Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017064.1 Corchorus olitorius cultivar O-4 contig17097, 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: 24156
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:14613 original size:12 final size:11
Alignment explanation
Indices: 14585--14654 Score: 55
Period size: 11 Copynumber: 6.8 Consensus size: 11
14575 ATACTACTAC
14585 TAATAT-TATA
1 TAATATATATA
14595 T-ATATATATA
1 TAATATATATA
*
14605 TAGTA-ATAT-
1 TAATATATATA
14614 TAATAT-TA-A
1 TAATATATATA
*
14623 TATTAATATATA
1 TAAT-ATATATA
14635 TAATATATATA
1 TAATATATATA
14646 CTAAT-TATA
1 -TAATATATA
14655 AAGTTAAGTT
Statistics
Matches: 48, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
9 13 0.27
10 12 0.25
11 15 0.31
12 8 0.17
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (11 bp):
TAATATATATA
Found at i:16248 original size:78 final size:78
Alignment explanation
Indices: 16154--16323 Score: 236
Period size: 78 Copynumber: 2.2 Consensus size: 78
16144 ATTGTTTAAA
*
16154 ATTTTA-TAATTTTACTCAACTAAAAACACTATCTTTATTTAATTAAATCTAATAT-CTTTATAA
1 ATTTTACT-ATTTTACTCAACTAAAAACACTATCTTTATTTAATTAAATCTAACATAC-TTATAA
*
16217 CTATTTTATTTTACC
64 CTATTTTAGTTTACC
* * * * *
16232 ATTTTACTATTTTACTCAACTAAAAACTCTATTTTTGTTTAATTAAATGTAACATACTTGTAACT
1 ATTTTACTATTTTACTCAACTAAAAACACTATCTTTATTTAATTAAATCTAACATACTTATAACT
*
16297 ATTTTAGTTTATC
66 ATTTTAGTTTACC
16310 ATTTTACTATTTTA
1 ATTTTACTATTTTA
16324 ATTAAAAAAA
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
78 80 0.98
79 2 0.02
ACGTcount: A:0.35, C:0.13, G:0.02, T:0.50
Consensus pattern (78 bp):
ATTTTACTATTTTACTCAACTAAAAACACTATCTTTATTTAATTAAATCTAACATACTTATAACT
ATTTTAGTTTACC
Found at i:19032 original size:12 final size:12
Alignment explanation
Indices: 19015--19040 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
19005 CTAAGGACAA
19015 AGATTAAATGTG
1 AGATTAAATGTG
19027 AGATTAAATGTG
1 AGATTAAATGTG
19039 AG
1 AG
19041 CTGTTGAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.31
Consensus pattern (12 bp):
AGATTAAATGTG
Found at i:20080 original size:22 final size:22
Alignment explanation
Indices: 20054--20108 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
20044 ACTATAATAT
*
20054 CAAAAAATTATAGGGAGATTAA
1 CAAAAAATCATAGGGAGATTAA
** * *
20076 CAAAACCTCATAGGGAGGTTAT
1 CAAAAAATCATAGGGAGATTAA
20098 C-AAAAATCATA
1 CAAAAAATCATA
20109 AGAAGGTTAC
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.49, C:0.13, G:0.16, T:0.22
Consensus pattern (22 bp):
CAAAAAATCATAGGGAGATTAA
Found at i:20149 original size:23 final size:21
Alignment explanation
Indices: 20091--20152 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
20081 CCTCATAGGG
*
20091 AGGTTATCAAAA-ATCATAAGA
1 AGGTTA-CAAAATTTCATAAGA
*
20112 AGGTTACAAAATTTCATAGGA
1 AGGTTACAAAATTTCATAAGA
20133 AGGTTTACTAAAATTTCATA
1 AGG-TTAC-AAAATTTCATA
20153 TTTAGCTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.14
21 16 0.44
22 4 0.11
23 11 0.31
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.31
Consensus pattern (21 bp):
AGGTTACAAAATTTCATAAGA
Found at i:20207 original size:21 final size:21
Alignment explanation
Indices: 20083--20261 Score: 132
Period size: 22 Copynumber: 8.2 Consensus size: 21
20073 TAACAAAACC
* *
20083 TCATAGGGAGGTTATCAAAA-A
1 TCATAGGTA-GTTATCAAAATT
* *
20104 TCATAAGAAGGTTA-CAAAATT
1 TCATAGGTA-GTTATCAAAATT
*
20125 TCATAGGAAGGTT-TACTAAAATT
1 TCATAGGTA-GTTAT-C-AAAATT
** *
20148 TCATATTTAGCTTATCAAAGTT
1 TCATAGGTAG-TTATCAAAATT
*
20170 TCATATGG-AGCTTATCACAATT
1 TCATA-GGTAG-TTATCAAAATT
*
20192 TCATAGGTAATTATCAAAATT
1 TCATAGGTAGTTATCAAAATT
*
20213 TCATAGTGTGGTTATCAAAATT
1 TCATAG-GTAGTTATCAAAATT
*
20235 TAATAGGGTAGTTATCAAAATT
1 TCATA-GGTAGTTATCAAAATT
20257 TCATA
1 TCATA
20262 AAAATATTCA
Statistics
Matches: 129, Mismatches: 19, Indels: 19
0.77 0.11 0.11
Matches are distributed among these distances:
20 5 0.04
21 42 0.33
22 65 0.50
23 16 0.12
24 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.36
Consensus pattern (21 bp):
TCATAGGTAGTTATCAAAATT
Found at i:20215 original size:43 final size:44
Alignment explanation
Indices: 20159--20261 Score: 131
Period size: 43 Copynumber: 2.4 Consensus size: 44
20149 CATATTTAGC
* * *
20159 TTATCAAAGTTTCATA-TG-GAGCTTATCACAATTTCATA-GGTAA
1 TTATCAAAATTTCATAGTGTG-G-TTATCAAAATTTAATAGGGTAA
*
20202 TTATCAAAATTTCATAGTGTGGTTATCAAAATTTAATAGGGTAG
1 TTATCAAAATTTCATAGTGTGGTTATCAAAATTTAATAGGGTAA
20246 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
20262 AAAATATTCA
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
43 29 0.55
44 23 0.43
45 1 0.02
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.39
Consensus pattern (44 bp):
TTATCAAAATTTCATAGTGTGGTTATCAAAATTTAATAGGGTAA
Done.