Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012420.1 Corchorus olitorius cultivar O-4 contig12453, 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: 24077
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:773 original size:11 final size:11
Alignment explanation
Indices: 757--781 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
747 AGAAAATTGT
757 TTGTTTTTGGA
1 TTGTTTTTGGA
768 TTGTTTTTGGA
1 TTGTTTTTGGA
779 TTG
1 TTG
782 ATTATTCCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.28, T:0.64
Consensus pattern (11 bp):
TTGTTTTTGGA
Found at i:850 original size:22 final size:23
Alignment explanation
Indices: 808--850 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
798 TAAAAAAAAA
**
808 AATTTAAAAAAAATTGATTTTCG
1 AATTTAAAAAAAAAAGATTTTCG
831 AATTTAAAAAAAAAAG-TTTT
1 AATTTAAAAAAAAAAGATTTT
851 GAGAATTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTTAAAAAAAAAAGATTTTCG
Found at i:856 original size:23 final size:23
Alignment explanation
Indices: 808--858 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
798 TAAAAAAAAA
** *
808 AATTTAAAAAAAATTGATTTTCG
1 AATTTAAAAAAAAAAGATTTTAG
831 AATTTAAAAAAAAAAG-TTTTGAG
1 AATTTAAAAAAAAAAGATTTT-AG
854 AATTT
1 AATTT
859 TGAATTTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.37
Consensus pattern (23 bp):
AATTTAAAAAAAAAAGATTTTAG
Found at i:2122 original size:12 final size:13
Alignment explanation
Indices: 2105--2134 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
2095 GTTTTCTTTA
2105 ATTTTCTTGATT-
1 ATTTTCTTGATTG
2117 ATTTTCTTGATTG
1 ATTTTCTTGATTG
2130 ATTTT
1 ATTTT
2135 AATTACTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.17, C:0.07, G:0.10, T:0.67
Consensus pattern (13 bp):
ATTTTCTTGATTG
Found at i:6872 original size:21 final size:21
Alignment explanation
Indices: 6832--6872 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6822 AGGGCTTGAA
*
6832 AACCTTGCCCAAGCGTGGCCC
1 AACCTTGCCCAAGCGCGGCCC
6853 AACCTTGCCC-AGACGCGGCC
1 AACCTTGCCCAAG-CGCGGCC
6873 TACCCCAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.20, C:0.44, G:0.24, T:0.12
Consensus pattern (21 bp):
AACCTTGCCCAAGCGCGGCCC
Found at i:18260 original size:76 final size:72
Alignment explanation
Indices: 18138--18279 Score: 187
Period size: 76 Copynumber: 1.9 Consensus size: 72
18128 ATTTGGACTA
* *
18138 TGAGCAAAGGAATGATGAGTATTAATCAAGCTTTTCAAAATCAGTTTTAATCAAAGCTATGATTT
1 TGAGCAAAGGAATGACGAGTATTAATCAAGCTTTTCAAAATCAGTTTTAATCAAAGCCATGATTT
18203 CGAGTTG
66 CGAGTTG
* **
18210 TGAGCAAAGGAATGACG-GTGACTTAATCAGAAGGTGTTTCAAAATCAGTTTTTGTCAAAGCCAT
1 TGAGCAAAGGAATGACGAGT-A-TTAATC--AAGCT-TTTCAAAATCAGTTTTAATCAAAGCCAT
18274 GATTTC
61 GATTTC
18280 AAAGGTAACT
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
71 2 0.03
72 17 0.28
73 6 0.10
75 4 0.07
76 31 0.52
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.32
Consensus pattern (72 bp):
TGAGCAAAGGAATGACGAGTATTAATCAAGCTTTTCAAAATCAGTTTTAATCAAAGCCATGATTT
CGAGTTG
Found at i:18704 original size:21 final size:21
Alignment explanation
Indices: 18680--18729 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
18670 ATAAAAATTA
*
18680 AAAAAAATCATAAAAAAAATC
1 AAAAAAATAATAAAAAAAATC
* * *
18701 AAAAAAAGAATGAAAAAAATG
1 AAAAAAATAATAAAAAAAATC
18722 AAAAAAAT
1 AAAAAAAT
18730 GGAAAAAGGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.78, C:0.04, G:0.06, T:0.12
Consensus pattern (21 bp):
AAAAAAATAATAAAAAAAATC
Found at i:18728 original size:12 final size:12
Alignment explanation
Indices: 18679--18719 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
18669 AATAAAAATT
*
18679 AAAAAAAATCAT
1 AAAAAAAATCAA
18691 AAAAAAAATCAA
1 AAAAAAAATCAA
* *
18703 AAAAAGAATGAA
1 AAAAAAAATCAA
18715 AAAAA
1 AAAAA
18720 TGAAAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.80, C:0.05, G:0.05, T:0.10
Consensus pattern (12 bp):
AAAAAAAATCAA
Found at i:18734 original size:10 final size:9
Alignment explanation
Indices: 18703--18736 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
18693 AAAAAATCAA
18703 AAAAAGAATG
1 AAAAA-AATG
18713 AAAAAAATG
1 AAAAAAATG
18722 AAAAAAATGG
1 AAAAAAAT-G
18732 AAAAA
1 AAAAA
18737 GGAAAAAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 12 0.52
10 11 0.48
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (9 bp):
AAAAAAATG
Found at i:18742 original size:6 final size:7
Alignment explanation
Indices: 18724--18756 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
18714 AAAAAATGAA
18724 AAAAATGG
1 AAAAA-GG
18732 AAAAAGG
1 AAAAAGG
18739 AAAAAGG
1 AAAAAGG
18746 AAAAAGG
1 AAAAAGG
18753 AAAA
1 AAAA
18757 TAAAGGCACT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 20 0.80
8 5 0.20
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.03
Consensus pattern (7 bp):
AAAAAGG
Found at i:19125 original size:3 final size:3
Alignment explanation
Indices: 19117--19148 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
19107 AAAAATATCG
19117 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
19149 ATCAAATCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:19833 original size:49 final size:49
Alignment explanation
Indices: 19761--19961 Score: 287
Period size: 49 Copynumber: 4.1 Consensus size: 49
19751 GAACAAGAAG
* **
19761 TTTTACAATAAAATAGCTTTCCATTTGAGAGTTCAAGAAAAAAATTCGC
1 TTTTACAATAAAATTGCTTTCCATTTGAGAGTTCAAGATCAAAATTCGC
19810 TTTTACAATAAAATTGCTTTCCATTTGAGAGTTCAAGATCAAAATTCGC
1 TTTTACAATAAAATTGCTTTCCATTTGAGAGTTCAAGATCAAAATTCGC
*
19859 TTTTACAATAAAATTGCTCTCCATTTGAGAGTTCAAGATCAAAATTCGC
1 TTTTACAATAAAATTGCTTTCCATTTGAGAGTTCAAGATCAAAATTCGC
* * * ** *
19908 TTTT-CAAAGTAAGATTGCATTCCCTTTTTGAGTCCAAGATCAAAATTCGC
1 TTTTAC-AA-TAAAATTGCTTTCCATTTGAGAGTTCAAGATCAAAATTCGC
19958 TTTT
1 TTTT
19962 CAAAGGGCAT
Statistics
Matches: 139, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
48 1 0.01
49 100 0.72
50 38 0.27
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.36
Consensus pattern (49 bp):
TTTTACAATAAAATTGCTTTCCATTTGAGAGTTCAAGATCAAAATTCGC
Found at i:20747 original size:50 final size:50
Alignment explanation
Indices: 20693--20789 Score: 149
Period size: 50 Copynumber: 1.9 Consensus size: 50
20683 GTTCCATCCA
* * **
20693 AGCAGCAGGGACTTTTCCATAAGTCAAACTGGTTTCCATACGAGTCAATT
1 AGCAGCAGGGACTTTTCCACAAGCCAAACTCATTTCCATACGAGTCAATT
*
20743 AGCAGCAGGGGCTTTTCCACAAGCCAAACTCATTTCCATACGAGTCA
1 AGCAGCAGGGACTTTTCCACAAGCCAAACTCATTTCCATACGAGTCA
20790 GTTCAAACCT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.25
Consensus pattern (50 bp):
AGCAGCAGGGACTTTTCCACAAGCCAAACTCATTTCCATACGAGTCAATT
Found at i:20794 original size:119 final size:118
Alignment explanation
Indices: 20583--20858 Score: 471
Period size: 119 Copynumber: 2.3 Consensus size: 118
20573 CGAATGCTTT
20583 GACTTTTCCATAAGTCAAACTCGTTTCCATACGAGTCAATTAGCAGCAGGGGCTTTTCCACAAGC
1 GACTTTTCCATAAGTCAAACT-GTTTCCATACGAGTCAATTAGCAGCAGGGGCTTTTCCACAAGC
*
20648 CAAACTCGTTTCCATACAAGTCAGTTCAAACCTTGGTTCCATCCAAGCAGCAGG
65 CAAACTCATTTCCATACAAGTCAGTTCAAACCTTGGTTCCATCCAAGCAGCAGG
20702 GACTTTTCCATAAGTCAAACTGGTTTCCATACGAGTCAATTAGCAGCAGGGGCTTTTCCACAAGC
1 GACTTTTCCATAAGTCAAACT-GTTTCCATACGAGTCAATTAGCAGCAGGGGCTTTTCCACAAGC
*
20767 CAAACTCATTTCCATACGAGTCAGTTCAAACCTTGGTTCCATCCAAGCAGCAGG
65 CAAACTCATTTCCATACAAGTCAGTTCAAACCTTGGTTCCATCCAAGCAGCAGG
* * * *
20821 GGCGTTTCCACAAGCCAAATCTGTTTCCATACGAGTCA
1 GACTTTTCCATAAGTCAAA-CTGTTTCCATACGAGTCA
20859 GTTCAAACCT
Statistics
Matches: 149, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
119 147 0.99
120 2 0.01
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (118 bp):
GACTTTTCCATAAGTCAAACTGTTTCCATACGAGTCAATTAGCAGCAGGGGCTTTTCCACAAGCC
AAACTCATTTCCATACAAGTCAGTTCAAACCTTGGTTCCATCCAAGCAGCAGG
Found at i:20816 original size:69 final size:69
Alignment explanation
Indices: 20743--20976 Score: 337
Period size: 69 Copynumber: 3.4 Consensus size: 69
20733 CGAGTCAATT
* *
20743 AGCAGCAGGGGCTTTTCCACAAGCCAAACTCATTTCCATACGAGTCAGTTCAAACCTTGGTTCCA
1 AGCAGCAGAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCA
20808 TCCA
66 TCCA
* * *
20812 AGCAGCAGGGGCGTTTCCACAAGCCAAA-TCTGTTTCCATACGAGTCAGTTCAAACCTTTGTTCC
1 AGCAGCAGAGGCTTTTCCACAAGCCAAACTC-GTTTCCATACGAGTCAGTTCAAACCTTGGTTCC
20876 ATCCA
65 ATCCA
* * * *
20881 AGCAGCAGAGGCTTTTCCACAAGGCAAACTCGTTTCCATATGAGTTAATTCAAACCTTGGTTCCA
1 AGCAGCAGAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCA
20946 TCCA
66 TCCA
*
20950 AGCCA-CATAGGCTTTTTCCACAAGCCA
1 AG-CAGCAGAGGC-TTTTCCACAAGCCA
20977 CATCCGTTTC
Statistics
Matches: 149, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
68 2 0.01
69 130 0.87
70 17 0.11
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.26
Consensus pattern (69 bp):
AGCAGCAGAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCA
TCCA
Found at i:21130 original size:50 final size:51
Alignment explanation
Indices: 21001--21135 Score: 211
Period size: 51 Copynumber: 2.7 Consensus size: 51
20991 CGGTGCATTA
*
21001 CCTTTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCAGAAGACAGT
1 CCTTTTTAAGATTGAATTGGAAGACAATTCAAAGGATAAGCAGAAGACAGT
* *
21052 CCTTTTTAAGATTGAATTGGAAGACAATTCAAAGGATAAGCGGAAGACGGT
1 CCTTTTTAAGATTGAATTGGAAGACAATTCAAAGGATAAGCAGAAGACAGT
*
21103 CC-TTTTAATATT-AGATTGGAAGACAATTCAAAG
1 CCTTTTTAAGATTGA-ATTGGAAGACAATTCAAAG
21136 AAATTGATTC
Statistics
Matches: 79, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
49 1 0.01
50 28 0.35
51 50 0.63
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.27
Consensus pattern (51 bp):
CCTTTTTAAGATTGAATTGGAAGACAATTCAAAGGATAAGCAGAAGACAGT
Done.