Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167982.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_24, 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: 18142777
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 63000 characters in sequence are not A, C, G, or T
File 26 of 84
Found at i:5627562 original size:19 final size:20
Alignment explanation
Indices: 5627535--5627577 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
5627525 AACAAATACT
*
5627535 AAAATCTAAA-AAAAAAAGA
1 AAAACCTAAAGAAAAAAAGA
* *
5627554 AAAACCTAAAGAAAGAGAGA
1 AAAACCTAAAGAAAAAAAGA
5627574 AAAA
1 AAAA
5627578 GTAGGTTCTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.74, C:0.07, G:0.12, T:0.07
Consensus pattern (20 bp):
AAAACCTAAAGAAAAAAAGA
Found at i:5627835 original size:21 final size:20
Alignment explanation
Indices: 5627815--5627868 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
5627805 AATAAAATTA
* *
5627815 ATAAATTTATTTATAATATT
1 ATAAATGTATATATAATATT
5627835 ATAATATGTATATATATATATT
1 ATAA-ATGTATATATA-ATATT
*
5627857 ATAAATGAATAT
1 ATAAATGTATAT
5627869 CGTGATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.14
21 16 0.55
22 9 0.31
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (20 bp):
ATAAATGTATATATAATATT
Found at i:5634461 original size:27 final size:28
Alignment explanation
Indices: 5634402--5634463 Score: 124
Period size: 28 Copynumber: 2.2 Consensus size: 28
5634392 AACGCACGTC
5634402 AAAAAAAATTTACAAATCATACCAATAT
1 AAAAAAAATTTACAAATCATACCAATAT
5634430 AAAAAAAATTTACAAATCATACCAATAT
1 AAAAAAAATTTACAAATCATACCAATAT
5634458 AAAAAA
1 AAAAAA
5634464 TTCACAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.65, C:0.13, G:0.00, T:0.23
Consensus pattern (28 bp):
AAAAAAAATTTACAAATCATACCAATAT
Found at i:5642038 original size:2 final size:2
Alignment explanation
Indices: 5642031--5642060 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5642021 ATGCATAGAT
5642031 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5642061 GAAGAGAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5642917 original size:2 final size:2
Alignment explanation
Indices: 5642910--5642934 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5642900 TGTTTTTGAG
5642910 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
5642935 TGCAAGTTGT
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:5658491 original size:13 final size:13
Alignment explanation
Indices: 5658475--5658506 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
5658465 TTTCTTTTGC
5658475 CTTTTTTTTTTCT
1 CTTTTTTTTTTCT
5658488 C--TTTTTTTTCT
1 CTTTTTTTTTTCT
5658499 CTTTTTTT
1 CTTTTTTT
5658507 CCTTTGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
11 11 0.65
13 6 0.35
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
CTTTTTTTTTTCT
Found at i:5658492 original size:10 final size:10
Alignment explanation
Indices: 5658479--5658516 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
5658469 TTTTGCCTTT
5658479 TTTTTTTCTC
1 TTTTTTTCTC
5658489 TTTTTTTTCTC
1 -TTTTTTTCTC
5658500 TTTTTTTC-C
1 TTTTTTTCTC
5658509 TTTGTTTT
1 TTT-TTTT
5658517 TGGATTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 4 0.15
10 12 0.46
11 10 0.38
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.82
Consensus pattern (10 bp):
TTTTTTTCTC
Found at i:5658860 original size:4 final size:4
Alignment explanation
Indices: 5658851--5658879 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
5658841 ATCCCAGTGT
5658851 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
5658880 ACTTGTAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:5663651 original size:7 final size:7
Alignment explanation
Indices: 5663639--5663669 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
5663629 AAAACTTGGG
5663639 CTTCAGC
1 CTTCAGC
5663646 CTTCAGC
1 CTTCAGC
5663653 CTTCAGC
1 CTTCAGC
5663660 CTTCAGC
1 CTTCAGC
5663667 CTT
1 CTT
5663670 TACTTTGTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.13, C:0.42, G:0.13, T:0.32
Consensus pattern (7 bp):
CTTCAGC
Found at i:5663928 original size:20 final size:20
Alignment explanation
Indices: 5663899--5663938 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5663889 CTTTTTAAAA
*
5663899 ATAAAATTTTGAAAAGTTAT
1 ATAAAATTTTAAAAAGTTAT
* *
5663919 ATAAATTTTTAAAAATTTAT
1 ATAAAATTTTAAAAAGTTAT
5663939 TTTTTAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
ATAAAATTTTAAAAAGTTAT
Found at i:5663953 original size:34 final size:34
Alignment explanation
Indices: 5663870--5664012 Score: 114
Period size: 34 Copynumber: 4.2 Consensus size: 34
5663860 CTTTTCTCGT
*
5663870 AATTTTTT-AAAATT-TATAACTTTTTAAAAATA
1 AATTTTTTAAAAATTATATAAATTTTTAAAAATA
* * * *
5663902 AAATTTTGAAAAGTTATATAAATTTTTAAAAATT
1 AATTTTTTAAAAATTATATAAATTTTTAAAAATA
* * ** *
5663936 TATTTTTTAAAAATTATA-AACCTTTTCGAAAGTA
1 AATTTTTTAAAAATTATATAA-ATTTTTAAAAATA
* * *
5663970 AATTTTTGAAAAATTATA-AATTTTTTCAAAAACTT
1 AATTTTTTAAAAATTATATAAATTTTT-AAAAA-TA
5664005 AATTTTTT
1 AATTTTTT
5664013 TAAATTTTAT
Statistics
Matches: 84, Mismatches: 22, Indels: 7
0.74 0.19 0.06
Matches are distributed among these distances:
32 6 0.07
33 11 0.13
34 59 0.70
35 8 0.10
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (34 bp):
AATTTTTTAAAAATTATATAAATTTTTAAAAATA
Found at i:5664000 original size:18 final size:18
Alignment explanation
Indices: 5663870--5664016 Score: 89
Period size: 18 Copynumber: 8.6 Consensus size: 18
5663860 CTTTTCTCGT
*
5663870 AATTTTTTAAAATTTAT-
1 AATTTTTTAAAAATTATA
*
5663887 AACTTTTTAAAAA-TA-A
1 AATTTTTTAAAAATTATA
* *
5663903 AA-TTTTGAAAAGTTATA
1 AATTTTTTAAAAATTATA
*
5663920 TAAATTTTTAAAAATT-T-
1 -AATTTTTTAAAAATTATA
5663937 -ATTTTTTAAAAATTATA
1 AATTTTTTAAAAATTATA
** ** *
5663954 AACCTTTTCGAAA--GTA
1 AATTTTTTAAAAATTATA
*
5663970 AATTTTTGAAAAATTATA
1 AATTTTTTAAAAATTATA
*
5663988 AATTTTTTCAAAAACT-TA
1 AATTTTTT-AAAAATTATA
*
5664006 ATTTTTTTAAA
1 AATTTTTTAAA
5664017 TTTTATTTTT
Statistics
Matches: 98, Mismatches: 21, Indels: 22
0.70 0.15 0.16
Matches are distributed among these distances:
15 21 0.21
16 17 0.17
17 15 0.15
18 29 0.30
19 16 0.16
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (18 bp):
AATTTTTTAAAAATTATA
Found at i:5664018 original size:68 final size:66
Alignment explanation
Indices: 5663869--5664019 Score: 178
Period size: 68 Copynumber: 2.2 Consensus size: 66
5663859 ACTTTTCTCG
* *
5663869 TAATTTTTTAAAATTTATAACTTTTTAAAAATAAAATTTTGAAAAGTTATATAAATTTTTAAAAA
1 TAATTTTTTAAAATTTATAACTTTTCAAAAATAAAATTTTGAAAAATTATATAAATTTTTAAAAA
5663934 T
66 T
* * * * * *
5663935 TTATTTTTTAAAAATTATAAACCTTTTCGAAAGTAAATTTTTGAAAAATTATA-AATTTTTTCAA
1 TAATTTTTTAAAATTTAT-AA-CTTTTCAAAAATAAAATTTTGAAAAATTATATAAATTTTT-AA
5663999 AAACT
63 AAA-T
*
5664004 TAATTTTTTTAAATTT
1 TAATTTTTTAAAATTT
5664020 TATTTTTAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
66 16 0.23
67 9 0.13
68 31 0.44
69 14 0.20
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.48
Consensus pattern (66 bp):
TAATTTTTTAAAATTTATAACTTTTCAAAAATAAAATTTTGAAAAATTATATAAATTTTTAAAAA
T
Found at i:5666390 original size:20 final size:19
Alignment explanation
Indices: 5666365--5666408 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
5666355 TCTAATCTAA
*
5666365 TTATATATTTTTATTAATTT
1 TTATATATTTTT-TAAATTT
5666385 TTATATATTTTTTAAATTT
1 TTATATATTTTTTAAATTT
5666404 TTATA
1 TTATA
5666409 AAATAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATATATTTTTTAAATTT
Found at i:5666412 original size:11 final size:10
Alignment explanation
Indices: 5666365--5666410 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
5666355 TCTAATCTAA
*
5666365 TTATATATTT
1 TTATAAATTT
*
5666375 TTATTAATTT
1 TTATAAATTT
*
5666385 TTATATATTT
1 TTATAAATTT
5666395 TT-TAAATTT
1 TTATAAATTT
5666404 TTATAAA
1 TTATAAA
5666411 ATAAAAATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
9 8 0.27
10 22 0.73
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTATAAATTT
Found at i:5668602 original size:39 final size:39
Alignment explanation
Indices: 5668559--5668634 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 39
5668549 AAATTTTTTT
*
5668559 AAAAAAATCTGAAATA-TTATAAAAATTATTAAAAAATAA
1 AAAAAAATATGAAATATTTATAAAAATTA-TAAAAAATAA
* *
5668598 AAAAATATATGAAATATTTATAGAAATTATAAAAAAT
1 AAAAAAATATGAAATATTTATAAAAATTATAAAAAAT
5668635 TATGAAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 22 0.67
40 11 0.33
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.30
Consensus pattern (39 bp):
AAAAAAATATGAAATATTTATAAAAATTATAAAAAATAA
Found at i:5668918 original size:18 final size:18
Alignment explanation
Indices: 5668893--5668931 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
5668883 AAAATATTTT
5668893 AAAATTAT-AAAAATTAA
1 AAAATTATGAAAAATTAA
*
5668910 AAAATTTATGAAAACTTAA
1 AAAA-TTATGAAAAATTAA
5668929 AAA
1 AAA
5668932 CTTCAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 4 0.21
19 11 0.58
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (18 bp):
AAAATTATGAAAAATTAA
Found at i:5669202 original size:30 final size:30
Alignment explanation
Indices: 5669141--5669203 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
5669131 TTTATTAAAA
* *
5669141 TTTTTATTTTTTATGAAAAATTGAGATTTT
1 TTTTTATTTTTCATGAAAAATTAAGATTTT
* *
5669171 TTTTTATTTTTCATTAAAATTTTAAGATTTT
1 TTTTTATTTTTCATGAAAA-ATTAAGATTTT
5669202 TT
1 TT
5669204 AATTTTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 17 0.61
31 11 0.39
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.63
Consensus pattern (30 bp):
TTTTTATTTTTCATGAAAAATTAAGATTTT
Found at i:5670343 original size:29 final size:30
Alignment explanation
Indices: 5670273--5670355 Score: 93
Period size: 30 Copynumber: 2.9 Consensus size: 30
5670263 TATATGTTTA
* *
5670273 AAGT-TTTAATTAAATAAAAATAAATATTT
1 AAGTATTTAATTAATTAAAAATAAAAATTT
*
5670302 AAGTATTCAATTAATTAAAAATAAAAATTT
1 AAGTATTTAATTAATTAAAAATAAAAATTT
*
5670332 -A-TATTGTAATTAATT-ATAATAAAA
1 AAGTATT-TAATTAATTAAAAATAAAA
5670356 TCAAAATTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
28 12 0.26
29 13 0.28
30 22 0.47
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.40
Consensus pattern (30 bp):
AAGTATTTAATTAATTAAAAATAAAAATTT
Found at i:5670549 original size:2 final size:2
Alignment explanation
Indices: 5670544--5670598 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
5670534 ACACACTCAG
5670544 AT AT AT AT AT AT AT 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 AT AT AT AT
5670586 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
5670599 CAACAGACAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5670636 original size:149 final size:149
Alignment explanation
Indices: 5670449--5670729 Score: 544
Period size: 149 Copynumber: 1.9 Consensus size: 149
5670439 TGCCAACAAG
*
5670449 ACAACAGACATGACACCCGCGATAATAATTTGGGAAATTAAACAGAAACCAAACGAGTTTTCATT
1 ACAACAGACATGACACCCGCGATAATAATTTGAGAAATTAAACAGAAACCAAACGAGTTTTCATT
*
5670514 GAAATTTTTTATATGGACACACACACTCAGATATATATATATATATATATATATATATATATATA
66 GAAAATTTTTATATGGACACACACACTCAGATATATATATATATATATATATATATATATATATA
5670579 TATATATATATATATATAT
131 TATATATATATATATATAT
5670598 ACAACAGACATGACACCCGCGATAATAATTTGAGAAATTAAACAGAAACCAAACGAGTTTTCATT
1 ACAACAGACATGACACCCGCGATAATAATTTGAGAAATTAAACAGAAACCAAACGAGTTTTCATT
5670663 GAAAATTTTTATATGGACACACACACTCAGATATATATATATATATATATATATATATATATATA
66 GAAAATTTTTATATGGACACACACACTCAGATATATATATATATATATATATATATATATATATA
5670728 TA
131 TA
5670730 GCCAGTTGAA
Statistics
Matches: 130, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 130 1.00
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.32
Consensus pattern (149 bp):
ACAACAGACATGACACCCGCGATAATAATTTGAGAAATTAAACAGAAACCAAACGAGTTTTCATT
GAAAATTTTTATATGGACACACACACTCAGATATATATATATATATATATATATATATATATATA
TATATATATATATATATAT
Found at i:5670698 original size:2 final size:2
Alignment explanation
Indices: 5670693--5670729 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5670683 ACACACTCAG
5670693 AT AT AT AT AT 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 AT AT AT AT AT A
5670730 GCCAGTTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5672998 original size:31 final size:31
Alignment explanation
Indices: 5672957--5673020 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
5672947 ATAAAAAAAT
5672957 TATAATTTACATCATAAACTTTTAAATAATA
1 TATAATTTACATCATAAACTTTTAAATAATA
* * * *
5672988 TATACTTTACATTATAAATTTTTAAATCATA
1 TATAATTTACATCATAAACTTTTAAATAATA
5673019 TA
1 TA
5673021 CCATATTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (31 bp):
TATAATTTACATCATAAACTTTTAAATAATA
Found at i:5678287 original size:276 final size:275
Alignment explanation
Indices: 5677794--5678346 Score: 770
Period size: 276 Copynumber: 2.0 Consensus size: 275
5677784 AAATGGGAAG
** *
5677794 GAGAATTAAGTTATGGTTCCTACAGTGCAGAACATTCGTAGTCAAAAAAGTACTCCTAAGCAACA
1 GAGAATTAAACTATGGTTCCTACAGTGCAGAACATTCATAGTCAAAAAAGTACTCCTAAGCAACA
* * * * * *
5677859 GCAAGGCCAAGCCAATGTGTCAGATACCCAAACTTAATTGAACGGGCCAAGCAAACAGTGTTGGA
66 GCAAGCCCAAGCCAATGTGTCAAATAACCAAACTGAATTGAACAGGCCAAGCAAACACTGTTGGA
** * * * *
5677924 TTCCATATTTTGACCTGTAGTTTTGCCAATAGTGTTAAATTTACGACGACTGTGGGTAATCTTGG
131 TTCCATAACTAGACCTATAGTTTTGCCAATACTGTTAAATTTACCACGAC-GTGGGTAATCTTGG
* * *
5677989 TGACTTTAGACTATCAGCTCCTCCTGTATGAAGCAAGAAAATATGATTTTGACCTGCCATGAGAG
195 TAACTTTAGACCATCAGCTCCTCCTGTATGAAGCAAGAAAATATAATTTTGACCTGCCATGAGAG
* *
5678054 GAATGTGAGTGTGAAT
260 GAAAGGGAGTGTGAAT
5678070 GAGAATTAAACTATGGTTCCTACAGTGCAGAACATTCATAGTCAAAAAAGTACTCCTAAGCAACA
1 GAGAATTAAACTATGGTTCCTACAGTGCAGAACATTCATAGTCAAAAAAGTACTCCTAAGCAACA
*
5678135 GCAAGACCCAAGCCAATGTGTCAAATAACCAAATCTGAATTGAACAGGTCAAGCAAACACTGTTG
66 GCAAG-CCCAAGCCAATGTGTCAAATAACCAAA-CTGAATTGAACAGGCCAAGCAAACACTGTTG
* ** * *
5678200 GATTCCATAACTAGACCTATCGTTTTGGTGACA-ACT-TTAAGTTTACCATGAC-TGGGTAATCT
129 GATTCCATAACTAGACCTATAGTTTT-GCCA-ATACTGTTAAATTTACCACGACGTGGGTAATCT
* * *
5678262 TGGTAACTTTAGACCATCAGCTCCTCCTGTGTGAAGCAAGAAAATATAATTTTGACCTTCCATTA
192 TGGTAACTTTAGACCATCAGCTCCTCCTGTATGAAGCAAGAAAATATAATTTTGACCTGCCATGA
*
5678327 GAGGAAAGGGAGTTTGAAT
257 GAGGAAAGGGAGTGTGAAT
5678346 G
1 G
5678347 TGATAGGGAC
Statistics
Matches: 243, Mismatches: 30, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
276 153 0.63
277 24 0.10
278 61 0.25
279 4 0.02
280 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.27
Consensus pattern (275 bp):
GAGAATTAAACTATGGTTCCTACAGTGCAGAACATTCATAGTCAAAAAAGTACTCCTAAGCAACA
GCAAGCCCAAGCCAATGTGTCAAATAACCAAACTGAATTGAACAGGCCAAGCAAACACTGTTGGA
TTCCATAACTAGACCTATAGTTTTGCCAATACTGTTAAATTTACCACGACGTGGGTAATCTTGGT
AACTTTAGACCATCAGCTCCTCCTGTATGAAGCAAGAAAATATAATTTTGACCTGCCATGAGAGG
AAAGGGAGTGTGAAT
Found at i:5680605 original size:23 final size:24
Alignment explanation
Indices: 5680555--5680606 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
5680545 TTAATTTGTA
*
5680555 TAATAAATTTTAAAAAATAACATC
1 TAATAAATTTTAAAAAATAAAATC
** *
5680579 TAATAAA-TTTAAAATTTAAAATT
1 TAATAAATTTTAAAAAATAAAATC
5680602 TAATA
1 TAATA
5680607 TTTACAACCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (24 bp):
TAATAAATTTTAAAAAATAAAATC
Found at i:5686042 original size:140 final size:140
Alignment explanation
Indices: 5685796--5686062 Score: 358
Period size: 140 Copynumber: 1.9 Consensus size: 140
5685786 ATTGTTAGGA
* * * * *
5685796 ATGGTTGATGTTCTTTGGATTCAATCATTTTTGTTTAAAAATCTTGTAGTTGTAGTTGCAACTTT
1 ATGGTTGATGTTCTTTAGATTCAATCATTCTTGTCTAAAAATCTTGTAGTTATAGTTCCAACTTT
* * * * *
5685861 CATTTTTTAATCCCTTGGATAATTAGAAACTGACATATTTAATTGGTTTGTGTAGGGCTCTTTTG
66 CATTTTCTAATCCCTTGGACAATGAGAAACTGAAATATTTAATTGGTTTGTATAGGGCTCTTTTG
5685926 ATTGTTGTGG
131 ATTGTTGTGG
*
5685936 ATGGTTGATGTTCTTTAGATTCAAT-ATTGCTTGTCTAAAAATCTTGTGGTTATAGTTCCAACTT
1 ATGGTTGATGTTCTTTAGATTCAATCATT-CTTGTCTAAAAATCTTGTAGTTATAGTTCCAACTT
* * * * *
5686000 TCATTTTCTAATTCCTTGTG-CAATGAGAAATTGAAATCTTTAATTTGTTTGTATAGTGCTCTT
65 TCATTTTCTAATCCCTTG-GACAATGAGAAACTGAAATATTTAATTGGTTTGTATAGGGCTCTT
5686063 GGGGCAGCAA
Statistics
Matches: 109, Mismatches: 16, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
139 3 0.03
140 105 0.96
141 1 0.01
ACGTcount: A:0.24, C:0.11, G:0.18, T:0.47
Consensus pattern (140 bp):
ATGGTTGATGTTCTTTAGATTCAATCATTCTTGTCTAAAAATCTTGTAGTTATAGTTCCAACTTT
CATTTTCTAATCCCTTGGACAATGAGAAACTGAAATATTTAATTGGTTTGTATAGGGCTCTTTTG
ATTGTTGTGG
Found at i:5695854 original size:2 final size:2
Alignment explanation
Indices: 5695847--5695872 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5695837 ATAAAATGAG
5695847 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
5695873 GAACTTATTC
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:5702373 original size:2 final size:2
Alignment explanation
Indices: 5702366--5702390 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5702356 TACAAAACAA
5702366 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
5702391 AAAAGAAGAA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5717795 original size:59 final size:59
Alignment explanation
Indices: 5717723--5717842 Score: 213
Period size: 59 Copynumber: 2.0 Consensus size: 59
5717713 GAGGGGTTTT
* *
5717723 ATAAGTATTAATTATTAAGTGATTGATTGAGATTATTTGTTTGTAATTTTTTATAATTA
1 ATAAGTATTAATTATTAAGTGATTGATTGAGATTATTTGTTTATAATTTTTCATAATTA
*
5717782 ATAAGTATTAATTATTAAGTGGTTGATTGAGATTATTTGTTTATAATTTTTCATAATTA
1 ATAAGTATTAATTATTAAGTGATTGATTGAGATTATTTGTTTATAATTTTTCATAATTA
5717841 AT
1 AT
5717843 TTTTTTTTAT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.34, C:0.01, G:0.13, T:0.52
Consensus pattern (59 bp):
ATAAGTATTAATTATTAAGTGATTGATTGAGATTATTTGTTTATAATTTTTCATAATTA
Found at i:5724369 original size:16 final size:16
Alignment explanation
Indices: 5724348--5724379 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5724338 AAAAGTGTAC
5724348 TTTCAATATAGAGAGG
1 TTTCAATATAGAGAGG
5724364 TTTCAATATAGAGAGG
1 TTTCAATATAGAGAGG
5724380 GTGGGAGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.31
Consensus pattern (16 bp):
TTTCAATATAGAGAGG
Found at i:5727715 original size:22 final size:22
Alignment explanation
Indices: 5727690--5727731 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5727680 TTGTCTATCC
* *
5727690 TAATTTTAGGGATACAAATACT
1 TAATTCTAGAGATACAAATACT
5727712 TAATTCTAGAGATACAAATA
1 TAATTCTAGAGATACAAATA
5727732 TAAATATACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (22 bp):
TAATTCTAGAGATACAAATACT
Found at i:5730226 original size:22 final size:22
Alignment explanation
Indices: 5730201--5730242 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5730191 TTGTCTATCC
* *
5730201 TAATTTTAGGGATACAAATACT
1 TAATTCTAGAGATACAAATACT
5730223 TAATTCTAGAGATACAAATA
1 TAATTCTAGAGATACAAATA
5730243 TAAATATACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (22 bp):
TAATTCTAGAGATACAAATACT
Found at i:5736878 original size:18 final size:18
Alignment explanation
Indices: 5736855--5736889 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5736845 TTTTTGATTT
*
5736855 AATATAAATATATTTATA
1 AATATAAATAAATTTATA
*
5736873 AATATACATAAATTTAT
1 AATATAAATAAATTTAT
5736890 GTATAATAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
AATATAAATAAATTTATA
Found at i:5746178 original size:18 final size:18
Alignment explanation
Indices: 5746143--5746183 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
5746133 GCAGCCGCAG
* *
5746143 GCAGC-ACAAGCACCACA
1 GCAGCAACAACCACAACA
5746160 GCAGCAACAACCACAACA
1 GCAGCAACAACCACAACA
5746178 GCAGCA
1 GCAGCA
5746184 GCAGCAGCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.44, C:0.39, G:0.17, T:0.00
Consensus pattern (18 bp):
GCAGCAACAACCACAACA
Found at i:5746875 original size:15 final size:15
Alignment explanation
Indices: 5746857--5746908 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
5746847 TTACATGAAC
*
5746857 CAGCAGCTGCAGCAG
1 CAGCAACTGCAGCAG
*
5746872 CAGCAATTGCAGCAG
1 CAGCAACTGCAGCAG
* * * *
5746887 CAACAACAGCAACAA
1 CAGCAACTGCAGCAG
5746902 CAGCAAC
1 CAGCAAC
5746909 AGTTACAGCA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.40, C:0.33, G:0.21, T:0.06
Consensus pattern (15 bp):
CAGCAACTGCAGCAG
Found at i:5746896 original size:9 final size:9
Alignment explanation
Indices: 5746884--5746909 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
5746874 GCAATTGCAG
5746884 CAGCAACAA
1 CAGCAACAA
5746893 CAGCAACAA
1 CAGCAACAA
5746902 CAGCAACA
1 CAGCAACA
5746910 GTTACAGCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.54, C:0.35, G:0.12, T:0.00
Consensus pattern (9 bp):
CAGCAACAA
Found at i:5749330 original size:2 final size:2
Alignment explanation
Indices: 5749323--5749349 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5749313 AAGATGTATG
5749323 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 T
5749350 CTGATAATAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5763895 original size:165 final size:163
Alignment explanation
Indices: 5763577--5763910 Score: 544
Period size: 165 Copynumber: 2.0 Consensus size: 163
5763567 CGTTGGGGTG
* *
5763577 TCTAATGGGCCCATAAAGTTTTATTGGGTCATGGAAGGTGGGCCCACTAAGCTCATTGCAGAAGT
1 TCTAATGGGCCCAAAAAGTTTTATTGGGTCATGGAAGGTAGGCCCACTAAGCTCATTGCAGAAGT
* *
5763642 TTAACTCTTTTTACTAAAGAAAAAAGTGACAATGGATTGGAGTTGCACTACTTAAAATATATAAT
66 TTAACTCTTTTTACTAAAAAAAAAAGTGAAAATGGATTGGAGTTGCACTACTTAAAATATATAAT
* *
5763707 AATGGCCAAAAGAAATTAATATATAACAATTCA
131 AATGGCCAAAACAAATAAATATATAACAATTCA
*
5763740 TTTAATGGGCCCAAAAAGTTTTATTGGGTCATTGG-AGGTAGGCCCACTAAGCTCATTGCAGAAG
1 TCTAATGGGCCCAAAAAGTTTTATTGGGTCA-TGGAAGGTAGGCCCACTAAGCTCATTGCAGAAG
* *
5763804 TTTAACTTTTTTTATTAAAAAAAAAAAAGTGAAAATGGATTGGAGTTGCACTACTTAAAATATAT
65 TTTAACTCTTTTTACT--AAAAAAAAAAGTGAAAATGGATTGGAGTTGCACTACTTAAAATATAT
*
5763869 AATAATGGCCAAAACAAATAAATATATAATAATTCA
128 AATAATGGCCAAAACAAATAAATATATAACAATTCA
5763905 TCTAAT
1 TCTAAT
5763911 CCTGTCTATG
Statistics
Matches: 157, Mismatches: 11, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
163 71 0.45
164 3 0.02
165 83 0.53
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.31
Consensus pattern (163 bp):
TCTAATGGGCCCAAAAAGTTTTATTGGGTCATGGAAGGTAGGCCCACTAAGCTCATTGCAGAAGT
TTAACTCTTTTTACTAAAAAAAAAAGTGAAAATGGATTGGAGTTGCACTACTTAAAATATATAAT
AATGGCCAAAACAAATAAATATATAACAATTCA
Found at i:5764057 original size:27 final size:27
Alignment explanation
Indices: 5764027--5764087 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
5764017 AAAAAAATTT
5764027 TTAATAAAAAATT-TATGTT-AATTTAA
1 TTAATAAAAAATTATAT-TTAAATTTAA
*
5764053 CTTAAT-TAAAATTAATATTTAAATTTAA
1 -TTAATAAAAAATT-ATATTTAAATTTAA
5764081 TTAATAA
1 TTAATAA
5764088 TATAATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
26 6 0.21
27 12 0.43
28 10 0.36
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (27 bp):
TTAATAAAAAATTATATTTAAATTTAA
Found at i:5765899 original size:2 final size:2
Alignment explanation
Indices: 5765892--5765921 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5765882 TCGAAGACAA
5765892 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5765922 AAAACGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5768040 original size:22 final size:23
Alignment explanation
Indices: 5767998--5768040 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
5767988 CTTACATGAG
*
5767998 AAAAAACATGTTATTTTTTCTTT
1 AAAAAACATGTTATTTATTCTTT
5768021 AAAAAA-ATGTT-TTTAATTCT
1 AAAAAACATGTTATTT-ATTCT
5768041 AAAATACAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 3 0.17
22 9 0.50
23 6 0.33
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.49
Consensus pattern (23 bp):
AAAAAACATGTTATTTATTCTTT
Found at i:5771223 original size:22 final size:22
Alignment explanation
Indices: 5771195--5771239 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
5771185 TTGTGGTAGG
5771195 AGATGTTGTTTCTACTACTAAA
1 AGATGTTGTTTCTACTACTAAA
5771217 AGATGTTGTTTCTACTACTAAA
1 AGATGTTGTTTCTACTACTAAA
5771239 A
1 A
5771240 TCTGAGTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (22 bp):
AGATGTTGTTTCTACTACTAAA
Found at i:5780173 original size:2 final size:2
Alignment explanation
Indices: 5780152--5780197 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
5780142 CAGGTTAGTA
* * *
5780152 AT AT AT AC AT AC AT AC 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 AT AT AT AT
5780194 AT AT
1 AT AT
5780198 TGATTGTGCA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:5791783 original size:34 final size:34
Alignment explanation
Indices: 5791740--5791805 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
5791730 GAACCCCACC
5791740 ACTAGGACAGGAAAACTATGTTGCCATGAAACCA
1 ACTAGGACAGGAAAACTATGTTGCCATGAAACCA
*
5791774 ACTAGGACAGGAAGACTATGTTGCCATGAAAC
1 ACTAGGACAGGAAAACTATGTTGCCATGAAAC
5791806 ATATTTGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (34 bp):
ACTAGGACAGGAAAACTATGTTGCCATGAAACCA
Found at i:5793821 original size:16 final size:16
Alignment explanation
Indices: 5793800--5793830 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5793790 AATAACCATC
5793800 CATGGTAATTTATAAT
1 CATGGTAATTTATAAT
*
5793816 CATGGTGATTTATAA
1 CATGGTAATTTATAA
5793831 AGTATCTTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.42
Consensus pattern (16 bp):
CATGGTAATTTATAAT
Found at i:5798545 original size:4 final size:4
Alignment explanation
Indices: 5798538--5798564 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5798528 ACAATGAGGT
5798538 TTTG TTTG TTTG TTTG TTTG TTTG TTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTT
5798565 ATGAAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (4 bp):
TTTG
Found at i:5808500 original size:23 final size:23
Alignment explanation
Indices: 5808468--5808534 Score: 68
Period size: 22 Copynumber: 2.9 Consensus size: 23
5808458 ATTTATCATC
5808468 ATTTT-TAATAAATTAATAAATT
1 ATTTTATAATAAATTAATAAATT
*
5808490 ATTTTATAATAAA-TAATTAATT
1 ATTTTATAATAAATTAATAAATT
5808512 -TTTTCAATAATATAATTATATAA
1 ATTTT--ATAATA-AATTA-ATAA
5808535 TATCATTGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
21 4 0.11
22 13 0.35
23 13 0.35
24 2 0.05
25 2 0.05
26 3 0.08
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTTTATAATAAATTAATAAATT
Found at i:5811109 original size:27 final size:29
Alignment explanation
Indices: 5811079--5811152 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
5811069 TTCAAGTATC
5811079 ATATTA-ATTAATATATTTAT-AA-TTTAA
1 ATATTACATTAA-ATATTTATAAATTTTAA
* * *
5811106 ATATTACATAAAATTTTTTTAAATTTTAA
1 ATATTACATTAAATATTTATAAATTTTAA
*
5811135 ATATTATATTAAATATTT
1 ATATTACATTAAATATTT
5811153 TATTAGAACT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
27 12 0.32
28 6 0.16
29 20 0.53
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (29 bp):
ATATTACATTAAATATTTATAAATTTTAA
Found at i:5814312 original size:21 final size:21
Alignment explanation
Indices: 5814287--5814333 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
5814277 CTAAATACCG
5814287 ATCTATAGTCCAAAATAGAGC
1 ATCTATAGTCCAAAATAGAGC
5814308 ATCTATAGTCCAAAATAGAGC
1 ATCTATAGTCCAAAATAGAGC
5814329 A-CTAT
1 ATCTAT
5814334 GTAACGAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.26
Consensus pattern (21 bp):
ATCTATAGTCCAAAATAGAGC
Found at i:5817131 original size:7 final size:7
Alignment explanation
Indices: 5817119--5817144 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5817109 AAATACACAA
5817119 AACCAGG
1 AACCAGG
5817126 AACCAGG
1 AACCAGG
5817133 AACCAGG
1 AACCAGG
5817140 AACCA
1 AACCA
5817145 AAATTACTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.31, G:0.23, T:0.00
Consensus pattern (7 bp):
AACCAGG
Found at i:5818653 original size:24 final size:22
Alignment explanation
Indices: 5818628--5818680 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
5818618 CTGTTTCAAT
*
5818628 TTTTAATTTATTTAATATTAAAA
1 TTTTAATTT-TTTAATATAAAAA
*
5818651 TTTCATATTTTTTAATATAAAAAA
1 TTTTA-ATTTTTTAATAT-AAAAA
5818675 TTTTAA
1 TTTTAA
5818681 AAATCATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 13 0.52
24 12 0.48
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTTAATTTTTTAATATAAAAA
Found at i:5827771 original size:13 final size:13
Alignment explanation
Indices: 5827739--5827764 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5827729 TCGTACATAA
5827739 AAATTTTAATTCT
1 AAATTTTAATTCT
5827752 AAATTTTAATTCT
1 AAATTTTAATTCT
5827765 TTATTTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
AAATTTTAATTCT
Found at i:5830971 original size:2 final size:2
Alignment explanation
Indices: 5830964--5830989 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5830954 ACTGTTTCTG
5830964 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
5830990 CTTGAAGTCG
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:5842615 original size:93 final size:93
Alignment explanation
Indices: 5842507--5842686 Score: 351
Period size: 93 Copynumber: 1.9 Consensus size: 93
5842497 AGGCTTGGGC
*
5842507 TTTGGTCTTTGGTTGTTTTTGTTGTTTTTATCAGTTTTGGGGATTAGGGTCTTGTTGGGTTTCTT
1 TTTGGTCTTTGGTTGTTTTTGTTGTTTTTATCAGTTCTGGGGATTAGGGTCTTGTTGGGTTTCTT
5842572 CTCAGGATCGGAACTTTGGTTTTTATAG
66 CTCAGGATCGGAACTTTGGTTTTTATAG
5842600 TTTGGTCTTTGGTTGTTTTTGTTGTTTTTATCAGTTCTGGGGATTAGGGTCTTGTTGGGTTTCTT
1 TTTGGTCTTTGGTTGTTTTTGTTGTTTTTATCAGTTCTGGGGATTAGGGTCTTGTTGGGTTTCTT
5842665 CTCAGGATCGGAACTTTGGTTT
66 CTCAGGATCGGAACTTTGGTTT
5842687 CATAGTTAAG
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 86 1.00
ACGTcount: A:0.10, C:0.09, G:0.28, T:0.52
Consensus pattern (93 bp):
TTTGGTCTTTGGTTGTTTTTGTTGTTTTTATCAGTTCTGGGGATTAGGGTCTTGTTGGGTTTCTT
CTCAGGATCGGAACTTTGGTTTTTATAG
Found at i:5842713 original size:93 final size:93
Alignment explanation
Indices: 5842523--5842713 Score: 287
Period size: 93 Copynumber: 2.1 Consensus size: 93
5842513 CTTTGGTTGT
*
5842523 TTTTGTTGTTTTTATCAGTTTTGGGGATTAGGGTCTTGTTGGGTTTCTTCTCAGGATCGGAACTT
1 TTTTGTTGTTTTTATCAGTTCTGGGGATTAGGGTCTTGTTGGGTTTCTTCTCAGGATCGGAACTT
* * * ** *
5842588 TGGTTTTTATAGTTTGGTCTTTGGTTGT
66 TGGTTTTCATAGTTGGGTCTTTCGCGGG
5842616 TTTTGTTGTTTTTATCAGTTCTGGGGATTAGGGTCTTGTTGGGTTTCTTCTCAGGATCGGAACTT
1 TTTTGTTGTTTTTATCAGTTCTGGGGATTAGGGTCTTGTTGGGTTTCTTCTCAGGATCGGAACTT
5842681 TGG-TTTCATAGTTAAGGGT-TTTCGCGGG
66 TGGTTTTCATAGTT--GGGTCTTTCGCGGG
5842709 TTTTG
1 TTTTG
5842714 GAGGTTTAAG
Statistics
Matches: 89, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
92 9 0.10
93 77 0.87
94 3 0.03
ACGTcount: A:0.12, C:0.10, G:0.29, T:0.50
Consensus pattern (93 bp):
TTTTGTTGTTTTTATCAGTTCTGGGGATTAGGGTCTTGTTGGGTTTCTTCTCAGGATCGGAACTT
TGGTTTTCATAGTTGGGTCTTTCGCGGG
Found at i:5848408 original size:34 final size:34
Alignment explanation
Indices: 5848336--5848400 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
5848326 TCAGAAATGG
* * *
5848336 ATTTTCAAGAATCCTCAAAGCTTCTCGGATGCCC
1 ATTTTCAAGAAACCTCAAAGCTTCTCGAATACCC
* *
5848370 ATTTTCGAGAAACTTCAAAGCTTCTCGAATA
1 ATTTTCAAGAAACCTCAAAGCTTCTCGAATA
5848401 TTCATTTTTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.31
Consensus pattern (34 bp):
ATTTTCAAGAAACCTCAAAGCTTCTCGAATACCC
Found at i:5859040 original size:8 final size:8
Alignment explanation
Indices: 5859027--5859052 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
5859017 GAAGCTCGAT
5859027 GACGATTG
1 GACGATTG
5859035 GACGATTG
1 GACGATTG
5859043 GACGATTG
1 GACGATTG
5859051 GA
1 GA
5859053 GATAGATGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.12, G:0.38, T:0.23
Consensus pattern (8 bp):
GACGATTG
Found at i:5860007 original size:19 final size:22
Alignment explanation
Indices: 5859975--5860023 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 22
5859965 TTCAACATAA
*
5859975 AAAAAATTACTTAAAC-CAA-T
1 AAAAAATTACTTAAACAAAACT
5859995 AAAAAATTA-TTAAACAAAACT
1 AAAAAATTACTTAAACAAAACT
5860016 AAAAAATT
1 AAAAAATT
5860024 CTTTATCACT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 6 0.23
20 11 0.42
21 9 0.35
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.24
Consensus pattern (22 bp):
AAAAAATTACTTAAACAAAACT
Found at i:5860856 original size:12 final size:12
Alignment explanation
Indices: 5860839--5860879 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
5860829 TTCAAAAATT
5860839 TTAAAATATATA
1 TTAAAATATATA
5860851 TTAAAATAT-TA
1 TTAAAATATATA
* *
5860862 -AAAAATATATT
1 TTAAAATATATA
5860873 TTAAAAT
1 TTAAAAT
5860880 TAAAATTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
10 7 0.29
11 3 0.12
12 14 0.58
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TTAAAATATATA
Found at i:5860862 original size:20 final size:20
Alignment explanation
Indices: 5860833--5860890 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
5860823 AAACAATTCA
*
5860833 AAAATTTTAAAATATATATT
1 AAAATATTAAAATATATATT
*
5860853 AAAATATTAAAAAATATATTT
1 AAAATATTAAAATATATA-TT
*
5860874 TAAA-ATTAAAAT-TATAT
1 AAAATATTAAAATATATAT
5860891 AAATTTATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 1 0.03
19 4 0.12
20 23 0.70
21 5 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATATTAAAATATATATT
Found at i:5863299 original size:21 final size:21
Alignment explanation
Indices: 5863275--5863342 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
5863265 TTTTATTTTT
5863275 TAAAAATATTATGTTTTTATA
1 TAAAAATATTATGTTTTTATA
5863296 TAAAAA-A--ATGTAATTTTA-A
1 TAAAAATATTATGT--TTTTATA
**
5863315 TAATAAATATTACATTTTTATA
1 TAA-AAATATTATGTTTTTATA
5863337 TAAAAA
1 TAAAAA
5863343 ATATAGTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
18 4 0.11
19 4 0.11
20 9 0.24
21 15 0.39
22 4 0.11
23 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.44
Consensus pattern (21 bp):
TAAAAATATTATGTTTTTATA
Found at i:5863301 original size:22 final size:20
Alignment explanation
Indices: 5863276--5863346 Score: 65
Period size: 22 Copynumber: 3.4 Consensus size: 20
5863266 TTTATTTTTT
5863276 AAAAATATTATGTTTTTATATA
1 AAAAATATTA--TTTTTATATA
*
5863298 AAAAA-ATGTAATTTTA-ATA
1 AAAAATAT-TATTTTTATATA
*
5863317 ATAAATATTACATTTTTATATA
1 AAAAATATT--ATTTTTATATA
5863339 AAAAATAT
1 AAAAATAT
5863347 AGTTAAAAGT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
19 8 0.20
20 7 0.17
21 8 0.20
22 17 0.43
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (20 bp):
AAAAATATTATTTTTATATA
Found at i:5863312 original size:20 final size:21
Alignment explanation
Indices: 5863288--5863343 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 21
5863278 AAATATTATG
5863288 TTTTTATATAAAAAAATGTA-A
1 TTTTTATATAAAAAAAT-TACA
*
5863309 -TTTTA-ATAATAAATATTACA
1 TTTTTATATAA-AAAAATTACA
5863329 TTTTTATATAAAAAA
1 TTTTTATATAAAAAA
5863344 TATAGTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
19 6 0.21
20 11 0.38
21 8 0.28
22 4 0.14
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
TTTTTATATAAAAAAATTACA
Found at i:5863650 original size:19 final size:20
Alignment explanation
Indices: 5863626--5863666 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
5863616 ACCAAATATG
5863626 AAAATTACAT-TAAAAAAAT
1 AAAATTACATATAAAAAAAT
**
5863645 AAAATTTTATATAAAAAAAT
1 AAAATTACATATAAAAAAAT
5863665 AA
1 AA
5863667 TTTTTTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAATTACATATAAAAAAAT
Found at i:5864828 original size:13 final size:13
Alignment explanation
Indices: 5864810--5864925 Score: 102
Period size: 13 Copynumber: 9.2 Consensus size: 13
5864800 AAATAATATT
*
5864810 ATATTAACAAATA
1 ATATTAATAAATA
5864823 ATATT-ATAATATA
1 ATATTAATAA-ATA
* *
5864836 TTAATAATAATATA
1 ATATTAATAA-ATA
* *
5864850 TTATTAATATAA-C
1 ATATTAATA-AATA
5864863 ATATTAATAAATA
1 ATATTAATAAATA
*
5864876 TTATTAATAAATA
1 ATATTAATAAATA
5864889 ATATT-AT-AAT-
1 ATATTAATAAATA
5864899 ATATTAATAAATA
1 ATATTAATAAATA
5864912 ATA-TAA-AAATA
1 ATATTAATAAATA
5864923 ATA
1 ATA
5864926 AATAGTTTTA
Statistics
Matches: 87, Mismatches: 9, Indels: 16
0.78 0.08 0.14
Matches are distributed among these distances:
10 5 0.06
11 13 0.15
12 13 0.15
13 38 0.44
14 17 0.20
15 1 0.01
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (13 bp):
ATATTAATAAATA
Found at i:5864847 original size:40 final size:44
Alignment explanation
Indices: 5864798--5864896 Score: 120
Period size: 40 Copynumber: 2.3 Consensus size: 44
5864788 AATTTTACTT
5864798 ATAAATAATATTATATTAACA-AATAATATT-AT-AATA-TATTA
1 ATAAATAATATTATATTAACATAA-AATATTAATAAATATTATTA
* *
5864839 AT-AATAATA-TATTATTAATATAACATATTAATAAATATTATTA
1 ATAAATAATATTA-TATTAACATAAAATATTAATAAATATTATTA
5864882 ATAAATAATATTATA
1 ATAAATAATATTATA
5864897 ATATATTAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
39 2 0.04
40 19 0.39
41 6 0.12
42 4 0.08
43 7 0.14
44 9 0.18
45 2 0.04
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (44 bp):
ATAAATAATATTATATTAACATAAAATATTAATAAATATTATTA
Found at i:5864882 original size:26 final size:26
Alignment explanation
Indices: 5864796--5864922 Score: 106
Period size: 26 Copynumber: 5.0 Consensus size: 26
5864786 ATAATTTTAC
* * *
5864796 TTATAAATAATATTATATTAACAAATA
1 TTATTAATAA-ATAATATTAATAAATA
* * *
5864823 ATATT-ATAATATATTAATAATAATATA
1 TTATTAATAA-ATAATATTAATAA-ATA
*
5864850 TTATTAATATAA-CATATTAATAAATA
1 TTATTAATA-AATAATATTAATAAATA
5864876 TTATTAATAAATAATATT-AT-AATA
1 TTATTAATAAATAATATTAATAAATA
5864900 -TATTAATAAATAATA-TAA-AAATA
1 TTATTAATAAATAATATTAATAAATA
5864923 ATAAATAGTT
Statistics
Matches: 83, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
22 1 0.01
23 20 0.24
24 4 0.05
25 4 0.05
26 31 0.37
27 18 0.22
28 4 0.05
29 1 0.01
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (26 bp):
TTATTAATAAATAATATTAATAAATA
Found at i:5864904 original size:36 final size:34
Alignment explanation
Indices: 5864818--5864925 Score: 116
Period size: 36 Copynumber: 3.2 Consensus size: 34
5864808 TTATATTAAC
*
5864818 AAATAATATTATAATATATTAAT-AATAATAT--
1 AAATAATATTATAACATATTAATAAATAATATAA
* * * *
5864849 -ATTATTAATATAACATATTAATAAATATTATTAA
1 AAATAATATTATAACATATTAATAAATAATA-TAA
*
5864883 TAAATAATATTATAATATATTAATAAATAATATAA
1 -AAATAATATTATAACATATTAATAAATAATATAA
5864918 AAATAATA
1 AAATAATA
5864926 AATAGTTTTA
Statistics
Matches: 61, Mismatches: 10, Indels: 9
0.76 0.12 0.11
Matches are distributed among these distances:
30 18 0.30
31 6 0.10
32 1 0.02
34 8 0.13
35 3 0.05
36 25 0.41
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (34 bp):
AAATAATATTATAACATATTAATAAATAATATAA
Found at i:5864963 original size:17 final size:18
Alignment explanation
Indices: 5864926--5864977 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
5864916 AAAAATAATA
5864926 AATAGTTTTAT-TTAAAGT
1 AATA-TTTTATATTAAAGT
5864944 AAT-TTTTATATTAACA-T
1 AATATTTTATATTAA-AGT
5864961 AATATTTTAATATTAAA
1 AATATTTT-ATATTAAA
5864978 TATTATTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
16 6 0.20
17 8 0.27
18 9 0.30
19 7 0.23
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (18 bp):
AATATTTTATATTAAAGT
Found at i:5864973 original size:19 final size:18
Alignment explanation
Indices: 5864937--5865016 Score: 62
Period size: 18 Copynumber: 4.5 Consensus size: 18
5864927 ATAGTTTTAT
5864937 TTAAAGTAAT-TTTT-ATA
1 TTAAA-TAATATTTTAATA
5864954 TTAACATAATATTTTAATA
1 TTAA-ATAATATTTTAATA
*
5864973 TTAAATATTATTATTAA-A
1 TTAAATAATATT-TTAATA
* *
5864991 ATATAATTAT-TTTTAATA
1 TTA-AATAATATTTTAATA
5865009 TT-AATAAT
1 TTAAATAAT
5865017 TTAATAATAA
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
16 5 0.10
17 12 0.24
18 19 0.37
19 15 0.29
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (18 bp):
TTAAATAATATTTTAATA
Found at i:5865017 original size:19 final size:19
Alignment explanation
Indices: 5864945--5865017 Score: 59
Period size: 19 Copynumber: 4.0 Consensus size: 19
5864935 ATTTAAAGTA
5864945 ATTTTT-ATATTAACATAA-T
1 ATTTTTAATATT-A-ATAATT
5864964 A-TTTTAATATTAA-ATATT
1 ATTTTTAATATTAATA-ATT
* *
5864982 ATTATTAA-AAT-ATAATT
1 ATTTTTAATATTAATAATT
5864999 ATTTTTAATATTAATAATT
1 ATTTTTAATATTAATAATT
5865018 TAATAATAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
16 1 0.02
17 13 0.30
18 12 0.28
19 17 0.40
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTTTAATATTAATAATT
Found at i:5865019 original size:14 final size:14
Alignment explanation
Indices: 5865002--5865059 Score: 52
Period size: 15 Copynumber: 4.2 Consensus size: 14
5864992 TATAATTATT
*
5865002 TTTAATATTAATAA
1 TTTAATATAAATAA
5865016 TTTAATAATAAATAA
1 TTTAAT-ATAAATAA
5865031 TTTCAATAT--AT--
1 TTT-AATATAAATAA
5865042 TTTAATAATAAATAA
1 TTTAAT-ATAAATAA
5865057 TTT
1 TTT
5865060 TTAATATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 13
0.72 0.02 0.26
Matches are distributed among these distances:
10 3 0.08
11 5 0.14
13 4 0.11
14 6 0.17
15 15 0.42
16 3 0.08
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (14 bp):
TTTAATATAAATAA
Found at i:5868855 original size:198 final size:195
Alignment explanation
Indices: 5868601--5868978 Score: 421
Period size: 198 Copynumber: 1.9 Consensus size: 195
5868591 GAAGAAATAA
* * * *
5868601 TTAAAAAAATTATAAAATAAAAACTCTAATAAAATTTTGAGGATTAATACTAATTA-T-AGAATG
1 TTAAAAAAAATATAAAATAAAAACTCTAATAAAAATTTGAGGATGAATAATAATTATTCA-AAT-
* * * * *
5868664 ATGAAATTTTTAAAAATTACAAATAATTA-A-TTTTTATAAAATTTATAAGTGAGAAATTTTTTT
64 ATGAAATTCTTAAAAATTACAAAT-ATTAGATTTTTTAAAAAATTT-TAAGTGAAAAATTTCTCT
* * *
5868727 AAAATTTAATCTAAATGGTGAAAA-ATTTTAGATAAAATTTTAATAATAA-TAATTAACATTTAT
127 -AAATTTAATCCAAAAGGT-AAAATAATTTAGAT-AAATTTTAATAA-AAGTAATTAACATTTAT
5868790 TTTTAATT
188 TTTTAATT
* *
5868798 TTAAAAAATAATATAAAATATAAA-TTTAATAAAAATTT-AGGAATGAATTAATAATTATTCAAA
1 TTAAAAAA-AATATAAAATAAAAACTCTAATAAAAATTTGAGG-ATGAA-TAATAATTATTCAAA
** * *
5868861 TATGAAATTCTTAAAAATTTTAAATGTTAGATTTTTTTAAAAAATTTTAGGTGAAAAATTTCTCT
63 TATGAAATTCTTAAAAATTACAAATATTAGA-TTTTTTAAAAAATTTTAAGTGAAAAATTTCTCT
*
5868926 AAATTTAATCCAAAAGGTAAAATAATTTAGATGAATTTTAATAAAAGTAATTA
127 AAATTTAATCCAAAAGGTAAAATAATTTAGATAAATTTTAATAAAAGTAATTA
5868979 TATTTTTTTA
Statistics
Matches: 152, Mismatches: 19, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
196 5 0.03
197 48 0.32
198 67 0.44
199 18 0.12
200 14 0.09
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (195 bp):
TTAAAAAAAATATAAAATAAAAACTCTAATAAAAATTTGAGGATGAATAATAATTATTCAAATAT
GAAATTCTTAAAAATTACAAATATTAGATTTTTTAAAAAATTTTAAGTGAAAAATTTCTCTAAAT
TTAATCCAAAAGGTAAAATAATTTAGATAAATTTTAATAAAAGTAATTAACATTTATTTTTAATT
Found at i:5869031 original size:13 final size:13
Alignment explanation
Indices: 5869000--5869033 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
5868990 ATAAAAAATT
5869000 TTAAAAATAAAAA
1 TTAAAAATAAAAA
* *
5869013 TAAAAAATAAAAC
1 TTAAAAATAAAAA
5869026 TTAAAAAT
1 TTAAAAAT
5869034 TTAGGTGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (13 bp):
TTAAAAATAAAAA
Found at i:5871546 original size:19 final size:20
Alignment explanation
Indices: 5871519--5871563 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
5871509 TTAATTTTAG
5871519 TTTTT-TTTTA-ACAAATTT
1 TTTTTATTTTATACAAATTT
**
5871537 TTTTTATTTTATTGAAATTT
1 TTTTTATTTTATACAAATTT
5871557 TTTTTAT
1 TTTTTAT
5871564 AAATACTCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 5 0.22
19 5 0.22
20 13 0.57
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTTTATTTTATACAAATTT
Found at i:5871839 original size:21 final size:22
Alignment explanation
Indices: 5871815--5871859 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
5871805 AAATATTAAT
*
5871815 AATAAT-TATTAAAATAA-CAAA
1 AATAATAT-TTAAAAAAATCAAA
5871836 AATAATATTTAAAAAAATCAAA
1 AATAATATTTAAAAAAATCAAA
5871858 AA
1 AA
5871860 ATTCAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (22 bp):
AATAATATTTAAAAAAATCAAA
Found at i:5872820 original size:15 final size:15
Alignment explanation
Indices: 5872791--5872837 Score: 51
Period size: 17 Copynumber: 3.0 Consensus size: 15
5872781 CCCATTTTTG
5872791 TATTTTTTTAATTTA
1 TATTTTTTTAATTTA
*
5872806 T-TTTTTTGTATTTTA
1 TATTTTTT-TAATTTA
5872821 TATTTTTATTTAATTTA
1 TA-TTTT-TTTAATTTA
5872838 ATAAAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 6 0.23
15 8 0.31
17 10 0.38
18 2 0.08
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (15 bp):
TATTTTTTTAATTTA
Found at i:5875485 original size:46 final size:46
Alignment explanation
Indices: 5875415--5875503 Score: 160
Period size: 46 Copynumber: 1.9 Consensus size: 46
5875405 GAAGCCTAGT
* *
5875415 TTGTAAGTTTTGAAGGGGAGTTGTCTTCTTCCATTATTGTCTTAGG
1 TTGTAAGTTTTGAAGGGGAATTGTCTTCTTCAATTATTGTCTTAGG
5875461 TTGTAAGTTTTGAAGGGGAATTGTCTTCTTCAATTATTGTCTT
1 TTGTAAGTTTTGAAGGGGAATTGTCTTCTTCAATTATTGTCTT
5875504 TATAAATATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.19, C:0.10, G:0.24, T:0.47
Consensus pattern (46 bp):
TTGTAAGTTTTGAAGGGGAATTGTCTTCTTCAATTATTGTCTTAGG
Found at i:5877206 original size:31 final size:31
Alignment explanation
Indices: 5877168--5877252 Score: 152
Period size: 31 Copynumber: 2.7 Consensus size: 31
5877158 AGGCTTTTAG
* *
5877168 CCCAACAAATGGTATCAGAGCTGTGGTGTTC
1 CCCAACAAGTGGTATCAGAGCTGTGGTGATC
5877199 CCCAACAAGTGGTATCAGAGCTGTGGTGATC
1 CCCAACAAGTGGTATCAGAGCTGTGGTGATC
5877230 CCCAACAAGTGGTATCAGAGCTG
1 CCCAACAAGTGGTATCAGAGCTG
5877253 AAGTTTCGAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (31 bp):
CCCAACAAGTGGTATCAGAGCTGTGGTGATC
Found at i:5880276 original size:2 final size:2
Alignment explanation
Indices: 5880271--5880295 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5880261 ACACACACAC
5880271 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 A
5880296 AATAAAATAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5883088 original size:21 final size:22
Alignment explanation
Indices: 5883063--5883103 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5883053 AAAGATAATG
5883063 GAAATGTTAGATAAA-AAATAT
1 GAAATGTTAGATAAATAAATAT
* *
5883084 GAAATTTTAGGTAAATAAAT
1 GAAATGTTAGATAAATAAAT
5883104 CTCTTTCATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.32
Consensus pattern (22 bp):
GAAATGTTAGATAAATAAATAT
Found at i:5884047 original size:2 final size:2
Alignment explanation
Indices: 5884040--5884070 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5884030 TAAAAGAAAC
5884040 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5884071 GAACACAACC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5899097 original size:27 final size:26
Alignment explanation
Indices: 5899059--5899121 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 26
5899049 TATAAAAAAG
* *
5899059 ATAATATTATTTAATTTAATTATATTT
1 ATAATTTTATTTAATTTAATTATA-TC
* *
5899086 ATAATTTTATTTTATTTTATTATATC
1 ATAATTTTATTTAATTTAATTATATC
5899112 ATAATTTTAT
1 ATAATTTTAT
5899122 ATACCAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 11 0.34
27 21 0.66
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (26 bp):
ATAATTTTATTTAATTTAATTATATC
Found at i:5900502 original size:23 final size:23
Alignment explanation
Indices: 5900451--5900597 Score: 108
Period size: 23 Copynumber: 6.5 Consensus size: 23
5900441 AATTTTTTTT
* * *
5900451 ATAAATAATATTACATTA-ATAA
1 ATAAATAATATTATAATATATTA
5900473 ATAAATAATATTATAATATATTA
1 ATAAATAATATTATAATATATTA
* * *
5900496 ATAAATAATACTATATTA-ATAA
1 ATAAATAATATTATAATATATTA
* **
5900518 AT-CAT-ATATTAATAA-ATAACA
1 ATAAATAATATT-ATAATATATTA
*
5900539 ATATAAT-ATATTAATAAAAATATTA
1 ATA-AATAATATT-AT-AATATATTA
* *
5900564 AGAAATAATACTATAATATATTA
1 ATAAATAATATTATAATATATTA
5900587 ATAAATAATAT
1 ATAAATAATAT
5900598 AATATTAATA
Statistics
Matches: 98, Mismatches: 19, Indels: 15
0.74 0.14 0.11
Matches are distributed among these distances:
20 5 0.05
21 9 0.09
22 21 0.21
23 46 0.47
24 7 0.07
25 10 0.10
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (23 bp):
ATAAATAATATTATAATATATTA
Found at i:5900570 original size:35 final size:36
Alignment explanation
Indices: 5900507--5900636 Score: 132
Period size: 35 Copynumber: 3.8 Consensus size: 36
5900497 TAAATAATAC
*
5900507 TATATTAATAAATCATATATTAATAAATAACAATATAA
1 TATATTAATAAAT-A-ATATTAAGAAATAACAATATAA
* *
5900545 TATATTAATAAA-AATATTAAGAAATAATACTATAA
1 TATATTAATAAATAATATTAAGAAATAACAATATAA
**
5900580 TATATTAATAAATAATA-T----AATATTAATATAA
1 TATATTAATAAATAATATTAAGAAATAACAATATAA
*
5900611 TATATTGATAAATAATA-TAA-AAATAA
1 TATATTAATAAATAATATTAAGAAATAA
5900637 TAAATACTTT
Statistics
Matches: 81, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
31 28 0.35
34 4 0.05
35 32 0.40
36 5 0.06
38 12 0.15
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (36 bp):
TATATTAATAAATAATATTAAGAAATAACAATATAA
Found at i:5900611 original size:23 final size:23
Alignment explanation
Indices: 5900451--5900642 Score: 92
Period size: 22 Copynumber: 8.7 Consensus size: 23
5900441 AATTTTTTTT
* *
5900451 ATAAATAATATTACATTAATA-A
1 ATAAATAATATAATATTAATATA
* *
5900473 ATAAATAATATTATAAT-ATATTA
1 ATAAATAATATAATATTAATA-TA
5900496 ATAAATAATACT-ATATTAATA-A
1 ATAAATAATA-TAATATTAATATA
**
5900518 ATCATATATTAATA-AATAACAATATA
1 AT-A-A-A-TAATATAATATTAATATA
* * *
5900544 ATATATTAATAAAAATATTAAGA-A
1 ATA-AATAAT-ATAATATTAATATA
*
5900568 AT-AATACTATAATA-T-AT-TA
1 ATAAATAATATAATATTAATATA
5900587 ATAAATAATATAATATTAATATA
1 ATAAATAATATAATATTAATATA
*
5900610 AT--ATATTGATAA-A-TAATATA
1 ATAAATAAT-ATAATATTAATATA
5900630 A-AAATAATA-AATA
1 ATAAATAATATAATA
5900643 CTTTTATTTT
Statistics
Matches: 133, Mismatches: 16, Indels: 44
0.69 0.08 0.23
Matches are distributed among these distances:
19 6 0.05
20 22 0.17
21 18 0.14
22 28 0.21
23 24 0.18
24 9 0.07
25 18 0.14
26 8 0.06
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (23 bp):
ATAAATAATATAATATTAATATA
Found at i:5900636 original size:15 final size:15
Alignment explanation
Indices: 5900451--5900636 Score: 100
Period size: 15 Copynumber: 12.3 Consensus size: 15
5900441 AATTTTTTTT
5900451 ATAAATAATATTACATTA
1 ATAAATAATA-TA-A-TA
5900469 ATAAATAA-ATAAT-
1 ATAAATAATATAATA
* *
5900482 AT-TATAATATATTA
1 ATAAATAATATAATA
5900496 ATAAATAATACTATATTA
1 ATAAATAATA-TA-A-TA
* *
5900514 ATAAATCATATATTA
1 ATAAATAATATAATA
*
5900529 ATAAATAACA-ATATA
1 ATAAATAATATA-ATA
*
5900544 ATATATTAATA-AA-A
1 ATA-AATAATATAATA
* *
5900558 AT-ATTAAGA-AATA
1 ATAAATAATATAATA
* *
5900571 ATACTATAATATATTA
1 ATA-AATAATATAATA
5900587 ATAAATAATATAATA
1 ATAAATAATATAATA
* * *
5900602 TTAATATAATATATTG
1 ATAA-ATAATATAATA
*
5900618 ATAAATAATATAAAA
1 ATAAATAATATAATA
5900633 ATAA
1 ATAA
5900637 TAAATACTTT
Statistics
Matches: 130, Mismatches: 25, Indels: 29
0.71 0.14 0.16
Matches are distributed among these distances:
12 12 0.09
13 9 0.07
14 7 0.05
15 52 0.40
16 28 0.22
17 3 0.02
18 19 0.15
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (15 bp):
ATAAATAATATAATA
Found at i:5900638 original size:31 final size:31
Alignment explanation
Indices: 5900529--5900642 Score: 124
Period size: 31 Copynumber: 3.5 Consensus size: 31
5900519 TCATATATTA
*
5900529 ATAAATAACAATATAATATATTAATAAA-AAT
1 ATAAA-AATAATATAATATATTAATAAATAAT
5900560 ATTAAGAAATAATACTATAATATATTAATAAATAAT
1 A-TAA-AAAT-A-A-TATAATATATTAATAAATAAT
* * *
5900596 ATAATATTAATATAATATATTGATAAATAAT
1 ATAAAAATAATATAATATATTAATAAATAAT
5900627 ATAAAAATAATA-AATA
1 ATAAAAATAATATAATA
5900643 CTTTTATTTT
Statistics
Matches: 71, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
30 4 0.06
31 31 0.44
32 6 0.08
33 3 0.04
34 3 0.04
35 20 0.28
36 4 0.06
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (31 bp):
ATAAAAATAATATAATATATTAATAAATAAT
Found at i:5900639 original size:9 final size:9
Alignment explanation
Indices: 5900450--5900642 Score: 55
Period size: 10 Copynumber: 20.9 Consensus size: 9
5900440 TAATTTTTTT
5900450 TATAAATAA
1 TATAAATAA
* *
5900459 TATTACATTA
1 TA-TAAATAA
5900469 -ATAAATAA
1 TATAAATAA
*
5900477 -AT-AATAT
1 TATAAATAA
*
5900484 TATAATATAT
1 TATAA-ATAA
5900494 TAATAAATAA
1 T-ATAAATAA
* *
5900504 TACTATATTA
1 TA-TAAATAA
5900514 -ATAAATCATA
1 TATAAAT-A-A
*
5900524 TATTAATAA
1 TATAAATAA
*
5900533 -AT-AACAA
1 TATAAATAA
*
5900540 TATAATATAT
1 TATAA-ATAA
5900550 TAATAAA-AA
1 T-ATAAATAA
* *
5900559 TATTAAGAA
1 TATAAATAA
*
5900568 -AT-AATAC
1 TATAAATAA
*
5900575 TATAATATAT
1 TATAA-ATAA
5900585 TAATAAATAA
1 T-ATAAATAA
5900595 TATAATATTAA
1 TATAA-A-TAA
*
5900606 TATAATATAT
1 TATAA-ATAA
5900616 TGATAAATAA
1 T-ATAAATAA
5900626 TATAAA-AA
1 TATAAATAA
5900634 TAATAAATA
1 T-ATAAATA
5900643 CTTTTATTTT
Statistics
Matches: 139, Mismatches: 22, Indels: 45
0.67 0.11 0.22
Matches are distributed among these distances:
7 11 0.08
8 28 0.20
9 27 0.19
10 42 0.30
11 31 0.22
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (9 bp):
TATAAATAA
Found at i:5900746 original size:36 final size:36
Alignment explanation
Indices: 5900678--5900746 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
5900668 TAACATAATA
* *
5900678 TTTTAATATTAAATATTATTATTAAAATTAATTATT
1 TTTTAATATTAAATATTATTAATAAAAATAATTATT
5900714 TTTTAATATT-AATAATT-TTAATAATAAATAATT
1 TTTTAATATTAAAT-ATTATTAATAA-AAATAATT
5900747 TTTAATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 9 0.31
36 20 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (36 bp):
TTTTAATATTAAATATTATTAATAAAAATAATTATT
Found at i:5902653 original size:27 final size:28
Alignment explanation
Indices: 5902598--5902662 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 28
5902588 CTTTATTACT
*
5902598 AAGAGACTAATTCGGATTCTCT-AACAA
1 AAGAGACTAATTCGGATTATCTAAACAA
*
5902625 AAGAGATTAATTCGGATTAGAT-TAAA-AA
1 AAGAGACTAATTCGGATT--ATCTAAACAA
5902653 AAGAGACTAA
1 AAGAGACTAA
5902663 ATAATTAGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 17 0.53
28 12 0.38
29 3 0.09
ACGTcount: A:0.48, C:0.11, G:0.17, T:0.25
Consensus pattern (28 bp):
AAGAGACTAATTCGGATTATCTAAACAA
Found at i:5905312 original size:13 final size:13
Alignment explanation
Indices: 5905296--5905341 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
5905286 TTAAATTATA
5905296 TTATTTTTGTATC
1 TTATTTTTGTATC
*
5905309 TTATTTTTATATC
1 TTATTTTTGTATC
* * *
5905322 ATATTATTGTATT
1 TTATTTTTGTATC
5905335 TTATTTT
1 TTATTTT
5905342 AAATTATCAG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.70
Consensus pattern (13 bp):
TTATTTTTGTATC
Found at i:5907112 original size:33 final size:33
Alignment explanation
Indices: 5907017--5907114 Score: 124
Period size: 36 Copynumber: 2.9 Consensus size: 33
5907007 GACATTACGA
* * *
5907017 TTTATCTTACAAAAGGCGCCTTACAAAAACGAT
1 TTTATCCTACAAAAGGCGCCTTACAAGAACAAT
5907050 TTTATCCTACAAAAGGTGGCGCCTTACAAGAACAAT
1 TTTATCCTACAAAA---GGCGCCTTACAAGAACAAT
* *
5907086 TTTGTCCTACAAAAGACGCCTTACAAGAA
1 TTTATCCTACAAAAGGCGCCTTACAAGAA
5907115 AGAGATGGTC
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
33 27 0.47
36 30 0.53
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (33 bp):
TTTATCCTACAAAAGGCGCCTTACAAGAACAAT
Found at i:5907186 original size:33 final size:33
Alignment explanation
Indices: 5907147--5907234 Score: 104
Period size: 36 Copynumber: 2.6 Consensus size: 33
5907137 CGATTTATCT
*
5907147 TACAAAAGGCGCCTTACAAAAACGATTTTGTCC
1 TACAAAAGGCGCCTTACAAAAACAATTTTGTCC
* *
5907180 TACAAAAGGTGGCGCCTCACAAGAACAATTTTGTCC
1 TACAAAA---GGCGCCTTACAAAAACAATTTTGTCC
**
5907216 TACAAAAGATGCCTTACAA
1 TACAAAAGGCGCCTTACAA
5907235 GAAAGAGATG
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
33 16 0.35
36 30 0.65
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.23
Consensus pattern (33 bp):
TACAAAAGGCGCCTTACAAAAACAATTTTGTCC
Found at i:5907211 original size:36 final size:36
Alignment explanation
Indices: 5907154--5907223 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
5907144 TCTTACAAAA
* *
5907154 GGCGCCTTACAAAAACGATTTTGTCCTACAAAAGGT
1 GGCGCCTCACAAAAACAATTTTGTCCTACAAAAGGT
*
5907190 GGCGCCTCACAAGAACAATTTTGTCCTACAAAAG
1 GGCGCCTCACAAAAACAATTTTGTCCTACAAAAG
5907224 ATGCCTTACA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (36 bp):
GGCGCCTCACAAAAACAATTTTGTCCTACAAAAGGT
Found at i:5907218 original size:123 final size:123
Alignment explanation
Indices: 5906999--5907246 Score: 469
Period size: 123 Copynumber: 2.0 Consensus size: 123
5906989 ATCCATTTTT
5906999 GTCCCTTCGACATTACGATTTATCTTACAAAAGGCGCCTTACAAAAACGATTTTATCCTACAAAA
1 GTCCCTTCGACATTACGATTTATCTTACAAAAGGCGCCTTACAAAAACGATTTTATCCTACAAAA
*
5907064 GGTGGCGCCTTACAAGAACAATTTTGTCCTACAAAAGACGCCTTACAAGAAAGAGATG
66 GGTGGCGCCTCACAAGAACAATTTTGTCCTACAAAAGACGCCTTACAAGAAAGAGATG
*
5907122 GTCCCTTCGACATTACGATTTATCTTACAAAAGGCGCCTTACAAAAACGATTTTGTCCTACAAAA
1 GTCCCTTCGACATTACGATTTATCTTACAAAAGGCGCCTTACAAAAACGATTTTATCCTACAAAA
*
5907187 GGTGGCGCCTCACAAGAACAATTTTGTCCTACAAAAGATGCCTTACAAGAAAGAGATG
66 GGTGGCGCCTCACAAGAACAATTTTGTCCTACAAAAGACGCCTTACAAGAAAGAGATG
5907245 GT
1 GT
5907247 GTGAACCTTT
Statistics
Matches: 122, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 122 1.00
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (123 bp):
GTCCCTTCGACATTACGATTTATCTTACAAAAGGCGCCTTACAAAAACGATTTTATCCTACAAAA
GGTGGCGCCTCACAAGAACAATTTTGTCCTACAAAAGACGCCTTACAAGAAAGAGATG
Found at i:5908339 original size:15 final size:15
Alignment explanation
Indices: 5908319--5908352 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
5908309 CCCCCCCCCA
5908319 AAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAG
*
5908334 AAAAAAGAAAAAAAG
1 AAAAAAAAAAAAAAG
5908349 AAAA
1 AAAA
5908353 CTAATCTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAG
Found at i:5909800 original size:18 final size:18
Alignment explanation
Indices: 5909773--5909809 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5909763 AAAAATTATA
5909773 TTTTTATATTTTTATGTT
1 TTTTTATATTTTTATGTT
* *
5909791 TTTTTTTATTTTTTTGTT
1 TTTTTATATTTTTATGTT
5909809 T
1 T
5909810 GAAAATAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.00, G:0.05, T:0.84
Consensus pattern (18 bp):
TTTTTATATTTTTATGTT
Found at i:5910506 original size:165 final size:166
Alignment explanation
Indices: 5910255--5910556 Score: 455
Period size: 165 Copynumber: 1.8 Consensus size: 166
5910245 GATCCTAGAA
* * * * * *
5910255 ATTTATTAACGCTTTAAATGACGTTATTTTACAGATGTATAAAAGGTTGAAATCAGTCTTTTTTA
1 ATTTATTAACGCTTTAAACGACGTCATTTTACAGATGTATAAAAAGCTAAAATCAATCTTTTTTA
* *
5910320 GAAGAATTCTCTTCCTCCTTCTTTCT-TTCCCCTCTTTTCTCTTCTCTCTCTCTACAAAATTCTA
66 GAAGAATTCTCCTCCTCCTTCTTTCTCTTCCCCTCTTTTCTCTCCTCTCTCTCTACAAAATTCTA
5910384 AAATCCGATTGTAACAAAAATGAGCGAATCCTGGGG
131 AAATCCGATTGTAACAAAAATGAGCGAATCCTGGGG
*
5910420 ATTTATTAACGCTTTAAACGACGTCATTTTGCAGA-GATATAAAAAGCTAAAATCAATCTTTTTT
1 ATTTATTAACGCTTTAAACGACGTCATTTTACAGATG-TATAAAAAGCTAAAATCAATCTTTTTT
* * * *
5910484 AGTAGAATTCTCCTCTTCCTTCTTTCTCTTCCCCTCTTTTTTCTCCTCTCTCTCTACAAGATTCT
65 AGAAGAATTCTCCTCCTCCTTCTTTCTCTTCCCCTCTTTTCTCTCCTCTCTCTCTACAAAATTCT
*
5910549 AGAATCCG
130 AAAATCCG
5910557 GTTGAATTTC
Statistics
Matches: 121, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
164 1 0.01
165 79 0.65
166 41 0.34
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.40
Consensus pattern (166 bp):
ATTTATTAACGCTTTAAACGACGTCATTTTACAGATGTATAAAAAGCTAAAATCAATCTTTTTTA
GAAGAATTCTCCTCCTCCTTCTTTCTCTTCCCCTCTTTTCTCTCCTCTCTCTCTACAAAATTCTA
AAATCCGATTGTAACAAAAATGAGCGAATCCTGGGG
Found at i:5910708 original size:20 final size:21
Alignment explanation
Indices: 5910682--5910723 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5910672 AAAATTTTTC
*
5910682 AAAAAAAAAAACCCAAAAATT
1 AAAAAAAAAATCCCAAAAATT
*
5910703 AAAAAAAAAATCCTAAAAATT
1 AAAAAAAAAATCCCAAAAATT
5910724 CTCAAACTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.74, C:0.12, G:0.00, T:0.14
Consensus pattern (21 bp):
AAAAAAAAAATCCCAAAAATT
Found at i:5911026 original size:6 final size:6
Alignment explanation
Indices: 5911001--5911063 Score: 72
Period size: 7 Copynumber: 9.5 Consensus size: 6
5910991 AGAAACCAAG
5911001 AAAATA GAAAATA GAAAATA AAAATA AAAATA AAAATAA AAAAGTA AAAAGTA
1 AAAATA -AAAATA -AAAATA AAAATA AAAATA AAAAT-A AAAA-TA AAAA-TA
5911054 AAATATA AAA
1 AAA-ATA AAA
5911064 TTAGGCCAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
6 17 0.32
7 34 0.64
8 2 0.04
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:5911026 original size:20 final size:20
Alignment explanation
Indices: 5911001--5911064 Score: 73
Period size: 20 Copynumber: 3.2 Consensus size: 20
5910991 AGAAACCAAG
5911001 AAAATAGAAAATAGAAAATA
1 AAAATAGAAAATAGAAAATA
5911021 AAAATA-AAAATA-AAAATA
1 AAAATAGAAAATAGAAAATA
5911039 AAAA-AGTAAAA-AGTAAAATA
1 AAAATAG-AAAATAG-AAAATA
5911059 TAAAAT
1 -AAAAT
5911065 TAGGCCAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
17 1 0.03
18 11 0.29
19 10 0.26
20 12 0.32
21 4 0.11
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (20 bp):
AAAATAGAAAATAGAAAATA
Found at i:5917472 original size:2 final size:2
Alignment explanation
Indices: 5917465--5917492 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5917455 GTAGCGATAC
5917465 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
5917493 TTTGCTTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5926547 original size:14 final size:15
Alignment explanation
Indices: 5926519--5926549 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
5926509 TGATTCAGAA
5926519 TAAAATATATATAAT
1 TAAAATATATATAAT
5926534 TAAAATAT-TATAAT
1 TAAAATATATATAAT
5926548 TA
1 TA
5926550 TGTAAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAAAATATATATAAT
Found at i:5926590 original size:19 final size:19
Alignment explanation
Indices: 5926568--5926617 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
5926558 TATATCTGAA
5926568 TTTTTAATTAATATTTTAT
1 TTTTTAATTAATATTTTAT
* *
5926587 TTTTTAAAAATAATTTTTTAT
1 TTTTT--AATTAATATTTTAT
*
5926608 TTTTTTATTA
1 TTTTTAATTA
5926618 TATAAATTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 8 0.32
21 17 0.68
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTTAATTAATATTTTAT
Found at i:5927373 original size:2 final size:2
Alignment explanation
Indices: 5927366--5927391 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5927356 AAATAAACAA
5927366 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
5927392 TTGAGAAAGA
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:5928553 original size:12 final size:12
Alignment explanation
Indices: 5928506--5928584 Score: 54
Period size: 12 Copynumber: 6.5 Consensus size: 12
5928496 ATGGATAGAG
* *
5928506 TATTTTTGTCTT
1 TATTTTTATATT
*
5928518 TATTTTTAAATT
1 TATTTTTATATT
5928530 T-TTATATTATATT
1 TATT-T-TTATATT
5928543 TATTTTTATATT
1 TATTTTTATATT
* *
5928555 TATATTTA-ATA
1 TATTTTTATATT
* *
5928566 AATATTTTAAATT
1 TAT-TTTTATATT
5928579 TATTTT
1 TATTTT
5928585 CATTCTTGCA
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
11 6 0.12
12 32 0.62
13 12 0.23
14 2 0.04
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (12 bp):
TATTTTTATATT
Found at i:5928557 original size:18 final size:17
Alignment explanation
Indices: 5928527--5928562 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
5928517 TTATTTTTAA
5928527 ATTTTTATATTATATTT
1 ATTTTTATATTATATTT
5928544 ATTTTTATATTTATATTT
1 ATTTTTATA-TTATATTT
5928562 A
1 A
5928563 ATAAATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTTATATTATATTT
Found at i:5938895 original size:105 final size:105
Alignment explanation
Indices: 5938713--5938922 Score: 384
Period size: 105 Copynumber: 2.0 Consensus size: 105
5938703 ATTTAAATAT
5938713 ACTTTCATGTTACTAAGAAGGTTTTGTTTCAATGACAAGGAAAATATTCCAAAAATGTTTAAATT
1 ACTTTCATGTTACTAAGAAGGTTTTGTTTCAATGACAAGGAAAATATTCCAAAAATGTTTAAATT
5938778 TCATATTCAATTTCATCATAAGAAATTTTGTCAAATTATA
66 TCATATTCAATTTCATCATAAGAAATTTTGTCAAATTATA
* * *
5938818 ACTTTCATGTTGCTAAGAAGGTTTTGTTTCAATGACAAGGAAAATATTCTAGAAATGTTTAAATT
1 ACTTTCATGTTACTAAGAAGGTTTTGTTTCAATGACAAGGAAAATATTCCAAAAATGTTTAAATT
*
5938883 TCATATTCAATTTCATCATAATAAATTTTGTCAAATTATA
66 TCATATTCAATTTCATCATAAGAAATTTTGTCAAATTATA
5938923 TGTTAGATTT
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 101 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (105 bp):
ACTTTCATGTTACTAAGAAGGTTTTGTTTCAATGACAAGGAAAATATTCCAAAAATGTTTAAATT
TCATATTCAATTTCATCATAAGAAATTTTGTCAAATTATA
Found at i:5939339 original size:22 final size:21
Alignment explanation
Indices: 5939308--5939348 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
5939298 TAATATAATT
*
5939308 TATAAGTTTAATAATAATTATA
1 TATAAATTTAATAA-AATTATA
5939330 TATAAATTTAATAAAATTA
1 TATAAATTTAATAAAATTA
5939349 AAAATATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
TATAAATTTAATAAAATTATA
Found at i:5939406 original size:18 final size:18
Alignment explanation
Indices: 5939385--5939433 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 18
5939375 CGATATAAAT
5939385 TATAATATATAATTTTTA
1 TATAATATATAATTTTTA
*
5939403 TATAA-A-AT-A-TTATA
1 TATAATATATAATTTTTA
5939417 TA-AATATATAATTTTTA
1 TATAATATATAATTTTTA
5939434 ATATTTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 9
0.69 0.06 0.25
Matches are distributed among these distances:
13 2 0.08
14 7 0.28
15 3 0.12
16 3 0.12
17 5 0.20
18 5 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATAATATATAATTTTTA
Found at i:5946708 original size:22 final size:22
Alignment explanation
Indices: 5946680--5946723 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
5946670 CTAAATCTTC
5946680 CTTAATTCTAG-GAATACAAATA
1 CTTAATTCTAGAG-ATACAAATA
5946702 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
5946724 TAAATATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:5950429 original size:23 final size:25
Alignment explanation
Indices: 5950374--5950432 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
5950364 AAAGGGTTCG
* * *
5950374 GCAATGAAGGCCTAAACAGGATTCG
1 GCAATGAAGGCCTAAACAGAAGTCA
5950399 GCAATGAAGGCCTAAA-A-AAGTCA
1 GCAATGAAGGCCTAAACAGAAGTCA
5950422 GCAATGAAGGC
1 GCAATGAAGGC
5950433 TGAAAATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 14 0.45
24 1 0.03
25 16 0.52
ACGTcount: A:0.41, C:0.19, G:0.27, T:0.14
Consensus pattern (25 bp):
GCAATGAAGGCCTAAACAGAAGTCA
Found at i:5950608 original size:22 final size:22
Alignment explanation
Indices: 5950580--5950623 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
5950570 CTAAATCTTC
5950580 CTTAATTCTAGTA-ATACAAATA
1 CTTAATTCTAG-AGATACAAATA
5950602 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
5950624 TAAATATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 1 0.05
22 20 0.95
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.34
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:5960123 original size:33 final size:33
Alignment explanation
Indices: 5960081--5960147 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 33
5960071 TTCAGGACCG
*
5960081 ACCGCTGGAGAGTAATGCAAGTC-TTTATGGACA
1 ACCGCTGGAGACTAATGCAAG-CATTTATGGACA
5960114 ACCGCTGGAGACTAATGCAAGCATTTATGGACA
1 ACCGCTGGAGACTAATGCAAGCATTTATGGACA
5960147 A
1 A
5960148 AGCAAGGACA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 1 0.03
33 31 0.97
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.22
Consensus pattern (33 bp):
ACCGCTGGAGACTAATGCAAGCATTTATGGACA
Found at i:5970095 original size:77 final size:77
Alignment explanation
Indices: 5969964--5970122 Score: 248
Period size: 77 Copynumber: 2.1 Consensus size: 77
5969954 AATGCATCTT
*
5969964 CCAGTGTCTACATTAAGAATAAAAAAAGTATTATAAAAAAAATTATCACACTAAAATGAACGGGT
1 CCAGTGTCTACATTAAGAATAAAAAAAGTATTATAAAAAAAAGTATCACACTAAAATGAACGGGT
*
5970029 GTAATCTTAAAA
66 GTAATCATAAAA
* **
5970041 CCAGTGTCTACATT-AGAAATAAAAAGAGTATTATAAAAAAAAGTATCATGCTAAAATGAACGGG
1 CCAGTGTCTACATTAAG-AATAAAAAAAGTATTATAAAAAAAAGTATCACACTAAAATGAACGGG
*
5970105 TGTAATCATAGAA
65 TGTAATCATAAAA
5970118 CCAGT
1 CCAGT
5970123 AGAAAGGGAC
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
76 2 0.03
77 73 0.97
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.25
Consensus pattern (77 bp):
CCAGTGTCTACATTAAGAATAAAAAAAGTATTATAAAAAAAAGTATCACACTAAAATGAACGGGT
GTAATCATAAAA
Found at i:5970221 original size:32 final size:32
Alignment explanation
Indices: 5970185--5970273 Score: 169
Period size: 32 Copynumber: 2.8 Consensus size: 32
5970175 GTAATTGATA
*
5970185 GAATTTTTTTTGGTCATATAATTTAGATAGGC
1 GAATTTTTGTTGGTCATATAATTTAGATAGGC
5970217 GAATTTTTGTTGGTCATATAATTTAGATAGGC
1 GAATTTTTGTTGGTCATATAATTTAGATAGGC
5970249 GAATTTTTGTTGGTCATATAATTTA
1 GAATTTTTGTTGGTCATATAATTTA
5970274 ACTCTCTTAC
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 56 1.00
ACGTcount: A:0.28, C:0.06, G:0.19, T:0.47
Consensus pattern (32 bp):
GAATTTTTGTTGGTCATATAATTTAGATAGGC
Found at i:5974020 original size:17 final size:17
Alignment explanation
Indices: 5973998--5974032 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5973988 TAAATTCCGG
5973998 GAGAAAGT-GTGATACCC
1 GAGAAAGTAG-GATACCC
5974015 GAGAAAGTAGGATACCC
1 GAGAAAGTAGGATACCC
5974032 G
1 G
5974033 GGGTTTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.94
18 1 0.06
ACGTcount: A:0.37, C:0.17, G:0.31, T:0.14
Consensus pattern (17 bp):
GAGAAAGTAGGATACCC
Found at i:5981820 original size:29 final size:29
Alignment explanation
Indices: 5981756--5981821 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
5981746 GAGTTTTTAG
* * *
5981756 TAAATTTTAATAAAATTTTTACTGTAAAG
1 TAAATATTAATAAAATTTTTACTATAAAA
*
5981785 TAAATATTAATTAAATTTTTA-TCATAAAA
1 TAAATATTAATAAAATTTTTACT-ATAAAA
*
5981814 TATATATT
1 TAAATATT
5981822 TTATATATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 1 0.03
29 30 0.97
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (29 bp):
TAAATATTAATAAAATTTTTACTATAAAA
Found at i:5990789 original size:19 final size:19
Alignment explanation
Indices: 5990762--5990846 Score: 71
Period size: 19 Copynumber: 4.3 Consensus size: 19
5990752 GATAAAAAAT
*
5990762 TATTAAATAAATTATTTCA
1 TATTAAATAAATTATTTAA
* *
5990781 TATTTAATAAATTTTTTAA
1 TATTAAATAAATTATTTAA
** *
5990800 TATTTTATAATATTATATTTA
1 TATTAAATAA-ATTAT-TTAA
**
5990821 TATTAAATATTTTTATTTAA
1 TATTAAATA-AATTATTTAA
5990841 TATTAA
1 TATTAA
5990847 TTAATTTTAA
Statistics
Matches: 52, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
19 25 0.48
20 13 0.25
21 14 0.27
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (19 bp):
TATTAAATAAATTATTTAA
Done.