Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013935.1 Corchorus capsularis cultivar CVL-1 contig13956, 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: 16075
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:265 original size:19 final size:18
Alignment explanation
Indices: 241--276 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
231 TGAAGATTTC
241 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
260 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
277 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:6300 original size:14 final size:14
Alignment explanation
Indices: 6277--6306 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
6267 TGCTTGTTTC
6277 TTCTCCTTTCTTCT
1 TTCTCCTTTCTTCT
*
6291 TTCTCTTTTCTTCT
1 TTCTCCTTTCTTCT
6305 TT
1 TT
6307 TTTCTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (14 bp):
TTCTCCTTTCTTCT
Found at i:6304 original size:17 final size:17
Alignment explanation
Indices: 6284--6318 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
6274 TTCTTCTCCT
6284 TTCTTCTTTCTCTTTTC
1 TTCTTCTTTCTCTTTTC
* *
6301 TTCTTTTTTCTTTTTTC
1 TTCTTCTTTCTCTTTTC
6318 T
1 T
6319 CTTTTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (17 bp):
TTCTTCTTTCTCTTTTC
Found at i:6310 original size:24 final size:24
Alignment explanation
Indices: 6273--6335 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
6263 TGTTTGCTTG
**
6273 TTTCTTCTCCTTTCTTCTTTCTCT
1 TTTCTTCTTTTTTCTTCTTTCTCT
*
6297 TTTCTTCTTTTTTCTTTTTTCTCT
1 TTTCTTCTTTTTTCTTCTTTCTCT
6321 TTT-TT-TTTATTTCTT
1 TTTCTTCTTT-TTTCTT
6336 TTTTTTCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
22 3 0.09
23 8 0.23
24 24 0.69
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (24 bp):
TTTCTTCTTTTTTCTTCTTTCTCT
Found at i:6318 original size:14 final size:14
Alignment explanation
Indices: 6283--6339 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 14
6273 TTTCTTCTCC
6283 TTTCTTCTTTCTCTTT
1 TTTCTT-TTT-TCTTT
6299 TCTTCTTTTTTCTTT
1 T-TTCTTTTTTCTTT
*
6314 TTTCTCTTTTTTTTT
1 TTTCT-TTTTTCTTT
6329 ATTTCTTTTTT
1 -TTTCTTTTTT
6340 TTCATTTTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 19 0.51
16 9 0.24
17 5 0.14
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTCTTTTTTCTTT
Found at i:6338 original size:24 final size:25
Alignment explanation
Indices: 6290--6366 Score: 81
Period size: 24 Copynumber: 3.1 Consensus size: 25
6280 TCCTTTCTTC
6290 TTTCTCTTTTCTTCTTT-TTTC-TTT
1 TTTCTCTTTTCTT-TTTATTTCTTTT
6314 TTTCTCTTTT-TTTTTATTTCTTTT
1 TTTCTCTTTTCTTTTTATTTCTTTT
* *
6338 TTT-TCATTTTCATTTCATTTCTCTTT
1 TTTCTC-TTTTCTTTTTATTTCT-TTT
6364 TTT
1 TTT
6367 TTTTAGACCT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
22 3 0.07
23 8 0.17
24 20 0.43
25 9 0.20
26 6 0.13
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (25 bp):
TTTCTCTTTTCTTTTTATTTCTTTT
Found at i:6340 original size:14 final size:14
Alignment explanation
Indices: 6301--6346 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
6291 TTCTCTTTTC
*
6301 TTCTTTTTTCTTTTT
1 TTCTTTTTT-TTTAT
6316 TCTCTTTTTTTTTAT
1 T-TCTTTTTTTTTAT
*
6331 TTCTTTTTTTTCAT
1 TTCTTTTTTTTTAT
6345 TT
1 TT
6347 TCATTTCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 14 0.50
15 6 0.21
16 8 0.29
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (14 bp):
TTCTTTTTTTTTAT
Found at i:6357 original size:25 final size:23
Alignment explanation
Indices: 6307--6371 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
6297 TTTCTTCTTT
* * *
6307 TTTCTTTTTTCTCTTTTTTTTTA
1 TTTCTTTTTTTTCTTTTATTTCA
6330 TTTCTTTTTTTTCATTTTCATTTCA
1 TTTCTTTTTTTTC-TTTT-ATTTCA
*
6355 TTTCTCTTTTTT-TTTTA
1 TTTCTTTTTTTTCTTTTA
6372 GACCTACTCG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 1 0.03
23 16 0.44
24 4 0.11
25 15 0.42
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTCTTTTTTTTCTTTTATTTCA
Found at i:6471 original size:47 final size:47
Alignment explanation
Indices: 6422--6703 Score: 368
Period size: 47 Copynumber: 6.0 Consensus size: 47
6412 AACCCGTTGA
* ** * *
6422 CCAACTTTGGTCACTAAATTGAAAATTCGCATGGAAGCGAGAGAA-G
1 CCAACTTTGGCCACTAAATTGCTAACTCGCGTGGAAGCGAGAGAATG
* * * * * * *
6468 ACCAGCTTTGGTCTCTAAATTGCCAACTCGCATGGAAGCGAGAAAAGG
1 -CCAACTTTGGCCACTAAATTGCTAACTCGCGTGGAAGCGAGAGAATG
** *
6516 CCAACTTTGGCCACTAAATTGGAAATTCGCGTGGAAGCGAGAGAATG
1 CCAACTTTGGCCACTAAATTGCTAACTCGCGTGGAAGCGAGAGAATG
*
6563 CCAACTTTGGCCACTAGATTGCTAACTCGCGTGGAAGCGAGAGAATG
1 CCAACTTTGGCCACTAAATTGCTAACTCGCGTGGAAGCGAGAGAATG
* *
6610 CCAACTTTGGCCACTGAATTGCTAACTCGCGTGGAAGCGAAAGAATG
1 CCAACTTTGGCCACTAAATTGCTAACTCGCGTGGAAGCGAGAGAATG
* *
6657 CCAACTTTGGCCACTGAATTGCTAGCTCGCGTGGAAGCGAGAGAATG
1 CCAACTTTGGCCACTAAATTGCTAACTCGCGTGGAAGCGAGAGAATG
6704 ATTGCCTGGA
Statistics
Matches: 210, Mismatches: 24, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
47 209 1.00
48 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (47 bp):
CCAACTTTGGCCACTAAATTGCTAACTCGCGTGGAAGCGAGAGAATG
Found at i:6930 original size:69 final size:69
Alignment explanation
Indices: 6838--7378 Score: 573
Period size: 69 Copynumber: 7.9 Consensus size: 69
6828 AGCCCCTGAT
* * ** * ** *
6838 TGCTTGGATGGAACCAAATCTTAAACTCTCTCGCGTGGAAGCGAGTTTAACTTATGGAAAAGCCT
1 TGCTTGGATGGAACCAAAGCTTAAACTCACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCT
*
6903 ATGC
66 CTGC
* ** *
6907 TGCTTGGATGGAACCAAATCTTAAACT-ATCTCGCGTGGAAGCGAGTTTGGCTTGTGGAAAAGCC
1 TGCTTGGATGGAACCAAAGCTTAAACTCA-CTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
6971 TCTGC
65 TCTGC
* * * * *
6976 TGCTTGGATGGAACCAAGGC-TAAACTGACTCGTATGGAAACGAATTTGGCTTGTTGAAAAGCCC
1 TGCTTGGATGGAACCAAAGCTTAAACTCACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCT
**
7040 CTAAA
66 CT-GC
* * * *
7045 TGTTTGGATGGAACCAAAACTTGAATTGC-CTCGTATGGAAACGAGTTTGGCTTGTGG-AAAGCC
1 TGCTTGGATGGAACCAAAGCTTAAACT-CACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
*
7108 CCTGC
65 TCTGC
* * *
7113 TGCTTGGATGGAACCAAGGC-TAAACTGACTCGTGTGGAAACGAGTTTGGCTTGTGGAAAAGCC-
1 TGCTTGGATGGAACCAAAGCTTAAACTCACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCT
*
7176 CTTGAA
66 C-TG-C
* *
7182 TGCTTGGATGGAACCAAAGCTTGAACT-ATCTCGTATGGAAACGAGTTTGTCTTGTGGAAAAGCC
1 TGCTTGGATGGAACCAAAGCTTAAACTCA-CTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
**
7246 TCTTT
65 TCTGC
*
7251 TGCTTGGATGGAACCAAGGC-TAAACT-ACCTCGTATGGAAACGAGTTTGGCTTGTGGAAAA-CC
1 TGCTTGGATGGAACCAAAGCTTAAACTCA-CTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
*
7313 CCTGC
65 TCTGC
* * ** * *
7318 TGCTTGGATGGAACC-AAGGTTAAACTGACTCGTGCGGAAACGAGTTTGACTTATGGAAAAG
1 TGCTTGGATGGAACCAAAGCTTAAACTCACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG
7379 TCAAAGCATT
Statistics
Matches: 405, Mismatches: 52, Indels: 31
0.83 0.11 0.06
Matches are distributed among these distances:
66 2 0.00
67 85 0.21
68 101 0.25
69 147 0.36
70 69 0.17
71 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27
Consensus pattern (69 bp):
TGCTTGGATGGAACCAAAGCTTAAACTCACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCT
CTGC
Found at i:7014 original size:137 final size:138
Alignment explanation
Indices: 6838--7378 Score: 641
Period size: 137 Copynumber: 3.9 Consensus size: 138
6828 AGCCCCTGAT
** ** ** * ** *
6838 TGCTTGGATGGAACCAAATCTTAAACTCTCTCGCGTGGAAGCGAGTTTAACTTATGGAAAAG-CC
1 TGCTTGGATGGAACCAAGGC-TAAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCC
* * ** *
6902 TATGCTGCTTGGATGGAACCAAATCTTAAACTATCTCGCGTGGAAGCGAGTTTGGCTTGTGGAAA
65 TATGATGCTTGGATGGAACCAAAGCTTAAACTATCTCGTATGGAAACGAGTTTGGCTTGTGGAAA
6967 AGCCTCTGC
130 AGCCTCTGC
* *
6976 TGCTTGGATGGAACCAAGGCTAAACTGACTCGTATGGAAACGAATTTGGCTTGTTGAAAAGCCCC
1 TGCTTGGATGGAACCAAGGCTAAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG-CCC
* * * * * **
7041 TA-AATGTTTGGATGGAACCAAAACTTGAATTGCCTCGTATGGAAACGAGTTTGGCTTGTGG-AA
65 TATGATGCTTGGATGGAACCAAAGCTTAAACTATCTCGTATGGAAACGAGTTTGGCTTGTGGAAA
*
7104 AGCCCCTGC
130 AGCCTCTGC
*
7113 TGCTTGGATGGAACCAAGGCTAAACTGACTCGTGTGGAAACGAGTTTGGCTTGTGGAAAAGCCCT
1 TGCTTGGATGGAACCAAGGCTAAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCT
* *
7178 -TGAATGCTTGGATGGAACCAAAGCTTGAACTATCTCGTATGGAAACGAGTTTGTCTTGTGGAAA
66 ATG-ATGCTTGGATGGAACCAAAGCTTAAACTATCTCGTATGGAAACGAGTTTGGCTTGTGGAAA
**
7242 AGCCTCTTT
130 AGCCTCTGC
7251 TGCTTGGATGGAACCAAGGCTAAACT-ACCTCGTATGGAAACGAGTTTGGCTTGTGGAAAA-CCC
1 TGCTTGGATGGAACCAAGGCTAAACTGA-CTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCC
* * * ** * *
7314 -CTGCTGCTTGGATGGAACC-AAGGTTAAACTGA-CTCGTGCGGAAACGAGTTTGACTTATGGAA
65 TATGATGCTTGGATGGAACCAAAGCTTAAACT-ATCTCGTATGGAAACGAGTTTGGCTTGTGGAA
7376 AAG
129 AAG
7379 TCAAAGCATT
Statistics
Matches: 350, Mismatches: 45, Indels: 19
0.85 0.11 0.05
Matches are distributed among these distances:
135 38 0.11
136 20 0.06
137 157 0.45
138 131 0.37
139 4 0.01
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27
Consensus pattern (138 bp):
TGCTTGGATGGAACCAAGGCTAAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCT
ATGATGCTTGGATGGAACCAAAGCTTAAACTATCTCGTATGGAAACGAGTTTGGCTTGTGGAAAA
GCCTCTGC
Found at i:7394 original size:67 final size:66
Alignment explanation
Indices: 6907--7399 Score: 420
Period size: 67 Copynumber: 7.2 Consensus size: 66
6897 AAGCCTATGC
** * ** *
6907 TGCTTGGATGGAACCAAATCTTAAACTATCTCGCGTGGAAGCGAGTTTGGCTTGTGGAAAAGCCT
1 TGCTTGGATGGAACCAAGGC-TAAACTACCTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG-CT
**
6972 CTGC
64 C-AA
* *
6976 TGCTTGGATGGAACCAAGGCTAAACTGA-CTCGTATGGAAACGAATTTGGCTTGTTGAAAAGCCC
1 TGCTTGGATGGAACCAAGGCTAAACT-ACCTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG---
*
7040 CTAAA
62 CTCAA
* ** * * * *
7045 TGTTTGGATGGAACCAAAACTTGAATTGCCTCGTATGGAAACGAGTTTGGCTTGTGG-AAAGCCC
1 TGCTTGGATGGAACCAAGGC-TAAACTACCTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG-CT
**
7109 CTGC
64 C-AA
*
7113 TGCTTGGATGGAACCAAGGCTAAACTGA-CTCGTGTGGAAACGAGTTTGGCTTGTGGAAAAGCCC
1 TGCTTGGATGGAACCAAGGCTAAACT-ACCTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG--C
*
7177 TTGAA
63 -TCAA
* * * *
7182 TGCTTGGATGGAACCAAAGCTTGAACTATCTCGTATGGAAACGAGTTTGTCTTGTGGAAAAGCCT
1 TGCTTGGATGGAACCAAGGC-TAAACTACCTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG-CT
**
7247 CTTT
64 C-AA
* *
7251 TGCTTGGATGGAACCAAGGCTAAACTACCTCGTATGGAAACGAGTTTGGCTTGTGGAAAACCCCT
1 TGCTTGGATGGAACCAAGGCTAAACTACCTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCTC-
**
7316 GC
65 AA
* ** * *
7318 TGCTTGGATGGAACCAAGGTTAAACTGA-CTCGTGCGGAAACGAGTTTGACTTATGGAAAAG-TC
1 TGCTTGGATGGAACCAAGGCTAAACT-ACCTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCTC
7381 AA
65 AA
*
7383 AGCATTCGGATGGAACC
1 TGC-TT-GGATGGAACC
7400 GAAGCAAAGT
Statistics
Matches: 350, Mismatches: 58, Indels: 34
0.79 0.13 0.08
Matches are distributed among these distances:
65 2 0.01
66 3 0.01
67 99 0.28
68 94 0.27
69 83 0.24
70 69 0.20
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (66 bp):
TGCTTGGATGGAACCAAGGCTAAACTACCTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCTCA
A
Found at i:8650 original size:24 final size:24
Alignment explanation
Indices: 8604--8650 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
8594 TCACCTTTCC
*
8604 TTTCACTTTCATTTTCAATTTTTA
1 TTTCACTTTCATTTTCAACTTTTA
8628 TTTCACTTTCAATTTTC-ACTTTT
1 TTTCACTTTC-ATTTTCAACTTTT
8651 TCTTCTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTCACTTTCATTTTCAACTTTTA
Found at i:10571 original size:19 final size:18
Alignment explanation
Indices: 10538--10573 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
10528 TTGAAATAAT
10538 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
10556 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
10574 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Done.