Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012583.1 Corchorus olitorius cultivar O-4 contig12616, 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: 7815
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:283 original size:29 final size:28
Alignment explanation
Indices: 150--308 Score: 180
Period size: 29 Copynumber: 5.6 Consensus size: 28
140 AAGTGAACTT
*
150 AAAATGACCAAAATG-CCCTGAACATGC
1 AAAATGACCAAAATGCCCCTGAATATGC
* *
177 -AAATGACCAAAATGCCCTTGAATGTGC
1 AAAATGACCAAAATGCCCCTGAATATGC
204 -AAATGACCAAAATGCCCCTGAATCATGC
1 AAAATGACCAAAATGCCCCTGAAT-ATGC
* * * *
232 AGAAACGACCAAAATACCACTGAATACGC
1 A-AAATGACCAAAATGCCCCTGAATATGC
*
261 AAAAATGACCAAAATGCCCCTGAATGTGC
1 -AAAATGACCAAAATGCCCCTGAATATGC
*
290 AGAAATGATCAAAATGCCC
1 A-AAATGACCAAAATGCCC
309 TTAAGTGACC
Statistics
Matches: 111, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
26 14 0.13
27 31 0.28
28 4 0.04
29 41 0.37
30 21 0.19
ACGTcount: A:0.43, C:0.25, G:0.16, T:0.16
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTGAATATGC
Found at i:814 original size:32 final size:32
Alignment explanation
Indices: 777--874 Score: 110
Period size: 32 Copynumber: 3.1 Consensus size: 32
767 CAGGATCGAA
* * *
777 ATTAACTCATAATGCAATAATCCTATATCGGG
1 ATTAACTCATAAAGCAATAATCCTAAATCAGG
* *
809 ATTAACTGATAAAGCAATGATCCTAAATCAGG
1 ATTAACTCATAAAGCAATAATCCTAAATCAGG
* * *
841 ATTAA--AATAAAGCAATGATCCTAAACCAGG
1 ATTAACTCATAAAGCAATAATCCTAAATCAGG
871 ATTA
1 ATTA
875 TGATAAAGTG
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
30 27 0.46
32 32 0.54
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.27
Consensus pattern (32 bp):
ATTAACTCATAAAGCAATAATCCTAAATCAGG
Found at i:853 original size:30 final size:29
Alignment explanation
Indices: 817--1247 Score: 418
Period size: 30 Copynumber: 14.2 Consensus size: 29
807 GGATTAACTG
817 ATAAAGCAATGATCCTAAATCAGGATTAAA
1 ATAAAGCAATGATCCTAAA-CAGGATTAAA
**
847 ATAAAGCAATGATCCTAAACCAGGATTATG
1 ATAAAGCAATGATCCTAAA-CAGGATTAAA
* *
877 ATAAAGTGAA-GATCCTCAACCAGGATTAAA
1 ATAAAG-CAATGATCCT-AAACAGGATTAAA
* *
907 ATAAAGCAACGATCCTCAAACATGATTAAA
1 ATAAAGCAATGATCCT-AAACAGGATTAAA
* * *
937 ATAAAGCAACGATTCTCAACCAGGATTAAA
1 ATAAAGCAATGATCCT-AAACAGGATTAAA
*
967 ATAAAGCAAAT-ATCCTCAACCAGGATTAAA
1 ATAAAGC-AATGATCCT-AAACAGGATTAAA
*
997 ACAAAGCAATGATCCTCAAACAGGATTAAAAA
1 ATAAAGCAATGATCCT-AAACAGGATT--AAA
*
1029 ATGAAGCAATGATCCTTAAACAGGATTAAA
1 ATAAAGCAATGATCC-TAAACAGGATTAAA
* * *
1059 ATAAAGCGACGATCCTCAACCAGGATTAAA
1 ATAAAGCAATGATCCT-AAACAGGATTAAA
* ** *
1089 CTAAAGTGATGATCCTCAAGCAGGATTAAAA
1 ATAAAGCAATGATCCT-AAACAGGATT-AAA
*
1120 ATGAAA-CAATGATCCTTAAACAGGATCAAA
1 AT-AAAGCAATGATCC-TAAACAGGATTAAA
* * *
1150 ATAAAGCGACGATCCTCAACCAGGATTAAA
1 ATAAAGCAATGATCCT-AAACAGGATTAAA
*
1180 ATAAAGCAATGTTCCTCAAACAGGATTAAAA
1 ATAAAGCAATGATCCT-AAACAGGATT-AAA
*
1211 ATAAAGCAATGATCCTCAAACAGGATTGAA
1 ATAAAGCAATGATCCT-AAACAGGATTAAA
*
1241 ATGAAGC
1 ATAAAGC
1248 TGATAAAGCA
Statistics
Matches: 343, Mismatches: 43, Indels: 30
0.82 0.10 0.07
Matches are distributed among these distances:
29 10 0.03
30 248 0.72
31 54 0.16
32 30 0.09
33 1 0.00
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.20
Consensus pattern (29 bp):
ATAAAGCAATGATCCTAAACAGGATTAAA
Found at i:1159 original size:91 final size:91
Alignment explanation
Indices: 817--1247 Score: 575
Period size: 91 Copynumber: 4.7 Consensus size: 91
807 GGATTAACTG
**
817 ATAAAGCAATGATCCT-AAATCAGGATT-AAAATAAAGCAATGATCC-TAAACCAGGATTATGAT
1 ATAAAGCAATGATCCTCAAA-CAGGATTAAAAATAAAGCAATGATCCTTAAA-CAGGATTAAAAT
*
879 AAAGTGAAGATCCTCAACCAGGATTAAA
64 AAAGCGAAGATCCTCAACCAGGATTAAA
* * * * * *
907 ATAAAGCAACGATCCTCAAACATGATT-AAAATAAAGCAACGATTCTCAACCAGGATTAAAATAA
1 ATAAAGCAATGATCCTCAAACAGGATTAAAAATAAAGCAATGATCCTTAAACAGGATTAAAATAA
* *
971 AGCAAATATCCTCAACCAGGATTAAA
66 AGCGAAGATCCTCAACCAGGATTAAA
* *
997 ACAAAGCAATGATCCTCAAACAGGATTAAAAAATGAAGCAATGATCCTTAAACAGGATTAAAATA
1 ATAAAGCAATGATCCTCAAACAGGATT-AAAAATAAAGCAATGATCCTTAAACAGGATTAAAATA
*
1062 AAGCGACGATCCTCAACCAGGATTAAA
65 AAGCGAAGATCCTCAACCAGGATTAAA
* ** * *
1089 CTAAAGTGATGATCCTCAAGCAGGATTAAAAATGAAA-CAATGATCCTTAAACAGGATCAAAATA
1 ATAAAGCAATGATCCTCAAACAGGATTAAAAAT-AAAGCAATGATCCTTAAACAGGATTAAAATA
*
1153 AAGCGACGATCCTCAACCAGGATTAAA
65 AAGCGAAGATCCTCAACCAGGATTAAA
* * * *
1180 ATAAAGCAATGTTCCTCAAACAGGATTAAAAATAAAGCAATGATCCTCAAACAGGATTGAAATGA
1 ATAAAGCAATGATCCTCAAACAGGATTAAAAATAAAGCAATGATCCTTAAACAGGATTAAAATAA
1245 AGC
66 AGC
1248 TGATAAAGCA
Statistics
Matches: 297, Mismatches: 38, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
90 99 0.33
91 119 0.40
92 79 0.27
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.20
Consensus pattern (91 bp):
ATAAAGCAATGATCCTCAAACAGGATTAAAAATAAAGCAATGATCCTTAAACAGGATTAAAATAA
AGCGAAGATCCTCAACCAGGATTAAA
Found at i:1722 original size:102 final size:101
Alignment explanation
Indices: 1557--1860 Score: 452
Period size: 102 Copynumber: 3.0 Consensus size: 101
1547 TTACCAACGT
* * * *
1557 AAACTTTGAATAGAGACCTT-AACCAAGGATTTTAAACTTAAACATGAACTTTTAATGACAAACT
1 AAACTCTGAATAGAGACCTTGAA-CAAGGATTTTAAACTTAAACATGAATTTTTGAT-AAAAACT
*
1621 TGATGAAATGAAATGATACCCGGAGGTTTTATCAATGC
64 TGATAAAATGAAATGATACCCGGAGGTTTTATCAATGC
1659 AAACTCTGAATAGAGACCTTGAACAAGGATTTTAAACTTAAACATGAATTTTTGATAATAAACTT
1 AAACTCTGAATAGAGACCTTGAACAAGGATTTTAAACTTAAACATGAATTTTTGATAA-AAACTT
*
1724 GATAAAATGAAATGGTACCCGGAGGTTTTA-CTAATGC
65 GATAAAATGAAATGATACCCGGAGGTTTTATC-AATGC
* *
1761 AAACTCTGAATCA-AGACCTTGAACAAGGATTTTAAACTTAAACATGATTTTTTTGGTGAAAAAC
1 AAACTCTGAAT-AGAGACCTTGAACAAGGATTTTAAACTTAAACATGA-ATTTTTGAT-AAAAAC
1825 TTGATAAAATGAAATGATACCCGGAGGTTTTATCAA
63 TTGATAAAATGAAATGATACCCGGAGGTTTTATCAA
1861 ATGGAATAAG
Statistics
Matches: 186, Mismatches: 9, Indels: 13
0.89 0.04 0.06
Matches are distributed among these distances:
101 2 0.01
102 134 0.72
103 47 0.25
104 3 0.02
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.30
Consensus pattern (101 bp):
AAACTCTGAATAGAGACCTTGAACAAGGATTTTAAACTTAAACATGAATTTTTGATAAAAACTTG
ATAAAATGAAATGATACCCGGAGGTTTTATCAATGC
Found at i:3638 original size:16 final size:15
Alignment explanation
Indices: 3619--3655 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
3609 TTCGACTTCG
3619 TTTTTTATTTGATTTT
1 TTTTTTATTTG-TTTT
*
3635 TTTTTTCTTTGTTTT
1 TTTTTTATTTGTTTT
3650 TTTTTT
1 TTTTTT
3656 GGAATTTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.05, C:0.03, G:0.05, T:0.86
Consensus pattern (15 bp):
TTTTTTATTTGTTTT
Found at i:4049 original size:8 final size:8
Alignment explanation
Indices: 4036--4071 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
4026 GTGCCTTAAT
4036 TTTTTTCA
1 TTTTTTCA
4044 TTTTTTTCA
1 -TTTTTTCA
4053 TTTTTTCA
1 TTTTTTCA
*
4061 GTTTTTCA
1 TTTTTTCA
4069 TTT
1 TTT
4072 CATCATCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 17 0.68
9 8 0.32
ACGTcount: A:0.11, C:0.11, G:0.03, T:0.75
Consensus pattern (8 bp):
TTTTTTCA
Done.