Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007166.1 Corchorus capsularis cultivar CVL-1 contig07187, 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: 35915
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.32
Found at i:2512 original size:10 final size:10
Alignment explanation
Indices: 2497--2521 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2487 GAGGACTCTA
2497 GAATTTTCTG
1 GAATTTTCTG
2507 GAATTTTCTG
1 GAATTTTCTG
2517 GAATT
1 GAATT
2522 GTCCACGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:6741 original size:189 final size:189
Alignment explanation
Indices: 6421--6768 Score: 606
Period size: 189 Copynumber: 1.8 Consensus size: 189
6411 TCATCATCAA
* *
6421 ATGGCAGACCCTATGCTTTAGGTTCACAGCAGATGCTATGGCTTCTGAAATTGGGACGGATCGAT
1 ATGGCAGACCCTATGCTTCAGGTTCACAGCAGATGCTATGCCTTCTGAAATTGGGACGGATCGAT
* * *
6486 GAAATTATGGAATTGGATTGCCAACGATCCACGATTGGGATCGTGCGATCCAATTCGCAGATCGT
66 GAAATTATGGAATTGGATCGCCAACAATCCACGATTGGGATCGTGCGATCCAATTCACAGATCGT
6551 AGCTTGAGGGGCGATTTATGGTAACTCTGCTTTAGACTTTAGAGTTAGATTTTAGTTTT
131 AGCTTGAGGGGCGATTTATGGTAACTCTGCTTTAGACTTTAGAGTTAGATTTTAGTTTT
* * *
6610 ATGGCAGACCCTATGCTTCAGGTTCACGGCAGATTCTATGCCTTCTGAGATTGGGACGGATCGAT
1 ATGGCAGACCCTATGCTTCAGGTTCACAGCAGATGCTATGCCTTCTGAAATTGGGACGGATCGAT
*
6675 GAAATTATGGAATTGGATCGCCAACAATCCGCGATTGGGATCGTGCGATCCAATTCACAGATCGT
66 GAAATTATGGAATTGGATCGCCAACAATCCACGATTGGGATCGTGCGATCCAATTCACAGATCGT
*
6740 AGGTTGAGGGGCGATTTATGGTAACTCTG
131 AGCTTGAGGGGCGATTTATGGTAACTCTG
6769 TCTTGTTCAT
Statistics
Matches: 149, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
189 149 1.00
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (189 bp):
ATGGCAGACCCTATGCTTCAGGTTCACAGCAGATGCTATGCCTTCTGAAATTGGGACGGATCGAT
GAAATTATGGAATTGGATCGCCAACAATCCACGATTGGGATCGTGCGATCCAATTCACAGATCGT
AGCTTGAGGGGCGATTTATGGTAACTCTGCTTTAGACTTTAGAGTTAGATTTTAGTTTT
Found at i:15162 original size:5 final size:5
Alignment explanation
Indices: 15152--15197 Score: 60
Period size: 5 Copynumber: 9.4 Consensus size: 5
15142 GCTTGTTCTC
*
15152 TCTTT TCTTT TCTTT TCTCT TCTTT T-TTT TCTTT TACTTT T-TTT TC
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T-CTTT TCTTT TC
15198 ATGCTTATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
4 8 0.22
5 23 0.64
6 5 0.14
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (5 bp):
TCTTT
Found at i:15171 original size:19 final size:19
Alignment explanation
Indices: 15147--15186 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
15137 CCACTGCTTG
15147 TTCTC-TCTTTTCTTTTCTT
1 TTCTCTTCTTTT-TTTTCTT
15166 TTCTCTTCTTTTTTTTCTT
1 TTCTCTTCTTTTTTTTCTT
15185 TT
1 TT
15187 ACTTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.78
Consensus pattern (19 bp):
TTCTCTTCTTTTTTTTCTT
Found at i:17720 original size:2 final size:2
Alignment explanation
Indices: 17713--17756 Score: 61
Period size: 2 Copynumber: 21.0 Consensus size: 2
17703 TCGAGAAATC
*
17713 AT AT AT AT CAT AT AT AT AT AT AT AT AT AT AG AT AT ACT AT AT AT
1 AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
17757 TATTTGAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 34 0.89
3 4 0.11
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:22762 original size:48 final size:47
Alignment explanation
Indices: 22663--22815 Score: 180
Period size: 48 Copynumber: 3.2 Consensus size: 47
22653 ATGTGGCAGC
* * ** **
22663 ATGGTGCTTGGCTTCTGCGGTAAAATTGTGGTTGGCTTCTGCGACGGA
1 ATGGTGCTTGACTTCTGCGGTAAAATTGTGATTAACTTCTGC-ACAAA
* *
22711 ATGGTGCTTGACTTCTGCGGTACAATTGTGATTAACTTTTGTCACAAA
1 ATGGTGCTTGACTTCTGCGGTAAAATTGTGATTAACTTCTG-CACAAA
* * *
22759 ATGGTGCTTGACTTCTGCAGTAGAATTGTGATTAACTTCTGCCGCAAA
1 ATGGTGCTTGACTTCTGCGGTAAAATTGTGATTAACTTCTG-CACAAA
22807 ATGGTGCTT
1 ATGGTGCTT
22816 AAGATTGGTG
Statistics
Matches: 91, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
48 90 0.99
49 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.35
Consensus pattern (47 bp):
ATGGTGCTTGACTTCTGCGGTAAAATTGTGATTAACTTCTGCACAAA
Found at i:22817 original size:24 final size:24
Alignment explanation
Indices: 22710--22817 Score: 81
Period size: 24 Copynumber: 4.5 Consensus size: 24
22700 TCTGCGACGG
* * * *
22710 AATGGTGCTTGACTTCTGCGGTAC
1 AATGGTGCTTAACTTCTGCCGCAA
* * * * *
22734 AATTGTGATTAACTTTTGTCACAA
1 AATGGTGCTTAACTTCTGCCGCAA
* * * *
22758 AATGGTGCTTGACTTCTGCAGTAG
1 AATGGTGCTTAACTTCTGCCGCAA
* *
22782 AATTGTGATTAACTTCTGCCGCAA
1 AATGGTGCTTAACTTCTGCCGCAA
22806 AATGGTGCTTAA
1 AATGGTGCTTAA
22818 GATTGGTGGT
Statistics
Matches: 58, Mismatches: 26, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (24 bp):
AATGGTGCTTAACTTCTGCCGCAA
Found at i:24880 original size:27 final size:27
Alignment explanation
Indices: 24829--24928 Score: 94
Period size: 27 Copynumber: 3.7 Consensus size: 27
24819 GCTGAAATTC
* *
24829 CCGCAGTTGGGACGCACGCCAAAGCCT
1 CCGCAGTTGGGACTCATGCCAAAGCCT
* **
24856 TCGCAGTTGGGACTCATGCTGAAG-CT
1 CCGCAGTTGGGACTCATGCCAAAGCCT
* *
24882 CCCGTAGTTGGGACTTATGCCAAAGCCT
1 -CCGCAGTTGGGACTCATGCCAAAGCCT
* * *
24910 CCGTAGTTAGGACTTATGC
1 CCGCAGTTGGGACTCATGC
24929 TGAAGGACTC
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
26 2 0.03
27 56 0.93
28 2 0.03
ACGTcount: A:0.21, C:0.28, G:0.28, T:0.23
Consensus pattern (27 bp):
CCGCAGTTGGGACTCATGCCAAAGCCT
Found at i:24891 original size:54 final size:54
Alignment explanation
Indices: 24806--24933 Score: 157
Period size: 54 Copynumber: 2.4 Consensus size: 54
24796 ATGCTCCCGT
* ** *
24806 AGTTGGCACTCATGCTGAAATTCCCGCAGTTGGGACGCACGCCAAAGCCTTCGC
1 AGTTGGGACTCATGCTGAAGCTCCCGCAGTTGGGACGCACGCCAAAGCCTCCGC
* ** * *
24860 AGTTGGGACTCATGCTGAAGCTCCCGTAGTTGGGACTTATGCCAAAGCCTCCGT
1 AGTTGGGACTCATGCTGAAGCTCCCGCAGTTGGGACGCACGCCAAAGCCTCCGC
* *
24914 AGTTAGGACTTATGCTGAAG
1 AGTTGGGACTCATGCTGAAG
24934 GACTCATGCC
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 63 1.00
ACGTcount: A:0.23, C:0.26, G:0.27, T:0.24
Consensus pattern (54 bp):
AGTTGGGACTCATGCTGAAGCTCCCGCAGTTGGGACGCACGCCAAAGCCTCCGC
Found at i:24985 original size:27 final size:27
Alignment explanation
Indices: 24955--25069 Score: 126
Period size: 27 Copynumber: 4.3 Consensus size: 27
24945 AAGCTCTTGT
* * *
24955 AGTTGGGATTCATGTTGAAGCTCCCGC
1 AGTTGGGACTCATGCTAAAGCTCCCGC
* *
24982 AGTTGGGACTCATACTAAAGCTCCCAC
1 AGTTGGGACTCATGCTAAAGCTCCCGC
*
25009 GGTTGGGACTCATG-TCAAAGC-CTCCGC
1 AGTTGGGACTCATGCT-AAAGCTC-CCGC
* *
25036 AGTTGGGATTCATGCTAAAGCTCCCGT
1 AGTTGGGACTCATGCTAAAGCTCCCGC
25063 AGTTGGG
1 AGTTGGG
25070 TTTTGTGTTG
Statistics
Matches: 73, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
26 2 0.03
27 69 0.95
28 2 0.03
ACGTcount: A:0.22, C:0.24, G:0.28, T:0.26
Consensus pattern (27 bp):
AGTTGGGACTCATGCTAAAGCTCCCGC
Found at i:25015 original size:54 final size:54
Alignment explanation
Indices: 24956--25060 Score: 149
Period size: 54 Copynumber: 1.9 Consensus size: 54
24946 AGCTCTTGTA
* **
24956 GTTGGGATTCATGTTGAAG-CTCCCGCAGTTGGGACTCATACTAAAGCTCCCACG
1 GTTGGGACTCATGTCAAAGCCT-CCGCAGTTGGGACTCATACTAAAGCTCCCACG
* *
25010 GTTGGGACTCATGTCAAAGCCTCCGCAGTTGGGATTCATGCTAAAGCTCCC
1 GTTGGGACTCATGTCAAAGCCTCCGCAGTTGGGACTCATACTAAAGCTCCC
25061 GTAGTTGGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
54 43 0.96
55 2 0.04
ACGTcount: A:0.22, C:0.27, G:0.26, T:0.26
Consensus pattern (54 bp):
GTTGGGACTCATGTCAAAGCCTCCGCAGTTGGGACTCATACTAAAGCTCCCACG
Found at i:25068 original size:54 final size:54
Alignment explanation
Indices: 24953--25069 Score: 146
Period size: 54 Copynumber: 2.2 Consensus size: 54
24943 CGAAGCTCTT
* **
24953 GTAGTTGGGATTCATGTTGAAGCTCCCGCAGTTGGGACTCATACTAAAGCTCCC
1 GTAGTTGGGACTCATGTCAAAGCTCCCGCAGTTGGGACTCATACTAAAGCTCCC
*** * *
25007 ACGGTTGGGACTCATGTCAAAGC-CTCCGCAGTTGGGATTCATGCTAAAGCTCCC
1 GTAGTTGGGACTCATGTCAAAGCTC-CCGCAGTTGGGACTCATACTAAAGCTCCC
25061 GTAGTTGGG
1 GTAGTTGGG
25070 TTTTGTGTTG
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
53 1 0.02
54 50 0.98
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.26
Consensus pattern (54 bp):
GTAGTTGGGACTCATGTCAAAGCTCCCGCAGTTGGGACTCATACTAAAGCTCCC
Found at i:26383 original size:19 final size:19
Alignment explanation
Indices: 26359--26404 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
26349 ATTTATATCA
26359 ATTCTTTTTACATGAACTG
1 ATTCTTTTTACATGAACTG
26378 ATTCTTTTTACATGAACTG
1 ATTCTTTTTACATGAACTG
*
26397 ATGCTTTT
1 ATTCTTTT
26405 GCTTTTCCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.24, C:0.15, G:0.11, T:0.50
Consensus pattern (19 bp):
ATTCTTTTTACATGAACTG
Found at i:26948 original size:19 final size:19
Alignment explanation
Indices: 26924--26960 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
26914 TAATTATATT
26924 TTAAAGGTTATATTTAATG
1 TTAAAGGTTATATTTAATG
26943 TTAAAGGTTATATTTAAT
1 TTAAAGGTTATATTTAAT
26961 TACATTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.49
Consensus pattern (19 bp):
TTAAAGGTTATATTTAATG
Done.