Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008172.1 Corchorus capsularis cultivar CVL-1 contig08193, 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: 33832
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31
Found at i:2783 original size:48 final size:48
Alignment explanation
Indices: 2712--2807 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
2702 TTGATAACTA
2712 TTCATGTTTTATTGGTAACTATTCAGTATCTATAAATACAGATTTCGT
1 TTCATGTTTTATTGGTAACTATTCAGTATCTATAAATACAGATTTCGT
2760 TTCATGTTTTATTGGTAACTATTCAGTATCTATAAATACAGATTTCGT
1 TTCATGTTTTATTGGTAACTATTCAGTATCTATAAATACAGATTTCGT
2808 CCACGTTTTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.46
Consensus pattern (48 bp):
TTCATGTTTTATTGGTAACTATTCAGTATCTATAAATACAGATTTCGT
Found at i:16450 original size:13 final size:13
Alignment explanation
Indices: 16432--16456 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16422 AAACCACCTT
16432 CTTTTTTTTTTTC
1 CTTTTTTTTTTTC
16445 CTTTTTTTTTTT
1 CTTTTTTTTTTT
16457 TGTCTCAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
CTTTTTTTTTTTC
Found at i:18029 original size:26 final size:26
Alignment explanation
Indices: 17995--18046 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
17985 CATAGCGGGT
*
17995 CGCGGCCCA-CCATGGTCCGGGTCGCG
1 CGCGACCCAGCCATGG-CCGGGTCGCG
*
18021 CGCGACCCAGCCGTGGCCGGGTCGCG
1 CGCGACCCAGCCATGGCCGGGTCGCG
18047 ACCCACTGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.08, C:0.42, G:0.40, T:0.10
Consensus pattern (26 bp):
CGCGACCCAGCCATGGCCGGGTCGCG
Found at i:18717 original size:22 final size:22
Alignment explanation
Indices: 18685--18727 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
18675 TATTATATCT
18685 ATATATATATATAATATATAAC
1 ATATATATATATAATATATAAC
* **
18707 ATATATTTATATTTTATATAA
1 ATATATATATATAATATATAA
18728 AAAATATCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
ATATATATATATAATATATAAC
Found at i:18734 original size:24 final size:24
Alignment explanation
Indices: 18684--18734 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
18674 ATATTATATC
* *
18684 TATATATATATATAATATATAACA
1 TATATATATATATAATATAAAAAA
* * *
18708 TATATTTATATTTTATATAAAAAA
1 TATATATATATATAATATAAAAAA
18732 TAT
1 TAT
18735 CTATTTGGTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
TATATATATATATAATATAAAAAA
Found at i:20086 original size:43 final size:43
Alignment explanation
Indices: 19987--20186 Score: 207
Period size: 41 Copynumber: 4.7 Consensus size: 43
19977 TTTCTTTCTG
19987 AAGTCCTCAAGCACATTTATAACACAGAGGCACC-C-ATATCA
1 AAGTCCTCAAGCACATTTATAACACAGAGGCACCTCTATATCA
* *
20028 AAGTACC-CAAGCACATTTATAACACAGGGGCACCTCTATTTCA
1 AAGT-CCTCAAGCACATTTATAACACAGAGGCACCTCTATATCA
*
20071 AAGTCCTCAAGCACATTTATAACATAGAGGCA--TCTATATCA
1 AAGTCCTCAAGCACATTTATAACACAGAGGCACCTCTATATCA
* * * * * *
20112 AAGTCCCCAAACACAATTATAACAAAGGGGCAATCCTCTCTA--A
1 AAGTCCTCAAGCACATTTATAACACAGAGGC-A-CCTCTATATCA
** * *
20155 AAGAACTCAAACACATTTATAACATAGAGGCA
1 AAGTCCTCAAGCACATTTATAACACAGAGGCA
20187 TCCATACTAA
Statistics
Matches: 134, Mismatches: 17, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
41 64 0.48
42 7 0.05
43 58 0.43
45 5 0.04
ACGTcount: A:0.41, C:0.26, G:0.12, T:0.21
Consensus pattern (43 bp):
AAGTCCTCAAGCACATTTATAACACAGAGGCACCTCTATATCA
Found at i:20101 original size:84 final size:82
Alignment explanation
Indices: 19987--20227 Score: 288
Period size: 84 Copynumber: 2.9 Consensus size: 82
19977 TTTCTTTCTG
* * * *
19987 AAGTCCTCAAGCACATTTATAACACAGAGGCACCCATATCAAAGTACCCAAGCACATTTATAACA
1 AAGTCCTCAAGCACATTTATAACATAGAGGCATCCATATCAAAGT-CCCAAACACAATTATAACA
* *
20052 CAGGGGCA-CCTCTATTTCA
65 CAGGGGCATCCTC--TCTAA
*
20071 AAGTCCTCAAGCACATTTATAACATAGAGGCATCTATATCAAAGTCCCCAAACACAATTATAACA
1 AAGTCCTCAAGCACATTTATAACATAGAGGCATCCATATCAAAGT-CCCAAACACAATTATAACA
*
20136 AAGGGGCAATCCTCTCTAA
65 CAGGGGC-ATCCTCTCTAA
** * *
20155 AAGAACTCAAACACATTTATAACATAGAGGCATCCATA-CTAAAGTCCCTAAATACAATTATAAC
1 AAGTCCTCAAGCACATTTATAACATAGAGGCATCCATATC-AAAGTCCC-AAACACAATTATAAC
*
20219 ACAAGGGCA
64 ACAGGGGCA
20228 ATTTCTATAT
Statistics
Matches: 137, Mismatches: 16, Indels: 9
0.85 0.10 0.06
Matches are distributed among these distances:
83 5 0.04
84 127 0.93
85 1 0.01
86 4 0.03
ACGTcount: A:0.41, C:0.25, G:0.12, T:0.22
Consensus pattern (82 bp):
AAGTCCTCAAGCACATTTATAACATAGAGGCATCCATATCAAAGTCCCAAACACAATTATAACAC
AGGGGCATCCTCTCTAA
Found at i:20219 original size:41 final size:42
Alignment explanation
Indices: 20082--20219 Score: 122
Period size: 41 Copynumber: 3.3 Consensus size: 42
20072 AGTCCTCAAG
* * * *
20082 CACATTTATAACATAGAGGCATCTATA-TCAAAGTCCCCAAA
1 CACAATTATAACATAGAGGCATCCATACTAAAAGTCCCTAAA
* * * **
20123 CACAATTATAACAAAGGGGCAATCC-TCTCTAAAAG-AACTCAAA
1 CACAATTATAACATAGAGGC-ATCCAT-ACTAAAAGTCCCT-AAA
*
20166 CACATTTATAACATAGAGGCATCCATACT-AAAGTCCCTAAA
1 CACAATTATAACATAGAGGCATCCATACTAAAAGTCCCTAAA
*
20207 TACAATTATAACA
1 CACAATTATAACA
20220 CAAGGGCAAT
Statistics
Matches: 74, Mismatches: 17, Indels: 12
0.72 0.17 0.12
Matches are distributed among these distances:
41 36 0.49
42 12 0.16
43 26 0.35
ACGTcount: A:0.44, C:0.23, G:0.09, T:0.23
Consensus pattern (42 bp):
CACAATTATAACATAGAGGCATCCATACTAAAAGTCCCTAAA
Found at i:24018 original size:10 final size:10
Alignment explanation
Indices: 24003--24038 Score: 72
Period size: 10 Copynumber: 3.6 Consensus size: 10
23993 ACTTTGGGAG
24003 AAAATGGTAA
1 AAAATGGTAA
24013 AAAATGGTAA
1 AAAATGGTAA
24023 AAAATGGTAA
1 AAAATGGTAA
24033 AAAATG
1 AAAATG
24039 CCCCTGAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.19, T:0.19
Consensus pattern (10 bp):
AAAATGGTAA
Found at i:28344 original size:10 final size:10
Alignment explanation
Indices: 28329--28353 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
28319 GTTGCTGCAT
28329 AATTCCAGAA
1 AATTCCAGAA
28339 AATTCCAGAA
1 AATTCCAGAA
28349 AATTC
1 AATTC
28354 TAGAGTCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (10 bp):
AATTCCAGAA
Done.