Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006784.1 Corchorus capsularis cultivar CVL-1 contig06805, 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: 42337
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Found at i:1416 original size:30 final size:29
Alignment explanation
Indices: 1395--1458 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 29
1385 AATCGACATC
1395 TCTTGCCCATCTTAGTAAACAAATTCAAGT
1 TCTTGCCCATCTTAGTAAAC-AATTCAAGT
1425 TCTTGCCCATCTTAGTAAACAAATTCAAGT
1 TCTTGCCCATCTTAGTAAAC-AATTCAAGT
1455 TCTT
1 TCTT
1459 TTGCATGCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.31, C:0.23, G:0.09, T:0.36
Consensus pattern (29 bp):
TCTTGCCCATCTTAGTAAACAATTCAAGT
Found at i:3486 original size:57 final size:57
Alignment explanation
Indices: 3394--3519 Score: 236
Period size: 57 Copynumber: 2.2 Consensus size: 57
3384 TTACTGCGTT
3394 CGTC-CCCTTGAGGACCAAACAAACGATCCTTGAATCGTAAACTTAAGTACGACAAA
1 CGTCTCCCTTGAGGACCAAACAAACGATCCTTGAATCGTAAACTTAAGTACGACAAA
*
3450 CGTCTCCCTTGAGGACCAAACAAACGATCCTTGAATCGTAAACTTAAGTATGACAAA
1 CGTCTCCCTTGAGGACCAAACAAACGATCCTTGAATCGTAAACTTAAGTACGACAAA
3507 CGTCTCCCTTGAG
1 CGTCTCCCTTGAG
3520 ACCGTTTTGC
Statistics
Matches: 68, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
56 4 0.06
57 64 0.94
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (57 bp):
CGTCTCCCTTGAGGACCAAACAAACGATCCTTGAATCGTAAACTTAAGTACGACAAA
Found at i:3586 original size:67 final size:67
Alignment explanation
Indices: 3471--3774 Score: 465
Period size: 67 Copynumber: 4.6 Consensus size: 67
3461 AGGACCAAAC
* *
3471 AAACGATCCTTGAATCGT-AAACTTAAG-TATGACAAACGTCTCCCTTGAGACCGTTTTGCTAAG
1 AAACGATCCTTGAATCGTAAAACTTAAGCGA-GACGAACGTCTCCCTTGAGACCGTTTTGCTAAG
3534 ATA
65 ATA
* * *
3537 AAACGATCCTTGAATCGTAAAACTTAAGCGAGACGAATGTCTCCCTTGAGACCGTTTGGCTAAAA
1 AAACGATCCTTGAATCGTAAAACTTAAGCGAGACGAACGTCTCCCTTGAGACCGTTTTGCTAAGA
3602 TGA
66 T-A
*
3605 AAACGATCCTTGAATCGT-AGACTTAAGCGAGACGAACGTCTCCCTTGAGACCGTTTTGCTAA-A
1 AAACGATCCTTGAATCGTAAAACTTAAGCGAGACGAACGTCTCCCTTGAGACCGTTTTGCTAAGA
3668 GT-
66 -TA
* * *
3670 GAACGGTCCTCGAATCGTAAAACTTAAGCGAGACGAACGTCTCCCTTGAGACCGTTTTGCTAAGA
1 AAACGATCCTTGAATCGTAAAACTTAAGCGAGACGAACGTCTCCCTTGAGACCGTTTTGCTAAGA
3735 TA
66 TA
3737 AAACGATCCTTGAATCGTAAAACTTAAGCGAGACGAAC
1 AAACGATCCTTGAATCGTAAAACTTAAGCGAGACGAAC
3775 TCCAAAAAAT
Statistics
Matches: 216, Mismatches: 15, Indels: 13
0.89 0.06 0.05
Matches are distributed among these distances:
65 15 0.07
66 63 0.29
67 118 0.55
68 20 0.09
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (67 bp):
AAACGATCCTTGAATCGTAAAACTTAAGCGAGACGAACGTCTCCCTTGAGACCGTTTTGCTAAGA
TA
Found at i:3762 original size:133 final size:134
Alignment explanation
Indices: 3471--3774 Score: 472
Period size: 133 Copynumber: 2.3 Consensus size: 134
3461 AGGACCAAAC
* *
3471 AAACGATCCTTGAATCGTAAACTTAAG-TATGACAAACGTCTCCCTTGAGACCGTTTTGCTAAGA
1 AAACGATCCTTGAATCGTAAACTTAAGCGA-GACGAACGTCTCCCTTGAGACCGTTTTGCTAAGA
* *
3535 TAAAACGATCCTTGAATCGTAAAACTTAAGCGAGACGAATGTCTCCCTTGAGACCGTTTGGCTAA
65 TAAAACGATCCTCGAATCGTAAAACTTAAGCGAGACGAACGTCTCCCTTGAGACCGTTTGGCTAA
3600 AATGA
130 AATGA
*
3605 AAACGATCCTTGAATCGTAGACTTAAGCGAGACGAACGTCTCCCTTGAGACCGTTTTGCTAA-AG
1 AAACGATCCTTGAATCGTAAACTTAAGCGAGACGAACGTCTCCCTTGAGACCGTTTTGCTAAGA-
* * *
3669 T-GAACGGTCCTCGAATCGTAAAACTTAAGCGAGACGAACGTCTCCCTTGAGACCGTTTTGCTAA
65 TAAAACGATCCTCGAATCGTAAAACTTAAGCGAGACGAACGTCTCCCTTGAGACCGTTTGGCTAA
*
3733 GAT-A
130 AATGA
3737 AAACGATCCTTGAATCGTAAAACTTAAGCGAGACGAAC
1 AAACGATCCTTGAATCGT-AAACTTAAGCGAGACGAAC
3775 TCCAAAAAAT
Statistics
Matches: 157, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
132 19 0.12
133 79 0.50
134 58 0.37
135 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (134 bp):
AAACGATCCTTGAATCGTAAACTTAAGCGAGACGAACGTCTCCCTTGAGACCGTTTTGCTAAGAT
AAAACGATCCTCGAATCGTAAAACTTAAGCGAGACGAACGTCTCCCTTGAGACCGTTTGGCTAAA
ATGA
Found at i:12455 original size:17 final size:18
Alignment explanation
Indices: 12433--12473 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
12423 AAAAAAAAAC
*
12433 TTGTTTGTACCTG-ATAT
1 TTGTTTGTAACTGTATAT
*
12450 TTGTTTGTAAGTGTATAT
1 TTGTTTGTAACTGTATAT
12468 TTGTTT
1 TTGTTT
12474 CCACACATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.17, C:0.05, G:0.20, T:0.59
Consensus pattern (18 bp):
TTGTTTGTAACTGTATAT
Found at i:27265 original size:7 final size:6
Alignment explanation
Indices: 27238--27270 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
27228 TTTTTCGTTA
*
27238 TTTTAT TTTTAT TTTTAT TTTTAC TTTT-T TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
27271 CGTTTTAGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Done.