Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01006155.1 Corchorus olitorius cultivar O-4 contig06180, 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, 666
Length: 1110
ACGTcount: A:0.49, C:0.11, G:0.13, T:0.28
Found at i:300 original size:4 final size:4
Alignment explanation
Indices: 291--539 Score: 103
Period size: 4 Copynumber: 63.8 Consensus size: 4
281 AGATAATAAT
* ** * *
291 AATA AATA AATA GAT- AATA GCTA AATT AATA AAGA AA-A AGATA AAT-
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA A-ATA AATA
* * * * *
337 AGTA AATA AATA GAT- AACA ATTA AATT AATA AATA AA-A AGATA AAT-
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA A-ATA AATA
* * * *
383 AGTA AATA AATA GAT- AATA ATTA AATT AATA AATA AA-A AGATA AAT-
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA A-ATA AATA
* * * * * *
429 AACA AATA AATA GATGA TAGTT AA-A AATA AATAA AAAA AATA AAT- AGTA
1 AATA AATA AATA AAT-A -AATA AATA AATA AAT-A AATA AATA AATA AATA
* * * *
478 AATA AATA GATA ATAGTT AA-A AATA AATA AAAA AATA AAT- AATG AATA
1 AATA AATA AATA A-A-TA AATA AATA AATA AATA AATA AATA AATA AATA
*
526 AAT- AATA AAAA AAT
1 AATA AATA AATA AAT
540 CTTTTTGGTC
Statistics
Matches: 175, Mismatches: 48, Indels: 44
0.66 0.18 0.16
Matches are distributed among these distances:
3 29 0.17
4 131 0.75
5 12 0.07
6 3 0.02
ACGTcount: A:0.67, C:0.01, G:0.07, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:320 original size:27 final size:27
Alignment explanation
Indices: 290--429 Score: 91
Period size: 23 Copynumber: 5.8 Consensus size: 27
280 AAGATAATAA
*
290 TAATAAATAAATAGAT-AATAGCTAAAT
1 TAATAAATAAAAAGATAAATAG-TAAAT
*
317 TAATAAAGAAAAAGATAAATAGT--A-
1 TAATAAATAAAAAGATAAATAGTAAAT
*
341 -AATAAAT----AGATAACA-ATTAAAT
1 TAATAAATAAAAAGATAA-ATAGTAAAT
363 TAATAAATAAAAAGATAAATAGT--A-
1 TAATAAATAAAAAGATAAATAGTAAAT
* *
387 -AATAAATAGATA-AT-AAT--TAAAT
1 TAATAAATAAAAAGATAAATAGTAAAT
409 TAATAAATAAAAAGATAAATA
1 TAATAAATAAAAAGATAAATA
430 ACAAATAAAT
Statistics
Matches: 86, Mismatches: 9, Indels: 37
0.65 0.07 0.28
Matches are distributed among these distances:
19 9 0.10
20 1 0.01
21 5 0.06
22 2 0.02
23 33 0.38
24 2 0.02
25 5 0.06
26 1 0.01
27 23 0.27
28 5 0.06
ACGTcount: A:0.65, C:0.01, G:0.07, T:0.26
Consensus pattern (27 bp):
TAATAAATAAAAAGATAAATAGTAAAT
Found at i:349 original size:46 final size:46
Alignment explanation
Indices: 278--533 Score: 333
Period size: 46 Copynumber: 5.6 Consensus size: 46
268 GTAGCTAAAG
* *
278 AAAAGATAATAATAATAAATAAATAGATAATAGCTAAATTAATAAAGA
1 AAAAGAT-A-AATAATAAATAAATAGATAATAGTTAAATTAATAAATA
* * *
326 AAAAGATAAATAGTAAATAAATAGATAACAATTAAATTAATAAATA
1 AAAAGATAAATAATAAATAAATAGATAATAGTTAAATTAATAAATA
* *
372 AAAAGATAAATAGTAAATAAATAGATAATAATTAAATTAATAAATA
1 AAAAGATAAATAATAAATAAATAGATAATAGTTAAATTAATAAATA
* *
418 AAAAGATAAATAACAAATAAATAGATGATAGTTAAA--AATAAATAA
1 AAAAGATAAATAATAAATAAATAGATAATAGTTAAATTAATAAAT-A
* *
463 AAAAAATAAATAGTAAATAAATAGATAATAGTTAAA--AATAAATA
1 AAAAGATAAATAATAAATAAATAGATAATAGTTAAATTAATAAATA
* *
507 AAAAAATAAATAATGAATAAATA-ATAA
1 AAAAGATAAATAATAAATAAATAGATAA
534 AAAAATCTTT
Statistics
Matches: 191, Mismatches: 16, Indels: 7
0.89 0.07 0.03
Matches are distributed among these distances:
43 4 0.02
44 29 0.15
45 40 0.21
46 110 0.58
47 1 0.01
48 7 0.04
ACGTcount: A:0.67, C:0.01, G:0.07, T:0.25
Consensus pattern (46 bp):
AAAAGATAAATAATAAATAAATAGATAATAGTTAAATTAATAAATA
Found at i:351 original size:19 final size:19
Alignment explanation
Indices: 306--508 Score: 66
Period size: 19 Copynumber: 10.5 Consensus size: 19
296 ATAAATAGAT
* * *
306 AATAGCTAAATTAATAAAGA
1 AATAGATAAA-TAGTAAATA
*
326 AAAAGATAAATAGTAAATA
1 AATAGATAAATAGTAAATA
*
345 AATAGATAACAATTAAATTAATAAATA
1 AATAGAT-A-AA-T--AGT-A-AA-TA
*
372 AAAAGATAAATAGTAAATA
1 AATAGATAAATAGTAAATA
* *
391 AATAGAT-AATAATTAAATT
1 AATAGATAAAT-AGTAAATA
* *
410 AATAAATAAAAAGATAAATA
1 AATAGATAAATAG-TAAATA
430 ACA-A-ATAAATAG---AT-
1 A-ATAGATAAATAGTAAATA
* * *
444 GATAGTTAAA-AATAAATAA
1 AATAGATAAATAGTAAAT-A
* *
463 AAAAAATAAATAGTAAATA
1 AATAGATAAATAGTAAATA
*
482 AATAGAT-AATAGTTAA-A
1 AATAGATAAATAGTAAATA
*
499 AATAAATAAA
1 AATAGATAAA
509 AAAATAAATA
Statistics
Matches: 134, Mismatches: 28, Indels: 44
0.65 0.14 0.21
Matches are distributed among these distances:
13 1 0.01
14 2 0.01
15 6 0.04
17 9 0.07
18 13 0.10
19 53 0.40
20 26 0.19
21 4 0.03
22 3 0.02
24 3 0.02
25 3 0.02
26 3 0.02
27 8 0.06
ACGTcount: A:0.66, C:0.01, G:0.07, T:0.25
Consensus pattern (19 bp):
AATAGATAAATAGTAAATA
Found at i:435 original size:27 final size:27
Alignment explanation
Indices: 385--440 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
375 AGATAAATAG
* * *
385 TAAATAAATAGATAATAATTAAATTAA
1 TAAATAAAAAGATAATAATCAAATAAA
412 TAAATAAAAAGATAAATAA-CAAATAAA
1 TAAATAAAAAGAT-AATAATCAAATAAA
439 TA
1 TA
441 GATGATAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.27
Consensus pattern (27 bp):
TAAATAAAAAGATAATAATCAAATAAA
Found at i:469 original size:9 final size:10
Alignment explanation
Indices: 364--538 Score: 79
Period size: 11 Copynumber: 16.1 Consensus size: 10
354 CAATTAAATT
364 AATAAATAAAA
1 AATAAAT-AAA
*
375 AGATAAATAGTA
1 A-ATAAATA-AA
*
387 AATAAATAGAT
1 AATAAATA-AA
*
398 AATAATTAAA
1 AATAAATAAA
408 TTAATAAATAAAA
1 --AATAAAT-AAA
421 AGATAAATAACA
1 A-ATAAATAA-A
*
433 AATAAATAGAT
1 AATAAATA-AA
* **
444 GATAGTTAAA
1 AATAAATAAA
454 AATAAATAAA
1 AATAAATAAA
464 AA-AAATAAA
1 AATAAATAAA
*
473 TAGTAAATAAA
1 -AATAAATAAA
484 TAGATAATAGTTAAA
1 -A-ATAA-A--TAAA
499 AATAAAT-AA
1 AATAAATAAA
508 AA-AAATAAA
1 AATAAATAAA
*
517 TAATGAATAAA
1 -AATAAATAAA
528 TAATAAA-AAA
1 -AATAAATAAA
538 A
1 A
539 TCTTTTTGGT
Statistics
Matches: 129, Mismatches: 18, Indels: 36
0.70 0.10 0.20
Matches are distributed among these distances:
8 4 0.03
9 14 0.11
10 18 0.14
11 53 0.41
12 27 0.21
13 8 0.06
14 1 0.01
15 4 0.03
ACGTcount: A:0.69, C:0.01, G:0.06, T:0.24
Consensus pattern (10 bp):
AATAAATAAA
Done.