Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011980.1 Corchorus capsularis cultivar CVL-1 contig12001, 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: 82535
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:409 original size:31 final size:29
Alignment explanation
Indices: 339--419 Score: 85
Period size: 29 Copynumber: 2.7 Consensus size: 29
329 GCTCAGTTAA
* *
339 CTCCACTTCAGGGACTAAATTGCATATTT
1 CTCCACTTGAGGGACTAATTTGCATATTT
368 -TCACACTTGAGGGACTAATTTGC-TATGTT
1 CTC-CACTTGAGGGACTAATTTGCATAT-TT
*
397 CGCTCCACTTGAGGGACCAATTT
1 --CTCCACTTGAGGGACTAATTT
420 TGTACTTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
28 5 0.11
29 20 0.45
31 17 0.39
32 2 0.05
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (29 bp):
CTCCACTTGAGGGACTAATTTGCATATTT
Found at i:5390 original size:2 final size:2
Alignment explanation
Indices: 5383--5410 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5373 ACAAATCATC
5383 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
5411 GTCAATCATT
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:9185 original size:3 final size:3
Alignment explanation
Indices: 9177--9208 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
9167 CCTTGCTTAC
9177 CTT CTT CTT CTT CTT CTT CTT CTT -TT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
9209 ACATGAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
CTT
Found at i:11141 original size:1 final size:1
Alignment explanation
Indices: 11135--11161 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
11125 TAGTACTGAG
11135 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
11162 AAGGAGAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:17398 original size:8 final size:8
Alignment explanation
Indices: 17387--17436 Score: 55
Period size: 8 Copynumber: 6.0 Consensus size: 8
17377 AAGGTTTGTT
*
17387 TTTTTTTT
1 TTTTTTTA
17395 TTTTTTTA
1 TTTTTTTA
17403 TTTTATTTTA
1 -TTT-TTTTA
*
17413 TTTATTTA
1 TTTTTTTA
*
17421 TTTATTTA
1 TTTTTTTA
17429 TTTTTTTA
1 TTTTTTTA
17437 AATTTCACCA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
8 26 0.70
9 6 0.16
10 5 0.14
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTTTA
Found at i:28354 original size:23 final size:23
Alignment explanation
Indices: 28324--28370 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
28314 CCTTTCAGTT
28324 AAAGAAACAAAAGGAAGTGCATC
1 AAAGAAACAAAAGGAAGTGCATC
28347 AAAGAAACAAAAGGAAGTGCATC
1 AAAGAAACAAAAGGAAGTGCATC
28370 A
1 A
28371 TGCAAAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.57, C:0.13, G:0.21, T:0.09
Consensus pattern (23 bp):
AAAGAAACAAAAGGAAGTGCATC
Found at i:39129 original size:2 final size:2
Alignment explanation
Indices: 39122--39153 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
39112 TTTTCCATGC
39122 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
39154 TCTTGTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60088 original size:14 final size:14
Alignment explanation
Indices: 60069--60097 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
60059 ATTTTGCATT
60069 TTATTATGGGCTTA
1 TTATTATGGGCTTA
60083 TTATTATGGGCTTA
1 TTATTATGGGCTTA
60097 T
1 T
60098 AATAATCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.21, T:0.52
Consensus pattern (14 bp):
TTATTATGGGCTTA
Found at i:62999 original size:2 final size:2
Alignment explanation
Indices: 62988--63025 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
62978 GTTATAATGT
*
62988 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TG 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
63026 GGGAAATCGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:65785 original size:75 final size:78
Alignment explanation
Indices: 65662--65839 Score: 254
Period size: 75 Copynumber: 2.3 Consensus size: 78
65652 CCTTTTTTCT
* *
65662 TTTTGGATGAATTATTATGGCCTTGTTCTTCAGACCCATTTTGCATTTTG-TT-T-TGGTCTTAA
1 TTTTGGATGAATTATTATGGCCTTGTTCTTCAGACCCATTTTACATTTTGCTTATATGGTCATAA
65724 AATGATCCATATG
66 AATGATCCATATG
* * *
65737 TTTTGGATTAATTATTATGGCCTTGTTCTTCTGACCTATTTTACATTTTGCTTTATATGGTCATA
1 TTTTGGATGAATTATTATGGCCTTGTTCTTCAGACCCATTTTACATTTTGC-TTATATGGTCATA
65802 AAATGATCCATATG
65 AAATGATCCATATG
**
65816 TTTTGGATGGGCTTATTATGGCCT
1 TTTTGGAT-GAATTATTATGGCCT
65840 AATAATCTTT
Statistics
Matches: 90, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
75 46 0.51
77 2 0.02
78 1 0.01
79 29 0.32
80 12 0.13
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.47
Consensus pattern (78 bp):
TTTTGGATGAATTATTATGGCCTTGTTCTTCAGACCCATTTTACATTTTGCTTATATGGTCATAA
AATGATCCATATG
Found at i:78762 original size:53 final size:53
Alignment explanation
Indices: 78682--78788 Score: 178
Period size: 53 Copynumber: 2.0 Consensus size: 53
78672 TGCCTGTTTT
* * *
78682 ATTTTATAAATTCTTTTAATAAAATTCAGTTAAGAAATCAAATTTTATTGTGA
1 ATTTTATAAATTCTCTTAAGAAAATTCAGTTAAGAAATCAAAATTTATTGTGA
*
78735 ATTTTATAAATTCTCTTAAGAAAATTCAGTTAAGAAATCAAAATTTGTTGTGA
1 ATTTTATAAATTCTCTTAAGAAAATTCAGTTAAGAAATCAAAATTTATTGTGA
78788 A
1 A
78789 ATAATAATAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (53 bp):
ATTTTATAAATTCTCTTAAGAAAATTCAGTTAAGAAATCAAAATTTATTGTGA
Found at i:80049 original size:13 final size:13
Alignment explanation
Indices: 80033--80059 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
80023 CTGTTACTTG
80033 TGGGTATATTTCT
1 TGGGTATATTTCT
80046 TGGGTATATTTCT
1 TGGGTATATTTCT
80059 T
1 T
80060 AGTTTGTGGG
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:0.15, C:0.07, G:0.22, T:0.56
Consensus pattern (13 bp):
TGGGTATATTTCT
Found at i:81315 original size:29 final size:30
Alignment explanation
Indices: 81283--81347 Score: 105
Period size: 31 Copynumber: 2.2 Consensus size: 30
81273 ATGCAATTTG
81283 GGATATAACGTTAC-AAAACAAGCAATTAA
1 GGATATAACGTTACAAAAACAAGCAATTAA
*
81312 GGATATAACGTTACGAAAAACGAGCAATTAA
1 GGATATAACGTTAC-AAAAACAAGCAATTAA
81343 GGATA
1 GGATA
81348 CAGCCCGTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
29 14 0.42
31 19 0.58
ACGTcount: A:0.49, C:0.12, G:0.18, T:0.20
Consensus pattern (30 bp):
GGATATAACGTTACAAAAACAAGCAATTAA
Found at i:81503 original size:31 final size:31
Alignment explanation
Indices: 81468--81577 Score: 136
Period size: 31 Copynumber: 3.6 Consensus size: 31
81458 CCCTAACTGA
81468 TTATATCCTTAATTGCTTGAAATCGAAAACG
1 TTATATCCTTAATTGCTTGAAATCGAAAACG
*
81499 TTATATCCTTAATTGCTCGAAATC-AAAGACG
1 TTATATCCTTAATTGCTTGAAATCGAAA-ACG
* ** * *
81530 TTATATTCTTAATTGCTTG-TTTTG-TAACG
1 TTATATCCTTAATTGCTTGAAATCGAAAACG
81559 TTATATCCTTAATTGCTTG
1 TTATATCCTTAATTGCTTG
81578 CGGCAGCAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
29 21 0.30
30 5 0.07
31 43 0.62
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (31 bp):
TTATATCCTTAATTGCTTGAAATCGAAAACG
Found at i:81646 original size:3 final size:3
Alignment explanation
Indices: 81638--81696 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
81628 AAAGCAACCC
81638 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
81686 ATA ATA ATA AT
1 ATA ATA ATA AT
81697 CCTAATTTCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:81934 original size:13 final size:14
Alignment explanation
Indices: 81916--81949 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
81906 TATTGGAACA
81916 TTTTAAAT-ATATT
1 TTTTAAATGATATT
81929 TTTTAAATGATATT
1 TTTTAAATGATATT
*
81943 GTTTAAA
1 TTTTAAA
81950 CTTTTATAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (14 bp):
TTTTAAATGATATT
Found at i:82279 original size:26 final size:27
Alignment explanation
Indices: 82250--82306 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 27
82240 TAGCATATCA
* * *
82250 TTAAAAG-AGAATAACTAAATATAATT
1 TTAAAAGTAAAATAAATAAACATAATT
82276 TT-AAAGTAAAATAAATAAACATAATT
1 TTAAAAGTAAAATAAATAAACATAATT
*
82302 ATAAA
1 TTAAA
82307 TAATATTCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
25 4 0.16
26 19 0.76
27 2 0.08
ACGTcount: A:0.61, C:0.04, G:0.05, T:0.30
Consensus pattern (27 bp):
TTAAAAGTAAAATAAATAAACATAATT
Done.