Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007366.1 Corchorus capsularis cultivar CVL-1 contig07387, 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: 13876
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Found at i:781 original size:60 final size:60
Alignment explanation
Indices: 688--815 Score: 184
Period size: 60 Copynumber: 2.1 Consensus size: 60
678 TTGGGCTAAT
* ** * * * *
688 TGCTCAAATAAGGTCTTGATCTTTTAATTTGGCCAAATAAGGGTATAACGTTTGTCAAAA
1 TGCTCAAACAAGAACTTGATCTTCTAATTTGGCCAAATAAGGGCATAACATTTGCCAAAA
*
748 TGCTCAAACAAGAACTTGATCTTCTAATTTGGCCAAATAAGGGCCTAACATTTGCCAAAA
1 TGCTCAAACAAGAACTTGATCTTCTAATTTGGCCAAATAAGGGCATAACATTTGCCAAAA
808 TGCTCAAA
1 TGCTCAAA
816 TAAGGGCCCG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.30
Consensus pattern (60 bp):
TGCTCAAACAAGAACTTGATCTTCTAATTTGGCCAAATAAGGGCATAACATTTGCCAAAA
Found at i:1015 original size:60 final size:60
Alignment explanation
Indices: 867--1026 Score: 198
Period size: 60 Copynumber: 2.7 Consensus size: 60
857 GACACCGGAT
* * ** * * *
867 CCTTATCTGAGCATTTTCAATAACGTTAAACCCTTATTTGGTCAAATTAAAAGATCGGGT
1 CCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGGC
* *
927 CCTTATTTGAGCATTTTCGATAATGTTAGGCCCTCATTTGGCCAAATTAAAAGATCAGGC
1 CCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGGC
*
987 CCTTATTTGATCATTTT-G-TCAAACGTTAGGCCCTTATTTG
1 CCTTATTTGAGCATTTTCGAT--AACGTTAGGCCCTTATTTG
1027 AACAATTAAC
Statistics
Matches: 86, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
58 1 0.01
59 1 0.01
60 84 0.98
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (60 bp):
CCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGGC
Found at i:1217 original size:17 final size:17
Alignment explanation
Indices: 1177--1249 Score: 69
Period size: 17 Copynumber: 4.4 Consensus size: 17
1167 TCGAGCTATT
* *
1177 TTCGGATTCGGGTTTAA
1 TTCGGGTTCGGGTTGAA
*
1194 GTCGGGTTCGGGTTGAA
1 TTCGGGTTCGGGTTGAA
* * *
1211 TTTGGG-TCAGG-TCAA
1 TTCGGGTTCGGGTTGAA
1226 TTCGGGTTCGGGTTGAA
1 TTCGGGTTCGGGTTGAA
*
1243 TTTGGGT
1 TTCGGGT
1250 CAGGTCAATT
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
15 8 0.19
16 8 0.19
17 27 0.63
ACGTcount: A:0.14, C:0.11, G:0.38, T:0.37
Consensus pattern (17 bp):
TTCGGGTTCGGGTTGAA
Found at i:1268 original size:32 final size:32
Alignment explanation
Indices: 1200--1268 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
1190 TTAAGTCGGG
**
1200 TTCGGGTTGAATTTGGGTCAGGTCAATTCGGG
1 TTCGGGTTGAATTTGGGTCAGGTCAATTCGAA
1232 TTCGGGTTGAATTTGGGTCAGGTCAATTCGAA
1 TTCGGGTTGAATTTGGGTCAGGTCAATTCGAA
1264 TTCGG
1 TTCGG
1269 ATTCAGTTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.17, C:0.13, G:0.35, T:0.35
Consensus pattern (32 bp):
TTCGGGTTGAATTTGGGTCAGGTCAATTCGAA
Found at i:1268 original size:38 final size:32
Alignment explanation
Indices: 1195--1261 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
1185 CGGGTTTAAG
1195 TCGGGTTCGGGTTGAATTTGGGTCAGGTCAAT
1 TCGGGTTCGGGTTGAATTTGGGTCAGGTCAAT
1227 TCGGGTTCGGGTTGAATTTGGGTCAGGTCAAT
1 TCGGGTTCGGGTTGAATTTGGGTCAGGTCAAT
1259 TCG
1 TCG
1262 AATTCGGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.15, C:0.13, G:0.37, T:0.34
Consensus pattern (32 bp):
TCGGGTTCGGGTTGAATTTGGGTCAGGTCAAT
Found at i:1503 original size:16 final size:16
Alignment explanation
Indices: 1426--1503 Score: 93
Period size: 16 Copynumber: 4.9 Consensus size: 16
1416 AACTTTCGGA
1426 TTCGGGTTCGGGTTTT
1 TTCGGGTTCGGGTTTT
* * *
1442 TTCAGGTTCTGATTTT
1 TTCGGGTTCGGGTTTT
* * *
1458 TTCGGGTTTGAGCTTT
1 TTCGGGTTCGGGTTTT
1474 TTCGGGTTCGGGTTTT
1 TTCGGGTTCGGGTTTT
*
1490 TTCGGGTTCAGGTT
1 TTCGGGTTCGGGTT
1504 CAGGCGGGTT
Statistics
Matches: 49, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.05, C:0.13, G:0.32, T:0.50
Consensus pattern (16 bp):
TTCGGGTTCGGGTTTT
Found at i:11662 original size:174 final size:176
Alignment explanation
Indices: 11364--11691 Score: 450
Period size: 174 Copynumber: 1.9 Consensus size: 176
11354 CTGGTTATCA
* * * *
11364 GATTAAGGTGATTTAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGGATGACTC
1 GATTAAGATGATTCAAGTGTCTATCAAAAGATTATTCCATGATCTACAACTTTCA-GGA-GACTC
* *
11429 GAAAACTAAATTTAATGTTTCAAGTATCAAAAATGCTTCCGAAAAATTTGTTGTTTCGGTTAACG
64 GAAAACTAAATTTAATGTTTCAAGTATCAAAAATGCTTCCGAAAAATTAGTTATTTCGGTTAACG
* **
11494 GGAATAGACGGTCCACTTAATATTTTATAACTTTTGCCCCATATGCCT
129 GAAATAGACAATCCACTTAATATTTTATAACTTTTGCCCCATATGCCT
* * *
11542 GATTAAGATGATTCAAGTGTCTCTCGAAAGGTTATTCCATGATCTACAACTTTCA-G-GACTCGA
1 GATTAAGATGATTCAAGTGTCTATCAAAAGATTATTCCATGATCTACAACTTTCAGGAGACTCGA
11605 AAACTAAATTTAATG-TTCAAGGTAT-ACAAAATGCTTCC-AAAGAATTAGTTATTTCGGTTAAC
66 AAACTAAATTTAATGTTTCAA-GTATCA-AAAATGCTTCCGAAA-AATTAGTTATTTCGGTTAAC
* *
11667 GGAAATGGACAATCTACTTAATATT
128 GGAAATAGACAATCCACTTAATATT
11692 AAATAATTTG
Statistics
Matches: 133, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
173 9 0.07
174 75 0.56
176 1 0.01
178 48 0.36
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (176 bp):
GATTAAGATGATTCAAGTGTCTATCAAAAGATTATTCCATGATCTACAACTTTCAGGAGACTCGA
AAACTAAATTTAATGTTTCAAGTATCAAAAATGCTTCCGAAAAATTAGTTATTTCGGTTAACGGA
AATAGACAATCCACTTAATATTTTATAACTTTTGCCCCATATGCCT
Found at i:12168 original size:2 final size:2
Alignment explanation
Indices: 12161--12201 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
12151 TAATACAATA
* *
12161 AT AT AT AT AT AT AT GT AT GT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12202 CTAGTTTTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12289 original size:22 final size:22
Alignment explanation
Indices: 12260--12446 Score: 106
Period size: 22 Copynumber: 8.5 Consensus size: 22
12250 TGAATATTTT
12260 TATGAAATTTTGATAACTATCC
1 TATGAAATTTTGATAACTATCC
* * * *
12282 TATTAAATTCTGATAACCA-CTT
1 TATGAAATTTTGATAACTATC-C
*
12304 TATGAAATTTTGATAA-TTTACC
1 TATGAAATTTTGATAACTAT-CC
*
12326 TATGAAATTGTGATAA--ACTCC
1 TATGAAATTTTGATAACTA-TCC
* *
12347 ATATGAAACTTTGATAACCTA-AC
1 -TATGAAATTTTGATAA-CTATCC
*
12370 TATGAAATTTTAATAAACCT-TCC
1 TATGAAATTTTGAT-AA-CTATCC
*
12393 TAAGAAATTTTG-TAACCT-TCC
1 TATGAAATTTTGATAA-CTATCC
* *
12414 TATG-ATTTTTGATAAC-CTCTC
1 TATGAAATTTTGATAACTATC-C
*
12435 TATGAGATTTTG
1 TATGAAATTTTG
12447 TTAATCTCCC
Statistics
Matches: 128, Mismatches: 23, Indels: 28
0.72 0.13 0.16
Matches are distributed among these distances:
20 9 0.07
21 22 0.17
22 78 0.61
23 18 0.14
25 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACTATCC
Found at i:12328 original size:44 final size:44
Alignment explanation
Indices: 12258--12446 Score: 129
Period size: 44 Copynumber: 4.3 Consensus size: 44
12248 ATTGAATATT
*
12258 TTTATGAAATTTTGATAACTATCCTATTAAATTCTGATAACCAC
1 TTTATGAAATTTTGATAACTATCCTATGAAATTCTGATAACCAC
* * * *
12302 TTTATGAAATTTTGATAA-TTTACCTATGAAATTGTGATAAACTC
1 TTTATGAAATTTTGATAACTAT-CCTATGAAATTCTGATAACCAC
** * * * * *
12346 CATATGAAACTTTGATAACCTA-ACTATGAAATTTTAATAAAC-C
1 TTTATGAAATTTTGATAA-CTATCCTATGAAATTCTGATAACCAC
* * * *
12389 TTCCTAAGAAATTTTG-TAACCT-TCCTATG-ATTTTTGATAACCTC
1 TT--TATGAAATTTTGATAA-CTATCCTATGAAATTCTGATAACCAC
* *
12433 TCTATGAGATTTTG
1 TTTATGAAATTTTG
12447 TTAATCTCCC
Statistics
Matches: 115, Mismatches: 23, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
42 10 0.09
43 13 0.11
44 81 0.70
45 10 0.09
46 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.41
Consensus pattern (44 bp):
TTTATGAAATTTTGATAACTATCCTATGAAATTCTGATAACCAC
Found at i:12399 original size:23 final size:21
Alignment explanation
Indices: 12373--12415 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12363 ACCTAACTAT
12373 GAAATTTTAATAAACCTTCCTAA
1 GAAATTTT-AT-AACCTTCCTAA
*
12396 GAAATTTTGTAACCTTCCTA
1 GAAATTTTATAACCTTCCTA
12416 TGATTTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 1 0.05
23 8 0.42
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (21 bp):
GAAATTTTATAACCTTCCTAA
Found at i:12459 original size:22 final size:21
Alignment explanation
Indices: 12398--12469 Score: 69
Period size: 22 Copynumber: 3.5 Consensus size: 21
12388 CTTCCTAAGA
*
12398 AATTTTG-TAACCTTCCTATG
1 AATTTTGTTAACCTCCCTATG
* * *
12418 ATTTTTGATAACCTCTCTATG
1 AATTTTGTTAACCTCCCTATG
*
12439 AGATTTTGTTAATCTCCCTAT-
1 A-ATTTTGTTAACCTCCCTATG
12460 AATTTT-TTAA
1 AATTTTGTTAA
12470 TACTATAGTA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
19 4 0.09
20 11 0.26
21 13 0.30
22 15 0.35
ACGTcount: A:0.26, C:0.17, G:0.08, T:0.49
Consensus pattern (21 bp):
AATTTTGTTAACCTCCCTATG
Found at i:13578 original size:2 final size:2
Alignment explanation
Indices: 13573--13605 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
13563 CACACACTAC
13573 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13606 ACTACTCCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.