Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016335.1 Corchorus capsularis cultivar CVL-1 contig16356, 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: 124029
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:3306 original size:11 final size:11
Alignment explanation
Indices: 3292--3329 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3282 ATTCATAACA
3292 AATTTATAATT
1 AATTTATAATT
3303 AATTTATAATT
1 AATTTATAATT
3314 -ATTTGATAATT
1 AATTT-ATAATT
*
3325 TATTT
1 AATTT
3330 TATATATAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:7110 original size:16 final size:14
Alignment explanation
Indices: 7089--7127 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
7079 TTAATATCTT
7089 TTCTTTTCTTTTTTC
1 TTCTTTT-TTTTTTC
7104 GTTCTTTATTTTTTTC
1 -TTCTTT-TTTTTTTC
7120 TTCTTTTT
1 TTCTTTTT
7128 ATTTCCTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 2 0.09
15 6 0.27
16 13 0.59
17 1 0.05
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (14 bp):
TTCTTTTTTTTTTC
Found at i:14454 original size:15 final size:15
Alignment explanation
Indices: 14434--14464 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
14424 ATTGAAGTAG
14434 TGGTAATAAATCAAA
1 TGGTAATAAATCAAA
14449 TGGTAATAAATCAAA
1 TGGTAATAAATCAAA
14464 T
1 T
14465 AATGATGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.06, G:0.13, T:0.29
Consensus pattern (15 bp):
TGGTAATAAATCAAA
Found at i:23664 original size:13 final size:14
Alignment explanation
Indices: 23646--23674 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
23636 GAATTCCTTA
23646 GAGAGAGAG-CTGT
1 GAGAGAGAGCCTGT
23659 GAGAGAGAGCCTGT
1 GAGAGAGAGCCTGT
23673 GA
1 GA
23675 TTGAAGAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.31, C:0.10, G:0.45, T:0.14
Consensus pattern (14 bp):
GAGAGAGAGCCTGT
Found at i:26844 original size:26 final size:26
Alignment explanation
Indices: 26815--26866 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
26805 ACCTAGTAAC
26815 TAACCACAACAAGAAAACAAGAGAAA
1 TAACCACAACAAGAAAACAAGAGAAA
26841 TAACCACAACAAGAAAACAAGAGAAA
1 TAACCACAACAAGAAAACAAGAGAAA
26867 CAACTCAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.65, C:0.19, G:0.12, T:0.04
Consensus pattern (26 bp):
TAACCACAACAAGAAAACAAGAGAAA
Found at i:33389 original size:33 final size:32
Alignment explanation
Indices: 33352--33418 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 32
33342 CCTAAGATGC
33352 TTAAAAATAAAATCCTAATCTAGAAAACATAAA
1 TTAAAAATAAAATCCTAAT-TAGAAAACATAAA
** * *
33385 TTAAACTTAAAATCCTAATTTGAAAACCTAAA
1 TTAAAAATAAAATCCTAATTAGAAAACATAAA
33417 TT
1 TT
33419 GGTTTAGGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 13 0.43
33 17 0.57
ACGTcount: A:0.54, C:0.13, G:0.03, T:0.30
Consensus pattern (32 bp):
TTAAAAATAAAATCCTAATTAGAAAACATAAA
Found at i:41649 original size:19 final size:18
Alignment explanation
Indices: 41616--41651 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
41606 TTGAAATAAT
41616 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
41634 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
41652 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:42410 original size:30 final size:29
Alignment explanation
Indices: 42376--42467 Score: 87
Period size: 30 Copynumber: 3.1 Consensus size: 29
42366 GGTAGCACCC
*
42376 CTTTTACCGCAGAACTCACGTTGCGAAGCA
1 CTTTTACCGCA-AACTCACTTTGCGAAGCA
* * * *
42406 CTTTTGCCGCAAGACTCGCTTTACGAAACA
1 CTTTTACCGCAA-ACTCACTTTGCGAAGCA
*
42436 C-TTTACAGCAAATCTCACTTTGCGATAGCA
1 CTTTTACCGCAAA-CTCACTTTGCGA-AGCA
42466 CT
1 CT
42468 ATCGCAGAGC
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
28 1 0.02
29 19 0.40
30 28 0.58
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.27
Consensus pattern (29 bp):
CTTTTACCGCAAACTCACTTTGCGAAGCA
Found at i:44434 original size:37 final size:37
Alignment explanation
Indices: 44349--44473 Score: 101
Period size: 37 Copynumber: 3.4 Consensus size: 37
44339 GACCGATCAA
* * * * *
44349 TAGCACACTCTTTACCGCAGAGCTC-CTCTTACTGCGA
1 TAGCACCCTCTTTACCGCAGACCTCTC-CTTACAGAGG
** *
44386 TAGCATACTCTTTGCCGCA-ATCCTCTCCTTACAGAGG
1 TAGCACCCTCTTTACCGCAGA-CCTCTCCTTACAGAGG
* * * * *
44423 TAGCACCCTCTTCACTGCAGAGCTCTCCTTACTGCGG
1 TAGCACCCTCTTTACCGCAGACCTCTCCTTACAGAGG
44460 TAGCACCCTCTTTA
1 TAGCACCCTCTTTA
44474 TCGTAGAGCT
Statistics
Matches: 70, Mismatches: 15, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
36 1 0.01
37 67 0.96
38 2 0.03
ACGTcount: A:0.20, C:0.35, G:0.16, T:0.29
Consensus pattern (37 bp):
TAGCACCCTCTTTACCGCAGACCTCTCCTTACAGAGG
Found at i:46252 original size:21 final size:21
Alignment explanation
Indices: 46228--46284 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
46218 AAAAACCCCT
*
46228 ACTTGGACAAAAAGATAAGCA
1 ACTTGGACAAAAAGAGAAGCA
*
46249 ACTTGGACAAAAAGAGAAGTA
1 ACTTGGACAAAAAGAGAAGCA
46270 ACTTGGACAAAAAGA
1 ACTTGGACAAAAAGA
46285 AACTAGCTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.53, C:0.12, G:0.21, T:0.14
Consensus pattern (21 bp):
ACTTGGACAAAAAGAGAAGCA
Found at i:61126 original size:12 final size:13
Alignment explanation
Indices: 61085--61129 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
61075 AATTATTGTT
61085 TGCTTTATTAATC
1 TGCTTTATTAATC
*
61098 TGCTTTATTAATT
1 TGCTTTATTAATC
61111 TGCTTTA-TAATC
1 TGCTTTATTAATC
61123 TGCTTTA
1 TGCTTTA
61130 GATTTAGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56
Consensus pattern (13 bp):
TGCTTTATTAATC
Found at i:61512 original size:39 final size:38
Alignment explanation
Indices: 61440--61520 Score: 110
Period size: 39 Copynumber: 2.1 Consensus size: 38
61430 TAGTTTTTGA
*
61440 TTTTCCGTTTTTTCTAAAAAAAAAAAAGTTTTTTCCGAT
1 TTTTCCGATTTTTCTAAAAAAAAAAAAGTTTTTTCCG-T
* *
61479 TTTTCCGATTTTTCTAAAAAAAATATA-TATTTTTCCGT
1 TTTTCCGATTTTTCTAAAAAAAAAAAAGT-TTTTTCCGT
61517 TTTT
1 TTTT
61521 AAAATTAGGG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
38 6 0.16
39 32 0.84
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.51
Consensus pattern (38 bp):
TTTTCCGATTTTTCTAAAAAAAAAAAAGTTTTTTCCGT
Found at i:61600 original size:36 final size:36
Alignment explanation
Indices: 61530--61606 Score: 104
Period size: 36 Copynumber: 2.1 Consensus size: 36
61520 TAAAATTAGG
61530 GTTTCCGATTTTTCTTTAAAAAAAATTAATTTTTCT
1 GTTTCCGATTTTTCTTTAAAAAAAATTAATTTTTCT
* *
61566 TTTTCCG-TTTTTCCTTTAAAAAAAATT-TTATTTTCT
1 GTTTCCGATTTTT-CTTTAAAAAAAATTAAT-TTTTCT
61602 GTTTC
1 GTTTC
61607 TGCTTTTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 6 0.17
36 30 0.83
ACGTcount: A:0.26, C:0.13, G:0.05, T:0.56
Consensus pattern (36 bp):
GTTTCCGATTTTTCTTTAAAAAAAATTAATTTTTCT
Found at i:68292 original size:12 final size:13
Alignment explanation
Indices: 68251--68295 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
68241 AATTATTGTT
68251 TGCTTTATTAATC
1 TGCTTTATTAATC
*
68264 TGCTTTATTAATT
1 TGCTTTATTAATC
68277 TGCTTTA-TAATC
1 TGCTTTATTAATC
68289 TGCTTTA
1 TGCTTTA
68296 GATTTAGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56
Consensus pattern (13 bp):
TGCTTTATTAATC
Found at i:75163 original size:6 final size:6
Alignment explanation
Indices: 75152--75178 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
75142 GTTGCATAGC
75152 TTTGTT TTTGTT TTTGTT TTTGTT TTT
1 TTTGTT TTTGTT TTTGTT TTTGTT TTT
75179 AATTACTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTTGTT
Found at i:81428 original size:21 final size:21
Alignment explanation
Indices: 81404--81446 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
81394 CGTTGAAATG
81404 TGAATTTGTGGTAGTCTTTAT
1 TGAATTTGTGGTAGTCTTTAT
*
81425 TGAATTTTTGGTAGTCTTTAT
1 TGAATTTGTGGTAGTCTTTAT
81446 T
1 T
81447 ACTCACGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.05, G:0.21, T:0.56
Consensus pattern (21 bp):
TGAATTTGTGGTAGTCTTTAT
Found at i:81489 original size:21 final size:21
Alignment explanation
Indices: 81463--81505 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
81453 GTTTGGAATG
81463 TGAATTTTTGGTAGTCTTTAT
1 TGAATTTTTGGTAGTCTTTAT
81484 TGAATTTTTGGTAGTCTTTAT
1 TGAATTTTTGGTAGTCTTTAT
81505 T
1 T
81506 ACTCACGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.05, G:0.19, T:0.58
Consensus pattern (21 bp):
TGAATTTTTGGTAGTCTTTAT
Found at i:81492 original size:59 final size:59
Alignment explanation
Indices: 81400--81514 Score: 221
Period size: 59 Copynumber: 1.9 Consensus size: 59
81390 GTCTCGTTGA
81400 AATGTGAATTTGTGGTAGTCTTTATTGAATTTTTGGTAGTCTTTATTACTCACGTTTGG
1 AATGTGAATTTGTGGTAGTCTTTATTGAATTTTTGGTAGTCTTTATTACTCACGTTTGG
*
81459 AATGTGAATTTTTGGTAGTCTTTATTGAATTTTTGGTAGTCTTTATTACTCACGTT
1 AATGTGAATTTGTGGTAGTCTTTATTGAATTTTTGGTAGTCTTTATTACTCACGTT
81515 AATGACAGTT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.21, C:0.09, G:0.20, T:0.50
Consensus pattern (59 bp):
AATGTGAATTTGTGGTAGTCTTTATTGAATTTTTGGTAGTCTTTATTACTCACGTTTGG
Found at i:86390 original size:24 final size:24
Alignment explanation
Indices: 86362--86442 Score: 67
Period size: 24 Copynumber: 3.2 Consensus size: 24
86352 TGATGATTAA
86362 ATTTGCGTAGCTTATAGCTGTTGT
1 ATTTGCGTAGCTTATAGCTGTTGT
** *
86386 ATTTGC-TATGGGTATCGAGATAGTTG-
1 ATTTGCGTA-GCTTAT--AGCT-GTTGT
*
86412 ATTTTGCGTAACTTATAGCTGTTGT
1 A-TTTGCGTAGCTTATAGCTGTTGT
86437 ATTTGC
1 ATTTGC
86443 TATGGACATC
Statistics
Matches: 43, Mismatches: 7, Indels: 14
0.67 0.11 0.22
Matches are distributed among these distances:
23 2 0.05
24 19 0.44
25 4 0.09
26 4 0.09
27 12 0.28
28 2 0.05
ACGTcount: A:0.20, C:0.11, G:0.25, T:0.44
Consensus pattern (24 bp):
ATTTGCGTAGCTTATAGCTGTTGT
Found at i:88105 original size:60 final size:60
Alignment explanation
Indices: 87947--88095 Score: 169
Period size: 60 Copynumber: 2.5 Consensus size: 60
87937 TCAATAGGGT
* * * *
87947 CCTAACATATGAGAAAATGTTCAAATAAGGGCTCAT-TCTTTTAATTTGATTAAATAGGAC
1 CCTAACATATGAGAAAATGCTCAAATAAGGGCCCATGT-TTTTAATTTGATCAAATAAGAC
* * * * *
88007 CCTAACGTAT-ACGAAAATACTCAAATAATGGTCCATGTTTTTAATTTGGTCAAATAAGAC
1 CCTAACATATGA-GAAAATGCTCAAATAAGGGCCCATGTTTTTAATTTGATCAAATAAGAC
*
88067 CCTAACAT-TGTGAAAATGCTCAAATAAGG
1 CCTAACATATGAGAAAATGCTCAAATAAGG
88096 CACCGATGTT
Statistics
Matches: 73, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
59 18 0.25
60 54 0.74
61 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (60 bp):
CCTAACATATGAGAAAATGCTCAAATAAGGGCCCATGTTTTTAATTTGATCAAATAAGAC
Found at i:101725 original size:6 final size:6
Alignment explanation
Indices: 101714--101746 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
101704 TTAAACAGCC
101714 ATATCT ATATCT ATATCT ATATCT ATA-CT ATAT
1 ATATCT ATATCT ATATCT ATATCT ATATCT ATAT
101747 ATAAAAGTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (6 bp):
ATATCT
Found at i:102114 original size:22 final size:22
Alignment explanation
Indices: 102072--102117 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
102062 TTTAGTTTTG
*
102072 TCAAAATTTCATAGAGTGGTTA
1 TCAAAATTTCATAGAGAGGTTA
* *
102094 TCAAAATTTCATTGGGAGGTTA
1 TCAAAATTTCATAGAGAGGTTA
102116 TC
1 TC
102118 CACCTTGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.37
Consensus pattern (22 bp):
TCAAAATTTCATAGAGAGGTTA
Found at i:104537 original size:3 final size:3
Alignment explanation
Indices: 104531--104566 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
104521 GCAGCAGCAG
104531 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
104567 GAATACCGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:104804 original size:2 final size:2
Alignment explanation
Indices: 104797--104837 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
104787 TATTTCTTGA
104797 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
104838 ATAATTCAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:114788 original size:22 final size:22
Alignment explanation
Indices: 114763--114807 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
114753 AAAAATTCCC
114763 AATTCTGTTGAAAACTAAATCA
1 AATTCTGTTGAAAACTAAATCA
* **
114785 AATTCTTTTGATGACTAAATCA
1 AATTCTGTTGAAAACTAAATCA
114807 A
1 A
114808 GAATTCCCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.36
Consensus pattern (22 bp):
AATTCTGTTGAAAACTAAATCA
Found at i:115943 original size:131 final size:131
Alignment explanation
Indices: 115709--115970 Score: 452
Period size: 131 Copynumber: 2.0 Consensus size: 131
115699 TGAGATCCAC
115709 TGCTCCATATCAAATCCAATAATAAAAAATGTAAAACAACACATAAATATTACTATTTTATCTAA
1 TGCTCCATATCAAATCCAATAATAAAAAATGTAAAACAACACATAAATATTACTATTTTATCTAA
* *
115774 AACTTTATGTCACATACAAAGTAGACATTCAAAAGTGAAACAACGGCAATAATTGTTTTATATAT
66 AACTTTATGTCACACACAAAGTAGACATTCAAAAGTGAAACAACGGCAATAATTGTTTGATATAT
115839 T
131 T
* *
115840 TGCTCCATATCAAATCCGATAATAAAAAATGTAAAACAACACATAAATATTATTATTTTATCTAA
1 TGCTCCATATCAAATCCAATAATAAAAAATGTAAAACAACACATAAATATTACTATTTTATCTAA
* * **
115905 AACTTTGTGTCATACACAAAGTAGACATTCAAAAGTGAAACAGTGGCAATAATTGTTTGATATAT
66 AACTTTATGTCACACACAAAGTAGACATTCAAAAGTGAAACAACGGCAATAATTGTTTGATATAT
115970 T
131 T
115971 ATAAACTAAT
Statistics
Matches: 123, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
131 123 1.00
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.32
Consensus pattern (131 bp):
TGCTCCATATCAAATCCAATAATAAAAAATGTAAAACAACACATAAATATTACTATTTTATCTAA
AACTTTATGTCACACACAAAGTAGACATTCAAAAGTGAAACAACGGCAATAATTGTTTGATATAT
T
Found at i:117197 original size:27 final size:26
Alignment explanation
Indices: 117166--117218 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
117156 TGTAATTAAT
117166 AATTA-AAAAATAAATTTTATTAAAATC
1 AATTACAAAAAT-AA-TTTATTAAAATC
*
117193 AATTACTAAGAATAATTTATTAAAAT
1 AATTAC-AAAAATAATTTATTAAAAT
117219 TATTATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 16 0.70
28 2 0.09
29 5 0.22
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (26 bp):
AATTACAAAAATAATTTATTAAAATC
Found at i:119527 original size:38 final size:38
Alignment explanation
Indices: 119485--119559 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
119475 AAATTCATAA
119485 TGATTGGAAAATATCAATTACTAATTACTTGATTGATT
1 TGATTGGAAAATATCAATTACTAATTACTTGATTGATT
119523 TGATTGGAAAATATCAATTACTAATTACTTGATTGAT
1 TGATTGGAAAATATCAATTACTAATTACTTGATTGAT
119560 GGTGTTAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.41
Consensus pattern (38 bp):
TGATTGGAAAATATCAATTACTAATTACTTGATTGATT
Found at i:120599 original size:2 final size:2
Alignment explanation
Indices: 120588--120622 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
120578 ACCGCCGGTG
120588 TA TA -A 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
120623 ATAACTAGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.