Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024553.1 Corchorus olitorius cultivar O-4 contig24586, 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: 33918
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:801 original size:19 final size:18
Alignment explanation
Indices: 768--803 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
758 TTGAAATTAT
768 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
786 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
804 TAAATCTTCA
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:7788 original size:76 final size:76
Alignment explanation
Indices: 7660--7802 Score: 173
Period size: 76 Copynumber: 1.9 Consensus size: 76
7650 CCTACTCTAC
* *
7660 CTGGGCGCCCACATGGTTGCCTTAAACACCCATGTGGTTTGCTTGAGAACCCAGGTGGGCAGTGT
1 CTGGGCGCCCACATGGTTGCCTTAAACACCCATGTGGTTTGCCTGAGAACCCAGATGGGCAGTGT
7725 CACGACTCCAG
66 CACGACTCCAG
* * * * ** *
7736 CTGGGTGCCCACATGGTTTGTC-TGAAGACCCATGT-GTTTCGCCTGATCACCCAGATGGGCTGT
1 CTGGGCGCCCACATGG-TTGCCTTAAACACCCATGTGGTTT-GCCTGAGAACCCAGATGGGCAGT
7799 GTCA
64 GTCA
7803 TAGCTCATCA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
75 4 0.07
76 48 0.86
77 4 0.07
ACGTcount: A:0.18, C:0.28, G:0.29, T:0.25
Consensus pattern (76 bp):
CTGGGCGCCCACATGGTTGCCTTAAACACCCATGTGGTTTGCCTGAGAACCCAGATGGGCAGTGT
CACGACTCCAG
Found at i:9954 original size:19 final size:18
Alignment explanation
Indices: 9921--9956 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
9911 TTGAAATTAT
9921 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
9939 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
9957 TAAATCTTCA
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:11615 original size:45 final size:46
Alignment explanation
Indices: 11551--11642 Score: 177
Period size: 45 Copynumber: 2.0 Consensus size: 46
11541 GCGGCCCAGC
11551 GCTCCGGGCATTAGCCTTGACCCAAACAAATAAAAAAAAA-AGAGA
1 GCTCCGGGCATTAGCCTTGACCCAAACAAATAAAAAAAAAGAGAGA
11596 GCTCCGGGCATTAGCCTTGACCCAAACAAATAAAAAAAAAGAGAGA
1 GCTCCGGGCATTAGCCTTGACCCAAACAAATAAAAAAAAAGAGAGA
11642 G
1 G
11643 ATGTATTTGA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 40 0.87
46 6 0.13
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.13
Consensus pattern (46 bp):
GCTCCGGGCATTAGCCTTGACCCAAACAAATAAAAAAAAAGAGAGA
Found at i:11714 original size:18 final size:17
Alignment explanation
Indices: 11671--11708 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
11661 CAATTGAAAT
11671 AAAAGAAAAGGAAAAGAG
1 AAAA-AAAAGGAAAAGAG
11689 AAAAAAAAGGGAAAAG-G
1 AAAAAAAA-GGAAAAGAG
11706 AAA
1 AAA
11709 TTAAAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (17 bp):
AAAAAAAAGGAAAAGAG
Found at i:14202 original size:41 final size:41
Alignment explanation
Indices: 14064--14303 Score: 277
Period size: 41 Copynumber: 5.8 Consensus size: 41
14054 GTTTGATTTG
* * * * *
14064 ATTTGATTCAAGGG--TCGAATGACTTGGTTTTAAATTGACA
1 ATTTAATTCAAGGGTCTCG-ATGACTTGATCTTGAATTGATA
** * * * *
14104 ATCCAATTCAAAGGTCTTGACGACTTGGTCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
* *
14145 ATAATTCGATTCAAGGGTCTCGATGACTTGTTCTTGAATTGATA
1 AT--TT-AATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
**
14189 ATTTAATTCAAGGGTCTCGATGACTCAATCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
**
14230 ATTTAATTCAAGGGTCTCGATGACTCAATCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
14271 ATTTAATTCAAGGGTCTCGATGACTTGATCTTG
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTG
14304 GACAAACGAA
Statistics
Matches: 173, Mismatches: 22, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
40 10 0.06
41 125 0.72
42 4 0.02
44 34 0.20
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (41 bp):
ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
Found at i:15190 original size:158 final size:157
Alignment explanation
Indices: 14760--15316 Score: 904
Period size: 157 Copynumber: 3.5 Consensus size: 157
14750 TTTTTCTACA
* * *
14760 GGGTATATATAAATAAGCTTTATACCAAAAAATCGAAATGGGGATGGTCCATATAAGTTTTTGGG
1 GGGTATATATGAATAAGCTTTATACC-AAAAA-CGAATTGGGGATGGTGCATATAAGTTTTTGGG
* *
14825 GATAATGAGATATATTTTGGGTATGAAGTTATCACGTCGGGGATATTCCAAAAGTTTCCACTTTG
64 GATAATGAGATATATTTTGGGTATGAAGTTATCACGTTGGGGATATTCCAAAAGTATCCACTTTG
*
14890 GGGAAAAAATCATT-TTTAAAGTTGGTTTT
129 GGGAGAAAATC-TTGTTTAAAGTTGGTTTT
*
14919 GGGTATATATGAATAAGCTTTATACCAAAAACGAATTGGGGATGGTGCATATAAATTTTTGGGGA
1 GGGTATATATGAATAAGCTTTATACCAAAAACGAATTGGGGATGGTGCATATAAGTTTTTGGGGA
*
14984 TAATGAGATATATTTTGGGTATGAAGTTATCACATTGGGGATATTCCAAAAGTATCCACTTTGGG
66 TAATGAGATATATTTTGGGTATGAAGTTATCACGTTGGGGATATTCCAAAAGTATCCACTTTGGG
*
15049 GAGAAAATCTTGTTTAAAGTTAGTTTT
131 GAGAAAATCTTGTTTAAAGTTGGTTTT
*
15076 GGGTATATATGAATAAGCTTTATACCAACAAACGGATTGGGGATGGTGCATATAAGTTTTTGGGG
1 GGGTATATATGAATAAGCTTTATACCAA-AAACGAATTGGGGATGGTGCATATAAGTTTTTGGGG
*
15141 ATAATGAGATATATTTTGGGTATGAAGTTATCACGTTGGGGATAATCCAAAAGTATCCA-TTTGG
65 ATAATGAGATATATTTTGGGTATGAAGTTATCACGTTGGGGATATTCCAAAAGTATCCACTTTGG
*
15205 GGAGAAAATCATGTTTAAAGTTGGTTTT
130 GGAGAAAATCTTGTTTAAAGTTGGTTTT
* * *
15233 GGGTATATATGAATAAGCTTTATACCAAAAAC-AGGTTGGGGATGGTGCTTATAAGTCTTTGGGG
1 GGGTATATATGAATAAGCTTTATACCAAAAACGA-ATTGGGGATGGTGCATATAAGTTTTTGGGG
*
15297 ATAATGAGAAATATTTTGGG
65 ATAATGAGATATATTTTGGG
15317 ATTAAAGTAT
Statistics
Matches: 375, Mismatches: 20, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
156 52 0.14
157 202 0.54
158 96 0.26
159 25 0.07
ACGTcount: A:0.33, C:0.08, G:0.25, T:0.34
Consensus pattern (157 bp):
GGGTATATATGAATAAGCTTTATACCAAAAACGAATTGGGGATGGTGCATATAAGTTTTTGGGGA
TAATGAGATATATTTTGGGTATGAAGTTATCACGTTGGGGATATTCCAAAAGTATCCACTTTGGG
GAGAAAATCTTGTTTAAAGTTGGTTTT
Found at i:16162 original size:18 final size:18
Alignment explanation
Indices: 16139--16195 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
16129 GGTTATCATC
*
16139 CTTCCCCTCCATGGGGCT
1 CTTCCCCTCAATGGGGCT
*
16157 CTTCCCCTTAATGGGGCAT
1 CTTCCCCTCAATGGGGC-T
*
16176 C-TCCCCTCTATGGGGTCT
1 CTTCCCCTCAATGGGG-CT
16194 CT
1 CT
16196 GCCTTGGAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
18 29 0.91
19 3 0.09
ACGTcount: A:0.09, C:0.39, G:0.21, T:0.32
Consensus pattern (18 bp):
CTTCCCCTCAATGGGGCT
Found at i:23225 original size:16 final size:15
Alignment explanation
Indices: 23187--23228 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
23177 ACAGAGATTG
*
23187 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
23202 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
23217 ACTAGAAAACAA
1 AC-AGAAAACAA
23229 AACAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:29206 original size:21 final size:21
Alignment explanation
Indices: 29167--29215 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
29157 TCAATGCTTT
*
29167 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCGATTTCAA
* *
29189 AGGAAGCAAGAGCTATTTCCA
1 AGGAAGCAAGAGCGATTTCAA
29210 A-GAAGC
1 AGGAAGC
29216 TACAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.41, C:0.14, G:0.29, T:0.16
Consensus pattern (21 bp):
AGGAAGCAAGAGCGATTTCAA
Found at i:33288 original size:18 final size:17
Alignment explanation
Indices: 33256--33289 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
33246 ATTGCATGCA
*
33256 TTTTTATTTTATTTGTG
1 TTTTAATTTTATTTGTG
33273 TTTTAATTTGTATTTGT
1 TTTTAATTT-TATTTGT
33290 CTTATGTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.74
Consensus pattern (17 bp):
TTTTAATTTTATTTGTG
Done.