Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024583.1 Corchorus olitorius cultivar O-4 contig24616, 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: 26792
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:210 original size:2 final size:2
Alignment explanation
Indices: 203--239 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
193 TATATTACAT
203 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
240 GAGGATTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:625 original size:107 final size:105
Alignment explanation
Indices: 453--715 Score: 411
Period size: 107 Copynumber: 2.5 Consensus size: 105
443 AGTTTAGCCA
* *
453 TAATTTCACTAAGTTTAGTCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
518 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
66 AATAA--TATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
* *
560 TAATTTCATTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
* *
625 AATAATATTGTTATAGGGTTTTAGAAATAAAATATATAAC
66 AATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
* ** *
665 TAA-TTCACTAAGTTTAACCCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
716 TAGAAAAATT
Statistics
Matches: 145, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
104 43 0.30
105 36 0.25
107 66 0.46
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (105 bp):
TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
AATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:1072 original size:42 final size:42
Alignment explanation
Indices: 1009--1095 Score: 149
Period size: 42 Copynumber: 2.1 Consensus size: 42
999 TGTCAAATAA
1009 CCTCCTTAGATTTAGGCACGATTTTAGC-CCAAGGTTTAGCCC
1 CCTCCTTAGATTTAGGCACGATTTTA-CTCCAAGGTTTAGCCC
*
1051 CCTCCTTAGATTTAGGTACGATTTTACTCCAAGGTTTAGCCC
1 CCTCCTTAGATTTAGGCACGATTTTACTCCAAGGTTTAGCCC
1093 CCT
1 CCT
1096 TTTAAAATAA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
41 1 0.02
42 42 0.98
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.33
Consensus pattern (42 bp):
CCTCCTTAGATTTAGGCACGATTTTACTCCAAGGTTTAGCCC
Found at i:12449 original size:11 final size:11
Alignment explanation
Indices: 12433--12458 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
12423 CCTTGCCTAA
12433 AAAACTAGAAG
1 AAAACTAGAAG
12444 AAAACTAGAAG
1 AAAACTAGAAG
12455 AAAA
1 AAAA
12459 GATCTAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:19459 original size:11 final size:11
Alignment explanation
Indices: 19443--19468 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
19433 CCTTGCCTAA
19443 AAAACTAGAAG
1 AAAACTAGAAG
19454 AAAACTAGAAG
1 AAAACTAGAAG
19465 AAAA
1 AAAA
19469 GATCTAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:20485 original size:71 final size:68
Alignment explanation
Indices: 20369--20510 Score: 223
Period size: 71 Copynumber: 2.0 Consensus size: 68
20359 TAAGCTTTTG
*
20369 TTAATATTAAGGATTTGACACATAAACCATTTTATAATTATTACTATATATATTTAATACTATTC
1 TTAATATTAAGGAGTTGACACATAAACCATTTTATAATTATTAC----TATATTTAATACTATTC
20434 AACAG-T
62 AACAGCT
*
20440 TTAATATTAAGGAGTTGACACATAATCCATTTTATAATTATTACTATATTTAATACTATTCAACA
1 TTAATATTAAGGAGTTGACACATAAACCATTTTATAATTATTACTATATTTAATACTATTCAACA
20505 GCT
66 GCT
20508 TTA
1 TTA
20511 GGGGACGGTG
Statistics
Matches: 68, Mismatches: 2, Indels: 5
0.91 0.03 0.07
Matches are distributed among these distances:
67 22 0.32
68 4 0.06
71 42 0.62
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.42
Consensus pattern (68 bp):
TTAATATTAAGGAGTTGACACATAAACCATTTTATAATTATTACTATATTTAATACTATTCAACA
GCT
Found at i:21089 original size:13 final size:13
Alignment explanation
Indices: 21071--21105 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
21061 CAAAGAGTGG
21071 TCAAGAAAATTTT
1 TCAAGAAAATTTT
21084 TCAAGAAAATTTT
1 TCAAGAAAATTTT
*
21097 CCAAGAAAA
1 TCAAGAAAA
21106 CAGAGTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (13 bp):
TCAAGAAAATTTT
Found at i:21186 original size:33 final size:31
Alignment explanation
Indices: 21148--21210 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 31
21138 AAAGAAAGGC
* *
21148 TAAAATTC-CAATTTGGTACTCTAAACGTTTAA
1 TAAAAATCTCAATTTGGTA-TCAAAAC-TTTAA
21180 TAAAAATCTCAATTTGGTATCAAAACTTTAA
1 TAAAAATCTCAATTTGGTATCAAAACTTTAA
21211 ACTGGCTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 5 0.18
32 13 0.46
33 10 0.36
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (31 bp):
TAAAAATCTCAATTTGGTATCAAAACTTTAA
Found at i:26691 original size:22 final size:21
Alignment explanation
Indices: 26650--26703 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
26640 CCATTAGTAC
*
26650 ATTATTTTTGGGGAGTCATTG
1 ATTATTTTTGGGGAGCCATTG
*
26671 ATTATTTTTGAGGGGGCCATTG
1 ATTATTTTTG-GGGAGCCATTG
*
26693 ATTGTTTTTGG
1 ATTATTTTTGG
26704 TATTATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 11 0.38
22 18 0.62
ACGTcount: A:0.17, C:0.06, G:0.30, T:0.48
Consensus pattern (21 bp):
ATTATTTTTGGGGAGCCATTG
Done.