Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010139.1 Corchorus capsularis cultivar CVL-1 contig10160, 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: 22093
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:7516 original size:21 final size:21
Alignment explanation
Indices: 7482--7528 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
7472 CTATGCCATA
*
7482 TTTGTAGTAGAATT-TTTTATAT
1 TTTGTAGTAAAATTATTTT-T-T
7504 TTTGT-GTAAAATTATTTTTT
1 TTTGTAGTAAAATTATTTTTT
7524 TTTGT
1 TTTGT
7529 TTTTTTTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 6 0.26
21 8 0.35
22 9 0.39
ACGTcount: A:0.23, C:0.00, G:0.13, T:0.64
Consensus pattern (21 bp):
TTTGTAGTAAAATTATTTTTT
Found at i:9475 original size:12 final size:12
Alignment explanation
Indices: 9450--9486 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
9440 ACAATCTTTC
*
9450 TTTTCATCTA-T
1 TTTTCTTCTAGT
9461 TTTTC-TCTAGT
1 TTTTCTTCTAGT
9472 TTTTCTTCTAGT
1 TTTTCTTCTAGT
9484 TTT
1 TTT
9487 AGCTAAGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.17
11 11 0.46
12 9 0.38
ACGTcount: A:0.11, C:0.16, G:0.05, T:0.68
Consensus pattern (12 bp):
TTTTCTTCTAGT
Found at i:10334 original size:28 final size:27
Alignment explanation
Indices: 10301--10360 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
10291 AGATTTGAAG
*
10301 GAGATGTACTGAGAAAGAAAAAAAGAGA
1 GAGATGGACTGAGAAA-AAAAAAAGAGA
**
10329 GAGATGGACTGAGGGAAAAAAAAGAGA
1 GAGATGGACTGAGAAAAAAAAAAGAGA
10356 GAGAT
1 GAGAT
10361 TACAATGTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 16 0.55
28 13 0.45
ACGTcount: A:0.53, C:0.03, G:0.33, T:0.10
Consensus pattern (27 bp):
GAGATGGACTGAGAAAAAAAAAAGAGA
Found at i:14119 original size:134 final size:134
Alignment explanation
Indices: 13906--14177 Score: 386
Period size: 134 Copynumber: 2.0 Consensus size: 134
13896 GTTTTTGCCT
*
13906 TAAGGATGGCGGTTTTTTAAGTACAAACGCCAACACACAAACAACTATTACGGCGTTTCAATAAC
1 TAAGGATGGCGGGTTTTTAAGTACAAACGCCAACACACAAACAACTATTACGGCGTTTCAATAAC
* * * *
13971 AAACACCGTTTATAGTTAATTTTCAGCTAATTTTCCAATTTTGCGC-TAAAAAAAAAAGTAAACT
66 AAACACCGTGTATAGTTAATTTTCAGCTAATTTTCCAATTTTGCGCGGAAAAAAAAAAGGAAACC
14035 AGAA
131 AGAA
** ** * * *
14039 TAAGGATGGCGGCGTTTTTAAGTACAAATTCCGCCACACTAACAACTATTATGGTGTTTCCAATA
1 TAAGGATGGCGG-GTTTTTAAGTACAAACGCCAACACACAAACAACTATTACGGCGTTT-CAATA
*
14104 ACAAACGCCG-GTATAGTTAATTTTCAGCTAATTTTCCAATTTTGCGCGGGAAAAAAAAAAGGAA
64 ACAAACACCGTGTATAGTTAATTTTCAGCTAATTTTCCAATTTTGCGC-GGAAAAAAAAAAGGAA
14168 ACCAGAA
128 ACCAGAA
14175 TAA
1 TAA
14178 CGCGCCTAAT
Statistics
Matches: 122, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
133 12 0.10
134 74 0.61
135 14 0.11
136 22 0.18
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (134 bp):
TAAGGATGGCGGGTTTTTAAGTACAAACGCCAACACACAAACAACTATTACGGCGTTTCAATAAC
AAACACCGTGTATAGTTAATTTTCAGCTAATTTTCCAATTTTGCGCGGAAAAAAAAAAGGAAACC
AGAA
Found at i:18581 original size:25 final size:25
Alignment explanation
Indices: 18547--18596 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
18537 CTATTGTCAA
18547 TTGATTTTAGGTTGGCATAATAATG
1 TTGATTTTAGGTTGGCATAATAATG
18572 TTGATTTTAGGTTGGCATAATAATG
1 TTGATTTTAGGTTGGCATAATAATG
18597 ATGCCAAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.04, G:0.24, T:0.44
Consensus pattern (25 bp):
TTGATTTTAGGTTGGCATAATAATG
Found at i:20543 original size:28 final size:28
Alignment explanation
Indices: 20502--20556 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
20492 GACAGCCAAT
* * *
20502 ACACACACATAGAGAGATAGAGAGATAG
1 ACACAAACACAGAGAGACAGAGAGATAG
20530 ACACAAACACAGAGAGACAGAGAGATA
1 ACACAAACACAGAGAGACAGAGAGATA
20557 CACCGGATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.53, C:0.16, G:0.24, T:0.07
Consensus pattern (28 bp):
ACACAAACACAGAGAGACAGAGAGATAG
Found at i:21303 original size:75 final size:82
Alignment explanation
Indices: 21205--21412 Score: 259
Period size: 75 Copynumber: 2.6 Consensus size: 82
21195 TAGTAATGGA
*
21205 AATATCTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAG-AAAT-AA-AAGAA
1 AATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAAATAAATAAGAA
*
21267 TAA-T-AA-AGT-TGAG
66 AAATTGAATAGTATGAG
* * *
21280 AATATTTTTTAAATCTTGTCAAATTGTGGAAGATTTAGGAGATATTTTAAGAAACAAATAAATAA
1 AATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAG--A-AAATAAATAA
*
21345 TAAAAATTGAATAGTAATGAG
63 GAAAAATTGAATAGT-ATGAG
*
21366 AATATTTCTCTAAATCTTGCCAGATTGTGGGAGATTTAGGAGATATT
1 AATATTT-TCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATT
21413 AAATAATAAT
Statistics
Matches: 111, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
75 47 0.42
79 4 0.04
80 2 0.02
81 6 0.05
82 1 0.01
83 2 0.02
84 3 0.03
86 11 0.10
87 35 0.32
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (82 bp):
AATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAAATAAATAAGAA
AAATTGAATAGTATGAG
Done.