Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 51 of 82
Found at i:18651137 original size:30 final size:32
Alignment explanation
Indices: 18651081--18651139 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
18651071 GTTAATTTTA
*
18651081 AATAGTTGAATGATCAAAATATTAATTTTGGT
1 AATAGTTGAATGATCAAAACATTAATTTTGGT
18651113 AATAGTTG-ATGA-CTAAAACA-TAATTTT
1 AATAGTTGAATGATC-AAAACATTAATTTT
18651140 TTATAATTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 8 0.32
31 9 0.36
32 8 0.32
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.39
Consensus pattern (32 bp):
AATAGTTGAATGATCAAAACATTAATTTTGGT
Found at i:18655566 original size:21 final size:21
Alignment explanation
Indices: 18655542--18655582 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
18655532 AGAGCTTTGA
18655542 TTTTAGTCTTTATTCTTTTTC
1 TTTTAGTCTTTATTCTTTTTC
**
18655563 TTTTTTTCTTTATTCTTTTT
1 TTTTAGTCTTTATTCTTTTT
18655583 TAAAAAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.07, C:0.12, G:0.02, T:0.78
Consensus pattern (21 bp):
TTTTAGTCTTTATTCTTTTTC
Found at i:18655573 original size:14 final size:15
Alignment explanation
Indices: 18655554--18655583 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
18655544 TTAGTCTTTA
18655554 TTCTTT-TTCTTTTT
1 TTCTTTATTCTTTTT
18655568 TTCTTTATTCTTTTT
1 TTCTTTATTCTTTTT
18655583 T
1 T
18655584 AAAAAGAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.83
Consensus pattern (15 bp):
TTCTTTATTCTTTTT
Found at i:18656836 original size:18 final size:18
Alignment explanation
Indices: 18656813--18656857 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
18656803 ATTCTCTTGC
*
18656813 ATTTATTATTATTATTAT
1 ATTTATTATTATCATTAT
18656831 ATTTATTATTATCATTAT
1 ATTTATTATTATCATTAT
*
18656849 -TTCATTATT
1 ATTTATTATT
18656858 TCTTTTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTATTATTATCATTAT
Found at i:18659307 original size:28 final size:30
Alignment explanation
Indices: 18659250--18659309 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 30
18659240 TTTTTGAAAT
* *
18659250 TTACATTTTTGCCCCCGAAAAAGTCAAAAA
1 TTACATTTTTGACCCCGAAAAACTCAAAAA
*
18659280 TTACATTTTT-ACCCC-AAAAACTGAAAAA
1 TTACATTTTTGACCCCGAAAAACTCAAAAA
18659308 TT
1 TT
18659310 GCCCATAGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 13 0.48
29 4 0.15
30 10 0.37
ACGTcount: A:0.42, C:0.22, G:0.07, T:0.30
Consensus pattern (30 bp):
TTACATTTTTGACCCCGAAAAACTCAAAAA
Found at i:18659505 original size:19 final size:19
Alignment explanation
Indices: 18659477--18659513 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
18659467 GCCAAACCCT
* *
18659477 CAAATTATACTTCAATAAA
1 CAAATCATACTCCAATAAA
18659496 CAAATCATACTCCAATAA
1 CAAATCATACTCCAATAA
18659514 GTTAATATGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (19 bp):
CAAATCATACTCCAATAAA
Found at i:18662187 original size:30 final size:29
Alignment explanation
Indices: 18662151--18662239 Score: 90
Period size: 30 Copynumber: 3.0 Consensus size: 29
18662141 CATTAAAGTG
18662151 TAACAAATTTTTTTTAAACATAGCGTGTAA
1 TAACAAATTTTTTTT-AACATAGCGTGTAA
* * ** *
18662181 TAACAAAATTTTTTCAACATAGTATATAA
1 TAACAAATTTTTTTTAACATAGCGTGTAA
*
18662210 CAACAACATTTTTTTTAACAT-GACGTGTAA
1 TAACAA-ATTTTTTTTAACATAG-CGTGTAA
18662240 CATGTTTTTG
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
29 17 0.37
30 29 0.63
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (29 bp):
TAACAAATTTTTTTTAACATAGCGTGTAA
Found at i:18662275 original size:54 final size:53
Alignment explanation
Indices: 18662210--18662404 Score: 134
Period size: 54 Copynumber: 3.6 Consensus size: 53
18662200 TAGTATATAA
*
18662210 CAACAACATTTTTTTTAACATGACGTGTAACATGTTTTTGTACATGACATGTAG
1 CAACAATATTTTTTTTAACATGACGTGTAACATGTTTTTGTACATGAC-TGTAG
* * * *
18662264 CAACAATA--TTTTTCAACAT-AGCGTGTAACAACAATATTTCTTTTCAACGTGAC-GT-G
1 CAACAATATTTTTTTTAACATGA-CGTGT---AAC-ATGTTT-TTGT--ACATGACTGTAG
* * * * *
18662320 TAAC-A-ACTTTCTTTAACCATGACGTGTAACATGTTTTTGTACATAACGTGTAA
1 CAACAATATTTTTTTTAA-CATGACGTGTAACATGTTTTTGTACATGAC-TGTAG
**
18662373 CAATTATATTTTTTTTAACATGACGTGTAACA
1 CAACAATATTTTTTTTAACATGACGTGTAACA
18662405 ACCTTTTTTA
Statistics
Matches: 107, Mismatches: 17, Indels: 34
0.68 0.11 0.22
Matches are distributed among these distances:
50 5 0.05
51 1 0.01
52 20 0.19
53 7 0.07
54 26 0.24
55 13 0.12
56 15 0.14
57 13 0.12
58 1 0.01
59 6 0.06
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (53 bp):
CAACAATATTTTTTTTAACATGACGTGTAACATGTTTTTGTACATGACTGTAG
Found at i:18662412 original size:28 final size:27
Alignment explanation
Indices: 18662218--18662405 Score: 97
Period size: 24 Copynumber: 6.9 Consensus size: 27
18662208 AACAACAACA
18662218 TTTTTTTTAACATGACGTGTAAC--AT
1 TTTTTTTTAACATGACGTGTAACAAAT
* * * * *
18662243 GTTTTTGT-ACATGACATGTAGCAACAA
1 TTTTTTTTAACATGACGTGTAACAA-AT
* *
18662270 TATTTTTCAACAT-AGCGTGTAACAACAAT
1 TTTTTTTTAACATGA-CGTGTAAC-A-AAT
* *
18662299 ATTTCTTTTCAACGTGACGTGTAAC-AA-
1 -TTT-TTTTTAACATGACGTGTAACAAAT
* *
18662326 CTTTCTTTAACCATGACGTGTAAC--AT
1 TTTTTTTTAA-CATGACGTGTAACAAAT
* * *
18662352 GTTTTTGT-ACATAACGTGTAACAATTAT
1 TTTTTTTTAACATGACGTGTAACAA--AT
18662380 ATTTTTTTTAACATGACGTGTAACAA
1 -TTTTTTTTAACATGACGTGTAACAA
18662406 CCTTTTTTAA
Statistics
Matches: 120, Mismatches: 25, Indels: 31
0.68 0.14 0.18
Matches are distributed among these distances:
24 24 0.20
25 13 0.11
26 19 0.16
27 6 0.05
28 14 0.12
29 8 0.07
30 18 0.15
31 17 0.14
32 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.39
Consensus pattern (27 bp):
TTTTTTTTAACATGACGTGTAACAAAT
Found at i:18662428 original size:80 final size:80
Alignment explanation
Indices: 18662279--18662473 Score: 252
Period size: 80 Copynumber: 2.4 Consensus size: 80
18662269 ATATTTTTCA
* *
18662279 ACATAGCGTGTAACAACAATATTTCTTTTCAACGTGACGTGTAACAACTTTCTTTAACCATGACG
1 ACATAGCGTGTAACAATAATATTT-TTTTCAACATGACGTGTAACAACTTTCTTTAACCATGACG
*
18662344 TGTAACATGTTTTTGT
65 TGTAACATGTTTTGGT
* * * * **
18662360 ACATAACGTGTAACAATTATATTTTTTTTAACATGACGTGTAACAACCTTT-TTTAACTATGGTG
1 ACATAGCGTGTAACAATAATATTTTTTTCAACATGACGTGTAACAA-CTTTCTTTAACCATGACG
18662424 TGTAACATGTTTTGGT
65 TGTAACATGTTTTGGT
*
18662440 ATC-TAGCGTGTAACAATAACA-TTTTTTCAACATG
1 A-CATAGCGTGTAACAATAATATTTTTTTCAACATG
18662474 GCATATAACA
Statistics
Matches: 99, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
79 12 0.12
80 61 0.62
81 26 0.26
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (80 bp):
ACATAGCGTGTAACAATAATATTTTTTTCAACATGACGTGTAACAACTTTCTTTAACCATGACGT
GTAACATGTTTTGGT
Found at i:18663002 original size:24 final size:24
Alignment explanation
Indices: 18662975--18663022 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
18662965 TACTGCTACT
18662975 TTGGCTTTTGGCTTTTCAACTTGC
1 TTGGCTTTTGGCTTTTCAACTTGC
*
18662999 TTGGCTTTTGGCTTTTGAACTTGC
1 TTGGCTTTTGGCTTTTCAACTTGC
18663023 CTGTGCATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.08, C:0.19, G:0.23, T:0.50
Consensus pattern (24 bp):
TTGGCTTTTGGCTTTTCAACTTGC
Found at i:18665401 original size:2 final size:2
Alignment explanation
Indices: 18665394--18665452 Score: 95
Period size: 2 Copynumber: 30.5 Consensus size: 2
18665384 ACTAGTTCCA
18665394 TC TC TC TC TC TC TC TC TC TC TC TC TC T- TC -C TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
18665434 TC TC GC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC T
18665453 TTCNNNNNNN
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
1 2 0.04
2 51 0.96
ACGTcount: A:0.00, C:0.49, G:0.02, T:0.49
Consensus pattern (2 bp):
TC
Found at i:18665531 original size:2 final size:2
Alignment explanation
Indices: 18665524--18665583 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
18665514 NNNNNNNNNN
18665524 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
18665566 CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT
18665584 TTTATTGTAG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:18667249 original size:25 final size:25
Alignment explanation
Indices: 18667197--18667249 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
18667187 CTTACTTGTG
* *
18667197 TTTTATTTCTTTTTTTTTTCTCTCT
1 TTTTATTTCTTATTTTTTTCTATCT
* *
18667222 TTTTCTTTCTTATTTTTTTTTAT-T
1 TTTTATTTCTTATTTTTTTCTATCT
18667246 TTTT
1 TTTT
18667250 CCTCAAAACT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.06, C:0.11, G:0.00, T:0.83
Consensus pattern (25 bp):
TTTTATTTCTTATTTTTTTCTATCT
Found at i:18683955 original size:17 final size:17
Alignment explanation
Indices: 18683933--18683966 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
18683923 TGCTCTGTGG
*
18683933 CAAAATTTTATCACTAC
1 CAAAATTCTATCACTAC
*
18683950 CAAAATTCTATTACTAC
1 CAAAATTCTATCACTAC
18683967 TTCAGCCTCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.35
Consensus pattern (17 bp):
CAAAATTCTATCACTAC
Found at i:18688716 original size:19 final size:18
Alignment explanation
Indices: 18688694--18688742 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
18688684 TGAAAAGCTC
**
18688694 TTAAAAAAAAAACTTTTTT
1 TTAAAAAAAAAA-AATTTT
18688713 TTAAAAAAAACAAAATTTT
1 TTAAAAAAAA-AAAATTTT
18688732 TTAAAAAAAAA
1 TTAAAAAAAAA
18688743 GCTTAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 1 0.04
19 24 0.89
20 2 0.07
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (18 bp):
TTAAAAAAAAAAAATTTT
Found at i:18703615 original size:2 final size:2
Alignment explanation
Indices: 18703603--18703652 Score: 70
Period size: 2 Copynumber: 26.5 Consensus size: 2
18703593 TTATTAATAG
*
18703603 TA TA GA TA TA TA TA TA TA TA TA TA -A TA T- TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18703642 TA TA TA TA TA T
1 TA TA TA TA TA T
18703653 NNNNNNNNNN
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
1 3 0.07
2 40 0.93
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18703725 original size:2 final size:2
Alignment explanation
Indices: 18703718--18703753 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
18703708 NNNNNNNNNN
18703718 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
18703754 CAATTGGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18715764 original size:3 final size:3
Alignment explanation
Indices: 18715751--18715780 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
18715741 CTCATTTTTA
*
18715751 ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
18715781 CTTTTTCACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:18725523 original size:21 final size:20
Alignment explanation
Indices: 18725494--18725532 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
18725484 CATCGGTCGA
18725494 GACAGCCAAGATGCTGGGGTTG
1 GACAGCCAAG--GCTGGGGTTG
18725516 GACA-CCAAGGCTGGGGT
1 GACAGCCAAGGCTGGGGT
18725533 AGCGAGCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.47
21 5 0.29
22 4 0.24
ACGTcount: A:0.23, C:0.21, G:0.41, T:0.15
Consensus pattern (20 bp):
GACAGCCAAGGCTGGGGTTG
Found at i:18728712 original size:64 final size:64
Alignment explanation
Indices: 18728639--18728763 Score: 198
Period size: 65 Copynumber: 2.0 Consensus size: 64
18728629 TATAAGTCAC
* * *
18728639 ATAGAATCAAAG-TTTTTATGAAAAAGATATTAAATGTTATTGCATAATCAATAAAATATTAGAA
1 ATAGAATCAAAGTTTTTTATAAAAAAGATATTAAATATTATTACATAATCAAT-AAATATTAGAA
*
18728703 ATAGAATCAAGGTTTTTTATAAAAAAGATATTAAATATTATTACATAATCAATAAATATTA
1 ATAGAATCAAAGTTTTTTATAAAAAAGATATTAAATATTATTACATAATCAATAAATATTA
18728764 CAAAAATATT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
64 19 0.34
65 37 0.66
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (64 bp):
ATAGAATCAAAGTTTTTTATAAAAAAGATATTAAATATTATTACATAATCAATAAATATTAGAA
Found at i:18731702 original size:19 final size:18
Alignment explanation
Indices: 18731673--18731708 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
18731663 TGTTAATATA
18731673 TATTTATTTATTAATTTT
1 TATTTATTTATTAATTTT
18731691 TATTTGATTTATTAATTT
1 TATTT-ATTTATTAATTT
18731709 CTTTAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
TATTTATTTATTAATTTT
Found at i:18738419 original size:63 final size:63
Alignment explanation
Indices: 18738287--18738424 Score: 163
Period size: 64 Copynumber: 2.2 Consensus size: 63
18738277 AAAAAAGTCA
* * * * *
18738287 AAAAAATTTTAAAATTTTTGTAGGGGAGAAATTATAAAATTTTTAAAAAGTAAAGGCAAATTAT
1 AAAAAA-TTAAAAATTATTGAAGGGGAGAAATTATAAAATTTTTAAAAAATAAAGACAAATTAT
*
18738351 AAAAAATTAAAAATTATTGAAGGGGAGAAATTA-AAATATTTTTTAAAAAATACAA-ATAAATTA
1 AAAAAATTAAAAATTATTGAAGGGGAGAAATTATAAA-A-TTTTTAAAAAATA-AAGACAAATTA
18738414 T
63 T
*
18738415 AAAAATTTAA
1 AAAAAATTAA
18738425 CCCTCCCGCC
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
62 3 0.05
63 25 0.39
64 34 0.53
65 2 0.03
ACGTcount: A:0.55, C:0.01, G:0.11, T:0.33
Consensus pattern (63 bp):
AAAAAATTAAAAATTATTGAAGGGGAGAAATTATAAAATTTTTAAAAAATAAAGACAAATTAT
Found at i:18739334 original size:24 final size:24
Alignment explanation
Indices: 18739302--18739349 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
18739292 TTGCATTTGC
*
18739302 CTTTAAAAAAGAATTCCTGGTGGT
1 CTTTAAAAAAGAATTCCTCGTGGT
18739326 CTTTAAAAAAGAATTCCTCGTGGT
1 CTTTAAAAAAGAATTCCTCGTGGT
18739350 TTTCATCAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (24 bp):
CTTTAAAAAAGAATTCCTCGTGGT
Found at i:18742131 original size:23 final size:23
Alignment explanation
Indices: 18742105--18742148 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
18742095 CAAAAGCATC
18742105 AAATAAAGAGATAGAGAAAAAAA
1 AAATAAAGAGATAGAGAAAAAAA
18742128 AAATAAAGAGATAGAGAAAAA
1 AAATAAAGAGATAGAGAAAAA
18742149 TAAGAGGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (23 bp):
AAATAAAGAGATAGAGAAAAAAA
Found at i:18743754 original size:23 final size:23
Alignment explanation
Indices: 18743726--18743787 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
18743716 AGTAATGCCT
18743726 AAGTCACACAATGCCTTACTAAC
1 AAGTCACACAATGCCTTACTAAC
** *
18743749 TGGTCACACAATGTCTTACTAAC
1 AAGTCACACAATGCCTTACTAAC
*
18743772 AAGTCACGCAATGCCT
1 AAGTCACACAATGCCT
18743788 ATCAACTAGT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.34, C:0.29, G:0.13, T:0.24
Consensus pattern (23 bp):
AAGTCACACAATGCCTTACTAAC
Found at i:18746085 original size:21 final size:19
Alignment explanation
Indices: 18746042--18746084 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 19
18746032 TTTTTTTGCA
18746042 TTTTGAAAAAATAAAAGCT
1 TTTTGAAAAAATAAAAGCT
18746061 TTTTGTAAAAGAATAAAA-CT
1 TTTTG-AAAA-AATAAAAGCT
18746081 TTTT
1 TTTT
18746085 TTTATACTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.23
20 10 0.45
21 7 0.32
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.40
Consensus pattern (19 bp):
TTTTGAAAAAATAAAAGCT
Found at i:18746251 original size:28 final size:28
Alignment explanation
Indices: 18746217--18746270 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
18746207 TAAGAATATT
* *
18746217 AGATTAAATTCAATAAAATT-AGATAAAA
1 AGATTAAAAT-AACAAAATTAAGATAAAA
18746245 AGATTAAAATAACAAAATTAAGATAA
1 AGATTAAAATAACAAAATTAAGATAA
18746271 TAGAGGGACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.63, C:0.04, G:0.07, T:0.26
Consensus pattern (28 bp):
AGATTAAAATAACAAAATTAAGATAAAA
Found at i:18747405 original size:15 final size:15
Alignment explanation
Indices: 18747371--18747406 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
18747361 GTTTTGCAAT
*
18747371 TAATTAAATTAATAA
1 TAATTTAATTAATAA
18747386 T-ATTTAATTAATAA
1 TAATTTAATTAATAA
18747400 TAATTTA
1 TAATTTA
18747407 TTATAATGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATTTAATTAATAA
Found at i:18747979 original size:21 final size:21
Alignment explanation
Indices: 18747940--18747978 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
18747930 TTGCATTTTG
18747940 AAAAAAATAGAAACTTTTTAT
1 AAAAAAATAGAAACTTTTTAT
18747961 AAAAAAATA-AAACTTTTT
1 AAAAAAATAGAAACTTTTT
18747979 TTTTACACTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (21 bp):
AAAAAAATAGAAACTTTTTAT
Found at i:18749095 original size:2 final size:2
Alignment explanation
Indices: 18749062--18749087 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18749052 TAAACACTTA
18749062 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
18749088 TGTATATAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18749136 original size:2 final size:2
Alignment explanation
Indices: 18749129--18749154 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18749119 TAGCATGNTA
18749129 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
18749155 TGTATATGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18749168 original size:65 final size:64
Alignment explanation
Indices: 18749060--18749190 Score: 203
Period size: 67 Copynumber: 2.0 Consensus size: 64
18749050 AGTAAACACT
18749060 TAATATATATATATATATATATATATATTGTATATAAGT-AAAAAATTAAGTAAATTAAGTAGCA
1 TAATATATATATATATATATATATATATTGTATAT-AGTAAAAAAATT-AG-AAATTAAGTAGCA
18749124 TG
63 TG
18749126 NTAATATATATATATATATATATATATATTGTATAT-GTAAAAAAAATTAGAAATTAAGTAGCAT
1 -TAATATATATATATATATATATATATATTGTATATAGT-AAAAAAATTAGAAATTAAGTAGCAT
18749190 G
64 G
18749191 CATGCTTGCA
Statistics
Matches: 62, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
65 17 0.27
66 2 0.03
67 43 0.69
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.39
Consensus pattern (64 bp):
TAATATATATATATATATATATATATATTGTATATAGTAAAAAAATTAGAAATTAAGTAGCATG
Found at i:18749445 original size:18 final size:19
Alignment explanation
Indices: 18749422--18749459 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
18749412 AATTGAAGTT
18749422 AAATAAAAATAAA-AAATA
1 AAATAAAAATAAATAAATA
*
18749440 AAATAATAATAAATAAATA
1 AAATAAAAATAAATAAATA
18749459 A
1 A
18749460 TGAATGAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (19 bp):
AAATAAAAATAAATAAATA
Found at i:18749452 original size:11 final size:11
Alignment explanation
Indices: 18749421--18749480 Score: 52
Period size: 11 Copynumber: 5.4 Consensus size: 11
18749411 TAATTGAAGT
18749421 TAAATAA-AAA
1 TAAATAATAAA
*
18749431 TAAAAAATAAA
1 TAAATAATAAA
18749442 -ATAATAATAAA
1 TA-AATAATAAA
*
18749453 TAAATAATGAA
1 TAAATAATAAA
*
18749464 TGAATGAATAAAA
1 TAAAT-AAT-AAA
18749477 TAAA
1 TAAA
18749481 AGAAGGAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
10 7 0.18
11 23 0.59
12 4 0.10
13 5 0.13
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (11 bp):
TAAATAATAAA
Found at i:18749865 original size:11 final size:11
Alignment explanation
Indices: 18749849--18749901 Score: 56
Period size: 10 Copynumber: 4.9 Consensus size: 11
18749839 AAAAGACAAG
*
18749849 AAAGAATGGAA
1 AAAGAAAGGAA
*
18749860 AAAG-AAGGAG
1 AAAGAAAGGAA
*
18749870 AAGGAAAGG-A
1 AAAGAAAGGAA
18749880 AAAGAAAGGAA
1 AAAGAAAGGAA
18749891 AAAGAGAAGGA
1 AAAGA-AAGGA
18749902 GAGAGAGAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
10 15 0.44
11 14 0.41
12 5 0.15
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (11 bp):
AAAGAAAGGAA
Found at i:18750066 original size:24 final size:24
Alignment explanation
Indices: 18750000--18750067 Score: 70
Period size: 22 Copynumber: 2.9 Consensus size: 24
18749990 CGAGGAGAAA
18750000 AGAAAGAAAAAGAAAGAAGA-AAGG
1 AGAAAGAAAAA-AAAGAAGAGAAGG
* **
18750024 AGAAAGGAAAGGAAG--GAGAAGG
1 AGAAAGAAAAAAAAGAAGAGAAGG
*
18750046 AGAGAGAAAAAAAAGAAGAGAA
1 AGAAAGAAAAAAAAGAAGAGAA
18750068 AAAGGGTGAG
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
21 2 0.06
22 15 0.44
23 3 0.09
24 14 0.41
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (24 bp):
AGAAAGAAAAAAAAGAAGAGAAGG
Found at i:18751106 original size:60 final size:59
Alignment explanation
Indices: 18750960--18751137 Score: 180
Period size: 59 Copynumber: 3.0 Consensus size: 59
18750950 ATATTTGATT
* * * *
18750960 GTAAAAAGGAAGACCTGAAGCCCCGATTTATATTAGGTGGCATGAGTAGTT-CTACGAGTAG
1 GTAAAAAGG-A-ACCTGAAGCCCCGATTTATAAT-GGTGGCGTGAGTAGTTCCCACGAGTAA
** * *
18751021 GTAAAGGGGGACTTGAAGCCCCGATTTATAATGGGTGGCGTGAGTAGTTCCCACGAGTAA
1 GTAAAAAGGAACCTGAAGCCCCGATTTATAAT-GGTGGCGTGAGTAGTTCCCACGAGTAA
* * * * * *
18751081 GTAAAAAGGAACCTAAAGCCCCGATTCAT-ATGATGGCGTGGGCAGTTCCCACAAGTA
1 GTAAAAAGGAACCTGAAGCCCCGATTTATAATGGTGGCGTGAGTAGTTCCCACGAGTA
18751138 GGTGATGATA
Statistics
Matches: 97, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
58 22 0.23
59 37 0.38
60 31 0.32
61 7 0.07
ACGTcount: A:0.31, C:0.18, G:0.29, T:0.22
Consensus pattern (59 bp):
GTAAAAAGGAACCTGAAGCCCCGATTTATAATGGTGGCGTGAGTAGTTCCCACGAGTAA
Found at i:18752582 original size:23 final size:23
Alignment explanation
Indices: 18752566--18752631 Score: 132
Period size: 23 Copynumber: 2.9 Consensus size: 23
18752556 TGTGAAACAA
18752566 CATGGTGGGAATGTGTGACATGT
1 CATGGTGGGAATGTGTGACATGT
18752589 CATGGTGGGAATGTGTGACATGT
1 CATGGTGGGAATGTGTGACATGT
18752612 CATGGTGGGAATGTGTGACA
1 CATGGTGGGAATGTGTGACA
18752632 CGGTTGTGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.23, C:0.09, G:0.39, T:0.29
Consensus pattern (23 bp):
CATGGTGGGAATGTGTGACATGT
Found at i:18752781 original size:23 final size:23
Alignment explanation
Indices: 18752701--18752825 Score: 94
Period size: 23 Copynumber: 5.5 Consensus size: 23
18752691 AACTCGAAAG
* * *
18752701 GAATATGTGAGATGACATGGTGA
1 GAATATGTGACACGCCATGGTGA
* * *
18752724 AAATATGTGACATGCCA-GTTTGA
1 GAATATGTGACACGCCATG-GTGA
* *
18752747 G-A-ATGTGGCACGCCATGGTGT
1 GAATATGTGACACGCCATGGTGA
18752768 GAATATGTGACACGCCATGGTGA
1 GAATATGTGACACGCCATGGTGA
* * * * *
18752791 GAATATGTAAGATGACATAGTGA
1 GAATATGTGACACGCCATGGTGA
*
18752814 GCATATGTGACA
1 GAATATGTGACA
18752826 TGGCTGTGAC
Statistics
Matches: 79, Mismatches: 19, Indels: 8
0.75 0.18 0.08
Matches are distributed among these distances:
21 14 0.18
22 4 0.05
23 61 0.77
ACGTcount: A:0.33, C:0.12, G:0.30, T:0.26
Consensus pattern (23 bp):
GAATATGTGACACGCCATGGTGA
Found at i:18752971 original size:46 final size:46
Alignment explanation
Indices: 18752904--18753045 Score: 123
Period size: 46 Copynumber: 3.1 Consensus size: 46
18752894 TTTAGAGTTG
*
18752904 GTGACACACCATGG-AGGGAATGTGTGACATGGCATGGTGAGAATAT
1 GTGACACACCATGGTA-AGAATGTGTGACATGGCATGGTGAGAATAT
* * * * *
18752950 GTGACACACTA-GTGTGAGAATGTG-G-CACGCCATGGTGTGAGA-AT
1 GTGACACACCATG-GTAAGAATGTGTGACATGGCATGGTGAGA-ATAT
* * * * *
18752994 GTTACACGCCATGGTAAGAATATGTGAGATGGCATGGTGAGCATAT
1 GTGACACACCATGGTAAGAATGTGTGACATGGCATGGTGAGAATAT
18753040 GTGACA
1 GTGACA
18753046 TGACAAGGTT
Statistics
Matches: 72, Mismatches: 17, Indels: 14
0.70 0.17 0.14
Matches are distributed among these distances:
44 31 0.43
45 6 0.08
46 35 0.49
ACGTcount: A:0.30, C:0.14, G:0.33, T:0.23
Consensus pattern (46 bp):
GTGACACACCATGGTAAGAATGTGTGACATGGCATGGTGAGAATAT
Found at i:18752987 original size:23 final size:23
Alignment explanation
Indices: 18752961--18753008 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
18752951 TGACACACTA
*
18752961 GTGTGAGAATGTGGCACGCCATG
1 GTGTGAGAATGTGACACGCCATG
*
18752984 GTGTGAGAATGTTACACGCCATG
1 GTGTGAGAATGTGACACGCCATG
18753007 GT
1 GT
18753009 AAGAATATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.23, C:0.17, G:0.35, T:0.25
Consensus pattern (23 bp):
GTGTGAGAATGTGACACGCCATG
Found at i:18753201 original size:23 final size:23
Alignment explanation
Indices: 18753166--18753217 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
18753156 TTTAGAGTTG
* *
18753166 GTGACACGCCATGGTGAGA-ATAT
1 GTGACACGACATGCTGA-ACATAT
*
18753189 GTGAGACGACATGCTGAACATAT
1 GTGACACGACATGCTGAACATAT
18753212 GTGACA
1 GTGACA
18753218 TGACTGTTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (23 bp):
GTGACACGACATGCTGAACATAT
Found at i:18753386 original size:23 final size:23
Alignment explanation
Indices: 18753338--18753415 Score: 77
Period size: 23 Copynumber: 3.4 Consensus size: 23
18753328 GTTTAGAGTT
* * *
18753338 TGTGAAATGCCATGG-TGAGAATA
1 TGTGACATGCCATGGCT-TGAACA
*
18753361 TGTGACATGGCATGGCTTGAACA
1 TGTGACATGCCATGGCTTGAACA
* * *
18753384 TGTGACACGCCATGGGTTGAATA
1 TGTGACATGCCATGGCTTGAACA
18753407 TGTGACATG
1 TGTGACATG
18753416 TGCCATAGTT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
23 44 0.98
24 1 0.02
ACGTcount: A:0.28, C:0.14, G:0.31, T:0.27
Consensus pattern (23 bp):
TGTGACATGCCATGGCTTGAACA
Found at i:18753429 original size:25 final size:24
Alignment explanation
Indices: 18753356--18753421 Score: 82
Period size: 23 Copynumber: 2.8 Consensus size: 24
18753346 GCCATGGTGA
18753356 GAATATGTGACATGG-CATGGCTT
1 GAATATGTGACATGGCCATGGCTT
* * *
18753379 GAACATGTGACA-CGCCATGGGTT
1 GAATATGTGACATGGCCATGGCTT
18753402 GAATATGTGACATGTGCCAT
1 GAATATGTGACATG-GCCAT
18753422 AGTTTGAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 1 0.03
23 29 0.83
25 5 0.14
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (24 bp):
GAATATGTGACATGGCCATGGCTT
Found at i:18753978 original size:31 final size:31
Alignment explanation
Indices: 18753940--18754044 Score: 140
Period size: 31 Copynumber: 3.4 Consensus size: 31
18753930 CCATGGTTGG
* *
18753940 CGTGTAACAACATTTGATTTGATATGCATGT
1 CGTGTAACAACATTTTACTTGATATGCATGT
* *
18753971 CGTGTAACAACATTTTACTTAATATGCATGG
1 CGTGTAACAACATTTTACTTGATATGCATGT
* *
18754002 CATGTAACAAAATTTTACTTGATATGCATGGT
1 CGTGTAACAACATTTTACTTGATATGCAT-GT
18754034 -GTGTAACAACA
1 CGTGTAACAACA
18754045 ACAATTATTT
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
31 62 0.98
32 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.35
Consensus pattern (31 bp):
CGTGTAACAACATTTTACTTGATATGCATGT
Found at i:18758856 original size:102 final size:103
Alignment explanation
Indices: 18758677--18758886 Score: 361
Period size: 102 Copynumber: 2.0 Consensus size: 103
18758667 AAATGTGAAC
18758677 ATCAACAAAATGAAAACCAATAGGAACCATTATCCAAATTCAGCCATCCAATATTTCCAGAATTT
1 ATCAACAAAATGAAAACCAATAGGAACCATTATCCAAATTCAGCCATCCAATATTTCCAGAATTT
* * *
18758742 TCATGCCTAGGTTACAGTACAAATCAG-AAAAGCTTTT
66 TCATGCCCAGGTTACAATACAAATCAGAAAAACCTTTT
*
18758779 ATCAACAAAATGAAAACCAATAGGAACCATTATCCAAATTCAGCCATCCAATCTTTCCA-ACATT
1 ATCAACAAAATGAAAACCAATAGGAACCATTATCCAAATTCAGCCATCCAATATTTCCAGA-ATT
18758843 TTCATGCCCAGGTTACAATACAAATCAGAAAAACCTTTT
65 TTCATGCCCAGGTTACAATACAAATCAGAAAAACCTTTT
18758882 ATCAA
1 ATCAA
18758887 ACCGATCTGT
Statistics
Matches: 102, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
101 1 0.01
102 87 0.85
103 14 0.14
ACGTcount: A:0.42, C:0.23, G:0.09, T:0.26
Consensus pattern (103 bp):
ATCAACAAAATGAAAACCAATAGGAACCATTATCCAAATTCAGCCATCCAATATTTCCAGAATTT
TCATGCCCAGGTTACAATACAAATCAGAAAAACCTTTT
Found at i:18759108 original size:24 final size:24
Alignment explanation
Indices: 18759046--18759110 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
18759036 AAAGTGCAGT
18759046 TGCACCAGCAGCAGCTTCACTTGG
1 TGCACCAGCAGCAGCTTCACTTGG
* * *
18759070 TGCAACAACAACAGCTTCACTTGG
1 TGCACCAGCAGCAGCTTCACTTGG
*
18759094 TGCACCAGTAGCAGCTT
1 TGCACCAGCAGCAGCTT
18759111 TAATCGCTCC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.26, C:0.31, G:0.22, T:0.22
Consensus pattern (24 bp):
TGCACCAGCAGCAGCTTCACTTGG
Found at i:18761556 original size:42 final size:42
Alignment explanation
Indices: 18761475--18761582 Score: 137
Period size: 42 Copynumber: 2.6 Consensus size: 42
18761465 CAGTAGCTTC
* * *
18761475 AGATAGGCCTTCAGCAG-TTTAAATTAACCTTCAGCAATTTT
1 AGATGGGCCGTCAGCAGCTTTAAATTAACCTCCAGCAATTTT
* * *
18761516 AGATGGGCCGTCAGCAGCTTTAACTTAGCCTCCAGTAATTTT
1 AGATGGGCCGTCAGCAGCTTTAAATTAACCTCCAGCAATTTT
* *
18761558 AAATGGGCCGTCAGTAGCTTTAAAT
1 AGATGGGCCGTCAGCAGCTTTAAAT
18761583 GGGCCTCCAA
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
41 15 0.26
42 42 0.74
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.31
Consensus pattern (42 bp):
AGATGGGCCGTCAGCAGCTTTAAATTAACCTCCAGCAATTTT
Found at i:18761572 original size:21 final size:21
Alignment explanation
Indices: 18761513--18761587 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
18761503 CTTCAGCAAT
* * *
18761513 TTTAGATGGGCCGTCAGCAGC
1 TTTAAATGGGCCGTCAGTAAC
* ** *
18761534 TTTAACTTAGCC-TCCAGTAAT
1 TTTAAATGGGCCGT-CAGTAAC
*
18761555 TTTAAATGGGCCGTCAGTAGC
1 TTTAAATGGGCCGTCAGTAAC
18761576 TTTAAATGGGCC
1 TTTAAATGGGCC
18761588 TCCAATAGCT
Statistics
Matches: 40, Mismatches: 12, Indels: 4
0.71 0.21 0.07
Matches are distributed among these distances:
20 1 0.03
21 38 0.95
22 1 0.03
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (21 bp):
TTTAAATGGGCCGTCAGTAAC
Found at i:18761596 original size:21 final size:21
Alignment explanation
Indices: 18761555--18761598 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
18761545 CTCCAGTAAT
*
18761555 TTTAAATGGGCCGTCAGTAGC
1 TTTAAATGGGCCGTCAATAGC
18761576 TTTAAATGGGCC-TCCAATAGC
1 TTTAAATGGGCCGT-CAATAGC
18761597 TT
1 TT
18761599 CAGATGAGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (21 bp):
TTTAAATGGGCCGTCAATAGC
Found at i:18765479 original size:19 final size:19
Alignment explanation
Indices: 18765427--18765480 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
18765417 AATTTCAACT
*
18765427 TAAAAAATATAACTTAAAATA
1 TAAAAAATA-AA-TAAAAATA
* *
18765448 TTAAACA-AAATAAAAATA
1 TAAAAAATAAATAAAAATA
18765466 TAAAAAATAAATAAA
1 TAAAAAATAAATAAA
18765481 TAATTGAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
18 12 0.44
19 9 0.33
20 1 0.04
21 5 0.19
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (19 bp):
TAAAAAATAAATAAAAATA
Found at i:18769258 original size:22 final size:23
Alignment explanation
Indices: 18769210--18769378 Score: 80
Period size: 22 Copynumber: 7.6 Consensus size: 23
18769200 AGTCATGTTA
18769210 TTACACGCCATGTTTAAAAAATG
1 TTACACGCCATGTTTAAAAAATG
* *
18769233 TTACACGTCATGTTT-AAATATG
1 TTACACGCCATGTTTAAAAAATG
** * * * **
18769255 TTACTTG-CAAGTTCACCATTATG
1 TTACACGCCATGTTTA-AAAAATG
* * * *
18769278 ATACACACCTTG-TTCAAAAATG
1 TTACACGCCATGTTTAAAAAATG
* * *
18769300 TTACACG-CAAGTTCAAAAATTG
1 TTACACGCCATGTTTAAAAAATG
* * *
18769322 TTACACACCTTG-TTCAAAAATG
1 TTACACGCCATGTTTAAAAAATG
* * *
18769344 TTACACG-CAAGTTCAAAAATTG
1 TTACACGCCATGTTTAAAAAATG
*
18769366 TTACATGCCATGT
1 TTACACGCCATGT
18769379 GCTAACACAT
Statistics
Matches: 99, Mismatches: 40, Indels: 14
0.65 0.26 0.09
Matches are distributed among these distances:
21 9 0.09
22 59 0.60
23 29 0.29
24 2 0.02
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.33
Consensus pattern (23 bp):
TTACACGCCATGTTTAAAAAATG
Found at i:18769314 original size:21 final size:22
Alignment explanation
Indices: 18769289--18769370 Score: 114
Period size: 22 Copynumber: 3.8 Consensus size: 22
18769279 TACACACCTT
18769289 GTTCAAAAA-TGTTACACGCAA
1 GTTCAAAAATTGTTACACGCAA
* **
18769310 GTTCAAAAATTGTTACACACCTT
1 GTTCAAAAATTGTTACAC-GCAA
18769333 GTTCAAAAA-TGTTACACGCAA
1 GTTCAAAAATTGTTACACGCAA
18769354 GTTCAAAAATTGTTACA
1 GTTCAAAAATTGTTACA
18769371 TGCCATGTGC
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
21 19 0.37
22 23 0.44
23 10 0.19
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.29
Consensus pattern (22 bp):
GTTCAAAAATTGTTACACGCAA
Found at i:18769338 original size:44 final size:44
Alignment explanation
Indices: 18769279--18769370 Score: 184
Period size: 44 Copynumber: 2.1 Consensus size: 44
18769269 ACCATTATGA
18769279 TACACACCTTGTTCAAAAATGTTACACGCAAGTTCAAAAATTGT
1 TACACACCTTGTTCAAAAATGTTACACGCAAGTTCAAAAATTGT
18769323 TACACACCTTGTTCAAAAATGTTACACGCAAGTTCAAAAATTGT
1 TACACACCTTGTTCAAAAATGTTACACGCAAGTTCAAAAATTGT
18769367 TACA
1 TACA
18769371 TGCCATGTGC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (44 bp):
TACACACCTTGTTCAAAAATGTTACACGCAAGTTCAAAAATTGT
Found at i:18774293 original size:16 final size:16
Alignment explanation
Indices: 18774247--18774294 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
18774237 CTTTTTAGTG
*
18774247 AGTTATT-TTAATTTT
1 AGTTATTATTTATTTT
18774262 ATGTTATTCCATTTATTTT
1 A-GTTATT--ATTTATTTT
18774281 AGTTATTATTTATT
1 AGTTATTATTTATT
18774295 GATTTTTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 1 0.04
16 13 0.46
18 6 0.21
19 8 0.29
ACGTcount: A:0.25, C:0.04, G:0.06, T:0.65
Consensus pattern (16 bp):
AGTTATTATTTATTTT
Found at i:18775398 original size:14 final size:14
Alignment explanation
Indices: 18775379--18775405 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18775369 TTGGTTTTAA
18775379 TTTTAGTTAATTAG
1 TTTTAGTTAATTAG
18775393 TTTTAGTTAATTA
1 TTTTAGTTAATTA
18775406 ATTAATTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (14 bp):
TTTTAGTTAATTAG
Found at i:18779005 original size:15 final size:13
Alignment explanation
Indices: 18778985--18779026 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
18778975 TTTACTTGAA
18778985 TTTTATTTATTTAT
1 TTTTATTT-TTTAT
18778999 TTATTA-TTTTTAT
1 TT-TTATTTTTTAT
*
18779012 TTTTATTTTTCAT
1 TTTTATTTTTTAT
18779025 TT
1 TT
18779027 GAAATCTTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 3 0.12
13 15 0.60
14 4 0.16
15 3 0.12
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTATTTTTTAT
Found at i:18786411 original size:22 final size:22
Alignment explanation
Indices: 18786383--18786425 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
18786373 AAAGTTCATA
*
18786383 TGAAAATTATACAAATAAATCC
1 TGAAAATTATACAAAGAAATCC
*
18786405 TGAAAATTATTCAAAGAAATC
1 TGAAAATTATACAAAGAAATC
18786426 AATCTTAATA
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:0.53, C:0.12, G:0.07, T:0.28
Consensus pattern (22 bp):
TGAAAATTATACAAAGAAATCC
Found at i:18787358 original size:63 final size:64
Alignment explanation
Indices: 18787265--18787401 Score: 165
Period size: 63 Copynumber: 2.2 Consensus size: 64
18787255 TAATATGTAA
* * * * *
18787265 AAAAATTTTAAAATTTTTGTAAGGATGAAATTATAAAATTTTTAAAAAGTA-A-AGGCAAATTAT
1 AAAAATTTAAAAATTATTGTAAGGATGAAATTA-AAAAATTTTAAAAAATATATAGACAAATTAT
*
18787328 AAAAATTTAAAAATTATTG-AAGGGGA-GAAATTAAAAAATTTTAAAAAATATATAGATAAATTA
1 AAAAATTTAAAAATTATTGTAA--GGATGAAATTAAAAAATTTTAAAAAATATATAGACAAATTA
18787391 T
64 T
18787392 AAAAATTTAA
1 AAAAATTTAA
18787402 CCCTCCCGTC
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
62 17 0.27
63 25 0.39
64 22 0.34
ACGTcount: A:0.55, C:0.01, G:0.10, T:0.34
Consensus pattern (64 bp):
AAAAATTTAAAAATTATTGTAAGGATGAAATTAAAAAATTTTAAAAAATATATAGACAAATTAT
Found at i:18794899 original size:22 final size:20
Alignment explanation
Indices: 18794860--18794898 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
18794850 TTACATTTTG
*
18794860 AAAAAAGAAAAACTTTTTAT
1 AAAAAAAAAAAACTTTTTAT
18794880 AAAAAAAAATAAACTTTTT
1 AAAAAAAAA-AAACTTTTT
18794899 TTTTACACTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.31
Consensus pattern (20 bp):
AAAAAAAAAAAACTTTTTAT
Found at i:18797924 original size:15 final size:15
Alignment explanation
Indices: 18797900--18797932 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
18797890 AACAAAACAC
18797900 TTTTCTTGCTCTTGAT
1 TTTTCTTGCTCTTG-T
18797916 TTTTC-TGCTCTTGT
1 TTTTCTTGCTCTTGT
18797930 TTT
1 TTT
18797933 GTTTTTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 8 0.47
16 5 0.29
ACGTcount: A:0.03, C:0.18, G:0.12, T:0.67
Consensus pattern (15 bp):
TTTTCTTGCTCTTGT
Found at i:18809263 original size:22 final size:22
Alignment explanation
Indices: 18809221--18809263 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
18809211 AAAGTTCATA
*
18809221 TGAAAATTATACAAATAAATCC
1 TGAAAATTATACAAAGAAATCC
* *
18809243 TGAAAATTATTCAAAGGAATC
1 TGAAAATTATACAAAGAAATC
18809264 AACCTTAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.51, C:0.12, G:0.09, T:0.28
Consensus pattern (22 bp):
TGAAAATTATACAAAGAAATCC
Found at i:18814396 original size:28 final size:29
Alignment explanation
Indices: 18814353--18814419 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 29
18814343 ATGTCTATGG
* *
18814353 GTAATTTTTCAGTTTT-TGGGGTAAAAAT
1 GTAATTTTTCACTTTTAGGGGGTAAAAAT
* *
18814381 GTAATTTTTGACTTTTACGGGGGTAAAAGT
1 GTAATTTTTCACTTTTA-GGGGGTAAAAAT
*
18814411 GTAAATTTT
1 GTAATTTTT
18814420 AAAAATTACG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 14 0.44
30 18 0.56
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.45
Consensus pattern (29 bp):
GTAATTTTTCACTTTTAGGGGGTAAAAAT
Found at i:18822618 original size:12 final size:11
Alignment explanation
Indices: 18822594--18822650 Score: 50
Period size: 10 Copynumber: 5.4 Consensus size: 11
18822584 AAAATGAAAA
18822594 TATTTAAATAT
1 TATTTAAATAT
18822605 TATTT-AATA-
1 TATTTAAATAT
18822614 TA-TTAAATAT
1 TATTTAAATAT
**
18822624 TATAAAAGCATAT
1 TATTTAA--ATAT
18822637 TATTT-AATAT
1 TATTTAAATAT
18822647 TATT
1 TATT
18822651 ATTTGAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
8 2 0.05
9 6 0.16
10 14 0.38
11 7 0.19
12 1 0.03
13 7 0.19
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (11 bp):
TATTTAAATAT
Found at i:18822650 original size:42 final size:43
Alignment explanation
Indices: 18822594--18822695 Score: 118
Period size: 45 Copynumber: 2.3 Consensus size: 43
18822584 AAAATGAAAA
* * *
18822594 TATTTAAATATTATTT-AATATATTAAATATTATAAAAGCATAT
1 TATTTAAATATTATTTGAATATAATAAATATAAT-AAAGAATAT
*
18822637 TATTTAATATTATTATTTGAATATAATAAATGTAATAAAGAATAT
1 TATTTAA-A-TATTATTTGAATATAATAAATATAATAAAGAATAT
*
18822682 TATTT-ATTATTATT
1 TATTTAAATATTATT
18822696 ATTTAAATTG
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
42 7 0.14
43 7 0.14
44 2 0.04
45 21 0.41
46 14 0.27
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (43 bp):
TATTTAAATATTATTTGAATATAATAAATATAATAAAGAATAT
Found at i:18822792 original size:23 final size:22
Alignment explanation
Indices: 18822736--18822809 Score: 69
Period size: 23 Copynumber: 3.3 Consensus size: 22
18822726 TTTTAATATT
*
18822736 AAATATTATTTAATTATAAT-A
1 AAATATTATTAAATTATAATAA
* ** *
18822757 AAATGTTTAATTAGCTTCTAATATA
1 AAAT-ATT-ATTAAATTATAATA-A
18822782 AAATATTATTAAATTATAATAA
1 AAATATTATTAAATTATAATAA
18822804 AAATAT
1 AAATAT
18822810 GTTTGTATTT
Statistics
Matches: 40, Mismatches: 9, Indels: 7
0.71 0.16 0.12
Matches are distributed among these distances:
21 4 0.10
22 9 0.22
23 20 0.50
24 2 0.05
25 5 0.12
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (22 bp):
AAATATTATTAAATTATAATAA
Found at i:18824923 original size:20 final size:20
Alignment explanation
Indices: 18824876--18824912 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
18824866 TTACATTGTG
18824876 AAAA-AATAAAATTTTTTAT
1 AAAAGAATAAAATTTTTTAT
18824895 AAAAGAATAAAATTTTTT
1 AAAAGAATAAAATTTTTT
18824913 TTATACTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (20 bp):
AAAAGAATAAAATTTTTTAT
Found at i:18826010 original size:18 final size:17
Alignment explanation
Indices: 18825983--18826016 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
18825973 TGGTAGAAGG
*
18825983 AAGGGGAAGAAAAGAGGA
1 AAGGGAAAG-AAAGAGGA
18826001 AAGGGAAAGAAAGAGG
1 AAGGGAAAGAAAGAGG
18826017 GAGTTGTTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (17 bp):
AAGGGAAAGAAAGAGGA
Found at i:18837702 original size:2 final size:2
Alignment explanation
Indices: 18837695--18837781 Score: 119
Period size: 2 Copynumber: 45.0 Consensus size: 2
18837685 ATGTTTACTA
* *
18837695 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T GT AG A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18837735 AT AT NAT -T 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
18837777 -T AT AT
1 AT AT AT
18837782 TGTAGAATAT
Statistics
Matches: 78, Mismatches: 2, Indels: 10
0.87 0.02 0.11
Matches are distributed among these distances:
1 4 0.05
2 72 0.92
3 2 0.03
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18839650 original size:30 final size:30
Alignment explanation
Indices: 18839609--18839672 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
18839599 ATCAGTGTAA
*
18839609 AGAATGAGCAGTAAATTTATTCTTGTTTAT
1 AGAAGGAGCAGTAAATTTATTCTTGTTTAT
*
18839639 AGAAGGAGCAGTAAATTTATTGTTGTTTAT
1 AGAAGGAGCAGTAAATTTATTCTTGTTTAT
18839669 AGAA
1 AGAA
18839673 TAGTACAGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (30 bp):
AGAAGGAGCAGTAAATTTATTCTTGTTTAT
Found at i:18851297 original size:23 final size:22
Alignment explanation
Indices: 18851254--18851297 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
18851244 TATTAATTCC
* *
18851254 TAACATAACAAATACAGAACAA
1 TAACATAACAAATAAAAAACAA
*
18851276 TAACATGACCAAATAAAAAACA
1 TAACAT-AACAAATAAAAAACA
18851298 TTTACCAGCA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.64, C:0.18, G:0.05, T:0.14
Consensus pattern (22 bp):
TAACATAACAAATAAAAAACAA
Found at i:18858421 original size:27 final size:27
Alignment explanation
Indices: 18858391--18858443 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
18858381 AAGTTTTGGG
* *
18858391 CATGAACATGTTTTTTTTCTTTTAATA
1 CATGAACATGCTTCTTTTCTTTTAATA
* *
18858418 CATGAGCCTGCTTCTTTTCTTTTAAT
1 CATGAACATGCTTCTTTTCTTTTAAT
18858444 GAGTTTAGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.21, C:0.17, G:0.09, T:0.53
Consensus pattern (27 bp):
CATGAACATGCTTCTTTTCTTTTAATA
Found at i:18880890 original size:13 final size:13
Alignment explanation
Indices: 18880872--18880899 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
18880862 CAAAAATTAT
18880872 AACTTATAAAAAA
1 AACTTATAAAAAA
18880885 AACTTATAAAAAA
1 AACTTATAAAAAA
18880898 AA
1 AA
18880900 ATTTACCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.21
Consensus pattern (13 bp):
AACTTATAAAAAA
Found at i:18884110 original size:17 final size:17
Alignment explanation
Indices: 18884088--18884121 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
18884078 AATAAGTTAT
18884088 TTAATATATTATAAATA
1 TTAATATATTATAAATA
* *
18884105 TTAATATTTTGTAAATA
1 TTAATATATTATAAATA
18884122 AATTTAAAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TTAATATATTATAAATA
Found at i:18884841 original size:28 final size:28
Alignment explanation
Indices: 18884809--18884897 Score: 76
Period size: 28 Copynumber: 3.2 Consensus size: 28
18884799 TTAATTCTAA
18884809 GAATAACTTTACCCTATTAGGAGTGGAT
1 GAATAACTTTACCCTATTAGGAGTGGAT
** * *
18884837 GAAT-ACTTTTAATCTATCAGGAGTAGAT
1 GAATAAC-TTTACCCTATTAGGAGTGGAT
**
18884865 GAATATTTTTAACCC-ATTAGGAGTGTG-T
1 GAATAACTTT-ACCCTATTAGGAGTG-GAT
18884893 GAATA
1 GAATA
18884898 GTGGAAAGAT
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
27 2 0.04
28 42 0.89
29 3 0.06
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.35
Consensus pattern (28 bp):
GAATAACTTTACCCTATTAGGAGTGGAT
Found at i:18885172 original size:11 final size:11
Alignment explanation
Indices: 18885149--18885201 Score: 63
Period size: 11 Copynumber: 4.7 Consensus size: 11
18885139 TATCATGAAG
18885149 ATATTTTTA-T
1 ATATTTTTATT
18885159 ATATTTTTATT
1 ATATTTTTATT
**
18885170 ATATTTAAATGAT
1 ATATTTTTAT--T
18885183 ATATTTTTATT
1 ATATTTTTATT
18885194 ATATTTTT
1 ATATTTTT
18885202 TAGTTAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
10 9 0.25
11 18 0.50
13 9 0.25
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (11 bp):
ATATTTTTATT
Found at i:18885173 original size:13 final size:13
Alignment explanation
Indices: 18885155--18885203 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 13
18885145 GAAGATATTT
18885155 TTATATATTTTTA
1 TTATATATTTTTA
**
18885168 -T-TATATTTAAA
1 TTATATATTTTTA
*
18885179 TGATATATTTTTA
1 TTATATATTTTTA
18885192 TTATAT-TTTTTA
1 TTATATATTTTTA
18885204 GTTAATAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
11 8 0.29
12 7 0.25
13 13 0.46
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (13 bp):
TTATATATTTTTA
Found at i:18885213 original size:34 final size:34
Alignment explanation
Indices: 18885149--18885222 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
18885139 TATCATGAAG
* *
18885149 ATATTTTTATATATTTTTATTATATTTAAATGAT
1 ATATTTTTATATATTTTTAGTATATATAAATGAT
*
18885183 ATATTTTTATTATATTTTTTAGT-TA-ATAAATTAT
1 ATATTTTTA-TATA-TTTTTAGTATATATAAATGAT
18885217 ATATTT
1 ATATTT
18885223 AATATTCTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
34 22 0.63
35 6 0.17
36 7 0.20
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (34 bp):
ATATTTTTATATATTTTTAGTATATATAAATGAT
Found at i:18891272 original size:22 final size:22
Alignment explanation
Indices: 18891244--18891285 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
18891234 TGCAACCATG
*
18891244 AACTTTGACAGTTCAATAGTGC
1 AACTTTGACAATTCAATAGTGC
18891266 AACTTTGACAATTCAATAGT
1 AACTTTGACAATTCAATAGT
18891286 CAAGGGGGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (22 bp):
AACTTTGACAATTCAATAGTGC
Found at i:18892001 original size:85 final size:85
Alignment explanation
Indices: 18891856--18892087 Score: 356
Period size: 85 Copynumber: 2.7 Consensus size: 85
18891846 TTCAAATAGC
* * * * *
18891856 TTAATATTTAGAATTATAGTTTAGATATTCAATTAAAACGATTGGCAATATACTAGAATTAAACA
1 TTAATGTTTAGAATTATTGTTTGGATATTCAATTAAAATGATTGGCAATATGCTAGAATTAAACA
18891921 TTAAGAATTATGTTTGGGAA
66 TTAAGAATTATGTTTGGGAA
* * *
18891941 TTAATGTTTAGAATTATTGTTTGGATATTCAATTAAAATGATTAGCAATATGCTATAATTAAATA
1 TTAATGTTTAGAATTATTGTTTGGATATTCAATTAAAATGATTGGCAATATGCTAGAATTAAACA
*
18892006 TTAAGAATTATGTTTTGGAA
66 TTAAGAATTATGTTTGGGAA
* * *
18892026 TTAATGTTTAAAATTATTATTTGGATATTCAATTAAAATGATTGGCAATATGTTAGAATTAA
1 TTAATGTTTAGAATTATTGTTTGGATATTCAATTAAAATGATTGGCAATATGCTAGAATTAA
18892088 TGATTACAGT
Statistics
Matches: 133, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
85 133 1.00
ACGTcount: A:0.41, C:0.04, G:0.14, T:0.41
Consensus pattern (85 bp):
TTAATGTTTAGAATTATTGTTTGGATATTCAATTAAAATGATTGGCAATATGCTAGAATTAAACA
TTAAGAATTATGTTTGGGAA
Found at i:18894727 original size:25 final size:25
Alignment explanation
Indices: 18894699--18894752 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
18894689 CTTTTGAAAC
* *
18894699 TAATGTTTGTTTATTATATAAAGAT
1 TAATGTTTATTTATTACATAAAGAT
*
18894724 TAATGTTTATTTATTACATGAAGAT
1 TAATGTTTATTTATTACATAAAGAT
18894749 TAAT
1 TAAT
18894753 ATTATTAGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.02, G:0.11, T:0.50
Consensus pattern (25 bp):
TAATGTTTATTTATTACATAAAGAT
Found at i:18907203 original size:42 final size:43
Alignment explanation
Indices: 18907151--18907231 Score: 128
Period size: 42 Copynumber: 1.9 Consensus size: 43
18907141 TATATTTGAT
*
18907151 TCTTAATAATCCAAAAACTGATTGACTATGGTC-TCACTTCAA
1 TCTTAATAATCCAAAAACTGATTGACTATAGTCTTCACTTCAA
* *
18907193 TCTTTATAATCCAGAAACTGATTGACTATAGTCTTCACT
1 TCTTAATAATCCAAAAACTGATTGACTATAGTCTTCACT
18907232 CCAAATAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 30 0.86
43 5 0.14
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (43 bp):
TCTTAATAATCCAAAAACTGATTGACTATAGTCTTCACTTCAA
Found at i:18912176 original size:23 final size:22
Alignment explanation
Indices: 18912150--18912193 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
18912140 TGAAACAGAG
18912150 ATCAAAATAAATAAAACCCTAAA
1 ATCAAAATAAA-AAAACCCTAAA
* *
18912173 ATCAAAATTAAGAAACCCTAA
1 ATCAAAATAAAAAAACCCTAA
18912194 GATGCAGACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.61, C:0.18, G:0.02, T:0.18
Consensus pattern (22 bp):
ATCAAAATAAAAAAACCCTAAA
Found at i:18916845 original size:105 final size:104
Alignment explanation
Indices: 18916584--18916846 Score: 292
Period size: 105 Copynumber: 2.5 Consensus size: 104
18916574 AAAAGAAAAG
* *
18916584 TCATTTTTGAGCTATAAGCTTTATCGCTCTTACTTTGGCTGTAATGTTATTATTGCACTTGGTCA
1 TCATTTTT-AGCTATAAGCTTTATCGCTCTTACTGTGGCTGTAATGTTATTATTGCACTTAGTCA
* * *
18916649 TAGGCTTTATCGCTCATTCTTTGACCATATAATTCATCAC
65 TAAGCTTTATCACTCATTCTTTGACCACATAATTCATCAC
* * *** * * * * * * * *
18916689 TTATATTTCAGCCGCAAGCTTTATTGCTTTTACTGTAGCTATGACGTTATTATTGCATTTAGTCG
1 TCAT-TTTTAGCTATAAGCTTTATCGCTCTTACTGTGGCTGTAATGTTATTATTGCACTTAGTCA
18916754 TAAGCTTTATCACTCATTCTTTGACCACATAATTCATCAC
65 TAAGCTTTATCACTCATTCTTTGACCACATAATTCATCAC
* * * * *
18916794 TCATGTTTTAGCTATAAACTTTAACGCTCATAATGTGGCTGTAATGATATTAT
1 TCAT-TTTTAGCTATAAGCTTTATCGCTCTTACTGTGGCTGTAATGTTATTAT
18916847 GCTATTGGCC
Statistics
Matches: 122, Mismatches: 35, Indels: 2
0.77 0.22 0.01
Matches are distributed among these distances:
105 119 0.98
106 3 0.02
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.43
Consensus pattern (104 bp):
TCATTTTTAGCTATAAGCTTTATCGCTCTTACTGTGGCTGTAATGTTATTATTGCACTTAGTCAT
AAGCTTTATCACTCATTCTTTGACCACATAATTCATCAC
Found at i:18918141 original size:3 final size:3
Alignment explanation
Indices: 18918133--18918167 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
18918123 TATGTTGCAA
18918133 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
18918168 ATTAAATCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:18918653 original size:26 final size:26
Alignment explanation
Indices: 18918624--18918693 Score: 86
Period size: 27 Copynumber: 2.7 Consensus size: 26
18918614 GCACGGAAGC
*
18918624 GCCCAGGGCGTTCCAAGTGTAGAAAT
1 GCCCAGGGCGTTCCAAGTGTAGAAAA
* *
18918650 GCCCAAGGGAGTTCCAAGTGTGGAAAA
1 GCCC-AGGGCGTTCCAAGTGTAGAAAA
* *
18918677 GCCCAGAGCATTCCAAG
1 GCCCAGGGCGTTCCAAG
18918694 CTCGGAGCCA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
26 14 0.38
27 23 0.62
ACGTcount: A:0.30, C:0.24, G:0.30, T:0.16
Consensus pattern (26 bp):
GCCCAGGGCGTTCCAAGTGTAGAAAA
Found at i:18923455 original size:19 final size:19
Alignment explanation
Indices: 18923428--18923465 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
18923418 CCATTTGACT
18923428 TATTAGAGTATGATTTGAG
1 TATTAGAGTATGATTTGAG
*
18923447 TATTGGAGTATGATTTGAG
1 TATTAGAGTATGATTTGAG
18923466 GTTAAGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTAGAGTATGATTTGAG
Found at i:18926319 original size:46 final size:46
Alignment explanation
Indices: 18926252--18926343 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
18926242 ATCATTTGGG
*
18926252 GTAATGAATCCTCTTTTAAGTACTCATTCACTTTCGCATGCTTCAT
1 GTAATGAATCCTCTCTTAAGTACTCATTCACTTTCGCATGCTTCAT
*
18926298 GTAATGAATCCTCTCTTAAGTACTCATTCATTTTCGCATGCTTCAT
1 GTAATGAATCCTCTCTTAAGTACTCATTCACTTTCGCATGCTTCAT
18926344 ACCATACCTA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.41
Consensus pattern (46 bp):
GTAATGAATCCTCTCTTAAGTACTCATTCACTTTCGCATGCTTCAT
Found at i:18927004 original size:18 final size:18
Alignment explanation
Indices: 18926959--18927015 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
18926949 TAACATAAGT
* *
18926959 AACATGATTAAAATTTTA
1 AACATGATTAATATATTA
**
18926977 AACAAAATTAATATATTA
1 AACATGATTAATATATTA
18926995 AACATGATTAATATGATTA
1 AACATGATTAATAT-ATTA
18927014 AA
1 AA
18927016 TTAAAATGTA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 26 0.81
19 6 0.19
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.35
Consensus pattern (18 bp):
AACATGATTAATATATTA
Found at i:18932051 original size:19 final size:19
Alignment explanation
Indices: 18932005--18932077 Score: 58
Period size: 19 Copynumber: 3.9 Consensus size: 19
18931995 ATCAGAAAAT
* *
18932005 AAAAATATATT-AACATAA
1 AAAAATACATTAAATATAA
* *
18932023 ATAAAGACATTAAATATAA
1 AAAAATACATTAAATATAA
* *
18932042 AAAAATACATTGAATATCA
1 AAAAATACATTAAATATAA
** *
18932061 TTAAATACAATAAATAT
1 AAAAATACATTAAATAT
18932078 CCACATATTT
Statistics
Matches: 42, Mismatches: 12, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
18 8 0.19
19 34 0.81
ACGTcount: A:0.62, C:0.07, G:0.03, T:0.29
Consensus pattern (19 bp):
AAAAATACATTAAATATAA
Found at i:18941720 original size:31 final size:29
Alignment explanation
Indices: 18941682--18941752 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
18941672 CTAGTTATTA
18941682 TGGATATTCAATATATCTTGCTTAGCTACTG
1 TGGATATT--ATATATCTTGCTTAGCTACTG
* * *
18941713 TGGATATTGTATATCTTGTTTAGTTACTG
1 TGGATATTATATATCTTGCTTAGCTACTG
* *
18941742 TAGATGTTATA
1 TGGATATTATA
18941753 AATATTTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 26 0.76
31 8 0.24
ACGTcount: A:0.25, C:0.10, G:0.18, T:0.46
Consensus pattern (29 bp):
TGGATATTATATATCTTGCTTAGCTACTG
Found at i:18947871 original size:86 final size:85
Alignment explanation
Indices: 18947769--18947978 Score: 233
Period size: 86 Copynumber: 2.5 Consensus size: 85
18947759 TAGAAATAGA
* * * * *
18947769 AAATCATGTTTTTTGATATATTAAATAGAAAATCATATTTTTGAAATTAAAAAGATAGTCTTCCA
1 AAATTATGTCTTTTGATATATTAAATAGAAAATCATATTTTTGAAAATAAAAAGATAGCCTTCAA
18947834 TTTGTTTCTAAAAAAAAAAAT
66 TTTGTTTC-AAAAAAAAAAAT
* * * * *
18947855 AAGTTATGTCTTTTGATATATGAAAT-GTAAAATCATATTTTTGAAAATAGAATGATGGCCTTCA
1 AAATTATGTCTTTTGATATATTAAATAG-AAAATCATATTTTTGAAAATAAAAAGATAGCCTTCA
* * **
18947919 ATTTTTTTCCAAAAAAAATGT
65 ATTTGTTTCAAAAAAAAAAAT
* * * *
18947940 AAATTACGTCTTTTGATAGATTAAATACAAATTCATATT
1 AAATTATGTCTTTTGATATATTAAATAGAAAATCATATT
18947979 ACCTTTTAAA
Statistics
Matches: 102, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
85 42 0.41
86 60 0.59
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (85 bp):
AAATTATGTCTTTTGATATATTAAATAGAAAATCATATTTTTGAAAATAAAAAGATAGCCTTCAA
TTTGTTTCAAAAAAAAAAAT
Found at i:18953016 original size:35 final size:36
Alignment explanation
Indices: 18952966--18953047 Score: 121
Period size: 35 Copynumber: 2.3 Consensus size: 36
18952956 GACTATGGAT
* *
18952966 GGCTGAGAGAGAGGGGAAGACCCACGGGTGAG-AGC
1 GGCTGAGAGAAAGGGGAAGACCCACGGCTGAGAAGC
*
18953001 GGTTGAGAGAAAGGGGAAGACCCACGGCTGAGATAGC
1 GGCTGAGAGAAAGGGGAAGACCCACGGCTGAGA-AGC
18953038 GGCTGAGAGA
1 GGCTGAGAGA
18953048 GAGGAAAAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 29 0.71
37 12 0.29
ACGTcount: A:0.30, C:0.16, G:0.45, T:0.09
Consensus pattern (36 bp):
GGCTGAGAGAAAGGGGAAGACCCACGGCTGAGAAGC
Found at i:18953092 original size:33 final size:33
Alignment explanation
Indices: 18953055--18953149 Score: 129
Period size: 32 Copynumber: 2.9 Consensus size: 33
18953045 AGAGAGGAAA
* *
18953055 AAGACCAGTTGAGAGAGGAGGGGAAGACGGGGG
1 AAGACCGGTTGAGAGAGGAGAGGAAGACGGGGG
* *
18953088 AAGACCGGTTGAGAGAGGAGATGTAGAC-GGGG
1 AAGACCGGTTGAGAGAGGAGAGGAAGACGGGGG
* *
18953120 AAGGCCGGCTGAGAGAGGAGAGGAAGACGG
1 AAGACCGGTTGAGAGAGGAGAGGAAGACGG
18953150 TCAAAGATTG
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
32 28 0.53
33 25 0.47
ACGTcount: A:0.33, C:0.11, G:0.49, T:0.07
Consensus pattern (33 bp):
AAGACCGGTTGAGAGAGGAGAGGAAGACGGGGG
Found at i:18954406 original size:32 final size:32
Alignment explanation
Indices: 18954365--18954432 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
18954355 GTTGTCGAAA
18954365 AAGATTGACATTACAACAATAATACTAATAAT
1 AAGATTGACATTACAACAATAATACTAATAAT
18954397 AAGATTGACATTACAACAATAATACTAATAAT
1 AAGATTGACATTACAACAATAATACTAATAAT
18954429 AAGA
1 AAGA
18954433 ATAAAAAAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.54, C:0.12, G:0.07, T:0.26
Consensus pattern (32 bp):
AAGATTGACATTACAACAATAATACTAATAAT
Found at i:18957080 original size:12 final size:12
Alignment explanation
Indices: 18957063--18957097 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
18957053 TCCTTTTTTT
18957063 AATTAATAAAAA
1 AATTAATAAAAA
*
18957075 AATTAATTAAAA
1 AATTAATAAAAA
18957087 AA-TAATAAAAA
1 AATTAATAAAAA
18957098 TTATATGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 8 0.38
12 13 0.62
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
AATTAATAAAAA
Found at i:18964837 original size:34 final size:34
Alignment explanation
Indices: 18964799--18964869 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
18964789 CTATTATGTA
18964799 CAAGATAATATCAAAGATAATTACAATGAAGGTT
1 CAAGATAATATCAAAGATAATTACAATGAAGGTT
*
18964833 CAAGATAATATCAAAGATTATTACAATGAAGGTT
1 CAAGATAATATCAAAGATAATTACAATGAAGGTT
18964867 CAA
1 CAA
18964870 ATGATATGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (34 bp):
CAAGATAATATCAAAGATAATTACAATGAAGGTT
Found at i:18967469 original size:6 final size:7
Alignment explanation
Indices: 18967443--18967482 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
18967433 TCTAGCTACA
18967443 CGCCCCC
1 CGCCCCC
*
18967450 CACCCCC
1 CGCCCCC
*
18967457 GGCCCCC
1 CGCCCCC
18967464 CGCCCCC
1 CGCCCCC
18967471 CGCCCCC
1 CGCCCCC
*
18967478 GGCCC
1 CGCCC
18967483 AGCTTTCCTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.03, C:0.80, G:0.17, T:0.00
Consensus pattern (7 bp):
CGCCCCC
Found at i:18967469 original size:21 final size:21
Alignment explanation
Indices: 18967443--18967482 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
18967433 TCTAGCTACA
18967443 CGCCCCCCACCCCCGGCCCCC
1 CGCCCCCCACCCCCGGCCCCC
*
18967464 CGCCCCCCGCCCCCGGCCC
1 CGCCCCCCACCCCCGGCCC
18967483 AGCTTTCCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.03, C:0.80, G:0.17, T:0.00
Consensus pattern (21 bp):
CGCCCCCCACCCCCGGCCCCC
Found at i:18978163 original size:18 final size:18
Alignment explanation
Indices: 18978125--18978166 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
18978115 GATTTTCTAG
18978125 AAAAAAGAGAGAATAAAT
1 AAAAAAGAGAGAATAAAT
18978143 AAAAATAGAG-GAA-AAATT
1 AAAAA-AGAGAGAATAAA-T
18978161 AAAAAA
1 AAAAAA
18978167 ATCAAATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 4 0.18
18 14 0.64
19 4 0.18
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (18 bp):
AAAAAAGAGAGAATAAAT
Found at i:18986312 original size:13 final size:13
Alignment explanation
Indices: 18986294--18986318 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18986284 TTTCAGAAAA
18986294 TTTATAAAATCAT
1 TTTATAAAATCAT
18986307 TTTATAAAATCA
1 TTTATAAAATCA
18986319 CAATTTCCCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:18987205 original size:30 final size:31
Alignment explanation
Indices: 18987150--18987208 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
18987140 CTTAATAGAA
18987150 AAAATCTCACCTTTTTCACTTAATTTTCTTG
1 AAAATCTCACCTTTTTCACTTAATTTTCTTG
*
18987181 AAAAT-TCACACTTTTTC-TTTAATTTTCT
1 AAAATCTCAC-CTTTTTCACTTAATTTTCT
18987209 CTCTCTAGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 14 0.54
31 12 0.46
ACGTcount: A:0.27, C:0.20, G:0.02, T:0.51
Consensus pattern (31 bp):
AAAATCTCACCTTTTTCACTTAATTTTCTTG
Found at i:18987516 original size:27 final size:28
Alignment explanation
Indices: 18987459--18987516 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
18987449 GGAAAAATGT
*
18987459 CCTGGTGGTGGAAAATTACAATTTTGCC
1 CCTGGTGGTGGAAAATTACAATTTTGAC
*
18987487 CCTGG-GGTGGTAAAATTACCATTTT-AC
1 CCTGGTGGTGG-AAAATTACAATTTTGAC
18987514 CCT
1 CCT
18987517 TTTACTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 9 0.33
28 18 0.67
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (28 bp):
CCTGGTGGTGGAAAATTACAATTTTGAC
Found at i:18987587 original size:20 final size:20
Alignment explanation
Indices: 18987570--18987607 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
18987560 CCTCAAATCT
18987570 TACTCCAATAAGTCAAATTA
1 TACTCCAATAAGTCAAATTA
18987590 TACTCCAATAAGTCAAAT
1 TACTCCAATAAGTCAAAT
18987608 GGGGCCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (20 bp):
TACTCCAATAAGTCAAATTA
Found at i:18988072 original size:19 final size:19
Alignment explanation
Indices: 18988008--18988059 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
18987998 TTAATATTTT
18988008 AATATTATTTTATTAATAA
1 AATATTATTTTATTAATAA
18988027 AATATTATTTTATTAATAA
1 AATATTATTTTATTAATAA
18988046 AATATTATTTTATT
1 AATATTATTTTATT
18988060 CTAAAACTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
AATATTATTTTATTAATAA
Found at i:18997066 original size:26 final size:27
Alignment explanation
Indices: 18997037--18997093 Score: 98
Period size: 26 Copynumber: 2.1 Consensus size: 27
18997027 GTATTATCTC
18997037 CAAATTATTCTTTGTTGTATCATTT-A
1 CAAATTATTCTTTGTTGTATCATTTAA
*
18997063 CAAATTATTCTTTTTTGTATCATTTAA
1 CAAATTATTCTTTGTTGTATCATTTAA
18997090 CAAA
1 CAAA
18997094 AAGAAAGGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 24 0.83
27 5 0.17
ACGTcount: A:0.32, C:0.12, G:0.05, T:0.51
Consensus pattern (27 bp):
CAAATTATTCTTTGTTGTATCATTTAA
Found at i:18997438 original size:23 final size:23
Alignment explanation
Indices: 18997412--18997525 Score: 138
Period size: 23 Copynumber: 5.0 Consensus size: 23
18997402 TGGTGTGTAT
*
18997412 GAATCACATGATTATTTGATATG
1 GAATCACATGACTATTTGATATG
* *
18997435 GAATCGCATGACTAGTTGATATG
1 GAATCACATGACTATTTGATATG
* *
18997458 GAATCGCGTGACTATTTGATATG
1 GAATCACATGACTATTTGATATG
** ** *
18997481 GAATCAGGTGACTAGCTAATATG
1 GAATCACATGACTATTTGATATG
18997504 GAATCACATGACTATTTGATAT
1 GAATCACATGACTATTTGATAT
18997526 AGTATTGTGG
Statistics
Matches: 76, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 76 1.00
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.33
Consensus pattern (23 bp):
GAATCACATGACTATTTGATATG
Found at i:18997474 original size:46 final size:46
Alignment explanation
Indices: 18997412--18997525 Score: 158
Period size: 46 Copynumber: 2.5 Consensus size: 46
18997402 TGGTGTGTAT
* * *
18997412 GAATCACATGATTATTTGATATGGAATC-GCATGACTAGTTGATATG
1 GAATCACATGACTATTTGATATGGAATCAG-ATGACTAGCTAATATG
* * *
18997458 GAATCGCGTGACTATTTGATATGGAATCAGGTGACTAGCTAATATG
1 GAATCACATGACTATTTGATATGGAATCAGATGACTAGCTAATATG
18997504 GAATCACATGACTATTTGATAT
1 GAATCACATGACTATTTGATAT
18997526 AGTATTGTGG
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
46 58 0.98
47 1 0.02
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.33
Consensus pattern (46 bp):
GAATCACATGACTATTTGATATGGAATCAGATGACTAGCTAATATG
Found at i:18999672 original size:211 final size:210
Alignment explanation
Indices: 18999354--18999859 Score: 681
Period size: 211 Copynumber: 2.4 Consensus size: 210
18999344 GTCACGCATC
**
18999354 GCCAGTCTCGCAATTTCTAATAATAAGTCACCCAATGCCTAATATCCACTCACGTTATGCCAAAA
1 GCCAGTCTCGCAATACCTAATAATAAGTCACCCAATGCCTAATATCCACTCACGTTATGCCAAAA
* * * * * *
18999419 TAATCAGTCATGTATTGGCCCAACGTCATGCAATACATAACAAGAAATCATGGAATACATAACAA
66 TAACCAGTCACGTATGGGCCCAACGTCACGCAATACATAACAACAAACCATGGAATACATAACAA
* * *
18999484 CCAGTCAAGCAATGCCTAAAAAGTAATCAAGAAATGTCTCAAAATACGATATGCATTGCATAATT
131 CCAGTCAACCAATGCCT-AAAAGTAATCAAGAAATGTCTCAAAATAAGATATGCATTGCACAATT
* * *
18999549 CACGCAATGCTTGTAA
195 CACGCAACGCCTATAA
* * * * * *
18999565 GTCAGTCTCGCAATACCTAATAATAAGTTACTCATTGTCTAATATCCACTCACGTTATACCAAAA
1 GCCAGTCTCGCAATACCTAATAATAAGTCACCCAATGCCTAATATCCACTCACGTTATGCCAAAA
* * * * *
18999630 TAACCAATCACGTATGGGCCTAATGTCACGCAATATATAACAACAAGCCATGGAATACATAACAA
66 TAACCAGTCACGTATGGGCCCAACGTCACGCAATACATAACAACAAACCATGGAATACATAACAA
* * *
18999695 TCAGTCATCCAATGCCTAAAAGTAGTCAAGAAATGTCTCAAAATAAGATATGCATTGCACAATTC
131 CCAGTCAACCAATGCCTAAAAGTAATCAAGAAATGTCTCAAAATAAGATATGCATTGCACAATTC
18999760 ACGCAACGCCTATAA
196 ACGCAACGCCTATAA
* ** * *
18999775 GCCAATCTCATAATACCTAATAATAAGTCACGCAATGCCTAATATCTACTCACGTTATGCCAAAA
1 GCCAGTCTCGCAATACCTAATAATAAGTCACCCAATGCCTAATATCCACTCACGTTATGCCAAAA
* *
18999840 T-ACCAGTCACGCATTGGCCC
66 TAACCAGTCACGTATGGGCCC
18999860 TATGTAACAT
Statistics
Matches: 253, Mismatches: 42, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
209 15 0.06
210 113 0.45
211 125 0.49
ACGTcount: A:0.39, C:0.24, G:0.13, T:0.25
Consensus pattern (210 bp):
GCCAGTCTCGCAATACCTAATAATAAGTCACCCAATGCCTAATATCCACTCACGTTATGCCAAAA
TAACCAGTCACGTATGGGCCCAACGTCACGCAATACATAACAACAAACCATGGAATACATAACAA
CCAGTCAACCAATGCCTAAAAGTAATCAAGAAATGTCTCAAAATAAGATATGCATTGCACAATTC
ACGCAACGCCTATAA
Found at i:18999819 original size:210 final size:211
Alignment explanation
Indices: 18999370--18999859 Score: 669
Period size: 210 Copynumber: 2.3 Consensus size: 211
18999360 CTCGCAATTT
* * *
18999370 CTAATAATAAGTCACCCAATGCCTAATATCCACTCACGTTATGCCAAAATAATCAGTCATGTATT
1 CTAATAATAAGTCACCCAATGCCTAATATCCACTCACGTTATGCCAAAATAACCAGTCACGTATG
* * * *
18999435 GGCCCAACGTCATGCAATACATAACAAGAAATCATGGAATACATAACAACCAGTCAAGCAATGCC
66 GGCCCAACGTCACGCAATACATAACAACAAACCATGGAATACATAACAACCAGTCAACCAATGCC
* * * * *
18999500 TAAAAAGTAATCAAGAAATGTCTCAAAATACGATATGCATTGCATAATTCACGCAATGCTTGTAA
131 TAAAAAGTAATCAAGAAATGTCTCAAAATAAGATATGCATTGCACAATTCACGCAACGCCTATAA
* * *
18999565 GTCAGTCTCGCAATAC
196 GCCAATCTCACAATAC
* * * * * *
18999581 CTAATAATAAGTTACTCATTGTCTAATATCCACTCACGTTATACCAAAATAACCAATCACGTATG
1 CTAATAATAAGTCACCCAATGCCTAATATCCACTCACGTTATGCCAAAATAACCAGTCACGTATG
* * * * * *
18999646 GGCCTAATGTCACGCAATATATAACAACAAGCCATGGAATACATAACAATCAGTCATCCAATGCC
66 GGCCCAACGTCACGCAATACATAACAACAAACCATGGAATACATAACAACCAGTCAACCAATGCC
*
18999711 T-AAAAGTAGTCAAGAAATGTCTCAAAATAAGATATGCATTGCACAATTCACGCAACGCCTATAA
131 TAAAAAGTAATCAAGAAATGTCTCAAAATAAGATATGCATTGCACAATTCACGCAACGCCTATAA
*
18999775 GCCAATCTCATAATAC
196 GCCAATCTCACAATAC
* * * *
18999791 CTAATAATAAGTCACGCAATGCCTAATATCTACTCACGTTATGCCAAAAT-ACCAGTCACGCATT
1 CTAATAATAAGTCACCCAATGCCTAATATCCACTCACGTTATGCCAAAATAACCAGTCACGTATG
18999855 GGCCC
66 GGCCC
18999860 TATGTAACAT
Statistics
Matches: 240, Mismatches: 39, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
209 15 0.06
210 113 0.47
211 112 0.47
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.24
Consensus pattern (211 bp):
CTAATAATAAGTCACCCAATGCCTAATATCCACTCACGTTATGCCAAAATAACCAGTCACGTATG
GGCCCAACGTCACGCAATACATAACAACAAACCATGGAATACATAACAACCAGTCAACCAATGCC
TAAAAAGTAATCAAGAAATGTCTCAAAATAAGATATGCATTGCACAATTCACGCAACGCCTATAA
GCCAATCTCACAATAC
Found at i:18999950 original size:210 final size:207
Alignment explanation
Indices: 18999370--18999922 Score: 621
Period size: 210 Copynumber: 2.6 Consensus size: 207
18999360 CTCGCAATTT
* *
18999370 CTAATAATAAGTCACCCAATGCCTAATATCCACTCACGTTATGCCAAAATAATCAGTCATGTATT
1 CTAATAATAAGTCACCCAATGCCTAATATCCACTCACGTTATGCCAAAATAACCAGTCACGTATT
* * * *
18999435 GGCCCAACGT-CATGCAATACATAACAAGAAATCATGGAATACATAACAACCAGTCA-AGCAATG
66 GGCCCTATGTACAT--AATACATAACAA-CAGTCATGGAATACATAACAACCAGTCACA-CAATG
* * * * *
18999498 CCTAAAAAGTAATCAAGAAATGTCTCAAAATACGATATGCATTGCATAATTCACGCAATGCTTGT
127 CCT-AAAA-TAATCAAGAAATGTCTCAAAATAAGATATGCATTGCACAATTCACGCAACGCCTAT
* * *
18999563 AAGTCAGTCTCGCAATAC
190 AAGCCAATCTCACAATAC
* * * * * *
18999581 CTAATAATAAGTTACTCATTGTCTAATATCCACTCACGTTATACCAAAATAACCAATCACGTA-T
1 CTAATAATAAGTCACCCAATGCCTAATATCCACTCACGTTATGCCAAAATAACCAGTCACGTATT
* ** * * *
18999645 GGGCCTAATGTCACGCAATATATAACAACAAGCCATGGAATACATAACAATCAGTCATC-CAATG
66 GGCCCT-ATGT-ACATAATACATAACAAC-AGTCATGGAATACATAACAACCAGTCA-CACAATG
*
18999709 CCTAAAAGTAGTCAAGAAATGTCTCAAAATAAGATATGCATTGCACAATTCACGCAACGCCTATA
127 CCTAAAA-TAATCAAGAAATGTCTCAAAATAAGATATGCATTGCACAATTCACGCAACGCCTATA
*
18999774 AGCCAATCTCATAATAC
191 AGCCAATCTCACAATAC
* * *
18999791 CTAATAATAAGTCACGCAATGCCTAATATCTACTCACGTTATGCCAAAAT-ACCAGTCACGCATT
1 CTAATAATAAGTCACCCAATGCCTAATATCCACTCACGTTATGCCAAAATAACCAGTCACGTATT
* * * ** *
18999855 GGCCCTATGTAACATAATACATAAAAATCAGTCACGAAATACATAACAACCAAACACATAATGCC
66 GGCCCTATGT-ACATAATACATAACAA-CAGTCATGGAATACATAACAACCAGTCACACAATGCC
18999920 TAA
129 TAA
18999923 TATCCATTCA
Statistics
Matches: 284, Mismatches: 49, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
208 1 0.00
209 56 0.20
210 125 0.44
211 101 0.36
213 1 0.00
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.24
Consensus pattern (207 bp):
CTAATAATAAGTCACCCAATGCCTAATATCCACTCACGTTATGCCAAAATAACCAGTCACGTATT
GGCCCTATGTACATAATACATAACAACAGTCATGGAATACATAACAACCAGTCACACAATGCCTA
AAATAATCAAGAAATGTCTCAAAATAAGATATGCATTGCACAATTCACGCAACGCCTATAAGCCA
ATCTCACAATAC
Found at i:19000846 original size:22 final size:21
Alignment explanation
Indices: 19000821--19000880 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 21
19000811 TCTTAATAAT
19000821 CAGTCATGCAATGCCTAATATC
1 CAGTCA-GCAATGCCTAATATC
19000843 CAGTCA-CACA--CCTTAATATC
1 CAGTCAGCA-ATGCC-TAATATC
*
19000863 CAGTGACGCAATGCCTAA
1 CAGTCA-GCAATGCCTAA
19000881 CAAATATTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 12
0.70 0.02 0.27
Matches are distributed among these distances:
19 2 0.06
20 14 0.45
21 2 0.06
22 11 0.35
23 2 0.06
ACGTcount: A:0.33, C:0.30, G:0.13, T:0.23
Consensus pattern (21 bp):
CAGTCAGCAATGCCTAATATC
Found at i:19001140 original size:38 final size:38
Alignment explanation
Indices: 19001068--19001141 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
19001058 GTTAGATAAC
* * *
19001068 GATATAAACCTCGATGGCATTGGAGAGTTTGATGGCTA
1 GATATAAACCTCGATGGCATTGGAAAGCTAGATGGCTA
*
19001106 GATATAGACCTCGATGGCATTGGAAAGCTAGATGGC
1 GATATAAACCTCGATGGCATTGGAAAGCTAGATGGC
19001142 GTGATAGCTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.26
Consensus pattern (38 bp):
GATATAAACCTCGATGGCATTGGAAAGCTAGATGGCTA
Found at i:19009846 original size:21 final size:21
Alignment explanation
Indices: 19009803--19009860 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
19009793 TAAAATTATT
*
19009803 AATATTTGAATTAT-AAT-AG
1 AATATTTAAATTATAAATAAG
19009822 --TATTTAAATTATAAATAAG
1 AATATTTAAATTATAAATAAG
*
19009841 AATA-TTAATATTTTAAATAA
1 AATATTTAA-ATTATAAATAA
19009861 ATTATTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
17 11 0.34
18 3 0.09
19 2 0.06
20 4 0.12
21 12 0.38
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (21 bp):
AATATTTAAATTATAAATAAG
Found at i:19012903 original size:17 final size:16
Alignment explanation
Indices: 19012881--19012914 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
19012871 GTTATTTTGC
*
19012881 TTTAAGTTTAGTTATTA
1 TTTAAGTTAAGTT-TTA
19012898 TTTAAGTTAAGTTTTA
1 TTTAAGTTAAGTTTTA
19012914 T
1 T
19012915 GTTTTTGTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (16 bp):
TTTAAGTTAAGTTTTA
Found at i:19016271 original size:3 final size:3
Alignment explanation
Indices: 19016263--19016332 Score: 86
Period size: 3 Copynumber: 23.3 Consensus size: 3
19016253 ATCACAACTA
* * * * *
19016263 AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAC AAC AAC AAC AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
19016311 AAT AAC AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
19016333 CATTCCAAGA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (3 bp):
AAT
Found at i:19018093 original size:44 final size:43
Alignment explanation
Indices: 19018028--19018115 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 43
19018018 TTACTTCGAT
* *
19018028 ATTTTTTTCTTTTAGCATTCAGTGATACTTGATAAAGTTTAAC
1 ATTTATTTCTTTTAGCATTCAGTGATACTTGATAAAGTTCAAC
19018071 ATTTATTTCTTTTTAGCATTCAGTGATACTTGATAAAGTTCAAC
1 ATTTATTTC-TTTTAGCATTCAGTGATACTTGATAAAGTTCAAC
19018115 A
1 A
19018116 AGATGTTTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
43 8 0.19
44 34 0.81
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.47
Consensus pattern (43 bp):
ATTTATTTCTTTTAGCATTCAGTGATACTTGATAAAGTTCAAC
Found at i:19018349 original size:28 final size:30
Alignment explanation
Indices: 19018274--19018353 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
19018264 CAATTTCTAA
* * *
19018274 TAGGTTAAAAACTATTCATCTACTTCTAGT
1 TAGGTTAAAAACTATTTATCCACTTCTAGC
*
19018304 TAGGTTAAAAAGTATTTATCCACTTCT-GC
1 TAGGTTAAAAACTATTTATCCACTTCTAGC
*
19018333 TAGGTT-AAAATTATTTATCCA
1 TAGGTTAAAAACTATTTATCCA
19018354 TGTCTAGTGG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
28 14 0.31
29 7 0.16
30 24 0.53
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (30 bp):
TAGGTTAAAAACTATTTATCCACTTCTAGC
Found at i:19029328 original size:6 final size:6
Alignment explanation
Indices: 19029310--19029368 Score: 56
Period size: 6 Copynumber: 10.5 Consensus size: 6
19029300 TTCTCTCATT
* *
19029310 AAATTA AAA-TA AATTTA AAATTA AAAGTA AAA--A AAATTA AAA--A
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
19029353 AAATTAA AAATTA AAA
1 AAATT-A AAATTA AAA
19029369 GATTTAAGTT
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
4 8 0.18
5 4 0.09
6 26 0.59
7 6 0.14
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (6 bp):
AAATTA
Done.