Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016692.1 Corchorus olitorius cultivar O-4 contig16725, 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: 52738
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:3140 original size:8 final size:9
Alignment explanation
Indices: 3120--3210 Score: 55
Period size: 8 Copynumber: 9.9 Consensus size: 9
3110 TTTTAACGTG
3120 TTTTCTTCT
1 TTTTCTTCT
3129 TTTTCTTCT
1 TTTTCTTCT
*
3138 TTTT-TTTT
1 TTTTCTTCT
*
3146 TTAAATTCTTTT
1 TT---TTCTTCT
*
3158 TCTTTATTCAT
1 T-TTTCTTC-T
3169 TTTTC-TCT
1 TTTTCTTCT
*
3177 TATTCTTTCT
1 TTTTC-TTCT
3187 TTTTCTT-T
1 TTTTCTTCT
3195 TTTTCTT-T
1 TTTTCTTCT
*
3203 CTTTCTTC
1 TTTTCTTC
3211 CTCCCTCACT
Statistics
Matches: 66, Mismatches: 7, Indels: 18
0.73 0.08 0.20
Matches are distributed among these distances:
8 25 0.38
9 17 0.26
10 14 0.21
11 4 0.06
12 5 0.08
13 1 0.02
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTCTTCT
Found at i:3185 original size:26 final size:22
Alignment explanation
Indices: 3156--3209 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 22
3146 TTAAATTCTT
3156 TTTCTTTATTCATTTTTCTCTTATTC
1 TTTCTTT-TTC-TTTTTCTC-T-TTC
*
3182 TTTCTTTTTCTTTTTTTCTTTC
1 TTTCTTTTTCTTTTTCTCTTTC
3204 TTTCTT
1 TTTCTT
3210 CCTCCCTCAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 9 0.33
23 1 0.04
24 7 0.26
25 3 0.11
26 7 0.26
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTCTTTTTCTTTTTCTCTTTC
Found at i:5826 original size:9 final size:9
Alignment explanation
Indices: 5808--5859 Score: 54
Period size: 9 Copynumber: 5.9 Consensus size: 9
5798 TAATTTTCTG
*
5808 TTTTTCCAT
1 TTTTTTCAT
5817 TTTTTTCA-
1 TTTTTTCAT
5825 TTTTTTC-T
1 TTTTTTCAT
* *
5833 TTTCTTCTT
1 TTTTTTCAT
5842 TTTTTTCAT
1 TTTTTTCAT
5851 TTTTCTTCA
1 TTTT-TTCA
5860 AAATTTGACC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 13 0.36
9 19 0.53
10 4 0.11
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTTTCAT
Found at i:5827 original size:24 final size:25
Alignment explanation
Indices: 5795--5857 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 25
5785 GAAAACACTC
* *
5795 TTTTAATTTTCTGTTTT-TCCATTT
1 TTTTCATTTTCTCTTTTCTCCATTT
* * *
5819 TTTTCATTTTTTCTTTTCTTCTTTT
1 TTTTCATTTTCTCTTTTCTCCATTT
5844 TTTTCATTTT-TCTT
1 TTTTCATTTTCTCTT
5858 CAAAATTTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
24 18 0.55
25 15 0.45
ACGTcount: A:0.08, C:0.14, G:0.02, T:0.76
Consensus pattern (25 bp):
TTTTCATTTTCTCTTTTCTCCATTT
Found at i:11211 original size:24 final size:25
Alignment explanation
Indices: 11184--11253 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
11174 CACCTGCCAA
*
11184 GCCTTGCACG-TGGGTCGCGCGTAG
1 GCCTTGCACGTTGGGCCGCGCGTAG
**
11208 GCCTTGTGCGTTGGGCCGCGCGTAG
1 GCCTTGCACGTTGGGCCGCGCGTAG
**
11233 GCCTTGTGCGTTGGGCCGCGC
1 GCCTTGCACGTTGGGCCGCGC
11254 ATGGCAGCCC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
24 8 0.19
25 34 0.81
ACGTcount: A:0.04, C:0.30, G:0.43, T:0.23
Consensus pattern (25 bp):
GCCTTGCACGTTGGGCCGCGCGTAG
Found at i:11227 original size:25 final size:25
Alignment explanation
Indices: 11194--11253 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
11184 GCCTTGCACG
*
11194 TGGGTCGCGCGTAGGCCTTGTGCGT
1 TGGGCCGCGCGTAGGCCTTGTGCGT
11219 TGGGCCGCGCGTAGGCCTTGTGCGT
1 TGGGCCGCGCGTAGGCCTTGTGCGT
11244 TGGGCCGCGC
1 TGGGCCGCGC
11254 ATGGCAGCCC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.03, C:0.28, G:0.45, T:0.23
Consensus pattern (25 bp):
TGGGCCGCGCGTAGGCCTTGTGCGT
Found at i:11289 original size:6 final size:6
Alignment explanation
Indices: 11276--11358 Score: 121
Period size: 6 Copynumber: 13.8 Consensus size: 6
11266 TAGCCTGCCT
* * * * *
11276 TCTCTC TGTCTC TGTCTC TGTCTC TGTCTC TGTCTC TCTCTC TCTCTC
1 TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC
11324 TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCT
1 TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCT
11359 TTTTAACATT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 75 1.00
ACGTcount: A:0.00, C:0.43, G:0.06, T:0.51
Consensus pattern (6 bp):
TCTCTC
Found at i:12960 original size:20 final size:20
Alignment explanation
Indices: 12923--12960 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12913 TTATTTCCTT
*
12923 TTTTAATATCTTCTAAATTC
1 TTTTAATATCTTCCAAATTC
*
12943 TTTTAATATTTTCCAAAT
1 TTTTAATATCTTCCAAAT
12961 CTTCCACACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTAATATCTTCCAAATTC
Found at i:14135 original size:42 final size:42
Alignment explanation
Indices: 14071--14150 Score: 151
Period size: 42 Copynumber: 1.9 Consensus size: 42
14061 ATACTTTTCA
*
14071 GTTTTGAGTTGGCACTAGAACATAACATTATGAACTGCTTCG
1 GTTTGGAGTTGGCACTAGAACATAACATTATGAACTGCTTCG
14113 GTTTGGAGTTGGCACTAGAACATAACATTATGAACTGC
1 GTTTGGAGTTGGCACTAGAACATAACATTATGAACTGC
14151 ATATTTGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (42 bp):
GTTTGGAGTTGGCACTAGAACATAACATTATGAACTGCTTCG
Found at i:25938 original size:15 final size:15
Alignment explanation
Indices: 25902--25931 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
25892 AATTGTTTCT
25902 GTGCAATACACGTGC
1 GTGCAATACACGTGC
25917 GTGCAATACACGTGC
1 GTGCAATACACGTGC
25932 CGTCAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (15 bp):
GTGCAATACACGTGC
Found at i:26708 original size:13 final size:14
Alignment explanation
Indices: 26687--26719 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
26677 GTTGTTCTTC
*
26687 TCTTTTTTTTTTTT
1 TCTTTTTTTTTTTG
26701 TCTTTTTTTTTTTG
1 TCTTTTTTTTTTTG
26715 TCTTT
1 TCTTT
26720 AACAAGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.88
Consensus pattern (14 bp):
TCTTTTTTTTTTTG
Found at i:29646 original size:19 final size:19
Alignment explanation
Indices: 29622--29659 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
29612 CTTCACACGT
29622 GCTTCTTCAAAACGACACC
1 GCTTCTTCAAAACGACACC
29641 GCTTCTTCAAAACGACACC
1 GCTTCTTCAAAACGACACC
29660 TCATATTGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.37, G:0.11, T:0.21
Consensus pattern (19 bp):
GCTTCTTCAAAACGACACC
Found at i:47287 original size:2 final size:2
Alignment explanation
Indices: 47282--47306 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
47272 TATTTTTTAG
47282 GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT G
47307 GCATTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:48157 original size:14 final size:14
Alignment explanation
Indices: 48138--48174 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
48128 CTTTAGTACG
*
48138 TAAAAACTACAAAA
1 TAAAAACTAAAAAA
*
48152 TAAAAAATAAAAAA
1 TAAAAACTAAAAAA
48166 TAAAAACTA
1 TAAAAACTA
48175 GCTAATAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (14 bp):
TAAAAACTAAAAAA
Found at i:48160 original size:7 final size:7
Alignment explanation
Indices: 48138--48171 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
48128 CTTTAGTACG
*
48138 TAAAAAC
1 TAAAAAA
*
48145 TACAAAA
1 TAAAAAA
48152 TAAAAAA
1 TAAAAAA
48159 TAAAAAA
1 TAAAAAA
48166 TAAAAA
1 TAAAAA
48172 CTAGCTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAAAAA
Found at i:48653 original size:115 final size:115
Alignment explanation
Indices: 48451--48680 Score: 460
Period size: 115 Copynumber: 2.0 Consensus size: 115
48441 AGGGGCTATA
48451 TGCATTGGGTGACTCCTTATTTCAACATCCCAAACTCCACCCACCACCACTCCAAAGTAGATTAA
1 TGCATTGGGTGACTCCTTATTTCAACATCCCAAACTCCACCCACCACCACTCCAAAGTAGATTAA
48516 TTTTGCTAAAAGCCCACATGATAAAGACAAGACTCAAAGCATGAGTAATT
66 TTTTGCTAAAAGCCCACATGATAAAGACAAGACTCAAAGCATGAGTAATT
48566 TGCATTGGGTGACTCCTTATTTCAACATCCCAAACTCCACCCACCACCACTCCAAAGTAGATTAA
1 TGCATTGGGTGACTCCTTATTTCAACATCCCAAACTCCACCCACCACCACTCCAAAGTAGATTAA
48631 TTTTGCTAAAAGCCCACATGATAAAGACAAGACTCAAAGCATGAGTAATT
66 TTTTGCTAAAAGCCCACATGATAAAGACAAGACTCAAAGCATGAGTAATT
48681 CCTGAATCAT
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
115 115 1.00
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.24
Consensus pattern (115 bp):
TGCATTGGGTGACTCCTTATTTCAACATCCCAAACTCCACCCACCACCACTCCAAAGTAGATTAA
TTTTGCTAAAAGCCCACATGATAAAGACAAGACTCAAAGCATGAGTAATT
Found at i:51394 original size:9 final size:9
Alignment explanation
Indices: 51376--51413 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
51366 TTCAAATTTT
51376 AAAA-AAAC
1 AAAACAAAC
51384 AAAACAAAC
1 AAAACAAAC
51393 -AAACAAAAC
1 AAAAC-AAAC
51402 AAAACAAAC
1 AAAACAAAC
51411 AAA
1 AAA
51414 GTCATCAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 8 0.30
9 15 0.56
10 4 0.15
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAACAAAC
Found at i:51402 original size:18 final size:18
Alignment explanation
Indices: 51379--51413 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
51369 AAATTTTAAA
51379 AAAACAAAACAAACAAAC
1 AAAACAAAACAAACAAAC
51397 AAAACAAAACAAACAAA
1 AAAACAAAACAAACAAA
51414 GTCATCAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (18 bp):
AAAACAAAACAAACAAAC
Found at i:52579 original size:60 final size:61
Alignment explanation
Indices: 52495--52626 Score: 144
Period size: 64 Copynumber: 2.1 Consensus size: 61
52485 TGTGGTAGGT
* * *
52495 CACGTCAGTGACCAAACTCGGTT-AAGTCCCACTGTCACGTGGAATTTCCACGT-AGCATGC
1 CACGTCAGTGACCAAACTCAGTTAAAGTCCCACTGCCACGTGGAATTTCAACGTGA-CATGC
* * *
52555 CACGTCAGTGACCTAAC-CTAGTTAACCAAGTCTCACTGCCACGTGGAATTTCAACGTGACTTGC
1 CACGTCAGTGACCAAACTC-AGTT-A--AAGTCCCACTGCCACGTGGAATTTCAACGTGACATGC
52619 CACGTCAG
1 CACGTCAG
52627 CGACTCTTAA
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
59 1 0.02
60 19 0.32
64 39 0.65
65 1 0.02
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.23
Consensus pattern (61 bp):
CACGTCAGTGACCAAACTCAGTTAAAGTCCCACTGCCACGTGGAATTTCAACGTGACATGC
Done.