Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019969.1 Corchorus olitorius cultivar O-4 contig20002, 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: 22904
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Found at i:1002 original size:33 final size:34
Alignment explanation
Indices: 976--1042 Score: 102
Period size: 33 Copynumber: 2.0 Consensus size: 34
966 TTTCAATGCT
*
976 ATGATCAACCAAAACA-AATTTGTTTTCATCACA
1 ATGAGCAACCAAAACAGAATTTGTTTTCATCACA
*
1009 ATGAGCATCCAAAACAGAATTTG-TTTCATCACA
1 ATGAGCAACCAAAACAGAATTTGTTTTCATCACA
1042 A
1 A
1043 ACAACACCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 25 0.81
34 6 0.19
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (34 bp):
ATGAGCAACCAAAACAGAATTTGTTTTCATCACA
Found at i:1056 original size:33 final size:32
Alignment explanation
Indices: 983--1087 Score: 115
Period size: 33 Copynumber: 3.2 Consensus size: 32
973 GCTATGATCA
** *
983 ACCAAAACA-AATTTGTTTTCATCACAATGAGC
1 ACCAAAACAGAATTTG-TTTCATCACAAACAAC
1015 ATCCAAAACAGAATTTGTTTCATCACAAACAAC
1 A-CCAAAACAGAATTTGTTTCATCACAAACAAC
*
1048 ACCTAAAACAG-ATTTAGTGTCATCACAAACAAC
1 ACC-AAAACAGAATTT-GTTTCATCACAAACAAC
1081 ACTCAAA
1 AC-CAAA
1088 TTAGTTTTAG
Statistics
Matches: 64, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
32 7 0.11
33 50 0.78
34 7 0.11
ACGTcount: A:0.45, C:0.24, G:0.08, T:0.24
Consensus pattern (32 bp):
ACCAAAACAGAATTTGTTTCATCACAAACAAC
Found at i:1097 original size:33 final size:33
Alignment explanation
Indices: 1019--1123 Score: 115
Period size: 33 Copynumber: 3.2 Consensus size: 33
1009 ATGAGCATCC
*
1019 AAAACAGAATTT-GTTTCATCACAAACAACACCT
1 AAAACAG-ATTTAGTATCATCACAAACAACACCT
*
1052 AAAACAGATTTAGTGTCATCACAAACAACA-CT
1 AAAACAGATTTAGTATCATCACAAACAACACCT
** * * *
1084 CAAATTAGTTTTAGTATCATCACTAACAACATCT
1 -AAAACAGATTTAGTATCATCACAAACAACACCT
1118 AAAACA
1 AAAACA
1124 CTCTTTGCAA
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
32 6 0.10
33 53 0.87
34 2 0.03
ACGTcount: A:0.46, C:0.22, G:0.07, T:0.26
Consensus pattern (33 bp):
AAAACAGATTTAGTATCATCACAAACAACACCT
Found at i:1721 original size:15 final size:15
Alignment explanation
Indices: 1701--1732 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1691 AAACTAAGTG
1701 GAGCTTGTTGATTTT
1 GAGCTTGTTGATTTT
1716 GAGCTTGTTGATTTT
1 GAGCTTGTTGATTTT
1731 GA
1 GA
1733 ACCTCGAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.16, C:0.06, G:0.28, T:0.50
Consensus pattern (15 bp):
GAGCTTGTTGATTTT
Found at i:2697 original size:25 final size:24
Alignment explanation
Indices: 2660--2706 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
2650 CTAGAAAATT
2660 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAACTTTGAT-GAT-AGATGGA
2686 TGAAAAAC-TTGATGATAGATG
1 TGAAAAACTTTGATGATAGATG
2707 AATAGAATGA
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:2716 original size:28 final size:26
Alignment explanation
Indices: 2660--2716 Score: 62
Period size: 28 Copynumber: 2.1 Consensus size: 26
2650 CTAGAAAATT
* *
2660 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAACTTTGATAGATGAGATGAA
2686 TGAAAAACTTGATGATAGATGA-ATAGAA
1 TGAAAAACTT--TGATAGATGAGAT-GAA
2714 TGA
1 TGA
2717 TAGATTTACC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 10 0.38
27 2 0.08
28 14 0.54
ACGTcount: A:0.44, C:0.04, G:0.26, T:0.26
Consensus pattern (26 bp):
TGAAAAACTTTGATAGATGAGATGAA
Found at i:3595 original size:21 final size:21
Alignment explanation
Indices: 3571--3662 Score: 141
Period size: 21 Copynumber: 4.4 Consensus size: 21
3561 CTTAGGCAAT
* *
3571 TCCAATGAGCTCGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
3592 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
3613 TCCAATGAGCTAGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
3634 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
3655 TCCAATGA
1 TCCAATGA
3663 TCTCCTAACA
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
20 3 0.05
21 63 0.95
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.26
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:6339 original size:43 final size:43
Alignment explanation
Indices: 6291--6375 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
6281 TCATTATCAA
6291 AATATATTTTAATAATGCCATTATTAAAATATATAAAATTGCT
1 AATATATTTTAATAATGCCATTATTAAAATATATAAAATTGCT
* *
6334 AATATATTTTTATTATGCCATTATTAAAATATATAAAATTGC
1 AATATATTTTAATAATGCCATTATTAAAATATATAAAATTGC
6376 CATTATTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.44
Consensus pattern (43 bp):
AATATATTTTAATAATGCCATTATTAAAATATATAAAATTGCT
Found at i:7796 original size:46 final size:46
Alignment explanation
Indices: 7742--8299 Score: 641
Period size: 46 Copynumber: 12.0 Consensus size: 46
7732 ACGAAAATTA
* * *
7742 GGACCTTCCGACCAGGAAGGGGCATTTTTGGAAATGAAGAAAACAT
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATAAAGAAAACAG
* * *
7788 GGACCTTCCAACCAGGAAAGGGTATTTTTGGAATAAAATAAAGAAAACGG
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGG----AAATAAAGAAAACAG
* *
7838 GGACCTTCCAACTAGGAAGGGGCATTTTTGGAATAAAATAAAGAAAACCG
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGG----AAATAAAGAAAACAG
* * * *
7888 GGACCTTCCAACCAGGAAGGGTCAATTTTGGAATAAAATGAAGAAAACGG
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGG----AAATAAAGAAAACAG
* **
7938 GGACCTTCCAACCAGGAAGGGGCGTTTTTGGAAATAAAGAAAATGG
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATAAAGAAAACAG
* * * *
7984 GGACCTTCCAACCAGGAAGGGGCATTTCTAG-ACTAGAAGAAAACAT
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATA-AAGAAAACAG
* * *
8030 GGACCTTCCAACCAGGAAGGGGCATTTCTAG-AATAGAAGAAAACAA
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATA-AAGAAAACAG
8076 GGACCTTCCAACCAGGAAGGGGCATTTTTTGGAAAT--A-AAAACAG
1 GGACCTTCCAACCAGGAAGGGGCA-TTTTTGGAAATAAAGAAAACAG
*
8120 GGATCTTCCAACCAGGAAGGGGCATTTTTGGAAATAAAGAAAAC-G
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATAAAGAAAACAG
* *
8165 GGAACCTTCCAACCAGGAAGGGGCATTTCTAG-AATAGAAGAAAACAG
1 GG-ACCTTCCAACCAGGAAGGGGCATTTTTGGAAATA-AAGAAAACAG
* *
8212 GGACCTTTCAACCAGGAAAGGGCATTTTTGGAAAT--A-AAAACAG
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATAAAGAAAACAG
*
8255 GGACCTTCAAACCAGGAAGGGGCATTTTTGGAAATAAAGAAAACA
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATAAAGAAAACA
8300 ATTCTTTTGA
Statistics
Matches: 452, Mismatches: 43, Indels: 34
0.85 0.08 0.06
Matches are distributed among these distances:
43 50 0.11
44 30 0.07
45 13 0.03
46 214 0.47
47 11 0.02
48 3 0.01
50 131 0.29
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (46 bp):
GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATAAAGAAAACAG
Found at i:9193 original size:11 final size:11
Alignment explanation
Indices: 9150--9187 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
9140 TTCCTATATA
*
9150 AAATAAATTAT
1 AAATTAATTAT
9161 CAAA-TAATTAT
1 -AAATTAATTAT
9172 AAATTAATTAT
1 AAATTAATTAT
9183 AAATT
1 AAATT
9188 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:9566 original size:28 final size:31
Alignment explanation
Indices: 9509--9569 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
9499 CAATATTTAT
* *
9509 TTTTTTGTGTATTATTAGTATGTAACATTAA
1 TTTTTTGTGTATTATTAATATATAACATTAA
9540 TTTTTTGTGTATTA-TAATA-ATAA-ATTAA
1 TTTTTTGTGTATTATTAATATATAACATTAA
9568 TT
1 TT
9570 ATAGTTTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 7 0.25
29 3 0.11
30 4 0.14
31 14 0.50
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.56
Consensus pattern (31 bp):
TTTTTTGTGTATTATTAATATATAACATTAA
Found at i:12732 original size:11 final size:11
Alignment explanation
Indices: 12712--12741 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
12702 CCAAGGGTAA
12712 AGGAAAGAGCT
1 AGGAAAGAGCT
*
12723 AGGAAGGAGCT
1 AGGAAAGAGCT
12734 AGGAAAGA
1 AGGAAAGA
12742 TCCTGCTCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.47, C:0.07, G:0.40, T:0.07
Consensus pattern (11 bp):
AGGAAAGAGCT
Found at i:13146 original size:21 final size:21
Alignment explanation
Indices: 13122--13192 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
13112 CTTAGGCAAT
13122 TCCAATGAGCTTGGAACCTT-C
1 TCCAATGAGCTTGGAA-CTTGC
13143 TCCAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
*
13164 TCTAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
13185 TCCAATGA
1 TCCAATGA
13193 ACTCCTAGCA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
20 3 0.06
21 44 0.94
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACTTGC
Found at i:17818 original size:49 final size:49
Alignment explanation
Indices: 17721--17850 Score: 190
Period size: 49 Copynumber: 2.6 Consensus size: 49
17711 CCAGAAAGAT
* * * * *
17721 CTCAGAAATGGAGTGCAATCTTATTTTGAAAAGCGAATTTTGATCTTGGA
1 CTCACAAATGGAATGCAATCTTATTAT-AAAAGCAAATTTTGACCTTGGA
17771 CTCACAAATGGAATGCAATCTTATTATAAAAGCAAATTTTGACCTTGGA
1 CTCACAAATGGAATGCAATCTTATTATAAAAGCAAATTTTGACCTTGGA
17820 CTCACAAAT-GAGATGCAATCTTATTATAAAA
1 CTCACAAATGGA-ATGCAATCTTATTATAAAA
17851 ATTCTTGTTC
Statistics
Matches: 74, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
48 2 0.03
49 48 0.65
50 24 0.32
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.32
Consensus pattern (49 bp):
CTCACAAATGGAATGCAATCTTATTATAAAAGCAAATTTTGACCTTGGA
Found at i:18924 original size:21 final size:21
Alignment explanation
Indices: 18900--18949 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
18890 CTTAGGCAAT
18900 TCCAATGAGCTTGAAACCTT-C
1 TCCAATGAGCTTGAAA-CTTGC
*
18921 TCCAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGAAACTTGC
18942 TCCAATGA
1 TCCAATGA
18950 TCTCCTAGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 3 0.11
21 24 0.89
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGAAACTTGC
Done.