Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014964.1 Corchorus olitorius cultivar O-4 contig14997, 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: 9962
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.31
Found at i:270 original size:17 final size:17
Alignment explanation
Indices: 248--283 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
238 TGTACTTTAT
*
248 TTTGTTTTTGTGTTTTG
1 TTTGTTTTTATGTTTTG
265 TTTGTTTTTATGTTTTG
1 TTTGTTTTTATGTTTTG
282 TT
1 TT
284 GGATCTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.03, C:0.00, G:0.19, T:0.78
Consensus pattern (17 bp):
TTTGTTTTTATGTTTTG
Found at i:1401 original size:15 final size:15
Alignment explanation
Indices: 1383--1412 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1373 GATATAAGTT
1383 GTCCTGATGGTGTGC
1 GTCCTGATGGTGTGC
1398 GTCCTGATGGTGTGC
1 GTCCTGATGGTGTGC
1413 TATTTCTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.20, G:0.40, T:0.33
Consensus pattern (15 bp):
GTCCTGATGGTGTGC
Found at i:1657 original size:27 final size:27
Alignment explanation
Indices: 1551--1659 Score: 139
Period size: 27 Copynumber: 4.0 Consensus size: 27
1541 GATCCAAATT
* ** **
1551 GCTCATGACCATCGGGATGTAATTTCA
1 GCTCATGACCATCAGGATCCAATTTTG
*
1578 TCTCATGACCATC-GGCATCCAATTTTG
1 GCTCATGACCATCAGG-ATCCAATTTTG
*
1605 ACTCATGACCATCAGGATCCAATTTTG
1 GCTCATGACCATCAGGATCCAATTTTG
1632 GCTCATGACCATCAGGATCCAATTTTG
1 GCTCATGACCATCAGGATCCAATTTTG
1659 G
1 G
1660 AAACCAAAGC
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
26 2 0.03
27 69 0.95
28 2 0.03
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (27 bp):
GCTCATGACCATCAGGATCCAATTTTG
Found at i:2250 original size:22 final size:22
Alignment explanation
Indices: 2224--2343 Score: 81
Period size: 22 Copynumber: 5.4 Consensus size: 22
2214 TGATGGTATA
2224 AATTTCTCACACCATCAGAACT
1 AATTTCTCACACCATCAGAACT
* * *
2246 AATTTTTC-CATCCTGAT-GGTA-T
1 AATTTCTCACA-CC--ATCAGAACT
2268 AAATTTCTCACACCATCAGAACT
1 -AATTTCTCACACCATCAGAACT
* *
2291 AATTTCTC-CATCCTGAT-GGTA-T
1 AATTTCTCACA-CC--ATCAGAACT
2313 AAATTTCTCACACCATCAGAACT
1 -AATTTCTCACACCATCAGAACT
2336 AATTTCTC
1 AATTTCTC
2344 CATCCTGATG
Statistics
Matches: 74, Mismatches: 10, Indels: 28
0.66 0.09 0.25
Matches are distributed among these distances:
21 8 0.11
22 33 0.45
23 25 0.34
24 8 0.11
ACGTcount: A:0.32, C:0.27, G:0.07, T:0.34
Consensus pattern (22 bp):
AATTTCTCACACCATCAGAACT
Found at i:2271 original size:45 final size:45
Alignment explanation
Indices: 2204--2729 Score: 785
Period size: 45 Copynumber: 11.6 Consensus size: 45
2194 CTTCATCAAA
2204 TTCTCCATCCTGATGGTATAAATTTCTCACACCATCAGAACTAAT
1 TTCTCCATCCTGATGGTATAAATTTCTCACACCATCAGAACTAAT
*
2249 TTTTCCATCCTGATGGTATAAATTTCTCACACCATCAGAACTAAT
1 TTCTCCATCCTGATGGTATAAATTTCTCACACCATCAGAACTAAT
2294 TTCTCCATCCTGATGGTATAAATTTCTCACACCATCAGAACTAAT
1 TTCTCCATCCTGATGGTATAAATTTCTCACACCATCAGAACTAAT
* *
2339 TTCTCCATCCTGATGGTATAAATATCTCACACCATCAGAACTAAA
1 TTCTCCATCCTGATGGTATAAATTTCTCACACCATCAGAACTAAT
* *
2384 TTCTCCATCCTGATGGTATAAATTTCTCACACCATCA-AGACCAAA
1 TTCTCCATCCTGATGGTATAAATTTCTCACACCATCAGA-ACTAAT
* *
2429 TTCTCCATCCTGATGGTATAAATTTCTTCACACCATCA-AGACCAAA
1 TTCTCCATCCTGATGGTATAAATTTC-TCACACCATCAGA-ACTAAT
** *
2475 TTCTCCATCCTGATGGTATAAACATCTCACACCATCAGAACTAAC
1 TTCTCCATCCTGATGGTATAAATTTCTCACACCATCAGAACTAAT
*
2520 TTCTCCATCCTGATGGTATAAATTTCTTCACACCATCA-AGACCAAT
1 TTCTCCATCCTGATGGTATAAATTTC-TCACACCATCAGA-ACTAAT
*
2566 TTCTCCATCCTGATGGTATAAATTTCTTCACACCATCTAG-ACCAAT
1 TTCTCCATCCTGATGGTATAAATTTC-TCACACCATC-AGAACTAAT
* *
2612 TTCTCCATTCTGATGGTATAAATTTCTTCACACCATCA-AGACCAAT
1 TTCTCCATCCTGATGGTATAAATTTC-TCACACCATCAGA-ACTAAT
2658 TTCTCCATCCTGATGGTAT-AATTTCTTCACACCATCAGAACTAAT
1 TTCTCCATCCTGATGGTATAAATTTC-TCACACCATCAGAACTAAT
*
2703 TTCTCCACCCTGATGGTATAAATTTCT
1 TTCTCCATCCTGATGGTATAAATTTCT
2730 TCTTTCGAGA
Statistics
Matches: 452, Mismatches: 18, Indels: 22
0.92 0.04 0.04
Matches are distributed among these distances:
44 1 0.00
45 281 0.62
46 169 0.37
47 1 0.00
ACGTcount: A:0.31, C:0.27, G:0.09, T:0.33
Consensus pattern (45 bp):
TTCTCCATCCTGATGGTATAAATTTCTCACACCATCAGAACTAAT
Found at i:2752 original size:91 final size:91
Alignment explanation
Indices: 2204--2731 Score: 827
Period size: 91 Copynumber: 5.8 Consensus size: 91
2194 CTTCATCAAA
*
2204 TTCTCCATCCTGATGGTATAAATTTCTCACACCATCAGAACTAATTTTTCCATCCTGATGGTATA
1 TTCTCCATCCTGATGGTATAAATTTCTCACACCATCAGAACTAATTTCTCCATCCTGATGGTATA
*
2269 AATTTC-TCACACCATC-AGAACTAAT
66 AATTTCTTCACACCATCAAG-ACCAAT
2294 TTCTCCATCCTGATGGTATAAATTTCTCACACCATCAGAACTAATTTCTCCATCCTGATGGTATA
1 TTCTCCATCCTGATGGTATAAATTTCTCACACCATCAGAACTAATTTCTCCATCCTGATGGTATA
* * *
2359 AATATC-TCACACCATC-AGAACTAAA
66 AATTTCTTCACACCATCAAG-ACCAAT
* *
2384 TTCTCCATCCTGATGGTATAAATTTCTCACACCATCA-AGACCAAATTCTCCATCCTGATGGTAT
1 TTCTCCATCCTGATGGTATAAATTTCTCACACCATCAGA-ACTAATTTCTCCATCCTGATGGTAT
*
2448 AAATTTCTTCACACCATCAAGACCAAA
65 AAATTTCTTCACACCATCAAGACCAAT
** *
2475 TTCTCCATCCTGATGGTATAAACATCTCACACCATCAGAACTAACTTCTCCATCCTGATGGTATA
1 TTCTCCATCCTGATGGTATAAATTTCTCACACCATCAGAACTAATTTCTCCATCCTGATGGTATA
2540 AATTTCTTCACACCATCAAGACCAAT
66 AATTTCTTCACACCATCAAGACCAAT
* *
2566 TTCTCCATCCTGATGGTATAAATTTCTTCACACCATCTAG-ACCAATTTCTCCATTCTGATGGTA
1 TTCTCCATCCTGATGGTATAAATTTC-TCACACCATC-AGAACTAATTTCTCCATCCTGATGGTA
2630 TAAATTTCTTCACACCATCAAGACCAAT
64 TAAATTTCTTCACACCATCAAGACCAAT
*
2658 TTCTCCATCCTGATGGTAT-AATTTCTTCACACCATCAGAACTAATTTCTCCACCCTGATGGTAT
1 TTCTCCATCCTGATGGTATAAATTTC-TCACACCATCAGAACTAATTTCTCCATCCTGATGGTAT
2722 AAATTTCTTC
65 AAATTTCTTC
2732 TTTCGAGATT
Statistics
Matches: 411, Mismatches: 20, Indels: 13
0.93 0.05 0.03
Matches are distributed among these distances:
89 1 0.00
90 155 0.38
91 172 0.42
92 81 0.20
93 2 0.00
ACGTcount: A:0.31, C:0.27, G:0.09, T:0.33
Consensus pattern (91 bp):
TTCTCCATCCTGATGGTATAAATTTCTCACACCATCAGAACTAATTTCTCCATCCTGATGGTATA
AATTTCTTCACACCATCAAGACCAAT
Found at i:6193 original size:18 final size:18
Alignment explanation
Indices: 6155--6194 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
6145 TTTAGCTCTT
* *
6155 CTCCTGAGCTCTCGCCTC
1 CTCCTGAGCTCTCACCCC
6173 CTCCTGAGCTCTCACCCC
1 CTCCTGAGCTCTCACCCC
6191 CTCC
1 CTCC
6195 ATGTCTTCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.07, C:0.55, G:0.12, T:0.25
Consensus pattern (18 bp):
CTCCTGAGCTCTCACCCC
Found at i:8063 original size:15 final size:15
Alignment explanation
Indices: 8043--8080 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
8033 CCTATTGTCA
8043 TTGCCATTATGCCCG
1 TTGCCATTATGCCCG
8058 TTGCCATTATGCCCG
1 TTGCCATTATGCCCG
*
8073 TTTCCATT
1 TTGCCATT
8081 CCTAACACGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.13, C:0.32, G:0.16, T:0.39
Consensus pattern (15 bp):
TTGCCATTATGCCCG
Found at i:9844 original size:27 final size:27
Alignment explanation
Indices: 9738--9846 Score: 137
Period size: 27 Copynumber: 4.0 Consensus size: 27
9728 GATCCAAATT
* * **
9738 GCTCATGACCATCGGGATCTAATTTCA
1 GCTCATGACCATCAGGATCCAATTTTG
* * * *
9765 TCTCATGAGCATCGGGATCAAATTTTG
1 GCTCATGACCATCAGGATCCAATTTTG
*
9792 ACTCATGACCATCAGGATCCAATTTTG
1 GCTCATGACCATCAGGATCCAATTTTG
9819 GCTCATGACCATCAGGATCCAATTTTG
1 GCTCATGACCATCAGGATCCAATTTTG
9846 G
1 G
9847 AAACCAAAGC
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 72 1.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (27 bp):
GCTCATGACCATCAGGATCCAATTTTG
Done.