Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006388.1 Corchorus capsularis cultivar CVL-1 contig06409, 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: 23565
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Found at i:3709 original size:33 final size:32
Alignment explanation
Indices: 3612--3716 Score: 129
Period size: 33 Copynumber: 3.2 Consensus size: 32
3602 TTGCAAAGAG
*
3612 TGTTTTAGATGTTGTTTGCGATGATACTAAACC
1 TGTTTTAG-TGTTGTTTGCGATGATACTAAATC
* * *
3645 TAATTTGAGTGTTGTTTGCGATGACACTAAATC
1 T-GTTTTAGTGTTGTTTGCGATGATACTAAATC
* *
3678 TGTTTTAAGTGTTGTTTGTGATGATAATAAATC
1 TGTTTT-AGTGTTGTTTGCGATGATACTAAATC
3711 TGTTTT
1 TGTTTT
3717 GGTTGATCAT
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
32 3 0.05
33 53 0.87
34 5 0.08
ACGTcount: A:0.25, C:0.09, G:0.21, T:0.46
Consensus pattern (32 bp):
TGTTTTAGTGTTGTTTGCGATGATACTAAATC
Found at i:3771 original size:32 final size:33
Alignment explanation
Indices: 3703--3783 Score: 119
Period size: 32 Copynumber: 2.5 Consensus size: 33
3693 TTGTGATGAT
* *
3703 AATAAATCTGTTTTGGTTGATCATAGCATTGGA
1 AATAATTCTGTTTTGGTTGATCATAGCATTGAA
* *
3736 AATAATTCTGTTTTGGTTGAT-GTGGCATTGAA
1 AATAATTCTGTTTTGGTTGATCATAGCATTGAA
3768 AATAATTCTGTTTTGG
1 AATAATTCTGTTTTGG
3784 GTGAAAAGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
32 24 0.55
33 20 0.45
ACGTcount: A:0.27, C:0.07, G:0.22, T:0.43
Consensus pattern (33 bp):
AATAATTCTGTTTTGGTTGATCATAGCATTGAA
Found at i:5407 original size:19 final size:18
Alignment explanation
Indices: 5383--5422 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5373 TTGAAGATTT
*
5383 ATTGAAGATAATTTGAAGA
1 ATTGAAGACAA-TTGAAGA
*
5402 ATTGAAGACCATTGAAGA
1 ATTGAAGACAATTGAAGA
5420 ATT
1 ATT
5423 ATTTCAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (18 bp):
ATTGAAGACAATTGAAGA
Found at i:8062 original size:32 final size:31
Alignment explanation
Indices: 8002--8063 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
7992 TAACCCTAAC
*
8002 AAATAGCGGCGTCTAGGACCCAAACGCCGCT
1 AAATAGCGGCATCTAGGACCCAAACGCCGCT
* * *
8033 AAATAGTGGCATCTGGGATCCCAGACGCCGC
1 AAATAGCGGCATCTAGGA-CCCAAACGCCGC
8064 CATACTTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 15 0.58
32 11 0.42
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.15
Consensus pattern (31 bp):
AAATAGCGGCATCTAGGACCCAAACGCCGCT
Found at i:8157 original size:31 final size:32
Alignment explanation
Indices: 8115--8190 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 32
8105 GAAGCCTAAC
* *
8115 AAATAGCGGCGT-ATAGGCCCTAAACGCCGCT
1 AAATAGTGGCGTCATAGGCCATAAACGCCGCT
* * * *
8146 AAATAGTGGCGTCTTATGTCATAGACGCCGCT
1 AAATAGTGGCGTCATAGGCCATAAACGCCGCT
*
8178 AAATGGTGGCGTC
1 AAATAGTGGCGTC
8191 TGGTATCTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 11 0.30
32 26 0.70
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.22
Consensus pattern (32 bp):
AAATAGTGGCGTCATAGGCCATAAACGCCGCT
Found at i:8176 original size:113 final size:112
Alignment explanation
Indices: 7892--8159 Score: 430
Period size: 112 Copynumber: 2.4 Consensus size: 112
7882 AAAATTGAAT
* * *
7892 ATAGCGGCGTCTTGACCATAAACGCCGCTAAATAGTGGCGTCTGGGATCCCAGACGCCGCCATAC
1 ATAGCGGCGTCTAGGCCCTAAACGCCGCTAAATAGTGGCGTCTGGGATCCCAGACGCCGCCATAC
* *
7957 TTGATTTTTCCGGAGAATTGCAAATTGAGTAAAAATAACCCTAACAA
66 TTAATTTTTCCGGAGAAATGCAAATTGAGTAAAAATAACCCTAACAA
*
8004 ATAGCGGCGTCTAGGACCC-AAACGCCGCTAAATAGTGGCATCTGGGATCCCAGACGCCGCCATA
1 ATAGCGGCGTCTAGG-CCCTAAACGCCGCTAAATAGTGGCGTCTGGGATCCCAGACGCCGCCATA
* *
8068 CTTAATTTTTTCGGAGAAATGCAAATTGAGTAAAAATGAAGCCTAACAA
65 CTTAATTTTTCCGGAGAAATGCAAATTGAGTAAAAAT-AACCCTAACAA
*
8117 ATAGCGGCGTATAGGCCCTAAACGCCGCTAAATAGTGGCGTCT
1 ATAGCGGCGTCTAGGCCCTAAACGCCGCTAAATAGTGGCGTCT
8160 TATGTCATAG
Statistics
Matches: 143, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
112 94 0.66
113 49 0.34
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.22
Consensus pattern (112 bp):
ATAGCGGCGTCTAGGCCCTAAACGCCGCTAAATAGTGGCGTCTGGGATCCCAGACGCCGCCATAC
TTAATTTTTCCGGAGAAATGCAAATTGAGTAAAAATAACCCTAACAA
Found at i:8285 original size:31 final size:31
Alignment explanation
Indices: 8243--8319 Score: 84
Period size: 32 Copynumber: 2.5 Consensus size: 31
8233 GAAGCCTAAC
* *
8243 AAATAGCGGCGTCTA-GGCCCTAAACGCCGCT
1 AAATAGTGGCGTCTATGGCAC-AAACGCCGCT
* *
8274 AAATAGTGGCGTCTTATGTCACAGACGCCGCT
1 AAATAGTGGCGTC-TATGGCACAAACGCCGCT
*
8306 AAATGGTGGCGTCT
1 AAATAGTGGCGTCT
8320 GGGATACCAG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
31 13 0.33
32 23 0.59
33 3 0.08
ACGTcount: A:0.25, C:0.26, G:0.27, T:0.22
Consensus pattern (31 bp):
AAATAGTGGCGTCTATGGCACAAACGCCGCT
Found at i:8300 original size:128 final size:133
Alignment explanation
Indices: 8064--8448 Score: 575
Period size: 128 Copynumber: 2.8 Consensus size: 133
8054 CAGACGCCGC
* *
8064 CATACTTAATTTTTTCGGAGAAATGCAAATTGAGTAAAAATGAAGCCTAACAAATAGCGGCGTAT
1 CATACTTAATTTTTTCGGAGAAATGCAAAGTGAGTAAAAATGAAGCCTAACAAATAGCGGCGTCT
*
8129 AGGCCCTAAACGCCGCTAAATAGTGGCGTCTTATGTCATAGACGCCGCTAAATGGTGGCGTCT-G
66 AGGCCCTAAACGCCGCTAAATAGTGGCGTCTTATGTCACAGACGCCGCTAAATGGTGGCGTCTGG
8193 G-T
131 GAT
8195 -AT-CTTAATTTTTTCGGAGAAATGC-AAGTGAGTAAAAATGAAGCCTAACAAATAGCGGCGTCT
1 CATACTTAATTTTTTCGGAGAAATGCAAAGTGAGTAAAAATGAAGCCTAACAAATAGCGGCGTCT
8257 AGGCCCTAAACGCCGCTAAATAGTGGCGTCTTATGTCACAGACGCCGCTAAATGGTGGCGTCTGG
66 AGGCCCTAAACGCCGCTAAATAGTGGCGTCTTATGTCACAGACGCCGCTAAATGGTGGCGTCTGG
8322 GAT
131 GAT
8325 ACCAGACGCCGCCATACTTAATTTTTTCGGAGAAATGCAAAGTGAGTAAAAATGAAGCCTAACAA
1 ------------CATACTTAATTTTTTCGGAGAAATGCAAAGTGAGTAAAAATGAAGCCTAACAA
* *
8390 ATAGCGGCGTCTAGGCCCTAAACGCTGCTAAATAGTGGCGT-TTATGTCCCAGACGCCGC
54 ATAGCGGCGTCTAGGCCCTAAACGCCGCTAAATAGTGGCGTCTTATGTCACAGACGCCGC
8449 CATACTTAAT
Statistics
Matches: 232, Mismatches: 5, Indels: 21
0.90 0.02 0.08
Matches are distributed among these distances:
128 98 0.42
129 24 0.10
130 3 0.01
143 2 0.01
144 39 0.17
145 66 0.28
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (133 bp):
CATACTTAATTTTTTCGGAGAAATGCAAAGTGAGTAAAAATGAAGCCTAACAAATAGCGGCGTCT
AGGCCCTAAACGCCGCTAAATAGTGGCGTCTTATGTCACAGACGCCGCTAAATGGTGGCGTCTGG
GAT
Found at i:16302 original size:19 final size:18
Alignment explanation
Indices: 16278--16313 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
16268 TGAAGATTTC
16278 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
16297 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
16314 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:23560 original size:20 final size:21
Alignment explanation
Indices: 23521--23561 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
23511 AGTCGACTAA
**
23521 GAGCAAAGTCGACTTTACAAG
1 GAGCAAAGTCGACTACACAAG
23542 GAGCAAA-TCGACTACACAAG
1 GAGCAAAGTCGACTACACAAG
23562 TCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.15
Consensus pattern (21 bp):
GAGCAAAGTCGACTACACAAG
Done.