Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 9 of 345
Found at i:3111361 original size:44 final size:44
Alignment explanation
Indices: 3111294--3111427 Score: 182
Period size: 44 Copynumber: 3.0 Consensus size: 44
3111284 ACAACATTGG
* * *
3111294 TTTGGCGA-CTCTGTATTGTCAGAGGGCAGATC-AAAGATAGCAGA
1 TTTGGC-ATCTCTGTATTGACAGAGAGCAGATCGAAA-ATAACAGA
*
3111338 TTTGGCATCTCTGTGTTGACAGAGAGCAGATCGAAAATAACAGA
1 TTTGGCATCTCTGTATTGACAGAGAGCAGATCGAAAATAACAGA
* *
3111382 TTTAGCATCTCTGTATTGGCAGAGAGCAGATCGAAAATAACAGA
1 TTTGGCATCTCTGTATTGACAGAGAGCAGATCGAAAATAACAGA
3111426 TT
1 TT
3111428 GGTGCTCCCG
Statistics
Matches: 81, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
43 1 0.01
44 77 0.95
45 3 0.04
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (44 bp):
TTTGGCATCTCTGTATTGACAGAGAGCAGATCGAAAATAACAGA
Found at i:3114689 original size:132 final size:131
Alignment explanation
Indices: 3114365--3114690 Score: 388
Period size: 131 Copynumber: 2.5 Consensus size: 131
3114355 ATCAAATATC
* * *
3114365 CCTTCAAAATTTCACTCATGTCTTCTAAAAACCCTTTAAAACGAAAGCAATACCCGGTGTTTGAT
1 CCTTCAAAATTTCACTCATGTTTTCTAAAAACCCTTTAAAACGAAGGCAATACTCGGTGTTTGAT
* * *
3114430 AATTCGAGAATCATGCCCTATCGTGTTGGGTTGTGATTTCTCTTTTGTTCAAAATAATCGAATAT
66 AATTCGAGAATCATGCCCTATCGTGTTGGGTTGTGATTTCCCTTTTGTTCAAAACAATCGAAGAT
3114495 T
131 T
* *** * * *
3114496 CCTTTAGGTTTTCACTCGTGTTTAT-TAAAAA-CCTTCCAAAACGAAGACAATACTCGGTGTTTG
1 CCTTCAAAATTTCACTCATGTTT-TCTAAAAACCCTT-TAAAACGAAGGCAATACTCGGTGTTTG
* * * *
3114559 ATAATTTGAGAATCGTGCTCTGA-CGTGTTGGGTTGTGATTTCCCGTTTTTTTCAAAACAATCGA
64 ATAATTCGAGAATCATGCCCT-ATCGTGTTGGGTTGTGATTTCCC-TTTTGTTCAAAACAATCGA
3114623 AGATT
127 AGATT
* ** * * *
3114628 CCTTCGAAATTTCACTCACATTTTCTAAAAACCCTTTAAAACGAAGGCGATATTCGATGTTTG
1 CCTTCAAAATTTCACTCATGTTTTCTAAAAACCCTTTAAAACGAAGGCAATACTCGGTGTTTG
3114691 GCAATTCGGG
Statistics
Matches: 159, Mismatches: 30, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
130 4 0.03
131 85 0.53
132 66 0.42
133 4 0.03
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (131 bp):
CCTTCAAAATTTCACTCATGTTTTCTAAAAACCCTTTAAAACGAAGGCAATACTCGGTGTTTGAT
AATTCGAGAATCATGCCCTATCGTGTTGGGTTGTGATTTCCCTTTTGTTCAAAACAATCGAAGAT
T
Found at i:3119605 original size:24 final size:25
Alignment explanation
Indices: 3119573--3119621 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
3119563 ACTGGAGACG
3119573 GGTTACCAT-TCCGCTGCCTTAGTA
1 GGTTACCATCTCCGCTGCCTTAGTA
3119597 GGTTACCATCTCCGCTGCCTTAGTA
1 GGTTACCATCTCCGCTGCCTTAGTA
3119622 TAAGAATCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.16, C:0.31, G:0.20, T:0.33
Consensus pattern (25 bp):
GGTTACCATCTCCGCTGCCTTAGTA
Found at i:3119772 original size:42 final size:42
Alignment explanation
Indices: 3119713--3119796 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
3119703 ATGACACAGC
3119713 TTTGCAATCGAGCTATATACCTTAGAAGTTACAAAAGTGCAG
1 TTTGCAATCGAGCTATATACCTTAGAAGTTACAAAAGTGCAG
3119755 TTTGCAATCGAGCTATATACCTTAGAAGTTACAAAAGTGCAG
1 TTTGCAATCGAGCTATATACCTTAGAAGTTACAAAAGTGCAG
3119797 AAGCTTGAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.29
Consensus pattern (42 bp):
TTTGCAATCGAGCTATATACCTTAGAAGTTACAAAAGTGCAG
Found at i:3133652 original size:2 final size:2
Alignment explanation
Indices: 3133645--3133671 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3133635 CAGCTGAAGC
3133645 AT 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 AT A
3133672 ATAACAAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3140011 original size:16 final size:17
Alignment explanation
Indices: 3139990--3140021 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3139980 AATATATTTT
3139990 TAAAAATATT-ATTAAA
1 TAAAAATATTAATTAAA
3140006 TAAAAATATTAATTAA
1 TAAAAATATTAATTAA
3140022 TCGATTTGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAAATATTAATTAAA
Found at i:3140627 original size:2 final size:2
Alignment explanation
Indices: 3140620--3140650 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3140610 AGATTGAAGA
*
3140620 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3140651 GAATATGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3147610 original size:15 final size:15
Alignment explanation
Indices: 3147583--3147630 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
3147573 AAATGATAAC
*
3147583 ATAAATAACTAAAAT
1 ATAAATAATTAAAAT
* *
3147598 AT-AATATTTTAAAT
1 ATAAATAATTAAAAT
3147612 ATAAATAATTAAAAT
1 ATAAATAATTAAAAT
3147627 ATAA
1 ATAA
3147631 CTTGAAATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
ATAAATAATTAAAAT
Found at i:3147611 original size:14 final size:14
Alignment explanation
Indices: 3147586--3147630 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
3147576 TGATAACATA
*
3147586 AATAACTAAAATAT
1 AATAATTAAAATAT
* *
3147600 AATATTTTAAATAT
1 AATAATTAAAATAT
3147614 AAATAATTAAAATAT
1 -AATAATTAAAATAT
3147629 AA
1 AA
3147631 CTTGAAATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (14 bp):
AATAATTAAAATAT
Found at i:3147644 original size:29 final size:31
Alignment explanation
Indices: 3147578--3147647 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 31
3147568 TAACAAAATG
* *
3147578 ATAACATAAATAACTAAAATATAATATTTTAA
1 ATAA-ATAAATAACTAAAATATAATACTTGAA
*
3147610 AT--ATAAATAATTAAAATAT-A-ACTTGAA
1 ATAAATAAATAACTAAAATATAATACTTGAA
3147637 ATAAATAAATA
1 ATAAATAAATA
3147648 GAAATATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
27 7 0.21
28 1 0.03
29 23 0.70
32 2 0.06
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.33
Consensus pattern (31 bp):
ATAAATAAATAACTAAAATATAATACTTGAA
Found at i:3153466 original size:13 final size:14
Alignment explanation
Indices: 3153450--3153485 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
3153440 CAATCTCATA
3153450 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
3153463 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
3153476 TCTC-ATTTCA
1 TCTCAATTTCA
3153486 TTCCAATAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:3153475 original size:18 final size:19
Alignment explanation
Indices: 3153437--3153477 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
3153427 TGGTTCATGT
3153437 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
3153456 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
3153474 TTTC
1 TTTC
3153478 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:3153664 original size:21 final size:22
Alignment explanation
Indices: 3153636--3153701 Score: 89
Period size: 21 Copynumber: 3.0 Consensus size: 22
3153626 CCTGATCAGT
3153636 ATACGACACATAAAGTGCCTAA
1 ATACGACACATAAAGTGCCTAA
** *
3153658 A-ACGACACACGAGGTGCCTGAA
1 ATACGACACATAAAGTGCCT-AA
3153680 ATACGACACATAAAGTGCCTAA
1 ATACGACACATAAAGTGCCTAA
3153702 TCGGTAAAGC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 15 0.42
22 6 0.17
23 15 0.42
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.15
Consensus pattern (22 bp):
ATACGACACATAAAGTGCCTAA
Found at i:3154013 original size:15 final size:15
Alignment explanation
Indices: 3153988--3154045 Score: 80
Period size: 15 Copynumber: 3.8 Consensus size: 15
3153978 TCATATATAT
3153988 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
*
3154004 TATAAATTCAATTAA
1 TATAAATTCAATCAA
* *
3154019 AATAATTTCAATCAA
1 TATAAATTCAATCAA
3154034 TATAAATTCAAT
1 TATAAATTCAAT
3154046 AAAACAGATA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
15 32 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:3154030 original size:30 final size:28
Alignment explanation
Indices: 3153991--3154049 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 28
3153981 TATATATTAT
3153991 ATAATTCAATCAATATAAATTCAATTAAA
1 ATAATTCAATCAATATAAATTCAA-TAAA
3154020 ATAATTTCAATCAATATAAATTCAATAAA
1 ATAA-TTCAATCAATATAAATTCAATAAA
3154049 A
1 A
3154050 CAGATATTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 9 0.31
30 20 0.69
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (28 bp):
ATAATTCAATCAATATAAATTCAATAAA
Found at i:3154208 original size:2 final size:2
Alignment explanation
Indices: 3154201--3154248 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
3154191 ATATCTCATT
*
3154201 CA CA CA CA CA CA CA CA CA TA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
3154243 CA CA CA
1 CA CA CA
3154249 TATATATATA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.48, G:0.00, T:0.02
Consensus pattern (2 bp):
CA
Found at i:3154253 original size:2 final size:2
Alignment explanation
Indices: 3154248--3154301 Score: 83
Period size: 2 Copynumber: 27.5 Consensus size: 2
3154238 ACACACACAC
*
3154248 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3154290 TT AT A- AT AT AT A
1 AT AT AT AT AT AT A
3154302 ATTCAATTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3157980 original size:2 final size:2
Alignment explanation
Indices: 3157973--3158008 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3157963 AAATAGACAT
3157973 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3158009 AACTATATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3158146 original size:22 final size:22
Alignment explanation
Indices: 3158118--3158163 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
3158108 CTTAGTCTAT
3158118 ATTTATTTTGATTTAAGTTAAA
1 ATTTATTTTGATTTAAGTTAAA
* * *
3158140 ATTTATTTTTATTTAGGTTTAA
1 ATTTATTTTGATTTAAGTTAAA
3158162 AT
1 AT
3158164 ATGTTATGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.59
Consensus pattern (22 bp):
ATTTATTTTGATTTAAGTTAAA
Found at i:3162217 original size:19 final size:21
Alignment explanation
Indices: 3162185--3162224 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
3162175 CCAATTTATT
3162185 ATTTATAGAGATAAATATTAA
1 ATTTATAGAGATAAATATTAA
*
3162206 ATTTATA-A-ATAAATTTTAA
1 ATTTATAGAGATAAATATTAA
3162225 TTCGTTGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 1 0.06
21 7 0.39
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (21 bp):
ATTTATAGAGATAAATATTAA
Found at i:3164886 original size:21 final size:21
Alignment explanation
Indices: 3164833--3164986 Score: 125
Period size: 21 Copynumber: 7.4 Consensus size: 21
3164823 TCGAAAGCTG
* * *
3164833 AACAGAAGCTCGTAAGAGCTA
1 AACAGAAACTCATAAGAGTTA
*
3164854 AAC-GAAAACTCATATGAGTTA
1 AACAG-AAACTCATAAGAGTTA
* * *
3164875 AACAGAAGCTCATAAGAGCTG
1 AACAGAAACTCATAAGAGTTA
* * *
3164896 AATAGAAAATCATAAGAGTTG
1 AACAGAAACTCATAAGAGTTA
* *
3164917 AACAGAAACTCAAAAGAGTTG
1 AACAGAAACTCATAAGAGTTA
*
3164938 AACGGAAACTCATATA-AGTTA
1 AACAGAAACTCATA-AGAGTTA
* * *
3164959 AATAGAAGCTCATAAGAGATA
1 AACAGAAACTCATAAGAGTTA
3164980 AAC-GAAA
1 AACAGAAA
3164987 AGTAAAACAC
Statistics
Matches: 105, Mismatches: 24, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
20 5 0.05
21 98 0.93
22 2 0.02
ACGTcount: A:0.49, C:0.14, G:0.19, T:0.18
Consensus pattern (21 bp):
AACAGAAACTCATAAGAGTTA
Found at i:3164892 original size:42 final size:42
Alignment explanation
Indices: 3164833--3164987 Score: 179
Period size: 42 Copynumber: 3.7 Consensus size: 42
3164823 TCGAAAGCTG
*
3164833 AACAGAAGCTCGTAAGAGCTAAACGAAAACTCATATGAGTTA
1 AACAGAAGCTCATAAGAGCTAAACGAAAACTCATATGAGTTA
* *
3164875 AACAGAAGCTCATAAGAGCTGAATA-GAAAA-TCATAAGAGTTG
1 AACAGAAGCTCATAAGAGCT-AA-ACGAAAACTCATATGAGTTA
* * * * * *
3164917 AACAGAAACTCAAAAGAGTTGAACGGAAACTCATATAAGTTA
1 AACAGAAGCTCATAAGAGCTAAACGAAAACTCATATGAGTTA
* *
3164959 AATAGAAGCTCATAAGAGATAAACGAAAA
1 AACAGAAGCTCATAAGAGCTAAACGAAAA
3164988 GTAAAACACA
Statistics
Matches: 92, Mismatches: 17, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
40 1 0.01
41 5 0.05
42 78 0.85
43 7 0.08
44 1 0.01
ACGTcount: A:0.50, C:0.14, G:0.19, T:0.18
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTAAACGAAAACTCATATGAGTTA
Found at i:3164912 original size:63 final size:63
Alignment explanation
Indices: 3164845--3164987 Score: 146
Period size: 63 Copynumber: 2.3 Consensus size: 63
3164835 CAGAAGCTCG
* * * * *
3164845 TAAGAGCTAAACGAAAACTCATATGAGTTAAACAGAAGCTCATA-AGAGCTGAATAGAAAATCA
1 TAAGAGATAAACGAAAACTCAAAAGAGTTAAACAGAAACTCATATA-AGCTAAATAGAAAATCA
* * * * * **
3164908 TAAGAGTTGAAC-AGAAACTCAAAAGAGTTGAACGGAAACTCATATAAGTTAAATAGAAGCTCA
1 TAAGAGATAAACGA-AAACTCAAAAGAGTTAAACAGAAACTCATATAAGCTAAATAGAAAATCA
3164971 TAAGAGATAAACGAAAA
1 TAAGAGATAAACGAAAA
3164988 GTAAAACACA
Statistics
Matches: 64, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
62 1 0.02
63 61 0.95
64 2 0.03
ACGTcount: A:0.50, C:0.13, G:0.18, T:0.19
Consensus pattern (63 bp):
TAAGAGATAAACGAAAACTCAAAAGAGTTAAACAGAAACTCATATAAGCTAAATAGAAAATCA
Found at i:3182696 original size:88 final size:88
Alignment explanation
Indices: 3182505--3182729 Score: 240
Period size: 88 Copynumber: 2.5 Consensus size: 88
3182495 CAAATATTCA
* *
3182505 AAAAATGAAATAAAATAAATAATTATTATAATTATTTCAAAAAATAAAAAAAATATTTATTGCAT
1 AAAAATGAAATAAAATAAATAATAATTATAATTATTTCAAAAAAT-AAAAAAATATTTATTGCAA
* * *
3182570 CACCAAACTCAAGCCTAATGCCCT
65 CACCAAACTCAAGCCAAATACACT
* **
3182594 AAAAATGAAATAAAATAATTATAATAATTATAATTCTTTCGGAAAAT-AAAAAA-ATTTATT-CA
1 AAAAATGAAATAAAATAA--ATAATAATTATAATTATTTCAAAAAATAAAAAAATATTTATTGCA
* * *
3182656 ACACTAGACTCTAGCCCAAATACACT
64 ACACCAAACTCAAG-CCAAATACACT
* *
3182682 GAAAATGAAATAAAATAAAATAATATTTATTATAATTATTTTAAAAAA
1 AAAAATGAAATAAAAT-AAATAATA---ATTATAATTATTTCAAAAAA
3182730 ATTTATTTTA
Statistics
Matches: 113, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
87 18 0.16
88 30 0.27
89 26 0.23
90 16 0.14
91 23 0.20
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.31
Consensus pattern (88 bp):
AAAAATGAAATAAAATAAATAATAATTATAATTATTTCAAAAAATAAAAAAATATTTATTGCAAC
ACCAAACTCAAGCCAAATACACT
Found at i:3186870 original size:4 final size:4
Alignment explanation
Indices: 3186861--3186887 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3186851 TCAATAGGAC
3186861 CATA CATA CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CAT
3186888 TGTTCCACGA
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:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:3187541 original size:20 final size:20
Alignment explanation
Indices: 3187490--3187529 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3187480 TCTAATATGT
3187490 AAAAATAATATAAGCTAACA
1 AAAAATAATATAAGCTAACA
3187510 AAAAATAATATAAGCTAACA
1 AAAAATAATATAAGCTAACA
3187530 TGATATTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.65, C:0.10, G:0.05, T:0.20
Consensus pattern (20 bp):
AAAAATAATATAAGCTAACA
Found at i:3191220 original size:18 final size:17
Alignment explanation
Indices: 3191187--3191234 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 17
3191177 GAAAATAGCA
3191187 AAAAAAAACTTGAAAAATC
1 AAAAAAAA-TT-AAAAATC
3191206 TAAAAAAAATTAAAAATC
1 -AAAAAAAATTAAAAATC
*
3191224 AAGAAAAATTA
1 AAAAAAAATTA
3191235 TAATATTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 10 0.37
18 7 0.26
19 2 0.07
20 8 0.30
ACGTcount: A:0.71, C:0.06, G:0.04, T:0.19
Consensus pattern (17 bp):
AAAAAAAATTAAAAATC
Found at i:3191735 original size:31 final size:31
Alignment explanation
Indices: 3191694--3191752 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
3191684 AATCTAACAG
* * *
3191694 TTTATATTTAAATCAATCAAATTCAAAAGTA
1 TTTACATTTAAATAAATCAAACTCAAAAGTA
*
3191725 TTTACATTTAAATAAATTAAACTCAAAA
1 TTTACATTTAAATAAATCAAACTCAAAA
3191753 TGGACTCAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (31 bp):
TTTACATTTAAATAAATCAAACTCAAAAGTA
Found at i:3202628 original size:3 final size:3
Alignment explanation
Indices: 3202622--3202647 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3202612 ACAAGAAGAA
3202622 GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GA
3202648 AAGGTGATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:3202660 original size:19 final size:20
Alignment explanation
Indices: 3202633--3202671 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
3202623 ATGATGATGA
3202633 TGATGATGATGATGA-AAGG
1 TGATGATGATGATGAGAAGG
* *
3202652 TGATTATGATTATGAGAAGG
1 TGATGATGATGATGAGAAGG
3202672 AAGCATTGCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.36, C:0.00, G:0.33, T:0.31
Consensus pattern (20 bp):
TGATGATGATGATGAGAAGG
Found at i:3211980 original size:13 final size:13
Alignment explanation
Indices: 3211962--3211989 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3211952 CCTAAAATCA
3211962 ATCCAACCCATGG
1 ATCCAACCCATGG
3211975 ATCCAACCCATGG
1 ATCCAACCCATGG
3211988 AT
1 AT
3211990 TTTGTAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.36, G:0.14, T:0.18
Consensus pattern (13 bp):
ATCCAACCCATGG
Found at i:3217384 original size:2 final size:2
Alignment explanation
Indices: 3217377--3217401 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3217367 GTTTGCAAAA
3217377 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
3217402 AAATAAGAAA
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:3223923 original size:22 final size:22
Alignment explanation
Indices: 3223886--3223928 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3223876 TAACAGAACT
3223886 TTGTTTAATGAATTTAACAATTA
1 TTGTTTAATGAATTTAA-AATTA
3223909 TTGTTTAA-GAATTTAAAATT
1 TTGTTTAATGAATTTAAAATT
3223929 TTAAGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.20
22 8 0.40
23 8 0.40
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (22 bp):
TTGTTTAATGAATTTAAAATTA
Found at i:3225556 original size:41 final size:43
Alignment explanation
Indices: 3225466--3225576 Score: 120
Period size: 41 Copynumber: 2.6 Consensus size: 43
3225456 AAATTTTTAT
* * * *
3225466 TTAATATTTGAAAGTTGAAATAAAAAAAAAACGTGGTATGGAAATA
1 TTAATATTTAAAAGTTGAAAT---AAAAAAACGTCGTATGAAAAAA
*
3225512 TTAATATTTAAAAG-TGAAATAAAAAAA-GTCGTGTGAAAAAA
1 TTAATATTTAAAAGTTGAAATAAAAAAACGTCGTATGAAAAAA
*
3225553 TTAATATTTAGAAGTTGAAA-AAAA
1 TTAATATTTAAAAGTTGAAATAAAA
3225577 TATTTAAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
41 27 0.47
42 12 0.21
45 6 0.10
46 13 0.22
ACGTcount: A:0.54, C:0.02, G:0.15, T:0.29
Consensus pattern (43 bp):
TTAATATTTAAAAGTTGAAATAAAAAAACGTCGTATGAAAAAA
Found at i:3226366 original size:16 final size:17
Alignment explanation
Indices: 3226345--3226378 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3226335 AGAGATTAAT
3226345 TTATTT-TTATATAAAA
1 TTATTTATTATATAAAA
*
3226361 TTATTTATTTTATAAAA
1 TTATTTATTATATAAAA
3226378 T
1 T
3226379 AAATTGTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATTTATTATATAAAA
Found at i:3231555 original size:2 final size:2
Alignment explanation
Indices: 3231548--3231579 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3231538 ACACCTACCC
3231548 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3231580 TTAAATTGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3232051 original size:23 final size:23
Alignment explanation
Indices: 3232025--3232071 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
3232015 GATGAATCCC
3232025 TTTTAAAAATTATAAT-ATATTAA
1 TTTT-AAAATTATAATAATATTAA
* *
3232048 TTTTATAATTATATTAATATTAA
1 TTTTAAAATTATAATAATATTAA
3232071 T
1 T
3232072 AATATTACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTTAAAATTATAATAATATTAA
Found at i:3232060 original size:17 final size:16
Alignment explanation
Indices: 3232034--3232076 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
3232024 CTTTTAAAAA
3232034 TTATAATATATTAATT
1 TTATAATATATTAATT
3232050 TTATAATTATATTAATAT
1 TTATAA-TATATTAAT-T
*
3232068 TAATAATAT
1 TTATAATAT
3232077 TACCATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 6 0.25
17 12 0.50
18 6 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATAATATATTAATT
Found at i:3251383 original size:44 final size:44
Alignment explanation
Indices: 3251333--3251459 Score: 120
Period size: 40 Copynumber: 3.0 Consensus size: 44
3251323 TCCAAAGTCG
* *
3251333 ACTGAATAATTTTTAACATGGAATGTTAAA-CATTGCGGATTTGA
1 ACTGAAT-ATTTTTAACATGGAATGCTAAATCATCGCGGATTTGA
* *** *
3251377 ACTGAATTTTTTTTTTATGGAATGCTAAATCATCGGGGATTTGA
1 ACTGAATATTTTTAACATGGAATGCTAAATCATCGCGGATTTGA
* * *
3251421 ACT-CAT-CTTTT--CATGGAATGCTAAATCATCGGGGATTTG
1 ACTGAATATTTTTAACATGGAATGCTAAATCATCGCGGATTTG
3251460 CTCTGATTTT
Statistics
Matches: 72, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
40 27 0.38
42 4 0.06
43 19 0.26
44 22 0.31
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.39
Consensus pattern (44 bp):
ACTGAATATTTTTAACATGGAATGCTAAATCATCGCGGATTTGA
Found at i:3252216 original size:2 final size:2
Alignment explanation
Indices: 3252211--3252240 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3252201 TGAAGAAATA
3252211 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3252241 TTTAGTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3253715 original size:20 final size:22
Alignment explanation
Indices: 3253676--3253720 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
3253666 AATACAGTTA
*
3253676 ATATTTTAATAATTTAATTACT
1 ATATTTTAATAATTTAATTAAT
*
3253698 ATATTTT-AT-ATTTCATTAAT
1 ATATTTTAATAATTTAATTAAT
3253718 ATA
1 ATA
3253721 AATTATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 2 0.10
22 7 0.33
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (22 bp):
ATATTTTAATAATTTAATTAAT
Found at i:3253717 original size:29 final size:29
Alignment explanation
Indices: 3253676--3253743 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 29
3253666 AATACAGTTA
* * *
3253676 ATATTTTAATAAT-TTAATTACTATATTTT
1 ATATTTCAATAATATAAATTA-TATATGTT
*
3253705 ATATTTCATTAATATAAATTATATATGTT
1 ATATTTCAATAATATAAATTATATATGTT
*
3253734 AAATTT-AATA
1 ATATTTCAATA
3253744 TAAATTAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
28 3 0.09
29 23 0.72
30 6 0.19
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (29 bp):
ATATTTCAATAATATAAATTATATATGTT
Found at i:3253909 original size:2 final size:2
Alignment explanation
Indices: 3253902--3253936 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
3253892 CCTTCCCTTT
* *
3253902 TA TA TA TA TA TA TA TA TT TA TA TA TT TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3253937 TTGATTCACT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:3253923 original size:18 final size:18
Alignment explanation
Indices: 3253900--3253938 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
3253890 TACCTTCCCT
3253900 TTTATATATATATATATA
1 TTTATATATATATATATA
*
3253918 TTTATATATTTATATATA
1 TTTATATATATATATATA
3253936 TTT
1 TTT
3253939 GATTCACTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTATATATATATATATA
Found at i:3254807 original size:22 final size:22
Alignment explanation
Indices: 3254779--3254823 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
3254769 TAACGCAAGG
3254779 TTTAAAAACATAAATATTAAAA
1 TTTAAAAACATAAATATTAAAA
* *
3254801 TTTAAAAATATAAGTATTAAAA
1 TTTAAAAACATAAATATTAAAA
3254823 T
1 T
3254824 ATTTTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
TTTAAAAACATAAATATTAAAA
Found at i:3258757 original size:28 final size:28
Alignment explanation
Indices: 3258717--3258774 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
3258707 CCATAAAGGG
3258717 TAAAACTCATGTATTAATTCTTGGCAAA
1 TAAAACTCATGTATTAATTCTTGGCAAA
3258745 TAAAACTCATGTATTAATTCTTGGCAAA
1 TAAAACTCATGTATTAATTCTTGGCAAA
3258773 TA
1 TA
3258775 TTACACCAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (28 bp):
TAAAACTCATGTATTAATTCTTGGCAAA
Found at i:3264623 original size:21 final size:20
Alignment explanation
Indices: 3264594--3264632 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
3264584 ATACCATAAT
3264594 TTATAAAAATATTTAAAAAA
1 TTATAAAAATATTTAAAAAA
3264614 TTATATAAAATATTTAAAA
1 TTATA-AAAATATTTAAAA
3264633 TATAGAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TTATAAAAATATTTAAAAAA
Found at i:3268034 original size:6 final size:6
Alignment explanation
Indices: 3268023--3268072 Score: 64
Period size: 6 Copynumber: 8.3 Consensus size: 6
3268013 TTTGATCCTC
* * * *
3268023 TACATA TACATA TACATA TACATA TACACA TACACA TACACA TATATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
3268071 TA
1 TA
3268073 TCATCGTGTG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (6 bp):
TACATA
Found at i:3268059 original size:20 final size:20
Alignment explanation
Indices: 3268030--3268068 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3268020 CTCTACATAT
* *
3268030 ACATATACATATACATATAC
1 ACATACACATACACATATAC
3268050 ACATACACATACACATATA
1 ACATACACATACACATATA
3268069 TATATCATCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (20 bp):
ACATACACATACACATATAC
Found at i:3278992 original size:29 final size:29
Alignment explanation
Indices: 3278938--3278994 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
3278928 TACACCAAAG
* **
3278938 TGCAATGATAGAATAGAATGGTACTGAAA
1 TGCAATGATAGAACAGAATGACACTGAAA
3278967 TGCAAT-ATCAGAACAGAATGACACTGAA
1 TGCAATGAT-AGAACAGAATGACACTGAA
3278995 GTTGATACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.46, C:0.12, G:0.21, T:0.21
Consensus pattern (29 bp):
TGCAATGATAGAACAGAATGACACTGAAA
Found at i:3280233 original size:16 final size:15
Alignment explanation
Indices: 3280214--3280248 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3280204 AAGTGATAAA
3280214 AAAAGTACAAAAAAAT
1 AAAA-TACAAAAAAAT
*
3280230 AAAATACGAAAAAAT
1 AAAATACAAAAAAAT
3280245 AAAA
1 AAAA
3280249 AAAAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.77, C:0.06, G:0.06, T:0.11
Consensus pattern (15 bp):
AAAATACAAAAAAAT
Found at i:3280259 original size:11 final size:10
Alignment explanation
Indices: 3280224--3280264 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
3280214 AAAAGTACAA
3280224 AAAAATAAAAT
1 AAAAA-AAAAT
**
3280235 ACGAAAAAAT
1 AAAAAAAAAT
3280245 AAAAAAAAAT
1 AAAAAAAAAT
3280255 AAAAAAAAAT
1 AAAAAAAAAT
3280265 TCTGTGGGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
10 23 0.88
11 3 0.12
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.12
Consensus pattern (10 bp):
AAAAAAAAAT
Found at i:3282179 original size:15 final size:15
Alignment explanation
Indices: 3282159--3282204 Score: 92
Period size: 15 Copynumber: 3.1 Consensus size: 15
3282149 AAATGAGGAG
3282159 TGGTTATGTTTTAAC
1 TGGTTATGTTTTAAC
3282174 TGGTTATGTTTTAAC
1 TGGTTATGTTTTAAC
3282189 TGGTTATGTTTTAAC
1 TGGTTATGTTTTAAC
3282204 T
1 T
3282205 AACTCTAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.20, C:0.07, G:0.20, T:0.54
Consensus pattern (15 bp):
TGGTTATGTTTTAAC
Found at i:3287997 original size:2 final size:2
Alignment explanation
Indices: 3287990--3288015 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3287980 ATGAAATTAA
3287990 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3288016 GTAAATAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3294168 original size:14 final size:14
Alignment explanation
Indices: 3294144--3294176 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3294134 TCCCTGCTTC
3294144 GTTTCTGTTTCTTTT
1 GTTTCTGTTTC-TTT
3294159 GTTT-TGTTTCTTT
1 GTTTCTGTTTCTTT
3294172 GTTTC
1 GTTTC
3294177 CTTAATTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.41
14 6 0.35
15 4 0.24
ACGTcount: A:0.00, C:0.12, G:0.15, T:0.73
Consensus pattern (14 bp):
GTTTCTGTTTCTTT
Found at i:3301958 original size:15 final size:14
Alignment explanation
Indices: 3301940--3301970 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
3301930 TTAATTTATT
3301940 TAATAATAATGCTAA
1 TAATAATAAT-CTAA
3301955 TAATAATAATCTAA
1 TAATAATAATCTAA
3301969 TA
1 TA
3301971 TAAAACCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (14 bp):
TAATAATAATCTAA
Found at i:3301981 original size:21 final size:20
Alignment explanation
Indices: 3301957--3302025 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
3301947 AATGCTAATA
3301957 ATAATAATCTAATATAAAACC
1 ATAATAAT-TAATATAAAACC
* **
3301978 ATAAT-GTTAAT-TAATAATT
1 ATAATAATTAATATAA-AACC
3301997 ATAATAATTTAATATAAAACC
1 ATAATAA-TTAATATAAAACC
3302018 ATAATAAT
1 ATAATAAT
3302026 AATCATTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
18 3 0.08
19 11 0.29
20 2 0.05
21 19 0.50
22 3 0.08
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.36
Consensus pattern (20 bp):
ATAATAATTAATATAAAACC
Found at i:3302474 original size:16 final size:17
Alignment explanation
Indices: 3302439--3302476 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
3302429 TTTCAGTCAT
*
3302439 TTGGGCCAGTTTTGTAA
1 TTGGGCCAGGTTTGTAA
*
3302456 TTGGGTCAGGTTT-TAA
1 TTGGGCCAGGTTTGTAA
3302472 TTGGG
1 TTGGG
3302477 GGTTTCGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.16, C:0.08, G:0.34, T:0.42
Consensus pattern (17 bp):
TTGGGCCAGGTTTGTAA
Found at i:3302609 original size:17 final size:17
Alignment explanation
Indices: 3302589--3302625 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
3302579 CCCATAAATA
3302589 ATTTGGTTTATTATTTT
1 ATTTGGTTTATTATTTT
3302606 ATTTGGTTTATTATTTT
1 ATTTGGTTTATTATTTT
3302623 ATT
1 ATT
3302626 ATTTTTGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.11, T:0.70
Consensus pattern (17 bp):
ATTTGGTTTATTATTTT
Found at i:3318818 original size:129 final size:127
Alignment explanation
Indices: 3318511--3318824 Score: 330
Period size: 127 Copynumber: 2.5 Consensus size: 127
3318501 TATTTAGTCC
* * * * **
3318511 AACAAAAAACCGAAACCCAGCACAGTAGGGCACGATTCCTCGAATTTCTAAACATTGAACATTGC
1 AACAGAAAATCGAAACCCAGCACGGTAGGGCACGATTCCTCGAATTTCCAAACATCAAACATTGC
* *
3318576 CTTGTTTTAAAATTTAGAAAACATGAGTGAAATTCTAAAGGAATATTCGATTATTTTGAACA
66 CTTGTTTTAAAATTTACAAAACAGGAGTGAAATTCTAAAGGAATATTCGATTATTTTGAACA
* * * * *
3318638 AACGGGAAATTGCAACCCAGCACGATAGGGCACGATTCC-CTGAATTTCCAAACATCAAACATTG
1 AACAGAAAATCGAAACCCAGCACGGTAGGGCACGATTCCTC-GAATTTCCAAACATCAAACATTG
* * * * * *
3318702 CCTTCGTTTTAAGGAATTTTCAAAATACGGA-TGAAATT-TCAAATGAATGTTTGATTA-TTTGG
65 CCTT-GTTTTAA--AATTTACAAAACA-GGAGTGAAATTCT-AAAGGAATATTCGATTATTTTGA
* *
3318764 GCG
125 ACA
* * *
3318767 AACAGAAAATCGAAACCCAGCACGGTTGGGCACGATTCCTCGAGTTCCCAAACATCAA
1 AACAGAAAATCGAAACCCAGCACGGTAGGGCACGATTCCTCGAATTTCCAAACATCAA
3318825 CTATTACTTT
Statistics
Matches: 151, Mismatches: 29, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
126 1 0.01
127 55 0.36
128 7 0.05
129 54 0.36
130 32 0.21
131 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.26
Consensus pattern (127 bp):
AACAGAAAATCGAAACCCAGCACGGTAGGGCACGATTCCTCGAATTTCCAAACATCAAACATTGC
CTTGTTTTAAAATTTACAAAACAGGAGTGAAATTCTAAAGGAATATTCGATTATTTTGAACA
Found at i:3321569 original size:42 final size:42
Alignment explanation
Indices: 3321521--3321717 Score: 130
Period size: 42 Copynumber: 4.6 Consensus size: 42
3321511 CGGCCTACTT
* * *
3321521 CACTACTTCTTAGGGAGATAGGATGGTGGCTTAAATCTGCTC
1 CACTACTGCTTAGGGAGACAAGATGGTGGCTTAAATCTGCTC
* ** * **
3321563 CACTACTGGTTAGGGAGACAAGATTCGACGTCTTCGATCTG-TCC
1 CACTACTGCTTAGGGAGACAAGA-T-GGTGGCTTAAATCTGCT-C
** * * * * *
3321607 CACTACAACTTTAGGGAGACAAGAT-CTGCAATCTTCAACCTACTC
1 CACTACTGC-TTAGGGAGACAAGATGGTG---GCTTAAATCTGCTC
* * *
3321652 CACTACTGCTTAGGGAGATAGGATGGTGGCTTAAATCTGTTC
1 CACTACTGCTTAGGGAGACAAGATGGTGGCTTAAATCTGCTC
3321694 CACTACTAGC-TAGGGAGACAAGAT
1 CACTACT-GCTTAGGGAGACAAGAT
3321718 TCACCGTCTT
Statistics
Matches: 116, Mismatches: 29, Indels: 20
0.70 0.18 0.12
Matches are distributed among these distances:
42 48 0.41
43 4 0.03
44 31 0.27
45 32 0.28
46 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.27
Consensus pattern (42 bp):
CACTACTGCTTAGGGAGACAAGATGGTGGCTTAAATCTGCTC
Found at i:3321611 original size:44 final size:45
Alignment explanation
Indices: 3321554--3321761 Score: 150
Period size: 44 Copynumber: 4.8 Consensus size: 45
3321544 TGGTGGCTTA
*
3321554 AATCTG-CTCCACTACTGGTTAGGGAGACAAGATTCGACGTCTTC
1 AATCTGTCTCCACTACTGCTTAGGGAGACAAGATTCGACGTCTTC
* ** *
3321598 GATCTGTC-CCACTACAACTTTAGGGAGACAAGA-TCTG-CAATCTTC
1 AATCTGTCTCCACTACTGC-TTAGGGAGACAAGATTC-GAC-GTCTTC
* * * * ** * *
3321643 AACCT-ACTCCACTACTGCTTAGGGAGATAGGA-T-GGTGGCTTA
1 AATCTGTCTCCACTACTGCTTAGGGAGACAAGATTCGACGTCTTC
3321685 AATCTGT-TCCACTACTAGC-TAGGGAGACAAGATTC-ACCGTCTTC
1 AATCTGTCTCCACTACT-GCTTAGGGAGACAAGATTCGA-CGTCTTC
* * *
3321729 GATCCG-CTCCACTACTGCTTAGGGAGATAAGAT
1 AATCTGTCTCCACTACTGCTTAGGGAGACAAGAT
3321762 CTAAAATTTC
Statistics
Matches: 124, Mismatches: 27, Indels: 26
0.70 0.15 0.15
Matches are distributed among these distances:
42 28 0.23
43 5 0.04
44 59 0.48
45 32 0.26
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.26
Consensus pattern (45 bp):
AATCTGTCTCCACTACTGCTTAGGGAGACAAGATTCGACGTCTTC
Found at i:3321668 original size:131 final size:130
Alignment explanation
Indices: 3321497--3321763 Score: 385
Period size: 131 Copynumber: 2.0 Consensus size: 130
3321487 AGGAGATACG
* ** * *
3321497 AGATTTGCAATCTTCGGCCTACTTCACTACTTCTTAGGGAGATAGGATGGTGGCTTAAATCTGCT
1 AGATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGATGGTGGCTTAAATCTGCT
* * *
3321562 CCACTACTGGTTAGGGAGACAAGATTCGA-CGTCTTCGATCTG-TCCCACTACAACTTTAGGGAG
66 CCACTACTAGCTAGGGAGACAAGATTC-ACCGTCTTCGATCCGCT-CCACTACAAC-TTAGGGAG
3321625 ACA
128 ACA
*
3321628 AGATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGATGGTGGCTTAAATCTGTT
1 AGATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGATGGTGGCTTAAATCTGCT
** *
3321693 CCACTACTAGCTAGGGAGACAAGATTCACCGTCTTCGATCCGCTCCACTACTGCTTAGGGAGATA
66 CCACTACTAGCTAGGGAGACAAGATTCACCGTCTTCGATCCGCTCCACTACAACTTAGGGAGACA
3321758 AGATCT
1 AGATCT
3321764 AAAATTTCTA
Statistics
Matches: 122, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
130 17 0.14
131 104 0.85
132 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (130 bp):
AGATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGATGGTGGCTTAAATCTGCT
CCACTACTAGCTAGGGAGACAAGATTCACCGTCTTCGATCCGCTCCACTACAACTTAGGGAGACA
Found at i:3321818 original size:88 final size:87
Alignment explanation
Indices: 3321718--3322745 Score: 774
Period size: 88 Copynumber: 11.7 Consensus size: 87
3321708 GAGACAAGAT
* * * *
3321718 TCACCGTCTTCGATCCGCTCCACTACTGCTTAGGGAGATAAGATCTAAAATTTCTAACCTGTTAC
1 TCACTGTCTTCGATCCGCTCCACTACTGCTTAGGGAGACAAGATCTACAATTTC-AGCCTGTTAC
* *
3321783 CCCACTGCTTAGGGGGTTAAGGC
65 CCTACTACTTAGGGGGTTAAGGC
* ** *
3321806 TCACCGTCTTCGATTTGCTCCACTACTGCTGAGGGAGACAAGATCTACAATCTTCAGCCTGTTAC
1 TCACTGTCTTCGATCCGCTCCACTACTGCTTAGGGAGACAAGATCTACAAT-TTCAGCCTGTTAC
3321871 CCTACTACTTAGGGGGGTTAAGGC
65 CCTACTACTTA-GGGGGTTAAGGC
* ** *
3321895 TCACTGTCTTTGATTTGCTCCACTACTGCTTAGGGAGACAAGATCTACAATCTTC-GTCTTGTTA
1 TCACTGTCTTCGATCCGCTCCACTACTGCTTAGGGAGACAAGATCTACAAT-TTCAG-CCTGTTA
* *
3321959 CCCTACTACTTAAGGGGTTAAGGG
64 CCCTACTACTTAGGGGGTTAAGGC
* * * ** * *
3321983 TCACTATCTTCGATCCGCTCCACTACTGCTTAGGGAGATAAGAT-TCGCCGTCTTC-GATCTATT
1 TCACTGTCTTCGATCCGCTCCACTACTGCTTAGGGAGACAAGATCT-ACAAT-TTCAG-CCTGTT
* * * * ** *
3322046 -CCACTGCAACTTTAAGGAGACAAGATC
63 ACC-CTACTAC-TTAGGGGGTTAAG-GC
* * * * * * * * * ** *
3322073 TGCA--ATCTTC-AACCTACTCCATTACTGCTTAGGGAGATAGGATGGTGGC---TTAAATCTGC
1 T-CACTGTCTTCGATCC-GCTCCACTACTGCTTAGGGAGACAAGAT-CT-ACAATTTCAGCCTGT
* ** ***
3322132 T-CCACTACTAGC-TAGGGAGACAATAT
62 TACC-CTACTA-CTTAGGGGGTTAAGGC
* * * * * *
3322158 TCGCCGTCTTCGATCCGCTCTACTACTGCTTAGGAAGATAAAATCTGA-AATTTCCAGCCTGTTA
1 TCACTGTCTTCGATCCGCTCCACTACTGCTTAGGGAGACAAGATCT-ACAATTT-CAGCCTGTTA
*
3322222 CCCTACTGCTTAGGGGGTTAAGGC
64 CCCTACTACTTAGGGGGTTAAGGC
* ** * * * * *
3322246 TCACCGTCTTCGATTTGCTCTATTACTGCTGAGGGAGACAAGATCTACAATCTTCGGCCTTTTAC
1 TCACTGTCTTCGATCCGCTCCACTACTGCTTAGGGAGACAAGATCTACAAT-TTCAGCCTGTTAC
*
3322311 CCTACTACTTAGGGGGTTAAAGC
65 CCTACTACTTAGGGGGTTAAGGC
* ** *** * *
3322334 TCACTATCTTTAATTTACTCCACTACTGCTTAGGGAGACAAGATCTACAATCTTCGGCTTGTTAC
1 TCACTGTCTTCGATCCGCTCCACTACTGCTTAGGGAGACAAGATCTACAAT-TTCAGCCTGTTAC
3322399 CCTACTACTTAGGGGGTTAAGGC
65 CCTACTACTTAGGGGGTTAAGGC
* * * *
3322422 TCACTGTCTTCGATCCACTCCACTACTGCTTAGGGAGACAAGATCTACAATCTCTTGCGTGTTAC
1 TCACTGTCTTCGATCCGCTCCACTACTGCTTAGGGAGACAAGATCTACAATTTC-AGCCTGTTAC
*
3322487 CCTACTACTTAAGGGGTTAAGGC
65 CCTACTACTTAGGGGGTTAAGGC
* * * * * *
3322510 TCACTGTCTTCGATCCACTCCACTATTACTTAAGGAGATAATATCTGA-AATTTCCAGCCTGTTA
1 TCACTGTCTTCGATCCGCTCCACTACTGCTTAGGGAGACAAGATCT-ACAATTT-CAGCCTGTTA
*
3322574 -CTTACTACTTAGGGGGTTAAGGC
64 CCCTACTACTTAGGGGGTTAAGGC
** * * * * * * *
3322597 TCACTGTCCCCGATCTGTTCCGCTATTGTTTAGGGAGACAAGATCTATAATTTTCAGCCTGTTAT
1 TCACTGTCTTCGATCCGCTCCACTACTGCTTAGGGAGACAAGATCTACAA-TTTCAGCCTGTTAC
*
3322662 CCTACTGCTTAGGGGGTTAAGGC
65 CCTACTACTTAGGGGGTTAAGGC
* * * ** * * *
3322685 TCA-TAGTCTTTGATCTGCTCCATTACAACTTCAGGAAGGCAAGATCTGCAATCTTCAGCCT
1 TCACT-GTCTTCGATCCGCTCCACTACTGCTT-AGGGAGACAAGATCTACAAT-TTCAGCCT
3322746 ACTTCACTAC
Statistics
Matches: 768, Mismatches: 139, Indels: 65
0.79 0.14 0.07
Matches are distributed among these distances:
84 1 0.00
85 3 0.00
86 38 0.05
87 94 0.12
88 471 0.61
89 155 0.20
90 1 0.00
91 5 0.01
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (87 bp):
TCACTGTCTTCGATCCGCTCCACTACTGCTTAGGGAGACAAGATCTACAATTTCAGCCTGTTACC
CTACTACTTAGGGGGTTAAGGC
Found at i:3321834 original size:44 final size:44
Alignment explanation
Indices: 3321692--3322024 Score: 141
Period size: 44 Copynumber: 7.5 Consensus size: 44
3321682 TTAAATCTGT
* ** **
3321692 TCCACTACTAGC-TAGGGAGACAA-GATTCACCGTCTTCGATCCGC
1 TCCACTACT-GCTTAGGGAGATAAGGA-TCACAATCTTCGATTTGC
* * ** *
3321736 TCCACTACTGCTTAGGGAGATAA-GATCTAAAAT-TTCTAACCTGT
1 TCCACTACTGCTTAGGGAGATAAGGATC-ACAATCTTC-GATTTGC
* * * * **
3321780 TACC-CCACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATTTGC
1 T-CCACTACTGCTTAGGGAGATAAGGATCACAATCTTCGATTTGC
* * ** *
3321824 TCCACTACTGCTGAGGGAGACAA-GATCTACAATCTTC-AGCCTGT
1 TCCACTACTGCTTAGGGAGATAAGGATC-ACAATCTTCGA-TTTGC
* * * * ** *
3321868 TACC-CTACTACTTAGGGGGGTTAAGGCTCACTGTCTTTGATTTGC
1 T-CCACTACTGCTTA-GGGAGATAAGGATCACAATCTTCGATTTGC
* *
3321913 TCCACTACTGCTTAGGGAGACAA-GATCTACAATCTTCG-TCTTGT
1 TCCACTACTGCTTAGGGAGATAAGGATC-ACAATCTTCGAT-TTGC
* * * * **
3321957 TACC-CTACTACTTAAGGG-GTTAAGGGTCACTATCTTCGATCCGC
1 T-CCACTACTGCTT-AGGGAGATAAGGATCACAATCTTCGATTTGC
3322001 TCCACTACTGCTTAGGGAGATAAG
1 TCCACTACTGCTTAGGGAGATAAG
3322025 ATTCGCCGTC
Statistics
Matches: 206, Mismatches: 61, Indels: 44
0.66 0.20 0.14
Matches are distributed among these distances:
43 23 0.11
44 135 0.66
45 44 0.21
46 4 0.02
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (44 bp):
TCCACTACTGCTTAGGGAGATAAGGATCACAATCTTCGATTTGC
Found at i:3322037 original size:44 final size:43
Alignment explanation
Indices: 3321989--3322198 Score: 129
Period size: 44 Copynumber: 4.8 Consensus size: 43
3321979 AGGGTCACTA
3321989 TCTTCGATCCGCTCCACTACTGCTTAGGGAGATAAGATTCGCCG
1 TCTTCGATCCGCTCCACTACTGCTTAGGGAGATAAGA-TCGCCG
*** * ** * * **
3322033 TCTTCGATCTATTCCACTGCAACTTTAAGGAGACAAGATCTGCAA
1 TCTTCGATCCGCTCCACTACTGC-TTAGGGAGATAAGATC-GCCG
* * * * **
3322078 TCTTC-AACCTACTCCATTACTGCTTAGGGAGATAGGAT-GGTG
1 TCTTCGATCC-GCTCCACTACTGCTTAGGGAGATAAGATCGCCG
* ** * * *
3322120 GCTTAAATCTGCTCCACTACTAGC-TAGGGAGACAATATTCGCCG
1 TCTTCGATCCGCTCCACTACT-GCTTAGGGAGATAAGA-TCGCCG
* *
3322164 TCTTCGATCCGCTCTACTACTGCTTAGGAAGATAA
1 TCTTCGATCCGCTCCACTACTGCTTAGGGAGATAA
3322199 AATCTGAAAT
Statistics
Matches: 117, Mismatches: 41, Indels: 16
0.67 0.24 0.09
Matches are distributed among these distances:
42 23 0.20
43 7 0.06
44 60 0.51
45 27 0.23
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.29
Consensus pattern (43 bp):
TCTTCGATCCGCTCCACTACTGCTTAGGGAGATAAGATCGCCG
Found at i:3322404 original size:44 final size:43
Alignment explanation
Indices: 3322277--3322412 Score: 118
Period size: 44 Copynumber: 3.1 Consensus size: 43
3322267 ATTACTGCTG
3322277 AGGGAGACAAGATCTACAATCTTCGGCCTTTTACCCTACTACTT
1 AGGGAGACAAGATCTACAATCTTCGG-CTTTTACCCTACTACTT
* * * *** *
3322321 AGGGGGTTA-AAGCTC-ACTATCTT--TAATTTACTCCACTACTGCTT
1 AGGGAG--ACAAGATCTACAATCTTCGGCTTTTA--CC-CTACTACTT
3322365 AGGGAGACAAGATCTACAATCTTCGGCTTGTTACCCTACTACTT
1 AGGGAGACAAGATCTACAATCTTCGGCTT-TTACCCTACTACTT
3322409 AGGG
1 AGGG
3322413 GGTTAAGGCT
Statistics
Matches: 68, Mismatches: 14, Indels: 20
0.67 0.14 0.20
Matches are distributed among these distances:
41 4 0.06
42 1 0.01
43 7 0.10
44 44 0.65
45 7 0.10
46 2 0.03
47 3 0.04
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.31
Consensus pattern (43 bp):
AGGGAGACAAGATCTACAATCTTCGGCTTTTACCCTACTACTT
Found at i:3322448 original size:44 final size:44
Alignment explanation
Indices: 3322400--3322541 Score: 121
Period size: 44 Copynumber: 3.2 Consensus size: 44
3322390 GCTTGTTACC
3322400 CTACTACTTAGGGGGTTAAGGCTCACTGTCTTCGATCCACTCCA
1 CTACTACTTAGGGGGTTAAGGCTCACTGTCTTCGATCCACTCCA
* * ** * * * **
3322444 CTACTGCTTAGGGAGACAAGATCTACAATCTCTTGCG-T--GTTACC-
1 CTACTACTTAGGGGGTTAAG-GCT-CACTGTCTT-CGATCCACT-CCA
*
3322488 CTACTACTTAAGGGGTTAAGGCTCACTGTCTTCGATCCACTCCA
1 CTACTACTTAGGGGGTTAAGGCTCACTGTCTTCGATCCACTCCA
*
3322532 CTATTACTTA
1 CTACTACTTA
3322542 AGGAGATAAT
Statistics
Matches: 70, Mismatches: 20, Indels: 16
0.66 0.19 0.15
Matches are distributed among these distances:
41 2 0.03
42 8 0.11
43 4 0.06
44 42 0.60
45 4 0.06
46 8 0.11
47 2 0.03
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.31
Consensus pattern (44 bp):
CTACTACTTAGGGGGTTAAGGCTCACTGTCTTCGATCCACTCCA
Found at i:3322657 original size:439 final size:437
Alignment explanation
Indices: 3321560--3322745 Score: 1320
Period size: 440 Copynumber: 2.7 Consensus size: 437
3321550 CTTAAATCTG
* * * *
3321560 CTCCACTACTGGTTAGGGAGACAAGATTCGA-CGTCTTCGATCTGTCCCACTACAACTTTAGGGA
1 CTCCACTACTGCTTAGGGAGACAAGATTC-ACCGTCTTCGATCTATACCACTACAACTTTAAGGA
* * * * *
3321624 GACAAGATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGATGGTGGCTTAAATC
65 GACAAGAGCTGCAATCTTCAACCTACTCCACTACTACTTAAGGAGATA-GATGAT-GCTGAAATC
* * * **
3321689 TGTTCCACTACTAGCTAGGGAGACAAGATTCACCGTCTTCGATCCGCTCCACTACTGCTTAGGGA
128 AGCTCCACTACTAGCTAGGGAGACAAGACTCACCGTCCCCGATCCGCTCCACTACTGCTTAGGGA
* * *
3321754 GATAAGATCTAAAATTTCTAACCTGTTACCCCACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGA
193 GATAAGATCTAAATTTTC-AGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGA
*
3321819 TTTGCTCCACTACTGCTGAGGGAGACAAGATCTACAATCTTCAGCCTGTTACCCTACTACTTAGG
257 TTTGCTCCATTACTGCTGAGGGAGACAAGATCTACAATCTTCAGCCTGTTACCCTACTACTTAGG
* * * *
3321884 GGGGTTAAGGCTCACTGTCTTTGATTTGCTCCACTACTGCTTAGGGAGACAAGATCTACAATCTT
322 GGGGTTAAAGCTCACTATCTTTAATTTACTCCACTACTGCTTAGGGAGACAAGATCTACAATCTT
* * *
3321949 CGTCTTGTTACCCTACTACTTAAGGGGTTAAGGGTCACTATCTTCGATCCG
387 CGGCTTGTTACCCTACTACTTAAGGGGTTAAGGCTCACTATCTTCGATCCA
* * * *
3322000 CTCCACTACTGCTTAGGGAGATAAGATTCGCCGTCTTCGATCTATTCCACTGCAACTTTAAGGAG
1 CTCCACTACTGCTTAGGGAGACAAGATTCACCGTCTTCGATCTATACCACTACAACTTTAAGGAG
* * * * * * *
3322065 ACAAGATCTGCAATCTTCAACCTACTCCATTACTGCTTAGGGAGATAGGATGGTGGCTTAAATCT
66 ACAAGAGCTGCAATCTTCAACCTACTCCACTACTACTTAAGGAGATA-GATGAT-GCTGAAATCA
* * * ** * *
3322130 GCTCCACTACTAGCTAGGGAGACAATATTCGCCGTCTTCGATCCGCTCTACTACTGCTTAGGAAG
129 GCTCCACTACTAGCTAGGGAGACAAGACTCACCGTCCCCGATCCGCTCCACTACTGCTTAGGGAG
* *
3322195 ATAAAATCTGAAATTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGAT
194 ATAAGATCT-AAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGAT
* * *
3322260 TTGCTCTATTACTGCTGAGGGAGACAAGATCTACAATCTTCGGCCTTTTACCCTACTACTTA-GG
258 TTGCTCCATTACTGCTGAGGGAGACAAGATCTACAATCTTCAGCCTGTTACCCTACTACTTAGGG
3322324 GGGTTAAAGCTCACTATCTTTAATTTACTCCACTACTGCTTAGGGAGACAAGATCTACAATCTTC
323 GGGTTAAAGCTCACTATCTTTAATTTACTCCACTACTGCTTAGGGAGACAAGATCTACAATCTTC
* *
3322389 GGCTTGTTACCCTACTACTTAGGGGGTTAAGGCTCACTGTCTTCGATCCA
388 GGCTTGTTACCCTACTACTTAAGGGGTTAAGGCTCACTATCTTCGATCCA
* * *
3322439 CTCCACTACTGCTTAGGGAGACAAGATCTACAATC-TCTTGCG-TGT-TACC-CTACTAC-TTAA
1 CTCCACTACTGCTTAGGGAGACAAGAT-T-C-ACCGTCTT-CGATCTATACCACTACAACTTTAA
* ** * * *
3322499 GGGGTTAAG-GCT-CACTGTCTTCGATCC-ACTCCACTATTACTTAAGGAGATA-AT-AT-CTGA
62 GGAGACAAGAGCTGCA--ATCTTC-AACCTACTCCACTACTACTTAAGGAGATAGATGATGCTGA
** * ** * * * * *
3322558 AATTTCCAGCCTGTTACTTACTA-CTTAGGGGGTTAAGGCTCACTGTCCCCGATCTGTTCCGCTA
124 AA--T-CAG-CT-CCAC-TACTAGC-TAGGGAGACAAGACTCACCGTCCCCGATCCGCTCCACTA
* * * *
3322622 TTGTTTAGGGAGACAAGATCTATAATTTTCAGCCTGTTATCCTACTGCTTAGGGGGTTAAGGCTC
182 CTGCTTAGGGAGATAAGATCTA-AATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTC
** * * ** * * * *
3322687 ATAGTCTTTGATCTGCTCCATTACAACTTCAGGAAGGCAAGATCTGCAATCTTCAGCCT
246 ACCGTCTTCGATTTGCTCCATTACTGC-TGAGGGAGACAAGATCTACAATCTTCAGCCT
3322746 ACTTCACTAC
Statistics
Matches: 642, Mismatches: 86, Indels: 36
0.84 0.11 0.05
Matches are distributed among these distances:
433 5 0.01
435 2 0.00
436 6 0.01
437 4 0.01
438 39 0.06
439 248 0.39
440 322 0.50
441 13 0.02
442 3 0.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (437 bp):
CTCCACTACTGCTTAGGGAGACAAGATTCACCGTCTTCGATCTATACCACTACAACTTTAAGGAG
ACAAGAGCTGCAATCTTCAACCTACTCCACTACTACTTAAGGAGATAGATGATGCTGAAATCAGC
TCCACTACTAGCTAGGGAGACAAGACTCACCGTCCCCGATCCGCTCCACTACTGCTTAGGGAGAT
AAGATCTAAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATTTG
CTCCATTACTGCTGAGGGAGACAAGATCTACAATCTTCAGCCTGTTACCCTACTACTTAGGGGGG
TTAAAGCTCACTATCTTTAATTTACTCCACTACTGCTTAGGGAGACAAGATCTACAATCTTCGGC
TTGTTACCCTACTACTTAAGGGGTTAAGGCTCACTATCTTCGATCCA
Found at i:3323035 original size:64 final size:64
Alignment explanation
Indices: 3322934--3323058 Score: 214
Period size: 64 Copynumber: 2.0 Consensus size: 64
3322924 TGTATCTATG
* *
3322934 CTTATGCCAAATAATTAGGATGTTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGATA
1 CTTATGCCAAATAATTAGGATGCTATAATCGAAATGAATCAAATGCTCCTAACTAGATGTGATA
* *
3322998 CTTATGTCAAATAATTAGGATGCTATAATCGACATGAATCAAATGCTCCTAACTAGATGTG
1 CTTATGCCAAATAATTAGGATGCTATAATCGAAATGAATCAAATGCTCCTAACTAGATGTG
3323059 TTATGAATGC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (64 bp):
CTTATGCCAAATAATTAGGATGCTATAATCGAAATGAATCAAATGCTCCTAACTAGATGTGATA
Found at i:3327472 original size:26 final size:26
Alignment explanation
Indices: 3327436--3327486 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
3327426 AACTGTTCTA
3327436 TTTAGCAATCAAATATGAATCAACAG
1 TTTAGCAATCAAATATGAATCAACAG
3327462 TTTAGCAATCAAATATGAATCAACA
1 TTTAGCAATCAAATATGAATCAACA
3327487 CCTCCTTTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.27
Consensus pattern (26 bp):
TTTAGCAATCAAATATGAATCAACAG
Found at i:3328821 original size:129 final size:127
Alignment explanation
Indices: 3328526--3328827 Score: 322
Period size: 129 Copynumber: 2.4 Consensus size: 127
3328516 CGAAAAACCA
* * * *
3328526 AAACCCAGCACAGTAAGGCACGATTCCTCGAATTTCTAAACATTAAACATTGCCTTGTTTTAGAA
1 AAACCCAGCACGGTAGGGCACGATTCCTCGAATTTCCAAACATCAAACATTGCCTTGTTTTAGAA
* * * * *
3328591 TTTAGAAAACATGAGTGAAATTCTAAAGGAATATTCGATTATTTCGAACAAACGGGAGATTG
66 TTTACAAAACAGGAGTGAAATTCTAAAGGAATATTCGATTATTTCGAACAAACAGAAAATTG
* * *
3328653 CAACCCAGCACGATAGGGCACGATTCCCCGAATTTCCAAACATCAAACATTGCCTTCGTTTTAAG
1 AAACCCAGCACGGTAGGGCACGATTCCTCGAATTTCCAAACATCAAACATTGCCTT-GTTTT-A-
* * * * * ** *
3328718 GAATTTTCAAAATACGGA-TGAAATT-TCAAATGAATGTTTGATTATTT-GGGCGAACAGAAAAT
63 GAATTTACAAAACA-GGAGTGAAATTCT-AAAGGAATATTCGATTATTTCGAACAAACAGAAAAT
3328780 TG
126 TG
* * * *
3328782 AAACCCAGCACGGTTGGGCACGATTCCTCGAGTTCCCAAATATCAA
1 AAACCCAGCACGGTAGGGCACGATTCCTCGAATTTCCAAACATCAA
3328828 CTATTACATT
Statistics
Matches: 143, Mismatches: 27, Indels: 8
0.80 0.15 0.04
Matches are distributed among these distances:
127 49 0.34
128 5 0.03
129 52 0.36
130 35 0.24
131 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (127 bp):
AAACCCAGCACGGTAGGGCACGATTCCTCGAATTTCCAAACATCAAACATTGCCTTGTTTTAGAA
TTTACAAAACAGGAGTGAAATTCTAAAGGAATATTCGATTATTTCGAACAAACAGAAAATTG
Found at i:3332006 original size:132 final size:130
Alignment explanation
Indices: 3331630--3332017 Score: 402
Period size: 131 Copynumber: 2.9 Consensus size: 130
3331620 AATTATTCAT
** ** * *
3331630 TTAAAAAC-CTTTCAAAACGAAGGTGACATTCGATGTTTGACAATCCGCGGAATCGTGCCCTATC
1 TTAAAAACTCTTT-AAAACGAAGGAAATGTTCGATGTTTGGCAATTCG-GGAATCGTGCCCTATC
* * * * * * ** *
3331694 GTGCTAGGTTGCAATTCCTCGTTTGCTCAAAGTAATCGAACGTCCTTTTAGAATTTCACTCATGA
64 GTGCTGGGTTGCAATTCC-CATTTGTTCAAAATAATCGAACATCCCTTCGGAATTTCACTCACGA
3331759 TTC
128 TTC
* * ** * *
3331762 TTAAAAACTCTTTGAAACGAAGGAAATGTTCAATGTTTGGTGATTTGAGAATCGTGCCCTATCGT
1 TTAAAAACTCTTTAAAACGAAGGAAATGTTCGATGTTTGGCAATTCGGGAATCGTGCCCTATCGT
** ** * * *
3331827 GCTGGGTTGCGCTTTTTCATTTGTTCAAAACAATCGAAGATTCCTTCGGAATTTCACTCACG-TT
66 GCTGGGTTGC-AATTCCCATTTGTTCAAAATAATCGAACATCCCTTCGGAATTTCACTCACGATT
*
3331891 T
130 C
* *
3331892 TCTAAAAACTCTTTAAAACGAGGGAAATGTTCGATGTTTGGCAATTCGGGAAATAGTGCCCTATC
1 T-TAAAAACTCTTTAAAACGAAGGAAATGTTCGATGTTTGGCAATTCGGG-AATCGTGCCCTATC
* *
3331957 GTGCTGGGTTGCAATCTCCCATTTGTTCAAAATAATCGAATATCCCTTCGGGATTTCACTC
64 GTGCTGGGTTGCAAT-TCCCATTTGTTCAAAATAATCGAACATCCCTTCGGAATTTCACTC
3332018 GTATTTTTCT
Statistics
Matches: 206, Mismatches: 45, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
130 3 0.01
131 102 0.50
132 97 0.47
133 4 0.02
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (130 bp):
TTAAAAACTCTTTAAAACGAAGGAAATGTTCGATGTTTGGCAATTCGGGAATCGTGCCCTATCGT
GCTGGGTTGCAATTCCCATTTGTTCAAAATAATCGAACATCCCTTCGGAATTTCACTCACGATTC
Found at i:3337362 original size:27 final size:26
Alignment explanation
Indices: 3337332--3337382 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
3337322 AATATTAACA
*
3337332 AAATAATTTTTAAAATTTTTATTTTTT
1 AAATAACTTTTAAAATTTTT-TTTTTT
* *
3337359 AAATAGCTTTTATAATTTTTTTTT
1 AAATAACTTTTAAAATTTTTTTTT
3337383 GAATTTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 4 0.19
27 17 0.81
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (26 bp):
AAATAACTTTTAAAATTTTTTTTTTT
Found at i:3340377 original size:1 final size:1
Alignment explanation
Indices: 3340371--3340401 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
3340361 CTTCTTCCTC
*
3340371 TTTTTTTTTTTTTTTTTTTTTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3340402 ATGTGGGGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:3341351 original size:17 final size:16
Alignment explanation
Indices: 3341321--3341357 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3341311 TAATTAATTC
*
3341321 TATTTT-ATTTTAT-T
1 TATTTTAATATTATAT
3341335 TATTTTAATATTATAT
1 TATTTTAATATTATAT
3341351 TATTTTA
1 TATTTTA
3341358 TAAAAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 6 0.30
15 6 0.30
16 8 0.40
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTTTAATATTATAT
Found at i:3341550 original size:15 final size:14
Alignment explanation
Indices: 3341523--3341561 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
3341513 CAATTTTATA
3341523 ACTTAAATTTCAAT
1 ACTTAAATTTCAAT
*
3341537 AGTTAAATTTTCAAT
1 ACTTAAA-TTTCAAT
3341552 ACTT-AATTTC
1 ACTTAAATTTC
3341562 TCAACTTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 4 0.18
14 8 0.36
15 10 0.45
ACGTcount: A:0.38, C:0.13, G:0.03, T:0.46
Consensus pattern (14 bp):
ACTTAAATTTCAAT
Found at i:3342176 original size:22 final size:22
Alignment explanation
Indices: 3342151--3342206 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
3342141 GAATAGTGTC
3342151 ACACGCCCGTGTGACCTAAGAG
1 ACACGCCCGTGTGACCTAAGAG
*
3342173 ACACGCCCATGTGACCTAAGAG
1 ACACGCCCGTGTGACCTAAGAG
3342195 ACACGCCCGTGT
1 ACACGCCCGTGT
3342207 ACCCTTCTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.27, C:0.34, G:0.25, T:0.14
Consensus pattern (22 bp):
ACACGCCCGTGTGACCTAAGAG
Found at i:3343787 original size:3 final size:3
Alignment explanation
Indices: 3343779--3343805 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3343769 ATTTAATACC
3343779 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
3343806 CTTACCATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3344490 original size:22 final size:21
Alignment explanation
Indices: 3344465--3344526 Score: 60
Period size: 22 Copynumber: 3.1 Consensus size: 21
3344455 TCCCCTGTTC
*
3344465 TTCTCTATTTCGTTTTCTTTGT
1 TTCTCTATTTC-ATTTCTTTGT
*
3344487 TTCTCTTTTTCATTTCTTT-T
1 TTCTCTATTTCATTTCTTTGT
*
3344507 AT-T-TATTT-ATTTCTTTGT
1 TTCTCTATTTCATTTCTTTGT
3344525 TT
1 TT
3344527 TTTTTAATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 8 0.24
18 6 0.18
19 1 0.03
20 2 0.06
21 7 0.21
22 10 0.29
ACGTcount: A:0.08, C:0.15, G:0.05, T:0.73
Consensus pattern (21 bp):
TTCTCTATTTCATTTCTTTGT
Found at i:3345286 original size:17 final size:16
Alignment explanation
Indices: 3345250--3345286 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
3345240 TTTAAACTCG
*
3345250 AAATTAATTCAATTTA
1 AAATTAATTCAATCTA
3345266 AAATTAATTCAAATCTA
1 AAATTAATTC-AATCTA
3345283 AAAT
1 AAAT
3345287 AGTTCAACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATTAATTCAATCTA
Found at i:3345503 original size:3 final size:3
Alignment explanation
Indices: 3345495--3345539 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
3345485 TTGAATCTCC
3345495 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3345540 TATTATAGTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3346561 original size:15 final size:15
Alignment explanation
Indices: 3346529--3346574 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
3346519 ATTTATCTAT
3346529 TTATATTTCTACTATTA
1 TTATATTTCTA-T-TTA
3346546 TTATATTTCTATTTA
1 TTATATTTCTATTTA
*
3346561 TTATATTTTTATTT
1 TTATATTTCTATTT
3346575 CAATTTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 16 0.57
16 1 0.04
17 11 0.39
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATATTTCTATTTA
Found at i:3346562 original size:18 final size:18
Alignment explanation
Indices: 3346454--3346564 Score: 67
Period size: 17 Copynumber: 6.4 Consensus size: 18
3346444 ATTATTGCTA
*
3346454 TTATTATTATGTTTCTAT
1 TTATTATTATATTTCTAT
*
3346472 TTA-TATT-TATTTTTTAT
1 TTATTATTATA-TTTCTAT
* * *
3346489 TCTAATACTAT-TAT-TAT
1 T-TATTATTATATTTCTAT
*
3346506 TTA-T-TTA-ATTTTTAT
1 TTATTATTATATTTCTAT
3346521 TTATCTATTTATATTTCTA-
1 TTAT-TA-TTATATTTCTAT
*
3346540 CTATTATTATATTTCTAT
1 TTATTATTATATTTCTAT
3346558 TTATTAT
1 TTATTAT
3346565 ATTTTTATTT
Statistics
Matches: 72, Mismatches: 9, Indels: 24
0.69 0.09 0.23
Matches are distributed among these distances:
14 4 0.06
15 7 0.10
16 3 0.04
17 27 0.38
18 15 0.21
19 9 0.12
20 7 0.10
ACGTcount: A:0.27, C:0.06, G:0.01, T:0.66
Consensus pattern (18 bp):
TTATTATTATATTTCTAT
Found at i:3346585 original size:20 final size:21
Alignment explanation
Indices: 3346549--3346587 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3346539 ACTATTATTA
*
3346549 TATTTCTATTTATTATATTTT
1 TATTTCAATTTATTATATTTT
3346570 TATTTCAATTTA-TATATT
1 TATTTCAATTTATTATATT
3346588 AATATTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (21 bp):
TATTTCAATTTATTATATTTT
Found at i:3346593 original size:20 final size:20
Alignment explanation
Indices: 3346544--3346593 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
3346534 TTTCTACTAT
*
3346544 TATTATATTTCTATTTATTA
1 TATTATATTTCAATTTATTA
*
3346564 TATTTTTATTTCAATTTA-TA
1 TA-TTATATTTCAATTTATTA
3346584 TATTAATATT
1 TATT-ATATT
3346594 ATTTTCATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 2 0.08
20 10 0.40
21 13 0.52
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTATATTTCAATTTATTA
Found at i:3346620 original size:86 final size:86
Alignment explanation
Indices: 3346440--3346620 Score: 192
Period size: 86 Copynumber: 2.1 Consensus size: 86
3346430 AACTAATTTA
* * *
3346440 ATATATTATTGCTATTATTATTATGTTTCTATTTATATTTATTTTTTATTCTAATACTATTATTA
1 ATATA-TATTGCTACTATTATTATATTTCTATTTATATATATTTTTTATTCTAATACTATTATTA
*
3346505 TTTATTTAATTTTTATTTATCT
65 TTTATTTAATTATTATTTATCT
* * *
3346527 ATTTATATTTCTACTATTATTATATTTCTATTTAT-TATA-TTTTTATT-TCAAT-TTATATATT
1 ATATATATTGCTACTATTATTATATTTCTATTTATATATATTTTTTATTCT-AATACTAT-TATT
* *
3346588 AATATTATTTTCATTATTATTTTTCT
64 -AT-TTA-TTTAATTATTATTTATCT
3346614 -TATATAT
1 ATATATAT
3346621 GTTTTTACTT
Statistics
Matches: 79, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
83 4 0.05
84 15 0.19
85 5 0.06
86 36 0.46
87 19 0.24
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.64
Consensus pattern (86 bp):
ATATATATTGCTACTATTATTATATTTCTATTTATATATATTTTTTATTCTAATACTATTATTAT
TTATTTAATTATTATTTATCT
Found at i:3346773 original size:25 final size:24
Alignment explanation
Indices: 3346712--3346773 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
3346702 TATAACGCTC
* *
3346712 ATTTCAAATTTTTATACATTATTT
1 ATTTCAAATTTTCATACATTATGT
*
3346736 ACTTT-AATATTTTCATATATTATGT
1 A-TTTCAA-ATTTTCATACATTATGT
3346761 ATTTCAAACTTTT
1 ATTTCAAA-TTTT
3346774 TTTTACACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
24 7 0.23
25 24 0.77
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (24 bp):
ATTTCAAATTTTCATACATTATGT
Found at i:3348453 original size:26 final size:27
Alignment explanation
Indices: 3348406--3348462 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 27
3348396 TTTTCCCCTA
*
3348406 TAAAAAAAATGTAATACATTAATATT-
1 TAAAAAAAATGTAATACATTAAAATTC
**
3348432 TAAAAATAAATGTAA-ATTTTAAAATTC
1 TAAAAA-AAATGTAATACATTAAAATTC
3348459 TAAA
1 TAAA
3348463 GTTCAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (27 bp):
TAAAAAAAATGTAATACATTAAAATTC
Found at i:3349963 original size:2 final size:2
Alignment explanation
Indices: 3349956--3349992 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
3349946 GTCATAATCC
3349956 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3349993 TAGTTAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3356863 original size:19 final size:19
Alignment explanation
Indices: 3356839--3356878 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
3356829 AGTTAAAAGT
*
3356839 AAAATTTT-TTATTGAAATA
1 AAAATTTTAATATT-AAATA
3356858 AAAATTTTAATATTAAATA
1 AAAATTTTAATATTAAATA
3356877 AA
1 AA
3356879 TTTATCAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
AAAATTTTAATATTAAATA
Found at i:3359653 original size:103 final size:103
Alignment explanation
Indices: 3359474--3359742 Score: 511
Period size: 103 Copynumber: 2.6 Consensus size: 103
3359464 GCGAGTTGCT
* *
3359474 ATTTGCATTATATATTCTGCAAGCATCCATTTTAAGTTCTTTTCCTTGCTACTCGAGTTTTTCAA
1 ATTTGCATTATATATTCTTCAAGCATCCATTTTAAGTTCTTTTCCTTGCTGCTCGAGTTTTTCAA
3359539 GCATCCATTTTAGGGGAAATGGAGTATTTATTGTATTC
66 GCATCCATTTTAGGGGAAATGGAGTATTTATTGTATTC
*
3359577 ATTTGCATTATATATTCTTCAAGCATCCATTTTAAGTTCTTCTCCTTGCTGCTCGAGTTTTTCAA
1 ATTTGCATTATATATTCTTCAAGCATCCATTTTAAGTTCTTTTCCTTGCTGCTCGAGTTTTTCAA
3359642 GCATCCATTTTAGGGGAAATGGAGTATTTATTGTATTC
66 GCATCCATTTTAGGGGAAATGGAGTATTTATTGTATTC
3359680 ATTTGCATTATATATTCTTCAAGCATCCATTTTAAGTTCTTTTCCTTGCTGCTCGAGTTTTTC
1 ATTTGCATTATATATTCTTCAAGCATCCATTTTAAGTTCTTTTCCTTGCTGCTCGAGTTTTTC
3359743 TTCATTTGTA
Statistics
Matches: 162, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 162 1.00
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.45
Consensus pattern (103 bp):
ATTTGCATTATATATTCTTCAAGCATCCATTTTAAGTTCTTTTCCTTGCTGCTCGAGTTTTTCAA
GCATCCATTTTAGGGGAAATGGAGTATTTATTGTATTC
Found at i:3362208 original size:30 final size:31
Alignment explanation
Indices: 3362174--3362233 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
3362164 TAACTCAATA
* *
3362174 ATTTAAAT-AAATTTTTTACATAATTAAATG
1 ATTTAAATGAAAATTTTTAAATAATTAAATG
3362204 ATTTAAATGAAAATTTTTAAATAATTAAAT
1 ATTTAAATGAAAATTTTTAAATAATTAAAT
3362234 AATTATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 8 0.30
31 19 0.70
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (31 bp):
ATTTAAATGAAAATTTTTAAATAATTAAATG
Found at i:3365324 original size:12 final size:12
Alignment explanation
Indices: 3365307--3365336 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3365297 ACCGTGGGGG
*
3365307 CGCACCTCTGGT
1 CGCACCTCCGGT
3365319 CGCACCTCCGGT
1 CGCACCTCCGGT
3365331 CGCACC
1 CGCACC
3365337 CCTAGTCGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.10, C:0.50, G:0.23, T:0.17
Consensus pattern (12 bp):
CGCACCTCCGGT
Found at i:3369427 original size:28 final size:28
Alignment explanation
Indices: 3369391--3369448 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
3369381 CATACTTGTA
3369391 TAAGCGTAAATTTTAATATAGTTGCTTG
1 TAAGCGTAAATTTTAATATAGTTGCTTG
3369419 TAAGCGTAAATTTTAATATAGTTGCTTG
1 TAAGCGTAAATTTTAATATAGTTGCTTG
3369447 TA
1 TA
3369449 TTAGTGCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (28 bp):
TAAGCGTAAATTTTAATATAGTTGCTTG
Found at i:3376758 original size:22 final size:21
Alignment explanation
Indices: 3376711--3376758 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
3376701 TTTTTCAAAA
*
3376711 TTTAAGAAAATAATTTATTTG
1 TTTAAGAAAATAATTAATTTG
*
3376732 TTTAAGTAAATATATTGAATTT-
1 TTTAAGAAAATA-ATT-AATTTG
3376754 TTTAA
1 TTTAA
3376759 TATTTATGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 11 0.48
22 8 0.35
23 4 0.17
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (21 bp):
TTTAAGAAAATAATTAATTTG
Found at i:3377397 original size:32 final size:33
Alignment explanation
Indices: 3377317--3377400 Score: 91
Period size: 32 Copynumber: 2.5 Consensus size: 33
3377307 ACAAATAATT
* * *
3377317 TAAAAATTATAAAATATTCAAAATTTTAAAATTCA
1 TAAAAATTATAAAATA-T-AAAATATAAAAAGTCA
* *
3377352 -AAAAAATATAAAATATAAAGTATAAAAAGTCA
1 TAAAAATTATAAAATATAAAATATAAAAAGTCA
3377384 TAAAAATTA-AAAATATA
1 TAAAAATTATAAAATATA
3377401 TATATGAAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
32 20 0.48
33 8 0.19
34 14 0.33
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (33 bp):
TAAAAATTATAAAATATAAAATATAAAAAGTCA
Found at i:3377529 original size:31 final size:32
Alignment explanation
Indices: 3377483--3377550 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 32
3377473 TTTAAATAGC
* *
3377483 AATTTGACTTTTTTTTAAAAGGTTGATGGTCA
1 AATTTGACTTCTTTTTAAAAGGTTGAGGGTCA
*
3377515 AATTTGAC-TCTTTTTAAATGGTTGAGGGTCA
1 AATTTGACTTCTTTTTAAAAGGTTGAGGGTCA
3377546 AATTT
1 AATTT
3377551 AGCTAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 25 0.76
32 8 0.24
ACGTcount: A:0.28, C:0.07, G:0.19, T:0.46
Consensus pattern (32 bp):
AATTTGACTTCTTTTTAAAAGGTTGAGGGTCA
Found at i:3385749 original size:21 final size:21
Alignment explanation
Indices: 3385725--3385765 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3385715 TAACAGAACC
*
3385725 GCTGATGTGGCAAGTTAACTA
1 GCTGACGTGGCAAGTTAACTA
*
3385746 GCTGACGTGGCCAGTTAACT
1 GCTGACGTGGCAAGTTAACT
3385766 TGGCCAGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (21 bp):
GCTGACGTGGCAAGTTAACTA
Found at i:3385771 original size:13 final size:13
Alignment explanation
Indices: 3385753--3385780 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3385743 CTAGCTGACG
3385753 TGGCCAGTTAACT
1 TGGCCAGTTAACT
3385766 TGGCCAGTTAACT
1 TGGCCAGTTAACT
3385779 TG
1 TG
3385781 CCACGTTGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.32
Consensus pattern (13 bp):
TGGCCAGTTAACT
Found at i:3386766 original size:21 final size:21
Alignment explanation
Indices: 3386740--3386801 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
3386730 CCATGTGGCA
3386740 AGTTAACTGGCCACGTCAGCT
1 AGTTAACTGGCCACGTCAGCT
3386761 AGTTAACTGGCCACGTCAGCT
1 AGTTAACTGGCCACGTCAGCT
* *
3386782 AGTTAACTTGCCACATCAGC
1 AGTTAACTGGCCACGTCAGC
3386802 GGTTCTGTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
AGTTAACTGGCCACGTCAGCT
Found at i:3389425 original size:16 final size:17
Alignment explanation
Indices: 3389393--3389475 Score: 56
Period size: 15 Copynumber: 5.1 Consensus size: 17
3389383 TAATTCTATA
3389393 TTAAAACACAT--ATAT
1 TTAAAACACATACATAT
3389408 TTAAAAC-CATACATATTT
1 TTAAAACACATACATA--T
* *
3389426 TTATAACTA-ATTTCATA-
1 TTAAAAC-ACA-TACATAT
3389443 TTAAAACACAT--ATAT
1 TTAAAACACATACATAT
3389458 TTAAAAC-CATACATAT
1 TTAAAACACATACATAT
3389474 TT
1 TT
3389476 GAATAATTAA
Statistics
Matches: 54, Mismatches: 3, Indels: 21
0.69 0.04 0.27
Matches are distributed among these distances:
14 9 0.17
15 14 0.26
16 11 0.20
17 7 0.13
18 7 0.13
19 1 0.02
20 5 0.09
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAAAACACATACATAT
Found at i:3389444 original size:50 final size:50
Alignment explanation
Indices: 3389377--3389475 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
3389367 CTTATTATAA
3389377 TATAACTAATTCTATATTAAAACACATATATTTAAAACCATACATATTTT
1 TATAACTAATTCTATATTAAAACACATATATTTAAAACCATACATATTTT
3389427 TATAACTAATT-TCATATTAAAACACATATATTTAAAACCATACATATTT
1 TATAACTAATTCT-ATATTAAAACACATATATTTAAAACCATACATATTT
3389476 GAATAATTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
49 1 0.02
50 47 0.98
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.39
Consensus pattern (50 bp):
TATAACTAATTCTATATTAAAACACATATATTTAAAACCATACATATTTT
Found at i:3389473 original size:18 final size:16
Alignment explanation
Indices: 3389389--3389464 Score: 61
Period size: 15 Copynumber: 4.8 Consensus size: 16
3389379 TAACTAATTC
3389389 TATA-TTAAAAC-ACA
1 TATATTTAAAACTACA
3389403 TATATTTAAAACCATACA
1 TATATTTAAAA-C-TACA
* *
3389421 TATTTTTATAACTA-A
1 TATATTTAAAACTACA
*
3389436 TTTCATATTAAAAC-ACA
1 TAT-AT-TTAAAACTACA
3389453 TATATTTAAAAC
1 TATATTTAAAAC
3389465 CATACATATT
Statistics
Matches: 49, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
14 4 0.08
15 16 0.33
16 7 0.14
17 10 0.20
18 12 0.24
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (16 bp):
TATATTTAAAACTACA
Found at i:3389487 original size:50 final size:50
Alignment explanation
Indices: 3389378--3389487 Score: 177
Period size: 50 Copynumber: 2.2 Consensus size: 50
3389368 TTATTATAAT
**
3389378 ATAACTAA-TTCTATATTAAAACACATATATTTAAAACCATACATATTTTT
1 ATAACTAATTTC-ATATTAAAACACATATATTTAAAACCATACATATTTGA
3389428 ATAACTAATTTCATATTAAAACACATATATTTAAAACCATACATATTTGA
1 ATAACTAATTTCATATTAAAACACATATATTTAAAACCATACATATTTGA
*
3389478 ATAATTAATT
1 ATAACTAATT
3389488 AACTTATTTA
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
50 53 0.95
51 3 0.05
ACGTcount: A:0.47, C:0.13, G:0.01, T:0.39
Consensus pattern (50 bp):
ATAACTAATTTCATATTAAAACACATATATTTAAAACCATACATATTTGA
Found at i:3398655 original size:23 final size:20
Alignment explanation
Indices: 3398629--3398682 Score: 58
Period size: 23 Copynumber: 2.6 Consensus size: 20
3398619 GCTTGTCAAA
3398629 TAATTAAAAATTAATTAAATTTT
1 TAATTAAAAATTAATT--A-TTT
*
3398652 TAATTGAAAATT-ATTATTT
1 TAATTAAAAATTAATTATTT
3398671 TAA-TAAAAATTA
1 TAATTAAAAATTA
3398683 GCAATCAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
18 7 0.25
19 6 0.21
20 1 0.04
22 3 0.11
23 11 0.39
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
TAATTAAAAATTAATTATTT
Found at i:3398914 original size:19 final size:19
Alignment explanation
Indices: 3398885--3398932 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
3398875 AAATTAAAGC
*
3398885 ATTAT-AAAAATTTAGAAA
1 ATTATAAAAAATATAGAAA
3398903 ATTATAAAAAATATAGAAA
1 ATTATAAAAAATATAGAAA
**
3398922 AAAATAAAAAA
1 ATTATAAAAAA
3398933 ATATTATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 5 0.19
19 21 0.81
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (19 bp):
ATTATAAAAAATATAGAAA
Found at i:3452162 original size:20 final size:22
Alignment explanation
Indices: 3452137--3452177 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3452127 ACTTAACCAA
3452137 AACTTTT-AAAT-TAAAAATTT
1 AACTTTTGAAATATAAAAATTT
*
3452157 AACTTTTGAAGTATAAAAATT
1 AACTTTTGAAATATAAAAATT
3452178 AAATATCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 8 0.44
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (22 bp):
AACTTTTGAAATATAAAAATTT
Found at i:3453729 original size:11 final size:11
Alignment explanation
Indices: 3453715--3453744 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
3453705 ATTAAATTAT
3453715 ATTTAATTAAA
1 ATTTAATTAAA
3453726 ATTT-ATTAAA
1 ATTTAATTAAA
3453736 ATTTAATTA
1 ATTTAATTA
3453745 TAATAACAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
ATTTAATTAAA
Found at i:3456126 original size:21 final size:21
Alignment explanation
Indices: 3456080--3456126 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
3456070 TTAAAGTGTA
*
3456080 AAAAAATTAATAATTTTAATT
1 AAAATATTAATAATTTTAATT
3456101 AAAATATTAAT-ATTTTGAATT
1 AAAATATTAATAATTTT-AATT
*
3456122 TAAAT
1 AAAAT
3456127 CTTATCACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
AAAATATTAATAATTTTAATT
Found at i:3459840 original size:29 final size:30
Alignment explanation
Indices: 3459792--3459851 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 30
3459782 TTGGTCATGC
3459792 ATTTTGAAAATTGAAAAGTA-AAGAAACTAA
1 ATTTTGAAAATTGAAAAGTACAAG-AACTAA
3459822 ATTTCTGAAAA-T-AAAAGTACAAGAACTAA
1 ATTT-TGAAAATTGAAAAGTACAAGAACTAA
3459851 A
1 A
3459852 ATCCAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
29 14 0.50
30 8 0.29
31 6 0.21
ACGTcount: A:0.57, C:0.07, G:0.12, T:0.25
Consensus pattern (30 bp):
ATTTTGAAAATTGAAAAGTACAAGAACTAA
Found at i:3466750 original size:25 final size:23
Alignment explanation
Indices: 3466724--3466768 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3466714 TATACTAAAT
* *
3466724 ATATATATTTTTTATTTTTAATC
1 ATATTTATATTTTATTTTTAATC
3466747 ATATTTATATTTTATTTTTAAT
1 ATATTTATATTTTATTTTTAAT
3466769 TTTAATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
ATATTTATATTTTATTTTTAATC
Found at i:3466765 original size:29 final size:27
Alignment explanation
Indices: 3466732--3466786 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 27
3466722 ATATATATAT
* *
3466732 TTTTTATTTTTAATCATATTTATATTTTA
1 TTTTTAATTTTAAT-ATAATTA-ATTTTA
3466761 TTTTTAATTTTAATATAATTAATTTT
1 TTTTTAATTTTAATATAATTAATTTT
3466787 TATTATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 5 0.21
28 6 0.25
29 13 0.54
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTTTAATTTTAATATAATTAATTTTA
Found at i:3466854 original size:39 final size:40
Alignment explanation
Indices: 3466784--3466868 Score: 109
Period size: 39 Copynumber: 2.1 Consensus size: 40
3466774 TATAATTAAT
*
3466784 TTTTATTATATTTTCAATTTGTGTATTGTTTTAAAAATTG
1 TTTTAATATATTTTCAATTTGTGTATTGTTTTAAAAATTG
* * * * *
3466824 TTTTAATATATTTT-TATTTGTTTTTTGTTTTAATATTTG
1 TTTTAATATATTTTCAATTTGTGTATTGTTTTAAAAATTG
3466863 TTTTAA
1 TTTTAA
3466869 ATGTATTTGA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 26 0.67
40 13 0.33
ACGTcount: A:0.25, C:0.01, G:0.08, T:0.66
Consensus pattern (40 bp):
TTTTAATATATTTTCAATTTGTGTATTGTTTTAAAAATTG
Found at i:3468324 original size:21 final size:22
Alignment explanation
Indices: 3468299--3468358 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 22
3468289 AATACATAAA
3468299 AAATATTTAAAAAATT-AAAAT
1 AAATATTTAAAAAATTGAAAAT
*
3468320 AAATATTTTCTAACAAATTGAAAAT
1 AAATA--TT-TAAAAAATTGAAAAT
3468345 AAAT-TTTAAAAAAT
1 AAATATTTAAAAAAT
3468359 ATGTAAACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
21 12 0.36
22 2 0.06
23 2 0.06
24 8 0.24
25 9 0.27
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (22 bp):
AAATATTTAAAAAATTGAAAAT
Found at i:3468436 original size:30 final size:30
Alignment explanation
Indices: 3468402--3468460 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
3468392 CTTAACAAGG
* * *
3468402 AAATATCTCTAAAATAATAATAAAATTAAC
1 AAATACCTCTAAAACAATAACAAAATTAAC
* *
3468432 AAATACCTTTATAACAATAACAAAATTAA
1 AAATACCTCTAAAACAATAACAAAATTAA
3468461 TAATAAAATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (30 bp):
AAATACCTCTAAAACAATAACAAAATTAAC
Found at i:3468939 original size:2 final size:2
Alignment explanation
Indices: 3468932--3468986 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
3468922 TTTATTATTA
3468932 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3468974 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
3468987 GTCCAAATGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3470234 original size:27 final size:26
Alignment explanation
Indices: 3470168--3470234 Score: 64
Period size: 27 Copynumber: 2.5 Consensus size: 26
3470158 TTAAAAGTTC
*
3470168 TATAAAATTTATTTAAAAATATAAAAA
1 TATAAAATTTA-TAAAAAATATAAAAA
* *
3470195 TAAAAAAAGTTATAAAAAATAT-AAAA
1 T-ATAAAATTTATAAAAAATATAAAAA
3470221 TCATAAATATTTAT
1 T-ATAAA-ATTTAT
3470235 CTTCTCGACT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
26 9 0.28
27 15 0.47
28 8 0.25
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (26 bp):
TATAAAATTTATAAAAAATATAAAAA
Found at i:3471537 original size:2 final size:2
Alignment explanation
Indices: 3471530--3471558 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3471520 TTATTCAAAC
3471530 AT AT 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 AT AT A
3471559 AAAGGTACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3474943 original size:2 final size:2
Alignment explanation
Indices: 3474938--3474963 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3474928 CACTAACTTT
3474938 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3474964 ATTTATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.