Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013470.1 Corchorus capsularis cultivar CVL-1 contig13491, 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: 96489
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:712 original size:2 final size:2
Alignment explanation
Indices: 707--738 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
697 AAGACTGCCC
707 TA 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
739 CACACGTATA
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):
TA
Found at i:28051 original size:38 final size:40
Alignment explanation
Indices: 27975--28051 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 40
27965 TGCAATTTTG
27975 TAAATCGCTACATAATGATGAGAGCAAATCAATAAAATAAA
1 TAAATCGCTACATAATGA-GAGAGCAAATCAATAAAATAAA
*
28016 TAAATCGCTACATAATGA-A-AGTAAATCAATAAAATA
1 TAAATCGCTACATAATGAGAGAGCAAATCAATAAAATA
28052 TAACAAATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
38 16 0.46
39 1 0.03
41 18 0.51
ACGTcount: A:0.55, C:0.12, G:0.10, T:0.23
Consensus pattern (40 bp):
TAAATCGCTACATAATGAGAGAGCAAATCAATAAAATAAA
Found at i:28736 original size:2 final size:2
Alignment explanation
Indices: 28729--28757 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
28719 TCTATTATTC
28729 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 T
28758 GCTAAATAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28917 original size:2 final size:2
Alignment explanation
Indices: 28912--28937 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28902 TCACGTGTTA
28912 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
28938 TTTTTCCGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32527 original size:15 final size:14
Alignment explanation
Indices: 32507--32536 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
32497 CATGAAAGGG
32507 ATATTGATTCATTGA
1 ATATTGATT-ATTGA
32522 ATATTGATTATTGA
1 ATATTGATTATTGA
32536 A
1 A
32537 GAACCACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47
Consensus pattern (14 bp):
ATATTGATTATTGA
Found at i:36328 original size:13 final size:14
Alignment explanation
Indices: 36304--36332 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
36294 ATAGGCAAGG
36304 TAAATAATAATATA
1 TAAATAATAATATA
36318 TAAAT-ATAATATA
1 TAAATAATAATATA
36331 TA
1 TA
36333 GTTTAGAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAATAATAATATA
Found at i:37512 original size:11 final size:11
Alignment explanation
Indices: 37488--37522 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
37478 TTGACAGCGT
37488 AACAAAAACAA
1 AACAAAAACAA
* *
37499 AACGAAAACGA
1 AACAAAAACAA
37510 AACAAAAACAA
1 AACAAAAACAA
37521 AA
1 AA
37523 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:44321 original size:21 final size:21
Alignment explanation
Indices: 44269--44325 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
44259 TTTCGCCTTC
* * *
44269 CCTTTCTTTGAAGAACTGGAT
1 CCTTTCTTTGCAGACCCGGAT
*
44290 CCTTTCTTTGCAGACCCGGGT
1 CCTTTCTTTGCAGACCCGGAT
44311 CCTTTCTTTGCAGAC
1 CCTTTCTTTGCAGAC
44326 TTCTTATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.16, C:0.28, G:0.19, T:0.37
Consensus pattern (21 bp):
CCTTTCTTTGCAGACCCGGAT
Found at i:53611 original size:48 final size:47
Alignment explanation
Indices: 53358--53730 Score: 190
Period size: 48 Copynumber: 7.9 Consensus size: 47
53348 ACCACTTTGA
*** * * * *
53358 GTCGTGATGGTTAATTTTGGACA-TTGTGGCCAATTTCGGTCACCATCG
1 GTCGTGATGGTTAGCCTTGGCCATTTG-GGCCAATTT-TGACACCATTG
* ***
53406 GTCATGATGGTTAGCCTTGGCCATTTTTAACCAATTTTGACCACC-TTAG
1 GTCGTGATGGTTAGCCTTGGCCA-TTTGGGCCAATTTTGA-CACCATT-G
** * * ** * *
53455 GTCGTGATGGTTAGCCTTAACCATTTTGGG-GAATATTGGTTACTATCG
1 GTCGTGATGGTTAGCCTTGGCCA-TTTGGGCCAAT-TTTGACACCATTG
* * ** *
53503 GTTGTGATGGTTAGCTTTGGTTATTTGGGCCAATTTTGATCA-CGTTG
1 GTCGTGATGGTTAGCCTTGGCCATTTGGGCCAATTTTGA-CACCATTG
*
53550 GTCGTGGTGGTTAGCCTTGGCCATTTGGGCCAATTTTGACAACCATTG
1 GTCGTGATGGTTAGCCTTGGCCATTTGGGCCAATTTTGAC-ACCATTG
* * * *
53598 GTCGTGGTGGTTAGCCTTTGG-CATTTTGGCCAATTTGGGTCACC-TTGG
1 GTCGTGATGGTTAGCC-TTGGCCATTTGGGCCAATTT-TGACACCATT-G
* * * **
53646 GTTGTGAT-G-T-GCCTTGGTCAATTT-GGCCAATTTCGAGCACCATCA
1 GTCGTGATGGTTAGCCTTGG-CCATTTGGGCCAATTTTGA-CACCATTG
* * * ***
53691 GTTGTGCTGGTTATCCTTGGCCATTTTAACCAATTTTGAC
1 GTCGTGATGGTTAGCCTTGGCCATTTGGGCCAATTTTGAC
53731 CACCTTACGT
Statistics
Matches: 246, Mismatches: 58, Indels: 43
0.71 0.17 0.12
Matches are distributed among these distances:
44 5 0.02
45 23 0.09
46 8 0.03
47 56 0.23
48 106 0.43
49 46 0.19
50 2 0.01
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (47 bp):
GTCGTGATGGTTAGCCTTGGCCATTTGGGCCAATTTTGACACCATTG
Found at i:54331 original size:48 final size:47
Alignment explanation
Indices: 54217--54332 Score: 115
Period size: 48 Copynumber: 2.4 Consensus size: 47
54207 GATTCTGAAA
* * * * *
54217 ATGGTTAGACTTGGCTATTTTGGCTAATTTTAGTCACCACCGGTTGTG
1 ATGGTTAGCCTTGGCCA-TTTGGCAAATTTTAGCCACCACCGGTCGTG
* ** * **
54265 ATGGTTAACCTTTTCCATTTGGCCAAATTTTGGCCACCATTGGTCGTG
1 ATGGTTAGCCTTGGCCATTTGG-CAAATTTTAGCCACCACCGGTCGTG
54313 ATGGTTAGCCTTGGCCATTT
1 ATGGTTAGCCTTGGCCATTT
54333 TATCCACCAT
Statistics
Matches: 53, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
47 5 0.09
48 48 0.91
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (47 bp):
ATGGTTAGCCTTGGCCATTTGGCAAATTTTAGCCACCACCGGTCGTG
Found at i:56232 original size:77 final size:77
Alignment explanation
Indices: 56120--56270 Score: 239
Period size: 77 Copynumber: 2.0 Consensus size: 77
56110 TTTATTAGTG
* * * *
56120 TTTAACATTTTGGTCATCTTATTATGTGTTGGTTAAGCTTAGTTATTTTGACCATCTCGAGTCGT
1 TTTAACATTTTGGTCATCTTATTATGTGTTAGTTAAGCTGAGCTATTTTGACCATCTCGAATCGT
*
56185 GATGATTAGCCT
66 GATAATTAGCCT
* *
56197 TTTAACATTTTGGTCATCTTATTCTGTGTTAGTTAAGCTGAGCTATTTTGACCATCTTGAATCGT
1 TTTAACATTTTGGTCATCTTATTATGTGTTAGTTAAGCTGAGCTATTTTGACCATCTCGAATCGT
56262 GATAATTAG
66 GATAATTAG
56271 TCTTAGTCAT
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
77 67 1.00
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.45
Consensus pattern (77 bp):
TTTAACATTTTGGTCATCTTATTATGTGTTAGTTAAGCTGAGCTATTTTGACCATCTCGAATCGT
GATAATTAGCCT
Found at i:64744 original size:5 final size:5
Alignment explanation
Indices: 64734--64763 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
64724 ACATGTACCC
64734 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
64764 GGAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:79005 original size:33 final size:32
Alignment explanation
Indices: 78942--79006 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
78932 AAGGTTGAAA
**
78942 ATTTTAGACCTTTCTAATGTTACATAGACCAT
1 ATTTTAGACCTTTCTAACCTTACATAGACCAT
*
78974 ATTTTGAGACCTTTCTTAACCTTCCAT-GACCAT
1 ATTTT-AGACCTTTC-TAACCTTACATAGACCAT
79007 CTCCTTCGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 5 0.18
33 15 0.54
34 8 0.29
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (32 bp):
ATTTTAGACCTTTCTAACCTTACATAGACCAT
Found at i:80312 original size:27 final size:27
Alignment explanation
Indices: 80282--80338 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
80272 TGAAACCAAA
*
80282 AAACAAAAGCT-T-TTTTTCTAGAGAGAG
1 AAACAAAAG-TGTCTTTTT-TAGACAGAG
*
80309 AAACTAAAGTGTCTTTTTTAGACAGAG
1 AAACAAAAGTGTCTTTTTTAGACAGAG
80336 AAA
1 AAA
80339 GAGTGGGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 1 0.04
27 20 0.77
28 5 0.19
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.30
Consensus pattern (27 bp):
AAACAAAAGTGTCTTTTTTAGACAGAG
Found at i:85738 original size:29 final size:30
Alignment explanation
Indices: 85687--85744 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
85677 CTCCCTATCT
* *
85687 TGAGGTTGGAATTCACATGGAGAGGTCTCA
1 TGAGGTTGGAATTCACATAGAGAAGTCTCA
85717 TGAGG-TGGAATTCATC-TAGAGAAGTCTC
1 TGAGGTTGGAATTCA-CATAGAGAAGTCTC
85745 GAGTTTGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.28, C:0.14, G:0.31, T:0.28
Consensus pattern (30 bp):
TGAGGTTGGAATTCACATAGAGAAGTCTCA
Found at i:85897 original size:14 final size:14
Alignment explanation
Indices: 85877--85912 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
85867 TAATACATCA
85877 TTTATTAT-CTTTT
1 TTTATTATCCTTTT
85890 TATTATTATCCTTTT
1 T-TTATTATCCTTTT
85905 TTTATTAT
1 TTTATTAT
85913 TTTATTATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.05
14 14 0.67
15 6 0.29
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTATTATCCTTTT
Found at i:90077 original size:18 final size:17
Alignment explanation
Indices: 90054--90087 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
90044 TGGTCGTTTA
*
90054 TGATTTTGTCCTTCTGAC
1 TGATTTT-TCCATCTGAC
90072 TGATTTTTCCATCTGA
1 TGATTTTTCCATCTGA
90088 AAAAGGGACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.15, C:0.21, G:0.15, T:0.50
Consensus pattern (17 bp):
TGATTTTTCCATCTGAC
Found at i:96480 original size:11 final size:11
Alignment explanation
Indices: 96464--96489 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
96454 AATAAAATAC
96464 TCTTTTCAACT
1 TCTTTTCAACT
96475 TCTTTTCAACT
1 TCTTTTCAACT
96486 TCTT
1 TCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.27, G:0.00, T:0.58
Consensus pattern (11 bp):
TCTTTTCAACT
Done.