Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018514.1 Corchorus olitorius cultivar O-4 contig18547, 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: 39268
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:428 original size:21 final size:21
Alignment explanation
Indices: 404--465 Score: 115
Period size: 21 Copynumber: 3.0 Consensus size: 21
394 GAAAACCAAA
404 GAGAATATGTTGAGACATGAG
1 GAGAATATGTTGAGACATGAG
425 GAGAATATGTTGAGACATGAG
1 GAGAATATGTTGAGACATGAG
*
446 AAGAATATGTTGAGACATGA
1 GAGAATATGTTGAGACATGA
466 AGAAGAGCTC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.40, C:0.05, G:0.31, T:0.24
Consensus pattern (21 bp):
GAGAATATGTTGAGACATGAG
Found at i:2371 original size:290 final size:290
Alignment explanation
Indices: 1846--2431 Score: 1100
Period size: 290 Copynumber: 2.0 Consensus size: 290
1836 TGGTTCAGAC
* *
1846 TCTGGCTCATTAGGCTTGAGAATCTCCTCAGATGTGCTAAATTGATGGATATTTTCGGCCATGAT
1 TCTGACTCATTAGGCTTGAGAATCTCCTCAGATGTGCTAAATTGATGGATATCTTCGGCCATGAT
*
1911 GTTGAGCAGCTTCCTCGCTTCTGTAGGTGTTTTAAGTGTTAGGCTACCTCCACTGGTTGCATCAA
66 ATTGAGCAGCTTCCTCGCTTCTGTAGGTGTTTTAAGTGTTAGGCTACCTCCACTGGTTGCATCAA
1976 TGTAGACTCGATCTTCATAAAACAATCCATCATAGAATTGCCGTATCAAGAGTTCCTCGCTGATG
131 TGTAGACTCGATCTTCATAAAACAATCCATCATAGAATTGCCGTATCAAGAGTTCCTCGCTGATG
*
2041 TTGTGGTAGGGGCAACTTTCACAAATCTTGTTGTACCTTTCCAAATATTGAAACTACTTCTCCTT
196 TTGTGGTAGGGGCAACTTTCACAAATCTTGTTGTACCTTTCCAAATATTGAAACCACTTCTCCTT
*
2106 AGGTAATTGTCGGCAAGAATTGATTTTACT
261 AGGTAATTGTCGACAAGAATTGATTTTACT
*
2136 TCTGACTCATTAGGCTTGAGAATCTCTTCAGATGTGCTAAATTGATGGATATCTTCGGCCATGAT
1 TCTGACTCATTAGGCTTGAGAATCTCCTCAGATGTGCTAAATTGATGGATATCTTCGGCCATGAT
*
2201 ATTGAGCAGCTTCCTTGCTTCTGTAGGTGTTTTAAGTGTTAGGCTACCTCCACTGGTTGCATCAA
66 ATTGAGCAGCTTCCTCGCTTCTGTAGGTGTTTTAAGTGTTAGGCTACCTCCACTGGTTGCATCAA
2266 TGTAGACTCGATCTTCATAAAACAATCCATCATAGAATTGCCGTATCAAGAGTTCCTCGCTGATG
131 TGTAGACTCGATCTTCATAAAACAATCCATCATAGAATTGCCGTATCAAGAGTTCCTCGCTGATG
*
2331 TTGTGGTAGGGGCAACTTTCACAGATCTTGTTGTACCTTTCCAAATATTGAAACCACTTCTCCTT
196 TTGTGGTAGGGGCAACTTTCACAAATCTTGTTGTACCTTTCCAAATATTGAAACCACTTCTCCTT
2396 AGGTAATTGTCGACAAGAATTGATTTTACT
261 AGGTAATTGTCGACAAGAATTGATTTTACT
2426 TCTGAC
1 TCTGAC
2432 ATCAGCACGT
Statistics
Matches: 288, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
290 288 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (290 bp):
TCTGACTCATTAGGCTTGAGAATCTCCTCAGATGTGCTAAATTGATGGATATCTTCGGCCATGAT
ATTGAGCAGCTTCCTCGCTTCTGTAGGTGTTTTAAGTGTTAGGCTACCTCCACTGGTTGCATCAA
TGTAGACTCGATCTTCATAAAACAATCCATCATAGAATTGCCGTATCAAGAGTTCCTCGCTGATG
TTGTGGTAGGGGCAACTTTCACAAATCTTGTTGTACCTTTCCAAATATTGAAACCACTTCTCCTT
AGGTAATTGTCGACAAGAATTGATTTTACT
Found at i:7701 original size:24 final size:25
Alignment explanation
Indices: 7674--7721 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
7664 GTGAACAATA
7674 AAAATAAATG-AACAAGA-AAATAGT
1 AAAATAAA-GCAACAAGATAAATAGT
*
7698 AAAATTAAGCAACAAGATAAATAG
1 AAAATAAAGCAACAAGATAAATAG
7722 ATACTCCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 1 0.05
24 14 0.67
25 6 0.29
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.17
Consensus pattern (25 bp):
AAAATAAAGCAACAAGATAAATAGT
Found at i:14518 original size:22 final size:20
Alignment explanation
Indices: 14492--14535 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
14482 AAATCCAGGT
14492 TTTCCAGCTCAATCCGATCCGA
1 TTTCCAGCTCAA-CC-ATCCGA
* *
14514 TTTCCGGTTCAACCATCCGA
1 TTTCCAGCTCAACCATCCGA
14534 TT
1 TT
14536 AAAACGATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 2 0.10
22 10 0.50
ACGTcount: A:0.20, C:0.34, G:0.14, T:0.32
Consensus pattern (20 bp):
TTTCCAGCTCAACCATCCGA
Found at i:19638 original size:16 final size:16
Alignment explanation
Indices: 19617--19648 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
19607 TCAATTTTCC
19617 TACGACAACCATACAT
1 TACGACAACCATACAT
*
19633 TACGACAACTATACAT
1 TACGACAACCATACAT
19649 GCTCTTTGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.28, G:0.06, T:0.22
Consensus pattern (16 bp):
TACGACAACCATACAT
Found at i:25891 original size:19 final size:18
Alignment explanation
Indices: 25845--25901 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 18
25835 TTCCCACATC
*
25845 ATTTTTAAAATGTAAATA
1 ATTTTTAAAATATAAATA
* **
25863 ATATAAAAAATTATAAATA
1 ATTTTTAAAA-TATAAATA
*
25882 ATTTTTAAAAAAT-AATA
1 ATTTTTAAAATATAAATA
25899 ATT
1 ATT
25902 GTAAACAATT
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
17 7 0.23
18 9 0.30
19 14 0.47
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
ATTTTTAAAATATAAATA
Found at i:26498 original size:10 final size:11
Alignment explanation
Indices: 26470--26499 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
26460 TCAAACAAAT
26470 ATAATTCACAA
1 ATAATTCACAA
26481 ATAATTCACAA
1 ATAATTCACAA
26492 A-AATTCAC
1 ATAATTCAC
26500 CATATGAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.37
11 12 0.63
ACGTcount: A:0.53, C:0.20, G:0.00, T:0.27
Consensus pattern (11 bp):
ATAATTCACAA
Found at i:28002 original size:49 final size:49
Alignment explanation
Indices: 27930--28058 Score: 181
Period size: 49 Copynumber: 2.7 Consensus size: 49
27920 TCAAAGCAAT
* *
27930 CTTTAATTTTCCTTGCACCTTTTTCTCAATTTTAACAACAAAATTGAAC
1 CTTTAATTTTCCTTGCACCTTTTTATCAATTTTAACAACAAAATAGAAC
* *
27979 CTTTATTTTTCCTTGCACCTTTTTATCAATTTTTACAACAAAATAGAAC
1 CTTTAATTTTCCTTGCACCTTTTTATCAATTTTAACAACAAAATAGAAC
* * *
28028 ATTTACTTTTCC-TGCA-CTTTTTATTAATTTT
1 CTTTAATTTTCCTTGCACCTTTTTATCAATTTT
28059 TGTAATGAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
47 14 0.19
48 4 0.05
49 55 0.75
ACGTcount: A:0.28, C:0.20, G:0.04, T:0.48
Consensus pattern (49 bp):
CTTTAATTTTCCTTGCACCTTTTTATCAATTTTAACAACAAAATAGAAC
Found at i:32119 original size:6 final size:6
Alignment explanation
Indices: 32108--32132 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
32098 ATAGTTCAAT
32108 TCCAAA TCCAAA TCCAAA TCCAAA T
1 TCCAAA TCCAAA TCCAAA TCCAAA T
32133 ATTAGTCATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.20
Consensus pattern (6 bp):
TCCAAA
Found at i:38320 original size:2 final size:2
Alignment explanation
Indices: 38313--38351 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
38303 ATACTTGGCA
38313 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
38352 GATACGAGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39227 original size:2 final size:2
Alignment explanation
Indices: 39220--39260 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
39210 AGGGGTTGAA
39220 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39261 CTTACGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.