Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009337.1 Corchorus capsularis cultivar CVL-1 contig09358, 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: 12273
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:4457 original size:40 final size:40
Alignment explanation
Indices: 4411--4502 Score: 166
Period size: 40 Copynumber: 2.3 Consensus size: 40
4401 GCTAAACCAT
4411 GTACTATTATACTTAGAGTTCTCATTGATTGTAAACTCTA
1 GTACTATTATACTTAGAGTTCTCATTGATTGTAAACTCTA
4451 GTACTATTATACTTAGAGTTCTCATTGATTGTAAACTCTA
1 GTACTATTATACTTAGAGTTCTCATTGATTGTAAACTCTA
*
4491 GTGCTATATATA
1 GTACTAT-TATA
4503 TTAAATGAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 46 0.92
41 4 0.08
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.42
Consensus pattern (40 bp):
GTACTATTATACTTAGAGTTCTCATTGATTGTAAACTCTA
Found at i:5944 original size:23 final size:23
Alignment explanation
Indices: 5917--5963 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
5907 GTATATGGAT
5917 ACAGGTGCCTCTTCTCATATGAC
1 ACAGGTGCCTCTTCTCATATGAC
5940 ACAGGTGCCTCTTCTCATATGAC
1 ACAGGTGCCTCTTCTCATATGAC
5963 A
1 A
5964 AACTCTCTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.30
Consensus pattern (23 bp):
ACAGGTGCCTCTTCTCATATGAC
Found at i:6075 original size:14 final size:14
Alignment explanation
Indices: 6056--6084 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
6046 TCAACTCAAA
6056 TGGCAATATGACTT
1 TGGCAATATGACTT
6070 TGGCAATATGACTT
1 TGGCAATATGACTT
6084 T
1 T
6085 TAACTCATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.38
Consensus pattern (14 bp):
TGGCAATATGACTT
Found at i:6406 original size:2 final size:2
Alignment explanation
Indices: 6399--6423 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6389 AACTGAATAA
6399 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
6424 ATTATAAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10448 original size:149 final size:147
Alignment explanation
Indices: 10167--10460 Score: 383
Period size: 149 Copynumber: 2.0 Consensus size: 147
10157 TTATTTTTTC
** *
10167 TAAGTTTTGCCTTAGGGATGGCGGTGTTTATAAGTACAAACGCCTGCAAATTAACAACTATAACG
1 TAAGTTTTGCCTTAGGGATGGCGGCATTTATAAGTACAAACGCCTGCAAACTAACAACTATAACG
* * * *
10232 GTGTTTACAATAACAAACGCTGTTATAGTTAATTTTCATCTAATTTTTCAATTTTGCGCAGAGAA
66 GCGTTTACAATAACAAACGCCGTTATAGTTAATTTTCAGCTAATTTTCCAATTTTGCGCAGAG-A
10297 AAAAAGAGAGGGAAACCA
130 AAAAAGAGAGGGAAACCA
* * * * *
10315 TAAGTTTTGCCTTCAGGGATGGTGGCATTTATAAGTACAAGCGCC-GCCACACTAAGAACTATTA
1 TAAGTTTTGCCTT-AGGGATGGCGGCATTTATAAGTACAAACGCCTG-CAAACTAACAACTATAA
* ** ** *
10379 CGGCGTTTGCAATAGTAAACGCCGTTATAGTTAATTTTCAGCTAATTTTCCAATTTTGCGTGGAT
64 CGGCGTTTACAATAACAAACGCCGTTATAGTTAATTTTCAGCTAATTTTCCAATTTTGCGCAGAG
*
10444 AAAAATGAGAGGGAAAC
129 AAAAAAGAGAGGGAAAC
10461 TAAAATAGAG
Statistics
Matches: 125, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
148 30 0.24
149 95 0.76
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.30
Consensus pattern (147 bp):
TAAGTTTTGCCTTAGGGATGGCGGCATTTATAAGTACAAACGCCTGCAAACTAACAACTATAACG
GCGTTTACAATAACAAACGCCGTTATAGTTAATTTTCAGCTAATTTTCCAATTTTGCGCAGAGAA
AAAAGAGAGGGAAACCA
Found at i:11287 original size:223 final size:224
Alignment explanation
Indices: 10716--11299 Score: 756
Period size: 223 Copynumber: 2.6 Consensus size: 224
10706 GATCATTTTG
* * * * *
10716 CTAAACCGGCACATTAAACTTTTAGCAACGCCGAAAAGGTGACGACT-GGTG-TGACGCTAAGAG
1 CTAAATCGTCACATTAAACTTTTAGCGACGCGGAAAAGGTGACGACTAGGTGTTG-CGCTAAGAA
* * * * * *
10779 AAATGACAGAAAATATAATATGTAACGAAATTATGATATTTAGTGACATTAATG-TGC-AAG-AA
65 AAACGTCACAAAATACAATATGTGACGAAATTATGATATTTAGTGACATTAATGCTGCTCAGAAA
***
10841 TTCACAATTTTGTGAATGAATGTCACAAAAGCCTCATTAAAAGATGGTGTTTTGTGTTTTTGTCA
130 TTCACAATTTTGTGAATGAATGTCACAAAAGCCTCATTAAAAGATAACGTTTTGTGTTTTTGTCA
10906 CAAAAAACTGATCATTTTGTGACAAAACAA
195 CAAAAAACTGATCATTTTGTGACAAAACAA
* * * * **
10936 CTAAATCGTCACATTAAACTTTTAGCGACGTGGAAAAGGTGACGACCA-CTATAACGCTAAGAAA
1 CTAAATCGTCACATTAAACTTTTAGCGACGCGGAAAAGGTGACGACTAGGTGTTGCGCTAAGAAA
* * * * *
11000 AACATCACAAAATACAATACGTGATGAAATTATGATATATAGTGACATTAATGC-GATGCAGAAA
66 AACGTCACAAAATACAATATGTGACGAAATTATGATATTTAGTGACATTAATGCTGCT-CAGAAA
*
11064 TTCACAATTTTGTGAATTAATGTCACAAAAGCCTCATTAAAAGATAACGTTTTGTGTTTTTGTCA
130 TTCACAATTTTGTGAATGAATGTCACAAAAGCCTCATTAAAAGATAACGTTTTGTGTTTTTGTCA
** * * *
11129 CGTAAAAGTGGTCATTTTGTGACGAAACAA
195 CAAAAAACTGATCATTTTGTGACAAAACAA
*
11159 CTAAATTGTCACATTAAACTTTTAGCGACGCGGAAAAGGTGACGA-TAGGTGTTGCGCTAAGAAA
1 CTAAATCGTCACATTAAACTTTTAGCGACGCGGAAAAGGTGACGACTAGGTGTTGCGCTAAGAAA
*
11223 AACGTTACAAAATACAATATGTGACGAAA-T-TGATATTTAGTGACATTAATGCCTGCGTCAGAA
66 AACGTCACAAAATACAATATGTGACGAAATTATGATATTTAGTGACATTAATG-CTGC-TCAGAA
*
11286 ATTCACAAATTTGT
129 ATTCACAATTTTGT
11300 TTTAGTGTGT
Statistics
Matches: 309, Mismatches: 45, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
220 96 0.31
221 20 0.06
222 5 0.02
223 187 0.61
224 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (224 bp):
CTAAATCGTCACATTAAACTTTTAGCGACGCGGAAAAGGTGACGACTAGGTGTTGCGCTAAGAAA
AACGTCACAAAATACAATATGTGACGAAATTATGATATTTAGTGACATTAATGCTGCTCAGAAAT
TCACAATTTTGTGAATGAATGTCACAAAAGCCTCATTAAAAGATAACGTTTTGTGTTTTTGTCAC
AAAAAACTGATCATTTTGTGACAAAACAA
Done.