Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12
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: 24583705
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1509421 characters in sequence are not A, C, G, or T
File 59 of 75
Found at i:18928115 original size:9 final size:9
Alignment explanation
Indices: 18928101--18928138 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
18928091 TTGAATTGAT
18928101 TTTTTATAA
1 TTTTTATAA
18928110 TTTTTATAA
1 TTTTTATAA
*
18928119 ATTTTA-AA
1 TTTTTATAA
18928127 TTTTTATAA
1 TTTTTATAA
18928136 TTT
1 TTT
18928139 ACTTATTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
8 7 0.27
9 19 0.73
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TTTTTATAA
Found at i:18928130 original size:17 final size:18
Alignment explanation
Indices: 18928102--18928135 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
18928092 TGAATTGATT
18928102 TTTTATAATTTTTATAAA
1 TTTTATAATTTTTATAAA
18928120 TTTTA-AATTTTTATAA
1 TTTTATAATTTTTATAA
18928136 TTTACTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTATAATTTTTATAAA
Found at i:18928315 original size:9 final size:9
Alignment explanation
Indices: 18928303--18928369 Score: 75
Period size: 9 Copynumber: 7.4 Consensus size: 9
18928293 AAATTTTAGA
18928303 ATTTTTTAT
1 ATTTTTTAT
18928312 ATTTTTTAT
1 ATTTTTTAT
*
18928321 ATTTTTTAA
1 ATTTTTTAT
18928330 ATTTTTT-T
1 ATTTTTTAT
18928338 ATTCTTTT-T
1 ATT-TTTTAT
*
18928347 ATTTTTCAT
1 ATTTTTTAT
*
18928356 AACTTTTTAT
1 -ATTTTTTAT
18928366 ATTT
1 ATTT
18928370 AAAAATTATA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
8 6 0.12
9 36 0.73
10 7 0.14
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.73
Consensus pattern (9 bp):
ATTTTTTAT
Found at i:18928336 original size:28 final size:27
Alignment explanation
Indices: 18928296--18928369 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 27
18928286 TAATATTAAA
18928296 TTTTAGAATTTTTTATATTTTTTATATT
1 TTTTAGAATTTTTTATATTTTTT-TATT
18928324 TTTTA-AATTTTTT-TATTCTTTTTATT
1 TTTTAGAATTTTTTATATT-TTTTTATT
* * *
18928350 TTTCATAACTTTTTATATTT
1 TTTTAGAATTTTTTATATTT
18928370 AAAAATTATA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
26 12 0.29
27 20 0.49
28 9 0.22
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.72
Consensus pattern (27 bp):
TTTTAGAATTTTTTATATTTTTTTATT
Found at i:18929649 original size:20 final size:20
Alignment explanation
Indices: 18929615--18929656 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
18929605 AACTATTTAA
** *
18929615 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
18929635 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
18929655 AT
1 AT
18929657 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:18931727 original size:15 final size:16
Alignment explanation
Indices: 18931702--18931735 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
18931692 AATATGAAGC
18931702 GTTTGATAAATTTAAA
1 GTTTGATAAATTTAAA
*
18931718 GTTT-ATAAATTTGAA
1 GTTTGATAAATTTAAA
18931733 GTT
1 GTT
18931736 GAAATTCAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (16 bp):
GTTTGATAAATTTAAA
Found at i:18937457 original size:21 final size:21
Alignment explanation
Indices: 18937433--18937488 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 21
18937423 CGGAACAATT
*
18937433 AAGAAAAAGA-GAAATACAAAA
1 AAGAAAAAGATCAAAT-CAAAA
*
18937454 AAG-AATAGATCAAATCAAAA
1 AAGAAAAAGATCAAATCAAAA
*
18937474 AAGAAATAGAATCAA
1 AAGAAAAAG-ATCAA
18937489 CAATTTGTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 13 0.43
21 12 0.40
22 5 0.17
ACGTcount: A:0.70, C:0.07, G:0.12, T:0.11
Consensus pattern (21 bp):
AAGAAAAAGATCAAATCAAAA
Found at i:18937474 original size:20 final size:23
Alignment explanation
Indices: 18937444--18937488 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
18937434 AGAAAAAGAG
18937444 AAATACAAAAAAG-AATAG-ATC
1 AAATACAAAAAAGAAATAGAATC
18937465 AAAT-CAAAAAAGAAATAGAATC
1 AAATACAAAAAAGAAATAGAATC
18937487 AA
1 AA
18937489 CAATTTGTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
21 9 0.41
22 5 0.23
ACGTcount: A:0.69, C:0.09, G:0.09, T:0.13
Consensus pattern (23 bp):
AAATACAAAAAAGAAATAGAATC
Found at i:18940350 original size:34 final size:35
Alignment explanation
Indices: 18940302--18940387 Score: 120
Period size: 34 Copynumber: 2.5 Consensus size: 35
18940292 AATGATACCA
18940302 AAAATGATGAGTGAACAGGAGAGATTCCCTGCAA-
1 AAAATGATGAGTGAACAGGAGAGATTCCCTGCAAC
* * *
18940336 GAAATGATGTGTGAACATGAGAGATTCCCTGCAAC
1 AAAATGATGAGTGAACAGGAGAGATTCCCTGCAAC
* *
18940371 AAAATAATGCGTGAACA
1 AAAATGATGAGTGAACA
18940388 TGAAATATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
34 31 0.69
35 14 0.31
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (35 bp):
AAAATGATGAGTGAACAGGAGAGATTCCCTGCAAC
Found at i:18943029 original size:32 final size:32
Alignment explanation
Indices: 18942984--18943057 Score: 112
Period size: 32 Copynumber: 2.3 Consensus size: 32
18942974 GTAGTCCATC
* *
18942984 ATTAATCACTATAACCATGTGTCTAAACCCAA
1 ATTAATCATTATAACCATGAGTCTAAACCCAA
*
18943016 ATTAATCATTATAACCATGAGTCTAAACCCTA
1 ATTAATCATTATAACCATGAGTCTAAACCCAA
*
18943048 GTTAATCATT
1 ATTAATCATT
18943058 GCAAGGTGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.39, C:0.22, G:0.07, T:0.32
Consensus pattern (32 bp):
ATTAATCATTATAACCATGAGTCTAAACCCAA
Found at i:18946420 original size:12 final size:11
Alignment explanation
Indices: 18946399--18946431 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
18946389 AAGTTATAAT
18946399 AAAAATAAAAG
1 AAAAATAAAAG
18946410 AAAATATAAAAG
1 AAAA-ATAAAAG
18946422 AAAAA-AAAAG
1 AAAAATAAAAG
18946432 TATGAAAGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 5 0.24
11 5 0.24
12 11 0.52
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (11 bp):
AAAAATAAAAG
Found at i:18946591 original size:16 final size:16
Alignment explanation
Indices: 18946572--18946615 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
18946562 CGGTTTTTTT
**
18946572 TTTTTTTTTTTTTGAA
1 TTTTTTTTTTTTCAAA
18946588 TTTTTTTTTTTTCAAA
1 TTTTTTTTTTTTCAAA
18946604 TTCTTTTTTTTT
1 TT-TTTTTTTTT
18946616 AAGCTTGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 16 0.64
17 9 0.36
ACGTcount: A:0.11, C:0.05, G:0.02, T:0.82
Consensus pattern (16 bp):
TTTTTTTTTTTTCAAA
Found at i:18947310 original size:35 final size:34
Alignment explanation
Indices: 18947257--18947382 Score: 92
Period size: 35 Copynumber: 3.6 Consensus size: 34
18947247 TCACACATAT
*
18947257 TTGTCGGTTTTAAC-GACCAGCGCAAGGCTCATTTA
1 TTGTCGGTTAT-ACTGACCAGCGC-AGGCTCATTTA
* * *
18947292 TTGTCGGTTATACTGACCAGTGCTAGGCACATATA
1 TTGTCGGTTATACTGACCAGCGC-AGGCTCATTTA
* * * * * * *
18947327 TTTGTTGATTTTATTAACTAGCGCAGGGTGCATTTA
1 -TTGTCGGTTATACTGACCAGCGCAGGCT-CATTTA
*
18947363 TTGTCGGTTATACCGACCAG
1 TTGTCGGTTATACTGACCAG
18947383 TGCTGGGCAC
Statistics
Matches: 66, Mismatches: 22, Indels: 6
0.70 0.23 0.06
Matches are distributed among these distances:
34 2 0.03
35 43 0.65
36 21 0.32
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (34 bp):
TTGTCGGTTATACTGACCAGCGCAGGCTCATTTA
Found at i:18947425 original size:71 final size:71
Alignment explanation
Indices: 18947272--18947442 Score: 209
Period size: 71 Copynumber: 2.4 Consensus size: 71
18947262 GGTTTTAACG
* * * *
18947272 ACCAGCGCAAGGCTCATTTATTGTCGGTTATACTGACCAGTGCTAGGCACATATATTTGTTGATT
1 ACCAGCGCAGGGCACATTTATTGTCGGTTATACCGACCAGTGCTAGGCACACATATTTGTTGATT
* *
18947337 TTATTA
66 CTACTA
* ** * *
18947343 ACTAGCGCAGGGTGCATTTATTGTCGGTTATACCGACCAGTGCTGGGCACACATATTT-TTCGGT
1 ACCAGCGCAGGGCACATTTATTGTCGGTTATACCGACCAGTGCTAGGCACACATATTTGTT-GAT
18947407 TCTACTA
65 TCTACTA
* *
18947414 ACCAGCTCAGGGCACATTTATTGCCGGTT
1 ACCAGCGCAGGGCACATTTATTGTCGGTT
18947443 TTATCGGCCA
Statistics
Matches: 84, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
70 2 0.02
71 82 0.98
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (71 bp):
ACCAGCGCAGGGCACATTTATTGTCGGTTATACCGACCAGTGCTAGGCACACATATTTGTTGATT
CTACTA
Found at i:18959666 original size:40 final size:40
Alignment explanation
Indices: 18959621--18959780 Score: 194
Period size: 40 Copynumber: 4.0 Consensus size: 40
18959611 GATAAAACAG
* ** * *
18959621 AAAAACGCTTCCTTAAAAAAACGCTTTGTCCATGTGGACA
1 AAAAACGCTTCCTCAAGGAAGCGCTTTGTCCACGTGGACA
*
18959661 AAAAACGCTCCCTCAAGGAAGCGCTTTGTCCACGTGGACA
1 AAAAACGCTTCCTCAAGGAAGCGCTTTGTCCACGTGGACA
* *
18959701 AAAAATGCTTCCTCAAGGAAGCACTTTGTCCACGTGGACA
1 AAAAACGCTTCCTCAAGGAAGCGCTTTGTCCACGTGGACA
* ** *
18959741 GAAAACGCTTCCTTGAGGGAGCGCTTTGTGTCCACGTGGA
1 AAAAACGCTTCCTCAAGGAAGCGC-TT-TGTCCACGTGGA
18959781 TAGGATTTAG
Statistics
Matches: 103, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
40 89 0.86
41 2 0.02
42 12 0.12
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (40 bp):
AAAAACGCTTCCTCAAGGAAGCGCTTTGTCCACGTGGACA
Found at i:18960534 original size:52 final size:52
Alignment explanation
Indices: 18960476--18960631 Score: 141
Period size: 52 Copynumber: 3.1 Consensus size: 52
18960466 AAACACTAAA
18960476 CCCTAATCTAATTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCCAAG
1 CCCTAATCTAATTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCCAAG
* ** ** * * * * *
18960528 CCCTAAT-TTATTTGATTT----TTT-TCTTTAA-AAACCCTA--AACACTAAA
1 CCCTAATCTAATTT--TTTAAAATTTATAATTAATTTACTCAAGTAACCCCAAG
18960573 CCCTAATCTAATTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCCAAG
1 CCCTAATCTAATTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCCAAG
18960625 CCCTAAT
1 CCCTAAT
18960632 TTATTTGATT
Statistics
Matches: 73, Mismatches: 20, Indels: 22
0.63 0.17 0.19
Matches are distributed among these distances:
44 3 0.04
45 13 0.18
46 5 0.07
47 4 0.05
48 8 0.11
49 8 0.11
50 4 0.05
51 5 0.07
52 20 0.27
53 3 0.04
ACGTcount: A:0.37, C:0.21, G:0.03, T:0.39
Consensus pattern (52 bp):
CCCTAATCTAATTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCCAAG
Found at i:18960536 original size:97 final size:97
Alignment explanation
Indices: 18960423--18960757 Score: 577
Period size: 97 Copynumber: 3.5 Consensus size: 97
18960413 ATTAACCCTA
18960423 AACCCC-AGCCCTAATTTATTTGATTTTTTTCTTTAAAAACCCTAAACACTAAACCCTAATCTAA
1 AACCCCAAGCCCTAATTTATTTGATTTTTTTCTTTAAAAACCCTAAACACTAAACCCTAATCTAA
18960487 TTTTTTAAAATTTATAATTAATTTACTCAAGT
66 TTTTTTAAAATTTATAATTAATTTACTCAAGT
18960519 AACCCCAAGCCCTAATTTATTTGATTTTTTTCTTTAAAAACCCTAAACACTAAACCCTAATCTAA
1 AACCCCAAGCCCTAATTTATTTGATTTTTTTCTTTAAAAACCCTAAACACTAAACCCTAATCTAA
18960584 TTTTTTAAAATTTATAATTAATTTACTCAAGT
66 TTTTTTAAAATTTATAATTAATTTACTCAAGT
18960616 AACCCCAAGCCCTAATTTATTTGATTTTTTTCTTTAAAAACCCTAAACACTAAACCCTAATCTAA
1 AACCCCAAGCCCTAATTTATTTGATTTTTTTCTTTAAAAACCCTAAACACTAAACCCTAATCTAA
* * *
18960681 TTTTTTAAAATTTATAATTAATTTAATTAAGG
66 TTTTTTAAAATTTATAATTAATTTACTCAAGT
* * * * *
18960713 AACCCTAAACCCTTATTTATTT-AATTTTTTCCTT-AAAACCCTAAA
1 AACCCCAAGCCCTAATTTATTTGATTTTTTTCTTTAAAAACCCTAAA
18960758 GTCTAAAAAT
Statistics
Matches: 230, Mismatches: 8, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
95 11 0.05
96 16 0.07
97 203 0.88
ACGTcount: A:0.37, C:0.20, G:0.03, T:0.40
Consensus pattern (97 bp):
AACCCCAAGCCCTAATTTATTTGATTTTTTTCTTTAAAAACCCTAAACACTAAACCCTAATCTAA
TTTTTTAAAATTTATAATTAATTTACTCAAGT
Found at i:18972817 original size:17 final size:17
Alignment explanation
Indices: 18972796--18972838 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
18972786 ATCGATGAAA
18972796 TTTTAAAATTTACAATTC
1 TTTTAAAATTTA-AATTC
* *
18972814 -TTTAAATTTTAATTTC
1 TTTTAAAATTTAAATTC
18972830 TTTTAAAAT
1 TTTTAAAAT
18972839 ATAGTTGTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTAAAATTTAAATTC
Found at i:18977834 original size:23 final size:22
Alignment explanation
Indices: 18977791--18977834 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
18977781 TTCTAAGTTG
18977791 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
18977814 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
18977835 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:18977944 original size:45 final size:45
Alignment explanation
Indices: 18977880--18977967 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 45
18977870 ACAAATCCTT
* *
18977880 GGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTCC
1 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCC
18977925 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
1 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
18977968 TCGTTTCACA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (45 bp):
GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCC
Found at i:18978042 original size:51 final size:50
Alignment explanation
Indices: 18977978--18978134 Score: 138
Period size: 51 Copynumber: 3.1 Consensus size: 50
18977968 TCGTTTCACA
*
18977978 TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATTCGATACACG
1 TAGTACCCTGCACATAGTACTACACATGTGACCA-TACCATTCGATACACG
** * * * * * * * * *
18978029 TAGTGTCCTGCACATAATACTACATACGTGATCAAAACTATCCGGTACGA-A
1 TAGTACCCTGCACATAGTACTACACATGTGA-CCATACCATTCGATAC-ACG
* *
18978080 TAGTACCCTGCACATAGTACTACACATGCGACC-TATCATTCCGATACACG
1 TAGTACCCTGCACATAGTACTACACATGTGACCATACCATT-CGATACACG
18978130 TAGTA
1 TAGTA
18978135 GCCTTTTAAC
Statistics
Matches: 78, Mismatches: 24, Indels: 9
0.70 0.22 0.08
Matches are distributed among these distances:
49 4 0.05
50 11 0.14
51 60 0.77
52 3 0.04
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.25
Consensus pattern (50 bp):
TAGTACCCTGCACATAGTACTACACATGTGACCATACCATTCGATACACG
Found at i:18979668 original size:30 final size:31
Alignment explanation
Indices: 18979610--18979668 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
18979600 TTGTCTTTAC
*
18979610 TTTTCTTTCATCTTTTTAGCTTTCTAGTTAG
1 TTTTCTTTCATCTTTTTAGCGTTCTAGTTAG
*
18979641 TTTTC-TTCATCTTTTCTAGGGTT-TAGTT
1 TTTTCTTTCATCTTTT-TAGCGTTCTAGTT
18979669 TAGAACTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.12, C:0.15, G:0.12, T:0.61
Consensus pattern (31 bp):
TTTTCTTTCATCTTTTTAGCGTTCTAGTTAG
Found at i:18987448 original size:19 final size:20
Alignment explanation
Indices: 18987411--18987448 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18987401 AATGAGTCAT
*
18987411 TTAAGAAAGAAATTAATTTC
1 TTAAAAAAGAAATTAATTTC
18987431 TTAAAAAAGAAA-TAATTT
1 TTAAAAAAGAAATTAATTT
18987449 AATTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.34
Consensus pattern (20 bp):
TTAAAAAAGAAATTAATTTC
Found at i:18988906 original size:41 final size:39
Alignment explanation
Indices: 18988789--18988910 Score: 124
Period size: 37 Copynumber: 3.1 Consensus size: 39
18988779 TTTGGTACCT
* * *
18988789 AGTGCCTCATCGGATAATTCGAAGTAATAAATTGACACCC
1 AGTGCCTCAT-TGATAATCCGAAGTAGTAAATTGACACCC
* * * *
18988829 AGTGTCTCATTGGCTAAACCG-A--AGTAAATTGGCACCC
1 AGTGCCTCATT-GATAATCCGAAGTAGTAAATTGACACCC
18988866 AGTGCCTCATTGAATTAATCCGAAGTAGTAAATTGACACCC
1 AGTGCCTCATTG-A-TAATCCGAAGTAGTAAATTGACACCC
18988907 AGTG
1 AGTG
18988911 TCTCGTCGAC
Statistics
Matches: 65, Mismatches: 11, Indels: 11
0.75 0.13 0.13
Matches are distributed among these distances:
36 1 0.02
37 23 0.35
38 6 0.09
39 2 0.03
40 15 0.23
41 18 0.28
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (39 bp):
AGTGCCTCATTGATAATCCGAAGTAGTAAATTGACACCC
Found at i:18989919 original size:7 final size:7
Alignment explanation
Indices: 18989907--18989955 Score: 98
Period size: 7 Copynumber: 7.0 Consensus size: 7
18989897 TATTATTATT
18989907 ATATATA
1 ATATATA
18989914 ATATATA
1 ATATATA
18989921 ATATATA
1 ATATATA
18989928 ATATATA
1 ATATATA
18989935 ATATATA
1 ATATATA
18989942 ATATATA
1 ATATATA
18989949 ATATATA
1 ATATATA
18989956 TACTTANNNN
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 42 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
ATATATA
Found at i:18992336 original size:38 final size:39
Alignment explanation
Indices: 18992243--18992336 Score: 102
Period size: 38 Copynumber: 2.4 Consensus size: 39
18992233 CGTTTGGATA
* * *
18992243 AAAACGCCGCTAAAGATTGAGCATTAGCGGCACTTTTTAG
1 AAAACGCCGC-AAAAAATAAGCATTAGCGGCACTTTTTAG
* *
18992283 AAAACGCCGCTAAAAATAAGCATTAGCGGC-GTTTTTA-
1 AAAACGCCGCAAAAAATAAGCATTAGCGGCACTTTTTAG
*
18992320 AGAAGCGCCGCAAAAAA
1 A-AAACGCCGCAAAAAA
18992337 CCTATGCCCA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 1 0.02
38 19 0.41
39 16 0.35
40 10 0.22
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.20
Consensus pattern (39 bp):
AAAACGCCGCAAAAAATAAGCATTAGCGGCACTTTTTAG
Found at i:18993481 original size:21 final size:22
Alignment explanation
Indices: 18993455--18993501 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
18993445 TATGAATTAA
* *
18993455 GGTTTATGGTTTAAGGGTT-GG
1 GGTTTAAGGTTTAAGAGTTAGG
18993476 GGTTTAAGGTTTAAGAGTTAGG
1 GGTTTAAGGTTTAAGAGTTAGG
18993498 GGTT
1 GGTT
18993502 AGGATTTATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.19, C:0.00, G:0.40, T:0.40
Consensus pattern (22 bp):
GGTTTAAGGTTTAAGAGTTAGG
Found at i:18993509 original size:28 final size:28
Alignment explanation
Indices: 18993437--18993532 Score: 70
Period size: 28 Copynumber: 3.4 Consensus size: 28
18993427 ATTTAAATAA
* * * *
18993437 TTAGGGATTATGAATTAAGGTTTATG-G
1 TTAGGGGTTAGGATTTAAGGTTTAAGAG
* * *
18993464 TTTAAGGGTTGGGGTTTAAGGTTTAAGAG
1 -TTAGGGGTTAGGATTTAAGGTTTAAGAG
* * *
18993493 TTAGGGGTTAGGATTTATGTTTTATA-AT
1 TTAGGGGTTAGGATTTAAGGTTTA-AGAG
18993521 TTAGGGGTTAGG
1 TTAGGGGTTAGG
18993533 GGATAGGGGT
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
28 51 0.96
29 2 0.04
ACGTcount: A:0.25, C:0.00, G:0.33, T:0.42
Consensus pattern (28 bp):
TTAGGGGTTAGGATTTAAGGTTTAAGAG
Found at i:18993531 original size:7 final size:7
Alignment explanation
Indices: 18993521--18993575 Score: 56
Period size: 7 Copynumber: 7.7 Consensus size: 7
18993511 GTTTTATAAT
18993521 TTAGGGG
1 TTAGGGG
18993528 TTAGGGG
1 TTAGGGG
*
18993535 ATAGGGG
1 TTAGGGG
*
18993542 TTAAGGG
1 TTAGGGG
*
18993549 TTAAGGG
1 TTAGGGG
*
18993556 TTAAGGGT
1 TT-AGGGG
*
18993564 TTAGGGT
1 TTAGGGG
18993571 TTAGG
1 TTAGG
18993576 TTTTAGATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
7 37 0.88
8 5 0.12
ACGTcount: A:0.22, C:0.00, G:0.47, T:0.31
Consensus pattern (7 bp):
TTAGGGG
Found at i:18993580 original size:7 final size:7
Alignment explanation
Indices: 18993520--18993581 Score: 52
Period size: 7 Copynumber: 8.7 Consensus size: 7
18993510 TGTTTTATAA
18993520 TTTAGGG
1 TTTAGGG
*
18993527 GTTAGGG
1 TTTAGGG
**
18993534 GATAGGGG
1 TTTA-GGG
*
18993542 TTAAGGG
1 TTTAGGG
*
18993549 TTAAGGG
1 TTTAGGG
*
18993556 TTAAGGG
1 TTTAGGG
18993563 TTTAGGG
1 TTTAGGG
*
18993570 TTTAGGT
1 TTTAGGG
18993577 TTTAG
1 TTTAG
18993582 ATTAATTAGT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
7 43 0.91
8 4 0.09
ACGTcount: A:0.21, C:0.00, G:0.44, T:0.35
Consensus pattern (7 bp):
TTTAGGG
Found at i:18993580 original size:14 final size:14
Alignment explanation
Indices: 18993539--18993581 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
18993529 TAGGGGATAG
*
18993539 GGGTTAAGGGTTAA
1 GGGTTAAGGGTTTA
18993553 GGGTTAAGGGTTTA
1 GGGTTAAGGGTTTA
* *
18993567 GGGTTTAGGTTTTA
1 GGGTTAAGGGTTTA
18993581 G
1 G
18993582 ATTAATTAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.21, C:0.00, G:0.42, T:0.37
Consensus pattern (14 bp):
GGGTTAAGGGTTTA
Found at i:18996987 original size:43 final size:44
Alignment explanation
Indices: 18996926--18997013 Score: 124
Period size: 43 Copynumber: 2.0 Consensus size: 44
18996916 GAGTTCGTTA
* * *
18996926 CAAGATTTCCTTGATTAAGTAAATGTATTATA-TCTTTTATTAC
1 CAAGATTTACTTGATTAAGAAAATGCATTATATTCTTTTATTAC
* *
18996969 CAAGATTTACTTGATTAAGAAAATGCATTGTATTTTTTTATTAC
1 CAAGATTTACTTGATTAAGAAAATGCATTATATTCTTTTATTAC
18997013 C
1 C
18997014 TTGCAATGTG
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
43 28 0.72
44 11 0.28
ACGTcount: A:0.33, C:0.11, G:0.10, T:0.45
Consensus pattern (44 bp):
CAAGATTTACTTGATTAAGAAAATGCATTATATTCTTTTATTAC
Found at i:18997460 original size:43 final size:43
Alignment explanation
Indices: 18997382--18997588 Score: 238
Period size: 43 Copynumber: 4.8 Consensus size: 43
18997372 TTTTTGCGAG
* * * * *
18997382 AAGCGTCGCTAAAGGT-TTGTTCTATAGCAGAGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTATTGATCTATAGCGGCGTTTGTGGAAA
* * *
18997424 AAGCACCGCTAAAGGTATTGAGCTATAGCGGCGTTTGTGAAAA
1 AAGCGCCGCTAAAGGTATTGATCTATAGCGGCGTTTGTGGAAA
*
18997467 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAA
1 AAGCGCCGCTAAAGGTATTGATCTATAGCGGCGTTTGTGGAAA
** * * * * *
18997510 AAATGCCGCTAAAGGTCTTGAGCTATAGCAGTGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTATTGATCTATAGCGGCGTTTGTGGAAA
*
18997553 AAGCGTCGCTAAAGGTCA-TGATCTATAGCGGCGTTT
1 AAGCGCCGCTAAAGGT-ATTGATCTATAGCGGCGTTT
18997589 ATTTCTAAAA
Statistics
Matches: 138, Mismatches: 25, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
42 14 0.10
43 124 0.90
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.27
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTATTGATCTATAGCGGCGTTTGTGGAAA
Found at i:18997531 original size:86 final size:86
Alignment explanation
Indices: 18997382--18997588 Score: 281
Period size: 86 Copynumber: 2.4 Consensus size: 86
18997372 TTTTTGCGAG
* * * * *
18997382 AAGCGTCGCTAAAGGT-TTGTTCTATAGCAGAGTTTGTGGGAAAAGCACCGCTAAAGGTATTGAG
1 AAGCGTCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAAAAACACCGCTAAAGGTATTGAG
*
18997446 CTATAGCGGCGTTTGTGAAAA
66 CTATAGCAGCGTTTGTGAAAA
* ** *
18997467 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAAAAATGCCGCTAAAGGTCTTGAG
1 AAGCGTCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAAAAACACCGCTAAAGGTATTGAG
* **
18997532 CTATAGCAGTGTTTGTGGGAA
66 CTATAGCAGCGTTTGTGAAAA
*
18997553 AAGCGTCGCTAAAGGTCATGATCTATAGCGGCGTTT
1 AAGCGTCGCTAAAGGTCTTGATCTATAGCGGCGTTT
18997589 ATTTCTAAAA
Statistics
Matches: 106, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
85 15 0.14
86 91 0.86
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.27
Consensus pattern (86 bp):
AAGCGTCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAAAAACACCGCTAAAGGTATTGAG
CTATAGCAGCGTTTGTGAAAA
Found at i:19000592 original size:2 final size:2
Alignment explanation
Indices: 19000585--19000609 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19000575 TGTGCATGCG
19000585 CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA C
19000610 TCTAGCAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:19001833 original size:30 final size:33
Alignment explanation
Indices: 19001772--19001833 Score: 76
Period size: 34 Copynumber: 1.9 Consensus size: 33
19001762 ACTATAAAAC
**
19001772 ATTTATTATTAAATATTTATAAATTGTAATATAT
1 ATTTATTATTAAATA-TTATAAATTACAATATAT
19001806 ATTTATTATTAAA-A-TA-AAATTACAATAT
1 ATTTATTATTAAATATTATAAATTACAATAT
19001834 TAAATCATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
30 10 0.38
31 2 0.08
33 1 0.04
34 13 0.50
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (33 bp):
ATTTATTATTAAATATTATAAATTACAATATAT
Found at i:19001852 original size:20 final size:18
Alignment explanation
Indices: 19001824--19001872 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
19001814 TTAAAATAAA
*
19001824 ATTACAATATTAAATCATTT
1 ATTAAAATATTAAAT--TTT
*
19001844 ATTAAAATAATAAATTTT
1 ATTAAAATATTAAATTTT
19001862 ATTAATAATAT
1 ATTAA-AATAT
19001873 AGTAATATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 8 0.32
19 4 0.16
20 13 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (18 bp):
ATTAAAATATTAAATTTT
Found at i:19011685 original size:15 final size:15
Alignment explanation
Indices: 19011665--19011693 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
19011655 ATATTTCCTC
19011665 TATTATAATTATAAT
1 TATTATAATTATAAT
19011680 TATTATAATTATAA
1 TATTATAATTATAA
19011694 AAAAATATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTATAATTATAAT
Found at i:19012327 original size:39 final size:39
Alignment explanation
Indices: 19012281--19012376 Score: 147
Period size: 39 Copynumber: 2.5 Consensus size: 39
19012271 GGAGTTGTAA
*
19012281 GTGACTATTCATCTACATCACTTAAGTGCTATAGGAGCT
1 GTGACTATTCATCTACATCACTTAAATGCTATAGGAGCT
* * *
19012320 GTGACTATTTATCTTCATCACTTAAATGCTATAGGAGTT
1 GTGACTATTCATCTACATCACTTAAATGCTATAGGAGCT
*
19012359 ATGACTATTCATCTACAT
1 GTGACTATTCATCTACAT
19012377 GCTTGTGTGT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (39 bp):
GTGACTATTCATCTACATCACTTAAATGCTATAGGAGCT
Found at i:19013461 original size:12 final size:12
Alignment explanation
Indices: 19013439--19013468 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
19013429 TTATAACCAT
19013439 GAATCTTCCTTGA
1 GAAT-TTCCTTGA
19013452 GAATTTCCTTGA
1 GAATTTCCTTGA
19013464 GAATT
1 GAATT
19013469 CTTTCAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.40
Consensus pattern (12 bp):
GAATTTCCTTGA
Found at i:19016771 original size:43 final size:42
Alignment explanation
Indices: 19016723--19016832 Score: 151
Period size: 39 Copynumber: 2.7 Consensus size: 42
19016713 TAACTCTTTA
*
19016723 TATAGGAGTTGTAAGTGACTATTCATCTACATCACTTAAGTGC
1 TATAGGAGTTGT-AGTGACTATTCATCTACATCACTTAAATGC
*
19016766 TATAGGAGTTGTA---ACTATTCATCTTCATCACTTAAATGC
1 TATAGGAGTTGTAGTGACTATTCATCTACATCACTTAAATGC
19016805 TATAGGAG-T-T-GTGACTATTCATCTACAT
1 TATAGGAGTTGTAGTGACTATTCATCTACAT
19016833 GCATGTGTGT
Statistics
Matches: 61, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
37 1 0.02
38 1 0.02
39 46 0.75
42 1 0.02
43 12 0.20
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.37
Consensus pattern (42 bp):
TATAGGAGTTGTAGTGACTATTCATCTACATCACTTAAATGC
Found at i:19016795 original size:39 final size:39
Alignment explanation
Indices: 19016740--19016832 Score: 159
Period size: 39 Copynumber: 2.4 Consensus size: 39
19016730 GTTGTAAGTG
*
19016740 ACTATTCATCTACATCACTTAAGTGCTATAGGAGTTGTA
1 ACTATTCATCTACATCACTTAAATGCTATAGGAGTTGTA
* *
19016779 ACTATTCATCTTCATCACTTAAATGCTATAGGAGTTGTG
1 ACTATTCATCTACATCACTTAAATGCTATAGGAGTTGTA
19016818 ACTATTCATCTACAT
1 ACTATTCATCTACAT
19016833 GCATGTGTGT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (39 bp):
ACTATTCATCTACATCACTTAAATGCTATAGGAGTTGTA
Found at i:19016866 original size:16 final size:16
Alignment explanation
Indices: 19016845--19016897 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 16
19016835 ATGTGTGTAG
19016845 CTCTTCATCTTCAAGT
1 CTCTTCATCTTCAAGT
19016861 CTCTTCA-CATTTCTAA--
1 CTCTTCATC--TTC-AAGT
19016877 CTCTTCATCTTCAAGT
1 CTCTTCATCTTCAAGT
19016893 CTCTT
1 CTCTT
19016898 TACATACCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
14 2 0.06
15 4 0.13
16 19 0.61
17 4 0.13
18 2 0.06
ACGTcount: A:0.19, C:0.32, G:0.04, T:0.45
Consensus pattern (16 bp):
CTCTTCATCTTCAAGT
Found at i:19023259 original size:37 final size:37
Alignment explanation
Indices: 19023149--19023616 Score: 471
Period size: 37 Copynumber: 12.6 Consensus size: 37
19023139 TAAGATAAGA
* * * **
19023149 TCTATCCCAAGCTTTTT-AAGTTTGGCTTAGA-TGGG
1 TCTATCCCAACCTTTTTAAAGGTTGCCTTAGACAAGG
* *
19023184 TCTACCCCAACCTTTTT-TAGGTTGCCTTAGAC--GTG
1 TCTATCCCAACCTTTTTAAAGGTTGCCTTAGACAAG-G
*
19023219 TCTATCCCAACCATTTTTAAAGATTGCCTTAGACAA-G
1 TCTATCCCAACC-TTTTTAAAGGTTGCCTTAGACAAGG
19023256 TCTATCCCAACCTTTTTTAAAGGTTG-CTTGAGACAAGG
1 TCTATCCCAACC-TTTTTAAAGGTTGCCTT-AGACAAGG
* *
19023294 TCTATCCTAACC-TTTT-AAGGTTGCCTTCA-AC-GGG
1 TCTATCCCAACCTTTTTAAAGGTTGCCTT-AGACAAGG
* * *
19023328 TCTATCCTAACCTTTTTTATAGGATGCCTTAGACAAGG
1 TCTATCCCAACC-TTTTTAAAGGTTGCCTTAGACAAGG
* *
19023366 TCTATTCCAACCTTTTTTTAAAGGTTACCTTAGACAAGG
1 TCTATCCCAACC--TTTTTAAAGGTTGCCTTAGACAAGG
*
19023405 TCTATCCCAACCTTTTTAAAGGTTGCTTTAGACAAGG
1 TCTATCCCAACCTTTTTAAAGGTTGCCTTAGACAAGG
* *
19023442 TCTATCCTAACCTTTTT-AAGGTTTCCTTAGACAAGG
1 TCTATCCCAACCTTTTTAAAGGTTGCCTTAGACAAGG
*
19023478 TCTA-CCCAACCTTTTTTAAAGGTTGCCTTAGATAAGAAGG
1 TCTATCCCAACC-TTTTTAAAGGTTGCCTTAG---ACAAGG
* * *
19023518 TCTATCCCAACCTTTTT-AAGGTTTCCTTAGA-TAGC
1 TCTATCCCAACCTTTTTAAAGGTTGCCTTAGACAAGG
* *
19023553 TCTATCCTAACCGTTTTTAAAAAGGTTTCCTTAGACAAGG
1 TCTATCCCAACC-TTTTT--AAAGGTTGCCTTAGACAAGG
19023593 TCTATCCCAACCTTTTTTAAAGGT
1 TCTATCCCAACC-TTTTTAAAGGT
19023617 CGACCTCGAC
Statistics
Matches: 369, Mismatches: 38, Indels: 49
0.81 0.08 0.11
Matches are distributed among these distances:
34 15 0.04
35 66 0.18
36 53 0.14
37 106 0.29
38 30 0.08
39 60 0.16
40 32 0.09
41 7 0.02
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (37 bp):
TCTATCCCAACCTTTTTAAAGGTTGCCTTAGACAAGG
Found at i:19023265 original size:72 final size:71
Alignment explanation
Indices: 19023149--19023609 Score: 405
Period size: 76 Copynumber: 6.2 Consensus size: 71
19023139 TAAGATAAGA
* * * *** *
19023149 TCTATCCCAAGCTTTTTAAGTTTGGCTTAGATGGGTCTACCCCAACCTTTTT-TAGGTTGCCTTA
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACAAGTCTATCCCAACCTTTTTATAGGTTGCCTTA
19023213 GAC-GTG
66 GACAG-G
* *
19023219 TCTATCCCAACCATTTTTAAAGATTGCCTTAGACAAGTCTATCCCAACCTTTTTTAAAGGTTG-C
1 TCTATCCCAACC-TTTTT-AAGGTTGCCTTAGACAAGTCTATCCCAACC-TTTTTATAGGTTGCC
19023283 TTGAGACAAGG
63 TT-AGAC-AGG
* ** * *
19023294 TCTATCCTAACC-TTTTAAGGTTGCCTTCA-ACGGGTCTATCCTAACCTTTTTTATAGGATGCCT
1 TCTATCCCAACCTTTTTAAGGTTGCCTT-AGACAAGTCTATCCCAACC-TTTTTATAGGTTGCCT
19023357 TAGACAAGG
64 TAGAC-AGG
* * *
19023366 TCTATTCCAACCTTTTTTTAAAGGTTACCTTAGACAAGGTCTATCCCAACCTTTTTAAAGGTTGC
1 TCTATCCCAACC--TTTTT-AAGGTTGCCTTAGACAA-GTCTATCCCAACCTTTTTATAGGTTGC
*
19023431 TTTAGACAAGG
62 CTTAGAC-AGG
* * *
19023442 TCTATCCTAACCTTTTTAAGGTTTCCTTAGACAAGGTCTA-CCCAACCTTTTTTAAAGGTTGCCT
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACAA-GTCTATCCCAACC-TTTTTATAGGTTGCCT
*
19023506 TAGATAAGAAGG
64 TAG---A-CAGG
* * * * *
19023518 TCTATCCCAACCTTTTTAAGGTTTCCTTAGA-TAGCTCTATCCTAACCGTTTTTAAAAAGGTTTC
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACAAG-TCTATCCCAACC-TTTTT--ATAGGTTGC
19023582 CTTAGACAAGG
62 CTTAGAC-AGG
19023593 TCTATCCCAACCTTTTT
1 TCTATCCCAACCTTTTT
19023610 TAAAGGTCGA
Statistics
Matches: 331, Mismatches: 35, Indels: 45
0.81 0.09 0.11
Matches are distributed among these distances:
70 11 0.03
71 5 0.02
72 85 0.26
73 56 0.17
74 16 0.05
75 43 0.13
76 90 0.27
77 12 0.04
78 13 0.04
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (71 bp):
TCTATCCCAACCTTTTTAAGGTTGCCTTAGACAAGTCTATCCCAACCTTTTTATAGGTTGCCTTA
GACAGG
Found at i:19023612 original size:76 final size:74
Alignment explanation
Indices: 19023149--19023609 Score: 498
Period size: 72 Copynumber: 6.2 Consensus size: 74
19023139 TAAGATAAGA
* * * ** *
19023149 TCTATCCCAAGCTTTTTAAGTTTGGCTTAGA-TGGGTCTACCCCAACCTTTTTT--AGGTTGCCT
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTTAAAGGTTGCCT
19023211 TAGAC--GTG
66 TAGACAAG-G
*
19023219 TCTATCCCAACCATTTTTAAAGATTGCCTTAGACAA-GTCTATCCCAACCTTTTTTAAAGGTTG-
1 TCTATCCCAACC-TTTTT-AAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTTAAAGGTTGC
19023282 CTTGAGACAAGG
64 CTT-AGACAAGG
* * * * *
19023294 TCTATCCTAACC-TTTTAAGGTTGCCTTCA-AC-GGGTCTATCCTAACCTTTTTTATAGGATGCC
1 TCTATCCCAACCTTTTTAAGGTTGCCTT-AGACAAGGTCTATCCCAACCTTTTTTAAAGGTTGCC
19023356 TTAGACAAGG
65 TTAGACAAGG
* *
19023366 TCTATTCCAACCTTTTTTTAAAGGTTACCTTAGACAAGGTCTATCCCAACC-TTTTTAAAGGTTG
1 TCTATCCCAACC--TTTTT-AAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTTAAAGGTTG
*
19023430 CTTTAGACAAGG
63 CCTTAGACAAGG
* *
19023442 TCTATCCTAACCTTTTTAAGGTTTCCTTAGACAAGGTCTA-CCCAACCTTTTTTAAAGGTTGCCT
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTTAAAGGTTGCCT
*
19023506 TAGATAAGAAGG
66 TAG---ACAAGG
* * * * * *
19023518 TCTATCCCAACCTTTTTAAGGTTTCCTTAGA-TAGCTCTATCCTAACCGTTTTTAAAAAGGTTTC
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACAAGGTCTATCCCAACC-TTTTT-TAAAGGTTGC
19023582 CTTAGACAAGG
64 CTTAGACAAGG
19023593 TCTATCCCAACCTTTTT
1 TCTATCCCAACCTTTTT
19023610 TAAAGGTCGA
Statistics
Matches: 335, Mismatches: 32, Indels: 43
0.82 0.08 0.10
Matches are distributed among these distances:
70 11 0.03
71 5 0.01
72 91 0.27
73 51 0.15
74 15 0.04
75 45 0.13
76 86 0.26
77 18 0.05
78 13 0.04
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (74 bp):
TCTATCCCAACCTTTTTAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTTAAAGGTTGCCT
TAGACAAGG
Found at i:19025065 original size:22 final size:22
Alignment explanation
Indices: 19025040--19025084 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
19025030 AAGTATGGAA
*
19025040 CAGTATGAATAAAGAACGTACC
1 CAGTATGAATAAAGAACGCACC
19025062 CAGTATGAATAAAGAACGCACC
1 CAGTATGAATAAAGAACGCACC
19025084 C
1 C
19025085 GCTACAACGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.44, C:0.22, G:0.18, T:0.16
Consensus pattern (22 bp):
CAGTATGAATAAAGAACGCACC
Found at i:19029466 original size:44 final size:44
Alignment explanation
Indices: 19029403--19029493 Score: 164
Period size: 44 Copynumber: 2.1 Consensus size: 44
19029393 AACTCTATTT
* *
19029403 TTAGTTTTCCACTTAAACTCTGATTAGTGTAGGTTATTTTAATA
1 TTAGTTTCCCACTTAAACTCTGATTAGTGTAGGTTACTTTAATA
19029447 TTAGTTTCCCACTTAAACTCTGATTAGTGTAGGTTACTTTAATA
1 TTAGTTTCCCACTTAAACTCTGATTAGTGTAGGTTACTTTAATA
19029491 TTA
1 TTA
19029494 TTAGACCTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.46
Consensus pattern (44 bp):
TTAGTTTCCCACTTAAACTCTGATTAGTGTAGGTTACTTTAATA
Found at i:19031944 original size:114 final size:115
Alignment explanation
Indices: 19031675--19031945 Score: 365
Period size: 115 Copynumber: 2.4 Consensus size: 115
19031665 ATATTGTATT
19031675 ATTTATATTTT-TTAAATGAAATAATATAGAAATATTCAAAATATTGCCTTATTTTAAAAAATTC
1 ATTT-TATTTTATTAAATGAAATAATATAGAAATATTCAAAATATTGCCTTATTTTAAAAAATTC
** * ** *
19031739 TATTTTATTAAAAATATTAAAGTAAATTACAATTACTTTATTCAAAACAAC
65 TATTTTATTAAAAATACAAAAGTAAATTACAATGAAATAATTCAAAACAAC
*
19031790 ATTTTATTTTATTAAATGAAATAATATAGAAATATTCAAAATATTGTCTTA-TTTAAAAGAATTT
1 ATTTTATTTTATTAAATGAAATAATATAGAAATATTCAAAATATTGCCTTATTTTAAAA-AA-TT
*
19031854 CTATTTTATTAAAAATACAAAAGTAAATTAC-ATGAAATAATAT-AAAA-GA-
64 CTATTTTATTAAAAATACAAAAGTAAATTACAATGAAATAAT-TCAAAACAAC
* *
19031903 ATTTCTATTTTATTACATGAAATAATATAAAAATATTCAAAAT
1 ATTT-TATTTTATTAAATGAAATAATATAGAAATATTCAAAAT
19031946 GTTTGTACAA
Statistics
Matches: 141, Mismatches: 10, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
113 4 0.03
114 50 0.35
115 55 0.39
116 32 0.23
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (115 bp):
ATTTTATTTTATTAAATGAAATAATATAGAAATATTCAAAATATTGCCTTATTTTAAAAAATTCT
ATTTTATTAAAAATACAAAAGTAAATTACAATGAAATAATTCAAAACAAC
Found at i:19037407 original size:114 final size:114
Alignment explanation
Indices: 19037199--19037415 Score: 289
Period size: 114 Copynumber: 1.9 Consensus size: 114
19037189 NNNNNNNNNN
** * ** *
19037199 TAAAAAATTCTATTTTATTAAAAATATTAAAGTAAATTACAATTACTTTATTCAAAACAACATTT
1 TAAAAAATTCTATTTTATTAAAAATACAAAAGTAAATTACAATGAAATAATTCAAAACAACATTT
*
19037264 TATTTTATTAAATGAAATAATATAGAAATATTCAAAATATTGTCTTATT
66 TATTTTATTAAATGAAATAATATAAAAATATTCAAAATATTGTCTTATT
*
19037313 TAAAAGAATTTCTATTTTATTAAAAATACAAAAGTAAATTAC-ATGAAATAATAT-AAAA-GA-A
1 TAAAA-AA-TTCTATTTTATTAAAAATACAAAAGTAAATTACAATGAAATAAT-TCAAAACAACA
*
19037374 TTTCTATTTTATTACATGAAATAATATAAAAATATTCAAAAT
63 TTT-TATTTTATTAAATGAAATAATATAAAAATATTCAAAAT
19037416 GTTTGTACAA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
113 4 0.04
114 42 0.47
115 12 0.13
116 32 0.36
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.39
Consensus pattern (114 bp):
TAAAAAATTCTATTTTATTAAAAATACAAAAGTAAATTACAATGAAATAATTCAAAACAACATTT
TATTTTATTAAATGAAATAATATAAAAATATTCAAAATATTGTCTTATT
Found at i:19037852 original size:18 final size:18
Alignment explanation
Indices: 19037811--19037853 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
19037801 GACTAGAAAA
* *
19037811 AGGAAACATAAAAGAGTT
1 AGGATACATAAAAGAGCT
*
19037829 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGAGCT
*
19037847 ATGATAC
1 AGGATAC
19037854 GCACCTGGCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.49, C:0.09, G:0.23, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGAGCT
Found at i:19037948 original size:30 final size:30
Alignment explanation
Indices: 19037914--19037970 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
19037904 TGTTGGGTCG
* *
19037914 GGTGACTGTGTCGGTGCTGTTGCTGGGCCT
1 GGTGACTGTGTCGGCGCTGTTGATGGGCCT
* *
19037944 GGTGATTGTGTGGGCGCTGTTGATGGG
1 GGTGACTGTGTCGGCGCTGTTGATGGG
19037971 ATTGCATCGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.05, C:0.14, G:0.47, T:0.33
Consensus pattern (30 bp):
GGTGACTGTGTCGGCGCTGTTGATGGGCCT
Found at i:19042727 original size:23 final size:22
Alignment explanation
Indices: 19042685--19042739 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
19042675 CAGCACAAAG
19042685 AAACAACA-AAAAGAAAGAAACAA
1 AAACAACAGAAAAGAAAG-AA-AA
*
19042708 AAACAACAGAAAAG-AGGAAAA
1 AAACAACAGAAAAGAAAGAAAA
*
19042729 AAAGAACAGAA
1 AAACAACAGAA
19042740 TAGGGGAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 12 0.41
22 2 0.07
23 10 0.34
24 5 0.17
ACGTcount: A:0.75, C:0.11, G:0.15, T:0.00
Consensus pattern (22 bp):
AAACAACAGAAAAGAAAGAAAA
Found at i:19042736 original size:24 final size:24
Alignment explanation
Indices: 19042681--19042736 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 24
19042671 AACACAGCAC
*
19042681 AAAGAAACAACAAAAAGAAAGAAAC
1 AAAG-AACAACAAAAAGAAAGAAAA
*
19042706 AAA-AACAACAGAAAAG-AGGAAAA
1 AAAGAACAACA-AAAAGAAAGAAAA
19042729 AAAGAACA
1 AAAGAACA
19042737 GAATAGGGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 15 0.56
24 9 0.33
25 3 0.11
ACGTcount: A:0.75, C:0.11, G:0.14, T:0.00
Consensus pattern (24 bp):
AAAGAACAACAAAAAGAAAGAAAA
Found at i:19043556 original size:3 final size:3
Alignment explanation
Indices: 19043548--19043589 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
19043538 TACTATGATT
19043548 TTA TTA TTA TTA TTA TTAA TT- TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
19043590 CTACTACTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:19043569 original size:21 final size:21
Alignment explanation
Indices: 19043545--19043586 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
19043535 TTATACTATG
19043545 ATTTTATTATTATTATTATTA
1 ATTTTATTATTATTATTATTA
19043566 ATTTTATTATTATTATTATTA
1 ATTTTATTATTATTATTATTA
19043587 TTACTACTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
ATTTTATTATTATTATTATTA
Found at i:19043876 original size:22 final size:23
Alignment explanation
Indices: 19043835--19043878 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
19043825 ACATGTACAT
* *
19043835 ATACATGTATTTTTATAATATTC
1 ATACATATATTTTTAAAATATTC
19043858 ATACATAT-TTTTTAAAATATT
1 ATACATATATTTTTAAAATATT
19043879 TATAAGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (23 bp):
ATACATATATTTTTAAAATATTC
Found at i:19048373 original size:22 final size:22
Alignment explanation
Indices: 19048334--19048375 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
19048324 ACCAATCCAT
*
19048334 TTTAACATATTTTCAAGATAGA
1 TTTAACATATTATCAAGATAGA
19048356 TTTAACATATTCAT-AAGATA
1 TTTAACATATT-ATCAAGATA
19048376 ACCTCATCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (22 bp):
TTTAACATATTATCAAGATAGA
Found at i:19052303 original size:31 final size:31
Alignment explanation
Indices: 19052265--19052336 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
19052255 ACCAATAATT
* *
19052265 ACTCAACTTTGATCTCAATGATAAAACGGTC
1 ACTCAACTTTGATCTCAATGACAAAACAGTC
*
19052296 ACTCAACTTTGGTCTCAATGACAAAACAGTC
1 ACTCAACTTTGATCTCAATGACAAAACAGTC
*
19052327 ACTCGACTTT
1 ACTCAACTTT
19052337 CAATTCAGTC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.29
Consensus pattern (31 bp):
ACTCAACTTTGATCTCAATGACAAAACAGTC
Found at i:19052347 original size:20 final size:20
Alignment explanation
Indices: 19052322--19052359 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
19052312 AATGACAAAA
*
19052322 CAGTCACTCGACTTTCAATT
1 CAGTCACTCAACTTTCAATT
19052342 CAGTCACTCAACTTTCAA
1 CAGTCACTCAACTTTCAA
19052360 AAAATAACAA
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:0.29, C:0.32, G:0.08, T:0.32
Consensus pattern (20 bp):
CAGTCACTCAACTTTCAATT
Found at i:19052537 original size:31 final size:31
Alignment explanation
Indices: 19052498--19052569 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
19052488 ACCCCAAATT
* **
19052498 ACTCAACTTTGATCTCAATGATAAAATGGTC
1 ACTCAACTTTGATCTCAATGACAAAACAGTC
* *
19052529 ACTTAACTTTGGTCTCAATGACAAAACAGTC
1 ACTCAACTTTGATCTCAATGACAAAACAGTC
19052560 ACTCAACTTT
1 ACTCAACTTT
19052570 CAATTCAGTC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.32
Consensus pattern (31 bp):
ACTCAACTTTGATCTCAATGACAAAACAGTC
Found at i:19052539 original size:233 final size:233
Alignment explanation
Indices: 19052261--19052728 Score: 864
Period size: 233 Copynumber: 2.0 Consensus size: 233
19052251 TTACACCAAT
19052261 AATTACTCAACTTTGATCTCAATGATAAAACGGTCACTCAACTTTGGTCTCAATGACAAAACAGT
1 AATTACTCAACTTTGATCTCAATGATAAAACGGTCACTCAACTTTGGTCTCAATGACAAAACAGT
* *
19052326 CACTCGACTTTCAATTCAGTCACTCAACTTTCAAAAAATAACAAATTAGTCCTACTAACTTTCAA
66 CACTCAACTTTCAATTCAGTCACTCAACTTTCAAAAAATAACAAATCAGTCCTACTAACTTTCAA
*
19052391 AAAACCAAACACCCAAAAAGAAGAACAAATAAAACCCTTGAATGAATTCTTCTTGTTCAAGAAGA
131 AAAACCAAACACCCAAAAAGAAGAACAAATAAAACCCTTGAATAAATTCTTCTTGTTCAAGAAGA
*
19052456 AAGTTGAGAACCATGGCTTCCTTATTGCCATTACCCCA
196 AAGTTGAGAACCATGGCTTCCTCATTGCCATTACCCCA
* *
19052494 AATTACTCAACTTTGATCTCAATGATAAAATGGTCACTTAACTTTGGTCTCAATGACAAAACAGT
1 AATTACTCAACTTTGATCTCAATGATAAAACGGTCACTCAACTTTGGTCTCAATGACAAAACAGT
19052559 CACTCAACTTTCAATTCAGTCACTCAACTTTCAAAAAATAACAAATCAGTCCTACTAACTTTCAA
66 CACTCAACTTTCAATTCAGTCACTCAACTTTCAAAAAATAACAAATCAGTCCTACTAACTTTCAA
* *
19052624 AAAACCAAACACTCAAAAAGAAGAACAAATAAAACCCTTGAATAAATTCTTCTTGTTCAGGAAGA
131 AAAACCAAACACCCAAAAAGAAGAACAAATAAAACCCTTGAATAAATTCTTCTTGTTCAAGAAGA
19052689 AAGTTGAGAACCATGGCTTCCTCATTGCCATTACCCCA
196 AAGTTGAGAACCATGGCTTCCTCATTGCCATTACCCCA
19052727 AA
1 AA
19052729 ATACCCTTTT
Statistics
Matches: 227, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
233 227 1.00
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27
Consensus pattern (233 bp):
AATTACTCAACTTTGATCTCAATGATAAAACGGTCACTCAACTTTGGTCTCAATGACAAAACAGT
CACTCAACTTTCAATTCAGTCACTCAACTTTCAAAAAATAACAAATCAGTCCTACTAACTTTCAA
AAAACCAAACACCCAAAAAGAAGAACAAATAAAACCCTTGAATAAATTCTTCTTGTTCAAGAAGA
AAGTTGAGAACCATGGCTTCCTCATTGCCATTACCCCA
Found at i:19052580 original size:20 final size:20
Alignment explanation
Indices: 19052555--19052592 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
19052545 AATGACAAAA
19052555 CAGTCACTCAACTTTCAATT
1 CAGTCACTCAACTTTCAATT
19052575 CAGTCACTCAACTTTCAA
1 CAGTCACTCAACTTTCAA
19052593 AAAATAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.32
Consensus pattern (20 bp):
CAGTCACTCAACTTTCAATT
Found at i:19053535 original size:29 final size:31
Alignment explanation
Indices: 19053471--19053527 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 31
19053461 GATGAAGAAG
* *
19053471 AAAAAGTATAAACATATTGGGTCATTTACAC
1 AAAAAGTATAAAAATATTGGGCCATTTACAC
19053502 AAAAAGTA-AAAAATATT-GGCCATTTA
1 AAAAAGTATAAAAATATTGGGCCATTTA
19053528 TTAAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.33
30 8 0.33
31 8 0.33
ACGTcount: A:0.49, C:0.11, G:0.12, T:0.28
Consensus pattern (31 bp):
AAAAAGTATAAAAATATTGGGCCATTTACAC
Found at i:19053536 original size:30 final size:31
Alignment explanation
Indices: 19053471--19053536 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 31
19053461 GATGAAGAAG
* * *
19053471 AAAAAGTATAAACATATTGGGTCATTTACAC
1 AAAAAGTATAAAAATATTGGGCCATTTACAA
*
19053502 AAAAAGTA-AAAAATATT-GGCCATTTATTAA
1 AAAAAGTATAAAAATATTGGGCCATTTA-CAA
19053532 AAAAA
1 AAAAA
19053537 TAGAAAAGGG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 8 0.27
30 14 0.47
31 8 0.27
ACGTcount: A:0.53, C:0.09, G:0.11, T:0.27
Consensus pattern (31 bp):
AAAAAGTATAAAAATATTGGGCCATTTACAA
Found at i:19054240 original size:12 final size:11
Alignment explanation
Indices: 19054219--19054243 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19054209 TTATTTCAAT
19054219 ATTGAAAAAAA
1 ATTGAAAAAAA
19054230 ATTGAAAAAAA
1 ATTGAAAAAAA
19054241 ATT
1 ATT
19054244 AGAATTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (11 bp):
ATTGAAAAAAA
Found at i:19054866 original size:19 final size:20
Alignment explanation
Indices: 19054822--19054866 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
19054812 GAAAAAATCC
*
19054822 TAAAAATTAAGTGATAAAAT
1 TAAAAATTAAGTGACAAAAT
* *
19054842 TGAAAA-TAAGTGACCAAAT
1 TAAAAATTAAGTGACAAAAT
19054861 TAAAAA
1 TAAAAA
19054867 AACTTTTAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.60, C:0.04, G:0.11, T:0.24
Consensus pattern (20 bp):
TAAAAATTAAGTGACAAAAT
Found at i:19063715 original size:17 final size:18
Alignment explanation
Indices: 19063690--19063733 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
19063680 TAATAACATG
*
19063690 AATAATAAATAAATT-TA
1 AATATTAAATAAATTGTA
19063707 AATATTAAA-AAATTGTA
1 AATATTAAATAAATTGTA
*
19063724 AATATAAAAT
1 AATATTAAAT
19063734 TAAGGTTGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (18 bp):
AATATTAAATAAATTGTA
Found at i:19063719 original size:16 final size:16
Alignment explanation
Indices: 19063694--19063732 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
19063684 AACATGAATA
19063694 ATAAATAAATT-TAAAT
1 ATAAA-AAATTGTAAAT
19063710 ATTAAAAAATTGTAAAT
1 A-TAAAAAATTGTAAAT
19063727 ATAAAA
1 ATAAAA
19063733 TTAAGGTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (16 bp):
ATAAAAAATTGTAAAT
Found at i:19073430 original size:15 final size:16
Alignment explanation
Indices: 19073410--19073449 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
19073400 TTAAAATAAA
19073410 TTTAAAATACTTT-TT
1 TTTAAAATACTTTATT
**
19073425 TTTAAAATTTTTTATT
1 TTTAAAATACTTTATT
19073441 TTTAAAATA
1 TTTAAAATA
19073450 AATTTTTAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTAAAATACTTTATT
Found at i:19077869 original size:18 final size:19
Alignment explanation
Indices: 19077846--19077901 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 19
19077836 TTTTATTACT
19077846 AGTGGTTTATCCACAACA-
1 AGTGGTTTATCCACAACAG
* *
19077864 AGTGGTTCATCCACAATGATG
1 AGTGGTTTATCCACAA-CA-G
19077885 AGTGGTTTATCCACAAC
1 AGTGGTTTATCCACAAC
19077902 GTGGTGTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
18 15 0.48
19 1 0.03
21 15 0.48
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (19 bp):
AGTGGTTTATCCACAACAG
Found at i:19087611 original size:34 final size:35
Alignment explanation
Indices: 19087555--19087621 Score: 93
Period size: 34 Copynumber: 1.9 Consensus size: 35
19087545 CTGTCACTGT
*
19087555 ACTGAATATTGATACTATAATGGGCTAAGGCCCTA
1 ACTGAATATTGAAACTATAATGGGCTAAGGCCCTA
*
19087590 ACTGAA-ATTGAAACTGA-AATGGGCTTAGGCCC
1 ACTGAATATTGAAACT-ATAATGGGCTAAGGCCC
19087622 AGACTATGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 22 0.76
35 7 0.24
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.25
Consensus pattern (35 bp):
ACTGAATATTGAAACTATAATGGGCTAAGGCCCTA
Found at i:19093382 original size:95 final size:95
Alignment explanation
Indices: 19093215--19093402 Score: 304
Period size: 95 Copynumber: 2.0 Consensus size: 95
19093205 TCCACAATTT
* * *
19093215 CAAATTTTTTCCTAAAATCATTTCAACACTCCCCCATCCAAATCTCCTTAATTATCTCCAACAAC
1 CAAATTTTCTCCTAAAATCACTCCAACACTCCCCCATCCAAATCTCCTTAATTATCTCCAACAAC
*
19093280 CTTTCCACTATCCGAATTTTAGTCCAACCC
66 CTCTCCACTATCCGAATTTTAGTCCAACCC
* * *
19093310 CAAATTTTCTCCTAAAATCACTCCAACACTCCTCCATCCAAATCTCCTTAATTATCTCTATCAAC
1 CAAATTTTCTCCTAAAATCACTCCAACACTCCCCCATCCAAATCTCCTTAATTATCTCCAACAAC
*
19093375 CTCTCCACTATCGGAATTTTAGTCCAAC
66 CTCTCCACTATCCGAATTTTAGTCCAAC
19093403 TCAAACTCAC
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
95 85 1.00
ACGTcount: A:0.30, C:0.35, G:0.03, T:0.32
Consensus pattern (95 bp):
CAAATTTTCTCCTAAAATCACTCCAACACTCCCCCATCCAAATCTCCTTAATTATCTCCAACAAC
CTCTCCACTATCCGAATTTTAGTCCAACCC
Found at i:19100051 original size:95 final size:94
Alignment explanation
Indices: 19099889--19100077 Score: 306
Period size: 95 Copynumber: 2.0 Consensus size: 94
19099879 ACTCCACAAT
* * *
19099889 CCCAAATTTTCTCCTAAAATCACTCCAACACTCGCCATCCAAATCTCTTTAATTATCTCCAACAA
1 CCCAAATTTTCTCCTAAAATCACTCCAAAACTCCCCATCCAAATCTCCTTAATTATCTCCAACAA
* *
19099954 CCTCTCTACTATCCGAATTTTAGTCCAAC
66 CCTCTCCACTATCAGAATTTTAGTCCAAC
*
19099983 CCCAAATTTTCTCCTAAAATCACTCCAAAACTCCCCCATCCAAATCTCCTTAATTATCTCCATCA
1 CCCAAATTTTCTCCTAAAATCACTCCAAAACT-CCCCATCCAAATCTCCTTAATTATCTCCAACA
*
19100048 ACCTCTCCACTATTAGAATTTTAGTCCAAC
65 ACCTCTCCACTATCAGAATTTTAGTCCAAC
19100078 ACAAACTCGC
Statistics
Matches: 87, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
94 31 0.36
95 56 0.64
ACGTcount: A:0.31, C:0.35, G:0.03, T:0.31
Consensus pattern (94 bp):
CCCAAATTTTCTCCTAAAATCACTCCAAAACTCCCCATCCAAATCTCCTTAATTATCTCCAACAA
CCTCTCCACTATCAGAATTTTAGTCCAAC
Found at i:19103714 original size:20 final size:20
Alignment explanation
Indices: 19103689--19103729 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
19103679 TCCTACTGAG
19103689 TAAGCTTATGTTATATTGTT
1 TAAGCTTATGTTATATTGTT
19103709 TAAGCTTATGTTATATTGTT
1 TAAGCTTATGTTATATTGTT
19103729 T
1 T
19103730 GTAAACTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.05, G:0.15, T:0.56
Consensus pattern (20 bp):
TAAGCTTATGTTATATTGTT
Found at i:19113679 original size:19 final size:18
Alignment explanation
Indices: 19113649--19113685 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
19113639 CTCCAATTAT
*
19113649 AATAAACATAATATAATA
1 AATAAACATAATAAAATA
19113667 AATAAATCATAATAAAATA
1 AATAAA-CATAATAAAATA
19113686 TATTTGAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (18 bp):
AATAAACATAATAAAATA
Found at i:19115528 original size:24 final size:26
Alignment explanation
Indices: 19115497--19115555 Score: 77
Period size: 24 Copynumber: 2.3 Consensus size: 26
19115487 AAATAAATAA
*
19115497 AAAATACTAAA-CTTGGTTTAAG-TT
1 AAAATACTAAAGCTTAGTTTAAGTTT
*
19115521 AAAATACTAAAGCTTAGTTTATGTTT
1 AAAATACTAAAGCTTAGTTTAAGTTT
19115547 ATAAATACT
1 A-AAATACT
19115556 CATGATTCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
24 11 0.37
25 9 0.30
26 3 0.10
27 7 0.23
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.39
Consensus pattern (26 bp):
AAAATACTAAAGCTTAGTTTAAGTTT
Found at i:19116670 original size:13 final size:14
Alignment explanation
Indices: 19116652--19116684 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
19116642 GAATGTTGGC
*
19116652 ATTATCTT-CATAA
1 ATTATCTTGAATAA
19116665 ATTATCTTGAATAA
1 ATTATCTTGAATAA
19116679 ATTATC
1 ATTATC
19116685 CCAATAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.39, C:0.12, G:0.03, T:0.45
Consensus pattern (14 bp):
ATTATCTTGAATAA
Found at i:19117990 original size:18 final size:18
Alignment explanation
Indices: 19117952--19117990 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
19117942 TTTGAGCATT
**
19117952 TATGTATTATTTTGCTTC
1 TATGTATTATTTTGCAAC
19117970 TATGTATTATTTTGCAAC
1 TATGTATTATTTTGCAAC
19117988 TAT
1 TAT
19117991 TTCTCTTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.56
Consensus pattern (18 bp):
TATGTATTATTTTGCAAC
Found at i:19119286 original size:126 final size:130
Alignment explanation
Indices: 19119120--19119356 Score: 279
Period size: 126 Copynumber: 1.9 Consensus size: 130
19119110 AAACTTGTAC
* * ** *
19119120 TTTGAAATTTTAAGAGGATATTTGGCTATTTGGTCGAACGA-AAA-ATTGAAACC-CAGCACGTT
1 TTTGAAATTTTAAAAGGATATTTGGCTATTAGGTCGAACGAGAAAGACCGAAACCAC-GCAAGTT
* * *
19119182 AGGGCAC-ATTTTCTTGAATTC-CCAA-ACGCAAAATATTGCCTTATTGAGATTCCTTTCATCAT
65 AGGACACAATTTTCTCGAA-TCGCCAATACACAAAATATTGCCTTATTGAGATTCCTTTCATCAT
19119244 TT
129 TT
* * * * **
19119246 TTTGAGATTTTAAAAGGGTATTTTGCTATTAGTTTTAACGAGAAAGACCGAAACCACGCAAGTTA
1 TTTGAAATTTTAAAAGGATATTTGGCTATTAGGTCGAACGAGAAAGACCGAAACCACGCAAGTTA
*
19119311 GGATACAATTTTCTCGAATCGCCAATACACAAAATATTGCCTTATT
66 GGACACAATTTTCTCGAATCGCCAATACACAAAATATTGCCTTATT
19119357 TGAAAATTTC
Statistics
Matches: 90, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
126 33 0.37
127 3 0.03
128 20 0.22
129 15 0.17
130 19 0.21
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (130 bp):
TTTGAAATTTTAAAAGGATATTTGGCTATTAGGTCGAACGAGAAAGACCGAAACCACGCAAGTTA
GGACACAATTTTCTCGAATCGCCAATACACAAAATATTGCCTTATTGAGATTCCTTTCATCATTT
Found at i:19119607 original size:23 final size:23
Alignment explanation
Indices: 19119579--19119622 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
19119569 AGTAAATAAT
*
19119579 AAATATTTAAAATGAATAATGCG
1 AAATATTCAAAATGAATAATGCG
*
19119602 AAATATTCAAAATTAATAATG
1 AAATATTCAAAATGAATAATG
19119623 TACAATTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.55, C:0.05, G:0.09, T:0.32
Consensus pattern (23 bp):
AAATATTCAAAATGAATAATGCG
Found at i:19119798 original size:26 final size:26
Alignment explanation
Indices: 19119769--19119818 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
19119759 AAATAACATA
* *
19119769 GAAAGCAATTTAAA-TAGGTAATATAT
1 GAAA-CAAGTTAAAGTAGCTAATATAT
19119795 GAAACAAGTTAAAGTAGCTAATAT
1 GAAACAAGTTAAAGTAGCTAATAT
19119819 CAAATATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.50, C:0.06, G:0.16, T:0.28
Consensus pattern (26 bp):
GAAACAAGTTAAAGTAGCTAATATAT
Found at i:19121657 original size:44 final size:44
Alignment explanation
Indices: 19121607--19122046 Score: 167
Period size: 44 Copynumber: 9.6 Consensus size: 44
19121597 ATTTTAATCC
* **
19121607 GCTCCACTGCAACTTCAGGGAGATAGGA-TTAGTAGCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTT-GTAGCTTCAACCT
* * * *
19121651 GTTCCACTGTAACTTCAGGGAAATAAGACTTGTATCTTCAACCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAACCT
* * * *
19121695 GCCCCACTGCAACTTCAGGGGGATAAGACTCT-CAACTTCAACCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACT-TGTAGCTTCAACCT
* * * * * * * * *
19121739 GCCCCACTACAAATTCGGGGAGATGAG-GTT-T-GATAT-GATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCT-TCAACCT
* * ** *
19121780 GCTCTATTGCAACTTCAGAAAGATAAGATCTGTAATGTATAGCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-C--T--TG--TAGCTTCAACCT
** * * * **
19121831 ATTCCACTGCTACTTCAGGGAAATAAGA-TTCGTTATCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTT-G-TAGCTTCAACCT
* *
19121876 CCTCCACTGCAACTTCAGGGAGATAAGACTTGATATGATCTACTCTACTGCAACT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTTG-TA-G--CT--TC-A----ACCT
* * **
19121931 GCCCCACTGCAACTTCAGGGGGATAAGGTTTGTTA-CTTCAACCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTTG-TAGCTTCAACCT
* * * * ** * * **
19121975 TCTCTACTGTAACTTCAGAGAGATAAGGTTTGTGGCTTTAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAACCT
*
19122019 GCTCCACTGCAACTTCAAGGAGATAAGA
1 GCTCCACTGCAACTTCAGGGAGATAAGA
19122047 TTCGCCATGA
Statistics
Matches: 290, Mismatches: 79, Indels: 54
0.69 0.19 0.13
Matches are distributed among these distances:
41 22 0.08
42 2 0.01
43 2 0.01
44 148 0.51
45 42 0.14
46 3 0.01
47 2 0.01
48 3 0.01
49 2 0.01
50 4 0.01
51 29 0.10
55 31 0.11
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAACCT
Found at i:19127579 original size:141 final size:136
Alignment explanation
Indices: 19127403--19127675 Score: 395
Period size: 136 Copynumber: 2.0 Consensus size: 136
19127393 AAAACCGGGC
*
19127403 CGGGCTTATTATTTTTTCCCGGGCCGGGCCTGGGCAAAATTTCAGGCTCATATTTCGGGCCGGGC
1 CGGGCTTATTATTTTTTCCCGGGCCGGGCCTGGGCAAAATTTCAGGCCCATATTT-----CGGGC
*
19127468 CGGGCCCGGGCCTAAGAGTCGGGCCAAAAAAATTTTCTGGGCCCGACTCGAACCCGGCCCATGGA
61 CGGGCCCGGGCCTAAGAGTCGGGCCAAAAAAATTTTCTGGGCCCGAC-CCAACCCGGCCCATGGA
19127533 CAGGTCTAGTCT
125 CAGGTCTAGTCT
19127545 CGGGCTTATT-TTTTTTCCCGGGCCGGGCCTGGGCAAAATTTCAGGCCCATATTTCGGGCCGGGC
1 CGGGCTTATTATTTTTTCCCGGGCCGGGCCTGGGCAAAATTTCAGGCCCATATTTCGGGCCGGGC
** *** * * *
19127609 CCGGGCCTAAGAGTCGGGCTGAAATTTTTTTCTGGGCCTGGCCCAGCCCGGCCCATGGACAGGTC
66 CCGGGCCTAAGAGTCGGGCCAAAAAAATTTTCTGGGCCCGACCCAACCCGGCCCATGGACAGGTC
19127674 TA
131 TA
19127676 ATCCTGCCAT
Statistics
Matches: 121, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
135 23 0.19
136 45 0.37
141 43 0.36
142 10 0.08
ACGTcount: A:0.16, C:0.29, G:0.31, T:0.24
Consensus pattern (136 bp):
CGGGCTTATTATTTTTTCCCGGGCCGGGCCTGGGCAAAATTTCAGGCCCATATTTCGGGCCGGGC
CCGGGCCTAAGAGTCGGGCCAAAAAAATTTTCTGGGCCCGACCCAACCCGGCCCATGGACAGGTC
TAGTCT
Found at i:19133592 original size:14 final size:14
Alignment explanation
Indices: 19133569--19133604 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
19133559 GATAAGATAT
19133569 AATACAAATGAATG
1 AATACAAATGAATG
*
19133583 AATGCAAATGAATG
1 AATACAAATGAATG
19133597 AATACAAA
1 AATACAAA
19133605 AAGAGGCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.58, C:0.08, G:0.14, T:0.19
Consensus pattern (14 bp):
AATACAAATGAATG
Found at i:19138758 original size:30 final size:32
Alignment explanation
Indices: 19138707--19138768 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
19138697 AATTTTTCGA
*
19138707 ATAAGGATTAATTTGTTAAATTAGT-AAAAAT
1 ATAAGGATTAATTTGTGAAATTAGTGAAAAAT
* *
19138738 ATAAGGATT-TTTTGTGAAATTATTGAAAAAT
1 ATAAGGATTAATTTGTGAAATTAGTGAAAAAT
19138769 GGGTTGTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 12 0.44
31 15 0.56
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (32 bp):
ATAAGGATTAATTTGTGAAATTAGTGAAAAAT
Found at i:19139347 original size:25 final size:26
Alignment explanation
Indices: 19139319--19139436 Score: 93
Period size: 25 Copynumber: 4.7 Consensus size: 26
19139309 ATCCCAATAT
*
19139319 TTGGCTCTCACGAGCTTCCTGG-TAC
1 TTGGCTCTCACGAGCTTCCTGGATAA
19139344 TTGGCTCTCACGAGCTT-CTGGATAA
1 TTGGCTCTCACGAGCTTCCTGGATAA
* * * *
19139369 TTAGCTCTAATGAGCTTCC-CGATTAA
1 TTGGCTCTCACGAGCTTCCTGGA-TAA
** * *
19139395 -TGGCTCTCTTGAGCTTCC-CGATAT
1 TTGGCTCTCACGAGCTTCCTGGATAA
* *
19139419 TTGGCTCGCATGAGCTTC
1 TTGGCTCTCACGAGCTTC
19139437 TTGATTTACA
Statistics
Matches: 78, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
24 6 0.08
25 68 0.87
26 4 0.05
ACGTcount: A:0.17, C:0.27, G:0.22, T:0.34
Consensus pattern (26 bp):
TTGGCTCTCACGAGCTTCCTGGATAA
Found at i:19141877 original size:22 final size:20
Alignment explanation
Indices: 19141841--19141899 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
19141831 GGCCCGGCCC
19141841 ATTT-TTTTAATAAATACCAAAA
1 ATTTATTTTAA-AAATA--AAAA
19141863 ATTTATTTTAAAAATTAAAAA
1 ATTTATTTTAAAAA-TAAAAA
* *
19141884 AATAATTTTAAAAATA
1 ATTTATTTTAAAAATA
19141900 TTTTAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 2 0.06
21 16 0.48
22 7 0.21
23 8 0.24
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (20 bp):
ATTTATTTTAAAAATAAAAA
Found at i:19141953 original size:39 final size:38
Alignment explanation
Indices: 19141870--19141958 Score: 151
Period size: 38 Copynumber: 2.3 Consensus size: 38
19141860 AAAATTTATT
*
19141870 TTAAAAATTAAAAAAATAATTTTAAAAATATTTTAAAA
1 TTAAAAAATAAAAAAATAATTTTAAAAATATTTTAAAA
*
19141908 TTAAAAAATAAAAAAATCATTTTAAAAATATTTTAAAA
1 TTAAAAAATAAAAAAATAATTTTAAAAATATTTTAAAA
19141946 TTAAAAAAATAAA
1 TT-AAAAAATAAA
19141959 TATATTTATT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 38 0.79
39 10 0.21
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (38 bp):
TTAAAAAATAAAAAAATAATTTTAAAAATATTTTAAAA
Found at i:19147113 original size:117 final size:118
Alignment explanation
Indices: 19146979--19147215 Score: 467
Period size: 117 Copynumber: 2.0 Consensus size: 118
19146969 ATAGATATAT
19146979 TTACAAAAAATATATAATAATTAATAAAAATATGATTTGAAATTAATTTATAATAATATATAAAA
1 TTACAAAAAATATATAATAATTAATAAAAATATGATTTGAAATTAATTTATAATAATATATAAAA
19147044 TAAGTACGATATTAAAATGTAAAAGAATAGATTAAATTGTGAGTAAAACGAAA
66 TAAGTACGATATTAAAATGTAAAAGAATAGATTAAATTGTGAGTAAAACGAAA
19147097 TTACAAAAAATA-ATAATAATTAATAAAAATATGATTTGAAATTAATTTATAATAATATATAAAA
1 TTACAAAAAATATATAATAATTAATAAAAATATGATTTGAAATTAATTTATAATAATATATAAAA
19147161 TAAGTACGATATTAAAATGTAAAAGAATAGATTAAATTGTGAGTAAAACGAAA
66 TAAGTACGATATTAAAATGTAAAAGAATAGATTAAATTGTGAGTAAAACGAAA
19147214 TT
1 TT
19147216 TAAATACAAA
Statistics
Matches: 119, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
117 107 0.90
118 12 0.10
ACGTcount: A:0.56, C:0.03, G:0.09, T:0.32
Consensus pattern (118 bp):
TTACAAAAAATATATAATAATTAATAAAAATATGATTTGAAATTAATTTATAATAATATATAAAA
TAAGTACGATATTAAAATGTAAAAGAATAGATTAAATTGTGAGTAAAACGAAA
Found at i:19149579 original size:138 final size:138
Alignment explanation
Indices: 19149343--19149594 Score: 378
Period size: 138 Copynumber: 1.8 Consensus size: 138
19149333 ATCTTATGAT
* * * * *
19149343 GGTAACACACTTACAAAGTCATTGGTTAAGAAGTTGATTAGCAGTTTCGTGATAGTATATAATAA
1 GGTAACACAATTACAAAGTCACTGGCTAAGAAGTTGATAAGCAGTTTCGTGATAGGATATAATAA
* *
19149408 TGAAGAGTTCAATCATGATACTTTAGTGGAATGACTTCATGACTAAATAATACTGTAACGAATAT
66 TGAAGAGCTCAATCATGATACTTTAGTGAAATGACTTCATGACTAAATAATACTGTAACGAATAT
19149473 CCTATTAG
131 CCTATTAG
* * * * * *
19149481 GGTAATACAATTACAAAGTCACTGGCTGAGAAGTTGATAAGTAGTTTTGTGATAGGGTATAATCA
1 GGTAACACAATTACAAAGTCACTGGCTAAGAAGTTGATAAGCAGTTTCGTGATAGGATATAATAA
*
19149546 TGGAGAGCTCAATCATGATACTTTAGTGAAATGACTTCATGACTAAATA
66 TGAAGAGCTCAATCATGATACTTTAGTGAAATGACTTCATGACTAAATA
19149595 CTGTTATAAT
Statistics
Matches: 100, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
138 100 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.32
Consensus pattern (138 bp):
GGTAACACAATTACAAAGTCACTGGCTAAGAAGTTGATAAGCAGTTTCGTGATAGGATATAATAA
TGAAGAGCTCAATCATGATACTTTAGTGAAATGACTTCATGACTAAATAATACTGTAACGAATAT
CCTATTAG
Found at i:19150011 original size:22 final size:21
Alignment explanation
Indices: 19149986--19150033 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
19149976 CCTTAATAGA
19149986 AATTAAAATGAATAGAGAAAAT
1 AATTAAAATG-ATAGAGAAAAT
** *
19150008 AATTTAATTTGATAGAGAAATT
1 AA-TTAAAATGATAGAGAAAAT
19150030 AATT
1 AATT
19150034 TAGTTAACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 2 0.09
22 14 0.64
23 6 0.27
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.33
Consensus pattern (21 bp):
AATTAAAATGATAGAGAAAAT
Found at i:19152136 original size:17 final size:18
Alignment explanation
Indices: 19152103--19152142 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
19152093 CATAAACAAC
*
19152103 ATAAACTTGATAAAATAA
1 ATAAACATGATAAAATAA
19152121 ATAAACATGA-AAAATAA
1 ATAAACATGATAAAATAA
19152138 ATAAA
1 ATAAA
19152143 GAGTAAGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.23
Consensus pattern (18 bp):
ATAAACATGATAAAATAA
Found at i:19154784 original size:40 final size:41
Alignment explanation
Indices: 19154703--19154784 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
19154693 TCGAACCTAA
* * *
19154703 AAATTCTTATTTTACCCTTATACCTGAAACAACCTTAAATC
1 AAATTCTCATTTTACCCTTATACCTCAAACAACCCTAAATC
19154744 AAATTCTCATTTTACCCTTATACC-CAAACAACCCTAAATC
1 AAATTCTCATTTTACCCTTATACCTCAAACAACCCTAAATC
19154784 A
1 A
19154785 CCTTTTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
40 15 0.39
41 23 0.61
ACGTcount: A:0.38, C:0.28, G:0.01, T:0.33
Consensus pattern (41 bp):
AAATTCTCATTTTACCCTTATACCTCAAACAACCCTAAATC
Found at i:19160359 original size:44 final size:44
Alignment explanation
Indices: 19160269--19160366 Score: 108
Period size: 44 Copynumber: 2.2 Consensus size: 44
19160259 AAACATAGTT
* * * * *
19160269 TTACACGTAGATCTTAAGTCGATGCCAACGCCCGATACGTGCTC
1 TTACACGAAAATCTCAAGTCGATGCCAACGCCCGAGACATGCTC
* * *
19160313 TTACATGAAAATCTCAAGTCGATGCCAACATCCC-AGACATGGTC
1 TTACACGAAAATCTCAAGTCGATGCCAAC-GCCCGAGACATGCTC
19160357 TTACACGAAA
1 TTACACGAAA
19160367 TCACATACCG
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
44 41 0.93
45 3 0.07
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (44 bp):
TTACACGAAAATCTCAAGTCGATGCCAACGCCCGAGACATGCTC
Found at i:19160692 original size:15 final size:15
Alignment explanation
Indices: 19160672--19160701 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19160662 CCGAACCTAG
19160672 CTTTCTATTTCTTTT
1 CTTTCTATTTCTTTT
*
19160687 CTTTCTTTTTCTTTT
1 CTTTCTATTTCTTTT
19160702 GTAGTTTCGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (15 bp):
CTTTCTATTTCTTTT
Found at i:19160900 original size:8 final size:8
Alignment explanation
Indices: 19160887--19160915 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
19160877 AATCAAATCA
19160887 TAACATAT
1 TAACATAT
19160895 TAACATAT
1 TAACATAT
19160903 TAACATAT
1 TAACATAT
19160911 TAACA
1 TAACA
19160916 ATGAGAATGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (8 bp):
TAACATAT
Found at i:19168183 original size:43 final size:42
Alignment explanation
Indices: 19168148--19168237 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 42
19168138 TCTTACATAT
*
19168148 AATCAAATATCGATGCCACTGTCCCAGACAGGGTCTTACACGA
1 AATCAAATA-CGATGCCAATGTCCCAGACAGGGTCTTACACGA
* * *
19168191 AGTCATATACGATGCCAATGTCCCAGACATGGTCTTACACGTA
1 AATCAAATACGATGCCAATGTCCCAGACAGGGTCTTACACG-A
19168234 AATC
1 AATC
19168238 TCAGGTTGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
42 30 0.73
43 11 0.27
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (42 bp):
AATCAAATACGATGCCAATGTCCCAGACAGGGTCTTACACGA
Found at i:19171050 original size:14 final size:14
Alignment explanation
Indices: 19171031--19171062 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
19171021 TGTTAATTTT
19171031 AAAGCTTATTAGAG
1 AAAGCTTATTAGAG
*
19171045 AAAGCTTATTAGCG
1 AAAGCTTATTAGAG
19171059 AAAG
1 AAAG
19171063 AGCATAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.09, G:0.22, T:0.25
Consensus pattern (14 bp):
AAAGCTTATTAGAG
Found at i:19172228 original size:10 final size:10
Alignment explanation
Indices: 19172202--19172242 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
19172192 ATTAAAATAC
*
19172202 AATAATTTGCA
1 AATAATTT-AA
19172213 AA-AATTTAA
1 AATAATTTAA
19172222 AATAATTTAA
1 AATAATTTAA
19172232 AATAATTTAA
1 AATAATTTAA
19172242 A
1 A
19172243 GAATGTCAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 3 0.11
10 23 0.82
11 2 0.07
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (10 bp):
AATAATTTAA
Found at i:19173938 original size:18 final size:18
Alignment explanation
Indices: 19173915--19173951 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
19173905 ACCAAACAAA
19173915 AAGGGTAAGTACATGGTC
1 AAGGGTAAGTACATGGTC
19173933 AAGGGTAAGTACATGGTC
1 AAGGGTAAGTACATGGTC
19173951 A
1 A
19173952 TTTTTGGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.11, G:0.32, T:0.22
Consensus pattern (18 bp):
AAGGGTAAGTACATGGTC
Found at i:19174408 original size:17 final size:17
Alignment explanation
Indices: 19174367--19174412 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
19174357 TTTGACAAGA
*
19174367 AAAATAAATGAAAAATCTT
1 AAAATAAA--AAAAATCCT
19174386 AGAAATAAAAAAAATCCT
1 A-AAATAAAAAAAATCCT
19174404 AAAATAAAA
1 AAAATAAAA
19174413 TTTAAATTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 8 0.32
18 9 0.36
19 1 0.04
20 7 0.28
ACGTcount: A:0.70, C:0.07, G:0.04, T:0.20
Consensus pattern (17 bp):
AAAATAAAAAAAATCCT
Found at i:19191859 original size:24 final size:24
Alignment explanation
Indices: 19191827--19191874 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
19191817 AGTAGAATTA
*
19191827 AAGAGCCAACGACGTCCCCGTGAT
1 AAGAGCCAACGACGTCCCCATGAT
19191851 AAGAGCCAACGACGTCCCCATGAT
1 AAGAGCCAACGACGTCCCCATGAT
19191875 GAATCCTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.33, G:0.23, T:0.12
Consensus pattern (24 bp):
AAGAGCCAACGACGTCCCCATGAT
Found at i:19193282 original size:27 final size:27
Alignment explanation
Indices: 19193222--19193275 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
19193212 TCCTTTCTTT
* *
19193222 AGAGTTTGTCATACGTACTATTCCTTC
1 AGAGTTCGTCACACGTACTATTCCTTC
19193249 AGAGTTCGTCACACGTACTATTCCTTC
1 AGAGTTCGTCACACGTACTATTCCTTC
19193276 CAAGTTCACC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (27 bp):
AGAGTTCGTCACACGTACTATTCCTTC
Found at i:19193385 original size:53 final size:53
Alignment explanation
Indices: 19193290--19193465 Score: 282
Period size: 53 Copynumber: 3.3 Consensus size: 53
19193280 TTCACCATGT
* * * *
19193290 ATATCATCCTTTCATGGTTT-CCATACTTATCATTCTTCAAAGTTAGCCAAAC
1 ATATCATTCTTTCAGGGTTTGCCATACTTACCATTCTTCAAAGTTAGCCATAC
*
19193342 ATATCATTCTTTCAGGGTTTGCCATACTTACCATTCTTCAAAGTTAACCATAC
1 ATATCATTCTTTCAGGGTTTGCCATACTTACCATTCTTCAAAGTTAGCCATAC
* *
19193395 ATATTATTCTTTTAGGGTTTGCCATACTTACCATTCTTCAAAGTTAGCCATAC
1 ATATCATTCTTTCAGGGTTTGCCATACTTACCATTCTTCAAAGTTAGCCATAC
19193448 ATATCATTCTTTCAGGGT
1 ATATCATTCTTTCAGGGT
19193466 CCGCCACAAA
Statistics
Matches: 113, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
52 18 0.16
53 95 0.84
ACGTcount: A:0.27, C:0.23, G:0.10, T:0.40
Consensus pattern (53 bp):
ATATCATTCTTTCAGGGTTTGCCATACTTACCATTCTTCAAAGTTAGCCATAC
Found at i:19193471 original size:27 final size:27
Alignment explanation
Indices: 19193290--19193465 Score: 144
Period size: 26 Copynumber: 6.7 Consensus size: 27
19193280 TTCACCATGT
* * *
19193290 ATATCATCCTTTCATGGTT-TCCATAC
1 ATATCATTCTTTCAGGGTTAGCCATAC
* ** *
19193316 TTATCATTC-TTCAAAGTTAGCCAAAC
1 ATATCATTCTTTCAGGGTTAGCCATAC
*
19193342 ATATCATTCTTTCAGGGTTTGCCATAC
1 ATATCATTCTTTCAGGGTTAGCCATAC
* * ** *
19193369 TTACCATTC-TTCAAAGTTAACCATAC
1 ATATCATTCTTTCAGGGTTAGCCATAC
* * *
19193395 ATATTATTCTTTTAGGGTTTGCCATAC
1 ATATCATTCTTTCAGGGTTAGCCATAC
* * **
19193422 TTACCATTC-TTCAAAGTTAGCCATAC
1 ATATCATTCTTTCAGGGTTAGCCATAC
19193448 ATATCATTCTTTCAGGGT
1 ATATCATTCTTTCAGGGT
19193466 CCGCCACAAA
Statistics
Matches: 110, Mismatches: 36, Indels: 7
0.72 0.24 0.05
Matches are distributed among these distances:
25 7 0.06
26 59 0.54
27 44 0.40
ACGTcount: A:0.27, C:0.23, G:0.10, T:0.40
Consensus pattern (27 bp):
ATATCATTCTTTCAGGGTTAGCCATAC
Found at i:19198801 original size:60 final size:61
Alignment explanation
Indices: 19198726--19198840 Score: 187
Period size: 60 Copynumber: 1.9 Consensus size: 61
19198716 TTCTGAGAAC
* *
19198726 TTCAAATCGTCACTCCTAAAATTTTGGGGAGCACTCTTCTCTTGAATCT-GGTTTTGGAAG
1 TTCAAATCGTCACTCCCAAAATTTTGGGGAGCACCCTTCTCTTGAATCTCGGTTTTGGAAG
* *
19198786 TTCAAATCGTTACTCCCAAAATTTTGGGGAGCACCCTTCTCTTGATTCTCGGTTT
1 TTCAAATCGTCACTCCCAAAATTTTGGGGAGCACCCTTCTCTTGAATCTCGGTTT
19198841 GTACTTTAGG
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
60 45 0.90
61 5 0.10
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (61 bp):
TTCAAATCGTCACTCCCAAAATTTTGGGGAGCACCCTTCTCTTGAATCTCGGTTTTGGAAG
Found at i:19202034 original size:101 final size:99
Alignment explanation
Indices: 19201894--19202086 Score: 260
Period size: 101 Copynumber: 1.9 Consensus size: 99
19201884 TGAATTGACG
** * * *
19201894 GATAAGACCATAACTGGGTTATGGCACTATGAACATAAGACCATGGTTGGACCATGACAGTGTTT
1 GATAAGACCATAACTGGGTTATGGCACTACAAACATAAGACCATGGTAGGACCATGACAATG--C
*
19201959 ATATGTAAGACCATAGCTGGGCTATGGCATTCTGAT
64 ATATGTAAGACCATAGCTGGACTATGGCATTCTGAT
** * *
19201995 GATAAGACCATAACTGGGTTATGGCACTACAAATGTAAGACCATGGTAGGGCCATGGCAATGCAT
1 GATAAGACCATAACTGGGTTATGGCACTACAAACATAAGACCATGGTAGGACCATGACAATGCAT
* *
19202060 GTGTAAGACCATAGTTGGACTATGGCA
66 ATGTAAGACCATAGCTGGACTATGGCA
19202087 CAAAAAGAAC
Statistics
Matches: 80, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
99 26 0.32
101 54 0.68
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (99 bp):
GATAAGACCATAACTGGGTTATGGCACTACAAACATAAGACCATGGTAGGACCATGACAATGCAT
ATGTAAGACCATAGCTGGACTATGGCATTCTGAT
Found at i:19202085 original size:33 final size:33
Alignment explanation
Indices: 19201962--19202086 Score: 103
Period size: 33 Copynumber: 3.8 Consensus size: 33
19201952 AGTGTTTATA
*
19201962 TGTAAGACCATAGCTGGGCTATGGC-ATTC-TG
1 TGTAAGACCATAGCTGGGCTATGGCAATACATG
* * * **
19201993 ATGATAAGACCATAACTGGGTTATGGCACTACAAA
1 -TG-TAAGACCATAGCTGGGCTATGGCAATACATG
* * *
19202028 TGTAAGACCAT-GGTAGGGCCATGGCAATGCATG
1 TGTAAGACCATAGCT-GGGCTATGGCAATACATG
* *
19202061 TGTAAGACCATAGTTGGACTATGGCA
1 TGTAAGACCATAGCTGGGCTATGGCA
19202087 CAAAAAGAAC
Statistics
Matches: 71, Mismatches: 17, Indels: 9
0.73 0.18 0.09
Matches are distributed among these distances:
32 3 0.04
33 62 0.87
34 6 0.08
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (33 bp):
TGTAAGACCATAGCTGGGCTATGGCAATACATG
Found at i:19208254 original size:20 final size:20
Alignment explanation
Indices: 19208229--19208275 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
19208219 ATTTTAAAAT
**
19208229 ATTTTTAAAATACTTTTTTA
1 ATTTTTAAAATAAATTTTTA
19208249 ATTTTTAAAATAAATTTTTA
1 ATTTTTAAAATAAATTTTTA
*
19208269 ATATTTA
1 ATTTTTA
19208276 TTAAAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTTTAAAATAAATTTTTA
Found at i:19210388 original size:18 final size:17
Alignment explanation
Indices: 19210356--19210407 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
19210346 NNNNNNNNNT
*
19210356 AAAATTATTTTTAATTTA
1 AAAATTA-TTATAATTTA
19210374 AAAATATATTATAATTT-
1 AAAAT-TATTATAATTTA
* *
19210391 TAAATTATTATATTTTA
1 AAAATTATTATAATTTA
19210408 TTAATTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 10 0.34
17 4 0.14
18 13 0.45
19 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AAAATTATTATAATTTA
Found at i:19210401 original size:16 final size:16
Alignment explanation
Indices: 19210375--19210407 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
19210365 TTTAATTTAA
19210375 AAATATATTATAATTTT
1 AAATATATTAT-ATTTT
19210392 AAAT-TATTATATTTT
1 AAATATATTATATTTT
19210407 A
1 A
19210408 TTAATTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 6 0.38
17 4 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AAATATATTATATTTT
Found at i:19213398 original size:43 final size:43
Alignment explanation
Indices: 19213304--19213390 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
19213294 ATGAAGGCAG
* * *
19213304 GATATGATATGTTACAAGATATGTTTCGATATGAATCTGATAT
1 GATATGATATGTTACAAGAAATGTTCCGAAATGAATCTGATAT
* *
19213347 GATATGATATG-TATAAGAAATGTTCCGAAATGGAGTCTGATAT
1 GATATGATATGTTACAAGAAATGTTCCGAAAT-GAATCTGATAT
19213390 G
1 G
19213391 CTTTGATACA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
42 16 0.42
43 22 0.58
ACGTcount: A:0.36, C:0.07, G:0.22, T:0.36
Consensus pattern (43 bp):
GATATGATATGTTACAAGAAATGTTCCGAAATGAATCTGATAT
Found at i:19214298 original size:13 final size:13
Alignment explanation
Indices: 19214280--19214335 Score: 85
Period size: 13 Copynumber: 4.2 Consensus size: 13
19214270 CATACTCATC
19214280 TAGGAAGTAATCA
1 TAGGAAGTAATCA
*
19214293 TAGGAAGTACTCA
1 TAGGAAGTAATCA
19214306 TCTAGGAAGTAATCA
1 --TAGGAAGTAATCA
19214321 TAGGAAGTAATCA
1 TAGGAAGTAATCA
19214334 TA
1 TA
19214336 CTCTTTCCTA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
13 27 0.69
15 12 0.31
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.25
Consensus pattern (13 bp):
TAGGAAGTAATCA
Found at i:19214312 original size:28 final size:28
Alignment explanation
Indices: 19214272--19214334 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
19214262 GTGCCAACCA
19214272 TACTCATCTAGGAAGTAATCATAGGAAG
1 TACTCATCTAGGAAGTAATCATAGGAAG
19214300 TACTCATCTAGGAAGTAATCATAGGAAG
1 TACTCATCTAGGAAGTAATCATAGGAAG
*
19214328 TAATCAT
1 TACTCAT
19214335 ACTCTTTCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (28 bp):
TACTCATCTAGGAAGTAATCATAGGAAG
Found at i:19214981 original size:43 final size:43
Alignment explanation
Indices: 19214924--19215107 Score: 219
Period size: 43 Copynumber: 4.3 Consensus size: 43
19214914 TTTTTCACAT
19214924 AAACGCCGCTAAAGAGCATGACCTTTAGCGGCGCTTTTATCAC
1 AAACGCCGCTAAAGAGCATGACCTTTAGCGGCGCTTTTATCAC
* ** *
19214967 ACACGCCGCTAAAGAGCATGACC-TTAGCAACGAC-TTCATCAC
1 AAACGCCGCTAAAGAGCATGACCTTTAGCGGCG-CTTTTATCAC
* * * * *
19215009 AAACACCGCTAAAGAACATGATCTTTAGTGGCACTTTTATCAC
1 AAACGCCGCTAAAGAGCATGACCTTTAGCGGCGCTTTTATCAC
* * * *
19215052 AAATGCTGCTAAAGAGCATGACCTTTAGCGGCGCTTTTATTAT
1 AAACGCCGCTAAAGAGCATGACCTTTAGCGGCGCTTTTATCAC
*
19215095 AAACGCTGCTAAA
1 AAACGCCGCTAAA
19215108 AGTACCGTTC
Statistics
Matches: 115, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
42 34 0.30
43 81 0.70
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGAGCATGACCTTTAGCGGCGCTTTTATCAC
Found at i:19215275 original size:4 final size:4
Alignment explanation
Indices: 19215263--19215293 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
19215253 TAAAATTAGT
19215263 TAAA T-AA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
19215294 AAGGATAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:19215635 original size:31 final size:32
Alignment explanation
Indices: 19215597--19215678 Score: 130
Period size: 32 Copynumber: 2.6 Consensus size: 32
19215587 AGGCAAATTA
*
19215597 CAAGAGTAATTCAATCCTAAT-AAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
*
19215628 CAAGAGTAAATGAATCCTAATAAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
*
19215660 AAAGAGTAATTGAATCCTA
1 CAAGAGTAATTGAATCCTA
19215679 NNNNNNNNNN
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
31 19 0.41
32 27 0.59
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.29
Consensus pattern (32 bp):
CAAGAGTAATTGAATCCTAATAAAAACTCTTT
Found at i:19238659 original size:100 final size:101
Alignment explanation
Indices: 19238527--19238743 Score: 285
Period size: 100 Copynumber: 2.2 Consensus size: 101
19238517 TAGAGTTGCA
** * * *
19238527 ATCATAAATCGGTGAACTCTTAATGAATTGTTCATGAT-AGTAAATCAATGAACCGAAGTTGTGA
1 ATCATAAATCAATGAACTCTTAATAAAGTGTTCATGATCA-TAAATCAATGAACAGAAGTTGTGA
* ** *
19238591 TCGT-AAATCAGTGAGCTTCAAAAGATGACAGCTGTG
65 TAGTAAAATCAACGAGCTTCAAAAAATGACAGCTGTG
*
19238627 ATCATAAATCAATGAACTGTTAATAAAGTGTTCATGATCATAAATCAATGAACAGAAGTTGTGAT
1 ATCATAAATCAATGAACTCTTAATAAAGTGTTCATGATCATAAATCAATGAACAGAAGTTGTGAT
* * *
19238692 AGTAAAATTAACGAGCTTTAAAAAATGACAGTTGTG
66 AGTAAAATCAACGAGCTTCAAAAAATGACAGCTGTG
*
19238728 ATCGTAAATCAATGAA
1 ATCATAAATCAATGAA
19238744 TTATTTCAAG
Statistics
Matches: 101, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
100 59 0.58
101 42 0.42
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (101 bp):
ATCATAAATCAATGAACTCTTAATAAAGTGTTCATGATCATAAATCAATGAACAGAAGTTGTGAT
AGTAAAATCAACGAGCTTCAAAAAATGACAGCTGTG
Found at i:19238767 original size:100 final size:98
Alignment explanation
Indices: 19238567--19238778 Score: 239
Period size: 101 Copynumber: 2.1 Consensus size: 98
19238557 TTCATGATAG
* * ** *
19238567 TAAATCAATGAACCGAAGTTGTGATCGTAAATCAGTGAGCTTCAAAAGATGACAGCTGTGATCAT
1 TAAATCAATGAACAGAAGTTGTGATAGTAAATCAACGAGCTTCAAAAAATGACAGCTGTGATCAT
* *
19238632 AAATCAATGAACTGTTAATAAAGTGTTCATGATCA
66 AAATCAATGAACTATT-ATAAAGAGTTCA-GATCA
* * * *
19238667 TAAATCAATGAACAGAAGTTGTGATAGTAAAATTAACGAGCTTTAAAAAATGACAGTTGTGATCG
1 TAAATCAATGAACAGAAGTTGTGATAGT-AAATCAACGAGCTTCAAAAAATGACAGCTGTGATCA
* *
19238732 TAAATCAATGAATTATT-TCAAGGGAGTTGCA-ATCA
65 TAAATCAATGAACTATTAT-AA-AGAGTT-CAGATCA
19238767 TAAATCAATGAA
1 TAAATCAATGAA
19238779 ATCTTCATGA
Statistics
Matches: 95, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
99 1 0.01
100 44 0.46
101 48 0.51
102 2 0.02
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (98 bp):
TAAATCAATGAACAGAAGTTGTGATAGTAAATCAACGAGCTTCAAAAAATGACAGCTGTGATCAT
AAATCAATGAACTATTATAAAGAGTTCAGATCA
Done.