Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022964.1 Corchorus olitorius cultivar O-4 contig22997, 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: 41642
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:2172 original size:27 final size:27
Alignment explanation
Indices: 2142--2210 Score: 111
Period size: 27 Copynumber: 2.6 Consensus size: 27
2132 TGTGAACTTA
*
2142 AAAAATGACCAAAATGCCCTTGAATGT
1 AAAAATGACCAAAATGCCCCTGAATGT
2169 AAAAATGACCAAAATGCCCCTGAATGT
1 AAAAATGACCAAAATGCCCCTGAATGT
**
2196 GCAAATGACCAAAAT
1 AAAAATGACCAAAAT
2211 ATCCCCCTAG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.46, C:0.20, G:0.14, T:0.19
Consensus pattern (27 bp):
AAAAATGACCAAAATGCCCCTGAATGT
Found at i:22620 original size:197 final size:197
Alignment explanation
Indices: 22285--22652 Score: 709
Period size: 197 Copynumber: 1.9 Consensus size: 197
22275 CTTCAGCCTT
22285 GAGATCATCAAGTTTCATGGGAGCATGGTCAAGTTCTTCCATGGTGATCCCATCTTGTATGTTTT
1 GAGATCATCAAGTTTCATGGGAGCATGGTCAAGTTCTTCCATGGTGATCCCATCTTGTATGTTTT
22350 TCACATCTTGATAAGCCGCATCAGCTGATGGGGCGGCTAAGTCCTCTAAGCTTTGGAGCTTCATA
66 TCACATCTTGATAAGCCGCATCAGCTGATGGGGCGGCTAAGTCCTCTAAGCTTTGGAGCTTCATA
22415 TCCAAGGCCAAGGTCGACAACTTTTTCAAGATGTCGTTGGCTAACACAACCTCTTCATCTTTTTC
131 TCCAAGGCCAAGGTCGACAACTTTTTCAAGATGTCGTTGGCTAACACAACCTCTTCATCTTTTTC
22480 AA
196 AA
* *
22482 GAGATCATCAAGTTTTATGGGAGCATGGTCAAGTTCTTCCATGGTGATCTCATCTTGTATGTTTT
1 GAGATCATCAAGTTTCATGGGAGCATGGTCAAGTTCTTCCATGGTGATCCCATCTTGTATGTTTT
*
22547 TCACATCTTGATAAGCTGCATCAGCTGATGGGGCGGCTAAGTCCTCTAAGCTTTGGAGCTTCATA
66 TCACATCTTGATAAGCCGCATCAGCTGATGGGGCGGCTAAGTCCTCTAAGCTTTGGAGCTTCATA
22612 TCCAAGGCCAAGGTCGACAACTTTTTCAAGATGTCGTTGGC
131 TCCAAGGCCAAGGTCGACAACTTTTTCAAGATGTCGTTGGC
22653 ACAACCTCTT
Statistics
Matches: 168, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
197 168 1.00
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.32
Consensus pattern (197 bp):
GAGATCATCAAGTTTCATGGGAGCATGGTCAAGTTCTTCCATGGTGATCCCATCTTGTATGTTTT
TCACATCTTGATAAGCCGCATCAGCTGATGGGGCGGCTAAGTCCTCTAAGCTTTGGAGCTTCATA
TCCAAGGCCAAGGTCGACAACTTTTTCAAGATGTCGTTGGCTAACACAACCTCTTCATCTTTTTC
AA
Found at i:27058 original size:11 final size:11
Alignment explanation
Indices: 27034--27067 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
27024 GTAAAACTGG
*
27034 AAAAGTAAATA
1 AAAAGTAAAGA
*
27045 AAAAGAAAAGA
1 AAAAGTAAAGA
27056 AAAAGTAAAGA
1 AAAAGTAAAGA
27067 A
1 A
27068 GGCAAACCCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (11 bp):
AAAAGTAAAGA
Found at i:32428 original size:17 final size:16
Alignment explanation
Indices: 32380--32438 Score: 66
Period size: 16 Copynumber: 3.6 Consensus size: 16
32370 AAGTCAACGT
*
32380 CCCGAACCCGCCCGAA
1 CCCGAACCCGCCCGAG
*
32396 CCCGAGA-CAGCCCGAG
1 CCCGA-ACCCGCCCGAG
32412 CCCGAACCCGACCCGAG
1 CCCGAACCCG-CCCGAG
*
32429 ACCGAACCCG
1 CCCGAACCCG
32439 ATCCCGTCCC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
15 1 0.03
16 19 0.53
17 16 0.44
ACGTcount: A:0.25, C:0.51, G:0.24, T:0.00
Consensus pattern (16 bp):
CCCGAACCCGCCCGAG
Found at i:32438 original size:23 final size:23
Alignment explanation
Indices: 32390--32463 Score: 78
Period size: 23 Copynumber: 3.3 Consensus size: 23
32380 CCCGAACCCG
** *
32390 CCCGAACCCGAGAC-AGCCCGAG
1 CCCGAACCCGACCCGAGCCCGAA
*
32412 CCCGAACCCGACCCGAGACCGAA
1 CCCGAACCCGACCCGAGCCCGAA
* * *
32435 CCCGATCCCGTCCCGAGCCCAAA
1 CCCGAACCCGACCCGAGCCCGAA
32458 CCCGAA
1 CCCGAA
32464 ATAATTTGAA
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
22 12 0.29
23 30 0.71
ACGTcount: A:0.27, C:0.49, G:0.22, T:0.03
Consensus pattern (23 bp):
CCCGAACCCGACCCGAGCCCGAA
Found at i:32439 original size:17 final size:18
Alignment explanation
Indices: 32406--32444 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
32396 CCCGAGACAG
*
32406 CCCGAGCCCGAACCCGA-
1 CCCGAGACCGAACCCGAT
32423 CCCGAGACCGAACCCGAT
1 CCCGAGACCGAACCCGAT
32441 CCCG
1 CCCG
32445 TCCCGAGCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.23, C:0.51, G:0.23, T:0.03
Consensus pattern (18 bp):
CCCGAGACCGAACCCGAT
Found at i:33402 original size:23 final size:23
Alignment explanation
Indices: 33355--33409 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
33345 ATCGAAATCA
**
33355 AACCCGAAACCGACCCGAGTTCG
1 AACCCGAAACCGACCCGAGACCG
* *
33378 AACCCGAACCCTACCCGAGACCG
1 AACCCGAAACCGACCCGAGACCG
*
33401 AATCCGAAA
1 AACCCGAAA
33410 ATACCCGAAC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.35, C:0.40, G:0.18, T:0.07
Consensus pattern (23 bp):
AACCCGAAACCGACCCGAGACCG
Found at i:33499 original size:15 final size:16
Alignment explanation
Indices: 33398--33487 Score: 130
Period size: 16 Copynumber: 5.7 Consensus size: 16
33388 CTACCCGAGA
*
33398 CCGAATCCGAAAATAC
1 CCGAACCCGAAAATAC
*
33414 CCGAACCCG-ACATAAC
1 CCGAACCCGAAAAT-AC
33430 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
33446 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
*
33462 CCGAACCC-AAAAAAC
1 CCGAACCCGAAAATAC
33477 CCGAACCCGAA
1 CCGAACCCGAA
33488 GTATCCGAAC
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
15 17 0.25
16 47 0.70
17 3 0.04
ACGTcount: A:0.43, C:0.39, G:0.12, T:0.06
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:36374 original size:22 final size:22
Alignment explanation
Indices: 36349--36390 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
36339 TTATTCACCT
36349 TGATTCCACATTTTTCTAAACC
1 TGATTCCACATTTTTCTAAACC
36371 TGATTCCACATTTTTCTAAA
1 TGATTCCACATTTTTCTAAA
36391 TCATTTTGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.29, C:0.24, G:0.05, T:0.43
Consensus pattern (22 bp):
TGATTCCACATTTTTCTAAACC
Found at i:37079 original size:116 final size:115
Alignment explanation
Indices: 36877--37188 Score: 490
Period size: 116 Copynumber: 2.7 Consensus size: 115
36867 CTGAATTTTA
* *
36877 TTCCATATTAAGAAAGTC-T-AA-AATAATAACAATTATTTTTACATTAAACAACTTATTATTAT
1 TTCCATATTAA-AAAGTCTTAAATAATACTAACAATT-TTTTTACGTTAAACAACTTATTATTAT
36939 AATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTTCT
64 AATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTTCT
36991 TTCCATATTATAAAAGTCTTAAATAATACTAACAATTTTTTTACGTTAAACAACTTATTATTATA
1 TTCCATATTA-AAAAGTCTTAAATAATACTAACAATTTTTTTACGTTAAACAACTTATTATTATA
37056 ATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTTCT
65 ATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTTCT
* * *
37107 TTCCATATTAAAAAAAT-TTAAAATAATACTAACAA-TTTTTTACGTTAAACATCTTCTTATTAT
1 TTCCATATT-AAAAAGTCTT-AAATAATACTAACAATTTTTTTACGTTAAACAACTTATTATTAT
*
37170 AATTATTAAACTTATTATT
64 AATTATTAAAATTATTATT
37189 CTTATAATAA
Statistics
Matches: 186, Mismatches: 6, Indels: 11
0.92 0.03 0.05
Matches are distributed among these distances:
114 16 0.09
115 48 0.26
116 109 0.59
117 13 0.07
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46
Consensus pattern (115 bp):
TTCCATATTAAAAAGTCTTAAATAATACTAACAATTTTTTTACGTTAAACAACTTATTATTATAA
TTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTTCT
Found at i:38642 original size:22 final size:22
Alignment explanation
Indices: 38612--38653 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
38602 GAGATAATAA
* *
38612 TATAGTTTTTAGAATAATCACT
1 TATACTTTTTAGAACAATCACT
38634 TATACTTTTTAGAACAATCA
1 TATACTTTTTAGAACAATCA
38654 TTAAAGCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (22 bp):
TATACTTTTTAGAACAATCACT
Found at i:38665 original size:23 final size:22
Alignment explanation
Indices: 38617--38665 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
38607 AATAATATAG
* *
38617 TTTTTAGAATAATCACTTATAC
1 TTTTTAGAACAATCACTTAAAC
38639 TTTTTAGAACAATCA-TTAAAGC
1 TTTTTAGAACAATCACTTAAA-C
38661 TTTTT
1 TTTTT
38666 TAGTAACTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (22 bp):
TTTTTAGAACAATCACTTAAAC
Done.