Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014344.1 Corchorus olitorius cultivar O-4 contig14377, 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: 44781
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Found at i:2253 original size:27 final size:27
Alignment explanation
Indices: 2215--2280 Score: 116
Period size: 27 Copynumber: 2.4 Consensus size: 27
2205 AGTGTATTTG
2215 AAATGACCAAAATGCCCCTGGAC-GTGC
1 AAATGACCAAAATGCCCCTGGACAG-GC
2242 AAATGACCAAAATGCCCCTGGACAGGC
1 AAATGACCAAAATGCCCCTGGACAGGC
2269 AAATGACCAAAA
1 AAATGACCAAAA
2281 GAAGTAAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
27 37 0.97
28 1 0.03
ACGTcount: A:0.41, C:0.27, G:0.20, T:0.12
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGGACAGGC
Found at i:2640 original size:50 final size:50
Alignment explanation
Indices: 2579--2723 Score: 281
Period size: 50 Copynumber: 2.9 Consensus size: 50
2569 TCCAATATAA
2579 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTCCCAATTCAATCTT
1 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTCCCAATTCAATCTT
2629 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTCCCAATTCAATCTT
1 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTCCCAATTCAATCTT
*
2679 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCA
1 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTCCCAATTCA
2724 CTCCTAGATA
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 94 1.00
ACGTcount: A:0.24, C:0.30, G:0.12, T:0.34
Consensus pattern (50 bp):
AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTCCCAATTCAATCTT
Found at i:12606 original size:11 final size:11
Alignment explanation
Indices: 12590--12637 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
12580 GAAGTTCGTG
12590 TTTGAAGACTA
1 TTTGAAGACTA
12601 TTTGAAGA-TAA
1 TTTGAAGACT-A
12612 TTTGAAGAC--
1 TTTGAAGACTA
12621 -TTGAAGACTA
1 TTTGAAGACTA
12631 -TTGAAGA
1 TTTGAAGA
12638 ATTATCTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
8 8 0.24
10 8 0.24
11 17 0.52
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33
Consensus pattern (11 bp):
TTTGAAGACTA
Found at i:13237 original size:11 final size:11
Alignment explanation
Indices: 13221--13246 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
13211 CATAGATATT
13221 TTTTCTTCTAG
1 TTTTCTTCTAG
13232 TTTTCTTCTAG
1 TTTTCTTCTAG
13243 TTTT
1 TTTT
13247 TTAAGCAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:14044 original size:15 final size:15
Alignment explanation
Indices: 14013--14054 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
14003 TTACTTTGCT
*
14013 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-TTTTAA
14029 TTGTTTTCTTTTTAA
1 TTGTTTTCTTTTTAA
14044 TTGTTCTTCTT
1 TTGTT-TTCTT
14055 AACCCTCTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.12, C:0.10, G:0.10, T:0.69
Consensus pattern (15 bp):
TTGTTTTCTTTTTAA
Found at i:15785 original size:20 final size:20
Alignment explanation
Indices: 15757--15800 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
15747 GTATGAAAAC
15757 CTTGCCCACAGACTCTTCAA
1 CTTGCCCACAGACTCTTCAA
*
15777 CTTGGCCACAGACTCTTCAA
1 CTTGCCCACAGACTCTTCAA
15797 CTTG
1 CTTG
15801 TCCAAAATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.36, G:0.14, T:0.27
Consensus pattern (20 bp):
CTTGCCCACAGACTCTTCAA
Found at i:18586 original size:27 final size:27
Alignment explanation
Indices: 18546--18611 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
18536 AGTGTATTTG
18546 AAATGACCAAAATGCCCCTGGACATGC
1 AAATGACCAAAATGCCCCTGGACATGC
* *
18573 AAATGACCATAATGCCCTTGGACATGC
1 AAATGACCAAAATGCCCCTGGACATGC
18600 AAATGACCAAAA
1 AAATGACCAAAA
18612 GAAGTAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.41, C:0.26, G:0.17, T:0.17
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGGACATGC
Found at i:19369 original size:2 final size:2
Alignment explanation
Indices: 19362--19390 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19352 TCCTAACTTT
19362 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19391 GTAGCAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27145 original size:22 final size:22
Alignment explanation
Indices: 27120--27172 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
27110 AAATCAAACT
**
27120 AACAATTAAGACTATCT-AAGAA
1 AACAATTAAGAAAAT-TAAAGAA
* *
27142 AACAGTCAAGAAAATTAAAGAA
1 AACAATTAAGAAAATTAAAGAA
27164 AACAATTAA
1 AACAATTAA
27173 TCAGAAAGCA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.60, C:0.11, G:0.09, T:0.19
Consensus pattern (22 bp):
AACAATTAAGAAAATTAAAGAA
Found at i:28430 original size:19 final size:18
Alignment explanation
Indices: 28397--28432 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
28387 TTGAAATTAT
28397 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
28415 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
28433 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:34844 original size:12 final size:12
Alignment explanation
Indices: 34827--34851 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34817 TAAATGAATA
34827 AGATCATGTCAT
1 AGATCATGTCAT
34839 AGATCATGTCAT
1 AGATCATGTCAT
34851 A
1 A
34852 TATCCATGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (12 bp):
AGATCATGTCAT
Found at i:36859 original size:11 final size:12
Alignment explanation
Indices: 36843--36874 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
36833 GAAGTTCGTG
36843 TTTGAAGACT-A
1 TTTGAAGACTAA
36854 TTTGAAGA-TAA
1 TTTGAAGACTAA
36865 TTTGAAGACT
1 TTTGAAGACT
36875 TGAAGATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.05
11 17 0.89
12 1 0.05
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (12 bp):
TTTGAAGACTAA
Found at i:36879 original size:19 final size:18
Alignment explanation
Indices: 36855--36890 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
36845 TGAAGACTAT
36855 TTGAAGATAATTTGAAGAC
1 TTGAAGAT-ATTTGAAGAC
*
36874 TTGAAGATTTTTGAAGA
1 TTGAAGATATTTGAAGA
36891 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATATTTGAAGAC
Found at i:39891 original size:11 final size:11
Alignment explanation
Indices: 39875--39903 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
39865 CTTTAAGGAG
39875 TGGAAAAGAGT
1 TGGAAAAGAGT
39886 TGGAAAAGAGT
1 TGGAAAAGAGT
39897 TGGAAAA
1 TGGAAAA
39904 CCCCTATCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.34, T:0.17
Consensus pattern (11 bp):
TGGAAAAGAGT
Found at i:41296 original size:21 final size:21
Alignment explanation
Indices: 41272--41316 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
41262 CCGAGCCGCG
*
41272 CCGAGACACATGCCCGGCCAT
1 CCGAGACACATGCCCGGACAT
*
41293 CCGAGCCACATGCCCGGACAT
1 CCGAGACACATGCCCGGACAT
41314 CCG
1 CCG
41317 CGCTATCCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.22, C:0.44, G:0.24, T:0.09
Consensus pattern (21 bp):
CCGAGACACATGCCCGGACAT
Found at i:43491 original size:11 final size:11
Alignment explanation
Indices: 43475--43508 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
43465 TCGAAGTTCG
43475 TATTTGAAGAC
1 TATTTGAAGAC
43486 TATTTGAAGA-
1 TATTTGAAGAC
43496 TAATTTGAAGAC
1 T-ATTTGAAGAC
43508 T
1 T
43509 TGAAGATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 19 0.90
12 1 0.05
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (11 bp):
TATTTGAAGAC
Done.