Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005227.1 Corchorus capsularis cultivar CVL-1 contig05245, 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: 2737
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.39
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1273 original size:15 final size:16
Alignment explanation
Indices: 1236--1376 Score: 99
Period size: 16 Copynumber: 8.5 Consensus size: 16
1226 CAGTCAGTTT
*
1236 TTTCAGGTCATTCGGG
1 TTTCGGGTCATTCGGG
*
1252 TTTCGGGTCATTTGGG
1 TTTCGGGTCATTCGGG
* *
1268 -TTCGGGTTAATCGGG
1 TTTCGGGTCATTCGGG
1283 TTTCGGGTCTCGGGTTATTCGGG
1 TTTCGGG--TC-----ATTCGGG
* *
1306 TCTCGGGTTATTCGGG
1 TTTCGGGTCATTCGGG
* * *
1322 TCTCGGGTTAATCGGG
1 TTTCGGGTCATTCGGG
1338 TTTCGGGTCATTC-GG
1 TTTCGGGTCATTCGGG
*
1353 TTCTCGGGTTATTCGGG
1 TT-TCGGGTCATTCGGG
1370 -TTCGGGT
1 TTTCGGGT
1377 TTAGACTTCG
Statistics
Matches: 101, Mismatches: 14, Indels: 21
0.74 0.10 0.15
Matches are distributed among these distances:
15 22 0.22
16 63 0.62
17 2 0.02
18 1 0.01
21 1 0.01
23 12 0.12
ACGTcount: A:0.08, C:0.17, G:0.37, T:0.38
Consensus pattern (16 bp):
TTTCGGGTCATTCGGG
Found at i:1320 original size:32 final size:31
Alignment explanation
Indices: 1284--1377 Score: 143
Period size: 32 Copynumber: 3.0 Consensus size: 31
1274 TTAATCGGGT
1284 TTCGGGTCTCGGGTTATTCGGGTCTCGGGTTA
1 TTCGGGTCTCGGGTTATTCGGGT-TCGGGTTA
* *
1316 TTCGGGTCTCGGGTTAATCGGGTTTCGGGTCA
1 TTCGGGTCTCGGGTTATTCGGG-TTCGGGTTA
*
1348 TTCGGTTCTCGGGTTATTCGGGTTCGGGTT
1 TTCGGGTCTCGGGTTATTCGGGTTCGGGTT
1378 TAGACTTCGG
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
31 7 0.12
32 48 0.86
33 1 0.02
ACGTcount: A:0.06, C:0.18, G:0.37, T:0.38
Consensus pattern (31 bp):
TTCGGGTCTCGGGTTATTCGGGTTCGGGTTA
Found at i:1337 original size:48 final size:45
Alignment explanation
Indices: 1278--1405 Score: 159
Period size: 48 Copynumber: 2.8 Consensus size: 45
1268 TTCGGGTTAA
*
1278 TCGGGTTTCGGGTCTCGGGTTATTCGGGTCTCGGGTTATTCGGGT
1 TCGGGTTTCGGGTCTCGGGTCATTCGGGTCTCGGGTTATTCGGGT
* *
1323 CTCGGGTTAATCGGGTTTCGGGTCATTCGGTTCTCGGGTTATTCGGGT
1 -TCGGGTT--TCGGGTCTCGGGTCATTCGGGTCTCGGGTTATTCGGGT
* ** *
1371 TCGGGTTTAGACT-TCGGGTCATTCGGATCTCGGGT
1 TCGGGTTTCGGGTCTCGGGTCATTCGGGTCTCGGGT
1406 CAAATGGGTC
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
44 21 0.29
45 3 0.04
46 7 0.10
47 7 0.10
48 35 0.48
ACGTcount: A:0.08, C:0.19, G:0.37, T:0.37
Consensus pattern (45 bp):
TCGGGTTTCGGGTCTCGGGTCATTCGGGTCTCGGGTTATTCGGGT
Found at i:1796 original size:13 final size:13
Alignment explanation
Indices: 1764--1800 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1754 AGAAAACAAG
1764 TTTATTCTATTTTC
1 TTTATTCTA-TTTC
*
1778 TATATTCTATTTC
1 TTTATTCTATTTC
1791 TTTATTCTAT
1 TTTATTCTAT
1801 AATTTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTATTCTATTTC
Found at i:1904 original size:19 final size:21
Alignment explanation
Indices: 1880--1918 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1870 TATCTAAATA
1880 ATAAAT-GAT-AACTTATAAT
1 ATAAATAGATAAACTTATAAT
*
1899 ATAAATAGGTAAACTTATAA
1 ATAAATAGATAAACTTATAA
1919 ATTCTCGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 2 0.12
21 9 0.53
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.33
Consensus pattern (21 bp):
ATAAATAGATAAACTTATAAT
Found at i:1980 original size:16 final size:16
Alignment explanation
Indices: 1961--2014 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
1951 CATTCAGGTC
*
1961 TCGGGTCTCACGAGTT
1 TCGGGTCTCACGGGTT
*
1977 TCGGGTTTCACGGGTT
1 TCGGGTCTCACGGGTT
1993 TCGGGTCAT-ACGGGTT
1 TCGGGTC-TCACGGGTT
2009 TCGGGT
1 TCGGGT
2015 TATACGGGTC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
16 33 0.97
17 1 0.03
ACGTcount: A:0.09, C:0.20, G:0.37, T:0.33
Consensus pattern (16 bp):
TCGGGTCTCACGGGTT
Found at i:1982 original size:32 final size:31
Alignment explanation
Indices: 1945--2030 Score: 77
Period size: 32 Copynumber: 2.7 Consensus size: 31
1935 GGTCAACTTA
1945 TCGGGTCATTCAGGTCTCGGGTC-TCACGAGTT
1 TCGGGT-ATTCAGGTCTCGGGTCAT-ACGAGTT
* *
1977 TCGGGT-TTCACGGGTTTCGGGTCATACGGGTT
1 TCGGGTATTCA--GGTCTCGGGTCATACGAGTT
* *
2009 TCGGGTTATACGGGTCTCGGGT
1 TCGGG-TATTCAGGTCTCGGGT
2031 TATTTGGGTC
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
30 4 0.09
32 36 0.82
33 2 0.05
34 2 0.05
ACGTcount: A:0.10, C:0.21, G:0.36, T:0.33
Consensus pattern (31 bp):
TCGGGTATTCAGGTCTCGGGTCATACGAGTT
Found at i:2019 original size:16 final size:16
Alignment explanation
Indices: 1974--2033 Score: 86
Period size: 16 Copynumber: 3.8 Consensus size: 16
1964 GGTCTCACGA
1974 GTTTCGGGTT-TCACGG
1 GTTTCGGGTTAT-ACGG
*
1990 GTTTCGGGTCATACGG
1 GTTTCGGGTTATACGG
2006 GTTTCGGGTTATACGG
1 GTTTCGGGTTATACGG
*
2022 GTCTCGGGTTAT
1 GTTTCGGGTTAT
2034 TTGGGTCACG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
16 39 0.98
17 1 0.03
ACGTcount: A:0.10, C:0.17, G:0.37, T:0.37
Consensus pattern (16 bp):
GTTTCGGGTTATACGG
Found at i:2039 original size:16 final size:16
Alignment explanation
Indices: 2003--2078 Score: 73
Period size: 16 Copynumber: 4.8 Consensus size: 16
1993 TCGGGTCATA
*
2003 CGGGTTTCGGGTTA-T
1 CGGGTCTCGGGTTAGT
*
2018 ACGGGTCTCGGGTTATT
1 -CGGGTCTCGGGTTAGT
* * *
2035 TGGGTCACGGGTCAGT
1 CGGGTCTCGGGTTAGT
*
2051 CGGGTCACGGGTTAGT
1 CGGGTCTCGGGTTAGT
*
2067 CGGGTTTCGGGT
1 CGGGTCTCGGGT
2079 CGGGCGTGTT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
16 49 0.98
17 1 0.02
ACGTcount: A:0.09, C:0.17, G:0.42, T:0.32
Consensus pattern (16 bp):
CGGGTCTCGGGTTAGT
Found at i:2078 original size:32 final size:32
Alignment explanation
Indices: 2003--2079 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 32
1993 TCGGGTCATA
* * *
2003 CGGGTTTCGGGTTATACGGGTCTCGGGTTATT
1 CGGGTTTCGGGTCATACGGGTCACGGGTTAGT
* **
2035 TGGGTCACGGGTCAGT-CGGGTCACGGGTTAGT
1 CGGGTTTCGGGTCA-TACGGGTCACGGGTTAGT
2067 CGGGTTTCGGGTC
1 CGGGTTTCGGGTC
2080 GGGCGTGTTC
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
32 34 0.97
33 1 0.03
ACGTcount: A:0.09, C:0.18, G:0.42, T:0.31
Consensus pattern (32 bp):
CGGGTTTCGGGTCATACGGGTCACGGGTTAGT
Found at i:2166 original size:27 final size:26
Alignment explanation
Indices: 2116--2168 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
2106 GTAGTCAAAT
2116 CGGGTTGGACGGGTTACGGGTTCGGG
1 CGGGTTGGACGGGTTACGGGTTCGGG
*
2142 CGGGTTGGGC-GGTTAATCGGGTTCGGG
1 CGGGTTGGACGGGTT-A-CGGGTTCGGG
2169 TCAGCTTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 4 0.17
26 10 0.42
27 10 0.42
ACGTcount: A:0.08, C:0.15, G:0.53, T:0.25
Consensus pattern (26 bp):
CGGGTTGGACGGGTTACGGGTTCGGG
Done.