Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012984.1 Corchorus capsularis cultivar CVL-1 contig13005, 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: 20631
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Found at i:5886 original size:122 final size:120
Alignment explanation
Indices: 5669--5911 Score: 423
Period size: 122 Copynumber: 2.0 Consensus size: 120
5659 TGGTATGATC
* * *
5669 CACCCTAACAAAGGGAGATGAAGGAAAGTTTTGCCAAAGACATTAAAGAAAAGCGCTGCTTGGGA
1 CACCCTAACAAAGGGAGATGAAGGAAAGTCTAGCCAAAGACATTAAAGAAAAGCACTGCTTGGGA
*
5734 GGCAACCCAAGATTTTACTAATATTTTAATTTTCTTTTTAGTTTTGTTTTTCTTTTT
66 GGCAACCCAAGATTTTACTAACATTTTAATTTTC-TTTTAG-TTTGTTTTTCTTTTT
*
5791 CACCCTAACAAAGGGAGATGAAGGAAAGTCTAGCCAAAGACATTAAAGAAAGGCACTGCTTGGGA
1 CACCCTAACAAAGGGAGATGAAGGAAAGTCTAGCCAAAGACATTAAAGAAAAGCACTGCTTGGGA
5856 GGCAACCCAAGATTTTACTAACATTTTAATTTTCTTTTAGTTTGTTTTTCTTTTT
66 GGCAACCCAAGATTTTACTAACATTTTAATTTTCTTTTAGTTTGTTTTTCTTTTT
5911 C
1 C
5912 TTTTTAGGAT
Statistics
Matches: 116, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
120 16 0.14
121 6 0.05
122 94 0.81
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (120 bp):
CACCCTAACAAAGGGAGATGAAGGAAAGTCTAGCCAAAGACATTAAAGAAAAGCACTGCTTGGGA
GGCAACCCAAGATTTTACTAACATTTTAATTTTCTTTTAGTTTGTTTTTCTTTTT
Found at i:9383 original size:46 final size:46
Alignment explanation
Indices: 9316--9425 Score: 220
Period size: 46 Copynumber: 2.4 Consensus size: 46
9306 TTGGGCAATT
9316 ATCACACTGGATCAAGAGGTAATTGTTTAAACAATAAAAGGGATAA
1 ATCACACTGGATCAAGAGGTAATTGTTTAAACAATAAAAGGGATAA
9362 ATCACACTGGATCAAGAGGTAATTGTTTAAACAATAAAAGGGATAA
1 ATCACACTGGATCAAGAGGTAATTGTTTAAACAATAAAAGGGATAA
9408 ATCACACTGGATCAAGAG
1 ATCACACTGGATCAAGAG
9426 TTTTATCTAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 64 1.00
ACGTcount: A:0.45, C:0.13, G:0.20, T:0.23
Consensus pattern (46 bp):
ATCACACTGGATCAAGAGGTAATTGTTTAAACAATAAAAGGGATAA
Found at i:18373 original size:33 final size:33
Alignment explanation
Indices: 18249--18369 Score: 136
Period size: 33 Copynumber: 3.7 Consensus size: 33
18239 GTGTTTTAGA
18249 TGTTGTTTGCGATAATACTAAACCTAATTTGAG
1 TGTTGTTTGCGATAATACTAAACCTAATTTGAG
** *
18282 TGTTGTTTTTGATGATACTAAACCTAATTTGAG
1 TGTTGTTTGCGATAATACTAAACCTAATTTGAG
* * * * *
18315 TGTTGTTTGCAATGACACTAAATCTGATTT-AGG
1 TGTTGTTTGCGATAATACTAAACCTAATTTGA-G
* *
18348 TGTTGTTTGTGATAAAACTAAA
1 TGTTGTTTGCGATAATACTAAA
18370 TCTGTTTTGG
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
32 1 0.01
33 73 0.99
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.41
Consensus pattern (33 bp):
TGTTGTTTGCGATAATACTAAACCTAATTTGAG
Found at i:18442 original size:33 final size:33
Alignment explanation
Indices: 18395--18474 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
18385 AATTGTGATG
* *
18395 AAAACAATTCTGTTTTGGTTGAACATAGCATTA
1 AAAATAATTTTGTTTTGGTTGAACATAGCATTA
*
18428 AAAATAATTTTGTTTTGGTTGATCATAGCATTA
1 AAAATAATTTTGTTTTGGTTGAACATAGCATTA
*
18461 CAAATAATTTTGTT
1 AAAATAATTTTGTT
18475 GATTATAGCA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (33 bp):
AAAATAATTTTGTTTTGGTTGAACATAGCATTA
Found at i:18482 original size:27 final size:28
Alignment explanation
Indices: 18407--18495 Score: 90
Period size: 33 Copynumber: 3.0 Consensus size: 28
18397 AACAATTCTG
* *
18407 TTTTGGTTGAACATAGCATTAAAAATAA
1 TTTTGGTTGATCATAGCATTACAAATAA
18435 TTTTGTTTTGGTTGATCATAGCATTACAAATAA
1 -----TTTTGGTTGATCATAGCATTACAAATAA
* *
18468 TTTT-GTTGATTATAGCATTGCAAATAA
1 TTTTGGTTGATCATAGCATTACAAATAA
18495 T
1 T
18496 CCTGTTTTGG
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
27 22 0.42
28 4 0.08
33 26 0.50
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.43
Consensus pattern (28 bp):
TTTTGGTTGATCATAGCATTACAAATAA
Found at i:18501 original size:27 final size:27
Alignment explanation
Indices: 18445--18501 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
18435 TTTTGTTTTG
**
18445 GTTGATCATAGCATTACAAATAATTTT
1 GTTGATCATAGCATTACAAATAATCCT
* *
18472 GTTGATTATAGCATTGCAAATAATCCT
1 GTTGATCATAGCATTACAAATAATCCT
18499 GTT
1 GTT
18502 TTGGCTAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.40
Consensus pattern (27 bp):
GTTGATCATAGCATTACAAATAATCCT
Done.