Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007596.1 Corchorus capsularis cultivar CVL-1 contig07617, 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: 3209
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Found at i:2026 original size:22 final size:22
Alignment explanation
Indices: 2001--2600 Score: 228
Period size: 22 Copynumber: 27.6 Consensus size: 22
1991 ATGATCCCAT
2001 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* ** *
2023 TATGAAATTTTAATAACAATAC
1 TATGAAATTTTGATAACCTTCC
* * * **
2045 TATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
* ** *
2067 TAT-AATTTTTTTTAACCTTCT
1 TATGAAATTTTGATAACCTTCC
* * * *
2088 TATGCAATTTGGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
2110 TAAGAAATTTTGA-AGATC-TCAA
1 TATGAAATTTTGATA-ACCTTC-C
**
2132 TATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* * *
2155 TATGAGATGTTGATAACCTTCA
1 TATGAAATTTTGATAACCTTCC
* * *
2177 TATGATATATTGATAATCACGT--
1 TATGAAATTTTGATAA-C-CTTCC
* * *
2199 TATGAAAATTTAAAAACC-TCC
1 TATGAAATTTTGATAACCTTCC
*
2220 ATATG-AATTGTT-AGTAA--TTAGAC
1 -TATGAAATT-TTGA-TAACCTT--CC
* ** *
2243 TCTGAAATTTTGATATTC-ACAC
1 TATGAAATTTTGATAACCTTC-C
*
2265 TATGAAATTGTGATAACC-TCGC
1 TATGAAATTTTGATAACCTTC-C
*
2287 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
* *
2310 TATAAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
* *
2333 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTTCC
* ** *
2356 TATAAAATTTTGATAATTTTCT
1 TATGAAATTTTGATAACCTTCC
*
2378 TATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTTCC
* *
2395 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
** *
2416 TATGATTTTTTGATAACC-TCAT
1 TATGAAATTTTGATAACCTTC-C
* * *
2438 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
2460 TATGAAATTTTGATCTA-CATAC
1 TATGAAATTTTGAT-AACCTTCC
* *
2482 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
* * *
2504 TGTGAAATTTTGA-AA-ATTAAAC
1 TATGAAATTTTGATAACCTT--CC
* *
2526 TATGAAATTTAGATAACCTTCA
1 TATGAAATTTTGATAACCTTCC
*
2548 TATGAAATTTTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
2569 -CTG-AATTTTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
2588 T-TGAAATTTTGAT
1 TATGAAATTTTGAT
2601 TACTCCATAA
Statistics
Matches: 430, Mismatches: 110, Indels: 78
0.70 0.18 0.13
Matches are distributed among these distances:
16 11 0.03
17 2 0.00
19 19 0.04
20 13 0.03
21 31 0.07
22 256 0.60
23 92 0.21
24 6 0.01
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:2317 original size:23 final size:23
Alignment explanation
Indices: 2286--2393 Score: 146
Period size: 23 Copynumber: 4.7 Consensus size: 23
2276 GATAACCTCG
*
2286 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAATCTTC
2309 CTATAAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAATCTTC
* *
2332 CTATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAATCTTC
*
2355 CTATAAAATTTTGAT-AATTTTC
1 CTATAAAATTTTGATAAATCTTC
* * *
2377 TTATGAAATCTTGATAA
1 CTATAAAATTTTGATAA
2394 CTACAAATTT
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
22 16 0.21
23 59 0.79
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (23 bp):
CTATAAAATTTTGATAAATCTTC
Found at i:2606 original size:19 final size:20
Alignment explanation
Indices: 2550--2600 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
2540 AACCTTCATA
2550 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
*
2570 TG-AATTTTGATATCCTCCT
1 TGAAATTTTGATATCCTCCC
2589 TGAAATTTTGAT
1 TGAAATTTTGAT
2601 TACTCCATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:2731 original size:22 final size:22
Alignment explanation
Indices: 2706--2921 Score: 95
Period size: 22 Copynumber: 9.8 Consensus size: 22
2696 AATCACATTT
2706 TGAAAATTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
*
2728 TGAAATTTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
* * * *
2750 T-AAAATTTTGTTGACCCCTCTA
1 TGAAAA-TTTGATAACCTCTTTA
* * *
2772 TG-AAATTCTGATAATCACATTA
1 TGAAAATT-TGATAACCTCTTTA
* * *
2794 TGTAATTTTGATAACCTCGCTT-
1 TGAAAATTTGATAACCTC-TTTA
* ** **
2816 TGAAATTTTGATAACAACACTA
1 TGAAAATTTGATAACCTCTTTA
* *
2838 TGAAATTTTGATAATCT-TTCTA
1 TGAAAATTTGATAACCTCTT-TA
* *
2860 T-AAATTTTGATAATCCGATCTCTA
1 TGAAAATTTGATAA-CC--TCTTTA
* * *
2884 TG-AAATTTCGATAATCACTCTA
1 TGAAAATTT-GATAACCTCTTTA
*
2906 TG-AGATTTGATAACCT
1 TGAAAATTTGATAACCT
2922 TCTATCAAAT
Statistics
Matches: 147, Mismatches: 34, Indels: 27
0.71 0.16 0.13
Matches are distributed among these distances:
21 24 0.16
22 101 0.69
23 6 0.04
24 10 0.07
25 6 0.04
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTTTA
Found at i:2774 original size:44 final size:44
Alignment explanation
Indices: 2681--2851 Score: 139
Period size: 44 Copynumber: 3.9 Consensus size: 44
2671 AGAAATACCA
* * * *
2681 CTATGAAATTTTTG-TAATCACATTTTGAAAA-TTTGATAACCTCT
1 CTATGAAA-TTTTGATAACCACATTAT-AAAATTTTGATAACCCCG
* * * * * *
2725 TTATGAAATTTTGATAACCTCTTTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAACCACATTATAAAATTTTGATAACCCCG
* * ** *
2769 CTATGAAATTCTGATAATCACATTATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAACCACATTATAAAATTTTGATAACCCCG
* * * *
2813 CTTTGAAATTTTGATAACAACACTATGAAATTTTGATAA
1 CTATGAAATTTTGATAACCACATTATAAAATTTTGATAA
2852 TCTTTCTATA
Statistics
Matches: 100, Mismatches: 25, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
43 9 0.09
44 91 0.91
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.42
Consensus pattern (44 bp):
CTATGAAATTTTGATAACCACATTATAAAATTTTGATAACCCCG
Found at i:2822 original size:66 final size:66
Alignment explanation
Indices: 2725--2853 Score: 161
Period size: 66 Copynumber: 2.0 Consensus size: 66
2715 GATAACCTCT
* * * ** *
2725 TTATGAAATTTTGATAACCTCTTTATAAAATTTTGTTGACCCCTCTATGAAATTCTGATAATCAC
1 TTATGAAATTTTGATAACCTCCTTATAAAATTTTGATAACAACACTATGAAATTCTGATAATCAC
2790 A
66 A
* * *
2791 TTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAACACTATGAAATTTTGATAATC
1 TTATGAAATTTTGATAACCTC-CTTATAAAATTTTGATAACAACACTATGAAATTCTGATAATC
2854 TTTCTATAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
66 51 0.96
67 2 0.04
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (66 bp):
TTATGAAATTTTGATAACCTCCTTATAAAATTTTGATAACAACACTATGAAATTCTGATAATCAC
A
Found at i:2844 original size:88 final size:88
Alignment explanation
Indices: 2681--2847 Score: 212
Period size: 88 Copynumber: 1.9 Consensus size: 88
2671 AGAAATACCA
* * * **
2681 CTATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTC
1 CTATGAAATTTCTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
**
2746 TTTATAAAATTTTGTTGACCCCT
66 ACTATAAAATTTTGTTGACCCCT
* *
2769 CTATGAAA-TTCTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACA
1 CTATGAAATTTCTG-TAATCACATTATGAAAATTTGATAACCTC-CTTATGAAATTTTGATAACA
*
2832 ACACTATGAAATTTTG
64 ACACTATAAAATTTTG
2848 ATAATCTTTC
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
87 4 0.06
88 61 0.91
89 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (88 bp):
CTATGAAATTTCTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
ACTATAAAATTTTGTTGACCCCT
Found at i:3023 original size:22 final size:22
Alignment explanation
Indices: 2977--3023 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
2967 CTTCATATGG
*
2977 AATTTTGATAACCACACTATAA
1 AATTTTGATAACCACACCATAA
* *
2999 AATTTTGATAACCACCCCATGA
1 AATTTTGATAACCACACCATAA
3021 AAT
1 AAT
3024 ATTTAATGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.43, C:0.21, G:0.06, T:0.30
Consensus pattern (22 bp):
AATTTTGATAACCACACCATAA
Done.