Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold273
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: 1282806
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 5 of 9
Found at i:612205 original size:20 final size:22
Alignment explanation
Indices: 612139--612205 Score: 70
Period size: 23 Copynumber: 3.1 Consensus size: 22
612129 ACAAATACCA
*
612139 AAATAAAAATTATTATAA-AATT
1 AAATATAAATTA-TATAATAATT
*
612161 CAAATATAAATTATAAAATAA-T
1 -AAATATAAATTATATAATAATT
612183 AAA-ATAAA-TATATAATAATT
1 AAATATAAATTATATAATAATT
612203 AAA
1 AAA
612206 CACATCTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
19 9 0.23
20 9 0.23
21 3 0.08
22 5 0.13
23 13 0.33
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (22 bp):
AAATATAAATTATATAATAATT
Found at i:612313 original size:15 final size:14
Alignment explanation
Indices: 612293--612322 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
612283 ATTTATAAAC
612293 AAATTAATAAACTAT
1 AAATTAATAAA-TAT
612308 AAATTAATAAATAT
1 AAATTAATAAATAT
612322 A
1 A
612323 TATTTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATTAATAAATAT
Found at i:613054 original size:308 final size:308
Alignment explanation
Indices: 612497--613109 Score: 874
Period size: 308 Copynumber: 2.0 Consensus size: 308
612487 TTCTCTCCTT
* *
612497 TGCCTTCTCATTGTTTAATGGTGACAGCAGTAGCACAACAAAATCATAAAAAACACAATGAATTA
1 TGCCTTCTCATTCTTTAATGGTGACAGCAGTAGCACAACAAAATCATAAAAAACACAAAGAATTA
* *
612562 AAGCCAAATATAAACAAAAAATACAAATAAATAAATACTTACTTGATTATTTTTATTAGATTTTT
66 AAGCCAAATATAAACAAAAAATACAAATAAATAAATACTCACTTGATTATTTTTATTAAATTTTT
* * * * *
612627 ATTTTTTCTTGAACAGATGCCTAAATTCCCCTACTTATTATCGTGATTGTGTGAAAGAAATTAAA
131 ATTTTTTCTTGAACAGATGCCGAAATTCCCATAATTATTATCGCGATTATGTGAAAGAAATTAAA
* * * * *
612692 ATTTAGTGTTGTTTTGAGTGAAATCTTTCTGCTTTTAATTTGATTGTTTGGTTCTAGCAAGTAAT
196 ATTTAGTATTATTTTAAGTAAAATCTTTCTGCTTTTAATTTGATTGTTTGGTTCTAACAAGTAAT
*
612757 CATATAAATTATAATTAAGG-TTTGAAATGATTGAATTTGATTTGATC
261 CATATAAATTATAATTAAGGTTTTAAAATGATTGAATTTGATTTGATC
*
612804 TGCCTTCTCATTCTTTAATGGTGACAGCAGTAGCACAACAAAATCA-CAAAAACACAAAGAA-TA
1 TGCCTTCTCATTCTTTAATGGTGACAGCAGTAGCACAACAAAATCATAAAAAACACAAAGAATTA
* * ** *
612867 AAGGTCAAATATGAACAAAAAATACAGGTAAATAAATACTCACTT-ATTTATTTTTGTTAAATTT
66 AA-GCCAAATATAAACAAAAAATACAAATAAATAAATACTCACTTGA-TTATTTTTATTAAA-TT
* * *
612931 TTTATTTTTTTCTTGAACAGATGCCGAAATTCCCATAATTGTTATTGCGATTATGTGAATGAAAT
128 TTTA-TTTTTTCTTGAACAGATGCCGAAATTCCCATAATTATTATCGCGATTATGTGAAAGAAAT
* * * * * *
612996 TGAAATTTGGTATTATTTTAATTAAAATCTTTTTGCTTTTAATTTGGTTGTTTGGTTCTAACACG
192 TAAAATTTAGTATTATTTTAAGTAAAATCTTTCTGCTTTTAATTTGATTGTTTGGTTCTAACAAG
* *
613061 TAGTCATATAAATTATATTTAAGGTTTTAAAATGATTGAATTTGATTTG
257 TAATCATATAAATTATAATTAAGGTTTTAAAATGATTGAATTTGATTTG
613110 GTTAGCTTTT
Statistics
Matches: 269, Mismatches: 32, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
305 5 0.02
306 62 0.23
307 51 0.19
308 128 0.48
309 23 0.09
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.39
Consensus pattern (308 bp):
TGCCTTCTCATTCTTTAATGGTGACAGCAGTAGCACAACAAAATCATAAAAAACACAAAGAATTA
AAGCCAAATATAAACAAAAAATACAAATAAATAAATACTCACTTGATTATTTTTATTAAATTTTT
ATTTTTTCTTGAACAGATGCCGAAATTCCCATAATTATTATCGCGATTATGTGAAAGAAATTAAA
ATTTAGTATTATTTTAAGTAAAATCTTTCTGCTTTTAATTTGATTGTTTGGTTCTAACAAGTAAT
CATATAAATTATAATTAAGGTTTTAAAATGATTGAATTTGATTTGATC
Found at i:615955 original size:16 final size:16
Alignment explanation
Indices: 615936--615966 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
615926 TTTATTATTA
*
615936 AATTAAATTATATTTT
1 AATTAAAATATATTTT
615952 AATTAAAATATATTT
1 AATTAAAATATATTT
615967 AAAATATTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTAAAATATATTTT
Found at i:616181 original size:16 final size:17
Alignment explanation
Indices: 616160--616192 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
616150 ATTATATTTT
*
616160 AATTAAGTAT-TTAATA
1 AATTAAATATGTTAATA
616176 AATTAAATATGTTAATA
1 AATTAAATATGTTAATA
616193 TAAATTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (17 bp):
AATTAAATATGTTAATA
Found at i:616453 original size:15 final size:15
Alignment explanation
Indices: 616433--616479 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
616423 AACAACTAAA
616433 ATTTATTAAAATTAT
1 ATTTATTAAAATTAT
616448 ATTTATTAAAA--A-
1 ATTTATTAAAATTAT
616460 A-TTATTAAAATTAT
1 ATTTATTAAAATTAT
616474 ATTTAT
1 ATTTAT
616480 ATTAATAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
11 9 0.32
12 1 0.04
13 2 0.07
14 1 0.04
15 15 0.54
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTTATTAAAATTAT
Found at i:616466 original size:26 final size:26
Alignment explanation
Indices: 616430--616479 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
616420 AATAACAACT
*
616430 AAAATTTATTAAAATTATATTTATTA
1 AAAAATTATTAAAATTATATTTATTA
616456 AAAAATTATTAAAATTATATTTAT
1 AAAAATTATTAAAATTATATTTAT
616480 ATTAATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
AAAAATTATTAAAATTATATTTATTA
Found at i:616908 original size:20 final size:20
Alignment explanation
Indices: 616883--616922 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
616873 ATATCCTATT
616883 TAATATTAAAAATAATTTTA
1 TAATATTAAAAATAATTTTA
* *
616903 TAATATTTAAAATTATTTTA
1 TAATATTAAAAATAATTTTA
616923 ATTAAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TAATATTAAAAATAATTTTA
Found at i:622379 original size:15 final size:15
Alignment explanation
Indices: 622359--622388 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
622349 CGTTTGCTGC
622359 TTCTAGATGGTGAAA
1 TTCTAGATGGTGAAA
622374 TTCTAGATGGTGAAA
1 TTCTAGATGGTGAAA
622389 GTTGATACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.27, T:0.33
Consensus pattern (15 bp):
TTCTAGATGGTGAAA
Found at i:622534 original size:2 final size:2
Alignment explanation
Indices: 622527--622571 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
622517 AGACGTGCTT
622527 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
622569 TA T
1 TA T
622572 TATCCCTATC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:624090 original size:4 final size:4
Alignment explanation
Indices: 624074--624104 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
624064 CCCTTTGCCA
*
624074 ATTC ATTC TTTC ATTC ATTC ATTC ATTC ATT
1 ATTC ATTC ATTC ATTC ATTC ATTC ATTC ATT
624105 TTATTGATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.55
Consensus pattern (4 bp):
ATTC
Found at i:625628 original size:23 final size:22
Alignment explanation
Indices: 625602--625658 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
625592 ATAAGAAAAA
*
625602 ATAATTAAAATATAATATTATAT
1 ATAATTAAAATATAAAATTA-AT
**
625625 ATAAAAAAAATATAAAATTAAT
1 ATAATTAAAATATAAAATTAAT
625647 ATGAATATAAAA
1 AT-AAT-TAAAA
625659 ATGTATCAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
22 4 0.15
23 19 0.70
24 4 0.15
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
ATAATTAAAATATAAAATTAAT
Found at i:625632 original size:30 final size:28
Alignment explanation
Indices: 625597--625659 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 28
625587 ACGTGATAAG
*
625597 AAAAAATAAT-TAAAATATAATATTATATAT
1 AAAAAA-AATATAAAAT-TAATATGA-ATAT
625627 AAAAAAAATATAAAATTAATATGAATAT
1 AAAAAAAATATAAAATTAATATGAATAT
625655 AAAAA
1 AAAAA
625660 TGTATCAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 9 0.29
29 10 0.32
30 12 0.39
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (28 bp):
AAAAAAAATATAAAATTAATATGAATAT
Found at i:625767 original size:9 final size:10
Alignment explanation
Indices: 625745--625770 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
625735 ATGAAATAAC
625745 AAAATATTTA
1 AAAATATTTA
625755 AAAATATTTA
1 AAAATATTTA
625765 AAAATA
1 AAAATA
625771 ATATAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
AAAATATTTA
Found at i:626275 original size:22 final size:22
Alignment explanation
Indices: 626250--626294 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
626240 AAGTTCATTT
*
626250 ATATTATTTT-TTTATTTTTTAA
1 ATATT-TTTTATTTAATTTTTAA
626272 ATATTTTTTAATTTAATTTTTAA
1 ATATTTTTT-ATTTAATTTTTAA
626295 TAATTTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
22 5 0.25
23 11 0.55
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
ATATTTTTTATTTAATTTTTAA
Found at i:626429 original size:16 final size:18
Alignment explanation
Indices: 626394--626432 Score: 55
Period size: 16 Copynumber: 2.2 Consensus size: 18
626384 AACTAGTAAA
626394 ATAAAATTATAATTATATT
1 ATAAAATTATAA-TATATT
626413 ATAAAA-TATAA-ATATT
1 ATAAAATTATAATATATT
626429 ATAA
1 ATAA
626433 TAAAAACATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 9 0.45
18 5 0.25
19 6 0.30
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATAAAATTATAATATATT
Found at i:626435 original size:19 final size:19
Alignment explanation
Indices: 626393--626437 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
626383 CAACTAGTAA
*
626393 AATAAAATTATAATTATAT
1 AATAAAATTATAAATATAT
*
626412 TATAAAA-TATAAATATTAT
1 AATAAAATTATAAATA-TAT
626431 AATAAAA
1 AATAAAA
626438 ACATAATTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AATAAAATTATAAATATAT
Found at i:627085 original size:15 final size:15
Alignment explanation
Indices: 627065--627098 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
627055 ATTCATTAGC
627065 ATAATTTTACAATAT
1 ATAATTTTACAATAT
**
627080 ATAATTTTTTAATAT
1 ATAATTTTACAATAT
627095 ATAA
1 ATAA
627099 AATATACATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
ATAATTTTACAATAT
Found at i:627183 original size:13 final size:14
Alignment explanation
Indices: 627163--627192 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
627153 TTTGGTGTAT
627163 ATATATATATATCTA
1 ATATATATATA-CTA
627178 ATATATATATACTA
1 ATATATATATACTA
627192 A
1 A
627193 AATCTAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATATATATACTA
Found at i:627197 original size:21 final size:19
Alignment explanation
Indices: 627160--627199 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
627150 ATTTTTGGTG
*
627160 TATATATATATATATCTAA
1 TATATATATATAAATCTAA
627179 TATATATATACTAAAATCTAA
1 TATATATATA-T-AAATCTAA
627200 AAGGAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 1 0.06
21 7 0.39
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (19 bp):
TATATATATATAAATCTAA
Found at i:628084 original size:19 final size:20
Alignment explanation
Indices: 628040--628086 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
628030 AAAAAAAAAG
*
628040 ATAAAAAAATAATAAATACA
1 ATAAATAAATAATAAATACA
*
628060 AGAAATAAA-AATAAATA-A
1 ATAAATAAATAATAAATACA
628078 CATAAATAA
1 -ATAAATAA
628087 CAATGTACGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 1 0.04
19 15 0.65
20 7 0.30
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.19
Consensus pattern (20 bp):
ATAAATAAATAATAAATACA
Found at i:629590 original size:11 final size:11
Alignment explanation
Indices: 629574--629615 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
629564 AATTCATATT
629574 TTTATATTATA
1 TTTATATTATA
*
629585 TTTATATATTTA
1 TTTATAT-TATA
629597 TTTATATTATA
1 TTTATATTATA
*
629608 ATTATATT
1 TTTATATT
629616 TAAGATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TTTATATTATA
Found at i:629648 original size:18 final size:17
Alignment explanation
Indices: 629622--629680 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 17
629612 TATTTAAGAT
629622 ATTTTATATATATATAA
1 ATTTTATATATATATAA
629639 ATTTTA-ATATATTAATAA
1 ATTTTATATATA-T-ATAA
*
629657 ATTTTCT-TATATAT-A
1 ATTTTATATATATATAA
*
629672 TTTTTATAT
1 ATTTTATAT
629681 TTATTATGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
15 6 0.17
16 8 0.23
17 8 0.23
18 13 0.37
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTTATATATATATAA
Found at i:629684 original size:18 final size:18
Alignment explanation
Indices: 629574--629715 Score: 59
Period size: 18 Copynumber: 8.1 Consensus size: 18
629564 AATTCATATT
*
629574 TTTATATTATATTTATATA
1 TTTATA-TATATTTTTATA
*
629593 TTTATTTATATTATAATTATA
1 TTTATATATATT-T--TTATA
*
629614 TTTA-AGATA-TTTTATA
1 TTTATATATATTTTTATA
* * *
629630 TATATATAAATTTTAATA
1 TTTATATATATTTTTATA
*
629648 TATTA-ATA-A-ATTT-T-
1 T-TTATATATATTTTTATA
*
629662 CTTATATATATTTTTATA
1 TTTATATATATTTTTATA
* *
629680 TTTAT-TATGTTTTAATTA
1 TTTATATATATTTTTA-TA
* *
629698 TTTTTAT-TATATTTATA
1 TTTATATATATTTTTATA
629715 T
1 T
629716 AATCTCATAT
Statistics
Matches: 90, Mismatches: 20, Indels: 28
0.65 0.14 0.20
Matches are distributed among these distances:
13 3 0.03
14 3 0.03
15 2 0.02
16 13 0.14
17 16 0.18
18 32 0.36
19 10 0.11
20 3 0.03
21 8 0.09
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (18 bp):
TTTATATATATTTTTATA
Found at i:630037 original size:28 final size:27
Alignment explanation
Indices: 629978--630030 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
629968 GTAAATTTTT
*
629978 TTTTATTTAAAAAATTTAAATTTAAAA
1 TTTTATTTAAAAAATATAAATTTAAAA
630005 TTTTATTTAAAAAA-ATAAATATTAAA
1 TTTTATTTAAAAAATATAAAT-TTAAA
630031 CTATTTAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 5 0.21
27 19 0.79
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
TTTTATTTAAAAAATATAAATTTAAAA
Found at i:633712 original size:2 final size:2
Alignment explanation
Indices: 633705--633731 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
633695 TTTCTCTACC
633705 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
633732 TGTGTGTGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:634716 original size:14 final size:14
Alignment explanation
Indices: 634697--634723 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
634687 TGTTGGATAG
634697 TTTTATTTATTTTA
1 TTTTATTTATTTTA
634711 TTTTATTTATTTT
1 TTTTATTTATTTT
634724 CTATTAGAAT
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:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTATTTATTTTA
Found at i:638934 original size:2 final size:2
Alignment explanation
Indices: 638896--638926 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
638886 CCCTCAAACG
638896 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
638927 AGTCTCTCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:641042 original size:30 final size:30
Alignment explanation
Indices: 640949--641084 Score: 116
Period size: 30 Copynumber: 4.5 Consensus size: 30
640939 AATTTCATCA
*
640949 TTTTATTTAAATAAATTTTTATATTTTT-A-
1 TTTTATTTAAATAAACTTTTA-ATTTTTAAT
* * *
640978 TTATATTCAAAT-AAGTTATTAATTTTTAAAT
1 TTTTATTTAAATAAACTT-TTAATTTTT-AAT
*
641009 TTTTATTTAAATAAACTTTTAACTTTTAAT
1 TTTTATTTAAATAAACTTTTAATTTTTAAT
* * * *
641039 TTTTACTCAAAAAAATTTTTAATTTTTAAT
1 TTTTATTTAAATAAACTTTTAATTTTTAAT
* * *
641069 TTATACTTAAACAAAC
1 TTTTATTTAAATAAAC
641085 CCTTAAATTA
Statistics
Matches: 86, Mismatches: 16, Indels: 9
0.77 0.14 0.08
Matches are distributed among these distances:
28 10 0.12
29 13 0.15
30 41 0.48
31 18 0.21
32 4 0.05
ACGTcount: A:0.40, C:0.06, G:0.01, T:0.54
Consensus pattern (30 bp):
TTTTATTTAAATAAACTTTTAATTTTTAAT
Found at i:641070 original size:60 final size:60
Alignment explanation
Indices: 640949--641084 Score: 150
Period size: 60 Copynumber: 2.3 Consensus size: 60
640939 AATTTCATCA
* * * * *
640949 TTTTATTTAAATAAATTTTTATATTTTTATTATATTCAAATAAGTTATTAATTTTTAAAT
1 TTTTATTTAAATAAACTTTTATATTTTAATTATACTCAAAAAAATTATTAATTTTTAAAT
* *
641009 TTTTATTTAAATAAACTTTTA-ACTTTTAATTTTTACTCAAAAAAATTTTTAATTTTT-AAT
1 TTTTATTTAAATAAACTTTTATA-TTTTAA-TTATACTCAAAAAAATTATTAATTTTTAAAT
* * *
641069 TTATACTTAAACAAAC
1 TTTTATTTAAATAAAC
641085 CCTTAAATTA
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
59 1 0.02
60 41 0.64
61 22 0.34
ACGTcount: A:0.40, C:0.06, G:0.01, T:0.54
Consensus pattern (60 bp):
TTTTATTTAAATAAACTTTTATATTTTAATTATACTCAAAAAAATTATTAATTTTTAAAT
Found at i:641623 original size:26 final size:24
Alignment explanation
Indices: 641540--641628 Score: 67
Period size: 26 Copynumber: 3.6 Consensus size: 24
641530 ATTATTTTAG
* *
641540 ATATGATATAAAAAAATATGATACGA
1 ATATGATAT-AATAAATATGATA-AA
* *
641566 ATATGATATATTAATAAAT-ATAAA
1 ATATGATATAATAA-ATATGATAAA
641590 ATA--ATATAATAAATATGATAATTA
1 ATATGATATAATAAATATGATAA--A
*
641614 ATATGATATATTAAA
1 ATATGATATAATAAA
641629 AATTATTAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
21 3 0.06
22 12 0.24
24 8 0.16
25 6 0.12
26 21 0.42
ACGTcount: A:0.57, C:0.01, G:0.07, T:0.35
Consensus pattern (24 bp):
ATATGATATAATAAATATGATAAA
Found at i:641623 original size:36 final size:38
Alignment explanation
Indices: 641540--641623 Score: 111
Period size: 38 Copynumber: 2.3 Consensus size: 38
641530 ATTATTTTAG
*
641540 ATATGATATAAAAAAATATGATACGAATATGATATATTA
1 ATATGATATAAAAAAATATAATAC-AATATGATATATTA
* *
641579 ATA-AATATAAAATAATATAATA-AATATGATA-ATTA
1 ATATGATATAAAAAAATATAATACAATATGATATATTA
641614 ATATGATATA
1 ATATGATATA
641624 TTAAAAATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
35 7 0.17
36 14 0.35
38 16 0.40
39 3 0.08
ACGTcount: A:0.57, C:0.01, G:0.07, T:0.35
Consensus pattern (38 bp):
ATATGATATAAAAAAATATAATACAATATGATATATTA
Found at i:643953 original size:19 final size:19
Alignment explanation
Indices: 643925--643980 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
643915 TATATTTATT
*
643925 TTTAAATTTTTTTTATATA
1 TTTAATTTTTTTTTATATA
643944 TTTAATTTTTTTTTA-A-A
1 TTTAATTTTTTTTTATATA
*
643961 TTATATATTTATTTTTATAT
1 TT-TA-ATTTTTTTTTATAT
643981 TTAAAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
17 3 0.10
18 3 0.10
19 24 0.77
20 1 0.03
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTAATTTTTTTTTATATA
Found at i:643969 original size:24 final size:25
Alignment explanation
Indices: 643914--643985 Score: 85
Period size: 24 Copynumber: 2.9 Consensus size: 25
643904 TGAAATATAA
* ***
643914 ATATATTTATTTTTAAATTTTTTTT
1 ATATATTTATTTTTATATTTAAATT
643939 ATATATTTAATTTTT-T-TTTAAATT
1 ATATATTT-ATTTTTATATTTAAATT
643963 ATATATTTATTTTTATATTTAAA
1 ATATATTTATTTTTATATTTAAA
643986 AATATATCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
23 6 0.15
24 14 0.35
25 14 0.35
26 6 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (25 bp):
ATATATTTATTTTTATATTTAAATT
Found at i:643990 original size:24 final size:24
Alignment explanation
Indices: 643912--643997 Score: 68
Period size: 24 Copynumber: 3.5 Consensus size: 24
643902 TATGAAATAT
* **
643912 AAATATATTTATTTTTAAATTTTTT
1 AAATATATTTATTTTTATA-TTTAA
**
643937 TTATATATTTAATTTTT-T-TTTAA
1 AAATATATTT-ATTTTTATATTTAA
*
643960 ATTATATATTTATTTTTATATTTAA
1 A-AATATATTTATTTTTATATTTAA
*
643985 AAATATATCTATT
1 AAATATATTTATT
643998 ATGAATCTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
23 9 0.18
24 20 0.41
25 14 0.29
26 6 0.12
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (24 bp):
AAATATATTTATTTTTATATTTAA
Found at i:646957 original size:22 final size:22
Alignment explanation
Indices: 646928--646984 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
646918 TTTCATTGTT
*
646928 CATCACTGTTTATGTATCGATA
1 CATCACTGTTCATGTATCGATA
*
646950 TATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
646972 CATCACTGTTCAT
1 CATCACTGTTCAT
646985 CACTATACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.40
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:647043 original size:19 final size:20
Alignment explanation
Indices: 647019--647056 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
647009 ATAATTTCAA
647019 ATGCA-TGTATCAATACATT
1 ATGCATTGTATCAATACATT
*
647038 ATGCATTGTATCGATACAT
1 ATGCATTGTATCAATACAT
647057 AAGAGCGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (20 bp):
ATGCATTGTATCAATACATT
Found at i:647526 original size:20 final size:20
Alignment explanation
Indices: 647501--647539 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
647491 AAAGGTTTTT
647501 ATCTTAGCCTTAAAAGATAC
1 ATCTTAGCCTTAAAAGATAC
*
647521 ATCTTAGCCTTGAAAGATA
1 ATCTTAGCCTTAAAAGATA
647540 GTATTGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (20 bp):
ATCTTAGCCTTAAAAGATAC
Found at i:648076 original size:20 final size:20
Alignment explanation
Indices: 648048--648122 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
648038 TTTTACCCAG
648048 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
648068 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
648088 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
648108 ATGTATCGATACATT
1 ATGTATCGATACATT
648123 ATGTCTTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:648108 original size:40 final size:39
Alignment explanation
Indices: 648048--648125 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
648038 TTTTACCCAG
*
648048 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTTCAATATATCGATACAT-TATGA
* *
648088 ATGTATCGATATATTCTTCAATGTATCGATACATTATG
1 ATGTATCGATACATTCTTCAATATATCGATACATTATG
648126 TCTTTTTACC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTTCAATATATCGATACATTATGA
Found at i:662125 original size:13 final size:13
Alignment explanation
Indices: 662107--662131 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
662097 GTCCTTTACA
662107 AAAAAAACAAAAC
1 AAAAAAACAAAAC
662120 AAAAAAACAAAA
1 AAAAAAACAAAA
662132 AACCAAGAAA
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:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAC
Found at i:663467 original size:57 final size:57
Alignment explanation
Indices: 663382--664085 Score: 932
Period size: 57 Copynumber: 12.2 Consensus size: 57
663372 TGTTCATCCC
* * * * *
663382 TTTCAAAGCTCACAAGTCTGTGGCACTCTTTTCAAAGCCCACGAGTTAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCT
* * * *
663439 TTTCAAAGCCCACAAGTCAGTGGGACTCTTTTTAAAGCCCACAAATCAGTGGCATTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA-CCT
*
663497 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CT
* * *
663555 TTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAATCAGTGACACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CT
* *
663612 TTTCAAAGCCCACAAGTAAGTGGCAC-CTTTTTAAAGCCCACAAGTCAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA-CCT
* * *
663669 TTT-AAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAATGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCT
*
663725 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CT
* * * * *
663783 TTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCTACAAGTTAGTGACACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCT
* * *
663840 TTTCAAAGCCCACAAATTAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTAGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CT
* * * * *
663898 TTTTAAAGCCCATAAGTTAGTGGCA-TCATTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCT
* *
663954 TTTCAAAACCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CT
* ** *
664011 TTTCGAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACACGAGTTGGTGGTAACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACA--AGTCAGTGG-CAC-CT
664072 TTTCAAAGCCCACA
1 TTTCAAAGCCCACA
664086 CAAGTTGGTG
Statistics
Matches: 575, Mismatches: 59, Indels: 22
0.88 0.09 0.03
Matches are distributed among these distances:
56 74 0.13
57 305 0.53
58 171 0.30
60 7 0.01
61 18 0.03
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.24
Consensus pattern (57 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCT
Found at i:663749 original size:257 final size:257
Alignment explanation
Indices: 663386--664085 Score: 1051
Period size: 257 Copynumber: 2.7 Consensus size: 257
663376 CATCCCTTTC
* * * * *
663386 AAAGCTCACAAGTCTGTGGCACTCTTTTCAAAGCCCACGAGTTAGTGGCACCCTTTCAAAGCCCA
1 AAAGCCCACAAGTCAGTGGCACCCTTTT-AAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCA
* * * * *
663451 CAAGTCAGTGGGACTCTTTTTAAAGCCCACAAATCAGTGGCATTCTTTTCAAAGCCCACAAGTCA
65 CAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCA
*
663516 GTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC
129 GTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGACAC
*
663581 CCTTTCAAAGCCCACAAATCAGTGACACTCTTTTCAAAGCCCACAAGTAAGTGGCAC-CTTTTT
194 CCTTTCAAAGCCCACAAATCAGTGACACTCTTTTCAAAGCCCACAAGTAAGTAGCACTCTTTTT
* *
663644 AAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCA
1 AAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCA
* *
663709 CAAGTCAATGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAG
65 CAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAG
* *
663774 TGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCTACAAGTTAGTGACACC
130 TGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGACACC
* * *
663839 CTTTCAAAGCCCACAAATTAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTAGCACTCTTTTT
195 CTTTCAAAGCCCACAAATCAGTGACACTCTTTTCAAAGCCCACAAGTAAGTAGCACTCTTTTT
* * * * * *
663902 AAAGCCCATAAGTTAGTGGCATCATTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAACCCAC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCAC
*
663967 AAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCGAAGCCCACAAGTCAGT
66 AAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGT
* ** *
664032 GGCACTCTTTTCAAAGCCCACACGAGTTGGTGGTAACTCTTTTCAAAGCCCACA
131 GGCACTCTTTTCAAAGCCCACA--AATCAGTGG-CACTCTTTTCAAAGCCCACA
664086 CAAGTTGGTG
Statistics
Matches: 400, Mismatches: 37, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
257 276 0.69
258 100 0.25
259 6 0.01
260 18 0.05
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (257 bp):
AAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCAC
AAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGT
GGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGACACCC
TTTCAAAGCCCACAAATCAGTGACACTCTTTTCAAAGCCCACAAGTAAGTAGCACTCTTTTT
Found at i:663922 original size:286 final size:286
Alignment explanation
Indices: 663379--664085 Score: 1024
Period size: 286 Copynumber: 2.5 Consensus size: 286
663369 GAATGTTCAT
* * * *
663379 CCCTTTCAAAGCTCACAAGTCTGTGGCACTCTTTTCAAAGCCCACGAGTTAGTGGCACCCTTTCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCA
* * * *
663444 AAGCCCACAAGTCAGTGGGACTCTTTTTAAAGCCCACAAATCAGTGGCATTCTTTTCAAAGCCCA
66 AAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCA
* * * *
663509 CAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCA
131 CAAATCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGACACTCCTTTCAAAGCCCACAAATCA
663574 GTGGCACCCTTTCAAAGCCCACAAATCAGTGACACTCTTTTCAAAGCCCACAAGTAAGTGGCACC
196 GTGGCACCCTTTCAAAGCCCACAAATCAGTGACACTCTTTTCAAAGCCCACAAGTAAGTGGCACC
* *
663639 TTTTTAAAGCCCACAAGTCAGTGGCA
261 ATTTCAAAGCCCACAAGTCAGTGGCA
* * *
663665 CCCTTTTAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAATGGCACCCTTTCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCA
*
663730 AAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCA
66 AAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCA
* * * *
663795 CAAATCAGTGGCACTCTTTTCAAAGCCTACAAGTTAGTGACAC-CCTTTCAAAGCCCACAAATTA
131 CAAATCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGACACTCCTTTCAAAGCCCACAAATCA
* * * * *
663859 GTGGCACTCTTTTCAAAGCCCACAAGTCAGT-AGCACTCTTTTTAAAGCCCATAAGTTAGTGGCA
196 GTGGCAC-CCTTTCAAAGCCCACAAATCAGTGA-CACTCTTTTCAAAGCCCACAAGTAAGTGGCA
*
663923 TCATTTCAAAGCCCACAAGTCAGTGGCA
259 CCATTTCAAAGCCCACAAGTCAGTGGCA
* * *
663951 CCCTTTCAAAACCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTC
* ** *
664015 GAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACACGAGTTGGTGGTAACTCTTTTCAAAG
65 AAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACA--AGTCAGTGG-CACTCTTTTCAAAG
664080 CCCACA
127 CCCACA
664086 CAAGTTGGTG
Statistics
Matches: 376, Mismatches: 39, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
285 52 0.14
286 298 0.79
288 7 0.02
289 19 0.05
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.24
Consensus pattern (286 bp):
CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCA
AAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCA
CAAATCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGACACTCCTTTCAAAGCCCACAAATCA
GTGGCACCCTTTCAAAGCCCACAAATCAGTGACACTCTTTTCAAAGCCCACAAGTAAGTGGCACC
ATTTCAAAGCCCACAAGTCAGTGGCA
Found at i:664096 original size:32 final size:29
Alignment explanation
Indices: 663382--664085 Score: 967
Period size: 29 Copynumber: 24.5 Consensus size: 29
663372 TGTTCATCCC
* *
663382 TTTCAAAGCTCACAAGTCTGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
663411 TTTCAAAGCCCACGAGTTAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
663439 TTTCAAAGCCCACAAGTCAGTGGGACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
663468 TTTTAAAGCCCACAAATCAGTGGCATTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
663497 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
663526 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
663555 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
663583 TTTCAAAGCCCACAAATCAGTGACACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
663612 TTTCAAAGCCCACAAGTAAGTGGCAC-CT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
663640 TTTTAAAGCCCACAAGTCAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
663669 TTT-AAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
663697 TTTCAAAGCCCACAAGTCAATGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
663725 TTTCAAAGCCCACAAGTCAGTGGCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
663754 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
663783 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * * *
663812 TTTCAAAGCCTACAAGTTAGTGACAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
663840 TTTCAAAGCCCACAAATTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
663869 TTTCAAAGCCCACAAGTCAGTAGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * * *
663898 TTTTAAAGCCCATAAGTTAGTGGCA-TCA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
663926 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
663954 TTTCAAAACCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
663982 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
664011 TTTCGAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
** *
664040 TTTCAAAGCCCACACGAGTTGGTGGTAACTCT
1 TTTCAAAGCCCACA--AGTCAGTGG-CACTCT
664072 TTTCAAAGCCCACA
1 TTTCAAAGCCCACA
664086 CAAGTTGGTG
Statistics
Matches: 600, Mismatches: 64, Indels: 19
0.88 0.09 0.03
Matches are distributed among these distances:
28 228 0.38
29 346 0.58
31 7 0.01
32 19 0.03
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.24
Consensus pattern (29 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTCT
Found at i:664686 original size:20 final size:20
Alignment explanation
Indices: 664658--664751 Score: 100
Period size: 20 Copynumber: 4.7 Consensus size: 20
664648 TTTTACCCAG
664658 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
664678 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
664698 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
**
664718 ATGTATCGATACATTGAAT-A
1 ATGTATCGATACATT-TTTCA
664738 ATGTATCGATACAT
1 ATGTATCGATACAT
664752 CTAGTTAAAA
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 59 0.98
21 1 0.02
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:664718 original size:40 final size:40
Alignment explanation
Indices: 664658--664751 Score: 136
Period size: 40 Copynumber: 2.4 Consensus size: 40
664648 TTTTACCCAG
* *
664658 ATGTATCGATACATTTTTCAATATATCGATACA-TGTATGA
1 ATGTATCGATACATTCTTCAATATATCGATACATTGAAT-A
* *
664698 ATGTATCGATATATTCTTCAATGTATCGATACATTGAATA
1 ATGTATCGATACATTCTTCAATATATCGATACATTGAATA
664738 ATGTATCGATACAT
1 ATGTATCGATACAT
664752 CTAGTTAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 44 0.92
41 4 0.08
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (40 bp):
ATGTATCGATACATTCTTCAATATATCGATACATTGAATA
Found at i:669367 original size:20 final size:20
Alignment explanation
Indices: 669339--669413 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
669329 TTTTACCCAG
669339 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
669359 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
669379 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
669399 ATGTATCGATACATT
1 ATGTATCGATACATT
669414 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:669406 original size:40 final size:39
Alignment explanation
Indices: 669339--669416 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
669329 TTTTACCCAG
* *
669339 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
669379 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
669417 TCTTTTTATC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:673109 original size:20 final size:21
Alignment explanation
Indices: 673084--673125 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
673074 AACCCTGATT
673084 TGTATCGATACA-TATGTAAA
1 TGTATCGATACATTATGTAAA
*
673104 TGTATCGATTCATTATGTAAA
1 TGTATCGATACATTATGTAAA
673125 T
1 T
673126 ATGTCAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTATGTAAA
Found at i:673158 original size:113 final size:113
Alignment explanation
Indices: 672960--673225 Score: 471
Period size: 113 Copynumber: 2.4 Consensus size: 113
672950 ACATATGCTA
* * * * *
672960 AAACCCTTATTTCTATCGATACA-AGTGAAAATATATTGATTCATTATGTAAATATGTCAATACA
1 AAACCCTGATTTGTATCGATACATA-TGTAAATGTATCGATTCATTATGTAAATATGTCAATACA
673024 GCATGTATTGTATCAATACATTTTGTTGGCAGTAGCTAAGGTAATTTTG
65 GCATGTATTGTATCAATACATTTTGTTGGCAGTAGCTAAGGTAATTTTG
673073 AAACCCTGATTTGTATCGATACATATGTAAATGTATCGATTCATTATGTAAATATGTCAATACAG
1 AAACCCTGATTTGTATCGATACATATGTAAATGTATCGATTCATTATGTAAATATGTCAATACAG
673138 CATGTATTGTATCAATACATTTTGTTGGCAGTAGCTAAGGTAATTTTG
66 CATGTATTGTATCAATACATTTTGTTGGCAGTAGCTAAGGTAATTTTG
673186 AAACCCTGATTTGTATCGATACATATGTAAATGTATCGAT
1 AAACCCTGATTTGTATCGATACATATGTAAATGTATCGAT
673226 ACAATTCAGA
Statistics
Matches: 147, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
113 146 0.99
114 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.38
Consensus pattern (113 bp):
AAACCCTGATTTGTATCGATACATATGTAAATGTATCGATTCATTATGTAAATATGTCAATACAG
CATGTATTGTATCAATACATTTTGTTGGCAGTAGCTAAGGTAATTTTG
Found at i:673222 original size:20 final size:19
Alignment explanation
Indices: 673197--673269 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
673187 AACCCTGATT
673197 TGTATCGATACATATGTAAA
1 TGTATCGATACATAT-TAAA
673217 TGTATCGATACA-ATTCAGAA
1 TGTATCGATACATATT-A-AA
* *
673237 TATATCGATACATCCTTAAA
1 TGTATCGATACAT-ATTAAA
673257 TGTATCGATACAT
1 TGTATCGATACAT
673270 TGAGTTTAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
18 1 0.02
19 3 0.07
20 39 0.85
21 1 0.02
22 2 0.04
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.34
Consensus pattern (19 bp):
TGTATCGATACATATTAAA
Found at i:674947 original size:20 final size:19
Alignment explanation
Indices: 674902--674949 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
674892 TAACACATTT
674902 ATTTAATATAAATATAACAC
1 ATTTAA-ATAAATATAACAC
* *
674922 A-ATAAATACAATATTACAC
1 ATTTAAATA-AATATAACAC
674941 ATTTAAATA
1 ATTTAAATA
674950 TGATTAAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 3 0.13
19 13 0.57
20 7 0.30
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTTAAATAAATATAACAC
Found at i:675298 original size:559 final size:559
Alignment explanation
Indices: 674226--675344 Score: 1701
Period size: 559 Copynumber: 2.0 Consensus size: 559
674216 CATAATGTGT
*
674226 TAATAGTAAAAAACCAATATTTAAGCACCTCAAGTTATATTTGAACTATAAGTAGATTTGACAAA
1 TAATAGTAAAAAACCAATATTTAAACACCTCAAGTTATATTTGAACTATAAGTAGATTTGACAAA
674291 TTTAAACATAAAACAAAAATGTTACACAAATATAAAAAATATTTAACATAAATATAACACAACAA
66 TTTAAACATAAAACAAAAATGTTACACAAATATAAAAAATATTTAACATAAATATAACACAACAA
* *
674356 ACATAACATTACACATTTAAATATAATTAAAACACATGTCATATTTGTGTTTAAAATTTTAACAA
131 ACACAACATTACACATTTAAATATAATTAAAACACATCTCATATTTGTG-TTAAAATTTTAACAA
*
674421 ATTTAATAATATATATTATATTTATATATATTCAACTAATAAAAAAACACGAAATAAACATATAC
195 ATTTAATAATATATATTATATTTATATATATTCAACTAATAAAAAAACACGAAATAAACATACAC
* ** * *
674486 AAATTATCAAGTTTTAACGTAAGTACATGAAATGCCAATAGCTCGACTCCTCATCCTAATTACTT
260 AAATTATCAAATTTTAACACAAGTACATGAAATGCCAATAGCCCGACTCCCCATCC--A-TA---
*
674551 TAGGAGAAAAGACCCACAATAGTCTAAAAGCCATAATTTGAAAGATATTTTACATCACCAATATA
319 TA-GAG--AAGACCCACAATAGTCCAAAAGCCATAATTTGAAAGATATTTTACATCACCAATATA
* *
674616 ATAATCTAGGTTGCTTTGAATATTCAGATGATTGATATAGTTATTCTAGTTTGGTTTATAAGCAG
381 ATAAGCTAGGTTGCTTTGAATATTCAGATGATTGATATAATTATTCTAGTTTGGTTTATAAGCAG
** * *
674681 GCCAAAATTTAGGGGAAAAAAAGTATGTGCCATGTGGAATAGAACATAGATGGAACCTTAAGAGT
446 GCCAAAATTTAGGAAAAAAAAAGTATATGCCATGTGGAATAGAACATAGATAGAACCTTAAGAGT
*
674746 ACTTGGTTAATCACTTTGATAAAAGTTTGAAAAATCGAAACTAATATGG
511 ACTTGGTTAATCACTTTGATAAAAGTTTGAAAAATAGAAACTAATATGG
** * *
674795 TAATAGTAAAAAAGTAATATTTAAACACCTTAAGTTATATTTGAACTATAAGTAGATTTGATAAA
1 TAATAGTAAAAAACCAATATTTAAACACCTCAAGTTATATTTGAACTATAAGTAGATTTGACAAA
* ** * *
674860 TTTAAATATAAAACAAAAATGTTACACAAATATAACACATTTATTTAATATAAATATAACACAAT
66 TTTAAACATAAAACAAAAATGTTACACAAATATAA-A-AAATATTTAACATAAATATAACACAAC
* * * *
674925 AAATACAATATTACACATTTAAATATGATTAAAACACATCTCATATTTGTG-TAAAATTTTAATA
129 AAACACAACATTACACATTTAAATATAATTAAAACACATCTCATATTTGTGTTAAAATTTTAACA
* **
674989 AATTTAATCATATTTATATTATATTTATATATATTCAACTAATAAAAAAAACACTTAATAAACAT
194 AATTTAAT-A-ATATATATTATATTTATATATATTCAACTAAT-AAAAAAACACGAAATAAACAT
*
675054 ACACAAATTATCAAATTTTAACACAAGTACATGAAATGCCAATAGCCCGGCTCCCCATCC-TA-A
256 ACACAAATTATCAAATTTTAACACAAGTACATGAAATGCCAATAGCCCGACTCCCCATCCATATA
* *
675117 -AG-AGACCCATAATAGTCCAAAAGTCATAATTTGAAAGATATTTTACATCACCAATATAATAAG
321 GAGAAGACCCACAATAGTCCAAAAGCCATAATTTGAAAGATATTTTACATCACCAATATAATAAG
* *
675180 CTAGGTTGCTTTGAGTATTCAGATGATTGATATAATTATTCTAGTTTGGTTTATAAGTAGGCCAA
386 CTAGGTTGCTTTGAATATTCAGATGATTGATATAATTATTCTAGTTTGGTTTATAAGCAGGCCAA
*
675245 AATTTA-GAAAAAAACAAGTATATGCCATGTGGAATAGAACATAGATAGAACCTTGAGAGTACTT
451 AATTTAGGAAAAAAA-AAGTATATGCCATGTGGAATAGAACATAGATAGAACCTTAAGAGTACTT
675309 GGTTAATCACTTTGATAAAAGTTTGAAAAATAGAAA
515 GGTTAATCACTTTGATAAAAGTTTGAAAAATAGAAA
675345 AAAAATGCAC
Statistics
Matches: 505, Mismatches: 39, Indels: 22
0.89 0.07 0.04
Matches are distributed among these distances:
558 6 0.01
559 206 0.41
562 2 0.00
564 1 0.00
568 2 0.00
569 114 0.23
570 2 0.00
571 100 0.20
572 72 0.14
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (559 bp):
TAATAGTAAAAAACCAATATTTAAACACCTCAAGTTATATTTGAACTATAAGTAGATTTGACAAA
TTTAAACATAAAACAAAAATGTTACACAAATATAAAAAATATTTAACATAAATATAACACAACAA
ACACAACATTACACATTTAAATATAATTAAAACACATCTCATATTTGTGTTAAAATTTTAACAAA
TTTAATAATATATATTATATTTATATATATTCAACTAATAAAAAAACACGAAATAAACATACACA
AATTATCAAATTTTAACACAAGTACATGAAATGCCAATAGCCCGACTCCCCATCCATATAGAGAA
GACCCACAATAGTCCAAAAGCCATAATTTGAAAGATATTTTACATCACCAATATAATAAGCTAGG
TTGCTTTGAATATTCAGATGATTGATATAATTATTCTAGTTTGGTTTATAAGCAGGCCAAAATTT
AGGAAAAAAAAAGTATATGCCATGTGGAATAGAACATAGATAGAACCTTAAGAGTACTTGGTTAA
TCACTTTGATAAAAGTTTGAAAAATAGAAACTAATATGG
Found at i:675612 original size:29 final size:29
Alignment explanation
Indices: 675569--675624 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
675559 GATCAGCATC
* *
675569 TTTTATTTTTTTATTATATAATATATTAT
1 TTTTATTTATATATTATATAATATATTAT
* *
675598 TTTTATTTATATATTATGTAATTTATT
1 TTTTATTTATATATTATATAATATATT
675625 TTATAAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (29 bp):
TTTTATTTATATATTATATAATATATTAT
Found at i:675621 original size:22 final size:22
Alignment explanation
Indices: 675576--675629 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
675566 ATCTTTTATT
*
675576 TTTTTA-TTATATAATATATTA
1 TTTTTATTTATATAATATATAA
* *
675597 TTTTTATTTATATATTATGTAA
1 TTTTTATTTATATAATATATAA
*
675619 TTTAT-TTTATA
1 TTTTTATTTATA
675630 AAAATTAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTTTATTTATATAATATATAA
Found at i:676600 original size:20 final size:21
Alignment explanation
Indices: 676565--676604 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
676555 TATAAAATAC
676565 ATATATAAATATTATCATATA
1 ATATATAAATATTATCATATA
*
676586 ATATATATA-ATTATCATAT
1 ATATATAAATATTATCATAT
676605 GTAGATTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (21 bp):
ATATATAAATATTATCATATA
Found at i:678521 original size:16 final size:15
Alignment explanation
Indices: 678498--678528 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
678488 TTTAGATATT
678498 TATTATTTTAATTTA
1 TATTATTTTAATTTA
678513 TATTAATTTTAATTTA
1 TATT-ATTTTAATTTA
678529 GATAGTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TATTATTTTAATTTA
Found at i:679269 original size:2 final size:2
Alignment explanation
Indices: 679256--679300 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
679246 TTACATGTCG
*
679256 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
679298 AT A
1 AT A
679301 AACACAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:680622 original size:10 final size:9
Alignment explanation
Indices: 680607--680663 Score: 53
Period size: 10 Copynumber: 5.9 Consensus size: 9
680597 TCTATCTCTC
680607 ATAATATTAA
1 ATAATA-TAA
680617 ATAATATATA
1 ATAATATA-A
680627 A-AATATTAA
1 ATAATA-TAA
*
680636 AAAATATAA
1 ATAATATAA
680645 TATAATATAA
1 -ATAATATAA
680655 ATATATATA
1 ATA-ATATA
680664 TTTTAAAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
9 14 0.34
10 27 0.66
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
ATAATATAA
Found at i:680633 original size:19 final size:19
Alignment explanation
Indices: 680609--680663 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
680599 TATCTCTCAT
680609 AATATTAAATAATATATAA
1 AATATTAAATAATATATAA
* *
680628 AATATTAAAAAATATAATAT
1 AATATTAAATAATAT-ATAA
680648 AATA-TAAAT-ATATATA
1 AATATTAAATAATATATA
680664 TTTTAAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 3 0.09
18 4 0.12
19 18 0.56
20 7 0.22
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AATATTAAATAATATATAA
Found at i:680658 original size:16 final size:16
Alignment explanation
Indices: 680637--680753 Score: 70
Period size: 16 Copynumber: 7.4 Consensus size: 16
680627 AAATATTAAA
680637 AAATATAATATAATAT
1 AAATATAATATAATAT
* *
680653 AAATAT-ATATATTTT
1 AAATATAATATAATAT
*
680668 AAA-ATTTATATAATAT
1 AAATA-TAATATAATAT
680684 AAAT-T-AT-TAATCTAT
1 AAATATAATATAA--TAT
680699 CAAAT-TAATATAAATAT
1 -AAATATAATAT-AATAT
* *
680716 AAA-ATATTTTAAATAT
1 AAATATAATAT-AATAT
*
680732 AATTATAATATAATA-
1 AAATATAATATAATAT
680747 AAATATA
1 AAATATA
680754 TAAATAAAAC
Statistics
Matches: 80, Mismatches: 10, Indels: 23
0.71 0.09 0.20
Matches are distributed among these distances:
13 3 0.04
14 3 0.04
15 21 0.26
16 40 0.50
17 10 0.12
18 1 0.01
19 2 0.03
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATATAATATAATAT
Found at i:680664 original size:22 final size:21
Alignment explanation
Indices: 680607--680664 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 21
680597 TCTATCTCTC
680607 ATAATATTAAATAATATATAAA
1 ATAATA-TAAATAATATATAAA
*
680629 AT-AT-TAAA-AA-ATATAAT
1 ATAATATAAATAATATATAAA
680646 ATAATATAAATATATATAT
1 ATAATATAAATA-ATATAT
680665 TTTAAAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
17 8 0.27
18 4 0.13
19 8 0.27
20 1 0.03
21 3 0.10
22 6 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAATATAAATAATATATAAA
Found at i:680691 original size:26 final size:26
Alignment explanation
Indices: 680647--680744 Score: 74
Period size: 26 Copynumber: 3.5 Consensus size: 26
680637 AAATATAATA
*
680647 TAATATAA-ATATATATATTTTAAAAT
1 TAATATAATATAAAT-TATTTTAAAAT
*
680673 TTATATAATATAAATTATTAATCTATCAAAT
1 TAATATAATATAAATTATT--T-TA--AAAT
*
680704 TAATATAAATATAAAATATTTT-AAAT
1 TAATAT-AATATAAATTATTTTAAAAT
680730 ATAATTATAATATAA
1 -TAA-TATAATATAA
680745 TAAAATATAT
Statistics
Matches: 59, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
26 15 0.25
27 15 0.25
28 4 0.07
29 3 0.05
30 1 0.02
31 9 0.15
32 12 0.20
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (26 bp):
TAATATAATATAAATTATTTTAAAAT
Found at i:680704 original size:31 final size:30
Alignment explanation
Indices: 680629--680723 Score: 93
Period size: 31 Copynumber: 3.0 Consensus size: 30
680619 AATATATAAA
*
680629 ATATTAAAAAATATAATATAATATAAATATAT
1 ATATTATAAAAT-TAATATAATATAAATAT-T
* *
680661 ATATTTTAAAATTTATATAATATAAATTATT
1 ATATTATAAAATTAATATAATATAAA-TATT
*
680692 A-ATCTATCAAATTAATATAAATATAAAATATT
1 ATAT-TATAAAATTAATAT-AATAT-AAATATT
680724 TTAAATATAA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
30 2 0.04
31 26 0.49
32 22 0.42
33 3 0.06
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (30 bp):
ATATTATAAAATTAATATAATATAAATATT
Found at i:680760 original size:16 final size:16
Alignment explanation
Indices: 680619--680760 Score: 57
Period size: 16 Copynumber: 8.8 Consensus size: 16
680609 AATATTAAAT
*
680619 AATATATAAAATATTAA
1 AATATAT-AAATAATAA
*
680636 AAAATATAATATAATATA
1 AATATATAA-ATAATA-A
* **
680654 AATATATATATTTTAA
1 AATATATAAATAATAA
*
680670 AAT-T-TATATAATATA
1 AATATATAAATAATA-A
* *
680685 AAT-TATTAATCTATCAA
1 AATATATAAAT-AAT-AA
*
680702 ATTAATATAAAT-ATAA
1 AAT-ATATAAATAATAA
*
680718 AATATTTTAAAT-AT--
1 AATA-TATAAATAATAA
680732 AAT-TATAATATAATAA
1 AATATATAA-ATAATAA
680748 AATATATAAATAA
1 AATATATAAATAA
680761 AACATAAATC
Statistics
Matches: 95, Mismatches: 16, Indels: 29
0.68 0.11 0.21
Matches are distributed among these distances:
12 4 0.04
13 2 0.02
14 12 0.13
15 7 0.07
16 28 0.29
17 27 0.28
18 9 0.09
19 6 0.06
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (16 bp):
AATATATAAATAATAA
Found at i:683856 original size:11 final size:11
Alignment explanation
Indices: 683840--683890 Score: 58
Period size: 11 Copynumber: 5.1 Consensus size: 11
683830 AAATAAAAAT
683840 ATTATTTATTA
1 ATTATTTATTA
683851 ATTATTTATTA
1 ATTATTTATTA
*
683862 ATTA--TA-AA
1 ATTATTTATTA
683870 ATTATTT-TTA
1 ATTATTTATTA
683880 ATTA-TTATTA
1 ATTATTTATTA
683890 A
1 A
683891 ATTAAATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
8 5 0.15
9 4 0.12
10 10 0.29
11 15 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
ATTATTTATTA
Found at i:683866 original size:18 final size:18
Alignment explanation
Indices: 683839--683886 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
683829 AAAATAAAAA
*
683839 TATTATTTATTAATTATT
1 TATTAATTATTAATTATT
*
683857 TATTAATTATAAAATTATT
1 TATTAATTAT-TAATTATT
683876 T-TTAATTATTA
1 TATTAATTATTA
683887 TTAAATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 1 0.04
18 17 0.65
19 8 0.31
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTAATTATTAATTATT
Found at i:683886 original size:21 final size:22
Alignment explanation
Indices: 683862--683904 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
683852 TTATTTATTA
*
683862 ATTATAAAATT-ATTTTTAATT
1 ATTATAAAATTAAATTTTAATT
*
683883 ATTATTAAATTAAATTTTAATT
1 ATTATAAAATTAAATTTTAATT
683905 TAAATATACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTATAAAATTAAATTTTAATT
Found at i:683891 original size:22 final size:21
Alignment explanation
Indices: 683859--683904 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 21
683849 TAATTATTTA
*
683859 TTAATTA-TA-AAATT-ATTT
1 TTAATTATTATAAATTAAATT
683877 TTAATTATTATTAAATTAAATT
1 TTAATTATTA-TAAATTAAATT
683899 TTAATT
1 TTAATT
683905 TAAATATACA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 7 0.30
19 2 0.09
21 5 0.22
22 9 0.39
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTAATTATTATAAATTAAATT
Found at i:684665 original size:2 final size:2
Alignment explanation
Indices: 684660--684688 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
684650 GTTAACTTGG
684660 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
684689 TATGCCAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:686789 original size:20 final size:19
Alignment explanation
Indices: 686744--686799 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 19
686734 CTTAACGAGG
686744 TTTTTATAT-TATTGATTAAT
1 TTTTTATATATA-T-ATTAAT
686764 TATTTTATATATATATTAAAT
1 T-TTTTATATATATATT-AAT
686785 TTTTTATATAT-TATT
1 TTTTTATATATATATT
686800 TATTCATGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
19 4 0.12
20 14 0.42
21 13 0.39
22 2 0.06
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTTTATATATATATTAAT
Found at i:687126 original size:22 final size:23
Alignment explanation
Indices: 687101--687143 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
687091 AAGTTTTATT
687101 GGCC-TTTTTTTAAGGCTTTAAC
1 GGCCTTTTTTTTAAGGCTTTAAC
687123 GGCCTTTTTTTTAAGGCTTTA
1 GGCCTTTTTTTTAAGGCTTTA
687144 GCGGTGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.49
Consensus pattern (23 bp):
GGCCTTTTTTTTAAGGCTTTAAC
Found at i:695120 original size:16 final size:16
Alignment explanation
Indices: 695099--695129 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
695089 TTTATTATTT
*
695099 TATTTTTTGTTTTATA
1 TATTTTTTATTTTATA
695115 TATTTTTTATTTTAT
1 TATTTTTTATTTTAT
695130 TAGAAGCCAA
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:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (16 bp):
TATTTTTTATTTTATA
Found at i:697073 original size:78 final size:78
Alignment explanation
Indices: 696871--697560 Score: 481
Period size: 78 Copynumber: 8.9 Consensus size: 78
696861 TAATGATCTA
* * * * *
696871 GGGTTGGAGTATCCCCGAAATGAAAAA-TTGATATTTTTGGAAATAAAAACGAGGCT-GAAATAT
1 GGGTTGGAGTAT-CCCGAGATGAAAAATTTAATA-TTTTGGAAATAAAAACGGGGTTAG-AGTAT
* * * * *
696934 CCCTTCAAAAATAAAG
63 CCCCTCGAAATTGATG
* * ** * **
696950 GGTTTGGAATA-CCCCCGA-GAAAAATTTAATAGTTTAAAAATAAAAACGGGGTTAGAGTATCCC
1 GGGTTGGAGTATCCCGAGATGAAAAATTTAATATTTTGGAAATAAAAACGGGGTTAGAGTATCCC
697013 CTCGAAATTGATG
66 CTCGAAATTGATG
* ** *
697026 GGGTTGGAGTATCTCGAGATGAAAAATTTAGCATTTTGGAAATAAAAACAGGGTTAGAGTATCCC
1 GGGTTGGAGTATCCCGAGATGAAAAATTTAATATTTTGGAAATAAAAACGGGGTTAGAGTATCCC
*
697091 CT-TAGAATTGATG
66 CTCGA-AATTGATG
* * * * * ** *
697104 GGATTGGAGTATCCCCAAATAAAAAATTTAATATTTTAGAAATAAAAATC-GAATTAGAGTATCT
1 GGGTTGGAGTATCCCGAGATGAAAAATTTAATATTTTGGAAATAAAAA-CGGGGTTAGAGTATCC
* **
697168 CCTCGGAAA-TAACA
65 CCTC-GAAATTGATG
* * ** *
697182 GGGTTGGAGCATCTCCGAAATGAAAAA-TCGATATTTTTGGAAATAAAAACGGGGTTGGAGTATC
1 GGGTTGGAGTATC-CCGAGATGAAAAATTTAATA-TTTTGGAAATAAAAACGGGGTTAGAGTATC
** * * * **
697246 CTATTGAAAATAACA
64 CCCTCGAAATTGATG
* ** * * * *
697261 GGGTTAGAGTA-CCCTTGA-GAAAAATTTAATATTTTGAAAATAAAAACGGGATTAAAGTATCGC
1 GGGTTGGAGTATCCCGAGATGAAAAATTTAATATTTTGGAAATAAAAACGGGGTTAGAGTATCCC
*
697324 CTCGGAATTGATG
66 CTCGAAATTGATG
* * * ** * * * * *
697337 AGGTTGAAGTATCCCGAGATGAAAAAATATAGCATTTTGAAAAT-TAAGCGGGGTTTGAGTATTC
1 GGGTTGGAGTATCCCGAGATG-AAAAATTTAATATTTTGGAAATAAAAACGGGGTTAGAGTATCC
*
697401 CCT-TAGAATTGATG
65 CCTCGA-AATTGATG
* * * *
697415 GGGTTGGAGTATCCCCAAGATGAAAAATTTAATATTTTGGAAATAAAAATGGTGTTGGAGTATCC
1 GGGTTGGAGTAT-CCCGAGATGAAAAATTTAATATTTTGGAAATAAAAACGGGGTTAGAGTATCC
* *
697480 CCTCAGAAA-TAATT
65 CCTC-GAAATTGATG
* * * * * *
697494 GAGTTGGAGCATCCCAAAAT-AAAAATTTTAATATTTTGGAAATAAAAGCGGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCGAGATGAAAAA-TTTAATATTTTGGAAATAAAAACGGGGTTAGAGTATCC
697558 CCT
65 CCT
697561 AAGATGAAAA
Statistics
Matches: 472, Mismatches: 117, Indels: 45
0.74 0.18 0.07
Matches are distributed among these distances:
76 93 0.20
77 32 0.07
78 224 0.47
79 119 0.25
80 3 0.01
81 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (78 bp):
GGGTTGGAGTATCCCGAGATGAAAAATTTAATATTTTGGAAATAAAAACGGGGTTAGAGTATCCC
CTCGAAATTGATG
Found at i:697375 original size:155 final size:151
Alignment explanation
Indices: 696872--697557 Score: 485
Period size: 157 Copynumber: 4.4 Consensus size: 151
696862 AATGATCTAG
* * * * * *
696872 GGTTGGAGTATCCCCGAAATGAAAAATTGATA--TTTTTGGAAATAAAAACGAGGCTGAAATATC
1 GGTTGGAGTAT-CCCGAGATGAAAAA-T-ATAGCATTTTGGAAATAAAAACGGGGTTGGAGTAT-
* * * * *
696935 CCTTCAAAAATAAAGGGTTTGGAATACCCCCGAGAAAAATTTAATAGTTTAAAAATAAAAACGGG
62 CCTT-TAAAATAAAGGGATTGGAGTACCCCAGAGAAAAATTTAATA-TTTTAAAATAAAAACGGG
* * *
697000 GTTAGAGTATCCCCTCGAAATTGATGG
125 ATTAGAGTATCCCCTCGGAATTGATGA
* * * * *
697027 GGTTGGAGTATCTCGAGATGAAAAATTTAGCATTTTGGAAATAAAAACAGGGTTAGAGTATCCCC
1 GGTTGGAGTATCCCGAGATGAAAAATATAGCATTTTGGAAATAAAAACGGGGTTGGAGTAT-CCT
* * * * * *
697092 TTAGAATTGATGGGATTGGAGTATCCCCAAATAAAAAATTTAATATTTTAGAAATAAAAATC-GA
65 TTA-AAATAAAGGGATTGGAGTA-CCCCAGA-GAAAAATTTAATATTTTA-AAATAAAAA-CGGG
* * **
697156 ATTAGAGTATCTCCTCGGAAAT-AACA
125 ATTAGAGTATCCCCTCGGAATTGATGA
* * *
697182 GGGTTGGAGCATCTCCGAAATGAAAAATCGATA--TTTTTGGAAATAAAAACGGGGTTGGAGTAT
1 -GGTTGGAGTATC-CCGAGATGAAAAAT--ATAGCATTTTGGAAATAAAAACGGGGTTGGAGTAT
* **
697245 CCTATTGAAAATAACAGGG-TTAGAGTACCCTTGAGAAAAATTTAATATTTTGAAAATAAAAACG
62 CCT-TT-AAAATAA-AGGGATTGGAGTACCCCAGAGAAAAATTTAATATTTT-AAAATAAAAACG
* *
697309 GGATTAAAGTATCGCCTCGGAATTGATGA
123 GGATTAGAGTATCCCCTCGGAATTGATGA
* * * * *
697338 GGTTGAAGTATCCCGAGATGAAAAAATATAGCATTTTGAAAAT-TAAGCGGGGTTTGAGTATTCC
1 GGTTGGAGTATCCCGAGATG-AAAAATATAGCATTTTGGAAATAAAAACGGGGTTGGAGTA-TCC
* * * * * * *
697402 CTTAGAATTGATGGGGTTGGAGTATCCCCAAGATGAAAAATTTAATATTTTGGAAATAAAAATGG
64 TTTA-AAATAAAGGGATTGGAGTA-CCCC-AGA-GAAAAATTTAATATTTT-AAAATAAAAACGG
* * * *
697467 TG-TTGGAGTATCCCCTCAGAAATAATTGA
124 -GATTAGAGTATCCCCTCGGAATTGA-TGA
* * * * ** *
697496 -GTTGGAGCATCCCAAAAT-AAAAATTTTAATATTTTGGAAATAAAAGCGGGGTTGGAGTATCC
1 GGTTGGAGTATCCCGAGATGAAAAA-TATAGCATTTTGGAAATAAAAACGGGGTTGGAGTATCC
697558 CCTAAGATGA
Statistics
Matches: 417, Mismatches: 84, Indels: 59
0.74 0.15 0.11
Matches are distributed among these distances:
152 2 0.00
153 9 0.02
154 88 0.21
155 102 0.24
156 78 0.19
157 128 0.31
158 8 0.02
159 2 0.00
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (151 bp):
GGTTGGAGTATCCCGAGATGAAAAATATAGCATTTTGGAAATAAAAACGGGGTTGGAGTATCCTT
TAAAATAAAGGGATTGGAGTACCCCAGAGAAAAATTTAATATTTTAAAATAAAAACGGGATTAGA
GTATCCCCTCGGAATTGATGA
Found at i:697533 original size:311 final size:310
Alignment explanation
Indices: 696873--697557 Score: 849
Period size: 311 Copynumber: 2.2 Consensus size: 310
696863 ATGATCTAGG
* * * ** * * * *
696873 GTTGGAGTATCCCCGAAATGAAAAATTGATATTTTTGGAAATAAAAACGAGGCTGAAATATCCCT
1 GTTGGAGCATCTCCAAAATGAAAAATCAATATTTTTGGAAATAAAAACGGGGTTGGAGTAT-CCT
* *
696938 TCAAAAATAAAGGGTTTGGAATACCCCCGAGAAAAATTTAATAGTTTAAAAATAAAAACGGGGTT
65 TCAAAAATAAAGGGTTTAGAATACCCCCGAGAAAAATTTAATAGTTTAAAAATAAAAACGGGATT
* * * * * *
697003 AGAGTATCCCCTCGAAATTGATGGGGTTGGAGTATCTCGAGATGAAAAATTTAGCATTTTGGAAA
130 AAAGTATCCCCTCGAAATTGATGAGGTTGAAGTATCCCGAGATGAAAAATATAGCATTTTGAAAA
697068 TAAAAACAGGGTTAGAGTATCCCCTTAGAATTGATGGGATTGGAGTATCCCCAAATAAAAAATTT
195 TAAAAACAGGGTTAGAGTATCCCCTTAGAATTGATGGGATTGGAGTATCCCCAAATAAAAAATTT
* * *
697133 AATATTTTAGAAATAAAAATCGAATTAGAGTATCTCCTCGGAAATAACAGG
260 AATATTTTAGAAATAAAAATCGAATTAGAGTATCCCCTCAGAAATAACAGA
* *
697184 GTTGGAGCATCTCCGAAATGAAAAATCGATATTTTTGGAAATAAAAACGGGGTTGGAGTATCCTA
1 GTTGGAGCATCTCCAAAATGAAAAATCAATATTTTTGGAAATAAAAACGGGGTTGGAGTATCCT-
** * ** * *
697249 TTGAAAATAACAGGG-TTAGAGTACCCTTGAGAAAAATTTAATATTTTGAAAATAAAAACGGGAT
65 TCAAAAATAA-AGGGTTTAGAATACCCCCGAGAAAAATTTAATAGTTTAAAAATAAAAACGGGAT
* *
697313 TAAAGTATCGCCTCGGAATTGATGAGGTTGAAGTATCCCGAGATGAAAAAATATAGCATTTTGAA
129 TAAAGTATCCCCTCGAAATTGATGAGGTTGAAGTATCCCGAGATG-AAAAATATAGCATTTTGAA
* * * * * * *
697378 AAT-TAAGCGGGGTTTGAGTATTCCCTTAGAATTGATGGGGTTGGAGTATCCCCAAGATGAAAAA
193 AATAAAAACAGGGTTAGAGTATCCCCTTAGAATTGATGGGATTGGAGTATCCCCAA-ATAAAAAA
* * ** * **
697442 TTTAATATTTTGGAAATAAAAATGGTGTTGGAGTATCCCCTCAGAAATAATTGA
257 TTTAATATTTTAGAAATAAAAATCGAATTAGAGTATCCCCTCAGAAATAACAGA
* *
697496 GTTGGAGCATC-CCAAAAT-AAAAATTTTAATA-TTTTGGAAATAAAAGCGGGGTTGGAGTATCC
1 GTTGGAGCATCTCCAAAATGAAAAA--TCAATATTTTTGGAAATAAAAACGGGGTTGGAGTATCC
697558 CCTAAGATGA
Statistics
Matches: 323, Mismatches: 45, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
310 8 0.02
311 225 0.70
312 90 0.28
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (310 bp):
GTTGGAGCATCTCCAAAATGAAAAATCAATATTTTTGGAAATAAAAACGGGGTTGGAGTATCCTT
CAAAAATAAAGGGTTTAGAATACCCCCGAGAAAAATTTAATAGTTTAAAAATAAAAACGGGATTA
AAGTATCCCCTCGAAATTGATGAGGTTGAAGTATCCCGAGATGAAAAATATAGCATTTTGAAAAT
AAAAACAGGGTTAGAGTATCCCCTTAGAATTGATGGGATTGGAGTATCCCCAAATAAAAAATTTA
ATATTTTAGAAATAAAAATCGAATTAGAGTATCCCCTCAGAAATAACAGA
Found at i:700030 original size:41 final size:41
Alignment explanation
Indices: 699985--700071 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 41
699975 GTTTTTATTA
* * * *
699985 TAAACGGCGCTAATGTAAATTATTTAGCAGTATTTCTATCT
1 TAAACGCCGCTAATATAAACTATTTAGCAGTATTTCTATCC
* * *
700026 TAAACGCCGCTAATATTAACTATTTAGCGGTGTTTCTATCC
1 TAAACGCCGCTAATATAAACTATTTAGCAGTATTTCTATCC
700067 TAAAC
1 TAAAC
700072 ACTGCTAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (41 bp):
TAAACGCCGCTAATATAAACTATTTAGCAGTATTTCTATCC
Found at i:701805 original size:18 final size:17
Alignment explanation
Indices: 701772--701805 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
701762 TTGTCACTAT
*
701772 AAATACTTTGATCACAA
1 AAATACTTTGAGCACAA
701789 AAATACTTTGCAGCACA
1 AAATACTTTG-AGCACA
701806 CATTGGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.44, C:0.21, G:0.09, T:0.26
Consensus pattern (17 bp):
AAATACTTTGAGCACAA
Found at i:701903 original size:3 final size:3
Alignment explanation
Indices: 701895--701923 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
701885 ATTCTTCCAT
701895 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
701924 GTTAATTGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:702366 original size:21 final size:21
Alignment explanation
Indices: 702327--702385 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
702317 AGCGAAATCC
* *
702327 ATTTTGAATGAAATAAATTTAA
1 ATTTT-AATTAAATTAATTTAA
*
702349 ATTTTAATTAAATTAATTTGA
1 ATTTTAATTAAATTAATTTAA
*
702370 ATTATT-ATTTAATTAA
1 ATT-TTAATTAAATTAA
702386 CAAATTAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 25 0.78
22 7 0.22
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (21 bp):
ATTTTAATTAAATTAATTTAA
Found at i:702501 original size:35 final size:32
Alignment explanation
Indices: 702462--702540 Score: 97
Period size: 32 Copynumber: 2.4 Consensus size: 32
702452 TTTAAAAAAA
*
702462 TAATATTAAATAGTTTTT-AAATTATTTAATAATTT
1 TAATA-TAAATAATTTTTGAAATTA---AATAATTT
*
702497 TAATATAAATAATTTTTGGAATTAAATAATTT
1 TAATATAAATAATTTTTGAAATTAAATAATTT
702529 TAATATAAATAA
1 TAATATAAATAA
702541 ATTACTTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
32 20 0.49
34 11 0.27
35 10 0.24
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (32 bp):
TAATATAAATAATTTTTGAAATTAAATAATTT
Found at i:702509 original size:15 final size:15
Alignment explanation
Indices: 702489--702540 Score: 70
Period size: 15 Copynumber: 3.3 Consensus size: 15
702479 TAAATTATTT
702489 AATAATTTTAATATA
1 AATAATTTTAATATA
702504 AATAATTTTTGGAAT-TA
1 AATAA-TTTT--AATATA
702521 AATAATTTTAATATA
1 AATAATTTTAATATA
702536 AATAA
1 AATAA
702541 ATTACTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
14 3 0.09
15 12 0.36
16 8 0.24
17 7 0.21
18 3 0.09
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (15 bp):
AATAATTTTAATATA
Found at i:702543 original size:16 final size:16
Alignment explanation
Indices: 702492--702543 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
702482 ATTATTTAAT
702492 AATTTTAATATAAATA
1 AATTTTAATATAAATA
*
702508 ATTTTTGGAAT-TAAAT-
1 AATTTT--AATATAAATA
702524 AATTTTAATATAAATA
1 AATTTTAATATAAATA
702540 AATT
1 AATT
702544 ACTTAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
14 3 0.10
15 5 0.17
16 14 0.47
17 5 0.17
18 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (16 bp):
AATTTTAATATAAATA
Found at i:702585 original size:36 final size:37
Alignment explanation
Indices: 702516--702614 Score: 137
Period size: 36 Copynumber: 2.6 Consensus size: 37
702506 TAATTTTTGG
*
702516 AATTAAATAATTTTAATATAAATAAATTACTTAAAAATAAT
1 AATTAAATAATTTT-CT-T-AA-AAATTACTTAAAAATAAT
*
702557 AATTAAA-AATTTTCTTAAAAATTTCTTAAAAATAAT
1 AATTAAATAATTTTCTTAAAAATTACTTAAAAATAAT
702593 AATTAAATAATTTTCTTAAAAA
1 AATTAAATAATTTTCTTAAAAA
702615 AATAATTAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
36 24 0.44
37 16 0.29
38 1 0.02
39 1 0.02
40 6 0.11
41 7 0.13
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (37 bp):
AATTAAATAATTTTCTTAAAAATTACTTAAAAATAAT
Found at i:702613 original size:25 final size:26
Alignment explanation
Indices: 702571--702628 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 26
702561 AAAAATTTTC
*
702571 TTAAA-AA-TTTCTTAAAAATAATAA
1 TTAAATAATTTTCTTAAAAAAAATAA
702595 TTAAATAATTTTCTT-AAAAAAATAA
1 TTAAATAATTTTCTTAAAAAAAATAA
702620 TT-AATAATT
1 TTAAATAATT
702629 ATCTATAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 12 0.39
25 13 0.42
26 6 0.19
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (26 bp):
TTAAATAATTTTCTTAAAAAAAATAA
Found at i:709988 original size:20 final size:20
Alignment explanation
Indices: 709963--710016 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
709953 AATTGTAAGC
* *
709963 ATGTATTGATACATTTACTT
1 ATGTATCGATACATGTACTT
709983 ATGTATCGATACATGTACTAT
1 ATGTATCGATACATGTACT-T
* *
710004 TTGCATCGATACA
1 ATGTATCGATACA
710017 AATTGTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATGTACTT
Found at i:710013 original size:21 final size:20
Alignment explanation
Indices: 709970--710016 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
709960 AGCATGTATT
* *
709970 GATACATTTACTTATGTATC
1 GATACATGTACTTATGCATC
*
709990 GATACATGTACTATTTGCATC
1 GATACATGTACT-TATGCATC
710011 GATACA
1 GATACA
710017 AATTGTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (20 bp):
GATACATGTACTTATGCATC
Found at i:711986 original size:394 final size:394
Alignment explanation
Indices: 711239--712030 Score: 1050
Period size: 394 Copynumber: 2.0 Consensus size: 394
711229 CCAGATTATC
* * * *
711239 ATGGCCACTATATAGCTTAGATACAGGCTATGAGGAATCATATAGTCGCCCAACAGGCCATTATA
1 ATGGCCACTATATAGCTCAGATACAGGCTATGACGAATCACATAGTCGCCCAACAAGCCATTATA
* * ** * * * *
711304 CAATAGTTCTTGCAGAAGTAAGAGAAGTGGCAAAATCCTTCAGCGTAAGTGAATGGCCAAAGTGT
66 CAATAGCTCTTGCAGAAGCAAGAGAAGCAGCAAAATCCTCCAGCGCAAGCGAATGGCCAAAGTGC
* * *
711369 GCAAACCCAGTCAAATCGCCAGAATAGAAAAGTTAAAAGCCATAATCACTTTGATCGACCTTTGA
131 GCAAACCCAGTCAAATCACCAGAATAGAAAAGTTAAAAGCCATAATCACTCTGATCGACCTCTGA
* * *
711434 GCCTAGAAAGTCAACTGAACTGGGAAAGTTTCTACTCGACTCCTAGTAAAGAACGTTTGACTAAA
196 GCCTAGAAAGTCAACTGAACTGGGAAAGTTCCTACTCGACTCCTACTAAAGAACGTTCGACTAAA
711499 AAAAAGAGAGGAGCGGGGCAAGAAGAGTTTGATAGACAAGCATACGCAACGTCAAACTCAACCTT
261 AAAAAGAGAGGAGCGGGGCAAGAAGAGTTTGATAGACAAGCATACGCAACGTCAAACTCAACCTT
* * * * * * *
711564 AACAGAACAGGTAGCCACTCTAAAACAAGAAATTAAGAACCTAAAGCAACCCCACAAAGACGACT
326 AACAGAACAAGTAACCACTCTAAAACAAGAAATAAAAAACCCAAAGCAACCCCACAAAAACAACT
711629 GGGA
391 GGGA
** * *
711633 ATGGCCACTATATAGCTCAGATGTAGGCTATGACTAATCACATAGTCGCCGAACAAGCCATTATA
1 ATGGCCACTATATAGCTCAGATACAGGCTATGACGAATCACATAGTCGCCCAACAAGCCATTATA
* *
711698 CAATAGCTCTTGCAGAAGCAAGAGAAGCAGTAAAATCCTCCAGTGCAAGCGAATGGCCAAAGTGC
66 CAATAGCTCTTGCAGAAGCAAGAGAAGCAGCAAAATCCTCCAGCGCAAGCGAATGGCCAAAGTGC
* * * *
711763 GCAAACCCAGTCAGATCACCAGAATAGAAAAGTTAGAAGCCATACTCGCTCTGATCGACCTCTGA
131 GCAAACCCAGTCAAATCACCAGAATAGAAAAGTTAAAAGCCATAATCACTCTGATCGACCTCTGA
* * * *
711828 G-CTTGAAAAGTCAACT-AGATTGGGAAAGTTCCTACTTGACTCCTACTAAGGAACGTTCGACTA
196 GCCTAG-AAAGTCAACTGA-ACTGGGAAAGTTCCTACTCGACTCCTACTAAAGAACGTTCGACTA
* ** * * * * * *
711891 GAAAACGGAGAGGGGCGGGGCAAGAGGAGTCTT-TTAGACAAGCATACGCAACGTCAGACTTAGC
259 AAAAAAAGAGAGGAGCGGGGCAAGAAGAGT-TTGATAGACAAGCATACGCAACGTCAAACTCAAC
* ** * * *
711955 CTTAGCAGAACAAGTAACTGCTCTGAAACAAGAAATAAAAAACCCAAAGCAACCCTACAAAAATA
323 CTTAACAGAACAAGTAACCACTCTAAAACAAGAAATAAAAAACCCAAAGCAACCCCACAAAAACA
712020 ACTGGGA
388 ACTGGGA
712027 ATGG
1 ATGG
712031 TTGGATGTTG
Statistics
Matches: 341, Mismatches: 54, Indels: 6
0.85 0.13 0.01
Matches are distributed among these distances:
393 4 0.01
394 335 0.98
395 2 0.01
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (394 bp):
ATGGCCACTATATAGCTCAGATACAGGCTATGACGAATCACATAGTCGCCCAACAAGCCATTATA
CAATAGCTCTTGCAGAAGCAAGAGAAGCAGCAAAATCCTCCAGCGCAAGCGAATGGCCAAAGTGC
GCAAACCCAGTCAAATCACCAGAATAGAAAAGTTAAAAGCCATAATCACTCTGATCGACCTCTGA
GCCTAGAAAGTCAACTGAACTGGGAAAGTTCCTACTCGACTCCTACTAAAGAACGTTCGACTAAA
AAAAAGAGAGGAGCGGGGCAAGAAGAGTTTGATAGACAAGCATACGCAACGTCAAACTCAACCTT
AACAGAACAAGTAACCACTCTAAAACAAGAAATAAAAAACCCAAAGCAACCCCACAAAAACAACT
GGGA
Found at i:726192 original size:52 final size:52
Alignment explanation
Indices: 726107--726231 Score: 187
Period size: 52 Copynumber: 2.4 Consensus size: 52
726097 ATATGAAAAG
* *
726107 TTGCTTGCATGTATCAATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCTTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
* *
726159 TTGCTTGCATGTATCGATACATTTTATAATGTATCGATACATTTGGGCAAAT
1 TTGCTTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
** *
726211 TTGCCCGTATGTATCGATACA
1 TTGCTTGCATGTATCGATACA
726232 AAGATCAGTG
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.38
Consensus pattern (52 bp):
TTGCTTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:726244 original size:52 final size:52
Alignment explanation
Indices: 726113--726251 Score: 156
Period size: 52 Copynumber: 2.7 Consensus size: 52
726103 AAAGTTGCTT
* * **
726113 GCATGTATCAATACATTTA-ATAGTGTATCGATACATCTGGGCAAATTTGCTT
1 GCATGTATCGATACA-TAAGATAGTGTATCGATACATCTGGGCAAATTTGCCC
*** * *
726165 GCATGTATCGATACATTTTATAATGTATCGATACATTTGGGCAAATTTGCCC
1 GCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGCCC
*
726217 GTATGTATCGATACA-AAGATCAGTGTATCGATACA
1 GCATGTATCGATACATAAGAT-AGTGTATCGATACA
726252 ATGTATCGAT
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
51 4 0.05
52 70 0.95
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (52 bp):
GCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGCCC
Found at i:726258 original size:13 final size:13
Alignment explanation
Indices: 726240--726264 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
726230 CAAAGATCAG
726240 TGTATCGATACAA
1 TGTATCGATACAA
726253 TGTATCGATACA
1 TGTATCGATACA
726265 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:726342 original size:33 final size:33
Alignment explanation
Indices: 726305--726371 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
726295 AATAGCTTAA
726305 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
726338 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
726371 A
1 A
726372 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:726345 original size:13 final size:13
Alignment explanation
Indices: 726327--726351 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
726317 CAAAAAAATA
726327 TGTATCGATACAT
1 TGTATCGATACAT
726340 TGTATCGATACA
1 TGTATCGATACA
726352 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:727613 original size:69 final size:69
Alignment explanation
Indices: 727502--727640 Score: 278
Period size: 69 Copynumber: 2.0 Consensus size: 69
727492 CCCAAATATT
727502 TTATACCTTAGATGATTATGAATTAAACAACCAATAAGATCCTATCTTTCATTTGTTTATTTAAT
1 TTATACCTTAGATGATTATGAATTAAACAACCAATAAGATCCTATCTTTCATTTGTTTATTTAAT
727567 TCAA
66 TCAA
727571 TTATACCTTAGATGATTATGAATTAAACAACCAATAAGATCCTATCTTTCATTTGTTTATTTAAT
1 TTATACCTTAGATGATTATGAATTAAACAACCAATAAGATCCTATCTTTCATTTGTTTATTTAAT
727636 TCAA
66 TCAA
727640 T
1 T
727641 CATTCTTTCC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.42
Consensus pattern (69 bp):
TTATACCTTAGATGATTATGAATTAAACAACCAATAAGATCCTATCTTTCATTTGTTTATTTAAT
TCAA
Found at i:730332 original size:28 final size:29
Alignment explanation
Indices: 730294--730354 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 29
730284 GAAAAAAATT
730294 TAAAAATAATAA-A-AAATATGATATAATA
1 TAAAAATAATAACATAAATATGATATAA-A
730322 TAAAAATAATAACATAAATATGATATAAA
1 TAAAAATAATAACATAAATATGATATAAA
730351 TAAA
1 TAAA
730355 TATATATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
28 12 0.39
29 6 0.19
30 13 0.42
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (29 bp):
TAAAAATAATAACATAAATATGATATAAA
Found at i:731647 original size:14 final size:14
Alignment explanation
Indices: 731622--731657 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
731612 TAATTTTTTT
731622 AATTTTTT-AAATA
1 AATTTTTTAAAATA
731635 AATTTTTTAAAATA
1 AATTTTTTAAAATA
*
731649 TATTTTTTA
1 AATTTTTTA
731658 TGAATATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
AATTTTTTAAAATA
Found at i:731663 original size:15 final size:13
Alignment explanation
Indices: 731623--731667 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 13
731613 AATTTTTTTA
*
731623 ATTTTTTAAATAA
1 ATTTTTTAAATAT
731636 ATTTTTTAAAATAT
1 ATTTTTT-AAATAT
731650 ATTTTTTATGAATAT
1 ATTTTTTA--AATAT
731665 ATT
1 ATT
731668 AAAAAATCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 8 0.29
14 12 0.43
15 8 0.29
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (13 bp):
ATTTTTTAAATAT
Found at i:732199 original size:23 final size:27
Alignment explanation
Indices: 732170--732228 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
732160 TTTAAAGTTA
732170 TTTTATTT-T-AAAGT-A-TGATTTAT
1 TTTTATTTATAAAAGTAATTGATTTAT
*
732193 TTTTATTTATAAAATTAATTTGATTTAT
1 TTTTATTTATAAAAGTAA-TTGATTTAT
732221 TTTTATTT
1 TTTTATTT
732229 GATTATGTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 8 0.27
24 1 0.03
25 4 0.13
26 1 0.03
28 16 0.53
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (27 bp):
TTTTATTTATAAAAGTAATTGATTTAT
Found at i:734713 original size:87 final size:88
Alignment explanation
Indices: 734460--734720 Score: 317
Period size: 89 Copynumber: 2.9 Consensus size: 88
734450 TTCACTTATG
** * * *
734460 ACATTTACAATCAATCAACTTTTCTGCTTCTCTATTAAAAGGAATCTGATTCTCAAATATAATTC
1 ACATTTACAATCAATCAACTTTT-T--TTC-CTACAAAAAAGAATCTGATTCTCAGATACAATTC
* ** *
734525 ATGCATTAATCTAATCATTGTAGTCTG
62 ATGCATTAATCTAATCCTTACAGTCTA
*
734552 ACATTTACAATCAATCAACTTTTTTTTCTTACAAAAAAGAATCTGATTCTCAGATACAATTCATG
1 ACATTTACAATCAATCAAC-TTTTTTTCCTACAAAAAAGAATCTGATTCTCAGATACAATTCATG
* *
734617 CATTGATCTAATCCTTACAGTTTA
65 CATTAATCTAATCCTTACAGTCTA
* * * * *
734641 ACATTCACAATCAATCAAC-TTTTTTCCTACCAAAATGAATCTGATTTTGAGATACAATTCATGC
1 ACATTTACAATCAATCAACTTTTTTTCCTACAAAAAAGAATCTGATTCTCAGATACAATTCATGC
734705 ATTAATCTAATCCTTA
66 ATTAATCTAATCCTTA
734721 TCGCCTGACA
Statistics
Matches: 149, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
87 55 0.37
89 67 0.45
90 3 0.02
92 20 0.13
93 4 0.03
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (88 bp):
ACATTTACAATCAATCAACTTTTTTTCCTACAAAAAAGAATCTGATTCTCAGATACAATTCATGC
ATTAATCTAATCCTTACAGTCTA
Found at i:735132 original size:39 final size:39
Alignment explanation
Indices: 735084--735201 Score: 96
Period size: 39 Copynumber: 3.1 Consensus size: 39
735074 CAATCATATT
* *
735084 TTTTGAATTTTAATAAAAAATTTATATATTATTCACATC
1 TTTTAAATTTTAATAAAAAATTTATATATTACTCACATC
* ** * *
735123 TTTTAAATTTCAATAAGTAATCTACA-ATTACT-ACTATC
1 TTTTAAATTTTAATAAAAAATTTATATATTACTCAC-ATC
* * * * * *
735161 ATTCAAAATTTAATAAAAAATTTATGTATTAGTCATATC
1 TTTTAAATTTTAATAAAAAATTTATATATTACTCACATC
735200 TT
1 TT
735202 GTAGATTTCA
Statistics
Matches: 57, Mismatches: 19, Indels: 6
0.70 0.23 0.07
Matches are distributed among these distances:
37 2 0.04
38 25 0.44
39 29 0.51
40 1 0.02
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (39 bp):
TTTTAAATTTTAATAAAAAATTTATATATTACTCACATC
Found at i:735822 original size:2 final size:2
Alignment explanation
Indices: 735815--735848 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
735805 TATACATATA
735815 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
735849 CTCTTGGCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:736102 original size:33 final size:33
Alignment explanation
Indices: 736060--736122 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
736050 ATCCTCCCGT
736060 GGCTCTTAATAAATTTATTAACAAATATATATA
1 GGCTCTTAATAAATTTATTAACAAATATATATA
* *
736093 GGCTCTTAATAAATTTATTAATATATATAT
1 GGCTCTTAATAAATTTATTAACAAATATAT
736123 GTGTGTGTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (33 bp):
GGCTCTTAATAAATTTATTAACAAATATATATA
Found at i:740199 original size:21 final size:21
Alignment explanation
Indices: 740174--740214 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
740164 ACATAATAAA
*
740174 AATATAAATATATTAATTTTT
1 AATATAAATATATGAATTTTT
740195 AATATAAATATATGAATTTT
1 AATATAAATATATGAATTTT
740215 CAATTAGTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
AATATAAATATATGAATTTTT
Found at i:741291 original size:26 final size:25
Alignment explanation
Indices: 741262--741319 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 25
741252 TTAATTACTA
* *
741262 TTAAATTAAATTCTTATTAAATTATT
1 TTAAATTAAATACATATTAAA-TATT
* * *
741288 TTAATTTAAGTACATGTTAAATATT
1 TTAAATTAAATACATATTAAATATT
741313 TTAAATT
1 TTAAATT
741320 TATCTTTAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.52
Consensus pattern (25 bp):
TTAAATTAAATACATATTAAATATT
Found at i:748258 original size:79 final size:79
Alignment explanation
Indices: 748125--748385 Score: 335
Period size: 79 Copynumber: 3.3 Consensus size: 79
748115 CTTCACATGC
* * * * *
748125 AACGCCCTGTGATGCCAAGTCACCTTCACTC-GAGTCGCCTCAATGGCGCACAATTGACCCCGCA
1 AACGCCCTGTGACGCCAAGTCACCCTCACTCTG-GTCGCCACCATGGCGCGCAATTGACCCCGCA
748189 TGACGCCGAGTCATT
65 TGACGCCGAGTCATT
748204 AACGCCCTGTGACGCCAAGTCACCCTCACTCTGGTCGCCACCATGGCGCGCAATTGACCCCGCAT
1 AACGCCCTGTGACGCCAAGTCACCCTCACTCTGGTCGCCACCATGGCGCGCAATTGACCCCGCAT
**
748269 GACGTTGAGTCATT
66 GACGCCGAGTCATT
* * ** *
748283 AACGCCTTGTGACGCCAAGACACCCTCACTCTGGTCGCCACCATGGCATGCAATTGACCCCACAT
1 AACGCCCTGTGACGCCAAGTCACCCTCACTCTGGTCGCCACCATGGCGCGCAATTGACCCCGCAT
* * *
748348 GATGCCAAGTTATT
66 GACGCCGAGTCATT
* * * *
748362 AGCGCTCTATGACACCAAGTCACC
1 AACGCCCTGTGACGCCAAGTCACC
748386 GCTACGCTTA
Statistics
Matches: 158, Mismatches: 23, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
79 157 0.99
80 1 0.01
ACGTcount: A:0.23, C:0.36, G:0.21, T:0.20
Consensus pattern (79 bp):
AACGCCCTGTGACGCCAAGTCACCCTCACTCTGGTCGCCACCATGGCGCGCAATTGACCCCGCAT
GACGCCGAGTCATT
Found at i:750329 original size:13 final size:13
Alignment explanation
Indices: 750311--750335 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
750301 GCCAAGAAAA
750311 TGTATCGATACAT
1 TGTATCGATACAT
750324 TGTATCGATACA
1 TGTATCGATACA
750336 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:750402 original size:52 final size:52
Alignment explanation
Indices: 750344--750469 Score: 234
Period size: 52 Copynumber: 2.4 Consensus size: 52
750334 CACTGATCTT
750344 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
750396 TGTATCGATACATTCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
750448 TGTATTGATACATGCAGGCAAA
1 TGTATCGATACATGCAGGCAAA
750470 ATTTCATATT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:755787 original size:17 final size:17
Alignment explanation
Indices: 755764--755799 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
755754 AATTTTATAG
*
755764 TTAAAAAAATTTAAAAAA
1 TTAAAAAAA-ATAAAAAA
755782 TTAAAAAAAATAAAAAA
1 TTAAAAAAAATAAAAAA
755799 T
1 T
755800 ATTACAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
TTAAAAAAAATAAAAAA
Found at i:756625 original size:17 final size:18
Alignment explanation
Indices: 756605--756642 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
756595 TTTATATTTT
756605 TTTAA-ATTTTT-TTATAA
1 TTTAATATTTTTATTA-AA
756622 TTTAATATTTTTATTAAA
1 TTTAATATTTTTATTAAA
756640 TTT
1 TTT
756643 TAAACTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 11 0.58
19 3 0.16
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTAATATTTTTATTAAA
Found at i:757289 original size:13 final size:12
Alignment explanation
Indices: 757263--757332 Score: 56
Period size: 13 Copynumber: 5.7 Consensus size: 12
757253 AAAAAGTATA
757263 AATTTAAA--TT
1 AATTTAAATTTT
757273 AATTTAAAATTTT
1 AATTT-AAATTTT
*
757286 AATTTAATTGTTT
1 AATTTAAAT-TTT
*
757299 GAATTTTAATTTT
1 -AATTTAAATTTT
757312 AAAATTTAAA-TTT
1 --AATTTAAATTTT
757325 AATTTAAA
1 AATTTAAA
757333 ATAAAATCGA
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
10 5 0.10
11 11 0.22
12 3 0.06
13 16 0.33
14 14 0.29
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (12 bp):
AATTTAAATTTT
Found at i:758487 original size:24 final size:24
Alignment explanation
Indices: 758442--758487 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
758432 TGAATTTATT
* ***
758442 TTAATTTTAAAATATTTTATTTAA
1 TTAATTATAAAATATAAAATTTAA
758466 TTAATTATAAAATATAAAATTT
1 TTAATTATAAAATATAAAATTT
758488 TATTTTTTTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TTAATTATAAAATATAAAATTTAA
Found at i:759347 original size:6 final size:7
Alignment explanation
Indices: 759320--759346 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
759310 TAAATTATAA
759320 ATTTTTT
1 ATTTTTT
759327 ATTTTTT
1 ATTTTTT
759334 ATTTTTT
1 ATTTTTT
759341 ATTTTT
1 ATTTTT
759347 AATTAAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
ATTTTTT
Found at i:759804 original size:25 final size:25
Alignment explanation
Indices: 759776--759823 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
759766 ATACATATAT
*
759776 ATTATATTATTCTTA-TTTAAAATAA
1 ATTA-ATTATTATTATTTTAAAATAA
*
759801 ATTAATTGTTATTATTTTAAAAT
1 ATTAATTATTATTATTTTAAAAT
759824 TTTAATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (25 bp):
ATTAATTATTATTATTTTAAAATAA
Found at i:760709 original size:20 final size:20
Alignment explanation
Indices: 760686--760756 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
760676 TGAAACTATT
760686 TACTTATTCTTGAAGTAGCA
1 TACTTATTCTTGAAGTAGCA
* **
760706 TACTTATT-TTGAAACTA-TT
1 TACTTATTCTTG-AAGTAGCA
760725 TACTTATTCTTGAAGTAGCA
1 TACTTATTCTTGAAGTAGCA
760745 TACTTACTTCTT
1 TACTTA-TTCTT
760757 AGTAATAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
19 15 0.37
20 21 0.51
21 5 0.12
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.46
Consensus pattern (20 bp):
TACTTATTCTTGAAGTAGCA
Found at i:760724 original size:39 final size:39
Alignment explanation
Indices: 760674--760750 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
760664 ATAAGAGTTA
760674 TTTGAAACTATTTACTTATTCTTGAAGTAGCATACTTAT
1 TTTGAAACTATTTACTTATTCTTGAAGTAGCATACTTAT
760713 TTTGAAACTATTTACTTATTCTTGAAGTAGCATACTTA
1 TTTGAAACTATTTACTTATTCTTGAAGTAGCATACTTA
760751 CTTCTTAGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.45
Consensus pattern (39 bp):
TTTGAAACTATTTACTTATTCTTGAAGTAGCATACTTAT
Found at i:760728 original size:19 final size:20
Alignment explanation
Indices: 760675--760738 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
760665 TAAGAGTTAT
760675 TTGAAACTATTTACTTATTC
1 TTGAAACTATTTACTTATTC
* **
760695 TTG-AAGTAGCATACTTATT-
1 TTGAAACTA-TTTACTTATTC
760714 TTGAAACTATTTACTTATTC
1 TTGAAACTATTTACTTATTC
760734 TTGAA
1 TTGAA
760739 GTAGCATACT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
19 15 0.43
20 20 0.57
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.47
Consensus pattern (20 bp):
TTGAAACTATTTACTTATTC
Found at i:760767 original size:3 final size:3
Alignment explanation
Indices: 760759--760815 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
760749 TACTTCTTAG
*
760759 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
760807 TAA TAA TAA
1 TAA TAA TAA
760816 ACTCACTTGT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:762460 original size:16 final size:16
Alignment explanation
Indices: 762441--762471 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
762431 TAAAAAAATT
762441 TAAATTTTTATATTTA
1 TAAATTTTTATATTTA
*
762457 TAAATTTTTTTATTT
1 TAAATTTTTATATTT
762472 TCATGATAAT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TAAATTTTTATATTTA
Found at i:764049 original size:22 final size:22
Alignment explanation
Indices: 764023--764085 Score: 108
Period size: 22 Copynumber: 2.9 Consensus size: 22
764013 TAATTACAAA
764023 ATTTACTATTATGTTATTAATT
1 ATTTACTATTATGTTATTAATT
* *
764045 ATTTACTATTATATTACTAATT
1 ATTTACTATTATGTTATTAATT
764067 ATTTACTATTATGTTATTA
1 ATTTACTATTATGTTATTA
764086 CGATACTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.57
Consensus pattern (22 bp):
ATTTACTATTATGTTATTAATT
Done.