Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014839.1 Corchorus capsularis cultivar CVL-1 contig14860, 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: 21154
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:5328 original size:8 final size:8
Alignment explanation
Indices: 5317--5349 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
5307 TTTGCTTTTT
5317 TATACATA
1 TATACATA
5325 TATACATA
1 TATACATA
*
5333 TATATATA
1 TATACATA
5341 TATACATA
1 TATACATA
5349 T
1 T
5350 TTTCTACTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.42
Consensus pattern (8 bp):
TATACATA
Found at i:5647 original size:10 final size:10
Alignment explanation
Indices: 5632--5669 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
5622 TCCCATTCTA
5632 AAAAAAAAAG
1 AAAAAAAAAG
5642 AAAAAAAAAG
1 AAAAAAAAAG
*
5652 AAAAAAGAAG
1 AAAAAAAAAG
5662 AAAAAAAA
1 AAAAAAAA
5670 CTTGGCCTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:5657 original size:17 final size:17
Alignment explanation
Indices: 5631--5669 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
5621 TTCCCATTCT
5631 AAAAAAAAAAGAA-AAA
1 AAAAAAAAAAGAAGAAA
5647 AAAAGAAAAAAGAAGAAA
1 AAAA-AAAAAAGAAGAAA
5665 AAAAA
1 AAAAA
5670 CTTGGCCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.19
17 10 0.48
18 7 0.33
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAGAAGAAA
Found at i:5783 original size:11 final size:12
Alignment explanation
Indices: 5759--5809 Score: 59
Period size: 12 Copynumber: 4.1 Consensus size: 12
5749 AAGCAACGAT
5759 GGTTTTCAAAAA
1 GGTTTTCAAAAA
5771 GGTTTTC-AAAA
1 GGTTTTCAAAAA
*
5782 GGTTTTGATAAAAAA
1 GG-TTT--TCAAAAA
5797 GGTTTTCAAAAA
1 GGTTTTCAAAAA
5809 G
1 G
5810 AGTCATGGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
11 6 0.18
12 17 0.52
14 4 0.12
15 6 0.18
ACGTcount: A:0.41, C:0.06, G:0.20, T:0.33
Consensus pattern (12 bp):
GGTTTTCAAAAA
Found at i:5820 original size:45 final size:45
Alignment explanation
Indices: 5771--5898 Score: 206
Period size: 45 Copynumber: 2.8 Consensus size: 45
5761 TTTTCAAAAA
5771 GGTTTTCAAAAGGTTTTGATAAAAAAGGTTTTCAAAAAGAGTCAT-
1 GGTTTTCAAAAGGTTTTGATAAAAAAGGTTTTCAAAAAGAGTC-TC
5816 GGTTTTCAAAAGGTTTTGATAAAAAAGGTTTTCAAAAAGAGTCTC
1 GGTTTTCAAAAGGTTTTGATAAAAAAGGTTTTCAAAAAGAGTCTC
* *
5861 GATTTTCAAAAGGTTTTGAT-AAAATGGTTTTCCAAAAA
1 GGTTTTCAAAAGGTTTTGATAAAAAAGGTTTT-CAAAAA
5899 TGATTTAAAA
Statistics
Matches: 79, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
44 11 0.14
45 68 0.86
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.34
Consensus pattern (45 bp):
GGTTTTCAAAAGGTTTTGATAAAAAAGGTTTTCAAAAAGAGTCTC
Found at i:6656 original size:5 final size:5
Alignment explanation
Indices: 6579--6637 Score: 86
Period size: 5 Copynumber: 11.8 Consensus size: 5
6569 AGTGCACTGA
6579 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA- AGAAAG -AAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG A-AAAG AAAAG
6628 AAAAAG AAAA
1 -AAAAG AAAA
6638 ATGAATGATG
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
4 5 0.10
5 41 0.82
6 4 0.08
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:7808 original size:36 final size:36
Alignment explanation
Indices: 7759--7866 Score: 110
Period size: 36 Copynumber: 3.0 Consensus size: 36
7749 CAGTTGACCC
* *
7759 AGGGTGATTTTTCTTCAGTTTATGTCGGAATGATCG
1 AGGGTGGTATTTCTTCAGTTTATGTCGGAATGATCG
* * * * *
7795 AGGGTGGTATTTCTTTAGTTTATTTCGG-TTGACCC
1 AGGGTGGTATTTCTTCAGTTTATGTCGGAATGATCG
* ** *
7830 AGGGCGGCCTTTCTTCAGTTTATGTCAGAATGATCG
1 AGGGTGGTATTTCTTCAGTTTATGTCGGAATGATCG
7866 A
1 A
7867 TTCAGTCGAC
Statistics
Matches: 55, Mismatches: 16, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
35 26 0.47
36 29 0.53
ACGTcount: A:0.19, C:0.15, G:0.27, T:0.40
Consensus pattern (36 bp):
AGGGTGGTATTTCTTCAGTTTATGTCGGAATGATCG
Found at i:7850 original size:35 final size:36
Alignment explanation
Indices: 7768--7862 Score: 102
Period size: 35 Copynumber: 2.7 Consensus size: 36
7758 CAGGGTGATT
* * * *
7768 TTTCTTCAGTTTATGTCGGAATGATCGAGGGTGGTA
1 TTTCTTCAGTTTATGTCGGAATGACCCAGGGCGGCA
* * * *
7804 TTTCTTTAGTTTATTTCGG-TTGACCCAGGGCGGCC
1 TTTCTTCAGTTTATGTCGGAATGACCCAGGGCGGCA
*
7839 TTTCTTCAGTTTATGTCAGAATGA
1 TTTCTTCAGTTTATGTCGGAATGA
7863 TCGATTCAGT
Statistics
Matches: 46, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
35 26 0.57
36 20 0.43
ACGTcount: A:0.18, C:0.16, G:0.25, T:0.41
Consensus pattern (36 bp):
TTTCTTCAGTTTATGTCGGAATGACCCAGGGCGGCA
Found at i:7921 original size:71 final size:71
Alignment explanation
Indices: 7846--8181 Score: 514
Period size: 71 Copynumber: 4.7 Consensus size: 71
7836 GCCTTTCTTC
*
7846 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTGTTTTCAAGTTT
*
7911 ATTCGA
66 ATTCCA
7917 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTGTTTTCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTGTTTTCAAGTTT
*
7982 ATTCGA
66 ATTCCA
* * * * *
7988 AGTTTATGTCAGAATGATCGATTCAGTCGATCCAGGGCGCTCTTTCTTCAGTTGTTTCCATGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTGTTTTCAAGTTT
8053 ATTCCA
66 ATTCCA
* * * *
8059 AGTTTATGTCAGAATGATCGATTCAGTCGACCTAGGGTGCTTTTTTTTTCAGTTG-TTTCAAGTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTG-GTCTTTCTTCAGTTGTTTTCAAGTT
8123 TA-TCCA
65 TATTCCA
* * *
8129 AGTTTATGTCAGAATGATCGATTCAGTTGACCCAGGGTGGTTTTTCTTTAGTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTT
8182 TATGTCGGAA
Statistics
Matches: 244, Mismatches: 20, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
69 11 0.05
70 41 0.17
71 180 0.74
72 12 0.05
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (71 bp):
AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTGTTTTCAAGTTT
ATTCCA
Found at i:8211 original size:36 final size:36
Alignment explanation
Indices: 8162--8269 Score: 128
Period size: 36 Copynumber: 3.0 Consensus size: 36
8152 CAGTTGACCC
*
8162 AGGGTGGTTTTTCTTTAGTTTATGTCGGAATGATCG
1 AGGGTGGTCTTTCTTTAGTTTATGTCGGAATGATCG
* * * *
8198 AGGGTGGTCTTTCTTTAGTTTATTTCGG-TTGACCC
1 AGGGTGGTCTTTCTTTAGTTTATGTCGGAATGATCG
* * * *
8233 AGGGCGGTCTTTCTTCAGTTTATGTCAGAAAGATCG
1 AGGGTGGTCTTTCTTTAGTTTATGTCGGAATGATCG
8269 A
1 A
8270 TTCAGTCGAC
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
35 28 0.48
36 30 0.52
ACGTcount: A:0.18, C:0.14, G:0.28, T:0.41
Consensus pattern (36 bp):
AGGGTGGTCTTTCTTTAGTTTATGTCGGAATGATCG
Found at i:8253 original size:35 final size:35
Alignment explanation
Indices: 8154--8258 Score: 138
Period size: 36 Copynumber: 3.0 Consensus size: 35
8144 GATCGATTCA
*
8154 GTTGACCCAGGGTGGTTTTTCTTTAGTTTATGTCG
1 GTTGACCCAGGGTGGTCTTTCTTTAGTTTATGTCG
* * * *
8189 GAATGATCGAGGGTGGTCTTTCTTTAGTTTATTTCG
1 G-TTGACCCAGGGTGGTCTTTCTTTAGTTTATGTCG
* *
8225 GTTGACCCAGGGCGGTCTTTCTTCAGTTTATGTC
1 GTTGACCCAGGGTGGTCTTTCTTTAGTTTATGTC
8259 AGAAAGATCG
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
35 28 0.48
36 30 0.52
ACGTcount: A:0.13, C:0.16, G:0.28, T:0.43
Consensus pattern (35 bp):
GTTGACCCAGGGTGGTCTTTCTTTAGTTTATGTCG
Found at i:8327 original size:71 final size:70
Alignment explanation
Indices: 8249--8529 Score: 400
Period size: 70 Copynumber: 4.0 Consensus size: 70
8239 GTCTTTCTTC
* * *
8249 AGTTTATGTCAGAAAGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTTAGTTGTTTTCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
*
8314 ATTCGA
66 A-TCCA
*
8320 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTATTTCCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
8385 ATCCA
66 ATCCA
* * * * * *
8390 AGTTTGTGTCAGAATGATCGATTCGGTCGACCCAGCGTGGTCTTTCTTCAGTAGTTTCCACGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
8455 ATCCA
66 ATCCA
* * * * * *
8460 AGTTTATGTTAGAATGATCAATTCAGTCGACCCAGGGCCGTTTTTCATCAGTTGTTTCCAAGTTG
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
8525 ATCCA
66 ATCCA
8530 GGTTGGTCTT
Statistics
Matches: 186, Mismatches: 24, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
70 124 0.67
71 62 0.33
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.36
Consensus pattern (70 bp):
AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
ATCCA
Found at i:8938 original size:27 final size:28
Alignment explanation
Indices: 8903--8976 Score: 98
Period size: 27 Copynumber: 2.7 Consensus size: 28
8893 AGGGTCACCT
*
8903 AGGGTCATTTTGGTCATTTTC-ACATTC
1 AGGGGCATTTTGGTCATTTTCTACATTC
* * *
8930 CGGGGCATTTTAGTCA-TTTCTGCATTC
1 AGGGGCATTTTGGTCATTTTCTACATTC
8957 AGGGGCATTTTGGTCATTTT
1 AGGGGCATTTTGGTCATTTT
8977 GAGTCCACTT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
26 4 0.10
27 32 0.82
28 3 0.08
ACGTcount: A:0.16, C:0.18, G:0.23, T:0.43
Consensus pattern (28 bp):
AGGGGCATTTTGGTCATTTTCTACATTC
Found at i:10443 original size:23 final size:23
Alignment explanation
Indices: 10416--10465 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
10406 TGCATTCATC
10416 ATTTCATACAGGCATTAGTTAAT
1 ATTTCATACAGGCATTAGTTAAT
* *
10439 ATTTCATGCATGCATTAGTTAAT
1 ATTTCATACAGGCATTAGTTAAT
10462 ATTT
1 ATTT
10466 AGGTCAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (23 bp):
ATTTCATACAGGCATTAGTTAAT
Found at i:13203 original size:15 final size:16
Alignment explanation
Indices: 13174--13203 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13164 GTGTGAAGTG
13174 AAATTGATCTTTTGAA
1 AAATTGATCTTTTGAA
13190 AAATTGAT-TTTTGA
1 AAATTGATCTTTTGA
13204 TTAAACTTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47
Consensus pattern (16 bp):
AAATTGATCTTTTGAA
Found at i:16260 original size:17 final size:17
Alignment explanation
Indices: 16223--16263 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
16213 AAAATCTCTT
* *
16223 TTTTTTATTTTTTTTAA
1 TTTTCTATTTTTTGTAA
16240 -TTTCTATTTTTTGTAA
1 TTTTCTATTTTTTGTAA
16256 TTTTCTAT
1 TTTTCTAT
16264 AATTAGGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (17 bp):
TTTTCTATTTTTTGTAA
Found at i:17848 original size:24 final size:26
Alignment explanation
Indices: 17815--17885 Score: 74
Period size: 29 Copynumber: 2.7 Consensus size: 26
17805 TCATTGATAT
* *
17815 AAAAATTTATTCTAACTT-GT-TAAA
1 AAAAAATTATTCTAACTTAGTGAAAA
*
17839 AAAAAATTATACTAACTTATAGTGGAAAA
1 AAAAAATTATTCTAAC-T-TAGT-GAAAA
17868 AAAAAATTATTCTAACTT
1 AAAAAATTATTCTAACTT
17886 TTTCTCCCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
24 14 0.37
25 1 0.03
26 1 0.03
27 3 0.08
28 1 0.03
29 18 0.47
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.35
Consensus pattern (26 bp):
AAAAAATTATTCTAACTTAGTGAAAA
Found at i:20433 original size:23 final size:23
Alignment explanation
Indices: 20406--20449 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
20396 TGGAAATAAC
*
20406 CTATTAA-CTTACTTAATTAACCA
1 CTATTAACCTTA-ATAATTAACCA
20429 CTATTAACCTTAATAATTAAC
1 CTATTAACCTTAATAATTAAC
20450 TACCAAGGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (23 bp):
CTATTAACCTTAATAATTAACCA
Done.