Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010066.1 Corchorus olitorius cultivar O-4 contig10098, 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: 5811
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Found at i:49 original size:21 final size:21
Alignment explanation
Indices: 25--90 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
15 CCTTAGAATT
*
25 TTATTAATGTAAGTATTTCAG
1 TTATTAATGTAAGTATTTAAG
* *
46 TTATT-A--T-AGTATTAAAT
1 TTATTAATGTAAGTATTTAAG
*
63 TTAATTAATGTAAGTATTTTAG
1 TT-ATTAATGTAAGTATTTAAG
85 TTATTA
1 TTATTA
91 TATATATTAC
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
17 9 0.26
18 4 0.12
19 1 0.03
20 1 0.03
21 10 0.29
22 9 0.26
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.52
Consensus pattern (21 bp):
TTATTAATGTAAGTATTTAAG
Found at i:329 original size:2 final size:2
Alignment explanation
Indices: 318--354 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
308 AGTTTAGACT
*
318 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
355 CTAGTTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:442 original size:22 final size:22
Alignment explanation
Indices: 413--493 Score: 110
Period size: 22 Copynumber: 3.7 Consensus size: 22
403 TGAATATTTT
413 TATAAAATTTTGATAATTACCC
1 TATAAAATTTTGATAATTACCC
* ** *
435 TATTAAATTTTGATAACCACCA
1 TATAAAATTTTGATAATTACCC
457 TATAAAATTTTGATAATTA-CC
1 TATAAAATTTTGATAATTACCC
*
478 TATAAAATTGTGATAA
1 TATAAAATTTTGATAA
494 ACTCCATATG
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 16 0.32
22 34 0.68
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (22 bp):
TATAAAATTTTGATAATTACCC
Found at i:501 original size:43 final size:44
Alignment explanation
Indices: 413--515 Score: 145
Period size: 43 Copynumber: 2.4 Consensus size: 44
403 TGAATATTTT
* * *
413 TATAAAATTTTGATAATTACCCTATTAAATTTTGATAACCACCA
1 TATAAAATTTTGATAATTACCCTATAAAATTGTGATAAACACCA
*
457 TATAAAATTTTGATAATTA-CCTATAAAATTGTGATAAACTCCA
1 TATAAAATTTTGATAATTACCCTATAAAATTGTGATAAACACCA
* *
500 TATGAAACTTTGATAA
1 TATAAAATTTTGATAA
516 CCTAACTATG
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 34 0.64
44 19 0.36
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.38
Consensus pattern (44 bp):
TATAAAATTTTGATAATTACCCTATAAAATTGTGATAAACACCA
Found at i:530 original size:65 final size:64
Alignment explanation
Indices: 413--537 Score: 146
Period size: 65 Copynumber: 1.9 Consensus size: 64
403 TGAATATTTT
* * * * *
413 TATAAAATTTTGATAATTACCCTATTAAATTTTGATAACCACCATATAAAATTTTGATAATTACC
1 TATAAAATTGTGATAA-TACCCTATGAAACTTTGATAACCAACATATAAAATTTTAATAATTACC
*
478 TATAAAATTGTGATAA-ACTCCATATGAAACTTTGATAACCTAAC-TATGAAATTTTAATAA
1 TATAAAATTGTGATAATAC-CC-TATGAAACTTTGATAACC-AACATATAAAATTTTAATAA
538 ATTTTCCTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
63 2 0.04
64 2 0.04
65 45 0.88
66 2 0.04
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.38
Consensus pattern (64 bp):
TATAAAATTGTGATAATACCCTATGAAACTTTGATAACCAACATATAAAATTTTAATAATTACC
Found at i:566 original size:20 final size:21
Alignment explanation
Indices: 462--609 Score: 79
Period size: 22 Copynumber: 6.9 Consensus size: 21
452 CACCATATAA
* *
462 AATTTTGATAAT-TACCTATAA
1 AATTTTGATAATCTTCCTAT-G
* *
483 AATTGTGATAAAC-TCCATATG
1 AATTTTGATAATCTTCC-TATG
* * **
504 AAACTTTGATAACCTAACTATG
1 -AATTTTGATAATCTTCCTATG
* *
526 AAATTTTAATAAATTTTCCTATG
1 -AATTTTGAT-AATCTTCCTATG
549 AATTTTG-TAATCTTCCTATG
1 AATTTTGATAATCTTCCTATG
* *
569 ATTTTTGATAATC-TCTCTGTG
1 AATTTTGATAATCTTC-CTATG
* *
590 AAATTTTGTTAATCTCCCTA
1 -AATTTTGATAATCTTCCTA
610 CAATTTTTTG
Statistics
Matches: 95, Mismatches: 23, Indels: 17
0.70 0.17 0.13
Matches are distributed among these distances:
20 19 0.20
21 22 0.23
22 44 0.46
23 10 0.11
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (21 bp):
AATTTTGATAATCTTCCTATG
Found at i:582 original size:21 final size:20
Alignment explanation
Indices: 541--609 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 20
531 TTAATAAATT
541 TTCCTATGAATTTTGTAATC
1 TTCCTATGAATTTTGTAATC
*
561 TTCCTATGATTTTTGATAATC
1 TTCCTATGAATTTTG-TAATC
*
582 -TCTCTGTGAAATTTTGTTAATC
1 TTC-CTATG-AATTTTG-TAATC
*
604 TCCCTA
1 TTCCTA
610 CAATTTTTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.41
21 9 0.23
22 13 0.33
23 1 0.03
ACGTcount: A:0.23, C:0.17, G:0.10, T:0.49
Consensus pattern (20 bp):
TTCCTATGAATTTTGTAATC
Found at i:1927 original size:2 final size:2
Alignment explanation
Indices: 1920--1948 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1910 CTGGCCAATA
1920 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1949 ACAATAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.