Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011315.1 Corchorus capsularis cultivar CVL-1 contig11336, 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: 50141
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2386 original size:16 final size:16
Alignment explanation
Indices: 2365--2399 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
2355 ACAATTCAGA
2365 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
2381 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
2397 AAG
1 AAG
2400 TATTTCAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:2601 original size:92 final size:91
Alignment explanation
Indices: 2444--2670 Score: 310
Period size: 92 Copynumber: 2.5 Consensus size: 91
2434 GCTTAAGAAG
* * *
2444 ATTGAAAGAAGATCCACGTATGTGGAAAATTCTTCTTTCAAAGAAGATTCAATTATTGGAGAATT
1 ATTGAAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAAGAAGATCCAATTATTGCAGAATT
* * * *
2509 ACTGAAGATCCAGTTATTGGGGGAGTT
66 ACTGAAGACCCAGTTATT-AGGAAATT
* * *
2536 ATTGAAAGAAGATCCATGTATGTGGAGTATTCTTCTTTCAAAGAATATCCAATTATTGCAGAATT
1 ATTGAAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAAGAAGATCCAATTATTGCAGAATT
2601 ACTGAAGACCCAGTTATTAGGAAATT
66 ACTGAAGACCCAGTTATTAGGAAATT
* * *
2627 ATTGAAAAAAAAAATCCACGTATGTGGAGGATTCTTCTTTCAAA
1 ATTG--AAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAA
2671 TTATCAAAGA
Statistics
Matches: 119, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
91 9 0.08
92 76 0.64
93 34 0.29
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (91 bp):
ATTGAAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAAGAAGATCCAATTATTGCAGAATT
ACTGAAGACCCAGTTATTAGGAAATT
Found at i:5087 original size:102 final size:102
Alignment explanation
Indices: 4961--5267 Score: 373
Period size: 102 Copynumber: 3.0 Consensus size: 102
4951 GTAATTTGAA
* * * * * * *
4961 TCTCTTAGACATCTCAAAAACAAACCATCTATGGTGTGATTGAACAAAGCATCTATAATATGCTT
1 TCTCTTAGACATCTCAAAATCAAACAATTTATGATGTAATTGAACAAAGCTTCTATAAGATGCTT
* *
5026 TGTCCAGGACCTTTTAACTATTCTGTGTAGTAGAAAC
66 TGTCCAGGACCTTTTAACTCTTCTGTGTAGTTGAAAC
* * * * * *
5063 TCTTTTAGACATCCCAAAATCAAACAATTTATGATCTAATAGAACAAAACTTCTATAAGATGCTA
1 TCTCTTAGACATCTCAAAATCAAACAATTTATGATGTAATTGAACAAAGCTTCTATAAGATGCTT
*
5128 TGT-CATGCACCTTTTAACTCTTCTGTGTAGTTGAAAC
66 TGTCCA-GGACCTTTTAACTCTTCTGTGTAGTTGAAAC
* * * *
5165 TCTCTTAGACATCTAAAAATCAAACGATTTATGATGTAATTAAACAAAGCTTCTATAAGATGCAT
1 TCTCTTAGACATCTCAAAATCAAACAATTTATGATGTAATTGAACAAAGCTTCTATAAGATGCTT
* * ** *
5230 TGCCCTGGAAATGTTAACTCTTCTGTGTAGTTGAAAC
66 TGTCCAGGACCTTTTAACTCTTCTGTGTAGTTGAAAC
5267 T
1 T
5268 ACCATTGGCA
Statistics
Matches: 171, Mismatches: 32, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
101 2 0.01
102 168 0.98
103 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.34
Consensus pattern (102 bp):
TCTCTTAGACATCTCAAAATCAAACAATTTATGATGTAATTGAACAAAGCTTCTATAAGATGCTT
TGTCCAGGACCTTTTAACTCTTCTGTGTAGTTGAAAC
Found at i:6424 original size:2 final size:2
Alignment explanation
Indices: 6417--6447 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6407 AACTCACTAC
6417 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 T
6448 TTAAAAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8395 original size:14 final size:14
Alignment explanation
Indices: 8372--8402 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
8362 TCCCCAAATA
*
8372 CCATGTTATATTTG
1 CCATGCTATATTTG
8386 CCATGCTATATTTG
1 CCATGCTATATTTG
8400 CCA
1 CCA
8403 ATAAACAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.42
Consensus pattern (14 bp):
CCATGCTATATTTG
Found at i:17481 original size:31 final size:31
Alignment explanation
Indices: 17443--17501 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
17433 TCAGTTAAAC
* *
17443 GACAATCAATTGAACCGAAAGAAAGACATAT
1 GACAATCAACTGAACCAAAAGAAAGACATAT
*
17474 GACAATCAACTGAACTAAAAGAAAGACA
1 GACAATCAACTGAACCAAAAGAAAGACA
17502 GCACAAACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.54, C:0.17, G:0.15, T:0.14
Consensus pattern (31 bp):
GACAATCAACTGAACCAAAAGAAAGACATAT
Found at i:18601 original size:79 final size:79
Alignment explanation
Indices: 18470--18626 Score: 296
Period size: 79 Copynumber: 2.0 Consensus size: 79
18460 TCGTCTTCTT
*
18470 GTCATATAAATCTTGCAATACTCTTAAAAAATTGCAATAGGTTTATATTTTTTATGAGCTATTAG
1 GTCATATAAATCTTGCAATACTCTTAAAAAATTGCAATAGGTTTATATTTTTTATAAGCTATTAG
18535 TGGACAGCTCGCGA
66 TGGACAGCTCGCGA
18549 GTCATATAAATCTTGCAATACTCTTAAAAAATTGCAATAGGTTTATATTTTTTATAAGCTATTAG
1 GTCATATAAATCTTGCAATACTCTTAAAAAATTGCAATAGGTTTATATTTTTTATAAGCTATTAG
*
18614 TGGACAGTTCGCG
66 TGGACAGCTCGCG
18627 TTTCGCGTGC
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
79 76 1.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (79 bp):
GTCATATAAATCTTGCAATACTCTTAAAAAATTGCAATAGGTTTATATTTTTTATAAGCTATTAG
TGGACAGCTCGCGA
Found at i:20744 original size:22 final size:22
Alignment explanation
Indices: 20716--20854 Score: 70
Period size: 22 Copynumber: 6.3 Consensus size: 22
20706 TATTTTTATA
*
20716 AAATTTTGATAACCATACTATG
1 AAATTTTAATAACCATACTATG
* **
20738 AAATTTTAATAATCATTTTATG
1 AAATTTTAATAACCATACTATG
* **
20760 AAATTGTT-ATAAAC-T-CCCTG
1 AAATT-TTAATAACCATACTATG
* ** *
20780 AAACTTTGGTAACC-TAGTTATG
1 AAATTTTAATAACCATA-CTATG
* *
20802 AAATTTTAATAAACAATCCTATG
1 AAATTTTAAT-AACCATACTATG
* * *
20825 AAAATTTAATAAACATTTCTATG
1 AAATTTTAATAACCA-TACTATG
20848 AAATTTT
1 AAATTTT
20855 GTTAATCTCC
Statistics
Matches: 85, Mismatches: 25, Indels: 13
0.69 0.20 0.11
Matches are distributed among these distances:
19 2 0.02
20 11 0.13
21 1 0.01
22 40 0.47
23 30 0.35
24 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.40
Consensus pattern (22 bp):
AAATTTTAATAACCATACTATG
Found at i:20825 original size:23 final size:23
Alignment explanation
Indices: 20798--20854 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
20788 GTAACCTAGT
20798 TATGAAATTTTAATAAACAATCC
1 TATGAAATTTTAATAAACAATCC
* * *
20821 TATGAAAATTTAATAAACATTTC
1 TATGAAATTTTAATAAACAATCC
20844 TATGAAATTTT
1 TATGAAATTTT
20855 GTTAATCTCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (23 bp):
TATGAAATTTTAATAAACAATCC
Found at i:22691 original size:37 final size:39
Alignment explanation
Indices: 22638--22716 Score: 108
Period size: 37 Copynumber: 2.1 Consensus size: 39
22628 TTTATATACT
* ** *
22638 TGATCAACATACATGTCTTTTCGTATAGACATAACTTTA
1 TGATCAACATACATGTCTTTCCAAACAGACATAACTTTA
22677 TGATCAA-A-ACATGTCTTTCCAAACAGACATAACTTTA
1 TGATCAACATACATGTCTTTCCAAACAGACATAACTTTA
22714 TGA
1 TGA
22717 ATAATTCTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
37 28 0.78
38 1 0.03
39 7 0.19
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (39 bp):
TGATCAACATACATGTCTTTCCAAACAGACATAACTTTA
Found at i:25148 original size:37 final size:37
Alignment explanation
Indices: 25089--25159 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
25079 CTTGATCAAC
* ** * *
25089 ATACATGTCTTTTCGTATAGACATAACTTTATGATCA
1 ATACATGTCTTTCCAAACAGACAAAACTTTATGATCA
25126 ATACATGTCTTTCCAAACAGACAAAACTTTATGA
1 ATACATGTCTTTCCAAACAGACAAAACTTTATGA
25160 ATAATTCTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (37 bp):
ATACATGTCTTTCCAAACAGACAAAACTTTATGATCA
Found at i:34815 original size:28 final size:28
Alignment explanation
Indices: 34779--34835 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
34769 GTTCCAAGAC
34779 TGATGATGTCATTAATGTAGCTGACTTG
1 TGATGATGTCATTAATGTAGCTGACTTG
34807 TGATGATGTCATTAATGTAGCTGACTTG
1 TGATGATGTCATTAATGTAGCTGACTTG
34835 T
1 T
34836 TCTTTAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.40
Consensus pattern (28 bp):
TGATGATGTCATTAATGTAGCTGACTTG
Found at i:37890 original size:19 final size:19
Alignment explanation
Indices: 37850--37886 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
37840 AATTTTTAAG
37850 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
*
37869 TAAAAATTTAATAT-TAAA
1 TAAAAATATAATATATAAA
37887 ATAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:38224 original size:33 final size:33
Alignment explanation
Indices: 38186--38270 Score: 116
Period size: 33 Copynumber: 2.6 Consensus size: 33
38176 GGCGCGAGTG
*
38186 ACCGGCCATGCGACTTGGAGAAGCCCAGCCAAC
1 ACCGGCCACGCGACTTGGAGAAGCCCAGCCAAC
* * * *
38219 ACCGGCCACGCGACTCGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACTTGGAGAAGCCCAGCCAAC
*
38252 ACCGGCCACGCGACATGGA
1 ACCGGCCACGCGACTTGGA
38271 TATGTCCGGC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.24, C:0.39, G:0.29, T:0.08
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAGAAGCCCAGCCAAC
Found at i:38280 original size:33 final size:31
Alignment explanation
Indices: 38186--38292 Score: 115
Period size: 33 Copynumber: 3.3 Consensus size: 31
38176 GGCGCGAGTG
* * *
38186 ACCGGCCATGCGACTTGGAGAAGCCCAGCCAAC
1 ACCGGCCACGCGAC-TGGAGATGCCCGGCC-AC
38219 ACCGGCCACGCGACTCGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACT-GGAGATGCCCGGCCA-C
* *
38252 ACCGGCCACGCGACATGGATATGTCCGGCCAC
1 ACCGGCCACGCGAC-TGGAGATGCCCGGCCAC
38284 AACCGGCCA
1 -ACCGGCCA
38293 TCGCTTGGCG
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
32 3 0.05
33 61 0.94
34 1 0.02
ACGTcount: A:0.23, C:0.39, G:0.28, T:0.09
Consensus pattern (31 bp):
ACCGGCCACGCGACTGGAGATGCCCGGCCAC
Found at i:44781 original size:33 final size:33
Alignment explanation
Indices: 44743--44822 Score: 115
Period size: 33 Copynumber: 2.4 Consensus size: 33
44733 GGCGCGAGTG
* *
44743 ACCGGCCATGCGACTTGGAGAAGCCCGGCCAAC
1 ACCGGCCACGCGACTCGGAGAAGCCCGGCCAAC
* * *
44776 ACCGGCAACGCGACTCGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACTCGGAGAAGCCCGGCCAAC
44809 ACCGGCCACGCGAC
1 ACCGGCCACGCGAC
44823 ATTGACATGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.23, C:0.40, G:0.30, T:0.07
Consensus pattern (33 bp):
ACCGGCCACGCGACTCGGAGAAGCCCGGCCAAC
Done.