Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008223.1 Corchorus capsularis cultivar CVL-1 contig08244, 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: 18564
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:2324 original size:68 final size:69
Alignment explanation
Indices: 2210--2343 Score: 198
Period size: 68 Copynumber: 2.0 Consensus size: 69
2200 CTCGTGCTCT
* * * **
2210 TCCCTATCCTAGCTATTTTCCATTCACCACCATTTCTACACTGTTACTGACACA-TTAGAAAGCA
1 TCCCTATCCTAGCCATTTCCCATTCACCACCATTTCTACACCGTTACCAACACATTTAGAAAGCA
2274 CCTC
66 CCTC
* *
2278 TCCCTATCCTAGCCATTTCCCCTTCACCACCATTTCTACACCGTTACCAACGCATTTAGAAAGCA
1 TCCCTATCCTAGCCATTTCCCATTCACCACCATTTCTACACCGTTACCAACACATTTAGAAAGCA
2343 C
66 C
2344 GACGGCCACC
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
68 47 0.81
69 11 0.19
ACGTcount: A:0.26, C:0.37, G:0.07, T:0.30
Consensus pattern (69 bp):
TCCCTATCCTAGCCATTTCCCATTCACCACCATTTCTACACCGTTACCAACACATTTAGAAAGCA
CCTC
Found at i:7351 original size:1 final size:1
Alignment explanation
Indices: 7345--7369 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
7335 AAAATTGCAA
7345 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
7370 GCAATATTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:10191 original size:22 final size:22
Alignment explanation
Indices: 10166--10637 Score: 188
Period size: 22 Copynumber: 21.6 Consensus size: 22
10156 ATGATCCCAT
10166 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* ** *
10188 TATGAAATTTTAATAACGATAC
1 TATGAAATTTTGATAACCTTCC
* * * **
10210 TATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
** *
10232 TAT-AAATTTTTTTAACCTTCT
1 TATGAAATTTTGATAACCTTCC
* * *
10253 TATGAAATTTGGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
10275 TAAGGAATTTTGA-AGACC-TCAA
1 TATGAAATTTTGATA-ACCTTC-C
10297 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* * **
10319 AATGAAATTTTAATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* *
10342 TATGAGATGTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * ****
10363 ATATGATATATTGATAACCAGGT
1 -TATGAAATTTTGATAACCTTCC
* * * * *
10386 TATGAAAATTTAAAAACCTACA
1 TATGAAATTTTGATAACCTTCC
* *
10408 TATG-AATTGTT-AGTAATC-ACAC
1 TATGAAATT-TTGA-TAACCTTC-C
* *
10430 TTTGAAATTTTGATAATCACAT--
1 TATGAAATTTTGATAA-C-CTTCC
*
10452 TATGAAATTGTGATAACC-TCGC
1 TATGAAATTTTGATAACCTTC-C
*
10474 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
* *
10497 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTTCC
* * *
10520 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTTCC
*
10542 TATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTTCC
* *
10559 TA-AAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
** * *
10580 TATGATTTTTTTATAACC-TCAT
1 TATGAAATTTTGATAACCTTC-C
* * *
10602 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
10624 TATGAAATTTTGAT
1 TATGAAATTTTGAT
10638 CTACATACTA
Statistics
Matches: 329, Mismatches: 90, Indels: 62
0.68 0.19 0.13
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
19 1 0.00
20 1 0.00
21 30 0.09
22 219 0.67
23 62 0.19
24 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:10504 original size:23 final size:23
Alignment explanation
Indices: 10473--10557 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
10463 GATAACCTCG
*
10473 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAATCTTC
* *
10496 CTATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAATCTTC
*
10519 CTATAAAATTTTGATAACT-TTC
1 CTATAAAATTTTGATAAATCTTC
* * *
10541 TTATGAAATCTTGATAA
1 CTATAAAATTTTGATAA
10558 CTAAAAATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 16 0.30
23 37 0.70
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (23 bp):
CTATAAAATTTTGATAAATCTTC
Found at i:10556 original size:45 final size:43
Alignment explanation
Indices: 10434--10557 Score: 124
Period size: 45 Copynumber: 2.7 Consensus size: 43
10424 TCACACTTTG
** * *
10434 AAATTTTGATAATCACATTATGAAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAATTTC-TTATGAAATT-TGATAAACCTCCCTATA
* *
10478 AAATTTTGATAAATCTTCCTATAAAATTTTGATAAACCTCCCTATA
1 AAATTTTGAT-AAT-TTCTTATGAAA-TTTGATAAACCTCCCTATA
10524 AAATTTTGATAACTTTCTTATGAAATCTTGATAA
1 AAATTTTGATAA-TTTCTTATGAAAT-TTGATAA
10558 CTAAAAATTT
Statistics
Matches: 66, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
44 11 0.17
45 31 0.47
46 24 0.36
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.40
Consensus pattern (43 bp):
AAATTTTGATAATTTCTTATGAAATTTGATAAACCTCCCTATA
Found at i:10748 original size:19 final size:20
Alignment explanation
Indices: 10692--10742 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
10682 AACTAAAATA
*
10692 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTTCC
*
10712 TG-AATTTTGATATCCTTCT
1 TGAAATTTTGATATCCTTCC
10731 TGAAATTTTGAT
1 TGAAATTTTGAT
10743 TACTTCATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.47
Consensus pattern (20 bp):
TGAAATTTTGATATCCTTCC
Found at i:10873 original size:22 final size:22
Alignment explanation
Indices: 10848--10971 Score: 92
Period size: 22 Copynumber: 5.6 Consensus size: 22
10838 AATCACATTT
10848 TGAAAATTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
*
10870 TGAAATTTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
* * * *
10892 T-AAAATTTTGTTGACCCCTCTA
1 TGAAAA-TTTGATAACCTCTTTA
* * *
10914 TG-AAATTCTGATAATCACATTA
1 TGAAAATT-TGATAACCTCTTTA
* * *
10936 TGTAATTTTGATAACCTCGCTT-
1 TGAAAATTTGATAACCTC-TTTA
*
10958 TGAAATTTTGATAA
1 TGAAAATTTGATAA
10972 TCCGATCTCT
Statistics
Matches: 80, Mismatches: 17, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
21 5 0.06
22 69 0.86
23 6 0.08
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTTTA
Found at i:10943 original size:44 final size:44
Alignment explanation
Indices: 10823--10973 Score: 160
Period size: 44 Copynumber: 3.4 Consensus size: 44
10813 AGAAATACCA
* *
10823 CTATGAAATTTTTG-TAATCACATTTTGAAAATTTGATAACCTCT
1 CTATGAAA-TTTTGATAATCACATTATGAAATTTTGATAACCTCT
* * * * * * * *
10867 TTATGAAATTTTGATAACCTCTTTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCT
* * *
10911 CTATGAAATTCTGATAATCACATTATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCT
*
10955 CTTTGAAATTTTGATAATC
1 CTATGAAATTTTGATAATC
10974 CGATCTCTAT
Statistics
Matches: 83, Mismatches: 23, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
43 5 0.06
44 78 0.94
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (44 bp):
CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCT
Found at i:11086 original size:22 final size:23
Alignment explanation
Indices: 11057--11111 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
11047 AAATTGGGAC
* *
11057 TTTT-ATAACCTTCA-TATGAAA
1 TTTTGATAACCTACACTATAAAA
11078 TTTTGATAACC-ACACTATAAAA
1 TTTTGATAACCTACACTATAAAA
11100 TTTTGATAACCT
1 TTTTGATAACCT
11112 CCTCATGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 6 0.21
22 23 0.79
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.40
Consensus pattern (23 bp):
TTTTGATAACCTACACTATAAAA
Found at i:11254 original size:22 final size:22
Alignment explanation
Indices: 11222--11383 Score: 105
Period size: 22 Copynumber: 7.3 Consensus size: 22
11212 TTGTGATAAT
* *
11222 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
* *
11244 TAACCAACCTAAGAGATTTTAA
1 TAACCAACCTATGAAATTTTAA
* **
11266 TAACCTGATCCTATGAAATTTTGG
1 TAACC--AACCTATGAAATTTTAA
**
11290 TAACC-ACACTATGAAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
* *
11312 TAACC-ACACTATGGAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
** *
11334 TAACC-TTCTGATGAAATTATAA
1 TAACCAACCT-ATGAAATTTTAA
* * *
11356 TAACCATCTTATGAAATTTTGA
1 TAACCAACCTATGAAATTTTAA
11378 TAACCA
1 TAACCA
11384 CATAGAGACA
Statistics
Matches: 114, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
21 3 0.03
22 92 0.81
23 2 0.02
24 17 0.15
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:11586 original size:20 final size:20
Alignment explanation
Indices: 11549--11591 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 20
11539 TATTAATATT
11549 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTAAAAAG
11568 TAAAATATT-AAATTTAAAAAG
1 TAAAA-ATTGAAA-TTAAAAAG
11589 TAA
1 TAA
11592 TAGTAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 8 0.38
20 5 0.24
21 8 0.38
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (20 bp):
TAAAAATTGAAATTAAAAAG
Done.