Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1143
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: 169065
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Found at i:2707 original size:15 final size:16
Alignment explanation
Indices: 2689--2718 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2679 ATTTCCTTTC
2689 TTCTTTCTT-TTTATT
1 TTCTTTCTTGTTTATT
2704 TTCTTTCTTGTTTAT
1 TTCTTTCTTGTTTAT
2719 CTATCAAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.07, C:0.13, G:0.03, T:0.77
Consensus pattern (16 bp):
TTCTTTCTTGTTTATT
Found at i:11521 original size:2 final size:2
Alignment explanation
Indices: 11514--11549 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
11504 AAAATAGGAA
11514 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
11550 GAAAAAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14094 original size:2 final size:2
Alignment explanation
Indices: 14089--14118 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
14079 GCCGTTTTTC
14089 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
14119 TTGGAACTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16306 original size:22 final size:22
Alignment explanation
Indices: 16278--16335 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 22
16268 TTTTAAATTG
*
16278 AATAATATTATAAACAAT-TAAT
1 AATAATACTATAAA-AATATAAT
16300 AATAATACTAGTAAAAATATAAT
1 AATAATACTA-TAAAAATATAAT
16323 AATATATACTATA
1 AATA-ATACTATA
16336 TATACTTAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
22 12 0.38
23 14 0.44
24 6 0.19
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (22 bp):
AATAATACTATAAAAATATAAT
Found at i:18114 original size:23 final size:24
Alignment explanation
Indices: 18096--18157 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
18086 AATAAAAATT
*
18096 AGCCACTAATTTTGATAAACAACA
1 AGCCACCAATTTTGATAAACAACA
* *
18120 AGCCACCAATTTTGACAAATAAACA
1 AGCCACCAATTTTGATAAA-CAACA
*
18145 AGCCTCCATATTT
1 AGCCACCA-ATTT
18158 GACAAATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 17 0.53
25 11 0.34
26 4 0.12
ACGTcount: A:0.42, C:0.24, G:0.08, T:0.26
Consensus pattern (24 bp):
AGCCACCAATTTTGATAAACAACA
Found at i:18158 original size:25 final size:25
Alignment explanation
Indices: 18096--18165 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
18086 AATAAAAATT
* * *
18096 AGCCACTAATTTTGATAAA-CAACA
1 AGCCACCAATTTTGACAAATAAACA
18120 AGCCACCAATTTTGACAAATAAACA
1 AGCCACCAATTTTGACAAATAAACA
*
18145 AGCCTCC-ATATTTGACAAATA
1 AGCCACCAAT-TTTGACAAATA
18166 CAAAGGAAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
24 19 0.47
25 21 0.52
ACGTcount: A:0.44, C:0.23, G:0.09, T:0.24
Consensus pattern (25 bp):
AGCCACCAATTTTGACAAATAAACA
Found at i:18211 original size:27 final size:27
Alignment explanation
Indices: 18150--18220 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
18140 AAACAAGCCT
* *
18150 CCATATTTGACAAATACAAAGGAAACCA
1 CCATTTTTGACAAACACAAA-GAAACCA
18178 CCATTTTTGACAAACACAAA-ATAACCA
1 CCATTTTTGACAAACACAAAGA-AACCA
18205 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
18221 AATGGGTGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAGAAACCA
Found at i:20142 original size:21 final size:22
Alignment explanation
Indices: 20104--20149 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
20094 ATTTGTTGAA
* **
20104 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
20125 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
20147 ACT
1 ACT
20150 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:22647 original size:20 final size:20
Alignment explanation
Indices: 22602--22641 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
22592 AAGAATTGAA
22602 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAT
* *
22622 GAGGGATGCAAGAGATGGAT
1 GAGGGATACAAGAGAGGGAT
22642 TTGGGAGCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.45, T:0.12
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAT
Found at i:22756 original size:25 final size:25
Alignment explanation
Indices: 22694--22763 Score: 90
Period size: 25 Copynumber: 2.8 Consensus size: 25
22684 AATAAAAATT
* *
22694 AGCCACTAATTTTGACAAA-CAACA
1 AGCCACCAATTTTGACAAATAAACA
22718 AGCCACCAATTTTGACAAATAAACA
1 AGCCACCAATTTTGACAAATAAACA
*
22743 AGCCTCC-ATATTTGACAAATA
1 AGCCACCAAT-TTTGACAAATA
22764 CAAAGGAAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
24 20 0.49
25 21 0.51
ACGTcount: A:0.44, C:0.24, G:0.09, T:0.23
Consensus pattern (25 bp):
AGCCACCAATTTTGACAAATAAACA
Found at i:22809 original size:27 final size:27
Alignment explanation
Indices: 22748--22818 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
22738 AAACAAGCCT
* *
22748 CCATATTTGACAAATACAAAGGAAACCA
1 CCATTTTTGACAAACACAAA-GAAACCA
22776 CCATTTTTGACAAACACAAA-ATAACCA
1 CCATTTTTGACAAACACAAAGA-AACCA
22803 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
22819 AATGGGTGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAGAAACCA
Found at i:26193 original size:27 final size:27
Alignment explanation
Indices: 26163--26214 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
26153 TATACATCTA
*
26163 AAGTTATG-TTACCAAGTGGTAAAATAG
1 AAGTT-TGCTTACCAAGTGGAAAAATAG
26190 AAGTTTGCTTACCAAGTGGAAAAAT
1 AAGTTTGCTTACCAAGTGGAAAAAT
26215 TACAAGATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (27 bp):
AAGTTTGCTTACCAAGTGGAAAAATAG
Found at i:31381 original size:13 final size:13
Alignment explanation
Indices: 31363--31394 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
31353 TAGTTTTTAG
31363 AAAATGAAAACAA
1 AAAATGAAAACAA
*
31376 AAAATGAAAATAA
1 AAAATGAAAACAA
31389 AAAATG
1 AAAATG
31395 TTTTTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.75, C:0.03, G:0.09, T:0.12
Consensus pattern (13 bp):
AAAATGAAAACAA
Found at i:33340 original size:24 final size:24
Alignment explanation
Indices: 33312--33381 Score: 113
Period size: 24 Copynumber: 2.9 Consensus size: 24
33302 AATAAAAATT
*
33312 AGCCACAAATTTTAACAAACAACA
1 AGCCACAAATTTTGACAAACAACA
33336 AGCCACAAATTTTGACAAACAACA
1 AGCCACAAATTTTGACAAACAACA
* *
33360 AGCCACCATTTTTGACAAACAA
1 AGCCACAAATTTTGACAAACAA
33382 AAAAGAACTA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.49, C:0.26, G:0.07, T:0.19
Consensus pattern (24 bp):
AGCCACAAATTTTGACAAACAACA
Found at i:33439 original size:27 final size:27
Alignment explanation
Indices: 33345--33440 Score: 126
Period size: 27 Copynumber: 3.7 Consensus size: 27
33335 AAGCCACAAA
*
33345 TTTTGACAAACAACAA-G--CCACCAT
1 TTTTGACAAACAAAAAGGAACCACCAT
* *
33369 TTTTGACAAACAAAAAAGAACTACCAT
1 TTTTGACAAACAAAAAGGAACCACCAT
*
33396 TTTTGACAAACACAAAGGAACCACCAT
1 TTTTGACAAACAAAAAGGAACCACCAT
*
33423 TTTTGACAAACATAAAGG
1 TTTTGACAAACAAAAAGG
33441 GTGACTTTTG
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.24
25 1 0.02
27 47 0.75
ACGTcount: A:0.46, C:0.22, G:0.10, T:0.22
Consensus pattern (27 bp):
TTTTGACAAACAAAAAGGAACCACCAT
Found at i:37915 original size:23 final size:25
Alignment explanation
Indices: 37881--37926 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
37871 AATAAAAATT
37881 AGCCACCAATTTT-GACAAACAACA
1 AGCCACCAATTTTGGACAAACAACA
37905 AGCCA-CAATTTTGGACAAACAA
1 AGCCACCAATTTTGGACAAACAA
37927 AAAAGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.46, C:0.26, G:0.11, T:0.17
Consensus pattern (25 bp):
AGCCACCAATTTTGGACAAACAACA
Found at i:37980 original size:27 final size:28
Alignment explanation
Indices: 37883--37984 Score: 99
Period size: 27 Copynumber: 3.9 Consensus size: 28
37873 TAAAAATTAG
* *
37883 CCACCAATTTTGACAAACA-ACA-AG--
1 CCACCATTTTTGACAAACACAAAGAGAA
* * *
37907 CCACAATTTTGGACAAACA-AAAAAGAA
1 CCACCATTTTTGACAAACACAAAGAGAA
*
37934 CCACCGTTTTTGACAAACACAAAGA-AA
1 CCACCATTTTTGACAAACACAAAGAGAA
*
37961 CTACCATTTTTGACAAACACAAAG
1 CCACCATTTTTGACAAACACAAAG
37985 GGTGGCTTTT
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
24 18 0.28
25 2 0.03
27 40 0.62
28 4 0.06
ACGTcount: A:0.47, C:0.25, G:0.10, T:0.19
Consensus pattern (28 bp):
CCACCATTTTTGACAAACACAAAGAGAA
Found at i:38570 original size:27 final size:26
Alignment explanation
Indices: 38530--38602 Score: 101
Period size: 27 Copynumber: 2.8 Consensus size: 26
38520 AAAAACCATC
* *
38530 CTTTGTGTTTGTCAAAAATGGTATTT
1 CTTTTTGTTTGTCAAAAATGGTAGTT
38556 CTTTTTTGTTTGTCAAAAATGGTAGTT
1 C-TTTTTGTTTGTCAAAAATGGTAGTT
* *
38583 CTTTTTGTTTATAAAAAATG
1 CTTTTTGTTTGTCAAAAATG
38603 ATGGCTTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 18 0.43
27 24 0.57
ACGTcount: A:0.26, C:0.07, G:0.16, T:0.51
Consensus pattern (26 bp):
CTTTTTGTTTGTCAAAAATGGTAGTT
Found at i:40262 original size:22 final size:22
Alignment explanation
Indices: 40210--40266 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
40200 ATGAAAATGT
* *
40210 TTGATAAAAAAGAGGGGAGGAG
1 TTGAAAAAAAAAAGGGGAGGAG
* *
40232 TCGAGAAAAAAAAGGGGA-GAGG
1 TTGAAAAAAAAAAGGGGAGGA-G
40254 TTGAAAAAAAAAA
1 TTGAAAAAAAAAA
40267 TCAAATCAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 2 0.07
22 27 0.93
ACGTcount: A:0.54, C:0.02, G:0.33, T:0.11
Consensus pattern (22 bp):
TTGAAAAAAAAAAGGGGAGGAG
Found at i:43887 original size:33 final size:33
Alignment explanation
Indices: 43850--43920 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
43840 AAAAAAAGAA
43850 AAAAAAACTAATGAA-ATTGTTGCTTATAAATAT
1 AAAAAAACTAAT-AACATTGTTGCTTATAAATAT
* * * *
43883 AAAAATACTAATAACTTTTTTTCTTATAAATAT
1 AAAAAAACTAATAACATTGTTGCTTATAAATAT
43916 AAAAA
1 AAAAA
43921 TATCCCTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 2 0.06
33 31 0.94
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (33 bp):
AAAAAAACTAATAACATTGTTGCTTATAAATAT
Found at i:44213 original size:21 final size:21
Alignment explanation
Indices: 44180--44221 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
44170 TTTCTACTAA
*
44180 TTTTATTTCTATTATTGTAAT
1 TTTTATTTCTATTATTATAAT
44201 TTTTAATTT-TATTATTATAAT
1 TTTT-ATTTCTATTATTATAAT
44222 AATTAATCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTATTTCTATTATTATAAT
Found at i:44227 original size:21 final size:21
Alignment explanation
Indices: 44184--44239 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
44174 TACTAATTTT
* **
44184 ATTTCTATTATTGTAATTTTTA
1 ATTT-TATTATTATAATAATTA
44206 ATTTTATTATTATAATAATTA
1 ATTTTATTATTATAATAATTA
* *
44227 ATCTTACTATTAT
1 ATTTTATTATTAT
44240 TATTGTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 25 0.86
22 4 0.14
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (21 bp):
ATTTTATTATTATAATAATTA
Found at i:46770 original size:28 final size:27
Alignment explanation
Indices: 46715--46780 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 27
46705 GCCATCCATT
46715 TGTTTGTCAAAAATAGTGGTTATTTTG
1 TGTTTGTCAAAAATAGTGGTTATTTTG
46742 TGTTTGTCAAAAAT-GATGGTT-TCCTTTG
1 TGTTTGTCAAAAATAG-TGGTTAT--TTTG
*
46770 TATTTGTCAAA
1 TGTTTGTCAAA
46781 TATGGAGGCT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
26 2 0.06
27 19 0.54
28 14 0.40
ACGTcount: A:0.26, C:0.08, G:0.20, T:0.47
Consensus pattern (27 bp):
TGTTTGTCAAAAATAGTGGTTATTTTG
Found at i:49385 original size:21 final size:22
Alignment explanation
Indices: 49356--49401 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
49346 TGTTCAGACA
** *
49356 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
49378 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
49399 AGT
1 AGT
49402 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:51320 original size:27 final size:27
Alignment explanation
Indices: 51286--51356 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
51276 GCCATCCATT
51286 TGTTTGTCAAAAATGGTGGTTAT-TTTG
1 TGTTTGTCAAAAATGGTGGTT-TCTTTG
*
51313 TGTTTGTCAAAAATGATGGTTTCCTTTG
1 TGTTTGTCAAAAATGGTGGTTT-CTTTG
* *
51341 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
51357 AGGCTTGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.53
28 17 0.45
ACGTcount: A:0.24, C:0.07, G:0.23, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTTCTTTG
Found at i:52551 original size:34 final size:33
Alignment explanation
Indices: 52507--52623 Score: 180
Period size: 34 Copynumber: 3.5 Consensus size: 33
52497 GTAAAAACCA
52507 CCATTTAATCAACAATGGTAAGCTACCAAATCT
1 CCATTTAATCAACAATGGTAAGCTACCAAATCT
*
52540 CTCATTTAATCAACAATGGTAAGCTACCAAATTT
1 C-CATTTAATCAACAATGGTAAGCTACCAAATCT
* * *
52574 CCCATTTAGTCAACAATGGTAAACTACCAAATCA
1 -CCATTTAATCAACAATGGTAAGCTACCAAATCT
52608 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
52624 TCTCCCACTT
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
33 16 0.21
34 59 0.78
35 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (33 bp):
CCATTTAATCAACAATGGTAAGCTACCAAATCT
Found at i:56716 original size:19 final size:19
Alignment explanation
Indices: 56689--56751 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
56679 TCACGTGTAC
* *
56689 AGTAACCGTATACTTAAAT
1 AGTACCCGTATACGTAAAT
56708 AGTACCCGTATACGTAAAT
1 AGTACCCGTATACGTAAAT
** *
56727 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTAAAT
56746 AGTACC
1 AGTACC
56752 TCGACAACCA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTAAAT
Found at i:57101 original size:34 final size:34
Alignment explanation
Indices: 57058--57240 Score: 307
Period size: 34 Copynumber: 5.4 Consensus size: 34
57048 GTAAAAACCA
57058 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
57092 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
*
57126 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
*
57160 TCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
* *
57194 CCATTTAGTCAACAATGGTAAACTACCAAA--TC
1 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
57226 ACCATTTAATCAACA
1 -CCATTTAATCAACA
57241 CAATGCCCAA
Statistics
Matches: 141, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
32 2 0.01
33 13 0.09
34 126 0.89
ACGTcount: A:0.39, C:0.24, G:0.08, T:0.28
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAAGCTACCAAATTTC
Found at i:58508 original size:26 final size:29
Alignment explanation
Indices: 58461--58514 Score: 78
Period size: 26 Copynumber: 1.9 Consensus size: 29
58451 AAAATAAAAA
58461 GTCAAATAAATTTTAACTTTTTCATTTTTT
1 GTCAAATAAATTTTAAC-TTTTCATTTTTT
58491 GTCAAATAAA-TTT-A-TTTTCATTTT
1 GTCAAATAAATTTTAACTTTTCATTTT
58515 GAGGTTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 10 0.42
28 1 0.04
29 3 0.12
30 10 0.42
ACGTcount: A:0.31, C:0.09, G:0.04, T:0.56
Consensus pattern (29 bp):
GTCAAATAAATTTTAACTTTTCATTTTTT
Found at i:60789 original size:23 final size:22
Alignment explanation
Indices: 60752--60805 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 22
60742 TTCAAATTTG
60752 ATTTAAATAAAAAAAATTAAAT
1 ATTTAAATAAAAAAAATTAAAT
*
60774 ATTTAAACTAAAAAAATTTAAAT
1 ATTTAAA-TAAAAAAAATTAAAT
*
60797 -TCTAAATAA
1 ATTTAAATAA
60806 TTAAAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 3 0.10
22 12 0.41
23 14 0.48
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (22 bp):
ATTTAAATAAAAAAAATTAAAT
Found at i:62049 original size:79 final size:79
Alignment explanation
Indices: 61966--62117 Score: 214
Period size: 79 Copynumber: 1.9 Consensus size: 79
61956 GTCAGCCCTA
* * * *
61966 TTGTCCAATCAATGCCACATCATCCAACCATCATCTGCCATGTGTCACCTATTATCACGCCATCA
1 TTGTCCAATCAATGCCACATCATCCAACCATCATCTACCACGTGTCACCTATTACCACACCATCA
62031 CCTAGTCAACTTTG
66 CCTAGTCAACTTTG
** ** * *
62045 TTGTCCAATCAATGCCATGTCATCCAATGATCATCTACCACGTGTCACCTATTGCCACATCATCA
1 TTGTCCAATCAATGCCACATCATCCAACCATCATCTACCACGTGTCACCTATTACCACACCATCA
62110 CCTAGTCA
66 CCTAGTCA
62118 TCATATTTTT
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
79 63 1.00
ACGTcount: A:0.27, C:0.34, G:0.11, T:0.29
Consensus pattern (79 bp):
TTGTCCAATCAATGCCACATCATCCAACCATCATCTACCACGTGTCACCTATTACCACACCATCA
CCTAGTCAACTTTG
Found at i:66391 original size:16 final size:16
Alignment explanation
Indices: 66370--66423 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
66360 TTAATAATAA
*
66370 ATTTTTGAAATCACAG
1 ATTTTTAAAATCACAG
* *
66386 ATTTTTAAGAATTATAG
1 ATTTTTAA-AATCACAG
**
66403 ATTTTTTTAATCACAG
1 ATTTTTAAAATCACAG
66419 ATTTT
1 ATTTT
66424 CAACTCCAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
16 18 0.60
17 12 0.40
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.48
Consensus pattern (16 bp):
ATTTTTAAAATCACAG
Found at i:69029 original size:23 final size:21
Alignment explanation
Indices: 68997--69053 Score: 78
Period size: 23 Copynumber: 2.6 Consensus size: 21
68987 TAGTTTAAAG
68997 TTATTTTATTTTAAAATATAAT
1 TTATTTTATTTTAAAAT-TAAT
69019 TTATTTTTATTTATAAAATTAAT
1 TTA-TTTTATTT-TAAAATTAAT
*
69042 TTAATTTATTTT
1 TTATTTTATTTT
69054 TTATTTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
21 1 0.03
22 10 0.31
23 15 0.47
24 6 0.19
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTATTTTATTTTAAAATTAAT
Found at i:71687 original size:14 final size:15
Alignment explanation
Indices: 71663--71691 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
71653 AAAAATTAAA
71663 AAATCTTTTTTATTT
1 AAATCTTTTTTATTT
71678 AAAT-TTTTTTATTT
1 AAATCTTTTTTATTT
71692 TTTTAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (15 bp):
AAATCTTTTTTATTT
Found at i:71769 original size:26 final size:29
Alignment explanation
Indices: 71747--71804 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
71737 TTTTTAAACT
71747 TAATTAA-ATATTA-TATTTATTAAAAAATAA
1 TAATTAATATATTATTATTTATT--AAAAT-A
71777 TAATTAATATATTATTATTTATTAAAAT
1 TAATTAATATATTATTATTTATTAAAAT
71805 TTTAAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 12 0.46
31 6 0.23
32 8 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
TAATTAATATATTATTATTTATTAAAATA
Found at i:71782 original size:122 final size:121
Alignment explanation
Indices: 71547--71783 Score: 354
Period size: 122 Copynumber: 2.0 Consensus size: 121
71537 CCCTTTTTAA
*
71547 TTTTTTAATTTAAAATTTTTTATTTTTAAAAAATATAATAATTAATATTTTAATTTGTTAATGTA
1 TTTTTTAATTTAAAATTTTTTATTTTTAAAAAATATAATAATTAATATTTTAATTTATTAATGTA
* * **
71612 AATATTTTAAACTTAATTAAATATTATTTTTTATTTTATTAAAAAATTAAAAAATC
66 AATATTTTAAACTTAATTAAATATTATTATTTATTTAAAAAAAAAATTAAAAAATC
*
71668 TTTTTT-ATTTAAATTTTTTTATTTTTTTAAAAAATATAATAATTAATATTTTAATTTATTAATG
1 TTTTTTAATTTAAAATTTTTTA--TTTTTAAAAAATATAATAATTAATATTTTAATTTATTAATG
*
71732 TAAATTTTTTAAACTTAATTAAATATTA-TATTTA-TTAAAAAATAATAATTAA
64 TAAATATTTTAAACTTAATTAAATATTATTATTTATTTAAAAAA-AA-AATTAA
71784 TATATTATTA
Statistics
Matches: 105, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
120 19 0.18
121 13 0.12
122 73 0.70
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (121 bp):
TTTTTTAATTTAAAATTTTTTATTTTTAAAAAATATAATAATTAATATTTTAATTTATTAATGTA
AATATTTTAAACTTAATTAAATATTATTATTTATTTAAAAAAAAAATTAAAAAATC
Found at i:72006 original size:2 final size:2
Alignment explanation
Indices: 72001--72027 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
71991 TCAGAGATAC
72001 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 T
72028 GTATGAGAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:73227 original size:24 final size:24
Alignment explanation
Indices: 73191--73237 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
73181 AATTTAGCTT
73191 ATCAGCATCAGCTCATATGATCTC
1 ATCAGCATCAGCTCATATGATCTC
* * *
73215 ATCAGCATTAGCTGATCTGATCT
1 ATCAGCATCAGCTCATATGATCT
73238 GATCCGATGT
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:0.28, C:0.26, G:0.15, T:0.32
Consensus pattern (24 bp):
ATCAGCATCAGCTCATATGATCTC
Found at i:73994 original size:21 final size:21
Alignment explanation
Indices: 73969--74009 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
73959 ATTTAAAATT
73969 ATTAAATATTAA-ACTTTAATC
1 ATTAAA-ATTAAGACTTTAATC
*
73990 ATTAAAATTAAGAGTTTAAT
1 ATTAAAATTAAGACTTTAAT
74010 GCTTTCGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (21 bp):
ATTAAAATTAAGACTTTAATC
Found at i:74708 original size:21 final size:22
Alignment explanation
Indices: 74678--74723 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
74668 AACATAAACA
* *
74678 AGAAAAAAAATAGAAAG-AAAT
1 AGAAAAAAAAAAAAAAGAAAAT
*
74699 AGAAAGAAAAAAAAAAGAAAAT
1 AGAAAAAAAAAAAAAAGAAAAT
74721 AGA
1 AGA
74724 GAACTTGATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (22 bp):
AGAAAAAAAAAAAAAAGAAAAT
Found at i:77028 original size:19 final size:19
Alignment explanation
Indices: 77004--77041 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
76994 CTACTCTTTT
77004 GTCTAACATACTACATTAC
1 GTCTAACATACTACATTAC
77023 GTCTAACATACTACATTAC
1 GTCTAACATACTACATTAC
77042 TATTTAGGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.26, G:0.05, T:0.32
Consensus pattern (19 bp):
GTCTAACATACTACATTAC
Found at i:78790 original size:13 final size:13
Alignment explanation
Indices: 78772--78798 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
78762 AGAGTTATTT
78772 TCAATTGGGACAA
1 TCAATTGGGACAA
78785 TCAATTGGGACAA
1 TCAATTGGGACAA
78798 T
1 T
78799 TAATATGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (13 bp):
TCAATTGGGACAA
Found at i:79029 original size:129 final size:129
Alignment explanation
Indices: 78799--79057 Score: 419
Period size: 129 Copynumber: 2.0 Consensus size: 129
78789 TTGGGACAAT
* * *
78799 TAATATGAAAGATACTTTCATGGTTGTAATTAAAGTCAATGTAATCTTCGATAAGGATATAAGCG
1 TAATATGAAAGATAATTTCATGGTTGTAATTAAAGTCAAGGTAATCTTCGATAAGGATATAAGCA
*
78864 CGTCAATTAATCATGACAGTAGCAATTTTCATCTTAGGAAACTATAATGGGACAAAATTTTCAA
66 CGTCAATTAATCATGACAGTAGCAATTTCCATCTTAGGAAACTATAATGGGACAAAATTTTCAA
* * * *
78928 TAATATGAAGGATAATTTTATGGTTGTAATTAAAGTTAAGGTAATCTTTGATAAGGATATAAGCA
1 TAATATGAAAGATAATTTCATGGTTGTAATTAAAGTCAAGGTAATCTTCGATAAGGATATAAGCA
* **
78993 CGTCAATTAATCATGACAGTAGCAATTTCCATCTTAGGAGACTATAATGGGGTAAAATTTTCAA
66 CGTCAATTAATCATGACAGTAGCAATTTCCATCTTAGGAAACTATAATGGGACAAAATTTTCAA
79057 T
1 T
79058 TTTAACTAGT
Statistics
Matches: 119, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
129 119 1.00
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (129 bp):
TAATATGAAAGATAATTTCATGGTTGTAATTAAAGTCAAGGTAATCTTCGATAAGGATATAAGCA
CGTCAATTAATCATGACAGTAGCAATTTCCATCTTAGGAAACTATAATGGGACAAAATTTTCAA
Found at i:79544 original size:2 final size:2
Alignment explanation
Indices: 79446--79531 Score: 172
Period size: 2 Copynumber: 43.0 Consensus size: 2
79436 TGTATTTGTC
79446 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
79488 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
79530 TA
1 TA
79532 CACACACATA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 84 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:79823 original size:14 final size:15
Alignment explanation
Indices: 79804--79833 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
79794 GGACATAAAC
79804 AAGAAAAA-AAAAGA
1 AAGAAAAAGAAAAGA
79818 AAGAAAAAGAAAAGA
1 AAGAAAAAGAAAAGA
79833 A
1 A
79834 GATAGGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAGAAAAAGAAAAGA
Found at i:81109 original size:32 final size:32
Alignment explanation
Indices: 81073--81139 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
81063 TTATTTCATC
* *
81073 GTTTGATTTTAGCTTTTTATTATATCAAAGTA
1 GTTTGATTTTAGCTTTCTATCATATCAAAGTA
81105 GTTTGATTTTAGCTTTCTATCATATCAAAGTA
1 GTTTGATTTTAGCTTTCTATCATATCAAAGTA
81137 GTT
1 GTT
81140 AGTAGCTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.27, C:0.09, G:0.13, T:0.51
Consensus pattern (32 bp):
GTTTGATTTTAGCTTTCTATCATATCAAAGTA
Found at i:82448 original size:33 final size:33
Alignment explanation
Indices: 82338--82487 Score: 228
Period size: 34 Copynumber: 4.5 Consensus size: 33
82328 ATAAAAACCA
*
82338 CCATTTAATCAACAATGGTAACCTACCAAATCT
1 CCATTTAATCAACAATGGTAAGCTACCAAATCT
* * * *
82371 CCCATTTAGTCAACAATGGTAAACCACCAAATCAC
1 -CCATTTAATCAACAATGGTAAGCTACCAAATC-T
82406 CCATTTAATCAACAATGGTAAGCTACCAAATCT
1 CCATTTAATCAACAATGGTAAGCTACCAAATCT
*
82439 CCATTTAATCAACAATGGTAAGCTACCAAATCA
1 CCATTTAATCAACAATGGTAAGCTACCAAATCT
82472 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
82488 TCTCCCACTT
Statistics
Matches: 106, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
33 48 0.45
34 58 0.55
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (33 bp):
CCATTTAATCAACAATGGTAAGCTACCAAATCT
Found at i:86616 original size:19 final size:20
Alignment explanation
Indices: 86559--86618 Score: 97
Period size: 19 Copynumber: 3.1 Consensus size: 20
86549 GTACAGTAAC
*
86559 CGTATACTTGAATAGTA-CT
1 CGTATACGTGAATAGTACCT
86578 CGTATACGTGAATAGTACCT
1 CGTATACGTGAATAGTACCT
86598 -GTATACGTGAATAGTACCT
1 CGTATACGTGAATAGTACCT
86617 CG
1 CG
86619 ACAACCAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
19 35 0.92
20 3 0.08
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (20 bp):
CGTATACGTGAATAGTACCT
Found at i:87034 original size:33 final size:33
Alignment explanation
Indices: 86922--87069 Score: 206
Period size: 34 Copynumber: 4.4 Consensus size: 33
86912 GTAAAAACCA
*
86922 CCATTTAATCAACAATGGTAACCTACCAAATCT
1 CCATTTAATCAACAATGGTAAGCTACCAAATCT
* * * *
86955 CCCATTTAGTCAACAATGGTAAACCACCAAATCAC
1 -CCATTTAATCAACAATGGTAAGCTACCAAATC-T
86990 CCATTTAATCAACAATGGTAAGCTACCAAATCT
1 CCATTTAATCAACAATGGTAAGCTACCAAATCT
* * *
87023 CAATTTAATCAACAATGATAAGCTACCAAATCA
1 CCATTTAATCAACAATGGTAAGCTACCAAATCT
87056 CCATTTAATCAACA
1 CCATTTAATCAACA
87070 CTAAGCATTA
Statistics
Matches: 101, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
33 43 0.43
34 58 0.57
ACGTcount: A:0.42, C:0.26, G:0.07, T:0.25
Consensus pattern (33 bp):
CCATTTAATCAACAATGGTAAGCTACCAAATCT
Found at i:93875 original size:21 final size:22
Alignment explanation
Indices: 93835--93875 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
93825 AGTAGAATAT
*
93835 AAAAATATAAATTGATTATGAA
1 AAAAATATAAATTGAATATGAA
*
93857 AAAAATTTAAATT-AATATG
1 AAAAATATAAATTGAATATG
93876 GCAATATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (22 bp):
AAAAATATAAATTGAATATGAA
Found at i:94904 original size:30 final size:30
Alignment explanation
Indices: 94868--94929 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
94858 TTTTTATGGT
94868 TTTCATATCTCTTCTTCATTTTCCAATTTC
1 TTTCATATCTCTTCTTCATTTTCCAATTTC
94898 TTTCATATCTCTTCTTCATTTTCCAATTTC
1 TTTCATATCTCTTCTTCATTTTCCAATTTC
94928 TT
1 TT
94930 GGAGGTGGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.16, C:0.26, G:0.00, T:0.58
Consensus pattern (30 bp):
TTTCATATCTCTTCTTCATTTTCCAATTTC
Found at i:96101 original size:6 final size:6
Alignment explanation
Indices: 96085--96122 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
96075 ACAGACTCAA
* *
96085 AATTAC TATTAC AATTAC AATTAC AATTAC AATAAC AA
1 AATTAC AATTAC AATTAC AATTAC AATTAC AATTAC AA
96123 CTTAATTCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.32
Consensus pattern (6 bp):
AATTAC
Found at i:96308 original size:3 final size:3
Alignment explanation
Indices: 96302--96328 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
96292 TATAAACAAT
96302 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
96329 AACTATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:97900 original size:17 final size:17
Alignment explanation
Indices: 97878--97914 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
97868 TCGCAGATAA
97878 TGAAAGGGAATTAAAGT
1 TGAAAGGGAATTAAAGT
97895 TGAAAGGGAATTAAAGT
1 TGAAAGGGAATTAAAGT
97912 TGA
1 TGA
97915 TGAATCTGGA
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:0.46, C:0.00, G:0.30, T:0.24
Consensus pattern (17 bp):
TGAAAGGGAATTAAAGT
Found at i:108564 original size:15 final size:15
Alignment explanation
Indices: 108544--108578 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
108534 ACACAGGATA
108544 ATGTATCCCAAGCCT
1 ATGTATCCCAAGCCT
108559 ATGTATCCCAAGCCT
1 ATGTATCCCAAGCCT
108574 ATGTA
1 ATGTA
108579 GATATCACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (15 bp):
ATGTATCCCAAGCCT
Found at i:109748 original size:19 final size:19
Alignment explanation
Indices: 109710--109748 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
109700 ATTGTATTAA
*
109710 AGTTTTTGACATTTGTTAT
1 AGTTTTTGACATTTGATAT
109729 AGTTTTTGAC-TTGTGATAT
1 AGTTTTTGACATT-TGATAT
109748 A
1 A
109749 AAGATAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.23, C:0.05, G:0.18, T:0.54
Consensus pattern (19 bp):
AGTTTTTGACATTTGATAT
Found at i:110094 original size:16 final size:16
Alignment explanation
Indices: 110075--110111 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
110065 AATAATTATG
110075 AAAAATAAAAATTACA
1 AAAAATAAAAATTACA
* *
110091 AAAATTAAAAATTAGA
1 AAAAATAAAAATTACA
110107 AAAAA
1 AAAAA
110112 AATTCTGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.19
Consensus pattern (16 bp):
AAAAATAAAAATTACA
Found at i:115761 original size:168 final size:163
Alignment explanation
Indices: 115315--115783 Score: 624
Period size: 166 Copynumber: 2.8 Consensus size: 163
115305 CTATTGTTAT
* *
115315 ATTTAATTTTATTCCT-TTTTTG-AAAATATCATTTCGTACCTTAAT-GAAAACCTGAAAAGATA
1 ATTTAATTTTATT--TATTTTTGAAAAATACCATTTCGTACCTTAATAG-AAACCCGAAAAGATA
115377 CGAAAAGTTTTTAAAATCTTTTATACCCCTACAGACCCCTATAGGAATATAAAAGATTTAAAAAA
63 -GAAAAGTTTTTAAAATCTTTTATACCCCTACAGACCCC-ATAGGAATATAAAAGA-TTAAAAAA
* * * *
115442 ATGATTAAAATTTATTTCAATTATGAAAGTGTTAGTCTA
125 ATGATTAATATTTATTTCAATTATGAAAATATTAATCTA
* * *
115481 ATTTAATTTTATTTATTTTTGAAAAATACCATTTCGTATCTTAATAGAAACTCGAAAAGATACAA
1 ATTTAATTTTATTTATTTTTGAAAAATACCATTTCGTACCTTAATAGAAACCCGAAAAGATAGAA
* * *
115546 AAGGTTTTTGAAATCTTTTATACCCCTACAGACCCTCATAAGAATATACAAGATTAAAAAGAATG
66 AA-GTTTTTAAAATCTTTTATACCCCTACAGACCC-CATAGGAATATAAAAGATTAAAAA-AATG
* *
115611 ATTAATATTTATTTCAATTATGAAAATATTAATTTT
128 ATTAATATTTATTTCAATTATGAAAATATTAATCTA
* *
115647 ATTTTA-TTTATTTATTCATTTCGAAAAATACCATTTCATACCTTAATAGAAACCCGAAAAGATA
1 ATTTAATTTTATTTATT--TTT-GAAAAATACCATTTCGTACCTTAATAGAAACCCGAAAAGATA
*
115711 GGAAAAGTTTTTAAAATCTTTTATACCCCTACGGACCTCCATAGGAATATAAAAGATT-AAAAAA
63 -GAAAAGTTTTTAAAATCTTTTATACCCCTACAGACC-CCATAGGAATATAAAAGATTAAAAAAA
115775 TGATTAATA
126 TGATTAATA
115784 GCTTAAATAT
Statistics
Matches: 269, Mismatches: 23, Indels: 22
0.86 0.07 0.07
Matches are distributed among these distances:
164 1 0.00
165 27 0.10
166 142 0.53
167 9 0.03
168 85 0.32
169 5 0.02
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.37
Consensus pattern (163 bp):
ATTTAATTTTATTTATTTTTGAAAAATACCATTTCGTACCTTAATAGAAACCCGAAAAGATAGAA
AAGTTTTTAAAATCTTTTATACCCCTACAGACCCCATAGGAATATAAAAGATTAAAAAAATGATT
AATATTTATTTCAATTATGAAAATATTAATCTA
Found at i:116618 original size:11 final size:11
Alignment explanation
Indices: 116597--116626 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
116587 TTTTCCTCGC
116597 CTTTCTTTCTCT
1 CTTT-TTTCTCT
116609 CTTTTTTCTCT
1 CTTTTTTCTCT
116620 CTTTTTT
1 CTTTTTT
116627 TCAGCTGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (11 bp):
CTTTTTTCTCT
Found at i:117445 original size:164 final size:164
Alignment explanation
Indices: 117089--117705 Score: 705
Period size: 164 Copynumber: 3.7 Consensus size: 164
117079 CAATGTATAT
* * * * *
117089 AAAAAATTCAAAATTCATG-AAAT-AATTTGAATTTTCAAAAACTGATTTAATATAATTTAATGA
1 AAAAAATTAAAAATTCATGAAAATGAA--TGAATTTTTAAAAACTGATTTAATATAAATAAATAA
* * *** * *
117152 AAATATTAGATGAATTTTCAAAAACTT-TAAATTGAGAAAAATTGCCT-CGAAAAAAATTTACGA
64 AAATATTTGATGAATTTT-AAAAA-TTAAAAACCAAGAAAAA-T-CCTCCCAAAAAAATTTACGG
* * * * *
117215 AGAAAAAAATTCTGTTTTTCAAAAAAGAGAAATTTCAAGG
125 AGTAAAAAACTCCGTATTTCAGAAAAGAGAAATTTCAAGG
* *
117255 AAAAAATCAAAAACTCATGAAAATGAATGAATTTTTAAAAACTGATTTAATATGAAATAAATAAA
1 AAAAAATTAAAAATTCATGAAAATGAATGAATTTTTAAAAACTGATTTAATAT-AAATAAATAAA
117320 AATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTCCC-AAAAAATTTACGGAGTAA
65 AATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTCCCAAAAAAATTTACGGAGTAA
*
117384 AAAACTCCATATTTCAGAAACATGA-AAATTTCAA-G
130 AAAACTCCGTATTTCAGAAA-A-GAGAAATTTCAAGG
* * * *
117419 AAAAAATTAAAAATTCATGAAAATGAATGAATTTCTGAAAACTGATTTAATGTGAAATAAATAAT
1 AAAAAATTAAAAATTCATGAAAATGAATGAATTTTTAAAAACTGATTTAATAT-AAATAAATAAA
* *
117484 AATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTCCCAAAAAAATTTACAGAGTAG
65 AATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTCCCAAAAAAATTTACGGAGTAA
*
117549 AAAACTCCGTATTTTAGAAATAGATG-AATTTCAAGG
130 AAAACTCCGTATTTCAGAAA-AGA-GAAATTTCAAGG
* * * * * * *
117585 AAAAAATGAAAAAATAATGAAAATGAATGAA-TTTTGAAAGCTGATTTACTATAAATTAAATAAT
1 AAAAAATTAAAAATTCATGAAAATGAATGAATTTTTAAAAACTGATTTAATATAAA-TAAATAAA
* * *
117649 AATATTTTATGAATTTTAAAAATTAAGAACCATG-AAAATCCTCCCGAAAAAAATTTA
65 AATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTCCC-AAAAAAATTTA
117706 TAAAAAAGAA
Statistics
Matches: 397, Mismatches: 41, Indels: 27
0.85 0.09 0.06
Matches are distributed among these distances:
164 156 0.39
165 124 0.31
166 87 0.22
167 28 0.07
168 2 0.01
ACGTcount: A:0.52, C:0.09, G:0.10, T:0.29
Consensus pattern (164 bp):
AAAAAATTAAAAATTCATGAAAATGAATGAATTTTTAAAAACTGATTTAATATAAATAAATAAAA
ATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTCCCAAAAAAATTTACGGAGTAAA
AAACTCCGTATTTCAGAAAAGAGAAATTTCAAGG
Found at i:120952 original size:12 final size:11
Alignment explanation
Indices: 120918--120954 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
120908 TTACTATCAT
120918 AAACAATTAAG
1 AAACAATTAAG
120929 AAACAATTAAG
1 AAACAATTAAG
*
120940 AAAGCAATAAAG
1 AAA-CAATTAAG
120952 AAA
1 AAA
120955 ATATAAACGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.68, C:0.08, G:0.11, T:0.14
Consensus pattern (11 bp):
AAACAATTAAG
Found at i:122397 original size:16 final size:16
Alignment explanation
Indices: 122378--122423 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
122368 TAATTTTTGT
122378 AAATAAATTTTTTATA
1 AAATAAATTTTTTATA
*
122394 AAAT--A--TTTTAAA
1 AAATAAATTTTTTATA
122406 AAATAAATTTTTTATA
1 AAATAAATTTTTTATA
122422 AA
1 AA
122424 TTTATTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 8
0.71 0.06 0.24
Matches are distributed among these distances:
12 10 0.42
14 2 0.08
16 12 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AAATAAATTTTTTATA
Found at i:125132 original size:27 final size:26
Alignment explanation
Indices: 125081--125134 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
125071 ATATTAATAT
*
125081 AATATTTTTCATAAAATTATTTTTAA
1 AATATTTTTCATAAAATTATATTTAA
*
125107 AATATTTGTTGATAAAATT-TAATTTAA
1 AATATTT-TTCATAAAATTAT-ATTTAA
125134 A
1 A
125135 CCTTAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 8 0.33
27 16 0.67
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (26 bp):
AATATTTTTCATAAAATTATATTTAA
Found at i:125902 original size:22 final size:22
Alignment explanation
Indices: 125875--125916 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
125865 TATTTATAGA
125875 TATTAAATTAAAATTATTTAAT
1 TATTAAATTAAAATTATTTAAT
* * *
125897 TATTAATTTTAAATTTTTTA
1 TATTAAATTAAAATTATTTA
125917 TATTTAATGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TATTAAATTAAAATTATTTAAT
Found at i:126125 original size:47 final size:46
Alignment explanation
Indices: 126085--126187 Score: 129
Period size: 47 Copynumber: 2.2 Consensus size: 46
126075 TAAAATTTTT
126085 TATTTAT-TTATATAATATT-AATAATTTATATAAATATTAAAATAAA
1 TATTTATATTATATAATATTAAAT-ATTT-TATAAATATTAAAATAAA
* **
126131 TATTTATATTATATTATATTAAATATTTTATAAATATTATATTTAAA
1 TATTTATATTATATAATATTAAATATTTTATAAATATTA-AAATAAA
*
126178 TAATTATATT
1 TATTTATATT
126188 TAAAATTACT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
46 18 0.36
47 29 0.58
48 3 0.06
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (46 bp):
TATTTATATTATATAATATTAAATATTTTATAAATATTAAAATAAA
Found at i:126133 original size:18 final size:20
Alignment explanation
Indices: 126093--126133 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
126083 TTTATTTATT
**
126093 TATATAATATTAATAATTTA
1 TATATAATATTAATAATAAA
126113 TATA-AATATTAA-AATAAA
1 TATATAATATTAATAATAAA
126131 TAT
1 TAT
126134 TTATATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
18 7 0.37
19 8 0.42
20 4 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TATATAATATTAATAATAAA
Found at i:126153 original size:28 final size:26
Alignment explanation
Indices: 126118--126193 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 26
126108 ATTTATATAA
*
126118 ATATTAAAATAAATATTTATATTATATT
1 ATATT-AAATAAATATTTATA-AATATT
126146 ATATTAAAT--AT-TTTATAAATATT
1 ATATTAAATAAATATTTATAAATATT
126169 ATATTTAAATAATTATATTTA-AAAT
1 ATA-TTAAATAA--ATATTTATAAAT
126194 TACTCGATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
23 8 0.20
24 12 0.29
25 2 0.05
27 4 0.10
28 11 0.27
29 4 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
ATATTAAATAAATATTTATAAATATT
Found at i:126185 original size:14 final size:13
Alignment explanation
Indices: 126141--126195 Score: 64
Period size: 14 Copynumber: 4.5 Consensus size: 13
126131 TATTTATATT
126141 ATATTATA-TTAA
1 ATATTATATTTAA
*
126153 ATATT-T-TATAA
1 ATATTATATTTAA
126164 ATATTATATTTAA
1 ATATTATATTTAA
126177 ATAATTATATTTAA
1 AT-ATTATATTTAA
126191 A-ATTA
1 ATATTA
126196 CTCGATTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
11 9 0.24
12 10 0.27
13 6 0.16
14 12 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
ATATTATATTTAA
Found at i:126692 original size:16 final size:18
Alignment explanation
Indices: 126657--126705 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
126647 TCAATTATGC
* * *
126657 TTTAACAATTATGTTATA
1 TTTAATAATTATTTTTTA
126675 TTT-AT-ATTATTTTTTA
1 TTTAATAATTATTTTTTA
126691 TTTAATAATTATTTT
1 TTTAATAATTATTTT
126706 AATATATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 12 0.46
17 3 0.12
18 11 0.42
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTAATAATTATTTTTTA
Found at i:126720 original size:44 final size:46
Alignment explanation
Indices: 126671--126758 Score: 119
Period size: 44 Copynumber: 1.9 Consensus size: 46
126661 ACAATTATGT
* *
126671 TATATTTATATTATTTTT-TAT-TTAAT-AATTATTTTAATATATTA
1 TATATTTATATAATTTTTATATGTTAATAAATTATATT-ATATATTA
126715 TATATTTATATAATTTTTAATATGTTAATAAATTATATTATATA
1 TATATTTATATAATTTTT-ATATGTTAATAAATTATATTATATA
126759 GATTTTGAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
44 17 0.45
46 3 0.08
47 10 0.26
48 8 0.21
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (46 bp):
TATATTTATATAATTTTTATATGTTAATAAATTATATTATATATTA
Found at i:132821 original size:16 final size:16
Alignment explanation
Indices: 132802--132840 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
132792 TTGAATCCAG
*
132802 AATAACTGAAACCTAA
1 AATAACTCAAACCTAA
* *
132818 AATAGCTCAAACTTAA
1 AATAACTCAAACCTAA
132834 AATAACT
1 AATAACT
132841 TGAATTTGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.54, C:0.18, G:0.05, T:0.23
Consensus pattern (16 bp):
AATAACTCAAACCTAA
Found at i:134107 original size:8 final size:8
Alignment explanation
Indices: 134094--134119 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
134084 GATTTTAATT
134094 TTTATATA
1 TTTATATA
134102 TTTATATA
1 TTTATATA
134110 TTTATATA
1 TTTATATA
134118 TT
1 TT
134120 AGAATGATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
TTTATATA
Found at i:135275 original size:19 final size:19
Alignment explanation
Indices: 135247--135285 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
135237 GTAAGTTAAC
135247 AACTAGTATTA-AAAACTAT
1 AACTAGTATTATAAAA-TAT
*
135266 AACTATTATTATAAAATAT
1 AACTAGTATTATAAAATAT
135285 A
1 A
135286 TAGTTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.36
Consensus pattern (19 bp):
AACTAGTATTATAAAATAT
Found at i:135287 original size:21 final size:20
Alignment explanation
Indices: 135263--135302 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
135253 TATTAAAAAC
135263 TATAACTATTATTATAAAATA
1 TATAACTA-TATTATAAAATA
**
135284 TATAGTTATATTATAAAAT
1 TATAACTATATTATAAAAT
135303 TAAATTTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (20 bp):
TATAACTATATTATAAAATA
Found at i:135813 original size:18 final size:20
Alignment explanation
Indices: 135787--135828 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
135777 AGGTCTCGTA
135787 AATATATATTAATATA-ATAT
1 AATATAT-TTAATATATATAT
*
135807 AATATATTTATTATATATAT
1 AATATATTTAATATATATAT
135827 AA
1 AA
135829 AAAAGTGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AATATATTTAATATATATAT
Found at i:138003 original size:29 final size:30
Alignment explanation
Indices: 137959--138035 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
137949 ATTTTATTTT
* *
137959 TTCAAATAAGTTTTTATATTTTT-A-TTATA
1 TTCAAATAAATCTTTAT-TTTTTGATTTATA
* * *
137988 TTTAAATATATCTTTATTTTTTGATTTGTA
1 TTCAAATAAATCTTTATTTTTTGATTTATA
138018 TTCAAATAAATCTTTATT
1 TTCAAATAAATCTTTATT
138036 CAAATGAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
28 5 0.13
29 14 0.36
30 20 0.51
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.58
Consensus pattern (30 bp):
TTCAAATAAATCTTTATTTTTTGATTTATA
Found at i:138031 original size:30 final size:28
Alignment explanation
Indices: 137950--138035 Score: 84
Period size: 30 Copynumber: 3.0 Consensus size: 28
137940 CTTTGAACTA
* * *
137950 TTTTATT-TTTTCAAATAAGTTTTTATAT
1 TTTTATTATATTCAAATAAATCTTTAT-T
* *
137978 TTTTATTATATTTAAATATATCTTTATT
1 TTTTATTATATTCAAATAAATCTTTATT
*
138006 TTTTGATTTGTATTCAAATAAATCTTTATT
1 TTTT-A-TTATATTCAAATAAATCTTTATT
138036 CAAATGAAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
28 12 0.26
29 15 0.32
30 20 0.43
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (28 bp):
TTTTATTATATTCAAATAAATCTTTATT
Found at i:140210 original size:26 final size:24
Alignment explanation
Indices: 140160--140210 Score: 59
Period size: 24 Copynumber: 2.0 Consensus size: 24
140150 GTTTATAACA
*
140160 TTTCATATTAAAAAAAAAATCAAT
1 TTTCATATTAAAAAAAAAATAAAT
140184 TTTCA-ATTAACAAAAAAGTAATAAAT
1 TTTCATATTAA-AAAAAA--AATAAAT
140210 T
1 T
140211 ATTTAAGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 5 0.22
24 11 0.48
26 7 0.30
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.33
Consensus pattern (24 bp):
TTTCATATTAAAAAAAAAATAAAT
Found at i:141552 original size:34 final size:32
Alignment explanation
Indices: 141506--141585 Score: 88
Period size: 35 Copynumber: 2.4 Consensus size: 32
141496 GATCAGTATC
*
141506 AATCACAAATTTTAAGAATCATAAATTTTCTAAA
1 AATCACAGATTTTAAGAATCATAAA-TTTCT-AA
* * *
141540 AATCACAGATTTTTAAGAATTATAGATTTCTAT
1 AATCACAGA-TTTTAAGAATCATAAATTTCTAA
*
141573 AATCATAGATTTT
1 AATCACAGATTTT
141586 CAACCCCAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
32 4 0.10
33 9 0.22
34 13 0.32
35 14 0.35
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (32 bp):
AATCACAGATTTTAAGAATCATAAATTTCTAA
Found at i:141568 original size:17 final size:17
Alignment explanation
Indices: 141515--141585 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 17
141505 CAATCACAAA
*
141515 TTTTAAGAATCATAAAT
1 TTTTAAGAATCATAGAT
* *
141532 TTTCTAAAAATCACAGAT
1 TTT-TAAGAATCATAGAT
*
141550 TTTTAAGAATTATAGAT
1 TTTTAAGAATCATAGAT
* *
141567 TTCT-ATAATCATAGAT
1 TTTTAAGAATCATAGAT
141583 TTT
1 TTT
141586 CAACCCCAAT
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
16 12 0.28
17 17 0.40
18 14 0.33
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (17 bp):
TTTTAAGAATCATAGAT
Found at i:145884 original size:17 final size:16
Alignment explanation
Indices: 145847--145943 Score: 88
Period size: 16 Copynumber: 5.8 Consensus size: 16
145837 GATAAGCATC
*
145847 AATCACAGATTTTAGG
1 AATCACAGATTTTAAG
145863 AATCACAGATTTCTAAG
1 AATCACAGATTT-TAAG
*
145880 AATCACAAATTTTTAAG
1 AATCACAGA-TTTTAAG
* * *
145897 AATTACAGATTTTTAT
1 AATCACAGATTTTAAG
*
145913 AATTACAGATTTTCAA-
1 AATCACAGATTTT-AAG
145929 ACCATCACAGATTTT
1 A--ATCACAGATTTT
145944 CAACCTTAAG
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
16 31 0.46
17 23 0.34
18 14 0.21
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.36
Consensus pattern (16 bp):
AATCACAGATTTTAAG
Found at i:147594 original size:21 final size:21
Alignment explanation
Indices: 147568--147613 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
147558 TCTTCTACAG
147568 TAGCATATTGTCATCTCTTGT
1 TAGCATATTGTCATCTCTTGT
147589 TAGCATATTGTCATCTCTTGT
1 TAGCATATTGTCATCTCTTGT
147610 TAGC
1 TAGC
147614 TTTTCAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.46
Consensus pattern (21 bp):
TAGCATATTGTCATCTCTTGT
Found at i:148316 original size:28 final size:28
Alignment explanation
Indices: 148280--148336 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
148270 TAATAGAATG
*
148280 AGTATATATTTATTTTATATAATTGTTA
1 AGTAAATATTTATTTTATATAATTGTTA
*
148308 AGTAAATATTTATTTTATATACTTGTTA
1 AGTAAATATTTATTTTATATAATTGTTA
148336 A
1 A
148337 TGTTGTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (28 bp):
AGTAAATATTTATTTTATATAATTGTTA
Found at i:148972 original size:69 final size:70
Alignment explanation
Indices: 148816--148996 Score: 222
Period size: 70 Copynumber: 2.6 Consensus size: 70
148806 CTAACATATC
* * * * * * *
148816 TTAAGTATTCAAATCTCTCTAACAGTCAGATTTC-GGAAAATATATTTCCCTTTAAGAGTTTAAT
1 TTAAGTATTTAGATCTCTCTAACAATCAGTTTTCTGG-AAATATATTCCCCCTCAAGAGTTTAAT
148880 ATCCTT
65 ATCCTT
* *
148886 TTGAGTATTTAGATCTCTCTAACAATCAGTTTTCTGGAAATATATTCCCCCTCATGAGTTTAATA
1 TTAAGTATTTAGATCTCTCTAACAATCAGTTTTCTGGAAATATATTCCCCCTCAAGAGTTTAATA
148951 T-CTT
66 TCCTT
** * *
148955 TTAAGTATTTAGATCTCTCTTTCAATTAGTTTTCTGAAAATA
1 TTAAGTATTTAGATCTCTCTAACAATCAGTTTTCTGGAAATA
148997 CATTTGTCCT
Statistics
Matches: 96, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
69 40 0.42
70 54 0.56
71 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.43
Consensus pattern (70 bp):
TTAAGTATTTAGATCTCTCTAACAATCAGTTTTCTGGAAATATATTCCCCCTCAAGAGTTTAATA
TCCTT
Found at i:151333 original size:27 final size:26
Alignment explanation
Indices: 151303--151404 Score: 71
Period size: 28 Copynumber: 3.7 Consensus size: 26
151293 TGTTCAGTAA
151303 TTTTTATATTTATATCATATTTATATT
1 TTTTTATATTTATAT-ATATTTATATT
* * *
151330 TTTTT-TATATTATAATAATATATAAAAT
1 TTTTTATAT-TTAT-AT-ATATTTATATT
* * * *
151358 ATTTTATATTTATATAAATTTTTATA
1 TTTTTATATTTATATATATTTATATT
*
151384 TATTTATAATTTATATTATAT
1 TTTTTAT-ATTTATA-TATAT
151405 AAATTTTAAA
Statistics
Matches: 56, Mismatches: 14, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
26 13 0.23
27 18 0.32
28 22 0.39
29 3 0.05
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (26 bp):
TTTTTATATTTATATATATTTATATT
Found at i:151371 original size:20 final size:20
Alignment explanation
Indices: 151348--151391 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
151338 ATTATAATAA
151348 TATATAAAATATTT-TATATT
1 TATAT-AAATATTTATATATT
*
151368 TATATAAATTTTTATATATT
1 TATATAAATATTTATATATT
151388 TATA
1 TATA
151392 ATTTATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATATAAATATTTATATATT
Found at i:151380 original size:18 final size:18
Alignment explanation
Indices: 151348--151411 Score: 66
Period size: 18 Copynumber: 3.7 Consensus size: 18
151338 ATTATAATAA
151348 TATATAAAATATTTTATATT
1 TATAT-AAAT-TTTTATATT
151368 TATATAAATTTTTATATAT
1 TATATAAATTTTTATAT-T
151387 T-TAT-AA--TTTATA-T
1 TATATAAATTTTTATATT
151400 TATATAAATTTT
1 TATATAAATTTT
151412 AAAATATATT
Statistics
Matches: 39, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 2 0.05
14 3 0.08
15 8 0.21
17 4 0.10
18 11 0.28
19 6 0.15
20 5 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TATATAAATTTTTATATT
Found at i:151385 original size:14 final size:15
Alignment explanation
Indices: 151367--151411 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
151357 TATTTTATAT
151367 TTATATAAATTTTTA
1 TTATATAAATTTTTA
* *
151382 TATATTTATAATTTATA
1 T-TATATA-AATTTTTA
151399 TTATATAAATTTT
1 TTATATAAATTTT
151412 AAAATATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
15 6 0.25
16 10 0.42
17 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATATAAATTTTTA
Found at i:151422 original size:27 final size:27
Alignment explanation
Indices: 151333--151424 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 27
151323 TTATATTTTT
*
151333 TTTATATTATA-ATAATATATAAAATAT-
1 TTTATATTATATA-AAT-TTTAAAATATA
*
151360 TTTATATTTATATAAATTTTTATATATTTATAA
1 TTTATA-TTATATAAA-TTTTA-A-A-ATAT-A
151393 TTTATATTATATAAATTTTAAAATATA
1 TTTATATTATATAAATTTTAAAATATA
151420 TTTAT
1 TTTAT
151425 GTATATATCG
Statistics
Matches: 54, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
27 12 0.22
28 13 0.24
29 4 0.07
30 2 0.04
31 8 0.15
32 9 0.17
33 6 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TTTATATTATATAAATTTTAAAATATA
Found at i:152026 original size:25 final size:25
Alignment explanation
Indices: 151994--152044 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
151984 TTCGGCATTT
151994 GGGTGAGAATCAGACTGGTAATGTG
1 GGGTGAGAATCAGACTGGTAATGTG
152019 GGGTGAGAATCAGACTGGTAATGTG
1 GGGTGAGAATCAGACTGGTAATGTG
152044 G
1 G
152045 ACTGGACCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.08, G:0.41, T:0.24
Consensus pattern (25 bp):
GGGTGAGAATCAGACTGGTAATGTG
Found at i:152772 original size:2 final size:2
Alignment explanation
Indices: 152765--152800 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
152755 TTTTCATTCC
152765 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
152801 GCATCTAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:155729 original size:13 final size:14
Alignment explanation
Indices: 155704--155734 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
155694 ATTTCGGATG
155704 AAATAATTTTTCTC
1 AAATAATTTTTCTC
155718 AAATAA-TTTTCTC
1 AAATAATTTTTCTC
155731 AAAT
1 AAAT
155735 CTCTATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (14 bp):
AAATAATTTTTCTC
Found at i:163764 original size:1 final size:1
Alignment explanation
Indices: 163753--163807 Score: 74
Period size: 1 Copynumber: 55.0 Consensus size: 1
163743 GGCAATTGTG
* * * *
163753 AAAAGAAAAAAAAAAAAAAAACAAAAAAAAAAAAAGAAAAAAACAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
163808 GTGAAGATTT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.93, C:0.04, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:163814 original size:25 final size:22
Alignment explanation
Indices: 163753--163807 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
163743 GGCAATTGTG
163753 AAAAGAAAAAAAAA-AAAAAAAC
1 AAAA-AAAAAAAAAGAAAAAAAC
163775 AAAAAAAAAAAAAGAAAAAAAC
1 AAAAAAAAAAAAAGAAAAAAAC
163797 AAAAAAAAAAA
1 AAAAAAAAAAA
163808 GTGAAGATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 9 0.28
22 23 0.72
ACGTcount: A:0.93, C:0.04, G:0.04, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAAAAAGAAAAAAAC
Found at i:166350 original size:20 final size:20
Alignment explanation
Indices: 166328--166368 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
166318 CATAAACAAG
166328 AAAGAAAAAATGAAAAAAAGAA
1 AAAG-AAAAA-GAAAAAAAGAA
*
166350 AAAGAAAAAGAAAAGAAGA
1 AAAGAAAAAGAAAAAAAGA
166369 TAGGAAACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 5 0.28
22 4 0.22
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (20 bp):
AAAGAAAAAGAAAAAAAGAA
Found at i:166530 original size:17 final size:18
Alignment explanation
Indices: 166498--166531 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
166488 AATCCTTCAA
166498 ATAACAAAATTATCATTG
1 ATAACAAAATTATCATTG
*
166516 ATAATAAAA-TATCATT
1 ATAACAAAATTATCATT
166532 ATATGCTTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.09, G:0.03, T:0.35
Consensus pattern (18 bp):
ATAACAAAATTATCATTG
Found at i:167326 original size:15 final size:15
Alignment explanation
Indices: 167306--167356 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
167296 CTATAAATAC
167306 ATTTTATGATATTAT
1 ATTTTATGATATTAT
167321 ATTTTATGAATAATTAT
1 ATTTTATG-AT-ATTAT
167338 -TTTTGAT-ATATTA-
1 ATTTT-ATGATATTAT
167351 ATTTTA
1 ATTTTA
167357 ATTTTAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 1 0.03
14 8 0.25
15 10 0.31
16 6 0.19
17 7 0.22
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (15 bp):
ATTTTATGATATTAT
Found at i:167993 original size:17 final size:18
Alignment explanation
Indices: 167961--167994 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
167951 AAGCCTTCAA
167961 ATAATAAAATTATCATTG
1 ATAATAAAATTATCATTG
167979 ATAATAAAA-TATCATT
1 ATAATAAAATTATCATT
167995 ATATACTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (18 bp):
ATAATAAAATTATCATTG
Found at i:168778 original size:15 final size:15
Alignment explanation
Indices: 168758--168808 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
168748 CTATAAATAC
168758 ATTTTATGATATTAT
1 ATTTTATGATATTAT
168773 ATTTTATGAATAATTAT
1 ATTTTATG-AT-ATTAT
168790 -TTTTGAT-ATATTA-
1 ATTTT-ATGATATTAT
168803 ATTTTA
1 ATTTTA
168809 ATTTAATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 1 0.03
14 8 0.25
15 10 0.31
16 6 0.19
17 7 0.22
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (15 bp):
ATTTTATGATATTAT
Done.