Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007410.1 Corchorus capsularis cultivar CVL-1 contig07431, 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: 43031
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:819 original size:20 final size:21
Alignment explanation
Indices: 794--839 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
784 TCAAATTAAA
*
794 ATAAAAACTACCCATTTTA-G
1 ATAAAAACTACCCATTATAGG
814 ATAAAAACTACCCATTATAGG
1 ATAAAAACTACCCATTATAGG
835 ATAAA
1 ATAAA
840 TATAATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.50, C:0.17, G:0.07, T:0.26
Consensus pattern (21 bp):
ATAAAAACTACCCATTATAGG
Found at i:2239 original size:13 final size:13
Alignment explanation
Indices: 2221--2246 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2211 TAAAAATTTT
2221 TGTGTATTTGTAC
1 TGTGTATTTGTAC
2234 TGTGTATTTGTAC
1 TGTGTATTTGTAC
2247 ATACATGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.23, T:0.54
Consensus pattern (13 bp):
TGTGTATTTGTAC
Found at i:8706 original size:20 final size:20
Alignment explanation
Indices: 8678--8719 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
8668 ATGAGTAAGA
8678 AAAATATAAAT-GAAATTAC
1 AAAATATAAATAGAAATTAC
*
8697 AAAATAATAACTAGAAATTAC
1 AAAAT-ATAAATAGAAATTAC
8718 AA
1 AA
8720 TAGGTTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 5 0.25
21 10 0.50
ACGTcount: A:0.64, C:0.07, G:0.05, T:0.24
Consensus pattern (20 bp):
AAAATATAAATAGAAATTAC
Found at i:15518 original size:37 final size:37
Alignment explanation
Indices: 15477--15743 Score: 283
Period size: 37 Copynumber: 7.2 Consensus size: 37
15467 TTAATAAATT
* * *
15477 TTTAAGGTCCCTGTTTAGGTATCTCATCAAAATCTTG
1 TTTAAGATCCCTGTTTAGGTGTCTTATCAAAATCTTG
* * *
15514 TTTAAGAAT-CATGTTTAGGTTTCTTAT-TAAATCCTTG
1 TTTAAG-ATCCCTGTTTAGGTGTCTTATCAAAAT-CTTG
* *
15551 TTTAAGATCCATGTTTAGGTGTCTCATCAAAATCTTG
1 TTTAAGATCCCTGTTTAGGTGTCTTATCAAAATCTTG
* * * *
15588 TTTAATATTCTTGTTTAGGAT-TCTTAT-TAAATCCTTG
1 TTTAAGATCCCTGTTTAGG-TGTCTTATCAAAAT-CTTG
*
15625 TTTAAGGTCCCTGTTTAGGTGTCTTATCAAAATCTTG
1 TTTAAGATCCCTGTTTAGGTGTCTTATCAAAATCTTG
* * *
15662 TTTAAGATTCCTGTTTAGGTTTCTTAT-TAAATCCTTG
1 TTTAAGATCCCTGTTTAGGTGTCTTATCAAAAT-CTTG
* * *
15699 TTTAAGATCCCTGTTTAGGCGTGTCATCAAAATCTTG
1 TTTAAGATCCCTGTTTAGGTGTCTTATCAAAATCTTG
15736 TTTAAGAT
1 TTTAAGAT
15744 TCCCATTTTT
Statistics
Matches: 192, Mismatches: 28, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
36 15 0.08
37 163 0.85
38 14 0.07
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (37 bp):
TTTAAGATCCCTGTTTAGGTGTCTTATCAAAATCTTG
Found at i:15746 original size:74 final size:74
Alignment explanation
Indices: 15477--15746 Score: 432
Period size: 74 Copynumber: 3.6 Consensus size: 74
15467 TTAATAAATT
* * * *
15477 TTTAAGGTCCCTGTTTAGGTATCTCATCAAAATCTTGTTTAAGAATCATGTTTAGGTTTCTTATT
1 TTTAAGATCCCTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATT
15542 AAATCCTTG
66 AAATCCTTG
* * * *
15551 TTTAAGATCCATGTTTAGGTGTCTCATCAAAATCTTGTTTAATATTCTTGTTTAGGATTCTTATT
1 TTTAAGATCCCTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATT
15616 AAATCCTTG
66 AAATCCTTG
* *
15625 TTTAAGGTCCCTGTTTAGGTGTCTTATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATT
1 TTTAAGATCCCTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATT
15690 AAATCCTTG
66 AAATCCTTG
* *
15699 TTTAAGATCCCTGTTTAGGCGTGTCATCAAAATCTTGTTTAAGATTCC
1 TTTAAGATCCCTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCC
15747 CATTTTTGTA
Statistics
Matches: 179, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
74 179 1.00
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.45
Consensus pattern (74 bp):
TTTAAGATCCCTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATT
AAATCCTTG
Found at i:19864 original size:83 final size:82
Alignment explanation
Indices: 19725--19884 Score: 268
Period size: 83 Copynumber: 1.9 Consensus size: 82
19715 ATAATTGAAC
*
19725 CGGGATGGTCAAACCGGTCATGCCAAACAATAAACATAATGCAATCAATAAACTTCTAGTTTACA
1 CGGGATGGCCAAACCGGTCATGCCAAACAATAAACATAATGCAATCAATAAACTTCT-GTTTACA
19790 AAAGCATAAGTTTATAAT
65 AAAGCATAAGTTTATAAT
*
19808 CGGGATGGCCTAAA-CGGTCATGTCAAACAATAAACATAATGCAATCAATAAACTTCTGTTTACA
1 CGGGATGGCC-AAACCGGTCATGCCAAACAATAAACATAATGCAATCAATAAACTTCTGTTTACA
*
19872 AAAGCATATGTTT
65 AAAGCATAAGTTT
19885 CAATCTTACC
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
82 19 0.26
83 51 0.70
84 3 0.04
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (82 bp):
CGGGATGGCCAAACCGGTCATGCCAAACAATAAACATAATGCAATCAATAAACTTCTGTTTACAA
AAGCATAAGTTTATAAT
Found at i:20173 original size:35 final size:35
Alignment explanation
Indices: 20127--20224 Score: 151
Period size: 35 Copynumber: 2.8 Consensus size: 35
20117 AACAATAGTA
*
20127 GCTCTTCTGGAGCCTTCAATCAAATTTGAATACTG
1 GCTCTTCTGGAGCCTTCAATCAAATTTGAAAACTG
* * *
20162 GCTCTTCTGGAGCCTTTAATCAATTTTAAAAACTG
1 GCTCTTCTGGAGCCTTCAATCAAATTTGAAAACTG
*
20197 GCTTTTCTGGAGCCTTCAATCAAATTTG
1 GCTCTTCTGGAGCCTTCAATCAAATTTG
20225 TACCATCTGA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 55 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (35 bp):
GCTCTTCTGGAGCCTTCAATCAAATTTGAAAACTG
Found at i:21646 original size:54 final size:54
Alignment explanation
Indices: 21563--21665 Score: 188
Period size: 54 Copynumber: 1.9 Consensus size: 54
21553 ATATAATTTA
* *
21563 AAGTGGATAGTATGACAACTTCGGGTGTCAAACTTTGGCAACAATTAAAGTTTT
1 AAGTGGATAGTATGACAACTTCAGATGTCAAACTTTGGCAACAATTAAAGTTTT
21617 AAGTGGATAGTATGACAACTTCAGATGTCAAACTTTGGCAACAATTAAA
1 AAGTGGATAGTATGACAACTTCAGATGTCAAACTTTGGCAACAATTAAA
21666 CAAATATTTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (54 bp):
AAGTGGATAGTATGACAACTTCAGATGTCAAACTTTGGCAACAATTAAAGTTTT
Found at i:21729 original size:29 final size:29
Alignment explanation
Indices: 21685--21745 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
21675 CCATCCTTAA
*
21685 TATGACAACTTTGGGTGTCAAAATGATAC
1 TATGACAACTTCGGGTGTCAAAATGATAC
* *
21714 TATGACAACTTCGGGTGTCATAGTGATAC
1 TATGACAACTTCGGGTGTCAAAATGATAC
21743 TAT
1 TAT
21746 ATTTTTGATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (29 bp):
TATGACAACTTCGGGTGTCAAAATGATAC
Found at i:21787 original size:33 final size:33
Alignment explanation
Indices: 21744--21815 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
21734 TAGTGATACT
* *
21744 ATATTTTTGATATGACAACTTCAGGTGCCACTG
1 ATATTCTTGATATGACAACTTCAGGTGCCACTA
*
21777 ATATTCTTGATGTGACAACTTCAGGTGCCACTA
1 ATATTCTTGATATGACAACTTCAGGTGCCACTA
21810 ATATTC
1 ATATTC
21816 AAGGATAGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (33 bp):
ATATTCTTGATATGACAACTTCAGGTGCCACTA
Found at i:24745 original size:79 final size:78
Alignment explanation
Indices: 24618--24851 Score: 391
Period size: 78 Copynumber: 3.0 Consensus size: 78
24608 CCATCAGGGT
24618 GTAATGTCTTAGTACATCAACAGCTGTGAAGGTTGGCGAAAAAAAAAAAACAGCTTCGTGAAGGG
1 GTAATGTCTTAGTACATCAACAGCTGTGAAGGTTGGCG-AAAAAAAAAAACAGCTTCGTGAAGGG
24683 CGAATATTAGATCA
65 CGAATATTAGATCA
* *
24697 GTAATGTCTTAGTACATCAACAGCTGTGAATGTTGGCCG-AAAAAAAAAACAGCTTCGTGAAGGA
1 GTAATGTCTTAGTACATCAACAGCTGTGAAGGTTGG-CGAAAAAAAAAAACAGCTTCGTGAAGGG
24761 CGAATATTAGATCA
65 CGAATATTAGATCA
* * *
24775 GTAATGTCTTAGTACATCAACAGCTATGAAGGTTGGC-AAAAAAAAAAAAAACTTCGTGAAGGGC
1 GTAATGTCTTAGTACATCAACAGCTGTGAAGGTTGGCGAAAAAAAAAAACAGCTTCGTGAAGGGC
24839 GAATATTAGATCA
66 GAATATTAGATCA
24852 TGGCACGCTA
Statistics
Matches: 146, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
77 37 0.25
78 72 0.49
79 35 0.24
80 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.24
Consensus pattern (78 bp):
GTAATGTCTTAGTACATCAACAGCTGTGAAGGTTGGCGAAAAAAAAAAACAGCTTCGTGAAGGGC
GAATATTAGATCA
Found at i:25542 original size:31 final size:32
Alignment explanation
Indices: 25498--25566 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
25488 CGTGGCCTTA
25498 CCACATGGCA-TTTTGGTCCAGCATG-A-CATTG
1 CCACATGGCATTTTTGGTCC--CATGTAGCATTG
* *
25529 CCACGTGGTATTTTTGGTCCCATGTAGCATTG
1 CCACATGGCATTTTTGGTCCCATGTAGCATTG
25561 CCACAT
1 CCACAT
25567 CAGCAATACT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
30 4 0.12
31 9 0.28
32 19 0.59
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.32
Consensus pattern (32 bp):
CCACATGGCATTTTTGGTCCCATGTAGCATTG
Found at i:27960 original size:153 final size:156
Alignment explanation
Indices: 27662--27971 Score: 493
Period size: 153 Copynumber: 2.0 Consensus size: 156
27652 ACCGTTAAAG
*
27662 TTAACGATGCGTTTTTTTCACATGCTAAAAGGTAGAATACCTCTATTTGACAATTTACCTCTATC
1 TTAACGACGCGTTTTTTTCACATGCTAAAAGGTA-AATACCTCTATTTGACAATTTACCTCTATC
*
27727 TGACACGAATTGATAACGTTTTGCCACAAATAGACCAAATTGAAAGCTTCTACCCCAAATTAGGC
65 TGACACAAATTGATAACGTTTTGCCACAAATAGACCAAATTGAAAGCTTCTACCCCAAATTAGGC
*
27792 CGAATCAGAAACGTTTTGCCCTTAATT
130 CGAACCAGAAACGTTTTGCCCTTAATT
* * * *
27819 TTAACGACGCGTTTTTTTCACATGCTAAAAGGT-ATTGCCTCTATTTGATAATTTGCCTCTAAT-
1 TTAACGACGCGTTTTTTTCACATGCTAAAAGGTAAATACCTCTATTTGACAATTTACCTCT-ATC
* *
27882 TGACACAAATTGATAACGTTTTG-C-CAAATAGACCAAATTGAATGCTTCTGCCCCAAATTAGGC
65 TGACACAAATTGATAACGTTTTGCCACAAATAGACCAAATTGAAAGCTTCTACCCCAAATTAGGC
27945 CGAACCAGAAACGTTTTGCCCTTAATT
130 CGAACCAGAAACGTTTTGCCCTTAATT
27972 AAGCAATTAG
Statistics
Matches: 143, Mismatches: 9, Indels: 6
0.91 0.06 0.04
Matches are distributed among these distances:
153 63 0.44
154 1 0.01
155 45 0.31
156 2 0.01
157 32 0.22
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.33
Consensus pattern (156 bp):
TTAACGACGCGTTTTTTTCACATGCTAAAAGGTAAATACCTCTATTTGACAATTTACCTCTATCT
GACACAAATTGATAACGTTTTGCCACAAATAGACCAAATTGAAAGCTTCTACCCCAAATTAGGCC
GAACCAGAAACGTTTTGCCCTTAATT
Found at i:29260 original size:6 final size:6
Alignment explanation
Indices: 29231--29273 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
29221 CATTTTAGAG
*
29231 GCTCGA GCTTGA -CTCGA GAC-CGA GCTCGA GCTCGA GCTCGA GC
1 GCTCGA GCTCGA GCTCGA G-CTCGA GCTCGA GCTCGA GCTCGA GC
29274 CTATAACGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 5 0.16
6 26 0.81
7 1 0.03
ACGTcount: A:0.19, C:0.33, G:0.33, T:0.16
Consensus pattern (6 bp):
GCTCGA
Found at i:32818 original size:11 final size:11
Alignment explanation
Indices: 32802--32827 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
32792 AGTAACAAAG
32802 TGAATAGTAAT
1 TGAATAGTAAT
32813 TGAATAGTAAT
1 TGAATAGTAAT
32824 TGAA
1 TGAA
32828 CAAGAAGGTA
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:0.46, C:0.00, G:0.19, T:0.35
Consensus pattern (11 bp):
TGAATAGTAAT
Found at i:33412 original size:20 final size:21
Alignment explanation
Indices: 33389--33438 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
33379 AATATGTAAA
*
33389 ATATTTTAT-TAAATAAGAAT
1 ATATTATATGTAAATAAGAAT
33409 ATA-TATATGTAAATAAGAAT
1 ATATTATATGTAAATAAGAAT
33429 ATATATATAT
1 ATAT-TATAT
33439 ATGTAAGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 4 0.15
20 17 0.65
22 5 0.19
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (21 bp):
ATATTATATGTAAATAAGAAT
Found at i:33445 original size:20 final size:20
Alignment explanation
Indices: 33398--33495 Score: 78
Period size: 20 Copynumber: 5.0 Consensus size: 20
33388 AATATTTTAT
*
33398 TAAATAAGAATATATATATG
1 TAAATAAGAATATATATATA
33418 TAAATAAGAATATATATATA
1 TAAATAAGAATATATATATA
** *
33438 TATGTAAGAAT-T-T-TATT
1 TAAATAAGAATATATATATA
* *
33455 TTAATATATAATATATAT-TA
1 TAAATA-AGAATATATATATA
* *
33475 TTAATATGTAATATATATATA
1 TAAATAAG-AATATATATATA
33496 ATATATTTAA
Statistics
Matches: 61, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
17 6 0.10
18 5 0.08
19 2 0.03
20 45 0.74
21 3 0.05
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (20 bp):
TAAATAAGAATATATATATA
Found at i:41937 original size:21 final size:18
Alignment explanation
Indices: 41899--41939 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 18
41889 GGAATATTCT
41899 TGCTTCCAATGACTTCAA
1 TGCTTCCAATGACTTCAA
41917 TGCTCTCCAATTGATCTTCAA
1 TGCT-TCCAA-TGA-CTTCAA
41938 TG
1 TG
41940 GTCTTCAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 5 0.25
20 3 0.15
21 8 0.40
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.37
Consensus pattern (18 bp):
TGCTTCCAATGACTTCAA
Done.