Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016144.1 Corchorus olitorius cultivar O-4 contig16177, 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: 18577
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:1247 original size:22 final size:22
Alignment explanation
Indices: 1217--1268 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
1207 CAATTCTTGC
*
1217 TCTTGAAATAATTCTTCAAA-AG
1 TCTTCAAATAA-TCTTCAAATAG
* *
1239 TCTTCAAATTATCTTCAAATGG
1 TCTTCAAATAATCTTCAAATAG
1261 TCTTCAAA
1 TCTTCAAA
1269 CACGAACTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (22 bp):
TCTTCAAATAATCTTCAAATAG
Found at i:5408 original size:29 final size:27
Alignment explanation
Indices: 5366--5420 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
5356 AGAGAAAGGC
5366 CAGAGAGATGGAAGCAAAGCTGAAGGAAG
1 CAGAGAGATGGAAG--AAGCTGAAGGAAG
*
5395 CAGAG-GATGTGAAGAAGTTGAAGGAA
1 CAGAGAGATG-GAAGAAGCTGAAGGAA
5421 AAAGCTGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 11 0.46
28 4 0.17
29 9 0.38
ACGTcount: A:0.44, C:0.07, G:0.38, T:0.11
Consensus pattern (27 bp):
CAGAGAGATGGAAGAAGCTGAAGGAAG
Found at i:7140 original size:15 final size:15
Alignment explanation
Indices: 7107--7151 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 15
7097 TTCCTTTGTT
*
7107 TTGTTTTCTAGTATAA
1 TTGTTTTCT-GTTTAA
7123 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
7138 TTGTTTTCT-TTTAA
1 TTGTTTTCTGTTTAA
7152 CCTCTGCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
14 5 0.18
15 14 0.50
16 9 0.32
ACGTcount: A:0.18, C:0.07, G:0.11, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:7540 original size:51 final size:54
Alignment explanation
Indices: 7458--7572 Score: 166
Period size: 51 Copynumber: 2.2 Consensus size: 54
7448 TTTTCTAAAA
* *
7458 AAAAAAAAAAGATTTTGATTTTTGCGTTTTTAATTTTTGTGTCTTTGCG-TTTTTG
1 AAAAAAAAAAGATTTTGA-TTTTGCGCTTTTAATTTGTGTGT-TTTGCGTTTTTTG
7513 AAAAAAAAAA-A-TTTG-TTTTGCGCTTTTAATTTGTGTGTTTTGCGTTTTTTG
1 AAAAAAAAAAGATTTTGATTTTGCGCTTTTAATTTGTGTGTTTTGCGTTTTTTG
7564 AAAAAAAAA
1 AAAAAAAAA
7573 GGAGTTTTTC
Statistics
Matches: 57, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
50 6 0.11
51 36 0.63
53 4 0.07
54 1 0.02
55 10 0.18
ACGTcount: A:0.31, C:0.05, G:0.16, T:0.48
Consensus pattern (54 bp):
AAAAAAAAAAGATTTTGATTTTGCGCTTTTAATTTGTGTGTTTTGCGTTTTTTG
Found at i:11114 original size:26 final size:26
Alignment explanation
Indices: 11085--11140 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
11075 TGCATCCCTC
11085 CTCTATTCTTGATCACTTGATCATTG
1 CTCTATTCTTGATCACTTGATCATTG
11111 CTCTATTCTTGATCACTTGATCATTG
1 CTCTATTCTTGATCACTTGATCATTG
11137 CTCT
1 CTCT
11141 TGGGCTTCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.18, C:0.25, G:0.11, T:0.46
Consensus pattern (26 bp):
CTCTATTCTTGATCACTTGATCATTG
Found at i:14974 original size:54 final size:53
Alignment explanation
Indices: 14915--15047 Score: 146
Period size: 52 Copynumber: 2.5 Consensus size: 53
14905 TTTTTAAGTC
* * *
14915 GGGAAAGTTCCCATCAGTTTTCAAAAAATACTCCATCTAGCTC-TTTTTCAAATT
1 GGGAAAGTTCCCATCA-TTTTCAAAAAATACTCAATCTAGC-CAGTCTTCAAATT
* * *
14969 GGGAAAGTTCCCATCTATTTTC--AAAGTATTCAATTTAGCCAGTCTTCAAATT
1 GGGAAAGTTCCCATC-ATTTTCAAAAAATACTCAATCTAGCCAGTCTTCAAATT
15021 GGGAAAGTTCCCATCCAATTTTCAAAA
1 GGGAAAGTTCCCAT-C-ATTTTCAAAA
15048 TTGTCAAAAT
Statistics
Matches: 67, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
51 1 0.01
52 36 0.54
53 7 0.10
54 20 0.30
55 3 0.04
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (53 bp):
GGGAAAGTTCCCATCATTTTCAAAAAATACTCAATCTAGCCAGTCTTCAAATT
Found at i:15055 original size:37 final size:37
Alignment explanation
Indices: 15013--15146 Score: 164
Period size: 37 Copynumber: 3.6 Consensus size: 37
15003 TTAGCCAGTC
*
15013 TTCAAATTGGGAAAGTTCCCATCCAATTTTCAAAATT
1 TTCAAATTGGGAAAGTTCCCATCCAATTTTCAAAGTT
* * *
15050 GTCAAAATTGGGAAAGTTCCCGT-CAAGTTTT-TAAGTT
1 TTC-AAATTGGGAAAGTTCCCATCCAA-TTTTCAAAGTT
* * *
15087 TTCAAATTGGGAATGTTCCCATTCAGTTTTCAAAGTT
1 TTCAAATTGGGAAAGTTCCCATCCAATTTTCAAAGTT
*
15124 TTTAAATTGGGAAAGTTCCCATC
1 TTCAAATTGGGAAAGTTCCCATC
15147 AGGTTTTAGT
Statistics
Matches: 81, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
36 21 0.26
37 38 0.47
38 22 0.27
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (37 bp):
TTCAAATTGGGAAAGTTCCCATCCAATTTTCAAAGTT
Found at i:15105 original size:74 final size:73
Alignment explanation
Indices: 15013--15178 Score: 201
Period size: 74 Copynumber: 2.3 Consensus size: 73
15003 TTAGCCAGTC
*
15013 TTCAAATTGGGAAAGTTCCCATCCAATTTTCAAAATTGTCAAAATTGGGAAAGTTCCCGTCAAGT
1 TTCAAATTGGGAAAGTTCCCATCCAATTTTCAAAATT-TCAAAATTGGGAAAGTTCCCATCAAGT
15078 TTTTAAGTT
65 TTTTAAGTT
* * * * ** *
15087 TTCAAATTGGGAATGTTCCCATTCAGTTTTCAAAGTTTTTAAATTGGGAAAGTTCCCATC-AGGT
1 TTCAAATTGGGAAAGTTCCCATCCAATTTTCAAAATTTCAAAATTGGGAAAGTTCCCATCAAGTT
15151 TTT-AGTT
66 TTTAAGTT
* * *
15158 TTTAATTTCGGAAAAGTTCCC
1 TTCAAATT-GGGAAAGTTCCC
15179 GTCATTTTCA
Statistics
Matches: 79, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
71 10 0.13
72 16 0.20
73 20 0.25
74 33 0.42
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.38
Consensus pattern (73 bp):
TTCAAATTGGGAAAGTTCCCATCCAATTTTCAAAATTTCAAAATTGGGAAAGTTCCCATCAAGTT
TTTAAGTT
Found at i:15153 original size:37 final size:35
Alignment explanation
Indices: 15016--15186 Score: 150
Period size: 37 Copynumber: 4.7 Consensus size: 35
15006 GCCAGTCTTC
* * **
15016 AAATTGGGAAAGTTCCCATCCAATTTTCAAAATTGTCA
1 AAATTGGGAAAGTTCCCAT-CAGTTTT-AAAGTT-TTT
* * *
15054 AAATTGGGAAAGTTCCCGTCAAGTTTTTAAGTTTTC
1 AAATTGGGAAAGTTCCCATC-AGTTTTAAAGTTTTT
*
15090 AAATTGGGAATGTTCCCATTCAGTTTTCAAAGTTTTT
1 AAATTGGGAAAGTTCCCA-TCAGTTTT-AAAGTTTTT
15127 AAATTGGGAAAGTTCCCATCAGGTTTT--AGTTTTT
1 AAATTGGGAAAGTTCCCATCA-GTTTTAAAGTTTTT
* * *
15161 AATTTCGGAAAAGTTCCCGTCA-TTTT
1 AAATT-GGGAAAGTTCCCATCAGTTTT
15187 CAGTTTTAGT
Statistics
Matches: 114, Mismatches: 14, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
33 4 0.04
34 11 0.10
35 14 0.12
36 26 0.23
37 36 0.32
38 23 0.20
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (35 bp):
AAATTGGGAAAGTTCCCATCAGTTTTAAAGTTTTT
Done.