Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007801.1 Hibiscus syriacus cultivar Beakdansim tig00110118_pilon, whole genome shotgun sequence
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: 951604
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:419574 original size:2 final size:2
Alignment explanation
Indices: 419567--419591 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
419557 GTGAGACATA
419567 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
419592 ACAATGCATT
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:419885 original size:18 final size:18
Alignment explanation
Indices: 419862--419896 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
419852 GACCACTGAT
419862 TGTTCCGAAGAACCACTA
1 TGTTCCGAAGAACCACTA
*
419880 TGTTCCGAAGGACCACT
1 TGTTCCGAAGAACCACT
419897 GATAATCCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.23
Consensus pattern (18 bp):
TGTTCCGAAGAACCACTA
Found at i:426449 original size:2 final size:2
Alignment explanation
Indices: 426436--426478 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
426426 GTGAGGCATA
*
426436 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
426478 A
1 A
426479 ACAATGCATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:426752 original size:18 final size:18
Alignment explanation
Indices: 426729--426801 Score: 74
Period size: 18 Copynumber: 3.9 Consensus size: 18
426719 ACTAAATATT
**
426729 TGTCCCGAAGGACCACTA
1 TGTCCCGAAAAACCACTA
*
426747 TGTCCCGAAAAACCATTGA
1 TGTCCCGAAAAACCACT-A
* *
426766 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAAAACCACTA
*
426785 TGTCCCGAAAGACCACT
1 TGTCCCGAAAAACCACT
426802 GATAATTCCT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
18 28 0.64
19 2 0.05
20 14 0.32
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAAAACCACTA
Found at i:426784 original size:38 final size:38
Alignment explanation
Indices: 426728--426804 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
426718 CACTAAATAT
* *
426728 TTGTCCCGAAGGACCACTATGTCCCGAAAAACCATTGA
1 TTGTCCCGAAGAACCACTATGTCCCGAAAAACCACTGA
* *
426766 TTGTTCCGAAGAACCACTATGTCCCGAAAGACCACTGA
1 TTGTCCCGAAGAACCACTATGTCCCGAAAAACCACTGA
426804 T
1 T
426805 AATTCCTCGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (38 bp):
TTGTCCCGAAGAACCACTATGTCCCGAAAAACCACTGA
Found at i:427463 original size:64 final size:64
Alignment explanation
Indices: 427377--427512 Score: 143
Period size: 64 Copynumber: 2.1 Consensus size: 64
427367 CTTGACGGGT
** * *
427377 GCATCGATGCACAATCTATGCATC-AGTACA-TAAATCCCATTCGATGTTTGTATTTTAAGGGGG
1 GCATCGATGCACAATCTATGCATCGA-TACACT-AATAACATTCGATGTTTGTATTTTAAAGGAG
427440 C
64 C
* * * * *
427441 GCATCGATGCACTA-CTTGTGCATCGATACACTAATAATATTCGATGTTTTTATTTTAAAGGAGT
1 GCATCGATGCACAATC-TATGCATCGATACACTAATAACATTCGATGTTTGTATTTTAAAGGAGC
427505 GCATCGAT
1 GCATCGAT
427513 ATACCTCATG
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
63 1 0.02
64 57 0.95
65 2 0.03
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (64 bp):
GCATCGATGCACAATCTATGCATCGATACACTAATAACATTCGATGTTTGTATTTTAAAGGAGC
Found at i:427525 original size:64 final size:64
Alignment explanation
Indices: 427415--427535 Score: 163
Period size: 64 Copynumber: 1.9 Consensus size: 64
427405 CATAAATCCC
* * * *
427415 ATTCGATGTTTGTATTTTAAGGGGGCGCATCGATGCACTACTTGTGCATCGATACACTAATAAT
1 ATTCGATGTTTGTATTTTAAAGGAGCGCATCGATACACTACATGTGCATCGATACACTAATAAT
* * *
427479 ATTCGATGTTTTTATTTTAAAGGAGTGCATCGATATACCT-CATGTGCATCGATACAC
1 ATTCGATGTTTGTATTTTAAAGGAGCGCATCGATACA-CTACATGTGCATCGATACAC
427536 CTTGAACAGT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
64 47 0.96
65 2 0.04
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (64 bp):
ATTCGATGTTTGTATTTTAAAGGAGCGCATCGATACACTACATGTGCATCGATACACTAATAAT
Found at i:431747 original size:16 final size:15
Alignment explanation
Indices: 431724--431811 Score: 54
Period size: 16 Copynumber: 5.5 Consensus size: 15
431714 TTTCAAATTA
431724 AAAT-TAATAACAAAT
1 AAATATAATAA-AAAT
*
431739 AAATATAATAATAAT
1 AAATATAATAAAAAT
* * *
431754 TAATA-ACAGTAATTATT
1 AAATATA-A-TAA-AAAT
431771 AAATATAATAAATAAGT
1 AAATATAATAAA-AA-T
431788 AAAATATAATAATAAAT
1 -AAATATAATAA-AAAT
431805 AAATATA
1 AAATATA
431812 GTAATTAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
14 1 0.02
15 12 0.21
16 20 0.34
17 10 0.17
18 14 0.24
19 1 0.02
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (15 bp):
AAATATAATAAAAAT
Found at i:431816 original size:16 final size:16
Alignment explanation
Indices: 431724--431838 Score: 78
Period size: 17 Copynumber: 7.1 Consensus size: 16
431714 TTTCAAATTA
*
431724 AAAT-TAATAACAAAT
1 AAATATAATAATAAAT
431739 AAATATAATAAT-AAT
1 AAATATAATAATAAAT
* * *
431754 TAATA-ACAGTAATTATT
1 AAATATA-A-TAATAAAT
*
431771 AAATATAATAAATAAGT
1 AAATATAAT-AATAAAT
431788 AAAATATAATAATAAAT
1 -AAATATAATAATAAAT
*
431805 AAATATAGTAATTAAA-
1 AAATATAATAA-TAAAT
*
431821 AAGATATTAT-ATAAAT
1 AA-ATATAATAATAAAT
431837 AA
1 AA
431839 TAATTATAAT
Statistics
Matches: 80, Mismatches: 10, Indels: 19
0.73 0.09 0.17
Matches are distributed among these distances:
14 1 0.01
15 16 0.20
16 26 0.32
17 27 0.34
18 10 0.12
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (16 bp):
AAATATAATAATAAAT
Found at i:432257 original size:23 final size:25
Alignment explanation
Indices: 432222--432267 Score: 62
Period size: 23 Copynumber: 1.9 Consensus size: 25
432212 GGTGAATTAA
432222 TTATATTATTTTGTATT-TTTAGTAT
1 TTATATTATTTTGT-TTGTTTAGTAT
432247 TTAT-TTA-TTTGTTTGTTTAGT
1 TTATATTATTTTGTTTGTTTAGT
432268 TTATTTGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 2 0.10
23 11 0.55
24 3 0.15
25 4 0.20
ACGTcount: A:0.20, C:0.00, G:0.11, T:0.70
Consensus pattern (25 bp):
TTATATTATTTTGTTTGTTTAGTAT
Found at i:432270 original size:17 final size:16
Alignment explanation
Indices: 432246--432277 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
432236 ATTTTTAGTA
432246 TTTATTTATTTGTTTG
1 TTTATTTATTTGTTTG
432262 TTTAGTTTATTTGTTT
1 TTTA-TTTATTTGTTT
432278 TGGTATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.75
Consensus pattern (16 bp):
TTTATTTATTTGTTTG
Found at i:432794 original size:24 final size:24
Alignment explanation
Indices: 432752--432814 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
432742 TTATTTATGA
* *
432752 ATATTTATTAATATTGAAATTTA-T
1 ATATTTATT-ATTTTGAAATTAAGT
432776 ATATTTATTATTTTGGAAATTAAGT
1 ATATTTATTATTTT-GAAATTAAGT
432801 A-ATTATATTATTTT
1 ATATT-TATTATTTT
432815 ATTAATTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 4 0.12
24 19 0.56
25 11 0.32
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (24 bp):
ATATTTATTATTTTGAAATTAAGT
Found at i:435691 original size:30 final size:28
Alignment explanation
Indices: 435611--435693 Score: 71
Period size: 28 Copynumber: 2.9 Consensus size: 28
435601 GCAAGAGAAA
* *
435611 AAAATAAACTTAAGGGATT-AAATAGCAC
1 AAAA-AAATTTAAAGGATTAAAATAGCAC
* **
435639 AAAAAAATTTAAAGTACCAAAATAGCAC
1 AAAAAAATTTAAAGGATTAAAATAGCAC
435667 AAACCGAAAA-TTAAAGGATTAAAATAG
1 AAA---AAAATTTAAAGGATTAAAATAG
435694 TATTAACAGA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
27 9 0.21
28 16 0.37
30 14 0.33
31 4 0.09
ACGTcount: A:0.58, C:0.11, G:0.12, T:0.19
Consensus pattern (28 bp):
AAAAAAATTTAAAGGATTAAAATAGCAC
Found at i:436851 original size:2 final size:2
Alignment explanation
Indices: 436841--436911 Score: 135
Period size: 2 Copynumber: 36.0 Consensus size: 2
436831 AAAAATGTAT
436841 TA TA T- TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
436882 TA TA 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 TA TA
436912 GGTTACATAT
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 67 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:437632 original size:85 final size:85
Alignment explanation
Indices: 437494--437978 Score: 557
Period size: 85 Copynumber: 5.7 Consensus size: 85
437484 ACACGGCCTC
* * *
437494 GAGCTGAATGGT-ATCAAACTCAGCA-GTGTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTAT
1 GAGCTGAAT-GTAATCAAACTC-GAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTAT
* *
437557 ACTGTAAATTTGATATGCCTCT
64 GCTGTAAATTTGATATGCCTTT
* * * * * * *
437579 GAGCTTAGTGTAATCAAACTCGAA-GTATTTTGATGAAATATAACCCTTTTCGCCTTGAGTTATG
1 GAGCTGAATGTAATCAAACTCGAAGGT-TTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
*
437643 CTATAAATTTGATATGCCTTT
65 CTGTAAATTTGATATGCCTTT
* * * * * *
437664 GAGTTGAGTGTAATCGAACTCGAAGGTCTTTGTT-AGCAGATACCCCTTCTCACCTTGAGCTATG
1 GAGCTGAATGTAATCAAACTCGAAGGTTTTTGTTGA-CAGATAACCCTTCTCGCCTTGAGCTATG
** *
437728 CTACAAATTTAATATGCCTTT
65 CTGTAAATTTGATATGCCTTT
** * * * * *
437749 GAGCTGAATGTAATTGAACACGAAGGTTTTTGCTGACAGATAACCCTTCTCACCTTGAGTTATGT
1 GAGCTGAATGTAATCAAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
* *
437814 TGTAAATTGGATATGCCTAT
66 TGTAAATTTGATATGCCTTT
*
437834 GAGCTGAATGTAAT-AGAACTCGAAGGTTTTTTGTTGATAGATAACCCTTCTCGCCTTGAGCTAT
1 GAGCTGAATGTAATCA-AACTCGAAGG-TTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTAT
*
437898 ACTGTAAATTTGATATGCCTTT
64 GCTGTAAATTTGATATGCCTTT
* * *
437920 AAGCTGAATGTAATCAAACTCGAAGGTCTTTGTTGACATATAACCCTTCTCGCCTTGAG
1 GAGCTGAATGTAATCAAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAG
437979 TTTTGTTGTA
Statistics
Matches: 338, Mismatches: 54, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
84 7 0.02
85 253 0.75
86 77 0.23
87 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (85 bp):
GAGCTGAATGTAATCAAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
TGTAAATTTGATATGCCTTT
Found at i:437829 original size:170 final size:171
Alignment explanation
Indices: 437522--437988 Score: 616
Period size: 170 Copynumber: 2.7 Consensus size: 171
437512 CTCAGCAGTG
* * * *
437522 TTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATACTGTAAATTTGATATGCCTCTGAGCTTAG
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATACTGTAAATTTGATATGCCTTTGAGCTGAA
* * * *
437587 TGTAATCAAACTCGAA-GTATTTTGATGAAATATAACCCTTTTCGCCTTGAGTTATGCTATAAAT
66 TGTAATCAAACTCGAAGGT-TTTTGATGACATATAACCCTTCTCGCCTTGAGTTATGTTGTAAAT
* * * * *
437651 TTGATATGCCTTTGAGTTGAGTGTAATCGAACTCGAAGG-TC
130 TGGATATGCCTATGAGCTGAATGTAATAGAACTCGAAGGTTC
* * * ** *
437692 TTTGTT-AGCAGATACCCCTTCTCACCTTGAGCTATGCTACAAATTTAATATGCCTTTGAGCTGA
1 TTTGTTGA-CAGATAACCCTTCTCGCCTTGAGCTATACTGTAAATTTGATATGCCTTTGAGCTGA
** * * * *
437756 ATGTAATTGAACACGAAGGTTTTTGCTGACAGATAACCCTTCTCACCTTGAGTTATGTTGTAAAT
65 ATGTAATCAAACTCGAAGGTTTTTGATGACATATAACCCTTCTCGCCTTGAGTTATGTTGTAAAT
*
437821 TGGATATGCCTATGAGCTGAATGTAATAGAACTCGAAGGTTT
130 TGGATATGCCTATGAGCTGAATGTAATAGAACTCGAAGGTTC
* *
437863 TTTGTTGATAGATAACCCTTCTCGCCTTGAGCTATACTGTAAATTTGATATGCCTTTAAGCTGAA
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATACTGTAAATTTGATATGCCTTTGAGCTGAA
* * *
437928 TGTAATCAAACTCGAAGGTCTTTGTTGACATATAACCCTTCTCGCCTTGAGTTTTGTTGTA
66 TGTAATCAAACTCGAAGGTTTTTGATGACATATAACCCTTCTCGCCTTGAGTTATGTTGTA
437989 TTTGGCTGGG
Statistics
Matches: 252, Mismatches: 41, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
169 1 0.00
170 139 0.55
171 111 0.44
172 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (171 bp):
TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATACTGTAAATTTGATATGCCTTTGAGCTGAA
TGTAATCAAACTCGAAGGTTTTTGATGACATATAACCCTTCTCGCCTTGAGTTATGTTGTAAATT
GGATATGCCTATGAGCTGAATGTAATAGAACTCGAAGGTTC
Found at i:438279 original size:124 final size:124
Alignment explanation
Indices: 438059--438282 Score: 333
Period size: 124 Copynumber: 1.8 Consensus size: 124
438049 ATCTATTTGA
*
438059 CACGATATCATTCTTCGTGAAGTTGAAATCGTGGATGGATCATTCGTTATGAAGTTGAGCTTTGA
1 CACGATATCATTCTTCGTGAAGTTGAAATCGTGAATGGATCATTCGTTATGAAGTTGAGCTTTGA
* * *
438124 ATTTGATATCCTTCGTTGTGATGTTAAAATCCAATCTAGAGATGGATGTTGCTTGTGGG
66 ATTAGATATCCTTCATTGTGAAGTTAAAATCCAATCTAGAGATGGATGTTGCTTGTGGG
* * * * *
438183 CACGATATCCTTCGTT-GTGAAGTTGAAATCGTGAATGGCTCATTCGTTGTGAATTTGATCTTTG
1 CACGATATCATTC-TTCGTGAAGTTGAAATCGTGAATGGATCATTCGTTATGAAGTTGAGCTTTG
* *
438247 AATTAGATATCCTTTATTGTGAAGTTGAAATCCAAT
65 AATTAGATATCCTTCATTGTGAAGTTAAAATCCAAT
438283 GGTTGTTTCA
Statistics
Matches: 88, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
124 86 0.98
125 2 0.02
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (124 bp):
CACGATATCATTCTTCGTGAAGTTGAAATCGTGAATGGATCATTCGTTATGAAGTTGAGCTTTGA
ATTAGATATCCTTCATTGTGAAGTTAAAATCCAATCTAGAGATGGATGTTGCTTGTGGG
Found at i:438439 original size:64 final size:64
Alignment explanation
Indices: 438368--438787 Score: 648
Period size: 64 Copynumber: 6.6 Consensus size: 64
438358 TTGTTTCGAT
* * * *
438368 TCCAATATCATTCGCTGTGAAGTTAAAATTGACTCTGAATGAATCTGGGAAGTTGTTTGTTGAG
1 TCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTGAG
438432 TCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTGAG
1 TCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTGAG
* *
438496 TCCAATATCCTTCGCTGTTAAGTTGAAATTGACTCTGAATGAAAATGGAAAGTTGTTTGTTGAG
1 TCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTGAG
* *
438560 TCCAATATCCTTCGTTATGAAGTTGAAATTGACTCTGAATGAAACTGTG-AAGTTGTTTGTTGAG
1 TCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTG-GAAAGTTGTTTGTTGAG
* * *
438624 TCCAATATCATTCGCTGTGAAGTTGAAATTAACTCTGAAT-AGAACTGGAAAGTTGTTTGTTAAG
1 TCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGA-AACTGGAAAGTTGTTTGTTGAG
*
438688 TCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTAGG-AAGTTATTTGTTGAG
1 TCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACT-GGAAAGTTGTTTGTTGAG
* * * *
438752 TCTAATATCCTTTGTTGTGTAGTTGAAATTGACTCT
1 TCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCT
438788 AAAAGCTGCA
Statistics
Matches: 328, Mismatches: 23, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
63 2 0.01
64 322 0.98
65 4 0.01
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (64 bp):
TCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTGAG
Found at i:439729 original size:95 final size:95
Alignment explanation
Indices: 439534--439794 Score: 344
Period size: 95 Copynumber: 2.7 Consensus size: 95
439524 GGCTAGCTGG
* * * * *
439534 ATCCATAAAGCCAGGGCATTTAACCAATTTCTCTATAGGGACAGCTCAATGTCATTGTA-TAGAT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAGCTCAA-G-C-TT-TATTATAT
* *
439598 ATTATAATCACTTTTATCAGGCTAGATGAATATT
62 ATTATAATCACCTTTATCAAGCTAGATGAATATT
* * *
439632 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGATGGACAACTCAAGCTTTATTATATATTA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAGCTCAAGCTTTATTATATATTA
*
439697 TAATCACCTTTATCAAGCTAGATGAATCTT
66 TAATCACCTTTATCAAGCTAGATGAATATT
* * *
439727 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGATAGCTAAAGCTTTATTGTATATAT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAGCTCAAGCTTTATTATATAT-T
439792 ATA
65 ATA
439795 TATTATTATA
Statistics
Matches: 144, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
94 2 0.01
95 94 0.65
96 5 0.03
97 1 0.01
98 42 0.29
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (95 bp):
ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAGCTCAAGCTTTATTATATATTA
TAATCACCTTTATCAAGCTAGATGAATATT
Found at i:442214 original size:12 final size:13
Alignment explanation
Indices: 442197--442225 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
442187 CTCAATTGCG
442197 AAAATTTAAA-TT
1 AAAATTTAAATTT
442209 AAAATTTAAATTT
1 AAAATTTAAATTT
442222 AAAA
1 AAAA
442226 ATTCGATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAAATTTAAATTT
Found at i:442527 original size:30 final size:28
Alignment explanation
Indices: 442447--442529 Score: 71
Period size: 28 Copynumber: 2.9 Consensus size: 28
442437 GCAAGAGAAA
* *
442447 AAAATAAACTTAAGGGATT-AAATAGCAC
1 AAAA-AAATTTAAAGGATTAAAATAGCAC
* **
442475 AAAAAAATTTAAAGTACCAAAATAGCAC
1 AAAAAAATTTAAAGGATTAAAATAGCAC
442503 AAACCGAAAA-TTAAAGGATTAAAATAG
1 AAA---AAAATTTAAAGGATTAAAATAG
442530 TATTAACAGA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
27 9 0.21
28 16 0.37
30 14 0.33
31 4 0.09
ACGTcount: A:0.58, C:0.11, G:0.12, T:0.19
Consensus pattern (28 bp):
AAAAAAATTTAAAGGATTAAAATAGCAC
Found at i:443571 original size:29 final size:30
Alignment explanation
Indices: 443518--443581 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
443508 TCTTCATCAA
* * *
443518 TTTTCCAAAATTTACGAATTTATCCCCAAC
1 TTTTCCAAAACTTACGAAATGATCCCCAAC
*
443548 TTTTCC-AAACTTACGAAATGATCCCCAAT
1 TTTTCCAAAACTTACGAAATGATCCCCAAC
443577 TTTTC
1 TTTTC
443582 TGAGGCTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 24 0.80
30 6 0.20
ACGTcount: A:0.31, C:0.27, G:0.05, T:0.38
Consensus pattern (30 bp):
TTTTCCAAAACTTACGAAATGATCCCCAAC
Found at i:447222 original size:29 final size:29
Alignment explanation
Indices: 447180--447266 Score: 158
Period size: 29 Copynumber: 3.0 Consensus size: 29
447170 ATTTTCACCT
447180 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
447209 AACTAAATTGATGTAAGCAATGACATC-A
1 AACTAAATTGATGTAAGCAATGACATCAA
*
447237 AACTAAATTAATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
447266 A
1 A
447267 TTAATTTAGG
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
28 27 0.48
29 29 0.52
ACGTcount: A:0.49, C:0.14, G:0.13, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:447250 original size:28 final size:28
Alignment explanation
Indices: 447180--447266 Score: 156
Period size: 28 Copynumber: 3.1 Consensus size: 28
447170 ATTTTCACCT
447180 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATC-A
447209 AACTAAATTGATGTAAGCAATGACATCA
1 AACTAAATTGATGTAAGCAATGACATCA
*
447237 AACTAAATTAATGTAAGCAATGACATCA
1 AACTAAATTGATGTAAGCAATGACATCA
447265 AA
1 AA
447267 TTAATTTAGG
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
28 30 0.53
29 27 0.47
ACGTcount: A:0.49, C:0.14, G:0.13, T:0.24
Consensus pattern (28 bp):
AACTAAATTGATGTAAGCAATGACATCA
Found at i:451786 original size:28 final size:29
Alignment explanation
Indices: 451755--451812 Score: 109
Period size: 28 Copynumber: 2.0 Consensus size: 29
451745 AATTTTCACC
451755 AAACTAAATTGATGTAAGC-ATGACATCA
1 AAACTAAATTGATGTAAGCAATGACATCA
451783 AAACTAAATTGATGTAAGCAATGACATCA
1 AAACTAAATTGATGTAAGCAATGACATCA
451812 A
1 A
451813 TTAATTTATG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 19 0.66
29 10 0.34
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AAACTAAATTGATGTAAGCAATGACATCA
Found at i:462993 original size:30 final size:30
Alignment explanation
Indices: 462958--463047 Score: 101
Period size: 32 Copynumber: 2.9 Consensus size: 30
462948 GAAGGACTTC
* *
462958 TCCATATGTTCCGAATAACATAGGTAACTG
1 TCCATATGTTCCAAATAACATAGGTAACTA
*
462988 TCCATATG-TCTCAAATGACATAGGTAATACTA
1 TCCATATGTTC-CAAATAACATAGGT-A-ACTA
* *
463020 TCCATATGTCCCAAAGAACATAGGTAAC
1 TCCATATGTTCCAAATAACATAGGTAAC
463048 CCTCGACTCT
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
29 2 0.04
30 22 0.44
31 2 0.04
32 23 0.46
33 1 0.02
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (30 bp):
TCCATATGTTCCAAATAACATAGGTAACTA
Found at i:468002 original size:2 final size:2
Alignment explanation
Indices: 467995--468025 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
467985 CTTATGTAAC
467995 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
468026 TATCTCATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:470284 original size:15 final size:16
Alignment explanation
Indices: 470260--470292 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
470250 TAAATTTTTT
470260 ATTTTGATATTTTAAA
1 ATTTTGATATTTTAAA
*
470276 ATTTT-ATATTTTGAA
1 ATTTTGATATTTTAAA
470291 AT
1 AT
470293 AAATTTGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (16 bp):
ATTTTGATATTTTAAA
Found at i:470955 original size:2 final size:2
Alignment explanation
Indices: 470948--471034 Score: 165
Period size: 2 Copynumber: 43.5 Consensus size: 2
470938 ATTGATACGA
470948 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
470990 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
471032 AT A
1 AT A
471035 ATTATTGACA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 83 1.00
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:471119 original size:2 final size:2
Alignment explanation
Indices: 471106--471138 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
471096 TATGCATAAA
*
471106 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
471139 GAGAGAGAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:471328 original size:16 final size:17
Alignment explanation
Indices: 471296--471328 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
471286 TATTTTAAGC
471296 TAAAAACAATTACTAAAA
1 TAAAAACAA-TACTAAAA
471314 TAAAAACAA-ACTAAA
1 TAAAAACAATACTAAA
471329 TTTAGGGTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.18
Consensus pattern (17 bp):
TAAAAACAATACTAAAA
Found at i:472864 original size:13 final size:13
Alignment explanation
Indices: 472845--472885 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
472835 ATTAACATTA
472845 AAATAATAATAAT
1 AAATAATAATAAT
* *
472858 TAATAATAGTAAT
1 AAATAATAATAAT
*
472871 AAATAATAAAAAT
1 AAATAATAATAAT
472884 AA
1 AA
472886 TGAACTTACA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (13 bp):
AAATAATAATAAT
Found at i:472865 original size:16 final size:16
Alignment explanation
Indices: 472841--472886 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
472831 TAATATTAAC
472841 ATTAA-AATAATAATA
1 ATTAATAATAATAATA
*
472856 ATTAATAATAGTAATA
1 ATTAATAATAATAATA
* *
472872 AATAATAAAAATAAT
1 ATTAATAATAATAAT
472887 GAACTTACAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
15 5 0.19
16 21 0.81
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (16 bp):
ATTAATAATAATAATA
Found at i:473384 original size:29 final size:29
Alignment explanation
Indices: 473342--473448 Score: 169
Period size: 29 Copynumber: 3.7 Consensus size: 29
473332 CAGTGGCCGG
*
473342 TATATTTACCGATCTAACACTAGTCAGAC
1 TATATTTCCCGATCTAACACTAGTCAGAC
* *
473371 TATATTTTCTGATCTAACACTAGTCAGAC
1 TATATTTCCCGATCTAACACTAGTCAGAC
* *
473400 TATATTTCCCGATTTAACACCAGTCAGAC
1 TATATTTCCCGATCTAACACTAGTCAGAC
473429 TATATTTCCCGATCTAACAC
1 TATATTTCCCGATCTAACAC
473449 CCTTAACAGT
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 71 1.00
ACGTcount: A:0.32, C:0.25, G:0.09, T:0.34
Consensus pattern (29 bp):
TATATTTCCCGATCTAACACTAGTCAGAC
Found at i:473749 original size:8 final size:10
Alignment explanation
Indices: 473725--473763 Score: 69
Period size: 10 Copynumber: 3.9 Consensus size: 10
473715 TCACACCAAA
*
473725 TTCTCTCAAT
1 TTCTCTCAAC
473735 TTCTCTCAAC
1 TTCTCTCAAC
473745 TTCTCTCAAC
1 TTCTCTCAAC
473755 TTCTCTCAA
1 TTCTCTCAA
473764 ATACTCTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.21, C:0.36, G:0.00, T:0.44
Consensus pattern (10 bp):
TTCTCTCAAC
Found at i:473770 original size:10 final size:10
Alignment explanation
Indices: 473721--473780 Score: 66
Period size: 10 Copynumber: 6.0 Consensus size: 10
473711 TTCATCACAC
473721 CAAATTCTCT
1 CAAATTCTCT
*
473731 CAATTTCTCT
1 CAAATTCTCT
*
473741 CAACTTCTCT
1 CAAATTCTCT
*
473751 CAACTTCTCT
1 CAAATTCTCT
*
473761 CAAATACTCT
1 CAAATTCTCT
* *
473771 TATATTCTCT
1 CAAATTCTCT
473781 GTTTAAGGTA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 43 1.00
ACGTcount: A:0.25, C:0.32, G:0.00, T:0.43
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:473770 original size:20 final size:20
Alignment explanation
Indices: 473721--473770 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
473711 TTCATCACAC
*
473721 CAAATTCTCTCAATTTCTCT
1 CAAATTCTCTCAACTTCTCT
*
473741 CAACTTCTCTCAACTTCTCT
1 CAAATTCTCTCAACTTCTCT
*
473761 CAAATACTCT
1 CAAATTCTCT
473771 TATATTCTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.26, C:0.34, G:0.00, T:0.40
Consensus pattern (20 bp):
CAAATTCTCTCAACTTCTCT
Found at i:473853 original size:16 final size:15
Alignment explanation
Indices: 473794--473853 Score: 50
Period size: 16 Copynumber: 3.9 Consensus size: 15
473784 TAAGGTATAT
*
473794 TTTATTATATTTTTAA
1 TTTATT-TATATTTAA
* *
473810 TAT-TTTGTATTTAA
1 TTTATTTATATTTAA
*
473824 TTTATTTTTAATTTAA
1 TTTATTTAT-ATTTAA
473840 TTTATTTAATATTT
1 TTTATTT-ATATTT
473854 TACTTATATA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
14 9 0.26
15 6 0.17
16 19 0.54
17 1 0.03
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (15 bp):
TTTATTTATATTTAA
Found at i:481230 original size:21 final size:22
Alignment explanation
Indices: 481206--481259 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
481196 TTTTTCAAAT
*
481206 TCCC-AATTTCCTGACTCACAA
1 TCCCTAATTTCCTGACCCACAA
* *
481227 TCCCTAA-TTCTTGACCCCCAA
1 TCCCTAATTTCCTGACCCACAA
481248 TCCCTAATTTCC
1 TCCCTAATTTCC
481260 CTCTAGGGCC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 22 0.81
22 5 0.19
ACGTcount: A:0.24, C:0.41, G:0.04, T:0.31
Consensus pattern (22 bp):
TCCCTAATTTCCTGACCCACAA
Found at i:484464 original size:27 final size:25
Alignment explanation
Indices: 484421--484471 Score: 59
Period size: 27 Copynumber: 2.0 Consensus size: 25
484411 TCCCCATTTT
*
484421 AACTTTTTACTCATAGCTGAACTGTAC
1 AACTTTTCACTCATAGC--AACTGTAC
484448 AACTTTTCAC-CATTAGCAACTGTA
1 AACTTTTCACTCA-TAGCAACTGTA
484472 ATAGTCAAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 7 0.32
26 2 0.09
27 13 0.59
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.35
Consensus pattern (25 bp):
AACTTTTCACTCATAGCAACTGTAC
Found at i:486314 original size:22 final size:22
Alignment explanation
Indices: 486286--486338 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
486276 TTTTCTAATT
*
486286 CCTAATTTCCTGACTCACAATC
1 CCTAATTTCCTGACCCACAATC
* * *
486308 CCTAA-TTCTTGACCCCCAATT
1 CCTAATTTCCTGACCCACAATC
486329 CCTAATTTCC
1 CCTAATTTCC
486339 CTCCAGGGCC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.25, C:0.38, G:0.04, T:0.34
Consensus pattern (22 bp):
CCTAATTTCCTGACCCACAATC
Found at i:487893 original size:14 final size:16
Alignment explanation
Indices: 487863--487897 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
487853 ATATAAAAAC
487863 ATAAAATATAGGATAA
1 ATAAAATATAGGATAA
487879 ATAAAA-ATA-GATAA
1 ATAAAATATAGGATAA
487893 ATAAA
1 ATAAA
487898 TGAGTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.53
15 3 0.16
16 6 0.32
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.23
Consensus pattern (16 bp):
ATAAAATATAGGATAA
Found at i:487922 original size:17 final size:17
Alignment explanation
Indices: 487807--487923 Score: 60
Period size: 17 Copynumber: 6.6 Consensus size: 17
487797 ACAACTAAAT
487807 AAAAATAAAATA-ATAA
1 AAAAATAAAATATATAA
** *
487823 TGCAAAT-AAATAAATAA
1 -AAAAATAAAATATATAA
*
487840 AACAAATAAAAGAATATAA
1 AA-AAATAAAA-TATATAA
* **
487859 AAACATAAAATATA-GG
1 AAAAATAAAATATATAA
* *
487875 ATAAATAAAAATAGATAA
1 AAAAAT-AAAATATATAA
487893 ATAAATGAGTAAAATATATAA
1 A-AAA--A-TAAAATATATAA
487914 AAAAATAAAA
1 AAAAATAAAA
487924 GCATATATAT
Statistics
Matches: 73, Mismatches: 17, Indels: 20
0.66 0.15 0.18
Matches are distributed among these distances:
16 9 0.12
17 27 0.37
18 12 0.16
19 9 0.12
20 3 0.04
21 12 0.16
22 1 0.01
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.21
Consensus pattern (17 bp):
AAAAATAAAATATATAA
Found at i:488545 original size:34 final size:34
Alignment explanation
Indices: 488491--488559 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
488481 GAATCCTAGC
*
488491 AAAATTTTATCATATCTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
* *
488525 AAAATTCTATCCTATTTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
488559 A
1 A
488560 GTAGGACGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (34 bp):
AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
Found at i:489308 original size:98 final size:97
Alignment explanation
Indices: 489155--489412 Score: 257
Period size: 98 Copynumber: 2.6 Consensus size: 97
489145 TGGAACCGGA
* * *
489155 AAATTGTTTGTTGCAACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAA
1 AAATTGTTTGTTGCAACCAGCCACCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCAA
* * *
489220 TATCCTTCGTTGTGAAGTTGAGATTGGCTCCG
66 TATCCTCCGCTGTGAAGTTGAAATTGGCTCCG
** * * * * *
489252 AAATTGTTTGTTGACAGTCAGCCGCCCCTTTGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCA
1 AAATTGTTTGTTG-CAACCAGCCACCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCA
489317 ATATCCTCCGCTGTGAAGTTGAAATTGGC-CCTG
65 ATATCCTCCGCTGTGAAGTTGAAATTGGCTCC-G
* ** * *
489350 AAACTGGGAAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTC
1 AAA-T-TG----T-TTGTTG-CAACCAGCCACCCCTTCGCTGTGAAGTTGAACTTGTGCTGTC
489413 ATAGGTAGCA
Statistics
Matches: 131, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
97 15 0.11
98 71 0.54
99 1 0.01
100 1 0.01
104 1 0.01
105 42 0.32
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.34
Consensus pattern (97 bp):
AAATTGTTTGTTGCAACCAGCCACCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCAA
TATCCTCCGCTGTGAAGTTGAAATTGGCTCCG
Found at i:489406 original size:105 final size:102
Alignment explanation
Indices: 489155--489546 Score: 307
Period size: 105 Copynumber: 3.8 Consensus size: 102
489145 TGGAACCGGA
* * *
489155 AAATTGTTTGTTG-CAACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-CC
1 AAATTG-TTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGGGTACC
* * ** * ** ** **
489218 A-ATATCCTTCGTTGT-GAAGTTGAG-ATTG-GCTCCG
65 AGATATCCTCCGTCGTGGAAAATCAGCCCTGAAATGGG
** * * * * *
489252 AAATTGTTTGTTGACAGTCAGCCGCCCCTTTGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGT-CC
1 AAATTG-TTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGGGTACC
* **
489316 A-ATATCCTCCG-CTGTGAAGTTGAAATTGGCCCTGAAACTGGG
65 AGATATCCTCCGTC-GTG--G--AAAATCAGCCCTGAAA-TGGG
* * *
489358 AAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCATAGGTAGCA
1 AAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGGGTACCA
** *
489423 TGATATCCTCCGTCGTGGAAAATCAGCTTTGAAATTGG
66 -GATATCCTCCGTCGTGGAAAATCAGCCCTGAAATGGG
* **
489461 AAAGTTGTTCGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTGG
1 AAA-TTGTT-GTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGGGTAC
*
489526 CACGATATCCTCCATCGTGGA
64 CA-GATATCCTCCGTCGTGGA
489547 GTTGAAATCG
Statistics
Matches: 234, Mismatches: 45, Indels: 24
0.77 0.15 0.08
Matches are distributed among these distances:
97 13 0.06
98 52 0.22
101 1 0.00
103 9 0.04
104 18 0.08
105 116 0.50
106 11 0.05
108 13 0.06
109 1 0.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (102 bp):
AAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGGGTACCA
GATATCCTCCGTCGTGGAAAATCAGCCCTGAAATGGG
Found at i:491151 original size:14 final size:14
Alignment explanation
Indices: 491134--491185 Score: 70
Period size: 15 Copynumber: 3.6 Consensus size: 14
491124 TTCTTTTTGA
491134 TTTTTGTTCTTTCTT
1 TTTTTGTTCTTTC-T
491149 TTTTTGTTC-TTCT
1 TTTTTGTTCTTTCT
491162 TTTTTGCTTCTTTTCT
1 TTTTTG-TTC-TTTCT
491178 TTTTTGTT
1 TTTTTGTT
491186 TTTGCCCTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.21
14 6 0.18
15 11 0.32
16 10 0.29
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (14 bp):
TTTTTGTTCTTTCT
Found at i:495624 original size:16 final size:18
Alignment explanation
Indices: 495592--495626 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
495582 ATATAAAAAC
495592 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
495610 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
495626 A
1 A
495627 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:495662 original size:20 final size:20
Alignment explanation
Indices: 495636--495687 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
495626 AAATGAGTAA
495636 AATATATAAAAAAGTAAAAG
1 AATATATAAAAAAGTAAAAG
* * * *
495656 CATATATATATAAGTAAAAT
1 AATATATAAAAAAGTAAAAG
495676 AATA-ATAAAAAA
1 AATATATAAAAAA
495688 AAGAAAATCA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (20 bp):
AATATATAAAAAAGTAAAAG
Found at i:495796 original size:32 final size:30
Alignment explanation
Indices: 495738--495830 Score: 87
Period size: 32 Copynumber: 2.9 Consensus size: 30
495728 GGAAATATAT
* *
495738 AAATATATATATATAATAACACTAATAAAAA
1 AAATATACATATATAATAA-AATAATAAAAA
*
495769 AACATATACATATATAATAAAATTAATAGAAAG
1 AA-ATATACATATATAATAAAA-TAATA-AAAA
* * *
495802 TAATATGCATATATAACAAGAATAATAAA
1 AAATATACATATATAATAA-AATAATAAA
495831 GTAGGAAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
31 5 0.10
32 41 0.79
33 6 0.12
ACGTcount: A:0.61, C:0.06, G:0.04, T:0.28
Consensus pattern (30 bp):
AAATATACATATATAATAAAATAATAAAAA
Found at i:496263 original size:34 final size:34
Alignment explanation
Indices: 496220--496288 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
496210 GAATCCTAGC
496220 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
* *
496254 AAAATTCTATCCTATTTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
496288 A
1 A
496289 GTAGGACGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (34 bp):
AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
Found at i:506985 original size:20 final size:20
Alignment explanation
Indices: 506962--507012 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
506952 AACGGAATAT
*
506962 AAGATTATCAGT-AGGAATTA
1 AAGATTACCAGTGA-GAATTA
506982 AAGATTACCAGTGAGAATTA
1 AAGATTACCAGTGAGAATTA
507002 AAGATTACCAG
1 AAGATTACCAG
507013 GGAATAGGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (20 bp):
AAGATTACCAGTGAGAATTA
Found at i:507244 original size:37 final size:38
Alignment explanation
Indices: 507164--507244 Score: 89
Period size: 37 Copynumber: 2.2 Consensus size: 38
507154 AACAAGTTAG
*
507164 AAAATATTTATATATTTTCTTTAAAAAAATTAAATTCAT
1 AAAA-ATTTATATATTTTCTTTAAAAAAATTAAAATCAT
*
507203 -AAAATTTATATAATTTT-TTT-ACAAAATTGAAAAT-AT
1 AAAAATTTATAT-ATTTTCTTTAAAAAAATT-AAAATCAT
507239 AAAAAT
1 AAAAAT
507245 ATTTAATGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
36 9 0.24
37 20 0.54
38 8 0.22
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (38 bp):
AAAAATTTATATATTTTCTTTAAAAAAATTAAAATCAT
Found at i:509361 original size:60 final size:60
Alignment explanation
Indices: 509291--509457 Score: 182
Period size: 60 Copynumber: 2.8 Consensus size: 60
509281 AGTATAACCC
* *
509291 TCATTTTAAATTGGTCCCTAAACTTTT-AA-ATGTTCCAAATTT-ATCCTTAAAGTATGACTA-
1 TCATTTTAAATTAGTCCCTAAACTTTTGAACAT-TT-C-AATTTCATCCCTAAAGTATGA-TAT
* * * *
509351 TCATTCTAAATTTGT-CCTCAAACTTTTGAACATTTCAATTTCATCCCTAAATTTTGATAT
1 TCATTTTAAATTAGTCCCT-AAACTTTTGAACATTTCAATTTCATCCCTAAAGTATGATAT
*
509411 TCATTTTAAATTAGTCCCTAAACTTTTTAAACATTTCAATTTCATCC
1 TCATTTTAAATTAGTCCCTAAAC-TTTTGAACATTTCAATTTCATCC
509458 AAAACTATAC
Statistics
Matches: 92, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
59 10 0.11
60 51 0.55
61 29 0.32
62 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.05, T:0.44
Consensus pattern (60 bp):
TCATTTTAAATTAGTCCCTAAACTTTTGAACATTTCAATTTCATCCCTAAAGTATGATAT
Found at i:510934 original size:34 final size:34
Alignment explanation
Indices: 510892--510978 Score: 122
Period size: 34 Copynumber: 2.5 Consensus size: 34
510882 AAAAATCTTT
* * *
510892 CAATATAATTT-TCATTAATTTATGGATGTGTTAG
1 CAATATAATTTAT-ATTAATTTATGAATGTATTAA
510926 CAATATAATTTATATTAATTTATGAATGTATTAA
1 CAATATAATTTATATTAATTTATGAATGTATTAA
510960 CAATATAATTTATTATTAA
1 CAATATAATTTA-TATTAA
510979 ATTTTATATT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
34 41 0.85
35 7 0.15
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.47
Consensus pattern (34 bp):
CAATATAATTTATATTAATTTATGAATGTATTAA
Found at i:514279 original size:20 final size:21
Alignment explanation
Indices: 514254--514305 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
514244 TTTTCACAAT
*
514254 TCGCAATGCGAATAAG-TAAA
1 TCGCAATGCGAATAAGAAAAA
**
514274 TCGCAATGCGAATTTGAAAAA
1 TCGCAATGCGAATAAGAAAAA
514295 TCGCAATGCGA
1 TCGCAATGCGA
514306 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATAAGAAAAA
Found at i:514303 original size:41 final size:40
Alignment explanation
Indices: 514254--514508 Score: 185
Period size: 41 Copynumber: 6.3 Consensus size: 40
514244 TTTTCACAAT
514254 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTTGAAAAA
1 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTTG-AAAA
* * ** *
514295 TCGCAATGCG-AT-ACTGACTATCGCAATGC-AATTTTCCTAAT
1 TCGCAATGCGAATAAGT-A-AATCGCAATGCGAA-TTT-GAAAA
* * * * ** * * *
514336 TCGCATTGCGATTTACGT-ATTCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGA-ATAAGTAAATCGCAATGCGAATTTGA-AAA
* ** *
514377 TCGCAATGCGAATACGTAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTTGAAAA
* * *
514417 TCGCAACGCGATTAAGTAAATCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAATGCGAATT-TGAAAA
* * **
514458 TCGCAATGCGAATACGTAAATCGCAATGCGAATCTGACTA
1 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTTGAAAA
514498 TCGCAATGCGA
1 TCGCAATGCGA
514509 TTTACATAGC
Statistics
Matches: 164, Mismatches: 39, Indels: 23
0.73 0.17 0.10
Matches are distributed among these distances:
39 2 0.01
40 57 0.35
41 102 0.62
42 1 0.01
43 1 0.01
44 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.26
Consensus pattern (40 bp):
TCGCAATGCGAATAAGTAAATCGCAATGCGAATTTGAAAA
Found at i:514349 original size:21 final size:21
Alignment explanation
Indices: 514212--514387 Score: 76
Period size: 21 Copynumber: 8.5 Consensus size: 21
514202 ATTATGACTA
* *
514212 TCGCAATGCAATTTTCCA-ATT
1 TCGCAATGCGATTTT-CATAAT
** * *
514233 TCGCGTTGCGTTTTTCACAAT
1 TCGCAATGCGATTTTCATAAT
* * *
514254 TCGCAATGCGA--ATAAGTAAA
1 TCGCAATGCGATTTTCA-TAAT
* * * *
514274 TCGCAATGCGAATTTGAAAAA
1 TCGCAATGCGATTTTCATAAT
** *
514295 TCGCAATGCGATACTGACT-A-
1 TCGCAATGCGATTTTCA-TAAT
* *
514315 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
514336 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
514356 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
514377 TCGCAATGCGA
1 TCGCAATGCGA
514388 ATACGTAAAT
Statistics
Matches: 114, Mismatches: 33, Indels: 16
0.70 0.20 0.10
Matches are distributed among these distances:
19 3 0.03
20 45 0.39
21 64 0.56
22 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:514402 original size:20 final size:20
Alignment explanation
Indices: 514377--514490 Score: 174
Period size: 20 Copynumber: 5.7 Consensus size: 20
514367 TTTTCATAAT
514377 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
514397 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
514417 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
514437 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
514458 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
514478 TCGCAATGCGAAT
1 TCGCAATGCGAAT
514491 CTGACTATCG
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
20 66 0.79
21 18 0.21
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:514428 original size:61 final size:63
Alignment explanation
Indices: 514239--514513 Score: 205
Period size: 61 Copynumber: 4.5 Consensus size: 63
514229 AATTTCGCGT
* * ** *
514239 TGCGTTTTTCAC-AATTCGCAATGCGAA-TAAGTAAATCGCAATGCGAATTTGAAAAATCGCAA
1 TGCGATTTTCACTAATTCGCAATGCGAATTACGTAAATCGCAATGCGAATACG-TAAATCGCAA
** * * * * * * * **
514301 TGCGATACTGACT-A-TCGCAATGC-AATTTTCCTAATTCGCATTGCGATTTACGT-ATTCGCGT
1 TGCGATTTTCACTAATTCGCAATGCGAA-TTACGTAAATCGCAATGCGA-ATACGTAAATCGCAA
514362 TGCGATTTTCA-TAATTCGCAATGCGAA-TACGTAAATCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTTCACTAATTCGCAATGCGAATTACGTAAATCGCAATGCGAATACGTAAATCGCAA
* * * * * *
514423 CGCGA--TTAAGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTTCACTAATTCGCAATGCGAATTACGTAAATCGCAATGCGAATACGTAAATCGCAA
* * * *
514484 TGCGAATCTGACT-A-TCGCAATGCGATTTAC
1 TGCGATTTTCACTAATTCGCAATGCGAATTAC
514514 ATAGCGCCAT
Statistics
Matches: 163, Mismatches: 38, Indels: 25
0.72 0.17 0.11
Matches are distributed among these distances:
59 3 0.02
60 23 0.14
61 97 0.60
62 33 0.20
63 7 0.04
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (63 bp):
TGCGATTTTCACTAATTCGCAATGCGAATTACGTAAATCGCAATGCGAATACGTAAATCGCAA
Found at i:515089 original size:33 final size:33
Alignment explanation
Indices: 515038--515119 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
515028 CGAGAATGAA
**
515038 AATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGC-GAAATGAAAATCGCAACGAGAG
* *
515072 AATCACAACGCGAAATGAAAATCGCAACGAGAT
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
515105 AATCGCAACGCGAAA
1 AATCGCAACGCGAAA
515120 CCAAAATCCC
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 33 0.77
34 10 0.23
ACGTcount: A:0.44, C:0.23, G:0.22, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:515126 original size:33 final size:33
Alignment explanation
Indices: 515059--515127 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
515049 GGAAATGACT
**
515059 ATCGCAACGAGAGAATCACAACGCGAAATGAAA
1 ATCGCAACGAGAGAATCACAACGCGAAACCAAA
* *
515092 ATCGCAACGAGATAATCGCAACGCGAAACCAAA
1 ATCGCAACGAGAGAATCACAACGCGAAACCAAA
515125 ATC
1 ATC
515128 CCATTGCGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.46, C:0.25, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGAGAGAATCACAACGCGAAACCAAA
Found at i:515215 original size:20 final size:19
Alignment explanation
Indices: 515131--515238 Score: 118
Period size: 20 Copynumber: 5.8 Consensus size: 19
515121 CAAAATCCCA
515131 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
515150 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
515169 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
**
515183 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCG
*
515203 TTGCGATTTTCATTATCTCG
1 TTGCGATTTTCATT-TCGCG
*
515223 TTACGATTTTCATTTC
1 TTGCGATTTTCATTTC
515239 AACCAAAAGA
Statistics
Matches: 75, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
14 10 0.13
16 2 0.03
17 3 0.04
19 28 0.37
20 31 0.41
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:517050 original size:94 final size:94
Alignment explanation
Indices: 516889--517104 Score: 405
Period size: 94 Copynumber: 2.3 Consensus size: 94
516879 TCACTTAGAT
516889 TAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAG
1 TAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAG
516954 TAAATTTGTTCGGTTGCTGCCAATTCTGC
66 TAAATTTGTTCGGTTGCTGCCAATTCTGC
516983 TAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAG
1 TAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAG
*
517048 TAAATTTGTTCGTTTGCTGCCAATTCTGC
66 TAAATTTGTTCGGTTGCTGCCAATTCTGC
* *
517077 TAAACTGTGTATTCTTTAATACTCTGAA
1 TAAACTGTGTATTCTTTAACACTGTGAA
517105 ACTATTCTTC
Statistics
Matches: 119, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 119 1.00
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.47
Consensus pattern (94 bp):
TAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAG
TAAATTTGTTCGGTTGCTGCCAATTCTGC
Found at i:518991 original size:13 final size:14
Alignment explanation
Indices: 518965--518995 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
518955 GTTTAATTGA
518965 TTGTAAAAGATGAT
1 TTGTAAAAGATGAT
518979 TTGTAAAAG-TGAT
1 TTGTAAAAGATGAT
518992 TTGT
1 TTGT
518996 TTAATTGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (14 bp):
TTGTAAAAGATGAT
Found at i:519162 original size:19 final size:19
Alignment explanation
Indices: 519102--519162 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
519092 AAAAATGACT
*
519102 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
519121 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
*
519135 ATCGTAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
519154 ATCGCAACG
1 ATCGCAACG
519163 AGAGAATCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
14 9 0.27
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 18 0.55
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:519172 original size:14 final size:14
Alignment explanation
Indices: 519120--519176 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
519110 GCGAAATGAA
519120 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
519134 AATCGTAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
519153 AATCGCAACGAGAG
1 AATCGCAACGAGAG
519167 AATCGCAACG
1 AATCGCAACG
519177 CGAAACTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:519192 original size:33 final size:33
Alignment explanation
Indices: 519102--519181 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
519092 AAAAATGACT
*
519102 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
519135 ATCGTAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
519168 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
519182 CTAAATTCGC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:519258 original size:32 final size:33
Alignment explanation
Indices: 519193--519316 Score: 187
Period size: 33 Copynumber: 3.8 Consensus size: 33
519183 TAAATTCGCA
* * *
519193 TTGCGATTTTTATTTCGCTTTGCGATTCCCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
519226 TTGCGATTTTCATTTCGCA-TGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
* *
519258 TTGCGATTTTTATTTTGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
519291 TTGTGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
519317 AGTCATTTCC
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
32 29 0.35
33 53 0.65
ACGTcount: A:0.12, C:0.21, G:0.19, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:519299 original size:65 final size:66
Alignment explanation
Indices: 519193--519316 Score: 205
Period size: 65 Copynumber: 1.9 Consensus size: 66
519183 TAAATTCGCA
*
519193 TTGCGATTTTTATTTCGCTTTGCGATTCCCTCGTTGCGATTTTCATTTCGCA-TGCGATTCTCTC
1 TTGCGATTTTTATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
519257 G
66 G
* * *
519258 TTGCGATTTTTATTTTGCATTGCGATTCTCTCGTTGTGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTTATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGAT
519317 AGTCATTTCC
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
65 48 0.89
66 6 0.11
ACGTcount: A:0.12, C:0.21, G:0.19, T:0.48
Consensus pattern (66 bp):
TTGCGATTTTTATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
G
Found at i:519324 original size:19 final size:19
Alignment explanation
Indices: 519300--519343 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
519290 GTTGTGATTT
519300 TCATTTCGCA-TTGCGATAG
1 TCATTTC-CACTTGCGATAG
519319 TCATTTCCACGTTGCGATAG
1 TCATTTCCAC-TTGCGATAG
*
519339 ACATT
1 TCATT
519344 AAGATGATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 2 0.09
19 7 0.32
20 13 0.59
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (19 bp):
TCATTTCCACTTGCGATAG
Found at i:519382 original size:20 final size:20
Alignment explanation
Indices: 519310--519382 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
519300 TCATTTCGCA
**
519310 TTGCGATAGTCATTTCCACG
1 TTGCGATAGTCATTTCCGTG
* **
519330 TTGCGATAGACA-TTAAGATG
1 TTGCGATAGTCATTTCCG-TG
519350 ATTGCGA-ACGTCATTTCCGTG
1 -TTGCGATA-GTCATTTCCGTG
519371 TTGCGATAGTCA
1 TTGCGATAGTCA
519383 AATAATTGCC
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 2 0.05
20 23 0.57
21 12 0.30
22 3 0.08
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGTG
Found at i:521659 original size:12 final size:12
Alignment explanation
Indices: 521642--521666 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
521632 TCTTCGGGGA
521642 CTTTTTCTTCTT
1 CTTTTTCTTCTT
521654 CTTTTTCTTCTT
1 CTTTTTCTTCTT
521666 C
1 C
521667 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:521873 original size:24 final size:23
Alignment explanation
Indices: 521835--521888 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 23
521825 CTGAAACATC
*
521835 ATCAAATCCGAGTATTGACCAAT
1 ATCAAATCCGAGTATTGACCAAG
*
521858 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAA-TCCGAGTATTGACCAAG
521882 ATCAAAT
1 ATCAAAT
521889 TTCGAATACT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 7 0.25
24 21 0.75
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (23 bp):
ATCAAATCCGAGTATTGACCAAG
Found at i:522798 original size:20 final size:20
Alignment explanation
Indices: 522624--522798 Score: 190
Period size: 20 Copynumber: 8.7 Consensus size: 20
522614 GATTCTTTAT
* *
522624 TATCTCGTTGCGATAGTCAA
1 TATCGCGTTGCGATAGTCAG
* * *
522644 AATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
522664 AATCGCGTTGCAAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
522684 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
522704 TATCGTGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
522724 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
522745 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
522765 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
522785 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
522799 TTTCCCAATT
Statistics
Matches: 137, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
19 3 0.02
20 118 0.86
21 14 0.10
22 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:522812 original size:61 final size:61
Alignment explanation
Indices: 522604--522819 Score: 206
Period size: 61 Copynumber: 3.6 Consensus size: 61
522594 AACTTTGAAA
* * * ** * *
522604 ATCGCATTGCGATTCTT-TATTATCTCGTTGCGATAGTCAAAATCTCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATT-TTCCAATATCGCGTTGCGATAGTCAGTATCGCGTTGCGAAAGTCAGT
* * *** * *
522665 ATCGCGTTGCAAAAGT-CAGA-ATCGCGTTGCGAAAGTCAGTATCGTGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCCA-ATATCGCGTTGCGATAGTCAGTATCGCGTTGCGAAAGTCAGT
* ** * *
522725 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGTATCGCGTTGCGAAAGTCAGT
522786 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
522820 TTACTTATTC
Statistics
Matches: 124, Mismatches: 27, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
60 47 0.38
61 75 0.60
62 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (61 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGTATCGCGTTGCGAAAGTCAGT
Found at i:522858 original size:21 final size:20
Alignment explanation
Indices: 522828--522880 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 20
522818 ATTTACTTAT
522828 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATT-GGAAAA
*
522849 TCGCAATGCGAAATTGGAAAA
1 TCGCATTGCG-AATTGGAAAA
522870 TCGCATTGCGA
1 TCGCATTGCGA
522881 TAGTCATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 1 0.03
21 24 0.83
22 4 0.14
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (20 bp):
TCGCATTGCGAATTGGAAAA
Found at i:524560 original size:22 final size:22
Alignment explanation
Indices: 524534--524611 Score: 111
Period size: 22 Copynumber: 3.5 Consensus size: 22
524524 TTAACAGAAA
* * *
524534 TGCCTTAGCATTGGTATTAAAG
1 TGCCTTAGCACTGATACTAAAG
*
524556 TGCCTCAGCACTGATACTAAAG
1 TGCCTTAGCACTGATACTAAAG
524578 TGCCTTAGCACTGATACTAAAG
1 TGCCTTAGCACTGATACTAAAG
*
524600 TGCTTTAGCACT
1 TGCCTTAGCACT
524612 ACTGAGAGTA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (22 bp):
TGCCTTAGCACTGATACTAAAG
Found at i:525735 original size:54 final size:54
Alignment explanation
Indices: 525663--526084 Score: 573
Period size: 54 Copynumber: 7.8 Consensus size: 54
525653 TAGTGCCCAT
* * *
525663 ACGGTCATTCATAAACATATGATGAATTCCGTGAATAGCACACTTAGTGCTGAA
1 ACGGTTATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCTGAA
* * * *
525717 ACAGCTATTCATTAACATATGATGAATTCCATGAATTGCACACTTAGTGAC-GAA
1 ACGGTTATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTG-CTGAA
* * * * *
525771 ACGATTATTCATCAACATATGATGAATTTCGTGAATTGAACACTTAGTGCCGCA
1 ACGGTTATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCTGAA
* * *
525825 ACGATTATTCATCAACATATGATGAATTCCGTGAATTGCACACTCAGTGCCGAA
1 ACGGTTATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCTGAA
* * *
525879 ACAGTTATTCATCAATATATGATGAATTCCGTGAATTGCACACTTAATG-TCGAA
1 ACGGTTATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCT-GAA
* *
525933 ACGGTTATTCATCAACATATGATGAATTCCGTGAATTGTACATTTAGTGCTGAA
1 ACGGTTATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCTGAA
* *
525987 ACGGTTATTCATCAACATATGATGAATTCCATGAATTGCACATTTAGTG-TCGAA
1 ACGGTTATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCT-GAA
* *
526041 ACGGTTATTTATCAACATATGATGAA-TCTGTGAATTGCACACTT
1 ACGGTTATTCATCAACATATGATGAATTCCGTGAATTGCACACTT
526085 TTATTTGGTA
Statistics
Matches: 328, Mismatches: 35, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
53 17 0.05
54 309 0.94
55 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Consensus pattern (54 bp):
ACGGTTATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCTGAA
Found at i:529695 original size:76 final size:77
Alignment explanation
Indices: 529511--529717 Score: 273
Period size: 75 Copynumber: 2.8 Consensus size: 77
529501 CAAAGCCAAA
* * **
529511 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCG-TT-CCCCCTAAATGGT
1 AATTCCAGAATGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
529574 TTTGGCCCTGAG
66 TTTGGCCCTGAG
* *
529586 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
529651 TTT-GCTCC-GAG
66 TTTGGC-CCTGAG
* * * *
529662 AATTCCAGTATGCTC-GAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCT
529718 TGTACAACGG
Statistics
Matches: 118, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
74 19 0.16
75 63 0.53
76 20 0.17
77 16 0.14
ACGTcount: A:0.24, C:0.32, G:0.23, T:0.21
Consensus pattern (77 bp):
AATTCCAGAATGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTTGGCCCTGAG
Found at i:534406 original size:21 final size:21
Alignment explanation
Indices: 534380--534419 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
534370 CCCCCTTTGA
*
534380 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
534401 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
534420 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:536647 original size:31 final size:30
Alignment explanation
Indices: 536612--536684 Score: 101
Period size: 30 Copynumber: 2.3 Consensus size: 30
536602 GGAGAAGAAT
*
536612 AGGTGTTAAATATTTTTACATAATAAATTGA
1 AGGTGTTAAAT-GTTTTACATAATAAATTGA
*
536643 AGGTGTTCAATGTTTTACATAATAAATTGA
1 AGGTGTTAAATGTTTTACATAATAAATTGA
536673 AGAAGTGTTAAA
1 AG--GTGTTAAA
536685 GTAAGGGGGA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 20 0.54
31 10 0.27
32 7 0.19
ACGTcount: A:0.41, C:0.04, G:0.16, T:0.38
Consensus pattern (30 bp):
AGGTGTTAAATGTTTTACATAATAAATTGA
Found at i:537153 original size:76 final size:77
Alignment explanation
Indices: 536993--537201 Score: 262
Period size: 76 Copynumber: 2.7 Consensus size: 77
536983 CAAAGCCAAA
* * * **
536993 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCCATAGGAGGAACCGATT-CCCCCTAAATG
1 AATTCCAGAATGCTCGGAGGGAACCGATT--CCCCCCATAGGAGGAACCGATTCCCCCCTAAACA
537057 GTTTTGGCCCCGAG
64 GTTTTGGCCCCGAG
*
537071 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
* *
537136 TTT-GCTCTGAG
66 TTTGGCCCCGAG
* * * * *
537147 AATTCCAGTATGCTCGGAGAGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCC
537202 TTGTACAACG
Statistics
Matches: 116, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
75 17 0.15
76 60 0.52
77 14 0.12
78 25 0.22
ACGTcount: A:0.25, C:0.32, G:0.23, T:0.20
Consensus pattern (77 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTTGGCCCCGAG
Found at i:541248 original size:40 final size:40
Alignment explanation
Indices: 541193--541275 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
541183 TCGTTAGTCT
541193 TAATCTACTACTCTATTCATTGAGTATATTTTTAATTGAA
1 TAATCTACTACTCTATTCATTGAGTATATTTTTAATTGAA
541233 TAATCTACTACTCTATTCATTGAGTATATTTTTAATTGAA
1 TAATCTACTACTCTATTCATTGAGTATATTTTTAATTGAA
541273 TAA
1 TAA
541276 ACCTTTCAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.47
Consensus pattern (40 bp):
TAATCTACTACTCTATTCATTGAGTATATTTTTAATTGAA
Found at i:544386 original size:16 final size:16
Alignment explanation
Indices: 544365--544399 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
544355 CCATCTGTTT
*
544365 TAATCCAAATGGATGC
1 TAATCCAAATGAATGC
544381 TAATCCAAATGAATGC
1 TAATCCAAATGAATGC
544397 TAA
1 TAA
544400 AAGATAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (16 bp):
TAATCCAAATGAATGC
Found at i:545134 original size:18 final size:17
Alignment explanation
Indices: 545088--545127 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
545078 CTGGGAGAAA
*
545088 ATGTATGTGTACATATGT
1 ATGTATTTGTACATA-GT
545106 ATGTATTTGTACATA-T
1 ATGTATTTGTACATAGT
545122 ATGTAT
1 ATGTAT
545128 GCTTGTAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.33
18 14 0.67
ACGTcount: A:0.30, C:0.05, G:0.17, T:0.47
Consensus pattern (17 bp):
ATGTATTTGTACATAGT
Found at i:555230 original size:19 final size:20
Alignment explanation
Indices: 555208--555276 Score: 65
Period size: 19 Copynumber: 3.6 Consensus size: 20
555198 AGAAAATAAA
555208 TAAATGAT-CAAACGAAATG
1 TAAATGATACAAACGAAATG
* * *
555227 TAAAAGATACAAA-TAAA-A
1 TAAATGATACAAACGAAATG
* *
555245 TAAACGAT-CAAACGAGATG
1 TAAATGATACAAACGAAATG
555264 TAAATGATACAAA
1 TAAATGATACAAA
555277 TAAAATAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
17 4 0.11
18 9 0.24
19 17 0.45
20 8 0.21
ACGTcount: A:0.58, C:0.10, G:0.13, T:0.19
Consensus pattern (20 bp):
TAAATGATACAAACGAAATG
Found at i:555254 original size:37 final size:37
Alignment explanation
Indices: 555201--555285 Score: 136
Period size: 37 Copynumber: 2.3 Consensus size: 37
555191 AACAATCAGA
*
555201 AAAT-AAATAAATGATCAAACGAAATGTAAAAGATAC
1 AAATAAAATAAACGATCAAACGAAATGTAAAAGATAC
* *
555237 AAATAAAATAAACGATCAAACGAGATGTAAATGATAC
1 AAATAAAATAAACGATCAAACGAAATGTAAAAGATAC
555274 AAATAAAATAAA
1 AAATAAAATAAA
555286 TATGTTCATT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
36 4 0.09
37 41 0.91
ACGTcount: A:0.62, C:0.08, G:0.11, T:0.19
Consensus pattern (37 bp):
AAATAAAATAAACGATCAAACGAAATGTAAAAGATAC
Found at i:564090 original size:93 final size:93
Alignment explanation
Indices: 563931--564105 Score: 244
Period size: 93 Copynumber: 1.9 Consensus size: 93
563921 CCGCTATCAC
* * *
563931 TCAGGGAATATCAAATCTTGGAAAAAAGGGACATGTTCCACTTTCTCTGAAATGAATATCAGATC
1 TCAGGGAAGATCAAATCTTGGAAAAAAGGGACATCTTCCACTTTCTCTGAAAGGAATATCAGATC
563996 TAGGGGAGTTGATCCATGCCACTGTTAT
66 TAGGGGAGTTGATCCATGCCACTGTTAT
* ** * * * *
564024 TCAGGGAAGATTAAATCTTGGAGAAGTA-GGACCTCTTCCGCTTTCTCTGAAGGGAATATCATAT
1 TCAGGGAAGATCAAATCTTGGA-AAAAAGGGACATCTTCCACTTTCTCTGAAAGGAATATCAGAT
564088 CTAGGGGAGTTGATCCAT
65 CTAGGGGAGTTGATCCAT
564106 TCTGCTATCA
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
93 68 0.96
94 3 0.04
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.29
Consensus pattern (93 bp):
TCAGGGAAGATCAAATCTTGGAAAAAAGGGACATCTTCCACTTTCTCTGAAAGGAATATCAGATC
TAGGGGAGTTGATCCATGCCACTGTTAT
Found at i:564129 original size:93 final size:93
Alignment explanation
Indices: 563921--564133 Score: 241
Period size: 93 Copynumber: 2.3 Consensus size: 93
563911 CATACTTGTT
* * *
563921 CCGCTATCACTCAGGGAAT-ATCAAATCTTGGAAAAAAGGGACATGTTCCACTTTCTCTGAAATG
1 CCGCTATCACTCAGGG-ATGATTAAATCTTGGAAAAAAGGGACATCTTCCACTTTCTCTGAAAGG
563985 AATATCAGATCTAGGGGAGTTGATCCATG
65 AATATCAGATCTAGGGGAGTTGATCCATG
* * * * * ** * * *
564014 CCACTGTTATTCAGGGAAGATTAAATCTTGGAGAAGTA-GGACCTCTTCCGCTTTCTCTGAAGGG
1 CCGCTATCACTCAGGGATGATTAAATCTTGGA-AAAAAGGGACATCTTCCACTTTCTCTGAAAGG
* *
564078 AATATCATATCTAGGGGAGTTGATCCATT
65 AATATCAGATCTAGGGGAGTTGATCCATG
* *
564107 CTGCTATCACTCACGGATGATTAAATC
1 CCGCTATCACTCAGGGATGATTAAATC
564134 GGGGCTAACT
Statistics
Matches: 96, Mismatches: 22, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
92 1 0.01
93 92 0.96
94 3 0.03
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.29
Consensus pattern (93 bp):
CCGCTATCACTCAGGGATGATTAAATCTTGGAAAAAAGGGACATCTTCCACTTTCTCTGAAAGGA
ATATCAGATCTAGGGGAGTTGATCCATG
Found at i:564257 original size:227 final size:227
Alignment explanation
Indices: 563847--564267 Score: 553
Period size: 227 Copynumber: 1.9 Consensus size: 227
563837 ACTGTCACTC
* * *
563847 AGGGAATATCAGATCTGGGGATGTTGATCCATTCCGCTGTTACTCAGTGAATATTGAATCAGAGC
1 AGGGAATATCAGATCTGGGGATGTTGATCCATTCCGCTATCACTCAGTGAATATTAAATCAGAGC
* *
563912 ATACTTGTTCCGCTATCACTCAGGGAATATCAAATCTTGGAAAAAAGGGACATGTTCCACTTTCT
66 ATACTTGTTCCACTATCACTCAAGGAATATCAAATCTTGGAAAAAAGGGACATGTTCCACTTTCT
* * * * *
563977 CTGAAATGAATATCAGATCTAGGGGAGTTGATCCATGCCACTGTTATTCAGGGAAGATTAAATCT
131 CTGAAAGGAATATCAAATATAGGGGAGTTGATCCATGCCACTATTACTCAGGGAAGATTAAATCT
564042 TGGAGAAGTAGGACCTCTTCCGCTTTCTCTGA
196 TGGAGAAGTAGGACCTCTTCCGCTTTCTCTGA
* * *
564074 AGGGAATATCATATCTAGGGGA-GTTGATCCATTCTGCTATCACTCACG-G-ATGATTAAATCGG
1 AGGGAATATCAGATCT-GGGGATGTTGATCCATTCCGCTATCACTCA-GTGAAT-ATTAAATCAG
* * * * **
564136 GGC-TAACTTGTTTCACTGTCACTCAAGGAATATCAAATCTTGGAAAAGAGGGACATGTTCTGCT
63 AGCAT-ACTTGTTCCACTATCACTCAAGGAATATCAAATCTTGGAAAAAAGGGACATGTTCCACT
* * * * * *
564200 TTCTCTGAAGGGAATATCAAATATGGGGGAGTTGATCCATTCCGCTATTACTCAGGGAATATTGA
127 TTCTCTGAAAGGAATATCAAATATAGGGGAGTTGATCCATGCCACTATTACTCAGGGAAGATTAA
564265 ATC
192 ATC
564268 GGGGCAAACT
Statistics
Matches: 165, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
226 3 0.02
227 156 0.95
228 6 0.04
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (227 bp):
AGGGAATATCAGATCTGGGGATGTTGATCCATTCCGCTATCACTCAGTGAATATTAAATCAGAGC
ATACTTGTTCCACTATCACTCAAGGAATATCAAATCTTGGAAAAAAGGGACATGTTCCACTTTCT
CTGAAAGGAATATCAAATATAGGGGAGTTGATCCATGCCACTATTACTCAGGGAAGATTAAATCT
TGGAGAAGTAGGACCTCTTCCGCTTTCTCTGA
Found at i:564268 original size:134 final size:133
Alignment explanation
Indices: 564036--564352 Score: 411
Period size: 134 Copynumber: 2.4 Consensus size: 133
564026 AGGGAAGATT
* * * * *
564036 AAATCTTGGAGAAGTAGGACCTCTTCCGCTTTCTCTGAAGGGAATATCATATCTAGGGGAGTTGA
1 AAATCTTGGAAAAG-AGGACATGTTCCGCTTTCTCTGAAGGGAATATCAAATATAGGGGAGTTGA
* * * *
564101 TCCATTCTGCTATCACTCACGGATGATTAAATCGGGGCTAACTTGTTTCACTGTCACTCAAGGAA
65 TCCATTCCGCTATCACTCACGGATGATTAAATCGGGGCAAACTTATTCCACTGTCACTCAAGGAA
564166 TATC
130 TATC
* *
564170 AAATCTTGGAAAAGAGGGACATGTTCTGCTTTCTCTGAAGGGAATATCAAATATGGGGGAGTTGA
1 AAATCTTGGAAAAGA-GGACATGTTCCGCTTTCTCTGAAGGGAATATCAAATATAGGGGAGTTGA
* * * * * *
564235 TCCATTCCGCTATTACTCAGGGAAT-ATTGAATCGGGGCAAACTTATTCCGCTGTCACTTAGGGA
65 TCCATTCCGCTATCACTCACGG-ATGATTAAATCGGGGCAAACTTATTCCACTGTCACTCAAGGA
564299 ATATC
129 ATATC
* * *
564304 AAATCTTGGAGAAAAAGGACATGTTCCGCTTTGTCCGAAGGGAATATCA
1 AAATCTTGGA-AAAGAGGACATGTTCCGCTTTCTCTGAAGGGAATATCA
564353 GATCTACAAA
Statistics
Matches: 159, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
133 1 0.01
134 152 0.96
135 6 0.04
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (133 bp):
AAATCTTGGAAAAGAGGACATGTTCCGCTTTCTCTGAAGGGAATATCAAATATAGGGGAGTTGAT
CCATTCCGCTATCACTCACGGATGATTAAATCGGGGCAAACTTATTCCACTGTCACTCAAGGAAT
ATC
Found at i:566276 original size:11 final size:11
Alignment explanation
Indices: 566260--566306 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
566250 TTATCCATTC
566260 TTTCTTTTTTT
1 TTTCTTTTTTT
566271 TTTC-TTTTTT
1 TTTCTTTTTTT
* *
566281 TTCCTCTTTTT
1 TTTCTTTTTTT
*
566292 TTTCTTTTTTG
1 TTTCTTTTTTT
566303 TTTC
1 TTTC
566307 GAGTGTGGTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 9 0.30
11 21 0.70
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:567849 original size:19 final size:18
Alignment explanation
Indices: 567825--567878 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
567815 AACAAAATAC
567825 TGTAAAAAATGATAAAGAA
1 TGTAAAAAATGATAAA-AA
*
567844 TGTAAAGAATGATAAAAA
1 TGTAAAAAATGATAAAAA
*
567862 TGT-GAAAATGTATAAAA
1 TGTAAAAAATG-ATAAAA
567879 TGATTGCCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 5 0.16
18 11 0.35
19 15 0.48
ACGTcount: A:0.59, C:0.00, G:0.17, T:0.24
Consensus pattern (18 bp):
TGTAAAAAATGATAAAAA
Found at i:567851 original size:9 final size:8
Alignment explanation
Indices: 567829--567880 Score: 50
Period size: 9 Copynumber: 5.9 Consensus size: 8
567819 AAATACTGTA
567829 AAAAATGAT
1 AAAAATG-T
567838 AAAGAATGT
1 AAA-AATGT
567847 AAAGAATGAT
1 AAA-AATG-T
567857 AAAAATGT
1 AAAAATGT
*
567865 GAAAATGT
1 AAAAATGT
567873 ATAAAATG
1 A-AAAATG
567881 ATTGCCATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
8 8 0.21
9 22 0.58
10 8 0.21
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (8 bp):
AAAAATGT
Found at i:567876 original size:18 final size:17
Alignment explanation
Indices: 567829--567878 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
567819 AAATACTGTA
567829 AAAAATGATAAAGAATGT
1 AAAAATGATAAA-AATGT
567847 AAAGAATGATAAAAATGT
1 AAA-AATGATAAAAATGT
*
567865 GAAAATGTATAAAA
1 AAAAATG-ATAAAA
567879 TGATTGCCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 4 0.14
18 16 0.55
19 9 0.31
ACGTcount: A:0.62, C:0.00, G:0.16, T:0.22
Consensus pattern (17 bp):
AAAAATGATAAAAATGT
Found at i:573671 original size:18 final size:18
Alignment explanation
Indices: 573636--573671 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
573626 AAAATGGGTA
* *
573636 CATATGTTATATGTATTG
1 CATATGTTACATGAATTG
573654 CATATGTTACATGAATTG
1 CATATGTTACATGAATTG
573672 AATGAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (18 bp):
CATATGTTACATGAATTG
Found at i:573894 original size:13 final size:13
Alignment explanation
Indices: 573874--573907 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
573864 TAGCAAGAGA
573874 AAATGATATAAAT
1 AAATGATATAAAT
* *
573887 AGATGATATATAT
1 AAATGATATAAAT
573900 AAATGATA
1 AAATGATA
573908 AGTTAAACGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (13 bp):
AAATGATATAAAT
Found at i:578770 original size:16 final size:16
Alignment explanation
Indices: 578748--578784 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
578738 CATATTACTT
*
578748 ATTCAAGTCATTTTAA
1 ATTCAAGTCAATTTAA
*
578764 GTTCAAGTCAATTTAA
1 ATTCAAGTCAATTTAA
578780 ATTCA
1 ATTCA
578785 GGTCCATTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.41
Consensus pattern (16 bp):
ATTCAAGTCAATTTAA
Found at i:578800 original size:16 final size:16
Alignment explanation
Indices: 578749--578801 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
578739 ATATTACTTA
* *
578749 TTCAAGTCATTTTAAG
1 TTCAAGTCAATTCAAG
* *
578765 TTCAAGTCAATTTAAA
1 TTCAAGTCAATTCAAG
* *
578781 TTCAGGTCCATTCAAG
1 TTCAAGTCAATTCAAG
578797 TTCAA
1 TTCAA
578802 ATTGAATAGG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (16 bp):
TTCAAGTCAATTCAAG
Found at i:579485 original size:32 final size:32
Alignment explanation
Indices: 579447--579509 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
579437 ATTTTACAAG
*
579447 TAGTTATAATTCAGTTACTTTGTTAGAGTGTA
1 TAGTTATAAATCAGTTACTTTGTTAGAGTGTA
*
579479 TAGTTATAAATCATTTACTTTGTTAGAGTGT
1 TAGTTATAAATCAGTTACTTTGTTAGAGTGT
579510 TGTTTGTGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.29, C:0.06, G:0.17, T:0.48
Consensus pattern (32 bp):
TAGTTATAAATCAGTTACTTTGTTAGAGTGTA
Found at i:582891 original size:81 final size:81
Alignment explanation
Indices: 582756--582983 Score: 330
Period size: 81 Copynumber: 2.8 Consensus size: 81
582746 GTTTATGTCA
* * * * * * * * * *
582756 AAATGCACTGTTAAGCATTTAGTCTTTTACCCAAAGGTATTTAGCATTTCATCTAACTTGCATGA
1 AAATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATAA
*
582821 TTGACACCTTTCTGCC
66 TTGACACATTTCTGCC
*
582837 AAATGCACAGCTAGGCATTTAATCTTTAACTCAAAGGCATTTAACCTTTCATCTAACTGGCATAA
1 AAATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATAA
*
582902 TTGACACATTTCTGTC
66 TTGACACATTTCTGCC
*
582918 AAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATAA
1 AAATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATAA
582983 T
66 T
582984 AAAGAATTGA
Statistics
Matches: 132, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 132 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (81 bp):
AAATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATAA
TTGACACATTTCTGCC
Found at i:583276 original size:32 final size:32
Alignment explanation
Indices: 583238--583300 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
583228 ATTTTATAAG
*
583238 TAGTTATAATTCATTTACTTTGTTAGAGTGTA
1 TAGTTATAAATCATTTACTTTGTTAGAGTGTA
583270 TAGTTATAAATCATTTACTTTGTTAGAGTGT
1 TAGTTATAAATCATTTACTTTGTTAGAGTGT
583301 TGTTTGTGGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.29, C:0.06, G:0.16, T:0.49
Consensus pattern (32 bp):
TAGTTATAAATCATTTACTTTGTTAGAGTGTA
Found at i:585285 original size:32 final size:32
Alignment explanation
Indices: 585246--585308 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
585236 ATTTTGTAAG
*
585246 TAGTTATAATTAAGTTATTTTGTTAGAGTGTA
1 TAGTTATAATTAAGTTACTTTGTTAGAGTGTA
*
585278 TAGTTATAATTTAGTTACTTTGTTAGAGTGT
1 TAGTTATAATTAAGTTACTTTGTTAGAGTGT
585309 TGTTTGTGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.19, T:0.51
Consensus pattern (32 bp):
TAGTTATAATTAAGTTACTTTGTTAGAGTGTA
Found at i:586744 original size:81 final size:81
Alignment explanation
Indices: 586587--587123 Score: 734
Period size: 81 Copynumber: 6.6 Consensus size: 81
586577 AGTCAAATCA
* * * * * * * *
586587 ATAAATGACACCGTTTATGTCAAAATGCACTGTTAAG-AATTTAGTCTTTTACCCAAAGGTATTT
1 ATAATTGACACC-TTTCTGTC-AAATGCACAGCTAGGCAA-TTAATCTTTTACTCAAAGGCATTT
* * *
586651 AGCATTTCATCTAACTTGC
63 AACCTTTCATCTAACTGGC
* * * * *
586670 ATGATTGACACCTTTCTGCCAAATGCACAGCTAGGCATTTAATCTTTAACTCAAAGGCATTTAGC
1 ATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGCATTTAAC
586735 CTTTCATCTAACTGGC
66 CTTTCATCTAACTGGC
* * *
586751 ATAATTGACACATTTCTATCAAATGCACAGCTAGACAATTAATCTTTTACTCAAAGGCATTTAAC
1 ATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGCATTTAAC
586816 CTTTCATCTAACTGGC
66 CTTTCATCTAACTGGC
* *
586832 ATAATTGACACCTTTCTCTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAATGCATTTAAC
1 ATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGCATTTAAC
586897 CTTTCATCTAACTGGC
66 CTTTCATCTAACTGGC
* *
586913 ATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAATATTTTACTCAAAGGTATTTAAC
1 ATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGCATTTAAC
* *
586978 CCTTCATCTAACTGAC
66 CTTTCATCTAACTGGC
* * * * *
586994 ATAATTGACATCTTTCTGTCAAATGCACATCTAGGCAATTAATATTTAACTCAAAGGTATTTAAC
1 ATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGCATTTAAC
* *
587059 CTTTCATCTAAGTGGT
66 CTTTCATCTAACTGGC
* *
587075 ATAATTGACACCTTTCTGTCAAATACACAGCTAGGTAATTAATCTTTTA
1 ATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAATCTTTTA
587124 TTTAAAACAA
Statistics
Matches: 408, Mismatches: 45, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
81 391 0.96
82 7 0.02
83 10 0.02
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (81 bp):
ATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGCATTTAAC
CTTTCATCTAACTGGC
Found at i:587220 original size:22 final size:21
Alignment explanation
Indices: 587179--587220 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
587169 ACATACATTA
*
587179 TAAAACATATATAATATAAAG
1 TAAAACATACATAATATAAAG
*
587200 TAAAACATACATTAATTTAAA
1 TAAAACATACA-TAATATAAA
587221 TTTTTGAGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.31
Consensus pattern (21 bp):
TAAAACATACATAATATAAAG
Found at i:587669 original size:94 final size:95
Alignment explanation
Indices: 587532--587713 Score: 278
Period size: 94 Copynumber: 1.9 Consensus size: 95
587522 ACCATGGTAT
* * *
587532 CGATACTTTTATAATGTGGTACCGATACTCCCTTTTAGTATCGATACCATTTCT-ACATTCTAG-
1 CGATACTTCTATAATATGGTACCGATACTCCCTTTCAGTATCGATACCATTT-TGACATTCTAGA
*
587595 ATCCATGGTATCGATACTTTCTTTCTAGTAC
65 ATCCATGGTATCAATACTTTCTTTCTAGTAC
* * *
587626 CGATACTTCTATACTATGGTACTGATACTCCCTTTCAGTATCGATACCATTTTGGCATTCTAGAA
1 CGATACTTCTATAATATGGTACCGATACTCCCTTTCAGTATCGATACCATTTTGACATTCTAGAA
587691 TCCATGGTATCAATACTTTCTTT
66 TCCATGGTATCAATACTTTCTTT
587714 TTTGGTATCG
Statistics
Matches: 79, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
93 1 0.01
94 55 0.70
95 23 0.29
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.40
Consensus pattern (95 bp):
CGATACTTCTATAATATGGTACCGATACTCCCTTTCAGTATCGATACCATTTTGACATTCTAGAA
TCCATGGTATCAATACTTTCTTTCTAGTAC
Found at i:591804 original size:19 final size:19
Alignment explanation
Indices: 591780--591817 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
591770 TGTGTTTAAG
*
591780 TTGACTTTATATGCAAAAT
1 TTGACTTTAGATGCAAAAT
*
591799 TTGACTTTAGATGCTAAAT
1 TTGACTTTAGATGCAAAAT
591818 ACTTGTATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (19 bp):
TTGACTTTAGATGCAAAAT
Found at i:594997 original size:13 final size:13
Alignment explanation
Indices: 594979--595005 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
594969 TTTTGTTCAC
594979 TGTTTTACTTGCT
1 TGTTTTACTTGCT
594992 TGTTTTACTTGCT
1 TGTTTTACTTGCT
595005 T
1 T
595006 AGGCTAGTAA
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:0.07, C:0.15, G:0.15, T:0.63
Consensus pattern (13 bp):
TGTTTTACTTGCT
Found at i:599516 original size:22 final size:22
Alignment explanation
Indices: 599485--599580 Score: 84
Period size: 22 Copynumber: 4.2 Consensus size: 22
599475 TTAAAATAAA
*
599485 TTATTATAAAATATGGATTGAT
1 TTATTTTAAAATATGGATTGAT
** * *
599507 TTATTTTAAAATAATTTATTTTAA
1 TTATTTTAAAAT-ATGGA-TTGAT
* * * *
599531 ATAATTTATTAGTATGGATTGAT
1 TTATTTTA-AAATATGGATTGAT
599554 TTATTTTAAAATATGGATTGAT
1 TTATTTTAAAATATGGATTGAT
599576 TTATT
1 TTATT
599581 ATTGTAGTTG
Statistics
Matches: 54, Mismatches: 17, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
22 28 0.52
23 12 0.22
24 12 0.22
25 2 0.04
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (22 bp):
TTATTTTAAAATATGGATTGAT
Found at i:599534 original size:14 final size:15
Alignment explanation
Indices: 599393--599540 Score: 181
Period size: 15 Copynumber: 9.5 Consensus size: 15
599383 TAATAAGGTT
599393 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
599408 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
599423 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
599438 GTTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
599453 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
599468 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
599483 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
599502 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
599520 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
599534 ATTTATT
1 ATTTATT
599541 AGTATGGATT
Statistics
Matches: 116, Mismatches: 10, Indels: 15
0.82 0.07 0.11
Matches are distributed among these distances:
14 12 0.10
15 84 0.72
16 4 0.03
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 4 0.03
22 6 0.05
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:599631 original size:32 final size:32
Alignment explanation
Indices: 599590--599707 Score: 218
Period size: 32 Copynumber: 3.7 Consensus size: 32
599580 TATTGTAGTT
599590 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
599622 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
599654 GTATGGATTGATTTATTTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
599686 GTATAGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
599708 ATATGGATTG
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 84 1.00
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:599637 original size:18 final size:18
Alignment explanation
Indices: 599614--599670 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
599604 ATTTTAAATA
599614 ATTTATTAGTATGGATTG
1 ATTTATTAGTATGGATTG
* * *
599632 ATTTATT--T-T-AAATA
1 ATTTATTAGTATGGATTG
599646 ATTTATTAGTATGGATTG
1 ATTTATTAGTATGGATTG
599664 ATTTATT
1 ATTTATT
599671 TTAAATAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
14 9 0.31
15 1 0.03
16 2 0.07
17 1 0.03
18 16 0.55
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (18 bp):
ATTTATTAGTATGGATTG
Found at i:599668 original size:144 final size:144
Alignment explanation
Indices: 599520--599787 Score: 473
Period size: 144 Copynumber: 1.9 Consensus size: 144
599510 TTTTAAAATA
*
599520 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
** *
599585 TAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTT
66 TAGTTGTATAAATTGATTTATTTTAAATAATTTATTAGTATGGATTAATTTATTTTAAATAATTT
599650 ATTAGTATGGATTG
131 ATTAGTATGGATTG
* *
599664 ATTTATTTTAAATAATTTATTTGTATAGATTGATTTATTTTAAAATATGGATTGATTTGTTATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
*
599729 TAGTTGTATAAATTGATTTATTTTAAATAATTTATTAGTATGTATTAATTTATTTTAAA
66 TAGTTGTATAAATTGATTTATTTTAAATAATTTATTAGTATGGATTAATTTATTTTAAA
599788 ATATGGATTG
Statistics
Matches: 117, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
144 117 1.00
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.54
Consensus pattern (144 bp):
ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
TAGTTGTATAAATTGATTTATTTTAAATAATTTATTAGTATGGATTAATTTATTTTAAATAATTT
ATTAGTATGGATTG
Found at i:599792 original size:22 final size:22
Alignment explanation
Indices: 599767--599809 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
599757 AATTTATTAG
*
599767 TATGTATTAATTTATTTTAAAA
1 TATGGATTAATTTATTTTAAAA
*
599789 TATGGATTGATTTATTTTAAA
1 TATGGATTAATTTATTTTAAA
599810 TAATTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.53
Consensus pattern (22 bp):
TATGGATTAATTTATTTTAAAA
Found at i:599869 original size:31 final size:31
Alignment explanation
Indices: 599834--599892 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
599824 AGTTGTATGG
* *
599834 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
599865 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
599893 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:605358 original size:20 final size:20
Alignment explanation
Indices: 605321--605359 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
605311 AGATTGAGTG
* * *
605321 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
605341 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
605360 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:605590 original size:21 final size:23
Alignment explanation
Indices: 605518--605590 Score: 73
Period size: 22 Copynumber: 3.3 Consensus size: 23
605508 CAGAACCCCA
* *
605518 GGGGGGTATCGATTCCCCTGT--T
1 GGGGGGAATCGGTTCCCCT-TCAT
*
605540 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTTCCCCTTCAT
*
605563 AGGGGGAATCGGTT-CCC-TCAT
1 GGGGGGAATCGGTTCCCCTTCAT
605584 GGGGGGA
1 GGGGGGA
605591 TCGATTCACT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
21 10 0.23
22 20 0.47
23 13 0.30
ACGTcount: A:0.15, C:0.22, G:0.40, T:0.23
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCCCTTCAT
Found at i:611962 original size:87 final size:86
Alignment explanation
Indices: 611860--612200 Score: 345
Period size: 87 Copynumber: 4.0 Consensus size: 86
611850 AGTCCATTAT
* *
611860 TCTTTTACTCAACAGTGCTTAACCATTCAACTAACCGGCATAATTGAAATC-TTTCTGCCAATTG
1 TCTTTTACTCAACAGTACTTAACCATTCAACTAACCGGCATAATTGACA-CATTTCTGCCAATTG
*
611924 CATAGTTAGGCCATTATCTTTA
65 CACAGTTAGGCCATTATCTTTA
* * * *
611946 TCTTTTTACTCAACAGTGCTTAACCATTCAGCTAACCGGCATAATTGACACATTTCTACTAATTG
1 TC-TTTTACTCAACAGTACTTAACCATTCAACTAACCGGCATAATTGACACATTTCTGCCAATTG
612011 CACAGTTAGGCCATTATCCTCTTA
65 CACAGTTAGGCCATTAT-CT-TTA
** * * * * * * *
612035 CTCAACTTACTCAACGGTATTTAACCGTTCATA-TAACTGGCATCATTGACACCTTTTTTGCCAA
1 -TC-TTTTACTCAACAGTACTTAACCATTCA-ACTAACCGGCATAATTGACA-CATTTCTGCCAA
* *
612099 TTGCATAGTTAGTCCATTATC----
62 TTGCACAGTTAGGCCATTATCTTTA
* * * * *
612120 -CTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCCAATTGC
1 TCTTTTACTCAACAGTACTTAACCATTCAACTAACCGGCATAATTGACACATTTCTGCCAATTGC
*
612184 ACAATTAGGCCATTATC
66 ACAGTTAGGCCATTATC
612201 CTTTTATTTT
Statistics
Matches: 217, Mismatches: 30, Indels: 21
0.81 0.11 0.08
Matches are distributed among these distances:
81 28 0.13
82 42 0.19
83 1 0.00
86 3 0.01
87 72 0.33
88 2 0.01
89 3 0.01
90 40 0.18
91 26 0.12
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (86 bp):
TCTTTTACTCAACAGTACTTAACCATTCAACTAACCGGCATAATTGACACATTTCTGCCAATTGC
ACAGTTAGGCCATTATCTTTA
Found at i:612450 original size:54 final size:54
Alignment explanation
Indices: 612323--613092 Score: 977
Period size: 54 Copynumber: 14.1 Consensus size: 54
612313 GATGCAAATG
* * **
612323 TAGTGCCTATATGG-TAGTTCATCAACTCATGATGAATTTTGT-GAATTTGCACACA
1 TAGTGCCTGTACGGTTA-TTCATCAACTCATGATGAATTCCGTGGAA--TGCACACA
* * * *
612378 TAGTGCTTGTAAGGTTATTTATCAACTCATGATGAATTCCGTGGAATGCACACT
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGAATGCACACA
* * *
612432 TAGTGCCTGTACGATTATTCATCAACTCATGATGAATTTCGTGGAATGCACACT
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGAATGCACACA
* * * * *
612486 TAGTGCATGTACGGTTATTCATCAACTCATGATGAATTTCTTGGAACGCACACT
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGAATGCACACA
* * *
612540 TAGTGCCTGTACAGTTATTCATCAACTCATGATAAATTCCGTGGATTTGCACACA
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGA-ATGCACACA
* * * * *
612595 TAGTGCATGTACGGTTATTCATAAACTCATTATGAATTCCATGGAATGCACACT
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGAATGCACACA
* * * *
612649 TAGTGCTTGTACGGTTATTCACCAACTCATGATGAATTCCATGGATTTGCACACA
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGA-ATGCACACA
* * * * * *
612704 TAGTGCTTGTACGATTATTCATCAACTCATGATGAATTCCATTGAATTCACACT
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGAATGCACACA
*
612758 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACA
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGA-ATGCACACA
* * *
612813 TAGTGCATGTACGATTATTCATCAACTCATGATGAATTCCGTGGAATGCACACT
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGAATGCACACA
* * *
612867 TAGTGCCTGTACGGATATTCATCAACTCATGATGAATTCTGTGGATTTGCACACA
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGA-ATGCACACA
* *
612922 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGAATGAACACT
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGAATGCACACA
* * * * * * * *
612976 TAGTGCATGTACGATTATTCATCAACTAACGATGAATTCCGTAGATTTTCACAAA
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGA-ATGCACACA
**
613031 TAGTGTTTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGAATGCACACA
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGAATGCACACA
613085 TAGTGCCT
1 TAGTGCCT
613093 TTTGGTAATC
Statistics
Matches: 621, Mismatches: 87, Indels: 15
0.86 0.12 0.02
Matches are distributed among these distances:
54 347 0.56
55 269 0.43
56 5 0.01
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (54 bp):
TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGAATGCACACA
Done.