Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 35 of 203
Found at i:11596512 original size:27 final size:26
Alignment explanation
Indices: 11596451--11596523 Score: 87
Period size: 25 Copynumber: 2.8 Consensus size: 26
11596441 AACCCGGATA
* *
11596451 AGCTTCCCGTTACATGGCTC-ACATG
1 AGCTTCCCGTTATATGGCTCGACAAG
*
11596476 AGCTTCCCGTTATATGGCTCGAGAGAG
1 AGCTTCCCGTTATATGGCTCGACA-AG
11596503 AGCTTCCCGTT-TATGTGCTCG
1 AGCTTCCCGTTATATG-GCTCG
11596524 TATGAGCATT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
25 19 0.45
26 6 0.14
27 17 0.40
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (26 bp):
AGCTTCCCGTTATATGGCTCGACAAG
Found at i:11599708 original size:21 final size:20
Alignment explanation
Indices: 11599661--11599709 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
11599651 GAAAATAATT
*
11599661 TCTA-AAAAATAGATTGATT
1 TCTATAAAAATAGATTGATG
* *
11599680 TTTCTAAAAATAGATTAGATG
1 TCTATAAAAATAGATT-GATG
11599701 TCTATAAAA
1 TCTATAAAA
11599710 CATTTTTTGG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 2 0.09
20 11 0.48
21 10 0.43
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (20 bp):
TCTATAAAAATAGATTGATG
Found at i:11608720 original size:51 final size:52
Alignment explanation
Indices: 11608658--11608879 Score: 231
Period size: 51 Copynumber: 4.4 Consensus size: 52
11608648 TTCGGTGGTT
* * *
11608658 TGCACATAGTACCACCCATGTGACCATTGTC-ATCCGATACACGTAGTAGCC
1 TGCACATAGTACTACACACGTGACCATTGTCTATCCGATACACGTAGTAGCC
* * * * *
11608709 TACACATAGTACTACACACGTGATCA-AG-CTTTCC-AGTTCACGTAGTAGCC
1 TGCACATAGTACTACACACGTGACCATTGTCTATCCGA-TACACGTAGTAGCC
** * * *
11608759 TGCACATAGTACTACACACGTGACCAAGGT-AATCCGGTACACATAGTAGCC
1 TGCACATAGTACTACACACGTGACCATTGTCTATCCGATACACGTAGTAGCC
* * *
11608810 TGTACATAGTACTACACATGTGACCATTGTCTAT-TGATACACGTAGTAGCC
1 TGCACATAGTACTACACACGTGACCATTGTCTATCCGATACACGTAGTAGCC
* *
11608861 TGCACTTAGTACTATACAC
1 TGCACATAGTACTACACAC
11608880 ATGTTCATAG
Statistics
Matches: 137, Mismatches: 28, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
49 2 0.01
50 41 0.30
51 92 0.67
52 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (52 bp):
TGCACATAGTACTACACACGTGACCATTGTCTATCCGATACACGTAGTAGCC
Found at i:11609937 original size:9 final size:9
Alignment explanation
Indices: 11609921--11609999 Score: 131
Period size: 9 Copynumber: 8.8 Consensus size: 9
11609911 GGTATTTTTC
11609921 GGTAATTCG
1 GGTAATTCG
*
11609930 GTTAATTCG
1 GGTAATTCG
*
11609939 GTTAATTCG
1 GGTAATTCG
*
11609948 GTTAATTCG
1 GGTAATTCG
11609957 GGTAATTCG
1 GGTAATTCG
11609966 GGTAATTCG
1 GGTAATTCG
11609975 GGTAATTCG
1 GGTAATTCG
11609984 GGTAATTCG
1 GGTAATTCG
11609993 GGTAATT
1 GGTAATT
11610000 TTTAACCAAA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 68 1.00
ACGTcount: A:0.23, C:0.10, G:0.29, T:0.38
Consensus pattern (9 bp):
GGTAATTCG
Found at i:11610177 original size:12 final size:12
Alignment explanation
Indices: 11610160--11610184 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11610150 AGTAATTTCG
11610160 GGTCGGTTAACC
1 GGTCGGTTAACC
11610172 GGTCGGTTAACC
1 GGTCGGTTAACC
11610184 G
1 G
11610185 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:11612276 original size:18 final size:17
Alignment explanation
Indices: 11612244--11612277 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
11612234 AAAATTATTC
*
11612244 ATATTTTATATTATAAA
1 ATATTTTAAATTATAAA
11612261 ATATTTATAAATTATAA
1 ATATTT-TAAATTATAA
11612278 TCTATACATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATTTTAAATTATAAA
Found at i:11612316 original size:22 final size:23
Alignment explanation
Indices: 11612288--11612332 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
11612278 TCTATACATT
11612288 TATTTT-CAAAATATTAATAAAA
1 TATTTTACAAAATATTAATAAAA
11612310 TATTTTCAACAAAATATTAATAA
1 TATTTT--ACAAAATATTAATAA
11612333 TATTATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 6 0.30
25 14 0.70
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (23 bp):
TATTTTACAAAATATTAATAAAA
Found at i:11613469 original size:28 final size:28
Alignment explanation
Indices: 11613438--11613498 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
11613428 AACATTGTTA
11613438 ATTTTTTTATTAAATTTATTGGTATGAT
1 ATTTTTTTATTAAATTTATTGGTATGAT
11613466 ATTTTTTTATTAAATTTATTGGTATGAT
1 ATTTTTTTATTAAATTTATTGGTATGAT
11613494 ATTTT
1 ATTTT
11613499 GAAAAATAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (28 bp):
ATTTTTTTATTAAATTTATTGGTATGAT
Found at i:11618005 original size:9 final size:9
Alignment explanation
Indices: 11617979--11618007 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
11617969 GTTGTTAACT
11617979 TTTCTTTTC
1 TTTCTTTTC
11617988 TTT-TTTTC
1 TTTCTTTTC
11617996 TTTCTTTTC
1 TTTCTTTTC
11618005 TTT
1 TTT
11618008 AATGTTTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTCTTTTC
Found at i:11622583 original size:4 final size:4
Alignment explanation
Indices: 11622576--11622611 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
11622566 CATACACACA
11622576 CATC CATC CATC CATC CATC CATC CATC CATC CATC
1 CATC CATC CATC CATC CATC CATC CATC CATC CATC
11622612 TTCTGTTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.25, C:0.50, G:0.00, T:0.25
Consensus pattern (4 bp):
CATC
Found at i:11627407 original size:31 final size:31
Alignment explanation
Indices: 11627361--11627420 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
11627351 TGATCTTTCC
*
11627361 TATGGGTGTTTTTTTATCTACCTGTGTTTGA
1 TATGGGTGTTGTTTTATCTACCTGTGTTTGA
*
11627392 TATGTGTGTTGTTTTATCTACCTGTGTTT
1 TATGGGTGTTGTTTTATCTACCTGTGTTT
11627421 TTTATCTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.12, C:0.10, G:0.22, T:0.57
Consensus pattern (31 bp):
TATGGGTGTTGTTTTATCTACCTGTGTTTGA
Found at i:11627425 original size:17 final size:18
Alignment explanation
Indices: 11627396--11627429 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
11627386 GTTTGATATG
11627396 TGTGTTGTTTTATCTACC
1 TGTGTTGTTTTATCTACC
11627414 TGTGTT-TTTTATCTAC
1 TGTGTTGTTTTATCTAC
11627430 ACATTTTGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.12, C:0.15, G:0.15, T:0.59
Consensus pattern (18 bp):
TGTGTTGTTTTATCTACC
Found at i:11631472 original size:21 final size:22
Alignment explanation
Indices: 11631446--11631492 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
11631436 CTCTGCTCAA
*
11631446 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
11631467 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
11631489 ACTC
1 ACTC
11631493 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:11636618 original size:19 final size:20
Alignment explanation
Indices: 11636581--11636621 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
11636571 TACAACACAA
*
11636581 TTCAATTTCATATTGAATAT
1 TTCAATTTCATATTCAATAT
*
11636601 TTCAATTT-TTATTCAATAT
1 TTCAATTTCATATTCAATAT
11636620 TT
1 TT
11636622 GCCTAAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (20 bp):
TTCAATTTCATATTCAATAT
Found at i:11643201 original size:19 final size:20
Alignment explanation
Indices: 11643164--11643204 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
11643154 TACAACACAA
*
11643164 TTCAATTTCATATTGAATAT
1 TTCAATTTCATATTCAATAT
*
11643184 TTCAATTT-TTATTCAATAT
1 TTCAATTTCATATTCAATAT
11643203 TT
1 TT
11643205 TACTAAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (20 bp):
TTCAATTTCATATTCAATAT
Found at i:11645356 original size:19 final size:19
Alignment explanation
Indices: 11645334--11645371 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
11645324 CAAACCTTAA
11645334 CTTGAGTTTCTCTTTCCTC
1 CTTGAGTTTCTCTTTCCTC
11645353 CTTGAGTTTCTCTTTCCTC
1 CTTGAGTTTCTCTTTCCTC
11645372 GAAGACGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.05, C:0.32, G:0.11, T:0.53
Consensus pattern (19 bp):
CTTGAGTTTCTCTTTCCTC
Found at i:11648746 original size:20 final size:21
Alignment explanation
Indices: 11648702--11648746 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
11648692 GAGATCATGC
11648702 AGATGTTTTGTTACTTCAATT
1 AGATGTTTTGTTACTTCAATT
*
11648723 AGATGTTTTGTTACTT-AGTT
1 AGATGTTTTGTTACTTCAATT
11648743 AGAT
1 AGAT
11648747 ATGAACTAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.24, C:0.07, G:0.18, T:0.51
Consensus pattern (21 bp):
AGATGTTTTGTTACTTCAATT
Found at i:11650690 original size:12 final size:12
Alignment explanation
Indices: 11650673--11650697 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11650663 GGTGTTCATT
11650673 CGGTTAACCGAC
1 CGGTTAACCGAC
11650685 CGGTTAACCGAC
1 CGGTTAACCGAC
11650697 C
1 C
11650698 CGAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:11650872 original size:9 final size:9
Alignment explanation
Indices: 11650858--11650934 Score: 93
Period size: 9 Copynumber: 8.4 Consensus size: 9
11650848 TTTGGTTAAA
11650858 AATTACCCG
1 AATTACCCG
11650867 AATTACCCG
1 AATTACCCG
*
11650876 AATTATCCG
1 AATTACCCG
*
11650885 AATTAACCG
1 AATTACCCG
*
11650894 AATTAACCG
1 AATTACCCG
11650903 AATTA-CCG
1 AATTACCCG
*
11650911 AAAAATACCCG
1 --AATTACCCG
11650922 AATTACCCG
1 AATTACCCG
11650931 AATT
1 AATT
11650935 TTTTTTATTT
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
8 3 0.05
9 51 0.84
10 4 0.07
11 3 0.05
ACGTcount: A:0.40, C:0.26, G:0.10, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:11650896 original size:27 final size:27
Alignment explanation
Indices: 11650857--11650934 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
11650847 TTTTGGTTAA
11650857 AAATTACCCGAATTACCCGAATTATCCG
1 AAATTACCCGAATTACCCGAATTA-CCG
* *
11650885 -AATTAACCGAATTAACCGAATTACCG
1 AAATTACCCGAATTACCCGAATTACCG
*
11650911 AAAAATACCCGAATTACCCGAATT
1 -AAATTACCCGAATTACCCGAATT
11650935 TTTTTTATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
26 3 0.07
27 21 0.49
28 19 0.44
ACGTcount: A:0.41, C:0.26, G:0.10, T:0.23
Consensus pattern (27 bp):
AAATTACCCGAATTACCCGAATTACCG
Found at i:11651735 original size:21 final size:21
Alignment explanation
Indices: 11651709--11651777 Score: 129
Period size: 21 Copynumber: 3.3 Consensus size: 21
11651699 GAATAGAAGT
*
11651709 TTGATGGATATGGCCAGATGC
1 TTGATGGATATGGCTAGATGC
11651730 TTGATGGATATGGCTAGATGC
1 TTGATGGATATGGCTAGATGC
11651751 TTGATGGATATGGCTAGATGC
1 TTGATGGATATGGCTAGATGC
11651772 TTGATG
1 TTGATG
11651778 TTTGAGAGAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.23, C:0.10, G:0.33, T:0.33
Consensus pattern (21 bp):
TTGATGGATATGGCTAGATGC
Found at i:11655884 original size:12 final size:12
Alignment explanation
Indices: 11655867--11655901 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
11655857 CCCAATTTTA
11655867 TTTTATTTTATT
1 TTTTATTTTATT
11655879 TTTTATTTTTATT
1 TTTTA-TTTTATT
11655892 TTTATATTTT
1 TTT-TATTTT
11655902 CTATTTTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 5 0.24
13 14 0.67
14 2 0.10
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTATTTTATT
Found at i:11658313 original size:20 final size:21
Alignment explanation
Indices: 11658278--11658316 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
11658268 CTTATCTTTA
*
11658278 CAATTTTAATTTCAATTAACG
1 CAATTTCAATTTCAATTAACG
11658299 CAATTTCAA-TTCAATTAA
1 CAATTTCAATTTCAATTAA
11658317 ACTTTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.41
Consensus pattern (21 bp):
CAATTTCAATTTCAATTAACG
Found at i:11665518 original size:32 final size:32
Alignment explanation
Indices: 11665430--11665519 Score: 78
Period size: 32 Copynumber: 2.8 Consensus size: 32
11665420 ACAGCAATTT
*
11665430 TAGCAGAATTTATCCATTTAAAAAT-GATTAA
1 TAGCAGAATTTATCCAATTAAAAATGGATTAA
** * * *
11665461 TTTCTATAACTTA--CAAATAAGAAATGGATTAA
1 TAGC-AGAATTTATCCAATTAA-AAATGGATTAA
*
11665493 TAGCAGAATTTATCCACTTAAAAATGG
1 TAGCAGAATTTATCCAATTAAAAATGG
11665520 TTTATTTCGA
Statistics
Matches: 42, Mismatches: 12, Indels: 9
0.67 0.19 0.14
Matches are distributed among these distances:
30 5 0.12
31 12 0.29
32 20 0.48
33 5 0.12
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (32 bp):
TAGCAGAATTTATCCAATTAAAAATGGATTAA
Found at i:11667476 original size:19 final size:17
Alignment explanation
Indices: 11667452--11667495 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
11667442 CAATGCATCT
*
11667452 AATAATTATACATATTGCC
1 AATAATAATACA-ATT-CC
*
11667471 AATAATAATTCAATTCC
1 AATAATAATACAATTCC
11667488 AATAATAA
1 AATAATAA
11667496 AATACATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 10 0.43
18 3 0.13
19 10 0.43
ACGTcount: A:0.50, C:0.14, G:0.02, T:0.34
Consensus pattern (17 bp):
AATAATAATACAATTCC
Found at i:11671481 original size:20 final size:20
Alignment explanation
Indices: 11671438--11671494 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
11671428 TTCGGGTGGA
* *
11671438 TCAGCTCTTTTGAGCTTCTGT
1 TCAGCTCTTATGAG-TTCTAT
*
11671459 TCAGCTCTTACGAGTTCTAT
1 TCAGCTCTTATGAGTTCTAT
11671479 TCAGCTCTTATGAGTT
1 TCAGCTCTTATGAGTT
11671495 TTCATTTGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 20 0.62
21 12 0.38
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.44
Consensus pattern (20 bp):
TCAGCTCTTATGAGTTCTAT
Found at i:11671543 original size:37 final size:37
Alignment explanation
Indices: 11671502--11671575 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
11671492 GTTTTCATTT
*
11671502 GTGTGTTCAAGTGGATCAGCTCTATGAGCTTCTGTTG
1 GTGTGTTCAAGTGGACCAGCTCTATGAGCTTCTGTTG
** *
11671539 GTGTGTTCGGGTGGACCAGCTCTATGAGCTTTTGTTG
1 GTGTGTTCAAGTGGACCAGCTCTATGAGCTTCTGTTG
11671576 ATGATGTACT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.14, C:0.16, G:0.32, T:0.38
Consensus pattern (37 bp):
GTGTGTTCAAGTGGACCAGCTCTATGAGCTTCTGTTG
Found at i:11672152 original size:15 final size:14
Alignment explanation
Indices: 11672132--11672161 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
11672122 TTTATGATGG
11672132 TATATATATACTAAA
1 TATATATATA-TAAA
11672147 TATATATATATAAA
1 TATATATATATAAA
11672161 T
1 T
11672162 TATTGAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (14 bp):
TATATATATATAAA
Found at i:11672482 original size:66 final size:65
Alignment explanation
Indices: 11672405--11672535 Score: 244
Period size: 66 Copynumber: 2.0 Consensus size: 65
11672395 TCAATGATTA
*
11672405 TAGGAAAAGAAAATAATAAAGAAAAGTAAGTGAGTGTGGGGTGGGGGGGGGGGGGAAATGTTTTT
1 TAGGAAAAGAAAATAATAAAGAAAAGTAAGTGAGTGTGGGGTGGGGGGGGGGGAGAAATGTTTTT
11672470 NTAGGAAAAGAAAATAATAAAGAAAAGTAAGTGAGTGTGGGGTGGGGGGGGGGGAGAAATGTTTT
1 -TAGGAAAAGAAAATAATAAAGAAAAGTAAGTGAGTGTGGGGTGGGGGGGGGGGAGAAATGTTTT
11672535 T
65 T
11672536 CTTCTTCCTT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.37, C:0.00, G:0.40, T:0.21
Consensus pattern (65 bp):
TAGGAAAAGAAAATAATAAAGAAAAGTAAGTGAGTGTGGGGTGGGGGGGGGGGAGAAATGTTTTT
Found at i:11673697 original size:75 final size:75
Alignment explanation
Indices: 11673602--11673743 Score: 221
Period size: 75 Copynumber: 1.9 Consensus size: 75
11673592 CACACAATCA
* * * *
11673602 TCGGTTTATCCGACTAGCGCTGGGTGCAAACACCGTTGGTTCATCCAACTAGAGTTGGGCTCACT
1 TCGGTATATCCGACTAGCGCTGGGCGCAAACACCATTGGTTCATCCAACTAGAGCTGGGCTCACT
11673667 TTTATTATTG
66 TTTATTATTG
** *
11673677 TCGGTATATCCGACTAGCGCTGGGCGCAAACATTATTGGTTTATCCAACTAGAGCTGGGCTCACT
1 TCGGTATATCCGACTAGCGCTGGGCGCAAACACCATTGGTTCATCCAACTAGAGCTGGGCTCACT
11673742 TT
66 TT
11673744 CAATATTTCC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
75 60 1.00
ACGTcount: A:0.21, C:0.23, G:0.24, T:0.32
Consensus pattern (75 bp):
TCGGTATATCCGACTAGCGCTGGGCGCAAACACCATTGGTTCATCCAACTAGAGCTGGGCTCACT
TTTATTATTG
Found at i:11673765 original size:75 final size:75
Alignment explanation
Indices: 11673611--11673782 Score: 204
Period size: 75 Copynumber: 2.3 Consensus size: 75
11673601 ATCGGTTTAT
* * * * *
11673611 CCGACTAGCGCTGGGTGCAAACACCGTTGGTTCATCCAACTAGAGTTGGGCTCACTTTTATTATT
1 CCGACTAGCGCTGGGCGCAAACACCATTGGTTCATCCAACTAGAGCTGGGCTCACTTTCAATATT
* *
11673676 GTCGGTATAT
66 GTCAGTATAC
** *
11673686 CCGACTAGCGCTGGGCGCAAACATTATTGGTTTATCCAACTAGAGCTGGGCTCACTTTCAATATT
1 CCGACTAGCGCTGGGCGCAAACACCATTGGTTCATCCAACTAGAGCTGGGCTCACTTTCAATATT
*
11673751 -TCCAAT-TAAC
66 GT-CAGTAT-AC
*
11673761 CCGACTAGCGTTGGGCGCAAAC
1 CCGACTAGCGCTGGGCGCAAAC
11673783 CTCTCTGCAG
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
74 2 0.02
75 81 0.98
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.28
Consensus pattern (75 bp):
CCGACTAGCGCTGGGCGCAAACACCATTGGTTCATCCAACTAGAGCTGGGCTCACTTTCAATATT
GTCAGTATAC
Found at i:11675516 original size:19 final size:19
Alignment explanation
Indices: 11675492--11675581 Score: 116
Period size: 19 Copynumber: 4.8 Consensus size: 19
11675482 AATCTTCGAG
*
11675492 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
11675511 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
11675530 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
11675551 GATATGTAATCTTAGA-A-
1 GATATGCAATCTTAGATAT
11675568 GATATG--ATCTTAGA
1 GATATGCAATCTTAGA
11675582 GATTTAATTT
Statistics
Matches: 67, Mismatches: 2, Indels: 8
0.87 0.03 0.10
Matches are distributed among these distances:
15 8 0.12
17 6 0.09
18 1 0.01
19 33 0.49
21 19 0.28
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:11675538 original size:21 final size:21
Alignment explanation
Indices: 11675493--11675555 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
11675483 ATCTTCGAGG
*
11675493 ATATGTAATCTTAGATATG--
1 ATATGCAATCTTAGATATGAT
11675512 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
11675533 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
11675554 AT
1 AT
11675556 GTAATCTTAG
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
19 18 0.44
21 23 0.56
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:11676355 original size:25 final size:25
Alignment explanation
Indices: 11676311--11676435 Score: 105
Period size: 25 Copynumber: 5.0 Consensus size: 25
11676301 TACACGTATA
*
11676311 TATATTTTTTTAAAACGAATATTTTCC
1 TATATTTTTTT--AATGAATATTTTCC
11676338 TATATTTTTTTAATGAATATTTT-C
1 TATATTTTTTTAATGAATATTTTCC
* * * * *
11676362 -ATATTTATATT-ATGTACATGTAT-A
1 TATATTT-TTTTAATGAATAT-TTTCC
* *
11676386 TATATTTTTTAAAACGAATATTTTCC
1 TATATTTTTT-TAATGAATATTTTCC
11676412 TATATTTTTTTAATGAATATTTTC
1 TATATTTTTTTAATGAATATTTTC
11676436 ATATTTATAT
Statistics
Matches: 77, Mismatches: 15, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
23 12 0.16
24 8 0.10
25 31 0.40
26 15 0.19
27 11 0.14
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (25 bp):
TATATTTTTTTAATGAATATTTTCC
Found at i:11676407 original size:74 final size:75
Alignment explanation
Indices: 11676297--11676445 Score: 282
Period size: 74 Copynumber: 2.0 Consensus size: 75
11676287 ATTCCTTTTA
11676297 TATGTACACGTATATATATTTTTTTAAAACGAATATTTTCCTATATTTTTTTAATGAATATTTTC
1 TATGTACACGTATATATATTTTTTTAAAACGAATATTTTCCTATATTTTTTTAATGAATATTTTC
11676362 ATATTTATAT
66 ATATTTATAT
*
11676372 TATGTACATGTATATATA-TTTTTTAAAACGAATATTTTCCTATATTTTTTTAATGAATATTTTC
1 TATGTACACGTATATATATTTTTTTAAAACGAATATTTTCCTATATTTTTTTAATGAATATTTTC
11676436 ATATTTATAT
66 ATATTTATAT
11676446 GCATATATTT
Statistics
Matches: 73, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
74 56 0.77
75 17 0.23
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.54
Consensus pattern (75 bp):
TATGTACACGTATATATATTTTTTTAAAACGAATATTTTCCTATATTTTTTTAATGAATATTTTC
ATATTTATAT
Found at i:11677228 original size:98 final size:98
Alignment explanation
Indices: 11677107--11677301 Score: 345
Period size: 98 Copynumber: 2.0 Consensus size: 98
11677097 AAAAATCATG
* * *
11677107 AAGGAAATATTTCGAGTTTGAGATTCTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTCTT
1 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGAGTGTGATTTCTT
11677172 AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
66 AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
*
11677205 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGGATCGTGCCCTAACGTATTGAGTGTGATTTCTT
1 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGAGTGTGATTTCTT
*
11677270 AAATCTTGGATGAGTGGATGTTCTTTTAAAGT
66 AAATCTTGGATAAGTGGATGTTCTTTTAAAGT
11677302 TTTATTGTAT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 92 1.00
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.37
Consensus pattern (98 bp):
AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGAGTGTGATTTCTT
AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
Found at i:11679003 original size:11 final size:11
Alignment explanation
Indices: 11678980--11679048 Score: 76
Period size: 11 Copynumber: 6.5 Consensus size: 11
11678970 AAAACAAAAA
11678980 TTAAAAAAGTATT
1 TTAAAAAA--ATT
*
11678993 TTAAAAATATT
1 TTAAAAAAATT
11679004 TT---AAAA-T
1 TTAAAAAAATT
11679011 T-AAAAAAATT
1 TTAAAAAAATT
11679021 TTAAAAAAATT
1 TTAAAAAAATT
11679032 TTAAAAAAATT
1 TTAAAAAAATT
11679043 TTAAAA
1 TTAAAA
11679049 TTTAAAAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
7 2 0.04
8 3 0.06
9 4 0.08
10 2 0.04
11 31 0.63
13 7 0.14
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (11 bp):
TTAAAAAAATT
Found at i:11679020 original size:9 final size:9
Alignment explanation
Indices: 11679006--11679066 Score: 52
Period size: 11 Copynumber: 6.4 Consensus size: 9
11678996 AAAATATTTT
11679006 AAAATTAAA
1 AAAATTAAA
11679015 AAAATTTTAAA
1 AAAA--TTAAA
11679026 AAAATTTTAAA
1 AAAA--TTAAA
**
11679037 AAAATT-TT
1 AAAATTAAA
*
11679045 AAAATTTAA
1 AAAATTAAA
11679054 AAAATTAAA
1 AAAATTAAA
11679063 AAAA
1 AAAA
11679067 AGTATTTTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
8 6 0.14
9 18 0.41
11 20 0.45
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
AAAATTAAA
Found at i:11679024 original size:28 final size:29
Alignment explanation
Indices: 11678976--11679037 Score: 99
Period size: 28 Copynumber: 2.1 Consensus size: 29
11678966 AATTAAAACA
*
11678976 AAAATTAAAAAAGTATTTTAAAAATATTTT
1 AAAATTAAAAAAG-ATTTTAAAAAAATTTT
11679006 AAAATTAAAAAA-ATTTTAAAAAAATTTT
1 AAAATTAAAAAAGATTTTAAAAAAATTTT
11679034 AAAA
1 AAAA
11679038 AAATTTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 19 0.61
30 12 0.39
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (29 bp):
AAAATTAAAAAAGATTTTAAAAAAATTTT
Found at i:11679049 original size:30 final size:30
Alignment explanation
Indices: 11679015--11679080 Score: 82
Period size: 28 Copynumber: 2.2 Consensus size: 30
11679005 TAAAATTAAA
**
11679015 AAAATTTTAAAAAAATTTTAAAAAA-ATTTT
1 AAAATTTT-AAAAAATTAAAAAAAAGATTTT
11679045 AAAA-TTTAAAAAATTAAAAAAAAGTATTTT
1 AAAATTTTAAAAAATTAAAAAAAAG-ATTTT
11679075 AAAATT
1 AAAATT
11679081 AAAATAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 14 0.45
29 3 0.10
30 13 0.42
31 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (30 bp):
AAAATTTTAAAAAATTAAAAAAAAGATTTT
Found at i:11679493 original size:20 final size:20
Alignment explanation
Indices: 11679470--11679512 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
11679460 ATATATTTGG
11679470 ATACATCCTCATCATTTTTT
1 ATACATCCTCATCATTTTTT
* **
11679490 ATACTTCCTCATTTTTTTTT
1 ATACATCCTCATCATTTTTT
11679510 ATA
1 ATA
11679513 TTTACTCAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.23, C:0.21, G:0.00, T:0.56
Consensus pattern (20 bp):
ATACATCCTCATCATTTTTT
Found at i:11679526 original size:20 final size:20
Alignment explanation
Indices: 11679484--11679526 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
11679474 ATCCTCATCA
* **
11679484 TTTTTTATACTTCCTCATTT
1 TTTTTTATACTTACTCAAGT
*
11679504 TTTTTTATATTTACTCAAGT
1 TTTTTTATACTTACTCAAGT
11679524 TTT
1 TTT
11679527 AGTGTATTCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.19, C:0.14, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTTTTATACTTACTCAAGT
Found at i:11679866 original size:20 final size:20
Alignment explanation
Indices: 11679841--11680241 Score: 128
Period size: 20 Copynumber: 20.9 Consensus size: 20
11679831 CTTGATATTC
*
11679841 CCTCATAATTTTTTGTACTT
1 CCTCATAATTTTTGGTACTT
*
11679861 CCTCAT-ATGTTTTGGTACAT
1 CCTCATAAT-TTTTGGTACTT
* * ** **
11679881 CATCAT-TTTTTTTATTTTT
1 CCTCATAATTTTTGGTACTT
11679900 CCTCA-AATTTTATGGTA-TT
1 CCTCATAATTTT-TGGTACTT
11679919 CTCTCATAA-TTTTGGTACTT
1 C-CTCATAATTTTTGGTACTT
* *
11679939 CCTCATATTTTTTAGTA-TT
1 CCTCATAATTTTTGGTACTT
* * *
11679958 CTATCATAATTTTTTTGTACAT
1 C-CTCATAA-TTTTTGGTACTT
* * *
11679980 CTTCATAATTTTTGGTGCAT
1 CCTCATAATTTTTGGTACTT
* *
11680000 CCACAT--TTTTTGGTAATT
1 CCTCATAATTTTTGGTACTT
** * *
11680018 CCT--TTTTTTTTTGTA-TC
1 CCTCATAATTTTTGGTACTT
* *
11680035 CCTCGTAATTTTTAGTA-TT
1 CCTCATAATTTTTGGTACTT
11680054 CGCTCATAATTTTTGGTACTT
1 C-CTCATAATTTTTGGTACTT
* * *
11680075 ACTCAT--TTTTTTGTATTT
1 CCTCATAATTTTTGGTACTT
** *
11680093 TGTCGTAATTTTT--TA--T
1 CCTCATAATTTTTGGTACTT
* *
11680109 --ACAT--CTTTTGGTACTT
1 CCTCATAATTTTTGGTACTT
*
11680125 CCTCATAATTTTTGGTAATT
1 CCTCATAATTTTTGGTACTT
* ** ** *
11680145 CATTGTGTTTTTTGGTATTT
1 CCTCATAATTTTTGGTACTT
* * *
11680165 CCTCATAAATTTTGATTCATT
1 CCTCATAATTTTTGGTAC-TT
* *
11680186 -CTCATAAGTTTTGGTAGTT
1 CCTCATAATTTTTGGTACTT
* * *
11680205 CTTTATAAATTTTGGTACTT
1 CCTCATAATTTTTGGTACTT
* * *
11680225 TCTTATAATTCTTGGTA
1 CCTCATAATTTTTGGTA
11680242 TCCTATTATA
Statistics
Matches: 277, Mismatches: 76, Indels: 56
0.68 0.19 0.14
Matches are distributed among these distances:
12 4 0.01
14 4 0.01
16 3 0.01
17 4 0.01
18 37 0.13
19 46 0.17
20 157 0.57
21 20 0.07
22 2 0.01
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.55
Consensus pattern (20 bp):
CCTCATAATTTTTGGTACTT
Found at i:11681026 original size:20 final size:20
Alignment explanation
Indices: 11680908--11681025 Score: 87
Period size: 20 Copynumber: 5.8 Consensus size: 20
11680898 AATTTTATTT
* *
11680908 TGAAAGCATACCAAAAATTA
1 TGAAAGAATAACAAAAATTA
*
11680928 TGAAA-AAAATACTAAAAATTA
1 TGAAAGAATA-AC-AAAAATTA
* * * *
11680949 TGAGAGATTACCAATAATTA
1 TGAAAGAATAACAAAAATTA
* * *
11680969 TGAAAGTATATCCAAAATTA
1 TGAAAGAATAACAAAAATTA
* *
11680989 TAACAAAAATAACAAAAATTA
1 TGA-AAGAATAACAAAAATTA
11681010 TGAAAGAATAA-AAAAA
1 TGAAAGAATAACAAAAA
11681026 AGGAATTTGA
Statistics
Matches: 73, Mismatches: 21, Indels: 9
0.71 0.20 0.09
Matches are distributed among these distances:
19 7 0.10
20 36 0.49
21 28 0.38
22 2 0.03
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.23
Consensus pattern (20 bp):
TGAAAGAATAACAAAAATTA
Found at i:11684062 original size:37 final size:37
Alignment explanation
Indices: 11684012--11684086 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
11684002 AGCTTTTTAA
11684012 TCTTGAAATAATTCTTAAATGTTGCATTAAATAGTAT
1 TCTTGAAATAATTCTTAAATGTTGCATTAAATAGTAT
11684049 TCTTGAAATAATTCTTAAATGTTGCATTAAATAGTAT
1 TCTTGAAATAATTCTTAAATGTTGCATTAAATAGTAT
11684086 T
1 T
11684087 TTTGTTTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.44
Consensus pattern (37 bp):
TCTTGAAATAATTCTTAAATGTTGCATTAAATAGTAT
Found at i:11684521 original size:17 final size:16
Alignment explanation
Indices: 11684488--11684521 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
11684478 ATTTCATATA
11684488 TAAAATTATATAAAAT
1 TAAAATTATATAAAAT
*
11684504 TAAAATTCATATATAAT
1 TAAAATT-ATATAAAAT
11684521 T
1 T
11684522 TTACGGATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAAATTATATAAAAT
Found at i:11686286 original size:22 final size:22
Alignment explanation
Indices: 11686252--11686294 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
11686242 TATACAAATA
*
11686252 ATATTACTCGAATAGTTATGAG
1 ATATTACTCGAATAATTATGAG
* *
11686274 ATATTAGTTGAATAATTATGA
1 ATATTACTCGAATAATTATGA
11686295 CCTCTATTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.40
Consensus pattern (22 bp):
ATATTACTCGAATAATTATGAG
Found at i:11692741 original size:5 final size:6
Alignment explanation
Indices: 11692727--11692776 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
11692717 TAAAGCAACT
* *
11692727 AAAACA AAAATA AAAATA AAAAT- AAAATA AAACGA-A AAAATA ATAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAA--ATA AAAATA AAAATA
11692775 AA
1 AA
11692777 CTCAATGATA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
5 6 0.16
6 26 0.70
7 4 0.11
8 1 0.03
ACGTcount: A:0.80, C:0.04, G:0.02, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:11692962 original size:12 final size:12
Alignment explanation
Indices: 11692886--11692973 Score: 60
Period size: 12 Copynumber: 7.4 Consensus size: 12
11692876 TAAGTATGAG
11692886 AATAATAAAT-A
1 AATAATAAATAA
11692897 AATAAATAAATAA
1 AAT-AATAAATAA
* **
11692910 AATAATTAGGAA
1 AATAATAAATAA
11692922 AATAA-AAATTAA
1 AATAATAAA-TAA
* *
11692934 TAAT-ATAACTATT
1 -AATAATAAATA-A
11692947 AATAATAAATAA
1 AATAATAAATAA
11692959 AAT-A-AAATAA
1 AATAATAAATAA
11692969 AATAA
1 AATAA
11692974 AAGGGGTAGC
Statistics
Matches: 59, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
10 9 0.15
11 6 0.10
12 29 0.49
13 15 0.25
ACGTcount: A:0.69, C:0.01, G:0.02, T:0.27
Consensus pattern (12 bp):
AATAATAAATAA
Found at i:11703278 original size:21 final size:21
Alignment explanation
Indices: 11703252--11703291 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
11703242 TTTAAGATAG
*
11703252 TTACTTGAATAGTTGTATCTC
1 TTACTTGAATAGTTATATCTC
*
11703273 TTACTTTAATAGTTATATC
1 TTACTTGAATAGTTATATC
11703292 GTTTTAAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.10, T:0.50
Consensus pattern (21 bp):
TTACTTGAATAGTTATATCTC
Found at i:11725417 original size:18 final size:19
Alignment explanation
Indices: 11725387--11725439 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
11725377 GTAACTTTTA
11725387 AATTTAGAAAATATTAAA-T
1 AATTTA-AAAATATTAAAGT
*
11725406 AATTTAAAAATATGAAAGT
1 AATTTAAAAATATTAAAGT
*
11725425 CA-TTAAAAAT-TTAAA
1 AATTTAAAAATATTAAA
11725440 AAATGATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 4 0.13
18 18 0.60
19 8 0.27
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (19 bp):
AATTTAAAAATATTAAAGT
Found at i:11726436 original size:15 final size:16
Alignment explanation
Indices: 11726416--11726445 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11726406 AAGTATAGTA
11726416 AAATAT-TTAAAAAAT
1 AAATATCTTAAAAAAT
11726431 AAATATCTTAAAAAA
1 AAATATCTTAAAAAA
11726446 ATAGACACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATATCTTAAAAAAT
Found at i:11727015 original size:20 final size:20
Alignment explanation
Indices: 11726990--11727029 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
11726980 AATGAGATTG
11726990 ATTTTGTAAGGGTAAATGCA
1 ATTTTGTAAGGGTAAATGCA
11727010 ATTTTGTAAGGGTAAATGCA
1 ATTTTGTAAGGGTAAATGCA
11727030 GGGATACCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (20 bp):
ATTTTGTAAGGGTAAATGCA
Found at i:11729233 original size:76 final size:77
Alignment explanation
Indices: 11729041--11729249 Score: 330
Period size: 76 Copynumber: 2.7 Consensus size: 77
11729031 AACCGTTATC
* * *
11729041 GGTGGATTCAACACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTTTTTAC
1 GGTGGAATCAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTTTTCAC
*
11729106 TTTCAAGGATAT
66 ATTCAAGGATAT
*
11729118 GGTGGAATCAGCACTTAGCAACCACCAGTGATTCGGGGAATCAACACTTAGCAACCCC-TTTCAC
1 GGTGGAATCAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTTTTCAC
11729182 ATTCAAGGATAT
66 ATTCAAGGATAT
** * *
11729194 GGTGGAATCAGCACTTAGCAACCACCAAAGAGTCAGGGAATCAGCACTTAGCAACC
1 GGTGGAATCAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACC
11729250 ACCAAAGAGT
Statistics
Matches: 122, Mismatches: 10, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
76 67 0.55
77 55 0.45
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.22
Consensus pattern (77 bp):
GGTGGAATCAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTTTTCAC
ATTCAAGGATAT
Found at i:11729239 original size:33 final size:33
Alignment explanation
Indices: 11729197--11729282 Score: 172
Period size: 33 Copynumber: 2.6 Consensus size: 33
11729187 AGGATATGGT
11729197 GGAATCAGCACTTAGCAACCACCAAAGAGTCAG
1 GGAATCAGCACTTAGCAACCACCAAAGAGTCAG
11729230 GGAATCAGCACTTAGCAACCACCAAAGAGTCAG
1 GGAATCAGCACTTAGCAACCACCAAAGAGTCAG
11729263 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
11729283 CTTTGTTATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.38, C:0.28, G:0.21, T:0.13
Consensus pattern (33 bp):
GGAATCAGCACTTAGCAACCACCAAAGAGTCAG
Found at i:11735968 original size:13 final size:13
Alignment explanation
Indices: 11735916--11735968 Score: 65
Period size: 13 Copynumber: 4.1 Consensus size: 13
11735906 AGTTCTTCAT
11735916 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
11735929 TG-TTGTGAAAAAG
1 TGCTTTTG-AAAAG
11735942 TGCTTTT-AAGAAG
1 TGCTTTTGAA-AAG
11735955 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
11735968 T
1 T
11735969 TTAGTTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
12 6 0.18
13 23 0.68
14 5 0.15
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:11740496 original size:3 final size:3
Alignment explanation
Indices: 11740488--11740535 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
11740478 TAATGTGTTC
11740488 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
11740536 TTGCCTTGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:11742462 original size:32 final size:31
Alignment explanation
Indices: 11742425--11742516 Score: 121
Period size: 32 Copynumber: 2.9 Consensus size: 31
11742415 TGTTAAATTT
* *
11742425 TTAATCAATCCTAATTTCTTCAAGGGTTTGTA
1 TTAATCAATCCCAATTT-TTCAAGGATTTGTA
*
11742457 TTAATCAATCCCAATTTTTTCCAGGATTTGTA
1 TTAATCAATCCCAA-TTTTTCAAGGATTTGTA
*
11742489 CTAATCAATCCCAATATTTTCAAGGATT
1 TTAATCAATCCCAAT-TTTTCAAGGATT
11742517 ATACTAATCA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
31 1 0.02
32 49 0.92
33 3 0.06
ACGTcount: A:0.30, C:0.18, G:0.10, T:0.41
Consensus pattern (31 bp):
TTAATCAATCCCAATTTTTCAAGGATTTGTA
Found at i:11742525 original size:31 final size:30
Alignment explanation
Indices: 11742426--11742527 Score: 114
Period size: 32 Copynumber: 3.2 Consensus size: 30
11742416 GTTAAATTTT
* * *
11742426 TAATCAATCCTAATTTCTTCAAGGGTTTGTAT
1 TAATCAATCCCAATTT-TTCAA-GGATTGTAC
*
11742458 TAATCAATCCCAATTTTTTCCAGGATTTGTAC
1 TAATCAATCCCAA-TTTTTCAAGGA-TTGTAC
*
11742490 TAATCAATCCCAATATTTTCAAGGATTATAC
1 TAATCAATCCCAAT-TTTTCAAGGATTGTAC
11742521 TAATCAA
1 TAATCAA
11742528 CGTCTAAAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
31 15 0.25
32 43 0.70
33 3 0.05
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (30 bp):
TAATCAATCCCAATTTTTCAAGGATTGTAC
Found at i:11743074 original size:23 final size:22
Alignment explanation
Indices: 11743047--11743097 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 22
11743037 TTGGTACTAC
*
11743047 AAAATACTGCAAGCTGTATTGT
1 AAAATACTGCAAACTGTATTGT
*
11743069 GAAAATATTGCAAACTGTATTGT
1 -AAAATACTGCAAACTGTATTGT
11743092 AAAATA
1 AAAATA
11743098 ATGCGAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 6 0.23
23 20 0.77
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.31
Consensus pattern (22 bp):
AAAATACTGCAAACTGTATTGT
Found at i:11743355 original size:94 final size:94
Alignment explanation
Indices: 11743194--11743381 Score: 270
Period size: 94 Copynumber: 2.0 Consensus size: 94
11743184 TTTTGCTACT
* *** * *
11743194 TTAAAATTGAAATCAACTGCATGAGAAAGTTGCAATCTTAAATTGGCAACTGCAAGATTTTGGAA
1 TTAAAATTGAAATCAACTGCATGAGAAAATTGCAATCTTAAACCAGCAACTGCAAGATTCTAGAA
11743259 ATCTTGTAAGTATAAGACT-AGGATCTTAA
66 ATCTTGTAAGTATAAGACTGA-GATCTTAA
* * *
11743288 TTAAAGTTGAAATCAATTGCATGAGAAAATTGTAATCTTAAACCAGCAACTGCAAGATTCTAGAA
1 TTAAAATTGAAATCAACTGCATGAGAAAATTGCAATCTTAAACCAGCAACTGCAAGATTCTAGAA
*
11743353 ATCTTGTAAGTATAAGGCTGAGATCTTAA
66 ATCTTGTAAGTATAAGACTGAGATCTTAA
11743382 ATCGATAAGC
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
94 82 0.99
95 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (94 bp):
TTAAAATTGAAATCAACTGCATGAGAAAATTGCAATCTTAAACCAGCAACTGCAAGATTCTAGAA
ATCTTGTAAGTATAAGACTGAGATCTTAA
Found at i:11743397 original size:54 final size:54
Alignment explanation
Indices: 11743339--11744282 Score: 673
Period size: 54 Copynumber: 17.5 Consensus size: 54
11743329 ACCAGCAACT
* * **
11743339 GCAAGATTCTAGAAATCTTGTAAGTATAAGGCTGAGATCTTAAATCGATAAGCC
1 GCAAGATTCAAAAAATCTTGTAAGTATAAGGCTGAGATCTTAAATCGACGAGCC
** * * * * **
11743393 GCAAGATTCAAAAAATCTTGTAAGTATAAGATTGTGGTCTTAAATATG-CAAATC
1 GCAAGATTCAAAAAATCTTGTAAGTATAAGGCTGAGATCTTAAAT-CGACGAGCC
* * ** * * **
11743447 GCAAGATTCAGAAAATCCTACAAGTATAAGGCTGCGATCTTAAATTGGTGAGCC
1 GCAAGATTCAAAAAATCTTGTAAGTATAAGGCTGAGATCTTAAATCGACGAGCC
* * * * * * * * * *
11743501 GCAAGATTTAGAAAATATTGTAAGTATAAGGTTGCGATATTAAATTGGCCAACC
1 GCAAGATTCAAAAAATCTTGTAAGTATAAGGCTGAGATCTTAAATCGACGAGCC
* * * * * * *
11743555 GTAAGATTCAGAAAATCTTATAAGTATAAGGTTGCGATCTTAAATCGGCGAGCT
1 GCAAGATTCAAAAAATCTTGTAAGTATAAGGCTGAGATCTTAAATCGACGAGCC
* * * * * *
11743609 GCAAGATTCAAAAAGTCTTGTAAGTATAATGTTGCA-ATCTTAAATCGACAAACT
1 GCAAGATTCAAAAAATCTTGTAAGTATAAGGCTG-AGATCTTAAATCGACGAGCC
** * * * * * * **
11743663 GCAAGATTTGAAAAATCCTATAAGTATAAGGGTGTGATCTTAAATCGGCAAGTT
1 GCAAGATTCAAAAAATCTTGTAAGTATAAGGCTGAGATCTTAAATCGACGAGCC
** * * * * *
11743717 GCAAGATTCAAAAAATCTTGTAAGTATAAGTTTGAGATCCTAAATTGGCCAACC
1 GCAAGATTCAAAAAATCTTGTAAGTATAAGGCTGAGATCTTAAATCGACGAGCC
** * * *
11743771 ATAAGATTCGAAAAATCTTGTAAGTATAAGGCTGCA-ATATTAAATCGGCGAGCC
1 GCAAGATTCAAAAAATCTTGTAAGTATAAGGCTG-AGATCTTAAATCGACGAGCC
* ** * *
11743825 ACAAGATTTGAAAAATCTTGTAAGTATAAGACTGCA-ATCTTAAATCGGCGAGCC
1 GCAAGATTCAAAAAATCTTGTAAGTATAAGGCTG-AGATCTTAAATCGACGAGCC
* *
11743879 GCAAGATTCAAAAAATCTTGTAAGTATAAGGCTGCGATTTTAAATCGACGAGCC
1 GCAAGATTCAAAAAATCTTGTAAGTATAAGGCTGAGATCTTAAATCGACGAGCC
* * * * ** **
11743933 -CTAAGATTCAAAAAATCGTGTAAGTACAA-GCATGTGATCTAAAATCGGTGAGTT
1 GC-AAGATTCAAAAAATCTTGTAAGTATAAGGC-TGAGATCTTAAATCGACGAGCC
* * * * * * *
11743987 GCAAGAGTCAAAAAATCCTGTAAGTATAAGGCTGCGATATTAAAT-TAGTGAGTC
1 GCAAGATTCAAAAAATCTTGTAAGTATAAGGCTGAGATCTTAAATCGA-CGAGCC
* * * * * * *
11744041 GCAAGATTCGAAAAATCTTGTAAGTATAAGGTTGCGATTTTAAATCGACCAACT
1 GCAAGATTCAAAAAATCTTGTAAGTATAAGGCTGAGATCTTAAATCGACGAGCC
* * * * *
11744095 ACAACATTCAAAAAATCTTATAAGTATAAGGCTGTGATCTTAAATC-AGTGAGCC
1 GCAAGATTCAAAAAATCTTGTAAGTATAAGGCTGAGATCTTAAATCGA-CGAGCC
** * * * * * * **
11744149 ATAAGATTCGAAAAATCTTGTAAGTACAAGGTTGTGATATTAAATTGACGAGTT
1 GCAAGATTCAAAAAATCTTGTAAGTATAAGGCTGAGATCTTAAATCGACGAGCC
* * * * * * * *
11744203 GCAAGTTTCGAAAAATCTTGTAAGTATAAGG-TTATAATCTTAAATCGGCAAACT
1 GCAAGATTCAAAAAATCTTGTAAGTATAAGGCTGA-GATCTTAAATCGACGAGCC
* *
11744257 GCAAGATTCGAAAAATCCTGTAAGTA
1 GCAAGATTCAAAAAATCTTGTAAGTA
11744283 GTAAATTGAG
Statistics
Matches: 714, Mismatches: 161, Indels: 30
0.79 0.18 0.03
Matches are distributed among these distances:
53 7 0.01
54 700 0.98
55 7 0.01
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (54 bp):
GCAAGATTCAAAAAATCTTGTAAGTATAAGGCTGAGATCTTAAATCGACGAGCC
Found at i:11743615 original size:162 final size:162
Alignment explanation
Indices: 11743339--11744282 Score: 778
Period size: 162 Copynumber: 5.8 Consensus size: 162
11743329 ACCAGCAACT
* * * **
11743339 GCAAGATTCTAG-AAATCTTGTAAGTATAAGGCTGAGATCTTAAA-TCGATAAGCCGCAAGATTC
1 GCAAGATT-TAGAAAATCTTGTAAGTATAAGGCTGCGATATTAAATTGGCGAA-CCGCAAGATTC
* * * ** * *
11743402 AAAAAATCTTGTAAGTATAAGATTGTGGTCTTAAATATG-CAAATCGCAAGATTCAGAAAATCCT
64 AAAAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGGCCAACT-GCAAGATTCAGAAAATCTT
** *
11743466 ACAAGTATAAGGCTGCGATCTTAAATTGGTGAGCC
128 GTAAGTATAAGGCTGCGATCTTAAATCGGTGAGCC
* * * * *
11743501 GCAAGATTTAGAAAATATTGTAAGTATAAGGTTGCGATATTAAATTGGCCAACCGTAAGATTCAG
1 GCAAGATTTAGAAAATCTTGTAAGTATAAGGCTGCGATATTAAATTGGCGAACCGCAAGATTCAA
* * *
11743566 AAAATCTTATAAGTATAAGGTTGCGATCTTAAATCGGCGAGCTGCAAGATTCA-AAAAGTCTTGT
66 AAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGGCCAACTGCAAGATTCAGAAAA-TCTTGT
* * * *** * *
11743630 AAGTATAATGTTGCAATCTTAAATCGACAAACT
130 AAGTATAAGGCTGCGATCTTAAATCGGTGAGCC
* * * * * * **
11743663 GCAAGATTT-GAAAAATCCTATAAGTATAAGGGTGTGATCTTAAATCGGC-AAGTTGCAAGATTC
1 GCAAGATTTAG-AAAATCTTGTAAGTATAAGGCTGCGATATTAAATTGGCGAA-CCGCAAGATTC
* * * * ***
11743726 AAAAAATCTTGTAAGTATAAGTTTGAGATCCTAAATTGGCCAACCATAAGATTC-GAAAAATCTT
64 AAAAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGGCCAACTGCAAGATTCAG-AAAATCTT
* * *
11743790 GTAAGTATAAGGCTGCAATATTAAATCGGCGAGCC
128 GTAAGTATAAGGCTGCGATCTTAAATCGGTGAGCC
* * * * * *
11743825 ACAAGATTT-GAAAAATCTTGTAAGTATAAGACTGCAATCTTAAATCGGCGAGCCGCAAGATTCA
1 GCAAGATTTAG-AAAATCTTGTAAGTATAAGGCTGCGATATTAAATTGGCGAACCGCAAGATTCA
* * * * * * * *
11743889 AAAAATCTTGTAAGTATAAGGCTGCGATTTTAAATCGACGAGC-CCTAAGATTCAAAAAATCGTG
65 AAAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGGCCAACTGC-AAGATTCAGAAAATCTTG
* * * **
11743953 TAAGTACAA-GCATGTGATCTAAAATCGGTGAGTT
129 TAAGTATAAGGC-TGCGATCTTAAATCGGTGAGCC
* * * * * * ** *
11743987 GCAAGAGTCAAAAAATCCTGTAAGTATAAGGCTGCGATATTAAATTAGTGAGTCGCAAGATTCGA
1 GCAAGATTTAGAAAATCTTGTAAGTATAAGGCTGCGATATTAAATTGGCGAACCGCAAGATTCAA
* * * * * *
11744052 AAAATCTTGTAAGTATAAGGTTGCGATTTTAAATCGACCAACTACAACATTCAAAAAATCTTATA
66 AAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGGCCAACTGCAAGATTCAGAAAATCTTGTA
* *
11744117 AGTATAAGGCTGTGATCTTAAATCAGTGAGCC
131 AGTATAAGGCTGCGATCTTAAATCGGTGAGCC
** * * * * * *** * *
11744149 ATAAGA-TTCGAAAAATCTTGTAAGTACAAGGTTGTGATATTAAATTGACGAGTTGCAAGTTTCG
1 GCAAGATTTAG-AAAATCTTGTAAGTATAAGGCTGCGATATTAAATTGGCGAACCGCAAGATTCA
*** * *
11744213 AAAAATCTTGTAAGTATAAGGTTATAATCTTAAATCGGCAAACTGCAAGATTC-GAAAAATCCTG
65 AAAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGGCCAACTGCAAGATTCAG-AAAATCTTG
11744277 TAAGTA
129 TAAGTA
11744283 GTAAATTGAG
Statistics
Matches: 626, Mismatches: 139, Indels: 34
0.78 0.17 0.04
Matches are distributed among these distances:
161 13 0.02
162 599 0.96
163 14 0.02
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (162 bp):
GCAAGATTTAGAAAATCTTGTAAGTATAAGGCTGCGATATTAAATTGGCGAACCGCAAGATTCAA
AAAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGGCCAACTGCAAGATTCAGAAAATCTTGTA
AGTATAAGGCTGCGATCTTAAATCGGTGAGCC
Found at i:11746149 original size:16 final size:16
Alignment explanation
Indices: 11746128--11746169 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
11746118 GAGTTGGGAA
11746128 AGTGGCGAGCAAGAGG
1 AGTGGCGAGCAAGAGG
* *
11746144 AGTGGCGAGCTAGTGG
1 AGTGGCGAGCAAGAGG
11746160 AGTGGCGAGC
1 AGTGGCGAGC
11746170 CAGATAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.24, C:0.14, G:0.50, T:0.12
Consensus pattern (16 bp):
AGTGGCGAGCAAGAGG
Found at i:11763452 original size:12 final size:12
Alignment explanation
Indices: 11763421--11763457 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
11763411 TGTATGGAAT
*
11763421 AATAGTAATCAA
1 AATAGTTATCAA
11763433 AATA-TTATCAA
1 AATAGTTATCAA
11763444 AATAGTTAT-AA
1 AATAGTTATCAA
11763455 AAT
1 AAT
11763458 TGAGTTGCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 15 0.65
12 8 0.35
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.32
Consensus pattern (12 bp):
AATAGTTATCAA
Found at i:11767765 original size:23 final size:25
Alignment explanation
Indices: 11767737--11767786 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
11767727 TTAACTTTTT
* *
11767737 ATATATATTTTT-TAATTTTTTTAAA
1 ATATA-ATTTTTGAAATTTTTATAAA
11767762 ATATAATTTTTGAAATTTTTATAAA
1 ATATAATTTTTGAAATTTTTATAAA
11767787 TATTTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (25 bp):
ATATAATTTTTGAAATTTTTATAAA
Found at i:11767797 original size:20 final size:19
Alignment explanation
Indices: 11767713--11767831 Score: 69
Period size: 19 Copynumber: 5.8 Consensus size: 19
11767703 TATTATTTAT
* * *
11767713 TTTTTTTAAAAATTTTAAC
1 TTTTTATAAATATTTTAAA
* *
11767732 TTTTTATATATATTTTTTAATT
1 TTTTTATA-A-ATATTTTAA-A
*
11767754 TTTTTAAAATATAATTTTTGAAA
1 TTTTTATAA-AT-A-TTTT-AAA
11767777 TTTTTATAAATATTTTAAA
1 TTTTTATAAATATTTTAAA
* *
11767796 ATTTTA-AAATTATTTTGAA
1 TTTTTATAAA-TATTTTAAA
*
11767815 TTATTTATAATTATTTT
1 TT-TTTATAAATATTTT
11767832 GTAATTTTTG
Statistics
Matches: 79, Mismatches: 12, Indels: 17
0.73 0.11 0.16
Matches are distributed among these distances:
18 3 0.04
19 24 0.30
20 15 0.19
21 14 0.18
22 9 0.11
23 12 0.15
24 2 0.03
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTTTATAAATATTTTAAA
Found at i:11767832 original size:20 final size:20
Alignment explanation
Indices: 11767769--11767840 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
11767759 AAAATATAAT
*
11767769 TTTTGAAATTTTTATAAATA
1 TTTTGAAATTTTTATAATTA
* *
11767789 TTTT-AAAATTTTAAAATTA
1 TTTTGAAATTTTTATAATTA
11767808 TTTTG-AATTATTTATAATTA
1 TTTTGAAATT-TTTATAATTA
*
11767828 TTTTGTAATTTTT
1 TTTTGAAATTTTT
11767841 GTTGTGAGAG
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
19 19 0.43
20 21 0.48
21 4 0.09
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTTGAAATTTTTATAATTA
Found at i:11767839 original size:39 final size:42
Alignment explanation
Indices: 11767755--11767831 Score: 108
Period size: 39 Copynumber: 1.9 Consensus size: 42
11767745 TTTTTAATTT
11767755 TTTTAAAATATAATTTTTGAAATTTTTATAAATATTTTAAAA
1 TTTTAAAATATAATTTTTGAAATTTTTATAAATATTTTAAAA
*
11767797 TTTTAAAAT-T-A-TTTTG-AATTATTTATAATTATTTT
1 TTTTAAAATATAATTTTTGAAATT-TTTATAAATATTTT
11767832 GTAATTTTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
38 4 0.12
39 18 0.55
40 1 0.03
41 1 0.03
42 9 0.27
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (42 bp):
TTTTAAAATATAATTTTTGAAATTTTTATAAATATTTTAAAA
Found at i:11772887 original size:23 final size:23
Alignment explanation
Indices: 11772857--11772902 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
11772847 CATCTATCAA
11772857 GTCCAATTGGAAGATGTTTTGTT
1 GTCCAATTGGAAGATGTTTTGTT
11772880 GTCCAATTGGAAGATGTTTTGTT
1 GTCCAATTGGAAGATGTTTTGTT
11772903 TTGAGTATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.09, G:0.26, T:0.43
Consensus pattern (23 bp):
GTCCAATTGGAAGATGTTTTGTT
Found at i:11777774 original size:21 final size:22
Alignment explanation
Indices: 11777745--11777791 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
11777735 CAGAAGGAGT
*
11777745 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
11777767 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
11777788 GAGT
1 GAGT
11777792 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:11780984 original size:21 final size:22
Alignment explanation
Indices: 11780955--11781001 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
11780945 CAGAAGGAGT
*
11780955 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
11780977 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
11780998 GAGT
1 GAGT
11781002 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:11783934 original size:16 final size:16
Alignment explanation
Indices: 11783913--11783944 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
11783903 TTTCTTTATG
11783913 AAAAAGTGAGTTGAAT
1 AAAAAGTGAGTTGAAT
11783929 AAAAAGTGAGTTGAAT
1 AAAAAGTGAGTTGAAT
11783945 TCACTTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (16 bp):
AAAAAGTGAGTTGAAT
Found at i:11785296 original size:20 final size:20
Alignment explanation
Indices: 11785273--11785332 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
11785263 CAAAGAATTT
**
11785273 ATTCAAACAATAATGAATCA
1 ATTCAAACAATAAAAAATCA
*
11785293 ATTCAAACAATAAAAAATCG
1 ATTCAAACAATAAAAAATCA
*
11785313 ATTCAAACAACAAAAGAATC
1 ATTCAAACAATAAAA-AATC
11785333 GAGTCAATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
20 31 0.89
21 4 0.11
ACGTcount: A:0.58, C:0.17, G:0.05, T:0.20
Consensus pattern (20 bp):
ATTCAAACAATAAAAAATCA
Found at i:11785920 original size:18 final size:19
Alignment explanation
Indices: 11785883--11785920 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
11785873 CTAAATCGCG
*
11785883 TATAGAGTAAAAATTGAAT
1 TATAGAGTAAAAATTCAAT
*
11785902 TATAGATTAAAAA-TCAAT
1 TATAGAGTAAAAATTCAAT
11785920 T
1 T
11785921 GAGGGATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.53, C:0.03, G:0.11, T:0.34
Consensus pattern (19 bp):
TATAGAGTAAAAATTCAAT
Found at i:11789394 original size:20 final size:20
Alignment explanation
Indices: 11789361--11789440 Score: 81
Period size: 20 Copynumber: 4.0 Consensus size: 20
11789351 GTTGGGTTTT
11789361 GAATCGAGTT-AAACAACAAA
1 GAATCGA-TTCAAACAACAAA
** * *
11789381 GAATTAATTCAAACAATAAT
1 GAATCGATTCAAACAACAAA
*
11789401 GAATCGATTCAAACAATAAA
1 GAATCGATTCAAACAACAAA
* *
11789421 CAATCGATTCAAACAGCAAA
1 GAATCGATTCAAACAACAAA
11789441 AGATTTAAGT
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
19 2 0.04
20 47 0.96
ACGTcount: A:0.54, C:0.16, G:0.10, T:0.20
Consensus pattern (20 bp):
GAATCGATTCAAACAACAAA
Found at i:11789415 original size:40 final size:40
Alignment explanation
Indices: 11789360--11789435 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
11789350 TGTTGGGTTT
* *
11789360 TGAATCGAGTTAAACAACAAAGAATTAATTCAAACAATAA
1 TGAATCGAGTTAAACAACAAACAATCAATTCAAACAATAA
* *
11789400 TGAATCGA-TTCAAACAATAAACAATCGATTCAAACA
1 TGAATCGAGTT-AAACAACAAACAATCAATTCAAACA
11789436 GCAAAAGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 2 0.06
40 29 0.94
ACGTcount: A:0.53, C:0.16, G:0.09, T:0.22
Consensus pattern (40 bp):
TGAATCGAGTTAAACAACAAACAATCAATTCAAACAATAA
Found at i:11806460 original size:21 final size:20
Alignment explanation
Indices: 11806422--11806464 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
11806412 GGCCATTCAT
11806422 AAGAATTTACAAAGATAAGTC
1 AAGAATTTACAAAGATAA-TC
*
11806443 AAGAATTTCACATA-ATAATC
1 AAGAATTT-ACAAAGATAATC
11806463 AA
1 AA
11806465 AATCAAGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.53, C:0.12, G:0.09, T:0.26
Consensus pattern (20 bp):
AAGAATTTACAAAGATAATC
Found at i:11813524 original size:20 final size:20
Alignment explanation
Indices: 11813499--11813539 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
11813489 AAGAGTAATC
11813499 AAACTCAATAATATTAAAAA
1 AAACTCAATAATATTAAAAA
11813519 AAACTCAATAATATTAAAAA
1 AAACTCAATAATATTAAAAA
11813539 A
1 A
11813540 GATGTGGGAT
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:0.66, C:0.10, G:0.00, T:0.24
Consensus pattern (20 bp):
AAACTCAATAATATTAAAAA
Found at i:11813942 original size:19 final size:19
Alignment explanation
Indices: 11813902--11813942 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
11813892 ACAAAATATT
* * *
11813902 TTTTTTCTTTTTTTTCATA
1 TTTTTTCTGTTTTTGCACA
11813921 TTTTTTCTGTTTTTGCACA
1 TTTTTTCTGTTTTTGCACA
11813940 TTT
1 TTT
11813943 CTTGATCACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.10, C:0.12, G:0.05, T:0.73
Consensus pattern (19 bp):
TTTTTTCTGTTTTTGCACA
Found at i:11818537 original size:3 final size:3
Alignment explanation
Indices: 11818529--11818553 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
11818519 TGATCATTTC
11818529 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
11818554 AAGTCTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:11818604 original size:3 final size:3
Alignment explanation
Indices: 11818596--11818628 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
11818586 AAGATAATTT
11818596 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
11818629 AAGTCTAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:11818646 original size:75 final size:75
Alignment explanation
Indices: 11818529--11818670 Score: 284
Period size: 75 Copynumber: 1.9 Consensus size: 75
11818519 TGATCATTTC
11818529 ATTATTATTATTATTATTATTATTAAAGTCTAATAATTATAGATTATGTGGTGTTGAAAGATAAT
1 ATTATTATTATTATTATTATTATTAAAGTCTAATAATTATAGATTATGTGGTGTTGAAAGATAAT
11818594 TTTTATTATT
66 TTTTATTATT
11818604 ATTATTATTATTATTATTATTATTAAAGTCTAATAATTATAGATTATGTGGTGTTGAAAGATAAT
1 ATTATTATTATTATTATTATTATTAAAGTCTAATAATTATAGATTATGTGGTGTTGAAAGATAAT
11818669 TT
66 TT
11818671 GTTGGAATAT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.37, C:0.01, G:0.11, T:0.51
Consensus pattern (75 bp):
ATTATTATTATTATTATTATTATTAAAGTCTAATAATTATAGATTATGTGGTGTTGAAAGATAAT
TTTTATTATT
Found at i:11818702 original size:75 final size:72
Alignment explanation
Indices: 11818529--11818704 Score: 255
Period size: 75 Copynumber: 2.4 Consensus size: 72
11818519 TGATCATTTC
*
11818529 ATTATTATTATTATTATTATTATTAAAGTCTAATAATTATAGATTATGTGGTGTTGAAAGATAAT
1 ATTATTATTATTAATATTATTATTAAAGTCTAATAATTATAGATTATGTGGTGTTGAAAGATAAT
11818594 TTTTATTATT
66 TTTTA--A-T
*
11818604 ATTATTATTATTATTATTATTATTAAAGTCTAATAATTATAGATTATGTGGTGTTGAAAGATAAT
1 ATTATTATTATTAATATTATTATTAAAGTCTAATAATTATAGATTATGTGGTGTTGAAAGATAAT
11818669 TTGTTGGAAT
66 TT-TT--AAT
*
11818679 ATT-TTATTATTAGATATTTTTATTAA
1 ATTATTATTATTA-ATATTATTATTAA
11818705 TTAATTAATG
Statistics
Matches: 95, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
74 9 0.09
75 82 0.86
76 3 0.03
78 1 0.01
ACGTcount: A:0.36, C:0.01, G:0.11, T:0.52
Consensus pattern (72 bp):
ATTATTATTATTAATATTATTATTAAAGTCTAATAATTATAGATTATGTGGTGTTGAAAGATAAT
TTTTAAT
Found at i:11820844 original size:9 final size:9
Alignment explanation
Indices: 11820830--11820857 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
11820820 TGAGTTTTCG
11820830 AATTCGAAT
1 AATTCGAAT
11820839 AATTCGAAT
1 AATTCGAAT
11820848 AATTCGAAT
1 AATTCGAAT
11820857 A
1 A
11820858 TCAAACTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:11827910 original size:29 final size:29
Alignment explanation
Indices: 11827877--11827944 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
11827867 ATAAATTAGT
11827877 AATGATAAAA-TTACACTTTAATT-TTTAAA
1 AATGATAAAATTTA-A-TTTAATTGTTTAAA
11827906 AATGATAAAAATTTAATTTAATTGTTTAAA
1 AATGAT-AAAATTTAATTTAATTGTTTAAA
*
11827936 AATTATAAA
1 AATGATAAA
11827945 CCGATAAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
29 16 0.46
30 16 0.46
31 3 0.09
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.41
Consensus pattern (29 bp):
AATGATAAAATTTAATTTAATTGTTTAAA
Found at i:11827934 original size:30 final size:30
Alignment explanation
Indices: 11827877--11827944 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
11827867 ATAAATTAGT
11827877 AATGAT-AAAATTACACTTTAATTTTTAAA
1 AATGATAAAAATTACACTTTAATTTTTAAA
11827906 AATGATAAAAATTTA-A-TTTAATTGTTTAAA
1 AATGATAAAAA-TTACACTTTAATT-TTTAAA
*
11827936 AATTATAAA
1 AATGATAAA
11827945 CCGATAAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
29 13 0.37
30 19 0.54
31 3 0.09
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.41
Consensus pattern (30 bp):
AATGATAAAAATTACACTTTAATTTTTAAA
Found at i:11829362 original size:33 final size:32
Alignment explanation
Indices: 11829322--11829614 Score: 249
Period size: 33 Copynumber: 10.1 Consensus size: 32
11829312 TTAAGTTAAG
11829322 GGTTAGGGTTAGGGTTTTTAAGTTAAGGGTTAA
1 GGTTAGGGTTAGGGTTTTTAAGTTAAGGGTT-A
*
11829355 GGTTAGGGTTAGGGTTTTTAAGTTAAAGGTTA
1 GGTTAGGGTTAGGGTTTTTAAGTTAAGGGTTA
*
11829387 GGGTTAGGGCTAGGGTTTTT--GTTAA-GGTT-
1 -GGTTAGGGTTAGGGTTTTTAAGTTAAGGGTTA
*
11829416 --TT--GG-T---GTTTTCAAGTTAAGGGT--
1 GGTTAGGGTTAGGGTTTTTAAGTTAAGGGTTA
11829438 ---TAGGGTTAGGGTTTTTAAGTTAAGGGTTAA
1 GGTTAGGGTTAGGGTTTTTAAGTTAAGGGTT-A
*
11829468 GGTTAGGGTTAGGGTTTTTAAGTTAAAGGTTA
1 GGTTAGGGTTAGGGTTTTTAAGTTAAGGGTTA
*
11829500 GGGTTAGGGCTAGGGTTTTT--GTTAA-GGTT-
1 -GGTTAGGGTTAGGGTTTTTAAGTTAAGGGTTA
*
11829529 --TT--GG-T---GTTTTCAAGTTAAGGGT--
1 GGTTAGGGTTAGGGTTTTTAAGTTAAGGGTTA
11829551 ---TAGGGTTAGGGTTTTTAAGTTAAGGGTTAA
1 GGTTAGGGTTAGGGTTTTTAAGTTAAGGGTT-A
11829581 GGTTAGGGTTAGGGTTTTTAAGTTAAGGGTTA
1 GGTTAGGGTTAGGGTTTTTAAGTTAAGGGTTA
11829613 GG
1 GG
11829615 GTGAAGGCTA
Statistics
Matches: 220, Mismatches: 8, Indels: 65
0.75 0.03 0.22
Matches are distributed among these distances:
20 10 0.05
21 2 0.01
22 10 0.05
23 12 0.05
24 6 0.03
26 4 0.02
27 32 0.15
30 8 0.04
31 10 0.05
32 5 0.02
33 121 0.55
ACGTcount: A:0.22, C:0.01, G:0.36, T:0.41
Consensus pattern (32 bp):
GGTTAGGGTTAGGGTTTTTAAGTTAAGGGTTA
Found at i:11829395 original size:113 final size:113
Alignment explanation
Indices: 11829265--11829664 Score: 674
Period size: 113 Copynumber: 3.5 Consensus size: 113
11829255 TTATATCAGA
* *
11829265 TTAGGGTTAGGGTTAGGGTTTTTGTTAGCATTAGAGTTTTGGTGTTTTTAAGTTAAGGGTTAGGG
1 TTAGGGTTAGGGCTAGGGTTTTTGTT---A--AG-GTTTTGGTGTTTTCAAGTTAAGGGTTAGGG
11829330 TTAGGGTTTTTAAGTTAAGGGTTAAGGTTAGGGTTAGGGTTTTTAAGTTAAAGG
60 TTAGGGTTTTTAAGTTAAGGGTTAAGGTTAGGGTTAGGGTTTTTAAGTTAAAGG
11829384 TTAGGGTTAGGGCTAGGGTTTTTGTTAAGGTTTTGGTGTTTTCAAGTTAAGGGTTAGGGTTAGGG
1 TTAGGGTTAGGGCTAGGGTTTTTGTTAAGGTTTTGGTGTTTTCAAGTTAAGGGTTAGGGTTAGGG
11829449 TTTTTAAGTTAAGGGTTAAGGTTAGGGTTAGGGTTTTTAAGTTAAAGG
66 TTTTTAAGTTAAGGGTTAAGGTTAGGGTTAGGGTTTTTAAGTTAAAGG
11829497 TTAGGGTTAGGGCTAGGGTTTTTGTTAAGGTTTTGGTGTTTTCAAGTTAAGGGTTAGGGTTAGGG
1 TTAGGGTTAGGGCTAGGGTTTTTGTTAAGGTTTTGGTGTTTTCAAGTTAAGGGTTAGGGTTAGGG
*
11829562 TTTTTAAGTTAAGGGTTAAGGTTAGGGTTAGGGTTTTTAAGTTAAGGG
66 TTTTTAAGTTAAGGGTTAAGGTTAGGGTTAGGGTTTTTAAGTTAAAGG
* * * * *
11829610 TTAGGGTGAAGGCTAAGGTTTTTGTTAGGGTTTTGGTGTTTTTAAGTTAAGGGTT
1 TTAGGGTTAGGGCTAGGGTTTTTGTTAAGGTTTTGGTGTTTTCAAGTTAAGGGTT
11829665 TTTAAGTTAA
Statistics
Matches: 273, Mismatches: 8, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
113 245 0.90
114 2 0.01
116 1 0.00
119 25 0.09
ACGTcount: A:0.21, C:0.01, G:0.35, T:0.42
Consensus pattern (113 bp):
TTAGGGTTAGGGCTAGGGTTTTTGTTAAGGTTTTGGTGTTTTCAAGTTAAGGGTTAGGGTTAGGG
TTTTTAAGTTAAGGGTTAAGGTTAGGGTTAGGGTTTTTAAGTTAAAGG
Found at i:11829601 original size:21 final size:21
Alignment explanation
Indices: 11829577--11829616 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
11829567 AAGTTAAGGG
11829577 TTAAGGTT-AGGGTTAGGGTTT
1 TTAA-GTTAAGGGTTAGGGTTT
11829598 TTAAGTTAAGGGTTAGGGT
1 TTAAGTTAAGGGTTAGGGT
11829617 GAAGGCTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.23, C:0.00, G:0.38, T:0.40
Consensus pattern (21 bp):
TTAAGTTAAGGGTTAGGGTTT
Found at i:11829627 original size:45 final size:46
Alignment explanation
Indices: 11829581--11829858 Score: 171
Period size: 53 Copynumber: 5.8 Consensus size: 46
11829571 TAAGGGTTAA
*
11829581 GGTTAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTGAAGGCTAAG
1 GGTTAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTAAGGCTAAG
* * *
11829627 GTTTTTGTTAGGGTTTTGGTGTTTTTAAGTTAAGGGTT---TTTAA-GTTAAG
1 G-----GTTAGGG-TTAGG-GTTTTTAAGTTAAGGGTTAGGGTTAAGGCTAAG
* *
11829676 GGTTAGGGCTT-GGGTTTTT-A-TT-AGGGTTTTGGTGTTTTTAA-GTTAAG
1 GGTTAGGG-TTAGGGTTTTTAAGTTAAGGG-TTAGG-G---TTAAGGCTAAG
* * *
11829723 GGTTAGGGTTAGGGTTTTTAAGTTTAGGGCTAGGGTTAGGGCT-AG
1 GGTTAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTAAGGCTAAG
**** *
11829768 GGTTTTTATTAGGGTTTTTAAGTTAAGGGTTAGGGTGAAGGCTAAG
1 GGTTAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTAAGGCTAAG
*
11829814 GTTTTTGTTAGGGTTTTGGTGTTTTTAAGTTAAGGGTTAGGGTTA
1 G-----GTTAGGG-TTAGG-GTTTTTAAGTTAAGGGTTAGGGTTA
11829859 GGGTTTTTAA
Statistics
Matches: 180, Mismatches: 24, Indels: 49
0.71 0.09 0.19
Matches are distributed among these distances:
39 4 0.02
40 4 0.02
41 1 0.01
42 6 0.03
43 2 0.01
44 9 0.05
45 40 0.22
46 8 0.04
47 26 0.14
48 2 0.01
49 11 0.06
50 7 0.04
51 10 0.06
52 8 0.04
53 42 0.23
ACGTcount: A:0.19, C:0.02, G:0.36, T:0.44
Consensus pattern (46 bp):
GGTTAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTAAGGCTAAG
Found at i:11829630 original size:33 final size:33
Alignment explanation
Indices: 11829560--11829632 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
11829550 TTAGGGTTAG
* * * *
11829560 GGTTTTTAAGTTAAGGGTTAAGGTTAGGGTTAG
1 GGTTTTTAAGTTAAGGGTTAAGGTGAAGGCTAA
*
11829593 GGTTTTTAAGTTAAGGGTTAGGGTGAAGGCTAA
1 GGTTTTTAAGTTAAGGGTTAAGGTGAAGGCTAA
11829626 GGTTTTT
1 GGTTTTT
11829633 GTTAGGGTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.23, C:0.01, G:0.36, T:0.40
Consensus pattern (33 bp):
GGTTTTTAAGTTAAGGGTTAAGGTGAAGGCTAA
Found at i:11829664 original size:68 final size:62
Alignment explanation
Indices: 11829591--11829726 Score: 191
Period size: 62 Copynumber: 2.1 Consensus size: 62
11829581 GGTTAGGGTT
*
11829591 AGGGTTTTTAAGTTAAGGGTTAGGGTGAAGGCTAAGGTTTTTGTTAGGGTTTTGGTGTTTTTAAG
1 AGGGTTTTTAAGTTAAGGGTTA----G--GGCTAAGGTTTTTATTAGGGTTTTGGTGTTTTTAAG
11829656 TTA
60 TTA
**
11829659 AGGGTTTTTAAGTTAAGGGTTAGGGCTTGGGTTTTTATTAGGGTTTTGGTGTTTTTAAGTTA
1 AGGGTTTTTAAGTTAAGGGTTAGGGCTAAGGTTTTTATTAGGGTTTTGGTGTTTTTAAGTTA
11829721 AGGGTT
1 AGGGTT
11829727 AGGGTTAGGG
Statistics
Matches: 65, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
62 42 0.65
64 1 0.02
68 22 0.34
ACGTcount: A:0.19, C:0.01, G:0.34, T:0.46
Consensus pattern (62 bp):
AGGGTTTTTAAGTTAAGGGTTAGGGCTAAGGTTTTTATTAGGGTTTTGGTGTTTTTAAGTTA
Found at i:11829667 original size:15 final size:15
Alignment explanation
Indices: 11829647--11829679 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
11829637 GGGTTTTGGT
11829647 GTTTTTAAGTTAAGG
1 GTTTTTAAGTTAAGG
11829662 GTTTTTAAGTTAAGG
1 GTTTTTAAGTTAAGG
11829677 GTT
1 GTT
11829680 AGGGCTTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.48
Consensus pattern (15 bp):
GTTTTTAAGTTAAGG
Found at i:11829690 original size:27 final size:26
Alignment explanation
Indices: 11829660--11829759 Score: 106
Period size: 27 Copynumber: 4.0 Consensus size: 26
11829650 TTTAAGTTAA
11829660 GGGTTTTTAAGTTAAGGGTTAGGGCTT
1 GGGTTTTTAAGTTAAGGGTTAGGG-TT
11829687 GGGTTTTT-A-TT-AGGGTT----TT
1 GGGTTTTTAAGTTAAGGGTTAGGGTT
11829706 GGTGTTTTTAAGTTAAGGGTTAGGGTT
1 GG-GTTTTTAAGTTAAGGGTTAGGGTT
* *
11829733 AGGGTTTTTAAGTTTAGGGCTAGGGTT
1 -GGGTTTTTAAGTTAAGGGTTAGGGTT
11829760 AGGGCTAGGG
Statistics
Matches: 62, Mismatches: 2, Indels: 18
0.76 0.02 0.22
Matches are distributed among these distances:
19 4 0.06
20 6 0.10
21 1 0.02
22 2 0.03
23 6 0.10
24 6 0.10
25 2 0.03
26 1 0.02
27 32 0.52
28 2 0.03
ACGTcount: A:0.17, C:0.02, G:0.36, T:0.45
Consensus pattern (26 bp):
GGGTTTTTAAGTTAAGGGTTAGGGTT
Found at i:11829701 original size:18 final size:20
Alignment explanation
Indices: 11829678--11829715 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
11829668 AAGTTAAGGG
11829678 TTAGGG-CTTGG-GTTTTTA
1 TTAGGGTCTTGGTGTTTTTA
*
11829696 TTAGGGTTTTGGTGTTTTTA
1 TTAGGGTCTTGGTGTTTTTA
11829716 AGTTAAGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 4 0.24
20 7 0.41
ACGTcount: A:0.11, C:0.03, G:0.32, T:0.55
Consensus pattern (20 bp):
TTAGGGTCTTGGTGTTTTTA
Found at i:11829712 original size:175 final size:178
Alignment explanation
Indices: 11829499--11829851 Score: 550
Period size: 187 Copynumber: 1.9 Consensus size: 178
11829489 GTTAAAGGTT
*
11829499 AGGGTTAGGGCTAGGGTTTTTGTTAAGGTTTTGGTGTTTTCAAGTTAAGGGTTAGGGTTAGGGTT
1 AGGGTTAGGGCTAGGGTTTTTATTAAGGTTTTGGTGTTTTCAAGTTAAGGGTTAGGGTTAGGGTT
*
11829564 TTTAAG-TTA-AGGGTTAAGGTTAGGG-TTAGGGTTTTTAAGTTAAGGGTTAGGGTGAAGGCTAA
66 TTTAAGTTTAGAGGGTTAAGGCTAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTGAAGGCTAA
11829626 GGTTTTTGTTAGGGTTTTGGTGTTTTTAAGTTAAGGGTTTTTAAGTTA
131 GGTTTTTGTTAGGGTTTTGGTGTTTTTAAGTTAAGGGTTTTTAAGTTA
* * *
11829674 AGGGTTAGGGCTTGGGTTTTTATTAGGGTTTTGGTGTTTTTAAGTTAAGGGTTAGGGTTAGGGTT
1 AGGGTTAGGGCTAGGGTTTTTATTAAGGTTTTGGTGTTTTCAAGTTAAGGGTTAGGGTTAGGGTT
*
11829739 TTTAAGTTTAGGGCTAGGGTTAGGGCTAGGGTTTTTATTAGGGTTTTTAAGTTAAGGGTTAGGGT
66 TTTAAGTTTA--G--AGGGTTAAGGCTAGGG----T-TTAGGGTTTTTAAGTTAAGGGTTAGGGT
11829804 GAAGGCTAAGGTTTTTGTTAGGGTTTTGGTGTTTTTAAGTTAAGGGTT
122 GAAGGCTAAGGTTTTTGTTAGGGTTTTGGTGTTTTTAAGTTAAGGGTT
11829852 AGGGTTAGGG
Statistics
Matches: 160, Mismatches: 6, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
175 67 0.42
176 3 0.02
181 14 0.09
187 76 0.47
ACGTcount: A:0.19, C:0.02, G:0.35, T:0.43
Consensus pattern (178 bp):
AGGGTTAGGGCTAGGGTTTTTATTAAGGTTTTGGTGTTTTCAAGTTAAGGGTTAGGGTTAGGGTT
TTTAAGTTTAGAGGGTTAAGGCTAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTGAAGGCTAA
GGTTTTTGTTAGGGTTTTGGTGTTTTTAAGTTAAGGGTTTTTAAGTTA
Found at i:11829763 original size:12 final size:12
Alignment explanation
Indices: 11829746--11829771 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11829736 GTTTTTAAGT
11829746 TTAGGGCTAGGG
1 TTAGGGCTAGGG
11829758 TTAGGGCTAGGG
1 TTAGGGCTAGGG
11829770 TT
1 TT
11829772 TTTATTAGGG
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:0.15, C:0.08, G:0.46, T:0.31
Consensus pattern (12 bp):
TTAGGGCTAGGG
Found at i:11829871 original size:27 final size:27
Alignment explanation
Indices: 11829820--11829890 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 27
11829810 TAAGGTTTTT
*
11829820 GTTAGGGTTTTGGTGTTTTTAAGTTAAGG
1 GTTAGGG-TTAGG-GTTTTTAAGTTAAGG
11829849 GTTAGGGTTAGGGTTTTTAAGTTAAGG
1 GTTAGGGTTAGGGTTTTTAAGTTAAGG
*
11829876 GTTAAGGTTAGGGTT
1 GTTAGGGTTAGGGTT
11829891 AGGGTTTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
27 29 0.73
28 4 0.10
29 7 0.17
ACGTcount: A:0.20, C:0.00, G:0.37, T:0.44
Consensus pattern (27 bp):
GTTAGGGTTAGGGTTTTTAAGTTAAGG
Found at i:11829935 original size:18 final size:18
Alignment explanation
Indices: 11829898--11829937 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
11829888 GTTAGGGTTT
11829898 TTATAAATTTAATTATAAA
1 TTATAAATTT-ATTATAAA
11829917 TTATAAATTT-TTAATAAA
1 TTATAAATTTATT-ATAAA
11829935 TTA
1 TTA
11829938 GTTTAGGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 2 0.10
18 8 0.40
19 10 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTATAAATTTATTATAAA
Found at i:11830969 original size:7 final size:7
Alignment explanation
Indices: 11830959--11830984 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
11830949 CATAATACAT
11830959 AATACTA
1 AATACTA
11830966 AATACTA
1 AATACTA
11830973 AATACTA
1 AATACTA
11830980 AATAC
1 AATAC
11830985 CAATTGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:11832103 original size:10 final size:11
Alignment explanation
Indices: 11832086--11832111 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
11832076 TTTTACGATC
11832086 TAAAAAAATTT
1 TAAAAAAATTT
11832097 TAAAAAAATTT
1 TAAAAAAATTT
11832108 TAAA
1 TAAA
11832112 TTTTTTTAAA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TAAAAAAATTT
Found at i:11832134 original size:22 final size:21
Alignment explanation
Indices: 11832094--11832134 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
11832084 TCTAAAAAAA
**
11832094 TTTTAAAAAAATTTTAAATTT
1 TTTTAAAAAAATTAAAAATTT
11832115 TTTTAAAAATAATTAAAAAT
1 TTTTAAAAA-AATTAAAAAT
11832135 AGGGATTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TTTTAAAAAAATTAAAAATTT
Found at i:11832169 original size:11 final size:11
Alignment explanation
Indices: 11832155--11832241 Score: 51
Period size: 11 Copynumber: 8.3 Consensus size: 11
11832145 GAGAAATTTA
11832155 AGAGGAAATTG
1 AGAGGAAATTG
*
11832166 AGAGCAAATTG
1 AGAGGAAATTG
**
11832177 AGATTAAA-T-
1 AGAGGAAATTG
* *
11832186 --ATGAATTTG
1 AGAGGAAATTG
11832195 AGA-GAAATTTG
1 AGAGGAAA-TTG
11832206 -GAAGGAAATTG
1 AG-AGGAAATTG
* *
11832217 AGAGCAATTTG
1 AGAGGAAATTG
11832228 AGAGGAAATTG
1 AGAGGAAATTG
11832239 AGA
1 AGA
11832242 AAATAATTGA
Statistics
Matches: 58, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
7 4 0.07
8 1 0.02
10 5 0.09
11 43 0.74
12 5 0.09
ACGTcount: A:0.45, C:0.02, G:0.29, T:0.24
Consensus pattern (11 bp):
AGAGGAAATTG
Found at i:11832169 original size:22 final size:22
Alignment explanation
Indices: 11832144--11832245 Score: 64
Period size: 22 Copynumber: 4.4 Consensus size: 22
11832134 TAGGGATTTA
11832144 AGAGAAATTTAAGAGGAAATTG
1 AGAGAAATTTAAGAGGAAATTG
* * *
11832166 AGAGCAAATTGAGATTAAATATGAATTTG
1 AGAG-AAA-T----TT-AAGAGGAAATTG
*
11832195 AGAGAAATTT-GGAAGGAAATTG
1 AGAGAAATTTAAG-AGGAAATTG
* *
11832217 AGAGCAATTTGAGAGGAAATTG
1 AGAGAAATTTAAGAGGAAATTG
11832239 AGA-AAAT
1 AGAGAAAT
11832246 AATTGAAAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 19
0.68 0.11 0.21
Matches are distributed among these distances:
21 3 0.05
22 32 0.52
23 6 0.10
24 1 0.02
27 1 0.02
28 5 0.08
29 13 0.21
ACGTcount: A:0.47, C:0.02, G:0.26, T:0.25
Consensus pattern (22 bp):
AGAGAAATTTAAGAGGAAATTG
Found at i:11832186 original size:51 final size:51
Alignment explanation
Indices: 11832131--11832230 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 51
11832121 AAATAATTAA
*
11832131 AAATAGGGATTTAAGAGAAATTTA-AGAGGAAATTGAGAGCAAATTGAGATT
1 AAATAGGAATTTAAGAGAAATTTAGA-AGGAAATTGAGAGCAAATTGAGATT
* * * *
11832182 AAATATGAATTTGAGAGAAATTTGGAAGGAAATTGAGAGCAATTTGAGA
1 AAATAGGAATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAGA
11832231 GGAAATTGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.26, T:0.26
Consensus pattern (51 bp):
AAATAGGAATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAGATT
Found at i:11833361 original size:7 final size:7
Alignment explanation
Indices: 11833349--11833375 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
11833339 TACCTTCTTA
11833349 TTTTTAT
1 TTTTTAT
11833356 TTTTTAT
1 TTTTTAT
11833363 TTTTTAT
1 TTTTTAT
11833370 TTTTTA
1 TTTTTA
11833376 AAGTTAATAC
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):
TTTTTAT
Found at i:11833616 original size:22 final size:22
Alignment explanation
Indices: 11833539--11833638 Score: 60
Period size: 22 Copynumber: 4.3 Consensus size: 22
11833529 TAAGTCAACT
*
11833539 TTTA-ATTTGAATATTTTTTAA
1 TTTATATTTAAATATTTTTTAA
* * *
11833560 TTTAAATTATAATTATCAATATTTTAT
1 TTTATATT-TAA--AT--ATTTTTTAA
11833587 TTTAATATTTAAATATTTTTTAA
1 TTT-ATATTTAAATATTTTTTAA
** *
11833610 TTTATATGCATAAT-TTTTTTAT
1 TTTATATTTA-AATATTTTTTAA
11833632 TTTATAT
1 TTTATAT
11833639 AAATAAATTC
Statistics
Matches: 62, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
21 4 0.06
22 22 0.35
23 15 0.24
25 4 0.06
27 13 0.21
28 4 0.06
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTATATTTAAATATTTTTTAA
Found at i:11833647 original size:23 final size:23
Alignment explanation
Indices: 11833581--11833647 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 23
11833571 ATTATCAATA
**
11833581 TTTTATTTTA-ATATTTAAATATT
1 TTTTATTTTATATAAATAAAT-TT
* **
11833604 TTTTAATTTATATGCAT-AATTT
1 TTTTATTTTATATAAATAAATTT
11833626 TTTTATTTTATATAAATAAATT
1 TTTTATTTTATATAAATAAATT
11833648 CATGGCATTG
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
22 16 0.46
23 16 0.46
24 3 0.09
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (23 bp):
TTTTATTTTATATAAATAAATTT
Found at i:11842533 original size:17 final size:17
Alignment explanation
Indices: 11842507--11842541 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
11842497 GACCATTTTG
*
11842507 ATAAACAATTAAAGAAA
1 ATAAAAAATTAAAGAAA
*
11842524 ATAAAAAATTAAATAAA
1 ATAAAAAATTAAAGAAA
11842541 A
1 A
11842542 ATTAAAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.20
Consensus pattern (17 bp):
ATAAAAAATTAAAGAAA
Found at i:11857790 original size:34 final size:34
Alignment explanation
Indices: 11857752--11857822 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
11857742 TCATGACAGA
11857752 AGTAAAGACAATTCACCTATAATAGCCCTTTTTT
1 AGTAAAGACAATTCACCTATAATAGCCCTTTTTT
11857786 AGTAAAGACAATTCACCTATAATAGCCCTTTTTT
1 AGTAAAGACAATTCACCTATAATAGCCCTTTTTT
11857820 AGT
1 AGT
11857823 GGTATCATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (34 bp):
AGTAAAGACAATTCACCTATAATAGCCCTTTTTT
Found at i:11860032 original size:17 final size:17
Alignment explanation
Indices: 11860010--11860179 Score: 146
Period size: 17 Copynumber: 10.0 Consensus size: 17
11860000 TACATATATA
11860010 TTTATATGTGAGTTATG
1 TTTATATGTGAGTTATG
** * *
11860027 TTTATAAATAAGCTATG
1 TTTATATGTGAGTTATG
* *
11860044 TTTCTATGCT-AGTTGTG
1 TTTATATG-TGAGTTATG
* *
11860061 TTTATATGCGAGCTATG
1 TTTATATGTGAGTTATG
*
11860078 TTTATATGTGAGTTGTG
1 TTTATATGTGAGTTATG
** *
11860095 TTTATATGCAAGTTGTG
1 TTTATATGTGAGTTATG
* *
11860112 TTTATATGCGAGCTATG
1 TTTATATGTGAGTTATG
** *
11860129 TTTATATGCAAGTTGTG
1 TTTATATGTGAGTTATG
*
11860146 TTTATATGCT-AGCTATG
1 TTTATATG-TGAGTTATG
11860163 TTTATATGTGAGTTATG
1 TTTATATGTGAGTTATG
11860180 CGAGCTGGCT
Statistics
Matches: 121, Mismatches: 28, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
16 1 0.01
17 119 0.98
18 1 0.01
ACGTcount: A:0.24, C:0.06, G:0.22, T:0.48
Consensus pattern (17 bp):
TTTATATGTGAGTTATG
Found at i:11860078 original size:51 final size:51
Alignment explanation
Indices: 11860010--11860179 Score: 214
Period size: 51 Copynumber: 3.3 Consensus size: 51
11860000 TACATATATA
* * ** * * *
11860010 TTTATATGTGAGTTATGTTTATAAATAAGCTATGTTTCTATGCTAGTTGTG
1 TTTATATGCGAGCTATGTTTATATGTAAGTTGTGTTTATATGCTAGTTGTG
* *
11860061 TTTATATGCGAGCTATGTTTATATGTGAGTTGTGTTTATATGCAAGTTGTG
1 TTTATATGCGAGCTATGTTTATATGTAAGTTGTGTTTATATGCTAGTTGTG
* * *
11860112 TTTATATGCGAGCTATGTTTATATGCAAGTTGTGTTTATATGCTAGCTATG
1 TTTATATGCGAGCTATGTTTATATGTAAGTTGTGTTTATATGCTAGTTGTG
* *
11860163 TTTATATGTGAGTTATG
1 TTTATATGCGAGCTATG
11860180 CGAGCTGGCT
Statistics
Matches: 103, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 103 1.00
ACGTcount: A:0.24, C:0.06, G:0.22, T:0.48
Consensus pattern (51 bp):
TTTATATGCGAGCTATGTTTATATGTAAGTTGTGTTTATATGCTAGTTGTG
Found at i:11865891 original size:25 final size:25
Alignment explanation
Indices: 11865857--11865905 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
11865847 AAAGAATAGA
11865857 GAAAGAGCCTCATGTGATCTACTAG
1 GAAAGAGCCTCATGTGATCTACTAG
*
11865882 GAAAGAGCCTCATGTTATCTACTA
1 GAAAGAGCCTCATGTGATCTACTA
11865906 CACTTCGAAA
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:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (25 bp):
GAAAGAGCCTCATGTGATCTACTAG
Found at i:11868151 original size:33 final size:32
Alignment explanation
Indices: 11868111--11868175 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 32
11868101 AACCAAACTA
11868111 ATCCCACCAAATTCTTCGTTACTGCATTCCTG
1 ATCCCACCAAATTCTTCGTTACTGCATTCCTG
*
11868143 NATCCCACCGAATTCTTCGTTACTGCATTCCTG
1 -ATCCCACCAAATTCTTCGTTACTGCATTCCTG
11868176 CAAAAGCCCC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.34, G:0.11, T:0.34
Consensus pattern (32 bp):
ATCCCACCAAATTCTTCGTTACTGCATTCCTG
Found at i:11876491 original size:14 final size:14
Alignment explanation
Indices: 11876472--11876511 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
11876462 TTGATTGGCA
11876472 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
11876486 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
11876500 GGAAAATGTTTT
1 GTAAAATGTTTT
11876512 ACATTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:11876533 original size:20 final size:20
Alignment explanation
Indices: 11876494--11876533 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
11876484 CCGTAAAATG
**
11876494 ATTTCTGGAAAATGTTTTAC
1 ATTTCTGGAAAATGACTTAC
*
11876514 ATTTCTGTAAAATGACTTAC
1 ATTTCTGGAAAATGACTTAC
11876534 TGGAAAATGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (20 bp):
ATTTCTGGAAAATGACTTAC
Found at i:11876541 original size:35 final size:34
Alignment explanation
Indices: 11876481--11876546 Score: 105
Period size: 35 Copynumber: 1.9 Consensus size: 34
11876471 AGTAAAATGT
*
11876481 TTTCCGTAAAATGATTTCTGGAAAATGTTTTACA
1 TTTCCGTAAAATGATTACTGGAAAATGTTTTACA
*
11876515 TTTCTGTAAAATGACTTACTGGAAAATGTTTT
1 TTTCCGTAAAATGA-TTACTGGAAAATGTTTT
11876547 TTGGTGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 13 0.45
35 16 0.55
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (34 bp):
TTTCCGTAAAATGATTACTGGAAAATGTTTTACA
Found at i:11877825 original size:18 final size:18
Alignment explanation
Indices: 11877791--11877825 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11877781 GCTTCGAAAC
*
11877791 GGGAAAGGGAAGGAGAAG
1 GGGAAAGGGAAGAAGAAG
*
11877809 GGGAAAGGGGAGAAGAA
1 GGGAAAGGGAAGAAGAA
11877826 TGGGTCATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (18 bp):
GGGAAAGGGAAGAAGAAG
Found at i:11885049 original size:6 final size:6
Alignment explanation
Indices: 11885034--11885067 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
11885024 AGACAGGCAA
*
11885034 GAACAT GAACAG GAACAG GAACAG GAACAG GAAC
1 GAACAG GAACAG GAACAG GAACAG GAACAG GAAC
11885068 GAGAGCAGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.50, C:0.18, G:0.29, T:0.03
Consensus pattern (6 bp):
GAACAG
Done.