Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009120.1 Corchorus capsularis cultivar CVL-1 contig09141, 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: 23075
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:114 original size:21 final size:21
Alignment explanation
Indices: 90--145 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
80 AAAAAGTGGG
90 GCGGTATTTAGCAAAACTAGA
1 GCGGTATTTAGCAAAACTAGA
*
111 GCGGTATTTAGCAAAACTAGG
1 GCGGTATTTAGCAAAACTAGA
*
132 GTGGTATTTAGCAA
1 GCGGTATTTAGCAA
146 CCCCATATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.34, C:0.12, G:0.27, T:0.27
Consensus pattern (21 bp):
GCGGTATTTAGCAAAACTAGA
Found at i:11830 original size:29 final size:28
Alignment explanation
Indices: 11771--11830 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
11761 ATGTTAATTA
**
11771 AAAAATCATAAACTATTTTTTTGCTACTT
1 AAAAATCATAAACTATTTAATTGCTA-TT
11800 AAAAATCATAAACTATTAGTAATTGCT-TT
1 AAAAATCATAAACTATT--TAATTGCTATT
11829 AA
1 AA
11831 GAGGTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 21 0.78
31 6 0.22
ACGTcount: A:0.43, C:0.12, G:0.05, T:0.40
Consensus pattern (28 bp):
AAAAATCATAAACTATTTAATTGCTATT
Found at i:17636 original size:28 final size:29
Alignment explanation
Indices: 17575--17646 Score: 92
Period size: 28 Copynumber: 2.5 Consensus size: 29
17565 GTTAGGTTGA
*
17575 GGGGGCAAAACGTCTCAAAATTAAAGTTC
1 GGGGGCAAAATGTCTCAAAATTAAAGTTC
* * *
17604 AGGGGCAAAATGTC-CAAGATTGAAGTTC
1 GGGGGCAAAATGTCTCAAAATTAAAGTTC
*
17632 GGGGGAAAAATGTCT
1 GGGGGCAAAATGTCT
17647 AAACGCTACA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
28 24 0.67
29 12 0.33
ACGTcount: A:0.36, C:0.14, G:0.29, T:0.21
Consensus pattern (29 bp):
GGGGGCAAAATGTCTCAAAATTAAAGTTC
Found at i:20189 original size:15 final size:15
Alignment explanation
Indices: 20166--20195 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20156 ATCGGTTGAA
*
20166 ATATTGTGTATCGTG
1 ATATCGTGTATCGTG
20181 ATATCGTGTATCGTG
1 ATATCGTGTATCGTG
20196 GCAGCCTGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.10, G:0.27, T:0.43
Consensus pattern (15 bp):
ATATCGTGTATCGTG
Found at i:21259 original size:22 final size:22
Alignment explanation
Indices: 21234--21504 Score: 78
Period size: 22 Copynumber: 12.5 Consensus size: 22
21224 CACATTTTGA
*
21234 AAATTTTGATAATCACACTATG
1 AAATTTTGATAACCACACTATG
* * *
21256 AAATTGTGATAACCTCGCTATG
1 AAATTTTGATAACCACACTATG
** *
21278 AAATTTTGATAAATCTTCA-TATA
1 AAATTTTGAT-AA-CCACACTATG
* * *
21301 AAATTTTAATAAACCTGC-CTATA
1 AAATTTTGAT-AACC-ACACTATG
** *
21324 AAATTTTGATAACTTTC-TTATG
1 AAATTTTGATAAC-CACACTATG
*
21346 AAATCTTTGAT----A-ACTA-C
1 AAAT-TTTGATAACCACACTATG
* * *
21363 AAATTTTGATAAGCTCCCTATG
1 AAATTTTGATAACCACACTATG
** ****
21385 ATTTTTTGATAACCTTTTTATG
1 AAATTTTGATAACCACACTATG
* * * *
21407 AAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAACCACACTATG
* *
21429 AAATTTTGATCTA-CATACTATG
1 AAATTTTGAT-AACCACACTATG
**
21451 AAATTTTGATAACC-CTGTTATG
1 AAATTTTGATAACCAC-ACTATG
* * *
21473 AAATTTTGAAAACTAAACTATG
1 AAATTTTGATAACCACACTATG
*
21495 AAAATTTGAT
1 AAATTTTGAT
21505 CAGTTTCATA
Statistics
Matches: 181, Mismatches: 51, Indels: 34
0.68 0.19 0.13
Matches are distributed among these distances:
16 6 0.03
17 4 0.02
18 2 0.01
21 4 0.02
22 124 0.69
23 38 0.21
24 3 0.02
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.41
Consensus pattern (22 bp):
AAATTTTGATAACCACACTATG
Found at i:21306 original size:23 final size:23
Alignment explanation
Indices: 21278--21358 Score: 83
Period size: 23 Copynumber: 3.5 Consensus size: 23
21268 CCTCGCTATG
21278 AAATTTTGATAAATCTTCATATA
1 AAATTTTGATAAATCTTCATATA
* * * *
21301 AAATTTTAATAAACCTGCCTATA
1 AAATTTTGATAAATCTTCATATA
* * *
21324 AAATTTTGATAACT-TTCTTATG
1 AAATTTTGATAAATCTTCATATA
21346 AAATCTTTGATAA
1 AAAT-TTTGATAA
21359 CTACAAATTT
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
22 9 0.19
23 38 0.81
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.42
Consensus pattern (23 bp):
AAATTTTGATAAATCTTCATATA
Found at i:21586 original size:19 final size:19
Alignment explanation
Indices: 21522--21580 Score: 82
Period size: 19 Copynumber: 3.1 Consensus size: 19
21512 ATATGAAATT
*
21522 TATCCTCACTGAATTTTGA
1 TATCCTCCCTGAATTTTGA
*
21541 TATCCTCCCTGAATTTTGG
1 TATCCTCCCTGAATTTTGA
*
21560 TATCCTCCTTGAAATTTTGA
1 TATCCTCCCTG-AATTTTGA
21580 T
1 T
21581 TACTCCATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
19 27 0.77
20 8 0.23
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (19 bp):
TATCCTCCCTGAATTTTGA
Found at i:21718 original size:22 final size:22
Alignment explanation
Indices: 21687--21878 Score: 138
Period size: 22 Copynumber: 8.6 Consensus size: 22
21677 AATCACATTT
*
21687 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
*
21709 TGAAATTTTGATAACATCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * * * *
21731 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTTTA
* * *
21753 TGAAATTTTGATAATCACATTA
1 TGAAATTTTGATAACCTCTTTA
* * *
21775 TGTAATTTTGATAATCTCGCTT-
1 TGAAATTTTGATAACCTC-TTTA
** **
21797 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTCTTTA
*
21819 TGAAATTTTGATAA--TCTTCA
1 TGAAATTTTGATAACCTCTTTA
*
21839 TAAAAATTTTGATAATCCTATCTTTA
1 T-GAAATTTTGATAA-CC--TCTTTA
*
21865 TGAAATTTCGATAA
1 TGAAATTTTGATAA
21879 TTACTCTATG
Statistics
Matches: 130, Mismatches: 32, Indels: 13
0.74 0.18 0.07
Matches are distributed among these distances:
20 3 0.02
21 13 0.10
22 95 0.73
23 2 0.02
25 11 0.08
26 6 0.05
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.42
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:21782 original size:44 final size:43
Alignment explanation
Indices: 21661--21853 Score: 167
Period size: 44 Copynumber: 4.4 Consensus size: 43
21651 AGAAATAGCA
* *
21661 CTATGAAATTTTTTG-TAATCACATTTTGAAAATTTGATAACCTCT
1 CTATGAAA--TTTTGATAA-CACATTATGAAATTTTGATAACCTCT
* * * * * *
21706 TTATGAAATTTTGATAACATCTTTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAACA-CATTATGAAATTTTGATAACCTCT
* * *
21750 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAATCTCG
1 CTATGAAATTTTGATAA-CACATTATGAAATTTTGATAACCTCT
* * *
21794 CTTTGAAATTTTGATAACAACACTATGAAATTTTGATAATCT-T
1 CTATGAAATTTTGATAAC-ACATTATGAAATTTTGATAACCTCT
*
21837 C-ATAAAAATTTTGATAA
1 CTAT-GAAATTTTGATAA
21854 TCCTATCTTT
Statistics
Matches: 120, Mismatches: 23, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
42 1 0.01
43 21 0.17
44 89 0.74
45 9 0.08
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (43 bp):
CTATGAAATTTTGATAACACATTATGAAATTTTGATAACCTCT
Found at i:22007 original size:22 final size:22
Alignment explanation
Indices: 21954--22015 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
21944 TAACCATCGT
*
21954 ATGAAATTTTGATAACCACACC
1 ATGAAATTTTGATAACCTCACC
*
21976 ATAAAATTTTGATAACCTC-CC
1 ATGAAATTTTGATAACCTCACC
*
21997 GATGAAGTTTTAGA-AACCT
1 -ATGAAATTTT-GATAACCT
22016 TCTAATGGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 30 0.88
23 2 0.06
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (22 bp):
ATGAAATTTTGATAACCTCACC
Found at i:22177 original size:24 final size:22
Alignment explanation
Indices: 22121--22318 Score: 111
Period size: 22 Copynumber: 8.9 Consensus size: 22
22111 ATTAACTACC
* *
22121 CTATGAAATTTCAATAACCAAC
1 CTATGAAATTTTAATAACCAAT
*
22143 CTAAGAAATTTTAATAACCTAAT
1 CTATGAAATTTTAATAACC-AAT
** *
22166 CTTATGAAATTTTGGTAACCACT
1 C-TATGAAATTTTAATAACCAAT
** *
22189 CTATGAAATTTTGGTAACTACA-
1 CTATGAAATTTTAATAACCA-AT
**
22211 CTATGAAATTTTGGTAACCACA-
1 CTATGAAATTTTAATAACCA-AT
**
22233 CTATGAAATTTTGGTAACCACA-
1 CTATGAAATTTTAATAACCA-AT
* *
22255 CTATGGAATTTTGATAACC--T
1 CTATGAAATTTTAATAACCAAT
* * *
22275 CCTCATGGAATTATAATAATC-AT
1 -CT-ATGAAATTTTAATAACCAAT
*
22298 CTTATGAAATTTTGATAACCA
1 C-TATGAAATTTTAATAACCA
22319 CATAGAAACA
Statistics
Matches: 148, Mismatches: 19, Indels: 17
0.80 0.10 0.09
Matches are distributed among these distances:
21 2 0.01
22 123 0.83
23 8 0.05
24 15 0.10
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.35
Consensus pattern (22 bp):
CTATGAAATTTTAATAACCAAT
Found at i:22185 original size:46 final size:44
Alignment explanation
Indices: 22113--22320 Score: 165
Period size: 44 Copynumber: 4.7 Consensus size: 44
22103 TTGTGATAAT
* *** *
22113 TAACTACCCTATGAAATTTCAATAACCA-ACCTAAGAAATTTTAA
1 TAACTACACTATGAAATTTTGGTAACCACA-CTATGAAATTTTAA
* **
22157 TAACCTA-ATCTTATGAAATTTTGGTAACCACTCTATGAAATTTTGG
1 TAA-CTACA-C-TATGAAATTTTGGTAACCACACTATGAAATTTTAA
**
22203 TAACTACACTATGAAATTTTGGTAACCACACTATGAAATTTTGG
1 TAACTACACTATGAAATTTTGGTAACCACACTATGAAATTTTAA
* * * * * *
22247 TAACCACACTATGGAATTTTGATAACCTC-CTCATGGAATTATAA
1 TAACTACACTATGAAATTTTGGTAACCACACT-ATGAAATTTTAA
*
22291 TAA-T-CATCTTATGAAATTTTGATAACCACA
1 TAACTACA-C-TATGAAATTTTGGTAACCACA
22321 TAGAAACAAG
Statistics
Matches: 135, Mismatches: 20, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
42 2 0.01
43 3 0.02
44 91 0.67
45 8 0.06
46 31 0.23
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (44 bp):
TAACTACACTATGAAATTTTGGTAACCACACTATGAAATTTTAA
Found at i:22225 original size:44 final size:44
Alignment explanation
Indices: 22168--22273 Score: 176
Period size: 44 Copynumber: 2.4 Consensus size: 44
22158 AACCTAATCT
* *
22168 TATGAAATTTTGGTAACCACTCTATGAAATTTTGGTAACTACAC
1 TATGAAATTTTGGTAACCACACTATGAAATTTTGGTAACCACAC
22212 TATGAAATTTTGGTAACCACACTATGAAATTTTGGTAACCACAC
1 TATGAAATTTTGGTAACCACACTATGAAATTTTGGTAACCACAC
* *
22256 TATGGAATTTTGATAACC
1 TATGAAATTTTGGTAACC
22274 TCCTCATGGA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 58 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (44 bp):
TATGAAATTTTGGTAACCACACTATGAAATTTTGGTAACCACAC
Found at i:22304 original size:66 final size:66
Alignment explanation
Indices: 22121--22320 Score: 183
Period size: 66 Copynumber: 3.0 Consensus size: 66
22111 ATTAACTACC
** * * *
22121 CTATGAAATTTCAATAACCA-ACCTAAGAAATTTTAATAACCTAATCTTATGAAATTTTGGTAAC
1 CTATGAAATTTTGATAACTACA-CTATGAAATTATAATAACC--ATCTTATGAAATTTTGGTAAC
*
22185 CACT
63 CACA
* * ** *
22189 CTATGAAATTTTGGTAACTACACTATGAAATTTTGGTAACCA-CACTATGAAATTTTGGTAACCA
1 CTATGAAATTTTGATAACTACACTATGAAATTATAATAACCATC-TTATGAAATTTTGGTAACCA
22253 CA
65 CA
* * * *
22255 CTATGGAATTTTGATAACCT-C-CTCATGGAATTATAATAATCATCTTATGAAATTTTGATAACC
1 CTATGAAATTTTGATAA-CTACACT-ATGAAATTATAATAACCATCTTATGAAATTTTGGTAACC
22318 ACA
64 ACA
22321 TAGAAACAAG
Statistics
Matches: 109, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
65 3 0.03
66 70 0.64
67 3 0.03
68 32 0.29
69 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.34
Consensus pattern (66 bp):
CTATGAAATTTTGATAACTACACTATGAAATTATAATAACCATCTTATGAAATTTTGGTAACCAC
A
Found at i:22461 original size:6 final size:6
Alignment explanation
Indices: 22450--22475 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
22440 AGTATTGTAC
22450 GTGTTA GTGTTA GTGTTA GTGTTA GT
1 GTGTTA GTGTTA GTGTTA GTGTTA GT
22476 TTAATCTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (6 bp):
GTGTTA
Found at i:22634 original size:29 final size:31
Alignment explanation
Indices: 22601--22664 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
22591 TGGCAGTTTA
22601 GAAATATGTTTT-AAAA-AAGGGTACAATTG
1 GAAATATGTTTTAAAAATAAGGGTACAATTG
* *
22630 GAAATATGTTTTAAAAATAAGGTTACAGTTG
1 GAAATATGTTTTAAAAATAAGGGTACAATTG
22661 GAAA
1 GAAA
22665 ACATAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 12 0.39
30 4 0.13
31 15 0.48
ACGTcount: A:0.45, C:0.03, G:0.20, T:0.31
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAGGGTACAATTG
Found at i:22709 original size:2 final size:2
Alignment explanation
Indices: 22702--22742 Score: 66
Period size: 2 Copynumber: 20.5 Consensus size: 2
22692 TTCGAACTTT
22702 TA TA TA TA GT- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22743 CACTGCCTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 35 0.95
3 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Done.