Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006929.1 Corchorus capsularis cultivar CVL-1 contig06950, 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: 10116
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Found at i:1293 original size:51 final size:51
Alignment explanation
Indices: 1234--1335 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
1224 TAAAATGGAC
*
1234 TTAAACCCAATAAGGAAAGGAAAGTTGAATTTGGGCTTTAAAAGTTTAATT
1 TTAAACCCAATAAGGAAAGAAAAGTTGAATTTGGGCTTTAAAAGTTTAATT
1285 TTAAACCCAATAAGGAAAGAAAAGTTGAATTTGGGCTTTAAAAGTTTAATT
1 TTAAACCCAATAAGGAAAGAAAAGTTGAATTTGGGCTTTAAAAGTTTAATT
1336 AATGAATTTG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.42, C:0.08, G:0.19, T:0.31
Consensus pattern (51 bp):
TTAAACCCAATAAGGAAAGAAAAGTTGAATTTGGGCTTTAAAAGTTTAATT
Found at i:1573 original size:14 final size:13
Alignment explanation
Indices: 1554--1596 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
1544 AATCCCCCCC
1554 TTTTGCTTTTTGCT
1 TTTTGCTTTTT-CT
1568 TTTTGCTTTTCTCT
1 TTTTGCTTTT-TCT
1582 TTTT--TTTTTCT
1 TTTTGCTTTTTCT
1593 TTTT
1 TTTT
1597 TCCTAGTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 7 0.25
12 4 0.14
14 16 0.57
15 1 0.04
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (13 bp):
TTTTGCTTTTTCT
Found at i:2009 original size:56 final size:57
Alignment explanation
Indices: 1923--2034 Score: 190
Period size: 56 Copynumber: 2.0 Consensus size: 57
1913 AAGGCTAAAT
* *
1923 TGACTCGTGTGGAAACAAGTTTGGCTTGTGGAAAAGCCCCTG-CTGCTTGGATGAAC
1 TGACTCGTATGGAAACAAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGAAC
*
1979 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGAA
1 TGACTCGTATGGAAACAAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGAA
2035 ACCAAAGCTT
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
56 40 0.77
57 12 0.23
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (57 bp):
TGACTCGTATGGAAACAAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGAAC
Found at i:2202 original size:69 final size:70
Alignment explanation
Indices: 1974--2501 Score: 794
Period size: 70 Copynumber: 7.6 Consensus size: 70
1964 GCTGCTTGGA
*
1974 TGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGAAACCA
1 TGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCA
2039 AAGCT
66 AAGCT
*
2044 TGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGAATGCTTGGATGGAACCA
1 TGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCA
2109 AAGCT
66 AAGCT
* * ** * *
2114 TGAATTGACTCGTACGGAAACGAGTTTGGCTTGTGGAAAAGCTGCT-ACTGTTTGGATGGAAGCC
1 TGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAA-CC
2178 -AAGCT
65 AAAGCT
*
2183 TGAACTGACTCGTCTGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCA
1 TGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCA
2248 AAGCT
66 AAGCT
* * * * *
2253 TGAACTGACTCGTACGGAAACGAGTTTGGCTTGTGGAAAAGTCGCTG-CTGTTTGGATGGAACCA
1 TGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCA
2317 AAGCT
66 AAGCT
* *
2322 TGAAATGGCTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCA
1 TGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCA
*
2387 AGGCT
66 AAGCT
* * * *
2392 TGAACTGACTCGTATAGAGACGAGTTTGGCTTGTGGAAAAGCCACT-ACTGCTTGGATGGAACCA
1 TGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCA
*
2456 AGGCT
66 AAGCT
* * *
2461 TGAACTGACTCGTAAGGAAACGAGTTTGACTTATGGAAAAG
1 TGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG
2502 TCGAAGCATT
Statistics
Matches: 413, Mismatches: 41, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
69 181 0.44
70 232 0.56
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.25
Consensus pattern (70 bp):
TGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCA
AAGCT
Found at i:2232 original size:139 final size:139
Alignment explanation
Indices: 1974--2501 Score: 824
Period size: 139 Copynumber: 3.8 Consensus size: 139
1964 GCTGCTTGGA
* * * *
1974 TGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGAAACCA
1 TGAACTGACTCGTACGGAAACGAGTTTGGCTTGTGGAAAAGCCGCT-ACTGCTTGGATGGAACCA
*
2039 AAGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGAATGCTTGGATGG
65 AAGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGG
2104 AACCAAAGCT
130 AACCAAAGCT
* * *
2114 TGAATTGACTCGTACGGAAACGAGTTTGGCTTGTGGAAAAGCTGCTACTGTTTGGATGGAAGCC-
1 TGAACTGACTCGTACGGAAACGAGTTTGGCTTGTGGAAAAGCCGCTACTGCTTGGATGGAA-CCA
*
2178 AAGCTTGAACTGACTCGTCTGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGG
65 AAGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGG
2243 AACCAAAGCT
130 AACCAAAGCT
* * *
2253 TGAACTGACTCGTACGGAAACGAGTTTGGCTTGTGGAAAAGTCGCTGCTGTTTGGATGGAACCAA
1 TGAACTGACTCGTACGGAAACGAGTTTGGCTTGTGGAAAAGCCGCTACTGCTTGGATGGAACCAA
* *
2318 AGCTTGAAATGGCTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGA
66 AGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGA
*
2383 ACCAAGGCT
131 ACCAAAGCT
** * *
2392 TGAACTGACTCGTATAGAGACGAGTTTGGCTTGTGGAAAAGCCACTACTGCTTGGATGGAACCAA
1 TGAACTGACTCGTACGGAAACGAGTTTGGCTTGTGGAAAAGCCGCTACTGCTTGGATGGAACCAA
* * * *
2457 GGCTTGAACTGACTCGTAAGGAAACGAGTTTGACTTATGGAAAAG
66 AGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG
2502 TCGAAGCATT
Statistics
Matches: 356, Mismatches: 30, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
138 2 0.01
139 310 0.87
140 44 0.12
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.25
Consensus pattern (139 bp):
TGAACTGACTCGTACGGAAACGAGTTTGGCTTGTGGAAAAGCCGCTACTGCTTGGATGGAACCAA
AGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGA
ACCAAAGCT
Found at i:2673 original size:30 final size:30
Alignment explanation
Indices: 2645--2703 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
2635 GTTCTGAATC
2645 TTTGCT-TTCTTGACTTTGCTTCCTTGAATCCT
1 TTTGCTCTTCTTGA-TTTG--TCCTTGAATCCT
*
2677 TTTGTTCTTCTTGATTTGTCCTTGAAT
1 TTTGCTCTTCTTGATTTGTCCTTGAAT
2704 TTGCTTCCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 9 0.36
32 9 0.36
33 7 0.28
ACGTcount: A:0.10, C:0.20, G:0.14, T:0.56
Consensus pattern (30 bp):
TTTGCTCTTCTTGATTTGTCCTTGAATCCT
Found at i:3049 original size:50 final size:50
Alignment explanation
Indices: 2985--3083 Score: 153
Period size: 50 Copynumber: 2.0 Consensus size: 50
2975 AAAATGCCCT
*
2985 TTGAAAAGCAAATTTTGATCTTGGACTCACAAATGGAACGCAATCTTATC
1 TTGAAAAGCAAATTTTGATATTGGACTCACAAATGGAACGCAATCTTATC
* * * *
3035 TTGAAAATCGAATTTTGATATTGGACTTACAAATGGAATGCAATCTTAT
1 TTGAAAAGCAAATTTTGATATTGGACTCACAAATGGAACGCAATCTTAT
3084 TATAAAACTT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.33
Consensus pattern (50 bp):
TTGAAAAGCAAATTTTGATATTGGACTCACAAATGGAACGCAATCTTATC
Found at i:3372 original size:14 final size:14
Alignment explanation
Indices: 3352--3413 Score: 74
Period size: 14 Copynumber: 4.5 Consensus size: 14
3342 ACCCTAGAGC
*
3352 TTCTTTTCTTCATT
1 TTCTTTTCTTCTTT
* *
3366 CTCTTTTTTTCTTT
1 TTCTTTTCTTCTTT
3380 TTCTTTTTCTT-TTT
1 TTC-TTTTCTTCTTT
3394 TTCTTTTCTTCTTT
1 TTCTTTTCTTCTTT
3408 TT-TTTT
1 TTCTTTT
3414 ACATGTACTT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
13 11 0.27
14 24 0.59
15 6 0.15
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.81
Consensus pattern (14 bp):
TTCTTTTCTTCTTT
Found at i:3378 original size:8 final size:8
Alignment explanation
Indices: 3367--3411 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
3357 TTCTTCATTC
3367 TCTTTTTT
1 TCTTTTTT
3375 TC--TTTT
1 TCTTTTTT
3381 TC--TTTT
1 TCTTTTTT
3387 TCTTTTTT
1 TCTTTTTT
*
3395 TCTTTTCT
1 TCTTTTTT
3403 TCTTTTTT
1 TCTTTTTT
3411 T
1 T
3412 TTACATGTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 12 0.36
8 21 0.64
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (8 bp):
TCTTTTTT
Found at i:3382 original size:6 final size:6
Alignment explanation
Indices: 3371--3412 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
3361 TCATTCTCTT
*
3371 TTTTTC TTTTTC TTTTTC TTTTTT TCTTTTC TTCTTT- TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC T-TTTTC TT-TTTC TTTTT
3413 TACATGTACT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
5 3 0.09
6 21 0.66
7 8 0.25
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:3392 original size:20 final size:20
Alignment explanation
Indices: 3352--3413 Score: 83
Period size: 19 Copynumber: 3.0 Consensus size: 20
3342 ACCCTAGAGC
3352 TTCTTTTCTTCATTCTCTTTTT
1 TTCTTTTCTTC-TT-TCTTTTT
3374 TTCTTTTTCTT-TTTCTTTTT
1 TTC-TTTTCTTCTTTCTTTTT
3394 TTCTTTTCTTCTTT-TTTTT
1 TTCTTTTCTTCTTTCTTTTT
3413 T
1 T
3414 ACATGTACTT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
19 13 0.34
20 13 0.34
21 2 0.05
22 3 0.08
23 7 0.18
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.81
Consensus pattern (20 bp):
TTCTTTTCTTCTTTCTTTTT
Found at i:4229 original size:30 final size:31
Alignment explanation
Indices: 4190--4249 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
4180 CCGTTTTATC
* *
4190 AAAACCTTTTGAAAATCATGACTCTTTTTGA
1 AAAACTTTTTAAAAATCATGACTCTTTTTGA
4221 AAAACTTTTTAAAAATCATGACTCTTTTT
1 AAAACTTTTTAAAAATCATGACTCTTTTT
4250 CTTTTTCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.42
Consensus pattern (31 bp):
AAAACTTTTTAAAAATCATGACTCTTTTTGA
Found at i:4254 original size:6 final size:6
Alignment explanation
Indices: 4243--4291 Score: 55
Period size: 6 Copynumber: 8.0 Consensus size: 6
4233 AAATCATGAC
* *
4243 TCTTTT TCTTTT TCTTTC TCTTTT T-TTTT CCTTTCT TCTTCTT TCTTTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTT-T TCTT-TT TCTTTT
4292 ATTATCCTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
5 4 0.11
6 22 0.61
7 9 0.25
8 1 0.03
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (6 bp):
TCTTTT
Found at i:4271 original size:17 final size:18
Alignment explanation
Indices: 4242--4291 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
4232 AAAATCATGA
*
4242 CTCTTTTTCTTTTTCTTT
1 CTCTTTTTCTTTTCCTTT
4260 CTCTTTTT-TTTTCCTTT
1 CTCTTTTTCTTTTCCTTT
4277 CTTCTTCTTTCTTTT
1 C-TCTT-TTTCTTTT
4292 ATTATCCTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 9 0.32
18 12 0.43
19 3 0.11
20 4 0.14
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (18 bp):
CTCTTTTTCTTTTCCTTT
Found at i:4315 original size:26 final size:25
Alignment explanation
Indices: 4261--4316 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
4251 TTTTTCTTTC
* * *
4261 TCTTTTTTTTTCCTTTCTTCTTCTT
1 TCTTTTATTATCCTTTCCTCTTCTT
4286 TCTTTTATTATCCTTCTCCTCTTCTT
1 TCTTTTATTATCCTT-TCCTCTTCTT
4312 TCTTT
1 TCTTT
4317 CTTTTTTTGC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 13 0.48
26 14 0.52
ACGTcount: A:0.04, C:0.27, G:0.00, T:0.70
Consensus pattern (25 bp):
TCTTTTATTATCCTTTCCTCTTCTT
Done.