Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005919.1 Corchorus capsularis cultivar CVL-1 contig05937, 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: 15418
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.37
Found at i:6 original size:1 final size:1
Alignment explanation
Indices: 1--28 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
29 AAATTACTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3898 original size:12 final size:12
Alignment explanation
Indices: 3881--3907 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3871 GATTTGAGGG
3881 TACTTGTTTATA
1 TACTTGTTTATA
3893 TACTTGTTTATA
1 TACTTGTTTATA
3905 TAC
1 TAC
3908 ACTGATGTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.11, G:0.07, T:0.56
Consensus pattern (12 bp):
TACTTGTTTATA
Found at i:9855 original size:21 final size:21
Alignment explanation
Indices: 9807--9856 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
9797 TTTGGATGAG
* **
9807 ATCAAATTTTGGAGTTTGATT
1 ATCAAAATTTGGAGTTTGACC
* *
9828 ATTAAAATTTGGATTTTGACC
1 ATCAAAATTTGGAGTTTGACC
9849 ATCAAAAT
1 ATCAAAAT
9857 ATAGCAAAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (21 bp):
ATCAAAATTTGGAGTTTGACC
Found at i:11897 original size:22 final size:22
Alignment explanation
Indices: 11872--11915 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
11862 AACCTCCCTA
*
11872 TGAAAATTTGATAACTACACTG
1 TGAAAATTTGAGAACTACACTG
* *
11894 TGAAATTTTGGGAACTACACTG
1 TGAAAATTTGAGAACTACACTG
11916 AAATTTCGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (22 bp):
TGAAAATTTGAGAACTACACTG
Found at i:12106 original size:22 final size:21
Alignment explanation
Indices: 12081--12155 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 21
12071 CTCTATGTAT
12081 TTTTGATAACCTCTCCATAAAA
1 TTTTGATAACCTC-CCATAAAA
*
12103 TTTTCATAACCTCCCTATAAAA
1 TTTTGATAACCTCCC-ATAAAA
* *
12125 TTTTGTTATCCTCCC-TAGGAAA
1 TTTTGATAACCTCCCATA--AAA
12147 TTTTGATAA
1 TTTTGATAA
12156 ACACAATTCC
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
20 2 0.05
21 2 0.05
22 40 0.91
ACGTcount: A:0.32, C:0.21, G:0.07, T:0.40
Consensus pattern (21 bp):
TTTTGATAACCTCCCATAAAA
Found at i:12199 original size:22 final size:21
Alignment explanation
Indices: 12171--12357 Score: 135
Period size: 22 Copynumber: 8.6 Consensus size: 21
12161 ATTCCCTCCC
*
12171 TATGAAATTTTGTTAACTTTCA
1 TATGAAATTTTGATAAC-TTCA
* *
12193 TATGAAATTTT-ATTAACATCC
1 TATGAAATTTTGA-TAACTTCA
* * **
12214 TAAGAAATTTTGGTAACCTTTT
1 TATGAAATTTTGATAA-CTTCA
* * *
12236 TATGAAATTTTGTTAACCTCTG
1 TATGAAATTTTGATAACTTC-A
* *
12258 TATGAAATTTTCATAACTACA
1 TATGAAATTTTGATAACTTCA
*
12279 CTATGAAGTTTTGATAACTTCTA
1 -TATGAAATTTTGATAACTTC-A
* *
12302 TATGAAATTTTGGTAACTACA
1 TATGAAATTTTGATAACTTCA
12323 CTATGAAATTTTGATAATCTTTC-
1 -TATGAAATTTTGATAA-C-TTCA
*
12346 TATGTAATTTTG
1 TATGAAATTTTG
12358 GTTTGATTGT
Statistics
Matches: 129, Mismatches: 27, Indels: 18
0.74 0.16 0.10
Matches are distributed among these distances:
21 18 0.14
22 107 0.83
23 2 0.02
24 2 0.02
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (21 bp):
TATGAAATTTTGATAACTTCA
Found at i:12284 original size:44 final size:44
Alignment explanation
Indices: 12236--12339 Score: 154
Period size: 44 Copynumber: 2.4 Consensus size: 44
12226 GTAACCTTTT
* *
12236 TATGAAATTTTGTTAACCTCTGTATGAAATTTTCATAACTACAC
1 TATGAAATTTTGATAACCTCTATATGAAATTTTCATAACTACAC
* * **
12280 TATGAAGTTTTGATAACTTCTATATGAAATTTTGGTAACTACAC
1 TATGAAATTTTGATAACCTCTATATGAAATTTTCATAACTACAC
12324 TATGAAATTTTGATAA
1 TATGAAATTTTGATAA
12340 TCTTTCTATG
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.41
Consensus pattern (44 bp):
TATGAAATTTTGATAACCTCTATATGAAATTTTCATAACTACAC
Found at i:12328 original size:66 final size:62
Alignment explanation
Indices: 12171--12339 Score: 162
Period size: 66 Copynumber: 2.6 Consensus size: 62
12161 ATTCCCTCCC
* *
12171 TATGAAATTTTGTTAACTTTCATATGAAATTTTATTAACATCCTAAGAAATTTTGGTAACCTTTT
1 TATGAAATTTTGTTAAC--TCATATGAAATTTTA-TAACATCCTAAGAAATTTTGATAACCTTTA
* * *
12236 TATGAAATTTTGTTAACCTCTGTATGAAATTTTCATAAC-TACACTATGAAGTTTTGATAA-CTT
1 TATGAAATTTTGTTAA-CTC-ATATGAAATTTT-ATAACAT-C-CTAAGAAATTTTGATAACCTT
12299 CTA
61 -TA
*
12302 TATGAAATTTTGGTAACTACACTATGAAATTTTGATAA
1 TATGAAATTTTGTTAACT-CA-TATGAAATTTT-ATAA
12340 TCTTTCTATG
Statistics
Matches: 88, Mismatches: 8, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
64 3 0.03
65 37 0.42
66 48 0.55
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (62 bp):
TATGAAATTTTGTTAACTCATATGAAATTTTATAACATCCTAAGAAATTTTGATAACCTTTA
Found at i:12355 original size:44 final size:43
Alignment explanation
Indices: 12171--12359 Score: 150
Period size: 44 Copynumber: 4.3 Consensus size: 43
12161 ATTCCCTCCC
* * * **
12171 TATGAAATTTTGTTAACTTTCA-TATGAAATTTT-ATTAACATCC
1 TATGAAATTTTGGTAAC-TACACTATGAAATTTTGA-TAACTTTA
* *** * * *
12214 TAAGAAATTTTGGTAACCT-TTTTATGAAATTTTGTTAACCTCTG
1 TATGAAATTTTGGTAA-CTACACTATGAAATTTTGATAA-CTTTA
** *
12258 TATGAAATTTTCATAACTACACTATGAAGTTTTGATAACTTCTA
1 TATGAAATTTTGGTAACTACACTATGAAATTTTGATAACTT-TA
*
12302 TATGAAATTTTGGTAACTACACTATGAAATTTTGATAATCTTTC
1 TATGAAATTTTGGTAACTACACTATGAAATTTTGATAA-CTTTA
*
12346 TATGTAATTTTGGT
1 TATGAAATTTTGGT
12360 TTGATTGTCA
Statistics
Matches: 115, Mismatches: 24, Indels: 13
0.76 0.16 0.09
Matches are distributed among these distances:
43 33 0.29
44 79 0.69
45 3 0.03
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (43 bp):
TATGAAATTTTGGTAACTACACTATGAAATTTTGATAACTTTA
Found at i:12778 original size:2 final size:2
Alignment explanation
Indices: 12733--12762 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12723 ACACACACAA
12733 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12763 GAACTTAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14342 original size:22 final size:22
Alignment explanation
Indices: 14332--14867 Score: 164
Period size: 22 Copynumber: 24.6 Consensus size: 22
14322 ATGATCTCAT
14332 TATGAAATTTTGATAATCTTCC
1 TATGAAATTTTGATAATCTTCC
* * *
14354 TATGAAATTTTAATAA-CAATAC
1 TATGAAATTTTGATAATC-TTCC
* * * * **
14376 TATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAATCTTCC
* ** * *
14398 TAT-AATTTTTTTTAACCTTCT
1 TATGAAATTTTGATAATCTTCC
* *
14419 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAATCTTCC
* * *
14441 TAAGGAATTTTGA-AGATC-TCAA
1 TATGAAATTTTGATA-ATCTTC-C
*
14463 TATAAAATTTTGATAA-CTTTCC
1 TATGAAATTTTGATAATC-TTCC
* * **
14485 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAATCTTC-C
* * *
14508 TATGAGATGTTGATAA-CCTCC
1 TATGAAATTTTGATAATCTTCC
* * ** *
14529 ATATGATATATTGATAA-CCGCGT
1 -TATGAAATTTTGATAATCTTC-C
* * *
14552 TATGAAAATTTAAAAATC-TCC
1 TATGAAATTTTGATAATCTTCC
*
14573 ATATG-AATTGTT-AGTAATC-ACAC
1 -TATGAAATT-TTGA-TAATCTTC-C
* *
14596 TCTGAAATTTTGATAATC-ACAC
1 TATGAAATTTTGATAATCTTC-C
* * *
14618 TATGAAATTGTGATAACCTTGC
1 TATGAAATTTTGATAATCTTCC
14640 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AATCTTCC
* * * *
14663 AATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AATCTTCC
* *
14686 TATAAAATTTTGATAA-CTTTCT
1 TATGAAATTTTGATAATC-TTCC
*
14708 TATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAATCTTCC
* * *
14725 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAATCTTCC
** * *
14746 TATGATTTTTTGATAA-CCTCAT
1 TATGAAATTTTGATAATCTTC-C
* *
14768 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAATCTTCC
* * *
14790 TATGAAATTTTGAT-CTACATAC
1 TATGAAATTTTGATAAT-CTTCC
* * *
14812 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAATCTTCC
* *
14834 TATAAAATTTTGAT-ATCCTCC
1 TATGAAATTTTGATAATCTTCC
*
14855 -CTGAAATTTTGAT
1 TATGAAATTTTGAT
14868 TACTCCATAA
Statistics
Matches: 380, Mismatches: 102, Indels: 66
0.69 0.19 0.12
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
20 11 0.03
21 35 0.09
22 255 0.67
23 66 0.17
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAATCTTCC
Found at i:14674 original size:23 final size:23
Alignment explanation
Indices: 14644--14701 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
14634 CCTTGCTATG
* *
14644 AAATTTTGATAAATCTTCCAATA
1 AAATTTTGATAAACCTCCCAATA
*
14667 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACCTCCCAATA
14690 AAATTTTGATAA
1 AAATTTTGATAA
14702 CTTTCTTATG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.38
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCAATA
Found at i:14816 original size:44 final size:44
Alignment explanation
Indices: 14332--15365 Score: 241
Period size: 44 Copynumber: 24.0 Consensus size: 44
14322 ATGATCTCAT
* * *
14332 TATGAAATTTTGATAATCTTCCTATGAAATTTTAATAACAAT-AC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAAC-ATCAC
* * * *** * ** * *
14376 TATGGAATTTCGAGAACCTTTTTAT-AATTTTTTTTAACCTTC-T
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAA-CATCAC
* * * * *
14419 TATGAAATTTTGTTAATCTCCCTAAGGAATTTTGA-AGATC-TCAA
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATA-A-CATCAC
* * * * *
14463 TATAAAATTTTGATAACTTTCCAATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAA-CATCAC
* * * * * ** **
14508 TATGAGATGTTGATAACCTCCATATGATATATTGATAACCGCGT
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATCAC
* * * * *
14552 TATGAAAATTTAAAAATCTCCATATG-AATTGTT-AGTAATCA-CAC
1 TATGAAATTTTGATAACCTCCCTATGAAATT-TTGA-TAA-CATCAC
* * * * * * **
14596 TCTGAAATTTTGATAATCACACTATGAAATTGTGATAACCTTGC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATCAC
* * * * * *
14640 TATGAAATTTTGATAAATCTTCCAATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTCCCTATGAAATTTTGAT-AACATCAC
* * * * *
14686 TATAAAATTTTGATAACTTTCTTATGAAATCTTGATAAC-T-AC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATCAC
** * *
14728 ----AAATTTTGATAACCTCCCTATGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATCAC
* * *
14768 TATGAAATTTTGTTAATCTCCCTATGAAATTTTGATCTACAT-AC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGAT-AACATCAC
* * * *
14812 TATGAAATTTTGATAACC-CTCTTATAAAATTTTGATATCCTC-C
1 TATGAAATTTTGATAACCTC-CCTATGAAATTTTGATAACATCAC
* * * * * * *
14855 -CTGAAATTTTGATTA-CTCCATAATAAAAGTTTAATAACCTTC-C
1 TATGAAATTTTGATAACCTCCCT-ATGAAATTTTGATAA-CATCAC
* * *
14898 --T--AA-TTTGGTAACCAT-ACTATGAAATTTTGATAACCTC-C
1 TATGAAATTTTGATAACC-TCCCTATGAAATTTTGATAACATCAC
* *
14936 TA-G-AA-----AT-A-C-CACTATGAAATTTTTG-TAATCA-CAT
1 TATGAAATTTTGATAACCTCCCTATGAAA-TTTTGATAA-CATCAC
* * ** * **
14970 TCTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTCTT
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATCAC
* * * *
15014 TAT-ACAATTTTGTTGACC-CCTTTATGAAATTCTT-AT-A-ATCAT
1 TATGA-AATTTTGATAACCTCC-CTATGAAATT-TTGATAACATCAC
* * * * * * * *
15056 TATGTAATTTTGATAATCTCGCTTTGAATTTTTGATAATAACGC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATCAC
* ** *
15100 TATGAAATTTTGATAATCTTTCTAT-AAATTTTGATAATCCGATCTC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAA--C-ATCAC
* * * * * * * *
15146 TATGAAATTTCGATAATCACTCTATGAGA-TTGGATAACCT-TC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATCAC
* * * * *
15188 TATCAAATTTTGGT-A-CTCCTTATGAAATTGAGACTTTTATAACCTTCA-
1 TATGAAATTTTGATAACCTCCCTATGAAA-T-----TTTGATAA-CATCAC
* ** * * *
15236 TATGAAATTTTGATAACCACAATATAAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATCAC
* * *
15280 CATGAAATATT-AGTAACCT-CCTAATGAAATTTTGTTAACCA-CAC
1 TATGAAATTTTGA-TAACCTCCCT-ATGAAATTTTGATAA-CATCAC
* *
15324 TATGAAATTCTT-ATAACCTCGCTATGACATTTTGATAACATC
1 TATGAAATT-TTGATAACCTCCCTATGAAATTTTGATAACATC
15366 TTTGATAACC
Statistics
Matches: 713, Mismatches: 199, Indels: 156
0.67 0.19 0.15
Matches are distributed among these distances:
33 13 0.02
34 8 0.01
35 2 0.00
36 3 0.00
38 33 0.05
39 19 0.03
40 15 0.02
41 9 0.01
42 67 0.09
43 73 0.10
44 307 0.43
45 81 0.11
46 51 0.07
47 8 0.01
48 14 0.02
49 2 0.00
50 8 0.01
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.40
Consensus pattern (44 bp):
TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATCAC
Found at i:15154 original size:25 final size:23
Alignment explanation
Indices: 14972--15361 Score: 134
Period size: 22 Copynumber: 17.6 Consensus size: 23
14962 AATCACATTC
* *
14972 TGAAAATTTGATAA-CCTCTTTA
1 TGAAATTTTGATAATCCTCTCTA
*
14994 TGAAATTTTGATAA-CCTCTTTA
1 TGAAATTTTGATAATCCTCTCTA
* * * *
15016 T-ACAATTTTGTTGA-CCCCTTTA
1 TGA-AATTTTGATAATCCTCTCTA
*
15038 TGAAATTCTT-ATAAT-C-AT-TA
1 TGAAATT-TTGATAATCCTCTCTA
* * *
15058 TGTAATTTTGATAAT-CTCGCTT
1 TGAAATTTTGATAATCCTCTCTA
* ** *
15080 TGAATTTTTGATAAT-AACGCTA
1 TGAAATTTTGATAATCCTCTCTA
*
15102 TGAAATTTTGATAAT-CTTTCTA
1 TGAAATTTTGATAATCCTCTCTA
15124 T-AAATTTTGATAATCCGATCTCTA
1 TGAAATTTTGATAATCC--TCTCTA
* *
15148 TGAAATTTCGATAAT-CACTCTA
1 TGAAATTTTGATAATCCTCTCTA
* *
15170 TGAGA-TTGGATAA-CCT-TCTA
1 TGAAATTTTGATAATCCTCTCTA
* * * *
15190 TCAAATTTTGGTACTCCT-TATGAAA
1 TGAAATTTTGATAATCCTCTCT---A
*
15215 TTGAGACTTTT-ATAA-CCT-TCATA
1 -TGA-AATTTTGATAATCCTCTC-TA
* **
15238 TGAAATTTTGATAA-CCACAATA
1 TGAAATTTTGATAATCCTCTCTA
* * *
15260 TAAAATTTTGATAA-CCTCCCCA
1 TGAAATTTTGATAATCCTCTCTA
*
15282 TGAAATATT-AGTAA-CCTC-CTAA
1 TGAAATTTTGA-TAATCCTCTCT-A
* * *
15304 TGAAATTTTGTTAA-CCACACTA
1 TGAAATTTTGATAATCCTCTCTA
*
15326 TGAAATTCTT-ATAA-CCTCGCTA
1 TGAAATT-TTGATAATCCTCTCTA
*
15348 TGACATTTTGATAA
1 TGAAATTTTGATAA
15362 CATCTTTGAT
Statistics
Matches: 283, Mismatches: 57, Indels: 56
0.71 0.14 0.14
Matches are distributed among these distances:
19 2 0.01
20 21 0.07
21 37 0.13
22 181 0.64
23 8 0.03
24 7 0.02
25 17 0.06
26 5 0.02
27 5 0.02
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (23 bp):
TGAAATTTTGATAATCCTCTCTA
Done.