Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021610.1 Corchorus olitorius cultivar O-4 contig21643, 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: 44347
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:92 original size:19 final size:18
Alignment explanation
Indices: 68--104 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
58 ATTTTGTTCA
68 TTTCATCATTTTCTTTCTT
1 TTTCAT-ATTTTCTTTCTT
*
87 TTTCATTTTTTCTTTCTT
1 TTTCATATTTTCTTTCTT
105 CCTCCCAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTCATATTTTCTTTCTT
Found at i:1176 original size:30 final size:31
Alignment explanation
Indices: 1142--1204 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 31
1132 TTGAGATAAG
*
1142 GTTAGATTCTCTGAAAT-TATTGGCTATTGT
1 GTTAGATTCTCTGAAATATATTGGATATTGT
* * *
1172 GTTAGATTTTCTGACATATCTTGGATATTGT
1 GTTAGATTCTCTGAAATATATTGGATATTGT
1203 GT
1 GT
1205 GGATGAGATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 15 0.54
31 13 0.46
ACGTcount: A:0.22, C:0.10, G:0.21, T:0.48
Consensus pattern (31 bp):
GTTAGATTCTCTGAAATATATTGGATATTGT
Found at i:1297 original size:136 final size:136
Alignment explanation
Indices: 942--1428 Score: 669
Period size: 136 Copynumber: 3.6 Consensus size: 136
932 TGTGGAACAT
* * * * *
942 ATAAGGATTCAAA-CAACGGTCACATTTCAATCTCACTTTGAATCCAACGGTTGGATTAAGATAA
1 ATAACGATTCAAATCAACGGTCACATTTGAATCTCACTTTTAATCCAACGGTTGAATTGAGATAA
* * * * * * * * *
1006 TGTTAAATTATCATCAATTTATTGACTGTTGTGTTATATTTTTTGACATATCTTGGATATTGTGT
66 GGTTAGATTCTC-TGAAATTATTGGCTATTGTGTTAGATTTTCTGACATATCTTGGATATTGTGT
*
1071 GGAAGAG
130 GGATGAG
* *** * *
1078 ATAA-GTTTTTCATCAACGGTCACATTTGATTC-CAAC-TTTAATCCAACGATTGAATTGAGATA
1 ATAACGATTCAAATCAACGGTCACATTTGAATCTC-ACTTTTAATCCAACGGTTGAATTGAGATA
1140 AGGTTAGATTCTCTGAAATTATTGGCTATTGTGTTAGATTTTCTGACATATCTTGGATATTGTGT
65 AGGTTAGATTCTCTGAAATTATTGGCTATTGTGTTAGATTTTCTGACATATCTTGGATATTGTGT
1205 GGATGAG
130 GGATGAG
*
1212 ATAACGATTCAAATTAACGGTCACATTTGAATCTCACTTTTAATCCAACGGTTGAATTGAGATAA
1 ATAACGATTCAAATCAACGGTCACATTTGAATCTCACTTTTAATCCAACGGTTGAATTGAGATAA
1277 GGTTAGATTCTCTGAAATTATTGGCTATTGTGTTAGATTTTCTGACATATCTTGGATATTGTGTG
66 GGTTAGATTCTCTGAAATTATTGGCTATTGTGTTAGATTTTCTGACATATCTTGGATATTGTGTG
1342 GATGAG
131 GATGAG
* * *
1348 ATAACTATTCAAATTAACGGTCACATTTGAATCTCACTTTTAATCTAACGGTT-AGATTGAGATA
1 ATAACGATTCAAATCAACGGTCACATTTGAATCTCACTTTTAATCCAACGGTTGA-ATTGAGATA
* *
1412 GGGTTAGATTCTGTGAA
65 AGGTTAGATTCTCTGAA
1429 GATAAAATTA
Statistics
Matches: 314, Mismatches: 31, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
134 56 0.18
135 62 0.20
136 196 0.62
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (136 bp):
ATAACGATTCAAATCAACGGTCACATTTGAATCTCACTTTTAATCCAACGGTTGAATTGAGATAA
GGTTAGATTCTCTGAAATTATTGGCTATTGTGTTAGATTTTCTGACATATCTTGGATATTGTGTG
GATGAG
Found at i:1312 original size:30 final size:31
Alignment explanation
Indices: 1278--1340 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 31
1268 TTGAGATAAG
*
1278 GTTAGATTCTCTGAAAT-TATTGGCTATTGT
1 GTTAGATTCTCTGAAATATATTGGATATTGT
* * *
1308 GTTAGATTTTCTGACATATCTTGGATATTGT
1 GTTAGATTCTCTGAAATATATTGGATATTGT
1339 GT
1 GT
1341 GGATGAGATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 15 0.54
31 13 0.46
ACGTcount: A:0.22, C:0.10, G:0.21, T:0.48
Consensus pattern (31 bp):
GTTAGATTCTCTGAAATATATTGGATATTGT
Found at i:8725 original size:11 final size:11
Alignment explanation
Indices: 8682--8719 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
8672 TTCCTATATA
*
8682 AAATAAATTAT
1 AAATTAATTAT
8693 CAAA-TAATTAT
1 -AAATTAATTAT
8704 AAATTAATTAT
1 AAATTAATTAT
8715 AAATT
1 AAATT
8720 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:9589 original size:85 final size:85
Alignment explanation
Indices: 9486--9656 Score: 290
Period size: 85 Copynumber: 2.0 Consensus size: 85
9476 TTGTTTAAAA
*
9486 TTTTATAGTTTTAGTCAACTAAAAACTCTATTATTATTTAATTAAATCTAATATCCTTATA-ACT
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTATTATTTAATTAAATCTAATATCCTTATACA-T
*
9550 ATTTTATTTTTACCATTTTAC
65 ATTTTATTTTTACCATATTAC
* *
9571 TTTTGTAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACATA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTATTATTTAATTAAATCTAATATCCTTATACATA
9636 TTTTATTTTTACCATATTAC
66 TTTTATTTTTACCATATTAC
9656 T
1 T
9657 AATTTAATTA
Statistics
Matches: 81, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
85 80 0.99
86 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.02, T:0.51
Consensus pattern (85 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTATTATTTAATTAAATCTAATATCCTTATACATA
TTTTATTTTTACCATATTAC
Found at i:12563 original size:22 final size:22
Alignment explanation
Indices: 12523--12565 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
12513 ACAAATCATG
* **
12523 GGATTTAATTGCATCAAATTAA
1 GGATTTAATTGAAGAAAATTAA
12545 GGATTTAATTGAAGAAAATTA
1 GGATTTAATTGAAGAAAATTA
12566 GAAATCTTAC
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:0.44, C:0.05, G:0.16, T:0.35
Consensus pattern (22 bp):
GGATTTAATTGAAGAAAATTAA
Found at i:15882 original size:27 final size:27
Alignment explanation
Indices: 15838--15911 Score: 85
Period size: 28 Copynumber: 2.7 Consensus size: 27
15828 AGTGAAATTA
* ** *
15838 AAATGACCAAAACACCCCTGAATGTGC
1 AAATGACTAAAATGCCCCTGAACGTGC
*
15865 AAATGACTAAAATGCCCCATGGACGTGC
1 AAATGACTAAAATGCCCC-TGAACGTGC
*
15893 AAATGAATAAAATGCCCCT
1 AAATGACTAAAATGCCCCT
15912 AGGTGACCCT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
27 16 0.40
28 24 0.60
ACGTcount: A:0.41, C:0.26, G:0.16, T:0.18
Consensus pattern (27 bp):
AAATGACTAAAATGCCCCTGAACGTGC
Found at i:16128 original size:64 final size:64
Alignment explanation
Indices: 16039--16165 Score: 191
Period size: 64 Copynumber: 2.0 Consensus size: 64
16029 CAATCGGACA
* * *
16039 GGTTGAACGGGTTTCGGGTTCGGGTCATCAGGGTTTAGCTTAAATGAGTCAGATAATTTTCTCG
1 GGTTGAACGGGTTTCAGGTTCGGGTCATCAGGATTTAGCTCAAATGAGTCAGATAATTTTCTCG
* * * *
16103 GGTTGGACGGGTTTTAGGTTTGGGTCATCAGGATTTAGCTCAAATGAGTCAGGTAATTTTCTC
1 GGTTGAACGGGTTTCAGGTTCGGGTCATCAGGATTTAGCTCAAATGAGTCAGATAATTTTCTC
16166 AGGTCATTCG
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
64 56 1.00
ACGTcount: A:0.20, C:0.13, G:0.31, T:0.35
Consensus pattern (64 bp):
GGTTGAACGGGTTTCAGGTTCGGGTCATCAGGATTTAGCTCAAATGAGTCAGATAATTTTCTCG
Found at i:17498 original size:22 final size:22
Alignment explanation
Indices: 17464--17523 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
17454 AAAATGGCAT
*
17464 GACACGGCACGACCCACGTGCC
1 GACACAGCACGACCCACGTGCC
*
17486 GGCACAGCACGACCCACGTGCC
1 GACACAGCACGACCCACGTGCC
**
17508 GATGCAGCACGACCCA
1 GACACAGCACGACCCA
17524 TTTTTAATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.25, C:0.43, G:0.27, T:0.05
Consensus pattern (22 bp):
GACACAGCACGACCCACGTGCC
Found at i:29989 original size:5 final size:6
Alignment explanation
Indices: 29966--30000 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
29956 GAAGAGGAAA
* *
29966 TGTTCT TGTTTT TATTTT TGTTTT TGTTTT TGTTT
1 TGTTTT TGTTTT TGTTTT TGTTTT TGTTTT TGTTT
30001 AGAAATTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.03, C:0.03, G:0.14, T:0.80
Consensus pattern (6 bp):
TGTTTT
Found at i:30272 original size:13 final size:13
Alignment explanation
Indices: 30243--30271 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
30233 TTTTAATGTG
30243 AAAAGGAAAAAGA
1 AAAAGGAAAAAGA
30256 AAAAGG-AAAAGA
1 AAAAGGAAAAAGA
30268 AAAA
1 AAAA
30272 ATAGAGTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAGGAAAAAGA
Found at i:34005 original size:36 final size:36
Alignment explanation
Indices: 33958--34027 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
33948 CTTTGGTTCT
33958 GTTTCGTCCATTAGATTTCCCTTTTCCCATTGAATA
1 GTTTCGTCCATTAGATTTCCCTTTTCCCATTGAATA
33994 GTTTCGTCCATTAGATTTCCCTTTTCCCATTGAA
1 GTTTCGTCCATTAGATTTCCCTTTTCCCATTGAA
34028 CATTTAGAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.19, C:0.26, G:0.11, T:0.44
Consensus pattern (36 bp):
GTTTCGTCCATTAGATTTCCCTTTTCCCATTGAATA
Found at i:36253 original size:20 final size:21
Alignment explanation
Indices: 36211--36253 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
36201 TCCTTTGTTG
36211 ATGATCTCCAATGGGCTTCAA
1 ATGATCTCCAATGGGCTTCAA
* *
36232 ATGATCTCCGAT-GGCTTTAA
1 ATGATCTCCAATGGGCTTCAA
36252 AT
1 AT
36254 TCTTCAAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (21 bp):
ATGATCTCCAATGGGCTTCAA
Found at i:36390 original size:21 final size:21
Alignment explanation
Indices: 36364--36405 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
36354 GCATCTTAGA
36364 CAACTCCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
*
36385 CAACTCTGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
36406 TTCTTCCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (21 bp):
CAACTCCGATGAGCTTGAAAC
Found at i:41363 original size:12 final size:12
Alignment explanation
Indices: 41346--41371 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41336 TACATAATTA
41346 TTGGTGTTTATT
1 TTGGTGTTTATT
41358 TTGGTGTTTATT
1 TTGGTGTTTATT
41370 TT
1 TT
41372 ATCAATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.23, T:0.69
Consensus pattern (12 bp):
TTGGTGTTTATT
Found at i:43477 original size:38 final size:38
Alignment explanation
Indices: 43413--43509 Score: 142
Period size: 38 Copynumber: 2.6 Consensus size: 38
43403 TTTAAAAAGA
** *
43413 CCTAAATTGAATGCTTTGAAAACTTGATGGGATTTTTC
1 CCTAAATTGAAAACTTTGAAAACTTGATGGGATCTTTC
43451 CCTAAATTGAAAACTTT-AAAATCTTGATGGGATCTTTC
1 CCTAAATTGAAAACTTTGAAAA-CTTGATGGGATCTTTC
*
43489 CTTAAATTGAAAACTTTGAAA
1 CCTAAATTGAAAACTTTGAAA
43510 GAAATTCTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
37 4 0.08
38 46 0.87
39 3 0.06
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.37
Consensus pattern (38 bp):
CCTAAATTGAAAACTTTGAAAACTTGATGGGATCTTTC
Found at i:44309 original size:2 final size:2
Alignment explanation
Indices: 44302--44339 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
44292 TAAAACCCAA
44302 AT AT 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 AT AT
44340 GAGAATAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.