Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold107
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2327068
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 25 characters in sequence are not A, C, G, or T
File 4 of 15
Found at i:426696 original size:79 final size:79
Alignment explanation
Indices: 426559--426733 Score: 233
Period size: 79 Copynumber: 2.2 Consensus size: 79
426549 AACAACGGGG
* * * * * * *
426559 TTAGAGTATCCCTGATTATGGAAAATCGGTGTTCTGGAAATAAAATCGAGGTTTGAGTATCCCCT
1 TTAGAGTATCCTTGATTATAGAAAATCAGTATTCTGAAAATAAAAACGAGGTTGGAGTATCCCCT
*
426624 CAAAAATAATAGGA
66 CAAAAATAACAGGA
* * *
426638 TTGGAGTATCCTTGATTATAGAAAATCAGTATTTTGAAAATAAAAACGGGGTTGGAGTATCCCCT
1 TTAGAGTATCCTTGATTATAGAAAATCAGTATTCTGAAAATAAAAACGAGGTTGGAGTATCCCCT
*
426703 CAAAAATAACAGGG
66 CAAAAATAACAGGA
*
426717 TTAGAGTATCCTCGATT
1 TTAGAGTATCCTTGATT
426734 GTGAAAAATC
Statistics
Matches: 82, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
79 82 1.00
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (79 bp):
TTAGAGTATCCTTGATTATAGAAAATCAGTATTCTGAAAATAAAAACGAGGTTGGAGTATCCCCT
CAAAAATAACAGGA
Found at i:426767 original size:79 final size:79
Alignment explanation
Indices: 426556--426780 Score: 226
Period size: 79 Copynumber: 2.8 Consensus size: 79
426546 GATAACAACG
* * * * *
426556 GGGTTAGAGTATCC-CTGATTATGGAAAATCGGTG-TTCTGGAAATAAAATCGAGGTTTGAGTAT
1 GGGTTAGAGTATCCTC-GATTATGAAAAATCGATGATT-TAGAAATAAAATCGGGGTTGGAGTAT
*
426619 CCCCTCAAAAATAATA
64 CCCCTCAAAAATAACA
* * * * *
426635 GGATTGGAGTATCCTTGATTAT-AGAAAATC-A-GTATTTTGAAAATAAAAACGGGGTTGGAGTA
1 GGGTTAGAGTATCCTCGATTATGA-AAAATCGATG-ATTTAG-AAATAAAATCGGGGTTGGAGTA
426697 TCCCCTCAAAAATAACA
63 TCCCCTCAAAAATAACA
* ** * *
426714 GGGTTAGAGTATCCTCGATTGTGAAAAATCGATGATTTAGAAATAAGGTCGGGGTTGAACTATCC
1 GGGTTAGAGTATCCTCGATTATGAAAAATCGATGATTTAGAAATAAAATCGGGGTTGGAGTATCC
426779 CC
66 CC
426781 GATTATGAGA
Statistics
Matches: 118, Mismatches: 20, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
77 1 0.01
78 2 0.02
79 107 0.91
80 7 0.06
81 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (79 bp):
GGGTTAGAGTATCCTCGATTATGAAAAATCGATGATTTAGAAATAAAATCGGGGTTGGAGTATCC
CCTCAAAAATAACA
Found at i:426785 original size:130 final size:130
Alignment explanation
Indices: 426651--426889 Score: 345
Period size: 130 Copynumber: 1.8 Consensus size: 130
426641 GAGTATCCTT
*
426651 GATTAT-AGAAAATCAGTATTTTGAAAATAAAAACGGGGTTGGAGTATCCCCTCAAAAATAACAG
1 GATTATGAG-AAATCAATATTTTGAAAATAAAAACGGGGTTGGAGTATCCCCTCAAAAATAACAG
* *
426715 GGTTAGAGTATCCTCGATTGTGAAAAATCGATGATTTAGAAATAAGGTCGGGGTTGAACTATCCC
65 GGTTAGAGTATCCCCGATTATGAAAAATCGATGATTTAGAAATAAGGTCGGGGTTGAACTATCCC
426780 C
130 C
* * * * *
426781 GATTATGAGAAATCAATATTTTGGAAATAAAGATGGGGTTGGAGTATCCCCTCGAAAATAACGGG
1 GATTATGAGAAATCAATATTTTGAAAATAAAAACGGGGTTGGAGTATCCCCTCAAAAATAACAGG
* * * * *
426846 GTTGGAGTATCCCCGATTATGGAAAATTGGTGTTTTAGAAATAA
66 GTTAGAGTATCCCCGATTATGAAAAATCGATGATTTAGAAATAA
426890 AACTGGGGTT
Statistics
Matches: 95, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
130 93 0.98
131 2 0.02
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (130 bp):
GATTATGAGAAATCAATATTTTGAAAATAAAAACGGGGTTGGAGTATCCCCTCAAAAATAACAGG
GTTAGAGTATCCCCGATTATGAAAAATCGATGATTTAGAAATAAGGTCGGGGTTGAACTATCCCC
Found at i:426848 original size:79 final size:78
Alignment explanation
Indices: 426763--427064 Score: 379
Period size: 79 Copynumber: 3.8 Consensus size: 78
426753 GAAATAAGGT
* * * **
426763 CGGGGTTGAACTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGATGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATATTTTGGAAATAAA-ATGGGGTTGGAGTAT
426828 CCCCTCGAAAATAA
65 CCCCTCGAAAATAA
* * * *
426842 CGGGGTTGGAGTATCCCCGATTATGGAAAATTGGTGTTTTAGAAATAAAACTGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATATTTTGGAAATAAAA-TGGGGTTGGAGTAT
*
426907 CCCCTCAAAAATAA
65 CCCCTCGAAAATAA
* * * * **
426921 CGGGGTTGGAGTATCCCCAATTGTGAAAAATTGGTATTTTGGGAATAAAATCGGGGTTATAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATATTTTGGAAATAAAAT-GGGGTTGGAGTAT
*
426986 CCCCTCGGAAATAA
65 CCCCTCGAAAATAA
* * * *
427000 CGGGATTGGAGTATCCCCGATTATGAAAAATTGATGTTTTGGAAATAAAACCGTGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATATTTTGGAAATAAAA-TGGGGTTGGAGTAT
427065 TCCTGAGATG
Statistics
Matches: 190, Mismatches: 30, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
78 2 0.01
79 188 0.99
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATATTTTGGAAATAAAATGGGGTTGGAGTATC
CCCTCGAAAATAA
Found at i:426989 original size:209 final size:207
Alignment explanation
Indices: 426536--426989 Score: 522
Period size: 209 Copynumber: 2.2 Consensus size: 207
426526 GAAAAATTTA
* ** *
426536 ATATTTTGGAGATAACAA-CGGGGTTAGAGTATCCCTGATTATGGAAAATCGGTGTTCTGGAAAT
1 ATATTTTGGA-ATAA-AATCGGGGTTA-AGTATCCCCGATTATGGAAAATCAATATTCTGGAAAT
* * **
426600 AAAATCGAGGTTTGAGTATCCCCTCAAAAATAATAGGATTGGAGTATCCTTGATTATAGAAAATC
63 AAAATCGAGGTTGGAGTATCCCCTCAAAAATAACAGGATTGGAGTATCCCCGATTATAGAAAATC
*
426665 AGTATTTTGAAAATAAAAACGGGGTTGGAGTATCCCCTCAAAAATAACAGGGTTAGAGTATCCTC
128 AGTATTTTGAAAATAAAAACGGGGTTGGAGTATCCCCTCAAAAATAACAGGGTTAGAGTATCCCC
*
426730 GATTGTGAAAAATCG
193 AATTGTGAAAAATCG
* * ** * *
426745 ATGATTTAGAAATAAGGTCGGGGTTGAACTATCCCCGATTAT-GAGAAATCAATATTTTGGAAAT
1 AT-ATTTTGGAATAAAATCGGGGTT-AAGTATCCCCGATTATGGA-AAATCAATATTCTGGAAAT
* * * * *
426809 AAAGAT-GGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGGAAAAT
63 AAA-ATCGAGGTTGGAGTATCCCCTCAAAAATAACAGGATTGGAGTATCCCCGATTATAGAAAAT
** * * *
426873 TGGTGTTTT-AGAAAT-AAAACTGGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATC
127 CAGTATTTTGA-AAATAAAAAC-GGGGTTGGAGTATCCCCTCAAAAATAACAGGGTTAGAGTATC
*
426936 CCCAATTGTGAAAAATTG
190 CCCAATTGTGAAAAATCG
*
426954 GTATTTTGGGAATAAAATCGGGGTTATAGTATCCCC
1 ATATTTT-GGAATAAAATCGGGGTTA-AGTATCCCC
426990 TCGGAAATAA
Statistics
Matches: 203, Mismatches: 33, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
208 13 0.06
209 181 0.89
210 9 0.04
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (207 bp):
ATATTTTGGAATAAAATCGGGGTTAAGTATCCCCGATTATGGAAAATCAATATTCTGGAAATAAA
ATCGAGGTTGGAGTATCCCCTCAAAAATAACAGGATTGGAGTATCCCCGATTATAGAAAATCAGT
ATTTTGAAAATAAAAACGGGGTTGGAGTATCCCCTCAAAAATAACAGGGTTAGAGTATCCCCAAT
TGTGAAAAATCG
Found at i:429422 original size:13 final size:13
Alignment explanation
Indices: 429401--429430 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
429391 GTGAACCCAG
*
429401 AATGTATCGATAC
1 AATGCATCGATAC
429414 AATGCATCGATAC
1 AATGCATCGATAC
429427 AATG
1 AATG
429431 AACAATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.27
Consensus pattern (13 bp):
AATGCATCGATAC
Found at i:430040 original size:40 final size:42
Alignment explanation
Indices: 429996--430096 Score: 127
Period size: 40 Copynumber: 2.4 Consensus size: 42
429986 GTCCTACTTT
* *
429996 TTGAGGACAAAGGAAAAGAG-AATGAAATAG-GTCTTGC-TCC
1 TTGAGGACAAAGGAAAAAAGAAAAGAAA-AGTGTCTTGCTTCC
* *
430036 TTGAGGACAAAGGAAAAAAGAAAAGGAAAGTGTCTTGCTTTC
1 TTGAGGACAAAGGAAAAAAGAAAAGAAAAGTGTCTTGCTTCC
430078 TTGAGGACAAAGTGAAAAA
1 TTGAGGACAAAG-GAAAAA
430097 GAGTACGTCC
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
40 21 0.40
41 12 0.23
42 14 0.26
43 6 0.11
ACGTcount: A:0.44, C:0.10, G:0.27, T:0.20
Consensus pattern (42 bp):
TTGAGGACAAAGGAAAAAAGAAAAGAAAAGTGTCTTGCTTCC
Found at i:430097 original size:42 final size:41
Alignment explanation
Indices: 429992--430098 Score: 123
Period size: 42 Copynumber: 2.6 Consensus size: 41
429982 AGGTGTCCTA
* *
429992 CTTT-TTGAGGACAAAGG-AAAAGAGAATGAAATAGGTCTTG
1 CTTTCTTGAGGACAAAGGAAAAAGAAAAGGAAATA-GTCTTG
*
430032 C-TCCTTGAGGACAAAGGAAAAAAGAAAAGGAAAGT-GTCTTG
1 CTTTCTTGAGGACAAAGG-AAAAAGAAAAGGAAA-TAGTCTTG
430073 CTTTCTTGAGGACAAAGTGAAAAAGA
1 CTTTCTTGAGGACAAAG-GAAAAAGA
430099 GTACGTCCTA
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
39 1 0.02
40 14 0.25
41 7 0.12
42 33 0.58
43 2 0.04
ACGTcount: A:0.42, C:0.10, G:0.26, T:0.21
Consensus pattern (41 bp):
CTTTCTTGAGGACAAAGGAAAAAGAAAAGGAAATAGTCTTG
Found at i:430191 original size:41 final size:43
Alignment explanation
Indices: 430116--430266 Score: 130
Period size: 41 Copynumber: 3.5 Consensus size: 43
430106 CTACTTTTCA
* *
430116 AGGACAAAGGAAAAAAGGAAAACGAAATGTGTCCTGCTCTTTG
1 AGGACAAAGGAAAAAAGGAAAACAAAATGCGTCCTGCTCTTTG
* *
430159 AGGACAAA-G-AAAGAGGAAAATAAAATGCGTCCTGCTCTTTG
1 AGGACAAAGGAAAAAAGGAAAACAAAATGCGTCCTGCTCTTTG
* * * * * * *
430200 AGGATAAAAGGGAAAAGAAGG-GAATAAAGTGTGTCCTACTCTTTA
1 AGGA-CAAA-GGAAAA-AAGGAAAACAAAATGCGTCCTGCTCTTTG
*
430245 AGGACAAA-GAAGAAATGGAAAA
1 AGGACAAAGGAA-AAAAGGAAAA
430267 GGCATCCTGC
Statistics
Matches: 87, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
41 32 0.37
42 10 0.11
43 12 0.14
44 4 0.05
45 26 0.30
46 3 0.03
ACGTcount: A:0.45, C:0.11, G:0.26, T:0.18
Consensus pattern (43 bp):
AGGACAAAGGAAAAAAGGAAAACAAAATGCGTCCTGCTCTTTG
Found at i:430215 original size:120 final size:117
Alignment explanation
Indices: 429986--430215 Score: 250
Period size: 120 Copynumber: 1.9 Consensus size: 117
429976 TGGAAGAGGT
** * * *
429986 GTCCTACTTTTTGAGGACAAAGGAAAAGAGAATGAAATAGGTCTTGCTCCTTGAGGACAAAGGAA
1 GTCCTACTTTTCAAGGACAAAGGAAAAGAAAACGAAATAGGTCCTGCTCCTTGAGGACAAAGGAA
* * * * * *
430051 AAAAGAAAAGGAAAGTGTCTTGCTTTCTTGAGGACAAAGTGAAAAAGAGTAC
66 AAAAGAAAAGAAAAGCGTCCTGCTCTCTTGAGGAAAAAGGGAAAAAGAGTAC
*
430103 GTCCTACTTTTCAAGGACAAAGGAAAAAAGGAAAACGAAAT-GTGTCCTGCTCTTTGAGGACAAA
1 GTCCTACTTTTCAAGGACAAAGG--AAAA-GAAAACGAAATAG-GTCCTGCTCCTTGAGGACAAA
* * *
430167 -GAAAGAGGAAAATAAAATGCGTCCTGCTCT-TTGAGGATAAAAGGGAAAA
62 GGAAAAAAGAAAAGAAAA-GCGTCCTGCTCTCTTGAGGA-AAAAGGGAAAA
430216 GAAGGGAATA
Statistics
Matches: 92, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
117 21 0.23
119 25 0.27
120 46 0.50
ACGTcount: A:0.41, C:0.13, G:0.25, T:0.21
Consensus pattern (117 bp):
GTCCTACTTTTCAAGGACAAAGGAAAAGAAAACGAAATAGGTCCTGCTCCTTGAGGACAAAGGAA
AAAAGAAAAGAAAAGCGTCCTGCTCTCTTGAGGAAAAAGGGAAAAAGAGTAC
Found at i:430337 original size:61 final size:60
Alignment explanation
Indices: 430262--430590 Score: 327
Period size: 61 Copynumber: 5.5 Consensus size: 60
430252 AGAAGAAATG
*
430262 GAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCATGTGGGCTTTGAAAA
1 GAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTATGTGGGCTTT-AAAA
* * * * * *
430323 GAAAAGGCGTCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTATGGGCTTTGGAAA
1 GAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTATGTGGGCTTT-AAAA
* * * * **
430383 GAGAAA-GCATCCTGCTCTCTGAGGACTAGAAGGTGCCACCAACTCGA-GTGGTTTTTAAAAA
1 GA-AAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACT-TATGTGGGCTTT-AAAA
* *
430444 GAGTAA-GCATCCTGCTCTTTGAGGACTGAAAAA-TGCCACCAACTTGTGTGGGCTTTAAAA
1 GA-AAAGGCATCCTGCTCTTTGAGGACT-AAAAAGTGCCACCAACTTATGTGGGCTTTAAAA
* * * *
430504 GGAAAAGGCACCCTACTCTTTGAGAACTAGAAAAGTTCCACCAACTTATGTGGGCTTT----
1 -GAAAAGGCATCCTGCTCTTTGAGGACTA-AAAAGTGCCACCAACTTATGTGGGCTTTAAAA
*
430562 -AAAAGGCATCTTGCTCTTTGAGGACTAAA
1 GAAAAGGCATCCTGCTCTTTGAGGACTAAA
430591 GGGCGAAAGG
Statistics
Matches: 225, Mismatches: 34, Indels: 24
0.80 0.12 0.08
Matches are distributed among these distances:
55 2 0.01
56 23 0.10
60 55 0.24
61 121 0.54
62 24 0.11
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (60 bp):
GAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTATGTGGGCTTTAAAA
Found at i:430406 original size:121 final size:121
Alignment explanation
Indices: 430261--430566 Score: 370
Period size: 121 Copynumber: 2.5 Consensus size: 121
430251 AAGAAGAAAT
430261 GGAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCATGTGGGCTTTGAAAAGA-
1 GGAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCATGTGGGCTTT-AAAAGAG
* ** *
430325 AAAGGCGTCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTATGGGCTTTGGAAA
65 AAA-GCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTATGGGCTTT-AAAA
* * * **
430383 -GAGAAA-GCATCCTGCTCTCTGAGGACTAGAAGGTGCCACCAACTCGA-GTGGTTTTTAAAAAG
1 GGA-AAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTC-ATGTGGGCTTT-AAAAG
* *
430445 AGTAAGCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAA
63 AGAAAGCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTATGGGCTTTAAAA
* * * * *
430504 GGAAAAGGCACCCTACTCTTTGAGAACTAGAAAAGTTCCACCAACTTATGTGGGCTTTAAAAG
1 GGAAAAGGCATCCTGCTCTTTGAGGACTA-AAAAGTGCCACCAACTCATGTGGGCTTTAAAAG
430567 GCATCTTGCT
Statistics
Matches: 154, Mismatches: 22, Indels: 16
0.80 0.11 0.08
Matches are distributed among these distances:
121 78 0.51
122 56 0.36
123 20 0.13
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.24
Consensus pattern (121 bp):
GGAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCATGTGGGCTTTAAAAGAGA
AAGCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTATGGGCTTTAAAA
Found at i:430733 original size:150 final size:152
Alignment explanation
Indices: 430449--430743 Score: 396
Period size: 150 Copynumber: 1.9 Consensus size: 152
430439 AAAAAGAGTA
*
430449 AGCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
1 AGCATCCTACTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTT---A--AAAAGGCA
* * * * *
430514 CCCTACTCTTTGAGAACTAGAAAAGTTCCACCAACTTATGTGGGCTTTAAAAGGCATCTTGCTCT
61 CCCTACTCTTTGAGAACTAAAAAAATGCCACAAACTTATGTGGGCTTTAAAAGGCATCCTGCTCT
430579 TTGAGGACT-AAAGGGCGAAAGGAGAG
126 TTGAGGACTGAAAGGGCGAAAGGAGAG
** * ** *
430605 AGCATCCTACTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGGCGTCCTG
1 AGCATCCTACTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGGCACCCTA
* * *
430669 CTCTTTGAGGACTAAAAAAATGCCACAAACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTGAG
66 CTCTTTGAGAACTAAAAAAATGCCACAAACTTATGTGGGCTTTAAAAGGCATCCTGCTCTTTGAG
430734 GACTGAAAGG
131 GACTGAAAGG
430744 TGCTACCAAC
Statistics
Matches: 123, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
150 71 0.58
151 5 0.04
156 47 0.38
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (152 bp):
AGCATCCTACTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGGCACCCTA
CTCTTTGAGAACTAAAAAAATGCCACAAACTTATGTGGGCTTTAAAAGGCATCCTGCTCTTTGAG
GACTGAAAGGGCGAAAGGAGAG
Found at i:430774 original size:55 final size:56
Alignment explanation
Indices: 430606--430793 Score: 263
Period size: 55 Copynumber: 3.4 Consensus size: 56
430596 AAAGGAGAGA
* *
430606 GCATCCTACTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAG
1 GCATCCTACTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG
* * * ** * *
430661 GCGTCCTGCTCTTTGAGGACTAAAAAAATGCCACAAACTTGTGTGGGCTTTGAAAG
1 GCATCCTACTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG
* *
430717 GCATCCTGCTCTTTGAGGACT-GAAAGGTGCTACCAACTTGTGTGGGCTTTAAAAG
1 GCATCCTACTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG
430772 GCATCCTACTCTTTGAGGACTA
1 GCATCCTACTCTTTGAGGACTA
430794 AAGGGTGAAA
Statistics
Matches: 115, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
55 69 0.60
56 46 0.40
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (56 bp):
GCATCCTACTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG
Found at i:430831 original size:205 final size:207
Alignment explanation
Indices: 430453--430866 Score: 593
Period size: 205 Copynumber: 2.0 Consensus size: 207
430443 AGAGTAAGCA
* *
430453 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCACCCT
1 TCCTGCTCTTTGAGGACTAAAAAATGCCACAAACTTGTGTGGGCTTT---A-GAAAAGGCACCCT
* * *
430518 ACTCTTTGAGAACTAGAAAAGTTCCACCAACTTATGTGGGCTTTAAAAGGCATCTTGCTCTTTGA
62 ACTCTTTGAGAACTAGAAAAGTGCCACCAACTTATGTGGGCTTTAAAAGGCATCCTACTCTTTGA
* * *
430583 GGACTAAAGGGCGAAAGGAGAGAGCATCCTACTCTTTGAGGACTGGGAA-GTGCCACCAACTTGT
127 GGACTAAAGGGCGAAAGGAGAGAGCATCATACTCTTTGAGGACT-AGAAGGTGACACCAACTTGT
430647 GTGGGCTTTAAAAGGCG
191 GTGGGCTTTAAAAGGCG
* *
430664 TCCTGCTCTTTGAGGACTAAAAAAATGCCACAAACTTGTGTGGGCTTT-G-AAAGGCATCCTGCT
1 TCCTGCTCTTTGAGGACT-AAAAAATGCCACAAACTTGTGTGGGCTTTAGAAAAGGCACCCTACT
* * * *
430727 CTTTGAGGACT-GAAAGGTGCTACCAACTTGTGTGGGCTTTAAAAGGCATCCTACTCTTTGAGGA
65 CTTTGAGAACTAGAAAAGTGCCACCAACTTATGTGGGCTTTAAAAGGCATCCTACTCTTTGAGGA
* * *
430791 CTAAAGGGTGAAAGGAGAGAGCGTCATGCTCTTTGAGGACTAGAAGGTGACACCAACTTGTGTGG
130 CTAAAGGGCGAAAGGAGAGAGCATCATACTCTTTGAGGACTAGAAGGTGACACCAACTTGTGTGG
430856 GCTTTAAAAGG
195 GCTTTAAAAGG
430867 AAAAGACGTC
Statistics
Matches: 184, Mismatches: 17, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
204 3 0.02
205 113 0.61
206 22 0.12
207 1 0.01
211 18 0.10
212 27 0.15
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (207 bp):
TCCTGCTCTTTGAGGACTAAAAAATGCCACAAACTTGTGTGGGCTTTAGAAAAGGCACCCTACTC
TTTGAGAACTAGAAAAGTGCCACCAACTTATGTGGGCTTTAAAAGGCATCCTACTCTTTGAGGAC
TAAAGGGCGAAAGGAGAGAGCATCATACTCTTTGAGGACTAGAAGGTGACACCAACTTGTGTGGG
CTTTAAAAGGCG
Found at i:431891 original size:22 final size:21
Alignment explanation
Indices: 431869--431909 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
431859 AGCAGGTTCT
431869 TTTCTTTTCTCTTTTTTTTTC
1 TTTCTTTTCTCTTTTTTTTTC
* * *
431890 TTTGTTTTGTTTTTTTTTTT
1 TTTCTTTTCTCTTTTTTTTT
431910 TTGTGTTGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (21 bp):
TTTCTTTTCTCTTTTTTTTTC
Found at i:431902 original size:16 final size:14
Alignment explanation
Indices: 431883--431936 Score: 63
Period size: 16 Copynumber: 3.6 Consensus size: 14
431873 TTTTCTCTTT
431883 TTTTTTCTTTGTTTTG
1 TTTTTT-TTT-TTTTG
431899 TTTTTTTTTTTTTG
1 TTTTTTTTTTTTTG
*
431913 TGTTGTATTTTTTTTG
1 T-TT-TTTTTTTTTTG
431929 TTTTTTTT
1 TTTTTTTT
431937 AAAAAAAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
14 10 0.29
15 7 0.21
16 17 0.50
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.85
Consensus pattern (14 bp):
TTTTTTTTTTTTTG
Found at i:431904 original size:19 final size:19
Alignment explanation
Indices: 431880--431927 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
431870 TTCTTTTCTC
*
431880 TTTTTTTTTCTTTGTTTTG
1 TTTTTTTTTCTTTGTGTTG
*
431899 TTTTTTTTTTTTTGTGTTG
1 TTTTTTTTTCTTTGTGTTG
431918 TATTTTTTTT
1 T-TTTTTTTT
431928 GTTTTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.85
Consensus pattern (19 bp):
TTTTTTTTTCTTTGTGTTG
Found at i:431904 original size:21 final size:19
Alignment explanation
Indices: 431880--431932 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 19
431870 TTCTTTTCTC
* *
431880 TTTTTTTTTCTTTGTTTTGT
1 TTTTTTTTT-TTTGTGTTGA
431900 TTTTTTTTTTTTGTGTTGTA
1 TTTTTTTTTTTTGTGTTG-A
431920 TTTTTTTTGTTTT
1 TTTTTTTT-TTTT
431933 TTTTAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 8 0.28
20 17 0.59
21 4 0.14
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.85
Consensus pattern (19 bp):
TTTTTTTTTTTTGTGTTGA
Found at i:444474 original size:79 final size:79
Alignment explanation
Indices: 444340--444556 Score: 230
Period size: 79 Copynumber: 2.7 Consensus size: 79
444330 GCCAGGCCGA
* * * *
444340 AGTATCCCCGATTATGGAAAATTGATATTCTTGAAATAAAATCGGGGTTGAAGTATCCTCTC-AG
1 AGTATCCCTGATTATGAAAAATCGATATTCTTGAAATAAAATCGGGGTTGAAGTATCCCCTCGA-
444404 AAATAATAGGG-TTGG
65 AAATAA-AGGGATTGG
* * *
444419 AGTATCCCTGATTATAAAAAATCGGTATT-TTGAAAATAAAATCGGGGTTGGAGTATCCCCTCGA
1 AGTATCCCTGATTATGAAAAATCGATATTCTTG-AAATAAAATCGGGGTTGAAGTATCCCCTCGA
*
444483 AAATAACGGGATTGG
65 AAATAAAGGGATTGG
* * **
444498 AGTAT-CCTCGATTATGAAAAATTGATGATT-TAGAAAT-AAGGCTGGGGTTGAAGTATCCC
1 AGTATCCCT-GATTATGAAAAATCGAT-ATTCTTGAAATAAAATC-GGGGTTGAAGTATCCC
444557 GGATTATGAG
Statistics
Matches: 117, Mismatches: 15, Indels: 12
0.81 0.10 0.08
Matches are distributed among these distances:
78 12 0.10
79 99 0.85
80 6 0.05
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (79 bp):
AGTATCCCTGATTATGAAAAATCGATATTCTTGAAATAAAATCGGGGTTGAAGTATCCCCTCGAA
AATAAAGGGATTGG
Found at i:444562 original size:130 final size:128
Alignment explanation
Indices: 444412--444816 Score: 426
Period size: 130 Copynumber: 3.1 Consensus size: 128
444402 AGAAATAATA
* *
444412 GGGTTGGAGTATCCCTGATTATAAAAAATCGGTATTTTGAAAATAAAATCGGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCGATTATGAAAAATCGGTATTTTGAAAATAAAA-CGGGGTTGGAGTATCC
* **
444477 CCTCGAAAATAAC-GGGATTGGAGTATCCTCGATTATGAAAAATT-GATGATTTAG-AAATAAGG
65 CCTCGAAAATAACAGGG-TTGGAGTATCC-CGATTGTGAAAAATTAG-TG-TTTAGAAAATAAAA
444539 CTG
126 CTG
* * * ** * *
444542 GGGTTGAAGTATCCCGGATTATGAGAAATCAATATTTTGAAAATAAAGCCAGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCGATTATGAAAAATCGGTATTTTGAAAATAAA-ACGGGGTTGGAGTATCC
* *
444607 CCTCGAAAATAACAGGGTTGGAGTATCACCGATTGTGAAAAATTAGTGTTTTGAAAATAAAATTG
65 CCTCGAAAATAACAGGGTTGGAGTATC-CCGATTGTGAAAAATTAGTGTTTAGAAAATAAAACTG
* * * * *
444672 GAGTTGGAGTATCCCCAATTGTGAAAAATTGGTGTTTT-AGAAATAAAACTGGGGTTGGAGTATC
1 GGGTTGGAGTATCCCCGATTATGAAAAATCGGTATTTTGA-AAATAAAAC-GGGGTTGGAGTATC
* * * * * * * *
444736 TCCTCG-AAATGACAGGGTTGGAGTATCCCCAATTGTGAAAAACTGGTATTTTGAGAATAAAA-T
64 CCCTCGAAAATAACAGGGTTGGAGTAT-CCCGATTGTGAAAAATTAGTGTTTAGAAAATAAAACT
444799 CG
128 -G
444801 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
444817 TCGGAAATAA
Statistics
Matches: 233, Mismatches: 33, Indels: 19
0.82 0.12 0.07
Matches are distributed among these distances:
128 1 0.00
129 70 0.30
130 157 0.67
131 5 0.02
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (128 bp):
GGGTTGGAGTATCCCCGATTATGAAAAATCGGTATTTTGAAAATAAAACGGGGTTGGAGTATCCC
CTCGAAAATAACAGGGTTGGAGTATCCCGATTGTGAAAAATTAGTGTTTAGAAAATAAAACTG
Found at i:444684 original size:51 final size:51
Alignment explanation
Indices: 444623--444735 Score: 165
Period size: 51 Copynumber: 2.2 Consensus size: 51
444613 AAATAACAGG
* *
444623 GTTGGAGTATCACCGATTGTGAAAAATTAGTGTTTT-GAAAATAAAATTGGA
1 GTTGGAGTATCACCAATTGTGAAAAATTAGTGTTTTAG-AAATAAAACTGGA
* * *
444674 GTTGGAGTATCCCCAATTGTGAAAAATTGGTGTTTTAGAAATAAAACTGGG
1 GTTGGAGTATCACCAATTGTGAAAAATTAGTGTTTTAGAAATAAAACTGGA
444725 GTTGGAGTATC
1 GTTGGAGTATC
444736 TCCTCGAAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
51 55 0.98
52 1 0.02
ACGTcount: A:0.34, C:0.08, G:0.26, T:0.33
Consensus pattern (51 bp):
GTTGGAGTATCACCAATTGTGAAAAATTAGTGTTTTAGAAATAAAACTGGA
Found at i:444765 original size:78 final size:77
Alignment explanation
Indices: 444674--444895 Score: 243
Period size: 78 Copynumber: 2.8 Consensus size: 77
444664 TAAAATTGGA
* * *
444674 GTTGGAGTATCCCCAATTGTGAAAAATTGGTGTTTTAGAAATAAAACTGGGGTTGGAGTATCTCC
1 GTTGGAGTATCCCCAATTGTGAAAAAATGGTATTTT-GAAATAAAACTGGGGTTGGAGTATCCCC
444739 TC-GAAATGACA-GG
65 TCGGAAAT-A-ATGG
*
444752 GTTGGAGTATCCCCAATTGTGAAAAACTGGTATTTTGAGAATAAAA-TCGGGGTTGGAGTATCCC
1 GTTGGAGTATCCCCAATTGTGAAAAAATGGTATTTTGA-AATAAAACT-GGGGTTGGAGTATCCC
444816 CTCGGAAATAATGG
64 CTCGGAAATAATGG
* ** * * * * * *
444830 GAATGGAGTATCTTCGATTATGAAAAAATGATCTTTTGGAAATAAAACCGGGGTTGAAGTATCCC
1 G-TTGGAGTATCCCCAATTGTGAAAAAATGGTATTTT-GAAATAAAACTGGGGTTGGAGTATCCC
444895 C
64 C
444896 GAGATGAAGA
Statistics
Matches: 124, Mismatches: 13, Indels: 13
0.83 0.09 0.09
Matches are distributed among these distances:
77 4 0.03
78 63 0.51
79 55 0.44
80 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.29
Consensus pattern (77 bp):
GTTGGAGTATCCCCAATTGTGAAAAAATGGTATTTTGAAATAAAACTGGGGTTGGAGTATCCCCT
CGGAAATAATGG
Found at i:444996 original size:18 final size:18
Alignment explanation
Indices: 444973--445009 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
444963 TTACAAAGAT
444973 ACGTCCGAATGTCTTGGG
1 ACGTCCGAATGTCTTGGG
444991 ACGTCCGAATGTCTTGGG
1 ACGTCCGAATGTCTTGGG
445009 A
1 A
445010 TGAAGTTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.19, C:0.22, G:0.32, T:0.27
Consensus pattern (18 bp):
ACGTCCGAATGTCTTGGG
Found at i:447236 original size:20 final size:20
Alignment explanation
Indices: 447211--447265 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
447201 AAAATACCTG
*
447211 AATGTATCAATACATTGCAA-
1 AATGTATCAATACAATG-AAC
447231 AATGTATCAATACAATGAAC
1 AATGTATCAATACAATGAAC
*
447251 AATGTATCGATACAA
1 AATGTATCAATACAA
447266 ATTGTAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.27
Consensus pattern (20 bp):
AATGTATCAATACAATGAAC
Found at i:447937 original size:13 final size:13
Alignment explanation
Indices: 447919--447945 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
447909 ACATTATGCT
447919 TTGTATCGATACA
1 TTGTATCGATACA
447932 TTGTATCGATACA
1 TTGTATCGATACA
447945 T
1 T
447946 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:447954 original size:19 final size:19
Alignment explanation
Indices: 447929--447987 Score: 82
Period size: 19 Copynumber: 3.1 Consensus size: 19
447919 TTGTATCGAT
*
447929 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGA
*
447948 TCATTGTATCGATACATGA
1 ACATTGTATCGATACATGA
*
447967 ACAAATGTATCGATACATGA
1 AC-ATTGTATCGATACATGA
447987 A
1 A
447988 ACCGGCAGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
19 18 0.51
20 17 0.49
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (19 bp):
ACATTGTATCGATACATGA
Found at i:447977 original size:20 final size:19
Alignment explanation
Indices: 447933--447987 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
447923 ATCGATACAT
** *
447933 TGTATCGATACATGTTCAT
1 TGTATCGATACATGAACAA
447952 TGTATCGATACATGAACAAA
1 TGTATCGATACATGAAC-AA
447972 TGTATCGATACATGAA
1 TGTATCGATACATGAA
447988 ACCGGCAGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (19 bp):
TGTATCGATACATGAACAA
Found at i:450958 original size:19 final size:18
Alignment explanation
Indices: 450908--450962 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
450898 AATATGTATT
*
450908 TTTAAATTATTAAAA-TA
1 TTTAAAATATTAAAATTA
* *
450925 TTTATCAATAATAAATATTA
1 TTTA-AAATATTAAA-ATTA
450945 TTTAAAATATTAAAATTA
1 TTTAAAATATTAAAATTA
450963 GTAAATTTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
17 4 0.13
18 11 0.37
19 9 0.30
20 6 0.20
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
TTTAAAATATTAAAATTA
Found at i:457081 original size:13 final size:13
Alignment explanation
Indices: 457063--457088 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
457053 TACACCAAGT
457063 ATGTATCGATACA
1 ATGTATCGATACA
457076 ATGTATCGATACA
1 ATGTATCGATACA
457089 CCAAAAAAAT
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):
ATGTATCGATACA
Found at i:458315 original size:277 final size:277
Alignment explanation
Indices: 457816--458376 Score: 1113
Period size: 277 Copynumber: 2.0 Consensus size: 277
457806 AAAGAACTAA
*
457816 TTCACCCCCCTTCTTGGCTCGTTACTTCATAAGCTTTCAATTGGTATCAGAGCTTAACCTCCGTT
1 TTCATCCCCCTTCTTGGCTCGTTACTTCATAAGCTTTCAATTGGTATCAGAGCTTAACCTCCGTT
457881 CAACGGATTCACACTCGGGAGAGACGATCAATTTCAAATCAAGAATGGAAGGCGCAATGATCAAC
66 CAACGGATTCACACTCGGGAGAGACGATCAATTTCAAATCAAGAATGGAAGGCGCAATGATCAAC
457946 AATTCAATCTTCATGAACCAAGAAGAAATATGTCTCATGGCATTAGAAAACAACTCAAATACCAT
131 AATTCAATCTTCATGAACCAAGAAGAAATATGTCTCATGGCATTAGAAAACAACTCAAATACCAT
458011 AGGACTCGAGGGACACTCAACCATGAGGCCTCCATACTTCAACGGTGACAACTTCTCATATTGGA
196 AGGACTCGAGGGACACTCAACCATGAGGCCTCCATACTTCAACGGTGACAACTTCTCATATTGGA
458076 AGACAAGGATGAGGTTG
261 AGACAAGGATGAGGTTG
458093 TTCATCCCCCTTCTTGGCTCGTTACTTCATAAGCTTTCAATTGGTATCAGAGCTTAACCTCCGTT
1 TTCATCCCCCTTCTTGGCTCGTTACTTCATAAGCTTTCAATTGGTATCAGAGCTTAACCTCCGTT
458158 CAACGGATTCACACTCGGGAGAGACGATCAATTTCAAATCAAGAATGGAAGGCGCAATGATCAAC
66 CAACGGATTCACACTCGGGAGAGACGATCAATTTCAAATCAAGAATGGAAGGCGCAATGATCAAC
458223 AATTCAATCTTCATGAACCAAGAAGAAATATGTCTCATGGCATTAGAAAACAACTCAAATACCAT
131 AATTCAATCTTCATGAACCAAGAAGAAATATGTCTCATGGCATTAGAAAACAACTCAAATACCAT
458288 AGGACTCGAGGGACACTCAACCATGAGGCCTCCATACTTCAACGGTGACAACTTCTCATATTGGA
196 AGGACTCGAGGGACACTCAACCATGAGGCCTCCATACTTCAACGGTGACAACTTCTCATATTGGA
458353 AGACAAGGATGAGGTTG
261 AGACAAGGATGAGGTTG
458370 TTCATCC
1 TTCATCC
458377 AAGCCAACGA
Statistics
Matches: 283, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
277 283 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.25
Consensus pattern (277 bp):
TTCATCCCCCTTCTTGGCTCGTTACTTCATAAGCTTTCAATTGGTATCAGAGCTTAACCTCCGTT
CAACGGATTCACACTCGGGAGAGACGATCAATTTCAAATCAAGAATGGAAGGCGCAATGATCAAC
AATTCAATCTTCATGAACCAAGAAGAAATATGTCTCATGGCATTAGAAAACAACTCAAATACCAT
AGGACTCGAGGGACACTCAACCATGAGGCCTCCATACTTCAACGGTGACAACTTCTCATATTGGA
AGACAAGGATGAGGTTG
Found at i:459005 original size:12 final size:12
Alignment explanation
Indices: 458973--459006 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
458963 AACCATCAAG
*
458973 GATGAAGAAGAT
1 GATGAAGATGAT
*
458985 GATGAAGATGTT
1 GATGAAGATGAT
458997 GATGAAGATG
1 GATGAAGATG
459007 GTGACTCGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.35, T:0.24
Consensus pattern (12 bp):
GATGAAGATGAT
Found at i:463556 original size:13 final size:13
Alignment explanation
Indices: 463538--463562 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
463528 CATTTTTCTT
463538 TGTATCGATACAC
1 TGTATCGATACAC
463551 TGTATCGATACA
1 TGTATCGATACA
463563 GGGGGATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:463708 original size:21 final size:20
Alignment explanation
Indices: 463684--463730 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
463674 AAATCTTTTG
463684 CAAAATAC-TTGTTTTTCACTT
1 CAAAATACTTTGTTTTTCA--T
*
463705 CAAATTACTTTGTTTTTCAT
1 CAAAATACTTTGTTTTTCAT
463725 CAAAAT
1 CAAAAT
463731 CAGCTTCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 6 0.26
21 7 0.30
22 10 0.43
ACGTcount: A:0.32, C:0.17, G:0.04, T:0.47
Consensus pattern (20 bp):
CAAAATACTTTGTTTTTCAT
Found at i:465988 original size:20 final size:19
Alignment explanation
Indices: 465934--465988 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
465924 AAAACCCTTA
*
465934 AAAGTATCGATACACAATTC
1 AAAGTATCGATACA-TATTC
465954 AAAGTATCGATACATATTGC
1 AAAGTATCGATACATATT-C
*
465974 AATGTATCGATACAT
1 AAAGTATCGATACAT
465989 GAAAAATATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 3 0.09
20 29 0.91
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (19 bp):
AAAGTATCGATACATATTC
Found at i:468167 original size:3 final size:3
Alignment explanation
Indices: 468159--468199 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
468149 TCAACCATCA
*
468159 ATG ATG ATG AAG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
468200 AAAGTTGACT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.37, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:474381 original size:35 final size:37
Alignment explanation
Indices: 474318--474402 Score: 93
Period size: 35 Copynumber: 2.4 Consensus size: 37
474308 TTATGTTTGC
* * * * *
474318 TTTCATGATTGTAATGAATATTTGCCTTGCT-A-TTT
1 TTTCATGAATGCAAAGAATATTTCCCTTGATAACTTT
*
474353 TTTCATGAATGCAAAGAATGTTTCCCTTGATAACTTT
1 TTTCATGAATGCAAAGAATATTTCCCTTGATAACTTT
*
474390 TTTTATGAATGCA
1 TTTCATGAATGCA
474403 TGGGGGAGAA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
35 25 0.61
36 1 0.02
37 15 0.37
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.46
Consensus pattern (37 bp):
TTTCATGAATGCAAAGAATATTTCCCTTGATAACTTT
Found at i:479535 original size:38 final size:38
Alignment explanation
Indices: 479493--479588 Score: 115
Period size: 38 Copynumber: 2.5 Consensus size: 38
479483 CCACTAGATA
* * *
479493 AGAATAATGGTTTTTATATT-GAATCGTGCCACCGGTTT
1 AGAATAATAGTTTTCAT-TTCGAACCGTGCCACCGGTTT
*
479531 AGAATAGTAGTTTTCATTTCGAACCGTGCCACCGGTTT
1 AGAATAATAGTTTTCATTTCGAACCGTGCCACCGGTTT
*
479569 AGAATAGT-GATTTTCATTTC
1 AGAATAATAG-TTTTCATTTC
479589 TAACTATGCC
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
37 3 0.06
38 49 0.94
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.39
Consensus pattern (38 bp):
AGAATAATAGTTTTCATTTCGAACCGTGCCACCGGTTT
Found at i:479599 original size:38 final size:38
Alignment explanation
Indices: 479519--479620 Score: 125
Period size: 38 Copynumber: 2.7 Consensus size: 38
479509 TATTGAATCG
*
479519 TGCCACCGGTTTAGAATAGT-AGTTTTCATTTCGAACCG
1 TGCCACCGGTTTAGAATAGTGA-TTTTCATTTCGAACCA
* *
479557 TGCCACCGGTTTAGAATAGTGATTTTCATTTCTAACTA
1 TGCCACCGGTTTAGAATAGTGATTTTCATTTCGAACCA
* * * *
479595 TGCCATCGATTTAAAATAGTGGTTTT
1 TGCCACCGGTTTAGAATAGTGATTTT
479621 TGTTCGTAAC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
38 55 0.98
39 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (38 bp):
TGCCACCGGTTTAGAATAGTGATTTTCATTTCGAACCA
Found at i:487039 original size:31 final size:31
Alignment explanation
Indices: 486954--487040 Score: 106
Period size: 30 Copynumber: 2.8 Consensus size: 31
486944 TCAAATCGCA
* *
486954 CCACCGGATAAGAATAGTAGTTTTTGCCATG
1 CCACCGGATAAGAATAGTGGTTTTTGACATG
*
486985 CCACC-GATAAGAATAGTGATTTTT-ACAGTG
1 CCACCGGATAAGAATAGTGGTTTTTGACA-TG
* *
487015 CCACCGGATAAGATTAATGGTTTTTG
1 CCACCGGATAAGAATAGTGGTTTTTG
487041 TATTGAATCG
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
29 2 0.04
30 24 0.51
31 21 0.45
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (31 bp):
CCACCGGATAAGAATAGTGGTTTTTGACATG
Found at i:487076 original size:38 final size:38
Alignment explanation
Indices: 487034--487156 Score: 160
Period size: 38 Copynumber: 3.2 Consensus size: 38
487024 AAGATTAATG
487034 GTTTTTGTATT-GAATCGTGCCACCGGTTTAGAATAGTA
1 GTTTTTGT-TTCGAATCGTGCCACCGGTTTAGAATAGTA
* * * *
487072 GTTTTCGTTTCGAATCATGTCACCGGTTTAGAATAATA
1 GTTTTTGTTTCGAATCGTGCCACCGGTTTAGAATAGTA
* *
487110 GTTTTTGTTTCTAATCGTGCCACCGGTTTAAAATAGT-
1 GTTTTTGTTTCGAATCGTGCCACCGGTTTAGAATAGTA
487147 GATTTTTGTT
1 G-TTTTTGTT
487157 CGTAGCTTGT
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
37 3 0.04
38 70 0.96
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.43
Consensus pattern (38 bp):
GTTTTTGTTTCGAATCGTGCCACCGGTTTAGAATAGTA
Found at i:487185 original size:2 final size:2
Alignment explanation
Indices: 487180--487220 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
487170 GAGAGTTAGT
*
487180 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
487221 TTTTGATCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:491245 original size:13 final size:13
Alignment explanation
Indices: 491227--491254 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
491217 ATACAAAGAT
491227 CAATGTATCGATA
1 CAATGTATCGATA
491240 CAATGTATCGATA
1 CAATGTATCGATA
491253 CA
1 CA
491255 TTGAATAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:500711 original size:22 final size:21
Alignment explanation
Indices: 500686--500729 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
500676 AAAGAGATAT
*
500686 ATAAAATATTTTAAAAAGTAAA
1 ATAAAA-ATTTTAAAAAATAAA
*
500708 ATAATAATTTTAAAAAATAAA
1 ATAAAAATTTTAAAAAATAAA
500729 A
1 A
500730 CAAGTATAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
ATAAAAATTTTAAAAAATAAA
Found at i:502594 original size:2 final size:2
Alignment explanation
Indices: 502587--502612 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
502577 GTCATCCGTG
502587 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
502613 GAAAACACTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:508456 original size:14 final size:13
Alignment explanation
Indices: 508438--508483 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 13
508428 GTTAATAGAA
508438 ATAAAATAATAATT
1 ATAAAA-AATAATT
*
508452 TTAAAAAAATAATT
1 AT-AAAAAATAATT
508466 ATAATAAAATAATT
1 ATAA-AAAATAATT
508480 ATAA
1 ATAA
508484 TTTAATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 2 0.07
14 22 0.79
15 4 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
ATAAAAAATAATT
Found at i:508484 original size:14 final size:14
Alignment explanation
Indices: 508445--508484 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
508435 GAAATAAAAT
* *
508445 AATAATTTTAAAAA
1 AATAATTATAATAA
508459 AATAATTATAATAA
1 AATAATTATAATAA
508473 AATAATTATAAT
1 AATAATTATAAT
508485 TTAATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AATAATTATAATAA
Found at i:508490 original size:14 final size:14
Alignment explanation
Indices: 508459--508528 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 14
508449 ATTTTAAAAA
**
508459 AATAATTATAATAA
1 AATAATTATAATTT
508473 AATAATTATAATTT
1 AATAATTATAATTT
*
508487 AAT-ATTTTAATTT
1 AATAATTATAATTT
* * * **
508500 AGTAAAATAAAATAA
1 AAT-AATTATAATTT
508515 AATAATTATAATTT
1 AATAATTATAATTT
508529 TTATTATTTA
Statistics
Matches: 40, Mismatches: 14, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
13 11 0.28
14 22 0.55
15 7 0.17
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (14 bp):
AATAATTATAATTT
Found at i:508647 original size:19 final size:19
Alignment explanation
Indices: 508623--508664 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
508613 AATGATAGTG
508623 AATTATTTATTAGGAAAAA
1 AATTATTTATTAGGAAAAA
508642 AATTATTTATTAGGAAAAA
1 AATTATTTATTAGGAAAAA
508661 AATT
1 AATT
508665 GCTTCATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (19 bp):
AATTATTTATTAGGAAAAA
Found at i:509221 original size:97 final size:96
Alignment explanation
Indices: 509082--509269 Score: 245
Period size: 97 Copynumber: 1.9 Consensus size: 96
509072 GTGAAGAATA
* * *
509082 GGGAAGAGTTTAAGTATATTAAAATTTCCTTAAATGGTTACACTAAGGAGAAGTAGATCACCATT
1 GGGAAGAGTCTAAGTATATTAAAATTTCCTTAAATGGCTACACTAAGAAGAAGTAGATCACCATT
509147 TTCTGTAAATATTGCG-GCATATATGAAATTTG
66 TTC-GTAAATATTG-GAGCATATATGAAATTTG
* *** * *
509179 GGGAAGAGTCT-AGATATATTAAGATTTCCTTGCGTGGCTACACTAAGAAGGAGTAGATCATCAT
1 GGGAAGAGTCTAAG-TATATTAAAATTTCCTTAAATGGCTACACTAAGAAGAAGTAGATCACCAT
*
509243 TTTCGTAAATATTGGAGCATATGTGAA
65 TTTCGTAAATATTGGAGCATATATGAA
509270 GCGTAAGAAA
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
95 1 0.01
96 22 0.28
97 56 0.71
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (96 bp):
GGGAAGAGTCTAAGTATATTAAAATTTCCTTAAATGGCTACACTAAGAAGAAGTAGATCACCATT
TTCGTAAATATTGGAGCATATATGAAATTTG
Found at i:510615 original size:14 final size:14
Alignment explanation
Indices: 510598--510656 Score: 50
Period size: 14 Copynumber: 4.2 Consensus size: 14
510588 TGAAAAAAAA
*
510598 TAAATATAATTTAT
1 TAAATATAATATAT
510612 TAAATATAAATATAT
1 TAAATAT-AATATAT
* *
510627 T-AATATATTTTCA-
1 TAAATATAATAT-AT
*
510640 TAAATATTATATAT
1 TAAATATAATATAT
510654 TAA
1 TAA
510657 TTTTAGAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
13 5 0.14
14 23 0.66
15 7 0.20
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (14 bp):
TAAATATAATATAT
Found at i:510632 original size:28 final size:27
Alignment explanation
Indices: 510600--510657 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
510590 AAAAAAAATA
510600 AATATAATTT-ATTAAATATAAATATATT
1 AATATAATTTCA-TAAATAT-AATATATT
* *
510628 AATATATTTTCATAAATATTATATATT
1 AATATAATTTCATAAATATAATATATT
510655 AAT
1 AAT
510658 TTTAGAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 10 0.37
28 16 0.59
29 1 0.04
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (27 bp):
AATATAATTTCATAAATATAATATATT
Found at i:511388 original size:10 final size:10
Alignment explanation
Indices: 511375--511428 Score: 54
Period size: 10 Copynumber: 5.0 Consensus size: 10
511365 ATTACTGTTC
511375 ATTTATCACT
1 ATTTATCACT
511385 ATTTATCACTGTTT
1 ATTTATCAC----T
*
511399 ATGTATCACT
1 ATTTATCACT
511409 ATTTATCACT
1 ATTTATCACT
*
511419 ATTCATCACT
1 ATTTATCACT
511429 GTTCATGTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 28 0.76
14 9 0.24
ACGTcount: A:0.28, C:0.20, G:0.04, T:0.48
Consensus pattern (10 bp):
ATTTATCACT
Found at i:511395 original size:24 final size:24
Alignment explanation
Indices: 511368--511424 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
511358 TTGATACATT
*
511368 ACTGTTCATTTATCACTATTTATC
1 ACTGTTCATGTATCACTATTTATC
*
511392 ACTGTTTATGTATCACTATTTATC
1 ACTGTTCATGTATCACTATTTATC
*
511416 ACTATTCAT
1 ACTGTTCAT
511425 CACTGTTCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.26, C:0.19, G:0.05, T:0.49
Consensus pattern (24 bp):
ACTGTTCATGTATCACTATTTATC
Found at i:511413 original size:34 final size:34
Alignment explanation
Indices: 511375--511439 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
511365 ATTACTGTTC
* *
511375 ATTTATCACTATTTATCACTGTTTATGTATCACT
1 ATTTATCACTATTCATCACTGTTCATGTATCACT
511409 ATTTATCACTATTCATCACTGTTCATGTATC
1 ATTTATCACTATTCATCACTGTTCATGTATC
511440 GATACAGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.48
Consensus pattern (34 bp):
ATTTATCACTATTCATCACTGTTCATGTATCACT
Found at i:511557 original size:15 final size:15
Alignment explanation
Indices: 511537--511568 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
511527 GTAAGTGCGG
511537 AAACAAGGTCCAAAC
1 AAACAAGGTCCAAAC
*
511552 AAACAAGGTCTAAAC
1 AAACAAGGTCCAAAC
511567 AA
1 AA
511569 GTCAATAACG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.56, C:0.22, G:0.12, T:0.09
Consensus pattern (15 bp):
AAACAAGGTCCAAAC
Found at i:517337 original size:21 final size:20
Alignment explanation
Indices: 517308--517350 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
517298 GACTAGTGTG
*
517308 GGGACTGCCCGGTTGCGACCT
1 GGGACTG-CCGGTCGCGACCT
*
517329 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
517349 GG
1 GG
517351 TGGTGCTGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.09, C:0.30, G:0.44, T:0.16
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:517809 original size:13 final size:13
Alignment explanation
Indices: 517791--517815 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
517781 ATAATCCCCC
517791 TGTATCGATACAT
1 TGTATCGATACAT
517804 TGTATCGATACA
1 TGTATCGATACA
517816 AAGAAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:519920 original size:15 final size:15
Alignment explanation
Indices: 519900--519930 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
519890 ATTTCGTTTG
*
519900 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
519915 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
519930 G
1 G
519931 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:522952 original size:13 final size:13
Alignment explanation
Indices: 522934--522959 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
522924 TACACCAAGT
522934 ATGTATCGATACA
1 ATGTATCGATACA
522947 ATGTATCGATACA
1 ATGTATCGATACA
522960 CAAAAAATTG
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):
ATGTATCGATACA
Found at i:522957 original size:32 final size:33
Alignment explanation
Indices: 522916--522979 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
522906 TAGCCAAACT
* **
522916 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
522948 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
522980 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:523275 original size:23 final size:22
Alignment explanation
Indices: 523249--523291 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
523239 TTTGTTCATA
523249 TTGTCATTATT-TTTCTAAGCTCT
1 TTGT-ATTATTATTTC-AAGCTCT
*
523272 TTGTATTCTTATTTCAAGCT
1 TTGTATTATTATTTCAAGCT
523292 TAAATTCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.19, C:0.16, G:0.09, T:0.56
Consensus pattern (22 bp):
TTGTATTATTATTTCAAGCTCT
Found at i:525203 original size:21 final size:21
Alignment explanation
Indices: 525170--525214 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
525160 TTGCAAGTTG
*
525170 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
525192 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
525212 AAA
1 AAA
525215 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:527041 original size:15 final size:15
Alignment explanation
Indices: 527021--527051 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
527011 TAAAAATGTC
*
527021 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
527036 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
527051 C
1 C
527052 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:529138 original size:13 final size:13
Alignment explanation
Indices: 529120--529158 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
529110 ACATTTTTCT
529120 TTGTATCGATACA
1 TTGTATCGATACA
529133 TTGTATCGATACA
1 TTGTATCGATACA
*
529146 CTGTATCGATACA
1 TTGTATCGATACA
529159 GGGGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:531725 original size:20 final size:20
Alignment explanation
Indices: 531680--531731 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
531670 GTAGCCAAAC
* **
531680 TTGTATCGATACACCAAGTA
1 TTGTATCGATACACAAAAAA
531700 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
531719 TTGTATCGATACA
1 TTGTATCGATACA
531732 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:534005 original size:13 final size:13
Alignment explanation
Indices: 533987--534012 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
533977 CAATTTTTTG
533987 TGTATCGATACAT
1 TGTATCGATACAT
534000 TGTATCGATACAT
1 TGTATCGATACAT
534013 ACTTTGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:537599 original size:19 final size:20
Alignment explanation
Indices: 537575--537613 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
537565 ATCTAAAATA
*
537575 CCAAAAAA-TACCATATTTT
1 CCAAAAAATTACCAAATTTT
537594 CCAAAAAATTACCAAATTTT
1 CCAAAAAATTACCAAATTTT
537614 AATCAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.31
Consensus pattern (20 bp):
CCAAAAAATTACCAAATTTT
Found at i:537845 original size:27 final size:27
Alignment explanation
Indices: 537807--537860 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
537797 CAACCAACCC
*
537807 TTTTTTTCATA-TT-TTATGTTCTTTAT
1 TTTTTTTAATATTTATTAT-TTCTTTAT
537833 TTTTTTGTAATATTTATTATTTCTTTAT
1 TTTTTT-TAATATTTATTATTTCTTTAT
537861 GCCTTGCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 6 0.25
27 4 0.17
28 10 0.42
29 4 0.17
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.72
Consensus pattern (27 bp):
TTTTTTTAATATTTATTATTTCTTTAT
Found at i:538791 original size:77 final size:75
Alignment explanation
Indices: 538676--538823 Score: 165
Period size: 76 Copynumber: 1.9 Consensus size: 75
538666 GAAAGCATTA
* ** *
538676 ACATGACCCTAAAAGTTTGGTTTCGAAGGGAAAAACTAAAAG-GACCTTAGGGGTTTAATTTTGG
1 ACATAACCCTAAAAGTTTGGTTTCGAAGGGAAAAACT-AAAGTGACCTTAAAGGTTCAATTTTGG
538740 CATGAAAAAGCT
65 CAT-AAAAAGCT
* * * * *
538752 ACATAACCCTAAAGGTTTGTTTTTG-AGGAGAATATACTAAAGTGACCTTAAAGGTTCAGTTTTG
1 ACATAACCCTAAAAGTTTGGTTTCGAAGG-GAA-AAACTAAAGTGACCTTAAAGGTTCAATTTTG
538816 GCATAAAA
64 GCATAAAA
538824 GTATTAACAT
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
75 3 0.05
76 32 0.53
77 25 0.42
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (75 bp):
ACATAACCCTAAAAGTTTGGTTTCGAAGGGAAAAACTAAAGTGACCTTAAAGGTTCAATTTTGGC
ATAAAAAGCT
Found at i:546259 original size:20 final size:19
Alignment explanation
Indices: 546236--546309 Score: 85
Period size: 20 Copynumber: 3.8 Consensus size: 19
546226 CACACCCAGA
* *
546236 TGTATTGATACATTATGCTT
1 TGTATTGATACATGAT-CAT
546256 TGTATTGATACATGATCAT
1 TGTATTGATACATGATCAT
* *
546275 TGTATCGATACATGAATAAT
1 TGTATTGATACATG-ATCAT
*
546295 TGTATCGATACATGA
1 TGTATTGATACATGA
546310 AACTTGCAGT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
19 16 0.33
20 33 0.67
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (19 bp):
TGTATTGATACATGATCAT
Found at i:546310 original size:20 final size:20
Alignment explanation
Indices: 546255--546310 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
546245 ACATTATGCT
* *
546255 TTGTATTGATACATG-ATCA
1 TTGTATCGATACATGAATAA
546274 TTGTATCGATACATGAATAA
1 TTGTATCGATACATGAATAA
546294 TTGTATCGATACATGAA
1 TTGTATCGATACATGAA
546311 ACTTGCAGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 14 0.41
20 20 0.59
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.38
Consensus pattern (20 bp):
TTGTATCGATACATGAATAA
Found at i:548843 original size:13 final size:13
Alignment explanation
Indices: 548827--548856 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
548817 ACAATTCATC
*
548827 ATGTATTGATACA
1 ATGTATCGATACA
548840 ATGTATCGATACA
1 ATGTATCGATACA
548853 ATGT
1 ATGT
548857 GCCATGTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:548863 original size:33 final size:32
Alignment explanation
Indices: 548805--548873 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 32
548795 CCGTTTGAAG
*
548805 CAATGTATCAATACAATTCATCATGTATTGATA
1 CAATGTATCAATACAATTCA-CATGTATCGATA
*
548838 CAATGTATCGATACAATGTGC-CATGTATCGATA
1 CAATGTATCAATACAAT-T-CACATGTATCGATA
548871 CAA
1 CAA
548874 ACAGTGGTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (32 bp):
CAATGTATCAATACAATTCACATGTATCGATA
Found at i:548935 original size:20 final size:20
Alignment explanation
Indices: 548902--548974 Score: 105
Period size: 20 Copynumber: 3.8 Consensus size: 20
548892 CTGCCAGTTT
548902 CATGTATC-ATACAATTGTC
1 CATGTATCGATACAATTGTC
548921 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGTC
**
548941 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGTC
*
548960 AATGTATCGATACAA
1 CATGTATCGATACAA
548975 AGCATAATGT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
19 24 0.48
20 26 0.52
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATTGTC
Found at i:548985 original size:20 final size:19
Alignment explanation
Indices: 548942--548993 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
548932 ACAATTGTCC
*
548942 ATGTATCGATACAATGAAA
1 ATGTATCGATACAAAGAAA
*
548961 ATGTATCGATACAAAGCATA
1 ATGTATCGATACAAAG-AAA
548981 ATGTATCGATACA
1 ATGTATCGATACA
548994 TCTGGGTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.27
Consensus pattern (19 bp):
ATGTATCGATACAAAGAAA
Found at i:551928 original size:13 final size:13
Alignment explanation
Indices: 551910--551934 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
551900 CATAAAGTGT
551910 TGTATCGATACAA
1 TGTATCGATACAA
551923 TGTATCGATACA
1 TGTATCGATACA
551935 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:551945 original size:32 final size:33
Alignment explanation
Indices: 551890--551953 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 33
551880 TTCAACGATT
551890 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
551923 TGTATCGATACAT-AAGTGTTGTATCGATACA
1 TGTATCGATACATAAAGTGTTGTATCGATACA
551954 TAAGTTTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 18 0.58
33 13 0.42
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:551947 original size:19 final size:19
Alignment explanation
Indices: 551889--551972 Score: 108
Period size: 19 Copynumber: 4.7 Consensus size: 19
551879 TTTCAACGAT
551889 TTGTATCGATACATAAAGTG
1 TTGTATCGATACAT-AAGTG
551909 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
551923 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
*
551941 TTGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
551960 TTGTATCGATACA
1 TTGTATCGATACA
551973 ATGTAAGCTA
Statistics
Matches: 57, Mismatches: 1, Indels: 13
0.80 0.01 0.18
Matches are distributed among these distances:
13 11 0.19
15 2 0.04
17 2 0.04
19 30 0.53
20 12 0.21
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:552012 original size:13 final size:13
Alignment explanation
Indices: 551994--552018 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
551984 TGCCAAAAAA
551994 TGTATCGATACAT
1 TGTATCGATACAT
552007 TGTATCGATACA
1 TGTATCGATACA
552019 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:552085 original size:52 final size:52
Alignment explanation
Indices: 552027--552155 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
552017 CACTGATCTT
552027 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
* *
552079 TGTATCGATACATGCGGGCAAATTTGCCTAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
552131 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
552156 TCATATTTCG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:553114 original size:32 final size:33
Alignment explanation
Indices: 553052--553120 Score: 113
Period size: 32 Copynumber: 2.1 Consensus size: 33
553042 TTCAATGATT
*
553052 TGTATCGATACATAAAGTGTTGTATTGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*
553085 TGTATCGATACAT-AAGTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
553117 TGTA
1 TGTA
553121 AGCTACTACC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 21 0.62
33 13 0.38
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:553176 original size:13 final size:13
Alignment explanation
Indices: 553158--553182 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
553148 ATTACTCAAA
553158 TGTATCGATACAT
1 TGTATCGATACAT
553171 TGTATCGATACA
1 TGTATCGATACA
553183 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:559107 original size:98 final size:97
Alignment explanation
Indices: 558942--559189 Score: 255
Period size: 98 Copynumber: 2.5 Consensus size: 97
558932 TTTAATTTTT
** * * * * *
558942 GTTAAAAAACGGGGTTAAAATATCCCCTC-AAAGAAATGGGGTTGGAGTGTCCCCGACGATGATA
1 GTTAAAAAACAAGGTTAGAGTATCCCCTCGGAAG-AATGGGGTTGGAGTATCCCCGACGATGACA
**** * * *
559006 ATTTAGGTGAAAATAAGATTTAAATTTTGATAA
65 ATTTAACCAAAAATAAGACTTAAATCTTGACAA
* * * *
559039 GTTAAAAAATAAGGTTAGAGTATTCCCTCGGAAGAATGGGAGTTAGAGTATCCCCGATGATGACA
1 GTTAAAAAACAAGGTTAGAGTATCCCCTCGGAAGAATGGG-GTTGGAGTATCCCCGACGATGACA
*
559104 ATTTAACCAAAAATAAGACTTAAATCTTGACGA
65 ATTTAACCAAAAATAAGACTTAAATCTTGACAA
* ** * *
559137 GTTTAAAAACGGGGTTAGAGTATCCCCTTGGAAGAATGAGGTTGGAGTATCCC
1 GTTAAAAAACAAGGTTAGAGTATCCCCTCGGAAGAATGGGGTTGGAGTATCCC
559190 AAATGATAGC
Statistics
Matches: 122, Mismatches: 27, Indels: 4
0.80 0.18 0.03
Matches are distributed among these distances:
97 41 0.34
98 81 0.66
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (97 bp):
GTTAAAAAACAAGGTTAGAGTATCCCCTCGGAAGAATGGGGTTGGAGTATCCCCGACGATGACAA
TTTAACCAAAAATAAGACTTAAATCTTGACAA
Found at i:559260 original size:88 final size:89
Alignment explanation
Indices: 559111--559280 Score: 227
Period size: 88 Copynumber: 1.9 Consensus size: 89
559101 ACAATTTAAC
* *
559111 CAAAAATAAGACTTAAATCTTGACGAGTTTAAAAACGGGGTTAGAGTATCCCCTTGGAAGAATGA
1 CAAAAATAAGACTTAAATCTTAACGAGTTTAAAAACGGGGTTAGAGTATCCCCTCGGAAGAAT-A
559176 -GGTTGGAGTATC-CCAAATGATAG
65 TGGTTGGAGTATCTCCAAATGATAG
** * * * * *
559199 CAAAAATAAGGTTTAAATTTTAATGAGTTTAAAAGCGGGGTTGGAGTATCCTCTCGGAAGAATAT
1 CAAAAATAAGACTTAAATCTTAACGAGTTTAAAAACGGGGTTAGAGTATCCCCTCGGAAGAATAT
*
559264 GGTTGGTGTATCTCCAA
66 GGTTGGAGTATCTCCAA
559281 TGAACAAAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
87 1 0.01
88 65 0.93
89 4 0.06
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.28
Consensus pattern (89 bp):
CAAAAATAAGACTTAAATCTTAACGAGTTTAAAAACGGGGTTAGAGTATCCCCTCGGAAGAATAT
GGTTGGAGTATCTCCAAATGATAG
Found at i:561712 original size:51 final size:52
Alignment explanation
Indices: 561606--561724 Score: 177
Period size: 51 Copynumber: 2.3 Consensus size: 52
561596 AATTGCCTGC
* * * *
561606 ATGTATCGATACATTTGTGTCAAAAACCTAAAATGTATAGATACAATGAAGA
1 ATGTATCGATACATTTGGGTCAAAAACCCAAAATGTATAGATACAATAAAAA
*
561658 ATGTATCGATACATTTGGGTC-AAAACCCAAAATGTATCGATACAATAAAAA
1 ATGTATCGATACATTTGGGTCAAAAACCCAAAATGTATAGATACAATAAAAA
*
561709 ATGTATCGATGCATTT
1 ATGTATCGATACATTT
561725 TCATTCTAGA
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
51 41 0.67
52 20 0.33
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.29
Consensus pattern (52 bp):
ATGTATCGATACATTTGGGTCAAAAACCCAAAATGTATAGATACAATAAAAA
Found at i:569094 original size:21 final size:21
Alignment explanation
Indices: 569070--569111 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
569060 AAAATAATTT
569070 TTTTTAAATAATTACATAAGC
1 TTTTTAAATAATTACATAAGC
569091 TTTTTAAATAATTACATAAGC
1 TTTTTAAATAATTACATAAGC
569112 AAAACGACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.43
Consensus pattern (21 bp):
TTTTTAAATAATTACATAAGC
Found at i:581665 original size:19 final size:18
Alignment explanation
Indices: 581641--581687 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
581631 GCTTTCAACT
* *
581641 AAAAAAAATAGAGAGCAAA
1 AAAAAAAAAAAAGAG-AAA
581660 AAAAAAAAAAAAGAGAAA
1 AAAAAAAAAAAAGAGAAA
581678 AAAGAAAAAA
1 AAA-AAAAAA
581688 GCAAAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.83, C:0.02, G:0.13, T:0.02
Consensus pattern (18 bp):
AAAAAAAAAAAAGAGAAA
Found at i:584406 original size:886 final size:885
Alignment explanation
Indices: 581794--585221 Score: 5521
Period size: 886 Copynumber: 3.9 Consensus size: 885
581784 TTCTTTTTTT
*
581794 TTGTAAGCTCTAGGAATAGATGAACCAAGAGGGAGGTGAATTGGATT-TTTCCAAAATTTGAATA
1 TTGTAAGCTCTAGGAATGGATGAACCAAGAGGGAGGTGAATTGG-TTCTTT-CAAAATTTGAATA
* * *
581858 TTTTGTAAGAATTGTTTTGAAAACAACTTGGAGATAAAGAGAATAGGGAAAAGAGAAAACTCGAC
64 TTTTGTAAGAATTGTTTCGAAAACAACTTGAAGATAAAGAGAATAGGGAAAAAAGAAAACTCGAC
* *
581923 ACAAGTGTTTATAGAGGTTCGGTCCAAACAC-AGCACCTACGTCCTCTCTCCTCGACACTTCTTT
129 ACAAGTGTTTATAGAGGTTCGGTCTAAACACGA-CACCTACGTCCTCTCTCCTCGACACTTCCTT
* * * * * *
581987 GTTGAGTGTTACCACAATCCACTACACGAATTGTTTACTTTTCATGAAA-GTATAACCTTACAAC
193 ATCGAGTGTAACCATAATCCACTACACGAATGGTTTACCTTTCATGAAAGGTATAACCTTACAAC
582051 ACGTATCTTTTCAAGGCTTAGATAAGAACCTCACAATCTCTTCAAGAATTATACCCCAAATTCTT
258 ACGTATCTTTTCAAGGCTTAGATAAGAACCTCACAATCTCTTCAAGAATTATACCCCAAATTCTT
* * * * *
582116 AAGAGATTGCAAACCAAGGTTGAATGCAATCTTAAATAATTCAAGGAAATTTTACAAATGAAAAC
323 AAGAGATTGTAAACCAAGGTTGAATGCAACCTTAAACAATTCAAGGAAATTTTACAAACGAAAAT
* * *
582181 TGCCTCTAGGTAGGCTGGTGTTTGTGAAAGAATAAGCATAAAATAAAGACAAAAGAGCTTTCAAA
388 TGCCTCTAGGTAGGCTGGTGTTTGTGAAAGAATAAGCACAAAATAAATACAAAAGAGCTTCCAAA
* * * *
582246 GAATGACAACAATGAGTTTAAAAGCTCTTGAAAAATGAGAAAAATGATACAACTTTGAATGCTTT
453 GAATAATAACAAAGAGTTTAAAAGCTCTTGAAAAATGAGAAAAATGATAAAACTTTGAATGCTTT
582311 GATCTCTTGATGTTTCTTAATGGTTCTCTTCTTCTTCAGCTGTTGGAAACTCAAATTTATAGGCT
518 GATCTCTTGATGTTTCTTAATGGTTCTCTTCTTCTTCAGCTGTTGGAAACTCAAATTTATAGGCT
* * * * * *
582376 AGAATGTTGACATACTCGTTGGAGGTTGAATGATTATGTTTGTAGCCGTTATTGACTTGTTTGGT
583 AAAATGTTGACATAATGGTTGAAGGTCGAATGATCATGTTTGTAGCCGTTATTGACTTGTTTGGT
* *
582441 GCTTGTTTCCATGCATTCCCGTTATTGTGTATCG---------AT-A-C-AT-G---CA--T-TT
648 GCTTGTTTCCATGCATGCCCGTTATTATGTATCGATACTTTTCATAATCTATCGATACATGTATT
* ** * * *
582487 -GAAAATTATAGTTGTCGGGCACAATGCATCGATACTTTTCACCATGTATTGATACACTTGCCTC
713 AGAAATTTATAGCCGTTGGGCACAATGCATCAATACTTTTCACCATGTATCGATACACTTGCCTC
* * * *
582551 ATTCTCCTGGGTTGAATGCATCAATACTTTTCAAGCTTTCCATTTGAGCTATAAAGATTGTTTCT
778 ATTCTCCCGGGTTGAATGCATCGATACTTTTCAAGTTTTCCATTTGAGCTATAAAGATCGTTTCT
* * *
582616 CCCGGGTGTTAATCCGATGAAGGA-ATTAGGCTCTGATACTAA
843 CTCGGGTGTTAATCCTATGAAGGAGATTAGGCTCTGATACTAG
*
582658 TTATAAGCTCTAGGAATGGATGAACCAAGAGGGAGGTGAATTGGTTCTTTCAAAAATTTGAATAT
1 TTGTAAGCTCTAGGAATGGATGAACCAAGAGGGAGGTGAATTGGTTCTTTC-AAAATTTGAATAT
* * *
582723 TTT-TAAGAATTGTTTCGAAAACAACTTGGAGATAAACAGAATAGGGAAAAGAGAAAACTCGACA
65 TTTGTAAGAATTGTTTCGAAAACAACTTGAAGATAAAGAGAATAGGGAAAAAAGAAAACTCGACA
* * * * * * *
582787 CAAGTATTTATAGAGGTTCGATCTAAACACGGCACTTACGTCCTCTCTTCTTGACACTTCCTTGT
130 CAAGTGTTTATAGAGGTTCGGTCTAAACACGACACCTACGTCCTCTCTCCTCGACACTTCCTTAT
* * *
582852 CGAGTGTTACCATAATCCACTAGACGAATTGTTTACCTTTCATGAAAGGTATAACCTTACAACAC
195 CGAGTGTAACCATAATCCACTACACGAATGGTTTACCTTTCATGAAAGGTATAACCTTACAACAC
582917 GTATCTTTTCAAGGCTTAGATAAGAACCTCACAATCTCTTCAAGAATTATACCCCAAATTCTTAA
260 GTATCTTTTCAAGGCTTAGATAAGAACCTCACAATCTCTTCAAGAATTATACCCCAAATTCTTAA
*
582982 GAGATTGTAAACCAAGGTTGAATGCAACCTTAAATAATTCAAGGAAATTTTACAAACGAAAATTG
325 GAGATTGTAAACCAAGGTTGAATGCAACCTTAAACAATTCAAGGAAATTTTACAAACGAAAATTG
* * *
583047 CCTCTAGATAAGCTGGTGTTTGTCAAAGAATAAG--C---------ACAAAAGAGCTTCCAAAGA
390 CCTCTAGGTAGGCTGGTGTTTGTGAAAGAATAAGCACAAAATAAATACAAAAGAGCTTCCAAAGA
* * *
583101 ACAATAACAATGAGTTTAAAAGCTTTTGAAAAATGAGAAAAATGATAAAACTTTGAATGCTTTGA
455 ATAATAACAAAGAGTTTAAAAGCTCTTGAAAAATGAGAAAAATGATAAAACTTTGAATGCTTTGA
*
583166 TCTCTTAATGTTTCTTAATGGTTCTCTTCTTCTTCAGCTGTTGGAAACTCAAATTTATAGGCTAA
520 TCTCTTGATGTTTCTTAATGGTTCTCTTCTTCTTCAGCTGTTGGAAACTCAAATTTATAGGCTAA
*
583231 AATGTTGACA-AATTGGTTGAAGGTCGAATGATTATGTTTGTAGCCGTTATTGACTTGTTTGGTG
585 AATGTTGACATAA-TGGTTGAAGGTCGAATGATCATGTTTGTAGCCGTTATTGACTTGTTTGGTG
*
583295 CTTGTTTCCATGCATGCCTGTTATTATGTATCGATACTTTTCATAATCTATCGATACATGTATTA
649 CTTGTTTCCATGCATGCCCGTTATTATGTATCGATACTTTTCATAATCTATCGATACATGTATTA
*
583360 GAAATTTATAGCCGTTGGGCACAATGCATCTATACTTTTCACCATGTATCGATACACTTGCCTCA
714 GAAATTTATAGCCGTTGGGCACAATGCATCAATACTTTTCACCATGTATCGATACACTTGCCTCA
583425 TTCTCCCGGGTTGAATGCATCGATACTTTTCAAGTTTTCCATTTGAGCTATAAAGATCGTTTCTC
779 TTCTCCCGGGTTGAATGCATCGATACTTTTCAAGTTTTCCATTTGAGCTATAAAGATCGTTTCTC
* *
583490 TCGGGTGTTAATCCTATGAAGGAGATTAGGCTTTGATACCAG
844 TCGGGTGTTAATCCTATGAAGGAGATTAGGCTCTGATACTAG
* *
583532 TTGTAAGCTCTAAGAATGGATGAACGAAGAGGGAGGTGAATTGGTTCATTTCAAAATTTGAATAT
1 TTGTAAGCTCTAGGAATGGATGAACCAAGAGGGAGGTGAATTGGTTC-TTTCAAAATTTGAATAT
* *
583597 TTTGTAAGAATTGTTTCGAAAATAACTTGAAGATAAATAGAATAGGGAAAAAAGAAAACTCGACA
65 TTTGTAAGAATTGTTTCGAAAACAACTTGAAGATAAAGAGAATAGGGAAAAAAGAAAACTCGACA
* *
583662 TAAGTGTTTATAGAGGTTCGGTCTAAACACGACACCTACGTCCTCTCTCCTCGACACTTCTTTAT
130 CAAGTGTTTATAGAGGTTCGGTCTAAACACGACACCTACGTCCTCTCTCCTCGACACTTCCTTAT
*
583727 CGAGTGTAACCATAGTCCACTACACGAATGGTTTACCTTTCA-GAAAAGGTATAACCTTACAACA
195 CGAGTGTAACCATAATCCACTACACGAATGGTTTACCTTTCATG-AAAGGTATAACCTTACAACA
*
583791 TGTATCTTTTCAAGGCTTAGATAAGAACCTCACAATCTCTTCAAGAATTATACCCCAAATTCTTA
259 CGTATCTTTTCAAGGCTTAGATAAGAACCTCACAATCTCTTCAAGAATTATACCCCAAATTCTTA
* *
583856 AGAGATTGTAAACCAAGGTTGAATGCAACCTTAAACAATTCAAGGAAATTTTAAAAACAAAAATT
324 AGAGATTGTAAACCAAGGTTGAATGCAACCTTAAACAATTCAAGGAAATTTTACAAACGAAAATT
583921 GCCTCTAGGTAGGCTGGTGTTTGTGAAAGAATAAGCACAAAATAAATACAAAAGAGCTTCCAAAG
389 GCCTCTAGGTAGGCTGGTGTTTGTGAAAGAATAAGCACAAAATAAATACAAAAGAGCTTCCAAAG
*
583986 AATAATAACAAAGAGTTTAAAAGCTCTTGAAAAATGAGAAAAATGATAAAACATTGAATGCTTTG
454 AATAATAACAAAGAGTTTAAAAGCTCTTGAAAAATGAGAAAAATGATAAAACTTTGAATGCTTTG
*
584051 ATCTCTTGATGTTTCTTAATGGTTCTCTTCTTCTTCAGCTATTGGAAACTCAAATTTATAGGCTA
519 ATCTCTTGATGTTTCTTAATGGTTCTCTTCTTCTTCAGCTGTTGGAAACTCAAATTTATAGGCTA
* * * *
584116 AAATATTGACATAATGGTTAAAGGTCAAATGATCATGTTTGTAGCCGTTATTGACTTGTTTAGTG
584 AAATGTTGACATAATGGTTGAAGGTCGAATGATCATGTTTGTAGCCGTTATTGACTTGTTTGGTG
*
584181 CTTGTTTCCATGCATGCCCGTTATTATGTATCGATACTTTTCATAATGTATCGATACATGTATTA
649 CTTGTTTCCATGCATGCCCGTTATTATGTATCGATACTTTTCATAATCTATCGATACATGTATTA
*
584246 GAAATTTATAGCCGTTGGGCACAATGCATTAATACTTTTCACCATGTATCGATACACTTGCCTCA
714 GAAATTTATAGCCGTTGGGCACAATGCATCAATACTTTTCACCATGTATCGATACACTTGCCTCA
584311 TTCTCCCGGGTTGAATGCATCGATACTTTTCAAGTTTTCCATTTGAGCTATAAAGATCGTTTCTC
779 TTCTCCCGGGTTGAATGCATCGATACTTTTCAAGTTTTCCATTTGAGCTATAAAGATCGTTTCTC
*
584376 TCGGGTGTTAAGCCTATGAAGGAGATTAGGCTCTGATACTAG
844 TCGGGTGTTAATCCTATGAAGGAGATTAGGCTCTGATACTAG
* * *
584418 CTGTAAGCTCTAGGAATGGATGAACAAAGAGGGAGGTGAATTGGTTCTTTTCAAAATTTAAATAT
1 TTGTAAGCTCTAGGAATGGATGAACCAAGAGGGAGGTGAATTGGTTC-TTTCAAAATTTGAATAT
584483 TTTGTAAGAATTGTTTCGAAAACAACTTGAAGATAAAGAGAATAGGGAAAAAAGAAAACTCGACA
65 TTTGTAAGAATTGTTTCGAAAACAACTTGAAGATAAAGAGAATAGGGAAAAAAGAAAACTCGACA
* *
584548 TAAGTGTTTATAGAGGTTCGGTCTAAACACGGCACCTACGTCCTCTCTCCTCGACACTTCCTTAT
130 CAAGTGTTTATAGAGGTTCGGTCTAAACACGACACCTACGTCCTCTCTCCTCGACACTTCCTTAT
*
584613 CGAGTGTAACCATAGTCCACTACACGAATGGTTTACCTTTCA-GAAAAGGTATAACCTTACAACA
195 CGAGTGTAACCATAATCCACTACACGAATGGTTTACCTTTCATG-AAAGGTATAACCTTACAACA
* *
584677 TGTATCTTTTCAAGGCTTAGATAAGAACCTCATAATCTCTTCAAGAATTATACCCCAAATTCTTA
259 CGTATCTTTTCAAGGCTTAGATAAGAACCTCACAATCTCTTCAAGAATTATACCCCAAATTCTTA
* *
584742 AGAGATTGTAAACTAAGGTTGAATGCAACCTTAAACAATTCAAGGAAATTTTGCAAACGAAAATT
324 AGAGATTGTAAACCAAGGTTGAATGCAACCTTAAACAATTCAAGGAAATTTTACAAACGAAAATT
* *
584807 GCCTCTAGGTAGGCTGGTGTTTGTGAAAGAATAAGCACACAATAAATACAAACGAGCTTCCAAAG
389 GCCTCTAGGTAGGCTGGTGTTTGTGAAAGAATAAGCACAAAATAAATACAAAAGAGCTTCCAAAG
*
584872 AATAATAACAAAGAGTTTAAAAGCTCTTGAAAAATAAGAAAAATGATAAAACTTTGAATGCTTTG
454 AATAATAACAAAGAGTTTAAAAGCTCTTGAAAAATGAGAAAAATGATAAAACTTTGAATGCTTTG
584937 ATCTCTTGATGTTTCTTAATGGTTCTCTTCTTCTTCAGCTGTTGGAAACTCAAATTTATAGGCTA
519 ATCTCTTGATGTTTCTTAATGGTTCTCTTCTTCTTCAGCTGTTGGAAACTCAAATTTATAGGCTA
* *
585002 AAATGTTGACATATTGGTTGAAGGTCGAATGATCATGTTTGTAGCTGTTATTGACTTGTTTGGTG
584 AAATGTTGACATAATGGTTGAAGGTCGAATGATCATGTTTGTAGCCGTTATTGACTTGTTTGGTG
*
585067 CTTGTTTCCATGCATGCACGTTATTATGTATCGATACTTTTCATAATCTATCGATACATGTATTA
649 CTTGTTTCCATGCATGCCCGTTATTATGTATCGATACTTTTCATAATCTATCGATACATGTATTA
*
585132 GAAATTTATAGCCATTGGGCACAATGCATCAATACTTTTCACCATGTATCGATACACTTGCCTCA
714 GAAATTTATAGCCGTTGGGCACAATGCATCAATACTTTTCACCATGTATCGATACACTTGCCTCA
*
585197 TTCTCCCGGGTTGAATACATCGATA
779 TTCTCCCGGGTTGAATGCATCGATA
585222 AAATTAAGTA
Statistics
Matches: 2394, Mismatches: 129, Indels: 60
0.93 0.05 0.02
Matches are distributed among these distances:
852 1 0.00
853 229 0.10
862 2 0.00
863 162 0.07
864 236 0.10
865 2 0.00
866 1 0.00
869 2 0.00
871 1 0.00
872 2 0.00
873 141 0.06
874 76 0.03
875 333 0.14
877 1 0.00
886 1203 0.50
887 2 0.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (885 bp):
TTGTAAGCTCTAGGAATGGATGAACCAAGAGGGAGGTGAATTGGTTCTTTCAAAATTTGAATATT
TTGTAAGAATTGTTTCGAAAACAACTTGAAGATAAAGAGAATAGGGAAAAAAGAAAACTCGACAC
AAGTGTTTATAGAGGTTCGGTCTAAACACGACACCTACGTCCTCTCTCCTCGACACTTCCTTATC
GAGTGTAACCATAATCCACTACACGAATGGTTTACCTTTCATGAAAGGTATAACCTTACAACACG
TATCTTTTCAAGGCTTAGATAAGAACCTCACAATCTCTTCAAGAATTATACCCCAAATTCTTAAG
AGATTGTAAACCAAGGTTGAATGCAACCTTAAACAATTCAAGGAAATTTTACAAACGAAAATTGC
CTCTAGGTAGGCTGGTGTTTGTGAAAGAATAAGCACAAAATAAATACAAAAGAGCTTCCAAAGAA
TAATAACAAAGAGTTTAAAAGCTCTTGAAAAATGAGAAAAATGATAAAACTTTGAATGCTTTGAT
CTCTTGATGTTTCTTAATGGTTCTCTTCTTCTTCAGCTGTTGGAAACTCAAATTTATAGGCTAAA
ATGTTGACATAATGGTTGAAGGTCGAATGATCATGTTTGTAGCCGTTATTGACTTGTTTGGTGCT
TGTTTCCATGCATGCCCGTTATTATGTATCGATACTTTTCATAATCTATCGATACATGTATTAGA
AATTTATAGCCGTTGGGCACAATGCATCAATACTTTTCACCATGTATCGATACACTTGCCTCATT
CTCCCGGGTTGAATGCATCGATACTTTTCAAGTTTTCCATTTGAGCTATAAAGATCGTTTCTCTC
GGGTGTTAATCCTATGAAGGAGATTAGGCTCTGATACTAG
Found at i:585240 original size:20 final size:19
Alignment explanation
Indices: 585215--585260 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
585205 GGTTGAATAC
* *
585215 ATCGATAAAATTAAGTATGT
1 ATCGATAAAATGAA-CATGT
*
585235 ATCGATACAATGAACATGT
1 ATCGATAAAATGAACATGT
585254 ATCGATA
1 ATCGATA
585261 CAAAGCATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.30
Consensus pattern (19 bp):
ATCGATAAAATGAACATGT
Found at i:586365 original size:20 final size:20
Alignment explanation
Indices: 586340--586383 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
586330 ATGACCTAGG
* *
586340 TTTTTATGTTATTTCATTCA
1 TTTTTATGTCATTTCAATCA
*
586360 TTTTTATGTCATTTTAATCA
1 TTTTTATGTCATTTCAATCA
586380 TTTT
1 TTTT
586384 CCATTACTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.09, G:0.05, T:0.66
Consensus pattern (20 bp):
TTTTTATGTCATTTCAATCA
Found at i:586474 original size:68 final size:68
Alignment explanation
Indices: 586380--586508 Score: 195
Period size: 68 Copynumber: 1.9 Consensus size: 68
586370 ATTTTAATCA
* * * * *
586380 TTTTCCATTACTTAGGAACTCTTATGACATTTCATGCATTTTAGTGCCTTTTAGTCATTTTCCCT
1 TTTTCCATAACTTAGGAACTCGTATGACATTTCATGCATTTTAATGCCATTTACTCATTTTCCCT
586445 AAC
66 AAC
* *
586448 TTTTCCCTAACTTAGGAACTCGTATGACATTTCATGCATTTTAATGTCATTTACTCATTTT
1 TTTTCCATAACTTAGGAACTCGTATGACATTTCATGCATTTTAATGCCATTTACTCATTTT
586509 TGATGACTTA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
68 54 1.00
ACGTcount: A:0.23, C:0.21, G:0.10, T:0.46
Consensus pattern (68 bp):
TTTTCCATAACTTAGGAACTCGTATGACATTTCATGCATTTTAATGCCATTTACTCATTTTCCCT
AAC
Found at i:586680 original size:114 final size:115
Alignment explanation
Indices: 586553--586817 Score: 349
Period size: 115 Copynumber: 2.3 Consensus size: 115
586543 TTTTAATGCT
* * * * *
586553 ATTTAAGTTATTTT-TCATGATTTAGGGACTTTTATGCATATTTATGTATATTAGGGTCA-TTAG
1 ATTTAAGTCATTTTCT-ATGATCTAAGGACTTTTATGCAAATGTATGTATATTAGGGTCATTTAG
* * *
586616 GTCATTTTCATGATCTAGGGACTTTCATGTCAA-TTTTAT-TATGTTAAGGTG
65 GTCATTTTCATGATCTA-GGACTTACATGT-AAGTTATATGTATATTAAGGTG
* * *
586667 ATTTAAGTCATTTTCTATGATCTAAGGACTTTTATGCAAATGTGTGTATGTTGGGGTCATTTAGG
1 ATTTAAGTCATTTTCTATGATCTAAGGACTTTTATGCAAATGTATGTATATTAGGGTCATTTAGG
**
586732 TCATTTTCATGATCTAGGACTTACATGTAAGTTATATGTATATTGGGGTG
66 TCATTTTCATGATCTAGGACTTACATGTAAGTTATATGTATATTAAGGTG
*
586782 ATTTAGGTCATTTTCTATGATCTAAGGACTTTTATG
1 ATTTAAGTCATTTTCTATGATCTAAGGACTTTTATG
586818 TAGTTGTTCC
Statistics
Matches: 133, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
113 2 0.02
114 65 0.49
115 66 0.50
ACGTcount: A:0.25, C:0.09, G:0.20, T:0.45
Consensus pattern (115 bp):
ATTTAAGTCATTTTCTATGATCTAAGGACTTTTATGCAAATGTATGTATATTAGGGTCATTTAGG
TCATTTTCATGATCTAGGACTTACATGTAAGTTATATGTATATTAAGGTG
Found at i:586697 original size:58 final size:58
Alignment explanation
Indices: 586564--586818 Score: 254
Period size: 57 Copynumber: 4.4 Consensus size: 58
586554 TTTAAGTTAT
* * * * * *
586564 TTTTCATGATTTAGGGACTTTTATG-CATATT-TATGTATATTAGGGTCA-TTAGGTCA
1 TTTTCATGATCTAAGGACTTTCATGTCA-ATTATATGTATGTTGGGGTGATTTAGGTCA
* * ** *
586620 TTTTCATGATCTAGGGACTTTCATGTCAATTTTAT-TATGTTAAGGTGATTTAAGTCA
1 TTTTCATGATCTAAGGACTTTCATGTCAATTATATGTATGTTGGGGTGATTTAGGTCA
* * * * *
586677 TTTTCTATGATCTAAGGACTTTTATG-CAAATGTGTGTATGTTGGGGTCATTTAGGTCA
1 TTTTC-ATGATCTAAGGACTTTCATGTCAATTATATGTATGTTGGGGTGATTTAGGTCA
* *
586735 TTTTCATGATCT-AGGACTTACATGT-AAGTTATATGTATATTGGGGTGATTTAGGTCA
1 TTTTCATGATCTAAGGACTTTCATGTCAA-TTATATGTATGTTGGGGTGATTTAGGTCA
*
586792 TTTTCTATGATCTAAGGACTTTTATGT
1 TTTTC-ATGATCTAAGGACTTTCATGT
586819 AGTTGTTCCA
Statistics
Matches: 166, Mismatches: 24, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
56 48 0.29
57 59 0.36
58 48 0.29
59 11 0.07
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.45
Consensus pattern (58 bp):
TTTTCATGATCTAAGGACTTTCATGTCAATTATATGTATGTTGGGGTGATTTAGGTCA
Found at i:586700 original size:29 final size:29
Alignment explanation
Indices: 586616--586700 Score: 68
Period size: 29 Copynumber: 3.0 Consensus size: 29
586606 GGGTCATTAG
* * *
586616 GTCATTTTC-ATGATCTAGGGACTTTCAT
1 GTCATTTTCTATGATCTAAGGACTTTTAA
* ***
586644 GTCAATTTTATTATG-T-TAAGGTGATTTAA
1 GTC-ATTTT-CTATGATCTAAGGACTTTTAA
586673 GTCATTTTCTATGATCTAAGGACTTTTA
1 GTCATTTTCTATGATCTAAGGACTTTTA
586701 TGCAAATGTG
Statistics
Matches: 41, Mismatches: 11, Indels: 9
0.67 0.18 0.15
Matches are distributed among these distances:
27 4 0.10
28 9 0.22
29 24 0.59
30 1 0.02
31 3 0.07
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.46
Consensus pattern (29 bp):
GTCATTTTCTATGATCTAAGGACTTTTAA
Found at i:589588 original size:253 final size:253
Alignment explanation
Indices: 589140--589643 Score: 1008
Period size: 253 Copynumber: 2.0 Consensus size: 253
589130 AAATCTTGAG
589140 GCTTGATCTAAGCACTAGGATGCTAAGTTAAGATTAAAGACCTAAAAATAAAATTCATAAGAATA
1 GCTTGATCTAAGCACTAGGATGCTAAGTTAAGATTAAAGACCTAAAAATAAAATTCATAAGAATA
589205 AACAAACTTATCTTAATACTCACCCTCGGTATGAAAACGAACCCGGTGGTTTCTTAAGATTTGGT
66 AACAAACTTATCTTAATACTCACCCTCGGTATGAAAACGAACCCGGTGGTTTCTTAAGATTTGGT
589270 TTCATAAGAAATTAGTGAAATATTCCCAAGACAAACCTACCCTTAATCTGTACCTTTGGCATTAA
131 TTCATAAGAAATTAGTGAAATATTCCCAAGACAAACCTACCCTTAATCTGTACCTTTGGCATTAA
589335 AGCGACTCGGTAATTTTGTAGGACTAGGTTTCGGAAACACGGCTGAAATTCCCCTAGT
196 AGCGACTCGGTAATTTTGTAGGACTAGGTTTCGGAAACACGGCTGAAATTCCCCTAGT
589393 GCTTGATCTAAGCACTAGGATGCTAAGTTAAGATTAAAGACCTAAAAATAAAATTCATAAGAATA
1 GCTTGATCTAAGCACTAGGATGCTAAGTTAAGATTAAAGACCTAAAAATAAAATTCATAAGAATA
589458 AACAAACTTATCTTAATACTCACCCTCGGTATGAAAACGAACCCGGTGGTTTCTTAAGATTTGGT
66 AACAAACTTATCTTAATACTCACCCTCGGTATGAAAACGAACCCGGTGGTTTCTTAAGATTTGGT
589523 TTCATAAGAAATTAGTGAAATATTCCCAAGACAAACCTACCCTTAATCTGTACCTTTGGCATTAA
131 TTCATAAGAAATTAGTGAAATATTCCCAAGACAAACCTACCCTTAATCTGTACCTTTGGCATTAA
589588 AGCGACTCGGTAATTTTGTAGGACTAGGTTTCGGAAACACGGCTGAAATTCCCCTA
196 AGCGACTCGGTAATTTTGTAGGACTAGGTTTCGGAAACACGGCTGAAATTCCCCTA
589644 ATGTTTACCA
Statistics
Matches: 251, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
253 251 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (253 bp):
GCTTGATCTAAGCACTAGGATGCTAAGTTAAGATTAAAGACCTAAAAATAAAATTCATAAGAATA
AACAAACTTATCTTAATACTCACCCTCGGTATGAAAACGAACCCGGTGGTTTCTTAAGATTTGGT
TTCATAAGAAATTAGTGAAATATTCCCAAGACAAACCTACCCTTAATCTGTACCTTTGGCATTAA
AGCGACTCGGTAATTTTGTAGGACTAGGTTTCGGAAACACGGCTGAAATTCCCCTAGT
Found at i:592068 original size:26 final size:26
Alignment explanation
Indices: 592037--592090 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
592027 CTTTTTTTAA
592037 TTAATTATTTAATTA-TTATTATTATT
1 TTAATTATTT-ATTATTTATTATTATT
*
592063 TTAATTATTTATTATTTATTTTTATT
1 TTAATTATTTATTATTTATTATTATT
592089 TT
1 TT
592091 TTGACAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 4 0.15
26 22 0.85
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (26 bp):
TTAATTATTTATTATTTATTATTATT
Found at i:602047 original size:52 final size:50
Alignment explanation
Indices: 601986--602082 Score: 158
Period size: 50 Copynumber: 1.9 Consensus size: 50
601976 TACATTTTTC
*
601986 AATGTATCGATACATCTGGGTAAAAAAAATAGAATGTATCGATACATTGAAA
1 AATGCATCGATACATCT-GG-AAAAAAAATAGAATGTATCGATACATTGAAA
*
602038 AATGCATCGATACATCTGGATAAAAAATAGAATGTATCGATACAT
1 AATGCATCGATACATCTGGAAAAAAAATAGAATGTATCGATACAT
602083 GTACCATTCA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
50 25 0.58
51 2 0.05
52 16 0.37
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.27
Consensus pattern (50 bp):
AATGCATCGATACATCTGGAAAAAAAATAGAATGTATCGATACATTGAAA
Found at i:602738 original size:16 final size:16
Alignment explanation
Indices: 602713--602748 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
602703 ACTTTTACTT
*
602713 CTTTGTTTGTTTTTAA
1 CTTTGATTGTTTTTAA
602729 CTTTGATTGTTTTTAA
1 CTTTGATTGTTTTTAA
602745 CTTT
1 CTTT
602749 TCTTAATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.14, C:0.08, G:0.11, T:0.67
Consensus pattern (16 bp):
CTTTGATTGTTTTTAA
Found at i:603016 original size:21 final size:23
Alignment explanation
Indices: 602992--603033 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
602982 TTTTTTTAGG
602992 GAAAATTTTT-ATT-AAGGGGGA
1 GAAAATTTTTAATTGAAGGGGGA
603013 GAAAATTTTTAATTGAAGGGG
1 GAAAATTTTTAATTGAAGGGG
603034 AGTTATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 10 0.53
22 3 0.16
23 6 0.32
ACGTcount: A:0.38, C:0.00, G:0.29, T:0.33
Consensus pattern (23 bp):
GAAAATTTTTAATTGAAGGGGGA
Found at i:603670 original size:33 final size:32
Alignment explanation
Indices: 603628--603690 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 32
603618 AGCCCAGAAG
*
603628 TATCGATACATGTTGCT-TTGTATCGATACATTA
1 TATCGATACATGTT--TATTATATCGATACATTA
603661 TATCGATACATGTTTATTATATCGATACAT
1 TATCGATACATGTTTATTATATCGATACAT
603691 GAAGAATTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 1 0.04
32 13 0.46
33 14 0.50
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (32 bp):
TATCGATACATGTTTATTATATCGATACATTA
Found at i:603786 original size:33 final size:33
Alignment explanation
Indices: 603740--603809 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 33
603730 CTACCACTGT
**
603740 TTGTATCGATACAT-GGGACATTGTATCGATACA
1 TTGTATCGATACATAGGGA-AAAGTATCGATACA
* * *
603773 TTGTATTGCTACATAGTGAAAAGTATCGATACA
1 TTGTATCGATACATAGGGAAAAGTATCGATACA
603806 TTGT
1 TTGT
603810 GCCTAACGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 28 0.90
34 3 0.10
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATAGGGAAAAGTATCGATACA
Found at i:605434 original size:2 final size:2
Alignment explanation
Indices: 605427--605451 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
605417 AAGGTGATAA
605427 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 A
605452 GTCCAAGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:606477 original size:17 final size:17
Alignment explanation
Indices: 606455--606488 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
606445 GTATTCACAA
606455 CTTTCTTATTTTTTTTC
1 CTTTCTTATTTTTTTTC
*
606472 CTTTCTTCTTTTTTTTC
1 CTTTCTTATTTTTTTTC
606489 TTGTCCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (17 bp):
CTTTCTTATTTTTTTTC
Found at i:610451 original size:3 final size:3
Alignment explanation
Indices: 610443--610485 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
610433 TTAAAAATCT
610443 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
610486 AAAAATCCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:612927 original size:37 final size:40
Alignment explanation
Indices: 612886--612961 Score: 104
Period size: 37 Copynumber: 2.0 Consensus size: 40
612876 AATATAAATA
* * *
612886 AAATTATATTTATGTTGAAAAAT-AATTA-TAAA-TTATT
1 AAATTACATTTATATTAAAAAATAAATTATTAAAGTTATT
612923 AAATTACATTTATATTAAAAAATAAATTATTAAAGTTAT
1 AAATTACATTTATATTAAAAAATAAATTATTAAAGTTAT
612962 ATTTATATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
37 20 0.61
38 5 0.15
39 4 0.12
40 4 0.12
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.43
Consensus pattern (40 bp):
AAATTACATTTATATTAAAAAATAAATTATTAAAGTTATT
Found at i:612982 original size:37 final size:35
Alignment explanation
Indices: 612862--612992 Score: 123
Period size: 32 Copynumber: 3.8 Consensus size: 35
612852 TTATTAAAAA
612862 TATATTAAATAATAAATATAAATA--AAATTATATT
1 TATATTAAATAATAAA-ATAAATATTAAATTATATT
* * *
612896 TATGTTGAAA-AATAATTATAAATTATTAAATTACATT
1 TATATT-AAATAATAA-AATAAA-TATTAAATTATATT
*
612933 TATATTAAAAAAT-AAAT---TATTAAAGTTATATT
1 TATATTAAATAATAAAATAAATATTAAA-TTATATT
*
612965 TATATTAAATAATAAAATAGATATTAAA
1 TATATTAAATAATAAAATAAATATTAAA
612993 ATTGGAAATT
Statistics
Matches: 79, Mismatches: 7, Indels: 20
0.75 0.07 0.19
Matches are distributed among these distances:
31 7 0.09
32 18 0.23
33 4 0.05
34 15 0.19
35 7 0.09
36 11 0.14
37 17 0.22
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (35 bp):
TATATTAAATAATAAAATAAATATTAAATTATATT
Found at i:614986 original size:20 final size:21
Alignment explanation
Indices: 614963--615001 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
614953 CAAAGCAATA
614963 TGTATCGATAC-TTCTAGGTT
1 TGTATCGATACTTTCTAGGTT
*
614983 TGTATCGATGCTTTCTAGG
1 TGTATCGATACTTTCTAGG
615002 GTTTTAACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.18, C:0.15, G:0.23, T:0.44
Consensus pattern (21 bp):
TGTATCGATACTTTCTAGGTT
Found at i:618644 original size:52 final size:51
Alignment explanation
Indices: 618503--618651 Score: 217
Period size: 52 Copynumber: 2.9 Consensus size: 51
618493 CGAAATATGA
*
618503 AAATTTGCCTGCATGTATCGATATATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* * *
618555 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGT
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
**
618607 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
618652 ATGTATCGAT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.95
53 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:618658 original size:13 final size:13
Alignment explanation
Indices: 618640--618664 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
618630 CAAAGATCAG
618640 TGTATCGATACAA
1 TGTATCGATACAA
618653 TGTATCGATACA
1 TGTATCGATACA
618665 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:618745 original size:13 final size:13
Alignment explanation
Indices: 618727--618751 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
618717 CAAAAAAATA
618727 TGTATCGATACAT
1 TGTATCGATACAT
618740 TGTATCGATACA
1 TGTATCGATACA
618752 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:618746 original size:33 final size:33
Alignment explanation
Indices: 618709--618771 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
618699 GCTTAAATTT
618709 TATCGATACAAAAAAATATGTATCGATACATTG
1 TATCGATACAAAAAAATATGTATCGATACATTG
* ***
618742 TATCGATACAACACTTTATGTATCGATACA
1 TATCGATACAAAAAAATATGTATCGATACA
618772 AATCGTTGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (33 bp):
TATCGATACAAAAAAATATGTATCGATACATTG
Found at i:619666 original size:55 final size:52
Alignment explanation
Indices: 619566--619850 Score: 199
Period size: 55 Copynumber: 5.7 Consensus size: 52
619556 GAAAAGTGAT
* * * * * **
619566 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAA
1 AAAG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG-GAA
* *
619620 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAA
1 AAA-G-TGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAA
* * *
619674 AAAGTGCCAATATGCTGATTCAAGGCTAGCTATATTGGACTT-AA-A--G--
1 AAAGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAA
* * *
619720 ---GTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTT-AAGTAT-G--
1 AAAGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAG-ATGGAA
* * * * * *
619766 AAGGTGCCAATATGCTGATTTAAGGCCAGCGATATTGGACTT-AA-A-GG-C
1 AAAGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAA
* *
619814 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTG
1 AAAGTGCCAATATGCTGATTCAAGGCCAGCTACATTG
619851 GGCTTAAAAG
Statistics
Matches: 197, Mismatches: 25, Indels: 24
0.80 0.10 0.10
Matches are distributed among these distances:
43 37 0.19
45 1 0.01
46 1 0.01
47 2 0.01
48 36 0.18
49 36 0.18
50 1 0.01
51 2 0.01
52 33 0.17
53 1 0.01
54 9 0.05
55 38 0.19
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (52 bp):
AAAGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAA
Found at i:619738 original size:43 final size:44
Alignment explanation
Indices: 619677--619861 Score: 210
Period size: 48 Copynumber: 4.0 Consensus size: 44
619667 GATGGAAAAA
*
619677 GTGCCAATATGCTGATTCAAGGCTAGCTATATTGGACTTA-AAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAGAAG
* * *
619720 GTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAGTATGAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T---TA-GAAG
* *
619769 GTGCCAATATGCTGATTTAAGGCCAGCGATATTGGACTTAAAGGCAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT--A-G-AAG
* *
619817 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAGAAG
619861 G
1 G
619862 AGACGCCACC
Statistics
Matches: 119, Mismatches: 14, Indels: 17
0.79 0.09 0.11
Matches are distributed among these distances:
43 33 0.28
44 5 0.04
45 1 0.01
46 1 0.01
47 4 0.03
48 40 0.34
49 35 0.29
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.28
Consensus pattern (44 bp):
GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAGAAG
Found at i:619747 original size:95 final size:93
Alignment explanation
Indices: 619619--619850 Score: 288
Period size: 92 Copynumber: 2.4 Consensus size: 93
619609 AAAGATGAGA
*
619619 AAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAG-ATGGAAAAAGTGCCA
1 AAAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTT-AAGTAT-G--AAAGTGCCA
* *
619683 ATATGCTGATTCAAGGCTAGCTATATTGGACTT
61 ATATGCTGATTCAAGGCCAGCGATATTGGACTT
* * *
619716 -AAAGGTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAGTATGAAGGTGCCAATATG
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAGTATGAAAGTGCCAATATG
*
619780 CTGATTTAAGGCCAGCGATATTGGACTT
66 CTGATTCAAGGCCAGCGATATTGGACTT
* *
619808 AAAGGCAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTG
1 -AA---AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTG
619851 GGCTTAAAAG
Statistics
Matches: 119, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
92 38 0.32
94 5 0.04
95 37 0.31
96 5 0.04
97 34 0.29
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (93 bp):
AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAGTATGAAAGTGCCAATATG
CTGATTCAAGGCCAGCGATATTGGACTT
Found at i:619809 original size:92 final size:94
Alignment explanation
Indices: 619619--619857 Score: 295
Period size: 97 Copynumber: 2.5 Consensus size: 94
619609 AAAGATGAGA
* *
619619 AAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAAGTGCCAA
1 AAAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT-AAGATGG-AAAAGTGCCAA
* *
619684 TATGCTGATTCAAGGCTAGCTATATTGGACTT
63 TATGCTGATTCAAGGCCAGCGATATTGGACTT
* *
619716 -AAAGGTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAGTAT-G-AAGGTGCCAATA
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAG-ATGGAAAAGTGCCAATA
*
619778 TGCTGATTTAAGGCCAGCGATATTGGACTT
65 TGCTGATTCAAGGCCAGCGATATTGGACTT
* * *
619808 AAAGGCAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAA
1 -AA---AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAA
619858 AAGGAGACGC
Statistics
Matches: 125, Mismatches: 11, Indels: 12
0.84 0.07 0.08
Matches are distributed among these distances:
92 38 0.30
94 5 0.04
95 37 0.30
96 5 0.04
97 40 0.32
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (94 bp):
AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAGATGGAAAAGTGCCAATAT
GCTGATTCAAGGCCAGCGATATTGGACTT
Found at i:619935 original size:28 final size:28
Alignment explanation
Indices: 619878--620001 Score: 126
Period size: 28 Copynumber: 4.3 Consensus size: 28
619868 CACCAACTTG
*
619878 TGTGGGCTTTTGAGAGGTTTG-CA-TCAACT
1 TGTGGGCTTTTGA-AGG-TTGCCACT-GACT
* * *
619907 TATGTGCTTTTGAAGGTTGCTACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
*
619935 TGTGGGCTTTTAAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* *
619963 TGTGGGCTTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTTG--AAGGTTGCCACTGACT
619993 TGTGGGCTT
1 TGTGGGCTT
620002 AAAAAGAAAA
Statistics
Matches: 80, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
27 3 0.04
28 42 0.52
29 12 0.15
30 23 0.29
ACGTcount: A:0.18, C:0.15, G:0.30, T:0.37
Consensus pattern (28 bp):
TGTGGGCTTTTGAAGGTTGCCACTGACT
Found at i:620106 original size:29 final size:29
Alignment explanation
Indices: 620042--620274 Score: 220
Period size: 29 Copynumber: 8.0 Consensus size: 29
620032 GCTTACAAAA
* * * *
620042 GAAAAAGAGTGCCACGGAGTTGTCGACTTT
1 GAAAAAGA-TGCCACTGACTTGTGGGCTTT
* * *
620072 GGAAAAGATGCCACCGACTTGTGGGCTTC
1 GAAAAAGATGCCACTGACTTGTGGGCTTT
* *
620101 GAAAAAGGGTGCCACTGATTTGTGGGCTTT
1 GAAAAA-GATGCCACTGACTTGTGGGCTTT
* *
620131 G--AAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAAGATGCCACTGACTTGTGGGC-TTT
* *
620159 GAAAAAAAATGACACTGACTTGTGGGCTTT
1 G-AAAAAGATGCCACTGACTTGTGGGCTTT
*
620189 GAAAAAGATGCCACTGACTTATGGGCTTT
1 GAAAAAGATGCCACTGACTTGTGGGCTTT
* * *
620218 -TAAAGGTTGCCACTGACTTGTGGGCTTT
1 GAAAAAGATGCCACTGACTTGTGGGCTTT
* * * *
620246 GAAAAATATGCCACTAACTTTTGGACTTT
1 GAAAAAGATGCCACTGACTTGTGGGCTTT
620275 TGAAGGGTGA
Statistics
Matches: 165, Mismatches: 32, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
27 18 0.11
28 30 0.18
29 67 0.41
30 31 0.19
31 19 0.12
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (29 bp):
GAAAAAGATGCCACTGACTTGTGGGCTTT
Found at i:620143 original size:27 final size:27
Alignment explanation
Indices: 620078--620248 Score: 144
Period size: 30 Copynumber: 6.0 Consensus size: 27
620068 CTTTGGAAAA
* *
620078 GATGCCACCGACTTGTGGGCTTCGAAAAAG
1 GATGCCACTGACTTGTGGGCTTTG---AAG
* *
620108 GGTGCCACTGATTTGTGGGCTTTGAAG
1 GATGCCACTGACTTGTGGGCTTTGAAG
* *
620135 GTTGCCACTGACTTGTGGGCTTTTGAAAAAA
1 GATGCCACTGACTTGTGGGC-TTTG---AAG
* * *
620166 AATGACACTGACTTGTGGGCTTTGAAAAA
1 GATGCCACTGACTTGTGGGCTTTG--AAG
* *
620195 GATGCCACTGACTTATGGGCTTTTAAAG
1 GATGCCACTGACTTGTGGGC-TTTGAAG
*
620223 GTTGCCACTGACTTGTGGGCTTTGAA
1 GATGCCACTGACTTGTGGGCTTTGAA
620249 AAATATGCCA
Statistics
Matches: 118, Mismatches: 18, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
27 26 0.22
28 24 0.20
29 22 0.19
30 27 0.23
31 19 0.16
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.30
Consensus pattern (27 bp):
GATGCCACTGACTTGTGGGCTTTGAAG
Found at i:620224 original size:88 final size:87
Alignment explanation
Indices: 620087--620251 Score: 260
Period size: 88 Copynumber: 1.9 Consensus size: 87
620077 AGATGCCACC
* * * *
620087 GACTTGTGGGCTTCGAAAAAGGGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTGACTTGTG
1 GACTTGTGGGCTTCGAAAAAGGATGCCACTGACTTATGGGCTTTAAAGGTTGCCACTGACTTGTG
620152 GGCTTTTGAAAAAAAATGACACT
66 GGC-TTTGAAAAAAAATGACACT
*
620175 GACTTGTGGGCTTTGAAAAA-GATGCCACTGACTTATGGGCTTTTAAAGGTTGCCACTGACTTGT
1 GACTTGTGGGCTTCGAAAAAGGATGCCACTGACTTATGGGC-TTTAAAGGTTGCCACTGACTTGT
620239 GGGCTTTGAAAAA
65 GGGCTTTGAAAAA
620252 TATGCCACTA
Statistics
Matches: 71, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
87 26 0.37
88 45 0.63
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.30
Consensus pattern (87 bp):
GACTTGTGGGCTTCGAAAAAGGATGCCACTGACTTATGGGCTTTAAAGGTTGCCACTGACTTGTG
GGCTTTGAAAAAAAATGACACT
Done.