Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022113.1 Corchorus olitorius cultivar O-4 contig22146, 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: 17069
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:2041 original size:65 final size:67
Alignment explanation
Indices: 1917--2074 Score: 173
Period size: 65 Copynumber: 2.4 Consensus size: 67
1907 TAACAAAAAC
* * * ** * *
1917 TCATATGGAGGTTA-CAAAATTTCATAGGAAGATTTTTTAAATTTTCATAGTTTGTTTATCAAAG
1 TCATATGGAGTTTATCAAAATTTCATAGGAAGATTTATTAAAATTTCATAGCGTGGTTATCAAAA
1981 TT
66 TT
* *
1983 TCATATGGAGTTTATCACAATTTCATAGGTA-A-TTATTAAAATTTCATAGCGTGGTTATCAAAA
1 TCATATGGAGTTTATCAAAATTTCATAGGAAGATTTATTAAAATTTCATAGCGTGGTTATCAAAA
2046 TT
66 TT
*
2048 TAATA-GGA-TAATTATCAAAATTTCATA
1 TCATATGGAGT--TTATCAAAATTTCATA
2075 AAAATATTCA
Statistics
Matches: 78, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
63 1 0.01
64 3 0.04
65 46 0.59
66 14 0.18
67 14 0.18
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (67 bp):
TCATATGGAGTTTATCAAAATTTCATAGGAAGATTTATTAAAATTTCATAGCGTGGTTATCAAAA
TT
Found at i:2045 original size:22 final size:21
Alignment explanation
Indices: 1972--2074 Score: 100
Period size: 22 Copynumber: 4.8 Consensus size: 21
1962 CATAGTTTGT
* *
1972 TTATCAAAGTTTCATATGG-AGT
1 TTATCAAAATTTCATA-GGTA-A
*
1994 TTATCACAATTTCATAGGTAA
1 TTATCAAAATTTCATAGGTAA
* **
2015 TTATTAAAATTTCATAGCGTGG
1 TTATCAAAATTTCATAG-GTAA
*
2037 TTATCAAAATTTAATAGGATAA
1 TTATCAAAATTTCATAGG-TAA
2059 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
2075 AAAATATTCA
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
21 18 0.27
22 48 0.73
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.40
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGTAA
Found at i:2875 original size:33 final size:32
Alignment explanation
Indices: 2788--2890 Score: 143
Period size: 32 Copynumber: 3.2 Consensus size: 32
2778 CCCTAAGGAT
** * *
2788 GCCTCCACCGTGGTGGGGCGCCCTTTGGAGAT
1 GCCTCCACCGTGGTGGGGCGCCCTCCGGGGAC
2820 GCCTCCACCGTGGTGGGGCGCCCTCCGGGGAC
1 GCCTCCACCGTGGTGGGGCGCCCTCCGGGGAC
* *
2852 GCCTCTCACTGTGCTGGGGCGCCCTCCGGGGAC
1 GCCTC-CACCGTGGTGGGGCGCCCTCCGGGGAC
2885 GCCTCC
1 GCCTCC
2891 GTGCCTAGAT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
32 34 0.53
33 30 0.47
ACGTcount: A:0.07, C:0.39, G:0.37, T:0.17
Consensus pattern (32 bp):
GCCTCCACCGTGGTGGGGCGCCCTCCGGGGAC
Found at i:4364 original size:22 final size:23
Alignment explanation
Indices: 4336--4382 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
4326 GATACATTTT
* *
4336 AAGCTCGGGCTCG-TTTGAGCTC
1 AAGCTCGAGCTCGATTGGAGCTC
4358 AAGCTCGAGCTCGATTGGAGCTC
1 AAGCTCGAGCTCGATTGGAGCTC
4381 AA
1 AA
4383 AAATTTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.21, C:0.26, G:0.30, T:0.23
Consensus pattern (23 bp):
AAGCTCGAGCTCGATTGGAGCTC
Found at i:4927 original size:2 final size:2
Alignment explanation
Indices: 4922--4953 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4912 GTGGTGTGTG
4922 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4954 AGCTTGAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7202 original size:22 final size:21
Alignment explanation
Indices: 7176--7225 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
7166 GAATTGATGA
*
7176 AGAGAGATAGTGAGTGGGAGG
1 AGAGAGAGAGTGAGTGGGAGG
* * *
7197 AGGAGAAAGAGTTAGTGGGGGG
1 A-GAGAGAGAGTGAGTGGGAGG
7219 AGAGAGA
1 AGAGAGA
7226 AGAAGGACAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.36, C:0.00, G:0.52, T:0.12
Consensus pattern (21 bp):
AGAGAGAGAGTGAGTGGGAGG
Found at i:8376 original size:23 final size:24
Alignment explanation
Indices: 8349--8393 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
8339 TGAAAAATTT
8349 ATATGTAATT-AAAATTTTAAAAA
1 ATATGTAATTGAAAATTTTAAAAA
**
8372 ATATGTTTTTGAAAATTTTAAA
1 ATATGTAATTGAAAATTTTAAA
8394 TTTTAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (24 bp):
ATATGTAATTGAAAATTTTAAAAA
Found at i:16232 original size:253 final size:252
Alignment explanation
Indices: 15783--16287 Score: 895
Period size: 253 Copynumber: 2.0 Consensus size: 252
15773 TAGCTCATTC
* *
15783 GGTAAAAGTACTCGGAGGTCCCTGTACTATATGAAATGTTGATTTTGGTCCCTGTACTTTTTTTT
1 GGTAAAAGTACCCGGAGGTCCCTGTACTATACGAAATGTTGATTTTGGTCCCTGTACTTTTTTTT
* * **
15848 TTCTACAAATTCGTTCCTCTACTATCAGAACCTATCACCCGAGGTCCCTTACGTTAGTGTGCCGT
66 TTCTACAAATTCGTCCCTCTACTATCAGAACCTATCACCCGAGGTCCCTCACGTTAGCATGCCGT
*
15913 GACAGACCCGTCAAATATGCTGACGTGGCACTAACACCGTCTTTTTTGCTGACGTGGCAAGTGAC
131 GACAGACCCGTCAAATATGCTGACGTGGCACTAACACCGTCTTTTTTGCTGACATGGCAAGTGAC
15978 ACGTGGAATAAAAATTAAATATTTTTTTAATATATTTTATTTTCATTGAAATTTATTT
196 ACGTGGAATAAAAATTAAATATTTTTTTAATATATTTTATTTT-ATTGAAATTTATTT
16036 GGTAAAAGTACCCGGGAGGTCCCTGTACTATACGAAATGTTGATTTTGGTCCCTGTACTTTTTTT
1 GGTAAAAGTACCC-GGAGGTCCCTGTACTATACGAAATGTTGATTTTGGTCCCTGTACTTTTTTT
16101 TTT-TACAAATTCGTCCCTCTACTATCAGAACCTATCACCCGAGGTCCCTCACGTTAGCATGCCG
65 TTTCTACAAATTCGTCCCTCTACTATCAGAACCTATCACCCGAGGTCCCTCACGTTAGCATGCCG
* * *
16165 TGACAGACCCGTCAAATGTGCTGACGTGGCACTAATACCGTCTTTTTTGCTGACATGGCAGGTGA
130 TGACAGACCCGTCAAATATGCTGACGTGGCACTAACACCGTCTTTTTTGCTGACATGGCAAGTGA
16230 CACGTGGAATAAAAATTAAATATTTTTTTAATATATTTTATTTTATTGAAATTTATTT
195 CACGTGGAATAAAAATTAAATATTTTTTTAATATATTTTATTTTATTGAAATTTATTT
16288 TTTTTTTTAA
Statistics
Matches: 241, Mismatches: 10, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
252 14 0.06
253 174 0.72
254 53 0.22
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (252 bp):
GGTAAAAGTACCCGGAGGTCCCTGTACTATACGAAATGTTGATTTTGGTCCCTGTACTTTTTTTT
TTCTACAAATTCGTCCCTCTACTATCAGAACCTATCACCCGAGGTCCCTCACGTTAGCATGCCGT
GACAGACCCGTCAAATATGCTGACGTGGCACTAACACCGTCTTTTTTGCTGACATGGCAAGTGAC
ACGTGGAATAAAAATTAAATATTTTTTTAATATATTTTATTTTATTGAAATTTATTT
Done.