Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022203.1 Corchorus olitorius cultivar O-4 contig22236, 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: 35169
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1738 original size:24 final size:25
Alignment explanation
Indices: 1709--1758 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
1699 TTATGTGAAC
*
1709 AATAAAATAAATAAACAAGA-AAAT
1 AATAAAATAAAGAAACAAGATAAAT
* *
1733 AATAAAATTAAGCAACAAGATAAAT
1 AATAAAATAAAGAAACAAGATAAAT
1758 A
1 A
1759 TGTACTCCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.70, C:0.06, G:0.06, T:0.18
Consensus pattern (25 bp):
AATAAAATAAAGAAACAAGATAAAT
Found at i:2247 original size:28 final size:28
Alignment explanation
Indices: 2206--2260 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
2196 AATAAGTATG
* *
2206 CATACAAATCAATTAGAAATCATAAAAA
1 CATAAAAATAAATTAGAAATCATAAAAA
*
2234 CATAAAAATAAATTTGAAATCATAAAA
1 CATAAAAATAAATTAGAAATCATAAAA
2261 TACCAAGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.62, C:0.11, G:0.04, T:0.24
Consensus pattern (28 bp):
CATAAAAATAAATTAGAAATCATAAAAA
Found at i:5287 original size:22 final size:22
Alignment explanation
Indices: 5262--5307 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
5252 AAGTTGTTGT
5262 TTCGACCTCTACAAAGGTTGAA
1 TTCGACCTCTACAAAGGTTGAA
* *
5284 TTCGACCTCTCCAGAGGTTGAA
1 TTCGACCTCTACAAAGGTTGAA
5306 TT
1 TT
5308 AGGAGATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (22 bp):
TTCGACCTCTACAAAGGTTGAA
Found at i:5511 original size:18 final size:19
Alignment explanation
Indices: 5470--5512 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 19
5460 GAGCTCTCCT
5470 TCATGTCTCAACATATTGTTC
1 TCATGTCTCAACATA-T-TTC
5491 TCATGTCTCAACATA-TTC
1 TCATGTCTCAACATATTTC
5509 TCAT
1 TCAT
5513 TAGTTTTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.32
21 15 0.68
ACGTcount: A:0.26, C:0.26, G:0.07, T:0.42
Consensus pattern (19 bp):
TCATGTCTCAACATATTTC
Found at i:6165 original size:24 final size:25
Alignment explanation
Indices: 6136--6186 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
6126 TTATGTGAAC
*
6136 AATAAAATAAATAAACAAGA-AAAT
1 AATAAAATAAAGAAACAAGATAAAT
* *
6160 AATAAAATTAAGCAACAAGATAAAT
1 AATAAAATAAAGAAACAAGATAAAT
6185 AA
1 AA
6187 ATACTCCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.18
Consensus pattern (25 bp):
AATAAAATAAAGAAACAAGATAAAT
Found at i:8050 original size:13 final size:13
Alignment explanation
Indices: 8032--8059 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
8022 TATAGATCTC
8032 AAGAGGTGTGTTA
1 AAGAGGTGTGTTA
8045 AAGAGGTGTGTTA
1 AAGAGGTGTGTTA
8058 AA
1 AA
8060 CACCCTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.29
Consensus pattern (13 bp):
AAGAGGTGTGTTA
Found at i:11029 original size:93 final size:93
Alignment explanation
Indices: 10927--11096 Score: 313
Period size: 93 Copynumber: 1.8 Consensus size: 93
10917 TTGTTTAAAT
* *
10927 TTTTATAGTTTTAGTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
1 TTTTATAGTTTTACTCAACTAAAAAATCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
10992 TTTTATTTTTACCATTTTATTATTTTAC
66 TTTTATTTTTACCATTTTATTATTTTAC
*
11020 TTTTATAGTTTTACTCAACTAAAAAATCTATTTTTATTTAATTAAATCTAATATCCTTATACCTA
1 TTTTATAGTTTTACTCAACTAAAAAATCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
11085 TTTTATTTTTAC
66 TTTTATTTTTAC
11097 GATATTACTA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.33, C:0.12, G:0.02, T:0.53
Consensus pattern (93 bp):
TTTTATAGTTTTACTCAACTAAAAAATCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
TTTTATTTTTACCATTTTATTATTTTAC
Found at i:11664 original size:35 final size:35
Alignment explanation
Indices: 11624--11695 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
11614 TCGTTTATGC
*
11624 TCACGAACAGGCTCGTTTATTGTTCATTTAAGTGT
1 TCACGAACAGACTCGTTTATTGTTCATTTAAGTGT
11659 TCACGAACAGACTCGTTTATTGTTCATTTAAGTGT
1 TCACGAACAGACTCGTTTATTGTTCATTTAAGTGT
11694 TC
1 TC
11696 GTTTATATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (35 bp):
TCACGAACAGACTCGTTTATTGTTCATTTAAGTGT
Found at i:11758 original size:16 final size:16
Alignment explanation
Indices: 11737--11768 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
11727 TATAATCATT
11737 TATATATTAATAATAA
1 TATATATTAATAATAA
*
11753 TATATATTATTAATAA
1 TATATATTAATAATAA
11769 AAATTATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATATATTAATAATAA
Found at i:11763 original size:19 final size:18
Alignment explanation
Indices: 11723--11790 Score: 59
Period size: 19 Copynumber: 3.8 Consensus size: 18
11713 ATGTTCATTA
* *
11723 ATTATATAATCATTTATAT
1 ATTA-ATAATAATATATAT
11742 ATTAATAATAATATATATT
1 ATTAATAATAATATATA-T
*
11761 ATTAATAAAAAT-TATA-
1 ATTAATAATAATATATAT
**
11777 AAAAATAATAATAT
1 ATTAATAATAATAT
11791 TCTATTATCT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
16 9 0.22
17 1 0.02
18 15 0.37
19 16 0.39
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTAATAATAATATATAT
Found at i:11850 original size:17 final size:16
Alignment explanation
Indices: 11828--11864 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
11818 ATTTAATTAT
11828 TATATATAATATATATA
1 TATATATAAT-TATATA
11845 TATATATAATTATATA
1 TATATATAATTATATA
11861 -ATAT
1 TATAT
11865 TTTGTTCGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 4 0.20
16 6 0.30
17 10 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TATATATAATTATATA
Found at i:11930 original size:18 final size:18
Alignment explanation
Indices: 11903--11937 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
11893 AATTATTACA
11903 TTGTTCATGAACAATTTT
1 TTGTTCATGAACAATTTT
*
11921 TTGTTTATGAACAATTT
1 TTGTTCATGAACAATTT
11938 CAATTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (18 bp):
TTGTTCATGAACAATTTT
Found at i:14335 original size:17 final size:17
Alignment explanation
Indices: 14313--14349 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
14303 GGCTATACTT
14313 ATTTTAAAG-TATTAGGA
1 ATTTTAAAGCT-TTAGGA
14330 ATTTTAAAGCTTTAGGA
1 ATTTTAAAGCTTTAGGA
14347 ATT
1 ATT
14350 GGGAGTTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 18 0.95
18 1 0.05
ACGTcount: A:0.38, C:0.03, G:0.16, T:0.43
Consensus pattern (17 bp):
ATTTTAAAGCTTTAGGA
Found at i:31722 original size:13 final size:13
Alignment explanation
Indices: 31704--31728 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31694 TTTTTTTTTT
31704 GTATAATCAATTG
1 GTATAATCAATTG
31717 GTATAATCAATT
1 GTATAATCAATT
31729 ACAATTAGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (13 bp):
GTATAATCAATTG
Found at i:31791 original size:13 final size:13
Alignment explanation
Indices: 31773--31798 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31763 TTTTTTCTTC
31773 GATTTGTTTGGGT
1 GATTTGTTTGGGT
31786 GATTTGTTTGGGT
1 GATTTGTTTGGGT
31799 TTGAGTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.38, T:0.54
Consensus pattern (13 bp):
GATTTGTTTGGGT
Done.