Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
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: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 38 of 141
Found at i:12469516 original size:6 final size:6
Alignment explanation
Indices: 12469505--12469567 Score: 72
Period size: 6 Copynumber: 10.3 Consensus size: 6
12469495 TTTTTCCTTT
* * *
12469505 TTTTTC TCTTTC TTTTTC TTTTTC TTTTTC TTTTTTC TTCTTC TTCTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC -TTTTTC TTTTTC TTTTTC
* *
12469554 TTCTTC TTCTTC TT
1 TTTTTC TTTTTC TT
12469568 CCTCCTTGAA
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
6 47 0.89
7 6 0.11
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTTTC
Found at i:12469520 original size:12 final size:12
Alignment explanation
Indices: 12469495--12469535 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
12469485 TATAATAAGT
12469495 TTTTTC-CTTT-
1 TTTTTCTCTTTC
12469505 TTTTTCTCTTTC
1 TTTTTCTCTTTC
*
12469517 TTTTTCTTTTTC
1 TTTTTCTCTTTC
12469529 TTTTTCT
1 TTTTTCT
12469536 TTTTTCTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
10 6 0.21
11 4 0.14
12 18 0.64
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTTCTCTTTC
Found at i:12469527 original size:22 final size:21
Alignment explanation
Indices: 12469494--12469567 Score: 69
Period size: 22 Copynumber: 3.5 Consensus size: 21
12469484 CTATAATAAG
* *
12469494 TTTTTTCCTTTTT-TTTCTCT
1 TTTTTTTCTTTTTCTTTTTCT
12469514 TTCTTTTTCTTTTTCTTTTTCT
1 TT-TTTTTCTTTTTCTTTTTCT
* *
12469536 TTTTTCTTCTTCTTCTTCTTCT
1 TTTTT-TTCTTTTTCTTTTTCT
* *
12469558 TCTTCTTCTT
1 TTTTTTTCTT
12469568 CCTCCTTGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
20 2 0.04
21 18 0.40
22 25 0.56
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTTTTTCTTTTTCTTTTTCT
Found at i:12469539 original size:19 final size:19
Alignment explanation
Indices: 12469505--12469555 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
12469495 TTTTTCCTTT
*
12469505 TTTTTCTCTTTC-TTTTTC
1 TTTTTCTTTTTCTTTTTTC
12469523 TTTTTCTTTTTCTTTTTTC
1 TTTTTCTTTTTCTTTTTTC
* *
12469542 TTCTTCTTCTTCTT
1 TTTTTCTTTTTCTT
12469556 CTTCTTCTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 11 0.38
19 18 0.62
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTTCTTTTTCTTTTTTC
Found at i:12469540 original size:34 final size:34
Alignment explanation
Indices: 12469495--12469570 Score: 91
Period size: 34 Copynumber: 2.2 Consensus size: 34
12469485 TATAATAAGT
* * *
12469495 TTTTTCCTTTTTTTTC-TCTTTCTTTTTCTTTTTC
1 TTTTTCCTTTTTCTTCTTC-TTCTTCTTCTTCTTC
*
12469529 TTTTTCTTTTTTCTTCTTCTTCTTCTTCTTCTTC
1 TTTTTCCTTTTTCTTCTTCTTCTTCTTCTTCTTC
*
12469563 TTCTTCCT
1 TTTTTCCT
12469571 CCTTGAACCT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
34 33 0.94
35 2 0.06
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (34 bp):
TTTTTCCTTTTTCTTCTTCTTCTTCTTCTTCTTC
Found at i:12469547 original size:3 final size:3
Alignment explanation
Indices: 12469514--12469568 Score: 69
Period size: 3 Copynumber: 19.0 Consensus size: 3
12469504 TTTTTTCTCT
* * *
12469514 TTC TTT TTC TTT TTC TTT TTC TT- TT- TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
12469560 TTC TTC TTC
1 TTC TTC TTC
12469569 CTCCTTGAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
2 4 0.09
3 41 0.91
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (3 bp):
TTC
Found at i:12469983 original size:29 final size:28
Alignment explanation
Indices: 12469927--12470052 Score: 144
Period size: 29 Copynumber: 4.2 Consensus size: 28
12469917 GGCCAAAACA
12469927 TAATTTTGAGAAAATTTAGGGGTCAAAATG
1 TAATTTT-A-AAAATTTAGGGGTCAAAATG
**
12469957 TAATTTTAAAAATTTTATAGGTCAAAATG
1 TAATTTTAAAAA-TTTAGGGGTCAAAATG
*
12469986 TAATTTTAGGAAAATTTAGGGGTTAAAATG
1 TAATTTTA--AAAATTTAGGGGTCAAAATG
* *
12470016 CAATTTTAAAAGGTTTAGGGGTCAAAATG
1 TAATTTTAAAA-ATTTAGGGGTCAAAATG
12470045 TAAATTTT
1 T-AATTTT
12470053 TTATTTTTTG
Statistics
Matches: 82, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
28 7 0.09
29 38 0.46
30 33 0.40
31 4 0.05
ACGTcount: A:0.40, C:0.03, G:0.19, T:0.37
Consensus pattern (28 bp):
TAATTTTAAAAATTTAGGGGTCAAAATG
Found at i:12470014 original size:59 final size:59
Alignment explanation
Indices: 12469927--12470052 Score: 173
Period size: 59 Copynumber: 2.1 Consensus size: 59
12469917 GGCCAAAACA
* * *
12469927 TAATTTTGAGAAAATTTAGGGGTCAAAATGTAATTTTAAAAATTTTATAGGTCAAAATG
1 TAATTTTGAGAAAATTTAGGGGTCAAAATGCAATTTTAAAAAGTTTAGAGGTCAAAATG
* * *
12469986 TAATTTT-AGGAAAATTTAGGGGTTAAAATGCAATTTTAAAAGGTTTAGGGGTCAAAATG
1 TAATTTTGA-GAAAATTTAGGGGTCAAAATGCAATTTTAAAAAGTTTAGAGGTCAAAATG
12470045 TAAATTTT
1 T-AATTTT
12470053 TTATTTTTTG
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
58 1 0.02
59 52 0.88
60 6 0.10
ACGTcount: A:0.40, C:0.03, G:0.19, T:0.37
Consensus pattern (59 bp):
TAATTTTGAGAAAATTTAGGGGTCAAAATGCAATTTTAAAAAGTTTAGAGGTCAAAATG
Found at i:12470340 original size:76 final size:76
Alignment explanation
Indices: 12470245--12470544 Score: 573
Period size: 76 Copynumber: 3.9 Consensus size: 76
12470235 ACATCGGCGT
* * *
12470245 GTGACCCGAGGCTTAACTCACCTCTCGTACTATGAGTTAATTTTTGAAAAACAACAGAAATTAAA
1 GTGACCCAAGGCTCAACTCACCTCTCGTACTATGAGTTGATTTTTGAAAAACAACAGAAATTAAA
12470310 AATACCTCAGC
66 AATACCTCAGC
12470321 GTGACCCAAGGCTCAACTCACCTCTCGTACTATGAGTTGATTTTTGAAAAACAACAGAAATTAAA
1 GTGACCCAAGGCTCAACTCACCTCTCGTACTATGAGTTGATTTTTGAAAAACAACAGAAATTAAA
12470386 AATACCTCAGC
66 AATACCTCAGC
12470397 GTGACCCAAGGCTCAACTCACCTCTCGTACTATGAGTTGATTTTTGAAAAACAACAGAAATTAAA
1 GTGACCCAAGGCTCAACTCACCTCTCGTACTATGAGTTGATTTTTGAAAAACAACAGAAATTAAA
12470462 AATACCTCAGC
66 AATACCTCAGC
12470473 GTGACCCAAGGCTCAACTCACCTCTCGTACTATGAGTTGATTTTTGAAAAACAACAGAAATTAAA
1 GTGACCCAAGGCTCAACTCACCTCTCGTACTATGAGTTGATTTTTGAAAAACAACAGAAATTAAA
12470538 AATACCT
66 AATACCT
12470545 GTTGGTAGTT
Statistics
Matches: 221, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 221 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (76 bp):
GTGACCCAAGGCTCAACTCACCTCTCGTACTATGAGTTGATTTTTGAAAAACAACAGAAATTAAA
AATACCTCAGC
Found at i:12471971 original size:76 final size:77
Alignment explanation
Indices: 12471845--12472007 Score: 319
Period size: 76 Copynumber: 2.1 Consensus size: 77
12471835 TTATTATTTT
12471845 ATATAAATTATAGATATCTATTATTTGCAGTCGTGACTCATCAACTCTTTTGTGGGCCAAGTCAA
1 ATATAAATTATAGATATCTATTATTTGCAGTCGTGACTCATCAACTCTTTTGTGGGCCAAGTCAA
12471910 GTTAATTCC-AA
66 GTTAATTCCAAA
12471921 ATATAAATTATAGATATCTATTATTTGCAGTCGTGACTCATCAACTCTTTTGTGGGCCAAGTCAA
1 ATATAAATTATAGATATCTATTATTTGCAGTCGTGACTCATCAACTCTTTTGTGGGCCAAGTCAA
12471986 GTTAATTCCAAA
66 GTTAATTCCAAA
12471998 ATATAAATTA
1 ATATAAATTA
12472008 ATTATTACTA
Statistics
Matches: 86, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
76 74 0.86
77 12 0.14
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (77 bp):
ATATAAATTATAGATATCTATTATTTGCAGTCGTGACTCATCAACTCTTTTGTGGGCCAAGTCAA
GTTAATTCCAAA
Found at i:12474440 original size:14 final size:14
Alignment explanation
Indices: 12474423--12474449 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12474413 GGGTTTATGA
12474423 GTTTTGGTTATAGG
1 GTTTTGGTTATAGG
12474437 GTTTTGGTTATAG
1 GTTTTGGTTATAG
12474450 ACAAATGATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.33, T:0.52
Consensus pattern (14 bp):
GTTTTGGTTATAGG
Found at i:12475235 original size:56 final size:56
Alignment explanation
Indices: 12475175--12475287 Score: 192
Period size: 56 Copynumber: 2.0 Consensus size: 56
12475165 TAACACTTTT
* *
12475175 ATTTCATTCCTACAGAATAAA-TTCTACTACAGCTCTATTTTATTCGAGCGAACCAA
1 ATTTCATTCCTACAGAATAAATTTC-ACTACAGCTCTATTTTATTCCAACGAACCAA
12475231 ATTTCATTCCTACAGAATAAATTTCACTACAGCTCTATTTTATTCCAACGAACCAA
1 ATTTCATTCCTACAGAATAAATTTCACTACAGCTCTATTTTATTCCAACGAACCAA
12475287 A
1 A
12475288 CATATCGTNN
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
56 51 0.94
57 3 0.06
ACGTcount: A:0.35, C:0.24, G:0.07, T:0.34
Consensus pattern (56 bp):
ATTTCATTCCTACAGAATAAATTTCACTACAGCTCTATTTTATTCCAACGAACCAA
Found at i:12475593 original size:2 final size:2
Alignment explanation
Indices: 12475586--12475628 Score: 77
Period size: 2 Copynumber: 21.0 Consensus size: 2
12475576 NNNNNNNNNN
12475586 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
12475629 AAAAAGTAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:12481596 original size:3 final size:3
Alignment explanation
Indices: 12481590--12481615 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12481580 AACTAATAAG
12481590 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
12481616 TATGTCTTGT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:12482026 original size:44 final size:43
Alignment explanation
Indices: 12481958--12482044 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 43
12481948 TAATTCGTAT
*
12481958 TGTTATCGTTGTTTTATTTGATATTTATTTATTCATTTATTGA
1 TGTTATCATTGTTTTATTTGATATTTATTTATTCATTTATTGA
12482001 TGTTATCATTGTTTTTATTTGATATTTATTTATTCATTTATTGA
1 TGTTATCATTG-TTTTATTTGATATTTATTTATTCATTTATTGA
12482045 AGTGTTCATT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
43 10 0.24
44 32 0.76
ACGTcount: A:0.22, C:0.05, G:0.10, T:0.63
Consensus pattern (43 bp):
TGTTATCATTGTTTTATTTGATATTTATTTATTCATTTATTGA
Found at i:12482054 original size:44 final size:44
Alignment explanation
Indices: 12481969--12482060 Score: 150
Period size: 44 Copynumber: 2.1 Consensus size: 44
12481959 GTTATCGTTG
* *
12481969 TTTTATTTGATATTTATTTATTCATTTATTGATGTTATCATTGT
1 TTTTATTTGATATTTATTTATTCATTTATTGAAGTTATCATTAT
12482013 TTTTATTTGATATTTATTTATTCATTTATTGAAGTGT-TCATTAT
1 TTTTATTTGATATTTATTTATTCATTTATTGAAGT-TATCATTAT
12482057 TTTT
1 TTTT
12482061 GTGAAATGCT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 44 0.98
45 1 0.02
ACGTcount: A:0.23, C:0.04, G:0.09, T:0.64
Consensus pattern (44 bp):
TTTTATTTGATATTTATTTATTCATTTATTGAAGTTATCATTAT
Found at i:12488853 original size:21 final size:21
Alignment explanation
Indices: 12488827--12488883 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
12488817 AAATAATAAA
12488827 TAAAAAACATAAATAAATTAT
1 TAAAAAACATAAATAAATTAT
*
12488848 TAAAAAATATAAATAAATTAT
1 TAAAAAACATAAATAAATTAT
12488869 T--AAAACATAAATAAA
1 TAAAAAACATAAATAAA
12488884 GATGGAGAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.38
21 21 0.62
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (21 bp):
TAAAAAACATAAATAAATTAT
Found at i:12489627 original size:9 final size:9
Alignment explanation
Indices: 12489615--12489694 Score: 56
Period size: 10 Copynumber: 8.6 Consensus size: 9
12489605 TATAAAATCG
12489615 TAAAAAATA
1 TAAAAAATA
12489624 TAAAAAAT-
1 TAAAAAATA
* * *
12489632 TGTAAAATTT
1 T-AAAAAATA
12489642 TATAAAAATAA
1 TA-AAAAAT-A
12489653 TAAAAAAT-
1 TAAAAAATA
*
12489661 TATAAAATA
1 TAAAAAATA
*
12489670 TATAGAAATA
1 TA-AAAAATA
12489680 TAAAAAATTA
1 TAAAAAA-TA
12489690 TAAAA
1 TAAAA
12489695 TTTTATAAAG
Statistics
Matches: 55, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
8 8 0.15
9 19 0.35
10 26 0.47
11 2 0.04
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (9 bp):
TAAAAAATA
Found at i:12489647 original size:20 final size:20
Alignment explanation
Indices: 12489622--12489703 Score: 75
Period size: 19 Copynumber: 4.3 Consensus size: 20
12489612 TCGTAAAAAA
*
12489622 TATAAAAAATTGTAAAATTT
1 TATAAAAAATTATAAAATTT
* **
12489642 TAT-AAAAATAATAAAAAAT
1 TATAAAAAATTATAAAATTT
*
12489661 TATAAAATA-TATAGAAA---
1 TATAAAAAATTATA-AAATTT
12489678 TATAAAAAATTATAAAATTT
1 TATAAAAAATTATAAAATTT
12489698 TATAAA
1 TATAAA
12489704 GTCGAAAGAA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
17 11 0.22
18 4 0.08
19 18 0.37
20 16 0.33
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (20 bp):
TATAAAAAATTATAAAATTT
Found at i:12489716 original size:56 final size:57
Alignment explanation
Indices: 12489615--12489741 Score: 154
Period size: 56 Copynumber: 2.2 Consensus size: 57
12489605 TATAAAATCG
*
12489615 TAAA-AAATATAAAAAATTGTAAAATTTTATAAAAATAATAAAAAATTAT-AAAATA
1 TAAAGAAATATAAAAAATTATAAAATTTTATAAAAATAATAAAAAATTATAAAAATA
* * * *
12489670 TATAGAAATATAAAAAATTATAAAATTTTAT-AAAGTCGAA-AGAAAATTATACAAAATG
1 TAAAGAAATATAAAAAATTATAAAATTTTATAAAAAT--AATAAAAAATTATA-AAAATA
12489728 TAAAGAAATATAAA
1 TAAAGAAATATAAA
12489742 TTTCTTAAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
55 7 0.11
56 34 0.56
57 2 0.03
58 18 0.30
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.29
Consensus pattern (57 bp):
TAAAGAAATATAAAAAATTATAAAATTTTATAAAAATAATAAAAAATTATAAAAATA
Found at i:12490066 original size:27 final size:24
Alignment explanation
Indices: 12490018--12490076 Score: 64
Period size: 27 Copynumber: 2.3 Consensus size: 24
12490008 AATTTTTATA
*
12490018 AAAATTCTAATTTTTAATAAATTT
1 AAAATTTTAATTTTTAATAAATTT
*
12490042 GAAAATTTTATATTTTTATTAAAATTT
1 -AAAATTTTA-ATTTTTAAT-AAATTT
12490069 AATAATTT
1 AA-AATTT
12490077 ATCTAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 8 0.28
26 10 0.34
27 11 0.38
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
AAAATTTTAATTTTTAATAAATTT
Found at i:12490069 original size:18 final size:20
Alignment explanation
Indices: 12490043--12490089 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
12490033 AATAAATTTG
*
12490043 AAAATTT-TATATTTTTAT-T
1 AAAATTTATATA-ATTTATCT
12490062 AAAATTTA-ATAATTTATCT
1 AAAATTTATATAATTTATCT
12490081 AAAATTTAT
1 AAAATTTAT
12490090 TTATTTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
AAAATTTATATAATTTATCT
Found at i:12490095 original size:19 final size:18
Alignment explanation
Indices: 12490043--12490095 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
12490033 AATAAATTTG
12490043 AAAATTTTATATT-TTTATT
1 AAAA-TTTAT-TTATTTATT
* *
12490062 AAAATTTAATAATTTATCT
1 AAAATTTATTTATTTAT-T
12490081 AAAATTTATTTATTT
1 AAAATTTATTTATTT
12490096 TAATTTATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 1 0.04
18 9 0.32
19 18 0.64
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
AAAATTTATTTATTTATT
Found at i:12490356 original size:96 final size:96
Alignment explanation
Indices: 12490176--12490356 Score: 226
Period size: 96 Copynumber: 1.9 Consensus size: 96
12490166 TTTTGATGCG
12490176 TTTTGAAAGTTCAAGTATCCAATTGAGTGCCAAAAAAAAAAAAGAGAACTTAATTGCTTTTTTTG
1 TTTTGAAAGTTCAAGTATCCAATTGAGTGCCAAAAAAAAAAAAGAGAACTTAATTGCTTTTTTTG
* *
12490241 AAGAAATTTGAGGGCTTTTTTTTTTTATACA
66 AAGAAATTTGACGACTTTTTTTTTTTATACA
* * * * **
12490272 TTTTGAAAGTTCAAGT-GCTCAATTGAGTG-CAAAAAAAGAGAGGAAGGGCTTAATTGCTTTTTT
1 TTTTGAAAGTTCAAGTATC-CAATTGAGTGCCAAAAAAAAAAAAG-AGAACTTAATTGCTTTTTT
*
12490335 TGAA-AAAGTTTTACGA-TTTTTT
64 TGAAGAAA-TTTGACGACTTTTTT
12490357 ACACCCTTAA
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
95 21 0.29
96 52 0.71
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (96 bp):
TTTTGAAAGTTCAAGTATCCAATTGAGTGCCAAAAAAAAAAAAGAGAACTTAATTGCTTTTTTTG
AAGAAATTTGACGACTTTTTTTTTTTATACA
Found at i:12493089 original size:19 final size:19
Alignment explanation
Indices: 12493065--12493101 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12493055 TAAATGAGCA
*
12493065 AATAATTACAATAATAACT
1 AATAATAACAATAATAACT
*
12493084 AATAATAACAGTAATAAC
1 AATAATAACAATAATAAC
12493102 ATCAAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.11, G:0.03, T:0.27
Consensus pattern (19 bp):
AATAATAACAATAATAACT
Found at i:12494920 original size:45 final size:45
Alignment explanation
Indices: 12494856--12495248 Score: 349
Period size: 45 Copynumber: 8.8 Consensus size: 45
12494846 CGATCTACTT
* *
12494856 CGCTGTCGGTACAGGAAGGCAAGATCTGCTATCTGCAGTCTGCTC
1 CGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTC
* * * * * *
12494901 CGCTGTTAGTACAGGAAGGCAAG-GCTGGTGTCTTC-GATCTACTT
1 CGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAG-TCTGCTC
* *
12494945 CACT-TCCAGTACAGGAAGGCAAGATCTGCTATCTACAGTCTGCTC
1 CGCTGT-CAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTC
* * * * * * *
12494990 CGCTGTTAGTATAGGAAGGCAAG-GCTGGTGTCTT-TGATCTGCTT
1 CGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAG-TCTGCTC
* * * *
12495034 CACCGTTAGTACAGGAAGGCAAGATTTGCTATCTTCAGTCTGCTC
1 CGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTC
* * * * * *
12495079 CACTGTCAGTACAGGAAGGAAAG-GCTGGTGTCTTC-GATCTGCTT
1 CGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAG-TCTGCTC
12495123 CGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTC
1 CGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTC
* * *
12495168 CGCTGTCAGTACAGGAAGGCAACG--CTGATGTCTTC-GATCTGCTT
1 CGCTGTCAGTACAGGAAGGCAA-GATCTGCTATCTTCAG-TCTGCTC
* * *
12495212 CGCCTAT-AGTATAGGAATGCAAGATCTGCTATCTTCA
1 CG-CTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCA
12495249 CTGATCTATT
Statistics
Matches: 275, Mismatches: 56, Indels: 33
0.76 0.15 0.09
Matches are distributed among these distances:
43 6 0.02
44 130 0.47
45 134 0.49
46 5 0.02
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (45 bp):
CGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTC
Found at i:12494988 original size:89 final size:88
Alignment explanation
Indices: 12494837--12495248 Score: 585
Period size: 89 Copynumber: 4.6 Consensus size: 88
12494827 CTGTAAACTA
* * *
12494837 TGGTGTCTTCGATCTACTTCGCTGTCGGTACAGGAAGGCAAGATCTGCTATCTGCAGTCTGCTCC
1 TGGTGTCTTCGATCTGCTTCGCT-TCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCC
*
12494902 GCTGTTAGTACAGGAAGGCAAGGC
65 GCTGTCAGTACAGGAAGGCAAGGC
* * *
12494926 TGGTGTCTTCGATCTACTTCACTTCCAGTACAGGAAGGCAAGATCTGCTATCTACAGTCTGCTCC
1 TGGTGTCTTCGATCTGCTTCGCTT-CAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCC
* *
12494991 GCTGTTAGTATAGGAAGGCAAGGC
65 GCTGTCAGTACAGGAAGGCAAGGC
* * *
12495015 TGGTGTCTTTGATCTGCTTCACCGTT-AGTACAGGAAGGCAAGATTTGCTATCTTCAGTCTGCTC
1 TGGTGTCTTCGATCTGCTTC-GC-TTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTC
* *
12495079 CACTGTCAGTACAGGAAGGAAAGGC
64 CGCTGTCAGTACAGGAAGGCAAGGC
12495104 TGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCC
1 TGGTGTCTTCGATCTGCTTCGCT-TCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCC
*
12495169 GCTGTCAGTACAGGAAGGCAACGC
65 GCTGTCAGTACAGGAAGGCAAGGC
* * *
12495193 TGATGTCTTCGATCTGCTTCGCCTAT-AGTATAGGAATGCAAGATCTGCTATCTTCA
1 TGGTGTCTTCGATCTGCTTCG-CT-TCAGTACAGGAAGGCAAGATCTGCTATCTTCA
12495249 CTGATCTATT
Statistics
Matches: 294, Mismatches: 23, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
87 1 0.00
88 3 0.01
89 284 0.97
90 4 0.01
91 2 0.01
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.29
Consensus pattern (88 bp):
TGGTGTCTTCGATCTGCTTCGCTTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCG
CTGTCAGTACAGGAAGGCAAGGC
Found at i:12495552 original size:22 final size:22
Alignment explanation
Indices: 12495524--12495565 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
12495514 AATCTTCAAG
12495524 GTTCAATCCACTGTAATTCTAT
1 GTTCAATCCACTGTAATTCTAT
* *
12495546 GTTCAATGCAGTGTAATTCT
1 GTTCAATCCACTGTAATTCT
12495566 GGGACATAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.40
Consensus pattern (22 bp):
GTTCAATCCACTGTAATTCTAT
Found at i:12500254 original size:9 final size:9
Alignment explanation
Indices: 12500240--12500270 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
12500230 GTTAAACAAA
12500240 TCGAGTTAT
1 TCGAGTTAT
*
12500249 TCGAGTTAA
1 TCGAGTTAT
12500258 TCGAGTTAT
1 TCGAGTTAT
12500267 TCGA
1 TCGA
12500271 ATCAAGTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:12502681 original size:9 final size:9
Alignment explanation
Indices: 12502669--12502697 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
12502659 CAAAATGAAC
12502669 AAAATTATA
1 AAAATTATA
12502678 AAAATTATA
1 AAAATTATA
12502687 AAAA-TATA
1 AAAATTATA
12502695 AAA
1 AAA
12502698 GATATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 7 0.35
9 13 0.65
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (9 bp):
AAAATTATA
Found at i:12502703 original size:17 final size:17
Alignment explanation
Indices: 12502669--12502734 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
12502659 CAAAATGAAC
*
12502669 AAAATTATAAAAATTAT
1 AAAAATATAAAAATTAT
12502686 AAAAATATAAAAGA-TAT
1 AAAAATATAAAA-ATTAT
* * *
12502703 ATATATGTATAAAATTAT
1 AAAAATATA-AAAATTAT
*
12502721 GAAAATATGAAAAA
1 AAAAATAT-AAAAA
12502735 CATATGCATG
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
17 21 0.57
18 15 0.41
19 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (17 bp):
AAAAATATAAAAATTAT
Found at i:12502746 original size:35 final size:35
Alignment explanation
Indices: 12502678--12502746 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
12502668 CAAAATTATA
* *
12502678 AAAATTATAAAAATATAAAAGATATATATATGTAT
1 AAAATTATAAAAATATAAAAGACATATACATGTAT
* *
12502713 AAAATTATGAAAATATGAAAA-ACATATGCATGTA
1 AAAATTATAAAAATAT-AAAAGACATATACATGTA
12502747 CACATATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 25 0.86
36 4 0.14
ACGTcount: A:0.58, C:0.03, G:0.09, T:0.30
Consensus pattern (35 bp):
AAAATTATAAAAATATAAAAGACATATACATGTAT
Found at i:12503130 original size:19 final size:19
Alignment explanation
Indices: 12503106--12503142 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12503096 TAAATGAGCA
*
12503106 AATAATTACAATAATAACT
1 AATAATAACAATAATAACT
*
12503125 AATAATAACAGTAATAAC
1 AATAATAACAATAATAAC
12503143 ATCAAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.11, G:0.03, T:0.27
Consensus pattern (19 bp):
AATAATAACAATAATAACT
Found at i:12506094 original size:17 final size:17
Alignment explanation
Indices: 12506066--12506098 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
12506056 TAACTCAAAA
12506066 ATAAATAAATATTAAATT
1 ATAAATAAATA-TAAATT
12506084 ATAAA-AAATATAAAT
1 ATAAATAAATATAAAT
12506099 ATTAAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAAATAAATATAAATT
Found at i:12506104 original size:16 final size:18
Alignment explanation
Indices: 12506066--12506113 Score: 54
Period size: 13 Copynumber: 3.0 Consensus size: 18
12506056 TAACTCAAAA
12506066 ATAAATAAATATTAAATT
1 ATAAATAAATATTAAATT
12506084 ATAAA-AAATA-TAAA-T
1 ATAAATAAATATTAAATT
12506099 AT---TAAATATTAAATT
1 ATAAATAAATATTAAATT
12506114 TATCCGTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
13 5 0.19
14 4 0.15
15 4 0.15
16 4 0.15
17 5 0.19
18 5 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAAATAAATATTAAATT
Found at i:12519125 original size:19 final size:19
Alignment explanation
Indices: 12519097--12519133 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12519087 CATTTACCCA
*
12519097 TTTTACCACTTTGGCCATT
1 TTTTACCACTATGGCCATT
*
12519116 TTTTATCACTATGGCCAT
1 TTTTACCACTATGGCCAT
12519134 CCACCTTCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.19, C:0.24, G:0.11, T:0.46
Consensus pattern (19 bp):
TTTTACCACTATGGCCATT
Found at i:12519335 original size:11 final size:10
Alignment explanation
Indices: 12519308--12519334 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
12519298 TAAAATTGTT
12519308 TATTTTTAAA
1 TATTTTTAAA
12519318 TATTTTTAAA
1 TATTTTTAAA
12519328 TATTTTT
1 TATTTTT
12519335 TTTGAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TATTTTTAAA
Found at i:12527881 original size:64 final size:64
Alignment explanation
Indices: 12527779--12527938 Score: 248
Period size: 64 Copynumber: 2.5 Consensus size: 64
12527769 TACCCAAACT
* * * * *
12527779 ATATAGCAAATTAAGACGTCAAGTTGGTAGGTGGAAGTACATAAAACAAATTAATAATTAATAA
1 ATATAGTAAACTAAGACGTCAGGTTGATAGGTGAAAGTACATAAAACAAATTAATAATTAATAA
*
12527843 ATATAGTAAACTAAGACGTCAGGTAGATAGGTGAAAGTACATAAAACAAATTAATAATTAATAA
1 ATATAGTAAACTAAGACGTCAGGTTGATAGGTGAAAGTACATAAAACAAATTAATAATTAATAA
* *
12527907 ATACAGTAAACTAAGAGGTCAGGTTGATAGGT
1 ATATAGTAAACTAAGACGTCAGGTTGATAGGT
12527939 AGAAGTAGAG
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 87 1.00
ACGTcount: A:0.47, C:0.08, G:0.19, T:0.26
Consensus pattern (64 bp):
ATATAGTAAACTAAGACGTCAGGTTGATAGGTGAAAGTACATAAAACAAATTAATAATTAATAA
Found at i:12528123 original size:7 final size:7
Alignment explanation
Indices: 12528098--12528159 Score: 99
Period size: 7 Copynumber: 9.0 Consensus size: 7
12528088 AAAAAAATAA
*
12528098 ATTTCTC
1 ATTTCCC
12528105 ATTTCCC
1 ATTTCCC
*
12528112 -CTTCCC
1 ATTTCCC
12528118 ATTTCCC
1 ATTTCCC
12528125 ATTTCCC
1 ATTTCCC
12528132 ATTTCCC
1 ATTTCCC
12528139 ATTTCCC
1 ATTTCCC
12528146 ATTTCCC
1 ATTTCCC
12528153 ATTTCCC
1 ATTTCCC
12528160 TAAGCCCGTA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
6 5 0.10
7 46 0.90
ACGTcount: A:0.13, C:0.44, G:0.00, T:0.44
Consensus pattern (7 bp):
ATTTCCC
Found at i:12528208 original size:14 final size:14
Alignment explanation
Indices: 12528189--12528236 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
12528179 ATTTATTTTT
12528189 ATTTTTAATTTAAA
1 ATTTTTAATTTAAA
**
12528203 ATTTTTAATTTTTA
1 ATTTTTAATTTAAA
*
12528217 ATTTTTATATTTCAA
1 ATTTTTA-ATTTAAA
12528232 ATTTT
1 ATTTT
12528237 AAAATTTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 19 0.66
15 10 0.34
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (14 bp):
ATTTTTAATTTAAA
Found at i:12528220 original size:28 final size:27
Alignment explanation
Indices: 12528183--12528253 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
12528173 TTTGAAATTT
12528183 ATTTTT-ATTTTTAATTTAAAATTTTTA
1 ATTTTTAATTTTTAATTTAAAA-TTTTA
*
12528210 ATTTTTAATTTTTATATTTCAAATTTTA
1 ATTTTTAATTTTTA-ATTTAAAATTTTA
**
12528238 AAATTTAA-TTTTAATT
1 ATTTTTAATTTTTAATT
12528254 ATTAGTATTG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
26 3 0.08
27 11 0.28
28 18 0.46
29 7 0.18
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (27 bp):
ATTTTTAATTTTTAATTTAAAATTTTA
Found at i:12528222 original size:8 final size:7
Alignment explanation
Indices: 12528183--12528228 Score: 58
Period size: 7 Copynumber: 6.6 Consensus size: 7
12528173 TTTGAAATTT
12528183 ATTTTT-
1 ATTTTTA
12528189 ATTTTTA
1 ATTTTTA
**
12528196 ATTTAAA
1 ATTTTTA
12528203 ATTTTTA
1 ATTTTTA
12528210 ATTTTTA
1 ATTTTTA
12528217 ATTTTTA
1 ATTTTTA
12528224 TATTT
1 -ATTT
12528229 CAAATTTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
6 6 0.18
7 24 0.71
8 4 0.12
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
ATTTTTA
Found at i:12531501 original size:21 final size:21
Alignment explanation
Indices: 12531442--12531511 Score: 54
Period size: 21 Copynumber: 3.4 Consensus size: 21
12531432 TCGAAGCAGT
* *
12531442 ATACAACACATAAAGTGCCTGA
1 ATACGACACATATAGTGCCT-A
* ** *
12531464 A-ATGACACACGTTGTGCCTA
1 ATACGACACATATAGTGCCTA
*
12531484 ATACGACACATATAGTGCCTG
1 ATACGACACATATAGTGCCTA
12531505 AT-CGACA
1 ATACGACA
12531512 AAGCCAATAA
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
20 7 0.19
21 28 0.78
22 1 0.03
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.21
Consensus pattern (21 bp):
ATACGACACATATAGTGCCTA
Found at i:12531990 original size:17 final size:18
Alignment explanation
Indices: 12531958--12531991 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12531948 AATTTCTTTT
12531958 CAATTTATACCCTAATTC
1 CAATTTATACCCTAATTC
*
12531976 CAATTTA-ATCCTAATT
1 CAATTTATACCCTAATT
12531992 AACTCATTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (18 bp):
CAATTTATACCCTAATTC
Found at i:12532457 original size:17 final size:18
Alignment explanation
Indices: 12532435--12532469 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
12532425 CTTTCTTTTG
*
12532435 TTCTTTTA-GTTTCTTTA
1 TTCTTTTATGTTTATTTA
12532452 TTCTTTTATGTTTATTTA
1 TTCTTTTATGTTTATTTA
12532470 CTTTATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.14, C:0.09, G:0.06, T:0.71
Consensus pattern (18 bp):
TTCTTTTATGTTTATTTA
Found at i:12532473 original size:23 final size:23
Alignment explanation
Indices: 12532439--12532482 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
12532429 CTTTTGTTCT
*
12532439 TTTAGTTTCTTTATTCTTTTATG
1 TTTAGTTTCTTTATTATTTTATG
12532462 TTTA-TTTACTTTATTATTTTA
1 TTTAGTTT-CTTTATTATTTTA
12532483 ATTGTCCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.18, C:0.07, G:0.05, T:0.70
Consensus pattern (23 bp):
TTTAGTTTCTTTATTATTTTATG
Found at i:12533200 original size:13 final size:12
Alignment explanation
Indices: 12533184--12533233 Score: 55
Period size: 13 Copynumber: 3.9 Consensus size: 12
12533174 TTTATATATA
12533184 TTTTTCTTTTTGC
1 TTTTTCTTTTT-C
12533197 TTTTTTCTTTTTC
1 -TTTTTCTTTTTC
*
12533210 TCCTTTCTTTTTC
1 T-TTTTCTTTTTC
*
12533223 TTTATCTTTTT
1 TTTTTCTTTTT
12533234 GATTTTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 9 0.28
13 12 0.38
14 11 0.34
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (12 bp):
TTTTTCTTTTTC
Found at i:12533207 original size:6 final size:6
Alignment explanation
Indices: 12533184--12533233 Score: 55
Period size: 6 Copynumber: 7.8 Consensus size: 6
12533174 TTTATATATA
* *
12533184 TTTTTC TTTTTGC TTTTTTC TTTTTC TCCTTTC TTTTTC TTTATC TTTTT
1 TTTTTC TTTTT-C -TTTTTC TTTTTC T-TTTTC TTTTTC TTTTTC TTTTT
12533234 GATTTTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
6 25 0.68
7 7 0.19
8 5 0.14
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTTTC
Found at i:12534187 original size:12 final size:11
Alignment explanation
Indices: 12534154--12534215 Score: 58
Period size: 10 Copynumber: 5.5 Consensus size: 11
12534144 TAAAATGCAT
12534154 AATAAAAT-AA
1 AATAAAATAAA
*
12534164 AAT-AACTAAA
1 AATAAAATAAA
12534174 AATAAAAGTAAA
1 AATAAAA-TAAA
12534186 AAT-AAATAAA
1 AATAAAATAAA
12534196 ATATAAAATATAA
1 A-ATAAAATA-AA
12534209 AACTAAA
1 AA-TAAA
12534216 TGAAATCACT
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
9 3 0.07
10 13 0.30
11 7 0.16
12 13 0.30
13 7 0.16
ACGTcount: A:0.74, C:0.03, G:0.02, T:0.21
Consensus pattern (11 bp):
AATAAAATAAA
Found at i:12534194 original size:16 final size:16
Alignment explanation
Indices: 12534173--12534205 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12534163 AAATAACTAA
12534173 AAATAAAAGTA-AAAAT
1 AAATAAAA-TATAAAAT
12534189 AAATAAAATATAAAAT
1 AAATAAAATATAAAAT
12534205 A
1 A
12534206 TAAAACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 14 0.88
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (16 bp):
AAATAAAATATAAAAT
Found at i:12534686 original size:12 final size:12
Alignment explanation
Indices: 12534666--12534697 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
12534656 AAAAAAATTT
*
12534666 AATTCTTTTTTC
1 AATTTTTTTTTC
12534678 AATTTTTTTTTC
1 AATTTTTTTTTC
12534690 AATTTTTT
1 AATTTTTT
12534698 CATTTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (12 bp):
AATTTTTTTTTC
Found at i:12538244 original size:361 final size:361
Alignment explanation
Indices: 12537580--12538303 Score: 1448
Period size: 361 Copynumber: 2.0 Consensus size: 361
12537570 AATGTTGAAT
12537580 GAAAGTATGTCTATGTTCATGAAATTGATGATTTCAAGTGAGATTATTCATGTCTAATGACTTAC
1 GAAAGTATGTCTATGTTCATGAAATTGATGATTTCAAGTGAGATTATTCATGTCTAATGACTTAC
12537645 CTTATGTTAATTCATGTGAATTATGAATTGATGCACTAACATGTGTTATTGATGATGCTTAGGCT
66 CTTATGTTAATTCATGTGAATTATGAATTGATGCACTAACATGTGTTATTGATGATGCTTAGGCT
12537710 TGTGCCATTGATTGGATTGTATTATGTTAGTTTTAAGGATTTGCATTGAAATGATAAGTGTCCAA
131 TGTGCCATTGATTGGATTGTATTATGTTAGTTTTAAGGATTTGCATTGAAATGATAAGTGTCCAA
12537775 ATGGAAATATGCTTATGTTCATGAAAGGGTGGTAAGAATGAAAGTATGTAATTTCTTATGAATGG
196 ATGGAAATATGCTTATGTTCATGAAAGGGTGGTAAGAATGAAAGTATGTAATTTCTTATGAATGG
12537840 TTTATCATGTAGTTGATTTCAAAAGAGTTATGTTTAAATGCACTAGCTTGTGGCTATGGTTGATG
261 TTTATCATGTAGTTGATTTCAAAAGAGTTATGTTTAAATGCACTAGCTTGTGGCTATGGTTGATG
12537905 TTCATGCTTACATATTGCGTGTTATGCAAATGAAAC
326 TTCATGCTTACATATTGCGTGTTATGCAAATGAAAC
12537941 GAAAGTATGTCTATGTTCATGAAATTGATGATTTCAAGTGAGATTATTCATGTCTAATGACTTAC
1 GAAAGTATGTCTATGTTCATGAAATTGATGATTTCAAGTGAGATTATTCATGTCTAATGACTTAC
12538006 CTTATGTTAATTCATGTGAATTATGAATTGATGCACTAACATGTGTTATTGATGATGCTTAGGCT
66 CTTATGTTAATTCATGTGAATTATGAATTGATGCACTAACATGTGTTATTGATGATGCTTAGGCT
12538071 TGTGCCATTGATTGGATTGTATTATGTTAGTTTTAAGGATTTGCATTGAAATGATAAGTGTCCAA
131 TGTGCCATTGATTGGATTGTATTATGTTAGTTTTAAGGATTTGCATTGAAATGATAAGTGTCCAA
12538136 ATGGAAATATGCTTATGTTCATGAAAGGGTGGTAAGAATGAAAGTATGTAATTTCTTATGAATGG
196 ATGGAAATATGCTTATGTTCATGAAAGGGTGGTAAGAATGAAAGTATGTAATTTCTTATGAATGG
12538201 TTTATCATGTAGTTGATTTCAAAAGAGTTATGTTTAAATGCACTAGCTTGTGGCTATGGTTGATG
261 TTTATCATGTAGTTGATTTCAAAAGAGTTATGTTTAAATGCACTAGCTTGTGGCTATGGTTGATG
12538266 TTCATGCTTACATATTGCGTGTTATGCAAATGAAAC
326 TTCATGCTTACATATTGCGTGTTATGCAAATGAAAC
12538302 GA
1 GA
12538304 GTGAGAATAG
Statistics
Matches: 363, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
361 363 1.00
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.39
Consensus pattern (361 bp):
GAAAGTATGTCTATGTTCATGAAATTGATGATTTCAAGTGAGATTATTCATGTCTAATGACTTAC
CTTATGTTAATTCATGTGAATTATGAATTGATGCACTAACATGTGTTATTGATGATGCTTAGGCT
TGTGCCATTGATTGGATTGTATTATGTTAGTTTTAAGGATTTGCATTGAAATGATAAGTGTCCAA
ATGGAAATATGCTTATGTTCATGAAAGGGTGGTAAGAATGAAAGTATGTAATTTCTTATGAATGG
TTTATCATGTAGTTGATTTCAAAAGAGTTATGTTTAAATGCACTAGCTTGTGGCTATGGTTGATG
TTCATGCTTACATATTGCGTGTTATGCAAATGAAAC
Found at i:12540122 original size:25 final size:26
Alignment explanation
Indices: 12540085--12540135 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
12540075 GTTATAAATA
12540085 AGAAAAATATCTTTAG-AAATTTTCT
1 AGAAAAATATCTTTAGAAAATTTTCT
* *
12540110 AGAATAATCTCTTTAGAAAATTTTCT
1 AGAAAAATATCTTTAGAAAATTTTCT
12540136 CTCTACAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (26 bp):
AGAAAAATATCTTTAGAAAATTTTCT
Found at i:12540390 original size:141 final size:142
Alignment explanation
Indices: 12540128--12540394 Score: 423
Period size: 141 Copynumber: 1.9 Consensus size: 142
12540118 CTCTTTAGAA
* *
12540128 AATTTTCTCTCTACAACTTTCTCTTGAATTCCAGTGTGTGAAAAATAATGACCCAATGCTCTCTT
1 AATTTTCTCTCTACAACTTTCTCTTGAATTCAAGTGTATGAAAAATAATGACCCAATGCTCTCTT
12540193 TATATAAAGAGAGTTTAGAGAGTTCAACTATGATTAAACTTAATCACTCTAATATTAAATTTAAT
66 TATATAAAGAGAGTTTAGAGAGTTCAACTATGATTAAACTTAATCACTCTAATATTAAATTTAAT
12540258 GATACTTCAAAG
131 GATACTTCAAAG
* * *
12540270 AATTTTCTCTTTACAACTTTCTTTTGAATTCAAGTGTATG-TAAATAATGACCCAA-GACAT-TC
1 AATTTTCTCTCTACAACTTTCTCTTGAATTCAAGTGTATGAAAAATAATGACCCAATG-C-TCTC
* * *
12540332 TTTATATAGAGAGAGTTTAGAGAGTTCAACTATGATTAAACTTAATCACTTTAGTATTAAATT
64 TTTATATAAAGAGAGTTTAGAGAGTTCAACTATGATTAAACTTAATCACTCTAATATTAAATT
12540395 AATATAATAT
Statistics
Matches: 115, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
140 1 0.01
141 77 0.67
142 37 0.32
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.38
Consensus pattern (142 bp):
AATTTTCTCTCTACAACTTTCTCTTGAATTCAAGTGTATGAAAAATAATGACCCAATGCTCTCTT
TATATAAAGAGAGTTTAGAGAGTTCAACTATGATTAAACTTAATCACTCTAATATTAAATTTAAT
GATACTTCAAAG
Found at i:12542136 original size:16 final size:16
Alignment explanation
Indices: 12542115--12542146 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12542105 CTCTATGCAT
*
12542115 GAAAAATTTAAAAGAC
1 GAAAAATATAAAAGAC
12542131 GAAAAATATAAAAGAC
1 GAAAAATATAAAAGAC
12542147 ATAGTAGTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.06, G:0.12, T:0.16
Consensus pattern (16 bp):
GAAAAATATAAAAGAC
Found at i:12544284 original size:15 final size:14
Alignment explanation
Indices: 12544246--12544293 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
12544236 AACAAATGAA
*
12544246 AAAAAAATTAGAAT
1 AAAAAAATTAAAAT
** *
12544260 GTAAAAATTAAATT
1 AAAAAAATTAAAAT
12544274 AAAAAATATTAAAAT
1 AAAAAA-ATTAAAAT
12544289 AAAAA
1 AAAAA
12544294 TAAAAATAAC
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (14 bp):
AAAAAAATTAAAAT
Found at i:12547997 original size:86 final size:86
Alignment explanation
Indices: 12547852--12548022 Score: 256
Period size: 86 Copynumber: 2.0 Consensus size: 86
12547842 CTATGTGGTA
* *
12547852 GGCCATGTGAGCCACTAACTTGGGTCACACGGCCGAGTGACATGGCAGTGTGCCCAAACCATGCT
1 GGCCATGTGAGCCACTAACTTAGGTCACACGGCCGAGTGACATGCCAGTGTGCCCAAACCATGCT
12547917 AGGGATTGACTTGAGCCACAT
66 AGGGATTGACTTGAGCCACAT
* * *
12547938 GGCCATGTGAGCCACTGACTTAGGTCACATGAG-C-ATGTGACATGCCTGTGTGCCCAAACCATG
1 GGCCATGTGAGCCACTAACTTAGGTCACACG-GCCGA-GTGACATGCCAGTGTGCCCAAACCATG
*
12548001 TTAGGGATTGACTTGAGCCACA
64 CTAGGGATTGACTTGAGCCACA
12548023 CGACTATGTG
Statistics
Matches: 77, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
85 1 0.01
86 75 0.97
87 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.28, T:0.22
Consensus pattern (86 bp):
GGCCATGTGAGCCACTAACTTAGGTCACACGGCCGAGTGACATGCCAGTGTGCCCAAACCATGCT
AGGGATTGACTTGAGCCACAT
Found at i:12549999 original size:32 final size:31
Alignment explanation
Indices: 12549929--12549996 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
12549919 ATTAGTAAAA
* *
12549929 ATAAAATTCCACTTTGGCCTCCCTAAAAATG
1 ATAAAATTCCACATTGCCCTCCCTAAAAATG
12549960 ATAAAATTACCACATTGCCCT-CCTAAAAATG
1 ATAAAATT-CCACATTGCCCTCCCTAAAAATG
*
12549991 TTAAAA
1 ATAAAA
12549997 ATTTGATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 23 0.70
32 10 0.30
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.28
Consensus pattern (31 bp):
ATAAAATTCCACATTGCCCTCCCTAAAAATG
Found at i:12550032 original size:27 final size:29
Alignment explanation
Indices: 12549994--12550047 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 29
12549984 AAAAATGTTA
* *
12549994 AAAATTTGATTT-AA-TCCTTTAAAAATT
1 AAAATTTAATTTCAATTCCTCTAAAAATT
12550021 AAAATTTAATTTCAATTCCTCTAAAAA
1 AAAATTTAATTTCAATTCCTCTAAAAA
12550048 AAATTCTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 11 0.48
28 2 0.09
29 10 0.43
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.41
Consensus pattern (29 bp):
AAAATTTAATTTCAATTCCTCTAAAAATT
Found at i:12551427 original size:2 final size:2
Alignment explanation
Indices: 12551420--12551460 Score: 73
Period size: 2 Copynumber: 20.0 Consensus size: 2
12551410 CAATTGTGTT
12551420 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
12551461 AAAAAAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:12554420 original size:12 final size:12
Alignment explanation
Indices: 12554403--12554427 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12554393 AAAAGAGAGG
12554403 GTTTGAAAAAGA
1 GTTTGAAAAAGA
12554415 GTTTGAAAAAGA
1 GTTTGAAAAAGA
12554427 G
1 G
12554428 ATGAGTGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.28, T:0.24
Consensus pattern (12 bp):
GTTTGAAAAAGA
Found at i:12556401 original size:23 final size:23
Alignment explanation
Indices: 12556367--12556419 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
12556357 TAATATTTGT
12556367 TTTTAATATGTC-TAGCTACAACA
1 TTTTAATATGTCTTAGCT-CAACA
* *
12556390 TTTTAATGTGTCTTTAGCTGAACA
1 TTTTAATATGTC-TTAGCTCAACA
12556414 TTTTAA
1 TTTTAA
12556420 ATGCATGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 11 0.42
24 10 0.38
25 5 0.19
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.45
Consensus pattern (23 bp):
TTTTAATATGTCTTAGCTCAACA
Found at i:12576089 original size:21 final size:21
Alignment explanation
Indices: 12576066--12576133 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
12576056 AATTTTAATG
* *
12576066 ATTTTTTTGGAATTTTGGAAG
1 ATTTTTTTGAAATTTTGGAAA
* *
12576087 ATTATTTTGAAATTTT-TAAA
1 ATTTTTTTGAAATTTTGGAAA
*
12576107 ATTCTTTTTGAAACTTTGGAAA
1 ATT-TTTTTGAAATTTTGGAAA
12576129 ATTTT
1 ATTTT
12576134 ATTAATTATT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
20 5 0.13
21 27 0.71
22 6 0.16
ACGTcount: A:0.31, C:0.03, G:0.13, T:0.53
Consensus pattern (21 bp):
ATTTTTTTGAAATTTTGGAAA
Found at i:12576104 original size:42 final size:42
Alignment explanation
Indices: 12576045--12576127 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
12576035 TATACTTTTT
* * *
12576045 ATTATTTTATAAATTTTAATGATT-TTTTTGGAATTTTGGAAG
1 ATTATTTTATAAATTTTAA-AATTCTTTTTGAAACTTTGGAAG
*
12576087 ATTATTTTGA-AATTTTTAAAATTCTTTTTGAAACTTTGGAA
1 ATTATTTT-ATAAATTTTAAAATTCTTTTTGAAACTTTGGAA
12576128 AATTTTATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
41 3 0.09
42 31 0.89
43 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (42 bp):
ATTATTTTATAAATTTTAAAATTCTTTTTGAAACTTTGGAAG
Found at i:12576162 original size:173 final size:173
Alignment explanation
Indices: 12575873--12576218 Score: 683
Period size: 173 Copynumber: 2.0 Consensus size: 173
12575863 TAATATTATT
12575873 TTATTTTATAAATTTTAATAATTTTTTTGGAATTTTGGAAGATTATTTTGAAATTTTTAAAATTC
1 TTATTTTATAAATTTTAATAATTTTTTTGGAATTTTGGAAGATTATTTTGAAATTTTTAAAATTC
12575938 TTTTTGAAACTTTGGAAAATTTTATTAATTATTAACTTTTTGAATTTTTATAATTTCAAGAAAAC
66 TTTTTGAAACTTTGGAAAATTTTATTAATTATTAACTTTTTGAATTTTTATAATTTCAAGAAAAC
12576003 TACAATTTTTTATTTTTAGATATTTAATATTCTATACTTTTTA
131 TACAATTTTTTATTTTTAGATATTTAATATTCTATACTTTTTA
*
12576046 TTATTTTATAAATTTTAATGATTTTTTTGGAATTTTGGAAGATTATTTTGAAATTTTTAAAATTC
1 TTATTTTATAAATTTTAATAATTTTTTTGGAATTTTGGAAGATTATTTTGAAATTTTTAAAATTC
12576111 TTTTTGAAACTTTGGAAAATTTTATTAATTATTAACTTTTTGAATTTTTATAATTTCAAGAAAAC
66 TTTTTGAAACTTTGGAAAATTTTATTAATTATTAACTTTTTGAATTTTTATAATTTCAAGAAAAC
12576176 TACAATTTTTTATTTTTAGATATTTAATATTCTATACTTTTTA
131 TACAATTTTTTATTTTTAGATATTTAATATTCTATACTTTTTA
12576219 AAACTATGAT
Statistics
Matches: 172, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
173 172 1.00
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.54
Consensus pattern (173 bp):
TTATTTTATAAATTTTAATAATTTTTTTGGAATTTTGGAAGATTATTTTGAAATTTTTAAAATTC
TTTTTGAAACTTTGGAAAATTTTATTAATTATTAACTTTTTGAATTTTTATAATTTCAAGAAAAC
TACAATTTTTTATTTTTAGATATTTAATATTCTATACTTTTTA
Found at i:12584519 original size:21 final size:21
Alignment explanation
Indices: 12584468--12584522 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
12584458 AATTTGGTTT
*
12584468 TGCTGCTGCTACTACTACTGA
1 TGCTGCTGCTTCTACTACTGA
* * *
12584489 TG-TCGATGCTTGTACTACTGC
1 TGCT-GCTGCTTCTACTACTGA
12584510 TGCTGCTGCTTCT
1 TGCTGCTGCTTCT
12584523 TTTGCTTTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.22, T:0.38
Consensus pattern (21 bp):
TGCTGCTGCTTCTACTACTGA
Found at i:12585396 original size:20 final size:21
Alignment explanation
Indices: 12585371--12585426 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
12585361 CGAAAATTTT
*
12585371 GAAACACGAGATTTT-TTTAG
1 GAAACACGAAATTTTCTTTAG
**
12585391 GAAACAC-AAATTTTCTTTTT
1 GAAACACGAAATTTTCTTTAG
12585411 GAAACACGAAAATTTT
1 GAAACACG-AAATTTT
12585427 TAAAACACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 6 0.20
20 17 0.57
22 7 0.23
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (21 bp):
GAAACACGAAATTTTCTTTAG
Found at i:12585443 original size:16 final size:17
Alignment explanation
Indices: 12585406--12585442 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
12585396 ACAAATTTTC
*
12585406 TTTTTGAAACACGAAAA
1 TTTTTAAAACACGAAAA
12585423 TTTTTAAAACAC--AAA
1 TTTTTAAAACACGAAAA
12585438 TTTTT
1 TTTTT
12585443 TTTTTGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 8 0.42
17 11 0.58
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (17 bp):
TTTTTAAAACACGAAAA
Found at i:12585447 original size:37 final size:39
Alignment explanation
Indices: 12585367--12585451 Score: 120
Period size: 37 Copynumber: 2.2 Consensus size: 39
12585357 AAAACGAAAA
**
12585367 TTTTGAAACACGAGATTTTTTTAGGAAACACAAATTTTCT
1 TTTTGAAACACGAGAAATTTTTA-GAAACACAAATTTTCT
*
12585407 TTTTGAAACACGA-AAATTTTTA-AAACACAAATTTTTT
1 TTTTGAAACACGAGAAATTTTTAGAAACACAAATTTTCT
12585444 TTTTGAAA
1 TTTTGAAA
12585452 ACATAATATT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
37 22 0.52
39 7 0.17
40 13 0.31
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (39 bp):
TTTTGAAACACGAGAAATTTTTAGAAACACAAATTTTCT
Found at i:12585518 original size:17 final size:17
Alignment explanation
Indices: 12585492--12585729 Score: 129
Period size: 17 Copynumber: 13.3 Consensus size: 17
12585482 GAGGATTTTT
12585492 TTTTTGAAACACGAAAA
1 TTTTTGAAACACGAAAA
* **
12585509 TTTATGAAACACGGTCAATT
1 TTTTTGAAACAC-G--AAAA
*
12585529 TTTTTGAAAATACGAAAA
1 TTTTTG-AAACACGAAAA
* * * **
12585547 TTTTTGAAAGATGGGATT
1 TTTTTGAAACA-CGAAAA
*
12585565 TTTTTGAAAACACGGAAA
1 TTTTTG-AAACACGAAAA
* *
12585583 TTTATGAAACACGGAAATT
1 TTTTTGAAACAC-GAAA-A
*
12585602 TTTTTGAAAACAAGAAAA
1 TTTTTG-AAACACGAAAA
* * *
12585620 TTTTCGAAATACG-AGA
1 TTTTTGAAACACGAAAA
* *
12585636 CTTTTGAAAACAAGGAAAA
1 TTTTTG-AAAC-ACGAAAA
*
12585655 TTTTTTGAAAACACGACAA
1 -TTTTTG-AAACACGAAAA
*
12585674 TTTTTGAAACACCG-GAA
1 TTTTTGAAACA-CGAAAA
** *
12585691 TTTTAAAAACACGAAGA
1 TTTTTGAAACACGAAAA
12585708 TTTTTGAAACACGAAAA
1 TTTTTGAAACACGAAAA
12585725 TTTTT
1 TTTTT
12585730 TTAAAACACG
Statistics
Matches: 164, Mismatches: 42, Indels: 30
0.69 0.18 0.13
Matches are distributed among these distances:
16 8 0.05
17 65 0.40
18 43 0.26
19 20 0.12
20 23 0.14
21 5 0.03
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.32
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:12585552 original size:18 final size:18
Alignment explanation
Indices: 12585492--12585739 Score: 129
Period size: 18 Copynumber: 13.8 Consensus size: 18
12585482 GAGGATTTTT
12585492 TTTTTG-AAACACGAAAA
1 TTTTTGAAAACACGAAAA
* **
12585509 TTTATG-AAACACGGTCAATT
1 TTTTTGAAAACAC-G--AAAA
*
12585529 TTTTTGAAAATACGAAAA
1 TTTTTGAAAACACGAAAA
** * **
12585547 TTTTTGAAAGA-TGGGATT
1 TTTTTGAAA-ACACGAAAA
*
12585565 TTTTTGAAAACACGGAAA
1 TTTTTGAAAACACGAAAA
* *
12585583 TTTATG-AAACACGGAAATT
1 TTTTTGAAAACAC-GAAA-A
*
12585602 TTTTTGAAAACAAGAAAA
1 TTTTTGAAAACACGAAAA
* * *
12585620 TTTTCG-AAATACG-AGA
1 TTTTTGAAAACACGAAAA
* *
12585636 CTTTTGAAAACAAGGAAAA
1 TTTTTGAAAAC-ACGAAAA
*
12585655 TTTTTTGAAAACACGACAA
1 -TTTTTGAAAACACGAAAA
*
12585674 TTTTTG-AAACACCG-GAA
1 TTTTTGAAAACA-CGAAAA
* *
12585691 -TTTTAAAAACACGAAGA
1 TTTTTGAAAACACGAAAA
12585708 TTTTTG-AAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
12585725 TTTTTTTAAAACACG
1 -TTTTTGAAAACACG
12585740 GAAACACGAA
Statistics
Matches: 171, Mismatches: 41, Indels: 36
0.69 0.17 0.15
Matches are distributed among these distances:
16 12 0.07
17 49 0.29
18 58 0.34
19 24 0.14
20 23 0.13
21 5 0.03
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:12585566 original size:36 final size:37
Alignment explanation
Indices: 12585490--12585622 Score: 171
Period size: 36 Copynumber: 3.6 Consensus size: 37
12585480 ACGAGGATTT
*
12585490 TTTTTTTG-AAACACGAAAATTTATGAAACACGGTCAA
1 TTTTTTTGAAAACACGAAAATTTATGAAACACGG-AAA
* * * * *
12585527 TTTTTTTGAAAATACGAAAATTTTTGAAAGATGG-GA
1 TTTTTTTGAAAACACGAAAATTTATGAAACACGGAAA
*
12585563 TTTTTTTGAAAACACGGAAATTTATGAAACACGGAAA
1 TTTTTTTGAAAACACGAAAATTTATGAAACACGGAAA
*
12585600 TTTTTTTGAAAACAAGAAAATTT
1 TTTTTTTGAAAACACGAAAATTT
12585623 TCGAAATACG
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
36 30 0.37
37 30 0.37
38 21 0.26
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.35
Consensus pattern (37 bp):
TTTTTTTGAAAACACGAAAATTTATGAAACACGGAAA
Found at i:12585576 original size:74 final size:72
Alignment explanation
Indices: 12585490--12585628 Score: 215
Period size: 73 Copynumber: 1.9 Consensus size: 72
12585480 ACGAGGATTT
* * * *
12585490 TTTTTTTGAAACACGAAAATTTATGAAACACGGTCAATTTTTTTGAAAATACGAAAATTTTTGAA
1 TTTTTTTGAAACACGAAAATTTATGAAACACGG-AAATTTTTTTGAAAACAAGAAAATTTTCGAA
12585555 AGATGGGA
65 AGATGGGA
*
12585563 TTTTTTTGAAAACACGGAAATTTATGAAACACGGAAATTTTTTTGAAAACAAGAAAATTTTCGAA
1 TTTTTTTG-AAACACGAAAATTTATGAAACACGGAAATTTTTTTGAAAACAAGAAAATTTTCGAA
12585628 A
65 A
12585629 TACGAGACTT
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
73 36 0.60
74 24 0.40
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.35
Consensus pattern (72 bp):
TTTTTTTGAAACACGAAAATTTATGAAACACGGAAATTTTTTTGAAAACAAGAAAATTTTCGAAA
GATGGGA
Found at i:12585700 original size:54 final size:53
Alignment explanation
Indices: 12585565--12585729 Score: 158
Period size: 54 Copynumber: 3.1 Consensus size: 53
12585555 AGATGGGATT
* * * * *
12585565 TTTTTGAAAACACGGAAATTTATGAAACACGGAAATTTTTTTGAAAACAAGAAAA
1 TTTTTGAAAAC-CGGAATTTTA-AAAACAAGGAAAATTTTTTGAAAACACGAAAA
* * * *
12585620 TTTTCGAAATA-CGAGACTTTTGAAAACAAGGAAAATTTTTTGAAAACACGACAA
1 TTTTTGAAA-ACCG-GAATTTTAAAAACAAGGAAAATTTTTTGAAAACACGAAAA
* *
12585674 TTTTTGAAACACCGGAATTTTAAAAAC-ACGAAGA-TTTTTG-AAACACGAAAA
1 TTTTTGAAA-ACCGGAATTTTAAAAACAAGGAAAATTTTTTGAAAACACGAAAA
12585725 TTTTT
1 TTTTT
12585730 TTAAAACACG
Statistics
Matches: 91, Mismatches: 16, Indels: 10
0.78 0.14 0.09
Matches are distributed among these distances:
51 15 0.16
52 6 0.07
53 5 0.05
54 49 0.54
55 15 0.16
56 1 0.01
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (53 bp):
TTTTTGAAAACCGGAATTTTAAAAACAAGGAAAATTTTTTGAAAACACGAAAA
Found at i:12586642 original size:19 final size:20
Alignment explanation
Indices: 12586607--12586659 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
12586597 TTATTTTTAT
12586607 TTTTTCTTTCTTATTCTCTC
1 TTTTTCTTTCTTATTCTCTC
*
12586627 TTTTTCTTT-TTTTTCTCTC
1 TTTTTCTTTCTTATTCTCTC
*
12586646 TTCTTCTTCTCTTA
1 TTTTTCTT-TCTTA
12586660 ACTTTCTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 16 0.57
20 10 0.36
21 2 0.07
ACGTcount: A:0.04, C:0.25, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTTCTTTCTTATTCTCTC
Found at i:12586664 original size:29 final size:29
Alignment explanation
Indices: 12586606--12586674 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
12586596 TTTATTTTTA
* **
12586606 TTTTTTCTTTCTTATTCTCTCTTTTTCTT
1 TTTTTTCTCTCTTATTCTCTCTTTAACTT
*
12586635 TTTTTTCTCTCTTCTTCT-TCTCTTAACTT
1 TTTTTTCTCTCTTATTCTCTCT-TTAACTT
12586664 TCTTTTT-TCTC
1 T-TTTTTCTCTC
12586675 CTTCGGCAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
28 3 0.09
29 26 0.76
30 5 0.15
ACGTcount: A:0.04, C:0.25, G:0.00, T:0.71
Consensus pattern (29 bp):
TTTTTTCTCTCTTATTCTCTCTTTAACTT
Found at i:12586807 original size:19 final size:20
Alignment explanation
Indices: 12586777--12586814 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
12586767 CCTTTTTTCC
12586777 CTTTTCCTTTTTCTTCTTTA
1 CTTTTCCTTTTTCTTCTTTA
*
12586797 CTTTT-CTTTTTTTTCTTT
1 CTTTTCCTTTTTCTTCTTT
12586815 TGCTTGCTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (20 bp):
CTTTTCCTTTTTCTTCTTTA
Found at i:12587242 original size:29 final size:29
Alignment explanation
Indices: 12587188--12587243 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
12587178 CAAAGTTTCT
*
12587188 GGGGTAAAAGTGTAATTTTGGCAAAATAC
1 GGGGTAAAAGTGTAATTTTGGAAAAATAC
*
12587217 GGGGTTAAAA-TGTAATTTTTGAAAAAT
1 GGGG-TAAAAGTGTAATTTTGGAAAAAT
12587244 TTGAGGGCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.32
Consensus pattern (29 bp):
GGGGTAAAAGTGTAATTTTGGAAAAATAC
Found at i:12587294 original size:30 final size:30
Alignment explanation
Indices: 12587260--12587372 Score: 133
Period size: 34 Copynumber: 3.7 Consensus size: 30
12587250 GCTAAAACGT
*
12587260 AATTT-AGAAGAGTTTAGGGGTAGAAATGTA
1 AATTTGAGAA-AGTTTAGGGGTTGAAATGTA
*
12587290 AATTTGAGAAAGTTTATGGGTTGAAATGTA
1 AATTTGAGAAAGTTTAGGGGTTGAAATGTA
12587320 ATTTCATTTGAGAAAGTTTAGGGGTTGAAATGT-
1 A----ATTTGAGAAAGTTTAGGGGTTGAAATGTA
12587353 AATTT-AGAAAAGTTTAGGGG
1 AATTTGAG-AAAGTTTAGGGG
12587373 CCAAAATGTA
Statistics
Matches: 74, Mismatches: 3, Indels: 13
0.82 0.03 0.14
Matches are distributed among these distances:
28 2 0.03
29 16 0.22
30 24 0.32
31 4 0.05
33 1 0.01
34 27 0.36
ACGTcount: A:0.36, C:0.01, G:0.28, T:0.35
Consensus pattern (30 bp):
AATTTGAGAAAGTTTAGGGGTTGAAATGTA
Found at i:12587367 original size:29 final size:29
Alignment explanation
Indices: 12587217--12587386 Score: 139
Period size: 29 Copynumber: 5.6 Consensus size: 29
12587207 GGCAAAATAC
* *
12587217 GGGGTTAAAATGTAATTTTTGAAAAATTT-
1 GGGGTTAAAATGTAA-TTTAGAAAAGTTTA
* * *
12587246 GAGGGCTAAAACGTAATTTAGAAGAGTTTA
1 G-GGGTTAAAATGTAATTTAGAAAAGTTTA
12587276 GGGG-TAGAAATGTAAATTT-GAGAAAGTTTA
1 GGGGTTA-AAATGT-AATTTAGA-AAAGTTTA
* *
12587306 TGGGTTGAAATGTAATTTCATTTGAGAAAGTTTA
1 GGGGTTAAAATGTAATTT-A---GA-AAAGTTTA
*
12587340 GGGGTTGAAATGTAATTTAGAAAAGTTTA
1 GGGGTTAAAATGTAATTTAGAAAAGTTTA
**
12587369 GGGGCCAAAATGTAATTT
1 GGGGTTAAAATGTAATTT
12587387 GTATTTTTTT
Statistics
Matches: 117, Mismatches: 13, Indels: 22
0.77 0.09 0.14
Matches are distributed among these distances:
28 2 0.02
29 49 0.42
30 36 0.31
31 1 0.01
33 1 0.01
34 28 0.24
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.34
Consensus pattern (29 bp):
GGGGTTAAAATGTAATTTAGAAAAGTTTA
Found at i:12587382 original size:63 final size:64
Alignment explanation
Indices: 12587261--12587386 Score: 168
Period size: 63 Copynumber: 2.0 Consensus size: 64
12587251 CTAAAACGTA
* ***
12587261 ATTTAGAAGAGTTTAGGGGTAGAAATGTAAATTTGAGAAAGTTTATGGGTTGAAATGTAATTTC
1 ATTTAGAAGAGTTTAGGGGTAGAAATGTAAATTTGAGAAAGTTTAGGGGCCAAAATGTAATTTC
*
12587325 ATTTGAGAA-AGTTTAGGGGTTGAAATGT-AATTT-AGAAAAGTTTAGGGGCCAAAATGTAATTT
1 ATTT-AGAAGAGTTTAGGGGTAGAAATGTAAATTTGAG-AAAGTTTAGGGGCCAAAATGTAATTT
12587387 GTATTTTTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
62 2 0.04
63 27 0.49
64 22 0.40
65 4 0.07
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.35
Consensus pattern (64 bp):
ATTTAGAAGAGTTTAGGGGTAGAAATGTAAATTTGAGAAAGTTTAGGGGCCAAAATGTAATTTC
Found at i:12588037 original size:157 final size:155
Alignment explanation
Indices: 12587755--12588305 Score: 585
Period size: 157 Copynumber: 3.4 Consensus size: 155
12587745 AAACAAAGAA
* * * *
12587755 AAAATTAAAAAATACCTCAGC-T-TGACTCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATT
1 AAAATTAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--
* *
12587818 TTTTTTTTTTTGAAAACA-TAAATTG-AAAATACCTCAGC-GTGACCTGAGGCTTAACTCACCTC
64 --TTTTTTTTT-AAAACAGT-AATTGAAAAATACCTCGGCTGTGACCTGAGGCTCAACTCACCTC
*
12587880 TCGCATTATGAGTTGA-TTTTTGAAAAACAG
125 TCGCAATATGAGTTGATTTTTTGAAAAACAG
* *
12587910 AAAATTGAAAAATACCTCGGCATGTGACCCGGGGCTCAACTCACCTCTCGCAATATGAGTTGATT
1 AAAATTAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
* *
12587975 GTTTTTTTAAAAGTAGTAATTGAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCG
66 -TTTTTTTAAAA-CAGTAATTGAAAAATACCTCGGC-TGTGACCTGAGGCTCAACTCACCTCTCG
12588040 CAATATGAGTTGATTTTTTTGAAAAACAG
128 CAATATGAGTTGA-TTTTTTGAAAAACAG
* * * *
12588069 AAATTTAAAAGAAATACCACGACATGTGACCCGAAGCTCAACTCACCTCTCGCAATATGAGTTGA
1 AAAATT-AAA-AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
* * * *
12588134 TTTTTTTTGAAAAAACAGAAATTTAAAAGAAATACCTCGGAATGTGACCTGAGGCTCAACTCACC
64 TTTTTTTT--TAAAACAGTAA-TT-GAA-AAATACCTCGG-CTGTGACCTGAGGCTCAACTCACC
**
12588199 TCTCGCAATATGAGTTGAATTTTTTTTTTTTAAAA-AG
123 TCTCGCAATATGAGTTG-A----TTTTTTGAAAAACAG
* * * * * *
12588236 TAGTAATTGAAAAATACCTCGGCGTGTGACCCGGGGCTCAACTCACCTCTGGCAATATGAGCTGA
1 -A-AAATTAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
12588301 TTTTT
64 TTTTT
12588306 GAAAAACAGA
Statistics
Matches: 337, Mismatches: 35, Indels: 36
0.83 0.09 0.09
Matches are distributed among these distances:
153 6 0.02
154 13 0.04
155 32 0.09
156 1 0.00
157 72 0.21
159 19 0.06
160 8 0.02
161 56 0.17
162 6 0.02
163 2 0.01
164 50 0.15
165 1 0.00
167 54 0.16
168 14 0.04
169 3 0.01
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.30
Consensus pattern (155 bp):
AAAATTAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
TTTTTTTAAAACAGTAATTGAAAAATACCTCGGCTGTGACCTGAGGCTCAACTCACCTCTCGCAA
TATGAGTTGATTTTTTGAAAAACAG
Found at i:12588191 original size:83 final size:79
Alignment explanation
Indices: 12587756--12588324 Score: 597
Period size: 80 Copynumber: 7.1 Consensus size: 79
12587746 AACAAAGAAA
* * * * *
12587756 AAATTAAAAAATACCTCAGC-T-TGACTCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTT
1 AAATTGAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---
*
12587819 TTTTTTTTTTG-AAAACAT
63 --TTTTTTTTGAAAAACAG
* * * *
12587837 AAATTG-AAAATACCTCAGC--GTGACCTGAGGCTTAACTCACCTCTCGCATTATGAGTTGA---
1 AAATTGAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
12587896 TTTTTGAAAAACAG
66 TTTTTGAAAAACAG
*
12587910 AAAATTGAAAAATACCTCGGCATGTGACCCGGGGCTCAACTCACCTCTCGCAATATGAGTTGATT
1 -AAATTGAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
* **
12587975 GTTTTTTTAAAAGTAG
65 -TTTTTTGAAAAACAG
* *
12587991 TAATTGAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TT
1 AAATTGAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
12588055 TTTTTGAAAAACAG
66 TTTTTGAAAAACAG
* * * *
12588069 AAATTTAAAAGAAATACCACGACATGTGACCCGAAGCTCAACTCACCTCTCGCAATATGAGTTGA
1 AAA-TT-GAA-AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
12588134 TTTTTTTTGAAAAAACAG
63 TTTTTTTTG-AAAAACAG
* * *
12588152 AAATTTAAAAGAAATACCTCGGAATGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 AAA-TT-GAA-AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG-
* *
12588217 ATTTTTTTTTTTTAAAAAGTAG
62 A---TTTTTTTTGAAAAA-CAG
* * * * *
12588239 TAATTGAAAAATACCTCGGCGTGTGACCCGGGGCTCAACTCACCTCTGGCAATATGAGCTGA---
1 AAATTGAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
12588301 TTTTTGAAAAACAG
66 TTTTTGAAAAACAG
*
12588315 AAATCGAAAA
1 AAATTGAAAA
12588325 TAATTCTTGA
Statistics
Matches: 423, Mismatches: 45, Indels: 45
0.82 0.09 0.09
Matches are distributed among these distances:
72 6 0.01
73 6 0.01
74 6 0.01
75 12 0.03
76 10 0.02
77 46 0.11
78 14 0.03
79 3 0.01
80 109 0.26
81 66 0.16
82 8 0.02
83 68 0.16
84 48 0.11
85 2 0.00
86 7 0.02
87 12 0.03
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (79 bp):
AAATTGAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
TTTTTGAAAAACAG
Found at i:12588304 original size:248 final size:236
Alignment explanation
Indices: 12587856--12588318 Score: 701
Period size: 248 Copynumber: 1.9 Consensus size: 236
12587846 ATACCTCAGC
* * * * *
12587856 GTGACCTGAGGCTTAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACAGAAAATTGAAAA
1 GTGACCCGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAAATTAAAAA
* *
12587921 ATACCTCGGCATGTGACCCGGGGCTCAACTCACCTCTCGCAATATGAGTTGATTGTTTTTTTAAA
66 ATACCTCGGAATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTGTTTTTTTAAA
*
12587986 AGTAGTAATTGAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
131 AGTAGTAATTGAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGCT
12588051 GATTTTTTTGAAAAACAGAAATTTAAAAGAAATACCACGACAT
196 GA--TTTTTGAAAAACAGAAATTTAAAAGAAATACCACGACAT
*
12588094 GTGACCCGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAAACAGAAATTTA
1 GTGACCCGAAGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTG-AAAAACAGAAAATT-
* *
12588159 AAAGAAATACCTCGGAATGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTT
61 AAA-AAATACCTCGGAATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG-A--TTGT
* *
12588224 TTTTTTAAAAAGTAGTAATTGAAAAATACCTCGGCGTGTGACCCGGGGCTCAACTCACCTCTGGC
122 TTTTTT-AAAAGTAGTAATTGAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGC
12588289 AATATGAGCTGATTTTTGAAAAACAGAAAT
186 AATATGAGCTGATTTTTGAAAAACAGAAAT
12588319 CGAAAATAAT
Statistics
Matches: 202, Mismatches: 13, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
238 36 0.18
241 6 0.03
242 13 0.06
243 2 0.01
244 50 0.25
245 1 0.00
246 18 0.09
247 9 0.04
248 67 0.33
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (236 bp):
GTGACCCGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAAATTAAAAA
ATACCTCGGAATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTGTTTTTTTAAA
AGTAGTAATTGAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGCT
GATTTTTGAAAAACAGAAATTTAAAAGAAATACCACGACAT
Found at i:12589958 original size:1 final size:1
Alignment explanation
Indices: 12589954--12590016 Score: 54
Period size: 1 Copynumber: 63.0 Consensus size: 1
12589944 ATTTTTCTTC
* * * * * * **
12589954 TTTTTTTATTTTTTTATTTTTTTATTTTTTTTGTTGTTTTTTTGTTTTTTTTCCTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12590017 AGGCATAATA
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.05, C:0.03, G:0.05, T:0.87
Consensus pattern (1 bp):
T
Found at i:12589967 original size:7 final size:8
Alignment explanation
Indices: 12589944--12589984 Score: 64
Period size: 8 Copynumber: 5.0 Consensus size: 8
12589934 TTTCATCTTG
12589944 ATTTTTCTT
1 ATTTTT-TT
*
12589953 CTTTTTTT
1 ATTTTTTT
12589961 ATTTTTTT
1 ATTTTTTT
12589969 ATTTTTTT
1 ATTTTTTT
12589977 ATTTTTTT
1 ATTTTTTT
12589985 TGTTGTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
8 25 0.83
9 5 0.17
ACGTcount: A:0.10, C:0.05, G:0.00, T:0.85
Consensus pattern (8 bp):
ATTTTTTT
Found at i:12590013 original size:20 final size:20
Alignment explanation
Indices: 12589945--12590017 Score: 66
Period size: 20 Copynumber: 3.9 Consensus size: 20
12589935 TTCATCTTGA
*
12589945 TTTTTCTTCTTTTTTTA---
1 TTTTTCTTGTTTTTTTATTT
*
12589962 TTTTT-TTATTTTTTTATTT
1 TTTTTCTTGTTTTTTTATTT
* *
12589981 TTTTTGTTGTTTTTTTGTTT
1 TTTTTCTTGTTTTTTTATTT
12590001 TTTTTCCTT-TTTTTTTA
1 TTTTT-CTTGTTTTTTTA
12590018 GGCATAATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
16 10 0.22
17 5 0.11
19 5 0.11
20 24 0.52
21 2 0.04
ACGTcount: A:0.05, C:0.05, G:0.04, T:0.85
Consensus pattern (20 bp):
TTTTTCTTGTTTTTTTATTT
Found at i:12596444 original size:20 final size:20
Alignment explanation
Indices: 12596397--12596481 Score: 63
Period size: 20 Copynumber: 4.4 Consensus size: 20
12596387 AAAACGAAAA
* *
12596397 TTTTGAAACACTAGATTTTT
1 TTTTGAAACACGAAATTTTT
**
12596417 TTAGGAAACAC-AAATTTTCT
1 TTTTGAAACACGAAATTTT-T
*
12596437 TTTTGAAACACGAAA---AT
1 TTTTGAAACACGAAATTTTT
*
12596454 TTTTAAAACAC-AAATTTTTT
1 TTTTGAAACACGAAA-TTTTT
12596474 TTTTGAAA
1 TTTTGAAA
12596482 ACATAATATT
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
16 3 0.06
17 11 0.22
19 6 0.12
20 27 0.54
21 3 0.06
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (20 bp):
TTTTGAAACACGAAATTTTT
Found at i:12596473 original size:16 final size:17
Alignment explanation
Indices: 12596436--12596472 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
12596426 ACAAATTTTC
*
12596436 TTTTTGAAACACGAAAA
1 TTTTTAAAACACGAAAA
12596453 TTTTTAAAACAC--AAA
1 TTTTTAAAACACGAAAA
12596468 TTTTT
1 TTTTT
12596473 TTTTTGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 8 0.42
17 11 0.58
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (17 bp):
TTTTTAAAACACGAAAA
Found at i:12596546 original size:17 final size:17
Alignment explanation
Indices: 12596520--12597106 Score: 185
Period size: 17 Copynumber: 32.8 Consensus size: 17
12596510 ACGAGGATTT
12596520 TTTTTGAAACACGAAAA
1 TTTTTGAAACACGAAAA
* **
12596537 TTTATGAAACACGGTCAATT
1 TTTTTGAAACAC-G--AAAA
12596557 TTTTTGAAAACACGAAAA
1 TTTTTG-AAACACGAAAA
* **
12596575 TTTTTGAAAGACGAGATT
1 TTTTTGAAACACGA-AAA
* *
12596593 TTTTTGAAAATACGGAAA
1 TTTTTG-AAACACGAAAA
* **
12596611 TTTATGAAACACGGAATT
1 TTTTTGAAACAC-GAAAA
*
12596629 TTTTTGAAAACAAGAAAA
1 TTTTTG-AAACACGAAAA
* * *
12596647 TTTTCGAAATACG-AGA
1 TTTTTGAAACACGAAAA
* *
12596663 CTTTTGAAAACAAGGAAAA
1 TTTTTG-AAAC-ACGAAAA
12596682 TTTTTTGAAAACAC-AACAA
1 -TTTTTG-AAACACGAA-AA
* *
12596701 TTTTTGAAACACCAGAA
1 TTTTTGAAACACGAAAA
*
12596718 -TTTTGAAAACACGAAGA
1 TTTTTG-AAACACGAAAA
12596735 TTTTTGAAACACGAAAA
1 TTTTTGAAACACGAAAA
**
12596752 TTTTTTTTGAAAACACGAATTTTC
1 ---TTTTTG-AAACACGAA---AA
12596776 TTTTTGAAACACGAAAA
1 TTTTTGAAACACGAAAA
* *
12596793 TTATTAAAACAC-AAAA
1 TTTTTGAAACACGAAAA
*
12596809 TTTGTTTTTGAAA-ACATAAAA
1 ----TTTTTGAAACAC-GAAAA
* *
12596830 TTTTTTATA-A--AAAA
1 TTTTTGAAACACGAAAA
* **
12596844 ----CGAAACACGAGGATTTT
1 TTTTTGAAACACGA--A--AA
12596861 TTTTTGAAACACGAAAA
1 TTTTTGAAACACGAAAA
* **
12596878 TTTATGAAACACGGTCAATT
1 TTTTTGAAACAC-G--AAAA
12596898 TTTTTGAAAACACGAAAA
1 TTTTTG-AAACACGAAAA
* * *
12596916 TTTTTGAAAGACGGGATA
1 TTTTTGAAACAC-GAAAA
*
12596934 TTTTTGAAAACACGGAAA
1 TTTTTG-AAACACGAAAA
* * *
12596952 TTTATGAAACACGGAAT
1 TTTTTGAAACACGAAAA
*
12596969 TTTGTTGTAAACAAGAAAA
1 TTT-TTG-AAACACGAAAA
* *
12596988 TTTTTGAAATACG-AGA
1 TTTTTGAAACACGAAAA
* * *
12597004 CTTTTGAAAAGAAGGAAAA
1 TTTTTG-AAA-CACGAAAA
* ** *
12597023 TTTTTTATTCACGAGAA
1 TTTTTGAAACACGAAAA
*
12597040 TTTTTGAAACACGAAGAT
1 TTTTTGAAACACGAA-AA
*
12597058 TTTTTGAAAACACGGAAA
1 TTTTTG-AAACACGAAAA
* **
12597076 -TTTTGAAAACATGAATTT
1 TTTTTG-AAACACGAA-AA
12597094 TTTTTGAAACACG
1 TTTTTGAAACACG
12597107 GGAGATTTTA
Statistics
Matches: 416, Mismatches: 99, Indels: 109
0.67 0.16 0.17
Matches are distributed among these distances:
10 2 0.00
11 1 0.00
13 1 0.00
14 4 0.01
15 1 0.00
16 22 0.05
17 141 0.34
18 102 0.25
19 54 0.13
20 48 0.12
21 40 0.10
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:12596594 original size:36 final size:36
Alignment explanation
Indices: 12596505--12597115 Score: 287
Period size: 36 Copynumber: 16.4 Consensus size: 36
12596495 GATAAAATAC
*
12596505 GAAACACGAGGATTTTTTTTG-AAACACGAAAATTTAT
1 GAAACACGA-GA-TTTTTTTGAAAACACGAAAATTTTT
12596542 GAAACACG-GTCAATTTTTTTGAAAACACGAAAATTTTT
1 GAAACACGAG---ATTTTTTTGAAAACACGAAAATTTTT
* * * *
12596580 GAAAGACGAGATTTTTTTGAAAATACGGAAATTTAT
1 GAAACACGAGATTTTTTTGAAAACACGAAAATTTTT
* *
12596616 GAAACACG-GAATTTTTTTGAAAACAAGAAAATTTTC
1 GAAACACGAG-ATTTTTTTGAAAACACGAAAATTTTT
* * *
12596652 GAAATACGAGA--CTTTTGAAAACAAGGAAAATTTTTT
1 GAAACACGAGATTTTTTTGAAAAC-ACGAAAA-TTTTT
* * * * *
12596688 GAAAACACAACA-ATTTTTG-AAACACCAGAA-TTTT
1 G-AAACACGAGATTTTTTTGAAAACACGAAAATTTTT
12596722 GAAAACACGAAGA--TTTTTG-AAACACGAAAATTTTTTTT
1 G-AAACACG-AGATTTTTTTGAAAACACGAAAA---TTTTT
*
12596760 GAAAACACGA-ATTTTCTTTTTG-AAACACGAAAATTATT
1 G-AAACACGAGA--TT-TTTTTGAAAACACGAAAATTTTT
* * * *
12596798 AAAACACAAAATTTGTTTTTGAAAACA-TAAAATTTTTTAT
1 GAAACACGAGA-TT-TTTTTGAAAACACGAAAA--TTTT-T
*
12596838 AAAAAACGAAACACGAGGATTTTTTTTTG-AAACACGAAAATTTAT
1 -------GAAACACGA-GA-T-TTTTTTGAAAACACGAAAATTTTT
12596883 GAAACACG-GTCAATTTTTTTGAAAACACGAAAATTTTT
1 GAAACACGAG---ATTTTTTTGAAAACACGAAAATTTTT
* * * * *
12596921 GAAAGACGGGATATTTTTGAAAACACGGAAATTTAT
1 GAAACACGAGATTTTTTTGAAAACACGAAAATTTTT
* * *
12596957 GAAACACG-GAATTTTGTTGTAAACAAGAAAATTTTT
1 GAAACACGAG-ATTTTTTTGAAAACACGAAAATTTTT
* * * *
12596993 GAAATACGAGA--CTTTTGAAAAGAAGGAAAATTTTT
1 GAAACACGAGATTTTTTTGAAAA-CACGAAAATTTTT
* ** * *
12597028 TATTCACGAGA-ATTTTTG-AAACACGAAGATTTTTT
1 GAAACACGAGATTTTTTTGAAAACACGAA-AATTTTT
** * **
12597063 GAAAACACG-GA-AATTTTGAAAACATGAATTTTTTTT
1 G-AAACACGAGATTTTTTTGAAAACACGAA-AATTTTT
12597099 GAAACACGGGAGATTTT
1 GAAACAC--GAGATTTT
12597116 ATTATTATTA
Statistics
Matches: 450, Mismatches: 72, Indels: 102
0.72 0.12 0.16
Matches are distributed among these distances:
34 48 0.11
35 52 0.12
36 153 0.34
37 58 0.13
38 84 0.19
39 7 0.02
40 1 0.00
41 17 0.04
45 1 0.00
46 3 0.01
47 12 0.03
48 13 0.03
49 1 0.00
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (36 bp):
GAAACACGAGATTTTTTTGAAAACACGAAAATTTTT
Found at i:12596763 original size:54 final size:51
Alignment explanation
Indices: 12596558--12596756 Score: 163
Period size: 54 Copynumber: 3.8 Consensus size: 51
12596548 CGGTCAATTT
* ** * *
12596558 TTTTGAAAACACGAAAATTTTTG-AAAGACGAGATTTTTTTGAAAATACGGAAA
1 TTTTGAAAACACGAAAATTTTTGAAAACACGA-AAATTTTTGAAAA-CCAG-AA
** * * * *
12596611 TTTATG-AAACACGGAATTTTTTTGAAAACAAGAAAATTTTCGAAATACGAGAC
1 TTT-TGAAAACAC-GAAAATTTTTGAAAACACGAAAATTTTTGAAA-ACCAGAA
*
12596664 TTTTGAAAACAAGGAAAATTTTTTGAAAACAC-AACAATTTTTGAAACACCAGAA
1 TTTTGAAAAC-ACGAAAA-TTTTTGAAAACACGAA-AATTTTTGAAA-ACCAGAA
*
12596718 TTTTGAAAACACGAAGATTTTTG-AAACACGAAAATTTTT
1 TTTTGAAAACACGAAAATTTTTGAAAACACGAAAATTTTT
12596757 TTTGAAAACA
Statistics
Matches: 116, Mismatches: 21, Indels: 20
0.74 0.13 0.13
Matches are distributed among these distances:
51 13 0.11
52 10 0.09
53 27 0.23
54 59 0.51
55 7 0.06
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (51 bp):
TTTTGAAAACACGAAAATTTTTGAAAACACGAAAATTTTTGAAAACCAGAA
Found at i:12596765 original size:21 final size:21
Alignment explanation
Indices: 12596718--12596848 Score: 99
Period size: 20 Copynumber: 6.8 Consensus size: 21
12596708 AACACCAGAA
*
12596718 TTTTGAAAACACGAAGA---T
1 TTTTGAAAACACGAAAATTTT
12596736 TTTTG-AAACACGAAAATTTT
1 TTTTGAAAACACGAAAATTTT
*
12596756 TTTTGAAAACACG-AATTTTCT
1 TTTTGAAAACACGAAAATTT-T
12596777 TTTTG-AAACACGAAAA---T
1 TTTTGAAAACACGAAAATTTT
*
12596794 TATT-AAAACAC-AAAATTTGT
1 TTTTGAAAACACGAAAATTT-T
*
12596814 TTTTGAAAACA-TAAAATTTT
1 TTTTGAAAACACGAAAATTTT
* *
12596834 TTAT-AAAAAACGAAA
1 TTTTGAAAACACGAAA
12596849 CACGAGGATT
Statistics
Matches: 91, Mismatches: 8, Indels: 26
0.73 0.06 0.21
Matches are distributed among these distances:
16 4 0.04
17 20 0.22
18 5 0.05
19 5 0.05
20 29 0.32
21 28 0.31
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.35
Consensus pattern (21 bp):
TTTTGAAAACACGAAAATTTT
Found at i:12596951 original size:341 final size:337
Alignment explanation
Indices: 12596385--12597106 Score: 1101
Period size: 341 Copynumber: 2.1 Consensus size: 337
12596375 TCTTTTTTAA
* * * * * *
12596385 AAAAAACGAAAATTTTGAAACACTAGATTTTTTTAGGAAACACAAATTTTCTTTTTGAAACACGA
1 AAAACACGGAAATTTTGAAACACAAAATTTTTTT-TGAAACACGAATTTTCTTTTTGAAACACGA
* * * * *
12596450 AAATTTTTAAAACACAAATTTTTTTTTTGAAAACATAATATTTTTGATAAAATACGAAACACGAG
65 AAATTATTAAAACACAAAATTTGTTTTTGAAAACATAAAATTTTTGATAAAAAACGAAACACGAG
12596515 GATTTTTTTTGAAACACGAAAATTTATGAAACACGGTCAATTTTTTTGAAAACACGAAAATTTTT
130 GATTTTTTTTGAAACACGAAAATTTATGAAACACGGTCAATTTTTTTGAAAACACGAAAATTTTT
* * *
12596580 GAAAGACGAGATTTTTTTGAAAATACGGAAATTTATGAAACACGGAATTTTTTTGAAAACAAGAA
195 GAAAGACGAGATATTTTTGAAAACACGGAAATTTATGAAACACGGAATTTTGTTGAAAACAAGAA
12596645 AATTTTCGAAATACGAGACTTTTGAAAACAAGGAAAATTTTTTGAAAACACAACAATTTTTGAAA
260 AATTTTCGAAATACGAGACTTTTGAAAACAAGGAAAATTTTTT--AAACACAACAATTTTTGAAA
*
12596710 CAC-CAGA-ATTTTG
323 CACGAAGATATTTTG
12596723 AAAACAC-GAAGATTTTTGAAACACGAAAATTTTTTTTGAAAACACGAATTTTCTTTTTGAAACA
1 AAAACACGGAA-A-TTTTGAAACAC-AAAATTTTTTTTG-AAACACGAATTTTCTTTTTGAAACA
*
12596787 CGAAAATTATTAAAACACAAAATTTGTTTTTGAAAACATAAAATTTTTTATAAAAAACGAAACAC
62 CGAAAATTATTAAAACACAAAATTTGTTTTTGAAAACATAAAATTTTTGATAAAAAACGAAACAC
12596852 GAGGATTTTTTTTTGAAACACGAAAATTTATGAAACACGGTCAATTTTTTTGAAAACACGAAAAT
127 GAGGA-TTTTTTTTGAAACACGAAAATTTATGAAACACGGTCAATTTTTTTGAAAACACGAAAAT
* *
12596917 TTTTGAAAGACGGGATATTTTTGAAAACACGGAAATTTATGAAACACGGAATTTTGTTGTAAACA
191 TTTTGAAAGACGAGATATTTTTGAAAACACGGAAATTTATGAAACACGGAATTTTGTTGAAAACA
* * ** * *
12596982 AGAAAATTTTTGAAATACGAGACTTTTGAAAAGAAGGAAAATTTTTTATTCACGAGAATTTTTGA
256 AGAAAATTTTCGAAATACGAGACTTTTGAAAACAAGGAAAATTTTTTAAACACAACAATTTTTGA
*
12597047 AACACGAAGATTTTTTG
321 AACACGAAGATATTTTG
*
12597064 AAAACACGGAAATTTTGAAA-ACATGAATTTTTTTTGAAACACG
1 AAAACACGGAAATTTTGAAACACA-AAATTTTTTTTGAAACACG
12597107 GGAGATTTTA
Statistics
Matches: 349, Mismatches: 26, Indels: 18
0.89 0.07 0.05
Matches are distributed among these distances:
337 2 0.01
338 15 0.04
339 44 0.13
340 108 0.31
341 177 0.51
342 3 0.01
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.33
Consensus pattern (337 bp):
AAAACACGGAAATTTTGAAACACAAAATTTTTTTTGAAACACGAATTTTCTTTTTGAAACACGAA
AATTATTAAAACACAAAATTTGTTTTTGAAAACATAAAATTTTTGATAAAAAACGAAACACGAGG
ATTTTTTTTGAAACACGAAAATTTATGAAACACGGTCAATTTTTTTGAAAACACGAAAATTTTTG
AAAGACGAGATATTTTTGAAAACACGGAAATTTATGAAACACGGAATTTTGTTGAAAACAAGAAA
ATTTTCGAAATACGAGACTTTTGAAAACAAGGAAAATTTTTTAAACACAACAATTTTTGAAACAC
GAAGATATTTTG
Found at i:12597676 original size:14 final size:14
Alignment explanation
Indices: 12597657--12597702 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
12597647 TGCCAAGGAA
*
12597657 CTGGGCCGAAGCTG
1 CTGGGCTGAAGCTG
*
12597671 CTGGGCTGGAGCTG
1 CTGGGCTGAAGCTG
*
12597685 CTGGGCTGTAGCTG
1 CTGGGCTGAAGCTG
12597699 CTGG
1 CTGG
12597703 ACTACTGCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.09, C:0.24, G:0.46, T:0.22
Consensus pattern (14 bp):
CTGGGCTGAAGCTG
Found at i:12597916 original size:28 final size:30
Alignment explanation
Indices: 12597873--12597950 Score: 88
Period size: 28 Copynumber: 2.6 Consensus size: 30
12597863 CCTGCTGTTT
* *
12597873 TTATTTTTATTTTTTCTTTCTTATTC-TCTC
1 TTATTTCT-TTTTTTCTCTCTTATTCTTCTC
*
12597903 TT-TTTCTTTTTTTCTCTCTTCTTCTTCTC
1 TTATTTCTTTTTTTCTCTCTTATTCTTCTC
12597932 TTAACTTTCTTTTTTTCTC
1 TT-A-TTTCTTTTTTTCTC
12597951 CTTCGGCAGC
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 15 0.37
29 10 0.24
30 2 0.05
32 14 0.34
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (30 bp):
TTATTTCTTTTTTTCTCTCTTATTCTTCTC
Found at i:12597919 original size:18 final size:20
Alignment explanation
Indices: 12597883--12597934 Score: 72
Period size: 18 Copynumber: 2.6 Consensus size: 20
12597873 TTATTTTTAT
12597883 TTTTTCTTTCTTATTCTCTC
1 TTTTTCTTTCTTATTCTCTC
12597903 TTTTTCTTT-TT-TTCTCTC
1 TTTTTCTTTCTTATTCTCTC
*
12597921 TTCTTCTTCTCTTA
1 TTTTTCTT-TCTTA
12597935 ACTTTCTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 14 0.50
19 3 0.11
20 11 0.39
ACGTcount: A:0.04, C:0.25, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTTCTTTCTTATTCTCTC
Found at i:12598076 original size:20 final size:21
Alignment explanation
Indices: 12598053--12598096 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
12598043 CCCTTTTTCC
12598053 CTTTTCCTTTTTCTTC-TTTG
1 CTTTTCCTTTTTCTTCTTTTG
* *
12598073 CTTTTCTTTTTTTTTCTTTTG
1 CTTTTCCTTTTTCTTCTTTTG
12598094 CTT
1 CTT
12598097 GCTGTTTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.00, C:0.20, G:0.05, T:0.75
Consensus pattern (21 bp):
CTTTTCCTTTTTCTTCTTTTG
Found at i:12598539 original size:30 final size:29
Alignment explanation
Indices: 12598470--12598526 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
12598460 CAAAGTTTCT
12598470 GGGGTAAAAGTGTAATTTTGGCAAAAATAC
1 GGGGTAAAA-TGTAATTTTGGCAAAAATAC
*
12598500 GGGGTTAAAATGTAATTTTTG-AAAAAT
1 GGGG-TAAAATGTAATTTTGGCAAAAAT
12598527 TTGGGGGCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 6 0.24
30 14 0.56
31 5 0.20
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.32
Consensus pattern (29 bp):
GGGGTAAAATGTAATTTTGGCAAAAATAC
Found at i:12598563 original size:59 final size:57
Alignment explanation
Indices: 12598500--12598666 Score: 156
Period size: 59 Copynumber: 2.8 Consensus size: 57
12598490 GCAAAAATAC
* * * *
12598500 GGGGTTAAAATGTAATTTTTGAAAAATTTGGGGGCTAAAACGTAATTTAGAAGAGTTTA
1 GGGGTTAAAATGTAA-TTTTGAAAAGTTTGGGGGCTAAAATGTAATTTA-AAAAGTTCA
* ** * *
12598559 GGGG-TAGAAATGTAAATTTGAGAAAGTTTATGGGTTGAAATGTAATTTCAAAAAGTTCA
1 GGGGTTA-AAATGTAATTTTGA-AAAGTTTGGGGGCTAAAATGTAATTT-AAAAAGTTCA
* * * *
12598618 GGGGTTGAAATGTAATTTAGAAAAGTTTAGGGGCCCAAAATGTAATTTA
1 GGGGTTAAAATGTAATTTTGAAAAGTTT-GGGGGCTAAAATGTAATTTA
12598667 TATTTTTTTT
Statistics
Matches: 85, Mismatches: 18, Indels: 11
0.75 0.16 0.10
Matches are distributed among these distances:
58 15 0.18
59 68 0.80
60 2 0.02
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.32
Consensus pattern (57 bp):
GGGGTTAAAATGTAATTTTGAAAAGTTTGGGGGCTAAAATGTAATTTAAAAAGTTCA
Found at i:12598573 original size:29 final size:30
Alignment explanation
Indices: 12598500--12598650 Score: 148
Period size: 29 Copynumber: 5.1 Consensus size: 30
12598490 GCAAAAATAC
* ** * *
12598500 GGGGTTAAAATGTAATTTTTGAAAAATTTG
1 GGGGTTGAAATGTAATTTCAGAAAAGTTTA
* * * *
12598530 GGGGCTAAAACGTAATTT-AGAAGAGTTTA
1 GGGGTTGAAATGTAATTTCAGAAAAGTTTA
* *
12598559 GGGGTAGAAATGTAAATTTGAG-AAAGTTTA
1 GGGGTTGAAATGT-AATTTCAGAAAAGTTTA
* *
12598589 TGGGTTGAAATGTAATTTCA-AAAAGTTCA
1 GGGGTTGAAATGTAATTTCAGAAAAGTTTA
12598618 GGGGTTGAAATGTAATTT-AGAAAAGTTTA
1 GGGGTTGAAATGTAATTTCAGAAAAGTTTA
12598647 GGGG
1 GGGG
12598651 CCCAAAATGT
Statistics
Matches: 100, Mismatches: 17, Indels: 9
0.79 0.13 0.07
Matches are distributed among these distances:
28 1 0.01
29 58 0.58
30 39 0.39
31 2 0.02
ACGTcount: A:0.37, C:0.03, G:0.28, T:0.32
Consensus pattern (30 bp):
GGGGTTGAAATGTAATTTCAGAAAAGTTTA
Found at i:12600555 original size:3 final size:3
Alignment explanation
Indices: 12600547--12600622 Score: 107
Period size: 3 Copynumber: 25.3 Consensus size: 3
12600537 TATTTTAGTG
12600547 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** * * *
12600595 TCC TTA GTA TTA TTA TTA ATA CTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
12600623 GACTATCATT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:12612962 original size:50 final size:50
Alignment explanation
Indices: 12612877--12613533 Score: 403
Period size: 50 Copynumber: 13.1 Consensus size: 50
12612867 TAACCATAGT
*
12612877 TTGCAAATT-AAAAGATTGAGGCCACAACGGCGAATCTCACTTCCTCGACA
1 TTGC-AATTGAAAAGATTGAAGCCACAACGGCGAATCTCACTTCCTCGACA
* * * *
12612927 TTGTAATTTAAAAGATTGAAGCCACAACGGTGAATCTTACTTCC-C-ATGCGA
1 TTGCAATTGAAAAGATTGAAGCCACAACGGCGAATCTCACTTCCTCGA--C-A
*** ** * * *
12612978 -TGCAGCGGAGCAGATTGAAGCTACAACAGCGAATCTCACTTCATCGACA
1 TTGCAATTGAAAAGATTGAAGCCACAACGGCGAATCTCACTTCCTCGACA
* * * * * * * *
12613027 TTGCAATTTAAAAGATTGAGGCCACAACAGTGAGTCTTACTTTCC-AGGCGA
1 TTGCAATTGAAAAGATTGAAGCCACAACGGCGAATCTCAC-TTCCTCGAC-A
** * *
12613078 -TGC-AGCGAAGCAGATTGAAGCTACAACGGCGAATCTCACTTCCTCGACA
1 TTGCAATTGAA-AAGATTGAAGCCACAACGGCGAATCTCACTTCCTCGACA
* * * **
12613127 TTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCC-C-AGG
1 TTGCAATTGAAAAGATTGAAGCCACAACGGCGAATCTCACTTCCTCGACA
*** ** * * *
12613175 TGATGCAGCGGAGCAGATTGAAGCTACAGCAGCGAATCTCACTTCCTCGACA
1 T--TGCAATTGAAAAGATTGAAGCCACAACGGCGAATCTCACTTCCTCGACA
* * * * *
12613227 TTGCAATTCAAAAGATTAAAGCCACAACGGTGAATCTTACTTCC-CAGGCGA
1 TTGCAATTGAAAAGATTGAAGCCACAACGGCGAATCTCACTTCCTC-GAC-A
*** * *
12613278 -TGCAGCAGAGCAA-ATTGAAGCTACAACGGCGAATCTCACTTCCTCGACA
1 TTGCAATTGA-AAAGATTGAAGCCACAACGGCGAATCTCACTTCCTCGACA
* * * * *
12613327 TTGTAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCC-CAAGCGA
1 TTGCAATTGAAAAGATTGAAGCCACAACGGCGAATCTCACTTCCTCGA-C-A
*** ** * * *
12613378 -TGCAGCGGAGCAGATTGAAGCTACAGCAGCGAATCTCACTTCCTCGACA
1 TTGCAATTGAAAAGATTGAAGCCACAACGGCGAATCTCACTTCCTCGACA
* * * * *
12613427 TTGCAATTCAAAAGATTAAAGCCACAACGGTGAATCTTACTTCC-CAGGCGA
1 TTGCAATTGAAAAGATTGAAGCCACAACGGCGAATCTCACTTCCTC-GAC-A
*** * *
12613478 -TGCAGCAGAGCAA-ATTGAAGCTACAACGGCGAATCTCACTTCCTCGACA
1 TTGCAATTGA-AAAGATTGAAGCCACAACGGCGAATCTCACTTCCTCGACA
12613527 TTGCAAT
1 TTGCAAT
12613534 CTTACTTCTC
Statistics
Matches: 440, Mismatches: 135, Indels: 64
0.69 0.21 0.10
Matches are distributed among these distances:
48 3 0.01
49 24 0.05
50 389 0.88
51 21 0.05
52 3 0.01
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (50 bp):
TTGCAATTGAAAAGATTGAAGCCACAACGGCGAATCTCACTTCCTCGACA
Found at i:12613065 original size:100 final size:100
Alignment explanation
Indices: 12612889--12613533 Score: 1056
Period size: 100 Copynumber: 6.5 Consensus size: 100
12612879 GCAAATTAAA
* * * *
12612889 AGATTGAGGCCACAACGGCGAATCTCACTTCCTCGACATTGTAATTTAAAAGATTGAAGCCACAA
1 AGATTGAAGCTACAACGGCGAATCTCACTTCCTCGACATTGCAATTCAAAAGATTGAAGCCACAA
*
12612954 CGGTGAATCTTACTTCCCATGCGATGCAGCGGAGC
66 CGGTGAATCTTACTTCCCAGGCGATGCAGCGGAGC
* * * *
12612989 AGATTGAAGCTACAACAGCGAATCTCACTTCATCGACATTGCAATTTAAAAGATTGAGGCCACAA
1 AGATTGAAGCTACAACGGCGAATCTCACTTCCTCGACATTGCAATTCAAAAGATTGAAGCCACAA
* * * *
12613054 CAGTGAGTCTTACTTTCCAGGCGATGCAGCGAAGC
66 CGGTGAATCTTACTTCCCAGGCGATGCAGCGGAGC
12613089 AGATTGAAGCTACAACGGCGAATCTCACTTCCTCGACATTGCAATTCAAAAGATTGAAGCCACAA
1 AGATTGAAGCTACAACGGCGAATCTCACTTCCTCGACATTGCAATTCAAAAGATTGAAGCCACAA
*
12613154 CGGTGAATCTTACTTCCCAGGTGATGCAGCGGAGC
66 CGGTGAATCTTACTTCCCAGGCGATGCAGCGGAGC
* * *
12613189 AGATTGAAGCTACAGCAGCGAATCTCACTTCCTCGACATTGCAATTCAAAAGATTAAAGCCACAA
1 AGATTGAAGCTACAACGGCGAATCTCACTTCCTCGACATTGCAATTCAAAAGATTGAAGCCACAA
*
12613254 CGGTGAATCTTACTTCCCAGGCGATGCAGCAGAGC
66 CGGTGAATCTTACTTCCCAGGCGATGCAGCGGAGC
* *
12613289 AAATTGAAGCTACAACGGCGAATCTCACTTCCTCGACATTGTAATTCAAAAGATTGAAGCCACAA
1 AGATTGAAGCTACAACGGCGAATCTCACTTCCTCGACATTGCAATTCAAAAGATTGAAGCCACAA
*
12613354 CGGTGAATCTTACTTCCCAAGCGATGCAGCGGAGC
66 CGGTGAATCTTACTTCCCAGGCGATGCAGCGGAGC
* * *
12613389 AGATTGAAGCTACAGCAGCGAATCTCACTTCCTCGACATTGCAATTCAAAAGATTAAAGCCACAA
1 AGATTGAAGCTACAACGGCGAATCTCACTTCCTCGACATTGCAATTCAAAAGATTGAAGCCACAA
*
12613454 CGGTGAATCTTACTTCCCAGGCGATGCAGCAGAGC
66 CGGTGAATCTTACTTCCCAGGCGATGCAGCGGAGC
*
12613489 AAATTGAAGCTACAACGGCGAATCTCACTTCCTCGACATTGCAAT
1 AGATTGAAGCTACAACGGCGAATCTCACTTCCTCGACATTGCAAT
12613534 CTTACTTCTC
Statistics
Matches: 503, Mismatches: 42, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
100 503 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.22
Consensus pattern (100 bp):
AGATTGAAGCTACAACGGCGAATCTCACTTCCTCGACATTGCAATTCAAAAGATTGAAGCCACAA
CGGTGAATCTTACTTCCCAGGCGATGCAGCGGAGC
Found at i:12615037 original size:3 final size:3
Alignment explanation
Indices: 12615029--12615063 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
12615019 TATTTTAGTG
12615029 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12615064 GCTTTTATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:12615112 original size:2 final size:2
Alignment explanation
Indices: 12615105--12615152 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
12615095 TAACTCATTT
* * *
12615105 TA TA TA TA TA TA TA GA TA TA TA TT TA TA TA TG TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
12615146 TT TA TA T
1 TA TA TA T
12615153 TTTTTTCTCA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (2 bp):
TA
Found at i:12615452 original size:17 final size:16
Alignment explanation
Indices: 12615425--12615459 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
12615415 TGAGTGAAGG
*
12615425 TTTTAATTTTATTTGT
1 TTTTAATTTTACTTGT
12615441 TTTTATATTTTACTTGT
1 TTTTA-ATTTTACTTGT
12615458 TT
1 TT
12615460 GGATGTTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.17, C:0.03, G:0.06, T:0.74
Consensus pattern (16 bp):
TTTTAATTTTACTTGT
Found at i:12616546 original size:3 final size:3
Alignment explanation
Indices: 12616538--12616568 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
12616528 ATTACTATTC
*
12616538 TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
12616569 TAATCAACTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:12617367 original size:330 final size:329
Alignment explanation
Indices: 12616716--12618033 Score: 1785
Period size: 330 Copynumber: 4.0 Consensus size: 329
12616706 CCTAAACCCG
* *
12616716 TTAGTTGCATAAAAGCTTAATATAATTAATTTCTTAATTT---AA-AAAG-A--AAG-ACT---T
1 TTAGTTGCATAAAAACTTAATATAATTAATTTCTTAATTTAAAAAGAAAGAATTAAGTAATAAAT
* * * * * * * *
12616770 AAATAATTTATTTAAAGTCAAACTTAAAAAATTTAATTCAAAATAAAGTAATTTGAATCGAATTA
66 AAATAATTTATTTAAAGTCAAGCCTAAAAAAATTAATTCAAGATAAAGCAATTTGAAACAAAGTA
* * * * **
12616835 CTATTCTAATAATCAT-AT--TTAATCGACTCTAATCTTATATAATAACAACAGGACTTTTCAAT
131 CTATTCTAATAATAATAATAATTAATCGACTGTAAGCATATATAATAACAACAGGGTTTTTCAAT
* * * * * * * *
12616897 TACCATTGGAGTCGTATAAGCCTCAGGTAAAAATTGTTGTTTACCAATATAAGTCACAGGCT-TA
196 TACCATTTGAGTCGTATAAGTCTCAGGTAAAGATTGTTGTTCATCAAAATAAATCACAGG-TACA
** * * * * * * * * * * *
12616961 GGCTGTGAAATCACACTCGTATAA-CATTATCGATTCATATAAGTCGCACTTGTAAGCTCCCCCT
260 GAATTTGCAGTCACACAC-TAGAATC-TTGTTGATTCGTATAAGTTGCACTTGGAAGCTCCCCAT
*
12617025 GAAACCA
323 GAAACTA
* * *
12617032 TTAGTTGCATAAAAGCTTAATATAATGAATTTCTTAATTTAAAAAGAAAGAATTAAGTAATAAGT
1 TTAGTTGCATAAAAACTTAATATAATTAATTTCTTAATTTAAAAAGAAAGAATTAAGTAATAAAT
12617097 AAATAATTTATTTAAAGTCAAGCCTAAAAAAATTAATTCAAGATAAAGCAATTTGAAACAAAGTA
66 AAATAATTTATTTAAAGTCAAGCCTAAAAAAATTAATTCAAGATAAAGCAATTTGAAACAAAGTA
12617162 CTATTCTAATAATAATAATAATTAATCGACTGTAAGCATATATAATAACAACAGGGTTTTTCAAT
131 CTATTCTAATAATAATAATAATTAATCGACTGTAAGCATATATAATAACAACAGGGTTTTTCAAT
* *
12617227 TACCATTTGAGTCGTATGAGTCTCAGGTAAAGATTGTTGTTCATCAAAATAAATCACAAGTACAG
196 TACCATTTGAGTCGTATAAGTCTCAGGTAAAGATTGTTGTTCATCAAAATAAATCACAGGTACAG
12617292 AATTTGCAGTCACACACTCAGAATCTTGTTGATTCGTATAAGTTGCACTTGGAAGCTCCCCATGA
261 AATTTGCAGTCACACACT-AGAATCTTGTTGATTCGTATAAGTTGCACTTGGAAGCTCCCCATGA
12617357 AACTA
325 AACTA
* ** *
12617362 TTAGTTGCATAAAAACATAGGATAATTAATTTCTTAATTTAAAAAGAAATAATTAAGTAATAAAT
1 TTAGTTGCATAAAAACTTAATATAATTAATTTCTTAATTTAAAAAGAAAGAATTAAGTAATAAAT
*
12617427 AAATAATTTATTTAAGGTCAAGCCTAAAAAAATTAATTCAAGATAAAGCAATTTGAAACAAAGTA
66 AAATAATTTATTTAAAGTCAAGCCTAAAAAAATTAATTCAAGATAAAGCAATTTGAAACAAAGTA
* * *
12617492 CTATTCTAATAATAATAATAATTAATTGACTGTAAACATATATAATAACAATAGGGTTTTTCAAT
131 CTATTCTAATAATAATAATAATTAATCGACTGTAAGCATATATAATAACAACAGGGTTTTTCAAT
12617557 TACCATTTGAGTCGTATAAGTCTCAGGTAAAGATTGTTGTTCATCAAAATAAATCACAGGTACAG
196 TACCATTTGAGTCGTATAAGTCTCAGGTAAAGATTGTTGTTCATCAAAATAAATCACAGGTACAG
* * *
12617622 AATTTGCAGTCGCACACTCAAAATCTTGTTGATTCGTATAAGTTGTACTTGGAAGCTCCCCATGA
261 AATTTGCAGTCACACACT-AGAATCTTGTTGATTCGTATAAGTTGCACTTGGAAGCTCCCCATGA
12617687 AACTA
325 AACTA
*
12617692 TTAGTTGCATAAAAAC--AATGGATAATTAATTTTTTAATTTAAAAAGAAAGAATTAAGTAATAA
1 TTAGTTGCATAAAAACTTAAT--ATAATTAATTTCTTAATTTAAAAAGAAAGAATTAAGTAATAA
* * *
12617755 ATAAATAATTTAGTTAAGGTCAAGCCTAAAAAAACTAATTCAAGATAAAGCAATTTGAAACAAAG
64 ATAAATAATTTATTTAAAGTCAAGCCTAAAAAAATTAATTCAAGATAAAGCAATTTGAAACAAAG
*
12617820 TACTATTCTAATAATAATAATAATTAATCGACTGTAAGCATATATAATAACAATAGGG-TTTTCA
129 TACTATTCTAATAATAATAATAATTAATCGACTGTAAGCATATATAATAACAACAGGGTTTTTCA
* * * * *
12617884 ATTATCATTTGAGTCGTATAAGTCTCAGATAAAGATTGTTGTTCATCAATATAAGTCACAGGTAG
194 ATTACCATTTGAGTCGTATAAGTCTCAGGTAAAGATTGTTGTTCATCAAAATAAATCACAGGTAC
* * * * * *
12617949 AGAATTTACAGTCGCTTGCA-TAGAATCTTGTTGATTCTTATAAATTGCACTTGGAAACTCCCCA
259 AGAATTTGCAGTCAC--ACACTAGAATCTTGTTGATTCGTATAAGTTGCACTTGGAAGCTCCCCA
12618013 TGAAACTA
322 TGAAACTA
12618021 TTAGTTGCATAAA
1 TTAGTTGCATAAA
12618034 TATATATTTG
Statistics
Matches: 905, Mismatches: 76, Indels: 29
0.90 0.08 0.03
Matches are distributed among these distances:
316 39 0.04
319 2 0.00
320 4 0.00
321 1 0.00
323 3 0.00
324 2 0.00
327 73 0.08
328 3 0.00
329 141 0.16
330 634 0.70
331 3 0.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.33
Consensus pattern (329 bp):
TTAGTTGCATAAAAACTTAATATAATTAATTTCTTAATTTAAAAAGAAAGAATTAAGTAATAAAT
AAATAATTTATTTAAAGTCAAGCCTAAAAAAATTAATTCAAGATAAAGCAATTTGAAACAAAGTA
CTATTCTAATAATAATAATAATTAATCGACTGTAAGCATATATAATAACAACAGGGTTTTTCAAT
TACCATTTGAGTCGTATAAGTCTCAGGTAAAGATTGTTGTTCATCAAAATAAATCACAGGTACAG
AATTTGCAGTCACACACTAGAATCTTGTTGATTCGTATAAGTTGCACTTGGAAGCTCCCCATGAA
ACTA
Found at i:12621278 original size:18 final size:18
Alignment explanation
Indices: 12621237--12621278 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
12621227 TTTAATCATT
*
12621237 AAATTTATCAATATATTT
1 AAATTTATCAATATATTA
*
12621255 ATATTTATC-ATATATATA
1 AAATTTATCAATATAT-TA
12621273 AAATTT
1 AAATTT
12621279 TTAATTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (18 bp):
AAATTTATCAATATATTA
Found at i:12621397 original size:34 final size:34
Alignment explanation
Indices: 12621334--12621401 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
12621324 ATACGAATAA
* **
12621334 AATAAAAACCAAGTCAAATAAATGGTAAATCATG
1 AATAAAAACCAAGTCAAACAAATCATAAATCATG
* *
12621368 AATAAAAACCAAGTCAGACGAATCATAAATCATG
1 AATAAAAACCAAGTCAAACAAATCATAAATCATG
12621402 CAACTATATA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.54, C:0.15, G:0.12, T:0.19
Consensus pattern (34 bp):
AATAAAAACCAAGTCAAACAAATCATAAATCATG
Found at i:12622233 original size:26 final size:26
Alignment explanation
Indices: 12622204--12622255 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
12622194 TGATAGTACC
12622204 ATCA-AAATGAGAGTGTTTT-GTAGTGT
1 ATCACAAATGAG-GT-TTTTCGTAGTGT
12622230 ATCATCAAATGAGGTTTTTCGTAGTG
1 ATCA-CAAATGAGGTTTTTCGTAGTG
12622256 GATTGCGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
26 8 0.35
27 8 0.35
28 7 0.30
ACGTcount: A:0.29, C:0.08, G:0.25, T:0.38
Consensus pattern (26 bp):
ATCACAAATGAGGTTTTTCGTAGTGT
Found at i:12622843 original size:27 final size:27
Alignment explanation
Indices: 12622780--12622864 Score: 82
Period size: 27 Copynumber: 3.1 Consensus size: 27
12622770 TAATACATAG
* * **
12622780 TAGTGGCGCCTATCTTAGAGGCGTTAA
1 TAGTGGTGCCTATCTGAGAGGCGCCAA
* * *
12622807 TGGTGATGCCTATCTGAGAGGCGCCAT
1 TAGTGGTGCCTATCTGAGAGGCGCCAA
*
12622834 TAGTGGTGCC-ATGTTGAGAGGCGCCAA
1 TAGTGGTGCCTAT-CTGAGAGGCGCCAA
12622861 TAGT
1 TAGT
12622865 CTTATTTTAT
Statistics
Matches: 46, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
26 2 0.04
27 44 0.96
ACGTcount: A:0.21, C:0.19, G:0.33, T:0.27
Consensus pattern (27 bp):
TAGTGGTGCCTATCTGAGAGGCGCCAA
Found at i:12622949 original size:15 final size:16
Alignment explanation
Indices: 12622929--12622965 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
12622919 ACAAAATCAA
12622929 ATAAAA-TTACATTAT
1 ATAAAAGTTACATTAT
12622944 ATAAAAGTTACATTAT
1 ATAAAAGTTACATTAT
12622960 ATAAAA
1 ATAAAA
12622966 ATTAAATGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (16 bp):
ATAAAAGTTACATTAT
Found at i:12623130 original size:19 final size:19
Alignment explanation
Indices: 12623106--12623268 Score: 154
Period size: 19 Copynumber: 8.2 Consensus size: 19
12623096 ATTATAAAAT
12623106 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
12623125 AATTACAATATTCATACAAAA
1 AATTACAATATTCATAC--AA
12623146 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
* * *
12623165 AA-TACTA-ATCCAAAACTATA
1 AATTACAATATTC-ATAC-A-A
*
12623185 AA-TACAAAATTAATT-ATAAAA
1 AATTAC--AA-T-ATTCATACAA
12623206 TAATTACAATATTCATACAA
1 -AATTACAATATTCATACAA
12623226 AATTACAATATTCATACAAAA
1 AATTACAATATTCATAC--AA
12623247 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
12623266 AAT
1 AAT
12623269 ACTAATCCAA
Statistics
Matches: 121, Mismatches: 8, Indels: 30
0.76 0.05 0.19
Matches are distributed among these distances:
17 3 0.02
18 7 0.06
19 47 0.39
20 12 0.10
21 41 0.34
22 4 0.03
23 5 0.04
25 2 0.02
ACGTcount: A:0.56, C:0.14, G:0.00, T:0.30
Consensus pattern (19 bp):
AATTACAATATTCATACAA
Found at i:12623160 original size:101 final size:101
Alignment explanation
Indices: 12623043--12623329 Score: 556
Period size: 101 Copynumber: 2.8 Consensus size: 101
12623033 TTTTTAATTC
* *
12623043 AAAATTACAACATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAATAA
1 AAAATTACAATATTCATACAAAATACTAATCCAAAACTATAAATACAAAATTAATTATAAAATAA
12623108 TTACAATATTCATACAAAATTACAATATTCATACAA
66 TTACAATATTCATACAAAATTACAATATTCATACAA
12623144 AAAATTACAATATTCATACAAAATACTAATCCAAAACTATAAATACAAAATTAATTATAAAATAA
1 AAAATTACAATATTCATACAAAATACTAATCCAAAACTATAAATACAAAATTAATTATAAAATAA
12623209 TTACAATATTCATACAAAATTACAATATTCATACAA
66 TTACAATATTCATACAAAATTACAATATTCATACAA
12623245 AAAATTACAATATTCATACAAAATACTAATCCAAAACTATAAATACAAAATTAATTATAAAATAA
1 AAAATTACAATATTCATACAAAATACTAATCCAAAACTATAAATACAAAATTAATTATAAAATAA
12623310 TTACAATATTCATACAAAAT
66 TTACAATATTCATACAAAAT
12623330 ACTAATCAAA
Statistics
Matches: 184, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
101 184 1.00
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (101 bp):
AAAATTACAATATTCATACAAAATACTAATCCAAAACTATAAATACAAAATTAATTATAAAATAA
TTACAATATTCATACAAAATTACAATATTCATACAA
Found at i:12623313 original size:61 final size:61
Alignment explanation
Indices: 12623243--12623389 Score: 269
Period size: 61 Copynumber: 2.4 Consensus size: 61
12623233 ATATTCATAC
*
12623243 AAAA-AATTACAATATTCATACAAAATACTAATCCAAAACTATAAATACAAAATTAATTAT
1 AAAATAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTAT
*
12623303 AAAATAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATATAAAATTAATTAT
1 AAAATAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTAT
12623364 AAAATAATTACAATATTCATACAAAA
1 AAAATAATTACAATATTCATACAAAA
12623390 AATTACAATA
Statistics
Matches: 84, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
60 4 0.05
61 80 0.95
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (61 bp):
AAAATAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTAT
Found at i:12623394 original size:21 final size:22
Alignment explanation
Indices: 12623364--12623411 Score: 80
Period size: 21 Copynumber: 2.2 Consensus size: 22
12623354 AATTAATTAT
12623364 AAAATAATTACAATATTCATAC
1 AAAATAATTACAATATTCATAC
*
12623386 AAAA-AATTACAATATTCATTC
1 AAAATAATTACAATATTCATAC
12623407 AAAAT
1 AAAAT
12623412 TACCCATTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAATAATTACAATATTCATAC
Found at i:12623480 original size:27 final size:27
Alignment explanation
Indices: 12623419--12623480 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
12623409 AATTACCCAT
* **
12623419 TGGCGCCTCCGTATGAGGCACTTTTAA
1 TGGCGCCTCCCTATGAGGCACAATTAA
* *
12623446 TGGTGCCTCCCTATGAGGCACAATTAG
1 TGGCGCCTCCCTATGAGGCACAATTAA
12623473 TGGCGCCT
1 TGGCGCCT
12623481 ACCTGACAGG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.27
Consensus pattern (27 bp):
TGGCGCCTCCCTATGAGGCACAATTAA
Found at i:12625003 original size:2 final size:2
Alignment explanation
Indices: 12624996--12625027 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
12624986 AAAAGTCAGA
12624996 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
12625028 GTCACAAGTT
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
Done.