Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024631.1 Corchorus olitorius cultivar O-4 contig24664, 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: 3821
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Found at i:128 original size:38 final size:39
Alignment explanation
Indices: 51--130 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 39
41 ATCTTTTTGA
* ** * *
51 AAAACATTTTTTCTCTTTTAAAAAGATTGCACTTTGAGG
1 AAAACATTTTTTCTCTTTGAAAAAGATCACACCTAGAGG
*
90 AAAACATTTTTTCT-TTTGAAAAAGATCACGCCTAGAGG
1 AAAACATTTTTTCTCTTTGAAAAAGATCACACCTAGAGG
128 AAA
1 AAA
131 GTTTCATTCC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
38 21 0.60
39 14 0.40
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (39 bp):
AAAACATTTTTTCTCTTTGAAAAAGATCACACCTAGAGG
Found at i:341 original size:20 final size:22
Alignment explanation
Indices: 307--354 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
297 TCCTTTCCTC
307 TTTCTTTTGCTTTTTCAACT-T
1 TTTCTTTTGCTTTTTCAACTCT
*
328 TTTCTTTT-CTTTTTCAATTCT
1 TTTCTTTTGCTTTTTCAACTCT
349 TTTCTT
1 TTTCTT
355 CATTTTCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.08, C:0.19, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTCTTTTGCTTTTTCAACTCT
Found at i:745 original size:14 final size:13
Alignment explanation
Indices: 710--757 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
700 AAAACCGATT
*
710 TTTTTGAAAACCC
1 TTTTTGAAAACAC
723 TTTTCTGAAAACAC
1 TTTT-TGAAAACAC
737 TTTCTTGAAAAGCA-
1 TTT-TTGAAAA-CAC
751 TTTTTGA
1 TTTTTGA
758 CTTTTGAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
13 8 0.26
14 20 0.65
15 3 0.10
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (13 bp):
TTTTTGAAAACAC
Found at i:3362 original size:4 final size:4
Alignment explanation
Indices: 3331--3569 Score: 95
Period size: 4 Copynumber: 60.5 Consensus size: 4
3321 AAAAATATTA
*
3331 AAAT AAAAT AAA- AAAGT -AAT AGAT AAAT AAAT AAAT AAAT AAAT AGAA-
1 AAAT -AAAT AAAT AAA-T AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT
* * * ** * *
3379 AAAT AAGT AAAA ATAAT AGAT AAAT AAA- AAGAT AAAT AGGT ATAT AGAT
1 AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT
* * ** * * *
3428 AATT AGAT AAAT AGGT AAGT AAA- AAA- AAGT AGAT AATAGT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA-A-T AAAT AAAT
* ** * * *
3476 AGAT -AAT AGCT AAAT TAAT AAAT AAAT AGAT AAAT -AGT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* ** * *
3522 AGAT -AAT AGTT AAAT TAAT AAAT AAA- AATAT AAAT -AGT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT
3568 AA
1 AA
3570 CAAAAAATCT
Statistics
Matches: 169, Mismatches: 48, Indels: 35
0.67 0.19 0.14
Matches are distributed among these distances:
3 23 0.14
4 128 0.76
5 15 0.09
6 3 0.02
ACGTcount: A:0.64, C:0.00, G:0.10, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:3415 original size:12 final size:12
Alignment explanation
Indices: 3348--3568 Score: 117
Period size: 12 Copynumber: 19.3 Consensus size: 12
3338 ATAAAAAAGT
3348 AATAGATAAATA
1 AATAGATAAATA
*
3360 AATAAATAAATA
1 AATAGATAAATA
*
3372 AATAGAAAAATA
1 AATAGATAAATA
*
3384 AGTA-A-AAAT-
1 AATAGATAAATA
3393 AATAGATAAATA
1 AATAGATAAATA
*
3405 AAAAGATAAATA
1 AATAGATAAATA
** * *
3417 GGTATATAGATA
1 AATAGATAAATA
*
3429 ATTAGATAAATA
1 AATAGATAAATA
**
3441 GGTA-AGTAAA-A
1 AATAGA-TAAATA
* *
3452 AAAAG-TAGAT-
1 AATAGATAAATA
3462 AATAG-TAAATA
1 AATAGATAAATA
3473 AATAGAT-AATA
1 AATAGATAAATA
** * *
3484 GCTAAATTAATA
1 AATAGATAAATA
* *
3496 AATAAATAGATA
1 AATAGATAAATA
3508 AATAG-TAAATA
1 AATAGATAAATA
3519 AATAGAT-AATA
1 AATAGATAAATA
** * *
3530 GTTAAATTAATA
1 AATAGATAAATA
*
3542 AATA-AAAATATA
1 AATAGATAA-ATA
3554 AATAG-TAAATA
1 AATAGATAAATA
3565 AATA
1 AATA
3569 ACAAAAAATC
Statistics
Matches: 156, Mismatches: 40, Indels: 27
0.70 0.18 0.12
Matches are distributed among these distances:
9 3 0.02
10 16 0.10
11 48 0.31
12 89 0.57
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.26
Consensus pattern (12 bp):
AATAGATAAATA
Found at i:3502 original size:27 final size:26
Alignment explanation
Indices: 3467--3569 Score: 94
Period size: 27 Copynumber: 4.1 Consensus size: 26
3457 TAGATAATAG
3467 TAAATAAATAGATAATAGCTAAATTAA
1 TAAATAAATAGATAATAG-TAAATTAA
*
3494 TAAATAAATAG-----A-TAAA-TAG
1 TAAATAAATAGATAATAGTAAATTAA
3513 TAAATAAATAGATAATAGTTAAATTAA
1 TAAATAAATAGATAATAG-TAAATTAA
* * *
3540 TAAATAAAAATATAAATAGTAAATAAA
1 TAAATAAATAGAT-AATAGTAAATTAA
3567 TAA
1 TAA
3570 CAAAAAATCT
Statistics
Matches: 62, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
19 13 0.21
20 4 0.06
22 1 0.02
24 1 0.02
26 4 0.06
27 34 0.55
28 5 0.08
ACGTcount: A:0.63, C:0.01, G:0.07, T:0.29
Consensus pattern (26 bp):
TAAATAAATAGATAATAGTAAATTAA
Found at i:3514 original size:46 final size:46
Alignment explanation
Indices: 3347--3568 Score: 203
Period size: 46 Copynumber: 5.0 Consensus size: 46
3337 AATAAAAAAG
* * * * *
3347 TAATAGATAAATAAATAAATAAATAAATAGAAAAATAAGTAAA-A-A
1 TAATAGATAAATTAATAAATAAATAGATA-AATAGTAAATAAATAGA
* * * *
3392 TAATAGATAAA-TAAAAAGATAAATAGGT--ATA-TAGATAATTAGA
1 TAATAGATAAATTAATAA-ATAAATAGATAAATAGTAAATAAATAGA
* *
3435 TAAATAGGT-AAGTAA-AAA-AAAGTAGAT-AATAGTAAATAAATAGA
1 T-AATAGATAAATTAATAAATAAA-TAGATAAATAGTAAATAAATAGA
*
3479 TAATAGCTAAATTAATAAATAAATAGATAAATAGTAAATAAATAGA
1 TAATAGATAAATTAATAAATAAATAGATAAATAGTAAATAAATAGA
* * *
3525 TAATAGTTAAATTAATAAATAAAAATATAAATAGTAAATAAATA
1 TAATAGATAAATTAATAAATAAATAGATAAATAGTAAATAAATA
3569 ACAAAAAATC
Statistics
Matches: 148, Mismatches: 17, Indels: 23
0.79 0.09 0.12
Matches are distributed among these distances:
41 8 0.05
42 8 0.05
43 15 0.10
44 29 0.20
45 27 0.18
46 61 0.41
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (46 bp):
TAATAGATAAATTAATAAATAAATAGATAAATAGTAAATAAATAGA
Done.