Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold320
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: 2598547
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 499 characters in sequence are not A, C, G, or T
File 13 of 17
Found at i:1845874 original size:14 final size:14
Alignment explanation
Indices: 1845857--1845906 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
1845847 ACACTATTTC
1845857 TTTTTCTCTATTC-
1 TTTTTCTCTATTCT
*
1845870 TTTTTCTTTA-TCT
1 TTTTTCTCTATTCT
1845883 TTTATTCTCTATCTCT
1 TTT-TTCTCTAT-TCT
*
1845899 TATTTCTC
1 TTTTTCTC
1845907 ATTTTTTCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 2 0.07
13 12 0.40
14 6 0.20
15 5 0.17
16 5 0.17
ACGTcount: A:0.10, C:0.22, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTTTCTCTATTCT
Found at i:1845912 original size:27 final size:27
Alignment explanation
Indices: 1845860--1845913 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
1845850 CTATTTCTTT
*
1845860 TTCTCTATTCTTTTTCTTTATCTTTTA
1 TTCTCTATTCTTTTTCTTCATCTTTTA
*
1845887 TTCTCTATCTCTTATTTC-TCATTTTTT
1 TTCTCTAT-TCTT-TTTCTTCATCTTTT
1845914 CTTTTTTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 8 0.35
28 11 0.48
29 4 0.17
ACGTcount: A:0.11, C:0.20, G:0.00, T:0.69
Consensus pattern (27 bp):
TTCTCTATTCTTTTTCTTCATCTTTTA
Found at i:1845939 original size:19 final size:19
Alignment explanation
Indices: 1845901--1845940 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1845891 CTATCTCTTA
* **
1845901 TTTCTCATTTTTTCTTTTT
1 TTTCTCAATTTTTCCCTTT
1845920 TTTCTCAATTTTTCCCTTT
1 TTTCTCAATTTTTCCCTTT
1845939 TT
1 TT
1845941 GTAAATGCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTCTCAATTTTTCCCTTT
Found at i:1849403 original size:23 final size:23
Alignment explanation
Indices: 1849350--1849405 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
1849340 TTTACTTTTC
*
1849350 ATTATTTTTTGTATTTTTTGTCT
1 ATTATTTTTTGTATTTTTTATCT
* *
1849373 CTTTTTTTTTGTATTTTATTAT-T
1 ATTATTTTTTGTATTTT-TTATCT
1849396 ATTATTTTTT
1 ATTATTTTTT
1849406 TTAAAAGCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 24 0.89
24 3 0.11
ACGTcount: A:0.14, C:0.04, G:0.05, T:0.77
Consensus pattern (23 bp):
ATTATTTTTTGTATTTTTTATCT
Found at i:1851730 original size:277 final size:277
Alignment explanation
Indices: 1851101--1851931 Score: 1370
Period size: 277 Copynumber: 3.0 Consensus size: 277
1851091 AATTAAAATT
* *
1851101 TTATGCATTTTACTCGATATTTCAACAAAAATGAAAAATAG-TGAAGATGCAAAGGTGATAAAGA
1 TTATGCATTTTACTCGATATTTCAGCAAAAATGAAAAATAGTTGAAGATGCAAAAGTGATAAAGA
*
1851165 TAAACGATCTATTTTCATTAAAAATTTTCAATTAATACTCATTAATTATTATATTAATAATTATA
66 TAAACGATCTATTTTCATTAAAAATTTTTAATTAATACTCATTAATTATTATATTAATAATTATA
*
1851230 AATAATCAACACTAATAAAAAAGATTTGTGAGTTTGAGTTTTTA--C-TTTTTTT-TTATGACAA
131 AATAATCAACACTAATAAAAAAGATTTGTGAGTTTGAGTTTTTACCCTTTTTTTTCTTAGGACAA
* * * * * *
1851291 AGTTACCTCCTTTTGTTATATAATTGTTAATTTTTTTAAATAGAAAAAGTATTATGATCTCTTAT
196 ATTTGCCTCCTTTTGTTATATCATTGTCAA-TTTTTCAAATAAAAAAAGTATTATGATCTCTTAT
1851356 TTTTGAAAATAATTCTAC
260 TTTTGAAAATAATTCTAC
* *
1851374 ATATGCATTTTACTCGATATTTCAGCAAAAATGAAAAATAGTTGAAGATGC-CAAGTTGATAAAG
1 TTATGCATTTTACTCGATATTTCAGCAAAAATGAAAAATAGTTGAAGATGCAAAAG-TGATAAAG
* *
1851438 ATAAACGATCTATTTTCATGAAAAATTTTTAATTAATACTCATTAATTATTATAATAATAATTAT
65 ATAAACGATCTATTTTCATTAAAAATTTTTAATTAATACTCATTAATTATTATATTAATAATTAT
*
1851503 AAATAATCAACGCTAATAAAAAAGATTTGTGAGTTTGAGTTTTTACCCTTTTTTTTCTTAGGACA
130 AAATAATCAACACTAATAAAAAAGATTTGTGAGTTTGAGTTTTTACCCTTTTTTTTCTTAGGACA
* *
1851568 AATTTGCCTCTTTTTGTTATATCATTGTCAATTTTTCAAATAAAAAAAGTATTATGATCTCTTGT
195 AATTTGCCTCCTTTTGTTATATCATTGTCAATTTTTCAAATAAAAAAAGTATTATGATCTCTTAT
* *
1851633 TTTTAAAAATAATTTTAC
260 TTTTGAAAATAATTCTAC
*
1851651 TTATGCATTTTACTCGACATTTCAGCAAAAATGAAAAATAGTTGAAGATGCAAAAGTGATAAAGA
1 TTATGCATTTTACTCGATATTTCAGCAAAAATGAAAAATAGTTGAAGATGCAAAAGTGATAAAGA
* *
1851716 TAAATGATCTATTTTTATTAAAAATTTTTAATTAATACTCATTAATTATTATATTAATAATTATA
66 TAAACGATCTATTTTCATTAAAAATTTTTAATTAATACTCATTAATTATTATATTAATAATTATA
*
1851781 AATAATCAACACTAATAAAAAAGATTTGTGAGTTTGAGTTTTTACCTTTTTTTTTTCTTAGGACA
131 AATAATCAACACTAATAAAAAAGATTTGTGAGTTTGAGTTTTTACC-CTTTTTTTTCTTAGGACA
*
1851846 AATTTGCCTCCTTTTGTTATATCATTGTCAAATTTTCAAAT-AAAAAAGTATTATGATCTCTTAT
195 AATTTGCCTCCTTTTGTTATATCATTGTCAATTTTTCAAATAAAAAAAGTATTATGATCTCTTAT
1851910 TTTTGAAAATAATTCTAC
260 TTTTGAAAATAATTCTAC
1851928 TTAT
1 TTAT
1851932 CCCATTAAGA
Statistics
Matches: 517, Mismatches: 33, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
273 41 0.08
274 123 0.24
276 1 0.00
277 260 0.50
278 92 0.18
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.42
Consensus pattern (277 bp):
TTATGCATTTTACTCGATATTTCAGCAAAAATGAAAAATAGTTGAAGATGCAAAAGTGATAAAGA
TAAACGATCTATTTTCATTAAAAATTTTTAATTAATACTCATTAATTATTATATTAATAATTATA
AATAATCAACACTAATAAAAAAGATTTGTGAGTTTGAGTTTTTACCCTTTTTTTTCTTAGGACAA
ATTTGCCTCCTTTTGTTATATCATTGTCAATTTTTCAAATAAAAAAAGTATTATGATCTCTTATT
TTTGAAAATAATTCTAC
Found at i:1853090 original size:27 final size:28
Alignment explanation
Indices: 1853060--1853113 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
1853050 AAACCTTCAA
1853060 AAATAATATTTCA-TTAATTTAAAATTT
1 AAATAATATTTCATTTAATTTAAAATTT
* * *
1853087 AAATTATATTTTATTTATTTTAAAATT
1 AAATAATATTTCATTTAATTTAAAATT
1853114 ACGATTTCCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (28 bp):
AAATAATATTTCATTTAATTTAAAATTT
Found at i:1853771 original size:2 final size:2
Alignment explanation
Indices: 1853764--1853789 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1853754 AAACGTAATG
1853764 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
1853790 TATGATAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1854839 original size:2 final size:2
Alignment explanation
Indices: 1854832--1854872 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1854822 GTCTCTTCTT
1854832 TA TA 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 TA TA T
1854873 TCTCTAGTAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1855459 original size:14 final size:15
Alignment explanation
Indices: 1855433--1855468 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
1855423 TCGAAGGCAA
1855433 ATTTA-ATTGTATTT
1 ATTTATATTGTATTT
1855447 ATTTATATT-TATTT
1 ATTTATATTGTATTT
1855461 ATTTATAT
1 ATTTATAT
1855469 CATTAGTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 18 0.86
15 3 0.14
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (15 bp):
ATTTATATTGTATTT
Found at i:1855698 original size:20 final size:21
Alignment explanation
Indices: 1855660--1855699 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1855650 TTCTAAAAAT
1855660 AAATAGAAATATTAATAATAA
1 AAATAGAAATATTAATAATAA
1855681 AAATA-AAA-ATTAAATAATA
1 AAATAGAAATATT-AATAATA
1855700 TTTTATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.17
20 10 0.56
21 5 0.28
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (21 bp):
AAATAGAAATATTAATAATAA
Found at i:1856228 original size:4 final size:4
Alignment explanation
Indices: 1856219--1856262 Score: 54
Period size: 4 Copynumber: 10.8 Consensus size: 4
1856209 AAAAATACAT
*
1856219 TAAA TAAA TAAA TAAA TAACA -AAA CAAAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAA-A TAAA -TAAA TAAA TAAA TAAA TAA
1856263 CAATAATTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
3 1 0.03
4 31 0.86
5 4 0.11
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (4 bp):
TAAA
Found at i:1856235 original size:21 final size:20
Alignment explanation
Indices: 1856224--1856284 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 20
1856214 TACATTAAAT
1856224 AAATAAATAAATAACAAAACA
1 AAATAAATAAAT-ACAAAACA
1856245 AAATAAATAAATA-AATAACA
1 AAATAAATAAATACAA-AACA
1856265 ATAATTAAA-AAA-ACAAAACA
1 A-AA-TAAATAAATACAAAACA
1856285 TCAATCAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
19 2 0.06
20 11 0.31
21 19 0.53
22 4 0.11
ACGTcount: A:0.75, C:0.08, G:0.00, T:0.16
Consensus pattern (20 bp):
AAATAAATAAATACAAAACA
Found at i:1858868 original size:31 final size:29
Alignment explanation
Indices: 1858802--1858873 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
1858792 CCACTACCTC
*
1858802 TCAAGAAAAAAAAAACAAAAACGAAGAAA
1 TCAAGCAAAAAAAAACAAAAACGAAGAAA
*
1858831 TCAAGCAAAAGAAAA-AAAAACGCAAAGAAAA
1 TCAAGCAAAAAAAAACAAAAACG--AAG-AAA
*
1858862 TTAAGCAAAAAA
1 TCAAGCAAAAAA
1858874 TGATCTTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 7 0.19
29 13 0.36
30 3 0.08
31 13 0.36
ACGTcount: A:0.72, C:0.11, G:0.11, T:0.06
Consensus pattern (29 bp):
TCAAGCAAAAAAAAACAAAAACGAAGAAA
Found at i:1859704 original size:22 final size:21
Alignment explanation
Indices: 1859676--1859720 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
1859666 GGTAATGTAA
*
1859676 ATATAATAAAAATAATTAAAAT
1 ATATAATAAAAAT-ATAAAAAT
*
1859698 ATATAATATAAATATAAAAAT
1 ATATAATAAAAATATAAAAAT
1859719 AT
1 AT
1859721 CGTAAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
ATATAATAAAAATATAAAAAT
Found at i:1859713 original size:6 final size:6
Alignment explanation
Indices: 1859673--1859833 Score: 56
Period size: 6 Copynumber: 27.3 Consensus size: 6
1859663 TCTGGTAATG
* *
1859673 TAAATA T-AATA -AAA-A TAATTA -AAATA TATAATA TAAATA TAAAAA
1 TAAATA TAAATA TAAATA TAAATA TAAATA TA-AATA TAAATA TAAATA
** * * *
1859718 TATCGTA -AAATTTA TATAATA AAAATTA TTAATA TATATA TTAAA-A
1 TA-AATA TAAA--TA TA-AATA TAAA-TA TAAATA TAAATA -TAAATA
** * *
1859764 TTTATA TAAATA TAAA-A T-AATT TAAATA TAATTA T-AATA T-AATA
1 TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA
* *
1859808 AAATATA TAAATA T-AATA TTAATA TA
1 TAA-ATA TAAATA TAAATA TAAATA TA
1859834 CAAAATATCA
Statistics
Matches: 112, Mismatches: 25, Indels: 36
0.65 0.14 0.21
Matches are distributed among these distances:
4 3 0.03
5 30 0.27
6 52 0.46
7 24 0.21
8 1 0.01
9 2 0.02
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.39
Consensus pattern (6 bp):
TAAATA
Found at i:1859755 original size:22 final size:22
Alignment explanation
Indices: 1859730--1859783 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
1859720 TCGTAAAATT
1859730 TATATAATAAAAATTAT-TAATA
1 TATATAATAAAAATTATATAA-A
* *
1859752 TATATATTAAAATTTATATAAA
1 TATATAATAAAAATTATATAAA
*
1859774 TATAAAATAA
1 TATATAATAA
1859784 TTTAAATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 24 0.89
23 3 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TATATAATAAAAATTATATAAA
Found at i:1859768 original size:36 final size:37
Alignment explanation
Indices: 1859723--1859820 Score: 105
Period size: 37 Copynumber: 2.6 Consensus size: 37
1859713 AAAAATATCG
*
1859723 TAAAATTTATAT-AATA-AAAATTA-TTAATATATATAT
1 TAAAATTTATATAAATATAAAATAATTTAA-ATATA-AT
1859759 TAAAATTTATATAAATATAAAATAATTTAAATATAAT
1 TAAAATTTATATAAATATAAAATAATTTAAATATAAT
* *
1859796 TATAATATA-ATAAAATATATAAATA
1 TAAAATTTATAT-AAATATA-AAATA
1859821 TAATATTAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
36 14 0.26
37 20 0.37
38 16 0.30
39 4 0.07
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (37 bp):
TAAAATTTATATAAATATAAAATAATTTAAATATAAT
Found at i:1859830 original size:29 final size:28
Alignment explanation
Indices: 1859768--1859841 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 28
1859758 TTAAAATTTA
*
1859768 TATAA-ATATAAAATAATTTAAATATAAT
1 TATAATATATAAAAT-ATATAAATATAAT
1859796 TATAATATAATAAAATATATAAATATAA-
1 TATAATAT-ATAAAATATATAAATATAAT
*
1859824 TATTAATATACAAAATAT
1 TA-TAATATATAAAATAT
1859842 CAAGTTTAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
28 15 0.37
29 19 0.46
30 7 0.17
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (28 bp):
TATAATATATAAAATATATAAATATAAT
Found at i:1862064 original size:2 final size:2
Alignment explanation
Indices: 1862057--1862082 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1862047 TTGGTAATTC
1862057 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
1862083 GTGTTGTGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1864071 original size:29 final size:29
Alignment explanation
Indices: 1864038--1864098 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
1864028 ATTTTTAATT
*
1864038 TAATTTGAA-TTATTATTTAATAATAAAAA
1 TAATTTGAATTTA-AATTTAATAATAAAAA
** *
1864067 TAATTTTTATTTAAATTTAATTATAAAAA
1 TAATTTGAATTTAAATTTAATAATAAAAA
1864096 TAA
1 TAA
1864099 ATTTTTTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 24 0.89
30 3 0.11
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (29 bp):
TAATTTGAATTTAAATTTAATAATAAAAA
Found at i:1864116 original size:29 final size:28
Alignment explanation
Indices: 1864055--1864136 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 28
1864045 AATTATTATT
* * *
1864055 TAATAATAAAAATAATTTTTATTTAAATT
1 TAATAATAAAAATAAATTTT-TTAAAATA
*
1864084 TAATTATAAAAATAAATTTTTTAATAATA
1 TAATAATAAAAATAAATTTTTTAA-AATA
1864113 TAATAAATAGTAAAATAAATTTTT
1 TAAT-AATA--AAAATAAATTTTT
1864137 GAAAGTAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
28 3 0.07
29 25 0.57
30 3 0.07
32 13 0.30
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (28 bp):
TAATAATAAAAATAAATTTTTTAAAATA
Found at i:1865353 original size:50 final size:50
Alignment explanation
Indices: 1865280--1865450 Score: 236
Period size: 50 Copynumber: 3.4 Consensus size: 50
1865270 GGTGCAAAAG
* *
1865280 AGGTGATCGTAATTGTTGACTATTCTTCATCAACCTTTGACAATCAAGAA
1 AGGTGATCGTAATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAA
* * * *
1865330 AAGTGATCGTAATTGTTGACTATTCCTCACCAATCTTTGGCAATCGAGAA
1 AGGTGATCGTAATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAA
* *
1865380 AGGTGATCATAATTGTTGACTATT-TCTCACCAACCTTTGACAATCGAGAG
1 AGGTGATCGTAATTGTTGACTATTCT-TCACCAACCTTTGACAATCGAGAA
* *
1865430 AGGTGGTTGTAATTGTTGACT
1 AGGTGATCGTAATTGTTGACT
1865451 CTAAACATCT
Statistics
Matches: 105, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
50 105 1.00
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (50 bp):
AGGTGATCGTAATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAA
Found at i:1869461 original size:50 final size:49
Alignment explanation
Indices: 1869386--1869523 Score: 197
Period size: 50 Copynumber: 2.8 Consensus size: 49
1869376 GGGTGCAAAG
* *
1869386 GAGGTGACCGTAATTGTTGACTATTCTTTACCAATCTTTGACAATCGAGA
1 GAGGTGACCGTAATTGTTGACTATTCTTCACCAA-CTTTGACAATCAAGA
*
1869436 GAGGTGACCGTAATTGTTGACTATTCCTCACCAACCTTTGACAATCAAGA
1 GAGGTGACCGTAATTGTTGACTATTCTTCACCAA-CTTTGACAATCAAGA
* *
1869486 GAGAT-AGTCGTAATTGTTGACTATTCTTCACCAACTTT
1 GAGGTGA-CCGTAATTGTTGACTATTCTTCACCAACTTT
1869524 TAACAATAAA
Statistics
Matches: 80, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
49 5 0.06
50 75 0.94
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33
Consensus pattern (49 bp):
GAGGTGACCGTAATTGTTGACTATTCTTCACCAACTTTGACAATCAAGA
Found at i:1869530 original size:50 final size:50
Alignment explanation
Indices: 1869390--1869553 Score: 190
Period size: 50 Copynumber: 3.3 Consensus size: 50
1869380 GCAAAGGAGG
* * *
1869390 TGACCGTAATTGTTGACTATTCTTTACCAA-TCTTTGACAATCGAGAGAGG
1 TGACCGTAATTGTTGACTATTCTTCACCAACT-TTTGACAATCAAGAGAGA
* *
1869440 TGACCGTAATTGTTGACTATTCCTCACCAACCTTTGACAATCAAGAGAGA
1 TGACCGTAATTGTTGACTATTCTTCACCAACTTTTGACAATCAAGAGAGA
* * * *
1869490 T-AGTCGTAATTGTTGACTATTCTTCACCAACTTTTAACAATAAAG-GAAA
1 TGA-CCGTAATTGTTGACTATTCTTCACCAACTTTTGACAATCAAGAGAGA
*
1869539 GTGACCATAATTGTT
1 -TGACCGTAATTGTT
1869554 AACTCTAAGC
Statistics
Matches: 97, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
49 4 0.04
50 92 0.95
51 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (50 bp):
TGACCGTAATTGTTGACTATTCTTCACCAACTTTTGACAATCAAGAGAGA
Found at i:1870660 original size:2 final size:2
Alignment explanation
Indices: 1870653--1870694 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1870643 CCGAAAAAGA
1870653 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1870695 TCCATATACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1871813 original size:12 final size:12
Alignment explanation
Indices: 1871798--1871822 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1871788 TATTAATAAT
1871798 TTTAAAATTAAA
1 TTTAAAATTAAA
1871810 TTTAAAATTAAA
1 TTTAAAATTAAA
1871822 T
1 T
1871823 ATTGATTGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TTTAAAATTAAA
Found at i:1872561 original size:71 final size:71
Alignment explanation
Indices: 1872431--1872565 Score: 166
Period size: 71 Copynumber: 1.9 Consensus size: 71
1872421 TTCCAAATAT
* * * * *
1872431 ACATCTATCATTGATTTTTATATTATCATTATAATATACAACTCCAAAGCTATAGTAATTAATCC
1 ACATCTATCATTGATTTTAATATCATCAATATAATATACAAATCCAAAGCTACAGTAATTAATCC
1872496 ACGTAC
66 ACGTAC
* * *
1872502 ACATTTATCATTGATTTTAATATCATTAATATAATAT-CAAATCTCACAA-CTACATTAATTAAT
1 ACATCTATCATTGATTTTAATATCATCAATATAATATACAAATC-CA-AAGCTACAGTAATTAAT
1872565 C
64 C
1872566 TTATTATTAT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
70 5 0.09
71 47 0.87
72 2 0.04
ACGTcount: A:0.40, C:0.17, G:0.04, T:0.39
Consensus pattern (71 bp):
ACATCTATCATTGATTTTAATATCATCAATATAATATACAAATCCAAAGCTACAGTAATTAATCC
ACGTAC
Found at i:1872725 original size:33 final size:33
Alignment explanation
Indices: 1872653--1872732 Score: 83
Period size: 33 Copynumber: 2.5 Consensus size: 33
1872643 AGGATAAAAA
* *
1872653 AAATTCTCCACA-AAAGCACAAGGGCTAGCAGAT
1 AAATTCTCCA-AGAAAGCACAAGGGCAAGCAGAC
** * *
1872686 GGATTCTCCAAGAAAGCATAAGGGCAAGTAGAC
1 AAATTCTCCAAGAAAGCACAAGGGCAAGCAGAC
1872719 AAATTCTCC-AGAAA
1 AAATTCTCCAAGAAA
1872733 AAACTAAGGC
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
32 6 0.16
33 32 0.84
ACGTcount: A:0.42, C:0.21, G:0.20, T:0.16
Consensus pattern (33 bp):
AAATTCTCCAAGAAAGCACAAGGGCAAGCAGAC
Found at i:1872884 original size:2 final size:2
Alignment explanation
Indices: 1872877--1872913 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1872867 TTATGGCGAG
1872877 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
1872914 TCACAAAAAC
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:1878366 original size:10 final size:10
Alignment explanation
Indices: 1878351--1878375 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1878341 CTGTAATAGA
1878351 TTTTTTTATT
1 TTTTTTTATT
1878361 TTTTTTTATT
1 TTTTTTTATT
1878371 TTTTT
1 TTTTT
1878376 GGCATGGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:1892493 original size:2 final size:2
Alignment explanation
Indices: 1892486--1892512 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1892476 TATTCATTTA
1892486 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1892513 AAAGGTAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1892595 original size:12 final size:11
Alignment explanation
Indices: 1892579--1892616 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
1892569 AAAAATTTAA
*
1892579 AATTTAAGTTT
1 AATTTAAATTT
1892590 AAATTTAAATTT
1 -AATTTAAATTT
1892602 AATTT-AATTT
1 AATTTAAATTT
1892612 AATTT
1 AATTT
1892617 TATAATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 10 0.40
11 5 0.20
12 10 0.40
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:1892596 original size:6 final size:6
Alignment explanation
Indices: 1892571--1892629 Score: 59
Period size: 6 Copynumber: 9.8 Consensus size: 6
1892561 ATGGTATAAA
* *
1892571 AAATTT AAAATTT AAGTTT AAATTT AAATTT -AATTT -AATTT AATTTT
1 AAATTT -AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
*
1892618 ATAATTT TAATT
1 A-AATTT AAATT
1892630 ATTATTTAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
5 10 0.22
6 25 0.56
7 10 0.22
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (6 bp):
AAATTT
Found at i:1893137 original size:20 final size:20
Alignment explanation
Indices: 1893114--1893152 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1893104 TTAAAATTTA
1893114 AAATTAAATATTTTATTAAT
1 AAATTAAATATTTTATTAAT
1893134 AAATTAAATATTTTATTAA
1 AAATTAAATATTTTATTAA
1893153 AATATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AAATTAAATATTTTATTAAT
Found at i:1896114 original size:25 final size:25
Alignment explanation
Indices: 1896080--1896135 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
1896070 TCCATAGTTA
1896080 AGAGTGATACTAGGATGTTTAGGTG
1 AGAGTGATACTAGGATGTTTAGGTG
*
1896105 AGAGTGATACTAGGATGTTTCGGTG
1 AGAGTGATACTAGGATGTTTAGGTG
1896130 AGAGTG
1 AGAGTG
1896136 GTATTAAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.27, C:0.05, G:0.38, T:0.30
Consensus pattern (25 bp):
AGAGTGATACTAGGATGTTTAGGTG
Found at i:1896146 original size:25 final size:25
Alignment explanation
Indices: 1896080--1896146 Score: 89
Period size: 25 Copynumber: 2.7 Consensus size: 25
1896070 TCCATAGTTA
*
1896080 AGAGTGATACTAGGATGTTTAGGTG
1 AGAGTGATACTAAGATGTTTAGGTG
* *
1896105 AGAGTGATACTAGGATGTTTCGGTG
1 AGAGTGATACTAAGATGTTTAGGTG
* *
1896130 AGAGTGGTATTAAGATG
1 AGAGTGATACTAAGATG
1896147 AGTAATCTCT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.28, C:0.04, G:0.36, T:0.31
Consensus pattern (25 bp):
AGAGTGATACTAAGATGTTTAGGTG
Found at i:1896237 original size:63 final size:63
Alignment explanation
Indices: 1896136--1896261 Score: 207
Period size: 63 Copynumber: 2.0 Consensus size: 63
1896126 GGTGAGAGTG
*
1896136 GTATTAAGATGAGTAATCTCTTAAAAAGTTTTTGTATCGTTTCTTATTTAATTTTAATTTTTT
1 GTATTAAGATGAGTAATCTCTTAAAAAGTTTTTCTATCGTTTCTTATTTAATTTTAATTTTTT
* * * *
1896199 GTATTAGGATGAGTAATCTTTTAAAAAGTTTTTCTATCGTTTTTTATTTAATTTTAGTTTTTT
1 GTATTAAGATGAGTAATCTCTTAAAAAGTTTTTCTATCGTTTCTTATTTAATTTTAATTTTTT
1896262 AACATTATTA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.27, C:0.06, G:0.12, T:0.56
Consensus pattern (63 bp):
GTATTAAGATGAGTAATCTCTTAAAAAGTTTTTCTATCGTTTCTTATTTAATTTTAATTTTTT
Found at i:1897451 original size:25 final size:24
Alignment explanation
Indices: 1897423--1897472 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1897413 ACTCACTTGT
1897423 AACTACCATCTTTTTACTTTAAAAA
1 AACTACCAT-TTTTTACTTTAAAAA
***
1897448 AACTTTTATTTTTTACTTTAAAAA
1 AACTACCATTTTTTACTTTAAAAA
1897472 A
1 A
1897473 TCAATTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.40, C:0.14, G:0.00, T:0.46
Consensus pattern (24 bp):
AACTACCATTTTTTACTTTAAAAA
Found at i:1899122 original size:10 final size:10
Alignment explanation
Indices: 1899103--1899131 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1899093 AATATTATTT
1899103 TATA-AAATA
1 TATATAAATA
1899112 TATATAAATA
1 TATATAAATA
1899122 TATATAAATA
1 TATATAAATA
1899132 ATTTTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.21
10 15 0.79
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
TATATAAATA
Found at i:1899188 original size:28 final size:27
Alignment explanation
Indices: 1899126--1899188 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
1899116 TAAATATATA
* * *
1899126 TAAATAATTTTTTTATTAAAATAATAT
1 TAAATAATTTATTTATGAAAATAAAAT
** *
1899153 TATTTAATTTATTTATGATATATAAAAT
1 TAAATAATTTATTTATGA-AAATAAAAT
1899181 TAAATAAT
1 TAAATAAT
1899189 AACGATGATG
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
27 14 0.52
28 13 0.48
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (27 bp):
TAAATAATTTATTTATGAAAATAAAAT
Found at i:1900970 original size:2 final size:2
Alignment explanation
Indices: 1900963--1901008 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1900953 AATGTCATGC
1900963 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1901005 AT AT
1 AT AT
1901009 TCCTATATGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1902098 original size:13 final size:14
Alignment explanation
Indices: 1902072--1902102 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
1902062 GTAAAAATAT
1902072 TTTAAATATTAAAA
1 TTTAAATATTAAAA
1902086 TTTAAAT-TTAAAA
1 TTTAAATATTAAAA
1902099 TTTA
1 TTTA
1902103 TTAAATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTTAAATATTAAAA
Found at i:1902682 original size:19 final size:19
Alignment explanation
Indices: 1902640--1902683 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1902630 AAGTTTAATA
*
1902640 AATTTTAAATTTTTATATT
1 AATTTTAAAATTTTATATT
*
1902659 TATTTTAATAATTTTAT-TT
1 AATTTTAA-AATTTTATATT
1902678 AATTTT
1 AATTTT
1902684 TTTATTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
AATTTTAAAATTTTATATT
Found at i:1903262 original size:194 final size:192
Alignment explanation
Indices: 1902974--1903361 Score: 593
Period size: 194 Copynumber: 2.0 Consensus size: 192
1902964 AAATATATTT
* * * * * *
1902974 ATCCTAAGGTTTTAAAAAATATATATTTACGCATTCTAATTTAAAAAATATCTACTTGCTCTTTA
1 ATCCTAAGGTTTTAAAAAATATATATTTACACA-TCTAATTTAAAAAATATCCACATACCCTTGA
* * *
1903039 AAGAAAAAAAATATATTAACCTTTAAGATTTATTTATTAATTAATTTTTTAATAAAAAATTTTAT
65 AAGAAAAAAAACATATTAACCTTTAAGATTTATTTATTAATTAAATTTTTAATAAAAAATTATAT
1903104 CCTTTTTAATCACTAATCATTTAATTTTATATTTAATTTTATTTTTTTACTCAATTTTTTTAC
130 CCTTTTTAATCACTAATCATTTAATTTTATATTTAATTTTATTTTTTTACTCAATTTTTTTAC
1903167 ATCCTAAGGTTTT-AAAAATATATATTTACACA-CT-ATTTAAAAAATATCCACATACCCTCTGA
1 ATCCTAAGGTTTTAAAAAATATATATTTACACATCTAATTTAAAAAATATCCACATACCCT-TGA
*
1903229 AAGTTTGAAGAAAAACATATTAACCTTTAAGATTTATTTATTAATTAAATTTTTAATAAAAAATT
65 AA----GAAAAAAAACATATTAACCTTTAAGATTTATTTATTAATTAAATTTTTAATAAAAAATT
* *
1903294 ATATCCTTTTTAATTACTAATCATTTAATTTTATATTTTATTTTATTTTTTTACTCAATTTTTTT
126 ATATCCTTTTTAATCACTAATCATTTAATTTTATATTTAATTTTATTTTTTTACTCAATTTTTTT
1903359 AC
191 AC
1903361 A
1 A
1903362 AAATAATAAA
Statistics
Matches: 178, Mismatches: 12, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
189 20 0.11
190 6 0.03
192 18 0.10
193 13 0.07
194 121 0.68
ACGTcount: A:0.39, C:0.11, G:0.03, T:0.47
Consensus pattern (192 bp):
ATCCTAAGGTTTTAAAAAATATATATTTACACATCTAATTTAAAAAATATCCACATACCCTTGAA
AGAAAAAAAACATATTAACCTTTAAGATTTATTTATTAATTAAATTTTTAATAAAAAATTATATC
CTTTTTAATCACTAATCATTTAATTTTATATTTAATTTTATTTTTTTACTCAATTTTTTTAC
Found at i:1903955 original size:30 final size:30
Alignment explanation
Indices: 1903888--1903955 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
1903878 TAAGATAAAA
* *
1903888 TACAAATTAAATGTTAAGCATTTAATTAAC
1 TACAAATAAAATATTAAGCATTTAATTAAC
* * *
1903918 TATAAATAAAATATTAAGCATTTAATTGAG
1 TACAAATAAAATATTAAGCATTTAATTAAC
1903948 TACAAATA
1 TACAAATA
1903956 TAAGTTAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.35
Consensus pattern (30 bp):
TACAAATAAAATATTAAGCATTTAATTAAC
Found at i:1905067 original size:32 final size:30
Alignment explanation
Indices: 1905028--1905100 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 30
1905018 TTAAAGTTTT
* * *
1905028 TTAATTAATCATTATTTTATTTTATTTAAAAA
1 TTAATTAATAATTA-CTAATTTTA-TTAAAAA
*
1905060 TTAATTAATTAATTACTAATTTTATTAAATA
1 TTAATTAA-TAATTACTAATTTTATTAAAAA
1905091 TTAATTAATA
1 TTAATTAATA
1905101 CTTATTATAC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
30 2 0.06
31 14 0.39
32 15 0.42
33 5 0.14
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (30 bp):
TTAATTAATAATTACTAATTTTATTAAAAA
Found at i:1905068 original size:36 final size:38
Alignment explanation
Indices: 1904992--1905072 Score: 103
Period size: 36 Copynumber: 2.2 Consensus size: 38
1904982 TACAAATACC
* * **
1904992 AATTAATAATTATTTTATTTATTATTTTAAAGTTTTTT
1 AATTAATAATTATTTTATTTATTATTTAAAAATTAATT
*
1905030 AATTAATCATTATTTTA-TT-TTATTTAAAAATTAATT
1 AATTAATAATTATTTTATTTATTATTTAAAAATTAATT
1905066 AATTAAT
1 AATTAAT
1905073 TACTAATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
36 20 0.53
37 2 0.05
38 16 0.42
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (38 bp):
AATTAATAATTATTTTATTTATTATTTAAAAATTAATT
Found at i:1905095 original size:16 final size:16
Alignment explanation
Indices: 1905046--1905096 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
1905036 TCATTATTTT
*
1905046 ATTTTATTTAAAAATTA
1 ATTTTA-TTAAATATTA
* * *
1905063 A-TTAATTAATTACTA
1 ATTTTATTAAATATTA
1905078 ATTTTATTAAATATTA
1 ATTTTATTAAATATTA
1905094 ATT
1 ATT
1905097 AATACTTATT
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
15 8 0.31
16 17 0.65
17 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTTATTAAATATTA
Found at i:1905300 original size:3 final size:3
Alignment explanation
Indices: 1905292--1905323 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1905282 AATTGGATCT
1905292 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1905324 GTGCTAATGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1907855 original size:21 final size:21
Alignment explanation
Indices: 1907831--1907873 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1907821 AAATATTAAA
*
1907831 ATATTTTTTAT-ATTAATATTT
1 ATATATTTTATAATTAA-ATTT
1907852 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
1907873 A
1 A
1907874 AATAATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:1907857 original size:23 final size:22
Alignment explanation
Indices: 1907822--1907877 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
1907812 ATTATTTAAA
* *
1907822 AATATTAAAATATTTTTTATATT
1 AATATTTAAATATTTTATA-ATT
*
1907845 AATATTTATATATTTTATAATT
1 AATATTTAAATATTTTATAATT
1907867 AA-ATTTAAATA
1 AATATTTAAATA
1907878 ATAAATAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 8 0.28
22 5 0.17
23 16 0.55
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
AATATTTAAATATTTTATAATT
Found at i:1908840 original size:27 final size:25
Alignment explanation
Indices: 1908800--1908892 Score: 71
Period size: 25 Copynumber: 3.6 Consensus size: 25
1908790 TGAATTATAT
* *
1908800 ATTTTATAAATAAAAAATATGTTTTTA
1 ATTTAATAATTAAAAAATA--TTTTTA
*
1908827 ATTTAATAATTAAATAATATTTTTA
1 ATTTAATAATTAAAAAATATTTTTA
* * *
1908852 ATTTATTAA-TAATAAATTATTATTTT
1 ATTTAATAATTAA-AAAATATT-TTTA
*
1908878 ATTAAATTAATTAAA
1 ATTTAA-TAATTAAA
1908893 CTATATAATA
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
24 3 0.06
25 20 0.38
26 7 0.13
27 20 0.38
28 3 0.06
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (25 bp):
ATTTAATAATTAAAAAATATTTTTA
Found at i:1908872 original size:25 final size:26
Alignment explanation
Indices: 1908802--1908872 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 26
1908792 AATTATATAT
* * *
1908802 TTTATAAATAAAAAATATGTTTTTAA
1 TTTATTAATAATAAATATATTTTTAA
*
1908828 TTTAATAAT--TAAATAATATTTTTAA
1 TTTATTAATAATAAAT-ATATTTTTAA
1908853 TTTATTAATAATAAAT-TATT
1 TTTATTAATAATAAATATATT
1908873 ATTTTATTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
24 4 0.11
25 21 0.57
26 7 0.19
27 5 0.14
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (26 bp):
TTTATTAATAATAAATATATTTTTAA
Found at i:1908881 original size:22 final size:23
Alignment explanation
Indices: 1908824--1908882 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 23
1908814 AAATATGTTT
* *
1908824 TTAATTTAATAATTAAATAATATTT
1 TTAATTTATTAA-T-AATAATATTA
1908849 TTAATTTATTAATAATAA-ATTA
1 TTAATTTATTAATAATAATATTA
*
1908871 TTATTTTATTAA
1 TTAATTTATTAA
1908883 ATTAATTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.45
23 5 0.16
24 1 0.03
25 11 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TTAATTTATTAATAATAATATTA
Found at i:1910109 original size:37 final size:37
Alignment explanation
Indices: 1910042--1910121 Score: 101
Period size: 36 Copynumber: 2.2 Consensus size: 37
1910032 AAATAATCTT
*
1910042 ATTTTATATTAATTTAATTTTTTTGAATTATTAA-TA
1 ATTTTATATTAAATTAATTTTTTTGAATTATTAATTA
**
1910078 ATTTTATATTTAAATT-ATTTTTTATTTATTATTAATTA
1 ATTTTATA-TTAAATTAATTTTTT-TGAATTATTAATTA
1910116 ATTTTA
1 ATTTTA
1910122 ATTGAATGCT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 15 0.39
37 15 0.39
38 8 0.21
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (37 bp):
ATTTTATATTAAATTAATTTTTTTGAATTATTAATTA
Found at i:1910484 original size:2 final size:2
Alignment explanation
Indices: 1910479--1910515 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1910469 AATGTGTGTG
1910479 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
1910516 CAAAGTTCCT
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:1911552 original size:34 final size:34
Alignment explanation
Indices: 1911514--1911584 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
1911504 ATTTATATCA
* * * *
1911514 TATTTTATA-TTATTTATTATAATAATTTAATTTT
1 TATTTTATATTTATTAATTA-AAAAATTAAATTAT
1911548 TATTTTATATTTATTAATTAAAAAATTAAATTAT
1 TATTTTATATTTATTAATTAAAAAATTAAATTAT
1911582 TAT
1 TAT
1911585 ATATTTTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 23 0.72
35 9 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (34 bp):
TATTTTATATTTATTAATTAAAAAATTAAATTAT
Found at i:1912393 original size:13 final size:13
Alignment explanation
Indices: 1912377--1912402 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1912367 AAAACAAGGG
1912377 AAAAAAAGGAGAA
1 AAAAAAAGGAGAA
1912390 AAAAAAAGGAGAA
1 AAAAAAAGGAGAA
1912403 TAAAGTAAAA
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:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AAAAAAAGGAGAA
Found at i:1912766 original size:17 final size:16
Alignment explanation
Indices: 1912736--1912778 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
1912726 ATATTTTAAA
*
1912736 AATAAAAATATTTATGT
1 AATAAAATTATTTAT-T
*
1912753 AATAAAATTTTTTATT
1 AATAAAATTATTTATT
*
1912769 TATAAAATTA
1 AATAAAATTA
1912779 AAAATTTCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
AATAAAATTATTTATT
Found at i:1913052 original size:16 final size:16
Alignment explanation
Indices: 1913020--1913053 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1913010 CAAGCCTTCG
**
1913020 TTTTTTATTTTGTTAT
1 TTTTTTATTTTCATAT
1913036 TTTTTTATTTTCATAT
1 TTTTTTATTTTCATAT
1913052 TT
1 TT
1913054 AATATATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (16 bp):
TTTTTTATTTTCATAT
Found at i:1914399 original size:21 final size:21
Alignment explanation
Indices: 1914370--1914421 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
1914360 TTTTTGATTT
*
1914370 TTAAATTTTTAAAGAGAATTA
1 TTAATTTTTTAAAGAGAATTA
* *
1914391 TTAATTTTTTAAATATAATTA
1 TTAATTTTTTAAAGAGAATTA
1914412 TTAATTTTTT
1 TTAATTTTTT
1914422 TTAATTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (21 bp):
TTAATTTTTTAAAGAGAATTA
Found at i:1916693 original size:2 final size:2
Alignment explanation
Indices: 1916675--1916720 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
1916665 ATCCTAGTAC
* * *
1916675 AT AT GT AT AT TT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1916717 AT AT
1 AT AT
1916721 CCCACTCAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (2 bp):
AT
Found at i:1918274 original size:21 final size:22
Alignment explanation
Indices: 1918245--1918285 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1918235 TATTGTGCTC
*
1918245 TATTCTTAA-AATATAAATTTT
1 TATTCTTAATAATAAAAATTTT
*
1918266 TATTTTTAATAATAAAAATT
1 TATTCTTAATAATAAAAATT
1918286 AAACAACTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TATTCTTAATAATAAAAATTTT
Found at i:1921429 original size:28 final size:28
Alignment explanation
Indices: 1921374--1921426 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
1921364 ATTAGTAATA
*
1921374 TAAATTAAAAAGATATTAATTTAATTAT
1 TAAATTAAAAAGATATTAATTAAATTAT
1921402 TAAATTTAAAAA-A-ATTAATTAAATT
1 TAAA-TTAAAAAGATATTAATTAAATT
1921427 TATGATATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 11 0.48
28 5 0.22
29 7 0.30
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (28 bp):
TAAATTAAAAAGATATTAATTAAATTAT
Found at i:1921565 original size:20 final size:20
Alignment explanation
Indices: 1921478--1921584 Score: 76
Period size: 20 Copynumber: 5.2 Consensus size: 20
1921468 ATTTTTAAAT
1921478 TTTAATTTTTTGAAAAAATTA
1 TTTAATTTTTT-AAAAAATTA
* *
1921499 -ATAATTTTTAATAAAAATTA
1 TTTAATTTTTTA-AAAAATTA
* *
1921519 CTT-GTTTTATCTAAAAAAATTA
1 TTTAATTTT-T-T-AAAAAATTA
1921541 TTTTAATTTTTTAAAAAATTA
1 -TTTAATTTTTTAAAAAATTA
**
1921562 TTT-ATAATTTATAAAAATTA
1 TTTAATTTTTTA-AAAAATTA
1921582 TTT
1 TTT
1921585 TTTAGTTATC
Statistics
Matches: 69, Mismatches: 9, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
19 7 0.10
20 34 0.49
21 11 0.16
22 9 0.13
23 4 0.06
24 4 0.06
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
TTTAATTTTTTAAAAAATTA
Found at i:1921578 original size:22 final size:21
Alignment explanation
Indices: 1921530--1921585 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
1921520 TTGTTTTATC
*
1921530 TAAAAAAATTATTTTAATTTT
1 TAAAAAAATTATTTTAATTTA
*
1921551 TTAAAAAATTATTTATAATTTA
1 TAAAAAAATTATTT-TAATTTA
1921573 T--AAAAATTATTTT
1 TAAAAAAATTATTTT
1921586 TTAGTTATCC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.03
20 11 0.34
21 13 0.41
22 7 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TAAAAAAATTATTTTAATTTA
Found at i:1921593 original size:20 final size:20
Alignment explanation
Indices: 1921509--1921593 Score: 73
Period size: 20 Copynumber: 4.1 Consensus size: 20
1921499 ATAATTTTTA
*
1921509 ATAAAAATTACTTGTTTTATCT
1 ATAAAAATTA-TT-TTTTATTT
* *
1921531 AAAAAAATTATTTTAATTTTTT
1 ATAAAAATTATTTT--TTATTT
* *
1921553 A-AAAAATTATTTATAATTT
1 ATAAAAATTATTTTTTATTT
*
1921572 ATAAAAATTATTTTTTAGTT
1 ATAAAAATTATTTTTTATTT
1921592 AT
1 AT
1921594 CCATTTGTAA
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
19 5 0.10
20 19 0.37
21 13 0.25
22 14 0.27
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (20 bp):
ATAAAAATTATTTTTTATTT
Found at i:1921890 original size:33 final size:33
Alignment explanation
Indices: 1921838--1921903 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1921828 TGTAAAGCAC
* *
1921838 AAAATATATTAAGATATGATATAAATATAATATA
1 AAAATATATTAACACATGATAT-AATATAATATA
*
1921872 AAAATA-ATTAACACATGATATATTATAATATA
1 AAAATATATTAACACATGATATAATATAATATA
1921904 TAATGATACA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 10 0.34
33 13 0.45
34 6 0.21
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.35
Consensus pattern (33 bp):
AAAATATATTAACACATGATATAATATAATATA
Found at i:1922730 original size:14 final size:14
Alignment explanation
Indices: 1922711--1922745 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1922701 AGTCATCAAT
1922711 TTGATTTAGTTTAC
1 TTGATTTAGTTTAC
* *
1922725 TTGATTTGGTTTAT
1 TTGATTTAGTTTAC
1922739 TTGATTT
1 TTGATTT
1922746 TGTAATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.17, C:0.03, G:0.17, T:0.63
Consensus pattern (14 bp):
TTGATTTAGTTTAC
Found at i:1924271 original size:2 final size:2
Alignment explanation
Indices: 1924264--1924295 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1924254 CTCAATCATA
*
1924264 AT AT AT AT AG 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
1924296 GTAAAATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1924601 original size:3 final size:3
Alignment explanation
Indices: 1924593--1924627 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1924583 ATATTACCAT
1924593 AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AG
1 AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AG
1924628 ATGCGGAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.31, G:0.34, T:0.00
Consensus pattern (3 bp):
AGC
Found at i:1926738 original size:2 final size:2
Alignment explanation
Indices: 1926731--1926769 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1926721 TTATAAAAGA
1926731 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1926770 CACACATTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1927939 original size:15 final size:16
Alignment explanation
Indices: 1927914--1927943 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1927904 TATTAAATAA
1927914 AAATATAATTTAAATC
1 AAATATAATTTAAATC
1927930 AAAT-TAATTTAAAT
1 AAATATAATTTAAAT
1927944 TTATAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATATAATTTAAATC
Found at i:1928154 original size:20 final size:20
Alignment explanation
Indices: 1928093--1928155 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
1928083 ACACATTTTT
* *
1928093 TATTTTATTATATTATAATA
1 TATTTTATTTTTTTATAATA
* * *
1928113 -ATATTTATATATTTATATTA
1 TAT-TTTATTTTTTTATAATA
1928133 TATTTTATTTTTTTATAATA
1 TATTTTATTTTTTTATAATA
1928153 TAT
1 TAT
1928156 CATACTTTCA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
19 2 0.06
20 29 0.88
21 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTTTATTTTTTTATAATA
Found at i:1928931 original size:17 final size:18
Alignment explanation
Indices: 1928909--1928942 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1928899 AAATAAAAAT
1928909 AAATAAAATT-TTTAATA
1 AAATAAAATTATTTAATA
*
1928926 AAATAATATTATTTAAT
1 AAATAAAATTATTTAAT
1928943 TTATTAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATAAAATTATTTAATA
Found at i:1928964 original size:19 final size:19
Alignment explanation
Indices: 1928926--1928976 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
1928916 ATTTTTAATA
*
1928926 AAATAATATTATTTAATTTAT
1 AAATAATA-TA-TGAATTTAT
*
1928947 TAATAATATATGAATTTAT
1 AAATAATATATGAATTTAT
1928966 AAATAATATAT
1 AAATAATATAT
1928977 AAAAAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 18 0.67
20 2 0.07
21 7 0.26
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
AAATAATATATGAATTTAT
Found at i:1929096 original size:16 final size:16
Alignment explanation
Indices: 1929061--1929104 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
1929051 AAAATGAAAT
*
1929061 ATAAATATAAAATATA
1 ATAAATAAAAAATATA
1929077 ATAAATAAAAAATAACATA
1 ATAAATAAAAAAT---ATA
1929096 ATAAATAAA
1 ATAAATAAA
1929105 TCTTGTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 12 0.50
19 12 0.50
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (16 bp):
ATAAATAAAAAATATA
Found at i:1929882 original size:23 final size:24
Alignment explanation
Indices: 1929813--1929882 Score: 58
Period size: 23 Copynumber: 2.9 Consensus size: 24
1929803 ACCTCTGATT
1929813 TATTATAATTTT-TTTAATATACTGA
1 TATTATAATTTTATTTAATATAC--A
* *
1929838 TATTAT-TTTTGTATGTT-TTATA-A
1 TATTATAATTT-TAT-TTAATATACA
1929861 TATTATAATTTTATTTAATATA
1 TATTATAATTTTATTTAATATA
1929883 TTTTATATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
22 2 0.06
23 14 0.39
24 6 0.17
25 7 0.19
26 5 0.14
27 2 0.06
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.60
Consensus pattern (24 bp):
TATTATAATTTTATTTAATATACA
Found at i:1929910 original size:47 final size:48
Alignment explanation
Indices: 1929813--1929934 Score: 124
Period size: 48 Copynumber: 2.5 Consensus size: 48
1929803 ACCTCTGATT
** * * ** *
1929813 TATTATAATTTT-TTTAATATACTGATATTATTTTTGTATGTTTTATAA
1 TATTATAATTTTATTTAATATA-TTTTATTATTTATATAAATTTTAAAA
1929861 TATTATAATTTTATTTAATATATTTTA-TATTTATATAAATTTTAAAA
1 TATTATAATTTTATTTAATATATTTTATTATTTATATAAATTTTAAAA
1929908 TATTAGTAATTTATATATTAAT-TATTT
1 TATTA-TAATTT-TAT-TTAATATATTT
1929935 AAATTTTTTA
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
47 20 0.32
48 21 0.33
49 17 0.27
50 5 0.08
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (48 bp):
TATTATAATTTTATTTAATATATTTTATTATTTATATAAATTTTAAAA
Found at i:1935117 original size:20 final size:20
Alignment explanation
Indices: 1935089--1935146 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 20
1935079 AAGAGAAGGC
1935089 AAAGCGAGAAGAAGAAGAACA
1 AAAGCGAGAAGAA-AAGAACA
*
1935110 AAAG-GAGAGGAAAAGAACA
1 AAAGCGAGAAGAAAAGAACA
*
1935129 AAAGAACGAGAAAAAAAG
1 AAAG--CGAGAAGAAAAG
1935147 CTCAGGAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 11 0.35
20 7 0.23
21 4 0.13
22 9 0.29
ACGTcount: A:0.66, C:0.07, G:0.28, T:0.00
Consensus pattern (20 bp):
AAAGCGAGAAGAAAAGAACA
Found at i:1935139 original size:22 final size:21
Alignment explanation
Indices: 1935089--1935132 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
1935079 AAGAGAAGGC
1935089 AAAGCGAGAAGAAGAAGAACA
1 AAAGCGAGAAGAAGAAGAACA
*
1935110 AAAG-GAGAGGAA-AAGAACA
1 AAAGCGAGAAGAAGAAGAACA
1935129 AAAG
1 AAAG
1935133 AACGAGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.50
20 7 0.32
21 4 0.18
ACGTcount: A:0.64, C:0.07, G:0.30, T:0.00
Consensus pattern (21 bp):
AAAGCGAGAAGAAGAAGAACA
Found at i:1938296 original size:4 final size:4
Alignment explanation
Indices: 1938289--1938314 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1938279 TTTTTTTCCA
1938289 AACG AACG AACG AACG AACG AACG AA
1 AACG AACG AACG AACG AACG AACG AA
1938315 ATTTCCCGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.23, G:0.23, T:0.00
Consensus pattern (4 bp):
AACG
Found at i:1940858 original size:16 final size:16
Alignment explanation
Indices: 1940811--1940858 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
1940801 TTTTTTCGTG
* *
1940811 TTGTGTTTTAATTATT
1 TTGTTTTTTAATTATA
* *
1940827 TTTTTTTTTATGTTATA
1 TTGTTTTTTA-ATTATA
1940844 TTGTTTTTTAATTAT
1 TTGTTTTTTAATTAT
1940859 TTTAATTGAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.73
Consensus pattern (16 bp):
TTGTTTTTTAATTATA
Found at i:1943274 original size:2 final size:2
Alignment explanation
Indices: 1943269--1943296 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1943259 CTTAAATTTG
1943269 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
1943297 TCCAATCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1945616 original size:13 final size:14
Alignment explanation
Indices: 1945598--1945627 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1945588 CACTTTTCGT
1945598 AATTAATTATA-TA
1 AATTAATTATAGTA
1945611 AATTAATTATAGTA
1 AATTAATTATAGTA
1945625 AAT
1 AAT
1945628 CTTAAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (14 bp):
AATTAATTATAGTA
Found at i:1950421 original size:101 final size:100
Alignment explanation
Indices: 1950314--1950842 Score: 451
Period size: 101 Copynumber: 5.2 Consensus size: 100
1950304 GGAAGAGATT
* ** * * ** *
1950314 ACAAATTAATTTAGTAATATCTAATAGAACACGCGTAAGTTAATAAACTCGTCACAACTTATAAT
1 ACAAATTAATTCAAAAATATATAATAGAACACGTGTAAGTCGATAAACTCGTTACAACTTATAA-
* *
1950379 GATCATAAATGTATATATTGACAATTATAAGAAATC
65 AATCATAAATGTATACATTGACAATTATAAGAAATC
* * * * **
1950415 ATAAATTAATTAAAAAATATATAAT-GAAACACGTGTAAATCAATAAACTCGTTACGTCTTACTA
1 ACAAATTAATTCAAAAATATATAATAG-AACACGTGTAAGTCGATAAACTCGTTACAACTTA-TA
* * * ** * * *
1950479 AAATCATAAATATTTACATTCACAAGCAAAAAAAATT
64 AAATCATAAATGTATACATTGACAATTATAAGAAATC
* * * **
1950516 ACAAATTAATTCAATAAATATATAACAGAACACGTGTAAGTTGATAAACTCATTGTAACTTATAG
1 ACAAATTAATTCAA-AAATATATAATAGAACACGTGTAAGTCGATAAACTCGTTACAACTTATA-
* * *
1950581 AAATTATTAATGTATA-AGTT-ATCAATTATTAGAAA-C
64 AAATCATAAATGTATACA-TTGA-CAATTATAAGAAATC
* * * * * *
1950617 GACAAATTGATTCAAAAATACATAATAAAACACGTGTAAGTCGATAAACTCATTACATCTTA-CA
1 -ACAAATTAATTCAAAAATATATAATAGAACACGTGTAAGTCGATAAACTCGTTACAACTTATAA
* * * *
1950681 AATCATAAATATTTACATTGACAAGTAAAAGAAAT-
65 AATCATAAATGTATACATTGACAATTATAAGAAATC
* * * *
1950716 ACAAATTAATTTAGAAAATATATAATAGAACAAGTATAAGTCGATAAACTCGTCACAACTTATAG
1 ACAAATTAATTCA-AAAATATATAATAGAACACGTGTAAGTCGATAAACTCGTTACAACTTATA-
* * * *
1950781 AAATC-TAAATGTGTATATTTGACAATTATAATAAACC
64 AAATCATAAATGTATACA-TTGACAATTATAAGAAATC
*
1950818 ACAAATTAATTGAAAAATATATAAT
1 ACAAATTAATTCAAAAATATATAAT
1950843 GAAACACAAG
Statistics
Matches: 336, Mismatches: 76, Indels: 32
0.76 0.17 0.07
Matches are distributed among these distances:
98 11 0.03
99 65 0.19
100 12 0.04
101 161 0.48
102 86 0.26
103 1 0.00
ACGTcount: A:0.49, C:0.12, G:0.09, T:0.31
Consensus pattern (100 bp):
ACAAATTAATTCAAAAATATATAATAGAACACGTGTAAGTCGATAAACTCGTTACAACTTATAAA
ATCATAAATGTATACATTGACAATTATAAGAAATC
Found at i:1950578 original size:203 final size:201
Alignment explanation
Indices: 1950311--1950849 Score: 653
Period size: 203 Copynumber: 2.7 Consensus size: 201
1950301 AATGGAAGAG
* * * *
1950311 ATTACAAATTAATTTAGT-AATATCTAATAGAACACGCGTAAGTTAATAAACTCGTCACAACTTA
1 ATTACAAATTAATTTAATAAATATATAATAGAACACGTGTAAGTTGATAAACTCGTCACAACTTA
* *
1950375 TA-ATGATCATAAATGTATATA-TTGACAATTATAAGAAATCATAAATTAATTAAAAAATATATA
66 TAGA-AATCATAAATGTATATAGTTGACAATTATAAGAAA-CACAAATTAATTAAAAAATATATA
* *
1950438 ATGAAACACGTGTAAATCAATAAACTCGTTACGTCTTACTAAAATCATAAATATTTACATTCACA
129 ATGAAACACGTGTAAATCAATAAACTCATTACATCTTAC--AAATCATAAATATTTACATTCACA
1950503 AGCAAAAAAA
192 AGCAAAAAAA
* * * ***
1950513 ATTACAAATTAATTCAATAAATATATAACAGAACACGTGTAAGTTGATAAACTCATTGTAACTTA
1 ATTACAAATTAATTTAATAAATATATAATAGAACACGTGTAAGTTGATAAACTCGTCACAACTTA
* * * * * *
1950578 TAGAAATTATTAATGTATA-AGTT-ATCAATTATTAGAAACGACAAATTGATTCAAAAATACATA
66 TAGAAATCATAAATGTATATAGTTGA-CAATTATAAGAAAC-ACAAATTAATTAAAAAATATATA
* * * *
1950641 ATAAAACACGTGTAAGTCGATAAACTCATTACATCTTACAAATCATAAATATTTACATTGACAAG
129 ATGAAACACGTGTAAATCAATAAACTCATTACATCTTACAAATCATAAATATTTACATTCACAAG
* *
1950706 TAAAAGAA
194 CAAAAAAA
* * *
1950714 A-TACAAATTAATTTAGA-AAATATATAATAGAACAAGTATAAGTCGATAAACTCGTCACAACTT
1 ATTACAAATTAATTTA-ATAAATATATAATAGAACACGTGTAAGTTGATAAACTCGTCACAACTT
* * * *
1950777 ATAGAAATC-TAAATGTGTATATTTGACAATTATAATAAACCACAAATTAATTGAAAAATATATA
65 ATAGAAATCATAAATGTATATAGTTGACAATTATAAGAAA-CACAAATTAATTAAAAAATATATA
1950841 ATGAAACAC
129 ATGAAACAC
1950850 AAGTAATAAA
Statistics
Matches: 283, Mismatches: 45, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
199 8 0.03
200 101 0.36
201 35 0.12
202 19 0.07
203 119 0.42
204 1 0.00
ACGTcount: A:0.49, C:0.12, G:0.09, T:0.30
Consensus pattern (201 bp):
ATTACAAATTAATTTAATAAATATATAATAGAACACGTGTAAGTTGATAAACTCGTCACAACTTA
TAGAAATCATAAATGTATATAGTTGACAATTATAAGAAACACAAATTAATTAAAAAATATATAAT
GAAACACGTGTAAATCAATAAACTCATTACATCTTACAAATCATAAATATTTACATTCACAAGCA
AAAAAA
Found at i:1952122 original size:5 final size:6
Alignment explanation
Indices: 1952111--1952139 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1952101 TTTATTCATA
1952111 TTTTTG -TTTTG TTTTTG TTTTTG TTTTTG
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
1952140 ATTTCTTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (6 bp):
TTTTTG
Found at i:1953422 original size:2 final size:2
Alignment explanation
Indices: 1953415--1953445 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1953405 ATAGGAAATA
1953415 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1953446 AAATTTTGTC
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1954059 original size:9 final size:9
Alignment explanation
Indices: 1954029--1954062 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
1954019 CTGAACTGAA
1954029 AAGCAATGT
1 AAGCAATGT
*
1954038 AAGGAAT-T
1 AAGCAATGT
1954046 AAGCAATGT
1 AAGCAATGT
1954055 AAGCAATG
1 AAGCAATG
1954063 AAGAGAGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.47, C:0.09, G:0.24, T:0.21
Consensus pattern (9 bp):
AAGCAATGT
Found at i:1954439 original size:20 final size:21
Alignment explanation
Indices: 1954414--1954453 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1954404 AAGATAATTA
1954414 ATTTTTT-AAAATAATTTTTT
1 ATTTTTTAAAAATAATTTTTT
1954434 ATTTTTTAAAAATAATTTTT
1 ATTTTTTAAAAATAATTTTT
1954454 GATAGTAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTTTTAAAAATAATTTTTT
Found at i:1954634 original size:12 final size:12
Alignment explanation
Indices: 1954617--1954647 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
1954607 TTATAAATTT
1954617 TCAAAAATTAAA
1 TCAAAAATTAAA
1954629 TC-AAAATTAAA
1 TCAAAAATTAAA
1954640 TCAAAAAT
1 TCAAAAAT
1954648 CATATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.26
Consensus pattern (12 bp):
TCAAAAATTAAA
Found at i:1969821 original size:21 final size:21
Alignment explanation
Indices: 1969797--1969878 Score: 77
Period size: 21 Copynumber: 4.0 Consensus size: 21
1969787 TATATTAATA
*
1969797 AATATTATTTATATAAATTTT
1 AATATTATTTATATATATTTT
1969818 AATA-TATTT-T-TATATTTT
1 AATATTATTTATATATATTTT
1969836 --TATTATTTTATATTATATTTT
1 AATATTA-TTTATA-TATATTTT
1969857 AATTATT-TTTATATCATATTTT
1 AA-TATTATTTATAT-ATATTTT
1969879 TATGTAATTT
Statistics
Matches: 51, Mismatches: 1, Indels: 17
0.74 0.01 0.25
Matches are distributed among these distances:
16 2 0.04
17 2 0.04
18 10 0.20
19 2 0.04
20 5 0.10
21 13 0.25
22 13 0.25
24 4 0.08
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (21 bp):
AATATTATTTATATATATTTT
Found at i:1969826 original size:10 final size:10
Alignment explanation
Indices: 1969780--1969870 Score: 57
Period size: 10 Copynumber: 9.0 Consensus size: 10
1969770 TATTATATAA
1969780 ATTTTAATAT
1 ATTTTAATAT
*
1969790 ATTAATAA-AT
1 ATT-TTAATAT
*
1969800 ATTATTTATATAA
1 A-T-TTTA-ATAT
1969813 ATTTTAATAT
1 ATTTTAATAT
1969823 ATTTT--TAT
1 ATTTTAATAT
*
1969831 ATTTTTAT-T
1 ATTTTAATAT
1969840 ATTTTATATTAT
1 ATTTTA-A-TAT
1969852 ATTTTAAT-T
1 ATTTTAATAT
*
1969861 ATTTTTATAT
1 ATTTTAATAT
1969871 CATATTTTTA
Statistics
Matches: 64, Mismatches: 6, Indels: 22
0.70 0.07 0.24
Matches are distributed among these distances:
8 8 0.12
9 14 0.22
10 18 0.28
11 12 0.19
12 10 0.16
13 2 0.03
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
ATTTTAATAT
Found at i:1969833 original size:8 final size:9
Alignment explanation
Indices: 1969799--1969868 Score: 61
Period size: 10 Copynumber: 7.3 Consensus size: 9
1969789 TATTAATAAA
*
1969799 TATTATTTA
1 TATTATTTT
*
1969808 TATAAATTTT
1 TAT-TATTTT
*
1969818 AATATATTTT
1 TAT-TATTTT
1969828 TA-TATTTT
1 TATTATTTT
1969836 TATTATTTT
1 TATTATTTT
1969845 ATATTATATTT
1 -TATTAT-TTT
1969856 TAATTATTTT
1 T-ATTATTTT
1969866 TAT
1 TAT
1969869 ATCATATTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
8 8 0.16
9 11 0.22
10 24 0.47
11 8 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TATTATTTT
Found at i:1969845 original size:27 final size:30
Alignment explanation
Indices: 1969813--1969868 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
1969803 ATTTATATAA
*
1969813 ATTTTA-A-TATATTTTTA-TATTTTTATT
1 ATTTTATATTATATTTTAATTATTTTTATT
1969840 ATTTTATATTATATTTTAATTATTTTTAT
1 ATTTTATATTATATTTTAATTATTTTTAT
1969869 ATCATATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 6 0.24
28 1 0.04
29 9 0.36
30 9 0.36
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (30 bp):
ATTTTATATTATATTTTAATTATTTTTATT
Found at i:1969864 original size:38 final size:37
Alignment explanation
Indices: 1969799--1969870 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 37
1969789 TATTAATAAA
1969799 TATTATTTATATAAATTTTAATATATTTTTATATTTT
1 TATTATTTATATAAATTTTAATATATTTTTATATTTT
*
1969836 TATTATTTTATATTATATTTTAAT-TATTTTTATAT
1 TATTA-TTTATA-TAAATTTTAATATATTTTTATAT
1969871 CATATTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
37 5 0.16
38 17 0.53
39 10 0.31
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (37 bp):
TATTATTTATATAAATTTTAATATATTTTTATATTTT
Found at i:1969875 original size:22 final size:21
Alignment explanation
Indices: 1969800--1969878 Score: 80
Period size: 22 Copynumber: 4.0 Consensus size: 21
1969790 ATTAATAAAT
*
1969800 ATTA-TTTATAT-AAATTTTA
1 ATTATTTTATATCATATTTTA
1969819 ATATATTTT-TAT-AT-TTTT-
1 AT-TATTTTATATCATATTTTA
*
1969837 ATTATTTTATATTATATTTTA
1 ATTATTTTATATCATATTTTA
1969858 ATTATTTTTATATCATATTTT
1 ATTA-TTTTATATCATATTTT
1969879 TATGTAATTT
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
17 6 0.12
18 5 0.10
19 8 0.16
20 10 0.20
21 7 0.14
22 15 0.29
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (21 bp):
ATTATTTTATATCATATTTTA
Found at i:1969878 original size:13 final size:12
Alignment explanation
Indices: 1969798--1969881 Score: 52
Period size: 13 Copynumber: 6.8 Consensus size: 12
1969788 ATATTAATAA
1969798 ATATTATTTATAT
1 ATATT-TTTATAT
*
1969811 A-AATTTTA-AT
1 ATATTTTTATAT
1969821 ATATTTTTATATTT
1 ATATTTTTATA--T
*
1969835 TTATTATTT-TAT
1 ATATT-TTTATAT
1969847 ATTATATTTTA-AT
1 A-TAT-TTTTATAT
1969860 -TATTTTTATAT
1 ATATTTTTATAT
1969871 CATATTTTTAT
1 -ATATTTTTAT
1969882 GTAATTTGAT
Statistics
Matches: 56, Mismatches: 4, Indels: 22
0.68 0.05 0.27
Matches are distributed among these distances:
10 8 0.14
11 15 0.27
12 4 0.07
13 18 0.32
14 8 0.14
15 3 0.05
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (12 bp):
ATATTTTTATAT
Found at i:1970251 original size:25 final size:23
Alignment explanation
Indices: 1970230--1970285 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
1970220 TATATAATAC
*
1970230 AAATTATATAATATATAAATAAA
1 AAATAATATAATATATAAATAAA
* *
1970253 AAATAATATATTATATAATTAAA
1 AAATAATATAATATATAAATAAA
*
1970276 AATTAA-ATAA
1 AAATAATATAA
1970286 AACCTTAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 3 0.11
23 25 0.89
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
AAATAATATAATATATAAATAAA
Found at i:1970256 original size:23 final size:22
Alignment explanation
Indices: 1970220--1970285 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
1970210 ATTTATTATT
*
1970220 TATATAAT-ACAAATTATATAA
1 TATATAATAAAAAATTATATAA
* *
1970241 TATATAAATAAAAAATAATATAT
1 TATAT-AATAAAAAATTATATAA
* *
1970264 TATATAATTAAAAATTAAATAA
1 TATATAATAAAAAATTATATAA
1970286 AACCTTAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
21 5 0.14
22 16 0.44
23 15 0.42
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
TATATAATAAAAAATTATATAA
Found at i:1970340 original size:18 final size:17
Alignment explanation
Indices: 1970319--1970361 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
1970309 TCTAATTCGA
1970319 TTTTAAAATAAATCTTAT
1 TTTTAAAATAAAT-TTAT
**
1970337 TTTTAATTTAAATTTAT
1 TTTTAAAATAAATTTAT
1970354 TTTTAAAA
1 TTTTAAAA
1970362 ATCTTTTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTAAAATAAATTTAT
Found at i:1971516 original size:2 final size:2
Alignment explanation
Indices: 1971511--1971547 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1971501 AAAAACACCC
*
1971511 AT AT AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1971548 GACACACACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1973796 original size:23 final size:22
Alignment explanation
Indices: 1973764--1973831 Score: 81
Period size: 19 Copynumber: 3.2 Consensus size: 22
1973754 TATTATTTAA
* *
1973764 ATAAAAATATTTAAAT-TTAATT
1 ATAAAAA-ATATAAATATTAACT
1973786 ATAAAAAATATAAATATTAACT
1 ATAAAAAATATAAATATTAACT
1973808 AT--AAAA-ATAAATATTAACT
1 ATAAAAAATATAAATATTAACT
1973827 ATAAA
1 ATAAA
1973832 TCAAGTTTGG
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
19 15 0.37
20 4 0.10
21 8 0.20
22 14 0.34
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (22 bp):
ATAAAAAATATAAATATTAACT
Found at i:1974775 original size:23 final size:22
Alignment explanation
Indices: 1974749--1974792 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
1974739 AGATGGTAAA
1974749 AAAAATTAA-ACAAAGAAAATATC
1 AAAAATTAATA-AAA-AAAATATC
1974772 AAAAATTAATAAAAAAAATAT
1 AAAAATTAATAAAAAAAATAT
1974793 GAAAGATACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 7 0.35
23 12 0.60
24 1 0.05
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (22 bp):
AAAAATTAATAAAAAAAATATC
Found at i:1974948 original size:2 final size:2
Alignment explanation
Indices: 1974936--1974994 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
1974926 TCTCAAATCT
*
1974936 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1974978 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
1974995 GAACTTGATC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1977627 original size:21 final size:19
Alignment explanation
Indices: 1977603--1977641 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
1977593 TTTAATTTTT
*
1977603 ATTTTATAAATGAAGATTTAA
1 ATTTCATAAAT-AA-ATTTAA
1977624 ATTTCATAAATAAATTTA
1 ATTTCATAAATAAATTTA
1977642 TAAGGTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.44
Consensus pattern (19 bp):
ATTTCATAAATAAATTTAA
Found at i:1978391 original size:4 final size:4
Alignment explanation
Indices: 1978382--1978422 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
1978372 CACCAAAAAC
1978382 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
1978423 AAGTGGCTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:1981930 original size:18 final size:18
Alignment explanation
Indices: 1981863--1981918 Score: 50
Period size: 17 Copynumber: 3.3 Consensus size: 18
1981853 ATGATTATTT
1981863 TAAAATTTAT-AT-AATA
1 TAAAATTTATAATAAATA
**
1981879 T-AAA-TTATTAATGTAT-
1 TAAAATTTA-TAATAAATA
1981895 TAAAATTTATAATAAATA
1 TAAAATTTATAATAAATA
1981913 TAAAAT
1 TAAAAT
1981919 ATTTTAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
14 3 0.10
15 4 0.13
16 4 0.13
17 11 0.35
18 9 0.29
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
TAAAATTTATAATAAATA
Found at i:1982433 original size:21 final size:20
Alignment explanation
Indices: 1982393--1982434 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
1982383 TATTTTTATT
*
1982393 TAAATTTAATTATAAAAATA
1 TAAATTTAATTAAAAAAATA
1982413 TAAATATTAA-TAAAAATAATA
1 TAAAT-TTAATTAAAAA-AATA
1982434 T
1 T
1982435 TTTAATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAATTTAATTAAAAAAATA
Found at i:1983102 original size:27 final size:28
Alignment explanation
Indices: 1983067--1983128 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
1983057 AGATCCGTCG
* * *
1983067 ATTTAATTATTAGT-ATTATATTT-ATAT
1 ATTTTATTATTA-TAATCATATTTAAAAT
1983094 ATTTTATTATTATAATCATATTTAAAAT
1 ATTTTATTATTATAATCATATTTAAAAT
1983122 ATTTTAT
1 ATTTTAT
1983129 ATTTATATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 1 0.03
27 19 0.63
28 10 0.33
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (28 bp):
ATTTTATTATTATAATCATATTTAAAAT
Found at i:1983218 original size:22 final size:22
Alignment explanation
Indices: 1983191--1983234 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1983181 TAATGATATA
*
1983191 TTTTATATTATA-TTATAATTAT
1 TTTTATATCATATTTAT-ATTAT
1983213 TTTTATATCATATTTATATTAT
1 TTTTATATCATATTTATATTAT
1983235 ATCTAATATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTTATATCATATTTATATTAT
Found at i:1983228 original size:11 final size:11
Alignment explanation
Indices: 1983187--1983236 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
1983177 ATTTTAATGA
1983187 TATATTTTATAT
1 TATA-TTTATAT
1983199 TATA-TTATAAT
1 TATATTTAT-AT
*
1983210 TATTTTTATAT
1 TATATTTATAT
*
1983221 CATATTTATAT
1 TATATTTATAT
1983232 TATAT
1 TATAT
1983237 CTAATATCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
10 4 0.12
11 20 0.62
12 8 0.25
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1985239 original size:35 final size:36
Alignment explanation
Indices: 1985161--1985239 Score: 90
Period size: 35 Copynumber: 2.2 Consensus size: 36
1985151 ATTAAATTCA
* *
1985161 ATTAATTTAATAAAAAAATTTATTATTAAATATAATT
1 ATTAA-TTAATAAAAAAATATATTATTAAATATAATG
* *
1985198 ATTAATTAAT-AAAAAATATA-TATTTAATTTAATG
1 ATTAATTAATAAAAAAATATATTATTAAATATAATG
1985232 ATATAATT
1 AT-TAATT
1985240 TTTAATATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
34 13 0.35
35 14 0.38
36 5 0.14
37 5 0.14
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (36 bp):
ATTAATTAATAAAAAAATATATTATTAAATATAATG
Found at i:1986377 original size:2 final size:2
Alignment explanation
Indices: 1986370--1986399 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1986360 GAAAACTTTA
1986370 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1986400 GGTCTATTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1986564 original size:21 final size:21
Alignment explanation
Indices: 1986540--1986586 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
1986530 TATCTTATAC
1986540 TTTTCAAAAACATAAAAT-AT
1 TTTTCAAAAACATAAAATAAT
* * *
1986560 TTTTTAAAAATATAAATTAAT
1 TTTTCAAAAACATAAAATAAT
1986581 TTTTCA
1 TTTTCA
1986587 TTGATCAAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (21 bp):
TTTTCAAAAACATAAAATAAT
Found at i:1986866 original size:20 final size:19
Alignment explanation
Indices: 1986819--1986869 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
1986809 TCATGTTTAA
1986819 AATATTATATATTAATATT
1 AATATTATATATTAATATT
* *
1986838 AATTTTTATATGTTAATAATT
1 AA-TATTATATATTAAT-ATT
*
1986859 TATATTATATA
1 AATATTATATA
1986870 GACTTTTACA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 2 0.08
20 19 0.76
21 4 0.16
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
AATATTATATATTAATATT
Found at i:1988563 original size:15 final size:14
Alignment explanation
Indices: 1988544--1988589 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
1988534 ATAAAAAAAA
1988544 TTTAATTTTTATAT
1 TTTAATTTTTATAT
* *
1988558 TATTAAATTTAATAT
1 T-TTAATTTTTATAT
*
1988573 TTTAATTATTATAT
1 TTTAATTTTTATAT
1988587 TTT
1 TTT
1988590 TAAAATTTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTAATTTTTATAT
Found at i:1988584 original size:29 final size:31
Alignment explanation
Indices: 1988544--1988602 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
1988534 ATAAAAAAAA
*
1988544 TTTAATTTTTATATTATT-AAA-TTTAATAT
1 TTTAATTATTATATTATTAAAATTTTAATAT
*
1988573 TTTAATTATTATATTTTTAAAATTTTAATA
1 TTTAATTATTATATTATTAAAATTTTAATA
1988603 AATAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 16 0.62
30 3 0.12
31 7 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (31 bp):
TTTAATTATTATATTATTAAAATTTTAATAT
Found at i:1988592 original size:23 final size:21
Alignment explanation
Indices: 1988541--1988588 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1988531 AAAATAAAAA
1988541 AAATTTAAT-TTTTATATTATT
1 AAATTTAATATTTTA-ATTATT
1988562 AAATTTAATATTTTAATTATT
1 AAATTTAATATTTTAATTATT
*
1988583 ATATTT
1 AAATTT
1988589 TTAAAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
AAATTTAATATTTTAATTATT
Done.