Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009863.1 Corchorus capsularis cultivar CVL-1 contig09884, 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: 42384
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1969 original size:22 final size:22
Alignment explanation
Indices: 1941--1996 Score: 112
Period size: 22 Copynumber: 2.5 Consensus size: 22
1931 TTTCTTCAAA
1941 AAATTCCCAATTCCAAAACCCT
1 AAATTCCCAATTCCAAAACCCT
1963 AAATTCCCAATTCCAAAACCCT
1 AAATTCCCAATTCCAAAACCCT
1985 AAATTCCCAATT
1 AAATTCCCAATT
1997 TCTAAATTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.41, C:0.34, G:0.00, T:0.25
Consensus pattern (22 bp):
AAATTCCCAATTCCAAAACCCT
Found at i:16219 original size:19 final size:19
Alignment explanation
Indices: 16192--16228 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
16182 TTTGGGACAG
* *
16192 GAAATTGAAATCTGAAAAT
1 GAAAGTGAAAACTGAAAAT
16211 GAAAGTGAAAACTGAAAA
1 GAAAGTGAAAACTGAAAA
16229 CTGATCAACG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.05, G:0.19, T:0.19
Consensus pattern (19 bp):
GAAAGTGAAAACTGAAAAT
Found at i:17359 original size:8 final size:8
Alignment explanation
Indices: 17346--17381 Score: 72
Period size: 8 Copynumber: 4.5 Consensus size: 8
17336 AAAGTAGATC
17346 GTTAAAAT
1 GTTAAAAT
17354 GTTAAAAT
1 GTTAAAAT
17362 GTTAAAAT
1 GTTAAAAT
17370 GTTAAAAT
1 GTTAAAAT
17378 GTTA
1 GTTA
17382 TCACCATACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39
Consensus pattern (8 bp):
GTTAAAAT
Found at i:24188 original size:100 final size:101
Alignment explanation
Indices: 24006--24208 Score: 363
Period size: 100 Copynumber: 2.0 Consensus size: 101
23996 TCCAACTTCC
* *
24006 AAGTGGCTTTTTTTAAATAACAACAAAGGCCCACCATTAGTAGCTACTTTTTTTTTTTTTCGGCC
1 AAGTGACTTTTTTTAAATAACAACAAAGGCCCACCATTACTAGCTAC-TTTTTTTTTTTTCGGCC
24071 ACACTTAGTGGCTACTTAGAGTTTCCCAATATAAGTT
65 ACACTTAGTGGCTACTTAGAGTTTCCCAATATAAGTT
24108 AAGTGACTTTTTTTAAATAACAACAAAGGCCCACCATTACTAGCTAC-TTTTTTTTTTTCGGCCA
1 AAGTGACTTTTTTTAAATAACAACAAAGGCCCACCATTACTAGCTACTTTTTTTTTTTTCGGCCA
*
24172 CACTTAGTGGCTACTTAGAGTTTCCGAATATAAGTT
66 CACTTAGTGGCTACTTAGAGTTTCCCAATATAAGTT
24208 A
1 A
24209 CGATAGTAGT
Statistics
Matches: 98, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
100 53 0.54
102 45 0.46
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (101 bp):
AAGTGACTTTTTTTAAATAACAACAAAGGCCCACCATTACTAGCTACTTTTTTTTTTTTCGGCCA
CACTTAGTGGCTACTTAGAGTTTCCCAATATAAGTT
Found at i:24615 original size:20 final size:21
Alignment explanation
Indices: 24580--24625 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
24570 AAATATTATA
24580 TTTATCCTATAATGGGTAGTT
1 TTTATCCTATAATGGGTAGTT
*
24601 TTTATCTTA-AATGGGTAGTT
1 TTTATCCTATAATGGGTAGTT
24621 TTTAT
1 TTTAT
24626 TTTATTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.24, C:0.07, G:0.17, T:0.52
Consensus pattern (21 bp):
TTTATCCTATAATGGGTAGTT
Found at i:31599 original size:11 final size:11
Alignment explanation
Indices: 31583--31614 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
31573 GAAGTTCGTG
31583 TTTGAAGATTA
1 TTTGAAGATTA
*
31594 TTTGAAGATAA
1 TTTGAAGATTA
31605 TTTGAAGATT
1 TTTGAAGATT
31615 TGAAGACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (11 bp):
TTTGAAGATTA
Found at i:37297 original size:15 final size:15
Alignment explanation
Indices: 37277--37339 Score: 55
Period size: 15 Copynumber: 4.4 Consensus size: 15
37267 AAAATTACTA
37277 ACATTTAATTATTTT
1 ACATTTAATTATTTT
*
37292 ACATTTAAGTA-TTT
1 ACATTTAATTATTTT
*
37306 --ATTTAATAATAATTT
1 ACATTTAAT--TATTTT
37321 --ATTTAATTATTTT
1 ACATTTAATTATTTT
37334 ACATTT
1 ACATTT
37340 TACATAAAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
12 6 0.15
13 5 0.12
14 5 0.12
15 24 0.60
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.57
Consensus pattern (15 bp):
ACATTTAATTATTTT
Found at i:37913 original size:21 final size:21
Alignment explanation
Indices: 37889--37932 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
37879 AGATTTACTC
37889 TTTTAAAAAATAAAAATATTT
1 TTTTAAAAAATAAAAATATTT
37910 TTTTAAAAAATAAAAATATTT
1 TTTTAAAAAATAAAAATATTT
37931 TT
1 TT
37933 ATAATTGGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TTTTAAAAAATAAAAATATTT
Found at i:42062 original size:439 final size:436
Alignment explanation
Indices: 41207--42241 Score: 1373
Period size: 439 Copynumber: 2.4 Consensus size: 436
41197 GTTCTTCATG
* * * * * * *
41207 TAGACTCTTGAATCACCTTAATGGGACAAAT----AAAACACAAAAACAAAAGTCAAAGCGTTAA
1 TAGACACTTGAATCACCTTGATCGGACAAATAAAAAAAATACAAAAATAAAAGCCGAAGCGTTAA
* * * * * * *
41268 ATCGTCCAACCTATAATTATAAAGGATTCAATAGCATAAAACATAAATGTATGAGGGTCATTAGA
66 ATCGTCCAACCCATAATTGTAAAGGATTAAATAGCATAAAACATAAAAGTATAAGGATCATTTGA
* * **
41333 TAAATAATCCAACAAAAAAAAATATTAGTTTATGAAGACAAAACATAAAAATTCCCTTTTGAATT
131 TAAATAATCCAAC-AAAAAAAATATTTGTTTATGAAGACAAAACATAAAAATTCCCTTTCGAACC
* * * *
41398 CTCCATGAAACTCATTAATCAAATTCAACTTTCATGCCCTTAATGAAAGTAGTAGATCACGCAAT
195 CTCCACGAAACTCATTAATCAAATTCAACTTTCAGGCCCTTAACGAAAGTAGTAGATCACACAAT
* * * *
41463 AACCTTTTAACCGACATTTGAACAACTTCAATCGGACAAGTGGACCGAAAATTATACGATATTAA
260 AACCTTTTAACCGACACTTGAACAACCTCAATCGGACAAATGGACCGAAAATTATACAATATTAA
* *
41528 ATAGACCGACAATCGAAACCACAAAATTTAAGAAACATTTTTTAGAATCAAAACATTAAAATTGA
325 ATAGACCAACAATCGAAACCACAAAATTTAAGAAACATTTTTTAGAATCAAAACATGAAAATTGA
* * * *
41593 CTTCTGAGTTTTTCATGAAAGTTGTAGATCATGAGATTACCTTTTGA
390 CTTCTCAGTCTTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAA
* *
41640 TAGACACTTGAATCACCTTGATTGGACAAATAGAACAGAAAATACAAAAATAAAAGCCGACGCGT
1 TAGACACTTGAATCACCTTGATCGGACAAATA-AA-A-AAAATACAAAAATAAAAGCCGAAGCGT
41705 TAAATCGTCCAACCCATAATTGTAAAGGATTAAATAGCATAAAACATAAAAGTATAAGGATCATT
63 TAAATCGTCCAACCCATAATTGTAAAGGATTAAATAGCATAAAACATAAAAGTATAAGGATCATT
* * * *
41770 TGATAAATAATCCAACAAAAAATATATTTGTTTATGGATACCAAACATAAAAATT-CCTTCTCGA
128 TGATAAATAATCCAACAAAAAAAATATTTGTTTATGAAGACAAAACATAAAAATTCCCTT-TCGA
* * * *
41834 ACCCTCCACGAAACTCATTAATCAAATTCAGCTTTTAGGTCCTTGACGAAAGTCA-TAGATCACA
192 ACCCTCCACGAAACTCATTAATCAAATTCAACTTTCAGGCCCTTAACGAAAGT-AGTAGATCACA
*
41898 CAATAACCTTTTAACCGACACTTGAACAACCTCAATCGGACAAATGGATCGAAAATTATACAATA
256 CAATAACCTTTTAACCGACACTTGAACAACCTCAATCGGACAAATGGACCGAAAATTATACAATA
* * * * *
41963 TTAGATAGACCAACAATCGAGACCACAAAATTTAAGAAGCATTTTTTAGAATCGAAAGATGAAAA
321 TTAAATAGACCAACAATCGAAACCACAAAATTTAAGAAACATTTTTTAGAATCAAAACATGAAAA
** *
42028 TTGGTTTTTCAGTCTTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAA
386 TTGACTTCTCAGTCTTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAA
* * * * *
42079 TAGACACTTGAATCACCTTGATCGGACAAGTAAAAAAAATA-AAAGATTTAAAGCCGAAACGTTC
1 TAGACACTTGAATCACCTTGATCGGACAAATAAAAAAAATACAAA-AATAAAAGCCGAAGCGTTA
* * * * * *
42143 AATCGTCCAACCCAGAATTTGTGAGGGGTTAAATAGCATAAAGCATAAAAGTATAGGGATCATTT
65 AATCGTCCAACCCATAA-TTGTAAAGGATTAAATAGCATAAAACATAAAAGTATAAGGATCATTT
**
42208 GATAAATAATCCAGTAAAAAAAATATTTGTTTAT
129 GATAAATAATCCAACAAAAAAAATATTTGTTTAT
42242 TGAAAGTGGG
Statistics
Matches: 525, Mismatches: 66, Indels: 18
0.86 0.11 0.03
Matches are distributed among these distances:
433 28 0.05
435 3 0.01
436 36 0.07
437 74 0.14
438 6 0.01
439 281 0.54
440 97 0.18
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (436 bp):
TAGACACTTGAATCACCTTGATCGGACAAATAAAAAAAATACAAAAATAAAAGCCGAAGCGTTAA
ATCGTCCAACCCATAATTGTAAAGGATTAAATAGCATAAAACATAAAAGTATAAGGATCATTTGA
TAAATAATCCAACAAAAAAAATATTTGTTTATGAAGACAAAACATAAAAATTCCCTTTCGAACCC
TCCACGAAACTCATTAATCAAATTCAACTTTCAGGCCCTTAACGAAAGTAGTAGATCACACAATA
ACCTTTTAACCGACACTTGAACAACCTCAATCGGACAAATGGACCGAAAATTATACAATATTAAA
TAGACCAACAATCGAAACCACAAAATTTAAGAAACATTTTTTAGAATCAAAACATGAAAATTGAC
TTCTCAGTCTTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAA
Done.