Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023784.1 Corchorus olitorius cultivar O-4 contig23817, 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: 45935
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:7056 original size:21 final size:21
Alignment explanation
Indices: 6993--7069 Score: 100
Period size: 22 Copynumber: 3.6 Consensus size: 21
6983 TACTTTTATG
*
6993 AAATTTTGATAATTATCCTATT
1 AAATTTTGATAATTA-CCTATA
**
7015 AAATTTTGATAACCACGCTATA
1 AAATTTTGATAATTAC-CTATA
7037 AAATTTTGATAATTACCTATA
1 AAATTTTGATAATTACCTATA
*
7058 AAATTGTGATAA
1 AAATTTTGATAA
7070 ACTCCATATG
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
21 17 0.35
22 31 0.65
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (21 bp):
AAATTTTGATAATTACCTATA
Found at i:7088 original size:43 final size:44
Alignment explanation
Indices: 6989--7091 Score: 129
Period size: 43 Copynumber: 2.4 Consensus size: 44
6979 TGAATACTTT
* * *
6989 TATGAAATTTTGATAATTATCCTATTAAATTTTGATAACCACGC
1 TATGAAATTTTGATAATTATCCTATAAAATTGTGATAAACACGC
* *
7033 TATAAAATTTTGATAATTA-CCTATAAAATTGTGATAAACTC-C
1 TATGAAATTTTGATAATTATCCTATAAAATTGTGATAAACACGC
*
7075 ATATGAAACTTTGATAA
1 -TATGAAATTTTGATAA
7092 CCTTAATATG
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
42 1 0.02
43 32 0.63
44 18 0.35
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.39
Consensus pattern (44 bp):
TATGAAATTTTGATAATTATCCTATAAAATTGTGATAAACACGC
Found at i:7100 original size:22 final size:22
Alignment explanation
Indices: 7075--7139 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
7065 GATAAACTCC
7075 ATATGAAACTTTGATAACCTTA
1 ATATGAAACTTTGATAACCTTA
* * *
7097 ATATGAAACTTTAATAAACTTTC
1 ATATGAAACTTTGAT-AACCTTA
* *
7120 CTATGAAATTTTG-TAACCTT
1 ATATGAAACTTTGATAACCTT
7140 TTTATGATTT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
21 5 0.14
22 15 0.43
23 15 0.43
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (22 bp):
ATATGAAACTTTGATAACCTTA
Found at i:7195 original size:22 final size:21
Alignment explanation
Indices: 7142--7194 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
7132 GTAACCTTTT
7142 TATGATTTTTGATAACCTCCC
1 TATGATTTTTGATAACCTCCC
* * * *
7163 TATGAGATTTTGTTAATCTCTC
1 TATGA-TTTTTGATAACCTCCC
7185 TATGATTTTT
1 TATGATTTTT
7195 TAATATTATA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.23, C:0.15, G:0.11, T:0.51
Consensus pattern (21 bp):
TATGATTTTTGATAACCTCCC
Found at i:15174 original size:30 final size:31
Alignment explanation
Indices: 15138--15212 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
15128 TTTAACTACA
* *
15138 AATTTGAGGCTAAACCTTT-AAAAGTTGTTC
1 AATTTGAGCCTAAACCTTTCAAAAGTTGATC
* *
15168 AATTTGAGTCTAAACCTTTCAAATGTTGATC
1 AATTTGAGCCTAAACCTTTCAAAAGTTGATC
15199 AATTTGAGCCTAAA
1 AATTTGAGCCTAAA
15213 AACAGAAACG
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 18 0.45
31 22 0.55
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (31 bp):
AATTTGAGCCTAAACCTTTCAAAAGTTGATC
Found at i:15335 original size:85 final size:85
Alignment explanation
Indices: 15192--15366 Score: 332
Period size: 85 Copynumber: 2.1 Consensus size: 85
15182 CCTTTCAAAT
* *
15192 GTTGATCAATTTGAGCCTAAAAACAGAAACGGTAACGACGCGTGCGTTTCACAGGCAGAGCATCG
1 GTTGACCAATTTGAGCCTAAAAACAGAAACGGTAACGACGCGTGCGTTTCACAGGCAGAGCACCG
15257 TCTAATTTAGGCCTAAATTG
66 TCTAATTTAGGCCTAAATTG
15277 GTTGACCAATTTGAGCCTAAAAACAGAAACGGTAACGACGCGTGCGTTTCACAGGCAGAGCACCG
1 GTTGACCAATTTGAGCCTAAAAACAGAAACGGTAACGACGCGTGCGTTTCACAGGCAGAGCACCG
15342 TCTAATTTAGGCCTAAATTG
66 TCTAATTTAGGCCTAAATTG
15362 GTTGA
1 GTTGA
15367 TTTCGATAAA
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 88 1.00
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (85 bp):
GTTGACCAATTTGAGCCTAAAAACAGAAACGGTAACGACGCGTGCGTTTCACAGGCAGAGCACCG
TCTAATTTAGGCCTAAATTG
Found at i:18870 original size:21 final size:21
Alignment explanation
Indices: 18844--18884 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
18834 TTGAAGCCCT
18844 ATTGGATAC-AAGTGGTACTAA
1 ATTGGAT-CTAAGTGGTACTAA
18865 ATTGGATCTAAGTGGTACTA
1 ATTGGATCTAAGTGGTACTA
18885 GGGTTTCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32
Consensus pattern (21 bp):
ATTGGATCTAAGTGGTACTAA
Found at i:20163 original size:15 final size:15
Alignment explanation
Indices: 20143--20174 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
20133 CTTGTAAAGG
20143 TCATCGATCTACTCA
1 TCATCGATCTACTCA
20158 TCATCGATCTACTCA
1 TCATCGATCTACTCA
20173 TC
1 TC
20175 TAGAAGTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.34, G:0.06, T:0.34
Consensus pattern (15 bp):
TCATCGATCTACTCA
Found at i:22939 original size:33 final size:33
Alignment explanation
Indices: 22867--22940 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 33
22857 CTATGATCAA
** *
22867 CCAAAACAGATTTGTTTTCATCACAATTAGCAT
1 CCAAAACAGATTTGTTTTCATCACAAACAACAT
22900 CCAAAACAGAATTTG-TTTCATCACAAACAACA-
1 CCAAAACAG-ATTTGTTTTCATCACAAACAACAT
22932 CCTAAAACA
1 CC-AAAACA
22941 CTCTTTGCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 2 0.06
33 29 0.81
34 5 0.14
ACGTcount: A:0.43, C:0.24, G:0.07, T:0.26
Consensus pattern (33 bp):
CCAAAACAGATTTGTTTTCATCACAAACAACAT
Found at i:33101 original size:7 final size:7
Alignment explanation
Indices: 33087--33116 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
33077 GCCCACTAGT
33087 ACTAGAA
1 ACTAGAA
*
33094 AGTAGAA
1 ACTAGAA
33101 ACTAGAA
1 ACTAGAA
33108 ACTAGAA
1 ACTAGAA
33115 AC
1 AC
33117 CACAAAAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.13, G:0.17, T:0.13
Consensus pattern (7 bp):
ACTAGAA
Found at i:34284 original size:6 final size:6
Alignment explanation
Indices: 34275--34348 Score: 66
Period size: 6 Copynumber: 12.8 Consensus size: 6
34265 CCAAATGCCT
* * * * *
34275 GGTGGA GGTGGT GGTGGT GGTGGT GGT-G- GGTGG- GGTGG- GTGGGGT
1 GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA G-GTGGA
34320 GGTGGA GGTGGA GGTGGA GGTGGA GGTGG
1 GGTGGA GGTGGA GGTGGA GGTGGA GGTGG
34349 GGGAGGGGGA
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
4 3 0.05
5 8 0.13
6 49 0.80
7 1 0.02
ACGTcount: A:0.07, C:0.00, G:0.70, T:0.23
Consensus pattern (6 bp):
GGTGGA
Found at i:34288 original size:9 final size:9
Alignment explanation
Indices: 34274--34354 Score: 76
Period size: 9 Copynumber: 9.0 Consensus size: 9
34264 ACCAAATGCC
34274 TGGTGGAGG
1 TGGTGGAGG
*
34283 TGGTGGTGG
1 TGGTGGAGG
*
34292 TGGTGGTGG
1 TGGTGGAGG
34301 TGGGTGG-GG
1 T-GGTGGAGG
34310 TGGGTGG-GG
1 T-GGTGGAGG
34319 TGGTGGAGG
1 TGGTGGAGG
* *
34328 TGGAGGTGG
1 TGGTGGAGG
*
34337 AGGTGGAGG
1 TGGTGGAGG
*
34346 TGGGGGAGG
1 TGGTGGAGG
34355 GGGAGGTATG
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
8 5 0.08
9 52 0.84
10 5 0.08
ACGTcount: A:0.07, C:0.00, G:0.70, T:0.22
Consensus pattern (9 bp):
TGGTGGAGG
Found at i:34291 original size:12 final size:12
Alignment explanation
Indices: 34274--34348 Score: 77
Period size: 12 Copynumber: 6.5 Consensus size: 12
34264 ACCAAATGCC
34274 TGGTGGAGGTGG
1 TGGTGGAGGTGG
*
34286 TGGTGGTGGTGG
1 TGGTGGAGGTGG
34298 TGGT-G-GGTGG
1 TGGTGGAGGTGG
*
34308 -GGTGG-GTGGGG
1 TGGTGGAG-GTGG
34319 TGGTGGAGGTGG
1 TGGTGGAGGTGG
*
34331 AGGTGGAGGTGG
1 TGGTGGAGGTGG
*
34343 AGGTGG
1 TGGTGG
34349 GGGAGGGGGA
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
9 3 0.05
10 7 0.13
11 4 0.07
12 40 0.73
13 1 0.02
ACGTcount: A:0.07, C:0.00, G:0.69, T:0.24
Consensus pattern (12 bp):
TGGTGGAGGTGG
Found at i:36141 original size:127 final size:126
Alignment explanation
Indices: 35893--36145 Score: 488
Period size: 127 Copynumber: 2.0 Consensus size: 126
35883 GTTTTGCCTA
35893 ATAATGGTGTATGAGCATTTCAGCCAGTCTTTTGAAATTCCCAACTAATTTGCCTTGCTTTTTTT
1 ATAATGGTGTATGAGCATTTCAGCCAGTCTTTTGAAATTCCCAACTAATTTGCCTTGCTTTTTTT
35958 GGTACTTGAGGCTGCTAGGGATCGAACCCTAGCCACTGGAACTAAGAGTCCAGCACTCTAC
66 GGTACTTGAGGCTGCTAGGGATCGAACCCTAGCCACTGGAACTAAGAGTCCAGCACTCTAC
*
36019 ATAATGGTGTATGAGCATTTCAGCCAGTCTTTTGAAATTCCCAACTAATTTTCCTTGCTTTTTTT
1 ATAATGGTGTATGAGCATTTCAGCCAGTCTTTTGAAATTCCCAACTAATTTGCCTTGC-TTTTTT
36084 TGGTACTTGAGGCTGCTAGGGATCGAACCCTAGCCACTGGAACTAAGAGTCCAGCACTCTAC
65 TGGTACTTGAGGCTGCTAGGGATCGAACCCTAGCCACTGGAACTAAGAGTCCAGCACTCTAC
36146 CACCTGGCCA
Statistics
Matches: 125, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
126 57 0.46
127 68 0.54
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (126 bp):
ATAATGGTGTATGAGCATTTCAGCCAGTCTTTTGAAATTCCCAACTAATTTGCCTTGCTTTTTTT
GGTACTTGAGGCTGCTAGGGATCGAACCCTAGCCACTGGAACTAAGAGTCCAGCACTCTAC
Found at i:41977 original size:31 final size:31
Alignment explanation
Indices: 41939--42029 Score: 182
Period size: 31 Copynumber: 2.9 Consensus size: 31
41929 GGGACACGCT
41939 ACTGAATTACTATAACCAAAAAGAAATAAGC
1 ACTGAATTACTATAACCAAAAAGAAATAAGC
41970 ACTGAATTACTATAACCAAAAAGAAATAAGC
1 ACTGAATTACTATAACCAAAAAGAAATAAGC
42001 ACTGAATTACTATAACCAAAAAGAAATAA
1 ACTGAATTACTATAACCAAAAAGAAATAA
42030 AGCTAATAAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 60 1.00
ACGTcount: A:0.56, C:0.15, G:0.09, T:0.20
Consensus pattern (31 bp):
ACTGAATTACTATAACCAAAAAGAAATAAGC
Found at i:42582 original size:15 final size:15
Alignment explanation
Indices: 42541--42570 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
42531 AACTTGATAT
42541 AAGTTTATATTTCAC
1 AAGTTTATATTTCAC
42556 AAGTTTATATTTCAC
1 AAGTTTATATTTCAC
42571 GGAGTTATAT
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:0.33, C:0.13, G:0.07, T:0.47
Consensus pattern (15 bp):
AAGTTTATATTTCAC
Done.