Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold77
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1619719
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29
Warning! 197531 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:822906 original size:433 final size:435
Alignment explanation
Indices: 822067--823292 Score: 2005
Period size: 433 Copynumber: 2.8 Consensus size: 435
822057 ATGAAAGGAG
* * *
822067 ATTCGTTACCGTTCTGGAGATATATGAGAAAGAAGGTTTTAGGGGCCGATCTCTTATCTCCTTAT
1 ATTCGTTACCATTCTGAAGATATATGAG-AAGAAGGTTTTAGGGGCCGATCCCTTATCTCCTTAT
** * * * *
822132 AGGGGCCGTTTGGCGAAATTTTGAAGATAGCATA-TGTTTAAGAACATCT-TTTTGAACAACTTT
65 AGGGGCCGTTTAACAAAATTTTGAAGGTTGCATATTG-TTAAGAACAT-TAATTTGAACAACTTT
* *
822195 TCTTCTGTATTGCATTTCAAAATG-TTTTTCCTTTCTGAGATATGGGTGATCAAAATTTTGGACT
128 TCTTCTGTATTGCATTACAAAA-GATTTTTCCTTTCTGAGATATGGGTGATCGAAATTTTGGACT
* * *
822259 TTTGGCCCCTAAAAACCTTTAATTACGTAATGCATGATAAAATCATTACATTGCTTGGACACATA
192 TTTGGCCCCTAAAAACC-TTAATTACGTAATACATGACAAAATCATTACATTGCTTGGATACATA
* * * *
822324 ACAGTGAGATAAACATATTTGCTTCTATAACCTTTCACAAAATATCTCCCATTAAAGAACTACAG
256 ACTGTGAGATAAACATATTTGCTTCTATAACCTTTCACAAAATATCTCTCAGTAAAGAGCTACAG
822389 ATTAAAGACTTTAGAGCCCTTTGGTCCCCTT-ATTTGAGGGGCCAGCCCCTTTTTCTTGATATTA
321 ATTAAAGACTTTAGAGCCCTTTGGT-CCCTTAATTTGAGGGGCCAGCCCCTTTTTCTTGATATTA
822453 AATGAAAGGTCATTTAATTCTAAACAAATTTTATTCAACAAGTGTTTAGAA
385 AATGAAAGGTCATTTAATTCTAAACAAATTTTATTCAACAAGTGTTTAGAA
* * * * *
822504 ATTCGTTACCTTTTTGTAGATATATGAG-A-AAGGTTTTAGGGGCTGATCCCTTACCTCCTTATA
1 ATTCGTTACCATTCTGAAGATATATGAGAAGAAGGTTTTAGGGGCCGATCCCTTATCTCCTTATA
*
822567 GGGGCCGTTTAACAAAATTTTGAAGGTTGCATATTGTTAAAAACATTAATTTGAACAACTTTTCT
66 GGGGCCGTTTAACAAAATTTTGAAGGTTGCATATTGTTAAGAACATTAATTTGAACAACTTTTCT
*
822632 TCTGTATTGCATTACAAAGGATTTTTCCTTTCTGAGATATGGGTGATCGAAATTTTGGACTTTTG
131 TCTGTATTGCATTACAAAAGATTTTTCCTTTCTGAGATATGGGTGATCGAAATTTTGGACTTTTG
*
822697 GCCCCTAAAAACCCTAATTACGTAATACATGACAAAATCATTACATTGCTTGGATACATAACTGT
196 GCCCCTAAAAACCTTAATTACGTAATACATGACAAAATCATTACATTGCTTGGATACATAACTGT
* *
822762 GAGATAAACATATTTGCTTCTATAACCTTTCACAAAATATCTCTCAGTAAAGGGCTACAGATTTA
261 GAGATAAACATATTTGCTTCTATAACCTTTCACAAAATATCTCTCAGTAAAGAGCTACAGATTAA
822827 AGACTTTAGAGCCCTTTGGTCCCTTAATTTGAGGGGCCAGCCCCTTTTTCTTGATATTAAATGAA
326 AGACTTTAGAGCCCTTTGGTCCCTTAATTTGAGGGGCCAGCCCCTTTTTCTTGATATTAAATGAA
*
822892 AGGTCATTTAATTCTAAACAAATTTTGTTCAACAAGTGTTTAGAA
391 AGGTCATTTAATTCTAAACAAATTTTATTCAACAAGTGTTTAGAA
*
822937 ATTCGTTACCATTCTGAAGATATATGAGAAAGAAGGTTTTAGGGGCCGATCCCTTATCTCCCTAT
1 ATTCGTTACCATTCTGAAGATATATGAG-AAGAAGGTTTTAGGGGCCGATCCCTTATCTCCTTAT
*
823002 AGGGGCCGTTTAACAAAATTTTAAAGGTTGCATATTGTTAAGAACATTAATTTGAACAACTTTTC
65 AGGGGCCGTTTAACAAAATTTTGAAGGTTGCATATTGTTAAGAACATTAATTTGAACAACTTTTC
*
823067 TTCTGTATTGCATTACAAAAGATTTTTCCTTTCTGAGATATGGGTGACCGAAATTTTGGACTTTT
130 TTCTGTATTGCATTACAAAAGATTTTTCCTTTCTGAGATATGGGTGATCGAAATTTTGGACTTTT
*
823132 GGCCCCTAAAAATTCTTAATTACGTAATACATGACAAAATCATTACATTGCTTGGATACATAACT
195 GGCCCCTAAAAA-CCTTAATTACGTAATACATGACAAAATCATTACATTGCTTGGATACATAACT
* * *
823197 GTGAGATAAACATATTTGCTTCTATAACCTTTCACAAAATATTTCTCAGTAAAAAGATACAGATT
259 GTGAGATAAACATATTTGCTTCTATAACCTTTCACAAAATATCTCTCAGTAAAGAGCTACAGATT
*
823262 AAAGACTTTAGAGCCCTTTGGTCCCCTAATT
324 AAAGACTTTAGAGCCCTTTGGTCCCTTAATT
823293 CTTGGTTTCA
Statistics
Matches: 736, Mismatches: 45, Indels: 16
0.92 0.06 0.02
Matches are distributed among these distances:
432 5 0.01
433 237 0.32
434 157 0.21
435 4 0.01
436 168 0.23
437 165 0.22
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (435 bp):
ATTCGTTACCATTCTGAAGATATATGAGAAGAAGGTTTTAGGGGCCGATCCCTTATCTCCTTATA
GGGGCCGTTTAACAAAATTTTGAAGGTTGCATATTGTTAAGAACATTAATTTGAACAACTTTTCT
TCTGTATTGCATTACAAAAGATTTTTCCTTTCTGAGATATGGGTGATCGAAATTTTGGACTTTTG
GCCCCTAAAAACCTTAATTACGTAATACATGACAAAATCATTACATTGCTTGGATACATAACTGT
GAGATAAACATATTTGCTTCTATAACCTTTCACAAAATATCTCTCAGTAAAGAGCTACAGATTAA
AGACTTTAGAGCCCTTTGGTCCCTTAATTTGAGGGGCCAGCCCCTTTTTCTTGATATTAAATGAA
AGGTCATTTAATTCTAAACAAATTTTATTCAACAAGTGTTTAGAA
Found at i:824795 original size:438 final size:435
Alignment explanation
Indices: 824003--824977 Score: 1377
Period size: 438 Copynumber: 2.2 Consensus size: 435
823993 ATTAAAAACT
* * * * *
824003 GATATTGTTACGATCAACAACTTTACTTTTTTAATGCATTACAAAATCTTGATCGTTTTTAAGGT
1 GATATTGTTACGATCAACAACTTTGCTTCTATAATGCATTACAAAATCTTTATCGTTTTTAAGTT
** * ** *
824068 ATGTGTACGAG-GCTTTACGAGTCTCTTGGCCCCTAATTACAGGGACCAGCCCCTTTTTCTTGAG
66 AT-TGTAATAGAG-TTTACGAGTGTCTTGGCCCCTAAAAAAAGGGACCAGCCCCTTTTTCTTGAG
* * * *
824132 TTCATTCAAAAGGTCCCACGATTACTAACATTTTTTGTTCTTACAACCATCTAAAATTGTTGTAT
129 TTCATTAAAAAGGTCCCAAGAATACCAACATTTTTTGTTCTTACAACCATCTAAAATTGTTGTAT
** * * *
824197 ATTTTTTCGATACAATTGATTGAATATTTTAGGGGCCGGCCCTCTTAATCTTTAATGGGGACAGA
194 ATTTTTGAGATACAAATGATTGAATATTTTAGGGGCCAGCCCTCTTAATCCTTAATGGGGACAGA
* *
824262 CATTGGTGTTTTATTAATGAAATCGATTAGAATCATCAATGCAAACATTCTCTCTTCTACATTGC
259 CATTGGTGTTTTATCAATGAAATCGATTAGAATCATCAATGCAAACATTCTCTCTTCTACAATGC
* *
824327 TTTACAAAATATGTCTCCTTTTCTAGATATATTGCGTCATAGTTTAAGTACTTTGGCCCCTAAAA
324 TTTACAAAATATGTCTCCTTTTCAAGATATATTGCGTCAAAGTTTAAGTACTTTGGCCCCTAAAA
*
824392 ATCCCTAATTGCGTAATAAATGGGCGTGGCAATGACTTTTTCTGATA
389 ATCCCTAATTACGTAATAAATGGGCGTGGCAATGACTTTTTCTGATA
* ** *
824439 GATATTGTTACGATCAACAACTTTGCCTCTATAATGCAAGACAAAATCTTTATGGTTTTTAAGTT
1 GATATTGTTACGATCAACAACTTTGCTTCTATAATGCATTACAAAATCTTTATCGTTTTTAAGTT
* * * *
824504 ATTCGTAATAGAGTTTACGAGTGTCTTGGCTCTTACAAAAAAGGGGCCAGCCCCTTTTTCTTGAT
66 ATT-GTAATAGAGTTTACGAGTGTCTTGGCCCCTA-AAAAAAGGGACCAGCCCCTTTTTCTTGAG
** **
824569 TTC-TTAAAAAAAGGTCTTAAGAATACCAATTTTTTTTGTTCTTAC-ACTCATCTAAAATT-TTG
129 TTCATT--AAAAAGGTCCCAAGAATACCAACATTTTTTGTTCTTACAAC-CATCTAAAATTGTTG
*
824631 -ATCATTTTTGAGATTCAAATGATTGAATATTTTAGGGGCCAGCCCTC-TAGATCCTTAATGGGG
191 TAT-ATTTTTGAGATACAAATGATTGAATATTTTAGGGGCCAGCCCTCTTA-ATCCTTAATGGGG
* * * *
824694 ACATACATTGGTGTTTTGATCAATGGAATCGATTAGAATCATTAATGCAAACATTTTCTCTTCTA
254 ACAGACATTGGTGTTTT-ATCAATGAAATCGATTAGAATCATCAATGCAAACATTCTCTCTTCTA
824759 CAATGCTTTACAAAATATGTCTCCTTTTCAAGATATATTGCGTCAAAGTTTAAGTACTTTGGCCC
318 CAATGCTTTACAAAATATGTCTCCTTTTCAAGATATATTGCGTCAAAGTTTAAGTACTTTGGCCC
* * *
824824 CTCAAAATCCCTAATTACGTAATAAATTGGCGTGGCAATGGCTTTTTCTGATA
383 CTAAAAATCCCTAATTACGTAATAAATGGGCGTGGCAATGACTTTTTCTGATA
* *
824877 GATATTGTTACGATCAACAACTATGCTTCTATAATGCATTACAAAATCTTTATCGTATTTAAGTT
1 GATATTGTTACGATCAACAACTTTGCTTCTATAATGCATTACAAAATCTTTATCGTTTTTAAGTT
*
824942 ATTTGTAATAGAGTCTACGAGTGTCTTGGCCCCTAA
66 A-TTGTAATAGAGTTTACGAGTGTCTTGGCCCCTAA
824978 TTTAAGGGGA
Statistics
Matches: 475, Mismatches: 54, Indels: 19
0.87 0.10 0.03
Matches are distributed among these distances:
435 1 0.00
436 88 0.19
437 101 0.21
438 283 0.60
439 2 0.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (435 bp):
GATATTGTTACGATCAACAACTTTGCTTCTATAATGCATTACAAAATCTTTATCGTTTTTAAGTT
ATTGTAATAGAGTTTACGAGTGTCTTGGCCCCTAAAAAAAGGGACCAGCCCCTTTTTCTTGAGTT
CATTAAAAAGGTCCCAAGAATACCAACATTTTTTGTTCTTACAACCATCTAAAATTGTTGTATAT
TTTTGAGATACAAATGATTGAATATTTTAGGGGCCAGCCCTCTTAATCCTTAATGGGGACAGACA
TTGGTGTTTTATCAATGAAATCGATTAGAATCATCAATGCAAACATTCTCTCTTCTACAATGCTT
TACAAAATATGTCTCCTTTTCAAGATATATTGCGTCAAAGTTTAAGTACTTTGGCCCCTAAAAAT
CCCTAATTACGTAATAAATGGGCGTGGCAATGACTTTTTCTGATA
Found at i:826420 original size:63 final size:61
Alignment explanation
Indices: 826347--826512 Score: 228
Period size: 60 Copynumber: 2.7 Consensus size: 61
826337 AAACAGTACG
*
826347 AAAACTATAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAATAGGGAAAAAGAAA-CAAAGCA
1 AAAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAATA--GAAAAAGAAACCAAAG-A
**
826410 AAAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAA-AGAAAAAGAAACCGTAGA
1 AAAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAATAGAAAAAGAAACCAAAGA
* * * *
826470 ATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCCTAATAAT
1 AAAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAAT
826513 TTGATGCTGA
Statistics
Matches: 94, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
60 49 0.52
61 3 0.03
62 1 0.01
63 41 0.44
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.18
Consensus pattern (61 bp):
AAAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAATAGAAAAAGAAACCAAAGA
Found at i:828640 original size:51 final size:51
Alignment explanation
Indices: 828516--828704 Score: 243
Period size: 51 Copynumber: 3.6 Consensus size: 51
828506 TGAGCTCAAA
* * * *
828516 GTATTGTATATGCCCGACTCTTGGGATAAAGGTACCTGTGCATTTATGGAGCTCACG
1 GTATTGTAAATGCCCGTCTCTTGGGATAAA--T---T-TGTATTTCTGGAGCTCACG
* *
828573 GTATTGTAAATGCCCGTCTCTTGGTATAAATTTGTATTTCTGGAGCTCACA
1 GTATTGTAAATGCCCGTCTCTTGGGATAAATTTGTATTTCTGGAGCTCACG
*
828624 GTATTGTAAATTCCCGTCTCTTGGGATAAATTTGTATTTCTGGAGCTCACG
1 GTATTGTAAATGCCCGTCTCTTGGGATAAATTTGTATTTCTGGAGCTCACG
**
828675 GTATTGTAAATGCCCGAGTCTTGGGATAAA
1 GTATTGTAAATGCCCGTCTCTTGGGATAAA
828705 GTTTCCTGTG
Statistics
Matches: 120, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
51 91 0.76
52 1 0.01
55 1 0.01
57 27 0.22
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.35
Consensus pattern (51 bp):
GTATTGTAAATGCCCGTCTCTTGGGATAAATTTGTATTTCTGGAGCTCACG
Found at i:830804 original size:2 final size:2
Alignment explanation
Indices: 830797--830822 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
830787 NNNNNNNNNN
830797 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
830823 GAACCGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:831192 original size:2 final size:2
Alignment explanation
Indices: 831185--831238 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
831175 GATACCAATT
831185 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
831227 GA GA GA GA GA GA
1 GA GA GA GA GA GA
831239 TGGTTTATAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:831440 original size:24 final size:24
Alignment explanation
Indices: 831413--831463 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
831403 CATACTGTGG
831413 TTTCATTATTATTCAAGGTATCAA
1 TTTCATTATTATTCAAGGTATCAA
831437 TTTCATTATTATTCAAGGTATCAA
1 TTTCATTATTATTCAAGGTATCAA
831461 TTT
1 TTT
831464 TTGTAGATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.49
Consensus pattern (24 bp):
TTTCATTATTATTCAAGGTATCAA
Found at i:837767 original size:2 final size:2
Alignment explanation
Indices: 837760--837793 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
837750 CTGGCGATCA
*
837760 TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
837794 CATAATTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:843220 original size:21 final size:21
Alignment explanation
Indices: 843196--843287 Score: 123
Period size: 21 Copynumber: 4.4 Consensus size: 21
843186 ATCTGCCACC
843196 ACTTGTCAGATAATTATGTCG
1 ACTTGTCAGATAATTATGTCG
*
843217 ACTTGTCAGAT-CTTGATGTCG
1 ACTTGTCAGATAATT-ATGTCG
843238 ACTTGTCAGATAATTATGTCG
1 ACTTGTCAGATAATTATGTCG
* ** *
843259 ACTTGTCAGTTCTTTAAGTCG
1 ACTTGTCAGATAATTATGTCG
843280 ACTTGTCA
1 ACTTGTCA
843288 CTTATTCACG
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
20 2 0.03
21 59 0.94
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (21 bp):
ACTTGTCAGATAATTATGTCG
Found at i:843243 original size:42 final size:42
Alignment explanation
Indices: 843196--843287 Score: 157
Period size: 42 Copynumber: 2.2 Consensus size: 42
843186 ATCTGCCACC
*
843196 ACTTGTCAGATAATTATGTCGACTTGTCAGATCTTGATGTCG
1 ACTTGTCAGATAATTATGTCGACTTGTCAGATCTTGAAGTCG
* *
843238 ACTTGTCAGATAATTATGTCGACTTGTCAGTTCTTTAAGTCG
1 ACTTGTCAGATAATTATGTCGACTTGTCAGATCTTGAAGTCG
843280 ACTTGTCA
1 ACTTGTCA
843288 CTTATTCACG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (42 bp):
ACTTGTCAGATAATTATGTCGACTTGTCAGATCTTGAAGTCG
Found at i:843390 original size:21 final size:21
Alignment explanation
Indices: 843366--843523 Score: 151
Period size: 21 Copynumber: 7.6 Consensus size: 21
843356 TAATATTTTT
**
843366 TGACAAGTCGACATAAGGATC
1 TGACAAGTCGACATAATTATC
* *
843387 TGACAAGTCGACATAATCAAC
1 TGACAAGTCGACATAATTATC
*** *
843408 TTTTAAGTCGATC-TAATTATT
1 TGACAAGTCGA-CATAATTATC
843429 TGACAAGTCGACATAATTATC
1 TGACAAGTCGACATAATTATC
*
843450 TGACAAGTCGACATAATTATT
1 TGACAAGTCGACATAATTATC
* *
843471 TGAAAAGAT-GACATAA-CATC
1 TGACAAG-TCGACATAATTATC
* * *
843491 TGACAAGACAACATCATTATC
1 TGACAAGTCGACATAATTATC
843512 TGACAAGTCGAC
1 TGACAAGTCGAC
843524 TTACAATATG
Statistics
Matches: 108, Mismatches: 24, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
20 14 0.13
21 92 0.85
22 2 0.02
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.27
Consensus pattern (21 bp):
TGACAAGTCGACATAATTATC
Found at i:843510 original size:41 final size:42
Alignment explanation
Indices: 843421--843523 Score: 120
Period size: 41 Copynumber: 2.5 Consensus size: 42
843411 TAAGTCGATC
* * * *
843421 TAATTATTTGACAAGTCGACATAATTATCTGACAAGTCGACA
1 TAATTATTTGAAAAGTCGACATAATCATCTGACAAGACAACA
843463 TAATTATTTGAAAAGAT-GACATAA-CATCTGACAAGACAACA
1 TAATTATTTGAAAAG-TCGACATAATCATCTGACAAGACAACA
* * *
843504 TCATTATCTGACAAGTCGAC
1 TAATTATTTGAAAAGTCGAC
843524 TTACAATATG
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
40 1 0.02
41 29 0.56
42 21 0.40
43 1 0.02
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (42 bp):
TAATTATTTGAAAAGTCGACATAATCATCTGACAAGACAACA
Found at i:843600 original size:21 final size:21
Alignment explanation
Indices: 843575--843701 Score: 146
Period size: 21 Copynumber: 6.0 Consensus size: 21
843565 TTATTTTTTC
*
843575 TGTCAGATAATTATGTTAACT
1 TGTCAGATAATTATGTCAACT
**
843596 TGTCAGATCTTTATGTCAACT
1 TGTCAGATAATTATGTCAACT
* *
843617 TGACAGATAATTATGTTAACT
1 TGTCAGATAATTATGTCAACT
** *
843638 TGTCAGATCTTTATGTCGACT
1 TGTCAGATAATTATGTCAACT
* *
843659 TGTCAGATGATTATGTAAACT
1 TGTCAGATAATTATGTCAACT
* *
843680 TGTCAGATATTTATGTCGACT
1 TGTCAGATAATTATGTCAACT
843701 T
1 T
843702 ATATGGTATT
Statistics
Matches: 86, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 86 1.00
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (21 bp):
TGTCAGATAATTATGTCAACT
Found at i:843626 original size:42 final size:42
Alignment explanation
Indices: 843578--843701 Score: 203
Period size: 42 Copynumber: 3.0 Consensus size: 42
843568 TTTTTTCTGT
*
843578 CAGATAATTATGTTAACTTGTCAGATCTTTATGTCAACTTGA
1 CAGATAATTATGTTAACTTGTCAGATCTTTATGTCGACTTGA
*
843620 CAGATAATTATGTTAACTTGTCAGATCTTTATGTCGACTTGT
1 CAGATAATTATGTTAACTTGTCAGATCTTTATGTCGACTTGA
* * *
843662 CAGATGATTATGTAAACTTGTCAGATATTTATGTCGACTT
1 CAGATAATTATGTTAACTTGTCAGATCTTTATGTCGACTT
843702 ATATGGTATT
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 77 1.00
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (42 bp):
CAGATAATTATGTTAACTTGTCAGATCTTTATGTCGACTTGA
Found at i:843652 original size:63 final size:63
Alignment explanation
Indices: 843575--843695 Score: 161
Period size: 63 Copynumber: 1.9 Consensus size: 63
843565 TTATTTTTTC
* * *
843575 TGTCAGATAATTATGTTAACTTGTCAGATCTTTATGTCAACTTGACAGATAATTATGTTAACT
1 TGTCAGATAATTATGTCAACTTGTCAGATCATTATGTAAACTTGACAGATAATTATGTTAACT
** * * * *
843638 TGTCAGATCTTTATGTCGACTTGTCAGATGATTATGTAAACTTGTCAGATATTTATGT
1 TGTCAGATAATTATGTCAACTTGTCAGATCATTATGTAAACTTGACAGATAATTATGT
843696 CGACTTATAT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
63 49 1.00
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (63 bp):
TGTCAGATAATTATGTCAACTTGTCAGATCATTATGTAAACTTGACAGATAATTATGTTAACT
Found at i:843842 original size:42 final size:42
Alignment explanation
Indices: 843795--843888 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 42
843785 ATGGTTATTT
* *
843795 TCTGACAAGTCAACATAAAGATCTGACAAGTGAACATAAATA
1 TCTGACAAGTCAACATAAACATATGACAAGTGAACATAAATA
* * * * *
843837 TCTGACAAGTCGACATTATCATATGAGAAGTGAACATAATTA
1 TCTGACAAGTCAACATAAACATATGACAAGTGAACATAAATA
843879 TCTGACAAGT
1 TCTGACAAGT
843889 GGTGGCAGAT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.26
Consensus pattern (42 bp):
TCTGACAAGTCAACATAAACATATGACAAGTGAACATAAATA
Found at i:843889 original size:21 final size:21
Alignment explanation
Indices: 843795--843889 Score: 104
Period size: 21 Copynumber: 4.5 Consensus size: 21
843785 ATGGTTATTT
* *
843795 TCTGACAAGTCAACATAAAGA
1 TCTGACAAGTGAACATAAATA
843816 TCTGACAAGTGAACATAAATA
1 TCTGACAAGTGAACATAAATA
*
843837 TCTGACAAGTCG-ACAT-TATCA
1 TCTGACAAGT-GAACATAAAT-A
* * *
843858 TATGAGAAGTGAACATAATTA
1 TCTGACAAGTGAACATAAATA
843879 TCTGACAAGTG
1 TCTGACAAGTG
843890 GTGGCAGATC
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
20 3 0.05
21 56 0.92
22 2 0.03
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.25
Consensus pattern (21 bp):
TCTGACAAGTGAACATAAATA
Found at i:846426 original size:21 final size:21
Alignment explanation
Indices: 846400--846439 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
846390 TTATTTGATT
* *
846400 TTTTGTTTATTATTTTTTTCA
1 TTTTGTTGATTACTTTTTTCA
846421 TTTTGTTGATTACTTTTTT
1 TTTTGTTGATTACTTTTTT
846440 AGTTGTGCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.75
Consensus pattern (21 bp):
TTTTGTTGATTACTTTTTTCA
Found at i:855874 original size:13 final size:13
Alignment explanation
Indices: 855858--855883 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
855848 GTTTTGGCAC
855858 TGGGTTCTTAACT
1 TGGGTTCTTAACT
855871 TGGGTTCTTAACT
1 TGGGTTCTTAACT
855884 CTTAACTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.46
Consensus pattern (13 bp):
TGGGTTCTTAACT
Found at i:859728 original size:182 final size:182
Alignment explanation
Indices: 859417--860482 Score: 1601
Period size: 182 Copynumber: 5.9 Consensus size: 182
859407 CCTGACGGAA
* * * *
859417 TCCCGGCACCAGGGCGCTGAGAT-ATCCCTTTCATACAGGTTCCAAACATTATTGTAGGGTCTCT
1 TCCCGGCGCCAGGGCGCTGAGTTGA-CCCTATCATACAGGTTCCATACATTATTGTAGGGTCTCT
* *
859481 AAACAGGGCACATAGCGCCCAAACTAGGAAGTGTGCCATCAAGCTGAGACCGGATCCTTGGGGGT
65 AAACAGGGCACATAGCGCCCAAACTAGGAAGTGTGCCATCTAGCTGAGACCGGATCCTCGGGGGT
859546 ACGGGTGTCTCCAGAAGGAATCCGGTCTCAAAAGGGGCCATACTGACACCGAT
130 ACGGGTGTCTCCAGAAGGAATCCGGTCTCAAAAGGGGCCATACTGACACCGAT
859599 TCCCGGCGCCAGGGCGCTGAGTTGACCCTATCATACAGGTTCCATACATTATTGTAGGGTCTCTA
1 TCCCGGCGCCAGGGCGCTGAGTTGACCCTATCATACAGGTTCCATACATTATTGTAGGGTCTCTA
* * *
859664 AACAGGGCGCATAGCGCCCAAACTAGGAAGTGAGCCATTTAGCTGAGACCGGATCCTCGGGGGTA
66 AACAGGGCACATAGCGCCCAAACTAGGAAGTGTGCCATCTAGCTGAGACCGGATCCTCGGGGGTA
859729 CGGGTGTCTCCAGAAGGAATCCGGTCTCAAAAGGGGCCATACTGACACCGAT
131 CGGGTGTCTCCAGAAGGAATCCGGTCTCAAAAGGGGCCATACTGACACCGAT
*
859781 TCCCGGCGCCAGGGCGCTGAGTTGACCCTATAATACAGGTTCCATACATTATTGTAGGGTCTCTA
1 TCCCGGCGCCAGGGCGCTGAGTTGACCCTATCATACAGGTTCCATACATTATTGTAGGGTCTCTA
* * * *
859846 AACAGGGCGCCTAGCACCTAAACTAGGAAGTGTGCCATCTAGCTGAGACCGGATCCTCGGGGGTA
66 AACAGGGCACATAGCGCCCAAACTAGGAAGTGTGCCATCTAGCTGAGACCGGATCCTCGGGGGTA
* * * * * * * *
859911 CGAGTG-CCCCTGACGGAATCCGGTCTCATAAGGGGCCAAATTGACACCGTT
131 CGGGTGTCTCCAGAAGGAATCCGGTCTCAAAAGGGGCCATACTGACACCGAT
*
859962 TCCCGGCGCCAGGGCGCTGAGTTGATCCTATCATACAGGTTCCATACATTATTGTAGGGTCTCTA
1 TCCCGGCGCCAGGGCGCTGAGTTGACCCTATCATACAGGTTCCATACATTATTGTAGGGTCTCTA
* *
860027 AACAGGGCACATAGCGCCCAAACTAGGAAGTGAGCCATCTAGCTGAGACCGGATCCTTGGGGGTA
66 AACAGGGCACATAGCGCCCAAACTAGGAAGTGTGCCATCTAGCTGAGACCGGATCCTCGGGGGTA
*
860092 CGGGTGTCTCCAGAAGGAATCCGGTCTCAAAAGGGGACATACTGACACCGAT
131 CGGGTGTCTCCAGAAGGAATCCGGTCTCAAAAGGGGCCATACTGACACCGAT
* * *
860144 TCCCCGGCGCCAGGGCGCTGAGTTGACCCTATAATACAGGTTCCTTACATTAATGTAGGGTCTCT
1 T-CCCGGCGCCAGGGCGCTGAGTTGACCCTATCATACAGGTTCCATACATTATTGTAGGGTCTCT
* *
860209 AAACAGGGCACATAGCGCCCAAAGTAGGAAGTGTGCCATCTAGCTGAGACCGGATCCT-TGGGG-
65 AAACAGGGCACATAGCGCCCAAACTAGGAAGTGTGCCATCTAGCTGAGACCGGATCCTCGGGGGT
* * * * * * *
860272 --GGGNG-CCCCTGACGGAATCCGATCTCAAAAGGGGCCAAATTGACACCGAT
130 ACGGGTGTCTCCAGAAGGAATCCGGTCTCAAAAGGGGCCATACTGACACCGAT
* * *
860322 TCCCGGCGCCAGGGCGCTGAGTTGAACCTATTATAGAGGTTCCATACATTATTGTAGGGTCTCTA
1 TCCCGGCGCCAGGGCGCTGAGTTGACCCTATCATACAGGTTCCATACATTATTGTAGGGTCTCTA
* * * *
860387 AACAGGGCGCCTAGCGCCCAAACTAGGAAGTGTGCCATCTAGTTGAGACCGGATCCTC-GGGGTT
66 AACAGGGCACATAGCGCCCAAACTAGGAAGTGTGCCATCTAGCTGAGACCGGATCCTCGGGGGTA
** * *
860451 CTAGTGTC-CCTTGACGGAATCCGGTCTCAAAA
131 CGGGTGTCTCC-AGAAGGAATCCGGTCTCAAAA
860483 TTGGCGTTAT
Statistics
Matches: 807, Mismatches: 68, Indels: 19
0.90 0.08 0.02
Matches are distributed among these distances:
177 116 0.14
178 39 0.05
179 4 0.00
180 4 0.00
181 186 0.23
182 342 0.42
183 116 0.14
ACGTcount: A:0.25, C:0.26, G:0.28, T:0.21
Consensus pattern (182 bp):
TCCCGGCGCCAGGGCGCTGAGTTGACCCTATCATACAGGTTCCATACATTATTGTAGGGTCTCTA
AACAGGGCACATAGCGCCCAAACTAGGAAGTGTGCCATCTAGCTGAGACCGGATCCTCGGGGGTA
CGGGTGTCTCCAGAAGGAATCCGGTCTCAAAAGGGGCCATACTGACACCGAT
Found at i:862977 original size:2 final size:2
Alignment explanation
Indices: 862972--862999 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
862962 GAGATGCATG
862972 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
863000 TTGTACATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:873076 original size:184 final size:181
Alignment explanation
Indices: 872634--873500 Score: 983
Period size: 182 Copynumber: 4.8 Consensus size: 181
872624 TTGGGCGCTA
* * * * *
872634 TCAACTCAGCGACTTGGCGCCAAGAATTGGTGTCAATGTGGCCCCTTTTGAGACCAGATTCCATC
1 TCAACTCAGCGCCCTGGCGCCAAGAATCGGTGTCAATATGGCCCCTTTTGAGACCAGATTCCGTC
* * * * * *
872699 AGGGGACACCCGTACCCCCG-GAGATCCGGTCTCAGCTAGGTGACACACTTTCTAGTTTGGCCGC
66 AGGGGACACCCGTA-TCCCGAG-GATCCGGTCTCAGCAAGATGGCACACTTCCTAGTTTGGGCGC
* ** *
872763 TAGGCGCCCTCTTTAGAGACCCTATTATAATGTATAGAACCTGTATGATAGGG
129 TAGGCGCCCTGTTTAGAGACCCTACAATAATGTATGGAACCTGTATGATAGGG
* * ** *
872816 TCAACTCAGCGCCCTGGCGCCAAGAATCAGTGTCATTATGGCAACTTTTGAGACCGGATTCCGTC
1 TCAACTCAGCGCCCTGGCGCCAAGAATCGGTGTCAATATGGCCCCTTTTGAGACCAGATTCCGTC
** * ** *
872881 AGGGGACACCCGTATTCCAAAGGATCTGGTCTCAGCTTGATGGCATACTTCCTAGTTTGGGCGCT
66 AGGGGACACCCGTA-TCCCGAGGATCCGGTCTCAGCAAGATGGCACACTTCCTAGTTTGGGCGCT
* * * * * * **
872946 ATGCGCCATGTATAGAGACCATATC-TTAATGTATGGAACCTTTGAATGATATCG
130 AGGCGCCCTGTTTAGAGACCCTA-CAATAATGTATGGAACC--TGTATGATAGGG
* * * * * * * * * *
873000 CCAAATGAGCGCCCTGGCTCCAAAAATTGGTGTCAATATCGCGCCTTTTGAGACCGGATTCCGTT
1 TCAACTCAGCGCCCTGGCGCCAAGAATCGGTGTCAATATGGCCCCTTTTGAGACCAGATTCCGTC
* * * * * *
873065 AGTGGACACCCGTCTTCCTGGGGATCTGGTCTCAGCAAGATGGTACACTTCCTAGTTTGGGCGCT
66 AGGGGACACCCGT-ATCCCGAGGATCCGGTCTCAGCAAGATGGCACACTTCCTAGTTTGGGCGCT
* *
873130 AGGCGCCCTGTTTAGAGACCCTACAATAATGTAGGGAACATGTATGATAGGG
130 AGGCGCCCTGTTTAGAGACCCTACAATAATGTATGGAACCTGTATGATAGGG
* *
873182 TCAACTC-GACGCCCTCGCGCCAAGAATCGGTGTCAATATGGCCCCTTTTGAGA-CTGAGTTCCG
1 TCAACTCAG-CGCCCTGGCGCCAAGAATCGGTGTCAATATGGCCCCTTTTGAGACCAGA-TTCCG
* *
873245 TCAGGGGACACCCGTACTACCGAGGATCCGGTCTCAGCAAGATGGCACACTTCCTATGCTT-GGC
64 TCAGGGGACACCCGTA-TCCCGAGGATCCGGTCTCAGCAAGATGGCACACTTCCTA-GTTTGGGC
* *
873309 GCTAAGCGCCCTGTTTAGAGACCCTACAATAATGTATTGAACCTGTATGATAGGG
127 GCTAGGCGCCCTGTTTAGAGACCCTACAATAATGTATGGAACCTGTATGATAGGG
* * *
873364 TCAACTCAGCGCCCTAGCGCC-AGAAATCGGTGTCAATATCGCGCCTTTTGAGACCAGATTCCGT
1 TCAACTCAGCGCCCTGGCGCCAAG-AATCGGTGTCAATATGGCCCCTTTTGAGACCAGATTCCGT
* * *
873428 CAGGGGATACCCGTACCCCGTAGGATCCGGTCTGAGCAAGATGGCACACTTCCTAGGTTT-GGCG
65 CAGGGGACACCCGTATCCCG-AGGATCCGGTCTCAGCAAGATGGCACACTTCCTA-GTTTGGGCG
873492 CTAGGCGCC
128 CTAGGCGCC
873501 GTTTTAAATT
Statistics
Matches: 574, Mismatches: 97, Indels: 28
0.82 0.14 0.04
Matches are distributed among these distances:
181 9 0.02
182 408 0.71
183 9 0.02
184 148 0.26
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (181 bp):
TCAACTCAGCGCCCTGGCGCCAAGAATCGGTGTCAATATGGCCCCTTTTGAGACCAGATTCCGTC
AGGGGACACCCGTATCCCGAGGATCCGGTCTCAGCAAGATGGCACACTTCCTAGTTTGGGCGCTA
GGCGCCCTGTTTAGAGACCCTACAATAATGTATGGAACCTGTATGATAGGG
Found at i:873330 original size:366 final size:363
Alignment explanation
Indices: 872648--873500 Score: 1054
Period size: 366 Copynumber: 2.3 Consensus size: 363
872638 CTCAGCGACT
* * * * *
872648 TGGCGCCAAGAATTGGTGTCAATGTGGCCCCTTTTGAGACCAGATTCCATCAGGGGACACCCGTA
1 TGGCGCCAAAAATTGGTGTCAATATCGCGCCTTTTGAGACCAGATTCCGTCAGGGGACACCCGTA
* * * * * *
872713 CCCCCGGAGATCCGGTCTCAGCTAGGTGACACACTTTCTAGTTTGGCCGCTAGGCGCCCTCTTTA
66 -CCCCGGGGATCCGGTCTCAGCAAGATGGCACACTTCCTAGTTTGGGCGCTAGGCGCCCTCTTTA
** * * *
872778 GAGACCCTATTATAATGTATAGAACCTGTATGATAGGGTCAACTCAGCGCCCTGGCGCCAAGAAT
130 GAGACCCTACAATAATGTAGAGAACATGTATGATAGGGTCAACTCAGCGCCCTCGCGCCAAGAAT
* * *
872843 CAGTGTCATTATGGCAACTTTTGAGACCGGATTCCGTCAGGGGACACCCGTATTCCAAAGGATCT
195 CAGTGTCAATATGGCAACTTTTGAGACCGGATTCCGTCAGGGGACACCCGTATACCAAAGGATCC
** * * * *
872908 GGTCTCAGCTTGATGGCATACTTCCTAGTTTGGGCGCTATGCGCCATGTATAGAGACCATATC-T
260 GGTCTCAGCAAGATGGCACACTTCCTAGCTTGGGCGCTAAGCGCCATGTATAGAGACCATA-CAA
* *
872972 TAATGTATGGAACCTTTGAATGATATCGCCAAATGAGCGCCC
324 TAATGTATGGAACC--TGAATGATAGCGCCAAATCAGCGCCC
* * * *
873014 TGGCTCCAAAAATTGGTGTCAATATCGCGCCTTTTGAGACCGGATTCCGTTAGTGGACACCCGT-
1 TGGCGCCAAAAATTGGTGTCAATATCGCGCCTTTTGAGACCAGATTCCGTCAGGGGACACCCGTA
* * * *
873078 CTTCCTGGGGATCTGGTCTCAGCAAGATGGTACACTTCCTAGTTTGGGCGCTAGGCGCCCTGTTT
66 C--CCCGGGGATCCGGTCTCAGCAAGATGGCACACTTCCTAGTTTGGGCGCTAGGCGCCCTCTTT
*
873143 AGAGACCCTACAATAATGTAGGGAACATGTATGATAGGGTCAACTC-GACGCCCTCGCGCCAAGA
129 AGAGACCCTACAATAATGTAGAGAACATGTATGATAGGGTCAACTCAG-CGCCCTCGCGCCAAGA
* ** * *
873207 ATCGGTGTCAATATGGCCCCTTTTGAGA-CTGAGTTCCGTCAGGGGACACCCGTACTACC-GAGG
193 ATCAGTGTCAATATGGCAACTTTTGAGACCGGA-TTCCGTCAGGGGACACCCGTA-TACCAAAGG
* * *
873270 ATCCGGTCTCAGCAAGATGGCACACTTCCTATGCTT-GGCGCTAAGCGCCCTGTTTAGAGACCCT
256 ATCCGGTCTCAGCAAGATGGCACACTTCCTA-GCTTGGGCGCTAAGCGCCATGTATAGAGACCAT
* * * * *
873334 ACAATAATGTATTGAACCTGTATGATAGGGTCAACTCAGCGCCC
320 ACAATAATGTATGGAACCTGAATGATAGCGCCAAATCAGCGCCC
* * * *
873378 TAGCGCCAGAAATCGGTGTCAATATCGCGCCTTTTGAGACCAGATTCCGTCAGGGGATACCCGTA
1 TGGCGCCAAAAATTGGTGTCAATATCGCGCCTTTTGAGACCAGATTCCGTCAGGGGACACCCGTA
* *
873443 CCCCGTAGGATCCGGTCTGAGCAAGATGGCACACTTCCTAGGTTT-GGCGCTAGGCGCC
66 CCCCG-GGGATCCGGTCTCAGCAAGATGGCACACTTCCTA-GTTTGGGCGCTAGGCGCC
873501 GTTTTAAATT
Statistics
Matches: 415, Mismatches: 62, Indels: 22
0.83 0.12 0.04
Matches are distributed among these distances:
363 3 0.01
364 120 0.29
365 10 0.02
366 276 0.67
367 6 0.01
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.25
Consensus pattern (363 bp):
TGGCGCCAAAAATTGGTGTCAATATCGCGCCTTTTGAGACCAGATTCCGTCAGGGGACACCCGTA
CCCCGGGGATCCGGTCTCAGCAAGATGGCACACTTCCTAGTTTGGGCGCTAGGCGCCCTCTTTAG
AGACCCTACAATAATGTAGAGAACATGTATGATAGGGTCAACTCAGCGCCCTCGCGCCAAGAATC
AGTGTCAATATGGCAACTTTTGAGACCGGATTCCGTCAGGGGACACCCGTATACCAAAGGATCCG
GTCTCAGCAAGATGGCACACTTCCTAGCTTGGGCGCTAAGCGCCATGTATAGAGACCATACAATA
ATGTATGGAACCTGAATGATAGCGCCAAATCAGCGCCC
Found at i:878024 original size:2 final size:2
Alignment explanation
Indices: 878019--878053 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
878009 ATATATATAT
878019 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
878054 TATTTGTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:878120 original size:2 final size:2
Alignment explanation
Indices: 878113--878141 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
878103 TTATAATTAT
878113 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
878142 TTTGTTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:879276 original size:22 final size:21
Alignment explanation
Indices: 879244--879289 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 21
879234 GCCCGTTGTC
*
879244 TGTCGTCGTTGTCGTTGGCGT
1 TGTCGTCGTTGGCGTTGGCGT
879265 TGTCGGTCGTTGGCGTTGGCGT
1 TGTC-GTCGTTGGCGTTGGCGT
879287 TGT
1 TGT
879290 TGTAAACTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.00, C:0.17, G:0.41, T:0.41
Consensus pattern (21 bp):
TGTCGTCGTTGGCGTTGGCGT
Found at i:879291 original size:25 final size:24
Alignment explanation
Indices: 879237--879292 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 24
879227 AAAATTTGCC
*
879237 CGTTGTCTGTCGTCGTTGTCGTTGG
1 CGTTGT-TGTCGTCGTTGGCGTTGG
*
879262 CGTTGTCG--GTCGTTGGCGTTGG
1 CGTTGTTGTCGTCGTTGGCGTTGG
879284 CGTTGTTGT
1 CGTTGTTGT
879293 AAACTTTACA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 20 0.74
24 1 0.04
25 6 0.22
ACGTcount: A:0.00, C:0.18, G:0.39, T:0.43
Consensus pattern (24 bp):
CGTTGTTGTCGTCGTTGGCGTTGG
Found at i:880736 original size:166 final size:164
Alignment explanation
Indices: 880455--880991 Score: 603
Period size: 166 Copynumber: 3.2 Consensus size: 164
880445 TAGATTTNAT
* * * *
880455 TTTTAAATAGGAATATATAGAGAAAATCTTTAACAACTCTTCTTCTAAAAAACTATCAGGCCAGA
1 TTTTACATAGGAATATATAGAGAAAATCTTTAA-AAATCCTCTTCTAAAAAACTATCAGGCCAGG
* * * * * *
880520 AAAGCTCAAATTCGAGTAGAGGAATCTTCAGTTACTGTAGATTCAAGTTTGTTCAAATCATGGTC
65 AAAGCTC-AATTTGAGTAGAAGCATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTC
880585 CCCGGGGGTAGGGAGGGGCCACAATGGAGGTATCAAG
129 CCCGGGGGTAGGGAGGGGCCACAATGG-GGTATCAAG
* * * * *
880622 TTTTACATAGGAATACATAGAGAAAATCTTTAATAATCGTCTTCTTAAAAACTATCAGACCAGGA
1 TTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCCTCTTCTAAAAAACTATCAGGCCAGGA
* *
880687 AAGCTCATATTTGAGTAGAAGCATCCTCAGATAGTGTAAATTCAAGTTTGTTCAAATCATGGTAC
66 AAGCTCA-ATTTGAGTAGAAGCATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCC
* * ** *
880752 CAGGGGGTAGGGTGTAGCCACAATTGGGGTATCACG
130 CCGGGGGTAGGGAGGGGCCACAA-TGGGGTATCAAG
* * * * * *
880788 TTTTACATGGGAATATATAGAGAAAATTTTTAAAAATCCTTTTCTCAAAAAGTATTAGGCCAGGA
1 TTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCCTCTTCTAAAAAACTATCAGGCCAGGA
* *
880853 AAGCTCAATTTGGAGT-GAAAGCATCCTCAGATTGTGTAGATTGAAGTTTGTTCAAATCATGGTC
66 AAGCTCAATTT-GAGTAG-AAGCATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTC
* * * * *
880917 CCCGGGGGGAAGGGCA-GGGCCACCATAGCGG-ATGAAT
129 CCC-GGGGGTAGGG-AGGGGCCACAAT-GGGGTATCAAG
* * **
880954 TTTTACATAGGAATTTTTTTTAGAAAATCTTTAAAAAT
1 TTTTACATAGGAA-TATATAGAGAAAATCTTTAAAAAT
880992 ATTCTTGAAA
Statistics
Matches: 311, Mismatches: 51, Indels: 16
0.82 0.13 0.04
Matches are distributed among these distances:
165 6 0.02
166 234 0.75
167 71 0.23
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (164 bp):
TTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCCTCTTCTAAAAAACTATCAGGCCAGGA
AAGCTCAATTTGAGTAGAAGCATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCC
CGGGGGTAGGGAGGGGCCACAATGGGGTATCAAG
Found at i:894219 original size:12 final size:12
Alignment explanation
Indices: 894202--894226 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
894192 ATGGTCGACT
894202 TGAATTCATCGA
1 TGAATTCATCGA
894214 TGAATTCATCGA
1 TGAATTCATCGA
894226 T
1 T
894227 TGGCGGCTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (12 bp):
TGAATTCATCGA
Found at i:904697 original size:169 final size:169
Alignment explanation
Indices: 904418--904756 Score: 669
Period size: 169 Copynumber: 2.0 Consensus size: 169
904408 TAAGTTGGCC
904418 TTGAATAAATTAAATGACGTTATAATACGATCGTTTTAAATCAAAACACCTCTGTCTAACAGAAT
1 TTGAATAAATTAAATGACGTTATAATACGATCGTTTTAAATCAAAACACCTCTGTCTAACAGAAT
904483 ATGCTCCACTTAGGCTTAGCATATTGATCAAATAATAATTTGTGCAGGAAAATAAAACAATTTTA
66 ATGCTCCACTTAGGCTTAGCATATTGATCAAATAATAATTTGTGCAGGAAAATAAAACAATTTTA
904548 TTTAAAGTCTACCAGGTTAATATAGTTTGCCATTCCTTA
131 TTTAAAGTCTACCAGGTTAATATAGTTTGCCATTCCTTA
904587 TTGAATAAATTAAATGACGTTATAATACGATCGTTTTAAATCAAAACACCTCTGTCTAACAGAAT
1 TTGAATAAATTAAATGACGTTATAATACGATCGTTTTAAATCAAAACACCTCTGTCTAACAGAAT
904652 ATGCTCCACTTAGGCTTAGCATATTGATCAAATAATAATTTGTGCAGGAAAATAAAACAATTTTA
66 ATGCTCCACTTAGGCTTAGCATATTGATCAAATAATAATTTGTGCAGGAAAATAAAACAATTTTA
*
904717 TTTAAAGTCTACCAGGTTAATATAGTTTGCCATTCTTTA
131 TTTAAAGTCTACCAGGTTAATATAGTTTGCCATTCCTTA
904756 T
1 T
904757 AAGGGTATAT
Statistics
Matches: 169, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
169 169 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (169 bp):
TTGAATAAATTAAATGACGTTATAATACGATCGTTTTAAATCAAAACACCTCTGTCTAACAGAAT
ATGCTCCACTTAGGCTTAGCATATTGATCAAATAATAATTTGTGCAGGAAAATAAAACAATTTTA
TTTAAAGTCTACCAGGTTAATATAGTTTGCCATTCCTTA
Found at i:916362 original size:13 final size:13
Alignment explanation
Indices: 916346--916372 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
916336 CTTTTAAAAA
916346 AGAATTGGACTTT
1 AGAATTGGACTTT
916359 AGAATTGGACTTT
1 AGAATTGGACTTT
916372 A
1 A
916373 TTTTAACAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.07, G:0.22, T:0.37
Consensus pattern (13 bp):
AGAATTGGACTTT
Found at i:917368 original size:15 final size:15
Alignment explanation
Indices: 917348--917376 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
917338 GCATTTGCTC
917348 ATATTGGGCACATAT
1 ATATTGGGCACATAT
917363 ATATTGGGCACATA
1 ATATTGGGCACATA
917377 CATTTAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (15 bp):
ATATTGGGCACATAT
Found at i:920725 original size:2 final size:2
Alignment explanation
Indices: 920718--920765 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
920708 GTCTCTGTTG
920718 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
920760 GA GA GA
1 GA GA GA
920766 TCGTTCAAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:923955 original size:2 final size:2
Alignment explanation
Indices: 923942--923993 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
923932 ACAGACATAA
*
923942 TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
923984 TC TC TC TC TC
1 TC TC TC TC TC
923994 ATCTTGCCAC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:932423 original size:2 final size:2
Alignment explanation
Indices: 932416--932488 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
932406 AAACCTTCGT
932416 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
932458 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
932489 GAAAATAGTA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:936951 original size:166 final size:165
Alignment explanation
Indices: 936668--937657 Score: 962
Period size: 166 Copynumber: 6.1 Consensus size: 165
936658 GGTATTTTTC
* * * * * * * * *
936668 AAAATCTTCGTCTCAAAAACTATTCGGCCTGAAAAGCTTTAACTTGTGTGGAGGTATCCTCAGGT
1 AAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGC-TCAAATTGAGTGGAAGCATCCTCAGAT
* * * *
936733 AGTGTAGATTCAAGTTTGTTCAAATCATGGT-CCTCGGGGGTAGAGAGGGGCCACAATTTGGGGA
65 AGTGTAGATTCAAGTTTGTTCAAATCATAGTCCCT-GGGGGTAGGGTGGGGCCACAATTGGGGGA
*
936797 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTTA
129 TCAATTTTTACATAGGAATATATAGAGAAAATCTTTA
* * *
936834 AAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGGT
1 AAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATT-GAGTGGAAGCATCCTCAGAT
* * *
936899 AGTGTAGATTCAAATTTGTTTAAATCATAGTCCCTGGGGGTAGGGTGGGGCCACAATTGGGGGAA
65 AGTGTAGATTCAAGTTTGTTCAAATCATAGTCCCTGGGGGTAGGGTGGGGCCACAATTGGGGGAT
*
936964 CAAGTTTTACATAGGAATATATAGAGAAAATCTTTA
130 CAATTTTTACATAGGAATATATAGAGAAAATCTTTA
* * *
937000 AAAATCTTCCTCTCAAAAACTACTAGGCCAGGAAAGCTCAAATTTGAGTGGAAGCATCCTCAGAT
1 AAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAA-TTGAGTGGAAGCATCCTCAGAT
* * * * *
937065 TGTGTAGATTCACGTTTGTTCAAATCATGGTCCCCGGGAGTAGGGTGGGGCCACAATTGGGGGAT
65 AGTGTAGATTCAAGTTTGTTCAAATCATAGTCCCTGGGGGTAGGGTGGGGCCACAATTGGGGGAT
* * *
937130 AAATTTTTATACAGGAATATATAGAGAAAATCTTTAA
130 CAATTTTTACATAGGAATATATAGAGAAAATCTTT-A
** * * * * * * *
937167 AAAAAATTCTT-TTAAAAACTGTTTGGCCA-AGAAAGCTCAAATTGGCGTGTAACCATCCTTAGA
1 AAAATCTTCTTCTCAAAAACTATTAGGCCAGA-AAAGCTCAAATT-GAGTGGAAGCATCCTCAGA
* * * *
937230 TAATGTAGATTCAAGTTTGTTCAAATCATGGTCCTTGGGGGTAGGGCGGGGCCACAA-TGGGGGA
64 TAGTGTAGATTCAAGTTTGTTCAAATCATAGTCCCTGGGGGTAGGGTGGGGCCACAATTGGGGGA
*
937294 T-AAATTTT---T----ATATATAGAGAAAATCTTTA
129 TCAATTTTTACATAGGAATATATAGAGAAAATCTTTA
* * *
937323 AAAATCTTCTTCTC-AAAACTA--A--CCAGGAAAGCCCAAACTTGAGTGGAAGCATCCCCAGAT
1 AAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAA-TTGAGTGGAAGCATCCTCAGAT
* * * * * * *
937383 CGTATAGATTCAAGTTTGTTTAAATAATAGT-CCAGGGGATAGGGTGAGGCCACAA-TGGGGGAT
65 AGTGTAGATTCAAGTTTGTTCAAATCATAGTCCCTGGGGGTAGGGTGGGGCCACAATTGGGGGAT
* * * *
937446 GAATTTTTACATAGGGACATATAGAGAACATCTTTA
130 CAATTTTTACATAGGAATATATAGAGAAAATCTTTA
* * * * * * * * * *
937482 AAAATCTTCTTTTTAAAGACTATTTGGCCAGAAAAGCTTAAACTTGTGTAGAGGCATCCTCGGGT
1 AAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAA-TTGAGTGGAAGCATCCTCAGAT
* * * * * * *** *
937547 AGTGTAAATTTAAGTTTG--CAAAATCACAGTCCCTAGTGGTAGGGGGCGGCGCCTTGA-TGGTG
65 AGTGTAGATTCAAGTTTGTTC-AAATCATAGTCCCTGGGGGTAGGGTG-GG-GCCACAATTGGGG
* * *
937609 GTTGAATTTTTACATAGGAATATATAAAGAAAATCTTTA
127 GATCAATTTTTACATAGGAATATATAGAGAAAATCTTTA
*
937648 AAAATATTCT
1 AAAATCTTCT
937658 GGGAAAGTTT
Statistics
Matches: 680, Mismatches: 118, Indels: 52
0.80 0.14 0.06
Matches are distributed among these distances:
151 27 0.04
152 58 0.09
153 2 0.00
155 1 0.00
156 16 0.02
157 20 0.03
159 30 0.04
160 6 0.01
163 8 0.01
164 59 0.09
165 16 0.02
166 423 0.62
167 14 0.02
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.29
Consensus pattern (165 bp):
AAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTGAGTGGAAGCATCCTCAGATA
GTGTAGATTCAAGTTTGTTCAAATCATAGTCCCTGGGGGTAGGGTGGGGCCACAATTGGGGGATC
AATTTTTACATAGGAATATATAGAGAAAATCTTTA
Found at i:938024 original size:3 final size:3
Alignment explanation
Indices: 938011--938049 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
938001 TTTATGGTGT
*
938011 TGA TAA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
938050 AAGTGATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.36, C:0.00, G:0.31, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:950466 original size:4 final size:4
Alignment explanation
Indices: 950452--950529 Score: 147
Period size: 4 Copynumber: 19.5 Consensus size: 4
950442 TTGTCCGTCC
*
950452 ATCT ATTT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT
1 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT
950500 ATCT ATCT ATCT ATCT ATCT ATCT ATCT AT
1 ATCT ATCT ATCT ATCT ATCT ATCT ATCT AT
950530 ATATATACAC
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 72 1.00
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.51
Consensus pattern (4 bp):
ATCT
Found at i:953589 original size:14 final size:14
Alignment explanation
Indices: 953572--953601 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
953562 CGTACAGAGA
953572 TGAATCTACATGGT
1 TGAATCTACATGGT
953586 TGAATCTACATGGT
1 TGAATCTACATGGT
953600 TG
1 TG
953602 TAAACCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (14 bp):
TGAATCTACATGGT
Found at i:954629 original size:2 final size:2
Alignment explanation
Indices: 954622--954700 Score: 149
Period size: 2 Copynumber: 39.5 Consensus size: 2
954612 TAGGCGCCGC
954622 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
954664 TG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
954701 TTTCTTTACC
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.01
Consensus pattern (2 bp):
AG
Found at i:970562 original size:33 final size:32
Alignment explanation
Indices: 970518--970584 Score: 80
Period size: 33 Copynumber: 2.1 Consensus size: 32
970508 TACAAAGAAA
* *
970518 TGGTGAATATAAAATGCCAAAAATCCTATCTGT
1 TGGTGAATATAAAATACC-AAAATCATATCTGT
* * *
970551 TGGTGAGTATAACATACCAATATCATATCTGT
1 TGGTGAATATAAAATACCAAAATCATATCTGT
970583 TG
1 TG
970585 CTGTCTTCGG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (32 bp):
TGGTGAATATAAAATACCAAAATCATATCTGT
Found at i:979702 original size:16 final size:16
Alignment explanation
Indices: 979681--979711 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
979671 AGGAAGGAAG
979681 GATAGAAAGAAAGAAT
1 GATAGAAAGAAAGAAT
*
979697 GATAGATAGAAAGAA
1 GATAGAAAGAAAGAA
979712 AGAAATGTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.26, T:0.13
Consensus pattern (16 bp):
GATAGAAAGAAAGAAT
Found at i:985044 original size:3 final size:3
Alignment explanation
Indices: 985036--985085 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
985026 GATTTGAGAT
985036 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
985084 TG
1 TG
985086 GGAAAGAACA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:999194 original size:29 final size:29
Alignment explanation
Indices: 999157--999419 Score: 400
Period size: 29 Copynumber: 9.1 Consensus size: 29
999147 AGCATCGGCT
999157 ACTACACCTCACAGCCCAGGTAAACACGC
1 ACTACACCTCACAGCCCAGGTAAACACGC
*
999186 ACTTCACCTCACAGCCCAGGTAAACACGC
1 ACTACACCTCACAGCCCAGGTAAACACGC
*
999215 ACTACACCTCACAACCCAGGTAAACACGC
1 ACTACACCTCACAGCCCAGGTAAACACGC
* *
999244 ACTACACCTCACAGCCAAGGTAAACATGC
1 ACTACACCTCACAGCCCAGGTAAACACGC
* * *
999273 ACTACACCTCACAACCCAGTTAAACATGC
1 ACTACACCTCACAGCCCAGGTAAACACGC
*
999302 ACTACACCTCACAGCCCAGGGAAACACGC
1 ACTACACCTCACAGCCCAGGTAAACACGC
*
999331 ACTACACCTCACAACCCAGGTAAACACGC
1 ACTACACCTCACAGCCCAGGTAAACACGC
* *
999360 ACTACACCTCACAGCCCATGTAAACATGC
1 ACTACACCTCACAGCCCAGGTAAACACGC
* * *
999389 ACTGCACCTCACAACCTAGGTAAACACGC
1 ACTACACCTCACAGCCCAGGTAAACACGC
999418 AC
1 AC
999420 GACTTCTCCT
Statistics
Matches: 211, Mismatches: 23, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 211 1.00
ACGTcount: A:0.36, C:0.40, G:0.12, T:0.13
Consensus pattern (29 bp):
ACTACACCTCACAGCCCAGGTAAACACGC
Found at i:1000639 original size:12 final size:12
Alignment explanation
Indices: 1000622--1000659 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
1000612 ACACAAGAGT
1000622 TTAAGTATAACA
1 TTAAGTATAACA
*
1000634 TTAAGTACAACA
1 TTAAGTATAACA
*
1000646 TCAAGTATAACA
1 TTAAGTATAACA
1000658 TT
1 TT
1000660 TATTGAAGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32
Consensus pattern (12 bp):
TTAAGTATAACA
Found at i:1004152 original size:22 final size:22
Alignment explanation
Indices: 1004113--1004155 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1004103 TAAAGGTGTA
*
1004113 ACGTTATATATACTTTTCCATG
1 ACGTTATATATACATTTCCATG
* *
1004135 ACGTTATATTTGCATTTCCAT
1 ACGTTATATATACATTTCCAT
1004156 TGTTCTTTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.19, G:0.09, T:0.47
Consensus pattern (22 bp):
ACGTTATATATACATTTCCATG
Found at i:1004192 original size:139 final size:139
Alignment explanation
Indices: 1004001--1004281 Score: 553
Period size: 139 Copynumber: 2.0 Consensus size: 139
1003991 GTATTTGTAA
1004001 ATATTTGCATTTCCATTGTTCTTTCCCACTGTAAGCCCATACGGAGGAGCTGCAATTATTTCTCT
1 ATATTTGCATTTCCATTGTTCTTTCCCACTGTAAGCCCATACGGAGGAGCTGCAATTATTTCTCT
1004066 ATAATCGCAATTGCTCTGTCAGTATACTATGACGTCATAAAGGTGTAACGTTATATATACTTTTC
66 ATAATCGCAATTGCTCTGTCAGTATACTATGACGTCATAAAGGTGTAACGTTATATATACTTTTC
1004131 CATGACGTT
131 CATGACGTT
*
1004140 ATATTTGCATTTCCATTGTTCTTTCCCACTGTAAGCCCATACGGAGGCGCTGCAATTATTTCTCT
1 ATATTTGCATTTCCATTGTTCTTTCCCACTGTAAGCCCATACGGAGGAGCTGCAATTATTTCTCT
1004205 ATAATCGCAATTGCTCTGTCAGTATACTATGACGTCATAAAGGTGTAACGTTATATATACTTTTC
66 ATAATCGCAATTGCTCTGTCAGTATACTATGACGTCATAAAGGTGTAACGTTATATATACTTTTC
1004270 CATGACGTT
131 CATGACGTT
1004279 ATA
1 ATA
1004282 GATTTAAACC
Statistics
Matches: 141, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 141 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (139 bp):
ATATTTGCATTTCCATTGTTCTTTCCCACTGTAAGCCCATACGGAGGAGCTGCAATTATTTCTCT
ATAATCGCAATTGCTCTGTCAGTATACTATGACGTCATAAAGGTGTAACGTTATATATACTTTTC
CATGACGTT
Found at i:1014437 original size:29 final size:29
Alignment explanation
Indices: 1014400--1014720 Score: 471
Period size: 29 Copynumber: 11.1 Consensus size: 29
1014390 AGCATCGGCT
1014400 ACTACACCTCACAGCCCAGGTAAACACGC
1 ACTACACCTCACAGCCCAGGTAAACACGC
*
1014429 ACTTCACCTCACAGCCCAGGTAAACACGC
1 ACTACACCTCACAGCCCAGGTAAACACGC
*
1014458 ACTACACCTCACAACCCAGGTAAACACGC
1 ACTACACCTCACAGCCCAGGTAAACACGC
* * *
1014487 ACTTCACCTCACAGCCAAGGTAAACATGC
1 ACTACACCTCACAGCCCAGGTAAACACGC
* *
1014516 ACTGCACCTCACAACCCAGGTAAACACGC
1 ACTACACCTCACAGCCCAGGTAAACACGC
* *
1014545 ACTACACCTCACAGCCAAGGTAAACATGC
1 ACTACACCTCACAGCCCAGGTAAACACGC
* * *
1014574 ACTACACCTCACAACCCAGTTAAACATGC
1 ACTACACCTCACAGCCCAGGTAAACACGC
*
1014603 ACTACACCTCACAGCCCAGGGAAACACGC
1 ACTACACCTCACAGCCCAGGTAAACACGC
*
1014632 ACTACACCTCACAACCCAGGTAAACACGC
1 ACTACACCTCACAGCCCAGGTAAACACGC
* *
1014661 ACTACACCTCACAGCCCATGTAAACATGC
1 ACTACACCTCACAGCCCAGGTAAACACGC
* * *
1014690 ACTGCACCTCACAACCTAGGTAAACACGC
1 ACTACACCTCACAGCCCAGGTAAACACGC
1014719 AC
1 AC
1014721 GACTTCTCCT
Statistics
Matches: 260, Mismatches: 32, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 260 1.00
ACGTcount: A:0.36, C:0.39, G:0.12, T:0.13
Consensus pattern (29 bp):
ACTACACCTCACAGCCCAGGTAAACACGC
Found at i:1015940 original size:12 final size:12
Alignment explanation
Indices: 1015923--1015960 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
1015913 ACACAAGAGT
1015923 TTAAGTATAACA
1 TTAAGTATAACA
*
1015935 TTAAGTACAACA
1 TTAAGTATAACA
*
1015947 TCAAGTATAACA
1 TTAAGTATAACA
1015959 TT
1 TT
1015961 TATTGAAGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32
Consensus pattern (12 bp):
TTAAGTATAACA
Found at i:1019453 original size:22 final size:22
Alignment explanation
Indices: 1019414--1019456 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1019404 TAAAGGTGTA
*
1019414 ACGTTATATATACTTTTCCATG
1 ACGTTATATATACATTTCCATG
* *
1019436 ACGTTATATTTGCATTTCCAT
1 ACGTTATATATACATTTCCAT
1019457 TGTTCTTTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.19, G:0.09, T:0.47
Consensus pattern (22 bp):
ACGTTATATATACATTTCCATG
Found at i:1019493 original size:139 final size:139
Alignment explanation
Indices: 1019302--1019582 Score: 553
Period size: 139 Copynumber: 2.0 Consensus size: 139
1019292 GTATTTGTAA
1019302 ATATTTGCATTTCCATTGTTCTTTCCCACTGTAAGCCCATACGGAGGAGCTGCAATTATTTCTCT
1 ATATTTGCATTTCCATTGTTCTTTCCCACTGTAAGCCCATACGGAGGAGCTGCAATTATTTCTCT
1019367 ATAATCGCAATTGCTCTGTCAGTATACTATGACGTCATAAAGGTGTAACGTTATATATACTTTTC
66 ATAATCGCAATTGCTCTGTCAGTATACTATGACGTCATAAAGGTGTAACGTTATATATACTTTTC
1019432 CATGACGTT
131 CATGACGTT
*
1019441 ATATTTGCATTTCCATTGTTCTTTCCCACTGTAAGCCCATACGGAGGCGCTGCAATTATTTCTCT
1 ATATTTGCATTTCCATTGTTCTTTCCCACTGTAAGCCCATACGGAGGAGCTGCAATTATTTCTCT
1019506 ATAATCGCAATTGCTCTGTCAGTATACTATGACGTCATAAAGGTGTAACGTTATATATACTTTTC
66 ATAATCGCAATTGCTCTGTCAGTATACTATGACGTCATAAAGGTGTAACGTTATATATACTTTTC
1019571 CATGACGTT
131 CATGACGTT
1019580 ATA
1 ATA
1019583 GATTTAAACC
Statistics
Matches: 141, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 141 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (139 bp):
ATATTTGCATTTCCATTGTTCTTTCCCACTGTAAGCCCATACGGAGGAGCTGCAATTATTTCTCT
ATAATCGCAATTGCTCTGTCAGTATACTATGACGTCATAAAGGTGTAACGTTATATATACTTTTC
CATGACGTT
Found at i:1022341 original size:2 final size:2
Alignment explanation
Indices: 1022334--1022391 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
1022324 ATTCGTAAAT
1022334 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1022376 TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC
1022392 GTTGTATCAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1039282 original size:2 final size:2
Alignment explanation
Indices: 1039265--1039314 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
1039255 CCCCTTCAAA
* *
1039265 TC TC TC TT TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1039307 TC TC TC TC
1 TC TC TC TC
1039315 ATAAATTCTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:1039370 original size:1 final size:1
Alignment explanation
Indices: 1039364--1039391 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
1039354 AAGTGTTATC
1039364 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1039392 ACATAAACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1042172 original size:3 final size:3
Alignment explanation
Indices: 1042164--1042204 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1042154 CAGAAATATA
1042164 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
1042205 GATGATGATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:1042211 original size:3 final size:3
Alignment explanation
Indices: 1042205--1042265 Score: 50
Period size: 3 Copynumber: 20.3 Consensus size: 3
1042195 ATCATCATCA
* * * * * *
1042205 GAT GAT GAT GAT GAT GAT AAA GTT GAT GAT GAT GAT AAG GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
**
1042253 GAT TTT GAT GAT G
1 GAT GAT GAT GAT G
1042266 CCAATTCTAA
Statistics
Matches: 43, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.36, C:0.00, G:0.31, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:1042250 original size:18 final size:18
Alignment explanation
Indices: 1042211--1042255 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1042201 ATCAGATGAT
**
1042211 GATGATGATGATAAAGTT
1 GATGATGATGATAAAGAA
*
1042229 GATGATGATGATAAGGAA
1 GATGATGATGATAAAGAA
1042247 GATGATGAT
1 GATGATGAT
1042256 TTTGATGATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.31, T:0.29
Consensus pattern (18 bp):
GATGATGATGATAAAGAA
Found at i:1042252 original size:21 final size:21
Alignment explanation
Indices: 1042204--1042255 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
1042194 CATCATCATC
* *
1042204 AGATGATGATGATGATGATAA
1 AGATGATGATGATGATAAGAA
* *
1042225 AGTTGATGATGATGATAAGGA
1 AGATGATGATGATGATAAGAA
1042246 AGATGATGAT
1 AGATGATGAT
1042256 TTTGATGATG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.40, C:0.00, G:0.31, T:0.29
Consensus pattern (21 bp):
AGATGATGATGATGATAAGAA
Found at i:1047529 original size:20 final size:20
Alignment explanation
Indices: 1047504--1047544 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1047494 ACAGTATAAA
1047504 CGTTCTAACGAGCAGCAATC
1 CGTTCTAACGAGCAGCAATC
1047524 CGTTCTAACGAGCAGCAATC
1 CGTTCTAACGAGCAGCAATC
1047544 C
1 C
1047545 ATATTCATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.32, G:0.20, T:0.20
Consensus pattern (20 bp):
CGTTCTAACGAGCAGCAATC
Found at i:1050530 original size:14 final size:14
Alignment explanation
Indices: 1050511--1050538 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1050501 GTGGAGGTTG
1050511 TTAACTTAACTTAA
1 TTAACTTAACTTAA
1050525 TTAACTTAACTTAA
1 TTAACTTAACTTAA
1050539 GTTTGTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAACTTAACTTAA
Found at i:1054287 original size:180 final size:180
Alignment explanation
Indices: 1053975--1054518 Score: 943
Period size: 180 Copynumber: 3.0 Consensus size: 180
1053965 GGCTGCCAAA
* *
1053975 AGGGTACCCTCATTGTAGGGACAA---CTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCA
* *
1054037 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTTGGA-TTTGATTTCCGATAATTTATCGA
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATATATCG-
*
1054101 AAAAAATACCAGCTTTTGAACTTACTCATTTTTTGGCAAAATATTGCATAT
130 AAAAAATACCAGCTTTTGAACTTACTCATTTTTTGGCAAAATGTTGCATAT
1054152 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCA
* *
1054217 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATGTATAGA
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATATATCGA
* *
1054282 AAAAATACTAGCTTTTGAACTTAGTCATTTTTTGGCAAAATGTTGCATAT
131 AAAAATACCAGCTTTTGAACTTACTCATTTTTTGGCAAAATGTTGCATAT
1054332 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCA
* *
1054397 GATCAATTGTACATATATCAGAGGTGTGCATATTGATAGGATTTTGATTTCTGATAATATATCGA
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATATATCGA
*
1054462 AAAAATACCAGCTTTTGAACTTATTCATTTTTTGGCAAAATGTTGCATAT
131 AAAAATACCAGCTTTTGAACTTACTCATTTTTTGGCAAAATGTTGCATAT
1054512 AGGGTAC
1 AGGGTAC
1054519 TCCATTTCAC
Statistics
Matches: 349, Mismatches: 14, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
177 22 0.06
180 307 0.88
181 20 0.06
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (180 bp):
AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCA
GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATATATCGA
AAAAATACCAGCTTTTGAACTTACTCATTTTTTGGCAAAATGTTGCATAT
Found at i:1055802 original size:24 final size:24
Alignment explanation
Indices: 1055775--1056540 Score: 685
Period size: 24 Copynumber: 30.3 Consensus size: 24
1055765 ACATGTACTG
*
1055775 GTATTAATATACTTCTACTTACAA
1 GTATAAATATACTTCTACTTACAA
*
1055799 GTATAAATATACTTCTACTTACTA
1 GTATAAATATACTTCTACTTACAA
*
1055823 GTATAAATATACTTCTACTTAC-T
1 GTATAAATATACTTCTACTTACAA
* * *
1055846 CTATAAATGTACTTCTACTTAC-T
1 GTATAAATATACTTCTACTTACAA
*
1055869 GTATAAATATA-TTTTACTTACAA
1 GTATAAATATACTTCTACTTACAA
*
1055892 TGGTACTAGTAAAATATACTTCTACTTACTA
1 --G---TA-T-AAATATACTTCTACTTACAA
* *
1055923 GTATAAATATACTTTTACTTAC-T
1 GTATAAATATACTTCTACTTACAA
*
1055946 CTATAAATATACTTTTACTTACAATGGTACAA
1 GTATAAATATAC--TT-C-TAC--T--TACAA
*
1055978 GTATAAATATACTTCTACTTAC-T
1 GTATAAATATACTTCTACTTACAA
* *
1056001 GTATAAATGTACTTCTACTTAC-T
1 GTATAAATATACTTCTACTTACAA
*
1056024 GTATAAATATACTTTTACTTATAATGGTACAA
1 GTATAAATATAC--TT-C---TACT--TACAA
*
1056056 GTATAAATATACTTCTACTTAC-T
1 GTATAAATATACTTCTACTTACAA
*
1056079 GTATAAATATACTTTTACTTACAGTGTACTA
1 GTATAAATATAC--TT-C-TAC--T-TACAA
* *
1056110 GTAAAAATATACTTCTACTTACTA
1 GTATAAATATACTTCTACTTACAA
*
1056134 GTATAAATATACTTCTACTTACTA
1 GTATAAATATACTTCTACTTACAA
*
1056158 GTATAAATATACTTCTACTTACTA
1 GTATAAATATACTTCTACTTACAA
*
1056182 GTATAAATATACTTTTAC-T-C--
1 GTATAAATATACTTCTACTTACAA
1056202 -TATAAATATACTTCTACTTACAA
1 GTATAAATATACTTCTACTTACAA
1056225 GTATAAATATACTTCTACTTACAA
1 GTATAAATATACTTCTACTTACAA
*
1056249 GTATAAATATACTTCTACTAACAA
1 GTATAAATATACTTCTACTTACAA
1056273 GTATAAATATACTTCTACTTACTAGTACAA
1 GTATAAATATAC-T-T-C-TACT--TACAA
*
1056303 GTATAAATATACTTCTACTTACTA
1 GTATAAATATACTTCTACTTACAA
*
1056327 GTATAAATATACTTATACTTACAA
1 GTATAAATATACTTCTACTTACAA
* *
1056351 GTATAATTATACTTCTACTTTCAA
1 GTATAAATATACTTCTACTTACAA
1056375 GTATAAATATACTTCTACTTACTAGTACAA
1 GTATAAATATAC-T-T-C-TACT--TACAA
**
1056405 GTATAAATATACTTCTACTTACTT
1 GTATAAATATACTTCTACTTACAA
*
1056429 GTATAAATATAGTTCTACTTACAA
1 GTATAAATATACTTCTACTTACAA
1056453 GTATAAATATACTTCTACTTACTAGTACTA
1 GTATAAATATACTTCTACTTAC----A--A
* *
1056483 GTATAAATATACTTTTACTTACTA
1 GTATAAATATACTTCTACTTACAA
*
1056507 GTATGAATATA-TTCTACTTAATACAA
1 GTATAAATATACTTCTAC-T--TACAA
1056533 GTATAAAT
1 GTATAAAT
1056541 GAAGCAATCA
Statistics
Matches: 630, Mismatches: 51, Indels: 120
0.79 0.06 0.15
Matches are distributed among these distances:
19 16 0.03
20 1 0.00
21 1 0.00
22 10 0.02
23 92 0.15
24 309 0.49
25 11 0.02
26 29 0.05
27 13 0.02
28 17 0.03
29 13 0.02
30 68 0.11
31 27 0.04
32 23 0.04
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (24 bp):
GTATAAATATACTTCTACTTACAA
Found at i:1056007 original size:78 final size:77
Alignment explanation
Indices: 1055822--1056540 Score: 640
Period size: 78 Copynumber: 9.1 Consensus size: 77
1055812 TCTACTTACT
* *
1055822 AGTATAAATATACTTCTACTTACTCTATAAATGTACTTCTACTTACTGTATAAATATA-TTTTAC
1 AGTATAAATATACTTCTACTTACTGTATAAATATACTTCTACTTACTGTATAAATATACTTTTAC
*
1055886 TTACAATGGTACT
66 TTACAAT-GTACA
* *
1055899 AGTA-AAATATACTTCTACTTACTAGTATAAATATACTTTTACTTACTCTATAAATATACTTTTA
1 AGTATAAATATACTTCTACTTACT-GTATAAATATACTTCTACTTACTGTATAAATATACTTTTA
1055963 CTTACAATGGTACA
65 CTTACAAT-GTACA
*
1055977 AGTATAAATATACTTCTACTTACTGTATAAATGTACTTCTACTTACTGTATAAATATACTTTTAC
1 AGTATAAATATACTTCTACTTACTGTATAAATATACTTCTACTTACTGTATAAATATACTTTTAC
*
1056042 TTATAATGGTACA
66 TTACAAT-GTACA
* * * ** *
1056055 AGTATAAATATACTTCTACTTACTGTATAAATATACTTTTACTTACAGTGTACT-AGTAAAAATA
1 AGTATAAATATACTTCTACTTACTGTATAAATATACTTCTACTTAC--TGTA-TAAATATACTTT
* *
1056119 TACTT-CTACT-TACT
63 TACTTAC-AATGTACA
1056133 AGTATAAATATACTTCTACTTACTAGTATAAATATACTTCTACTTACTAGTATAAATATACTTTT
1 AGTATAAATATACTTCTACTTACT-GTATAAATATACTTCTACTTACT-GTATAAATATACTTTT
* *
1056198 ACTCTATAAATATACTTCTACTTACA
64 A--CT-T--ACA-A----T--GTACA
* * * *
1056224 AGTATAAATATACTTCTACTTACAAGTATAAATATACTTCTACTAACAAGTATAAATATACTTCT
1 AGTATAAATATACTTCTACTTAC-TGTATAAATATACTTCTACTTAC-TGTATAAATATACTTTT
*
1056289 ACTTACTA-GTACA
64 ACTTACAATGTACA
* * * *
1056302 AGTATAAATATACTTCTACTTACTAGTATAAATATACTTATACTTACAAGTATAATTATACTTCT
1 AGTATAAATATACTTCTACTTACT-GTATAAATATACTTCTACTTAC-TGTATAAATATACTTTT
* *
1056367 ACTTTCAA-GTATA
64 ACTTACAATGTACA
* ** * * * * *
1056380 AATATACTTCTACTTACTA-GTACAAGTATAAATATACTTCTACTTACTTGTATAAATATAGTTC
1 AGTATAAATATACTT-CTACTTAC-TGTATAAATATACTTCTACTTAC-TGTATAAATATACTTT
*
1056444 TACTTACAA-GTATA
63 TACTTACAATGTACA
* ** * * * * *
1056458 AATATACTTCTACTTACTA-GTACTAGTATAAATATACTTTTACTTACTAGTATGAATATA-TTC
1 AGTATAAATATACTT-CTACTTACT-GTATAAATATACTTCTACTTACT-GTATAAATATACTTT
1056521 TACTT--AA--TACA
63 TACTTACAATGTACA
1056532 AGTATAAAT
1 AGTATAAAT
1056541 GAAGCAATCA
Statistics
Matches: 550, Mismatches: 61, Indels: 65
0.81 0.09 0.10
Matches are distributed among these distances:
74 9 0.02
75 2 0.00
76 19 0.03
77 45 0.08
78 342 0.62
79 43 0.08
80 18 0.03
81 2 0.00
83 1 0.00
85 1 0.00
86 1 0.00
88 2 0.00
89 2 0.00
91 63 0.11
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (77 bp):
AGTATAAATATACTTCTACTTACTGTATAAATATACTTCTACTTACTGTATAAATATACTTTTAC
TTACAATGTACA
Found at i:1056060 original size:55 final size:55
Alignment explanation
Indices: 1055918--1056526 Score: 280
Period size: 54 Copynumber: 11.9 Consensus size: 55
1055908 TACTTCTACT
* * *
1055918 TACTAGTATAAATATACTTTTACTTACT-CTATAAATATACTTTTACTTACAATGG
1 TACTAGTATAAATATACTTCTACTTACTAGTATAAATATACTTTTACTTATAAT-G
* * *
1055973 TACAAGTATAAATATACTTCTACTTACT-GTATAAATGTAC--TT-C---TACT-
1 TACTAGTATAAATATACTTCTACTTACTAGTATAAATATACTTTTACTTATAATG
* * * ** * * *
1056020 TACT-GTATAAATATACTTTTACTTA-TAATGGTACAAGTATAAATATACTTCTACT-
1 TACTAGTATAAATATACTTCTACTTACT-A--GTATAAATATACTTTTACTTATAATG
* * * * ** * * *
1056075 TACT-GTATAAATATACTTTTACTTAC-AGTGTACTAGTAAAAATATACTTCTACT-
1 TACTAGTATAAATATACTTCTACTTACTAGTATA--AATATACTTTTACTTATAATG
*
1056129 TACTAGTATAAATATACTTCTACTTACTAGTATAAATATAC--TT-C---TACT-
1 TACTAGTATAAATATACTTCTACTTACTAGTATAAATATACTTTTACTTATAATG
* *
1056177 TACTAGTATAAATATAC-T-T--TTACT-CTATAAATATAC--TT-C---TACT-
1 TACTAGTATAAATATACTTCTACTTACTAGTATAAATATACTTTTACTTATAATG
* * *
1056220 TACAAGTATAAATATACTTCTACTTACAAGTATAAATATACTTCTAC---T-A--
1 TACTAGTATAAATATACTTCTACTTACTAGTATAAATATACTTTTACTTATAATG
* * * ** * * *
1056269 -ACAAGTATAAATATACTTCTACTTACTAGTACAAGTATAAATATACTTCTACT-
1 TACTAGTATAAATATACTTCTACTTACTAGTATAAATATACTTTTACTTATAATG
* * * *
1056322 TACTAGTATAAATATACTTATACTTACAAGTATAATTATACTTCTAC---T--T-
1 TACTAGTATAAATATACTTCTACTTACTAGTATAAATATACTTTTACTTATAATG
* * * ** * * *
1056371 T-CAAGTATAAATATACTTCTACTTACTAGTACAAGTATAAATATACTTCTACT-
1 TACTAGTATAAATATACTTCTACTTACTAGTATAAATATACTTTTACTTATAATG
* * * *
1056424 TACTTGTATAAATATAGTTCTACTTACAAGTATAAATATACTTCTACTTACT-A-G
1 TACTAGTATAAATATACTTCTACTTACTAGTATAAATATACTTTTACTTA-TAATG
* * *
1056478 TACTAGTATAAATATACTTTTACTTACTAGTATGAATATA-TTCTACTTA
1 TACTAGTATAAATATACTTCTACTTACTAGTATAAATATACTTTTACTTA
1056527 ATACAAGTAT
Statistics
Matches: 450, Mismatches: 67, Indels: 76
0.76 0.11 0.13
Matches are distributed among these distances:
43 34 0.08
44 6 0.01
45 2 0.00
46 21 0.05
47 8 0.02
48 109 0.24
49 12 0.03
50 1 0.00
51 7 0.02
52 6 0.01
53 13 0.03
54 139 0.31
55 87 0.19
56 5 0.01
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (55 bp):
TACTAGTATAAATATACTTCTACTTACTAGTATAAATATACTTTTACTTATAATG
Found at i:1056177 original size:102 final size:101
Alignment explanation
Indices: 1055798--1056509 Score: 778
Period size: 102 Copynumber: 7.0 Consensus size: 101
1055788 TCTACTTACA
** *
1055798 AGTATAAATATACTTCTACTTACTAGTATAAATATACTTCTACTTAC-TCTATAAATGTACTTCT
1 AGTATAAATATACTTCTACTTACTAGTATAAATATACTTCTACTTACAAGTATAAATATACTTCT
*
1055862 ACTTACTGTATAAATATA-TTTTACTTACAATGGTACT
66 ACTTACTGTATAAATATACTTTTACTTAC--TAGTACT
* ** *
1055899 AGTA-AAATATACTTCTACTTACTAGTATAAATATACTTTTACTTAC-TCTATAAATATACTTTT
1 AGTATAAATATACTTCTACTTACTAGTATAAATATACTTCTACTTACAAGTATAAATATACTTCT
* * ** * *
1055962 ACTTACAATGGTACAAGTATAAATATACTT-CTACTTACT
66 ACTTAC--T-GTATAAATATACTTTTACTTACTA-GTACT
* *
1056001 -GTATAAATGTACTTCTACTTACT-GTATAAATATACTTTTACTTATAATGGTACAAGTATAAAT
1 AGTATAAATATACTTCTACTTACTAGTATAAATATAC--TT-C---TACT--TACAAGTATAAAT
1056064 ATACTTCTACTTACTGTATAAATATACTTTTACTTAC-AGTGTACT
58 ATACTTCTACTTACTGTATAAATATACTTTTACTTACTA--GTACT
* *
1056109 AGTAAAAATATACTTCTACTTACTAGTATAAATATACTTCTACTTACTAGTATAAATATACTTCT
1 AGTATAAATATACTTCTACTTACTAGTATAAATATACTTCTACTTACAAGTATAAATATACTTCT
1056174 ACTTACTAGTATAAATATAC--TT--TTAC---T-C-
66 ACTTACT-GTATAAATATACTTTTACTTACTAGTACT
*
1056202 --TATAAATATACTTCTACTTACAAGTATAAATATACTTCTACTTACAAGTATAAATATACTTCT
1 AGTATAAATATACTTCTACTTACTAGTATAAATATACTTCTACTTACAAGTATAAATATACTTCT
* * * *
1056265 ACTAACAAGTATAAATATACTTCTACTTACTAGTACA
66 ACTTAC-TGTATAAATATACTTTTACTTACTAGTACT
* *
1056302 AGTATAAATATACTTCTACTTACTAGTATAAATATACTTATACTTACAAGTATAATTATACTTCT
1 AGTATAAATATACTTCTACTTACTAGTATAAATATACTTCTACTTACAAGTATAAATATACTTCT
* * * *
1056367 ACTTTCAAGTATAAATATACTTCTACTTACTAGTACA
66 ACTTAC-TGTATAAATATACTTTTACTTACTAGTACT
* *
1056404 AGTATAAATATACTTCTACTTACTTGTATAAATATAGTTCTACTTACAAGTATAAATATACTTCT
1 AGTATAAATATACTTCTACTTACTAGTATAAATATACTTCTACTTACAAGTATAAATATAC-T-T
1056469 ACTTACTAGTACTAGTATAAATATACTTTTACTTACTAGTA
64 -C-TACT--TACT-GTATAAATATACTTTTACTTACTAGTA
1056510 TGAATATATT
Statistics
Matches: 528, Mismatches: 44, Indels: 71
0.82 0.07 0.11
Matches are distributed among these distances:
91 77 0.15
93 1 0.00
94 1 0.00
95 5 0.01
98 1 0.00
99 5 0.01
100 62 0.12
101 22 0.04
102 202 0.38
103 25 0.05
104 10 0.02
105 1 0.00
106 4 0.01
107 20 0.04
108 36 0.07
109 24 0.05
110 32 0.06
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (101 bp):
AGTATAAATATACTTCTACTTACTAGTATAAATATACTTCTACTTACAAGTATAAATATACTTCT
ACTTACTGTATAAATATACTTTTACTTACTAGTACT
Found at i:1060984 original size:37 final size:37
Alignment explanation
Indices: 1060936--1061158 Score: 272
Period size: 37 Copynumber: 6.0 Consensus size: 37
1060926 CCTGTAGTAC
*
1060936 GTGTCTCTGTAGCTGTATCTTGTTTGTTGTCTCTGTA
1 GTGTCTCTGTAGCAGTATCTTGTTTGTTGTCTCTGTA
* * * * *
1060973 GTGTCTCTGTAGTAATGTCTAGTTTGTTTTCTCTGTA
1 GTGTCTCTGTAGCAGTATCTTGTTTGTTGTCTCTGTA
*
1061010 GTGTCTCTGTAGCAGTATATT-TTGTGTTGTCTCTGTA
1 GTGTCTCTGTAGCAGTATCTTGTT-TGTTGTCTCTGTA
*
1061047 GTGTAAT-TGTAGCAGTATCTTGTTTGTTGTCTTCT-TA
1 GTGT-CTCTGTAGCAGTATCTTGTTTGTTGTC-TCTGTA
* * * *
1061084 TTTTCTCTGTAGCAATATCTTGTTAGTTGTCTCTGTA
1 GTGTCTCTGTAGCAGTATCTTGTTTGTTGTCTCTGTA
* *
1061121 GTGTCTCTGTAGCTGTAACTTGTTTGTTGTCTCTGTA
1 GTGTCTCTGTAGCAGTATCTTGTTTGTTGTCTCTGTA
1061158 G
1 G
1061159 CAGTATCTTG
Statistics
Matches: 155, Mismatches: 25, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
36 6 0.04
37 143 0.92
38 6 0.04
ACGTcount: A:0.13, C:0.14, G:0.22, T:0.50
Consensus pattern (37 bp):
GTGTCTCTGTAGCAGTATCTTGTTTGTTGTCTCTGTA
Found at i:1061119 original size:111 final size:111
Alignment explanation
Indices: 1060943--1061158 Score: 303
Period size: 111 Copynumber: 1.9 Consensus size: 111
1060933 TACGTGTCTC
* * * * *
1060943 TGTAGCTGTATCTTGTTTGTTGTCTCTGTAGTGTCTCTGTAGTAATGTCTAGTTTGTTTTCTCTG
1 TGTAGCAGTATCTTGTTTGTTGTCTCTGTAGTGTCTCTGTAGCAATATCTAGTTAGTTGTCTCTG
1061008 TAGTGTCTCTGTAGCAGTATA-TT-TTGTGTTGTCTCTGTAGTGTAAT
66 TAGTGTCTCTGTAGCAGTA-ACTTGTT-TGTTGTCTCTGTAGTGTAAT
* * *
1061054 TGTAGCAGTATCTTGTTTGTTGTCTTCT-TATTTTCTCTGTAGCAATATCTTGTTAGTTGTCTCT
1 TGTAGCAGTATCTTGTTTGTTGTC-TCTGTAGTGTCTCTGTAGCAATATCTAGTTAGTTGTCTCT
*
1061118 GTAGTGTCTCTGTAGCTGTAACTTGTTTGTTGTCTCTGTAG
65 GTAGTGTCTCTGTAGCAGTAACTTGTTTGTTGTCTCTGTAG
1061159 CAGTATCTTG
Statistics
Matches: 93, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
110 1 0.01
111 87 0.94
112 5 0.05
ACGTcount: A:0.13, C:0.14, G:0.22, T:0.50
Consensus pattern (111 bp):
TGTAGCAGTATCTTGTTTGTTGTCTCTGTAGTGTCTCTGTAGCAATATCTAGTTAGTTGTCTCTG
TAGTGTCTCTGTAGCAGTAACTTGTTTGTTGTCTCTGTAGTGTAAT
Found at i:1061158 original size:26 final size:26
Alignment explanation
Indices: 1061122--1061188 Score: 107
Period size: 26 Copynumber: 2.6 Consensus size: 26
1061112 GTCTCTGTAG
1061122 TGTCTCTGTAGCTGTAACTTGTTTGT
1 TGTCTCTGTAGCTGTAACTTGTTTGT
* *
1061148 TGTCTCTGTAGCAGTATCTTGTTTGT
1 TGTCTCTGTAGCTGTAACTTGTTTGT
*
1061174 TGTTTCTGTAGCTGT
1 TGTCTCTGTAGCTGT
1061189 GTTTTGATTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.10, C:0.15, G:0.24, T:0.51
Consensus pattern (26 bp):
TGTCTCTGTAGCTGTAACTTGTTTGT
Found at i:1061199 original size:26 final size:26
Alignment explanation
Indices: 1061126--1061210 Score: 82
Period size: 26 Copynumber: 3.3 Consensus size: 26
1061116 CTGTAGTGTC
* * * *
1061126 TCTGTAGCTGTAACTTGTTTGTTGTC
1 TCTGTAGCAGTATCTTGATTGTTGTT
*
1061152 TCTGTAGCAGTATCTTGTTTGTTGTT
1 TCTGTAGCAGTATCTTGATTGTTGTT
* * *
1061178 TCTGTAGCTGTGTTTTGATTGTTGTCT
1 TCTGTAGCAGTATCTTGATTGTTGT-T
1061205 T-TGTAG
1 TCTGTAG
1061211 GGTTGTATAG
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
26 49 0.96
27 2 0.04
ACGTcount: A:0.11, C:0.12, G:0.25, T:0.53
Consensus pattern (26 bp):
TCTGTAGCAGTATCTTGATTGTTGTT
Found at i:1063216 original size:49 final size:49
Alignment explanation
Indices: 1063123--1063216 Score: 138
Period size: 49 Copynumber: 1.9 Consensus size: 49
1063113 GGTTCGAATG
*
1063123 TTTACATAGGAATATATAGAGAAAAATCTTTAAAAGTCTTCTTTTCTTT
1 TTTACATAGGAATATATAGAGAAAAATCTTTAAAAATCTTCTTTTCTTT
*
1063172 TTTA-ATAGGAATATATAGGGAAAAAATCTTTAAAAAT-TATCTTTT
1 TTTACATAGGAATATATAGAG-AAAAATCTTTAAAAATCT-TCTTTT
1063217 AAAACACAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
48 16 0.39
49 25 0.61
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.41
Consensus pattern (49 bp):
TTTACATAGGAATATATAGAGAAAAATCTTTAAAAATCTTCTTTTCTTT
Found at i:1068049 original size:165 final size:165
Alignment explanation
Indices: 1067771--1068099 Score: 595
Period size: 165 Copynumber: 2.0 Consensus size: 165
1067761 AGCACATACT
*
1067771 ATAGTACTTTGCGCCTACAAGAAATGCCTTAATTAAACGCACTATAAGAGATTTTACATGCAGAT
1 ATAGTACTTTGCGCCTACAAGAAATGCCTTAATTAAACGCACTATAAGAGATTTTACATGCAGAA
*
1067836 TGAAGTAACCAAAAATATCACTGTAAGCCTTAACCCTTTGGCAACCCGAAACTTGCCATGTGTTT
66 TGAAGTAACCAAAAATACCACTGTAAGCCTTAACCCTTTGGCAACCCGAAACTTGCCATGTGTTT
* *
1067901 TTATTATGAAAGAAAGTGAAATCATGATTCGATAA
131 TTATCATGAAAGAAAGTGAAATCACGATTCGATAA
*
1067936 ATAGTTCTTTGCGCCTACAAGAAATGCCTTAATTAAACGCACTATAAGAGATTTTACATGCAGAA
1 ATAGTACTTTGCGCCTACAAGAAATGCCTTAATTAAACGCACTATAAGAGATTTTACATGCAGAA
*
1068001 TGAAGTAACCAAAAATACCACTGTAAGCCTTAACCCTTTGGGAACCCGAAACTTGCCATGTGTTT
66 TGAAGTAACCAAAAATACCACTGTAAGCCTTAACCCTTTGGCAACCCGAAACTTGCCATGTGTTT
*
1068066 TTATCATGAAAGAAAGTGAAATCACGATTGGATA
131 TTATCATGAAAGAAAGTGAAATCACGATTCGATA
1068100 CCTTGTAGAA
Statistics
Matches: 157, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
165 157 1.00
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (165 bp):
ATAGTACTTTGCGCCTACAAGAAATGCCTTAATTAAACGCACTATAAGAGATTTTACATGCAGAA
TGAAGTAACCAAAAATACCACTGTAAGCCTTAACCCTTTGGCAACCCGAAACTTGCCATGTGTTT
TTATCATGAAAGAAAGTGAAATCACGATTCGATAA
Found at i:1070596 original size:15 final size:15
Alignment explanation
Indices: 1070576--1070609 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1070566 TTCATAAGGA
1070576 CGTAATGGTTAGATG
1 CGTAATGGTTAGATG
*
1070591 CGTAATGTTTAGATG
1 CGTAATGGTTAGATG
1070606 CGTA
1 CGTA
1070610 TATTTATCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.09, G:0.29, T:0.35
Consensus pattern (15 bp):
CGTAATGGTTAGATG
Found at i:1072224 original size:2 final size:2
Alignment explanation
Indices: 1072217--1072262 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
1072207 AAGAATGTAA
1072217 TC TC TC TC TC TC TC T- TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1072258 TC TC T
1 TC TC T
1072263 GTGCACTTCT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1075531 original size:2 final size:2
Alignment explanation
Indices: 1075524--1075580 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
1075514 CAGAAAATAT
1075524 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1075566 TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC T
1075581 AACACCAGAC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1080004 original size:2 final size:2
Alignment explanation
Indices: 1079997--1080041 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1079987 CAGAAAATAT
1079997 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1080039 TC T
1 TC T
1080042 AATATCAGAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1087404 original size:22 final size:22
Alignment explanation
Indices: 1087379--1087444 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
1087369 TGAACGATCC
*
1087379 ATGAATACATATTGATAGCATA
1 ATGAATACATATTGATTGCATA
* *
1087401 ATGAATATATATTGATTGCGTA
1 ATGAATACATATTGATTGCATA
1087423 ATGAATACATATTGATTGCATA
1 ATGAATACATATTGATTGCATA
1087445 GTGATCTAGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (22 bp):
ATGAATACATATTGATTGCATA
Found at i:1092542 original size:8 final size:8
Alignment explanation
Indices: 1092529--1092581 Score: 88
Period size: 8 Copynumber: 6.6 Consensus size: 8
1092519 TGGTTTCACC
1092529 CTGTCCGT
1 CTGTCCGT
1092537 CTGTCCGT
1 CTGTCCGT
*
1092545 CTGTCTGT
1 CTGTCCGT
*
1092553 CCGTCCGT
1 CTGTCCGT
1092561 CTGTCCGT
1 CTGTCCGT
1092569 CTGTCCGT
1 CTGTCCGT
1092577 CTGTC
1 CTGTC
1092582 TGTAGACGCA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 41 1.00
ACGTcount: A:0.00, C:0.38, G:0.25, T:0.38
Consensus pattern (8 bp):
CTGTCCGT
Found at i:1092552 original size:4 final size:4
Alignment explanation
Indices: 1092529--1092584 Score: 58
Period size: 4 Copynumber: 14.0 Consensus size: 4
1092519 TGGTTTCACC
* * * * * *
1092529 CTGT CCGT CTGT CCGT CTGT CTGT CCGT CCGT CTGT CCGT CTGT CCGT
1 CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT
1092577 CTGT CTGT
1 CTGT CTGT
1092585 AGACGCAACT
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.00, C:0.36, G:0.25, T:0.39
Consensus pattern (4 bp):
CTGT
Found at i:1092552 original size:12 final size:12
Alignment explanation
Indices: 1092535--1092584 Score: 73
Period size: 12 Copynumber: 4.2 Consensus size: 12
1092525 CACCCTGTCC
1092535 GTCTGTCCGTCT
1 GTCTGTCCGTCT
*
1092547 GTCTGTCCGTCC
1 GTCTGTCCGTCT
1092559 GTCTGTCCGTCT
1 GTCTGTCCGTCT
* *
1092571 GTCCGTCTGTCT
1 GTCTGTCCGTCT
1092583 GT
1 GT
1092585 AGACGCAACT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.00, C:0.34, G:0.26, T:0.40
Consensus pattern (12 bp):
GTCTGTCCGTCT
Found at i:1109200 original size:12 final size:12
Alignment explanation
Indices: 1109183--1109213 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1109173 GTTTTCAGGC
*
1109183 GGTATGGGAGGT
1 GGTATGGGAAGT
1109195 GGTATGGGAAGT
1 GGTATGGGAAGT
1109207 GGTATGG
1 GGTATGG
1109214 CGTCACCAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.55, T:0.26
Consensus pattern (12 bp):
GGTATGGGAAGT
Found at i:1110008 original size:28 final size:28
Alignment explanation
Indices: 1109977--1110056 Score: 115
Period size: 28 Copynumber: 2.9 Consensus size: 28
1109967 GGAGGACGGC
* *
1109977 CAAACTCCACCAATAGGGATACATTATT
1 CAAAATCCACCTATAGGGATACATTATT
* *
1110005 CAAAATCCACCTGTAGGGGTACATTATT
1 CAAAATCCACCTATAGGGATACATTATT
*
1110033 CAAAATCCAACTATAGGGATACAT
1 CAAAATCCACCTATAGGGATACAT
1110057 CAGTTGAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.25
Consensus pattern (28 bp):
CAAAATCCACCTATAGGGATACATTATT
Found at i:1112221 original size:21 final size:21
Alignment explanation
Indices: 1112196--1112375 Score: 238
Period size: 21 Copynumber: 8.6 Consensus size: 21
1112186 CATAATATGA
*
1112196 TGATACTTCAACATCACATGC
1 TGATACTTCAACATTACATGC
1112217 TGATACTTTC-ACATTACATGC
1 TGATAC-TTCAACATTACATGC
*
1112238 TGATACTT-AACATTATATGC
1 TGATACTTCAACATTACATGC
* * *
1112258 TGATTCTTTAACATCACATGC
1 TGATACTTCAACATTACATGC
*
1112279 TGATACTTCAACATTACATGA
1 TGATACTTCAACATTACATGC
* *
1112300 TGATACTTTAACATTACATGA
1 TGATACTTCAACATTACATGC
* *
1112321 TGGTACTTTAACATTACATGC
1 TGATACTTCAACATTACATGC
1112342 TGATACTTCAACATTACATGC
1 TGATACTTCAACATTACATGC
*
1112363 GGATACTTCAACA
1 TGATACTTCAACA
1112376 AAGTGCTGAT
Statistics
Matches: 141, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
20 19 0.13
21 119 0.84
22 3 0.02
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (21 bp):
TGATACTTCAACATTACATGC
Found at i:1112243 original size:42 final size:42
Alignment explanation
Indices: 1112196--1112484 Score: 258
Period size: 42 Copynumber: 6.7 Consensus size: 42
1112186 CATAATATGA
* *
1112196 TGATACTTCAACATCACATGCTGATACTTTCACATTACATGC
1 TGATACTTCAACATTACATGCTGATACTTTAACATTACATGC
* * *
1112238 TGATACTT-AACATTATATGCTGATTCTTTAACATCACATGC
1 TGATACTTCAACATTACATGCTGATACTTTAACATTACATGC
* *
1112279 TGATACTTCAACATTACATGATGATACTTTAACATTACATGA
1 TGATACTTCAACATTACATGCTGATACTTTAACATTACATGC
* * *
1112321 TGGTACTTTAACATTACATGCTGATACTTCAACATTACATGC
1 TGATACTTCAACATTACATGCTGATACTTTAACATTACATGC
* * * *
1112363 GGATACTTCAACAAAGTGCTGATACATGATGATACTTCAACATTACATGA
1 TGATACTTCAAC--A----T--TACATGCTGATACTTTAACATTACATGC
* * * * ** * *
1112413 TGATACTTTAACCTTATATTCTGATA-TTTCTTCATTATATGT
1 TGATACTTCAACATTACATGCTGATACTTT-AACATTACATGC
* * *
1112455 TGATACTTCTACATTATATGTTGATACTTT
1 TGATACTTCAACATTACATGCTGATACTTT
1112485 GTCTTTATAT
Statistics
Matches: 200, Mismatches: 36, Indels: 21
0.78 0.14 0.08
Matches are distributed among these distances:
41 38 0.19
42 120 0.60
43 3 0.01
44 2 0.01
48 1 0.00
50 36 0.18
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (42 bp):
TGATACTTCAACATTACATGCTGATACTTTAACATTACATGC
Found at i:1112343 original size:63 final size:63
Alignment explanation
Indices: 1112192--1112375 Score: 264
Period size: 63 Copynumber: 2.9 Consensus size: 63
1112182 TCTTCATAAT
* *
1112192 ATGATGATACTTCAACATCACATGCTGATACTTTC-ACATTACATGCTGATAC-TTAACATTAT
1 ATGATGATACTTTAACATCACATGCTGATAC-TTCAACATTACATGCTGATACTTTAACATTAC
* * *
1112254 ATGCTGATTCTTTAACATCACATGCTGATACTTCAACATTACATGATGATACTTTAACATTAC
1 ATGATGATACTTTAACATCACATGCTGATACTTCAACATTACATGCTGATACTTTAACATTAC
* * * *
1112317 ATGATGGTACTTTAACATTACATGCTGATACTTCAACATTACATGCGGATACTTCAACA
1 ATGATGATACTTTAACATCACATGCTGATACTTCAACATTACATGCTGATACTTTAACA
1112376 AAGTGCTGAT
Statistics
Matches: 108, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
61 3 0.03
62 44 0.41
63 61 0.56
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.35
Consensus pattern (63 bp):
ATGATGATACTTTAACATCACATGCTGATACTTCAACATTACATGCTGATACTTTAACATTAC
Found at i:1112494 original size:21 final size:21
Alignment explanation
Indices: 1112392--1112483 Score: 98
Period size: 21 Copynumber: 4.4 Consensus size: 21
1112382 TGATACATGA
* * *
1112392 TGATACTTCAACATTACATGA
1 TGATACTTCTACATTATATGT
*
1112413 TGATACTT-TAACCTTATAT-T
1 TGATACTTCT-ACATTATATGT
* *
1112433 CTGATATTTCTTCATTATATGT
1 -TGATACTTCTACATTATATGT
1112455 TGATACTTCTACATTATATGT
1 TGATACTTCTACATTATATGT
1112476 TGATACTT
1 TGATACTT
1112484 TGTCTTTATA
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
21 56 0.97
22 2 0.03
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.47
Consensus pattern (21 bp):
TGATACTTCTACATTATATGT
Found at i:1112507 original size:63 final size:63
Alignment explanation
Indices: 1112392--1112526 Score: 146
Period size: 63 Copynumber: 2.1 Consensus size: 63
1112382 TGATACATGA
* * * *
1112392 TGATACTTCAACATTACATGATGATACTTTAACCTTATATTCTGATATTTCTTCATTATATGT
1 TGATACTTCAACATTACATGATGATACTTTAACCTTATATACTGATAGTTCTTAATTATATGC
* * * ** * *
1112455 TGATACTTCTACATTATATGTTGATACTTTGTCTTTATATAAC-GATAGTTCTTAATTTTATGC
1 TGATACTTCAACATTACATGATGATACTTTAACCTTATAT-ACTGATAGTTCTTAATTATATGC
*
1112518 TGATTCTTC
1 TGATACTTC
1112527 CTCATAATAT
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
63 58 0.98
64 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (63 bp):
TGATACTTCAACATTACATGATGATACTTTAACCTTATATACTGATAGTTCTTAATTATATGC
Found at i:1123212 original size:22 final size:22
Alignment explanation
Indices: 1123187--1123249 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
1123177 GAAATAATGC
* *
1123187 TTTATTTGTGTCCCAATAAGGT
1 TTTATTTGTGTCCAAATAAGGA
*
1123209 TTTATTTGTGTCCAAATAATGA
1 TTTATTTGTGTCCAAATAAGGA
*
1123231 TTTATTTGTGACCTAAATA
1 TTTATTTGTGTCC-AAATA
1123250 TATTGTACTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 31 0.86
23 5 0.14
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (22 bp):
TTTATTTGTGTCCAAATAAGGA
Found at i:1124758 original size:15 final size:15
Alignment explanation
Indices: 1124738--1124767 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1124728 ATCGGCTGAC
*
1124738 TTTTGTTGATCACAT
1 TTTTGTTGACCACAT
1124753 TTTTGTTGACCACAT
1 TTTTGTTGACCACAT
1124768 GACAGTTGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.50
Consensus pattern (15 bp):
TTTTGTTGACCACAT
Found at i:1127283 original size:4 final size:4
Alignment explanation
Indices: 1127214--1127283 Score: 70
Period size: 4 Copynumber: 17.8 Consensus size: 4
1127204 GATCACATTT
* * * *
1127214 TGTC TGTC -GTC CGTC TGTC TGTC TGTC TGTC CGTC TGTC CGTC CGTC
1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC
* * *
1127261 GGTC CGTC TGTC CGTC TGTC TGT
1 TGTC TGTC TGTC TGTC TGTC TGT
1127284 AAACTTTTCA
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
3 3 0.05
4 53 0.95
ACGTcount: A:0.00, C:0.33, G:0.27, T:0.40
Consensus pattern (4 bp):
TGTC
Found at i:1127710 original size:166 final size:166
Alignment explanation
Indices: 1127435--1128301 Score: 1242
Period size: 166 Copynumber: 5.2 Consensus size: 166
1127425 AAAAATTTTC
* * *
1127435 AAAAATCTTCTTCTCATG-AAC-CATAAGACCAGGAAAGCTGAAACTTGTGTGGAAGCATCATCA
1 AAAAATCTTCTTCTCA-GAAACTAATCAG-CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCA
* *
1127498 GGTAGTGTAGATTCTAATTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGG
64 GGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGG
*
1127563 GTCGAAGTTTTACATAGGAATATACAGAGTAAATCTTT
129 GTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
* * *
1127601 GAAAATCTTCTTCTCATG-AAC-CATAAGACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCA
1 AAAAATCTTCTTCTCA-GAAACTAATCAG-CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCA
* * * *
1127664 GGTAGTGTAGATTCTAATTTGTGAAATTCATGACCCCCGGGGGTAGGATGGGGCCACAATGGGGG
64 GGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGG
*
1127729 GTCGAAGTTTTACATAGGAATATACAGAGTAAATCTTT
129 GTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
*
1127767 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* *
1127832 TAGTGTAGATTCATAGTTGTGAAAATCATGACCCCCCGGGGGTAGGGTGGGGCCACAATGGGGGA
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGA-CCCCCGGGGGTAGGGTGGGGCCACAATGGGGGG
* *
1127897 TTGAAGTTTTACATAGGAATATATAGAGTCAATCTTT
130 TCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
* *
1127934 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGTAAAGCTGACACTTGTGTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* * * * **
1127999 TAGGGTAGATACAAAGTTGTGAAAATCATGACCCCCGAGGGTAGGGTGGGGCCAAAATGGAAGGT
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGT
**
1128064 AAAAGTTTTACATAGGAATATATAGAGTAAATCTTT
131 CGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
* *
1128100 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTTAAACTTGTGTGGAAGCGTCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* * *
1128165 TAGTGTAAATTCAAAGTTGTGAAAATCATGATCCCCAGGGGTAGGGT-GGGCCACAATGGGGGGG
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAAT-----GG
* * * *
1128229 GGGGGCAAAGTTTAACAAAGGAATATATATG-GTAAATCTTT
126 GGGGTCGAAGTTTTACATAGGAATATATA-GAGTAAATCTTT
*
1128270 AAAAATCTTCTTCTCAGAAATTAATCAGCCAG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAG
1128302 ATGATTCTTT
Statistics
Matches: 643, Mismatches: 49, Indels: 14
0.91 0.07 0.02
Matches are distributed among these distances:
165 10 0.02
166 407 0.63
167 159 0.25
170 66 0.10
171 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (166 bp):
AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGT
CGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
Found at i:1128043 original size:333 final size:332
Alignment explanation
Indices: 1127435--1128301 Score: 1235
Period size: 333 Copynumber: 2.6 Consensus size: 332
1127425 AAAAATTTTC
* * *
1127435 AAAAATCTTCTTCTCATG-AAC-CATAAGACCAGGAAAGCTGAAACTTGTGTGGAAGCATCATCA
1 AAAAATCTTCTTCTCA-GAAACTAATCAG-CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCA
*
1127498 GGTAGTGTAGATTC-TAATTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGG
64 GGTAGTGTAGATTCAT-AGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGG
* * *
1127562 GGTCGAAGTTTTACATAGGAATATACAGAGTAAATCTTTGAAAATCTTCTTCTCATG-AAC-CAT
128 GGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCA-GAAACTAAT
* * * * *
1127625 AAGACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCTAATTTGTGAAA
192 CAG-CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGGGTAGATACAAAGTTGTGAAA
* * * ** **
1127690 TTCATGACCCCCGGGGGTAGGATGGGGCCACAATGGGGGGTCGAAGTTTTACATAGGAATATACA
256 ATCATGACCCCCGAGGGTAGGATGGGGCCAAAATGGAAGGTAAAAGTTTTACATAGGAATATACA
1127755 GAGTAAATCTTT
321 GAGTAAATCTTT
*
1127767 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
*
1127832 TAGTGTAGATTCATAGTTGTGAAAATCATGACCCCCCGGGGGTAGGGTGGGGCCACAATGGGGGA
66 TAGTGTAGATTCATAGTTGTGAAAATCATGA-CCCCCGGGGGTAGGGTGGGGCCACAATGGGGGG
* *
1127897 TTGAAGTTTTACATAGGAATATATAGAGTCAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAG
130 TCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAG
* *
1127962 CCAGTAAAGCTGACACTTGTGTGGAAGCATCCTCAGGTAGGGTAGATACAAAGTTGTGAAAATCA
195 CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGGGTAGATACAAAGTTGTGAAAATCA
* *
1128027 TGACCCCCGAGGGTAGGGTGGGGCCAAAATGGAAGGTAAAAGTTTTACATAGGAATATATAGAGT
260 TGACCCCCGAGGGTAGGATGGGGCCAAAATGGAAGGTAAAAGTTTTACATAGGAATATACAGAGT
1128092 AAATCTTT
325 AAATCTTT
* *
1128100 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTTAAACTTGTGTGGAAGCGTCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* * * *
1128165 TAGTGTAAATTCAAAGTTGTGAAAATCATGATCCCCAGGGGTAGGGT-GGGCCACAATGGGGGGG
66 TAGTGTAGATTCATAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAAT-----GG
* * * * *
1128229 GGGGGCAAAGTTTAACAAAGGAATATATATG-GTAAATCTTTAAAAATCTTCTTCTCAGAAATTA
126 GGGGTCGAAGTTTTACATAGGAATATATA-GAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTA
1128293 ATCAGCCAG
190 ATCAGCCAG
1128302 ATGATTCTTT
Statistics
Matches: 481, Mismatches: 42, Indels: 20
0.89 0.08 0.04
Matches are distributed among these distances:
331 11 0.02
332 97 0.20
333 303 0.63
334 4 0.01
336 65 0.14
337 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (332 bp):
AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
TAGTGTAGATTCATAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGT
CGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGC
CAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGGGTAGATACAAAGTTGTGAAAATCAT
GACCCCCGAGGGTAGGATGGGGCCAAAATGGAAGGTAAAAGTTTTACATAGGAATATACAGAGTA
AATCTTT
Found at i:1129771 original size:2 final size:2
Alignment explanation
Indices: 1129766--1129794 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1129756 ATCTAATACA
1129766 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1129795 GTAAATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1137033 original size:14 final size:14
Alignment explanation
Indices: 1137014--1137041 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1137004 ACTCTTTCAT
1137014 TATTATGATGCATA
1 TATTATGATGCATA
1137028 TATTATGATGCATA
1 TATTATGATGCATA
1137042 AGTGAAACTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (14 bp):
TATTATGATGCATA
Found at i:1139506 original size:21 final size:21
Alignment explanation
Indices: 1139476--1139515 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1139466 GGTAGCTGCT
*
1139476 ACTTAATTATGTTGGCATGCA
1 ACTTAATTATGTTGACATGCA
*
1139497 ACTTATTTATGTTGACATG
1 ACTTAATTATGTTGACATG
1139516 TGAGTTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.42
Consensus pattern (21 bp):
ACTTAATTATGTTGACATGCA
Found at i:1139693 original size:20 final size:20
Alignment explanation
Indices: 1139668--1139705 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1139658 CATAAGTAAG
1139668 AAGTTGCAAGTAAACATAAA
1 AAGTTGCAAGTAAACATAAA
* *
1139688 AAGTTGCATGTCAACATA
1 AAGTTGCAAGTAAACATA
1139706 TTTACGTCGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (20 bp):
AAGTTGCAAGTAAACATAAA
Found at i:1139738 original size:21 final size:21
Alignment explanation
Indices: 1139690--1139743 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1139680 AACATAAAAA
*
1139690 GTTGCATGTCAACATATTTAC
1 GTTGCATGTCAACATAATTAC
*
1139711 GTCGCATGTCAACATAAATTA-
1 GTTGCATGTCAACAT-AATTAC
*
1139732 TTTGCATGTCAA
1 GTTGCATGTCAA
1139744 TATTATAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 24 0.86
22 4 0.14
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (21 bp):
GTTGCATGTCAACATAATTAC
Found at i:1166258 original size:28 final size:28
Alignment explanation
Indices: 1166211--1166266 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
1166201 CACAATAAAT
1166211 CGGATAAAAACGAAATTTTAAC-AAAAAA
1 CGGATAAAAACGAAATTTT-ACGAAAAAA
1166239 CGGATAAAAACGGAAA-TTTACGAAAAAA
1 CGGATAAAAAC-GAAATTTTACGAAAAAA
1166267 AACTCGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 2 0.08
28 20 0.77
29 4 0.15
ACGTcount: A:0.59, C:0.11, G:0.14, T:0.16
Consensus pattern (28 bp):
CGGATAAAAACGAAATTTTACGAAAAAA
Found at i:1167384 original size:28 final size:28
Alignment explanation
Indices: 1167337--1167392 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
1167327 CACAATAAAT
1167337 CGGATAAAAACGAAATTTTAAC-AAAAAA
1 CGGATAAAAACGAAATTTT-ACGAAAAAA
1167365 CGGATAAAAACGGAAA-TTTACGAAAAAA
1 CGGATAAAAAC-GAAATTTTACGAAAAAA
1167393 AACTCGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 2 0.08
28 20 0.77
29 4 0.15
ACGTcount: A:0.59, C:0.11, G:0.14, T:0.16
Consensus pattern (28 bp):
CGGATAAAAACGAAATTTTACGAAAAAA
Found at i:1167545 original size:28 final size:28
Alignment explanation
Indices: 1167508--1167583 Score: 134
Period size: 28 Copynumber: 2.7 Consensus size: 28
1167498 CATTATTGAC
*
1167508 TAATAACTTGGTAATTCATTGTTGACAA
1 TAATTACTTGGTAATTCATTGTTGACAA
*
1167536 TAATTACTTGGTAATTCATTGTTGACAG
1 TAATTACTTGGTAATTCATTGTTGACAA
1167564 TAATTACTTGGTAATTCATT
1 TAATTACTTGGTAATTCATT
1167584 AGTAATTTTG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 46 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (28 bp):
TAATTACTTGGTAATTCATTGTTGACAA
Found at i:1167774 original size:22 final size:22
Alignment explanation
Indices: 1167747--1167790 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1167737 GGTAAATAAC
* *
1167747 ATGACGCCACAATGCTTTAAAT
1 ATGACGCCACAATACATTAAAT
*
1167769 ATGACGTCACAATACATTAAAT
1 ATGACGCCACAATACATTAAAT
1167791 GCGTAAATGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.27
Consensus pattern (22 bp):
ATGACGCCACAATACATTAAAT
Found at i:1169428 original size:34 final size:34
Alignment explanation
Indices: 1169380--1169450 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
1169370 TATTGGTGTC
*
1169380 ATTCCCATTCAGATTAACATTGACCTACATTCAG
1 ATTCCCATTCAGATTAACATTGACCAACATTCAG
* * * *
1169414 ATTCCCATTTAGATTCATATTGACGAACATTCAG
1 ATTCCCATTCAGATTAACATTGACCAACATTCAG
1169448 ATT
1 ATT
1169451 AACATTGACC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.32, C:0.23, G:0.10, T:0.35
Consensus pattern (34 bp):
ATTCCCATTCAGATTAACATTGACCAACATTCAG
Found at i:1175468 original size:22 final size:20
Alignment explanation
Indices: 1175434--1175473 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1175424 ATGATGTTTG
1175434 AAAAAGATCAAGTTAGTGATC
1 AAAAAGATCAAGTT-GTGATC
*
1175455 AAAAAGATATAAGTTGTGA
1 AAAAAGAT-CAAGTTGTGA
1175474 AGAAATTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.50, C:0.05, G:0.20, T:0.25
Consensus pattern (20 bp):
AAAAAGATCAAGTTGTGATC
Found at i:1184974 original size:13 final size:13
Alignment explanation
Indices: 1184956--1184980 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1184946 TTTCAGTTAT
1184956 TTGCGTGTTTGAA
1 TTGCGTGTTTGAA
1184969 TTGCGTGTTTGA
1 TTGCGTGTTTGA
1184981 GAGTTTGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.08, G:0.32, T:0.48
Consensus pattern (13 bp):
TTGCGTGTTTGAA
Found at i:1185905 original size:164 final size:165
Alignment explanation
Indices: 1185515--1185962 Score: 445
Period size: 164 Copynumber: 2.7 Consensus size: 165
1185505 TTCCCCTACA
* *
1185515 GCCTGAACCCCTGACCCAGGGGCCATGAATTTCACAATTTAGGTAGAGGAG-TTCGTGGACATCA
1 GCCT-AACCCCTGACCAAGGGGCCATGAATTTCACAATTTAGGTAGAGG-GCTTCATGGACATCA
* ** * * *
1185579 TAAACATGCATTCAGTTTTTCCCCACATGTGTGGGAGTAAAGAAGAAGATTTTCTAAGATTTAAT
64 TAACCATGCATTCAGTTTTTCCAAACATATATGGGAGT-AAGAAGAAGATTTTCTAAGATCTAAT
* * * *
1185644 ACATTTTCACCATATGGCTACATTGACCCCGCTCTAGG
128 ACATTTTCACCAAATGGCCACATTGACCCCACCCTAGG
* * * ** * * * * * *
1185682 GCCTAAACCCTTACCTAGGGGTAATGAATTTCAAAATTAAGTTAGAAGACTTTATGGACATCATA
1 GCCTAACCCCTGACCAAGGGGCCATGAATTTCACAATTTAGGTAGAGGGCTTCATGGACATCATA
* * *
1185747 ACCATGCATTTAGTTTTTATCAAATATATATGGGAGT-AGAA-AAGATTTTCTAAGATCTAATAC
66 ACCATGCATTCAGTTTTT-CCAAACATATATGGGAGTAAGAAGAAGATTTTCTAAGATCTAATAC
* ** * * *
1185810 ATTTTTAGTAAATGGCCATATTGCCCCCACCCTAGAT
130 ATTTTCACCAAATGGCCACATTGACCCCACCCTAG-G
* *
1185847 TCC-AACCCCTGACCAAGGGGCCATGAATTTCACAATTTTGGTAGAGGGCTTCATGGACATCATA
1 GCCTAACCCCTGACCAAGGGGCCATGAATTTCACAATTTAGGTAGAGGGCTTCATGGACATCATA
* * ** * *
1185911 ACCATACATTCAGTTTTTTCTCACATGTGTGGGAGTAGAGAAGAAGAATTTT
66 ACCATGCATTCAGTTTTTCCAAACATATATGGGAGTA-AGAAGAAG-ATTTT
1185963 GAAAATTTGC
Statistics
Matches: 223, Mismatches: 51, Indels: 14
0.77 0.18 0.05
Matches are distributed among these distances:
163 13 0.06
164 112 0.50
165 10 0.04
166 67 0.30
167 21 0.09
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (165 bp):
GCCTAACCCCTGACCAAGGGGCCATGAATTTCACAATTTAGGTAGAGGGCTTCATGGACATCATA
ACCATGCATTCAGTTTTTCCAAACATATATGGGAGTAAGAAGAAGATTTTCTAAGATCTAATACA
TTTTCACCAAATGGCCACATTGACCCCACCCTAGG
Found at i:1187048 original size:166 final size:166
Alignment explanation
Indices: 1186570--1187200 Score: 900
Period size: 166 Copynumber: 3.8 Consensus size: 166
1186560 TTAGTTTCTG
* *
1186570 AGAAGA-TTTTAAAAGATTTACTCTATATATTCCTATGTAAAACTTTGACCCCCCATTGTCGCCC
1 AGAAGACTTTTAAAAGATTTACTCTATATATTCCTATGTAAAACTTCGACCCCCCATTGTGGCCC
* *
1186634 CACCCTACCCCCAGGGGTCATGATTTTCACAACTTGGAATCTACACTACCTGAGGATACTTCCAC
66 CACCCTACCCCC-GGGGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCAC
1186699 ACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGA
130 ACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGA
* * * * *
1186736 AGAAGACTTTT-AAATATTTACTCTATATATTTCTATCTAAAACTTCGACTCTCCATTGT-GCCC
1 AGAAGACTTTTAAAAGATTTACTCTATATATTCCTATGTAAAACTTCGACCCCCCATTGTGGCCC
* * * * * *
1186799 CAACCTACCCCCAGGGATCATGATTATCACAAGTTTGAATTTACACTACATGAGGATGCTTCCAC
66 CACCCTACCCCC-GGGGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCAC
* *
1186864 ACAAGTTTTAGCTTTCCTGGCTGATTAGTTTTTGAGA
130 ACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGA
*
1186901 AGAAGA-TTTTAAAAGATTTACTCTATATATTCCTATGTAAAACTTTGACCCCCCATTGTGGCCC
1 AGAAGACTTTTAAAAGATTTACTCTATATATTCCTATGTAAAACTTCGACCCCCCATTGTGGCCC
1186965 CACCCTACCCCCGGGGTTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCAC
66 CACCCTACCCCCGGGG-TCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCAC
1187030 ACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGA
130 ACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGA
* * **
1187067 AGAGGATTTTTAAAA-ATTTACTCTATAGATATATTCCTACATAAAACTTCGACCCCCC-TTGTG
1 AGAAGACTTTTAAAAGATTTACTC--T--ATATATTCCTATGTAAAACTTCGACCCCCCATTGTG
** *
1187130 GCCCCACCCTACCCTTGGGGGTCATGA-TTTCACAACTTTGAATCTACACTACTTGAGGAAT-CT
62 GCCCCACCCTACCC-CCGGGGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGG-ATGCT
1187193 TCCACACA
125 TCCACACA
1187201 GGTGTTTTCC
Statistics
Matches: 417, Mismatches: 37, Indels: 20
0.88 0.08 0.04
Matches are distributed among these distances:
164 4 0.01
165 147 0.35
166 155 0.37
167 12 0.03
168 41 0.10
169 27 0.06
170 31 0.07
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (166 bp):
AGAAGACTTTTAAAAGATTTACTCTATATATTCCTATGTAAAACTTCGACCCCCCATTGTGGCCC
CACCCTACCCCCGGGGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACA
CAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGA
Found at i:1189664 original size:147 final size:144
Alignment explanation
Indices: 1189326--1190206 Score: 1146
Period size: 146 Copynumber: 6.0 Consensus size: 144
1189316 TTTAACTGTT
* * **
1189326 GGTCATAAGCAATATTTGTGTGAAGTAAAAACATT-CAATACTTCTCCATAAGAAAGATAAT-GA
1 GGTCATAAGCAATCTTTGTGTGAAGTAAGAAC-TTCCAATGTTTCTCCATAAGAAAGAT-ATGGA
* *
1189389 CCGGACACGAATTTTGCACTT-TTTCTGCCAGTGACCTTCACCTTGCCCAAATGACCTTGGGTCA
64 CCGGACACGAATTTT--ACTTATTT-TTCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCA
*
1189453 AGGTCATGACACACCCTTT
126 AGGTCATGACACACCCTTA
* * * * *
1189472 GGTCCTAAGCAATATTTGTGTAAAGTTAGAACATT-CAATGCTTCTCCATAAGAAAGATAAT-GA
1 GGTCATAAGCAATCTTTGTGTGAAGTAAGAAC-TTCCAATGTTTCTCCATAAGAAAGAT-ATGGA
** * **
1189535 CCGGACACGAATTTTACTCTATTTTTCCTAACGACCTTGATCTTGCCCAAATGAACCTTGCATCA
64 CCGGACACGAATTTTACT-TATTTTTCC-AGTGACCTTGACCTTGCCCAAATG-ACCTTGGGTCA
1189600 AGGTCATGACACACCCTTA
126 AGGTCATGACACACCCTTA
* *
1189619 GGTCATAAGCAATCTTTGTGTGAATTAAGAACTTCCAATGTTTCTCCATAAGAAAGAGATGGACC
1 GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
* * *
1189684 GGACACAAATTTTGCACTTATTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGG
66 GGACACGAATTTT--ACTTATTTTTCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGG
1189749 TCATGACACACCCTTA
129 TCATGACACACCCTTA
* * * *
1189765 GGTCATAAGCAATCTTTGTATGAAGAAAGAACTTCCAATGTTTCTCTATAAGAAAGATATGGACT
1 GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
** * *
1189830 GGACACGAATTTTTGTATGTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTTAAG
66 GGACACGAATTTTACT-TATTTT-T-CCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAG
*
1189895 GTCATGACACAGCCTTA
128 GTCATGACACACCCTTA
* * *
1189912 GGTCATAAGCAATCTTTTTATGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGTACC
1 GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
* * *
1189977 GGACACGAATTTT-GTATGTTTTCTGCCAGTGACCTTGACCTTGCCCGAATGACCTTGGGTCAAG
66 GGACACGAATTTTACT-TATTTT-T-CCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAG
1190041 GTCATGACACACCCTTA
128 GTCATGACACACCCTTA
* *
1190058 GGTCATAAACAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATAGACC
1 GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
* *
1190123 GGACACGAATTTGCACTT-TTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGG
66 GGACACGAATTT-TACTTATTT-TTCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGG
* *
1190187 TCATGACACATCCTTT
129 TCATGACACACCCTTA
1190203 GGTC
1 GGTC
1190207 CTGACACAGA
Statistics
Matches: 660, Mismatches: 61, Indels: 29
0.88 0.08 0.04
Matches are distributed among these distances:
144 4 0.01
145 65 0.10
146 339 0.51
147 241 0.37
148 8 0.01
149 3 0.00
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (144 bp):
GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
GGACACGAATTTTACTTATTTTTCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTC
ATGACACACCCTTA
Found at i:1189898 original size:293 final size:291
Alignment explanation
Indices: 1189326--1190206 Score: 1256
Period size: 293 Copynumber: 3.0 Consensus size: 291
1189316 TTTAACTGTT
* * **
1189326 GGTCATAAGCAATATTTGTGTGAAGTAAAAACATT-CAATACTTCTCCATAAGAAAGATAAT-GA
1 GGTCATAAGCAATCTTTGTGTGAAGTAAGAAC-TTCCAATGTTTCTCCATAAGAAAGA-AATGGA
*
1189389 CCGGACACGAATTTTGCACTTTTTCTGCCAGTGACCTTCACCTTGCCCAAATGACCTTGGGTCAA
64 CCGGACACGAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAA
* * * * * *
1189454 GGTCATGACACACCCTTTGGTCCTAAGCAATATTTGTGTAAAGTTAGAACATT-CAATGCTTCTC
129 GGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAAC-TTCCAATGTTTCTC
* * ** *
1189518 CATAAGAAAGATAATGACCGGACACGAATTTTACTCTATTTTTC--CTAACGACCTTGATCTTGC
193 CATAAGAAAGAT-ATGACCGGACACGAATTTT--TGTATTTTTCTGCCAGTGACCTTGACCTTGC
**
1189581 CCAAATGAACCTTGCATCAAGGTCATGACACACCCTTA
255 CCAAATG-ACCTTGGGTCAAGGTCATGACACACCCTTA
* *
1189619 GGTCATAAGCAATCTTTGTGTGAATTAAGAACTTCCAATGTTTCTCCATAAGAAAGAGATGGACC
1 GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGAAATGGACC
* *
1189684 GGACACAAATTTTGCACTTATTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGG
66 GGACACGAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGG
* * *
1189749 TCATGACACACCCTTAGGTCATAAGCAATCTTTGTATGAAGAAAGAACTTCCAATGTTTCTCTAT
131 TCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCAT
*
1189814 AAGAAAGATATGGACTGGACACGAATTTTTGTATGTTTTCTGCCAGTGACCTTGACCTTGCCCAA
196 AAGAAAGATAT-GACCGGACACGAATTTTTGTAT-TTTTCTGCCAGTGACCTTGACCTTGCCCAA
* *
1189879 ATGACCTTGGGTTAAGGTCATGACACAGCCTTA
259 ATGACCTTGGGTCAAGGTCATGACACACCCTTA
* * * *
1189912 GGTCATAAGCAATCTTTTTATGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGTACC
1 GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGAAATGGACC
* *
1189977 GGACACGAATTTTGTA-TGTTTTCTGCCAGTGACCTTGACCTTGCCCGAATGACCTTGGGTCAAG
66 GGACACGAATTTTGCACT-TTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAG
*
1190041 GTCATGACACACCCTTAGGTCATAAACAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCA
130 GTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCA
*
1190106 TAAGAAAGATATAGACCGGACACGAA--TTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCA
195 TAAGAAAGATAT-GACCGGACACGAATTTTTGTA-TTTTTCTGCCAGTGACCTTGACCTTGCCCA
* *
1190169 AATGACCTTGGGTCAAGGTCATGACACATCCTTT
258 AATGACCTTGGGTCAAGGTCATGACACACCCTTA
1190203 GGTC
1 GGTC
1190207 CTGACACAGA
Statistics
Matches: 532, Mismatches: 47, Indels: 20
0.89 0.08 0.03
Matches are distributed among these distances:
291 73 0.14
292 15 0.03
293 422 0.79
294 22 0.04
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (291 bp):
GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGAAATGGACC
GGACACGAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGG
TCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCAT
AAGAAAGATATGACCGGACACGAATTTTTGTATTTTTCTGCCAGTGACCTTGACCTTGCCCAAAT
GACCTTGGGTCAAGGTCATGACACACCCTTA
Found at i:1193501 original size:62 final size:62
Alignment explanation
Indices: 1193404--1193536 Score: 221
Period size: 62 Copynumber: 2.1 Consensus size: 62
1193394 GTAACAATTC
* *
1193404 GTTTTATTATACTTTCATGTTAAATACTGAAATCTGATTGGTTTAGACGCAGTTGATAATCT
1 GTTTTATTATACTTTCATGTTAAATACTGAAATCTGATTGGTTAAGACGCAGTTCATAATCT
* *
1193466 GTTTTGTTATACTTTCATGTTAAATACTGAAATCTGATTGGTTAAGACGCAGTTCATAATCC
1 GTTTTATTATACTTTCATGTTAAATACTGAAATCTGATTGGTTAAGACGCAGTTCATAATCT
*
1193528 GTTCTATTA
1 GTTTTATTA
1193537 CCCTCAGCGT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 65 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.43
Consensus pattern (62 bp):
GTTTTATTATACTTTCATGTTAAATACTGAAATCTGATTGGTTAAGACGCAGTTCATAATCT
Found at i:1222001 original size:31 final size:31
Alignment explanation
Indices: 1221767--1221988 Score: 354
Period size: 31 Copynumber: 7.2 Consensus size: 31
1221757 NNNNNNNNNN
*
1221767 GAACTTACACAGCAGTAATCAGAACCAATCG
1 GAACTGACACAGCAGTAATCAGAACCAATCG
1221798 GAACTGACACAGCAGTAATCAGAACCAATCG
1 GAACTGACACAGCAGTAATCAGAACCAATCG
* *
1221829 GAACTGACACAGCAGTAATCAGAACCAAACA
1 GAACTGACACAGCAGTAATCAGAACCAATCG
* * * *
1221860 GAATTGACAAAGCAGTAATCGGAACCAATCA
1 GAACTGACACAGCAGTAATCAGAACCAATCG
*
1221891 GAACTGACACAGCAGTAATCAGAACCAATCA
1 GAACTGACACAGCAGTAATCAGAACCAATCG
*
1221922 GAACTGACACAGCAGTAATCATAACCAATCG
1 GAACTGACACAGCAGTAATCAGAACCAATCG
*
1221953 GAACTTACACAGCAGTAATCAGAACCAATCG
1 GAACTGACACAGCAGTAATCAGAACCAATCG
1221984 GAACT
1 GAACT
1221989 TATACACCAG
Statistics
Matches: 177, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 177 1.00
ACGTcount: A:0.44, C:0.25, G:0.17, T:0.14
Consensus pattern (31 bp):
GAACTGACACAGCAGTAATCAGAACCAATCG
Found at i:1222446 original size:31 final size:31
Alignment explanation
Indices: 1222361--1222671 Score: 291
Period size: 31 Copynumber: 10.1 Consensus size: 31
1222351 TAAATATAAC
* * *
1222361 CTGATACAGTAGTAATCAGAACCAATCAAAA
1 CTGACACAGCAGTAATCAGAACCAATCAGAA
* *** * * * *
1222392 CTAATGTAGAATTAATAAAAACCAATCAGAA
1 CTGACACAGCAGTAATCAGAACCAATCAGAA
* * *
1222423 CTGACACAGCAGTAATCTGAACCAATCGGAG
1 CTGACACAGCAGTAATCAGAACCAATCAGAA
* *
1222454 CTTACACAACAGTAATCAGAACCAATCAGAA
1 CTGACACAGCAGTAATCAGAACCAATCAGAA
*
1222485 CTGACACAGCAGTAAACAGAACCAATCAGAA
1 CTGACACAGCAGTAATCAGAACCAATCAGAA
* *
1222516 CTTACCCAGCAGTAATCAGAACCAATCAGAA
1 CTGACACAGCAGTAATCAGAACCAATCAGAA
*
1222547 CTGACACAGTAGTAATCAGAACCAATCA-AA
1 CTGACACAGCAGTAATCAGAACCAATCAGAA
* ** ** * * * *
1222577 CTAATGCAAAATTAATAAAAACCAACCAGAA
1 CTGACACAGCAGTAATCAGAACCAATCAGAA
* ** *
1222608 CTGACACAGTAGTAAAAAGAACCAATCGGAA
1 CTGACACAGCAGTAATCAGAACCAATCAGAA
* * *
1222639 CTTACACAACAGTAATCAGAACCAATCAAAA
1 CTGACACAGCAGTAATCAGAACCAATCAGAA
1222670 CT
1 CT
1222672 AATTCAGAAT
Statistics
Matches: 220, Mismatches: 59, Indels: 2
0.78 0.21 0.01
Matches are distributed among these distances:
30 21 0.10
31 199 0.90
ACGTcount: A:0.48, C:0.23, G:0.13, T:0.16
Consensus pattern (31 bp):
CTGACACAGCAGTAATCAGAACCAATCAGAA
Found at i:1222477 original size:62 final size:62
Alignment explanation
Indices: 1222411--1222671 Score: 335
Period size: 62 Copynumber: 4.2 Consensus size: 62
1222401 AATTAATAAA
* * *
1222411 AACCAATCAGAACTGACACAGCAGTAATCTGAACCAATCGGAGCTTACACAACAGTAATCAG
1 AACCAATCAGAACTGACACAGCAGTAAACAGAACCAATCGGAACTTACACAACAGTAATCAG
* * *
1222473 AACCAATCAGAACTGACACAGCAGTAAACAGAACCAATCAGAACTTACCCAGCAGTAATCAG
1 AACCAATCAGAACTGACACAGCAGTAAACAGAACCAATCGGAACTTACACAACAGTAATCAG
* * * * ** * * * *
1222535 AACCAATCAGAACTGACACAGTAGTAATCAGAACCAATC-AAACTAATGCAAAATTAATAAA
1 AACCAATCAGAACTGACACAGCAGTAAACAGAACCAATCGGAACTTACACAACAGTAATCAG
* * *
1222596 AACCAACCAGAACTGACACAGTAGTAAAAAGAACCAATCGGAACTTACACAACAGTAATCAG
1 AACCAATCAGAACTGACACAGCAGTAAACAGAACCAATCGGAACTTACACAACAGTAATCAG
*
1222658 AACCAATCAAAACT
1 AACCAATCAGAACT
1222672 AATTCAGAAT
Statistics
Matches: 168, Mismatches: 30, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
61 49 0.29
62 119 0.71
ACGTcount: A:0.48, C:0.25, G:0.13, T:0.15
Consensus pattern (62 bp):
AACCAATCAGAACTGACACAGCAGTAAACAGAACCAATCGGAACTTACACAACAGTAATCAG
Found at i:1226280 original size:15 final size:15
Alignment explanation
Indices: 1226260--1226289 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1226250 ATTAACATAA
1226260 TCTGAGGCTCTATTG
1 TCTGAGGCTCTATTG
*
1226275 TCTGAGGCTGTATTG
1 TCTGAGGCTCTATTG
1226290 CGCTTGCTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.17, G:0.30, T:0.40
Consensus pattern (15 bp):
TCTGAGGCTCTATTG
Found at i:1227887 original size:2 final size:2
Alignment explanation
Indices: 1227828--1227868 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1227818 GGAGTATAAT
1227828 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1227869 GTGTGTGTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1229177 original size:29 final size:29
Alignment explanation
Indices: 1229135--1229190 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
1229125 TTACTAATCA
1229135 CCCGCCGTGGCCACAGGTGATCACGTTCT
1 CCCGCCGTGGCCACAGGTGATCACGTTCT
1229164 CCCGCCGTGGCCACAGGTGATCACGTT
1 CCCGCCGTGGCCACAGGTGATCACGTT
1229191 TTACCCGAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.14, C:0.38, G:0.29, T:0.20
Consensus pattern (29 bp):
CCCGCCGTGGCCACAGGTGATCACGTTCT
Found at i:1230947 original size:11 final size:11
Alignment explanation
Indices: 1230928--1230960 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
1230918 TCGTTAATCA
*
1230928 ATATTGAATGT
1 ATATGGAATGT
1230939 ATATGGAATGT
1 ATATGGAATGT
1230950 ATATGGAATGT
1 ATATGGAATGT
1230961 TTACAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.39
Consensus pattern (11 bp):
ATATGGAATGT
Found at i:1232352 original size:71 final size:70
Alignment explanation
Indices: 1232244--1232835 Score: 659
Period size: 71 Copynumber: 8.4 Consensus size: 70
1232234 TGTACCGGCA
* *
1232244 CCTATATCTTGGTTTGTAACGCCCCTATGTCTTGGTTTGTAACGCCCCCTGTGTCTTGGTTTGTA
1 CCTATGTCTTGGTTTGTAACGCCCCTATGTCTTGGTTTGTAACG-CCCCTATGTCTTGGTTTGTA
1232309 ACGCCC
65 ACGCCC
* * * * *
1232315 CCTGTGTCTTGGTTTGTAACGCCCCTATGTCTCGGTTTGTGACGCCACCTATGTCTCGGTTTGTG
1 CCTATGTCTTGGTTTGTAACGCCCCTATGTCTTGGTTTGTAACGCC-CCTATGTCTTGGTTTGTA
*
1232380 ACGCCA
65 ACGCCC
* *
1232386 CCTATGTCTTGGTTTGTAACGCCCCCTATGTCTTGGTTTGTAACGCCCCTATGTCTCGGTTTGTG
1 CCTATGTCTTGGTTTGTAACG-CCCCTATGTCTTGGTTTGTAACGCCCCTATGTCTTGGTTTGTA
*
1232451 ACGCCA
65 ACGCCC
* *
1232457 CCTATGTCTTGGTTTGTAACGCCCCCTATGTCTTGGTTTGTAACGCCCCTATGTCTCGGTTTGTG
1 CCTATGTCTTGGTTTGTAACG-CCCCTATGTCTTGGTTTGTAACGCCCCTATGTCTTGGTTTGTA
1232522 ACG-CC
65 ACGCCC
*
1232527 CCTATGTCTTGGTTTGTAACGCCCATATGTCTTGGTTTGTAACGCCCCTATGTCTTGGTTTGTAA
1 CCTATGTCTTGGTTTGTAACGCCCCTATGTCTTGGTTTGTAACGCCCCTATGTCTTGGTTTGTAA
1232592 CG-CC
66 CGCCC
* * * * *
1232596 CCTTTGTCTTGGTTTGGAACACCCCCTATGTCTTGGTTTGTAACGCCCCTATGTCTGGGTTTTTA
1 CCTATGTCTTGGTTTGTAAC-GCCCCTATGTCTTGGTTTGTAACGCCCCTATGTCTTGGTTTGTA
*
1232661 ATGCCC
65 ACGCCC
* * ** * * ** * ** * * *
1232667 CCTTTGTTTTGAATTGAAATGCCATTTATGGCTTGAATTGTAATGCCCCCTATATTTTGGTTTGT
1 CCTATGTCTTGGTTTGTAACGCC-CCTATGTCTTGGTTTGTAACG-CCCCTATGTCTTGGTTTGT
**
1232732 AATTCCC
64 AACGCCC
* * * * *
1232739 CCTGTGTCTTGGTATGTAACGCCTCCTATGAT-TTGGTATGTAATGCCCCCTATGTCTTGGCTTG
1 CCTATGTCTTGGTTTGTAACGCC-CCTATG-TCTTGGTTTGTAACG-CCCCTATGTCTTGGTTTG
**
1232803 TAACGCTA
63 TAACGCCC
* * *
1232811 CCTGTATGTTGGTTTGTAACGCCCC
1 CCTATGTCTTGGTTTGTAACGCCCC
1232836 CTGTATCTTG
Statistics
Matches: 451, Mismatches: 63, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
69 63 0.14
70 68 0.15
71 206 0.46
72 114 0.25
ACGTcount: A:0.14, C:0.26, G:0.22, T:0.38
Consensus pattern (70 bp):
CCTATGTCTTGGTTTGTAACGCCCCTATGTCTTGGTTTGTAACGCCCCTATGTCTTGGTTTGTAA
CGCCC
Found at i:1232841 original size:24 final size:24
Alignment explanation
Indices: 1232244--1232837 Score: 668
Period size: 24 Copynumber: 25.1 Consensus size: 24
1232234 TGTACCGGCA
*
1232244 CCTATATCTTGGTTTGTAACG-CC
1 CCTATGTCTTGGTTTGTAACGCCC
1232267 CCTATGTCTTGGTTTGTAACGCCC
1 CCTATGTCTTGGTTTGTAACGCCC
*
1232291 CCTGTGTCTTGGTTTGTAACGCCC
1 CCTATGTCTTGGTTTGTAACGCCC
*
1232315 CCTGTGTCTTGGTTTGTAACG-CC
1 CCTATGTCTTGGTTTGTAACGCCC
* * *
1232338 CCTATGTCTCGGTTTGTGACGCCA
1 CCTATGTCTTGGTTTGTAACGCCC
* * *
1232362 CCTATGTCTCGGTTTGTGACGCCA
1 CCTATGTCTTGGTTTGTAACGCCC
1232386 CCTATGTCTTGGTTTGTAACGCCC
1 CCTATGTCTTGGTTTGTAACGCCC
1232410 CCTATGTCTTGGTTTGTAACG-CC
1 CCTATGTCTTGGTTTGTAACGCCC
* * *
1232433 CCTATGTCTCGGTTTGTGACGCCA
1 CCTATGTCTTGGTTTGTAACGCCC
1232457 CCTATGTCTTGGTTTGTAACGCCC
1 CCTATGTCTTGGTTTGTAACGCCC
1232481 CCTATGTCTTGGTTTGTAACG-CC
1 CCTATGTCTTGGTTTGTAACGCCC
* *
1232504 CCTATGTCTCGGTTTGTGACG-CC
1 CCTATGTCTTGGTTTGTAACGCCC
1232527 CCTATGTCTTGGTTTGTAACG-CC
1 CCTATGTCTTGGTTTGTAACGCCC
*
1232550 CATATGTCTTGGTTTGTAACG-CC
1 CCTATGTCTTGGTTTGTAACGCCC
1232573 CCTATGTCTTGGTTTGTAACG-CC
1 CCTATGTCTTGGTTTGTAACGCCC
* * *
1232596 CCTTTGTCTTGGTTTGGAACACCC
1 CCTATGTCTTGGTTTGTAACGCCC
1232620 CCTATGTCTTGGTTTGTAACG-CC
1 CCTATGTCTTGGTTTGTAACGCCC
* * *
1232643 CCTATGTCTGGGTTTTTAATGCCC
1 CCTATGTCTTGGTTTGTAACGCCC
* * ** * * *
1232667 CCTTTGTTTTGAATTGAAATGCCA
1 CCTATGTCTTGGTTTGTAACGCCC
** * ** *
1232691 TTTATGGCTTGAATTGTAATGCCC
1 CCTATGTCTTGGTTTGTAACGCCC
* * **
1232715 CCTATATTTTGGTTTGTAATTCCC
1 CCTATGTCTTGGTTTGTAACGCCC
* * *
1232739 CCTGTGTCTTGGTATGTAACGCCT
1 CCTATGTCTTGGTTTGTAACGCCC
* *
1232763 CCTATGAT-TTGGTATGTAATGCCC
1 CCTATG-TCTTGGTTTGTAACGCCC
* **
1232787 CCTATGTCTTGGCTTGTAACGCTA
1 CCTATGTCTTGGTTTGTAACGCCC
* * *
1232811 CCTGTATGTTGGTTTGTAACGCCC
1 CCTATGTCTTGGTTTGTAACGCCC
1232835 CCT
1 CCT
1232838 GTATCTTGTT
Statistics
Matches: 490, Mismatches: 74, Indels: 13
0.85 0.13 0.02
Matches are distributed among these distances:
23 188 0.38
24 301 0.61
25 1 0.00
ACGTcount: A:0.14, C:0.26, G:0.22, T:0.38
Consensus pattern (24 bp):
CCTATGTCTTGGTTTGTAACGCCC
Found at i:1234253 original size:22 final size:22
Alignment explanation
Indices: 1234213--1234254 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1234203 GAATTATGTG
*
1234213 CTGTAAAGAAATACTAAAATGA
1 CTGTAAAGAAATACAAAAATGA
1234235 CTGTGAAAGAAA-ACAAAAAT
1 CTGT-AAAGAAATACAAAAAT
1234255 TGAATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.57, C:0.10, G:0.14, T:0.19
Consensus pattern (22 bp):
CTGTAAAGAAATACAAAAATGA
Found at i:1234698 original size:29 final size:29
Alignment explanation
Indices: 1234665--1234759 Score: 181
Period size: 29 Copynumber: 3.3 Consensus size: 29
1234655 ATAATTAGGG
*
1234665 AATTTTCATTTGTAAACATAATGCAGTGT
1 AATTTTCATTTGTAGACATAATGCAGTGT
1234694 AATTTTCATTTGTAGACATAATGCAGTGT
1 AATTTTCATTTGTAGACATAATGCAGTGT
1234723 AATTTTCATTTGTAGACATAATGCAGTGT
1 AATTTTCATTTGTAGACATAATGCAGTGT
1234752 AATTTTCA
1 AATTTTCA
1234760 AATAACGAAA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 65 1.00
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.42
Consensus pattern (29 bp):
AATTTTCATTTGTAGACATAATGCAGTGT
Found at i:1242869 original size:159 final size:158
Alignment explanation
Indices: 1242580--1242876 Score: 585
Period size: 159 Copynumber: 1.9 Consensus size: 158
1242570 ATTTATCGAT
1242580 ATTAAAGGCCAAAAATTCAAGTTTGTTATTTTAATATAGTAGTATAGATGTGGTAACAATTCCAA
1 ATTAAAGGCCAAAAATTCAAGTTTGTTATTTTAATATAGTAGTATAGATGTGGTAACAATTCCAA
1242645 CCGGACTCGAACATCAAAAGTTACACATCGCTGGATAAACTTTAAACTAACTAAGCCACGATGTT
66 CCGGACTCGAACATCAAAAGTTACACATCGCTGGATAAACTTTAAACTAACTAAGCCACGATGTT
1242710 AGACATTAAAACTAGGGGGGGGGGGGGG
131 AGACATTAAAACTAGGGGGGGGGGGGGG
1242738 NATTAAAGGCCAAAAATTCAAGTTTGTTATTTTAATATAGTAGTATAGATGTGGTAACAATTCCA
1 -ATTAAAGGCCAAAAATTCAAGTTTGTTATTTTAATATAGTAGTATAGATGTGGTAACAATTCCA
1242803 ACCGGACTCGAACATCAAAAGTTACACATCGCTGGATAAACTTTAAACTAACTAAGCCACGATGT
65 ACCGGACTCGAACATCAAAAGTTACACATCGCTGGATAAACTTTAAACTAACTAAGCCACGATGT
1242868 TAGACATTA
130 TAGACATTA
1242877 NGCTCAGAAC
Statistics
Matches: 138, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
159 138 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (158 bp):
ATTAAAGGCCAAAAATTCAAGTTTGTTATTTTAATATAGTAGTATAGATGTGGTAACAATTCCAA
CCGGACTCGAACATCAAAAGTTACACATCGCTGGATAAACTTTAAACTAACTAAGCCACGATGTT
AGACATTAAAACTAGGGGGGGGGGGGGG
Done.