Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 177 of 185
Found at i:53798742 original size:17 final size:17
Alignment explanation
Indices: 53798722--53798755 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
53798712 TTTATGTGTT
*
53798722 ATAAATTATATAACATA
1 ATAAAATATATAACATA
*
53798739 ATAAAATATATTACATA
1 ATAAAATATATAACATA
53798756 CTTAGGAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAAAATATATAACATA
Found at i:53799275 original size:21 final size:21
Alignment explanation
Indices: 53799234--53799275 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
53799224 AGTTCTGCCC
**
53799234 ATATTATTTTTAAATTTTTAA
1 ATATTATTTTTAAATACTTAA
53799255 ATATATATTTTT-AATACTTAA
1 ATAT-TATTTTTAAATACTTAA
53799276 TAATTTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATTATTTTTAAATACTTAA
Found at i:53799662 original size:3 final size:3
Alignment explanation
Indices: 53799654--53799690 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
53799644 TTACGTTGTG
53799654 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
53799691 AGTAAGAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:53802800 original size:11 final size:10
Alignment explanation
Indices: 53802784--53802847 Score: 50
Period size: 9 Copynumber: 6.8 Consensus size: 10
53802774 GTACAAAAAA
53802784 ATTTTTAAGAT
1 ATTTTTAA-AT
53802795 ATTTTT--AT
1 ATTTTTAAAT
*
53802803 AGTTTTTTAAT
1 A-TTTTTAAAT
*
53802814 A-CTTTAAAT
1 ATTTTTAAAT
53802823 ATTTTT-AAT
1 ATTTTTAAAT
53802832 ATTTTT-AAT
1 ATTTTTAAAT
53802841 -TTTTTAA
1 ATTTTTAA
53802848 TTTTAAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
8 8 0.18
9 25 0.56
10 3 0.07
11 9 0.20
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (10 bp):
ATTTTTAAAT
Found at i:53802836 original size:8 final size:9
Alignment explanation
Indices: 53802793--53802848 Score: 62
Period size: 9 Copynumber: 6.2 Consensus size: 9
53802783 AATTTTTAAG
53802793 ATATTTTT-
1 ATATTTTTA
53802801 ATAGTTTTTTA
1 ATA--TTTTTA
* *
53802812 ATACTTTAA
1 ATATTTTTA
53802821 ATATTTTTA
1 ATATTTTTA
53802830 ATATTTTTA
1 ATATTTTTA
53802839 AT-TTTTTA
1 ATATTTTTA
53802847 AT
1 AT
53802849 TTTAAAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
8 11 0.27
9 22 0.54
10 5 0.12
11 3 0.07
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (9 bp):
ATATTTTTA
Found at i:53810709 original size:20 final size:17
Alignment explanation
Indices: 53810675--53810716 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 17
53810665 TCTGATCGCG
53810675 TATTGTAATTTTGATTA
1 TATTGTAATTTTGATTA
53810692 TGATTGTAACTATTTGATTA
1 T-ATTGTAA-T-TTTGATTA
53810712 TATTG
1 TATTG
53810717 GTTGTAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 1 0.05
18 7 0.32
19 5 0.23
20 9 0.41
ACGTcount: A:0.29, C:0.02, G:0.14, T:0.55
Consensus pattern (17 bp):
TATTGTAATTTTGATTA
Found at i:53819217 original size:13 final size:13
Alignment explanation
Indices: 53819199--53819226 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
53819189 ATAAATACTT
53819199 GTCTGTATAAGAG
1 GTCTGTATAAGAG
53819212 GTCTGTATAAGAG
1 GTCTGTATAAGAG
53819225 GT
1 GT
53819227 GAGAGAAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.07, G:0.32, T:0.32
Consensus pattern (13 bp):
GTCTGTATAAGAG
Found at i:53821398 original size:21 final size:21
Alignment explanation
Indices: 53821372--53821427 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
53821362 AACAGTGGTG
*
53821372 GTGGTGAGATTAGTTACTATA
1 GTGGTGAGATTAGATACTATA
* *
53821393 GTGGTGAGATTGGATACTGTA
1 GTGGTGAGATTAGATACTATA
**
53821414 GCAGTGAGATTAGA
1 GTGGTGAGATTAGA
53821428 AATAGCGGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.29, C:0.05, G:0.34, T:0.32
Consensus pattern (21 bp):
GTGGTGAGATTAGATACTATA
Found at i:53821703 original size:33 final size:34
Alignment explanation
Indices: 53821636--53821703 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 34
53821626 AATAAAATTT
* *
53821636 AAATATTTTTAACTTATATTAATAATAAATAATA
1 AAATATATTTAAATTATATTAATAATAAATAATA
* *
53821670 AAATATATTTAAATTAT-TTTATATTAAATAATA
1 AAATATATTTAAATTATATTAATAATAAATAATA
53821703 A
1 A
53821704 TTAAACTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 15 0.50
34 15 0.50
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (34 bp):
AAATATATTTAAATTATATTAATAATAAATAATA
Found at i:53823584 original size:29 final size:29
Alignment explanation
Indices: 53823529--53823589 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
53823519 TGGAATTAAA
*
53823529 TTTATATTTTTAAAAATTTTACTCTTTAT
1 TTTATATTTTTAAAAATTTCACTCTTTAT
53823558 TTTA-ATTTTTAATTAAATTTCAC-CTTTAT
1 TTTATATTTTTAA--AAATTTCACTCTTTAT
53823587 TTT
1 TTT
53823590 TTAAAAAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 8 0.28
29 13 0.45
30 8 0.28
ACGTcount: A:0.30, C:0.08, G:0.00, T:0.62
Consensus pattern (29 bp):
TTTATATTTTTAAAAATTTCACTCTTTAT
Found at i:53825624 original size:16 final size:15
Alignment explanation
Indices: 53825599--53825632 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
53825589 ATTATAATTT
53825599 AAAATTTAAAAACTA
1 AAAATTTAAAAACTA
53825614 AAAAGTTTAAAAACTA
1 AAAA-TTTAAAAACTA
53825630 AAA
1 AAA
53825633 TTAACCAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.24
Consensus pattern (15 bp):
AAAATTTAAAAACTA
Found at i:53827109 original size:14 final size:14
Alignment explanation
Indices: 53827090--53827116 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53827080 TGATAAAGAT
53827090 AAAAAAATTCAATC
1 AAAAAAATTCAATC
53827104 AAAAAAATTCAAT
1 AAAAAAATTCAAT
53827117 TAATTTTCTG
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:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAAAAATTCAATC
Found at i:53845847 original size:19 final size:19
Alignment explanation
Indices: 53845823--53845884 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 19
53845813 AAGCAATAGT
53845823 TTATTAAAGTAAAATAGAG
1 TTATTAAAGTAAAATAGAG
*** ** * *
53845842 TTATTACTTTTTAATAAAC
1 TTATTAAAGTAAAATAGAG
*
53845861 TTGTTAAAGTAAAATAGAG
1 TTATTAAAGTAAAATAGAG
53845880 TTATT
1 TTATT
53845885 GCTTAATTAG
Statistics
Matches: 27, Mismatches: 16, Indels: 0
0.63 0.37 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.44, C:0.03, G:0.11, T:0.42
Consensus pattern (19 bp):
TTATTAAAGTAAAATAGAG
Found at i:53852503 original size:21 final size:21
Alignment explanation
Indices: 53852477--53852517 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
53852467 ATCTGCTCAA
* *
53852477 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
53852498 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
53852518 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:53858239 original size:31 final size:31
Alignment explanation
Indices: 53858204--53858269 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
53858194 AACAGCCTAT
*
53858204 TGACTTAAATAAAAACTTTTAAATAGTTCAG
1 TGACTTAAATAAAAACTTTCAAATAGTTCAG
*
53858235 TGACTTAAATGAAAACTTTCAAATAGTTCAG
1 TGACTTAAATAAAAACTTTCAAATAGTTCAG
53858266 TGAC
1 TGAC
53858270 CGGATTGTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTCAAATAGTTCAG
Found at i:53864963 original size:79 final size:79
Alignment explanation
Indices: 53864832--53864989 Score: 280
Period size: 79 Copynumber: 2.0 Consensus size: 79
53864822 TAATAATTGT
* *
53864832 TGATTATTTGAGCAGGCCTTATGGATAGAGGTAAAAAGCCTCTAAAAGAAATAGTTGATGAATGG
1 TGATTATTTGAGCAGGCCTCATGGATAGAGGTAAAAAGCATCTAAAAGAAATAGTTGATGAATGG
53864897 ACTACTGTTCATAA
66 ACTACTGTTCATAA
*
53864911 TGATTATTTGAGCAGGCCTCATGGATAGAGGTAAAAAGCATCTAAAAGAAATAGTTGGTGAATGG
1 TGATTATTTGAGCAGGCCTCATGGATAGAGGTAAAAAGCATCTAAAAGAAATAGTTGATGAATGG
*
53864976 ACTACTGTTTATAA
66 ACTACTGTTCATAA
53864990 AAAAAACCAA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
79 75 1.00
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (79 bp):
TGATTATTTGAGCAGGCCTCATGGATAGAGGTAAAAAGCATCTAAAAGAAATAGTTGATGAATGG
ACTACTGTTCATAA
Found at i:53872216 original size:18 final size:19
Alignment explanation
Indices: 53872193--53872229 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
53872183 TGATTTAAGT
53872193 CTAAATT-TTTAATTTCTC
1 CTAAATTATTTAATTTCTC
*
53872211 CTAAATTATTTACTTTCTC
1 CTAAATTATTTAATTTCTC
53872230 TTCTACCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.27, C:0.19, G:0.00, T:0.54
Consensus pattern (19 bp):
CTAAATTATTTAATTTCTC
Found at i:53873059 original size:31 final size:31
Alignment explanation
Indices: 53873024--53873089 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
53873014 AACAGCCTAT
*
53873024 TGACTTAAATAAAAACTTTTAAATAGTTCAG
1 TGACTTAAATAAAAACTTTCAAATAGTTCAG
*
53873055 TGACTTAAATGAAAACTTTCAAATAGTTCAG
1 TGACTTAAATAAAAACTTTCAAATAGTTCAG
53873086 TGAC
1 TGAC
53873090 CGGATTGTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTCAAATAGTTCAG
Found at i:53880465 original size:16 final size:16
Alignment explanation
Indices: 53880440--53880480 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
53880430 TATTGTGGTA
*
53880440 AATA-TGTTAATA-AT
1 AATAGTGTTAACAGAT
53880454 AATAGCTGTTAACAGAT
1 AATAG-TGTTAACAGAT
53880471 AATAGTGTTA
1 AATAGTGTTA
53880481 TGAGTAGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 4 0.17
16 12 0.52
17 7 0.30
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.37
Consensus pattern (16 bp):
AATAGTGTTAACAGAT
Found at i:53886097 original size:39 final size:39
Alignment explanation
Indices: 53886044--53886131 Score: 117
Period size: 39 Copynumber: 2.3 Consensus size: 39
53886034 GGATCAACCA
**
53886044 TTCTCAT-CACTAGCTAGCCACTT-GCTCTTGTTGGAAGG
1 TTCTCATCCACTAGCTAGCCA-TTCGCTCTTGCCGGAAGG
*
53886082 TTCTCATCCACTAGCTAGCCATTCGTTCTTGCCGGAAGG
1 TTCTCATCCACTAGCTAGCCATTCGCTCTTGCCGGAAGG
*
53886121 TTCTCGTCCAC
1 TTCTCATCCAC
53886132 CCATTCTTCA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
38 9 0.20
39 35 0.80
ACGTcount: A:0.17, C:0.31, G:0.19, T:0.33
Consensus pattern (39 bp):
TTCTCATCCACTAGCTAGCCATTCGCTCTTGCCGGAAGG
Found at i:53886618 original size:19 final size:19
Alignment explanation
Indices: 53886594--53886634 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
53886584 AACCCAGAAA
53886594 AATTATAAAATAATAATAT
1 AATTATAAAATAATAATAT
* *
53886613 AATTATGAAATAATAATTT
1 AATTATAAAATAATAATAT
53886632 AAT
1 AAT
53886635 CCCTCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
AATTATAAAATAATAATAT
Found at i:53888948 original size:23 final size:23
Alignment explanation
Indices: 53888930--53888983 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
53888920 GGTATACACG
53888930 TACATAATAAAAATATATACTAA
1 TACATAATAAAAATATATACTAA
* **
53888953 TACATAATAATAATA-ATGGTAA
1 TACATAATAAAAATATATACTAA
53888975 TAC-TAATAA
1 TACATAATAA
53888984 TACTAATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 6 0.21
22 8 0.29
23 14 0.50
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.31
Consensus pattern (23 bp):
TACATAATAAAAATATATACTAA
Found at i:53888964 original size:3 final size:3
Alignment explanation
Indices: 53888933--53889003 Score: 54
Period size: 3 Copynumber: 23.3 Consensus size: 3
53888923 ATACACGTAC
* * * * *
53888933 ATA ATA AAA ATA TATA CTA ATA CATA ATA ATA ATA ATG GTA ATA CTA
1 ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* *
53888980 ATA ATA CTA ATA AT- ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
53889004 CAAGGATATT
Statistics
Matches: 51, Mismatches: 14, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
2 2 0.04
3 43 0.84
4 6 0.12
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:53889490 original size:18 final size:18
Alignment explanation
Indices: 53889463--53889500 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
53889453 AAAGAAAAAA
*
53889463 AGAAGAGAGAGGGAAGAG
1 AGAAGAGAGAGAGAAGAG
*
53889481 AGAAGGGAGAGAGAAGAG
1 AGAAGAGAGAGAGAAGAG
53889499 AG
1 AG
53889501 GGGAATCCGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (18 bp):
AGAAGAGAGAGAGAAGAG
Found at i:53889495 original size:11 final size:12
Alignment explanation
Indices: 53889464--53889496 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
53889454 AAGAAAAAAA
53889464 GAAGAGAG-AGG
1 GAAGAGAGAAGG
53889475 GAAGAGAGAAGG
1 GAAGAGAGAAGG
53889487 G-AGAGAGAAG
1 GAAGAGAGAAG
53889497 AGAGGGGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (12 bp):
GAAGAGAGAAGG
Found at i:53890936 original size:10 final size:10
Alignment explanation
Indices: 53890909--53890969 Score: 54
Period size: 10 Copynumber: 5.9 Consensus size: 10
53890899 ACGTCAGTAA
53890909 TTAAATAATTT
1 TTAAA-AATTT
*
53890920 TT-TAAATTT
1 TTAAAAATTT
53890929 TTAAAAATTT
1 TTAAAAATTT
53890939 TTAAAAA-TT
1 TTAAAAATTT
*
53890948 ATAAAATTTATTT
1 TTAAAA---ATTT
53890961 TTAAAAATT
1 TTAAAAATT
53890970 AAAAAGTATA
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
9 14 0.34
10 17 0.41
11 2 0.05
12 1 0.02
13 7 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TTAAAAATTT
Found at i:53890972 original size:29 final size:30
Alignment explanation
Indices: 53890925--53890983 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 30
53890915 AATTTTTTAA
*
53890925 ATTTTTAAAAATTTTTAAAAATTATAAAATTT
1 ATTTTTAAAAA--TTTAAAAAGTATAAAATTT
53890957 ATTTTTAAAAA-TTAAAAAGTATAAAAT
1 ATTTTTAAAAATTTAAAAAGTATAAAAT
53890984 CATAAAGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 15 0.58
32 11 0.42
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (30 bp):
ATTTTTAAAAATTTAAAAAGTATAAAATTT
Found at i:53896451 original size:31 final size:30
Alignment explanation
Indices: 53896414--53896497 Score: 87
Period size: 31 Copynumber: 2.7 Consensus size: 30
53896404 TGGGAGGGTC
*
53896414 TAATTAAAATTTCAAAAAATTTTAAAGGGCT
1 TAATTAAAATTTC-AAAAATTTTAAAGGGCA
* *
53896445 TAATTAAAATTTTCAAATATTTTGAAGGGCA
1 TAATTAAAA-TTTCAAAAATTTTAAAGGGCA
** *
53896476 TAAAGAAAATTTCCCAAAATTT
1 TAATTAAAATTT-CAAAAATTT
53896498 GCGATAGGGG
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
30 3 0.07
31 37 0.84
32 4 0.09
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (30 bp):
TAATTAAAATTTCAAAAATTTTAAAGGGCA
Found at i:53905038 original size:13 final size:13
Alignment explanation
Indices: 53904999--53905048 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
53904989 AGTTCTTAAT
53904999 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
53905012 TGC-TGTGAAAAAG
1 TGCTTTTG-AAAAG
*
53905025 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
*
53905038 T-ATTTTGAAAA
1 TGCTTTTGAAAA
53905049 TTTTGAGTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
12 11 0.37
13 16 0.53
14 3 0.10
ACGTcount: A:0.34, C:0.06, G:0.24, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:53905046 original size:26 final size:26
Alignment explanation
Indices: 53904999--53905048 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
53904989 AGTTCTTAAT
*
53904999 TGCTTTTGAAAAGTGCTGTGAAAAAG
1 TGCTTTTGAAAAGTACTGTGAAAAAG
* * *
53905025 TGCTTTTGAGAAGTATTTTGAAAA
1 TGCTTTTGAAAAGTACTGTGAAAA
53905049 TTTTGAGTGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.34, C:0.06, G:0.24, T:0.36
Consensus pattern (26 bp):
TGCTTTTGAAAAGTACTGTGAAAAAG
Found at i:53905243 original size:26 final size:30
Alignment explanation
Indices: 53905211--53905269 Score: 88
Period size: 27 Copynumber: 2.1 Consensus size: 30
53905201 TTATAACTTG
*
53905211 TTTTTAATATTT-TAA-TAA-TAATATTAA
1 TTTTAAATATTTCTAAGTAATTAATATTAA
53905238 TTTTAAATATTTCTAAGTAATTAATATTAA
1 TTTTAAATATTTCTAAGTAATTAATATTAA
53905268 TT
1 TT
53905270 ATTTATTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 11 0.39
28 3 0.11
29 3 0.11
30 11 0.39
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (30 bp):
TTTTAAATATTTCTAAGTAATTAATATTAA
Found at i:53910009 original size:21 final size:22
Alignment explanation
Indices: 53909964--53910014 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
53909954 TTTGAACCGT
* *
53909964 TACCAATTCGTACCAAATACCA
1 TACCATTTCATACCAAATACCA
*
53909986 TACCATTTCATACC-AATTCCA
1 TACCATTTCATACCAAATACCA
53910007 TACCATTT
1 TACCATTT
53910015 TGTACTAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.35, C:0.31, G:0.02, T:0.31
Consensus pattern (22 bp):
TACCATTTCATACCAAATACCA
Found at i:53911413 original size:23 final size:23
Alignment explanation
Indices: 53911387--53911432 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
53911377 AGAAGTGAGC
*
53911387 AAAAAAAGAAAAAAAAGTAAAAA
1 AAAAAAACAAAAAAAAGTAAAAA
* *
53911410 AAAAGAACAAAAAAAAGTGAAAA
1 AAAAAAACAAAAAAAAGTAAAAA
53911433 GTCTTGTGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.83, C:0.02, G:0.11, T:0.04
Consensus pattern (23 bp):
AAAAAAACAAAAAAAAGTAAAAA
Found at i:53916036 original size:10 final size:10
Alignment explanation
Indices: 53916021--53916082 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
53916011 TTTGAACCGT
*
53916021 TACCAATTCG
1 TACCAATTCA
*
53916031 TACCAAATACCA
1 TACC-AAT-TCA
*
53916043 TACCATTTCA
1 TACCAATTCA
53916053 TACCAATTCCA
1 TACCAATT-CA
* *
53916064 TACCATTTCG
1 TACCAATTCA
53916074 TACCAATTC
1 TACCAATTC
53916083 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:53916066 original size:21 final size:21
Alignment explanation
Indices: 53916021--53916083 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
53916011 TTTGAACCGT
* *
53916021 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
53916043 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
53916064 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
53916084 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:53918140 original size:18 final size:18
Alignment explanation
Indices: 53918119--53918153 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
53918109 TTTTTCTTTT
53918119 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
53918137 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
53918154 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:53919068 original size:16 final size:15
Alignment explanation
Indices: 53919049--53919101 Score: 67
Period size: 16 Copynumber: 3.6 Consensus size: 15
53919039 TTTAACTTGA
53919049 TTTTTTTTGCTCACCT
1 TTTTTTTTGCTCA-CT
53919065 TTTTTTTTGCTCGA-T
1 TTTTTTTTGCTC-ACT
53919080 TTTTTTTT--TCACT
1 TTTTTTTTGCTCACT
53919093 TTTTTTTTG
1 TTTTTTTTG
53919102 AATTTTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
12 1 0.03
13 11 0.32
15 9 0.26
16 12 0.35
17 1 0.03
ACGTcount: A:0.06, C:0.15, G:0.08, T:0.72
Consensus pattern (15 bp):
TTTTTTTTGCTCACT
Found at i:53919070 original size:30 final size:29
Alignment explanation
Indices: 53919029--53919100 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 29
53919019 GCAAGACTTT
*
53919029 TCACTTTTTTTTTAACTTGATTTTTTTTGC
1 TCACTTTTTTTTTAACTCGATTTTTTTT-C
* *
53919059 TCACCTTTTTTTTT-GCTCGATTTTTTTTT
1 TCA-CTTTTTTTTTAACTCGATTTTTTTTC
53919088 TCACTTTTTTTTT
1 TCACTTTTTTTTT
53919101 GAATTTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 10 0.26
29 3 0.08
30 15 0.39
31 10 0.26
ACGTcount: A:0.10, C:0.15, G:0.06, T:0.69
Consensus pattern (29 bp):
TCACTTTTTTTTTAACTCGATTTTTTTTC
Found at i:53919108 original size:13 final size:13
Alignment explanation
Indices: 53919078--53919143 Score: 62
Period size: 13 Copynumber: 4.9 Consensus size: 13
53919068 TTTTTGCTCG
*
53919078 ATTTTTTTTTT-C
1 ATTTTTTTTTTGA
*
53919090 ACTTTTTTTTTGA
1 ATTTTTTTTTTGA
*
53919103 ATTTTTTTTTCAATCA
1 ATTTTTTTTT---TGA
*
53919119 ATTTTTTTTTCGA
1 ATTTTTTTTTTGA
53919132 ATTTTTTTTTTG
1 ATTTTTTTTTTG
53919144 TTACTCCAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
12 10 0.23
13 21 0.49
16 12 0.28
ACGTcount: A:0.15, C:0.08, G:0.05, T:0.73
Consensus pattern (13 bp):
ATTTTTTTTTTGA
Found at i:53919111 original size:29 final size:29
Alignment explanation
Indices: 53919026--53919142 Score: 78
Period size: 28 Copynumber: 4.0 Consensus size: 29
53919016 CTCGCAAGAC
*
53919026 TTTTCACTTTTTTTTT-AACTTGATTTTTTT
1 TTTTCACTTTTTTTTTGAA-TT-TTTTTTTT
** * ***
53919056 TGCTCACCTTTTTTTTTG-CTCGATTTTTT
1 TTTTCA-CTTTTTTTTTGAATTTTTTTTTT
53919085 TTTTCACTTTTTTTTTGAA-TTTTTTTTT
1 TTTTCACTTTTTTTTTGAATTTTTTTTTT
*** *
53919113 CAATCAATTTTTTTTTCGAATTTTTTTTTT
1 TTTTCACTTTTTTTTT-GAATTTTTTTTTT
53919143 GTTACTCCAA
Statistics
Matches: 66, Mismatches: 16, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
28 29 0.44
29 13 0.20
30 14 0.21
31 10 0.15
ACGTcount: A:0.13, C:0.12, G:0.05, T:0.70
Consensus pattern (29 bp):
TTTTCACTTTTTTTTTGAATTTTTTTTTT
Found at i:53920515 original size:11 final size:10
Alignment explanation
Indices: 53920490--53920550 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
53920480 ACCAATAAAA
53920490 TAAA-TGAGC
1 TAAATTGAGC
*
53920499 TGAATTGTAGC
1 TAAATTG-AGC
53920510 TAAATTGAGC
1 TAAATTGAGC
**
53920520 TCGATTGAGC
1 TAAATTGAGC
53920530 TGAAA-TGAGC
1 T-AAATTGAGC
*
53920540 TCAATTGAGC
1 TAAATTGAGC
53920550 T
1 T
53920551 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:53920551 original size:20 final size:20
Alignment explanation
Indices: 53920491--53920551 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
53920481 CCAATAAAAT
*
53920491 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
53920511 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
53920532 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
53920552 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:53922742 original size:24 final size:24
Alignment explanation
Indices: 53922715--53922774 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
53922705 AAAGAGATAT
53922715 ATATGTATATAACTATAAATTA-AA
1 ATATGTATATAAC-ATAAATTACAA
* *
53922739 ATATGTGTGTATACATAAATTACAA
1 ATATGTATATA-ACATAAATTACAA
*
53922764 AT-TATATATAA
1 ATATGTATATAA
53922775 AGTATATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
23 1 0.03
24 22 0.76
25 6 0.21
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (24 bp):
ATATGTATATAACATAAATTACAA
Found at i:53922825 original size:18 final size:18
Alignment explanation
Indices: 53922804--53922838 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53922794 AGAAAGAAAG
*
53922804 AAATATGTATATATATAA
1 AAATATGTACATATATAA
*
53922822 AAATGTGTACATATATA
1 AAATATGTACATATATA
53922839 TATAGGTGTA
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:0.51, C:0.03, G:0.09, T:0.37
Consensus pattern (18 bp):
AAATATGTACATATATAA
Found at i:53923217 original size:3 final size:3
Alignment explanation
Indices: 53923206--53923255 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
53923196 CAATAATACC
* * *
53923206 AAT ACT AAT AAT AGT AA- AGAT AAT AGT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
53923251 AAT AA
1 AAT AA
53923256 GACTAGATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 1 0.03
3 37 0.95
4 1 0.03
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:53923240 original size:12 final size:12
Alignment explanation
Indices: 53923211--53923254 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
53923201 ATACCAATAC
53923211 TAATAATAGTAA
1 TAATAATAGTAA
53923223 -AGATAATAGTAA
1 TA-ATAATAGTAA
*
53923235 TAATAATAATAA
1 TAATAATAGTAA
53923247 TAATAATA
1 TAATAATA
53923255 AGACTAGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 1 0.03
12 27 0.93
13 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (12 bp):
TAATAATAGTAA
Found at i:53925381 original size:17 final size:18
Alignment explanation
Indices: 53925352--53925387 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
53925342 AAAGAAATTG
53925352 TGGGAATTTCTTTTTCCC
1 TGGGAATTTCTTTTTCCC
53925370 TGGGAA-TTCTTTTTCCC
1 TGGGAATTTCTTTTTCCC
53925387 T
1 T
53925388 TTTTGTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.11, C:0.22, G:0.17, T:0.50
Consensus pattern (18 bp):
TGGGAATTTCTTTTTCCC
Found at i:53932121 original size:27 final size:28
Alignment explanation
Indices: 53932091--53932144 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
53932081 CTTTAGATAA
*
53932091 TTATA-TGGATATCATTCTAATATTTCC
1 TTATAGTGGATATCATTATAATATTTCC
*
53932118 TTATATGTGGATATCATTATGATATTT
1 TTATA-GTGGATATCATTATAATATTT
53932145 TCTTTTACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 5 0.22
29 18 0.78
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.50
Consensus pattern (28 bp):
TTATAGTGGATATCATTATAATATTTCC
Found at i:53932325 original size:24 final size:23
Alignment explanation
Indices: 53932298--53932342 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
53932288 CGAATAAAAA
*
53932298 TTATAGGATTTGAAATTTTATAAC
1 TTAT-GGATTTGAAAATTTATAAC
* *
53932322 TTATGGTTTTTAAAATTTATA
1 TTATGGATTTGAAAATTTATA
53932343 GAAATTTCCA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.51
Consensus pattern (23 bp):
TTATGGATTTGAAAATTTATAAC
Found at i:53934709 original size:23 final size:22
Alignment explanation
Indices: 53934675--53934723 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
53934665 AGAAATATAT
* *
53934675 AAAAATACATAA-ATATTTTCAA
1 AAAAATAAATAATAAATTTT-AA
53934697 AAAAATATAATAATAAATTTTAA
1 AAAAATA-AATAATAAATTTTAA
53934720 AAAA
1 AAAA
53934724 TATTACTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 7 0.30
23 10 0.43
24 6 0.26
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAAATAAATAATAAATTTTAA
Found at i:53934781 original size:16 final size:17
Alignment explanation
Indices: 53934760--53934796 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
53934750 TAAATTTTAA
*
53934760 AAATATAAAAATA-AAT
1 AAATATAAAAACATAAT
53934776 AAATATAAAAACATAAT
1 AAATATAAAAACATAAT
53934793 AAAT
1 AAAT
53934797 TTATTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATATAAAAACATAAT
Found at i:53934816 original size:6 final size:6
Alignment explanation
Indices: 53934805--53934846 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
53934795 ATTTATTTTT
53934805 TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA
1 TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA
53934847 ATAAAATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TATTAA
Found at i:53934855 original size:18 final size:18
Alignment explanation
Indices: 53934805--53934851 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
53934795 ATTTATTTTT
*
53934805 TATTAATATTAATATTAA
1 TATTAATATAAATATTAA
*
53934823 TATTAATATTAATATTAA
1 TATTAATATAAATATTAA
53934841 TATTAA-ATAAA
1 TATTAATATAAA
53934852 ATATAATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 4 0.14
18 24 0.86
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTAATATAAATATTAA
Found at i:53935242 original size:9 final size:9
Alignment explanation
Indices: 53935224--53935263 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
53935214 TTTGGTTAAA
53935224 AATTAACCG
1 AATTAACCG
*
53935233 AATTACCCG
1 AATTAACCG
53935242 AATTAACCG
1 AATTAACCG
*
53935251 AATTACCCG
1 AATTAACCG
53935260 AATT
1 AATT
53935264 GAATCACAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:53935247 original size:18 final size:18
Alignment explanation
Indices: 53935224--53935263 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
53935214 TTTGGTTAAA
53935224 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
53935242 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
53935260 AATT
1 AATT
53935264 GAATCACAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:53935377 original size:6 final size:6
Alignment explanation
Indices: 53935303--53935361 Score: 118
Period size: 6 Copynumber: 9.8 Consensus size: 6
53935293 ACTTTTAGAC
53935303 TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT
1 TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT
53935351 TTTAGT TTTAG
1 TTTAGT TTTAG
53935362 GATTTTATTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (6 bp):
TTTAGT
Found at i:53935425 original size:13 final size:13
Alignment explanation
Indices: 53935407--53935431 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53935397 TTATGATTGG
53935407 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
53935420 ATTGGGTTGGGT
1 ATTGGGTTGGGT
53935432 TGAATACTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:53936535 original size:25 final size:25
Alignment explanation
Indices: 53936507--53936555 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
53936497 ATAAATTGAA
53936507 TTTGTATTCAAATCCTATTCTCTCT
1 TTTGTATTCAAATCCTATTCTCTCT
53936532 TTTGTATTCAAATCCTATTCTCTC
1 TTTGTATTCAAATCCTATTCTCTC
53936556 AGTTCTGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.20, C:0.24, G:0.04, T:0.51
Consensus pattern (25 bp):
TTTGTATTCAAATCCTATTCTCTCT
Found at i:53954192 original size:31 final size:31
Alignment explanation
Indices: 53954164--53954233 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
53954154 CTATTAAAGG
53954164 TTTTGGAAGACCTAATTAAAAT-TTTTAAAAA
1 TTTTGGAAGACCTAATTAAAATCTTTT-AAAA
* * * *
53954195 TTATGGAGGATCTAATTAAAATCTTCTAAAA
1 TTTTGGAAGACCTAATTAAAATCTTTTAAAA
53954226 TTTTGGAA
1 TTTTGGAA
53954234 AGCTTAGTGA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
31 29 0.91
32 3 0.09
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (31 bp):
TTTTGGAAGACCTAATTAAAATCTTTTAAAA
Found at i:53954287 original size:31 final size:29
Alignment explanation
Indices: 53954175--53954318 Score: 107
Period size: 31 Copynumber: 4.8 Consensus size: 29
53954165 TTTGGAAGAC
53954175 CTAATTAAAATTTTT-AAAAATTATGGAGG
1 CTAATTAAAATTTTTAAAAAATT-TGGAGG
* * *
53954204 ATCTAATTAAAATCTTCT-AAAATTTTGGAAAG
1 --CTAATTAAAAT-TTTTAAAAAATTTGG-AGG
* * * *
53954236 CTTAGTGAGAATTTTCAAAAAATTTGGAGG
1 C-TAATTAAAATTTTTAAAAAATTTGGAGG
*
53954266 TCTAATTAAAATTTTTAAAAAAATTAGGA-G
1 -CTAATTAAAATTTTT-AAAAAATTTGGAGG
53954296 CTAATTAAAA-TTTTAAATAAATT
1 CTAATTAAAATTTTTAAA-AAATT
53954319 AACAAAAACT
Statistics
Matches: 91, Mismatches: 15, Indels: 17
0.74 0.12 0.14
Matches are distributed among these distances:
27 3 0.03
28 9 0.10
29 10 0.11
30 16 0.18
31 42 0.46
32 11 0.12
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.38
Consensus pattern (29 bp):
CTAATTAAAATTTTTAAAAAATTTGGAGG
Found at i:53957813 original size:15 final size:16
Alignment explanation
Indices: 53957774--53957814 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
53957764 ATATATTAAG
53957774 TTATATAAATTTGAAAA
1 TTATATAAA-TTGAAAA
53957791 TTCA-ATAAA-TGAAAA
1 TT-ATATAAATTGAAAA
53957806 TTATATAAA
1 TTATATAAA
53957815 ATTAAACACA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.05
15 13 0.59
17 7 0.32
18 1 0.05
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (16 bp):
TTATATAAATTGAAAA
Found at i:53961341 original size:24 final size:24
Alignment explanation
Indices: 53961314--53961369 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
53961304 CATTTAATAA
*
53961314 AATAAAAATTGTTTTTA-ATATTTT
1 AATAAAAATTATTTTTATAT-TTTT
*
53961338 AATAGTAAATTATTTTTATATTTTT
1 AATA-AAAATTATTTTTATATTTTT
53961363 AATAAAA
1 AATAAAA
53961370 TAGAAGTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 6 0.22
25 19 0.70
26 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (24 bp):
AATAAAAATTATTTTTATATTTTT
Found at i:53961353 original size:25 final size:25
Alignment explanation
Indices: 53961319--53961366 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
53961309 AATAAAATAA
*
53961319 AAATTGTTTTTA-ATATTTTAATAGT
1 AAATTATTTTTATAT-TTTTAATAGT
53961344 AAATTATTTTTATATTTTTAATA
1 AAATTATTTTTATATTTTTAATA
53961367 AAATAGAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (25 bp):
AAATTATTTTTATATTTTTAATAGT
Found at i:53964171 original size:126 final size:124
Alignment explanation
Indices: 53963944--53964341 Score: 503
Period size: 126 Copynumber: 3.2 Consensus size: 124
53963934 TAAGGCCAAA
* *
53963944 CAGGAACTACTGTAGAAAAAGAGCGTCTACGTGGGAGCTTTTTTCATCAATTTTACTGACAGTGC
1 CAGGAACTACTGTAGAAAAAGAGCGTCCACGT-GGAGCTTTTTTCAT-AATTTTGCTGACAGTGC
*
53964009 ATCCTGCTTAAAGCA-TTTTTGACACCATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTT
64 ATCCTGCTTGAAG-AGTTTTTGACACCATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTT
* * * * *
53964070 TAGGAACTACTATAGAAAAAGAGTGTCCACGTAGGAGCTTTTTTCAGTATTTTTGCTGATAGTGC
1 CAGGAACTACTGTAGAAAAAGAGCGTCCACGT-GGAGCTTTTTTCA-TAATTTTGCTGACAGTGC
* * * *
53964135 ATCCTGCTTGAAGAGTTTTTGACACCATTTGCTCAGAACTGTCTTTTCAGAATTATTTTTT
64 ATCCTGCTTGAAGAGTTTTTGACACCATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTT
* *
53964196 CAGGAACTACTGTAGAAAAAGAGCATCCACGTGGTAGCTTTTTTTAATAATTTTGCTGACAGTGC
1 CAGGAACTACTGTAGAAAAAGAGCGTCCACGTGG-AGC-TTTTTTCATAATTTTGCTGACAGTGC
* * * ** * * *
53964261 ATCCTGTTTGAAGTGTTTTTGGCATTATCTT-TTCAGAATCATCTTCTTAAAATTATTTTTT
64 ATCCTGCTTGAAGAGTTTTTGACACCAT-TTGTTCAGAACCGTCTTCTCAAAATTATTTTTT
*
53964322 CAAGAACTACTGTAGAAAAA
1 CAGGAACTACTGTAGAAAAA
53964342 AAAATCCTTA
Statistics
Matches: 234, Mismatches: 33, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
125 3 0.01
126 221 0.94
127 10 0.04
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.37
Consensus pattern (124 bp):
CAGGAACTACTGTAGAAAAAGAGCGTCCACGTGGAGCTTTTTTCATAATTTTGCTGACAGTGCAT
CCTGCTTGAAGAGTTTTTGACACCATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTT
Found at i:53964449 original size:34 final size:34
Alignment explanation
Indices: 53964410--53964527 Score: 125
Period size: 34 Copynumber: 3.4 Consensus size: 34
53964400 TAAGAAAAAA
*
53964410 CTAAACCATAATTTAATTAATTTTCTTAAAAACC
1 CTAAACCTTAATTTAATTAATTTTCTTAAAAACC
* **
53964444 CTAAACCTTAATTTAATTAATTTAAAC-CCAAAACC
1 CTAAACCTTAATTTAATTAATTT--TCTTAAAAACC
*
53964479 CAAAAACC-TAATTTAATTAATTTT-TTAAAAAACC
1 C-TAAACCTTAATTTAATTAATTTTCTT-AAAAACC
*
53964513 TTAAACCTTAATTTA
1 CTAAACCTTAATTTA
53964528 TTCCTTAAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
33 5 0.07
34 35 0.51
35 22 0.32
36 6 0.09
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (34 bp):
CTAAACCTTAATTTAATTAATTTTCTTAAAAACC
Found at i:53964602 original size:15 final size:16
Alignment explanation
Indices: 53964569--53964603 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
53964559 ACAAAACCTT
*
53964569 AACCCTAAACCCTAAA
1 AACCCTAAACCCAAAA
53964585 AACCCTAAA-CCAAAA
1 AACCCTAAACCCAAAA
53964600 AACC
1 AACC
53964604 TTAGGGACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.54, C:0.37, G:0.00, T:0.09
Consensus pattern (16 bp):
AACCCTAAACCCAAAA
Found at i:53968403 original size:9 final size:9
Alignment explanation
Indices: 53968389--53968454 Score: 98
Period size: 9 Copynumber: 7.4 Consensus size: 9
53968379 GTAGTGATTC
53968389 AATTCGGTT
1 AATTCGGTT
53968398 AATTCGGTT
1 AATTCGGTT
*
53968407 AATTCGGGT
1 AATTCGGTT
53968416 AATTCGGTT
1 AATTCGGTT
*
53968425 AATTCGGGT
1 AATTCGGTT
*
53968434 AATCCGG-T
1 AATTCGGTT
53968442 AATTCGGTT
1 AATTCGGTT
53968451 AATT
1 AATT
53968455 TTTAACCAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
8 7 0.14
9 44 0.86
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.39
Consensus pattern (9 bp):
AATTCGGTT
Found at i:53970745 original size:14 final size:14
Alignment explanation
Indices: 53970718--53970754 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
53970708 TCTCAACCTG
53970718 TAAATCTT--ACCC
1 TAAATCTTAAACCC
53970730 TAAATCTTAAACCC
1 TAAATCTTAAACCC
*
53970744 TAAATATTAAA
1 TAAATCTTAAA
53970755 GTAGTGGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 8 0.36
14 14 0.64
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
TAAATCTTAAACCC
Found at i:53971058 original size:38 final size:37
Alignment explanation
Indices: 53971023--53971131 Score: 168
Period size: 38 Copynumber: 2.9 Consensus size: 37
53971013 TAAAAAAATT
53971023 TATTTTAAAATATTTTAAAATTAAAAAAATTAAAAAG
1 TATTTTAAAATATTTTAAAATTAAAAAAATTAAAAAG
53971060 TATTTTAAAAATATTTTAAAATTAAAAAAATTTAAAAAG
1 TATTTT-AAAATATTTTAAAATTAAAAAAA-TTAAAAAG
* *
53971099 TATTTTAAAAT-TTTAAAAAATAAAAAAA-TAAAA
1 TATTTTAAAATATTTTAAAATTAAAAAAATTAAAA
53971132 TAATTTATTA
Statistics
Matches: 68, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
35 5 0.07
37 21 0.31
38 28 0.41
39 14 0.21
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (37 bp):
TATTTTAAAATATTTTAAAATTAAAAAAATTAAAAAG
Found at i:53971074 original size:11 final size:12
Alignment explanation
Indices: 53971052--53971080 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
53971042 ATTAAAAAAA
53971052 TTAAAAAGTATT
1 TTAAAAAGTATT
53971064 TTAAAAA-TATT
1 TTAAAAAGTATT
53971075 TTAAAA
1 TTAAAA
53971081 TTAAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (12 bp):
TTAAAAAGTATT
Found at i:53971086 original size:28 final size:29
Alignment explanation
Indices: 53971048--53971119 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 29
53971038 TAAAATTAAA
* *
53971048 AAAATTAAAAAGTATTTTAAAAA-TATTTT
1 AAAATTAAAAA-AAATTTAAAAAGTATTTT
53971077 AAAATT-AAAAAAATTTAAAAAGTATTTT
1 AAAATTAAAAAAAATTTAAAAAGTATTTT
**
53971105 AAAATTTTAAAAAAT
1 AAAATTAAAAAAAAT
53971120 AAAAAAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 9 0.24
28 16 0.42
29 13 0.34
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (29 bp):
AAAATTAAAAAAAATTTAAAAAGTATTTT
Found at i:53976143 original size:54 final size:54
Alignment explanation
Indices: 53976084--53976191 Score: 189
Period size: 54 Copynumber: 2.0 Consensus size: 54
53976074 ATTTCGAATT
* *
53976084 GTTATCAATGTCAACCATAGTTTATATGTTTCAGAAAATGAGATAATATGGTTA
1 GTTATCAATGTCAACCATAGTTTATATGATTCAGAAAATGAAATAATATGGTTA
*
53976138 GTTATCAATGTCAACCATAGTTTGTATGATTCAGAAAATGAAATAATATGGTTA
1 GTTATCAATGTCAACCATAGTTTATATGATTCAGAAAATGAAATAATATGGTTA
53976192 ACCAAATGCT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (54 bp):
GTTATCAATGTCAACCATAGTTTATATGATTCAGAAAATGAAATAATATGGTTA
Found at i:53990047 original size:14 final size:14
Alignment explanation
Indices: 53990016--53990075 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
53990006 TGATTTTAGT
* **
53990016 ATATTTGATATATT
1 ATATTTTATATAAA
53990030 ATATTTTATATAAA
1 ATATTTTATATAAA
53990044 ATATTTT-T-TAAA
1 ATATTTTATATAAA
53990056 ATTATTTTTATATAAA
1 A-TA-TTTTATATAAA
53990072 ATAT
1 ATAT
53990076 AATATTAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
12 5 0.13
13 3 0.08
14 23 0.59
15 3 0.08
16 5 0.13
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (14 bp):
ATATTTTATATAAA
Found at i:53990048 original size:28 final size:28
Alignment explanation
Indices: 53990016--53990075 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
53990006 TGATTTTAGT
*
53990016 ATATTTGAT-ATATTATATTTTATATAAA
1 ATATTTGATAAAATTAT-TTTTATATAAA
**
53990044 ATATTTTTTAAAATTATTTTTATATAAA
1 ATATTTGATAAAATTATTTTTATATAAA
53990072 ATAT
1 ATAT
53990076 AATATTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 22 0.79
29 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (28 bp):
ATATTTGATAAAATTATTTTTATATAAA
Found at i:53991895 original size:12 final size:12
Alignment explanation
Indices: 53991878--53991905 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
53991868 AAATACTTTT
53991878 AAATTAATAATA
1 AAATTAATAATA
53991890 AAATTAATAATA
1 AAATTAATAATA
53991902 AAAT
1 AAAT
53991906 AAAAGTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAATTAATAATA
Found at i:53992509 original size:24 final size:26
Alignment explanation
Indices: 53992452--53992510 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 26
53992442 CCTGAAAATT
53992452 TTAAAAAGAATATAAACTTTTATAAAA
1 TTAAAAA-AATATAAACTTTTATAAAA
* *
53992479 -TATAAAATTAT-AACTTTT-TAAAA
1 TTAAAAAAATATAAACTTTTATAAAA
53992502 TTAAAAAAA
1 TTAAAAAAA
53992511 ATATTTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
23 5 0.19
24 13 0.48
25 4 0.15
26 5 0.19
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (26 bp):
TTAAAAAAATATAAACTTTTATAAAA
Found at i:54002027 original size:21 final size:22
Alignment explanation
Indices: 54001986--54002027 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
54001976 TTATGAAAGA
54001986 AATTGGAAAATCTTGTGATGAT
1 AATTGGAAAATCTTGTGATGAT
54002008 AATTGGAATAAT-TT-TGATGA
1 AATTGGAA-AATCTTGTGATGA
54002028 AGAAGGTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 10 0.53
23 3 0.16
ACGTcount: A:0.38, C:0.02, G:0.21, T:0.38
Consensus pattern (22 bp):
AATTGGAAAATCTTGTGATGAT
Found at i:54019388 original size:23 final size:23
Alignment explanation
Indices: 54019345--54019389 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
54019335 CCTAAAAGTT
* *
54019345 TAAAAATTTAAAAGTTCAAGTAC
1 TAAAAATATAAAAGTTAAAGTAC
54019368 TAAAAATGATAAAA-TTAAAGTA
1 TAAAAAT-ATAAAAGTTAAAGTA
54019390 TAGAGATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.58, C:0.04, G:0.09, T:0.29
Consensus pattern (23 bp):
TAAAAATATAAAAGTTAAAGTAC
Found at i:54023507 original size:124 final size:128
Alignment explanation
Indices: 54023188--54023519 Score: 336
Period size: 124 Copynumber: 2.6 Consensus size: 128
54023178 CTTTGAACTT
*
54023188 AAAAAACTC-AAACTCGAAAAC-CTCCAAAATCCTAAAACAACTAAAACCCAAAATTACATGATC
1 AAAAAACTCAAAACTCGAAAACAC-CC-AAA-CTTAAAACAACTAAAACCCAAAATTACATGATC
* * * * * * * * *
54023251 TAAACCTGAATCAAGTTGTTATCTTTATACCTGCAAACAACATTCACACTCAAACTTTGAACTAC
63 TAAACCCGAATCAAATTGCTACCTTTATACATGCAAACAACACTAACACTCAAACTCTCAACTAC
54023316 A
128 A
* *** * * * *
54023317 AAAAAACTCAAAACTCGAAAATACTTGAACTTGAAACAATTAAAACCCAAAATTAAATTATCTAA
1 AAAAAACTCAAAACTCGAAAACACCCAAACTTAAAACAACTAAAACCCAAAATTACATGATCTAA
* ** *
54023382 ACCCGAATCAAATT-CTACCTTTATA-AT-TACCCAACACTAACACTCAAACTCTCAACTATA
66 ACCCGAATCAAATTGCTACCTTTATACATGCAAACAACACTAACACTCAAACTCTCAACTACA
* * * * *
54023442 AAAACATTC-AAAC-CAGAAAACACCCAAATTTAAAACAACTAAATCCCAAAATTACATGATATA
1 AAAAAACTCAAAACTC-GAAAACACCCAAACTTAAAACAACTAAAACCCAAAATTACATGATCTA
54023505 AACCCGAATCAAATT
65 AACCCGAATCAAATT
54023520 ACTATATTTA
Statistics
Matches: 165, Mismatches: 35, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
123 1 0.01
124 56 0.34
125 32 0.19
126 1 0.01
127 9 0.05
128 43 0.26
129 11 0.07
130 11 0.07
131 1 0.01
ACGTcount: A:0.48, C:0.24, G:0.04, T:0.23
Consensus pattern (128 bp):
AAAAAACTCAAAACTCGAAAACACCCAAACTTAAAACAACTAAAACCCAAAATTACATGATCTAA
ACCCGAATCAAATTGCTACCTTTATACATGCAAACAACACTAACACTCAAACTCTCAACTACA
Found at i:54023555 original size:125 final size:125
Alignment explanation
Indices: 54023188--54023557 Score: 372
Period size: 125 Copynumber: 2.9 Consensus size: 125
54023178 CTTTGAACTT
*
54023188 AAAAAACTC-AAACTCGAAAAC-CTCCAAAATCCTAAAACAACTAAAACCCAAAATTACATGATC
1 AAAAAACTCAAAACTCGAAAACAC-CC-AAA-CTTAAAACAACTAAAACCCAAAATTACATGATC
* * * * * * *
54023251 TAAACCTGAATCAAGTTGTTATCTTTATACCTGCAAACAACATTCACACTCAAACTTTGAACTAC
63 TAAACCCGAATCAAATT-CTATCTTTATACCT--ACACAACACTCACACTCAAACTCTCAACTAC
54023316 A
125 A
* *** * * * *
54023317 AAAAAACTCAAAACTCGAAAATACTTGAACTTGAAACAATTAAAACCCAAAATTAAATTATCTAA
1 AAAAAACTCAAAACTCGAAAACACCCAAACTTAAAACAACTAAAACCCAAAATTACATGATCTAA
* ** * * *
54023382 ACCCGAATCAAATTCTACCTTTATAATTACCCAACACTAACACTCAAACTCTCAACTATA
66 ACCCGAATCAAATTCTATCTTTATACCTACACAACACTCACACTCAAACTCTCAACTACA
* * * * *
54023442 AAAACATTC-AAAC-CAGAAAACACCCAAATTTAAAACAACTAAATCCCAAAATTACATGATATA
1 AAAAAACTCAAAACTC-GAAAACACCCAAACTTAAAACAACTAAAACCCAAAATTACATGATCTA
*
54023505 AACCCGAATCAAATTACTATATTTATACCTACACAACACTCACA-TCCAAACTC
65 AACCCGAATCAAATT-CTATCTTTATACCTACACAACACTCACACT-CAAACTC
54023558 GAGCAACTTA
Statistics
Matches: 195, Mismatches: 41, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
123 1 0.01
124 57 0.29
125 61 0.31
127 10 0.05
128 43 0.22
129 11 0.06
130 11 0.06
131 1 0.01
ACGTcount: A:0.48, C:0.25, G:0.04, T:0.23
Consensus pattern (125 bp):
AAAAAACTCAAAACTCGAAAACACCCAAACTTAAAACAACTAAAACCCAAAATTACATGATCTAA
ACCCGAATCAAATTCTATCTTTATACCTACACAACACTCACACTCAAACTCTCAACTACA
Found at i:54024527 original size:51 final size:51
Alignment explanation
Indices: 54024467--54024567 Score: 141
Period size: 51 Copynumber: 2.0 Consensus size: 51
54024457 GTTGTTAGAC
54024467 AGAATATGTAAATG-TTACGAGTTAAATTTGTTAAATCAAGACCAAATTGAT
1 AGAATATGTAAATGTTTACGAGTTAAATTTGTTAAA-CAAGACCAAATTGAT
** * * *
54024518 AGAATATGTAAATGTTTGTGGGTTAAATTTGTTAAACAATACCAATTTGA
1 AGAATATGTAAATGTTTACGAGTTAAATTTGTTAAACAAGACCAAATTGA
54024568 CACAATGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
51 26 0.59
52 18 0.41
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.36
Consensus pattern (51 bp):
AGAATATGTAAATGTTTACGAGTTAAATTTGTTAAACAAGACCAAATTGAT
Found at i:54024596 original size:51 final size:52
Alignment explanation
Indices: 54024464--54024598 Score: 125
Period size: 51 Copynumber: 2.6 Consensus size: 52
54024454 TGTGTTGTTA
* * *
54024464 GACAGAATATGTAAATG-TT-ACGAGTTAAATTTGTTAAATCAAGACCAAATT
1 GACACAATATGTAAATGTTTGAGGA-CTAAATTTGTTAAATCAAGACCAAATT
* * * ** * *
54024515 GATAGAATATGTAAATGTTTGTGGGTTAAATTTGTTAAA-CAATACCAATTT
1 GACACAATATGTAAATGTTTGAGGACTAAATTTGTTAAATCAAGACCAAATT
*
54024566 GACACAATGTGTAAAAT-TTTGAGGACTAAATTT
1 GACACAATATGT-AAATGTTTGAGGACTAAATTT
54024599 ATTATTATAC
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
51 48 0.70
52 20 0.29
53 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (52 bp):
GACACAATATGTAAATGTTTGAGGACTAAATTTGTTAAATCAAGACCAAATT
Found at i:54027147 original size:27 final size:28
Alignment explanation
Indices: 54027094--54027159 Score: 116
Period size: 27 Copynumber: 2.4 Consensus size: 28
54027084 TTTTTTTGGT
54027094 ATATTTTGGTAAATAAAAAAAAGATATA
1 ATATTTTGGTAAATAAAAAAAAGATATA
*
54027122 ATATTTTGGTAAAT-AAAAAAATATATA
1 ATATTTTGGTAAATAAAAAAAAGATATA
54027149 ATATTTTGGTA
1 ATATTTTGGTA
54027160 TTTTTTTATA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 23 0.62
28 14 0.38
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.38
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGATATA
Found at i:54029241 original size:3 final size:3
Alignment explanation
Indices: 54029233--54029352 Score: 84
Period size: 3 Copynumber: 39.7 Consensus size: 3
54029223 CAAAACTTAG
* * * * * *
54029233 ATT ATT ATT ATG ATT GTT ATT ATT GTC ATT ATT ATA ATC ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
54029281 ATGT -TT -TT ATTT ATT AAT ATT AAT ATTT ATT ATT ACT ATT ATT ATT
1 AT-T ATT ATT A-TT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT
* *
54029327 ATCT -TT ATT ATT ACT ATT AGT ATT AT
1 AT-T ATT ATT ATT ATT ATT ATT ATT AT
54029353 ATTTAATCTT
Statistics
Matches: 90, Mismatches: 21, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
2 4 0.04
3 79 0.88
4 7 0.08
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:54029301 original size:24 final size:23
Alignment explanation
Indices: 54029274--54029356 Score: 62
Period size: 22 Copynumber: 3.5 Consensus size: 23
54029264 TTATAATCAT
54029274 TATTATTATGTTTTTATTTATTAA
1 TATTATTAT-TTTTTATTTATTAA
* * * *
54029298 TATTAATATTTATTA-TTACTAT
1 TATTATTATTTTTTATTTATTAA
*
54029320 TATTATTATCTTTATTATTACTATTAG
1 TATTATTAT-TTT-TTATT--TATTAA
54029347 TATTA-TATTT
1 TATTATTATTT
54029357 AATCTTATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
22 13 0.28
23 7 0.15
24 11 0.24
25 3 0.07
26 3 0.07
27 9 0.20
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (23 bp):
TATTATTATTTTTTATTTATTAA
Found at i:54029315 original size:19 final size:20
Alignment explanation
Indices: 54029286--54029336 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
54029276 TTATTATGTT
54029286 TTTATTTATTAATATTAATA
1 TTTATTTATTAATATTAATA
* *
54029306 TTTA-TTATTACTATTATTA
1 TTTATTTATTAATATTAATA
*
54029325 TTATCTTTATTA
1 TT-TATTTATTA
54029337 TTACTATTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 15 0.58
20 5 0.19
21 6 0.23
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTATTTATTAATATTAATA
Found at i:54030330 original size:50 final size:51
Alignment explanation
Indices: 54030246--54030371 Score: 166
Period size: 51 Copynumber: 2.5 Consensus size: 51
54030236 CTAGTGACTA
* *
54030246 AAGTGTGGTACTATGTGAAGGCCACTTTGAGAAG-AGATAGTTTTGG-TCAC
1 AAGTGTGGTACTATGTGAAGGCCACTCTGAGAAGAAGATAGCTTTGGCT-AC
* * *
54030296 AATTGTGGTACTATGTGAAGGCCACTCTGTGAAGAAGGTAGCTTTGGCTAC
1 AAGTGTGGTACTATGTGAAGGCCACTCTGAGAAGAAGATAGCTTTGGCTAC
* *
54030347 AAGGGTGGTACTATGTGCAGGCCAC
1 AAGTGTGGTACTATGTGAAGGCCAC
54030372 CGGGTATCTG
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
50 31 0.47
51 34 0.52
52 1 0.02
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (51 bp):
AAGTGTGGTACTATGTGAAGGCCACTCTGAGAAGAAGATAGCTTTGGCTAC
Found at i:54031932 original size:17 final size:17
Alignment explanation
Indices: 54031905--54031965 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 17
54031895 ACTCCCCCTA
54031905 TTTACTTTCCCTCAAACT
1 TTTACTTTCCC-CAAACT
*
54031923 TTTA-TTTCCCAAAACTT
1 TTTACTTTCCCCAAAC-T
*
54031940 TTTATTTTCCCCCTAAACT
1 TTTACTTT-CCCC-AAACT
54031959 TTTACTT
1 TTTACTT
54031966 CTCACCCTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
16 4 0.11
17 11 0.31
18 7 0.19
19 10 0.28
20 4 0.11
ACGTcount: A:0.23, C:0.28, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTACTTTCCCCAAACT
Found at i:54033506 original size:6 final size:6
Alignment explanation
Indices: 54033489--54033527 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
54033479 ATGTGAGGTA
* * *
54033489 AGTATT AATATT AGTATT AGTATT ATTATT ATTATT AGT
1 AGTATT AGTATT AGTATT AGTATT AGTATT AGTATT AGT
54033528 GGGAATTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (6 bp):
AGTATT
Found at i:54039210 original size:51 final size:52
Alignment explanation
Indices: 54039083--54039216 Score: 132
Period size: 51 Copynumber: 2.6 Consensus size: 52
54039073 TGTTAGAGAG
* * *
54039083 AATATGTAAATG-TT-ACGAGCTAAATTTGTTAAATCAAGATCAAATTGATAT
1 AATATGTAAATGTTTAAGGA-CTAAATTTGTTAAATCAAGACCAAATTGACAT
** ** * *
54039134 AATATGTAAATGTTTGTGGGTTAAATTTGTTAAA-CAATACCAATTTGACAT
1 AATATGTAAATGTTTAAGGACTAAATTTGTTAAATCAAGACCAAATTGACAT
*
54039185 AATGTGTAAAAT-TTTAAGGACTAAATTTGTTA
1 AATATGT-AAATGTTTAAGGACTAAATTTGTTA
54039217 TTATACCAAT
Statistics
Matches: 67, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
51 47 0.70
52 19 0.28
53 1 0.01
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (52 bp):
AATATGTAAATGTTTAAGGACTAAATTTGTTAAATCAAGACCAAATTGACAT
Found at i:54044120 original size:23 final size:23
Alignment explanation
Indices: 54044077--54044120 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
54044067 ATGTTTAAGT
**
54044077 TTAATATATTTTTAAGTTTATTA
1 TTAATATATTTTTAAAATTATTA
54044100 TTAATACTA-TTTTAAAATTAT
1 TTAATA-TATTTTTAAAATTAT
54044121 AATATATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 16 0.89
24 2 0.11
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (23 bp):
TTAATATATTTTTAAAATTATTA
Found at i:54047645 original size:18 final size:17
Alignment explanation
Indices: 54047624--54047675 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 17
54047614 TACAAAATTT
54047624 TATATTTTATATTTTCTA
1 TATATTTTATATTTT-TA
54047642 TATATTTTATAATTTTTA
1 TATATTTTAT-ATTTTTA
*
54047660 CA-ATTTTTATATTTTT
1 TATA-TTTTATATTTTT
54047676 TTCTAATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
17 7 0.23
18 19 0.61
19 5 0.16
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (17 bp):
TATATTTTATATTTTTA
Found at i:54047675 original size:9 final size:9
Alignment explanation
Indices: 54047628--54047676 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
54047618 AAATTTTATA
54047628 TTTTATATT
1 TTTTATATT
* *
54047637 TTCTATATA
1 TTTTATATT
*
54047646 TTTTATAAT
1 TTTTATATT
* *
54047655 TTTTACAAT
1 TTTTATATT
54047664 TTTTATATT
1 TTTTATATT
54047673 TTTT
1 TTTT
54047677 TCTAATTTTT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTTATATT
Found at i:54047676 original size:18 final size:18
Alignment explanation
Indices: 54047628--54047692 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 18
54047618 AAATTTTATA
* *
54047628 TTTTATATTTTCTA-TAT
1 TTTTATATTTTTTACAAT
*
54047645 ATTTTATAATTTTTACAAT
1 -TTTTATATTTTTTACAAT
*
54047664 TTTTATATTTTTTTCTAAT
1 TTTTATATTTTTTAC-AAT
54047683 TTTTAATATT
1 TTTT-ATATT
54047693 AATTTTTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
18 25 0.64
19 9 0.23
20 5 0.13
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTATATTTTTTACAAT
Found at i:54050655 original size:91 final size:90
Alignment explanation
Indices: 54050490--54050658 Score: 205
Period size: 91 Copynumber: 1.9 Consensus size: 90
54050480 ATATAGGTAT
* * * * *
54050490 GTATCCAACATGGGTACCGTTAGATTTTTCAAAGTTGTTCCATATATTTGGAAGATCATTGAAGT
1 GTATCAAACACGGGCACCGTTAGATTTTTCAAAGTTGTTCCACATATTTGGAAGATCATTGAAGA
54050555 TCATATCCCCATAATCAGGATGTAA
66 TCATATCCCCATAATCAGGATGTAA
* * * * * *
54050580 GTATCAAACACGGGCACGGTTAGATTTTTTACAAGTTTTTCCACCA-ATTTGGAAGGTCTTTTAA
1 GTATCAAACACGGGCACCGTTAGATTTTTCA-AAGTTGTTCCA-CATATTTGGAAGATCATTGAA
*
54050644 GATCATGTCCCCATA
64 GATCATATCCCCATA
54050659 TCCATGTGCT
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
90 26 0.40
91 38 0.58
92 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (90 bp):
GTATCAAACACGGGCACCGTTAGATTTTTCAAAGTTGTTCCACATATTTGGAAGATCATTGAAGA
TCATATCCCCATAATCAGGATGTAA
Found at i:54051844 original size:17 final size:17
Alignment explanation
Indices: 54051824--54051865 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
54051814 TTTACGAAAT
*
54051824 CAAATCTTTTAAGATTA
1 CAAATCTTTTAAAATTA
54051841 CAAAAT-TTTTAAAATTA
1 C-AAATCTTTTAAAATTA
*
54051858 CATATCTT
1 CAAATCTT
54051866 CAAAAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
16 3 0.14
17 14 0.67
18 4 0.19
ACGTcount: A:0.43, C:0.12, G:0.02, T:0.43
Consensus pattern (17 bp):
CAAATCTTTTAAAATTA
Found at i:54056321 original size:17 final size:16
Alignment explanation
Indices: 54056294--54056325 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
54056284 GTCTTTCATG
54056294 CTTTAGTTTCTCTTTA
1 CTTTAGTTTCTCTTTA
54056310 CTTTATGTTTCTCTTT
1 CTTTA-GTTTCTCTTT
54056326 CAAGTGTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.09, C:0.19, G:0.06, T:0.66
Consensus pattern (16 bp):
CTTTAGTTTCTCTTTA
Found at i:54057407 original size:55 final size:55
Alignment explanation
Indices: 54057323--54057432 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 55
54057313 TATTCTAATA
54057323 TTGTGATGATTTAGATGTAGTGGCTTATCTTTGACAAAAAGAGTCATTTGTAGTG
1 TTGTGATGATTTAGATGTAGTGGCTTATCTTTGACAAAAAGAGTCATTTGTAGTG
*
54057378 TTGTGATGATTTAGATGTAGTGGCTTATCTTTGACTAAAAGAGTCATTTGTAGTG
1 TTGTGATGATTTAGATGTAGTGGCTTATCTTTGACAAAAAGAGTCATTTGTAGTG
54057433 ACAAGAGGTC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.26, C:0.07, G:0.25, T:0.41
Consensus pattern (55 bp):
TTGTGATGATTTAGATGTAGTGGCTTATCTTTGACAAAAAGAGTCATTTGTAGTG
Found at i:54064893 original size:20 final size:20
Alignment explanation
Indices: 54064870--54064912 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
54064860 GAAAATTGGG
*
54064870 TAATTTATGGAGAAAAATGA
1 TAATTTATGGAGAAAAAAGA
*
54064890 TAATTTATGGATAAAAAAGA
1 TAATTTATGGAGAAAAAAGA
54064910 TAA
1 TAA
54064913 GACCTTTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.30
Consensus pattern (20 bp):
TAATTTATGGAGAAAAAAGA
Found at i:54067506 original size:4 final size:4
Alignment explanation
Indices: 54067497--54067526 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
54067487 CTACCACAGC
54067497 TACA TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TA
54067527 TAAAGATTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:54067649 original size:12 final size:12
Alignment explanation
Indices: 54067632--54067674 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
54067622 CGGCCAGGTA
54067632 TGTATGTATATG
1 TGTATGTATATG
* *
54067644 TGTATGTAAATA
1 TGTATGTATATG
*
54067656 TGTATATATATG
1 TGTATGTATATG
*
54067668 TATATGT
1 TGTATGT
54067675 TTTTAGTATA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.49
Consensus pattern (12 bp):
TGTATGTATATG
Found at i:54078856 original size:23 final size:23
Alignment explanation
Indices: 54078829--54078885 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
54078819 TGACCATTGA
*
54078829 CGTCCCGATGAGAAGAGATTCCT
1 CGTCCCGATGAGAAGAGATGCCT
*
54078852 CGTCCTGATGAGAAGAGATGCCT
1 CGTCCCGATGAGAAGAGATGCCT
*
54078875 CGTCCGGATGA
1 CGTCCCGATGA
54078886 CCCAATGAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.25, C:0.25, G:0.30, T:0.21
Consensus pattern (23 bp):
CGTCCCGATGAGAAGAGATGCCT
Found at i:54079485 original size:59 final size:59
Alignment explanation
Indices: 54079411--54079530 Score: 231
Period size: 59 Copynumber: 2.0 Consensus size: 59
54079401 CCGAATAGTC
54079411 TTCTTCGTTATCCTCAAGCTCACATCTGGCAAATGTGGGCTCGCTTCAAATTAGAACTT
1 TTCTTCGTTATCCTCAAGCTCACATCTGGCAAATGTGGGCTCGCTTCAAATTAGAACTT
*
54079470 TTCTTCGTTATCCTCAAGCTCACATCTGGCAAATGTGGGCTCGCTTCAAATTAGAATTT
1 TTCTTCGTTATCCTCAAGCTCACATCTGGCAAATGTGGGCTCGCTTCAAATTAGAACTT
54079529 TT
1 TT
54079531 TTTAAAAAAA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (59 bp):
TTCTTCGTTATCCTCAAGCTCACATCTGGCAAATGTGGGCTCGCTTCAAATTAGAACTT
Found at i:54099615 original size:23 final size:26
Alignment explanation
Indices: 54099571--54099622 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 26
54099561 ACATGCAATC
54099571 AAAGTAAAATATAAAATTTTCCAAGAA
1 AAAGTAAAATATAAAA-TTTCCAAGAA
*
54099598 AAAGTAAAA-A-AAAA-TTCCCAGAA
1 AAAGTAAAATATAAAATTTCCAAGAA
54099621 AA
1 AA
54099623 CTGGTTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 10 0.42
25 4 0.17
26 1 0.04
27 9 0.38
ACGTcount: A:0.63, C:0.10, G:0.08, T:0.19
Consensus pattern (26 bp):
AAAGTAAAATATAAAATTTCCAAGAA
Found at i:54104243 original size:15 final size:15
Alignment explanation
Indices: 54104223--54104251 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
54104213 TGCTTTCATT
54104223 CTTTATTTAATTCAC
1 CTTTATTTAATTCAC
54104238 CTTTATTTAATTCA
1 CTTTATTTAATTCA
54104252 ATTTTTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.55
Consensus pattern (15 bp):
CTTTATTTAATTCAC
Found at i:54104309 original size:28 final size:31
Alignment explanation
Indices: 54104258--54104315 Score: 86
Period size: 28 Copynumber: 2.0 Consensus size: 31
54104248 TTCAATTTTT
*
54104258 TAAATATTCGCTTTATTAATTTTTT-TAATA
1 TAAATATTCGCTTTAATAATTTTTTATAATA
54104288 TAAATATT-G-TTTAATAATTTTTTATAAT
1 TAAATATTCGCTTTAATAATTTTTTATAAT
54104316 TATTTAAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 13 0.50
29 5 0.19
30 8 0.31
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.57
Consensus pattern (31 bp):
TAAATATTCGCTTTAATAATTTTTTATAATA
Found at i:54106719 original size:49 final size:49
Alignment explanation
Indices: 54106662--54106756 Score: 172
Period size: 49 Copynumber: 1.9 Consensus size: 49
54106652 CTCGATGTTT
54106662 TCCTGGTTGATCCACCTAAGCCTGCTCTCGCTACATTTTGAATCAGGTC
1 TCCTGGTTGATCCACCTAAGCCTGCTCTCGCTACATTTTGAATCAGGTC
* *
54106711 TCCTGGTTGATCCACCTGAGCCTGCTCTTGCTACATTTTGAATCAG
1 TCCTGGTTGATCCACCTAAGCCTGCTCTCGCTACATTTTGAATCAG
54106757 ACTTGATTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.18, C:0.29, G:0.19, T:0.34
Consensus pattern (49 bp):
TCCTGGTTGATCCACCTAAGCCTGCTCTCGCTACATTTTGAATCAGGTC
Found at i:54110798 original size:14 final size:14
Alignment explanation
Indices: 54110779--54110805 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54110769 TTTAAGCATA
54110779 TTATTATTATTATC
1 TTATTATTATTATC
54110793 TTATTATTATTAT
1 TTATTATTATTAT
54110806 TATCTACGTT
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:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTATTATTATC
Found at i:54110799 original size:17 final size:17
Alignment explanation
Indices: 54110755--54110810 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 17
54110745 CATGAATCTA
54110755 TATCTATATTATTATT-T
1 TATCT-TATTATTATTAT
* * *
54110772 AAGCATATTATTATTAT
1 TATCTTATTATTATTAT
54110789 TATCTTATTATTATTAT
1 TATCTTATTATTATTAT
54110806 TATCT
1 TATCT
54110811 ACGTTAATGC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
16 10 0.31
17 22 0.69
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (17 bp):
TATCTTATTATTATTAT
Found at i:54112653 original size:4 final size:4
Alignment explanation
Indices: 54112644--54112686 Score: 77
Period size: 4 Copynumber: 10.8 Consensus size: 4
54112634 AAGTTAGGAA
*
54112644 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGA ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
54112687 CCCTACAGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.47
Consensus pattern (4 bp):
ATGT
Found at i:54113816 original size:15 final size:15
Alignment explanation
Indices: 54113796--54113826 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
54113786 GTTATGTAAG
54113796 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
*
54113811 TGAAAGGTTAAGAGT
1 TGAAAGGTCAAGAGT
54113826 T
1 T
54113827 ATGTTGTTTT
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:0.39, C:0.03, G:0.32, T:0.26
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:54118176 original size:15 final size:15
Alignment explanation
Indices: 54118156--54118186 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
54118146 GTTATGTAAG
54118156 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
*
54118171 TGAAAGGTTAAGAGT
1 TGAAAGGTCAAGAGT
54118186 T
1 T
54118187 ATGTTGTTTT
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:0.39, C:0.03, G:0.32, T:0.26
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:54119482 original size:37 final size:37
Alignment explanation
Indices: 54119417--54119525 Score: 177
Period size: 37 Copynumber: 3.0 Consensus size: 37
54119407 TACGTATGAT
* *
54119417 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
54119452 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
54119489 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
54119526 TAAAGCTATC
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
35 10 0.14
36 3 0.04
37 56 0.81
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:54119542 original size:46 final size:46
Alignment explanation
Indices: 54119489--54119757 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
54119479 TAAGTGTAGC
* **
54119489 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
54119535 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
54119581 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
54119633 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
54119679 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
54119731 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
54119758 AGTACTCAAA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
46 112 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:54119608 original size:52 final size:52
Alignment explanation
Indices: 54119532--54119751 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
54119522 TAGCTAAAGC
* *
54119532 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
54119585 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
54119637 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
54119683 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
54119735 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
54119752 ATCAGAAGTA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 86 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:54119654 original size:98 final size:98
Alignment explanation
Indices: 54119489--54119757 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
54119479 TAAGTGTAGC
* * *
54119489 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
54119554 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
54119588 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
54119653 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
54119686 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
54119751 GATCAGA
66 GATCAGA
54119758 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 151 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:54125731 original size:21 final size:21
Alignment explanation
Indices: 54125705--54125765 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
54125695 AGCTTTGCCG
54125705 ATTAGGCACTATATGTGTCGT
1 ATTAGGCACTATATGTGTCGT
* ** *
54125726 ATTAGGCACCACGTGTGTTGT
1 ATTAGGCACTATATGTGTCGT
*
54125747 -TTCAGGCACTTTATGTGTC
1 ATT-AGGCACTATATGTGTC
54125766 ATATACTGCT
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
20 2 0.07
21 28 0.93
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.38
Consensus pattern (21 bp):
ATTAGGCACTATATGTGTCGT
Found at i:54128933 original size:36 final size:37
Alignment explanation
Indices: 54128857--54128933 Score: 86
Period size: 36 Copynumber: 2.1 Consensus size: 37
54128847 ATGATTTTAG
* *
54128857 TAAATTCATATAATAATAATTTTATTAAGAATTTTAT
1 TAAATTCATATAATAATAATTTTAATAAGAATTATAT
* * *
54128894 TAAATT-ATATAA-AATTATATTTAATAATAATTATGT
1 TAAATTCATATAATAATAAT-TTTAATAAGAATTATAT
54128930 TAAA
1 TAAA
54128934 ATATGGTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
35 5 0.15
36 23 0.68
37 6 0.18
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (37 bp):
TAAATTCATATAATAATAATTTTAATAAGAATTATAT
Found at i:54129180 original size:16 final size:16
Alignment explanation
Indices: 54129159--54129213 Score: 76
Period size: 16 Copynumber: 3.4 Consensus size: 16
54129149 TGAATTACTG
*
54129159 ATTACAGCTTTATTCA
1 ATTACAGCTCTATTCA
*
54129175 ATTACAACTCTATTCA
1 ATTACAGCTCTATTCA
54129191 ATTACAGCTCTATTTC-
1 ATTACAGCTCTA-TTCA
54129207 ATTACAG
1 ATTACAG
54129214 TGAACCAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
16 32 0.91
17 3 0.09
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.40
Consensus pattern (16 bp):
ATTACAGCTCTATTCA
Found at i:54133465 original size:90 final size:90
Alignment explanation
Indices: 54133363--54133543 Score: 281
Period size: 90 Copynumber: 2.0 Consensus size: 90
54133353 CTAATCATAA
* * * *
54133363 ATTACTAGCAAAATAACTATAAAATTAATTTTTAAAAAAATTTCATTACTAAAAAGTCACGAAAC
1 ATTACTAACAAAATAACTATAAAATTAATTTTTAAAAAAATTACATTACTAAAAAATCACAAAAC
*
54133428 ACTAAACTAACCACTAACAATTTAT
66 ACTAAACTAAACACTAACAATTTAT
* *
54133453 ATTACTAACAAAATAACTATAAAATTATTTTTTTAAAAAATTACATTACTAAAAAATCACAAAAC
1 ATTACTAACAAAATAACTATAAAATTAATTTTTAAAAAAATTACATTACTAAAAAATCACAAAAC
* *
54133518 CCTAAACTAAACACTTACAATTTAT
66 ACTAAACTAAACACTAACAATTTAT
54133543 A
1 A
54133544 ACCTAATCCC
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
90 82 1.00
ACGTcount: A:0.52, C:0.15, G:0.02, T:0.31
Consensus pattern (90 bp):
ATTACTAACAAAATAACTATAAAATTAATTTTTAAAAAAATTACATTACTAAAAAATCACAAAAC
ACTAAACTAAACACTAACAATTTAT
Done.