Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012127.1 Corchorus olitorius cultivar O-4 contig12160, 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: 31217
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:998 original size:13 final size:13
Alignment explanation
Indices: 980--1013 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
970 GTTGAGGAAC
980 TGTTTTATTAATA
1 TGTTTTATTAATA
993 TGTTTTATTAATA
1 TGTTTTATTAATA
1006 TGTTTTAT
1 TGTTTTAT
1014 AAATGGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (13 bp):
TGTTTTATTAATA
Found at i:1034 original size:25 final size:26
Alignment explanation
Indices: 980--1036 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 26
970 GTTGAGGAAC
*
980 TGTTTTATTAATATGTTTTATTAATA
1 TGTTTTATTAATATGTTTTATAAATA
1006 TGTTTTA-TAA-ATGGTTTTAATAAAT-
1 TGTTTTATTAATAT-GTTTT-ATAAATA
1031 TGTTTT
1 TGTTTT
1037 GGGTGCATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 2 0.07
25 14 0.50
26 12 0.43
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (26 bp):
TGTTTTATTAATATGTTTTATAAATA
Found at i:1035 original size:13 final size:13
Alignment explanation
Indices: 980--1036 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
970 GTTGAGGAAC
*
980 TGTTTTATTAATA
1 TGTTTTATAAATA
*
993 TGTTTTATTAATA
1 TGTTTTATAAATA
1006 TGTTTTATAAAT-
1 TGTTTTATAAATA
*
1018 GGTTTTAATAAAT-
1 TGTTTT-ATAAATA
1031 TGTTTT
1 TGTTTT
1037 GGGTGCATGA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
12 5 0.12
13 35 0.88
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (13 bp):
TGTTTTATAAATA
Found at i:7867 original size:29 final size:31
Alignment explanation
Indices: 7835--7902 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 31
7825 CCCTTAAAAA
* *
7835 AAGCCCCTATACTT-TTGTTT-TAATCAAAT
1 AAGCCCCTATACTTCTTATTTGCAATCAAAT
** *
7864 AAGCCTTTATACTTCTTATTTGCAATCACAT
1 AAGCCCCTATACTTCTTATTTGCAATCAAAT
7895 AAGCCCCT
1 AAGCCCCT
7903 CAAATTTTTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
29 12 0.40
30 5 0.17
31 13 0.43
ACGTcount: A:0.29, C:0.25, G:0.07, T:0.38
Consensus pattern (31 bp):
AAGCCCCTATACTTCTTATTTGCAATCAAAT
Found at i:12274 original size:24 final size:24
Alignment explanation
Indices: 12246--12298 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
12236 TGGATCTAAG
*
12246 TGTTTCAGTCATAGGGTTAAGTAT
1 TGTTTAAGTCATAGGGTTAAGTAT
* * *
12270 TGTTTAATTCATAGGGTTTAGTTT
1 TGTTTAAGTCATAGGGTTAAGTAT
12294 TGTTT
1 TGTTT
12299 GGTAAACATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.21, C:0.06, G:0.23, T:0.51
Consensus pattern (24 bp):
TGTTTAAGTCATAGGGTTAAGTAT
Found at i:19077 original size:6 final size:6
Alignment explanation
Indices: 19067--19100 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
19057 GGATTTGAAG
* *
19067 AACCCG AACCCG AACCCA AACCCA AACCCA AACC
1 AACCCA AACCCA AACCCA AACCCA AACCCA AACC
19101 GTAGTTCTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.44, C:0.50, G:0.06, T:0.00
Consensus pattern (6 bp):
AACCCA
Found at i:22076 original size:15 final size:16
Alignment explanation
Indices: 22046--22080 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
22036 TAAAGATTAA
22046 TATTTAAAATATAATT
1 TATTTAAAATATAATT
*
22062 TATTTATAA-ATAATT
1 TATTTAAAATATAATT
22077 TATT
1 TATT
22081 AACCACATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATTTAAAATATAATT
Found at i:23333 original size:200 final size:199
Alignment explanation
Indices: 22953--23696 Score: 1229
Period size: 200 Copynumber: 3.7 Consensus size: 199
22943 GATTTCAAAA
*
22953 AATATTAATACATATTCCCTAAGGGGACACATGCCAACCCTTAAACCCCGCACGTGCAGTCTGCT
1 AATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCT
* * *
23018 AAACTCCACTGACTGTGTATTGTACAATTTTTCTTATAGGGATTATTATACAATACACTGTCAGC
66 AAACTCCACTGACGGTGTATTGTATAATTTTTCTTATA-GGATTATTATACAATACACTGTCAGT
*
23083 GTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAA
130 GTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATATCCCATTTCATAATTAATTAAA
23148 TATTT
195 TATTT
*
23153 AATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCACACGTGCAGTCTGCT
1 AATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCT
*
23218 AAATTCCACTGACGGTGTATTGTATAATTTTTCTTATAGGGATTATTATACAATACACTGTCAGT
66 AAACTCCACTGACGGTGTATTGTATAATTTTTCTTATA-GGATTATTATACAATACACTGTCAGT
* *
23283 GTAAATTTTGGACTCCATAAGCGGTTTAGGAAGTTGACACATATCCCATTTCATAATTAATTAAA
130 GTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATATCCCATTTCATAATTAATT-AA
23348 TATATTT
194 -ATATTT
* *
23355 AATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTATATCCCGCACGTGCAGTCTGCT
1 AATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCT
* * * *
23420 AAACTCCACTTATGGTGTATTGCATAATTTTTCTTATAGTATTATTATACAATACACTGTCAGTG
66 AAACTCCACTGACGGTGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTG
23485 TAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACAT-TCCCAATTTCATAATTAATTAAA
131 TAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATATCCC-ATTTCATAATTAATTAAA
23549 TATTT
195 TATTT
* * *
23554 AATATTAATACATATTCCCTAAGGGGATACATGTCAACCCTTATACCCCGTACGTGCAGTCTGCT
1 AATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCT
* * * * *
23619 AAACTCTACTGACGGTGTATTGTATAATATTTCGTATAGGACTATTATACGATACACTGTCAGTG
66 AAACTCCACTGACGGTGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTG
23684 TAAATTTTGGACT
131 TAAATTTTGGACT
23697 TAATAAAGTT
Statistics
Matches: 510, Mismatches: 31, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
199 137 0.27
200 189 0.37
201 82 0.16
202 102 0.20
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34
Consensus pattern (199 bp):
AATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCT
AAACTCCACTGACGGTGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTG
TAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATATCCCATTTCATAATTAATTAAAT
ATTT
Found at i:26248 original size:18 final size:19
Alignment explanation
Indices: 26226--26272 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
26216 ATATAAAAAA
26226 AAGAAAGAAAAGAAA-AAG
1 AAGAAAGAAAAGAAAGAAG
* *
26244 GAGAAAAAAAAGAAAGAAG
1 AAGAAAGAAAAGAAAGAAG
*
26263 AAGAAGGAAA
1 AAGAAAGAAA
26273 TAAGGAAATT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (19 bp):
AAGAAAGAAAAGAAAGAAG
Done.