Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013417.1 Corchorus capsularis cultivar CVL-1 contig13438, 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: 30259
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1386 original size:30 final size:30
Alignment explanation
Indices: 1340--1400 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
1330 CTTGTAGTGA
* *
1340 TTGGACGTTTTGTCCCTATAAACT-TCAATT
1 TTGGACATTTTATCCCT-TAAACTCTCAATT
*
1370 TTGGACATTTTATCCCTTAAATTCTCAATT
1 TTGGACATTTTATCCCTTAAACTCTCAATT
1400 T
1 T
1401 GAACCTCCGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 5 0.19
30 22 0.81
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.46
Consensus pattern (30 bp):
TTGGACATTTTATCCCTTAAACTCTCAATT
Found at i:3839 original size:21 final size:21
Alignment explanation
Indices: 3815--3858 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
3805 ACCATTTCTC
3815 ACGATGGTACCACTTCCGGAA
1 ACGATGGTACCACTTCCGGAA
3836 ACGATGGTACCACTTCCGGAA
1 ACGATGGTACCACTTCCGGAA
3857 AC
1 AC
3859 ATTCTTTCGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.30, G:0.23, T:0.18
Consensus pattern (21 bp):
ACGATGGTACCACTTCCGGAA
Found at i:5201 original size:91 final size:91
Alignment explanation
Indices: 5080--5262 Score: 348
Period size: 91 Copynumber: 2.0 Consensus size: 91
5070 CTCAACAAGT
5080 TTCGGCTCAAAGACCCAAATCCCATCACTGCCAACTTAGAGTTTCCCCAACCCGTTCGAGTTGAT
1 TTCGGCTCAAAGACCCAAATCCCATCACTGCCAACTTAGAGTTTCCCCAACCCGTTCGAGTTGAT
*
5145 GCCGTGGTGCTCGAGGGATGCGAGGA
66 GCCATGGTGCTCGAGGGATGCGAGGA
*
5171 TTCGGTTCAAAGACCCAAATCCCATCACTGCCAACTTAGAGTTTCCCCAACCCGTTCGAGTTGAT
1 TTCGGCTCAAAGACCCAAATCCCATCACTGCCAACTTAGAGTTTCCCCAACCCGTTCGAGTTGAT
5236 GCCATGGTGCTCGAGGGATGCGAGGA
66 GCCATGGTGCTCGAGGGATGCGAGGA
5262 T
1 T
5263 GTAGCGACTC
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 90 1.00
ACGTcount: A:0.23, C:0.29, G:0.25, T:0.23
Consensus pattern (91 bp):
TTCGGCTCAAAGACCCAAATCCCATCACTGCCAACTTAGAGTTTCCCCAACCCGTTCGAGTTGAT
GCCATGGTGCTCGAGGGATGCGAGGA
Found at i:8729 original size:22 final size:22
Alignment explanation
Indices: 8704--8747 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
8694 AAAATTTGGC
*
8704 TTTTAGTTTATGATTTATGAGT
1 TTTTAGTTTATGATTAATGAGT
8726 TTTTAGTTTATGATTAATGAGT
1 TTTTAGTTTATGATTAATGAGT
8748 AGATCTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.00, G:0.18, T:0.57
Consensus pattern (22 bp):
TTTTAGTTTATGATTAATGAGT
Found at i:9228 original size:35 final size:35
Alignment explanation
Indices: 9188--10015 Score: 1139
Period size: 35 Copynumber: 23.9 Consensus size: 35
9178 GTGGGTCAGT
*
9188 AGTAATCAACTTAATTCAGGGTAATTAAGTAAATC
1 AGTAATCAACTTAATTCAGGGTAATTAAGTAAGTC
*
9223 AGTAATCAACTTAATTCATGGTAATTAAGTAAGTC
1 AGTAATCAACTTAATTCAGGGTAATTAAGTAAGTC
*
9258 AGTAATCAACTTAATTCAGGGTAATTAAGTAAATC
1 AGTAATCAACTTAATTCAGGGTAATTAAGTAAGTC
*
9293 AGTAATCAACTTAATTCATGGTAATTAAGTAAGTC
1 AGTAATCAACTTAATTCAGGGTAATTAAGTAAGTC
9328 AGTAATCAACTTAATTCAGGGTAATTAAGTAAGTC
1 AGTAATCAACTTAATTCAGGGTAATTAAGTAAGTC
*
9363 ATTAATCAACTTAATTCAGGGTAATTAAGTAAGTC
1 AGTAATCAACTTAATTCAGGGTAATTAAGTAAGTC
9398 AGTAATCAACTTAATTCAGGGTAATTAAGTAAGTC
1 AGTAATCAACTTAATTCAGGGTAATTAAGTAAGTC
* *
9433 ATTAATCAACTTAATTCAGGGTAATTAAGTAAATC
1 AGTAATCAACTTAATTCAGGGTAATTAAGTAAGTC
9468 AGTAATCAACTTAATTCAGGGTAATTAAGTAAGTC
1 AGTAATCAACTTAATTCAGGGTAATTAAGTAAGTC
*
9503 ATTAATCAACTTAATTCAGGGTAATTAAGTAAGTC
1 AGTAATCAACTTAATTCAGGGTAATTAAGTAAGTC
* *
9538 AATAATCAACTTAATTCAGGGTAATTAAGAAAGTC
1 AGTAATCAACTTAATTCAGGGTAATTAAGTAAGTC
* *
9573 AGTAGTCAACTTAATTCAAGGTAATTAAGTAAGTC
1 AGTAATCAACTTAATTCAGGGTAATTAAGTAAGTC
* *
9608 ATTAATCAACTTAATTCAGGGTAATTAAGTGAGTC
1 AGTAATCAACTTAATTCAGGGTAATTAAGTAAGTC
* * *
9643 GGTGATCAACTTAATTCAGGGTAATTAAGTGAGTC
1 AGTAATCAACTTAATTCAGGGTAATTAAGTAAGTC
9678 AGTAATCAACTTAATTCAGGGTAATTAAGTAAGTC
1 AGTAATCAACTTAATTCAGGGTAATTAAGTAAGTC
* **
9713 ATTAATCAACTTAATTCAGGGTAATTAAGTGGGTC
1 AGTAATCAACTTAATTCAGGGTAATTAAGTAAGTC
*
9748 AGTAATCAACTTAATTCAGGGTAATTAAGTGAGTC
1 AGTAATCAACTTAATTCAGGGTAATTAAGTAAGTC
* * *
9783 TGTGAAT-AACTTAATTCAAGGTAATTAAGTTAGT-
1 AGT-AATCAACTTAATTCAGGGTAATTAAGTAAGTC
** *
9817 A--AAT-AGTTTAATTCAGGGTAATTAAGTGAGTC
1 AGTAATCAACTTAATTCAGGGTAATTAAGTAAGTC
* *
9849 AGTTAAT-GACTTAATTCA-GG--A-TAATTAAGTC
1 AG-TAATCAACTTAATTCAGGGTAATTAAGTAAGTC
* *
9880 AGTAAGT-AGCTTAATTCAGGGTAATTAAGTGAA-TT
1 AGTAA-TCAACTTAATTCAGGGTAATTAAGT-AAGTC
*
9915 AGTAATCAACTTTAATTCAGGGTAATTAAGTGAA-TT
1 AGTAATCAAC-TTAATTCAGGGTAATTAAGT-AAGTC
* *
9951 AATGAA-AAACTTAATTCAGGGTAATTAAGT-AGTTC
1 AGT-AATCAACTTAATTCAGGGTAATTAAGTAAG-TC
* *
9986 AATAAGT-AGCTTAATTCAGGGTAATTAAGT
1 AGTAA-TCAACTTAATTCAGGGTAATTAAGT
10016 TTAGTAAGCA
Statistics
Matches: 718, Mismatches: 57, Indels: 36
0.89 0.07 0.04
Matches are distributed among these distances:
30 3 0.00
31 46 0.06
32 4 0.01
33 1 0.00
34 6 0.01
35 621 0.86
36 35 0.05
37 2 0.00
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.33
Consensus pattern (35 bp):
AGTAATCAACTTAATTCAGGGTAATTAAGTAAGTC
Found at i:13641 original size:2 final size:2
Alignment explanation
Indices: 13634--13660 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13624 TAAGATCATA
13634 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
13661 GGCTTTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16777 original size:29 final size:29
Alignment explanation
Indices: 16722--16779 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
16712 GCCAGTTTAA
*
16722 ATTTTGAATTCCACAAGCGTGTTGTGGAG
1 ATTTTGAATTCCACAAGCGTGTCGTGGAG
16751 ATTTTGAACTT-CACAAGCG-GATCGTGGAG
1 ATTTTGAA-TTCCACAAGCGTG-TCGTGGAG
16780 TTGACACATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 1 0.04
29 23 0.88
30 2 0.08
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.31
Consensus pattern (29 bp):
ATTTTGAATTCCACAAGCGTGTCGTGGAG
Found at i:18481 original size:6 final size:6
Alignment explanation
Indices: 18470--18508 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
18460 TGGCACTGAT
*
18470 TCTGGC TCTGGC TCTGGC TCTAGC TCTGGC TCTGGC TCT
1 TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC TCT
18509 AATCCTGCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.03, C:0.33, G:0.28, T:0.36
Consensus pattern (6 bp):
TCTGGC
Found at i:19251 original size:14 final size:14
Alignment explanation
Indices: 19232--19294 Score: 54
Period size: 14 Copynumber: 4.3 Consensus size: 14
19222 TTGATAAAAT
*
19232 TGAAAATTAAGTGC
1 TGAAAATTAAGTAC
19246 TGAAAAATTAAGTAC
1 TG-AAAATTAAGTAC
* * *
19261 TGAAATTTTAGTTC
1 TGAAAATTAAGTAC
*
19275 TGAATCATATAAGTAC
1 TGAA-AAT-TAAGTAC
19291 TGAA
1 TGAA
19295 TTCAAATCAT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
14 15 0.39
15 14 0.37
16 9 0.24
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.33
Consensus pattern (14 bp):
TGAAAATTAAGTAC
Found at i:19254 original size:15 final size:15
Alignment explanation
Indices: 19234--19265 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
19224 GATAAAATTG
*
19234 AAAATTAAGTGCTGA
1 AAAATTAAGTACTGA
19249 AAAATTAAGTACTGA
1 AAAATTAAGTACTGA
19264 AA
1 AA
19266 TTTTAGTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.06, G:0.16, T:0.25
Consensus pattern (15 bp):
AAAATTAAGTACTGA
Found at i:19265 original size:29 final size:30
Alignment explanation
Indices: 19232--19294 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
19222 TTGATAAAAT
19232 TGAAAATTAAGTGCTGAAAAAT-TAAGTAC
1 TGAAAATTAAGTGCTGAAAAATATAAGTAC
* * * **
19261 TGAAATTTTAGTTCTGAATCATATAAGTAC
1 TGAAAATTAAGTGCTGAAAAATATAAGTAC
19291 TGAA
1 TGAA
19295 TTCAAATCAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.33
Consensus pattern (30 bp):
TGAAAATTAAGTGCTGAAAAATATAAGTAC
Found at i:21103 original size:22 final size:22
Alignment explanation
Indices: 21075--21117 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
21065 GAGGAGACTT
21075 CTAAATCCTTCGTTCATAGTTG
1 CTAAATCCTTCGTTCATAGTTG
21097 CTAAATCCTTCGTTCATAGTT
1 CTAAATCCTTCGTTCATAGTT
21118 ATTATAGCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (22 bp):
CTAAATCCTTCGTTCATAGTTG
Done.