Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016896.1 Corchorus olitorius cultivar O-4 contig16929, 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: 43274
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1120 original size:85 final size:86
Alignment explanation
Indices: 993--1168 Score: 284
Period size: 85 Copynumber: 2.1 Consensus size: 86
983 TTATTTAAAC
*
993 TTTTATAGTTTTACTCAACTAAAAACTCTATGTTTATTTAATTAAATCTAATATCTTTATAACTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATGTTTATTTAATTAAATCTAATATCCTTATAACTA
* *
1058 CTTTATTTTACCGTTTTACTA
66 CTTTAGTTTACCATTTTACTA
*
1079 TTTTACTA-TTTTACTCAACT-AAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACT
1 TTTTA-TAGTTTTACTCAACTAAAAACTCTATGTTTATTTAATTAAATCTAATATCCTTATAACT
*
1142 ATTTTAGTTTACCATTTTACTA
65 ACTTTAGTTTACCATTTTACTA
1164 TTTTA
1 TTTTA
1169 ATTATAAAAG
Statistics
Matches: 84, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
85 65 0.77
86 17 0.20
87 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.02, T:0.51
Consensus pattern (86 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATGTTTATTTAATTAAATCTAATATCCTTATAACTA
CTTTAGTTTACCATTTTACTA
Found at i:1315 original size:14 final size:14
Alignment explanation
Indices: 1291--1324 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1281 AATATTTTAA
*
1291 TAAATATTTTATTTT
1 TAAA-ATTTTAATTT
1306 TAAAATTTTAATTT
1 TAAAATTTTAATTT
1320 TAAAA
1 TAAAA
1325 AATTTGAGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TAAAATTTTAATTT
Found at i:1325 original size:15 final size:16
Alignment explanation
Indices: 1284--1329 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
1274 TAAATTCAAT
*
1284 ATTTTAATAAATATTTT
1 ATTTTAA-AAATATTTA
*
1301 ATTTTTAAAAT-TTTA
1 ATTTTAAAAATATTTA
1316 ATTTTAAAAA-ATTT
1 ATTTTAAAAATATTT
1330 GAGACTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 15 0.60
16 4 0.16
17 6 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTTAAAAATATTTA
Found at i:5111 original size:11 final size:11
Alignment explanation
Indices: 5095--5121 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
5085 TTTGCGAGTC
5095 TAAATATTTGA
1 TAAATATTTGA
5106 TAAATATTTGA
1 TAAATATTTGA
5117 TAAAT
1 TAAAT
5122 GATTATGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (11 bp):
TAAATATTTGA
Found at i:10063 original size:2 final size:2
Alignment explanation
Indices: 10056--10081 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10046 ATTGCTTTTG
10056 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
10082 TATTTACTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22028 original size:15 final size:15
Alignment explanation
Indices: 22008--22038 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
21998 GAAATTATCT
22008 AATGGTTGTAATGAG
1 AATGGTTGTAATGAG
22023 AATGGTTGTAATGAG
1 AATGGTTGTAATGAG
22038 A
1 A
22039 TTTGAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (15 bp):
AATGGTTGTAATGAG
Found at i:26118 original size:22 final size:25
Alignment explanation
Indices: 26092--26149 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 25
26082 ATTTAAGTAG
*
26092 GGATCAAACCATTTTT-TT-T-AAA
1 GGATCCAACCATTTTTGTTATGAAA
26114 GGATCCAACCATTTTTGTTATGAAA
1 GGATCCAACCATTTTTGTTATGAAA
26139 GGATCCAACCA
1 GGATCCAACCA
26150 AATTTGGTCC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
22 15 0.47
23 2 0.06
24 1 0.03
25 14 0.44
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (25 bp):
GGATCCAACCATTTTTGTTATGAAA
Found at i:26816 original size:178 final size:179
Alignment explanation
Indices: 26456--26905 Score: 505
Period size: 178 Copynumber: 2.5 Consensus size: 179
26446 TTTCAGAAAC
* * * * * *
26456 TTTTTGATACTTGAAACATCAAATTTAGCTTTGGAATCCTTCATGAAAGTTGTAGATTATGCAAC
1 TTTTTTATACTTGAAACATTAAATTTAGCTTTCGAGTCCTTCATGAAAGTTGTAGATAATGGAAC
* * * *
26521 AACCTTTTAATAGACATTTGAATCA-CTTCAATCGGACATCTGGAGCAAAAATTATGCAATATTT
66 AACCTTTTAATAGACACTTGAATCACCTTCAATCAGACATCTGGAACAAAAATTAAGCAATATTT
* * *
26585 GAGTACACCGTCCATTCCCGCAAACCGAAACAACTATTTTCTTGAATCA
131 AAGTACACCGTCCATTCCCGCAAACCGAAACAACTATTTTCTGGAAGCA
* * *
26634 TTTTTTTATATTTGGAACATTAAA-TTAGCTTTCGAGTCCTTAATGAAAGTTGTAGATAATGGAA
1 -TTTTTTATACTTGAAACATTAAATTTAGCTTTCGAGTCCTTCATGAAAGTTGTAGATAATGGAA
* * * * * ***
26698 CAATCTTTTAAGAGACACTTGAATCACCTT-AATTAGACATGTGGAACAAAAGTTAAGTGTTA-T
65 CAACCTTTTAATAGACACTTGAATCACCTTCAATCAGACATCTGGAACAAAAATTAAGCAATATT
** * **
26761 TAAGTGGAGCGTCCATTCCCGTTAACCGAAACAACTAATTTT-TCGGAAGCA
130 TAAGTACACCGTCCATTCCCGCAAACCGAAACAACT-ATTTTCT-GGAAGCA
* * * * * *
26812 TTTTTTATACTTGAAACATTAAATTTAGTTTTCGAGTTCTTCATTAAAGTTGTAGATCATGGGAT
1 TTTTTTATACTTGAAACATTAAATTTAGCTTTCGAGTCCTTCATGAAAGTTGTAGATAATGGAAC
* *
26877 AACCTTTAAATAGACACTCGAATCACCTT
66 AACCTTTTAATAGACACTTGAATCACCTT
26906 GATCGGATAT
Statistics
Matches: 225, Mismatches: 42, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
177 53 0.24
178 150 0.67
179 22 0.10
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (179 bp):
TTTTTTATACTTGAAACATTAAATTTAGCTTTCGAGTCCTTCATGAAAGTTGTAGATAATGGAAC
AACCTTTTAATAGACACTTGAATCACCTTCAATCAGACATCTGGAACAAAAATTAAGCAATATTT
AAGTACACCGTCCATTCCCGCAAACCGAAACAACTATTTTCTGGAAGCA
Found at i:27064 original size:23 final size:24
Alignment explanation
Indices: 27029--27073 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
27019 TCAAAGGTTT
*
27029 GTGAGAATAACAAAAATACCAAAA
1 GTGAGAATAACAAAAAAACCAAAA
*
27053 GTGA-AATGACAAAAAAACCAA
1 GTGAGAATAACAAAAAAACCAA
27074 GGTGAATAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.62, C:0.13, G:0.13, T:0.11
Consensus pattern (24 bp):
GTGAGAATAACAAAAAAACCAAAA
Found at i:27078 original size:22 final size:23
Alignment explanation
Indices: 27029--27090 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 23
27019 TCAAAGGTTT
*
27029 GTGAGAATAACAAAAATACCAAAA
1 GTGA-AATAACAAAAAAACCAAAA
* *
27053 GTGAAATGACAAAAAAACC-AAG
1 GTGAAATAACAAAAAAACCAAAA
27075 GTGAATAGTAACAAAA
1 GTGAA-A-TAACAAAA
27091 TCAACATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 7 0.22
23 14 0.44
24 11 0.34
ACGTcount: A:0.60, C:0.11, G:0.16, T:0.13
Consensus pattern (23 bp):
GTGAAATAACAAAAAAACCAAAA
Found at i:36607 original size:15 final size:16
Alignment explanation
Indices: 36587--36620 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
36577 TTAAGCAATT
36587 CAAATT-AACAGAAAG
1 CAAATTAAACAGAAAG
*
36602 CAAATTAAATAGAAAG
1 CAAATTAAACAGAAAG
36618 CAA
1 CAA
36621 TTGATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.62, C:0.12, G:0.12, T:0.15
Consensus pattern (16 bp):
CAAATTAAACAGAAAG
Found at i:41616 original size:22 final size:22
Alignment explanation
Indices: 41588--41630 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
41578 GCGCAAAAAA
41588 CAAAGCTAC-GTGCTTATTCTCT
1 CAAAGCT-CTGTGCTTATTCTCT
*
41610 CAAAGCTCTGTGCTTTTTCTC
1 CAAAGCTCTGTGCTTATTCTC
41631 AGGAATCTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.19, C:0.28, G:0.14, T:0.40
Consensus pattern (22 bp):
CAAAGCTCTGTGCTTATTCTCT
Found at i:41786 original size:51 final size:51
Alignment explanation
Indices: 41686--41789 Score: 122
Period size: 51 Copynumber: 2.0 Consensus size: 51
41676 TTCTTTAATA
** * **
41686 TTTCCTTGTTTCAATCTTGTCTCCGGACAAAAGAACACTCTTTTAGTGTTT
1 TTTCCTTGTTTCAATCCCGTCTCCGGACAAAAGAACACTCGTACAGTGTTT
*
41737 TTTCCTTGTTTCAATCCCGTCTCCGGACATACA-AACACT-GTACACGTGTTT
1 TTTCCTTGTTTCAATCCCGTCTCCGGACA-AAAGAACACTCGTACA-GTGTTT
41788 TT
1 TT
41790 CTCTCATAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
50 2 0.04
51 41 0.91
52 2 0.04
ACGTcount: A:0.21, C:0.25, G:0.13, T:0.40
Consensus pattern (51 bp):
TTTCCTTGTTTCAATCCCGTCTCCGGACAAAAGAACACTCGTACAGTGTTT
Found at i:42847 original size:29 final size:30
Alignment explanation
Indices: 42787--42847 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
42777 GAAGTTCGTG
**
42787 TTTGAAGACTCATTGAAGACTTATTTGGAGA
1 TTTGAAGACT-ATTGAAGACTTATTTCAAGA
*
42818 TTTGAAGACT-TTGAAGATTTATTTCAAGA
1 TTTGAAGACTATTGAAGACTTATTTCAAGA
42847 T
1 T
42848 GAAGAATTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 17 0.63
31 10 0.37
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (30 bp):
TTTGAAGACTATTGAAGACTTATTTCAAGA
Done.