Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013344.1 Corchorus olitorius cultivar O-4 contig13377, 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: 23682
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:12415 original size:4 final size:4
Alignment explanation
Indices: 12408--12613 Score: 61
Period size: 4 Copynumber: 52.2 Consensus size: 4
12398 TTTATAACTA
* * *
12408 TTAT TTAT CTT-T TTAT TTA- TTAGT TTAG CTA- TTAT CTAT TTAT TTA-
1 TTAT TTAT -TTAT TTAT TTAT TTA-T TTAT TTAT TTAT TTAT TTAT TTAT
* * * * * *
12454 CTAT TTAT TCTTT TTAT TTAT TAAT TTAG CTA- TTAT CTAT TTAT TTA-
1 TTAT TTAT T-TAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * * * * * * *
12501 TTA- TTAT CTCTTT TTCT TTTT TTCT TT-T TTAC CTAT CTAT TTAT CTAT
1 TTAT TTAT -T-TAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * * * * * * * *
12549 TTAT GGTAC CTAT TTAT CTAT TTAT CTAT ATAC CTAT TTAT CT-T TTAT
1 TTAT -TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
12597 TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT T
12614 ATTATTATTA
Statistics
Matches: 147, Mismatches: 41, Indels: 28
0.68 0.19 0.13
Matches are distributed among these distances:
3 22 0.15
4 111 0.76
5 12 0.08
6 2 0.01
ACGTcount: A:0.22, C:0.11, G:0.02, T:0.65
Consensus pattern (4 bp):
TTAT
Found at i:12449 original size:27 final size:26
Alignment explanation
Indices: 12412--12505 Score: 101
Period size: 27 Copynumber: 3.8 Consensus size: 26
12402 TAACTATTAT
*
12412 TTATCTTTTTATTTATTAGTTTAGCTA
1 TTATCTATTTATTTATTA-TTTAGCTA
*
12439 TTATCTATTTATTTACTA-TT---TA
1 TTATCTATTTATTTATTATTTAGCTA
*
12461 -T-TCTTTTTATTTATTAATTTAGCTA
1 TTATCTATTTATTTATT-ATTTAGCTA
12486 TTATCTATTTATTTATTATT
1 TTATCTATTTATTTATTATT
12506 ATCTCTTTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
20 12 0.22
21 2 0.04
22 4 0.07
25 4 0.07
26 4 0.07
27 29 0.53
ACGTcount: A:0.24, C:0.07, G:0.03, T:0.65
Consensus pattern (26 bp):
TTATCTATTTATTTATTATTTAGCTA
Found at i:12450 original size:8 final size:8
Alignment explanation
Indices: 12421--12616 Score: 74
Period size: 8 Copynumber: 24.5 Consensus size: 8
12411 TTTATCTTTT
12421 TATTTAT-
1 TATTTATC
*
12428 TAGTTTAGC
1 TA-TTTATC
12437 TA-TTATC
1 TATTTATC
12444 TATTTATTTAC
1 TATTTA--T-C
12455 TATTTAT-
1 TATTTATC
*
12462 TCTTT-T-
1 TATTTATC
12468 TATTTAT-
1 TATTTATC
*
12475 TAATTTAGC
1 T-ATTTATC
12484 TA-TTATC
1 TATTTATC
*
12491 TATTTATT
1 TATTTATC
12499 TATTATTATC
1 TA-T-TTATC
* *
12509 TCTTTTTC
1 TATTTATC
* *
12517 TTTTTTTC
1 TATTTATC
12525 T-TTT-T-
1 TATTTATC
**
12530 TACCTATC
1 TATTTATC
12538 TATTTATC
1 TATTTATC
12546 TATTTATGGTACC
1 TATTTA---T--C
12559 TATTTATC
1 TATTTATC
12567 TATTTATC
1 TATTTATC
* *
12575 TATATACC
1 TATTTATC
12583 TATTTATC
1 TATTTATC
*
12591 T-TTTATT
1 TATTTATC
*
12598 TATTTATT
1 TATTTATC
12606 TATTTAT-
1 TATTTATC
12613 TATT
1 TATT
12617 ATTATTATCA
Statistics
Matches: 148, Mismatches: 20, Indels: 42
0.70 0.10 0.20
Matches are distributed among these distances:
5 1 0.01
6 7 0.05
7 34 0.23
8 78 0.53
9 6 0.04
10 7 0.05
11 8 0.05
13 7 0.05
ACGTcount: A:0.23, C:0.11, G:0.03, T:0.64
Consensus pattern (8 bp):
TATTTATC
Found at i:12468 original size:47 final size:47
Alignment explanation
Indices: 12409--12515 Score: 173
Period size: 47 Copynumber: 2.3 Consensus size: 47
12399 TTATAACTAT
*
12409 TATTTA-TCTTTTTATTTATTAGTTTAGCTATTATCTATTTATTTAC
1 TATTTATTCTTTTTATTTATTAATTTAGCTATTATCTATTTATTTAC
*
12455 TATTTATTCTTTTTATTTATTAATTTAGCTATTATCTATTTATTTAT
1 TATTTATTCTTTTTATTTATTAATTTAGCTATTATCTATTTATTTAC
12502 TA-TTATCTCTTTTT
1 TATTTAT-TCTTTTT
12516 CTTTTTTTCT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
46 10 0.18
47 47 0.82
ACGTcount: A:0.23, C:0.08, G:0.03, T:0.65
Consensus pattern (47 bp):
TATTTATTCTTTTTATTTATTAATTTAGCTATTATCTATTTATTTAC
Found at i:12475 original size:28 final size:27
Alignment explanation
Indices: 12439--12503 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 27
12429 AGTTTAGCTA
* * *
12439 TTATCTATTTATTTA-CTATTTATTCTTT
1 TTATTTATTAATTTAGCTA-TTA-TCTAT
12467 TTATTTATTAATTTAGCTATTATCTAT
1 TTATTTATTAATTTAGCTATTATCTAT
12494 TTATTTATTA
1 TTATTTATTA
12504 TTATCTCTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 14 0.42
28 16 0.48
29 3 0.09
ACGTcount: A:0.26, C:0.08, G:0.02, T:0.65
Consensus pattern (27 bp):
TTATTTATTAATTTAGCTATTATCTAT
Found at i:12617 original size:3 final size:3
Alignment explanation
Indices: 12609--12671 Score: 117
Period size: 3 Copynumber: 21.0 Consensus size: 3
12599 ATTTATTTAT
*
12609 TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12657 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
12672 ACTTATTTTT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:17948 original size:19 final size:18
Alignment explanation
Indices: 17924--17959 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
17914 TGAAGACTTA
17924 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
17943 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
17960 ATTATCTCGA
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
Done.