Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 172 of 202
Found at i:53668935 original size:16 final size:16
Alignment explanation
Indices: 53668913--53668951 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
53668903 GCGACAGTTA
*
53668913 TCTAAAAC-ACGGTTT
1 TCTAAAACAAAGGTTT
53668928 TACTAAAACAAAGGTTT
1 T-CTAAAACAAAGGTTT
53668945 TCTAAAA
1 TCTAAAA
53668952 ATACGAACGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 13 0.62
17 7 0.33
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (16 bp):
TCTAAAACAAAGGTTT
Found at i:53670648 original size:85 final size:84
Alignment explanation
Indices: 53670500--53670660 Score: 223
Period size: 85 Copynumber: 1.9 Consensus size: 84
53670490 TTACAAATTT
* * * *
53670500 CCAAGGTTTAATATAAGACGCATGCATCATTATTAGTGCATTACGTAAGTTGCAAAACGTTTTTT
1 CCAAGGTTTAATATAAGACACATGCAACATTATTAATGCATTACGTAAGTTGCAAAAC-ATTTTT
*
53670565 TTTCAAATATTTACTTAATA
65 TTCCAAATATTTACTTAATA
* * * * *
53670585 CCAATGTTTAATATAAGACACATGCAACATTGTTAATGCATTATGTATGTTGCAAAGCATTTTTT
1 CCAAGGTTTAATATAAGACACATGCAACATTATTAATGCATTACGTAAGTTGCAAAACATTTTTT
53670650 TCCAAATATTT
66 TCCAAATATTT
53670661 GTTTAATCCA
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
84 16 0.24
85 50 0.76
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.39
Consensus pattern (84 bp):
CCAAGGTTTAATATAAGACACATGCAACATTATTAATGCATTACGTAAGTTGCAAAACATTTTTT
TCCAAATATTTACTTAATA
Found at i:53674675 original size:2 final size:2
Alignment explanation
Indices: 53674668--53674705 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
53674658 ATTATATTTC
53674668 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53674706 AAAGAAAGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53689641 original size:22 final size:22
Alignment explanation
Indices: 53689616--53689669 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
53689606 TTTCACTACA
* *
53689616 GTGCCTTCTAATTTGCACTTTG
1 GTGCCTACTAATTCGCACTTTG
* **
53689638 GTGCCTACTGATTCGCACTTCA
1 GTGCCTACTAATTCGCACTTTG
53689660 GTGCCTACTA
1 GTGCCTACTA
53689670 TTAAAGCATT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.17, C:0.28, G:0.19, T:0.37
Consensus pattern (22 bp):
GTGCCTACTAATTCGCACTTTG
Found at i:53692203 original size:46 final size:46
Alignment explanation
Indices: 53692114--53692203 Score: 112
Period size: 46 Copynumber: 2.0 Consensus size: 46
53692104 AGATCAGATA
*
53692114 TATGTGGTCAAACCACTATATTACAGCCAAGCTGTCAGAACAAATG
1 TATGTGGTCAAACCACTATATTACAGACAAGCTGTCAGAACAAATG
* * *
53692160 TATGTGGTCAAGCCA-TCATACTTGCAGACAAGTTGTCAG-ACAAA
1 TATGTGGTCAAACCACT-ATA-TTACAGACAAGCTGTCAGAACAAA
53692204 AATGTGGATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
45 1 0.03
46 22 0.58
47 15 0.39
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (46 bp):
TATGTGGTCAAACCACTATATTACAGACAAGCTGTCAGAACAAATG
Found at i:53694122 original size:22 final size:22
Alignment explanation
Indices: 53694094--53694139 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
53694084 TAAATGTGTT
53694094 AAAATAATTA-TACATAAAATAA
1 AAAATAATTAGTACA-AAAATAA
*
53694116 AAAATAATTAGTATAAAAATAA
1 AAAATAATTAGTACAAAAATAA
53694138 AA
1 AA
53694140 CCTCTTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (22 bp):
AAAATAATTAGTACAAAAATAA
Found at i:53699868 original size:39 final size:38
Alignment explanation
Indices: 53699825--53699908 Score: 89
Period size: 39 Copynumber: 2.2 Consensus size: 38
53699815 TTTTACAAAT
*
53699825 TTTTTTATTTTTTTACAATTTTTATAAAAAAATTT-CTAA
1 TTTTTTATTTTTTT-CAATTTTT-TAAAAAAATTTAATAA
* * **
53699864 TTTTTAAATTTTTTTTAATTTTTTATTAAAATTTAATAA
1 TTTTT-TATTTTTTTCAATTTTTTAAAAAAATTTAATAA
53699903 TTTTTT
1 TTTTTT
53699909 TAAAATTTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
38 9 0.24
39 20 0.54
40 8 0.22
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (38 bp):
TTTTTTATTTTTTTCAATTTTTTAAAAAAATTTAATAA
Found at i:53699908 original size:40 final size:39
Alignment explanation
Indices: 53699804--53699908 Score: 99
Period size: 40 Copynumber: 2.6 Consensus size: 39
53699794 TAATTTATGC
*
53699804 TTTTTATAAAATTTTACA-AATTTTTTTATTTTTTTACAAT
1 TTTTTATAAAA-TTTA-ATAATTTTTTAATTTTTTTACAAT
* * * *
53699844 TTTTATAAAAAAATTT-CTAATTTTTAAATTTTTTT-TAAT
1 TTTT-T-ATAAAATTTAATAATTTTTTAATTTTTTTACAAT
53699883 TTTTTATTAAAATTTAATAATTTTTT
1 TTTTTA-TAAAATTTAATAATTTTTT
53699909 TAAAATTTAT
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
37 1 0.02
38 8 0.15
39 15 0.29
40 19 0.37
41 4 0.08
42 5 0.10
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (39 bp):
TTTTTATAAAATTTAATAATTTTTTAATTTTTTTACAAT
Found at i:53699925 original size:19 final size:20
Alignment explanation
Indices: 53699881--53699928 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
53699871 ATTTTTTTTA
53699881 ATTTTTTATTAAAATTTAAT
1 ATTTTTTATTAAAATTTAAT
* *
53699901 AATTTTT-TTAAAATTTATT
1 ATTTTTTATTAAAATTTAAT
53699920 ATTTTTTAT
1 ATTTTTTAT
53699929 AATTTTTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
ATTTTTTATTAAAATTTAAT
Found at i:53710027 original size:24 final size:24
Alignment explanation
Indices: 53710000--53710049 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
53709990 ATAAGGAAAG
53710000 TTTGATTTCCATTGGGAGCAAGCC
1 TTTGATTTCCATTGGGAGCAAGCC
53710024 TTTGATTTCCATTGGGAGCAAGCC
1 TTTGATTTCCATTGGGAGCAAGCC
53710048 TT
1 TT
53710050 GGAAATCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (24 bp):
TTTGATTTCCATTGGGAGCAAGCC
Found at i:53714262 original size:21 final size:21
Alignment explanation
Indices: 53714236--53714279 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
53714226 TAGATTGGCG
53714236 GTGCGTTTACCTGCGGTTAGT
1 GTGCGTTTACCTGCGGTTAGT
*
53714257 GTGCGTTTACTTGCGGTTAGT
1 GTGCGTTTACCTGCGGTTAGT
53714278 GT
1 GT
53714280 AAAAGCAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.09, C:0.16, G:0.34, T:0.41
Consensus pattern (21 bp):
GTGCGTTTACCTGCGGTTAGT
Found at i:53720136 original size:18 final size:18
Alignment explanation
Indices: 53720115--53720151 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
53720105 GAGTAATAAG
53720115 AGCAGTTAGAAGTCAGTT
1 AGCAGTTAGAAGTCAGTT
53720133 AGCAGTTAGAAGTCAGTT
1 AGCAGTTAGAAGTCAGTT
53720151 A
1 A
53720152 ACACAAACTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.11, G:0.27, T:0.27
Consensus pattern (18 bp):
AGCAGTTAGAAGTCAGTT
Found at i:53726585 original size:43 final size:43
Alignment explanation
Indices: 53726450--53726586 Score: 177
Period size: 43 Copynumber: 3.2 Consensus size: 43
53726440 TGTATTTTGT
* * * *
53726450 CAATGGGTGAATTGTTTAAAGTCTGCTTATGTATAGCATTCGC
1 CAATGGGCGAATTGTATAAAGTCTGCTTGTGTATAGTATTCGC
* * **
53726493 CAAT-GTCTGAATTGTATAAAGTATGCTTGCATATAGTATTCGC
1 CAATGGGC-GAATTGTATAAAGTCTGCTTGTGTATAGTATTCGC
*
53726536 CAATGGGCGAATTGTATAAAGTCTGCTTGTGTATAGTATTTGC
1 CAATGGGCGAATTGTATAAAGTCTGCTTGTGTATAGTATTCGC
53726579 CAATGGGC
1 CAATGGGC
53726587 AAACTATGTG
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
42 1 0.01
43 76 0.96
44 2 0.03
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (43 bp):
CAATGGGCGAATTGTATAAAGTCTGCTTGTGTATAGTATTCGC
Found at i:53727555 original size:10 final size:11
Alignment explanation
Indices: 53727525--53727554 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
53727515 TCAAACTTGT
*
53727525 AAATATTTTTA
1 AAATATTTTAA
53727536 AAATATTTTAA
1 AAATATTTTAA
53727547 AAATATTT
1 AAATATTT
53727555 ACAAAGTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AAATATTTTAA
Found at i:53728622 original size:16 final size:17
Alignment explanation
Indices: 53728591--53728623 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
53728581 ACTATTGTAC
53728591 TTTATAATTGAATTGAA
1 TTTATAATTGAATTGAA
*
53728608 TTTATAGTT-AATTGAA
1 TTTATAATTGAATTGAA
53728624 ATGGATTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (17 bp):
TTTATAATTGAATTGAA
Found at i:53729558 original size:26 final size:25
Alignment explanation
Indices: 53729504--53729558 Score: 58
Period size: 26 Copynumber: 2.2 Consensus size: 25
53729494 AAATTGAGTT
* *
53729504 ATAAATATAATGTTGGTTTGAATAT
1 ATAAATATAATGTTGGTTTGAAGAC
*
53729529 ATAAATAT-ATGTTGGTGTTTGAAGCC
1 ATAAATATAATGTT-G-GTTTGAAGAC
53729555 ATAA
1 ATAA
53729559 TTTGGCATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 5 0.20
25 9 0.36
26 11 0.44
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (25 bp):
ATAAATATAATGTTGGTTTGAAGAC
Found at i:53736278 original size:43 final size:43
Alignment explanation
Indices: 53736230--53736370 Score: 174
Period size: 43 Copynumber: 3.3 Consensus size: 43
53736220 AGTTTTGTAT
* * * *
53736230 TTCACCAATGGGCGAATTGTATAAAGTTTGCTTGTGTATACTA
1 TTCACCAATAGGCAAATTGTATAAAGTCTGCTTGTGTATAGTA
* * *
53736273 TTCACCAATTGGAAAATAGTATAAAGTCTGCTTGTGTATAGTA
1 TTCACCAATAGGCAAATTGTATAAAGTCTGCTTGTGTATAGTA
** * *
53736316 TTTGCCAATAGACAAATTGTATAAAGCCTGCTTGTGTATAGTA
1 TTCACCAATAGGCAAATTGTATAAAGTCTGCTTGTGTATAGTA
*
53736359 TTCGCCAATAGG
1 TTCACCAATAGG
53736371 TGAACTATGT
Statistics
Matches: 83, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 83 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (43 bp):
TTCACCAATAGGCAAATTGTATAAAGTCTGCTTGTGTATAGTA
Found at i:53741865 original size:13 final size:13
Alignment explanation
Indices: 53741847--53741891 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
53741837 AACATGGTTT
53741847 TTTATTTATTTTA
1 TTTATTTATTTTA
53741860 TTTATTTATTTTA
1 TTTATTTATTTTA
*
53741873 TCTTATCT-TTTTA
1 T-TTATTTATTTTA
53741886 TTTATT
1 TTTATT
53741892 ACCCTAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 4 0.14
13 20 0.69
14 5 0.17
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTATTTTA
Found at i:53742648 original size:61 final size:62
Alignment explanation
Indices: 53742532--53742650 Score: 168
Period size: 62 Copynumber: 1.9 Consensus size: 62
53742522 AAGGATCGGC
* * * *
53742532 GGCGACTCCATTTTTATTTTTTAAAATAAAAGTCGATTTCAAAAAAAAGGTTTCGACAGCTT
1 GGCGACTCCATTTTCATTTTTTAAAATAAAAATCGATTTAAAAAAAAAAGTTTCGACAGCTT
* **
53742594 GGCGACTCCGTTTTCATTTTTTAAAATAAAAATTTA-TTAAAAAAAAAAGTTTCGACA
1 GGCGACTCCATTTTCATTTTTTAAAATAAAAATCGATTTAAAAAAAAAAGTTTCGACA
53742651 ATCTCCTTTG
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
61 19 0.38
62 31 0.62
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (62 bp):
GGCGACTCCATTTTCATTTTTTAAAATAAAAATCGATTTAAAAAAAAAAGTTTCGACAGCTT
Found at i:53758563 original size:15 final size:15
Alignment explanation
Indices: 53758543--53758573 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
53758533 GCCCATATGG
53758543 ATCATCTTCATCTTC
1 ATCATCTTCATCTTC
*
53758558 ATCATCTTCTTCTTC
1 ATCATCTTCATCTTC
53758573 A
1 A
53758574 CTTTTAACTC
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:0.19, C:0.32, G:0.00, T:0.48
Consensus pattern (15 bp):
ATCATCTTCATCTTC
Found at i:53759716 original size:8 final size:8
Alignment explanation
Indices: 53759703--53759750 Score: 55
Period size: 8 Copynumber: 6.2 Consensus size: 8
53759693 AATGTGTAAA
53759703 TTATATAT
1 TTATATAT
53759711 TTATATAT
1 TTATATAT
53759719 TTATA-A-
1 TTATATAT
*
53759725 ATATATAT
1 TTATATAT
*
53759733 ATATATAT
1 TTATATAT
*
53759741 TTATAAAT
1 TTATATAT
53759749 TT
1 TT
53759751 TCGTTTATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
6 4 0.11
7 2 0.06
8 29 0.83
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
TTATATAT
Found at i:53763426 original size:24 final size:24
Alignment explanation
Indices: 53763398--53763449 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
53763388 TTAGTAAGTC
* *
53763398 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
53763422 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
53763446 AAAT
1 AAAT
53763450 CTTTTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:53765586 original size:2 final size:2
Alignment explanation
Indices: 53765579--53765603 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
53765569 TTTATAAAAT
53765579 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
53765604 TAAAGCAAGG
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:53766556 original size:23 final size:23
Alignment explanation
Indices: 53766526--53766572 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
53766516 ATTCTGAGTA
53766526 GGCGTCGGGCATGTTGAACACGT
1 GGCGTCGGGCATGTTGAACACGT
53766549 GGCGTCGGGCATGTTGAACACGT
1 GGCGTCGGGCATGTTGAACACGT
53766572 G
1 G
53766573 TACTGTTCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.17, C:0.21, G:0.40, T:0.21
Consensus pattern (23 bp):
GGCGTCGGGCATGTTGAACACGT
Found at i:53781150 original size:73 final size:73
Alignment explanation
Indices: 53781061--53781214 Score: 238
Period size: 73 Copynumber: 2.1 Consensus size: 73
53781051 ACGAAACTTA
* * *
53781061 TAACATTT-TCATGTTATAAAACATATACAAGTAAACACATTAGACATATCATTTATTCAACATC
1 TAACATTTCACATGTTATAAAACATATACAAGTAAACACATTAGACATACCATTCATTCAACATC
*
53781125 TATTCATT
66 TATTAATT
* * *
53781133 TAACATTTCACATGTTATAAAACGTGTACAAGTAAACACATTAGATATACCATTCATTCAACATC
1 TAACATTTCACATGTTATAAAACATATACAAGTAAACACATTAGACATACCATTCATTCAACATC
53781198 TATTAATT
66 TATTAATT
53781206 TAACATTTC
1 TAACATTTC
53781215 CCATTTCCCA
Statistics
Matches: 74, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
72 8 0.11
73 66 0.89
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (73 bp):
TAACATTTCACATGTTATAAAACATATACAAGTAAACACATTAGACATACCATTCATTCAACATC
TATTAATT
Found at i:53781219 original size:7 final size:7
Alignment explanation
Indices: 53781209--53781235 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
53781199 ATTAATTTAA
53781209 CATTTCC
1 CATTTCC
53781216 CATTTCC
1 CATTTCC
53781223 CATTTCC
1 CATTTCC
53781230 CATTTC
1 CATTTC
53781236 AAGCGTTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.41, G:0.00, T:0.44
Consensus pattern (7 bp):
CATTTCC
Found at i:53781669 original size:45 final size:45
Alignment explanation
Indices: 53781620--53781718 Score: 105
Period size: 45 Copynumber: 2.2 Consensus size: 45
53781610 ACAGTTACGG
*
53781620 TCTTACACACTTCCGAT-ATGAT-GTCATAGTGTCTTTCAACAATGA
1 TCTTACACACTTCCG-TCATGATAG-CATAATGTCTTTCAACAATGA
* * * *
53781665 TCTTATC-CATTTCCGTCATGTTAGCATAATGTCTTTCAACTATGG
1 TCTTA-CACACTTCCGTCATGATAGCATAATGTCTTTCAACAATGA
53781710 TCTTACACA
1 TCTTACACA
53781719 TTGAATCGTG
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
44 2 0.04
45 41 0.91
46 2 0.04
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.38
Consensus pattern (45 bp):
TCTTACACACTTCCGTCATGATAGCATAATGTCTTTCAACAATGA
Found at i:53781781 original size:45 final size:44
Alignment explanation
Indices: 53781696--53781809 Score: 156
Period size: 45 Copynumber: 2.6 Consensus size: 44
53781686 TAGCATAATG
* * *
53781696 TCTTTCAACTATGGTCTTACACATTGAATCGTGATGCCATAGCA
1 TCTTTCAGCTATGGTCTTACTCATTGAATCATGATGCCATAGCA
* * *
53781740 TCTTTTAGCTATGGTCTTACTCGTTTGAATCATGATGCCATAGCG
1 TCTTTCAGCTATGGTCTTACTC-ATTGAATCATGATGCCATAGCA
*
53781785 TCTTTCAGCTATGATCTTACTCATT
1 TCTTTCAGCTATGGTCTTACTCATT
53781810 TCCAGTATAG
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
44 21 0.35
45 39 0.65
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (44 bp):
TCTTTCAGCTATGGTCTTACTCATTGAATCATGATGCCATAGCA
Found at i:53783603 original size:24 final size:27
Alignment explanation
Indices: 53783576--53783625 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
53783566 CAAATACTCA
53783576 TTTATA-TA-ATTAAAATAT-TCATAT
1 TTTATACTAGATTAAAATATGTCATAT
53783600 TTTATACTAGATTAAAATATGTCATA
1 TTTATACTAGATTAAAATATGTCATA
53783626 AGTCCATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.26
25 2 0.09
26 10 0.43
27 5 0.22
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (27 bp):
TTTATACTAGATTAAAATATGTCATAT
Found at i:53784042 original size:23 final size:23
Alignment explanation
Indices: 53784001--53784044 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
53783991 CTATAAAAAA
*
53784001 TTATTATTAATATTGTAATATAT
1 TTATTATTAAAATTGTAATATAT
53784024 TTATTATTAAAATAT-TAATAT
1 TTATTATTAAAAT-TGTAATAT
53784045 TAATATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
TTATTATTAAAATTGTAATATAT
Found at i:53784045 original size:6 final size:6
Alignment explanation
Indices: 53784034--53784069 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
53784024 TTATTATTAA
53784034 AATATT AATATT AATATT AATATT AATATT AATATT
1 AATATT AATATT AATATT AATATT AATATT AATATT
53784070 GTTCATTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AATATT
Found at i:53784245 original size:39 final size:38
Alignment explanation
Indices: 53784202--53784277 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 38
53784192 AATATGTATG
53784202 TTTAATA-ATATTGAAAATTACAATATTTTATT-TTAATAT
1 TTTAATATAT-TTGAAAATTA-AA-ATTTTATTATTAATAT
*
53784241 TTTAATATATTTTAAAATTAAAATTTTATTATTAATA
1 TTTAATATATTTGAAAATTAAAATTTTATTATTAATA
53784278 GAATAATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
37 8 0.24
38 8 0.24
39 16 0.47
40 2 0.06
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (38 bp):
TTTAATATATTTGAAAATTAAAATTTTATTATTAATAT
Found at i:53803189 original size:16 final size:17
Alignment explanation
Indices: 53803149--53803190 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
53803139 TTCTCCACAT
53803149 AGTTATTCCCAATATAG
1 AGTTATTCCCAATATAG
*
53803166 AGGTTATTCCGAATA-AG
1 A-GTTATTCCCAATATAG
53803183 AGTTATTC
1 AGTTATTC
53803191 TGTAATAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 7 0.30
17 4 0.17
18 12 0.52
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (17 bp):
AGTTATTCCCAATATAG
Found at i:53803254 original size:15 final size:16
Alignment explanation
Indices: 53803234--53803272 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
53803224 GAATAATGGC
*
53803234 TCTAAATAC-ATTTGT
1 TCTAAATACAAGTTGT
53803249 TCTAAATACAAGTTGT
1 TCTAAATACAAGTTGT
*
53803265 TCCAAATA
1 TCTAAATA
53803273 ATGGTTGGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (16 bp):
TCTAAATACAAGTTGT
Found at i:53803352 original size:26 final size:26
Alignment explanation
Indices: 53803316--53803368 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
53803306 CCATATTCTA
53803316 AACAAGAGTTATTTCGAACTTTAATC
1 AACAAGAGTTATTTCGAACTTTAATC
53803342 AACAAGAGTTATTTCGAACTTTAATC
1 AACAAGAGTTATTTCGAACTTTAATC
53803368 A
1 A
53803369 TTCTCAATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (26 bp):
AACAAGAGTTATTTCGAACTTTAATC
Found at i:53810499 original size:2 final size:2
Alignment explanation
Indices: 53810492--53810523 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
53810482 GAGTGACCAA
53810492 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
53810524 TGGTATGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53817767 original size:17 final size:16
Alignment explanation
Indices: 53817742--53817814 Score: 58
Period size: 17 Copynumber: 4.4 Consensus size: 16
53817732 TTTAAACTAC
*
53817742 AAAAGATTATAAAAATT
1 AAAAAATTAT-AAAATT
* * *
53817759 ACAAAATTAGT-TATTT
1 AAAAAATTA-TAAAATT
*
53817775 AAAAAATTATAATATT
1 AAAAAATTATAAAATT
53817791 AAACAAATTATAAAATT
1 AAA-AAATTATAAAATT
53817808 ACAAAAA
1 A-AAAAA
53817815 AGAATATATA
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
15 1 0.02
16 16 0.37
17 23 0.53
18 3 0.07
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.32
Consensus pattern (16 bp):
AAAAAATTATAAAATT
Found at i:53818199 original size:21 final size:21
Alignment explanation
Indices: 53818162--53818231 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
53818152 AAATTTTTTT
* *
53818162 ATTTTTATATTATTTTTTGTA
1 ATTTTTATAATATTTTTTGGA
53818183 ATTTTTA-AATATGTTTTTGGA
1 ATTTTTATAATAT-TTTTTGGA
*
53818204 ATTTTTTTATAA-CTTTTTTGGA
1 A--TTTTTATAATATTTTTTGGA
*
53818226 TTTTTT
1 ATTTTT
53818232 TCATTTAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
20 9 0.22
21 15 0.37
22 8 0.20
23 7 0.17
24 2 0.05
ACGTcount: A:0.23, C:0.01, G:0.09, T:0.67
Consensus pattern (21 bp):
ATTTTTATAATATTTTTTGGA
Found at i:53825378 original size:91 final size:91
Alignment explanation
Indices: 53825193--53825460 Score: 369
Period size: 92 Copynumber: 2.9 Consensus size: 91
53825183 TGCCAGATGC
* * * *
53825193 ACATAGTGCAAACCCGTAGGCTAAATATTCT-CCTCGATAACACGCCAGATTTCTTATAAGAGCT
1 ACATAGTGCAAAGCCGTAGGCTAAATATTCTCCCCCGATAACACGCCAGATTGCTCATAAGAGCT
* * * *
53825257 ATTCTAATCAATAACATGCTAGATGC
66 ATTCTAATCAAGAACACGCTAAATGA
* * *
53825283 ACATAGTGCAAAGCCATAGGCTAAATATTCTCCCCCGATAACATGCCAGATTGCGCATAAGAGCT
1 ACATAGTGCAAAGCCGTAGGCTAAATATTCTCCCCCGATAACACGCCAGATTGCTCATAAGAGCT
*
53825348 ATTCTAATCGAGAACACG-TCAAATGA
66 ATTCTAATCAAGAACACGCT-AAATGA
*
53825374 ACATAGTGCAAAGCCTGTAGGCTAAATATTCTCCCCTGATAACACGCCAGATTGCTCATAAGAGC
1 ACATAGTGCAAAGCC-GTAGGCTAAATATTCTCCCCCGATAACACGCCAGATTGCTCATAAGAGC
* *
53825439 TATTCCAATCTAGAACACGCTA
65 TATTCTAATCAAGAACACGCTA
53825461 GAATCTCTGA
Statistics
Matches: 156, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
90 30 0.19
91 62 0.40
92 63 0.40
93 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.25
Consensus pattern (91 bp):
ACATAGTGCAAAGCCGTAGGCTAAATATTCTCCCCCGATAACACGCCAGATTGCTCATAAGAGCT
ATTCTAATCAAGAACACGCTAAATGA
Found at i:53825425 original size:92 final size:90
Alignment explanation
Indices: 53825193--53825460 Score: 367
Period size: 91 Copynumber: 2.9 Consensus size: 90
53825183 TGCCAGATGC
* * * *
53825193 ACATAGTGCAAACCCGTAGGCTAAATATTCTCCTCGATAACACGCCAGATTTCTTATAAGAGCTA
1 ACATAGTGCAAAGCCGTAGGCTAAATATTCTCCCCGATAACACGCCAGATTGCTCATAAGAGCTA
* * * *
53825258 TTCTAATCAATAACATGCTAGATGC
66 TTCTAATCAAGAACACGCTAAATGA
* * *
53825283 ACATAGTGCAAAGCCATAGGCTAAATATTCTCCCCCGATAACATGCCAGATTGCGCATAAGAGCT
1 ACATAGTGCAAAGCCGTAGGCTAAATATTCT-CCCCGATAACACGCCAGATTGCTCATAAGAGCT
*
53825348 ATTCTAATCGAGAACACG-TCAAATGA
65 ATTCTAATCAAGAACACGCT-AAATGA
53825374 ACATAGTGCAAAGCCTGTAGGCTAAATATTCTCCCCTGATAACACGCCAGATTGCTCATAAGAGC
1 ACATAGTGCAAAGCC-GTAGGCTAAATATTCTCCCC-GATAACACGCCAGATTGCTCATAAGAGC
* *
53825439 TATTCCAATCTAGAACACGCTA
64 TATTCTAATCAAGAACACGCTA
53825461 GAATCTCTGA
Statistics
Matches: 156, Mismatches: 17, Indels: 8
0.86 0.09 0.04
Matches are distributed among these distances:
90 30 0.19
91 66 0.42
92 59 0.38
93 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.25
Consensus pattern (90 bp):
ACATAGTGCAAAGCCGTAGGCTAAATATTCTCCCCGATAACACGCCAGATTGCTCATAAGAGCTA
TTCTAATCAAGAACACGCTAAATGA
Found at i:53830035 original size:22 final size:24
Alignment explanation
Indices: 53830010--53830058 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 24
53830000 CTCTTGAAAG
* *
53830010 AATACCTAAAAGAGAGT-CA-CAA
1 AATAACTAAAAGAAAGTACACCAA
*
53830032 AATAACTACAAGAAAGTACACCAA
1 AATAACTAAAAGAAAGTACACCAA
53830056 AAT
1 AAT
53830059 TGTGAACAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 14 0.64
23 2 0.09
24 6 0.27
ACGTcount: A:0.57, C:0.18, G:0.10, T:0.14
Consensus pattern (24 bp):
AATAACTAAAAGAAAGTACACCAA
Found at i:53831408 original size:109 final size:107
Alignment explanation
Indices: 53831290--53831523 Score: 330
Period size: 109 Copynumber: 2.2 Consensus size: 107
53831280 ATGTGAAAGG
*
53831290 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTAATTCCACCG-AATCCTT
1 GGTTGCTAAGTGCTGATTCCCCAAATCACTGGTGGTTGCTAAGTGCTAATTCCACCGTAAT--TT
*
53831354 -AATTGTAAAC-GGGGTTGCTAAGTGCTGATTCCCCGAATCAATAGT
64 GAA---TAAACAGGGGTTGCTAAGTGCTGATTCCCCAAATCAATAGT
* * *
53831399 GGTTGCTAAGTGTTGATTCCCCAAATCACTGGTGGTTGGTAAGTGCTGATTCCACCGTAATTTGA
1 GGTTGCTAAGTGCTGATTCCCCAAATCACTGGTGGTTGCTAAGTGCTAATTCCACCGTAATTTGA
* *
53831464 ATAAGCGAGGGGTTGCTAAGTGCTGATTCCCCAAATCAATGGT
66 ATAAAC-AGGGGTTGCTAAGTGCTGATTCCCCAAATCAATAGT
53831507 GGTTGCTAAGTGCTGAT
1 GGTTGCTAAGTGCTGAT
53831524 CCCATCGTAT
Statistics
Matches: 113, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
106 4 0.04
108 51 0.45
109 55 0.49
110 3 0.03
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.31
Consensus pattern (107 bp):
GGTTGCTAAGTGCTGATTCCCCAAATCACTGGTGGTTGCTAAGTGCTAATTCCACCGTAATTTGA
ATAAACAGGGGTTGCTAAGTGCTGATTCCCCAAATCAATAGT
Found at i:53831418 original size:76 final size:75
Alignment explanation
Indices: 53831169--53831410 Score: 373
Period size: 76 Copynumber: 3.2 Consensus size: 75
53831159 TGAATGTAAA
* * *
53831169 GGTGGTTGCTGAGTGCTGATTCCACCGAATCCTTAATTGTAAATGGGGTTGCTAAGTGTTGATTC
1 GGTGGTTGCTAAGTGCTAATTCCACCGAATCCTTAATTGTAAA-GGGGTTGCTAAGTGCTGATTC
53831234 CCCGAATCAAT
65 CCCGAATCAAT
53831245 GGTGGTTGCTAAGTGCTAATTCCACCGTAAT--TTGAA-TGTGAAAGGGGTTGCTAAGTGCTGAT
1 GGTGGTTGCTAAGTGCTAATTCCACCG-AATCCTT-AATTGT-AAAGGGGTTGCTAAGTGCTGAT
*
53831307 TCCCCGAATCACT
63 TCCCCGAATCAAT
53831320 GGTGGTTGCTAAGTGCTAATTCCACCGAATCCTTAATTGTAAACGGGGTTGCTAAGTGCTGATTC
1 GGTGGTTGCTAAGTGCTAATTCCACCGAATCCTTAATTGTAAA-GGGGTTGCTAAGTGCTGATTC
53831385 CCCGAATCAAT
65 CCCGAATCAAT
*
53831396 AGTGGTTGCTAAGTG
1 GGTGGTTGCTAAGTG
53831411 TTGATTCCCC
Statistics
Matches: 153, Mismatches: 6, Indels: 14
0.88 0.03 0.08
Matches are distributed among these distances:
74 3 0.02
75 67 0.44
76 80 0.52
77 3 0.02
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (75 bp):
GGTGGTTGCTAAGTGCTAATTCCACCGAATCCTTAATTGTAAAGGGGTTGCTAAGTGCTGATTCC
CCGAATCAAT
Found at i:53831478 original size:151 final size:147
Alignment explanation
Indices: 53831364--53831756 Score: 487
Period size: 151 Copynumber: 2.7 Consensus size: 147
53831354 AATTGTAAAC
* * *
53831364 GGGGTTGCTAAGTGCTGATTCCC-CG-A-ATC-AA-T-AGTGGTTGCTAAGTGTTGATTCCCCAA
1 GGGGTTGCTAAGTGCTGA-TCCCACGTACATCGAAGTAAGGGGTTGATAAGTGCTGATTCCCCAA
* *
53831423 ATCACTGGTGGTTGGTAAGTGCTGATTCCACCGTAATTTGAATAAGCGAGGGGTTGCTAAGTGCT
65 ATCACTGGTGGTTGCTAAGTGCTGACTCCACCGTAATTTGAATAAGCGAGGGGTTGCTAAGTGCT
*
53831488 GATTCCCCAAAT-CAATG
130 GATTCCCCGAATCCAATG
* *
53831505 GTGGTTGCTAAGTGCTGATCCCATCGTATCTTCGAATGTGAAAGGGGTTGATAAGTGCTGATTCC
1 GGGGTTGCTAAGTGCTGATCCCA-CGTA-CATCGAA-GT--AAGGGGTTGATAAGTGCTGATTCC
*
53831570 CCGAATCACTGGTGGTTGCTAAGTGCTGACTCCACCGTAATTTGAATAAGCGAGGGGTTGCTAAG
61 CCAAATCACTGGTGGTTGCTAAGTGCTGACTCCACCGTAATTTGAATAAGCGAGGGGTTGCTAAG
53831635 TGCTGATTCCCCGAAT-CAATG
126 TGCTGATTCCCCGAATCCAATG
* * * *
53831656 GTGGTTGCTAAGTGCTGATCCCATCGTATCTTCAAATGTGAAAGGGGTTGCTAAGTGCTGATTCC
1 GGGGTTGCTAAGTGCTGATCCCA-CGTA-CATCGAA-GT--AAGGGGTTGATAAGTGCTGATTCC
* * *
53831721 CCGAATCACTGGTGGTTGCTAAGTGTTGAATCCACC
61 CCAAATCACTGGTGGTTGCTAAGTGCTGACTCCACC
53831757 AACTAACGGA
Statistics
Matches: 228, Mismatches: 13, Indels: 12
0.90 0.05 0.05
Matches are distributed among these distances:
140 4 0.02
141 17 0.07
142 2 0.01
143 1 0.00
145 2 0.01
146 2 0.01
148 1 0.00
151 199 0.87
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (147 bp):
GGGGTTGCTAAGTGCTGATCCCACGTACATCGAAGTAAGGGGTTGATAAGTGCTGATTCCCCAAA
TCACTGGTGGTTGCTAAGTGCTGACTCCACCGTAATTTGAATAAGCGAGGGGTTGCTAAGTGCTG
ATTCCCCGAATCCAATG
Found at i:53831522 original size:75 final size:75
Alignment explanation
Indices: 53831399--53831756 Score: 461
Period size: 75 Copynumber: 4.7 Consensus size: 75
53831389 AATCAATAGT
* * *
53831399 GGTTGCTAAGTGTTGATTCCCCAAATCACTGGTGGTTGGTAAGTGCTGATTCCACCGTAAT-TTG
1 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGATTCCACCGT-ATCTTG
53831463 AATAAGCGAGG
65 AATAAGCGAGG
* * * *
53831474 GGTTGCTAAGTGCTGATTCCCCAAATCAATGGTGGTTGCTAAGTGCTGATCCCATCGTATCTTCG
1 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTT-G
** **
53831539 AATGTGAAAGG
65 AATAAGCGAGG
* *
53831550 GGTTGATAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGACTCCACCGTAAT-TTG
1 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGATTCCACCGT-ATCTTG
53831614 AATAAGCGAGG
65 AATAAGCGAGG
* * * *
53831625 GGTTGCTAAGTGCTGATTCCCCGAATCAATGGTGGTTGCTAAGTGCTGATCCCATCGTATCTTCA
1 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTGA
* *
53831690 A-ATGTGAAAGG
66 ATAAGCG--AGG
* *
53831701 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGTTGAATCCACC
1 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGATTCCACC
53831757 AACTAACGGA
Statistics
Matches: 245, Mismatches: 32, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
74 7 0.03
75 120 0.49
76 116 0.47
77 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (75 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTGA
ATAAGCGAGG
Found at i:53831554 original size:184 final size:184
Alignment explanation
Indices: 53831215--53831594 Score: 559
Period size: 184 Copynumber: 2.1 Consensus size: 184
53831205 TTGTAAATGG
*
53831215 GGTTGCTAAGTGTTGATTCCCCGAATCAATGGTGGTTGCTAAGTGCTAATTCCACCGTAATTTGA
1 GGTTGCTAAGTGTTGATTCCCCAAATCAATGGTGGTTGCTAAGTGCTAATTCCACCGTAATTTGA
** * * *
53831280 ATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTAATTCCAC
66 ATAAGAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCAATGGTGGTTGCTAAGTGCTAATCCCAC
*
53831345 CGAATCCTTAATTGTAAACGGGGTTGCTAAGTGCTGATTCCCCGAATCAATAGT
131 CGAATCCTTAATTGTAAACGGGGTTGATAAGTGCTGATTCCCCGAATCAATAGT
* * *
53831399 GGTTGCTAAGTGTTGATTCCCCAAATCACTGGTGGTTGGTAAGTGCTGATTCCACCGTAATTTGA
1 GGTTGCTAAGTGTTGATTCCCCAAATCAATGGTGGTTGCTAAGTGCTAATTCCACCGTAATTTGA
** * *
53831464 ATAAGCGAGGGGTTGCTAAGTGCTGATTCCCCAAATCAATGGTGGTTGCTAAGTGCTGATCCCAT
66 ATAAGAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCAATGGTGGTTGCTAAGTGCTAATCCCAC
* * *
53831529 CGTAT-CTTCGAA-TGTGAAA-GGGGTTGATAAGTGCTGATTCCCCGAATCACTGGT
131 CGAATCCTT--AATTGT-AAACGGGGTTGATAAGTGCTGATTCCCCGAATCAATAGT
53831583 GGTTGCTAAGTG
1 GGTTGCTAAGTG
53831595 CTGACTCCAC
Statistics
Matches: 176, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
183 3 0.02
184 168 0.95
185 5 0.03
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.31
Consensus pattern (184 bp):
GGTTGCTAAGTGTTGATTCCCCAAATCAATGGTGGTTGCTAAGTGCTAATTCCACCGTAATTTGA
ATAAGAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCAATGGTGGTTGCTAAGTGCTAATCCCAC
CGAATCCTTAATTGTAAACGGGGTTGATAAGTGCTGATTCCCCGAATCAATAGT
Found at i:53831664 original size:184 final size:180
Alignment explanation
Indices: 53831215--53831674 Score: 445
Period size: 184 Copynumber: 2.5 Consensus size: 180
53831205 TTGTAAATGG
* * * * * *
53831215 GGTTGCTAAGTGTTGATTCCCCGAATCAA-TGGTGGTTGCTAAGTGCTAATTCCACCGTAATTTG
1 GGTTGCTAAGTGCTGACTCCCCAAAT-AACTGGGGGTTGCTAAGTGCTGATTCCACCGTAA-TTC
* * * *
53831279 AATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTAATTCCA
64 AA--T-AGAGGGGTTGCTAAGTGCTGATTCCCCAAATCAATGGTGGTTGCTAAGTGCTAATCCCA
*
53831344 CCGAATCCTTAATTGTAAACGGGGTTGCTAAGTGCTGATTCCCCGAATCAATAGT
126 CCGAATCCTTAATTGTAAACGGGGTTGATAAGTGCTGATTCCCCGAATCAATAGT
* * * * * *
53831399 GGTTGCTAAGTGTTGATTCCCCAAATCACTGGTGGTTGGTAAGTGCTGATTCCACCGTAATTTGA
1 GGTTGCTAAGTGCTGACTCCCCAAATAACTGGGGGTTGCTAAGTGCTGATTCCACCGTAA-TTCA
* *
53831464 ATAAGCGAGGGGTTGCTAAGTGCTGATTCCCCAAATCAATGGTGGTTGCTAAGTGCTGATCCCAT
65 AT-A--GAGGGGTTGCTAAGTGCTGATTCCCCAAATCAATGGTGGTTGCTAAGTGCTAATCCCAC
* * *
53831529 CGTAT-CTTCGAA-TGTGAAA-GGGGTTGATAAGTGCTGATTCCCCGAATCACTGGT
127 CGAATCCTT--AATTGT-AAACGGGGTTGATAAGTGCTGATTCCCCGAATCAATAGT
53831583 GGTTGCTAAGTGCTGACTCCACCGTAATTTGAATAAGC-GAGGGGTTGCTAAGTGCTGATTCC-C
1 GGTTGCTAAGTGCTGACTCC-CC---A----AATAA-CTG-GGGGTTGCTAAGTGCTGATTCCAC
*
53831646 CG-AA-TCAAT-G-GTGGTTGCTAAGTGCTGAT
56 CGTAATTCAATAGAGGGGTTGCTAAGTGCTGAT
53831675 CCCATCGTAT
Statistics
Matches: 238, Mismatches: 22, Indels: 32
0.82 0.08 0.11
Matches are distributed among these distances:
182 2 0.01
183 4 0.02
184 188 0.79
185 8 0.03
188 1 0.00
189 4 0.02
191 2 0.01
192 8 0.03
193 21 0.09
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (180 bp):
GGTTGCTAAGTGCTGACTCCCCAAATAACTGGGGGTTGCTAAGTGCTGATTCCACCGTAATTCAA
TAGAGGGGTTGCTAAGTGCTGATTCCCCAAATCAATGGTGGTTGCTAAGTGCTAATCCCACCGAA
TCCTTAATTGTAAACGGGGTTGATAAGTGCTGATTCCCCGAATCAATAGT
Found at i:53833034 original size:26 final size:26
Alignment explanation
Indices: 53833004--53833063 Score: 102
Period size: 26 Copynumber: 2.3 Consensus size: 26
53832994 GTCAAAGCTA
*
53833004 CTGCAAAAAAATTTTTAGCACCACTG
1 CTGCAAAAAAAATTTTAGCACCACTG
53833030 CTGCAAAAAAAATTTTAGCACCACTG
1 CTGCAAAAAAAATTTTAGCACCACTG
*
53833056 CTCCAAAA
1 CTGCAAAA
53833064 TTTGTTCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.42, C:0.25, G:0.10, T:0.23
Consensus pattern (26 bp):
CTGCAAAAAAAATTTTAGCACCACTG
Found at i:53835062 original size:12 final size:12
Alignment explanation
Indices: 53835042--53835080 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
53835032 TTTAAAATTT
53835042 AAAAA-TTATAA
1 AAAAATTTATAA
*
53835053 CAAAATTTATAA
1 AAAAATTTATAA
53835065 AAAAATTTATTAA
1 AAAAATTTA-TAA
53835078 AAA
1 AAA
53835081 TAACAATACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 4 0.17
12 14 0.58
13 6 0.25
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAAATTTATAA
Found at i:53835209 original size:13 final size:13
Alignment explanation
Indices: 53835193--53835233 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
53835183 ATAATTTTAA
53835193 TTTTTTATAAATT
1 TTTTTTATAAATT
53835206 TTTTTTATAAATT
1 TTTTTTATAAATT
*
53835219 TTGTTTAT-AATT
1 TTTTTTATAAATT
53835231 TTT
1 TTT
53835234 ATGATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 6 0.23
13 20 0.77
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (13 bp):
TTTTTTATAAATT
Found at i:53836629 original size:21 final size:22
Alignment explanation
Indices: 53836598--53836639 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
53836588 TAATTTTGGT
53836598 TTTGTTTTTCTTTTCTTCTTTC
1 TTTGTTTTTCTTTTCTTCTTTC
*
53836620 TTTG-TTTTCTTTTGTTCTTT
1 TTTGTTTTTCTTTTCTTCTTT
53836640 TGGTTCTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (22 bp):
TTTGTTTTTCTTTTCTTCTTTC
Found at i:53840626 original size:30 final size:30
Alignment explanation
Indices: 53840568--53840623 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 30
53840558 ATACTTTTCT
* **
53840568 AATACTTTTAATCTTTTTTTTATTTTTAAA
1 AATAATTTTAATCTTTTTTGAATTTTTAAA
53840598 AATAATTTTAAT-TTTTTTGAATTTTT
1 AATAATTTTAATCTTTTTTGAATTTTT
53840624 TAATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
29 12 0.52
30 11 0.48
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (30 bp):
AATAATTTTAATCTTTTTTGAATTTTTAAA
Found at i:53841162 original size:20 final size:19
Alignment explanation
Indices: 53841139--53841180 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
53841129 AAAAAGAACT
53841139 TATAAATGAAAATTAAAATA
1 TATAAATGAAAATTAAAA-A
**
53841159 TATATTTGAAAATTAAAAA
1 TATAAATGAAAATTAAAAA
53841178 TAT
1 TAT
53841181 TAAAAAAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (19 bp):
TATAAATGAAAATTAAAAA
Found at i:53841827 original size:2 final size:2
Alignment explanation
Indices: 53841820--53841851 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
53841810 GCCATGGGAG
53841820 TA 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 TA
53841852 AGTGTGTGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:53844091 original size:19 final size:21
Alignment explanation
Indices: 53844064--53844102 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
53844054 TTCTACCAAA
*
53844064 ATTCTTCAAT-ATAT-TTACT
1 ATTCCTCAATCATATCTTACT
53844083 ATTCCTCAATCATATCTTAC
1 ATTCCTCAATCATATCTTAC
53844103 ATCATATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 4 0.24
21 4 0.24
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (21 bp):
ATTCCTCAATCATATCTTACT
Found at i:53846444 original size:17 final size:17
Alignment explanation
Indices: 53846422--53846456 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
53846412 AAATAGGAAA
*
53846422 GTAATTTTAAAAGATTT
1 GTAATTTGAAAAGATTT
*
53846439 GTAATTTGATAAGATTT
1 GTAATTTGAAAAGATTT
53846456 G
1 G
53846457 ATTTTGTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (17 bp):
GTAATTTGAAAAGATTT
Found at i:53854724 original size:6 final size:6
Alignment explanation
Indices: 53854713--53854743 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
53854703 AACGCACATG
53854713 CTGTTC CTGTTC CTGTTC CTGTTC CTGTTC C
1 CTGTTC CTGTTC CTGTTC CTGTTC CTGTTC C
53854744 AGCACTGCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.35, G:0.16, T:0.48
Consensus pattern (6 bp):
CTGTTC
Found at i:53856210 original size:101 final size:104
Alignment explanation
Indices: 53856019--53856218 Score: 289
Period size: 101 Copynumber: 1.9 Consensus size: 104
53856009 AAAAGGAAAA
* *
53856019 TTTTGGGTGTTGGCCTGTCAATGGCCGACACCCAGTACAATTTAAAAAAAATTTCTTTTTTTTCG
1 TTTTGGGTGCTGGCCTGTCAATGGCCGACACCCAATACAATTT---AAAAA-TTCTTTTTTTTCG
*
53856084 TGTCAGAATCAGATATCAGTATACGAAAAAAATAATAAATTTT
62 TGTCAGAATCAAATATCAGTATACGAAAAAAATAATAAATTTT
*
53856127 TTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAATACAATTT-AAAA-T-TTTTTTTTCGTGTC
1 TTTTGGGTGCTGGCCTGTCAATGGCCGACACCCAATACAATTTAAAAATTCTTTTTTTTCGTGTC
* *
53856189 TGAATCAAATATCTGTATACGAAAAAAATA
66 AGAATCAAATATCAGTATACGAAAAAAATA
53856219 TTGTTTTCTC
Statistics
Matches: 86, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
101 41 0.48
102 1 0.01
104 4 0.05
108 40 0.47
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Consensus pattern (104 bp):
TTTTGGGTGCTGGCCTGTCAATGGCCGACACCCAATACAATTTAAAAATTCTTTTTTTTCGTGTC
AGAATCAAATATCAGTATACGAAAAAAATAATAAATTTT
Found at i:53859082 original size:18 final size:17
Alignment explanation
Indices: 53859059--53859093 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
53859049 GCCACATAAT
*
53859059 ATATATTTTTATTTAAAA
1 ATATATATTTA-TTAAAA
53859077 ATATATATTTATTAAAA
1 ATATATATTTATTAAAA
53859094 TTAAATTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATATATTTATTAAAA
Found at i:53859182 original size:26 final size:26
Alignment explanation
Indices: 53859153--53859202 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
53859143 CAAATAAACC
53859153 TAGCCCAATACACCACAACCCAAAAA
1 TAGCCCAATACACCACAACCCAAAAA
* *
53859179 TAGCCCAATACACTACAACTCAAA
1 TAGCCCAATACACCACAACCCAAA
53859203 TCAGAAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.48, C:0.36, G:0.04, T:0.12
Consensus pattern (26 bp):
TAGCCCAATACACCACAACCCAAAAA
Found at i:53869897 original size:23 final size:23
Alignment explanation
Indices: 53869866--53869941 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
53869856 NGTGTTATTG
53869866 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
53869889 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
53869912 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
53869935 ATCAGTG
1 ATCAGTG
53869942 TGGCACTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:53881971 original size:98 final size:98
Alignment explanation
Indices: 53881802--53881993 Score: 307
Period size: 98 Copynumber: 2.0 Consensus size: 98
53881792 TACAGCGGAG
*
53881802 CAGATTGAAGATAGTAATCCTATCTCCCTGAAATTACAGTGGAGCGGATTAAAATAAAGGATTTT
1 CAGATTGAAGATAGTAATCCTATCTCCCTGAAATTACAGTGGAGCGGATTAAAATAAAGGATCTT
53881867 ATCTCTCTGAAGTTACAGTAGAGTAGATCACAT
66 ATCTCTCTGAAGTTACAGTAGAGTAGATCACAT
* * * *
53881900 CAGATTGAAG-TCGATAATCCTATCTCCCTGAAGTTACAGTGGAGTGGATTAAAATCACA-GATC
1 CAGATTGAAGATAG-TAATCCTATCTCCCTGAAATTACAGTGGAGCGGATTAAAAT-AAAGGATC
53881963 TTATCTCTCTGAAGTTACAGTAGAGTAGATC
64 TTATCTCTCTGAAGTTACAGTAGAGTAGATC
53881994 GTATCCGGTC
Statistics
Matches: 87, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
97 2 0.02
98 83 0.95
99 2 0.02
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.30
Consensus pattern (98 bp):
CAGATTGAAGATAGTAATCCTATCTCCCTGAAATTACAGTGGAGCGGATTAAAATAAAGGATCTT
ATCTCTCTGAAGTTACAGTAGAGTAGATCACAT
Found at i:53881983 original size:44 final size:43
Alignment explanation
Indices: 53881920--53882687 Score: 339
Period size: 44 Copynumber: 17.7 Consensus size: 43
53881910 TCGATAATCC
*
53881920 TATCTCCCTGAAGTTACAGTGGAGTGGATTAAAATCACAGATCT
1 TATCTCCCTGAAGTTACAGTGGAGTAGATTAAAAT-ACAGATCT
* * *** * *
53881964 TATCTCTCTGAAGTTACAGTAGAGTAGA-TCGTAT-CCGGTCT
1 TATCTCCCTGAAGTTACAGTGGAGTAGATTAAAATACAGATCT
* * ** * *
53882005 TATCTCCCTG-AGATTACAGCGGAGCAGATTGAAGTTGATA-ATCC
1 TATCTCCCTGAAG-TTACAGTGGAGTAGATT-AAAAT-ACAGATCT
* *
53882049 TATCTCCCTG-AGATTACAGTGGAGTGGATTAAAATAAATGATCT
1 TATCTCCCTGAAG-TTACAGTGGAGTAGATTAAAATACA-GATCT
* * * *** *
53882093 TATCTCTCTGAAGTTACAGTAGAGTGGA-TCGTAT-CAGGTCT
1 TATCTCCCTGAAGTTACAGTGGAGTAGATTAAAATACAGATCT
* ** * *
53882134 TATCTCCCTG-AGATTACAGCGGAGTAGATTGAAGCTAGTA-ATCC
1 TATCTCCCTGAAG-TTACAGTGGAGTAGATT-AAAATA-CAGATCT
* ** *
53882178 TATCTCCCTG-AGATTACAGTGGGGCGGATTAAAATAAAGGATCT
1 TATCTCCCTGAAG-TTACAGTGGAGTAGATTAAAATACA-GATCT
* ** ** *
53882222 TATCTCTCTGAAGTTACAGCAGAGTAGATT-GCAT-CAGGTCT
1 TATCTCCCTGAAGTTACAGTGGAGTAGATTAAAATACAGATCT
* * * ** *
53882263 TATTTCCCTGAGGTTACAGTGGAATAGACCGAAGAATTTCAGATCT
1 TATCTCCCTGAAGTTACAGTGGAGTAGA-TTAA-AA-TACAGATCT
* * *** *
53882309 TATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCT
1 TATCTCCCTGAAGTTACAGTGGAGTAGATT-AAAATACAGATCT
* * ** * * *
53882353 TATCTCCCTG-AGATTACAGCGGAGCAGA-TCCAAGACACTATCC
1 TATCTCCCTGAAG-TTACAGTGGAGTAGATTAAAATACA-GATCT
** *
53882396 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCT
1 TATCTCCCTGAAGTTACAGTGGAGTAGATTAAAATACA-GATCT
* * * *** *
53882440 CATCTCTCTGAAGTTACAGTAGAGTAGA-TCGCAT-CAGGTCT
1 TATCTCCCTGAAGTTACAGTGGAGTAGATTAAAATACAGATCT
* * ** *
53882481 TATCTCCCTGAGGTTACAGTAGAGTAGACCGAAGAATTTCAGATCT
1 TATCTCCCTGAAGTTACAGTGGAGTAGA-TTAA-AA-TACAGATCT
** * *** *
53882527 TATCTCCCTGTGGTTACAGTGGAGCAGATTGAAGCCAGAGATCT
1 TATCTCCCTGAAGTTACAGTGGAGTAGATT-AAAATACAGATCT
* ** ** * *
53882571 TATCTCCCTG-AGATTATAACGGAGTAGATTGAAGCTAGTA-ATCC
1 TATCTCCCTGAAG-TTACAGTGGAGTAGATT-AAAATA-CAGATCT
* * * * *
53882615 TAACTCTCTAAAGTTACAGTGGAGTGGATTAAAATAAAGGATCT
1 TATCTCCCTGAAGTTACAGTGGAGTAGATTAAAATACA-GATCT
* *
53882659 TATCTCTCTGAAGTTACAGTAGAGTAGAT
1 TATCTCCCTGAAGTTACAGTGGAGTAGAT
53882688 CACATCAGAT
Statistics
Matches: 533, Mismatches: 154, Indels: 74
0.70 0.20 0.10
Matches are distributed among these distances:
40 4 0.01
41 106 0.20
42 11 0.02
43 53 0.10
44 283 0.53
45 10 0.02
46 66 0.12
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (43 bp):
TATCTCCCTGAAGTTACAGTGGAGTAGATTAAAATACAGATCT
Found at i:53882133 original size:129 final size:128
Alignment explanation
Indices: 53881900--53882281 Score: 588
Period size: 129 Copynumber: 3.0 Consensus size: 128
53881890 TAGATCACAT
* *
53881900 CAGATTGAAGTCGATAATCCTATCTCCCTGA-AGTTACAGTGGAGTGGATTAAAATCACAGATCT
1 CAGATTGAAGTTGATAATCCTATCTCCCTGAGA-TTACAGTGGAGTGGATTAAAAT-AAAGATCT
*
53881964 TATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCCGGTCTTATCTCCCTGAGATTACAGCGGAG
64 TATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCAGGTCTTATCTCCCTGAGATTACAGCGGAG
53882029 CAGATTGAAGTTGATAATCCTATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAAATGATCTT
1 CAGATTGAAGTTGATAATCCTATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAAA-GATCTT
*
53882094 ATCTCTCTGAAGTTACAGTAGAGTGGATCGTATCAGGTCTTATCTCCCTGAGATTACAGCGGAG
65 ATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCAGGTCTTATCTCCCTGAGATTACAGCGGAG
* * * *
53882158 TAGATTGAAGCT-AGTAATCCTATCTCCCTGAGATTACAGTGGGGCGGATTAAAATAAAGGATCT
1 CAGATTGAAGTTGA-TAATCCTATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAAA-GATCT
* * * * *
53882222 TATCTCTCTGAAGTTACAGCAGAGTAGATTGCATCAGGTCTTATTTCCCTGAGGTTACAG
64 TATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCAGGTCTTATCTCCCTGAGATTACAG
53882282 TGGAATAGAC
Statistics
Matches: 235, Mismatches: 15, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
128 3 0.01
129 231 0.98
130 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.30
Consensus pattern (128 bp):
CAGATTGAAGTTGATAATCCTATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAAAGATCTTA
TCTCTCTGAAGTTACAGTAGAGTAGATCGTATCAGGTCTTATCTCCCTGAGATTACAGCGGAG
Found at i:53882425 original size:218 final size:219
Alignment explanation
Indices: 53882131--53882695 Score: 920
Period size: 218 Copynumber: 2.6 Consensus size: 219
53882121 TCGTATCAGG
53882131 TCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAATCCTATCTCCCTG-AGATTAC
1 TCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAATCCTATCTCCCTGAAG-TTAC
* * *
53882195 AGTGGGGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATTGCATCAGG
65 AGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGG
* *
53882260 TCTTATTTCCCTGAGGTTACAGTGGAATAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTTA
130 TCTTATCTCCCTGAGGTTACAGTAGAATAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTTA
53882325 CAGTGGAGCAGATTGAAGCCAGAGA
195 CAGTGGAGCAGATTGAAGCCAGAGA
* ** *
53882350 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCCAAGAC-ACT-ATCCTATCTCCCTGAAGTTAC
1 TCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAG-CTAGTAATCCTATCTCCCTGAAGTTAC
*
53882413 AGTGGAGCGGATTAAAATAAAGGATCTCATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGG
65 AGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGG
* *
53882478 TCTTATCTCCCTGAGGTTACAGTAGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGTGGTTA
130 TCTTATCTCCCTGAGGTTACAGTAGAATAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTTA
53882543 CAGTGGAGCAGATTGAAGCCAGAGA
195 CAGTGGAGCAGATTGAAGCCAGAGA
* * * * *
53882568 TCTTATCTCCCTGAGATTATAACGGAGTAGATTGAAGCTAGTAATCCTAACTCTCTAAAGTTACA
1 TCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAATCCTATCTCCCTGAAGTTACA
* *
53882633 GTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCAG
66 GTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
53882696 ATTGAAACTG
Statistics
Matches: 318, Mismatches: 24, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
217 1 0.00
218 199 0.63
219 117 0.37
220 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (219 bp):
TCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAATCCTATCTCCCTGAAGTTACA
GTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGT
CTTATCTCCCTGAGGTTACAGTAGAATAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTTAC
AGTGGAGCAGATTGAAGCCAGAGA
Found at i:53882469 original size:87 final size:87
Alignment explanation
Indices: 53882309--53882469 Score: 191
Period size: 87 Copynumber: 1.9 Consensus size: 87
53882299 TTTCAGATCT
* * ** * *
53882309 TATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCG
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGAAAGAGATCTCATCTCCCTGAGATTACAGCA
53882374 GAGCAGATCCAAGACACTATCC
66 GAGCAGATCCAAGACACTATCC
* * *
53882396 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAG-GATCTCATCTCTCTGA-AGTTACAG
1 TATCTCCCTGAAGTTACAGTGGAGCAGATT-AAAGAAAGAGATCTCATCTCCCTGAGA-TTACAG
* *
53882459 TAGAGTAGATC
64 CAGAGCAGATC
53882470 GCATCAGGTC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
86 1 0.02
87 56 0.92
88 4 0.07
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.25
Consensus pattern (87 bp):
TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGAAAGAGATCTCATCTCCCTGAGATTACAGCA
GAGCAGATCCAAGACACTATCC
Found at i:53883593 original size:41 final size:41
Alignment explanation
Indices: 53883509--53883706 Score: 306
Period size: 41 Copynumber: 4.8 Consensus size: 41
53883499 TTGTATATAA
* ** * * *
53883509 CACCGGCATAAAGTCTGCTAGGCACCAAGCCCGATACATTT
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGATATAATT
* * * *
53883550 CACTGGCACAAAGCCTGCTAGACATAAAGTCTGATATAATT
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGATATAATT
53883591 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGATATAATT
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGATATAATT
53883632 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGATATAATT
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGATATAATT
53883673 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGA
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGA
53883707 ACTTACAAAA
Statistics
Matches: 143, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 143 1.00
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (41 bp):
CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGATATAATT
Found at i:53884887 original size:16 final size:17
Alignment explanation
Indices: 53884866--53884897 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
53884856 AAATATGCAA
53884866 TCACATAA-TTCATATT
1 TCACATAACTTCATATT
53884882 TCACATAACTTCATAT
1 TCACATAACTTCATAT
53884898 CATCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCACATAACTTCATATT
Found at i:53885147 original size:41 final size:41
Alignment explanation
Indices: 53885059--53885213 Score: 163
Period size: 41 Copynumber: 3.7 Consensus size: 41
53885049 GGCTCGTACA
** * *
53885059 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATG
1 ATGCCAACGTCCCAGACGTGGTCTTACA-CAAATCAAATACG
53885101 ATGCC-ACTGTCCCAGACAG-GGTCTTACACAAATCAAATACG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACAAATCAAATACG
* * **
53885142 ATGCCAATGTCCCAGACATGGTCTTACACGTATACACAAGT-CG
1 ATGCCAACGTCCCAGACGTGGTCTTACACAAAT-CA-AA-TACG
53885185 ATGCCAACGTCCCAGACGTGGTCTTACAC
1 ATGCCAACGTCCCAGACGTGGTCTTACAC
53885214 GAAAATACAT
Statistics
Matches: 96, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
41 37 0.39
42 26 0.27
43 32 0.33
44 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.23
Consensus pattern (41 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACAAATCAAATACG
Found at i:53886084 original size:28 final size:31
Alignment explanation
Indices: 53886052--53886110 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 31
53886042 CCTTTCCTTT
53886052 TTATTATAATAAC-ATTAT-AATA-TATAAA
1 TTATTATAATAACTATTATAAATAGTATAAA
* *
53886080 TTATTATTATAACTTTTATAAATAGTATAAA
1 TTATTATAATAACTATTATAAATAGTATAAA
53886111 AACTATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 12 0.46
29 4 0.15
30 4 0.15
31 6 0.23
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (31 bp):
TTATTATAATAACTATTATAAATAGTATAAA
Found at i:53886678 original size:26 final size:25
Alignment explanation
Indices: 53886649--53886698 Score: 91
Period size: 26 Copynumber: 2.0 Consensus size: 25
53886639 CAAATAAACC
53886649 TAGCCCAATACACTACAACCCAAAAA
1 TAGCCCAATACACTACAA-CCAAAAA
53886675 TAGCCCAATACACTACAACCAAAA
1 TAGCCCAATACACTACAACCAAAA
53886699 TCAGAAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.50, C:0.34, G:0.04, T:0.12
Consensus pattern (25 bp):
TAGCCCAATACACTACAACCAAAAA
Found at i:53888327 original size:7 final size:7
Alignment explanation
Indices: 53888315--53888340 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
53888305 TCAATATTAT
53888315 TTTATGC
1 TTTATGC
53888322 TTTATGC
1 TTTATGC
53888329 TTTATGC
1 TTTATGC
53888336 TTTAT
1 TTTAT
53888341 TATTTATTTT
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:0.15, C:0.12, G:0.12, T:0.62
Consensus pattern (7 bp):
TTTATGC
Found at i:53888346 original size:14 final size:14
Alignment explanation
Indices: 53888309--53888347 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
53888299 ATTATGTCAA
53888309 TATTATTTTATGCTT
1 TATTA-TTTATGCTT
**
53888324 TATGCTTTATGCTT
1 TATTATTTATGCTT
53888338 TATTATTTAT
1 TATTATTTAT
53888348 TTTTATATCT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
14 17 0.85
15 3 0.15
ACGTcount: A:0.21, C:0.08, G:0.08, T:0.64
Consensus pattern (14 bp):
TATTATTTATGCTT
Found at i:53889720 original size:2 final size:2
Alignment explanation
Indices: 53889715--53889791 Score: 127
Period size: 2 Copynumber: 38.5 Consensus size: 2
53889705 AAATAGATAC
* *
53889715 AT AT AT AT AT AC AT AT AT AT TT 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
*
53889757 AT AT AT AT AT AT AT AT AT AT CT 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 A
53889792 CTTATAAACA
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53892233 original size:40 final size:40
Alignment explanation
Indices: 53892165--53892288 Score: 117
Period size: 40 Copynumber: 3.1 Consensus size: 40
53892155 GCGTTTGGAT
*
53892165 AAAAAACGCCGCTTAAAATTAAGCATTAGCGGCGCTTTTA
1 AAAAAACGCCACTTAAAATTAAGCATTAGCGGCGCTTTTA
* * *
53892205 AAAAAACGCCAC-TAAAGATTGAGTATTAGCGGCGCTTTTT
1 AAAAAACGCCACTTAAA-ATTAAGCATTAGCGGCGCTTTTA
** * * * * * *
53892245 GGAAAATGCCGCTAAAAATT-AGCATTAGCAGCGATTTTC
1 AAAAAACGCCACTTAAAATTAAGCATTAGCGGCGCTTTTA
53892284 AAAAA
1 AAAAA
53892289 GCGCTGCAAA
Statistics
Matches: 67, Mismatches: 15, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
39 22 0.33
40 42 0.63
41 3 0.04
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.25
Consensus pattern (40 bp):
AAAAAACGCCACTTAAAATTAAGCATTAGCGGCGCTTTTA
Found at i:53892370 original size:13 final size:13
Alignment explanation
Indices: 53892354--53892382 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
53892344 TGGCGTTTTT
53892354 TAAAAAGCGCCGC
1 TAAAAAGCGCCGC
53892367 TAAAAAGCGCCGC
1 TAAAAAGCGCCGC
53892380 TAA
1 TAA
53892383 TACTCGGGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.28, G:0.21, T:0.10
Consensus pattern (13 bp):
TAAAAAGCGCCGC
Found at i:53892426 original size:41 final size:40
Alignment explanation
Indices: 53892368--53892478 Score: 177
Period size: 41 Copynumber: 2.7 Consensus size: 40
53892358 AAGCGCCGCT
53892368 AAAAAGCGCCGCTAATACTCGGGGCTTTAGCGGCGTTTCTG
1 AAAAAGCG-CGCTAATACTCGGGGCTTTAGCGGCGTTTCTG
*
53892409 GAAAAGCGACGCTAATACTCGGGGCTTTAGCGGCGTTTCTG
1 AAAAAGCG-CGCTAATACTCGGGGCTTTAGCGGCGTTTCTG
*
53892450 AAAAAGCGCTGCTAAAACTCGGGGCTTTA
1 AAAAAGCGC-GCTAATACTCGGGGCTTTA
53892479 ACGGTATTTT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
40 1 0.02
41 64 0.98
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.23
Consensus pattern (40 bp):
AAAAAGCGCGCTAATACTCGGGGCTTTAGCGGCGTTTCTG
Found at i:53892645 original size:13 final size:14
Alignment explanation
Indices: 53892616--53892642 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53892606 GAAAATCGAC
53892616 CCCCCTTCTTTTTT
1 CCCCCTTCTTTTTT
53892630 CCCCCTTCTTTTT
1 CCCCCTTCTTTTT
53892643 CCCAAAATCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (14 bp):
CCCCCTTCTTTTTT
Found at i:53896713 original size:43 final size:43
Alignment explanation
Indices: 53896646--53896738 Score: 132
Period size: 43 Copynumber: 2.2 Consensus size: 43
53896636 AGGTTATGTT
* * *
53896646 TTTAGCGGCGTTTTTGCGAGAAGCGCCGCTAAAGATCATGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGATCATGGTC
* * *
53896689 TTTAGCGGCGTTTGTGAGAAAAGCGTCGCTAAAGGTCATTGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGATCATGGTC
53896732 TTTAGCG
1 TTTAGCG
53896739 CCGCTAAAGG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGATCATGGTC
Found at i:53896738 original size:25 final size:25
Alignment explanation
Indices: 53896710--53896763 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
53896700 TTGTGAGAAA
* *
53896710 AGCGTCGCTAAAGGTCATTGTCTTT
1 AGCGCCGCTAAAGGTCATAGTCTTT
53896735 AGCGCCGCTAAAGGTCATAGTCTTT
1 AGCGCCGCTAAAGGTCATAGTCTTT
53896760 AGCG
1 AGCG
53896764 GCGTTTGTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (25 bp):
AGCGCCGCTAAAGGTCATAGTCTTT
Found at i:53896779 original size:68 final size:68
Alignment explanation
Indices: 53896667--53896806 Score: 228
Period size: 68 Copynumber: 2.1 Consensus size: 68
53896657 TTTTGCGAGA
* * *
53896667 AGCGCCGCTAAAGATCATGGTCTTTAGCGGCGTTTGTGAGAAAAGCGTCGCTAAAGGTCATTG-T
1 AGCGCCGCTAAAGATCATAGTCTTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTC-TTGTT
53896731 CTTT
65 CTTT
*
53896735 AGCGCCGCTAAAGGTCATAGTCTTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCTTGTTC
1 AGCGCCGCTAAAGATCATAGTCTTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCTTGTTC
53896800 TTT
66 TTT
53896803 AGCG
1 AGCG
53896807 GCGTTTATTT
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
67 3 0.04
68 64 0.96
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.29
Consensus pattern (68 bp):
AGCGCCGCTAAAGATCATAGTCTTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCTTGTTC
TTT
Found at i:53896934 original size:22 final size:22
Alignment explanation
Indices: 53896906--53896948 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
53896896 TAGTGACGCT
*
53896906 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
53896928 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
53896949 GTTTTGGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.28, G:0.21, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:53898194 original size:30 final size:31
Alignment explanation
Indices: 53898158--53898224 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
53898148 ATACATGAAT
53898158 TTTAATT-TGATGC-AATTATACATATGAAAC
1 TTTAATTGTGATGCAAATT-TACATATGAAAC
* * *
53898188 TTTAATTGTGGTTCAAATTTATATATGAAAC
1 TTTAATTGTGATGCAAATTTACATATGAAAC
53898219 TTTAAT
1 TTTAAT
53898225 CTTAAAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 7 0.22
31 21 0.66
32 4 0.12
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.45
Consensus pattern (31 bp):
TTTAATTGTGATGCAAATTTACATATGAAAC
Found at i:53898952 original size:16 final size:16
Alignment explanation
Indices: 53898923--53898956 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
53898913 AAATTAAAGC
53898923 TAATTGTTATTAAAAT
1 TAATTGTTATTAAAAT
53898939 TAATTGTT-TGTAAAAT
1 TAATTGTTAT-TAAAAT
53898955 TA
1 TA
53898957 TCAAATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.06
16 16 0.94
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (16 bp):
TAATTGTTATTAAAAT
Found at i:53899030 original size:59 final size:61
Alignment explanation
Indices: 53898966--53899145 Score: 274
Period size: 68 Copynumber: 2.9 Consensus size: 61
53898956 ATCAAATTAT
53898966 TAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTA
1 TAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATC--A--A
53899031 TTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATC-A
1 -TAA-T-TATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAA
*
53899094 -AATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAA
1 TAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA
53899146 ACAAACTTGA
Statistics
Matches: 111, Mismatches: 1, Indels: 11
0.90 0.01 0.09
Matches are distributed among these distances:
59 48 0.43
60 1 0.01
61 2 0.02
63 1 0.01
66 3 0.03
67 1 0.01
68 55 0.50
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.46
Consensus pattern (61 bp):
TAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAA
Found at i:53899059 original size:68 final size:68
Alignment explanation
Indices: 53898948--53899115 Score: 313
Period size: 68 Copynumber: 2.5 Consensus size: 68
53898938 TTAATTGTTT
*
53898948 GTAAAATTATCAAATTATTAA-T-TATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGA
1 GTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGA
53899011 TTA
66 TTA
53899014 GTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGA
1 GTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGA
53899079 TTA
66 TTA
53899082 GTAAATTTATCAAATTATTAATTGTATTAATTGT
1 GTAAATTTATCAAATTATTAATTGTATTAATTGT
53899116 TGTAACAAAA
Statistics
Matches: 99, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
66 20 0.20
67 1 0.01
68 78 0.79
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.47
Consensus pattern (68 bp):
GTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGA
TTA
Found at i:53899062 original size:9 final size:9
Alignment explanation
Indices: 53899029--53899056 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
53899019 TTTATCAAAT
53899029 TATTAATTG
1 TATTAATTG
53899038 TATTAATTG
1 TATTAATTG
53899047 TATTAATTG
1 TATTAATTG
53899056 T
1 T
53899057 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:53899249 original size:22 final size:24
Alignment explanation
Indices: 53899209--53899252 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
53899199 AAATAAACTT
53899209 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
53899233 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
53899253 AATATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:53899937 original size:95 final size:95
Alignment explanation
Indices: 53899802--53900103 Score: 347
Period size: 95 Copynumber: 3.0 Consensus size: 95
53899792 GGAAAAAGAA
* *
53899802 GAAAAAGAAAAAAAAAATTTGGGTGTTGGCCTGTCAATGGCCGGCACCCAGTACAA-TTAAAAAA
1 GAAAAAGTAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAA
* * * *
53899866 AATTTCGTGTTAGAATTAGATATCAGTATAT
66 AATTT-GTGTCAAAATCAGATATCAGTATAC
*
53899897 GAAAACAGTAAAAAAAAA-TTGGATGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAGAAA
1 GAAAA-AGTAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTT----A
53899961 AAAAATTAATTTTTTGTGTCAAAATCAGATATCAGTATAAC
61 AAAAA--AA---TTTGTGTCAAAATCAGATATCAGTAT-AC
*
53900002 GAAAAAAATAAAAAAAATAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATT
1 G-AAAAAGT----AAAA-AAAAA-TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATT
53900067 TAAAAAAAATTTGTGTCAAAATCAGATATCAGTATAC
59 TAAAAAAAATTTGTGTCAAAATCAGATATCAGTATAC
53900104 CCAGTACAAT
Statistics
Matches: 178, Mismatches: 9, Indels: 33
0.81 0.04 0.15
Matches are distributed among these distances:
95 41 0.23
96 13 0.07
100 6 0.03
102 4 0.02
103 26 0.15
104 20 0.11
105 7 0.04
106 6 0.03
108 6 0.03
109 4 0.02
110 5 0.03
112 40 0.22
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.25
Consensus pattern (95 bp):
GAAAAAGTAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAA
AATTTGTGTCAAAATCAGATATCAGTATAC
Found at i:53900225 original size:48 final size:47
Alignment explanation
Indices: 53900124--53900266 Score: 236
Period size: 47 Copynumber: 3.0 Consensus size: 47
53900114 TTAAAAAAAA
53900124 TTCGTATACTGATATCCGATTCTGACAACGAAAAAAAAGAAC-TTTTT
1 TTCGTATACTGATATCCGATTCTGAC-ACGAAAAAAAAGAACTTTTTT
53900171 TTCGTATACTGATATCCGATTCTGACACGAAAAAAAAAGAACTTTTTT
1 TTCGTATACTGATATCCGATTCTGACACG-AAAAAAAAGAACTTTTTT
* *
53900219 TTCGTATATTGATATCTGATTCTGACACGAAAAAAAAGAA-TTTTTT
1 TTCGTATACTGATATCCGATTCTGACACGAAAAAAAAGAACTTTTTT
53900265 TT
1 TT
53900267 AAATTGTACT
Statistics
Matches: 92, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
46 11 0.12
47 49 0.53
48 32 0.35
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.36
Consensus pattern (47 bp):
TTCGTATACTGATATCCGATTCTGACACGAAAAAAAAGAACTTTTTT
Found at i:53901022 original size:19 final size:19
Alignment explanation
Indices: 53901000--53901041 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
53900990 CATGCAAATT
*
53901000 TATTACCAAAAATAAAACG
1 TATTACCAAAAAGAAAACG
* *
53901019 TATTTCCAAAAAGAAAACT
1 TATTACCAAAAAGAAAACG
53901038 TATT
1 TATT
53901042 GCCATAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.52, C:0.14, G:0.05, T:0.29
Consensus pattern (19 bp):
TATTACCAAAAAGAAAACG
Found at i:53902053 original size:39 final size:39
Alignment explanation
Indices: 53901925--53902054 Score: 147
Period size: 40 Copynumber: 3.3 Consensus size: 39
53901915 CGTTAGGACA
* * *
53901925 AAAAACGCCACTAAAAATCAAGCATTAGCGGTGCTTTTAC
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGATTTT-C
* * *
53901965 AAAAACGCCGCTAAAGATCGAGCATTAGCGGCGGATTTTG
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGC-GATTTTC
*
53902005 GAAAACGCCGCTAAAAAT-AAGCATTAGCGGCG-TTTTCC
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGATTTT-C
53902043 AAAAAGCGCCGC
1 AAAAA-CGCCGC
53902055 ACAAAACCTA
Statistics
Matches: 76, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
37 4 0.05
38 5 0.07
39 18 0.24
40 44 0.58
41 5 0.07
ACGTcount: A:0.36, C:0.23, G:0.22, T:0.19
Consensus pattern (39 bp):
AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGATTTTC
Found at i:53902174 original size:41 final size:42
Alignment explanation
Indices: 53902099--53902255 Score: 248
Period size: 41 Copynumber: 3.8 Consensus size: 42
53902089 TTTTTGGGGT
*
53902099 CTTTAGTGGCGTTTTTTGAAAAAGCGCCGCTAATGCTCGTAC
1 CTTTAGCGGCGTTTTTTGAAAAAGCGCCGCTAATGCTCGTAC
* * *
53902141 CTTTAGCGGCGTTTTGT-AATAAGCGCCGCTAATGCTCCTAC
1 CTTTAGCGGCGTTTTTTGAAAAAGCGCCGCTAATGCTCGTAC
*
53902182 CTTTAGCGGCG-TTTTTGAAGAAGCGCCGCTAATGCTCGTAC
1 CTTTAGCGGCGTTTTTTGAAAAAGCGCCGCTAATGCTCGTAC
53902223 CTTTAGCGGCGTTTTTT-AAAAAGCGCCGCTAAT
1 CTTTAGCGGCGTTTTTTGAAAAAGCGCCGCTAAT
53902256 AATAAAATCT
Statistics
Matches: 105, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
40 4 0.04
41 81 0.77
42 20 0.19
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.32
Consensus pattern (42 bp):
CTTTAGCGGCGTTTTTTGAAAAAGCGCCGCTAATGCTCGTAC
Found at i:53903560 original size:20 final size:20
Alignment explanation
Indices: 53903538--53903600 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
53903528 TTTGTGATTT
53903538 AAAATTTTAAAATGAATTTTA
1 AAAATTTTAAAATG-ATTTTA
**
53903559 AAAGATTTT-AAATTTTTTTA
1 AAA-ATTTTAAAATGATTTTA
*
53903579 AAAATTTTAAAAAGATTTTA
1 AAAATTTTAAAATGATTTTA
53903599 AA
1 AA
53903601 CTTTTATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
19 5 0.14
20 18 0.51
21 7 0.20
22 5 0.14
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (20 bp):
AAAATTTTAAAATGATTTTA
Found at i:53903568 original size:10 final size:10
Alignment explanation
Indices: 53903541--53903600 Score: 59
Period size: 10 Copynumber: 5.8 Consensus size: 10
53903531 GTGATTTAAA
53903541 ATTTTAAAATG
1 ATTTTAAAA-G
53903552 AATTTTAAAAG
1 -ATTTTAAAAG
**
53903563 ATTTTAAATT
1 ATTTTAAAAG
*
53903573 TTTTTAAAA-
1 ATTTTAAAAG
53903582 ATTTTAAAAAG
1 ATTTT-AAAAG
53903593 ATTTTAAA
1 ATTTTAAA
53903601 CTTTTATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
9 4 0.10
10 22 0.54
11 6 0.15
12 9 0.22
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (10 bp):
ATTTTAAAAG
Found at i:53908535 original size:43 final size:43
Alignment explanation
Indices: 53908419--53908733 Score: 290
Period size: 43 Copynumber: 7.3 Consensus size: 43
53908409 ATGATATGTT
* * * * * * *
53908419 TTTAGCGGTGTTTTTGTGAGAAGCGTCGCTAAAGGT-TTGTTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
* * * * *
53908461 TATAGCGGTGTTTGTGATAAAAAGTGCCGCTAAAGGTCATGCTC
1 TTTAGCGGCGTTTGTGA-GAAAAGCGCCGCTAAAGGTCATGGTC
* * * *
53908505 TATAGCGGCGTTTGTGACAAATGCGTCGCTAAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCT-AAAGGTCATGGTC
* * *
53908549 TTTATCGGCGTTTGTGGGAAAAGTGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
* * * *
53908592 TATAGCGGTGTTTGTGACAAAAGCGCAGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
* * * * *
53908635 TTTAGCGACGTTTGTGGGAAAAGCACCGCTAAAGGTCCTAGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
* * * ** **
53908678 TTTAGCGGCGTTTGTGGGAAAAGTGTCGCTAAAGACCATGACC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
53908721 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
53908734 ATTTCTAAAA
Statistics
Matches: 222, Mismatches: 48, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
42 14 0.06
43 153 0.69
44 55 0.25
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
Found at i:53908824 original size:22 final size:22
Alignment explanation
Indices: 53908798--53908839 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
53908788 GGTGCTTCTC
*
53908798 AAAAGCGCAGCTAAAGGCCTAA
1 AAAAGCGCAGCTAAAAGCCTAA
*
53908820 AAAAGCGCCGCTAAAAGCCT
1 AAAAGCGCAGCTAAAAGCCT
53908840 GTTTTGGTGT
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:0.43, C:0.26, G:0.21, T:0.10
Consensus pattern (22 bp):
AAAAGCGCAGCTAAAAGCCTAA
Found at i:53915493 original size:15 final size:14
Alignment explanation
Indices: 53915475--53915530 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 14
53915465 ATTAATTTAA
53915475 TATTATTATTACCAT
1 TATTATTATTACC-T
53915490 TATTATT-TTACCCT
1 TATTATTATTA-CCT
53915504 TATTATTTATATA-CT
1 TATTA-TTAT-TACCT
53915519 TATTATTATTAC
1 TATTATTATTAC
53915531 TATATTGTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
13 2 0.06
14 13 0.36
15 18 0.50
16 1 0.03
17 2 0.06
ACGTcount: A:0.30, C:0.12, G:0.00, T:0.57
Consensus pattern (14 bp):
TATTATTATTACCT
Found at i:53915500 original size:14 final size:14
Alignment explanation
Indices: 53915475--53915511 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
53915465 ATTAATTTAA
53915475 TATTATTATTACCAT
1 TATTATT-TTACCAT
*
53915490 TATTATTTTACCCT
1 TATTATTTTACCAT
53915504 TATTATTT
1 TATTATTT
53915512 ATATACTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.27, C:0.14, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTATTTTACCAT
Found at i:53915671 original size:3 final size:3
Alignment explanation
Indices: 53915663--53915702 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
53915653 GACTATTTAT
53915663 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
53915703 AACTCTAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:53915802 original size:15 final size:15
Alignment explanation
Indices: 53915755--53915793 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
53915745 ACTGTATTTT
*
53915755 TTATTGTTACTATCA
1 TTATTATTACTATCA
*
53915770 TTATTATTACTCTCA
1 TTATTATTACTATCA
53915785 TTATTATTA
1 TTATTATTA
53915794 TTATTATTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.28, C:0.13, G:0.03, T:0.56
Consensus pattern (15 bp):
TTATTATTACTATCA
Found at i:53922967 original size:18 final size:18
Alignment explanation
Indices: 53922944--53922978 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53922934 CTTAGCAATG
53922944 TTTTTATCTCAAAAGTGT
1 TTTTTATCTCAAAAGTGT
* *
53922962 TTTTTATTTTAAAAGTG
1 TTTTTATCTCAAAAGTG
53922979 CTTCTTAAAA
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:0.29, C:0.06, G:0.11, T:0.54
Consensus pattern (18 bp):
TTTTTATCTCAAAAGTGT
Found at i:53923566 original size:59 final size:59
Alignment explanation
Indices: 53923458--53923582 Score: 153
Period size: 59 Copynumber: 2.1 Consensus size: 59
53923448 TTTTTAAAAC
* *
53923458 TTTTAGAATTAGAATTAAGTTGAAAAATTTTGTAAATGTTCAAGATAAATTTATTGAAT
1 TTTTAGAATTAGAATTAAGATGAAAAATTTTGTAAATATTCAAGATAAATTTATTGAAT
* * * * * * *
53923517 TTTTAGAATTAGAATTAA-ATGACAAATTTTGTAGATATTGAGGGCTAAATTTGTTTAAT
1 TTTTAGAATTAGAATTAAGATGAAAAATTTTGTAAATATTCA-AGATAAATTTATTGAAT
53923576 TTTTAGA
1 TTTTAGA
53923583 TTTAAGATCA
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
58 18 0.32
59 38 0.68
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.43
Consensus pattern (59 bp):
TTTTAGAATTAGAATTAAGATGAAAAATTTTGTAAATATTCAAGATAAATTTATTGAAT
Found at i:53930039 original size:17 final size:17
Alignment explanation
Indices: 53930017--53930080 Score: 101
Period size: 17 Copynumber: 3.8 Consensus size: 17
53930007 GACTAATCCC
*
53930017 TATACATCACTTAGGTA
1 TATACATTACTTAGGTA
53930034 TATACATTACTTAGGTA
1 TATACATTACTTAGGTA
*
53930051 TGTACATTACTTAGGTA
1 TATACATTACTTAGGTA
*
53930068 TGTACATTACTTA
1 TATACATTACTTA
53930081 AGTACATGCC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 45 1.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (17 bp):
TATACATTACTTAGGTA
Found at i:53930854 original size:23 final size:23
Alignment explanation
Indices: 53930784--53930868 Score: 108
Period size: 21 Copynumber: 3.9 Consensus size: 23
53930774 CCTGATCAGT
53930784 ATACGACACAT-AAGTGCCTGA-
1 ATACGACACATAAAGTGCCTGAG
** *
53930805 A-ACGACACACGAGGTGCCT--G
1 ATACGACACATAAAGTGCCTGAG
53930825 ATACGACACATAAAGTGCCTGAG
1 ATACGACACATAAAGTGCCTGAG
53930848 ATACGACACATAAAGTGCCTG
1 ATACGACACATAAAGTGCCTG
53930869 GTCGGCAAAG
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
20 9 0.17
21 23 0.43
23 22 0.41
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.16
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAG
Found at i:53930866 original size:44 final size:41
Alignment explanation
Indices: 53930784--53930868 Score: 116
Period size: 44 Copynumber: 2.0 Consensus size: 41
53930774 CCTGATCAGT
* *
53930784 ATACGACACATAAGTGCCTGAAACGACACACGAGGTGCCTG
1 ATACGACACATAAGTGCCTGAAACGACACACAAAGTGCCTG
*
53930825 ATACGACACATAAAGTGCCTGAGATACGACACATAAAGTGCCTG
1 ATACGACACAT-AAGTGCCTGA-A-ACGACACACAAAGTGCCTG
53930869 GTCGGCAAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 11 0.29
42 10 0.26
43 1 0.03
44 16 0.42
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.16
Consensus pattern (41 bp):
ATACGACACATAAGTGCCTGAAACGACACACAAAGTGCCTG
Found at i:53931601 original size:13 final size:13
Alignment explanation
Indices: 53931572--53931609 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
53931562 CCCGTTTTGC
53931572 TCTCTGTTTCT-T
1 TCTCTGTTTCTAT
53931584 TCTCTGTTTCTAT
1 TCTCTGTTTCTAT
*
53931597 TCTCTTTTTCTAT
1 TCTCTGTTTCTAT
53931610 CCTTTCTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.05, C:0.24, G:0.05, T:0.66
Consensus pattern (13 bp):
TCTCTGTTTCTAT
Found at i:53931639 original size:8 final size:8
Alignment explanation
Indices: 53931628--53931655 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
53931618 TGTTATATAC
53931628 ATATAATA
1 ATATAATA
53931636 ATATAATA
1 ATATAATA
53931644 ATATAATA
1 ATATAATA
53931652 ATAT
1 ATAT
53931656 TTTTTTTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATAATA
Found at i:53932440 original size:18 final size:18
Alignment explanation
Indices: 53932404--53932451 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
53932394 ATCTACCATT
*
53932404 TCATATTCCACTTCACATC
1 TCAT-TTCCATTTCACATC
*
53932423 TCATTTCCATTTCTCATC
1 TCATTTCCATTTCACATC
*
53932441 -CTTTTCCATTT
1 TCATTTCCATTT
53932452 TAATATCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 10 0.38
18 12 0.46
19 4 0.15
ACGTcount: A:0.19, C:0.33, G:0.00, T:0.48
Consensus pattern (18 bp):
TCATTTCCATTTCACATC
Found at i:53932833 original size:24 final size:25
Alignment explanation
Indices: 53932790--53932838 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
53932780 AATTTCATAA
53932790 ATGTATATTATCACATATTCAATTT
1 ATGTATATTATCACATATTCAATTT
53932815 ATGTATATTATCACA-ATTCAATTT
1 ATGTATATTATCACATATTCAATTT
53932839 GATAGCAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.37, C:0.12, G:0.04, T:0.47
Consensus pattern (25 bp):
ATGTATATTATCACATATTCAATTT
Found at i:53934390 original size:2 final size:2
Alignment explanation
Indices: 53934383--53934416 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
53934373 ACTTTAGATA
* *
53934383 AT AT AT AT AT AT AT AT AC AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53934417 GATTTTGTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:53935589 original size:14 final size:14
Alignment explanation
Indices: 53935570--53935603 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
53935560 TAATGCACAT
*
53935570 ACAAATTTTATTAA
1 ACAAATTTTAATAA
53935584 ACAAATTTTAATAA
1 ACAAATTTTAATAA
*
53935598 GCAAAT
1 ACAAAT
53935604 GTGCTAATGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.53, C:0.09, G:0.03, T:0.35
Consensus pattern (14 bp):
ACAAATTTTAATAA
Found at i:53936532 original size:10 final size:10
Alignment explanation
Indices: 53936517--53936575 Score: 59
Period size: 10 Copynumber: 6.0 Consensus size: 10
53936507 ATTTTTATTT
53936517 TTATATTAAA
1 TTATATTAAA
53936527 TTATATTAAA
1 TTATATTAAA
*
53936537 ATAT-TTAAA
1 TTATATTAAA
*
53936546 ATATTATTAAA
1 TTA-TATTAAA
*
53936557 TCATATTAAA
1 TTATATTAAA
*
53936567 CTAT-TTAAA
1 TTATATTAAA
53936576 AATATTTTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
9 13 0.31
10 23 0.55
11 6 0.14
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (10 bp):
TTATATTAAA
Found at i:53936556 original size:30 final size:31
Alignment explanation
Indices: 53936520--53936581 Score: 99
Period size: 30 Copynumber: 2.0 Consensus size: 31
53936510 TTTATTTTTA
*
53936520 TATTAAATTATATTAAAATATTT-AAAATAT
1 TATTAAATCATATTAAAATATTTAAAAATAT
*
53936550 TATTAAATCATATTAAACTATTTAAAAATAT
1 TATTAAATCATATTAAAATATTTAAAAATAT
53936581 T
1 T
53936582 TTATTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 21 0.72
31 8 0.28
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (31 bp):
TATTAAATCATATTAAAATATTTAAAAATAT
Found at i:53936581 original size:10 final size:9
Alignment explanation
Indices: 53936522--53936582 Score: 50
Period size: 10 Copynumber: 6.2 Consensus size: 9
53936512 TATTTTTATA
*
53936522 TTAAATTAT
1 TTAAAATAT
53936531 ATTAAAATAT
1 -TTAAAATAT
53936541 TTAAAATAT
1 TTAAAATAT
*
53936550 TATTAAATCAT
1 T-TAAAAT-AT
*
53936561 ATTAAACTAT
1 -TTAAAATAT
53936571 TTAAAAATAT
1 TT-AAAATAT
53936581 TT
1 TT
53936583 TATTTTTTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
9 12 0.29
10 23 0.55
11 6 0.14
12 1 0.02
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (9 bp):
TTAAAATAT
Found at i:53936648 original size:25 final size:25
Alignment explanation
Indices: 53936614--53936696 Score: 116
Period size: 25 Copynumber: 3.4 Consensus size: 25
53936604 AATTGGAAAT
*
53936614 AATATTTTATTTTAAATTATATTAA
1 AATATTTTATATTAAATTATATTAA
* *
53936639 AATATTTTATATTAAA-TAAATT-T
1 AATATTTTATATTAAATTATATTAA
*
53936662 AATATTTAATATTAAATTATATTAA
1 AATATTTTATATTAAATTATATTAA
53936687 AATATTTTAT
1 AATATTTTAT
53936697 TTTTAAAATT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
23 15 0.31
24 10 0.20
25 24 0.49
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
AATATTTTATATTAAATTATATTAA
Found at i:53936650 original size:15 final size:15
Alignment explanation
Indices: 53936630--53936709 Score: 65
Period size: 15 Copynumber: 5.1 Consensus size: 15
53936620 TTATTTTAAA
53936630 TTATATTAAAATATT
1 TTATATTAAAATATT
*
53936645 TTATATTAAATAAATT
1 TTATATTAAA-ATATT
* *
53936661 TAATATT-TAATATT
1 TTATATTAAAATATT
53936675 AAATTATATTAAAATATT
1 ---TTATATTAAAATATT
*
53936693 TTATTTTTAAAAT-TT
1 TTA-TATTAAAATATT
53936708 TT
1 TT
53936710 GAAATTTGGA
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
14 4 0.08
15 18 0.35
16 18 0.35
17 6 0.12
18 6 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTATATTAAAATATT
Found at i:53937022 original size:2 final size:2
Alignment explanation
Indices: 53937015--53937053 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
53937005 TATCAAAATT
*
53937015 TC TC TC TC TC TC TC TC TC TC TG TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
53937054 TTTAAAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.46, G:0.03, T:0.51
Consensus pattern (2 bp):
TC
Found at i:53940313 original size:37 final size:37
Alignment explanation
Indices: 53940251--53940349 Score: 126
Period size: 37 Copynumber: 2.7 Consensus size: 37
53940241 TTCGAAGTAA
* * * *
53940251 TAAAATGACACCCAGTGTCTCATCGGCTAAACCGAAG
1 TAAATTGACACACAGTGCCTCATCGGCTAAACCAAAG
* *
53940288 TAAATTGGCACACAGTGCCTAATCGGCTAAACCAAAG
1 TAAATTGACACACAGTGCCTCATCGGCTAAACCAAAG
* *
53940325 TAAATTGACACCCAATGCCTCATCG
1 TAAATTGACACACAGTGCCTCATCG
53940350 AATTAATCCG
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.20
Consensus pattern (37 bp):
TAAATTGACACACAGTGCCTCATCGGCTAAACCAAAG
Found at i:53948753 original size:17 final size:16
Alignment explanation
Indices: 53948716--53948754 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
53948706 AATAAATAAT
53948716 TAAA-TAAATTGGAAA
1 TAAATTAAATTGGAAA
53948731 TAAAATTAAATTGGGAAA
1 T-AAATTAAATT-GGAAA
53948749 TAAATT
1 TAAATT
53948755 TGAATTTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 1 0.05
16 3 0.14
17 11 0.52
18 6 0.29
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (16 bp):
TAAATTAAATTGGAAA
Done.