Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012275.1 Corchorus capsularis cultivar CVL-1 contig12296, 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: 13489
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:86 original size:29 final size:29
Alignment explanation
Indices: 19--91 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
9 ATCAAGGTAG
* *
19 GAAAAATAAAAAAATCCAGAAAAGCAGAAA
1 GAAAAATAAAAAAATCCAGAAAAACA-CAA
* *
49 GAAAGATAAAAAAAT-CAGAAAAACTCAA
1 GAAAAATAAAAAAATCCAGAAAAACACAA
77 GAAAACATAAAAAAA
1 GAAAA-ATAAAAAAA
92 AGGGAAAACA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 6 0.16
29 17 0.46
30 14 0.38
ACGTcount: A:0.71, C:0.10, G:0.11, T:0.08
Consensus pattern (29 bp):
GAAAAATAAAAAAATCCAGAAAAACACAA
Found at i:1612 original size:99 final size:99
Alignment explanation
Indices: 1441--1917 Score: 337
Period size: 99 Copynumber: 4.8 Consensus size: 99
1431 TTCGATTTTC
** * * * ** * * *
1441 ACTTGCATTTCCCCCAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTATTTCCCA
1 ACTTGCATTTTTCCCAAAATGCCCGTCCCGGATAGAAGGCATTCATTTTTACTTGCTTTTTCCTA
* * *
1506 AAGCGCCCTTCCCAGACGGAAGCCATTTAT-TTT
66 AAGCGCCCTTCCCAGATGGAAGCCACTAATCTTT
* * * * *
1539 ACTTGCTTTTTTTTCTCAAAATGCCCGTCCCGGACT-GCAGGCATTTATTTTTACCTG-TTTTTC
1 ACTTGC--ATTTTTCCCAAAATGCCCGTCCCGGA-TAGAAGGCATTCATTTTTACTTGCTTTTTC
* *
1602 CTAAAACGCCCTTCCCAGATGGAAGGCACTAATCTTT
63 CTAAAGCGCCCTTCCCAGATGGAAGCCACTAATCTTT
* * * * *
1639 ACTTGCATTTTTCCCAAAGTGCCCTTCCCGGATAGAAGGCACTGATTTTTACTTGCTTTGTCCTA
1 ACTTGCATTTTTCCCAAAATGCCCGTCCCGGATAGAAGGCATTCATTTTTACTTGCTTTTTCCTA
* * * *
1704 AAGCGCCATTCCCGGATGGAAGGCACTAATCTCT
66 AAGCGCCCTTCCCAGATGGAAGCCACTAATCTTT
* * * **
1738 ACCTG--TTTTTCTCAAAATGCTC-TCCCCGGACGGAAGGCACTT-A-TTTTACTTGCTATTTTC
1 ACTTGCATTTTTCCCAAAATGCCCGT-CCCGGATAGAAGGCA-TTCATTTTTACTTGCT-TTTTC
* * * ** * *
1798 CGAAAACGCCCTTCCCGGATGGAAAACGCTCA-CTTTT
63 CTAAAGCGCCCTTCCCAGATGGAAGCCACTAATC-TTT
* * * * * * * *
1835 AC--CCACTTTTCCCCAAAGTGCCCTTCCCCGACAGAAAGGCACTAATTTTTACTTGCTTTTTCC
1 ACTTGCA-TTTTTCCCAAAATGCCCGTCCCGGATAG-AAGGCATTCATTTTTACTTGCTTTTTCC
* *
1898 TAAAACGCCCTTCCCGGATG
64 TAAAGCGCCCTTCCCAGATG
1918 AAAGGCATTA
Statistics
Matches: 305, Mismatches: 57, Indels: 33
0.77 0.14 0.08
Matches are distributed among these distances:
96 13 0.04
97 62 0.20
98 67 0.22
99 107 0.35
100 56 0.18
ACGTcount: A:0.22, C:0.30, G:0.16, T:0.32
Consensus pattern (99 bp):
ACTTGCATTTTTCCCAAAATGCCCGTCCCGGATAGAAGGCATTCATTTTTACTTGCTTTTTCCTA
AAGCGCCCTTCCCAGATGGAAGCCACTAATCTTT
Found at i:1944 original size:49 final size:49
Alignment explanation
Indices: 1456--1972 Score: 307
Period size: 49 Copynumber: 10.5 Consensus size: 49
1446 CATTTCCCCC
* * * * * *
1456 AAAACGCCCTTCCCAGACGGAAGCCA-TTCATTTTTACTTGCTATTTCCC
1 AAAACGCCCTTCCCGGATGAAAGGCACTT-ATTTTTACTTGCTTTTTCCT
* * * * * * *
1505 AAAGCGCCCTTCCCAGACGGAAGCCATTTA-TTTTACTTGCTTTTTTTTCT
1 AAAACGCCCTTCCCGGATGAAAGGCACTTATTTTTACTTGC--TTTTTCCT
* * * * *
1555 CAAAATGCCCGTCCCGGACTG-CAGGCATTTATTTTTACCTG-TTTTTCCT
1 -AAAACGCCCTTCCCGGA-TGAAAGGCACTTATTTTTACTTGCTTTTTCCT
* * * * *
1604 AAAACGCCCTTCCCAGATGGAAGGCACTAATCTTTACTTGCATTTTTCCC
1 AAAACGCCCTTCCCGGATGAAAGGCACTTATTTTTACTTGC-TTTTTCCT
** * *
1654 AAAGTGCCCTTCCCGGAT-AGAAGGCACTGATTTTTACTTGCTTTGTCCT
1 AAAACGCCCTTCCCGGATGA-AAGGCACTTATTTTTACTTGCTTTTTCCT
* * * * * * *
1703 AAAGCGCCATTCCCGGATGGAAGGCACTAATCTCTACCTG-TTTTT-CT
1 AAAACGCCCTTCCCGGATGAAAGGCACTTATTTTTACTTGCTTTTTCCT
* * * * * *
1750 CAAAATGCTCTCCCCGGACGGAAGGCACTTA-TTTTACTTGCTATTTTCCG
1 -AAAACGCCCTTCCCGGATGAAAGGCACTTATTTTTACTTGCT-TTTTCCT
* * * * *** * *
1800 AAAACGCCCTTCCCGGATGGAAA-ACGCTCACTTTTACCCACTTTTCCCC
1 AAAACGCCCTTCCCGGAT-GAAAGGCACTTATTTTTACTTGCTTTTTCCT
** * * *
1849 AAAGTGCCCTTCCCCGACAGAAAGGCACTAATTTTTACTTGCTTTTTCCT
1 AAAACGCCCTTCCCGGA-TGAAAGGCACTTATTTTTACTTGCTTTTTCCT
* * **
1899 AAAACGCCCTTCCCGGATGAAAGGCA-TTAGTTTCACTTGCTTTTTTTT
1 AAAACGCCCTTCCCGGATGAAAGGCACTTATTTTTACTTGCTTTTTCCT
* * * *
1947 AAAATGCCTTTTCCGGACGAAAGGCA
1 AAAACGCCCTTCCCGGATGAAAGGCA
1973 AGTTCGCTTT
Statistics
Matches: 361, Mismatches: 88, Indels: 39
0.74 0.18 0.08
Matches are distributed among these distances:
47 10 0.03
48 106 0.29
49 124 0.34
50 91 0.25
51 21 0.06
52 9 0.02
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.32
Consensus pattern (49 bp):
AAAACGCCCTTCCCGGATGAAAGGCACTTATTTTTACTTGCTTTTTCCT
Found at i:1953 original size:196 final size:193
Alignment explanation
Indices: 1446--1972 Score: 506
Period size: 196 Copynumber: 2.7 Consensus size: 193
1436 TTTTCACTTG
* ** * * * * * * *
1446 CATTTCCCCCAAAACGCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTATTTCCCAAAGCG
1 CATTTTCCCCAAAGTGCCCTTCCCCGACAGAAGGCACTAATTTTTACTTGCTTTTTCCTAAAGCG
* * * * *
1511 CCCTTCCCAGACGGAAGCCATTTATTTTACTTGCTTTTTTTTCTCAAAATGCCCGTCCCGGACTG
66 CCCTTCCCGGATGGAAGGCA-TTATTTCACTTGC-TTTTTTT-T-AAAATGCCCGTCCCGGACGG
* * * **
1576 CAGGCATTTATTTTTACCTGTTTTTCCTAAAACGCCCTTCCCAGATGGAAGGCACTAATCTTTAC
127 AAGGCACTTATTTTTACCTGTTTTTCCGAAAACGCCCTTCCCAGATGGAAAACACTAATCTTTAC
*
1641 TTG
192 -TC
* * * * *
1644 CATTTTTCCCAAAGTGCCCTTCCCGGATAGAAGGCACTGATTTTTACTTGCTTTGTCCTAAAGCG
1 CATTTTCCCCAAAGTGCCCTTCCCCGACAGAAGGCACTAATTTTTACTTGCTTTTTCCTAAAGCG
* * * * * * *
1709 CCATTCCCGGATGGAAGGCACTAATCTCTACCTG-TTTTTCTCAAAATGCTC-TCCCCGGACGGA
66 CCCTTCCCGGATGGAAGGCA-TTATTTC-ACTTGCTTTTTTTTAAAATGCCCGT-CCCGGACGGA
* * * *
1772 AGGCACTTA-TTTTACTTGCTATTTTCCGAAAACGCCCTTCCCGGATGGAAAACGCTCA-CTTTT
128 AGGCACTTATTTTTACCTG-T-TTTTCCGAAAACGCCCTTCCCAGATGGAAAACACTAATC-TTT
1835 AC-C
190 ACTC
*
1838 CACTTTTCCCCAAAGTGCCCTTCCCCGACAGAAAGGCACTAATTTTTACTTGCTTTTTCCTAAAA
1 CA-TTTTCCCCAAAGTGCCCTTCCCCGACAG-AAGGCACTAATTTTTACTTGCTTTTTCCTAAAG
* ** * *
1903 CGCCCTTCCCGGATGAAAGGCATTAGTTTCACTTGCTTTTTTTTAAAATGCCTTTTCCGGACGAA
64 CGCCCTTCCCGGATGGAAGGCATTA-TTTCACTTGCTTTTTTTTAAAATGCCCGTCCCGGACGGA
1968 AGGCA
128 AGGCA
1973 AGTTCGCTTT
Statistics
Matches: 266, Mismatches: 53, Indels: 22
0.78 0.16 0.06
Matches are distributed among these distances:
194 11 0.04
195 57 0.21
196 115 0.43
197 7 0.03
198 72 0.27
199 4 0.02
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.32
Consensus pattern (193 bp):
CATTTTCCCCAAAGTGCCCTTCCCCGACAGAAGGCACTAATTTTTACTTGCTTTTTCCTAAAGCG
CCCTTCCCGGATGGAAGGCATTATTTCACTTGCTTTTTTTTAAAATGCCCGTCCCGGACGGAAGG
CACTTATTTTTACCTGTTTTTCCGAAAACGCCCTTCCCAGATGGAAAACACTAATCTTTACTC
Found at i:7496 original size:9 final size:9
Alignment explanation
Indices: 7484--7594 Score: 61
Period size: 9 Copynumber: 13.8 Consensus size: 9
7474 CCCAACCCGA
7484 GACCCGAAT
1 GACCCGAAT
7493 GACCCG-A-
1 GACCCGAAT
**
7500 GACCTTAAT
1 GACCCGAAT
7509 GACCCGAA-
1 GACCCGAAT
*
7517 -ACCCGTAT
1 GACCCGAAT
*
7525 AACCCG-A-
1 GACCCGAAT
7532 GACCCGAAT
1 GACCCGAAT
7541 GACCCGAA-
1 GACCCGAAT
*
7549 -ACCCGTAT
1 GACCCGAAT
*
7557 AACCCG-A-
1 GACCCGAAT
7564 -ACCC-AGAT
1 GACCCGA-AT
7572 GACCCGAA-
1 GACCCGAAT
7580 -ACCCGAAT
1 GACCCGAAT
7588 GACCCGA
1 GACCCGA
7595 GAAAGCTACC
Statistics
Matches: 80, Mismatches: 7, Indels: 30
0.68 0.06 0.26
Matches are distributed among these distances:
6 4 0.05
7 29 0.36
8 5 0.06
9 41 0.51
10 1 0.01
ACGTcount: A:0.34, C:0.37, G:0.19, T:0.10
Consensus pattern (9 bp):
GACCCGAAT
Found at i:7497 original size:16 final size:16
Alignment explanation
Indices: 7478--7596 Score: 134
Period size: 16 Copynumber: 7.5 Consensus size: 16
7468 AACCCGCCCA
7478 ACCCGAGACCCGAATG
1 ACCCGAGACCCGAATG
**
7494 ACCCGAGACCTTAATG
1 ACCCGAGACCCGAATG
* * *
7510 ACCCGAAACCCGTATA
1 ACCCGAGACCCGAATG
7526 ACCCGAGACCCGAATG
1 ACCCGAGACCCGAATG
* * *
7542 ACCCGAAACCCGTATA
1 ACCCGAGACCCGAATG
7558 ACCCGA-ACCC-AGATG
1 ACCCGAGACCCGA-ATG
*
7573 ACCCGAAACCCGAATG
1 ACCCGAGACCCGAATG
7589 ACCCGAGA
1 ACCCGAGA
7597 AAGCTACCTG
Statistics
Matches: 84, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
15 12 0.14
16 71 0.85
17 1 0.01
ACGTcount: A:0.34, C:0.37, G:0.19, T:0.09
Consensus pattern (16 bp):
ACCCGAGACCCGAATG
Found at i:7529 original size:48 final size:47
Alignment explanation
Indices: 7477--7596 Score: 154
Period size: 48 Copynumber: 2.5 Consensus size: 47
7467 GAACCCGCCC
* *
7477 AACCCGAGACCCGAATGACCCGAGA-CCTTAATGACCCGAAACCC-GTAT
1 AACCCGAGACCCGAATGACCCGAGACCCGT-ATAACCCG-AACCCAG-AT
*
7525 AACCCGAGACCCGAATGACCCGAAACCCGTATAACCCGAACCCAGAT
1 AACCCGAGACCCGAATGACCCGAGACCCGTATAACCCGAACCCAGAT
* *
7572 GACCCGAAACCCGAATGACCCGAGA
1 AACCCGAGACCCGAATGACCCGAGA
7597 AAGCTACCTG
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
47 29 0.45
48 32 0.50
49 3 0.05
ACGTcount: A:0.35, C:0.37, G:0.19, T:0.09
Consensus pattern (47 bp):
AACCCGAGACCCGAATGACCCGAGACCCGTATAACCCGAACCCAGAT
Found at i:7577 original size:31 final size:32
Alignment explanation
Indices: 7478--7596 Score: 152
Period size: 32 Copynumber: 3.8 Consensus size: 32
7468 AACCCGCCCA
* * * **
7478 ACCCGAGACCCGAATGACCCGAGACCTTAATG
1 ACCCGAAACCCGTATAACCCGAGACCCGAATG
7510 ACCCGAAACCCGTATAACCCGAGACCCGAATG
1 ACCCGAAACCCGTATAACCCGAGACCCGAATG
7542 ACCCGAAACCCGTATAACCCGA-ACCC-AGATG
1 ACCCGAAACCCGTATAACCCGAGACCCGA-ATG
* *
7573 ACCCGAAACCCGAATGACCCGAGA
1 ACCCGAAACCCGTATAACCCGAGA
7597 AAGCTACCTG
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
30 1 0.01
31 27 0.35
32 50 0.64
ACGTcount: A:0.34, C:0.37, G:0.19, T:0.09
Consensus pattern (32 bp):
ACCCGAAACCCGTATAACCCGAGACCCGAATG
Found at i:10589 original size:120 final size:120
Alignment explanation
Indices: 10347--10589 Score: 299
Period size: 119 Copynumber: 2.0 Consensus size: 120
10337 CACATGTCCA
* *
10347 TTTTTTTAATTAATTAAGTTTTAAATATTTTCAATCTAGTCCCTAAGGGACACATGTCACCCTTC
1 TTTTTTTAATTAATTAAATTTTAAATATTTTCAATCTAGTCCCTAAGGGACACATGTCACACTTC
** ** * * ** * **
10412 AAGACCCGCTTGTGTAGTTTTCTAAACTCACCGCCGGTGTATTGTATAATTTGCC
66 AAGACCCGCACGTACAGTCTACTAAACTCACCAACAGTGTATTAAATAATTTGCC
* * *
10467 TTTTTTTAATTAATTAAATTTTAAATA-TTTCAATCTAGTCCCTAGGGGATACATGTCACATTTC
1 TTTTTTTAATTAATTAAATTTTAAATATTTTCAATCTAGTCCCTAAGGGACACATGTCACACTTC
* * *
10531 TAGACCCGCACGTACAGTCTACTAAACTCCACTAACAGTGTATTAAATAATTTTCC
66 AAGACCCGCACGTACAGTCTACTAAACT-CACCAACAGTGTATTAAATAATTTGCC
10587 TTT
1 TTT
10590 AATTATAGAA
Statistics
Matches: 103, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
119 54 0.52
120 49 0.48
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (120 bp):
TTTTTTTAATTAATTAAATTTTAAATATTTTCAATCTAGTCCCTAAGGGACACATGTCACACTTC
AAGACCCGCACGTACAGTCTACTAAACTCACCAACAGTGTATTAAATAATTTGCC
Done.