Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023643.1 Corchorus olitorius cultivar O-4 contig23676, 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: 27844
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Found at i:201 original size:57 final size:56
Alignment explanation
Indices: 110--223 Score: 192
Period size: 57 Copynumber: 2.0 Consensus size: 56
100 TATACGTTTC
*
110 CTTTCACACAATAAATGTTATAATAAATCTTATCCCTCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCCTATCCC-CCTATCTCTACTTAATTATT
* *
167 CTTTCACACAATTAATGTTATATTAAATCCTATCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
223 C
1 C
224 GACAAAATAA
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
56 21 0.39
57 33 0.61
ACGTcount: A:0.32, C:0.25, G:0.02, T:0.42
Consensus pattern (56 bp):
CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
Found at i:1881 original size:11 final size:11
Alignment explanation
Indices: 1861--1895 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
1851 TTGACAATGC
1861 AACAAAAACAA
1 AACAAAAACAA
*
1872 AACGAAAACAA
1 AACAAAAACAA
1883 AACAAAAACAA
1 AACAAAAACAA
1894 AA
1 AA
1896 AACAGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:1886 original size:16 final size:16
Alignment explanation
Indices: 1865--1924 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
1855 CAATGCAACA
1865 AAAACAAAACGAAAAC
1 AAAACAAAACGAAAAC
1881 AAAACAAAAAC-AAAA-
1 AAAAC-AAAACGAAAAC
1896 AACAGA-AAAACGAAAAC
1 AA-A-ACAAAACGAAAAC
* *
1913 AATACCAAACGA
1 AAAACAAAACGA
1925 CCCCTTAGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
15 8 0.22
16 20 0.56
17 8 0.22
ACGTcount: A:0.73, C:0.18, G:0.07, T:0.02
Consensus pattern (16 bp):
AAAACAAAACGAAAAC
Found at i:4287 original size:61 final size:61
Alignment explanation
Indices: 4182--4303 Score: 190
Period size: 61 Copynumber: 2.0 Consensus size: 61
4172 ATATTTTTGC
* * *
4182 CCTTGACTTCATTTTCTTTAAACTCTCTAACTTTAAATCCTCTAAAACCATCAAACTAAAA
1 CCTTGACTTCATTTTCTTCAAACTCTCTAACTTCAAATCATCTAAAACCATCAAACTAAAA
* * *
4243 CCTTTACTTCATTTTCTTCAAACTTTCTAACTTCAAATCATCTAAAACCTTCAAACTAAAA
1 CCTTGACTTCATTTTCTTCAAACTCTCTAACTTCAAATCATCTAAAACCATCAAACTAAAA
4304 TCTCAAATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.36, C:0.26, G:0.01, T:0.37
Consensus pattern (61 bp):
CCTTGACTTCATTTTCTTCAAACTCTCTAACTTCAAATCATCTAAAACCATCAAACTAAAA
Found at i:4647 original size:4 final size:4
Alignment explanation
Indices: 4640--4676 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
4630 AATTAATTAA
* *
4640 TTAT TTAT TTAT TTAT TGAT TTAT TGAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
4677 ATTATTATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.70
Consensus pattern (4 bp):
TTAT
Found at i:4751 original size:18 final size:19
Alignment explanation
Indices: 4730--4774 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
4720 GTTAATTAGT
*
4730 GTTTATTAGTTA-TAATTA
1 GTTTATTAGATATTAATTA
4748 GTTTATTA-ATATTAATTA
1 GTTTATTAGATATTAATTA
*
4766 GTTTGTTAG
1 GTTTATTAG
4775 GGTTAATTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 21 0.91
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (19 bp):
GTTTATTAGATATTAATTA
Found at i:6034 original size:22 final size:22
Alignment explanation
Indices: 5973--6027 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
5963 TGCAGAACAC
5973 GTCCTGTCCAGATCTTGGCCAA
1 GTCCTGTCCAGATCTTGGCCAA
5995 GTCCTGTCCAGATCTTGGCCAA
1 GTCCTGTCCAGATCTTGGCCAA
6017 GTCCTGTCCAG
1 GTCCTGTCCAG
6028 GACTTGGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.16, C:0.33, G:0.24, T:0.27
Consensus pattern (22 bp):
GTCCTGTCCAGATCTTGGCCAA
Found at i:6159 original size:69 final size:70
Alignment explanation
Indices: 6013--6173 Score: 243
Period size: 69 Copynumber: 2.3 Consensus size: 70
6003 CAGATCTTGG
* * * *
6013 CCAAGTCCTGTCCAGGACTTGGGCTGTTGAGGAATGCAAAAATACAGGACAAGACCTGGGCAGGA
1 CCAAGTCCTGTCCAGGACTTGTGCTGTTGAAGAACGCAAAAATAAAGGACAAGACCTGGGCAGGA
6078 GTTAC
66 GTTAC
* * *
6083 CCAAGTCCTGTCCCGGACTTGTGCTGTTGAAGAGCGC-AAATTAAAGGACAAGACCTGGGCAGGA
1 CCAAGTCCTGTCCAGGACTTGTGCTGTTGAAGAACGCAAAAATAAAGGACAAGACCTGGGCAGGA
6147 GTTAC
66 GTTAC
*
6152 CCAAGTCCTGTCCAGGAGTTGT
1 CCAAGTCCTGTCCAGGACTTGT
6174 TGCGGGAAAT
Statistics
Matches: 82, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
69 50 0.61
70 32 0.39
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.20
Consensus pattern (70 bp):
CCAAGTCCTGTCCAGGACTTGTGCTGTTGAAGAACGCAAAAATAAAGGACAAGACCTGGGCAGGA
GTTAC
Found at i:8473 original size:49 final size:49
Alignment explanation
Indices: 8413--8511 Score: 137
Period size: 49 Copynumber: 2.0 Consensus size: 49
8403 TTTGGCTGAC
* * * *
8413 TGATTTATATTTTCATTTCTTGTATGATTAC-TTTATACATTTTTATTTG
1 TGATTTATATTTTCATTTCTTCTAT-ATAACATTTATACAGTTGTATTTG
*
8462 TGATTTGTATTTTCATTTCTTCTATATAACATTTATACAGTTGTATTTG
1 TGATTTATATTTTCATTTCTTCTATATAACATTTATACAGTTGTATTTG
8511 T
1 T
8512 AAATTGGGGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
48 4 0.09
49 40 0.91
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.59
Consensus pattern (49 bp):
TGATTTATATTTTCATTTCTTCTATATAACATTTATACAGTTGTATTTG
Found at i:12138 original size:32 final size:32
Alignment explanation
Indices: 12096--12164 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
12086 GCGTCCCCAA
*
12096 AGGG-CACCTCCCCATGGGCGAGGCACCCCCT
1 AGGGACACCTCCCCATGGGCGAAGCACCCCCT
* *
12127 AGGGACACCTCCCCATGGTCGAAGCGCCCCCT
1 AGGGACACCTCCCCATGGGCGAAGCACCCCCT
12159 AGGGAC
1 AGGGAC
12165 GCCGCACCTC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 4 0.12
32 30 0.88
ACGTcount: A:0.19, C:0.42, G:0.29, T:0.10
Consensus pattern (32 bp):
AGGGACACCTCCCCATGGGCGAAGCACCCCCT
Found at i:14336 original size:43 final size:41
Alignment explanation
Indices: 14282--14442 Score: 207
Period size: 43 Copynumber: 3.8 Consensus size: 41
14272 ATAAAGAGAA
14282 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGGAATAGAG
1 ATGCC-CTGTGTTATATATGTGTTTGAGGACTTT-GAATAGAG
* * *
14325 ATGACCCTGTGTTATATATGTGATTGGGGACTTTG-ATATAG
1 ATG-CCCTGTGTTATATATGTGTTTGAGGACTTTGAATAGAG
* *
14366 ATGCCTTTGTGTTATATATGTGTTTGAGAACTTTGATATAGAG
1 ATGCC-CTGTGTTATATATGTGTTTGAGGACTTTGA-ATAGAG
*
14409 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
1 ATG-CCCTGTGTTATATATGTGTTTGAGGACTTT
14443 TGGTTATTGG
Statistics
Matches: 102, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
40 2 0.02
41 33 0.32
42 1 0.01
43 62 0.61
44 4 0.04
ACGTcount: A:0.22, C:0.10, G:0.26, T:0.42
Consensus pattern (41 bp):
ATGCCCTGTGTTATATATGTGTTTGAGGACTTTGAATAGAG
Found at i:14377 original size:84 final size:84
Alignment explanation
Indices: 14282--14442 Score: 270
Period size: 84 Copynumber: 1.9 Consensus size: 84
14272 ATAAAGAGAA
*
14282 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGGA-ATAGAGATGACCCTGTGTTATATATGT
1 ATGCCTCTGTGTTATATATGTGTTTGAGAACTTT-GATATAGAGATGACCCTGTGTTATATATGT
14346 GATTGGGGACTTTGATATAG
65 GATTGGGGACTTTGATATAG
* *
14366 ATGCCTTTGTGTTATATATGTGTTTGAGAACTTTGATATAGAGATGCCCCTGTGTTATATATGTG
1 ATGCCTCTGTGTTATATATGTGTTTGAGAACTTTGATATAGAGATGACCCTGTGTTATATATGTG
*
14431 TTTGGGGACTTT
66 ATTGGGGACTTT
14443 TGGTTATTGG
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
83 2 0.03
84 70 0.97
ACGTcount: A:0.22, C:0.10, G:0.26, T:0.42
Consensus pattern (84 bp):
ATGCCTCTGTGTTATATATGTGTTTGAGAACTTTGATATAGAGATGACCCTGTGTTATATATGTG
ATTGGGGACTTTGATATAG
Found at i:26776 original size:13 final size:12
Alignment explanation
Indices: 26744--26777 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
26734 TTTTTCATCA
26744 TTTTTT-GGTAT
1 TTTTTTGGGTAT
26755 TTTTTTGGGTAT
1 TTTTTTGGGTAT
26767 TTTTTGTGGGT
1 TTTTT-TGGGT
26778 TTTCGGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 6 0.29
12 10 0.48
13 5 0.24
ACGTcount: A:0.06, C:0.00, G:0.26, T:0.68
Consensus pattern (12 bp):
TTTTTTGGGTAT
Done.