Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015148.1 Corchorus olitorius cultivar O-4 contig15181, 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: 33118
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:1535 original size:29 final size:27
Alignment explanation
Indices: 1482--1535 Score: 65
Period size: 29 Copynumber: 1.9 Consensus size: 27
1472 ATAAGGGGGG
*
1482 TTTTAACATAATTAATATGTTTTTTAT
1 TTTTAACATAATTAATAAGTTTTTTAT
1509 TTTTAATCATAAATTAA-AAGTTATTTT
1 TTTTAA-CAT-AATTAATAAGTT-TTTT
1536 TTATTTCAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 6 0.26
28 7 0.30
29 10 0.43
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (27 bp):
TTTTAACATAATTAATAAGTTTTTTAT
Found at i:1862 original size:37 final size:37
Alignment explanation
Indices: 1821--1898 Score: 140
Period size: 36 Copynumber: 2.1 Consensus size: 37
1811 GTTCAACTCC
*
1821 TCTGCCGGAATTTCAAAGGATTTGTGCTATAAATGTA
1 TCTGCCGGAATTCCAAAGGATTTGTGCTATAAATGTA
1858 TCTG-CGGAATTCCAAAGGATTTGTGCTATAAATGTA
1 TCTGCCGGAATTCCAAAGGATTTGTGCTATAAATGTA
1894 TCTGC
1 TCTGC
1899 AATAATAGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
36 35 0.90
37 4 0.10
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (37 bp):
TCTGCCGGAATTCCAAAGGATTTGTGCTATAAATGTA
Found at i:13187 original size:13 final size:13
Alignment explanation
Indices: 13169--13194 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13159 CTTGGCATGA
13169 GTGATGATTTTTG
1 GTGATGATTTTTG
13182 GTGATGATTTTTG
1 GTGATGATTTTTG
13195 TTGTTACCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (13 bp):
GTGATGATTTTTG
Found at i:14989 original size:51 final size:51
Alignment explanation
Indices: 14934--15039 Score: 126
Period size: 51 Copynumber: 2.1 Consensus size: 51
14924 ACGAGTTCTT
14934 CACTCGTTCA-TCAAATTTTC-CTTGTTTCAATCTTGTCTCAGGACAAACAAA
1 CACTCGTTCAGT--AATTTTCTCTTGTTTCAATCTTGTCTCAGGACAAACAAA
* * ** * *
14985 CACTCTTTTAGTGTTTTTCTCTTGTTTCAATCTTGTCTCCGGACATACAAA
1 CACTCGTTCAGTAATTTTCTCTTGTTTCAATCTTGTCTCAGGACAAACAAA
15036 CACT
1 CACT
15040 GTACACGTGT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
50 5 0.11
51 41 0.87
52 1 0.02
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.40
Consensus pattern (51 bp):
CACTCGTTCAGTAATTTTCTCTTGTTTCAATCTTGTCTCAGGACAAACAAA
Found at i:15050 original size:51 final size:51
Alignment explanation
Indices: 14949--15055 Score: 137
Period size: 51 Copynumber: 2.1 Consensus size: 51
14939 GTTCATCAAA
* **
14949 TTTTC-CTTGTTTCAATCTTGTCTCAGGACAAACAAACACTCTTTTAGTGT
1 TTTTCTCTTGTTTCAATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
* *
14999 TTTTCTCTTGTTTCAATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
1 TTTTCTCTTGTTTCAATCTTGTCTCAGGACAAACAAACACTCGTACA-GTGT
*
15050 TCTTCT
1 TTTTCT
15056 TTCAGAAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
50 7 0.14
51 42 0.86
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.42
Consensus pattern (51 bp):
TTTTCTCTTGTTTCAATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
Found at i:17703 original size:35 final size:35
Alignment explanation
Indices: 17664--17736 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
17654 AACTATTCTC
* *
17664 TTGATTTTTCCAATTGGTAAATTCCAATCTTAAGT
1 TTGATTTTTCCAATTGGTAAATTCCAAACATAAGT
*
17699 TTGATTTTTCCAATTGGTAAATTCTAAACATAAGT
1 TTGATTTTTCCAATTGGTAAATTCCAAACATAAGT
17734 TTG
1 TTG
17737 CTTAGGTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (35 bp):
TTGATTTTTCCAATTGGTAAATTCCAAACATAAGT
Found at i:22903 original size:44 final size:44
Alignment explanation
Indices: 22847--22944 Score: 196
Period size: 44 Copynumber: 2.2 Consensus size: 44
22837 GACTTTAAAC
22847 CAAAACCCAATAGCTCATAAGTTTGTCTTAGCCACTCTTAAAAT
1 CAAAACCCAATAGCTCATAAGTTTGTCTTAGCCACTCTTAAAAT
22891 CAAAACCCAATAGCTCATAAGTTTGTCTTAGCCACTCTTAAAAT
1 CAAAACCCAATAGCTCATAAGTTTGTCTTAGCCACTCTTAAAAT
22935 CAAAACCCAA
1 CAAAACCCAA
22945 AAGGTATTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 54 1.00
ACGTcount: A:0.39, C:0.27, G:0.08, T:0.27
Consensus pattern (44 bp):
CAAAACCCAATAGCTCATAAGTTTGTCTTAGCCACTCTTAAAAT
Found at i:30644 original size:16 final size:15
Alignment explanation
Indices: 30606--30647 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
30596 ACAGAGATTG
*
30606 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
30621 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
30636 ACTAGAAAACAA
1 AC-AGAAAACAA
30648 AGCAAAGTAA
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:32077 original size:29 final size:29
Alignment explanation
Indices: 32021--32078 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
32011 CTTGAAATAA
* *
32021 ATCTTCAATGGTCTTCAAGTCTCCAATTT
1 ATCTTCAATGGTCTTCAAGACACCAATTT
*
32050 ATCTTCAAATGGTCTTCAA-ACACGAATTT
1 ATCTTC-AATGGTCTTCAAGACACCAATTT
32079 CGAATCTCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.38
Consensus pattern (29 bp):
ATCTTCAATGGTCTTCAAGACACCAATTT
Done.