Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012819.1 Corchorus capsularis cultivar CVL-1 contig12840, 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: 26084
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:3249 original size:21 final size:20
Alignment explanation
Indices: 3212--3250 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3202 TTTAGAAGCA
*
3212 ATTAATTAAAAGCATTAAAC
1 ATTAATTAAAAACATTAAAC
3232 ATTAATTAAAAACAATTAA
1 ATTAATTAAAAAC-ATTAA
3251 GGAAGAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.31
Consensus pattern (20 bp):
ATTAATTAAAAACATTAAAC
Found at i:3410 original size:74 final size:74
Alignment explanation
Indices: 3257--3413 Score: 262
Period size: 74 Copynumber: 2.1 Consensus size: 74
3247 TTAAGGAAGA
* *
3257 GAAATGTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATGGGGGAAACTCATAAAGGGGCTTTT
1 GAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAAAGGGGCTTTT
3322 TAGTCATCC
66 TAGTCATCC
* *
3331 AAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTT
1 GAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAAAGGGGCTTTT
3396 TAGTCA-CC
66 TAGTCATCC
3404 TGAAAAGTGT
1 -GAAAAGTGT
3414 GAAAAGACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
73 2 0.03
74 75 0.97
ACGTcount: A:0.41, C:0.09, G:0.29, T:0.21
Consensus pattern (74 bp):
GAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAAAGGGGCTTTT
TAGTCATCC
Found at i:3510 original size:2 final size:2
Alignment explanation
Indices: 3497--3538 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
3487 GTTAAAAATA
3497 AT AT AT AGT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3539 GATTAATTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3517 original size:17 final size:17
Alignment explanation
Indices: 3497--3537 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
3487 GTTAAAAATA
*
3497 ATATATAGTATATATAT
1 ATATATAATATATATAT
3514 ATATATAATATATATAT
1 ATATATAATATATATAT
3531 ATATATA
1 ATATATA
3538 TGATTAATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
ATATATAATATATATAT
Found at i:5496 original size:27 final size:27
Alignment explanation
Indices: 5466--5530 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
5456 ATTTCTGGAA
5466 AACAAGGGAAAGAGACAATTAAAAAGG
1 AACAAGGGAAAGAGACAATTAAAAAGG
* *
5493 AACAAGGGAAAGTGACAATTAAAAATG
1 AACAAGGGAAAGAGACAATTAAAAAGG
5520 AACAGAGGGAA
1 AACA-AGGGAA
5531 GAGTATATTC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 29 0.83
28 6 0.17
ACGTcount: A:0.57, C:0.08, G:0.26, T:0.09
Consensus pattern (27 bp):
AACAAGGGAAAGAGACAATTAAAAAGG
Found at i:6731 original size:2 final size:2
Alignment explanation
Indices: 6724--6758 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6714 TGACCAAATC
6724 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 T
6759 TTTAACAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16503 original size:17 final size:18
Alignment explanation
Indices: 16481--16522 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
16471 GTGTAAACCC
*
16481 AAACATGACT-ACTAATT
1 AAACATGACTAAATAATT
*
16498 AAACATGATTAAATAATT
1 AAACATGACTAAATAATT
16516 AAACATG
1 AAACATG
16523 GTTATTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.52, C:0.12, G:0.07, T:0.29
Consensus pattern (18 bp):
AAACATGACTAAATAATT
Found at i:17402 original size:15 final size:15
Alignment explanation
Indices: 17379--17408 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17369 TCCGTGGTTC
*
17379 TGACCAATAAGATTT
1 TGACAAATAAGATTT
17394 TGACAAATAAGATTT
1 TGACAAATAAGATTT
17409 CTTCATACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.33
Consensus pattern (15 bp):
TGACAAATAAGATTT
Found at i:19860 original size:24 final size:25
Alignment explanation
Indices: 19832--19882 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
19822 ATATACTGAA
* * *
19832 TTTAATTAAATGAAA-AATAAATTT
1 TTTAATAAAATAAAACAATAAAATT
19856 TTTAATAAAATAAAACAATAAAATT
1 TTTAATAAAATAAAACAATAAAATT
19881 TT
1 TT
19883 AAACAATGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (25 bp):
TTTAATAAAATAAAACAATAAAATT
Found at i:23257 original size:26 final size:26
Alignment explanation
Indices: 23219--23289 Score: 76
Period size: 28 Copynumber: 2.7 Consensus size: 26
23209 ACCGAAATTA
23219 ATATATAT-A-ATTAAATA-AATATT
1 ATATATATAATATTAAATATAATATT
*
23242 ATTATATATAATATTAGATATATAATACT
1 A-TATATATAATATTA-A-ATATAATATT
23271 ATATATATAATTATTAAAT
1 ATATATATAA-TATTAAAT
23290 GGTCTAAACT
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
23 1 0.03
24 7 0.17
25 1 0.03
26 4 0.10
27 3 0.08
28 13 0.32
29 11 0.28
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (26 bp):
ATATATATAATATTAAATATAATATT
Found at i:23262 original size:14 final size:14
Alignment explanation
Indices: 23245--23286 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
23235 AAATATTATT
23245 ATATATAATATTAG
1 ATATATAATATTAG
* *
23259 ATATATAATACTAT
1 ATATATAATATTAG
23273 ATATATAATTATTA
1 ATATATAA-TATTA
23287 AATGGTCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 20 0.83
15 4 0.17
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (14 bp):
ATATATAATATTAG
Done.