Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011676.1 Corchorus capsularis cultivar CVL-1 contig11697, 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: 5026
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--98 Score: 189
Period size: 2 Copynumber: 49.5 Consensus size: 2
1 TC TC TC TC TC TC TC TC TC -C TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
42 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
84 TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC T
99 AATCAAATTC
Statistics
Matches: 95, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 94 0.99
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1001 original size:14 final size:14
Alignment explanation
Indices: 968--1001 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
958 ATAAATGTAA
968 TTTTTAAATATTTT
1 TTTTTAAATATTTT
**
982 ACTTTAAATATTTT
1 TTTTTAAATATTTT
996 TTTTTA
1 TTTTTA
1002 TAAATAATAA
Statistics
Matches: 16, Mismatches: 4, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTTTAAATATTTT
Found at i:1417 original size:20 final size:20
Alignment explanation
Indices: 1369--1444 Score: 66
Period size: 20 Copynumber: 3.6 Consensus size: 20
1359 TATTCATATC
* *
1369 AAATTTTGATAACCACACTTTTT
1 AAATTTTGATAA-TAC-C-TTTA
1392 AAATTTTGATAATACCTTTA
1 AAATTTTGATAATACCTTTA
1412 AAATTTTGAT-A-ACCTTCTCA
1 AAATTTTGATAATACCTT-T-A
*
1432 TAATTTTGATAAT
1 AAATTTTGATAAT
1445 CTCACTATGA
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
18 5 0.11
19 2 0.04
20 23 0.50
21 2 0.04
22 2 0.04
23 12 0.26
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (20 bp):
AAATTTTGATAATACCTTTA
Found at i:1461 original size:22 final size:21
Alignment explanation
Indices: 1369--1511 Score: 96
Period size: 22 Copynumber: 6.6 Consensus size: 21
1359 TATTCATATC
* * *
1369 AAATTTTGATAACCACACTTTTT
1 AAATTTTGATAACC-TAC-TATG
* *
1392 AAATTTTGATAA--TACCTTTA
1 AAATTTTGATAACCTA-CTATG
*
1412 AAATTTTGATAACCTTCTCAT-
1 AAATTTTGATAACCTACT-ATG
*
1433 -AATTTTGATAATCTCACTATG
1 AAATTTTGATAACCT-ACTATG
* *
1454 AAATTTTGATAACCATATTACG
1 AAATTTTGATAACC-TACTATG
*
1476 AAATTTCGATAACCTTACTATAG
1 AAATTTTGATAACC-TACTAT-G
1499 AAATTTTGATAAC
1 AAATTTTGATAAC
1512 TTCATAACAT
Statistics
Matches: 97, Mismatches: 14, Indels: 18
0.75 0.11 0.14
Matches are distributed among these distances:
20 31 0.32
21 5 0.05
22 35 0.36
23 26 0.27
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.41
Consensus pattern (21 bp):
AAATTTTGATAACCTACTATG
Found at i:1552 original size:22 final size:22
Alignment explanation
Indices: 1529--1671 Score: 115
Period size: 22 Copynumber: 6.5 Consensus size: 22
1519 CATCCCTGTA
* *
1529 AAATTTTGATTATCTCCCTATA
1 AAATTTTGATAATCTCCCTATG
* * * * * *
1551 AAATGTTGGTAACCACACTATA
1 AAATTTTGATAATCTCCCTATG
* * *
1573 AAATTTTGATAACCACACTATG
1 AAATTTTGATAATCTCCCTATG
* *
1595 AAATTGTGATAATCTCCTTATG
1 AAATTTTGATAATCTCCCTATG
***
1617 AAATTTTGATAAATCTTTTTATG
1 AAATTTTGAT-AATCTCCCTATG
**
1640 AAATTTTGATAATCTCTTTATG
1 AAATTTTGATAATCTCCCTATG
1662 AAATTTTGAT
1 AAATTTTGAT
1672 TATAAATTTT
Statistics
Matches: 102, Mismatches: 18, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
22 82 0.80
23 20 0.20
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.42
Consensus pattern (22 bp):
AAATTTTGATAATCTCCCTATG
Found at i:1638 original size:23 final size:22
Alignment explanation
Indices: 1573--1671 Score: 126
Period size: 22 Copynumber: 4.5 Consensus size: 22
1563 CCACACTATA
* * **
1573 AAATTTTGATAACCACACTATG
1 AAATTTTGATAATCTCTTTATG
* *
1595 AAATTGTGATAATCTCCTTATG
1 AAATTTTGATAATCTCTTTATG
*
1617 AAATTTTGATAAATCTTTTTATG
1 AAATTTTGAT-AATCTCTTTATG
1640 AAATTTTGATAATCTCTTTATG
1 AAATTTTGATAATCTCTTTATG
1662 AAATTTTGAT
1 AAATTTTGAT
1672 TATAAATTTT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
22 47 0.70
23 20 0.30
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.44
Consensus pattern (22 bp):
AAATTTTGATAATCTCTTTATG
Found at i:1682 original size:45 final size:44
Alignment explanation
Indices: 1573--1671 Score: 126
Period size: 45 Copynumber: 2.2 Consensus size: 44
1563 CCACACTATA
* ***
1573 AAATTTTGATAACCACACTATGAAATTGTGATAATCTCCTTATG
1 AAATTTTGATAAACATTTTATGAAATTGTGATAATCTCCTTATG
* * *
1617 AAATTTTGATAAATCTTTTTATGAAATTTTGATAATCTCTTTATG
1 AAATTTTGATAAA-CATTTTATGAAATTGTGATAATCTCCTTATG
1662 AAATTTTGAT
1 AAATTTTGAT
1672 TATAAATTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 12 0.26
45 35 0.74
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.44
Consensus pattern (44 bp):
AAATTTTGATAAACATTTTATGAAATTGTGATAATCTCCTTATG
Found at i:1709 original size:22 final size:22
Alignment explanation
Indices: 1675--1731 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
1665 TTTTGATTAT
1675 AAATTTT-AGTAACATCCCTATG
1 AAATTTTGA-TAACATCCCTATG
* *
1697 AAATTTTGATAACTTCCTTATG
1 AAATTTTGATAACATCCCTATG
* *
1719 ATATTCTGATAAC
1 AAATTTTGATAAC
1732 TTTCCAATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 29 0.97
23 1 0.03
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (22 bp):
AAATTTTGATAACATCCCTATG
Found at i:1732 original size:22 final size:22
Alignment explanation
Indices: 1684--1733 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
1674 TAAATTTTAG
* *
1684 TAACATCCCTATGAAATTTTGA
1 TAACTTCCCTATGAAATTCTGA
* *
1706 TAACTTCCTTATGATATTCTGA
1 TAACTTCCCTATGAAATTCTGA
1728 TAACTT
1 TAACTT
1734 TCCAATGTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.32, C:0.18, G:0.08, T:0.42
Consensus pattern (22 bp):
TAACTTCCCTATGAAATTCTGA
Found at i:1863 original size:22 final size:22
Alignment explanation
Indices: 1791--2227 Score: 354
Period size: 22 Copynumber: 19.9 Consensus size: 22
1781 CAAGCATACA
*
1791 ATGAAA-TTTGATAATCTTC-CT
1 ATGAAATTTTGATAA-CCTCACT
* *
1812 ATGAAATTTTTCGATAAACCTCCCA
1 ATGAAA-TTTT-GAT-AACCTCACT
*
1837 ATGAAATTTTGATAACCACACT
1 ATGAAATTTTGATAACCTCACT
* *
1859 TTGAAATTTTGGT-ACCTC-CT
1 ATGAAATTTTGATAACCTCACT
**
1879 AATGAAATTTTGATAACCAAACT
1 -ATGAAATTTTGATAACCTCACT
* *
1902 ATGAAATTTTGAT-ACCTCGCA
1 ATGAAATTTTGATAACCTCACT
*
1923 ATGAAATTTTGATAACCACACT
1 ATGAAATTTTGATAACCTCACT
*
1945 ATGAAATTTTGATAACCTCCCT
1 ATGAAATTTTGATAACCTCACT
* * *
1967 ATTAAATTTTGATAACCACACA
1 ATGAAATTTTGATAACCTCACT
* * *
1989 ATGGAATTTTGATAATCTCTCT
1 ATGAAATTTTGATAACCTCACT
* * *
2011 ATGAAATCTCGATAACCAC-CAT
1 ATGAAATTTTGATAACCTCAC-T
*
2033 ATGAAATTTTGATAACCACACT
1 ATGAAATTTTGATAACCTCACT
* *
2055 ATGAAAATTTTGGT-ACCTC-CGA
1 ATG-AAATTTTGATAACCTCAC-T
* **
2077 ATGAACTTTTGATAA-CTGCGTT
1 ATGAAATTTTGATAACCT-CACT
*
2099 ATGAAATTTTGATAGCCTCACT
1 ATGAAATTTTGATAACCTCACT
* * *
2121 ATGAAATTTTAATAATCTCCCT
1 ATGAAATTTTGATAACCTCACT
* * *
2143 ATAAAATTTTGATAACCCCACA
1 ATGAAATTTTGATAACCTCACT
2165 ATGAAATTTTGATAACCTTC-CT
1 ATGAAATTTTGATAACC-TCACT
* * * *
2187 ATGAAAATTCGATAATCACACT
1 ATGAAATTTTGATAACCTCACT
* *
2209 ATAAAATTTTTATAACCTC
1 ATGAAATTTTGATAACCTC
2228 TTTGATAACT
Statistics
Matches: 325, Mismatches: 72, Indels: 37
0.75 0.17 0.09
Matches are distributed among these distances:
20 2 0.01
21 51 0.16
22 232 0.71
23 21 0.06
24 10 0.03
25 9 0.03
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.35
Consensus pattern (22 bp):
ATGAAATTTTGATAACCTCACT
Found at i:1978 original size:44 final size:44
Alignment explanation
Indices: 1810--2451 Score: 414
Period size: 44 Copynumber: 14.9 Consensus size: 44
1800 GATAATCTTC
*
1810 CTATGAAATTTTTCGATAAACCTCCCAATGAAATTTTGATAACCACA
1 CTATGAAA-TTTT-GAT-AACCTCCCTATGAAATTTTGATAACCACA
* * *
1857 CTTTGAAATTTTGGT-ACCT-CCTAATGAAATTTTGATAACCAAA
1 CTATGAAATTTTGATAACCTCCCT-ATGAAATTTTGATAACCACA
* *
1900 CTATGAAATTTTGAT-ACCTCGCAATGAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCACA
*
1943 CTATGAAATTTTGATAACCTCCCTATTAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCACA
* * * * * *
1987 CAATGGAATTTTGATAATCTCTCTATGAAATCTCGATAACCAC-
1 CTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCACA
* * * *
2030 CATATGAAATTTTGATAACCACACTATGAAAATTTTGGT-ACCTC-
1 C-TATGAAATTTTGATAACCTCCCTATG-AAATTTTGATAACCACA
* * ** * *
2074 CGAATGAACTTTTGATAA-CTGCGTTATGAAATTTTGATAGCCTCA
1 C-TATGAAATTTTGATAACCT-CCCTATGAAATTTTGATAACCACA
* * * *
2119 CTATGAAATTTTAATAATCTCCCTATAAAATTTTGATAACCCCA
1 CTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCACA
* * * * *
2163 CAATGAAATTTTGATAACCTTCCTATGAAAATTCGATAATCACA
1 CTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCACA
* * **
2207 CTATAAAATTTTTATAACCT--C--------TTTGATAACTTC-
1 CTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCACA
* * * * *
2240 CTTATGAAAGTTTGATAACCACACTATAAAATTTTGAT-ATC-C-
1 C-TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCACA
* * *** * ** *
2282 CTATGCAATTTTGGT-TTTTACACTATGAAATTTTGATAACTTCC
1 CTATGAAATTTTGATAACCT-CCCTATGAAATTTTGATAACCACA
* * * ** * ***
2326 CTATAAAATTTTGGTAACCACATTATGAAATTGTGATTGTCACA
1 CTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCACA
* * * *
2370 CTATGGAATTGTGATAACCT--CTATGAAATTTTGATAACCTCC
1 CTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCACA
** ** *
2412 CTATGACTTTTTGATAACCTTACTATGATATTTTGATAAC
1 CTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAAC
2452 AACATAGAGA
Statistics
Matches: 461, Mismatches: 107, Indels: 57
0.74 0.17 0.09
Matches are distributed among these distances:
33 1 0.00
34 23 0.05
36 1 0.00
41 27 0.06
42 37 0.08
43 87 0.19
44 262 0.57
45 12 0.03
46 4 0.01
47 7 0.02
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (44 bp):
CTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCACA
Found at i:2081 original size:66 final size:66
Alignment explanation
Indices: 1837--2451 Score: 326
Period size: 66 Copynumber: 9.6 Consensus size: 66
1827 AAACCTCCCA
* * *
1837 ATGAAATTTTGATAACCACACTTTGAAATTTTGGT-ACCTC-CTAATGAAATTTTGATAACCA-A
1 ATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCAC-AATGAAATTTTGATAACCACC
1899 ACT
65 A-T
* * * * * * *
1902 ATGAAATTTTGAT-ACCTCGCAATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCCC
1 ATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCACAATGAAATTTTGATAACCACCA
1966 T
66 T
* * * * * * * *
1967 ATTAAATTTTGATAACCACACAATGGAATTTTGATAATCTCTCTATGAAATCTCGATAACCACCA
1 ATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCACAATGAAATTTTGATAACCACCA
2032 T
66 T
* * **
2033 ATGAAATTTTGATAACCACACTATGAAAATTTTGGT-ACCTC-CGAATGAACTTTTGATAACTGC
1 ATGAAATTTTGATAACCACACTATG-AAATTTTGATAACCTCAC-AATGAAATTTTGATAACCAC
**
2096 GTT
64 CAT
* * * * * * *
2099 ATGAAATTTTGATAGCCTCACTATGAAATTTTAATAATCTCCCTATAAAATTTTGATAACC-CCA
1 ATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCACAATGAAATTTTGATAACCACCA
*
2163 CA
66 -T
* * * * * * * *
2165 ATGAAATTTTGATAACCTTC-CTATGAAAATTCGATAATCACACTATAAAATTTTTAT-A--ACC
1 ATGAAATTTTGATAACC-ACACTATGAAATTTTGATAACCTCACAATGAAATTTTGATAACCACC
2226 --
65 AT
* ** * * * * *
2226 -T----CTTTGATAACTTC-CTTATGAAAGTTTGATAACCACACTATAAAATTTTGAT-ATC-CC
1 ATGAAATTTTGATAACCACAC-TATGAAATTTTGATAACCTCACAATGAAATTTTGATAACCACC
2283 -T
65 AT
* * **** * * * * *
2284 ATGCAATTTTGGTTTTTACACTATGAAATTTTGATAACTTCCCTATAAAATTTTGGTAACCA-CA
1 ATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCACAATGAAATTTTGATAACCACCA
2348 TT
66 -T
* *** * * * * *
2350 ATGAAATTGTGATTGTCACACTATGGAATTGTGATAACCT--CTATGAAATTTTGATAACCTCCC
1 ATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCACAATGAAATTTTGATAACCACCA
2413 T
66 T
** ** *
2414 ATGACTTTTTGATAACCTTACTATGATATTTTGATAAC
1 ATGAAATTTTGATAACCACACTATGAAATTTTGATAAC
2452 AACATAGAGA
Statistics
Matches: 430, Mismatches: 94, Indels: 53
0.75 0.16 0.09
Matches are distributed among these distances:
55 3 0.01
56 42 0.10
57 2 0.00
59 1 0.00
60 1 0.00
63 38 0.09
64 67 0.16
65 59 0.14
66 206 0.48
67 11 0.03
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.37
Consensus pattern (66 bp):
ATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCACAATGAAATTTTGATAACCACCA
T
Found at i:2275 original size:22 final size:22
Alignment explanation
Indices: 2242--2451 Score: 124
Period size: 22 Copynumber: 9.8 Consensus size: 22
2232 ATAACTTCCT
*
2242 TATGAAAGTTTGATAACCACAC
1 TATGAAATTTTGATAACCACAC
* *
2264 TATAAAATTTTGAT-ATC-C-C
1 TATGAAATTTTGATAACCACAC
* * ****
2283 TATGCAATTTTGGTTTTTACAC
1 TATGAAATTTTGATAACCACAC
** *
2305 TATGAAATTTTGATAACTTCCC
1 TATGAAATTTTGATAACCACAC
* * *
2327 TATAAAATTTTGGTAACCACAT
1 TATGAAATTTTGATAACCACAC
* ***
2349 TATGAAATTGTGATTGTCACAC
1 TATGAAATTTTGATAACCACAC
* * *
2371 TATGGAATTGTGATAA-C-CTC
1 TATGAAATTTTGATAACCACAC
* *
2391 TATGAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCACAC
** **
2413 TATGACTTTTTGATAACCTTAC
1 TATGAAATTTTGATAACCACAC
*
2435 TATGATATTTTGATAAC
1 TATGAAATTTTGATAAC
2452 AACATAGAGA
Statistics
Matches: 142, Mismatches: 41, Indels: 10
0.74 0.21 0.05
Matches are distributed among these distances:
19 12 0.08
20 18 0.13
21 5 0.04
22 107 0.75
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAC
Found at i:2737 original size:22 final size:22
Alignment explanation
Indices: 2696--2737 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
2686 TTTAATTTAA
2696 TTAAATGAAAATAGAGTTTTTT
1 TTAAATGAAAATAGAGTTTTTT
2718 TTAAA-GAAAATAGAGTTTTT
1 TTAAATGAAAATAGAGTTTTT
2738 AGTATAGTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (22 bp):
TTAAATGAAAATAGAGTTTTTT
Found at i:2974 original size:8 final size:8
Alignment explanation
Indices: 2961--2988 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
2951 CATATTGTGA
2961 TAGTTAAC
1 TAGTTAAC
2969 TAGTTAAC
1 TAGTTAAC
2977 TAGTTAAC
1 TAGTTAAC
2985 TAGT
1 TAGT
2989 AAAAAGAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (8 bp):
TAGTTAAC
Done.