Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 177 of 226
Found at i:56645392 original size:16 final size:18
Alignment explanation
Indices: 56645360--56645392 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
56645350 ATATATTATA
56645360 ATAATTAAAATGAAAGAT
1 ATAATTAAAATGAAAGAT
56645378 ATAA-TAAAA-GAAAGA
1 ATAATTAAAATGAAAGA
56645393 AAAAGAGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (18 bp):
ATAATTAAAATGAAAGAT
Found at i:56646109 original size:25 final size:25
Alignment explanation
Indices: 56646061--56646109 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
56646051 CATAACTGAA
* *
56646061 ATGAAATGAATTGATTTTGTATATT
1 ATGAAATGAATTGATTATGAATATT
56646086 ATGAAAT-ATATTGATTATGAATAT
1 ATGAAATGA-ATTGATTATGAATAT
56646110 ATGTGTATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (25 bp):
ATGAAATGAATTGATTATGAATATT
Found at i:56646535 original size:25 final size:25
Alignment explanation
Indices: 56646507--56646554 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
56646497 TGTCATTAAC
*
56646507 ATTGAAATGGCAAAGATGAGAAAAT
1 ATTGAAATGACAAAGATGAGAAAAT
* *
56646532 ATTGAAATTACAAATATGAGAAA
1 ATTGAAATGACAAAGATGAGAAA
56646555 TGATTATGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.54, C:0.04, G:0.19, T:0.23
Consensus pattern (25 bp):
ATTGAAATGACAAAGATGAGAAAAT
Found at i:56647872 original size:49 final size:49
Alignment explanation
Indices: 56647793--56647886 Score: 143
Period size: 49 Copynumber: 1.9 Consensus size: 49
56647783 TCAAGAAGGG
* *
56647793 ATAAATAGTGATAAGAGTGTAGACAATGGAAGACTAAGTTTAGCAATGT
1 ATAAATAGTGATAAAAGTGTAGACAATGGAAGACCAAGTTTAGCAATGT
* * *
56647842 ATAAATAGTGATAAAAGTGTAGATAGTGGAAGACCAATTTTAGCA
1 ATAAATAGTGATAAAAGTGTAGACAATGGAAGACCAAGTTTAGCA
56647887 TTGCATAGCA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 40 1.00
ACGTcount: A:0.44, C:0.06, G:0.23, T:0.27
Consensus pattern (49 bp):
ATAAATAGTGATAAAAGTGTAGACAATGGAAGACCAAGTTTAGCAATGT
Found at i:56652804 original size:16 final size:18
Alignment explanation
Indices: 56652783--56652816 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
56652773 TGTAGCTAAT
56652783 TAAATTTT-TG-AATTAG
1 TAAATTTTGTGAAATTAG
56652799 TAAATTTTGTGAAATTAG
1 TAAATTTTGTGAAATTAG
56652817 GAGTTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 2 0.12
18 6 0.38
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (18 bp):
TAAATTTTGTGAAATTAG
Found at i:56653042 original size:16 final size:18
Alignment explanation
Indices: 56653010--56653042 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
56653000 ATATATTATA
56653010 ATAATTAAAATGAAAGAT
1 ATAATTAAAATGAAAGAT
56653028 ATAA-TAAAA-GAAAGA
1 ATAATTAAAATGAAAGA
56653043 AAAAGAGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (18 bp):
ATAATTAAAATGAAAGAT
Found at i:56654249 original size:43 final size:43
Alignment explanation
Indices: 56654201--56654286 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
56654191 TATATGATTG
* *
56654201 ATATTGGAATGGAAAAGATGATAAATGAAAACGAGATGAGAAA
1 ATATTGAAATGGAAAAGATGAAAAATGAAAACGAGATGAGAAA
** ** *
56654244 ATATTGAAATGGAAATTATGAAAAATGATTATGAGATGAGAAA
1 ATATTGAAATGGAAAAGATGAAAAATGAAAACGAGATGAGAAA
56654287 TGAAATATGA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.52, C:0.01, G:0.23, T:0.23
Consensus pattern (43 bp):
ATATTGAAATGGAAAAGATGAAAAATGAAAACGAGATGAGAAA
Found at i:56655578 original size:49 final size:49
Alignment explanation
Indices: 56655506--56655599 Score: 179
Period size: 49 Copynumber: 1.9 Consensus size: 49
56655496 TCAAGAAGGA
*
56655506 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACTAAGTTTAGCAAAGT
1 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACCAAGTTTAGCAAAGT
56655555 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACCAAGTTTAGCA
1 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACCAAGTTTAGCA
56655600 TTGCATAGCA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.43, C:0.07, G:0.27, T:0.23
Consensus pattern (49 bp):
ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACCAAGTTTAGCAAAGT
Found at i:56656646 original size:100 final size:99
Alignment explanation
Indices: 56656460--56656651 Score: 269
Period size: 100 Copynumber: 1.9 Consensus size: 99
56656450 ATTTAAAATA
* * **
56656460 TTCAATGTTCAAATGTTTAAATGTTTCCGATTGTATGGTAATGCTCCGTAACCCTAATCTGGCGA
1 TTCAATGTTAAAATGTTTAAATGTTTCCGATTGTACGGTAATGCTCCGTAACCCTAATCCAGCGA
* * *
56656525 CGGAGACGGGTTAGGGGTGTTACATTTAGAAATTC
66 CGAAGACAGGTTAGGGATGTTAC-TTTAGAAATTC
* * *
56656560 TTCAGTGTTAAAATGTTTAAATGTTTTCGATTGTACGGTAATGCAT-CGTAACCCTAATCCAGTG
1 TTCAATGTTAAAATGTTTAAATGTTTCCGATTGTACGGTAATGC-TCCGTAACCCTAATCCAGCG
56656624 ACGAAGACAGGTTAGGGATGTTACTTTA
65 ACGAAGACAGGTTAGGGATGTTACTTTA
56656652 TATGTAGGTA
Statistics
Matches: 81, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
99 4 0.05
100 76 0.94
101 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (99 bp):
TTCAATGTTAAAATGTTTAAATGTTTCCGATTGTACGGTAATGCTCCGTAACCCTAATCCAGCGA
CGAAGACAGGTTAGGGATGTTACTTTAGAAATTC
Found at i:56667250 original size:11 final size:11
Alignment explanation
Indices: 56667234--56667259 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
56667224 AGGTCCAAGG
56667234 TAAGTTGATTT
1 TAAGTTGATTT
56667245 TAAGTTGATTT
1 TAAGTTGATTT
56667256 TAAG
1 TAAG
56667260 GTTGTTTACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (11 bp):
TAAGTTGATTT
Found at i:56671132 original size:32 final size:32
Alignment explanation
Indices: 56671096--56671178 Score: 114
Period size: 32 Copynumber: 2.6 Consensus size: 32
56671086 ACAATTATGG
* * *
56671096 AACCTAGTTTTGAGGTTTACTTATGATTTAA-A
1 AACCTAGTTGTGAGGCTTACTGATGA-TTAAGA
*
56671128 AACCTAGTTGTAAGGCTTACTGATGATTAAGA
1 AACCTAGTTGTGAGGCTTACTGATGATTAAGA
56671160 AACCTAGTTGTGAGGCTTA
1 AACCTAGTTGTGAGGCTTA
56671179 TTGAGGTTCA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
31 4 0.09
32 41 0.91
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.36
Consensus pattern (32 bp):
AACCTAGTTGTGAGGCTTACTGATGATTAAGA
Found at i:56671536 original size:31 final size:32
Alignment explanation
Indices: 56671501--56671565 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
56671491 AAGCCGAGCA
*
56671501 TTAAGGTCCATGTTAA-TTTATAA-ACCTAGTT
1 TTAAGGCCCATGTTAATTTTA-AAGACCTAGTT
* *
56671532 TTAAGGCCCATTTTTATTTTAAAGACCTAGTT
1 TTAAGGCCCATGTTAATTTTAAAGACCTAGTT
56671564 TT
1 TT
56671566 GACATTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 15 0.52
32 14 0.48
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (32 bp):
TTAAGGCCCATGTTAATTTTAAAGACCTAGTT
Found at i:56675206 original size:29 final size:30
Alignment explanation
Indices: 56675163--56675233 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 30
56675153 TGGATCAAAT
56675163 CAAAATTTTATATATAAAATT-ACATAAAAC
1 CAAAA-TTTATATATAAAATTAACATAAAAC
* *
56675193 CAAAATTTATATATACAATTACACATTAAAC
1 CAAAATTTATATATAAAATTA-ACATAAAAC
*
56675224 CATAATTTAT
1 CAAAATTTAT
56675234 TTTGCCCCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 14 0.39
30 5 0.14
31 17 0.47
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (30 bp):
CAAAATTTATATATAAAATTAACATAAAAC
Found at i:56680115 original size:18 final size:19
Alignment explanation
Indices: 56680065--56680115 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
56680055 GTAATAAAAT
* *
56680065 AAAATAAAAACAAATGAA-
1 AAAATAAAAATAAATTAAG
*
56680083 AAAATGAAAA-AAATTAAG
1 AAAATAAAAATAAATTAAG
56680101 AAAAT-AAAATAAATT
1 AAAATAAAAATAAATT
56680116 GGTAAATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 10 0.34
18 19 0.66
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.18
Consensus pattern (19 bp):
AAAATAAAAATAAATTAAG
Found at i:56680970 original size:23 final size:23
Alignment explanation
Indices: 56680938--56680982 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
56680928 AGATTTTTCC
56680938 TAAATATTATCACTAAATAATTT
1 TAAATATTATCACTAAATAATTT
*
56680961 TAAATGTTATCACTAAATAATT
1 TAAATATTATCACTAAATAATT
56680983 CAAAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (23 bp):
TAAATATTATCACTAAATAATTT
Found at i:56680988 original size:23 final size:23
Alignment explanation
Indices: 56680939--56680988 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
56680929 GATTTTTCCT
**
56680939 AAATATTATCACTAAATAATTTT
1 AAATATTATCACTAAATAATTCA
*
56680962 AAATGTTATCACTAAATAATTCA
1 AAATATTATCACTAAATAATTCA
56680985 AAAT
1 AAAT
56680989 TTAAAAATCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.50, C:0.10, G:0.02, T:0.38
Consensus pattern (23 bp):
AAATATTATCACTAAATAATTCA
Found at i:56682472 original size:23 final size:23
Alignment explanation
Indices: 56682440--56682504 Score: 121
Period size: 23 Copynumber: 2.8 Consensus size: 23
56682430 TAGATTTTTC
*
56682440 CTAAACATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
56682463 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
56682486 CTAAATATTATCACTAAAT
1 CTAAATATTATCACTAAAT
56682505 TTGAAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:56682481 original size:13 final size:13
Alignment explanation
Indices: 56682440--56682504 Score: 61
Period size: 13 Copynumber: 5.5 Consensus size: 13
56682430 TAGATTTTTC
*
56682440 CTAAACATTATCA
1 CTAAATATTATCA
*
56682453 CTAAATA--AT-T
1 CTAAATATTATCA
56682463 CTAAATATTATCA
1 CTAAATATTATCA
*
56682476 CTAAATA--AT-T
1 CTAAATATTATCA
56682486 CTAAATATTATCA
1 CTAAATATTATCA
56682499 CTAAAT
1 CTAAAT
56682505 TTGAAATTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
10 14 0.34
11 4 0.10
12 4 0.10
13 19 0.46
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:56683406 original size:8 final size:8
Alignment explanation
Indices: 56683380--56683418 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
56683370 TTAACCAAGC
56683380 TATTTAAT
1 TATTTAAT
*
56683388 TAATTAAT
1 TATTTAAT
*
56683396 TATTTATT
1 TATTTAAT
*
56683404 TATTTATT
1 TATTTAAT
56683412 TATTTAA
1 TATTTAA
56683419 AAGAGTACTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TATTTAAT
Found at i:56686882 original size:35 final size:35
Alignment explanation
Indices: 56686843--56686918 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 35
56686833 TAATTAAGAT
* *
56686843 AATAAAA-AAAG-AAAATATGAAGTGTAATAAAATAA
1 AATAAAATAAAGCAAAA-AT-AAATGTAAGAAAATAA
* *
56686878 AATAAAATAATGCAAAAATAAATTTAAGAAAATAA
1 AATAAAATAAAGCAAAAATAAATGTAAGAAAATAA
56686913 AATAAA
1 AATAAA
56686919 TTGGTAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
35 26 0.74
36 5 0.14
37 4 0.11
ACGTcount: A:0.70, C:0.01, G:0.08, T:0.21
Consensus pattern (35 bp):
AATAAAATAAAGCAAAAATAAATGTAAGAAAATAA
Found at i:56688953 original size:20 final size:20
Alignment explanation
Indices: 56688928--56688974 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
56688918 ATATCTCGTT
56688928 TTGATTTGATTTTAATCAAA
1 TTGATTTGATTTTAATCAAA
*
56688948 TTGATTTGATTTTATTCAAA
1 TTGATTTGATTTTAATCAAA
56688968 TTGATTT
1 TTGATTT
56688975 AAAGGCTCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.55
Consensus pattern (20 bp):
TTGATTTGATTTTAATCAAA
Found at i:56691302 original size:76 final size:77
Alignment explanation
Indices: 56691176--56691329 Score: 274
Period size: 76 Copynumber: 2.0 Consensus size: 77
56691166 GTTTGGGTAA
* *
56691176 TCCACGGGTAGTTAGAGGACTTCGGCATGTGCTAAAGATGTATAATCCCCAGGTAGTC-TTTTTT
1 TCCACGGGCAGTTAGAAGACTTCGGCATGTGCTAAAGATGTATAATCCCCAGGTAGTCTTTTTTT
56691240 GTGGAGACTAAG
66 GTGGAGACTAAG
*
56691252 TCCACGGGCAGTTAGAAGACTTCGGCATGTGCTGAAGATGTATAATCCCCAGGTAGTCTTTTTTT
1 TCCACGGGCAGTTAGAAGACTTCGGCATGTGCTAAAGATGTATAATCCCCAGGTAGTCTTTTTTT
56691317 GTGGAGACTAAG
66 GTGGAGACTAAG
56691329 T
1 T
56691330 TATGCAAGGT
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
76 55 0.74
77 19 0.26
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.31
Consensus pattern (77 bp):
TCCACGGGCAGTTAGAAGACTTCGGCATGTGCTAAAGATGTATAATCCCCAGGTAGTCTTTTTTT
GTGGAGACTAAG
Found at i:56697747 original size:228 final size:228
Alignment explanation
Indices: 56697345--56697803 Score: 855
Period size: 228 Copynumber: 2.0 Consensus size: 228
56697335 GTGGGACAGT
* *
56697345 TGACCAGATTAAATGCAAATGTATATTATGAACATTTTGATAGTGTGTTGCATTCTAACTTGTTG
1 TGACCAGAGTAAACGCAAATGTATATTATGAACATTTTGATAGTGTGTTGCATTCTAACTTGTTG
*
56697410 ACTTGGCAAGAACGTAGGGGCCCTTTCGAAGTTCTTGAGTAAAGAGGCCGAGAGACTGTGGGCAA
66 ACTTGGCAAGAACATAGGGGCCCTTTCGAAGTTCTTGAGTAAAGAGGCCGAGAGACTGTGGGCAA
*
56697475 AACGAAGCCAAGTGTTGTGAATCAAGAGGATTCTGTTCGAGTCAAGTTAGAATGTGGACAAGAGA
131 AACGAAGCCAAGTGTTGTGAATCAAGAGGATTATGTTCGAGTCAAGTTAGAATGTGGACAAGAGA
*
56697540 GTGACATAGCTTCTTGTCGTTGAGATGTACAAA
196 GTGACATAGCTTCTTGTCATTGAGATGTACAAA
56697573 TGACCAGAGTAAACGCAAATGTATATTATGAACATTTTGATAGTGTGTTGCATTCTAACTTGTTG
1 TGACCAGAGTAAACGCAAATGTATATTATGAACATTTTGATAGTGTGTTGCATTCTAACTTGTTG
56697638 ACTTGGCAAGAACATAGGGGCCCTTTCGAAGTTCTTGAGTAAAGAGGCCGAGAGACTGTGGGCAA
66 ACTTGGCAAGAACATAGGGGCCCTTTCGAAGTTCTTGAGTAAAGAGGCCGAGAGACTGTGGGCAA
*
56697703 AACGAAGCCAAGTGTTGTGAATCAAGAGGATTATGTTTGAGTCAAGTTAGAATGTGGACAAGAGA
131 AACGAAGCCAAGTGTTGTGAATCAAGAGGATTATGTTCGAGTCAAGTTAGAATGTGGACAAGAGA
*
56697768 GTGACATAGCTTTTTGTCATTGAGATGTACAAA
196 GTGACATAGCTTCTTGTCATTGAGATGTACAAA
56697801 TGA
1 TGA
56697804 GTAGGACGGT
Statistics
Matches: 224, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
228 224 1.00
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.29
Consensus pattern (228 bp):
TGACCAGAGTAAACGCAAATGTATATTATGAACATTTTGATAGTGTGTTGCATTCTAACTTGTTG
ACTTGGCAAGAACATAGGGGCCCTTTCGAAGTTCTTGAGTAAAGAGGCCGAGAGACTGTGGGCAA
AACGAAGCCAAGTGTTGTGAATCAAGAGGATTATGTTCGAGTCAAGTTAGAATGTGGACAAGAGA
GTGACATAGCTTCTTGTCATTGAGATGTACAAA
Found at i:56700763 original size:9 final size:9
Alignment explanation
Indices: 56700746--56700776 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
56700736 TCGAGTTGAT
56700746 TCGAATAAC
1 TCGAATAAC
*
56700755 TCGATTAAC
1 TCGAATAAC
56700764 TCGAATAAC
1 TCGAATAAC
56700773 TCGA
1 TCGA
56700777 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:56701763 original size:50 final size:50
Alignment explanation
Indices: 56701708--56701862 Score: 113
Period size: 50 Copynumber: 3.1 Consensus size: 50
56701698 GCTAAAATAC
56701708 AGAATTATTTGATTCTCTTAAGACATTGGTCTAATCTGGCTAATATACCA
1 AGAATTATTTGATTCTCTTAAGACATTGGTCTAATCTGGCTAATATACCA
* ** *** **** *
56701758 AGAATTCTGTCAACTTC-AAAAAGA-ATTTTTGGCTTCGCCCCT-GCTAAAATA-C-
1 AGAATTAT-TTGA-TTCTCTTAAGACA---TTGG--TCTAATCTGGCTAATATACCA
56701810 AGAATTATTTGATTCTCTTAAGACATTGGTCTAATCTGGCTAATATACCA
1 AGAATTATTTGATTCTCTTAAGACATTGGTCTAATCTGGCTAATATACCA
56701860 AGA
1 AGA
56701863 GAATAATGAA
Statistics
Matches: 71, Mismatches: 22, Indels: 24
0.61 0.19 0.21
Matches are distributed among these distances:
47 4 0.06
48 8 0.11
49 5 0.07
50 14 0.20
51 12 0.17
52 11 0.15
53 5 0.07
54 8 0.11
55 4 0.06
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (50 bp):
AGAATTATTTGATTCTCTTAAGACATTGGTCTAATCTGGCTAATATACCA
Found at i:56701810 original size:102 final size:102
Alignment explanation
Indices: 56701634--56701862 Score: 458
Period size: 102 Copynumber: 2.2 Consensus size: 102
56701624 GGGGGCGGTT
56701634 GTCTAATCTGGCTAATATACCAAGAATTCTGTCAACTTCAAAAAGAATTTTTGGCTTCGCCCCTG
1 GTCTAATCTGGCTAATATACCAAGAATTCTGTCAACTTCAAAAAGAATTTTTGGCTTCGCCCCTG
56701699 CTAAAATACAGAATTATTTGATTCTCTTAAGACATTG
66 CTAAAATACAGAATTATTTGATTCTCTTAAGACATTG
56701736 GTCTAATCTGGCTAATATACCAAGAATTCTGTCAACTTCAAAAAGAATTTTTGGCTTCGCCCCTG
1 GTCTAATCTGGCTAATATACCAAGAATTCTGTCAACTTCAAAAAGAATTTTTGGCTTCGCCCCTG
56701801 CTAAAATACAGAATTATTTGATTCTCTTAAGACATTG
66 CTAAAATACAGAATTATTTGATTCTCTTAAGACATTG
56701838 GTCTAATCTGGCTAATATACCAAGA
1 GTCTAATCTGGCTAATATACCAAGA
56701863 GAATAATGAA
Statistics
Matches: 127, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 127 1.00
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.34
Consensus pattern (102 bp):
GTCTAATCTGGCTAATATACCAAGAATTCTGTCAACTTCAAAAAGAATTTTTGGCTTCGCCCCTG
CTAAAATACAGAATTATTTGATTCTCTTAAGACATTG
Found at i:56704988 original size:31 final size:31
Alignment explanation
Indices: 56704944--56705020 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
56704934 ATCACACTAG
* *
56704944 TAGTC-TCCTAACTATTAGTCAATTTCTTTTT
1 TAGTCATCC-AACTATTAGTAAATTTATTTTT
56704975 TAGTCATCCAACTATTAGTAAATTTATTTTT
1 TAGTCATCCAACTATTAGTAAATTTATTTTT
* *
56705006 TGGTCATCTAACTAT
1 TAGTCATCCAACTAT
56705021 GAAAAGTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 38 0.93
32 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (31 bp):
TAGTCATCCAACTATTAGTAAATTTATTTTT
Found at i:56705598 original size:18 final size:17
Alignment explanation
Indices: 56705570--56705603 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
56705560 TTAATCACTT
56705570 TAATATTAAATTTAATC
1 TAATATTAAATTTAATC
56705587 TAATATTTAAATTTAAT
1 TAATA-TTAAATTTAAT
56705604 ATTAAATCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATATTAAATTTAATC
Found at i:56707723 original size:29 final size:29
Alignment explanation
Indices: 56707659--56707723 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
56707649 ACAAAATTGA
* *
56707659 ATAATTAGGTGATCATTCTGTAACTTTTC
1 ATAATTGGGTGACCATTCTGTAACTTTTC
*
56707688 ATAATTGGGTGACCATTTTGTAACTTTTC
1 ATAATTGGGTGACCATTCTGTAACTTTTC
56707717 ATAATTG
1 ATAATTG
56707724 AGTGGCCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (29 bp):
ATAATTGGGTGACCATTCTGTAACTTTTC
Found at i:56709171 original size:24 final size:24
Alignment explanation
Indices: 56709133--56709280 Score: 113
Period size: 24 Copynumber: 6.2 Consensus size: 24
56709123 CTAGCATGTA
* * *
56709133 ACCTGCAAACCCCTATCACCAAAT
1 ACCTGCGAACACCTATCACCAGAT
* * * *
56709157 ACCTACGAACACCTATTACTAGAC
1 ACCTGCGAACACCTATCACCAGAT
*
56709181 ACATGCGAAC-CCTATCACCAGAT
1 ACCTGCGAACACCTATCACCAGAT
*
56709204 ACCTGCGAACACCTATCACCAGAC
1 ACCTGCGAACACCTATCACCAGAT
* * * * *
56709228 ACATGC-AAAACACTACCACTAGAC
1 ACCTGCGAACAC-CTATCACCAGAT
* *
56709252 ACATGCGAAC-CCATATCACCAGAC
1 ACCTGCGAACACC-TATCACCAGAT
56709276 ACCTG
1 ACCTG
56709281 TGAATCCCTA
Statistics
Matches: 98, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
23 24 0.24
24 72 0.73
25 2 0.02
ACGTcount: A:0.37, C:0.37, G:0.10, T:0.16
Consensus pattern (24 bp):
ACCTGCGAACACCTATCACCAGAT
Found at i:56709213 original size:47 final size:47
Alignment explanation
Indices: 56709143--56709233 Score: 146
Period size: 47 Copynumber: 1.9 Consensus size: 47
56709133 ACCTGCAAAC
* *
56709143 CCCTATCACCAAATACCTACGAACACCTATTACTAGACACATGCGAA
1 CCCTATCACCAAATACCTACGAACACCTATCACCAGACACATGCGAA
* *
56709190 CCCTATCACCAGATACCTGCGAACACCTATCACCAGACACATGC
1 CCCTATCACCAAATACCTACGAACACCTATCACCAGACACATGC
56709234 AAAACACTAC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 40 1.00
ACGTcount: A:0.35, C:0.37, G:0.10, T:0.18
Consensus pattern (47 bp):
CCCTATCACCAAATACCTACGAACACCTATCACCAGACACATGCGAA
Found at i:56711338 original size:46 final size:46
Alignment explanation
Indices: 56711281--56711389 Score: 173
Period size: 46 Copynumber: 2.4 Consensus size: 46
56711271 ATTGAATCGG
* * *
56711281 GCCTTGAGCCTAGCAGGTTTTATGCCGGTGTATTTTAATGTATCAA
1 GCCTTGTGCCTAGCAGGTTTTATGCCGGTGTACTATAATGTATCAA
*
56711327 GCCTTGTGCCTAGCAGGTTTTATGCCGGTGTACTATAATGTATCAG
1 GCCTTGTGCCTAGCAGGTTTTATGCCGGTGTACTATAATGTATCAA
*
56711373 GCCTTGTACCTAGCAGG
1 GCCTTGTGCCTAGCAGG
56711390 CTTCATATCG
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 58 1.00
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (46 bp):
GCCTTGTGCCTAGCAGGTTTTATGCCGGTGTACTATAATGTATCAA
Found at i:56712862 original size:24 final size:24
Alignment explanation
Indices: 56712800--56712876 Score: 102
Period size: 24 Copynumber: 3.2 Consensus size: 24
56712790 GTGTTACAAT
* **
56712800 CCCTATCACCAGACACCTGCGAAC
1 CCCTATCACTAGACACCTATGAAC
*
56712824 CCCTAT-ACTAGACACCTATGGAC
1 CCCTATCACTAGACACCTATGAAC
*
56712847 CCCTATCACTAGACACATATGAAC
1 CCCTATCACTAGACACCTATGAAC
56712871 CCCTAT
1 CCCTAT
56712877 TTCCAGATAC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 19 0.41
24 27 0.59
ACGTcount: A:0.31, C:0.39, G:0.10, T:0.19
Consensus pattern (24 bp):
CCCTATCACTAGACACCTATGAAC
Found at i:56716044 original size:15 final size:16
Alignment explanation
Indices: 56716020--56716056 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
56716010 TTTAGTTACC
*
56716020 ATTAAGGCCTAAC-AT
1 ATTAAAGCCTAACTAT
56716035 ATTAAAGCCTAACTAT
1 ATTAAAGCCTAACTAT
56716051 ATTAAA
1 ATTAAA
56716057 CCCAAAGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.46, C:0.16, G:0.08, T:0.30
Consensus pattern (16 bp):
ATTAAAGCCTAACTAT
Found at i:56718434 original size:25 final size:23
Alignment explanation
Indices: 56718406--56718452 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
56718396 ATCCGGATAA
56718406 TATAACAGAAAGCTCACAAAGAGCC
1 TATAAC-GAAAGCTC-CAAAGAGCC
**
56718431 TATAACGGTAGCTCCAAAGAGC
1 TATAACGAAAGCTCCAAAGAGC
56718453 AATTAACGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 6 0.30
25 6 0.30
ACGTcount: A:0.43, C:0.23, G:0.19, T:0.15
Consensus pattern (23 bp):
TATAACGAAAGCTCCAAAGAGCC
Found at i:56718450 original size:23 final size:24
Alignment explanation
Indices: 56718416--56718483 Score: 77
Period size: 24 Copynumber: 2.8 Consensus size: 24
56718406 TATAACAGAA
*
56718416 AGCTCACAAAGAGC-CTATAACG-GT
1 AGCTC-CAAAGAGCAAT-TAACGAGT
56718440 AGCTCCAAAGAGCAATTAACGAGT
1 AGCTCCAAAGAGCAATTAACGAGT
* *
56718464 AGCTCCGAAGATCAATTAAC
1 AGCTCCAAAGAGCAATTAAC
56718484 AGGAAGCACC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
23 13 0.33
24 26 0.67
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.18
Consensus pattern (24 bp):
AGCTCCAAAGAGCAATTAACGAGT
Found at i:56720838 original size:25 final size:24
Alignment explanation
Indices: 56720810--56720857 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
56720800 AGATACTTTT
*
56720810 TTTATTATAAAATATCACATTTTAG
1 TTTATTATAAAATAT-AAATTTTAG
56720835 TTTATTATAAAATATAAATTTTA
1 TTTATTATAAAATATAAATTTTA
56720858 AAAATGTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (24 bp):
TTTATTATAAAATATAAATTTTAG
Found at i:56720890 original size:22 final size:20
Alignment explanation
Indices: 56720857--56720896 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
56720847 TATAAATTTT
*
56720857 AAAAATGTAAAATTTTATTA
1 AAAAATGTAAAAGTTTATTA
56720877 AAAATATGTAAAAAGTTTAT
1 AAAA-ATGT-AAAAGTTTAT
56720897 AATGTTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 4 0.24
22 9 0.53
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (20 bp):
AAAAATGTAAAAGTTTATTA
Found at i:56721771 original size:23 final size:23
Alignment explanation
Indices: 56721743--56721786 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
56721733 TAATACTATT
56721743 TAATAA-TGGTAACAATAGTAAAA
1 TAATAAGTGG-AACAATAGTAAAA
*
56721766 TAATAAGTGGAACATTAGTAA
1 TAATAAGTGGAACAATAGTAA
56721787 TAACCAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.52, C:0.05, G:0.16, T:0.27
Consensus pattern (23 bp):
TAATAAGTGGAACAATAGTAAAA
Found at i:56723524 original size:28 final size:27
Alignment explanation
Indices: 56723489--56723541 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
56723479 TTTTTATTAA
56723489 TTTTTATA-TTTAAAATTTTTAAAATGT
1 TTTTTATATTTTAAAA-TTTTAAAATGT
*
56723516 TTTTATATATTTTTAAATTTTAAAAT
1 TTTT-TATATTTTAAAATTTTAAAAT
56723542 AATAATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
28 13 0.57
29 6 0.26
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTTATATTTTAAAATTTTAAAATGT
Found at i:56736013 original size:18 final size:19
Alignment explanation
Indices: 56735970--56736023 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
56735960 GGTCAAATCC
* *
56735970 AACTCTCTCTATTCTGTCT
1 AACTCTCTCAATTCTCTCT
*
56735989 AA-ACTCTCAATTCTCT-T
1 AACTCTCTCAATTCTCTCT
*
56736006 AACTCTCTCAATTTTCTC
1 AACTCTCTCAATTCTCTC
56736024 AAGTTTTGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
17 3 0.11
18 23 0.82
19 2 0.07
ACGTcount: A:0.22, C:0.31, G:0.02, T:0.44
Consensus pattern (19 bp):
AACTCTCTCAATTCTCTCT
Found at i:56737975 original size:24 final size:24
Alignment explanation
Indices: 56737943--56738025 Score: 89
Period size: 24 Copynumber: 3.5 Consensus size: 24
56737933 GGAGATGGAA
56737943 ATGAAGATGAAAACGAGGGTA-GAG
1 ATGAAGATGAAAACGAGGG-ACGAG
* *
56737967 ATGAAGATGAAGACGAGGGACTAG
1 ATGAAGATGAAAACGAGGGACGAG
* *
56737991 ATGAAGATGAATAC-AGGGATCGGG
1 ATGAAGATGAAAACGAGGGA-CGAG
*
56738015 GTGAAGATGAA
1 ATGAAGATGAA
56738026 GAAGATGAAG
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
23 6 0.12
24 45 0.88
ACGTcount: A:0.42, C:0.06, G:0.37, T:0.14
Consensus pattern (24 bp):
ATGAAGATGAAAACGAGGGACGAG
Found at i:56753709 original size:136 final size:137
Alignment explanation
Indices: 56753398--56753954 Score: 775
Period size: 138 Copynumber: 4.1 Consensus size: 137
56753388 TAGAAAAAAG
** * * *
56753398 AATTATATTCTTTCCAAAAGAATATTAATTTCCGTGTCATTTATATTTTGGCCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCTATGTCTTTTATATTTTGACTGAAATTAATTAA
*
56753463 TATAACTGCTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAA-T
66 TATAACTGATTATATTAATAAATTCGGT-AAATATATACAATTAATATTTTGTATGAATCAAATT
56753527 CTATATATT
130 C-ATATATT
* * * * *
56753536 AATTATATTCTTCCCAAAAGAAAATTAATTTCTATGTCTTTAATATTTTGACTAAAATTAATCAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCTATGTCTTTTATATTTTGACTGAAATTAATTAA
* *
56753601 TATAACTGATTATATTAATAAATTCGGT-AATATATATAATTAATATTTTTTATGAATCAAATTC
66 TATAACTGATTATATTAATAAATTCGGTAAATATATACAATTAATATTTTGTATGAATCAAATTC
56753665 ATATATT
131 ATATATT
* * *
56753672 AATTATATTTTTTTCAAAAGAATATTAATTT-TCATGTCTTTTATATTTTGACTGAAATTATTTA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCT-ATGTCTTTTATATTTTGACTGAAATTAATTA
* * * *
56753736 ATATATCT-ATTTATATTATTAAATTCGGTAAAATATATATAATTAATATTTT-TATGAATCACA
65 ATATAACTGA-TTATATTAATAAATTCGGT-AAATATATACAATTAATATTTTGTATGAATCAAA
*
56753799 TTCAGATATT
128 TTCATATATT
*
56753809 AATTATATTCTTTCCAAAAGAATATTAATTTCTATATCTTTTATATTTTGA-TCGAAATTAATTA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCTATGTCTTTTATATTTTGACT-GAAATTAATTA
* * * *
56753873 ATATAATTGTTTATATTAATAAATTTGGTAAAATATATACAATTATTATTTTGTATGAATCAAAT
65 ATATAACTGATTATATTAATAAATTCGGT-AAATATATACAATTAATATTTTGTATGAATCAAAT
56753938 TCATATATT
129 TCATATATT
56753947 AATTATAT
1 AATTATAT
56753955 CTATGTTCTC
Statistics
Matches: 372, Mismatches: 38, Indels: 18
0.87 0.09 0.04
Matches are distributed among these distances:
135 2 0.01
136 118 0.32
137 121 0.33
138 131 0.35
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (137 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTCTATGTCTTTTATATTTTGACTGAAATTAATTAA
TATAACTGATTATATTAATAAATTCGGTAAATATATACAATTAATATTTTGTATGAATCAAATTC
ATATATT
Found at i:56762420 original size:32 final size:31
Alignment explanation
Indices: 56762365--56762535 Score: 177
Period size: 32 Copynumber: 5.4 Consensus size: 31
56762355 GAATGGCTAC
* * *
56762365 AAGCCATAAGTACAGTAATATGATTGGCACA
1 AAGCCATCAGTATAGTAATATGATCGGCACA
* * *
56762396 AAGCCATCAGTAGTAGTGATATGATCGACATA
1 AAGCCATCAGTA-TAGTAATATGATCGGCACA
* *
56762428 CAA-CCATCAGTAATGGTAATATGATCGACACA
1 -AAGCCATCAGT-ATAGTAATATGATCGGCACA
56762460 AAGCCATCAGTA-ATGATAATATGATCGGCACA
1 AAGCCATCAGTATA-G-TAATATGATCGGCACA
*
56762492 AAGCCATCAGTA-ACGATAATATTATCGGCACA
1 AAGCCATCAGTATA-G-TAATATGATCGGCACA
56762524 AAGCCATCAGTA
1 AAGCCATCAGTA
56762536 CCATCGCAGT
Statistics
Matches: 121, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
31 15 0.12
32 103 0.85
33 3 0.02
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.22
Consensus pattern (31 bp):
AAGCCATCAGTATAGTAATATGATCGGCACA
Found at i:56762463 original size:64 final size:64
Alignment explanation
Indices: 56762365--56762535 Score: 204
Period size: 64 Copynumber: 2.7 Consensus size: 64
56762355 GAATGGCTAC
* * * * * *
56762365 AAGCCATAAGT-ACAGTAATATGATTGGCACAAAGCCATCAGTAGT-AGTGATATGATCGACATA
1 AAGCCATCAGTAACGGTAATATGATCGGCACAAAGCCATCAGTAATGA-TAATATGATCGACACA
* * *
56762428 CAA-CCATCAGTAATGGTAATATGATCGACACAAAGCCATCAGTAATGATAATATGATCGGCACA
1 -AAGCCATCAGTAACGGTAATATGATCGGCACAAAGCCATCAGTAATGATAATATGATCGACACA
* *
56762492 AAGCCATCAGTAACGATAATATTATCGGCACAAAGCCATCAGTA
1 AAGCCATCAGTAACGGTAATATGATCGGCACAAAGCCATCAGTA
56762536 CCATCGCAGT
Statistics
Matches: 91, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
63 9 0.10
64 81 0.89
65 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.22
Consensus pattern (64 bp):
AAGCCATCAGTAACGGTAATATGATCGGCACAAAGCCATCAGTAATGATAATATGATCGACACA
Found at i:56762576 original size:26 final size:26
Alignment explanation
Indices: 56762546--56762617 Score: 108
Period size: 26 Copynumber: 2.8 Consensus size: 26
56762536 CCATCGCAGT
*
56762546 AAAGCTACCAGCAACAGTATCACAGC
1 AAAGCTGCCAGCAACAGTATCACAGC
*
56762572 AAAGCTGCCAGCAACAGTATCGCAGC
1 AAAGCTGCCAGCAACAGTATCACAGC
* *
56762598 AAAGCTGCCAGTAATAGTAT
1 AAAGCTGCCAGCAACAGTAT
56762618 ATGTGGCCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.15
Consensus pattern (26 bp):
AAAGCTGCCAGCAACAGTATCACAGC
Found at i:56762635 original size:27 final size:27
Alignment explanation
Indices: 56762605--56762664 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 27
56762595 AGCAAAGCTG
56762605 CCAGTAATAGT-ATATGTGGCCA-AGCCA
1 CCAGTAATAGTGAT-TGTGG-CAGAGCCA
56762632 CCAGTAATAGTGATTGTGGCAGAGCCA
1 CCAGTAATAGTGATTGTGGCAGAGCCA
56762659 CCAGTA
1 CCAGTA
56762665 CAAAACTTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
26 2 0.06
27 27 0.87
28 2 0.06
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.22
Consensus pattern (27 bp):
CCAGTAATAGTGATTGTGGCAGAGCCA
Found at i:56762858 original size:27 final size:27
Alignment explanation
Indices: 56762812--56762956 Score: 175
Period size: 27 Copynumber: 5.4 Consensus size: 27
56762802 GGGAAATATA
* *
56762812 GTCA-TTTACCCTCCAGGGGCATTACG
1 GTCATTTTACCCTACAAGGGCATTACG
*
56762838 ATCATTTTACCCTACAAGGGCATTACG
1 GTCATTTTACCCTACAAGGGCATTACG
*
56762865 GTCATTTTACCCTACAGGGGCATTACG
1 GTCATTTTACCCTACAAGGGCATTACG
* * * *
56762892 GTCATTTTACCTTATATGGGCATTATG
1 GTCATTTTACCCTACAAGGGCATTACG
* * *
56762919 GTCATTTTGCCCTACAAGGGTATTACA
1 GTCATTTTACCCTACAAGGGCATTACG
*
56762946 GTCATTATACC
1 GTCATTTTACC
56762957 TATTTTAGGG
Statistics
Matches: 100, Mismatches: 18, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
26 3 0.03
27 97 0.97
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (27 bp):
GTCATTTTACCCTACAAGGGCATTACG
Found at i:56768234 original size:3 final size:3
Alignment explanation
Indices: 56768228--56768299 Score: 99
Period size: 3 Copynumber: 24.0 Consensus size: 3
56768218 ATTTTTTTAG
* *
56768228 ATT ATT ATT ATT ATT ATT ATT ATT ATT ACT ATT ATT ACT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
56768276 ACT ATT ATT ATT ATG ATT TTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT
56768300 TTGTTTTATT
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:56768332 original size:25 final size:23
Alignment explanation
Indices: 56768291--56768336 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
56768281 TATTATTATG
56768291 ATTTTTATTTTGTTTTATTTAAT
1 ATTTTTATTTTGTTTTATTTAAT
*
56768314 ATTTTTATTCTTTTATTTATTTA
1 ATTTTTATT-TTGT-TTTATTTA
56768337 CTTATTTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 3 0.15
25 8 0.40
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (23 bp):
ATTTTTATTTTGTTTTATTTAAT
Found at i:56769541 original size:23 final size:23
Alignment explanation
Indices: 56769493--56769541 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
56769483 TCTTCTGCCT
* *
56769493 TTTCTATCTTTCTTTTTCTTTCA
1 TTTCTATCTTTCTTTTTATTTAA
*
56769516 TTTCTTTC-TTCTTTTTAATTTAA
1 TTTCTATCTTTCTTTTT-ATTTAA
56769539 TTT
1 TTT
56769542 GCATGCCACC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTCTATCTTTCTTTTTATTTAA
Found at i:56770630 original size:29 final size:31
Alignment explanation
Indices: 56770597--56770660 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 31
56770587 ATGGTGAAAT
56770597 TGTTAAGGAGAAG-CCCTT-GTGGCTGATTC
1 TGTTAAGGAGAAGACCCTTCGTGGCTGATTC
* *
56770626 TGTT-ATGAGAAGAGCCTTCGTGGCTGATTC
1 TGTTAAGGAGAAGACCCTTCGTGGCTGATTC
56770656 TGTTA
1 TGTTA
56770661 GAAGCGCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 7 0.23
29 8 0.27
30 15 0.50
ACGTcount: A:0.20, C:0.16, G:0.30, T:0.34
Consensus pattern (31 bp):
TGTTAAGGAGAAGACCCTTCGTGGCTGATTC
Found at i:56770635 original size:28 final size:30
Alignment explanation
Indices: 56770604--56770660 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
56770594 AATTGTTAAG
56770604 GAGAAG-CCCTT-GTGGCTGATTCTGTTAT
1 GAGAAGACCCTTCGTGGCTGATTCTGTTAT
*
56770632 GAGAAGAGCCTTCGTGGCTGATTCTGTTA
1 GAGAAGACCCTTCGTGGCTGATTCTGTTA
56770661 GAAGCGCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 6 0.23
29 4 0.15
30 16 0.62
ACGTcount: A:0.19, C:0.18, G:0.30, T:0.33
Consensus pattern (30 bp):
GAGAAGACCCTTCGTGGCTGATTCTGTTAT
Found at i:56770675 original size:27 final size:30
Alignment explanation
Indices: 56770613--56770676 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 30
56770603 GGAGAAGCCC
*
56770613 TTGTGGCTGATTCTGTTATGAGAAGAGCCT
1 TTGTGGCTGATTCTGTTATGAGAAGAGCAT
* *
56770643 TCGTGGCTGATTCTG-T-T-AGAAGCGCAT
1 TTGTGGCTGATTCTGTTATGAGAAGAGCAT
56770670 TTGTGGC
1 TTGTGGC
56770677 AAAGTTTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 14 0.47
28 1 0.03
29 1 0.03
30 14 0.47
ACGTcount: A:0.17, C:0.16, G:0.31, T:0.36
Consensus pattern (30 bp):
TTGTGGCTGATTCTGTTATGAGAAGAGCAT
Found at i:56780318 original size:70 final size:70
Alignment explanation
Indices: 56780185--56780323 Score: 197
Period size: 70 Copynumber: 2.0 Consensus size: 70
56780175 AGTACTAGGC
* * * * *
56780185 ACAACTATTGTCGGTTATCCGACTAGCATTGGGCGCAATAATTTGTCGACTCGTTCGACTAGTGC
1 ACAACTATCGTCGGTTATCCGACTAGCACTGGGCGCAATAATTTGTCGACTCATTCAACTAGTGA
56780250 TGGGT
66 TGGGT
* * * *
56780255 ACAACTATCGTCGGTTATCCGACTAGCGCTGGGCGTAATAATTTTTCGACTCATTCAATTAGTGA
1 ACAACTATCGTCGGTTATCCGACTAGCACTGGGCGCAATAATTTGTCGACTCATTCAACTAGTGA
56780320 TGGG
66 TGGG
56780324 CACACAAATG
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
70 60 1.00
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (70 bp):
ACAACTATCGTCGGTTATCCGACTAGCACTGGGCGCAATAATTTGTCGACTCATTCAACTAGTGA
TGGGT
Found at i:56786485 original size:65 final size:65
Alignment explanation
Indices: 56786410--56786540 Score: 262
Period size: 65 Copynumber: 2.0 Consensus size: 65
56786400 ATATAACAAG
56786410 TATGTGACTAATGATCTTTCGTATCACATTGATAACATAAGTTATCTCTCCCCTGTGAATGGTTA
1 TATGTGACTAATGATCTTTCGTATCACATTGATAACATAAGTTATCTCTCCCCTGTGAATGGTTA
56786475 TATGTGACTAATGATCTTTCGTATCACATTGATAACATAAGTTATCTCTCCCCTGTGAATGGTTA
1 TATGTGACTAATGATCTTTCGTATCACATTGATAACATAAGTTATCTCTCCCCTGTGAATGGTTA
56786540 T
1 T
56786541 CTTGAGAACT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.39
Consensus pattern (65 bp):
TATGTGACTAATGATCTTTCGTATCACATTGATAACATAAGTTATCTCTCCCCTGTGAATGGTTA
Found at i:56788457 original size:21 final size:18
Alignment explanation
Indices: 56788419--56788464 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 18
56788409 TTTATGCAAT
56788419 AATAGTATTTTAATTTTATA
1 AATA-TATTTTAATTTTA-A
56788439 ACATATATTTTATATTTTAA
1 A-ATATATTTTA-ATTTTAA
56788459 AATATA
1 AATATA
56788465 ATTATCTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 5 0.21
20 10 0.42
21 9 0.38
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
AATATATTTTAATTTTAA
Found at i:56792729 original size:24 final size:24
Alignment explanation
Indices: 56792696--56792749 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
56792686 CATCAGAAGA
56792696 GGCACACAAAATGAGAGATATCGTG
1 GGCA-ACAAAATGAGAGATATCGTG
* *
56792721 GGCAACAAAATGTGAGATATTGTG
1 GGCAACAAAATGAGAGATATCGTG
*
56792745 AGCAA
1 GGCAA
56792750 TAAATAATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.41, C:0.13, G:0.28, T:0.19
Consensus pattern (24 bp):
GGCAACAAAATGAGAGATATCGTG
Found at i:56796593 original size:23 final size:23
Alignment explanation
Indices: 56796557--56796600 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
56796547 TAGGAAAGTA
*
56796557 GTCTGCTACCCTAGCACGTCTCT
1 GTCTGCTACCCTAGCAAGTCTCT
* *
56796580 GTCTGCTTCTCTAGCAAGTCT
1 GTCTGCTACCCTAGCAAGTCT
56796601 TTAGGTTTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.14, C:0.34, G:0.18, T:0.34
Consensus pattern (23 bp):
GTCTGCTACCCTAGCAAGTCTCT
Found at i:56802778 original size:24 final size:23
Alignment explanation
Indices: 56802727--56802803 Score: 72
Period size: 24 Copynumber: 3.3 Consensus size: 23
56802717 ACACATTAAA
56802727 TAAATA-AAAAATATAAAATTTCAA-
1 TAAATATAAAAATATAAAA--T-AAT
56802751 TAAATATAAAATATATAAAATAAT
1 TAAATATAAAA-ATATAAAATAAT
*
56802775 TAAATAT-TAAAT-TAAAATAAT
1 TAAATATAAAAATATAAAATAAT
56802796 ATAAATAT
1 -TAAATAT
56802804 TTTTGAAAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
21 9 0.19
22 9 0.19
23 4 0.08
24 14 0.29
25 4 0.08
26 8 0.17
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (23 bp):
TAAATATAAAAATATAAAATAAT
Found at i:56827804 original size:41 final size:41
Alignment explanation
Indices: 56827654--56827821 Score: 160
Period size: 41 Copynumber: 4.1 Consensus size: 41
56827644 GTACAATTTG
* * * **
56827654 CCTGATACAATACACCGACACGAAGCCTG-CTAGGCTCAAGG
1 CCTGATACAATACACCGGCACGAAGCC-GACAAGGCACAAAA
** *
56827695 CCTGATACAATACACCGGCACGAAGCCTTCTAGGCACAAAA
1 CCTGATACAATACACCGGCACGAAGCCGACAAGGCACAAAA
**
56827736 CCTGATACAATACACTAGCACGAAGCCGACAAGGCA-AAAA
1 CCTGATACAATACACCGGCACGAAGCCGACAAGGCACAAAA
* * * ** *
56827776 CCCTGATCCAAGACACCGGTACGAAGCCGACTGGGCTCAAAA
1 -CCTGATACAATACACCGGCACGAAGCCGACAAGGCACAAAA
56827818 CCTG
1 CCTG
56827822 CTAGGCTCAA
Statistics
Matches: 106, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
40 4 0.04
41 98 0.92
42 4 0.04
ACGTcount: A:0.35, C:0.32, G:0.20, T:0.13
Consensus pattern (41 bp):
CCTGATACAATACACCGGCACGAAGCCGACAAGGCACAAAA
Found at i:56848597 original size:27 final size:27
Alignment explanation
Indices: 56848557--56848619 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
56848547 ATACTTTAAT
** *
56848557 TCATTTCAAGTTTCACATCCCATTTCA
1 TCATTTCATTTTTCACATCCCATCTCA
**
56848584 TCATTTCATTTTTCATTTCCCATCTCA
1 TCATTTCATTTTTCACATCCCATCTCA
56848611 T-A-TTCATTT
1 TCATTTCATTT
56848620 CTCATATTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 7 0.23
26 1 0.03
27 23 0.74
ACGTcount: A:0.22, C:0.27, G:0.02, T:0.49
Consensus pattern (27 bp):
TCATTTCATTTTTCACATCCCATCTCA
Found at i:56848624 original size:25 final size:27
Alignment explanation
Indices: 56848574--56848624 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
56848564 AAGTTTCACA
* *
56848574 TCCCATTTCATCATTTCATTTTTCATT
1 TCCCATCTCATCATTTCATTTCTCATT
56848601 TCCCATCTCAT-A-TTCATTTCTCAT
1 TCCCATCTCATCATTTCATTTCTCAT
56848625 ATTTTCCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 11 0.50
26 1 0.05
27 10 0.45
ACGTcount: A:0.20, C:0.29, G:0.00, T:0.51
Consensus pattern (27 bp):
TCCCATCTCATCATTTCATTTCTCATT
Found at i:56848628 original size:27 final size:25
Alignment explanation
Indices: 56848598--56848649 Score: 59
Period size: 27 Copynumber: 2.0 Consensus size: 25
56848588 TTCATTTTTC
*
56848598 ATTTCCCATCTCATATTCATTTCTCAT
1 ATTTCCCATCTCA-ATAC-TTTCTCAT
* *
56848625 ATTTTCCATTTCAATACTTTCTCAT
1 ATTTCCCATCTCAATACTTTCTCAT
56848650 CTCATATTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 8 0.36
26 3 0.14
27 11 0.50
ACGTcount: A:0.23, C:0.27, G:0.00, T:0.50
Consensus pattern (25 bp):
ATTTCCCATCTCAATACTTTCTCAT
Found at i:56848653 original size:43 final size:43
Alignment explanation
Indices: 56848599--56848683 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
56848589 TCATTTTTCA
56848599 TTTCCCATCTCATATTCATTTCTCATATTT-TCCATTTCAATAC
1 TTTCCCATCTCATATTCATTTCTCATATTTGT-CATTTCAATAC
* *
56848642 TTTCTCATCTCATATTCATTTCTCATCTTTGTCATTTCAATA
1 TTTCCCATCTCATATTCATTTCTCATATTTGTCATTTCAATA
56848684 TCAATAACAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
43 38 0.97
44 1 0.03
ACGTcount: A:0.22, C:0.26, G:0.01, T:0.51
Consensus pattern (43 bp):
TTTCCCATCTCATATTCATTTCTCATATTTGTCATTTCAATAC
Found at i:56851155 original size:16 final size:16
Alignment explanation
Indices: 56851136--56851166 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56851126 CTCTTAAAGT
*
56851136 TTATTTTTCTTTTATG
1 TTATTTTGCTTTTATG
56851152 TTATTTTGCTTTTAT
1 TTATTTTGCTTTTAT
56851167 TACTAGTACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.06, G:0.06, T:0.74
Consensus pattern (16 bp):
TTATTTTGCTTTTATG
Found at i:56859441 original size:16 final size:16
Alignment explanation
Indices: 56859422--56859452 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56859412 CTCTTGAAAT
56859422 TTATTTTTCTCTTATG
1 TTATTTTTCTCTTATG
*
56859438 TTATTTTTCTTTTAT
1 TTATTTTTCTCTTAT
56859453 TACTAGTACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.10, G:0.03, T:0.74
Consensus pattern (16 bp):
TTATTTTTCTCTTATG
Found at i:56863672 original size:138 final size:138
Alignment explanation
Indices: 56863359--56864519 Score: 1654
Period size: 137 Copynumber: 8.4 Consensus size: 138
56863349 TAGAAAAAGG
* * * *
56863359 AATTATATTGTTTCCAAAAGAATATTAATTTCCATATCTTTTATATTTTGACCAAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
*
56863424 TATAATTTTTTATATTAATAAATTCGGTAAAAATATATACAATTAATATTTTATATCAATCAAAT
66 TATAATTGTTTATATTAATAAATTCGGT-AAAATATATACAATTAATATTTTATATCAATCAAAT
56863489 TCATATATT
130 TCATATATT
* * *
56863498 AATTTTATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATAATTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
*
56863563 TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATCAATCAAATT
66 TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTATATCAATCAAATT
56863628 CATATATT
131 CATATATT
* * * *
56863636 AATTATATTCTTTCCAAAATAATATTAATTTTCATGTCTTTTATATATTTTG-GCAAAATGAATT
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTC-TTT-TATATTTTGACCGAAATTAATT
* * * * * * *
56863700 AATATAATTGTTTATATTAATAAACTCGGTAAATTGTATACAATTAAAAGTTTATATGAATCAAG
64 AATATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTATATCAATCAAA
56863765 TTCATATATT
129 TTCATATATT
* *
56863775 AATTATATTCTTTCCAAAAGAATATTAA-TTTCTATGTCTTTTATATTTTAACCGAAATTTATTA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTC-ATGTCTTTTATATTTTGACCGAAATTAATTA
* * * * *
56863839 ATATAACTGTTTATATTGATAAATTCAGTAATATATATATAATTAATATTTTATATCAATCAAAT
65 ATATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTATATCAATCAAAT
*
56863904 TCATATACT
130 TCATATATT
* * *
56863913 AATTATATTCTTTCCAAAA-AATATTAATTTTCATATCTTTTATATTTTGACTGAAATTAGTTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
* ** *
56863977 TATAACTT-TTTATATTAATAATTTTAGTAAAATATATACAATTAATATTTTGTATCAATCAAAT
66 TATAA-TTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTATATCAATCAAAT
56864041 TCATATATT
130 TCATATATT
* * *
56864050 AATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATGAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
* * * * * *
56864115 TATAATTATTTATATTAATAAATTCGGTAAAATATAAACAACTAAAATTTTGTATGAATCAAATT
66 TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTATATCAATCAAATT
*
56864180 TATATA-T
131 CATATATT
* * *
56864187 AATTATTTTCTTTCCAAAAGAATATTAATTTTCATGTCTTTAATATTTTGATCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
* * *
56864252 TAT-ATCTGATTATATTAATAAATTCGGTAAAATATATAAAATTAATATTTTATATCAATGAAAT
66 TATAAT-TGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTATATCAATCAAAT
56864316 TCATATATT
130 TCATATATT
* *
56864325 ACTTATATTCTTTCCAAAA-AATAATAATTTTCATGTCTTTTATATTTTGACCG-AATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
* * *** *
56864388 TATAACTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGGGTAAATCAAATT
66 TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTATATCAATCAAATT
56864453 CATATATT
131 CATATATT
* * *
56864461 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTATTATAGTTTGACCGAAATT
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATT
56864520 GAAAATATAT
Statistics
Matches: 907, Mismatches: 102, Indels: 27
0.88 0.10 0.03
Matches are distributed among these distances:
136 92 0.10
137 307 0.34
138 302 0.33
139 198 0.22
140 8 0.01
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (138 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTATATCAATCAAATT
CATATATT
Found at i:56864089 original size:275 final size:276
Alignment explanation
Indices: 56863359--56864519 Score: 1677
Period size: 275 Copynumber: 4.2 Consensus size: 276
56863349 TAGAAAAAGG
* * * *
56863359 AATTATATTGTTTCCAAAAGAATATTAATTTCCATATCTTTTATATTTTGACCAAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
*
56863424 TATAATTTTTTATATTAATAAATTCGGTAAAAATATATACAATTAATATTTTATATCAATCAAAT
66 TATAACTTTTTATATTAATAAATTCGGT-AAAATATATACAATTAATATTTTATATCAATCAAAT
* * *
56863489 TCATATATTAATTTTATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATAATTTGACCGAA
130 TCATATATTAATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGACCGAA
*
56863554 ATTAATTAATATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATC
195 ATTAATTAATATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATC
56863619 AATCAAATTCATATATT
260 AATCAAATTCATATATT
* * * *
56863636 AATTATATTCTTTCCAAAATAATATTAATTTTCATGTCTTTTATATATTTTG-GCAAAATGAATT
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTC-TTT-TATATTTTGACCGAAATTAATT
* * * * * *
56863700 AATATAA-TTGTTTATATTAATAAACTCGGTAAATTGTATACAATTAAAAGTTTATATGAATCAA
64 AATATAACTT-TTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTATATCAATCAA
* * * *
56863764 GTTCATATATTAATTATATTCTTTCCAAAAGAATATTAATTTCTATGTCTTTTATATTTTAACCG
128 ATTCATATATTAATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGACCG
* * * * * *
56863829 AAATTTATTAATATAACTGTTTATATTGATAAATTCAGTAATATATATATAATTAATATTTTATA
193 AAATTAATTAATATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTA
*
56863894 TCAATCAAATTCATATACT
258 TCAATCAAATTCATATATT
* * *
56863913 AATTATATTCTTTCCAAAA-AATATTAATTTTCATATCTTTTATATTTTGACTGAAATTAGTTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
* ** *
56863977 TATAACTTTTTATATTAATAATTTTAGTAAAATATATACAATTAATATTTTGTATCAATCAAATT
66 TATAACTTTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTATATCAATCAAATT
56864042 CATATATTAATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGACCGAAA
131 CATATATTAATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGACCGAAA
* * * * * * *
56864107 TGAATTAATATAATTATTTATATTAATAAATTCGGTAAAATATAAACAACTAAAATTTTGTATGA
196 TTAATTAATATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATCA
*
56864172 ATCAAATTTATATA-T
261 ATCAAATTCATATATT
* * *
56864187 AATTATTTTCTTTCCAAAAGAATATTAATTTTCATGTCTTTAATATTTTGATCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
* ** * *
56864252 TATATCTGATTATATTAATAAATTCGGTAAAATATATAAAATTAATATTTTATATCAATGAAATT
66 TATAACTTTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTATATCAATCAAATT
* * *
56864317 CATATATTACTTATATTCTTTCC-AAAAAATAATAATTTTCATGTCTTTTATATTTTGACCG-AA
131 CATATATTAATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGACCGAAA
* ** *
56864380 TTAATTAATATAACTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGGGTAA
196 TTAATTAATATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATCA
56864445 ATCAAATTCATATATT
261 ATCAAATTCATATATT
* * *
56864461 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTATTATAGTTTGACCGAAATT
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATT
56864520 GAAAATATAT
Statistics
Matches: 783, Mismatches: 94, Indels: 17
0.88 0.11 0.02
Matches are distributed among these distances:
273 70 0.09
274 118 0.15
275 308 0.39
276 19 0.02
277 220 0.28
278 39 0.05
279 9 0.01
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (276 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
TATAACTTTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTATATCAATCAAATT
CATATATTAATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGACCGAAA
TTAATTAATATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATCA
ATCAAATTCATATATT
Found at i:56879576 original size:28 final size:28
Alignment explanation
Indices: 56879537--56879740 Score: 288
Period size: 28 Copynumber: 7.3 Consensus size: 28
56879527 CTATTAAGTG
56879537 ACAGT-ACAGTGTGGGCCTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
* *
56879564 ACAGTAACAGTGTAGGCTTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
* *
56879592 ACAGTAATAATGTGGGCCTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
*
56879620 ATAGTAACAGTGTGGGCCTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
*
56879648 ACAG-AATCACTGTGGGCCTTAGCCCAAT
1 ACAGTAA-CAGTGTGGGCCTTAGCCCAAT
*
56879676 ACAG-AATCAGTATGGGCCTTAGCCCAAT
1 ACAGTAA-CAGTGTGGGCCTTAGCCCAAT
* *
56879704 ACAGTAACAATGTTGGCCTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
56879732 ACAGTAACA
1 ACAGTAACA
56879741 TTGTAGTGAA
Statistics
Matches: 158, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
27 7 0.04
28 149 0.94
29 2 0.01
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (28 bp):
ACAGTAACAGTGTGGGCCTTAGCCCAAT
Found at i:56879923 original size:26 final size:26
Alignment explanation
Indices: 56879844--56879924 Score: 110
Period size: 26 Copynumber: 3.1 Consensus size: 26
56879834 AACACACCAA
56879844 TATCGCAGCAAAGCTGCCAGTAATAG
1 TATCGCAGCAAAGCTGCCAGTAATAG
* * * *
56879870 CATCGCAGCAGAGCTACTAGT-ATCAG
1 TATCGCAGCAAAGCTGCCAGTAAT-AG
56879896 TATCGCAGCAAAGCTGCCAGTAATAG
1 TATCGCAGCAAAGCTGCCAGTAATAG
56879922 TAT
1 TAT
56879925 ATGTGGCAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
25 2 0.04
26 41 0.91
27 2 0.04
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.21
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAGTAATAG
Found at i:56880203 original size:54 final size:54
Alignment explanation
Indices: 56880145--56880520 Score: 381
Period size: 54 Copynumber: 6.9 Consensus size: 54
56880135 TTTTATCTCC
* **
56880145 TAGGGGTATAATAGTCATTTTACCCTATAAAGGTATTTCGGTCATTTTACCCTA
1 TAGGGGTATTATAGTCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCTA
* * * *
56880199 TAGGGGTATTTTAGACATTTTACCCTAT-GAAGGTATTTCGATCATTTTACCCTA
1 TAGGGGTATTATAGTCATTTTACCCTATAG-GGGTATTTCGGTCATTTTACCCTA
* *
56880253 TGGGGGTATT-TCAATCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCTA
1 TAGGGGTATTAT-AGTCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCTA
* * **
56880307 T-GGGAGTATTATGGTCATTTTATCCTAT-GGGAGTATTTTAGTCATTTTACCCTA
1 TAGGG-GTATTATAGTCATTTTACCCTATAGGG-GTATTTCGGTCATTTTACCCTA
* * *
56880361 TGGGGGTATTTCTA-TTATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCTA
1 TAGGGGTA-TTATAGTCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCTA
* * * * **
56880415 TGGGGGTATTTTAGTCATTTTACCCTAT-GGGGATATTTCAGTTATTTT-CATATA
1 TAGGGGTATTATAGTCATTTTACCCTATAGGGG-TATTTCGGTCATTTTAC-CCTA
* ** *
56880469 TTATGGGTAAAATAGTCATTTTACCCT-TCAGGGGTATTTTGGTCATTTTACC
1 -TAGGGGTATTATAGTCATTTTACCCTAT-AGGGGTATTTCGGTCATTTTACC
56880521 TATTTTGGGG
Statistics
Matches: 270, Mismatches: 36, Indels: 31
0.80 0.11 0.09
Matches are distributed among these distances:
53 16 0.06
54 205 0.76
55 44 0.16
56 5 0.02
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (54 bp):
TAGGGGTATTATAGTCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCTA
Found at i:56880443 original size:27 final size:27
Alignment explanation
Indices: 56880130--56880462 Score: 341
Period size: 27 Copynumber: 12.3 Consensus size: 27
56880120 AAGCCATAAC
**
56880130 AGTCATTTTATCTCCTA--GGGGTATAAT
1 AGTCATTTTA-C-CCTATGGGGGTATTTT
*** *
56880157 AGTCATTTTACCCTATAAAGGTATTTC
1 AGTCATTTTACCCTATGGGGGTATTTT
* *
56880184 GGTCATTTTACCCTATAGGGGTATTTT
1 AGTCATTTTACCCTATGGGGGTATTTT
* **
56880211 AGACATTTTACCCTATGAAGGTA-TTT
1 AGTCATTTTACCCTATGGGGGTATTTT
* *
56880237 CGATCATTTTACCCTATGGGGGTATTTC
1 AG-TCATTTTACCCTATGGGGGTATTTT
* * *
56880265 AATCATTTTACCCTATAGGGGTATTTC
1 AGTCATTTTACCCTATGGGGGTATTTT
* * *
56880292 GGTCATTTTACCCTATGGGAGTATTAT
1 AGTCATTTTACCCTATGGGGGTATTTT
* * *
56880319 GGTCATTTTATCCTATGGGAGTATTTT
1 AGTCATTTTACCCTATGGGGGTATTTT
56880346 AGTCATTTTACCCTATGGGGGTATTTCT
1 AGTCATTTTACCCTATGGGGGTATTT-T
* * *
56880374 A-TTATTTTACCCTATAGGGGTATTTC
1 AGTCATTTTACCCTATGGGGGTATTTT
*
56880400 GGTCATTTTACCCTATGGGGGTATTTT
1 AGTCATTTTACCCTATGGGGGTATTTT
* *
56880427 AGTCATTTTACCCTATGGGGATATTTC
1 AGTCATTTTACCCTATGGGGGTATTTT
*
56880454 AGTTATTTT
1 AGTCATTTT
56880463 CATATATTAT
Statistics
Matches: 256, Mismatches: 44, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
25 4 0.02
26 5 0.02
27 243 0.95
28 4 0.02
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (27 bp):
AGTCATTTTACCCTATGGGGGTATTTT
Found at i:56880780 original size:18 final size:17
Alignment explanation
Indices: 56880750--56880784 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
56880740 CATCTGTGTG
56880750 GGGCCCACAAGCCCATT
1 GGGCCCACAAGCCCATT
*
56880767 GGGCCTACACAGCCCATT
1 GGGCCCACA-AGCCCATT
56880785 TCGGCCCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.23, C:0.40, G:0.23, T:0.14
Consensus pattern (17 bp):
GGGCCCACAAGCCCATT
Found at i:56889787 original size:19 final size:20
Alignment explanation
Indices: 56889691--56889789 Score: 75
Period size: 19 Copynumber: 5.2 Consensus size: 20
56889681 GGGTGGTACA
* *
56889691 CATACTAGCATATG-AAGTG
1 CATACTAGCACACGAAAGTG
*
56889710 CATCCT-GACACAC-AAAGTG
1 CATACTAG-CACACGAAAGTG
*
56889729 CATACTAGCACA-AAAAGTG
1 CATACTAGCACACGAAAGTG
* * *
56889748 CATCCTAGCATATG-AAGTG
1 CATACTAGCACACGAAAGTG
*
56889767 CATACTGGCACACGAAA-TG
1 CATACTAGCACACGAAAGTG
56889786 CATA
1 CATA
56889790 AACCCGTACA
Statistics
Matches: 63, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
18 1 0.02
19 59 0.94
20 3 0.05
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.20
Consensus pattern (20 bp):
CATACTAGCACACGAAAGTG
Found at i:56889920 original size:21 final size:20
Alignment explanation
Indices: 56889889--56889929 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
56889879 TATGAACCAA
56889889 TTCATTTATCAT-AATCTCAT
1 TTCATTTATCATCAAT-TCAT
56889909 TTCATTTCATCATCAATTCAT
1 TTCATTT-ATCATCAATTCAT
56889930 GTATGTCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
21 9 0.47
22 3 0.16
ACGTcount: A:0.29, C:0.22, G:0.00, T:0.49
Consensus pattern (20 bp):
TTCATTTATCATCAATTCAT
Found at i:56890604 original size:37 final size:37
Alignment explanation
Indices: 56890562--56890638 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
56890552 TAACTTGCTA
56890562 AAAACTTAATAATTGAACAAATTGATATGGGCTACCT
1 AAAACTTAATAATTGAACAAATTGATATGGGCTACCT
56890599 AAAACTTAATAATTGAACAAATTGATATGGGCTACCT
1 AAAACTTAATAATTGAACAAATTGATATGGGCTACCT
56890636 AAA
1 AAA
56890639 TCAAACTCTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (37 bp):
AAAACTTAATAATTGAACAAATTGATATGGGCTACCT
Found at i:56890929 original size:22 final size:22
Alignment explanation
Indices: 56890884--56890931 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
56890874 ATACACGTTA
*
56890884 GAAATAAGTCGGGACTAAATTT
1 GAAATAAGTCGGGACTAAAATT
56890906 GAAATAAGTCGGGAC-AAACATT
1 GAAATAAGTCGGGACTAAA-ATT
56890928 GAAA
1 GAAA
56890932 ATTTTCAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.46, C:0.10, G:0.23, T:0.21
Consensus pattern (22 bp):
GAAATAAGTCGGGACTAAAATT
Found at i:56892453 original size:25 final size:25
Alignment explanation
Indices: 56892370--56892463 Score: 109
Period size: 25 Copynumber: 3.8 Consensus size: 25
56892360 TCTTGTACAC
* * *
56892370 GTATGCTCAT-ACGAGCTATGAATTG
1 GTATGCTC-TCACGAGCTGTAAATCG
* * *
56892395 GTATGCTCACTCGAGCTGTAAATCA
1 GTATGCTCTCACGAGCTGTAAATCG
56892420 GTATGCTCTCACGAGCTGTAAATCG
1 GTATGCTCTCACGAGCTGTAAATCG
*
56892445 GTATGCTCTCACAAGCTGT
1 GTATGCTCTCACGAGCTGT
56892464 GGGTCGGAAC
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
25 58 1.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (25 bp):
GTATGCTCTCACGAGCTGTAAATCG
Found at i:56897041 original size:17 final size:17
Alignment explanation
Indices: 56897019--56897052 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
56897009 ACAAATTTTA
56897019 ATATGACTTAAAATCAT
1 ATATGACTTAAAATCAT
56897036 ATATGACTTAAAATCAT
1 ATATGACTTAAAATCAT
56897053 TTCCAGGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.35
Consensus pattern (17 bp):
ATATGACTTAAAATCAT
Found at i:56907763 original size:2 final size:2
Alignment explanation
Indices: 56907756--56907783 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
56907746 TAAAGTTGGT
56907756 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
56907784 CATTCCTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:56914893 original size:27 final size:27
Alignment explanation
Indices: 56914763--56914923 Score: 144
Period size: 27 Copynumber: 6.0 Consensus size: 27
56914753 CATGACAGCT
*
56914763 AAAGAATAGCCTTTGTGGCAAACTCTG
1 AAAGAATAGCCTTTGTGGCGAACTCTG
* *
56914790 AAAGGATAGCCTTTGTGGCGAACTCTA
1 AAAGAATAGCCTTTGTGGCGAACTCTG
* * ** *
56914817 AAAGAATAACCCTTACGGCAAACTCTG
1 AAAGAATAGCCTTTGTGGCGAACTCTG
*
56914844 AAAGAATAGCCTTTGTGGCGAACTTTG
1 AAAGAATAGCCTTTGTGGCGAACTCTG
* * * *
56914871 AAAGGAAT-GTCTTTGTTGTGAACTCGG
1 AAA-GAATAGCCTTTGTGGCGAACTCTG
* * * * *
56914898 AATGGATCGCCTTAGTGGCGTACTCT
1 AAAGAATAGCCTTTGTGGCGAACTCT
56914924 ATCTGATTTC
Statistics
Matches: 103, Mismatches: 29, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
26 3 0.03
27 96 0.93
28 4 0.04
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (27 bp):
AAAGAATAGCCTTTGTGGCGAACTCTG
Found at i:56919503 original size:5 final size:5
Alignment explanation
Indices: 56919493--56919524 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
56919483 GGAAAATATT
56919493 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TA
56919525 TTACAATAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:56921995 original size:5 final size:5
Alignment explanation
Indices: 56921966--56922004 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
56921956 TAAATTTAGC
* *
56921966 TCAAT TTAAT ACAAT TCATAT TCAAT TCAAT TCAAT TCA
1 TCAAT TCAAT TCAAT TCA-AT TCAAT TCAAT TCAAT TCA
56922005 CATCCTAGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (5 bp):
TCAAT
Found at i:56925535 original size:3 final size:3
Alignment explanation
Indices: 56925529--56925596 Score: 127
Period size: 3 Copynumber: 22.7 Consensus size: 3
56925519 CTAGTACTCT
*
56925529 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTT TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
56925577 TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TT
56925597 TTTGAGTCGG
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:56930463 original size:101 final size:101
Alignment explanation
Indices: 56930288--56930479 Score: 303
Period size: 101 Copynumber: 1.9 Consensus size: 101
56930278 AGGATGCTTA
* * * *
56930288 AAGTGTGGATCCAAAGAACATATGCTTAGGGACTGGTTGGAACGCGTGGAGAGGTCACAAACTCA
1 AAGTGTGGATCCAAAGAACATATGCTAAAGGACTGGCTGAAACGCGTGGAGAGGTCACAAACTCA
*
56930353 GAGTTTAATCCCCATACCACTGCAAGTAGGTAAAGC
66 GAGTTTAATCCCCATACCACTACAAGTAGGTAAAGC
* * * *
56930389 AAGTGTGGATCCAAAGAACATATGGTAAAGGACTTGCTGAAACGGGTGGAGAGGTCGCAAACTCA
1 AAGTGTGGATCCAAAGAACATATGCTAAAGGACTGGCTGAAACGCGTGGAGAGGTCACAAACTCA
56930454 GAGTTTAATCCCCATACCACTACAAG
66 GAGTTTAATCCCCATACCACTACAAG
56930480 CAGATGCTCA
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
101 82 1.00
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.20
Consensus pattern (101 bp):
AAGTGTGGATCCAAAGAACATATGCTAAAGGACTGGCTGAAACGCGTGGAGAGGTCACAAACTCA
GAGTTTAATCCCCATACCACTACAAGTAGGTAAAGC
Found at i:56934703 original size:53 final size:53
Alignment explanation
Indices: 56934623--56934723 Score: 148
Period size: 53 Copynumber: 1.9 Consensus size: 53
56934613 TCACAGCACT
* ** *
56934623 GAAGACCATATCGTATAAGACTTTAACTGGTGGATTATGGCATCATATATACA
1 GAAGACCATATCATATAAGACCATAACTGGTGGATTATGACATCATATATACA
* *
56934676 GAAGACTATATCATGTAAGACCATAACTGGTGGATTATGACATCATAT
1 GAAGACCATATCATATAAGACCATAACTGGTGGATTATGACATCATAT
56934724 GGAAGAATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 42 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (53 bp):
GAAGACCATATCATATAAGACCATAACTGGTGGATTATGACATCATATATACA
Found at i:56934948 original size:61 final size:61
Alignment explanation
Indices: 56934846--56935010 Score: 206
Period size: 60 Copynumber: 2.7 Consensus size: 61
56934836 CAGGAAAGGA
* * * * *
56934846 AAAGCCTTTTGTGGCGAGTACTGGATGTAAAAGAATGCCTTTGTTGCAAAACTTTGGATAGG
1 AAAGCC-TTTGTGGTGAGTACTGAATGTAAAAGAATGCCTTTGTTGCAAAAATCTGGACAGG
* * * * * *
56934908 AAAGCCTTTGTCGTGAGTACTAAATGTAAATGAATTCCTTT-ATGTAAAAATCTGGACAGG
1 AAAGCCTTTGTGGTGAGTACTGAATGTAAAAGAATGCCTTTGTTGCAAAAATCTGGACAGG
*
56934968 AAAGCCTTTGTGGTGAGTATTGAATGTAAAAGAATGCCTTTGT
1 AAAGCCTTTGTGGTGAGTACTGAATGTAAAAGAATGCCTTTGT
56935011 GGTGATTACT
Statistics
Matches: 85, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
60 50 0.59
61 29 0.34
62 6 0.07
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (61 bp):
AAAGCCTTTGTGGTGAGTACTGAATGTAAAAGAATGCCTTTGTTGCAAAAATCTGGACAGG
Found at i:56935027 original size:32 final size:32
Alignment explanation
Indices: 56934971--56935045 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
56934961 GGACAGGAAA
* *
56934971 GCCTTTGTGGTGAGTATTGAATGTAAAAGAAT
1 GCCTTTGTGGTGAGTACTGAATGTAAAAGAAC
* *
56935003 GCCTTTGTGGTGATTACT-ATATGTAAAGGAAC
1 GCCTTTGTGGTGAGTACTGA-ATGTAAAAGAAC
*
56935035 GTCTTTGTGGT
1 GCCTTTGTGGT
56935046 AAAAATTTGG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 1 0.03
32 36 0.97
ACGTcount: A:0.25, C:0.09, G:0.28, T:0.37
Consensus pattern (32 bp):
GCCTTTGTGGTGAGTACTGAATGTAAAAGAAC
Found at i:56939305 original size:28 final size:27
Alignment explanation
Indices: 56939274--56939346 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
56939264 ATTTTAGGGT
*
56939274 TTAAATGCAGGGAAAAGACATTAAAGCA
1 TTAAATGTAGGGAAAAG-CATTAAAGCA
* * *
56939302 TTAAATGTAGGGATAATGCATTAACGTA
1 TTAAATGTAGGGA-AAAGCATTAAAGCA
*
56939330 TTAAATGTTGGGAAAAG
1 TTAAATGTAGGGAAAAG
56939347 GCTATTGTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
27 3 0.08
28 32 0.84
29 3 0.08
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.26
Consensus pattern (27 bp):
TTAAATGTAGGGAAAAGCATTAAAGCA
Found at i:56940353 original size:42 final size:42
Alignment explanation
Indices: 56940289--56940433 Score: 218
Period size: 42 Copynumber: 3.5 Consensus size: 42
56940279 NNNNNNNNNN
*
56940289 GGTCTATAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACAT
1 GGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACAT
* *
56940331 GGTCTTTAGCGGCATTTCTTTCTAAGCGCCGCTAAAGAACAT
1 GGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACAT
*
56940373 GGTCTCTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACAT
1 GGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACAT
** **
56940415 TATCTTTAGATGCGTTTTT
1 GGTCTTTAGCGGCGTTTTT
56940434 ATACAAAAAT
Statistics
Matches: 92, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 92 1.00
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.34
Consensus pattern (42 bp):
GGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACAT
Found at i:56940818 original size:21 final size:21
Alignment explanation
Indices: 56940750--56940820 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
56940740 TTTTGCTCTG
* * *
56940750 CTCTGCTTCTCTTGCTGCTGC
1 CTCTGCTTCCCTCGCTGCAGC
* * *
56940771 CTTTTCTTCCCTCGCTGTAG-
1 CTCTGCTTCCCTCGCTGCAGC
*
56940791 CTGCTGCTTCCCTCGCTGCCGC
1 CT-CTGCTTCCCTCGCTGCAGC
56940813 CTCTGCTT
1 CTCTGCTT
56940821 TAAGTTGTAG
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
20 2 0.05
21 34 0.89
22 2 0.05
ACGTcount: A:0.01, C:0.41, G:0.18, T:0.39
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:56944031 original size:14 final size:15
Alignment explanation
Indices: 56943992--56944062 Score: 58
Period size: 14 Copynumber: 4.7 Consensus size: 15
56943982 ATAAAAATTA
56943992 ATAACCCCTAAATCCC
1 ATAACCCCT-AATCCC
*
56944008 A-AATCCCTAA-CCC
1 ATAACCCCTAATCCC
56944021 ATAACCCCTAAATCTCC
1 ATAACCCCT-AATC-CC
* **
56944038 CTAACCCCTAA-AGC
1 ATAACCCCTAATCCC
56944052 ATAACCCCTAA
1 ATAACCCCTAA
56944063 AAAAAATTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
13 4 0.09
14 19 0.42
15 8 0.18
16 4 0.09
17 10 0.22
ACGTcount: A:0.38, C:0.42, G:0.01, T:0.18
Consensus pattern (15 bp):
ATAACCCCTAATCCC
Found at i:56944055 original size:31 final size:29
Alignment explanation
Indices: 56943992--56944063 Score: 90
Period size: 31 Copynumber: 2.4 Consensus size: 29
56943982 ATAAAAATTA
* *
56943992 ATAACCCCTAAATCCCAAATCCCTAACCC
1 ATAACCCCTAAATCCCAAACCCCTAAACC
* *
56944021 ATAACCCCTAAATCTCCCTAACCCCTAAAGC
1 ATAACCCCTAAA--TCCCAAACCCCTAAACC
56944052 ATAACCCCTAAA
1 ATAACCCCTAAA
56944064 AAAAATTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 12 0.32
31 25 0.68
ACGTcount: A:0.39, C:0.42, G:0.01, T:0.18
Consensus pattern (29 bp):
ATAACCCCTAAATCCCAAACCCCTAAACC
Found at i:56944345 original size:7 final size:7
Alignment explanation
Indices: 56944333--56944423 Score: 51
Period size: 7 Copynumber: 12.4 Consensus size: 7
56944323 CTTACCGTTG
56944333 AAACCCT
1 AAACCCT
56944340 AAACCCT
1 AAACCCT
*
56944347 AAATCCAT
1 AAA-CCCT
*
56944355 AATCCCT
1 AAACCCT
*
56944362 AACCCCT
1 AAACCCT
56944369 AAATCCTCTT
1 AAA-CC-C-T
* *
56944379 AAAGCAT
1 AAACCCT
56944386 -AACACCT
1 AAAC-CCT
*
56944393 AACCCCT
1 AAACCCT
*
56944400 AAACCTT
1 AAACCCT
56944407 AAATCCC-
1 AAA-CCCT
56944414 AAACCCT
1 AAACCCT
56944421 AAA
1 AAA
56944424 TCCATACCCC
Statistics
Matches: 63, Mismatches: 13, Indels: 16
0.68 0.14 0.17
Matches are distributed among these distances:
6 5 0.08
7 41 0.65
8 11 0.17
9 2 0.03
10 4 0.06
ACGTcount: A:0.42, C:0.37, G:0.01, T:0.20
Consensus pattern (7 bp):
AAACCCT
Found at i:56944838 original size:114 final size:114
Alignment explanation
Indices: 56944638--56944850 Score: 336
Period size: 114 Copynumber: 1.9 Consensus size: 114
56944628 TAAATTATTT
* * * * *
56944638 TAAATCCCTGAGCATTAGCGGCGCTTCCCTAAAAATGCCGTTAAATCCCCGAAAGCACAGACAAC
1 TAAATCCCTGAGCATTAGCAGCGCATCCCTAAAAACGCCGCTAAATCCCCGAAAGCACAGAAAAC
*
56944703 GGCACCGTTGGGCTTAGTTTTTTTTGTGGCGCTACACCTAAAACGACGC
66 GGCACCGTTGGGCTTAGTTTTTTTTGCGGCGCTACACCTAAAACGACGC
* *
56944752 TAAATCCCTGAGCATTAGCAGCGCATCCTTAAAAACGCCGCTAAATCCCCGAAAGCACAGAAAAT
1 TAAATCCCTGAGCATTAGCAGCGCATCCCTAAAAACGCCGCTAAATCCCCGAAAGCACAGAAAAC
**
56944817 GGTGCCGTTGGGCTTAGTTTTTTTTGCGGCGCTA
66 GGCACCGTTGGGCTTAGTTTTTTTTGCGGCGCTA
56944851 TTCCAAAAAC
Statistics
Matches: 89, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
114 89 1.00
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (114 bp):
TAAATCCCTGAGCATTAGCAGCGCATCCCTAAAAACGCCGCTAAATCCCCGAAAGCACAGAAAAC
GGCACCGTTGGGCTTAGTTTTTTTTGCGGCGCTACACCTAAAACGACGC
Found at i:56944908 original size:76 final size:76
Alignment explanation
Indices: 56944792--56944939 Score: 199
Period size: 76 Copynumber: 1.9 Consensus size: 76
56944782 AAAAACGCCG
* * *
56944792 CTAAATCCCCGAAAGCACAGAAAATGGTGCCGTTGGGCTTAGTTTTTTTTGCGGCGCTATTCCAA
1 CTAAATCCCCGAAAGCACAGAAAACGGTGCCGTTGGGCTTAGGTTTTCTTGCGGCGCTATTCCAA
56944857 AAACGCCACTA
66 AAACGCCACTA
* * * * * *
56944868 CTAAATCCCCGAAAAGCTCAG-AAACGGTGTCGTTGTGCTTAGGTTTTCTTGCTGCGCTTTTTCA
1 CTAAATCCCCG-AAAGCACAGAAAACGGTGCCGTTGGGCTTAGGTTTTCTTGCGGCGCTATTCCA
56944932 AAAACGCC
65 AAAACGCC
56944940 GCTAAAGCCC
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
76 54 0.87
77 8 0.13
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (76 bp):
CTAAATCCCCGAAAGCACAGAAAACGGTGCCGTTGGGCTTAGGTTTTCTTGCGGCGCTATTCCAA
AAACGCCACTA
Found at i:56945048 original size:114 final size:113
Alignment explanation
Indices: 56944867--56945172 Score: 334
Period size: 114 Copynumber: 2.7 Consensus size: 113
56944857 AAACGCCACT
* * * * *
56944867 ACTAAATCCCCGAAAAGCTCAGAAACGGTGTCGTTGTGCTTAGGTTTTCTTGCTGCGCTTTTTCA
1 ACTAAATTCCCG-AAAGCTCAGAAACGGTGTCGTTGAGCTTAGGTTTTTTTGCAGCGCTTTCTCA
*
56944932 AAAACGCCGCTAAAGCCCT-AAGCATTAGCG-GCATGTTATTAAAAATGCC
65 AAAACGCCGCTAAAGCCCTGAA-CATTAGCGCGC-TGTTATTAAAAACGCC
* * * *
56944981 ACT-AA-TCACTCGAAAGCTCAGAAAATGGTGTCGTTGGGATTAGGTTTTTTTGCAGCGCTTTCC
1 ACTAAATTC-C-CGAAAGCTCAG-AAACGGTGTCGTTGAGCTTAGGTTTTTTTGCAGCGCTTTCT
* * *
56945044 CAAAAACGCCGCTAAAGCCCTGAACGTTAGCGTCGCTTTTATTACAAACGCC
63 CAAAAACGCCGCTAAAGCCCTGAACATTAGCG-CGCTGTTATTAAAAACGCC
* * ** * *
56945096 GCTAAATTCCCGAAAGCTCGGTAAACGACGTCGTTCAGCTTAGG-TTTTTTGCAGCGCTTTCTCT
1 ACTAAATTCCCGAAAGCTCAG-AAACGGTGTCGTTGAGCTTAGGTTTTTTTGCAGCGCTTTCTCA
56945160 AAAACGCCGCTAA
65 AAAACGCCGCTAA
56945173 TTCTTATTTT
Statistics
Matches: 161, Mismatches: 23, Indels: 16
0.81 0.12 0.08
Matches are distributed among these distances:
112 1 0.01
113 12 0.07
114 98 0.61
115 43 0.27
116 5 0.03
117 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.28
Consensus pattern (113 bp):
ACTAAATTCCCGAAAGCTCAGAAACGGTGTCGTTGAGCTTAGGTTTTTTTGCAGCGCTTTCTCAA
AAACGCCGCTAAAGCCCTGAACATTAGCGCGCTGTTATTAAAAACGCC
Found at i:56952328 original size:26 final size:26
Alignment explanation
Indices: 56952267--56952344 Score: 75
Period size: 26 Copynumber: 3.0 Consensus size: 26
56952257 AAGAGAGGAG
* **
56952267 TGGTAAGTATGGAAAACCCTAAAGAA
1 TGGTAAGTATGGCAAACTTTAAAGAA
** * *
56952293 TTATATGTATGGCTAACTTTAAAGAA
1 TGGTAAGTATGGCAAACTTTAAAGAA
* *
56952319 TGGTAAGTATGACAAACTTTGAAGAA
1 TGGTAAGTATGGCAAACTTTAAAGAA
56952345 ATGATATGTG
Statistics
Matches: 39, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.42, C:0.09, G:0.21, T:0.28
Consensus pattern (26 bp):
TGGTAAGTATGGCAAACTTTAAAGAA
Found at i:56954617 original size:328 final size:328
Alignment explanation
Indices: 56954008--56954648 Score: 1192
Period size: 328 Copynumber: 2.0 Consensus size: 328
56953998 ACAGCTCCGT
* *
56954008 AAATATTTTTATTAAAAATTTACTAACTCGGTTTATAGAAACGAGGTCCCAAAATCTCATTTTCC
1 AAATATTTTTATTAAAAATTTACGAACTCAGTTTATAGAAACGAGGTCCCAAAATCTCATTTTCC
56954073 AAAACCACTTGACTTTTGGTACGCACCACTTGTACCTTGACTAATTGACCAGTTAATAAAATATA
66 AAAACCACTTGACTTTTGGTACGCACCACTTGTACCTTGACTAATTGACCAGTTAATAAAATATA
*
56954138 TTAAATCATGATTCAATATTACACTATATTTAACTCATAAATATTAATTAAATATATCTATGGAC
131 TTAAATCATGATTCAATATTACACTATATTTAACTCATAAATATTAATTAAATATATCTATGGAA
56954203 TCTCTTGTTTGAATTATCGTCCCAGAACCACTATTTTCAATAACACTGAAAAATGAGTTTTACAT
196 TCTCTTGTTTGAATTATCGTCCCAGAACCACTATTTTCAATAACACTGAAAAATGAGTTTTACAT
*
56954268 TTAATATTCCTCTTAATACATTCGTCTAAAATAATCAATTGTTTGGTTAAAAATAATCAATTCGT
261 TTAATATGCCTCTTAATACATTCGTCTAAAATAATCAATTGTTTGGTTAAAAATAATCAATTCGT
56954333 CTA
326 CTA
*
56954336 AAATATTTTTATTAAATATTTACGAACTCAGTTTATAGAAACGAGGTCCCAAAATCTCATTTTCC
1 AAATATTTTTATTAAAAATTTACGAACTCAGTTTATAGAAACGAGGTCCCAAAATCTCATTTTCC
56954401 AAAACCACTTGACTTTTGGTACGCACCACTTGTACCTTGACTAATTGACCAGTTAATAAAATATA
66 AAAACCACTTGACTTTTGGTACGCACCACTTGTACCTTGACTAATTGACCAGTTAATAAAATATA
*
56954466 TTAAATCATGATTCAATATTACACTATATTTAACTCATAAATATTAATTAAATATGTCTATGGAA
131 TTAAATCATGATTCAATATTACACTATATTTAACTCATAAATATTAATTAAATATATCTATGGAA
* **
56954531 TCTCTTGTTTGAATTATCGTCCCGGAACCACTATTTTTGATAACACTGAAAAATGAGTTTTACAT
196 TCTCTTGTTTGAATTATCGTCCCAGAACCACTATTTTCAATAACACTGAAAAATGAGTTTTACAT
*
56954596 TTAATATGCCTCTTCATACATTCGTCTAAAATAATCAATTGTTTGGTTAAAAA
261 TTAATATGCCTCTTAATACATTCGTCTAAAATAATCAATTGTTTGGTTAAAAA
56954649 ATTTAACACA
Statistics
Matches: 303, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
328 303 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (328 bp):
AAATATTTTTATTAAAAATTTACGAACTCAGTTTATAGAAACGAGGTCCCAAAATCTCATTTTCC
AAAACCACTTGACTTTTGGTACGCACCACTTGTACCTTGACTAATTGACCAGTTAATAAAATATA
TTAAATCATGATTCAATATTACACTATATTTAACTCATAAATATTAATTAAATATATCTATGGAA
TCTCTTGTTTGAATTATCGTCCCAGAACCACTATTTTCAATAACACTGAAAAATGAGTTTTACAT
TTAATATGCCTCTTAATACATTCGTCTAAAATAATCAATTGTTTGGTTAAAAATAATCAATTCGT
CTA
Found at i:56957613 original size:50 final size:50
Alignment explanation
Indices: 56957526--56957658 Score: 153
Period size: 50 Copynumber: 2.7 Consensus size: 50
56957516 CAATATCATA
* ** ***
56957526 TCCCAGATATGGTCTTA-GATGGGAGTTCTCATATCGGTGCCCCTGCCATG
1 TCCCAGACATGGTCTTACG-TGGGACCTCTCATATCGGTGCCAAGGCCATG
* *
56957576 TCCTAGACATGGTCTTACG-GCGGACCTCTCATCTCGGTGCCAAGGCCATG
1 TCCCAGACATGGTCTTACGTG-GGACCTCTCATATCGGTGCCAAGGCCATG
*
56957626 TCCCAGACATGGTCTTATGTGGGACCTCTCATA
1 TCCCAGACATGGTCTTACGTGGGACCTCTCATA
56957659 ACTTCAATAA
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
49 1 0.01
50 66 0.96
51 2 0.03
ACGTcount: A:0.19, C:0.29, G:0.25, T:0.28
Consensus pattern (50 bp):
TCCCAGACATGGTCTTACGTGGGACCTCTCATATCGGTGCCAAGGCCATG
Found at i:56962980 original size:13 final size:13
Alignment explanation
Indices: 56962964--56963052 Score: 81
Period size: 13 Copynumber: 6.7 Consensus size: 13
56962954 AAATGAATAA
56962964 ATGAAATGGTTAT
1 ATGAAATGGTTAT
**
56962977 ATGAACCGGTTAT
1 ATGAAATGGTTAT
* *
56962990 ATAGAAATAGATAT
1 AT-GAAATGGTTAT
56963004 ATGAAATGGTTAT
1 ATGAAATGGTTAT
*
56963017 ATG-AATCGATTAT
1 ATGAAAT-GGTTAT
* *
56963030 ATAGAAATAGATAT
1 AT-GAAATGGTTAT
56963044 ATGAAATGG
1 ATGAAATGG
56963053 AACATTAGAT
Statistics
Matches: 59, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
12 3 0.05
13 38 0.64
14 15 0.25
15 3 0.05
ACGTcount: A:0.44, C:0.03, G:0.20, T:0.33
Consensus pattern (13 bp):
ATGAAATGGTTAT
Found at i:56963019 original size:40 final size:40
Alignment explanation
Indices: 56962964--56963052 Score: 160
Period size: 40 Copynumber: 2.2 Consensus size: 40
56962954 AAATGAATAA
*
56962964 ATGAAATGGTTATATGAACCGGTTATATAGAAATAGATAT
1 ATGAAATGGTTATATGAACCGATTATATAGAAATAGATAT
*
56963004 ATGAAATGGTTATATGAATCGATTATATAGAAATAGATAT
1 ATGAAATGGTTATATGAACCGATTATATAGAAATAGATAT
56963044 ATGAAATGG
1 ATGAAATGG
56963053 AACATTAGAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.44, C:0.03, G:0.20, T:0.33
Consensus pattern (40 bp):
ATGAAATGGTTATATGAACCGATTATATAGAAATAGATAT
Found at i:56965474 original size:49 final size:49
Alignment explanation
Indices: 56965381--56965474 Score: 111
Period size: 49 Copynumber: 1.9 Consensus size: 49
56965371 AGAATACCCA
* * * * *
56965381 GCATGGCATATTATGCGATGCAATATAATAATCAGATCAGATACAGATG
1 GCATGGCATATCATGCGATGCAACATAATAATCAAAACAAATACAGATG
56965430 GCATGGCATATCATGCGATGCAACACT--TAATACAAAACAAATACA
1 GCATGGCATATCATGCGATGCAACA-TAATAAT-CAAAACAAATACA
56965475 AATCCTAACC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
48 4 0.11
49 33 0.87
50 1 0.03
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.23
Consensus pattern (49 bp):
GCATGGCATATCATGCGATGCAACATAATAATCAAAACAAATACAGATG
Found at i:56993625 original size:16 final size:15
Alignment explanation
Indices: 56993586--56993627 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
56993576 CATTTTCACT
56993586 AAAATATTTTA-AAA
1 AAAATATTTTATAAA
* *
56993600 TAAATTTTTTATAAA
1 AAAATATTTTATAAA
56993615 AAAGATATTTTAT
1 AAA-ATATTTTAT
56993628 TTTTAAAGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 9 0.41
15 5 0.23
16 8 0.36
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (15 bp):
AAAATATTTTATAAA
Found at i:56993727 original size:10 final size:10
Alignment explanation
Indices: 56993709--56993786 Score: 56
Period size: 10 Copynumber: 7.9 Consensus size: 10
56993699 TAAAAAAAAC
56993709 AATAATTTTT
1 AATAATTTTT
*
56993719 AATAGTTTTT
1 AATAATTTTT
*
56993729 -ACAATCTTTT
1 AATAAT-TTTT
**
56993739 -GCAATTTTT
1 AATAATTTTT
56993748 AATAATTATTTT
1 AATAA-T-TTTT
56993760 AATAATTTTT
1 AATAATTTTT
*
56993770 AAT-TTTTTT
1 AATAATTTTT
56993779 AAT-ATTTT
1 AATAATTTT
56993787 AACATATTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
9 19 0.34
10 26 0.46
11 2 0.04
12 9 0.16
ACGTcount: A:0.33, C:0.04, G:0.03, T:0.60
Consensus pattern (10 bp):
AATAATTTTT
Found at i:56993778 original size:19 final size:18
Alignment explanation
Indices: 56993750--56993786 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
56993740 CAATTTTTAA
56993750 TAATTATTTTAATAATTTT
1 TAATTATTTTAAT-ATTTT
*
56993769 TAATTTTTTTAATATTTT
1 TAATTATTTTAATATTTT
56993787 AACATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TAATTATTTTAATATTTT
Found at i:56993796 original size:19 final size:19
Alignment explanation
Indices: 56993756--56993798 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
56993746 TTAATAATTA
* *
56993756 TTTTAATAATTTTTAATTT
1 TTTTAATAATTTTAAATAT
56993775 TTTTAAT-ATTTTAACATAT
1 TTTTAATAATTTTAA-ATAT
56993794 TTTTA
1 TTTTA
56993799 TTTTTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTAATAATTTTAAATAT
Found at i:56993820 original size:27 final size:28
Alignment explanation
Indices: 56993764--56993824 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
56993754 TATTTTAATA
**
56993764 ATTTTTAATTTTTTTAATATTTTAACAT
1 ATTTTTAATTTTTTTAATATCATAACAT
*
56993792 ATTTTT-ATTTTTTTAA-ATCATATATAT
1 ATTTTTAATTTTTTTAATATCATA-ACAT
56993819 ATTTTT
1 ATTTTT
56993825 GGTGTTTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 4 0.14
27 19 0.66
28 6 0.21
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (28 bp):
ATTTTTAATTTTTTTAATATCATAACAT
Found at i:57015864 original size:58 final size:59
Alignment explanation
Indices: 57015788--57015943 Score: 183
Period size: 58 Copynumber: 2.7 Consensus size: 59
57015778 TCTAAAAATG
* * * * * * *
57015788 GCCACGAAGGCGTCCTTTTAACAGAAATAGCCACAAAGGCATATTTTTAATAGAGAT-A
1 GCCACAAAGGCATTCTTTTAACAGAGATAGCCACAAAGGCAAACTTATAATAGAGATCA
* * *
57015846 GCCACAAAGGCATTCTTTTAACTGAGATAGCCACAAATGAAAACTTATAATAGAGATCA
1 GCCACAAAGGCATTCTTTTAACAGAGATAGCCACAAAGGCAAACTTATAATAGAGATCA
*
57015905 -CCACAAAGGTATTCTTTTAACTA-AGATAGCCACAAAGGC
1 GCCACAAAGGCATTCTTTTAAC-AGAGATAGCCACAAAGGC
57015944 TTCCTTTCAG
Statistics
Matches: 82, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
58 81 0.99
59 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.24
Consensus pattern (59 bp):
GCCACAAAGGCATTCTTTTAACAGAGATAGCCACAAAGGCAAACTTATAATAGAGATCA
Found at i:57015950 original size:29 final size:30
Alignment explanation
Indices: 57015788--57015969 Score: 127
Period size: 29 Copynumber: 6.4 Consensus size: 30
57015778 TCTAAAAATG
* * * *
57015788 GCCACGAAGGCGTCCTTTTAAC-AGAAATA
1 GCCACAAAGGCTTACTTTTAACTAGAGATA
* *
57015817 GCCACAAAGGCATATTTTTAA-TAGAGATA
1 GCCACAAAGGCTTACTTTTAACTAGAGATA
57015846 GCCACAAAGGCATT-CTTTTAACT-GAGATA
1 GCCACAAAGGC-TTACTTTTAACTAGAGATA
* *** *
57015875 GCCACAAATGAAAACTTATAA-TAGAGATCA
1 GCCACAAAGGCTTACTTTTAACTAGAGAT-A
*
57015905 -CCACAAAGG-TATTCTTTTAACTA-AGATA
1 GCCACAAAGGCT-TACTTTTAACTAGAGATA
*
57015933 GCCACAAAGGCTT-CCTTT--C-AGAGATA
1 GCCACAAAGGCTTACTTTTAACTAGAGATA
*
57015959 ACCACAAAGGC
1 GCCACAAAGGC
57015970 GTGCATTCAG
Statistics
Matches: 123, Mismatches: 19, Indels: 25
0.74 0.11 0.15
Matches are distributed among these distances:
25 1 0.01
26 16 0.13
28 6 0.05
29 94 0.76
30 6 0.05
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (30 bp):
GCCACAAAGGCTTACTTTTAACTAGAGATA
Found at i:57015964 original size:26 final size:26
Alignment explanation
Indices: 57015928--57015996 Score: 93
Period size: 26 Copynumber: 2.7 Consensus size: 26
57015918 CTTTTAACTA
*
57015928 AGATAGCCACAAAGGCTTCCTTTCAG
1 AGATAGCCACAAAGGCTTCCATTCAG
* * *
57015954 AGATAACCACAAAGGCGTGCATTCAG
1 AGATAGCCACAAAGGCTTCCATTCAG
*
57015980 AGATAGCCGCAAAGGCT
1 AGATAGCCACAAAGGCT
57015997 CTATAACCCC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (26 bp):
AGATAGCCACAAAGGCTTCCATTCAG
Found at i:57019279 original size:26 final size:27
Alignment explanation
Indices: 57019250--57019306 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
57019240 TAAAACGGTA
57019250 ATTTTACCCCTAG-GGGTATTTTGGTC
1 ATTTTACCCCTAGAGGGTATTTTGGTC
* *
57019276 ATTTTACCCTTTGAGGGTATTTTGGTC
1 ATTTTACCCCTAGAGGGTATTTTGGTC
57019303 ATTT
1 ATTT
57019307 AATAAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 11 0.39
27 17 0.61
ACGTcount: A:0.16, C:0.16, G:0.21, T:0.47
Consensus pattern (27 bp):
ATTTTACCCCTAGAGGGTATTTTGGTC
Found at i:57024130 original size:12 final size:12
Alignment explanation
Indices: 57024113--57024142 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
57024103 TTTGAAAGTT
57024113 ACACGGCCTAGC
1 ACACGGCCTAGC
57024125 ACACGGCCTAGC
1 ACACGGCCTAGC
*
57024137 ATACGG
1 ACACGG
57024143 GCGTGTGGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.37, G:0.27, T:0.10
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:57030322 original size:42 final size:42
Alignment explanation
Indices: 57030258--57030397 Score: 140
Period size: 50 Copynumber: 3.2 Consensus size: 42
57030248 ATACTGACCT
57030258 TAAAGTAAGTC--AGCTTTCTGGTTCCACAAACGTCTAATAG
1 TAAAGTAAGTCATAGCTTTCTGGTTCCACAAACGTCTAATAG
* * * *
57030298 TAAAGTAAGTCATAGCTTTCTGGTTCCACATATGTCTCGACTTCTAAA
1 TAAAGTAAGTCATAGCTTTCTGGTTCCACAAACGTCT--A---AT-AG
* *
57030346 TAAGAAGTAAGTCATGGCTTTCTGGTTCCACAAACATCTAATAG
1 T-A-AAGTAAGTCATAGCTTTCTGGTTCCACAAACGTCTAATAG
57030390 TAAAGTAA
1 TAAAGTAA
57030398 AAAATGTCTA
Statistics
Matches: 80, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
40 11 0.14
42 28 0.35
43 1 0.01
44 3 0.04
45 1 0.01
47 1 0.01
48 3 0.04
49 1 0.01
50 31 0.39
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (42 bp):
TAAAGTAAGTCATAGCTTTCTGGTTCCACAAACGTCTAATAG
Found at i:57036775 original size:18 final size:18
Alignment explanation
Indices: 57036752--57036787 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
57036742 CTTATTTCCA
*
57036752 TATTAGTACGTCCTAGGT
1 TATTAGCACGTCCTAGGT
57036770 TATTAGCACGTCCTAGGT
1 TATTAGCACGTCCTAGGT
57036788 CTACATAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.36
Consensus pattern (18 bp):
TATTAGCACGTCCTAGGT
Found at i:57042472 original size:31 final size:30
Alignment explanation
Indices: 57042400--57042474 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 30
57042390 AAATATGTAT
*
57042400 TTTTTATTTTTTA-AATAA-ATTTA-ATAA
1 TTTTTATTTTTTATAATAATTTTTATATAA
**
57042427 TTATTTATGATTTATAATAATTTTTATATAA
1 TT-TTTATTTTTTATAATAATTTTTATATAA
57042458 TTTTATATTTTTTATAA
1 TTTT-TATTTTTTATAA
57042475 CTACAATTGT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
27 2 0.05
28 9 0.24
29 5 0.13
30 6 0.16
31 16 0.42
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (30 bp):
TTTTTATTTTTTATAATAATTTTTATATAA
Found at i:57042628 original size:16 final size:17
Alignment explanation
Indices: 57042607--57042645 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
57042597 TTTTAAATAA
57042607 TTATTTTAAA-ATTTAT
1 TTATTTTAAAGATTTAT
*
57042623 TTA-TTTAAAGTTTTAT
1 TTATTTTAAAGATTTAT
57042639 TTATTTT
1 TTATTTT
57042646 TTAAAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 6 0.30
16 11 0.55
17 3 0.15
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
TTATTTTAAAGATTTAT
Found at i:57046349 original size:9 final size:9
Alignment explanation
Indices: 57046335--57046450 Score: 58
Period size: 10 Copynumber: 12.4 Consensus size: 9
57046325 CATGTGACAA
57046335 AAAAATTAT
1 AAAAATTAT
57046344 AAAAA-T-T
1 AAAAATTAT
*
57046351 AAAAATCAAT
1 AAAAAT-TAT
*
57046361 AAAAGTTAT
1 AAAAATTAT
57046370 AAAAATT-T
1 AAAAATTAT
* *
57046378 TAAATTTACT
1 AAAAATTA-T
*
57046388 AAAAATTAGAA
1 AAAAATT--AT
*
57046399 AAAAGAATAT
1 AAAA-ATTAT
*
57046409 AAAAATTGT
1 AAAAATTAT
*
57046418 AAAATTTTAT
1 AAAA-ATTAT
* *
57046428 AAATATCAT
1 AAAAATTAT
57046437 AAAAAATTAT
1 -AAAAATTAT
57046447 AAAA
1 AAAA
57046451 TAAATTAAAA
Statistics
Matches: 77, Mismatches: 20, Indels: 20
0.66 0.17 0.17
Matches are distributed among these distances:
7 6 0.08
8 7 0.09
9 27 0.35
10 30 0.39
11 4 0.05
12 3 0.04
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:57046805 original size:29 final size:30
Alignment explanation
Indices: 57046771--57046832 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
57046761 TTTTTTCTAA
57046771 TTTTTATTAAAAATTAAAAAATTTTAT-AT
1 TTTTTATTAAAAATTAAAAAATTTTATCAT
* * * *
57046800 TTTTTATTAACATTTAATAATTTTTATCAT
1 TTTTTATTAAAAATTAAAAAATTTTATCAT
57046830 TTT
1 TTT
57046833 GCCACATGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 23 0.82
30 5 0.18
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (30 bp):
TTTTTATTAAAAATTAAAAAATTTTATCAT
Done.