Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1532
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: 1715538
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.29
Warning! 192937 characters in sequence are not A, C, G, or T
File 2 of 5
Found at i:643 original size:89 final size:89
Alignment explanation
Indices: 487--666 Score: 333
Period size: 89 Copynumber: 2.0 Consensus size: 89
477 TTCATATTAA
*
487 AACATTCCTTTATAAAACATTTAGAATATTGAAAACAAAATTCCTACTTTTAAGATACAAAATGG
1 AACAATCCTTTATAAAACATTTAGAATATTGAAAACAAAATTCCTACTTTTAAGATACAAAATGG
552 TGTGATTAAGTAGTACATCATATG
66 TGTGATTAAGTAGTACATCATATG
*
576 AACAATCCTTTATAAAACATTTAGAATATTGATAACAAAATTCCTACTTTTAAGATACAAAATGG
1 AACAATCCTTTATAAAACATTTAGAATATTGAAAACAAAATTCCTACTTTTAAGATACAAAATGG
*
641 TGTGATTAAGTTGTACATCATATG
66 TGTGATTAAGTAGTACATCATATG
665 AA
1 AA
667 AGTAATCTCC
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
89 88 1.00
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.34
Consensus pattern (89 bp):
AACAATCCTTTATAAAACATTTAGAATATTGAAAACAAAATTCCTACTTTTAAGATACAAAATGG
TGTGATTAAGTAGTACATCATATG
Found at i:924 original size:287 final size:286
Alignment explanation
Indices: 408--980 Score: 1137
Period size: 287 Copynumber: 2.0 Consensus size: 286
398 TTGTGTATGT
408 ATGTACAATGCAATATGATCGGTCGGTTAGAGAGGAATCATTTGATGTTACACGTTATCGGGTCG
1 ATGTACAATGCAATATGATCGGTCGGTTAGAGAGGAATCATTTGATGTTACACGTTATCGGGTCG
473 ATTATTCATATTAAAACATTCCTTTATAAAACATTTAGAATATTGAAAACAAAATTCCTACTTTT
66 ATTATTCATATTAAAACATTCCTTTATAAAACATTTAGAATATTGAAAACAAAATTCCTACTTTT
538 AAGATACAAAATGGTGTGATTAAGTAGTACATCATATGAACAATCCTTTATAAAACATTTAGAAT
131 AAGATACAAAATGGTGTGATTAAGTAGTACATCATATGAACAATCCTTTATAAAACATTTAGAAT
603 ATTGATAACAAAATTCCTACTTTTAAGATACAAAATGGTGTGATTAAGTTGTACATCATATGAAA
196 ATTGATAACAAAATTCCTACTTTTAAGATACAAAATGGTGTGATTAAGTTGTACATCATATGAAA
668 GTAATCTCCCACGCTTGGTAGGTGCA
261 GTAATCTCCCACGCTTGGTAGGTGCA
694 NATGTACAATGCAATATGATCGGTCGGTTAGAGAGGAATCATTTGATGTTACACGTTATCGGGTC
1 -ATGTACAATGCAATATGATCGGTCGGTTAGAGAGGAATCATTTGATGTTACACGTTATCGGGTC
759 GATTATTCATATTAAAACATTCCTTTATAAAACATTTAGAATATTGAAAACAAAATTCCTACTTT
65 GATTATTCATATTAAAACATTCCTTTATAAAACATTTAGAATATTGAAAACAAAATTCCTACTTT
824 TAAGATACAAAATGGTGTGATTAAGTAGTACATCATATGAACAATCCTTTATAAAACATTTAGAA
130 TAAGATACAAAATGGTGTGATTAAGTAGTACATCATATGAACAATCCTTTATAAAACATTTAGAA
889 TATTGATAACAAAATTCCTACTTTTAAGATACAAAATGGTGTGATTAAGTTGTACATCATATGAA
195 TATTGATAACAAAATTCCTACTTTTAAGATACAAAATGGTGTGATTAAGTTGTACATCATATGAA
954 AGTAATCTCCCACGCTTGGTAGGTGCA
260 AGTAATCTCCCACGCTTGGTAGGTGCA
981 TTGGGAATAG
Statistics
Matches: 286, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
287 286 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (286 bp):
ATGTACAATGCAATATGATCGGTCGGTTAGAGAGGAATCATTTGATGTTACACGTTATCGGGTCG
ATTATTCATATTAAAACATTCCTTTATAAAACATTTAGAATATTGAAAACAAAATTCCTACTTTT
AAGATACAAAATGGTGTGATTAAGTAGTACATCATATGAACAATCCTTTATAAAACATTTAGAAT
ATTGATAACAAAATTCCTACTTTTAAGATACAAAATGGTGTGATTAAGTTGTACATCATATGAAA
GTAATCTCCCACGCTTGGTAGGTGCA
Found at i:930 original size:89 final size:89
Alignment explanation
Indices: 774--953 Score: 333
Period size: 89 Copynumber: 2.0 Consensus size: 89
764 TTCATATTAA
*
774 AACATTCCTTTATAAAACATTTAGAATATTGAAAACAAAATTCCTACTTTTAAGATACAAAATGG
1 AACAATCCTTTATAAAACATTTAGAATATTGAAAACAAAATTCCTACTTTTAAGATACAAAATGG
839 TGTGATTAAGTAGTACATCATATG
66 TGTGATTAAGTAGTACATCATATG
*
863 AACAATCCTTTATAAAACATTTAGAATATTGATAACAAAATTCCTACTTTTAAGATACAAAATGG
1 AACAATCCTTTATAAAACATTTAGAATATTGAAAACAAAATTCCTACTTTTAAGATACAAAATGG
*
928 TGTGATTAAGTTGTACATCATATG
66 TGTGATTAAGTAGTACATCATATG
952 AA
1 AA
954 AGTAATCTCC
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
89 88 1.00
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.34
Consensus pattern (89 bp):
AACAATCCTTTATAAAACATTTAGAATATTGAAAACAAAATTCCTACTTTTAAGATACAAAATGG
TGTGATTAAGTAGTACATCATATG
Found at i:7948 original size:12 final size:12
Alignment explanation
Indices: 7931--7956 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
7921 CTTCAGTTAA
7931 TAGGGGTTTATT
1 TAGGGGTTTATT
7943 TAGGGGTTTATT
1 TAGGGGTTTATT
7955 TA
1 TA
7957 CTTTTTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (12 bp):
TAGGGGTTTATT
Found at i:8266 original size:10 final size:10
Alignment explanation
Indices: 8248--8298 Score: 93
Period size: 10 Copynumber: 5.0 Consensus size: 10
8238 AAAACGTAAA
8248 ATGACGTTGCG
1 ATGA-GTTGCG
8259 ATGAGTTGCG
1 ATGAGTTGCG
8269 ATGAGTTGCG
1 ATGAGTTGCG
8279 ATGAGTTGCG
1 ATGAGTTGCG
8289 ATGAGTTGCG
1 ATGAGTTGCG
8299 CCAAGTCATT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
10 36 0.90
11 4 0.10
ACGTcount: A:0.20, C:0.12, G:0.39, T:0.29
Consensus pattern (10 bp):
ATGAGTTGCG
Found at i:21461 original size:39 final size:39
Alignment explanation
Indices: 21407--21489 Score: 130
Period size: 39 Copynumber: 2.1 Consensus size: 39
21397 GGGGAGGAGC
* *
21407 CAGAGGGCCCAATCACCCTAGGTAAAGACGCCAGTGGTA
1 CAGAGGACCCAATCACCCCAGGTAAAGACGCCAGTGGTA
* *
21446 CAGAGGACCCAATCACCCCAGGTACAGAGGCCAGTGGTA
1 CAGAGGACCCAATCACCCCAGGTAAAGACGCCAGTGGTA
21485 CAGAG
1 CAGAG
21490 TCTGGATCCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.31, C:0.29, G:0.29, T:0.11
Consensus pattern (39 bp):
CAGAGGACCCAATCACCCCAGGTAAAGACGCCAGTGGTA
Found at i:22478 original size:1 final size:1
Alignment explanation
Indices: 22472--22496 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
22462 GTGGGCTGAT
22472 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
22497 AGTCCGGGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:29444 original size:12 final size:14
Alignment explanation
Indices: 29412--29445 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
29402 AATTATGAAA
29412 TTGTGTGACATTGT
1 TTGTGTGACATTGT
29426 TTGTGTGACATTGT
1 TTGTGTGACATTGT
29440 TTGTGT
1 TTGTGT
29446 TCATGACCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.12, C:0.06, G:0.29, T:0.53
Consensus pattern (14 bp):
TTGTGTGACATTGT
Found at i:34574 original size:8 final size:8
Alignment explanation
Indices: 34561--34613 Score: 88
Period size: 8 Copynumber: 6.6 Consensus size: 8
34551 TGGTTTCACC
34561 CTGTCCGT
1 CTGTCCGT
34569 CTGTCCGT
1 CTGTCCGT
*
34577 CTGTCTGT
1 CTGTCCGT
*
34585 CCGTCCGT
1 CTGTCCGT
34593 CTGTCCGT
1 CTGTCCGT
34601 CTGTCCGT
1 CTGTCCGT
34609 CTGTC
1 CTGTC
34614 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:34584 original size:4 final size:4
Alignment explanation
Indices: 34561--34616 Score: 58
Period size: 4 Copynumber: 14.0 Consensus size: 4
34551 TGGTTTCACC
* * * * * *
34561 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
34609 CTGT CTGT
1 CTGT CTGT
34617 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:34584 original size:12 final size:12
Alignment explanation
Indices: 34567--34616 Score: 73
Period size: 12 Copynumber: 4.2 Consensus size: 12
34557 CACCCTGTCC
34567 GTCTGTCCGTCT
1 GTCTGTCCGTCT
*
34579 GTCTGTCCGTCC
1 GTCTGTCCGTCT
34591 GTCTGTCCGTCT
1 GTCTGTCCGTCT
* *
34603 GTCCGTCTGTCT
1 GTCTGTCCGTCT
34615 GT
1 GT
34617 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:39663 original size:2 final size:2
Alignment explanation
Indices: 39658--39704 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
39648 TTTTTTTTCT
*
39658 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39700 TA TA T
1 TA TA T
39705 GTACTTGATA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:41532 original size:22 final size:22
Alignment explanation
Indices: 41507--41598 Score: 89
Period size: 22 Copynumber: 4.2 Consensus size: 22
41497 GATGTTGATT
*
41507 TTTTGACAGTATTTTGTTGTTG
1 TTTTGACAATATTTTGTTGTTG
*
41529 TTTT-ATCAATATTTTGTTGTTA
1 TTTTGA-CAATATTTTGTTGTTG
* *
41551 TTTTGACACTATCTTGTTGTTG
1 TTTTGACAATATTTTGTTGTTG
* * *
41573 TATTGACGAT-TTTTCATTGTTG
1 TTTTGACAATATTTT-GTTGTTG
41595 TTTT
1 TTTT
41599 AACTATAGAT
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
21 4 0.07
22 51 0.91
23 1 0.02
ACGTcount: A:0.16, C:0.08, G:0.16, T:0.60
Consensus pattern (22 bp):
TTTTGACAATATTTTGTTGTTG
Found at i:47561 original size:2 final size:2
Alignment explanation
Indices: 47554--47587 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
47544 AAATATACTC
47554 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
47588 GAATCCTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:59854 original size:162 final size:162
Alignment explanation
Indices: 59562--59878 Score: 492
Period size: 162 Copynumber: 2.0 Consensus size: 162
59552 ATTTTCTTGG
* * *
59562 CAGAGGATGAACATATTGAAATGAAGTTTGATATACAGGTTTATCATGATAATATCTAGGTCAAG
1 CAGAGGATGAACATATTGAAATGAAATTTGATATACAGGTTTATCAAGATAATATCCAGGTCAAG
* * *
59627 TTCGAATATTGGGTACGATAAAGCAATTTTCGACAGAGTTATGCCCCTTTGACATAGAGAAATTC
66 TTCGAATATTGGGTACGATAAAGCAATTTTCGACAGAGTTATGCCCCTTGGACATAAAAAAATTC
*
59692 CAATTATTTGCAGTTTCCGCTCATTGTCTTCA
131 CAATTATTTGCAGTTTACGCTCATTGTCTTCA
*
59724 CAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTATCAAGATAATATCCAGGTCAAG
1 CAGAGGATGAACATATTGAAATGAAATTTGATATACAGGTTTATCAAGATAATATCCAGGTCAAG
* ** * *
59789 TTCG-ATATTGGGTATGATTGAGCAATTTTTGACAGAGTTATGCCCCTTGGACTTAAAAAAAATT
66 TTCGAATATTGGGTACGATAAAGCAATTTTCGACAGAGTTATGCCCCTTGGACAT-AAAAAAATT
*
59853 CCAATTATTTGCAGTTTACGTTCATT
130 CCAATTATTTGCAGTTTACGCTCATT
59879 TTCTATGTGG
Statistics
Matches: 140, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
161 44 0.31
162 96 0.69
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (162 bp):
CAGAGGATGAACATATTGAAATGAAATTTGATATACAGGTTTATCAAGATAATATCCAGGTCAAG
TTCGAATATTGGGTACGATAAAGCAATTTTCGACAGAGTTATGCCCCTTGGACATAAAAAAATTC
CAATTATTTGCAGTTTACGCTCATTGTCTTCA
Found at i:71028 original size:436 final size:434
Alignment explanation
Indices: 69963--71134 Score: 1708
Period size: 436 Copynumber: 2.7 Consensus size: 434
69953 TATGGTTGTA
* * *
69963 CATTGTTAAGCTCAATATTTTGAGCATCTTTTGTTAAATATTGCTT-TCCAAA-GTTTTCCTCTA
1 CATTGTTAAGCTCTATATTTTGAGCAT-TTTTGTTAAATATTGCTTATCAAAATG-TTTCTTC-A
* * * * *
70026 TTTTGAGATATTAAACATCAAAGCTTTAGACCTCTGGTCCCTTAAAATCCCTAATTACGTAACAT
63 TTTTGAGATATT-AGCATCAAAGTTTTGGACTTCTGGCCCCTTAAAATCCCTAATTACGTAACAT
* * * *
70091 A-AGTGTAAATGATTGCCATGTACAGGTACATAACATTAGAATGAACATAATTGCTTCTATAACG
127 AGA-AGTAAATGATTGCCATGTATAGGTAAATAACCTTAGAATGAACATAATTGCTTCTATAACG
* * * * *
70155 TATCACCAAATATTTAACAGTAAAAAGTTATCATTAATAGACTTAAGAGCCCCCTCAGCCCCTTA
191 CATCACAAAATATTTCACGGTAAAAAGTTATCATTAAAAGACTTAAGAGCCCCCTCAGCCCCTTA
* * * *
70220 TTAGAAGGGCCAGCACCTTTTTCATGATTTCAAATGAAAGCTATTGTCAATTCTAACACTTTTTG
256 TTTGAAGGGCCAGCCCCTTTTTCATGATTTCAAATGAAAGCTATTGTCAATTCAAACACATTTTG
* *
70285 TTCAACAAGTAATTACAAATTTTGTACCGTTCTCGAGATATCTTGAGAGGGTCGTGTTAGGGGCC
321 TTCAAAAAGTAATTACAAATTATGTACCGTTCTCGAGATATCTTGAGAGGGTCGTGTTAGGGGCC
*
70350 AGCCCTGTATCTCCTTTTAGGGACCGCATAACAAAGAAATTATAGTTGAT
386 AGCCCTGTAACTCCTTTTAGGGACCGCATAACAAAGAAATTATAGTT-AT
* * * * *
70400 TATTGTTAAGCTCTATATTTTGAGCATCTTTGTTAAATATTTCTTATCGAAATGTTTCTTCATTC
1 CATTGTTAAGCTCTATATTTTGAGCATTTTTGTTAAATATTGCTTATCAAAATGTTTCTTCATTT
* **
70465 TGAGATATTATGCATTAAAGTTTTGGACTTCTGGCCCCTTAAAAATTACTAATTACGTAACATAG
66 TGAGATATTA-GCATCAAAGTTTTGGACTTCTGGCCCCTT-AAAATCCCTAATTACGTAACATAG
* *
70530 GAGTAAATGATTGCCATGTATAGGTAAATAATCTTAGAATGAACATAATTGCTTCTATAACGCAT
129 AAGTAAATGATTGCCATGTATAGGTAAATAACCTTAGAATGAACATAATTGCTTCTATAACGCAT
* * * *
70595 CACAAAATATTTCACGGTAAAAGGTTATCATTAAAAGACTTCAGAGCTCCCTCAGCCCCTAATTT
194 CACAAAATATTTCACGGTAAAAAGTTATCATTAAAAGACTTAAGAGCCCCCTCAGCCCCTTATTT
* *
70660 GAAGGGCCAGCCCCTTTTTCTTGATTTCAAATGAAAGCTTTTGTCAATTCAAACACATTTTGTTC
259 GAAGGGCCAGCCCCTTTTTCATGATTTCAAATGAAAGCTATTGTCAATTCAAACACATTTTGTTC
** *
70725 AAAAAGTGTTTACAAA-TATGTACCGTTCTCGAGATATCTTGAGAGGGTCGTTTTAGGGGCC-GA
324 AAAAAGTAATTACAAATTATGTACCGTTCTCGAGATATCTTGAGAGGGTCGTGTTAGGGGCCAG-
* *
70788 CCCTGTAACTCCTTTTAGGGACCGCATAACAAGGAAATTATGGTT-T
388 CCCTGTAACTCCTTTTAGGGACCGCATAACAAAGAAATTATAGTTAT
70834 CAGGTTGTTAAGCTCTATATTTTGAGCATGTTTTGTTAAATATTGCTTATCAAAATGTTTCTTCA
1 CA--TTGTTAAGCTCTATATTTTGAGCAT-TTTTGTTAAATATTGCTTATCAAAATGTTTCTTCA
*
70899 TTTTGAGATATTGAGCATCAAAGTTTTGGACTTCTGGCCCCTTAAAATCCCTAATTACGTAATAT
63 TTTTGAGATATT-AGCATCAAAGTTTTGGACTTCTGGCCCCTTAAAATCCCTAATTACGTAACAT
* *
70964 AGAAGTAAATGATTGCCATGTATAGGTAAATAACCTAAGAATAAACATAATTGCTTCTATAACGC
127 AGAAGTAAATGATTGCCATGTATAGGTAAATAACCTTAGAATGAACATAATTGCTTCTATAACGC
* * *
71029 ATCACAAAATATTTCACGGTAAAAAGTTATTATTAAAATACTTTAGAGCCCCCTCAGCCCCTTAT
192 ATCACAAAATATTTCACGGTAAAAAGTTATCATTAAAAGACTTAAGAGCCCCCTCAGCCCCTTAT
**
71094 TTGAAGGGCCAGCCCCTTTTTCATGATCCCAAATGAAAGCT
257 TTGAAGGGCCAGCCCCTTTTTCATGATTTCAAATGAAAGCT
71135 CTTGATTTAA
Statistics
Matches: 659, Mismatches: 66, Indels: 21
0.88 0.09 0.03
Matches are distributed among these distances:
434 2 0.00
435 2 0.00
436 338 0.51
437 315 0.48
438 2 0.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (434 bp):
CATTGTTAAGCTCTATATTTTGAGCATTTTTGTTAAATATTGCTTATCAAAATGTTTCTTCATTT
TGAGATATTAGCATCAAAGTTTTGGACTTCTGGCCCCTTAAAATCCCTAATTACGTAACATAGAA
GTAAATGATTGCCATGTATAGGTAAATAACCTTAGAATGAACATAATTGCTTCTATAACGCATCA
CAAAATATTTCACGGTAAAAAGTTATCATTAAAAGACTTAAGAGCCCCCTCAGCCCCTTATTTGA
AGGGCCAGCCCCTTTTTCATGATTTCAAATGAAAGCTATTGTCAATTCAAACACATTTTGTTCAA
AAAGTAATTACAAATTATGTACCGTTCTCGAGATATCTTGAGAGGGTCGTGTTAGGGGCCAGCCC
TGTAACTCCTTTTAGGGACCGCATAACAAAGAAATTATAGTTAT
Found at i:72474 original size:63 final size:63
Alignment explanation
Indices: 72375--72493 Score: 188
Period size: 63 Copynumber: 1.9 Consensus size: 63
72365 GAATAAGAAA
72375 AAAAAGAAACCGTAGAAAAACAAAAGGGTCTTCCGTTGAAAACGGAAGACCCTAATAATAGGG
1 AAAAAGAAACCGTAGAAAAACAAAAGGGTCTTCCGTTGAAAACGGAAGACCCTAATAATAGGG
* *
72438 AAAAAGAAACC-TAAGAAAAACAATAA-GGTCTTCCGTTGGAAACGGAAGACCTTAAT
1 AAAAAGAAACCGT-AGAAAAACAA-AAGGGTCTTCCGTTGAAAACGGAAGACCCTAAT
72494 TAAAGCCTTA
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
62 1 0.02
63 49 0.94
64 2 0.04
ACGTcount: A:0.48, C:0.16, G:0.20, T:0.16
Consensus pattern (63 bp):
AAAAAGAAACCGTAGAAAAACAAAAGGGTCTTCCGTTGAAAACGGAAGACCCTAATAATAGGG
Found at i:73360 original size:38 final size:38
Alignment explanation
Indices: 73310--73565 Score: 322
Period size: 38 Copynumber: 6.8 Consensus size: 38
73300 CGAAGAATGG
**
73310 TGTCTATATCAACTTGGCCAATGTAGTCACTGAGGTAT
1 TGTCTATATCAACTCAGCCAATGTAGTCACTGAGGTAT
* *
73348 TGTCTTTATCAACTCAGCCAATGAAGTCACTGAGGTAT
1 TGTCTATATCAACTCAGCCAATGTAGTCACTGAGGTAT
73386 TGTCTATATCAACTCAGCCAATGTAGTCACTGAGGTAT
1 TGTCTATATCAACTCAGCCAATGTAGTCACTGAGGTAT
* * *
73424 TGTCTAT-T-AACTCAGCCAA--TAGTCATTGAAGAAT
1 TGTCTATATCAACTCAGCCAATGTAGTCACTGAGGTAT
* **
73458 GGTGTCTATATCAACTCGGCCAGGGTAGTCACTGAGGTAT
1 --TGTCTATATCAACTCAGCCAATGTAGTCACTGAGGTAT
* * * *
73498 TATCTATATTAACCTCAGCCAATGTAGTCACTTAAGTAT
1 TGTCTATATCAA-CTCAGCCAATGTAGTCACTGAGGTAT
*
73537 TGTCTACATCAACTCAGCCAATGTAGTCA
1 TGTCTATATCAACTCAGCCAATGTAGTCA
73566 TTGAAGAAAG
Statistics
Matches: 187, Mismatches: 24, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
34 12 0.06
36 18 0.10
37 2 0.01
38 113 0.60
39 30 0.16
40 12 0.06
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (38 bp):
TGTCTATATCAACTCAGCCAATGTAGTCACTGAGGTAT
Found at i:73486 original size:74 final size:75
Alignment explanation
Indices: 73281--73565 Score: 321
Period size: 74 Copynumber: 3.7 Consensus size: 75
73271 ATATGCAACT
* *
73281 ACTCAGCCAAAGTAGTCATCGAAGAATGGTGTCTATATCAACTTGGCCAATGTAGTCACTGAGGT
1 ACTCAGCC-AA-TAGTCATTGAAGAATGGTGTCTATATCAACTCGGCCAATGTAGTCACTGAGGT
*
73346 ATTGTCTTTATCA
64 ATTGTC-TTATTA
* * * *
73359 ACTCAGCCAATGAAGTCACTGAGGTAT--TGTCTATATCAACTCAGCCAATGTAGTCACTGAGGT
1 ACTCAGCCAAT--AGTCATTGAAGAATGGTGTCTATATCAACTCGGCCAATGTAGTCACTGAGGT
73422 ATTGTC-TATTA
64 ATTGTCTTATTA
**
73433 ACTCAGCCAATAGTCATTGAAGAATGGTGTCTATATCAACTCGGCCAGGGTAGTCACTGAGGTAT
1 ACTCAGCCAATAGTCATTGAAGAATGGTGTCTATATCAACTCGGCCAATGTAGTCACTGAGGTAT
*
73498 TATCTATATTA
66 TGTCT-TATTA
* * *
73509 ACCTCAGCCAATGTAGTCACTT-AAGTAT--TGTCTACATCAACTCAGCCAATGTAGTCA
1 A-CTCAGCCAA--TAGTCA-TTGAAGAATGGTGTCTATATCAACTCGGCCAATGTAGTCA
73566 TTGAAGAAAG
Statistics
Matches: 178, Mismatches: 19, Indels: 21
0.82 0.09 0.10
Matches are distributed among these distances:
72 11 0.06
74 53 0.30
76 47 0.26
77 36 0.20
78 18 0.10
79 11 0.06
80 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (75 bp):
ACTCAGCCAATAGTCATTGAAGAATGGTGTCTATATCAACTCGGCCAATGTAGTCACTGAGGTAT
TGTCTTATTA
Found at i:73587 original size:17 final size:17
Alignment explanation
Indices: 73561--73600 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
73551 CAGCCAATGT
73561 AGTC-ATTGAAGAAAGG
1 AGTCTATTGAAGAAAGG
73577 AGTCTATTGAAGAAAGG
1 AGTCTATTGAAGAAAGG
73594 AGTCTAT
1 AGTCTAT
73601 ATCAATTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.40, C:0.07, G:0.28, T:0.25
Consensus pattern (17 bp):
AGTCTATTGAAGAAAGG
Found at i:82997 original size:37 final size:37
Alignment explanation
Indices: 82956--83059 Score: 117
Period size: 37 Copynumber: 2.9 Consensus size: 37
82946 TTGAACTGCT
*
82956 TAATATTGTTTCGTAAAATCTTGTTTTCTGCAGAACA
1 TAATATTGTTTCATAAAATCTTGTTTTCTGCAGAACA
* * * *
82993 TAATATTATTTCATAAAATATTTTTTTCTGCAGGACA
1 TAATATTGTTTCATAAAATCTTGTTTTCTGCAGAACA
*
83030 T-ATA--GTTTAATAAAATC-TGTTTTTCTGCAG
1 TAATATTGTTTCATAAAATCTTG-TTTTCTGCAG
83060 GACAATGGTG
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
33 1 0.02
34 20 0.35
36 3 0.05
37 33 0.58
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.45
Consensus pattern (37 bp):
TAATATTGTTTCATAAAATCTTGTTTTCTGCAGAACA
Found at i:83053 original size:34 final size:35
Alignment explanation
Indices: 82969--83063 Score: 104
Period size: 34 Copynumber: 2.7 Consensus size: 35
82959 TATTGTTTCG
* *
82969 TAAAATCTTGTTTTCTGCAGAACATAATATTATTTCA
1 TAAAATCTT-TTTTCTGCAGGACATAATA-TATTTAA
* *
83006 TAAAATATTTTTTTCTGCAGGACAT-ATA-GTTTAA
1 TAAAAT-CTTTTTTCTGCAGGACATAATATATTTAA
83040 TAAAATCTGTTTTTCTGCAGGACA
1 TAAAATCT-TTTTTCTGCAGGACA
83064 ATGGTGGAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
33 1 0.02
34 25 0.49
36 3 0.06
37 20 0.39
38 2 0.04
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.42
Consensus pattern (35 bp):
TAAAATCTTTTTTCTGCAGGACATAATATATTTAA
Found at i:86116 original size:21 final size:23
Alignment explanation
Indices: 86091--86150 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
86081 TTTTACAGAG
86091 ACTTT-CTT-GTCATGATATAAA
1 ACTTTGCTTAGTCATGATATAAA
* *
86112 ACTTTGTTTAGTCATGTTATAAA
1 ACTTTGCTTAGTCATGATATAAA
*
86135 ACTTTGTTTAGTCATG
1 ACTTTGCTTAGTCATG
86151 TTCATATTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.14
22 2 0.06
23 28 0.80
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.47
Consensus pattern (23 bp):
ACTTTGCTTAGTCATGATATAAA
Found at i:86151 original size:23 final size:23
Alignment explanation
Indices: 86099--86152 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
86089 AGACTTTCTT
*
86099 GTCATGATATAAAACTTTGTTTA
1 GTCATGTTATAAAACTTTGTTTA
86122 GTCATGTTATAAAACTTTGTTTA
1 GTCATGTTATAAAACTTTGTTTA
86145 GTCATGTT
1 GTCATGTT
86153 CATATTACAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.46
Consensus pattern (23 bp):
GTCATGTTATAAAACTTTGTTTA
Found at i:88626 original size:31 final size:31
Alignment explanation
Indices: 88591--88655 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
88581 TCATGTACTG
*
88591 CATTAAAACCTCATTGACAGTTTCGAGTGAC
1 CATTAAAACCTCAGTGACAGTTTCGAGTGAC
*
88622 CATTAAAACCTCAGTGACAGTTTTGAGTGAC
1 CATTAAAACCTCAGTGACAGTTTCGAGTGAC
88653 CAT
1 CAT
88656 GTCATATACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (31 bp):
CATTAAAACCTCAGTGACAGTTTCGAGTGAC
Found at i:90199 original size:13 final size:13
Alignment explanation
Indices: 90181--90207 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
90171 ACAGATGACA
90181 GGGTTGTATGCAT
1 GGGTTGTATGCAT
90194 GGGTTGTATGCAT
1 GGGTTGTATGCAT
90207 G
1 G
90208 TTAATTAGGA
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:0.15, C:0.07, G:0.41, T:0.37
Consensus pattern (13 bp):
GGGTTGTATGCAT
Found at i:93133 original size:11 final size:12
Alignment explanation
Indices: 93114--93143 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
93104 TGAAATTAAT
93114 GATACATAAATA
1 GATACATAAATA
93126 GA-ACATAAATA
1 GATACATAAATA
93137 GATACAT
1 GATACAT
93144 TATGGTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.57, C:0.10, G:0.10, T:0.23
Consensus pattern (12 bp):
GATACATAAATA
Found at i:108222 original size:55 final size:55
Alignment explanation
Indices: 108151--108298 Score: 233
Period size: 55 Copynumber: 2.7 Consensus size: 55
108141 CCCAAACAAA
* * *
108151 AACATATATCTAGCAAATTCTCAAGAATATTTGATTTGTCCTTAAACTACTGTAC
1 AACAGATATCTAGCAAATTCTCAAGAATATCTGATTTGTCATTAAACTACTGTAC
*
108206 AACAGATATCTAGCAAATTCTCAAGAATATCTGATTTGTCATTTAACTACTGTAC
1 AACAGATATCTAGCAAATTCTCAAGAATATCTGATTTGTCATTAAACTACTGTAC
* * *
108261 AACAGATATCTAGCAAATTCACAAGGATATCTAATTTG
1 AACAGATATCTAGCAAATTCTCAAGAATATCTGATTTG
108299 ACTCCAAACA
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 86 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.34
Consensus pattern (55 bp):
AACAGATATCTAGCAAATTCTCAAGAATATCTGATTTGTCATTAAACTACTGTAC
Found at i:108337 original size:56 final size:50
Alignment explanation
Indices: 108128--108403 Score: 216
Period size: 55 Copynumber: 5.2 Consensus size: 50
108118 ATTCACTACA
* * * * *
108128 ATATATAATTTGACCC-AAACAAAAACATATATCTAGCAAATTCTCAAGA
1 ATATCTAATTTGACCCTAAACAACAACAGATATCTAGCAAATTCACAAGG
* * * * * *
108177 ATATTTGATTTGTCCTTAAACTACTGTACAACAGATATCTAGCAAATTCTCAAGA
1 ATATCTAATTTGACCCTAAAC-A----ACAACAGATATCTAGCAAATTCACAAGG
* * ** *
108232 ATATCTGATTTGTCATTTAACTACTGTACAACAGATATCTAGCAAATTCACAAGG
1 ATATCTAATTTGAC-CCTAA--AC--AACAACAGATATCTAGCAAATTCACAAGG
*
108287 ATATCTAATTTGACTCC-AAACAACACCATAAACATG-TATCTAGCACATTCACAAGG
1 ATATCTAATTTGAC-CCTAAAC-A-A-C---AACA-GATATCTAGCAAATTCACAAGG
108343 ATATCTAATTTGACCCTAAACAACAACAGATATCTAGCAAATTCACAAGG
1 ATATCTAATTTGACCCTAAACAACAACAGATATCTAGCAAATTCACAAGG
108393 ATATCTAATTT
1 ATATCTAATTT
108404 ATCCCCAAAC
Statistics
Matches: 188, Mismatches: 21, Indels: 35
0.77 0.09 0.14
Matches are distributed among these distances:
49 13 0.07
50 38 0.20
51 1 0.01
52 3 0.02
53 2 0.01
54 3 0.02
55 80 0.43
56 45 0.24
57 1 0.01
58 2 0.01
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (50 bp):
ATATCTAATTTGACCCTAAACAACAACAGATATCTAGCAAATTCACAAGG
Found at i:120381 original size:28 final size:29
Alignment explanation
Indices: 120341--120466 Score: 193
Period size: 28 Copynumber: 4.4 Consensus size: 29
120331 TAACAAAAAT
120341 AATGAACACAAACAATGGTAAACCAATG-
1 AATGAACACAAACAATGGTAAACCAATGA
120369 AATGAACACAAACAATGGTAAACCAATG-
1 AATGAACACAAACAATGGTAAACCAATGA
120397 AATGAACACAAACAATGGTAAACCAATGA
1 AATGAACACAAACAATGGTAAACCAATGA
* * * * *
120426 AATAAAAAAAAACATTGGTAAACCATTGA
1 AATGAACACAAACAATGGTAAACCAATGA
120455 AATGAACACAAA
1 AATGAACACAAA
120467 TAGTTTTAAG
Statistics
Matches: 89, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
28 56 0.63
29 33 0.37
ACGTcount: A:0.56, C:0.16, G:0.13, T:0.15
Consensus pattern (29 bp):
AATGAACACAAACAATGGTAAACCAATGA
Found at i:124723 original size:2 final size:2
Alignment explanation
Indices: 124716--124767 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
124706 CTAACAACAA
124716 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
124758 TC TC TC TC TC
1 TC TC TC TC TC
124768 GTTGAGAAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:144555 original size:102 final size:102
Alignment explanation
Indices: 144411--144603 Score: 287
Period size: 102 Copynumber: 1.9 Consensus size: 102
144401 GTTCTATATA
* * * * * *
144411 CAGAATTGTTCTGGATTGGTACTGGGTTCATAGTCCTTGGCTGAATAACATTATCTGGTTGACGG
1 CAGAATTGTGCTGGATGGGTACTGGATTCACAGTCCTCGGCTGAATAACATTATCCGGTTGACGG
*
144476 GAAAAATGTTCAGCGATATATGGCTCGGTCCTATCTT
66 GAAAAATGTTCAGCGATATATCGCTCGGTCCTATCTT
* * *
144513 CAGAATTGTGCTGGATGGGTACTGGATTCACAGTCCTCGGCTGAATAATATTCTCCGGTTGATGG
1 CAGAATTGTGCTGGATGGGTACTGGATTCACAGTCCTCGGCTGAATAACATTATCCGGTTGACGG
*
144578 GAAAAATGTTCAGTGATATATCGCTC
66 GAAAAATGTTCAGCGATATATCGCTC
144604 AGTACGAGTT
Statistics
Matches: 80, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
102 80 1.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (102 bp):
CAGAATTGTGCTGGATGGGTACTGGATTCACAGTCCTCGGCTGAATAACATTATCCGGTTGACGG
GAAAAATGTTCAGCGATATATCGCTCGGTCCTATCTT
Found at i:146138 original size:2 final size:2
Alignment explanation
Indices: 146131--146167 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
146121 TAACCATTAT
* *
146131 GA GA GA GA GA GA GA GA GA GA GA AA GT GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
146168 GGGGCATGGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.03
Consensus pattern (2 bp):
GA
Found at i:149459 original size:15 final size:15
Alignment explanation
Indices: 149439--149468 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
149429 GAGTTGTTGA
149439 TTTGGTTGTTTGTGG
1 TTTGGTTGTTTGTGG
*
149454 TTTGGTTTTTTGTGG
1 TTTGGTTGTTTGTGG
149469 ATTGCCACAT
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:0.00, C:0.00, G:0.37, T:0.63
Consensus pattern (15 bp):
TTTGGTTGTTTGTGG
Found at i:154973 original size:22 final size:20
Alignment explanation
Indices: 154928--154975 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 20
154918 ATCTTCTTTG
*
154928 AAATATATGATAAACATACC
1 AAATATATGATAAACATACA
154948 AAATATATCGATAGAA-ATATCA
1 AAATATAT-GATA-AACATA-CA
154970 AAATAT
1 AAATAT
154976 TGTTTAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 8 0.33
21 7 0.29
22 9 0.38
ACGTcount: A:0.56, C:0.10, G:0.06, T:0.27
Consensus pattern (20 bp):
AAATATATGATAAACATACA
Found at i:168379 original size:145 final size:146
Alignment explanation
Indices: 168115--168410 Score: 576
Period size: 145 Copynumber: 2.0 Consensus size: 146
168105 TTGCGTTTTT
168115 TAAATATCCTCAAAAAATTATCTCTAGAAGGCTACAATAGTTGTAATATGATATGTTTACATAGT
1 TAAATATCCTCAAAAAATTATCTCTAGAAGGCTACAATAGTTGTAATATGATATGTTTACATAGT
168180 GTATTATAAAGCATGAATAATTACATGTTCTGTCAGCATGGGATGTATATATTTTCATAATAAAA
66 GTATTATAAAGCATGAATAATTACATGTTCTGTCAGCATGGGATGTATATATTTTCATAATAAAA
*
168245 CAAAAAATTTTTGAAA
131 CAAAAAAATTTTGAAA
168261 -AAATATCCTCAAAAAATTATCTCTAGAAGGCTACAATAGTTGTAATATGATATGTTTACATAGT
1 TAAATATCCTCAAAAAATTATCTCTAGAAGGCTACAATAGTTGTAATATGATATGTTTACATAGT
168325 GTATTATAAAGCATGAATAATTACATGTTCTGTCAGCATGGGATGTATATATTTTCATAATAAAA
66 GTATTATAAAGCATGAATAATTACATGTTCTGTCAGCATGGGATGTATATATTTTCATAATAAAA
168390 CAAAAAAATTTTGAAA
131 CAAAAAAATTTTGAAA
168406 TAAAT
1 TAAAT
168411 CTTTAGCAGA
Statistics
Matches: 148, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
145 144 0.97
146 4 0.03
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (146 bp):
TAAATATCCTCAAAAAATTATCTCTAGAAGGCTACAATAGTTGTAATATGATATGTTTACATAGT
GTATTATAAAGCATGAATAATTACATGTTCTGTCAGCATGGGATGTATATATTTTCATAATAAAA
CAAAAAAATTTTGAAA
Found at i:178636 original size:20 final size:21
Alignment explanation
Indices: 178608--178647 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
178598 ACATACTAAG
178608 CAATATGCTAAGT-CAAATTT
1 CAATATGCTAAGTACAAATTT
*
178628 CAATCTGCTAAGTACAAATT
1 CAATATGCTAAGTACAAATT
178648 CTGTACTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (21 bp):
CAATATGCTAAGTACAAATTT
Found at i:179777 original size:27 final size:28
Alignment explanation
Indices: 179747--179821 Score: 91
Period size: 27 Copynumber: 2.6 Consensus size: 28
179737 ACAGGCATGG
179747 ATATTTTATTTTATAATTATTA-TAATT
1 ATATTTTATTTTATAATTATTATTAATT
179774 ATATATTTATTTTTTATAATTATTATTAATT
1 ATAT-TTTA--TTTTATAATTATTATTAATT
* *
179805 ATA-ATAATTTTATAATT
1 ATATTTTATTTTATAATT
179822 TGTTTCATGG
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
27 14 0.33
28 4 0.10
29 2 0.05
30 14 0.33
31 8 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (28 bp):
ATATTTTATTTTATAATTATTATTAATT
Found at i:182408 original size:16 final size:16
Alignment explanation
Indices: 182387--182424 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
182377 CCACAACAAC
182387 ATGAAATGTATTAGGT
1 ATGAAATGTATTAGGT
182403 ATGAAATGTATTAGGT
1 ATGAAATGTATTAGGT
182419 ATGAAA
1 ATGAAA
182425 GGACAGTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.24, T:0.34
Consensus pattern (16 bp):
ATGAAATGTATTAGGT
Found at i:188753 original size:20 final size:19
Alignment explanation
Indices: 188724--188761 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
188714 TATTATTATT
188724 AAATTAGATAGATAGATAC
1 AAATTAGATAGATAGATAC
188743 AAATGTAGATAGATAGATA
1 AAAT-TAGATAGATAGATA
188762 GATAAAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.53, C:0.03, G:0.18, T:0.26
Consensus pattern (19 bp):
AAATTAGATAGATAGATAC
Found at i:190516 original size:12 final size:12
Alignment explanation
Indices: 190499--190528 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
190489 AAAAATTAAA
190499 CTCTCTGTCTCT
1 CTCTCTGTCTCT
190511 CTCTCTGTCTCT
1 CTCTCTGTCTCT
190523 CTCTCT
1 CTCTCT
190529 ATATATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.43, G:0.07, T:0.50
Consensus pattern (12 bp):
CTCTCTGTCTCT
Found at i:197184 original size:19 final size:18
Alignment explanation
Indices: 197144--197186 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
197134 AGATCCCAGA
197144 CTTTTAAAGATAAAATCT
1 CTTTTAAAGATAAAATCT
*
197162 -TTTTAAAGATATAATCTT
1 CTTTTAAAGATAAAATC-T
197180 CTTTTAA
1 CTTTTAA
197187 CTATGTATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 15 0.68
18 1 0.05
19 6 0.27
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.47
Consensus pattern (18 bp):
CTTTTAAAGATAAAATCT
Found at i:199301 original size:21 final size:21
Alignment explanation
Indices: 199228--199322 Score: 102
Period size: 21 Copynumber: 4.5 Consensus size: 21
199218 TATATTTAAG
**
199228 AAGTATCAGCATGTAATAATA
1 AAGTATCAGCATGTAATGTTA
* * * * *
199249 AAGTAACGGGATGCAATTTTA
1 AAGTATCAGCATGTAATGTTA
*
199270 AAGTCTCAGCATGTAATGTTTA
1 AAGTATCAGCATGTAATG-TTA
199292 AA-TATCAGCATGTAATGTTA
1 AAGTATCAGCATGTAATGTTA
199312 AAGTATCAGCA
1 AAGTATCAGCA
199323 CATACTGAAG
Statistics
Matches: 59, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
20 5 0.08
21 49 0.83
22 5 0.08
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.31
Consensus pattern (21 bp):
AAGTATCAGCATGTAATGTTA
Found at i:211806 original size:20 final size:20
Alignment explanation
Indices: 211781--211825 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
211771 GGCGAATTAA
211781 GATTTGTTCTCACAAAATAG
1 GATTTGTTCTCACAAAATAG
* *
211801 GATTTGTTCTGACAAATTAG
1 GATTTGTTCTCACAAAATAG
211821 GATTT
1 GATTT
211826 CTTATCAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (20 bp):
GATTTGTTCTCACAAAATAG
Found at i:217080 original size:19 final size:17
Alignment explanation
Indices: 217056--217090 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 17
217046 TCTAGCTGTT
217056 AACAAACAAAAAACATGTA
1 AACAAA-AAAAAA-ATGTA
217075 AACAAAAAAAAAATGT
1 AACAAAAAAAAAATGT
217091 CTTGCTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 6 0.38
19 6 0.38
ACGTcount: A:0.71, C:0.11, G:0.06, T:0.11
Consensus pattern (17 bp):
AACAAAAAAAAAATGTA
Found at i:228159 original size:63 final size:60
Alignment explanation
Indices: 228058--228237 Score: 222
Period size: 63 Copynumber: 3.0 Consensus size: 60
228048 GGTAAAAGCG
* *
228058 AAGAAAAAGAAACAGAACGAA-AACAAGAAGGTCTTCCGTTGGAAACGGAAGACCTTAATG
1 AAGAAAAAGAAACCGAA-GAATAACAAGAAGGTCTTCCGTTGGAAACGGAAGACCTTAATC
* *
228118 ATAGGGAAAAAGAAACCGAAGAATAACAATAAGGTCTTCCGTTGGAAACGGAAGACTTTAA-C
1 A-A--GAAAAAGAAACCGAAGAATAACAAGAAGGTCTTCCGTTGGAAACGGAAGACCTTAATC
* * * * *
228180 AATAAAAAGAAA-CGTAGAATAACAAGAGGGTCTTCCGTTGGAAAAGGAAGACCCTAAT
1 AAGAAAAAGAAACCGAAGAATAACAAGAAGGTCTTCCGTTGGAAACGGAAGACCTTAAT
228238 TATCATTTCT
Statistics
Matches: 104, Mismatches: 11, Indels: 11
0.83 0.09 0.09
Matches are distributed among these distances:
58 39 0.38
59 9 0.09
60 1 0.01
61 2 0.02
62 4 0.04
63 49 0.47
ACGTcount: A:0.47, C:0.14, G:0.23, T:0.16
Consensus pattern (60 bp):
AAGAAAAAGAAACCGAAGAATAACAAGAAGGTCTTCCGTTGGAAACGGAAGACCTTAATC
Found at i:235268 original size:31 final size:31
Alignment explanation
Indices: 235230--235295 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
235220 GAAATCAGAT
*
235230 TGTTAAGTATGTTTTTTACACTTGAATTATA
1 TGTTAAGTATGTTATTTACACTTGAATTATA
235261 TGTTAAGTATGTTATTTACACTTGAATTATA
1 TGTTAAGTATGTTATTTACACTTGAATTATA
235292 TGTT
1 TGTT
235296 TTGTACACGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.29, C:0.06, G:0.14, T:0.52
Consensus pattern (31 bp):
TGTTAAGTATGTTATTTACACTTGAATTATA
Found at i:247054 original size:21 final size:21
Alignment explanation
Indices: 247029--247074 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
247019 AACAGGAAGA
* *
247029 TGAAATTAAACACACCATTTC
1 TGAAATCAAACACACCATTGC
* *
247050 TGAAATCACACAGACCATTGC
1 TGAAATCAAACACACCATTGC
247071 TGAA
1 TGAA
247075 CTGAAGACGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.24, G:0.11, T:0.24
Consensus pattern (21 bp):
TGAAATCAAACACACCATTGC
Found at i:248373 original size:27 final size:29
Alignment explanation
Indices: 248308--248368 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
248298 TGCAGCTCAT
*
248308 TTATACATTAGAGTGTATGTATACATATG
1 TTATACATTGGAGTGTATGTATACATATG
* *
248337 TTATACATTGGAGTGTATGTGTACATGTG
1 TTATACATTGGAGTGTATGTATACATATG
248366 TTA
1 TTA
248369 CATTGTCAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.30, C:0.07, G:0.21, T:0.43
Consensus pattern (29 bp):
TTATACATTGGAGTGTATGTATACATATG
Found at i:251526 original size:15 final size:16
Alignment explanation
Indices: 251508--251548 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
251498 AATTGATGTA
251508 TATAACGAA-CACGGC
1 TATAACGAATCACGGC
*
251523 TATAACGAATTTACGGC
1 TATAACGAA-TCACGGC
251540 TATAACGAA
1 TATAACGAA
251549 GTAATTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.39
17 14 0.61
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (16 bp):
TATAACGAATCACGGC
Found at i:252065 original size:29 final size:29
Alignment explanation
Indices: 252026--252091 Score: 114
Period size: 29 Copynumber: 2.2 Consensus size: 29
252016 CTATTAAGTT
*
252026 AACATGTCATTGAATACACATTTTTGGTGA
1 AACAT-TCATTGAATACACAATTTTGGTGA
252056 AACATTCATTGAATACACAATTTTGGTGA
1 AACATTCATTGAATACACAATTTTGGTGA
252085 AACATTC
1 AACATTC
252092 TAAAATTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 30 0.86
30 5 0.14
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (29 bp):
AACATTCATTGAATACACAATTTTGGTGA
Found at i:252362 original size:2 final size:2
Alignment explanation
Indices: 252355--252391 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
252345 CGTAACATTG
*
252355 CT CT CT CT CT CT CT CT CT CT TT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
252392 AGAGCAGAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:254779 original size:30 final size:30
Alignment explanation
Indices: 254745--254851 Score: 128
Period size: 30 Copynumber: 3.6 Consensus size: 30
254735 ACTCATCCGC
*
254745 TGCGACATATTTGGATTTTCACTTGACTGA
1 TGCGACATATTTGAATTTTCACTTGACTGA
* *
254775 TGCGACATATATGAATTTACACTTGACTGA
1 TGCGACATATTTGAATTTTCACTTGACTGA
*
254805 TG-GTACACATTTGAATTTAT-ACTTGACTGA
1 TGCG-ACATATTTGAATTT-TCACTTGACTGA
* *
254835 TGGGACATATTTAAATT
1 TGCGACATATTTGAATT
254852 GCCAATCATC
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
29 1 0.02
30 64 0.97
31 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (30 bp):
TGCGACATATTTGAATTTTCACTTGACTGA
Found at i:254905 original size:30 final size:30
Alignment explanation
Indices: 254838--254913 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
254828 TGACTGATGG
* *
254838 GACATATTTAAATTGCCAATCATCTCGTGC
1 GACATATTTGAATTGCCAATCATATCGTGC
* * * **
254868 GATATATTTGAATTGCCACTCATATGGTTT
1 GACATATTTGAATTGCCAATCATATCGTGC
254898 GACATATTTGAATTGC
1 GACATATTTGAATTGC
254914 TATTTAACTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (30 bp):
GACATATTTGAATTGCCAATCATATCGTGC
Found at i:265598 original size:5 final size:5
Alignment explanation
Indices: 265588--265619 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
265578 TTGGTAATAA
265588 ACAAT ACAAT ACAAT ACAAT ACAAT ACAAT AC
1 ACAAT ACAAT ACAAT ACAAT ACAAT ACAAT AC
265620 GATATAATGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.59, C:0.22, G:0.00, T:0.19
Consensus pattern (5 bp):
ACAAT
Found at i:268659 original size:10 final size:10
Alignment explanation
Indices: 268644--268684 Score: 64
Period size: 10 Copynumber: 4.1 Consensus size: 10
268634 GTCTGAAATT
268644 AATCTGAATG
1 AATCTGAATG
268654 AATCTGAATG
1 AATCTGAATG
*
268664 AATCTGCATG
1 AATCTGAATG
*
268674 AATCTTAATG
1 AATCTGAATG
268684 A
1 A
268685 CCTGTAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (10 bp):
AATCTGAATG
Found at i:271449 original size:2 final size:2
Alignment explanation
Indices: 271442--271485 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
271432 TTCGATTAAG
271442 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
271484 AT
1 AT
271486 CACATATTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:271986 original size:2 final size:2
Alignment explanation
Indices: 271979--272015 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
271969 CGTTACATTG
271979 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
272016 AGAGCAGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:272938 original size:21 final size:21
Alignment explanation
Indices: 272914--272956 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
272904 AGTTTTTGAC
272914 TTAAATTGCATTTTATAGAAA
1 TTAAATTGCATTTTATAGAAA
272935 TTAAATTGCATTTTATAGAAA
1 TTAAATTGCATTTTATAGAAA
272956 T
1 T
272957 AAAGATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (21 bp):
TTAAATTGCATTTTATAGAAA
Found at i:274445 original size:30 final size:29
Alignment explanation
Indices: 274355--274488 Score: 126
Period size: 30 Copynumber: 4.5 Consensus size: 29
274345 ATCTGGTGTA
* ** *
274355 ACATATTGGAATTTTCACCCATCTGCTGCG
1 ACATATTTGAATTGCCACTCATCTG-TGCG
* *
274385 ACATATTTGAATTTCCACTTGA-CTGATGCG
1 ACATATTTGAATTGCCAC-TCATCTG-TGCG
274415 ACATATTTGAATTGCCACTCATCTCGTGCG
1 ACATATTTGAATTGCCACTCATCT-GTGCG
* * * *
274445 ATAAATTTGAATTGCCACTCATATGGTGTG
1 ACATATTTGAATTGCCACTCATCT-GTGCG
274475 ACATATTTGAATTG
1 ACATATTTGAATTG
274489 TTATTCAACT
Statistics
Matches: 87, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
29 2 0.02
30 83 0.95
31 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (29 bp):
ACATATTTGAATTGCCACTCATCTGTGCG
Found at i:280328 original size:2 final size:2
Alignment explanation
Indices: 280321--280356 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
280311 AACATCGCAT
280321 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
280357 AGAGCAGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:282775 original size:30 final size:30
Alignment explanation
Indices: 282741--282818 Score: 120
Period size: 30 Copynumber: 2.6 Consensus size: 30
282731 ACTTGAGTGA
*
282741 TGCGACATATTTGAATTGCCACTCATCTCG
1 TGCGACATATTTGAATTGCCACTCATATCG
* *
282771 TGCGATATATTTGAATTGCCACTCATATGG
1 TGCGACATATTTGAATTGCCACTCATATCG
*
282801 TGTGACATATTTGAATTG
1 TGCGACATATTTGAATTG
282819 TTATTCAACT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (30 bp):
TGCGACATATTTGAATTGCCACTCATATCG
Found at i:285961 original size:2 final size:2
Alignment explanation
Indices: 285954--285988 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
285944 ATTTTATTTT
285954 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
285989 TTAAAATTTT
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:296896 original size:21 final size:21
Alignment explanation
Indices: 296872--296917 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
296862 AACAGGAAGA
*
296872 TGAAATCAAACACACCATTTC
1 TGAAATCAAACACACCATTAC
* *
296893 TGAAATCACACAGACCATTAC
1 TGAAATCAAACACACCATTAC
296914 TGAA
1 TGAA
296918 CTAAAGACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.43, C:0.26, G:0.09, T:0.22
Consensus pattern (21 bp):
TGAAATCAAACACACCATTAC
Found at i:300252 original size:2 final size:2
Alignment explanation
Indices: 300245--300305 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
300235 CGTAACATTG
*
300245 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
300287 CT CT CT CT CT AT CT CT CT C
1 CT CT CT CT CT CT CT CT CT C
300306 AGGGCAGAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.02, C:0.48, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:301583 original size:22 final size:22
Alignment explanation
Indices: 301558--301650 Score: 143
Period size: 22 Copynumber: 4.3 Consensus size: 22
301548 TAAGTAAACA
*
301558 GCTATAGAGTACACAGTACATT
1 GCTATAGAGTACACAGTACACT
301580 GCTATAGAGTACACAGTACACT
1 GCTATAGAGTACACAGTACACT
301602 GCTATAGAGTACACAGTACACT
1 GCTATAGAGTACACAGTACACT
* **
301624 GTTATA-AAAACACAGTACACT
1 GCTATAGAGTACACAGTACACT
301645 GCTATA
1 GCTATA
301651 ATATTAAAAT
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
21 18 0.27
22 48 0.73
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (22 bp):
GCTATAGAGTACACAGTACACT
Found at i:310478 original size:125 final size:125
Alignment explanation
Indices: 310256--310505 Score: 473
Period size: 125 Copynumber: 2.0 Consensus size: 125
310246 AGAGGTCACT
310256 TGTCCTACTGTTTCGTCGTGGTTGCCCACTAAGACTTTAGCAATTTTAGCACAGTTCTTGTGTGA
1 TGTCCTACTGTTTCGTCGTGGTTGCCCACTAAGACTTTAGCAATTTTAGCACAGTTCTTGTGTGA
*
310321 TATTGCACAGGTACTGGACAGACTATTAGTGAAATCCTCTGATCCGTAGAAGCAGCAGAG
66 TATGGCACAGGTACTGGACAGACTATTAGTGAAATCCTCTGATCCGTAGAAGCAGCAGAG
*
310381 TGTCCTACTGTTTCGTCGTGGTTGCCCACTAAGACTTTAGCAATTTTAGCACAGTTCTTGTGTGG
1 TGTCCTACTGTTTCGTCGTGGTTGCCCACTAAGACTTTAGCAATTTTAGCACAGTTCTTGTGTGA
*
310446 TATGGCACAGGTACTGGACAGACTATTAGTGAAATCCTCTGATCCGTAGAGGCAGCAGAG
66 TATGGCACAGGTACTGGACAGACTATTAGTGAAATCCTCTGATCCGTAGAAGCAGCAGAG
310506 ATGCTCTATT
Statistics
Matches: 122, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
125 122 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (125 bp):
TGTCCTACTGTTTCGTCGTGGTTGCCCACTAAGACTTTAGCAATTTTAGCACAGTTCTTGTGTGA
TATGGCACAGGTACTGGACAGACTATTAGTGAAATCCTCTGATCCGTAGAAGCAGCAGAG
Found at i:316804 original size:2 final size:2
Alignment explanation
Indices: 316797--316844 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
316787 TCGTCATATA
316797 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
316839 AG AG AG
1 AG AG AG
316845 TACCAGTATG
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):
AG
Found at i:317169 original size:2 final size:2
Alignment explanation
Indices: 317162--317209 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
317152 TTGTAAAATA
*
317162 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
317204 TC TC TC
1 TC TC TC
317210 AGTGTGTACT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:319897 original size:2 final size:2
Alignment explanation
Indices: 319890--319934 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
319880 TGATCGTTAT
*
319890 GA GA GA GA GA GA GA GA GA GA GA GA TA 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
319932 GA G
1 GA G
319935 TTAATTATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.02
Consensus pattern (2 bp):
GA
Found at i:326849 original size:2 final size:2
Alignment explanation
Indices: 326842--326887 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
326832 CGTAACATTG
326842 CT CT CT CT CT CT CT 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 CT CT CT CT CT CT CT
326884 CT CT
1 CT CT
326888 GAGCAGAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:332393 original size:54 final size:51
Alignment explanation
Indices: 332311--332420 Score: 175
Period size: 54 Copynumber: 2.1 Consensus size: 51
332301 AACAACTTGA
332311 ATTTCTCACAGCGTTTAGAATTTCTGAATACTGGTATATAAAATAAACTAATAT
1 ATTTCTCACAGCGTTTAGAATTTCTGAATACTGG--TATAAAA-AAACTAATAT
*
332365 ATTTCTCAGAGCGTTTAGAATTTCTGAATACTGGTATAAAAAAACTAATAT
1 ATTTCTCACAGCGTTTAGAATTTCTGAATACTGGTATAAAAAAACTAATAT
*
332416 CTTTC
1 ATTTC
332421 CAAATATTTA
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
51 14 0.26
52 7 0.13
54 33 0.61
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (51 bp):
ATTTCTCACAGCGTTTAGAATTTCTGAATACTGGTATAAAAAAACTAATAT
Found at i:332538 original size:2 final size:2
Alignment explanation
Indices: 332533--332584 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
332523 AGAAAGAACG
332533 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
332575 TC TC TC TC TC
1 TC TC TC TC TC
332585 ATTTAAAGAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:334323 original size:15 final size:17
Alignment explanation
Indices: 334303--334337 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
334293 ATAATAAAAA
334303 AAATGG-TT-TAAAATT
1 AAATGGTTTATAAAATT
334318 AAATGGTTTATAAAATT
1 AAATGGTTTATAAAATT
334335 AAA
1 AAA
334338 ATGTTGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 2 0.11
17 10 0.56
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.37
Consensus pattern (17 bp):
AAATGGTTTATAAAATT
Found at i:360366 original size:18 final size:18
Alignment explanation
Indices: 360343--360391 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
360333 TGCTAGGTTT
360343 ACAGCATTTTGATCTTTC
1 ACAGCATTTTGATCTTTC
* *
360361 ACAGCATGTTGATCTTTT
1 ACAGCATTTTGATCTTTC
*
360379 GCAGCATTTTGAT
1 ACAGCATTTTGAT
360392 GATATTTTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.22, C:0.18, G:0.16, T:0.43
Consensus pattern (18 bp):
ACAGCATTTTGATCTTTC
Found at i:365296 original size:49 final size:49
Alignment explanation
Indices: 365239--365338 Score: 121
Period size: 49 Copynumber: 2.0 Consensus size: 49
365229 TTAAAAAATA
* * *
365239 TTTTCAAAGTGCGTTAAA-TTGGGAACAAATCAACGCACTATCAAAATTT
1 TTTTCAAAGAGCGTGAAATTTGGGAACAAATCAACCCACTATC-AAATTT
* * * *
365288 TTTTCAAAGAGCGTGAAATTTGGGACCAAGTTAACCCACTTTCAAATTT
1 TTTTCAAAGAGCGTGAAATTTGGGAACAAATCAACCCACTATCAAATTT
365337 TT
1 TT
365339 ATTTTTGTGC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
49 24 0.56
50 19 0.44
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (49 bp):
TTTTCAAAGAGCGTGAAATTTGGGAACAAATCAACCCACTATCAAATTT
Found at i:372402 original size:4 final size:4
Alignment explanation
Indices: 372393--372465 Score: 146
Period size: 4 Copynumber: 18.2 Consensus size: 4
372383 TGAACAATGT
372393 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
372441 TATC TATC TATC TATC TATC TATC T
1 TATC TATC TATC TATC TATC TATC T
372466 GTCTGTCTGT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 69 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.51
Consensus pattern (4 bp):
TATC
Found at i:372470 original size:4 final size:4
Alignment explanation
Indices: 372463--372491 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
372453 TATCTATCTA
372463 TCTG TCTG TCTG TCTG TCTG TCTG TCTG T
1 TCTG TCTG TCTG TCTG TCTG TCTG TCTG T
372492 ATAAATCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.24, T:0.52
Consensus pattern (4 bp):
TCTG
Found at i:382792 original size:4 final size:4
Alignment explanation
Indices: 382783--382859 Score: 154
Period size: 4 Copynumber: 19.2 Consensus size: 4
382773 TGAACAATGT
382783 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
382831 TATC TATC TATC TATC TATC TATC TATC T
1 TATC TATC TATC TATC TATC TATC TATC T
382860 GTCTGTCTGT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 73 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.51
Consensus pattern (4 bp):
TATC
Found at i:382864 original size:4 final size:4
Alignment explanation
Indices: 382857--382889 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
382847 TATCTATCTA
*
382857 TCTG TCTG TCTG TCTG TCTC TCTG TCTG TCTG T
1 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG T
382890 ATTTATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.27, G:0.21, T:0.52
Consensus pattern (4 bp):
TCTG
Found at i:386073 original size:12 final size:12
Alignment explanation
Indices: 386050--386094 Score: 67
Period size: 12 Copynumber: 3.8 Consensus size: 12
386040 TAACCTTTTC
386050 TCTGTC-GTCCG
1 TCTGTCTGTCCG
386061 TCTGTCTGTCCG
1 TCTGTCTGTCCG
386073 TCCT-TCTGTCCG
1 T-CTGTCTGTCCG
386085 TCTGTCTGTC
1 TCTGTCTGTC
386095 TGAAAACTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.26
12 21 0.68
13 2 0.06
ACGTcount: A:0.00, C:0.36, G:0.22, T:0.42
Consensus pattern (12 bp):
TCTGTCTGTCCG
Found at i:387062 original size:2 final size:2
Alignment explanation
Indices: 387055--387089 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
387045 GTCACAACAG
387055 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
387090 GGGGGGGGGG
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:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (2 bp):
GT
Found at i:390539 original size:100 final size:101
Alignment explanation
Indices: 390366--390639 Score: 397
Period size: 100 Copynumber: 2.8 Consensus size: 101
390356 GACGTGATAT
* *
390366 ATATTGTGGGTGTAACCGTTAACGCCAATAACTTGTTATCAGCTAAAATATTTTTCTGTGACGTC
1 ATATTGTGGATGTAACCGTTAACGCCCATAACTTGTTATCAGCTAAAATATTTTTCTGTGACGTC
390431 AGTGACTGTGTAGTCACCCCTTGACTGTGTACTCA-
66 AGTGACTGTGTAGTCACCCCTTGACTGTGTACTCAC
390466 ATATTGTGGATGTAACCGTTAACGCCCATAACTTGTTATCAGCTAAAATATTTTTCTGTGACGTC
1 ATATTGTGGATGTAACCGTTAACGCCCATAACTTGTTATCAGCTAAAATATTTTTCTGTGACGTC
390531 AGTGACTGTGTAGTCACCCCTTGACTGTGTACTCAC
66 AGTGACTGTGTAGTCACCCCTTGACTGTGTACTCAC
* * *** * *
390567 CTCTTGACTATG--ACC--TCAC-CCC---A-TGGTTATCAGCTAAAATATTTTTCTGTGACGTC
1 ATATTGTGGATGTAACCGTTAACGCCCATAACTTGTTATCAGCTAAAATATTTTTCTGTGACGTC
390623 AGTGACTGTGTAGTCAC
66 AGTGACTGTGTAGTCAC
390640 ATCTCAACCA
Statistics
Matches: 164, Mismatches: 9, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
92 49 0.30
93 1 0.01
96 3 0.02
97 3 0.02
99 3 0.02
100 98 0.60
101 7 0.04
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (101 bp):
ATATTGTGGATGTAACCGTTAACGCCCATAACTTGTTATCAGCTAAAATATTTTTCTGTGACGTC
AGTGACTGTGTAGTCACCCCTTGACTGTGTACTCAC
Found at i:390557 original size:19 final size:19
Alignment explanation
Indices: 390533--390588 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
390523 GTGACGTCAG
*
390533 TGACTGTGTAGTCACCCCT
1 TGACTGTGTACTCACCCCT
*
390552 TGACTGTGTACTCACCTCT
1 TGACTGTGTACTCACCCCT
*
390571 TGACTATG-ACCTCACCCC
1 TGACTGTGTA-CTCACCCC
390589 ATGGTTATCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 1 0.03
19 31 0.97
ACGTcount: A:0.18, C:0.36, G:0.16, T:0.30
Consensus pattern (19 bp):
TGACTGTGTACTCACCCCT
Found at i:396350 original size:15 final size:15
Alignment explanation
Indices: 396330--396359 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
396320 TCGTCTCCAT
*
396330 TTCAGAGGATGATGA
1 TTCAGAAGATGATGA
396345 TTCAGAAGATGATGA
1 TTCAGAAGATGATGA
396360 GGACACCCCT
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:0.37, C:0.07, G:0.30, T:0.27
Consensus pattern (15 bp):
TTCAGAAGATGATGA
Found at i:397831 original size:11 final size:11
Alignment explanation
Indices: 397815--397851 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
397805 AGCTATGCCA
397815 TTCAGTCACAT
1 TTCAGTCACAT
* *
397826 TTCAGTTACCT
1 TTCAGTCACAT
397837 TTCAGTCACAT
1 TTCAGTCACAT
397848 TTCA
1 TTCA
397852 ATTGACTGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.24, C:0.27, G:0.08, T:0.41
Consensus pattern (11 bp):
TTCAGTCACAT
Found at i:400025 original size:26 final size:26
Alignment explanation
Indices: 399996--400047 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
399986 AGTCTAGTAC
399996 AAATAGAAAATTGTTAGCCGCCCTGG
1 AAATAGAAAATTGTTAGCCGCCCTGG
*
400022 AAATTGAAAATTGTTAGCCGCCCTGG
1 AAATAGAAAATTGTTAGCCGCCCTGG
400048 CAAAGACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (26 bp):
AAATAGAAAATTGTTAGCCGCCCTGG
Found at i:404013 original size:12 final size:11
Alignment explanation
Indices: 403993--404031 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
403983 TAAAAAAGGG
*
403993 TTTTGTTTTGT
1 TTTTTTTTTGT
404004 TTTTTATTTTGT
1 TTTTT-TTTTGT
404016 TTTTTTTTT-T
1 TTTTTTTTTGT
404026 TTTTTT
1 TTTTTT
404032 GGGGGGGGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 7 0.27
11 8 0.31
12 11 0.42
ACGTcount: A:0.03, C:0.00, G:0.08, T:0.90
Consensus pattern (11 bp):
TTTTTTTTTGT
Found at i:404030 original size:17 final size:17
Alignment explanation
Indices: 403993--404028 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
403983 TAAAAAAGGG
403993 TTTTGTTTTGTTTTTTA
1 TTTTGTTTTGTTTTTTA
404010 TTTTGTTTT-TTTTTT-
1 TTTTGTTTTGTTTTTTA
404025 TTTT
1 TTTT
404029 TTTGGGGGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.21
16 6 0.32
17 9 0.47
ACGTcount: A:0.03, C:0.00, G:0.08, T:0.89
Consensus pattern (17 bp):
TTTTGTTTTGTTTTTTA
Found at i:407135 original size:23 final size:21
Alignment explanation
Indices: 407104--407148 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 21
407094 ATTTCGGGGG
407104 GGGGGGGGGGTATCAAAACAAA
1 GGGGGGGGGG-ATCAAAACAAA
407126 GNGGGGGGGGGATCAAAACAAA
1 G-GGGGGGGGGATCAAAACAAA
407148 G
1 G
407149 AAGATATAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.36, C:0.09, G:0.47, T:0.07
Consensus pattern (21 bp):
GGGGGGGGGGATCAAAACAAA
Found at i:408091 original size:2 final size:2
Alignment explanation
Indices: 408086--408151 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
408076 AATGTAAGAA
408086 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
408128 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
408152 GTGTCACGTA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:409100 original size:4 final size:4
Alignment explanation
Indices: 409084--409125 Score: 68
Period size: 4 Copynumber: 10.8 Consensus size: 4
409074 TTAATGATTT
*
409084 TTTG TTTG CTTG TTTG TTTG TTTG TTTG TTTG TTTG -TTG TTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTT
409126 TTTTTGGGGG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 3 0.09
4 32 0.91
ACGTcount: A:0.00, C:0.02, G:0.24, T:0.74
Consensus pattern (4 bp):
TTTG
Found at i:415288 original size:19 final size:19
Alignment explanation
Indices: 415264--415301 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
415254 ATTTTATTAT
415264 ATAATTAAATAATTGAAAA
1 ATAATTAAATAATTGAAAA
415283 ATAATTAAATAATTGAAAA
1 ATAATTAAATAATTGAAAA
415302 TGTCTTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (19 bp):
ATAATTAAATAATTGAAAA
Found at i:425983 original size:29 final size:28
Alignment explanation
Indices: 425941--425998 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 28
425931 GGTCCACATC
*
425941 GGAAGAGTTTAAACAATTCAAGTTGGTT
1 GGAAGAGTTCAAACAATTCAAGTTGGTT
425969 NGGAAGAGTTCAAACAATTCAAGTTGGTT
1 -GGAAGAGTTCAAACAATTCAAGTTGGTT
425998 G
1 G
425999 AGAGTTTAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 1 0.04
29 27 0.96
ACGTcount: A:0.34, C:0.09, G:0.26, T:0.29
Consensus pattern (28 bp):
GGAAGAGTTCAAACAATTCAAGTTGGTT
Found at i:434935 original size:14 final size:14
Alignment explanation
Indices: 434916--434946 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
434906 TCAAGATGAG
434916 ATTCAAAATACGAA
1 ATTCAAAATACGAA
434930 ATTCAAAATACGAA
1 ATTCAAAATACGAA
434944 ATT
1 ATT
434947 TAAGATTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.06, T:0.26
Consensus pattern (14 bp):
ATTCAAAATACGAA
Found at i:435203 original size:21 final size:21
Alignment explanation
Indices: 435177--435322 Score: 130
Period size: 21 Copynumber: 7.0 Consensus size: 21
435167 TACAAGATAA
435177 ACGATAGGATAGGATTCACGC
1 ACGATAGGATAGGATTCACGC
* *
435198 ACGATAGGATAGAATTAACGC
1 ACGATAGGATAGGATTCACGC
* * * *
435219 ACGATAGAACAGTATACACGC
1 ACGATAGGATAGGATTCACGC
* *
435240 ACGAAAGGATAGGATTAACGC
1 ACGATAGGATAGGATTCACGC
* * * *
435261 ACGATAGAACAGTATACACGC
1 ACGATAGGATAGGATTCACGC
* * **
435282 ACGATATGATAGGATTGATAC
1 ACGATAGGATAGGATTCACGC
* *
435303 ACGATAGGAAAGGATACACG
1 ACGATAGGATAGGATTCACG
435323 ATGTTCATGA
Statistics
Matches: 92, Mismatches: 33, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 92 1.00
ACGTcount: A:0.41, C:0.17, G:0.25, T:0.17
Consensus pattern (21 bp):
ACGATAGGATAGGATTCACGC
Found at i:435309 original size:42 final size:42
Alignment explanation
Indices: 435193--435297 Score: 183
Period size: 42 Copynumber: 2.5 Consensus size: 42
435183 GGATAGGATT
*
435193 CACGCACGATAGGATAGAATTAACGCACGATAGAACAGTATA
1 CACGCACGATAGGATAGGATTAACGCACGATAGAACAGTATA
*
435235 CACGCACGAAAGGATAGGATTAACGCACGATAGAACAGTATA
1 CACGCACGATAGGATAGGATTAACGCACGATAGAACAGTATA
*
435277 CACGCACGATATGATAGGATT
1 CACGCACGATAGGATAGGATT
435298 GATACACGAT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.17
Consensus pattern (42 bp):
CACGCACGATAGGATAGGATTAACGCACGATAGAACAGTATA
Found at i:435320 original size:42 final size:42
Alignment explanation
Indices: 435177--435322 Score: 168
Period size: 42 Copynumber: 3.5 Consensus size: 42
435167 TACAAGATAA
* * * * *
435177 ACGATAGGATAGGATTCACGCACGATAGGATAGAATTAACGC
1 ACGATAGAACAGGATACACGCACGATAGGATAGGATTAACAC
* * *
435219 ACGATAGAACAGTATACACGCACGAAAGGATAGGATTAACGC
1 ACGATAGAACAGGATACACGCACGATAGGATAGGATTAACAC
* * * *
435261 ACGATAGAACAGTATACACGCACGATATGATAGGATTGATAC
1 ACGATAGAACAGGATACACGCACGATAGGATAGGATTAACAC
435303 ACGATAGGAA-AGGATACACG
1 ACGATA-GAACAGGATACACG
435323 ATGTTCATGA
Statistics
Matches: 91, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
42 88 0.97
43 3 0.03
ACGTcount: A:0.41, C:0.17, G:0.25, T:0.17
Consensus pattern (42 bp):
ACGATAGAACAGGATACACGCACGATAGGATAGGATTAACAC
Found at i:437315 original size:21 final size:21
Alignment explanation
Indices: 437291--437356 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
437281 ACCCCCGCGA
*
437291 ATAGAACAGGATACACGCACG
1 ATAGAACAGAATACACGCACG
* *
437312 ATAGGATAGAATTA-ACGCACG
1 ATAGAACAGAA-TACACGCACG
*
437333 ATAGAACAGTATACACGCACG
1 ATAGAACAGAATACACGCACG
437354 ATA
1 ATA
437357 CGATAGGATT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
20 2 0.05
21 33 0.89
22 2 0.05
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.15
Consensus pattern (21 bp):
ATAGAACAGAATACACGCACG
Found at i:437375 original size:42 final size:42
Alignment explanation
Indices: 437291--437377 Score: 120
Period size: 42 Copynumber: 2.1 Consensus size: 42
437281 ACCCCCGCGA
* *
437291 ATAGAACAGGATACACGCACGATAGGATAGAATTAACGCACG
1 ATAGAACAGGATACACGCACGATACGATAGAATTAACACACG
* * * *
437333 ATAGAACAGTATACACGCACGATACGATAGGATTGATACACG
1 ATAGAACAGGATACACGCACGATACGATAGAATTAACACACG
437375 ATA
1 ATA
437378 CGATAGGATA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.17
Consensus pattern (42 bp):
ATAGAACAGGATACACGCACGATACGATAGAATTAACACACG
Found at i:449030 original size:15 final size:15
Alignment explanation
Indices: 449010--449039 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
449000 AACAAACACA
449010 TACAGGTAAGTTTTT
1 TACAGGTAAGTTTTT
*
449025 TACAGGTAGGTTTTT
1 TACAGGTAAGTTTTT
449040 CCCATAATTA
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:0.23, C:0.07, G:0.23, T:0.47
Consensus pattern (15 bp):
TACAGGTAAGTTTTT
Found at i:463774 original size:2 final size:2
Alignment explanation
Indices: 463769--463800 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
463759 CCCCCCCCCC
463769 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
463801 ACAAACCATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:473831 original size:17 final size:17
Alignment explanation
Indices: 473801--473836 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
473791 ACTCTGCAAA
* *
473801 AATTTCCGGTTATAACG
1 AATTTACGGATATAACG
473818 AATTTACGGATATAACG
1 AATTTACGGATATAACG
473835 AA
1 AA
473837 CTGATTTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.31
Consensus pattern (17 bp):
AATTTACGGATATAACG
Found at i:479118 original size:200 final size:201
Alignment explanation
Indices: 478774--479179 Score: 805
Period size: 200 Copynumber: 2.0 Consensus size: 201
478764 AAGTTATCTC
478774 TCTTTGTTTGATCAAATCATTTATATTTAATGAAAATATACATAAATGTTTACATGACATGCTAA
1 TCTTTGTTTGATCAAATCATTTATATTTAATGAAAATATACATAAATGTTTACATGACATGCTAA
478839 AAAAAGTGATGTCTACGGGGATTTTGTATTGCAGTTAGCCCGGATGATAACGTTGTAAAATTGCG
66 AAAAAGTGATGTCTACGGGGATTTTGTATTGCAGTTAGCCCGGATGATAACGTTGTAAAATTGCG
478904 CGATATATTCCGAGTGTATTCCGAATGGAGAAAAGATGTAAACATTCCCCTTTATAAATCTCCGT
131 CGATATATTCCGAGTGTATTCCGAATGGAGAAAAGATGTAAACATTCCCCTTTATAAATCTCCGT
478969 AAGGAA
196 AAGGAA
478975 -CTTTGTTTGATCAAATCATTTATATTTAATGAAAATATACATAAATGTTTACATGACATGCTAA
1 TCTTTGTTTGATCAAATCATTTATATTTAATGAAAATATACATAAATGTTTACATGACATGCTAA
479039 AAAAAGTGATGTCTACGGGGATTTTGTATTGCAGTTAGCCCGGATGATAACGTTGTAAAATTGCG
66 AAAAAGTGATGTCTACGGGGATTTTGTATTGCAGTTAGCCCGGATGATAACGTTGTAAAATTGCG
479104 CGATATATTCCGAGTGTATTCCGAATGGAGAAAAGATGTAAACATTCCCCTTTATAAATCTCCGT
131 CGATATATTCCGAGTGTATTCCGAATGGAGAAAAGATGTAAACATTCCCCTTTATAAATCTCCGT
479169 AAGGAA
196 AAGGAA
479175 TCTTT
1 TCTTT
479180 TTTCGTTTCT
Statistics
Matches: 204, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
200 200 0.98
201 4 0.02
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (201 bp):
TCTTTGTTTGATCAAATCATTTATATTTAATGAAAATATACATAAATGTTTACATGACATGCTAA
AAAAAGTGATGTCTACGGGGATTTTGTATTGCAGTTAGCCCGGATGATAACGTTGTAAAATTGCG
CGATATATTCCGAGTGTATTCCGAATGGAGAAAAGATGTAAACATTCCCCTTTATAAATCTCCGT
AAGGAA
Found at i:479940 original size:12 final size:11
Alignment explanation
Indices: 479916--479968 Score: 76
Period size: 10 Copynumber: 5.0 Consensus size: 11
479906 CCCCCCCCCC
479916 CAAAA-AAAAA
1 CAAAACAAAAA
479926 -AAAACAAAAA
1 CAAAACAAAAA
479936 CAAAAACAAAAA
1 C-AAAACAAAAA
479948 CAAAAC-AAAA
1 CAAAACAAAAA
479958 CAAAACAAAAA
1 CAAAACAAAAA
479969 ACCACAGAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
9 4 0.10
10 15 0.38
11 9 0.23
12 11 0.28
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (11 bp):
CAAAACAAAAA
Found at i:479962 original size:27 final size:26
Alignment explanation
Indices: 479916--479968 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
479906 CCCCCCCCCC
479916 CAAAAAAAAAAAAACAAAAACAAAAA
1 CAAAAAAAAAAAAACAAAAACAAAAA
479942 CAAAAACAAAACAAAAC-AAAACAAAAA
1 CAAAAA-AAAA-AAAACAAAAACAAAAA
479969 ACCACAGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 6 0.24
27 14 0.56
28 5 0.20
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (26 bp):
CAAAAAAAAAAAAACAAAAACAAAAA
Found at i:479969 original size:12 final size:12
Alignment explanation
Indices: 479919--479970 Score: 58
Period size: 12 Copynumber: 4.6 Consensus size: 12
479909 CCCCCCCCAA
*
479919 AAAAAAAAAAAC
1 AAAAAACAAAAC
479931 -AAAAACAAAA-
1 AAAAAACAAAAC
479941 ACAAAAACAAAAC
1 A-AAAAACAAAAC
479954 --AAAACAAAAC
1 AAAAAACAAAAC
479964 AAAAAAC
1 AAAAAAC
479971 CACAGAAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
10 10 0.29
11 9 0.26
12 15 0.44
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAACAAAAC
Found at i:487213 original size:196 final size:195
Alignment explanation
Indices: 486879--487269 Score: 773
Period size: 196 Copynumber: 2.0 Consensus size: 195
486869 TTTAGCTCGG
486879 TACAGTCAAGAATAGCTAAACAGTTTGGAAAATCATGTTTGTAAGATTCTGGCATGATTCCTATG
1 TACAGTCAAGAATAGCTAAACAGTTTGGAAAATCATGTTTGTAAGATTCTGGCATGATTCCTATG
486944 ATTGTATTTCGATGGGGCCAATAACTTAAGGAACCTAATCTCAAATACATGTACTTCGCTACCCC
66 ATTGTATTTCGATGGGGCCAATAACTTAAGGAACCTAATCTCAAATACATGTACTTCGCTACCCC
487009 ATTAATTACTGTTGACACAGTTTGAACCTTAATATTGAATCTGAATGCTAAATCTTTCACATTTA
131 ATTAATTACTGTTGACACAGTTTGAACCTTAATATTGAATCTGAATGCTAAATCTTTCACATTTA
487074 NTACAGTCAAGAATAGCTAAACAGTTTGGAAAATCATGTTTGTAAGATTCTGGCATGATTCCTAT
1 -TACAGTCAAGAATAGCTAAACAGTTTGGAAAATCATGTTTGTAAGATTCTGGCATGATTCCTAT
487139 GATTGTATTTCGATGGGGCCAATAACTTAAGGAACCTAATCTCAAATACATGTACTTCGCTACCC
65 GATTGTATTTCGATGGGGCCAATAACTTAAGGAACCTAATCTCAAATACATGTACTTCGCTACCC
487204 CATTAATTACTGTTGACACAGTTTGAACCTTAATATTGAATCTGAATGCTAAATCTTTCACATTT
130 CATTAATTACTGTTGACACAGTTTGAACCTTAATATTGAATCTGAATGCTAAATCTTTCACATTT
487269 A
195 A
487270 AAGCATTTCT
Statistics
Matches: 195, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
196 195 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (195 bp):
TACAGTCAAGAATAGCTAAACAGTTTGGAAAATCATGTTTGTAAGATTCTGGCATGATTCCTATG
ATTGTATTTCGATGGGGCCAATAACTTAAGGAACCTAATCTCAAATACATGTACTTCGCTACCCC
ATTAATTACTGTTGACACAGTTTGAACCTTAATATTGAATCTGAATGCTAAATCTTTCACATTTA
Found at i:510977 original size:21 final size:21
Alignment explanation
Indices: 510951--511138 Score: 176
Period size: 21 Copynumber: 9.2 Consensus size: 21
510941 AAAATATTTT
510951 ATCTCGTTATTACGAGAAAAG
1 ATCTCGTTATTACGAGAAAAG
* * **
510972 ATCTCGTTACTACGAGTTAATT
1 ATCTCGTTATTACGAG-AAAAG
*
510994 ATCTCGGTATTACGAGAAAAG
1 ATCTCGTTATTACGAGAAAAG
511015 ATCTCGTTATTACGAGAAAAG
1 ATCTCGTTATTACGAGAAAAG
* *
511036 ATATCGTTATTTC--G---AG
1 ATCTCGTTATTACGAGAAAAG
** *
511052 -T-TAATTATTACGAGAAAAA
1 ATCTCGTTATTACGAGAAAAG
511071 ATCTCG-TATTTACGAGAAAAG
1 ATCTCGTTA-TTACGAGAAAAG
* **
511092 ATCTCGTTATTACGAGGTAATT
1 ATCTCGTTATTACGA-GAAAAG
511114 ATCTCGTTATTACGAGAAAAG
1 ATCTCGTTATTACGAGAAAAG
511135 ATCT
1 ATCT
511139 ATTTAAAATG
Statistics
Matches: 131, Mismatches: 25, Indels: 22
0.74 0.14 0.12
Matches are distributed among these distances:
14 7 0.05
15 1 0.01
16 3 0.02
19 2 0.02
20 3 0.02
21 79 0.60
22 36 0.27
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.33
Consensus pattern (21 bp):
ATCTCGTTATTACGAGAAAAG
Found at i:510997 original size:43 final size:42
Alignment explanation
Indices: 510949--511138 Score: 189
Period size: 43 Copynumber: 4.6 Consensus size: 42
510939 AAAAAATATT
* *
510949 TTATCTCGTTATTACGAGAAAAGATCTCGTTACTACGAGTTAA
1 TTATCTCGTTATTACGAGAAAAGATCTCGTTATTACGAG-AAA
*
510992 TTATCTCGGTATTACGAGAAAAGATCTCGTTATTACGAGAAA
1 TTATCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGAAA
** * * **
511034 AGATATCGTTATTTC--G---AG-T-TAATTATTACGAGAAA
1 TTATCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGAAA
** *
511069 AAATCTCG-TATTTACGAGAAAAGATCTCGTTATTACGAGGTAA
1 TTATCTCGTTA-TTACGAGAAAAGATCTCGTTATTACGA-GAAA
511112 TTATCTCGTTATTACGAGAAAAGATCT
1 TTATCTCGTTATTACGAGAAAAGATCT
511139 ATTTAAAATG
Statistics
Matches: 119, Mismatches: 18, Indels: 20
0.76 0.11 0.13
Matches are distributed among these distances:
34 2 0.02
35 23 0.19
36 1 0.01
37 3 0.03
40 3 0.03
41 1 0.01
42 22 0.18
43 62 0.52
44 2 0.02
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (42 bp):
TTATCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGAAA
Found at i:511087 original size:56 final size:56
Alignment explanation
Indices: 511001--511115 Score: 178
Period size: 56 Copynumber: 2.1 Consensus size: 56
510991 ATTATCTCGG
* * *
511001 TATTACGAGAAAAGATCTCGTTATTACGAGAAAAGATATCGTTATTTCGAGTTAAT
1 TATTACGAGAAAAAATCTCGTTATTACGAGAAAAGATATCGTTATTACGAGGTAAT
*
511057 TATTACGAGAAAAAATCTCG-TATTTACGAGAAAAGATCTCGTTATTACGAGGTAAT
1 TATTACGAGAAAAAATCTCGTTA-TTACGAGAAAAGATATCGTTATTACGAGGTAAT
511113 TAT
1 TAT
511116 CTCGTTATTA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
55 2 0.04
56 52 0.96
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.33
Consensus pattern (56 bp):
TATTACGAGAAAAAATCTCGTTATTACGAGAAAAGATATCGTTATTACGAGGTAAT
Found at i:511890 original size:21 final size:21
Alignment explanation
Indices: 511810--512045 Score: 175
Period size: 22 Copynumber: 11.0 Consensus size: 21
511800 ATATAGATTC
* *
511810 TTTTCTCGTGATAACAAGATAA
1 TTTTCTCGTAATAACGAGAT-A
**
511832 TTAACTCGTAATAACGAGATAA
1 TTTTCTCGTAATAACGAGAT-A
***
511854 TCAGCTCGTAATAACGAGATA
1 TTTTCTCGTAATAACGAGATA
* * *
511875 TTTTCTTGTCATAACGAGAAAA
1 TTTTCTCGTAATAACGAG-ATA
* * *
511897 TTATCTCGTTATAACGAGATC
1 TTTTCTCGTAATAACGAGATA
* * * *
511918 TTTTCTCGTTATTATGAGATC
1 TTTTCTCGTAATAACGAGATA
511939 TTTTCTCGTAATAACGAGATAA
1 TTTTCTCGTAATAACGAGAT-A
* * * *
511961 TTATCTCGTAATTACAAGATC
1 TTTTCTCGTAATAACGAGATA
511982 TTTTCTCGTAATAACGAGATAA
1 TTTTCTCGTAATAACGAGAT-A
** * *
512004 TTAACTCGTAATTACGAGATC
1 TTTTCTCGTAATAACGAGATA
* * *
512025 GTTGCTCGTAATTACGAGATA
1 TTTTCTCGTAATAACGAGATA
512046 AAAATATTTT
Statistics
Matches: 171, Mismatches: 40, Indels: 7
0.78 0.18 0.03
Matches are distributed among these distances:
21 84 0.49
22 87 0.51
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.36
Consensus pattern (21 bp):
TTTTCTCGTAATAACGAGATA
Found at i:511953 original size:107 final size:107
Alignment explanation
Indices: 511836--512044 Score: 283
Period size: 107 Copynumber: 2.0 Consensus size: 107
511826 AGATAATTAA
* * * *
511836 CTCGTAATAACGAGATAATCAGCTCGTAATAACGAGATATTTTCTTGTCATAACGAGAAAATTAT
1 CTCGTAATAACGAGATAATCAGCTCGTAATAACAAGATATTTTCTCGTAATAACGAGAAAATTAA
* * * * *
511901 CTCGTTATAACGAGATCTTTTCTCGTTATTATGAGATCTTTT
66 CTCGTAATAACGAGATCGTTGCTCGTAATTACGAGATCTTTT
* * * * *
511943 CTCGTAATAACGAGATAATTATCTCGTAATTACAAGATCTTTTCTCGTAATAACGAGATAATTAA
1 CTCGTAATAACGAGATAATCAGCTCGTAATAACAAGATATTTTCTCGTAATAACGAGAAAATTAA
*
512008 CTCGTAATTACGAGATCGTTGCTCGTAATTACGAGAT
66 CTCGTAATAACGAGATCGTTGCTCGTAATTACGAGAT
512045 AAAAATATTT
Statistics
Matches: 87, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
107 87 1.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Consensus pattern (107 bp):
CTCGTAATAACGAGATAATCAGCTCGTAATAACAAGATATTTTCTCGTAATAACGAGAAAATTAA
CTCGTAATAACGAGATCGTTGCTCGTAATTACGAGATCTTTT
Found at i:511954 original size:64 final size:64
Alignment explanation
Indices: 511808--512001 Score: 226
Period size: 64 Copynumber: 3.0 Consensus size: 64
511798 ATATATAGAT
* * * * ***
511808 TCTTTTCTCGTGATAACAAGATAATTAACTCGTAATAACGAGATAATCAGCTCGTAATAACGAGA
1 TCTTTTCTCGTAATAACGAGATAATTATCTCGTAATAACGAGAT-CTTTTCTCGTAATAACGAGA
* * * * * * * *
511873 TATTTTCTTGTCATAACGAGAAAATTATCTCGTTATAACGAGATCTTTTCTCGTTATTATGAGA
1 TCTTTTCTCGTAATAACGAGATAATTATCTCGTAATAACGAGATCTTTTCTCGTAATAACGAGA
* *
511937 TCTTTTCTCGTAATAACGAGATAATTATCTCGTAATTACAAGATCTTTTCTCGTAATAACGAGA
1 TCTTTTCTCGTAATAACGAGATAATTATCTCGTAATAACGAGATCTTTTCTCGTAATAACGAGA
512001 T
1 T
512002 AATTAACTCG
Statistics
Matches: 105, Mismatches: 24, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
64 68 0.65
65 37 0.35
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.37
Consensus pattern (64 bp):
TCTTTTCTCGTAATAACGAGATAATTATCTCGTAATAACGAGATCTTTTCTCGTAATAACGAGA
Found at i:512003 original size:43 final size:43
Alignment explanation
Indices: 511808--512046 Score: 221
Period size: 43 Copynumber: 5.6 Consensus size: 43
511798 ATATATAGAT
* * * *
511808 TCTTTTCTCGTGATAACAAGATAATTAACTCGTAATAACGAGA
1 TCTTTTCTCGTAATAACGAGATAATTATCTCGTAATTACGAGA
* *** * * * *
511851 TAATCAGCTCGTAATAACGAGAT-ATTTTCTTGTCATAACGAGAA
1 T-CTTTTCTCGTAATAACGAGATAATTATCTCGTAATTACGAG-A
** * * * * * *
511895 AATTATCTCGTTATAACGAGAT-CTTTTCTCGTTATTATGAGA
1 TCTTTTCTCGTAATAACGAGATAATTATCTCGTAATTACGAGA
*
511937 TCTTTTCTCGTAATAACGAGATAATTATCTCGTAATTACAAGA
1 TCTTTTCTCGTAATAACGAGATAATTATCTCGTAATTACGAGA
*
511980 TCTTTTCTCGTAATAACGAGATAATTAACTCGTAATTACGAGA
1 TCTTTTCTCGTAATAACGAGATAATTATCTCGTAATTACGAGA
* * *
512023 TCGTTGCTCGTAATTACGAGATAA
1 TCTTTTCTCGTAATAACGAGATAA
512047 AAATATTTTT
Statistics
Matches: 160, Mismatches: 33, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
42 19 0.12
43 125 0.78
44 16 0.10
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.36
Consensus pattern (43 bp):
TCTTTTCTCGTAATAACGAGATAATTATCTCGTAATTACGAGA
Found at i:521890 original size:2 final size:2
Alignment explanation
Indices: 521883--521967 Score: 163
Period size: 2 Copynumber: 43.0 Consensus size: 2
521873 ACGCTAACAT
521883 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA -A GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
521924 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
521966 GA
1 GA
521968 TTTAAGAAGA
Statistics
Matches: 82, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 81 0.99
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:525518 original size:2 final size:2
Alignment explanation
Indices: 525511--525548 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
525501 CAAATCAATG
525511 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
525549 ATATTATATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:531225 original size:6 final size:6
Alignment explanation
Indices: 531214--531287 Score: 121
Period size: 6 Copynumber: 12.3 Consensus size: 6
531204 TGTGAATAAC
* * *
531214 AGAGAT AGAGAT AGATAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG
1 AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG
531262 AGAGAG AGAGAG AGAGAG AGAGAG AG
1 AGAGAG AGAGAG AGAGAG AGAGAG AG
531288 GATAAATATC
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 65 1.00
ACGTcount: A:0.50, C:0.00, G:0.46, T:0.04
Consensus pattern (6 bp):
AGAGAG
Found at i:531231 original size:10 final size:10
Alignment explanation
Indices: 531214--531287 Score: 121
Period size: 10 Copynumber: 7.4 Consensus size: 10
531204 TGTGAATAAC
*
531214 AGAGATAGAG
1 AGAGAGAGAG
* *
531224 ATAGATAGAG
1 AGAGAGAGAG
531234 AGAGAGAGAG
1 AGAGAGAGAG
531244 AGAGAGAGAG
1 AGAGAGAGAG
531254 AGAGAGAGAG
1 AGAGAGAGAG
531264 AGAGAGAGAG
1 AGAGAGAGAG
531274 AGAGAGAGAG
1 AGAGAGAGAG
531284 AGAG
1 AGAG
531288 GATAAATATC
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 61 1.00
ACGTcount: A:0.50, C:0.00, G:0.46, T:0.04
Consensus pattern (10 bp):
AGAGAGAGAG
Found at i:531237 original size:4 final size:4
Alignment explanation
Indices: 531214--531287 Score: 121
Period size: 4 Copynumber: 18.5 Consensus size: 4
531204 TGTGAATAAC
* * *
531214 AGAG ATAG AGAT AGAT AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG
1 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG
531262 AGAG AGAG AGAG AGAG AGAG AGAG AG
1 AGAG AGAG AGAG AGAG AGAG AGAG AG
531288 GATAAATATC
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.46, T:0.04
Consensus pattern (4 bp):
AGAG
Done.