Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 179 of 313
Found at i:55576663 original size:102 final size:101
Alignment explanation
Indices: 55576497--55576694 Score: 276
Period size: 102 Copynumber: 2.0 Consensus size: 101
55576487 AAAACTGTCG
* * *
55576497 CTAATGCTTGACTTTTGCGGCGTTTTTTGTAAAGCACCACTAATGTCTCTAAAGCTCAACAAAAA
1 CTAATGCTTGAATTTTGCGGCGTTTTTTGAAAAGCACCACTAATGTCTCTAAAACTCAACAAAAA
*
55576562 AACGAAT-CCGTTTGCTTAAAATTTTTTGCGGCGCTTC
66 AACG-ATGCCGTTTGCTTAAAA-ATTTTGCGGCGCTTC
*
55576599 CTAATGCTTGAATTTTGCGGCGTTTTTAT-AAAAG-AGCCACTAATGTGTCTAAAACTCAACAAA
1 CTAATGCTTGAATTTTGCGGCGTTTTT-TGAAAAGCA-CCACTAATGTCTCTAAAACTCAACAAA
* *
55576662 AAAACGTTGTCGTTTGCTTAAAAATTTTGCGGC
64 AAAACGATGCCGTTTGCTTAAAAATTTTGCGGC
55576695 TCTATTGTGA
Statistics
Matches: 86, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
101 11 0.13
102 74 0.86
103 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (101 bp):
CTAATGCTTGAATTTTGCGGCGTTTTTTGAAAAGCACCACTAATGTCTCTAAAACTCAACAAAAA
AACGATGCCGTTTGCTTAAAAATTTTGCGGCGCTTC
Found at i:55576836 original size:111 final size:110
Alignment explanation
Indices: 55576599--55576916 Score: 363
Period size: 111 Copynumber: 2.8 Consensus size: 110
55576589 GCGGCGCTTC
* * * * *
55576599 CTAATGCTTGAATTTTGCGGCGTTTTT-ATAAAAGAGCCACTAATGTGTCTAAAACTCAACAA-A
1 CTAATGCTTGACTTTTGCGGCGTTTTTCA-GAAAGCGCCACTAATGTCTCTAAAGCT-AA-AAGA
* * * * *
55576662 AAAACGTTGTCGTTTGCTTAAAAATTTTGCGGCTCTATTGTGAAAGCACTG
63 ACAAC---GTCGTTTGCTTAAAACTTTTGCGGCACTATTGAGAAAGCACCG
* *
55576713 CTAATTCTTGACTTTTGCAGCGTTTTTCAGAAAGCGCCACTAATGTCTCTAAAGCTGAAAAGAAC
1 CTAATGCTTGACTTTTGCGGCGTTTTTCAGAAAGCGCCACTAATGTCTCTAAAGCT-AAAAGAAC
* *
55576778 AACGTCGTTTGCTTAAAACTTTTGTGGCACTTTTGAGAAAGCACCG
65 AACGTCGTTTGCTTAAAACTTTTGCGGCACTATTGAGAAAGCACCG
* * *
55576824 CTAATGCTTGACTTTTGCGGCG-TTTCCTGATAAGCGCCACTAATTTCTCTAAAGCTAAAAGAAA
1 CTAATGCTTGACTTTTGCGGCGTTTTTCAGA-AAGCGCCACTAATGTCTCTAAAGCTAAAAG--A
*
55576888 ACAACGTCGTTTGCTTAAGACTTTTGCGG
63 ACAACGTCGTTTGCTTAAAACTTTTGCGG
55576917 TGCTCTTGAC
Statistics
Matches: 177, Mismatches: 22, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
110 11 0.06
111 81 0.46
112 28 0.16
113 2 0.01
114 54 0.31
115 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Consensus pattern (110 bp):
CTAATGCTTGACTTTTGCGGCGTTTTTCAGAAAGCGCCACTAATGTCTCTAAAGCTAAAAGAACA
ACGTCGTTTGCTTAAAACTTTTGCGGCACTATTGAGAAAGCACCG
Found at i:55587520 original size:33 final size:31
Alignment explanation
Indices: 55587483--55587558 Score: 77
Period size: 31 Copynumber: 2.4 Consensus size: 31
55587473 ATATTTAAAA
55587483 ATTTTAAAAATA-AAAAAT-TCAAACAAATATAT
1 ATTTTAAAAATATAAAAATGTC--A-AAATATAT
* *
55587515 CATTTT-CAAATATTAAAATGTCAAAATATAT
1 -ATTTTAAAAATATAAAAATGTCAAAATATAT
55587546 ATTTTAAAAATAT
1 ATTTTAAAAATAT
55587559 TTAAAATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
30 5 0.14
31 14 0.38
32 6 0.16
33 10 0.27
34 2 0.05
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.37
Consensus pattern (31 bp):
ATTTTAAAAATATAAAAATGTCAAAATATAT
Found at i:55587613 original size:19 final size:19
Alignment explanation
Indices: 55587546--55587619 Score: 59
Period size: 19 Copynumber: 3.9 Consensus size: 19
55587536 CAAAATATAT
*
55587546 ATTTTAAAAATATT-TAAA-
1 ATTTTAAAAA-ATTAAAAAC
*
55587564 ATTTTCAACAAAA-TAAATA-
1 ATTTT-AA-AAAATTAAAAAC
55587583 ATTTTAAAAAATTATAAAAC
1 ATTTTAAAAAATTA-AAAAC
55587603 ATTTT-AAAAATTAAAAA
1 ATTTTAAAAAATTAAAAA
55587620 TTAAAAATTA
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
17 4 0.09
18 14 0.30
19 21 0.45
20 8 0.17
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.36
Consensus pattern (19 bp):
ATTTTAAAAAATTAAAAAC
Found at i:55587625 original size:6 final size:7
Alignment explanation
Indices: 55587606--55587633 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
55587596 ATAAAACATT
55587606 TTAAAAA
1 TTAAAAA
55587613 TTAAAAA
1 TTAAAAA
55587620 TTAAAAA
1 TTAAAAA
55587627 TTAAAAA
1 TTAAAAA
55587634 AATAAATATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
TTAAAAA
Found at i:55588213 original size:67 final size:67
Alignment explanation
Indices: 55588135--55588275 Score: 239
Period size: 67 Copynumber: 2.1 Consensus size: 67
55588125 GGAGCAAAAG
* *
55588135 ATTTTTTCAATTTTTTGTCTTTCAGAGTTTAAAAA-ATTTAATTTTAATATTTTCAAAAACTAAA
1 ATTTTTTCAATTTTTTATCTTTCAGAGTTTAAAAATA-TTAATTTTAACATTTTCAAAAACTAAA
55588199 ATT
65 ATT
*
55588202 ATTTTTTCAATTTTTTATCTTTCAGAGTTTAAAAATATTAATTTTAACATTTTCAAAAATTAAAA
1 ATTTTTTCAATTTTTTATCTTTCAGAGTTTAAAAATATTAATTTTAACATTTTCAAAAACTAAAA
55588267 TT
66 TT
55588269 ATTTTTT
1 ATTTTTT
55588276 AAAATCTGAA
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
67 69 0.99
68 1 0.01
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (67 bp):
ATTTTTTCAATTTTTTATCTTTCAGAGTTTAAAAATATTAATTTTAACATTTTCAAAAACTAAAA
TT
Found at i:55591435 original size:184 final size:185
Alignment explanation
Indices: 55591123--55591497 Score: 725
Period size: 184 Copynumber: 2.0 Consensus size: 185
55591113 CAGTAGCAAT
55591123 ATTCCACAGAATGGTTTTGGAGATAGTTTTGAAAATCTACAAAAGAAAGGTTGCCAAAGTTAAAA
1 ATTCCACAGAATGGTTTTGGAGATAGTTTTGAAAATCTACAAAAGAAAGGTTGCCAAAGTT-AAA
55591188 AATCTCAGTTCATCTCCTTCAATTAAGGAACTAACAATCTTTTCTAACATCAACCAGATTGAACT
65 AATCTCAGTTCATCTCCTTCAATTAAGGAACTAACAATCTTTTCTAACATCAACCAGATTGAACT
55591253 GTATCTCCTACTTATTTGCTACAAATTTCTTACCCTAACTACTCCAAGATTTCAAG
130 GTATCTCCTACTTATTTGCTACAAATTTCTTACCCTAACTACTCCAAGATTTCAAG
55591309 ATTCCACAGAATGGTTTTGGAGATAGTTTTGAAAATCTACAAAAGAAAGGTTGCCAAAGTT-AAA
1 ATTCCACAGAATGGTTTTGGAGATAGTTTTGAAAATCTACAAAAGAAAGGTTGCCAAAGTTAAAA
*
55591373 ATCTCAGTTCATCTCCTTCAATTAAGGAGCTAACAATCTTTTCTAACATCAACCAGATTGAACTG
66 ATCTCAGTTCATCTCCTTCAATTAAGGAACTAACAATCTTTTCTAACATCAACCAGATTGAACTG
55591438 TATCTCCTACTTATTTGCTACAAATTTCTTACCCTAACTACTCCAAGATTTCAAG
131 TATCTCCTACTTATTTGCTACAAATTTCTTACCCTAACTACTCCAAGATTTCAAG
55591493 ATTCC
1 ATTCC
55591498 TTTTTTTCCC
Statistics
Matches: 188, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
184 127 0.68
186 61 0.32
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (185 bp):
ATTCCACAGAATGGTTTTGGAGATAGTTTTGAAAATCTACAAAAGAAAGGTTGCCAAAGTTAAAA
ATCTCAGTTCATCTCCTTCAATTAAGGAACTAACAATCTTTTCTAACATCAACCAGATTGAACTG
TATCTCCTACTTATTTGCTACAAATTTCTTACCCTAACTACTCCAAGATTTCAAG
Found at i:55599765 original size:14 final size:13
Alignment explanation
Indices: 55599746--55599807 Score: 61
Period size: 14 Copynumber: 4.5 Consensus size: 13
55599736 AGCTCGTTTG
*
55599746 TTTATTTCTCGTTA
1 TTTATTTCT-TTTA
*
55599760 TTTATTTCTTTTT
1 TTTATTTCTTTTA
*
55599773 TTTATTTGCTTTTT
1 TTTATTT-CTTTTA
*
55599787 TTTATTTCTCTTAA
1 TTTATTTCT-TTTA
55599801 TTTATTT
1 TTTATTT
55599808 TATGGTTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.26
14 31 0.74
ACGTcount: A:0.13, C:0.10, G:0.03, T:0.74
Consensus pattern (13 bp):
TTTATTTCTTTTA
Found at i:55601276 original size:23 final size:23
Alignment explanation
Indices: 55601250--55601296 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
55601240 ACATACTTAG
55601250 TTACCTTTGAATATTAACCATTC
1 TTACCTTTGAATATTAACCATTC
55601273 TTACCTTTGAATATTAACCATTC
1 TTACCTTTGAATATTAACCATTC
55601296 T
1 T
55601297 ATAATGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.21, G:0.04, T:0.45
Consensus pattern (23 bp):
TTACCTTTGAATATTAACCATTC
Found at i:55603891 original size:19 final size:18
Alignment explanation
Indices: 55603869--55603916 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
55603859 TTCTAATATT
55603869 TTTTAATTATTTTAGTAAA
1 TTTTAATT-TTTTAGTAAA
* * *
55603888 TTTTTATTTTTTTGTAAT
1 TTTTAATTTTTTAGTAAA
55603906 TTTGTAATTTT
1 TTT-TAATTTT
55603917 ATACTCTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
TTTTAATTTTTTAGTAAA
Found at i:55604000 original size:26 final size:25
Alignment explanation
Indices: 55603966--55604016 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
55603956 TTTAAATAAC
*
55603966 TTTTTTGTAATTATATTTATTGTAAA
1 TTTTGTGTAATT-TATTTATTGTAAA
* *
55603992 TTTTGTGTAATTTTTTTATTTTAAA
1 TTTTGTGTAATTTATTTATTGTAAA
55604017 AGATTTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (25 bp):
TTTTGTGTAATTTATTTATTGTAAA
Found at i:55615253 original size:45 final size:45
Alignment explanation
Indices: 55615188--55615275 Score: 167
Period size: 45 Copynumber: 2.0 Consensus size: 45
55615178 TTCACTAACG
*
55615188 GTACTCATTTATTTCTGAGTTCTTTAATTTCCCGAACTAGAATCT
1 GTACTCATTTATTTCCGAGTTCTTTAATTTCCCGAACTAGAATCT
55615233 GTACTCATTTATTTCCGAGTTCTTTAATTTCCCGAACTAGAAT
1 GTACTCATTTATTTCCGAGTTCTTTAATTTCCCGAACTAGAAT
55615276 ATTTCTTACC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.25, C:0.20, G:0.11, T:0.43
Consensus pattern (45 bp):
GTACTCATTTATTTCCGAGTTCTTTAATTTCCCGAACTAGAATCT
Found at i:55615642 original size:17 final size:17
Alignment explanation
Indices: 55615602--55615644 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
55615592 AAGTTCTAAT
**
55615602 GAAAAAAAAGATTAAAA
1 GAAAAAAAAGAAGAAAA
* *
55615619 TATAAAAAAGAAGAAAA
1 GAAAAAAAAGAAGAAAA
55615636 GAAAAAAAA
1 GAAAAAAAA
55615645 TCATCAAAGT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (17 bp):
GAAAAAAAAGAAGAAAA
Found at i:55615735 original size:19 final size:19
Alignment explanation
Indices: 55615708--55615748 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
55615698 GAAAAATAAT
* *
55615708 AAAATAGAAGACAAAAGTA
1 AAAAGAGAAGACAAAAATA
*
55615727 AAAAGAGAAGAGAAAAATA
1 AAAAGAGAAGACAAAAATA
55615746 AAA
1 AAA
55615749 TGTAATTATC
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:0.73, C:0.02, G:0.17, T:0.07
Consensus pattern (19 bp):
AAAAGAGAAGACAAAAATA
Found at i:55621652 original size:25 final size:25
Alignment explanation
Indices: 55621624--55621684 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
55621614 TAAAATATGT
* *
55621624 TATGTTATGATTCGATATAACATGA
1 TATGTTAAGATTCAATATAACATGA
* * *
55621649 TATGCTAAGATTCAATATGATATGA
1 TATGTTAAGATTCAATATAACATGA
55621674 TATGTTAAGAT
1 TATGTTAAGAT
55621685 ATGATTTGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.39
Consensus pattern (25 bp):
TATGTTAAGATTCAATATAACATGA
Found at i:55624415 original size:26 final size:26
Alignment explanation
Indices: 55624381--55624444 Score: 112
Period size: 26 Copynumber: 2.5 Consensus size: 26
55624371 TGTTAATTTC
*
55624381 AAGACTTATTTAATGTTAGTGATTCA
1 AAGACTTATGTAATGTTAGTGATTCA
55624407 AAGACTTATGTAATGTTAGTGATTCA
1 AAGACTTATGTAATGTTAGTGATTCA
55624433 AAGACTTA-GTAA
1 AAGACTTATGTAA
55624445 AACCATAGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
25 4 0.11
26 33 0.89
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.38
Consensus pattern (26 bp):
AAGACTTATGTAATGTTAGTGATTCA
Found at i:55630407 original size:73 final size:73
Alignment explanation
Indices: 55630330--55630484 Score: 186
Period size: 73 Copynumber: 2.1 Consensus size: 73
55630320 AGCTGTATAA
* * * * * *
55630330 CAGGAAGCTCATAAGAGCCATAT-TTAGGAAGCTCATGTGAGCCAATAACGGGTAGCTCTGAAGA
1 CAGGAAGCTCAGAAGAGCCATATATCAGGAAGCTCAAGCGAGCC-ATAACGGGAAGCTCCGAAGA
55630394 GCCATTAAT
65 GCCATTAAT
* * * * * *
55630403 CAGGAAGCTCCGGATAGCCATATATCAGGAAGTTCAAGCGAGCCATATCGGGAAGCTCCGGAGAG
1 CAGGAAGCTCAGAAGAGCCATATATCAGGAAGCTCAAGCGAGCCATAACGGGAAGCTCCGAAGAG
55630468 CCATTAAT
66 CCATTAAT
55630476 CAGGAAGCT
1 CAGGAAGCT
55630485 TACAAAGAGC
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
73 53 0.77
74 16 0.23
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.19
Consensus pattern (73 bp):
CAGGAAGCTCAGAAGAGCCATATATCAGGAAGCTCAAGCGAGCCATAACGGGAAGCTCCGAAGAG
CCATTAAT
Found at i:55630461 original size:48 final size:51
Alignment explanation
Indices: 55630390--55630536 Score: 155
Period size: 48 Copynumber: 2.9 Consensus size: 51
55630380 GGTAGCTCTG
*
55630390 AAGAGCC-ATTAATCAGGAAGCTCCGGATAGCCATATATCAGGAAG-TT-CA
1 AAGAGCCTA-TAATCGGGAAGCTCCGGATAGCCATATATCAGGAAGCTTACA
* *
55630439 AGCGAGCC-AT-ATCGGGAAGCTCCGGAGAGCCAT-TAATCAGGAAGCTTACA
1 A-AGAGCCTATAATCGGGAAGCTCCGGATAGCCATAT-ATCAGGAAGCTTACA
* **
55630489 AAGAGCCTTTAATCGGGAAGCTCACAAATAGCCATATATCAGG-AGCTT
1 AAGAGCCTATAATCGGGAAGCTC-CGGATAGCCATATATCAGGAAGCTT
55630537 CCTGATATAT
Statistics
Matches: 82, Mismatches: 8, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
47 1 0.01
48 30 0.37
49 9 0.11
50 10 0.12
51 17 0.21
52 14 0.17
53 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.20
Consensus pattern (51 bp):
AAGAGCCTATAATCGGGAAGCTCCGGATAGCCATATATCAGGAAGCTTACA
Found at i:55630500 original size:26 final size:26
Alignment explanation
Indices: 55630390--55630532 Score: 102
Period size: 25 Copynumber: 5.7 Consensus size: 26
55630380 GGTAGCTCTG
*
55630390 AAGAGCCATTAATCAGGAAGCTC-CG
1 AAGAGCCATTAATCAGGAAGCTCACA
* * *
55630415 GATAGCCA-TATATCAGGAAGTTCA-A
1 AAGAGCCATTA-ATCAGGAAGCTCACA
** * *
55630440 GCGAGCCA-T-ATCGGGAAGCTC-CG
1 AAGAGCCATTAATCAGGAAGCTCACA
* *
55630463 GAGAGCCATTAATCAGGAAGCTTACA
1 AAGAGCCATTAATCAGGAAGCTCACA
* *
55630489 AAGAGCCTTTAATCGGGAAGCTCACA
1 AAGAGCCATTAATCAGGAAGCTCACA
*
55630515 AATAGCCA-TATATCAGGA
1 AAGAGCCATTA-ATCAGGA
55630533 GCTTCCTGAT
Statistics
Matches: 91, Mismatches: 20, Indels: 13
0.73 0.16 0.10
Matches are distributed among these distances:
23 17 0.19
24 3 0.03
25 36 0.40
26 35 0.38
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.19
Consensus pattern (26 bp):
AAGAGCCATTAATCAGGAAGCTCACA
Found at i:55632436 original size:28 final size:29
Alignment explanation
Indices: 55632404--55632477 Score: 69
Period size: 30 Copynumber: 2.6 Consensus size: 29
55632394 AATACATTTT
*
55632404 TAAAATTTTTAAAATTCA-AAAAATATTA
1 TAAAATTTTTAAAAATCATAAAAATATTA
** *
55632432 TAAAAAATTTAAAAATCATTAAAATTATTA
1 TAAAATTTTTAAAAATCA-TAAAAATATTA
* * *
55632462 AAAAATTATAAAAAAT
1 TAAAATTTTTAAAAAT
55632478 TATTTTTAAT
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
28 15 0.43
30 20 0.57
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (29 bp):
TAAAATTTTTAAAAATCATAAAAATATTA
Found at i:55632473 original size:10 final size:10
Alignment explanation
Indices: 55632422--55632480 Score: 61
Period size: 10 Copynumber: 6.0 Consensus size: 10
55632412 TTAAAATTCA
55632422 AAAAATATTAT
1 AAAAA-ATTAT
55632433 AAAAAATT-T
1 AAAAAATTAT
*
55632442 -AAAAATCAT
1 AAAAAATTAT
*
55632451 -TAAAATTATT
1 AAAAAATTA-T
55632461 AAAAAATTAT
1 AAAAAATTAT
55632471 AAAAAATTAT
1 AAAAAATTAT
55632481 TTTTAATATA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
8 6 0.15
9 8 0.20
10 15 0.37
11 12 0.29
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:55632479 original size:27 final size:26
Alignment explanation
Indices: 55632428--55632479 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 26
55632418 TTCAAAAAAT
55632428 ATTATAAAAAATTTAAAAATCATTAAA
1 ATTATAAAAAATTTAAAAA-CATTAAA
55632455 ATTATTAAAAAATTATAAAAA-ATTA
1 ATTA-TAAAAAATT-TAAAAACATTA
55632480 TTTTTAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
27 8 0.35
28 9 0.39
29 6 0.26
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (26 bp):
ATTATAAAAAATTTAAAAACATTAAA
Found at i:55633861 original size:43 final size:43
Alignment explanation
Indices: 55633798--55634045 Score: 361
Period size: 43 Copynumber: 5.8 Consensus size: 43
55633788 CGTCGCTAAT
* * * *
55633798 TTTAGTGGCGCTTTTTCCACAAATGCCGCTAAAGACCAGAACC
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAGGACC
* * *
55633841 TTTAGCGACGCTTTTCCCACAAACACCGCTAAAGACTAGGACC
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAGGACC
* * *
55633884 TTTAGCGGCGCTTTTTCTATAAACGCCGCTAAAGACCAGGACC
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAGGACC
55633927 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAGGACC
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAGGACC
55633970 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAGGACC
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAGGACC
* * * * *
55634013 TTTAGCGTCACTTTTACCATAAATGCCGCTAAA
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAA
55634046 AACATGACTT
Statistics
Matches: 184, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 184 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (43 bp):
TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAGGACC
Found at i:55640461 original size:41 final size:40
Alignment explanation
Indices: 55640397--55640590 Score: 197
Period size: 41 Copynumber: 5.0 Consensus size: 40
55640387 TCAAAAACGG
* * *
55640397 GCATTAGCGGCACTTTTTAAAAAACGCCACTAAAGGCCCGA
1 GCATTAGCGGCGC-TTTTCAAAAACGCCGCTAAAGGCCCGA
* *
55640438 GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGTCTGA
1 GCATTAGCGGCGCTT-TTCAAAAACGCCGCTAAAGGCCCGA
* **
55640479 GCATTAGCGGCGC-TTT-------GCTGCTAAAGAACCGA
1 GCATTAGCGGCGCTTTTCAAAAACGCCGCTAAAGGCCCGA
* *
55640511 GCATTAGCAGCGCATTTTCAAAAACGCCGCTAAAGTCCCGA
1 GCATTAGCGGCGC-TTTTCAAAAACGCCGCTAAAGGCCCGA
*
55640552 GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAATGCCC
1 GCATTAGCGGCGCTT-TTCAAAAACGCCGCTAAAGGCCC
55640591 CAAAAACTCA
Statistics
Matches: 126, Mismatches: 16, Indels: 22
0.77 0.10 0.13
Matches are distributed among these distances:
32 24 0.19
34 3 0.02
39 2 0.02
40 5 0.04
41 92 0.73
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.21
Consensus pattern (40 bp):
GCATTAGCGGCGCTTTTCAAAAACGCCGCTAAAGGCCCGA
Found at i:55640750 original size:40 final size:39
Alignment explanation
Indices: 55640631--55640760 Score: 138
Period size: 40 Copynumber: 3.3 Consensus size: 39
55640621 TAGGCTTGTT
* *
55640631 GCGGCGCTTTTCAAAAAACGCCGCTAATGCTT-ATTTTTA
1 GCGGCG-TTTTTAAAAAGCGCCGCTAATGCTTGATTTTTA
* * **
55640670 GCGGCGTTTTCCAAAAAGCGCCGCTAATGCTCGACCTTTA
1 GCGGCGTTTT-TAAAAAGCGCCGCTAATGCTTGATTTTTA
*
55640710 GCGACGTTTTTAGAAAAGCGCC-CTTAATGCTTGATTTTTA
1 GCGGCGTTTTTA-AAAAGCGCCGC-TAATGCTTGATTTTTA
*
55640750 GTGGCGTTTTT
1 GCGGCGTTTTT
55640761 TGTCCAAACG
Statistics
Matches: 76, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
38 4 0.05
39 27 0.36
40 45 0.59
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (39 bp):
GCGGCGTTTTTAAAAAGCGCCGCTAATGCTTGATTTTTA
Found at i:55641502 original size:9 final size:9
Alignment explanation
Indices: 55641488--55641518 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
55641478 GTAGTAATTC
55641488 AATTCGGTT
1 AATTCGGTT
*
55641497 AATTCGGGT
1 AATTCGGTT
55641506 AATTCGGTT
1 AATTCGGTT
55641515 AATT
1 AATT
55641519 TTTAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:55643030 original size:43 final size:43
Alignment explanation
Indices: 55642955--55643063 Score: 130
Period size: 43 Copynumber: 2.6 Consensus size: 43
55642945 AATGTCATAT
* * * * *
55642955 CCCAGATATGGTCTTACATGTAATCTCGTATCGATGCCAATAA
1 CCCAGACATGGTCTTACACGAAATCACATATCGATGCCAATAA
* **
55642998 CCCAGCCATGGTCTTACACGAAATCACATATCGATGCCAATGT
1 CCCAGACATGGTCTTACACGAAATCACATATCGATGCCAATAA
*
55643041 CCTAGACATGGTCTTACAC-AAAT
1 CCCAGACATGGTCTTACACGAAAT
55643064 TCTTATATTG
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
42 4 0.07
43 52 0.93
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.27
Consensus pattern (43 bp):
CCCAGACATGGTCTTACACGAAATCACATATCGATGCCAATAA
Found at i:55649908 original size:5 final size:5
Alignment explanation
Indices: 55649898--55649923 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
55649888 TGAGCATTCG
55649898 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
55649924 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:55650436 original size:19 final size:19
Alignment explanation
Indices: 55650403--55650450 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
55650393 TAAACAATTC
55650403 AATAATATAAA--TAATAT
1 AATAATATAAATTTAATAT
*
55650420 AA-AATATGAAATTTAATTT
1 AATAATAT-AAATTTAATAT
55650439 AATAATATAAAT
1 AATAATATAAAT
55650451 AGAAGATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 5 0.19
17 5 0.19
19 11 0.42
20 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
AATAATATAAATTTAATAT
Found at i:55650960 original size:9 final size:9
Alignment explanation
Indices: 55650946--55650982 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
55650936 TATAGTTTGA
55650946 TATTCGAAT
1 TATTCGAAT
55650955 TATTCGAAT
1 TATTCGAAT
*
55650964 TATTCGAGT
1 TATTCGAAT
55650973 TATTCGAAT
1 TATTCGAAT
55650982 T
1 T
55650983 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:55656282 original size:12 final size:12
Alignment explanation
Indices: 55656255--55656295 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
55656245 CAAATGAAAT
*
55656255 ATTTCTCATTTTC
1 ATTTCT-ATTTCC
55656268 ATTTCTATTTCC
1 ATTTCTATTTCC
*
55656280 ATTTCCATTTCC
1 ATTTCTATTTCC
55656292 ATTT
1 ATTT
55656296 TTTTGAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 20 0.77
13 6 0.23
ACGTcount: A:0.17, C:0.24, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTTCTATTTCC
Found at i:55656288 original size:18 final size:19
Alignment explanation
Indices: 55656254--55656295 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
55656244 GCAAATGAAA
*
55656254 TATTTCTCATTTTCATTTC
1 TATTTCTCATTTCCATTTC
55656273 TATTTC-CATTTCCATTTC
1 TATTTCTCATTTCCATTTC
*
55656291 CATTT
1 TATTT
55656296 TTTTGAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.17, C:0.24, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTTCTCATTTCCATTTC
Found at i:55661058 original size:43 final size:43
Alignment explanation
Indices: 55660978--55661212 Score: 294
Period size: 43 Copynumber: 5.5 Consensus size: 43
55660968 GCTAATTTTT
* * * *
55660978 GCGGCGCTTACAGAAAAAAAACGCCTCTAAAGGTCATGTTCTTTA
1 GCGGCGCTT--AGGAAAAAAACGCCGCTAATGATCATGTTCTTTA
*
55661023 GCGGCGCTTAGGAAAAAAACGTCGCTAATGATCATGTTCTTTA
1 GCGGCGCTTAGGAAAAAAACGCCGCTAATGATCATGTTCTTTA
* * *
55661066 GCAGCGCTTAGGAAAAAAATGCCGTTAATGATCATGTTCTTTA
1 GCGGCGCTTAGGAAAAAAACGCCGCTAATGATCATGTTCTTTA
* *
55661109 GCAGCGCTTAGG-AAAAAACGCCCCTAATGATCATGTTCTTTA
1 GCGGCGCTTAGGAAAAAAACGCCGCTAATGATCATGTTCTTTA
* * * *
55661151 GCGGCGCTTTGG-AAAAAACGCCGCTAAAGAACATGATCTTTA
1 GCGGCGCTTAGGAAAAAAACGCCGCTAATGATCATGTTCTTTA
* *
55661193 GTGGCGTTTAGGAAAAAAAC
1 GCGGCGCTTAGGAAAAAAAC
55661213 ACCGTTAAAA
Statistics
Matches: 168, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
42 72 0.43
43 87 0.52
45 9 0.05
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.26
Consensus pattern (43 bp):
GCGGCGCTTAGGAAAAAAACGCCGCTAATGATCATGTTCTTTA
Found at i:55661138 original size:42 final size:42
Alignment explanation
Indices: 55660993--55661210 Score: 283
Period size: 42 Copynumber: 5.1 Consensus size: 42
55660983 GCTTACAGAA
* * *
55660993 AAAAAACGCCTCTAAAGGTCATGTTCTTTAGCGGCGCTTAGG
1 AAAAAACGCCGCTAATGATCATGTTCTTTAGCGGCGCTTAGG
* *
55661035 AAAAAAACGTCGCTAATGATCATGTTCTTTAGCAGCGCTTAGG
1 -AAAAAACGCCGCTAATGATCATGTTCTTTAGCGGCGCTTAGG
* * *
55661078 AAAAAAATGCCGTTAATGATCATGTTCTTTAGCAGCGCTTAGG
1 -AAAAAACGCCGCTAATGATCATGTTCTTTAGCGGCGCTTAGG
* *
55661121 AAAAAACGCCCCTAATGATCATGTTCTTTAGCGGCGCTTTGG
1 AAAAAACGCCGCTAATGATCATGTTCTTTAGCGGCGCTTAGG
* * * * *
55661163 AAAAAACGCCGCTAAAGAACATGATCTTTAGTGGCGTTTAGG
1 AAAAAACGCCGCTAATGATCATGTTCTTTAGCGGCGCTTAGG
55661205 AAAAAA
1 AAAAAA
55661211 ACACCGTTAA
Statistics
Matches: 155, Mismatches: 20, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
42 78 0.50
43 77 0.50
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.27
Consensus pattern (42 bp):
AAAAAACGCCGCTAATGATCATGTTCTTTAGCGGCGCTTAGG
Found at i:55661230 original size:85 final size:86
Alignment explanation
Indices: 55660978--55661276 Score: 306
Period size: 85 Copynumber: 3.5 Consensus size: 86
55660968 GCTAATTTTT
* * *
55660978 GCGGCGCTTACAGAAAAAAAACGCCTCTAAAGGTCATGTTCTTTAGCGGCGCTTAGGAAAAAAAC
1 GCGGCGCTT--AGGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAAAC
*
55661043 GTCGCTAATGATCATGTTCTTTA
64 GCCGCTAATGATCATGTTCTTTA
* * * * *
55661066 GCAGCGCTTAGGAAAAAAATGCCGTTAATGATCATGTTCTTTAGCAGCGCTTAGG-AAAAAACGC
1 GCGGCGCTTAGGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAAACGC
*
55661130 CCCTAATGATCATGTTCTTTA
66 CGCTAATGATCATGTTCTTTA
* * * * * *
55661151 GCGGCGCTTTGG-AAAAAACGCCGCTAAAGAACATGATCTTTAGTGGCGTTTAGGAAAAAAACAC
1 GCGGCGCTTAGGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAAACGC
* * * *
55661215 CGTTAA-AAGTAATGTTCTATA
66 CGCTAATGA-TCATGTTCTTTA
* * *
55661236 GCGGCGC---GGTAAAAAACGCCACTAAA-AGTAATGTTCTTTAG
1 GCGGCGCTTAGGAAAAAAACGCCGCTAAAGA-TCATGTTCTTTAG
55661277 TGACGCTTCA
Statistics
Matches: 177, Mismatches: 30, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
82 3 0.02
83 25 0.14
84 35 0.20
85 67 0.38
86 39 0.22
88 8 0.05
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (86 bp):
GCGGCGCTTAGGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAAACGC
CGCTAATGATCATGTTCTTTA
Found at i:55661742 original size:21 final size:21
Alignment explanation
Indices: 55661718--55661758 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
55661708 TCGCTGTTTC
*
55661718 TCTTGCTGCGGCCTCTGCTTT
1 TCTTGCTGCAGCCTCTGCTTT
55661739 TCTTGCTGCAGCCTCTGCTT
1 TCTTGCTGCAGCCTCTGCTT
55661759 CCCTCGTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.02, C:0.34, G:0.22, T:0.41
Consensus pattern (21 bp):
TCTTGCTGCAGCCTCTGCTTT
Found at i:55664568 original size:27 final size:27
Alignment explanation
Indices: 55664520--55664571 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
55664510 TCTTACTTTT
* *
55664520 AAATAATTAATTACCAATTTATTTAAC
1 AAATAAATAATTACCAACTTATTTAAC
**
55664547 AAATAAATAATTACTTACTTATTTA
1 AAATAAATAATTACCAACTTATTTA
55664572 TTTGTTTATT
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:0.10, G:0.00, T:0.42
Consensus pattern (27 bp):
AAATAAATAATTACCAACTTATTTAAC
Found at i:55664652 original size:10 final size:10
Alignment explanation
Indices: 55664637--55664665 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
55664627 ATTAATAACT
55664637 ATATATATCC
1 ATATATATCC
55664647 ATATATATCC
1 ATATATATCC
55664657 ATATATATC
1 ATATATATC
55664666 AAAAAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (10 bp):
ATATATATCC
Found at i:55666418 original size:14 final size:14
Alignment explanation
Indices: 55666399--55666466 Score: 61
Period size: 14 Copynumber: 4.9 Consensus size: 14
55666389 ATGACCGTTG
55666399 AAACCCTAAATCTC
1 AAACCCTAAATCTC
*
55666413 AAACCCTTAAACCTC
1 AAACCC-TAAATCTC
*
55666428 TAACCCCTAAAT-T-
1 -AAACCCTAAATCTC
*
55666441 -AACCTTAAATCTC
1 AAACCCTAAATCTC
*
55666454 AAACCTTAAATCT
1 AAACCCTAAATCT
55666467 ATACCCCGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
11 8 0.18
12 1 0.02
14 19 0.43
15 11 0.25
16 5 0.11
ACGTcount: A:0.41, C:0.32, G:0.00, T:0.26
Consensus pattern (14 bp):
AAACCCTAAATCTC
Found at i:55667013 original size:41 final size:40
Alignment explanation
Indices: 55666949--55667188 Score: 210
Period size: 41 Copynumber: 5.9 Consensus size: 40
55666939 TTTTGTTACT
* * * *
55666949 ATTAACGGCGCTTCGGTAAAAACGCCGCTAAAGGTAAATGC
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGTAGA-GC
* * * *
55666990 ATTAGCGGCGCTTAGCTACAAACGCCGCTAAAGGCCAGAGA
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGG-TAGAGC
* * * * * *
55667031 ATTAGTGGTGCTCAGATAAAAATGCCGCTAAAGATCCGAGC
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGT-AGAGC
* *
55667072 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAGA
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGG-TAGAGC
* * * ** * *
55667113 ATTAGCAGCGCTGAGGTAAAAACGCCGCTAAATATCCGAGT
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGT-AGAGC
**
55667154 ATTAGCGGCGCTTAGATAAAAACGTTGCTAAAGGT
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGT
55667189 TTAAAAAATC
Statistics
Matches: 155, Mismatches: 40, Indels: 8
0.76 0.20 0.04
Matches are distributed among these distances:
41 153 0.99
42 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.19
Consensus pattern (40 bp):
ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGTAGAGC
Found at i:55667102 original size:82 final size:82
Alignment explanation
Indices: 55666965--55667187 Score: 295
Period size: 82 Copynumber: 2.7 Consensus size: 82
55666955 GGCGCTTCGG
* ** * *
55666965 TAAAAACGCCGCTAAAGGT-AAATGCATTAGCGGCGCTTAGCTACAAACGCCGCTAAAGGCCAGA
1 TAAAAACGCCGCTAAAGATCCGA-GCATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGA
** *
55667029 GAATTAGTGGTGCTCAGA
65 GAATTAGCAGCGCTCAGA
*
55667047 TAAAAATGCCGCTAAAGATCCGAGCATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAG
1 TAAAAACGCCGCTAAAGATCCGAGCATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAG
* *
55667112 AATTAGCAGCGCTGAGG
66 AATTAGCAGCGCTCAGA
* * **
55667129 TAAAAACGCCGCTAAATATCCGAGTATTAGCGGCGCTTAGATAAAAACGTTGCTAAAGG
1 TAAAAACGCCGCTAAAGATCCGAGCATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGG
55667188 TTTAAAAAAT
Statistics
Matches: 124, Mismatches: 16, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
82 123 0.99
83 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.18
Consensus pattern (82 bp):
TAAAAACGCCGCTAAAGATCCGAGCATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAG
AATTAGCAGCGCTCAGA
Found at i:55667173 original size:123 final size:123
Alignment explanation
Indices: 55666949--55667175 Score: 278
Period size: 123 Copynumber: 1.8 Consensus size: 123
55666939 TTTTGTTACT
* * * * * * *
55666949 ATTAACGGCGCTTCGGTAAAAACGCCGCTAAAGGTAAATGCATTAGCGGCGCTTAGCTACAAACG
1 ATTAACGGCGCTTAGATAAAAACGCCGCTAAAGGCAAATGAATTAGCAGCGCTGAGCTAAAAACG
* * *
55667014 CCGCTAAAGGCCAGAGAATTAGTGGTGCTCAGATAAAAATGCCGCTAAAGATCCGAGC
66 CCGCTAAAAGCCAGAGAATTAGCGGCGCTCAGATAAAAATGCCGCTAAAGATCCGAGC
* * *
55667072 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGA-GAATTAGCAGCGCTGAGGTAAAAAC
1 ATTAACGGCGCTTAGATAAAAACGCCGCTAAAGG-CAAATGAATTAGCAGCGCTGAGCTAAAAAC
* * *
55667136 GCCGCTAAATATCC-GAGTATTAGCGGCGCTTAGATAAAAA
65 GCCGCTAAA-AGCCAGAGAATTAGCGGCGCTCAGATAAAAA
55667176 CGTTGCTAAA
Statistics
Matches: 86, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
123 82 0.95
124 4 0.05
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.19
Consensus pattern (123 bp):
ATTAACGGCGCTTAGATAAAAACGCCGCTAAAGGCAAATGAATTAGCAGCGCTGAGCTAAAAACG
CCGCTAAAAGCCAGAGAATTAGCGGCGCTCAGATAAAAATGCCGCTAAAGATCCGAGC
Found at i:55672433 original size:19 final size:19
Alignment explanation
Indices: 55672408--55672469 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
55672398 AATGGAAGAT
*
55672408 TTATAAATAAATAATAATC
1 TTATAAATAAATAATAATA
* *
55672427 TTTTAAATATAATTA-AATA
1 TTATAAATA-AATAATAATA
*
55672446 TTATAAATAAATATTAATAA
1 TTATAAATAAATAATAAT-A
55672466 TTAT
1 TTAT
55672470 TGAGGTTTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
18 3 0.09
19 22 0.65
20 9 0.26
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
TTATAAATAAATAATAATA
Found at i:55681449 original size:33 final size:33
Alignment explanation
Indices: 55681399--55681475 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 33
55681389 TATATACATG
* * * *
55681399 TGTAAGGCCATAGCTGGGCTATGGCA-TTCTAA
1 TGTAAGACCATAACTGGGCTATGGCACTACAAA
*
55681431 TGATAAGACCATAACTGGGTTATGGCACTACAAA
1 TG-TAAGACCATAACTGGGCTATGGCACTACAAA
55681465 TGTAAGACCAT
1 TGTAAGACCAT
55681476 GGCAGGGCCA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
32 2 0.05
33 30 0.79
34 6 0.16
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.26
Consensus pattern (33 bp):
TGTAAGACCATAACTGGGCTATGGCACTACAAA
Found at i:55681488 original size:11 final size:11
Alignment explanation
Indices: 55681472--55681498 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
55681462 AAATGTAAGA
55681472 CCATGGCAGGG
1 CCATGGCAGGG
55681483 CCATGGCAGGG
1 CCATGGCAGGG
55681494 CCATG
1 CCATG
55681499 TAAGACCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.19, C:0.30, G:0.41, T:0.11
Consensus pattern (11 bp):
CCATGGCAGGG
Found at i:55687426 original size:19 final size:19
Alignment explanation
Indices: 55687378--55687491 Score: 120
Period size: 19 Copynumber: 6.0 Consensus size: 19
55687368 AGCACACGAA
* *
55687378 CCTGGCACACAAAGTGCAT
1 CCTGGCACACGAAGCGCAT
* * * *
55687397 ACTAGCGCACGAAGAGCAT
1 CCTGGCACACGAAGCGCAT
55687416 CCTGGCACACGAAGCGCAT
1 CCTGGCACACGAAGCGCAT
*
55687435 CCTGGCACATGAAGCGCAT
1 CCTGGCACACGAAGCGCAT
* *
55687454 CCTGGCACATGAAGTGCAT
1 CCTGGCACACGAAGCGCAT
* * *
55687473 CATGGCACATGAACCGCAT
1 CCTGGCACACGAAGCGCAT
55687492 AAACCCATAC
Statistics
Matches: 81, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 81 1.00
ACGTcount: A:0.30, C:0.31, G:0.25, T:0.15
Consensus pattern (19 bp):
CCTGGCACACGAAGCGCAT
Found at i:55687454 original size:38 final size:38
Alignment explanation
Indices: 55687378--55687491 Score: 138
Period size: 38 Copynumber: 3.0 Consensus size: 38
55687368 AGCACACGAA
* * * * * *
55687378 CCTGGCACACAAAGTGCATACTAGCGCACGAAGAGCAT
1 CCTGGCACACGAAGTGCATCCTGGCACATGAAGCGCAT
*
55687416 CCTGGCACACGAAGCGCATCCTGGCACATGAAGCGCAT
1 CCTGGCACACGAAGTGCATCCTGGCACATGAAGCGCAT
* * *
55687454 CCTGGCACATGAAGTGCATCATGGCACATGAACCGCAT
1 CCTGGCACACGAAGTGCATCCTGGCACATGAAGCGCAT
55687492 AAACCCATAC
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 65 1.00
ACGTcount: A:0.30, C:0.31, G:0.25, T:0.15
Consensus pattern (38 bp):
CCTGGCACACGAAGTGCATCCTGGCACATGAAGCGCAT
Found at i:55691320 original size:13 final size:13
Alignment explanation
Indices: 55691302--55691354 Score: 63
Period size: 13 Copynumber: 4.1 Consensus size: 13
55691292 AGTTTAGCAA
55691302 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
55691315 TGCTTTTGAAAGG
1 TGCTTTTGAAAAG
*
55691328 TG-TTATGGAAAAG
1 TGCTT-TTGAAAAG
*
55691341 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
55691354 T
1 T
55691355 TTGGTTTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
12 2 0.06
13 29 0.88
14 2 0.06
ACGTcount: A:0.28, C:0.06, G:0.28, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:55691873 original size:13 final size:14
Alignment explanation
Indices: 55691857--55691885 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
55691847 CTCCTTTTAG
55691857 AAGTGCTTTT-AAA
1 AAGTGCTTTTGAAA
55691870 AAGTGCTTTTGAAA
1 AAGTGCTTTTGAAA
55691884 AA
1 AA
55691886 TAAAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.34
Consensus pattern (14 bp):
AAGTGCTTTTGAAA
Found at i:55692212 original size:19 final size:19
Alignment explanation
Indices: 55692173--55692212 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
55692163 CACCAATGAA
*
55692173 TTAAAAAATATTAATTTTT
1 TTAAAAAATATTAATTATT
55692192 TTAATAAAATATT-ATTATT
1 TTAA-AAAATATTAATTATT
55692211 TT
1 TT
55692213 TAAATATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTAAAAAATATTAATTATT
Found at i:55692218 original size:21 final size:20
Alignment explanation
Indices: 55692173--55692215 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
55692163 CACCAATGAA
55692173 TTAA-AAAATATTAATTTTT
1 TTAATAAAATATTAATTTTT
55692192 TTAATAAAATATT-ATTATTT
1 TTAATAAAATATTAATT-TTT
55692212 TTAA
1 TTAA
55692216 ATATTTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTAATAAAATATTAATTTTT
Found at i:55692696 original size:21 final size:22
Alignment explanation
Indices: 55692669--55692717 Score: 91
Period size: 21 Copynumber: 2.3 Consensus size: 22
55692659 TTTGGATTAG
55692669 TATTTTGTATGAATATTGTAAT
1 TATTTTGTATGAATATTGTAAT
55692691 T-TTTTGTATGAATATTGTAAT
1 TATTTTGTATGAATATTGTAAT
55692712 TATTTT
1 TATTTT
55692718 ATAATTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (22 bp):
TATTTTGTATGAATATTGTAAT
Found at i:55692747 original size:33 final size:32
Alignment explanation
Indices: 55692710--55692806 Score: 91
Period size: 33 Copynumber: 3.1 Consensus size: 32
55692700 GAATATTGTA
55692710 ATTATTTTATAATTAATTTGTTAGTAATTTAGG
1 ATTATTTTATAATTAATTT-TTAGTAATTTAGG
*
55692743 ATTATGTTATAA--AATTTTGT-GT--TTGTA--
1 ATTATTTTATAATTAATTTT-TAGTAATT-TAGG
*
55692770 ATTATTTTAAAATTAATTTATTAGTAATTTAGG
1 ATTATTTTATAATTAATTT-TTAGTAATTTAGG
55692803 ATTA
1 ATTA
55692807 AGTTATAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 20
0.69 0.04 0.27
Matches are distributed among these distances:
27 10 0.20
28 2 0.04
29 8 0.16
30 6 0.12
31 8 0.16
32 2 0.04
33 15 0.29
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (32 bp):
ATTATTTTATAATTAATTTTTAGTAATTTAGG
Found at i:55692776 original size:60 final size:60
Alignment explanation
Indices: 55692705--55692826 Score: 201
Period size: 60 Copynumber: 2.0 Consensus size: 60
55692695 TGTATGAATA
* * *
55692705 TTGTAATTATTTTATAATTAATTTGTTAGTAATTTAGGATTATGTTATAAAATT-TTGTGT
1 TTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTAT-AAATTGTTGTGT
55692765 TTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAATTGTTGTGT
1 TTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAATTGTTGTGT
55692825 TT
1 TT
55692827 AGTTTAGTAT
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
59 5 0.09
60 53 0.91
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (60 bp):
TTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAATTGTTGTGT
Found at i:55692961 original size:16 final size:16
Alignment explanation
Indices: 55692940--55692977 Score: 69
Period size: 15 Copynumber: 2.4 Consensus size: 16
55692930 TTAACTCATT
55692940 TAATTTTTATATAATG
1 TAATTTTTATATAATG
55692956 TAA-TTTTATATAATG
1 TAATTTTTATATAATG
55692971 TAATTTT
1 TAATTTT
55692978 ATTTGATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (16 bp):
TAATTTTTATATAATG
Found at i:55692964 original size:15 final size:15
Alignment explanation
Indices: 55692944--55692979 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
55692934 CTCATTTAAT
55692944 TTTTATATAATGTAA
1 TTTTATATAATGTAA
55692959 TTTTATATAATGTAA
1 TTTTATATAATGTAA
55692974 TTTTAT
1 TTTTAT
55692980 TTGATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (15 bp):
TTTTATATAATGTAA
Found at i:55694552 original size:6 final size:6
Alignment explanation
Indices: 55694526--55694580 Score: 65
Period size: 6 Copynumber: 9.2 Consensus size: 6
55694516 CATGCACCAA
* * * *
55694526 AGCCAA AGCCAG AGCCAG AGCCGG AGCCAG AGCTAG AGCCGG AGCCAG
1 AGCCAG AGCCAG AGCCAG AGCCAG AGCCAG AGCCAG AGCCAG AGCCAG
*
55694574 AGGCAG A
1 AGCCAG A
55694581 AACGAAACTA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.33, C:0.29, G:0.36, T:0.02
Consensus pattern (6 bp):
AGCCAG
Found at i:55694553 original size:18 final size:18
Alignment explanation
Indices: 55694532--55694580 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
55694522 CCAAAGCCAA
55694532 AGCCAGAGCCAGAGCCGG
1 AGCCAGAGCCAGAGCCGG
*
55694550 AGCCAGAGCTAGAGCCGG
1 AGCCAGAGCCAGAGCCGG
*
55694568 AGCCAGAGGCAGA
1 AGCCAGAGCCAGA
55694581 AACGAAACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.31, C:0.29, G:0.39, T:0.02
Consensus pattern (18 bp):
AGCCAGAGCCAGAGCCGG
Found at i:55698179 original size:27 final size:27
Alignment explanation
Indices: 55698113--55698181 Score: 68
Period size: 27 Copynumber: 2.6 Consensus size: 27
55698103 GAAAAATAAG
55698113 ACCATTGGCGCCTCTCAACATAGCACA
1 ACCATTGGCGCCTCTCAACATAGCACA
* * * * * *
55698140 ACTAATGGTGCCTGTC-AGATAAGCACC
1 ACCATTGGCGCCTCTCAACAT-AGCACA
55698167 ACCATTGGCGCCTCT
1 ACCATTGGCGCCTCT
55698182 GAGATAGGCG
Statistics
Matches: 31, Mismatches: 10, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
26 3 0.10
27 28 0.90
ACGTcount: A:0.26, C:0.33, G:0.19, T:0.22
Consensus pattern (27 bp):
ACCATTGGCGCCTCTCAACATAGCACA
Found at i:55698271 original size:21 final size:22
Alignment explanation
Indices: 55698232--55698272 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
55698222 TTGACCCTGG
55698232 AAAAAATTAATTATATTTTATT
1 AAAAAATTAATTATATTTTATT
*
55698254 AAAAAATTAA-TATTTTTTA
1 AAAAAATTAATTATATTTTA
55698273 ATTCATTGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AAAAAATTAATTATATTTTATT
Found at i:55698730 original size:20 final size:21
Alignment explanation
Indices: 55698705--55698744 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
55698695 ATAAAAAGGA
*
55698705 ATTAAATTATTTTTT-TTATG
1 ATTAAAATATTTTTTATTATG
55698725 ATTAAAATATTTTTTATTAT
1 ATTAAAATATTTTTTATTAT
55698745 ATTCTAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (21 bp):
ATTAAAATATTTTTTATTATG
Found at i:55698738 original size:21 final size:20
Alignment explanation
Indices: 55698705--55698744 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
55698695 ATAAAAAGGA
* *
55698705 ATTAAATTATTTTTTTTATG
1 ATTAAAATATTTTTATTATG
55698725 ATTAAAATATTTTTTATTAT
1 ATTAAAATA-TTTTTATTAT
55698745 ATTCTAAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
ATTAAAATATTTTTATTATG
Found at i:55701893 original size:161 final size:161
Alignment explanation
Indices: 55701628--55702106 Score: 775
Period size: 161 Copynumber: 3.0 Consensus size: 161
55701618 CTGGTGAGAA
* *
55701628 GTCCAATGTACAAGTTGCCAAAGATCATTAACCAACAATCAATGAAGTTTCCAGTGTTGGTCAAC
1 GTCCAATGTACAAGTTGCCAAAGATCTTTAACCAACAATCAATGAAGTTTTCAGTGTTGGTCAAC
* *
55701693 TCAAAGAGCTCATCAAAGAAGCTATAAAAGACCAATTTGAAAGTGTTGATCCACATTTATATACA
66 TCAAAGAGCTCATCAAAAAAGCTATAAAAGACCAATTTGAAAGTGTTGATCCACCTTTATATACA
*
55701758 TAATCAAATCCATACACACAAAGGATTGACC
131 TACTCAAATCCATACACACAAAGGATTGACC
*
55701789 GTCCAATGTACAAGTTGCCAAAGATCTTTAACCAACAATCAATGAAGTTTTCAGTGTTGGTTAAC
1 GTCCAATGTACAAGTTGCCAAAGATCTTTAACCAACAATCAATGAAGTTTTCAGTGTTGGTCAAC
* * *
55701854 TCAAAGAGCTCATCAAATAAGCTATAAAAGACCAATTTGAAAGTGTTGATCTACCTTCATATACA
66 TCAAAGAGCTCATCAAAAAAGCTATAAAAGACCAATTTGAAAGTGTTGATCCACCTTTATATACA
* * *
55701919 TACTCAAATCCATACACACGAGGGATTGATC
131 TACTCAAATCCATACACACAAAGGATTGACC
*
55701950 GTCCAATGTACAAGTTGCCAAAAAAT-TTTAACCAACAATCAATGAAGTTTTCA--GTTGGTCAA
1 GTCCAATGTACAAGTTGCC-AAAGATCTTTAACCAACAATCAATGAAGTTTTCAGTGTTGGTCAA
* * *
55702012 CTCAAAGAGCTCCTCAAAAAAGCTATAAAAGGCCAATTTGAAAGTGTTGATCCACCTTTATATAT
65 CTCAAAGAGCTCATCAAAAAAGCTATAAAAGACCAATTTGAAAGTGTTGATCCACCTTTATATAC
*
55702077 ATACTCAAATCCATACACACAAATGATTGA
130 ATACTCAAATCCATACACACAAAGGATTGA
55702107 TCGTTTGAGA
Statistics
Matches: 295, Mismatches: 22, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
159 94 0.32
161 196 0.66
162 5 0.02
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (161 bp):
GTCCAATGTACAAGTTGCCAAAGATCTTTAACCAACAATCAATGAAGTTTTCAGTGTTGGTCAAC
TCAAAGAGCTCATCAAAAAAGCTATAAAAGACCAATTTGAAAGTGTTGATCCACCTTTATATACA
TACTCAAATCCATACACACAAAGGATTGACC
Found at i:55705297 original size:42 final size:41
Alignment explanation
Indices: 55705187--55705301 Score: 140
Period size: 43 Copynumber: 2.7 Consensus size: 41
55705177 AGCGCCGCTA
* * *
55705187 AAAACGTCGCTATAGATCAAGACCTATAGCGGCGCTTTTTCC
1 AAAACGCCGCTATAGATCAA-ACCTTTAGCGGCGCTTTTCCC
* *
55705229 ACAAACGCCACTATAGATCAGGACCTTTAGCGGCGCTTTTCCC
1 A-AAACGCCGCTATAGATCA-AACCTTTAGCGGCGCTTTTCCC
*
55705272 GAAAACGCCGCTATAGAACAAACCTTTAGC
1 -AAAACGCCGCTATAGATCAAACCTTTAGC
55705302 AACACTTCTC
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
42 10 0.16
43 51 0.82
44 1 0.02
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (41 bp):
AAAACGCCGCTATAGATCAAACCTTTAGCGGCGCTTTTCCC
Found at i:55710383 original size:98 final size:98
Alignment explanation
Indices: 55710263--55710557 Score: 536
Period size: 98 Copynumber: 3.0 Consensus size: 98
55710253 TTAAAAATAA
* * * *
55710263 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTGACGTATTGGGTGTGATTTC
55710328 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
55710361 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTGACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTGACGTATTGGGTGTGATTTC
55710426 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
*
55710459 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTGACGTATTGGGTGCGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTGACGTATTGGGTGTGATTTC
*
55710524 TTAAATCTTGGATGAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
55710557 T
1 T
55710558 TTTATTGTAC
Statistics
Matches: 191, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 191 1.00
ACGTcount: A:0.27, C:0.11, G:0.26, T:0.36
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTGACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:55716533 original size:132 final size:132
Alignment explanation
Indices: 55716292--55716944 Score: 1056
Period size: 132 Copynumber: 4.9 Consensus size: 132
55716282 CTGCATTGAC
*
55716292 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCTAAGATAGTGGGAAGCAGATTTAAGCCAC
1 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAC
* * *
55716357 CAAGCCTTGTCTCCCTGAGCAGCAACGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGTA
66 CAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCA
55716422 GT
131 GT
* *
55716424 AGTGGAGCAGATCGAAGACGACGAATCTTATCTTTCTAAGATAGTGGGAAGCAGATTTAAGCCAC
1 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAC
* * * * *
55716489 CAAGCATTGTCGCCCTAAGCAACAGCGGAGAAGGTTGAAAATTGTAGATCTTATCTCCCTAAACA
66 CAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCA
55716554 GT
131 GT
* * *
55716556 AGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGCAGCAGATTTAAGCTAC
1 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAC
* * * *
55716621 TAAGCCTTGTCTCTCTCAGCAGCAGCAGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCA
66 CAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCA
55716686 GT
131 GT
*
55716688 AGTGGAGCAGATCGAAGACGGTGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAC
1 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAC
* * *
55716753 CAAGCCTTGTCCCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAAATCTTATCTCCCTAAGCA
66 CAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCA
55716818 GT
131 GT
* *
55716820 AGTGGAGCAGATCGAAGACGACGAATCTTAACTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAC
1 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAC
* *
55716885 CAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAAGGTTGAAGATGGCA-AGTCTTATCTCCCT
66 CAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAAGGTTGAAGATTGTAGA-TCTTATCTCCCT
55716945 GAAGTTGCAG
Statistics
Matches: 480, Mismatches: 40, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
131 1 0.00
132 479 1.00
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (132 bp):
AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAC
CAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCA
GT
Found at i:55716847 original size:44 final size:44
Alignment explanation
Indices: 55716292--55716849 Score: 152
Period size: 44 Copynumber: 12.7 Consensus size: 44
55716282 CTGCATTGAC
* * **
55716292 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCTAAG-A-T
1 AGTGGAGCAGATTGAAGACGACGAATCTTATCTCCCTAAGCAGT
* * * * * * *
55716334 AGTGGGAAGCAGATTTAAG-CCACCAAGCCTTGTCTCCCTGAGCAGC
1 AGT-GG-AGCAGATTGAAGACGACGAA-TCTTATCTCCCTAAGCAGT
** * * * *
55716380 AACGGAGAAGGTTGAAGATTGTA-G-ATCTTATCTCCCTAAGTAGT
1 AGTGGAGCAGATTGAAGA-CG-ACGAATCTTATCTCCCTAAGCAGT
* **
55716424 AGTGGAGCAGATCGAAGACGACGAATCTTATCTTTCTAAG-A-T
1 AGTGGAGCAGATTGAAGACGACGAATCTTATCTCCCTAAGCAGT
* * * * * * **
55716466 AGTGGGAAGCAGATTTAAG-CCACCAAGCATTGTCGCCCTAAGCAAC
1 AGT-GG-AGCAGATTGAAGACGACGAATC-TTATCTCCCTAAGCAGT
* * * * * *
55716512 AGCGGAGAAGGTTGAAAATTGTA-G-ATCTTATCTCCCTAAACAGT
1 AGTGGAGCAGATTGAAGA-CG-ACGAATCTTATCTCCCTAAGCAGT
* * * *
55716556 AGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCC-AAG-A-T
1 AGTGGAGCAGATTGAAGACGACGAATCTTATC-TCCCTAAGCAGT
* * * * * * * *
55716598 AGTGGGCAGCAGATTTAAG-CTACTAAGCCTTGTCTCTCTCAGCAGC
1 AGT-GG-AGCAGATTGAAGACGACGAA-TCTTATCTCCCTAAGCAGT
** * * *
55716644 AGCAGAGAAGGTTGAAGATTGTA-G-ATCTTATCTCCCTAAGCAGT
1 AGTGGAGCAGATTGAAGA-CG-ACGAATCTTATCTCCCTAAGCAGT
* ** *
55716688 AGTGGAGCAGATCGAAGACGGTGAATCTTATCTTTCC-AAG-A-T
1 AGTGGAGCAGATTGAAGACGACGAATCTTATC-TCCCTAAGCAGT
* * * * * * * *
55716730 AGTGGGAAGCAGATTTAAG-CCACCAAGCCTTGTCCCCCTGAGCAGC
1 AGT-GG-AGCAGATTGAAGACGACGAA-TCTTATCTCCCTAAGCAGT
* * * *
55716776 AGCGGAGAAGGTTGAAGATTGTA--AATCTTATCTCCCTAAGCAGT
1 AGTGGAGCAGATTGAAGA-CG-ACGAATCTTATCTCCCTAAGCAGT
*
55716820 AGTGGAGCAGATCGAAGACGACGAATCTTA
1 AGTGGAGCAGATTGAAGACGACGAATCTTA
55716850 ACTTTCCAAG
Statistics
Matches: 346, Mismatches: 126, Indels: 86
0.62 0.23 0.15
Matches are distributed among these distances:
42 17 0.05
43 38 0.11
44 257 0.74
45 23 0.07
46 7 0.02
47 4 0.01
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (44 bp):
AGTGGAGCAGATTGAAGACGACGAATCTTATCTCCCTAAGCAGT
Found at i:55716984 original size:44 final size:43
Alignment explanation
Indices: 55716931--55717562 Score: 356
Period size: 44 Copynumber: 14.6 Consensus size: 43
55716921 GAAGATGGCA
*
55716931 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCGAT
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC-AT
* *
55716975 AGTCCTATCTCCCTGAAGTTGCAGTGGAGC-GAATTAAAACC-T
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAG-ATTAAAGCCAT
* * ** * * * *** *
55717017 CAAATATTATCTCTTTGAAATTGCAG-AGAACAGATCGCA-TC-T
1 --AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAT
* * *
55717059 AGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGGCTAAGTAAG-CA-
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCA-GATTA--AAGCCAT
* * *
55717103 AGTCTTATC-CTCCTGAAGTTGCAGTGGGGCAGACTAAAGATGGCA-
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGAGCAGA-TTAA-A-GCCAT
*
55717148 AGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCGAT
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC-AT
* * ** * * * *
55717192 AATCCTATCTCATTGAAGTTGCATTAGAGCGGATTAAAACC-T
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAT
* * *** *
55717234 CAGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGATCGCA-TC-T
1 -AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAT
*
55717276 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAG-CA-
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTA--AAGCCAT
* * *
55717320 AGTCTTATC-CTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCA-
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGAGCAGA-TTAA-A-GCCAT
*
55717365 AGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCGAT
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC-AT
* * * * * *
55717409 AATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCTT
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAT
* * *** *
55717452 AGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGATCGCA-TC-T
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAT
* * * *
55717493 AGTCATATCTCCCTAAAGTTGCAGTGAAGCAGACTAAATAAG-CA-
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-T-TA-AAGCCAT
55717537 AGTCTTATC-CTCCTGAAGTTGCAGTG
1 AGTCTTATCTC-CCTGAAGTTGCAGTG
55717563 AGGCAGACTA
Statistics
Matches: 458, Mismatches: 89, Indels: 82
0.73 0.14 0.13
Matches are distributed among these distances:
40 58 0.13
41 22 0.05
42 17 0.04
43 36 0.08
44 261 0.57
45 62 0.14
46 2 0.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28
Consensus pattern (43 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAT
Found at i:55717304 original size:217 final size:217
Alignment explanation
Indices: 55716922--55717581 Score: 1095
Period size: 217 Copynumber: 3.0 Consensus size: 217
55716912 GAGAAGGTTG
* *
55716922 AAGATGGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCGATAGTCCTATCTCC
1 AAGATGGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCC
* * * * * *
55716987 CTGAAGTTGCAGTGGAGCGAATTAAAACCTCAAATATTATCTCTTTGAAATTGCAGAGAACAGAT
66 CTGAAGTTGCAGTGGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGAT
* *
55717052 CGCATCTAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGGCTAAGTAAGCAAGTCTTATCCTCCT
131 CGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCT
55717117 GAAGTTGCAGTGGGGCAGACTA
196 GAAGTTGCAGTGGGGCAGACTA
* *
55717139 AAGATGGCAAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCA
1 AAGATGGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCC
* * *
55717204 TTGAAGTTGCATTAGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGAT
66 CTGAAGTTGCAGTGGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGAT
55717269 CGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCT
131 CGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCT
*
55717334 GAAGTTGCAGTGGGGCAGACTG
196 GAAGTTGCAGTGGGGCAGACTA
*
55717356 AAGATGGCAAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCGATAATCCTATCTCC
1 AAGATGGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCC
* *
55717421 CTGAAGTTACAGTGGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGAT
66 CTGAAGTTGCAGTGGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGAT
* * * *
55717486 CGCATCTAGTCATATCTCCCTAAAGTTGCAGTGAAGCAGACTAAATAAGCAAGTCTTATCCTCCT
131 CGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCT
*
55717551 GAAGTTGCAGTGAGGCAGACTA
196 GAAGTTGCAGTGGGGCAGACTA
*
55717573 AATATGGCA
1 AAGATGGCA
55717582 CTAATTCCTA
Statistics
Matches: 412, Mismatches: 31, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
217 412 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (217 bp):
AAGATGGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCC
CTGAAGTTGCAGTGGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGAT
CGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCT
GAAGTTGCAGTGGGGCAGACTA
Found at i:55717427 original size:173 final size:173
Alignment explanation
Indices: 55717103--55717428 Score: 385
Period size: 173 Copynumber: 1.9 Consensus size: 173
55717093 TAAGTAAGCA
* *
55717103 AGTCTTATCCTCCTGAAGTTGCAGTGGGGCAGACTAAAGATGGCAAGTCTTATCTCCTTGAAGTT
1 AGTCTTATCCTCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCAAGTCTTATCTCCTTGAAGTT
* * * * * *
55717168 GCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCATTGAAGTTGCATTAGAGCGGATTAAAACC
66 GCAGTGGAGCAGACTAAAGACGACAATCCTATCTCACTGAAGTTGCAGTAGAGCAGATTAAAACC
* *
55717233 TCAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCT
131 TCAGATCCTATCTCCCTGAAGTTGCAGAGAGCAGATCGCATCT
55717276 AGTCTTAT-CTCCCTGAAGTTGCAGTGGAGCAGACT-AAG-TAAGCAAGTCTTATCCTCC-TGAA
1 AGTCTTATCCT-CCTGAAGTTGCAGTGGAGCAGACTAAAGAT-AGCAAGTCTTAT-CTCCTTGAA
* * * * * * * *
55717337 GTTGCAGTGGGGCAGACTGAAGATGGCAAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAA
63 GTTGCAGTGGAGCAGACTAAAGACGACAA-TCCTATCTCACTGAAGTTGCAGTAGAGCAGATTAA
*
55717402 AGCCGAT-A-ATCCTATCTCCCTGAAGTT
127 AACC--TCAGATCCTATCTCCCTGAAGTT
55717429 ACAGTGGAGC
Statistics
Matches: 128, Mismatches: 19, Indels: 12
0.81 0.12 0.08
Matches are distributed among these distances:
171 1 0.01
172 42 0.33
173 83 0.65
174 1 0.01
175 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (173 bp):
AGTCTTATCCTCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCAAGTCTTATCTCCTTGAAGTT
GCAGTGGAGCAGACTAAAGACGACAATCCTATCTCACTGAAGTTGCAGTAGAGCAGATTAAAACC
TCAGATCCTATCTCCCTGAAGTTGCAGAGAGCAGATCGCATCT
Found at i:55719431 original size:7 final size:7
Alignment explanation
Indices: 55719419--55719480 Score: 54
Period size: 7 Copynumber: 8.7 Consensus size: 7
55719409 CTAATTAATT
55719419 TAAACCC
1 TAAACCC
55719426 TAAACCC
1 TAAACCC
*
55719433 T-GACTCC
1 TAAAC-CC
*
55719440 TAAATCC
1 TAAACCC
*
55719447 TAAAGCC
1 TAAACCC
55719454 TAAACCCC
1 TAAA-CCC
*
55719462 TAACCCC
1 TAAACCC
*
55719469 TAAACCT
1 TAAACCC
55719476 TAAAC
1 TAAAC
55719481 TCCAGCCCTT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
6 2 0.05
7 36 0.82
8 6 0.14
ACGTcount: A:0.39, C:0.39, G:0.03, T:0.19
Consensus pattern (7 bp):
TAAACCC
Found at i:55719502 original size:7 final size:7
Alignment explanation
Indices: 55719490--55719550 Score: 59
Period size: 7 Copynumber: 8.6 Consensus size: 7
55719480 CTCCAGCCCT
55719490 TAAACCA
1 TAAACCA
55719497 TAAACCA
1 TAAACCA
*
55719504 TAAATCA
1 TAAACCA
*
55719511 TAAATCA
1 TAAACCA
* *
55719518 TAAGCCC
1 TAAACCA
55719525 TAAACCCA
1 TAAA-CCA
*
55719533 TAATCCA
1 TAAACCA
*
55719540 TAAACCT
1 TAAACCA
55719547 TAAA
1 TAAA
55719551 TAATATCTTT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
7 39 0.89
8 5 0.11
ACGTcount: A:0.51, C:0.26, G:0.02, T:0.21
Consensus pattern (7 bp):
TAAACCA
Found at i:55719551 original size:36 final size:36
Alignment explanation
Indices: 55719452--55719551 Score: 98
Period size: 36 Copynumber: 2.8 Consensus size: 36
55719442 AATCCTAAAG
* * * *
55719452 CCTAAACCCCTAACCCCTAAACCTTAAA-CTCCAGC
1 CCTAAACCCATAAACCATAAACCTTAAATCTCAAGC
* *
55719487 CCTTAAA-CCATAAACCATAAATCATAAATCAT-AAGC
1 CC-TAAACCCATAAACCATAAACCTTAAATC-TCAAGC
*
55719523 CCTAAACCCATAATCCATAAACCTTAAAT
1 CCTAAACCCATAAACCATAAACCTTAAAT
55719552 AATATCTTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
35 22 0.42
36 29 0.56
37 1 0.02
ACGTcount: A:0.43, C:0.34, G:0.02, T:0.21
Consensus pattern (36 bp):
CCTAAACCCATAAACCATAAACCTTAAATCTCAAGC
Found at i:55719578 original size:14 final size:14
Alignment explanation
Indices: 55719561--55719606 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
55719551 TAATATCTTT
55719561 TAAACCTTAAACCC
1 TAAACCTTAAACCC
* *
55719575 TAAACCATATACCC
1 TAAACCTTAAACCC
*
55719589 -CAACCTTAAACCC
1 TAAACCTTAAACCC
55719602 TAAAC
1 TAAAC
55719607 TATAATGATA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.43, C:0.37, G:0.00, T:0.20
Consensus pattern (14 bp):
TAAACCTTAAACCC
Found at i:55719734 original size:19 final size:19
Alignment explanation
Indices: 55719710--55719841 Score: 201
Period size: 19 Copynumber: 6.8 Consensus size: 19
55719700 AACTTTTGAG
*
55719710 GATATGCAATCTTATATAT
1 GATATGCAATCTTAGATAT
*
55719729 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
55719748 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
55719767 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
55719788 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
55719807 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
55719826 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
55719842 ATATATGATT
Statistics
Matches: 104, Mismatches: 7, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
19 85 0.82
21 19 0.18
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:55719777 original size:59 final size:57
Alignment explanation
Indices: 55719710--55719848 Score: 201
Period size: 59 Copynumber: 2.4 Consensus size: 57
55719700 AACTTTTGAG
* *
55719710 GATATGCAATCTTATATATGATATGCAATCCTAGATATGATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATACAATCTTAGATAT
* * *
55719767 GATATATGCAATCTTAGATATGATATGTAATCTTAGATATGATATATAATCTTAGATAT
1 G--ATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATACAATCTTAGATAT
55719826 GATATGCAATCTTAGA-AT-ATATG
1 GATATGCAATCTTAGATATGATATG
55719849 ATTTTGTAAT
Statistics
Matches: 75, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
55 5 0.07
56 2 0.03
57 16 0.21
59 52 0.69
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.38
Consensus pattern (57 bp):
GATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATACAATCTTAGATAT
Found at i:55719881 original size:57 final size:57
Alignment explanation
Indices: 55719711--55719864 Score: 184
Period size: 59 Copynumber: 2.6 Consensus size: 57
55719701 ACTTTTGAGG
* * * **
55719711 ATATGCAATCTTATATATGATATGCAATCCTAGATATGATATGCAATCTTAGATATGA
1 ATATGCAATCTTAGATATGATATGTAATCTTAGA-ATGATATATAATCTTAGATATGA
55719769 TATATGCAATCTTAGATATGATATGTAATCTTAGATATGATATATAATCTTAGATATG-
1 -ATATGCAATCTTAGATATGATATGTAATCTTAGA-ATGATATATAATCTTAGATATGA
*
55719827 ATATGCAATCTTAGAATATATGATTTTGTAATCTTAGA
1 ATATGCAATCTTAG---ATATGA-TATGTAATCTTAGA
55719865 GATTTAATTT
Statistics
Matches: 85, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
57 14 0.16
59 52 0.61
60 6 0.07
61 13 0.15
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.40
Consensus pattern (57 bp):
ATATGCAATCTTAGATATGATATGTAATCTTAGAATGATATATAATCTTAGATATGA
Found at i:55720191 original size:6 final size:7
Alignment explanation
Indices: 55720174--55720210 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
55720164 GTAATTAAGT
55720174 TTTTTTA
1 TTTTTTA
55720181 TTTTTTA
1 TTTTTTA
55720188 TTTTTTA
1 TTTTTTA
55720195 TTTTTTA
1 TTTTTTA
55720202 -TTTTTA
1 TTTTTTA
55720208 TTT
1 TTT
55720211 ATTTTAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTTA
Found at i:55720655 original size:25 final size:26
Alignment explanation
Indices: 55720612--55720661 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
55720602 TGTACATGTA
55720612 TATATTTTTTTAAACGAATATTTTCC
1 TATATTTTTTTAAACGAATATTTTCC
*
55720638 TATATTTTTTT-AATGAATATTTTC
1 TATATTTTTTTAAACGAATATTTTC
55720662 ATATTTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.30, C:0.08, G:0.04, T:0.58
Consensus pattern (26 bp):
TATATTTTTTTAAACGAATATTTTCC
Found at i:55721459 original size:98 final size:98
Alignment explanation
Indices: 55721336--55721530 Score: 354
Period size: 98 Copynumber: 2.0 Consensus size: 98
55721326 AAAAATCATG
*
55721336 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTCTT
1 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
55721401 AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
66 AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
* *
55721434 AAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
1 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
*
55721499 AAATCTTGGATGAGTGGATGTTCTTTTAAAGT
66 AAATCTTGGATAAGTGGATGTTCTTTTAAAGT
55721531 TTTATTGTAC
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.28, C:0.11, G:0.25, T:0.36
Consensus pattern (98 bp):
AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
Found at i:55726006 original size:11 final size:10
Alignment explanation
Indices: 55725990--55726014 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
55725980 AGTTCAGATT
55725990 AAAAAAAACA
1 AAAAAAAACA
55726000 AAAAAAAACA
1 AAAAAAAACA
55726010 AAAAA
1 AAAAA
55726015 TAAAAGTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:55727552 original size:44 final size:44
Alignment explanation
Indices: 55727376--55727552 Score: 101
Period size: 44 Copynumber: 4.0 Consensus size: 44
55727366 AAGGTTGAAA
*
55727376 ATTGTAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAG
1 ATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAG
** * * * **
55727420 ACGGCAAATCTTATCTTTCC-AAG-A-TAGTGGGCAGCAGATTTAAG
1 ATTGTAGATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATCGAAG
* ** * * * * * ** * * *
55727464 CTACTA-AGCCTTGTCTCTCTCAGCAGCAGCAGAGAAGGTTGAAG
1 ATTGTAGA-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAG
55727508 ATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAG
1 ATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAG
55727552 A
1 A
55727553 CGACGAATCT
Statistics
Matches: 88, Mismatches: 37, Indels: 16
0.62 0.26 0.11
Matches are distributed among these distances:
42 4 0.05
43 6 0.07
44 70 0.80
45 6 0.07
46 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.26
Consensus pattern (44 bp):
ATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAG
Found at i:55727639 original size:132 final size:132
Alignment explanation
Indices: 55727271--55727659 Score: 609
Period size: 132 Copynumber: 2.9 Consensus size: 132
55727261 CTGCATTGAC
*
55727271 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCTAAGATAGTGGGAAGCAGATTTAAGCCAC
1 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAC
* * * *
55727336 CAAGCATTGTCGCCCTAAGCAACAGCGGAGAAGGTTGAAAATTGTAGATCTTATCTCCCTAAACA
66 CAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAACA
55727401 GT
131 GT
* * *
55727403 AGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGCAGCAGATTTAAGCTAC
1 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAC
* * * * *
55727468 TAAGCCTTGTCTCTCTCAGCAGCAGCAGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCA
66 CAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAACA
55727533 GT
131 GT
* *
55727535 AGTGGAGCAGATCGAAGACGACGAATCTTAACTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAC
1 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAC
* *
55727600 CAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAAGGTTGAAGATGGCA-AGTCTTATCTCCCT
66 CAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAAGGTTGAAGATTGTAGA-TCTTATCTCCCT
55727660 GAAGTTGCAG
Statistics
Matches: 232, Mismatches: 24, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
131 1 0.00
132 231 1.00
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.24
Consensus pattern (132 bp):
AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAC
CAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAACA
GT
Found at i:55727699 original size:44 final size:44
Alignment explanation
Indices: 55727646--55728200 Score: 296
Period size: 44 Copynumber: 12.8 Consensus size: 44
55727636 GAAGATGGCA
*
55727646 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCGAT
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGAT
* * *
55727690 AGTCCTATCTCCCTGAAGTTGCAGTGGAGC-GAATTAAAACCTCA-
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAG-ATTAAAGCC-GAT
* * ** * * * * ***
55727734 AATATTATCTCTTTGAAATTGCAG-AGAACAGA-T--CGCATCT
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGAT
* * *
55727774 AGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGGCTAAGTAAG-C-A-
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCA-GATTA--AAGCCGAT
* * **
55727818 AGTCTTATC-CTCCTGAAGTTGCAGTGGGGCAGACTAAAGATGGCA-
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGAGCAGATTAAAG-CCG-AT
*
55727863 AGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCGAT
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGAT
* * ** * * * *
55727907 AATCCTATCTCATTGAAGTTGCATTAGAGCGGATTAAAACC--T
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGAT
* * * ***
55727949 CAGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T--CGCATCT
1 -AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGAT
*
55727991 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAG-C-A-
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTA--AAGCCGAT
* * **
55728035 AGTCTTATC-CTCCTGAAGTTGCAGTGGGGCAGACTAAAGATGGCA-
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGAGCAGATTAAAG-CCG-AT
*
55728080 AGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCGAT
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGAT
* * ** * * * *
55728124 AATCCTATCTCATTGAAGTTGCATTAGAGCGGATTAAAACC--T
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGAT
* *
55728166 CAGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGAT
1 -AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
55728201 CGCATCTAGT
Statistics
Matches: 388, Mismatches: 85, Indels: 77
0.71 0.15 0.14
Matches are distributed among these distances:
40 41 0.11
41 19 0.05
42 6 0.02
43 28 0.07
44 219 0.56
45 71 0.18
46 2 0.01
47 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (44 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGAT
Found at i:55728019 original size:217 final size:217
Alignment explanation
Indices: 55727637--55728296 Score: 1122
Period size: 217 Copynumber: 3.0 Consensus size: 217
55727627 GAGAAGGTTG
* * * *
55727637 AAGATGGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCGATAGTCCTATCTCC
1 AAGATGGCAAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCA
* * * * * * * * *
55727702 CTGAAGTTGCAGTGGAGCGAATTAAAACCTCAAATATTATCTCTTTGAAATTGCAGAGAACAGAT
66 TTGAAGTTGCATTAGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGAT
* *
55727767 CGCATCTAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGGCTAAGTAAGCAAGTCTTATCCTCCT
131 CGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCT
55727832 GAAGTTGCAGTGGGGCAGACTA
196 GAAGTTGCAGTGGGGCAGACTA
55727854 AAGATGGCAAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCA
1 AAGATGGCAAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCA
55727919 TTGAAGTTGCATTAGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGAT
66 TTGAAGTTGCATTAGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGAT
55727984 CGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCT
131 CGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCT
55728049 GAAGTTGCAGTGGGGCAGACTA
196 GAAGTTGCAGTGGGGCAGACTA
55728071 AAGATGGCAAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCA
1 AAGATGGCAAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCA
55728136 TTGAAGTTGCATTAGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGAT
66 TTGAAGTTGCATTAGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGAT
* * * * *
55728201 CGCATCTAGTCATATCTCCGTAAAGTTGCAGTGAAGCAGACTAAATAAGCAAGTCTTATCCTCCT
131 CGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCT
*
55728266 GAAGTTGCAGTGAGGCAGACTA
196 GAAGTTGCAGTGGGGCAGACTA
*
55728288 AATATGGCA
1 AAGATGGCA
55728297 CTAATTCCTA
Statistics
Matches: 421, Mismatches: 22, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
217 421 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (217 bp):
AAGATGGCAAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCA
TTGAAGTTGCATTAGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGAT
CGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCT
GAAGTTGCAGTGGGGCAGACTA
Found at i:55728143 original size:173 final size:173
Alignment explanation
Indices: 55727818--55728146 Score: 411
Period size: 173 Copynumber: 1.9 Consensus size: 173
55727808 TAAGTAAGCA
* *
55727818 AGTCTTATCCTCCTGAAGTTGCAGTGGGGCAGACTAAAGATGGCAAGTCTTATCTCCTTGAAGTT
1 AGTCTTATCCTCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCAAGTCTTATCTCCTTGAAGTT
* * * * *
55727883 GCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCATTGAAGTTGCATTAGAGCGGATTAAAACC
66 GCAGTGGAGCAGACTAAAGACGACAATCCTATCTCATTGAAGTTGCAGTAGAGCAGATTAAAACC
*
55727948 TCAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCT
131 TCAGATCCTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCT
55727991 AGTCTTAT-CTCCCTGAAGTTGCAGTGGAGCAGACT-AAG-TAAGCAAGTCTTATCCTCC-TGAA
1 AGTCTTATCCT-CCTGAAGTTGCAGTGGAGCAGACTAAAGAT-AGCAAGTCTTAT-CTCCTTGAA
* * * * * *
55728052 GTTGCAGTGGGGCAGACTAAAGATGGCAAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAA
63 GTTGCAGTGGAGCAGACTAAAGACGACAA-TCCTATCTCATTGAAGTTGCAGTAGAGCAGATTAA
*
55728117 AGCCGAT-A-ATCCTATCTCAT-TGAAGTTGCA
127 AACC--TCAGATCCTATCTC-TCTGAAGTTGCA
55728147 TTAGAGCGGA
Statistics
Matches: 134, Mismatches: 15, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
171 1 0.01
172 43 0.32
173 87 0.65
174 2 0.01
175 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (173 bp):
AGTCTTATCCTCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCAAGTCTTATCTCCTTGAAGTT
GCAGTGGAGCAGACTAAAGACGACAATCCTATCTCATTGAAGTTGCAGTAGAGCAGATTAAAACC
TCAGATCCTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCT
Found at i:55728272 original size:44 final size:43
Alignment explanation
Indices: 55727774--55728291 Score: 287
Period size: 44 Copynumber: 11.9 Consensus size: 43
55727764 GATCGCATCT
* * *
55727774 AGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGGCTAAGTAAGCA
1 AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGACTAAATAAGCA
* * *
55727818 AGTCTTATCCTCCTGAAGTTGCAGTGGGGCAGACTAAAGATGGCA
1 AGTCTTAT-CTCCTGAAGTTGCAGTGGAGCAGACTAAATA-AGCA
* ***
55727863 AGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCG-A
1 AGTCTTATCTCC-TGAAGTTGCAGTGGAGCAGACTAAATAAGCA
* * * * * * * * *
55727906 TAATCCTATCTCATTGAAGTTGCATTAGAGCGGA-TTAA-AACCTC
1 -AGTCTTATCTC-CTGAAGTTGCAGTGGAGCAGACTAAATAAGC-A
* ** *
55727950 AGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-TCGCAT---CT
1 AG-TCTTATCTC-CTGAAGTTGCAGTGGAGCAGACT-AAATAAGCA
*
55727991 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
1 AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGACTAAATAAGCA
* * *
55728035 AGTCTTATCCTCCTGAAGTTGCAGTGGGGCAGACTAAAGATGGCA
1 AGTCTTAT-CTCCTGAAGTTGCAGTGGAGCAGACTAAATA-AGCA
* ***
55728080 AGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCG-A
1 AGTCTTATCTCC-TGAAGTTGCAGTGGAGCAGACTAAATAAGCA
* * * * * * * * *
55728123 TAATCCTATCTCATTGAAGTTGCATTAGAGCGGA-TTAA-AACCTC
1 -AGTCTTATCTC-CTGAAGTTGCAGTGGAGCAGACTAAATAAGC-A
* ** *
55728167 AGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-TCGCAT---CT
1 AG-TCTTATCTC-CTGAAGTTGCAGTGGAGCAGACT-AAATAAGCA
* * *
55728208 AGTCATATCTCCGTAAAGTTGCAGTGAAGCAGACTAAATAAGCA
1 AGTCTTATCTCC-TGAAGTTGCAGTGGAGCAGACTAAATAAGCA
55728252 AGTCTTATCCTCCTGAAGTTGCAGT-GAGGCAGACTAAATA
1 AGTCTTAT-CTCCTGAAGTTGCAGTGGA-GCAGACTAAATA
55728292 TGGCACTAAT
Statistics
Matches: 367, Mismatches: 73, Indels: 68
0.72 0.14 0.13
Matches are distributed among these distances:
39 1 0.00
40 38 0.10
41 21 0.06
42 4 0.01
43 27 0.07
44 198 0.54
45 78 0.21
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (43 bp):
AGTCTTATCTCCTGAAGTTGCAGTGGAGCAGACTAAATAAGCA
Found at i:55728486 original size:19 final size:19
Alignment explanation
Indices: 55728462--55728574 Score: 172
Period size: 19 Copynumber: 5.8 Consensus size: 19
55728452 AATTTTTGAG
*
55728462 GATATGCAATCTTATATAT
1 GATATGCAATCTTAGATAT
*
55728481 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
55728500 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
55728519 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
**
55728540 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
55728559 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
55728575 ATATATGATT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
19 66 0.78
21 19 0.22
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:55728529 original size:59 final size:59
Alignment explanation
Indices: 55728463--55728574 Score: 188
Period size: 59 Copynumber: 1.9 Consensus size: 59
55728453 ATTTTTGAGG
* *
55728463 ATATGCAATCTTATATATGATATGCAATCCTAGATATGATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGATATACAATCCTAGATATGATATGCAATCTTAGATATGAT
* *
55728522 ATATGCAATCTTAGATATGATATATAATCTTAGATATGATATGCAATCTTAGA
1 ATATGCAATCTTAGATATGATATACAATCCTAGATATGATATGCAATCTTAGA
55728575 ATATATGATT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (59 bp):
ATATGCAATCTTAGATATGATATACAATCCTAGATATGATATGCAATCTTAGATATGAT
Found at i:55728537 original size:40 final size:38
Alignment explanation
Indices: 55728462--55728581 Score: 172
Period size: 40 Copynumber: 3.2 Consensus size: 38
55728452 AATTTTTGAG
* *
55728462 GATATGCAATCTTATATATGATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATATGATATGCAATCTTAGATAT
55728500 GATATGCAATCTTAGATATGATATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATATG--ATATGCAATCTTAGATAT
**
55728540 GATATATAATCTTAGATATGATATGCAATCTTAGA-AT
1 GATATGCAATCTTAGATATGATATGCAATCTTAGATAT
55728577 -ATATG
1 GATATG
55728582 ATTTTGTAAT
Statistics
Matches: 75, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
36 4 0.05
37 2 0.03
38 34 0.45
40 35 0.47
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (38 bp):
GATATGCAATCTTAGATATGATATGCAATCTTAGATAT
Found at i:55728898 original size:7 final size:7
Alignment explanation
Indices: 55728886--55728915 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
55728876 TAATTAAGTT
55728886 TTTTTTA
1 TTTTTTA
55728893 TTTTTTA
1 TTTTTTA
55728900 -TTTTTA
1 TTTTTTA
55728906 TTTTTTA
1 TTTTTTA
55728913 TTT
1 TTT
55728916 ATTTTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTTA
Found at i:55728903 original size:13 final size:13
Alignment explanation
Indices: 55728887--55728915 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
55728877 AATTAAGTTT
55728887 TTTTTATTTTTTA
1 TTTTTATTTTTTA
55728900 TTTTTATTTTTTA
1 TTTTTATTTTTTA
55728913 TTT
1 TTT
55728916 ATTTTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:55730135 original size:98 final size:98
Alignment explanation
Indices: 55730002--55730198 Score: 349
Period size: 98 Copynumber: 2.0 Consensus size: 98
55729992 TTAAAAATAA
* *
55730002 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
55730067 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
* *
55730100 TAAATGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
*
55730165 TTAAATCTTGGATGAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
55730198 T
1 T
55730199 TTTATTATAC
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.27, C:0.10, G:0.25, T:0.38
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:55731182 original size:41 final size:42
Alignment explanation
Indices: 55731097--55731211 Score: 144
Period size: 41 Copynumber: 2.8 Consensus size: 42
55731087 TAAAATATCT
* * *
55731097 TTAGCGGCGCTTTTCCAAAAACGCCACTAAAG-CCAAGAGAA
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGAACAACAGAA
* *
55731138 TTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGAAC-ACAGTA
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGAACAACAGAA
***
55731179 TTAGCGGCGCTTTTTTGAAAACGCCGCTAAAGA
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGA
55731212 TCCGAAAGGT
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
41 63 0.98
42 1 0.02
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.20
Consensus pattern (42 bp):
TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGAACAACAGAA
Found at i:55731321 original size:39 final size:38
Alignment explanation
Indices: 55731268--55731384 Score: 117
Period size: 40 Copynumber: 3.0 Consensus size: 38
55731258 CATTTTTATA
*
55731268 AAAAACGCCGCTAATGCTCATTTTTAGCGGCGTTTTTC
1 AAAAATGCCGCTAATGCTCATTTTTAGCGGCGTTTTTC
* * * * *
55731306 AGAAAATGCCACTAATGCTTGATCTTTAGTGGCGATTTTC
1 A-AAAATGCCGCTAATGC-TCATTTTTAGCGGCGTTTTTC
* * *
55731346 ATAAATCGCCGCTAATGCTCGATTTTTACCGACGTTTTT
1 AAAAAT-GCCGCTAATGCTC-ATTTTTAGCGGCGTTTTT
55731385 TTCTAAGCGT
Statistics
Matches: 61, Mismatches: 14, Indels: 6
0.75 0.17 0.07
Matches are distributed among these distances:
38 1 0.02
39 19 0.31
40 41 0.67
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (38 bp):
AAAAATGCCGCTAATGCTCATTTTTAGCGGCGTTTTTC
Found at i:55733261 original size:18 final size:19
Alignment explanation
Indices: 55733238--55733282 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
55733228 AAATTTACTA
55733238 ATTAATTT-TTTGGACCAC
1 ATTAATTTCTTTGGACCAC
55733256 ATTAATTTCTTTGGACCAC
1 ATTAATTTCTTTGGACCAC
55733275 ATTAATTT
1 ATTAATTT
55733283 AAGATCTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 8 0.31
19 18 0.69
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.47
Consensus pattern (19 bp):
ATTAATTTCTTTGGACCAC
Found at i:55733935 original size:6 final size:6
Alignment explanation
Indices: 55733924--55733956 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
55733914 AAAAAAATTA
55733924 TCAATG TCAATG TCAATG TCAATG TCAATG TCA
1 TCAATG TCAATG TCAATG TCAATG TCAATG TCA
55733957 TCAATGATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (6 bp):
TCAATG
Found at i:55743869 original size:54 final size:54
Alignment explanation
Indices: 55743786--55743920 Score: 189
Period size: 54 Copynumber: 2.5 Consensus size: 54
55743776 CACACAGCCG
* * * *
55743786 TGTGTCTTAAAATAGTGAGTAACACGGTCTGAGACACGACCAATGACATGACTA
1 TGTGTCTTAAAACAGTGAGTAACACGGTCTGAAACACGACCAACGACATGACCA
* * * *
55743840 TGTGTTTTAAAACAGTGAGTAACATGGTCTGAAACACGGCCAACGACATGACCG
1 TGTGTCTTAAAACAGTGAGTAACACGGTCTGAAACACGACCAACGACATGACCA
*
55743894 TGTGTCTTAAAACAGTGAGTTACACGG
1 TGTGTCTTAAAACAGTGAGTAACACGG
55743921 GTAGGTACAC
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 70 1.00
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (54 bp):
TGTGTCTTAAAACAGTGAGTAACACGGTCTGAAACACGACCAACGACATGACCA
Found at i:55745818 original size:21 final size:21
Alignment explanation
Indices: 55745782--55745835 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
55745772 CAAAACTGAA
* *
55745782 CAATTCAACTAGATCAAAATC
1 CAATTAAACTAAATCAAAATC
55745803 C-ATCTAAACTAAATCAAAATC
1 CAAT-TAAACTAAATCAAAATC
55745824 CAATTAAACTAA
1 CAATTAAACTAA
55745836 CCATGCCTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 2 0.07
21 25 0.86
22 2 0.07
ACGTcount: A:0.52, C:0.22, G:0.02, T:0.24
Consensus pattern (21 bp):
CAATTAAACTAAATCAAAATC
Found at i:55753320 original size:36 final size:37
Alignment explanation
Indices: 55753255--55753336 Score: 103
Period size: 36 Copynumber: 2.2 Consensus size: 37
55753245 TTCTAATTGG
* * **
55753255 AACACACCAGATGCTTATAAGAGATAATCCATTCGA-
1 AACACACCAGATGCTCATAAGAGACAATCCACCCGAT
* *
55753291 AACACACCAGATGCTCATATGAGCCAATCCACCCGAT
1 AACACACCAGATGCTCATAAGAGACAATCCACCCGAT
55753328 AACACACCA
1 AACACACCA
55753337 ATGGCTCCGA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
36 30 0.77
37 9 0.23
ACGTcount: A:0.40, C:0.30, G:0.12, T:0.17
Consensus pattern (37 bp):
AACACACCAGATGCTCATAAGAGACAATCCACCCGAT
Found at i:55759491 original size:17 final size:17
Alignment explanation
Indices: 55759466--55759505 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
55759456 TAGAATTGGG
* *
55759466 TTGAGAAAATTATTTAA
1 TTGAAAAAATTAATTAA
55759483 TTGAAAAAATTAATTAA
1 TTGAAAAAATTAATTAA
55759500 TT-AAAA
1 TTGAAAA
55759506 CTAATTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (17 bp):
TTGAAAAAATTAATTAA
Found at i:55760345 original size:30 final size:31
Alignment explanation
Indices: 55760299--55760389 Score: 78
Period size: 30 Copynumber: 3.0 Consensus size: 31
55760289 ATACATATTA
* *
55760299 CATTTTCATACTTTGTATTCATTCACATTTG
1 CATTATCATACCTTGTATTCATTCACATTTG
* **
55760330 TA-TATCATACCTTGTAATT-GGTCACATTTG
1 CATTATCATACCTTGT-ATTCATTCACATTTG
* * * *
55760360 CATTTTCATACCCTGTAATCATTCATATTT
1 CATTATCATACCTTGTATTCATTCACATTT
55760390 TCACATATAT
Statistics
Matches: 45, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
30 23 0.51
31 22 0.49
ACGTcount: A:0.25, C:0.20, G:0.08, T:0.47
Consensus pattern (31 bp):
CATTATCATACCTTGTATTCATTCACATTTG
Found at i:55760377 original size:31 final size:30
Alignment explanation
Indices: 55760321--55760378 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
55760311 TTGTATTCAT
* *
55760321 TCACATTTGTATATCATACCTTGTAATTGG
1 TCACATTTGCATATCATACCCTGTAATTGG
*
55760351 TCACATTTGCATTTTCATACCCTGTAAT
1 TCACATTTGCA-TATCATACCCTGTAAT
55760379 CATTCATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 10 0.42
31 14 0.58
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (30 bp):
TCACATTTGCATATCATACCCTGTAATTGG
Found at i:55766295 original size:46 final size:46
Alignment explanation
Indices: 55766242--55766381 Score: 210
Period size: 46 Copynumber: 3.0 Consensus size: 46
55766232 CCATGGCAAA
*
55766242 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATTCTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
* * *
55766288 TTGTGAAAAGTAGGTGTGGTGTGTCAATGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
* *
55766334 TTGTGAAAAGTAGGTATGGTATTTCAGTGAA-AGAAACTATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGA-AAACCATACTGAG
55766380 TT
1 TT
55766382 ATAGCATTGT
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
45 1 0.01
46 83 0.99
ACGTcount: A:0.34, C:0.08, G:0.28, T:0.30
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
Found at i:55769310 original size:7 final size:7
Alignment explanation
Indices: 55769293--55769324 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
55769283 ATAATATGCC
55769293 TTAGTTAT
1 TTAG-TAT
55769301 TTAGTAT
1 TTAGTAT
55769308 TTAGTAT
1 TTAGTAT
55769315 TTAGTAT
1 TTAGTAT
55769322 TTA
1 TTA
55769325 TTTGTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 20 0.83
8 4 0.17
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.59
Consensus pattern (7 bp):
TTAGTAT
Found at i:55769654 original size:69 final size:69
Alignment explanation
Indices: 55769550--55769707 Score: 210
Period size: 69 Copynumber: 2.3 Consensus size: 69
55769540 GTGGTATTGG
* * * * *
55769550 ACCTGTGAGCCCTAAAATGACAGTTAGAAGTTTTTAGCTCTCGCTAACTGTTTGGGGCTACAATG
1 ACCTGCGAGCCATAAAATGAAAGTTAGAAGCTTTTAACTCTCGCTAACTGTTTGGGGCTACAATG
*
55769615 TTTG
66 TTTA
* * * *
55769619 ACGTGCGAGCCATAAAATGAAAGTT-GATAGCTTTTAACTCTCGTTAACTGTTTGGGGCTGCAGT
1 ACCTGCGAGCCATAAAATGAAAGTTAGA-AGCTTTTAACTCTCGCTAACTGTTTGGGGCTACAAT
55769683 GTTTA
65 GTTTA
55769688 ACCTGCGAGCCATAAAATGA
1 ACCTGCGAGCCATAAAATGA
55769708 CACTCGTTAA
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
68 2 0.03
69 75 0.97
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.31
Consensus pattern (69 bp):
ACCTGCGAGCCATAAAATGAAAGTTAGAAGCTTTTAACTCTCGCTAACTGTTTGGGGCTACAATG
TTTA
Found at i:55769719 original size:52 final size:52
Alignment explanation
Indices: 55769658--55769757 Score: 146
Period size: 52 Copynumber: 1.9 Consensus size: 52
55769648 GCTTTTAACT
* * *
55769658 CTCGTTAACTGTTTGGGGCTGCAGTGTTTAACCTGCGAGCCATAAAATGACA
1 CTCGTTAACTATTTGGGGCTGCAGTGTTTAACCTACAAGCCATAAAATGACA
* * *
55769710 CTCGTTAACTATTTGGGGTTGCGGTGTTTAACCTACAAGCCTTAAAAT
1 CTCGTTAACTATTTGGGGCTGCAGTGTTTAACCTACAAGCCATAAAAT
55769758 TATAGTTGGG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 42 1.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (52 bp):
CTCGTTAACTATTTGGGGCTGCAGTGTTTAACCTACAAGCCATAAAATGACA
Found at i:55769841 original size:69 final size:69
Alignment explanation
Indices: 55769731--55769999 Score: 304
Period size: 69 Copynumber: 3.9 Consensus size: 69
55769721 TTTGGGGTTG
* * * * * * * * *
55769731 CGGTGTTTAACCTACAAGCCTTAAAATTATAGTTGGGAGCTTTTAACTCTCGCTAATTGTTTAGG
1 CGGTGTTTAACCTGCGAGCCATAAAATGACAGCTAGGAGCTTTTAACTCTCACTAACTGTTTAGG
*
55769796 GTTA
66 GCTA
* ** * *
55769800 CGGTGTTCAACCTGCGAGCCATAAAATGACAGCTAAAAGCTTTTAACTCTCAATAACTGTTTGGG
1 CGGTGTTTAACCTGCGAGCCATAAAATGACAGCTAGGAGCTTTTAACTCTCACTAACTGTTTAGG
55769865 GCTA
66 GCTA
* * * * * * *
55769869 TGGTGTTTAACTTGCGAGCCATGAAATGACAGCTAGGAGTTTTTAACTATCACCAATTGTTTAGG
1 CGGTGTTTAACCTGCGAGCCATAAAATGACAGCTAGGAGCTTTTAACTCTCACTAACTGTTTAGG
*
55769934 GCTG
66 GCTA
* * *
55769938 CGGTGTTTAACCTACGAGCCATAAAATGACAGCTCGGAGCTTTTAACTCTCGCTAACTGTTT
1 CGGTGTTTAACCTGCGAGCCATAAAATGACAGCTAGGAGCTTTTAACTCTCACTAACTGTTT
55770000 TGGTTTTCGA
Statistics
Matches: 162, Mismatches: 38, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
69 162 1.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.32
Consensus pattern (69 bp):
CGGTGTTTAACCTGCGAGCCATAAAATGACAGCTAGGAGCTTTTAACTCTCACTAACTGTTTAGG
GCTA
Found at i:55772058 original size:88 final size:88
Alignment explanation
Indices: 55771898--55772065 Score: 192
Period size: 88 Copynumber: 1.9 Consensus size: 88
55771888 ACTCCGTCGT
* * * **
55771898 TCCTAATACTGACACTCCGTGCGAGCTTCAAGCCTGTTGGACACGTGTCTCACTTTGGGTCACCA
1 TCCTAATACTAACACTCCATGCGAGCTTCAAGCCTGCTGGACACGTGTCTCACCCTGGGTCACCA
*
55771963 ACGGAGCATGCGGTCCTTTTCGA
66 ACAGAGCATGCGGTCCTTTTCGA
* * * * * * * * *
55771986 TCCTAGTACTAACATTCCATGCGGGCTTCAGGCCTGCTGGACAGGTGTTTTACCCTGGGTCGCCT
1 TCCTAATACTAACACTCCATGCGAGCTTCAAGCCTGCTGGACACGTGTCTCACCCTGGGTCACCA
*
55772051 ACAGAGCATGTGGTC
66 ACAGAGCATGCGGTC
55772066 TCCCTTTTGC
Statistics
Matches: 64, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
88 64 1.00
ACGTcount: A:0.18, C:0.29, G:0.26, T:0.27
Consensus pattern (88 bp):
TCCTAATACTAACACTCCATGCGAGCTTCAAGCCTGCTGGACACGTGTCTCACCCTGGGTCACCA
ACAGAGCATGCGGTCCTTTTCGA
Found at i:55773922 original size:21 final size:21
Alignment explanation
Indices: 55773896--55773949 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
55773886 AATAGCGGTG
*
55773896 GCGGTGAGATTAATTACTGTA
1 GCGGTGAGATTAAGTACTGTA
**
55773917 GCGGTGAGATTGGGTACTGTA
1 GCGGTGAGATTAAGTACTGTA
55773938 GCGGTGAGATTA
1 GCGGTGAGATTA
55773950 GAAACAATGG
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:0.24, C:0.09, G:0.37, T:0.30
Consensus pattern (21 bp):
GCGGTGAGATTAAGTACTGTA
Found at i:55774265 original size:22 final size:22
Alignment explanation
Indices: 55774214--55774265 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
55774204 TTTTATAGTT
*
55774214 ATAATTAAATATTTTTTATAACA
1 ATAA-TAAATATTATTTATAACA
* *
55774237 ATGATAAATATTATTT-TCACAA
1 ATAATAAATATTATTTATAAC-A
55774259 ATAATAA
1 ATAATAA
55774266 CATTATACTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 3 0.12
22 18 0.75
23 3 0.12
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (22 bp):
ATAATAAATATTATTTATAACA
Found at i:55777619 original size:64 final size:64
Alignment explanation
Indices: 55777518--55777664 Score: 285
Period size: 64 Copynumber: 2.3 Consensus size: 64
55777508 ATGTTATATT
55777518 AGTTCGAATCCTCTAATTTTGATTGAATTAATAAGGTTAGAAATTTGAGAATTTTAAAATCTTA
1 AGTTCGAATCCTCTAATTTTGATTGAATTAATAAGGTTAGAAATTTGAGAATTTTAAAATCTTA
*
55777582 AGTTCGAATCCTTTAATTTTGATTGAATTAATAAGGTTAGAAATTTGAGAATTTTAAAATCTTA
1 AGTTCGAATCCTCTAATTTTGATTGAATTAATAAGGTTAGAAATTTGAGAATTTTAAAATCTTA
55777646 AGTTCGAATCCTCTAATTT
1 AGTTCGAATCCTCTAATTT
55777665 AAATACTATA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 81 1.00
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (64 bp):
AGTTCGAATCCTCTAATTTTGATTGAATTAATAAGGTTAGAAATTTGAGAATTTTAAAATCTTA
Found at i:55778317 original size:15 final size:15
Alignment explanation
Indices: 55778297--55778328 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
55778287 TGTAAGTTTC
55778297 TTAGAAATAAAATGA
1 TTAGAAATAAAATGA
*
55778312 TTAGAAATAAGATGA
1 TTAGAAATAAAATGA
55778327 TT
1 TT
55778329 GGGGAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.31
Consensus pattern (15 bp):
TTAGAAATAAAATGA
Found at i:55779011 original size:379 final size:379
Alignment explanation
Indices: 55778312--55779056 Score: 1481
Period size: 379 Copynumber: 2.0 Consensus size: 379
55778302 AATAAAATGA
55778312 TTAGAAATAAGATGATTGGGGAAATTTGGGTCAAAATTGAGGAAAAAGCAGTGAAGATAATCCTG
1 TTAGAAATAAGATGATTGGGGAAATTTGGGTCAAAATTGAGGAAAAAGCAGTGAAGATAATCCTG
55778377 GGAAGTGAATGGGAAACTTCCCAATCCAGGTGTTGAATGCAACAGTTTTTTCCTTTGAAATGAAC
66 GGAAGTGAATGGGAAACTTCCCAATCCAGGTGTTGAATGCAACAGTTTTTTCCTTTGAAATGAAC
55778442 GACCGAAAGAGTGAGCTCTTTTTTTTCCTTCTTGTTGTTGATTTAATTTGTGCTTTCTTTGCTTC
131 GACCGAAAGAGTGAGCTCTTTTTTTTCCTTCTTGTTGTTGATTTAATTTGTGCTTTCTTTGCTTC
55778507 TTTTCATTTGGTTAACGAATCTCTGAATCTTTTCATTTGATTTAATTTGTGCTTTCTTCGCTTTT
196 TTTTCATTTGGTTAACGAATCTCTGAATCTTTTCATTTGATTTAATTTGTGCTTTCTTCGCTTTT
55778572 TTTCATTTGGTTTGATTTATCCTCTCCCTCTCTCTTTGTCTCACACATATGCACATCAACAGACG
261 TTTCATTTGGTTTGATTTATCCTCTCCCTCTCTCTTTGTCTCACACATATGCACATCAACAGACG
*
55778637 CAATTGTGTGTTCATCTCTTGTTTTCATTATAATTTATTGCATTTGTAAGTTTC
326 CAATTGTGTGTTCATCTCTTGTTCTCATTATAATTTATTGCATTTGTAAGTTTC
55778691 TTAGAAATAAGATGATTGGGGAAATTTGGGTCAAAATTGAGGAAAAAGCAGTGAAGATAATCCTG
1 TTAGAAATAAGATGATTGGGGAAATTTGGGTCAAAATTGAGGAAAAAGCAGTGAAGATAATCCTG
55778756 GGAAGTGAATGGGAAACTTCCCAATCCAGGTGTTGAATGCAACAGTTTTTTCCTTTGAAATGAAC
66 GGAAGTGAATGGGAAACTTCCCAATCCAGGTGTTGAATGCAACAGTTTTTTCCTTTGAAATGAAC
55778821 GACCGAAAGAGTGAGCTCTTTTTTTTCCTTCTTGTTGTTGATTTAATTTGTGCTTTCTTTGCTTC
131 GACCGAAAGAGTGAGCTCTTTTTTTTCCTTCTTGTTGTTGATTTAATTTGTGCTTTCTTTGCTTC
55778886 TTTTCATTTGGTTAACGAATCTCTGAATCTTTTCATTTGATTTAATTTGTGCTTTCTTCGCTTTT
196 TTTTCATTTGGTTAACGAATCTCTGAATCTTTTCATTTGATTTAATTTGTGCTTTCTTCGCTTTT
55778951 TTTCATTTGGTTTGATTTATCCTCTCCCTCTCTCTTTGTCTCACACATATGCACATCAACAGACG
261 TTTCATTTGGTTTGATTTATCCTCTCCCTCTCTCTTTGTCTCACACATATGCACATCAACAGACG
55779016 CAATTGTGTGTTCATCTCTTGTTCTCATTATAATTTATTGC
326 CAATTGTGTGTTCATCTCTTGTTCTCATTATAATTTATTGC
55779057 TATTGAATGC
Statistics
Matches: 365, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
379 365 1.00
ACGTcount: A:0.24, C:0.17, G:0.18, T:0.42
Consensus pattern (379 bp):
TTAGAAATAAGATGATTGGGGAAATTTGGGTCAAAATTGAGGAAAAAGCAGTGAAGATAATCCTG
GGAAGTGAATGGGAAACTTCCCAATCCAGGTGTTGAATGCAACAGTTTTTTCCTTTGAAATGAAC
GACCGAAAGAGTGAGCTCTTTTTTTTCCTTCTTGTTGTTGATTTAATTTGTGCTTTCTTTGCTTC
TTTTCATTTGGTTAACGAATCTCTGAATCTTTTCATTTGATTTAATTTGTGCTTTCTTCGCTTTT
TTTCATTTGGTTTGATTTATCCTCTCCCTCTCTCTTTGTCTCACACATATGCACATCAACAGACG
CAATTGTGTGTTCATCTCTTGTTCTCATTATAATTTATTGCATTTGTAAGTTTC
Found at i:55781380 original size:21 final size:21
Alignment explanation
Indices: 55781354--55781397 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
55781344 AAATAGAGCT
55781354 TCTTTGAGTCTGCTGTGAGTG
1 TCTTTGAGTCTGCTGTGAGTG
55781375 TCTTTGAGTCTGCTGTGAGTG
1 TCTTTGAGTCTGCTGTGAGTG
55781396 TC
1 TC
55781398 AATTGAAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.09, C:0.16, G:0.32, T:0.43
Consensus pattern (21 bp):
TCTTTGAGTCTGCTGTGAGTG
Found at i:55789201 original size:30 final size:28
Alignment explanation
Indices: 55789167--55789224 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 28
55789157 TTTGAATAAT
55789167 TTTTTAAAATTTTAAAAGTTATAAAAAATA
1 TTTTTAAAATTTTAAAA-TT-TAAAAAATA
* *
55789197 TTTTTAATATTTTTAAATTTAAAAAATA
1 TTTTTAAAATTTTAAAATTTAAAAAATA
55789225 ATTAAATGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 9 0.35
29 2 0.08
30 15 0.58
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (28 bp):
TTTTTAAAATTTTAAAATTTAAAAAATA
Found at i:55798092 original size:26 final size:26
Alignment explanation
Indices: 55798058--55798107 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
55798048 TGAGCGTTCC
55798058 ATTATATGGCTCTTCGTGAGCTTCTTG
1 ATTATATGGCTCTTCG-GAGCTTCTTG
55798085 ATTA-ATGGCTCTTCGGAGCTTCT
1 ATTATATGGCTCTTCGGAGCTTCT
55798108 CGACATGGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 8 0.35
26 11 0.48
27 4 0.17
ACGTcount: A:0.16, C:0.20, G:0.22, T:0.42
Consensus pattern (26 bp):
ATTATATGGCTCTTCGGAGCTTCTTG
Found at i:55798212 original size:73 final size:73
Alignment explanation
Indices: 55798076--55798213 Score: 170
Period size: 73 Copynumber: 1.9 Consensus size: 73
55798066 GCTCTTCGTG
* * * * * *
55798076 AGCTTCTTGATTAATGGCTCTTCGGAGCTTCTCGACATGGCTCGCTTGAACTTTCTGATATATGG
1 AGCTTATTGATTAATGGCTCTTCAGAGCTACTCGACATGGCTCACATGAACTTTCCGATATATGG
55798141 TTATCCGA
66 TTATCCGA
* ** *
55798149 AGCTTATTGATTAATGGCTTTTCAGAGCTACTCGTTATTGGCTCACATGAGCTTTCCGA-ATATG
1 AGCTTATTGATTAATGGCTCTTCAGAGCTACTCGACA-TGGCTCACATGAACTTTCCGATATATG
55798213 G
65 G
55798214 CTCTTATGAG
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
73 37 0.69
74 17 0.31
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (73 bp):
AGCTTATTGATTAATGGCTCTTCAGAGCTACTCGACATGGCTCACATGAACTTTCCGATATATGG
TTATCCGA
Found at i:55798226 original size:73 final size:73
Alignment explanation
Indices: 55798060--55798226 Score: 162
Period size: 73 Copynumber: 2.3 Consensus size: 73
55798050 AGCGTTCCAT
* * * * * *
55798060 TATATGGCTCTTCGTGAGCTTCTTGATTAATGGCTCTTCGGAGCTTCTCGACATGGCTCGCTTGA
1 TATATGGCTCTT-ATGAGCTTATTGATTAATGGCTCTTCAGAGCTACTCGACATGGCTCACATGA
*
55798125 ACTTTCTGA
65 ACTTTCCGA
* **
55798134 TATATGG---TTATCCGAAGCTTATTGATTAATGGCTTTTCAGAGCTACTCGTTATTGGCTCACA
1 TATATGGCTCTTAT--G-AGCTTATTGATTAATGGCTCTTCAGAGCTACTCGACA-TGGCTCACA
*
55798196 TGAGCTTTCCGA
62 TGAACTTTCCGA
55798208 -ATATGGCTCTTATGAGCTT
1 TATATGGCTCTTATGAGCTT
55798227 CTCGTTATAC
Statistics
Matches: 75, Mismatches: 11, Indels: 15
0.74 0.11 0.15
Matches are distributed among these distances:
70 1 0.01
71 2 0.03
72 1 0.01
73 42 0.56
74 25 0.33
76 4 0.05
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (73 bp):
TATATGGCTCTTATGAGCTTATTGATTAATGGCTCTTCAGAGCTACTCGACATGGCTCACATGAA
CTTTCCGA
Found at i:55798258 original size:25 final size:25
Alignment explanation
Indices: 55798222--55798285 Score: 58
Period size: 25 Copynumber: 2.6 Consensus size: 25
55798212 GGCTCTTATG
**
55798222 AGCTT-CTCGTTATACAGCCCGGATA
1 AGCTTCCT-GTTATACAGCCCACATA
* * *
55798247 AGCTTCCTGTTACACGGCTCACATA
1 AGCTTCCTGTTATACAGCCCACATA
*
55798272 AGCTTCATGTTATA
1 AGCTTCCTGTTATA
55798286 TGGCTCGAGA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
25 29 0.94
26 2 0.06
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (25 bp):
AGCTTCCTGTTATACAGCCCACATA
Done.