Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 54 of 318
Found at i:19582522 original size:22 final size:21
Alignment explanation
Indices: 19582497--19582665 Score: 79
Period size: 22 Copynumber: 8.1 Consensus size: 21
19582487 GAATATTTTA
19582497 ATATTAAGAATTTTATTAAATT
1 ATATTAA-AATTTTATTAAATT
19582519 ATATT----TTTTATTAAATT
1 ATATTAAAATTTTATTAAATT
19582536 ATATTTAATAATTATTATTTTAAATT
1 ATA-TTAA-AATT-TTA--TTAAATT
** **
19582562 ATATT-TTATACTATT--A-T
1 ATATTAAAATTTTATTAAATT
*
19582579 ATATTAAAATTTTAGTAAATT
1 ATATTAAAATTTTATTAAATT
19582600 CATA-TAAGAATTTTATTAAATT
1 -ATATTAA-AATTTTATTAAATT
* * *
19582622 ATAAT-ATATTTAATTATAATT
1 ATATTAAAATTTTATTA-AATT
* * * *
19582643 ATGTTTAAATATGATTAAATT
1 ATATTAAAATTTTATTAAATT
19582664 AT
1 AT
19582666 TTATTATTGA
Statistics
Matches: 112, Mismatches: 17, Indels: 37
0.67 0.10 0.22
Matches are distributed among these distances:
17 21 0.19
18 8 0.07
20 11 0.10
21 21 0.19
22 32 0.29
23 4 0.04
24 3 0.03
25 2 0.02
26 10 0.09
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (21 bp):
ATATTAAAATTTTATTAAATT
Found at i:19582527 original size:17 final size:17
Alignment explanation
Indices: 19582507--19582541 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
19582497 ATATTAAGAA
19582507 TTTTATTAAATTATATT
1 TTTTATTAAATTATATT
19582524 TTTTATTAAATTATATT
1 TTTTATTAAATTATATT
19582541 T
1 T
19582542 AATAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTATTAAATTATATT
Found at i:19582531 original size:120 final size:120
Alignment explanation
Indices: 19582308--19582614 Score: 519
Period size: 120 Copynumber: 2.6 Consensus size: 120
19582298 CCACAAAATC
*
19582308 AATTATTTTAGATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCGTATAAGAATAT
1 AATTATTTTAGATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATAT
19582373 TTAATACTAAGAATTTTATTAAATTATATATTTATATTAAATTATATTTAATAAT
66 TTAATACTAAGAATTTTATTAAATTATATATTTATATTAAATTATATTTAATAAT
19582428 AATTATTTTAGATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATAT
1 AATTATTTTAGATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATA-
* *
19582493 TTTAATATTAAGAATTTTATTAAATTATAT-TTTTTATTAAATTATATTTAATAAT
65 TTTAATACTAAGAATTTTATTAAATTATATATTTATATTAAATTATATTTAATAAT
* * * **
19582548 TATTATTTTAAATTATATTTTATACTATTATATATTAAAATTTTAGTAAATTCATATAAGAAT-T
1 AATTATTTTAGATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATAT
19582612 TTA
66 TTA
19582615 TTAAATTATA
Statistics
Matches: 178, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
118 4 0.02
120 145 0.81
121 29 0.16
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (120 bp):
AATTATTTTAGATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATAT
TTAATACTAAGAATTTTATTAAATTATATATTTATATTAAATTATATTTAATAAT
Found at i:19582638 original size:60 final size:58
Alignment explanation
Indices: 19582453--19582643 Score: 142
Period size: 60 Copynumber: 3.2 Consensus size: 58
19582443 TATTTTATAG
** *
19582453 TATTATATATTATGATTTTAGTAAATTCATATAAGAATATT-TTAATATTA-AGA-AT-TT
1 TATTATA-ATTAAAATTTTAGTAAATTCATATAAGAATTTTATTAA-ATTATA-ATATATT
** * * * * *
19582510 TATTA-AATTATATTTTTTATTAAATT-ATATTTAATAATTATTATTTTAAATTATATTTTATAC
1 TATTATAATTA-AAATTTTAGTAAATTCATA--TAAGAATT-TTA--TTAAATTATAATATAT-T
19582573 TATTATATATTAAAATTTTAGTAAATTCATATAAGAATTTTATTAAATTATAATATATT
1 TATTATA-ATTAAAATTTTAGTAAATTCATATAAGAATTTTATTAAATTATAATATATT
19582632 TAATTATAATTA
1 T-ATTATAATTA
19582644 TGTTTAAATA
Statistics
Matches: 103, Mismatches: 16, Indels: 28
0.70 0.11 0.19
Matches are distributed among these distances:
55 7 0.07
56 12 0.12
57 11 0.11
58 2 0.02
59 5 0.05
60 24 0.23
61 6 0.06
62 4 0.04
63 12 0.12
64 13 0.13
65 7 0.07
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (58 bp):
TATTATAATTAAAATTTTAGTAAATTCATATAAGAATTTTATTAAATTATAATATATT
Found at i:19582885 original size:16 final size:16
Alignment explanation
Indices: 19582864--19582933 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
19582854 TTGATTTGTT
19582864 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
19582880 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
* *
19582896 ATTACATCTCTATTCC
1 ATTACACCTCTAATCC
*
19582912 ATTACGCCTCTAATCC
1 ATTACACCTCTAATCC
*
19582928 AATACA
1 ATTACA
19582934 GCGAACCAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.31, C:0.34, G:0.01, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:19585539 original size:22 final size:19
Alignment explanation
Indices: 19585511--19585560 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 19
19585501 AATTTTTAAT
19585511 TTTTTAAATATAAAGTTTAGAA
1 TTTTTAAA-A-AAA-TTTAGAA
*
19585533 TTTTTAAAAATATTTAGAA
1 TTTTTAAAAAAATTTAGAA
19585552 -TTTTAAAAA
1 TTTTTAAAAA
19585561 TTATTTTGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 9 0.33
19 7 0.26
20 2 0.07
21 1 0.04
22 8 0.30
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (19 bp):
TTTTTAAAAAAATTTAGAA
Found at i:19585550 original size:19 final size:20
Alignment explanation
Indices: 19585526--19585572 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
19585516 AAATATAAAG
19585526 TTTAGAATTTTTAAAAA-TA
1 TTTAGAATTTTTAAAAATTA
19585545 TTTAGAA-TTTTAAAAATTA
1 TTTAGAATTTTTAAAAATTA
*
19585564 TTTTGAATT
1 TTTAGAATT
19585573 ATTTTATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 9 0.36
19 15 0.60
20 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (20 bp):
TTTAGAATTTTTAAAAATTA
Found at i:19585804 original size:3 final size:3
Alignment explanation
Indices: 19585798--19585826 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
19585788 AATAATAATA
19585798 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
19585827 GAAAAACGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:19587110 original size:17 final size:18
Alignment explanation
Indices: 19587077--19587111 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
19587067 TATTTGACTC
*
19587077 TAAAATATAAAATATATT
1 TAAAATATAAAAAATATT
19587095 TAAAATA-AAAAAATATT
1 TAAAATATAAAAAATATT
19587112 AAAGATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TAAAATATAAAAAATATT
Found at i:19589002 original size:11 final size:11
Alignment explanation
Indices: 19588986--19589016 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
19588976 AGGTATAGGT
19588986 AGGTATGGGAA
1 AGGTATGGGAA
*
19588997 AGGTATGGGCA
1 AGGTATGGGAA
19589008 AGGTATGGG
1 AGGTATGGG
19589017 GTATATTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.48, T:0.19
Consensus pattern (11 bp):
AGGTATGGGAA
Found at i:19593080 original size:18 final size:18
Alignment explanation
Indices: 19593057--19593113 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
19593047 CAATCCCAAC
*
19593057 TACTGTATACGTGAAAAG
1 TACTGTATACGTGAATAG
19593075 TACTGTATACGTGAATAG
1 TACTGTATACGTGAATAG
*
19593093 TATTGTATACGTGAATAG
1 TACTGTATACGTGAATAG
19593111 TAC
1 TAC
19593114 CGTAAACGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (18 bp):
TACTGTATACGTGAATAG
Found at i:19593675 original size:21 final size:22
Alignment explanation
Indices: 19593649--19593690 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
19593639 TGACCTTTCC
*
19593649 AAGGTATGGG-TAGGTATGGGA
1 AAGGTATGGGCAAGGTATGGGA
19593670 AAGGTATGGGCAAGGTATGGG
1 AAGGTATGGGCAAGGTATGGG
19593691 GTATATTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.29, C:0.02, G:0.48, T:0.21
Consensus pattern (22 bp):
AAGGTATGGGCAAGGTATGGGA
Found at i:19593676 original size:11 final size:10
Alignment explanation
Indices: 19593649--19593690 Score: 57
Period size: 11 Copynumber: 4.0 Consensus size: 10
19593639 TGACCTTTCC
19593649 AAGGTATGGG
1 AAGGTATGGG
*
19593659 TAGGTATGGG
1 AAGGTATGGG
19593669 AAAGGTATGGG
1 -AAGGTATGGG
19593680 CAAGGTATGGG
1 -AAGGTATGGG
19593691 GTATATTCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.29, C:0.02, G:0.48, T:0.21
Consensus pattern (10 bp):
AAGGTATGGG
Found at i:19596529 original size:3 final size:3
Alignment explanation
Indices: 19596521--19596551 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
19596511 TTATACTTTT
19596521 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
19596552 ACTTTATTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:19596729 original size:3 final size:3
Alignment explanation
Indices: 19596721--19596751 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
19596711 ATTGTTTTGA
19596721 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
19596752 GTTGTTGTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:19599310 original size:43 final size:43
Alignment explanation
Indices: 19599262--19599349 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
19599252 AATAAAAAAA
19599262 TCCATGTCTCGAGACTAGATCTCGAGACCAACCTCTCATGTTT
1 TCCATGTCTCGAGACTAGATCTCGAGACCAACCTCTCATGTTT
19599305 TCCATGTCTCGAGACTAGATCTCGAGACCAACCTCTCATGTTT
1 TCCATGTCTCGAGACTAGATCTCGAGACCAACCTCTCATGTTT
19599348 TC
1 TC
19599350 TTATTTTAGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.23, C:0.31, G:0.16, T:0.31
Consensus pattern (43 bp):
TCCATGTCTCGAGACTAGATCTCGAGACCAACCTCTCATGTTT
Found at i:19601315 original size:23 final size:23
Alignment explanation
Indices: 19601262--19601326 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 23
19601252 TGAGTGTCGT
*
19601262 TCTAGTGTGTTTGGGTGGATTAC
1 TCTAGTGTGTTTGGTTGGATTAC
*
19601285 TCTGGTGTGTTTGGTTGGATTA-
1 TCTAGTGTGTTTGGTTGGATTAC
*
19601307 TTTCAGTGTGTTTGGTTGGA
1 TCT-AGTGTGTTTGGTTGGA
19601327 ATCCGTGTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
22 2 0.05
23 35 0.95
ACGTcount: A:0.11, C:0.06, G:0.35, T:0.48
Consensus pattern (23 bp):
TCTAGTGTGTTTGGTTGGATTAC
Found at i:19609210 original size:54 final size:54
Alignment explanation
Indices: 19609152--19609272 Score: 224
Period size: 54 Copynumber: 2.2 Consensus size: 54
19609142 ATTACCAAAG
19609152 TACCCTCGATTTATAGAATTACTGTTTTACCATTGATTTACAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACTGTTTTACCATTGATTTACAGAATTACCGTTT
* *
19609206 TACCCTCGATTTATAGAATTACTGTTTTACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTATAGAATTACTGTTTTACCATTGATTTACAGAATTACCGTTT
19609260 TACCCTCGATTTA
1 TACCCTCGATTTA
19609273 CAAAATTGCT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 65 1.00
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.43
Consensus pattern (54 bp):
TACCCTCGATTTATAGAATTACTGTTTTACCATTGATTTACAGAATTACCGTTT
Found at i:19609273 original size:27 final size:27
Alignment explanation
Indices: 19609152--19609279 Score: 193
Period size: 27 Copynumber: 4.7 Consensus size: 27
19609142 ATTACCAAAG
*
19609152 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* * *
19609179 TACCATTGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
19609206 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
19609233 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
19609260 TACCCTCGATTTACAAAATT
1 TACCCTCGATTTACAGAATT
19609280 GCTAAAATAC
Statistics
Matches: 89, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 89 1.00
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.42
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACTGTTT
Found at i:19609290 original size:27 final size:27
Alignment explanation
Indices: 19609260--19609534 Score: 152
Period size: 27 Copynumber: 10.2 Consensus size: 27
19609250 ATTACTGTTT
* *
19609260 TACCCTCGATTTACAAAATTGCTAAAA
1 TACCCTCGATTTACAAAATTACCAAAA
*
19609287 TACCCT-TAGTTTACAAAATTACCAAAA
1 TACCCTCGA-TTTACAAAATTACCAAAA
* *
19609314 TACCCTCGA-TCAGTAAAATTACCAAAA
1 TACCCTCGATTTA-CAAAATTACCAAAA
* ** * *
19609341 TACCCTAG-TTTGTAAAATTGCTAAAA
1 TACCCTCGATTTACAAAATTACCAAAA
* ** *
19609367 TACCC-CTAGTTTGTAAAATTACCGAAA
1 TACCCTCGA-TTTACAAAATTACCAAAA
* ** *
19609394 TACCCTCAATTTGTAAAATGACCAAAA
1 TACCCTCGATTTACAAAATTACCAAAA
* **
19609421 TACCC-CTAGTTTGTAAAATTACCAAAA
1 TACCCTCGA-TTTACAAAATTACCAAAA
* ** * *
19609448 TACCACT-GGTTTGTAAAATTATCGAAA
1 TACC-CTCGATTTACAAAATTACCAAAA
* ** *
19609475 TACCCTCAATTTGTAAAATTAGCAAAA
1 TACCCTCGATTTACAAAATTACCAAAA
*
19609502 TA-CCTCTGATTTACAAAGTTA-CAGAAA
1 TACCCTC-GATTTACAAAATTACCA-AAA
19609529 TACCCT
1 TACCCT
19609535 TGACTTTTTA
Statistics
Matches: 201, Mismatches: 33, Indels: 27
0.77 0.13 0.10
Matches are distributed among these distances:
26 30 0.15
27 164 0.82
28 7 0.03
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACCAAAA
Found at i:19609291 original size:54 final size:54
Alignment explanation
Indices: 19609152--19609309 Score: 156
Period size: 54 Copynumber: 2.9 Consensus size: 54
19609142 ATTACCAAAG
* * **** *
19609152 TACCCTCGATTTATAGAATTACTGTTTTACCATTGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAAAATTACTAAAATACCCTTGATTTACAGAATTACCGTTT
* * **** *
19609206 TACCCTCGATTTATAGAATTACTGTTTTACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTAAAATACCCTTGATTTACAGAATTACCGTTT
* *
19609260 TACCCTCGATTTACAAAATTGCTAAAATACCCTT-AGTTTACAAAATTACC
1 TACCCTCGATTTACAAAATTACTAAAATACCCTTGA-TTTACAGAATTACC
19609310 AAAATACCCT
Statistics
Matches: 92, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
53 1 0.01
54 91 0.99
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.40
Consensus pattern (54 bp):
TACCCTCGATTTACAAAATTACTAAAATACCCTTGATTTACAGAATTACCGTTT
Found at i:19609468 original size:81 final size:81
Alignment explanation
Indices: 19609274--19609505 Score: 306
Period size: 81 Copynumber: 2.9 Consensus size: 81
19609264 CTCGATTTAC
* * ** * * **
19609274 AAAATTGCTAAAATACC-CTTAGTTTACAAAATTACCAAAATACCCTCGATCAGTAAAATTACCA
1 AAAATTACCAAAATACCAC-TAGTTTGTAAAATTACCGAAATACCCTCAATTTGTAAAATTACCA
19609338 AAATA-CCCTAGTTTGT
65 AAATACCCCTAGTTTGT
* * * *
19609354 AAAATTGCTAAAATACCCCTAGTTTGTAAAATTACCGAAATACCCTCAATTTGTAAAATGACCAA
1 AAAATTACCAAAATACCACTAGTTTGTAAAATTACCGAAATACCCTCAATTTGTAAAATTACCAA
19609419 AATACCCCTAGTTTGT
66 AATACCCCTAGTTTGT
* * *
19609435 AAAATTACCAAAATACCACTGGTTTGTAAAATTATCGAAATACCCTCAATTTGTAAAATTAGCAA
1 AAAATTACCAAAATACCACTAGTTTGTAAAATTACCGAAATACCCTCAATTTGTAAAATTACCAA
19609500 AATACC
66 AATACC
19609506 TCTGATTTAC
Statistics
Matches: 136, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
80 60 0.44
81 76 0.56
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.29
Consensus pattern (81 bp):
AAAATTACCAAAATACCACTAGTTTGTAAAATTACCGAAATACCCTCAATTTGTAAAATTACCAA
AATACCCCTAGTTTGT
Found at i:19609575 original size:26 final size:26
Alignment explanation
Indices: 19609541--19609595 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
19609531 CCCTTGACTT
*
19609541 TTTAAAAATTA-TGGAAATACCATTGG
1 TTTAAAAATTACT-AAAATACCATTGG
* *
19609567 TTTACAAATTACTAAAATACCCTTGG
1 TTTAAAAATTACTAAAATACCATTGG
19609593 TTT
1 TTT
19609596 GTAGATTTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (26 bp):
TTTAAAAATTACTAAAATACCATTGG
Found at i:19609670 original size:27 final size:27
Alignment explanation
Indices: 19609640--19609735 Score: 115
Period size: 27 Copynumber: 3.6 Consensus size: 27
19609630 GACTAAAATA
*
19609640 CCCCTATTA-GGTAAAAAGACCGTAAAG
1 CCCCTA-TAGGGTAAAGAGACCGTAAAG
*
19609667 CCCCTGTAGGGTAAAGAGACCGTAAAG
1 CCCCTATAGGGTAAAGAGACCGTAAAG
*
19609694 CCCCTATAGGGTAAAGTGACCGTAATA-
1 CCCCTATAGGGTAAAGAGACCGTAA-AG
* *
19609721 CCCCTGTATGGTAAA
1 CCCCTATAGGGTAAA
19609736 ATGACAAATA
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
26 2 0.03
27 58 0.95
28 1 0.02
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (27 bp):
CCCCTATAGGGTAAAGAGACCGTAAAG
Found at i:19610638 original size:25 final size:26
Alignment explanation
Indices: 19610541--19610663 Score: 196
Period size: 26 Copynumber: 4.8 Consensus size: 26
19610531 GAGGAAGTGC
*
19610541 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACTG
19610567 AAAAGGGCTTATGCCCCAGTTTACTG
1 AAAAGGGCTTATGCCCCAGTTTACTG
*
19610593 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACTG
*
19610619 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACTG
*
19610644 AAAAGGGCTT-TTCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
19610664 ATTAAAGAGT
Statistics
Matches: 92, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
25 32 0.35
26 60 0.65
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACTG
Found at i:19610867 original size:42 final size:42
Alignment explanation
Indices: 19610808--19610899 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
19610798 TAGTCTCCCC
* * ** *
19610808 AAATGGGCTTGTATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
19610850 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
19610892 AAATGGGC
1 AAATGGGC
19610900 CTAAGGGCCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:19611000 original size:31 final size:31
Alignment explanation
Indices: 19610923--19611001 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
19610913 CGTTTACAGT
*
19610923 AAAGGCTTCGGCCCAATGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
19610954 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
19610985 AAAGGCTTTGGCCCAGT
1 AAAGGCTTCGGCCCAGT
19611002 AACCGTTAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:19611819 original size:6 final size:6
Alignment explanation
Indices: 19611808--19611852 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
19611798 GTACTGATAT
19611808 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATA
19611853 ATATATTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (6 bp):
ATATAC
Found at i:19611840 original size:24 final size:24
Alignment explanation
Indices: 19611808--19611887 Score: 90
Period size: 24 Copynumber: 3.2 Consensus size: 24
19611798 GTACTGATAT
19611808 ATATACATATACATATACATATAC
1 ATATACATATACATATACATATAC
*
19611832 ATATACATATACATATACATAATAT
1 ATATACATATACATATACAT-ATAC
* *
19611857 ATTTA-AAATGAACATATACAATATAC
1 ATATACATAT--ACATATAC-ATATAC
19611883 ATATA
1 ATATA
19611888 TAATAAAATA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
24 23 0.49
25 7 0.15
26 15 0.32
27 2 0.04
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (24 bp):
ATATACATATACATATACATATAC
Found at i:19611873 original size:56 final size:55
Alignment explanation
Indices: 19611812--19611930 Score: 145
Period size: 57 Copynumber: 2.1 Consensus size: 55
19611802 TGATATATAT
*
19611812 ACATATAC-ATATACATATACATATACATATACAT-ATAC-ATAATATATTTAAAATGA
1 ACATATACAATATACATATACA-ATA-AAATACATAATACTATAATAT-TTTAAAA-GA
* *
19611868 ACATATACAATATACATATATAATAAAATACATGAATACTATGATATTTTAAAAGA
1 ACATATACAATATACATATACAATAAAATACAT-AATACTATAATATTTTAAAAGA
19611924 ACATATA
1 ACATATA
19611931 TACGTAATAT
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
55 7 0.12
56 20 0.36
57 23 0.41
58 6 0.11
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.33
Consensus pattern (55 bp):
ACATATACAATATACATATACAATAAAATACATAATACTATAATATTTTAAAAGA
Found at i:19612345 original size:27 final size:27
Alignment explanation
Indices: 19612300--19612351 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
19612290 TGTACATGAT
* * *
19612300 ATATATAATATGATGTTAAGAGTATAC
1 ATATAAAATATGATATTAAAAGTATAC
*
19612327 ATATAAAATATGGTATTAAAAGTAT
1 ATATAAAATATGATATTAAAAGTAT
19612352 GTATACGTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.48, C:0.02, G:0.13, T:0.37
Consensus pattern (27 bp):
ATATAAAATATGATATTAAAAGTATAC
Found at i:19612475 original size:17 final size:17
Alignment explanation
Indices: 19612455--19612503 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
19612445 TAATACTTCA
19612455 TAAATATATATACATAC
1 TAAATATATATACATAC
*
19612472 TAAA-A-ATATACATAA
1 TAAATATATATACATAC
19612487 T-AATAATATATACATAC
1 TAAAT-ATATATACATAC
19612504 AAAGTACACT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 2 0.07
15 10 0.37
16 2 0.07
17 13 0.48
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAATATATATACATAC
Found at i:19612482 original size:15 final size:17
Alignment explanation
Indices: 19612460--19612503 Score: 65
Period size: 15 Copynumber: 2.7 Consensus size: 17
19612450 CTTCATAAAT
19612460 ATATATACATACTAA-A
1 ATATATACATACTAATA
*
19612476 A-ATATACATAATAATA
1 ATATATACATACTAATA
19612492 ATATATACATAC
1 ATATATACATAC
19612504 AAAGTACACT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 12 0.50
16 3 0.12
17 9 0.38
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (17 bp):
ATATATACATACTAATA
Found at i:19612550 original size:18 final size:18
Alignment explanation
Indices: 19612524--19612558 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19612514 AATATTTAAA
19612524 AATAATAATAGTAAATAT
1 AATAATAATAGTAAATAT
* *
19612542 AATACTAATATTAAATA
1 AATAATAATAGTAAATA
19612559 AAATTAATAT
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:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (18 bp):
AATAATAATAGTAAATAT
Found at i:19614596 original size:13 final size:14
Alignment explanation
Indices: 19614569--19614602 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
19614559 GTTGATTTTT
*
19614569 TTGAAAAATACAAA
1 TTGAAAAATAAAAA
19614583 TTGAAAAA-AAAAA
1 TTGAAAAATAAAAA
19614596 TTGAAAA
1 TTGAAAA
19614603 CTCCTCAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.68, C:0.03, G:0.09, T:0.21
Consensus pattern (14 bp):
TTGAAAAATAAAAA
Found at i:19614732 original size:97 final size:89
Alignment explanation
Indices: 19614445--19614861 Score: 400
Period size: 89 Copynumber: 4.6 Consensus size: 89
19614435 GTGAGCCAAA
* * * * * * **
19614445 GCTCAACTCACCTCTCGCCATATGAGTTGGTCTTTTTGAAACTTAATTTG--AAAAGTAGATTTT
1 GCTCAACTCACTTCTTGCAATATGAGTT-G-ATTTTTGAAACATAAATTGAAAAAAAAAGATTTT
* * *** *
19614508 GAAAATACCTTGTCATGTGACCCGAA
64 GAAAATACCTCGACATGTGGTTCGAG
* * *
19614534 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATACAAATTGAAAAAAAAA-A--
1 GCTCAACTCACTTCTTGCAATATGAGTTGA--TTTTTGAAACAT--AAATTGAAAAAAAAAGATT
* *
19614596 TTGAAAACT-CCTC-AGCATGTGAG-CCAAG
62 TTGAAAA-TACCTCGA-CATGTG-GTTCGAG
*
19614624 GCTCAACTCACTTCTTGCAATATGAGTTGATTTTTGACAAACAGAAATTTGAAAAAAAAAGAAAA
1 GCTCAACTCACTTCTTGCAATATGAGTTGATTTTTG--AAACATAAA-TTGAAAAAAAAAG---A
19614689 GGTTTTGAAAATACCTCGACATGTGGTTCGAG
60 --TTTTGAAAATACCTCGACATGTGGTTCGAG
* * *
19614721 GCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAAATAACAGATTTTGA
1 GCTCAACTCACTTCTTGCAATATGAGTTGATTTTTGAAACATAAATTGAAAAAAAAAGATTTTGA
19614786 AAATACCTCGACATGTGGTTCGAG
66 AAATACCTCGACATGTGGTTCGAG
* *
19614810 GCTCAACTTACTTCTTGCAATATGAGTTGATTCTTGAAACATAAATTGAAAA
1 GCTCAACTCACTTCTTGCAATATGAGTTGATTTTTGAAACATAAATTGAAAA
19614862 TACCTCAACG
Statistics
Matches: 280, Mismatches: 25, Indels: 46
0.80 0.07 0.13
Matches are distributed among these distances:
88 10 0.04
89 128 0.46
90 51 0.18
91 7 0.03
92 1 0.00
93 6 0.02
94 11 0.04
95 8 0.03
96 2 0.01
97 55 0.20
98 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (89 bp):
GCTCAACTCACTTCTTGCAATATGAGTTGATTTTTGAAACATAAATTGAAAAAAAAAGATTTTGA
AAATACCTCGACATGTGGTTCGAG
Found at i:19615157 original size:252 final size:247
Alignment explanation
Indices: 19614718--19615183 Score: 537
Period size: 252 Copynumber: 1.9 Consensus size: 247
19614708 CATGTGGTTC
* *
19614718 GAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAAATAACAGATTT
1 GAGGCTCAACTCAC-TCTCGCAATATGAGTTGATTTTTGAAACAGAAATTGAAAAT-A-AGAATT
*** * * * *
19614783 TGAAAATACCTCGACATGTGGTTCGAGGCTCAACTTACTTCTTGCAATATGAGTTGATTCTTGAA
63 TGAAAATACCTCGACATGTGACCCGAGGCTCAACTCACTTCTCGCAATATGAATTGATTCTTAAA
* *** * *
19614848 ACATAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
128 ACATAAATTGAAAATACCTCAACGTGACCCAAGGCTCAACTCACCTCTAGCAATATGAATTGA-T
* *
19614913 TTTTTTTTGAAACACATAAATTGAAAAGCATAATTTGCAAATACCTCAGCATGTCCT
192 TTTTGTTTGAAA-ACAGAAATTGAAAAGCATAATTTGCAAATACCTCAGCATGTCCT
* *
19614970 GAGGCTCAACTCAC-CTCGGCAATATGAGTTGCTTTTTGAAAAGAGAAATT-AAAAT-AGAATTT
1 GAGGCTCAACTCACTCTC-GCAATATGAGTTGATTTTTG-AAACAGAAATTGAAAATAAGAATTT
* * * *
19615032 GAAAATACCTCGGCATGTGACCCTAGGCTCAACTCACCTT-TCGTAATATGAATTGATTTTTTTA
64 GAAAATACCTCGACATGTGACCCGAGGCTCAACTCA-CTTCTCGCAATATGAATTGA--TTCTTA
* * * *
19615096 AAACATAAATTGAAAA-ATCCTCGGCATGTGACCCAAGGCTCAATTCACCTCTAGTAATATGAAT
126 AAACATAAATTGAAAATA-CCTC--AACGTGACCCAAGGCTCAACTCACCTCTAGCAATATGAAT
19615160 TGATTTTTGTTTGAAAACAGAAAT
188 TGATTTTTGTTTGAAAACAGAAAT
19615184 AAAAAACATC
Statistics
Matches: 179, Mismatches: 27, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
248 49 0.27
249 4 0.02
250 34 0.19
251 36 0.20
252 56 0.31
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (247 bp):
GAGGCTCAACTCACTCTCGCAATATGAGTTGATTTTTGAAACAGAAATTGAAAATAAGAATTTGA
AAATACCTCGACATGTGACCCGAGGCTCAACTCACTTCTCGCAATATGAATTGATTCTTAAAACA
TAAATTGAAAATACCTCAACGTGACCCAAGGCTCAACTCACCTCTAGCAATATGAATTGATTTTT
GTTTGAAAACAGAAATTGAAAAGCATAATTTGCAAATACCTCAGCATGTCCT
Found at i:19628068 original size:16 final size:18
Alignment explanation
Indices: 19628028--19628074 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
19628018 AATATTTAAA
* *
19628028 AATAATAATAGTAAATAT
1 AATATTAATATTAAATAT
19628046 AATATTAATATTAAATA-
1 AATATTAATATTAAATAT
19628063 AA-ATTAATATTA
1 AATATTAATATTA
19628075 CAAATTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 10 0.37
17 2 0.07
18 15 0.56
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
AATATTAATATTAAATAT
Found at i:19637410 original size:21 final size:21
Alignment explanation
Indices: 19637386--19637438 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
19637376 CATTGTTTCT
*
19637386 AATCTCACCGCTACAGTACCC
1 AATCTCACCGCTACAGTAACC
*
19637407 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
19637428 AATCTCACCGC
1 AATCTCACCGC
19637439 CACCGCTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.40, G:0.09, T:0.21
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:19639798 original size:11 final size:12
Alignment explanation
Indices: 19639771--19639797 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
19639761 CAAAACAGAC
19639771 TTTTAGCGGCGT
1 TTTTAGCGGCGT
19639783 TTTTAGCGGCGT
1 TTTTAGCGGCGT
19639795 TTT
1 TTT
19639798 AAAAGAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.15, G:0.30, T:0.48
Consensus pattern (12 bp):
TTTTAGCGGCGT
Found at i:19640822 original size:25 final size:24
Alignment explanation
Indices: 19640772--19640823 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
19640762 TAACTTATTT
**
19640772 TTTAAATGAATTTAAAATTTTCTA
1 TTTAAATGAATTTAAAATTTAATA
* *
19640796 TTTAAACTGATTTTTAAATTTAATA
1 TTTAAA-TGAATTTAAAATTTAATA
19640821 TTT
1 TTT
19640824 TTATAGGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 6 0.26
25 17 0.74
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (24 bp):
TTTAAATGAATTTAAAATTTAATA
Found at i:19640858 original size:14 final size:13
Alignment explanation
Indices: 19640835--19640881 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 13
19640825 TATAGGTTTA
19640835 AGGGTTATGATTT
1 AGGGTTATGATTT
19640848 AGGGTTGATGATTT
1 AGGGTT-ATGATTT
**
19640862 ATGTTTTATGATTT
1 A-GGGTTATGATTT
19640876 AGGGTT
1 AGGGTT
19640882 TGAGGTTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 9 0.32
14 16 0.57
15 3 0.11
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.49
Consensus pattern (13 bp):
AGGGTTATGATTT
Found at i:19640897 original size:28 final size:28
Alignment explanation
Indices: 19640839--19640897 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
19640829 GGTTTAAGGG
**
19640839 TTATGATTTAGGGTTGATGATTTATGTT
1 TTATGATTTAGGGTTGATGATTTATAAT
*
19640867 TTATGATTTAGGGTTTGA-GGTTTATAAT
1 TTATGATTTAGGG-TTGATGATTTATAAT
19640895 TTA
1 TTA
19640898 AAAGGTTATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 23 0.85
29 4 0.15
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.53
Consensus pattern (28 bp):
TTATGATTTAGGGTTGATGATTTATAAT
Found at i:19641055 original size:14 final size:14
Alignment explanation
Indices: 19641038--19641067 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
19641028 GTGTTTTAAA
19641038 GTTTATTATTTAGG
1 GTTTATTATTTAGG
19641052 GTTTATTATTTAGG
1 GTTTATTATTTAGG
19641066 GT
1 GT
19641068 CTAAGATATT
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:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (14 bp):
GTTTATTATTTAGG
Found at i:19641107 original size:8 final size:8
Alignment explanation
Indices: 19641094--19641137 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 8
19641084 TAGCAATATT
19641094 AGGGTTTA
1 AGGGTTTA
19641102 AGGGTTTA
1 AGGGTTTA
19641110 A-GGTTT-
1 AGGGTTTA
*
19641116 AGGGCTTA
1 AGGGTTTA
*
19641124 AGAGTTTA
1 AGGGTTTA
19641132 AGGGTT
1 AGGGTT
19641138 AATGGTTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
6 1 0.03
7 9 0.30
8 20 0.67
ACGTcount: A:0.25, C:0.02, G:0.36, T:0.36
Consensus pattern (8 bp):
AGGGTTTA
Found at i:19641116 original size:15 final size:15
Alignment explanation
Indices: 19641096--19641137 Score: 59
Period size: 14 Copynumber: 2.8 Consensus size: 15
19641086 GCAATATTAG
19641096 GGTTTAAGGGTTTAA
1 GGTTTAAGGGTTTAA
*
19641111 GGTTT-AGGGCTTAA
1 GGTTTAAGGGTTTAA
19641125 GAGTTTAAGGGTT
1 G-GTTTAAGGGTT
19641138 AATGGTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 9 0.39
15 9 0.39
16 5 0.22
ACGTcount: A:0.24, C:0.02, G:0.36, T:0.38
Consensus pattern (15 bp):
GGTTTAAGGGTTTAA
Found at i:19641118 original size:22 final size:22
Alignment explanation
Indices: 19641092--19641134 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
19641082 TTTAGCAATA
* *
19641092 TTAGGGTTTAAGGGTTTAAGGT
1 TTAGGGCTTAAGAGTTTAAGGT
19641114 TTAGGGCTTAAGAGTTTAAGG
1 TTAGGGCTTAAGAGTTTAAGG
19641135 GTTAATGGTT
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:0.26, C:0.02, G:0.35, T:0.37
Consensus pattern (22 bp):
TTAGGGCTTAAGAGTTTAAGGT
Found at i:19641139 original size:15 final size:15
Alignment explanation
Indices: 19641096--19641144 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
19641086 GCAATATTAG
*
19641096 GGTTTAAGGGTTTAA
1 GGTTTAAGGGCTTAA
19641111 GGTTT-AGGGCTTAA
1 GGTTTAAGGGCTTAA
19641125 GAGTTTAAGGG-TTAA
1 G-GTTTAAGGGCTTAA
19641140 TGGTT
1 -GGTT
19641145 AATGGTTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
14 9 0.30
15 16 0.53
16 5 0.17
ACGTcount: A:0.24, C:0.02, G:0.35, T:0.39
Consensus pattern (15 bp):
GGTTTAAGGGCTTAA
Found at i:19641146 original size:22 final size:22
Alignment explanation
Indices: 19641094--19641139 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
19641084 TAGCAATATT
* * *
19641094 AGGGTTTAAGGGTTTAAGGTTT
1 AGGGCTTAAGAGTTTAAGGTTA
19641116 AGGGCTTAAGAGTTTAAGGGTTA
1 AGGGCTTAAGAGTTTAA-GGTTA
19641139 A
1 A
19641140 TGGTTAATGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.28, C:0.02, G:0.35, T:0.35
Consensus pattern (22 bp):
AGGGCTTAAGAGTTTAAGGTTA
Found at i:19641258 original size:7 final size:7
Alignment explanation
Indices: 19641242--19641300 Score: 55
Period size: 7 Copynumber: 8.4 Consensus size: 7
19641232 GGTTAATTAA
19641242 GGTTTAG
1 GGTTTAG
*
19641249 GGTCTAG
1 GGTTTAG
*
19641256 GGTTTGG
1 GGTTTAG
19641263 GGTTTAG
1 GGTTTAG
*
19641270 GGTTTAT
1 GGTTTAG
* *
19641277 AGCTTAG
1 GGTTTAG
*
19641284 GGTTTAT
1 GGTTTAG
*
19641291 GGTATAG
1 GGTTTAG
19641298 GGT
1 GGT
19641301 CAGGGTCTTA
Statistics
Matches: 39, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.15, C:0.03, G:0.41, T:0.41
Consensus pattern (7 bp):
GGTTTAG
Found at i:19641522 original size:7 final size:7
Alignment explanation
Indices: 19641512--19641619 Score: 51
Period size: 7 Copynumber: 15.6 Consensus size: 7
19641502 GATTTAGGAT
19641512 TTTAGGG
1 TTTAGGG
*
19641519 TTTATGG
1 TTTAGGG
19641526 TTTAGGG
1 TTTAGGG
*
19641533 ATT-GGG
1 TTTAGGG
*
19641539 TTTTATGG
1 -TTTAGGG
*
19641547 -TTATGG
1 TTTAGGG
***
19641553 TACGGGG
1 TTTAGGG
* *
19641560 CTTATGG
1 TTTAGGG
*
19641567 TTTGGGG
1 TTTAGGG
19641574 TTT-GGG
1 TTTAGGG
19641580 ATTTAGGG
1 -TTTAGGG
*
19641588 TTTGGGG
1 TTTAGGG
*
19641595 TTTGGGG
1 TTTAGGG
*
19641602 TTTAAGG
1 TTTAGGG
*
19641609 TTTAGTG
1 TTTAGGG
19641616 TTTA
1 TTTA
19641620 ATTTTAGAAA
Statistics
Matches: 74, Mismatches: 22, Indels: 10
0.70 0.21 0.09
Matches are distributed among these distances:
6 12 0.16
7 57 0.77
8 5 0.07
ACGTcount: A:0.13, C:0.02, G:0.40, T:0.45
Consensus pattern (7 bp):
TTTAGGG
Found at i:19641591 original size:21 final size:21
Alignment explanation
Indices: 19641565--19641611 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
19641555 CGGGGCTTAT
*
19641565 GGTTTGGGGTTTGGGATTTAG
1 GGTTTGGGGTTTGGGATTTAA
*
19641586 GGTTTGGGGTTTGGGGTTTAA
1 GGTTTGGGGTTTGGGATTTAA
19641607 GGTTT
1 GGTTT
19641612 AGTGTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.09, C:0.00, G:0.47, T:0.45
Consensus pattern (21 bp):
GGTTTGGGGTTTGGGATTTAA
Found at i:19641618 original size:21 final size:21
Alignment explanation
Indices: 19641565--19641618 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
19641555 CGGGGCTTAT
* *
19641565 GGTTTGGGGTTTGGGATTTAG
1 GGTTTAGGGTTTGGGATTTAA
* *
19641586 GGTTTGGGGTTTGGGGTTTAA
1 GGTTTAGGGTTTGGGATTTAA
*
19641607 GGTTTAGTGTTT
1 GGTTTAGGGTTT
19641619 AATTTTAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.09, C:0.00, G:0.44, T:0.46
Consensus pattern (21 bp):
GGTTTAGGGTTTGGGATTTAA
Found at i:19641838 original size:41 final size:40
Alignment explanation
Indices: 19641774--19641884 Score: 118
Period size: 41 Copynumber: 2.8 Consensus size: 40
19641764 AATTGTGAAT
* *
19641774 TAGTGGCGTTTT-TTAAAAAACGCCACAAAAAATGAGCTA
1 TAGTGGCGTTTTAATAAAAAACGCCACAAAAAATGACCTA
**
19641813 TAGTGGCGTTTATAATAAAAAACGCCACTAAAAGTTGACCTA
1 TAGTGGCGTTT-TAATAAAAAACGCCAC-AAAAAATGACCTA
** *
19641855 TACCGGCGTTTTAA-ATAAAAACGCCGCAAA
1 TAGTGGCGTTTTAATA-AAAAACGCCACAAA
19641885 TATTTGAGTT
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
39 11 0.18
40 5 0.08
41 26 0.43
42 19 0.31
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.24
Consensus pattern (40 bp):
TAGTGGCGTTTTAATAAAAAACGCCACAAAAAATGACCTA
Found at i:19642558 original size:24 final size:24
Alignment explanation
Indices: 19642528--19642573 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
19642518 GTCAAGTAAC
19642528 TTTAATTCCTAAGTCTCTGTTTCT
1 TTTAATTCCTAAGTCTCTGTTTCT
*
19642552 TTTAATTTCTAAGTCTCTGTTT
1 TTTAATTCCTAAGTCTCTGTTT
19642574 ACAAATACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.17, C:0.17, G:0.09, T:0.57
Consensus pattern (24 bp):
TTTAATTCCTAAGTCTCTGTTTCT
Found at i:19643356 original size:24 final size:24
Alignment explanation
Indices: 19643293--19643362 Score: 72
Period size: 24 Copynumber: 2.9 Consensus size: 24
19643283 TTTGTGACTG
*
19643293 TGAAAATCGTATTATAATAATGTTA
1 TGAAAATTGTATTATAAT-ATGTTA
**
19643318 T-ACTATCT-TATTTATAATATGTTA
1 TGAAAAT-TGTA-TTATAATATGTTA
19643342 TGAAAATTGTATTATAATATG
1 TGAAAATTGTATTATAATATG
19643363 CTTTGGTTAG
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
24 23 0.64
25 13 0.36
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.46
Consensus pattern (24 bp):
TGAAAATTGTATTATAATATGTTA
Found at i:19646536 original size:9 final size:9
Alignment explanation
Indices: 19646522--19646638 Score: 117
Period size: 9 Copynumber: 12.3 Consensus size: 9
19646512 TCTTAAAAAA
19646522 TTACATAAC
1 TTACATAAC
19646531 TTACATAAC
1 TTACATAAC
* *
19646540 TCATATAAC
1 TTACATAAC
*
19646549 TTACATAAT
1 TTACATAAC
19646558 TTACATAACAAC
1 TTACAT---AAC
19646570 TTACATAAC
1 TTACATAAC
*
19646579 TCACATAAC
1 TTACATAAC
*
19646588 TTACATAAT
1 TTACATAAC
19646597 TTACATAAC
1 TTACATAAC
*
19646606 TCACATAAC
1 TTACATAAC
*
19646615 GTACATAACAAC
1 TTACAT---AAC
19646627 TTACATAAC
1 TTACATAAC
19646636 TTA
1 TTA
19646639 ACTAATACAT
Statistics
Matches: 88, Mismatches: 14, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
9 72 0.82
12 16 0.18
ACGTcount: A:0.45, C:0.22, G:0.01, T:0.32
Consensus pattern (9 bp):
TTACATAAC
Found at i:19646575 original size:39 final size:39
Alignment explanation
Indices: 19646528--19646605 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
19646518 AAAATTACAT
*
19646528 AACTTACATAACTCATATAACTTACATAATTTACATAAC
1 AACTTACATAACTCACATAACTTACATAATTTACATAAC
19646567 AACTTACATAACTCACATAACTTACATAATTTACATAAC
1 AACTTACATAACTCACATAACTTACATAATTTACATAAC
19646606 TCACATAACG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (39 bp):
AACTTACATAACTCACATAACTTACATAATTTACATAAC
Found at i:19646612 original size:57 final size:57
Alignment explanation
Indices: 19646524--19646636 Score: 172
Period size: 57 Copynumber: 2.0 Consensus size: 57
19646514 TTAAAAAATT
* * **
19646524 ACATAACTTACATAACTCATATAACTTACATAATTTACATAACAACTTACATAACTC
1 ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACTC
* *
19646581 ACATAACTTACATAATTTACATAACTCACATAACGTACATAACAACTTACATAACT
1 ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACT
19646637 TAACTAATAC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.46, C:0.23, G:0.01, T:0.30
Consensus pattern (57 bp):
ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACTC
Found at i:19646628 original size:39 final size:36
Alignment explanation
Indices: 19646523--19646634 Score: 129
Period size: 39 Copynumber: 2.9 Consensus size: 36
19646513 CTTAAAAAAT
19646523 TACATAACTTACATAACT-CATATAACTTACATAATT
1 TACATAACTTACATAACTACATA-AACTTACATAATT
19646559 TACATAACAACTTACATAACTCACAT-AACTTACATAATT
1 TACAT---AACTTACATAACT-ACATAAACTTACATAATT
*
19646598 TACATAACTCACATAACGTACATAACAACTTACATAA
1 TACATAACTTACATAAC-TACAT-A-AACTTACATAA
19646635 CTTAACTAAT
Statistics
Matches: 66, Mismatches: 1, Indels: 15
0.80 0.01 0.18
Matches are distributed among these distances:
36 20 0.30
37 1 0.02
39 42 0.64
41 3 0.05
ACGTcount: A:0.46, C:0.22, G:0.01, T:0.30
Consensus pattern (36 bp):
TACATAACTTACATAACTACATAAACTTACATAATT
Found at i:19652218 original size:21 final size:21
Alignment explanation
Indices: 19652194--19652238 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
19652184 ACTTAGAGCT
*
19652194 GAGGCAGCAGCGCGGGAGGCG
1 GAGGCAGCAGCGAGGGAGGCG
19652215 GAGGCAGCAGCGAGGGAGGCG
1 GAGGCAGCAGCGAGGGAGGCG
19652236 GAG
1 GAG
19652239 CAGAACAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.22, C:0.20, G:0.58, T:0.00
Consensus pattern (21 bp):
GAGGCAGCAGCGAGGGAGGCG
Found at i:19652605 original size:40 final size:42
Alignment explanation
Indices: 19652527--19652650 Score: 126
Period size: 40 Copynumber: 2.9 Consensus size: 42
19652517 ACAAAACTGG
*
19652527 GCAAATTAGCGGCGTTTTTTAAAAAAAGCGCCGCTAAAAGTATT
1 GCAAATTAGCGGCGATTTTT--AAAAAGCGCCGCTAAAAGTATT
* *
19652571 GCAAATTAGCGGC-ATTTTT-AAAAGTGCCGCTAAAAGTACT
1 GCAAATTAGCGGCGATTTTTAAAAAGCGCCGCTAAAAGTATT
**** * *
19652611 GGTCTTTAGTGGCGTTTTTTAAAAAAGCGCCGCTAAAAGT
1 GCAAATTAGCGGCGATTTTT-AAAAAGCGCCGCTAAAAGT
19652651 CCTGGTCTTT
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
40 27 0.40
41 5 0.07
43 22 0.33
44 13 0.19
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (42 bp):
GCAAATTAGCGGCGATTTTTAAAAAGCGCCGCTAAAAGTATT
Found at i:19652656 original size:43 final size:43
Alignment explanation
Indices: 19652532--19652724 Score: 221
Period size: 43 Copynumber: 4.5 Consensus size: 43
19652522 ACTGGGCAAA
* ****
19652532 TTAGCGGCGTTTTTTAAAAAAAGCGCCGCTAAAAGTATTGCAAA
1 TTAGCGGCGTTTTTT-AAAAAAGCGCCGCTAAAAGTACTGGTCT
* *
19652576 TTAGCGGC-ATTTTT--AAAAGTGCCGCTAAAAGTACTGGTCT
1 TTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTACTGGTCT
* *
19652616 TTAGTGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTCCTGGTCT
1 TTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTACTGGTCT
* * ** *
19652659 TTAGCGGCGTTTATTAAAAAATCATCGCTAAAAGTCCTGGTCT
1 TTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTACTGGTCT
*
19652702 TTAGCGGCGTTTTTTAAGAAAGC
1 TTAGCGGCGTTTTTTAAAAAAGC
19652725 ATCGCGAAAG
Statistics
Matches: 127, Mismatches: 19, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
40 27 0.21
41 5 0.04
43 87 0.69
44 8 0.06
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.32
Consensus pattern (43 bp):
TTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTACTGGTCT
Found at i:19655119 original size:28 final size:28
Alignment explanation
Indices: 19655076--19655147 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 28
19655066 ATATTAAAAT
*
19655076 ATAATTTTT-ATATTTTCATGCT-TTTTA
1 ATAATTTTTAAT-TTTTCATACTATTTTA
*
19655103 AGTAATTTTTAATTTTTCATATTATTTTA
1 A-TAATTTTTAATTTTTCATACTATTTTA
19655132 ATAAATTTTTAATTTT
1 AT-AATTTTTAATTTT
19655148 AAAATTTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
27 1 0.03
28 17 0.44
29 21 0.54
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (28 bp):
ATAATTTTTAATTTTTCATACTATTTTA
Found at i:19656961 original size:22 final size:22
Alignment explanation
Indices: 19656927--19656984 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 22
19656917 ATTTTCTTGT
* *
19656927 ATTTTCTTTTTATTTTGCGACC
1 ATTTTATTATTATTTTGCGACC
* ** *
19656949 ATTTTATTATTATGTTGTTACT
1 ATTTTATTATTATTTTGCGACC
*
19656971 ATTTTATTGTTATT
1 ATTTTATTATTATT
19656985 ATTTGAATAT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.19, C:0.09, G:0.09, T:0.64
Consensus pattern (22 bp):
ATTTTATTATTATTTTGCGACC
Found at i:19657047 original size:30 final size:30
Alignment explanation
Indices: 19657013--19657075 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
19657003 ACTTATTTTA
19657013 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
* *
19657043 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
19657073 TTG
1 TTG
19657076 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:19657179 original size:18 final size:20
Alignment explanation
Indices: 19657158--19657198 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
19657148 GAAATATTTA
*
19657158 TTTTGATGT-TTTTA-ATAT
1 TTTTGATGTATTATATATAT
19657176 TTTTGATGTATTATATATAT
1 TTTTGATGTATTATATATAT
19657196 TTT
1 TTT
19657199 AAAATTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 4 0.20
20 7 0.35
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.66
Consensus pattern (20 bp):
TTTTGATGTATTATATATAT
Found at i:19662092 original size:2 final size:2
Alignment explanation
Indices: 19662085--19662115 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
19662075 ATTGGTATAA
19662085 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
19662116 TTTTCTCGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:19664368 original size:111 final size:108
Alignment explanation
Indices: 19664229--19664426 Score: 251
Period size: 111 Copynumber: 1.8 Consensus size: 108
19664219 CTGGCACCAG
* * * * *
19664229 GTAAAATTTTCGGTTCCCAAGATATTTTTTTTTACTTTAGGAA-ACTGATGGTCGGCACCAGTGT
1 GTAAAATTTTCGGTTCCCAAGATATTTTTTATTA-TTTAGGAATACTAATGGCCGACACCAATGT
19664293 ATTTAAAAAAAAAATTTGGGTGCTGACCATATAATGGGCAGCAGCAA
65 ATTT--AAAAAAAA-TTGGGTGCTGACCATATAATGGGCAGCAGCAA
*
19664340 GTAAAA-TTTCGGCTT-CCAATGCAT-TTTTTTATTATTTTGGAATACTAATGGCCGACACCAAT
1 GTAAAATTTTCGG-TTCCCAA-G-ATATTTTTTATTATTTAGGAATACTAATGGCCGACACCAAT
19664402 GTATTTAAAAAAAATTGGGTGCTGA
63 GTATTTAAAAAAAATTGGGTGCTGA
19664427 TATTGAGAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
108 11 0.14
109 8 0.10
110 17 0.22
111 39 0.51
112 2 0.03
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.34
Consensus pattern (108 bp):
GTAAAATTTTCGGTTCCCAAGATATTTTTTATTATTTAGGAATACTAATGGCCGACACCAATGTA
TTTAAAAAAAATTGGGTGCTGACCATATAATGGGCAGCAGCAA
Found at i:19664655 original size:20 final size:19
Alignment explanation
Indices: 19664602--19664659 Score: 66
Period size: 20 Copynumber: 3.1 Consensus size: 19
19664592 CTAATTAATA
* *
19664602 TGAAAAAATATGAAGTGAAT
1 TGAAAAAA-ATAAATTGAAT
19664622 TG-AAAAAA-AAATTGAAT
1 TGAAAAAAATAAATTGAAT
19664639 TGAAAAAAGATAAATTGAAT
1 TGAAAAAA-ATAAATTGAAT
19664659 T
1 T
19664660 TGTGATTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 9 0.27
18 6 0.18
19 6 0.18
20 12 0.36
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.26
Consensus pattern (19 bp):
TGAAAAAAATAAATTGAAT
Found at i:19664732 original size:20 final size:21
Alignment explanation
Indices: 19664695--19664736 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
19664685 GTATATTAGG
*
19664695 AAAAAAATAAATTTAAATGAA
1 AAAAAAATAAATTGAAATGAA
*
19664716 AAAAAAATTAA-TGAAATGAA
1 AAAAAAATAAATTGAAATGAA
19664736 A
1 A
19664737 TGTTAAATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (21 bp):
AAAAAAATAAATTGAAATGAA
Found at i:19664891 original size:19 final size:19
Alignment explanation
Indices: 19664840--19664900 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
19664830 AACTGAAATG
*
19664840 AAAAAA-AATTGAAATGCGA
1 AAAAAATAATTTAAATG-GA
* *
19664859 AATAATTAAATTTAAATGGA
1 AAAAAAT-AATTTAAATGGA
19664879 AAAAAATAATTTAAAT-GA
1 AAAAAATAATTTAAATGGA
19664897 AAAA
1 AAAA
19664901 GGAAATGTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 6 0.17
19 13 0.37
20 7 0.20
21 9 0.26
ACGTcount: A:0.64, C:0.02, G:0.10, T:0.25
Consensus pattern (19 bp):
AAAAAATAATTTAAATGGA
Found at i:19664904 original size:25 final size:24
Alignment explanation
Indices: 19664858--19664905 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
19664848 TTGAAATGCG
** *
19664858 AAATAATTAAATTTAAATGGAAAA
1 AAATAATTAAATGAAAAAGGAAAA
19664882 AAATAATTTAAATGAAAAAGGAAA
1 AAATAA-TTAAATGAAAAAGGAAA
19664906 TGTAAATGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.25
Consensus pattern (24 bp):
AAATAATTAAATGAAAAAGGAAAA
Found at i:19665294 original size:16 final size:16
Alignment explanation
Indices: 19665273--19665340 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
19665263 TTTGGTTCGC
19665273 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
19665289 TGTATTGGATTAGAGA
1 TGTATTGGATTAGAGG
*
19665305 TATATTGGATTAGAGG
1 TGTATTGGATTAGAGG
19665321 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
19665337 TGTA
1 TGTA
19665341 ATAGCAAATC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.28, C:0.00, G:0.34, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:19665597 original size:18 final size:17
Alignment explanation
Indices: 19665576--19665610 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
19665566 TTATTATTAA
*
19665576 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
19665594 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
19665611 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:19665717 original size:18 final size:17
Alignment explanation
Indices: 19665696--19665730 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
19665686 TTATTATTAA
*
19665696 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
19665714 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
19665731 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:19665772 original size:120 final size:120
Alignment explanation
Indices: 19665559--19666301 Score: 1432
Period size: 120 Copynumber: 6.2 Consensus size: 120
19665549 ATCATATTTA
19665559 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
19665624 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
19665679 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
19665744 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
19665799 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
19665864 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
19665919 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
19665984 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
19666039 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
19666104 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
19666159 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
19666224 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
19666279 AACATAATTATTATTAAATATAT
1 AACATAATTATTATTAAATATAT
19666302 AACTTGAAAA
Statistics
Matches: 619, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 619 1.00
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:19669371 original size:33 final size:33
Alignment explanation
Indices: 19669332--19669441 Score: 159
Period size: 33 Copynumber: 3.3 Consensus size: 33
19669322 ATTATAAAGC
19669332 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
* *
19669365 ATGTATAATTGACCTAAAATTAATTCTTGGTTT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
* * *
19669398 AT-TTTTATTTACCCTAAAATTAATTGTTGGTGT
1 ATGTATAATTGA-CCTAAAATTAATTGTTGGTGT
19669431 ATGTATAATTG
1 ATGTATAATTG
19669442 TTGGTGTATG
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
32 6 0.09
33 54 0.83
34 5 0.08
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.46
Consensus pattern (33 bp):
ATGTATAATTGACCTAAAATTAATTGTTGGTGT
Found at i:19669441 original size:18 final size:18
Alignment explanation
Indices: 19669418--19669459 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
19669408 ACCCTAAAAT
19669418 TAATTGTTGGTGTATGTA
1 TAATTGTTGGTGTATGTA
19669436 TAATTGTTGGTGTATGTA
1 TAATTGTTGGTGTATGTA
19669454 TAATTG
1 TAATTG
19669460 ACCTAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (18 bp):
TAATTGTTGGTGTATGTA
Found at i:19670842 original size:28 final size:28
Alignment explanation
Indices: 19670809--19670921 Score: 75
Period size: 28 Copynumber: 3.6 Consensus size: 28
19670799 TTTTTATTAT
19670809 AATATTTTATTATTTCAGTTTATTTCAC
1 AATATTTTATTATTTCAGTTTATTTCAC
* * *
19670837 AATATTTATTTTAAGTATT-AGATATATTATACATT
1 AATATTT-TATT-A-T-TTCAG-TTTATT-T-CA-C
*
19670872 AATATTTATTTTATTATTTCAGTTCATTTCAC
1 AATA--T--TTTATTATTTCAGTTTATTTCAC
19670904 AATATTTTATTATTTCAG
1 AATATTTTATTATTTCAG
19670922 CTTTTATTAT
Statistics
Matches: 65, Mismatches: 7, Indels: 26
0.66 0.07 0.27
Matches are distributed among these distances:
28 20 0.31
29 3 0.05
30 2 0.03
31 3 0.05
32 11 0.17
33 3 0.05
34 3 0.05
35 10 0.15
36 3 0.05
37 2 0.03
38 3 0.05
39 2 0.03
ACGTcount: A:0.33, C:0.08, G:0.04, T:0.55
Consensus pattern (28 bp):
AATATTTTATTATTTCAGTTTATTTCAC
Found at i:19670847 original size:32 final size:32
Alignment explanation
Indices: 19670811--19670910 Score: 105
Period size: 32 Copynumber: 3.0 Consensus size: 32
19670801 TTTATTATAA
19670811 TATTTTATTATTTCAGTTTATTTCACAATATT
1 TATTTTATTATTTCAGTTTATTTCACAATATT
* * *
19670843 TATTTTAAGTA-TT-AGATATATTATACATTAATATT
1 TATTTT-ATTATTTCAG-TTTATT-T-CA-CAATATT
*
19670878 TATTTTATTATTTCAGTTCATTTCACAATATT
1 TATTTTATTATTTCAGTTTATTTCACAATATT
19670910 T
1 T
19670911 TATTATTTCA
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
31 2 0.04
32 20 0.37
33 6 0.11
34 6 0.11
35 18 0.33
36 2 0.04
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (32 bp):
TATTTTATTATTTCAGTTTATTTCACAATATT
Found at i:19670928 original size:15 final size:15
Alignment explanation
Indices: 19670908--19670936 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
19670898 TTTCACAATA
19670908 TTTTATTATTTCAGC
1 TTTTATTATTTCAGC
19670923 TTTTATTATTTCAG
1 TTTTATTATTTCAG
19670937 TTTATTTCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.10, G:0.07, T:0.62
Consensus pattern (15 bp):
TTTTATTATTTCAGC
Found at i:19676104 original size:17 final size:17
Alignment explanation
Indices: 19676082--19676120 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
19676072 TAAACCCCAA
19676082 TTTCTCCCTTTT-CTTTC
1 TTTCT-CCTTTTCCTTTC
*
19676099 TTTCTCTTTTTCCTTTC
1 TTTCTCCTTTTCCTTTC
19676116 TTTCT
1 TTTCT
19676121 TTCTCCCCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTCTCCTTTTCCTTTC
Found at i:19683788 original size:39 final size:38
Alignment explanation
Indices: 19683728--19683929 Score: 314
Period size: 39 Copynumber: 5.2 Consensus size: 38
19683718 GCTCTGATGA
*
19683728 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTT-AGGCTTCCGTTTAGCACTTATGT
*
19683767 GCTTTAGTTAGCCTCTAGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCT-TAGGCTTCCGTTTAGCACTTATGT
*
19683806 GCTTCAGTTAGCCTTCAGGCTTCCATTTAGCACTTATGT
1 GCTTCAGTTAGCCTT-AGGCTTCCGTTTAGCACTTATGT
*
19683845 GCTTCAGTTAGCCTCTGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCT-TAGGCTTCCGTTTAGCACTTATGT
*
19683884 GCTTCAGTTAGCCTTCGAGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTAG-GCTTCCGTTTAGCACTTATGT
19683923 GCTTCAG
1 GCTTCAG
19683930 CTAGATTTCG
Statistics
Matches: 152, Mismatches: 7, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
38 3 0.02
39 147 0.97
40 2 0.01
ACGTcount: A:0.15, C:0.25, G:0.21, T:0.39
Consensus pattern (38 bp):
GCTTCAGTTAGCCTTAGGCTTCCGTTTAGCACTTATGT
Found at i:19683814 original size:78 final size:78
Alignment explanation
Indices: 19683728--19683929 Score: 359
Period size: 78 Copynumber: 2.6 Consensus size: 78
19683718 GCTCTGATGA
*
19683728 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGTGCTTTAGTTAGCCTCTAGGCTTCCGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGTGCTTCAGTTAGCCTCTAGGCTTCCGT
19683793 TTAGCACTTATGT
66 TTAGCACTTATGT
* * *
19683806 GCTTCAGTTAGCCTTCAGGCTTCCATTTAGCACTTATGTGCTTCAGTTAGCCTCTGGGCTTCCGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGTGCTTCAGTTAGCCTCTAGGCTTCCGT
19683871 TTAGCACTTATGT
66 TTAGCACTTATGT
*
19683884 GCTTCAGTTAGCCTTCGAGCTTCCGTTTAGCACTTATGTGCTTCAG
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGTGCTTCAG
19683930 CTAGATTTCG
Statistics
Matches: 117, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 117 1.00
ACGTcount: A:0.15, C:0.25, G:0.21, T:0.39
Consensus pattern (78 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGTGCTTCAGTTAGCCTCTAGGCTTCCGT
TTAGCACTTATGT
Found at i:19683944 original size:117 final size:117
Alignment explanation
Indices: 19683728--19683945 Score: 350
Period size: 117 Copynumber: 1.9 Consensus size: 117
19683718 GCTCTGATGA
* *
19683728 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGTGCTTTAGTTAGCCTCTAGGCTTCCGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGTGCTTCAGTTAGCCTCGAGGCTTCCGT
* *
19683793 TTAGCACTTATGTGCTTCAGTTAGCCTTCAGGCTTCCATTTAGCACTTATGT
66 TTAGCACTTATGTGCTTCAGCTAGACTTCAGGCTTCCATTTAGCACTTATGT
19683845 GCTTCAGTTAGCC-TCTGGGCTTCCGTTTAGCACTTATGTGCTTCAGTTAGCCTTCGA-GCTTCC
1 GCTTCAGTTAGCCTTC-GGGCTTCCGTTTAGCACTTATGTGCTTCAGTTAGCC-TCGAGGCTTCC
* *
19683908 GTTTAGCACTTATGTGCTTCAGCTAGATTTCGGGCTTC
64 GTTTAGCACTTATGTGCTTCAGCTAGACTTCAGGCTTC
19683946 AGATCACGAT
Statistics
Matches: 93, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
116 2 0.02
117 88 0.95
118 3 0.03
ACGTcount: A:0.15, C:0.25, G:0.22, T:0.39
Consensus pattern (117 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGTGCTTCAGTTAGCCTCGAGGCTTCCGT
TTAGCACTTATGTGCTTCAGCTAGACTTCAGGCTTCCATTTAGCACTTATGT
Found at i:19686978 original size:12 final size:11
Alignment explanation
Indices: 19686961--19687000 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
19686951 GAAAAGCAGG
19686961 GAAAGAAAGAAA
1 GAAAGAAAG-AA
*
19686973 GAAAGAAAGGA
1 GAAAGAAAGAA
19686984 GAAAAGAAAGAA
1 G-AAAGAAAGAA
19686996 GAAAG
1 GAAAG
19687001 GGAAAATTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 6 0.24
12 19 0.76
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (11 bp):
GAAAGAAAGAA
Found at i:19686991 original size:20 final size:18
Alignment explanation
Indices: 19686966--19687006 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
19686956 GCAGGGAAAG
19686966 AAAGAAAGAAAGAAAGGAGA
1 AAAGAAAG-AAGAAAGG-GA
19686986 AAAGAAAGAAGAAAGGGA
1 AAAGAAAGAAGAAAGGGA
19687004 AAA
1 AAA
19687007 TTGAATGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 5 0.24
19 8 0.38
20 8 0.38
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (18 bp):
AAAGAAAGAAGAAAGGGA
Found at i:19688409 original size:7 final size:7
Alignment explanation
Indices: 19688397--19688421 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
19688387 ATGAATTAAT
19688397 TGAAAAG
1 TGAAAAG
19688404 TGAAAAG
1 TGAAAAG
19688411 TGAAAAG
1 TGAAAAG
19688418 TGAA
1 TGAA
19688422 TTAAATACCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.28, T:0.16
Consensus pattern (7 bp):
TGAAAAG
Found at i:19688670 original size:53 final size:53
Alignment explanation
Indices: 19688604--19688724 Score: 206
Period size: 53 Copynumber: 2.3 Consensus size: 53
19688594 TACTGTTACC
*
19688604 GTTACTGTTACTGTTTCAGATTTGTTCCGATGAGGTACTCTGTGTACCGTAAT
1 GTTACTGTTACTGTTTCAGATCTGTTCCGATGAGGTACTCTGTGTACCGTAAT
* *
19688657 GTTACTGTTACTGTTTCGGATCTGTTCCGATGAGGTACTCTGTGTACCGTATT
1 GTTACTGTTACTGTTTCAGATCTGTTCCGATGAGGTACTCTGTGTACCGTAAT
*
19688710 GCTACTGTTACTGTT
1 GTTACTGTTACTGTT
19688725 ACTGTTCCGG
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 64 1.00
ACGTcount: A:0.17, C:0.18, G:0.23, T:0.42
Consensus pattern (53 bp):
GTTACTGTTACTGTTTCAGATCTGTTCCGATGAGGTACTCTGTGTACCGTAAT
Found at i:19688893 original size:18 final size:18
Alignment explanation
Indices: 19688852--19688886 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
19688842 GATTATTTCT
19688852 GAATAAATGACTGTTACC
1 GAATAAATGACTGTTACC
*
19688870 GAATAATTGACTGTTAC
1 GAATAAATGACTGTTAC
19688887 TGGATAACCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.31
Consensus pattern (18 bp):
GAATAAATGACTGTTACC
Found at i:19688953 original size:18 final size:18
Alignment explanation
Indices: 19688932--19688972 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
19688922 GGTTATTATT
* *
19688932 GAATAATTGATTGTTACC
1 GAATAACTGACTGTTACC
*
19688950 GAATAACTGACTGTTACT
1 GAATAACTGACTGTTACC
19688968 GAATA
1 GAATA
19688973 GATAATTGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (18 bp):
GAATAACTGACTGTTACC
Found at i:19691022 original size:21 final size:21
Alignment explanation
Indices: 19690981--19691022 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
19690971 CACTACAATA
* *
19690981 TTTCCTATCACTTCCTTTTAT
1 TTTCCTATCACTTCATATTAT
19691002 TTTCCT-TCACTATCATATTAT
1 TTTCCTATCACT-TCATATTAT
19691023 GAACATAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.19, C:0.26, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTCCTATCACTTCATATTAT
Found at i:19692798 original size:17 final size:17
Alignment explanation
Indices: 19692776--19692814 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
19692766 TAAACCCCAA
19692776 TTTCTCCCTTTT-CTTTC
1 TTTCT-CCTTTTCCTTTC
*
19692793 TTTCTCTTTTTCCTTTC
1 TTTCTCCTTTTCCTTTC
19692810 TTTCT
1 TTTCT
19692815 TTCTCCCCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTCTCCTTTTCCTTTC
Found at i:19695574 original size:21 final size:21
Alignment explanation
Indices: 19695542--19695605 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
19695532 ATTATATTAT
* *
19695542 AATAAAACAAAATAAATAAAG
1 AATAAAACAAAAGAAAGAAAG
19695563 AATAAATA-AAAAGAAAGAAAG
1 AATAAA-ACAAAAGAAAGAAAG
19695584 -ATAGAAACGAAACAGAAAGAAA
1 AATA-AAAC-AAA-AGAAAGAAA
19695606 AAGAAAGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
20 4 0.11
21 19 0.53
22 4 0.11
23 9 0.25
ACGTcount: A:0.73, C:0.05, G:0.12, T:0.09
Consensus pattern (21 bp):
AATAAAACAAAAGAAAGAAAG
Found at i:19695579 original size:4 final size:4
Alignment explanation
Indices: 19695572--19695640 Score: 63
Period size: 4 Copynumber: 17.0 Consensus size: 4
19695562 GAATAAATAA
*
19695572 AAAG AAAG AAAG ATAG AAACG AAACAG AAAG -AA- AAAG AAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAA-G -AA-AG AAAG AAAG AAAG AAAG AAAG AAAG
*
19695621 AAAAG AAA- AAGG AAAG AAAG
1 -AAAG AAAG AAAG AAAG AAAG
19695641 GAAGGAGAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
3 6 0.11
4 37 0.69
5 7 0.13
6 3 0.06
7 1 0.02
ACGTcount: A:0.72, C:0.03, G:0.23, T:0.01
Consensus pattern (4 bp):
AAAG
Found at i:19695612 original size:33 final size:34
Alignment explanation
Indices: 19695570--19695639 Score: 106
Period size: 33 Copynumber: 2.1 Consensus size: 34
19695560 AAGAATAAAT
* * *
19695570 AAAAAGAAAGAAAGATAGAAACGAAACA-GAAAG
1 AAAAAGAAAGAAAGAAAGAAAAGAAAAAGGAAAG
19695603 AAAAAGAAAGAAAGAAAGAAAAGAAAAAGGAAAG
1 AAAAAGAAAGAAAGAAAGAAAAGAAAAAGGAAAG
19695637 AAA
1 AAA
19695640 GGAAGGAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 25 0.76
34 8 0.24
ACGTcount: A:0.74, C:0.03, G:0.21, T:0.01
Consensus pattern (34 bp):
AAAAAGAAAGAAAGAAAGAAAAGAAAAAGGAAAG
Found at i:19695631 original size:29 final size:28
Alignment explanation
Indices: 19695559--19695640 Score: 87
Period size: 29 Copynumber: 2.9 Consensus size: 28
19695549 CAAAATAAAT
* *
19695559 AAAGAATAAATAAAAAGAAAGAAAGATAG
1 AAAGAA-AAAGAAAAAGAAAGAAAGAAAG
*
19695588 AAACGAAACAGAAAGAA-AAAGAAAGAAAG
1 AAA-GAAAAAGAAA-AAGAAAGAAAGAAAG
19695617 AAAG-AAAAGAAAAAGGAAAGAAAG
1 AAAGAAAAAGAAAAA-GAAAGAAAG
19695641 GAAGGAGAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
26 2 0.04
27 7 0.16
28 9 0.20
29 22 0.49
30 5 0.11
ACGTcount: A:0.73, C:0.02, G:0.21, T:0.04
Consensus pattern (28 bp):
AAAGAAAAAGAAAAAGAAAGAAAGAAAG
Found at i:19695651 original size:20 final size:20
Alignment explanation
Indices: 19695572--19695651 Score: 74
Period size: 20 Copynumber: 4.0 Consensus size: 20
19695562 GAATAAATAA
* *
19695572 AAAGAAAGAAAGATAGAAACGA
1 AAAGAAAGAAA-AGAGAAA-GG
19695594 AACAGAAAGAAAA-AGAAA-G
1 AA-AGAAAGAAAAGAGAAAGG
*
19695613 AAAGAAAGAAAAGAAAAAGG
1 AAAGAAAGAAAAGAGAAAGG
* *
19695633 AAAGAAAGGAAGGAGAAAG
1 AAAGAAAGAAAAGAGAAAG
19695652 CCACTGCCTT
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
18 10 0.20
19 6 0.12
20 17 0.34
21 5 0.10
22 3 0.06
23 9 0.18
ACGTcount: A:0.70, C:0.03, G:0.26, T:0.01
Consensus pattern (20 bp):
AAAGAAAGAAAAGAGAAAGG
Found at i:19696817 original size:23 final size:25
Alignment explanation
Indices: 19696791--19696837 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
19696781 TATCATTCAT
*
19696791 TTCATTATAT-CA-ATATTTTATGC
1 TTCATCATATCCATATATTTTATGC
*
19696814 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
19696838 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGC
Found at i:19697149 original size:46 final size:47
Alignment explanation
Indices: 19697098--19697400 Score: 301
Period size: 46 Copynumber: 6.9 Consensus size: 47
19697088 TTTGACGTGA
* * * * *
19697098 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TTTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCACGT
* *
19697144 TGCCATGGTATCTTTCAACCATGGTCTTATTC-TTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCACGT
* * *
19697190 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCACGT
* *
19697236 TGCCATGGTATCTTTCAACCATGGT-TT--T-A----CACA-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCACGT
* *
19697274 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCACGT
*
19697320 TGCCATGGTATCTTTCAACCATGGTCTTA--CA----C--A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCACGT
*
19697358 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCA
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCA
19697401 GAGAGCACAC
Statistics
Matches: 224, Mismatches: 15, Indels: 36
0.81 0.05 0.13
Matches are distributed among these distances:
38 64 0.29
39 6 0.03
40 2 0.01
41 1 0.00
42 2 0.01
43 1 0.00
44 2 0.01
45 11 0.05
46 135 0.60
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.38
Consensus pattern (47 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCACGT
Found at i:19697282 original size:38 final size:38
Alignment explanation
Indices: 19697231--19697390 Score: 239
Period size: 38 Copynumber: 4.0 Consensus size: 38
19697221 CATCTCATAT
*
19697231 CAGGTTGCCATGGTATCTTTCAACCATGGTTTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
19697269 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--A
19697314 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 -CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
19697353 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
19697391 TTTCATATCA
Statistics
Matches: 113, Mismatches: 1, Indels: 16
0.87 0.01 0.12
Matches are distributed among these distances:
38 70 0.62
39 1 0.01
40 3 0.03
41 1 0.01
43 1 0.01
44 3 0.03
45 1 0.01
46 33 0.29
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (38 bp):
CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
Found at i:19697329 original size:84 final size:84
Alignment explanation
Indices: 19697188--19697401 Score: 410
Period size: 84 Copynumber: 2.5 Consensus size: 84
19697178 TTCATGTCAC
*
19697188 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGTTGCCATGGTATCTTTCA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCA
*
19697253 ACCATGGTTTTACACACAG
66 ACCATGGTCTTACACACAG
19697272 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCA
19697337 ACCATGGTCTTACACACAG
66 ACCATGGTCTTACACACAG
19697356 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
19697402 AGAGCACACT
Statistics
Matches: 128, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 128 1.00
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (84 bp):
GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCA
ACCATGGTCTTACACACAG
Found at i:19697339 original size:130 final size:122
Alignment explanation
Indices: 19697142--19697390 Score: 372
Period size: 130 Copynumber: 2.0 Consensus size: 122
19697132 TTTCTTTCAT
** * *
19697142 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGTTGCCATGGTATCTTTCA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATGGTATCTTTCA
*
19697207 ACCATGGTCTTACACATCTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTTTTACACACAG
66 ACCATGGTCTT--ACA---C--A-CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACACAG
*
19697272 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATGGTATCTTTCA
19697337 ACCATGGTCTTACACACAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
66 ACCATGGTCTTACACACAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
19697391 TTTCATATCA
Statistics
Matches: 113, Mismatches: 6, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
122 37 0.33
123 1 0.01
125 1 0.01
128 3 0.03
130 71 0.63
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.36
Consensus pattern (122 bp):
GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATGGTATCTTTCA
ACCATGGTCTTACACACAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACACAG
Found at i:19710237 original size:23 final size:25
Alignment explanation
Indices: 19710211--19710257 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
19710201 TATCATTCAT
*
19710211 TTCATTATAT-CA-ATATTTTATGC
1 TTCATCATATCCATATATTTTATGC
*
19710234 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
19710258 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGC
Found at i:19710569 original size:46 final size:47
Alignment explanation
Indices: 19710518--19710766 Score: 218
Period size: 46 Copynumber: 5.8 Consensus size: 47
19710508 TTTGACGTGA
* * * * *
19710518 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TTTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCACGT
* *
19710564 TGCCATGGTATCTTTCAACCATGGTCTTATTC-TTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCACGT
* * *
19710610 TGCCATGGT-TCTTTCAACCATGGTCTTACACA-TCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCACGT
*
19710655 TGCCATGGTATCTTTCAACCATGGTCTTA--CA----C--A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCACGT
* *
19710693 TGCCATGGTATCTTTCAACCATGGT-TT--T-A----CACA-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCACGT
*
19710731 TGCCATGGTATCTTTCAACCATGGTCTTACACATTT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTT
19710767 CATTTCAGAA
Statistics
Matches: 178, Mismatches: 12, Indels: 27
0.82 0.06 0.12
Matches are distributed among these distances:
36 2 0.01
37 2 0.01
38 61 0.34
39 3 0.02
41 1 0.01
42 1 0.01
44 2 0.01
45 44 0.25
46 62 0.35
ACGTcount: A:0.21, C:0.24, G:0.16, T:0.39
Consensus pattern (47 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCACGT
Found at i:19710701 original size:38 final size:38
Alignment explanation
Indices: 19710650--19710763 Score: 219
Period size: 38 Copynumber: 3.0 Consensus size: 38
19710640 CATCTCATAT
19710650 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
*
19710688 CAGGTTGCCATGGTATCTTTCAACCATGGTTTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
19710726 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
19710764 TTTCATTTCA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 74 1.00
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.32
Consensus pattern (38 bp):
CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
Found at i:19712511 original size:11 final size:11
Alignment explanation
Indices: 19712495--19712542 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
19712485 CTTTATATAC
19712495 TAATAAAATAA
1 TAATAAAATAA
*
19712506 TAATAAAATATCT
1 TAATAAAATA--A
* *
19712519 TATTAAAATAT
1 TAATAAAATAA
19712530 TAATAAAATAA
1 TAATAAAATAA
19712541 TA
1 TA
19712543 TTTATCTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 22 0.71
13 9 0.29
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:19716139 original size:39 final size:39
Alignment explanation
Indices: 19716049--19716344 Score: 486
Period size: 39 Copynumber: 7.5 Consensus size: 39
19716039 ACAAAGCATG
* * *
19716049 CGGGACTTTAAGCCCGGATATAATACCAGCAC-AAAGCCTG
1 CGGGAC-TT-AGCCCGGATATAACACCAGCACGAATGCCTT
* *
19716089 CGGGACTTTAGCCCGGATATAACACCACCACGAATGCCTG
1 CGGGAC-TTAGCCCGGATATAACACCAGCACGAATGCCTT
19716129 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
19716168 CGGGACTTAGTCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
19716207 CGGGACTTAGCCCGGATATAATACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
19716246 CGGGACTTAGCCCGGATATAACACCAGCACGAATACCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
19716285 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
19716324 CGGGACTTAGCCCGGATATAA
1 CGGGACTTAGCCCGGATATAA
19716345 TTCTCCATTA
Statistics
Matches: 244, Mismatches: 11, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
39 222 0.91
40 22 0.09
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.19
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
Found at i:19718040 original size:86 final size:85
Alignment explanation
Indices: 19717895--19718074 Score: 344
Period size: 86 Copynumber: 2.1 Consensus size: 85
19717885 ATATATATAT
19717895 AATACATATATTTATCTCAAGCAATCAACATGGTCGGCCACTAATTTGGAAATGGCAAAATTGAC
1 AATACATATATTTATCTCAAGCAATCAACATGGTCGGCCACTAATTTGGAAATGGCAAAATTGAC
19717960 ATGCAAATCCATATCTATTAA
66 ATGCAAATCCATATCTATT-A
19717981 AATACATATATTTATCTCAAGCAATCAACATGGTCGGCCACTAATTTGGAAATGGCAAAATTGAC
1 AATACATATATTTATCTCAAGCAATCAACATGGTCGGCCACTAATTTGGAAATGGCAAAATTGAC
19718046 ATGCAAATCCATATCTATTA
66 ATGCAAATCCATATCTATTA
19718066 AAT-CATATA
1 AATACATATA
19718075 ATGTTTGGCC
Statistics
Matches: 94, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
84 6 0.06
85 4 0.04
86 84 0.89
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.29
Consensus pattern (85 bp):
AATACATATATTTATCTCAAGCAATCAACATGGTCGGCCACTAATTTGGAAATGGCAAAATTGAC
ATGCAAATCCATATCTATTA
Found at i:19718372 original size:6 final size:6
Alignment explanation
Indices: 19718361--19718405 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
19718351 AGTCCATCTA
* *
19718361 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT CTTTAT TTTCAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
19718406 GTCTTTCTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTAT
Found at i:19718410 original size:17 final size:16
Alignment explanation
Indices: 19718359--19718420 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 16
19718349 TGAGTCCATC
*
19718359 TATTTTATTTTTATTTT
1 TATTTTA-TTTTATCTT
19718376 TATTTTTATTTTTATCTT
1 TA-TTTTA-TTTTATCTT
*
19718394 TATTTTCATTTTGTCTT
1 TATTTT-ATTTTATCTT
*
19718411 TCTTTTATTT
1 TATTTTATTT
19718421 ATTTTTGAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
16 4 0.10
17 19 0.47
18 17 0.43
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (16 bp):
TATTTTATTTTATCTT
Found at i:19728927 original size:53 final size:53
Alignment explanation
Indices: 19728786--19728951 Score: 203
Period size: 53 Copynumber: 3.1 Consensus size: 53
19728776 GACGAAAAAT
* * **
19728786 ATGTGATAAGTGTG-C-CCGTTTAAGACCATAGATGGGCTATGGCATCGGTGCA
1 ATGTGATAA-TGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
19728838 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
1 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
* * * *
19728891 ATGTGATAATGTGATTTCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGA
1 ATGTGATAATGTGACTCCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A
19728945 TATGTGA
1 -ATGTGA
19728952 ACCGTGTAAG
Statistics
Matches: 101, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
51 4 0.04
52 11 0.11
53 79 0.78
54 1 0.01
55 6 0.06
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (53 bp):
ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
Found at i:19735111 original size:32 final size:32
Alignment explanation
Indices: 19735070--19735134 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
19735060 CAAAAAAATG
19735070 TAAGACATTTAAGTTCATATATTTGTTGTGCT
1 TAAGACATTTAAGTTCATATATTTGTTGTGCT
19735102 TAAGACATTTAAGTTCATATATTTGTTGTGCT
1 TAAGACATTTAAGTTCATATATTTGTTGTGCT
19735134 T
1 T
19735135 TCGGCAGCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.28, C:0.09, G:0.15, T:0.48
Consensus pattern (32 bp):
TAAGACATTTAAGTTCATATATTTGTTGTGCT
Found at i:19741310 original size:30 final size:30
Alignment explanation
Indices: 19741266--19741324 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
19741256 AACTTTTTAT
19741266 TTTCCCCCAAAATTTTTACTT-CTTCCCAC
1 TTTCCCCCAAAATTTTTACTTCCTTCCCAC
19741295 TTTCCCCCTAAAATTTTTACTTCCTTCCCA
1 TTTCCCCC-AAAATTTTTACTTCCTTCCCA
19741325 TCCCACCTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 8 0.29
30 13 0.46
31 7 0.25
ACGTcount: A:0.20, C:0.37, G:0.00, T:0.42
Consensus pattern (30 bp):
TTTCCCCCAAAATTTTTACTTCCTTCCCAC
Found at i:19745155 original size:13 final size:13
Alignment explanation
Indices: 19745137--19745168 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
19745127 GTGATTTGGT
19745137 GCCACACGGCCTG
1 GCCACACGGCCTG
*
19745150 GCCACACGGCTTG
1 GCCACACGGCCTG
19745163 GCCACA
1 GCCACA
19745169 TGATTATGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.19, C:0.44, G:0.28, T:0.09
Consensus pattern (13 bp):
GCCACACGGCCTG
Found at i:19747199 original size:23 final size:23
Alignment explanation
Indices: 19747146--19747200 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
19747136 ATGCATACAT
19747146 ACATATATCACTCATACTCATATC
1 ACATATAT-ACTCATACTCATATC
*
19747170 ACA-ATATACTTCATTCTCATA-C
1 ACATATATAC-TCATACTCATATC
*
19747192 CCATATATA
1 ACATATATA
19747201 AGTTGGTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 5 0.19
23 19 0.70
24 3 0.11
ACGTcount: A:0.38, C:0.27, G:0.00, T:0.35
Consensus pattern (23 bp):
ACATATATACTCATACTCATATC
Found at i:19747745 original size:21 final size:21
Alignment explanation
Indices: 19747672--19747785 Score: 108
Period size: 21 Copynumber: 5.5 Consensus size: 21
19747662 CCTCCCAATT
*
19747672 GAGC-GAACAGAAGCTTG-AA
1 GAGCTGAACAGAAGCTCGTAA
* *
19747691 -AGCTAAATAGAAGCTCGTAAA
1 GAGCTGAACAGAAGCTCGT-AA
* * *
19747712 GAGCTAAACAGAAACTCATAA
1 GAGCTGAACAGAAGCTCGTAA
* * *
19747733 GAGTTGAATAGAAGCTTGTAA
1 GAGCTGAACAGAAGCTCGTAA
19747754 GAGCTGAACAGAAGCTCGTAA
1 GAGCTGAACAGAAGCTCGTAA
*
19747775 GAGCTAAACAG
1 GAGCTGAACAG
19747786 CAAGTAAAAC
Statistics
Matches: 75, Mismatches: 16, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
18 3 0.04
19 10 0.13
21 47 0.63
22 15 0.20
ACGTcount: A:0.44, C:0.15, G:0.25, T:0.17
Consensus pattern (21 bp):
GAGCTGAACAGAAGCTCGTAA
Found at i:19747764 original size:42 final size:43
Alignment explanation
Indices: 19747696--19747777 Score: 121
Period size: 42 Copynumber: 1.9 Consensus size: 43
19747686 TTGAAAGCTA
19747696 AATAGAAGCTCGTAAAGAGCTAAACAGAAACTCATAAGAGTTG
1 AATAGAAGCTCGTAAAGAGCTAAACAGAAACTCATAAGAGTTG
* * * *
19747739 AATAGAAGCTTGT-AAGAGCTGAACAGAAGCTCGTAAGAG
1 AATAGAAGCTCGTAAAGAGCTAAACAGAAACTCATAAGAG
19747778 CTAAACAGCA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
42 23 0.66
43 12 0.34
ACGTcount: A:0.44, C:0.13, G:0.24, T:0.18
Consensus pattern (43 bp):
AATAGAAGCTCGTAAAGAGCTAAACAGAAACTCATAAGAGTTG
Found at i:19750190 original size:17 final size:17
Alignment explanation
Indices: 19750168--19750209 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
19750158 ACTGGAATAA
19750168 AATGTGTCGATTTAGCC
1 AATGTGTCGATTTAGCC
19750185 AATGTGTCGATTTAGCC
1 AATGTGTCGATTTAGCC
*
19750202 AATCTGTC
1 AATGTGTC
19750210 AACAATCACC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (17 bp):
AATGTGTCGATTTAGCC
Done.