Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012403.1 Corchorus capsularis cultivar CVL-1 contig12424, 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: 3986
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Found at i:1284 original size:31 final size:31
Alignment explanation
Indices: 1246--1317 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
1236 CCCAAATTAA
1246 CCCCTTAACTATCCATTTTGGGACAAATTGG
1 CCCCTTAACTATCCATTTTGGGACAAATTGG
* * ***
1277 CCTCTTAACTTTTTTTTTTGGGACAAATTGG
1 CCCCTTAACTATCCATTTTGGGACAAATTGG
1308 CCCCTTAACT
1 CCCCTTAACT
1318 TTAAAAAACG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.39
Consensus pattern (31 bp):
CCCCTTAACTATCCATTTTGGGACAAATTGG
Found at i:1318 original size:31 final size:31
Alignment explanation
Indices: 1261--1319 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
1251 TAACTATCCA
*
1261 TTTTGGGACAAATTGGCCTCTTAACTTTTTT
1 TTTTGGGACAAATTGGCCCCTTAACTTTTTT
1292 TTTTGGGACAAATTGGCCCCTTAACTTT
1 TTTTGGGACAAATTGGCCCCTTAACTTT
1320 AAAAAACGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.20, C:0.19, G:0.17, T:0.44
Consensus pattern (31 bp):
TTTTGGGACAAATTGGCCCCTTAACTTTTTT
Found at i:2086 original size:31 final size:29
Alignment explanation
Indices: 2015--2096 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 29
2005 TCTCATTTTT
* *
2015 AAAATTTAAGGGGGTCAATTTGTCCCAAAA
1 AAAAGTTAA-GGGGCCAATTTGTCCCAAAA
2045 AAAAGTTAAGGGGCCAATTTGTCCCAAAA
1 AAAAGTTAAGGGGCCAATTTGTCCCAAAA
* *
2074 TAGATAGTTAAGGGGCTAATTTG
1 -A-AAAGTTAAGGGGCCAATTTG
2097 GATATTAAGC
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
29 19 0.41
30 9 0.20
31 18 0.39
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (29 bp):
AAAAGTTAAGGGGCCAATTTGTCCCAAAA
Found at i:3107 original size:109 final size:110
Alignment explanation
Indices: 2889--3184 Score: 443
Period size: 109 Copynumber: 2.7 Consensus size: 110
2879 TAAATTAAAA
** * *
2889 TGGTAAAAATAAAAAAGATTATATAAAATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGT
1 TGGTAAAAATAAAGTA-ATTATA-AAGATATTAGAATTTAATTGAATGAAAATAGAGTTTTTAGT
2953 AGAATAAAATTGTATATTAGAAAAAATTTAAATATATCCAAATTTTT
64 AGAATAAAATTGTATATTAGAAAAAATTTAAATATATCCAAATTTTT
*
3000 TGGTAAAAATAAAGTAATTATAAAGATATTAG-ATTTAATTGAATGAAAATTGAGTTTTTAGTAG
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGAATTTAATTGAATGAAAATAGAGTTTTTAGTAG
* *
3064 AATAAAATTGTATATTAGAAAAAATTTTAGTATATCCAAATTTTT
66 AATAAAATTGTATATTAGAAAAAATTTAAATATATCCAAATTTTT
* *
3109 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAG----AATTTAATTGAATGAAAATAGAGTTTTTA
3174 GTAGAATAAAA
62 GTAGAATAAAA
3185 CTATAATAGT
Statistics
Matches: 169, Mismatches: 10, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
109 112 0.66
110 7 0.04
111 14 0.08
114 36 0.21
ACGTcount: A:0.49, C:0.02, G:0.12, T:0.37
Consensus pattern (110 bp):
TGGTAAAAATAAAGTAATTATAAAGATATTAGAATTTAATTGAATGAAAATAGAGTTTTTAGTAG
AATAAAATTGTATATTAGAAAAAATTTAAATATATCCAAATTTTT
Found at i:3831 original size:6 final size:7
Alignment explanation
Indices: 3814--3879 Score: 64
Period size: 7 Copynumber: 9.4 Consensus size: 7
3804 ATGGGGTTCA
*
3814 AAAAAGA
1 AAAAAGT
3821 AAAAAGT
1 AAAAAGT
3828 AAAAAGT
1 AAAAAGT
*
3835 AAAAAGG
1 AAAAAGT
3842 AAAAGAG-
1 AAAA-AGT
3849 AAAAACGT
1 AAAAA-GT
*
3857 AAAAAAT
1 AAAAAGT
*
3864 AAAAAAT
1 AAAAAGT
3871 AAAAA-T
1 AAAAAGT
3877 AAA
1 AAA
3880 GCCCAAATTA
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
6 5 0.09
7 41 0.77
8 7 0.13
ACGTcount: A:0.77, C:0.02, G:0.12, T:0.09
Consensus pattern (7 bp):
AAAAAGT
Found at i:3850 original size:29 final size:29
Alignment explanation
Indices: 3813--3868 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
3803 AATGGGGTTC
*
3813 AAAAAAGAAAAAAGTAAAAAGTAAAAAGG
1 AAAAAAGAAAAAAGTAAAAAATAAAAAGG
* *
3842 AAAAGAGAAAAACGTAAAAAATAAAAA
1 AAAAAAGAAAAAAGTAAAAAATAAAAA
3869 ATAAAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.77, C:0.02, G:0.14, T:0.07
Consensus pattern (29 bp):
AAAAAAGAAAAAAGTAAAAAATAAAAAGG
Found at i:3874 original size:29 final size:29
Alignment explanation
Indices: 3813--3875 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
3803 AATGGGGTTC
* *
3813 AAAAAAGAAAAAAGTAAAAAGTAAAAAGG
1 AAAAAAGAAAAAAGTAAAAAATAAAAAAG
* * *
3842 AAAAGAGAAAAACGTAAAAAATAAAAAAT
1 AAAAAAGAAAAAAGTAAAAAATAAAAAAG
3871 AAAAA
1 AAAAA
3876 TAAAGCCCAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.78, C:0.02, G:0.13, T:0.08
Consensus pattern (29 bp):
AAAAAAGAAAAAAGTAAAAAATAAAAAAG
Done.