Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014880.1 Corchorus capsularis cultivar CVL-1 contig14901, 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: 12475
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Found at i:743 original size:8 final size:8
Alignment explanation
Indices: 730--766 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
720 ACAACCGGCC
730 AAAAAGAA
1 AAAAAGAA
738 AAAAAGAA
1 AAAAAGAA
*
746 AGAAAGAA
1 AAAAAGAA
*
754 AGAAAGAA
1 AAAAAGAA
762 AAAAA
1 AAAAA
767 ACTATTACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:749 original size:12 final size:12
Alignment explanation
Indices: 732--766 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
722 AACCGGCCAA
732 AAAGAAAAAAAG
1 AAAGAAAAAAAG
*
744 AAAGAAAGAAAG
1 AAAGAAAAAAAG
756 AAAGAAAAAAA
1 AAAGAAAAAAA
767 ACTATTACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAAG
Found at i:767 original size:4 final size:4
Alignment explanation
Indices: 732--762 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
722 AACCGGCCAA
*
732 AAAG AAAA AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
763 AAAAACTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:4317 original size:347 final size:345
Alignment explanation
Indices: 3682--4373 Score: 1348
Period size: 347 Copynumber: 2.0 Consensus size: 345
3672 ATGTCTAATG
3682 GCATCTCCAATCTTCATAAAAACAGCATCTGCAGTCTGAGCTTGTCTTCCATAATACCTTGCATT
1 GCATCTCCAATCTTCATAAAAACAGCATCTGCAGTCTGAGCTTGTCTTCCATAATACCTTGCATT
3747 TCTTTCAAGCCAAATGTAATAACAGAATGCCATCTATTAATTATTTTAAATTTTAATACACATAA
66 TCTTTCAAGCCAAATGTAATAACAGAATGCCATCTATTAATTATTTTAAATTTTAATACACATAA
3812 GTGAAATTTTTCCTAAATAGAATAGGCAATGATTTTGTACACCCCAATTGTTCATCTACCCATTC
131 GTGAAATTTTTCCTAAATAGAATAGGCAATGATTTTGTACACCCCAATTGTTCATCTACCCATTC
3877 CTCTCAATCTTGAACTTTTTTTTTGGGTGAAACTCAATCTTGAACTTTAATTGAAAGGTGAAATT
196 CTCTCAATCTTGAACTTTTTTTTTGGGTGAAACTCAATCTTGAACTTTAATTGAAAGGTGAAATT
3942 ATCCTATAATAATATATATATGGACTTAAGAGATAGATGGCGTGAGATGTCCATAAAAAAAAATT
261 ATCCTATAATAATATATATATGGACTTAAGAGATAGATGGCGTGAGATGTCC--AAAAAAAAATT
4007 TATATATACCATTACATATATA
324 TATATATACCATTACATATATA
4029 GCATCTCCAATCTTCATAAAAACAGCATCTGCAGTCTGAGCTTGTCTTCCATAATACCTTGCATT
1 GCATCTCCAATCTTCATAAAAACAGCATCTGCAGTCTGAGCTTGTCTTCCATAATACCTTGCATT
4094 TCTTTCAAGCCAAATGTAATAACAGAATGCCATCTATTAATTATTTTAAATTTTAATACACATAA
66 TCTTTCAAGCCAAATGTAATAACAGAATGCCATCTATTAATTATTTTAAATTTTAATACACATAA
4159 GTGAAATTTTTCCTAAATAGAATAGGCAATGATTTTGTACACCCCAATTGTTCATCTACCCATTC
131 GTGAAATTTTTCCTAAATAGAATAGGCAATGATTTTGTACACCCCAATTGTTCATCTACCCATTC
4224 CTCTCAATCTTGAACTTTTTTTTTGGGTGAAACTCAATCTTGAACTTTAATTGAAAGGTGAAATT
196 CTCTCAATCTTGAACTTTTTTTTTGGGTGAAACTCAATCTTGAACTTTAATTGAAAGGTGAAATT
**
4289 ATCCTATAATAATATATATATGGACTTAAGAGATAGATGGCGTGAGATGTCCAAAAAATCATTTA
261 ATCCTATAATAATATATATATGGACTTAAGAGATAGATGGCGTGAGATGTCCAAAAAAAAATTTA
4354 TATATACCATTACATATATA
326 TATATACCATTACATATATA
4374 CCAAAAAATA
Statistics
Matches: 343, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
345 31 0.09
347 312 0.91
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (345 bp):
GCATCTCCAATCTTCATAAAAACAGCATCTGCAGTCTGAGCTTGTCTTCCATAATACCTTGCATT
TCTTTCAAGCCAAATGTAATAACAGAATGCCATCTATTAATTATTTTAAATTTTAATACACATAA
GTGAAATTTTTCCTAAATAGAATAGGCAATGATTTTGTACACCCCAATTGTTCATCTACCCATTC
CTCTCAATCTTGAACTTTTTTTTTGGGTGAAACTCAATCTTGAACTTTAATTGAAAGGTGAAATT
ATCCTATAATAATATATATATGGACTTAAGAGATAGATGGCGTGAGATGTCCAAAAAAAAATTTA
TATATACCATTACATATATA
Found at i:5063 original size:105 final size:105
Alignment explanation
Indices: 4954--5356 Score: 279
Period size: 104 Copynumber: 4.0 Consensus size: 105
4944 TGGCAGAATT
* * * * * * ***
4954 TAAACTTAGTTATATACATTGATTTTTTTTTTCCTAAAATCATTTAATAGTACATTTTTGCTTAA
1 TAAACTTAGTAAAATTCATTGATTTTTTTTTTCCTAAAACCATATAATAATACATTTCAACTTAA
* * *
5019 TGATTTACCCTTAAAATGAATTAAATTTTTAATTTTGAGC
66 TGACTTACCCTTAAAATGAATTAAATTTTTAAATTGGAGC
* * * * * *
5059 TAAACTTAATAAAATTCATTGA-CTTGTGTTTCCTAAAACCCTATAATAATACATTTCAATTTAA
1 TAAACTTAGTAAAATTCATTGATTTTTTTTTTCCTAAAACCATATAATAATACATTTCAACTTAA
*
5123 TGACTTACCCTTAAAATGAATTAAATTTTTAAATTGGGGC
66 TGACTTACCCTTAAAATGAATTAAATTTTTAAATTGGAGC
* * * * * *
5163 TAAACTTTAGTGAAATTCATTG---TTTTTTTT-ATAAAA-CACTATAACACTACAATTTAAATT
1 TAAAC-TTAGTAAAATTCATTGATTTTTTTTTTCCTAAAACCA-TATAATAATAC-ATTTCAACT
* * *
5223 TAATGTCTTGCCCTT-AAAT-AA-T---TTTTT---GT-GA-C
63 TAATGACTTACCCTTAAAATGAATTAAATTTTTAAATTGGAGC
** * * * * *
5255 TAGGCTTAGTGAAATTCATTGATTTTTTTTTT-CTAAAACCCTATAGTAACAAATTTACAACTTA
1 TAAACTTAGTAAAATTCATTGATTTTTTTTTTCCTAAAACCATATAATAATACATTT-CAACTTA
* *
5319 ATGACTTAACCCTTACAAA--AATTAAAATTTTAATTTGG
65 ATGACTT-ACCCTTA-AAATGAATTAAATTTTTAAATTGG
5357 GGGTTAAAGT
Statistics
Matches: 232, Mismatches: 47, Indels: 39
0.73 0.15 0.12
Matches are distributed among these distances:
91 16 0.07
92 4 0.02
93 5 0.02
94 31 0.13
95 6 0.03
96 2 0.01
97 9 0.04
100 5 0.02
101 3 0.01
102 18 0.08
103 28 0.12
104 73 0.31
105 32 0.14
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.43
Consensus pattern (105 bp):
TAAACTTAGTAAAATTCATTGATTTTTTTTTTCCTAAAACCATATAATAATACATTTCAACTTAA
TGACTTACCCTTAAAATGAATTAAATTTTTAAATTGGAGC
Found at i:5685 original size:116 final size:119
Alignment explanation
Indices: 5448--5668 Score: 261
Period size: 119 Copynumber: 1.9 Consensus size: 119
5438 GCACCAAATT
* *
5448 AAAAAAATTAATTCATTTCAAGGGTAAAAGTCATGAAATTAAAGATTTATTATTATAGGTTTTAG
1 AAAAAAAATAATTCATTTCAAGGGTAAAAGTCATGAAATCAAAGATTTATTATTATAGGTTTTAG
* * *
5513 AAAAAAAAATTTAAAATATCAATTTAACTAGGTTTAGCTCCAAAGTTTTTTTTTTA
66 AAAAAAAAA--TAAAATACCAATTTAACTAAGTTTAGCTCCAAAGTTTTATTTTTA
* * ** *
5569 AAAAAAAATAGTTCATTTTAAGGGT-AAA-TTGTGAAATCAATGATTTATTATTATAGGGTTTTA
1 AAAAAAAATAATTCATTTCAAGGGTAAAAGTCATGAAATCAAAGATTTATTATTATA-GGTTTTA
* * * *
5632 GGAAAATAAA-AATA-ACCAATTTCACTAAGTTTAGCTC
65 GAAAAAAAAATAAAATACCAATTTAACTAAGTTTAGCTC
5669 TAATTTAATA
Statistics
Matches: 86, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
116 20 0.23
117 3 0.03
119 23 0.27
120 18 0.21
121 22 0.26
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.37
Consensus pattern (119 bp):
AAAAAAAATAATTCATTTCAAGGGTAAAAGTCATGAAATCAAAGATTTATTATTATAGGTTTTAG
AAAAAAAAATAAAATACCAATTTAACTAAGTTTAGCTCCAAAGTTTTATTTTTA
Found at i:6326 original size:25 final size:26
Alignment explanation
Indices: 6292--6347 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
6282 TACCATTTTA
6292 CTATTTTAATT-AAAAAAACTTAGAT
1 CTATTTTAATTAAAAAAAACTTAGAT
6317 CTATTTTAATTAAAAAAAACTTAGAT
1 CTATTTTAATTAAAAAAAACTTAGAT
*
6343 GTATT
1 CTATT
6348 AGAAAATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 11 0.38
26 18 0.62
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.41
Consensus pattern (26 bp):
CTATTTTAATTAAAAAAAACTTAGAT
Found at i:8227 original size:13 final size:13
Alignment explanation
Indices: 8209--8233 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8199 TCTCATAAAT
8209 ATTTTTATTTATA
1 ATTTTTATTTATA
8222 ATTTTTATTTAT
1 ATTTTTATTTAT
8234 TTATTTAATT
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTTATTTATA
Found at i:8861 original size:14 final size:15
Alignment explanation
Indices: 8834--8874 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
8824 GACTTTAATT
8834 TTTAA-GAA-ATTAA
1 TTTAATGAATATTAA
8847 TTT-ATGAATATTAA
1 TTTAATGAATATTAA
*
8861 TTTAATTAATATTA
1 TTTAATGAATATTA
8875 TTTTTAGTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 1 0.04
13 6 0.25
14 8 0.33
15 9 0.38
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (15 bp):
TTTAATGAATATTAA
Found at i:9646 original size:20 final size:20
Alignment explanation
Indices: 9623--9661 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
9613 TGGAAAGATA
9623 TTATAAATTAAT-ATTATTTT
1 TTAT-AATTAATAATTATTTT
*
9643 TTATAATTTATAATTATTT
1 TTATAATTAATAATTATTT
9662 ACTGTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATAATTAATAATTATTTT
Done.