Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023409.1 Corchorus olitorius cultivar O-4 contig23442, 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: 31436
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:219 original size:21 final size:21
Alignment explanation
Indices: 193--233 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
183 AAGGCACGGA
193 TGGCCGGGCTGG-TGGCGCGGC
1 TGGCCGGGC-GGATGGCGCGGC
*
214 TGGCCGGTCGGATGGCGCGG
1 TGGCCGGGCGGATGGCGCGG
234 ATGAGGTCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.02, C:0.27, G:0.56, T:0.15
Consensus pattern (21 bp):
TGGCCGGGCGGATGGCGCGGC
Found at i:3048 original size:14 final size:15
Alignment explanation
Indices: 3029--3060 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
3019 AGCTTCCTAG
3029 AAAAACTCAAAA-AA
1 AAAAACTCAAAAGAA
3043 AAAAACTCAAAAGAA
1 AAAAACTCAAAAGAA
3058 AAA
1 AAA
3061 TTGTTAGTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.78, C:0.12, G:0.03, T:0.06
Consensus pattern (15 bp):
AAAAACTCAAAAGAA
Found at i:4383 original size:11 final size:11
Alignment explanation
Indices: 4367--4392 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4357 CCTTTGCCTA
4367 AAAACTAGAAG
1 AAAACTAGAAG
4378 AAAACTAGAAG
1 AAAACTAGAAG
4389 AAAA
1 AAAA
4393 GAAATTATCT
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:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:5959 original size:17 final size:15
Alignment explanation
Indices: 5916--5967 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
5906 CAAGAAGGAA
*
5916 AAATGAAAAAAAGA-
1 AAATGAAGAAAAGAT
*
5930 AAAAG-AGAAAAGAT
1 AAATGAAGAAAAGAT
5944 AGAATGAAGAAGAAGAT
1 A-AATGAAGAA-AAGAT
5961 AAATGAA
1 AAATGAA
5968 CAAGTTCAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 7 0.23
14 5 0.16
15 3 0.10
16 10 0.32
17 6 0.19
ACGTcount: A:0.69, C:0.00, G:0.21, T:0.10
Consensus pattern (15 bp):
AAATGAAGAAAAGAT
Found at i:10877 original size:50 final size:50
Alignment explanation
Indices: 10820--10964 Score: 211
Period size: 50 Copynumber: 2.9 Consensus size: 50
10810 TGGTTAAGTT
10820 GAAATAAAAATGAAATCTTTAAGTTAAAAAGATTGAATTTTGATAAATTA
1 GAAATAAAAATGAAATCTTTAAGTTAAAAAGATTGAATTTTGATAAATTA
* * ** *
10870 GGAATAAAAATGAAATCTTTAAGTTGAAAAGATTGAATTTTGATAGTTTT
1 GAAATAAAAATGAAATCTTTAAGTTAAAAAGATTGAATTTTGATAAATTA
* *
10920 GAAATAAAAATGAAATCTTGAACTTAAAAAGATT-AATTTTTGATA
1 GAAATAAAAATGAAATCTTTAAGTTAAAAAGATTGAA-TTTTGATA
10965 TTATTTGATA
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
49 2 0.02
50 83 0.98
ACGTcount: A:0.48, C:0.03, G:0.14, T:0.35
Consensus pattern (50 bp):
GAAATAAAAATGAAATCTTTAAGTTAAAAAGATTGAATTTTGATAAATTA
Found at i:11194 original size:50 final size:50
Alignment explanation
Indices: 11046--11228 Score: 149
Period size: 51 Copynumber: 3.6 Consensus size: 50
11036 AATTTCAAAG
* * * * *
11046 GATTGAATTTTGAATGAAA-TTGGAATAAAGATGTAACCTTTGGTTCAAAGA
1 GATTGAATTTAG-AT-AAATTTGGAATAAAAATGCAACCTATGGTTCAAAAA
* * * *
11097 GATCGAACCTT-GATAAAATTTGGAATAAAAATGCAACCTTTGTTTCAAAAA
1 GATTGAA-TTTAGAT-AAATTTGGAATAAAAATGCAACCTATGGTTCAAAAA
* * *
11148 GATT-AATTTATGGTAAATTTGGAATAAAAATGAGAACC-ATGGTTCAAAAG
1 GATTGAATTTA-GATAAATTTGGAATAAAAATG-CAACCTATGGTTCAAAAA
* *
11198 GTTTGACTTTAGATAAATCTTGGAATAAAAA
1 GATTGAATTTAGATAAAT-TTGGAATAAAAA
11229 GATAACCCTT
Statistics
Matches: 108, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
49 2 0.02
50 43 0.40
51 61 0.56
52 2 0.02
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (50 bp):
GATTGAATTTAGATAAATTTGGAATAAAAATGCAACCTATGGTTCAAAAA
Found at i:11857 original size:49 final size:49
Alignment explanation
Indices: 11740--12010 Score: 291
Period size: 49 Copynumber: 5.6 Consensus size: 49
11730 TTTCCCAAAA
* * * * *
11740 TGCCCTTCCTAGTCGGAAGGTGCTGTTTAAGTATT-TCGTTTT-CTGATT
1 TGCCTTTCCCAGTCGGAAGGTGTTGTTTAAGT-TTGTCTTTTTCCTAATT
* * *
11788 CGCCTTTCTCGGTCGGAAGGTGTTGTTTAAGTTTGTCTTTTTCCTAATT
1 TGCCTTTCCCAGTCGGAAGGTGTTGTTTAAGTTTGTCTTTTTCCTAATT
* * *
11837 TGCCTTTCCCAGTCGGAAGGTGTTGTTTAAGGTTGTCTTTTTCCCAAAT
1 TGCCTTTCCCAGTCGGAAGGTGTTGTTTAAGTTTGTCTTTTTCCTAATT
* **
11886 TGCCCTTT-CCGGTCGGAAGGTGTTTGTTTAAG-TTGTCTTTTTCCCCATT
1 TG-CCTTTCCCAGTCGGAAGGTG-TTGTTTAAGTTTGTCTTTTTCCTAATT
* * **
11935 TGTCC-TTCCCAGTCGGAAGGTGTTGTTTCAGTTTGTCTTATTCCTGTTT
1 TG-CCTTTCCCAGTCGGAAGGTGTTGTTTAAGTTTGTCTTTTTCCTAATT
* *
11984 TACCCTTCCCAGTCGGAAGGTGTTGTT
1 TGCCTTTCCCAGTCGGAAGGTGTTGTT
12011 CTGCCCTTTC
Statistics
Matches: 191, Mismatches: 25, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
47 2 0.01
48 44 0.23
49 131 0.69
50 14 0.07
ACGTcount: A:0.13, C:0.21, G:0.23, T:0.44
Consensus pattern (49 bp):
TGCCTTTCCCAGTCGGAAGGTGTTGTTTAAGTTTGTCTTTTTCCTAATT
Found at i:12070 original size:41 final size:41
Alignment explanation
Indices: 12012--12241 Score: 295
Period size: 41 Copynumber: 5.6 Consensus size: 41
12002 GGTGTTGTTC
* * * *
12012 TGCCCTTTCTAGTCGGAAGGTGTTGTTTACTTTTCCTAGTC
1 TGCCCTTCCCAGTCGGAAGGTGTTGTTTACTTTTCCCAGTT
*
12053 CGCCCTTCCCAGTCGGAAGGTGTTGTTTACTTTT-CCAGTT
1 TGCCCTTCCCAGTCGGAAGGTGTTGTTTACTTTTCCCAGTT
* *
12093 TGCCCTTCCCAGTCGGAAGGTATTGTTTACTTCTCCCAGTT
1 TGCCCTTCCCAGTCGGAAGGTGTTGTTTACTTTTCCCAGTT
* *
12134 TGCCCTTCCCCA-CCGGAAGGTGTTGTTTAGTTTTCCCAGTT
1 TGCCCTT-CCCAGTCGGAAGGTGTTGTTTACTTTTCCCAGTT
* *
12175 TGCCCTTCCCCA-TCGGAAGGTGTTGTTTACTTTTACCAATT
1 TGCCCTT-CCCAGTCGGAAGGTGTTGTTTACTTTTCCCAGTT
* **
12216 TACCCTTTACAGTCGGAAGGTGTTGT
1 TGCCCTTCCCAGTCGGAAGGTGTTGT
12242 CTAATTTCGT
Statistics
Matches: 167, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
40 37 0.22
41 126 0.75
42 4 0.02
ACGTcount: A:0.14, C:0.26, G:0.21, T:0.38
Consensus pattern (41 bp):
TGCCCTTCCCAGTCGGAAGGTGTTGTTTACTTTTCCCAGTT
Found at i:12113 original size:81 final size:82
Alignment explanation
Indices: 12012--12208 Score: 274
Period size: 81 Copynumber: 2.4 Consensus size: 82
12002 GGTGTTGTTC
* * * *
12012 TGCCCTTTCTAGTCGGAAGGTGTTGTTTACTTTTCCTAGTCCGCCCTT-CCCAGTCGGAAGGTGT
1 TGCCCTTCCCAGTCGGAAGGTGTTGTTTACTTTTCCCAGTCCGCCCTTCCCCA-CCGGAAGGTGT
12076 TGTTTACTTTT-CCAGTT
65 TGTTTACTTTTCCCAGTT
* * **
12093 TGCCCTTCCCAGTCGGAAGGTATTGTTTACTTCTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTT
1 TGCCCTTCCCAGTCGGAAGGTGTTGTTTACTTTTCCCAGTCCGCCCTTCCCCACCGGAAGGTGTT
*
12158 GTTTAGTTTTCCCAGTT
66 GTTTACTTTTCCCAGTT
12175 TGCCCTTCCCCA-TCGGAAGGTGTTGTTTACTTTT
1 TGCCCTT-CCCAGTCGGAAGGTGTTGTTTACTTTT
12209 ACCAATTTAC
Statistics
Matches: 102, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
81 61 0.60
82 37 0.36
83 4 0.04
ACGTcount: A:0.13, C:0.27, G:0.21, T:0.39
Consensus pattern (82 bp):
TGCCCTTCCCAGTCGGAAGGTGTTGTTTACTTTTCCCAGTCCGCCCTTCCCCACCGGAAGGTGTT
GTTTACTTTTCCCAGTT
Found at i:15680 original size:18 final size:19
Alignment explanation
Indices: 15652--15688 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
15642 CTTCATCTAT
15652 TTTTCTCTTCTAGTTTTAG
1 TTTTCTCTTCTAGTTTTAG
15671 TTTT-TCTTCTAGTTTTAG
1 TTTTCTCTTCTAGTTTTAG
15689 ACTAGGGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.11, C:0.14, G:0.11, T:0.65
Consensus pattern (19 bp):
TTTTCTCTTCTAGTTTTAG
Found at i:16285 original size:15 final size:15
Alignment explanation
Indices: 16256--16304 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
16246 TGGTATGAAG
*
16256 GAAATGGGAAGGAAA
1 GAAAGGGGAAGGAAA
16271 GAAGAGGGG-AGGAAA
1 GAA-AGGGGAAGGAAA
*
16286 GAAAGGGGAAGGAAG
1 GAAAGGGGAAGGAAA
16301 GAAA
1 GAAA
16305 AGGGTTCCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 5 0.17
15 21 0.70
16 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.47, T:0.02
Consensus pattern (15 bp):
GAAAGGGGAAGGAAA
Found at i:16369 original size:11 final size:11
Alignment explanation
Indices: 16353--16377 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16343 AAAGAATTAA
16353 GAGGGAAGTGG
1 GAGGGAAGTGG
16364 GAGGGAAGTGG
1 GAGGGAAGTGG
16375 GAG
1 GAG
16378 ACCCAATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.64, T:0.08
Consensus pattern (11 bp):
GAGGGAAGTGG
Found at i:20908 original size:17 final size:16
Alignment explanation
Indices: 20873--20925 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
20863 TATGACTTCC
*
20873 TTTCCCTTCCTCCCTA
1 TTTCCCTTCCTTCCTA
*
20889 TTTCCCTTCCCTTGCTA
1 TTTCCCTT-CCTTCCTA
*
20906 TTTCCTTTCCTTCCTA
1 TTTCCCTTCCTTCCTA
20922 TTTC
1 TTTC
20926 TTACCTCTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
16 19 0.59
17 13 0.41
ACGTcount: A:0.06, C:0.42, G:0.02, T:0.51
Consensus pattern (16 bp):
TTTCCCTTCCTTCCTA
Found at i:26654 original size:21 final size:21
Alignment explanation
Indices: 26630--26671 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
26620 AATTTTATTA
*
26630 ATTTCCAAAATCTTCTTTTGG
1 ATTTCCAAAATCTTCCTTTGG
26651 ATTTCCAAAATCTTCCTTTGG
1 ATTTCCAAAATCTTCCTTTGG
26672 GATTATCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.45
Consensus pattern (21 bp):
ATTTCCAAAATCTTCCTTTGG
Done.