Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
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: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 53 of 153
Found at i:17454179 original size:7 final size:7
Alignment explanation
Indices: 17454167--17454196 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
17454157 GTCATGATGG
17454167 CATGGTA
1 CATGGTA
17454174 CATGGTA
1 CATGGTA
17454181 CATGGTA
1 CATGGTA
17454188 CATGGTA
1 CATGGTA
17454195 CA
1 CA
17454197 CGGTGTAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.27
Consensus pattern (7 bp):
CATGGTA
Found at i:17454399 original size:33 final size:33
Alignment explanation
Indices: 17454345--17454435 Score: 112
Period size: 33 Copynumber: 2.8 Consensus size: 33
17454335 GCATCCACAA
*
17454345 AGTAAGTCCACCAGGATAGTAAACACGGAATAG
1 AGTAAGTCCACCAGGACAGTAAACACGGAATAG
* * *
17454378 AGTAAGTTCACCGGGACAGTAAACACGGAATAA
1 AGTAAGTCCACCAGGACAGTAAACACGGAATAG
* *
17454411 AG-ATAGTCCATCAAGACAGTAAACA
1 AGTA-AGTCCACCAGGACAGTAAACA
17454436 TGAGATAGTC
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
32 1 0.02
33 48 0.98
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (33 bp):
AGTAAGTCCACCAGGACAGTAAACACGGAATAG
Found at i:17456175 original size:28 final size:28
Alignment explanation
Indices: 17456135--17456201 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
17456125 GTACAGCTCA
17456135 TGTGAGCAAATTCAAATATCACAACTCG
1 TGTGAGCAAATTCAAATATCACAACTCG
* * * *
17456163 TGTGAGCAAATTCAAATATTATAGCTTG
1 TGTGAGCAAATTCAAATATCACAACTCG
17456191 TGTGAGCAAAT
1 TGTGAGCAAAT
17456202 CGGCCTCGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (28 bp):
TGTGAGCAAATTCAAATATCACAACTCG
Found at i:17461777 original size:9 final size:9
Alignment explanation
Indices: 17461763--17461791 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
17461753 TTTCAAATCA
17461763 CAACCAATT
1 CAACCAATT
17461772 CAACCAATT
1 CAACCAATT
17461781 CAACCAATT
1 CAACCAATT
17461790 CA
1 CA
17461792 TTTCACATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (9 bp):
CAACCAATT
Found at i:17462452 original size:45 final size:45
Alignment explanation
Indices: 17462392--17462546 Score: 238
Period size: 45 Copynumber: 3.4 Consensus size: 45
17462382 AGTATACAGT
* * *
17462392 AATCAGTAACGGTAACAGTAACAGTATTCAACACACAAAGTGCTG
1 AATCAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
* * *
17462437 AACCTGTAACAGTAACGGTAACAGTATTCGACACACAAAGTGCCG
1 AATCAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
* *
17462482 AGTCGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
1 AATCAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
17462527 AATCAGTAACAGTAACAGTA
1 AATCAGTAACAGTAACAGTA
17462547 GTCGGCACAT
Statistics
Matches: 98, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 98 1.00
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.19
Consensus pattern (45 bp):
AATCAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
Found at i:17462491 original size:39 final size:39
Alignment explanation
Indices: 17462403--17462573 Score: 148
Period size: 45 Copynumber: 4.1 Consensus size: 39
17462393 ATCAGTAACG
* *
17462403 GTAACAGTAACAGTATTCAACACACAAAGTGCTGAACCTGTAACA
1 GTAACAGTAACAGTATTCGACACACAAAGTGCCG-A---GT--CA
*
17462448 GTAACGGTAACAGTATTCGACACACAAAGTGCCGAGTCGGTAACA
1 GTAACAGTAACAGTATTCGACACACAAAGTGCCGA----GT--CA
*
17462493 GTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCA
1 GTAACAGTAACAGTATTCGACACACAAAGTGCCGAGTCA
* * *
17462532 GTAACAGTAACAGTAGTCGGCACA-TAAGTGCCTGA-TCA
1 GTAACAGTAACAGTATTCGACACACAAAGTGCC-GAGTCA
17462570 GTAA
1 GTAA
17462574 GCCGGCAAAT
Statistics
Matches: 114, Mismatches: 10, Indels: 11
0.84 0.07 0.08
Matches are distributed among these distances:
38 14 0.12
39 26 0.23
41 1 0.01
44 1 0.01
45 72 0.63
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (39 bp):
GTAACAGTAACAGTATTCGACACACAAAGTGCCGAGTCA
Found at i:17463519 original size:9 final size:9
Alignment explanation
Indices: 17463505--17463549 Score: 58
Period size: 9 Copynumber: 5.1 Consensus size: 9
17463495 CATTTAAATA
17463505 AATAATTAT
1 AATAATTAT
17463514 AATAATTAT
1 AATAATTAT
17463523 AATAATTAT
1 AATAATTAT
17463532 -ATACA-TAT
1 AATA-ATTAT
*
17463540 AATATTTAT
1 AATAATTAT
17463549 A
1 A
17463550 TATCTAACTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
8 6 0.19
9 26 0.81
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (9 bp):
AATAATTAT
Found at i:17469546 original size:6 final size:6
Alignment explanation
Indices: 17469520--17469569 Score: 64
Period size: 6 Copynumber: 8.2 Consensus size: 6
17469510 ACAGTACCTA
* * *
17469520 AACAGT AATCAAT AACAGT AGCAGT AGCAGT AACAGT AACAGT AACAGT
1 AACAGT AA-CAGT AACAGT AACAGT AACAGT AACAGT AACAGT AACAGT
17469569 A
1 A
17469570 TTCAACATAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
6 34 0.87
7 5 0.13
ACGTcount: A:0.48, C:0.16, G:0.18, T:0.18
Consensus pattern (6 bp):
AACAGT
Found at i:17469627 original size:45 final size:45
Alignment explanation
Indices: 17469549--17469650 Score: 125
Period size: 45 Copynumber: 2.3 Consensus size: 45
17469539 AGCAGTAGCA
* * * * *
17469549 GTAACAGTAACAGTAACAGTATTCAACATACAAAGTG-CTGAATCT
1 GTAACAGTAACGGCAACAATATTCAACACACAAAGTGTC-GAATCG
* *
17469594 GTAATAGTAACGGCAACAATATTCGACACACAAAGTGTCGAATCG
1 GTAACAGTAACGGCAACAATATTCAACACACAAAGTGTCGAATCG
17469639 GTAACAGTAACG
1 GTAACAGTAACG
17469651 ATAACAGAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
45 47 0.98
46 1 0.02
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (45 bp):
GTAACAGTAACGGCAACAATATTCAACACACAAAGTGTCGAATCG
Found at i:17469920 original size:40 final size:40
Alignment explanation
Indices: 17469860--17469943 Score: 105
Period size: 40 Copynumber: 2.1 Consensus size: 40
17469850 AATTCATTGC
* * * * *
17469860 TTCAGTAATTTCACAGTTCAATGCAGTACACATAACAATA
1 TTCAATAACTTCACAATTCAATGCAATACACAAAACAATA
* *
17469900 TTCAATAACTTCACAATTCAATTCAATACTCAAAACAATA
1 TTCAATAACTTCACAATTCAATGCAATACACAAAACAATA
17469940 TTCA
1 TTCA
17469944 GTATTCTATA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (40 bp):
TTCAATAACTTCACAATTCAATGCAATACACAAAACAATA
Found at i:17470714 original size:4 final size:4
Alignment explanation
Indices: 17470705--17470729 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
17470695 CTCTGTTTCT
17470705 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
17470730 GCTTTAGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:17474420 original size:9 final size:9
Alignment explanation
Indices: 17474406--17474434 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
17474396 TTTCAAATCA
17474406 CAACCAATT
1 CAACCAATT
17474415 CAACCAATT
1 CAACCAATT
17474424 CAACCAATT
1 CAACCAATT
17474433 CA
1 CA
17474435 TTTCACATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (9 bp):
CAACCAATT
Found at i:17475244 original size:10 final size:10
Alignment explanation
Indices: 17475229--17475263 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
17475219 CTCTGTTTCT
17475229 TTTTATGTTC
1 TTTTATGTTC
17475239 TTTTATGTTC
1 TTTTATGTTC
*
17475249 TTTTGT-TTC
1 TTTTATGTTC
17475258 TTTTAT
1 TTTTAT
17475264 TTTACTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.09, C:0.09, G:0.09, T:0.74
Consensus pattern (10 bp):
TTTTATGTTC
Found at i:17475614 original size:9 final size:9
Alignment explanation
Indices: 17475570--17475614 Score: 58
Period size: 9 Copynumber: 5.1 Consensus size: 9
17475560 TATTTAAATA
17475570 AATAATTAT
1 AATAATTAT
17475579 AATAATTAT
1 AATAATTAT
17475588 AATAATTAT
1 AATAATTAT
17475597 -ATACA-TAT
1 AATA-ATTAT
*
17475605 AATATTTAT
1 AATAATTAT
17475614 A
1 A
17475615 TATCTAACTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
8 6 0.19
9 26 0.81
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (9 bp):
AATAATTAT
Found at i:17476379 original size:27 final size:26
Alignment explanation
Indices: 17475978--17476390 Score: 384
Period size: 27 Copynumber: 15.3 Consensus size: 26
17475968 ACCCCCATAA
**
17475978 GGTAAAATGATCGAAATACCCCCATAG
1 GGTAAAATGATCGAAATACCCTGA-AG
* *
17476005 GATAAAATGA-CAGAAATACCC-CATAG
1 GGTAAAATGATC-GAAATACCCTGA-AG
* *
17476031 GATAAAATGA-CTGAAATACCCCTTAAG
1 GGTAAAATGATC-GAAATA-CCCTGAAG
* *
17476058 GGTAAAATGATCAAAATACCCCTAAAG
1 GGTAAAATGATCGAAATA-CCCTGAAG
* * *
17476085 GGTAAAATGA-CTAAAATACCCTCAAAT
1 GGTAAAATGATC-GAAATACCCT-GAAG
* * * *
17476112 GGTAAAATGACCAAAATATCGTCGAAG
1 GGTAAAATGATCGAAATACCCT-GAAG
*
17476139 GGTAAAATGATCGAAATACCTTCGAAG
1 GGTAAAATGATCGAAATACCCT-GAAG
*
17476166 GATAAAATGATCGAAATACCCTCGAAG
1 GGTAAAATGATCGAAATACCCT-GAAG
*
17476193 GATAAAATGATCGAAATACCCTCGAAG
1 GGTAAAATGATCGAAATACCCT-GAAG
* * *
17476220 GGTAAAATCACCAAAATACCCCCTGAAG
1 GGTAAAATGATCGAAATA--CCCTGAAG
* *
17476248 GGTAAAATAATCGAAATACCCCCGAAG
1 GGTAAAATGATCGAAATA-CCCTGAAG
17476275 GGTAAAATGATCGAAATACTCCTGAAG
1 GGTAAAATGATCGAAATAC-CCTGAAG
*
17476302 GGTAAAATGACCGAAATACCCTCGAAG
1 GGTAAAATGATCGAAATACCCT-GAAG
* *
17476329 GGTAAAATGATCAAAATACCCCTGATG
1 GGTAAAATGATCGAAATA-CCCTGAAG
*
17476356 GGTAAATTGATCGAAATACTCCTGAAG
1 GGTAAAATGATCGAAATAC-CCTGAAG
17476383 GGTAAAAT
1 GGTAAAAT
17476391 AACTGTTATG
Statistics
Matches: 338, Mismatches: 35, Indels: 26
0.85 0.09 0.07
Matches are distributed among these distances:
26 33 0.10
27 275 0.81
28 26 0.08
29 4 0.01
ACGTcount: A:0.44, C:0.19, G:0.18, T:0.19
Consensus pattern (26 bp):
GGTAAAATGATCGAAATACCCTGAAG
Found at i:17476405 original size:54 final size:54
Alignment explanation
Indices: 17475978--17476390 Score: 450
Period size: 54 Copynumber: 7.6 Consensus size: 54
17475968 ACCCCCATAA
* *
17475978 GGTAAAATGATCGAAATACCC-CCATAGGATAAAATGA-CAGAAATACCCC--ATAG
1 GGTAAAATGATCGAAATACCCTCGA-AGGGTAAAATGATCA-AAATACCCCTGA-AG
* * *
17476031 GATAAAATGA-CTGAAATACCC-CTTAAGGGTAAAATGATCAAAATACCCCTAAAG
1 GGTAAAATGATC-GAAATACCCTC-GAAGGGTAAAATGATCAAAATACCCCTGAAG
* * * * * *
17476085 GGTAAAATGA-CTAAAATACCCTCAAATGGTAAAATGACCAAAATA-TCGTCGAAG
1 GGTAAAATGATC-GAAATACCCTCGAAGGGTAAAATGATCAAAATACCCCT-GAAG
* * *
17476139 GGTAAAATGATCGAAATACCTTCGAAGGATAAAATGATCGAAATA-CCCTCGAAG
1 GGTAAAATGATCGAAATACCCTCGAAGGGTAAAATGATCAAAATACCCCT-GAAG
* * *
17476193 GATAAAATGATCGAAATACCCTCGAAGGGTAAAATCACCAAAATACCCCCTGAAG
1 GGTAAAATGATCGAAATACCCTCGAAGGGTAAAATGATCAAAATA-CCCCTGAAG
* * * *
17476248 GGTAAAATAATCGAAATACCCCCGAAGGGTAAAATGATCGAAATACTCCTGAAG
1 GGTAAAATGATCGAAATACCCTCGAAGGGTAAAATGATCAAAATACCCCTGAAG
* *
17476302 GGTAAAATGACCGAAATACCCTCGAAGGGTAAAATGATCAAAATACCCCTGATG
1 GGTAAAATGATCGAAATACCCTCGAAGGGTAAAATGATCAAAATACCCCTGAAG
*
17476356 GGTAAATTGATCGAAATACTCCT-GAAGGGTAAAAT
1 GGTAAAATGATCGAAATAC-CCTCGAAGGGTAAAAT
17476391 AACTGTTATG
Statistics
Matches: 308, Mismatches: 41, Indels: 21
0.83 0.11 0.06
Matches are distributed among these distances:
52 1 0.00
53 41 0.13
54 213 0.69
55 49 0.16
56 4 0.01
ACGTcount: A:0.44, C:0.19, G:0.18, T:0.19
Consensus pattern (54 bp):
GGTAAAATGATCGAAATACCCTCGAAGGGTAAAATGATCAAAATACCCCTGAAG
Found at i:17476587 original size:27 final size:27
Alignment explanation
Indices: 17476542--17476615 Score: 73
Period size: 25 Copynumber: 2.9 Consensus size: 27
17476532 AAAGGGGAAG
**
17476542 TATACTG-TACTGGTGGCTTTGCCACA
1 TATACTGTTACTGGCAGCTTTGCCACA
**
17476568 TATACTGTTACTGGCAGCTTTGCTGCA
1 TATACTGTTACTGGCAGCTTTGCCACA
* *
17476595 T-T-CTATTACTGGCAACTTTGC
1 TATACTGTTACTGGCAGCTTTGC
17476616 TGCATTATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
25 17 0.41
26 8 0.20
27 16 0.39
ACGTcount: A:0.19, C:0.23, G:0.20, T:0.38
Consensus pattern (27 bp):
TATACTGTTACTGGCAGCTTTGCCACA
Found at i:17476669 original size:25 final size:26
Alignment explanation
Indices: 17476570--17476668 Score: 132
Period size: 25 Copynumber: 3.9 Consensus size: 26
17476560 TTGCCACATA
* *
17476570 TACTGTTACTGGCAGCTTTGCTGCAT
1 TACTATTACTGGCAACTTTGCTGCAT
17476596 T-CTATTACTGGCAACTTTGCTGCAT
1 TACTATTACTGGCAACTTTGCTGCAT
* *
17476621 TATTATT-CTGGCAACTTTGCTGCGT
1 TACTATTACTGGCAACTTTGCTGCAT
*
17476646 TACTATTA-TGGCAGCTTTGCTGC
1 TACTATTACTGGCAACTTTGCTGC
17476669 GATATTGGTG
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
25 60 0.92
26 5 0.08
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.40
Consensus pattern (26 bp):
TACTATTACTGGCAACTTTGCTGCAT
Found at i:17476817 original size:28 final size:28
Alignment explanation
Indices: 17476779--17476861 Score: 94
Period size: 28 Copynumber: 3.0 Consensus size: 28
17476769 TATTTTGTTT
* *
17476779 ACTGTATTGGGCTAAAGCCCACATTGTC
1 ACTGTAATGGGCTAAAGCCCACACTGTC
* * * *
17476807 ACTGTACTGGGCTAAGGTCCACACTGTT
1 ACTGTAATGGGCTAAAGCCCACACTGTC
* *
17476835 ACTGTAATGGGCTAAGGCTCACACTGT
1 ACTGTAATGGGCTAAAGCCCACACTGT
17476862 ACCGATATTG
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (28 bp):
ACTGTAATGGGCTAAAGCCCACACTGTC
Found at i:17482465 original size:41 final size:41
Alignment explanation
Indices: 17482420--17482547 Score: 157
Period size: 41 Copynumber: 3.1 Consensus size: 41
17482410 AGAATATTGT
*
17482420 TGAATTGCATATACGTGACCTTATTTGTACTTTGGTACCCC
1 TGAATTGCATATACGTGACCTTATTTGTACTTCGGTACCCC
* * * * **
17482461 TGAATTGCATATACGTGTCCCTGTTTATACTTCAATACCCC
1 TGAATTGCATATACGTGACCTTATTTGTACTTCGGTACCCC
* * * *
17482502 TGAATTGCACATACGTGCCCTTCTTTGTACTTCGGTGCCCC
1 TGAATTGCATATACGTGACCTTATTTGTACTTCGGTACCCC
17482543 TGAAT
1 TGAAT
17482548 GCACTTTTGT
Statistics
Matches: 72, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 72 1.00
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (41 bp):
TGAATTGCATATACGTGACCTTATTTGTACTTCGGTACCCC
Found at i:17490339 original size:22 final size:21
Alignment explanation
Indices: 17490309--17490361 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
17490299 GGTTAGATTA
*
17490309 TCTCGAGACATAAGGTGCCAA-G
1 TCTCAAGACAT-AGGT-CCAATG
*
17490331 TCTCAAGACATAGGTTCAATG
1 TCTCAAGACATAGGTCCAATG
17490352 TCTCAAGACA
1 TCTCAAGACA
17490362 CTGTCCCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 3 0.11
21 15 0.54
22 10 0.36
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.23
Consensus pattern (21 bp):
TCTCAAGACATAGGTCCAATG
Found at i:17502142 original size:30 final size:31
Alignment explanation
Indices: 17502086--17502143 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
17502076 ATTTATTATC
17502086 AAATTTATCGTACGTAGTCAAAAACGACGTT
1 AAATTTATCGTACGTAGTCAAAAACGACGTT
*
17502117 AAATTTATCGTATGTAGTC-AAAACGAC
1 AAATTTATCGTACGTAGTCAAAAACGAC
17502144 ATTAGGTAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 8 0.31
31 18 0.69
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (31 bp):
AAATTTATCGTACGTAGTCAAAAACGACGTT
Found at i:17513424 original size:110 final size:110
Alignment explanation
Indices: 17513025--17513701 Score: 968
Period size: 110 Copynumber: 6.1 Consensus size: 110
17513015 TGGATTAAGA
* * * *
17513025 TTTAAGAGGATATTCGGCTATTTGGTCCAACGAG--AAATCGAAACCCAACGCATTAGGGCACGT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAACACATTAGGGCACGT
*
17513088 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTG-AAGTT
66 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTT
* * * *
17513132 TTTAAAAGGATATTTGGCCATTTGGTCGAATGAGAAAAATCGAAACCCAGCACATTAGGGCACAT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAACACATTAGGGCACGT
*
17513197 TTTCTCGAATTTCCAAACGCAAAACATTG-CTTCATTTTGAATTTTTT
66 TTTCTCGAATTTCCAAACGCAAAACATTGCCTT-ATTTTGAA--ATTT
* *
17513244 TTTAAAAGAGGATATTTGGCTATTTGGTCGAACGGGAAAGATCGAAACCCAACACATTAGGGCAC
1 TTT-AAA-AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAACACATTAGGGCAC
17513309 GTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTT
64 GTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTT
* * *
17513356 TTTAAAAGGATATTTAGCTATTTGGTCGAACGAGAAAAATCGAAACTCAACACATTAGGGCACAT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAACACATTAGGGCACGT
* * *
17513421 TTTCTCGAATTTCCAAAAGCAAAACATTACCTCATTTTGAAATTTTT
66 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAA--TTT
* * * **
17513468 TTTAAAAGAGGATATTTGGCTATTTGGTCGAA-TAGGAAAGATCGAAGCCCGGCACATTAGGGCA
1 TTT-AAA-AGGATATTTGGCTATTTGGTCGAACGA-GAAAAATCGAAACCCAACACATTAGGGCA
* *
17513532 CGTTTTCTCGAATTTCGAAACGCAAAACATTACCTTATTTTGAAATTT
63 CGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTT
* *
17513580 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATTGAAACCCAACACATTTGGGCACGT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAACACATTAGGGCACGT
* *
17513645 TTTCTCGAATTTCCAAATGCAAAATATTGCCTTATTTTGAAATTT
66 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTT
17513690 TTTAAAAGGATA
1 TTTAAAAGGATA
17513702 ATTAGTATGC
Statistics
Matches: 508, Mismatches: 47, Indels: 27
0.87 0.08 0.05
Matches are distributed among these distances:
107 29 0.06
108 3 0.01
109 61 0.12
110 197 0.39
111 7 0.01
112 23 0.05
113 7 0.01
114 178 0.35
115 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (110 bp):
TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAACACATTAGGGCACGT
TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTT
Found at i:17513429 original size:224 final size:224
Alignment explanation
Indices: 17513028--17513692 Score: 1059
Period size: 224 Copynumber: 3.0 Consensus size: 224
17513018 ATTAAGATTT
* * * *
17513028 AAGAGGATATTCGGCTATTTGGTCCAACGAG-AA-ATCGAAACCCAACGCATTAGGGCACGTTTT
1 AAGAGGATATTTGGCTATTTGGTCGAACGGGAAAGATCGAAACCCAACACATTAGGGCACGTTTT
* *
17513091 CTCGAATTTCCAAACGCAAAACATTGCCTTATTTTG-AAGTTTTTAAAAGGATATTTGGCCATTT
66 CTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTTAAAAGGATATTTGGCTATTT
* * *
17513155 GGTCGAATGAGAAAAATCGAAACCCAGCACATTAGGGCACATTTTCTCGAATTTCCAAACGCAAA
131 GGTCGAACGAGAAAAATCGAAACCCAACACATTAGGGCACATTTTCTCGAATTTCCAAAAGCAAA
*
17513220 ACATTGCTTCATTTTGAATTTTTTTTTAA
196 ACATTGCTTCATTTTGAAATTTTTTTTAA
17513249 AAGAGGATATTTGGCTATTTGGTCGAACGGGAAAGATCGAAACCCAACACATTAGGGCACGTTTT
1 AAGAGGATATTTGGCTATTTGGTCGAACGGGAAAGATCGAAACCCAACACATTAGGGCACGTTTT
*
17513314 CTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTTAAAAGGATATTTAGCTATTT
66 CTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTTAAAAGGATATTTGGCTATTT
*
17513379 GGTCGAACGAGAAAAATCGAAACTCAACACATTAGGGCACATTTTCTCGAATTTCCAAAAGCAAA
131 GGTCGAACGAGAAAAATCGAAACCCAACACATTAGGGCACATTTTCTCGAATTTCCAAAAGCAAA
* *
17513444 ACATTACCTCATTTTGAAATTTTTTTTAA
196 ACATTGCTTCATTTTGAAATTTTTTTTAA
** * **
17513473 AAGAGGATATTTGGCTATTTGGTCGAATAGGAAAGATCGAAGCCCGGCACATTAGGGCACGTTTT
1 AAGAGGATATTTGGCTATTTGGTCGAACGGGAAAGATCGAAACCCAACACATTAGGGCACGTTTT
* *
17513538 CTCGAATTTCGAAACGCAAAACATTACCTTATTTTGAAATTTTTTAAAAGGATATTTGGCTATTT
66 CTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTTAAAAGGATATTTGGCTATTT
* * * *
17513603 GGTCGAACGAGAAAAATTGAAACCCAACACATTTGGGCACGTTTTCTCGAATTTCCAAATGCAAA
131 GGTCGAACGAGAAAAATCGAAACCCAACACATTAGGGCACATTTTCTCGAATTTCCAAAAGCAAA
*
17513668 ATATTGCCTT-ATTTTGAAATTTTTT
196 ACATTG-CTTCATTTTGAAATTTTTT
17513693 AAAAGGATAA
Statistics
Matches: 410, Mismatches: 30, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
221 28 0.07
222 2 0.00
223 65 0.16
224 313 0.76
225 2 0.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Consensus pattern (224 bp):
AAGAGGATATTTGGCTATTTGGTCGAACGGGAAAGATCGAAACCCAACACATTAGGGCACGTTTT
CTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTTAAAAGGATATTTGGCTATTT
GGTCGAACGAGAAAAATCGAAACCCAACACATTAGGGCACATTTTCTCGAATTTCCAAAAGCAAA
ACATTGCTTCATTTTGAAATTTTTTTTAA
Found at i:17515294 original size:23 final size:23
Alignment explanation
Indices: 17515264--17515311 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
17515254 GTGGACTCGC
17515264 TTATTAAGGGGCTACACCTAAGG
1 TTATTAAGGGGCTACACCTAAGG
17515287 TTATTAAGGGGCTACACCTAAGG
1 TTATTAAGGGGCTACACCTAAGG
17515310 TT
1 TT
17515312 TTATAAAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (23 bp):
TTATTAAGGGGCTACACCTAAGG
Found at i:17518736 original size:29 final size:30
Alignment explanation
Indices: 17518675--17518765 Score: 89
Period size: 30 Copynumber: 3.1 Consensus size: 30
17518665 AAAAATTTAT
17518675 AAAAATGA-TTAAATTTTAATAAAACTATAA
1 AAAAAT-ATTTAAATTTTAATAAAACTATAA
* * *
17518705 AAAAATATTTAAATTTTATTAAAATTAGAA
1 AAAAATATTTAAATTTTAATAAAACTATAA
** *
17518735 AAAAATTATAAAAATTGTAA-AAAA-TATAA
1 AAAAA-TATTTAAATTTTAATAAAACTATAA
17518764 AA
1 AA
17518766 TATATAGAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
29 7 0.14
30 34 0.67
31 10 0.20
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (30 bp):
AAAAATATTTAAATTTTAATAAAACTATAA
Found at i:17518743 original size:20 final size:19
Alignment explanation
Indices: 17518720--17518765 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
17518710 TATTTAAATT
*
17518720 TTATTAAAATTAGAAAAAAA
1 TTATAAAAATT-GAAAAAAA
*
17518740 TTATAAAAATTGTAAAAAA
1 TTATAAAAATTGAAAAAAA
17518759 -TATAAAA
1 TTATAAAA
17518766 TATATAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 7 0.29
19 7 0.29
20 10 0.42
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.30
Consensus pattern (19 bp):
TTATAAAAATTGAAAAAAA
Found at i:17518834 original size:19 final size:19
Alignment explanation
Indices: 17518821--17518871 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
17518811 GAAAATTATA
*
17518821 AAAAAATATAAAAAAATAT
1 AAAAATTATAAAAAAATAT
* *
17518840 -AAAATTCGTAAAAAATTAT
1 AAAAATT-ATAAAAAAATAT
17518859 AAAAATTATAAAA
1 AAAAATTATAAAA
17518872 TACTTCTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 5 0.19
19 15 0.58
20 6 0.23
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (19 bp):
AAAAATTATAAAAAAATAT
Found at i:17518861 original size:10 final size:10
Alignment explanation
Indices: 17518812--17518871 Score: 63
Period size: 10 Copynumber: 6.2 Consensus size: 10
17518802 AAGTCGTAAG
17518812 AAAATTATAA
1 AAAATTATAA
*
17518822 AAAAATATAA
1 AAAATTATAA
*
17518832 AAAA--ATAT
1 AAAATTATAA
*
17518840 AAAATTCGTAA
1 AAAATT-ATAA
17518851 AAAATTAT-A
1 AAAATTATAA
17518860 AAAATTATAA
1 AAAATTATAA
17518870 AA
1 AA
17518872 TACTTCTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
8 7 0.17
9 9 0.22
10 17 0.41
11 8 0.20
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.27
Consensus pattern (10 bp):
AAAATTATAA
Found at i:17518872 original size:8 final size:9
Alignment explanation
Indices: 17518735--17518871 Score: 57
Period size: 9 Copynumber: 14.4 Consensus size: 9
17518725 AAAATTAGAA
17518735 AAAAATTAT
1 AAAAATTAT
*
17518744 AAAAATTGT
1 AAAAATTAT
*
17518753 AAAAAATAT
1 AAAAATTAT
17518762 -AAAATATAT
1 AAAAAT-TAT
* *
17518771 AGAAATATAG
1 AAAAAT-TAT
17518781 AAAAAGTTAT
1 AAAAA-TTAT
* *
17518791 -AAGATTTT
1 AAAAATTAT
*
17518799 ATAAAGTCGTA-
1 A-AAAAT--TAT
17518810 AGAAAATTAT
1 A-AAAATTAT
*
17518820 AAAAAAATAT
1 -AAAAATTAT
*
17518830 AAAAA-AAT
1 AAAAATTAT
*
17518838 ATAAAATTCGT
1 A-AAAATT-AT
17518849 AAAAAATTAT
1 -AAAAATTAT
17518859 AAAAATTAT
1 AAAAATTAT
17518868 AAAA
1 AAAA
17518872 TACTTCTTTT
Statistics
Matches: 95, Mismatches: 20, Indels: 26
0.67 0.14 0.18
Matches are distributed among these distances:
8 10 0.11
9 45 0.47
10 24 0.25
11 14 0.15
12 2 0.02
ACGTcount: A:0.64, C:0.01, G:0.07, T:0.28
Consensus pattern (9 bp):
AAAAATTAT
Found at i:17519036 original size:20 final size:20
Alignment explanation
Indices: 17519013--17519051 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
17519003 TTAAATGACC
17519013 TTTTTAATG-TATTTTATAAT
1 TTTTTAATGAT-TTTTATAAT
*
17519033 TTTTTTATGATTTTTATAA
1 TTTTTAATGATTTTTATAA
17519052 AAGTTTACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (20 bp):
TTTTTAATGATTTTTATAAT
Found at i:17519110 original size:28 final size:27
Alignment explanation
Indices: 17519078--17519146 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
17519068 ATTATATTTA
*
17519078 TAATTTATTTCTA-ATTTTTAATAAGATT
1 TAATTT-TTT-TATATTTTTAATAAAATT
*
17519106 TAATTTTTTTATATTTTTATTAAAATT
1 TAATTTTTTTATATTTTTAATAAAATT
*
17519133 TAATAATTTTTATA
1 TAAT-TTTTTTATA
17519147 AATTTTATTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
26 2 0.06
27 20 0.56
28 14 0.39
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (27 bp):
TAATTTTTTTATATTTTTAATAAAATT
Found at i:17529357 original size:29 final size:29
Alignment explanation
Indices: 17529335--17529397 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
17529325 AAAAGTTATT
*
17529335 AAATTTTAATAAAAATATAAAAAATATAA
1 AAATTTTAATAAAAATAGAAAAAATATAA
*
17529364 AAATTTTATTAAAAATAGAAAATATATATAA
1 AAATTTTAATAAAAATAGAAAA-A-ATATAA
17529395 AAA
1 AAA
17529398 ATTGTAAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 20 0.67
30 1 0.03
31 9 0.30
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (29 bp):
AAATTTTAATAAAAATAGAAAAAATATAA
Found at i:17529385 original size:19 final size:20
Alignment explanation
Indices: 17529354--17529418 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
17529344 TAAAAATATA
17529354 AAAAATA-TAAAAATTTTATT
1 AAAAATAGT-AAAATTTTATT
* *
17529374 AAAAATAG-AAAATATATATA
1 AAAAATAGTAAAAT-TTTATT
* *
17529394 AAAAATTGTAAGATTTTA-T
1 AAAAATAGTAAAATTTTATT
17529413 AAAAAT
1 AAAAAT
17529419 TATTAAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
19 11 0.31
20 21 0.58
21 4 0.11
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.34
Consensus pattern (20 bp):
AAAAATAGTAAAATTTTATT
Found at i:17529397 original size:20 final size:20
Alignment explanation
Indices: 17529349--17529399 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
17529339 TTTAATAAAA
*
17529349 ATATAAAAAATATAAAAATT
1 ATATAAAAAATAGAAAAATT
* *
17529369 TTATTAAAAATAG-AAAATAT
1 ATATAAAAAATAGAAAAAT-T
17529389 ATATAAAAAAT
1 ATATAAAAAAT
17529400 TGTAAGATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (20 bp):
ATATAAAAAATAGAAAAATT
Found at i:17535756 original size:25 final size:25
Alignment explanation
Indices: 17535726--17535817 Score: 89
Period size: 25 Copynumber: 3.6 Consensus size: 25
17535716 CTTATAAGAG
*
17535726 TCCCGA-TATATGGCTCTCCAGAGCT
1 TCCCGATTA-ATGGCTCTTCAGAGCT
* * *
17535751 TTCCGATTAAAGGCTCTTTTATGAGCT
1 TCCCGATTAATGGCTC-TTCA-GAGCT
*
17535778 TCCCGATTAATGGCTCTTCGGAGCT
1 TCCCGATTAATGGCTCTTCAGAGCT
*
17535803 TCCCGA-TATTGGCTC
1 TCCCGATTAATGGCTC
17535818 ACTTGAACTT
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
24 8 0.15
25 22 0.40
26 6 0.11
27 19 0.35
ACGTcount: A:0.18, C:0.27, G:0.21, T:0.34
Consensus pattern (25 bp):
TCCCGATTAATGGCTCTTCAGAGCT
Found at i:17542464 original size:66 final size:65
Alignment explanation
Indices: 17542377--17542510 Score: 180
Period size: 66 Copynumber: 2.0 Consensus size: 65
17542367 ATTCTGAAGC
**
17542377 TGTAACTGGAGTTCGTCATATTTTCTGCTT-GCCTCTACTTCCCTCGCTGCTGCCTCCGCTTTAA
1 TGTAACTGGAGTTCGTCATATTTTCT--TTAGCCTCTACTTCCCTCAATGCTGCCTCCGCTTTAA
17542441 GT
64 GT
* * * *
17542443 TGTAGCTGGAGTTCTTCATATTTTCTTTGAGCCTCTGCTTCTCTCAATGCTGCCTCCGCTTTAAG
1 TGTAACTGGAGTTCGTCATATTTTCTTT-AGCCTCTACTTCCCTCAATGCTGCCTCCGCTTTAAG
17542508 T
65 T
17542509 TG
1 TG
17542511 AGCAATTTGC
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
64 2 0.03
66 58 0.97
ACGTcount: A:0.13, C:0.28, G:0.19, T:0.41
Consensus pattern (65 bp):
TGTAACTGGAGTTCGTCATATTTTCTTTAGCCTCTACTTCCCTCAATGCTGCCTCCGCTTTAAGT
Found at i:17548131 original size:85 final size:85
Alignment explanation
Indices: 17548003--17548227 Score: 425
Period size: 85 Copynumber: 2.6 Consensus size: 85
17547993 TTCTGATCCA
17548003 AAAT-TTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAGTTATGTAAGTTATGAT
1 AAATGTTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAGTTATGTAAGTTATGAT
17548067 CCAAAGTTTTTTTATTCTTT
66 CCAAAGTTTTTTTATTCTTT
17548087 AAATGTTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAGTTATGTAAGTTATGAT
1 AAATGTTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAGTTATGTAAGTTATGAT
17548152 CCAAAGTTTTTTTATTCTTT
66 CCAAAGTTTTTTTATTCTTT
17548172 AAATGTTTATGTAAGTTATGATATGATATATATTTATGTAAGTTATGTAAGTTATG
1 AAATGTTTATGTAAGTTATGATATGATATATATTTATGT-A-TTATGTAAGTTATG
17548228 GTATGATATA
Statistics
Matches: 138, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
84 4 0.03
85 119 0.86
86 1 0.01
87 14 0.10
ACGTcount: A:0.33, C:0.03, G:0.15, T:0.50
Consensus pattern (85 bp):
AAATGTTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAGTTATGTAAGTTATGAT
CCAAAGTTTTTTTATTCTTT
Found at i:17548217 original size:9 final size:9
Alignment explanation
Indices: 17548205--17548270 Score: 66
Period size: 9 Copynumber: 7.6 Consensus size: 9
17548195 TGATATATAT
17548205 TTATGTAAG
1 TTATGTAAG
17548214 TTATGTAAG
1 TTATGTAAG
*
17548223 TTATGGTATG
1 TTAT-GTAAG
* * *
17548233 ATATAT-AT
1 TTATGTAAG
17548241 TTATGT-A-
1 TTATGTAAG
17548248 TTATGTAAG
1 TTATGTAAG
17548257 TTATGTAAG
1 TTATGTAAG
17548266 TTATG
1 TTATG
17548271 ATCCAAAGGT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
7 6 0.13
8 6 0.13
9 28 0.60
10 7 0.15
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:17548225 original size:36 final size:34
Alignment explanation
Indices: 17548174--17548261 Score: 142
Period size: 36 Copynumber: 2.6 Consensus size: 34
17548164 TATTCTTTAA
17548174 ATGT-TTATGTAAGTTATGATATGATATATATTT
1 ATGTATTATGTAAGTTATGATATGATATATATTT
*
17548207 ATGTAAGTTATGTAAGTTATGGTATGATATATATTT
1 ATGT-A-TTATGTAAGTTATGATATGATATATATTT
17548243 ATGTATTATGTAAGTTATG
1 ATGTATTATGTAAGTTATG
17548262 TAAGTTATGA
Statistics
Matches: 51, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
33 4 0.08
34 14 0.27
35 1 0.02
36 32 0.63
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (34 bp):
ATGTATTATGTAAGTTATGATATGATATATATTT
Found at i:17548240 original size:121 final size:124
Alignment explanation
Indices: 17548093--17548323 Score: 378
Period size: 121 Copynumber: 1.8 Consensus size: 124
17548083 CTTTAAATGT
17548093 TTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAGTTATGTAAGTTATGATCCAAA-
1 TTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAGTTATGTAAGTTATGATCCAAAG
17548157 G-TTTT-TTTATTCTTTAAATGTTTATGTAAGTTATGATATGATATATATTTATGTAAG
66 GTTTTTATTTATTCTTTAAATGTTTATGTAAGTTATGATATGATATATATTTATGTAAG
*
17548214 TTATGTAAGTTATGGTATGATATATATTTATGTATTATGTAAGTTATGTAAGTTATGATCCAAAG
1 TTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAGTTATGTAAGTTATGATCCAAAG
17548279 GTTTTTTTTTTTATTTATTCTTTAAATGTTTATGTAAGTTATGAT
66 G------TTTTTATTTATTCTTTAAATGTTTATGTAAGTTATGAT
17548324 TATCATCTTT
Statistics
Matches: 100, Mismatches: 1, Indels: 9
0.91 0.01 0.08
Matches are distributed among these distances:
121 63 0.63
122 1 0.01
129 4 0.04
130 32 0.32
ACGTcount: A:0.31, C:0.03, G:0.15, T:0.51
Consensus pattern (124 bp):
TTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAGTTATGTAAGTTATGATCCAAAG
GTTTTTATTTATTCTTTAAATGTTTATGTAAGTTATGATATGATATATATTTATGTAAG
Found at i:17548348 original size:13 final size:13
Alignment explanation
Indices: 17548330--17548356 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17548320 TGATTATCAT
17548330 CTTTAAATTTTAA
1 CTTTAAATTTTAA
17548343 CTTTAAATTTTAA
1 CTTTAAATTTTAA
17548356 C
1 C
17548357 CTTTTAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (13 bp):
CTTTAAATTTTAA
Found at i:17548365 original size:14 final size:14
Alignment explanation
Indices: 17548330--17548381 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
17548320 TGATTATCAT
17548330 CTTTAAATTTTAA-
1 CTTTAAATTTTAAC
17548343 CTTTAAATTTTAAC
1 CTTTAAATTTTAAC
* * *
17548357 CTTTTAATTGTACC
1 CTTTAAATTTTAAC
*
17548371 CTTTTAATTTT
1 CTTTAAATTTT
17548382 TAAATTTGTG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 13 0.38
14 21 0.62
ACGTcount: A:0.29, C:0.13, G:0.02, T:0.56
Consensus pattern (14 bp):
CTTTAAATTTTAAC
Found at i:17549202 original size:8 final size:8
Alignment explanation
Indices: 17549175--17549220 Score: 67
Period size: 8 Copynumber: 5.9 Consensus size: 8
17549165 TTATTTTAGC
17549175 TAAAATTA
1 TAAAATTA
*
17549183 -AAAATAA
1 TAAAATTA
*
17549190 AAAAATTA
1 TAAAATTA
17549198 TAAAATTA
1 TAAAATTA
17549206 TAAAATTA
1 TAAAATTA
17549214 TAAAATT
1 TAAAATT
17549221 TAACATAGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
7 6 0.18
8 28 0.82
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
TAAAATTA
Found at i:17550221 original size:22 final size:22
Alignment explanation
Indices: 17550191--17550233 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
17550181 ATACCAAAAC
*
17550191 AGGCTTTTAGCGGCGTTTTTTT
1 AGGCCTTTAGCGGCGTTTTTTT
17550213 AGGCCTTTAGCGGCGTTTTTT
1 AGGCCTTTAGCGGCGTTTTTT
17550234 AGCGCCGCAA
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:0.09, C:0.16, G:0.28, T:0.47
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGTTTTTTT
Found at i:17550448 original size:86 final size:86
Alignment explanation
Indices: 17550293--17550564 Score: 323
Period size: 86 Copynumber: 3.2 Consensus size: 86
17550283 TTTATTTAAA
* *
17550293 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCACAAACGCCGCTAAAGAATATGAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCACAAACGCCACTAAAGAATAGGAC
*
17550358 CTTTAGCGACGCTTTTTCCAC
66 CTTTAGCGACGCTTTTCCCAC
* * *
17550379 AAACGCCGCTAAAGAACATGATCTTTAGCGACGCTTTACCCACAAACGCCACTAAA-AGTCAGGT
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCACAAACGCCACTAAAGAAT-AGGA
* *
17550443 TCTTTAGCGGCGCTTTTCCCAC
65 CCTTTAGCGACGCTTTTCCCAC
* * * * * ** * ***
17550465 AAACACCGCTAAAGAACCTGACCTTT-GCGGCGCTTTTCCTATTAACACCACTAAAGAACCTGAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCACAAACGCCACTAAAGAATAGGAC
* *
17550529 CTTTAGCGGCGCTTTTCCCAA
66 CTTTAGCGACGCTTTTCCCAC
*
17550550 AAACGCCACTAAAGA
1 AAACGCCGCTAAAGA
17550565 TCATAAAAAA
Statistics
Matches: 158, Mismatches: 26, Indels: 5
0.84 0.14 0.03
Matches are distributed among these distances:
85 59 0.37
86 99 0.63
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.23
Consensus pattern (86 bp):
AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCACAAACGCCACTAAAGAATAGGAC
CTTTAGCGACGCTTTTCCCAC
Found at i:17550512 original size:42 final size:43
Alignment explanation
Indices: 17550301--17550564 Score: 262
Period size: 43 Copynumber: 6.2 Consensus size: 43
17550291 AAAAACGCCG
* * * * *
17550301 CTAAAGAACATGATCTTTAGCGGCGCTTTACCCACAAACGCCG
1 CTAAAGAACCTGACCTTTAGCGGCGCTTTTCCCACAAACACCA
** * * * *
17550344 CTAAAGAATATGACCTTTAGCGACGCTTTTTCCACAAACGCCG
1 CTAAAGAACCTGACCTTTAGCGGCGCTTTTCCCACAAACACCA
* * * * *
17550387 CTAAAGAACATGATCTTTAGCGACGCTTTACCCACAAACGCCA
1 CTAAAGAACCTGACCTTTAGCGGCGCTTTTCCCACAAACACCA
* ** ** *
17550430 CTAAA-AGTCAGGTTCTTTAGCGGCGCTTTTCCCACAAACACCG
1 CTAAAGA-ACCTGACCTTTAGCGGCGCTTTTCCCACAAACACCA
* **
17550473 CTAAAGAACCTGACCTTT-GCGGCGCTTTTCCTATTAACACCA
1 CTAAAGAACCTGACCTTTAGCGGCGCTTTTCCCACAAACACCA
* *
17550515 CTAAAGAACCTGACCTTTAGCGGCGCTTTTCCCAAAAACGCCA
1 CTAAAGAACCTGACCTTTAGCGGCGCTTTTCCCACAAACACCA
17550558 CTAAAGA
1 CTAAAGA
17550565 TCATAAAAAA
Statistics
Matches: 188, Mismatches: 30, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
42 39 0.21
43 148 0.79
44 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.23
Consensus pattern (43 bp):
CTAAAGAACCTGACCTTTAGCGGCGCTTTTCCCACAAACACCA
Found at i:17552864 original size:13 final size:13
Alignment explanation
Indices: 17552846--17552871 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17552836 GCTGAAGCTT
17552846 TGTAAAATGTAAA
1 TGTAAAATGTAAA
17552859 TGTAAAATGTAAA
1 TGTAAAATGTAAA
17552872 AATTTTATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTAAAATGTAAA
Found at i:17554985 original size:21 final size:20
Alignment explanation
Indices: 17554939--17554990 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
17554929 CACTAACTTT
* *
17554939 TAACCTCTAATCCCTAATCC
1 TAACCTCTAACCCCTAATAC
17554959 TAAACCTCTAACCCCTAATTAC
1 T-AACCTCTAACCCCTAA-TAC
*
17554981 TAACCCCTAA
1 TAACCTCTAA
17554991 ACATTATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.04
21 23 0.85
22 3 0.11
ACGTcount: A:0.35, C:0.38, G:0.00, T:0.27
Consensus pattern (20 bp):
TAACCTCTAACCCCTAATAC
Found at i:17555024 original size:21 final size:21
Alignment explanation
Indices: 17554998--17555058 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
17554988 TAAACATTAT
*
17554998 TTAGCCTCTAAACCTTAAACC
1 TTAGCCTCTAAACCATAAACC
*
17555019 TTAGCCTTTAAACCATAAACC
1 TTAGCCTCTAAACCATAAACC
* * *
17555040 ATAACCCCTAAACCCATAA
1 TTAGCCTCTAAA-CCATAA
17555059 TCCATAAACC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 27 0.82
22 6 0.18
ACGTcount: A:0.39, C:0.33, G:0.03, T:0.25
Consensus pattern (21 bp):
TTAGCCTCTAAACCATAAACC
Found at i:17555058 original size:15 final size:15
Alignment explanation
Indices: 17555031--17555068 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
17555021 AGCCTTTAAA
17555031 CCATAAA-CCATAAC
1 CCATAAACCCATAAC
* *
17555045 CCCTAAACCCATAAT
1 CCATAAACCCATAAC
17555060 CCATAAACC
1 CCATAAACC
17555069 TTAAAATGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.45, C:0.39, G:0.00, T:0.16
Consensus pattern (15 bp):
CCATAAACCCATAAC
Found at i:17555073 original size:22 final size:21
Alignment explanation
Indices: 17555026--17555125 Score: 69
Period size: 22 Copynumber: 4.7 Consensus size: 21
17555016 ACCTTAGCCT
*
17555026 TTAAACCATAAACCATAACCC
1 TTAAACCATAAACCATAAACC
* *
17555047 CTAAACCCATAATCCATAAACC
1 TTAAA-CCATAAACCATAAACC
***
17555069 TTAAAATGGTAACACC-TAAACC
1 TT-AAACCATAA-ACCATAAACC
*
17555091 TTAAACTC-TAAACCATATACC
1 TTAAAC-CATAAACCATAAACC
* *
17555112 CTAAACCAAAAACC
1 TTAAACCATAAACC
17555126 CTAACTATAG
Statistics
Matches: 60, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
20 4 0.07
21 25 0.42
22 26 0.43
23 5 0.08
ACGTcount: A:0.47, C:0.31, G:0.02, T:0.20
Consensus pattern (21 bp):
TTAAACCATAAACCATAAACC
Found at i:17555103 original size:14 final size:14
Alignment explanation
Indices: 17555083--17555129 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
17555073 AATGGTAACA
*
17555083 CCTAAACCTTAAAC
1 CCTAAACCATAAAC
* *
17555097 TCTAAACCATATAC
1 CCTAAACCATAAAC
*
17555111 CCTAAACCAAAAAC
1 CCTAAACCATAAAC
17555125 CCTAA
1 CCTAA
17555130 CTATAGTGAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.47, C:0.34, G:0.00, T:0.19
Consensus pattern (14 bp):
CCTAAACCATAAAC
Found at i:17555471 original size:114 final size:114
Alignment explanation
Indices: 17555340--17555678 Score: 529
Period size: 114 Copynumber: 3.0 Consensus size: 114
17555330 CCCCGAAAGC
** *
17555340 GCTTAGGTTTTTTGCGGCGCTTTCTTAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCACTTCC
1 GCTTAGGTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCC
17555405 TTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTT-G
66 TTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTC-TTTTCG
* *
17555454 GCTTAGGTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGACGTTTCC
1 GCTTAGGTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCC
* * * * *
17555519 TTAAAAACGCTGCTAAATCCTCAAAAGCTCAAAAAACAGCGTCTTTTCG
66 TTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCTTTTCG
* * *
17555568 GCTTAAGTTTTTTGCGGCGCTTTCCCAAAAACGTCGCTAAAGCCTTGAGCATTAGCGGCGCTTCC
1 GCTTAGGTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCC
17555633 TTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACCGGCG-CTTT
66 TTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAA-CGGCGTCTTT
17555679 CCCAAAAACG
Statistics
Matches: 203, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
113 4 0.02
114 195 0.96
115 4 0.02
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (114 bp):
GCTTAGGTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCC
TTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCTTTTCG
Found at i:17555733 original size:88 final size:87
Alignment explanation
Indices: 17555582--17555766 Score: 282
Period size: 88 Copynumber: 2.1 Consensus size: 87
17555572 AAGTTTTTTG
* * *
17555582 CGGCGCTTTCCCAAAAACGTCGCTAAAGCCTTGAGCATTAGCGGCGCTTCCTTAAAAACGCCGCT
1 CGGCGCTTTCCCAAAAACGTCGCTAAAGCCCTGAGCAGTAGCGACGCTTCCTTAAAAACGCCGCT
*
17555647 AAATCCCCGAAAGCTCACAAAA
66 AAATCCCCAAAAGCTCACAAAA
* *
17555669 CCGGCGCTTTCCCAAAAACG-CTGCTAAAGCCCTGAGCAGTAGCGACGCTTCTTTAAAAATGCCG
1 -CGGCGCTTTCCCAAAAACGTC-GCTAAAGCCCTGAGCAGTAGCGACGCTTCCTTAAAAACGCCG
17555733 CTAAATCCCCAAAAGCTCACAAAA
64 CTAAATCCCCAAAAGCTCACAAAA
17555757 CGGCGTCTTT
1 CGGCG-CTTT
17555767 TTGGCTTAGA
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
87 6 0.07
88 83 0.93
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.19
Consensus pattern (87 bp):
CGGCGCTTTCCCAAAAACGTCGCTAAAGCCCTGAGCAGTAGCGACGCTTCCTTAAAAACGCCGCT
AAATCCCCAAAAGCTCACAAAA
Found at i:17555806 original size:73 final size:73
Alignment explanation
Indices: 17555723--17555883 Score: 277
Period size: 73 Copynumber: 2.2 Consensus size: 73
17555713 ACGCTTCTTT
*
17555723 AAAAATGCCGCTAAATCCCCAAAAGCTCACAAAACGGCGTCTTTTTGGCTTAGATTATTTGCGGC
1 AAAAATGCCGCTAAATCCCCAAAAGCTCACAAAACGGCGTCATTTTGGCTTAGATTATTTGCGGC
*
17555788 GCTTTCTC
66 GCTTTCCC
* * *
17555796 AAAAACGCCGCTAAATCCCCAAAAGCTCACAAAACGGCGTCATTTTGGCTTAGGTTTTTTGCGGC
1 AAAAATGCCGCTAAATCCCCAAAAGCTCACAAAACGGCGTCATTTTGGCTTAGATTATTTGCGGC
17555861 GCTTTCCC
66 GCTTTCCC
17555869 AAAAATGCCGCTAAA
1 AAAAATGCCGCTAAA
17555884 GCCCTGAGCA
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 82 1.00
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (73 bp):
AAAAATGCCGCTAAATCCCCAAAAGCTCACAAAACGGCGTCATTTTGGCTTAGATTATTTGCGGC
GCTTTCCC
Found at i:17555985 original size:187 final size:186
Alignment explanation
Indices: 17555670--17556040 Score: 553
Period size: 187 Copynumber: 2.0 Consensus size: 186
17555660 CTCACAAAAC
* * *
17555670 CGGCGCTTTCCCAAAAACGCTGCTAAAGCCCTGAGCAGTAGCGACGCTTCTTTAAAAATGCCGCT
1 CGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCAGTAGCGACGCTTCCTTAAAAACGCCGCT
* * *
17555735 AAATCCCCAAAAGCTCACAAAACGGCGTCTTTTTGGCTTAGATTATTTGCGGCGCTTTCTCAAAA
66 AAATCCCCAAAAGCTCACAAAACGGCATCGTTTTGGCTTAGATTATTTGCGACGCTTTCTCAAAA
* * *
17555800 ACGCCGCTAAATCCCCAAAAGCTCACAAAACGGCGTCATTTTGGCTTAGGTTTTTTG
131 ACACCGCTAAATCCCCAAAAGCTCACAAAACGGCGTC-GTTGGGCTTAGGTTTTTTG
* * * * *
17555857 CGGCGCTTTCCCAAAAATGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCTTGAAAACGCTGCT
1 CGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCAGTAGCGACGCTTCCTTAAAAACGCCGCT
* * * * *
17555922 AAATTCCCGAAAGCTCACAAAACGGCATCGTTTTGGCTTAGGTTTTTTGCGACTCTTTCTCAAAA
66 AAATCCCCAAAAGCTCACAAAACGGCATCGTTTTGGCTTAGATTATTTGCGACGCTTTCTCAAAA
*
17555987 ACACCGCTAAATCCCCAAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTT
131 ACACCGCTAAATCCCCAAAAGCTCACAAAACGGCGTCGTTGGGCTTAGGTTTTT
17556041 GTGGTGCTTT
Statistics
Matches: 164, Mismatches: 20, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
186 15 0.09
187 149 0.91
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (186 bp):
CGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCAGTAGCGACGCTTCCTTAAAAACGCCGCT
AAATCCCCAAAAGCTCACAAAACGGCATCGTTTTGGCTTAGATTATTTGCGACGCTTTCTCAAAA
ACACCGCTAAATCCCCAAAAGCTCACAAAACGGCGTCGTTGGGCTTAGGTTTTTTG
Found at i:17555986 original size:114 final size:114
Alignment explanation
Indices: 17555783--17555997 Score: 313
Period size: 114 Copynumber: 1.9 Consensus size: 114
17555773 TAGATTATTT
* *
17555783 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCAAAAGCTCACAAAACGGCGTCATTTTGGCTTA
1 GCGGCGCTTCCTCAAAAACGCCGCTAAATCCCCAAAAGCTCACAAAACGGCATCATTTTGGCTTA
* **
17555848 GGTTTTTTGCGGCGCTTTCCCAAAAATGCCGCTAAAGCCCTGAGCATTA
66 GGTTTTTTGCGACGCTTTCCCAAAAACACCGCTAAAGCCCTGAGCATTA
** * * * *
17555897 GCGGCGCTTCCTTGAAAACGCTGCTAAATTCCCGAAAGCTCACAAAACGGCATCGTTTTGGCTTA
1 GCGGCGCTTCCTCAAAAACGCCGCTAAATCCCCAAAAGCTCACAAAACGGCATCATTTTGGCTTA
* *
17555962 GGTTTTTTGCGACTCTTTCTCAAAAACACCGCTAAA
66 GGTTTTTTGCGACGCTTTCCCAAAAACACCGCTAAA
17555998 TCCCCAAAAG
Statistics
Matches: 88, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
114 88 1.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.26
Consensus pattern (114 bp):
GCGGCGCTTCCTCAAAAACGCCGCTAAATCCCCAAAAGCTCACAAAACGGCATCATTTTGGCTTA
GGTTTTTTGCGACGCTTTCCCAAAAACACCGCTAAAGCCCTGAGCATTA
Found at i:17558404 original size:50 final size:50
Alignment explanation
Indices: 17558221--17558405 Score: 226
Period size: 50 Copynumber: 3.7 Consensus size: 50
17558211 GATAATAACA
* * * ** * *
17558221 TGCCAAAGACATGTCCCAGACATTGTCTTACATGGGATGTTCTCATATCGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * * **
17558272 TGCCCATGCCATGTCCCAAACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
17558322 TGCCAACACCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
17558372 TGCCAACGCCATGTCCCAGGCATGGTCTTACATG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATG
17558406 AGATCTCTTT
Statistics
Matches: 113, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
50 83 0.73
51 30 0.27
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:17563039 original size:34 final size:35
Alignment explanation
Indices: 17563001--17563088 Score: 97
Period size: 34 Copynumber: 2.5 Consensus size: 35
17562991 TACATGTTTA
* *
17563001 ACCATCCAACACACCAGATGCTTATAAGAGCTA-T
1 ACCATCCAACACACCAGATGCTCATAAGAGCCAGT
* * * *
17563035 ACCATCTAGCACACCAAATGCTCATAATAGCCAGT
1 ACCATCCAACACACCAGATGCTCATAAGAGCCAGT
* *
17563070 ACCAACCATCACACCAGAT
1 ACCATCCAACACACCAGAT
17563089 AACACTGTAA
Statistics
Matches: 43, Mismatches: 10, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
34 27 0.63
35 16 0.37
ACGTcount: A:0.39, C:0.33, G:0.10, T:0.18
Consensus pattern (35 bp):
ACCATCCAACACACCAGATGCTCATAAGAGCCAGT
Found at i:17563590 original size:31 final size:31
Alignment explanation
Indices: 17563548--17563614 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
17563538 TCCATGGCTC
*
17563548 AATTTTCAACCCATTCTTGATTTAGAATAAT
1 AATTTTCAACCCATTCTTGATCTAGAATAAT
*
17563579 AATTTTTAACCCATTCTTGATCTAGAATAAT
1 AATTTTCAACCCATTCTTGATCTAGAATAAT
17563610 AATTT
1 AATTT
17563615 CATTCAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.36, C:0.15, G:0.06, T:0.43
Consensus pattern (31 bp):
AATTTTCAACCCATTCTTGATCTAGAATAAT
Found at i:17568058 original size:29 final size:28
Alignment explanation
Indices: 17568024--17568122 Score: 72
Period size: 29 Copynumber: 3.4 Consensus size: 28
17568014 AATTGAATAA
*
17568024 TTGGTGACCATTTTATAACTTTTCATAG
1 TTGGTGACCATTTTATAAATTTTCATAG
* **** *
17568052 TTAGGTGACTAAAAAATAAATTTACTAATAG
1 TT-GGTGACCATTTTATAAATTT--TCATAG
* *
17568083 TTGGATAACCATTTTATAATTTTTCATAG
1 TTGG-TGACCATTTTATAAATTTTCATAG
17568112 TTGGGTGACCA
1 TT-GGTGACCA
17568123 AAAATGAAAA
Statistics
Matches: 50, Mismatches: 16, Indels: 9
0.67 0.21 0.12
Matches are distributed among these distances:
28 2 0.04
29 26 0.52
30 4 0.08
31 18 0.36
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.40
Consensus pattern (28 bp):
TTGGTGACCATTTTATAAATTTTCATAG
Found at i:17568143 original size:60 final size:59
Alignment explanation
Indices: 17568030--17568145 Score: 135
Period size: 60 Copynumber: 1.9 Consensus size: 59
17568020 ATAATTGGTG
* * ***
17568030 ACCATTTTATAACTTTTCATAGTTAGGTGACTAAAAAATAAATTTACTAATAGTTGGATA
1 ACCATTTTATAACTTTTCATAGTTAGGTGACCAAAAAAAAAAAAAAC-AATAGTTGGATA
* *
17568090 ACCATTTTATAATTTTTCATAGTTGGGTGACCAAAAATGAAAAAAAAAC-ATAGTTG
1 ACCATTTTATAACTTTTCATAGTTAGGTGACCAAAAA--AAAAAAAAACAATAGTTG
17568146 AATGACTTCT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
60 41 0.87
62 6 0.13
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.35
Consensus pattern (59 bp):
ACCATTTTATAACTTTTCATAGTTAGGTGACCAAAAAAAAAAAAAACAATAGTTGGATA
Found at i:17573350 original size:16 final size:16
Alignment explanation
Indices: 17573329--17573359 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17573319 AAATAAAGTA
17573329 TAATAAAACAAATAGG
1 TAATAAAACAAATAGG
*
17573345 TAATAAAAGAAATAG
1 TAATAAAACAAATAG
17573360 AAATCCATGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.03, G:0.13, T:0.19
Consensus pattern (16 bp):
TAATAAAACAAATAGG
Found at i:17580485 original size:52 final size:52
Alignment explanation
Indices: 17580311--17580499 Score: 220
Period size: 52 Copynumber: 3.6 Consensus size: 52
17580301 TGTACCGGAA
* * * * *
17580311 TAGCAGGCCTTGAGCC-AGTGTTTACTTAGCAAGCCTTAAGCCAGTGTTTATT
1 TAGCAGGCTTTGAGCCGA-TGATTACTTAGCAGGCCTTGAGCCGGTGTTTATT
* * *
17580363 TAGCAGGCTTTGAGCTGATGTTTACTTAGCAGGCCTTGAGCCGATGTTTATT
1 TAGCAGGCTTTGAGCCGATGATTACTTAGCAGGCCTTGAGCCGGTGTTTATT
* * *
17580415 TAGTAGGTTTTGAGCCGATGATTACTTAGTAGG-CTATGAGCCGGTGTTTATT
1 TAGCAGGCTTTGAGCCGATGATTACTTAGCAGGCCT-TGAGCCGGTGTTTATT
* * *
17580467 TAGCAGGCTTTGAACCGATGAATAGTTAGCAGG
1 TAGCAGGCTTTGAGCCGATGATTACTTAGCAGG
17580500 TATTATGTAC
Statistics
Matches: 117, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
51 2 0.02
52 114 0.97
53 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (52 bp):
TAGCAGGCTTTGAGCCGATGATTACTTAGCAGGCCTTGAGCCGGTGTTTATT
Found at i:17580499 original size:26 final size:26
Alignment explanation
Indices: 17580311--17580486 Score: 176
Period size: 26 Copynumber: 6.8 Consensus size: 26
17580301 TGTACCGGAA
*
17580311 TAGCAGGCCTTGAGCC-AGTGTTTACT
1 TAGCAGGCTTTGAGCCGA-TGTTTACT
* * * *
17580337 TAGCAAGCCTTAAGCC-AGTGTTTATT
1 TAGCAGGCTTTGAGCCGA-TGTTTACT
*
17580363 TAGCAGGCTTTGAGCTGATGTTTACT
1 TAGCAGGCTTTGAGCCGATGTTTACT
* *
17580389 TAGCAGGCCTTGAGCCGATGTTTATT
1 TAGCAGGCTTTGAGCCGATGTTTACT
* * *
17580415 TAGTAGGTTTTGAGCCGATGATTACT
1 TAGCAGGCTTTGAGCCGATGTTTACT
* * * *
17580441 TAGTAGGCTATGAGCCGGTGTTTATT
1 TAGCAGGCTTTGAGCCGATGTTTACT
*
17580467 TAGCAGGCTTTGAACCGATG
1 TAGCAGGCTTTGAGCCGATG
17580487 AATAGTTAGC
Statistics
Matches: 124, Mismatches: 25, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
26 123 0.99
27 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.35
Consensus pattern (26 bp):
TAGCAGGCTTTGAGCCGATGTTTACT
Found at i:17581110 original size:12 final size:13
Alignment explanation
Indices: 17581095--17581129 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
17581085 TAAAAATAGA
*
17581095 TATATGAATTG-T
1 TATATGAAGTGTT
17581107 TATATGAAGTGTT
1 TATATGAAGTGTT
17581120 TATATGAAGT
1 TATATGAAGT
17581130 ATTTGTTGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (13 bp):
TATATGAAGTGTT
Found at i:17583163 original size:42 final size:42
Alignment explanation
Indices: 17583102--17583218 Score: 157
Period size: 42 Copynumber: 2.8 Consensus size: 42
17583092 GATATGTGTT
*
17583102 TTCGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGA
1 TTCGTGTAAGACCACGTCTGGGACGTTGGCATCGACATGTGA
17583144 TTCGTGTAAGACC-CTGTCTGGGACAG-TGGCATCGACATGTGA
1 TTCGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGACATGTGA
* * *
17583186 TTACATGTAAGACCACGTTTGTGACGTTGGCAT
1 TT-CGTGTAAGACCACGTCTGGGACGTTGGCAT
17583219 TGTACGGAGT
Statistics
Matches: 66, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
41 1 0.02
42 40 0.61
43 24 0.36
44 1 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (42 bp):
TTCGTGTAAGACCACGTCTGGGACGTTGGCATCGACATGTGA
Found at i:17586297 original size:36 final size:36
Alignment explanation
Indices: 17586250--17586324 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
17586240 GAGGAAAACA
17586250 TATCTACTAGTATTAATCGAGGGAACTGTTCCTTTC
1 TATCTACTAGTATTAATCGAGGGAACTGTTCCTTTC
17586286 TATCTACTAGTATTAATCGAGGGAACTGTTCCTTTC
1 TATCTACTAGTATTAATCGAGGGAACTGTTCCTTTC
17586322 TAT
1 TAT
17586325 GGAGAGCTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (36 bp):
TATCTACTAGTATTAATCGAGGGAACTGTTCCTTTC
Found at i:17587038 original size:9 final size:9
Alignment explanation
Indices: 17587024--17587060 Score: 74
Period size: 9 Copynumber: 4.1 Consensus size: 9
17587014 TGAGTTTTCG
17587024 AATTCGAAT
1 AATTCGAAT
17587033 AATTCGAAT
1 AATTCGAAT
17587042 AATTCGAAT
1 AATTCGAAT
17587051 AATTCGAAT
1 AATTCGAAT
17587060 A
1 A
17587061 TCAAAATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:17587143 original size:30 final size:30
Alignment explanation
Indices: 17587109--17587165 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
17587099 AAACCTTTTT
* *
17587109 ACTTTTCCCTCAAAACTTTTACTCCTTCCC
1 ACTTTCCCCCCAAAACTTTTACTCCTTCCC
17587139 ACTTTCCCCCCAAAACTTTTACTCCTT
1 ACTTTCCCCCCAAAACTTTTACTCCTT
17587166 TCCCCTCCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.21, C:0.40, G:0.00, T:0.39
Consensus pattern (30 bp):
ACTTTCCCCCCAAAACTTTTACTCCTTCCC
Found at i:17587311 original size:30 final size:31
Alignment explanation
Indices: 17587275--17587334 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
17587265 AAACCTTTTA
*
17587275 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
17587305 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
17587335 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:17587453 original size:19 final size:17
Alignment explanation
Indices: 17587403--17587459 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 17
17587393 CTATTTACTT
17587403 TCCCTCAAACTTTTATTC
1 TCCCT-AAACTTTTATTC
*
17587421 T-CCAAAACTTTTTATTTTC
1 TCCCTAAAC-TTTTA--TTC
17587440 TCCCTAAACTTTTACTTC
1 TCCCTAAACTTTTA-TTC
17587458 TC
1 TC
17587460 ACCATTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 4 0.12
17 7 0.22
18 6 0.19
19 9 0.28
20 6 0.19
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (17 bp):
TCCCTAAACTTTTATTC
Found at i:17589435 original size:3 final size:3
Alignment explanation
Indices: 17589427--17589454 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
17589417 ACTGATATTG
17589427 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
17589455 TGTATATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:17590903 original size:17 final size:17
Alignment explanation
Indices: 17590881--17590931 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
17590871 TTTTATTTTT
17590881 ATATAAAAAATTAAAAA
1 ATATAAAAAATTAAAAA
* * *
17590898 ATATAATACA-TCAAAA
1 ATATAAAAAATTAAAAA
17590914 ATACTAAAAACATTAAAA
1 ATA-TAAAAA-ATTAAAA
17590932 TAAATGTTTC
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
16 8 0.32
17 12 0.48
18 1 0.04
19 4 0.16
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.24
Consensus pattern (17 bp):
ATATAAAAAATTAAAAA
Found at i:17591132 original size:22 final size:22
Alignment explanation
Indices: 17591104--17591169 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
17591094 TAGTGAAATG
*
17591104 ACAACAATACAGTGGGAAAACA
1 ACAACAAAACAGTGGGAAAACA
* * *
17591126 ACAACAAAATAGTGAGAAAGCA
1 ACAACAAAACAGTGGGAAAACA
* * *
17591148 ACAGCAAAAGAGAGGGAAAACA
1 ACAACAAAACAGTGGGAAAACA
17591170 TCAATTTCTT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.58, C:0.15, G:0.21, T:0.06
Consensus pattern (22 bp):
ACAACAAAACAGTGGGAAAACA
Found at i:17592501 original size:24 final size:24
Alignment explanation
Indices: 17592472--17592543 Score: 74
Period size: 28 Copynumber: 2.8 Consensus size: 24
17592462 GAAAAAAAAA
17592472 ACTTAAACATAGAATTTTATAAAT
1 ACTTAAACATAGAATTTTATAAAT
* *
17592496 AGTT-AACATGAAGTGTTATTTTATAAAT
1 ACTTAAACAT--A--G-AATTTTATAAAT
17592524 ACTTAAACATAGAATTTTAT
1 ACTTAAACATAGAATTTTAT
17592544 TGTTGCCTAG
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
23 5 0.13
24 10 0.26
25 2 0.05
27 2 0.05
28 14 0.37
29 5 0.13
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.40
Consensus pattern (24 bp):
ACTTAAACATAGAATTTTATAAAT
Found at i:17594215 original size:23 final size:23
Alignment explanation
Indices: 17594184--17594236 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
17594174 TGATTTAAAC
* *
17594184 AAATGTTCATA-TTTATATTATTA
1 AAATATTCATATTTTATACTA-TA
17594207 AAATATTCATATTTTATACTATA
1 AAATATTCATATTTTATACTATA
17594230 AAATATT
1 AAATATT
17594237 TTTACTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (23 bp):
AAATATTCATATTTTATACTATA
Found at i:17594282 original size:22 final size:23
Alignment explanation
Indices: 17594257--17594312 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 23
17594247 TTATAAATTG
*
17594257 TAATATATTTTT-ATTAAAATAT
1 TAATATATTTTTCAATAAAATAT
17594279 TAATATGATTTTTCAATAAAATAT
1 TAATAT-ATTTTTCAATAAAATAT
17594303 TAATAATATT
1 TAAT-ATATT
17594313 ACTTCAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 6 0.20
23 6 0.20
24 16 0.53
25 2 0.07
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
TAATATATTTTTCAATAAAATAT
Found at i:17599024 original size:13 final size:13
Alignment explanation
Indices: 17599000--17599024 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17598990 ATTTTTTTAA
17599000 TGAATAATTTTTT
1 TGAATAATTTTTT
17599013 TGAATAATTTTT
1 TGAATAATTTTT
17599025 ATTTTAATTA
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:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (13 bp):
TGAATAATTTTTT
Found at i:17607952 original size:84 final size:85
Alignment explanation
Indices: 17607830--17608009 Score: 335
Period size: 84 Copynumber: 2.1 Consensus size: 85
17607820 TAGCAACAAA
17607830 AAAATATATAAAATAAAAAATAAAAAAATCCAACAAACTTTAAAAAGAAAAAATCTTCTCCTTCC
1 AAAA-ATATAAAATAAAAAATAAAAAAATCCAACAAACTTTAAAAAGAAAAAATCTTCTCCTTCC
17607895 TTTATTATTATTCTTCTATCC
65 TTTATTATTATTCTTCTATCC
17607916 AAAAATATAAAATAAAAAAT-AAAAAATCCAACAAACTTTAAAAAGAAAAAATCTTCTCCTTCCT
1 AAAAATATAAAATAAAAAATAAAAAAATCCAACAAACTTTAAAAAGAAAAAATCTTCTCCTTCCT
17607980 TTATTATTATTCTTCTATCC
66 TTATTATTATTCTTCTATCC
*
17608000 AAACATATAA
1 AAAAATATAA
17608010 CAGAAAATAA
Statistics
Matches: 93, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
84 73 0.78
85 16 0.17
86 4 0.04
ACGTcount: A:0.51, C:0.16, G:0.01, T:0.32
Consensus pattern (85 bp):
AAAAATATAAAATAAAAAATAAAAAAATCCAACAAACTTTAAAAAGAAAAAATCTTCTCCTTCCT
TTATTATTATTCTTCTATCC
Found at i:17610450 original size:16 final size:15
Alignment explanation
Indices: 17610429--17610458 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
17610419 AAGTTTTAAA
17610429 AAAACTTTAACAAAAT
1 AAAACTTTAA-AAAAT
17610445 AAAACTTTAAAAAA
1 AAAACTTTAAAAAA
17610459 GTTTAAGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAACTTTAAAAAAT
Found at i:17615562 original size:18 final size:18
Alignment explanation
Indices: 17615518--17615553 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
17615508 TTTCTTATAG
* *
17615518 AATTTAGTTTTTTTAATA
1 AATTTAATTCTTTTAATA
17615536 AATTTAATTCTTTTAATA
1 AATTTAATTCTTTTAATA
17615554 TTTTTAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (18 bp):
AATTTAATTCTTTTAATA
Found at i:17617805 original size:13 final size:14
Alignment explanation
Indices: 17617768--17617811 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
17617758 GAAAAAAATT
17617768 ATATATATTTAATA
1 ATATATATTTAATA
17617782 ATATTATTATTTAA-A
1 ATA-TA-TATTTAATA
*
17617797 TTATATATTTAATA
1 ATATATATTTAATA
17617811 A
1 A
17617812 AATTTATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 7 0.28
14 6 0.24
15 5 0.20
16 7 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATATATATTTAATA
Found at i:17617812 original size:16 final size:16
Alignment explanation
Indices: 17617769--17617812 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
17617759 AAAAAAATTA
17617769 TATATATTTAATAATAT
1 TATATATTTAATAA-AT
17617786 TAT-TA-TT--TAAAT
1 TATATATTTAATAAAT
17617798 TATATATTTAATAAA
1 TATATATTTAATAAA
17617813 ATTTATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 9
0.72 0.00 0.28
Matches are distributed among these distances:
12 5 0.22
13 5 0.22
14 2 0.09
15 2 0.09
16 6 0.26
17 3 0.13
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATATATTTAATAAAT
Found at i:17617814 original size:17 final size:17
Alignment explanation
Indices: 17617769--17617819 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
17617759 AAAAAAATTA
*
17617769 TATATATTTAATAATAT
1 TATATATTTAATAAAAT
17617786 TAT-TA-TT--T-AAAT
1 TATATATTTAATAAAAT
17617798 TATATATTTAATAAAAT
1 TATATATTTAATAAAAT
17617815 T-TATA
1 TATATA
17617820 AATGTAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 11
0.70 0.03 0.28
Matches are distributed among these distances:
12 6 0.21
13 3 0.11
14 2 0.07
15 2 0.07
16 7 0.25
17 8 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATATTTAATAAAAT
Found at i:17617828 original size:31 final size:29
Alignment explanation
Indices: 17617769--17617830 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
17617759 AAAAAAATTA
* * *
17617769 TATATATTTAATAATATTATTATTTAAAT
1 TATATATTTAATAAAATTATAATGTAAAT
17617798 TATATATTTAATAAAATTTATAAATGTAAAT
1 TATATATTTAATAAAA-TTAT-AATGTAAAT
17617829 TA
1 TA
17617831 AGATTAGTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 15 0.54
30 4 0.14
31 9 0.32
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (29 bp):
TATATATTTAATAAAATTATAATGTAAAT
Found at i:17618653 original size:14 final size:15
Alignment explanation
Indices: 17618636--17618665 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
17618626 TTGATTAAAT
17618636 TAATAAAG-TTAAGA
1 TAATAAAGATTAAGA
17618650 TAATAAAGATTAAGA
1 TAATAAAGATTAAGA
17618665 T
1 T
17618666 GTTTTGATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.57, C:0.00, G:0.13, T:0.30
Consensus pattern (15 bp):
TAATAAAGATTAAGA
Found at i:17623612 original size:21 final size:21
Alignment explanation
Indices: 17623567--17623612 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
17623557 AGTTGACAAT
* *
17623567 GAAACAATCGATTGAAAATAA
1 GAAACAATCAATTGAAAAGAA
* *
17623588 GAAACAATCAATTGAACAGAG
1 GAAACAATCAATTGAAAAGAA
17623609 GAAA
1 GAAA
17623613 GAATGAATCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.57, C:0.11, G:0.17, T:0.15
Consensus pattern (21 bp):
GAAACAATCAATTGAAAAGAA
Found at i:17625309 original size:2 final size:2
Alignment explanation
Indices: 17625302--17625332 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
17625292 CTCCAAACTC
17625302 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
17625333 GGTCCAAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:17631038 original size:25 final size:25
Alignment explanation
Indices: 17630974--17631059 Score: 97
Period size: 25 Copynumber: 3.5 Consensus size: 25
17630964 GCGGGCACAG
*
17630974 CACAGCTTGTACT-AGCTTACCGATT
1 CACAGCTCGTA-TGAGCTTACCGATT
*
17630999 -TCAGCTCGTGA-GAGCTTACCGATT
1 CACAGCTCGT-ATGAGCTTACCGATT
*
17631023 CACAGCTTGTATGAGCTTACCGATT
1 CACAGCTCGTATGAGCTTACCGATT
*
17631048 TACAGCTCGTAT
1 CACAGCTCGTAT
17631060 AAGCATACAT
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
24 20 0.39
25 31 0.61
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (25 bp):
CACAGCTCGTATGAGCTTACCGATT
Found at i:17635944 original size:27 final size:27
Alignment explanation
Indices: 17635895--17635949 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
17635885 GTATAGCAAC
* *
17635895 CAAGGTAGTCCACTGGGATAGTAAACA
1 CAAGGTAGTCCACTGGCACAGTAAACA
* *
17635922 CAAGGTAGTCTACTGTCACAGTAAACA
1 CAAGGTAGTCCACTGGCACAGTAAACA
17635949 C
1 C
17635950 GATGATTACG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (27 bp):
CAAGGTAGTCCACTGGCACAGTAAACA
Found at i:17640599 original size:26 final size:26
Alignment explanation
Indices: 17640557--17640643 Score: 102
Period size: 26 Copynumber: 3.3 Consensus size: 26
17640547 ATTACTGGCG
*
17640557 AACCCTATGGTAGACACACTCTAGCA
1 AACCCTATGGTAAACACACTCTAGCA
* **
17640583 AACCCTATGGCAAACACACTCTAGTG
1 AACCCTATGGTAAACACACTCTAGCA
* * * *
17640609 AACCCTATAGTGAACTCACTCTAACA
1 AACCCTATGGTAAACACACTCTAGCA
17640635 AACCCTATG
1 AACCCTATG
17640644 CCTGGAGAAC
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.36, C:0.31, G:0.13, T:0.21
Consensus pattern (26 bp):
AACCCTATGGTAAACACACTCTAGCA
Found at i:17643402 original size:49 final size:47
Alignment explanation
Indices: 17643277--17643425 Score: 226
Period size: 47 Copynumber: 3.1 Consensus size: 47
17643267 CAGCCAAGAG
* *
17643277 AGTGTATATGTGTGATAAGGCCTAATTGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * *
17643324 AGTGTATATATATAATAAGGCCTAATGGCCGATGTGATAAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
17643371 AGTGTATGTATATGTGATAAGGCCTAATGGCCGATGTGATGGATGTGAA
1 AGTGTA--TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
17643420 AGTGTA
1 AGTGTA
17643426 ATTAACGGCA
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
47 48 0.53
49 43 0.47
ACGTcount: A:0.32, C:0.08, G:0.29, T:0.31
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:17643822 original size:47 final size:47
Alignment explanation
Indices: 17643741--17643991 Score: 328
Period size: 47 Copynumber: 5.4 Consensus size: 47
17643731 TAATTGAATA
* * *
17643741 AATGTGAA-AGTGTATATGTGTGAATAGGGCCGAATGGCCAATGTGATG
1 AATGTGAACA-TGTGTATGTGAG-ATAAGGCCGAATGGCCAATGTGATG
** *
17643789 AATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTGTATGTGAGATAAGGCCGAATGGCCAATGTGATG
*
17643836 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTGTATGTGAGATAAGGCCGAATGGCCAATGTGATG
* * * *
17643883 AAAGTGAACAGGTGTATGTGTGATAAGGCCGAGTGGCCAATGTGATG
1 AATGTGAACATGTGTATGTGAGATAAGGCCGAATGGCCAATGTGATG
* * * *
17643930 AATGTGAGCATGTGTATGTGAGATAGGGCCTAATGGCCGATGTGATG
1 AATGTGAACATGTGTATGTGAGATAAGGCCGAATGGCCAATGTGATG
17643977 AATGTGAA-A-GTGTAT
1 AATGTGAACATGTGTAT
17643992 AATTGTGATA
Statistics
Matches: 182, Mismatches: 20, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
45 6 0.03
46 1 0.01
47 157 0.86
48 17 0.09
49 1 0.01
ACGTcount: A:0.31, C:0.10, G:0.33, T:0.26
Consensus pattern (47 bp):
AATGTGAACATGTGTATGTGAGATAAGGCCGAATGGCCAATGTGATG
Found at i:17644178 original size:37 final size:37
Alignment explanation
Indices: 17644122--17644201 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
17644112 CCGGACTCTA
* * *
17644122 AAGACCCGATGACTGCGTGTGG-GAATTTTGTCCGGGT
1 AAGACTCGATAACTGCGTGTGGAG-ATTATGTCCGGGT
*
17644159 AAGACTCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACTCGATAACTGCGTGTGGAGATTATGTCCGGGT
17644196 AAGACT
1 AAGACT
17644202 TCGTAATAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (37 bp):
AAGACTCGATAACTGCGTGTGGAGATTATGTCCGGGT
Found at i:17644478 original size:307 final size:307
Alignment explanation
Indices: 17643907--17644519 Score: 987
Period size: 307 Copynumber: 2.0 Consensus size: 307
17643897 TATGTGTGAT
* * * * * * * *
17643907 AAGGCCGAGTGGCCAATGTGATGAATGTGAGCATGTGTATGTGAGATAGGGCCTAATGGCCGATG
1 AAGGCCGAATGGCCAATGTGATGAATGTGAGAATGTATATATGAGACAGGGCCGAATGGCCAACG
* * * * *
17643972 TGATGAATGTGAAAGTGTATAATTGTGATAAGTCCCGAAGGGCATTTGTGTCAGTACTATATCCG
66 TAATGAATGTGAAAGTGCATAAATGTGATAAGTCCCGAAAGGAATTTGTGTCAGTACTATATCCG
17644037 GGTTAAAACCCCGCAGGCTTTATGCGAGAATATTATCACTGATTAATGTCCGTAAGCTTCGTGCT
131 GGTTAAAACCCCGCAGGCTTTATGCGAGAATATTATCACTGATTAATGTCCGTAAGCTTCGTGCT
* *
17644102 CGTACTATATCCGGACTCTAAAGACCCGATGACTGCGTGTGGGAATTTTGTCCGGGTAAGACTCG
196 CGTACTATATCCGGACTCTAAAGACCCGATGACTACGTGTGGGAATTTTGTCCGGGTAAGACCCG
17644167 ATAACTTCGTGTGGAGATTATGTCCGGGTAAGACTTCGTAATAAGAG
261 ATAACTTCGTGTGGAGATTATGTCCGGGTAAGACTTCGTAATAAGAG
* * * *
17644214 AAGGCCTAATGGCCGATGTGATGAATGTGA-AAGTGTATATATGTGACAGGGCCGAGTGGCCAAC
1 AAGGCCGAATGGCCAATGTGATGAATGTGAGAA-TGTATATATGAGACAGGGCCGAATGGCCAAC
*
17644278 GTAATGGATGTGAAAGTGCATAAATGTGATAAGTCCCGAAAGGAATTTGTGTCAGTACTATATCC
65 GTAATGAATGTGAAAGTGCATAAATGTGATAAGTCCCGAAAGGAATTTGTGTCAGTACTATATCC
*
17644343 GGGTTAAAACCCCGCAGGCTTTATGCGAGAATATTATCACTGATTAATGTCCTTAAGCTTCGTGC
130 GGGTTAAAACCCCGCAGGCTTTATGCGAGAATATTATCACTGATTAATGTCCGTAAGCTTCGTGC
* *
17644408 TTGTACTATATCC-GAGCTCTAAAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGTAAGACC
195 TCGTACTATATCCGGA-CTCTAAAGACCCGATGACTACGTGTGGGAATTTTGTCCGGGTAAGACC
17644472 CGATAACTTCGTGTGGAGATTATGTCCGGGTAAGACTTCGTAATAAGA
259 CGATAACTTCGTGTGGAGATTATGTCCGGGTAAGACTTCGTAATAAGA
17644520 ATTGCTTATA
Statistics
Matches: 281, Mismatches: 23, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
306 3 0.01
307 278 0.99
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (307 bp):
AAGGCCGAATGGCCAATGTGATGAATGTGAGAATGTATATATGAGACAGGGCCGAATGGCCAACG
TAATGAATGTGAAAGTGCATAAATGTGATAAGTCCCGAAAGGAATTTGTGTCAGTACTATATCCG
GGTTAAAACCCCGCAGGCTTTATGCGAGAATATTATCACTGATTAATGTCCGTAAGCTTCGTGCT
CGTACTATATCCGGACTCTAAAGACCCGATGACTACGTGTGGGAATTTTGTCCGGGTAAGACCCG
ATAACTTCGTGTGGAGATTATGTCCGGGTAAGACTTCGTAATAAGAG
Found at i:17644485 original size:37 final size:37
Alignment explanation
Indices: 17644429--17644507 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
17644419 CCGAGCTCTA
* * *
17644429 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
17644466 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
17644503 AAGAC
1 AAGAC
17644508 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:17644995 original size:278 final size:277
Alignment explanation
Indices: 17644499--17645054 Score: 988
Period size: 278 Copynumber: 2.0 Consensus size: 277
17644489 GATTATGTCC
17644499 GGGTAAGACTTCGTAATAAGAATTGCTTATAAATATATTCAATGCGAAAGGTTAAACAGGTATGT
1 GGGTAAGACTTCGTAATAAGAATTGCTTATAAATATATTCAATGCGAAAGGTTAAACAGGTATGT
** *
17644564 ACTCCAAGTCTATATGTGAGCTTGATTGCACTAAATCATAAGGTAGTTATGTGATGCATGTGAGA
66 ACTCCAAGTCTATATGTGAGCTTGATTGCACTAAATCATAAGGTAGTTATGTGATGCATACGAAA
* *
17644629 GCAATCTATGAGACTACTCTTATGATTATGTGATATCGGATCAGTGTGAGAGGTGATGGGAAATC
131 GCAATCTATGAGACTACTCCTATGATTATGTGACATCGGATCAGTGTGAGAGGTGATGGGAAATC
17644694 ATACGATATATCTATGTCACATGAGCTCACTTTTACGTGAAAGTTTATCTGCCTATTGTATATGA
196 ATACGATATATCTATGTCACATGAGCTCACTTTTACGTGAAAGTTTATCTGCCTATTGTATATGA
17644759 TGAGACGTGC-GTATTCG
261 TGAGACGTGCAG-ATTCG
17644776 GGGTAAGACTTCGTAATAAGAATTGCTTATAAATATATTCAATGCGAAAGGTTAAACAGGTATGT
1 GGGTAAGACTTCGTAATAAGAATTGCTTATAAATATATTCAATGCGAAAGGTTAAACAGGTATGT
* *
17644841 ACTTCAAGTTTATATGTGAGCTTGATTTGCACTAAATCATAAGGTAGTTATGTGATGCATACGAA
66 ACTCCAAGTCTATATGTGAGCTTGA-TTGCACTAAATCATAAGGTAGTTATGTGATGCATACGAA
* *
17644906 AGCAATCTATGAGACTATTCCTATGATTATGTGACATCGGATCAGTGTGAGAGGTGATGTGAAAT
130 AGCAATCTATGAGACTACTCCTATGATTATGTGACATCGGATCAGTGTGAGAGGTGATGGGAAAT
*
17644971 CATACGATATATCTATGTCACATGAGCTCACTTTTATGTGAAAGTTTATCTGCCTATTGTATATG
195 CATACGATATATCTATGTCACATGAGCTCACTTTTACGTGAAAGTTTATCTGCCTATTGTATATG
*
17645036 ATGAGATGTGCAGATTCG
260 ATGAGACGTGCAGATTCG
17645054 G
1 G
17645055 TAAAGGGATG
Statistics
Matches: 266, Mismatches: 11, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
277 88 0.33
278 177 0.67
279 1 0.00
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.33
Consensus pattern (277 bp):
GGGTAAGACTTCGTAATAAGAATTGCTTATAAATATATTCAATGCGAAAGGTTAAACAGGTATGT
ACTCCAAGTCTATATGTGAGCTTGATTGCACTAAATCATAAGGTAGTTATGTGATGCATACGAAA
GCAATCTATGAGACTACTCCTATGATTATGTGACATCGGATCAGTGTGAGAGGTGATGGGAAATC
ATACGATATATCTATGTCACATGAGCTCACTTTTACGTGAAAGTTTATCTGCCTATTGTATATGA
TGAGACGTGCAGATTCG
Found at i:17647470 original size:21 final size:23
Alignment explanation
Indices: 17647431--17647472 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
17647421 TTCGTAACTC
17647431 AATATTTTAATTCTAATTATTTT
1 AATATTTTAATTCTAATTATTTT
17647454 AATATTTT-ATT-TAATTATT
1 AATATTTTAATTCTAATTATT
17647473 CCTAATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 8 0.42
22 3 0.16
23 8 0.42
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
AATATTTTAATTCTAATTATTTT
Found at i:17647480 original size:10 final size:8
Alignment explanation
Indices: 17647460--17647493 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
17647450 TTTTAATATT
17647460 TTATTTAA
1 TTATTTAA
17647468 TTATTCCTAA
1 TTATT--TAA
17647478 TTATTTAA
1 TTATTTAA
17647486 TTATTTAA
1 TTATTTAA
17647494 CCTAAATACG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 16 0.67
10 8 0.33
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (8 bp):
TTATTTAA
Found at i:17647482 original size:23 final size:23
Alignment explanation
Indices: 17647431--17647487 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
17647421 TTCGTAACTC
*
17647431 AATATTTTAATTCTAATTATTTT
1 AATATTTTAATTCTAATTATTCT
17647454 AATATTTT-ATT-TAATTATTCCT
1 AATATTTTAATTCTAATTATT-CT
17647476 AAT-TATTTAATT
1 AATAT-TTTAATT
17647488 ATTTAACCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
21 9 0.30
22 10 0.33
23 11 0.37
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (23 bp):
AATATTTTAATTCTAATTATTCT
Found at i:17648726 original size:25 final size:26
Alignment explanation
Indices: 17648678--17648728 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
17648668 ATTTTTCAAA
* *
17648678 AGTATGAATTTTGGACTGAATTGAAT
1 AGTATGAATATTGAACTGAATTGAAT
*
17648704 AGTATGAATATT-AACTGGATTGAAT
1 AGTATGAATATTGAACTGAATTGAAT
17648729 TTACTTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.37
Consensus pattern (26 bp):
AGTATGAATATTGAACTGAATTGAAT
Found at i:17652958 original size:32 final size:31
Alignment explanation
Indices: 17652911--17652986 Score: 134
Period size: 32 Copynumber: 2.4 Consensus size: 31
17652901 ATTTTGCTTC
17652911 AATAAAAAAATATATATGTAGTGTATTTTAAA
1 AATAAAAAAA-ATATATGTAGTGTATTTTAAA
17652943 AATAATAAAAAATATATGTAGTGTATTTTAAA
1 AATAA-AAAAAATATATGTAGTGTATTTTAAA
17652975 AATAAAAAAAAT
1 AATAAAAAAAAT
17652987 TTAATCTGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
31 7 0.16
32 31 0.72
33 5 0.12
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (31 bp):
AATAAAAAAAATATATGTAGTGTATTTTAAA
Found at i:17653098 original size:21 final size:22
Alignment explanation
Indices: 17653074--17653127 Score: 85
Period size: 21 Copynumber: 2.5 Consensus size: 22
17653064 TACCATTGTT
17653074 TCTAATCTCACCGCTACAGT-A
1 TCTAATCTCACCGCTACAGTAA
*
17653095 TCTAATCTTACCGCTACAGTAA
1 TCTAATCTCACCGCTACAGTAA
17653117 T-TAATCTCACC
1 TCTAATCTCACC
17653128 ACCACCGCTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 28 0.93
22 2 0.07
ACGTcount: A:0.30, C:0.31, G:0.07, T:0.31
Consensus pattern (22 bp):
TCTAATCTCACCGCTACAGTAA
Found at i:17654433 original size:31 final size:31
Alignment explanation
Indices: 17654398--17654474 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
17654388 TGTATGATTA
*
17654398 AATCAAAATTAAAGTTTCATGTATACATTTG
1 AATCAAAATTAAAATTTCATGTATACATTTG
* * * * *
17654429 AATCATAATCAAAATTTCTTGTGTATATTTG
1 AATCAAAATTAAAATTTCATGTATACATTTG
*
17654460 CATC-AAATTAAAATT
1 AATCAAAATTAAAATT
17654475 CAGGTATCAA
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
30 9 0.24
31 28 0.76
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (31 bp):
AATCAAAATTAAAATTTCATGTATACATTTG
Found at i:17663949 original size:29 final size:30
Alignment explanation
Indices: 17663906--17663970 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
17663896 GCAAAGTGAA
** *
17663906 GAGCTCGCAGGTGAGCTCTCATGC-TTGGT
1 GAGCTCGCAAATGAGCTCTCAGGCTTTGGT
*
17663935 TAGCTCGCAAATGAGCTCTCAGGCTTTGGT
1 GAGCTCGCAAATGAGCTCTCAGGCTTTGGT
17663965 GAGCTC
1 GAGCTC
17663971 ACAGTGTTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 20 0.67
30 10 0.33
ACGTcount: A:0.17, C:0.25, G:0.31, T:0.28
Consensus pattern (30 bp):
GAGCTCGCAAATGAGCTCTCAGGCTTTGGT
Found at i:17664001 original size:17 final size:18
Alignment explanation
Indices: 17663959--17664005 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
17663949 GCTCTCAGGC
17663959 TTTGGTGAGCT--CACAG
1 TTTGGTGAGCTCGCACAG
*
17663975 TGTTGATGAGCTCGCACA-
1 T-TTGGTGAGCTCGCACAG
17663993 TTTGGTGAGCTCG
1 TTTGGTGAGCTCG
17664006 TATATTTTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 1 0.04
17 20 0.77
18 1 0.04
19 4 0.15
ACGTcount: A:0.17, C:0.19, G:0.32, T:0.32
Consensus pattern (18 bp):
TTTGGTGAGCTCGCACAG
Found at i:17664012 original size:17 final size:17
Alignment explanation
Indices: 17663981--17664041 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 17
17663971 ACAGTGTTGA
* *
17663981 TGAGCTCGCACATTTGG
1 TGAGCTCGTATATTTGG
17663998 TGAGCTCGTATATTTTGG
1 TGAGCTCGTATA-TTTGG
*
17664016 TGAACTCGTAGT-TCTTGG
1 TGAGCTCGTA-TAT-TTGG
17664034 TGAGCTCG
1 TGAGCTCG
17664042 CAATTCGCAG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 11 0.30
18 25 0.68
19 1 0.03
ACGTcount: A:0.16, C:0.18, G:0.30, T:0.36
Consensus pattern (17 bp):
TGAGCTCGTATATTTGG
Found at i:17664016 original size:18 final size:18
Alignment explanation
Indices: 17663993--17664041 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
17663983 AGCTCGCACA
17663993 TTTGGTGAGCTCGTA-TAT
1 TTTGGTGAGCTCGTAGT-T
*
17664011 TTTGGTGAACTCGTAGTT
1 TTTGGTGAGCTCGTAGTT
*
17664029 CTTGGTGAGCTCG
1 TTTGGTGAGCTCG
17664042 CAATTCGCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 26 0.96
19 1 0.04
ACGTcount: A:0.14, C:0.14, G:0.31, T:0.41
Consensus pattern (18 bp):
TTTGGTGAGCTCGTAGTT
Found at i:17664423 original size:3 final size:3
Alignment explanation
Indices: 17664415--17664466 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
17664405 TAAGTTTGTT
17664415 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
17664463 TTA T
1 TTA T
17664467 GGCTTCGTGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:17669185 original size:11 final size:11
Alignment explanation
Indices: 17669171--17669200 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
17669161 GCTTTTGTTA
17669171 AATAATATAGC
1 AATAATATAGC
*
17669182 AATAATAGAGC
1 AATAATATAGC
17669193 AATAATAT
1 AATAATAT
17669201 CAATTGCACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.07, G:0.10, T:0.27
Consensus pattern (11 bp):
AATAATATAGC
Found at i:17672419 original size:19 final size:20
Alignment explanation
Indices: 17672383--17672421 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
17672373 AACAGTTTTG
*
17672383 TTTTTCTTTTCTTTTTTTAT
1 TTTTTCTTTTCTTCTTTTAT
*
17672403 TTTTTTTTTTC-TCTTTTAT
1 TTTTTCTTTTCTTCTTTTAT
17672422 GATGGGTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.05, C:0.10, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTTTCTTTTCTTCTTTTAT
Found at i:17672480 original size:30 final size:29
Alignment explanation
Indices: 17672424--17672483 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
17672414 TCTTTTATGA
17672424 TGGGTTACGACTAAATTACCAAAAAAAAT
1 TGGGTTACGACTAAATTACCAAAAAAAAT
17672453 TGGGTTACGACTAAATTACCAAAAAAAAT
1 TGGGTTACGACTAAATTACCAAAAAAAAT
17672482 TG
1 TG
17672484 CTTGCTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.47, C:0.13, G:0.15, T:0.25
Consensus pattern (29 bp):
TGGGTTACGACTAAATTACCAAAAAAAAT
Found at i:17680129 original size:12 final size:12
Alignment explanation
Indices: 17680109--17680153 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
17680099 CACAAACAAG
17680109 CTCGTTTATTGA
1 CTCGTTTATTGA
*
17680121 CTTGTTTATT-A
1 CTCGTTTATTGA
17680132 GCTCGTTTA-TGA
1 -CTCGTTTATTGA
17680144 CTCGTTTATT
1 CTCGTTTATT
17680154 TATTAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 10 0.36
12 18 0.64
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.53
Consensus pattern (12 bp):
CTCGTTTATTGA
Found at i:17680150 original size:23 final size:24
Alignment explanation
Indices: 17680107--17680153 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
17680097 TTCACAAACA
*
17680107 AGCTCGTTTATTGACTTGTTTATT
1 AGCTCGTTTATTGACTCGTTTATT
17680131 AGCTCGTTTA-TGACTCGTTTATT
1 AGCTCGTTTATTGACTCGTTTATT
17680154 TATTAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.17, C:0.15, G:0.17, T:0.51
Consensus pattern (24 bp):
AGCTCGTTTATTGACTCGTTTATT
Found at i:17680385 original size:12 final size:12
Alignment explanation
Indices: 17680349--17680410 Score: 56
Period size: 12 Copynumber: 5.2 Consensus size: 12
17680339 ATTAACATTA
17680349 TTCATGAACATG
1 TTCATGAACATG
*
17680361 TTCAATTAA-ATG
1 TTC-ATGAACATG
17680373 TTCATGAACATG
1 TTCATGAACATG
* **
17680385 TTCGTTTA-ATG
1 TTCATGAACATG
*
17680396 TTCGTGAACATG
1 TTCATGAACATG
17680408 TTC
1 TTC
17680411 GATTAAATTA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
11 13 0.32
12 23 0.57
13 4 0.10
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (12 bp):
TTCATGAACATG
Found at i:17680426 original size:23 final size:24
Alignment explanation
Indices: 17680349--17680418 Score: 106
Period size: 23 Copynumber: 3.0 Consensus size: 24
17680339 ATTAACATTA
*
17680349 TTCATGAACATGTTCAATTAAATG
1 TTCATGAACATGTTCGATTAAATG
*
17680373 TTCATGAACATGTTCG-TTTAATG
1 TTCATGAACATGTTCGATTAAATG
*
17680396 TTCGTGAACATGTTCGATTAAAT
1 TTCATGAACATGTTCGATTAAAT
17680419 TAAATGAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 21 0.51
24 20 0.49
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (24 bp):
TTCATGAACATGTTCGATTAAATG
Found at i:17680443 original size:23 final size:23
Alignment explanation
Indices: 17680400--17680445 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
17680390 TTAATGTTCG
*
17680400 TGAACATGTTCGATTAAATTAAA
1 TGAACATGTTCGATGAAATTAAA
*
17680423 TGAATATGTTCG-TGAATATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
17680446 CAAACAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:17682880 original size:20 final size:20
Alignment explanation
Indices: 17682855--17682892 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
17682845 GTAATAACGG
17682855 GATTTTAATATCAATTGTCA
1 GATTTTAATATCAATTGTCA
* *
17682875 GATTTTGATATGAATTGT
1 GATTTTAATATCAATTGT
17682893 GAAATGTGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.47
Consensus pattern (20 bp):
GATTTTAATATCAATTGTCA
Done.