Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016103.1 Corchorus olitorius cultivar O-4 contig16136, 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: 25928
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:244 original size:84 final size:84
Alignment explanation
Indices: 99--258 Score: 284
Period size: 84 Copynumber: 1.9 Consensus size: 84
89 AGAAGCAAAT
*
99 ATTGTTAGAATTCTAACCATGGTTTTTGTAACCGGACCGGATCGATCGGTCCAACCGGTTGACAG
1 ATTGTTAGAATTCTAACCATGGTTTTTGTAACCGGACCGGATCGATCGGTCCAACCAGTTGACAG
164 TATGCCAAATTAAGGAAAA
66 TATGCCAAATTAAGGAAAA
* * *
183 ATTGTTAGAATTCTAACCATGGTTTTTGTAATCGGACCGGATCGGTCGGTTCAACCAGTTGACAG
1 ATTGTTAGAATTCTAACCATGGTTTTTGTAACCGGACCGGATCGATCGGTCCAACCAGTTGACAG
248 TATGCCAAATT
66 TATGCCAAATT
259 TTCGGTAGGT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 72 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.30
Consensus pattern (84 bp):
ATTGTTAGAATTCTAACCATGGTTTTTGTAACCGGACCGGATCGATCGGTCCAACCAGTTGACAG
TATGCCAAATTAAGGAAAA
Found at i:15682 original size:7 final size:7
Alignment explanation
Indices: 15659--15865 Score: 382
Period size: 7 Copynumber: 29.9 Consensus size: 7
15649 GAAAAAGAAG
15659 TGAAAAT
1 TGAAAAT
*
15666 TG-AAAG
1 TGAAAAT
15672 TGAAAAT
1 TGAAAAT
15679 TGAAAAT
1 TGAAAAT
15686 TGAAAAT
1 TGAAAAT
15693 TGAAAAT
1 TGAAAAT
15700 TGAAAAT
1 TGAAAAT
15707 TGAAAAT
1 TGAAAAT
15714 TGAAAAT
1 TGAAAAT
15721 TGAAAAT
1 TGAAAAT
15728 TGAAAAT
1 TGAAAAT
15735 TGAAAAT
1 TGAAAAT
15742 TGAAAAT
1 TGAAAAT
15749 TGAAAAT
1 TGAAAAT
15756 TGAAAAT
1 TGAAAAT
15763 TGAAAAT
1 TGAAAAT
15770 TGAAAAT
1 TGAAAAT
15777 TGAAAAT
1 TGAAAAT
15784 TGAAAAT
1 TGAAAAT
15791 TG-AAAT
1 TGAAAAT
15797 TGAAAAT
1 TGAAAAT
15804 TGAAAAT
1 TGAAAAT
15811 TGAAAAT
1 TGAAAAT
15818 TGAAAAT
1 TGAAAAT
15825 TGAAAAT
1 TGAAAAT
*
15832 TGAAAAC
1 TGAAAAT
15839 TGAAAAT
1 TGAAAAT
15846 TGAAAAT
1 TGAAAAT
15853 TGAAAAT
1 TGAAAAT
15860 TGAAAA
1 TGAAAA
15866 AGCATAAGAT
Statistics
Matches: 194, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
6 11 0.06
7 183 0.94
ACGTcount: A:0.57, C:0.00, G:0.15, T:0.28
Consensus pattern (7 bp):
TGAAAAT
Found at i:16664 original size:20 final size:20
Alignment explanation
Indices: 16639--16676 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
16629 AATTGGCATG
16639 TTGCATGCATGACATTCTTT
1 TTGCATGCATGACATTCTTT
16659 TTGCATGCATGACATTCT
1 TTGCATGCATGACATTCT
16677 CATTGGGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.42
Consensus pattern (20 bp):
TTGCATGCATGACATTCTTT
Found at i:17296 original size:145 final size:145
Alignment explanation
Indices: 17046--17612 Score: 712
Period size: 145 Copynumber: 3.9 Consensus size: 145
17036 CCATTTTGGT
*
17046 AAGTTTTTCAA-CAAAGTTGTGTTTAAGTTTC--AAT--AAACCTTGCTCAAGGTTGAGTTTGCA
1 AAGTTTTT-AATCAAAGTTGCGTTTAAGTTTCAAAATCAAAACCTTGCTCAAGGTTGAGTTTGCA
* *
17106 TTTGTAAGACCTCCGGGCACAATTTCAGAATCCTCCGGGTATTAATTCTGATAAATCCTTCGGGT
65 TTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGT
*
17171 ATCATATCATTTCATC
130 ATCATTTCATTTCATC
* *
17187 AAGTTTTTAATCAAAGTTGCATTTAAGTTTCAAAATCAAAACCTTACTCAAGGTTGAGTTTGCAT
1 AAGTTTTTAATCAAAGTTGCGTTTAAGTTTCAAAATCAAAACCTTGCTCAAGGTTGAGTTTGCAT
* * *
17252 TTGTAAGTCCTCCGGGTACCATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTA
66 TTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTA
*
17317 TTATTTCATTTCATC
131 TCATTTCATTTCATC
* * * ** *
17332 AAATTTTTAATCAAAGCTGTGTTTACCTTTCAAAATCACAACCTTGCTCAAGGTCTCAATTCAGA
1 AAGTTTTTAATCAAAGTTGCGTTTAAGTTTCAAAATCAAAACCTTGCTCAAGG------TT--GA
* * * *
17397 ATTTGCATTTGTAAGACCTCCAGGCACAATTTCAAAAACCTCCGGGTATTAATTCTGATAAATTC
58 GTTTGCATTTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCC
* *
17462 TCAGGGTAACATTTCATTTCATC
123 TCCGGGTATCATTTCATTTCATC
* * ** * *
17485 CAGTTTTTAATCAAAGTTGCGTTTAAATTTCAAAATGGAAACCTTGCTCAAGGTCGAGTGTGCAT
1 AAGTTTTTAATCAAAGTTGCGTTTAAGTTTCAAAATCAAAACCTTGCTCAAGGTTGAGTTTGCAT
* * * * * *
17550 CTGTAAGACCTCCGCGTATAATTTCAGAAACCTCTGGGTATTAATTATGATAAATCCTCCGGG
66 TTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGG
17613 CATTCCATAG
Statistics
Matches: 363, Mismatches: 50, Indels: 22
0.83 0.11 0.05
Matches are distributed among these distances:
140 2 0.01
141 26 0.07
143 3 0.01
145 205 0.56
147 1 0.00
151 2 0.01
153 124 0.34
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.35
Consensus pattern (145 bp):
AAGTTTTTAATCAAAGTTGCGTTTAAGTTTCAAAATCAAAACCTTGCTCAAGGTTGAGTTTGCAT
TTGTAAGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTA
TCATTTCATTTCATC
Found at i:18028 original size:198 final size:196
Alignment explanation
Indices: 17687--18190 Score: 609
Period size: 198 Copynumber: 2.5 Consensus size: 196
17677 TTATTAGTCG
* * *
17687 ATTTCAAAATCCTGCTCAGGATCATTTCTTTTTATC-GATCAATTTCAGAATCCTGCTCAGGATC
1 ATTTCAAAATCCTACTCAGGATCA--T-TTTTTATCAAATTAATTTCAGAATCCTGCTCAGGATC
* **
17751 ATTTCTTTTTATCGGTCAATTTCAGATTCCTGCTCAGGATCATTGTTGTATCAAATTAATTTCAG
63 ATTTC--TTTATCAGTCAATTTCA-A-TCCTATTCAGGATCATTGTTGTATCAAATTAATTTCAG
* *
17816 AATCCTGCTCAGGATCATTGT-TGTATCAAATTAATTTCAAAATCCTACTCAGGATCATTGATGC
124 AATCCTACTCAGGATAATT-TCTGTATCAAATTAATTTCAAAATCCTACTCAGGATCATTGATGC
17880 ATCAAATTA
188 ATCAAATTA
* * **
17889 ATTTCAAAATCCTACTCAGTATCATTGTTGTATCAAATTAATTTCAGAATCCCACTCAGGATCAT
1 ATTTCAAAATCCTACTCAGGATCATT-TTTTATCAAATTAATTTCAGAATCCTGCTCAGGATCAT
* * *
17954 TGCTTTATCAAATCAATTTCAATCCTATTCAGGATCATT-TCTTTATCAAATTAATTTCAGAATC
65 TTCTTTATC-AGTCAATTTCAATCCTATTCAGGATCATTGT-TGTATCAAATTAATTTCAGAATC
* * * * ** **
18018 CTATTCAGGATAATTTCTTTATCAAATTAATTTCAGAATCCTACTCGGGATCATTTCTTTATCAA
128 CTACTCAGGATAATTTCTGTATCAAATTAATTTCAAAATCCTACTCAGGATCATTGATGCATCAA
18083 ATTA
193 ATTA
* * *
18087 ATTTCAGAATCCTACTCGGGATCATTTCTTTATCAAATTAATTTCAGAATCCTGTTCAGGATCAT
1 ATTTCAAAATCCTACTCAGGATCATTT-TTTATCAAATTAATTTCAGAATCCTGCTCAGGATCAT
* *
18152 TTTTTTATCAGTTAATTTCAGAATCCTATTCAGGATCAT
65 TTCTTTATCAGTCAATTTC--AATCCTATTCAGGATCAT
18191 CTTTTTTTAC
Statistics
Matches: 260, Mismatches: 34, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
197 11 0.04
198 157 0.60
199 26 0.10
200 16 0.06
201 28 0.11
202 22 0.08
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (196 bp):
ATTTCAAAATCCTACTCAGGATCATTTTTTATCAAATTAATTTCAGAATCCTGCTCAGGATCATT
TCTTTATCAGTCAATTTCAATCCTATTCAGGATCATTGTTGTATCAAATTAATTTCAGAATCCTA
CTCAGGATAATTTCTGTATCAAATTAATTTCAAAATCCTACTCAGGATCATTGATGCATCAAATT
A
Found at i:18196 original size:40 final size:40
Alignment explanation
Indices: 17687--18229 Score: 576
Period size: 40 Copynumber: 13.6 Consensus size: 40
17677 TTATTAGTCG
* * * *
17687 ATTTCAAAATCCTGCTCAGGATCATTTCTTTTTATC-GATCA
1 ATTTCAGAATCCTACTCAGGATCA-TT-TTTTTATCAAATTA
* ** *
17728 ATTTCAGAATCCTGCTCAGGATCATTTCTTTTTATC-GGTCA
1 ATTTCAGAATCCTACTCAGGATCA-TT-TTTTTATCAAATTA
* * * *
17769 ATTTCAGATTCCTGCTCAGGATCATTGTTGTATCAAATTA
1 ATTTCAGAATCCTACTCAGGATCATTTTTTTATCAAATTA
* * *
17809 ATTTCAGAATCCTGCTCAGGATCATTGTTGTATCAAATTA
1 ATTTCAGAATCCTACTCAGGATCATTTTTTTATCAAATTA
* ** **
17849 ATTTCAAAATCCTACTCAGGATCATTGATGCATCAAATTA
1 ATTTCAGAATCCTACTCAGGATCATTTTTTTATCAAATTA
* * * *
17889 ATTTCAAAATCCTACTCAGTATCATTGTTGTATCAAATTA
1 ATTTCAGAATCCTACTCAGGATCATTTTTTTATCAAATTA
* ** *
17929 ATTTCAGAATCCCACTCAGGATCATTGCTTTATCAAATCA
1 ATTTCAGAATCCTACTCAGGATCATTTTTTTATCAAATTA
* *
17969 ATTTC--AATCCTATTCAGGATCATTTCTTTATCAAATTA
1 ATTTCAGAATCCTACTCAGGATCATTTTTTTATCAAATTA
* * *
18007 ATTTCAGAATCCTATTCAGGATAATTTCTTTATCAAATTA
1 ATTTCAGAATCCTACTCAGGATCATTTTTTTATCAAATTA
* *
18047 ATTTCAGAATCCTACTCGGGATCATTTCTTTATCAAATTA
1 ATTTCAGAATCCTACTCAGGATCATTTTTTTATCAAATTA
* *
18087 ATTTCAGAATCCTACTCGGGATCATTTCTTTATCAAATTA
1 ATTTCAGAATCCTACTCAGGATCATTTTTTTATCAAATTA
** *
18127 ATTTCAGAATCCTGTTCAGGATCATTTTTTTATC-AGTTA
1 ATTTCAGAATCCTACTCAGGATCATTTTTTTATCAAATTA
* * * *
18166 ATTTCAGAATCCTATTCAGGATCATCTTTTTT-TACCAGTTG
1 ATTTCAGAATCCTACTCAGGATCAT-TTTTTTAT-CAAATTA
* *
18207 ATTTCAGCATCCAACTCAGGATC
1 ATTTCAGAATCCTACTCAGGATC
18230 CTGATTTAGG
Statistics
Matches: 456, Mismatches: 40, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
38 34 0.07
39 35 0.08
40 301 0.66
41 86 0.19
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.40
Consensus pattern (40 bp):
ATTTCAGAATCCTACTCAGGATCATTTTTTTATCAAATTA
Found at i:22242 original size:13 final size:13
Alignment explanation
Indices: 22220--22252 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
22210 CTATTAACAA
22220 TTTTTCTTTTGAG
1 TTTTTCTTTTGAG
*
22233 TTTTTTTTTTGAG
1 TTTTTCTTTTGAG
22246 TTTTTCT
1 TTTTTCT
22253 AGGAAGCTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.06, C:0.06, G:0.12, T:0.76
Consensus pattern (13 bp):
TTTTTCTTTTGAG
Found at i:24185 original size:14 final size:13
Alignment explanation
Indices: 24158--24193 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
24148 TCTTGGCAAC
*
24158 AAAAATAAAGAAA
1 AAAAATACAGAAA
24171 AAAAATACAGAAA
1 AAAAATACAGAAA
24184 AAAATATACA
1 AAAA-ATACA
24194 AGAAGAGCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 16 0.76
14 5 0.24
ACGTcount: A:0.78, C:0.06, G:0.06, T:0.11
Consensus pattern (13 bp):
AAAAATACAGAAA
Done.