Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020288.1 Corchorus olitorius cultivar O-4 contig20321, 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: 20164
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1118 original size:27 final size:27
Alignment explanation
Indices: 1080--1131 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
1070 CGTCCCTTGC
1080 ATCACCTACATTTGCATCATCTACAAA
1 ATCACCTACATTTGCATCATCTACAAA
1107 ATCACCTACATTTGCATCATCTACA
1 ATCACCTACATTTGCATCATCTACA
1132 TTTGCATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.35, C:0.31, G:0.04, T:0.31
Consensus pattern (27 bp):
ATCACCTACATTTGCATCATCTACAAA
Found at i:1141 original size:15 final size:15
Alignment explanation
Indices: 1076--1142 Score: 77
Period size: 15 Copynumber: 4.7 Consensus size: 15
1066 TCTTCGTCCC
*
1076 TTGCATCACCTACAT
1 TTGCATCATCTACAT
1091 TTGCATCATCTACA-
1 TTGCATCATCTACAT
** *
1105 --AAATCACCTACAT
1 TTGCATCATCTACAT
1118 TTGCATCATCTACAT
1 TTGCATCATCTACAT
1133 TTGCATCATC
1 TTGCATCATC
1143 ACCAACTTCA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
12 9 0.21
15 33 0.79
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.34
Consensus pattern (15 bp):
TTGCATCATCTACAT
Found at i:1917 original size:32 final size:33
Alignment explanation
Indices: 1874--1970 Score: 121
Period size: 32 Copynumber: 3.0 Consensus size: 33
1864 CTGGATTGCA
*
1874 AATTAGGGGCGTTTT-CTTCATAAAACGCCACT
1 AATTAGTGGCGTTTTACTTCATAAAACGCCACT
*
1906 AATTAGTGGCGTTTTAC-TCA-ATAAATGCCACT
1 AATTAGTGGCGTTTTACTTCATA-AAACGCCACT
**
1938 AATTAGTGGCGTTTTACTAAAT-AAACGCCACT
1 AATTAGTGGCGTTTTACTTCATAAAACGCCACT
1970 A
1 A
1971 TTTGCAAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
31 1 0.02
32 53 0.95
33 2 0.04
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (33 bp):
AATTAGTGGCGTTTTACTTCATAAAACGCCACT
Found at i:8470 original size:124 final size:129
Alignment explanation
Indices: 8254--8495 Score: 386
Period size: 124 Copynumber: 1.9 Consensus size: 129
8244 TAAAAAATTC
8254 TAATATATATAAGTTTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATA
1 TAATATATATAAG-TTTTTTTAATTAAAATAGTAAAATGGTAAAAAT---ATA-GTATAAGGATA
*
8319 TTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAAGTATATTTAAAATT
61 TTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATATTTAAAATT
8384 TTTT
126 TTTT
8388 TAATATATATAAG-TTTTTTAATTAAAATAGTAAAATGGTAAAAAT-TA-TA-AA-GATATTAGA
1 TAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAGTATAAGGATATTAGA
*
8448 TTTAATTAAATAAAAATTGAGTTTTTAGTTGAGTAAAACTATAAAAGT
66 TTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGT
8496 TTAAATAATG
Statistics
Matches: 106, Mismatches: 2, Indels: 10
0.90 0.02 0.08
Matches are distributed among these distances:
124 55 0.52
125 2 0.02
126 2 0.02
128 2 0.02
132 32 0.30
134 13 0.12
ACGTcount: A:0.48, C:0.01, G:0.12, T:0.40
Consensus pattern (129 bp):
TAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAGTATAAGGATATTAGA
TTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATATTTAAAATTTTTT
Found at i:10355 original size:35 final size:35
Alignment explanation
Indices: 10311--10400 Score: 153
Period size: 35 Copynumber: 2.6 Consensus size: 35
10301 AGAACGGAAG
10311 AAAAAGGGAATTAACCCAATTTATATATGAAAGGA
1 AAAAAGGGAATTAACCCAATTTATATATGAAAGGA
* *
10346 AAAAAGGGAATAAACCCAGTTTATATATGAAAGGA
1 AAAAAGGGAATTAACCCAATTTATATATGAAAGGA
*
10381 AAAAAGGGAATTGACCCAAT
1 AAAAAGGGAATTAACCCAAT
10401 CCGCTTTTCT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 50 1.00
ACGTcount: A:0.51, C:0.10, G:0.19, T:0.20
Consensus pattern (35 bp):
AAAAAGGGAATTAACCCAATTTATATATGAAAGGA
Found at i:14075 original size:24 final size:26
Alignment explanation
Indices: 14017--14080 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 26
14007 CCTCTCCATC
*
14017 ATGGTGTGAATAATGCAAATCAAGTGA
1 ATGGTGTGAATAATGCAAATCAAG-CA
*
14044 ATGGTGTGAATAATGC-CATCAA-CA
1 ATGGTGTGAATAATGCAAATCAAGCA
*
14068 ATGGTGTGGATAA
1 ATGGTGTGAATAA
14081 CCAAAATCCT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 13 0.38
26 5 0.15
27 16 0.47
ACGTcount: A:0.38, C:0.09, G:0.27, T:0.27
Consensus pattern (26 bp):
ATGGTGTGAATAATGCAAATCAAGCA
Found at i:14279 original size:15 final size:15
Alignment explanation
Indices: 14259--14295 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
14249 TGCTAGGGTG
14259 AATGGTGCAAACAAC
1 AATGGTGCAAACAAC
* *
14274 AATGGTGCGAATAAC
1 AATGGTGCAAACAAC
14289 AATGGTG
1 AATGGTG
14296 TGAACAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.41, C:0.14, G:0.27, T:0.19
Consensus pattern (15 bp):
AATGGTGCAAACAAC
Found at i:15905 original size:15 final size:15
Alignment explanation
Indices: 15885--15921 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
15875 TTATTGTTCA
15885 CACCATTGTTATTCG
1 CACCATTGTTATTCG
* *
15900 CACCATTGTTGTTTG
1 CACCATTGTTATTCG
15915 CACCATT
1 CACCATT
15922 CACCCTAGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.19, C:0.27, G:0.14, T:0.41
Consensus pattern (15 bp):
CACCATTGTTATTCG
Found at i:16132 original size:24 final size:26
Alignment explanation
Indices: 16100--16163 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 26
16090 AGGATTTTGG
* *
16100 TTATCCACACCATT-GTTGA-TGGCA
1 TTATTCACACCATTACTTGATTGGCA
*
16124 TTATTCACACCATTCACTTGATTTGCA
1 TTATTCACACCATT-ACTTGATTGGCA
16151 TTATTCACACCAT
1 TTATTCACACCAT
16164 GATGGAGAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 13 0.38
26 4 0.12
27 17 0.50
ACGTcount: A:0.27, C:0.27, G:0.09, T:0.38
Consensus pattern (26 bp):
TTATTCACACCATTACTTGATTGGCA
Found at i:19176 original size:6 final size:6
Alignment explanation
Indices: 19165--19197 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
19155 TATATCATCA
19165 TATATC TATATC TATATC TATA-C TATA-C TATAT
1 TATATC TATATC TATATC TATATC TATATC TATAT
19198 ATAAAAGTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.38
6 16 0.62
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (6 bp):
TATATC
Done.