Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023584.1 Corchorus olitorius cultivar O-4 contig23617, 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: 12213
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Found at i:3814 original size:43 final size:43
Alignment explanation
Indices: 3494--3822 Score: 440
Period size: 43 Copynumber: 7.8 Consensus size: 43
3484 CCAATAACCA
* * * *
3494 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTCC
1 AAAGTCCTCAAACACATATATAACACAGAGGCATCTCTATTAC
3537 AAAGTCCTCAAACACATATATAACACAGAGGCA--TCTATTAC
1 AAAGTCCTCAAACACATATATAACACAGAGGCATCTCTATTAC
* *
3578 AAAGTCCCCAAACACATATATAACACA-AGGGCAACTCTATTAC
1 AAAGTCCTCAAACACATATATAACACAGA-GGCATCTCTATTAC
* *
3621 AAAGTCCTCAAACATATATATAACACAGAGGCATCTATA-T-C
1 AAAGTCCTCAAACACATATATAACACAGAGGCATCTCTATTAC
* * *
3662 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTAC
1 AAAGTCCTCAAACACATATATAACACAGAGGCATCTCTATTAC
*
3705 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATA-T-C
1 AAAGTCCTCAAACACATATATAACACAGAGGCATCTCTATTAC
* *
3746 AAAGT-CTCCAAACACATATATAACATAGGGGCATCTCTATTAC
1 AAAGTCCT-CAAACACATATATAACACAGAGGCATCTCTATTAC
* *
3789 ATAGTCCTCAAACACATATATAACATAGAGGCAT
1 AAAGTCCTCAAACACATATATAACACAGAGGCAT
3823 TTCTCCTTAT
Statistics
Matches: 254, Mismatches: 22, Indels: 20
0.86 0.07 0.07
Matches are distributed among these distances:
40 3 0.01
41 106 0.42
42 4 0.02
43 138 0.54
44 3 0.01
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.22
Consensus pattern (43 bp):
AAAGTCCTCAAACACATATATAACACAGAGGCATCTCTATTAC
Found at i:3851 original size:84 final size:84
Alignment explanation
Indices: 3494--3822 Score: 561
Period size: 84 Copynumber: 3.9 Consensus size: 84
3484 CCAATAACCA
*
3494 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTCCAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
3559 ACACAGAGGCATCTAT-TAC
66 ACACAGAGGCATCTATAT-C
* * *
3578 AAAGTCCCCAAACACATATATAACACAAGGGCAACTCTATTACAAAGTCCTCAAACATATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
3643 ACACAGAGGCATCTATATC
66 ACACAGAGGCATCTATATC
3662 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
3727 ACACAGAGGCATCTATATC
66 ACACAGAGGCATCTATATC
* * * *
3746 AAAGTCTCCAAACACATATATAACATAGGGGCATCTCTATTACATAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
*
3811 ACATAGAGGCAT
66 ACACAGAGGCAT
3823 TTCTCCTTAT
Statistics
Matches: 232, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
84 231 1.00
85 1 0.00
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.22
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATC
Found at i:5965 original size:11 final size:10
Alignment explanation
Indices: 5949--5995 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
5939 AAACTCGTGT
5949 TTGAAGACTCA
1 TTGAAGA-TCA
*
5960 TTGAAGATAA
1 TTGAAGATCA
5970 TTTGAAGAT--
1 -TTGAAGATCA
5979 TTGAAGATCA
1 TTGAAGATCA
5989 TTGAAGA
1 TTGAAGA
5996 ATTATTTCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 8 0.25
10 9 0.28
11 15 0.47
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.32
Consensus pattern (10 bp):
TTGAAGATCA
Found at i:5984 original size:19 final size:18
Alignment explanation
Indices: 5960--5995 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5950 TGAAGACTCA
5960 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
5979 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
5996 ATTATTTCAA
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
Found at i:9408 original size:51 final size:52
Alignment explanation
Indices: 9352--9450 Score: 182
Period size: 51 Copynumber: 1.9 Consensus size: 52
9342 TTGTTTGTCT
9352 TATCTTCATCTCCATCTATTTTTAATCCA-TCTTTTGATTAATAAACCCGAA
1 TATCTTCATCTCCATCTATTTTTAATCCATTCTTTTGATTAATAAACCCGAA
*
9403 TATCTTCATCTCCATCTATTTTTAATCCATTTTTTTGATTAATAAACC
1 TATCTTCATCTCCATCTATTTTTAATCCATTCTTTTGATTAATAAACC
9451 TGAAGCTGAA
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
51 29 0.63
52 17 0.37
ACGTcount: A:0.28, C:0.22, G:0.03, T:0.46
Consensus pattern (52 bp):
TATCTTCATCTCCATCTATTTTTAATCCATTCTTTTGATTAATAAACCCGAA
Found at i:10648 original size:15 final size:16
Alignment explanation
Indices: 10624--10663 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
10614 AGAGGTTGAA
*
10624 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
10639 CGAAAACAATTAAACT
1 AGAAAACAATTAAACT
10655 AGAAAACAA
1 AGAAAACAA
10664 AGCAAAGTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.62, C:0.15, G:0.10, T:0.12
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:12024 original size:19 final size:18
Alignment explanation
Indices: 11991--12026 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
11981 TTGAAACAGA
11991 TCTTCAAAAATCTTCAAG
1 TCTTCAAAAATCTTCAAG
*
12009 TCTTCAAATTATCTTCAA
1 TCTTCAAA-AATCTTCAA
12027 ATGGTCTTCA
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:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (18 bp):
TCTTCAAAAATCTTCAAG
Done.