Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold354
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: 1591162
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29
Warning! 188200 characters in sequence are not A, C, G, or T
File 5 of 5
Found at i:1501201 original size:24 final size:24
Alignment explanation
Indices: 1501143--1501206 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
1501133 ATTAGTATTA
* *
1501143 TTTAAACTTATCATACATTATAGC
1 TTTAAACTTATCATATACTATAGC
* * * *
1501167 TTGAAATTTATTATATACTATAGT
1 TTTAAACTTATCATATACTATAGC
1501191 TTTAAACTTATCATAT
1 TTTAAACTTATCATAT
1501207 GTTATTATTT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.47
Consensus pattern (24 bp):
TTTAAACTTATCATATACTATAGC
Found at i:1502608 original size:12 final size:12
Alignment explanation
Indices: 1502593--1502630 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
1502583 TAAGTATTAA
1502593 ATTAAATTTATT
1 ATTAAATTTATT
1502605 ATTAAATTTATT
1 ATTAAATTTATT
1502617 A--AAATATTATT
1 ATTAAAT-TTATT
1502628 ATT
1 ATT
1502631 CTTGGAATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
10 4 0.17
11 6 0.26
12 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
ATTAAATTTATT
Found at i:1502845 original size:24 final size:24
Alignment explanation
Indices: 1502818--1502870 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
1502808 TTTTGATTAA
1502818 CGGTTAATTCAGTTCGAAACTGGT
1 CGGTTAATTCAGTTCGAAACTGGT
* *
1502842 CGGTTAATTCGGTTCGAAATTGGT
1 CGGTTAATTCAGTTCGAAACTGGT
1502866 CGGTT
1 CGGTT
1502871 CGAAACTTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.21, C:0.15, G:0.28, T:0.36
Consensus pattern (24 bp):
CGGTTAATTCAGTTCGAAACTGGT
Found at i:1505431 original size:23 final size:24
Alignment explanation
Indices: 1505398--1505455 Score: 91
Period size: 23 Copynumber: 2.5 Consensus size: 24
1505388 ATTCAATGTT
*
1505398 TGCAATTTCTTATCCATTTTCATA
1 TGCAATTTCTTATCCACTTTCATA
*
1505422 T-TAATTTCTTATCCACTTTCATA
1 TGCAATTTCTTATCCACTTTCATA
1505445 TGCAATTTCTT
1 TGCAATTTCTT
1505456 CATGCTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 21 0.70
24 9 0.30
ACGTcount: A:0.24, C:0.21, G:0.03, T:0.52
Consensus pattern (24 bp):
TGCAATTTCTTATCCACTTTCATA
Found at i:1505441 original size:12 final size:12
Alignment explanation
Indices: 1505400--1505455 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
1505390 TCAATGTTTG
1505400 CAATTTCTTATC
1 CAATTTCTTATC
* *
1505412 CATTTTCATAT-
1 CAATTTCTTATC
*
1505423 TAATTTCTTATC
1 CAATTTCTTATC
* * *
1505435 CACTTTCATATG
1 CAATTTCTTATC
1505447 CAATTTCTT
1 CAATTTCTT
1505456 CATGCTTTTA
Statistics
Matches: 32, Mismatches: 11, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
11 8 0.25
12 24 0.75
ACGTcount: A:0.25, C:0.21, G:0.02, T:0.52
Consensus pattern (12 bp):
CAATTTCTTATC
Found at i:1507712 original size:43 final size:42
Alignment explanation
Indices: 1507664--1507805 Score: 160
Period size: 43 Copynumber: 3.3 Consensus size: 42
1507654 TTTAAAAAAA
* *
1507664 AAACGCCGCTAAA-ACATATGACCATTAGCGGCGCTTTTATCAC
1 AAACGCCGCTAAAGA-ACATGA-CTTTAGCGGCGCTTTTATCAC
* ** *
1507707 AAACGCCGCTAAAGAACATGACTTTGAGCGACTTTTTTTTCAC
1 AAACGCCGCTAAAGAACATGACTTT-AGCGGCGCTTTTATCAC
*
1507750 AAATGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTATCAC
1 AAACGCCGCTAAAGAACATGA-CTTTAGCGGCGCTTTTATCAC
* *
1507793 AAATGCCACTAAA
1 AAACGCCGCTAAA
1507806 AGTACCGTTC
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
42 3 0.04
43 76 0.90
44 5 0.06
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (42 bp):
AAACGCCGCTAAAGAACATGACTTTAGCGGCGCTTTTATCAC
Found at i:1507818 original size:43 final size:41
Alignment explanation
Indices: 1507688--1507846 Score: 106
Period size: 43 Copynumber: 3.8 Consensus size: 41
1507678 CATATGACCA
* * * * *
1507688 TTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAACATGACT
1 TTAGCGGCGCTTTTATCACAAATGCCACTAAAGACCGT-TCT
* ** * * * *
1507730 TTGAGCGACTTTTTTTTCACAAATGCCGCTAAAGAACATGATCT
1 TT-AGCGGCGCTTTTATCACAAATGCCACTAAAG-AC-CGTTCT
1507774 TTAGCGGCGCTTTTATCACAAATGCCACTAAAAGTACCGTTCT
1 TTAGCGGCGCTTTTATCACAAATGCCACT-AAAG-ACCGTTCT
* * *
1507817 TTAGAGGCG--TTTATGAAAAAATGCCACTAA
1 TTAGCGGCGCTTTTAT-CACAAATGCCACTAA
1507847 CTTTGGCAGA
Statistics
Matches: 91, Mismatches: 21, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
41 7 0.08
42 13 0.14
43 60 0.66
44 11 0.12
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (41 bp):
TTAGCGGCGCTTTTATCACAAATGCCACTAAAGACCGTTCT
Found at i:1510605 original size:7 final size:6
Alignment explanation
Indices: 1510595--1510701 Score: 52
Period size: 7 Copynumber: 15.7 Consensus size: 6
1510585 CCCTAAACTA
* *
1510595 TAAACAC TAAATCC TAAACC ATAAACC TACACCC TAAACTG TAAACAC
1 TAAAC-C TAAA-CC TAAACC -TAAACC TA-AACC TAAAC-C TAAAC-C
* * *
1510643 TAAACTC TTAACAC TAAATCA TAAACC TTAAACC ATAAACC TACACCC
1 TAAAC-C TAAAC-C TAAA-CC TAAACC -TAAACC -TAAACC TA-AACC
1510691 TAAACCC TAAA
1 TAAA-CC TAAA
1510702 TATATATATT
Statistics
Matches: 78, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
6 10 0.13
7 66 0.85
8 2 0.03
ACGTcount: A:0.48, C:0.31, G:0.01, T:0.21
Consensus pattern (6 bp):
TAAACC
Found at i:1510699 original size:14 final size:14
Alignment explanation
Indices: 1510545--1510701 Score: 72
Period size: 14 Copynumber: 11.3 Consensus size: 14
1510535 GGCTTGTTTA
**
1510545 TAAACCATAAACTT
1 TAAACCATAAACCC
*
1510559 TAAATGCA-AAACCC
1 TAAA-CCATAAACCC
* * *
1510573 TAAGCCCCTAACCCC
1 TAA-ACCATAAACCC
* *
1510588 TAAACTATAAACAC
1 TAAACCATAAACCC
*
1510602 TAAATCC-TAAACCA
1 TAAA-CCATAAACCC
*
1510616 TAAACC-TACACCC
1 TAAACCATAAACCC
** *
1510629 TAAACTGTAAACAC
1 TAAACCATAAACCC
* *
1510643 TAAACTC-TTAACAC
1 TAAAC-CATAAACCC
* *
1510657 TAAATCATAAACCT
1 TAAACCATAAACCC
1510671 TAAACCATAAA-CC
1 TAAACCATAAACCC
* *
1510684 TACACCCTAAACCC
1 TAAACCATAAACCC
1510698 TAAA
1 TAAA
1510702 TATATATATT
Statistics
Matches: 104, Mismatches: 31, Indels: 16
0.69 0.21 0.11
Matches are distributed among these distances:
13 23 0.22
14 70 0.67
15 11 0.11
ACGTcount: A:0.46, C:0.31, G:0.02, T:0.20
Consensus pattern (14 bp):
TAAACCATAAACCC
Found at i:1510891 original size:21 final size:21
Alignment explanation
Indices: 1510867--1510918 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
1510857 TATAAAATAA
* *
1510867 TAAACCCTAAACCCTAAGCTC
1 TAAACACTAAACCCTAAACTC
*
1510888 TAAACAATAAACCCTAAACTC
1 TAAACACTAAACCCTAAACTC
* *
1510909 AAAACTCTAA
1 TAAACACTAA
1510919 TCCCAAAATA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.48, C:0.31, G:0.02, T:0.19
Consensus pattern (21 bp):
TAAACACTAAACCCTAAACTC
Found at i:1510916 original size:28 final size:28
Alignment explanation
Indices: 1510865--1510918 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
1510855 ATTATAAAAT
* *
1510865 AATAAACCCTAAACCCTAAGCTCTAAAC
1 AATAAACCCTAAACCCAAAACTCTAAAC
*
1510893 AATAAACCCTAAACTCAAAACTCTAA
1 AATAAACCCTAAACCCAAAACTCTAA
1510919 TCCCAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.50, C:0.30, G:0.02, T:0.19
Consensus pattern (28 bp):
AATAAACCCTAAACCCAAAACTCTAAAC
Found at i:1511499 original size:41 final size:40
Alignment explanation
Indices: 1511431--1511518 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 40
1511421 AAAAGTGCCA
* * *
1511431 CTAATGCTCGATCTATAGCGGCGTTTTTCAAATATCACCG
1 CTAATGCTCGATCTATAGCGACGTTTTTCAAAAAGCACCG
* * * *
1511471 CTAATGCTCGATCTATTGCGACATTTTTTTAAAAAGCACTG
1 CTAATGCTCGATCTATAGCGAC-GTTTTTCAAAAAGCACCG
1511512 CTAATGC
1 CTAATGC
1511519 CACTAAAGCT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 20 0.50
41 20 0.50
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (40 bp):
CTAATGCTCGATCTATAGCGACGTTTTTCAAAAAGCACCG
Found at i:1511518 original size:156 final size:154
Alignment explanation
Indices: 1511027--1511669 Score: 610
Period size: 156 Copynumber: 4.2 Consensus size: 154
1511017 TTTTGCAGCG
* * * * *
1511027 TTTTTATAAAAA-CGCCGCTAATGCCACTAAAGCTTAACAACAAACGACA-TCATTTT-CTCAAC
1 TTTTTTTAAAAAGCGCTGCTAATGCCACTAAAGCTCAACAACAAAC-AAAGT-GTTTTGCTCAAC
* * * **
1511089 TTTTTTACGGTC-TTTTGTGAAAAGAGCCACTAAAGCTCGATCTATAGTAGCGTTTTTC-AACAA
64 TTTTTTACGG-CGTTTTTTGAAAAGTGCCACTAATGCTCGATCTATAGCGGCGTTTTTCGAA-AA
* * *
1511152 -GCGCTGCTAATTCTTGATCTATTGTGGCA
127 TGC-C-GCTAATGCTCGATCTATTGCGGCA
* * * *
1511181 TTTTTTAAAAAAGTGCTACTAATGCCACTAAAGCTCAACAACAAACAACACTGTTTTGCTCAACT
1 TTTTTTTAAAAAGCGCTGCTAATGCCACTAAAGCTCAACAACAAACAA-AGTGTTTTGCTCAACT
* * * * *
1511246 TTTTTAAGGCGTTTTTTTTAAAAGTGCTACTAATGCTCAATCTATAGCGGTGTTTTTCGACAAAA
65 TTTTTACGGCG-TTTTTTGAAAAGTGCCACTAATGCTCGATCTATAGCGGCGTTTTTCG--AAAA
* * *
1511311 TGCCGCTAATTCTCCATCTATTGTGG-A
127 TGCCGCTAATGCTCGATCTATTGCGGCA
* * ** * *
1511338 GTTTTTTAAAAATCGCCACTAATGCCACTAAAGCTCAACAACAAACAAAGTCGTTTTGCTTAAGT
1 TTTTTTTAAAAAGCGCTGCTAATGCCACTAAAGCTCAACAACAAACAAAGT-GTTTTGCTCAACT
* *
1511403 TTTTTACGGCGTTTTCTAAAAAGTGCCACTAATGCTCGATCTATAGCGGCGTTTTTC-AAATATC
65 TTTTTACGGCGTTTTTTGAAAAGTGCCACTAATGCTCGATCTATAGCGGCGTTTTTCGAAA-AT-
* *
1511467 ACCGCTAATGCTCGATCTATTGCGACA
128 GCCGCTAATGCTCGATCTATTGCGGCA
* * * * *
1511494 TTTTTTTAAAAAGCACTGCTAATGCCACTAAAGCTCAACAACAAACGACGTGTTTTGCTTAGAAT
1 TTTTTTTAAAAAGCGCTGCTAATGCCACTAAAGCTCAACAACAAACAAAGTGTTTTGCTCA-ACT
* ** * * *
1511559 TTTTGTA--GCATTTTTTGAAAAGCCCCGCTAATGCTCGATCTATACCGGCATTTTTCGAAAAGT
65 TTTT-TACGGCGTTTTTTGAAAAGTGCCACTAATGCTCGATCTATAGCGGCGTTTTTCGAAAA-T
*
1511622 G-C-CTAATGCTCGATCTATAGCGGC-
128 GCCGCTAATGCTCGATCTATTGCGGCA
* *
1511646 GTTTTTCAAAAAGCGCTGCTAATG
1 TTTTTTTAAAAAGCGCTGCTAATG
1511670 TTTGAACTAT
Statistics
Matches: 410, Mismatches: 61, Indels: 38
0.81 0.12 0.07
Matches are distributed among these distances:
152 21 0.05
153 23 0.06
154 14 0.03
155 107 0.26
156 114 0.28
157 104 0.25
158 20 0.05
159 3 0.01
160 4 0.01
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (154 bp):
TTTTTTTAAAAAGCGCTGCTAATGCCACTAAAGCTCAACAACAAACAAAGTGTTTTGCTCAACTT
TTTTACGGCGTTTTTTGAAAAGTGCCACTAATGCTCGATCTATAGCGGCGTTTTTCGAAAATGCC
GCTAATGCTCGATCTATTGCGGCA
Found at i:1511637 original size:38 final size:38
Alignment explanation
Indices: 1511586--1511658 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
1511576 AAAAGCCCCG
*
1511586 CTAATGCTCGATCTATACCGGCATTTTTCGAAAAGTGC
1 CTAATGCTCGATCTATACCGGCATTTTTCAAAAAGTGC
* *
1511624 CTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAG
1 CTAATGCTCGATCTATACCGGCATTTTTCAAAAAG
1511659 CGCTGCTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (38 bp):
CTAATGCTCGATCTATACCGGCATTTTTCAAAAAGTGC
Found at i:1512474 original size:22 final size:22
Alignment explanation
Indices: 1512423--1512466 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1512413 TCAACTAAAC
1512423 AACCA-AAATTAGGCATAAAAT
1 AACCATAAATTAGGCATAAAAT
*
1512444 AACCATAAATTAGGCTTAAAAT
1 AACCATAAATTAGGCATAAAAT
1512466 A
1 A
1512467 TGCGTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.55, C:0.14, G:0.09, T:0.23
Consensus pattern (22 bp):
AACCATAAATTAGGCATAAAAT
Found at i:1513398 original size:15 final size:16
Alignment explanation
Indices: 1513375--1513411 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1513365 AATTTGAGAG
1513375 GAGAAAAAAAGA-AAT
1 GAGAAAAAAAGAGAAT
*
1513390 GAGAGAAAAAGAGAAT
1 GAGAAAAAAAGAGAAT
1513406 GA-AAAA
1 GAGAAAA
1513412 GAAATAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.70, C:0.00, G:0.24, T:0.05
Consensus pattern (16 bp):
GAGAAAAAAAGAGAAT
Found at i:1513501 original size:18 final size:18
Alignment explanation
Indices: 1513480--1513524 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1513470 AGAGTGTGAC
* * *
1513480 AAAAGAGATTGAGATTGA
1 AAAAGAAATCGAGAATGA
1513498 AAAAGAAATCGAGAATGA
1 AAAAGAAATCGAGAATGA
1513516 AGAAAGAAA
1 A-AAAGAAA
1513525 AACAAGTGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.60, C:0.02, G:0.24, T:0.13
Consensus pattern (18 bp):
AAAAGAAATCGAGAATGA
Found at i:1515074 original size:20 final size:21
Alignment explanation
Indices: 1515034--1515075 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1515024 TCTTTTTATT
1515034 GCATGTTTATTATGCGTCTTAA
1 GCATGTTTA-TATGCGTCTTAA
*
1515056 GCATGTTTA-ATGTGTCTTAA
1 GCATGTTTATATGCGTCTTAA
1515076 AAGTGTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.24, C:0.12, G:0.19, T:0.45
Consensus pattern (21 bp):
GCATGTTTATATGCGTCTTAA
Found at i:1528342 original size:21 final size:21
Alignment explanation
Indices: 1528316--1528361 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
1528306 AGTTTCTTGG
1528316 GATTAGCCGGATACTATCGGT
1 GATTAGCCGGATACTATCGGT
1528337 GATTAGCCGGATACTATCGGT
1 GATTAGCCGGATACTATCGGT
1528358 GATT
1 GATT
1528362 TGTTAAAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.30
Consensus pattern (21 bp):
GATTAGCCGGATACTATCGGT
Found at i:1528516 original size:18 final size:18
Alignment explanation
Indices: 1528495--1528533 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
1528485 CTCCAGTGTT
1528495 AACTCAGCATGAATCTGG
1 AACTCAGCATGAATCTGG
1528513 AACTCAGCATGAATCTGG
1 AACTCAGCATGAATCTGG
1528531 AAC
1 AAC
1528534 GACATATGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.21
Consensus pattern (18 bp):
AACTCAGCATGAATCTGG
Found at i:1529847 original size:14 final size:14
Alignment explanation
Indices: 1529828--1529854 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1529818 TAAAGGCACA
1529828 AAAAAGAAAAAAAG
1 AAAAAGAAAAAAAG
1529842 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
1529855 TAAATGCGCG
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:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:1529914 original size:19 final size:19
Alignment explanation
Indices: 1529892--1529935 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1529882 AAACAATTTT
*
1529892 AAATATTAACAAAGTAAAG
1 AAATAATAACAAAGTAAAG
* *
1529911 AAATAATAACTAAGTAAAT
1 AAATAATAACAAAGTAAAG
1529930 AAATAA
1 AAATAA
1529936 ATAAAGGACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.66, C:0.05, G:0.07, T:0.23
Consensus pattern (19 bp):
AAATAATAACAAAGTAAAG
Found at i:1530910 original size:12 final size:11
Alignment explanation
Indices: 1530870--1530909 Score: 53
Period size: 12 Copynumber: 3.4 Consensus size: 11
1530860 TTGATTGTTG
1530870 TTTTTTACTAT
1 TTTTTTACTAT
1530881 TTATTTCTACTAT
1 TT-TTT-TACTAT
1530894 TTTTGTTACTAT
1 TTTT-TTACTAT
1530906 TTTT
1 TTTT
1530910 GCATGTTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.08
12 15 0.58
13 9 0.35
ACGTcount: A:0.17, C:0.10, G:0.03, T:0.70
Consensus pattern (11 bp):
TTTTTTACTAT
Found at i:1531624 original size:44 final size:44
Alignment explanation
Indices: 1531561--1531704 Score: 252
Period size: 44 Copynumber: 3.3 Consensus size: 44
1531551 TTAATCCGAC
* *
1531561 CCACTGCAACTTCAGAGGTATAGGACTTTTCGTTTCAATATGCT
1 CCACTGCAACTTCAGAGGTATAGGACTTGTCGCTTCAATATGCT
* *
1531605 CCACTGCAACTTCAGAGGTATAGGACTTGTCGCTTCAATAAGTT
1 CCACTGCAACTTCAGAGGTATAGGACTTGTCGCTTCAATATGCT
1531649 CCACTGCAACTTCAGAGGTATAGGACTTGTCGCTTCAATATGCT
1 CCACTGCAACTTCAGAGGTATAGGACTTGTCGCTTCAATATGCT
1531693 CCACTGCAACTT
1 CCACTGCAACTT
1531705 TAGGGAGATA
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 94 1.00
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.31
Consensus pattern (44 bp):
CCACTGCAACTTCAGAGGTATAGGACTTGTCGCTTCAATATGCT
Found at i:1531751 original size:51 final size:48
Alignment explanation
Indices: 1531673--1531851 Score: 159
Period size: 51 Copynumber: 3.7 Consensus size: 48
1531663 GAGGTATAGG
* * * *
1531673 ACTTGTCGCTTCAATATGCTCCACTGCAACTTTAGGGAGATAAGGTTTGTA
1 ACTTGTAGCTTTAATCTGTTCCACTGCAACTTTA--GAGATAA-GTTTGTA
* **
1531724 ACTTGTAGCTTTAATCTATTCCACTGCAACTTTCAGAGA-AA-TAAG--
1 ACTTGTAGCTTTAATCTGTTCCACTGCAACTTT-AGAGATAAGTTTGTA
* * * *
1531769 ATTTGTAGCTTTAATTTGCTCCACTGTAACTTTAAAGAGATAAGATTTGTA
1 ACTTGTAGCTTTAATCTGTTCCACTGCAACTTT--AGAGATAAG-TTTGTA
*
1531820 ACTTGTAACTTTAATCTGTTCCACTGCAACTT
1 ACTTGTAGCTTTAATCTGTTCCACTGCAACTT
1531852 CAAGAAAATA
Statistics
Matches: 101, Mismatches: 20, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
45 28 0.28
46 5 0.05
47 4 0.04
49 4 0.04
50 4 0.04
51 55 0.54
52 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (48 bp):
ACTTGTAGCTTTAATCTGTTCCACTGCAACTTTAGAGATAAGTTTGTA
Found at i:1531800 original size:96 final size:95
Alignment explanation
Indices: 1531647--1531915 Score: 360
Period size: 96 Copynumber: 2.8 Consensus size: 95
1531637 CTTCAATAAG
** * * * *
1531647 TTCCACTGCAACTTCAGAGGTATAGGACTTGTCGCTTCAATATGCTCCACTGCAACTTTAGGGAG
1 TTCCACTGCAACTTCAGAGAAATAAGATTTGTAGCTTCAATATGCTCCACTGTAACTTTAGGGAG
* *
1531712 ATAAGGTTTGTAACTTGTAGCTTTAATCTA
66 ATAAGATTTGTAACTTGTAACTTTAATCTA
* * **
1531742 TTCCACTGCAACTTTCAGAGAAATAAGATTTGTAGCTTTAATTTGCTCCACTGTAACTTTAAAGA
1 TTCCACTGCAAC-TTCAGAGAAATAAGATTTGTAGCTTCAATATGCTCCACTGTAACTTTAGGGA
*
1531807 GATAAGATTTGTAACTTGTAACTTTAATCTG
65 GATAAGATTTGTAACTTGTAACTTTAATCTA
* *
1531838 TTCCACTGCAACTTCA-AGAAAATAAGATTTGCTATCTTCAATCTGCTCCACTGTAACTTTAGGG
1 TTCCACTGCAACTTCAGAG-AAATAAGATTTG-TAGCTTCAATATGCTCCACTGTAACTTTAGGG
*
1531902 AGATAAAATTTGTA
64 AGATAAGATTTGTA
1531916 GCTTCAATCT
Statistics
Matches: 152, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
94 2 0.01
95 28 0.18
96 122 0.80
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.35
Consensus pattern (95 bp):
TTCCACTGCAACTTCAGAGAAATAAGATTTGTAGCTTCAATATGCTCCACTGTAACTTTAGGGAG
ATAAGATTTGTAACTTGTAACTTTAATCTA
Found at i:1531863 original size:51 final size:51
Alignment explanation
Indices: 1531771--1531868 Score: 119
Period size: 51 Copynumber: 1.9 Consensus size: 51
1531761 GAAATAAGAT
* * * * *
1531771 TTGTAGCTTTAATTTGCTCCACTGTAACTTTAA-AGAGATAAGATTTGTAAC
1 TTGTA-CTTTAATCTGTTCCACTGCAACTTCAAGAGAAATAAGATTTGTAAC
1531822 TTGTAACTTTAATCTGTTCCACTGCAACTTCAAGA-AAATAAGATTTG
1 TTGT-ACTTTAATCTGTTCCACTGCAACTTCAAGAGAAATAAGATTTG
1531869 CTATCTTCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
51 38 0.95
52 2 0.05
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (51 bp):
TTGTACTTTAATCTGTTCCACTGCAACTTCAAGAGAAATAAGATTTGTAAC
Found at i:1531933 original size:44 final size:44
Alignment explanation
Indices: 1531726--1531999 Score: 208
Period size: 44 Copynumber: 6.0 Consensus size: 44
1531716 GGTTTGTAAC
** * *
1531726 TTGTAGCTTTAATCTATTCCACTGCAACTTTCAGAGAAATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTT-AGGGAGATAAGAT
* * **
1531771 TTGTAGCTTTAATTTGCTCCACTGTAACTTTAAAGAGATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGAT
* * * * *
1531815 TTGTAACTTGTAACTTTAATCTGTTCCACTGCAACTTCAAGAAAATAAGAT
1 TTGT-A---G---CTTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGAT
* * * *
1531866 TTGCTATCTTCAATCTGCTCCACTGTAACTTTAGGGAGATAAAAT
1 TTG-TAGCTTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGAT
* * * * *
1531911 TTGTAGCTTCAATCTGCTCCACTACAA-TTTCTGGGAGAAAATAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTT-AGGGAGATAAGAT
* * * * *
1531955 TTGTGGCTTTAATCTACTTCACTGCAACTTCAGGGATATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGAT
1531999 T
1 T
1532000 CGCTACAATG
Statistics
Matches: 181, Mismatches: 38, Indels: 21
0.75 0.16 0.09
Matches are distributed among these distances:
43 3 0.02
44 78 0.43
45 63 0.35
48 1 0.01
51 35 0.19
52 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (44 bp):
TTGTAGCTTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGAT
Found at i:1537881 original size:14 final size:14
Alignment explanation
Indices: 1537862--1537889 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1537852 CCAATTTATT
1537862 AATGAATTATTAAA
1 AATGAATTATTAAA
1537876 AATGAATTATTAAA
1 AATGAATTATTAAA
1537890 TATAACTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
AATGAATTATTAAA
Found at i:1547837 original size:24 final size:23
Alignment explanation
Indices: 1547784--1547842 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
1547774 ATAGATGATA
*
1547784 ATAAAATAATAATAATAAAGACAC
1 ATAAAATAA-AAAAATAAAGACAC
*
1547808 AAAAAATAAAAAAATAAATG-CAC
1 ATAAAATAAAAAAATAAA-GACAC
*
1547831 GATAAAAGAAAA
1 -ATAAAATAAAA
1547843 TAAAAAAACA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 11 0.38
24 18 0.62
ACGTcount: A:0.71, C:0.07, G:0.07, T:0.15
Consensus pattern (23 bp):
ATAAAATAAAAAAATAAAGACAC
Found at i:1549559 original size:11 final size:11
Alignment explanation
Indices: 1549543--1549568 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1549533 TGATCTGGGT
1549543 GATTGTTGATA
1 GATTGTTGATA
1549554 GATTGTTGATA
1 GATTGTTGATA
1549565 GATT
1 GATT
1549569 AACTAAGTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (11 bp):
GATTGTTGATA
Found at i:1553711 original size:19 final size:19
Alignment explanation
Indices: 1553683--1553726 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1553673 AAAAAATTTT
*
1553683 AAATATTAACAAAGTAAAG
1 AAATAATAACAAAGTAAAG
* *
1553702 AAATAATAACTAAGTAAAT
1 AAATAATAACAAAGTAAAG
1553721 AAATAA
1 AAATAA
1553727 AGGACTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.66, C:0.05, G:0.07, T:0.23
Consensus pattern (19 bp):
AAATAATAACAAAGTAAAG
Found at i:1555405 original size:11 final size:11
Alignment explanation
Indices: 1555389--1555414 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1555379 TGTTCTAGGT
1555389 GATTGTTGATA
1 GATTGTTGATA
1555400 GATTGTTGATA
1 GATTGTTGATA
1555411 GATT
1 GATT
1555415 AACTAAGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (11 bp):
GATTGTTGATA
Found at i:1557390 original size:17 final size:17
Alignment explanation
Indices: 1557363--1557401 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1557353 AGATGCAAGT
*
1557363 CTGTCTACCAGGCGATA
1 CTGTCTACCAGACGATA
* *
1557380 TTGTCTGCCAGACGATA
1 CTGTCTACCAGACGATA
1557397 CTGTC
1 CTGTC
1557402 CTCCAAGCGT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.28
Consensus pattern (17 bp):
CTGTCTACCAGACGATA
Found at i:1558350 original size:15 final size:16
Alignment explanation
Indices: 1558332--1558367 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
1558322 GGATGTAATT
1558332 TAAAACAAAGT-AAAA
1 TAAAACAAAGTAAAAA
*
1558347 TAAAATAAAGTAAAAA
1 TAAAACAAAGTAAAAA
1558363 TAAAA
1 TAAAA
1558368 GTTCCAATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.17
Consensus pattern (16 bp):
TAAAACAAAGTAAAAA
Found at i:1563299 original size:54 final size:53
Alignment explanation
Indices: 1563147--1563439 Score: 193
Period size: 54 Copynumber: 5.5 Consensus size: 53
1563137 ATTTGGATCA
* * * * * *
1563147 AAATACCCCCAAAGGTTAAAATGACCAAAATAGCCTCGAAGGGTAAAATGATTG
1 AAATA-CCCCATAGGGTAAAATGACCAAAATACCCCCGTAGGGTAAAATGACTG
* * *
1563201 AAATACCCTCGAT-GGGAAAAATGACCAAAATACCCTC-AATGGGTAAAATGACTG
1 AAATACCC-C-ATAGGGTAAAATGACCAAAATACCCCCGTA-GGGTAAAATGACTG
* * *
1563255 AAATGCCTCCATAGGGTAAAATGACCAAAATACCCCCGTAGGGTAGAAT-A-TCA
1 AAATACC-CCATAGGGTAAAATGACCAAAATACCCCCGTAGGGTAAAATGACT-G
* * ** * *
1563308 AAATAACCCCATATGGT-AAATAACCGTAATACCCCTGTAGGGTAAAAT-AATCG
1 AAAT-ACCCCATAGGGTAAAATGACCAAAATACCCCCGTAGGGTAAAATGACT-G
* * *** * ** *
1563361 TAATGCCCCTATAGGGTAAAATGACTGTAATACCTCTATAGGGTAAAATGACCG
1 AAATACCCC-ATAGGGTAAAATGACCAAAATACCCCCGTAGGGTAAAATGACTG
* *
1563415 TAATACCCCTGTAGGGTAAAATGAC
1 AAATACCCC-ATAGGGTAAAATGAC
1563440 TGTAATACCC
Statistics
Matches: 197, Mismatches: 30, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
52 32 0.16
53 31 0.16
54 130 0.66
55 4 0.02
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.21
Consensus pattern (53 bp):
AAATACCCCATAGGGTAAAATGACCAAAATACCCCCGTAGGGTAAAATGACTG
Found at i:1563316 original size:27 final size:27
Alignment explanation
Indices: 1563145--1563439 Score: 157
Period size: 27 Copynumber: 11.0 Consensus size: 27
1563135 ATATTTGGAT
** *
1563145 CAAAATACCCCCAAAGGTTAAAATGAC
1 CAAAATACCCCCGTAGGGTAAAATGAC
* * * *
1563172 CAAAATAGCCTCGAAGGGTAAAATGAT
1 CAAAATACCCCCGTAGGGTAAAATGAC
** * *
1563199 TGAAATACCCTCG-ATGGGAAAAATGAC
1 CAAAATACCCCCGTA-GGGTAAAATGAC
* *
1563226 CAAAATACCCTC-AATGGGTAAAATGAC
1 CAAAATACCCCCGTA-GGGTAAAATGAC
** * * *
1563253 TGAAATGCCTCCATAGGGTAAAATGAC
1 CAAAATACCCCCGTAGGGTAAAATGAC
* *
1563280 CAAAATACCCCCGTAGGGTAGAAT-AT
1 CAAAATACCCCCGTAGGGTAAAATGAC
* * * *
1563306 CAAAATAACCCCATATGGT-AAATAAC
1 CAAAATACCCCCGTAGGGTAAAATGAC
** * * *
1563332 CGTAATACCCCTGTAGGGTAAAATAAT
1 CAAAATACCCCCGTAGGGTAAAATGAC
** * **
1563359 CGTAATGCCCCTATAGGGTAAAATGAC
1 CAAAATACCCCCGTAGGGTAAAATGAC
*** * **
1563386 TGTAATACCTCTATAGGGTAAAATGAC
1 CAAAATACCCCCGTAGGGTAAAATGAC
** *
1563413 CGTAATACCCCTGTAGGGTAAAATGAC
1 CAAAATACCCCCGTAGGGTAAAATGAC
1563440 TGTAATACCC
Statistics
Matches: 215, Mismatches: 48, Indels: 10
0.79 0.18 0.04
Matches are distributed among these distances:
25 3 0.01
26 32 0.15
27 179 0.83
28 1 0.00
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.21
Consensus pattern (27 bp):
CAAAATACCCCCGTAGGGTAAAATGAC
Found at i:1563440 original size:54 final size:54
Alignment explanation
Indices: 1563265--1563472 Score: 224
Period size: 54 Copynumber: 3.9 Consensus size: 54
1563255 AAATGCCTCC
*** ** * **
1563265 ATAGGGTAAAATGACCAAAATACCCCCGTAGGGTAGAAT-ATCAAAATAACCCC-
1 ATAGGGTAAAATGACTGTAATACCCCTATAGGGTAAAATAATCGTAAT-ACCCCT
* * * * *
1563318 ATATGGT-AAATAACCGTAATACCCCTGTAGGGTAAAATAATCGTAATGCCCCT
1 ATAGGGTAAAATGACTGTAATACCCCTATAGGGTAAAATAATCGTAATACCCCT
* * *
1563371 ATAGGGTAAAATGACTGTAATACCTCTATAGGGTAAAATGACCGTAATACCCCT
1 ATAGGGTAAAATGACTGTAATACCCCTATAGGGTAAAATAATCGTAATACCCCT
* *
1563425 GTAGGGTAAAATGACTGTAATACCCCTATAAGGTAAAATAATCGTAAT
1 ATAGGGTAAAATGACTGTAATACCCCTATAGGGTAAAATAATCGTAAT
1563473 GCCCTAGTGG
Statistics
Matches: 130, Mismatches: 22, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
52 30 0.23
53 18 0.14
54 82 0.63
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (54 bp):
ATAGGGTAAAATGACTGTAATACCCCTATAGGGTAAAATAATCGTAATACCCCT
Found at i:1563444 original size:27 final size:27
Alignment explanation
Indices: 1563186--1563463 Score: 194
Period size: 27 Copynumber: 10.4 Consensus size: 27
1563176 ATAGCCTCGA
* * *
1563186 AGGGTAAAATGATTGAAATACCCTCGAT
1 AGGGTAAAATGACTGTAATACCC-CTAT
* *** *
1563214 -GGGAAAAATGACCAAAATACCCTCAAT
1 AGGGTAAAATGACTGTAATACCC-CTAT
* *
1563241 -GGGTAAAATGACTGAAATGCCTCC-AT
1 AGGGTAAAATGACTGTAATACC-CCTAT
*** **
1563267 AGGGTAAAATGACCAAAATACCCCCGT
1 AGGGTAAAATGACTGTAATACCCCTAT
* **
1563294 AGGGTAGAAT-A-TCAAAATAACCCC-AT
1 AGGGTAAAATGACT-GTAAT-ACCCCTAT
* * * *
1563320 ATGGT-AAATAACCGTAATACCCCTGT
1 AGGGTAAAATGACTGTAATACCCCTAT
* *
1563346 AGGGTAAAAT-AATCGTAATGCCCCTAT
1 AGGGTAAAATGACT-GTAATACCCCTAT
*
1563373 AGGGTAAAATGACTGTAATACCTCTAT
1 AGGGTAAAATGACTGTAATACCCCTAT
* *
1563400 AGGGTAAAATGACCGTAATACCCCTGT
1 AGGGTAAAATGACTGTAATACCCCTAT
1563427 AGGGTAAAATGACTGTAATACCCCTAT
1 AGGGTAAAATGACTGTAATACCCCTAT
*
1563454 AAGGTAAAAT
1 AGGGTAAAAT
1563464 AATCGTAATG
Statistics
Matches: 203, Mismatches: 36, Indels: 23
0.77 0.14 0.09
Matches are distributed among these distances:
25 8 0.04
26 25 0.12
27 167 0.82
28 3 0.01
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.23
Consensus pattern (27 bp):
AGGGTAAAATGACTGTAATACCCCTAT
Found at i:1563472 original size:81 final size:79
Alignment explanation
Indices: 1563322--1563492 Score: 222
Period size: 81 Copynumber: 2.1 Consensus size: 79
1563312 AACCCCATAT
* * * *
1563322 GGTAAATAACCGTAATACCCCTGTAGGGTAAAATAATCGTAATGCCCCTATAGGGTAAAATGACT
1 GGTAAATGACCGTAATACCCCTGTAGGGTAAAATAATCGTAATACCCCTATAAGGTAAAATAACT
1563387 GTAATACCTCTA-TAG
66 GTAATACC-CTAGT-G
*
1563402 GGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGA-CTGTAATACCCCTATAAGGTAAAATAA
1 GGT-AAATGACCGTAATACCCCTGTAGGGTAAAATAATC-GTAATACCCCTATAAGGTAAAATAA
*
1563466 -TCGTAATGCCCTAGTG
64 CT-GTAATACCCTAGTG
1563482 GGTAAATGACC
1 GGTAAATGACC
1563493 ATTTTTTCCC
Statistics
Matches: 81, Mismatches: 6, Indels: 9
0.84 0.06 0.09
Matches are distributed among these distances:
79 8 0.10
80 12 0.15
81 61 0.75
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (79 bp):
GGTAAATGACCGTAATACCCCTGTAGGGTAAAATAATCGTAATACCCCTATAAGGTAAAATAACT
GTAATACCCTAGTG
Found at i:1563551 original size:23 final size:24
Alignment explanation
Indices: 1563512--1563577 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
1563502 CCTCGAGGTC
* *
1563512 AAATGA-TTATTTCTCTGTGGTT-
1 AAATGACTAATTTGTCTGTGGTTG
*
1563534 AAATGACTAATTTGTCTGTGTTTG
1 AAATGACTAATTTGTCTGTGGTTG
** *
1563558 GTATGACTGATTTGTCTGTG
1 AAATGACTAATTTGTCTGTG
1563578 ATTTGAATGA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
22 6 0.17
23 13 0.36
24 17 0.47
ACGTcount: A:0.21, C:0.09, G:0.23, T:0.47
Consensus pattern (24 bp):
AAATGACTAATTTGTCTGTGGTTG
Found at i:1563570 original size:24 final size:24
Alignment explanation
Indices: 1563535--1563593 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
1563525 TCTGTGGTTA
*
1563535 AATGACTAATTTGTCTGTG-TTTGG
1 AATGACTGATTTGTCTGTGATTT-G
*
1563559 TATGACTGATTTGTCTGTGATTTG
1 AATGACTGATTTGTCTGTGATTTG
1563583 AATGACTGATT
1 AATGACTGATT
1563594 CTGAACATGG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 28 0.90
25 3 0.10
ACGTcount: A:0.22, C:0.08, G:0.24, T:0.46
Consensus pattern (24 bp):
AATGACTGATTTGTCTGTGATTTG
Found at i:1563760 original size:26 final size:26
Alignment explanation
Indices: 1563709--1563762 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
1563699 TTGGCCACAT
**
1563709 ATACTATTACTGGCAGCTTTGTTGCG
1 ATACTATTACTGGCAGCTTTACTGCG
*
1563735 ATACTGTTACTGGCAGCTTTACTGCG
1 ATACTATTACTGGCAGCTTTACTGCG
1563761 AT
1 AT
1563763 GCTACTGATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.37
Consensus pattern (26 bp):
ATACTATTACTGGCAGCTTTACTGCG
Found at i:1563806 original size:32 final size:32
Alignment explanation
Indices: 1563765--1563856 Score: 157
Period size: 32 Copynumber: 2.9 Consensus size: 32
1563755 ACTGCGATGC
*
1563765 TACTGATGGCTTTGTGTCGATCATAGTACCGT
1 TACTGATGGCTTTGTGCCGATCATAGTACCGT
* *
1563797 TACTGATGGCTTTATACCGATCATAGTACCGT
1 TACTGATGGCTTTGTGCCGATCATAGTACCGT
1563829 TACTGATGGCTTTGTGCCGATCATAGTA
1 TACTGATGGCTTTGTGCCGATCATAGTA
1563857 TCATCATATT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 55 1.00
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.36
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATAGTACCGT
Found at i:1563929 original size:32 final size:32
Alignment explanation
Indices: 1563880--1563992 Score: 111
Period size: 32 Copynumber: 3.5 Consensus size: 32
1563870 TTGTTACTCG
* * * *
1563880 TGGCTATGTGCCGATCATATCACTACTATTGA
1 TGGCTTTGTGCCAATCATATCACTGCTACTGA
* * ** * *
1563912 TGGCTTTGTACCAATCATGTTGCCGTTACTGA
1 TGGCTTTGTGCCAATCATATCACTGCTACTGA
*
1563944 TGG-TTGTGTGCCGATCATATCACTGCTACTGA
1 TGGCTT-TGTGCCAATCATATCACTGCTACTGA
1563976 TGGCTTTGTGCCAATCA
1 TGGCTTTGTGCCAATCA
1563993 CATTATTGTA
Statistics
Matches: 61, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
31 2 0.03
32 57 0.93
33 2 0.03
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.35
Consensus pattern (32 bp):
TGGCTTTGTGCCAATCATATCACTGCTACTGA
Found at i:1575409 original size:33 final size:33
Alignment explanation
Indices: 1575372--1575479 Score: 180
Period size: 33 Copynumber: 3.3 Consensus size: 33
1575362 ATCCCTCAAA
*
1575372 CACACCAAAGTTCATAAGAGCTAATCCAACCAT
1 CACACCAAAGCTCATAAGAGCTAATCCAACCAT
* *
1575405 CACACCAATGCTCATAAGAGCTAAACCAACCAT
1 CACACCAAAGCTCATAAGAGCTAATCCAACCAT
*
1575438 CACACCAATGCTCATAAGAGCTAATCCAACCAT
1 CACACCAAAGCTCATAAGAGCTAATCCAACCAT
1575471 CACACCAAA
1 CACACCAAA
1575480 CAAAGAGTAT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 70 1.00
ACGTcount: A:0.43, C:0.33, G:0.08, T:0.16
Consensus pattern (33 bp):
CACACCAAAGCTCATAAGAGCTAATCCAACCAT
Found at i:1583607 original size:33 final size:33
Alignment explanation
Indices: 1583539--1583691 Score: 152
Period size: 33 Copynumber: 4.6 Consensus size: 33
1583529 GTACATCTTC
* **
1583539 AATCCAACCAAACACACCAGATGCTCACCCA-AGCT
1 AATCCAACC-TACACACCA-ATGCTCA-TAAGAGCT
**
1583574 AATCCTTCCTACACACCAATGCTCATAAGAGCT
1 AATCCAACCTACACACCAATGCTCATAAGAGCT
1583607 AATCCAACC-ATCACACCAATGCTCATAAGAGCT
1 AATCCAACCTA-CACACCAATGCTCATAAGAGCT
* * *
1583640 AAACCAGCCGT-CACACCAATGCTCATAAGGGCT
1 AATCCAACC-TACACACCAATGCTCATAAGAGCT
1583673 AATCCAACC-ATCACACCAA
1 AATCCAACCTA-CACACCAA
1583692 ACAAAGAGTA
Statistics
Matches: 100, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
32 2 0.02
33 83 0.83
34 8 0.08
35 7 0.07
ACGTcount: A:0.38, C:0.36, G:0.10, T:0.16
Consensus pattern (33 bp):
AATCCAACCTACACACCAATGCTCATAAGAGCT
Found at i:1584334 original size:9 final size:9
Alignment explanation
Indices: 1584320--1584348 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
1584310 TTTGATCACT
1584320 TAATTACTA
1 TAATTACTA
1584329 TAATTACTA
1 TAATTACTA
1584338 TAATTACTA
1 TAATTACTA
1584347 TA
1 TA
1584349 TTTTTCACCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (9 bp):
TAATTACTA
Found at i:1587009 original size:64 final size:65
Alignment explanation
Indices: 1586931--1587076 Score: 231
Period size: 64 Copynumber: 2.2 Consensus size: 65
1586921 AGGTTTAAAT
* * *
1586931 TGTAAGACCATGGCTCGACCATGGCAACATAGATAGTCCGCCAGGACATTGAACATGGGGTAT-G
1 TGTAAGACCATGGCTCGACCATGGCAACATAGATAGTCCACCAGGACATTAAAAATGGGGTATAG
*
1586995 TGTAAGACCATGGCTCGACCATGGCAACATAGATAGTCCACTAGGACATTAAAAATGGGGTATGA
1 TGTAAGACCATGGCTCGACCATGGCAACATAGATAGTCCACCAGGACATTAAAAATGGGGTAT-A
1587060 CG
65 -G
1587062 TGTAAGACCATGGCT
1 TGTAAGACCATGGCT
1587077 TGGCTATGAC
Statistics
Matches: 75, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
64 59 0.79
67 16 0.21
ACGTcount: A:0.32, C:0.21, G:0.27, T:0.21
Consensus pattern (65 bp):
TGTAAGACCATGGCTCGACCATGGCAACATAGATAGTCCACCAGGACATTAAAAATGGGGTATAG
Found at i:1588844 original size:272 final size:272
Alignment explanation
Indices: 1588469--1589009 Score: 931
Period size: 272 Copynumber: 2.0 Consensus size: 272
1588459 AGAACCAGTC
*
1588469 TGAATTTAACAAATGGTTTAGATAAGAATGGAAAGTGATTATGGTTATAAAAAGGAAAAATGGGA
1 TGAATTTAACAAATGGTTTACATAAGAATGGAAAGTGATTATGGTTATAAAAAGGAAAAATGGGA
1588534 ATTGTGATTAGAGATTTATTCGATGGTTGAGATCCAGCACAAATTGTGGATTCCCGACAACTCGA
66 ATTGTGATTAGAGATTTATTCGATGGTTGAGATCCAGCACAAATTGTGGATTCCCGACAACTCGA
* * *
1588599 CTAAGCAGTGTCGGATCATTATATAGCAATCTATGATGA-TTAGTCCTTGAAACGTTCTAGTTGC
131 CTAAGCAGTATCGGATCATTATATAGCAATCTATGAT-ATTTAATCCCTGAAACGTTCTAGTTGC
*
1588663 CATTTTCTATGTAAGTTCATATGGAACTTACAGCATTTTCGTATTATATTTTAATTGTGTTTTTG
195 CATTTTCTAGGTAAGTTCATATGGAACTTACAGCATTTTCGTATTATATTTTAATTGTGTTTTTG
1588728 TATATATATTGTA
260 TATATATATTGTA
1588741 TGAATTTAACAAATGGTTTACATAAGAATGGAAAGTGATTATGGTTATAAAAAGGAAAAATGGGA
1 TGAATTTAACAAATGGTTTACATAAGAATGGAAAGTGATTATGGTTATAAAAAGGAAAAATGGGA
*
1588806 ATTGTGATTAGAGATTTATTCGATGGTTGAGATCCAGCACAAATTGTGGATTCCCGACAGCTCGA
66 ATTGTGATTAGAGATTTATTCGATGGTTGAGATCCAGCACAAATTGTGGATTCCCGACAACTCGA
* * * *
1588871 CTGAGCAGTATCGGATCATTATATAGTAATCTGTGATATTTAATCCCTGAAACTTTCTAGTTGCC
131 CTAAGCAGTATCGGATCATTATATAGCAATCTATGATATTTAATCCCTGAAACGTTCTAGTTGCC
* ** * *
1588936 ATTTTCTAGGTAAGTTCATATGGAATTTAGTGTATTTTCGTATTTTATTTTAATTGTGTTTTTGT
196 ATTTTCTAGGTAAGTTCATATGGAACTTACAGCATTTTCGTATTATATTTTAATTGTGTTTTTGT
1589001 ATATATATT
261 ATATATATT
1589010 TTAAATATAT
Statistics
Matches: 253, Mismatches: 15, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
271 1 0.00
272 252 1.00
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.38
Consensus pattern (272 bp):
TGAATTTAACAAATGGTTTACATAAGAATGGAAAGTGATTATGGTTATAAAAAGGAAAAATGGGA
ATTGTGATTAGAGATTTATTCGATGGTTGAGATCCAGCACAAATTGTGGATTCCCGACAACTCGA
CTAAGCAGTATCGGATCATTATATAGCAATCTATGATATTTAATCCCTGAAACGTTCTAGTTGCC
ATTTTCTAGGTAAGTTCATATGGAACTTACAGCATTTTCGTATTATATTTTAATTGTGTTTTTGT
ATATATATTGTA
Found at i:1588998 original size:25 final size:26
Alignment explanation
Indices: 1588965--1589013 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
1588955 ATGGAATTTA
*
1588965 GTGTATTTTCGTAT-TTTATTTTAATT
1 GTGTATTTT-GTATATATATTTTAATT
1588991 GTGT-TTTTGTATATATATTTTAA
1 GTGTATTTTGTATATATATTTTAA
1589014 ATATATAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 13 0.62
26 4 0.19
ACGTcount: A:0.22, C:0.02, G:0.12, T:0.63
Consensus pattern (26 bp):
GTGTATTTTGTATATATATTTTAATT
Done.