Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 55 of 322
Found at i:17159481 original size:24 final size:24
Alignment explanation
Indices: 17159432--17159478 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
17159422 AAATCAAAAA
*
17159432 GAAAAAGAAAAAGAAAATGAGATT
1 GAAAAAGAAAAAGAAAATGAAATT
* *
17159456 GAAAAAGAGAATGAAAA-GAAATT
1 GAAAAAGAAAAAGAAAATGAAATT
17159479 TGAGAGTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.66, C:0.00, G:0.21, T:0.13
Consensus pattern (24 bp):
GAAAAAGAAAAAGAAAATGAAATT
Found at i:17169069 original size:19 final size:19
Alignment explanation
Indices: 17169045--17169104 Score: 111
Period size: 19 Copynumber: 3.2 Consensus size: 19
17169035 ATATTTTTTC
17169045 TAAGATTTATCTACTTAAA
1 TAAGATTTATCTACTTAAA
17169064 TAAGATTTATCTACTTAAA
1 TAAGATTTATCTACTTAAA
*
17169083 TAAGATTTATCTACCTAAA
1 TAAGATTTATCTACTTAAA
17169102 TAA
1 TAA
17169105 CTTTAAAATA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.43, C:0.12, G:0.05, T:0.40
Consensus pattern (19 bp):
TAAGATTTATCTACTTAAA
Found at i:17173701 original size:42 final size:41
Alignment explanation
Indices: 17173605--17173701 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 41
17173595 TCCTAATTGG
*
17173605 AAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAA
1 AAAAATAGTTCCTTTATTCTAATAAACTACTAAAACATAAA
* *
17173646 AGAAATTAGTTCCTTTATTCTAATAAACTACTAAAAGATATAA
1 A-AAAATAGTTCCTTTATTCTAATAAACTACTAAAACATA-AA
17173689 TAAAAATA-TTCCT
1 -AAAAATAGTTCCT
17173702 AGAATATGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
41 1 0.02
42 40 0.82
43 7 0.14
44 1 0.02
ACGTcount: A:0.48, C:0.14, G:0.04, T:0.33
Consensus pattern (41 bp):
AAAAATAGTTCCTTTATTCTAATAAACTACTAAAACATAAA
Found at i:17173740 original size:19 final size:18
Alignment explanation
Indices: 17173718--17173757 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
17173708 TGAATAAAAC
17173718 TTATCTACAAAAATAAGAT
1 TTATCTACAAAAATAA-AT
**
17173737 TTATCTACCTAAATAAAT
1 TTATCTACAAAAATAAAT
17173755 TTA
1 TTA
17173758 AAATATATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (18 bp):
TTATCTACAAAAATAAAT
Found at i:17180849 original size:24 final size:25
Alignment explanation
Indices: 17180817--17180869 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
17180807 AAAGGTTCCA
* *
17180817 GTATATGAGTG-CCCTTTATGGGAC
1 GTATATGAGAGCCCCTTTATAGGAC
*
17180841 GTATATGAGAGCCCCTTTATAGGAT
1 GTATATGAGAGCCCCTTTATAGGAC
17180866 GTAT
1 GTAT
17180870 GAATGTAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (25 bp):
GTATATGAGAGCCCCTTTATAGGAC
Found at i:17182600 original size:51 final size:51
Alignment explanation
Indices: 17182545--17182709 Score: 120
Period size: 51 Copynumber: 3.1 Consensus size: 51
17182535 AACCAGCCCA
17182545 TTCATGAATCATCTTTAATTGTGTTCCCACATCATGCATTGTAAGTAGACG
1 TTCATGAATCATCTTTAATTGTGTTCCCACATCATGCATTGTAAGTAGACG
* * * * ** * ** * *
17182596 TTCATGCACCTAGCTTGAA-TG-AATCTCCACATTCGGCTGGTTCATTG-AACCAGCCCA
1 TTCATGAATC-ATCTTTAATTGTGTTC-CCACA-TC--AT-G--CATTGTAAGTAG-ACG
*
17182653 TTCATGAATCATCTTTAATTGTGTTCCCACATCATGCATTGTAAGTAAACG
1 TTCATGAATCATCTTTAATTGTGTTCCCACATCATGCATTGTAAGTAGACG
17182704 TTCATG
1 TTCATG
17182710 CACCTAGCTT
Statistics
Matches: 79, Mismatches: 23, Indels: 24
0.63 0.18 0.19
Matches are distributed among these distances:
50 2 0.03
51 27 0.34
52 11 0.14
53 1 0.01
54 2 0.03
55 1 0.01
56 12 0.15
57 21 0.27
58 2 0.03
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.35
Consensus pattern (51 bp):
TTCATGAATCATCTTTAATTGTGTTCCCACATCATGCATTGTAAGTAGACG
Found at i:17182716 original size:108 final size:108
Alignment explanation
Indices: 17182527--17182742 Score: 423
Period size: 108 Copynumber: 2.0 Consensus size: 108
17182517 TCATCCTTAC
17182527 GTTCATTGAACCAGCCCATTCATGAATCATCTTTAATTGTGTTCCCACATCATGCATTGTAAGTA
1 GTTCATTGAACCAGCCCATTCATGAATCATCTTTAATTGTGTTCCCACATCATGCATTGTAAGTA
*
17182592 GACGTTCATGCACCTAGCTTGAATGAATCTCCACATTCGGCTG
66 AACGTTCATGCACCTAGCTTGAATGAATCTCCACATTCGGCTG
17182635 GTTCATTGAACCAGCCCATTCATGAATCATCTTTAATTGTGTTCCCACATCATGCATTGTAAGTA
1 GTTCATTGAACCAGCCCATTCATGAATCATCTTTAATTGTGTTCCCACATCATGCATTGTAAGTA
17182700 AACGTTCATGCACCTAGCTTGAATGAATCTCCACATTCGGCTG
66 AACGTTCATGCACCTAGCTTGAATGAATCTCCACATTCGGCTG
17182743 TACCTACATG
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
108 107 1.00
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.32
Consensus pattern (108 bp):
GTTCATTGAACCAGCCCATTCATGAATCATCTTTAATTGTGTTCCCACATCATGCATTGTAAGTA
AACGTTCATGCACCTAGCTTGAATGAATCTCCACATTCGGCTG
Found at i:17182985 original size:10 final size:10
Alignment explanation
Indices: 17182953--17183009 Score: 60
Period size: 10 Copynumber: 5.6 Consensus size: 10
17182943 ATAAAATAAA
*
17182953 TGAGCTGAAT
1 TGAGCTCAAT
*
17182963 TGTAGCTAAAT
1 TG-AGCTCAAT
*
17182974 TGAGCTCGAT
1 TGAGCTCAAT
* *
17182984 TGAGCTTAAA
1 TGAGCTCAAT
17182994 TGAGCTCAAT
1 TGAGCTCAAT
17183004 TGAGCT
1 TGAGCT
17183010 GGTCGGAGTT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
10 29 0.76
11 9 0.24
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.32
Consensus pattern (10 bp):
TGAGCTCAAT
Found at i:17182989 original size:20 final size:19
Alignment explanation
Indices: 17182949--17183009 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 19
17182939 ACCAATAAAA
17182949 TAAATGAGCT-GAATTGTAGC
1 TAAATGAGCTCG-ATTG-AGC
17182969 TAAATTGAGCTCGATTGAGC
1 TAAA-TGAGCTCGATTGAGC
*
17182989 TTAAATGAGCTCAATTGAGC
1 -TAAATGAGCTCGATTGAGC
17183009 T
1 T
17183010 GGTCGGAGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
19 1 0.03
20 21 0.57
21 14 0.38
22 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (19 bp):
TAAATGAGCTCGATTGAGC
Found at i:17185130 original size:18 final size:18
Alignment explanation
Indices: 17185109--17185143 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
17185099 TTTTTCTTTT
17185109 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
17185127 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
17185144 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:17186055 original size:15 final size:14
Alignment explanation
Indices: 17186037--17186086 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 14
17186027 TTTAACTTGA
17186037 TTTTTTTTGCTCACC
1 TTTTTTTTGCTCA-C
17186052 TTTTTTTTTGCTCGA-
1 -TTTTTTTTGCTC-AC
17186067 TTTTTTTT--TCAC
1 TTTTTTTTGCTCAC
17186079 TTTTTTTT
1 TTTTTTTT
17186087 TGAATTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 1 0.03
12 10 0.31
14 8 0.25
16 12 0.38
17 1 0.03
ACGTcount: A:0.06, C:0.16, G:0.06, T:0.72
Consensus pattern (14 bp):
TTTTTTTTGCTCAC
Found at i:17186057 original size:30 final size:28
Alignment explanation
Indices: 17186015--17186087 Score: 85
Period size: 30 Copynumber: 2.6 Consensus size: 28
17186005 CTCGCAAGAC
*
17186015 TTTTCA-CTTTTTTTTAACTTGATTTTT
1 TTTTCACCTTTTTTTTAACTCGATTTTT
**
17186042 TTTGCTCACCTTTTTTTTTGCTCGATTTTT
1 TTT--TCACCTTTTTTTTAACTCGATTTTT
*
17186072 TTTTCACTTTTTTTTT
1 TTTTCACCTTTTTTTT
17186088 GAATTTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
27 3 0.08
28 12 0.31
29 3 0.08
30 21 0.54
ACGTcount: A:0.10, C:0.15, G:0.05, T:0.70
Consensus pattern (28 bp):
TTTTCACCTTTTTTTTAACTCGATTTTT
Found at i:17186082 original size:12 final size:12
Alignment explanation
Indices: 17186066--17186103 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
17186056 TTTTTGCTCG
17186066 ATTTTTTTTTCA
1 ATTTTTTTTTCA
* *
17186078 CTTTTTTTTTGA
1 ATTTTTTTTTCA
17186090 ATTTTTTTTTCA
1 ATTTTTTTTTCA
17186102 AT
1 AT
17186104 CAATTTTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.16, C:0.08, G:0.03, T:0.74
Consensus pattern (12 bp):
ATTTTTTTTTCA
Found at i:17186096 original size:14 final size:14
Alignment explanation
Indices: 17186079--17186128 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
17186069 TTTTTTTCAC
17186079 TTTTTTTTTGAATT
1 TTTTTTTTTGAATT
* *
17186093 TTTTTTTCAATCAATT
1 TTTTTTT--TTGAATT
*
17186109 TTTTTTTTCGAATT
1 TTTTTTTTTGAATT
17186123 TTTTTT
1 TTTTTT
17186129 GATTTTTTTG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
14 17 0.59
16 12 0.41
ACGTcount: A:0.16, C:0.06, G:0.04, T:0.74
Consensus pattern (14 bp):
TTTTTTTTTGAATT
Found at i:17187285 original size:109 final size:109
Alignment explanation
Indices: 17187155--17187372 Score: 418
Period size: 109 Copynumber: 2.0 Consensus size: 109
17187145 CCTTAGCCTT
17187155 GAAGAATCTCCATAATTCCATGAATGTGCAGCTCTTTAATGATCCTACATCTCCCTTGGCTGAAT
1 GAAGAATCTCCATAATTCCATGAATGTGCAGCTCTTTAATGATCCTACATCTCCCTTGGCTGAAT
*
17187220 GAGGCATTAATGTGCCTAAAATACTTGAATGGTCATCTTGAAAA
66 GAGGCATTAATATGCCTAAAATACTTGAATGGTCATCTTGAAAA
*
17187264 GAAGAATCTCCATAATTCCATGAATGTGCAGCTCTTTAATGATCCTACATCTCCCTTGGTTGAAT
1 GAAGAATCTCCATAATTCCATGAATGTGCAGCTCTTTAATGATCCTACATCTCCCTTGGCTGAAT
17187329 GAGGCATTAATATGCCTAAAATACTTGAATGGTCATCTTGAAAA
66 GAGGCATTAATATGCCTAAAATACTTGAATGGTCATCTTGAAAA
17187373 TGCATGAATC
Statistics
Matches: 107, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
109 107 1.00
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Consensus pattern (109 bp):
GAAGAATCTCCATAATTCCATGAATGTGCAGCTCTTTAATGATCCTACATCTCCCTTGGCTGAAT
GAGGCATTAATATGCCTAAAATACTTGAATGGTCATCTTGAAAA
Found at i:17187897 original size:20 final size:20
Alignment explanation
Indices: 17187874--17187920 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
17187864 AGGTTAAGAT
*
17187874 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
17187894 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
17187914 TGAGCTG
1 TGAGCTG
17187921 GAAACAAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:17189719 original size:48 final size:48
Alignment explanation
Indices: 17189664--17189769 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
17189654 TTGTCTTTTC
*
17189664 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
17189712 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
17189760 TTTCTTTTTC
1 TTTCTTTTTC
17189770 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:17190453 original size:30 final size:30
Alignment explanation
Indices: 17190419--17190515 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
17190409 AGCTCACTCC
17190419 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
17190449 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
17190479 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
17190509 TAGCTCA
1 TAGCTCA
17190516 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:17198990 original size:9 final size:9
Alignment explanation
Indices: 17198976--17199005 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
17198966 TTTTCTTATG
17198976 TTTTGGCTA
1 TTTTGGCTA
17198985 TTTTGGCTA
1 TTTTGGCTA
17198994 TTTTGGCT-
1 TTTTGGCTA
17199002 TTTT
1 TTTT
17199006 AATTCATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.19
9 17 0.81
ACGTcount: A:0.07, C:0.10, G:0.20, T:0.63
Consensus pattern (9 bp):
TTTTGGCTA
Found at i:17200633 original size:15 final size:15
Alignment explanation
Indices: 17200592--17200654 Score: 63
Period size: 15 Copynumber: 4.2 Consensus size: 15
17200582 GAAAACCATA
*
17200592 ATAAAGAAATCCATG
1 ATAAAGAAATCCAAG
* * *
17200607 ACAGAGGAATCCAAG
1 ATAAAGAAATCCAAG
*
17200622 ATAAAGATATCCAAG
1 ATAAAGAAATCCAAG
* *
17200637 GTACAGAAATCCAAG
1 ATAAAGAAATCCAAG
17200652 ATA
1 ATA
17200655 CCATATCATA
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.51, C:0.16, G:0.17, T:0.16
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:17202384 original size:40 final size:40
Alignment explanation
Indices: 17202291--17202507 Score: 271
Period size: 40 Copynumber: 5.5 Consensus size: 40
17202281 AAGCCAAGTA
* * *
17202291 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTC-AATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
17202329 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
17202369 CCTTCGGGACTTAGCCCGGATATAGTAGCTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
17202409 CCTTCGGGACTTAGCCCAGATGTAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
17202449 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATA
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
17202489 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
17202508 TTATCATCCG
Statistics
Matches: 157, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
38 12 0.08
39 17 0.11
40 128 0.82
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:17206213 original size:37 final size:37
Alignment explanation
Indices: 17206163--17206241 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
17206153 TTATTACGAA
* *
17206163 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
17206200 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
17206237 GTCTT
1 GTCTT
17206242 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:17206429 original size:47 final size:47
Alignment explanation
Indices: 17206360--17206519 Score: 302
Period size: 47 Copynumber: 3.4 Consensus size: 47
17206350 CCCTTCGGGA
17206360 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
17206407 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
17206454 CTTATCACACATATACACTTTCACATTCATCACATCGGCCAGTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
17206501 CTTATCACATATATACACT
1 CTTATCACATATATACACT
17206520 GTCTTGGCTG
Statistics
Matches: 110, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 110 1.00
ACGTcount: A:0.31, C:0.30, G:0.08, T:0.31
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:17214495 original size:15 final size:15
Alignment explanation
Indices: 17214455--17214517 Score: 72
Period size: 15 Copynumber: 4.2 Consensus size: 15
17214445 GAAAACCAGA
*
17214455 ATAAAGAAATCCATG
1 ATAAAGAAATCCAAG
* *
17214470 ATAGAGGAATCCAAG
1 ATAAAGAAATCCAAG
*
17214485 ATAAAGAAATCTAAG
1 ATAAAGAAATCCAAG
* *
17214500 GTACAGAAATCCAAG
1 ATAAAGAAATCCAAG
17214515 ATA
1 ATA
17214518 CCATATCATA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.52, C:0.13, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:17218668 original size:9 final size:9
Alignment explanation
Indices: 17218654--17218679 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
17218644 TTTTCTTATG
17218654 TTTTGGCTA
1 TTTTGGCTA
17218663 TTTTGGCTA
1 TTTTGGCTA
17218672 TTTTGGCT
1 TTTTGGCT
17218680 TTTGAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.58
Consensus pattern (9 bp):
TTTTGGCTA
Found at i:17230038 original size:13 final size:13
Alignment explanation
Indices: 17230020--17230048 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
17230010 CATAATATGT
17230020 ATTTGGTATGTTA
1 ATTTGGTATGTTA
17230033 ATTTGGTATGTTA
1 ATTTGGTATGTTA
17230046 ATT
1 ATT
17230049 AGTTTGTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (13 bp):
ATTTGGTATGTTA
Found at i:17234966 original size:7 final size:7
Alignment explanation
Indices: 17234954--17234978 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
17234944 GGGATATATT
17234954 ATTTTTA
1 ATTTTTA
17234961 ATTTTTA
1 ATTTTTA
17234968 ATTTTTA
1 ATTTTTA
17234975 ATTT
1 ATTT
17234979 GAATTTGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
ATTTTTA
Found at i:17237207 original size:42 final size:43
Alignment explanation
Indices: 17237106--17237212 Score: 126
Period size: 43 Copynumber: 2.5 Consensus size: 43
17237096 TCCCAGATTG
* * **
17237106 GGTCTTACATGTTATCACATATCGATGCTAATAGCCCAGTTAT
1 GGTCTTACATGTAATCACATAACGATGCTAATAGCCCAGACAT
* * * *
17237149 GGTCTTACATGAAATCAAATAACGATGCTAAT-TCCCTGACAT
1 GGTCTTACATGTAATCACATAACGATGCTAATAGCCCAGACAT
*
17237191 GGTCTTACACGTAATCACATAA
1 GGTCTTACATGTAATCACATAA
17237213 TGGTAATCCT
Statistics
Matches: 53, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
42 25 0.47
43 28 0.53
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (43 bp):
GGTCTTACATGTAATCACATAACGATGCTAATAGCCCAGACAT
Found at i:17246697 original size:39 final size:40
Alignment explanation
Indices: 17246626--17246726 Score: 118
Period size: 40 Copynumber: 2.5 Consensus size: 40
17246616 CTCGTACAAG
* * * *
17246626 TGCCTTCGGGACATAGCCCGG-TTATAGTAACT-CATGCAA
1 TGCCTTCGGGACTTAACCCGGATTATAGAAACTCCACG-AA
*
17246665 TGCCTTCGGGACTTAACCCGGATTTTA-AAACTCGCACGAA
1 TGCCTTCGGGACTTAACCCGGATTATAGAAACTC-CACGAA
17246705 TGCCTTCGGGACTTAACCCGGA
1 TGCCTTCGGGACTTAACCCGGA
17246727 AAGCATTCAA
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
39 23 0.43
40 28 0.52
41 3 0.06
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
TGCCTTCGGGACTTAACCCGGATTATAGAAACTCCACGAA
Found at i:17250415 original size:40 final size:39
Alignment explanation
Indices: 17250317--17250579 Score: 278
Period size: 40 Copynumber: 6.6 Consensus size: 39
17250307 TCCTCGTTCA
* * * *
17250317 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
17250356 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
17250395 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
17250435 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
17250475 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
17250515 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
17250556 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
17250580 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 21, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
39 40 0.20
40 145 0.74
41 12 0.06
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:17250539 original size:120 final size:119
Alignment explanation
Indices: 17250317--17250579 Score: 307
Period size: 120 Copynumber: 2.2 Consensus size: 119
17250307 TCCTCGTTCA
* * *
17250317 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
* * *
17250382 TAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAAC-TCGCAC
66 TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
* * * * *
17250435 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGACATAACCCGG-
* * ** * *
17250500 ATTT-GTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
63 ATTTAATAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAATAACTTAGCAC
*
17250556 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
17250580 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 37 0.31
120 75 0.62
121 9 0.07
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
Found at i:17250588 original size:41 final size:41
Alignment explanation
Indices: 17250511--17250588 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
17250501 TTTGTATCTC
* * *
17250511 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
17250552 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
17250589 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:17258351 original size:39 final size:40
Alignment explanation
Indices: 17258306--17258490 Score: 178
Period size: 40 Copynumber: 4.7 Consensus size: 40
17258296 GCTCCTCGTT
* * *
17258306 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
**
17258346 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
17258385 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * * * * *
17258425 CAAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CATAACCCGGATTTAGTAAC-TCGCA
* *
17258466 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACATAACCCGGA
17258491 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
39 37 0.30
40 74 0.61
41 11 0.09
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:17258406 original size:40 final size:39
Alignment explanation
Indices: 17258273--17258490 Score: 165
Period size: 40 Copynumber: 5.5 Consensus size: 39
17258263 AAATCACGTA
* * **
17258273 CCTTCGGGATTTAA-CCGGATATAGCTCCTCGTTCA-AATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCG--CACAATG
* * * * *
17258312 CCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCACAATG
* *
17258351 CCTTCGGGACATAACCCGGATTTAACAACTCGCACGAATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCAC-AATG
* * *
17258391 CCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCAC-AATG
* * * * *
17258431 CCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCACAAAG
1 CCTTCGGGA-CTTAACCCGGATTTA-GCAAC-TCGCACAATG
*
17258471 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAACCCGGA
17258491 CAGCATTCAA
Statistics
Matches: 143, Mismatches: 29, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
38 2 0.01
39 48 0.34
40 85 0.59
41 8 0.06
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (39 bp):
CCTTCGGGACTTAACCCGGATTTAGCAACTCGCACAATG
Found at i:17268349 original size:13 final size:12
Alignment explanation
Indices: 17268329--17268368 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 12
17268319 CAACTTCAAA
17268329 TCAAATTTTTTT
1 TCAAATTTTTTT
17268341 TCGAAATTTTTTTT
1 TC-AAA-TTTTTTT
17268355 TCAAGATTTTTTT
1 TCAA-ATTTTTTT
17268368 T
1 T
17268369 ACTACAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.08
13 13 0.52
14 10 0.40
ACGTcount: A:0.23, C:0.07, G:0.05, T:0.65
Consensus pattern (12 bp):
TCAAATTTTTTT
Found at i:17268353 original size:14 final size:14
Alignment explanation
Indices: 17268334--17268368 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
17268324 TCAAATCAAA
17268334 TTTTTTTTCGAA-AT
1 TTTTTTTTC-AAGAT
17268348 TTTTTTTTCAAGAT
1 TTTTTTTTCAAGAT
17268362 TTTTTTT
1 TTTTTTT
17268369 ACTACAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 2 0.10
14 18 0.90
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.71
Consensus pattern (14 bp):
TTTTTTTTCAAGAT
Found at i:17273374 original size:43 final size:43
Alignment explanation
Indices: 17273284--17273390 Score: 119
Period size: 43 Copynumber: 2.5 Consensus size: 43
17273274 TGAGATTACT
* * *
17273284 TGTAAGACCATATATGGGATA-TGACATCGATATGAGACTTCG
1 TGTAAGACCATATATGGGATATTGACATCAATATGAGACTCCA
** *
17273326 TGTAAGACCATAGCTGGGATATTGGCATCAATATGAGA-TCCCA
1 TGTAAGACCATATATGGGATATTGACATCAATATGAGACT-CCA
* *
17273369 TGTAAGACAATATTTGGGATAT
1 TGTAAGACCATATATGGGATAT
17273391 GGGATTGGTA
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
42 20 0.37
43 34 0.63
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (43 bp):
TGTAAGACCATATATGGGATATTGACATCAATATGAGACTCCA
Found at i:17280620 original size:16 final size:16
Alignment explanation
Indices: 17280585--17280626 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
17280575 GTAGATCGGC
*
17280585 AAAAGCCGAAATGCCA
1 AAAAGCTGAAATGCCA
**
17280601 AAAAGCTGAAATGCTG
1 AAAAGCTGAAATGCCA
17280617 AAAAGCTGAA
1 AAAAGCTGAA
17280627 GGCTTGGCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.21, T:0.12
Consensus pattern (16 bp):
AAAAGCTGAAATGCCA
Found at i:17280929 original size:29 final size:28
Alignment explanation
Indices: 17280886--17280963 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 28
17280876 AGATTGAGCC
* *
17280886 ATATGAATGTGAATTGGGCTAGATGGGCA
1 ATATGAATG-AAATTGGGCCAGATGGGCA
* *
17280915 ATATGAATGCAAATTGGGCCGGATGGGCC
1 ATATGAATG-AAATTGGGCCAGATGGGCA
* *
17280944 ATATAAATGAGATTGGGCCA
1 ATATGAATGAAATTGGGCCA
17280964 TATGCATGTA
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
28 9 0.22
29 32 0.78
ACGTcount: A:0.32, C:0.12, G:0.32, T:0.24
Consensus pattern (28 bp):
ATATGAATGAAATTGGGCCAGATGGGCA
Found at i:17280993 original size:17 final size:17
Alignment explanation
Indices: 17280971--17281005 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
17280961 CCATATGCAT
*
17280971 GTATGTAGGGGTTTTGG
1 GTATGTAAGGGTTTTGG
17280988 GTATGTAAGGGTTTTGG
1 GTATGTAAGGGTTTTGG
17281005 G
1 G
17281006 CTTAGTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.46, T:0.40
Consensus pattern (17 bp):
GTATGTAAGGGTTTTGG
Found at i:17289033 original size:28 final size:26
Alignment explanation
Indices: 17288958--17289086 Score: 68
Period size: 26 Copynumber: 4.8 Consensus size: 26
17288948 TACTATTATT
*
17288958 TAATAATAATTTA-AAAAAAATTTAAAA
1 TAATAATAATTTATAATAAAA--TAAAA
** * *
17288985 TCTTACATAATTAATGA-AAAATAAAAA
1 TAATA-ATAATTTATAATAAAAT-AAAA
*
17289012 TAATACATAATTTATAATAAAATGCAAA
1 TAATA-ATAATTTATAATAAAAT-AAAA
* * * *
17289040 GAATAAT-ATATATAGTAAAAT-ATA
1 TAATAATAATTTATAATAAAATAAAA
*
17289064 TAATATATAATATATAATAAAAT
1 TAATA-ATAATTTATAATAAAAT
17289087 TTATAAATAA
Statistics
Matches: 80, Mismatches: 16, Indels: 13
0.73 0.15 0.12
Matches are distributed among these distances:
24 6 0.08
25 2 0.03
26 26 0.32
27 22 0.28
28 23 0.29
29 1 0.01
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.33
Consensus pattern (26 bp):
TAATAATAATTTATAATAAAATAAAA
Found at i:17289064 original size:12 final size:12
Alignment explanation
Indices: 17289041--17289136 Score: 70
Period size: 12 Copynumber: 7.6 Consensus size: 12
17289031 AAATGCAAAG
*
17289041 AATAATATATAT
1 AATAAAATATAT
*
17289053 AGTAAAATATAT
1 AATAAAATATAT
17289065 AATATATAATATAT
1 AATA-A-AATATAT
*
17289079 AATAAAATTTAT
1 AATAAAATATAT
17289091 AAATAAAATGA-AT
1 -AATAAAAT-ATAT
*
17289104 AATAATAT-TAT
1 AATAAAATATAT
*
17289115 AATGGATAATATAT
1 AAT--AAAATATAT
17289129 GAATAAAA
1 -AATAAAA
17289137 ATAATATATA
Statistics
Matches: 66, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
11 5 0.08
12 26 0.39
13 18 0.27
14 14 0.21
15 3 0.05
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (12 bp):
AATAAAATATAT
Found at i:17289070 original size:7 final size:7
Alignment explanation
Indices: 17289042--17289193 Score: 66
Period size: 7 Copynumber: 21.3 Consensus size: 7
17289032 AATGCAAAGA
17289042 ATAATAT
1 ATAATAT
17289049 AT-ATAGT
1 ATAATA-T
*
17289056 AAAATAT
1 ATAATAT
17289063 ATAATAT
1 ATAATAT
17289070 ATAATAT
1 ATAATAT
17289077 ATAATA-
1 ATAATAT
*
17289083 A-AATTT
1 ATAATAT
17289089 ATAA-AT
1 ATAATAT
*
17289095 AAAATGAAT
1 ATAAT--AT
17289104 AATAATATT
1 -ATAATA-T
**
17289113 ATAATGG
1 ATAATAT
17289120 ATAATAT
1 ATAATAT
17289127 ATGAATA-
1 AT-AATAT
*
17289134 AAAATA-
1 ATAATAT
17289140 ATATATACT
1 ATA-ATA-T
**
17289149 ATTTTAT
1 ATAATAT
17289156 ATAACTAGT
1 ATAA-TA-T
*
17289165 AT-TTAT
1 ATAATAT
*
17289171 AAAATAT
1 ATAATAT
17289178 ATAATAT
1 ATAATAT
*
17289185 ATAAGAT
1 ATAATAT
17289192 AT
1 AT
17289194 TTAATAAATA
Statistics
Matches: 108, Mismatches: 21, Indels: 32
0.67 0.13 0.20
Matches are distributed among these distances:
5 3 0.03
6 17 0.16
7 59 0.55
8 17 0.16
9 8 0.07
10 4 0.04
ACGTcount: A:0.55, C:0.01, G:0.05, T:0.39
Consensus pattern (7 bp):
ATAATAT
Found at i:17289083 original size:38 final size:37
Alignment explanation
Indices: 17289041--17289193 Score: 93
Period size: 41 Copynumber: 4.0 Consensus size: 37
17289031 AAATGCAAAG
17289041 AATAATATATATAGTAAAATATATAATATATAATATAT
1 AATAATATATATA-TAAAATATATAATATATAATATAT
* *
17289079 AATAA-A-ATTTAT-AAATAAAATGAATA-ATAATATTAT
1 AATAATATATATATAAAAT-ATAT-AATATATAATA-TAT
* * * *
17289115 AATGGATA-ATATATGAATAA-AAATAATATATACTATTTT
1 AAT-AATATATATAT-AA-AATATATAATATATAATA-TAT
* *
17289154 ATATAACTAGTATTTATAAAATATATAATATATAAGATAT
1 A-ATAA-TA-TATATATAAAATATATAATATATAATATAT
17289194 TTAATAAATA
Statistics
Matches: 89, Mismatches: 12, Indels: 26
0.70 0.09 0.20
Matches are distributed among these distances:
34 4 0.04
35 10 0.11
36 14 0.16
37 2 0.02
38 15 0.17
39 14 0.16
40 9 0.10
41 16 0.18
42 5 0.06
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.39
Consensus pattern (37 bp):
AATAATATATATATAAAATATATAATATATAATATAT
Found at i:17290738 original size:44 final size:44
Alignment explanation
Indices: 17290690--17291152 Score: 676
Period size: 44 Copynumber: 10.5 Consensus size: 44
17290680 ACTCACGAAC
** *
17290690 GCCAAATCTATTATC-TCTGATCTGCTCTTTGACAATACAGAGAT
1 GCCAAATCTGCTATCTTC-GATCTGCTCTCTGACAATACAGAGAT
* * * * *
17290734 GCCAAATCTGTTGTCTTTGATCTACTCTCTGACAATACAGGGAT
1 GCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGAT
* *
17290778 GCCAAATCCGCTATCTTCGATATGCTCTCTGACAATACAGAGAT
1 GCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGAT
*
17290822 GCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGAC
1 GCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGAT
*
17290866 GCCAAATTTGCTATCTTCGATCTGCTCTCTGACAATACAGAGAT
1 GCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGAT
* * *
17290910 GCCACATCTGCTATCTTCGATTTGCTCTCTGACAATACAGAGAC
1 GCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGAT
* * * *
17290954 ACCAAATCTTCTATCTTCGATCTGCTCTTTGACAATACAAAGAT
1 GCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGAT
* *
17290998 GCCAAATCTACTATCTTCGATCTGCTCTTTGACAATACAGAGAT
1 GCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGAT
*
17291042 GCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGAC
1 GCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGAT
* *
17291086 GCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATATAGATAT
1 GCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGAT
* *
17291130 GCCAAATCAGTTATCTTCGATCT
1 GCCAAATCTGCTATCTTCGATCT
17291153 ACATTGTCCT
Statistics
Matches: 378, Mismatches: 40, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
44 377 1.00
45 1 0.00
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (44 bp):
GCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGAT
Found at i:17306991 original size:21 final size:21
Alignment explanation
Indices: 17306966--17307006 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17306956 GTTAGGGCTA
17306966 AATTG-AATAAAATAAAAATGG
1 AATTGTAA-AAAATAAAAATGG
*
17306987 AATTGTAAATAATAAAAATG
1 AATTGTAAAAAATAAAAATG
17307007 AGGGAGAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.61, C:0.00, G:0.12, T:0.27
Consensus pattern (21 bp):
AATTGTAAAAAATAAAAATGG
Found at i:17308792 original size:57 final size:55
Alignment explanation
Indices: 17308725--17308870 Score: 150
Period size: 57 Copynumber: 2.5 Consensus size: 55
17308715 GTGAGCATGA
**
17308725 ATATAATGTGATTTGGGCCGGATGGGCCATATAAATGAG-ATTGGGCTTAATGGGCC
1 ATATAATGTGA-TTGGGCC-GATGGGCCATATAAATGAGAATTGGGCCGAATGGGCC
* * * *
17308781 ATATGAATGTGAATTGGGCATGATGGGCCATATGAATGCGAATTGGGCCGGATGGGCC
1 ATAT-AATGTG-ATTGGGC-CGATGGGCCATATAAATGAGAATTGGGCCGAATGGGCC
* *
17308839 ATATAAATGAGATTGGGCCTAGTGGGCCATAT
1 ATAT-AATGTGATTGGGCCGA-TGGGCCATAT
17308871 GCATGTATGT
Statistics
Matches: 75, Mismatches: 10, Indels: 9
0.80 0.11 0.10
Matches are distributed among these distances:
56 5 0.07
57 46 0.61
58 24 0.32
ACGTcount: A:0.27, C:0.13, G:0.33, T:0.27
Consensus pattern (55 bp):
ATATAATGTGATTGGGCCGATGGGCCATATAAATGAGAATTGGGCCGAATGGGCC
Found at i:17308806 original size:29 final size:29
Alignment explanation
Indices: 17308725--17308876 Score: 159
Period size: 29 Copynumber: 5.3 Consensus size: 29
17308715 GTGAGCATGA
* *
17308725 ATAT-AATGTGATTTGGGCCGGATGGGCC
1 ATATGAATGTGAATTGGGCCTGATGGGCC
* * * *
17308753 ATATAAATGAG-ATTGGGCTTAATGGGCC
1 ATATGAATGTGAATTGGGCCTGATGGGCC
*
17308781 ATATGAATGTGAATTGGGCATGATGGGCC
1 ATATGAATGTGAATTGGGCCTGATGGGCC
* *
17308810 ATATGAATGCGAATTGGGCCGGATGGGCC
1 ATATGAATGTGAATTGGGCCTGATGGGCC
* *
17308839 ATATAAATGAG-ATTGGGCCT-AGTGGGCC
1 ATATGAATGTGAATTGGGCCTGA-TGGGCC
*
17308867 ATATGCATGT
1 ATATGAATGT
17308877 ATGTAGGGGT
Statistics
Matches: 103, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
27 1 0.01
28 47 0.46
29 55 0.53
ACGTcount: A:0.27, C:0.13, G:0.33, T:0.27
Consensus pattern (29 bp):
ATATGAATGTGAATTGGGCCTGATGGGCC
Found at i:17311140 original size:36 final size:36
Alignment explanation
Indices: 17311088--17311204 Score: 144
Period size: 36 Copynumber: 3.1 Consensus size: 36
17311078 GTTAGTTGAG
*
17311088 ATTACGTGTAAGACCATACTGGGATATGGCATCGAT
1 ATTACGTGTAAAACCATACTGGGATATGGCATCGAT
17311124 ATTACGTGTAAAACCATACTGGGATATGGCATCGAT
1 ATTACGTGTAAAACCATACTGGGATATGGCATCGAT
* *
17311160 ATGAGACTTCGTGTAAAACCATAACTGGGCTATTGGCATCGAT
1 AT-----TACGTGTAAAACCAT-ACTGGGATA-TGGCATCGAT
17311203 AT
1 AT
17311205 GAGACCCCAT
Statistics
Matches: 71, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
36 37 0.52
41 14 0.20
42 8 0.11
43 12 0.17
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (36 bp):
ATTACGTGTAAAACCATACTGGGATATGGCATCGAT
Found at i:17311206 original size:43 final size:41
Alignment explanation
Indices: 17311084--17311240 Score: 164
Period size: 43 Copynumber: 3.9 Consensus size: 41
17311074 TAGGGTTAGT
*
17311084 TGAGA-TTACGTGTAAGACCATACTGGGATATGGCATCGATA
1 TGAGACTT-CGTGTAAAACCATACTGGGATATGGCATCGATA
*
17311125 T-----TACGTGTAAAACCATACTGGGATATGGCATCGATA
1 TGAGACTTCGTGTAAAACCATACTGGGATATGGCATCGATA
*
17311161 TGAGACTTCGTGTAAAACCATAACTGGGCTATTGGCATCGATA
1 TGAGACTTCGTGTAAAACCAT-ACTGGGATA-TGGCATCGATA
** * * *
17311204 TGAGACCCCATGTAAGACCATATTTGGGATATGGCAT
1 TGAGACTTCGTGTAAAACCATA-CTGGGATATGGCAT
17311241 TGCTATGGTA
Statistics
Matches: 98, Mismatches: 10, Indels: 15
0.80 0.08 0.12
Matches are distributed among these distances:
36 33 0.34
37 1 0.01
41 15 0.15
42 15 0.15
43 34 0.35
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.27
Consensus pattern (41 bp):
TGAGACTTCGTGTAAAACCATACTGGGATATGGCATCGATA
Found at i:17311369 original size:20 final size:20
Alignment explanation
Indices: 17311323--17311369 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
17311313 CAGCAAAGTT
*
17311323 TAAGTTGTGAAAGACTATTG
1 TAAGTTGTGAAAGACTATGG
* * *
17311343 TATGTTGTGATAGATTATGG
1 TAAGTTGTGAAAGACTATGG
17311363 TAAGTTG
1 TAAGTTG
17311370 CAAATTTGGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.02, G:0.28, T:0.40
Consensus pattern (20 bp):
TAAGTTGTGAAAGACTATGG
Found at i:17323747 original size:27 final size:27
Alignment explanation
Indices: 17323708--17323768 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
17323698 ATTTGCTAGT
*
17323708 CTAGATCAAGAAAAAAGGTGTCTAGAC
1 CTAGACCAAGAAAAAAGGTGTCTAGAC
*
17323735 CTAGACCAGGAAAAAAGGTGTCTAGAC
1 CTAGACCAAGAAAAAAGGTGTCTAGAC
17323762 CTAGACC
1 CTAGACC
17323769 GGGGAAAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.16
Consensus pattern (27 bp):
CTAGACCAAGAAAAAAGGTGTCTAGAC
Found at i:17328096 original size:29 final size:29
Alignment explanation
Indices: 17328061--17328134 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
17328051 GTTGTGAGAT
* *
17328061 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
* *
17328090 TGGCACTAAGTGTGCGAGTTTAAAGTATA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
17328119 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
17328135 TGGTTGATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 5 0.12
29 35 0.88
ACGTcount: A:0.26, C:0.15, G:0.32, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:17328495 original size:40 final size:40
Alignment explanation
Indices: 17328447--17328629 Score: 233
Period size: 40 Copynumber: 4.6 Consensus size: 40
17328437 TCGAATGATG
*
17328447 TCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
* * *
17328487 TCCGGACTAAATTCCAAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
17328527 TCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
1 TCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
*** * *
17328567 TCCGTG-CTAAACCCCGAAGAGCATTCGTGCTGGTGTTATA
1 TCCG-GACTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
* * * *
17328607 TTCGGGCTAGGTCCCGAAGAGCA
1 TCCGGACTAAGTTCCGAAGAGCA
17328630 ATCATGCTGG
Statistics
Matches: 127, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
39 1 0.01
40 125 0.98
41 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (40 bp):
TCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
Found at i:17334620 original size:14 final size:16
Alignment explanation
Indices: 17334596--17334628 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
17334586 AATTGAAATG
17334596 GAAAAATGAGAGAA-A
1 GAAAAATGAGAGAAGA
17334611 GAAAAA-GAGAGAAGA
1 GAAAAATGAGAGAAGA
17334626 GAA
1 GAA
17334629 GTGTTGTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.03
Consensus pattern (16 bp):
GAAAAATGAGAGAAGA
Found at i:17337383 original size:2 final size:2
Alignment explanation
Indices: 17337376--17337400 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17337366 GAGACTAGTC
17337376 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
17337401 CATGTCATGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17339440 original size:30 final size:30
Alignment explanation
Indices: 17339406--17339466 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
17339396 TCCTTAACTC
17339406 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
17339436 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
17339466 A
1 A
17339467 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:17366827 original size:27 final size:27
Alignment explanation
Indices: 17366797--17367016 Score: 164
Period size: 27 Copynumber: 8.1 Consensus size: 27
17366787 GTAAATCTAC
17366797 AAACCAAGGGTATTTTAGTAATTTTGT
1 AAACCAAGGGTATTTTAGTAATTTTGT
*
17366824 AAACCAATGGTATTTCTA-TAATTTT-T
1 AAACCAAGGGTATTT-TAGTAATTTTGT
*
17366850 AGAAAGTCAAGGGTA-TTTATGTAATTTTGT
1 --AAA-CCAAGGGTATTTTA-GTAATTTTGT
* * **
17366880 AAATC-AGTGGTATTTTGGTAATTTTAC
1 AAACCAAG-GGTATTTTAGTAATTTTGT
*** ** * ***
17366907 AAATTGAGGGTATTTCGGCAATTTCAC
1 AAACCAAGGGTATTTTAGTAATTTTGT
* **
17366934 AAACC-AGTGGTATTTTGGTAATTTTAC
1 AAACCAAG-GGTATTTTAGTAATTTTGT
*
17366961 AAACC-AGGGTATTTTGGTAATTTTGT
1 AAACCAAGGGTATTTTAGTAATTTTGT
17366987 AAACCAAGGGTATTTTAGTAATTTTGT
1 AAACCAAGGGTATTTTAGTAATTTTGT
17367014 AAA
1 AAA
17367017 TTGAGGGTAA
Statistics
Matches: 163, Mismatches: 18, Indels: 24
0.80 0.09 0.12
Matches are distributed among these distances:
26 27 0.17
27 106 0.65
28 15 0.09
29 14 0.09
30 1 0.01
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (27 bp):
AAACCAAGGGTATTTTAGTAATTTTGT
Found at i:17366942 original size:54 final size:54
Alignment explanation
Indices: 17366884--17367025 Score: 171
Period size: 53 Copynumber: 2.6 Consensus size: 54
17366874 TTTTGTAAAT
17366884 CAGTGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGCAATTTCACAAAC
1 CAGTGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGCAATTTCACAAAC
** * * ***
17366938 CAGTGGTATTTTGGTAATTTTACAAA-CCAGGGTATTTTGGTAATTTTGTAAAC
1 CAGTGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGCAATTTCACAAAC
* **
17366991 CAAG-GGTATTTTAGTAATTTTGTAAATTGAGGGTA
1 C-AGTGGTATTTTGGTAATTTTACAAATTGAGGGTA
17367026 AAACAATAAT
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
53 40 0.54
54 34 0.46
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.39
Consensus pattern (54 bp):
CAGTGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGCAATTTCACAAAC
Found at i:17367035 original size:27 final size:27
Alignment explanation
Indices: 17367005--17367133 Score: 141
Period size: 27 Copynumber: 4.8 Consensus size: 27
17366995 GGTATTTTAG
* *
17367005 TAATTTTGTAAATTGAGGGTAAAACAA
1 TAATTCTGTAAATCGAGGGTAAAACAA
* * *
17367032 TAATTCTGTAAATCAAGGGTAAAATAG
1 TAATTCTGTAAATCGAGGGTAAAACAA
* ***
17367059 TAATTCTATAAATCGAGGGTAAAATGG
1 TAATTCTGTAAATCGAGGGTAAAACAA
* *
17367086 TAATTCTGTAAATCGAGGGTCAAACGA
1 TAATTCTGTAAATCGAGGGTAAAACAA
* *
17367113 TAATTATGTAAATCGGGGGTA
1 TAATTCTGTAAATCGAGGGTA
17367134 CTTTGGTAAT
Statistics
Matches: 87, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 87 1.00
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.30
Consensus pattern (27 bp):
TAATTCTGTAAATCGAGGGTAAAACAA
Found at i:17367049 original size:54 final size:54
Alignment explanation
Indices: 17366978--17367105 Score: 148
Period size: 54 Copynumber: 2.4 Consensus size: 54
17366968 GGTATTTTGG
* * *** * * *
17366978 TAATTTTGTAAACCAAGGGTATTTTAGTAATTTTGTAAATTGAGGGTAAAACAA
1 TAATTCTGTAAATCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACAA
***
17367032 TAATTCTGTAAATCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAATGG
1 TAATTCTGTAAATCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACAA
*
17367086 TAATTCTGTAAATCGAGGGT
1 TAATTCTGTAAATCAAGGGT
17367106 CAAACGATAA
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 62 1.00
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34
Consensus pattern (54 bp):
TAATTCTGTAAATCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACAA
Found at i:17367144 original size:54 final size:54
Alignment explanation
Indices: 17366975--17367133 Score: 140
Period size: 54 Copynumber: 2.9 Consensus size: 54
17366965 CAGGGTATTT
* * **** * * *
17366975 TGGTAATTTTGTAAACCAAGGGTATTTTAGTAATTTTGTAAATTGAGGGTAAAA
1 TGGTAATTCTGTAAATCAAGGGTAAAAGAGTAATTATATAAATCGAGGGTAAAA
*** * *
17367029 CAATAATTCTGTAAATCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAA
1 TGGTAATTCTGTAAATCAAGGGTAAAAGAGTAATTATATAAATCGAGGGTAAAA
* * * *
17367083 TGGTAATTCTGTAAATCGAGGGTCAAACGA-TAATTATGTAAATCGGGGGTA
1 TGGTAATTCTGTAAATCAAGGGT-AAAAGAGTAATTATATAAATCGAGGGTA
17367134 CTTTGGTAAT
Statistics
Matches: 84, Mismatches: 20, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
54 80 0.95
55 4 0.05
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (54 bp):
TGGTAATTCTGTAAATCAAGGGTAAAAGAGTAATTATATAAATCGAGGGTAAAA
Found at i:17367171 original size:81 final size:81
Alignment explanation
Indices: 17366993--17367171 Score: 187
Period size: 81 Copynumber: 2.2 Consensus size: 81
17366983 TTGTAAACCA
* * *
17366993 AGGGTATTTTAGTAATTTTGTAAATTGAGGGTAAAACAATAATTCTGTAAATCAAGGGTAAAATA
1 AGGGTATTTTAGTAATTCTGTAAATCGAGGGTAAAACAATAATTATGTAAATCAAGGGTAAAATA
*
17367058 GTAATTCTATAAATCG
66 GTAATTCTACAAATCG
*** * * * ** *** *
17367074 AGGGTAAAATGGTAATTCTGTAAATCGAGGGTCAAACGATAATTATGTAAATCGGGGGTACTTTG
1 AGGGTATTTTAGTAATTCTGTAAATCGAGGGTAAAACAATAATTATGTAAATCAAGGGTAAAATA
* *
17367139 GTAATTTTACAAGTCG
66 GTAATTCTACAAATCG
*
17367155 AGGGTATTTTAATAATT
1 AGGGTATTTTAGTAATT
17367172 GGTAAACTAA
Statistics
Matches: 75, Mismatches: 23, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
81 75 1.00
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (81 bp):
AGGGTATTTTAGTAATTCTGTAAATCGAGGGTAAAACAATAATTATGTAAATCAAGGGTAAAATA
GTAATTCTACAAATCG
Found at i:17369920 original size:31 final size:31
Alignment explanation
Indices: 17369876--17369951 Score: 116
Period size: 31 Copynumber: 2.4 Consensus size: 31
17369866 ACCACTACTA
*
17369876 GGCCGTAGCCCTTTTCATATTTCATAACACTG
1 GGCCGAAG-CCTTTTCATATTTCATAACACTG
**
17369908 GGCCGAAGCCTTTTCATATTTCATATTACTG
1 GGCCGAAGCCTTTTCATATTTCATAACACTG
17369939 GGCCGAAGCCTTT
1 GGCCGAAGCCTTT
17369952 AATTGTAAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
31 34 0.83
32 7 0.17
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.34
Consensus pattern (31 bp):
GGCCGAAGCCTTTTCATATTTCATAACACTG
Found at i:17370235 original size:47 final size:47
Alignment explanation
Indices: 17370170--17370308 Score: 190
Period size: 47 Copynumber: 3.0 Consensus size: 47
17370160 AGCCTCTTTT
* * *
17370170 AATAACTGGGGCAAAAGCCCTTTTTATAACTGGGGCATAATCCCTTC
1 AATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTC
* * * * *
17370217 AATAGCTGGGGCGTAAGCCCTTTTGATAACTAGGGCATAAGCCCTTT
1 AATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTC
*
17370264 AATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCGTAAGCCCTT
1 AATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTT
17370309 TTTCACTTCC
Statistics
Matches: 80, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
46 22 0.28
47 58 0.73
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (47 bp):
AATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTC
Found at i:17370237 original size:23 final size:23
Alignment explanation
Indices: 17370167--17370309 Score: 187
Period size: 23 Copynumber: 6.1 Consensus size: 23
17370157 CCTAGCCTCT
*
17370167 TTTAATAACTGGGGCAAAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
* *
17370190 TTTTTATAACTGGGGCATAATCCC
1 -TTTAATAACTGGGGCATAAGCCC
* * *
17370214 TTCAATAGCTGGGGCGTAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
* *
17370237 TTTTGATAACTAGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
17370261 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
17370284 TTTAATAACTGGGGCGTAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
17370307 TTT
1 TTT
17370310 TTCACTTCCT
Statistics
Matches: 102, Mismatches: 16, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
23 64 0.63
24 38 0.37
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:17370296 original size:70 final size:71
Alignment explanation
Indices: 17370146--17370310 Score: 226
Period size: 70 Copynumber: 2.3 Consensus size: 71
17370136 GCTTTATCAT
* * *
17370146 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTTATAACTGGGGCATAA
1 ATAACTGG-GGCGTAAGCC-CTTTTAATAACTAGGGCAAAAGCCCTTTTAATAACTGGGGCATAA
*
17370210 TCCCTTCA
64 GCCCTTCA
* * *
17370218 ATAGCTGGGGCGTAAGCCCTTTTGATAACTAGGGCATAAGCCC-TTTAATAACTGGGGCATAAGC
1 ATAACTGGGGCGTAAGCCCTTTTAATAACTAGGGCAAAAGCCCTTTTAATAACTGGGGCATAAGC
*
17370282 CCTTTA
66 CCTTCA
17370288 ATAACTGGGGCGTAAGCCCTTTT
1 ATAACTGGGGCGTAAGCCCTTTT
17370311 TCACTTCCTC
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
70 46 0.55
71 26 0.31
72 11 0.13
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.28
Consensus pattern (71 bp):
ATAACTGGGGCGTAAGCCCTTTTAATAACTAGGGCAAAAGCCCTTTTAATAACTGGGGCATAAGC
CCTTCA
Found at i:17370388 original size:20 final size:20
Alignment explanation
Indices: 17370360--17370426 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
17370350 TTATGATTAC
*
17370360 ATCACGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
17370380 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
17370400 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
17370420 ACCATGT
1 ATCATGT
17370427 TTATCAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:17371701 original size:27 final size:27
Alignment explanation
Indices: 17371671--17371735 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
17371661 GGGCATATTC
17371671 GTCATTTTACCATACAAGGG-TATTACG
1 GTCATTTTACCATACAAGGGCT-TTACG
* * *
17371698 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCATTTTACCATACAAGGGCTTTACG
*
17371725 GTCTTTTTACC
1 GTCATTTTACC
17371736 TATTAGGGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCATACAAGGGCTTTACG
Found at i:17371819 original size:27 final size:27
Alignment explanation
Indices: 17371793--17372098 Score: 158
Period size: 27 Copynumber: 11.3 Consensus size: 27
17371783 ATCTACAAAC
* *
17371793 CAAGGGTATTTCAGTAATTTTGTAAAC
1 CAAGGGTATTTTAGTAATTTTGTAAAT
*
17371820 CAATGGTATTTCTA-TAATTTT-TAGAAAGT
1 CAAGGGTATTT-TAGTAATTTTGT--AAA-T
17371849 CAAGGGTA-TTTATGTAATTTTGTAAAT
1 CAAGGGTATTTTA-GTAATTTTGTAAAT
* **
17371876 C-AGTGGTATTTTGGTAATTTTACAAAT
1 CAAG-GGTATTTTAGTAATTTTGTAAAT
** ** ***
17371903 TGAGGGTATTTCGGTAATTTCACAAA-
1 CAAGGGTATTTTAGTAATTTTGTAAAT
* * **
17371929 CTAGTGGTATTTTGGTAATTTTACAAA-
1 CAAG-GGTATTTTAGTAATTTTGTAAAT
* * **
17371956 CTAGTGGTATTTTGGTAATTTTACAAAT
1 CAAG-GGTATTTTAGTAATTTTGTAAAT
* * *
17371984 C-AGGGTATTTTGGTAATTTTGTTAAC
1 CAAGGGTATTTTAGTAATTTTGTAAAT
17372010 CAAGGGTATTTTAGTAATTTTGTAAAT
1 CAAGGGTATTTTAGTAATTTTGTAAAT
* **** * *
17372037 CCAGGGTAAAACAATAATTCTGTAAAT
1 CAAGGGTATTTTAGTAATTTTGTAAAT
*** * *
17372064 CAAGGGTAAAATAGTAATTCTATAAAT
1 CAAGGGTATTTTAGTAATTTTGTAAAT
*
17372091 CGAGGGTA
1 CAAGGGTA
17372099 AAATGGTAAT
Statistics
Matches: 233, Mismatches: 33, Indels: 26
0.80 0.11 0.09
Matches are distributed among these distances:
26 25 0.11
27 178 0.76
28 15 0.06
29 14 0.06
30 1 0.00
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.40
Consensus pattern (27 bp):
CAAGGGTATTTTAGTAATTTTGTAAAT
Found at i:17371935 original size:54 final size:54
Alignment explanation
Indices: 17371872--17372003 Score: 198
Period size: 54 Copynumber: 2.5 Consensus size: 54
17371862 GTAATTTTGT
*
17371872 AAATCAGTGGTATTTTGGTAATTTTACAAATTGAG-GGTATTTCGGTAATTTCAC
1 AAATCAGTGGTATTTTGGTAATTTTACAAACT-AGTGGTATTTCGGTAATTTCAC
* *
17371926 AAA-CTAGTGGTATTTTGGTAATTTTACAAACTAGTGGTATTTTGGTAATTTTAC
1 AAATC-AGTGGTATTTTGGTAATTTTACAAACTAGTGGTATTTCGGTAATTTCAC
17371980 AAATCAG-GGTATTTTGGTAATTTT
1 AAATCAGTGGTATTTTGGTAATTTT
17372004 GTTAACCAAG
Statistics
Matches: 72, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
53 20 0.28
54 51 0.71
55 1 0.01
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.43
Consensus pattern (54 bp):
AAATCAGTGGTATTTTGGTAATTTTACAAACTAGTGGTATTTCGGTAATTTCAC
Found at i:17372099 original size:27 final size:27
Alignment explanation
Indices: 17372021--17372128 Score: 144
Period size: 27 Copynumber: 4.0 Consensus size: 27
17372011 AAGGGTATTT
* * *
17372021 TAGTAATTTTGTAAATCCAGGGTAAAA
1 TAGTAATTCTATAAATCGAGGGTAAAA
* * * *
17372048 CAATAATTCTGTAAATCAAGGGTAAAA
1 TAGTAATTCTATAAATCGAGGGTAAAA
17372075 TAGTAATTCTATAAATCGAGGGTAAAA
1 TAGTAATTCTATAAATCGAGGGTAAAA
*
17372102 TGGTAATTCTATAAATCGAGGGTAAAA
1 TAGTAATTCTATAAATCGAGGGTAAAA
17372129 CGATAATTAT
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 72 1.00
ACGTcount: A:0.44, C:0.08, G:0.19, T:0.30
Consensus pattern (27 bp):
TAGTAATTCTATAAATCGAGGGTAAAA
Found at i:17372135 original size:27 final size:27
Alignment explanation
Indices: 17372032--17372152 Score: 136
Period size: 27 Copynumber: 4.5 Consensus size: 27
17372022 AGTAATTTTG
* * *
17372032 TAAATCCAGGGTAAAACAATAATTCTG
1 TAAATCGAGGGTAAAACGATAATTCTA
* *
17372059 TAAATCAAGGGTAAAA-TAGTAATTCTA
1 TAAATCGAGGGTAAAACGA-TAATTCTA
* *
17372086 TAAATCGAGGGTAAAATGGTAATTCTA
1 TAAATCGAGGGTAAAACGATAATTCTA
* *
17372113 TAAATCGAGGGTAAAACGATAATTATG
1 TAAATCGAGGGTAAAACGATAATTCTA
*
17372140 TAAATCGGGGGTA
1 TAAATCGAGGGTA
17372153 CTTTGGTAAT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
26 1 0.01
27 80 0.99
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.27
Consensus pattern (27 bp):
TAAATCGAGGGTAAAACGATAATTCTA
Found at i:17372136 original size:54 final size:54
Alignment explanation
Indices: 17372022--17372179 Score: 138
Period size: 54 Copynumber: 2.9 Consensus size: 54
17372012 AGGGTATTTT
* * * *** * * *
17372022 AGTAATTTTGTAAATCCAGGGTAAAACAATAATTCTGTAAATCAAGGGTAAAAT
1 AGTAATTATATAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAAG
*
17372076 AGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACG
1 AGTAATTATATAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAA-G
* * *** * * *
17372131 A-TAATTATGTAAATCGGGGGTACTTTGGTAATTTTACAAGTCGAGGGTA
1 AGTAATTATATAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTA
17372180 TTTCAATAAT
Statistics
Matches: 85, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
54 84 0.99
55 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.30
Consensus pattern (54 bp):
AGTAATTATATAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAAG
Found at i:17374230 original size:40 final size:40
Alignment explanation
Indices: 17374158--17374303 Score: 172
Period size: 40 Copynumber: 3.6 Consensus size: 40
17374148 GCTAATCGTT
* *
17374158 CAAATGCCTTCGGGACATAGCCCAG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
17374198 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
17374238 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
17374279 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
17374304 CATCATTCAA
Statistics
Matches: 92, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
39 3 0.03
40 76 0.83
41 13 0.14
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:17380702 original size:21 final size:21
Alignment explanation
Indices: 17380669--17380724 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
17380659 TTGACAGGGG
17380669 CACACGCCTGTGTGGAAGGGTGA
1 CACAC-CC-GTGTGGAAGGGTGA
**
17380692 CATGCCCGTGTGGAAGGGTGA
1 CACACCCGTGTGGAAGGGTGA
17380713 CACACCCGTGTG
1 CACACCCGTGTG
17380725 TCTTCTTAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 24 0.83
22 2 0.07
23 3 0.10
ACGTcount: A:0.20, C:0.25, G:0.38, T:0.18
Consensus pattern (21 bp):
CACACCCGTGTGGAAGGGTGA
Found at i:17382426 original size:47 final size:48
Alignment explanation
Indices: 17382307--17382445 Score: 172
Period size: 48 Copynumber: 2.9 Consensus size: 48
17382297 TACCACAGTT
* * * *
17382307 ATACGTGTAACGTGGTGCTAAGTGAATATACCACGATTACACATATTG
1 ATACATGTAACGTGGTGCTAAGTGGATATACCACGGTTACACATATCG
* * * *
17382355 ATACATGTGACGTGGTGCTAAGTGGATATGCCATGGTTACATATATCG
1 ATACATGTAACGTGGTGCTAAGTGGATATACCACGGTTACACATATCG
* * *
17382403 ATTCAT-TAATGTGGTGCTAAGTGGATATACCACGGTTAAACAT
1 ATACATGTAACGTGGTGCTAAGTGGATATACCACGGTTACACAT
17382446 GTAACGTGGT
Statistics
Matches: 76, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
47 31 0.41
48 45 0.59
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (48 bp):
ATACATGTAACGTGGTGCTAAGTGGATATACCACGGTTACACATATCG
Found at i:17382464 original size:38 final size:38
Alignment explanation
Indices: 17382413--17382485 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
17382403 ATTCATTAAT
17382413 GTGGTGCTAAGTGGATATACCACGGTTAAACATGTAAC
1 GTGGTGCTAAGTGGATATACCACGGTTAAACATGTAAC
* *
17382451 GTGGTGCTAAGTGGATATGCCACGGTTATACATGT
1 GTGGTGCTAAGTGGATATACCACGGTTAAACATGT
17382486 TAATTTGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (38 bp):
GTGGTGCTAAGTGGATATACCACGGTTAAACATGTAAC
Found at i:17388294 original size:167 final size:167
Alignment explanation
Indices: 17388013--17388345 Score: 657
Period size: 167 Copynumber: 2.0 Consensus size: 167
17388003 GGTTGAGCAT
17388013 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGGGGCGGGTTACATGATTTCTTGATTACATAT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGGGGCGGGTTACATGATTTCTTGATTACATAT
17388078 GAGGCACTTATGTGCAAATTATCCGTGTATCCGAGTTGTATTCCGATGTGTTCAACGGGTGAAAT
66 GAGGCACTTATGTGCAAATTATCCGTGTATCCGAGTTGTATTCCGATGTGTTCAACGGGTGAAAT
17388143 TTCTAGTGAAATGAAAGAACACTTAAGATGCAAGCGC
131 TTCTAGTGAAATGAAAGAACACTTAAGATGCAAGCGC
*
17388180 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTAGGGGCGGGTTACATGATTTCTTGATTACATAT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGGGGCGGGTTACATGATTTCTTGATTACATAT
17388245 GAGGCACTTATGTGCAAATTATCCGTGTATCCGAGTTGTATTCCGATGTGTTCAACGGGTGAAAT
66 GAGGCACTTATGTGCAAATTATCCGTGTATCCGAGTTGTATTCCGATGTGTTCAACGGGTGAAAT
17388310 TTCTAGTGAAATGAAAGAACACTTAAGATGCAAGCG
131 TTCTAGTGAAATGAAAGAACACTTAAGATGCAAGCG
17388346 ACGTTTTGGT
Statistics
Matches: 165, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
167 165 1.00
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.31
Consensus pattern (167 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGGGGCGGGTTACATGATTTCTTGATTACATAT
GAGGCACTTATGTGCAAATTATCCGTGTATCCGAGTTGTATTCCGATGTGTTCAACGGGTGAAAT
TTCTAGTGAAATGAAAGAACACTTAAGATGCAAGCGC
Found at i:17392445 original size:47 final size:47
Alignment explanation
Indices: 17392388--17392517 Score: 163
Period size: 47 Copynumber: 2.8 Consensus size: 47
17392378 GTGCGAATAA
* * *
17392388 TACCTTGATTTGGCTACGGACCATGGTATAGGTATTTTGAGAGGAGC
1 TACCTTGATTTGGCTACGGACCATGGTATAGGTACTCTGAGAGAAGC
* * * * *
17392435 TACTTTGATTTGGCTATGGGCCATGGTATAGGTACTCTGAGATAAGT
1 TACCTTGATTTGGCTACGGACCATGGTATAGGTACTCTGAGAGAAGC
*
17392482 TACCTTGATTTAGCTAC-GAGCCATGGTATAGGTACT
1 TACCTTGATTTGGCTACGGA-CCATGGTATAGGTACT
17392518 TATCGATTGT
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
46 1 0.01
47 69 0.99
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (47 bp):
TACCTTGATTTGGCTACGGACCATGGTATAGGTACTCTGAGAGAAGC
Found at i:17395016 original size:24 final size:24
Alignment explanation
Indices: 17394984--17395053 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
17394974 CCTCTTTATC
* *
17394984 ATATCCATCTTCACCTTGACCCTT
1 ATATTCATCTTCACCTCGACCCTT
* *
17395008 ATATTCATCTTTATCTCGACCCTT
1 ATATTCATCTTCACCTCGACCCTT
* *
17395032 GTCTTCATCTTCATCCTC-ACCC
1 ATATTCATCTTCA-CCTCGACCC
17395054 CTGTCTTCAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
24 34 0.92
25 3 0.08
ACGTcount: A:0.19, C:0.37, G:0.04, T:0.40
Consensus pattern (24 bp):
ATATTCATCTTCACCTCGACCCTT
Found at i:17395058 original size:24 final size:24
Alignment explanation
Indices: 17395011--17395065 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
17395001 GACCCTTATA
* *
17395011 TTCATCTTTATCTCGACCCTTGTC
1 TTCATCTTCATCTCGACCCCTGTC
17395035 TTCATCTTCATCCTC-ACCCCTGTC
1 TTCATCTTCAT-CTCGACCCCTGTC
17395059 TTCATCT
1 TTCATCT
17395066 ATGTACTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 25 0.89
25 3 0.11
ACGTcount: A:0.13, C:0.38, G:0.05, T:0.44
Consensus pattern (24 bp):
TTCATCTTCATCTCGACCCCTGTC
Found at i:17397307 original size:139 final size:140
Alignment explanation
Indices: 17397039--17397330 Score: 482
Period size: 139 Copynumber: 2.1 Consensus size: 140
17397029 AATAGAGAAC
*
17397039 ATAG-ATATAATTAATATATGAATTTGATTCATAAAAAATATTAATTGTATATATTTTACTGAAT
1 ATAGAATATAATTAATATATGAATTTGATTCATAAAAAATATTAATTGTATATATTTTACCGAAT
* * *
17397103 TTATTAATATATAAACAGTTATACTAATTAATTTTGGTCAAAATATAAAAGATATGGAGATTAAT
66 TTATTAATATATAAACAGTTATACTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAAT
17397168 ATTCTTTTGG
131 ATTCTTTTGG
*
17397178 ATAGAATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAAT
1 ATAGAATATAATTAATATATGAATTTGATTCATAAAAAATATTAATTGTATATATTTTACCGAA-
* *
17397243 TTTATT-A-ATATAAATAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAA
65 TTTATTAATATATAAACAGTTATACTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAA
17397306 TATTCTTTTGG
130 TATTCTTTTGG
*
17397317 AAAGAATATAATTA
1 ATAGAATATAATTA
17397331 CTTTTTCTAA
Statistics
Matches: 143, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
139 79 0.55
140 58 0.41
141 6 0.04
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (140 bp):
ATAGAATATAATTAATATATGAATTTGATTCATAAAAAATATTAATTGTATATATTTTACCGAAT
TTATTAATATATAAACAGTTATACTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAAT
ATTCTTTTGG
Found at i:17397398 original size:75 final size:75
Alignment explanation
Indices: 17397305--17397446 Score: 234
Period size: 75 Copynumber: 1.9 Consensus size: 75
17397295 ATGGAAATTA
**
17397305 ATATTCTTTTGGAAAGAATATAATT-ACTTTTTCTAACTTTTC-ATTTGTCTTCTCTATTAATAA
1 ATATTCTTTTGGAAAGAATATAATTCA-TTTTTCTAAC-TTTCAATTTACCTTCTCTATTAATAA
17397368 GGGAATAATCCT
64 GGGAATAATCCT
17397380 ATATTCTTTTGGAAAGAATATAATTCATTTTTCTAACTTTCAATTTACCTTCTCTATTAATAAGG
1 ATATTCTTTTGGAAAGAATATAATTCATTTTTCTAACTTTCAATTTACCTTCTCTATTAATAAGG
17397445 GA
66 GA
17397447 CAAATCTTGG
Statistics
Matches: 63, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
74 4 0.06
75 58 0.92
76 1 0.02
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.46
Consensus pattern (75 bp):
ATATTCTTTTGGAAAGAATATAATTCATTTTTCTAACTTTCAATTTACCTTCTCTATTAATAAGG
GAATAATCCT
Found at i:17402236 original size:43 final size:42
Alignment explanation
Indices: 17402185--17402284 Score: 130
Period size: 43 Copynumber: 2.3 Consensus size: 42
17402175 ATCTGCCAAA
*
17402185 TTTAGCGGCGTTTGT-AAAAAAAGCGTCGCTAAAAGCCTTGACC
1 TTTAGCGGCGTTT-TCAAAAAAA-CGCCGCTAAAAGCCTTGACC
** *
17402228 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAAGCCTTGACC
1 TTTAGCGGCG-TTTTCAAAAAAACGCCGCTAAAAGCCTTGACC
17402271 TTTAGCGGCGTTTT
1 TTTAGCGGCGTTTT
17402285 TTTCCAATAA
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
42 4 0.08
43 40 0.78
44 7 0.14
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (42 bp):
TTTAGCGGCGTTTTCAAAAAAACGCCGCTAAAAGCCTTGACC
Found at i:17409736 original size:27 final size:27
Alignment explanation
Indices: 17409705--17409807 Score: 80
Period size: 27 Copynumber: 3.5 Consensus size: 27
17409695 GTTGGATTTA
*
17409705 AGCACTATGTGTGTGAATTAATTTCTG
1 AGCACTAAGTGTGTGAATTAATTTCTG
* * *
17409732 AGCACTAAGTGTGCGAATGTGTACGAGTTGGATTTA
1 AGCACTAAGTGTGTGAA--T-TA--A-TT---TCTG
*
17409768 AGCACTATGTGTGTGAATTAATTTCTG
1 AGCACTAAGTGTGTGAATTAATTTCTG
17409795 AGCACTAAGTGTG
1 AGCACTAAGTGTG
17409808 CGAAGTCAGT
Statistics
Matches: 58, Mismatches: 9, Indels: 18
0.68 0.11 0.21
Matches are distributed among these distances:
27 29 0.50
29 1 0.02
30 4 0.07
31 1 0.02
32 1 0.02
33 4 0.07
34 1 0.02
36 17 0.29
ACGTcount: A:0.27, C:0.12, G:0.26, T:0.35
Consensus pattern (27 bp):
AGCACTAAGTGTGTGAATTAATTTCTG
Found at i:17409791 original size:63 final size:63
Alignment explanation
Indices: 17409687--17409811 Score: 241
Period size: 63 Copynumber: 2.0 Consensus size: 63
17409677 TGACCATTAA
*
17409687 GTGTGCGAGTTGGATTTAAGCACTATGTGTGTGAATTAATTTCTGAGCACTAAGTGTGCGAAT
1 GTGTACGAGTTGGATTTAAGCACTATGTGTGTGAATTAATTTCTGAGCACTAAGTGTGCGAAT
17409750 GTGTACGAGTTGGATTTAAGCACTATGTGTGTGAATTAATTTCTGAGCACTAAGTGTGCGAA
1 GTGTACGAGTTGGATTTAAGCACTATGTGTGTGAATTAATTTCTGAGCACTAAGTGTGCGAA
17409812 GTCAGTTATT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.26, C:0.11, G:0.28, T:0.34
Consensus pattern (63 bp):
GTGTACGAGTTGGATTTAAGCACTATGTGTGTGAATTAATTTCTGAGCACTAAGTGTGCGAAT
Found at i:17410405 original size:38 final size:38
Alignment explanation
Indices: 17410352--17410543 Score: 294
Period size: 38 Copynumber: 5.0 Consensus size: 38
17410342 TAAGATTTTA
17410352 GTTATAATCCCGCAGGCTTCGTGCTGGTCTTATATCCGG
1 GTTA-AATCCCGCAGGCTTCGTGCTGGTCTTATATCCGG
*
17410391 GTTAAATCTCGCAGGCTTCGTGCTGGTCTTATATCCGG
1 GTTAAATCCCGCAGGCTTCGTGCTGGTCTTATATCCGG
* *
17410429 GTTAAATCCCGCAGGCTTCGTGCTGGTCTTATTTCTGG
1 GTTAAATCCCGCAGGCTTCGTGCTGGTCTTATATCCGG
* *
17410467 GTTAAATCTCGCAGGCTTCGTGCTGGTCTTATATTCGG
1 GTTAAATCCCGCAGGCTTCGTGCTGGTCTTATATCCGG
* * * *
17410505 GTTAAATCCCGCAGGCCTAGTGCTGGTATTATATTCGG
1 GTTAAATCCCGCAGGCTTCGTGCTGGTCTTATATCCGG
17410543 G
1 G
17410544 CCTTTAGGCC
Statistics
Matches: 141, Mismatches: 12, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
38 137 0.97
39 4 0.03
ACGTcount: A:0.16, C:0.23, G:0.27, T:0.34
Consensus pattern (38 bp):
GTTAAATCCCGCAGGCTTCGTGCTGGTCTTATATCCGG
Found at i:17415445 original size:25 final size:25
Alignment explanation
Indices: 17415408--17415502 Score: 129
Period size: 25 Copynumber: 3.8 Consensus size: 25
17415398 CACCGAACAC
* *
17415408 GACATA-TAACTGGAAAGCTTTTGT
1 GACATATTATCTGGAAAGCCTTTGT
**
17415432 GGTATATTATCTGGAAAGCCTTTGT
1 GACATATTATCTGGAAAGCCTTTGT
* *
17415457 GACATCTTATTTGGAAAGCCTTTGT
1 GACATATTATCTGGAAAGCCTTTGT
17415482 GACATATTATCTGGAAAGCCT
1 GACATATTATCTGGAAAGCCT
17415503 GTATGGTGAT
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
24 4 0.07
25 56 0.93
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (25 bp):
GACATATTATCTGGAAAGCCTTTGT
Found at i:17416340 original size:37 final size:34
Alignment explanation
Indices: 17416290--17416361 Score: 81
Period size: 37 Copynumber: 2.0 Consensus size: 34
17416280 AGTTGTGCCA
* *
17416290 TTTTTCTGACCATCTTTCCTCCTCCTCCTTTCTTTTC
1 TTTTTCTCACCATC-TACCTCCTCCT-C-TTCTTTTC
* *
17416327 TTTTTCTCTCCATCTACCTTCTCCTCTTCTTTTC
1 TTTTTCTCACCATCTACCTCCTCCTCTTCTTTTC
17416361 T
1 T
17416362 CCATAGCTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
34 9 0.29
35 1 0.03
36 9 0.29
37 12 0.39
ACGTcount: A:0.06, C:0.38, G:0.01, T:0.56
Consensus pattern (34 bp):
TTTTTCTCACCATCTACCTCCTCCTCTTCTTTTC
Found at i:17417137 original size:8 final size:8
Alignment explanation
Indices: 17417124--17417156 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
17417114 CTAGATCGGC
17417124 AAAAGCCG
1 AAAAGCCG
17417132 AAAAGCC-
1 AAAAGCCG
17417139 AAAATGCCG
1 AAAA-GCCG
17417148 AAAAGCCG
1 AAAAGCCG
17417156 A
1 A
17417157 TATTTTGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 4 0.17
8 15 0.65
9 4 0.17
ACGTcount: A:0.52, C:0.24, G:0.21, T:0.03
Consensus pattern (8 bp):
AAAAGCCG
Found at i:17417612 original size:27 final size:26
Alignment explanation
Indices: 17417571--17417682 Score: 102
Period size: 27 Copynumber: 4.2 Consensus size: 26
17417561 AGGAAGCGTC
17417571 CTGGTGGCTAC-GCCACAATTATCTGAT
1 CTGGTGGCT-CTGCCAC-ATTATCTGAT
*
17417598 CTAGTGGCTCTGCCACATATATCT-ATT
1 CTGGTGGCTCTGCCACAT-TATCTGA-T
*
17417625 CTGGTGGTTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* * * *
17417653 TTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGAT
17417679 CTGG
1 CTGG
17417683 CAGCCATGCT
Statistics
Matches: 70, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
26 8 0.11
27 46 0.66
28 15 0.21
29 1 0.01
ACGTcount: A:0.18, C:0.23, G:0.21, T:0.38
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:17430958 original size:27 final size:27
Alignment explanation
Indices: 17430928--17431105 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
17430918 ATATTGAGTC
* * * *
17430928 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
17430955 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
17430982 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
17431010 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
17431037 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
17431064 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
17431091 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
17431106 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:17431067 original size:82 final size:81
Alignment explanation
Indices: 17430949--17431104 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
17430939 TGCTATATAA
* *
17430949 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
17431014 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
17431031 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
17431095 CACTTAGTGC
65 CACTTAGTGC
17431105 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:17434416 original size:40 final size:40
Alignment explanation
Indices: 17434333--17434556 Score: 285
Period size: 40 Copynumber: 5.5 Consensus size: 40
17434323 ACCCAAGTAT
* * *
17434333 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGT
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* **
17434372 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
17434412 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
17434452 CTTCGGGACTTAGCCCGGGTATAG-CAACTACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATGC
* *
17434495 CTTCGGGACTTAACCCGGATATAGTAACTTA-CACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCAC-TAGCACAAATGC
17434535 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
17434557 CATCCGAATA
Statistics
Matches: 163, Mismatches: 14, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
39 12 0.07
40 114 0.70
41 1 0.01
43 34 0.21
44 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:17434530 original size:83 final size:80
Alignment explanation
Indices: 17434333--17434556 Score: 274
Period size: 83 Copynumber: 2.8 Consensus size: 80
17434323 ACCCAAGTAT
* * * ** * *
17434333 CTTCGGGA-TTTAGCCGGATATAGCAACTCGCACAAATGTCTTCGGGTCTTAGCCCGGATATAGT
1 CTTCGGGACTTAACCCGGATATAGTAACTTACACAAATGCCTTCGGGACTTAGCCCGGATATAGT
**
17434397 CACTAGCATGAATGC
66 CACTAGCACAAATGC
* * *
17434412 CTTCGGGACTTAGCCCGGATATAGTCAC-TAGCACAAATGCCTTCGGGACTTAGCCCGGGTATAG
1 CTTCGGGACTTAACCCGGATATAGTAACTTA-CACAAATGCCTTCGGGACTTAGCCCGGATATAG
17434476 -CAACTACTCGCACAAATGC
65 TC-ACTA---GCACAAATGC
17434495 CTTCGGGACTTAACCCGGATATAGTAACTTACACAAATGCCTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAACCCGGATATAGTAACTTACACAAATGCCTTCGGGACTTAGCCCGGATAT
17434557 CATCCGAATA
Statistics
Matches: 123, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
79 9 0.07
80 48 0.39
83 64 0.52
84 2 0.02
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (80 bp):
CTTCGGGACTTAACCCGGATATAGTAACTTACACAAATGCCTTCGGGACTTAGCCCGGATATAGT
CACTAGCACAAATGC
Found at i:17443039 original size:21 final size:20
Alignment explanation
Indices: 17443015--17443079 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
17443005 AAGTCTAGCT
*
17443015 GAAGCACATAAGTGCTACACG
1 GAAGCACACAAGTGCTA-ACG
*
17443036 GAAGC-C-CGAAG-GCTAACT
1 GAAGCACAC-AAGTGCTAACG
17443054 GAAGCACACAAGTGCTAAACG
1 GAAGCACACAAGTGCT-AACG
17443075 GAAGC
1 GAAGC
17443080 CCGAAGGCTA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
18 7 0.19
19 8 0.22
20 8 0.22
21 13 0.36
ACGTcount: A:0.38, C:0.25, G:0.26, T:0.11
Consensus pattern (20 bp):
GAAGCACACAAGTGCTAACG
Found at i:17443040 original size:39 final size:39
Alignment explanation
Indices: 17442997--17443097 Score: 166
Period size: 39 Copynumber: 2.6 Consensus size: 39
17442987 ATCGTGATCT
* * * *
17442997 GAAGCCCGAAGTCTAGCTGAAGCACATAAGTGCTACACG
1 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
17443036 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
17443075 GAAGCCCGAAGGCTAACTGAAGC
1 GAAGCCCGAAGGCTAACTGAAGC
17443098 TTATCAAAGC
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 58 1.00
ACGTcount: A:0.36, C:0.26, G:0.27, T:0.12
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
Found at i:17444901 original size:46 final size:46
Alignment explanation
Indices: 17444851--17444944 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
17444841 GCCCTTGCCG
17444851 TCCAGCCCAAATAGACCTTAGGTCTATTTGCTTTTTAAACCCTCTT
1 TCCAGCCCAAATAGACCTTAGGTCTATTTGCTTTTTAAACCCTCTT
*
17444897 TCCAGCCCAAATAGACCTTGGGTCTATTTGCTTTTTAAACCCTCTT
1 TCCAGCCCAAATAGACCTTAGGTCTATTTGCTTTTTAAACCCTCTT
17444943 TC
1 TC
17444945 TTTTATCATT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.22, C:0.29, G:0.12, T:0.37
Consensus pattern (46 bp):
TCCAGCCCAAATAGACCTTAGGTCTATTTGCTTTTTAAACCCTCTT
Found at i:17446579 original size:4 final size:4
Alignment explanation
Indices: 17446570--17446596 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
17446560 TAAGTTAAAA
17446570 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
17446597 TAGAAAAGGG
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:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:17453132 original size:4 final size:4
Alignment explanation
Indices: 17453123--17453203 Score: 72
Period size: 4 Copynumber: 19.8 Consensus size: 4
17453113 TAAGTTAAAA
* *** * *
17453123 AAAG AAAG AAAG AAAG AAAG AAAG ATAG AAAG AGTT ACAG AGAG CAAACG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG -AAA-G
**
17453173 TGAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
17453204 TAGAAAAGGG
Statistics
Matches: 61, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
4 57 0.93
5 3 0.05
6 1 0.02
ACGTcount: A:0.65, C:0.04, G:0.26, T:0.05
Consensus pattern (4 bp):
AAAG
Found at i:17454575 original size:176 final size:176
Alignment explanation
Indices: 17454281--17454632 Score: 686
Period size: 176 Copynumber: 2.0 Consensus size: 176
17454271 TTTGTTTCCG
17454281 TGCGCAGGCTAGGTACGAAAATATAAGGACTCAGCATACAAGCCGATCCCCAAACTCAAATTGGT
1 TGCGCAGGCTAGGTACGAAAATATAAGGACTCAGCATACAAGCCGATCCCCAAACTCAAATTGGT
17454346 GAAATTTCTATCTTTTTGGAAAATGGCATTGTACCTAGGATGTCTTTTGGTCATTTTGAAAGTAT
66 GAAATTTCTATCTTTTTGGAAAATGGCATTGTACCTAGGATGTCTTTTGGTCATTTTGAAAGTAT
17454411 CTAAGTTGTTAAGTGATATTTTGGTATGTTTTGTAAATGTTACCAA
131 CTAAGTTGTTAAGTGATATTTTGGTATGTTTTGTAAATGTTACCAA
* *
17454457 TGCGCAGGCTAGGTACGAAAGTATAAGGACTCAGCATACAAGCCGATCCCCGAACTCAAATTGGT
1 TGCGCAGGCTAGGTACGAAAATATAAGGACTCAGCATACAAGCCGATCCCCAAACTCAAATTGGT
17454522 GAAATTTCTATCTTTTTGGAAAATGGCATTGTACCTAGGATGTCTTTTGGTCATTTTGAAAGTAT
66 GAAATTTCTATCTTTTTGGAAAATGGCATTGTACCTAGGATGTCTTTTGGTCATTTTGAAAGTAT
17454587 CTAAGTTGTTAAGTGATATTTTGGTATGTTTTGTAAATGTTACCAA
131 CTAAGTTGTTAAGTGATATTTTGGTATGTTTTGTAAATGTTACCAA
17454633 AACCTTAAGT
Statistics
Matches: 174, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
176 174 1.00
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.35
Consensus pattern (176 bp):
TGCGCAGGCTAGGTACGAAAATATAAGGACTCAGCATACAAGCCGATCCCCAAACTCAAATTGGT
GAAATTTCTATCTTTTTGGAAAATGGCATTGTACCTAGGATGTCTTTTGGTCATTTTGAAAGTAT
CTAAGTTGTTAAGTGATATTTTGGTATGTTTTGTAAATGTTACCAA
Found at i:17462344 original size:31 final size:30
Alignment explanation
Indices: 17462279--17462345 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
17462269 AAGGGTTAGT
* ** * *
17462279 GTGACTGTTTTGTTATTTTTCGAAAGTTGG
1 GTGACTGTTTTGTTACTACTCCAAAGTTGA
17462309 GTGACTGTTTTGTTAGCTACTCCAAAGTTGA
1 GTGACTGTTTTGTTA-CTACTCCAAAGTTGA
17462340 GTGACT
1 GTGACT
17462346 ATTAGTGTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 15 0.48
31 16 0.52
ACGTcount: A:0.19, C:0.12, G:0.25, T:0.43
Consensus pattern (30 bp):
GTGACTGTTTTGTTACTACTCCAAAGTTGA
Found at i:17470080 original size:6 final size:6
Alignment explanation
Indices: 17470058--17470107 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
17470048 AATATAGTTC
* * * * *
17470058 AAAATA TAAAGA AAAATA AAAATA AAACTA AAAATA ACAATA AACATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
17470106 AA
1 AA
17470108 GACAAATGGA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.76, C:0.06, G:0.02, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:17477735 original size:47 final size:47
Alignment explanation
Indices: 17477665--17477824 Score: 266
Period size: 47 Copynumber: 3.4 Consensus size: 47
17477655 ACCTTCGAGA
*
17477665 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
* * * *
17477712 CTTATCACATATATACACCTTCACATCCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
*
17477759 CTTATCTCATATATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
17477806 CTTATCACATATATACACT
1 CTTATCACATATATACACT
17477825 ATTGATCACA
Statistics
Matches: 102, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 102 1.00
ACGTcount: A:0.28, C:0.31, G:0.07, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
Found at i:17478178 original size:47 final size:47
Alignment explanation
Indices: 17478109--17478217 Score: 173
Period size: 47 Copynumber: 2.3 Consensus size: 47
17478099 ACCTTCGAGA
* * * *
17478109 CTTATCACATTTATACGCTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
17478156 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
17478203 CTTGTCACATATATA
1 CTTATCACATATATA
17478218 TATCTTGTAC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 57 1.00
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.35
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:17478216 original size:444 final size:444
Alignment explanation
Indices: 17477380--17478217 Score: 1613
Period size: 444 Copynumber: 1.9 Consensus size: 444
17477370 GAAGTTATAA
17477380 TATTGATCACATTTACATACCTTTTTTATACTAATAATTCACTTTGAAATCAATCCACCGACGAG
1 TATTGATCACATTTACATACCTTTTTTATACTAATAATTCACTTTGAAATCAATCCACCGACGAG
17477445 TAAGTAATACGTACCTGAACATCTTTAAATACGTAATACTTATTTGATGGTAACTTACTGCGGAT
66 TAAGTAATACGTACCTGAACATCTTTAAATACGTAATACTTATTTGATGGTAACTTACTGCGGAT
17477510 ACTCAATATCAAAGTCTTACTTGAATCTTCGGGTCTTCAAAACCCGGATATAGTACGAGCACGAA
131 ACTCAATATCAAAGTCTTACTTGAATCTTCGGGTCTTCAAAACCCGGATATAGTACGAGCACGAA
17477575 TCATACGGACATTAATTCAGAATAATATTCCCGCATAAAGCCTGCGGGATCTTAACCCGGATATA
196 TCATACGGACATTAATTCAGAATAATATTCCCGCATAAAGCCTGCGGGATCTTAACCCGGATATA
17477640 GTACTGGCACAAATGACCTTCGAGACTTATCACATTTATACACTTTCACATCCATCACATTGGCC
261 GTACTGGCACAAATGACCTTCGAGACTTATCACATTTATACACTTTCACATCCATCACATTGGCC
* *
17477705 ATTCGGCCTTATCACATATATACACCTTCACATCCATCACATCGGCCATTAGGTCTTATCTCATA
326 ATTCGGCCTTATCACATATATACACCTTCACATCCATCACATCGGCCATTAGGCCTTATCACATA
17477770 TATACACTTTCACATCCATCACATTGGCCATTCGGCCTTATCACATATATACAC
391 TATACACTTTCACATCCATCACATTGGCCATTCGGCCTTATCACATATATACAC
17477824 TATTGATCACATTTACATACCTTTTTTATACTAATAATTCACTTTGAAATCAATCCACCGACGAG
1 TATTGATCACATTTACATACCTTTTTTATACTAATAATTCACTTTGAAATCAATCCACCGACGAG
17477889 TAAGTAATACGTACCTGAACATCTTTAAATACGTAATACTTATTTGATGGTAACTTACTGCGGAT
66 TAAGTAATACGTACCTGAACATCTTTAAATACGTAATACTTATTTGATGGTAACTTACTGCGGAT
17477954 ACTCAATATCAAAGTCTTACTTGAATCTTCGGGTCTTCAAAACCCGGATATAGTACGAGCACGAA
131 ACTCAATATCAAAGTCTTACTTGAATCTTCGGGTCTTCAAAACCCGGATATAGTACGAGCACGAA
17478019 TCATACGGACATTAATTCAGAATAATATTCCCGCATAAAGCCTGCGGGATCTTAACCCGGATATA
196 TCATACGGACATTAATTCAGAATAATATTCCCGCATAAAGCCTGCGGGATCTTAACCCGGATATA
* *
17478084 GTACTGGCACAAATGACCTTCGAGACTTATCACATTTATACGCTTTCACATTCATCACATTGGCC
261 GTACTGGCACAAATGACCTTCGAGACTTATCACATTTATACACTTTCACATCCATCACATTGGCC
* * *
17478149 ATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTGTCACATA
326 ATTCGGCCTTATCACATATATACACCTTCACATCCATCACATCGGCCATTAGGCCTTATCACATA
17478214 TATA
391 TATA
17478218 TATCTTGTAC
Statistics
Matches: 387, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
444 387 1.00
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.31
Consensus pattern (444 bp):
TATTGATCACATTTACATACCTTTTTTATACTAATAATTCACTTTGAAATCAATCCACCGACGAG
TAAGTAATACGTACCTGAACATCTTTAAATACGTAATACTTATTTGATGGTAACTTACTGCGGAT
ACTCAATATCAAAGTCTTACTTGAATCTTCGGGTCTTCAAAACCCGGATATAGTACGAGCACGAA
TCATACGGACATTAATTCAGAATAATATTCCCGCATAAAGCCTGCGGGATCTTAACCCGGATATA
GTACTGGCACAAATGACCTTCGAGACTTATCACATTTATACACTTTCACATCCATCACATTGGCC
ATTCGGCCTTATCACATATATACACCTTCACATCCATCACATCGGCCATTAGGCCTTATCACATA
TATACACTTTCACATCCATCACATTGGCCATTCGGCCTTATCACATATATACAC
Found at i:17493513 original size:29 final size:29
Alignment explanation
Indices: 17493442--17493547 Score: 119
Period size: 29 Copynumber: 3.7 Consensus size: 29
17493432 TTCACATACC
* * *
17493442 TGTATCTGGCCCATTAAGCCC-ATTCATA
1 TGTATATGGCCCATTAGGCCCAAATCATA
17493470 T-TCATATGGCCCATTAGGCCCAAATCACT-
1 TGT-ATATGGCCCATTAGGCCCAAATCA-TA
17493499 TGTATATGGCCCATTAGGCCCAAATCATA
1 TGTATATGGCCCATTAGGCCCAAATCATA
* * *
17493528 TTTATATGGCTCGTTAGGCC
1 TGTATATGGCCCATTAGGCC
17493548 ATGTCACATT
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
27 1 0.01
28 18 0.27
29 46 0.69
30 2 0.03
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.31
Consensus pattern (29 bp):
TGTATATGGCCCATTAGGCCCAAATCATA
Found at i:17493574 original size:18 final size:17
Alignment explanation
Indices: 17493547--17493592 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
17493537 CTCGTTAGGC
* *
17493547 CATGTCACATTCATATT
1 CATGTCACATACAAATT
17493564 CATGCTCACATACAAATT
1 CATG-TCACATACAAATT
*
17493582 CATATCACATA
1 CATGTCACATA
17493593 GCATCAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (17 bp):
CATGTCACATACAAATT
Found at i:17493792 original size:8 final size:8
Alignment explanation
Indices: 17493781--17493832 Score: 68
Period size: 8 Copynumber: 6.5 Consensus size: 8
17493771 ACTTTCGAGT
17493781 TTTCGGCA
1 TTTCGGCA
**
17493789 TTTCGGGT
1 TTTCGGCA
17493797 TTTCGGCA
1 TTTCGGCA
* *
17493805 TTTTGGCT
1 TTTCGGCA
17493813 TTTCGGCA
1 TTTCGGCA
17493821 TTTCGGCA
1 TTTCGGCA
17493829 TTTC
1 TTTC
17493833 AGCTTTTGCC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
8 36 1.00
ACGTcount: A:0.08, C:0.21, G:0.25, T:0.46
Consensus pattern (8 bp):
TTTCGGCA
Found at i:17493798 original size:16 final size:16
Alignment explanation
Indices: 17493773--17493826 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
17493763 GTAGCCAAAC
*
17493773 TTTCGAGTTTTCGGCA
1 TTTCGGGTTTTCGGCA
17493789 TTTCGGGTTTTCGGCA
1 TTTCGGGTTTTCGGCA
* *
17493805 TTTTGGCTTTTCGGCA
1 TTTCGGGTTTTCGGCA
17493821 TTTCGG
1 TTTCGG
17493827 CATTTCAGCT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.07, C:0.19, G:0.28, T:0.46
Consensus pattern (16 bp):
TTTCGGGTTTTCGGCA
Found at i:17493832 original size:16 final size:16
Alignment explanation
Indices: 17493780--17493832 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
17493770 AACTTTCGAG
*
17493780 TTTTCGGCATTTCGGG
1 TTTTCGGCATTTCGGC
*
17493796 TTTTCGGCATTTTGGC
1 TTTTCGGCATTTCGGC
17493812 TTTTCGGCATTTCGGC
1 TTTTCGGCATTTCGGC
*
17493828 ATTTC
1 TTTTC
17493833 AGCTTTTGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.08, C:0.21, G:0.25, T:0.47
Consensus pattern (16 bp):
TTTTCGGCATTTCGGC
Found at i:17497062 original size:15 final size:15
Alignment explanation
Indices: 17497038--17497112 Score: 69
Period size: 15 Copynumber: 5.0 Consensus size: 15
17497028 TTATGATATG
17497038 CTATCTTGGATTTCT
1 CTATCTTGGATTTCT
* * *
17497053 GTACCTTGGATATCT
1 CTATCTTGGATTTCT
* * *
17497068 TTATCTAGGATTCCT
1 CTATCTTGGATTTCT
17497083 CTATCTTGGATTTCT
1 CTATCTTGGATTTCT
* * *
17497098 TTATTTTGGTTTTCT
1 CTATCTTGGATTTCT
17497113 TGTTATCTTC
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 46 1.00
ACGTcount: A:0.15, C:0.17, G:0.15, T:0.53
Consensus pattern (15 bp):
CTATCTTGGATTTCT
Found at i:17497073 original size:30 final size:30
Alignment explanation
Indices: 17497039--17497112 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 30
17497029 TATGATATGC
*
17497039 TATCTTGGATTTCTGTACCTTGGATATCTT
1 TATCTTGGATTTCTCTACCTTGGATATCTT
* * * *
17497069 TATCTAGGATTCCTCTATCTTGGATTTCTT
1 TATCTTGGATTTCTCTACCTTGGATATCTT
* *
17497099 TATTTTGGTTTTCT
1 TATCTTGGATTTCT
17497113 TGTTATCTTC
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.15, C:0.16, G:0.15, T:0.54
Consensus pattern (30 bp):
TATCTTGGATTTCTCTACCTTGGATATCTT
Found at i:17502307 original size:75 final size:75
Alignment explanation
Indices: 17502246--17502457 Score: 271
Period size: 75 Copynumber: 2.8 Consensus size: 75
17502236 CGGTAACGAA
* * * * *
17502246 TGTGAACCCAGCTCTAGTTAGATAATCCTACAATTTTTGCACCCAGTGCTAGTCGGATTAACTGA
1 TGTGAGCCCAGCTCTAGTTGGATAAACCAACAATATTTGCACCCAGTGCTAGTCGGATTAACTGA
*
17502311 TGATAATAAT
66 AGATAATAAT
* * * * * *
17502321 TGTGAGCCCAACTCTAGTTGGATAAACCAATAATATATGAACCCAGTGCTACTCGGATTAATTGA
1 TGTGAGCCCAGCTCTAGTTGGATAAACCAACAATATTTGCACCCAGTGCTAGTCGGATTAACTGA
*
17502386 AAATAATAAT
66 AGATAATAAT
* * * *
17502396 TGTGAGCCTAGCTCTAGTTGGATAAACCAACAATATTTCCACCCAATGTTAGTCGGATTAAC
1 TGTGAGCCCAGCTCTAGTTGGATAAACCAACAATATTTGCACCCAGTGCTAGTCGGATTAAC
17502458 CGATAGTTGT
Statistics
Matches: 114, Mismatches: 23, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
75 114 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (75 bp):
TGTGAGCCCAGCTCTAGTTGGATAAACCAACAATATTTGCACCCAGTGCTAGTCGGATTAACTGA
AGATAATAAT
Found at i:17503831 original size:116 final size:117
Alignment explanation
Indices: 17503626--17503859 Score: 452
Period size: 116 Copynumber: 2.0 Consensus size: 117
17503616 TATTTCATCC
17503626 TTGCTCCCCCATTTTGCAGAAACTAGAAGAAAAAAAAAAGGCTTCATCCTCTTTGTTTTTCTTGA
1 TTGCTCCCCCATTTTGCAGAAACTAGAAGAAAAAAAAAAGGCTTCATCCTCTTTGTTTTTCTTGA
17503691 CCGAAAAATCAAAGGAAGAAGAAAGAGCTCTCTTGCTTATGTTCGGTTTGGA
66 CCGAAAAATCAAAGGAAGAAGAAAGAGCTCTCTTGCTTATGTTCGGTTTGGA
*
17503743 TTGCTCCCCCATTTTGCCGAAACTAGAAG-AAAAAAAAAGGCTTCATCCTCTTTGTTTTTCTTGA
1 TTGCTCCCCCATTTTGCAGAAACTAGAAGAAAAAAAAAAGGCTTCATCCTCTTTGTTTTTCTTGA
17503807 CCGAAAAATCAAAGGAAGAAGAAAGAGCTCTCTTGCTTATGTTCGGTTTGGA
66 CCGAAAAATCAAAGGAAGAAGAAAGAGCTCTCTTGCTTATGTTCGGTTTGGA
17503859 T
1 T
17503860 GAGGATTAAG
Statistics
Matches: 116, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
116 88 0.76
117 28 0.24
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (117 bp):
TTGCTCCCCCATTTTGCAGAAACTAGAAGAAAAAAAAAAGGCTTCATCCTCTTTGTTTTTCTTGA
CCGAAAAATCAAAGGAAGAAGAAAGAGCTCTCTTGCTTATGTTCGGTTTGGA
Found at i:17519553 original size:7 final size:7
Alignment explanation
Indices: 17519541--17519565 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
17519531 AGGAAAAAGT
17519541 GAGAGAA
1 GAGAGAA
17519548 GAGAGAA
1 GAGAGAA
17519555 GAGAGAA
1 GAGAGAA
17519562 GAGA
1 GAGA
17519566 TGTGAATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (7 bp):
GAGAGAA
Found at i:17522844 original size:32 final size:32
Alignment explanation
Indices: 17522805--17522865 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
17522795 ACTTCAGTTT
17522805 TTGATAATTTTTACGTTTTTGAGATCATTTTC
1 TTGATAATTTTTACGTTTTTGAGATCATTTTC
17522837 TTGATAATTTTTACGTTTTTGAGATCATT
1 TTGATAATTTTTACGTTTTTGAGATCATT
17522866 GCTTCGAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.23, C:0.08, G:0.13, T:0.56
Consensus pattern (32 bp):
TTGATAATTTTTACGTTTTTGAGATCATTTTC
Found at i:17523933 original size:35 final size:35
Alignment explanation
Indices: 17523867--17523999 Score: 126
Period size: 35 Copynumber: 3.8 Consensus size: 35
17523857 CATAGGTAAG
* * * *
17523867 TATATGTAAGCTTATATTGAACTTGAATATTCGAT
1 TATATGTGAGTTTATATTGAATTTGAATATTCGGT
* **
17523902 TACATGTGAGTTTATATTGAATTTGTGTATTCGGT
1 TATATGTGAGTTTATATTGAATTTGAATATTCGGT
* * * * *
17523937 CATATGTGGAG-TTATCTTGAATGTGCATATTCGGC
1 TATATGT-GAGTTTATATTGAATTTGAATATTCGGT
17523972 TATATGTGATGTTT-TATTGAATTTGAAT
1 TATATGTGA-GTTTATATTGAATTTGAAT
17524000 TATAAGTTAC
Statistics
Matches: 77, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
34 2 0.03
35 70 0.91
36 5 0.06
ACGTcount: A:0.27, C:0.08, G:0.20, T:0.45
Consensus pattern (35 bp):
TATATGTGAGTTTATATTGAATTTGAATATTCGGT
Found at i:17532830 original size:26 final size:26
Alignment explanation
Indices: 17532801--17532853 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
17532791 TGAGAGAGAG
17532801 TTAGGGAGGGAAGAATTTGGATGTTT
1 TTAGGGAGGGAAGAATTTGGATGTTT
17532827 TTAGGGAGGGAAGAATTTGGATGTTT
1 TTAGGGAGGGAAGAATTTGGATGTTT
17532853 T
1 T
17532854 CAAACTCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.38, T:0.36
Consensus pattern (26 bp):
TTAGGGAGGGAAGAATTTGGATGTTT
Done.