Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold204
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: 1152859
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.31
Warning! 64757 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:352889 original size:431 final size:428
Alignment explanation
Indices: 352074--353111 Score: 1398
Period size: 431 Copynumber: 2.4 Consensus size: 428
352064 CCCCAAAACA
* * * *
352074 TACAAAGTTATTGCCCTTGTTTACGAAAAGCTTGTTATCGCTACTCCTCTGAAACCATATGAGAT
1 TACAGAGTTATTGCCCCTATTTACGAAAAGCTTGTTATCGCTACTCCTCTGAAACCATAAGAGAT
* * *
352139 AGAAACTTGGAACTTTTACCAATGTCTTCAGTACATTTAGAGGGTTCTTCAA-CATATTCATACC
66 AGAGACTT-GAAATTTTACCAATGTCTTCAGTACACTTAGAGGGTTCTTCAATC-TATTCATACC
** * * * *
352203 GAAAGGATCTGAGCCCCCCCCCCTTCTCGTAGTAATTGCCCCTGAAAGTATTTACATTTCTATAA
129 GAAAGGATCTGAG-----GTCCCTTTTAGTAGTTATTGCCCCTGAAAATATTTACATTTCTATAA
* *
352268 AGTCACGTCCAACTTTTTTATTTTTTGTCATAGAGACTTCGGACTACTTGGGACGGAAGCATCTA
189 AGTCACGTCCAACTTTTTTATTATTTGTCATAGAGACTTAGGACTACTTGGGACGGAAGCATCTA
** * * * *
352333 CCTTGGCCGATCAAAATGACATAAAGGTCAAAGGTCAAGGTCATTTGGAAACCTGTTAATTAATG
254 CCTTAACCAAACAAAATGACATAAAGGTCAAAGGTCAAAGTCACTTGGAAACCTGTTAATTAATG
* *
352398 AGCTTTTAGATCTCTTTTGTTAAGGCTGGTTGAGAAAAACTTTCTCATGGATGAAGTAGGACATC
319 AGCTTTTAGATCTCTTTTGTTAAGGATGGTAGAGAAAAACTTTCTCATGGATGAAGTAGGACATC
* *** * * *
352463 -TAAGACATTTTAAAATATAACCCCTTGGCCCCTT-CCGTTAAATAAT
384 ATAAGACA-TTTAAAA-A-AACCCATTAAACCCTTACCATGAAACAAT
* *
352509 TACAGGGTTATTGCCCCTATTTAGGAAAAGCTTGTTATCGCTACTCCTCTGAAACCATAAGAGAT
1 TACAGAGTTATTGCCCCTATTTACGAAAAGCTTGTTATCGCTACTCCTCTGAAACCATAAGAGAT
** *
352574 AGAGACTTGAAATGTTTACCAATGTCTTCAGTACACTTAGAGATTTCTTCAATCTATTCATACCA
66 AGAGACTTGAAAT-TTTACCAATGTCTTCAGTACACTTAGAGGGTTCTTCAATCTATTCATACCG
*
352639 AAAGGATCTGAGGTTCCCTTTTAGTAGTTATTGCCCCTGAAAATATTTACTTTTCTATAAAGTCA
130 AAAGGATCTGAGG-TCCCTTTTAGTAGTTATTGCCCCTGAAAATATTTACATTTCTATAAAGTCA
352704 CGTCCAACTTTTTTATTATTTGTCATAGAGACTTAGGACTACTTGGGACGGAAGCATCTACCTTA
194 CGTCCAACTTTTTTATTATTTGTCATAGAGACTTAGGACTACTTGGGACGGAAGCATCTACCTTA
* * *
352769 ACCAAACAAAATGGCATAAAGGTCAAAGGTCAAAGTCACTTGGAAACTTGTTAATTAATGAGTTT
259 ACCAAACAAAATGACATAAAGGTCAAAGGTCAAAGTCACTTGGAAACCTGTTAATTAATGAGCTT
* * * * *
352834 TTGGATCTCTTTTGTTTAGGATGGTAGAGAAACACTTTTTCATGGATGTAGTAGGACATCATAAG
324 TTAGATCTCTTTTGTTAAGGATGGTAGAGAAAAACTTTCTCATGGATGAAGTAGGACATCATAAG
352899 ACATTTAAAAAAACCCATTAAACCCTTACCATGAAACAAT
389 ACATTTAAAAAAACCCATTAAACCCTTACCATGAAACAAT
* * * *
352939 TATAGAGTTATTGCCCCTATTGTACGAAATGCTTGTTATCGCTACTCCTTTGAAACCATTAGAGA
1 TACAGAGTTATTGCCCCTATT-TACGAAAAGCTTGTTATCGCTACTCCTCTGAAACCATAAGAGA
* * * *
353004 TAGCGACTTGAAATTTTTACTAATGTATTCAGTACACTTAGAGGGTTCTTCAATCTATTCGTACC
65 TAGAGACTTGAAA-TTTTACCAATGTCTTCAGTACACTTAGAGGGTTCTTCAATCTATTCATACC
* ** * * *
353069 GAAAGGGTCCAAAGTCCTTTTCTAGTAGTTATTGCCTCTGAAA
129 GAAAGGATCTGAGGTCCCTTT-TAGTAGTTATTGCCCCTGAAA
353112 GGTTTAAATA
Statistics
Matches: 532, Mismatches: 63, Indels: 20
0.87 0.10 0.03
Matches are distributed among these distances:
429 12 0.02
430 35 0.07
431 349 0.66
432 8 0.02
434 4 0.01
435 123 0.23
436 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (428 bp):
TACAGAGTTATTGCCCCTATTTACGAAAAGCTTGTTATCGCTACTCCTCTGAAACCATAAGAGAT
AGAGACTTGAAATTTTACCAATGTCTTCAGTACACTTAGAGGGTTCTTCAATCTATTCATACCGA
AAGGATCTGAGGTCCCTTTTAGTAGTTATTGCCCCTGAAAATATTTACATTTCTATAAAGTCACG
TCCAACTTTTTTATTATTTGTCATAGAGACTTAGGACTACTTGGGACGGAAGCATCTACCTTAAC
CAAACAAAATGACATAAAGGTCAAAGGTCAAAGTCACTTGGAAACCTGTTAATTAATGAGCTTTT
AGATCTCTTTTGTTAAGGATGGTAGAGAAAAACTTTCTCATGGATGAAGTAGGACATCATAAGAC
ATTTAAAAAAACCCATTAAACCCTTACCATGAAACAAT
Found at i:355451 original size:2 final size:2
Alignment explanation
Indices: 355444--355493 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
355434 AGAAAACTAT
355444 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
355486 GA GA GA GA
1 GA GA GA GA
355494 ATTCGCAGCC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:356033 original size:10 final size:10
Alignment explanation
Indices: 356020--356053 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
356010 CTTCAAATTT
356020 CATAGCATAC
1 CATAGCATAC
*
356030 CATAGCATAG
1 CATAGCATAC
*
356040 CATAACATAC
1 CATAGCATAC
356050 CATA
1 CATA
356054 ACTATCTCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.44, C:0.26, G:0.09, T:0.21
Consensus pattern (10 bp):
CATAGCATAC
Found at i:356040 original size:15 final size:15
Alignment explanation
Indices: 356020--356053 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
356010 CTTCAAATTT
* *
356020 CATAGCATACCATAG
1 CATAGCATAACATAC
356035 CATAGCATAACATAC
1 CATAGCATAACATAC
356050 CATA
1 CATA
356054 ACTATCTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.26, G:0.09, T:0.21
Consensus pattern (15 bp):
CATAGCATAACATAC
Found at i:356095 original size:21 final size:21
Alignment explanation
Indices: 356071--356150 Score: 115
Period size: 21 Copynumber: 3.8 Consensus size: 21
356061 CTTTTAAATT
356071 TCTCATAGCATAGCATACAAA
1 TCTCATAGCATAGCATACAAA
*
356092 TCTCATAGCATAGCATAAAAA
1 TCTCATAGCATAGCATACAAA
*
356113 TCTCGTAGCATAGCATACAAA
1 TCTCATAGCATAGCATACAAA
* * *
356134 TCCCATACCATATCATA
1 TCTCATAGCATAGCATA
356151 GCATAAAATT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.41, C:0.25, G:0.09, T:0.25
Consensus pattern (21 bp):
TCTCATAGCATAGCATACAAA
Found at i:358206 original size:21 final size:21
Alignment explanation
Indices: 358180--358301 Score: 208
Period size: 21 Copynumber: 5.8 Consensus size: 21
358170 TCATCCTGGC
358180 ATCACGTAAGTCCCTTTGTAT
1 ATCACGTAAGTCCCTTTGTAT
358201 ATCACGTAAGTCCCTTTGTAT
1 ATCACGTAAGTCCCTTTGTAT
358222 ATCACGTAAGTCCCTTTGTAT
1 ATCACGTAAGTCCCTTTGTAT
358243 ATCACGTAAGTCCCTTTGTAT
1 ATCACGTAAGTCCCTTTGTAT
* * *
358264 ATCACGTGAGTCCCTTTGGAA
1 ATCACGTAAGTCCCTTTGTAT
*
358285 ATCAGGTAAGTCCCTTT
1 ATCACGTAAGTCCCTTT
358302 TTACAAAGGA
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 96 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (21 bp):
ATCACGTAAGTCCCTTTGTAT
Found at i:378295 original size:17 final size:18
Alignment explanation
Indices: 378270--378315 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
378260 TTAAAAACTA
*
378270 AGATGCATGT-ATATTTT
1 AGATCCATGTAATATTTT
378287 AGATCCATGTTAATATTTT
1 AGATCCATG-TAATATTTT
*
378306 AGCTCCATGT
1 AGATCCATGT
378316 CCAAAGTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 8 0.32
18 2 0.08
19 15 0.60
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.43
Consensus pattern (18 bp):
AGATCCATGTAATATTTT
Found at i:405653 original size:22 final size:22
Alignment explanation
Indices: 405621--405856 Score: 190
Period size: 22 Copynumber: 10.7 Consensus size: 22
405611 GCAGAAACCA
* *
405621 TTCAGTGACCATTTATTTACCT
1 TTCAGTGACCATTAAGTTACCT
*
405643 TTCAGTTACCATTAAGTTACCT
1 TTCAGTGACCATTAAGTTACCT
*
405665 TTCAGTGACCATTAAGTTACTT
1 TTCAGTGACCATTAAGTTACCT
*
405687 TTCAGTGACCATTAAAG-TACAT
1 TTCAGTGACCATT-AAGTTACCT
* * * *
405709 TTCAGCGACCATTTAGTAACAT
1 TTCAGTGACCATTAAGTTACCT
** *
405731 TTCAGTGACCATTAAGTTGTCA
1 TTCAGTGACCATTAAGTTACCT
* * * * *
405753 TTCAGTTACCTTTCAGTGACCA
1 TTCAGTGACCATTAAGTTACCT
* * *
405775 TTAAGTTG-TCATTCAGTTACCT
1 TTCAG-TGACCATTAAGTTACCT
* *
405797 TTTAGTGACCATTAAGCTACCT
1 TTCAGTGACCATTAAGTTACCT
* ** *
405819 TTCAATG-CCTATTCTGTTACTT
1 TTCAGTGACC-ATTAAGTTACCT
405841 TTCAGTGACCATTAAG
1 TTCAGTGACCATTAAG
405857 CCACTTTTCA
Statistics
Matches: 167, Mismatches: 41, Indels: 12
0.76 0.19 0.05
Matches are distributed among these distances:
21 6 0.04
22 155 0.93
23 6 0.04
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (22 bp):
TTCAGTGACCATTAAGTTACCT
Found at i:405683 original size:33 final size:33
Alignment explanation
Indices: 405646--405822 Score: 151
Period size: 33 Copynumber: 5.4 Consensus size: 33
405636 TTTACCTTTC
*
405646 AGTTACCATTAAGTTACCTTTCAGTGACCATTA
1 AGTTACCATTCAGTTACCTTTCAGTGACCATTA
** * ** *
405679 AGTTACTTTTCAGTGACCATTAAAGT-A-CATTTC
1 AGTTACCATTCAGTTACC-TTTCAGTGACCA-TTA
** * * *
405712 AGCGACCATTTAGTAACATTTCAGTGACCATTA
1 AGTTACCATTCAGTTACCTTTCAGTGACCATTA
**
405745 AGTTGTCATTCAGTTACCTTTCAGTGACCATTA
1 AGTTACCATTCAGTTACCTTTCAGTGACCATTA
** *
405778 AGTTGTCATTCAGTTACCTTTTAGTGACCATTA
1 AGTTACCATTCAGTTACCTTTCAGTGACCATTA
* *
405811 AGCTACCTTTCA
1 AGTTACCATTCA
405823 ATGCCTATTC
Statistics
Matches: 111, Mismatches: 29, Indels: 8
0.75 0.20 0.05
Matches are distributed among these distances:
32 7 0.06
33 97 0.87
34 7 0.06
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (33 bp):
AGTTACCATTCAGTTACCTTTCAGTGACCATTA
Found at i:411829 original size:13 final size:13
Alignment explanation
Indices: 411811--411836 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
411801 TTTTTATGGA
411811 TATGACTTAACAG
1 TATGACTTAACAG
411824 TATGACTTAACAG
1 TATGACTTAACAG
411837 AGGAAATTCT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TATGACTTAACAG
Found at i:412677 original size:10 final size:10
Alignment explanation
Indices: 412662--412686 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
412652 CTTGTAGCTT
412662 TTCATGATAA
1 TTCATGATAA
412672 TTCATGATAA
1 TTCATGATAA
412682 TTCAT
1 TTCAT
412687 TACAAAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (10 bp):
TTCATGATAA
Found at i:422739 original size:21 final size:21
Alignment explanation
Indices: 422715--423035 Score: 198
Period size: 21 Copynumber: 15.6 Consensus size: 21
422705 TGGTAATCTT
*
422715 CATTATATGATGATACTTTAA
1 CATTACATGATGATACTTTAA
422736 CATTACAT-ACTGAT-CATTTAA
1 CATTACATGA-TGATAC-TTTAA
* *
422757 CATTATATGATGGTACTTTAA
1 CATTACATGATGATACTTTAA
* *
422778 CATTACATGCTGATACTTCAA
1 CATTACATGATGATACTTTAA
*
422799 CATTACATGATGGTACTTTAA
1 CATTACATGATGATACTTTAA
* * * * *
422820 CATTACGTGCTGATACCTCAG
1 CATTACATGATGATACTTTAA
* * *
422841 CATCACATGATGGTACTCTAA
1 CATTACATGATGATACTTTAA
* *
422862 CATTACATGATGGTACTCTAA
1 CATTACATGATGATACTTTAA
* *
422883 CATTA-AGTGCTTATACTTTAA
1 CATTACA-TGATGATACTTTAA
* *
422904 CATTA-AGTGCTGATACTTCT-T
1 CATTACA-TGATGATACTT-TAA
* *
422925 CATT--AT-ATGATACTGTAT
1 CATTACATGATGATACTTTAA
* * * * *
422943 TATAAAATGCTGATAGTTTAA
1 CATTACATGATGATACTTTAA
*
422964 CATTACATGCTGATA-TTTCAA
1 CATTACATGATGATACTTT-AA
* * * *
422985 CATCACATGCTGATACCTCAA
1 CATTACATGATGATACTTTAA
*
423006 CATTACATGCTGATA-TTT--
1 CATTACATGATGATACTTTAA
*
423024 CATTAAATGATG
1 CATTACATGATG
423036 GTATTTCAGT
Statistics
Matches: 238, Mismatches: 50, Indels: 27
0.76 0.16 0.09
Matches are distributed among these distances:
17 1 0.00
18 20 0.08
19 1 0.00
20 10 0.04
21 202 0.85
22 4 0.02
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.37
Consensus pattern (21 bp):
CATTACATGATGATACTTTAA
Found at i:422774 original size:42 final size:42
Alignment explanation
Indices: 422715--423014 Score: 238
Period size: 42 Copynumber: 7.2 Consensus size: 42
422705 TGGTAATCTT
* * * *
422715 CATTATATGATGATACTTTAACATTACATACTGAT-CATTTAA
1 CATTACATGATGGTACTTTAACATTACATGCTGATAC-TTCAA
*
422757 CATTATATGATGGTACTTTAACATTACATGCTGATACTTCAA
1 CATTACATGATGGTACTTTAACATTACATGCTGATACTTCAA
* * *
422799 CATTACATGATGGTACTTTAACATTACGTGCTGATACCTCAG
1 CATTACATGATGGTACTTTAACATTACATGCTGATACTTCAA
* * * *
422841 CATCACATGATGGTACTCTAACATTACATGATGGTAC-TCTAA
1 CATTACATGATGGTACTTTAACATTACATGCTGATACTTC-AA
* ** **
422883 CATTA-AGTGCTTATACTTTAACATTA-AGTGCTGATACTTCTT
1 CATTACA-TGATGGTACTTTAACATTACA-TGCTGATACTTCAA
* * ** * * * *
422925 CATT--AT-ATGATACTGTATTATAAAATGCTGATAGTTTAA
1 CATTACATGATGGTACTTTAACATTACATGCTGATACTTCAA
* * * *
422964 CATTACATGCTGATA-TTTCAACATCACATGCTGATACCTCAA
1 CATTACATGATGGTACTTT-AACATTACATGCTGATACTTCAA
423006 CATTACATG
1 CATTACATG
423015 CTGATATTTC
Statistics
Matches: 207, Mismatches: 41, Indels: 20
0.77 0.15 0.07
Matches are distributed among these distances:
39 25 0.12
40 2 0.01
41 9 0.04
42 168 0.81
43 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (42 bp):
CATTACATGATGGTACTTTAACATTACATGCTGATACTTCAA
Found at i:422819 original size:63 final size:62
Alignment explanation
Indices: 422715--423020 Score: 230
Period size: 63 Copynumber: 4.9 Consensus size: 62
422705 TGGTAATCTT
* * * * *
422715 CATTATATGATGATACTTTAACATTACAT-ACTGAT-CATTTAACATTATATGATGGTACTTTAA
1 CATTACATGCTGATACTTCAACATTACATGA-TGATAC-TTTAACATTA-ATGCTGATACTTTAA
* * * * *
422778 CATTACATGCTGATACTTCAACATTACATGATGGTACTTTAACATTACGTGCTGATACCTCAG
1 CATTACATGCTGATACTTCAACATTACATGATGATACTTTAACATTA-ATGCTGATACTTTAA
* * * * * *
422841 CATCACATGATGGTAC-TCTAACATTACATGATGGTACTCTAACATTAAGTGCTTATACTTTAA
1 CATTACATGCTGATACTTC-AACATTACATGATGATACTTTAACATTAA-TGCTGATACTTTAA
** * ** * *
422904 CATTA-AGTGCTGATACTTCTTCATT--AT-ATGATACTGTATTATAAAATGCTGATAGTTTAA
1 CATTACA-TGCTGATACTTCAACATTACATGATGATACTTTAACAT-TAATGCTGATACTTTAA
* * * * *
422964 CATTACATGCTGATATTTCAACATCACATGCTGATACCTCAACATTACATGCTGATA
1 CATTACATGCTGATACTTCAACATTACATGATGATACTTTAACATTA-ATGCTGATA
423021 TTTCATTAAA
Statistics
Matches: 188, Mismatches: 43, Indels: 24
0.74 0.17 0.09
Matches are distributed among these distances:
60 42 0.22
61 5 0.03
62 6 0.03
63 131 0.70
64 4 0.02
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (62 bp):
CATTACATGCTGATACTTCAACATTACATGATGATACTTTAACATTAATGCTGATACTTTAA
Found at i:423636 original size:42 final size:42
Alignment explanation
Indices: 423599--423870 Score: 436
Period size: 42 Copynumber: 6.5 Consensus size: 42
423589 GAAGTATCAG
* * *
423599 CATGTAATGTTAAAGTATCAGCATGTAATGTTGAAGTACCAT
1 CATGTAATGTTGAAGTATCAGCACGTAATGTTAAAGTACCAT
423641 CATGTAATGTTGAAGTATCAGCACGTAATGTTAAAGTACCAT
1 CATGTAATGTTGAAGTATCAGCACGTAATGTTAAAGTACCAT
* *
423683 CATGTAATGTTGAAGTATCAGCACGTTATGTAAAAGTACCAT
1 CATGTAATGTTGAAGTATCAGCACGTAATGTTAAAGTACCAT
* *
423725 CAAGTAATGTTGAAGTATCAGCACGTAATGATAAAGTACCAT
1 CATGTAATGTTGAAGTATCAGCACGTAATGTTAAAGTACCAT
* * * *
423767 CATGCAATGTTGAAGTATCAGCATGTAATGTGAAAGTACTAT
1 CATGTAATGTTGAAGTATCAGCACGTAATGTTAAAGTACCAT
423809 CATGTAATGTTGAAGTATCAGCACGTAATGTTAAAGTACCAT
1 CATGTAATGTTGAAGTATCAGCACGTAATGTTAAAGTACCAT
*
423851 CATGTAATGTTAAAGTATCA
1 CATGTAATGTTGAAGTATCA
423871 TCATATTATG
Statistics
Matches: 210, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 210 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (42 bp):
CATGTAATGTTGAAGTATCAGCACGTAATGTTAAAGTACCAT
Found at i:423874 original size:21 final size:21
Alignment explanation
Indices: 423590--423870 Score: 303
Period size: 21 Copynumber: 13.4 Consensus size: 21
423580 TATAATGAAG
423590 AAGTATCAGCATGTAATGTTA
1 AAGTATCAGCATGTAATGTTA
*
423611 AAGTATCAGCATGTAATGTTG
1 AAGTATCAGCATGTAATGTTA
* * *
423632 AAGTACCATCATGTAATGTTG
1 AAGTATCAGCATGTAATGTTA
*
423653 AAGTATCAGCACGTAATGTTA
1 AAGTATCAGCATGTAATGTTA
* * *
423674 AAGTACCATCATGTAATGTTG
1 AAGTATCAGCATGTAATGTTA
* * *
423695 AAGTATCAGCACGTTATGTAA
1 AAGTATCAGCATGTAATGTTA
* * * *
423716 AAGTACCATCAAGTAATGTTG
1 AAGTATCAGCATGTAATGTTA
* *
423737 AAGTATCAGCACGTAATGATA
1 AAGTATCAGCATGTAATGTTA
* * * *
423758 AAGTACCATCATGCAATGTTG
1 AAGTATCAGCATGTAATGTTA
*
423779 AAGTATCAGCATGTAATGTGA
1 AAGTATCAGCATGTAATGTTA
* *
423800 AAGTA-CTATCATGTAATGTTG
1 AAGTATC-AGCATGTAATGTTA
*
423821 AAGTATCAGCACGTAATGTTA
1 AAGTATCAGCATGTAATGTTA
* *
423842 AAGTACCATCATGTAATGTTA
1 AAGTATCAGCATGTAATGTTA
423863 AAGTATCA
1 AAGTATCA
423871 TCATATTATG
Statistics
Matches: 209, Mismatches: 49, Indels: 4
0.80 0.19 0.02
Matches are distributed among these distances:
20 1 0.00
21 207 0.99
22 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (21 bp):
AAGTATCAGCATGTAATGTTA
Found at i:435659 original size:31 final size:31
Alignment explanation
Indices: 435572--435649 Score: 149
Period size: 31 Copynumber: 2.5 Consensus size: 31
435562 TATTTTAGAT
435572 TTAAGC-TTGAATATTTACTAGATCTTGACC
1 TTAAGCTTTGAATATTTACTAGATCTTGACC
435602 TTAAGCTTTGAATATTTACTAGATCTTGACC
1 TTAAGCTTTGAATATTTACTAGATCTTGACC
435633 TTAAGCTTTGAATATTT
1 TTAAGCTTTGAATATTT
435650 GCCATATCTT
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 6 0.13
31 41 0.87
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (31 bp):
TTAAGCTTTGAATATTTACTAGATCTTGACC
Found at i:436351 original size:16 final size:16
Alignment explanation
Indices: 436327--436358 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
436317 GTCCATGTCA
436327 TTCAAGTCTTTAGTAT
1 TTCAAGTCTTTAGTAT
*
436343 TTCAGGTCTTTAGTAT
1 TTCAAGTCTTTAGTAT
436359 GTCCCGTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.50
Consensus pattern (16 bp):
TTCAAGTCTTTAGTAT
Found at i:436971 original size:123 final size:123
Alignment explanation
Indices: 436752--436997 Score: 465
Period size: 123 Copynumber: 2.0 Consensus size: 123
436742 GCGAGTGGAT
436752 TTATCCAAACATTTTTGTGTCATGTGTCGTTTAAGCCTGCGTGTCTAAAATTGAGAACTGCGCAC
1 TTATCCAAACATTTTTGTGTCATGTGTCGTTTAAGCCTGCGTGTCTAAAATTGAGAACTGCGCAC
436817 CCGAGCTTATAAGTTGAGATCGACTATAGGGTGAAAGAGATCTAAGGTAGGGTAGTAG
66 CCGAGCTTATAAGTTGAGATCGACTATAGGGTGAAAGAGATCTAAGGTAGGGTAGTAG
* *
436875 TTATCCAAACATTTTTGTGTCATGTGTCGTTTAAGCCTGTGTGTCTAAAATTGAGAACTGCGTAC
1 TTATCCAAACATTTTTGTGTCATGTGTCGTTTAAGCCTGCGTGTCTAAAATTGAGAACTGCGCAC
*
436940 CCGAGCTTGTAAGTTGAGATCGACTATAGGGTGAAAGAGATCTAAGGTAGGGTAGTAG
66 CCGAGCTTATAAGTTGAGATCGACTATAGGGTGAAAGAGATCTAAGGTAGGGTAGTAG
436998 ACTCGTATTA
Statistics
Matches: 120, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 120 1.00
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (123 bp):
TTATCCAAACATTTTTGTGTCATGTGTCGTTTAAGCCTGCGTGTCTAAAATTGAGAACTGCGCAC
CCGAGCTTATAAGTTGAGATCGACTATAGGGTGAAAGAGATCTAAGGTAGGGTAGTAG
Found at i:439223 original size:2 final size:2
Alignment explanation
Indices: 439216--439268 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
439206 ACCCCTCTCC
439216 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A- AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
439257 AG AG AG AG AG AG
1 AG AG AG AG AG AG
439269 CCGGTACCTG
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:441956 original size:21 final size:21
Alignment explanation
Indices: 441931--441971 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
441921 GTACACTGAT
441931 TTAAAATGTAAAATTTACACA
1 TTAAAATGTAAAATTTACACA
* *
441952 TTAAAATGTTAATTTTACAC
1 TTAAAATGTAAAATTTACAC
441972 TTTTTTGAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (21 bp):
TTAAAATGTAAAATTTACACA
Found at i:448499 original size:7 final size:7
Alignment explanation
Indices: 448487--448511 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
448477 GTTTTTAGAA
448487 CGCAGTT
1 CGCAGTT
448494 CGCAGTT
1 CGCAGTT
448501 CGCAGTT
1 CGCAGTT
448508 CGCA
1 CGCA
448512 ATTGAATAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.32, G:0.28, T:0.24
Consensus pattern (7 bp):
CGCAGTT
Found at i:448583 original size:56 final size:56
Alignment explanation
Indices: 448512--448617 Score: 212
Period size: 56 Copynumber: 1.9 Consensus size: 56
448502 GCAGTTCGCA
448512 ATTGAATAGTGAACTGCGTTCTATAGAACGCAGTTCGCAATTCAAAATTTTGTGCG
1 ATTGAATAGTGAACTGCGTTCTATAGAACGCAGTTCGCAATTCAAAATTTTGTGCG
448568 ATTGAATAGTGAACTGCGTTCTATAGAACGCAGTTCGCAATTCAAAATTT
1 ATTGAATAGTGAACTGCGTTCTATAGAACGCAGTTCGCAATTCAAAATTT
448618 AGAATTCATA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 50 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (56 bp):
ATTGAATAGTGAACTGCGTTCTATAGAACGCAGTTCGCAATTCAAAATTTTGTGCG
Found at i:459532 original size:86 final size:86
Alignment explanation
Indices: 459387--459610 Score: 439
Period size: 86 Copynumber: 2.6 Consensus size: 86
459377 TTCAATCGCA
459387 CTAAATTTTGAATTGCGAACTGCGTTCTATAGAACGCAGTTCACTATTCAATTGCATATAAGGCA
1 CTAAATTTTGAATTGCGAACTGCGTTCTATAGAACGCAGTTCACTATTCAATTGCATATAAGGCA
459452 AGCGGGCCCCAAATATGAATT
66 AGCGGGCCCCAAATATGAATT
459473 CTAAATTTTGAATTGCGAACTGCGTTCTATAGAACGCAGTTCACTATTCAATTGCATATAAGGCA
1 CTAAATTTTGAATTGCGAACTGCGTTCTATAGAACGCAGTTCACTATTCAATTGCATATAAGGCA
459538 AGCGGGCCCCAAATATGAATT
66 AGCGGGCCCCAAATATGAATT
*
459559 CTAAATTTTGAATTTCGAACTGCGTTCTATAGAACGCAGTTCACTATTCAAT
1 CTAAATTTTGAATTGCGAACTGCGTTCTATAGAACGCAGTTCACTATTCAAT
459611 CGCACAAAAT
Statistics
Matches: 137, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 137 1.00
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (86 bp):
CTAAATTTTGAATTGCGAACTGCGTTCTATAGAACGCAGTTCACTATTCAATTGCATATAAGGCA
AGCGGGCCCCAAATATGAATT
Found at i:459647 original size:56 final size:56
Alignment explanation
Indices: 459561--459666 Score: 194
Period size: 56 Copynumber: 1.9 Consensus size: 56
459551 TATGAATTCT
*
459561 AAATTTTGAATTTCGAACTGCGTTCTATAGAACGCAGTTCACTATTCAATCGCACA
1 AAATTTTGAATTGCGAACTGCGTTCTATAGAACGCAGTTCACTATTCAATCGCACA
*
459617 AAATTTTGAATTGCGAACTGCGTTCTATAGAACGCAGTTCATTATTCAAT
1 AAATTTTGAATTGCGAACTGCGTTCTATAGAACGCAGTTCACTATTCAAT
459667 TGCGAACTGC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (56 bp):
AAATTTTGAATTGCGAACTGCGTTCTATAGAACGCAGTTCACTATTCAATCGCACA
Found at i:459677 original size:7 final size:7
Alignment explanation
Indices: 459667--459691 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
459657 ATTATTCAAT
459667 TGCGAAC
1 TGCGAAC
459674 TGCGAAC
1 TGCGAAC
459681 TGCGAAC
1 TGCGAAC
459688 TGCG
1 TGCG
459692 TTCTAAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.28, G:0.32, T:0.16
Consensus pattern (7 bp):
TGCGAAC
Found at i:467040 original size:21 final size:21
Alignment explanation
Indices: 467016--467081 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
467006 ATATTGTAAT
*
467016 TACGAGAAAAGATCTCGTTAA
1 TACGAGAAAAAATCTCGTTAA
* ***
467037 TACGAGTTATTTATCTCG-TAA
1 TACGAG-AAAAAATCTCGTTAA
467058 TAACGAGAAAAAATCTCGTTAA
1 T-ACGAGAAAAAATCTCGTTAA
467080 TA
1 TA
467082 ATTACAAGCT
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
21 18 0.53
22 16 0.47
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (21 bp):
TACGAGAAAAAATCTCGTTAA
Found at i:467058 original size:43 final size:42
Alignment explanation
Indices: 467011--467175 Score: 168
Period size: 43 Copynumber: 3.8 Consensus size: 42
467001 ATTTCATATT
467011 GTAATTACGAGAAAAGATCTCGTTAATACGAGTTATTTATCTC
1 GTAATTACGAGAAAAGATCTCGTTAATACGAGTTATTT-TCTC
* * * *
467054 GTAATAACGAGAAAAAATCTCGTTAATAATTACAAGCTAATTTTCTC
1 GTAATTACGAGAAAAGATCTCG-T--TAA-TACGAG-TTATTTTCTC
* * * *
467101 GTTATTACGAGAAAAGATCTTGTTATTATGAGTTAATTTTCTC
1 GTAATTACGAGAAAAGATCTCGTTAATACGAGTT-ATTTTCTC
* * *
467144 GTACTTACGAGAAAAGATCTCGGTATTACGAG
1 GTAATTACGAGAAAAGATCTCGTTAATACGAG
467176 AAAAAAACTT
Statistics
Matches: 99, Mismatches: 17, Indels: 12
0.77 0.13 0.09
Matches are distributed among these distances:
42 1 0.01
43 59 0.60
44 3 0.03
46 4 0.04
47 27 0.27
48 5 0.05
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (42 bp):
GTAATTACGAGAAAAGATCTCGTTAATACGAGTTATTTTCTC
Found at i:467080 original size:22 final size:22
Alignment explanation
Indices: 467012--467082 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
467002 TTTCATATTG
* *
467012 TAATTACGAGAAAAGATCTCGT
1 TAATAACGAGAAAAAATCTCGT
* ***
467034 TAAT-ACGAGTTATTTATCTCG-
1 TAATAACGAG-AAAAAATCTCGT
467055 TAATAACGAGAAAAAATCTCGT
1 TAATAACGAGAAAAAATCTCGT
467077 TAATAA
1 TAATAA
467083 TTACAAGCTA
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
21 16 0.42
22 22 0.58
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (22 bp):
TAATAACGAGAAAAAATCTCGT
Found at i:467126 original size:21 final size:21
Alignment explanation
Indices: 467097--467217 Score: 82
Period size: 21 Copynumber: 5.7 Consensus size: 21
467087 AAGCTAATTT
467097 TCTCGTTATTACGAGAAAAGA
1 TCTCGTTATTACGAGAAAAGA
* * * ***
467118 TCTTGTTATTATGAGTTAATTT
1 TCTCGTTATTACGAG-AAAAGA
467140 TCTCG-TACTTACGAGAAAAGA
1 TCTCGTTA-TTACGAGAAAAGA
* *
467161 TCTCGGTATTACGAGAAAAAA
1 TCTCGTTATTACGAGAAAAGA
* * * * *
467182 ACTTGTAAATTGCAAGAAAAGA
1 TCTCGT-TATTACGAGAAAAGA
*
467204 TCTCGTTTTTACGA
1 TCTCGTTATTACGA
467218 TATAATTATC
Statistics
Matches: 70, Mismatches: 26, Indels: 8
0.67 0.25 0.08
Matches are distributed among these distances:
21 41 0.59
22 29 0.41
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (21 bp):
TCTCGTTATTACGAGAAAAGA
Found at i:467541 original size:21 final size:21
Alignment explanation
Indices: 467514--467597 Score: 87
Period size: 21 Copynumber: 4.0 Consensus size: 21
467504 AAATCTGTTC
*
467514 TCGTAATAACGAGATCTTTTT
1 TCGTAATAACGAGATCTTTTA
* * *
467535 TCATAATTACGAGATCTTTTC
1 TCGTAATAACGAGATCTTTTA
* * * *
467556 TCGTAATAGCGTGATAGTTATA
1 TCGTAATAACGAGAT-CTTTTA
467578 TCGTAATAACGAGATCTTTT
1 TCGTAATAACGAGATCTTTT
467598 CTTGGAATTT
Statistics
Matches: 48, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
21 32 0.67
22 16 0.33
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.40
Consensus pattern (21 bp):
TCGTAATAACGAGATCTTTTA
Found at i:467669 original size:22 final size:21
Alignment explanation
Indices: 467603--467676 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
467593 CTTTTCTTGG
*
467603 AATTTCGAGAAAAGATCTCGT
1 AATTACGAGAAAAGATCTCGT
467624 AATTACGAGAAAAGATCTCGT
1 AATTACGAGAAAAGATCTCGT
* *
467645 AATTACGAGAAAATTATCTCAT
1 AATTACGAGAAAA-GATCTCGT
*
467667 AATAACGAGA
1 AATTACGAGA
467677 TCTTTTTTCT
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
21 33 0.69
22 15 0.31
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.26
Consensus pattern (21 bp):
AATTACGAGAAAAGATCTCGT
Found at i:467737 original size:21 final size:21
Alignment explanation
Indices: 467707--467756 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
467697 AGAAAACTAA
* *
467707 CTCGTAATAACGAGATCTTTT
1 CTCGTTATAAAGAGATCTTTT
467728 CTCGTTATAAAGAGATCTTTT
1 CTCGTTATAAAGAGATCTTTT
*
467749 TTCGTTAT
1 CTCGTTAT
467757 TTCGAAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (21 bp):
CTCGTTATAAAGAGATCTTTT
Found at i:468127 original size:48 final size:49
Alignment explanation
Indices: 468028--468128 Score: 141
Period size: 48 Copynumber: 2.0 Consensus size: 49
468018 GCAGCCTTTT
* *
468028 CAGTTCTAACATTATCTACCTATTAAGTGGAACATATAACAATTATAGCAA
1 CAGTTCTAACATTATCTACC--TTAAGTGGAACACATAAAAATTATAGCAA
* *
468079 CAGTTCTAACATTATCTACC-TAGGTGGAACACATAAAAATTATCGCAA
1 CAGTTCTAACATTATCTACCTTAAGTGGAACACATAAAAATTATAGCAA
468127 CA
1 CA
468129 TCTTATCAGC
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
48 26 0.57
51 20 0.43
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.29
Consensus pattern (49 bp):
CAGTTCTAACATTATCTACCTTAAGTGGAACACATAAAAATTATAGCAA
Found at i:470685 original size:2 final size:2
Alignment explanation
Indices: 470678--470743 Score: 123
Period size: 2 Copynumber: 33.0 Consensus size: 2
470668 CTGTGCTAAA
*
470678 CT CT CT CT CT CT CT CT CT CT CT CG 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
470720 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
470744 GTGTAAACGG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.00, C:0.50, G:0.02, T:0.48
Consensus pattern (2 bp):
CT
Found at i:475388 original size:46 final size:46
Alignment explanation
Indices: 475321--475463 Score: 277
Period size: 46 Copynumber: 3.1 Consensus size: 46
475311 TGCGTACCTG
*
475321 TATTGATACTCTTTTAAACTCTCGAGTTCCTCTGCTTCTGGATGCT
1 TATTGATACTTTTTTAAACTCTCGAGTTCCTCTGCTTCTGGATGCT
475367 TATTGATACTTTTTTAAACTCTCGAGTTCCTCTGCTTCTGGATGCT
1 TATTGATACTTTTTTAAACTCTCGAGTTCCTCTGCTTCTGGATGCT
475413 TATTGATACTTTTTTAAACTCTCGAGTTCCTCTGCTTCTGGATGCT
1 TATTGATACTTTTTTAAACTCTCGAGTTCCTCTGCTTCTGGATGCT
475459 TATTG
1 TATTG
475464 GTGTCTTACT
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
46 96 1.00
ACGTcount: A:0.17, C:0.22, G:0.15, T:0.45
Consensus pattern (46 bp):
TATTGATACTTTTTTAAACTCTCGAGTTCCTCTGCTTCTGGATGCT
Found at i:489100 original size:19 final size:19
Alignment explanation
Indices: 489039--489369 Score: 100
Period size: 19 Copynumber: 17.4 Consensus size: 19
489029 CTCCAAAAAC
* *
489039 ACATGTTGTGATATAACTTG
1 ACATGTTGTGAGAT-ATTTG
* * *
489059 A-ATATTGTGAGTTAACTTG
1 ACATGTTGTGAGAT-ATTTG
*
489078 -CATGGTGTGAGATATTTG
1 ACATGTTGTGAGATATTTG
* *
489096 ACATGTTCTGAGATATTTT
1 ACATGTTGTGAGATATTTG
*
489115 ACATGTTGTGAGAAAACTTT-
1 ACATGTTGTGAG-ATA-TTTG
*
489135 -CTTGTTGTGAGATAACTTT-
1 ACATGTTGTGAGAT-A-TTTG
* * *
489154 -CTTGTTGTGATAAATCTT-
1 ACATGTTGTGAGATAT-TTG
* * *
489172 ACATGTTGTAAGACACCTTG
1 ACATGTTGTGAGATA-TTTG
* *
489192 -CATGTTGTAAGATAAATT-
1 ACATGTTGTGAGAT-ATTTG
*
489210 ACATGTTGTGAGATAAATT-
1 ACATGTTGTGAGAT-ATTTG
*
489229 ACATATTGTGAGATATCTT-
1 ACATGTTGTGAGATAT-TTG
* * *
489248 ATATGTTGTGGGATAACTTG
1 ACATGTTGTGAGAT-ATTTG
* * *
489268 -CATTTTCTGAGATAACTT-
1 ACATGTTGTGAGAT-ATTTG
* *
489286 ACAAGTTGTGATATATCTT-
1 ACATGTTGTGAGATAT-TTG
*** *
489305 ATGCGTTGTGAGATATTTT
1 ACATGTTGTGAGATATTTG
*
489324 ACATGTTGTGAGATGACTT-
1 ACATGTTGTGAGAT-ATTTG
*
489343 ACATGGTGTGAGATATTTTG
1 ACATGTTGTGAGATA-TTTG
489363 -CATGTTG
1 ACATGTTG
489370 CGTGATAACT
Statistics
Matches: 241, Mismatches: 50, Indels: 41
0.73 0.15 0.12
Matches are distributed among these distances:
17 1 0.00
18 13 0.05
19 216 0.90
20 8 0.03
21 3 0.01
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.41
Consensus pattern (19 bp):
ACATGTTGTGAGATATTTG
Found at i:489133 original size:57 final size:57
Alignment explanation
Indices: 489039--489394 Score: 256
Period size: 57 Copynumber: 6.2 Consensus size: 57
489029 CTCCAAAAAC
* * * *
489039 ACATGTTGTGATATAACTTGA-ATATTGTGAGTTAACTTGCATGGTGTGAGAT-ATTT
1 ACATGTTGTGAGATAACTT-ACATGTTGTGAGATAACTTGCATGTTGTGAGATAATTT
* ** * * *
489095 GACATGTTCTGAGATATTTTACATGTTGTGAGAAAACTTTCTTGTTGTGAGATAACTTT
1 -ACATGTTGTGAGATAACTTACATGTTGTGAGATAACTTGCATGTTGTGAGATAA-TTT
* * * * * * *
489154 -CTTGTTGTGATA-AATCTTACATGTTGTAAGACACCTTGCATGTTGTAAGATAAATT
1 ACATGTTGTGAGATAA-CTTACATGTTGTGAGATAACTTGCATGTTGTGAGATAATTT
* * * ** * *
489210 ACATGTTGTGAGATAAATTACATATTGTGAGATATCTTATATGTTGTGGGATAACTT
1 ACATGTTGTGAGATAACTTACATGTTGTGAGATAACTTGCATGTTGTGAGATAATTT
* * * * * * *
489267 GCATTTTCTGAGATAACTTACAAGTTGTGATATATCTT--ATGCGTTGTGAGATATTTT
1 ACATGTTGTGAGATAACTTACATGTTGTGAGATAACTTGCAT--GTTGTGAGATAATTT
* * ** * * *
489324 ACATGTTGTGAGATGACTTACATGGTGTGAGATATTTTGCATGTTGCGTGATAACTT
1 ACATGTTGTGAGATAACTTACATGTTGTGAGATAACTTGCATGTTGTGAGATAATTT
* *
489381 ACGTGTTATGAGAT
1 ACATGTTGTGAGAT
489395 GAGCTGATGT
Statistics
Matches: 231, Mismatches: 58, Indels: 20
0.75 0.19 0.06
Matches are distributed among these distances:
55 2 0.01
56 4 0.02
57 217 0.94
58 3 0.01
59 5 0.02
ACGTcount: A:0.28, C:0.10, G:0.22, T:0.41
Consensus pattern (57 bp):
ACATGTTGTGAGATAACTTACATGTTGTGAGATAACTTGCATGTTGTGAGATAATTT
Found at i:489356 original size:38 final size:38
Alignment explanation
Indices: 489063--489394 Score: 243
Period size: 38 Copynumber: 8.7 Consensus size: 38
489053 AACTTGAATA
* * * *
489063 TTGTGAGTTAACTTGCATGGTGTGAGATATTTGACATG
1 TTGTGAGATAACTTACATGTTGTGAGATATTTTACATG
* ** * * *
489101 TTCTGAGATATTTTACATGTTGTGAGAAAACTTT-CTTG
1 TTGTGAGATAACTTACATGTTGTGAG-ATATTTTACATG
* * * * *
489139 TTGTGAGATAACTTTCTTGTTGTGATAAATCTTACATG
1 TTGTGAGATAACTTACATGTTGTGAGATATTTTACATG
* * * * * **
489177 TTGTAAGACACCTTGCATGTTGTAAGATAAATTACATG
1 TTGTGAGATAACTTACATGTTGTGAGATATTTTACATG
* * * *
489215 TTGTGAGATAAATTACATATTGTGAGATATCTTATATG
1 TTGTGAGATAACTTACATGTTGTGAGATATTTTACATG
* * * * ** *
489253 TTGTGGGATAACTTGCATTTTCTGAGATAACTTACAAG
1 TTGTGAGATAACTTACATGTTGTGAGATATTTTACATG
* * ***
489291 TTGTGATATATCTTATGCGTTGTGAGATATTTTACATG
1 TTGTGAGATAACTTACATGTTGTGAGATATTTTACATG
* * *
489329 TTGTGAGATGACTTACATGGTGTGAGATATTTTGCATG
1 TTGTGAGATAACTTACATGTTGTGAGATATTTTACATG
* * * *
489367 TTGCGTGATAACTTACGTGTTATGAGAT
1 TTGTGAGATAACTTACATGTTGTGAGAT
489395 GAGCTGATGT
Statistics
Matches: 219, Mismatches: 73, Indels: 4
0.74 0.25 0.01
Matches are distributed among these distances:
37 5 0.02
38 210 0.96
39 4 0.02
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (38 bp):
TTGTGAGATAACTTACATGTTGTGAGATATTTTACATG
Found at i:489878 original size:21 final size:19
Alignment explanation
Indices: 489852--489893 Score: 66
Period size: 21 Copynumber: 2.1 Consensus size: 19
489842 TGTCTCCCAC
489852 CTACTGCTTTTATTCAATAAT
1 CTACTGCTTTTA-TCAA-AAT
489873 CTACTGCTTTTATCAAAAT
1 CTACTGCTTTTATCAAAAT
489892 CT
1 CT
489894 GCTTTGTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.24
20 4 0.19
21 12 0.57
ACGTcount: A:0.29, C:0.21, G:0.05, T:0.45
Consensus pattern (19 bp):
CTACTGCTTTTATCAAAAT
Found at i:499740 original size:2 final size:2
Alignment explanation
Indices: 499733--499763 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
499723 AGTTTTTCAA
499733 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
499764 NNNNNNNNNN
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:501261 original size:24 final size:24
Alignment explanation
Indices: 501234--501281 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
501224 AATTAACTTT
501234 AAATATCTCCACAGATTGGCTGAC
1 AAATATCTCCACAGATTGGCTGAC
501258 AAATATCTCCACAGATTGGCTGAC
1 AAATATCTCCACAGATTGGCTGAC
501282 TATTTCTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (24 bp):
AAATATCTCCACAGATTGGCTGAC
Found at i:509406 original size:2 final size:2
Alignment explanation
Indices: 509401--509455 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
509391 AAAAGTTGAT
509401 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
*
509443 TC TC TT TC TC TC T
1 TC TC TC TC TC TC T
509456 GTGCCGTGAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:510790 original size:2 final size:2
Alignment explanation
Indices: 510783--510840 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
510773 GATAAAAGTG
*
510783 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CG 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
510825 CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT
510841 GTGTATATGC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.00, C:0.50, G:0.02, T:0.48
Consensus pattern (2 bp):
CT
Found at i:513067 original size:37 final size:38
Alignment explanation
Indices: 513023--513099 Score: 129
Period size: 38 Copynumber: 2.1 Consensus size: 38
513013 TATAATAACT
513023 TTCATAAATAAACTTCG-CTTTTTTATGAATGTATAAA
1 TTCATAAATAAACTTCGTCTTTTTTATGAATGTATAAA
* *
513060 TTCATAAATAAACTTCGTTTTTTTTATGAATTTATAAA
1 TTCATAAATAAACTTCGTCTTTTTTATGAATGTATAAA
513098 TT
1 TT
513100 GTTGAAATTG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
37 17 0.46
38 20 0.54
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.48
Consensus pattern (38 bp):
TTCATAAATAAACTTCGTCTTTTTTATGAATGTATAAA
Found at i:514217 original size:1 final size:1
Alignment explanation
Indices: 514213--514241 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
514203 ATTTATGTAT
514213 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
514242 GTTCAATGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:519352 original size:36 final size:36
Alignment explanation
Indices: 519289--519357 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
519279 ACAAAAGTAA
* *
519289 TTTACCAGTGTTGTACAGACTTTACTGTACATTTAC
1 TTTACCAGTGTTGTAAAGACTTAACTGTACATTTAC
* *
519325 TTTACCTGTGTTGTAAAGA-TTGAACTGTTCATT
1 TTTACCAGTGTTGTAAAGACTT-AACTGTACATT
519358 AATTATGTCG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 2 0.07
36 26 0.93
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.43
Consensus pattern (36 bp):
TTTACCAGTGTTGTAAAGACTTAACTGTACATTTAC
Found at i:519431 original size:30 final size:30
Alignment explanation
Indices: 519377--519674 Score: 463
Period size: 30 Copynumber: 9.9 Consensus size: 30
519367 GTACAAATAA
519377 TACAGTACATTACCTGTG-TGTACAGATTT
1 TACAGTACATTACCTGTGTTGTACAGATTT
*
519406 TACGGTACATTACCTGTGTTGTACAGATTT
1 TACAGTACATTACCTGTGTTGTACAGATTT
519436 TACAGTACATTACCTGTGTTGTACAGATTT
1 TACAGTACATTACCTGTGTTGTACAGATTT
519466 TACAGTACATTACCTGTGTTGTACAGATTT
1 TACAGTACATTACCTGTGTTGTACAGATTT
519496 TACAGTACATTACCTGTGTTGTACAGATTT
1 TACAGTACATTACCTGTGTTGTACAGATTT
** *
519526 TATGGTACAGTACCTGTGTTGTACAGATTT
1 TACAGTACATTACCTGTGTTGTACAGATTT
* *
519556 TACGGTACATTATTACCGGTGTTGTACAGATTT
1 TACAGTAC---ATTACCTGTGTTGTACAGATTT
* *
519589 TACAGTTCATTGCCTGTGTTGTACAGATTT
1 TACAGTACATTACCTGTGTTGTACAGATTT
* * *
519619 TGCAGTACATTACCTGAGTTTTACAGATTT
1 TACAGTACATTACCTGTGTTGTACAGATTT
519649 TACAGTACATTACCTGTGTTGTACAG
1 TACAGTACATTACCTGTGTTGTACAG
519675 TCCCAGCCGT
Statistics
Matches: 245, Mismatches: 20, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
29 17 0.07
30 202 0.82
33 26 0.11
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (30 bp):
TACAGTACATTACCTGTGTTGTACAGATTT
Found at i:519616 original size:153 final size:149
Alignment explanation
Indices: 519381--519674 Score: 489
Period size: 153 Copynumber: 1.9 Consensus size: 149
519371 AAATAATACA
* *
519381 GTACATTACCTGTGTGTACAGATTTTACGGTACATTACCTGTGTTGTACAGATTTTACAGTACAT
1 GTACAGTACCTGTGTGTACAGATTTTACGGTACATTACCGGTGTTGTACAGATTTTACAGTACAT
*
519446 TACCTGTGTTGTACAGATTTTACAGTACATTACCTGTGTTGTACAGATTTTACAGTACATTACCT
66 TACCTGTGTTGTACAGATTTTACAGTACATTACCTGAGTTGTACAGATTTTACAGTACATTACCT
519511 GTGTTGTACAGATTTTATG
131 GTGTTGTACAGATTTTATG
519530 GTACAGTACCTGTGTTGTACAGATTTTACGGTACATTATTACCGGTGTTGTACAGATTTTACAGT
1 GTACAGTACCTGTG-TGTACAGATTTTACGGTAC---ATTACCGGTGTTGTACAGATTTTACAGT
* * * *
519595 TCATTGCCTGTGTTGTACAGATTTTGCAGTACATTACCTGAGTTTTACAGATTTTACAGTACATT
62 ACATTACCTGTGTTGTACAGATTTTACAGTACATTACCTGAGTTGTACAGATTTTACAGTACATT
519660 ACCTGTGTTGTACAG
127 ACCTGTGTTGTACAG
519675 TCCCAGCCGT
Statistics
Matches: 134, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
149 13 0.10
150 19 0.14
153 102 0.76
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (149 bp):
GTACAGTACCTGTGTGTACAGATTTTACGGTACATTACCGGTGTTGTACAGATTTTACAGTACAT
TACCTGTGTTGTACAGATTTTACAGTACATTACCTGAGTTGTACAGATTTTACAGTACATTACCT
GTGTTGTACAGATTTTATG
Found at i:527465 original size:14 final size:14
Alignment explanation
Indices: 527442--527479 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
527432 ACAGGCTGCA
*
527442 AAACAGACACACAT
1 AAACATACACACAT
*
527456 AAACGTACACACAT
1 AAACATACACACAT
527470 AAACATACAC
1 AAACATACAC
527480 CAAAAGCTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.55, C:0.29, G:0.05, T:0.11
Consensus pattern (14 bp):
AAACATACACACAT
Found at i:528820 original size:52 final size:52
Alignment explanation
Indices: 528764--528927 Score: 132
Period size: 52 Copynumber: 3.0 Consensus size: 52
528754 ATCTTGGTGT
*** * *
528764 TACATTGCAGTTGCTTGCTATAC-TTGAGTGCAATATTGCCTTAATTTGAAGC
1 TACATTGCAGTTGCTTGCTATACACAAAG-GAAATATTGCCTTAACTTGAAGC
*
528816 TACATGTATGTTGCAGTTGCTTGCTATACACAAAGGAAATGTTGCCTTAACTTGAAGC
1 TAC----A--TTGCAGTTGCTTGCTATACACAAAGGAAATATTGCCTTAACTTGAAGC
** ** * * * *
528874 TATGTTGCAGTTGCTTGCTATACACAGGGGATATGTTGCCTTACCTGGAAGC
1 TACATTGCAGTTGCTTGCTATACACAAAGGAAATATTGCCTTAACTTGAAGC
528926 TA
1 TA
528928 TGTTGCTGTT
Statistics
Matches: 92, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
52 48 0.52
56 1 0.01
58 41 0.45
59 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.35
Consensus pattern (52 bp):
TACATTGCAGTTGCTTGCTATACACAAAGGAAATATTGCCTTAACTTGAAGC
Found at i:528928 original size:52 final size:52
Alignment explanation
Indices: 528822--528940 Score: 184
Period size: 52 Copynumber: 2.3 Consensus size: 52
528812 AAGCTACATG
*
528822 TATGTTGCAGTTGCTTGCTATACACAAAGGAAATGTTGCCTTAACTTGAAGC
1 TATGTTGCAGTTGCTTGCTATACACAAAGGAAATGTTGCCTTAACTGGAAGC
** * *
528874 TATGTTGCAGTTGCTTGCTATACACAGGGGATATGTTGCCTTACCTGGAAGC
1 TATGTTGCAGTTGCTTGCTATACACAAAGGAAATGTTGCCTTAACTGGAAGC
*
528926 TATGTTGCTGTTGCT
1 TATGTTGCAGTTGCT
528941 GGTGCTCTCC
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 61 1.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (52 bp):
TATGTTGCAGTTGCTTGCTATACACAAAGGAAATGTTGCCTTAACTGGAAGC
Found at i:534095 original size:12 final size:12
Alignment explanation
Indices: 534078--534107 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
534068 TTAATTGAAT
534078 GTAAAGTAAACA
1 GTAAAGTAAACA
534090 GTAAAGTAAACA
1 GTAAAGTAAACA
534102 GTAAAG
1 GTAAAG
534108 CCATCTTCTC
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:0.57, C:0.07, G:0.20, T:0.17
Consensus pattern (12 bp):
GTAAAGTAAACA
Found at i:550248 original size:16 final size:16
Alignment explanation
Indices: 550227--550261 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
550217 ACCCTTGTGT
550227 GTCTGTCTGTCCGTCC
1 GTCTGTCTGTCCGTCC
*
550243 GTCTGTCTGTCTGTCC
1 GTCTGTCTGTCCGTCC
550259 GTC
1 GTC
550262 CGTAACAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.34, G:0.26, T:0.40
Consensus pattern (16 bp):
GTCTGTCTGTCCGTCC
Found at i:550251 original size:20 final size:20
Alignment explanation
Indices: 550226--550264 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
550216 TACCCTTGTG
550226 TGTCTGTCTGTCCGTCCGTC
1 TGTCTGTCTGTCCGTCCGTC
550246 TGTCTGTCTGTCCGTCCGT
1 TGTCTGTCTGTCCGTCCGT
550265 AACAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.00, C:0.33, G:0.26, T:0.41
Consensus pattern (20 bp):
TGTCTGTCTGTCCGTCCGTC
Found at i:550670 original size:166 final size:165
Alignment explanation
Indices: 550288--551209 Score: 1375
Period size: 166 Copynumber: 5.6 Consensus size: 165
550278 GTCGCATTTA
* *
550288 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTGTTTGTTAAGGCATGCCATAT
1 TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTT-AGGCATGCCATAT
* *
550353 CGTGGGAAATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
65 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTA-TTT
550418 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
129 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* * **
550455 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTGT-ACACAGTATTTGTATAGGCATGCTTTA
1 TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTT-TAACACAGTATTTGT-TAGGCATGCCATA
* **
550519 TCGTGGGATGTATTTTTGTACCAATCAAACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTT
64 TCGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTT
550584 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
129 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* * *
550621 TCTCAGCAGCTATTTTTCGCAGATGCTTGAAATTTTTACACAATATTTGTATAGGCATGCCATAT
1 TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGT-TAGGCATGCCATAT
* **
550686 CGTGGGATATATTTCTGTACCAATCGGGTGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
65 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
*
550751 TAGCCAAAATTTTCAACCAAATTTTCGTCAAAGATT
130 TAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* * * *
550787 TCCCAGCAGCTATTTTTCGCAGATGCTTGAAATTTTAACACACTATTTGTTTTGGCATGCCATAT
1 TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTG-TTAGGCATGCCATAT
* * * * *
550852 CGTGGGATATATTTTTGTATCTATCGGACGTCAACATCCTGTTAAATAATGACTTTGTTTATTTT
65 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
* *
550917 TTGCCAACATTTTCAAACAAATTTTCGTCAAAGATT
130 TAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* * *
550953 TCTCAGCAGCTATTTATCGGAGATGCTTGAAATTTTTACACAGTGTTTGTTAAGGCATGCCATAT
1 TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTT-AGGCATGCCATAT
*
551018 TGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGA-GTACTTTGTTTA-TT
65 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACG-ACTTTGTTTATTT
*
551081 TTAGCCAAAATTTTCAAACAAATTTTCCTCAAAGATT
129 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* * *
551118 TCTCGGCAGCTGTTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATAT
1 TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTG-TTAGGCATGCCATAT
* * *
551183 TGTTGGATATA-TTCTGTACCAATCGGA
65 CGTGGGATATATTTTTGTACCAATCGGA
551210 TGCCAGCTTT
Statistics
Matches: 688, Mismatches: 60, Indels: 17
0.90 0.08 0.02
Matches are distributed among these distances:
164 15 0.02
165 106 0.15
166 451 0.66
167 114 0.17
168 2 0.00
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (165 bp):
TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTTAGGCATGCCATATC
GTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTTT
AGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
Found at i:560453 original size:185 final size:179
Alignment explanation
Indices: 559848--560507 Score: 981
Period size: 179 Copynumber: 3.7 Consensus size: 179
559838 GGCTGCCAAA
* * *
559848 AGGGTACCCTCATTGTACAGATAATTCCTCCTGCAGTTTTCAAGATAAGAAATTGTTCTTTTGCA
1 AGGGTACCCTCATTGTACGGATAATTCCTCCTACAGTTTTCAAGATAGGAAATTGTTCTTTTGCA
* * * * *
559913 GGTTAATTGTACATATATCAGAGGTGTGCGTATTGCTAGGAATTTGATTTCTGATGATTTATGAA
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTATGAA
* *
559978 AAAACACTAGCTTTT-AAACTTAATCATTTTTTGGCAAAATATTGCATAT
131 AAAA-ACCAGCTTTTGAAACTTAGTCATTTTTTGGCAAAATATTGCATAT
* * *
560027 AGGGTACCCTCATTGTACGGATAATTCCTCCTGCAGTTTTCAAGATAGGAAATTGTTCTTTAGTA
1 AGGGTACCCTCATTGTACGGATAATTCCTCCTACAGTTTTCAAGATAGGAAATTGTTCTTTTGCA
*
560092 GATCAATTGTACATATA-CTAGAGGTGTGCATATTGCTA-GATTTTGAATTCTGATAATTTATGA
66 GATCAATTGTACATATATC-AGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTATG-
560155 AAAAAAACCCAGCTTTTG-AACTTAGTCATTTTTTGGCAAAATATTGCATAT
129 AAAAAAA-CCAGCTTTTGAAACTTAGTCATTTTTTGGCAAAATATTGCATAT
*
560206 AGGGTACCCTCATTGTACGGATAATTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCA
1 AGGGTACCCTCATTGTACGGATAATTCCTCCTACAGTTTTCAAGATAGGAAATTGTTCTTTTGCA
560271 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTA-GATTTTGATTTCTGATAATTTATGAA
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTATGAA
560335 AAAAACCAGCTTTTGAACATACCGTGGTAGTCATTTTTTGGCAAAATATTGCATAT
131 AAAAACCAGCTTTTG-A-A-A-C-T--TAGTCATTTTTTGGCAAAATATTGCATAT
* * * * * * *
560391 AGGGCACCATCATTTTATGGATAACTCCACCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCA
1 AGGGTACCCTCATTGTACGGATAATTCCTCCTACAGTTTTCAAGATAGGAAATTGTTCTTTTGCA
560456 GATCAATTGTACATATATCAGAGGTGTGCA-ATTGCTAGGATTTTGATTTCTG
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTG
560508 CATATTGCTA
Statistics
Matches: 444, Mismatches: 23, Indels: 22
0.91 0.05 0.04
Matches are distributed among these distances:
177 10 0.02
178 30 0.07
179 260 0.59
180 2 0.00
181 1 0.00
182 1 0.00
183 1 0.00
184 7 0.02
185 132 0.30
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (179 bp):
AGGGTACCCTCATTGTACGGATAATTCCTCCTACAGTTTTCAAGATAGGAAATTGTTCTTTTGCA
GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTATGAA
AAAAACCAGCTTTTGAAACTTAGTCATTTTTTGGCAAAATATTGCATAT
Found at i:560521 original size:24 final size:24
Alignment explanation
Indices: 560482--560531 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
560472 ATCAGAGGTG
560482 TGCAATTGCTAGGATTTTGATTTC
1 TGCAATTGCTAGGATTTTGATTTC
560506 TGCATATTGCTA-GATTTTGATTTC
1 TGCA-ATTGCTAGGATTTTGATTTC
560530 TG
1 TG
560532 ATAATTTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.48
Consensus pattern (24 bp):
TGCAATTGCTAGGATTTTGATTTC
Found at i:562530 original size:38 final size:37
Alignment explanation
Indices: 562479--562606 Score: 175
Period size: 38 Copynumber: 3.4 Consensus size: 37
562469 GATGTTAGGA
*
562479 TAGAGAATGTTGATCAGCCCAGTCATCAGGAATCAGAC
1 TAGAGAATGTTGATCAGCCCAATCATCA-GAATCAGAC
562517 TAGAGAATGTTGATCAGCCCAATCATCCAGAATCAGAC
1 TAGAGAATGTTGATCAGCCCAATCAT-CAGAATCAGAC
* * * *
562555 TAAAGAGTGTTGATCAGCCCAATCATTTAGAATCAGAA
1 TAGAGAATGTTGATCAGCCCAATCA-TCAGAATCAGAC
*
562593 TTGAGAATGTTGAT
1 TAGAGAATGTTGAT
562607 AAACCTAGCA
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
38 77 0.96
39 3 0.04
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (37 bp):
TAGAGAATGTTGATCAGCCCAATCATCAGAATCAGAC
Found at i:565189 original size:17 final size:17
Alignment explanation
Indices: 565167--565199 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
565157 CTGGTACTGT
565167 ACCAGTTATCGGCTAAG
1 ACCAGTTATCGGCTAAG
565184 ACCAGTTATCGGCTAA
1 ACCAGTTATCGGCTAA
565200 ACTGAGAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24
Consensus pattern (17 bp):
ACCAGTTATCGGCTAAG
Found at i:569785 original size:4 final size:4
Alignment explanation
Indices: 569778--569807 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
569768 GCTGCTGTCT
*
569778 GTCG GTCG GTCG GTCG GTCG GTCT GTCG GT
1 GTCG GTCG GTCG GTCG GTCG GTCG GTCG GT
569808 TTACCAACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.23, G:0.47, T:0.30
Consensus pattern (4 bp):
GTCG
Found at i:570177 original size:162 final size:163
Alignment explanation
Indices: 569818--570455 Score: 1084
Period size: 162 Copynumber: 3.9 Consensus size: 163
569808 TTACCAACAG
* * * *
569818 TTCCGTTCATTTTCTTTGCAGAGGATAAACATATTGAAATGAAATTTAGTTTACAGGTTTATCAT
1 TTCCGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTAGTATACAGGTTTATCAT
* *
569883 GATAATGTCTAGGTCAAGTTCGATATTGGGTACGATCGAGCCATTTTCGACAGAGTTATGGCCCT
66 GATAATATCTAGGTCAAGTTCGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATGGCCCT
*
569948 TGGACGTAGAACAATTCTAGTTTTTTTTGCAGT
131 TGGACGTAGAAAAATTCTAGTTTTTTTTGCAGT
* *
569981 TTCCGCTCATTTTCTTCGCAGAGGATGGACATATTGAAATGAAATTTGGTATACAGGTTTATCAT
1 TTCCGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTAGTATACAGGTTTATCAT
570046 GATAATATCTAGGTCAAGTTCGATATTGGGTACGATCGAGCAATTTT-GACAGAGTTATGGCCCT
66 GATAATATCTAGGTCAAGTTCGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATGGCCCT
*
570110 TGGACGTAGAAAAAATCTAGTTTTTTTTGCAGT
131 TGGACGTAGAAAAATTCTAGTTTTTTTTGCAGT
570143 TTCCGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTAGTATACAGGTTTATCAT
1 TTCCGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTAGTATACAGGTTTATCAT
* * *
570208 GATAATATCTAGGTCGAGTTCGATATTGGGTACGGTCGAGCCATTTTCGACAGAGTTATGGCCCT
66 GATAATATCTAGGTCAAGTTCGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATGGCCCT
570273 TGGACGTAGAAAAATTCTAG--TTTTTTGCAGT
131 TGGACGTAGAAAAATTCTAGTTTTTTTTGCAGT
*
570304 TTCCGTTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTAGTATACAGGTTTATCAT
1 TTCCGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTAGTATACAGGTTTATCAT
* * *
570369 GATAATATCTAGGTCAAGTTTGATATTGGGTATGATAGAGCAATTTTCGACAGAGTTATGGCCCT
66 GATAATATCTAGGTCAAGTTCGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATGGCCCT
* *
570434 TGGACTTAGAAAAATTCGAGTT
131 TGGACGTAGAAAAATTCTAGTT
570456 ATTTAAGTTT
Statistics
Matches: 447, Mismatches: 25, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
161 152 0.34
162 155 0.35
163 140 0.31
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (163 bp):
TTCCGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTAGTATACAGGTTTATCAT
GATAATATCTAGGTCAAGTTCGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATGGCCCT
TGGACGTAGAAAAATTCTAGTTTTTTTTGCAGT
Found at i:570351 original size:161 final size:162
Alignment explanation
Indices: 569818--570479 Score: 1080
Period size: 161 Copynumber: 4.1 Consensus size: 162
569808 TTACCAACAG
* * *
569818 TTCCGTTCATTTTCTTTGCAGAGGATAAACATATTGAAATGAAATTTAGTTTACAGGTTTATCAT
1 TTCCGTTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTAGTATACAGGTTTATCAT
* *
569883 GATAATGTCTAGGTCAAGTTCGATATTGGGTACGATCGAGCCATTTTCGACAGAGTTATGGCCCT
66 GATAATATCTAGGTCAAGTTCGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATGGCCCT
*
569948 TGGACGTAGAACAATTCTAGTTTTTTTTGCAGT
131 TGGACGTAGAAAAATTCTAG-TTTTTTTGCAGT
* * *
569981 TTCCGCTCATTTTCTTCGCAGAGGATGGACATATTGAAATGAAATTTGGTATACAGGTTTATCAT
1 TTCCGTTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTAGTATACAGGTTTATCAT
570046 GATAATATCTAGGTCAAGTTCGATATTGGGTACGATCGAGCAATTTT-GACAGAGTTATGGCCCT
66 GATAATATCTAGGTCAAGTTCGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATGGCCCT
*
570110 TGGACGTAGAAAAAATCTAGTTTTTTTTGCAGT
131 TGGACGTAGAAAAATTCTAG-TTTTTTTGCAGT
*
570143 TTCCGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTAGTATACAGGTTTATCAT
1 TTCCGTTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTAGTATACAGGTTTATCAT
* * *
570208 GATAATATCTAGGTCGAGTTCGATATTGGGTACGGTCGAGCCATTTTCGACAGAGTTATGGCCCT
66 GATAATATCTAGGTCAAGTTCGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATGGCCCT
570273 TGGACGTAGAAAAATTCTAG-TTTTTTGCAGT
131 TGGACGTAGAAAAATTCTAGTTTTTTTGCAGT
570304 TTCCGTTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTAGTATACAGGTTTATCAT
1 TTCCGTTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTAGTATACAGGTTTATCAT
* * *
570369 GATAATATCTAGGTCAAGTTTGATATTGGGTATGATAGAGCAATTTTCGACAGAGTTATGGCCCT
66 GATAATATCTAGGTCAAGTTCGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATGGCCCT
* * * *
570434 TGGACTTAGAAAAATTCGAG-TTATTT-AAGT
131 TGGACGTAGAAAAATTCTAGTTTTTTTGCAGT
*
570464 TTACGTTCATTTTCTT
1 TTCCGTTCATTTTCTT
570480 TGTGGATGTT
Statistics
Matches: 470, Mismatches: 28, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
160 18 0.04
161 157 0.33
162 155 0.33
163 140 0.30
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (162 bp):
TTCCGTTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTAGTATACAGGTTTATCAT
GATAATATCTAGGTCAAGTTCGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATGGCCCT
TGGACGTAGAAAAATTCTAGTTTTTTTGCAGT
Found at i:576378 original size:19 final size:19
Alignment explanation
Indices: 576350--576392 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
576340 TTTCAGATAC
*
576350 TGGAGGAGG-TTAAGGTTTT
1 TGGAGAAGGTTTAA-GTTTT
576369 TGGAGAAGGTTTAAGTTTT
1 TGGAGAAGGTTTAAGTTTT
576388 TGGAG
1 TGGAG
576393 GATAAAATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.23, C:0.00, G:0.40, T:0.37
Consensus pattern (19 bp):
TGGAGAAGGTTTAAGTTTT
Found at i:580341 original size:5 final size:5
Alignment explanation
Indices: 580322--580412 Score: 98
Period size: 5 Copynumber: 18.4 Consensus size: 5
580312 CTGTAAAGTG
* *
580322 CGAAA CGAAA TCGAAA CGAAA CGAAA TCG-AA CGAAA CGAAA CCAAT CGAAA
1 CGAAA CGAAA -CGAAA CGAAA CGAAA -CGAAA CGAAA CGAAA CGAAA CGAAA
* * *
580373 CGAAA CCAAA CGAAA CCAAA --AAT CGAAA CGAAA CGAAA CG
1 CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA CG
580413 GAATTTAAAC
Statistics
Matches: 72, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
3 2 0.03
4 2 0.03
5 61 0.85
6 7 0.10
ACGTcount: A:0.56, C:0.23, G:0.16, T:0.04
Consensus pattern (5 bp):
CGAAA
Found at i:580657 original size:2 final size:2
Alignment explanation
Indices: 580650--580688 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
580640 TCAGACGTTT
580650 AG AG 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 AG A
580689 TGCCTTAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:581539 original size:15 final size:16
Alignment explanation
Indices: 581510--581545 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
581500 CCCTATAAAT
581510 TGGGTACGTTTTCTCC
1 TGGGTACGTTTTCTCC
*
581526 TGGGTACG-TTTCTCT
1 TGGGTACGTTTTCTCC
581541 TGGGT
1 TGGGT
581546 TTTCTCCAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.06, C:0.19, G:0.31, T:0.44
Consensus pattern (16 bp):
TGGGTACGTTTTCTCC
Found at i:582488 original size:21 final size:21
Alignment explanation
Indices: 582451--582490 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
582441 GTTGGTCGGA
**
582451 ATTTTTTTTTTTTTTTTAAAT
1 ATTTTTTTTTTCCTTTTAAAT
582472 ATTTTTTTTTTCCTTTTAA
1 ATTTTTTTTTTCCTTTTAA
582491 TTTTGCAGTA
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:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (21 bp):
ATTTTTTTTTTCCTTTTAAAT
Found at i:583910 original size:15 final size:14
Alignment explanation
Indices: 583876--583911 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
583866 ACAAACAAAA
583876 TAATTTTTTTTTTT
1 TAATTTTTTTTTTT
583890 TAATTTTTTTTTTT
1 TAATTTTTTTTTTT
583904 TAGATTTT
1 TA-ATTTT
583912 GTCCATCTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.81
Consensus pattern (14 bp):
TAATTTTTTTTTTT
Found at i:602031 original size:145 final size:145
Alignment explanation
Indices: 601741--602032 Score: 446
Period size: 145 Copynumber: 2.0 Consensus size: 145
601731 ACCCTCATTG
* * * *
601741 TACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAATTGTTCCTTTGCAGATTGTACATATATC
1 TACGGATAACTCCCCCTACAGTTCTCAAGATAGGAAATTGTTCCTTTGCAGATTGAACACATATC
* * *
601806 AGAGGTGTGCATATTGCTAGGATTTTGATTTTCGATAATTTATGATGAAAAAATACTAGCTTTTG
66 AGAGGTATGCATATTGCTAGGATTTTGATTTCCGATAATTTATGATGAAAAAATACCAGCTTTTG
601871 AACTTAGTCATTTTT
131 AACTTAGTCATTTTT
*
601886 TACGGATAACTCCCCCTACAGTTCTCAAGATAGGAAATTGTTCTTTTGCAGATCAATTGAACACA
1 TACGGATAACTCCCCCTACAGTTCTCAAGATAGGAAATTGTTCCTTTGCAG----ATTGAACACA
*
601951 TATCAGAGGTATGCATATTGGTAGGATTTTGATTTCCGATAA-TT-T-ATGAAAAAATACCAGCT
62 TATCAGAGGTATGCATATTGCTAGGATTTTGATTTCCGATAATTTATGATGAAAAAATACCAGCT
602013 TTTGAACTTAGTCATTTTT
127 TTTGAACTTAGTCATTTTT
602032 T
1 T
602033 GGCAAAATAT
Statistics
Matches: 134, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
145 48 0.36
146 36 0.27
147 1 0.01
148 2 0.01
149 47 0.35
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (145 bp):
TACGGATAACTCCCCCTACAGTTCTCAAGATAGGAAATTGTTCCTTTGCAGATTGAACACATATC
AGAGGTATGCATATTGCTAGGATTTTGATTTCCGATAATTTATGATGAAAAAATACCAGCTTTTG
AACTTAGTCATTTTT
Found at i:602289 original size:131 final size:129
Alignment explanation
Indices: 602107--602367 Score: 405
Period size: 131 Copynumber: 2.0 Consensus size: 129
602097 GGAAGTTGTT
* *
602107 CTTTTACAGATCAATTAAACATATATCAGAGGTGTGCATATTGCTATGATTTTGATATCTGATAA
1 CTTTTACAGATCAATTAAACATATATAAGAGGTGTGCATATTGCTAGGATTTTGATATCTGATAA
*
602172 TTTTTGAAAAAAATACCAGCTTTTGAACTTAGTCAGTTTTTGGCAAAATATTGCATATAGGGTAC
66 TTTATG-AAAAAATACCAGCTTTTGAACTTAGTCA-TTTTTGGCAAAATATTGCATATAGGGTAC
602237 C
129 C
* ** * * *
602238 CTTTTGCAGATCAATTGTACATATTTAAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATCA
1 CTTTTACAGATCAATTAAACATATATAAGAGGTGTGCATATTGCTAGGATTTTGATATCTGATAA
* *
602303 TTTATGAAATAATACTAGCTTTTGAACTTAGTCATTTTTGGCAAAATATTGCATATAGGGTACC
66 TTTATGAAAAAATACCAGCTTTTGAACTTAGTCATTTTTGGCAAAATATTGCATATAGGGTACC
602367 C
1 C
602368 CATTTCACTG
Statistics
Matches: 119, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
129 31 0.26
130 26 0.22
131 62 0.52
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (129 bp):
CTTTTACAGATCAATTAAACATATATAAGAGGTGTGCATATTGCTAGGATTTTGATATCTGATAA
TTTATGAAAAAATACCAGCTTTTGAACTTAGTCATTTTTGGCAAAATATTGCATATAGGGTACC
Found at i:609177 original size:13 final size:11
Alignment explanation
Indices: 609149--609175 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
609139 CAGATAAAGA
609149 ATATACAGAAT
1 ATATACAGAAT
609160 ATATACAGAAT
1 ATATACAGAAT
609171 ATATA
1 ATATA
609176 TATACACGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (11 bp):
ATATACAGAAT
Found at i:620839 original size:12 final size:12
Alignment explanation
Indices: 620816--620848 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
620806 ATCACATTTT
620816 GTCTGT-CGTCC
1 GTCTGTCCGTCC
620827 GTCTGTCCGTCC
1 GTCTGTCCGTCC
620839 GTCTGTCCGT
1 GTCTGTCCGT
620849 AAACTTTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.29
12 15 0.71
ACGTcount: A:0.00, C:0.36, G:0.27, T:0.36
Consensus pattern (12 bp):
GTCTGTCCGTCC
Found at i:621292 original size:166 final size:166
Alignment explanation
Indices: 621018--621660 Score: 1125
Period size: 166 Copynumber: 3.9 Consensus size: 166
621008 AGATATTTTC
621018 AAAAATCTTCTTCTCAAGAACCAGAA-AGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG
1 AAAAATCTTCTTCTCAAGAACCA-AACAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG
621082 GTAGTGTAGATTCAAAGTTGTGAAATTCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGG
65 GTAGTGTAGATTCAAAGTTGTGAAATTCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGG
621147 TCGAAGTTTTACATAGGAATATATAAGGTAAATCTTT
130 TCGAAGTTTTACATAGGAATATATAAGGTAAATCTTT
621184 AAAAATCTTCTTCTCAAGAACCAGAA-AGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG
1 AAAAATCTTCTTCTCAAGAACCA-AACAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG
*
621248 GTAATGTAGATTCAAAGTTGTGAAATTCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGG
65 GTAGTGTAGATTCAAAGTTGTGAAATTCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGG
621313 TCGAAGTTTTACATAGGAATATATAAGGTAAATCTTT
130 TCGAAGTTTTACATAGGAATATATAAGGTAAATCTTT
* * * *
621350 AAAAATCTTCTTCTCAGGAACTAAACAGCCAGGAAAGCTGAAACTTGTGTTGAAGCTTCCTCAGG
1 AAAAATCTTCTTCTCAAGAACCAAACAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
*
621415 TAGTGTAGACTCAAAGTTGTGAAATTCATGACCCCCGGGGGTAGGGTGGGGCCACAAT-GGGGGT
66 TAGTGTAGATTCAAAGTTGTGAAATTCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGT
621479 CGAAGTTTTACATAGGAATATAT-AGAGTAAATCTTT
131 CGAAGTTTTACATAGGAATATATAAG-GTAAATCTTT
* * * *
621515 AATAATCTTCTCCTC-AGAAACTAAACAGCCAGGAAAGCTGAAACTTGTGTTGAAGCATCCTCAG
1 AAAAATCTTCTTCTCAAG-AACCAAACAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG
621579 GTAGTGTAGATTCAAAGTTGTGAAATTCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGG
65 GTAGTGTAGATTCAAAGTTGTGAAATTCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGG
621644 TCGAAGTTTTACATAGG
130 TCGAAGTTTTACATAGG
621661 NNNNNNNNNN
Statistics
Matches: 461, Mismatches: 12, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
164 3 0.01
165 157 0.34
166 301 0.65
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (166 bp):
AAAAATCTTCTTCTCAAGAACCAAACAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
TAGTGTAGATTCAAAGTTGTGAAATTCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGT
CGAAGTTTTACATAGGAATATATAAGGTAAATCTTT
Found at i:621621 original size:331 final size:332
Alignment explanation
Indices: 621018--621660 Score: 1125
Period size: 331 Copynumber: 1.9 Consensus size: 332
621008 AGATATTTTC
621018 AAAAATCTTCTTCTCAAGAACCAGAAAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAAGAACCAGAAAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
*
621083 TAGTGTAGATTCAAAGTTGTGAAATTCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGT
66 TAGTGTAGACTCAAAGTTGTGAAATTCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGT
*
621148 CGAAGTTTTACATAGGAATATATAAGGTAAATCTTTAAAAATCTTCTTCTCAAGAACCAGAAAGC
131 CGAAGTTTTACATAGGAATATATAAGGTAAATCTTTAAAAATCTTCTCCTCAAGAACCAGAAAGC
621213 CAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAATGTAGATTCAAAGTTGTGAAATTCAT
196 CAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAATGTAGATTCAAAGTTGTGAAATTCAT
621278 GACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTTACATAGGAATATATAAGGTA
261 GACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTTACATAGGAATATATAAGGTA
621343 AATCTTT
326 AATCTTT
* * * *
621350 AAAAATCTTCTTCTCAGGAACTA-AACAGCCAGGAAAGCTGAAACTTGTGTTGAAGCTTCCTCAG
1 AAAAATCTTCTTCTCAAGAACCAGAA-AGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG
621414 GTAGTGTAGACTCAAAGTTGTGAAATTCATGACCCCCGGGGGTAGGGTGGGGCCACAAT-GGGGG
65 GTAGTGTAGACTCAAAGTTGTGAAATTCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGG
* *
621478 TCGAAGTTTTACATAGGAATATAT-AGAGTAAATCTTTAATAATCTTCTCCTC-AGAAACTA-AA
130 TCGAAGTTTTACATAGGAATATATAAG-GTAAATCTTTAAAAATCTTCTCCTCAAG-AACCAGAA
* *
621540 CAGCCAGGAAAGCTGAAACTTGTGTTGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAT
193 -AGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAATGTAGATTCAAAGTTGTGAAAT
621605 TCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTTACATAGG
257 TCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTTACATAGG
621661 NNNNNNNNNN
Statistics
Matches: 297, Mismatches: 10, Indels: 9
0.94 0.03 0.03
Matches are distributed among these distances:
330 6 0.02
331 176 0.59
332 115 0.39
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (332 bp):
AAAAATCTTCTTCTCAAGAACCAGAAAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
TAGTGTAGACTCAAAGTTGTGAAATTCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGT
CGAAGTTTTACATAGGAATATATAAGGTAAATCTTTAAAAATCTTCTCCTCAAGAACCAGAAAGC
CAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAATGTAGATTCAAAGTTGTGAAATTCAT
GACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTTACATAGGAATATATAAGGTA
AATCTTT
Found at i:622991 original size:40 final size:40
Alignment explanation
Indices: 622947--623026 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
622937 AAGTGTGCGG
*
622947 TTATCCCTACTTGTGTTAACGTTGGTACCTGTTGAGTTGT
1 TTATCCCTACTTGCGTTAACGTTGGTACCTGTTGAGTTGT
622987 TTATCCCTACTTGCGTTAACGTTGGTACCTGTTGAGTTGT
1 TTATCCCTACTTGCGTTAACGTTGGTACCTGTTGAGTTGT
623027 GTAGGTGTGC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.15, C:0.19, G:0.23, T:0.44
Consensus pattern (40 bp):
TTATCCCTACTTGCGTTAACGTTGGTACCTGTTGAGTTGT
Found at i:626555 original size:166 final size:166
Alignment explanation
Indices: 626281--627054 Score: 1110
Period size: 166 Copynumber: 4.7 Consensus size: 166
626271 GTGAATATGC
* * * * *
626281 AAAATAAGCAAAGTCGA-CATTTAACAGAAAGCTGGA-ATCCGATTGGTACAGAAATATATCCCA
1 AAAATAAACAAAGTC-ATCATTTAACAGGAAG-TTGACGTCCGATTGGTACAAAAATATATCCCA
*
626344 CAATATGGCATGCCAAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAATAGCTGCTGA
64 CGATATGGCATGCCAAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAATAGCTGCTGA
* *
626409 GAAATCTTTGACAAAAATTTGTTTAAAAAATTTTGGCT-
129 GAAATCTTTGACGAAAATTTGTTT-GAAAATTTTGGCTA
*
626447 AAAATAAACAAAGT-ACTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCAT
1 AAAATAAACAAAGTCA-TCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCAC
** * *
626511 GATATGGCATGCCTTAACAAACAGTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAG
65 GATATGGCATGCCAAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAG
* *
626576 AAATCTTTGACGAAAGTTTGTTCGAAAATTTTGGCTA
130 AAATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTA
* * *
626613 AAAATAAACAAAGTCATTATTTAACAGGAAGTTGACGTCCGATTGATAAAAAAATATATCCCACG
1 AAAATAAACAAAGTCATCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
* * * * *
626678 ATATGACATGCCTATACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAG-TAGCTGAG
66 ATATGGCATGCCAAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAATAGCT-GCTGAG
* ** *
626742 AAATCTTTGATGGTAATTTGTTTGAAAATGTTGGCTA
130 AAATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTA
*
626779 AAAATAAACAAAGTCATCATTTAACAGGAAGTTGACGCCCGATTGGTACAAAAATATATCCCAC-
1 AAAATAAACAAAGTCATCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
* * * *
626843 ATTATGGCTTGCCTAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAAGAGTTGCTGAG
66 A-TATGGCATGCCAAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAG
*
626908 AAATCTTTGACGAAAATTTGTTTGAAAATTTTGGTTAA
130 AAATCTTTGACGAAAATTTGTTTGAAAATTTTGGCT-A
* * *
626946 AAAATAAGCAAAGTCATCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCATG
1 AAAATAAACAAAGTCATCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
*
627011 ATATGGCATGCCAAAACAAATAGTGTGTTAAAATTTCCAGCATC
66 ATATGGCATGCCAAAACAAATAGTGTGTTAAAATTTCAAGCATC
627055 ATTCGGAGCG
Statistics
Matches: 546, Mismatches: 52, Indels: 19
0.88 0.08 0.03
Matches are distributed among these distances:
164 1 0.00
165 17 0.03
166 424 0.78
167 103 0.19
168 1 0.00
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (166 bp):
AAAATAAACAAAGTCATCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
ATATGGCATGCCAAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGA
AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTA
Found at i:628771 original size:47 final size:47
Alignment explanation
Indices: 628720--628829 Score: 177
Period size: 47 Copynumber: 2.3 Consensus size: 47
628710 TTGAATGACT
*
628720 GTAGTGACATAGTCCTTAGTACATTAATACTTACAGCTGGAGTGTAG
1 GTAGTGACATAGTCCTTAGTACATTAACACTTACAGCTGGAGTGTAG
* *
628767 GTAGTTG-CATAGTCCTTAGTACATTAACACTTACCGCTGGAGTGTAT
1 GTAG-TGACATAGTCCTTAGTACATTAACACTTACAGCTGGAGTGTAG
628814 GTAGTGACATAGTCCT
1 GTAGTGACATAGTCCT
628830 CCCCTGATGA
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
46 2 0.03
47 54 0.93
48 2 0.03
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (47 bp):
GTAGTGACATAGTCCTTAGTACATTAACACTTACAGCTGGAGTGTAG
Found at i:631078 original size:15 final size:15
Alignment explanation
Indices: 631058--631087 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
631048 GTTTATTTGA
631058 TTTGGTGGAACTTGC
1 TTTGGTGGAACTTGC
631073 TTTGGTGGAACTTGC
1 TTTGGTGGAACTTGC
631088 GGCAAACTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.13, G:0.33, T:0.40
Consensus pattern (15 bp):
TTTGGTGGAACTTGC
Found at i:632147 original size:31 final size:31
Alignment explanation
Indices: 632109--632170 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
632099 TATTTTCATA
*
632109 GGGTACGTTTTCTCTTGGAGAAAACGTACCC
1 GGGTACGTTTTCTCCTGGAGAAAACGTACCC
632140 GGGTACGTTTTCTCCTGGAGAAAACGTACCC
1 GGGTACGTTTTCTCCTGGAGAAAACGTACCC
632171 TAGAGATTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.27
Consensus pattern (31 bp):
GGGTACGTTTTCTCCTGGAGAAAACGTACCC
Found at i:632197 original size:16 final size:16
Alignment explanation
Indices: 632178--632225 Score: 96
Period size: 16 Copynumber: 3.0 Consensus size: 16
632168 CCCTAGAGAT
632178 TGGGTACGTTTTCTCC
1 TGGGTACGTTTTCTCC
632194 TGGGTACGTTTTCTCC
1 TGGGTACGTTTTCTCC
632210 TGGGTACGTTTTCTCC
1 TGGGTACGTTTTCTCC
632226 AGCATTCAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.06, C:0.25, G:0.25, T:0.44
Consensus pattern (16 bp):
TGGGTACGTTTTCTCC
Found at i:637800 original size:161 final size:161
Alignment explanation
Indices: 637424--637904 Score: 581
Period size: 161 Copynumber: 3.0 Consensus size: 161
637414 CCACCAACAG
637424 TTTCCGTTCATTTTCTTTGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTATCA
1 TTTCCGTTCATTTTCTTTGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTATCA
* * * ** * **
637489 TGATAATATCTAGGTAAAGTTTGAAATTTGG-AACATCGAGCAATTTTTGACAGAGTTATGACCC
66 TGATAATATCTAGGTCAAGTTTGATATTGGGTATGATAGAGCAATTTTCAACAGAGTTATGACCC
*
637553 TTGAACGTAGAAAAATTCCAGCTATTTGCAG
131 TTGAACGTAGAAAAATTCCAGCTATTTGCAA
* * * * *
637584 TTTCTGTTCATTTTCTTTGCAGAGGATAAAC-TGATTGAAATAAAATTTTGTATACAGATTTATC
1 TTTCCGTTCATTTTCTTTGCAGAGGATGAACAT-ATTGAAATGAAATTTGGTATACAGGTTTATC
* * * *
637648 ATGATAATATCTAAGTCAAGTTTGATATTGGGTATGATTGAGCAATTTTCAACAGAGTTATGGCT
65 ATGATAATATCTAGGTCAAGTTTGATATTGGGTATGATAGAGCAATTTTCAACAGAGTTATGACC
* * *
637713 CTTGGACGTAGAAGAATTCCAGTTATTTGCAA
130 CTTGAACGTAGAAAAATTCCAGCTATTTGCAA
* * * * *
637745 TTTCCGCTCATTTTCTTCGCAGAGGGTGCACATATTGATATGAAATTTGGTATACAGGTTTATC-
1 TTTCCGTTCATTTTCTTTGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTATCA
* * * * * *
637809 TAATTAATGTCTAGGTCAACTTTGATTTTGGGTATGAAAGAGCAATTTTCAACAGAGTTATGCCC
66 TGA-TAATATCTAGGTCAAGTTTGATATTGGGTATGATAGAGCAATTTTCAACAGAGTTATGACC
* * * * **
637874 CATGGACTTAAAAAAATTCCAAATATTTGCA
130 CTTGAACGTAGAAAAATTCCAGCTATTTGCA
637905 TTTGGAATTC
Statistics
Matches: 272, Mismatches: 45, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
159 1 0.00
160 87 0.32
161 183 0.67
162 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (161 bp):
TTTCCGTTCATTTTCTTTGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTATCA
TGATAATATCTAGGTCAAGTTTGATATTGGGTATGATAGAGCAATTTTCAACAGAGTTATGACCC
TTGAACGTAGAAAAATTCCAGCTATTTGCAA
Found at i:637939 original size:1 final size:1
Alignment explanation
Indices: 637935--637982 Score: 78
Period size: 1 Copynumber: 48.0 Consensus size: 1
637925 TTTGTGGATG
* *
637935 TTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTGTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
637983 CTCTTTTATT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.00, C:0.00, G:0.04, T:0.96
Consensus pattern (1 bp):
T
Found at i:637948 original size:26 final size:27
Alignment explanation
Indices: 637919--637976 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 27
637909 GAATTCATTC
637919 TTTTTCTTTGTGGATGTTTTTTTTTT-
1 TTTTTCTTTGTGGATGTTTTTTTTTTG
* * ***
637945 TTTTTTTTTTTTTTTGTTTTTTTTTTG
1 TTTTTCTTTGTGGATGTTTTTTTTTTG
637972 TTTTT
1 TTTTT
637977 TTTTTTCTCT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.86
Consensus pattern (27 bp):
TTTTTCTTTGTGGATGTTTTTTTTTTG
Found at i:637977 original size:26 final size:26
Alignment explanation
Indices: 637933--637982 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
637923 TCTTTGTGGA
*
637933 TGTTTTTTTTTTTTTTTTTTTTTTTT
1 TGTTTTTTTTTTGTTTTTTTTTTTTT
637959 TGTTTTTTTTTTGTTTTTTTTTTT
1 TGTTTTTTTTTTGTTTTTTTTTTT
637983 CTCTTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.06, T:0.94
Consensus pattern (26 bp):
TGTTTTTTTTTTGTTTTTTTTTTTTT
Found at i:640182 original size:38 final size:39
Alignment explanation
Indices: 640131--640208 Score: 113
Period size: 38 Copynumber: 2.0 Consensus size: 39
640121 ATATATACAA
*** *
640131 GTATTACAATAAATGGCTTTTTT-CAATTATTGAAATAT
1 GTATTACAATAAATAAATTTTTTAAAATTATTGAAATAT
640169 GTATTACAATAAATAAATTTTTTAAAATTATTGAAATAT
1 GTATTACAATAAATAAATTTTTTAAAATTATTGAAATAT
640208 G
1 G
640209 CATGCATGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
38 20 0.57
39 15 0.43
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (39 bp):
GTATTACAATAAATAAATTTTTTAAAATTATTGAAATAT
Found at i:644547 original size:46 final size:46
Alignment explanation
Indices: 644480--644567 Score: 167
Period size: 46 Copynumber: 1.9 Consensus size: 46
644470 TCTGTTAAAG
644480 ATACAGGCATTGTTTATCATATGTACAACAATTATAAAAAAAATTA
1 ATACAGGCATTGTTTATCATATGTACAACAATTATAAAAAAAATTA
*
644526 ATACAGGCATTGTTTATCATATGTACACCAATTATAAAAAAA
1 ATACAGGCATTGTTTATCATATGTACAACAATTATAAAAAAA
644568 TAATTAATTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.32
Consensus pattern (46 bp):
ATACAGGCATTGTTTATCATATGTACAACAATTATAAAAAAAATTA
Found at i:644888 original size:20 final size:20
Alignment explanation
Indices: 644860--644897 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
644850 ATATTTGTGC
*
644860 CCCCTGCTTAAGGAAAGAGT
1 CCCCAGCTTAAGGAAAGAGT
644880 CCCCAGCTTAAGGAAAGA
1 CCCCAGCTTAAGGAAAGA
644898 AAGAGATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.26, G:0.24, T:0.16
Consensus pattern (20 bp):
CCCCAGCTTAAGGAAAGAGT
Found at i:653530 original size:2 final size:2
Alignment explanation
Indices: 653523--653579 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
653513 AGAATATTTG
653523 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
653565 GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA G
653580 CCTTGACATG
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:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:660274 original size:6 final size:6
Alignment explanation
Indices: 660263--660315 Score: 79
Period size: 6 Copynumber: 8.8 Consensus size: 6
660253 GTTGGTGTAT
* * *
660263 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAT ATATAT ATATAT
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG
660311 ATATA
1 ATATA
660316 ACACAATTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (6 bp):
ATATAG
Found at i:660831 original size:2 final size:2
Alignment explanation
Indices: 660824--660891 Score: 111
Period size: 2 Copynumber: 34.5 Consensus size: 2
660814 AAACAAATAA
* *
660824 TC TC TC TC TC TC TC TT TC TC TC TT TC TC TC TC TC TC -C TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
660865 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 T
660892 GGTATTTTAT
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:663776 original size:79 final size:79
Alignment explanation
Indices: 663645--663883 Score: 471
Period size: 79 Copynumber: 3.0 Consensus size: 79
663635 NNNNNNNNNN
663645 ATATATATATATCTTAAGTGGTGCTTGAAGTTCGACTATAAAATGATTTTTTTTCAATCTTTTTC
1 ATATATATATATCTTAAGTGGTGCTTGAAGTTCGACTATAAAATGATTTTTTTTCAATCTTTTTC
663710 TGAACTTTGTAATA
66 TGAACTTTGTAATA
663724 ATATATATATATCTTAAGTGGTGCTTGAAGTTCGACTATAAAATGATTTTTTTTCAATCTTTTTC
1 ATATATATATATCTTAAGTGGTGCTTGAAGTTCGACTATAAAATGATTTTTTTTCAATCTTTTTC
663789 TGAACTTTGTAATA
66 TGAACTTTGTAATA
663803 ATATATATATATCTTAAGTGGTGCTTGAAGTTCGACTATAAAATGA-TTTTTTTCAATCTTTTTC
1 ATATATATATATCTTAAGTGGTGCTTGAAGTTCGACTATAAAATGATTTTTTTTCAATCTTTTTC
663867 TGAACTTTGTAATA
66 TGAACTTTGTAATA
663881 ATA
1 ATA
663884 AAAATAGACA
Statistics
Matches: 160, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
78 35 0.22
79 125 0.78
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (79 bp):
ATATATATATATCTTAAGTGGTGCTTGAAGTTCGACTATAAAATGATTTTTTTTCAATCTTTTTC
TGAACTTTGTAATA
Found at i:671583 original size:30 final size:30
Alignment explanation
Indices: 671547--671633 Score: 147
Period size: 30 Copynumber: 2.9 Consensus size: 30
671537 ATACGTTGCC
*
671547 GTCCAATAGATCGCAGTCTATTGACTGGCG
1 GTCCAATAGATCGCAGTCTATTGACCGGCG
*
671577 GTCCAATAGATCACAGTCTATTGACCGGCG
1 GTCCAATAGATCGCAGTCTATTGACCGGCG
*
671607 GTCTAATAGATCGCAGTCTATTGACCG
1 GTCCAATAGATCGCAGTCTATTGACCG
671634 ACAATTCAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.26
Consensus pattern (30 bp):
GTCCAATAGATCGCAGTCTATTGACCGGCG
Found at i:671645 original size:30 final size:29
Alignment explanation
Indices: 671550--671648 Score: 117
Period size: 30 Copynumber: 3.3 Consensus size: 29
671540 CGTTGCCGTC
* *
671550 CAATAGATCGCAGTCTATTGACTGGCGGTC
1 CAATAGATCGCAGTCTATTGACCGGC-GTT
* *
671580 CAATAGATCACAGTCTATTGACCGGCGGT
1 CAATAGATCGCAGTCTATTGACCGGCGTT
* *
671609 CTAATAGATCGCAGTCTATTGACCGACAATT
1 C-AATAGATCGCAGTCTATTGACCGGC-GTT
671640 CAATAGATC
1 CAATAGATC
671649 ACTTTCAAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
29 2 0.03
30 55 0.93
31 2 0.03
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.26
Consensus pattern (29 bp):
CAATAGATCGCAGTCTATTGACCGGCGTT
Found at i:683938 original size:2 final size:2
Alignment explanation
Indices: 683931--684009 Score: 149
Period size: 2 Copynumber: 39.5 Consensus size: 2
683921 TGAAGTTTTA
683931 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
*
683973 AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
684010 ANGTTTTAAA
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:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:684200 original size:2 final size:2
Alignment explanation
Indices: 684176--684223 Score: 61
Period size: 2 Copynumber: 26.5 Consensus size: 2
684166 TTGCGTATTT
684176 GA GA GA G- GA G- GA -A GA G- GA G- 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
684213 GA GA GA GA GA G
1 GA GA GA GA GA G
684224 TATGTTATGT
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
1 5 0.12
2 36 0.88
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
GA
Found at i:684222 original size:12 final size:10
Alignment explanation
Indices: 684176--684223 Score: 55
Period size: 9 Copynumber: 4.7 Consensus size: 10
684166 TTGCGTATTT
684176 GAGAGAGGAG
1 GAGAGAGGAG
684186 GA-AGAGGAG
1 GAGAGAGGAG
684195 GAGAGA-GAG
1 GAGAGAGGAG
684204 AGAGAGAGAGAG
1 -GAGAGAG-GAG
684216 AGAGAGAG
1 -GAGAGAG
684224 TATGTTATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
9 12 0.35
10 11 0.32
12 11 0.32
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (10 bp):
GAGAGAGGAG
Found at i:685782 original size:2 final size:2
Alignment explanation
Indices: 685775--685849 Score: 123
Period size: 2 Copynumber: 37.5 Consensus size: 2
685765 ATTTCAATAT
*
685775 GA GA GA GA GA GA GC 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
* *
685817 GA GA GA GA AA GA GA GA GA GA GA AA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
685850 CATTACACAT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.01, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:697370 original size:41 final size:41
Alignment explanation
Indices: 697308--697386 Score: 133
Period size: 41 Copynumber: 1.9 Consensus size: 41
697298 AAGCCTGATC
697308 AAGGGGTAAGTTTCAGAATCAGGTTCAAAGATGATCAGTTT
1 AAGGGGTAAGTTTCAGAATCAGGTTCAAAGATGATCAGTTT
*
697349 AAGGGGTAAGGTTT-AGGATCAGGTTCAAAGATGATCAG
1 AAGGGGTAA-GTTTCAGAATCAGGTTCAAAGATGATCAG
697387 CATTATAGAG
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
41 32 0.89
42 4 0.11
ACGTcount: A:0.34, C:0.09, G:0.30, T:0.27
Consensus pattern (41 bp):
AAGGGGTAAGTTTCAGAATCAGGTTCAAAGATGATCAGTTT
Found at i:697413 original size:42 final size:41
Alignment explanation
Indices: 697311--697528 Score: 147
Period size: 42 Copynumber: 5.2 Consensus size: 41
697301 CCTGATCAAG
* *
697311 GGGTAAGTT-TCAGAATCAGGTTCAAAGATGATCAG-TTTAA
1 GGGTAAGTTAT-AGGATCAGGTTCAAAGATGATCAGCATTAA
697351 GGGGTAAGGTT-TAGGATCAGGTTCAAAGATGATCAGCATTATA
1 -GGGTAA-GTTATAGGATCAGGTTCAAAGATGATCAGCATTA-A
* * * * ** *
697394 GAGTAAGTTATAGGATCAGGTTTAAATAAGATTGGCATCAAA
1 GGGTAAGTTATAGGATCAGGTTCAAAGATGATCAGCAT-TAA
* * * * *
697436 GGGGAAGTAATAGGATCAGGTTCAGAGATAATCAGCATCAAA
1 GGGTAAGTTATAGGATCAGGTTCAAAGATGATCAGCAT-TAA
* ** * * * *
697478 GGCTAAGGTT-TATTATTAGGTTCAAAGATGGTAAGCATCAA
1 GGGTAA-GTTATAGGATCAGGTTCAAAGATGATCAGCATTAA
697519 GGGGTAAGTT
1 -GGGTAAGTT
697529 GTATGATGTG
Statistics
Matches: 139, Mismatches: 31, Indels: 14
0.76 0.17 0.08
Matches are distributed among these distances:
41 37 0.27
42 98 0.71
43 4 0.03
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.28
Consensus pattern (41 bp):
GGGTAAGTTATAGGATCAGGTTCAAAGATGATCAGCATTAA
Found at i:700943 original size:2 final size:2
Alignment explanation
Indices: 700938--700979 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
700928 ATATATATAT
700938 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
700980 ATTTTCAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:704032 original size:2 final size:2
Alignment explanation
Indices: 704025--704061 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
704015 TTTGAATTTT
704025 GA GA GA GA GA GA GA GA GA GA GA GA GA 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
704062 GGGGGGGGGT
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:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:711640 original size:13 final size:13
Alignment explanation
Indices: 711622--711676 Score: 60
Period size: 12 Copynumber: 4.2 Consensus size: 13
711612 TAAATATTGG
711622 AATATATCTGAAA
1 AATATATCTGAAA
711635 AATATATCT-AAA
1 AATATATCTGAAA
* *
711647 AATAAAGCTG-AA
1 AATATATCTGAAA
711659 AATATAATCTGAATA
1 AATAT-ATCTGAA-A
711674 AAT
1 AAT
711677 TAGTTGTACA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
12 16 0.47
13 13 0.38
14 1 0.03
15 4 0.12
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.29
Consensus pattern (13 bp):
AATATATCTGAAA
Found at i:713056 original size:2 final size:2
Alignment explanation
Indices: 713051--713085 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
713041 AAAAAACATC
713051 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
713086 ATAGTCGTAA
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:717485 original size:49 final size:49
Alignment explanation
Indices: 717414--717509 Score: 192
Period size: 49 Copynumber: 2.0 Consensus size: 49
717404 TTAAGTTTAT
717414 TTTTTATTTTCTGAATGAACAAATCGCATGTTTATTGCATTTGACATAA
1 TTTTTATTTTCTGAATGAACAAATCGCATGTTTATTGCATTTGACATAA
717463 TTTTTATTTTCTGAATGAACAAATCGCATGTTTATTGCATTTGACAT
1 TTTTTATTTTCTGAATGAACAAATCGCATGTTTATTGCATTTGACAT
717510 TATAAAAAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.46
Consensus pattern (49 bp):
TTTTTATTTTCTGAATGAACAAATCGCATGTTTATTGCATTTGACATAA
Found at i:725952 original size:2 final size:2
Alignment explanation
Indices: 725945--725983 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
725935 TAAGCTTGGT
725945 GA GA GA GA GA GA GA GA GA GA GA GA GA GA 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 GA G
725984 TTCTTGGCGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:731975 original size:36 final size:36
Alignment explanation
Indices: 731934--732008 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
731924 GCTTTCAAAT
*
731934 AATGACAAGTTCTGTGAAACTCTGTTTGAGAATAAA
1 AATGACAAGTTCTGTGAAACTCTGTTTGAGAAAAAA
731970 AATGACAAGTTCTGTGAAACTCTGTTTGAGAAAAAA
1 AATGACAAGTTCTGTGAAACTCTGTTTGAGAAAAAA
732006 AAT
1 AAT
732009 CATCATATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29
Consensus pattern (36 bp):
AATGACAAGTTCTGTGAAACTCTGTTTGAGAAAAAA
Found at i:732548 original size:21 final size:21
Alignment explanation
Indices: 732514--732593 Score: 99
Period size: 21 Copynumber: 3.8 Consensus size: 21
732504 AATTTAATGC
* * *
732514 TATGCTATGGTATGCGATTT-
1 TATGATATGCTATGAGATTTG
732534 TAATGATATGCTATGAGATTTG
1 T-ATGATATGCTATGAGATTTG
*
732556 TATGGTATGCTATGAGATTTG
1 TATGATATGCTATGAGATTTG
*
732577 TATGCTATGCTATGAGA
1 TATGATATGCTATGAGA
732594 AATTGAAATG
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
20 1 0.02
21 51 0.96
22 1 0.02
ACGTcount: A:0.26, C:0.07, G:0.25, T:0.41
Consensus pattern (21 bp):
TATGATATGCTATGAGATTTG
Found at i:732810 original size:10 final size:10
Alignment explanation
Indices: 732792--732825 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
732782 AATAATGTTG
*
732792 TATGCTATGC
1 TATGGTATGC
732802 TATGGTATGC
1 TATGGTATGC
*
732812 TATGGTATGA
1 TATGGTATGC
732822 TATG
1 TATG
732826 ACGAATGCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.24, C:0.09, G:0.26, T:0.41
Consensus pattern (10 bp):
TATGGTATGC
Found at i:732811 original size:15 final size:15
Alignment explanation
Indices: 732791--732825 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
732781 AAATAATGTT
732791 GTATGCTATGCTATG
1 GTATGCTATGCTATG
*
732806 GTATGCTATGGTATG
1 GTATGCTATGCTATG
*
732821 ATATG
1 GTATG
732826 ACGAATGCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.23, C:0.09, G:0.29, T:0.40
Consensus pattern (15 bp):
GTATGCTATGCTATG
Found at i:732883 original size:21 final size:21
Alignment explanation
Indices: 732850--732904 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
732840 ATGAGATTGT
*
732850 ATGCTATGGTATGAGATTCCA
1 ATGCTATGCTATGAGATTCCA
* *
732871 ATGCTTTGCTATGAGATTTCA
1 ATGCTATGCTATGAGATTCCA
732892 ATGCTATGCTATG
1 ATGCTATGCTATG
732905 CTATGCTGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (21 bp):
ATGCTATGCTATGAGATTCCA
Found at i:735794 original size:17 final size:17
Alignment explanation
Indices: 735772--735808 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
735762 AGCCTGGTTT
735772 AAACAAATTTGAATATC
1 AAACAAATTTGAATATC
735789 AAACAAATTTGAATATC
1 AAACAAATTTGAATATC
735806 AAA
1 AAA
735809 AAGTCGACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.57, C:0.11, G:0.05, T:0.27
Consensus pattern (17 bp):
AAACAAATTTGAATATC
Found at i:746282 original size:21 final size:21
Alignment explanation
Indices: 746258--746349 Score: 107
Period size: 21 Copynumber: 4.4 Consensus size: 21
746248 ATCTGCCACC
746258 ACTTGTCAGATAATTATGTCG
1 ACTTGTCAGATAATTATGTCG
*
746279 ACTTGTCAGAT-CTTGATGTCG
1 ACTTGTCAGATAATT-ATGTCG
746300 ACTTGTCAGATAATTATGTTC-
1 ACTTGTCAGATAATTATG-TCG
* ** *
746321 ACTTGTCAGTTCTTTAAGTCG
1 ACTTGTCAGATAATTATGTCG
746342 ACTTGTCA
1 ACTTGTCA
746350 TTTATTTACG
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
20 4 0.07
21 53 0.87
22 4 0.07
ACGTcount: A:0.24, C:0.17, G:0.18, T:0.40
Consensus pattern (21 bp):
ACTTGTCAGATAATTATGTCG
Found at i:746305 original size:42 final size:42
Alignment explanation
Indices: 746258--746349 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
746248 ATCTGCCACC
*
746258 ACTTGTCAGATAATTATG-TCGACTTGTCAGATCTTGATGTCG
1 ACTTGTCAGATAATTATGTTC-ACTTGTCAGATCTTGAAGTCG
* *
746300 ACTTGTCAGATAATTATGTTCACTTGTCAGTTCTTTAAGTCG
1 ACTTGTCAGATAATTATGTTCACTTGTCAGATCTTGAAGTCG
746342 ACTTGTCA
1 ACTTGTCA
746350 TTTATTTACG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
42 44 0.96
43 2 0.04
ACGTcount: A:0.24, C:0.17, G:0.18, T:0.40
Consensus pattern (42 bp):
ACTTGTCAGATAATTATGTTCACTTGTCAGATCTTGAAGTCG
Found at i:746450 original size:21 final size:21
Alignment explanation
Indices: 746426--746585 Score: 187
Period size: 21 Copynumber: 7.7 Consensus size: 21
746416 AATAATATTT
**
746426 TCTGACAAGTCGACATAAGGA
1 TCTGACAAGTCGACATAATTA
*
746447 TCTGACAAGTCGACATAATCA
1 TCTGACAAGTCGACATAATTA
*** *
746468 TCTTTTAAGTCGATATAATTA
1 TCTGACAAGTCGACATAATTA
*
746489 TTTGACAAGTCGACATAATTA
1 TCTGACAAGTCGACATAATTA
746510 TCTGACAAGTCGACATAATTA
1 TCTGACAAGTCGACATAATTA
* * *
746531 TTTGACAAGACGACATAA-CA
1 TCTGACAAGTCGACATAATTA
* * *
746551 TCTGACAAGACAACATCATTA
1 TCTGACAAGTCGACATAATTA
746572 TCTGACAAGTCGAC
1 TCTGACAAGTCGAC
746586 TTACAATATA
Statistics
Matches: 116, Mismatches: 22, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
20 16 0.14
21 100 0.86
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (21 bp):
TCTGACAAGTCGACATAATTA
Found at i:746685 original size:42 final size:42
Alignment explanation
Indices: 746637--746721 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
746627 TTATTTTTTC
* *
746637 TGTCAGATAATTATGTTAACTTGTCAGATCTTTATGTCGACT
1 TGTCAGATAATTATGTAAACTTGTCAGATATTTATGTCGACT
*
746679 TGTCAGATGATTATGTAAACTTGTCAGATATTTATGTCGACT
1 TGTCAGATAATTATGTAAACTTGTCAGATATTTATGTCGACT
746721 T
1 T
746722 ATATGGTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (42 bp):
TGTCAGATAATTATGTAAACTTGTCAGATATTTATGTCGACT
Found at i:746721 original size:21 final size:21
Alignment explanation
Indices: 746637--746721 Score: 100
Period size: 21 Copynumber: 4.0 Consensus size: 21
746627 TTATTTTTTC
* *
746637 TGTCAGATAATTATGTTAACT
1 TGTCAGATATTTATGTCAACT
* *
746658 TGTCAGATCTTTATGTCGACT
1 TGTCAGATATTTATGTCAACT
*
746679 TGTCAGATGA-TTATGTAAACT
1 TGTCAGAT-ATTTATGTCAACT
*
746700 TGTCAGATATTTATGTCGACT
1 TGTCAGATATTTATGTCAACT
746721 T
1 T
746722 ATATGGTATT
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
20 1 0.02
21 52 0.98
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (21 bp):
TGTCAGATATTTATGTCAACT
Found at i:746840 original size:21 final size:21
Alignment explanation
Indices: 746815--746908 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
746805 ATGGTTATTT
*
746815 TCTGACAAGTCAACATAAAGA
1 TCTGACAAGTCAACATAAATA
**
746836 TCTGACAAGTTGACATAAATA
1 TCTGACAAGTCAACATAAATA
*
746857 TCTGACAAGTCGACAT-AATCA
1 TCTGACAAGTCAACATAAAT-A
* * * *
746878 TATGAGAAGTTAACATAATTA
1 TCTGACAAGTCAACATAAATA
746899 TCTGACAAGT
1 TCTGACAAGT
746909 GGTGGCAGAT
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
20 3 0.05
21 55 0.92
22 2 0.03
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.27
Consensus pattern (21 bp):
TCTGACAAGTCAACATAAATA
Found at i:746862 original size:42 final size:42
Alignment explanation
Indices: 746815--746908 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 42
746805 ATGGTTATTT
* * *
746815 TCTGACAAGTCAACATAAAGATCTGACAAGTTGACATAAATA
1 TCTGACAAGTCAACATAAACATATGACAAGTTAACATAAATA
* * * *
746857 TCTGACAAGTCGACATAATCATATGAGAAGTTAACATAATTA
1 TCTGACAAGTCAACATAAACATATGACAAGTTAACATAAATA
746899 TCTGACAAGT
1 TCTGACAAGT
746909 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:0.15, T:0.27
Consensus pattern (42 bp):
TCTGACAAGTCAACATAAACATATGACAAGTTAACATAAATA
Found at i:747425 original size:12 final size:11
Alignment explanation
Indices: 747402--747433 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
747392 AATTATAGAT
747402 GATAAAAAATA
1 GATAAAAAATA
747413 GATAAAAACATA
1 GATAAAAA-ATA
747425 GATAAAAAA
1 GATAAAAAA
747434 AAATAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.72, C:0.03, G:0.09, T:0.16
Consensus pattern (11 bp):
GATAAAAAATA
Done.