Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010468.1 Corchorus capsularis cultivar CVL-1 contig10489, 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: 47099
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:6927 original size:22 final size:22
Alignment explanation
Indices: 6880--6954 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 22
6870 AGAGCCACTC
*** *
6880 AAATTTCATAAGGAGGCAATTG
1 AAATTTCATAAGGAGATTATTA
*
6902 AAATTTCGTACA-GAGATTATTA
1 AAATTTCATA-AGGAGATTATTA
*
6924 AAATTTCATAAGGAGTTTATTA
1 AAATTTCATAAGGAGATTATTA
*
6946 AGATTTCAT
1 AAATTTCAT
6955 GGTGTGGTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 1 0.02
22 41 0.95
23 1 0.02
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (22 bp):
AAATTTCATAAGGAGATTATTA
Found at i:7013 original size:44 final size:44
Alignment explanation
Indices: 6948--7043 Score: 113
Period size: 44 Copynumber: 2.2 Consensus size: 44
6938 GTTTATTAAG
* * * * *
6948 ATTTCATGGTGTGGTTTCCAAAGTTTCGTACAGA-GATTATCAAA
1 ATTTCATAGTGTGGTTACCAAAATTTCATACAAACG-TTATCAAA
*
6992 ATTTCATAGTGTTGTTACCAAAATTTCATACAAACGTTATCAAA
1 ATTTCATAGTGTGGTTACCAAAATTTCATACAAACGTTATCAAA
*
7036 TTTTCATA
1 ATTTCATA
7044 ATTTGCTTAT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 43 0.98
45 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.39
Consensus pattern (44 bp):
ATTTCATAGTGTGGTTACCAAAATTTCATACAAACGTTATCAAA
Found at i:7134 original size:22 final size:23
Alignment explanation
Indices: 7085--7136 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
7075 ATAGTTATCG
* *
7085 AATTTTTATAAGGAGATTATTAT
1 AATTTTTATAAGGAGATTATCAA
* *
7108 GATTTTT-TAATGAGATTATCAA
1 AATTTTTATAAGGAGATTATCAA
7130 AATTTTT
1 AATTTTT
7137 GAAATTTCGT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.50
Consensus pattern (23 bp):
AATTTTTATAAGGAGATTATCAA
Found at i:8019 original size:35 final size:35
Alignment explanation
Indices: 7973--8044 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
7963 AATAAGAAGT
7973 AAGCAACCAATAATAATGACTCCTATACACGTGCA
1 AAGCAACCAATAATAATGACTCCTATACACGTGCA
8008 AAGCAACCAATAATAATGACTCCTATACACGTGCA
1 AAGCAACCAATAATAATGACTCCTATACACGTGCA
8043 AA
1 AA
8045 CCCATTTAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.44, C:0.25, G:0.11, T:0.19
Consensus pattern (35 bp):
AAGCAACCAATAATAATGACTCCTATACACGTGCA
Found at i:10023 original size:31 final size:31
Alignment explanation
Indices: 9987--10078 Score: 121
Period size: 31 Copynumber: 3.0 Consensus size: 31
9977 TGGTTAATTA
*
9987 AGTCCCTAACATTGCAAAATCGGTTAAAATC
1 AGTCCCTAACATTGCAAAATCGGCTAAAATC
* * *
10018 AGTCCCTAACGTTGCAAAATCCGCTCAAATC
1 AGTCCCTAACATTGCAAAATCGGCTAAAATC
* * *
10049 AGTCCCTAATATTTCAAAATCGGCTCAAAT
1 AGTCCCTAACATTGCAAAATCGGCTAAAAT
10079 TAGCCTAATG
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.36, C:0.26, G:0.12, T:0.26
Consensus pattern (31 bp):
AGTCCCTAACATTGCAAAATCGGCTAAAATC
Found at i:10476 original size:14 final size:15
Alignment explanation
Indices: 10452--10481 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
10442 TTACTATTAT
10452 TTTACTTTATATTTA
1 TTTACTTTATATTTA
10467 TTTA-TTTATATTTA
1 TTTACTTTATATTTA
10481 T
1 T
10482 ATCTAAACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTACTTTATATTTA
Found at i:16091 original size:27 final size:27
Alignment explanation
Indices: 16061--16113 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
16051 CTAAAATGAA
16061 ATTCTCCCTATTAGTTTTGAGTTTTTT
1 ATTCTCCCTATTAGTTTTGAGTTTTTT
16088 ATTCTCCCTATTAGTTTTGAGTTTTT
1 ATTCTCCCTATTAGTTTTGAGTTTTT
16114 ATTTTATGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.15, C:0.15, G:0.11, T:0.58
Consensus pattern (27 bp):
ATTCTCCCTATTAGTTTTGAGTTTTTT
Found at i:16131 original size:27 final size:27
Alignment explanation
Indices: 16101--16154 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
16091 CTCCCTATTA
*
16101 GTTTTGAGTTTT-TATTTTATGCACTGT
1 GTTTTGA-TTTTATATTTGATGCACTGT
*
16128 GTTTTGATTTTATATTTGATGCGCTGT
1 GTTTTGATTTTATATTTGATGCACTGT
16155 TAGTGTATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.15, C:0.07, G:0.20, T:0.57
Consensus pattern (27 bp):
GTTTTGATTTTATATTTGATGCACTGT
Found at i:16377 original size:2 final size:2
Alignment explanation
Indices: 16365--16419 Score: 57
Period size: 2 Copynumber: 29.5 Consensus size: 2
16355 TTATGTAATT
16365 TA TA TA T- TA TA TA T- TA TA TA TA TA -A TA TGA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
*
16404 TA TA T- TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA T
16420 TATTAATCTT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
1 5 0.11
2 38 0.84
3 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (2 bp):
TA
Found at i:16382 original size:5 final size:5
Alignment explanation
Indices: 16374--16422 Score: 55
Period size: 5 Copynumber: 9.6 Consensus size: 5
16364 TTATATATTA
* *
16374 TATAT TATA- TATAT AATAT GATAT ATATAT TATAT TATATT TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT -TATAT TATAT TATA-T TATAT TAT
16423 TAATCTTAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
4 4 0.11
5 25 0.66
6 9 0.24
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (5 bp):
TATAT
Found at i:16383 original size:14 final size:14
Alignment explanation
Indices: 16364--16424 Score: 63
Period size: 14 Copynumber: 4.2 Consensus size: 14
16354 TTTATGTAAT
16364 TTATATATTATATA
1 TTATATATTATATA
16378 TTATATA-TATAATA
1 TTATATATTAT-ATA
*
16392 TGATATATATATTATA
1 TTATATAT-TA-TATA
16408 TTATAT-TTATATTA
1 TTATATATTATA-TA
16422 TTA
1 TTA
16425 ATCTTAATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
13 5 0.12
14 23 0.57
15 1 0.03
16 10 0.25
17 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
TTATATATTATATA
Found at i:16384 original size:16 final size:16
Alignment explanation
Indices: 16365--16422 Score: 66
Period size: 16 Copynumber: 3.6 Consensus size: 16
16355 TTATGTAATT
16365 TATATATTATATATTA
1 TATATATTATATATTA
*
16381 TATATATAATATGA-TA
1 TATATATTATAT-ATTA
16397 TATATATTATAT-TATA
1 TATATATTATATAT-TA
*
16413 TTTATATTAT
1 TATATATTAT
16423 TAATCTTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
16 35 0.97
17 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
TATATATTATATATTA
Found at i:19868 original size:14 final size:14
Alignment explanation
Indices: 19851--19889 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
19841 CAAATGACAA
19851 CTGACTTGCTGTTG
1 CTGACTTGCTGTTG
*
19865 CTGAGTTGCTGTTG
1 CTGACTTGCTGTTG
*
19879 CTGGCTTGCTG
1 CTGACTTGCTG
19890 CATTCTGGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.05, C:0.21, G:0.33, T:0.41
Consensus pattern (14 bp):
CTGACTTGCTGTTG
Found at i:20702 original size:17 final size:17
Alignment explanation
Indices: 20680--20714 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
20670 AGATAAATCA
20680 TTATTATTTCTAACGTT
1 TTATTATTTCTAACGTT
20697 TTATTATTTCTAACGTT
1 TTATTATTTCTAACGTT
20714 T
1 T
20715 CCTCTTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.11, G:0.06, T:0.60
Consensus pattern (17 bp):
TTATTATTTCTAACGTT
Found at i:26564 original size:61 final size:62
Alignment explanation
Indices: 26433--26564 Score: 194
Period size: 61 Copynumber: 2.1 Consensus size: 62
26423 TGTCAGTGTA
* * * *
26433 TCAAATAAAAAACAACTTAGACCCTTCCATAAAAAAATGTTGAAGCTTAAGAATAGCACAAT
1 TCAATTAAGAAACAACTTAGACCCTTCCATAAAAAAAGGTTGAAGCTTAAGAATAGCACAAC
* *
26495 TCATTTAAGAAACAACTT-GACCCTTCCATAAAAAAAGGTTGAAGCTTAAGAATAGCCCAAC
1 TCAATTAAGAAACAACTTAGACCCTTCCATAAAAAAAGGTTGAAGCTTAAGAATAGCACAAC
*
26556 TGAATTAAG
1 TCAATTAAG
26565 CCGAGTAGAA
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
61 47 0.76
62 15 0.24
ACGTcount: A:0.46, C:0.18, G:0.12, T:0.23
Consensus pattern (62 bp):
TCAATTAAGAAACAACTTAGACCCTTCCATAAAAAAAGGTTGAAGCTTAAGAATAGCACAAC
Found at i:39211 original size:2 final size:2
Alignment explanation
Indices: 39204--39233 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
39194 TTTAGAGTTA
39204 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39234 TGTTATTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44160 original size:16 final size:16
Alignment explanation
Indices: 44139--44171 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
44129 AACACACAAT
44139 GCAGAAAAGCTCTGAA
1 GCAGAAAAGCTCTGAA
44155 GCAGAAAAGCTCTGAA
1 GCAGAAAAGCTCTGAA
44171 G
1 G
44172 TATTTCAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.18, G:0.27, T:0.12
Consensus pattern (16 bp):
GCAGAAAAGCTCTGAA
Found at i:44627 original size:67 final size:68
Alignment explanation
Indices: 44540--44716 Score: 304
Period size: 68 Copynumber: 2.6 Consensus size: 68
44530 AATTCCCAAG
* *
44540 TCATCAA-TTCAAGATTAAGTCATTCGACTCTTGAATCAAATCAAATCAAATCAAG-TTCTCAAA
1 TCATCAAGTTCAAGATCAAGTCATTCGACCCTTGAATCAAATCAAATCAAATCAAGATTCTCAAA
44603 TTA
66 TTA
*
44606 TCATCAAGTTCAAGACCAAGTCATTCGACCCTTGAATCAAATCAAATCAAATCAAGATTCTCAAA
1 TCATCAAGTTCAAGATCAAGTCATTCGACCCTTGAATCAAATCAAATCAAATCAAGATTCTCAAA
44671 TTA
66 TTA
*
44674 TCATCAAGTTCAAGATCAAGTCATTCGACCCTTGAAGCAAATC
1 TCATCAAGTTCAAGATCAAGTCATTCGACCCTTGAATCAAATC
44717 TTGAAGCATA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
66 7 0.07
67 45 0.43
68 52 0.50
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.28
Consensus pattern (68 bp):
TCATCAAGTTCAAGATCAAGTCATTCGACCCTTGAATCAAATCAAATCAAATCAAGATTCTCAAA
TTA
Found at i:46542 original size:64 final size:66
Alignment explanation
Indices: 46451--46592 Score: 252
Period size: 64 Copynumber: 2.2 Consensus size: 66
46441 TCAGTCAACC
* *
46451 CAAAAAAAAAAAGGCTCGCTAAGTTGAAAATCCTGCAAATGACGGCTTAGGCAAAAGTTAGAG-C
1 CAAAAAAAAAAAGGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAACTTAGAGAC
46515 A
66 A
46516 -AAAAAAAAAAAGGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAACTTAGAGAC
1 CAAAAAAAAAAAGGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAACTTAGAGAC
46580 A
66 A
46581 CAAAAAAAAAAA
1 CAAAAAAAAAAA
46593 ATGAATGAAC
Statistics
Matches: 73, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
64 60 0.82
65 2 0.03
66 11 0.15
ACGTcount: A:0.49, C:0.16, G:0.20, T:0.15
Consensus pattern (66 bp):
CAAAAAAAAAAAGGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAACTTAGAGAC
A
Done.