Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023375.1 Corchorus olitorius cultivar O-4 contig23408, 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: 15653
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Found at i:5590 original size:33 final size:33
Alignment explanation
Indices: 5553--5748 Score: 184
Period size: 33 Copynumber: 5.9 Consensus size: 33
5543 ATTAGCATCC
*
5553 AAAACAGAATTT-GTTTCATCACAAACAACACCT
1 AAAACAG-ATTTAGTGTCATCACAAACAACACCT
5586 AAAACAGATTTAGTGTCATCACAAACAACA-CT
1 AAAACAGATTTAGTGTCATCACAAACAACACCT
** * * *
5618 CAAATTAGTTTTAGTATCATCACAAACAACATCT
1 -AAAACAGATTTAGTGTCATCACAAACAACACCT
*
5652 AAAACAGATTTAGTGTCATCGCAAACAACA-CT
1 AAAACAGATTTAGTGTCATCACAAACAACACCT
** * * *
5684 CAAATTAGGTTTAGTATCATCACTAACAACA-CT
1 -AAAACAGATTTAGTGTCATCACAAACAACACCT
* * **
5717 AAAATCAGATTTCGAGTCATTGCAAACAACAC
1 AAAA-CAGATTTAGTGTCATCACAAACAACAC
5749 TCAAATTAGG
Statistics
Matches: 132, Mismatches: 25, Indels: 11
0.79 0.15 0.07
Matches are distributed among these distances:
32 11 0.08
33 119 0.90
34 2 0.02
ACGTcount: A:0.43, C:0.22, G:0.09, T:0.26
Consensus pattern (33 bp):
AAAACAGATTTAGTGTCATCACAAACAACACCT
Found at i:5747 original size:99 final size:99
Alignment explanation
Indices: 5548--5728 Score: 231
Period size: 99 Copynumber: 1.8 Consensus size: 99
5538 TCACAATTAG
* *
5548 CATCCAAAACAGAATTTGTTTCATCACAAACAACACCTAAAACAGATTTAGTGTCATCACAAACA
1 CATCCAAAACAGAATTTGTGTCATCACAAACAACACCTAAAACAGATTTAGTATCATCACAAACA
* * *
5613 ACACTCAAATTAGTTTTAGTATCATCACAAACAA
66 ACACTAAAATCAGATTTAGTATCATCACAAACAA
* * ** * *
5647 CATCTAAAACAG-ATTTAGTGTCATCGCAAACAACA-CTCAAATTAGGTTTAGTATCATCACTAA
1 CATCCAAAACAGAATTT-GTGTCATCACAAACAACACCT-AAAACAGATTTAGTATCATCACAAA
5710 CAACACTAAAATCAGATTT
64 CAACACTAAAATCAGATTT
5729 CGAGTCATTG
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
98 6 0.09
99 63 0.91
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.27
Consensus pattern (99 bp):
CATCCAAAACAGAATTTGTGTCATCACAAACAACACCTAAAACAGATTTAGTATCATCACAAACA
ACACTAAAATCAGATTTAGTATCATCACAAACAA
Found at i:5754 original size:66 final size:66
Alignment explanation
Indices: 5568--5760 Score: 307
Period size: 66 Copynumber: 2.9 Consensus size: 66
5558 AGAATTTGTT
* *
5568 TCATCACAAACAACACCTAAAACAGATTTAGTGTCATCACAAACAACACTCAAATTAGTTTTAGT
1 TCATCACAAACAACACCTAAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTTTAGT
5633 A
66 A
*
5634 TCATCACAAACAACATCTAAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTTTAGT
1 TCATCACAAACAACACCTAAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTTTAGT
5699 A
66 A
* * * *
5700 TCATCACTAACAACA-CTAAAATCAGATTTCGAGTCATTGCAAACAACACTCAAATTAGGTT
1 TCATCACAAACAACACCTAAAA-CAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTT
5761 CAGAATTACT
Statistics
Matches: 119, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
65 6 0.05
66 113 0.95
ACGTcount: A:0.42, C:0.22, G:0.09, T:0.26
Consensus pattern (66 bp):
TCATCACAAACAACACCTAAAACAGATTTAGTGTCATCGCAAACAACACTCAAATTAGGTTTAGT
A
Found at i:7337 original size:25 final size:24
Alignment explanation
Indices: 7300--7346 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
7290 CTAGAAAATT
7300 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAACTTTGAT-GAT-AGATGGA
7326 TGAAAAAC-TTGATGATAGATG
1 TGAAAAACTTTGATGATAGATG
7347 AATAGAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (24 bp):
TGAAAAACTTTGATGATAGATGGA
Found at i:10786 original size:37 final size:37
Alignment explanation
Indices: 10734--10810 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
10724 GCTCATCGAT
* *
10734 TTCAAGAAGAGTGCACAACTTGGAATCGATGGGAATA
1 TTCAAGAAGAATGCACAACTTGGAATCGATGGAAATA
10771 TTCAAGAAGAATGCACAACTTGGAATCGATGGAAATA
1 TTCAAGAAGAATGCACAACTTGGAATCGATGGAAATA
10808 TTC
1 TTC
10811 CTTTGTTGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.23
Consensus pattern (37 bp):
TTCAAGAAGAATGCACAACTTGGAATCGATGGAAATA
Found at i:11000 original size:21 final size:21
Alignment explanation
Indices: 10976--11109 Score: 191
Period size: 21 Copynumber: 6.4 Consensus size: 21
10966 CTTAGGCAAT
*
10976 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
10997 TCCAATGATCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
11018 TCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
* *
11039 TCCAATGAACTTGGAACCCTC
1 TCCAATGAGCTTGGAACCTTC
11060 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
11081 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
11102 TCCAATGA
1 TCCAATGA
11110 ACTTCTAGCA
Statistics
Matches: 106, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
20 2 0.02
21 104 0.98
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:12968 original size:33 final size:33
Alignment explanation
Indices: 12931--13042 Score: 120
Period size: 33 Copynumber: 3.4 Consensus size: 33
12921 ATTAGCATCC
*
12931 AAAACAGAATTT-GTTTCATCACAAACAACACCT
1 AAAACAG-ATTTAGTGTCATCACAAACAACACCT
12964 AAAACAGATTTAGTGTCATCACAAACAACA-CT
1 AAAACAGATTTAGTGTCATCACAAACAACACCT
** * * * * *
12996 CAAATTAGGTTTAGTATTATCGCAAACAACATCT
1 -AAAACAGATTTAGTGTCATCACAAACAACACCT
13030 AAAACAGATTTAG
1 AAAACAGATTTAG
13043 AATTACTCTT
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
32 6 0.09
33 58 0.88
34 2 0.03
ACGTcount: A:0.45, C:0.20, G:0.10, T:0.26
Consensus pattern (33 bp):
AAAACAGATTTAGTGTCATCACAAACAACACCT
Found at i:15531 original size:21 final size:21
Alignment explanation
Indices: 15507--15640 Score: 191
Period size: 21 Copynumber: 6.4 Consensus size: 21
15497 CTTAGGCAAT
*
15507 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
15528 TCCAATGATCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
15549 TCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
15570 TCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
15591 TCCAATGAGCTTGGAA-CTTGT
1 TCCAATGAGCTTGGAACCTT-C
15612 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
15633 TCCAATGA
1 TCCAATGA
15641 ACTTCATAGC
Statistics
Matches: 106, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
20 3 0.03
21 103 0.97
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Done.