Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 3 of 438
Found at i:759783 original size:46 final size:46
Alignment explanation
Indices: 759718--759903 Score: 257
Period size: 46 Copynumber: 4.0 Consensus size: 46
759708 TTATCTTTGA
* * * * * *
759718 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATAT
***
759764 CATGTTGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
759810 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* *
759856 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
759902 CA
1 CA
759904 GGGAGCACAC
Statistics
Matches: 127, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 4 0.03
46 123 0.97
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.41
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
Found at i:762056 original size:11 final size:11
Alignment explanation
Indices: 762040--762091 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
762030 TATACTAAAT
762040 AAATAATAATA
1 AAATAATAATA
*
762051 AAATAAT-ATT
1 AAATAATAATA
* *
762061 AAATATCTCATA
1 AAATA-ATAATA
*
762073 AAATATTAATA
1 AAATAATAATA
762084 AAATAATA
1 AAATAATA
762092 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:763241 original size:27 final size:28
Alignment explanation
Indices: 763205--763280 Score: 73
Period size: 32 Copynumber: 2.6 Consensus size: 28
763195 TAAATATAAC
*
763205 AAATTTAATTAATCAAT-ATGAGTTATT
1 AAATTAAATTAATCAATCATGAGTTATT
*
763232 AAATTAAATTAATTATTTTATCATGAGTTATT
1 AAATTAAATTAATCA----ATCATGAGTTATT
* *
763264 AAATTCAAGTAATCAAT
1 AAATTAAATTAATCAAT
763281 TTATAAGTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
27 13 0.33
28 2 0.05
31 2 0.05
32 22 0.56
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (28 bp):
AAATTAAATTAATCAATCATGAGTTATT
Found at i:763284 original size:32 final size:32
Alignment explanation
Indices: 763222--763284 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
763212 ATTAATCAAT
* * *
763222 ATGAGTTATTAAATTAAATTAATTATTTTATC
1 ATGAGTTATTAAATTAAAGTAATCAATTTATC
*
763254 ATGAGTTATTAAATTCAAGTAATCAATTTAT
1 ATGAGTTATTAAATTAAAGTAATCAATTTAT
763285 AAGTTTGTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (32 bp):
ATGAGTTATTAAATTAAAGTAATCAATTTATC
Found at i:767077 original size:510 final size:511
Alignment explanation
Indices: 766053--767098 Score: 1896
Period size: 510 Copynumber: 2.0 Consensus size: 511
766043 TTCTGATGGG
* *
766053 ATTTGATCACGATAAACCTTGGCGACGCAAATGGCTTATTCGCAAGCAACTCCCAGTCAATGACA
1 ATTTGAGCACCATAAACCTTGGCGACGCAAATGGCTTATTCGCAAGCAA--CCCAGTCAATGACA
766118 GTGAAGAGATCACAGGAATTACCATCGAAAACTTTGTAGTTTGCCAACACACAGTTATTAAACGT
64 GTGAAGAGATCACAGGAATTACCATCGAAAACTTTGTAGTTTGCCAACACACAGTTATTAAACGT
766183 TGGAGAATCTACCCACCATAAGCATAAATAGCAACCTGACTGCACATGCATAATTCGGATCTTAT
129 TGGAGAATCTACCCACCATAAGCATAAATAGCAACCTGACTGCACATGCATAATTCGGATCTTAT
*
766248 TTGTTGCAGTGTCCACCGGGATAAGTTTGAACAACGTGCACGACTCCTCGGATCGGCCTTCCACC
194 TTGTTGCAGTGTCCACCGGGATAAGCTTGAACAACGTGCACGACTCCTCGGATCGGCCTTCCACC
766313 GGCTTGTCGGCTGCTGCAGAAATCCAATACTGCTCTGTTGAGTTTCCAGTGATGGAAACATTTTT
259 GGCTTGTCGGCTGCTGCAGAAATCCAATACTGCTCTGTTGAGTTTCCAGTGATGGAAACATTTTT
* *
766378 GACTCGTTTGCAGTATTTTTTGTTGTGGCAGCTCTTTATGTGCACCAACCCATCTTCCCCACCGC
324 GACTCGTTTGCAGTATTTGTTGTTCTGGCAGCTCTTTATGTGCACCAACCCATCTTCCCCACCGC
* *
766443 ATTTGGCCCTTTCCACCTCAAATTTTGTGTATGGACTGAAAGCCAAAGTTTCCGAAAATTTGAGA
389 ATTTGGCCCTCTCCACCTCAAATTTTGTGTATGGACTGAAAGCCAAAGTTTCCGAAAATCTGAGA
*
766508 TACCCATTACAATCGTAACTCTCATGCATATAGCTCAAATATTTGTTCCTCGCCTCAC
454 TACCCATGACAATCGTAACTCTCATGCATATAGCTCAAATATTTGTTCCTCGCCTCAC
* * *
766566 ATTTGAGCACCATAAACCTTGGCGACGCAAATGGCTTATTCGCAAGCGA-CCAGTCGATGACTGT
1 ATTTGAGCACCATAAACCTTGGCGACGCAAATGGCTTATTCGCAAGCAACCCAGTCAATGACAGT
766630 GAAGAGATCACAGGAATTACCATCGAAAACTTTGTAGTTTGCCAACACACAGTTATTAAACGTTG
66 GAAGAGATCACAGGAATTACCATCGAAAACTTTGTAGTTTGCCAACACACAGTTATTAAACGTTG
*
766695 GAGAATCTACCCACCATAAGCATAAATAGCAACCTGATTGCACATGCATAATTCGGATCTTATTT
131 GAGAATCTACCCACCATAAGCATAAATAGCAACCTGACTGCACATGCATAATTCGGATCTTATTT
* *
766760 GTTGCAGTGTCCACTGGGATAAGCTTGAACAACGTGCACGACTCCTCGGATCGGCCTTCCTCCGG
196 GTTGCAGTGTCCACCGGGATAAGCTTGAACAACGTGCACGACTCCTCGGATCGGCCTTCCACCGG
* * *
766825 TTTGTCTGCTGCTGCAGAAATCCAATACTGCTCTTTTGAGTTTCCAGTGATGGAAACATTTTTGA
261 CTTGTCGGCTGCTGCAGAAATCCAATACTGCTCTGTTGAGTTTCCAGTGATGGAAACATTTTTGA
*
766890 CTCGTTTGCAGTATTTGTTGTTCTGGCAGCTCTTTATGTGCACCAACCCATCTTCCCCACTGCAT
326 CTCGTTTGCAGTATTTGTTGTTCTGGCAGCTCTTTATGTGCACCAACCCATCTTCCCCACCGCAT
*
766955 TTGGCCCTCTCCACCTCAAATTTTGTGTATGGACTGCAAGCCAAAGTTTCCGAAAATCTGAGATA
391 TTGGCCCTCTCCACCTCAAATTTTGTGTATGGACTGAAAGCCAAAGTTTCCGAAAATCTGAGATA
767020 CCCATGACAATCGTAACTCTCATGCATATAGCTCAAATATTTGTTCCTCGCCTCAC
456 CCCATGACAATCGTAACTCTCATGCATATAGCTCAAATATTTGTTCCTCGCCTCAC
767076 ATTTGAGCACCATAAACCTTGGC
1 ATTTGAGCACCATAAACCTTGGC
767099 CATGCAATTG
Statistics
Matches: 514, Mismatches: 19, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
510 468 0.91
513 46 0.09
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (511 bp):
ATTTGAGCACCATAAACCTTGGCGACGCAAATGGCTTATTCGCAAGCAACCCAGTCAATGACAGT
GAAGAGATCACAGGAATTACCATCGAAAACTTTGTAGTTTGCCAACACACAGTTATTAAACGTTG
GAGAATCTACCCACCATAAGCATAAATAGCAACCTGACTGCACATGCATAATTCGGATCTTATTT
GTTGCAGTGTCCACCGGGATAAGCTTGAACAACGTGCACGACTCCTCGGATCGGCCTTCCACCGG
CTTGTCGGCTGCTGCAGAAATCCAATACTGCTCTGTTGAGTTTCCAGTGATGGAAACATTTTTGA
CTCGTTTGCAGTATTTGTTGTTCTGGCAGCTCTTTATGTGCACCAACCCATCTTCCCCACCGCAT
TTGGCCCTCTCCACCTCAAATTTTGTGTATGGACTGAAAGCCAAAGTTTCCGAAAATCTGAGATA
CCCATGACAATCGTAACTCTCATGCATATAGCTCAAATATTTGTTCCTCGCCTCAC
Found at i:770443 original size:15 final size:15
Alignment explanation
Indices: 770423--770465 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
770413 TGGATAAATG
770423 AAAAATTAAGTATTC
1 AAAAATTAAGTATTC
* * *
770438 AAAAATTAAATGTTG
1 AAAAATTAAGTATTC
770453 AAAAATT-AGTATT
1 AAAAATTAAGTATT
770466 GAATATTAGA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 4 0.17
15 19 0.83
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.35
Consensus pattern (15 bp):
AAAAATTAAGTATTC
Found at i:773661 original size:24 final size:24
Alignment explanation
Indices: 773632--773686 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
773622 GAATTTTTAG
*
773632 AATATTTAATATTTATTAATATAA
1 AATATTTAACATTTATTAATATAA
* *
773656 TATATTTAACATTTATTAGTATAA
1 AATATTTAACATTTATTAATATAA
773680 AATATTT
1 AATATTT
773687 TTTTTTATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (24 bp):
AATATTTAACATTTATTAATATAA
Found at i:781250 original size:30 final size:30
Alignment explanation
Indices: 781214--781273 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
781204 ATAGACAAAT
*
781214 ATGATGTAATACCCTACACCTGGCCTAAAC
1 ATGATGTAACACCCTACACCTGGCCTAAAC
781244 ATGATGTAACACCCTACACCTGGCCTAAAC
1 ATGATGTAACACCCTACACCTGGCCTAAAC
781274 GTTATGGTCG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.33, C:0.32, G:0.13, T:0.22
Consensus pattern (30 bp):
ATGATGTAACACCCTACACCTGGCCTAAAC
Found at i:786671 original size:2 final size:2
Alignment explanation
Indices: 786664--786695 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
786654 CTCCAATGCC
786664 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
786696 TATGGGCTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:803681 original size:16 final size:15
Alignment explanation
Indices: 803646--803679 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
803636 GAAATAATTT
803646 AAAATGAAAATTTTA
1 AAAATGAAAATTTTA
803661 AAAATGAAAATTTTA
1 AAAATGAAAATTTTA
803676 AAAA
1 AAAA
803680 ATATATTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (15 bp):
AAAATGAAAATTTTA
Found at i:803829 original size:44 final size:44
Alignment explanation
Indices: 803734--803829 Score: 99
Period size: 44 Copynumber: 2.2 Consensus size: 44
803724 TATTCGCACT
* *
803734 CATTTT-TTTTTAGTTTTATTTTTTATTTTAAAAATTATGTAGCAA
1 CATTTTATTTTTA-TTTTAATTTTTATTTT-AAAATTATGTAACAA
* *
803779 CGTTTTATTTTT-TTTTAATTTTTATTTT-AAATTATGTCATATAA
1 CATTTTATTTTTATTTTAATTTTTATTTTAAAATTATGT-A-ACAA
803823 CATTTTA
1 CATTTTA
803830 CATGACATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
42 9 0.21
43 1 0.02
44 23 0.53
45 5 0.12
46 5 0.12
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.61
Consensus pattern (44 bp):
CATTTTATTTTTATTTTAATTTTTATTTTAAAATTATGTAACAA
Found at i:810830 original size:21 final size:21
Alignment explanation
Indices: 810802--810847 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
810792 AATAATTATA
810802 ATGA-ATGAAAAAGGAACCTC
1 ATGATATGAAAAAGGAACCTC
*
810822 ATGATATGAAAAAGGAACCTT
1 ATGATATGAAAAAGGAACCTC
810843 ATGAT
1 ATGAT
810848 TGTCCTAAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.48, C:0.11, G:0.20, T:0.22
Consensus pattern (21 bp):
ATGATATGAAAAAGGAACCTC
Found at i:814399 original size:31 final size:30
Alignment explanation
Indices: 814321--814402 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 30
814311 TTCTCCTTTT
* * *
814321 AGGTAGACAATTTT-CTTGATTTAAGAGAG
1 AGGTGGACGATTTTGCTTGATTCAAGAGAG
*
814350 AGAGTGGACGA-TTTGCTTGATTCAAGGGAG
1 AG-GTGGACGATTTTGCTTGATTCAAGAGAG
814380 AAGGTGGACGATTTTGCTTGATT
1 -AGGTGGACGATTTTGCTTGATT
814403 TGTGGAGAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
29 5 0.11
30 27 0.60
31 13 0.29
ACGTcount: A:0.28, C:0.09, G:0.30, T:0.33
Consensus pattern (30 bp):
AGGTGGACGATTTTGCTTGATTCAAGAGAG
Found at i:818483 original size:14 final size:15
Alignment explanation
Indices: 818449--818494 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
818439 TAGCAAAGAA
818449 GAACCCCTCACCTCAT
1 GAACCCCTCACCTC-T
818465 GAACCCC-CACCTCT
1 GAACCCCTCACCTCT
818479 GAACCCCTCACCTCT
1 GAACCCCTCACCTCT
818494 G
1 G
818495 GAAATTCTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.28
15 14 0.48
16 7 0.24
ACGTcount: A:0.22, C:0.52, G:0.09, T:0.17
Consensus pattern (15 bp):
GAACCCCTCACCTCT
Found at i:818843 original size:14 final size:15
Alignment explanation
Indices: 818817--818845 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
818807 CGCACTTTTT
818817 TTTTTTTAGTTTTAG
1 TTTTTTTAGTTTTAG
818832 TTTTTTTA-TTTTAG
1 TTTTTTTAGTTTTAG
818846 AAATTATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.14, C:0.00, G:0.10, T:0.76
Consensus pattern (15 bp):
TTTTTTTAGTTTTAG
Found at i:833250 original size:15 final size:15
Alignment explanation
Indices: 833217--833246 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
833207 TCCTCTCCCC
833217 TCTCCCTCTCTCCTT
1 TCTCCCTCTCTCCTT
833232 TCTCCC-CTCTCCTT
1 TCTCCCTCTCTCCTT
833246 T
1 T
833247 TCTCTCTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (15 bp):
TCTCCCTCTCTCCTT
Found at i:833256 original size:22 final size:22
Alignment explanation
Indices: 833204--833256 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
833194 GGCCAGAGCC
*
833204 CTCTCCTCTCCCCTCTCCCTCT
1 CTCTCTTCTCCCCTCTCCCTCT
* *
833226 CTC-CTTTCTCCCCTCTCCTTTT
1 CTCTC-TTCTCCCCTCTCCCTCT
833248 CTCTCTTCT
1 CTCTCTTCT
833257 TTTTTTTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 1 0.04
22 24 0.92
23 1 0.04
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (22 bp):
CTCTCTTCTCCCCTCTCCCTCT
Found at i:833753 original size:17 final size:18
Alignment explanation
Indices: 833727--833776 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 18
833717 ATATTGTTAC
*
833727 TATTATTTTTATTAATA-
1 TATTAATTTTATTAATAG
*
833744 TATTAATTTTTTTAA-AG
1 TATTAATTTTATTAATAG
833761 TATT-ATTATTATTAAT
1 TATTAATT-TTATTAAT
833777 GGTTGTTGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
16 4 0.15
17 23 0.85
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
TATTAATTTTATTAATAG
Found at i:833833 original size:13 final size:14
Alignment explanation
Indices: 833809--833839 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
833799 ATTATTATCA
833809 ATATTGATATATGT
1 ATATTGATATATGT
833823 ATATT-ATATATGT
1 ATATTGATATATGT
833836 ATAT
1 ATAT
833840 ATTCATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.52
Consensus pattern (14 bp):
ATATTGATATATGT
Found at i:842342 original size:15 final size:15
Alignment explanation
Indices: 842322--842381 Score: 86
Period size: 15 Copynumber: 4.1 Consensus size: 15
842312 TAGCAAAGAA
*
842322 GAACCCCTCACCTCT
1 GAACCCCCCACCTCT
*
842337 GAACCCCCCACCTTT
1 GAACCCCCCACCTCT
*
842352 GTACCCCCCACCTCT
1 GAACCCCCCACCTCT
842367 GAA-CCCCCACCTCT
1 GAACCCCCCACCTCT
842381 G
1 G
842382 GGAATCAGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
14 12 0.30
15 28 0.70
ACGTcount: A:0.18, C:0.55, G:0.08, T:0.18
Consensus pattern (15 bp):
GAACCCCCCACCTCT
Found at i:842462 original size:25 final size:25
Alignment explanation
Indices: 842428--842479 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
842418 AATTTTAAAA
842428 AATATATTGTAAAAATTTTCATTTT
1 AATATATTGTAAAAATTTTCATTTT
842453 AATATATTGTAAAAATTTTCATTTT
1 AATATATTGTAAAAATTTTCATTTT
842478 AA
1 AA
842480 AGTTTTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (25 bp):
AATATATTGTAAAAATTTTCATTTT
Found at i:847414 original size:21 final size:21
Alignment explanation
Indices: 847390--847429 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
847380 CACTAATCTG
847390 TTGTATTAATCGTCAAATCCA
1 TTGTATTAATCGTCAAATCCA
847411 TTGTATTAATCGTCAAATC
1 TTGTATTAATCGTCAAATC
847430 GTTGCTAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (21 bp):
TTGTATTAATCGTCAAATCCA
Found at i:850195 original size:17 final size:18
Alignment explanation
Indices: 850168--850202 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
850158 TTAAAACATA
*
850168 TAAAAACTAAATAAAAAG
1 TAAAAACTAAAGAAAAAG
850186 TAAAAA-TAAAGAAAAAG
1 TAAAAACTAAAGAAAAAG
850203 AGGCAACTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.74, C:0.03, G:0.09, T:0.14
Consensus pattern (18 bp):
TAAAAACTAAAGAAAAAG
Found at i:850789 original size:3 final size:3
Alignment explanation
Indices: 850781--850855 Score: 150
Period size: 3 Copynumber: 25.0 Consensus size: 3
850771 CTACTTTAAT
850781 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
850829 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
850856 CTTCTAATGT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:851338 original size:24 final size:24
Alignment explanation
Indices: 851310--851356 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
851300 TAATACATGT
*
851310 TTTTTATATGTATA-TATTATGTATA
1 TTTTAATAT-TATATTA-TATGTATA
851335 TTTTAATATTATATTATATGTA
1 TTTTAATATTATATTATATGTA
851357 CGTACTCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (24 bp):
TTTTAATATTATATTATATGTATA
Found at i:851434 original size:21 final size:20
Alignment explanation
Indices: 851400--851438 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
851390 TTTTGTACTA
*
851400 TATTATTTTATTAGTTTTGC
1 TATTATTGTATTAGTTTTGC
851420 TATTATTAGTATTAGTTTT
1 TATTATT-GTATTAGTTTT
851439 AGTTTTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.23, C:0.03, G:0.10, T:0.64
Consensus pattern (20 bp):
TATTATTGTATTAGTTTTGC
Found at i:851671 original size:31 final size:31
Alignment explanation
Indices: 851636--851700 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
851626 AAATACTATG
851636 TATAGTATATTTATGACTCTATTACTATATA
1 TATAGTATATTTATGACTCTATTACTATATA
851667 TATAGTATATTTATGACTCTATTACTATATA
1 TATAGTATATTTATGACTCTATTACTATATA
851698 TAT
1 TAT
851701 TCTATGTACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.35, C:0.09, G:0.06, T:0.49
Consensus pattern (31 bp):
TATAGTATATTTATGACTCTATTACTATATA
Found at i:855527 original size:21 final size:21
Alignment explanation
Indices: 855503--855548 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
855493 GATGGGCACT
*
855503 AATCTATTGTATTAATCGTCA
1 AATCCATTGTATTAATCGTCA
855524 AATCCATTGTATTAATCGTCA
1 AATCCATTGTATTAATCGTCA
855545 AATC
1 AATC
855549 GTTGCTAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (21 bp):
AATCCATTGTATTAATCGTCA
Found at i:862123 original size:3 final size:3
Alignment explanation
Indices: 862117--862154 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
862107 TCCCTCTTCT
862117 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
862155 GTGGATTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:865976 original size:28 final size:30
Alignment explanation
Indices: 865910--865976 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
865900 ACTAGAGTTT
*
865910 TTAAA-TTTAAAAGTAAGAGGATTAAATTT
1 TTAAATTTTAAAAGTAAGAGGATTAAATTC
*
865939 TTAACTTTTAAAA-TACAG-GGATTAAA-TC
1 TTAAATTTTAAAAGTA-AGAGGATTAAATTC
865967 TTAAATTTTA
1 TTAAATTTTA
865977 TAAAATAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 10 0.30
29 14 0.42
30 9 0.27
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.40
Consensus pattern (30 bp):
TTAAATTTTAAAAGTAAGAGGATTAAATTC
Found at i:867606 original size:3 final size:3
Alignment explanation
Indices: 867598--867625 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
867588 AAAGTGTTTG
867598 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
867626 GGGTACATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:869686 original size:17 final size:17
Alignment explanation
Indices: 869664--869698 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
869654 TATTTTTTAA
869664 ATTTAAATCCAAAATAT
1 ATTTAAATCCAAAATAT
*
869681 ATTTAAATTCAAAATAT
1 ATTTAAATCCAAAATAT
869698 A
1 A
869699 CCTACATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (17 bp):
ATTTAAATCCAAAATAT
Found at i:871611 original size:6 final size:6
Alignment explanation
Indices: 871600--871631 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
871590 TAACGATCCT
*
871600 CCATAG CCATAG CCATGG CCATAG CCATAG CC
1 CCATAG CCATAG CCATAG CCATAG CCATAG CC
871632 TGCTGACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.28, C:0.38, G:0.19, T:0.16
Consensus pattern (6 bp):
CCATAG
Found at i:872015 original size:22 final size:21
Alignment explanation
Indices: 871969--872009 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
871959 ATAATTATTT
871969 TAAATTTTTATTATATAAAAA
1 TAAATTTTTATTATATAAAAA
*
871990 TAAATATTTTA-TATTTAAAA
1 TAAAT-TTTTATTATATAAAA
872010 TGTAAAGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TAAATTTTTATTATATAAAAA
Found at i:875085 original size:19 final size:18
Alignment explanation
Indices: 875042--875106 Score: 60
Period size: 17 Copynumber: 3.5 Consensus size: 18
875032 AATAACTAAT
* *
875042 TTTAAAAATATACAAATA
1 TTTAAAAATATTCAAAAA
875060 TTT-AAAATATTCAAAAA
1 TTTAAAAATATTCAAAAA
*
875077 TTATAAAAAAATTCATAAAAA
1 TT-TAAAAATATTC--AAAAA
*
875098 TTTTAAAAT
1 TTTAAAAAT
875107 TAACTTCAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
17 14 0.37
18 4 0.11
19 8 0.21
20 5 0.13
21 7 0.18
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (18 bp):
TTTAAAAATATTCAAAAA
Found at i:878329 original size:22 final size:20
Alignment explanation
Indices: 878291--878330 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
878281 TGGTTTTTGG
*
878291 TTTATTTTGTCTTTAGTACT
1 TTTATTTTGTCCTTAGTACT
878311 TTTATGTTTGCTCCTTAGTA
1 TTTAT-TTTG-TCCTTAGTA
878331 GTTACCTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 4 0.24
22 8 0.47
ACGTcount: A:0.15, C:0.12, G:0.12, T:0.60
Consensus pattern (20 bp):
TTTATTTTGTCCTTAGTACT
Found at i:889471 original size:5 final size:5
Alignment explanation
Indices: 889465--889503 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
889455 TGAATTTTAA
* *
889465 ATTAA ATTAA ATTAT ATTAT ATTAT ATTAT ATTACT ATT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTA-T ATT
889504 TTTTAAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
5 28 0.88
6 4 0.12
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (5 bp):
ATTAT
Found at i:889530 original size:17 final size:19
Alignment explanation
Indices: 889486--889531 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
889476 TTATATTATA
889486 TTATAT-TATATTACTATT
1 TTATATATATATTACTATT
* *
889504 TTTTAAATAT-TTACTA-T
1 TTATATATATATTACTATT
889521 TTATATATATA
1 TTATATATATA
889532 AATATATCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
17 9 0.41
18 10 0.45
19 3 0.14
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (19 bp):
TTATATATATATTACTATT
Found at i:889534 original size:23 final size:23
Alignment explanation
Indices: 889507--889561 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
889497 TACTATTTTT
*
889507 TAAATATTTAC-TATTTATATATA
1 TAAATATTT-CTTAATTATATATA
*
889530 TAAATATATCTTAATTATATATA
1 TAAATATTTCTTAATTATATATA
889553 TAAATATTT
1 TAAATATTT
889562 TTGTATCTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 1 0.04
23 27 0.96
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (23 bp):
TAAATATTTCTTAATTATATATA
Found at i:890545 original size:30 final size:29
Alignment explanation
Indices: 890490--890546 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
890480 TCTTTATATT
* *
890490 TTTTAAATAATTAAATCAAATTTTTATAA
1 TTTTAAAAAATTAAATCAAAATTTTATAA
890519 TTTTAAGAAAATTAAAGT-AAAATTTTAT
1 TTTTAA-AAAATTAAA-TCAAAATTTTAT
890547 TTTTACTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.25
30 17 0.71
31 1 0.04
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.46
Consensus pattern (29 bp):
TTTTAAAAAATTAAATCAAAATTTTATAA
Found at i:892893 original size:213 final size:213
Alignment explanation
Indices: 892506--892923 Score: 520
Period size: 213 Copynumber: 2.0 Consensus size: 213
892496 GGATTGATTT
* * * *
892506 TTAACTCGATCGATATGAATATTGTTGTCAATATAAGATGATGTGGGTACGAGTGCGCTGAAACG
1 TTAACTCGATCGATATGAATATTGTTATCAATATAAGATGACGTGAGTACGAATGCGCTGAAACG
* * * * *
892571 CATTATCCTCCTATTAATGTGTTAGTGAGGAGTTGTAGGTAGTTTTAAGCATTGTGTAAAAGAAA
66 CATTAGCCTCCTATTAATGTATTAGTGAGGAGTTATAGGTAGTTTTAAGCATTATATAAAAGAAA
* * * * * *
892636 ACATATATGATCAGAACCTACAGTGAAATTATGTAAAGAAGTTATAGATTTAGTCTTTGTGCTTT
131 ACAGATATGATCAAAACCTACAATGAAATTATGTAAAAAAGTTATAGATTTAGTCGTCGTGCTTT
892701 TATTTGATCAATTGAGTC
196 TATTTGATCAATTGAGTC
* * **
892719 TTAACTCGATTGGTAT-AAGTATTGTTATCAATATAAGA-GAACGTGAGTTTGAATGCGCTGAAA
1 TTAACTCGATCGATATGAA-TATTGTTATCAATATAAGATG-ACGTGAGTACGAATGCGCTGAAA
* * *
892782 CGCATTAGCCTCCTATTAATAG-ATTGGTGAAGG-GTTATGGGTAGTTTTAGGCATTATATAAAA
64 CGCATTAGCCTCCTATTAAT-GTATTAGTG-AGGAGTTATAGGTAGTTTTAAGCATTATATAAAA
* * * * *
892845 GAAAACAGATATGGTCAAAACTTATAATGAGATTGTGTAAAAAAGTTATAGATTTAGTCGTCGTG
127 GAAAACAGATATGATCAAAACCTACAATGAAATTATGTAAAAAAGTTATAGATTTAGTCGTCGTG
*
892910 TTTTTATTTGATCA
192 CTTTTATTTGATCA
892924 CTTTTAATCT
Statistics
Matches: 173, Mismatches: 28, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
212 3 0.02
213 166 0.96
214 4 0.02
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.35
Consensus pattern (213 bp):
TTAACTCGATCGATATGAATATTGTTATCAATATAAGATGACGTGAGTACGAATGCGCTGAAACG
CATTAGCCTCCTATTAATGTATTAGTGAGGAGTTATAGGTAGTTTTAAGCATTATATAAAAGAAA
ACAGATATGATCAAAACCTACAATGAAATTATGTAAAAAAGTTATAGATTTAGTCGTCGTGCTTT
TATTTGATCAATTGAGTC
Found at i:908878 original size:3 final size:3
Alignment explanation
Indices: 908870--908896 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
908860 TATTTCTTTT
908870 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
908897 ATGAAACCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:914209 original size:7 final size:6
Alignment explanation
Indices: 914189--914220 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
914179 GACTAATAAC
914189 TTAAAA TTAAAA TTAAAAA TTAAAA TTAAAA T
1 TTAAAA TTAAAA TT-AAAA TTAAAA TTAAAA T
914221 ACAAATATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
TTAAAA
Found at i:914209 original size:13 final size:13
Alignment explanation
Indices: 914191--914219 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
914181 CTAATAACTT
914191 AAAATTAAAATTA
1 AAAATTAAAATTA
914204 AAAATTAAAATTA
1 AAAATTAAAATTA
914217 AAA
1 AAA
914220 TACAAATATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAATTAAAATTA
Found at i:922060 original size:13 final size:12
Alignment explanation
Indices: 922038--922064 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
922028 TTTAATTTAA
922038 TATTTTAAAAAT
1 TATTTTAAAAAT
922050 TATTTTAAAAAT
1 TATTTTAAAAAT
922062 TAT
1 TAT
922065 AAAATATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TATTTTAAAAAT
Found at i:922482 original size:16 final size:16
Alignment explanation
Indices: 922460--922497 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
922450 AAAAAATGGT
922460 AATTTTATACTTTTTA
1 AATTTTATACTTTTTA
* *
922476 TATTTTATATTTTTTA
1 AATTTTATACTTTTTA
922492 AATTTT
1 AATTTT
922498 TATTTAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
AATTTTATACTTTTTA
Found at i:928428 original size:20 final size:18
Alignment explanation
Indices: 928374--928424 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
928364 AGCCCAAAAA
*
928374 TATTGAATTTTAATTTTC
1 TATTTAATTTTAATTTTC
* *
928392 TATTTACTGTTTTATTTTC
1 TATTTAAT-TTTAATTTTC
928411 TGATTTAATTTTAA
1 T-ATTTAATTTTAA
928425 ATTTATTTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 6 0.23
19 14 0.54
20 6 0.23
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.63
Consensus pattern (18 bp):
TATTTAATTTTAATTTTC
Found at i:928855 original size:2 final size:2
Alignment explanation
Indices: 928848--928878 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
928838 TGCAATATGA
928848 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
928879 GATGTATGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:930873 original size:23 final size:25
Alignment explanation
Indices: 930842--930889 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
930832 TTCTGTTATT
930842 AACAGAGA-TTCCCGATCTTTGCCA
1 AACAGAGATTTCCCGATCTTTGCCA
930866 AACA-AGATTTCCCGATCTTTGCCA
1 AACAGAGATTTCCCGATCTTTGCCA
930890 CATCAAAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (25 bp):
AACAGAGATTTCCCGATCTTTGCCA
Found at i:935469 original size:6 final size:6
Alignment explanation
Indices: 935458--935489 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
935448 AGGTGACATG
935458 CATATA CATATA CATATA CATATA CATATA CA
1 CATATA CATATA CATATA CATATA CATATA CA
935490 GGTATTAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (6 bp):
CATATA
Found at i:945288 original size:18 final size:19
Alignment explanation
Indices: 945248--945302 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
945238 TGCTCTTATT
* *
945248 AAAAATTAAAAAAATTATA-
1 AAAAATT-AATAAATTTTAG
945267 AAAAA-TAATAAATTTTAG
1 AAAAATTAATAAATTTTAG
*
945285 AAAAATTATTAAATTTTA
1 AAAAATTAATAAATTTTA
945303 ATAAAAACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
17 9 0.29
18 6 0.19
19 16 0.52
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
AAAAATTAATAAATTTTAG
Found at i:945380 original size:46 final size:46
Alignment explanation
Indices: 945253--945380 Score: 118
Period size: 47 Copynumber: 2.8 Consensus size: 46
945243 TTATTAAAAA
* * *
945253 TTAA-AAAAATTATAAAAAATAATAAATTTTAGAAAAATTATTAAATT
1 TTAATAAAAATCATAAAAAATAAAAAATTTT--AAAAATTATGAAATT
* * * *
945300 TTAATAAAAA-CTTAAAAAATTAAAAGTTATTAAAAATTA-GAATTTT
1 TTAATAAAAATCATAAAAAATAAAAAATT-TTAAAAATTATGAA-ATT
* *
945346 TTTATAAAAATCATAAAAAATAAAAAATTGTAAAA
1 TTAATAAAAATCATAAAAAATAAAAAATTTTAAAA
945381 TTTTATAAAT
Statistics
Matches: 65, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
45 2 0.03
46 24 0.37
47 32 0.49
48 7 0.11
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (46 bp):
TTAATAAAAATCATAAAAAATAAAAAATTTTAAAAATTATGAAATT
Found at i:954768 original size:13 final size:13
Alignment explanation
Indices: 954750--954777 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
954740 TATTAAATAG
954750 AAGCAATTACCAA
1 AAGCAATTACCAA
954763 AAGCAATTACCAA
1 AAGCAATTACCAA
954776 AA
1 AA
954778 ACAAAATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.21, G:0.07, T:0.14
Consensus pattern (13 bp):
AAGCAATTACCAA
Found at i:955067 original size:23 final size:22
Alignment explanation
Indices: 955032--955095 Score: 60
Period size: 23 Copynumber: 2.9 Consensus size: 22
955022 AATAATTCAT
955032 TTTTTTAGT-TTAAAATTTAAAA
1 TTTTTTA-TATTAAAATTTAAAA
* *
955054 TATTTTTATATTAATA-TTAATA
1 T-TTTTTATATTAAAATTTAAAA
*
955076 TTTTTTATAATTAAATTTTA
1 TTTTTTAT-ATTAAAATTTA
955096 GTTTTAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
21 7 0.21
22 13 0.38
23 14 0.41
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
TTTTTTATATTAAAATTTAAAA
Found at i:955073 original size:22 final size:22
Alignment explanation
Indices: 955048--955089 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
955038 AGTTTAAAAT
955048 TTAAAATATTTTTAT-ATTAATA
1 TTAAAAT-TTTTTATAATTAATA
*
955070 TTAATATTTTTTATAATTAA
1 TTAAAATTTTTTATAATTAA
955090 ATTTTAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTAAAATTTTTTATAATTAATA
Found at i:955428 original size:19 final size:19
Alignment explanation
Indices: 955406--955442 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
955396 AAAAAATTAT
955406 AAAAAATAATAAATTTTAG
1 AAAAAATAATAAATTTTAG
* *
955425 AAAAATTATTAAATTTTA
1 AAAAAATAATAAATTTTA
955443 ATAAAAACTC
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:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
AAAAAATAATAAATTTTAG
Found at i:955481 original size:24 final size:25
Alignment explanation
Indices: 955454--955514 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 25
955444 TAAAAACTCA
* *
955454 AAAAATAAAAAAT-TAGAATTTTTT
1 AAAAATAAAAAATGTAAAATTTTAT
*
955478 AAAAA-AAAAATTGTAAAATTTTAT
1 AAAAATAAAAAATGTAAAATTTTAT
*
955502 AAATATAATAAAA
1 AAAAATAA-AAAA
955515 AAAGTGACCT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
23 6 0.21
24 18 0.62
25 2 0.07
26 3 0.10
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (25 bp):
AAAAATAAAAAATGTAAAATTTTAT
Found at i:959543 original size:2 final size:2
Alignment explanation
Indices: 959538--959584 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
959528 TCACACACAC
*
959538 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
959580 AT AT A
1 AT AT A
959585 AAAAGAAGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:966389 original size:2 final size:2
Alignment explanation
Indices: 966339--966378 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
966329 AAACATAAAC
966339 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
966379 GTAGCTATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:969025 original size:16 final size:16
Alignment explanation
Indices: 969004--969036 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
968994 AAAATTCACT
969004 TTGTAAAAGTTGTTTA
1 TTGTAAAAGTTGTTTA
969020 TTGTAAAAGTTGTTTA
1 TTGTAAAAGTTGTTTA
969036 T
1 T
969037 CTATCAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.52
Consensus pattern (16 bp):
TTGTAAAAGTTGTTTA
Found at i:973013 original size:29 final size:29
Alignment explanation
Indices: 972977--973043 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
972967 ACTAAAAACA
972977 AAATTTGAAATCGCACTCTAAATGAAAAT
1 AAATTTGAAATCGCACTCTAAATGAAAAT
* * *
973006 AATTTTGAAATTGTACTCTAAATGAAAAT
1 AAATTTGAAATCGCACTCTAAATGAAAAT
973035 AAATTTGAA
1 AAATTTGAA
973044 GGTCTTTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.48, C:0.09, G:0.10, T:0.33
Consensus pattern (29 bp):
AAATTTGAAATCGCACTCTAAATGAAAAT
Found at i:976423 original size:61 final size:62
Alignment explanation
Indices: 976317--976439 Score: 239
Period size: 61 Copynumber: 2.0 Consensus size: 62
976307 TATTACTATT
976317 TTTTTAACTCCACTATTCTTCCCCCCAACTCTCTAGGCTACTATGGTCTAATCTAAACCCCA
1 TTTTTAACTCCACTATTCTTCCCCCCAACTCTCTAGGCTACTATGGTCTAATCTAAACCCCA
976379 TTTTTAACTCCACTATTCTT-CCCCCAACTCTCTAGGCTACTATGGTCTAATCTAAACCCCA
1 TTTTTAACTCCACTATTCTTCCCCCCAACTCTCTAGGCTACTATGGTCTAATCTAAACCCCA
976440 AAGCTTCGGC
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
61 41 0.67
62 20 0.33
ACGTcount: A:0.24, C:0.35, G:0.07, T:0.34
Consensus pattern (62 bp):
TTTTTAACTCCACTATTCTTCCCCCCAACTCTCTAGGCTACTATGGTCTAATCTAAACCCCA
Found at i:977451 original size:46 final size:46
Alignment explanation
Indices: 977399--977664 Score: 343
Period size: 46 Copynumber: 6.0 Consensus size: 46
977389 TTTGACATGA
* * * * *
977399 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATATCAGGT
* ** *
977445 TGCCATAGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
*
977491 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
* *
977537 TGCCATGGTATCTTTCAACCATGGTCTTACGCATTTTATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
977583 TGCCATGGTATCTTTCAACCATGGTCTTA--CA---C---TCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
*
977621 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAG
977665 AGAGCACACT
Statistics
Matches: 197, Mismatches: 14, Indels: 18
0.86 0.06 0.08
Matches are distributed among these distances:
38 35 0.18
40 2 0.01
43 1 0.01
44 2 0.01
45 4 0.02
46 153 0.78
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
Found at i:977628 original size:38 final size:38
Alignment explanation
Indices: 977577--977652 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
977567 GCATTTTATA
977577 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
977615 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
977653 ATTTCATATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.34
Consensus pattern (38 bp):
TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
Found at i:979816 original size:11 final size:11
Alignment explanation
Indices: 979800--979851 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
979790 TATACTAAAT
979800 AAATAATAATA
1 AAATAATAATA
*
979811 AAATAAT-ATT
1 AAATAATAATA
* *
979821 AAATATCTCATA
1 AAATA-ATAATA
*
979833 AAATATTAATA
1 AAATAATAATA
979844 AAATAATA
1 AAATAATA
979852 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:981931 original size:28 final size:27
Alignment explanation
Indices: 981887--981990 Score: 86
Period size: 28 Copynumber: 3.7 Consensus size: 27
981877 CTGCACAATC
*
981887 GATGTCTT-GCACGCTAAGTGCTATACCG
1 GATGT-TTCGCACACTAAGTGCTAT-CCG
* * *
981915 GATGTTTCGCACACTAAGCGCCATCCTC
1 GATGTTTCGCACACTAAGTGCTATCC-G
** *
981943 GATACTTCGCACACTAAGTG-TCATTTCG
1 GATGTTTCGCACACTAAGTGCT-A-TCCG
981971 GATGTTTCGCACACTAAGTG
1 GATGTTTCGCACACTAAGTG
981991 TCATCATCAA
Statistics
Matches: 60, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
27 4 0.07
28 54 0.90
29 2 0.03
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (27 bp):
GATGTTTCGCACACTAAGTGCTATCCG
Found at i:981973 original size:56 final size:56
Alignment explanation
Indices: 981895--982109 Score: 286
Period size: 56 Copynumber: 3.8 Consensus size: 56
981885 TCGATGTCTT
* * ** * * *
981895 GCACGCTAAGTGCTATACCGGATGTTTCGCACACTAAGCGCCATCCTCGATACTTC
1 GCACACTAAGTGCCATTTCGGATGTCTCGCACACTAAGTGCCATCCTCAATACTTC
* * * *
981951 GCACACTAAGTGTCATTTCGGATGTTTCGCACACTAAGTGTCATCATCAATACTTC
1 GCACACTAAGTGCCATTTCGGATGTCTCGCACACTAAGTGCCATCCTCAATACTTC
* *
982007 GTATACTAAGTGCCATTTCGGATGTCTCGCACACTAAGTGCCATCCTCAATACTTC
1 GCACACTAAGTGCCATTTCGGATGTCTCGCACACTAAGTGCCATCCTCAATACTTC
* **
982063 GCACGCTAAGTGCCATTTCAAATGTCTCGCACACTAAGTGCCATCCT
1 GCACACTAAGTGCCATTTCGGATGTCTCGCACACTAAGTGCCATCCT
982110 ACTAAGGGCC
Statistics
Matches: 139, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
56 139 1.00
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.28
Consensus pattern (56 bp):
GCACACTAAGTGCCATTTCGGATGTCTCGCACACTAAGTGCCATCCTCAATACTTC
Found at i:981991 original size:28 final size:28
Alignment explanation
Indices: 981915--982107 Score: 158
Period size: 28 Copynumber: 6.9 Consensus size: 28
981905 TGCTATACCG
* *
981915 GATGTTTCGCACACTAAGCGCCATCCTC
1 GATGTTTCGCACACTAAGTGCCATCTTC
** *
981943 GATACTTCGCACACTAAGTGTCAT-TTC
1 GATGTTTCGCACACTAAGTGCCATCTTC
* *
981970 GGATGTTTCGCACACTAAGTGTCATCATC
1 -GATGTTTCGCACACTAAGTGCCATCTTC
* ** * *
981999 AATACTTCGTATACTAAGTGCCAT-TTC
1 GATGTTTCGCACACTAAGTGCCATCTTC
* *
982026 GGATGTCTCGCACACTAAGTGCCATCCTC
1 -GATGTTTCGCACACTAAGTGCCATCTTC
* ** *
982055 AATACTTCGCACGCTAAGTGCCAT-TTC
1 GATGTTTCGCACACTAAGTGCCATCTTC
* *
982082 AAATGTCTCGCACACTAAGTGCCATC
1 -GATGTTTCGCACACTAAGTGCCATC
982108 CTACTAAGGG
Statistics
Matches: 127, Mismatches: 32, Indels: 11
0.75 0.19 0.06
Matches are distributed among these distances:
27 6 0.05
28 117 0.92
29 4 0.03
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (28 bp):
GATGTTTCGCACACTAAGTGCCATCTTC
Found at i:982131 original size:43 final size:43
Alignment explanation
Indices: 982068--982152 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 43
982058 ACTTCGCACG
*
982068 CTAAGTGCCATTTCAAATGTCTCGCACACTAAGTGCCATCCTA
1 CTAAGGGCCATTTCAAATGTCTCGCACACTAAGTGCCATCCTA
* *
982111 CTAAGGGCCATTTCAGATGTCTCGCACACTAAGTGTCATCCT
1 CTAAGGGCCATTTCAAATGTCTCGCACACTAAGTGCCATCCT
982153 CAATACTTCG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.28
Consensus pattern (43 bp):
CTAAGGGCCATTTCAAATGTCTCGCACACTAAGTGCCATCCTA
Found at i:984477 original size:41 final size:40
Alignment explanation
Indices: 984393--984487 Score: 100
Period size: 41 Copynumber: 2.3 Consensus size: 40
984383 ATAATAAATC
*
984393 AAATATATTTAAAATAAATATTAAAACAAGAAACAAATAAA
1 AAATATA-ATAAAATAAATATTAAAACAAGAAACAAATAAA
* * * * * * *
984434 AAATGATACTAAAATAATTCTTAAAACAATACATAAATTAA
1 AAAT-ATAATAAAATAAATATTAAAACAAGAAACAAATAAA
984475 AAATATAATAAAA
1 AAATATAATAAAA
984488 AAGTGATTAT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
40 8 0.18
41 34 0.76
42 3 0.07
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.26
Consensus pattern (40 bp):
AAATATAATAAAATAAATATTAAAACAAGAAACAAATAAA
Found at i:984960 original size:29 final size:31
Alignment explanation
Indices: 984928--984996 Score: 83
Period size: 29 Copynumber: 2.3 Consensus size: 31
984918 AACTGATCTT
984928 TTATTTAAAA-AAATTAAAA-ATATATAAA-G-
1 TTATTTAAAACAAA-TAAAAGA-ATATAAATGA
*
984957 TTATTTAAAACACATAAAAGAATATAAATGA
1 TTATTTAAAACAAATAAAAGAATATAAATGA
984988 TTATTTAAA
1 TTATTTAAA
984997 TATGAAAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
29 22 0.63
30 4 0.11
31 9 0.26
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.35
Consensus pattern (31 bp):
TTATTTAAAACAAATAAAAGAATATAAATGA
Found at i:985479 original size:20 final size:19
Alignment explanation
Indices: 985408--985476 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 19
985398 AACCGACAAG
*
985408 ATTTTAAATTAAATAATTTT
1 ATTTTAAATTAAATAA-TAT
*
985428 ATTTTAAATTTAATTATAGTAT
1 ATTTTAAA-TTAA--ATAATAT
* *
985450 ATATTAATATTAAATGATAT
1 ATTTTAA-ATTAAATAATAT
985470 ATTTTAA
1 ATTTTAA
985477 TATCTTATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
20 19 0.49
21 4 0.10
22 12 0.31
23 4 0.10
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (19 bp):
ATTTTAAATTAAATAATAT
Found at i:987766 original size:23 final size:23
Alignment explanation
Indices: 987740--987788 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
987730 GTACAATGGC
987740 TGAGTACGGATTGTATGAAATTG
1 TGAGTACGGATTGTATGAAATTG
*
987763 TGAGTATGGATTGTATGAAATTG
1 TGAGTACGGATTGTATGAAATTG
987786 TGA
1 TGA
987789 TTCCACGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.02, G:0.31, T:0.37
Consensus pattern (23 bp):
TGAGTACGGATTGTATGAAATTG
Found at i:990142 original size:20 final size:20
Alignment explanation
Indices: 990117--990157 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
990107 TTACATAGCC
990117 ACCAATAATAGTAGTCAATG
1 ACCAATAATAGTAGTCAATG
990137 ACCAATAATAGTAGTCAATG
1 ACCAATAATAGTAGTCAATG
990157 A
1 A
990158 AAGGATCGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (20 bp):
ACCAATAATAGTAGTCAATG
Found at i:996973 original size:5 final size:5
Alignment explanation
Indices: 996963--996997 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
996953 ATATAAATTA
* *
996963 TGATT TGATT TGATT TGATT TGATT CGATT AGATT
1 TGATT TGATT TGATT TGATT TGATT TGATT TGATT
996998 CAATTCTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.23, C:0.03, G:0.20, T:0.54
Consensus pattern (5 bp):
TGATT
Found at i:1000966 original size:5 final size:5
Alignment explanation
Indices: 1000948--1000983 Score: 63
Period size: 5 Copynumber: 7.0 Consensus size: 5
1000938 TAGGAAGATA
1000948 TTATT TTGATT TTATT TTATT TTATT TTATT TTATT
1 TTATT TT-ATT TTATT TTATT TTATT TTATT TTATT
1000984 ATTAAATTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (5 bp):
TTATT
Found at i:1001562 original size:15 final size:15
Alignment explanation
Indices: 1001544--1001613 Score: 56
Period size: 15 Copynumber: 4.7 Consensus size: 15
1001534 TATTCTAATA
1001544 CTAATTATTATTTAT
1 CTAATTATTATTTAT
*
1001559 CTAATTTTTATTTAT
1 CTAATTATTATTTAT
* * *
1001574 TTATTTA-TATTTCT
1 CTAATTATTATTTAT
1001588 ACT-ATTATTATATT-T
1 -CTAATTATTAT-TTAT
*
1001603 CTATTTATTAT
1 CTAATTATTAT
1001614 ATTTTTATTT
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
14 11 0.26
15 30 0.70
16 2 0.05
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (15 bp):
CTAATTATTATTTAT
Found at i:1001595 original size:44 final size:45
Alignment explanation
Indices: 1001542--1001660 Score: 112
Period size: 44 Copynumber: 2.7 Consensus size: 45
1001532 GTTATTCTAA
1001542 TACTAATTATTAT-TTATCTAATTT-TTAT-TTATTTATTTATATTTC
1 TACTAATTATTATATT-TCT-ATTTATTATATT-TTTATTTATATTTC
* *
1001587 TACT-ATTATTATATTTCTATTTATTATATTTTTATTTCTATTTATA
1 TACTAATTATTATATTTCTATTTATTATATTTTTATTTATA-TT-TC
1001633 TACTAA-TATTAT-TTTC-A-TTATTAT-TTTT
1 TACTAATTATTATATTTCTATTTATTATATTTT
1001661 CTTATATATG
Statistics
Matches: 66, Mismatches: 2, Indels: 15
0.80 0.02 0.18
Matches are distributed among these distances:
42 4 0.06
43 11 0.17
44 25 0.38
45 14 0.21
46 11 0.17
47 1 0.02
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.65
Consensus pattern (45 bp):
TACTAATTATTATATTTCTATTTATTATATTTTTATTTATATTTC
Found at i:1001614 original size:15 final size:15
Alignment explanation
Indices: 1001571--1001623 Score: 70
Period size: 15 Copynumber: 3.3 Consensus size: 15
1001561 AATTTTTATT
1001571 TATTTATTTATATTTC
1 TATTTA-TTATATTTC
1001587 TACTATTATTATATTTC
1 TA-T-TTATTATATTTC
*
1001604 TATTTATTATATTTT
1 TATTTATTATATTTC
1001619 TATTT
1 TATTT
1001624 CTATTTATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
15 16 0.47
16 3 0.09
17 12 0.35
18 3 0.09
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTTATTATATTTC
Found at i:1003226 original size:10 final size:9
Alignment explanation
Indices: 1003139--1003281 Score: 51
Period size: 9 Copynumber: 15.7 Consensus size: 9
1003129 CTGCTCTTAT
1003139 TAAAAATTA
1 TAAAAATTA
*
1003148 GAAAAAATTA
1 -TAAAAATTA
*
1003158 TAGAAAATAA
1 TA-AAAATTA
**
1003168 TAAATTTTA
1 TAAAAATTA
*
1003177 GAAAAATTA
1 TAAAAATTA
**
1003186 TTAAATTTTAA
1 -TAAAAATT-A
1003197 TAAAAAGTTA
1 TAAAAA-TTA
1003207 -AAAAA--A
1 TAAAAATTA
1003213 TAAAAATTA
1 TAAAAATTA
*
1003222 TTAAAATTA
1 TAAAAATTA
****
1003231 TATTTTTTA
1 TAAAAATTA
*
1003240 TAAAAATTG
1 TAAAAATTA
*
1003249 TAAAAA-AA
1 TAAAAATTA
*
1003257 TAAAATTTTA
1 TAAAA-ATTA
* *
1003267 TAAATATCA
1 TAAAAATTA
1003276 TAAAAA
1 TAAAAA
1003282 ATGACCTCTA
Statistics
Matches: 91, Mismatches: 33, Indels: 19
0.64 0.23 0.13
Matches are distributed among these distances:
6 1 0.01
7 5 0.05
8 5 0.05
9 46 0.51
10 31 0.34
11 3 0.03
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (9 bp):
TAAAAATTA
Found at i:1003963 original size:17 final size:16
Alignment explanation
Indices: 1003936--1003967 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1003926 TTATAATATT
1003936 TAATATATAATTAAAC
1 TAATATATAATTAAAC
1003952 TAATACTATAATTAAA
1 TAATA-TATAATTAAA
1003968 ATAACTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATATATAATTAAAC
Found at i:1004420 original size:15 final size:15
Alignment explanation
Indices: 1004400--1004430 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1004390 CCTTCAAATG
1004400 CCTCTATGTTGCACT
1 CCTCTATGTTGCACT
1004415 CCTCTATGTTGCACT
1 CCTCTATGTTGCACT
1004430 C
1 C
1004431 GCACTCATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.35, G:0.13, T:0.39
Consensus pattern (15 bp):
CCTCTATGTTGCACT
Found at i:1011839 original size:20 final size:21
Alignment explanation
Indices: 1011789--1011840 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1011779 CGCTTGGAGT
*
1011789 ACTCTTTTCGATATTACTCTA
1 ACTCTTTTCAATATTACTCTA
* *
1011810 ACTTTTTTCAATATTATTCTA
1 ACTCTTTTCAATATTACTCTA
1011831 A-TCTTTTCAA
1 ACTCTTTTCAA
1011841 ATCTGGGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 8 0.30
21 19 0.70
ACGTcount: A:0.27, C:0.19, G:0.02, T:0.52
Consensus pattern (21 bp):
ACTCTTTTCAATATTACTCTA
Found at i:1013180 original size:24 final size:24
Alignment explanation
Indices: 1013151--1013197 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1013141 ATTTAGCCTG
*
1013151 AATTTAAATAAAAAAATTTATTTA
1 AATTTAAATAAAAAAATATATTTA
* *
1013175 AATTTAATTATAAAAATATATTT
1 AATTTAAATAAAAAAATATATTT
1013198 TATTATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
AATTTAAATAAAAAAATATATTTA
Found at i:1019066 original size:18 final size:18
Alignment explanation
Indices: 1019043--1019081 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1019033 GTACCTTTTA
*
1019043 TTTACTTATTATCTTACC
1 TTTACTTATTATCGTACC
1019061 TTTACTTATTATCGTACC
1 TTTACTTATTATCGTACC
1019079 TTT
1 TTT
1019082 CTTTTTTCGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.21, G:0.03, T:0.56
Consensus pattern (18 bp):
TTTACTTATTATCGTACC
Found at i:1021318 original size:33 final size:33
Alignment explanation
Indices: 1021281--1021346 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1021271 AGGAGATTGA
*
1021281 ATTTTTAACTTTTTAAGTGCAGGGATTAAATCT
1 ATTTTTAACTTTTTAAGTACAGGGATTAAATCT
*
1021314 ATTTTTAACTTTTTAAGTATAGGGATTAAATCT
1 ATTTTTAACTTTTTAAGTACAGGGATTAAATCT
1021347 CAAATTCTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.47
Consensus pattern (33 bp):
ATTTTTAACTTTTTAAGTACAGGGATTAAATCT
Found at i:1021499 original size:9 final size:9
Alignment explanation
Indices: 1021487--1021511 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1021477 TCAAGTCTTT
1021487 CAATTCCTC
1 CAATTCCTC
1021496 CAATTCCTC
1 CAATTCCTC
1021505 CAATTCC
1 CAATTCC
1021512 GACTCTGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.44, G:0.00, T:0.32
Consensus pattern (9 bp):
CAATTCCTC
Found at i:1022586 original size:9 final size:9
Alignment explanation
Indices: 1022572--1022639 Score: 82
Period size: 9 Copynumber: 7.6 Consensus size: 9
1022562 ATAAGTATAA
1022572 AATTAACCG
1 AATTAACCG
*
1022581 AATTAATCG
1 AATTAACCG
*
1022590 AATTAATCG
1 AATTAACCG
*
1022599 AATTAACTG
1 AATTAACCG
* *
1022608 AATTACCCA
1 AATTAACCG
1022617 AATTAACCG
1 AATTAACCG
*
1022626 AATAAACCG
1 AATTAACCG
1022635 AATTA
1 AATTA
1022640 TTTGTATAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 49 1.00
ACGTcount: A:0.47, C:0.18, G:0.09, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:1022674 original size:5 final size:6
Alignment explanation
Indices: 1022659--1022698 Score: 62
Period size: 6 Copynumber: 6.5 Consensus size: 6
1022649 AATTATATGT
*
1022659 TTTTTA TTTTTA TTTTTA TTTTTA GATTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA -TTTTTA TTTTTA TTT
1022699 ATTAAATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:1022897 original size:5 final size:6
Alignment explanation
Indices: 1022880--1022904 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1022870 CCATGCCTAC
1022880 TCTTTT TCTTTT TCTTTT TCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT T
1022905 TTCTAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TCTTTT
Found at i:1027622 original size:24 final size:24
Alignment explanation
Indices: 1027578--1027625 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1027568 GATACATCCA
**
1027578 TACTAAAATAAATTATTTTAAAAT
1 TACTAAAATAAATTAAGTTAAAAT
1027602 TACTAAAAATAAA-TAAGTTAAAAT
1 TACT-AAAATAAATTAAGTTAAAAT
1027626 AAATTGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.35
Consensus pattern (24 bp):
TACTAAAATAAATTAAGTTAAAAT
Found at i:1027826 original size:9 final size:9
Alignment explanation
Indices: 1027812--1027863 Score: 68
Period size: 9 Copynumber: 5.7 Consensus size: 9
1027802 TAATTTTTAT
*
1027812 TAAAAATAA
1 TAAAAATTA
1027821 TAAAAATTA
1 TAAAAATTA
**
1027830 TAATCATTA
1 TAAAAATTA
1027839 TAAAAAATTA
1 T-AAAAATTA
1027849 TAAAAATTA
1 TAAAAATTA
1027858 TAAAAA
1 TAAAAA
1027864 ACTATTTTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
9 30 0.81
10 7 0.19
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (9 bp):
TAAAAATTA
Found at i:1027844 original size:19 final size:19
Alignment explanation
Indices: 1027812--1027864 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
1027802 TAATTTTTAT
*
1027812 TAAAAATAAT-AAAAATTA
1 TAAAAATTATAAAAAATTA
**
1027830 TAATCATTATAAAAAATTA
1 TAAAAATTATAAAAAATTA
1027849 TAAAAATTATAAAAAA
1 TAAAAATTATAAAAAA
1027865 CTATTTTAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 7 0.24
19 22 0.76
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (19 bp):
TAAAAATTATAAAAAATTA
Found at i:1027899 original size:24 final size:23
Alignment explanation
Indices: 1027859--1027908 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
1027849 TAAAAATTAT
* *
1027859 AAAAAACTATTTTAAAAAATACA
1 AAAAAAATATTTGAAAAAATACA
* *
1027882 AAAAAAATATATTGAAAATATAGA
1 AAAAAAATAT-TTGAAAAAATACA
1027906 AAA
1 AAA
1027909 GTGCACAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.24
Consensus pattern (23 bp):
AAAAAAATATTTGAAAAAATACA
Found at i:1033607 original size:21 final size:22
Alignment explanation
Indices: 1033558--1033608 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
1033548 TATCTTGCCA
* *
1033558 AAAATTATTGGTATTTTAAAAT
1 AAAATTATTAGTATATTAAAAT
* *
1033580 GAAATTATTAGTATATT-ATAT
1 AAAATTATTAGTATATTAAAAT
1033601 AAAATTAT
1 AAAATTAT
1033609 ATAAAGAGAG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (22 bp):
AAAATTATTAGTATATTAAAAT
Found at i:1041730 original size:5 final size:5
Alignment explanation
Indices: 1041720--1041766 Score: 51
Period size: 5 Copynumber: 9.0 Consensus size: 5
1041710 TTTGAAGGTA
*
1041720 CTTTT CTTTT CTTTT CTTTT -TTAAATT ATTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTT---TT CTTTT CTTTT CTTTT CTTTT
1041767 TTAAATTATA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
4 2 0.05
5 31 0.84
7 2 0.05
8 2 0.05
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.77
Consensus pattern (5 bp):
CTTTT
Found at i:1041759 original size:27 final size:27
Alignment explanation
Indices: 1041721--1041775 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1041711 TTGAAGGTAC
1041721 TTTTCTTTTCTTTTCTTTTTTAAATTA
1 TTTTCTTTTCTTTTCTTTTTTAAATTA
1041748 TTTTCTTTTCTTTTCTTTTTTAAATTA
1 TTTTCTTTTCTTTTCTTTTTTAAATTA
1041775 T
1 T
1041776 ATAAAGGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.75
Consensus pattern (27 bp):
TTTTCTTTTCTTTTCTTTTTTAAATTA
Found at i:1042265 original size:21 final size:20
Alignment explanation
Indices: 1042235--1042275 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
1042225 TTTTATAATC
1042235 TTTTTTTTATAAATTTTTAT
1 TTTTTTTTATAAATTTTTAT
*
1042255 TTTTATTTTATATATTTTTAT
1 TTTT-TTTTATAAATTTTTAT
1042276 GATTTTCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTTTTATAAATTTTTAT
Found at i:1042270 original size:9 final size:8
Alignment explanation
Indices: 1042238--1042301 Score: 51
Period size: 9 Copynumber: 7.6 Consensus size: 8
1042228 TATAATCTTT
1042238 TTTTTATAA
1 TTTTTAT-A
*
1042247 ATTTT-TA
1 TTTTTATA
1042254 TTTTTAT-
1 TTTTTATA
*
1042261 TTTATATA
1 TTTTTATA
1042269 TTTTTATGA
1 TTTTTAT-A
1042278 TTTTCTATA
1 TTTT-TATA
1042287 TTTTTTATA
1 -TTTTTATA
1042296 GTTTTT
1 -TTTTT
1042302 TGCCGGGTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
7 11 0.24
8 8 0.18
9 19 0.42
10 7 0.16
ACGTcount: A:0.23, C:0.02, G:0.03, T:0.72
Consensus pattern (8 bp):
TTTTTATA
Found at i:1042273 original size:10 final size:9
Alignment explanation
Indices: 1042260--1042302 Score: 50
Period size: 10 Copynumber: 4.4 Consensus size: 9
1042250 TTTATTTTTA
1042260 TTTTATATAT
1 TTTTATAT-T
1042270 TTTTATGATT
1 TTTTAT-ATT
*
1042280 TTCTATATT
1 TTTTATATT
1042289 TTTTATAGTT
1 TTTTATA-TT
1042299 TTTT
1 TTTT
1042303 GCCGGGTGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 9 0.31
10 18 0.62
11 2 0.07
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.72
Consensus pattern (9 bp):
TTTTATATT
Found at i:1050475 original size:3 final size:3
Alignment explanation
Indices: 1050467--1050502 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1050457 AATTACCTCT
1050467 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1050503 GAAGTGTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1055293 original size:2 final size:2
Alignment explanation
Indices: 1055286--1055327 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1055276 GAGCATGTTC
*
1055286 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1055328 TAGGAAATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1058001 original size:20 final size:20
Alignment explanation
Indices: 1057972--1058025 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1057962 AAAATAGTTT
1057972 TTAATAAAAAAACTGAAATA
1 TTAATAAAAAAACTGAAATA
* *
1057992 TTAATTAAAAAACTTAAATAAA
1 TTAATAAAAAAACTGAAAT--A
*
1058014 TTTATAAAAAAA
1 TTAATAAAAAAA
1058026 TAACTTATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 17 0.61
22 11 0.39
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.30
Consensus pattern (20 bp):
TTAATAAAAAAACTGAAATA
Found at i:1063713 original size:20 final size:21
Alignment explanation
Indices: 1063670--1063721 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1063660 AACAACCAAG
*
1063670 TAAAATATTATACTCAAGTAT
1 TAAAATATTATACACAAGTAT
1063691 TAAAATATTCATA-ACAA-TAT
1 TAAAATATT-ATACACAAGTAT
1063711 TAAAAATATTA
1 T-AAAATATTA
1063722 ACATATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 5 0.18
21 20 0.71
22 3 0.11
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.37
Consensus pattern (21 bp):
TAAAATATTATACACAAGTAT
Found at i:1065403 original size:29 final size:31
Alignment explanation
Indices: 1065363--1065425 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
1065353 ATACTTTATA
*
1065363 TTTTATATATTTTTTAAA-ATTAAATTA-AAT
1 TTTTATATA-TTTTAAAATATTAAATTATAAT
1065393 TTTTAT-TATTTTAAAATATTAAATTATAAT
1 TTTTATATATTTTAAAATATTAAATTATAAT
1065423 TTT
1 TTT
1065426 ATCATTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 7 0.23
29 11 0.37
30 12 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (31 bp):
TTTTATATATTTTAAAATATTAAATTATAAT
Found at i:1065426 original size:29 final size:28
Alignment explanation
Indices: 1065336--1065427 Score: 81
Period size: 29 Copynumber: 3.4 Consensus size: 28
1065326 GAATTTTTAC
*
1065336 ATAATTTTATTATTTT-AATACT---TT
1 ATAATTTTATTATTTTAAATATTAAATT
1065360 AT-ATTTTATATATTTTTTAAA-ATTAAATT
1 ATAATTTTAT-TA--TTTTAAATATTAAATT
1065389 A-AATTTTTATTATTTTAAAATATTAAATT
1 ATAA-TTTTATTATTTT-AAATATTAAATT
1065418 ATAATTTTAT
1 ATAATTTTAT
1065428 CATTAATAAT
Statistics
Matches: 55, Mismatches: 1, Indels: 19
0.73 0.01 0.25
Matches are distributed among these distances:
23 7 0.13
24 4 0.07
26 6 0.11
27 6 0.11
28 3 0.05
29 21 0.38
30 8 0.15
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (28 bp):
ATAATTTTATTATTTTAAATATTAAATT
Found at i:1068325 original size:299 final size:293
Alignment explanation
Indices: 1067880--1068631 Score: 852
Period size: 299 Copynumber: 2.5 Consensus size: 293
1067870 GAGTATTTTT
* * **
1067880 ACGGTAGTGATTGGAAAGAAGAAGGTTCTGGAAGCTTTTGGTCAAACAGTTTGACTGTAGTGTAT
1 ACGGTAGTGATAGG-AA-AAGAAGATTCTGGAA-AATTTGGTCAAACAGTTTGACTGTAGT-TAT
* * * *
1067945 TGTGCTTCTAATTATTGTTTTCAATGATGGATCCTGTGTATTTCAATGATTGGAATTGATTTATT
62 TGTGCTTGTAGTTATCGTTTTCAATGATGGATCCTGTGTATTTCAATGATTTGAATT-ATTTATT
* * * *
1068010 ATGAGTGAAGTGTGATTGCTTATGAAAATGATATTCGATTTTTCTTCTTTTGGTTTCC-GGAATG
126 -TGAGT-AAATGTGATTGCTTATGAAAATGATATTCGATTTTTCAT-TTTTGG-TTCCTAGAATA
* * ** * *
1068074 CTTTTGGATTTAATTTGTTCTTTGCAAAGTAGCCAA-AAAGTTCCTGTTCTCTTCTTTTAGGATT
187 CTTTTGGA--TAACTTGTTCTTAGCAAACCAGCCAAGAAA-TTCATATTCTCTTCTTTTAGGATT
* ** *
1068138 TAGT-AACGAGAA-TTTTGTAGCTAAATCAAACATAAAGGATTTTTG
249 TAGTGAA-G-GAACATTTGTAGCTAAATCAAACATAAAGGAGGTTTA
* *
1068183 A-GGTATTGATAGGAAAAGAAGATTCTGGAAAATTTGGTCAAATAGTTTGACTGTAGCTTATTGT
1 ACGGTAGTGATAGGAAAAGAAGATTCTGGAAAATTTGGTCAAACAGTTTGACTGTAG-TTATTGT
1068247 GCTTGTAGTTATCGTTTTCAATGATGGATCCTGTGTATTTCAATGATTTGAATCTATTTAGTTTG
65 GCTTGTAGTTATCGTTTTCAATGATGGATCCTGTGTATTTCAATGATTTGAAT-TATTTA-TTTG
* * *
1068312 AGTAACATGTGATTGCTTATGAAAAATGATATTTGATTTTTCATTTTTGGTTCCTAGAGTATTTT
128 AGTAA-ATGTGATTGCTTATG-AAAATGATATTCGATTTTTCATTTTTGGTTCCTAGAATACTTT
** * *
1068377 TGGATAACTTGTTCTTAGCAAACCAGTGAAGAAATTTATATTTTCTTCTTTTAGGATTTAGTGAA
191 TGGATAACTTGTTCTTAGCAAACCAGCCAAGAAATTCATATTCTCTTCTTTTAGGATTTAGTGAA
* * *
1068442 GGAACATTTGTAGCTAAATTAAACATAGAGGGGGTTTA
256 GGAACATTTGTAGCTAAATCAAACATAAAGGAGGTTTA
* * * * *
1068480 ACTGTAGTGATAGGAAAAGAAGATTCTGG-AAGTTGTGGTCAAACAGTTTGACTGGA-TCATTAT
1 ACGGTAGTGATAGGAAAAGAAGATTCTGGAAAATT-TGGTCAAACAGTTTGACTGTAGTTATTGT
* *** *
1068543 ACTTGTAGTTATCACGTTCAATGATGGATCCTGTGTATTTGAATGATTTGAATTTATTTATTTGA
65 GCTTGTAGTTATCGTTTTCAATGATGGATCCTGTGTATTTCAATGATTTGAA-TTATTTATTTGA
*
1068608 GTAAAGTGTGATTACTTATGAAAA
129 GTAAA-TGTGATTGCTTATGAAAA
1068632 GATTTTTGAT
Statistics
Matches: 389, Mismatches: 47, Indels: 35
0.83 0.10 0.07
Matches are distributed among these distances:
294 5 0.01
295 22 0.06
296 61 0.16
297 77 0.20
298 55 0.14
299 118 0.30
300 38 0.10
301 2 0.01
302 10 0.03
303 1 0.00
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.40
Consensus pattern (293 bp):
ACGGTAGTGATAGGAAAAGAAGATTCTGGAAAATTTGGTCAAACAGTTTGACTGTAGTTATTGTG
CTTGTAGTTATCGTTTTCAATGATGGATCCTGTGTATTTCAATGATTTGAATTATTTATTTGAGT
AAATGTGATTGCTTATGAAAATGATATTCGATTTTTCATTTTTGGTTCCTAGAATACTTTTGGAT
AACTTGTTCTTAGCAAACCAGCCAAGAAATTCATATTCTCTTCTTTTAGGATTTAGTGAAGGAAC
ATTTGTAGCTAAATCAAACATAAAGGAGGTTTA
Found at i:1072481 original size:11 final size:11
Alignment explanation
Indices: 1072465--1072489 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1072455 GCGTACGTAT
1072465 ACATATTATAC
1 ACATATTATAC
1072476 ACATATTATAC
1 ACATATTATAC
1072487 ACA
1 ACA
1072490 CGCCAACGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (11 bp):
ACATATTATAC
Found at i:1083391 original size:16 final size:15
Alignment explanation
Indices: 1083370--1083400 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1083360 AGAGCAGAAG
1083370 TTTTAATCAATATTTT
1 TTTTAATCAA-ATTTT
1083386 TTTTAATCAAATTTT
1 TTTTAATCAAATTTT
1083401 ATTCAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTTAATCAAATTTT
Found at i:1093435 original size:14 final size:14
Alignment explanation
Indices: 1093416--1093457 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
1093406 TGAACGAAAA
*
1093416 TTAAAAATAATTTT
1 TTAAAAATAATTAT
*
1093430 TTAAAAA-AATCAT
1 TTAAAAATAATTAT
*
1093443 TTGAAAATAATTAT
1 TTAAAAATAATTAT
1093457 T
1 T
1093458 AAGGAAACCG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (14 bp):
TTAAAAATAATTAT
Found at i:1094586 original size:17 final size:18
Alignment explanation
Indices: 1094566--1094600 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1094556 AAAAAGTGCC
*
1094566 AAAATGAAAAA-AAAAAA
1 AAAAAGAAAAAGAAAAAA
1094583 AAAAAGAAAAAGAAAAAA
1 AAAAAGAAAAAGAAAAAA
1094601 TAGCAGCCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.89, C:0.00, G:0.09, T:0.03
Consensus pattern (18 bp):
AAAAAGAAAAAGAAAAAA
Found at i:1096463 original size:13 final size:13
Alignment explanation
Indices: 1096445--1096470 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1096435 ACTAAAGCCC
1096445 TTATAAACTAGAA
1 TTATAAACTAGAA
1096458 TTATAAACTAGAA
1 TTATAAACTAGAA
1096471 ACCTTCCATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (13 bp):
TTATAAACTAGAA
Found at i:1104984 original size:31 final size:31
Alignment explanation
Indices: 1104926--1104992 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
1104916 TAACTTTTGG
*
1104926 GTAAACCACACAAGTAGTAATCCAACTATTA
1 GTAAACCACACAAGTAATAATCCAACTATTA
* * * *
1104957 GTAAACTACACTAGTAATCATCTAACTATTA
1 GTAAACCACACAAGTAATAATCCAACTATTA
1104988 GTAAA
1 GTAAA
1104993 AAAAAAAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.45, C:0.19, G:0.09, T:0.27
Consensus pattern (31 bp):
GTAAACCACACAAGTAATAATCCAACTATTA
Found at i:1105316 original size:59 final size:59
Alignment explanation
Indices: 1105225--1105407 Score: 183
Period size: 59 Copynumber: 3.1 Consensus size: 59
1105215 GACAGGATTG
* * ** * *
1105225 AATAGTTCAATAATCATTTTGTAACTCGTCATAATTGAGTGAACAAAAAGAAATATACT
1 AATAGTTGAATAATTATTTTGTAACTTTTCATAGTTGAGTGAACAAAAAGAAATTTACT
* * * * *
1105284 AATAGTTGGATAATTATTTTGTAAGTTTTCATAGTT-AATGACCTAAGAAGAAATTTACT
1 AATAGTTGAATAATTATTTTGTAACTTTTCATAGTTGAGTGAAC-AAAAAGAAATTTACT
* * * * **
1105343 AATAGTTGAATGACTATTTTCTAACTTTTTATAGTTGAGT-AATTAAAA-AAATTTACT
1 AATAGTTGAATAATTATTTTGTAACTTTTCATAGTTGAGTGAACAAAAAGAAATTTACT
1105400 AATAGTTG
1 AATAGTTG
1105408 GATGACTACT
Statistics
Matches: 100, Mismatches: 22, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
57 17 0.17
58 8 0.08
59 73 0.73
60 2 0.02
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (59 bp):
AATAGTTGAATAATTATTTTGTAACTTTTCATAGTTGAGTGAACAAAAAGAAATTTACT
Found at i:1112305 original size:2 final size:2
Alignment explanation
Indices: 1112298--1112334 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1112288 TATAATCATG
1112298 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1112335 TCTTAATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1114125 original size:21 final size:21
Alignment explanation
Indices: 1114078--1114129 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
1114068 TGAGTGCATT
* *
1114078 ATATTTAAATATTAAAAATTA
1 ATATTTAAAAATTAAAAACTA
* **
1114099 AGATTTAAAAATTAAAGCCTA
1 ATATTTAAAAATTAAAAACTA
1114120 ATATTTAAAA
1 ATATTTAAAA
1114130 TAATTATTAA
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:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (21 bp):
ATATTTAAAAATTAAAAACTA
Found at i:1115852 original size:60 final size:59
Alignment explanation
Indices: 1115745--1116251 Score: 425
Period size: 60 Copynumber: 8.6 Consensus size: 59
1115735 TCTCAAGATA
* * ** * * *
1115745 TTAATTTGTCGTTAGCTTAAATCCAGCATTAAGCCTTTTGCTTCGAGTTCCATGTGATG
1 TTAATTTGTTGTTAGCTTAAATCCAGCATTAAGCCTTTCGCAACGTGCTCCACGTGATG
* * *
1115804 TTAATTTGTTGTTAGCTTAAATACCAGCATTAAGCCTTTCGCAACGAGTTCCATGTGATG
1 TTAATTTGTTGTTAGCTTAAAT-CCAGCATTAAGCCTTTCGCAACGTGCTCCACGTGATG
* * * * *
1115864 TTAATTTGTTGTTAGCTTAAATCCCTGCATTAA--ATGTTCACAATGTGCTCCACATGTTGTTG
1 TTAATTTGTTGTTAGCTTAAAT-CCAGCATTAAGCCT-TTCGCAACGTGCTCCAC--G-TGATG
*
1115926 TTAATTTCTTGTTAGCTTAAAGTCCAGCATTAAGCCTTT--C-A--TG----AC---ATG
1 TTAATTTGTTGTTAGCTTAAA-TCCAGCATTAAGCCTTTCGCAACGTGCTCCACGTGATG
* * * *
1115974 CTAATTTGTTGTTAGCTTAAAGTCCAGCCTTAAGCCTTTTGTAACGTGCTCCACGTGATG
1 TTAATTTGTTGTTAGCTTAAA-TCCAGCATTAAGCCTTTCGCAACGTGCTCCACGTGATG
** * * * *
1116034 TTAATTTGCCGTTAGCTTAAAGTCCAGCCTTAAGCCTTTTGTAACGTGCTGCACGTGATG
1 TTAATTTGTTGTTAGCTTAAA-TCCAGCATTAAGCCTTTCGCAACGTGCTCCACGTGATG
* * * * * *
1116094 TTAATTTGTTGTTTGCTTAAATCCCAGCATTAAACCTTTC-CGATGTGCTCCGCGTG-TCA
1 TTAATTTGTTGTTAGCTTAAAT-CCAGCATTAAGCCTTTCGCAACGTGCTCCACGTGAT-G
* ** * ** *
1116153 TTAGTTTGTTGTTAGCTTAAAGTCTTGGATTAAGCCTTTCATAACGTGCTCCACATGATG
1 TTAATTTGTTGTTAGCTTAAA-TCCAGCATTAAGCCTTTCGCAACGTGCTCCACGTGATG
*
1116213 TTAATTTGTTGTTAGCTTAAATCCCAGCATTAAGTCTTT
1 TTAATTTGTTGTTAGCTTAAAT-CCAGCATTAAGCCTTT
1116252 TCCAATTTGC
Statistics
Matches: 368, Mismatches: 54, Indels: 51
0.78 0.11 0.11
Matches are distributed among these distances:
48 38 0.10
51 1 0.00
53 2 0.01
54 2 0.01
57 2 0.01
58 4 0.01
59 78 0.21
60 201 0.55
61 3 0.01
62 33 0.09
63 3 0.01
64 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.39
Consensus pattern (59 bp):
TTAATTTGTTGTTAGCTTAAATCCAGCATTAAGCCTTTCGCAACGTGCTCCACGTGATG
Found at i:1119194 original size:17 final size:17
Alignment explanation
Indices: 1119172--1119208 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
1119162 AGTGTGAGTA
1119172 TTTGTCATGTTTTTTTG
1 TTTGTCATGTTTTTTTG
1119189 TTTGTCATGTTTTTTTG
1 TTTGTCATGTTTTTTTG
1119206 TTT
1 TTT
1119209 TTTGCATCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.05, C:0.05, G:0.16, T:0.73
Consensus pattern (17 bp):
TTTGTCATGTTTTTTTG
Found at i:1119341 original size:25 final size:25
Alignment explanation
Indices: 1119307--1119357 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
1119297 CTCTATCTTG
1119307 ACTTGAAAGTGTAATACAAAAGGCA
1 ACTTGAAAGTGTAATACAAAAGGCA
*
1119332 ACTTGAAAGTGTAATACAGAAGGCA
1 ACTTGAAAGTGTAATACAAAAGGCA
1119357 A
1 A
1119358 TGTGTGACTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.47, C:0.12, G:0.22, T:0.20
Consensus pattern (25 bp):
ACTTGAAAGTGTAATACAAAAGGCA
Found at i:1127459 original size:3 final size:3
Alignment explanation
Indices: 1127451--1127489 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1127441 TAGTTTACCC
1127451 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1127490 CTCCTATAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Done.