Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012576.1 Corchorus capsularis cultivar CVL-1 contig12597, 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: 54490
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:164 original size:18 final size:21
Alignment explanation
Indices: 121--178 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 21
111 AAATTATCAT
121 ATATATAATAATTTA-TA-TA
1 ATATATAATAATTTATTATTA
*
140 ATATTAAAATAAAATTTATTATTA
1 ATA-TATAAT--AATTTATTATTA
164 ATATATAATAATTTA
1 ATATATAATAATTTA
179 AATACTATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
19 3 0.09
20 5 0.16
21 6 0.19
22 6 0.19
23 7 0.22
24 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATATATAATAATTTATTATTA
Found at i:12910 original size:24 final size:24
Alignment explanation
Indices: 12819--12910 Score: 62
Period size: 24 Copynumber: 3.8 Consensus size: 24
12809 TAGGATGATA
*
12819 CTTGACTTCTGCAGTAGAATGTCG
1 CTTGACTTCTGCGGTAGAATGTCG
** * *
12843 CTTGACTTCTATGGTATAATTGTGG
1 CTTGACTTCTGCGGTAGAA-TGTCG
* ****
12868 TTTG-CTTCTGCCACGGAATGAT-G
1 CTTGACTTCTGCGGTAGAATG-TCG
12891 CTTGACTTCTGCGGTAGAAT
1 CTTGACTTCTGCGGTAGAAT
12911 TGTCTCACCA
Statistics
Matches: 47, Mismatches: 18, Indels: 6
0.66 0.25 0.08
Matches are distributed among these distances:
23 6 0.13
24 34 0.72
25 7 0.15
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (24 bp):
CTTGACTTCTGCGGTAGAATGTCG
Found at i:16186 original size:24 final size:23
Alignment explanation
Indices: 16147--16202 Score: 85
Period size: 24 Copynumber: 2.4 Consensus size: 23
16137 CTTTCCCCCC
*
16147 TTTTTTTTTGGGAATTTCGCTCT
1 TTTTTTTTTGGAAATTTCGCTCT
*
16170 TTTTTTTTATGGAAATTTTGCTCT
1 TTTTTTTT-TGGAAATTTCGCTCT
16194 TTTTTTTTT
1 TTTTTTTTT
16203 TTTGCCGCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 9 0.30
24 21 0.70
ACGTcount: A:0.11, C:0.09, G:0.12, T:0.68
Consensus pattern (23 bp):
TTTTTTTTTGGAAATTTCGCTCT
Found at i:16572 original size:27 final size:27
Alignment explanation
Indices: 16532--16612 Score: 117
Period size: 27 Copynumber: 3.0 Consensus size: 27
16522 TCATGCTGGA
* *
16532 GACTCATGCCGAAGCTCCTGCAGTTGG
1 GACTCATGCTGAAGCTCCCGCAGTTGG
16559 GACTCATGCTGAAGCTCCCGCAGTTGG
1 GACTCATGCTGAAGCTCCCGCAGTTGG
* * *
16586 GACTCATGCTAAAGCTCACGTAGTTGG
1 GACTCATGCTGAAGCTCCCGCAGTTGG
16613 CTTTTGTGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.21, C:0.27, G:0.28, T:0.23
Consensus pattern (27 bp):
GACTCATGCTGAAGCTCCCGCAGTTGG
Found at i:19349 original size:20 final size:20
Alignment explanation
Indices: 19305--19343 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
19295 TAGAACAATT
*
19305 ATAAAGAAAAGTAATTAAAA
1 ATAAAGAAAAGTAAATAAAA
*
19325 ATAAAGCAAAGTAAATAAA
1 ATAAAGAAAAGTAAATAAA
19344 TCTAAATCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.69, C:0.03, G:0.10, T:0.18
Consensus pattern (20 bp):
ATAAAGAAAAGTAAATAAAA
Found at i:21270 original size:13 final size:13
Alignment explanation
Indices: 21252--21276 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21242 GAAAATATAA
21252 AAAAAATTAAAAT
1 AAAAAATTAAAAT
21265 AAAAAATTAAAA
1 AAAAAATTAAAA
21277 AATTTTCGAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAAAATTAAAAT
Found at i:21954 original size:2 final size:2
Alignment explanation
Indices: 21947--21972 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21937 TGGTAAAAAT
21947 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
21973 TCTTTGTGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:27543 original size:33 final size:33
Alignment explanation
Indices: 27473--27549 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 33
27463 TTGCAAAGAG
* * *
27473 TGTTTTAGATGTTGTTTGCAATGACACTAAATC
1 TGTTTTAGATGTTGTTTGCAACGAAACAAAATC
* ** *
27506 TGTTTTAGGTGTTGTTTGTGACGAAACAAAATT
1 TGTTTTAGATGTTGTTTGCAACGAAACAAAATC
*
27539 TGTTTTTGATG
1 TGTTTTAGATG
27550 CTAATTGTGA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.25, C:0.08, G:0.22, T:0.45
Consensus pattern (33 bp):
TGTTTTAGATGTTGTTTGCAACGAAACAAAATC
Found at i:28028 original size:30 final size:30
Alignment explanation
Indices: 27992--28049 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 30
27982 AAGGGGGAAA
27992 GAATGATGCGCCCAAGG-CTTATCATGGAGG
1 GAATGATGCG-CCAAGGACTTATCATGGAGG
28022 GAATGATGCGCCAAGGACTTATCATGGA
1 GAATGATGCGCCAAGGACTTATCATGGA
28050 CTTGAAGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.29, C:0.19, G:0.31, T:0.21
Consensus pattern (30 bp):
GAATGATGCGCCAAGGACTTATCATGGAGG
Found at i:28107 original size:8 final size:8
Alignment explanation
Indices: 28094--28127 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
28084 TGCATGGGCT
28094 GCATGGAG
1 GCATGGAG
28102 GCATGGAG
1 GCATGGAG
28110 GCATGGAG
1 GCATGGAG
28118 ATGCATGGAG
1 --GCATGGAG
28128 ACCATGGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 16 0.67
10 8 0.33
ACGTcount: A:0.26, C:0.12, G:0.47, T:0.15
Consensus pattern (8 bp):
GCATGGAG
Found at i:28135 original size:19 final size:18
Alignment explanation
Indices: 28102--28138 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
28092 CTGCATGGAG
*
28102 GCATGGAGGCATGGAGAT
1 GCATGGAGCCATGGAGAT
28120 GCATGGAGACCATGGAGAT
1 GCATGGAG-CCATGGAGAT
28139 AACGATGGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.30, C:0.14, G:0.41, T:0.16
Consensus pattern (18 bp):
GCATGGAGCCATGGAGAT
Found at i:38068 original size:50 final size:50
Alignment explanation
Indices: 37997--38097 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
37987 GAAAGAGGGA
37997 GATGCCTATCAATCACATTTTATAGGTACATTTAATAGGTTTTCTAAGAT
1 GATGCCTATCAATCACATTTTATAGGTACATTTAATAGGTTTTCTAAGAT
38047 GATGCCTATCAATCACATTTTATAGGTACATTTAATAGGTTTTCTAAGAT
1 GATGCCTATCAATCACATTTTATAGGTACATTTAATAGGTTTTCTAAGAT
38097 G
1 G
38098 GCACACTTTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.40
Consensus pattern (50 bp):
GATGCCTATCAATCACATTTTATAGGTACATTTAATAGGTTTTCTAAGAT
Found at i:44615 original size:18 final size:18
Alignment explanation
Indices: 44592--44628 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
44582 GCTTTTTGCC
44592 TGCGCTCCGCTGCGGGGT
1 TGCGCTCCGCTGCGGGGT
44610 TGCGCTCCGCTGCGGGGT
1 TGCGCTCCGCTGCGGGGT
44628 T
1 T
44629 TTAATGGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.00, C:0.32, G:0.43, T:0.24
Consensus pattern (18 bp):
TGCGCTCCGCTGCGGGGT
Found at i:44715 original size:15 final size:15
Alignment explanation
Indices: 44695--44724 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
44685 TAGGTATGTT
44695 AAAATGTAATAAGGA
1 AAAATGTAATAAGGA
44710 AAAATGTAATAAGGA
1 AAAATGTAATAAGGA
44725 GTTGAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (15 bp):
AAAATGTAATAAGGA
Found at i:46788 original size:11 final size:10
Alignment explanation
Indices: 46770--46803 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
46760 GAAGTTTGTG
46770 TTTTGAAGAT
1 TTTTGAAGAT
46780 TTCTTGAAGAT
1 TT-TTGAAGAT
46791 ATTTTGAAGAT
1 -TTTTGAAGAT
46802 TT
1 TT
46804 GAAGACAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (10 bp):
TTTTGAAGAT
Found at i:53863 original size:11 final size:10
Alignment explanation
Indices: 53845--53878 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
53835 GAAGTTTGTG
53845 TTTTGAAGAT
1 TTTTGAAGAT
53855 TTCTTGAAGAT
1 TT-TTGAAGAT
53866 ATTTTGAAGAT
1 -TTTTGAAGAT
53877 TT
1 TT
53879 GAAGACAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (10 bp):
TTTTGAAGAT
Done.