Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010883.1 Corchorus capsularis cultivar CVL-1 contig10904, whole genome shotgun sequence
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: 214122
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--93 Score: 177
Period size: 2 Copynumber: 46.0 Consensus size: 2
1 CT CT CT CAT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT C-T CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
44 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
86 CT CT CT CT
1 CT CT CT CT
94 TTTGCTTCCT
Statistics
Matches: 90, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 88 0.98
3 2 0.02
ACGTcount: A:0.01, C:0.49, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:15525 original size:14 final size:13
Alignment explanation
Indices: 15506--15535 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
15496 TTTCTTGCAC
15506 TTTTTTATTGATTT
1 TTTTTTA-TGATTT
15520 TTTTTTATGATTT
1 TTTTTTATGATTT
15533 TTT
1 TTT
15536 GTTTTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.13, C:0.00, G:0.07, T:0.80
Consensus pattern (13 bp):
TTTTTTATGATTT
Found at i:16236 original size:2 final size:2
Alignment explanation
Indices: 16229--16256 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16219 AAATACAATC
16229 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
16257 CTATCATTTG
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:17314 original size:29 final size:30
Alignment explanation
Indices: 17268--17326 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
17258 TCTTTACTCC
*
17268 TTTTTTCGCCAAGTCCACTACTCAATTCTT
1 TTTTTTCGCCAAGACCACTACTCAATTCTT
*
17298 TTTTTTGGCC-AGACCACTACTCAATTCTT
1 TTTTTTCGCCAAGACCACTACTCAATTCTT
17327 CAGTACTCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.20, C:0.29, G:0.08, T:0.42
Consensus pattern (30 bp):
TTTTTTCGCCAAGACCACTACTCAATTCTT
Found at i:18448 original size:31 final size:33
Alignment explanation
Indices: 18385--18450 Score: 100
Period size: 35 Copynumber: 2.0 Consensus size: 33
18375 CCAATTATCC
18385 AATCACAATCTTATATTATAAATACATTCAAAATT
1 AATCACAATCTTATATTAT-AATA-ATTCAAAATT
18420 AATCACAATCTTATATTAT-AT-ATTCAAAATT
1 AATCACAATCTTATATTATAATAATTCAAAATT
18451 TCTATTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
31 10 0.32
33 2 0.06
35 19 0.61
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (33 bp):
AATCACAATCTTATATTATAATAATTCAAAATT
Found at i:18591 original size:17 final size:17
Alignment explanation
Indices: 18569--18608 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
18559 TCACCCATAA
*
18569 ATCACTGGTGAT-TTAAG
1 ATCACTGGAGATCTT-AG
18586 ATCACTGGAGATCTTAG
1 ATCACTGGAGATCTTAG
18603 ATCACT
1 ATCACT
18609 TGGGCTTAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 19 0.90
18 2 0.10
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (17 bp):
ATCACTGGAGATCTTAG
Found at i:22851 original size:12 final size:12
Alignment explanation
Indices: 22834--22868 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
22824 TGTTACTACG
22834 ATTTTTCTTTTT
1 ATTTTTCTTTTT
*
22846 ATTTTTATTTTT
1 ATTTTTCTTTTT
*
22858 ATTTTCCTTTT
1 ATTTTTCTTTT
22869 GGGTTCACTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (12 bp):
ATTTTTCTTTTT
Found at i:53097 original size:48 final size:51
Alignment explanation
Indices: 53023--53162 Score: 207
Period size: 48 Copynumber: 2.8 Consensus size: 51
53013 TAAATATTTA
53023 TTTGCACCATTACACCTTTCACTATGTAATAGGAATGCACC-A-AAC-CACG
1 TTTGCACCATTACACCTTTCACTATGTAATAGGAATGCACCGACAACTC-CG
*
53072 -TTGCACCATTACACCTTTCATTATGTAATAGGAATGCACCGTACCAACTCCG
1 TTTGCACCATTACACCTTTCACTATGTAATAGGAATGCACCG-A-CAACTCCG
*
53124 TTTGCACCATTACACCTTTCACAATGTAATAGGAATGCA
1 TTTGCACCATTACACCTTTCACTATGTAATAGGAATGCA
53163 GTATATGGCT
Statistics
Matches: 82, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
48 39 0.48
50 1 0.01
52 5 0.06
53 37 0.45
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (51 bp):
TTTGCACCATTACACCTTTCACTATGTAATAGGAATGCACCGACAACTCCG
Found at i:53571 original size:53 final size:53
Alignment explanation
Indices: 53481--53604 Score: 176
Period size: 53 Copynumber: 2.3 Consensus size: 53
53471 ACCATTACAC
* *
53481 CTATGTAATAGGAATGCACCAAACCATCTTCGGTTGCACCATTACACCTTTCA
1 CTATGTAATAGGAATGCACCAAACCAACTCCGGTTGCACCATTACACCTTTCA
* *** *
53534 TTATGTAATAGGAATGCACTGTACCAACTCCGTTTGCACCATTACACCTTTCA
1 CTATGTAATAGGAATGCACCAAACCAACTCCGGTTGCACCATTACACCTTTCA
*
53587 CAATGTAATAGGAATGCA
1 CTATGTAATAGGAATGCA
53605 GTATATGGCT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
53 62 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (53 bp):
CTATGTAATAGGAATGCACCAAACCAACTCCGGTTGCACCATTACACCTTTCA
Found at i:67596 original size:24 final size:24
Alignment explanation
Indices: 67569--67614 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
67559 AACTATATTT
*
67569 AGAATCCAAACTTTCCA-TAACACC
1 AGAAACCAAAC-TTCCAGTAACACC
*
67593 AGAAACTAAACTTCCAGTAACA
1 AGAAACCAAACTTCCAGTAACA
67615 TTAAAATTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.46, C:0.28, G:0.07, T:0.20
Consensus pattern (24 bp):
AGAAACCAAACTTCCAGTAACACC
Found at i:68311 original size:7 final size:7
Alignment explanation
Indices: 68299--68331 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
68289 TTGGAAATGG
68299 AGAAAGA
1 AGAAAGA
68306 AGAAAGA
1 AGAAAGA
68313 AGAAAGA
1 AGAAAGA
68320 AGAAAGA
1 AGAAAGA
68327 A-AAAG
1 AGAAAG
68332 TCTCAGAGCG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.15
7 22 0.85
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (7 bp):
AGAAAGA
Found at i:75621 original size:1 final size:1
Alignment explanation
Indices: 75615--75658 Score: 88
Period size: 1 Copynumber: 44.0 Consensus size: 1
75605 CATTTACAAG
75615 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
75659 CTCTTCTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:75912 original size:3 final size:3
Alignment explanation
Indices: 75904--75935 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
75894 AGTAAAACAA
*
75904 AAG AAG AAG AAG AAG AAG AAG AAG AAG GAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
75936 AATGTTGCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:84473 original size:19 final size:20
Alignment explanation
Indices: 84436--84473 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
84426 TCGATTCTTA
84436 AAAACCAAAAGCAAACGAAC
1 AAAACCAAAAGCAAACGAAC
*
84456 AAAACCAGAAGC-AACGAA
1 AAAACCAAAAGCAAACGAA
84474 TGAATACCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.63, C:0.24, G:0.13, T:0.00
Consensus pattern (20 bp):
AAAACCAAAAGCAAACGAAC
Found at i:85158 original size:13 final size:13
Alignment explanation
Indices: 85140--85225 Score: 75
Period size: 13 Copynumber: 6.2 Consensus size: 13
85130 CCCAAATATC
85140 AAATTACAAAAGA
1 AAATTACAAAAGA
85153 AAATTATGCAAGAAGAA
1 AAATTA--CAA-AAG-A
*
85170 AAATGTA-AGAAGA
1 AAAT-TACAAAAGA
85183 AAATTACAAAAGA
1 AAATTACAAAAGA
* *
85196 AACTATGCAATAAGA
1 AAAT-TACAA-AAGA
85211 AAATTACAAAAGA
1 AAATTACAAAAGA
85224 AA
1 AA
85226 CCAATGCATT
Statistics
Matches: 59, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
12 2 0.03
13 25 0.42
14 11 0.19
15 11 0.19
16 3 0.05
17 5 0.08
18 2 0.03
ACGTcount: A:0.64, C:0.07, G:0.13, T:0.16
Consensus pattern (13 bp):
AAATTACAAAAGA
Found at i:88904 original size:4 final size:4
Alignment explanation
Indices: 88895--88927 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
88885 TAGTTACTGA
*
88895 TGTT TGTT TGTT TGTT TGTT TGTT TGTC TGTT T
1 TGTT TGTT TGTT TGTT TGTT TGTT TGTT TGTT T
88928 TTGCTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.03, G:0.24, T:0.73
Consensus pattern (4 bp):
TGTT
Found at i:89752 original size:49 final size:49
Alignment explanation
Indices: 89690--89794 Score: 201
Period size: 49 Copynumber: 2.1 Consensus size: 49
89680 TCATCAGAGA
*
89690 GATTAAATTTGATGACATTTTCATATCAAGGTTGTAATTTATTCTGCTT
1 GATTCAATTTGATGACATTTTCATATCAAGGTTGTAATTTATTCTGCTT
89739 GATTCAATTTGATGACATTTTCATATCAAGGTTGTAATTTATTCTGCTT
1 GATTCAATTTGATGACATTTTCATATCAAGGTTGTAATTTATTCTGCTT
89788 GATTCAA
1 GATTCAA
89795 CTGGCTTTAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 55 1.00
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (49 bp):
GATTCAATTTGATGACATTTTCATATCAAGGTTGTAATTTATTCTGCTT
Found at i:104483 original size:2 final size:2
Alignment explanation
Indices: 104476--104503 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
104466 TTTCTAAAAC
104476 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
104504 TTCAATCTTT
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:120773 original size:156 final size:154
Alignment explanation
Indices: 120437--120918 Score: 458
Period size: 156 Copynumber: 3.1 Consensus size: 154
120427 ATAACAATTG
* * *
120437 GAGGAAATCATTTT-TTCTTTGCTACCAAATCAACCT-ACAAACGAAATA-AAATTTATTAAGAA
1 GAGGGAATCATTTTCTTCTTTGCT-CCAAATCAACATAACAAACAAAATATAAA-TTATTAAGAA
* * * ***
120499 ATAGGGAAAACAACAAATCAAAAAATGAAAGAGATAATAAACATACTTTCAATGAAACTTCTGCA
64 ATAGGGAAAACAACAAAGCAAAAAACGTAAGAGATAATAAACATAAGATCAATGAAACTTCTGCA
120564 ACATATCACAGTATTAATCACAGTTT
129 ACATATCACAGTATTAATCACAGTTT
* * *
120590 GAGGGAATCATTTTCTTTTTTGCCTCCAAATCAA-ATAACAAACAAAATATATATTATTATGAAA
1 GAGGGAATCATTTTCTTCTTTG-CTCCAAATCAACATAACAAACAAAATATAAATTATTAAGAAA
* * *
120654 TACGGAAAACAAACAAAGCAAAAAAACGTAAGAGATAATAAACGTAAGATCAATGAAACTTTTGC
65 TAGGGAAAAC-AACAAAGC-AAAAAACGTAAGAGATAATAAACATAAGATCAATGAAACTTCTGC
* * * * * *
120719 AATATGTTATAGT-TATAGTCATAG-TT
128 AACATATCACAGTAT-TAATCACAGTTT
* * * * *
120745 GAAGGTAATCGTTTTCTTCTTTGACTCCAAATCAACTTAA-AAACAAAATATAAATTTTTAGGAA
1 G-AGGGAATCATTTTCTTCTTTG-CTCCAAATCAACATAACAAACAAAATATAAATTATTAAGAA
* * * * * *
120809 ATAGGGAAAATAACTAAAGCAAAAAAGGTAAGAGATAATAAATATATGTTCAATTAAAACTT-TG
64 ATAGGGAAAACAAC-AAAGCAAAAAACGTAAGAGATAATAAACATAAGATCAA-TGAAACTTCTG
* * * * * *
120873 CAATATGTCACAGTAATATTTACAGTTA
127 CAACATATCACAGTATTAATCACAGTTT
*
120901 GATGAGAATCATTTTCTT
1 GA-GGGAATCATTTTCTT
120919 TTCTTTTTTT
Statistics
Matches: 268, Mismatches: 47, Indels: 25
0.79 0.14 0.07
Matches are distributed among these distances:
153 14 0.05
154 45 0.17
155 67 0.25
156 139 0.52
157 3 0.01
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.29
Consensus pattern (154 bp):
GAGGGAATCATTTTCTTCTTTGCTCCAAATCAACATAACAAACAAAATATAAATTATTAAGAAAT
AGGGAAAACAACAAAGCAAAAAACGTAAGAGATAATAAACATAAGATCAATGAAACTTCTGCAAC
ATATCACAGTATTAATCACAGTTT
Found at i:121694 original size:158 final size:158
Alignment explanation
Indices: 121366--121944 Score: 496
Period size: 155 Copynumber: 3.7 Consensus size: 158
121356 TTGATAGAAT
* * * * * ** *
121366 ATGTCACAGAAATAATCACAGTTGGAGGGAATCATTTTCTTTTTTTGCCTCTAAATCATTCTATA
1 ATGTCACAGTAATAATCACAGTTGGAGGAAATTATTTTC-TTTTTTGCCTCCAAATTAAACTACA
* * * * * * * * *
121431 AACAAATTACAAA-T-TTTTT-GAAAAT-AGAGAAAACAATCAAAACAAAAAATGAAAGAAATAA
65 AACAAAATATAAATTATTTTTAGGAAATAAGA-AAAACAAACAAAGCATAAACTGCAAGAGATAA
* * **
121492 TAAACATATATTTAATAAAAAAAACTTTTGCAAC
129 TAAAC--ATATGT--TCAACGAAACTTTTGCAAC
* * * *
121526 ATGTCACAGTAATAAACACAGTTGGAGAAAATTATTTTCTTTTTTGCCTCCAAATT-AATTCATA
1 ATGTCACAGTAATAATCACAGTTGGAGGAAATTATTTTCTTTTTTGCCTCCAAATTAAACT-ACA
* * *
121590 AACAAAATATGAATTATTTTTAGGAAATAAGGAAAACAAACAAAGCAATAAA-TGTAAGAGATAA
65 AACAAAATATAAATTATTTTTAGGAAATAAGAAAAACAAACAAAGC-ATAAACTGCAAGAGATAA
* * *
121654 TAGATAT-TCGTTCAACGAAACATTTGCAAC
129 TAAACATAT-GTTCAACGAAACTTTTGCAAC
* * * ** * *
121684 ATGTCACAGTAATAGTCACAGTTGAAGGTAATTATTTTAATCTTTGCCTCCAAATCAAACTACAA
1 ATGTCACAGTAATAATCACAGTTGGAGGAAATTATTTTCTTTTTTGCCTCCAAATTAAACTACAA
* * * ** *
121749 ACAAAAT-TTAA-T-TTATTGGGAAATAAGAAAAACAAATGAAGCATAAACTGCAAGAGATACTA
66 ACAAAATATAAATTATTTTTAGGAAATAAGAAAAACAAACAAAGCATAAACTGCAAGAGATAATA
* *
121811 AACATATGTTTAATGAAACTTTTGCAAC
131 AACATATGTTCAACGAAACTTTTGCAAC
* * * * * *
121839 ATGTCACAGTAATAATCATATTTGGAGGGAATTATTTTCTTTTCTGCCTTCAAATTAACCTACAA
1 ATGTCACAGTAATAATCACAGTTGGAGGAAATTATTTTCTTTTTTGCCTCCAAATTAAACTACAA
* * * *
121904 ATAAAATATAAATTACTTTTAAGAAAT-AGAAAAAAAAACAA
66 ACAAAATATAAATTATTTTTAGGAAATAAGAAAAACAAACAA
121945 TAAAAGTAAA
Statistics
Matches: 334, Mismatches: 72, Indels: 29
0.77 0.17 0.07
Matches are distributed among these distances:
154 5 0.01
155 117 0.35
156 5 0.01
157 15 0.04
158 81 0.24
159 32 0.10
160 38 0.11
161 5 0.01
162 30 0.09
163 6 0.02
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (158 bp):
ATGTCACAGTAATAATCACAGTTGGAGGAAATTATTTTCTTTTTTGCCTCCAAATTAAACTACAA
ACAAAATATAAATTATTTTTAGGAAATAAGAAAAACAAACAAAGCATAAACTGCAAGAGATAATA
AACATATGTTCAACGAAACTTTTGCAAC
Found at i:126593 original size:2 final size:2
Alignment explanation
Indices: 126586--126621 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
126576 GCTTAGAATA
126586 AT AT AT AT AT AT AT AT AT AT AT -T A- 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
126622 TGACAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:128017 original size:1 final size:1
Alignment explanation
Indices: 128011--128039 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
128001 ATATAGTATG
128011 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
128040 GAAGAAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:128655 original size:27 final size:27
Alignment explanation
Indices: 128617--128669 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
128607 ATTTCTGGAA
*
128617 AACAAGGGAAATGGATAATTAAAAAGT
1 AACAAGGGAAATGGACAATTAAAAAGT
*
128644 AACAAGGGAAATTGACAATTAAAAAG
1 AACAAGGGAAATGGACAATTAAAAAG
128670 GAAGAGAGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.57, C:0.06, G:0.21, T:0.17
Consensus pattern (27 bp):
AACAAGGGAAATGGACAATTAAAAAGT
Found at i:130176 original size:63 final size:62
Alignment explanation
Indices: 130077--130194 Score: 164
Period size: 63 Copynumber: 1.9 Consensus size: 62
130067 GGCATGCTAC
* * ** *
130077 GTGTCACTTTTTGGTACACGTGGTGTGATATGTGTCACTTTTTTGTACACGTGGCGTGACAT
1 GTGTCACTTTTTGGTACACATGGTGTGACACATGTCACTTTTTGGTACACGTGGCGTGACAT
* *
130139 GTGTCACTTTTTCTGTACACATGGTGTGCCACATGTCACTTTTTGGTACACGTGGC
1 GTGTCACTTTTT-GGTACACATGGTGTGACACATGTCACTTTTTGGTACACGTGGC
130195 ATGCCACGTC
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
62 12 0.25
63 36 0.75
ACGTcount: A:0.16, C:0.19, G:0.25, T:0.39
Consensus pattern (62 bp):
GTGTCACTTTTTGGTACACATGGTGTGACACATGTCACTTTTTGGTACACGTGGCGTGACAT
Found at i:130200 original size:31 final size:31
Alignment explanation
Indices: 130046--130203 Score: 154
Period size: 31 Copynumber: 5.1 Consensus size: 31
130036 GGCATGCAAT
** * * *
130046 GTGTCACTTTTTGAAACATGTGGCATGCTAC
1 GTGTCACTTTTTGGTACACGTGGCGTGCCAC
* ** *
130077 GTGTCACTTTTTGGTACACGTGGTGTGATAT
1 GTGTCACTTTTTGGTACACGTGGCGTGCCAC
* * *
130108 GTGTCACTTTTTTGTACACGTGGCGTGACAT
1 GTGTCACTTTTTGGTACACGTGGCGTGCCAC
* * *
130139 GTGTCACTTTTTCTGTACACATGGTGTGCCAC
1 GTGTCACTTTTT-GGTACACGTGGCGTGCCAC
* *
130171 ATGTCACTTTTTGGTACACGTGGCATGCCAC
1 GTGTCACTTTTTGGTACACGTGGCGTGCCAC
130202 GT
1 GT
130204 CGAATACCGT
Statistics
Matches: 106, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
31 80 0.75
32 26 0.25
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (31 bp):
GTGTCACTTTTTGGTACACGTGGCGTGCCAC
Found at i:131155 original size:1 final size:1
Alignment explanation
Indices: 131149--131182 Score: 59
Period size: 1 Copynumber: 34.0 Consensus size: 1
131139 ACCATTAAAC
*
131149 AAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
131183 GAGGCTTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.97, C:0.03, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:131162 original size:14 final size:14
Alignment explanation
Indices: 131145--131182 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
131135 CAAAACCATT
131145 AAACAAAAAAAAAA
1 AAACAAAAAAAAAA
131159 AAACAAAAAAAAAA
1 AAACAAAAAAAAAA
131173 AAA-AAAAAAA
1 AAACAAAAAAA
131183 GAGGCTTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 7 0.29
14 17 0.71
ACGTcount: A:0.95, C:0.05, G:0.00, T:0.00
Consensus pattern (14 bp):
AAACAAAAAAAAAA
Found at i:142887 original size:22 final size:22
Alignment explanation
Indices: 142859--142903 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
142849 TTGGCACAAT
142859 TTCCAATAGAACCAGATACGTA
1 TTCCAATAGAACCAGATACGTA
142881 TTCCAATAGAACCAGATACGTA
1 TTCCAATAGAACCAGATACGTA
142903 T
1 T
142904 GCTTCTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.24
Consensus pattern (22 bp):
TTCCAATAGAACCAGATACGTA
Found at i:144747 original size:272 final size:271
Alignment explanation
Indices: 143240--145394 Score: 2629
Period size: 272 Copynumber: 7.9 Consensus size: 271
143230 TTACCGCTTA
** * * * *
143240 ATCTAGAAATGATTCCTTTAGCAATCCCTCATGTGTGTACGCAAACCCTCCATGAGTTTCAGGAG
1 ATCTAGAAATGATTCCTTTAATAGTCCCTCATGTGTGTACGCAAACTCTCCACGAGTTTCAGCAG
* * * *
143305 CACATGCTTAAGGTGGCTCCGATGACAAACAATTCCCAAGGCAATCTGAACAGCAGTTATCATCT
66 CACATGCTTAAGGTGGCTTCGATGACAAACAATCCCCAAGGCAATCTGAACAGCAGTTATCGTCC
* * * *
143370 GATATTCGAGCTAGGGAAAAGATCACAATAAAATTTTTGAATGTCATGTTCTTGGAAATGTAGGA
131 GATATTCGAGCTAGCGAAAAGGTCACAATAGAATCTTTGAATGTCATGTTCTTGGAAATGTAGGA
* * * * * * * *
143435 AAATTTAGGCAACTCCATGGCTTTGTTGTCGTTTAGTTAAAGGATTTTTATGTTTTTCTTATCAT
196 AAATTTAGGCAACTCCATGGCATTGTTGTCATTTAG-CAAGGGATTTCTATGTTTTCCCTACCAT
* * * *
143500 AGCATTATTATT
260 GGCATTGTTGTC
* *
143512 ATCTAGAAATGATCCCTTTAGA-AGTCCCTCATTTGTGTACGCAAACTCTCCACGAGTTTCAGCA
1 ATCTAGAAATGATTCCTTTA-ATAGTCCCTCATGTGTGTACGCAAACTCTCCACGAGTTTCAGCA
* * * * * * * *
143576 GCACATGCTTAAGGTGGATCCAATGACAAACAGTTCCCAAGTCAATCTGAATAACAGTTATCGTC
65 GCACATGCTTAAGGTGGCTTCGATGACAAACAATCCCCAAGGCAATCTGAACAGCAGTTATCGTC
* * * *
143641 CGATATTCGAGTTAGCGCGAAAAGGTCACAATAGAATCTTTAAATGCCATGTTCTAT-GAGATGT
130 CGATATTCGAGCTA--GCGAAAAGGTCACAATAGAATCTTTGAATGTCATGTTCT-TGGAAATGT
* * * * * *
143705 AGGAAAATATAGGCAACTCCATGGCATTGTCGTCATTTAGCATGTGGATTTCAACGTTTTTCCTA
192 AGGAAAATTTAGGCAACTCCATGGCATTGTTGTCATTTAGCAAG-GGATTTCTATGTTTTCCCTA
143770 CCATGGCCATTGTTGTC
256 CCATGG-CATTGTTGTC
* * * * * * *
143787 ATTTAGAAATGATTCCATTAGTAGTCCCTTATATGTGTGCGCAAACTCTACACGAGTTTCAGC-G
1 ATCTAGAAATGATTCCTTTAATAGTCCCTCATGTGTGTACGCAAACTCTCCACGAGTTTCAGCAG
* * *
143851 ACACATGCTTAAGGTGG-ATCGATGACAAACAATCCCTAAGGCAATCTGAACAGCAGTTATCATC
66 -CACATGCTTAAGGTGGCTTCGATGACAAACAATCCCCAAGGCAATCTGAACAGCAGTTATCGTC
* * * *
143915 CGATATTCGAGTTAGCGAAAAGGTCATAATAGAATCTTTGAATGTCATGTTCTTAGAGATGTAGG
130 CGATATTCGAGCTAGCGAAAAGGTCACAATAGAATCTTTGAATGTCATGTTCTTGGAAATGTAGG
* * * **
143980 -AAATTTAGACAACTCAATGGCATTATTGTCATTTAGCAAGGGTATTTCTACATTTTCCCTACCA
195 AAAATTTAGGCAACTCCATGGCATTGTTGTCATTTAGCAAGGG-ATTTCTATGTTTTCCCTACCA
144044 TGGCATTGTTGTC
259 TGGCATTGTTGTC
*
144057 ATCTAAAAATGATTCCTTTAATAGTCCCTCATGTGTGTACGCAAACTCTCCACGAGTTTCAGACA
1 ATCTAGAAATGATTCCTTTAATAGTCCCTCATGTGTGTACGCAAACTCTCCACGAGTTTCAG-CA
144122 -CACATGCTTAAGGTGGCTTCGATGACAAACAATCCCCAAGGCAATCTGAACAGCAGTTATCGTC
65 GCACATGCTTAAGGTGGCTTCGATGACAAACAATCCCCAAGGCAATCTGAACAGCAGTTATCGTC
* *
144186 CTATATTCGAGCTAGCGAAAAGGTCACAATAGAATCTTTGAATGCCATGTTCTTGGAAATGTAGG
130 CGATATTCGAGCTAGCGAAAAGGTCACAATAGAATCTTTGAATGTCATGTTCTTGGAAATGTAGG
** *
144251 AAAATTTAGGCAACTCCATGGCATTGTTGTCAAAT-GCAAGGGGATTTCTATGTTTTCCCTAGCA
195 AAAATTTAGGCAACTCCATGGCATTGTTGTCATTTAGCAA-GGGATTTCTATGTTTTCCCTACCA
*
144315 TGACATTGTTGTC
259 TGGCATTGTTGTC
* ** * * ** * * *
144328 ATATAGAAATGATTCCTTTAGCAGTCCCTTATGTGTGTACGCAAACTCTCCATGTTTTTTAACAC
1 ATCTAGAAATGATTCCTTTAATAGTCCCTCATGTGTGTACGCAAACTCTCCACGAGTTTCAGCAG
* * * ** * ** *
144393 CACATGCTTAAGGTGGTTTCGGTGAAAAACAATCCCTTAGGCAATCTGAATTA-CAGAAATCGTT
66 CACATGCTTAAGGTGGCTTCGATGACAAACAATCCCCAAGGCAATCTGAA-CAGCAGTTATCGTC
* * * * * *
144457 CGATATTCGAGTTAGCGAAAAGGCCACAATAGAATCTTTGAATGCCACGTTATTGGAAAAGTAGG
130 CGATATTCGAGCTAGCGAAAAGGTCACAATAGAATCTTTGAATGTCATGTTCTTGGAAATGTAGG
* * * * * *
144522 AAAATTTAGGCAACTACATGACATTGTTGTCATTTAGCAAGGAGATCTCAACGTTTTCCCTACTA
195 AAAATTTAGGCAACTCCATGGCATTGTTGTCATTTAGCAAGG-GATTTCTATGTTTTCCCTACCA
* * *
144587 TCGCGTTGCTGTC
259 TGGCATTGTTGTC
* * * * * * *
144600 ATGTAGAAATGATTCTTTTAACAGTCTCTTATATGTGTACGCAAACTCTCCACGAGTTTCAACAG
1 ATCTAGAAATGATTCCTTTAATAGTCCCTCATGTGTGTACGCAAACTCTCCACGAGTTTCAGCAG
* * * *
144665 CACATGATTAAGATGGCTTCGATGACAAACAATCCCCAAGGCAATCTGAACAGCAGTTATCATTC
66 CACATGCTTAAGGTGGCTTCGATGACAAACAATCCCCAAGGCAATCTGAACAGCAGTTATCGTCC
* * * *
144730 GATATTTGAGCTAGCGAAAAGGTTACAATAAAATCTTTGAATGTCATGTTCTTGGAAATATAGGA
131 GATATTCGAGCTAGCGAAAAGGTCACAATAGAATCTTTGAATGTCATGTTCTTGGAAATGTAGGA
* * *
144795 AAATTTAGGCAACTCCATGGCATTATTGTTATTTAGCAAGAAGATTTCTATGTTTTCCCTACCAT
196 AAATTTAGGCAACTCCATGGCATTGTTGTCATTTAGCAAG-GGATTTCTATGTTTTCCCTACCAT
*
144860 GGCATTGCTGTC
260 GGCATTGTTGTC
* * * * * *
144872 ATCAAGAAATAATTCCTTTAATAGTCTCTTATGTGTGTACGCAAACTCTCCACGGGTTTCAGCCG
1 ATCTAGAAATGATTCCTTTAATAGTCCCTCATGTGTGTACGCAAACTCTCCACGAGTTTCAGCAG
* *
144937 CACATGCTTAAGGTGGCTCCGATGACAAACAATCCCCAAGGCAATCTGAACAACAGTTATCGTCC
66 CACATGCTTAAGGTGGCTTCGATGACAAACAATCCCCAAGGCAATCTGAACAGCAGTTATCGTCC
* * * * * * * *
145002 GATATTGGAGCTAGAGAAAAAGTCACAACATAATTTTTGAATGTCATGTTCTTGGAGATGCAGGA
131 GATATTCGAGCTAGCGAAAAGGTCACAATAGAATCTTTGAATGTCATGTTCTTGGAAATGTAGGA
* * * * * * *
145067 AAATTTAGGCAACTCAATGTCATTGTTGTCATTTAACAAGGGGATTTTTATGTTTTTCTTACGAT
196 AAATTTAGGCAACTCCATGGCATTGTTGTCATTTAGCAA-GGGATTTCTATGTTTTCCCTACCAT
145132 GGCATTGTTGTC
260 GGCATTGTTGTC
* * * *
145144 ATCTAGAATTGATTCCTTTAGTAGTCCCTCATGCGTGTACGCAAACTCTCCACGAGTTTTAGCAG
1 ATCTAGAAATGATTCCTTTAATAGTCCCTCATGTGTGTACGCAAACTCTCCACGAGTTTCAGCAG
* * *** * *
145209 CACATGCTTAAAGTGGC-TCTGATGACAAACAGTTTTCAAAGTAATCTGAACAGCAGTTATCGTC
66 CACATGCTTAAGGTGGCTTC-GATGACAAACAATCCCCAAGGCAATCTGAACAGCAGTTATCGTC
145273 CGATATTCGAGCTAGCGAAAAGGTCACAATAGAATCTTTGAATGTCATGTTCTTGGAAATGTAGG
130 CGATATTCGAGCTAGCGAAAAGGTCACAATAGAATCTTTGAATGTCATGTTCTTGGAAATGTAGG
* * *
145338 AAAATTTAGGCAACTACATGGCATTGTTATCATTTAGCAAGGGCATTTC-ACGTTTTC
195 AAAATTTAGGCAACTCCATGGCATTGTTGTCATTTAGCAAGGG-ATTTCTATGTTTTC
145395 AAAATTTTCT
Statistics
Matches: 1613, Mismatches: 246, Indels: 49
0.85 0.13 0.03
Matches are distributed among these distances:
270 84 0.05
271 402 0.25
272 900 0.56
273 2 0.00
274 147 0.09
275 78 0.05
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Consensus pattern (271 bp):
ATCTAGAAATGATTCCTTTAATAGTCCCTCATGTGTGTACGCAAACTCTCCACGAGTTTCAGCAG
CACATGCTTAAGGTGGCTTCGATGACAAACAATCCCCAAGGCAATCTGAACAGCAGTTATCGTCC
GATATTCGAGCTAGCGAAAAGGTCACAATAGAATCTTTGAATGTCATGTTCTTGGAAATGTAGGA
AAATTTAGGCAACTCCATGGCATTGTTGTCATTTAGCAAGGGATTTCTATGTTTTCCCTACCATG
GCATTGTTGTC
Found at i:164800 original size:2 final size:2
Alignment explanation
Indices: 164793--164822 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
164783 TAATCATGTA
164793 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
164823 TATGATAAAA
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:167268 original size:54 final size:50
Alignment explanation
Indices: 167173--167274 Score: 150
Period size: 54 Copynumber: 2.0 Consensus size: 50
167163 TTTATTTTAA
* *
167173 GCAAATTATACAATACACCGTGGAGTTTAGCAGACTACACAAGCGGGTTG
1 GCAAATTATACAATACACCGTGGAATTTAGCAAACTACACAAGCGGGTTG
167223 GCAAATTATACAATACACCGTTAGTGGAATTTAGCAAACTACACAAGCGGGT
1 GCAAATTATACAATACACC----GTGGAATTTAGCAAACTACACAAGCGGGT
167275 CTTGAATGGT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
50 19 0.41
54 27 0.59
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.23
Consensus pattern (50 bp):
GCAAATTATACAATACACCGTGGAATTTAGCAAACTACACAAGCGGGTTG
Found at i:172783 original size:37 final size:37
Alignment explanation
Indices: 172693--172803 Score: 161
Period size: 37 Copynumber: 2.9 Consensus size: 37
172683 GTTATGGGAT
172693 CTTCTTAAGGTTAAGGATGATGGGTCTAAATACAACTTGAA
1 CTTCTTAAGGTTAA-G--GAT-GGTCTAAATACAACTTGAA
* *
172734 CTTCTTAA-GTTAAGGATGGTCTAAATAAAACTTGAG
1 CTTCTTAAGGTTAAGGATGGTCTAAATACAACTTGAA
172770 CTTCTTAAGGTTAAGGATGGTCTAAATACAACTT
1 CTTCTTAAGGTTAAGGATGGTCTAAATACAACTT
172804 AAGTCCTTCC
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
36 25 0.38
37 27 0.41
39 1 0.02
40 5 0.08
41 8 0.12
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (37 bp):
CTTCTTAAGGTTAAGGATGGTCTAAATACAACTTGAA
Found at i:174174 original size:18 final size:18
Alignment explanation
Indices: 174153--174194 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
174143 TCACCACCAC
174153 CACCACCACCCCCACCCT
1 CACCACCACCCCCACCCT
*
174171 CACC-CACACCCCCATCCT
1 CACCAC-CACCCCCACCCT
174189 C-CCACC
1 CACCACC
174195 CCTCCCCCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.21, C:0.71, G:0.00, T:0.07
Consensus pattern (18 bp):
CACCACCACCCCCACCCT
Found at i:174313 original size:48 final size:48
Alignment explanation
Indices: 174273--174398 Score: 173
Period size: 48 Copynumber: 2.6 Consensus size: 48
174263 ACCACCGCAC
* *
174273 CCAGTTTACCCTCCGACCAAGCCACCAACTAAGGCACCACCCAAGCCA
1 CCAGTTTACCCTCCAACCAAGCCACCAACTAACGCACCACCCAAGCCA
* * * * *
174321 CCAG-TGAGCCCACCAACCAAGCCACCAACTTACTCGCCACCCAAGCCA
1 CCAGTTTA-CCCTCCAACCAAGCCACCAACTAACGCACCACCCAAGCCA
174369 CCAGTTTACCCTCCAACCAAGCCACCAACT
1 CCAGTTTACCCTCCAACCAAGCCACCAACT
174399 CAGCCCCCGG
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
47 2 0.03
48 63 0.94
49 2 0.03
ACGTcount: A:0.31, C:0.47, G:0.11, T:0.11
Consensus pattern (48 bp):
CCAGTTTACCCTCCAACCAAGCCACCAACTAACGCACCACCCAAGCCA
Found at i:174316 original size:24 final size:24
Alignment explanation
Indices: 174289--174403 Score: 81
Period size: 24 Copynumber: 4.8 Consensus size: 24
174279 TACCCTCCGA
*
174289 CCAAGCCACCAACTAAGGCACCAC
1 CCAAGCCACCAACTAAGCCACCAC
* * *
174313 CCAAGCCACC-AGTGAGCCCACCAA
1 CCAAGCCACCAACTAAG-CCACCAC
* *
174337 CCAAGCCACCAACTTA-CTCGCCAC
1 CCAAGCCACCAACTAAGC-CACCAC
** * * * *
174361 CCAAGCCACCAGTTTACCCTCCAA
1 CCAAGCCACCAACTAAGCCACCAC
*
174385 CCAAGCCACCAACTCAGCC
1 CCAAGCCACCAACTAAGCC
174404 CCCGGTTAAG
Statistics
Matches: 71, Mismatches: 16, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
23 5 0.07
24 62 0.87
25 4 0.06
ACGTcount: A:0.32, C:0.48, G:0.11, T:0.09
Consensus pattern (24 bp):
CCAAGCCACCAACTAAGCCACCAC
Found at i:174322 original size:12 final size:12
Alignment explanation
Indices: 174288--174349 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
174278 TTACCCTCCG
174288 ACCAAGCCACCA
1 ACCAAGCCACCA
* *
174300 ACTAAGGCACCA
1 ACCAAGCCACCA
*
174312 CCCAAGCCACC-
1 ACCAAGCCACCA
***
174323 AGTGAGCCCACCA
1 ACCAAG-CCACCA
174336 ACCAAGCCACCA
1 ACCAAGCCACCA
174348 AC
1 AC
174350 TTACTCGCCA
Statistics
Matches: 36, Mismatches: 12, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
11 2 0.06
12 31 0.86
13 3 0.08
ACGTcount: A:0.37, C:0.47, G:0.13, T:0.03
Consensus pattern (12 bp):
ACCAAGCCACCA
Found at i:190882 original size:1 final size:1
Alignment explanation
Indices: 190878--190916 Score: 78
Period size: 1 Copynumber: 39.0 Consensus size: 1
190868 ATCCATCTGG
190878 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
190917 CTCCTCAAGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:197040 original size:18 final size:19
Alignment explanation
Indices: 197017--197057 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
197007 CCAAGGGTTT
197017 AAAAAGAAAAG-AAAAGAA
1 AAAAAGAAAAGAAAAAGAA
*
197035 AAAAAGAGAAGAAAAAGAA
1 AAAAAGAAAAGAAAAAGAA
197054 AAAA
1 AAAA
197058 TTCCGTTGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (19 bp):
AAAAAGAAAAGAAAAAGAA
Found at i:201577 original size:21 final size:20
Alignment explanation
Indices: 201551--201598 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
201541 GTAGGCAAAA
*
201551 TTAACGGTGTTAAGTAATTTG
1 TTAACGG-GCTAAGTAATTTG
*
201572 TTAACGGGCTATGTAATTTG
1 TTAACGGGCTAAGTAATTTG
*
201592 CTAACGG
1 TTAACGG
201599 AAAATAAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.27, C:0.10, G:0.25, T:0.38
Consensus pattern (20 bp):
TTAACGGGCTAAGTAATTTG
Found at i:202404 original size:30 final size:30
Alignment explanation
Indices: 202362--202419 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 30
202352 CTAAAATAAA
202362 TTGTACTACTTGCCATCTAATATTCATCTT
1 TTGTACTACTTGCCATCTAATATTCATCTT
202392 TTGTA-TATCTTGCCATCTAATATTCATC
1 TTGTACTA-CTTGCCATCTAATATTCATC
202420 GCTAAGCATC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 2 0.07
30 25 0.93
ACGTcount: A:0.24, C:0.22, G:0.07, T:0.47
Consensus pattern (30 bp):
TTGTACTACTTGCCATCTAATATTCATCTT
Found at i:211124 original size:2 final size:2
Alignment explanation
Indices: 211119--211157 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
211109 TATGTGTGTG
211119 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 T
211158 TTCACCTTAC
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:213521 original size:440 final size:435
Alignment explanation
Indices: 212712--213725 Score: 1232
Period size: 440 Copynumber: 2.3 Consensus size: 435
212702 GTATTTTTTT
* * * * *
212712 TTCTATTTGTCCGATTAAGGTGATTCAAGTATCTATTAAAAGGTAATTTCATGATCTACAATTTT
1 TTCTATTTGTCCAATTAAGGTAATTCATGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTT
* * * * *
212777 CATGAAGAACTCAAAAGCCAATTTTAATGTCTTGATTCAAAAAAATGCTTCCGAAATTTTGTGGT
66 CATGAAGAACTCAAAAGCAAATTTTAATGTTTTAATTCAAAAAAATACTTCCGAAATTTGGTGGT
* * * * *
212842 TTTGATTACCGGTCAATTTAATATCATATAATTTTTTTTGTCCACATGTCTGATTGAAGTTAATG
131 TTCGATTACCGGTCAATTTAATACCATATAA--TTTTTCGTCCACATGTCTGATTAAAGTTAATC
* * *
212907 AAATGTCAATTAAAAGGTTATTGCATGATTTACAACTTTCATGAAGGACCCGAAAGTTAAATTTG
194 AAATGTCAATTAAAAGGTTACTGCATGATCTACAACTTTCATGAAGAACCCGAAAGTTAAATTTG
* * *
212972 ATCTATGAATTTCATGAAGGGTTCAAAAGGGAGTTTTTATGCTTCAAGATCTCCATTAACAAACA
259 ATCTACGAATTTCATGAAGGGTTCAAAAGGGAATTTTCATGCTTCAAGATCTCCATTAACAAACA
* * ** * *
213037 TTTTCTTATTTGGATTATTTATCAAATGACCCTCATGTTTTTCTACTTTATACGACTTAGTCCTT
324 TTTTCTTATTTGAATTAGTTATCAAATGACCCTCATACTTTTCTACTTTATACGACTTACTCATT
* *
213102 TACAAATTCTACCTTAATCTAACG-TTTAA-GATTTATTTTTTTTATTCTTTG
389 TACAAATTCTACCTT-AT-T--CGATTTAACGATTCA-TTTTTTT-TTCTTAG
* ** * * *
213153 TTCTGTTTGTCCGGTTAAGTTTTGATTTATGTGTCTATTAAAAGGTAATTTCATGATCTACAACT
1 TTCTATTTGTCCAATTAAG--GTAATTCATGTGTCTATTAAAAGGTAATTTCATGATCTACAACT
* * *
213218 TTCATGAAGAACTCAAAAGCAAATTTTTATGTTTTAATTCAAAAAAATACTTCCTAAATTTGGTT
64 TTCATGAAGAACTCAAAAGCAAATTTTAATGTTTTAATTCAAAAAAATACTTCCGAAATTTGGTG
*** *
213283 GTTTCGATTGTTGGT-ATATTTAATACCATATAA-TTTTCGATCCACATGTCTGATTAAAGTTAT
129 GTTTCGATTACCGGTCA-ATTTAATACCATATAATTTTTCG-TCCACATGTCTGATTAAAGTTAA
* * * * *
213346 TCAAGTGTCGATTAAAATGTTACTGCATGATCTACAACTTTCATTAAGAACCTGAAAGTT-AATT
192 TCAAATGTCAATTAAAAGGTTACTGCATGATCTACAACTTTCATGAAGAACCCGAAAGTTAAATT
* * * *
213410 TGATCTACGAGTTTCATGAATGGTTCAAAAGGGAATTTTCATGTTTCAAGA-CATCCATTAAGAA
257 TGATCTACGAATTTCATGAAGGGTTCAAAAGGGAATTTTCATGCTTCAAGATC-TCCATTAACAA
* * * * *
213474 ATATTTTCTTATTTGAATTAGTTATCAAATGACCCTCATACTTTTCTATTTTATGCTATTTACTC
321 ACATTTTCTTATTTGAATTAGTTATCAAATGACCCTCATACTTTTCTACTTTATACGACTTACTC
* *
213539 ATTTACAAATTCTATCTTATTCGATTTAACGCTTCATTTTTTTTTCTTAG
386 ATTTACAAATTCTACCTTATTCGATTTAACGATTCATTTTTTTTTCTTAG
* *
213589 TTCTATTTGTCCAATTAAGGTAATTCATGTGTCTATTAAAAGGTAATTTTATGATCGACAACTTT
1 TTCTATTTGTCCAATTAAGGTAATTCATGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTT
* * * * * ** * *
213654 CATGAA-AGACTCAAAAGCTAATTTTCATGTTTCAATTCTAAAAGATACTTTTGAAATTTTGTGA
66 CATGAAGA-ACTCAAAAGCAAATTTTAATGTTTTAATTCAAAAAAATACTTCCGAAATTTGGTGG
213718 TTTCGATT
130 TTTCGATT
213726 GACAATCTAT
Statistics
Matches: 492, Mismatches: 73, Indels: 23
0.84 0.12 0.04
Matches are distributed among these distances:
433 1 0.00
434 100 0.20
436 24 0.05
437 12 0.02
438 5 0.01
439 3 0.01
440 135 0.27
441 89 0.18
442 1 0.00
443 122 0.25
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (435 bp):
TTCTATTTGTCCAATTAAGGTAATTCATGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTT
CATGAAGAACTCAAAAGCAAATTTTAATGTTTTAATTCAAAAAAATACTTCCGAAATTTGGTGGT
TTCGATTACCGGTCAATTTAATACCATATAATTTTTCGTCCACATGTCTGATTAAAGTTAATCAA
ATGTCAATTAAAAGGTTACTGCATGATCTACAACTTTCATGAAGAACCCGAAAGTTAAATTTGAT
CTACGAATTTCATGAAGGGTTCAAAAGGGAATTTTCATGCTTCAAGATCTCCATTAACAAACATT
TTCTTATTTGAATTAGTTATCAAATGACCCTCATACTTTTCTACTTTATACGACTTACTCATTTA
CAAATTCTACCTTATTCGATTTAACGATTCATTTTTTTTTCTTAG
Done.