Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004918.1 Corchorus capsularis cultivar CVL-1 contig04936, 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: 6436
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:675 original size:23 final size:23
Alignment explanation
Indices: 645--690 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
635 ATAAGTCTAA
645 AGCTCAAATTTCAC-AGCTTTCTG
1 AGCTCAAATTTCACAAG-TTTCTG
668 AGCTCAAATTTCACAAGTTTCTG
1 AGCTCAAATTTCACAAGTTTCTG
691 GTCGAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (23 bp):
AGCTCAAATTTCACAAGTTTCTG
Found at i:730 original size:6 final size:5
Alignment explanation
Indices: 698--732 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
688 CTGGTCGAAA
698 ATTTT -TTTT ATTTT ATTTT ATTTT ATTTAT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTT-T ATTTT
733 TCGATATAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.14
5 19 0.68
6 5 0.18
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:1809 original size:33 final size:33
Alignment explanation
Indices: 1733--1856 Score: 135
Period size: 33 Copynumber: 3.7 Consensus size: 33
1723 TAGACAAAGG
* *
1733 GTCGCGTGGCCGGTTGTGGCCGGGCATGGCCGA-
1 GTCGCGTGGCCGGTTGTGGCCGGACATGTCC-AT
** * *
1766 GTCGTTTGGCCGGTTGTAGCCGGTCATGTCCAT
1 GTCGCGTGGCCGGTTGTGGCCGGACATGTCCAT
1799 GTCGCGTGGCCGG-TGATGGCCGGACATGTCCAT
1 GTCGCGTGGCCGGTTG-TGGCCGGACATGTCCAT
*
1832 GTCGCGTTGCCGGTCTTGTGGCCGG
1 GTCGCGTGGCCGG--TTGTGGCCGG
1857 TGTTGCGCAG
Statistics
Matches: 76, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
32 3 0.04
33 64 0.84
35 7 0.09
36 2 0.03
ACGTcount: A:0.07, C:0.27, G:0.41, T:0.25
Consensus pattern (33 bp):
GTCGCGTGGCCGGTTGTGGCCGGACATGTCCAT
Found at i:2778 original size:108 final size:103
Alignment explanation
Indices: 2514--3002 Score: 400
Period size: 104 Copynumber: 4.6 Consensus size: 103
2504 ATATTCTTTA
* * * *
2514 TTTTT-TTT-AAAACCCTATAATAATATATTCTTAATTTAACAACTCACCCTTTAAATGAATTAA
1 TTTTTATTTCAAAACCCTATAAGAATATATT-TTAATTTAATAACTTACCCTTAAAATGAATTAA
** * * *
2577 A-ACTTTAGTTTGGGGTTAAAATTAGTAAAATTCATTATTT
65 ATTTTTTA-TTTGGGGCTAAACTTAGTGAAATTCA-TATTT
* * * * *
2617 TTTATT-TTT-AAAACCCCATATGAATACATTTTCAGTTTAATAATTTACCCTTAAAATGAATTA
1 TTT-TTATTTCAAAACCCTATAAGAATATATTTT-AATTTAATAACTTACCCTTAAAATGAATTA
**
2680 AATTTTTTATTTGAAGCTAAACTTAGTGAAATTCACTATTT
64 AATTTTTTATTTGGGGCTAAACTTAGTGAAATTCA-TATTT
*
2721 TTTTTAAATTTCCAAAACCCTATAAGAATATATTTTAAGTTTAATAACTTACTCTTAAAATGAAT
1 TTTTT--ATTT-CAAAACCCTATAAGAATATATTTTAA-TTTAATAACTTACCCTTAAAATGAAT
* * * **
2786 TAAAATTTTTATTT-GGGTTAAATTTAGTGAAATTCAT-TAA
62 TAAATTTTTTATTTGGGGCTAAACTTAGTGAAATTCATATTT
* *
2826 TTTTTATTTCTAAAACCCTATATAATAATAATATATTTCAATTTAATGACTTACCCTTAAAATGA
1 TTTTTATTTC-AAAACCC--TATAAGAAT-ATAT-TTT-AATTTAATAACTTACCCTTAAAATGA
** * **
2891 ATTATTTTTTTTATTTGGGGCTAAACTTAGTGAGATTTGTTGATTCT
60 ATTAAATTTTTTATTTGGGGCTAAACTTAGTGA-AATTCAT-ATT-T
* * * * * *
2938 TTTTT-TTTCTAGAACCCAATAAGAATACAATTTCAATTTATTGACTTATACCCTTAAAATGAAT
1 TTTTTATTTC-AAAACCCTATAAGAATA-TATTTTAATTTAATAAC-T-TACCCTTAAAATGAAT
3002 T
62 T
3003 TTTATATGTT
Statistics
Matches: 314, Mismatches: 49, Indels: 40
0.78 0.12 0.10
Matches are distributed among these distances:
102 1 0.00
103 18 0.06
104 78 0.25
105 18 0.06
106 8 0.03
107 67 0.21
108 77 0.25
109 30 0.10
111 12 0.04
112 5 0.02
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (103 bp):
TTTTTATTTCAAAACCCTATAAGAATATATTTTAATTTAATAACTTACCCTTAAAATGAATTAAA
TTTTTTATTTGGGGCTAAACTTAGTGAAATTCATATTT
Found at i:2891 original size:107 final size:106
Alignment explanation
Indices: 2514--3002 Score: 432
Period size: 108 Copynumber: 4.6 Consensus size: 106
2504 ATATTCTTTA
* * * *
2514 TTTT-TTT-TAAAACCC-TATAATAATATAT-TCTT-AATTTAACAACTCACCCTTTAAATGAAT
1 TTTTATTTCTAAAACCCATATAAGAATATATAT-TTCAATTTAATAACTTACCCTTAAAATGAAT
* * * *
2574 TAAAA-CTTTAGTTTGGGGTTAAAATTAGTAAAATTCATTATT
65 TAAAATTTTTA-TTTGGGGCTAAACTTAGTGAAATTCATTATT
* * * *
2616 TTTTATTTTTAAAACCCCATAT--GAATACAT-TTTCAGTTTAATAATTTACCCTTAAAATGAAT
1 TTTTATTTCTAAAA-CCCATATAAGAATATATATTTCAATTTAATAACTTACCCTTAAAATGAAT
* ** *
2678 TAAATTTTTTATTTGAAGCTAAACTTAGTGAAATTCACTATTTT
65 TAAAATTTTTATTTGGGGCTAAACTTAGTGAAATTCA-T-TATT
* *
2722 TTTTAAATTTCCAAAACCC-TATAAGAATATAT-TTT-AAGTTTAATAACTTACTCTTAAAATGA
1 TTTT--ATTTCTAAAACCCATATAAGAATATATATTTCAA-TTTAATAACTTACCCTTAAAATGA
* * *
2784 ATTAAAATTTTTATTT-GGGTTAAATTTAGTGAAATTCATTAAT
63 ATTAAAATTTTTATTTGGGGCTAAACTTAGTGAAATTCATTATT
* *
2827 TTTTATTTCTAAAACCCTATATAATAATAATATATTTCAATTTAATGACTTACCCTTAAAATGAA
1 TTTTATTTCTAAAACCC-ATATAAGAAT-ATATATTTCAATTTAATAACTTACCCTTAAAATGAA
*** * **
2892 TTATTTTTTTTATTTGGGGCTAAACTTAGTGAGATTTGTTGATTCT
64 TTAAAATTTTTATTTGGGGCTAAACTTAGTGAAATTCATT-A-T-T
* * * * *
2938 TTTTTTTTCTAGAACCCA-ATAAGAATACA-ATTTCAATTTATTGACTTATACCCTTAAAATGAA
1 TTTTATTTCTAAAACCCATATAAGAATATATATTTCAATTTAATAAC-T-TACCCTTAAAATGAA
3001 TT
64 TT
3003 TTTATATGTT
Statistics
Matches: 317, Mismatches: 46, Indels: 41
0.78 0.11 0.10
Matches are distributed among these distances:
102 4 0.01
103 17 0.05
104 60 0.19
105 22 0.07
106 18 0.06
107 75 0.24
108 79 0.25
109 25 0.08
110 1 0.00
111 16 0.05
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (106 bp):
TTTTATTTCTAAAACCCATATAAGAATATATATTTCAATTTAATAACTTACCCTTAAAATGAATT
AAAATTTTTATTTGGGGCTAAACTTAGTGAAATTCATTATT
Found at i:3065 original size:26 final size:26
Alignment explanation
Indices: 3035--3117 Score: 82
Period size: 26 Copynumber: 3.2 Consensus size: 26
3025 CTTAAGGAAA
3035 ATAAATACCAAAATTGTCATTGCATT
1 ATAAATACCAAAATTGTCATTGCATT
* * * **
3061 ATAAAT--CTAAATTTTC-TTAAGGAAA
1 ATAAATACCAAAATTGTCATT--GCATT
3086 ATAAATACCAAAATTGTCATTGCATT
1 ATAAATACCAAAATTGTCATTGCATT
3112 ATAAAT
1 ATAAAT
3118 CTAACACATG
Statistics
Matches: 42, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
23 2 0.05
24 8 0.19
25 8 0.19
26 14 0.33
27 8 0.19
28 2 0.05
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.35
Consensus pattern (26 bp):
ATAAATACCAAAATTGTCATTGCATT
Found at i:3118 original size:51 final size:51
Alignment explanation
Indices: 3017--3121 Score: 210
Period size: 51 Copynumber: 2.1 Consensus size: 51
3007 TATGTTAGTA
3017 TAAATTTTCTTAAGGAAAATAAATACCAAAATTGTCATTGCATTATAAATC
1 TAAATTTTCTTAAGGAAAATAAATACCAAAATTGTCATTGCATTATAAATC
3068 TAAATTTTCTTAAGGAAAATAAATACCAAAATTGTCATTGCATTATAAATC
1 TAAATTTTCTTAAGGAAAATAAATACCAAAATTGTCATTGCATTATAAATC
3119 TAA
1 TAA
3122 CACATGAAAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.35
Consensus pattern (51 bp):
TAAATTTTCTTAAGGAAAATAAATACCAAAATTGTCATTGCATTATAAATC
Found at i:6206 original size:2 final size:2
Alignment explanation
Indices: 6199--6232 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6189 TTTCTAAATA
6199 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6233 GGTCATAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.