Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018996.1 Corchorus olitorius cultivar O-4 contig19029, 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: 10644
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--59 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
43 TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC T
60 TTTTCATCTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1836 original size:56 final size:55
Alignment explanation
Indices: 1772--2097 Score: 371
Period size: 53 Copynumber: 6.0 Consensus size: 55
1762 AAAAAACATT
* * *
1772 TCATTGTACTTGCATATTCAAACTCCAAAGTTTGATAGTCAAACCACAAAAAAACA
1 TCATTGTACATGCATAGTCAAACCCCAAAGTTTGATAGTCAAACCACAAAAAAA-A
* * *
1828 TCACTGTACATGCATGGTCAAACCCCAAAGTTTGATAGTCAAACAACAAAAAGAATA
1 TCATTGTACATGCATAGTCAAACCCCAAAGTTTGATAGTCAAACCACAAAAA-AA-A
* * * * *
1885 TCATTATAAATGCATAGTCAGATCCCAAAGTTTGATAGTTAAACCACAAAAAAAA
1 TCATTGTACATGCATAGTCAAACCCCAAAGTTTGATAGTCAAACCACAAAAAAAA
* *
1940 TCATTGCACATGCAT-GATCAAACCCCAAAGTTTGATAGTCAAA-C-CATAAAAAA
1 TCATTGTACATGCATAG-TCAAACCCCAAAGTTTGATAGTCAAACCACAAAAAAAA
* * *
1993 TCATTATACATGCATAGTTAAACCCCAAAGTTT-ACTAGTCAAA-C-CATAAAAAA
1 TCATTGTACATGCATAGTCAAACCCCAAAGTTTGA-TAGTCAAACCACAAAAAAAA
* **
2046 TCATTGTACATGCATGGTC-AACCCTCAAAGTTCAATAGTCAAACCA-AAAAAA
1 TCATTGTACATGCATAGTCAAACCC-CAAAGTTTGATAGTCAAACCACAAAAAA
2098 GCATTTCATT
Statistics
Matches: 232, Mismatches: 30, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
52 6 0.03
53 85 0.37
54 10 0.04
55 36 0.16
56 48 0.21
57 47 0.20
ACGTcount: A:0.44, C:0.21, G:0.11, T:0.24
Consensus pattern (55 bp):
TCATTGTACATGCATAGTCAAACCCCAAAGTTTGATAGTCAAACCACAAAAAAAA
Found at i:1981 original size:112 final size:112
Alignment explanation
Indices: 1782--2131 Score: 430
Period size: 112 Copynumber: 3.2 Consensus size: 112
1772 TCATTGTACT
* * *
1782 TGCATATTCAAACTCCAAAGTTTGATAGTCAAACCACAAAAAAACATCACTGTACATGCATGGTC
1 TGCATAGTCAAACCCCAAAGTTTGATAGTCAAACCACAAAAAAA-ATCATTGTACATGCATGGTC
1847 AAACCCCAAAGTTTGATAGTCAAACAACAAAAAGAATATCATTATAAA
65 AAACCCCAAAGTTTGATAGTCAAACAACAAAAAGAATATCATTATAAA
* * * * *
1895 TGCATAGTCAGATCCCAAAGTTTGATAGTTAAACCACAAAAAAAATCATTGCACATGCATGATCA
1 TGCATAGTCAAACCCCAAAGTTTGATAGTCAAACCACAAAAAAAATCATTGTACATGCATGGTCA
* *
1960 AACCCCAAAGTTTGATAGTCAAAC--CATAAA-AA-ATCATTATACA
66 AACCCCAAAGTTTGATAGTCAAACAACAAAAAGAATATCATTATAAA
* *
2003 TGCATAGTTAAACCCCAAAGTTT-ACTAGTCAAA-C-CATAAAAAATCATTGTACATGCATGGTC
1 TGCATAGTCAAACCCCAAAGTTTGA-TAGTCAAACCACAAAAAAAATCATTGTACATGCATGGTC
** * * *
2065 -AACCCTCAAAGTTCAATAGTCAAACCAA-AAAAAGCATTTCATTATATA
65 AAACCC-CAAAGTTTGATAGTCAAA-CAACAAAAAGAATATCATTATAAA
* *
2113 TACATGGTCAAACCCCAAA
1 TGCATAGTCAAACCCCAAA
2132 TGTTGGTCAA
Statistics
Matches: 204, Mismatches: 26, Indels: 17
0.83 0.11 0.07
Matches are distributed among these distances:
105 5 0.02
106 41 0.20
107 3 0.01
108 41 0.20
109 3 0.01
110 30 0.15
112 42 0.21
113 39 0.19
ACGTcount: A:0.44, C:0.21, G:0.11, T:0.24
Consensus pattern (112 bp):
TGCATAGTCAAACCCCAAAGTTTGATAGTCAAACCACAAAAAAAATCATTGTACATGCATGGTCA
AACCCCAAAGTTTGATAGTCAAACAACAAAAAGAATATCATTATAAA
Found at i:2161 original size:21 final size:20
Alignment explanation
Indices: 2116--2191 Score: 75
Period size: 21 Copynumber: 3.8 Consensus size: 20
2106 TTATATATAC
2116 ATGGTCAAACCCC-AA-ATG
1 ATGGTCAAACCCCAAAGATG
*
2134 TTGGTCAAACCCCAAAGGATG
1 ATGGTCAAACCCCAAA-GATG
* *
2155 ATGGTCAAATCCCAAAGTTCG
1 ATGGTCAAACCCCAAAGAT-G
* *
2176 ATAGTCAAACCACAAA
1 ATGGTCAAACCCCAAA
2192 AAACATTATT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
18 12 0.26
19 2 0.04
20 2 0.04
21 31 0.66
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.18
Consensus pattern (20 bp):
ATGGTCAAACCCCAAAGATG
Found at i:2219 original size:34 final size:36
Alignment explanation
Indices: 2176--2244 Score: 115
Period size: 34 Copynumber: 2.0 Consensus size: 36
2166 CCAAAGTTCG
2176 ATAGTCAAACCAC-AAAAAA-CATTATTGTACATGC
1 ATAGTCAAACCACAAAAAAATCATTATTGTACATGC
*
2210 ATAGTCAAACCACAAAAAAATCATTTTTGTACATG
1 ATAGTCAAACCACAAAAAAATCATTATTGTACATG
2245 GTCAAACCCC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 13 0.41
35 6 0.19
36 13 0.41
ACGTcount: A:0.46, C:0.19, G:0.09, T:0.26
Consensus pattern (36 bp):
ATAGTCAAACCACAAAAAAATCATTATTGTACATGC
Found at i:2287 original size:21 final size:20
Alignment explanation
Indices: 2242--2317 Score: 75
Period size: 21 Copynumber: 3.8 Consensus size: 20
2232 ATTTTTGTAC
2242 ATGGTCAAACCCC-AA-ATG
1 ATGGTCAAACCCCAAAGATG
*
2260 TTGGTCAAACCCCAAAGGATG
1 ATGGTCAAACCCCAAA-GATG
* *
2281 ATGGTCAAATCCCAAAGTTCG
1 ATGGTCAAACCCCAAAGAT-G
* *
2302 ATAGTCAAACCACAAA
1 ATGGTCAAACCCCAAA
2318 AAACATTATT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
18 12 0.26
19 2 0.04
20 2 0.04
21 31 0.66
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.18
Consensus pattern (20 bp):
ATGGTCAAACCCCAAAGATG
Found at i:2366 original size:33 final size:34
Alignment explanation
Indices: 2302--2376 Score: 116
Period size: 33 Copynumber: 2.2 Consensus size: 34
2292 CCAAAGTTCG
* *
2302 ATAGTCAAACCACAAAAAACATTATTGTACATGC
1 ATAGTCAAACCACAAAAAACATCATTATACATGC
2336 ATAGTCAAACCACAAAAAA-ATCATTATACATGC
1 ATAGTCAAACCACAAAAAACATCATTATACATGC
*
2369 ATGGTCAA
1 ATAGTCAA
2377 CCCCCAAAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
33 19 0.50
34 19 0.50
ACGTcount: A:0.48, C:0.20, G:0.09, T:0.23
Consensus pattern (34 bp):
ATAGTCAAACCACAAAAAACATCATTATACATGC
Found at i:2379 original size:126 final size:127
Alignment explanation
Indices: 2080--2384 Score: 515
Period size: 126 Copynumber: 2.4 Consensus size: 127
2070 TCAAAGTTCA
2080 ATAGTCAAACCA-AAAAAAGCATTTCATTATATATACATGGTCAAACCCCAAATGTTGGTCAAAC
1 ATAGTCAAACCACAAAAAA--A--TCATTATATATACATGGTCAAACCCCAAATGTTGGTCAAAC
2144 CCCAAAGGATGATGGTCAAATCCCAAAGTTCGATAGTCAAACCACAAAAAACATTATTGTACATG
62 CCCAAAGGATGATGGTCAAATCCCAAAGTTCGATAGTCAAACCACAAAAAACATTATTGTACATG
2209 C
127 C
* *
2210 ATAGTCAAACCACAAAAAAATCATT-TTTGTACATGGTCAAACCCCAAATGTTGGTCAAACCCCA
1 ATAGTCAAACCACAAAAAAATCATTATATATACATGGTCAAACCCCAAATGTTGGTCAAACCCCA
2274 AAGGATGATGGTCAAATCCCAAAGTTCGATAGTCAAACCACAAAAAACATTATTGTACATGC
66 AAGGATGATGGTCAAATCCCAAAGTTCGATAGTCAAACCACAAAAAACATTATTGTACATGC
* * *
2336 ATAGTCAAACCACAAAAAAATCATTATACATGCATGGTCAACCCCCAAA
1 ATAGTCAAACCACAAAAAAATCATTATATATACATGGTCAAACCCCAAA
2385 GTTCGATAGT
Statistics
Matches: 166, Mismatches: 7, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
126 124 0.75
127 23 0.14
129 1 0.01
130 12 0.07
131 6 0.04
ACGTcount: A:0.43, C:0.23, G:0.12, T:0.22
Consensus pattern (127 bp):
ATAGTCAAACCACAAAAAAATCATTATATATACATGGTCAAACCCCAAATGTTGGTCAAACCCCA
AAGGATGATGGTCAAATCCCAAAGTTCGATAGTCAAACCACAAAAAACATTATTGTACATGC
Found at i:2432 original size:56 final size:54
Alignment explanation
Indices: 2336--2440 Score: 147
Period size: 56 Copynumber: 1.9 Consensus size: 54
2326 TTGTACATGC
*
2336 ATAGTCAAACCACAAAAAAATCATTATACATGCATGGTCAACCCCCAAAGTTCG
1 ATAGTCAAACCACAAAAAAATCATTATACATGCATGGTCAAACCCCAAAGTTCG
** * *
2390 ATAGTCAAACCACAAAATCATTTCATTGTATATGCATGGTCAAACCCCAAA
1 ATAGTCAAACCACAAAA--AAATCATTATACATGCATGGTCAAACCCCAAA
2441 TGATGATGGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
54 17 0.39
56 27 0.61
ACGTcount: A:0.42, C:0.25, G:0.10, T:0.23
Consensus pattern (54 bp):
ATAGTCAAACCACAAAAAAATCATTATACATGCATGGTCAAACCCCAAAGTTCG
Found at i:2453 original size:56 final size:54
Alignment explanation
Indices: 2336--2456 Score: 145
Period size: 56 Copynumber: 2.2 Consensus size: 54
2326 TTGTACATGC
* *
2336 ATAGTCAAACCACAAAAAAATCATTATACATGCATGGTCAACCCCCAAAGTTCG
1 ATAGTCAAACCACAAAAAAATCATTATACATGCATGGTCAAACCCCAAAGATCG
** * *
2390 ATAGTCAAACCACAAAATCATTTCATTGTATATGCATGGTCAAACCCCAAATGAT-G
1 ATAGTCAAACCACAAAA--AAATCATTATACATGCATGGTCAAACCCCAAA-GATCG
*
2446 ATGGTCAAACC
1 ATAGTCAAACC
2457 TTAAAGTTTG
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
54 17 0.30
56 38 0.67
57 2 0.04
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.23
Consensus pattern (54 bp):
ATAGTCAAACCACAAAAAAATCATTATACATGCATGGTCAAACCCCAAAGATCG
Found at i:4306 original size:15 final size:16
Alignment explanation
Indices: 4261--4309 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 16
4251 GGAGGTTTAT
4261 ATTAATTGTTTTCTTG
1 ATTAATTGTTTTCTTG
*
4277 ATTATTCACTGTTTTCTTG
1 ATTA---ATTGTTTTCTTG
4296 -TTAATTGTTTTCTT
1 ATTAATTGTTTTCTT
4310 TAATTTTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
15 10 0.36
16 4 0.14
18 3 0.11
19 11 0.39
ACGTcount: A:0.16, C:0.10, G:0.10, T:0.63
Consensus pattern (16 bp):
ATTAATTGTTTTCTTG
Done.