Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A03
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: 108673976
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 5040000 characters in sequence are not A, C, G, or T
File 37 of 333
Found at i:10255308 original size:15 final size:16
Alignment explanation
Indices: 10255281--10255310 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
10255271 TATAACAATT
10255281 AATATATATTATATAA
1 AATATATATTATATAA
10255297 AATATA-ATTATATA
1 AATATATATTATATA
10255311 TTAGTTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATATATATTATATAA
Found at i:10255311 original size:22 final size:21
Alignment explanation
Indices: 10255271--10255313 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
10255261 ATGTAATGTT
10255271 TATAACAATTAATATATATTA
1 TATAACAATTAATATATATTA
10255292 TATAA-AATATAATTATATATTA
1 TATAACAAT-TAA-TATATATTA
10255314 GTTATTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 3 0.15
21 8 0.40
22 9 0.45
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
TATAACAATTAATATATATTA
Found at i:10258409 original size:27 final size:27
Alignment explanation
Indices: 10258379--10258434 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
10258369 AGTTGAGCTA
10258379 TTGATGATAATATGAGCTTTATGAAGT
1 TTGATGATAATATGAGCTTTATGAAGT
*
10258406 TTGATGATAATATGAGCTTTATTAAGT
1 TTGATGATAATATGAGCTTTATGAAGT
10258433 TT
1 TT
10258435 TGTCTTTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.32, C:0.04, G:0.20, T:0.45
Consensus pattern (27 bp):
TTGATGATAATATGAGCTTTATGAAGT
Found at i:10259063 original size:44 final size:42
Alignment explanation
Indices: 10259013--10259162 Score: 121
Period size: 44 Copynumber: 3.6 Consensus size: 42
10259003 TGTGTTTTGG
*
10259013 TGTAAGACCACATCTGGGACATTGGTATC-CACTTATGATTTACA
1 TGTAAGACCACATCTGGGACATTGGAATCGCA-TT-TGATTT-CA
* * * *
10259057 TGTAAGACCACGTTTGGGACGTTGGAATCGTATTTGATTTCA
1 TGTAAGACCACATCTGGGACATTGGAATCGCATTTGATTTCA
* * * * *
10259099 TGTAAGA-C-C--CTGAGACAGTGGCATCGATATTTGATTACA
1 TGTAAGACCACATCTGGGACATTGGAATCG-CATTTGATTTCA
* *
10259138 TGTAAGACCACGTCTGGGACGTTGG
1 TGTAAGACCACATCTGGGACATTGG
10259163 CATTGTACGA
Statistics
Matches: 86, Mismatches: 14, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
38 12 0.14
39 18 0.21
40 2 0.02
41 2 0.02
42 9 0.10
43 15 0.17
44 27 0.31
45 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.31
Consensus pattern (42 bp):
TGTAAGACCACATCTGGGACATTGGAATCGCATTTGATTTCA
Found at i:10263046 original size:18 final size:18
Alignment explanation
Indices: 10263023--10263057 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
10263013 GAGTTTTTAT
10263023 TTATGCCTTTCAGATTAG
1 TTATGCCTTTCAGATTAG
*
10263041 TTATGCCTTTCGGATTA
1 TTATGCCTTTCAGATTA
10263058 ACGAATGCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.17, G:0.17, T:0.46
Consensus pattern (18 bp):
TTATGCCTTTCAGATTAG
Found at i:10272528 original size:9 final size:9
Alignment explanation
Indices: 10272505--10272540 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
10272495 ATTGATAGGC
10272505 TATTTTATT
1 TATTTTATT
10272514 TA-TTTATT
1 TATTTTATT
10272522 TATTTTATT
1 TATTTTATT
10272531 TATTTTATT
1 TATTTTATT
10272540 T
1 T
10272541 TTGTTGTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.31
9 18 0.69
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TATTTTATT
Found at i:10272528 original size:13 final size:13
Alignment explanation
Indices: 10272505--10272540 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
10272495 ATTGATAGGC
10272505 TATTTTATTTATT
1 TATTTTATTTATT
10272518 TA-TTTATTTTATT
1 TATTTTA-TTTATT
10272531 TATTTTATTT
1 TATTTTATTT
10272541 TTGTTGTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 4 0.19
13 13 0.62
14 4 0.19
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
TATTTTATTTATT
Found at i:10280494 original size:49 final size:49
Alignment explanation
Indices: 10280437--10280531 Score: 145
Period size: 49 Copynumber: 1.9 Consensus size: 49
10280427 TGTCCTAACA
10280437 GACTTCATATGTTACCATAGCCCAACTATGGTCTTACACAACATAAGCG
1 GACTTCATATGTTACCATAGCCCAACTATGGTCTTACACAACATAAGCG
*** * *
10280486 GACTTCATATGTTGTTATAGCCCAGCTATGGTCTTATACAACATAA
1 GACTTCATATGTTACCATAGCCCAACTATGGTCTTACACAACATAA
10280532 TCTCGTGTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.31
Consensus pattern (49 bp):
GACTTCATATGTTACCATAGCCCAACTATGGTCTTACACAACATAAGCG
Found at i:10281413 original size:2 final size:2
Alignment explanation
Indices: 10281406--10281441 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
10281396 TTTCTCCCTT
10281406 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
10281442 TATATACACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:10282015 original size:20 final size:18
Alignment explanation
Indices: 10281990--10282037 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 18
10281980 TATTGTTTTT
10281990 TATTTTTTTAATATTTATA
1 TATTTTTTTAATATTTA-A
10282009 CTATTTTAATTTAATATTTAA
1 -TATTTT--TTTAATATTTAA
10282030 TATTTTTT
1 TATTTTTT
10282038 ATTTTTTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 2 0.08
20 12 0.46
21 1 0.04
22 11 0.42
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
TATTTTTTTAATATTTAA
Found at i:10282038 original size:22 final size:22
Alignment explanation
Indices: 10281996--10282035 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
10281986 TTTTTATTTT
10281996 TTTAATATTTATACTATTTTAA
1 TTTAATATTTATACTATTTTAA
10282018 TTTAATATTTA-A-TATTTT
1 TTTAATATTTATACTATTTT
10282036 TTATTTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 1 0.06
22 11 0.61
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTAATATTTATACTATTTTAA
Found at i:10284009 original size:28 final size:28
Alignment explanation
Indices: 10283969--10284026 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
10283959 ATTTTTTTAA
*
10283969 CTTGAACCCTAAACCATAGATCTTGGAC
1 CTTGAACCCTAAACCATAGACCTTGGAC
*
10283997 CTTGGACCCTAAACCATAGACCTTGGAC
1 CTTGAACCCTAAACCATAGACCTTGGAC
10284025 CT
1 CT
10284027 AGGATTCCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.24
Consensus pattern (28 bp):
CTTGAACCCTAAACCATAGACCTTGGAC
Found at i:10285573 original size:20 final size:21
Alignment explanation
Indices: 10285548--10285589 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
10285538 AAATTTTCAA
10285548 TAAATA-AAAAATAAAATTAT
1 TAAATATAAAAATAAAATTAT
* *
10285568 TAAATATTAAATTAAAATTAT
1 TAAATATAAAAATAAAATTAT
10285589 T
1 T
10285590 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATATAAAAATAAAATTAT
Found at i:10306140 original size:23 final size:23
Alignment explanation
Indices: 10306106--10306168 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
10306096 TGCACTGAAA
* *
10306106 TGCCAC-TACACTTGCATCGTAG
1 TGCCACTTTCACTTGCATCATAG
*
10306128 TGCCACTTTCACTTGCACCATAG
1 TGCCACTTTCACTTGCATCATAG
* *
10306151 TGCCACTATCATTTGCAT
1 TGCCACTTTCACTTGCAT
10306169 TCTTACTCAC
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 6 0.18
23 28 0.82
ACGTcount: A:0.22, C:0.32, G:0.14, T:0.32
Consensus pattern (23 bp):
TGCCACTTTCACTTGCATCATAG
Found at i:10308511 original size:26 final size:26
Alignment explanation
Indices: 10308482--10308533 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
10308472 GACAACTAAG
*
10308482 AATAGCCTCTATGGCGAACTCTGAAA
1 AATAGCATCTATGGCGAACTCTGAAA
* *
10308508 AATAGCATTTGTGGCGAACTCTGAAA
1 AATAGCATCTATGGCGAACTCTGAAA
10308534 GGAAAGCCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (26 bp):
AATAGCATCTATGGCGAACTCTGAAA
Found at i:10308559 original size:27 final size:27
Alignment explanation
Indices: 10308493--10308570 Score: 70
Period size: 27 Copynumber: 2.9 Consensus size: 27
10308483 ATAGCCTCTA
* *
10308493 TGGCGAACTCTGAAA--AATAGCATTTG
1 TGGCAAACTCTGAAAGGAA-AGCCTTTG
*
10308519 TGGCGAACTCTGAAAGGAAAGCCTTTG
1 TGGCAAACTCTGAAAGGAAAGCCTTTG
* * * *
10308546 TGGCAAATTTTGAATGGAATGCCTT
1 TGGCAAACTCTGAAAGGAAAGCCTT
10308571 GGAGGCATAC
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
26 15 0.34
27 27 0.61
28 2 0.05
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (27 bp):
TGGCAAACTCTGAAAGGAAAGCCTTTG
Found at i:10315670 original size:19 final size:19
Alignment explanation
Indices: 10315646--10315685 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
10315636 TACCAATGCC
10315646 TAAGTCGAAATTTGAGGAA
1 TAAGTCGAAATTTGAGGAA
10315665 TAAGTCGAAATTTGAGGAA
1 TAAGTCGAAATTTGAGGAA
10315684 TA
1 TA
10315686 TTGAAGGCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.05, G:0.25, T:0.28
Consensus pattern (19 bp):
TAAGTCGAAATTTGAGGAA
Found at i:10319644 original size:42 final size:38
Alignment explanation
Indices: 10319588--10319682 Score: 163
Period size: 38 Copynumber: 2.5 Consensus size: 38
10319578 TGAACTAACA
*
10319588 GTATGATGCAGATTGATTGCAAAAAGAAGACATGAAAT
1 GTATGCTGCAGATTGATTGCAAAAAGAAGACATGAAAT
*
10319626 GTATGTTGCAGATTGATTGCAAAAAGAAGACATGAAAT
1 GTATGCTGCAGATTGATTGCAAAAAGAAGACATGAAAT
*
10319664 GTATGCTGCAGATCGATTG
1 GTATGCTGCAGATTGATTG
10319683 GAACCAGATT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.39, C:0.09, G:0.25, T:0.26
Consensus pattern (38 bp):
GTATGCTGCAGATTGATTGCAAAAAGAAGACATGAAAT
Found at i:10321817 original size:22 final size:22
Alignment explanation
Indices: 10321792--10321835 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
10321782 AATTATTAAC
*
10321792 ATAATGAATTTTAATTAATTTT
1 ATAATAAATTTTAATTAATTTT
*
10321814 ATAATAAATTTTGATTAATTTT
1 ATAATAAATTTTAATTAATTTT
10321836 GGTCATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
ATAATAAATTTTAATTAATTTT
Found at i:10323607 original size:20 final size:20
Alignment explanation
Indices: 10323563--10323607 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
10323553 TAGGCTTCGA
* *
10323563 CTCACAGGAGTTGAAGGGAG
1 CTCACAGGAGTTAAAGAGAG
10323583 CTCACAGGAGTTAAAGAGAG
1 CTCACAGGAGTTAAAGAGAG
*
10323603 TTCAC
1 CTCAC
10323608 GGTCCCAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.18, G:0.31, T:0.18
Consensus pattern (20 bp):
CTCACAGGAGTTAAAGAGAG
Found at i:10327107 original size:53 final size:53
Alignment explanation
Indices: 10327006--10327111 Score: 144
Period size: 53 Copynumber: 2.0 Consensus size: 53
10326996 GAAGCGTCCT
*
10327006 GGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCTGTTC
1 GGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCTGTTC
* * *
10327059 GGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCT-CTCACAT-TATCTGTTC
1 GGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCTGC-CACATATATCTGTTC
10327112 TGGCAGCCAT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
53 30 0.64
54 17 0.36
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (53 bp):
GGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCTGTTC
Found at i:10327108 original size:27 final size:26
Alignment explanation
Indices: 10327004--10327114 Score: 127
Period size: 27 Copynumber: 4.2 Consensus size: 26
10326994 AGGAAGCGTC
* * *
10327004 CTGGTGGCTATGCCACAAATATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGTT
10327031 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGTT
10327058 C-GGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTGT-T
*
10327085 CTGGTGACTCT-CTCACATTATCTGTT
1 CTGGTGGCTCTGC-CACATTATCTGTT
10327111 CTGG
1 CTGG
10327115 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 4, Indels: 11
0.83 0.04 0.12
Matches are distributed among these distances:
26 27 0.36
27 37 0.49
28 11 0.15
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGTT
Found at i:10332780 original size:70 final size:71
Alignment explanation
Indices: 10332351--10333127 Score: 517
Period size: 70 Copynumber: 11.1 Consensus size: 71
10332341 ATCCTCTAAA
* * * * * *
10332351 AAAAATAGTTAGCGAAAGCTAAGGCTCCCAGCTGTAATCTTAAGGCTCACATGTTTAATACCACA
1 AAAAATAGTTAGCGAGAGCTAAGGCTCCCAGCTGTGATCTTAAGGCTCGCAGGTTCAATACCATA
*
10332416 GCCCCC
66 GCCTCC
* * * * * * *
10332422 AAAAACATTTAACTAGAGCTAAGGCTCCCA-TTGTTATCTTAAGGCTCGCAGGTTCAATACCACA
1 AAAAATAGTTAGCGAGAGCTAAGGCTCCCAGCTGTGATCTTAAGGCTCGCAGGTTCAATACCATA
*
10332486 TCCT-C
66 GCCTCC
* * * ** * * *
10332491 TAAAATAGATA-CGAAGAACTAAGGCTCCCAATTATGATCTTAAGGCTCGCAGGTTTAATACCAC
1 AAAAATAGTTAGCG-AGAGCTAAGGCTCCCAGCTGTGATCTTAAGGCTCGCAGGTTCAATACCAT
*
10332555 AGCCTCT
65 AGCCTCC
* * ** * * * * *
10332562 AAAAA-AGTTAGCAAGAGTTCAA-GCTCTAAGCTGTGATCTTAGGGCTTGCAGTTTTAATACCGT
1 AAAAATAGTTAGCGAGAGCT-AAGGCTCCCAGCTGTGATCTTAAGGCTCGCAGGTTCAATACCAT
*
10332625 AGCCCCC
65 AGCCTCC
* * * * * * * * *
10332632 AAAAATAGTTAACGAAAGCTAAAGCTCCCAGCTAT-AGTATTAAGGCTTGTAAGTTCAACACCAT
1 AAAAATAGTTAGCGAGAGCTAAGGCTCCCAGCTGTGA-TCTTAAGGCTCGCAGGTTCAATACCAT
10332696 AGCCT-C
65 AGCCTCC
* * * * *
10332702 TAAAATAGTTAGCTAGAGCTAA-GCTCCCAGCTGTAATCTTAAGGCCCGCAGGCTCAATATCC-T
1 AAAAATAGTTAGCGAGAGCTAAGGCTCCCAGCTGTGATCTTAAGGCTCGCAGGTTCAATA-CCAT
10332765 AGCCTCC
65 AGCCTCC
** * * * ** * * *
10332772 AAAAATAGTTAATGAGGGTTAAGGCTCTCAGCTACGATATTAATGCTAGCAGGTTCAATATCGCA
1 AAAAATAGTTAGCGAGAGCTAAGGCTCCCAGCTGTGATCTTAAGGCTCGCAGGTTCAATA-C-CA
**
10332837 -A-CCTTG
64 TAGCCTCC
* * ** * * * **
10332843 AAAAATAGTTAACAAGAGCTAAGGCTCTTAGTTTTGATCTTAAGGCTCGCAGGCTCAATACTGTA
1 AAAAATAGTTAGCGAGAGCTAAGGCTCCCAGCTGTGATCTTAAGGCTCGCAGGTTCAATACCATA
*
10332908 TCCT-C
66 GCCTCC
* * * * * * *
10332913 TAAAACAGTTAGCGAGAGTTAAGGCTCCCAACTATGATCTTAAGGCTCGTAGGTTCAATACCGTA
1 AAAAATAGTTAGCGAGAGCTAAGGCTCCCAGCTGTGATCTTAAGGCTCGCAGGTTCAATACCATA
10332978 GCCT-C
66 GCCTCC
* * * * * ** **
10332983 TAAAATAGTTAGCGAGAGCTCAA-GCTCTCAGCTGTGATCTTAAGGTTTGCAGGATCAATGTCGC
1 AAAAATAGTTAGCGAGAGCT-AAGGCTCCCAGCTGTGATCTTAAGGCTCGCAGGTTCAATACCAT
*
10333047 AGCCTCT
65 AGCCTCC
* * ** *
10333054 AAAACT-GTTAGCGAGAGCTCAA-GCTCCTA-CTTGTGATCTTAAGGCTCATAGGTTCAACACCA
1 AAAAATAGTTAGCGAGAGCT-AAGGCTCCCAGC-TGTGATCTTAAGGCTCGCAGGTTCAATACCA
*
10333116 CAGCCTCC
64 TAGCCTCC
10333124 AAAA
1 AAAA
10333128 CAGTTAGTAC
Statistics
Matches: 546, Mismatches: 141, Indels: 39
0.75 0.19 0.05
Matches are distributed among these distances:
68 1 0.00
69 57 0.10
70 322 0.59
71 164 0.30
72 2 0.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (71 bp):
AAAAATAGTTAGCGAGAGCTAAGGCTCCCAGCTGTGATCTTAAGGCTCGCAGGTTCAATACCATA
GCCTCC
Found at i:10333012 original size:211 final size:209
Alignment explanation
Indices: 10332352--10333015 Score: 586
Period size: 211 Copynumber: 3.2 Consensus size: 209
10332342 TCCTCTAAAA
* * *** * * * *
10332352 AAAATAGTTAGCGAAAGCT-AAGGCTCCCAGCTGTAATCTTAAGGCTCA-CATGTTTAATACCAC
1 AAAATAGTTAGCGAGAGCTCAA-GCTCTCAGCTACGATATTAAGGCT-AGCAGGTTCAATACCGC
* * * *
10332415 AGCCCCCAAAAACATTTAACTAGAGCTAAGGCTCCCA-TTGTTATCTTAAGGCTCGCAGGTTCAA
64 AACCCCCAAAAATAGTTAACAAGAGCTAAGGCTCCCAGTT-TTATCTTAAGGCTCGCAGGTTCAA
* * * *
10332479 TACCACATCCTCTAAAATAGATA-CGAAGAACTAAGGCTCCCAATTATGATCTTAAGGCTCGCAG
128 TACCATATCCTCTAAAATAGTTAGCG-AGAGCTAAGGCTCCCAACTATGATCTTAAGGCTCGCAG
* *
10332543 GTTTAATACCACAGCCTCT
192 GTTCAATACC-TAGCCTCT
* * * * ** * * * * * * *
10332562 AAAAAAGTTAGCAAGAGTTCAAGCTCTAAGCTGTGATCTTAGGGCTTGCAGTTTTAATACCGTAG
1 AAAATAGTTAGCGAGAGCTCAAGCTCTCAGCTACGATATTAAGGCTAGCAGGTTCAATACCGCAA
* * * * * * * *
10332627 CCCCCAAAAATAGTTAACGAA-AGCTAAAGCTCCCAGCTATAGTATTAAGGCTTGTAAGTTCAAC
66 CCCCCAAAAATAGTTAAC-AAGAGCTAAGGCTCCCAGTTTTA-TCTTAAGGCTCGCAGGTTCAAT
* * * * * * *
10332691 ACCATAGCCTCTAAAATAGTTAGCTAGAGCTAA-GCTCCCAGCTGTAATCTTAAGGCCCGCAGGC
129 ACCATATCCTCTAAAATAGTTAGCGAGAGCTAAGGCTCCCAACTATGATCTTAAGGCTCGCAGGT
*
10332755 TCAATATCCTAGCCTCCA
194 TCAATA-CCTAGCCT-CT
** * * * *
10332773 AAAATAGTTAATGAG-GGTTAAGGCTCTCAGCTACGATATTAATGCTAGCAGGTTCAATATCGCA
1 AAAATAGTTAGCGAGAGCTCAA-GCTCTCAGCTACGATATTAAGGCTAGCAGGTTCAATACCGCA
*** ** *
10332837 ACCTTGAAAAATAGTTAACAAGAGCTAAGGCTCTTAGTTTTGATCTTAAGGCTCGCAGGCTCAAT
65 ACCCCCAAAAATAGTTAACAAGAGCTAAGGCTCCCAGTTTT-ATCTTAAGGCTCGCAGGTTCAAT
** * * *
10332902 ACTGTATCCTCTAAAACAGTTAGCGAGAGTTAAGGCTCCCAACTATGATCTTAAGGCTCGTAGGT
129 ACCATATCCTCTAAAATAGTTAGCGAGAGCTAAGGCTCCCAACTATGATCTTAAGGCTCGCAGGT
10332967 TCAATACCGTAGCCTCT
194 TCAATACC-TAGCCTCT
10332984 AAAATAGTTAGCGAGAGCTCAAGCTCTCAGCT
1 AAAATAGTTAGCGAGAGCTCAAGCTCTCAGCT
10333016 GTGATCTTAA
Statistics
Matches: 353, Mismatches: 87, Indels: 27
0.76 0.19 0.06
Matches are distributed among these distances:
210 120 0.34
211 190 0.54
212 43 0.12
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.26
Consensus pattern (209 bp):
AAAATAGTTAGCGAGAGCTCAAGCTCTCAGCTACGATATTAAGGCTAGCAGGTTCAATACCGCAA
CCCCCAAAAATAGTTAACAAGAGCTAAGGCTCCCAGTTTTATCTTAAGGCTCGCAGGTTCAATAC
CATATCCTCTAAAATAGTTAGCGAGAGCTAAGGCTCCCAACTATGATCTTAAGGCTCGCAGGTTC
AATACCTAGCCTCT
Found at i:10334215 original size:24 final size:24
Alignment explanation
Indices: 10334181--10334232 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
10334171 TGACACAGAG
* *
10334181 CTAGCTTACCATTGTTTTCAGTAA
1 CTAGCTCACCACTGTTTTCAGTAA
*
10334205 CTAGCTCACCACTGTTTTCAGTAG
1 CTAGCTCACCACTGTTTTCAGTAA
10334229 CTAG
1 CTAG
10334233 TTCCCTAGCG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.37
Consensus pattern (24 bp):
CTAGCTCACCACTGTTTTCAGTAA
Found at i:10336122 original size:33 final size:33
Alignment explanation
Indices: 10336085--10336147 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
10336075 AGGGAAGCTT
* *
10336085 GCGATATCGGCTCACAGGAGTTGAAGGGAGTTC
1 GCGATATCAGCTCACAAGAGTTGAAGGGAGTTC
**
10336118 GCGATATCAGCTTGCAAGAGTTGAAGGGAG
1 GCGATATCAGCTCACAAGAGTTGAAGGGAG
10336148 CTCATAGCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.27, C:0.16, G:0.37, T:0.21
Consensus pattern (33 bp):
GCGATATCAGCTCACAAGAGTTGAAGGGAGTTC
Found at i:10338530 original size:13 final size:14
Alignment explanation
Indices: 10338488--10338532 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 14
10338478 TAATAATGAT
10338488 TAAAGTATATTATAA
1 TAAAGTA-ATTATAA
10338503 TAATA-TAA-TATAA
1 TAA-AGTAATTATAA
10338516 TAAAGTAATTA-AA
1 TAAAGTAATTATAA
10338529 TAAA
1 TAAA
10338533 AAAATAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 1 0.04
13 17 0.63
14 3 0.11
15 5 0.19
16 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (14 bp):
TAAAGTAATTATAA
Found at i:10339408 original size:20 final size:20
Alignment explanation
Indices: 10339385--10339423 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
10339375 TGTGTCCATA
10339385 AGACACTATATCTGTCGACG
1 AGACACTATATCTGTCGACG
*
10339405 AGACACTATATGTGTCGAC
1 AGACACTATATCTGTCGAC
10339424 TACTGTGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.26
Consensus pattern (20 bp):
AGACACTATATCTGTCGACG
Found at i:10341822 original size:17 final size:17
Alignment explanation
Indices: 10341797--10341833 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
10341787 TTGTTAAAGA
*
10341797 ATCTATTTGGATTTTGC
1 ATCTATTTGGATTTTAC
*
10341814 ATCTGTTTGGATTTTAC
1 ATCTATTTGGATTTTAC
10341831 ATC
1 ATC
10341834 AATCTGTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.19, C:0.14, G:0.16, T:0.51
Consensus pattern (17 bp):
ATCTATTTGGATTTTAC
Found at i:10341856 original size:3 final size:3
Alignment explanation
Indices: 10341848--10341938 Score: 182
Period size: 3 Copynumber: 30.3 Consensus size: 3
10341838 TGTTGAAGAA
10341848 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
10341896 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
10341939 TTATGCTTTA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 88 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:10344322 original size:21 final size:22
Alignment explanation
Indices: 10344298--10344352 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
10344288 TTTAACATAA
* *
10344298 TAAAATATTT-TTTTTACAATT
1 TAAAATATTTAATTTTAAAATT
*
10344319 TAAAGTATTTAATTTTAAAATT
1 TAAAATATTTAATTTTAAAATT
*
10344341 TAAAATAATTAA
1 TAAAATATTTAA
10344353 GTCCAAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 9 0.32
22 19 0.68
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
TAAAATATTTAATTTTAAAATT
Found at i:10346547 original size:6 final size:6
Alignment explanation
Indices: 10346536--10346573 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
10346526 ACACCGTAGG
* *
10346536 GTAACA GTAACA ATAAGA GTAACA GTAACA GTAACA GT
1 GTAACA GTAACA GTAACA GTAACA GTAACA GTAACA GT
10346574 CATAGTCAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.50, C:0.13, G:0.18, T:0.18
Consensus pattern (6 bp):
GTAACA
Found at i:10347491 original size:8 final size:8
Alignment explanation
Indices: 10347475--10347507 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
10347465 TAATCATTCT
*
10347475 TTATTTTA
1 TTATATTA
10347483 TTATATTA
1 TTATATTA
10347491 TTATATTA
1 TTATATTA
10347499 TTATATTA
1 TTATATTA
10347507 T
1 T
10347508 ATTTAGTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TTATATTA
Found at i:10355859 original size:27 final size:27
Alignment explanation
Indices: 10355815--10355901 Score: 84
Period size: 27 Copynumber: 3.0 Consensus size: 27
10355805 TTTTGAAATT
* * *
10355815 ATTATGTCTTGAATTTGTTAGATATTG
1 ATTATGTTTTAAACTTGTTAGATATTG
10355842 ATTATGTTTTAAACTTGTTAGATATTG
1 ATTATGTTTTAAACTTGTTAGATATTG
* *
10355869 AATTTATTATGTTTTAAGCTTGTTGGATATTG
1 -----ATTATGTTTTAAACTTGTTAGATATTG
10355901 A
1 A
10355902 ATTTATTATG
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
27 25 0.50
32 25 0.50
ACGTcount: A:0.28, C:0.03, G:0.17, T:0.52
Consensus pattern (27 bp):
ATTATGTTTTAAACTTGTTAGATATTG
Found at i:10355881 original size:32 final size:32
Alignment explanation
Indices: 10355842--10355934 Score: 150
Period size: 32 Copynumber: 2.9 Consensus size: 32
10355832 TTAGATATTG
*
10355842 ATTATGTTTTAAACTTGTTAGATATTGAATTT
1 ATTATGTTTTAAACTTGTTGGATATTGAATTT
*
10355874 ATTATGTTTTAAGCTTGTTGGATATTGAATTT
1 ATTATGTTTTAAACTTGTTGGATATTGAATTT
* *
10355906 ATTATGTTTCAAACTTGTTGGATTTTGAA
1 ATTATGTTTTAAACTTGTTGGATATTGAA
10355935 ATTGACAATG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 56 1.00
ACGTcount: A:0.28, C:0.04, G:0.16, T:0.52
Consensus pattern (32 bp):
ATTATGTTTTAAACTTGTTGGATATTGAATTT
Found at i:10356918 original size:29 final size:29
Alignment explanation
Indices: 10356879--10356938 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
10356869 TTTTAATGTG
10356879 GTGTAATATTAGTTATGCACTTGGACAAT
1 GTGTAATATTAGTTATGCACTTGGACAAT
10356908 GTGTAATATTAGTTATGCACTTGGACAAT
1 GTGTAATATTAGTTATGCACTTGGACAAT
10356937 GT
1 GT
10356939 TGTTGTTATT
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:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (29 bp):
GTGTAATATTAGTTATGCACTTGGACAAT
Found at i:10357226 original size:22 final size:22
Alignment explanation
Indices: 10357201--10357242 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
10357191 ATAATTTAAA
10357201 ATATAAATTTATTAATATATAT
1 ATATAAATTTATTAATATATAT
*
10357223 ATATAAATTTATTTATATAT
1 ATATAAATTTATTAATATAT
10357243 GTAAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATATAAATTTATTAATATATAT
Found at i:10357374 original size:14 final size:15
Alignment explanation
Indices: 10357355--10357385 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
10357345 AAAAGTAAAT
10357355 CATTTT-CTGGAAAA
1 CATTTTACTGGAAAA
10357369 CATTTTACTGGAAAA
1 CATTTTACTGGAAAA
10357384 CA
1 CA
10357386 AACGGACCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (15 bp):
CATTTTACTGGAAAA
Found at i:10358416 original size:20 final size:21
Alignment explanation
Indices: 10358374--10358416 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
10358364 TATTATTATT
* *
10358374 AAAAGTAAAGTAAATAAAAAG
1 AAAAGTAAAGGAAAGAAAAAG
*
10358395 AAAA-TAAAGGAAAGAAACAG
1 AAAAGTAAAGGAAAGAAAAAG
10358415 AA
1 AA
10358417 TAGCAGGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.72, C:0.02, G:0.16, T:0.09
Consensus pattern (21 bp):
AAAAGTAAAGGAAAGAAAAAG
Found at i:10359687 original size:14 final size:15
Alignment explanation
Indices: 10359663--10359711 Score: 75
Period size: 14 Copynumber: 3.4 Consensus size: 15
10359653 TTTATTGGAT
10359663 TTATATTGATTGAAA
1 TTATATTGATTGAAA
*
10359678 TTAT-TTGATTGAAT
1 TTATATTGATTGAAA
10359692 TTATATTGATTG-AA
1 TTATATTGATTGAAA
10359706 TTATAT
1 TTATAT
10359712 AATATATATG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
14 20 0.65
15 11 0.35
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
TTATATTGATTGAAA
Found at i:10359693 original size:29 final size:27
Alignment explanation
Indices: 10359652--10359709 Score: 89
Period size: 29 Copynumber: 2.1 Consensus size: 27
10359642 TATGCGATGA
*
10359652 ATTTATTGGATTTATATTGATTGAAATT
1 ATTTATTGAATTTATATTGATTG-AATT
10359680 ATTTGATTGAATTTATATTGATTGAATT
1 ATTT-ATTGAATTTATATTGATTGAATT
10359708 AT
1 AT
10359710 ATAATATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 10 0.36
29 18 0.64
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (27 bp):
ATTTATTGAATTTATATTGATTGAATT
Found at i:10360113 original size:23 final size:23
Alignment explanation
Indices: 10360083--10360169 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
10360073 GCTTTATCGA
* *
10360083 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
10360106 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
10360127 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* *
10360149 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
10360170 ACTGATCAGG
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
21 35 0.64
22 2 0.04
23 18 0.33
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:10375584 original size:104 final size:105
Alignment explanation
Indices: 10375375--10375586 Score: 363
Period size: 104 Copynumber: 2.0 Consensus size: 105
10375365 TGTTGCTCTA
*
10375375 ATACAAATGTTATTATAGTACTACTCTAATTTGTTTCCTCAAGTGTGTTTTTTTTTGTTGTTGTA
1 ATACAAATGTTATTATAGTACTACTCTAATTTGTTTCCTCAAGTGTG-TCTTTTTTGTTGTTGTA
*
10375440 ATAAAGCATGTTATGAAGAGTTAGTATGCTTTTAATTGTGC
65 ATAAAGCATGTTATGAAGAGTTAGTATGCTTTGAATTGTGC
* *
10375481 ATACAGATGTTATTATAGTACTACTCTAATTTGTTTCCTCAAGTGTG-CTTTTTTGTTGTTGTAC
1 ATACAAATGTTATTATAGTACTACTCTAATTTGTTTCCTCAAGTGTGTCTTTTTTGTTGTTGTAA
*
10375545 TGAAGCATGTTATGAAGAGTTAGTATGCTTTGAATTGTGC
66 TAAAGCATGTTATGAAGAGTTAGTATGCTTTGAATTGTGC
10375585 AT
1 AT
10375587 TTGTATATAG
Statistics
Matches: 101, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
104 55 0.54
106 46 0.46
ACGTcount: A:0.25, C:0.10, G:0.18, T:0.46
Consensus pattern (105 bp):
ATACAAATGTTATTATAGTACTACTCTAATTTGTTTCCTCAAGTGTGTCTTTTTTGTTGTTGTAA
TAAAGCATGTTATGAAGAGTTAGTATGCTTTGAATTGTGC
Found at i:10392869 original size:6 final size:6
Alignment explanation
Indices: 10392858--10392908 Score: 102
Period size: 6 Copynumber: 8.5 Consensus size: 6
10392848 TATACACAAT
10392858 TGCATG TGCATG TGCATG TGCATG TGCATG TGCATG TGCATG TGCATG
1 TGCATG TGCATG TGCATG TGCATG TGCATG TGCATG TGCATG TGCATG
10392906 TGC
1 TGC
10392909 CTGGCCTTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.16, C:0.18, G:0.33, T:0.33
Consensus pattern (6 bp):
TGCATG
Found at i:10399583 original size:127 final size:127
Alignment explanation
Indices: 10399431--10399687 Score: 340
Period size: 127 Copynumber: 2.0 Consensus size: 127
10399421 AAAATGGAAA
* * *
10399431 AACTCCTCAATAGAAGATAAGAAACTACAGACAAAAGGAGATTTCACTATAATCAATGAGAGTAC
1 AACTCCTCAAAAGAAGATAAAAAACTACAGACAAAAGGAGATTTCACTATAATAAATGAGAGTAC
* * *
10399496 AAAATAT-AGAGAGAATTAAAAGAAAAACTCGAAA-CCCACAAGAAAAAC-CCTTTGAAACAAAG
66 AAAAGATGA-AGAGAATTAAAA-AAAAACTCAAAACCCCACAAG-AAAACTCCTTCGAAACAAAG
* * * ** *
10399558 AACTCCTTAAAAGAGGATAAAAAACTACGGACAAAAGGAGATTTTGCTATAATAAATTAGAGTAC
1 AACTCCTCAAAAGAAGATAAAAAACTACAGACAAAAGGAGATTTCACTATAATAAATGAGAGTAC
* *
10399623 AAAAGATGAAGAGGATTAAAAAAAAACTCAAAACCCCATAAGAAAACTCCTTCGAAACAAAG
66 AAAAGATGAAGAGAATTAAAAAAAAACTCAAAACCCCACAAGAAAACTCCTTCGAAACAAAG
10399685 AAC
1 AAC
10399688 GAAATTCTCT
Statistics
Matches: 113, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
126 16 0.14
127 96 0.85
128 1 0.01
ACGTcount: A:0.53, C:0.16, G:0.14, T:0.17
Consensus pattern (127 bp):
AACTCCTCAAAAGAAGATAAAAAACTACAGACAAAAGGAGATTTCACTATAATAAATGAGAGTAC
AAAAGATGAAGAGAATTAAAAAAAAACTCAAAACCCCACAAGAAAACTCCTTCGAAACAAAG
Found at i:10402118 original size:5 final size:5
Alignment explanation
Indices: 10402108--10402141 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
10402098 AAATGCATCG
*
10402108 AATTA AATTA AATTA AATT- AATTA GATTA AATTA
1 AATTA AATTA AATTA AATTA AATTA AATTA AATTA
10402142 TCTTTTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (5 bp):
AATTA
Found at i:10402130 original size:14 final size:14
Alignment explanation
Indices: 10402108--10402141 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
10402098 AAATGCATCG
10402108 AATTAAATTAAATTA
1 AATT-AATTAAATTA
*
10402123 AATTAATTAGATTA
1 AATTAATTAAATTA
10402137 AATTA
1 AATTA
10402142 TCTTTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (14 bp):
AATTAATTAAATTA
Found at i:10407256 original size:21 final size:21
Alignment explanation
Indices: 10407232--10407302 Score: 60
Period size: 21 Copynumber: 3.3 Consensus size: 21
10407222 TTTATTTTAA
10407232 TATTATACATATTTCATGTGT
1 TATTATACATATTTCATGTGT
10407253 TATTATTA-ATTTATTT-AT-T-T
1 TATTA-TACA--TATTTCATGTGT
10407273 TAATACTATACATATTTCATGTGT
1 T-AT--TATACATATTTCATGTGT
10407297 TATTAT
1 TATTAT
10407303 TAAGTAATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 20
0.67 0.00 0.33
Matches are distributed among these distances:
20 2 0.05
21 17 0.43
22 8 0.20
23 11 0.28
24 2 0.05
ACGTcount: A:0.31, C:0.07, G:0.06, T:0.56
Consensus pattern (21 bp):
TATTATACATATTTCATGTGT
Found at i:10407262 original size:44 final size:44
Alignment explanation
Indices: 10407214--10407305 Score: 175
Period size: 44 Copynumber: 2.1 Consensus size: 44
10407204 TATTCATAAT
*
10407214 TTAATTTATTTATTTTAATATTATACATATTTCATGTGTTATTA
1 TTAATTTATTTATTTTAATACTATACATATTTCATGTGTTATTA
10407258 TTAATTTATTTATTTTAATACTATACATATTTCATGTGTTATTA
1 TTAATTTATTTATTTTAATACTATACATATTTCATGTGTTATTA
10407302 TTAA
1 TTAA
10407306 GTAATATAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.33, C:0.05, G:0.04, T:0.58
Consensus pattern (44 bp):
TTAATTTATTTATTTTAATACTATACATATTTCATGTGTTATTA
Found at i:10407375 original size:19 final size:20
Alignment explanation
Indices: 10407348--10407385 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
10407338 TATATGTTAC
*
10407348 TTTTAAATATGT-ATTTTTA
1 TTTTAAATACGTAATTTTTA
*
10407367 TTTTGAATACGTAATTTTT
1 TTTTAAATACGTAATTTTT
10407386 TTACATCTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.29, C:0.03, G:0.08, T:0.61
Consensus pattern (20 bp):
TTTTAAATACGTAATTTTTA
Found at i:10410610 original size:10 final size:10
Alignment explanation
Indices: 10410580--10410604 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
10410570 ATAATATATT
10410580 ATTTTAGATA
1 ATTTTAGATA
10410590 ATTTTAGATA
1 ATTTTAGATA
10410600 ATTTT
1 ATTTT
10410605 GAATAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (10 bp):
ATTTTAGATA
Found at i:10415659 original size:20 final size:22
Alignment explanation
Indices: 10415617--10415661 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
10415607 ATAACTTGAG
*
10415617 TTTTATTATATATAAATTTTAT
1 TTTTATTATATATAAATTGTAT
*
10415639 TTTTATT-TAT-TTAATTGTAT
1 TTTTATTATATATAAATTGTAT
10415659 TTT
1 TTT
10415662 GTAATGATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
21 3 0.14
22 7 0.33
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTTATTATATATAAATTGTAT
Found at i:10416165 original size:37 final size:36
Alignment explanation
Indices: 10416095--10416167 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 36
10416085 GTTGCTACCA
*
10416095 TTTTGTTGTTAATGTTTGAATATTGTATAACATTTG
1 TTTTATTGTTAATGTTTGAATATTGTATAACATTTG
10416131 TTTTATTGTTAAT-TTTGCTAATATT-TATAGACATTTG
1 TTTTATTGTTAATGTTTG--AATATTGTATA-ACATTTG
10416168 CTTGTTAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
35 4 0.12
36 16 0.48
37 13 0.39
ACGTcount: A:0.26, C:0.04, G:0.14, T:0.56
Consensus pattern (36 bp):
TTTTATTGTTAATGTTTGAATATTGTATAACATTTG
Found at i:10424630 original size:30 final size:31
Alignment explanation
Indices: 10424553--10424631 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 31
10424543 AAAATTTTAA
*
10424553 ATTAATAAAAATAAAAATTAAATTTTAACTTC
1 ATTAA-AAACATAAAAATTAAATTTTAACTTC
* * *
10424585 TTTAAAAACATAAAAATTTAA-TTT-ATTTC
1 ATTAAAAACATAAAAATTAAATTTTAACTTC
*
10424614 ATTAAAAATTATAAAAAT
1 ATTAAAAA-CATAAAAAT
10424632 ACAAATTTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 11 0.28
30 11 0.28
31 14 0.35
32 4 0.10
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (31 bp):
ATTAAAAACATAAAAATTAAATTTTAACTTC
Found at i:10425031 original size:12 final size:12
Alignment explanation
Indices: 10425014--10425038 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10425004 AATTTAGATT
10425014 AAATAATTTTAA
1 AAATAATTTTAA
10425026 AAATAATTTTAA
1 AAATAATTTTAA
10425038 A
1 A
10425039 TATATTAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATAATTTTAA
Found at i:10429744 original size:29 final size:31
Alignment explanation
Indices: 10429711--10429776 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
10429701 TTTAAATTAC
*
10429711 GTTTTGATCATTGAAC-TT-T-AATTTGTTAT
1 GTTTTGATCATT-AACATTATCAATTTGTAAT
*
10429740 GTTTTGGTCATTAACATTATCAATTTGTAAT
1 GTTTTGATCATTAACATTATCAATTTGTAAT
10429771 GTTTTG
1 GTTTTG
10429777 GTCACTCTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 3 0.09
29 13 0.41
30 1 0.03
31 15 0.47
ACGTcount: A:0.24, C:0.08, G:0.15, T:0.53
Consensus pattern (31 bp):
GTTTTGATCATTAACATTATCAATTTGTAAT
Found at i:10431275 original size:8 final size:8
Alignment explanation
Indices: 10431262--10431286 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
10431252 AAAAAAAGAT
10431262 ATTCAAAA
1 ATTCAAAA
10431270 ATTCAAAA
1 ATTCAAAA
10431278 ATTCAAAA
1 ATTCAAAA
10431286 A
1 A
10431287 AGTAAAACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (8 bp):
ATTCAAAA
Found at i:10433554 original size:20 final size:20
Alignment explanation
Indices: 10433525--10433570 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
10433515 GAGAGTGATT
*
10433525 AATTAAAGTTTAATGAAGCA
1 AATTAGAGTTTAATGAAGCA
10433545 AATTAGAGTTTAATGAAGCA
1 AATTAGAGTTTAATGAAGCA
10433565 AATTAG
1 AATTAG
10433571 CTTAAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.48, C:0.04, G:0.17, T:0.30
Consensus pattern (20 bp):
AATTAGAGTTTAATGAAGCA
Found at i:10434122 original size:85 final size:85
Alignment explanation
Indices: 10433979--10434145 Score: 325
Period size: 85 Copynumber: 2.0 Consensus size: 85
10433969 AACCCTGTTC
*
10433979 TGGCGACAGTATAGGGTTAGGAGACGTTACAAAGTAAGTTTTTTTGGAACTGCCATTCAAAAAAA
1 TGGCGACAGTATAGGGTTAGGAGACATTACAAAGTAAGTTTTTTTGGAACTGCCATTCAAAAAAA
10434044 AGTTATTCAGTGCTATATTA
66 AGTTATTCAGTGCTATATTA
10434064 TGGCGACAGTATAGGGTTAGGAGACATTACAAAGTAAGTTTTTTTGGAACTGCCATTCAAAAAAA
1 TGGCGACAGTATAGGGTTAGGAGACATTACAAAGTAAGTTTTTTTGGAACTGCCATTCAAAAAAA
10434129 AGTTATTCAGTGCTATA
66 AGTTATTCAGTGCTATA
10434146 GTCGGATGTC
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 81 1.00
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (85 bp):
TGGCGACAGTATAGGGTTAGGAGACATTACAAAGTAAGTTTTTTTGGAACTGCCATTCAAAAAAA
AGTTATTCAGTGCTATATTA
Found at i:10447780 original size:20 final size:20
Alignment explanation
Indices: 10447755--10447792 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
10447745 AAGTATTATT
*
10447755 AGATATTTATTATTTAAAAA
1 AGATATTTATTAATTAAAAA
10447775 AGATATTTATTAATTAAA
1 AGATATTTATTAATTAAA
10447793 TAATTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
AGATATTTATTAATTAAAAA
Found at i:10449205 original size:18 final size:18
Alignment explanation
Indices: 10449184--10449260 Score: 66
Period size: 18 Copynumber: 4.3 Consensus size: 18
10449174 GACTGACTGC
**
10449184 TACTGAATAATTGACTAT
1 TACTGAATAAACGACTAT
10449202 TACTGAATAAACGACTGA-
1 TACTGAATAAACGACT-AT
* * *
10449220 TACTGAATAAATGATTGT
1 TACTGAATAAACGACTAT
* * *
10449238 TACTGATTAATCGATTAT
1 TACTGAATAAACGACTAT
10449256 TACTG
1 TACTG
10449261 TTGACTGACT
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
18 47 0.98
19 1 0.02
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (18 bp):
TACTGAATAAACGACTAT
Found at i:10456728 original size:27 final size:26
Alignment explanation
Indices: 10456683--10456737 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
10456673 CTCATAATAG
* *
10456683 TTACAATTTCATCAATTTTTACGACTT
1 TTACAATTTAATCAATTTTCAC-ACTT
**
10456710 TTACAATTTAATCTTTTTTCACACTT
1 TTACAATTTAATCAATTTTCACACTT
10456736 TT
1 TT
10456738 CTTTCACCCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.27, C:0.18, G:0.02, T:0.53
Consensus pattern (26 bp):
TTACAATTTAATCAATTTTCACACTT
Found at i:10466570 original size:53 final size:53
Alignment explanation
Indices: 10466482--10466632 Score: 196
Period size: 53 Copynumber: 2.8 Consensus size: 53
10466472 CTTACACGGT
* * *
10466482 TCACATATCATACCGAAGCCATATCCCAAAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCC-AGCTATGGTCTTATACGGAATCACATTA
*
10466537 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** * *
10466590 TCACATTGCACCGATGCTATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
10466633 GCACACTTAT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
52 2 0.02
53 78 0.90
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:10478574 original size:5 final size:5
Alignment explanation
Indices: 10478564--10478608 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 5
10478554 AATTTTTTTA
* * *
10478564 AAAAT AAAAT AAAAT AAAAAT AAAAG AAAAT TAAAT AAAGT AAAA
1 AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
10478609 AGTTATTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
5 28 0.85
6 5 0.15
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:10478581 original size:16 final size:16
Alignment explanation
Indices: 10478562--10478608 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
10478552 ATAATTTTTT
10478562 TAAAAATAAAATAAAA
1 TAAAAATAAAATAAAA
*
10478578 TAAAAATAAAAGAAAA
1 TAAAAATAAAATAAAA
* *
10478594 T-TAAATAAAGTAAAA
1 TAAAAATAAAATAAAA
10478609 AGTTATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
15 11 0.41
16 16 0.59
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (16 bp):
TAAAAATAAAATAAAA
Found at i:10481940 original size:40 final size:39
Alignment explanation
Indices: 10481776--10481961 Score: 158
Period size: 41 Copynumber: 4.6 Consensus size: 39
10481766 GACAAATCAA
* * * *
10481776 CTATATGTGGCACTTAGTGTGCGATTCAACATAG-TTTCGG
1 CTATATATGGCACTTAGTGTGCAATT-GAGATAGCTTT-GG
* * * *
10481816 CTATATATGGCATTTCGTGTGCGAGATTGAGATAACTTTGT
1 CTATATATGGCACTTAGTGTGC-A-ATTGAGATAGCTTTGG
* * *
10481857 CTATATATGGCACTTTGTATGCGAGATTGAGATAGCTTCGG
1 CTATATATGGCACTTAGTGTGC-A-ATTGAGATAGCTTTGG
*
10481898 CTATATATGGCACTTAGTGTGCAATTTGAGATGGCTTTGG
1 CTATATATGGCACTTAGTGTGCAA-TTGAGATAGCTTTGG
* * * *
10481938 CTATGTACGACACTTAATGTGCAA
1 CTATATATGGCACTTAGTGTGCAA
10481962 GATATCGAGT
Statistics
Matches: 120, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
39 1 0.01
40 53 0.44
41 60 0.50
42 6 0.05
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (39 bp):
CTATATATGGCACTTAGTGTGCAATTGAGATAGCTTTGG
Found at i:10486252 original size:22 final size:22
Alignment explanation
Indices: 10486219--10486287 Score: 93
Period size: 22 Copynumber: 3.1 Consensus size: 22
10486209 TATGCACTAT
* *
10486219 TAAATAGAGAGCACTAAAGTGT
1 TAAACAGAGAGCACTAAAGTGC
* *
10486241 TATACAGAGAGCACTAATGTGC
1 TAAACAGAGAGCACTAAAGTGC
*
10486263 TAAACAGAGAGCACTAACGTGC
1 TAAACAGAGAGCACTAAAGTGC
10486285 TAA
1 TAA
10486288 TAATCAGAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.20
Consensus pattern (22 bp):
TAAACAGAGAGCACTAAAGTGC
Found at i:10488426 original size:64 final size:64
Alignment explanation
Indices: 10488358--10488563 Score: 179
Period size: 64 Copynumber: 3.2 Consensus size: 64
10488348 GATTGTTCAT
*
10488358 GATATTAAATCGAATGAACTTAGGTTGCGATATTAAATCAGTGAACCTTAATGATATCAGCTGC
1 GATATTAAATCGAATGAACTTAGGTTGCGATATTAAATCAGTGAACCTAAATGATATCAGCTGC
* * * * * *
10488422 GATATTAAATCAGCAA-GCTATTTGGAGTTGCGATATTAAATCAAGT-AA-CTCAAATAAGAT-T
1 GATATTAAATC-G-AATG-AACTTAG-GTTGCGATATTAAATC-AGTGAACCT-AAATGATATCA
*
10488483 G-TTC
60 GCTGC
** * *
10488487 ATGATATTAAATCGAATGAACTTAGGTTGCGATATTAAATCAACGAACCTCAATGATATCAACTG
1 --GATATTAAATCGAATGAACTTAGGTTGCGATATTAAATCAGTGAACCTAAATGATATCAGCTG
*
10488552 T
64 C
*
10488553 AATATTAAATC
1 GATATTAAATC
10488564 AGCTAGCTAT
Statistics
Matches: 108, Mismatches: 21, Indels: 26
0.70 0.14 0.17
Matches are distributed among these distances:
63 1 0.01
64 45 0.42
65 12 0.11
66 12 0.11
67 35 0.32
68 3 0.03
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (64 bp):
GATATTAAATCGAATGAACTTAGGTTGCGATATTAAATCAGTGAACCTAAATGATATCAGCTGC
Found at i:10488459 original size:67 final size:67
Alignment explanation
Indices: 10488381--10488595 Score: 176
Period size: 67 Copynumber: 3.3 Consensus size: 67
10488371 ATGAACTTAG
*
10488381 GTTGCGATATTAAATCAGTGAACCTTAATGATATCAGCTGCGATATTAAATCAGCAAGCTATTTG
1 GTTGCGATATTAAATCAGTGAACCTAAATGATATCAGCTGCGATATTAAATCAGCAAGCTATTTG
10488446 GA
66 GA
* * * * *
10488448 GTTGCGATATTAAATCAAGT-AA-CTCAAATAAGAT-TG-TTCATGATATTAAATC-G-AATG-A
1 GTTGCGATATTAAATC-AGTGAACCT-AAATGATATCAGCTGC--GATATTAAATCAGCAA-GCT
* *
10488506 ACTTAG-
61 ATTTGGA
** * * ** *
10488512 GTTGCGATATTAAATCAACGAACCTCAATGATATCAACTGTAATATTAAATCAGCTAGCTATTTG
1 GTTGCGATATTAAATCAGTGAACCTAAATGATATCAGCTGCGATATTAAATCAGCAAGCTATTTG
10488577 GA
66 GA
* *
10488579 GTTGTGATTTTAAATCA
1 GTTGCGATATTAAATCA
10488596 TTTAAGTCAA
Statistics
Matches: 111, Mismatches: 24, Indels: 26
0.69 0.15 0.16
Matches are distributed among these distances:
63 1 0.01
64 34 0.31
65 12 0.11
66 11 0.10
67 50 0.45
68 3 0.03
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (67 bp):
GTTGCGATATTAAATCAGTGAACCTAAATGATATCAGCTGCGATATTAAATCAGCAAGCTATTTG
GA
Found at i:10488625 original size:67 final size:65
Alignment explanation
Indices: 10488422--10488761 Score: 180
Period size: 67 Copynumber: 5.2 Consensus size: 65
10488412 TATCAGCTGC
* * * **
10488422 GATATTAAATCAGCAAGCTATTTGGAGTTGCGATATTAAATCAAGTAACTCAAATAAGATTGTTC
1 GATATTAAATCAACTAG-TATTTGGAGTTGTGATATTAAATCATTTAA-TCAAATAAGATTGTTC
10488487 AT
64 AT
* * * * *** *
10488489 GATATTAAATCGAA-T-GAACTTAG-GTTGCGATATTAAATCAACGAACCTC-AAT--GA-T-AT
1 GATATTAAATC-AACTAGTATTTGGAGTTGTGATATTAAATCATTTAA--TCAAATAAGATTGTT
10488546 CAACT
63 C-A-T
* *
10488551 GTAATATTAAATCAGCTAGCTATTTGGAGTTGTGATTTTAAATCATTTAAGTCAAATAAGATTGT
1 G--ATATTAAATCAACTAG-TATTTGGAGTTGTGATATTAAATCATTTAA-TCAAATAAGATTGT
10488616 TCAT
62 TCAT
* * * * * ** * * * * *
10488620 GATATTAAATCAAAT-GAACTTAG-GTTGTGATCTTAAATCATAGAACCTTAACAATATCAGTT-
1 GATATTAAATCAACTAGTATTTGGAGTTGTGATATTAAATCATTTAATC-AAATAAGAT-TGTTC
*
10488682 GT
64 AT
* * * *
10488684 GATATTAAATCAACGAGTTGTTTGGAGTTGCGATATTAAATCAATTAACTCAAATAAGATTGTTC
1 GATATTAAATCAACTAG-TATTTGGAGTTGTGATATTAAATCATTTAA-TCAAATAAGATTGTTC
10488749 AT
64 AT
10488751 GATATTAAATC
1 GATATTAAATC
10488762 GAATGAACTT
Statistics
Matches: 201, Mismatches: 50, Indels: 44
0.68 0.17 0.15
Matches are distributed among these distances:
60 2 0.01
61 2 0.01
62 4 0.02
63 2 0.01
64 73 0.36
65 16 0.08
66 14 0.07
67 78 0.39
68 2 0.01
69 4 0.02
70 2 0.01
71 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (65 bp):
GATATTAAATCAACTAGTATTTGGAGTTGTGATATTAAATCATTTAATCAAATAAGATTGTTCAT
Found at i:10488798 original size:131 final size:131
Alignment explanation
Indices: 10488205--10488828 Score: 764
Period size: 131 Copynumber: 4.8 Consensus size: 131
10488195 GAAAATTAGC
* * * * * *
10488205 TAACACAAATGAA-ATTGTTCATGATACTAAATCGAATGAACTTAGATTACGAAATTAAATCAAC
1 TAACTCAAAT-AAGATTGTTCATGATATTAAATCGAATGAACTTAGGTTGCGATATTAAATCAGC
* * * * * * * * *
10488269 GAACCTTAACGATATCAATTGCGATTTTTAATCAGCGAGTTGTTTGGAGATGCGATCTTAAATTA
65 GAACCTTAACGATATCAGTTGTGATATTAAATCAGCGAGCTATTTGGAGTTGCGATATTAAATCA
**
10488334 GC
130 AT
* * *
10488336 TAAATCAAATATGATTGTTCATGATATTAAATCGAATGAACTTAGGTTGCGATATTAAATCAGTG
1 TAACTCAAATAAGATTGTTCATGATATTAAATCGAATGAACTTAGGTTGCGATATTAAATCAGCG
* * * *
10488401 AACCTTAATGATATCAGCTGCGATATTAAATCAGCAAGCTATTTGGAGTTGCGATATTAAATCAA
66 AACCTTAACGATATCAGTTGTGATATTAAATCAGCGAGCTATTTGGAGTTGCGATATTAAATCAA
*
10488466 G
131 T
*
10488467 TAACTCAAATAAGATTGTTCATGATATTAAATCGAATGAACTTAGGTTGCGATATTAAATCAACG
1 TAACTCAAATAAGATTGTTCATGATATTAAATCGAATGAACTTAGGTTGCGATATTAAATCAGCG
* * ** * * * * *
10488532 AACCTCAATGATATCAACTGTAATATTAAATCAGCTAGCTATTTGGAGTTGTGATTTTAAATCAT
66 AACCTTAACGATATCAGTTGTGATATTAAATCAGCGAGCTATTTGGAGTTGCGATATTAAATCAA
10488597 T
131 T
* * * * **
10488598 TAAGTCAAATAAGATTGTTCATGATATTAAATCAAATGAACTTAGGTTGTGATCTTAAATCATAG
1 TAACTCAAATAAGATTGTTCATGATATTAAATCGAATGAACTTAGGTTGCGATATTAAATCAGCG
* * * *
10488663 AACCTTAACAATATCAGTTGTGATATTAAATCAACGAGTTGTTTGGAGTTGCGATATTAAATCAA
66 AACCTTAACGATATCAGTTGTGATATTAAATCAGCGAGCTATTTGGAGTTGCGATATTAAATCAA
10488728 T
131 T
* *
10488729 TAACTCAAATAAGATTGTTCATGATATTAAATCGAATGAACTTAGGTTGCGATATTAAATTAGCA
1 TAACTCAAATAAGATTGTTCATGATATTAAATCGAATGAACTTAGGTTGCGATATTAAATCAGCG
** * * *
10488794 AACCTTAAATATTTCAGTTATGATCTTAAATCAGC
66 AACCTTAACGATATCAGTTGTGATATTAAATCAGC
10488829 TGACTCAAAT
Statistics
Matches: 424, Mismatches: 68, Indels: 2
0.86 0.14 0.00
Matches are distributed among these distances:
130 1 0.00
131 423 1.00
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.34
Consensus pattern (131 bp):
TAACTCAAATAAGATTGTTCATGATATTAAATCGAATGAACTTAGGTTGCGATATTAAATCAGCG
AACCTTAACGATATCAGTTGTGATATTAAATCAGCGAGCTATTTGGAGTTGCGATATTAAATCAA
T
Found at i:10493118 original size:4 final size:4
Alignment explanation
Indices: 10493109--10493135 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
10493099 AAATTATATA
10493109 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
10493136 GATTTGCGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:10499565 original size:19 final size:20
Alignment explanation
Indices: 10499522--10499572 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
10499512 GAAAAAAATT
10499522 ATAAAAATAATAAATTTTAG
1 ATAAAAATAATAAATTTTAG
* *
10499542 A-AAAATTATTAAATTTTA-
1 ATAAAAATAATAAATTTTAG
10499560 ATAAAAAT-ATAAA
1 ATAAAAATAATAAA
10499573 AAATTAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 5 0.19
19 20 0.77
20 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (20 bp):
ATAAAAATAATAAATTTTAG
Found at i:10499578 original size:26 final size:25
Alignment explanation
Indices: 10499549--10499597 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
10499539 TAGAAAAATT
*
10499549 ATTAAATTTTAATAAAAATATAAAAA
1 ATTAAAATTTAATAAAAAT-TAAAAA
*
10499575 ATTAAAATTTATTAAAAATTAAA
1 ATTAAAATTTAATAAAAATTAAA
10499598 TTTTTTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
ATTAAAATTTAATAAAAATTAAAAA
Found at i:10507378 original size:14 final size:14
Alignment explanation
Indices: 10507359--10507388 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
10507349 CTATCCCTAT
*
10507359 TTCTATTTTTAAAA
1 TTCTATTTTGAAAA
10507373 TTCTATTTTGAAAA
1 TTCTATTTTGAAAA
10507387 TT
1 TT
10507389 TAAATTATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (14 bp):
TTCTATTTTGAAAA
Found at i:10507467 original size:13 final size:13
Alignment explanation
Indices: 10507449--10507474 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10507439 ATTATTTATC
10507449 ATTTAAATATATA
1 ATTTAAATATATA
10507462 ATTTAAATATATA
1 ATTTAAATATATA
10507475 TAAATTTAAG
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:0.00, T:0.46
Consensus pattern (13 bp):
ATTTAAATATATA
Found at i:10507482 original size:16 final size:15
Alignment explanation
Indices: 10507455--10507511 Score: 57
Period size: 16 Copynumber: 3.9 Consensus size: 15
10507445 TATCATTTAA
10507455 ATATATAATTTAAAT
1 ATATATAATTTAAAT
*
10507470 ATATATAAATTTAAGT
1 ATATAT-AATTTAAAT
10507486 ATAT-TAA--TAATAT
1 ATATATAATTTAA-AT
*
10507499 ATAAATAATTTAA
1 ATATATAATTTAA
10507512 CAATATAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
12 3 0.09
13 4 0.12
14 5 0.15
15 7 0.21
16 15 0.44
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
ATATATAATTTAAAT
Found at i:10511326 original size:21 final size:21
Alignment explanation
Indices: 10511302--10511342 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
10511292 ATTTGATCAA
* *
10511302 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTATGGAGTAC
10511323 ACTCCACCTGCTATGGAGTA
1 ACTCCACCTGCTATGGAGTA
10511343 TCGCTCGTCT
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:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTATGGAGTAC
Found at i:10516383 original size:31 final size:32
Alignment explanation
Indices: 10516345--10516410 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
10516335 TGATTTTTTA
*
10516345 ATTTAAAAAATTACAATTTGA-TCA-TTAAATT
1 ATTTAAAAAATTAC-ATTTAAGTCACTTAAATT
* *
10516376 ATTTAAAAATTTTCATTTAAGTCACTTAAATT
1 ATTTAAAAAATTACATTTAAGTCACTTAAATT
10516408 ATT
1 ATT
10516411 AAATTTGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 5 0.17
31 15 0.50
32 10 0.33
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (32 bp):
ATTTAAAAAATTACATTTAAGTCACTTAAATT
Found at i:10527681 original size:9 final size:9
Alignment explanation
Indices: 10527667--10527701 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
10527657 CCCAAATAGT
*
10527667 CTTCTTCGC
1 CTTCTTCTC
10527676 CTTCTTCTC
1 CTTCTTCTC
10527685 CTTCTTCTC
1 CTTCTTCTC
10527694 CTTCTTCT
1 CTTCTTCT
10527702 TTTATCTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.00, C:0.43, G:0.03, T:0.54
Consensus pattern (9 bp):
CTTCTTCTC
Found at i:10527682 original size:3 final size:3
Alignment explanation
Indices: 10527666--10527722 Score: 53
Period size: 3 Copynumber: 19.0 Consensus size: 3
10527656 ACCCAAATAG
* * * * *
10527666 TCT TCT TCG CCT TCT TCT CCT TCT TCT CCT TCT TCT TTT ATCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT -TCT TCT
10527712 T-T TCT TCT TCT
1 TCT TCT TCT TCT
10527723 AGAAGAAGAT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
2 2 0.05
3 38 0.90
4 2 0.05
ACGTcount: A:0.02, C:0.35, G:0.02, T:0.61
Consensus pattern (3 bp):
TCT
Found at i:10528464 original size:19 final size:18
Alignment explanation
Indices: 10528435--10528476 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
10528425 GTGTTGATCC
*
10528435 AATTGTAATTTTTGTTTT
1 AATTTTAATTTTTGTTTT
*
10528453 ATATTTTAATTTTTTTTTT
1 A-ATTTTAATTTTTGTTTT
10528472 AATTT
1 AATTT
10528477 CTTTGGCATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (18 bp):
AATTTTAATTTTTGTTTT
Found at i:10531962 original size:21 final size:21
Alignment explanation
Indices: 10531936--10531976 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
10531926 AGACGAGCAA
* *
10531936 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
10531957 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
10531977 TTGAGCAGAT
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:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:10533915 original size:16 final size:16
Alignment explanation
Indices: 10533882--10533915 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
10533872 GGAGATTGTT
* *
10533882 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
10533898 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
10533914 AA
1 AA
10533916 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:10534112 original size:15 final size:13
Alignment explanation
Indices: 10534079--10534115 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
10534069 CCAACCAATC
10534079 TTTCTCTCTTCGT
1 TTTCTCTCTTCGT
10534092 TTTCTCTCTTCGT
1 TTTCTCTCTTCGT
10534105 TTTCTCTCTTC
1 TTTCTCTCTTC
10534116 TCCCATTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.00, C:0.32, G:0.05, T:0.62
Consensus pattern (13 bp):
TTTCTCTCTTCGT
Found at i:10537004 original size:17 final size:19
Alignment explanation
Indices: 10536967--10537004 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
10536957 TAATACTTCA
10536967 AAAAATACATTGTTAATAT
1 AAAAATACATTGTTAATAT
*
10536986 AAAAATATATT-TT-ATAT
1 AAAAATACATTGTTAATAT
10537003 AA
1 AA
10537005 TATATTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 2 0.11
19 10 0.56
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (19 bp):
AAAAATACATTGTTAATAT
Found at i:10541664 original size:13 final size:13
Alignment explanation
Indices: 10541646--10541675 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
10541636 TTCTTGTAAA
10541646 CATTTCACATAAC
1 CATTTCACATAAC
*
10541659 CATTTCATATAAC
1 CATTTCACATAAC
10541672 CATT
1 CATT
10541676 CGTTATCTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.27, G:0.00, T:0.37
Consensus pattern (13 bp):
CATTTCACATAAC
Found at i:10541818 original size:46 final size:46
Alignment explanation
Indices: 10541759--10541988 Score: 318
Period size: 46 Copynumber: 5.0 Consensus size: 46
10541749 TTATCTTTGA
* * * * *
10541759 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATAT
* *
10541805 CATGTTGCCATAGTATCTTTCAACCATGGTCTTATTCATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
* * *
10541851 CATGTTGCCATGGTATCTTTCAACCATGGTTTTATTCATTCCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
* *
10541897 CACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
* *
10541943 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
10541989 TAGAGAGCAC
Statistics
Matches: 169, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 4 0.02
46 165 0.98
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.41
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
Found at i:10542611 original size:55 final size:55
Alignment explanation
Indices: 10542542--10542660 Score: 213
Period size: 55 Copynumber: 2.2 Consensus size: 55
10542532 ATTTCATTTA
*
10542542 ATTTATTA-ATTTAGATAATAAAACAATTCATTCTCTTCAATTTGTTCATTTTGAC
1 ATTT-TTACATTTAGATAATAAAACAATTCATTCTCTTCAATTTGTTCATTTTAAC
10542597 ATTTTTACATTTAGATAATAAAACAATTCATTCTCTTCAATTTGTTCATTTTAAC
1 ATTTTTACATTTAGATAATAAAACAATTCATTCTCTTCAATTTGTTCATTTTAAC
10542652 ATTTTTACA
1 ATTTTTACA
10542661 AAATTGCCCC
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
54 3 0.05
55 59 0.95
ACGTcount: A:0.34, C:0.13, G:0.04, T:0.48
Consensus pattern (55 bp):
ATTTTTACATTTAGATAATAAAACAATTCATTCTCTTCAATTTGTTCATTTTAAC
Found at i:10543488 original size:10 final size:11
Alignment explanation
Indices: 10543462--10543494 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
10543452 TTCTACACTA
10543462 TTTCTCTTCAC
1 TTTCTCTTCAC
*
10543473 TTTCTCTT-AT
1 TTTCTCTTCAC
10543483 TTTCTCTTCAC
1 TTTCTCTTCAC
10543494 T
1 T
10543495 AACATGACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.09, C:0.30, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTCTCTTCAC
Found at i:10545228 original size:25 final size:25
Alignment explanation
Indices: 10545195--10545276 Score: 137
Period size: 25 Copynumber: 3.3 Consensus size: 25
10545185 CTGTAAGCGA
* *
10545195 TAAGCTCCTCCAAGCTGAATAACGG
1 TAAGCTCCTTCGAGCTGAATAACGG
*
10545220 TAAGTTCCTTCGAGCTGAATAACGG
1 TAAGCTCCTTCGAGCTGAATAACGG
10545245 TAAGCTCCTTCGAGCTGAATAACGG
1 TAAGCTCCTTCGAGCTGAATAACGG
10545270 TAAGCTC
1 TAAGCTC
10545277 ATAACTGAGT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 53 1.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (25 bp):
TAAGCTCCTTCGAGCTGAATAACGG
Found at i:10548966 original size:6 final size:6
Alignment explanation
Indices: 10548918--10548978 Score: 50
Period size: 6 Copynumber: 9.5 Consensus size: 6
10548908 AAAAAGTTTA
* * * *
10548918 AAAACAT AACAAT AAACAT AAAAAT AGAAAT AAAACTAA AAAAAT AAAAAT
1 AAAA-AT AAAAAT AAAAAT AAAAAT AAAAAT AAAA--AT AAAAAT AAAAAT
10548969 AAATAAT AAA
1 AAA-AAT AAA
10548979 TAGACTCAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
6 29 0.67
7 9 0.21
8 5 0.12
ACGTcount: A:0.75, C:0.07, G:0.02, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:10556643 original size:21 final size:21
Alignment explanation
Indices: 10556617--10556659 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
10556607 GGCCATTAGG
10556617 AATGCTTAAGTGTGTCTAAAT
1 AATGCTTAAGTGTGTCTAAAT
10556638 AATGCTTAAGTGTGTCTAAAT
1 AATGCTTAAGTGTGTCTAAAT
10556659 A
1 A
10556660 TGACTATCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGCTTAAGTGTGTCTAAAT
Found at i:10558619 original size:11 final size:11
Alignment explanation
Indices: 10558600--10558628 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
10558590 ACTCCTGTGA
10558600 AAAAT-AAAAT
1 AAAATAAAAAT
10558610 AAAATAAAAAT
1 AAAATAAAAAT
10558621 AAAATAAA
1 AAAATAAA
10558629 GAACACACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:10563023 original size:11 final size:11
Alignment explanation
Indices: 10563004--10563032 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
10562994 CAATTTGTGA
10563004 AAAAT-AAAAT
1 AAAATAAAAAT
10563014 AAAATAAAAAT
1 AAAATAAAAAT
10563025 AAAATAAA
1 AAAATAAA
10563033 GAACACACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:10565937 original size:11 final size:11
Alignment explanation
Indices: 10565921--10565949 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
10565911 ATATATATAC
10565921 TAATTACTCTA
1 TAATTACTCTA
10565932 TAATTACTCTA
1 TAATTACTCTA
10565943 TAATTAC
1 TAATTAC
10565950 AAGTCATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.45
Consensus pattern (11 bp):
TAATTACTCTA
Found at i:10569279 original size:45 final size:45
Alignment explanation
Indices: 10569215--10569306 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
10569205 TTCTGATATT
10569215 TTCTTTTATTGCCCTTGTCTTTAGAGGCATTGACCAAATGAGCAC
1 TTCTTTTATTGCCCTTGTCTTTAGAGGCATTGACCAAATGAGCAC
10569260 TTCTTTTATTGCCCTTGTCTTTAGAGGCATTGACCAAATGAGCAC
1 TTCTTTTATTGCCCTTGTCTTTAGAGGCATTGACCAAATGAGCAC
10569305 TT
1 TT
10569307 TCAGACTTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (45 bp):
TTCTTTTATTGCCCTTGTCTTTAGAGGCATTGACCAAATGAGCAC
Found at i:10573491 original size:37 final size:37
Alignment explanation
Indices: 10573441--10573552 Score: 206
Period size: 37 Copynumber: 3.0 Consensus size: 37
10573431 ATGATAAGGA
*
10573441 GAATGTACTGTGACATACTGCTGTGCACCCTTTTGCT
1 GAATGTACTGTGACATACTGCTGTGCACCCTTATGCT
10573478 GAATGTACTGTGACATACTGCTGTGCACCCTTATGCT
1 GAATGTACTGTGACATACTGCTGTGCACCCTTATGCT
*
10573515 GAATGTACTGTGACATACTGCTGTGCACCCTCATGCT
1 GAATGTACTGTGACATACTGCTGTGCACCCTTATGCT
10573552 G
1 G
10573553 CCTGGACTTG
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 73 1.00
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.32
Consensus pattern (37 bp):
GAATGTACTGTGACATACTGCTGTGCACCCTTATGCT
Found at i:10581695 original size:19 final size:18
Alignment explanation
Indices: 10581673--10581730 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 18
10581663 TAAAAAAATT
10581673 AAAATTACTAAAAATATAG
1 AAAATTA-TAAAAATATAG
*
10581692 AAAATTATTAAAAATATTAT
1 AAAATTA-TAAAAATA-TAG
*
10581712 AAAA-TATAAACATATAG
1 AAAATTATAAAAATATAG
10581729 AA
1 AA
10581731 TTATCTGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
17 4 0.12
18 7 0.21
19 17 0.50
20 6 0.18
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.29
Consensus pattern (18 bp):
AAAATTATAAAAATATAG
Found at i:10581704 original size:37 final size:37
Alignment explanation
Indices: 10581636--10581730 Score: 102
Period size: 37 Copynumber: 2.5 Consensus size: 37
10581626 AATTATTAAA
** *
10581636 AAAACTATAAAAATATTTAAATTTTATTAAAAAAATTA-
1 AAAA-TATAAAAATATAGAAA-ATTATTAAAAAAATTAT
* *
10581674 AAATTACTAAAAATATAGAAAATTATTAAAAATATTAT
1 AAAATA-TAAAAATATAGAAAATTATTAAAAAAATTAT
*
10581712 AAAATATAAACATATAGAA
1 AAAATATAAAAATATAGAA
10581731 TTATCTGAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
37 28 0.58
38 20 0.42
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (37 bp):
AAAATATAAAAATATAGAAAATTATTAAAAAAATTAT
Found at i:10581878 original size:21 final size:21
Alignment explanation
Indices: 10581854--10581893 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
10581844 TAAAATCAAT
10581854 AAAAACATAAAAATATTATAG
1 AAAAACATAAAAATATTATAG
* * *
10581875 AAAAATATTAAAATTTTAT
1 AAAAACATAAAAATATTAT
10581894 TAAAATGCTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (21 bp):
AAAAACATAAAAATATTATAG
Found at i:10582278 original size:12 final size:10
Alignment explanation
Indices: 10582237--10582277 Score: 64
Period size: 10 Copynumber: 3.9 Consensus size: 10
10582227 AAATTTTTCT
10582237 ATATTTTTAA
1 ATATTTTTAA
10582247 ATATTTTTAA
1 ATATTTTTAA
10582257 ATATTTTTATA
1 ATATTTTTA-A
10582268 TATATTTTTA
1 -ATATTTTTA
10582278 TTGTTTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 19 0.66
11 1 0.03
12 9 0.31
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
ATATTTTTAA
Found at i:10582289 original size:14 final size:13
Alignment explanation
Indices: 10582257--10582303 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
10582247 ATATTTTTAA
*
10582257 ATATTTTTA-TAT
1 ATATTTTTATTTT
10582269 ATATTTTTATTGTT
1 ATATTTTTATT-TT
* *
10582283 TTATTTTTGTTTT
1 ATATTTTTATTTT
10582296 ATATTTTT
1 ATATTTTT
10582304 TTCATCATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 9 0.31
13 10 0.34
14 10 0.34
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.74
Consensus pattern (13 bp):
ATATTTTTATTTT
Found at i:10582719 original size:22 final size:22
Alignment explanation
Indices: 10582691--10582743 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
10582681 AAATACGTTC
* *
10582691 GGTGGTGATTGAGACTAATGTA
1 GGTGGTGATTAAGACTAATGCA
*
10582713 GGTGGTGATTAAGACTGATGCA
1 GGTGGTGATTAAGACTAATGCA
*
10582735 GATGGTGAT
1 GGTGGTGAT
10582744 GATGGATATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.26, C:0.06, G:0.38, T:0.30
Consensus pattern (22 bp):
GGTGGTGATTAAGACTAATGCA
Found at i:10592851 original size:18 final size:18
Alignment explanation
Indices: 10592815--10592853 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
10592805 TGTAATTCGA
* *
10592815 TCTTTTTTTTGTAAGTTT
1 TCTTTTCTTTGTAACTTT
*
10592833 TCTTTTCTTTGTGACTTT
1 TCTTTTCTTTGTAACTTT
10592851 TCT
1 TCT
10592854 AAGATAATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.13, G:0.10, T:0.69
Consensus pattern (18 bp):
TCTTTTCTTTGTAACTTT
Found at i:10592943 original size:18 final size:19
Alignment explanation
Indices: 10592912--10592947 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
10592902 ATGTCACAAA
10592912 AAAAAAACCAAAATTACAG
1 AAAAAAACCAAAATTACAG
*
10592931 AAAACAACC-AAATTACA
1 AAAAAAACCAAAATTACA
10592948 CAATGTGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.67, C:0.19, G:0.03, T:0.11
Consensus pattern (19 bp):
AAAAAAACCAAAATTACAG
Found at i:10596869 original size:45 final size:45
Alignment explanation
Indices: 10596801--10596933 Score: 176
Period size: 45 Copynumber: 3.0 Consensus size: 45
10596791 TAGGATTTTG
* * * *
10596801 ATATGTATTTTCGAGTAAGACCACGTCAGGGACGTTGGCATCGAT
1 ATATGTGTTTTCGTGTAAGACCACGTCTGGGACATTGGCATCGAT
*
10596846 ATATGTGTTTTCGTGTAAAACCACGTCTGGGACATTGGCATCGAT
1 ATATGTGTTTTCGTGTAAGACCACGTCTGGGACATTGGCATCGAT
* * * * *
10596891 ATATGTGGTTACGTGTGAGACCATGTCTGGAACATTGGCATCG
1 ATATGTGTTTTCGTGTAAGACCACGTCTGGGACATTGGCATCG
10596934 TATTAGATTC
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 77 1.00
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (45 bp):
ATATGTGTTTTCGTGTAAGACCACGTCTGGGACATTGGCATCGAT
Found at i:10597804 original size:2 final size:2
Alignment explanation
Indices: 10597799--10597835 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
10597789 ATGATATATA
*
10597799 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TA TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
10597836 ATTGTTAGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.03, C:0.00, G:0.46, T:0.51
Consensus pattern (2 bp):
TG
Found at i:10607077 original size:17 final size:18
Alignment explanation
Indices: 10607047--10607080 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
10607037 ATTTAAATTG
10607047 CGGTCGCGGTCGCGTTTT
1 CGGTCGCGGTCGCGTTTT
10607065 CGGTCGC-GTCGCGTTT
1 CGGTCGCGGTCGCGTTT
10607081 GTCGCGGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.00, C:0.29, G:0.38, T:0.32
Consensus pattern (18 bp):
CGGTCGCGGTCGCGTTTT
Found at i:10610665 original size:55 final size:56
Alignment explanation
Indices: 10610604--10610730 Score: 197
Period size: 55 Copynumber: 2.3 Consensus size: 56
10610594 TGTCTTGGCC
*
10610604 GTGGTCGACACTGACTTGGGTCACACGGCTAGCCACACGCCCGTGTGCCTT-AGCT
1 GTGGTCGACACTGACTTGGGTCACACGGCTAGCCACACGCCCGTGTGCCTTGACCT
* *
10610659 GTGGTCGGCATTGACTTGGGTCACACGGCTAGCCACACGCCCGTGTGCCTTGACCT
1 GTGGTCGACACTGACTTGGGTCACACGGCTAGCCACACGCCCGTGTGCCTTGACCT
10610715 -TGGTCGAGC-CTGACTT
1 GTGGTCGA-CACTGACTT
10610731 ACAAATGTAG
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
55 61 0.94
56 4 0.06
ACGTcount: A:0.15, C:0.31, G:0.30, T:0.24
Consensus pattern (56 bp):
GTGGTCGACACTGACTTGGGTCACACGGCTAGCCACACGCCCGTGTGCCTTGACCT
Found at i:10611780 original size:40 final size:41
Alignment explanation
Indices: 10611732--10611822 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 41
10611722 CTCAATATTG
**
10611732 CACACTTAGTGGC-ACATATAGCCGAAGCTATTCCAATTCA
1 CACACTTAGTGGCTACATATAGCCGAAGCTATTCCAAACCA
** * *
10611772 CACACTTAGT-GCTATTTATAGCCGAAGCTATTTCAAACCG
1 CACACTTAGTGGCTACATATAGCCGAAGCTATTCCAAACCA
10611812 CACACTTAGTG
1 CACACTTAGTG
10611823 CCGAACATAG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
39 2 0.05
40 41 0.95
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.27
Consensus pattern (41 bp):
CACACTTAGTGGCTACATATAGCCGAAGCTATTCCAAACCA
Found at i:10617718 original size:55 final size:56
Alignment explanation
Indices: 10617525--10617723 Score: 280
Period size: 55 Copynumber: 3.6 Consensus size: 56
10617515 CACAATACAT
* *
10617525 GCCCGTGTGTCTTGGCCGTGGTCGA-CACTGACTTGGGTCACACAACTAGCCACAC
1 GCCCGTGTGCCTTGGCCGTGGTCGAGCACTGACTTGGGTCACACAGCTAGCCACAC
* * *
10617580 GCCCGTGTGCCTTGGCCGTGGTCG-GCAATGAATTGGGTCACACAGCTAGCCACAT
1 GCCCGTGTGCCTTGGCCGTGGTCGAGCACTGACTTGGGTCACACAGCTAGCCACAC
* * *
10617635 GTCCGTGTGCCTTGGCCATGATCGAGC-CTGACTTGGGTCACACAGCTAGCCACAC
1 GCCCGTGTGCCTTGGCCGTGGTCGAGCACTGACTTGGGTCACACAGCTAGCCACAC
* *
10617690 GCCCATGTGCCTTGGCCGTGGTCAAGC-CTGACTT
1 GCCCGTGTGCCTTGGCCGTGGTCGAGCACTGACTT
10617724 ACAAATGTAA
Statistics
Matches: 126, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
55 124 0.98
56 2 0.02
ACGTcount: A:0.17, C:0.32, G:0.29, T:0.23
Consensus pattern (56 bp):
GCCCGTGTGCCTTGGCCGTGGTCGAGCACTGACTTGGGTCACACAGCTAGCCACAC
Found at i:10618603 original size:19 final size:19
Alignment explanation
Indices: 10618579--10618620 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
10618569 ACAAACTCGT
10618579 ACTTAACTATTACATTATC
1 ACTTAACTATTACATTATC
*
10618598 ACTTAACTATTATATTATC
1 ACTTAACTATTACATTATC
10618617 ACTT
1 ACTT
10618621 CAATGCTCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.36, C:0.19, G:0.00, T:0.45
Consensus pattern (19 bp):
ACTTAACTATTACATTATC
Found at i:10618760 original size:39 final size:40
Alignment explanation
Indices: 10618715--10618807 Score: 118
Period size: 40 Copynumber: 2.4 Consensus size: 40
10618705 ATAAAATATT
* *
10618715 GCACACTTAGTGCCA-TCATAACTGAAGCTA-TTCTAATTC
1 GCACACTTAGTGCCATTCATAACCGAAGCTATTTC-AAATC
* * *
10618754 GCACACTTAGTGCTATTTATAGCCGAAGCTATTTCAAATC
1 GCACACTTAGTGCCATTCATAACCGAAGCTATTTCAAATC
10618794 GCACACTTAGTGCC
1 GCACACTTAGTGCC
10618808 GAAAATAGTC
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
39 14 0.30
40 29 0.63
41 3 0.07
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (40 bp):
GCACACTTAGTGCCATTCATAACCGAAGCTATTTCAAATC
Found at i:10630898 original size:20 final size:21
Alignment explanation
Indices: 10630870--10630910 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
10630860 GAATACCATT
*
10630870 AATATTGATTGAATATTAATA
1 AATATTGATAGAATATTAATA
*
10630891 AATA-TGATAGTATATTAATA
1 AATATTGATAGAATATTAATA
10630911 TAAAATTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (21 bp):
AATATTGATAGAATATTAATA
Found at i:10631385 original size:9 final size:9
Alignment explanation
Indices: 10631373--10631399 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
10631363 CAAAAAATGT
10631373 AAAAATTAA
1 AAAAATTAA
10631382 AAAAATTAA
1 AAAAATTAA
10631391 AAAAATTAA
1 AAAAATTAA
10631400 GAAACATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (9 bp):
AAAAATTAA
Found at i:10633149 original size:17 final size:18
Alignment explanation
Indices: 10633099--10633149 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
10633089 ATTTTTTATA
*
10633099 ATAATATTTTTACAAATTT
1 ATAATCTTTTTA-AAATTT
*
10633118 ATAATCTTTTAAAAATATT
1 ATAATCTTTTTAAAAT-TT
10633137 -TAA-CTTTTTAAAA
1 ATAATCTTTTTAAAA
10633150 AATTAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 9 0.32
18 7 0.25
19 12 0.43
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (18 bp):
ATAATCTTTTTAAAATTT
Found at i:10639807 original size:19 final size:20
Alignment explanation
Indices: 10639783--10639823 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
10639773 ATAGTCCAAT
* *
10639783 TAGTTT-TATTTTTTTTATA
1 TAGTTTCTATTATTTTAATA
10639802 TAGTTTCTATTATTTTAATA
1 TAGTTTCTATTATTTTAATA
10639822 TA
1 TA
10639824 AATTTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (20 bp):
TAGTTTCTATTATTTTAATA
Found at i:10639817 original size:20 final size:19
Alignment explanation
Indices: 10639783--10639837 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
10639773 ATAGTCCAAT
* *
10639783 TAGTTTTATTTTTTTTATA
1 TAGTTTTATTATTTTAATA
10639802 TAGTTTCTATTATTTTAATA
1 TAGTTT-TATTATTTTAATA
* *
10639822 TAAATTTTTTTATTTT
1 T-AGTTTTATTATTTT
10639838 TTTATGTAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 6 0.20
20 20 0.67
21 4 0.13
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (19 bp):
TAGTTTTATTATTTTAATA
Found at i:10652583 original size:14 final size:14
Alignment explanation
Indices: 10652564--10652592 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
10652554 TACTCTTCTA
10652564 ATCAAATTCTAATT
1 ATCAAATTCTAATT
10652578 ATCAAATTCTAATT
1 ATCAAATTCTAATT
10652592 A
1 A
10652593 ATGATGGGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (14 bp):
ATCAAATTCTAATT
Done.