Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016901.1 Corchorus olitorius cultivar O-4 contig16934, 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: 54808
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:448 original size:31 final size:31
Alignment explanation
Indices: 410--491 Score: 128
Period size: 31 Copynumber: 2.6 Consensus size: 31
400 CGTTACAAAA
* **
410 CAAGCAATTAAGGATATAATGTTTTTTATTT
1 CAAGCAATTAAGAATATAATGTTTTCGATTT
*
441 CAAGCAATTAAGAATATAACGTTTTCGATTT
1 CAAGCAATTAAGAATATAATGTTTTCGATTT
472 CAAGCAATTAAGAATATAAT
1 CAAGCAATTAAGAATATAAT
492 CAATTAGGGC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (31 bp):
CAAGCAATTAAGAATATAATGTTTTCGATTT
Found at i:686 original size:29 final size:31
Alignment explanation
Indices: 621--686 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
611 CTAACGGACT
* *
621 ATATCCTTAATTGCTCGCTTTTCGTAACGTT
1 ATATCCTTAATTGCTCGATTTTCGTAACGTA
*
652 ATATCCTTAATTGCT-TATTTT-GTAACGTA
1 ATATCCTTAATTGCTCGATTTTCGTAACGTA
681 ATATCC
1 ATATCC
687 CAAATTACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 13 0.41
30 4 0.12
31 15 0.47
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.45
Consensus pattern (31 bp):
ATATCCTTAATTGCTCGATTTTCGTAACGTA
Found at i:1366 original size:31 final size:31
Alignment explanation
Indices: 1331--1502 Score: 150
Period size: 31 Copynumber: 5.6 Consensus size: 31
1321 GGCATGTCAG
*
1331 GTGTACCAAAAAGCGACATATGGCACGCCAC
1 GTGTACCAAAAAGCGACACATGGCACGCCAC
** *
1362 GTGTACCAAAAAGCGACATGTGGCACGCCTC
1 GTGTACCAAAAAGCGACACATGGCACGCCAC
* * * * *
1393 ATATACCAAAAAGCGACACGTGACACGACAC
1 GTGTACCAAAAAGCGACACATGGCACGCCAC
* * * * *
1424 ATATACCAAAAAGTGACACATGTCACGCCAT
1 GTGTACCAAAAAGCGACACATGGCACGCCAC
** * * *
1455 GTGTACCAAAAAATGACACGTGGCATGCCTC
1 GTGTACCAAAAAGCGACACATGGCACGCCAC
*
1486 GTGCA-CAAAAAG-GACAC
1 GTGTACCAAAAAGCGACAC
1503 GTGCCACGTA
Statistics
Matches: 118, Mismatches: 23, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
29 5 0.04
30 6 0.05
31 107 0.91
ACGTcount: A:0.38, C:0.27, G:0.20, T:0.15
Consensus pattern (31 bp):
GTGTACCAAAAAGCGACACATGGCACGCCAC
Found at i:1478 original size:93 final size:91
Alignment explanation
Indices: 1334--1510 Score: 228
Period size: 93 Copynumber: 1.9 Consensus size: 91
1324 ATGTCAGGTG
* * * *
1334 TACCAAAAAGCGACATATGGCACGCCACGTGTACCAAAAAGCGACATGTGGCACGCCTCATATAC
1 TACCAAAAAGCGACACATGGCACGCCACGTGTACCAAAAAACGACACGTGGCACGCCTCATACA-
1399 CAAAAAGCGACACGTGACACGACACATA
65 CAAAAAG-GACACGTGACACGACACATA
* * * * * * *
1427 TACCAAAAAGTGACACATGTCACGCCATGTGTACCAAAAAATGACACGTGGCATGCCTCGTGCAC
1 TACCAAAAAGCGACACATGGCACGCCACGTGTACCAAAAAACGACACGTGGCACGCCTCATACAC
*
1492 AAAAAGGACACGTGCCACG
66 AAAAAGGACACGTGACACG
1511 TATCATTTTT
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
91 12 0.17
92 7 0.10
93 53 0.74
ACGTcount: A:0.37, C:0.28, G:0.20, T:0.14
Consensus pattern (91 bp):
TACCAAAAAGCGACACATGGCACGCCACGTGTACCAAAAAACGACACGTGGCACGCCTCATACAC
AAAAAGGACACGTGACACGACACATA
Found at i:3308 original size:136 final size:123
Alignment explanation
Indices: 3113--3373 Score: 344
Period size: 136 Copynumber: 2.0 Consensus size: 123
3103 ATTTAAGAAA
**
3113 TATATTTAAAAATTCTAATATATATAAGTTTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAA
1 TATATTTAAAAATTCTAATATATATAAG-TTTAATTAATTAAAATAGTAAAATGGTAAAAAT---
3178 AAAGGTATAAGGATATTAGATTTAATTAAATAAATAAAAATAGAGTTTTTAGTTGAGTTAAAACT
62 -----TATAAGGATATTAGATTTAA-T---TAAATAAAAATAGAGTTTTTAGTTGAG-TAAAACT
*
3243 GTAAAAG
117 ATAAAAG
*
3250 TATATTTAAAAAATTCTAATATATATAAG-TTAATTATTTAAAATAGTAAAATGGTAAAAATTAT
1 TATATTT-AAAAATTCTAATATATATAAGTTTAATTAATTAAAATAGTAAAATGGTAAAAATTAT
3314 AAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
65 AAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
3373 T
1 T
3374 TTAAACAATG
Statistics
Matches: 119, Mismatches: 4, Indels: 16
0.86 0.03 0.12
Matches are distributed among these distances:
123 14 0.12
124 27 0.23
127 1 0.01
128 20 0.17
136 29 0.24
137 7 0.06
138 21 0.18
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.38
Consensus pattern (123 bp):
TATATTTAAAAATTCTAATATATATAAGTTTAATTAATTAAAATAGTAAAATGGTAAAAATTATA
AGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
Found at i:4129 original size:35 final size:35
Alignment explanation
Indices: 4089--4163 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
4079 AGTTCGTTTA
* *
4089 TGTTCACGAACATGCTCGTTTATTGTTCATTTAAG
1 TGTTCACGAACAGGCTCATTTATTGTTCATTTAAG
*
4124 TGTTCACGAATAGGCTCATTTATTGTTCATTTAAG
1 TGTTCACGAACAGGCTCATTTATTGTTCATTTAAG
4159 TGTTC
1 TGTTC
4164 GTTTATATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.23, C:0.16, G:0.17, T:0.44
Consensus pattern (35 bp):
TGTTCACGAACAGGCTCATTTATTGTTCATTTAAG
Found at i:4243 original size:13 final size:16
Alignment explanation
Indices: 4205--4236 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
4195 TATAATTATT
4205 TATATATTATTAATAA
1 TATATATTATTAATAA
4221 TATATATTATTAATAA
1 TATATATTATTAATAA
4237 AAATTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TATATATTATTAATAA
Found at i:4309 original size:9 final size:9
Alignment explanation
Indices: 4295--4323 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
4285 ATTTAATTAT
4295 TATATATAA
1 TATATATAA
4304 TATATATAA
1 TATATATAA
4313 T-TATATAA
1 TATATATAA
4321 TAT
1 TAT
4324 TTTGTTCGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
TATATATAA
Found at i:4498 original size:42 final size:39
Alignment explanation
Indices: 4451--4552 Score: 122
Period size: 35 Copynumber: 2.6 Consensus size: 39
4441 GAACATTTTC
* *
4451 TTAAACGAGCCGAGCTTGAACGAGCTTCGAACACTCTAAATT
1 TTAAACGAGTCGAGCTTGAACGA---ACGAACACTCTAAATT
4493 TTAAACGAGTCGAGC-T---CGAACGAACACTCTAAATT
1 TTAAACGAGTCGAGCTTGAACGAACGAACACTCTAAATT
*
4528 TTAAACGAGTCGAGCTCGAACGAAC
1 TTAAACGAGTCGAGCTTGAACGAAC
4553 ACCAAAATAT
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
35 30 0.57
38 3 0.06
39 5 0.09
41 1 0.02
42 14 0.26
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.22
Consensus pattern (39 bp):
TTAAACGAGTCGAGCTTGAACGAACGAACACTCTAAATT
Found at i:4518 original size:35 final size:35
Alignment explanation
Indices: 4478--4570 Score: 161
Period size: 35 Copynumber: 2.7 Consensus size: 35
4468 GAACGAGCTT
4478 CGAACACTCTAAATTTTAAACGAGTCGAGCTCGAA
1 CGAACACTCTAAATTTTAAACGAGTCGAGCTCGAA
4513 CGAACACTCTAAATTTTAAACGAGTCGAGCTCGAA
1 CGAACACTCTAAATTTTAAACGAGTCGAGCTCGAA
*
4548 CGAACAC-CAAAATATTTAAACGA
1 CGAACACTCTAAAT-TTTAAACGA
4571 ACACGAGCCG
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
34 5 0.09
35 51 0.91
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.22
Consensus pattern (35 bp):
CGAACACTCTAAATTTTAAACGAGTCGAGCTCGAA
Found at i:4701 original size:16 final size:15
Alignment explanation
Indices: 4673--4726 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 15
4663 TCAAATGTCA
*
4673 GGTCATTTGGGTTTG
1 GGTCATTTTGGTTTG
*
4688 GGTCAATTTTGGTTCG
1 GGTC-ATTTTGGTTTG
*
4704 GGTCTTTTTCGGTTTCG
1 GGTCATTTT-GGTTT-G
4721 GGTCAT
1 GGTCAT
4727 ATGGTTCCGA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
15 8 0.26
16 17 0.55
17 6 0.19
ACGTcount: A:0.07, C:0.13, G:0.33, T:0.46
Consensus pattern (15 bp):
GGTCATTTTGGTTTG
Found at i:12248 original size:5 final size:5
Alignment explanation
Indices: 12238--12271 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
12228 AGAAGAAGAA
12238 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
12272 AAGACAGAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:17965 original size:2 final size:2
Alignment explanation
Indices: 17958--17988 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
17948 TGAAACTGTA
17958 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17989 GTATTTTACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31907 original size:2 final size:2
Alignment explanation
Indices: 31902--31939 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
31892 TAATTTTTTA
*
31902 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31940 GGGAATTGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:32232 original size:33 final size:33
Alignment explanation
Indices: 32195--32318 Score: 221
Period size: 33 Copynumber: 3.8 Consensus size: 33
32185 GGCGTCTCCC
32195 ACCGTGGCGGGGCGCCCCCTGGGGACGCCACCT
1 ACCGTGGCGGGGCGCCCCCTGGGGACGCCACCT
32228 ACCGTGGCGGGGCGCCCCCTGGGGACGCCACCT
1 ACCGTGGCGGGGCGCCCCCTGGGGACGCCACCT
32261 ACCGTGGCGGGGCGCCCCCTGGGGACGCCACCT
1 ACCGTGGCGGGGCGCCCCCTGGGGACGCCACCT
* * *
32294 ACCGTGGTGTGGCGCCCCCCGGGGA
1 ACCGTGGCGGGGCGCCCCCTGGGGA
32319 TGCCTCCACG
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 88 1.00
ACGTcount: A:0.09, C:0.41, G:0.40, T:0.10
Consensus pattern (33 bp):
ACCGTGGCGGGGCGCCCCCTGGGGACGCCACCT
Found at i:34556 original size:149 final size:149
Alignment explanation
Indices: 34286--34591 Score: 452
Period size: 149 Copynumber: 2.1 Consensus size: 149
34276 TCCGGTCATG
34286 TCAAACATAACCAATATTTTGGGATATTAATTACCACTCTAACACGCCCCCTCACGTATAGCTCG
1 TCAAACATAACCAATATTTTGGGATATTAATTACCACTCTAACACGCCCCCTCACGTATAGCTCG
** * * * ** *
34351 GGACAACATTTGAAATAGAACGGGCCTACACGTGGACACAATTGGGTTTGGGGCAACGGGGCAGA
66 GGACAACACCTGAAACAAAACGGGCCTACACGTGAACACAACCGGGTTTGGAGCAACGGGGCAGA
34416 CCTGAGCTCTGATACCATA
131 CCTGAGCTCTGATACCATA
* * * *
34435 TCAAACATGACCAATATTTTGGGATATTAATTACCACTCTAACATGCCCCCTCACGTGTA-ATCC
1 TCAAACATAACCAATATTTTGGGATATTAATTACCACTCTAACACGCCCCCTCACGTATAGCT-C
*
34499 GGGACAACACCTGAAACAAAACGGGCCTACATGTGAACACAACCGGGTTTGGAGCAACGGGGCAG
65 GGGACAACACCTGAAACAAAACGGGCCTACACGTGAACACAACCGGGTTTGGAGCAACGGGGCAG
* * *
34564 ACCTGATCTCTGATATCATG
130 ACCTGAGCTCTGATACCATA
34584 TCAAACAT
1 TCAAACAT
34592 CTAACCTAAA
Statistics
Matches: 140, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
148 1 0.01
149 139 0.99
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (149 bp):
TCAAACATAACCAATATTTTGGGATATTAATTACCACTCTAACACGCCCCCTCACGTATAGCTCG
GGACAACACCTGAAACAAAACGGGCCTACACGTGAACACAACCGGGTTTGGAGCAACGGGGCAGA
CCTGAGCTCTGATACCATA
Found at i:39115 original size:20 final size:20
Alignment explanation
Indices: 39087--39125 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39077 GAATTCAATG
* *
39087 AATGGGGAGAGATGAAGGGA
1 AATGAGGAGAAATGAAGGGA
39107 AATGAGGAGAAATGAAGGG
1 AATGAGGAGAAATGAAGGG
39126 TATATATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.46, T:0.10
Consensus pattern (20 bp):
AATGAGGAGAAATGAAGGGA
Done.