Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007895.1 Corchorus capsularis cultivar CVL-1 contig07916, 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: 9949
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.32
Found at i:1805 original size:167 final size:166
Alignment explanation
Indices: 1337--1820 Score: 636
Period size: 167 Copynumber: 2.9 Consensus size: 166
1327 TGAGTCATTT
*
1337 GTCAATTGAGATATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* * *
1402 TTAAGTAATCTGCCAAGTAGGTAAAGACG-AAAAAAATTAGTTCTCTAGCTCATC-ATCAATCAT
65 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAAATTAGTTCTCTAGCTCCTCAAT-AATCCT
* * * *
1465 TGATGGGGATCTTTTATTAATTCCACTACTCTATTCAA
129 TGGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
* * * *
1503 GTCCATTGAGAATTGACCAAAAAAATTACTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACC-AAAAAGTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* * * * *
1568 TTAAGTAATCTACCAAGTAGGAAAAGACGAAAAAAAGA--AGTTCTCTAACT-CTAAAAGCAAGC
65 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAA-ATTAGTTCTCTAGCTCCT-CAA-TAATC
*
1630 CTTGGTAGGGATCTTTTAGTAATTCCACTACTTTATTAAA
127 CTTGGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
* *
1670 GTCAATTGAGAAATGACCAAAAAGTCTAGTTATTTAATCACCTCAAGAATCAAAAGTTAGGGCAT
1 GTCAATTGAGAAATGACCAAAAAGT-TAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* * * * * *
1735 TTAAGTAACCGGTCAAGTGGGAAAAGACGAAAAAAAATTAGTTCTCTCGCTCCTCAATAATCCGT
65 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAAATTAGTTCTCTAGCTCCTCAATAATCCTT
1800 GGTAGGGATCTTTTAGTAATT
130 GGTAGGGATCTTTTAGTAATT
1821 TTCATATGTT
Statistics
Matches: 273, Mismatches: 35, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
165 1 0.00
166 99 0.36
167 158 0.58
168 13 0.05
169 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (166 bp):
GTCAATTGAGAAATGACCAAAAAGTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATT
TAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAAATTAGTTCTCTAGCTCCTCAATAATCCTTG
GTAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
Found at i:7914 original size:22 final size:22
Alignment explanation
Indices: 7889--8383 Score: 122
Period size: 22 Copynumber: 22.7 Consensus size: 22
7879 ATGATTTCAT
7889 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* *** *
7911 TATGAAATTTTAATAATGATAC
1 TATGAAATTTTGATAACCTTCC
* * * ** **
7933 TATGGAATTTCGAGAATTTTTT
1 TATGAAATTTTGATAACCTTCC
* **
7955 TAT-AAATTGTT-TTAACCTTAT
1 TATGAAATT-TTGATAACCTTCC
*
7976 TATGAAATTTTGTTAA-CTTCC
1 TATGAAATTTTGATAACCTTCC
* * * * *
7997 CAAGGAATTTTGATGACC-TCAA
1 TATGAAATTTTGATAACCTTC-C
*
8019 TATGAAATTTTGATAA-CTTTC
1 TATGAAATTTTGATAACCTTCC
**
8040 TAATGAAATTTTGATAACCAACAC
1 T-ATGAAATTTTGATAACCTTC-C
* * *
8064 TATGAGATGTTGACAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * *
8085 ATATGATATATTGATAATCACGT--
1 -TATGAAATTTTGATAA-C-CTTCC
* * *
8108 TATGAAAATTTAAAAACC-TCC
1 TATGAAATTTTGATAACCTTCC
8129 ATATG-AATTGTT-AGTAATCACATT-C
1 -TATGAAATT-TTGA-TAA-C-C-TTCC
*
8154 --TGAAATTTTGTTAA-C-TCGC
1 TATGAAATTTTGATAACCTTC-C
**
8173 TATGAAATTTTGATAAATATTCC
1 TATGAAATTTTGAT-AACCTTCC
* *
8196 TATAAAATTTTGATATAAACCTTCT
1 TATGAAATTTTG--AT-AACCTTCC
* * *
8221 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTTCC
*
8243 TATGAAATCTTGATAA---T--
1 TATGAAATTTTGATAACCTTCC
* *
8260 TA-CAAATTTTAATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
** *
8280 TTATGATTTTTTGATAACC-TCAT
1 -TATGAAATTTTGATAACCTTC-C
* * *
8303 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
* **
8325 TATGAAATTTTGATAACCCTAT
1 TATGAAATTTTGATAACCTTCC
* **
8347 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
8369 TATGAAATTTTGATA
1 TATGAAATTTTGATA
8384 TCCTCCATGA
Statistics
Matches: 345, Mismatches: 85, Indels: 85
0.67 0.17 0.17
Matches are distributed among these distances:
16 10 0.03
17 3 0.01
18 1 0.00
19 4 0.01
20 1 0.00
21 54 0.16
22 206 0.60
23 37 0.11
24 6 0.02
25 22 0.06
26 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:8556 original size:22 final size:22
Alignment explanation
Indices: 8465--8614 Score: 96
Period size: 22 Copynumber: 6.8 Consensus size: 22
8455 GAAATACCAC
8465 TATGAAATTTTTG-TAATCACAT
1 TATGAAA-TTTTGATAATCACAT
* * * * *
8487 TTTGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAATCACAT
* * * *
8509 TATAAAATTTT-ATTGA-CCCCT
1 TATGAAATTTTGA-TAATCACAT
8530 CTATGAAATTTTGATAATCACAT
1 -TATGAAATTTTGATAATCACAT
* *
8553 TATGCAATTTTGATAACCTCGC-T
1 TATGAAATTTTGATAA--TCACAT
*
8576 T-TGAAATTTTGATAA-CAACAC
1 TATGAAATTTTGATAATC-ACAT
8597 TATGAAATTTTGATAATC
1 TATGAAATTTTGATAATC
8615 TTCCTATAAA
Statistics
Matches: 97, Mismatches: 20, Indels: 21
0.70 0.14 0.15
Matches are distributed among these distances:
19 1 0.01
20 1 0.01
21 9 0.09
22 76 0.78
23 7 0.07
24 3 0.03
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAATCACAT
Found at i:8562 original size:44 final size:44
Alignment explanation
Indices: 8524--8633 Score: 118
Period size: 44 Copynumber: 2.5 Consensus size: 44
8514 AATTTTATTG
* * *
8524 ACCCCTCTATGAAATTTTGATAATC-ACATTATGCAATTTTGATA
1 ACCCCGCTATGAAATTTTGATAA-CAACACTATGAAATTTTGATA
* *
8568 ACCTCGCTTTGAAATTTTGATAACAACACTATGAAATTTTGATA
1 ACCCCGCTATGAAATTTTGATAACAACACTATGAAATTTTGATA
**
8612 ATCTTC-CTAT-AAATTTTGATAA
1 A-CCCCGCTATGAAATTTTGATAA
8634 TTTGATCTCT
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
43 13 0.23
44 41 0.72
45 3 0.05
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.39
Consensus pattern (44 bp):
ACCCCGCTATGAAATTTTGATAACAACACTATGAAATTTTGATA
Found at i:8583 original size:66 final size:66
Alignment explanation
Indices: 8462--8614 Score: 177
Period size: 66 Copynumber: 2.3 Consensus size: 66
8452 CCAGAAATAC
* * *
8462 CACTATGAAATTTTTG-TAATCACATTTTGAAAATTTGATAACCTCTTTATAAAATTTT-ATTGA
1 CACTATGAAA-TTTTGATAATCACATTATGAAAATTTGATAACCTCCTTATAAAATTTTGA-TAA
**
8525 CCC
64 CAA
* * * *
8528 CTCTATGAAATTTTGATAATCACATTATGCAATTTTGATAACCTCGCTT-TGAAATTTTGATAAC
1 CACTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTC-CTTATAAAATTTTGATAAC
8592 AA
65 AA
8594 CACTATGAAATTTTGATAATC
1 CACTATGAAATTTTGATAATC
8615 TTCCTATAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
65 5 0.07
66 66 0.89
67 3 0.04
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (66 bp):
CACTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCCTTATAAAATTTTGATAACA
A
Found at i:8627 original size:21 final size:23
Alignment explanation
Indices: 8530--8634 Score: 103
Period size: 22 Copynumber: 4.8 Consensus size: 23
8520 ATTGACCCCT
8530 CTATGAAATTTTGATAATC-ACA
1 CTATGAAATTTTGATAATCAACA
* * ** *
8552 TTATGCAATTTTGATAA-CCTCG
1 CTATGAAATTTTGATAATCAACA
*
8574 CTTTGAAATTTTGATAA-CAACA
1 CTATGAAATTTTGATAATCAACA
**
8596 CTATGAAATTTTGATAATCTTC-
1 CTATGAAATTTTGATAATCAACA
8618 CTAT-AAATTTTGATAAT
1 CTATGAAATTTTGATAAT
8635 TTGATCTCTA
Statistics
Matches: 68, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
21 14 0.21
22 52 0.76
23 2 0.03
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (23 bp):
CTATGAAATTTTGATAATCAACA
Found at i:8946 original size:31 final size:31
Alignment explanation
Indices: 8910--8970 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
8900 TAATGATAAT
*
8910 TTAGAAATATGTTTT-AAAATAAAGGGTACAG
1 TTAGAAATATATTTTAAAAAT-AAGGGTACAG
8941 TTAGAAATATATTTTAAAAATAAGGGTACA
1 TTAGAAATATATTTTAAAAATAAGGGTACA
8971 ATCGAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 23 0.82
32 5 0.18
ACGTcount: A:0.48, C:0.03, G:0.16, T:0.33
Consensus pattern (31 bp):
TTAGAAATATATTTTAAAAATAAGGGTACAG
Found at i:8981 original size:32 final size:31
Alignment explanation
Indices: 8914--8983 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 31
8904 GATAATTTAG
* * * *
8914 AAATATGTTTTAAAATAAAGGGTACAGTTAG
1 AAATATATTTTAAAATAAAGGGTACAATGAA
8945 AAATATATTTTAAAA-ATAAGGGTACAATCGAA
1 AAATATATTTTAAAATA-AAGGGTACAAT-GAA
8977 AAATATA
1 AAATATA
8984 AAATTTCCCC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 1 0.03
31 24 0.73
32 8 0.24
ACGTcount: A:0.51, C:0.04, G:0.14, T:0.30
Consensus pattern (31 bp):
AAATATATTTTAAAATAAAGGGTACAATGAA
Done.