Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008135.1 Corchorus capsularis cultivar CVL-1 contig08156, 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: 18268
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:1075 original size:22 final size:22
Alignment explanation
Indices: 1050--1098 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
1040 TTCATTTCCT
1050 ATAATTATTGCTTTTTT-TAATA
1 ATAATTATTG-TTTTTTATAATA
*
1072 ATAATTATTGTTTTTTATAATT
1 ATAATTATTGTTTTTTATAATA
1094 ATAAT
1 ATAAT
1099 ATATCAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (22 bp):
ATAATTATTGTTTTTTATAATA
Found at i:1923 original size:22 final size:21
Alignment explanation
Indices: 1898--2308 Score: 133
Period size: 22 Copynumber: 19.0 Consensus size: 21
1888 ATGACGTCCT
1898 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACC-TCC
* * *
1920 TATGAAA-TTTCATTAACGATAC
1 TATGAAATTTTGA-TAAC-CTCC
* * *
1942 TATGGAATTTCGAGAACCT--
1 TATGAAATTTTGATAACCTCC
* * ** *
1961 TTTTATAATTTTTTTAACCTTCT
1 TATGA-AATTTTGATAACC-TCC
*
1984 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCT-CC
* * *
2006 TAAGGAATTTTGA-AGACCTCAA
1 TATGAAATTTTGATA-ACCTC-C
*
2028 TATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACC-TC-C
*
2051 TAT-AAGATGTTGATAACCTCC
1 TATGAA-ATTTTGATAACCTCC
* * * *
2072 ATATGATATATTGATAACCACGT
1 -TATGAAATTTTGATAACCTC-C
* ** *
2095 TATGAAAATTCAAAAACCTCC
1 TATGAAATTTTGATAACCTCC
* * * *
2116 ATATG-AATTGTCAGTAATCACAC
1 -TATGAAATTTTGA-TAACCTC-C
* * *
2139 TCTGAAATTTTGATAATCACAC
1 TATGAAATTTTGATAACCTC-C
* *
2161 TATAAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAACCTC-C
*
2183 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AA-CCTCC
* *
2206 TATAAAATTTTGATAAATCTCCC
1 TATGAAATTTTGAT-AACCT-CC
* * *
2229 TATAAAATTTTGATAATCGCC
1 TATGAAATTTTGATAACCTCC
*
2250 TTATGAAATCTTGATAA----C
1 -TATGAAATTTTGATAACCTCC
*
2268 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCT-CC
**
2289 TATGATTTTTTGATAACCTC
1 TATGAAATTTTGATAACCTC
2309 ATTATTCTCC
Statistics
Matches: 288, Mismatches: 71, Indels: 61
0.69 0.17 0.15
Matches are distributed among these distances:
16 11 0.04
17 2 0.01
18 1 0.00
19 2 0.01
20 9 0.03
21 20 0.07
22 174 0.60
23 66 0.23
24 3 0.01
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (21 bp):
TATGAAATTTTGATAACCTCC
Found at i:2210 original size:45 final size:46
Alignment explanation
Indices: 2141--2244 Score: 133
Period size: 46 Copynumber: 2.3 Consensus size: 46
2131 AATCACACTC
*
2141 TGAAATTTTGAT-AATCACACTATAAAATTGTGAT-AACCTCGCTA
1 TGAAATTTTGATAAATCACACTATAAAATTGTGATAAACCTCCCTA
* * *
2185 TGAAATTTTGATAAATCTTC-CTATAAAATTTTGATAAATCTCCCTA
1 TGAAATTTTGATAAATC-ACACTATAAAATTGTGATAAACCTCCCTA
*
2231 TAAAATTTTGATAA
1 TGAAATTTTGATAA
2245 TCGCCTTATG
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
44 12 0.23
45 18 0.35
46 22 0.42
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.38
Consensus pattern (46 bp):
TGAAATTTTGATAAATCACACTATAAAATTGTGATAAACCTCCCTA
Found at i:2213 original size:23 final size:24
Alignment explanation
Indices: 2143--2244 Score: 108
Period size: 23 Copynumber: 4.5 Consensus size: 24
2133 TCACACTCTG
*
2143 AAATTTTGAT-AATC-ACACTATA
1 AAATTTTGATAAATCTTCACTATA
* * * *
2165 AAATTGTGAT-AA-CCTCGCTATG
1 AAATTTTGATAAATCTTCACTATA
2187 AAATTTTGATAAATCTTC-CTATA
1 AAATTTTGATAAATCTTCACTATA
*
2210 AAATTTTGATAAATC-TCCCTATA
1 AAATTTTGATAAATCTTCACTATA
2233 AAATTTTGATAA
1 AAATTTTGATAA
2245 TCGCCTTATG
Statistics
Matches: 69, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.01
22 27 0.39
23 38 0.55
24 3 0.04
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (24 bp):
AAATTTTGATAAATCTTCACTATA
Found at i:2265 original size:45 final size:43
Alignment explanation
Indices: 2143--2266 Score: 124
Period size: 45 Copynumber: 2.7 Consensus size: 43
2133 TCACACTCTG
* *
2143 AAATTTTGATAATCACACTATAAAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAATCAC-CTATAAAATT-TGATAAACCTCCCTATA
* *
2187 AAATTTTGATAAATCTTCCTATAAAATTTTGATAAATCTCCCTATA
1 AAATTTTGAT-AATC-ACCTATAAAA-TTTGATAAACCTCCCTATA
* *
2233 AAATTTTGATAATCGCCTTATGAAATCTTGATAA
1 AAATTTTGATAATCACC-TATAAAAT-TTGATAA
2267 CTACAAATTT
Statistics
Matches: 68, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
44 13 0.19
45 33 0.49
46 22 0.32
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.38
Consensus pattern (43 bp):
AAATTTTGATAATCACCTATAAAATTTGATAAACCTCCCTATA
Found at i:2393 original size:22 final size:22
Alignment explanation
Indices: 2368--2422 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
2358 CCCTTTTATA
2368 AAATTTTGA-AAACTAAACTATG
1 AAATTTTGATAAACTAAA-TATG
* **
2390 AAATTTTGATAACCTTCATATG
1 AAATTTTGATAAACTAAATATG
2412 AAATTTTGATA
1 AAATTTTGATA
2423 TCCTCCCTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 24 0.83
23 5 0.17
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (22 bp):
AAATTTTGATAAACTAAATATG
Found at i:2599 original size:22 final size:22
Alignment explanation
Indices: 2547--2651 Score: 81
Period size: 22 Copynumber: 4.8 Consensus size: 22
2537 AATCACATTT
* *
2547 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTATA
*
2569 TGAAATTTTGATAATCTCTATA
1 TGAAATTTTGATAACCTCTATA
* * * *
2591 T-AAATTTTTGTTGACCCCTCTA
1 TGAAA-TTTTGATAACCTCTATA
*
2613 TGAAATTTTGATAA-TTAC-ATTA
1 TGAAATTTTGATAACCT-CTA-TA
*
2635 TGTAATTTTGATAACCT
1 TGAAATTTTGATAACCT
2652 AAGACAAAAG
Statistics
Matches: 63, Mismatches: 15, Indels: 9
0.72 0.17 0.10
Matches are distributed among these distances:
21 3 0.05
22 56 0.89
23 4 0.06
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTATA
Found at i:2644 original size:44 final size:44
Alignment explanation
Indices: 2522--2650 Score: 129
Period size: 44 Copynumber: 2.9 Consensus size: 44
2512 AAAAATACCA
* * * * *
2522 CTATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAATTACATTATGAAATTTTGATAACCCCT
* * *
2566 TTATGAAATTTTGATAATCT-C-TATAT-AAATTTTTGTTGACCCCT
1 CTATGAAATTTTGATAAT-TACAT-TATGAAA-TTTTGATAACCCCT
*
2610 CTATGAAATTTTGATAATTACATTATGTAATTTTGATAACC
1 CTATGAAATTTTGATAATTACATTATGAAATTTTGATAACC
2651 TAAGACAAAA
Statistics
Matches: 67, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
43 5 0.07
44 59 0.88
45 3 0.04
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.44
Consensus pattern (44 bp):
CTATGAAATTTTGATAATTACATTATGAAATTTTGATAACCCCT
Found at i:2859 original size:31 final size:31
Alignment explanation
Indices: 2824--2888 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
2814 TGGTAATTTA
* *
2824 GAAATATGTTTTTTAAAA-AAGGGTACAATTG
1 GAAATATG-TTTTAAAAATAAGGGTACAATCG
2855 GAAATATGTTTTAAAAATAAGGGTACAATCG
1 GAAATATGTTTTAAAAATAAGGGTACAATCG
2886 GAA
1 GAA
2889 TGTTTTCCCC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 8 0.26
31 23 0.74
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.31
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAGGGTACAATCG
Found at i:6231 original size:23 final size:24
Alignment explanation
Indices: 6194--6241 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
6184 TCAAGGTAAC
*
6194 TAAAAAAAATCATTTAACTTTTTT
1 TAAAAAAAATAATTTAACTTTTTT
* *
6218 TAAAAAAAA-AATTTGAGTTTTTT
1 TAAAAAAAATAATTTAACTTTTTT
6241 T
1 T
6242 TTTTTTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (24 bp):
TAAAAAAAATAATTTAACTTTTTT
Done.