Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024109.1 Corchorus olitorius cultivar O-4 contig24142, 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: 34369
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Found at i:1280 original size:41 final size:41
Alignment explanation
Indices: 1235--1337 Score: 134
Period size: 41 Copynumber: 2.5 Consensus size: 41
1225 TTTTTCCGTT
* * * *
1235 TTCAATATAGTCCCTGATTTAGGTTTATACTTGTTAATTTA
1 TTCAATTTAGTCCCTGATTTAGGGTAATACTTGTTAATTGA
* *
1276 TTCAATTTTGTCCCTGATTTAGGGTAATATTTGTTAATTGA
1 TTCAATTTAGTCCCTGATTTAGGGTAATACTTGTTAATTGA
* *
1317 TTCAATTTCGCCCCTGATTTA
1 TTCAATTTAGTCCCTGATTTA
1338 AGATTTTATT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.24, C:0.15, G:0.14, T:0.48
Consensus pattern (41 bp):
TTCAATTTAGTCCCTGATTTAGGGTAATACTTGTTAATTGA
Found at i:1348 original size:41 final size:41
Alignment explanation
Indices: 1246--1354 Score: 123
Period size: 41 Copynumber: 2.7 Consensus size: 41
1236 TCAATATAGT
* * * *
1246 CCCTGATTT-AGGTTTATACTTGTTAATTTATTCAATTTTGT
1 CCCTGATTTAAGGTTT-TATTTGTTAATTGATTCAATTTCGC
* **
1287 CCCTGATTTAGGGTAATATTTGTTAATTGATTCAATTTCGC
1 CCCTGATTTAAGGTTTTATTTGTTAATTGATTCAATTTCGC
*
1328 CCCTGATTTAAGATTTTATTT-TTAATT
1 CCCTGATTTAAGGTTTTATTTGTTAATT
1355 TATGCGGCCT
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
40 6 0.11
41 47 0.84
42 3 0.05
ACGTcount: A:0.24, C:0.13, G:0.13, T:0.50
Consensus pattern (41 bp):
CCCTGATTTAAGGTTTTATTTGTTAATTGATTCAATTTCGC
Found at i:2525 original size:24 final size:25
Alignment explanation
Indices: 2483--2530 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
2473 TTAATTGAAC
2483 AAAAATAAAATAAAATAAAAAATGG
1 AAAAATAAAATAAAATAAAAAATGG
* *
2508 AAAAATCAAA-AAATTAAAAAATG
1 AAAAATAAAATAAAATAAAAAATG
2531 TAATAAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.17
Consensus pattern (25 bp):
AAAAATAAAATAAAATAAAAAATGG
Found at i:4341 original size:20 final size:20
Alignment explanation
Indices: 4320--4387 Score: 118
Period size: 20 Copynumber: 3.4 Consensus size: 20
4310 CAGAGGCAGG
*
4320 TGTTGATTCATAAGACCAGG
1 TGTTGATTCATAAGACCAGC
4340 TGTTGATTCATAAGACCAGC
1 TGTTGATTCATAAGACCAGC
*
4360 TGTTGATTCATAAGCCCAGC
1 TGTTGATTCATAAGACCAGC
4380 TGTTGATT
1 TGTTGATT
4388 TGTGGTTCTA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (20 bp):
TGTTGATTCATAAGACCAGC
Found at i:9649 original size:75 final size:75
Alignment explanation
Indices: 9525--9715 Score: 253
Period size: 75 Copynumber: 2.6 Consensus size: 75
9515 TTAAAATGTC
* * * * * *
9525 GTTGCGTAAAAGATAATT-TTTTAGCAACGAATATATAT--TGTTGTTAAAATATTTTTACGTAG
1 GTTGCGTAAAATATAATTCTTTTAGCAAC-AATA-AAATGGCGTTGTTAAAATATTTTCACGCAA
***
9587 CAATATTTTTTT
64 CAATATTGAGTT
*
9599 GTTGCGTAAAATATAATTCTTTTAGAAACAATAAAATGGCGTTGTTAAAATATTTTCACGCAACA
1 GTTGCGTAAAATATAATTCTTTTAGCAACAATAAAATGGCGTTGTTAAAATATTTTCACGCAACA
9664 ATATTGAGTT
66 ATATTGAGTT
9674 GTTGCGTAAAATATAATTCTTTTAGCAACAATAAAATGGCGT
1 GTTGCGTAAAATATAATTCTTTTAGCAACAATAAAATGGCGT
9716 AACGAAAGGA
Statistics
Matches: 103, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
73 3 0.03
74 21 0.20
75 79 0.77
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (75 bp):
GTTGCGTAAAATATAATTCTTTTAGCAACAATAAAATGGCGTTGTTAAAATATTTTCACGCAACA
ATATTGAGTT
Found at i:14130 original size:18 final size:19
Alignment explanation
Indices: 14107--14142 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
14097 CTGAAATTAT
14107 TCTTCAAA-GGTCTTCAAA
1 TCTTCAAATGGTCTTCAAA
*
14125 TCTTCAAATTGTCTTCAA
1 TCTTCAAATGGTCTTCAA
14143 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (19 bp):
TCTTCAAATGGTCTTCAAA
Found at i:15329 original size:22 final size:22
Alignment explanation
Indices: 15297--15346 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
15287 AAAGGTTTTG
*
15297 AAAAATTCGAAATTTTATCTTC
1 AAAAATCCGAAATTTTATCTTC
* * *
15319 AAAAATCCGAATTTTTTTTTTC
1 AAAAATCCGAAATTTTATCTTC
15341 AAAAAT
1 AAAAAT
15347 TGGGGAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.42
Consensus pattern (22 bp):
AAAAATCCGAAATTTTATCTTC
Found at i:16482 original size:16 final size:17
Alignment explanation
Indices: 16451--16482 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
16441 GCTTAGGCTC
16451 CCCTGTTGCGGCAGCAG
1 CCCTGTTGCGGCAGCAG
16468 CCCTGTTGC-GCAGCA
1 CCCTGTTGCGGCAGCA
16483 ACAACAGCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.12, C:0.38, G:0.31, T:0.19
Consensus pattern (17 bp):
CCCTGTTGCGGCAGCAG
Done.