Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010395.1 Corchorus capsularis cultivar CVL-1 contig10416, 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: 37951
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:13370 original size:29 final size:29
Alignment explanation
Indices: 13320--13378 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
13310 AATTTATTCC
* * *
13320 CTTTTTTTTCATGACATGATATCTTTGTA
1 CTTTTTTTTCAAGAAATGATATCTTGGTA
* *
13349 CTTTTTTTTGAAGAAATTATATCTTGGTA
1 CTTTTTTTTCAAGAAATGATATCTTGGTA
13378 C
1 C
13379 ATATAACATA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.53
Consensus pattern (29 bp):
CTTTTTTTTCAAGAAATGATATCTTGGTA
Found at i:30851 original size:33 final size:33
Alignment explanation
Indices: 30798--30928 Score: 163
Period size: 33 Copynumber: 4.0 Consensus size: 33
30788 ATTTGTCTAG
* * *
30798 CGCCATGGCAGAACCATCCTAGTGGGGAGGCTT
1 CGCCGTGGCGGAACCATCCTAGTGGGGAGGCTC
* * *
30831 GGCCGTGGCGGAACCGTCCTAGTGGGGAGACTC
1 CGCCGTGGCGGAACCATCCTAGTGGGGAGGCTC
* *
30864 CGCCGTGGCGGACCCGTCCTAGTGGGGAGGCTC
1 CGCCGTGGCGGAACCATCCTAGTGGGGAGGCTC
* * *
30897 CGCCATGGTGGAGCCATCCTAGTGGGGAGGCT
1 CGCCGTGGCGGAACCATCCTAGTGGGGAGGCT
30929 AGTGTAAAAA
Statistics
Matches: 85, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 85 1.00
ACGTcount: A:0.15, C:0.28, G:0.40, T:0.17
Consensus pattern (33 bp):
CGCCGTGGCGGAACCATCCTAGTGGGGAGGCTC
Found at i:32348 original size:19 final size:20
Alignment explanation
Indices: 32302--32349 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
32292 TGTGGTACGC
*
32302 CACATGTACCAAAAAGTCGTGC
1 CACATGTACCAAAAA--CGTGA
32324 CACATGTACCAAAAA-GTGA
1 CACATGTACCAAAAACGTGA
32343 CACATGT
1 CACATGT
32350 CACGCCACGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
22 15 0.60
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CACATGTACCAAAAACGTGA
Found at i:32355 original size:53 final size:53
Alignment explanation
Indices: 32269--32371 Score: 163
Period size: 53 Copynumber: 1.9 Consensus size: 53
32259 GACTTGGCAC
**
32269 GCCACATGTACCAAAAAGTGACATGTGGTACGCCACATGTACCAAAAAGTCGT
1 GCCACATGTACCAAAAAGTGACACATGGTACGCCACATGTACCAAAAAGTCGT
*
32322 GCCACATGTACCAAAAAGTGACACAT-GTCACGCCACGTGTACCAAAAAGT
1 GCCACATGTACCAAAAAGTGACACATGGT-ACGCCACATGTACCAAAAAGT
32372 GACACGTGGC
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
52 2 0.04
53 44 0.96
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.17
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGGTACGCCACATGTACCAAAAAGTCGT
Found at i:32407 original size:30 final size:31
Alignment explanation
Indices: 32321--32417 Score: 133
Period size: 31 Copynumber: 3.2 Consensus size: 31
32311 CAAAAAGTCG
* *
32321 TGCCACATGTACCAAAAAGTGACACATGTCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
* *
32352 CGCCACGTGTACCAAAAAGTGACACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
**
32383 TGCCACATGTTTCAAAAA-TGACACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
32413 TGCCA
1 TGCCA
32418 TGTGCACAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
30 17 0.29
31 41 0.71
ACGTcount: A:0.34, C:0.27, G:0.21, T:0.19
Consensus pattern (31 bp):
TGCCACATGTACCAAAAAGTGACACGTGGCA
Found at i:34097 original size:33 final size:32
Alignment explanation
Indices: 34035--34097 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
34025 GGGGTTGAAG
** **
34035 CAAAGAAAGGAAAGGAATTTTCTTTTTTGGCA
1 CAAAGAAAGGAAAGGAATTTAATCATTTGGCA
34067 CAAAGAAAAGGAAAGGAATTTAATCATTTGG
1 CAAAG-AAAGGAAAGGAATTTAATCATTTGG
34098 ATAGAAAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 5 0.19
33 21 0.81
ACGTcount: A:0.43, C:0.08, G:0.22, T:0.27
Consensus pattern (32 bp):
CAAAGAAAGGAAAGGAATTTAATCATTTGGCA
Found at i:37513 original size:333 final size:332
Alignment explanation
Indices: 36892--37933 Score: 1417
Period size: 333 Copynumber: 3.1 Consensus size: 332
36882 GCTTTTTTGT
* * * *
36892 TTAGAAATTAATTCGGAAAAAATAGGATAAATGATAATAGAAGCATGAGAAGCCCTTCAATCA-T
1 TTAGAAATTAATTCGAAAAAAATAGGATAAATGATATTAGAAGCATGAAAAGCCATTCAAT-ATT
*
36956 TATGGCGATGAATTATATATTTATTTTGAGTATTGTGGCCAAAAATTGAGGAAAAATCTTTCGGG
65 TTTGGCGATGAATTATATATTT-TTTTGAGTATTGTGGCCAAAAATTGAGGAAAAATCTTTCGGG
*
37021 TCAATTTTCGCAAAATTTTAGCCGAAATCGTGTACTAAC-ACCATCACAGTTTTTGGCGAAAAAC
129 TCAATTTTCGCAAAATTTTAGCTGAAAT--TGTACTAACTACCATCACAGTTTTTGGCGAAAAAC
* *
37085 GTGTTC-CGGGGGCCCGACTCAGTTTTGCTTGATTTTTGACGCCAAGACTCGTTAAAATATCTGT
192 GTGTTCTC-GGGTCCCGACTCAGTTTTGCTTGATTTTTGGCGCCAAGACTCGTTAAAATATCTGT
* *
37149 ATTCATCTAAT-CAAATCTTAGTCACATTGGATTTAAGGATTTGTTTTTACGAGCATCAGAAACT
256 ATTCATCT-ATCCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCAGAAACT
*
37213 TTTTTCGATTTAA
320 TGTTTCGATTTAA
*
37226 TTAGAAATTAATTCGAAAAAAAATAGGATAAATGATATTAGAAGCATGAAAAGCCATTCAATGTT
1 TTAGAAATTAATTCG-AAAAAAATAGGATAAATGATATTAGAAGCATGAAAAGCCATTCAATATT
*
37291 TTTAGCGATGAATTATATATTTTTTT-AGTATTGTGGCCAAAAATTGAGGAAAAATCTTTCGGGT
65 TTTGGCGATGAATTATATATTTTTTTGAGTATTGTGGCCAAAAATTGAGGAAAAATCTTTCGGGT
* * * *
37355 CAATTTTTGCAAAATTTTAGCTGAAATTGTA-TACACGTTCCATCACAGTTTTGGGCTAAAAACG
130 CAATTTTCGCAAAATTTTAGCTGAAATTGTACTA-AC-TACCATCACAGTTTTTGGCGAAAAACG
* ** *
37419 TGTTCTTGGGTCCCGACTCAGTTTTGCTTGATTTTTGGCATCAAGACTCATTAAAATATCTGTAT
193 TGTTCTCGGGTCCCGACTCAGTTTTGCTTGATTTTTGGCGCCAAGACTCGTTAAAATATCTGTAT
* * *
37484 TCATCTATCCAAATCTCAGCCACATTGGATTTAAGGATATGTTTTTACTAGCATCA-AAATCATG
258 TCATCTATCCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCAGAAA-CTTG
* *
37548 TTTCTAATTAA
322 TTTCGATTTAA
* * ** ** * *
37559 ATAAAAATTAATTCTGAAAAAAATAGGATAAATGATATCGGAAAAATGAAAAGTCTTTCAATATT
1 TTAGAAATTAATTC-GAAAAAAATAGGATAAATGATATTAGAAGCATGAAAAGCCATTCAATATT
* *
37624 TTTGGC-ATTGAATTATATATTTTTTATGAGTATTATGGCCAAAAATTGAGGAAAAATATTTCGG
65 TTTGGCGA-TGAATTATATATTTTTT-TGAGTATTGTGGCCAAAAATTGAGGAAAAATCTTTCGG
* * * * *
37688 GTCAATTTTCGCAAAATTTTAGCTGAAATCG-AGT-ACTAACCAACATAGTTTTTTTGCGAAAAA
128 GTCAATTTTCGCAAAATTTTAGCTGAAATTGTACTAACT-ACCATCACAG-TTTTTGGCGAAAAA
* *
37751 TGTG-TCTCGAGGTCCCGACTCAGTTTTGCTTGATTTTTAGCGCCAAGACTCGTTAAAATATCTG
191 CGTGTTCTCG-GGTCCCGACTCAGTTTTGCTTGATTTTTGGCGCCAAGACTCGTTAAAATATCTG
* * *
37815 TATTCATCTAACCAAATCTCAGCCACATTGGATTTAA-GAATT-TTTTTACGAGCATCAGAATCT
255 TATTCATCTATCCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCAGAAACT
37878 TGTTTCGATTTAA
320 TGTTTCGATTTAA
* *
37891 TTAGAAATTAATTCGGAAAAAATAGGATAAACGATATTAGAAG
1 TTAGAAATTAATTCGAAAAAAATAGGATAAATGATATTAGAAG
37934 TGCGTAAAGC
Statistics
Matches: 624, Mismatches: 67, Indels: 37
0.86 0.09 0.05
Matches are distributed among these distances:
330 2 0.00
331 30 0.05
332 45 0.07
333 298 0.48
334 122 0.20
335 127 0.20
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (332 bp):
TTAGAAATTAATTCGAAAAAAATAGGATAAATGATATTAGAAGCATGAAAAGCCATTCAATATTT
TTGGCGATGAATTATATATTTTTTTGAGTATTGTGGCCAAAAATTGAGGAAAAATCTTTCGGGTC
AATTTTCGCAAAATTTTAGCTGAAATTGTACTAACTACCATCACAGTTTTTGGCGAAAAACGTGT
TCTCGGGTCCCGACTCAGTTTTGCTTGATTTTTGGCGCCAAGACTCGTTAAAATATCTGTATTCA
TCTATCCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCAGAAACTTGTTTC
GATTTAA
Done.