Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A04
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: 81554553
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2322942 characters in sequence are not A, C, G, or T
File 47 of 253
Found at i:12338426 original size:26 final size:26
Alignment explanation
Indices: 12338396--12338445 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
12338386 GCAATTTAAC
12338396 CATTTTTATTCAATTTCAAGTTTAGT
1 CATTTTTATTCAATTTCAAGTTTAGT
12338422 CATTTTTATTCAATTTCAAGTTTA
1 CATTTTTATTCAATTTCAAGTTTA
12338446 ACCGAATAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.28, C:0.12, G:0.06, T:0.54
Consensus pattern (26 bp):
CATTTTTATTCAATTTCAAGTTTAGT
Found at i:12339670 original size:24 final size:24
Alignment explanation
Indices: 12339615--12339672 Score: 82
Period size: 24 Copynumber: 2.3 Consensus size: 24
12339605 AATGTACGTG
12339615 AAAAATATTAATTTATTAATATTTA
1 AAAAATA-TAATTTATTAATATTTA
12339640 AATAAATATAATTTATT-ATATTTA
1 AA-AAATATAATTTATTAATATTTA
12339664 TAAAAATAT
1 -AAAAATAT
12339673 TGGTATTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
24 13 0.42
25 13 0.42
26 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
AAAAATATAATTTATTAATATTTA
Found at i:12341387 original size:15 final size:15
Alignment explanation
Indices: 12341344--12341389 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
12341334 TCGGGTTACA
12341344 TTTTAGTCACTTATG
1 TTTTAGTCACTTATG
**
12341359 -TTT-GAAATCTTATG
1 TTTTAGTCA-CTTATG
12341373 TTTTAGTCACTTATG
1 TTTTAGTCACTTATG
12341388 TT
1 TT
12341390 ATTGTGTTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
13 2 0.08
14 9 0.38
15 11 0.46
16 2 0.08
ACGTcount: A:0.22, C:0.11, G:0.13, T:0.54
Consensus pattern (15 bp):
TTTTAGTCACTTATG
Found at i:12344500 original size:65 final size:65
Alignment explanation
Indices: 12344425--12344567 Score: 191
Period size: 65 Copynumber: 2.2 Consensus size: 65
12344415 TGAATGTAAT
* ** * * *
12344425 TGAAATATATTTGCATGTTTATATAATTTATTAAGAAATTAAAAATTAGACAATAAATATATATG
1 TGAAAAATATTTAAATGTGTATATAATTTATCAAGAAACTAAAAATTAGACAATAAATATATATG
**
12344490 TGAAAAATATTTAAATGTGTATATAATTTATCAAGAAACTAAAAATTAGATTATAAATATATA--
1 TGAAAAATATTTAAATGTGTATATAATTTATCAAGAAACTAAAAATTAGACAATAAATATATATG
*
12344553 TGAGAAATATTTAAA
1 TGAAAAATATTTAAA
12344568 AACATTGATA
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
63 14 0.20
65 55 0.80
ACGTcount: A:0.50, C:0.03, G:0.09, T:0.38
Consensus pattern (65 bp):
TGAAAAATATTTAAATGTGTATATAATTTATCAAGAAACTAAAAATTAGACAATAAATATATATG
Found at i:12346547 original size:20 final size:20
Alignment explanation
Indices: 12346489--12346554 Score: 68
Period size: 19 Copynumber: 3.4 Consensus size: 20
12346479 ATTACAATTT
12346489 TATTTTAATAATAGATTTTAA
1 TATTTTAATAATA-ATTTTAA
*
12346510 CA--TTAATAATAATTTTAA
1 TATTTTAATAATAATTTTAA
12346528 -ATTTTAAGTAAT-ATTCTTAA
1 TATTTTAA-TAATAATT-TTAA
12346548 TATTTTA
1 TATTTTA
12346555 TTGAAAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
17 1 0.03
18 7 0.18
19 16 0.41
20 8 0.21
21 7 0.18
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (20 bp):
TATTTTAATAATAATTTTAA
Found at i:12346600 original size:19 final size:20
Alignment explanation
Indices: 12346572--12346610 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
12346562 AATTATATTA
*
12346572 ATATTTCAA-TAATAAATAT
1 ATATTACAATTAATAAATAT
*
12346591 ATATTACAATTTATAAATAT
1 ATATTACAATTAATAAATAT
12346611 TTAGTAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (20 bp):
ATATTACAATTAATAAATAT
Found at i:12352346 original size:6 final size:6
Alignment explanation
Indices: 12352327--12352358 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
12352317 GATTGGTAGG
*
12352327 AGTTAC AGTGAC AGTTAC AGTTAC AGTTAC AG
1 AGTTAC AGTTAC AGTTAC AGTTAC AGTTAC AG
12352359 CATTCTATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (6 bp):
AGTTAC
Found at i:12354046 original size:39 final size:39
Alignment explanation
Indices: 12353871--12354049 Score: 173
Period size: 39 Copynumber: 4.6 Consensus size: 39
12353861 TTTTGCTATT
* * * *
12353871 TCAGGGCCAAAGAGGAAAAT-AGAAGTTTCCTATGATTTT
1 TCAGGGCCAAAGA-GAAAATCAGAAGATTCCTGTAATTTC
* * * * * *
12353910 TCAGGGGCAAAGCGAAAACCAGAAGATTCTTGTGATCTC
1 TCAGGGCCAAAGAGAAAATCAGAAGATTCCTGTAATTTC
* * * *
12353949 TCAGGGGCAAAGAGAAAAT-ATGGAGATTCCTCTAATTCC
1 TCAGGGCCAAAGAGAAAATCA-GAAGATTCCTGTAATTTC
* * *
12353988 TCAGGACCAAAGAGAAAATCTGAAGATTCCTGTAATTTA
1 TCAGGGCCAAAGAGAAAATCAGAAGATTCCTGTAATTTC
12354027 TCAGGGCCAAAGAGAAAATCAGA
1 TCAGGGCCAAAGAGAAAATCAGA
12354050 GGACTCTTCC
Statistics
Matches: 112, Mismatches: 25, Indels: 6
0.78 0.17 0.04
Matches are distributed among these distances:
38 6 0.05
39 106 0.95
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (39 bp):
TCAGGGCCAAAGAGAAAATCAGAAGATTCCTGTAATTTC
Found at i:12357047 original size:68 final size:68
Alignment explanation
Indices: 12356930--12357068 Score: 260
Period size: 68 Copynumber: 2.0 Consensus size: 68
12356920 CAATTGAATG
12356930 TCACATTCTAATTATTTTCGTCTAAGTACACTTGTAATTTTTTCAAACATATTGGTTAATATAAT
1 TCACATTCTAATTATTTTCGTCTAAGTACACTTGTAATTTTTTCAAACATATTGGTTAATATAAT
12356995 TAT
66 TAT
* *
12356998 TCACGTTCTAATTATTTTCGTCTAAGTACACTTGTAATTTTTTCGAACATATTGGTTAATATAAT
1 TCACATTCTAATTATTTTCGTCTAAGTACACTTGTAATTTTTTCAAACATATTGGTTAATATAAT
12357063 TAT
66 TAT
12357066 TCA
1 TCA
12357069 TGAATTATAT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.47
Consensus pattern (68 bp):
TCACATTCTAATTATTTTCGTCTAAGTACACTTGTAATTTTTTCAAACATATTGGTTAATATAAT
TAT
Found at i:12358112 original size:6 final size:6
Alignment explanation
Indices: 12358096--12358160 Score: 69
Period size: 6 Copynumber: 10.7 Consensus size: 6
12358086 GGTTTTCTCA
* * *
12358096 AAATGG GAATGG AAATGG AAATGG AAATGG AAATGA AAATGA AAAT-G
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG
*
12358143 AACATGA AAATGAG AAAT
1 AA-ATGG AAATG-G AAAT
12358161 AATTCAGTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
5 2 0.04
6 42 0.84
7 6 0.12
ACGTcount: A:0.55, C:0.02, G:0.26, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:12358119 original size:18 final size:18
Alignment explanation
Indices: 12358095--12358160 Score: 80
Period size: 18 Copynumber: 3.6 Consensus size: 18
12358085 TGGTTTTCTC
*
12358095 AAAATGGGAATGGAAATG
1 AAAATGGAAATGGAAATG
*
12358113 GAAATGGAAATGGAAATG
1 AAAATGGAAATGGAAATG
*
12358131 AAAATGAAAAT-GAACATG
1 AAAATGGAAATGGAA-ATG
12358149 AAAATGAGAAAT
1 AAAATG-GAAAT
12358161 AATTCAGTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
17 3 0.07
18 34 0.83
19 4 0.10
ACGTcount: A:0.56, C:0.02, G:0.26, T:0.17
Consensus pattern (18 bp):
AAAATGGAAATGGAAATG
Found at i:12359178 original size:41 final size:41
Alignment explanation
Indices: 12359133--12359224 Score: 123
Period size: 41 Copynumber: 2.2 Consensus size: 41
12359123 TTACCGAATC
* *
12359133 AATGAAAAGGTTGAAAACGATGTTATCCAAAAATGATATA-A
1 AATGAAAAGGTTGAAAACGATGCTATCCAAAAAGGATA-ACA
** *
12359174 AATGAAAATATTGAAAAGGATGCTATCCAAAAAGGATAACA
1 AATGAAAAGGTTGAAAACGATGCTATCCAAAAAGGATAACA
12359215 AATGAAAAGG
1 AATGAAAAGG
12359225 ATGTTGTAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 1 0.02
41 42 0.98
ACGTcount: A:0.53, C:0.08, G:0.18, T:0.21
Consensus pattern (41 bp):
AATGAAAAGGTTGAAAACGATGCTATCCAAAAAGGATAACA
Found at i:12382466 original size:17 final size:18
Alignment explanation
Indices: 12382444--12382477 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
12382434 CTGATTTGGG
12382444 TCGTGTGAG-CCACACGA
1 TCGTGTGAGCCCACACGA
12382461 TCGTGTGAGCCCACACG
1 TCGTGTGAGCCCACACG
12382478 GGTGAACAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.21, C:0.32, G:0.29, T:0.18
Consensus pattern (18 bp):
TCGTGTGAGCCCACACGA
Found at i:12382575 original size:17 final size:18
Alignment explanation
Indices: 12382549--12382582 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12382539 CATATAGGGT
12382549 CGTGTAGG-CCACACGGG
1 CGTGTAGGCCCACACGGG
*
12382566 CGTGTGGGCCCACACGG
1 CGTGTAGGCCCACACGG
12382583 ACAAACAACG
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:0.15, C:0.32, G:0.41, T:0.12
Consensus pattern (18 bp):
CGTGTAGGCCCACACGGG
Found at i:12383885 original size:19 final size:19
Alignment explanation
Indices: 12383861--12383900 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
12383851 ATGCTATAGA
*
12383861 TAGTAAATACTGAGACTAT
1 TAGTAAACACTGAGACTAT
12383880 TAGTAAACACTGAGACTAT
1 TAGTAAACACTGAGACTAT
12383899 TA
1 TA
12383901 TAGATAGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (19 bp):
TAGTAAACACTGAGACTAT
Found at i:12395187 original size:19 final size:19
Alignment explanation
Indices: 12395163--12395199 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12395153 TTAAAAATTG
*
12395163 TATTTCCTCATTTTTTTGA
1 TATTTCCTCATATTTTTGA
*
12395182 TATTTCTTCATATTTTTG
1 TATTTCCTCATATTTTTG
12395200 GAGTAAATAG
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:0.16, C:0.14, G:0.05, T:0.65
Consensus pattern (19 bp):
TATTTCCTCATATTTTTGA
Found at i:12395467 original size:39 final size:39
Alignment explanation
Indices: 12395424--12395519 Score: 99
Period size: 39 Copynumber: 2.5 Consensus size: 39
12395414 TCCCCACATT
*
12395424 TTTTTGGTATTTCCTCGT-AATTTTAGTATTTCTTCATAA
1 TTTTTGGTATTTCCTCATCAATTTTAGTATTTCTT-ATAA
* * *
12395463 TTTTT--TAATATTCCTCATCATTTTTGGTATTTCTTATAT
1 TTTTTGGT-AT-TTCCTCATCAATTTTAGTATTTCTTATAA
*
12395502 TTTTTGGTATTCCCTCAT
1 TTTTTGGTATTTCCTCAT
12395520 ATTAGTATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
37 1 0.02
38 2 0.04
39 27 0.57
40 16 0.34
41 1 0.02
ACGTcount: A:0.19, C:0.15, G:0.08, T:0.58
Consensus pattern (39 bp):
TTTTTGGTATTTCCTCATCAATTTTAGTATTTCTTATAA
Found at i:12395493 original size:19 final size:19
Alignment explanation
Indices: 12395423--12395522 Score: 69
Period size: 19 Copynumber: 5.1 Consensus size: 19
12395413 ATCCCCACAT
*
12395423 TTTTTTGGTATTTCCTCGTA
1 TTTTTTGGTA-TTCCTCATA
* * *
12395443 -ATTTTAGTATTTCTTCATAA
1 TTTTTTGGTA-TTCCTCAT-A
**
12395463 TTTTTTAATATTCCTCATCA
1 TTTTTTGGTATTCCTCAT-A
* *
12395483 -TTTTTGGTATTTCTTATA
1 TTTTTTGGTATTCCTCATA
12395501 TTTTTTGGTATTCCCTCATA
1 TTTTTTGGTATT-CCTCATA
12395521 TT
1 TT
12395523 AGTATTTTGA
Statistics
Matches: 62, Mismatches: 14, Indels: 8
0.74 0.17 0.10
Matches are distributed among these distances:
18 1 0.02
19 38 0.61
20 16 0.26
21 7 0.11
ACGTcount: A:0.19, C:0.14, G:0.08, T:0.59
Consensus pattern (19 bp):
TTTTTTGGTATTCCTCATA
Found at i:12401218 original size:34 final size:35
Alignment explanation
Indices: 12401180--12401246 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
12401170 CAGTAAAATG
*
12401180 TTTTCCGTAAAATAATTT-CTGGAAAATATTTTAC
1 TTTTCCGTAAAATAATTTACTAGAAAATATTTTAC
* *
12401214 TTTTCTGTAAAATGATTTACTAGAAAATATTTT
1 TTTTCCGTAAAATAATTTACTAGAAAATATTTT
12401247 TTAGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATAATTTACTAGAAAATATTTTAC
Found at i:12401358 original size:20 final size:20
Alignment explanation
Indices: 12401333--12401371 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
12401323 GTTTTTACAT
12401333 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
12401353 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
12401372 TTTTAAATTA
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:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:12401440 original size:17 final size:18
Alignment explanation
Indices: 12401403--12401452 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
12401393 ATTGCAATGA
*
12401403 TTTATTTATAAATAATTT
1 TTTATTAATAAATAATTT
*
12401421 TTTATTAATAAA-AGTTT
1 TTTATTAATAAATAATTT
12401438 TTTATCTAATTAAAT
1 TTTAT-TAA-TAAAT
12401453 TCTAAATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 9 0.33
18 14 0.52
19 4 0.15
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (18 bp):
TTTATTAATAAATAATTT
Found at i:12404587 original size:11 final size:11
Alignment explanation
Indices: 12404571--12404596 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
12404561 AACCATCTGT
12404571 ATATAACCAAA
1 ATATAACCAAA
12404582 ATATAACCAAA
1 ATATAACCAAA
12404593 ATAT
1 ATAT
12404597 CATCCAGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (11 bp):
ATATAACCAAA
Found at i:12404832 original size:25 final size:25
Alignment explanation
Indices: 12404784--12404833 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
12404774 AGAAGAGAAG
*
12404784 ATGAAGAACAGAAGAAGAAAAAGGA
1 ATGAAAAACAGAAGAAGAAAAAGGA
* *
12404809 ATGAAAAACGGAAGAAGAAGAAGGA
1 ATGAAAAACAGAAGAAGAAAAAGGA
12404834 GCCTTACCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.62, C:0.04, G:0.30, T:0.04
Consensus pattern (25 bp):
ATGAAAAACAGAAGAAGAAAAAGGA
Found at i:12410473 original size:21 final size:21
Alignment explanation
Indices: 12410443--12410531 Score: 90
Period size: 21 Copynumber: 4.1 Consensus size: 21
12410433 CTCACAAAGA
* *
12410443 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTAGAC
* *
12410463 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
12410484 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
12410505 AAAAAGAAACGAAGTGACTTAGAC
1 AAAAAG--A-GAAGTAACTTAGAC
12410529 AAA
1 AAA
12410532 TCTTTTTTGT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
20 6 0.10
21 36 0.62
23 1 0.02
24 15 0.26
ACGTcount: A:0.54, C:0.10, G:0.24, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTAGAC
Found at i:12410524 original size:24 final size:21
Alignment explanation
Indices: 12410443--12410511 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
12410433 CTCACAAAGA
* * *
12410443 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTGGAC
*
12410463 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
12410484 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
12410505 AAAAAGA
1 AAAAAGA
12410512 AACGAAGTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 6 0.14
21 37 0.86
ACGTcount: A:0.55, C:0.09, G:0.25, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTGGAC
Found at i:12412693 original size:18 final size:18
Alignment explanation
Indices: 12412660--12412753 Score: 131
Period size: 18 Copynumber: 5.4 Consensus size: 18
12412650 AAGGTTTTCT
12412660 TATTGATGATA-T--CGA
1 TATTGATGATAGTGACGA
12412675 TATTGATGATAGTGACGA
1 TATTGATGATAGTGACGA
*
12412693 TATTGATGCTAGTGACGA
1 TATTGATGATAGTGACGA
* *
12412711 TATTGATGCTAGTGACGC
1 TATTGATGATAGTGACGA
*
12412729 TATTGATGATAGTGACGC
1 TATTGATGATAGTGACGA
12412747 TATTGAT
1 TATTGAT
12412754 CGTGACCTTG
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
15 11 0.15
16 1 0.01
18 61 0.84
ACGTcount: A:0.29, C:0.10, G:0.26, T:0.36
Consensus pattern (18 bp):
TATTGATGATAGTGACGA
Found at i:12419364 original size:19 final size:19
Alignment explanation
Indices: 12419340--12419379 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
12419330 TTGTTTTTTT
* *
12419340 ATTAGAATCGAAAAGTTTA
1 ATTAGAATAGAAAAGTGTA
12419359 ATTAGAATAGAAAAGTGTA
1 ATTAGAATAGAAAAGTGTA
12419378 AT
1 AT
12419380 AAAAGTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.50, C:0.03, G:0.17, T:0.30
Consensus pattern (19 bp):
ATTAGAATAGAAAAGTGTA
Found at i:12421089 original size:20 final size:19
Alignment explanation
Indices: 12421035--12421092 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 19
12421025 ATAAAAAACA
* *
12421035 AAATAGAGTAGAAAAAAAT
1 AAATAAAGTAGAACAAAAT
* *
12421054 AAATCATA-TAGTACAAAAT
1 AAAT-AAAGTAGAACAAAAT
12421073 CAAATAAAGTAGAACAAAAT
1 -AAATAAAGTAGAACAAAAT
12421093 TGAATGGTAC
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.64, C:0.07, G:0.10, T:0.19
Consensus pattern (19 bp):
AAATAAAGTAGAACAAAAT
Found at i:12421139 original size:15 final size:15
Alignment explanation
Indices: 12421119--12421148 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12421109 GAGCAAAATT
*
12421119 GAACAAAATAGAACA
1 GAACAAAACAGAACA
12421134 GAACAAAACAGAACA
1 GAACAAAACAGAACA
12421149 AAATAGAGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.17, G:0.13, T:0.03
Consensus pattern (15 bp):
GAACAAAACAGAACA
Found at i:12423223 original size:26 final size:26
Alignment explanation
Indices: 12423192--12423272 Score: 92
Period size: 26 Copynumber: 3.1 Consensus size: 26
12423182 TTTGCCACAT
* *
12423192 ATACTGATATTGGCAGCTCTGCTGCG
1 ATACTGATACTGGCAGCTTTGCTGCG
* * *
12423218 TTACTGTTACTGGCGGCTTTGCTGCG
1 ATACTGATACTGGCAGCTTTGCTGCG
*
12423244 ATA-TTATTACTGGCAGCTTTGCTGCG
1 ATACTGA-TACTGGCAGCTTTGCTGCG
12423270 ATA
1 ATA
12423273 TTAGTGTGTT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
25 1 0.02
26 44 0.98
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (26 bp):
ATACTGATACTGGCAGCTTTGCTGCG
Found at i:12423273 original size:26 final size:26
Alignment explanation
Indices: 12423202--12423275 Score: 103
Period size: 26 Copynumber: 2.8 Consensus size: 26
12423192 ATACTGATAT
* * * *
12423202 TGGCAGCTCTGCTGCGTTACTGTTAC
1 TGGCAGCTTTGCTGCGATATTATTAC
*
12423228 TGGCGGCTTTGCTGCGATATTATTAC
1 TGGCAGCTTTGCTGCGATATTATTAC
12423254 TGGCAGCTTTGCTGCGATATTA
1 TGGCAGCTTTGCTGCGATATTA
12423276 GTGTGTTGGC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.15, C:0.22, G:0.27, T:0.36
Consensus pattern (26 bp):
TGGCAGCTTTGCTGCGATATTATTAC
Found at i:12430865 original size:26 final size:25
Alignment explanation
Indices: 12430836--12430885 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
12430826 TGTGTTACTG
*
12430836 TTACTGGTAGCTTTGCTGCGATATTA
1 TTACTGGCAGCTTTGCTGCG-TATTA
12430862 TTACTGGCAGCTTTGCTGCGTATT
1 TTACTGGCAGCTTTGCTGCGTATT
12430886 GGCTGGGTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.42
Consensus pattern (25 bp):
TTACTGGCAGCTTTGCTGCGTATTA
Found at i:12432397 original size:14 final size:14
Alignment explanation
Indices: 12432366--12432412 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
12432356 TTAAAATAAG
12432366 AAACGAAAATGATG-
1 AAAC-AAAATGATGA
**
12432380 AAACTGAATGATGA
1 AAACAAAATGATGA
12432394 AAACAAAATGATAGA
1 AAACAAAATGAT-GA
12432409 AAAC
1 AAAC
12432413 GTTGCAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 7 0.26
14 14 0.52
15 6 0.22
ACGTcount: A:0.60, C:0.09, G:0.17, T:0.15
Consensus pattern (14 bp):
AAACAAAATGATGA
Found at i:12434028 original size:13 final size:13
Alignment explanation
Indices: 12434010--12434035 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12434000 TAAGACAAAG
12434010 GGTTTTAGAAAAT
1 GGTTTTAGAAAAT
12434023 GGTTTTAGAAAAT
1 GGTTTTAGAAAAT
12434036 AAGGTATTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (13 bp):
GGTTTTAGAAAAT
Found at i:12438515 original size:22 final size:22
Alignment explanation
Indices: 12438485--12438527 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
12438475 AACCATGTCA
* *
12438485 TATAGCATATTAGAGCATATCT
1 TATAACATATCAGAGCATATCT
12438507 TATAACATATCAGAGCATATC
1 TATAACATATCAGAGCATATC
12438528 CTACCCCCAT
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:0.40, C:0.16, G:0.12, T:0.33
Consensus pattern (22 bp):
TATAACATATCAGAGCATATCT
Found at i:12439681 original size:22 final size:22
Alignment explanation
Indices: 12439650--12439741 Score: 64
Period size: 22 Copynumber: 4.0 Consensus size: 22
12439640 TATTCAATGT
12439650 AGAATAAAAATAAAAGAG-AAAA
1 AGAA-AAAAATAAAAGAGCAAAA
*
12439672 AGAAAGAAAATAAGAAATGGGCCAAAA
1 AGAAA-AAAAT-A-AAA-GAG-CAAAA
* * *
12439699 AGAAAACAATAACAGAGAAAAA
1 AGAAAAAAATAAAAGAGCAAAA
12439721 AGAAAAAAA-AAAGAGAG-AAAA
1 AGAAAAAAATAAA-AGAGCAAAA
12439742 CATTAAAGGG
Statistics
Matches: 56, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
21 7 0.12
22 25 0.45
23 3 0.05
24 5 0.09
25 3 0.05
26 4 0.07
27 9 0.16
ACGTcount: A:0.73, C:0.04, G:0.17, T:0.05
Consensus pattern (22 bp):
AGAAAAAAATAAAAGAGCAAAA
Found at i:12445105 original size:28 final size:28
Alignment explanation
Indices: 12445074--12445144 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
12445064 CGATATTTTG
*
12445074 CACACTAAGTGTCATTCTCAATATCTCC
1 CACACTAAGTGCCATTCTCAATATCTCC
* *
12445102 CACACTAAGTGCCATTCTCAATATTTCG
1 CACACTAAGTGCCATTCTCAATATCTCC
* *
12445130 TACACTAAGTACCAT
1 CACACTAAGTGCCAT
12445145 ATTTGATTGC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.31, C:0.30, G:0.08, T:0.31
Consensus pattern (28 bp):
CACACTAAGTGCCATTCTCAATATCTCC
Found at i:12450138 original size:28 final size:28
Alignment explanation
Indices: 12450104--12450258 Score: 166
Period size: 28 Copynumber: 5.5 Consensus size: 28
12450094 AACCGATCTT
* *
12450104 GCACACACAGTGCTTGGTTACGGAACTC
1 GCACACACAGTGCTCGATTACGGAACTC
* ** * *
12450132 GCACACACAGTGCCTCAACAACCGATCTC
1 GCACACACAGTG-CTCGATTACGGAACTC
*
12450161 GCACACACAGTGCTCGGTTACGGAACTC
1 GCACACACAGTGCTCGATTACGGAACTC
* ** * *
12450189 GCACACACAGTGCCTCAACAACCGATCTC
1 GCACACACAGTG-CTCGATTACGGAACTC
12450218 GCACACACAGTGCTCGATTACGGAACTC
1 GCACACACAGTGCTCGATTACGGAACTC
*
12450246 ACACACACAGTGC
1 GCACACACAGTGC
12450259 CTATGTTCAC
Statistics
Matches: 100, Mismatches: 25, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
28 57 0.57
29 43 0.43
ACGTcount: A:0.29, C:0.35, G:0.19, T:0.16
Consensus pattern (28 bp):
GCACACACAGTGCTCGATTACGGAACTC
Found at i:12450144 original size:57 final size:57
Alignment explanation
Indices: 12450074--12450260 Score: 311
Period size: 57 Copynumber: 3.2 Consensus size: 57
12450064 GATCTCATTT
* * *
12450074 CACACACTTAGTGCCCCAACAACCGATCTTGCACACACAGTGCTTGGTTACGGAACTCG
1 CACACAC--AGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
12450133 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
1 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
* *
12450190 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGATTACGGAACTCA
1 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
12450247 CACACACAGTGCCT
1 CACACACAGTGCCT
12450261 ATGTTCACTT
Statistics
Matches: 123, Mismatches: 5, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
57 116 0.94
59 7 0.06
ACGTcount: A:0.29, C:0.36, G:0.18, T:0.17
Consensus pattern (57 bp):
CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
Found at i:12450170 original size:29 final size:29
Alignment explanation
Indices: 12450074--12450230 Score: 147
Period size: 29 Copynumber: 5.4 Consensus size: 29
12450064 GATCTCATTT
* *
12450074 CACACACTTAGTGCCCCAACAACCGATCTTG
1 CACACAC--AGTGCCTCAACAACCGATCTCG
***** * *
12450105 CACACACAGTG-CTTGGTTACGGAACTCG
1 CACACACAGTGCCTCAACAACCGATCTCG
12450133 CACACACAGTGCCTCAACAACCGATCTCG
1 CACACACAGTGCCTCAACAACCGATCTCG
**** * *
12450162 CACACACAGTG-CTCGGTTACGGAACTCG
1 CACACACAGTGCCTCAACAACCGATCTCG
12450190 CACACACAGTGCCTCAACAACCGATCTCG
1 CACACACAGTGCCTCAACAACCGATCTCG
12450219 CACACACAGTGC
1 CACACACAGTGC
12450231 TCGATTACGG
Statistics
Matches: 96, Mismatches: 28, Indels: 6
0.74 0.22 0.05
Matches are distributed among these distances:
28 41 0.43
29 48 0.50
31 7 0.07
ACGTcount: A:0.29, C:0.37, G:0.18, T:0.17
Consensus pattern (29 bp):
CACACACAGTGCCTCAACAACCGATCTCG
Found at i:12452258 original size:26 final size:26
Alignment explanation
Indices: 12452229--12452309 Score: 72
Period size: 28 Copynumber: 3.0 Consensus size: 26
12452219 TCCCTTTGAA
* * *
12452229 TCATTCGATATTTTGCACACTAAGTG
1 TCATTCAATATCTCGCACACTAAGTG
12452255 TCATTCTCAATATCTCGCACACTAAGTG
1 TCA-T-TCAATATCTCGCACACTAAGTG
* * *
12452283 CCATTCTCAATATTTCGTACACTAAGT
1 TCA-T-TCAATATCTCGCACACTAAGT
12452310 ACCATATTTG
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
26 3 0.06
27 1 0.02
28 43 0.91
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (26 bp):
TCATTCAATATCTCGCACACTAAGTG
Found at i:12452274 original size:28 final size:28
Alignment explanation
Indices: 12452243--12452314 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
12452233 TCGATATTTT
*
12452243 GCACACTAAGTGTCATTCTCAATATCTC
1 GCACACTAAGTGCCATTCTCAATATCTC
*
12452271 GCACACTAAGTGCCATTCTCAATATTTC
1 GCACACTAAGTGCCATTCTCAATATCTC
* *
12452299 GTACACTAAGTACCAT
1 GCACACTAAGTGCCAT
12452315 ATTTGATTGC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.31
Consensus pattern (28 bp):
GCACACTAAGTGCCATTCTCAATATCTC
Found at i:12458578 original size:40 final size:40
Alignment explanation
Indices: 12458503--12458578 Score: 91
Period size: 40 Copynumber: 1.9 Consensus size: 40
12458493 TCAATTACCA
* * *
12458503 TATAGTCGAAACTATTCCAATTCGCACACTAAGTGCTTTC
1 TATAGCCGAAACTATCCCAATTCGCACAATAAGTGCTTTC
* *
12458543 TATAGCCGAAGCTATCCCGAATT-GCACAATGAGTGC
1 TATAGCCGAAACTATCCC-AATTCGCACAATAAGTGC
12458579 CAAACATAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
40 26 0.87
41 4 0.13
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (40 bp):
TATAGCCGAAACTATCCCAATTCGCACAATAAGTGCTTTC
Found at i:12461135 original size:104 final size:105
Alignment explanation
Indices: 12461004--12461195 Score: 235
Period size: 105 Copynumber: 1.8 Consensus size: 105
12460994 CTAAGTCGTG
* ** * * *
12461004 TAACTCACTGTTTGTGATTTAGGACCACATAGCCAG-GGACAT-AGGCGTGTGCCTAGGCCGTGT
1 TAACTCACTGTTTATGATTTAAAACCACAAAGCCAGAGGACATGA-ACATGTGCCTAGGCCGTGT
*
12461067 GAGTCACACAGGAAAGGACATGGGAATTTGTTTAGGCCGTT
65 GAGCCACACAGGAAAGGACATGGGAATTTGTTTAGGCCGTT
* ** * *
12461108 TAACTCACTGTTTATGTTTTAAAACCACAAAGGTAGAGGACATGAACATGTGTCTAGGCCTTGTG
1 TAACTCACTGTTTATGATTTAAAACCACAAAGCCAGAGGACATGAACATGTGCCTAGGCCGTGTG
* *
12461173 AGCCACACGGGCAAGGACATGGG
66 AGCCACACAGGAAAGGACATGGG
12461196 CTTGTGTCTA
Statistics
Matches: 72, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
104 29 0.40
105 42 0.58
106 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (105 bp):
TAACTCACTGTTTATGATTTAAAACCACAAAGCCAGAGGACATGAACATGTGCCTAGGCCGTGTG
AGCCACACAGGAAAGGACATGGGAATTTGTTTAGGCCGTT
Found at i:12462677 original size:87 final size:87
Alignment explanation
Indices: 12462531--12462700 Score: 331
Period size: 87 Copynumber: 2.0 Consensus size: 87
12462521 TTGGTGTAAC
12462531 TCATCCAAGTTCGGCTTAAACTTCTATGCCAGGTTTGGGGTGTTACACTATATTTTATTTCAACA
1 TCATCCAAGTTCGGCTTAAACTTCTATGCCAGGTTTGGGGTGTTACACTATATTTTATTTCAACA
12462596 AGGATTCAAGTCACTCAATAAG
66 AGGATTCAAGTCACTCAATAAG
*
12462618 TCATCCAAGTTCGGCTTAAACTTCTATGCCAGGTTTGGGGTGTTACACTATATTTTATTTTAACA
1 TCATCCAAGTTCGGCTTAAACTTCTATGCCAGGTTTGGGGTGTTACACTATATTTTATTTCAACA
12462683 AGGATTCAAGTCACTCAA
66 AGGATTCAAGTCACTCAA
12462701 CTCTAACAAT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 82 1.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.35
Consensus pattern (87 bp):
TCATCCAAGTTCGGCTTAAACTTCTATGCCAGGTTTGGGGTGTTACACTATATTTTATTTCAACA
AGGATTCAAGTCACTCAATAAG
Found at i:12464532 original size:16 final size:16
Alignment explanation
Indices: 12464508--12464538 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12464498 TAAGTAAATA
*
12464508 AAATGAAATAAAGAAT
1 AAATAAAATAAAGAAT
12464524 AAATAAAATAAAGAA
1 AAATAAAATAAAGAA
12464539 ACAAAAGAAG
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:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (16 bp):
AAATAAAATAAAGAAT
Found at i:12466531 original size:20 final size:20
Alignment explanation
Indices: 12466506--12466556 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
12466496 GCCCATGGGT
*
12466506 AGGCCACACGGGCATGTTCC
1 AGGCCACACGGGCATGTCCC
12466526 AGGCCACACGGGCATGTCCC
1 AGGCCACACGGGCATGTCCC
12466546 AGGCCACACGG
1 AGGCCACACGG
12466557 ACGTGTGCCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.22, C:0.37, G:0.31, T:0.10
Consensus pattern (20 bp):
AGGCCACACGGGCATGTCCC
Found at i:12468474 original size:48 final size:47
Alignment explanation
Indices: 12468402--12468574 Score: 123
Period size: 48 Copynumber: 3.6 Consensus size: 47
12468392 TCCAAATATT
* * * * * **
12468402 GATGCCATATCCCGGATATGGTCTTATACGAAGTCTC-ATATCAGTGCC
1 GATGCCATGTCCCAGACATGGTCTTACAC-AAG-CACAATATCAACGCC
* * *
12468450 TATGCCATGTCCCAGACATGGTCTTACACTAGCACATATATCAACGTC
1 GATGCCATGTCCCAGACATGGTCTTACACAAGCACA-ATATCAACGCC
**** * * **
12468498 GATGCCATGTCCCAGACATGGTCTTACGTTGGCTCACATATCAATGTT
1 GATGCCATGTCCCAGACATGGTCTTACACAAGCACA-ATATCAACGCC
* *
12468546 GATTCCATGTCCTAGACATGGTCTTACAC
1 GATGCCATGTCCCAGACATGGTCTTACAC
12468575 TGGCTCTCAT
Statistics
Matches: 101, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
46 2 0.02
47 2 0.02
48 97 0.96
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.29
Consensus pattern (47 bp):
GATGCCATGTCCCAGACATGGTCTTACACAAGCACAATATCAACGCC
Found at i:12468579 original size:48 final size:48
Alignment explanation
Indices: 12468451--12468580 Score: 179
Period size: 48 Copynumber: 2.7 Consensus size: 48
12468441 ATCAGTGCCT
* * *
12468451 ATGCCATGTCCCAGACATGGTCTTACACTAGCACATATATCAACGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCAACGTCG
** * *
12468499 ATGCCATGTCCCAGACATGGTCTTACGTTGGCTCACATATCAATGTTG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCAACGTCG
* *
12468547 ATTCCATGTCCTAGACATGGTCTTACACTGGCTC
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTC
12468581 TCATTAACCA
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 71 1.00
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCAACGTCG
Found at i:12492871 original size:28 final size:29
Alignment explanation
Indices: 12492806--12492870 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
12492796 TTATGGATTG
* *
12492806 ATGGATTTTGTTTGTTATGTTAATTTTTT
1 ATGGATTTTGTTTGTGATATTAATTTTTT
12492835 ATGGATTTTGTTTGTGATATT-A-TTTTT
1 ATGGATTTTGTTTGTGATATTAATTTTTT
*
12492862 ATTGATTTT
1 ATGGATTTT
12492871 TTAATGGAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 13 0.39
28 1 0.03
29 19 0.58
ACGTcount: A:0.18, C:0.00, G:0.17, T:0.65
Consensus pattern (29 bp):
ATGGATTTTGTTTGTGATATTAATTTTTT
Found at i:12507280 original size:43 final size:43
Alignment explanation
Indices: 12507219--12507375 Score: 169
Period size: 43 Copynumber: 3.7 Consensus size: 43
12507209 TAAGTGTATT
* * *
12507219 CATGTAAGACCACATCTGGGACGTTGGCATTGATATGTGATTA
1 CATGTAAGACCACGTCTGGGACGTTGGCATCGATATATGATTA
* * * *
12507262 CATGTAAGACCATGTCTGGGACATCGGCATCG-TATTTGATT-
1 CATGTAAGACCACGTCTGGGACGTTGGCATCGATATATGATTA
* * *
12507303 CGTGTAAGACC-CTGTCTGGGACAG-TGGCATCAAGATATGATTA
1 CATGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATATGATTA
*
12507346 CATGTAAGACCACGTCTGGAACGTTGGCAT
1 CATGTAAGACCACGTCTGGGACGTTGGCAT
12507376 TGTACGATAT
Statistics
Matches: 93, Mismatches: 15, Indels: 12
0.77 0.12 0.10
Matches are distributed among these distances:
41 25 0.27
42 16 0.17
43 51 0.55
44 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (43 bp):
CATGTAAGACCACGTCTGGGACGTTGGCATCGATATATGATTA
Found at i:12516576 original size:35 final size:35
Alignment explanation
Indices: 12516500--12516629 Score: 120
Period size: 37 Copynumber: 3.6 Consensus size: 35
12516490 CTAAAACTAT
* * *
12516500 ATACACATATATATA-AATTATATAAAATAAGACCC
1 ATACACATATTTATATTA-TATATAAAACAAGACCC
*
12516535 ATATACACATATTTATATTATATATAAAACAGGACCC
1 --ATACACATATTTATATTATATATAAAACAAGACCC
*
12516572 ATACACGAGTATTTATATTATATATATAACAAGA-CC
1 ATACAC-A-TATTTATATTATATATAAAACAAGACCC
**
12516608 ATGTATGCATATTTATATTATA
1 A--TACACATATTTATATTATA
12516630 CATACCTATT
Statistics
Matches: 80, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
35 6 0.08
36 17 0.21
37 53 0.66
38 4 0.05
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (35 bp):
ATACACATATTTATATTATATATAAAACAAGACCC
Found at i:12521363 original size:25 final size:25
Alignment explanation
Indices: 12521335--12521387 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
12521325 TTCATTTTAT
*
12521335 ATTTATTTAT-TGCATACAAAAATAA
1 ATTTATTTATCT-AATACAAAAATAA
*
12521360 ATTTATTTATCTAATATAAAAATAA
1 ATTTATTTATCTAATACAAAAATAA
12521385 ATT
1 ATT
12521388 AATGTGTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 24 0.96
26 1 0.04
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (25 bp):
ATTTATTTATCTAATACAAAAATAA
Found at i:12526486 original size:5 final size:5
Alignment explanation
Indices: 12526476--12526510 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
12526466 CAATTTGAGA
12526476 AAAAT AAAAT AAAAT AAAAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT --AAAAT AAAAT AAAAT AAA
12526511 GAACACACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 23 0.82
7 5 0.18
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:12526497 original size:17 final size:17
Alignment explanation
Indices: 12526475--12526510 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
12526465 CCAATTTGAG
12526475 AAAAATAAAATAAAATA
1 AAAAATAAAATAAAATA
12526492 AAAAATAAAATAAAATA
1 AAAAATAAAATAAAATA
12526509 AA
1 AA
12526511 GAACACACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (17 bp):
AAAAATAAAATAAAATA
Found at i:12526498 original size:12 final size:12
Alignment explanation
Indices: 12526481--12526506 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12526471 TGAGAAAAAT
12526481 AAAATAAAATAA
1 AAAATAAAATAA
12526493 AAAATAAAATAA
1 AAAATAAAATAA
12526505 AA
1 AA
12526507 TAAAGAACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:12527008 original size:39 final size:40
Alignment explanation
Indices: 12526952--12527078 Score: 118
Period size: 39 Copynumber: 3.2 Consensus size: 40
12526942 AAAAAATTGG
* **
12526952 TATTC-CTTATAATTTTTGGTATCCCCTCATGGTTTTTTA
1 TATTCTCTCATAATTTTTGGTATCCCCTCATATTTTTTTA
* * **
12526991 TATTCTCTCATAA-TTTTGATGTTTCCTCATATTTTTTTA
1 TATTCTCTCATAATTTTTGGTATCCCCTCATATTTTTTTA
* * *
12527030 -ATTCTCTCTCATAATTTTTTGTA-CCTCTCATATTTTTTTG
1 TA-T-TCTCTCATAATTTTTGGTATCCCCTCATATTTTTTTA
12527070 TATTCTCTC
1 TATTCTCTC
12527079 GTGTTAGCGT
Statistics
Matches: 69, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
38 1 0.01
39 32 0.46
40 30 0.43
41 6 0.09
ACGTcount: A:0.18, C:0.19, G:0.06, T:0.57
Consensus pattern (40 bp):
TATTCTCTCATAATTTTTGGTATCCCCTCATATTTTTTTA
Found at i:12527040 original size:21 final size:20
Alignment explanation
Indices: 12527016--12527078 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 20
12527006 TTGATGTTTC
12527016 CTCATATTTTTTTAATTCTCT
1 CTCATATTTTTTT-ATTCTCT
* * *
12527037 CTCATAATTTTTTGTAC-CT
1 CTCATATTTTTTTATTCTCT
12527056 CTCATATTTTTTTGTATTCTCT
1 CTCATA-TTTTTT-TATTCTCT
12527078 C
1 C
12527079 GTGTTAGCGT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
19 8 0.24
20 7 0.21
21 15 0.45
22 3 0.09
ACGTcount: A:0.17, C:0.21, G:0.03, T:0.59
Consensus pattern (20 bp):
CTCATATTTTTTTATTCTCT
Found at i:12527076 original size:18 final size:19
Alignment explanation
Indices: 12527035--12527071 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
12527025 TTTTAATTCT
12527035 CTCTCATAATTTTTTGTAC
1 CTCTCATAATTTTTTGTAC
*
12527054 CTCTCATATTTTTTTGTA
1 CTCTCATAATTTTTTGTA
12527072 TTCTCTCGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.19, C:0.19, G:0.05, T:0.57
Consensus pattern (19 bp):
CTCTCATAATTTTTTGTAC
Found at i:12527184 original size:25 final size:25
Alignment explanation
Indices: 12527156--12527204 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
12527146 AATGGTATTA
*
12527156 GAACAAATGTATCAATCTAGCTAAT
1 GAACAAATGTATCAATCTAACTAAT
12527181 GAACAAATGTATCAATCTAACTAA
1 GAACAAATGTATCAATCTAACTAA
12527205 CGAAATGCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.27
Consensus pattern (25 bp):
GAACAAATGTATCAATCTAACTAAT
Found at i:12540160 original size:10 final size:10
Alignment explanation
Indices: 12540133--12540171 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
12540123 TTAAATTCTA
12540133 AAAGATAAAT
1 AAAGATAAAT
12540143 ACAA-ATAAAT
1 A-AAGATAAAT
*
12540153 AAAGATAACT
1 AAAGATAAAT
12540163 AAAGATAAA
1 AAAGATAAA
12540172 AGCTAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.69, C:0.05, G:0.08, T:0.18
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:12542329 original size:30 final size:30
Alignment explanation
Indices: 12542272--12542329 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
12542262 TTTTCGAGCT
* **
12542272 TAGGGGCAAAATGGTTATTTTGTCAAAGTC
1 TAGGGGCAAAATGGTCATTTTACCAAAGTC
12542302 TAGGGGCAAAATGGTCATTTTACCAAAG
1 TAGGGGCAAAATGGTCATTTTACCAAAG
12542330 ATGTGAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (30 bp):
TAGGGGCAAAATGGTCATTTTACCAAAGTC
Found at i:12542840 original size:94 final size:96
Alignment explanation
Indices: 12542667--12543030 Score: 403
Period size: 94 Copynumber: 3.9 Consensus size: 96
12542657 GGTGAATTGT
* *
12542667 GTGCTAGTGTAAGACATGTCTGGGACATGCATCAGCACGCAT-CTATGAGAGCCAATATAAGACC
1 GTGCTAGTGTAAGACATGTCTGGGACATGCATCAG-ACGCATACTATGAGAGCCAGTGTAAGACC
* *
12542731 ATGTCTGGGACATGGCATCGACATCCAGACGA
65 ATGTCTGGGACATGGCATCGGCATCAAGACGA
* * * * * *
12542763 GGGCTAGTGCAAGACATGTCCGGGACATGCATCAG-C-CATACTATGATAGCCAGTGTAACACAA
1 GTGCTAGTGTAAGACATGTCTGGGACATGCATCAGACGCATACTATGAGAGCCAGTGTAAGACCA
12542826 TGTCTGGGACATGGCATCGGCA-CAGAGACGA
66 TGTCTGGGACATGGCATCGGCATCA-AGACGA
* * * * * *
12542857 GTGCCAGTGTAAAACATGTCTGGGACATGCATCTGCCTC-GAC-A-GAGATAGCCAGTGTAAGA-
1 GTGCTAGTGTAAGACATGTCTGGGACATGCATCAGACGCATACTATGAG--AGCCAGTGTAAGAC
* * *
12542918 CGTGTCTGGGACA-CGCATCGGC-T-AAGA-GTT
64 CATGTCTGGGACATGGCATCGGCATCAAGACG-A
*
12542948 GTGCTAGTGTAAGACATGTCTGGGACATGCATCAGCACGCGTA-TATGAGAGCCAGTGTAAGACC
1 GTGCTAGTGTAAGACATGTCTGGGACATGCATCAG-ACGCATACTATGAGAGCCAGTGTAAGACC
12543012 ATGTCTGGGACATGGCATC
65 ATGTCTGGGACATGGCATC
12543031 AGCAATATAT
Statistics
Matches: 223, Mismatches: 31, Indels: 30
0.79 0.11 0.11
Matches are distributed among these distances:
90 1 0.00
91 35 0.16
92 16 0.07
93 28 0.13
94 95 0.43
95 15 0.07
96 33 0.15
ACGTcount: A:0.28, C:0.22, G:0.29, T:0.21
Consensus pattern (96 bp):
GTGCTAGTGTAAGACATGTCTGGGACATGCATCAGACGCATACTATGAGAGCCAGTGTAAGACCA
TGTCTGGGACATGGCATCGGCATCAAGACGA
Found at i:12542876 original size:47 final size:46
Alignment explanation
Indices: 12542667--12543030 Score: 215
Period size: 47 Copynumber: 7.7 Consensus size: 46
12542657 GGTGAATTGT
* * * *
12542667 GTGCTAGTGTAAGACATGTCTGGGACATGCATCAGCAC-GCATCTATGA
1 GTGCCAGTGTAAGACATGTCTGGGACATGCATCGGCACAG-A--GACGA
* * * * *
12542715 GAGCCAATATAAGACCATGTCTGGGACATGGCATCGACATC-CAGACGA
1 GTGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCA-CAGAGACGA
* * * * * * * *
12542763 GGGCTAGTGCAAGACATGTCCGGGACATGCATCAGC-CATACTATGA
1 GTGCCAGTGTAAGACATGTCTGGGACATGCATCGGCACAGA-GACGA
*
12542809 -TAGCCAGTGTAACACAATGTCTGGGACATGGCATCGGCACAGAGACGA
1 GT-GCCAGTGTAAGAC-ATGTCTGGGACAT-GCATCGGCACAGAGACGA
* * **
12542857 GTGCCAGTGTAAAACATGTCTGGGACATGCATCTGC-C-TCGACAGA
1 GTGCCAGTGTAAGACATGTCTGGGACATGCATCGGCACAGAGAC-GA
* * **
12542902 GATAGCCAGTGTAAGACGTGTCTGGGACACGCATCGGCTA-AGAG--TT
1 G-T-GCCAGTGTAAGACATGTCTGGGACATGCATCGGC-ACAGAGACGA
* * * * *
12542948 GTGCTAGTGTAAGACATGTCTGGGACATGCATCAGCACGCGTATATGA
1 GTGCCAGTGTAAGACATGTCTGGGACATGCATCGGCAC-AG-AGACGA
*
12542996 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATC
1 GTGCCAGTGTAAGA-CATGTCTGGGACAT-GCATC
12543031 AGCAATATAT
Statistics
Matches: 242, Mismatches: 51, Indels: 44
0.72 0.15 0.13
Matches are distributed among these distances:
43 1 0.00
44 34 0.14
45 7 0.03
46 29 0.12
47 68 0.28
48 56 0.23
49 33 0.14
50 13 0.05
51 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.29, T:0.21
Consensus pattern (46 bp):
GTGCCAGTGTAAGACATGTCTGGGACATGCATCGGCACAGAGACGA
Found at i:12549935 original size:30 final size:30
Alignment explanation
Indices: 12549878--12549935 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
12549868 TTTTCGAGCT
* **
12549878 TAGGGGCAAAATGGTTATTTTGTCAAAGTC
1 TAGGGGCAAAATGGTCATTTTACCAAAGTC
12549908 TAGGGGCAAAATGGTCATTTTACCAAAG
1 TAGGGGCAAAATGGTCATTTTACCAAAG
12549936 ATGTGAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (30 bp):
TAGGGGCAAAATGGTCATTTTACCAAAGTC
Found at i:12550309 original size:50 final size:50
Alignment explanation
Indices: 12550277--12550639 Score: 159
Period size: 47 Copynumber: 7.7 Consensus size: 50
12550267 TTTGTGTGCT
12550277 AGTATAAGA-CATGTCTGGGACAT-GCATCAGCATACGTATATGAGAGCC
1 AGTATAAGACCATGTCTGGGACATGGCATCAGCATACGTATATGAGAGCC
* * * *
12550325 AGTATAAGACCATGTCTGGGACATGGCATC-GACAT-C-CAGACGA-AGGCT
1 AGTATAAGACCATGTCTGGGACATGGCATCAG-CATACGTATATGAGA-GCC
* * * *
12550373 AGTGTAAGA-CATGTCCGGAACAT-GCATCAGCCATAC---TATGATAGCC
1 AGTATAAGACCATGTCTGGGACATGGCATCAG-CATACGTATATGAGAGCC
* * * * * * * *
12550419 AGTGTAACACAATGTCTGGGACATGGCATCGGCACA-G-AGACGAGTGCC
1 AGTATAAGACCATGTCTGGGACATGGCATCAGCATACGTATATGAGAGCC
* * * * * *
12550467 AGTGTAA-AACATGTCTGGGACAT-GCATCGGCCTTGAC--AGA-GATAGCC
1 AGTATAAGACCATGTCTGGGACATGGCATCAG-CAT-ACGTATATGAGAGCC
* * * * * * * *
12550514 AGTGTAAGA-CGTGTCTAGGACA-CGCATCGGC-TAAG-AGT-T--GTGCT
1 AGTATAAGACCATGTCTGGGACATGGCATCAGCATACGTA-TATGAGAGCC
** ** *
12550558 AGTGCAAGA-CATGTCTGGGACAT-GCATCAGCACGCGTATATGAGAGCT
1 AGTATAAGACCATGTCTGGGACATGGCATCAGCATACGTATATGAGAGCC
*
12550606 AGTGTAAGACCATGTCTGGGACATGGCATCAGCA
1 AGTATAAGACCATGTCTGGGACATGGCATCAGCA
12550640 ATATATCCCA
Statistics
Matches: 245, Mismatches: 43, Indels: 52
0.72 0.13 0.15
Matches are distributed among these distances:
44 29 0.12
45 4 0.02
46 28 0.11
47 77 0.31
48 60 0.24
49 30 0.12
50 17 0.07
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.21
Consensus pattern (50 bp):
AGTATAAGACCATGTCTGGGACATGGCATCAGCATACGTATATGAGAGCC
Found at i:12550446 original size:94 final size:94
Alignment explanation
Indices: 12550272--12550635 Score: 363
Period size: 94 Copynumber: 3.9 Consensus size: 94
12550262 GGTGATTTGT
* *
12550272 GTGCTAGTATAAGACATGTCTGGGACATGCATCAG-CATACGTATATGAGAGCCAGTATAAGACC
1 GTGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCATAC---TATGAGAGCCAGTGTAAGACC
* *
12550336 ATGTCTGGGACATGGCATCGACATCCAGACGAA
63 ATGTCTGGGACATGGCATCGGCATCAAGACG-A
* * * * *
12550369 G-GCTAGTGTAAGACATGTCCGGAACATGCATCAGCCATACTATGATAGCCAGTGTAACACAATG
1 GTGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCATACTATGAGAGCCAGTGTAAGACCATG
12550433 TCTGGGACATGGCATCGGCA-CAGAGACGA
66 TCTGGGACATGGCATCGGCATCA-AGACGA
* * * *
12550462 GTGCCAGTGTAAAACATGTCTGGGACATGCATCGGCCTTGAC-A-GAGATAGCCAGTGTAAGA-C
1 GTGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCAT-ACTATGAG--AGCCAGTGTAAGACC
* * * *
12550524 GTGTCTAGGACA-CGCATCGGC-T-AAGA-GTT
63 ATGTCTGGGACATGGCATCGGCATCAAGACG-A
* * *
12550553 GTGCTAGTGCAAGACATGTCTGGGACATGCATCAGCACGCGTA-TATGAGAGCTAGTGTAAGACC
1 GTGCTAGTGTAAGACATGTCTGGGACATGCATCAG--C-CATACTATGAGAGCCAGTGTAAGACC
12550617 ATGTCTGGGACATGGCATC
63 ATGTCTGGGACATGGCATC
12550636 AGCAATATAT
Statistics
Matches: 221, Mismatches: 31, Indels: 33
0.78 0.11 0.12
Matches are distributed among these distances:
90 1 0.00
91 34 0.15
92 13 0.06
93 27 0.12
94 96 0.43
95 14 0.06
96 30 0.14
97 6 0.03
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.21
Consensus pattern (94 bp):
GTGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCATACTATGAGAGCCAGTGTAAGACCATG
TCTGGGACATGGCATCGGCATCAAGACGA
Found at i:12556382 original size:90 final size:91
Alignment explanation
Indices: 12556260--12556500 Score: 396
Period size: 90 Copynumber: 2.7 Consensus size: 91
12556250 TGCTAATAAC
* * * *
12556260 TATGTTTCTTAAATAAGCGGGTACTTAGTTGTGCCGTGGATGGTGATTTGATATTTGTTTTG-TT
1 TATGTTTCTTAAATAAACGGGCACTTAATTGTGCCTTGGATGGTGATTTGATATTTGTTTTGTTT
12556324 TAAGGAGTGGAATTAATTATAATTTT
66 TAAGGAGTGGAATTAATTATAATTTT
*
12556350 TATGTTTCTTAAATAAATGGGCACTTAATTGTG-CTTGGATGGTGATTTGATATTTGTTTTGTTT
1 TATGTTTCTTAAATAAACGGGCACTTAATTGTGCCTTGGATGGTGATTTGATATTTGTTTTGTTT
* *
12556414 TAAGGTGTGGAATTAATTGTAATTTT
66 TAAGGAGTGGAATTAATTATAATTTT
*
12556440 TATGTTTCTTAAATAAACCGGCACTTAATTGTGCCTTGGATGGTGATTTGATATTTGTTTT
1 TATGTTTCTTAAATAAACGGGCACTTAATTGTGCCTTGGATGGTGATTTGATATTTGTTTT
12556501 TTCCCTTAAT
Statistics
Matches: 140, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
89 27 0.19
90 86 0.61
91 27 0.19
ACGTcount: A:0.24, C:0.07, G:0.22, T:0.47
Consensus pattern (91 bp):
TATGTTTCTTAAATAAACGGGCACTTAATTGTGCCTTGGATGGTGATTTGATATTTGTTTTGTTT
TAAGGAGTGGAATTAATTATAATTTT
Found at i:12557866 original size:39 final size:39
Alignment explanation
Indices: 12557811--12557922 Score: 140
Period size: 39 Copynumber: 2.8 Consensus size: 39
12557801 CTTTAGTGGC
12557811 TTTAGCGGCGCTTTTTAAAAACGCCGCTAAAGAT-CGAGTA
1 TTTAGCGGCGCTTTTTAAAAACGCCGCTAAAGATAC-A-TA
* *
12557851 -TTAGCGGCGCTTTTTAAAAACGCCGCTGTATG-TACATA
1 TTTAGCGGCGCTTTTTAAAAACGCCGCT-AAAGATACATA
*
12557889 TTTAGCGGCGCTTTTTAGAAAATGCCGCTAAAGA
1 TTTAGCGGCGCTTTTTA-AAAACGCCGCTAAAGA
12557923 ATTTTGCAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
38 2 0.03
39 47 0.76
40 13 0.21
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (39 bp):
TTTAGCGGCGCTTTTTAAAAACGCCGCTAAAGATACATA
Found at i:12558249 original size:22 final size:22
Alignment explanation
Indices: 12558224--12558269 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
12558214 GAGTTACTAT
* *
12558224 TTTAAGGTTTATGGATTATGGG
1 TTTAAGGATTATGGATTAAGGG
* *
12558246 TTTAGGGATTATGGTTTAAGGG
1 TTTAAGGATTATGGATTAAGGG
12558268 TT
1 TT
12558270 AGGTGCTAGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.46
Consensus pattern (22 bp):
TTTAAGGATTATGGATTAAGGG
Found at i:12558267 original size:15 final size:15
Alignment explanation
Indices: 12558229--12558263 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
12558219 ACTATTTTAA
*
12558229 GGTTTATGGATTATG
1 GGTTTAGGGATTATG
12558244 GGTTTAGGGATTAT-
1 GGTTTAGGGATTATG
12558258 GGTTTA
1 GGTTTA
12558264 AGGGTTAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.20, C:0.00, G:0.34, T:0.46
Consensus pattern (15 bp):
GGTTTAGGGATTATG
Found at i:12558282 original size:21 final size:21
Alignment explanation
Indices: 12558258--12558305 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
12558248 TAGGGATTAT
12558258 GGTTTAAGGGTTAGGTGCTAG
1 GGTTTAAGGGTTAGGTGCTAG
*
12558279 GGTTTAAGGGTTAGGTTCTAG
1 GGTTTAAGGGTTAGGTGCTAG
12558300 GGTTTA
1 GGTTTA
12558306 GGATTTATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.19, C:0.04, G:0.40, T:0.38
Consensus pattern (21 bp):
GGTTTAAGGGTTAGGTGCTAG
Found at i:12558307 original size:7 final size:7
Alignment explanation
Indices: 12558224--12558340 Score: 53
Period size: 7 Copynumber: 16.6 Consensus size: 7
12558214 GAGTTACTAT
*
12558224 TTTAAGG
1 TTTAGGG
*
12558231 TTTATGG
1 TTTAGGG
*
12558238 ATTATGGG
1 TTTA-GGG
12558246 TTTAGGG
1 TTTAGGG
* *
12558253 ATTATGG
1 TTTAGGG
12558260 TTTAAGGG
1 TTT-AGGG
12558268 -TTA-GG
1 TTTAGGG
*
12558273 TGCTAGGG
1 T-TTAGGG
12558281 TTTAAGGG
1 TTT-AGGG
12558289 -TTA-GG
1 TTTAGGG
12558294 TTCTAGGG
1 TT-TAGGG
*
12558302 TTTAGGA
1 TTTAGGG
* *
12558309 TTTATGT
1 TTTAGGG
* *
12558316 TTTAAGA
1 TTTAGGG
*
12558323 TTTATGG
1 TTTAGGG
12558330 TTTAGGG
1 TTTAGGG
12558337 TTTA
1 TTTA
12558341 AGAATTTGGA
Statistics
Matches: 83, Mismatches: 18, Indels: 18
0.70 0.15 0.15
Matches are distributed among these distances:
5 4 0.05
6 3 0.04
7 57 0.69
8 19 0.23
ACGTcount: A:0.21, C:0.02, G:0.32, T:0.44
Consensus pattern (7 bp):
TTTAGGG
Found at i:12558589 original size:14 final size:15
Alignment explanation
Indices: 12558565--12558598 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
12558555 TTATAGTTTT
*
12558565 TGGTATAAGGGTTAG
1 TGGTTTAAGGGTTAG
12558580 -GGTTTAAGGGTTAG
1 TGGTTTAAGGGTTAG
12558594 TGGTT
1 TGGTT
12558599 AGGGGTTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.21, C:0.00, G:0.41, T:0.38
Consensus pattern (15 bp):
TGGTTTAAGGGTTAG
Found at i:12558598 original size:21 final size:22
Alignment explanation
Indices: 12558574--12558628 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
12558564 TTGGTATAAG
12558574 GGTTAGGGTTTAAGGGTTA-GT
1 GGTTAGGGTTTAAGGGTTAGGT
* *
12558595 GGTTAGGGGTTAAGTGTTAGGT
1 GGTTAGGGTTTAAGGGTTAGGT
**
12558617 TTTTAGGGTTTA
1 GGTTAGGGTTTA
12558629 TAGATTATGT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.18, C:0.00, G:0.40, T:0.42
Consensus pattern (22 bp):
GGTTAGGGTTTAAGGGTTAGGT
Found at i:12559062 original size:25 final size:23
Alignment explanation
Indices: 12559019--12559070 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 23
12559009 ACATCATTTT
*
12559019 ATATTTATATATTGCATATATAA
1 ATATTTATATATTGCATATAAAA
12559042 ATATTTATATTTATT-CAATATAAAA
1 ATATTTATA--TATTGC-ATATAAAA
12559067 ATAT
1 ATAT
12559071 ATTGATGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 9 0.36
24 1 0.04
25 15 0.60
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (23 bp):
ATATTTATATATTGCATATAAAA
Found at i:12563200 original size:7 final size:7
Alignment explanation
Indices: 12563190--12563247 Score: 50
Period size: 7 Copynumber: 8.4 Consensus size: 7
12563180 AATAAATAAC
12563190 AAATATT
1 AAATATT
*
12563197 AAAT-TA
1 AAATATT
*
12563203 AAATA-A
1 AAATATT
12563209 ATAATATT
1 A-AATATT
*
12563217 AAAGCAT-
1 AAA-TATT
12563224 AAATATT
1 AAATATT
12563231 AAATATT
1 AAATATT
12563238 AAATATT
1 AAATATT
12563245 AAA
1 AAA
12563248 GTATAATATT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
6 9 0.21
7 30 0.71
8 3 0.07
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (7 bp):
AAATATT
Found at i:12563201 original size:24 final size:24
Alignment explanation
Indices: 12563163--12563212 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
12563153 TCAAAAATTA
12563163 AACATAATATTAATTAAAATAAAT
1 AACATAATATTAATTAAAATAAAT
12563187 AACA-AATATTAAATTAAAATAAAT
1 AACATAATATT-AATTAAAATAAAT
12563211 AA
1 AA
12563213 TATTAAAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (24 bp):
AACATAATATTAATTAAAATAAAT
Found at i:12563230 original size:14 final size:14
Alignment explanation
Indices: 12563211--12563257 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
12563201 TAAAATAAAT
*
12563211 AATATTAAAGCATA
1 AATATTAAAGTATA
12563225 AATATTAAA-TATTA
1 AATATTAAAGTA-TA
12563239 AATATTAAAGTAT-
1 AATATTAAAGTATA
12563252 AATATT
1 AATATT
12563258 TATCATAGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 7 0.23
14 21 0.70
15 2 0.07
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.38
Consensus pattern (14 bp):
AATATTAAAGTATA
Found at i:12563234 original size:28 final size:27
Alignment explanation
Indices: 12563203--12563257 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
12563193 TATTAAATTA
12563203 AAATAA-ATAATATTAAAGCATAAATATT
1 AAATAATA-AATATTAAAGCAT-AATATT
* *
12563231 AAATATTAAATATTAAAGTATAATATT
1 AAATAATAAATATTAAAGCATAATATT
12563258 TATCATAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 6 0.25
28 17 0.71
29 1 0.04
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (27 bp):
AAATAATAAATATTAAAGCATAATATT
Found at i:12563235 original size:41 final size:40
Alignment explanation
Indices: 12563157--12563241 Score: 102
Period size: 41 Copynumber: 2.1 Consensus size: 40
12563147 CAAATTTCAA
*
12563157 AAATTAAACATAATATTAATTAAAATAAATAACAAATATT
1 AAATTAAACATAATAATAATTAAAATAAATAACAAATATT
**
12563197 AAATTAAA-ATAAATAAT-ATTAAAGCATAAATATTAAATATT
1 AAATTAAACAT-AATAATAATTAAA--ATAAATAACAAATATT
12563238 AAAT
1 AAAT
12563242 ATTAAAGTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
39 8 0.21
40 13 0.33
41 18 0.46
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (40 bp):
AAATTAAACATAATAATAATTAAAATAAATAACAAATATT
Found at i:12563247 original size:21 final size:20
Alignment explanation
Indices: 12563182--12563247 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
12563172 TTAATTAAAA
12563182 TAAATAACAAATATTAAAT-T
1 TAAATAA-AAATATTAAATAT
* *
12563202 AAAATAAATAATATTAAAGCA-
1 TAAATAAA-AATATTAAA-TAT
*
12563223 TAAATATTAAATATTAAATAT
1 TAAATA-AAAATATTAAATAT
12563244 TAAA
1 TAAA
12563248 GTATAATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
19 1 0.03
20 16 0.44
21 18 0.50
22 1 0.03
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (20 bp):
TAAATAAAAATATTAAATAT
Found at i:12563502 original size:43 final size:43
Alignment explanation
Indices: 12563455--12563539 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 43
12563445 TTTTTATCGG
* * * *
12563455 CGTTTGTGGGAAAAGTGCCGCTAAAAATCATAGTT-TTTAGCAA
1 CGTTTGTAGAAAAAGCGCCACTAAAAATCAT-GTTCTTTAGCAA
**
12563498 CGTTTGTAGAAAAAGCGCCACTAAATGTCATGTTCTTTAGCA
1 CGTTTGTAGAAAAAGCGCCACTAAAAATCATGTTCTTTAGCA
12563540 GCATTTTTTG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
42 3 0.09
43 32 0.91
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (43 bp):
CGTTTGTAGAAAAAGCGCCACTAAAAATCATGTTCTTTAGCAA
Found at i:12575692 original size:36 final size:36
Alignment explanation
Indices: 12575652--12575725 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
12575642 AGTATTGATT
*
12575652 TTGATTTATAAATTTTGCTTGATACATTATTTAAAA
1 TTGATTTATAAACTTTGCTTGATACATTATTTAAAA
* *
12575688 TTGATTTATAAACTTTGTTTGATATATTATTTAAAA
1 TTGATTTATAAACTTTGCTTGATACATTATTTAAAA
12575724 TT
1 TT
12575726 AAGTATAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.53
Consensus pattern (36 bp):
TTGATTTATAAACTTTGCTTGATACATTATTTAAAA
Found at i:12578009 original size:37 final size:37
Alignment explanation
Indices: 12577948--12578046 Score: 119
Period size: 37 Copynumber: 2.7 Consensus size: 37
12577938 ATAATCACAT
* * * * *
12577948 ATTTACATGTCACTTTTTAATATATTAAATAAATATC
1 ATTTCCATATCACGTTTCAATATATCAAATAAATATC
*
12577985 ATTTCCATATCACGTTTCAATATATCAAGTAAATATC
1 ATTTCCATATCACGTTTCAATATATCAAATAAATATC
*
12578022 ATTTCCA-AGACACGTTTCAATATAT
1 ATTTCCATA-TCACGTTTCAATATAT
12578047 ATATACCGAT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
36 1 0.02
37 53 0.98
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.40
Consensus pattern (37 bp):
ATTTCCATATCACGTTTCAATATATCAAATAAATATC
Found at i:12587063 original size:18 final size:18
Alignment explanation
Indices: 12587040--12587081 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
12587030 TCTAGATGCA
*
12587040 TATCCTAGCCCTTATATG
1 TATCCTAACCCTTATATG
*
12587058 TATCCTAACCCTTTTATG
1 TATCCTAACCCTTATATG
*
12587076 TTTCCT
1 TATCCT
12587082 TTTCCTAGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.19, C:0.29, G:0.07, T:0.45
Consensus pattern (18 bp):
TATCCTAACCCTTATATG
Found at i:12587779 original size:129 final size:130
Alignment explanation
Indices: 12587490--12587991 Score: 723
Period size: 128 Copynumber: 3.9 Consensus size: 130
12587480 TAGAAACTTA
* * * *
12587490 TTTTATATGGTTT-CATATAATAAAATAAAAATTGTTTTTATTATTTTAATTGTACTTTACTTTT
1 TTTTATATAGTTTGAAT-TAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTTT
*
12587554 TTT-ACTTTATTAAAATAAATGTTCTTTTAAATTAAGAAATATTTTTTTATTATTTTTATATTTA
65 TTTAATTTTATTAAAATAAATGTTCTTTTAAATTAAGAAATA-TTTTTTATTATTTTTATATTTA
12587618 AT
129 AT
12587620 TTTTATATAGTTTGAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTTTT
1 TTTTATATAGTTTGAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTTTT
* * * *
12587685 TTAGTTTTATTAAAATAAATTTTCTTTTAGATTAAGAAATATTTTTTATT-TTTTTGTATTTAAT
66 TTAATTTTATTAAAATAAATGTTCTTTTAAATTAAGAAATATTTTTTATTATTTTTATATTTAAT
*
12587749 TTTTATATAGTTTGAATTGATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTA-TTTTT
1 TTTTATATAGTTTGAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTTTT
* * * **
12587813 TAAATTTTATTAAAATAAATGTTATTTTAAATT-AGCCAATA-TTTTTATTATTTTTATATTTGT
66 TTAATTTTATTAAAATAAATGTTCTTTTAAATTAAG-AAATATTTTTTATTATTTTTATATTTAA
12587876 T
130 T
* *
12587877 TTTTATATAGTTTTAAATAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTAC-TTACTTTTT
1 TTTTATATAGTTTGAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTTTT
* * * *
12587941 TTAATTTTAATACAATAAATGTTCTTTTAAATT-AGCTAATAATTTTTATTA
66 TTAATTTTATTAAAATAAATGTTCTTTTAAATTAAG-AAATATTTTTTATTA
12587992 AAATAAGTGT
Statistics
Matches: 339, Mismatches: 27, Indels: 13
0.89 0.07 0.03
Matches are distributed among these distances:
127 13 0.04
128 141 0.42
129 80 0.24
130 69 0.20
131 36 0.11
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (130 bp):
TTTTATATAGTTTGAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTTTT
TTAATTTTATTAAAATAAATGTTCTTTTAAATTAAGAAATATTTTTTATTATTTTTATATTTAAT
Found at i:12591129 original size:126 final size:126
Alignment explanation
Indices: 12590904--12591338 Score: 654
Period size: 126 Copynumber: 3.5 Consensus size: 126
12590894 AGTCTAAGTC
* * * *
12590904 TTTTTCAAATACTACTGTAGCAAAAGAGCGTCCACGTAAGAGATTTTTTCCTTAATTTTGCTGAC
1 TTTTTCAGATACTACTGTAGCAAAAGAGCGTCCACGTGAGAGCTTTTTTCCGTAATTTTGCTGAC
* * * *
12590969 AGTGCATCCTTCTTGAAGTATTTTTGACACTATTTTTTCAAAAACATCTTATCAAAATTAA
66 AGTGCATCCTTCTTGAAGCATTTTTGACACTATTTATTCAAAAACATCTTCTCAAAATTAT
* * *
12591030 TTTTTCAGATACTACTGTAGCAAAAGAGCGCCCACGTGAGAGCTGTTTTCCGTAATTTTACTGAC
1 TTTTTCAGATACTACTGTAGCAAAAGAGCGTCCACGTGAGAGCTTTTTTCCGTAATTTTGCTGAC
*
12591095 AGTGCATCCTTCTTGAAGCATTTTTGACACTATTTGTTCAAAAACATCTTCTCAAAATTAT
66 AGTGCATCCTTCTTGAAGCATTTTTGACACTATTTATTCAAAAACATCTTCTCAAAATTAT
* * * *
12591156 TTTTTCAGATACTACTGTAGTAAAAGAGCGTCCATGTGGGAGCTTTTTTCCATAATTTTGCTGAC
1 TTTTTCAGATACTACTGTAGCAAAAGAGCGTCCACGTGAGAGCTTTTTTCCGTAATTTTGCTGAC
* * * *
12591221 AGTGTATCCTTCTTGAAGCATTTTTGACACTATTCATTCAGAAACATCTTCTCAAAGTTAT
66 AGTGCATCCTTCTTGAAGCATTTTTGACACTATTTATTCAAAAACATCTTCTCAAAATTAT
* * * *
12591282 TTTTTTAGATACTATTGTAGCAAAAAAGCGTCCACGTGGGAGCTTTTTTCCGTAATT
1 TTTTTCAGATACTACTGTAGCAAAAGAGCGTCCACGTGAGAGCTTTTTTCCGTAATT
12591339 AATAGTTAAT
Statistics
Matches: 280, Mismatches: 29, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
126 280 1.00
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (126 bp):
TTTTTCAGATACTACTGTAGCAAAAGAGCGTCCACGTGAGAGCTTTTTTCCGTAATTTTGCTGAC
AGTGCATCCTTCTTGAAGCATTTTTGACACTATTTATTCAAAAACATCTTCTCAAAATTAT
Found at i:12591487 original size:16 final size:17
Alignment explanation
Indices: 12591465--12591502 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
12591455 CTTAAAAAAT
*
12591465 ACTAAAACCCA-AAACC
1 ACTAAAAACCATAAACC
12591481 -CTAAAAACCATAAACC
1 ACTAAAAACCATAAACC
12591497 ACTAAA
1 ACTAAA
12591503 CCCTAGCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 9 0.47
16 5 0.26
17 5 0.26
ACGTcount: A:0.58, C:0.32, G:0.00, T:0.11
Consensus pattern (17 bp):
ACTAAAAACCATAAACC
Found at i:12591766 original size:35 final size:33
Alignment explanation
Indices: 12591718--12591789 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 33
12591708 CATATAATAC
*
12591718 ATATAATATATAATATATATACTTAAACATTAAAA
1 ATATAATATATAATATATATA-ATAAAC-TTAAAA
*
12591753 ATAT-ATATAATAATATATATAATAAACTTATAA
1 ATATAATAT-ATAATATATATAATAAACTTAAAA
12591786 ATAT
1 ATAT
12591790 TTAACTTCTG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 9 0.26
34 9 0.26
35 16 0.47
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (33 bp):
ATATAATATATAATATATATAATAAACTTAAAA
Found at i:12592700 original size:70 final size:67
Alignment explanation
Indices: 12592577--12592709 Score: 176
Period size: 70 Copynumber: 1.9 Consensus size: 67
12592567 ATAAACAATA
* **
12592577 TAATGGTTTTGCCTTTTAACTTAATTAGTAAACATTTATCAAAACAACATAGTTTTACCTTTTAA
1 TAATGGTTTTGACTTTTAACTTAAAAAGTAAACATTTATCAAAACAACATAGTTTTACCTTTTAA
12592642 CT
66 CT
** * *
12592644 TAATGGTTTTGACTTTTAACTTTAGAAAAGGTAAACATTTATCAAAATGACGTAGTTTTGCCTTT
1 TAATGGTTTTGACTTTTAAC-TTA-AAAA-GTAAACATTTATCAAAACAACATAGTTTTACCTTT
12592709 T
63 T
12592710 CTTATTCGGA
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
67 19 0.34
68 3 0.05
69 2 0.04
70 32 0.57
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (67 bp):
TAATGGTTTTGACTTTTAACTTAAAAAGTAAACATTTATCAAAACAACATAGTTTTACCTTTTAA
CT
Found at i:12593352 original size:30 final size:30
Alignment explanation
Indices: 12593318--12593377 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
12593308 ACTTAACAAG
12593318 CAAATACCTCTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
* *
12593348 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
12593378 TAATAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.58, C:0.15, G:0.02, T:0.25
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:12595050 original size:22 final size:23
Alignment explanation
Indices: 12595027--12595152 Score: 116
Period size: 22 Copynumber: 5.5 Consensus size: 23
12595017 TGAGTTGATG
12595027 AACAGTAAGCTCTAATGAGCTGA
1 AACAGTAAGCTCTAATGAGCTGA
*
12595050 AACGGTAAGCTCT-ATCGAGCTG-
1 AACAGTAAGCTCTAAT-GAGCTGA
* * *
12595072 AATAGTAAGCTCTATTGAGTTG-
1 AACAGTAAGCTCTAATGAGCTGA
* *
12595094 AATAGTAAGCTC-ATACGAGCTGA
1 AACAGTAAGCTCTA-ATGAGCTGA
* * *
12595117 AACGGTAAGCTCCAATTAGCTGAA
1 AACAGTAAGCTCTAATGAGCTG-A
12595141 AACAGTAAGCTC
1 AACAGTAAGCTC
12595153 CTACGAGCTA
Statistics
Matches: 84, Mismatches: 13, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
21 1 0.01
22 35 0.42
23 35 0.42
24 13 0.15
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (23 bp):
AACAGTAAGCTCTAATGAGCTGA
Found at i:12596791 original size:14 final size:14
Alignment explanation
Indices: 12596772--12596801 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
12596762 TGATAAATTG
12596772 ATTATGAATTTAGC
1 ATTATGAATTTAGC
12596786 ATTATGAATTTAGC
1 ATTATGAATTTAGC
12596800 AT
1 AT
12596802 GATAAAGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (14 bp):
ATTATGAATTTAGC
Found at i:12600884 original size:34 final size:34
Alignment explanation
Indices: 12600821--12600885 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
12600811 TACTTTTCTT
* *
12600821 AAAAATCAAAACCTTATTTCGAAATAATTAACAA
1 AAAAATCAAAACCTTATTTCAAAAAAATTAACAA
* * *
12600855 AAAAATCAAAACTTTGTTTTAAAAAAATTAA
1 AAAAATCAAAACCTTATTTCAAAAAAATTAA
12600886 ACTTTCCTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.57, C:0.11, G:0.03, T:0.29
Consensus pattern (34 bp):
AAAAATCAAAACCTTATTTCAAAAAAATTAACAA
Found at i:12600887 original size:21 final size:22
Alignment explanation
Indices: 12600853--12600899 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
12600843 AATAATTAAC
**
12600853 AAAAAAATCAAAACTTTGTTTT
1 AAAAAAATCAAAACTTTCCTTT
*
12600875 AAAAAAAT-TAAACTTTCCTTT
1 AAAAAAATCAAAACTTTCCTTT
12600896 AAAA
1 AAAA
12600900 TGTCTTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.53, C:0.11, G:0.02, T:0.34
Consensus pattern (22 bp):
AAAAAAATCAAAACTTTCCTTT
Found at i:12601052 original size:158 final size:153
Alignment explanation
Indices: 12600853--12601255 Score: 537
Period size: 158 Copynumber: 2.6 Consensus size: 153
12600843 AATAATTAAC
* * **
12600853 AAAAAAATCAAAACTTTGTTTTAAAAAAATTAAACTTTCCTTTAAAATGTCTTAAAAAAACAGAT
1 AAAAAAATAAAAACTTTGTTTT-AAAAATTTAAACTTTCCTTTAAAATAAC-TAAAAAAACAGAT
*
12600918 ATTTATTTTTCAAATTCTAAACTTTCTCCCTTTTTTTTTAAAAAAAATACACTATTTTTTCTTAA
64 ATTTATTTTTCAAAATCTAAACTTTCT-CC-TTTTTTTT--AAAAAATACACTA-TTTTTCTTAA
* *
12600983 AGATTAAAGCTTTTATTTTGAAGTAGTT-A
124 AGATTAAAGCTTTTACTTTGAAATAGTTGA
12601012 AAAAAAATAAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAATAACTACAAAAAACA-ATT
1 AAAAAAATAAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAATAACTA-AAAAAACAGA-T
* *
12601076 ATTTATTTTTCAAAATCTAAA-TTTCT-CTTTTTTTTAAAAAATACATTATTTTTCTTAAATATT
64 ATTTATTTTTCAAAATCTAAACTTTCTCCTTTTTTTTAAAAAATACACTATTTTTCTTAAAGATT
*
12601139 AAAGTTTTTACTTTGAAATAGTTGA
129 AAAGCTTTTACTTTGAAATAGTTGA
* * * *
12601164 AAAACAAATAAAAATTTTGTTTTAAAAATTTAAACTTTCCTTTAAGATAACT-AAAAAATAGATT
1 AAAA-AAATAAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAATAACTAAAAAAACAGATA
*
12601228 TTTATTTCTTCAAAATCTAATCTTTCTC
65 TTTATTT-TTCAAAATCTAAACTTTCTC
12601256 ATTTAAAAAA
Statistics
Matches: 221, Mismatches: 15, Indels: 21
0.86 0.06 0.08
Matches are distributed among these distances:
151 49 0.22
152 30 0.14
153 50 0.23
154 8 0.04
155 1 0.00
157 8 0.04
158 54 0.24
159 21 0.10
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.43
Consensus pattern (153 bp):
AAAAAAATAAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAATAACTAAAAAAACAGATAT
TTATTTTTCAAAATCTAAACTTTCTCCTTTTTTTTAAAAAATACACTATTTTTCTTAAAGATTAA
AGCTTTTACTTTGAAATAGTTGA
Found at i:12601622 original size:9 final size:9
Alignment explanation
Indices: 12601604--12601638 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
12601594 TAATAGTATT
12601604 TAATAATAG
1 TAATAATAG
*
12601613 TAATAGTAG
1 TAATAATAG
*
12601622 TGATAATAG
1 TAATAATAG
12601631 TAATAATA
1 TAATAATA
12601639 ATTTGGGCCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.34
Consensus pattern (9 bp):
TAATAATAG
Found at i:12611550 original size:36 final size:36
Alignment explanation
Indices: 12611482--12611567 Score: 111
Period size: 36 Copynumber: 2.4 Consensus size: 36
12611472 TCGAGGCCAT
* * * *
12611482 TGGTGTGTTATAGGGTGGATTGGCTCGTATGAGCATC
1 TGGTGTGTT-TCGGATGGATTAGCTCGTATGAGCATA
12611519 TGGTGTGTTTCGGATGGATTAGCTC-TCATGAGCATA
1 TGGTGTGTTTCGGATGGATTAGCTCGT-ATGAGCATA
12611555 TGGTGTGTTTCGG
1 TGGTGTGTTTCGG
12611568 TTGTAATATT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
35 1 0.02
36 34 0.77
37 9 0.20
ACGTcount: A:0.15, C:0.12, G:0.36, T:0.37
Consensus pattern (36 bp):
TGGTGTGTTTCGGATGGATTAGCTCGTATGAGCATA
Found at i:12612499 original size:76 final size:75
Alignment explanation
Indices: 12612373--12612516 Score: 218
Period size: 76 Copynumber: 1.9 Consensus size: 75
12612363 AATCTGAGAC
* * * *
12612373 ATGAGTTCTTTAGGATTCAAGTCAGTGAGTTACAGGGCCTAACACACGGCCTGGCGATAC-GGCT
1 ATGAGTTCTTTAGGATGCAAGTCAATGAGTTACACGACCTAACACACGGCCTGGC-ATACAGGCT
12612437 GTGTGTCATCTG
65 -TGTGTCATCTG
*
12612449 ATGAGTTCTTTAGGGTGCAAGTCAATGAGTTACACGACCTAACACACGGCCTGGCATACAGGCTT
1 ATGAGTTCTTTAGGATGCAAGTCAATGAGTTACACGACCTAACACACGGCCTGGCATACAGGCTT
12612514 GTG
66 GTG
12612517 ACACGGCCAT
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
75 8 0.13
76 54 0.87
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (75 bp):
ATGAGTTCTTTAGGATGCAAGTCAATGAGTTACACGACCTAACACACGGCCTGGCATACAGGCTT
GTGTCATCTG
Found at i:12620060 original size:60 final size:59
Alignment explanation
Indices: 12619988--12620173 Score: 189
Period size: 60 Copynumber: 3.1 Consensus size: 59
12619978 CGTGTCCATT
* *
12619988 GGACACATAGCCATGTGACTGCTTTGGGCAATTAGGGCTTCCACACGGGCATGTGTTATG
1 GGACACACAGCCATGTGACTGATTTGGGCAATTAGGG-TTCCACACGGGCATGTGTTATG
* * * * *
12620048 GGACACACAGCCATGTAACTGAGTTGGGAAATTAGGGTTCCCACACTGGCATGTGCTT-CG
1 GGACACACAGCCATGTGACTGATTTGGGCAATTAGGGTT-CCACACGGGCATGTG-TTATG
* * ** * *
12620108 GGACATACGGCGGTGTGACTGATTTGGGGC--CTAGAGATTCCACACGGGCATGTGTTATG
1 GGACACACAGCCATGTGACTGATTT-GGGCAATTAG-GGTTCCACACGGGCATGTGTTATG
12620167 GGACACA
1 GGACACA
12620174 TGGCAGTGAC
Statistics
Matches: 102, Mismatches: 19, Indels: 11
0.77 0.14 0.08
Matches are distributed among these distances:
58 2 0.02
59 26 0.25
60 69 0.68
61 5 0.05
ACGTcount: A:0.23, C:0.22, G:0.31, T:0.24
Consensus pattern (59 bp):
GGACACACAGCCATGTGACTGATTTGGGCAATTAGGGTTCCACACGGGCATGTGTTATG
Found at i:12636833 original size:44 final size:44
Alignment explanation
Indices: 12636783--12636871 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
12636773 GAAAAAATGT
* *
12636783 ATGATATATAGAATGAATTTATGGTCATGTTTGTGTGTGTTGGA
1 ATGATATATAGAATCAATTTATGGTCATGTTTGTGCGTGTTGGA
12636827 ATGATATATAGAATCAATTTATGGTCATGTTTGTGCGTGTTGGA
1 ATGATATATAGAATCAATTTATGGTCATGTTTGTGCGTGTTGGA
12636871 A
1 A
12636872 GTTGGTTCTG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.28, C:0.04, G:0.26, T:0.42
Consensus pattern (44 bp):
ATGATATATAGAATCAATTTATGGTCATGTTTGTGCGTGTTGGA
Found at i:12646391 original size:47 final size:46
Alignment explanation
Indices: 12646331--12646501 Score: 157
Period size: 47 Copynumber: 3.6 Consensus size: 46
12646321 TTAGGATTTT
**
12646331 ATGTGATGGATGTGAATGTGTATATATGTGATAAGACCGAATGGCCA
1 ATGTGATAAATGTGAATGTGTATATATGTGATAAG-CCGAATGGCCA
** * *
12646378 ATGTGATAAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCA
1 ATGTGATAAATGTGAATGTGTATATATGTGATAA-GCCGAATGGCCA
* * *
12646425 ATGTGATGAACGTGGAA-GTGTATATATGTGGGA-AAGCCGAATGGCTA
1 ATGTGATAAATGT-GAATGTGTATATATGT--GATAAGCCGAATGGCCA
* *
12646472 ATGTGAGATATGTATGAGATGTGTATATAT
1 ATGTGATAAATG--TGA-ATGTGTATATAT
12646502 ATATTGTGGC
Statistics
Matches: 100, Mismatches: 16, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
47 78 0.78
48 8 0.08
49 4 0.04
50 10 0.10
ACGTcount: A:0.34, C:0.08, G:0.29, T:0.29
Consensus pattern (46 bp):
ATGTGATAAATGTGAATGTGTATATATGTGATAAGCCGAATGGCCA
Found at i:12650166 original size:49 final size:49
Alignment explanation
Indices: 12650109--12650206 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 49
12650099 ATTAATCATC
12650109 AATTGGAGTAAGGCATTTTACATCA-TTTTTAAATTCTATTTTTGATGGA
1 AATTGGAGTAAGGCATTTTACAT-ATTTTTTAAATTCTATTTTTGATGGA
12650158 AATTGGAGTAAGGCATTTTACATATTTTTTAAATTCTATTTTTGATGGA
1 AATTGGAGTAAGGCATTTTACATATTTTTTAAATTCTATTTTTGATGGA
12650207 GTTTCTTGAA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
48 1 0.02
49 47 0.98
ACGTcount: A:0.31, C:0.07, G:0.16, T:0.46
Consensus pattern (49 bp):
AATTGGAGTAAGGCATTTTACATATTTTTTAAATTCTATTTTTGATGGA
Found at i:12652660 original size:20 final size:20
Alignment explanation
Indices: 12652635--12652675 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
12652625 ATGAAATTAA
12652635 ATCAATAAAATTTTTCTATT
1 ATCAATAAAATTTTTCTATT
12652655 ATCAATAAAATTTTTCTATT
1 ATCAATAAAATTTTTCTATT
12652675 A
1 A
12652676 ACTTAGCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (20 bp):
ATCAATAAAATTTTTCTATT
Found at i:12659700 original size:21 final size:21
Alignment explanation
Indices: 12659674--12659723 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
12659664 CCCATATGGT
*
12659674 CATGTACCTTAGCCACAC-AGC
1 CATGTACCTCAGCCACACGA-C
* *
12659695 CATGTATCTCAGCCATACGAC
1 CATGTACCTCAGCCACACGAC
12659716 CATGTACC
1 CATGTACC
12659724 CCTGTCACAC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.28, C:0.36, G:0.14, T:0.22
Consensus pattern (21 bp):
CATGTACCTCAGCCACACGAC
Found at i:12662066 original size:33 final size:33
Alignment explanation
Indices: 12662024--12662092 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
12662014 ATAGAAACCA
12662024 ATTACTTAGTCTAGAATTCTTCTTTTAAATTCC
1 ATTACTTAGTCTAGAATTCTTCTTTTAAATTCC
12662057 ATTACTTAGTCTAGAATTCTTCTTTTAAATTCC
1 ATTACTTAGTCTAGAATTCTTCTTTTAAATTCC
12662090 ATT
1 ATT
12662093 TAGTTTTTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.49
Consensus pattern (33 bp):
ATTACTTAGTCTAGAATTCTTCTTTTAAATTCC
Found at i:12666113 original size:20 final size:20
Alignment explanation
Indices: 12666088--12666139 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
12666078 AATTATTGAA
*
12666088 TGTTTGCACATATGTACCCC
1 TGTTTGCACATAGGTACCCC
* * *
12666108 TGTTTGTACTTCGGTACCCC
1 TGTTTGCACATAGGTACCCC
*
12666128 TGGTTGCACATA
1 TGTTTGCACATA
12666140 CGTGCCCTTA
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.17, C:0.27, G:0.19, T:0.37
Consensus pattern (20 bp):
TGTTTGCACATAGGTACCCC
Found at i:12666154 original size:40 final size:40
Alignment explanation
Indices: 12666091--12666209 Score: 157
Period size: 40 Copynumber: 3.0 Consensus size: 40
12666081 TATTGAATGT
* * *
12666091 TTGCACATATGTACCCCTGTTTGTACTTCGGTACCCCTGG
1 TTGCACATATGTGCCCCTATTTGTACTTCGGTACCCCTAG
* * *
12666131 TTGCACATACGTGCCCTTATTTGTACTTCGGTACCCCTAT
1 TTGCACATATGTGCCCCTATTTGTACTTCGGTACCCCTAG
* * *
12666171 TTTCACACATGTGCCCCTATTTGTACTTTGGTACCCCTA
1 TTGCACATATGTGCCCCTATTTGTACTTCGGTACCCCTA
12666210 AATACATTTA
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 68 1.00
ACGTcount: A:0.17, C:0.30, G:0.16, T:0.37
Consensus pattern (40 bp):
TTGCACATATGTGCCCCTATTTGTACTTCGGTACCCCTAG
Found at i:12666207 original size:20 final size:20
Alignment explanation
Indices: 12666101--12666209 Score: 71
Period size: 20 Copynumber: 5.5 Consensus size: 20
12666091 TTGCACATAT
*
12666101 GTACCCCTGTTTGTACTTCG
1 GTACCCCTATTTGTACTTCG
** * *
12666121 GTACCCCTGGTTGCACATAC-
1 GTACCCCTATTTGTAC-TTCG
* *
12666141 GTGCCCTTATTTGTACTTCG
1 GTACCCCTATTTGTACTTCG
* *
12666161 GTACCCCTATTT-TCAC-ACAT
1 GTACCCCTATTTGT-ACTTC-G
* *
12666181 GTGCCCCTATTTGTACTTTG
1 GTACCCCTATTTGTACTTCG
12666201 GTACCCCTA
1 GTACCCCTA
12666210 AATACATTTA
Statistics
Matches: 65, Mismatches: 18, Indels: 12
0.68 0.19 0.13
Matches are distributed among these distances:
19 4 0.06
20 58 0.89
21 3 0.05
ACGTcount: A:0.16, C:0.31, G:0.17, T:0.37
Consensus pattern (20 bp):
GTACCCCTATTTGTACTTCG
Found at i:12675467 original size:118 final size:118
Alignment explanation
Indices: 12675259--12675493 Score: 443
Period size: 118 Copynumber: 2.0 Consensus size: 118
12675249 TCTGAAATTC
12675259 TTTTTACACATGAAAATTCATTGAATTTGAGCAATACATCGTATTTCAGTTCATATAAACATGTT
1 TTTTTACACATGAAAATTCATTGAATTTGAGCAATACATCGTATTTCAGTTCATATAAACATGTT
*
12675324 TTTAAAAGAAAAAAAATTAAGAGTTTGGAAAGGGCCGTGAAAGCTTATTTTAT
66 TTTAAAAGAAAAAAAATTAAGAGTTTGGAAAGGGCCGTGAAAGCCTATTTTAT
* *
12675377 TTTTTACACATGAAAATTCATTGAATTTGAGCAATACATCGTATTTGATTTCATATAAACATGTT
1 TTTTTACACATGAAAATTCATTGAATTTGAGCAATACATCGTATTTCAGTTCATATAAACATGTT
12675442 TTTAAAAGAAAAAAAATTAAGAGTTTGGAAAGGGCCGTGAAAGCCTATTTTA
66 TTTAAAAGAAAAAAAATTAAGAGTTTGGAAAGGGCCGTGAAAGCCTATTTTA
12675494 CCTTTAAAAT
Statistics
Matches: 114, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
118 114 1.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.35
Consensus pattern (118 bp):
TTTTTACACATGAAAATTCATTGAATTTGAGCAATACATCGTATTTCAGTTCATATAAACATGTT
TTTAAAAGAAAAAAAATTAAGAGTTTGGAAAGGGCCGTGAAAGCCTATTTTAT
Found at i:12683377 original size:18 final size:18
Alignment explanation
Indices: 12683340--12683377 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
12683330 ACTTAACTAA
*
12683340 AACACATTTTCCCCTGCC
1 AACACATTTTCCCATGCC
12683358 AACACA-TTTCCCATGTCC
1 AACACATTTTCCCATG-CC
12683376 AA
1 AA
12683378 GGTGAGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.29, C:0.39, G:0.05, T:0.26
Consensus pattern (18 bp):
AACACATTTTCCCATGCC
Found at i:12683682 original size:25 final size:26
Alignment explanation
Indices: 12683653--12683708 Score: 105
Period size: 25 Copynumber: 2.2 Consensus size: 26
12683643 GTCCATCCGA
12683653 TAACAAATTAGTGTGCTCATAAGAG-
1 TAACAAATTAGTGTGCTCATAAGAGC
12683678 TAACAAATTAGTGTGCTCATAAGAGC
1 TAACAAATTAGTGTGCTCATAAGAGC
12683704 TAACA
1 TAACA
12683709 TTGGAAATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 25 0.83
26 5 0.17
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (26 bp):
TAACAAATTAGTGTGCTCATAAGAGC
Found at i:12685843 original size:39 final size:41
Alignment explanation
Indices: 12685748--12685983 Score: 182
Period size: 40 Copynumber: 5.6 Consensus size: 41
12685738 CTAACAGGGT
* * * *
12685748 TAAGTCCCGAAGACATTTGTGCTAGTGATTAATT-TCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCTCGGGC
12685788 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCT-GGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCTCGGGC
*
12685828 -ACGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGACTAATTCTGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT------C----TC-GGGC
*
12685879 TAAGTCCCGAAAGCATTTGTGCGAGTTACT-ATATC-CGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCTCGGGC
* * * *
12685919 TAAGTCCCGAAGACATTTGTGCTAGTGAC-CATATC-CGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCTCGGGC
* * *
12685959 TAAGGCCCGACGGC-CTTGTGCGAGT
1 TAAGTCCCGAAGGCATTTGTGCGAGT
12685984 GGTTATATCC
Statistics
Matches: 164, Mismatches: 16, Indels: 33
0.77 0.08 0.15
Matches are distributed among these distances:
39 41 0.25
40 84 0.51
41 2 0.01
45 1 0.01
46 1 0.01
49 1 0.01
51 6 0.04
52 28 0.17
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (41 bp):
TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCTCGGGC
Found at i:12685895 original size:52 final size:51
Alignment explanation
Indices: 12685815--12685921 Score: 164
Period size: 52 Copynumber: 2.1 Consensus size: 51
12685805 TGTGCGAGTT
* *
12685815 ACTAATTCTGGGCACGTCCCGAAGGCATTTGTGCGAGTTACTA-ATTCCGGG
1 ACTAATTCTGGGCAAGTCCCGAAAGCATTTGTGCGAGTTACTATA-TCCGGG
12685866 ACTAATTCTGGGCTAAGTCCCGAAAGCATTTGTGCGAGTTACTATATCCGGG
1 ACTAATTCTGGGC-AAGTCCCGAAAGCATTTGTGCGAGTTACTATATCCGGG
12685918 -CTAA
1 ACTAA
12685922 GTCCCGAAGA
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
51 17 0.33
52 34 0.65
53 1 0.02
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.28
Consensus pattern (51 bp):
ACTAATTCTGGGCAAGTCCCGAAAGCATTTGTGCGAGTTACTATATCCGGG
Found at i:12685982 original size:131 final size:131
Alignment explanation
Indices: 12685748--12685983 Score: 291
Period size: 131 Copynumber: 1.8 Consensus size: 131
12685738 CTAACAGGGT
* * * *
12685748 TAAGTCCCGAAGACATTTGTGCTAGTGATTAATTTCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
1 TAAGTCCCGAAGACATTTGTGCGAGTGACTAATTCCGGGCTAAGTCCCGAAGACATTTGTGCGAG
* * * * * *
12685813 TTACTAATTCTGGGCACGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGACTAATTCTGGG
66 TGACCAATTCCGGGCAAGGCCCGAAGGCACTTGTGCGAGTTACTAATTCCGGGACTAATTCTGGG
12685878 C
131 C
* *
12685879 TAAGTCCCGAA-AGCATTTGTGCGAGTTACT-ATATCCGGGCTAAGTCCCGAAGACATTTGTGCT
1 TAAGTCCCGAAGA-CATTTGTGCGAGTGACTAAT-TCCGGGCTAAGTCCCGAAGACATTTGTGCG
*
12685942 AGTGACC-ATATCCGGGCTAAGGCCCGACGGC-CTTGTGCGAGT
64 AGTGACCAAT-TCCGGGC-AAGGCCCGAAGGCACTTGTGCGAGT
12685984 GGTTATATCC
Statistics
Matches: 88, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
130 5 0.06
131 73 0.83
132 10 0.11
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (131 bp):
TAAGTCCCGAAGACATTTGTGCGAGTGACTAATTCCGGGCTAAGTCCCGAAGACATTTGTGCGAG
TGACCAATTCCGGGCAAGGCCCGAAGGCACTTGTGCGAGTTACTAATTCCGGGACTAATTCTGGG
C
Found at i:12685992 original size:39 final size:40
Alignment explanation
Indices: 12685875--12686009 Score: 123
Period size: 40 Copynumber: 3.4 Consensus size: 40
12685865 GACTAATTCT
* * *
12685875 GGGCTAAGTCCCGAA-AGCATTTGTGCGAGTTACTATATCC
1 GGGCTAAGGCCCGAAGA-CACTTGTGCGAGTGACTATATCC
* * * *
12685915 GGGCTAAGTCCCGAAGACATTTGTGCTAGTGACCATATCC
1 GGGCTAAGGCCCGAAGACACTTGTGCGAGTGACTATATCC
* * **
12685955 GGGCTAAGGCCCGACGGC-CTTGTGCGAGTGGTTATATCC
1 GGGCTAAGGCCCGAAGACACTTGTGCGAGTGACTATATCC
**
12685994 -GGCTAAATCCCGAAGA
1 GGGCTAAGGCCCGAAGA
12686010 TAATTGGGTT
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
38 12 0.15
39 16 0.20
40 50 0.63
41 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
GGGCTAAGGCCCGAAGACACTTGTGCGAGTGACTATATCC
Found at i:12694056 original size:39 final size:40
Alignment explanation
Indices: 12693961--12694202 Score: 312
Period size: 40 Copynumber: 6.1 Consensus size: 40
12693951 CTAACGGGGT
* * * * *
12693961 TAAGTCCCGAAGACATTTGTGCTAGTGATTAATTCCGAGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
12694001 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
* * *
12694041 -AAGTCTCAAAGGCATTTGTGCGAGTTACTAATTCTGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
*
12694080 -ACGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
*
12694119 TAAGTCCCGAAGGCATTTGTGTGAGTTACT-ATATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCCGGGC
* * * *
12694159 TAAGTCCCGAAGACATTTGTGCTAGTGAC-CATATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCCGGGC
12694199 TAAG
1 TAAG
12694203 GCCTGACGGC
Statistics
Matches: 181, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
39 73 0.40
40 108 0.60
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.28
Consensus pattern (40 bp):
TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
Found at i:12694101 original size:78 final size:80
Alignment explanation
Indices: 12693961--12694202 Score: 287
Period size: 79 Copynumber: 3.0 Consensus size: 80
12693951 CTAACGGGGT
* * * * * *
12693961 TAAGTCCCGAAGACATTTGTGCTAGTGATTA-ATTCCGAGCTAAGTCCCGAAGGCATTTGTGCGA
1 TAAGTCCCAAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCCCGAAGGCATTTGTGCGA
12694025 GTTACTAATTCCGGGC
65 GTTACTAATTCCGGGC
* * *
12694041 -AAGTCTCAAAGGCATTTGTGCGAGTTACTA-ATTCTGGGC-ACGTCCCGAAGGCATTTGTGCGA
1 TAAGTCCCAAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCCCGAAGGCATTTGTGCGA
12694103 GTTACTAATTCCGGGC
65 GTTACTAATTCCGGGC
* * * *
12694119 TAAGTCCCGAAGGCATTTGTGTGAGTTACTATATCCGGGCTAAGTCCCGAAGACATTTGTGCTAG
1 TAAGTCCCAAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
* *
12694184 TGAC-CATATCCGGGC
66 TTACTAAT-TCCGGGC
12694199 TAAG
1 TAAG
12694203 GCCTGACGGC
Statistics
Matches: 140, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
78 38 0.27
79 66 0.47
80 36 0.26
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.28
Consensus pattern (80 bp):
TAAGTCCCAAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
TTACTAATTCCGGGC
Found at i:12711563 original size:27 final size:27
Alignment explanation
Indices: 12711526--12711730 Score: 241
Period size: 27 Copynumber: 7.6 Consensus size: 27
12711516 TAAATTGTAC
*
12711526 AGCACTAAGTGTGTGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
12711553 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
12711580 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
12711606 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
12711634 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* * *
12711662 AGCACTAAGTGTGCGATTTTATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
12711689 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
12711716 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
12711731 GACTCAATAT
Statistics
Matches: 153, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
27 130 0.85
28 23 0.15
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Done.