Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012800.1 Corchorus olitorius cultivar O-4 contig12833, 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: 9609
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2809 original size:315 final size:319
Alignment explanation
Indices: 2209--2854 Score: 1129
Period size: 315 Copynumber: 2.0 Consensus size: 319
2199 TTATCTTTTA
2209 CAACCGTTGGAATAAAACAATATATTCCTTTAAAAGAATCTATCATCATATCAAGTCTCCTTTCA
1 CAACCGTTGGAATAAAACAATATATTCCTTTAAAAGAATCTATCATCATATCAAGTCTCCTTTCA
*
2274 TTTCAATAGAATATATTCCTTCCCTTTAGAATATATTCCTTTGAATATAATGTCATTGTATGACA
66 TTTCAATAGAATAGATTCCTTCCCTTTAGAATATATTCCTTTGAATATAATGTCATTGTATGAC-
*
2339 AAAAAAGAAGAAGAATATAATGCCATTCAATAGAATATATTTGTTTCCTTTCTTTTCATTGCATT
130 AAAAAAGAAGAAGAATATAATGCCATTCAATAGAATATATTCGTTTCCTTTCTTTTCATTGCATT
* *
2404 GTATTGTCATTCAAGTCTCAATAATACAAATTATATTTCCTATACCTTTTCAGTGTAATGTCATT
195 GTATTGTCATTCAAATCTCAAGAATACAAATTATATTTCCTATACCTTTTCAGTGTAATGTCATT
*
2469 CAAGTATCAGACTCAATTCTACCCTTGTAATTGCAAACATACT-TTGCTGCAACCTACTC
260 CAAGTATCAGACTCAATTCTACCCTTGTAATTGCAAACATACTATTACTGCAACCTACTC
* *
2528 CAACCGCTGGAATAAAAGAATATATTCCTTTAAAAGAATCTATCATCATATCAAGTCTCCTTTCA
1 CAACCGTTGGAATAAAACAATATATTCCTTTAAAAGAATCTATCATCATATCAAGTCTCCTTTCA
*
2593 TTTCAATAGAATAGATTCCTTCCCTTTAGAATATATTGCTTTGAATATAATGTCATTGTATGAC-
66 TTTCAATAGAATAGATTCCTTCCCTTTAGAATATATTCCTTTGAATATAATGTCATTGTATGACA
* *
2657 AAAAA-AA-AAGAATATAATGTCATTCAATAGAATATATTCGTTTCCTTTCTTTTCATTGTATTG
131 AAAAAGAAGAAGAATATAATGCCATTCAATAGAATATATTCGTTTCCTTTCTTTTCATTGCATTG
*
2720 TATTGTCATTCAAATCTCAAGAATACAGATTATATTTCCTATACCTTTTCAGTGTAATGTCATTC
196 TATTGTCATTCAAATCTCAAGAATACAAATTATATTTCCTATACCTTTTCAGTGTAATGTCATTC
* * *
2785 AAGTATGAGACTCAATTTTACCCTTGTAATTGCAACCATACTATTACTGCAACCTACTC
261 AAGTATCAGACTCAATTCTACCCTTGTAATTGCAAACATACTATTACTGCAACCTACTC
2844 CAACCGTTGGA
1 CAACCGTTGGA
2855 TTCAAAGTGG
Statistics
Matches: 311, Mismatches: 15, Indels: 5
0.94 0.05 0.02
Matches are distributed among these distances:
315 154 0.50
316 27 0.09
317 5 0.02
319 125 0.40
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (319 bp):
CAACCGTTGGAATAAAACAATATATTCCTTTAAAAGAATCTATCATCATATCAAGTCTCCTTTCA
TTTCAATAGAATAGATTCCTTCCCTTTAGAATATATTCCTTTGAATATAATGTCATTGTATGACA
AAAAAGAAGAAGAATATAATGCCATTCAATAGAATATATTCGTTTCCTTTCTTTTCATTGCATTG
TATTGTCATTCAAATCTCAAGAATACAAATTATATTTCCTATACCTTTTCAGTGTAATGTCATTC
AAGTATCAGACTCAATTCTACCCTTGTAATTGCAAACATACTATTACTGCAACCTACTC
Found at i:3811 original size:18 final size:16
Alignment explanation
Indices: 3770--3817 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 16
3760 ATTGGGAGGA
3770 AGAAAGAAA-AAAATG
1 AGAAAGAAACAAAATG
*
3785 AAAAAGAAACAAAATG
1 AGAAAGAAACAAAATG
3801 AGGAAATGAAACAAAAT
1 A-GAAA-GAAACAAAAT
3818 TTTCAGTCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 8 0.29
16 7 0.25
17 3 0.11
18 10 0.36
ACGTcount: A:0.71, C:0.04, G:0.17, T:0.08
Consensus pattern (16 bp):
AGAAAGAAACAAAATG
Found at i:4335 original size:17 final size:17
Alignment explanation
Indices: 4287--4332 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
4277 CTTTTTAATC
*
4287 TATGGTGTAATTTATGT
1 TATGTTGTAATTTATGT
*
4304 TAT-TTTTAACTTTAT-T
1 TATGTTGTAA-TTTATGT
4320 TATGTTGTAATTT
1 TATGTTGTAATTT
4333 TATCTTAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.24, C:0.02, G:0.13, T:0.61
Consensus pattern (17 bp):
TATGTTGTAATTTATGT
Found at i:5972 original size:29 final size:31
Alignment explanation
Indices: 5928--5996 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
5918 CGAAAGTACA
5928 AATTG-GTCCCTCAAGT-GA-AAAAATGAGC
1 AATTGAGTCCCTCAAGTAGAGAAAAATGAGC
* ** *
5956 AATTGAGTCCCTGAAGTAGAGTTAACTGAGC
1 AATTGAGTCCCTCAAGTAGAGAAAAATGAGC
5987 AATTGAGTCC
1 AATTGAGTCC
5997 TTTCCGTTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 5 0.15
29 10 0.29
30 2 0.06
31 17 0.50
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (31 bp):
AATTGAGTCCCTCAAGTAGAGAAAAATGAGC
Found at i:7504 original size:21 final size:21
Alignment explanation
Indices: 7480--7546 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
7470 AATTCTCTGT
7480 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * * *
7501 AAATCATAGAAA-ATTC-TCTGT
1 AAATTA-AGAAATACTCAACT-C
*
7522 AAATTCAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
7543 AAAT
1 AAAT
7547 CCTGATCCTT
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
20 7 0.21
21 19 0.58
22 7 0.21
ACGTcount: A:0.49, C:0.18, G:0.06, T:0.27
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:7526 original size:42 final size:42
Alignment explanation
Indices: 7467--7547 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
7457 GCTAAGTCTT
7467 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
*
7509 GAAAATTCTCTGTAAATTCAGAAATACTCAACTCAAATC
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATC
7548 CTGATCCTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.46, C:0.19, G:0.07, T:0.28
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:8106 original size:42 final size:43
Alignment explanation
Indices: 8055--8148 Score: 147
Period size: 45 Copynumber: 2.2 Consensus size: 43
8045 AGTGCATTAC
*
8055 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
8096 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
8141 CTAATATT
1 CTAATATT
8149 AATTGTTGCT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
41 4 0.08
42 6 0.12
45 38 0.79
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Done.