Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019296.1 Corchorus olitorius cultivar O-4 contig19329, 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: 10232
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.31
Found at i:799 original size:25 final size:25
Alignment explanation
Indices: 769--848 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
759 TTGCGAGTTC
769 AAGATCAAAATTCGCTTTTCAAAAT
1 AAGATCAAAATTCGCTTTTCAAAAT
* * ****
794 AAGATC-ACATTC-CATTTGTGAGTCC
1 AAGATCAAAATTCGC-TTT-TCAAAAT
*
819 AAGATCAAAGTTCGCTTTTCAAAAT
1 AAGATCAAAATTCGCTTTTCAAAAT
844 AAGAT
1 AAGAT
849 TGCATTCTAT
Statistics
Matches: 38, Mismatches: 13, Indels: 8
0.64 0.22 0.14
Matches are distributed among these distances:
23 1 0.03
24 8 0.21
25 21 0.55
26 7 0.18
27 1 0.03
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.31
Consensus pattern (25 bp):
AAGATCAAAATTCGCTTTTCAAAAT
Found at i:822 original size:50 final size:50
Alignment explanation
Indices: 751--891 Score: 210
Period size: 50 Copynumber: 2.8 Consensus size: 50
741 ATAAGATTTG
* * *
751 CATTCCATTTGCGAGTTCAAGATCAAAATTCGCTTTTCAAAATAAGATCA
1 CATTCCATTTGTGAGTCCAAGATCAAAGTTCGCTTTTCAAAATAAGATCA
**
801 CATTCCATTTGTGAGTCCAAGATCAAAGTTCGCTTTTCAAAATAAGATTG
1 CATTCCATTTGTGAGTCCAAGATCAAAGTTCGCTTTTCAAAATAAGATCA
* * *
851 CATTCTATTTGTGAGACCAAGACCAAAGTTCGCTTTTCAAA
1 CATTCCATTTGTGAGTCCAAGATCAAAGTTCGCTTTTCAAA
892 GAGCATTTTA
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 83 1.00
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (50 bp):
CATTCCATTTGTGAGTCCAAGATCAAAGTTCGCTTTTCAAAATAAGATCA
Found at i:1238 original size:69 final size:68
Alignment explanation
Indices: 1148--1646 Score: 643
Period size: 68 Copynumber: 7.3 Consensus size: 68
1138 TGAATGTTTC
* *
1148 GGCTTTTCCATAAGTCAAAACTCGTTTCCATACGAGTCAGTTGAAGCCTTGGTTCCATCCAAGCC
1 GGCTTTTCCACAAG-CCAAACTCGTTTCCATACGAGTCAGTT-AAGCCTTGGTTCCATCCAAG-C
1213 A-CGTA
63 AGCGTA
* *
1218 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTAAGCCTTGGTTCCACCCAAGGAGC
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTAAGCCTTGGTTCCATCCAAGCAGC
**
1283 GGG
66 GTA
*
1286 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTATGCCTTGGTTCCATCCAAGCAGC
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTAAGCCTTGGTTCCATCCAAGCAGC
1351 AG-A
66 -GTA
* *
1354 GGCTTTTCCACAAGCCAAACTCGTTTCCATGCGAGTCAGTTAAGCCTTGGTTCCATCTAAGCAGC
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTAAGCCTTGGTTCCATCCAAGCAGC
*
1419 AG-G
66 -GTA
* * *
1422 GGCTTTTCCACAAGCAAAACTCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCATCCAAGTA-
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTT-AAGCCTTGGTTCCATCCAAGCAG
1486 -GTAA
65 CGT-A
* * *
1490 GTGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAACCATGGTTCCATCCAAGCA
1 G-GCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTT-AAGCCTTGGTTCCATCCAAGCA
* *
1555 ACAT-
64 GCGTA
* *
1559 GTGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTCAAGCCTTGGTTCCATCCAAGCA
1 G-GCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTT-AAGCCTTGGTTCCATCCAAGCA
*
1624 GCAG-G
64 GC-GTA
*
1629 GGCTTTTCCATAAGCCAA
1 GGCTTTTCCACAAGCCAA
1647 GTTCATTTCT
Statistics
Matches: 389, Mismatches: 30, Indels: 21
0.88 0.07 0.05
Matches are distributed among these distances:
66 1 0.00
67 1 0.00
68 187 0.48
69 185 0.48
70 14 0.04
71 1 0.00
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (68 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTAAGCCTTGGTTCCATCCAAGCAGC
GTA
Found at i:1291 original size:68 final size:69
Alignment explanation
Indices: 1148--1646 Score: 702
Period size: 69 Copynumber: 7.3 Consensus size: 69
1138 TGAATGTTTC
* * *
1148 GGCTTTTCCATAAGTCAAAACTCGTTTCCATACGAGTCAGTTGAAGCCTTGGTTCCATCCAAGC-
1 GGCTTTTCCACAAG-CCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCA
*
1212 -CACGTA
65 GCA-G-G
* *
1218 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTT-AAGCCTTGGTTCCACCCAAGGAG
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAG
*
1282 CGGG
66 CAGG
*
1286 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTT-ATGCCTTGGTTCCATCCAAGCAG
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAG
*
1350 CAGA
66 CAGG
* *
1354 GGCTTTTCCACAAGCCAAACTCGTTTCCATGCGAGTCAGTT-AAGCCTTGGTTCCATCTAAGCAG
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAG
1418 CAGG
66 CAGG
* * *
1422 GGCTTTTCCACAAGCAAAACTCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCATCCAAGTAG
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAG
* *
1487 TAAG
66 CAGG
* * * * *
1491 TGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAACCATGGTTCCATCCAAGCAA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAG
*
1556 CATG
66 CAGG
* * *
1560 TGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTCAAGCCTTGGTTCCATCCAAGCAG
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAG
1625 CAGG
66 CAGG
*
1629 GGCTTTTCCATAAGCCAA
1 GGCTTTTCCACAAGCCAA
1647 GTTCATTTCT
Statistics
Matches: 390, Mismatches: 36, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
68 185 0.47
69 191 0.49
70 14 0.04
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (69 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAG
CAGG
Found at i:1372 original size:136 final size:137
Alignment explanation
Indices: 1148--1646 Score: 718
Period size: 136 Copynumber: 3.6 Consensus size: 137
1138 TGAATGTTTC
* *
1148 GGCTTTTCCATAAGTCAAAACTCGTTTCCATACGAGTCAGTTGAAGCCTTGGTTCCATCCAAGC-
1 GGCTTTTCCACAAG-CAAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCA
*
1212 -CACGTAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTAAGCCTTGGTTCCACCC
65 GCA-G-AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTAAGCCTTGGTTCCATCC
* *
1276 AAGGAGCGGG
128 AAGCAGCAGG
* *
1286 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTT-ATGCCTTGGTTCCATCCAAGCAG
1 GGCTTTTCCACAAGCAAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAG
* *
1350 CAGAGGCTTTTCCACAAGCCAAACTCGTTTCCATGCGAGTCAGTTAAGCCTTGGTTCCATCTAAG
66 CAGAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTAAGCCTTGGTTCCATCCAAG
1415 CAGCAGG
131 CAGCAGG
* *
1422 GGCTTTTCCACAAGCAAAACTCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCATCCAAGTAG
1 GGCTTTTCCACAAGCAAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAG
* * * *
1487 TA-AGTGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAACCATGGTTCCATCCA
66 CAGAG-GCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTT-AAGCCTTGGTTCCATCCA
* *
1551 AGCAACATG
129 AGCAGCAGG
* * * *
1560 TGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTCAAGCCTTGGTTCCATCCAAGCAG
1 GGCTTTTCCACAAGCAAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAG
* *
1625 CAGGGGCTTTTCCATAAGCCAA
66 CAGAGGCTTTTCCACAAGCCAA
1647 GTTCATTTCT
Statistics
Matches: 327, Mismatches: 28, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
136 126 0.39
137 86 0.26
138 114 0.35
139 1 0.00
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (137 bp):
GGCTTTTCCACAAGCAAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAG
CAGAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTAAGCCTTGGTTCCATCCAAG
CAGCAGG
Found at i:2619 original size:2 final size:2
Alignment explanation
Indices: 2612--2652 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2602 TTCTGGGTTT
2612 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2653 GTGTGTGTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2657 original size:2 final size:2
Alignment explanation
Indices: 2652--2676 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2642 TATATATATA
2652 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
2677 TTTGATTGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:4581 original size:21 final size:21
Alignment explanation
Indices: 4557--4648 Score: 159
Period size: 21 Copynumber: 4.4 Consensus size: 21
4547 CTTAGGCAAT
*
4557 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
4578 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
4599 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
4620 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
4641 TCCAATGA
1 TCCAATGA
4649 TCTCCTAACA
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
20 3 0.04
21 66 0.96
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Done.