Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016898.1 Corchorus olitorius cultivar O-4 contig16931, 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: 20481
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:253 original size:45 final size:45
Alignment explanation
Indices: 189--316 Score: 247
Period size: 45 Copynumber: 2.8 Consensus size: 45
179 AGCAACAATT
189 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
*
234 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAT
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
279 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGA
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGA
317 ATAGATTTTA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
45 82 1.00
ACGTcount: A:0.34, C:0.07, G:0.22, T:0.38
Consensus pattern (45 bp):
AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
Found at i:8255 original size:99 final size:99
Alignment explanation
Indices: 8083--8281 Score: 371
Period size: 99 Copynumber: 2.0 Consensus size: 99
8073 GTGCTTATTC
* *
8083 TCAAGAATCTCCGTGATTTCCTTTTGTTCATCACGAGTTCTTACTCGTTTTTTAATATTTCCTTG
1 TCAAGAATCTCCGTGATTTCCTCTTGTTCATCACAAGTTCTTACTCGTTTTTTAATATTTCCTTG
*
8148 TTTTAATCTTGTCTCCGGACAAAAGAACACTCTT
66 TTTCAATCTTGTCTCCGGACAAAAGAACACTCTT
8182 TCAAGAATCTCCGTGATTTCCTCTTGTTCATCACAAGTTCTTACTCGTTTTTTAATATTTCCTTG
1 TCAAGAATCTCCGTGATTTCCTCTTGTTCATCACAAGTTCTTACTCGTTTTTTAATATTTCCTTG
8247 TTTCAATCTTGTCTCCGGACAAAAGAACACTCTT
66 TTTCAATCTTGTCTCCGGACAAAAGAACACTCTT
8281 T
1 T
8282 TAGTGTTATT
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
99 97 1.00
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.43
Consensus pattern (99 bp):
TCAAGAATCTCCGTGATTTCCTCTTGTTCATCACAAGTTCTTACTCGTTTTTTAATATTTCCTTG
TTTCAATCTTGTCTCCGGACAAAAGAACACTCTT
Found at i:11142 original size:8 final size:8
Alignment explanation
Indices: 11129--11158 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
11119 TAAATTCCTT
11129 TAATTTCC
1 TAATTTCC
11137 TAATTTCC
1 TAATTTCC
11145 TAATTTCC
1 TAATTTCC
11153 ATAATT
1 -TAATT
11159 AATTTAGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 16 0.76
9 5 0.24
ACGTcount: A:0.30, C:0.20, G:0.00, T:0.50
Consensus pattern (8 bp):
TAATTTCC
Found at i:13478 original size:53 final size:53
Alignment explanation
Indices: 13421--13523 Score: 179
Period size: 53 Copynumber: 1.9 Consensus size: 53
13411 GAGCATCCCA
* *
13421 TCACATGTGAACGGGGGAGTTTGTTGGAGTTCATATGTGAGTGTCGCATCCTG
1 TCACATGTGAACGGGGGAGTTTGTTAGAGTTCATATGTGAGTATCGCATCCTG
*
13474 TCACATGTGAACGGGGGAGTTTGTTATAGTTCATATGTGAGTATCGCATC
1 TCACATGTGAACGGGGGAGTTTGTTAGAGTTCATATGTGAGTATCGCATC
13524 GCACATCACA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.21, C:0.15, G:0.31, T:0.33
Consensus pattern (53 bp):
TCACATGTGAACGGGGGAGTTTGTTAGAGTTCATATGTGAGTATCGCATCCTG
Found at i:16184 original size:8 final size:8
Alignment explanation
Indices: 16171--16200 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
16161 ACTTATGGAG
16171 TATAAATA
1 TATAAATA
16179 TATAAATA
1 TATAAATA
*
16187 TATATATA
1 TATAAATA
16195 TATAAA
1 TATAAA
16201 ATCTTGTCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TATAAATA
Found at i:16980 original size:12 final size:13
Alignment explanation
Indices: 16951--16984 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
16941 AGTATATACC
*
16951 AATTACTCTCTCT
1 AATTTCTCTCTCT
16964 AATTTCTCTCT-T
1 AATTTCTCTCTCT
16976 AATTTCTCT
1 AATTTCTCT
16985 TTTTTGTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.21, C:0.26, G:0.00, T:0.53
Consensus pattern (13 bp):
AATTTCTCTCTCT
Found at i:17107 original size:2 final size:2
Alignment explanation
Indices: 17100--17131 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
17090 TTGGCGACAA
17100 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17132 TGTTGTAATT
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):
AT
Found at i:18695 original size:4 final size:4
Alignment explanation
Indices: 18686--18747 Score: 115
Period size: 4 Copynumber: 15.5 Consensus size: 4
18676 ATGTGGTGAG
*
18686 ATAC ATAC ATAC TTAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
18734 ATAC ATAC ATAC AT
1 ATAC ATAC ATAC AT
18748 TCCATTGATT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 56 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Done.