Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006836.1 Corchorus capsularis cultivar CVL-1 contig06857, 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: 38691
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Found at i:6855 original size:20 final size:19
Alignment explanation
Indices: 6817--6855 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
6807 CTAAACAAGT
*
6817 CTAAACTAAATATAATTAA
1 CTAAACTAAATAGAATTAA
*
6836 CTAATCTAAGATAGAATTAA
1 CTAAACTAA-ATAGAATTAA
6856 GGCCCATATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.54, C:0.10, G:0.05, T:0.31
Consensus pattern (19 bp):
CTAAACTAAATAGAATTAA
Found at i:7082 original size:21 final size:21
Alignment explanation
Indices: 7058--7100 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
7048 CTTGCTCTTG
*
7058 TCATCGGACCTAAA-GGCATCT
1 TCATAGGACC-AAATGGCATCT
*
7079 TCATAGGATCAAATGGCATCT
1 TCATAGGACCAAATGGCATCT
7100 T
1 T
7101 TGGTGCGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (21 bp):
TCATAGGACCAAATGGCATCT
Found at i:7124 original size:30 final size:30
Alignment explanation
Indices: 7090--7175 Score: 145
Period size: 30 Copynumber: 2.9 Consensus size: 30
7080 CATAGGATCA
7090 AATGGCATCTTTGGTGCGATTCCATCAACT
1 AATGGCATCTTTGGTGCGATTCCATCAACT
* * *
7120 AATGGCATCTTAGGCGCGATTCCATCACCT
1 AATGGCATCTTTGGTGCGATTCCATCAACT
7150 AATGGCATCTTTGGTGCGATTCCATC
1 AATGGCATCTTTGGTGCGATTCCATC
7176 TCTTGCTTGC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.31
Consensus pattern (30 bp):
AATGGCATCTTTGGTGCGATTCCATCAACT
Found at i:8112 original size:33 final size:33
Alignment explanation
Indices: 8014--8117 Score: 102
Period size: 33 Copynumber: 3.2 Consensus size: 33
8004 TTGCAAAGAG
* * * * *
8014 TGTTTTAGATGTTGTTTGCGATGATACTAAACC
1 TGTTTCAGGTGTTGTTTGCGATGAAACAAAATC
** * *
8047 TAATTC-GAGTGTTGTTTGCGATGACACTAAATC
1 TGTTTCAG-GTGTTGTTTGCGATGAAACAAAATC
*
8080 TGTTTCAGGTGTTGTTTGTGATGAAACAAAATC
1 TGTTTCAGGTGTTGTTTGCGATGAAACAAAATC
8113 TGTTT
1 TGTTT
8118 TGGATGCTAA
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
32 1 0.02
33 56 0.97
34 1 0.02
ACGTcount: A:0.25, C:0.12, G:0.22, T:0.41
Consensus pattern (33 bp):
TGTTTCAGGTGTTGTTTGCGATGAAACAAAATC
Found at i:10638 original size:17 final size:17
Alignment explanation
Indices: 10590--10626 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
10580 TCCCCCTCAT
* *
10590 GGTACCAGGTAGCATGA
1 GGTACTAGGTAACATGA
10607 GGTACTAGGTAACATGA
1 GGTACTAGGTAACATGA
10624 GGT
1 GGT
10627 GCTGGATAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.30, C:0.14, G:0.35, T:0.22
Consensus pattern (17 bp):
GGTACTAGGTAACATGA
Found at i:14979 original size:72 final size:72
Alignment explanation
Indices: 14894--15041 Score: 278
Period size: 72 Copynumber: 2.1 Consensus size: 72
14884 TCACTTATGT
*
14894 AATGTCTAACTAATTGCTAAATTGAGGGTTAATTAATCAATGAACTAAATTGAGCTTAAGCTACA
1 AATGTCTAACTAATTGCTAAATTGAGGGTTAATTAATCAATGAACTAAATTGAACTTAAGCTACA
14959 TGATTAA
66 TGATTAA
*
14966 AATGTCTAACTAATTGCTCAATTGAGGGTTAATTAATCAATGAACTAAATTGAACTTAAGCTACA
1 AATGTCTAACTAATTGCTAAATTGAGGGTTAATTAATCAATGAACTAAATTGAACTTAAGCTACA
15031 TGATTAA
66 TGATTAA
15038 AATG
1 AATG
15042 CAACAATACT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (72 bp):
AATGTCTAACTAATTGCTAAATTGAGGGTTAATTAATCAATGAACTAAATTGAACTTAAGCTACA
TGATTAA
Found at i:15388 original size:217 final size:217
Alignment explanation
Indices: 15013--15449 Score: 838
Period size: 217 Copynumber: 2.0 Consensus size: 217
15003 CAATGAACTA
*
15013 AATTGAACTTAAGCTACATGATTAAAATGCAACAATACTAAATTACCAATTGAAGCTAAGCTGAA
1 AATTGAACTTAAACTACATGATTAAAATGCAACAATACTAAATTACCAATTGAAGCTAAGCTGAA
15078 ATATGCAAAAATGCCAAAGGTGCACATTAAGATTTTTTGGTTTTTTCAAATGCAATTTTGATGAC
66 ATATGCAAAAATGCCAAAGGTGCACATTAAGATTTTTTGGTTTTTTCAAATGCAATTTTGATGAC
*
15143 TAAAGTGAATTAGAAAATCTAAATTAAGAGTGGACTCAAAATGACGAAAATGCCCCCTAAATGCA
131 TAAAATGAATTAGAAAATCTAAATTAAGAGTGGACTCAAAATGACGAAAATGCCCCCTAAATGCA
15208 AGAATGACAAAAATGCCCCCTG
196 AGAATGACAAAAATGCCCCCTG
* *
15230 AATTGAACTTAAACTACATGGTTAAAATGCAACAATACTAAATTACCTATTGAAGCTAAGCTGAA
1 AATTGAACTTAAACTACATGATTAAAATGCAACAATACTAAATTACCAATTGAAGCTAAGCTGAA
15295 ATATGCAAAAATGCCAAAGGTGCACATTAAGATTTTTTGGTTTTTTCAAATGCAATTTTGATGAC
66 ATATGCAAAAATGCCAAAGGTGCACATTAAGATTTTTTGGTTTTTTCAAATGCAATTTTGATGAC
15360 TAAAATGAATTAGAAAATCTAAATTAAGAGTGGACTCAAAATGACGAAAATGCCCCCTAAATGCA
131 TAAAATGAATTAGAAAATCTAAATTAAGAGTGGACTCAAAATGACGAAAATGCCCCCTAAATGCA
15425 AGAATGACAAAAATGCCCCCTG
196 AGAATGACAAAAATGCCCCCTG
15447 AAT
1 AAT
15450 GTTAAAATGA
Statistics
Matches: 216, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
217 216 1.00
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (217 bp):
AATTGAACTTAAACTACATGATTAAAATGCAACAATACTAAATTACCAATTGAAGCTAAGCTGAA
ATATGCAAAAATGCCAAAGGTGCACATTAAGATTTTTTGGTTTTTTCAAATGCAATTTTGATGAC
TAAAATGAATTAGAAAATCTAAATTAAGAGTGGACTCAAAATGACGAAAATGCCCCCTAAATGCA
AGAATGACAAAAATGCCCCCTG
Found at i:15431 original size:28 final size:28
Alignment explanation
Indices: 15395--15471 Score: 102
Period size: 28 Copynumber: 2.8 Consensus size: 28
15385 AAGAGTGGAC
*
15395 TCAAAATGACGAAAATGCCCCCTAAATG
1 TCAAAATGACAAAAATGCCCCCTAAATG
*
15423 -CAAGAATGACAAAAATGCCCCCTGAATG
1 TCAA-AATGACAAAAATGCCCCCTAAATG
* *
15451 TTAAAATGACCAAAATGCCCC
1 TCAAAATGACAAAAATGCCCC
15472 AGGGTGACCC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
27 3 0.07
28 38 0.88
29 2 0.05
ACGTcount: A:0.43, C:0.26, G:0.14, T:0.17
Consensus pattern (28 bp):
TCAAAATGACAAAAATGCCCCCTAAATG
Found at i:17206 original size:32 final size:32
Alignment explanation
Indices: 17178--17246 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 32
17168 TAGTGGCTAT
* * *
17178 GCCGCCCTAGGGGTGCGGCTTGCCGTGGCAAA
1 GCCGCCCCAGGGGTGCGACCTGCCGTGGCAAA
*
17210 GCCGCCCCAGGTGTGCGACCTGCCGTGGCAAA
1 GCCGCCCCAGGGGTGCGACCTGCCGTGGCAAA
17242 GCCGC
1 GCCGC
17247 ACACCTGGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.13, C:0.36, G:0.38, T:0.13
Consensus pattern (32 bp):
GCCGCCCCAGGGGTGCGACCTGCCGTGGCAAA
Found at i:17605 original size:27 final size:27
Alignment explanation
Indices: 17581--17715 Score: 155
Period size: 27 Copynumber: 5.0 Consensus size: 27
17571 AGTTTGAGCG
*
17581 TGCTCAGCCGGGCTACTATGATGAGGG-
1 TGCTCAGCCGGGTTACTATGATG-GGGC
* * *
17608 TGCACAACCCGGTTACTATGATGGGGC
1 TGCTCAGCCGGGTTACTATGATGGGGC
* * *
17635 AGCTCAGCCGAGTTACTATGATGTGGC
1 TGCTCAGCCGGGTTACTATGATGGGGC
* *
17662 TGCTCAACCGGGTCACTATGATGGGGC
1 TGCTCAGCCGGGTTACTATGATGGGGC
* *
17689 TGCTCAGCTGGGTTATTATGATGGGGC
1 TGCTCAGCCGGGTTACTATGATGGGGC
17716 CGAGGATTAT
Statistics
Matches: 88, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
26 3 0.03
27 85 0.97
ACGTcount: A:0.19, C:0.22, G:0.33, T:0.25
Consensus pattern (27 bp):
TGCTCAGCCGGGTTACTATGATGGGGC
Found at i:17902 original size:13 final size:14
Alignment explanation
Indices: 17886--17921 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
17876 ATTTTATATT
*
17886 ATTAGTTTAG-TAA
1 ATTAATTTAGTTAA
17899 ATTAATTTAGTTAA
1 ATTAATTTAGTTAA
17913 ATTAATTTA
1 ATTAATTTA
17922 CTTATTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (14 bp):
ATTAATTTAGTTAA
Found at i:19846 original size:10 final size:10
Alignment explanation
Indices: 19831--19855 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
19821 GTCGCTGCTC
19831 AATTCCAGAA
1 AATTCCAGAA
19841 AATTCCAGAA
1 AATTCCAGAA
19851 AATTC
1 AATTC
19856 TAGAGTCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (10 bp):
AATTCCAGAA
Found at i:20787 original size:12 final size:13
Alignment explanation
Indices: 20762--20795 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
20752 ATAATTATTG
20762 TTTGCTTTATTAA
1 TTTGCTTTATTAA
20775 TTTGCTTTA-TAA
1 TTTGCTTTATTAA
*
20787 TTTGTTTTA
1 TTTGCTTTA
20796 GATTTAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.21, C:0.06, G:0.09, T:0.65
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:24541 original size:21 final size:21
Alignment explanation
Indices: 24480--24542 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
24470 CCAGCATCTG
*
24480 CCGTGCCGCCTGCCCGGCCCAG
1 CCGTGCCGCCTGCCCGG-CCAT
*
24502 CCAG-GCC-ACTG-CCGCGCCAT
1 CC-GTGCCGCCTGCCCG-GCCAT
24522 CCGTGCCGCCTGCCCGGCCAT
1 CCGTGCCGCCTGCCCGGCCAT
24543 GCTCGGCCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 11
0.70 0.06 0.23
Matches are distributed among these distances:
19 1 0.03
20 11 0.33
21 12 0.36
22 8 0.24
23 1 0.03
ACGTcount: A:0.08, C:0.52, G:0.29, T:0.11
Consensus pattern (21 bp):
CCGTGCCGCCTGCCCGGCCAT
Found at i:27909 original size:12 final size:13
Alignment explanation
Indices: 27884--27917 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
27874 ATAATTATTG
27884 TTTGCTTTATTAA
1 TTTGCTTTATTAA
27897 TTTGCTTTA-TAA
1 TTTGCTTTATTAA
*
27909 TTTGTTTTA
1 TTTGCTTTA
27918 GATTTAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.21, C:0.06, G:0.09, T:0.65
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:27925 original size:6 final size:6
Alignment explanation
Indices: 27914--27940 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
27904 TATAATTTGT
27914 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
27941 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:29356 original size:21 final size:21
Alignment explanation
Indices: 29330--29373 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
29320 CAAACGTGTA
29330 AAAAAAGG-GACGGTGTTTAGC
1 AAAAAAGGTG-CGGTGTTTAGC
29351 AAAAAAGGTGCGGTGTTTAGC
1 AAAAAAGGTGCGGTGTTTAGC
29372 AA
1 AA
29374 TACCTTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.39, C:0.09, G:0.32, T:0.20
Consensus pattern (21 bp):
AAAAAAGGTGCGGTGTTTAGC
Found at i:29740 original size:6 final size:6
Alignment explanation
Indices: 29709--29738 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
29699 TCTGCTTCAC
*
29709 AATTTG AATTTG AATTTG AATTTG CATTTG
1 AATTTG AATTTG AATTTG AATTTG AATTTG
29739 CAATAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.30, C:0.03, G:0.17, T:0.50
Consensus pattern (6 bp):
AATTTG
Done.