Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021321.1 Corchorus olitorius cultivar O-4 contig21354, 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: 14764
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:9648 original size:24 final size:21
Alignment explanation
Indices: 9622--9705 Score: 73
Period size: 24 Copynumber: 3.8 Consensus size: 21
9612 AATTCAAAAA
9622 AAATCAATCAATCAAAAATCATC
1 AAATCAATCAATCAAAAA--ATC
**
9645 AAAAGAAATC-ATCAAAAAATC
1 -AAATCAATCAATCAAAAAATC
9666 AAATCAAAGTCAATCAAAAAAATC
1 AAATC-AA-TCAATC-AAAAAATC
*
9690 AAATCAA-AAATCAAAA
1 AAATCAATCAATCAAAA
9706 TCAAAATCAA
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
20 7 0.14
21 9 0.18
22 2 0.04
23 13 0.25
24 20 0.39
ACGTcount: A:0.64, C:0.17, G:0.02, T:0.17
Consensus pattern (21 bp):
AAATCAATCAATCAAAAAATC
Found at i:9671 original size:13 final size:13
Alignment explanation
Indices: 9655--9711 Score: 59
Period size: 13 Copynumber: 4.5 Consensus size: 13
9645 AAAAGAAATC
9655 ATCAAAAAATCAA
1 ATCAAAAAATCAA
*
9668 ATC--AAAGTC-A
1 ATCAAAAAATCAA
9678 ATCAAAAAAATCAA
1 ATC-AAAAAATCAA
9692 ATC-AAAAATCAAA
1 ATCAAAAAATC-AA
9705 ATCAAAA
1 ATCAAAA
9712 TCAAAAGAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
10 4 0.11
11 5 0.14
12 7 0.19
13 13 0.36
14 7 0.19
ACGTcount: A:0.67, C:0.16, G:0.02, T:0.16
Consensus pattern (13 bp):
ATCAAAAAATCAA
Found at i:9707 original size:6 final size:6
Alignment explanation
Indices: 9684--9717 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
9674 GTCAATCAAA
9684 AAAATC -AAATC AAAAATC AAAATC AAAATC AAAA
1 AAAATC AAAATC -AAAATC AAAATC AAAATC AAAA
9718 GAGAATTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.19
6 16 0.62
7 5 0.19
ACGTcount: A:0.71, C:0.15, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATC
Found at i:9716 original size:24 final size:22
Alignment explanation
Indices: 9622--9705 Score: 75
Period size: 21 Copynumber: 3.8 Consensus size: 22
9612 AATTCAAAAA
* *
9622 AAATCAATCAATCAAAAATCATC
1 AAATCAAACAATCAAAAA-AATC
**
9645 AAAAGAAATC-ATC-AAAAAATC
1 AAATCAAA-CAATCAAAAAAATC
9666 AAATCAAAGTCAATCAAAAAAATC
1 AAATCAAA--CAATCAAAAAAATC
9690 AAATCAAA-AATCAAAA
1 AAATCAAACAATCAAAA
9706 TCAAAATCAA
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
21 17 0.33
22 6 0.12
23 11 0.22
24 17 0.33
ACGTcount: A:0.64, C:0.17, G:0.02, T:0.17
Consensus pattern (22 bp):
AAATCAAACAATCAAAAAAATC
Found at i:10394 original size:50 final size:50
Alignment explanation
Indices: 10319--10555 Score: 336
Period size: 50 Copynumber: 4.7 Consensus size: 50
10309 AGATTTCTTT
* *
10319 CCATTT-ATGAGTTCAAGATCAAAATTCACTGTTCAAAATAAAATTGCTTA
1 CCATTTGA-GAGTTCAAGATCAAAATTCGCTTTTCAAAATAAAATTGCTTA
*
10369 CCATTTGAGAGTTCAAGATCAAAATTCGCTTTTCAAAATAAAATTGCTTT
1 CCATTTGAGAGTTCAAGATCAAAATTCGCTTTTCAAAATAAAATTGCTTA
*
10419 CCATTTAAGAGTTCAAGATCAAAATTCGCTTTTCAAAATAAAATTGCTTGA
1 CCATTTGAGAGTTCAAGATCAAAATTCGCTTTTCAAAATAAAATTGCTT-A
* * *
10470 -CATTTGAGAGTTCAAGATTAAAATTCGCTTTTCAAAGTAAGATTGCATT-
1 CCATTTGAGAGTTCAAGATCAAAATTCGCTTTTCAAAATAAAATTGC-TTA
* * *
10519 CCAGTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAA
1 CCATTTGAGAGTTCAAGATCAAAATTCGCTTTTCAAA
10556 GGACATTTAA
Statistics
Matches: 170, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
50 167 0.98
51 3 0.02
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (50 bp):
CCATTTGAGAGTTCAAGATCAAAATTCGCTTTTCAAAATAAAATTGCTTA
Found at i:10493 original size:100 final size:100
Alignment explanation
Indices: 10315--10555 Score: 376
Period size: 100 Copynumber: 2.4 Consensus size: 100
10305 AACAAGATTT
* *
10315 CTTTCCATTTATGAGTTCAAGATCAAAATTCACTGTTCAAAATAAAATTGCTTACCATTTGAGAG
1 CTTTCCATTTATGAGTTCAAGATCAAAATTCGCTTTTCAAAATAAAATTGCTTACCATTTGAGAG
10380 TTCAAGATCAAAATTCGCTTTTCAAAATAAAATTG
66 TTCAAGATCAAAATTCGCTTTTCAAAATAAAATTG
*
10415 CTTTCCATTTAAGAGTTCAAGATCAAAATTCGCTTTTCAAAATAAAATTGCTTGA-CATTTGAGA
1 CTTTCCATTTATGAGTTCAAGATCAAAATTCGCTTTTCAAAATAAAATTGCTT-ACCATTTGAGA
* * *
10479 GTTCAAGATTAAAATTCGCTTTTCAAAGTAAGATTG
65 GTTCAAGATCAAAATTCGCTTTTCAAAATAAAATTG
* * * *
10515 CATTCCAGTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAA
1 CTTTCCATTTATGAGTTCAAGATCAAAATTCGCTTTTCAAA
10556 GGACATTTAA
Statistics
Matches: 129, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
100 128 0.99
101 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (100 bp):
CTTTCCATTTATGAGTTCAAGATCAAAATTCGCTTTTCAAAATAAAATTGCTTACCATTTGAGAG
TTCAAGATCAAAATTCGCTTTTCAAAATAAAATTG
Found at i:11214 original size:50 final size:50
Alignment explanation
Indices: 11155--11587 Score: 751
Period size: 50 Copynumber: 8.7 Consensus size: 50
11145 CGAATGTTTT
* *
11155 GGCTTTTCCATAAGTCAAACTCGTTTCCATACGAGTCGATTATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACACA
11205 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACACA
11255 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACACA
11305 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACACA
*
11355 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACACA
* *
11405 GGATTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACACA
*
11455 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACACA
* * * *
11505 GGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGACAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACACA
*
11555 GGCTTTTCCACAAGCCACA-TCTGTTTCCATACG
1 GGCTTTTCCACAAGCCAAACTC-GTTTCCATACG
11588 GTGCATTACC
Statistics
Matches: 372, Mismatches: 10, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
49 2 0.01
50 370 0.99
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (50 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACACA
Found at i:11672 original size:50 final size:50
Alignment explanation
Indices: 11599--11729 Score: 201
Period size: 50 Copynumber: 2.6 Consensus size: 50
11589 TGCATTACCT
*
11599 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAACGGAAGACGGTCC
*
11649 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAACGGAAGACGGTTC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAACGGAAGACGGTCC
* * *
11699 TTTTAATATT-AGATTGGAAGACAATTCAAAG
1 TTTTAAGATTGA-ATTGGTAGACAGTTCAAAG
11730 AAGTTGATCG
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
49 1 0.01
50 74 0.99
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.29
Consensus pattern (50 bp):
TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAACGGAAGACGGTCC
Found at i:12064 original size:28 final size:27
Alignment explanation
Indices: 11984--12073 Score: 92
Period size: 28 Copynumber: 3.3 Consensus size: 27
11974 GGAATTTTGG
*
11984 GTCATTTTCAAAATCCAGGGGCATTTTGA
1 GTCATTTTC-ACATCCAGGGGCATTTT-A
* * *
12013 G-CATTTTCATATTCAGGGGTATTTTA
1 GTCATTTTCACATCCAGGGGCATTTTA
* *
12039 GTCATTTTGCACGTCCAGGGGCATTTTG
1 GTCATTTT-CACATCCAGGGGCATTTTA
12067 GTCATTT
1 GTCATTT
12074 CTACTCCATT
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
26 2 0.04
27 20 0.39
28 28 0.55
29 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (27 bp):
GTCATTTTCACATCCAGGGGCATTTTA
Done.