Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012110.1 Corchorus olitorius cultivar O-4 contig12143, 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: 29366
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Found at i:833 original size:154 final size:154
Alignment explanation
Indices: 553--841 Score: 429
Period size: 154 Copynumber: 1.9 Consensus size: 154
543 TCTGCATTTA
* * * ** *
553 ATTGATATAAATGCACAAAATCCAAGTGGATTACATAATTAATTAGAAGATTACATTTTTAATGC
1 ATTGATATAAAGGCACAAAATCCAAGTGGATTAAATAATTAATTACAAGAAGACATATTTAATGC
*
618 TATGTAGGAATATAGCGAAATAAGACAAAAGGAAAATCCATTCAGATTTTTTGCATCTTTAGCAG
66 TATGTAGGAATATAGCGAAATAAGACAAAAGGAAAATCCATTCAGATTTTTTGCATCTTTAGCAA
683 TAATGATATGTCTATATTTGGATT
131 TAATGATATGTCTATATTTGGATT
* *
707 ATTGATATAAAGGCAGAAAATCCAAGTGGATTAAATAATTAATTACTAGAAGACATAATTT-ATG
1 ATTGATATAAAGGCACAAAATCCAAGTGGATTAAATAATTAATTACAAGAAGACAT-ATTTAATG
* * **
771 CTAT-TAAGGAATTTAGCGAAATAAGACAAAAGGGAAATCCATTTGGATTTTTTGCATCTTTAGC
65 CTATGT-AGGAATATAGCGAAATAAGACAAAAGGAAAATCCATTCAGATTTTTTGCATCTTTAGC
835 AATAATG
129 AATAATG
842 TCTATATTTG
Statistics
Matches: 120, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
153 1 0.01
154 116 0.97
155 3 0.03
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (154 bp):
ATTGATATAAAGGCACAAAATCCAAGTGGATTAAATAATTAATTACAAGAAGACATATTTAATGC
TATGTAGGAATATAGCGAAATAAGACAAAAGGAAAATCCATTCAGATTTTTTGCATCTTTAGCAA
TAATGATATGTCTATATTTGGATT
Found at i:5631 original size:14 final size:13
Alignment explanation
Indices: 5588--5634 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
5578 TTTCCTTTAG
5588 TTTTGTTTTTAT-T
1 TTTTGTTTTT-TGT
* *
5601 TTTCGTATTTTGT
1 TTTTGTTTTTTGT
5614 TTTTGTTTTTGTGT
1 TTTTGTTTTT-TGT
5628 TTTTGTT
1 TTTTGTT
5635 AATTGTGCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
12 1 0.04
13 17 0.61
14 10 0.36
ACGTcount: A:0.04, C:0.02, G:0.15, T:0.79
Consensus pattern (13 bp):
TTTTGTTTTTTGT
Found at i:5634 original size:6 final size:6
Alignment explanation
Indices: 5588--5630 Score: 50
Period size: 6 Copynumber: 6.7 Consensus size: 6
5578 TTTCCTTTAG
*
5588 TTTTGT TTTTAT TTTTCGT ATTTTGT TTTTGT TTTTGT GTTTT
1 TTTTGT TTTTGT TTTT-GT -TTTTGT TTTTGT TTTTGT -TTTT
5631 TGTTAATTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
6 21 0.66
7 7 0.22
8 4 0.12
ACGTcount: A:0.05, C:0.02, G:0.14, T:0.79
Consensus pattern (6 bp):
TTTTGT
Found at i:11157 original size:20 final size:20
Alignment explanation
Indices: 11132--11172 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
11122 TAGAATTTGA
11132 CAAATCTCTCTTCTCTCCGT
1 CAAATCTCTCTTCTCTCCGT
*
11152 CAAATCTCTCTTCTCTTCGT
1 CAAATCTCTCTTCTCTCCGT
11172 C
1 C
11173 GCTTTTCTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.39, G:0.05, T:0.41
Consensus pattern (20 bp):
CAAATCTCTCTTCTCTCCGT
Found at i:18607 original size:19 final size:19
Alignment explanation
Indices: 18580--18616 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
18570 AATTTATATA
* *
18580 TTTTGATTTATATTTCAAT
1 TTTTAATTTACATTTCAAT
18599 TTTTAATTTACATTTCAA
1 TTTTAATTTACATTTCAA
18617 ATCAATTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.08, G:0.03, T:0.59
Consensus pattern (19 bp):
TTTTAATTTACATTTCAAT
Found at i:20876 original size:22 final size:20
Alignment explanation
Indices: 20832--20880 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
20822 GGATGACTTT
* *
20832 AATAAATAATAAATAATGGA
1 AATAGATAATAAATAAGGGA
20852 AATAGATAATAGAATTAAGGGA
1 AATAGATAATA-AA-TAAGGGA
20874 AATAGAT
1 AATAGAT
20881 TAAATGGAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.40
21 2 0.08
22 13 0.52
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.24
Consensus pattern (20 bp):
AATAGATAATAAATAAGGGA
Found at i:21310 original size:27 final size:27
Alignment explanation
Indices: 21272--21349 Score: 120
Period size: 27 Copynumber: 2.9 Consensus size: 27
21262 CACCAATGTC
21272 TTGCCACGTATTACAGTGGGCTTTATA
1 TTGCCACGTATTACAGTGGGCTTTATA
* *
21299 TTGCAACGTATTACAGTGGGCTTTGTA
1 TTGCCACGTATTACAGTGGGCTTTATA
* *
21326 TTGCCACTTATTACTGTGGGCTTT
1 TTGCCACGTATTACAGTGGGCTTT
21350 TAATGAAGTA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.40
Consensus pattern (27 bp):
TTGCCACGTATTACAGTGGGCTTTATA
Found at i:28741 original size:15 final size:16
Alignment explanation
Indices: 28718--28756 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
28708 GAGATTGACT
*
28718 GAAAGCAATTAAAC-A
1 GAAAACAATTAAACTA
28733 GAAAACAATTAAACTA
1 GAAAACAATTAAACTA
28749 GAAAACAA
1 GAAAACAA
28757 AGCAAAGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.64, C:0.13, G:0.10, T:0.13
Consensus pattern (16 bp):
GAAAACAATTAAACTA
Done.