Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, whole genome shotgun sequence
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: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 95 of 105
Found at i:16866493 original size:40 final size:40
Alignment explanation
Indices: 16866438--16866515 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
16866428 TGAAGACAGC
* *
16866438 TTGAATGATGAGTTCTGGATTGATATTAATATATATATGG
1 TTGAATGATGAGTTCTGGACTGATATAAATATATATATGG
16866478 TTGAATGATGAGTTCTGGACTGATATAAATATATATAT
1 TTGAATGATGAGTTCTGGACTGATATAAATATATATAT
16866516 ATATATATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.35, C:0.04, G:0.21, T:0.41
Consensus pattern (40 bp):
TTGAATGATGAGTTCTGGACTGATATAAATATATATATGG
Found at i:16866513 original size:2 final size:2
Alignment explanation
Indices: 16866500--16866533 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
16866490 TTCTGGACTG
*
16866500 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16866534 TCATTCTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:16867239 original size:15 final size:15
Alignment explanation
Indices: 16867219--16867247 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
16867209 GGTAGGATTT
16867219 TTTTTTAAAAAAATA
1 TTTTTTAAAAAAATA
16867234 TTTTTTAAAAAAAT
1 TTTTTTAAAAAAAT
16867248 TTATTAAGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTTTTAAAAAAATA
Found at i:16867431 original size:15 final size:15
Alignment explanation
Indices: 16867411--16867442 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
16867401 AATAATATTT
16867411 TATCATGCAACAATA
1 TATCATGCAACAATA
*
16867426 TATCATGCAATAATA
1 TATCATGCAACAATA
16867441 TA
1 TA
16867443 ATATATAAAC
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:0.47, C:0.16, G:0.06, T:0.31
Consensus pattern (15 bp):
TATCATGCAACAATA
Found at i:16868847 original size:23 final size:23
Alignment explanation
Indices: 16868821--16868865 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
16868811 TAACTAAAAA
*
16868821 AATTTTGAAATCTAAAGATTCAC
1 AATTTGGAAATCTAAAGATTCAC
* *
16868844 AATTTGGAAATTTAAAGGTTCA
1 AATTTGGAAATCTAAAGATTCA
16868866 TAAATTTTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (23 bp):
AATTTGGAAATCTAAAGATTCAC
Found at i:16869066 original size:52 final size:53
Alignment explanation
Indices: 16868964--16869085 Score: 147
Period size: 52 Copynumber: 2.3 Consensus size: 53
16868954 AAATTTTCAA
* * * **
16868964 AGATTCAAGATTTGTAAAGGTTTTCAAATTCACAAGAATTTCAAGTTTCACAG
1 AGATTCTAGATTCGCAAAGGTTTTCAAATTCACAAGAATTTCAAAATTCACAG
* * * *
16869017 AGATTTTAGATTCGCAAAGG-TTTCATATTTACAAGGATTTCAAAATTCACAG
1 AGATTCTAGATTCGCAAAGGTTTTCAAATTCACAAGAATTTCAAAATTCACAG
*
16869069 AGATTCTAGATTTGCAA
1 AGATTCTAGATTCGCAA
16869086 GATTCTAGAT
Statistics
Matches: 58, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
52 42 0.72
53 16 0.28
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (53 bp):
AGATTCTAGATTCGCAAAGGTTTTCAAATTCACAAGAATTTCAAAATTCACAG
Found at i:16869103 original size:16 final size:16
Alignment explanation
Indices: 16869061--16869109 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
16869051 GGATTTCAAA
16869061 ATTCACAGAGATTCTAG
1 ATTCACA-AGATTCTAG
**
16869078 ATTTGCAAGATTCTAG
1 ATTCACAAGATTCTAG
*
16869094 ATTCATAAGAATTCTA
1 ATTCACAAG-ATTCTA
16869110 AGTTTTGTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 15 0.58
17 11 0.42
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (16 bp):
ATTCACAAGATTCTAG
Found at i:16869332 original size:35 final size:35
Alignment explanation
Indices: 16869293--16869359 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
16869283 AAAAAACTTC
* *
16869293 AGATTCATAAGAAATTT-AGTTTCATAAGAATTGGT
1 AGATTCACAA-AAATTTCAGATTCATAAGAATTGGT
* *
16869328 AGATTCGCAAAATTTTCAGATTCATAAGAATT
1 AGATTCACAAAAATTTCAGATTCATAAGAATT
16869360 TTACGTTTGC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 5 0.19
35 22 0.81
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (35 bp):
AGATTCACAAAAATTTCAGATTCATAAGAATTGGT
Found at i:16884864 original size:12 final size:12
Alignment explanation
Indices: 16884847--16884876 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
16884837 AAAATTCATA
16884847 GAGTATGAGTCC
1 GAGTATGAGTCC
*
16884859 GAGTATGAGTTC
1 GAGTATGAGTCC
16884871 GAGTAT
1 GAGTAT
16884877 TCATCACTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.10, G:0.33, T:0.30
Consensus pattern (12 bp):
GAGTATGAGTCC
Found at i:16888017 original size:116 final size:116
Alignment explanation
Indices: 16887757--16888052 Score: 308
Period size: 116 Copynumber: 2.5 Consensus size: 116
16887747 ATTATCCCAC
* * * * * * * *
16887757 TCACTGGATCTTGGCTTAGTCCAAATGATTCTTCTTGATTCATGGTT-TCATCCCGATCATTTAT
1 TCACTTGATCTTGACTCAATCCAGATCATTCTTCATGATTCATGGTTCT-GTCCCGATCA-TT-T
* * * * * **
16887821 TTTGATCTTGACTCGATCCTGGTCGCTTTATTTTGGCTTGTGGTTTCATTTCGG
63 TTTGACCTCGACTCGATCCTGGTCACTTCATTTTGACTTGTGGTTTCATCCCGG
** * *
16887875 TCACTTGATCTTGGTTCAGTCCAGATCATTCTTCATGATTCATGGTTCTGTCCTGATCATTTTTT
1 TCACTTGATCTTGACTCAATCCAGATCATTCTTCATGATTCATGGTTCTGTCCCGATCATTTTTT
* *
16887940 -ACCTCGACTCGATCTTGGTCACTTCATTTTTGACTTGTGGTTTCATCCCTG
66 GACCTCGACTCGATCCTGGTCACTTCA-TTTTGACTTGTGGTTTCATCCCGG
* * * * *
16887991 TCACTTGGTCTTGACTCAATCTAGATCATTTTTCATGATTCGTAGTTCTGTCCCGATCATTT
1 TCACTTGATCTTGACTCAATCCAGATCATTCTTCATGATTCATGGTTCTGTCCCGATCATTT
16888053 ATTTTCGACC
Statistics
Matches: 150, Mismatches: 26, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
115 21 0.14
116 77 0.51
117 2 0.01
118 49 0.33
119 1 0.01
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.44
Consensus pattern (116 bp):
TCACTTGATCTTGACTCAATCCAGATCATTCTTCATGATTCATGGTTCTGTCCCGATCATTTTTT
GACCTCGACTCGATCCTGGTCACTTCATTTTGACTTGTGGTTTCATCCCGG
Found at i:16888395 original size:26 final size:26
Alignment explanation
Indices: 16888366--16888421 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
16888356 CTATAGACAT
* * *
16888366 CCATTTTGATCCGGGCCCTATTAGGC
1 CCATTTTGATACAGGCCCTATTAAGC
*
16888392 CCATTTTGGTACAGGCCCTATTAAGC
1 CCATTTTGATACAGGCCCTATTAAGC
16888418 CCAT
1 CCAT
16888422 CTTGGTTCGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (26 bp):
CCATTTTGATACAGGCCCTATTAAGC
Found at i:16889066 original size:17 final size:17
Alignment explanation
Indices: 16889044--16889077 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
16889034 TATCTGGGAA
16889044 TTTTTTTGGGTTTTTTT
1 TTTTTTTGGGTTTTTTT
16889061 TTTTTTTGGGTTTTTTT
1 TTTTTTTGGGTTTTTTT
16889078 AAGAACATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (17 bp):
TTTTTTTGGGTTTTTTT
Found at i:16889607 original size:9 final size:8
Alignment explanation
Indices: 16889587--16889616 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
16889577 AAAAATTTCT
*
16889587 AAAAAAAG
1 AAAAAAAC
16889595 AAAAAAAC
1 AAAAAAAC
16889603 AAAAAAAC
1 AAAAAAAC
16889611 AAAAAA
1 AAAAAA
16889617 GGGAAAGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.90, C:0.07, G:0.03, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:16890543 original size:13 final size:13
Alignment explanation
Indices: 16890525--16890565 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
16890515 GAAATTCATA
16890525 AAAAATTTAATAT
1 AAAAATTTAATAT
*
16890538 AAAAATTCAAT-T
1 AAAAATTTAATAT
*
16890550 AAAATTTTAATA-
1 AAAAATTTAATAT
16890562 AAAA
1 AAAA
16890566 TTCAAATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (13 bp):
AAAAATTTAATAT
Found at i:16890552 original size:12 final size:12
Alignment explanation
Indices: 16890516--16890570 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 12
16890506 AATTTTAATG
*
16890516 AAATTC-ATAAA
1 AAATTCAATTAA
*
16890527 AAATTTAATATAA
1 AAATTCAAT-TAA
16890540 AAATTCAATTAA
1 AAATTCAATTAA
* *
16890552 AATTTTAA-TAA
1 AAATTCAATTAA
16890563 AAATTCAA
1 AAATTCAA
16890571 ATTGATAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
11 14 0.40
12 11 0.31
13 10 0.29
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (12 bp):
AAATTCAATTAA
Found at i:16890566 original size:23 final size:24
Alignment explanation
Indices: 16890502--16890570 Score: 81
Period size: 23 Copynumber: 3.0 Consensus size: 24
16890492 AATTAAAAGA
*
16890502 AAAAAATTTTAAT-GAAATTC-AT
1 AAAAAATTTTAATAAAAATTCAAT
*
16890524 AAAAAATTTAATATAAAAATTCAAT
1 AAAAAATTTTA-ATAAAAATTCAAT
*
16890549 -TAAAATTTTAATAAAAATTCAA
1 AAAAAATTTTAATAAAAATTCAA
16890571 ATTGATAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
22 10 0.25
23 14 0.35
24 14 0.35
25 2 0.05
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.35
Consensus pattern (24 bp):
AAAAAATTTTAATAAAAATTCAAT
Found at i:16890573 original size:24 final size:24
Alignment explanation
Indices: 16890504--16890573 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
16890494 TTAAAAGAAA
*
16890504 AAAATTTTAAT-GAAATTCATAA--
1 AAAATTTTAATAAAAATTCA-AATT
*
16890526 AAAATTTAATATAAAAATTC-AATT
1 AAAATTTTA-ATAAAAATTCAAATT
16890550 AAAATTTTAATAAAAATTCAAATT
1 AAAATTTTAATAAAAATTCAAATT
16890574 GATAAATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
22 10 0.25
23 12 0.30
24 18 0.45
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.37
Consensus pattern (24 bp):
AAAATTTTAATAAAAATTCAAATT
Found at i:16897339 original size:34 final size:34
Alignment explanation
Indices: 16897296--16897365 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
16897286 AGAAGGCCAG
*
16897296 GACTATTATAACAAGGTTTAAATCTACTACCCAT
1 GACTATTATAAAAAGGTTTAAATCTACTACCCAT
16897330 GACTATTATAAAAAGGTTTAAATCTACTACCCAT
1 GACTATTATAAAAAGGTTTAAATCTACTACCCAT
16897364 GA
1 GA
16897366 GAATTCATAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (34 bp):
GACTATTATAAAAAGGTTTAAATCTACTACCCAT
Found at i:16906453 original size:15 final size:15
Alignment explanation
Indices: 16906418--16906472 Score: 94
Period size: 15 Copynumber: 3.7 Consensus size: 15
16906408 AATGAATATA
16906418 AAATAATTTAA-TTT
1 AAATAATTTAATTTT
*
16906432 AATTAATTTAATTTT
1 AAATAATTTAATTTT
16906447 AAATAATTTAATTTT
1 AAATAATTTAATTTT
16906462 AAATAATTTAA
1 AAATAATTTAA
16906473 AATAAAAGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
14 10 0.26
15 28 0.74
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AAATAATTTAATTTT
Found at i:16906478 original size:29 final size:29
Alignment explanation
Indices: 16906418--16906478 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
16906408 AATGAATATA
* **
16906418 AAATAATTTAATTTAATTAATTTAATTTT
1 AAATAATTTAATTTAAATAATTTAATAAT
16906447 AAATAATTTAATTTTAAATAATTTAA-AAT
1 AAATAATTTAA-TTTAAATAATTTAATAAT
16906476 AAA
1 AAA
16906479 AGTTAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
AAATAATTTAATTTAAATAATTTAATAAT
Found at i:16906581 original size:19 final size:17
Alignment explanation
Indices: 16906545--16906585 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
16906535 AAAGGCTCAA
16906545 TTAATAAATTAACCAAT
1 TTAATAAATTAACCAAT
*
16906562 TTAATCAAATTCATCCAAT
1 TTAAT-AAATT-AACCAAT
16906581 TTAAT
1 TTAAT
16906586 TTAATTGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 5 0.24
19 11 0.52
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAATAAATTAACCAAT
Found at i:16906675 original size:15 final size:15
Alignment explanation
Indices: 16906655--16906685 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
16906645 ATAATTCAAT
*
16906655 TAATTTAATTTTAAA
1 TAATTTAATTTAAAA
16906670 TAATTTAATTTAAAA
1 TAATTTAATTTAAAA
16906685 T
1 T
16906686 TAATCGAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TAATTTAATTTAAAA
Found at i:16912297 original size:22 final size:20
Alignment explanation
Indices: 16912266--16912310 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
16912256 AATTTAAAAT
16912266 TTTAACAAAAATTATAAATAAA
1 TTTAAC-AAAATTA-AAATAAA
* *
16912288 TTTAATAAAATTAAAATATA
1 TTTAACAAAATTAAAATAAA
16912308 TTT
1 TTT
16912311 TATATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 9 0.43
21 7 0.33
22 5 0.24
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
TTTAACAAAATTAAAATAAA
Found at i:16912312 original size:21 final size:22
Alignment explanation
Indices: 16912263--16912312 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
16912253 TATAATTTAA
16912263 AATTTTAACAAAAATTATAAAT
1 AATTTTAACAAAAATTATAAAT
* *
16912285 AAATTTAA-TAAAATTA-AAAT
1 AATTTTAACAAAAATTATAAAT
16912305 ATATTTTA
1 A-ATTTTA
16912313 TATTTTTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 5 0.21
21 12 0.50
22 7 0.29
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
AATTTTAACAAAAATTATAAAT
Found at i:16914234 original size:5 final size:5
Alignment explanation
Indices: 16914224--16914249 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
16914214 CCGTACATAT
16914224 ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA A
16914250 AATCTATTTT
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:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:16918949 original size:12 final size:12
Alignment explanation
Indices: 16918932--16918987 Score: 67
Period size: 12 Copynumber: 4.6 Consensus size: 12
16918922 AGTATATAAA
16918932 ATATTAAAATTT
1 ATATTAAAATTT
* *
16918944 ATATTATATTTT
1 ATATTAAAATTT
*
16918956 ATATAAAAATTAT
1 ATATTAAAATT-T
*
16918969 ATATTATAATTT
1 ATATTAAAATTT
16918981 ATATTAA
1 ATATTAA
16918988 TATAAAAACA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
12 25 0.71
13 10 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
ATATTAAAATTT
Found at i:16918968 original size:23 final size:25
Alignment explanation
Indices: 16918932--16918984 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
16918922 AGTATATAAA
* *
16918932 ATATTAAAATT-TATATTATATTTT
1 ATATAAAAATTATATATTATAATTT
16918956 ATATAAAAATTATATATTATAATTT
1 ATATAAAAATTATATATTATAATTT
16918981 ATAT
1 ATAT
16918985 TAATATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 10 0.38
25 16 0.62
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
ATATAAAAATTATATATTATAATTT
Found at i:16927821 original size:33 final size:33
Alignment explanation
Indices: 16927778--16927843 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
16927768 GCTGCAACAT
*
16927778 AATCACGCCCCCCGATCTTATTGCTGTTTCTAC
1 AATCACGCCCCCCAATCTTATTGCTGTTTCTAC
*
16927811 AATCAGGCCCCCCAATCTTATTGCTGTTTCTAC
1 AATCACGCCCCCCAATCTTATTGCTGTTTCTAC
16927844 CTAACCGTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.35, G:0.12, T:0.33
Consensus pattern (33 bp):
AATCACGCCCCCCAATCTTATTGCTGTTTCTAC
Found at i:16930079 original size:2 final size:2
Alignment explanation
Indices: 16930072--16930105 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
16930062 ACTTTGTATG
16930072 TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16930106 CAAGTGTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16933957 original size:2 final size:2
Alignment explanation
Indices: 16933950--16933974 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16933940 AACTATAGTT
16933950 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
16933975 TCACAGTGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16935063 original size:11 final size:11
Alignment explanation
Indices: 16935038--16935076 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
16935028 TTAAATCGTG
16935038 TTATTTTTATA
1 TTATTTTTATA
*
16935049 TATTTTATTTATA
1 T-TATT-TTTATA
16935062 TTATTTTTATA
1 TTATTTTTATA
16935073 TTAT
1 TTAT
16935077 ATATATTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 11 0.46
12 6 0.25
13 7 0.29
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATTTTTATA
Found at i:16944939 original size:20 final size:20
Alignment explanation
Indices: 16944914--16944968 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
16944904 GTTTATTTAT
16944914 TTTATATAAAATATTAATAA
1 TTTATATAAAATATTAATAA
** *
16944934 TTTATATATTTATATT-ATAT
1 TTTATATA-AAATATTAATAA
16944954 TTTATATAAAA-ATTA
1 TTTATATAAAATATTA
16944969 TATATAATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 3 0.11
19 1 0.04
20 19 0.68
21 5 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTATATAAAATATTAATAA
Found at i:16944968 original size:18 final size:18
Alignment explanation
Indices: 16944911--16944981 Score: 61
Period size: 18 Copynumber: 3.7 Consensus size: 18
16944901 TTCGTTTATT
16944911 TATTTTATATAAAATATTAA
1 TATTTTATATAAAA-ATT-A
** *
16944931 TAATTTATATATTTATATTA
1 T-ATTT-TATATAAAAATTA
16944951 TATTTTATATAAAAATTA
1 TATTTTATATAAAAATTA
* *
16944969 TATATAATATAAA
1 TATTTTATATAAA
16944982 TAATAAATAA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
18 21 0.51
19 4 0.10
20 3 0.07
21 7 0.17
22 6 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTTTATATAAAAATTA
Found at i:16944972 original size:20 final size:20
Alignment explanation
Indices: 16944906--16944973 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
16944896 ATTAATTCGT
*
16944906 TTATTTATTTTATATAAAATA
1 TTATATATTTTATATAAAA-A
* ***
16944927 TTA-ATAATTTATATATTTA
1 TTATATATTTTATATAAAAA
16944946 -TATTATATTTTATATAAAAA
1 TTA-TATATTTTATATAAAAA
16944966 TTATATAT
1 TTATATAT
16944974 AATATAAATA
Statistics
Matches: 35, Mismatches: 9, Indels: 7
0.69 0.18 0.14
Matches are distributed among these distances:
18 2 0.06
19 1 0.03
20 27 0.77
21 5 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTATATATTTTATATAAAAA
Found at i:16945059 original size:21 final size:20
Alignment explanation
Indices: 16945026--16945066 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
16945016 TATATATTAC
16945026 TTTTATTAAAATTTTAAATAT
1 TTTTATTAAAA-TTTAAATAT
* *
16945047 TTTTTTTATAATTTAAATAT
1 TTTTATTAAAATTTAAATAT
16945067 CATTGTACGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTTATTAAAATTTAAATAT
Found at i:16945267 original size:19 final size:19
Alignment explanation
Indices: 16945245--16945282 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
16945235 TTGTTAACAG
*
16945245 GAATTGGGATGTGACCACC
1 GAATTGGGATATGACCACC
16945264 GAATTGGGATATGACCACC
1 GAATTGGGATATGACCACC
16945283 ACTTTGAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (19 bp):
GAATTGGGATATGACCACC
Found at i:16945444 original size:29 final size:31
Alignment explanation
Indices: 16945413--16945488 Score: 88
Period size: 29 Copynumber: 2.5 Consensus size: 31
16945403 TAAAATATCT
16945413 AATATAATATTTAAAGTT-TAAA-A-ACTT-TT
1 AATATAATATTTAAA-TTATAAATATA-TTATT
*
16945442 AATATAATATCTAAATTATAAATATATTAATT
1 AATATAATATTTAAATTATAAATATATT-ATT
16945474 AATATAATATTTAAA
1 AATATAATATTTAAA
16945489 AAATTATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
28 2 0.05
29 18 0.45
30 3 0.08
31 1 0.03
32 16 0.40
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (31 bp):
AATATAATATTTAAATTATAAATATATTATT
Found at i:16945473 original size:15 final size:16
Alignment explanation
Indices: 16945440--16945487 Score: 55
Period size: 15 Copynumber: 3.0 Consensus size: 16
16945430 TTAAAAACTT
*
16945440 TTAATATAATATCTAAA
1 TTAATATAATAT-TTAA
16945457 TT-ATA-AATATATTAA
1 TTAATATAATAT-TTAA
16945472 TTAATATAATATTTAA
1 TTAATATAATATTTAA
16945488 AAAATTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 10 0.37
16 10 0.37
17 7 0.26
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
TTAATATAATATTTAA
Found at i:16948087 original size:39 final size:39
Alignment explanation
Indices: 16948041--16948119 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
16948031 AAAACCAAAG
16948041 TATGACTTAAAGATAGTTTAATTGGTACTCATAAAATTT
1 TATGACTTAAAGATAGTTTAATTGGTACTCATAAAATTT
16948080 TATGACTTAAAGATAGTTTAATTGGTACTCATAAAATTT
1 TATGACTTAAAGATAGTTTAATTGGTACTCATAAAATTT
16948119 T
1 T
16948120 TTTATAGTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.42
Consensus pattern (39 bp):
TATGACTTAAAGATAGTTTAATTGGTACTCATAAAATTT
Found at i:16953972 original size:14 final size:14
Alignment explanation
Indices: 16953950--16953979 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
16953940 GTTAGATTAT
*
16953950 AAAAGTAAAAAATA
1 AAAACTAAAAAATA
16953964 AAAACTAAAAAATA
1 AAAACTAAAAAATA
16953978 AA
1 AA
16953980 TAAAATATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.13
Consensus pattern (14 bp):
AAAACTAAAAAATA
Found at i:16954415 original size:19 final size:19
Alignment explanation
Indices: 16954391--16954433 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
16954381 GTATTATATA
*
16954391 TATTTAATAAAATAATTTT
1 TATTTAATAAAATAAATTT
*
16954410 TATTTAATAATATAAATTT
1 TATTTAATAAAATAAATTT
16954429 TATTT
1 TATTT
16954434 TAGATTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TATTTAATAAAATAAATTT
Found at i:16955932 original size:10 final size:10
Alignment explanation
Indices: 16955917--16955958 Score: 50
Period size: 9 Copynumber: 4.1 Consensus size: 10
16955907 TAAAATAAAT
16955917 ATTTTTTTTA
1 ATTTTTTTTA
16955927 A-TTTTTTTA
1 ATTTTTTTTA
16955936 ATTTTATTTATA
1 ATTTT-TTT-TA
*
16955948 ATTTTTATTA
1 ATTTTTTTTA
16955958 A
1 A
16955959 AATTTAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
9 9 0.32
10 7 0.25
11 5 0.18
12 7 0.25
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
ATTTTTTTTA
Found at i:16955996 original size:12 final size:12
Alignment explanation
Indices: 16955915--16955996 Score: 52
Period size: 12 Copynumber: 7.3 Consensus size: 12
16955905 TATAAAATAA
16955915 ATATTTTT-TTT
1 ATATTTTTATTT
16955926 A-A-TTTT-TTT
1 ATATTTTTATTT
16955935 A-A-TTTTATTT
1 ATATTTTTATTT
*
16955945 ATAATTTTTATTA
1 AT-ATTTTTATTT
* ** *
16955958 AAATTTAAAATT
1 ATATTTTTATTT
*
16955970 ATATTATT-TTT
1 ATATTTTTATTT
16955981 ATATTTTTATTT
1 ATATTTTTATTT
16955993 ATAT
1 ATAT
16955997 CATTACATTT
Statistics
Matches: 54, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
9 13 0.24
10 5 0.09
11 10 0.19
12 18 0.33
13 8 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTTTTATTT
Found at i:16962611 original size:13 final size:13
Alignment explanation
Indices: 16962589--16962635 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
16962579 AAAATTATAC
16962589 TTATAATTAAATA
1 TTATAATTAAATA
*
16962602 TTATATTTAAATA
1 TTATAATTAAATA
* *
16962615 AT-TAATTAATAAA
1 TTATAATTAA-ATA
16962628 TTATAATT
1 TTATAATT
16962636 TAATTAAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
12 6 0.22
13 16 0.59
14 5 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TTATAATTAAATA
Found at i:16962903 original size:2 final size:2
Alignment explanation
Indices: 16962896--16962930 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
16962886 TCGATTAAAT
16962896 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16962931 GAATGAAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16964836 original size:15 final size:16
Alignment explanation
Indices: 16964803--16964837 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
16964793 ATAAATATCA
16964803 AGAAGTTATAGATTCG
1 AGAAGTTATAGATTCG
16964819 AGAAGTTATAGA-TCG
1 AGAAGTTATAGATTCG
16964834 AGAA
1 AGAA
16964838 AATTTTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.43, C:0.06, G:0.26, T:0.26
Consensus pattern (16 bp):
AGAAGTTATAGATTCG
Found at i:16976660 original size:11 final size:11
Alignment explanation
Indices: 16976640--16976668 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
16976630 ATGGTTTAGA
16976640 ATAT-ATATAT
1 ATATAATATAT
16976650 ATATAATATAT
1 ATATAATATAT
16976661 ATATAATA
1 ATATAATA
16976669 CTATTATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
ATATAATATAT
Found at i:16982691 original size:21 final size:21
Alignment explanation
Indices: 16982667--16982723 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 21
16982657 AATACCTTTA
16982667 ATTTATTATTTTAAAA-ATAAT
1 ATTTA-TATTTTAAAATATAAT
** *
16982688 ATTTAATAAATTAAAATTTTAAT
1 ATTT-ATATTTTAAAA-TATAAT
16982711 ATTTATATTTTAA
1 ATTTATATTTTAA
16982724 TGATGGAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
21 12 0.43
22 8 0.29
23 8 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTATATTTTAAAATATAAT
Found at i:16983259 original size:18 final size:19
Alignment explanation
Indices: 16983238--16983288 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
16983228 CTATATTAAT
16983238 TATAATATATAAT-TTTTA
1 TATAATATATAATATTTTA
16983256 TATAA-ATTATAATATTTTA
1 TATAATA-TATAATATTTTA
*
16983275 TATTATATA-AATAT
1 TATAATATATAATAT
16983289 ATGAATCATC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 1 0.03
18 16 0.55
19 11 0.38
20 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TATAATATATAATATTTTA
Found at i:16990204 original size:3 final size:3
Alignment explanation
Indices: 16990186--16990224 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
16990176 GGAAAGGGGA
* * *
16990186 GAG GAG CAG AAG GAG GAG GAG GAG GAG GAA GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
16990225 AAGAGAGAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.38, C:0.03, G:0.59, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:17001219 original size:14 final size:14
Alignment explanation
Indices: 17001200--17001227 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
17001190 CCCAGCGCTT
17001200 TTCATCCTATTGGG
1 TTCATCCTATTGGG
17001214 TTCATCCTATTGGG
1 TTCATCCTATTGGG
17001228 GTCACTAGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.43
Consensus pattern (14 bp):
TTCATCCTATTGGG
Found at i:17002957 original size:11 final size:11
Alignment explanation
Indices: 17002945--17002988 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
17002935 TAAATATATT
*
17002945 AAAATTTTATT
1 AAAATTTTATA
17002956 AAAATTATATATA
1 AAAATT-T-TATA
*
17002969 AAAATTTTAAA
1 AAAATTTTATA
17002980 AAAATTTTA
1 AAAATTTTA
17002989 AATTGATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 18 0.62
12 2 0.07
13 9 0.31
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
AAAATTTTATA
Found at i:17002983 original size:24 final size:24
Alignment explanation
Indices: 17002938--17002985 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
17002928 ATCTATTTAA
* **
17002938 ATATATTAAAATTTTATTAAAATT
1 ATATATAAAAATTTTAAAAAAATT
17002962 ATATATAAAAATTTTAAAAAAATT
1 ATATATAAAAATTTTAAAAAAATT
17002986 TTAAATTGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
ATATATAAAAATTTTAAAAAAATT
Found at i:17005271 original size:12 final size:13
Alignment explanation
Indices: 17005254--17005283 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
17005244 TAAGGTTTTT
*
17005254 ATTTTTATTTTAA
1 ATTTTTATTTAAA
17005267 ATTTTTATTTAAA
1 ATTTTTATTTAAA
17005280 ATTT
1 ATTT
17005284 ATGAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
ATTTTTATTTAAA
Found at i:17005460 original size:6 final size:6
Alignment explanation
Indices: 17005438--17005507 Score: 54
Period size: 6 Copynumber: 11.2 Consensus size: 6
17005428 TTATCATTCC
* * *
17005438 AATTTT TATTATT AATTTT AATTTT ATTATTAT AATAATT AATTTT -ATTTT
1 AATTTT AATT-TT AATTTT AATTTT A--ATTTT AAT-TTT AATTTT AATTTT
17005489 AATTATT -ATTTT AATTTT A
1 AATT-TT AATTTT AATTTT A
17005508 TCAAAATTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
5 7 0.14
6 28 0.55
7 11 0.22
8 5 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
AATTTT
Found at i:17005462 original size:18 final size:18
Alignment explanation
Indices: 17005441--17005501 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
17005431 TCATTCCAAT
17005441 TTTTATTATTAATTTTAA
1 TTTTATTATTAATTTTAA
*
17005459 TTTTATTATTATAATAATTAA
1 TTTTATTA-T-TAAT-TTTAA
17005480 TTTTATT-TTAATTATT-A
1 TTTTATTATTAATT-TTAA
17005497 TTTTA
1 TTTTA
17005502 ATTTTATCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
17 6 0.16
18 14 0.38
19 2 0.05
20 4 0.11
21 11 0.30
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTATTATTAATTTTAA
Found at i:17008816 original size:9 final size:9
Alignment explanation
Indices: 17008799--17008856 Score: 55
Period size: 9 Copynumber: 6.3 Consensus size: 9
17008789 GGATTTTTGG
17008799 TATTT-TTT
1 TATTTATTT
17008807 TATTTATTT
1 TATTTATTT
*
17008816 TATTTAATT
1 TATTTATTT
*
17008825 TATTTGTTT
1 TATTTATTT
*
17008834 TACTTGTTTTT
1 TA-TT-TATTT
*
17008845 TTTTTATTT
1 TATTTATTT
17008854 TAT
1 TAT
17008857 CAAAATAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
8 5 0.12
9 26 0.65
10 4 0.10
11 5 0.12
ACGTcount: A:0.17, C:0.02, G:0.03, T:0.78
Consensus pattern (9 bp):
TATTTATTT
Found at i:17015581 original size:19 final size:19
Alignment explanation
Indices: 17015559--17015601 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
17015549 TGAAAAAGAG
17015559 AAAAAAAGA-GAAAATGAAA
1 AAAAAAAGATG-AAATGAAA
*
17015578 AAAAAAAGATGAAATGAAG
1 AAAAAAAGATGAAATGAAA
17015597 AAAAA
1 AAAAA
17015602 GGTAGACTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 21 0.95
20 1 0.05
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (19 bp):
AAAAAAAGATGAAATGAAA
Found at i:17017599 original size:123 final size:122
Alignment explanation
Indices: 17017377--17017687 Score: 333
Period size: 123 Copynumber: 2.5 Consensus size: 122
17017367 ATGATTGTTA
** * * * *
17017377 ATGAGTAATTTATTTTTTTTCAAAGTTCTGTTGTTTCTGTTTAGAGGAGCAATTTATTTTTTAAA
1 ATGAGTAATTTA--TTTTTT-AAAGTTCTGTTGCCTCTATTCAGAGGAGCCATTTATTTTTAAAA
* * * * *
17017442 GTCGTGATGCCTCTGTTTAGAGGAGCAATTTA-TTTTTCAAAG-TCATGGTGCCTCTGTTTAG
63 GTCGT-ATGCCTCTATTCAGAGGAACAATTTATTTTTTCAAAGTTCAT--TGCCTCTATTCAG
17017503 ATGAGTAATTTATTTTTTAAAGTTCTGTTGCCTCTATTCAGAGGAGCCATTTGATTTTTAAAAGT
1 ATGAGTAATTTATTTTTTAAAGTTCTGTTGCCTCTATTCAGAGGAGCCATTT-ATTTTTAAAAG-
*
17017568 TCGT-TGCCTCTATTCAGAGGAACAATTTATTTTTTTAAAGTTCATTGCCTCTATTCAG
64 TCGTATGCCTCTATTCAGAGGAACAATTTATTTTTTCAAAGTTCATTGCCTCTATTCAG
* *** * * *
17017626 ATGAGTCATTTATTTCCCCAAAGTTC-ATTGCCTCTATTCAAAGAAGCCATTTATTTTCTAAA
1 ATGAGTAATTTATTT-TTTAAAGTTCTGTTGCCTCTATTCAGAGGAGCCATTTATTTT-TAAA
17017688 GTTTTGTTGC
Statistics
Matches: 160, Mismatches: 19, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
122 5 0.03
123 103 0.64
124 32 0.20
125 8 0.05
126 12 0.08
ACGTcount: A:0.26, C:0.14, G:0.16, T:0.44
Consensus pattern (122 bp):
ATGAGTAATTTATTTTTTAAAGTTCTGTTGCCTCTATTCAGAGGAGCCATTTATTTTTAAAAGTC
GTATGCCTCTATTCAGAGGAACAATTTATTTTTTCAAAGTTCATTGCCTCTATTCAG
Found at i:17017609 original size:41 final size:41
Alignment explanation
Indices: 17017391--17017713 Score: 271
Period size: 41 Copynumber: 7.9 Consensus size: 41
17017381 GTAATTTATT
** * *
17017391 TTTTTTCAAAGTTCTGTTGTTTCTGTTTAGAGGAGCAATTTA
1 TTTTTT-AAAGTTCTGTTGCCTCTATTCAGAGGAGCAATTTA
* * *
17017433 TTTTTTAAAG-TCGTGATGCCTCTGTTTAGAGGAGCAATTTA
1 TTTTTTAAAGTTC-TGTTGCCTCTATTCAGAGGAGCAATTTA
* * * * * *
17017474 TTTTTCAAAG-TCATGGTGCCTCTGTTTAGATGAGTAATTTA
1 TTTTTTAAAGTTC-TGTTGCCTCTATTCAGAGGAGCAATTTA
*
17017515 TTTTTTAAAGTTCTGTTGCCTCTATTCAGAGGAGCCATTTGA
1 TTTTTTAAAGTTCTGTTGCCTCTATTCAGAGGAGCAATTT-A
* *
17017557 TTTTTAAAAGTTC-GTTGCCTCTATTCAGAGGAACAATTTA
1 TTTTTTAAAGTTCTGTTGCCTCTATTCAGAGGAGCAATTTA
* *
17017597 TTTTTTTAAAGTTC-ATTGCCTCTATTCAGATGAGTC-ATTTA
1 -TTTTTTAAAGTTCTGTTGCCTCTATTCAGAGGAG-CAATTTA
*** * * * *
17017638 TTTCCCCAAAGTTC-ATTGCCTCTATTCAAAGAAGCCATTTA
1 TTT-TTTAAAGTTCTGTTGCCTCTATTCAGAGGAGCAATTTA
* * * * *
17017679 TTTTCTAAAGTTTTGTTGCCTTTGTTTAGAGGAGC
1 TTTTTTAAAGTTCTGTTGCCTCTATTCAGAGGAGC
17017714 TTTGTTTACT
Statistics
Matches: 236, Mismatches: 37, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
40 14 0.06
41 200 0.85
42 22 0.09
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.44
Consensus pattern (41 bp):
TTTTTTAAAGTTCTGTTGCCTCTATTCAGAGGAGCAATTTA
Found at i:17018399 original size:19 final size:19
Alignment explanation
Indices: 17018363--17018399 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
17018353 AATCCGATAA
*
17018363 AATTTTTCGATGAATTTTG
1 AATTTTTCGACGAATTTTG
*
17018382 AATTTTTCGACGAGTTTT
1 AATTTTTCGACGAATTTT
17018400 TAAGCCAGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.51
Consensus pattern (19 bp):
AATTTTTCGACGAATTTTG
Found at i:17018510 original size:17 final size:17
Alignment explanation
Indices: 17018484--17018517 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
17018474 GAGAGAAAAA
*
17018484 AGAGAAAAAAAGGGAAG
1 AGAGAAAAAAAGAGAAG
*
17018501 AGAGAGAAAAAGAGAAG
1 AGAGAAAAAAAGAGAAG
17018518 GGAATTCTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (17 bp):
AGAGAAAAAAAGAGAAG
Found at i:17018787 original size:9 final size:9
Alignment explanation
Indices: 17018775--17018838 Score: 60
Period size: 9 Copynumber: 7.2 Consensus size: 9
17018765 CCATTTTTGG
*
17018775 ATTTTTTTT
1 ATTTATTTT
*
17018784 ATTT-TCTT
1 ATTTATTTT
17018792 ATTTATTTT
1 ATTTATTTT
*
17018801 ATTTAATTT
1 ATTTATTTT
*
17018810 ATTTGTTTT
1 ATTTATTTT
*
17018819 ACTTATGTTT
1 ATTTAT-TTT
17018829 -TTTATTTT
1 ATTTATTTT
17018837 AT
1 AT
17018839 CAAAATAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
8 10 0.23
9 31 0.70
10 3 0.07
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.75
Consensus pattern (9 bp):
ATTTATTTT
Found at i:17024294 original size:16 final size:16
Alignment explanation
Indices: 17024270--17024306 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
17024260 AAATTCAAAA
* *
17024270 TTTTAAATTATTAGAT
1 TTTTGAATTATTAAAT
17024286 TTTTGAATTATTAAAT
1 TTTTGAATTATTAAAT
17024302 TTTTG
1 TTTTG
17024307 GTTGTTTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.59
Consensus pattern (16 bp):
TTTTGAATTATTAAAT
Found at i:17025128 original size:14 final size:15
Alignment explanation
Indices: 17025101--17025131 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
17025091 AAAAATTTAA
17025101 ATTATAATTAATTAT
1 ATTATAATTAATTAT
17025116 ATTATAA-TAATTAT
1 ATTATAATTAATTAT
17025130 AT
1 AT
17025132 ACGATATACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTATAATTAATTAT
Found at i:17025631 original size:2 final size:2
Alignment explanation
Indices: 17025624--17025649 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17025614 ATGAATCATA
17025624 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
17025650 GCTATTTGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17025832 original size:2 final size:2
Alignment explanation
Indices: 17025820--17025850 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
17025810 ATTCATCTGT
*
17025820 TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17025851 CCTTATCACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:17028386 original size:22 final size:22
Alignment explanation
Indices: 17028361--17028402 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
17028351 AATATTTTTG
17028361 AAATATTTTGAAATTTAGCCTC
1 AAATATTTTGAAATTTAGCCTC
17028383 AAATATTTTGAAATTTAGCC
1 AAATATTTTGAAATTTAGCC
17028403 ATAATCACGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (22 bp):
AAATATTTTGAAATTTAGCCTC
Found at i:17034630 original size:2 final size:2
Alignment explanation
Indices: 17034625--17034660 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
17034615 TTTGTTGTGC
17034625 AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17034661 AAGCAAAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:17034647 original size:17 final size:17
Alignment explanation
Indices: 17034625--17034658 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
17034615 TTTGTTGTGC
17034625 ATATATATATATATATA
1 ATATATATATATATATA
17034642 ATATATATATATATATA
1 ATATATATATATATATA
17034659 TAAAGCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATATATATATATA
Found at i:17034649 original size:19 final size:19
Alignment explanation
Indices: 17034625--17034661 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
17034615 TTTGTTGTGC
17034625 ATATATATATATATATAAT
1 ATATATATATATATATAAT
17034644 ATATATATATATATATAA
1 ATATATATATATATATAA
17034662 AGCAAAAGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATATATATATATATATAAT
Found at i:17038775 original size:36 final size:36
Alignment explanation
Indices: 17038728--17038799 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
17038718 TAAAATTGTG
*
17038728 AAAGTCTGTCATACTTACCTTGTGAGATCAGTCTGT
1 AAAGTCTGTCATACTTACCCTGTGAGATCAGTCTGT
17038764 AAAGTCTGTCATACTTACCCTGTGAGATCAGTCTGT
1 AAAGTCTGTCATACTTACCCTGTGAGATCAGTCTGT
17038800 TTTCCTTCTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (36 bp):
AAAGTCTGTCATACTTACCCTGTGAGATCAGTCTGT
Found at i:17041847 original size:2 final size:2
Alignment explanation
Indices: 17041840--17041866 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17041830 ATTAAATTTC
17041840 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
17041867 GGATGTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17042155 original size:26 final size:24
Alignment explanation
Indices: 17042125--17042186 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 24
17042115 TAAGCAATAT
17042125 ATGTAAGTATATTTCTTTGGTTAGGG
1 ATGTAAGTATATTT-TTTGGTTA-GG
* *
17042151 ATGTAAATGTA-TTTTTGGTTAGG
1 ATGTAAGTATATTTTTTGGTTAGG
*
17042174 ATTTAAGATATAT
1 ATGTAAG-TATAT
17042187 GCTTATATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
23 7 0.24
24 11 0.38
25 2 0.07
26 9 0.31
ACGTcount: A:0.29, C:0.02, G:0.23, T:0.47
Consensus pattern (24 bp):
ATGTAAGTATATTTTTTGGTTAGG
Found at i:17049044 original size:434 final size:437
Alignment explanation
Indices: 17048260--17049045 Score: 908
Period size: 434 Copynumber: 1.8 Consensus size: 437
17048250 TTAAAAAATA
* * *
17048260 TTTTATTTAAATAAAATATATTTATCTTTTAAATTATTTAAAATTTAAAAAATCTTGATTGTGAT
1 TTTTATTTAAATAAAATATATTTATCTTTTAAATAACTTAAAATTT-AAAAATCTTGATTATGAT
* * * *
17048325 TTAAAATTAACTTTTTGTATAAAAATCGTATTATTTGCTTTTTAATTAAATACCATGTTTTCACT
65 TCAAAATTAACTTTTTGTATAAAAATCGTATTATTGGCTTTTTAATGAAATACCACGTTTTCACT
** * * * *
17048390 TAAAAAATGTAGTGTTTAAAATATACAATTAAATACTTCATTTGTAAAATGATAAACATGATATT
130 TAAAAAATGTAGTACTTAAAATATAAAATTAAATACTCCATTTATAAAATGATAAACATGATAGT
* * * * * *
17048455 TATAATTTTTATTTATTTATTTATCGTTGTTTAAACAAACCCTATGATTTTATAGTTTTCATTCA
195 TATAATGTTTATTTATTTATTTATCGCTATTTAAACAAACCCTATAATCTTATAGTTTCCATTCA
* * * * **
17048520 TAAAAATAAAGTCTATGCTTTTAAGTTTTAGAATTTTATTTCTTAAGTGGTTTACTGGTACTGTA
260 TAAAAATAAAGTCTATGCTTTTAAGTTTTAGAATTTTATGTCTTAACTAGTTTACTGATACCATA
* * *
17048585 TTTCTAAAAATAAATTTATAATTATCACTTAAATATAATTTTTATTATCAAATAATCAACTTATA
325 TTCCCAAAAATAAATTTACAATTATCACTTAAATATAATTTTTATTATCAAATAATCAACTTATA
17048650 CTTTTATAAACACTCCTTTCTTACTTTAGAAAACGTAGTACTAAATTT
390 CTTTTATAAACACTCCTTTCTTACTTTAGAAAACGTAGTACTAAATTT
* **
17048698 TTTTATTTAAATAAAATATATTTTTAC-TTTAAATAACTTAAAATTT-AAAAT-TTTTTTCATGA
1 TTTTATTTAAATAAAATATATTTAT-CTTTTAAATAACTTAAAATTTAAAAATCTTGATT-ATGA
* * *
17048760 TTCAAAGTT-ACATTTGTT-TCTAAAAAT-GATATTATTGGCATTTTTAATGAAATACCCCGTTT
64 TTCAAAATTAAC-TTT-TTGTATAAAAATCG-TATTATTGGC-TTTTTAATGAAATACCACGTTT
* * * * ** *
17048822 TTACATTTAAAAATGTAGTACTTATAATCTAAAATTAAATACTCCATTTATATTATGATAAATAT
125 TCAC-TTAAAAAATGTAGTACTTAAAATATAAAATTAAATACTCCATTTATAAAATGATAAACAT
* * * * * * *
17048887 GGTGGTTATCA-GTTTA-TT-TTT-TTTATTGCTATTTAAACAAATCTTATAATCTTATTGTTTC
189 GATAGTTATAATGTTTATTTATTTATTTATCGCTATTTAAACAAACCCTATAATCTTATAGTTTC
* **** * * * *
17048948 CATTCATAAAAATAAAGTTTATGCTTTTAAGTTTTTTCTTTTTGTGTGTTATCTAGTTTACTTAT
254 CATTCATAAAAATAAAGTCTATGCTTTTAAGTTTTAGAATTTTATGTCTTAACTAGTTTACTGAT
*
17049013 ACCATATTCCCAAATATAAATTTACAATTATCA
319 ACCATATTCCCAAAAATAAATTTACAATTATCA
17049046 TTTATTTTAT
Statistics
Matches: 283, Mismatches: 58, Indels: 18
0.79 0.16 0.05
Matches are distributed among these distances:
434 110 0.39
435 10 0.04
436 37 0.13
437 28 0.10
438 97 0.34
439 1 0.00
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.47
Consensus pattern (437 bp):
TTTTATTTAAATAAAATATATTTATCTTTTAAATAACTTAAAATTTAAAAATCTTGATTATGATT
CAAAATTAACTTTTTGTATAAAAATCGTATTATTGGCTTTTTAATGAAATACCACGTTTTCACTT
AAAAAATGTAGTACTTAAAATATAAAATTAAATACTCCATTTATAAAATGATAAACATGATAGTT
ATAATGTTTATTTATTTATTTATCGCTATTTAAACAAACCCTATAATCTTATAGTTTCCATTCAT
AAAAATAAAGTCTATGCTTTTAAGTTTTAGAATTTTATGTCTTAACTAGTTTACTGATACCATAT
TCCCAAAAATAAATTTACAATTATCACTTAAATATAATTTTTATTATCAAATAATCAACTTATAC
TTTTATAAACACTCCTTTCTTACTTTAGAAAACGTAGTACTAAATTT
Found at i:17053146 original size:30 final size:30
Alignment explanation
Indices: 17053110--17053256 Score: 197
Period size: 30 Copynumber: 4.9 Consensus size: 30
17053100 GAGGAGGAGC
*
17053110 TAACTCTACTGGAACACATGCTTCTTCAAA
1 TAACTCTACTGGAACACATGCTTCTTCAAG
17053140 TAACTCTACTGGAACACATGC-TCTTTCAAG
1 TAACTCTACTGGAACACATGCTTC-TTCAAG
* * * * *
17053170 TACCGCTACTGCAACAAATGCTCCTTCAAG
1 TAACTCTACTGGAACACATGCTTCTTCAAG
* *
17053200 TAACTCTACTGCAACACATGCTCCTTCAAG
1 TAACTCTACTGGAACACATGCTTCTTCAAG
*
17053230 TAACTCTACTGGAACACTTGCTTCTTC
1 TAACTCTACTGGAACACATGCTTCTTC
17053257 TTGTAATTGT
Statistics
Matches: 103, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
29 2 0.02
30 100 0.97
31 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.12, T:0.29
Consensus pattern (30 bp):
TAACTCTACTGGAACACATGCTTCTTCAAG
Found at i:17064624 original size:22 final size:22
Alignment explanation
Indices: 17064598--17064639 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
17064588 GCCTCTGATA
17064598 GATATAGACATATTAATAGTGT
1 GATATAGACATATTAATAGTGT
17064620 GATATAGACATATTAATAGT
1 GATATAGACATATTAATAGT
17064640 ATGGAATGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.05, G:0.17, T:0.36
Consensus pattern (22 bp):
GATATAGACATATTAATAGTGT
Found at i:17066889 original size:3 final size:3
Alignment explanation
Indices: 17066881--17066907 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
17066871 ACTGCGACCT
17066881 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
17066908 CATCAGAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:17068794 original size:24 final size:25
Alignment explanation
Indices: 17068750--17068802 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
17068740 TAAAAAAAAT
*
17068750 AAAATTTATTATAATTGTAA-TTAA
1 AAAATTTATTATAATTATAATTTAA
*
17068774 AAAATTTACTT-TAGTTATAATTTAA
1 AAAATTTA-TTATAATTATAATTTAA
17068799 AAAA
1 AAAA
17068803 ATTTTAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 15 0.60
25 10 0.40
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (25 bp):
AAAATTTATTATAATTATAATTTAA
Found at i:17068843 original size:39 final size:40
Alignment explanation
Indices: 17068752--17068844 Score: 102
Period size: 39 Copynumber: 2.4 Consensus size: 40
17068742 AAAAAAATAA
* *
17068752 AATTTATTATAATTGTAATTAAAAAATTTACTTTAGTTAT
1 AATTTATTAAAATTGTAATTAAAAAATTTACTTTAATTAT
** *
17068792 AATTTAAAAAAATTTTAA-TAAAAAATTTA-TATTAATT-T
1 AATTTATTAAAATTGTAATTAAAAAATTTACT-TTAATTAT
17068830 AATTTTATTAAAATT
1 AA-TTTATTAAAATT
17068845 AACGTTCGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
38 4 0.09
39 26 0.59
40 14 0.32
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (40 bp):
AATTTATTAAAATTGTAATTAAAAAATTTACTTTAATTAT
Found at i:17069217 original size:24 final size:23
Alignment explanation
Indices: 17069178--17069222 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
17069168 ATAAAATTTA
17069178 ATATAATAAATAAATTTAATAATT
1 ATATAATAAATAAA-TTAATAATT
17069202 ATATAATAAACT-AATTAATAA
1 ATATAATAAA-TAAATTAATAA
17069223 ACAAAAGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 7 0.35
24 12 0.60
25 1 0.05
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
ATATAATAAATAAATTAATAATT
Found at i:17071800 original size:12 final size:12
Alignment explanation
Indices: 17071785--17071823 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
17071775 TTGGTATTTT
17071785 TTTTATTTAGTA
1 TTTTATTTAGTA
17071797 TTTTATTTATGTA
1 TTTTATTTA-GTA
17071810 TTTT-TTTAGT-
1 TTTTATTTAGTA
17071820 TTTT
1 TTTT
17071824 TTTGCATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 4 0.15
11 2 0.08
12 13 0.50
13 7 0.27
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.74
Consensus pattern (12 bp):
TTTTATTTAGTA
Found at i:17072044 original size:15 final size:15
Alignment explanation
Indices: 17072022--17072057 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
17072012 TATTTATTTT
*
17072022 TAAAAAAAAGAAAAAA
1 TAAAAAATA-AAAAAA
17072038 TAAAAAATAAAAAAA
1 TAAAAAATAAAAAAA
17072053 TAAAA
1 TAAAA
17072058 TTTTGGTCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.11
Consensus pattern (15 bp):
TAAAAAATAAAAAAA
Found at i:17072315 original size:55 final size:54
Alignment explanation
Indices: 17072242--17072363 Score: 190
Period size: 55 Copynumber: 2.2 Consensus size: 54
17072232 AAAATAAAAG
*
17072242 AAAAAAGAAAAAAAGAATTTTTAAATAGGCCCAAATTATGAAAAATTTAGAAATCC
1 AAAAAAG--AAAAAGAATTTTTAAATAGACCCAAATTATGAAAAATTTAGAAATCC
* *
17072298 AATAAAAGAAAAAGAATTTTTAAATAGACCCAAATTGTGAAAAATTTAGAAATTC
1 AA-AAAAGAAAAAGAATTTTTAAATAGACCCAAATTATGAAAAATTTAGAAATCC
17072353 AAAAAAGAAAA
1 AAAAAAGAAAA
17072364 TATTTCTAAT
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
54 9 0.15
55 46 0.74
56 2 0.03
57 5 0.08
ACGTcount: A:0.59, C:0.07, G:0.11, T:0.23
Consensus pattern (54 bp):
AAAAAAGAAAAAGAATTTTTAAATAGACCCAAATTATGAAAAATTTAGAAATCC
Found at i:17076291 original size:24 final size:22
Alignment explanation
Indices: 17076263--17076312 Score: 55
Period size: 24 Copynumber: 2.2 Consensus size: 22
17076253 CTAATGGATG
*
17076263 AAAAATGAGAAGAAAAAAAATAAA
1 AAAAAGGAGAA-AAAAAAAA-AAA
* *
17076287 AAAAAGGTGAAAAAATAAAAAA
1 AAAAAGGAGAAAAAAAAAAAAA
17076309 AAAA
1 AAAA
17076313 TAAAAAAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 7 0.30
23 7 0.30
24 9 0.39
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (22 bp):
AAAAAGGAGAAAAAAAAAAAAA
Found at i:17076318 original size:19 final size:19
Alignment explanation
Indices: 17076276--17076319 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
17076266 AATGAGAAGA
**
17076276 AAAAAAATAAAAAAAAGGT
1 AAAAAAATAAAAAAAAAAT
*
17076295 GAAAAAATAAAAAAAAAAT
1 AAAAAAATAAAAAAAAAAT
17076314 AAAAAA
1 AAAAAA
17076320 GAAAGAAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.84, C:0.00, G:0.07, T:0.09
Consensus pattern (19 bp):
AAAAAAATAAAAAAAAAAT
Found at i:17077032 original size:8 final size:9
Alignment explanation
Indices: 17077015--17077044 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
17077005 AGAAGCTGAG
17077015 AAGTTAAAA
1 AAGTTAAAA
17077024 AAGTTAAAA
1 AAGTTAAAA
17077033 AAGTTAAAA
1 AAGTTAAAA
17077042 AAG
1 AAG
17077045 AAAAATATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20
Consensus pattern (9 bp):
AAGTTAAAA
Found at i:17077412 original size:25 final size:24
Alignment explanation
Indices: 17077352--17077623 Score: 145
Period size: 21 Copynumber: 11.8 Consensus size: 24
17077342 AAGTCCTGAA
17077352 TCTTCAAATGAGAATCTTT-A-AG-
1 TCTT-AAATGAGAATCTTTAAGAGT
*
17077374 TCTCAAATGAGAATCTTTAAGACGT
1 TCTTAAATGAGAATCTTTAAGA-GT
* *
17077399 TCTTAAATAAGAATATTT--GAG-
1 TCTTAAATGAGAATCTTTAAGAGT
*
17077420 TCTTAGATGAGAATCTTTAAGACGT
1 TCTTAAATGAGAATCTTTAAGA-GT
*
17077445 TATTAAATGAGAATCTTT--GAG-
1 TCTTAAATGAGAATCTTTAAGAGT
* **
17077466 TCTTAAATGAAAATCTTTATTATGT
1 TCTTAAATGAGAATCTTTAAGA-GT
17077491 T-TTCAAATGAGAA-CATTT--GAG-
1 TCTT-AAATGAGAATC-TTTAAGAGT
* * *
17077512 TCTTAAATTAGAATTTTTAAGACAT
1 TCTTAAATGAGAATCTTTAAGA-GT
*
17077537 TCTCAAATGAGAATCTTTAA-A--
1 TCTTAAATGAGAATCTTTAAGAGT
* * * *
17077558 TCTTAAATGAGTATGTTTAGGACAT
1 TCTTAAATGAGAATCTTTAAGA-GT
* *
17077583 T-TTCAAATAAGAA-CTTT-TGAG-
1 TCTT-AAATGAGAATCTTTAAGAGT
*
17077604 TCTTAAATGAGAATATTTAA
1 TCTTAAATGAGAATCTTTAA
17077624 AAATCTTTGA
Statistics
Matches: 190, Mismatches: 32, Indels: 55
0.69 0.12 0.20
Matches are distributed among these distances:
21 82 0.43
22 15 0.08
23 13 0.07
24 12 0.06
25 68 0.36
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (24 bp):
TCTTAAATGAGAATCTTTAAGAGT
Found at i:17077430 original size:46 final size:47
Alignment explanation
Indices: 17077352--17077623 Score: 288
Period size: 46 Copynumber: 5.9 Consensus size: 47
17077342 AAGTCCTGAA
* *
17077352 TCTTCAAATGAGAATCTTTAAGTCTCAAATGAGAATCTTTAAGACGT
1 TCTTCAAATGAGAATCTTTGAGTCTTAAATGAGAATCTTTAAGACGT
* * *
17077399 TCTT-AAATAAGAATATTTGAGTCTTAGATGAGAATCTTTAAGACGT
1 TCTTCAAATGAGAATCTTTGAGTCTTAAATGAGAATCTTTAAGACGT
* * ** *
17077445 TATT-AAATGAGAATCTTTGAGTCTTAAATGAAAATCTTTATTATGT
1 TCTTCAAATGAGAATCTTTGAGTCTTAAATGAGAATCTTTAAGACGT
* * *
17077491 T-TTCAAATGAGAA-CATTTGAGTCTTAAATTAGAATTTTTAAGACAT
1 TCTTCAAATGAGAATC-TTTGAGTCTTAAATGAGAATCTTTAAGACGT
* * * * * *
17077537 TC-TCAAATGAGAATCTTTAAATCTTAAATGAGTATGTTTAGGACAT
1 TCTTCAAATGAGAATCTTTGAGTCTTAAATGAGAATCTTTAAGACGT
* *
17077583 T-TTCAAATAAGAA-CTTTTGAGTCTTAAATGAGAATATTTAA
1 TCTTCAAATGAGAATC-TTTGAGTCTTAAATGAGAATCTTTAA
17077624 AAATCTTTGA
Statistics
Matches: 187, Mismatches: 32, Indels: 13
0.81 0.14 0.06
Matches are distributed among these distances:
45 4 0.02
46 178 0.95
47 5 0.03
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (47 bp):
TCTTCAAATGAGAATCTTTGAGTCTTAAATGAGAATCTTTAAGACGT
Found at i:17077514 original size:92 final size:92
Alignment explanation
Indices: 17077355--17077623 Score: 333
Period size: 92 Copynumber: 2.9 Consensus size: 92
17077345 TCCTGAATCT
* *
17077355 TCAAATGAGAATCTTTAAGTCTCAAATGAGAATCTTTAAGACGTTCTT-AAATAAGAATATTTGA
1 TCAAATGAGAATCTTTAAGTCTTAAATGAGAATCTTTAAGACGTT-TTCAAATAAGAACATTTGA
* * *
17077419 GTCTTAGATGAGAATCTTTAAGACGTTA
65 GTCTTAAATGAGAATATTTAAGACATTA
* * * ** * *
17077447 TTAAATGAGAATCTTTGAGTCTTAAATGAAAATCTTTATTATGTTTTCAAATGAGAACATTTGAG
1 TCAAATGAGAATCTTTAAGTCTTAAATGAGAATCTTTAAGACGTTTTCAAATAAGAACATTTGAG
* * *
17077512 TCTTAAATTAGAATTTTTAAGACATTC
66 TCTTAAATGAGAATATTTAAGACATTA
* * * * * *
17077539 TCAAATGAGAATCTTTAAATCTTAAATGAGTATGTTTAGGACATTTTCAAATAAGAACTTTTGAG
1 TCAAATGAGAATCTTTAAGTCTTAAATGAGAATCTTTAAGACGTTTTCAAATAAGAACATTTGAG
17077604 TCTTAAATGAGAATATTTAA
66 TCTTAAATGAGAATATTTAA
17077624 AAATCTTTGA
Statistics
Matches: 148, Mismatches: 28, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
91 2 0.01
92 146 0.99
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.38
Consensus pattern (92 bp):
TCAAATGAGAATCTTTAAGTCTTAAATGAGAATCTTTAAGACGTTTTCAAATAAGAACATTTGAG
TCTTAAATGAGAATATTTAAGACATTA
Found at i:17077605 original size:138 final size:138
Alignment explanation
Indices: 17077354--17077622 Score: 328
Period size: 138 Copynumber: 1.9 Consensus size: 138
17077344 GTCCTGAATC
* * *
17077354 TTCAAATGAGAATCTTTAAGTCTCAAATGAGAATCTTTAAGACGTTCTTAAATAAGAATATTTGA
1 TTCAAATGAGAATCTTTAAGTCTCAAATGAGAATCTTTAAGACATTCTCAAATAAGAATATTTAA
* * * * *
17077419 GTCTTAGATGAGAATCTTTAAGACGTTATTAAATGAGAATCTTTGAGTCTTAAATGAAAATCTTT
66 ATCTTAAATGAGAATCTTTAAGACATTATTAAATAAGAATCTTTGAGTCTTAAATGAAAATATTT
17077484 ATTATGTT
131 ATTATGTT
* * * * * *
17077492 TTCAAATGAGAA-CATTTGAGTCTTAAATTAGAATTTTTAAGACATTCTCAAATGAGAATCTTTA
1 TTCAAATGAGAATC-TTTAAGTCTCAAATGAGAATCTTTAAGACATTCTCAAATAAGAATATTTA
* * * *
17077556 AATCTTAAATGAGTATGTTTAGGACATT-TTCAAATAAGAA-CTTTTGAGTCTTAAATGAGAATA
65 AATCTTAAATGAGAATCTTTAAGACATTATT-AAATAAGAATC-TTTGAGTCTTAAATGAAAATA
17077619 TTTA
128 TTTA
17077623 AAAATCTTTG
Statistics
Matches: 110, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
137 4 0.04
138 106 0.96
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.38
Consensus pattern (138 bp):
TTCAAATGAGAATCTTTAAGTCTCAAATGAGAATCTTTAAGACATTCTCAAATAAGAATATTTAA
ATCTTAAATGAGAATCTTTAAGACATTATTAAATAAGAATCTTTGAGTCTTAAATGAAAATATTT
ATTATGTT
Found at i:17077742 original size:20 final size:20
Alignment explanation
Indices: 17077709--17077747 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
17077699 AAAATTTATT
*
17077709 GAATGTGAACCTTTAAACTC
1 GAATGAGAACCTTTAAACTC
* *
17077729 GAATGAGAAGCTTTGAACT
1 GAATGAGAACCTTTAAACT
17077748 TTTGGATGTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (20 bp):
GAATGAGAACCTTTAAACTC
Found at i:17077820 original size:44 final size:43
Alignment explanation
Indices: 17077730--17077812 Score: 116
Period size: 43 Copynumber: 2.0 Consensus size: 43
17077720 TTTAAACTCG
* * *
17077730 AATGAGAAGCTTTGAACTTTTGGATGTGAATATCCAAAATTCA
1 AATGAAAAGCTTTAAACTTTTGGATGTGAATACCCAAAATTCA
17077773 AATGAAAAGCTTTAAACTTTTTGGATGTG-AT-CCCAAAATT
1 AATGAAAAGCTTTAAAC-TTTTGGATGTGAATACCCAAAATT
17077813 GTTAAATGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
42 8 0.22
43 17 0.47
44 11 0.31
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (43 bp):
AATGAAAAGCTTTAAACTTTTGGATGTGAATACCCAAAATTCA
Found at i:17078353 original size:82 final size:83
Alignment explanation
Indices: 17078159--17078616 Score: 329
Period size: 83 Copynumber: 5.6 Consensus size: 83
17078149 TCAATAAGTC
* * * * ** * *
17078159 TTTTATTTTTTAAAGTTATTATGCTTATACATAG-AGAAGCCTTTTATTTTTC-AAAGTTATTGT
1 TTTTATTTTTCAAAGTTGTTATGCCTCTATTTAGAAG-AGCTTTTTATTTTTCTAAAGTTATTGA
17078222 GCCTCTATTTAGA-AGAGCCT
65 GCCTCTATTTAGAGA-AG-CT
* * * *
17078242 TTTTATTTTTCAAAGTTGTTATACTTCTATTTAAAAGAGCTTTTTATTTTTC-AAAGTTATTGAA
1 TTTTATTTTTCAAAGTTGTTATGCCTCTATTTAGAAGAGCTTTTTATTTTTCTAAAGTTATTGAG
*
17078306 CCTCTATTTAGAGAAGTT
66 CCTCTATTTAGAGAAGCT
* * * * *
17078324 TTTTATTTTTCAAAGTTGTTGTGCCTCTATTTATAGGTGCATTTTA-TTTTCTAAAGTTATT-AT
1 TTTTATTTTTCAAAGTTGTTATGCCTCTATTTAGAAGAGCTTTTTATTTTTCTAAAGTTATTGA-
* * *
17078387 GCCTCTGTTTAAAGGAGC-
65 GCCTCTATTTAGAGAAGCT
* * * * * * *
17078405 TTTTATTTTTCAAAATTGTTATGCCTCTGTTTAGAAGAGC-CTTTAATTTTCTAAA---CTCGTG
1 TTTTATTTTTCAAAGTTGTTATGCCTCTATTTAGAAGAGCTTTTTATTTTTCTAAAGTTATTGAG
*
17078466 CCTCTATTTAGA-ATAGCA
66 CCTCTATTTAGAGA-AGCT
* * * * **
17078484 TTTTATTTTTTAAAGTTGTTGTGCCTTTATTTAGATGAGCATTTATT-TTTTTCTAAAGTCGTTG
1 TTTTATTTTTCAAAGTTGTTATGCCTCTATTTAGAAGAGC-TTT-TTATTTTTCTAAAGTTATTG
* *
17078548 AGCCTCTGTTTATATG-AGCTT
64 AGCCTCTATTTAGA-GAAGC-T
* *
17078569 TATTTACTTTTTCAAAGTCATG-GA-GCCTCTATTTAGAGGAG-TTTTTAT
1 T-TTTA-TTTTTCAAAGT--TGTTATGCCTCTATTTAGAAGAGCTTTTTAT
17078617 ATTATTCAAG
Statistics
Matches: 298, Mismatches: 55, Indels: 42
0.75 0.14 0.11
Matches are distributed among these distances:
78 15 0.05
79 34 0.11
80 4 0.01
81 59 0.20
82 64 0.21
83 65 0.22
84 21 0.07
85 5 0.02
86 4 0.01
87 25 0.08
89 2 0.01
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.48
Consensus pattern (83 bp):
TTTTATTTTTCAAAGTTGTTATGCCTCTATTTAGAAGAGCTTTTTATTTTTCTAAAGTTATTGAG
CCTCTATTTAGAGAAGCT
Found at i:17078516 original size:41 final size:41
Alignment explanation
Indices: 17078159--17078605 Score: 300
Period size: 41 Copynumber: 10.9 Consensus size: 41
17078149 TCAATAAGTC
* * * * ** *
17078159 TTTTATTTTTTAAAGTTATTATGCTTATACATAG-AGAAGCC
1 TTTTATTTTTCAAAGTTATTGTGCCTCTATTTAGAAG-AGCA
*
17078200 TTTTATTTTTCAAAGTTATTGTGCCTCTATTTAGAAGAGCCT
1 TTTTATTTTTCAAAGTTATTGTGCCTCTATTTAGAAGAG-CA
* * * * * *
17078242 TTTTATTTTTCAAAGTTGTTATACTTCTATTTAAAAGAGCT
1 TTTTATTTTTCAAAGTTATTGTGCCTCTATTTAGAAGAGCA
** **
17078283 TTTTATTTTTCAAAGTTATTGAACCTCTATTTAG-AGAAGTT
1 TTTTATTTTTCAAAGTTATTGTGCCTCTATTTAGAAG-AGCA
* * * *
17078324 TTTTATTTTTCAAAGTTGTTGTGCCTCTATTTATAGGTGCA
1 TTTTATTTTTCAAAGTTATTGTGCCTCTATTTAGAAGAGCA
* *
17078365 TTTTA-TTTTCTAAAGTTATTATGCCTCTGTTTA-AAGGAGC-
1 TTTTATTTTTC-AAAGTTATTGTGCCTCTATTTAGAA-GAGCA
* * * *
17078405 TTTTATTTTTCAAAATTGTTATGCCTCTGTTTAGAAGAGC-
1 TTTTATTTTTCAAAGTTATTGTGCCTCTATTTAGAAGAGCA
* * * * *
17078445 CTTTAATTTTCTAAA---CTCGTGCCTCTATTTAGAATAGCA
1 TTTTATTTTTC-AAAGTTATTGTGCCTCTATTTAGAAGAGCA
* * * *
17078484 TTTTATTTTTTAAAGTTGTTGTGCCTTTATTTAGATGAGCA
1 TTTTATTTTTCAAAGTTATTGTGCCTCTATTTAGAAGAGCA
* ** * * * * *
17078525 TTTATTTTTTTCTAAAGTCGTTGAGCCTCTGTTTATATGAGCTT
1 TTT-TATTTTTC-AAAGTTATTGTGCCTCTATTTAGAAGAGC-A
* * *
17078569 TATTTACTTTTTCAAAGTCATGGAGCCTCTATTTAGA
1 T-TTTA-TTTTTCAAAGTTATTGTGCCTCTATTTAGA
17078606 GGAGTTTTTA
Statistics
Matches: 327, Mismatches: 61, Indels: 33
0.78 0.14 0.08
Matches are distributed among these distances:
38 21 0.06
39 8 0.02
40 46 0.14
41 154 0.47
42 44 0.13
43 24 0.07
44 22 0.07
45 8 0.02
ACGTcount: A:0.25, C:0.13, G:0.14, T:0.48
Consensus pattern (41 bp):
TTTTATTTTTCAAAGTTATTGTGCCTCTATTTAGAAGAGCA
Found at i:17078565 original size:43 final size:42
Alignment explanation
Indices: 17078465--17078605 Score: 144
Period size: 43 Copynumber: 3.3 Consensus size: 42
17078455 CTAAACTCGT
* * *
17078465 GCCTCTATTTAGAAT-AGCATTT-TATTTTTTAAAGTTGTTGT
1 GCCTCTATTTAG-ATGAGCATTTATTTTTTTTAAAGTCGTTGA
*
17078506 GCCTTTATTTAGATGAGCATTTATTTTTTTCTAAAGTCGTTGA
1 GCCTCTATTTAGATGAGCATTTATTTTTTT-TAAAGTCGTTGA
* * * *
17078549 GCCTCTGTTTATATGAGC-TTTATTTACTTTTTCAAAGTCATGGA
1 GCCTCTATTTAGATGAGCATTTATTT--TTTTT-AAAGTCGTTGA
17078593 GCCTCTATTTAGA
1 GCCTCTATTTAGA
17078606 GGAGTTTTTA
Statistics
Matches: 83, Mismatches: 11, Indels: 9
0.81 0.11 0.09
Matches are distributed among these distances:
40 2 0.02
41 18 0.22
42 13 0.16
43 26 0.31
44 24 0.29
ACGTcount: A:0.23, C:0.13, G:0.16, T:0.48
Consensus pattern (42 bp):
GCCTCTATTTAGATGAGCATTTATTTTTTTTAAAGTCGTTGA
Found at i:17079755 original size:25 final size:25
Alignment explanation
Indices: 17079727--17079800 Score: 78
Period size: 26 Copynumber: 2.9 Consensus size: 25
17079717 TTAATTATCC
17079727 AATGATGAAATTTTTA-AAAATTTTA
1 AATGAT-AAATTTTTATAAAATTTTA
*
17079752 AATGGTAAATTTTTATAAAATTTTTA
1 AATGATAAATTTTTATAAAA-TTTTA
** * *
17079778 TGTGAGAAATTTTTTTAAAATTT
1 AATGATAAATTTTTATAAAATTT
17079801 ATCCCAAATG
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
24 9 0.22
25 12 0.29
26 20 0.49
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (25 bp):
AATGATAAATTTTTATAAAATTTTA
Found at i:17079890 original size:8 final size:8
Alignment explanation
Indices: 17079877--17079905 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
17079867 AAAAAGAGAG
17079877 AAAAAAAT
1 AAAAAAAT
17079885 AAAAAAAT
1 AAAAAAAT
17079893 AAAAAAAT
1 AAAAAAAT
17079901 AAAAA
1 AAAAA
17079906 TTTGGTTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:17080152 original size:49 final size:48
Alignment explanation
Indices: 17080093--17080285 Score: 122
Period size: 49 Copynumber: 3.8 Consensus size: 48
17080083 ATAAAAAGAG
* *
17080093 AAAAAGAATTTCTAAATAGGGTCAAATGGTGAAAAATTTAGAAATTTCA
1 AAAAAAAATTTCTAAATAGGATCAAATGGTGAAAAATTTA-AAATTTCA
* * * * *
17080142 AAAAAAAATTTCTAGAT-TGACCTAAATGGTGGAAAATTTAAAATTCCAATAAA
1 AAAAAAAATTTCTAAATAGGATC-AAATGGTGAAAAATTTAAAATT----T-CA
* * *
17080195 AGAAAAAGAATTTCTAAATAGGCTCAAATAGTAAAAAATTTTAAAA-TTCA
1 A-AAAAA-AATTTCTAAATAGGATCAAATGGTGAAAAA-TTTAAAATTTCA
* * *
17080245 AAAAAATATATTTTTAATTTGGCA-CAAATGGTGAAATAATT
1 AAAAAA-A-ATTTCTAAATAGG-ATCAAATGGTGAAA-AATT
17080286 AGATATATTT
Statistics
Matches: 109, Mismatches: 22, Indels: 25
0.70 0.14 0.16
Matches are distributed among these distances:
48 7 0.06
49 37 0.34
50 24 0.22
51 3 0.03
52 1 0.01
53 2 0.02
54 5 0.05
55 21 0.19
56 9 0.08
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.30
Consensus pattern (48 bp):
AAAAAAAATTTCTAAATAGGATCAAATGGTGAAAAATTTAAAATTTCA
Found at i:17080843 original size:13 final size:14
Alignment explanation
Indices: 17080817--17080845 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
17080807 TATTTTTATA
17080817 TAATTATAATATTT
1 TAATTATAATATTT
17080831 TAATTAT-ATATTT
1 TAATTATAATATTT
17080844 TA
1 TA
17080846 TTCAAATTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAATTATAATATTT
Found at i:17081837 original size:27 final size:27
Alignment explanation
Indices: 17081805--17081856 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
17081795 TAAAAATTAT
17081805 AATTTAAATATTATATTAAAATTTTTA
1 AATTTAAATATTATATTAAAATTTTTA
* *
17081832 AATTTAAATATTTTATTAATATTTT
1 AATTTAAATATTATATTAAAATTTT
17081857 ATTATAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
AATTTAAATATTATATTAAAATTTTTA
Found at i:17085405 original size:23 final size:23
Alignment explanation
Indices: 17085379--17085431 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
17085369 TTTTATCAAA
**
17085379 AATTTTTTAATTGTAATTATAAT
1 AATTTTTTAATTACAATTATAAT
17085402 AATTTTTTAATTACAATTATAAT
1 AATTTTTTAATTACAATTATAAT
17085425 AATTTTT
1 AATTTTT
17085432 ATTATAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (23 bp):
AATTTTTTAATTACAATTATAAT
Found at i:17088739 original size:18 final size:18
Alignment explanation
Indices: 17088713--17088752 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
17088703 TACAGCAAGA
*
17088713 AATTTCAATT-CAGTTGTC
1 AATTCCAATTCCAGTT-TC
17088731 AATTCCAATTCCAGTTTC
1 AATTCCAATTCCAGTTTC
17088749 AATT
1 AATT
17088753 TCAAGTCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.42
Consensus pattern (18 bp):
AATTCCAATTCCAGTTTC
Found at i:17093677 original size:18 final size:18
Alignment explanation
Indices: 17093656--17093693 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
17093646 ACAATCTAAA
17093656 ATAATATGA-AAAAATCGT
1 ATAATATGAGAAAAAT-GT
*
17093674 ATAATATTAGAAAAATGT
1 ATAATATGAGAAAAATGT
17093692 AT
1 AT
17093694 TTGGCGATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.55, C:0.03, G:0.11, T:0.32
Consensus pattern (18 bp):
ATAATATGAGAAAAATGT
Found at i:17094224 original size:12 final size:12
Alignment explanation
Indices: 17094203--17094232 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
17094193 TACTCATAAT
17094203 AATT-TATTATA
1 AATTATATTATA
17094214 AATTATATTATA
1 AATTATATTATA
17094226 AATTATA
1 AATTATA
17094233 AAAAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
AATTATATTATA
Found at i:17096025 original size:11 final size:11
Alignment explanation
Indices: 17095993--17096026 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
17095983 ATTAATTTCA
*
17095993 TATATTAAATA
1 TATATTAAATT
17096004 TATATTAAATT
1 TATATTAAATT
*
17096015 TATATCAAATT
1 TATATTAAATT
17096026 T
1 T
17096027 TGAATTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (11 bp):
TATATTAAATT
Found at i:17096085 original size:18 final size:19
Alignment explanation
Indices: 17096062--17096102 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
17096052 TCAAACCGAA
*
17096062 TATATATATT-TTAATTTT
1 TATATATATTCTAAATTTT
*
17096080 TATATATCTTCTAAATTTT
1 TATATATATTCTAAATTTT
17096099 TATA
1 TATA
17096103 AAAAAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (19 bp):
TATATATATTCTAAATTTT
Found at i:17096192 original size:5 final size:5
Alignment explanation
Indices: 17096178--17096256 Score: 52
Period size: 5 Copynumber: 15.2 Consensus size: 5
17096168 TAAAAATTAA
* * * * *
17096178 TAAAT CAAAT TAAAT TAAAT T-AAT AAAAT TTAAT TCGATT TAAAT TAAAT
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT T-AAAT TAAAT TAAAT
* *
17096228 ATAAATT TTATT TAAAT TAAAAT TAAAT T
1 -TAAA-T TAAAT TAAAT T-AAAT TAAAT T
17096257 TTAAAATATT
Statistics
Matches: 56, Mismatches: 13, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
4 3 0.05
5 38 0.68
6 14 0.25
7 1 0.02
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (5 bp):
TAAAT
Found at i:17096253 original size:11 final size:10
Alignment explanation
Indices: 17096178--17096256 Score: 52
Period size: 11 Copynumber: 7.6 Consensus size: 10
17096168 TAAAAATTAA
*
17096178 TAAATCAAAT
1 TAAATTAAAT
17096188 TAAATTAAAT
1 TAAATTAAAT
*
17096198 T-AATAAAAT
1 TAAATTAAAT
* * *
17096207 TTAATTCGATT
1 TAAATT-AAAT
17096218 TAAATTAAAT
1 TAAATTAAAT
* *
17096228 ATAAATTTTATT
1 -TAAA-TTAAAT
17096240 TAAATTAAAAT
1 TAAATT-AAAT
17096251 TAAATT
1 TAAATT
17096257 TTAAAATATT
Statistics
Matches: 52, Mismatches: 12, Indels: 9
0.71 0.16 0.12
Matches are distributed among these distances:
9 8 0.15
10 17 0.33
11 23 0.44
12 4 0.08
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (10 bp):
TAAATTAAAT
Found at i:17096257 original size:22 final size:22
Alignment explanation
Indices: 17096201--17096259 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
17096191 ATTAAATTAA
* **
17096201 TAAAATTTAATTCGATTTAAAT
1 TAAAATTAAATTTTATTTAAAT
17096223 T-AAATATAAATTTTATTTAAAT
1 TAAAAT-TAAATTTTATTTAAAT
17096245 TAAAATTAAATTTTA
1 TAAAATTAAATTTTA
17096260 AAATATTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 4 0.12
22 24 0.75
23 4 0.12
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
TAAAATTAAATTTTATTTAAAT
Found at i:17096790 original size:28 final size:30
Alignment explanation
Indices: 17096726--17096780 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
17096716 TTTTTTATTT
* *
17096726 ATATATATATTTATATAATAATATTTTTAA
1 ATATTTATATTTATATAAAAATATTTTTAA
17096756 ATATTTATATTT-TA-AAAAATATTTT
1 ATATTTATATTTATATAAAAATATTTT
17096781 ATTAATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 10 0.43
29 2 0.09
30 11 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (30 bp):
ATATTTATATTTATATAAAAATATTTTTAA
Found at i:17105498 original size:19 final size:21
Alignment explanation
Indices: 17105476--17105534 Score: 58
Period size: 19 Copynumber: 3.1 Consensus size: 21
17105466 TTTGTGAGCC
17105476 TAATTAAAAT-TTTA-TATTT
1 TAATTAAAATATTTATTATTT
*
17105495 TAA-T-ATATATTTATTATTT
1 TAATTAAAATATTTATTATTT
*
17105514 TAATTAAAA-A-TTATTGTTT
1 TAATTAAAATATTTATTATTT
17105533 TA
1 TA
17105535 TTCTTATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
17 3 0.09
18 5 0.15
19 21 0.64
20 2 0.06
21 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
TAATTAAAATATTTATTATTT
Found at i:17106515 original size:3 final size:3
Alignment explanation
Indices: 17106507--17106545 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
17106497 TATTTTTGAG
17106507 ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
17106546 AGCCCTGTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:17110802 original size:23 final size:21
Alignment explanation
Indices: 17110776--17110833 Score: 53
Period size: 23 Copynumber: 2.6 Consensus size: 21
17110766 ATTAAGAAAC
17110776 AAATACCAGTAAAAACACCAAAA
1 AAATACCA-TAAAAACACC-AAA
** *
17110799 AAATATTATAAAAAATACCAAA
1 AAATACCAT-AAAAACACCAAA
17110821 AAATACCAATAAA
1 AAATACC-ATAAA
17110834 TTTATCGAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
22 12 0.43
23 16 0.57
ACGTcount: A:0.67, C:0.16, G:0.02, T:0.16
Consensus pattern (21 bp):
AAATACCATAAAAACACCAAA
Found at i:17111189 original size:130 final size:130
Alignment explanation
Indices: 17110956--17111218 Score: 481
Period size: 130 Copynumber: 2.0 Consensus size: 130
17110946 AGTCCCATTC
*
17110956 TACAAGGTAACTAGTTGAAATTAACTTATACTTATTTATATCATAAGACCCTCATCTAGAAACCC
1 TACAAGGTAACTAGCTGAAATTAACTTATACTTATTTATATCATAAGACCCTCATCTAGAAACCC
*
17111021 TGTAATTTTAATATTTTGAAGAACAAATTCAAAAAAATTAGAGCATAAGAAAAACCTAAAATTTA
66 TGTAATTTTAATATTTTGAAGAACAAATTCAAAAAAATTAAAGCATAAGAAAAACCTAAAATTTA
* *
17111086 TACAAGGTAACTAGCTGAAATTAACTTATACTTGTTTATATCATAAGACCCTCATTTAGAAACCC
1 TACAAGGTAACTAGCTGAAATTAACTTATACTTATTTATATCATAAGACCCTCATCTAGAAACCC
*
17111151 TGTAATTTTAATATTTTGAAGAACAAATTCAAAAAAATTAAAGCATGAGAAAAACCTAAAATTTA
66 TGTAATTTTAATATTTTGAAGAACAAATTCAAAAAAATTAAAGCATAAGAAAAACCTAAAATTTA
17111216 TAC
1 TAC
17111219 CAACCTTAAA
Statistics
Matches: 128, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
130 128 1.00
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.32
Consensus pattern (130 bp):
TACAAGGTAACTAGCTGAAATTAACTTATACTTATTTATATCATAAGACCCTCATCTAGAAACCC
TGTAATTTTAATATTTTGAAGAACAAATTCAAAAAAATTAAAGCATAAGAAAAACCTAAAATTTA
Found at i:17113067 original size:12 final size:12
Alignment explanation
Indices: 17113052--17113089 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
17113042 CCAACAGCAG
*
17113052 CTCCAACCGCTT
1 CTCCAACCACTT
17113064 CTCCAACCACTT
1 CTCCAACCACTT
17113076 CTCC-ACCAACTT
1 CTCCAACC-ACTT
17113088 CT
1 CT
17113090 TCACCACCAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 3 0.12
12 21 0.88
ACGTcount: A:0.21, C:0.50, G:0.03, T:0.26
Consensus pattern (12 bp):
CTCCAACCACTT
Found at i:17113912 original size:4 final size:4
Alignment explanation
Indices: 17113903--17113944 Score: 54
Period size: 4 Copynumber: 11.0 Consensus size: 4
17113893 ATTTAATTCG
17113903 ATTA ATTA ATTA ATTA ATT- ATTAA ATTA ATT- -TTA ATTA ATTA
1 ATTA ATTA ATTA ATTA ATTA ATT-A ATTA ATTA ATTA ATTA ATTA
17113945 TCAAATAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 2 0.06
3 3 0.09
4 26 0.76
5 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
ATTA
Found at i:17113920 original size:12 final size:11
Alignment explanation
Indices: 17113903--17113945 Score: 61
Period size: 12 Copynumber: 3.8 Consensus size: 11
17113893 ATTTAATTCG
17113903 ATTAATTAATTA
1 ATTAATT-ATTA
17113915 ATTAATTATTAA
1 ATTAATTATT-A
17113927 ATTAATT-TTA
1 ATTAATTATTA
17113937 ATTAATTAT
1 ATTAATTAT
17113946 CAAATAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 8 0.28
11 6 0.21
12 15 0.52
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
ATTAATTATTA
Found at i:17114263 original size:21 final size:20
Alignment explanation
Indices: 17114237--17114278 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
17114227 TAAAATTAAA
17114237 ATTTTGAATTTAATT-AATTTG
1 ATTTTGAA--TAATTCAATTTG
17114258 ATTTTGAATAATTCAATTTG
1 ATTTTGAATAATTCAATTTG
17114278 A
1 A
17114279 AATTAATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 7 0.35
21 8 0.40
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.52
Consensus pattern (20 bp):
ATTTTGAATAATTCAATTTG
Found at i:17114840 original size:18 final size:21
Alignment explanation
Indices: 17114779--17114845 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
17114769 AATAATGATA
* *
17114779 AATG-TGAAATTAATTATTAT
1 AATGATGAAATTAAATATTGT
17114799 AATGATGAAATTAAATATTGT
1 AATGATGAAATTAAATATTGT
*
17114820 AATGATGAGATTAAA-A-T-T
1 AATGATGAAATTAAATATTGT
17114838 AATGATGA
1 AATGATGA
17114846 TATATATATT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
18 9 0.21
19 1 0.02
20 5 0.12
21 28 0.65
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.37
Consensus pattern (21 bp):
AATGATGAAATTAAATATTGT
Done.