Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016257.1 Corchorus capsularis cultivar CVL-1 contig16278, 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: 11595
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:1208 original size:56 final size:56
Alignment explanation
Indices: 1079--1220 Score: 178
Period size: 56 Copynumber: 2.5 Consensus size: 56
1069 GATTTAGATT
* * * *
1079 GAAGACGGTCATC-CTCTCCAGTTTTCAGCAGTTTTAAGTAGTTACTCAACTTGATC
1 GAAGACGATCATCTTTCT-CAGTTTTCATCAGTTTTAAGTAATTACTCAACTTGATC
* *
1135 GAAGACGATCATCTTTCTCAGTTTTCATCAGTTTTTAGTAATTACTCAAGTTGATC
1 GAAGACGATCATCTTTCTCAGTTTTCATCAGTTTTAAGTAATTACTCAACTTGATC
* * * *
1191 GAAGATGATCATTTTTCTTAGATTTCATCA
1 GAAGACGATCATCTTTCTCAGTTTTCATCA
1221 ATATTCAGTG
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
56 72 0.96
57 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (56 bp):
GAAGACGATCATCTTTCTCAGTTTTCATCAGTTTTAAGTAATTACTCAACTTGATC
Found at i:3471 original size:56 final size:56
Alignment explanation
Indices: 3393--3534 Score: 187
Period size: 56 Copynumber: 2.5 Consensus size: 56
3383 GATTTAGATT
* *
3393 GAAGACGGTGATCCTTTC-CAGTTTTCAGCAGTTTTAAGTAGTTACTCAAGTTGATC
1 GAAGACGGTCAT-CTTTCTCAGTTTTCAGCAGTTTTAAGTAATTACTCAAGTTGATC
* *
3449 GAAGACGGTCATCTTTCTCAGTTTTCATCAGTTTTTAGTAATTACTCAAGTTGATC
1 GAAGACGGTCATCTTTCTCAGTTTTCAGCAGTTTTAAGTAATTACTCAAGTTGATC
** * * *
3505 GAAGACTATCATTTTTCTTAGATTTCAGCA
1 GAAGACGGTCATCTTTCTCAGTTTTCAGCA
3535 ATATTCAGTG
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
55 5 0.07
56 70 0.93
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.39
Consensus pattern (56 bp):
GAAGACGGTCATCTTTCTCAGTTTTCAGCAGTTTTAAGTAATTACTCAAGTTGATC
Found at i:4301 original size:20 final size:22
Alignment explanation
Indices: 4276--4329 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
4266 GTTTTTATAG
4276 CTATTTTTCTATA-CTTTTTA-
1 CTATTTTTCTATATCTTTTTAC
* *
4296 CTATTTTTATATATGTTTTTACC
1 CTATTTTTCTATATCTTTTTA-C
4319 CTATTTTTCTA
1 CTATTTTTCTA
4330 GTATTTGTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 12 0.43
21 6 0.21
23 10 0.36
ACGTcount: A:0.20, C:0.15, G:0.02, T:0.63
Consensus pattern (22 bp):
CTATTTTTCTATATCTTTTTAC
Found at i:7609 original size:56 final size:56
Alignment explanation
Indices: 7525--7781 Score: 302
Period size: 56 Copynumber: 4.6 Consensus size: 56
7515 TTTTAAGATT
* * * *
7525 TAGATTGAAGACGGTCGTCCTTTC-CAGTTTTCAGCAGTTTTAAGTAGTTACTCAAC
1 TAGATCGAAGACGGTCAT-CTTTCTCAGTTTTCAGCAGTTTTAAGTAATTACTCAAG
* * * * *
7581 TTGATCGGAGACGGTCATCTTTCTCAGTTTTCATCAATTTTTAGTAATTACTCAAG
1 TAGATCGAAGACGGTCATCTTTCTCAGTTTTCAGCAGTTTTAAGTAATTACTCAAG
* * *
7637 TAGATTGAAGATGGTCATCCTTTC-CAGTTTTCAGCAGTTTTAAGTAGTTACTCAAG
1 TAGATCGAAGACGGTCAT-CTTTCTCAGTTTTCAGCAGTTTTAAGTAATTACTCAAG
* * * *
7693 TTGATCGAAGACGATCATCTTTCTCAGTTTTCATCAGTTTTTAGTAATTACTCAAG
1 TAGATCGAAGACGGTCATCTTTCTCAGTTTTCAGCAGTTTTAAGTAATTACTCAAG
* * * *
7749 TAGATCGAAGACGATCATTTTTCTTAGATTTCA
1 TAGATCGAAGACGGTCATCTTTCTCAGTTTTCA
7782 ACAATATTTA
Statistics
Matches: 170, Mismatches: 28, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
55 10 0.06
56 155 0.91
57 5 0.03
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (56 bp):
TAGATCGAAGACGGTCATCTTTCTCAGTTTTCAGCAGTTTTAAGTAATTACTCAAG
Found at i:7722 original size:112 final size:112
Alignment explanation
Indices: 7525--7766 Score: 412
Period size: 112 Copynumber: 2.2 Consensus size: 112
7515 TTTTAAGATT
* *
7525 TAGATTGAAGACGGTCGTCCTTTCCAGTTTTCAGCAGTTTTAAGTAGTTACTCAACTTGATCGGA
1 TAGATTGAAGACGGTCATCCTTTCCAGTTTTCAGCAGTTTTAAGTAGTTACTCAACTTGATCGAA
*
7590 GACGGTCATCTTTCTCAGTTTTCATCAATTTTTAGTAATTACTCAAG
66 GACGATCATCTTTCTCAGTTTTCATCAATTTTTAGTAATTACTCAAG
* *
7637 TAGATTGAAGATGGTCATCCTTTCCAGTTTTCAGCAGTTTTAAGTAGTTACTCAAGTTGATCGAA
1 TAGATTGAAGACGGTCATCCTTTCCAGTTTTCAGCAGTTTTAAGTAGTTACTCAACTTGATCGAA
*
7702 GACGATCATCTTTCTCAGTTTTCATCAGTTTTTAGTAATTACTCAAG
66 GACGATCATCTTTCTCAGTTTTCATCAATTTTTAGTAATTACTCAAG
* *
7749 TAGATCGAAGACGATCAT
1 TAGATTGAAGACGGTCAT
7767 TTTTCTTAGA
Statistics
Matches: 121, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
112 121 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.38
Consensus pattern (112 bp):
TAGATTGAAGACGGTCATCCTTTCCAGTTTTCAGCAGTTTTAAGTAGTTACTCAACTTGATCGAA
GACGATCATCTTTCTCAGTTTTCATCAATTTTTAGTAATTACTCAAG
Found at i:10144 original size:112 final size:112
Alignment explanation
Indices: 9947--10182 Score: 409
Period size: 112 Copynumber: 2.1 Consensus size: 112
9937 GATTTAGATT
* *
9947 GAAGACGGTCGTCCTTTCCAGTTTTCAGCAGTTTTAAGTAGTTACTCAACTTGATCGGAGACGGT
1 GAAGACGGTCATCCTTTCCAGTTTTCAGCAGTTTTAAGTAGTTACTCAACTTGATCGAAGACGGT
10012 CATCTTTCTCAGTTTTCATCAGTTTTTAGTAATTACTCAAGTAGGTA
66 CATCTTTCTCAGTTTTCATCAGTTTTTAGTAATTACTCAAGTAGGTA
* *
10059 GAAGATGGTCATCCTTTCCAGTTTTCAGCAGTTTTAAGTAGTTACTCAAGTTGATCGAAGACGGT
1 GAAGACGGTCATCCTTTCCAGTTTTCAGCAGTTTTAAGTAGTTACTCAACTTGATCGAAGACGGT
* *
10124 CATCTTTCTCAGTTTTCATCAGTTTTTAGTAATTACTCAAGTAGATC
66 CATCTTTCTCAGTTTTCATCAGTTTTTAGTAATTACTCAAGTAGGTA
*
10171 GAAGACGATCAT
1 GAAGACGGTCAT
10183 TTGTCTTAGA
Statistics
Matches: 116, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
112 116 1.00
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (112 bp):
GAAGACGGTCATCCTTTCCAGTTTTCAGCAGTTTTAAGTAGTTACTCAACTTGATCGAAGACGGT
CATCTTTCTCAGTTTTCATCAGTTTTTAGTAATTACTCAAGTAGGTA
Found at i:10197 original size:56 final size:56
Alignment explanation
Indices: 9941--10182 Score: 308
Period size: 56 Copynumber: 4.3 Consensus size: 56
9931 TTTTAAGATT
* * * *
9941 TAGATTGAAGACGGTCGTCCTTTC-CAGTTTTCAGCAGTTTTAAGTAGTTACTCAAC
1 TAGATCGAAGACGGTCAT-CTTTCTCAGTTTTCAGCAGTTTTAAGTAATTACTCAAG
* * * *
9997 TTGATCGGAGACGGTCATCTTTCTCAGTTTTCATCAGTTTTTAGTAATTACTCAAG
1 TAGATCGAAGACGGTCATCTTTCTCAGTTTTCAGCAGTTTTAAGTAATTACTCAAG
* * * *
10053 TAGGTAGAAGATGGTCATCCTTTC-CAGTTTTCAGCAGTTTTAAGTAGTTACTCAAG
1 TAGATCGAAGACGGTCAT-CTTTCTCAGTTTTCAGCAGTTTTAAGTAATTACTCAAG
* * *
10109 TTGATCGAAGACGGTCATCTTTCTCAGTTTTCATCAGTTTTTAGTAATTACTCAAG
1 TAGATCGAAGACGGTCATCTTTCTCAGTTTTCAGCAGTTTTAAGTAATTACTCAAG
*
10165 TAGATCGAAGACGATCAT
1 TAGATCGAAGACGGTCAT
10183 TTGTCTTAGA
Statistics
Matches: 158, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
55 10 0.06
56 143 0.91
57 5 0.03
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (56 bp):
TAGATCGAAGACGGTCATCTTTCTCAGTTTTCAGCAGTTTTAAGTAATTACTCAAG
Found at i:10209 original size:56 final size:56
Alignment explanation
Indices: 9983--10209 Score: 163
Period size: 56 Copynumber: 4.1 Consensus size: 56
9973 AGCAGTTTTA
* * * * * * * * **
9983 AGTAGTTACTCAACTTGATCGGAGACGGTCATCTTTCTCAGTTTTCATCAGTTTTT
1 AGTAATTACTCAAGTAGATCGAAGACGATCATCTTTCTCAGATTTCAACAATACTT
* * * * * * * *
10039 AGTAATTACTCAAGTAGGTAGAAGATGGTCATCCTTTC-CAGTTTTCAGCAGT-TTT
1 AGTAATTACTCAAGTAGATCGAAGACGATCAT-CTTTCTCAGATTTCAACAATACTT
* * * * * * **
10094 AAGTAGTTACTCAAGTTGATCGAAGACGGTCATCTTTCTCAGTTTTCATCAGTTTTT
1 -AGTAATTACTCAAGTAGATCGAAGACGATCATCTTTCTCAGATTTCAACAATACTT
*
10151 AGTAATTACTCAAGTAGATCGAAGACGATCAT-TTGTCTTAGATTTCAACAATACTT
1 AGTAATTACTCAAGTAGATCGAAGACGATCATCTT-TCTCAGATTTCAACAATACTT
10207 AGT
1 AGT
10210 GCAGACGTCA
Statistics
Matches: 143, Mismatches: 23, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
55 10 0.07
56 125 0.87
57 8 0.06
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (56 bp):
AGTAATTACTCAAGTAGATCGAAGACGATCATCTTTCTCAGATTTCAACAATACTT
Done.