Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007240.1 Corchorus capsularis cultivar CVL-1 contig07261, 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: 34690
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:2766 original size:36 final size:35
Alignment explanation
Indices: 2702--2774 Score: 103
Period size: 36 Copynumber: 2.1 Consensus size: 35
2692 GCAGAAACAG
* *
2702 AAAATAAAAATATTTTTTTTTAAGGAAAAA-CGGA
1 AAAATAAAAATAATTTTTTTTAAAGAAAAATCGGA
2736 AAAATAAAAAATTAATTTTTTTTAAAGAAAAATCGGA
1 AAAAT-AAAAA-TAATTTTTTTTAAAGAAAAATCGGA
2773 AA
1 AA
2775 CCGTAATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
34 5 0.15
35 5 0.15
36 18 0.53
37 6 0.18
ACGTcount: A:0.56, C:0.03, G:0.10, T:0.32
Consensus pattern (35 bp):
AAAATAAAAATAATTTTTTTTAAAGAAAAATCGGA
Found at i:3184 original size:11 final size:11
Alignment explanation
Indices: 3164--3193 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
3154 AAAGCAAAGG
*
3164 AAATCAAATCT
1 AAATCTAATCT
3175 AAATCTAATCT
1 AAATCTAATCT
3186 AAATCTAA
1 AAATCTAA
3194 AGCAGATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (11 bp):
AAATCTAATCT
Found at i:3208 original size:12 final size:13
Alignment explanation
Indices: 3191--3235 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
3181 AATCTAAATC
3191 TAAAGCAGATT-A
1 TAAAGCAGATTAA
*
3203 TAAAGCAAATTAA
1 TAAAGCAGATTAA
3216 TAAAGCAGATTAA
1 TAAAGCAGATTAA
3229 TAAAGCA
1 TAAAGCA
3236 AACAATAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22
Consensus pattern (13 bp):
TAAAGCAGATTAA
Found at i:3242 original size:25 final size:25
Alignment explanation
Indices: 3191--3243 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
3181 AATCTAAATC
*
3191 TAAAGCAGATTATAAAGCAAATTAA
1 TAAAGCAGATTATAAAGCAAATCAA
3216 TAAAGCAGATTAATAAAGCAAA-CAA
1 TAAAGCAGATT-ATAAAGCAAATCAA
3241 TAA
1 TAA
3244 TTATAAAGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.58, C:0.09, G:0.11, T:0.21
Consensus pattern (25 bp):
TAAAGCAGATTATAAAGCAAATCAA
Found at i:5079 original size:27 final size:30
Alignment explanation
Indices: 5025--5094 Score: 76
Period size: 27 Copynumber: 2.5 Consensus size: 30
5015 CCCAGGGGCA
**
5025 TTTTGGTCATTTTATTACATTCGGGGGCTC
1 TTTTGGTCATTTTATTACATTCAAGGGCTC
*
5055 TTTTGGT-A-TTT-TTACATTCAAGGGC-A
1 TTTTGGTCATTTTATTACATTCAAGGGCTC
*
5081 TTTAGGTCATTTTA
1 TTTTGGTCATTTTA
5095 AGTTTACTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
26 6 0.18
27 13 0.39
28 6 0.18
29 1 0.03
30 7 0.21
ACGTcount: A:0.19, C:0.13, G:0.20, T:0.49
Consensus pattern (30 bp):
TTTTGGTCATTTTATTACATTCAAGGGCTC
Found at i:6016 original size:12 final size:12
Alignment explanation
Indices: 5999--6035 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
5989 TCTGATCAAA
5999 ACAGTGAGCAAT
1 ACAGTGAGCAAT
6011 ACAGTGAGCAAT
1 ACAGTGAGCAAT
6023 ACAGTGAGCAAT
1 ACAGTGAGCAAT
6035 A
1 A
6036 AGGCTCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.43, C:0.16, G:0.24, T:0.16
Consensus pattern (12 bp):
ACAGTGAGCAAT
Found at i:10370 original size:9 final size:9
Alignment explanation
Indices: 10352--10388 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
10342 GGCCCCGAAG
10352 TATATATAT
1 TATATATAT
*
10361 TATGTATAT
1 TATATATAT
10370 TATATATAT
1 TATATATAT
10379 TAATATATAT
1 T-ATATATAT
10389 GTTTTTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (9 bp):
TATATATAT
Found at i:10485 original size:20 final size:20
Alignment explanation
Indices: 10460--10518 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
10450 AGATATGTTT
10460 TACTAATAAATAATAATATA
1 TACTAATAAATAATAATATA
*
10480 TACTAATAAAT-A-AATATT
1 TACTAATAAATAATAATATA
* *
10498 TACTAATTTACTAATAATATA
1 TACTAA-TAAATAATAATATA
10519 AATATATATT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
18 11 0.34
19 4 0.12
20 12 0.38
21 5 0.16
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (20 bp):
TACTAATAAATAATAATATA
Found at i:15712 original size:69 final size:69
Alignment explanation
Indices: 15601--15881 Score: 429
Period size: 69 Copynumber: 4.1 Consensus size: 69
15591 AAAGCCCCTA
* * *
15601 AAAAGCCCTTGCTGCTTGGAGGGAACCAAGGCTTAAATTGACTCGTAAGGAAACGAGTTTGGCTT
1 AAAAGCCCATGCTGCTTGGATGGAACCAAGGCTTAAATTGACTCGTATGGAAACGAGTTTGGCTT
15666 GTGG
66 GTGG
* *
15670 AAAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAATTGACTCGTATGGAAACGAGTTTGTCTT
1 AAAAGCCCATGCTGCTTGGATGGAACCAAGGCTTAAATTGACTCGTATGGAAACGAGTTTGGCTT
15735 GTGG
66 GTGG
* *
15739 AAAAGCCCATGTTGTTTGGATGGAACCAAGGCTTAAATTGACTCGTATGGAAACGAGTTTGGCTT
1 AAAAGCCCATGCTGCTTGGATGGAACCAAGGCTTAAATTGACTCGTATGGAAACGAGTTTGGCTT
15804 GT-G
66 GTGG
* * * * *
15807 AAAATGCCCATCCTACTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACAAGTTTGACT
1 AAAA-GCCCATGCTGCTTGGATGGAACCAAGGCTTAAATTGACTCGTATGGAAACGAGTTTGGCT
*
15872 TATGG
65 TGTGG
15877 AAAAG
1 AAAAG
15882 TCAAAGTATT
Statistics
Matches: 195, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
68 5 0.03
69 185 0.95
70 5 0.03
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.27
Consensus pattern (69 bp):
AAAAGCCCATGCTGCTTGGATGGAACCAAGGCTTAAATTGACTCGTATGGAAACGAGTTTGGCTT
GTGG
Found at i:17416 original size:23 final size:22
Alignment explanation
Indices: 17381--17440 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 22
17371 TTCACTTCCA
17381 ATTTTC-TCTTCTTTTTTGTTTC
1 ATTTTCTTCTTCTTTTTT-TTTC
17403 ATTTTCTTCTTCTTTTTTTTTC
1 ATTTTCTTCTTCTTTTTTTTTC
*
17425 ATTTTCGTTTTTCTTT
1 ATTTTC-TTCTTCTTT
17441 CCTTCTTCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
22 16 0.46
23 19 0.54
ACGTcount: A:0.05, C:0.17, G:0.03, T:0.75
Consensus pattern (22 bp):
ATTTTCTTCTTCTTTTTTTTTC
Found at i:28973 original size:12 final size:13
Alignment explanation
Indices: 28956--29000 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
28946 AATCTAAATC
28956 TAAAGCAGATT-A
1 TAAAGCAGATTAA
*
28968 TAAAGCAAATTAA
1 TAAAGCAGATTAA
28981 TAAAGCAGATTAA
1 TAAAGCAGATTAA
28994 TAAAGCA
1 TAAAGCA
29001 AACAATAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22
Consensus pattern (13 bp):
TAAAGCAGATTAA
Found at i:29007 original size:25 final size:25
Alignment explanation
Indices: 28956--29008 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
28946 AATCTAAATC
*
28956 TAAAGCAGATTATAAAGCAAATTAA
1 TAAAGCAGATTATAAAGCAAATCAA
28981 TAAAGCAGATTAATAAAGCAAA-CAA
1 TAAAGCAGATT-ATAAAGCAAATCAA
29006 TAA
1 TAA
29009 TTATAAAGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.58, C:0.09, G:0.11, T:0.21
Consensus pattern (25 bp):
TAAAGCAGATTATAAAGCAAATCAA
Done.