Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013096.1 Corchorus olitorius cultivar O-4 contig13129, 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: 25212
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:522 original size:19 final size:18
Alignment explanation
Indices: 484--522 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
474 TTTGTATTGC
**
484 AATATTTAATTAAGGGTA
1 AATATTTAATTAAGACTA
502 AATATTTAAATTAAGACTA
1 AATATTT-AATTAAGACTA
521 AA
1 AA
523 AGTTTGGGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36
Consensus pattern (18 bp):
AATATTTAATTAAGACTA
Found at i:4896 original size:22 final size:22
Alignment explanation
Indices: 4870--4914 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
4860 TCACTTGTTC
4870 CCCTTGAACAAGATCTCGGATT
1 CCCTTGAACAAGATCTCGGATT
4892 CCCTTGAACAAGATCTCGGATT
1 CCCTTGAACAAGATCTCGGATT
4914 C
1 C
4915 GAATCTTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.27
Consensus pattern (22 bp):
CCCTTGAACAAGATCTCGGATT
Found at i:5963 original size:32 final size:33
Alignment explanation
Indices: 5905--5983 Score: 101
Period size: 32 Copynumber: 2.5 Consensus size: 33
5895 TATAATTTTG
*
5905 TGTGATATAAAATAATGTAATAAATTTCTAATTA
1 TGTGATAT-ATATAATGTAATAAATTTCTAATTA
*
5939 TGTGATATATATAAT-TAATAAATTTCTAGTTA
1 TGTGATATATATAATGTAATAAATTTCTAATTA
*
5971 -GT-ACATATATAAT
1 TGTGATATATATAAT
5984 ATGGCAATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
30 10 0.24
31 2 0.05
32 16 0.38
33 6 0.14
34 8 0.19
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (33 bp):
TGTGATATATATAATGTAATAAATTTCTAATTA
Found at i:7282 original size:3 final size:3
Alignment explanation
Indices: 7274--7334 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
7264 TAGTACACAA
7274 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
7322 TAT TAT TAT TAT T
1 TAT TAT TAT TAT T
7335 TTACATTGGG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:8089 original size:122 final size:124
Alignment explanation
Indices: 7890--8144 Score: 361
Period size: 122 Copynumber: 2.0 Consensus size: 124
7880 CATTGTTTAA
*
7890 ACTTTTATAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCTTTATGAT
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCTTTATGAT
**
7955 TTTTACCATTTTACTATTTTAATT-AAAAAACTTATATATATTAGAA-TTTTTAAATAT
66 TTTTATAATTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAATAT
*
8012 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATATC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATAT-CTT-TAT-
* * *
8077 TATTTTATTTTTACCATTTTACTATTTTATTTAAAAAAACTTATATATATTAGAATTTTTTAAAT
63 GA--TT-TTTATA--ATTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAAT
8142 AT
123 AT
8144 A
1 A
8145 TTTCTTAAAT
Statistics
Matches: 116, Mismatches: 7, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
122 54 0.47
123 3 0.03
124 3 0.03
125 1 0.01
127 2 0.02
128 3 0.03
130 16 0.14
131 22 0.19
132 12 0.10
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (124 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCTTTATGAT
TTTTATAATTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:8166 original size:14 final size:13
Alignment explanation
Indices: 8130--8168 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
8120 TATATATTAG
8130 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
8143 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
8157 AATTTTTTAAAT
1 AATTTTTTAAAT
8169 TTTACAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Found at i:13583 original size:22 final size:22
Alignment explanation
Indices: 13527--13594 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 22
13517 TTTAGTAATT
*
13527 AAATATATATTATTTATTTATTTTG
1 AAATATAT-TTATTT-TTTA-TTTA
*
13552 AACTA-A-TTATTTTTTATTTA
1 AAATATATTTATTTTTTATTTA
*
13572 AAATATATTTATTATTTATTTA
1 AAATATATTTATTTTTTATTTA
13594 A
1 A
13595 TAGTATATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
20 7 0.19
21 5 0.14
22 20 0.54
24 1 0.03
25 4 0.11
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (22 bp):
AAATATATTTATTTTTTATTTA
Found at i:23010 original size:33 final size:33
Alignment explanation
Indices: 22963--23052 Score: 110
Period size: 33 Copynumber: 2.8 Consensus size: 33
22953 TGTAAAGGCG
22963 TGATGAAGGCCCGTGAACTTCATTGAAAAGACA
1 TGATGAAGGCCCGTGAACTTCATTGAAAAGACA
* * * * * *
22996 TGATAAAGGCCCGTGAATTTTATTGAAACGGCG
1 TGATGAAGGCCCGTGAACTTCATTGAAAAGACA
*
23029 TGATGAAGACCCGT-AACTTCATTG
1 TGATGAAGGCCCGTGAACTTCATTG
23053 GTTGTAAGAG
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
32 8 0.17
33 39 0.83
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (33 bp):
TGATGAAGGCCCGTGAACTTCATTGAAAAGACA
Done.