Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018066.1 Corchorus olitorius cultivar O-4 contig18099, 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: 64982
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:3167 original size:17 final size:17
Alignment explanation
Indices: 3141--3174 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3131 TGATTCAACA
3141 TGCATCAGAATAGCTGG
1 TGCATCAGAATAGCTGG
*
3158 TGCATGAGAATAGCTGG
1 TGCATCAGAATAGCTGG
3175 AGAGACTTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.15, G:0.32, T:0.24
Consensus pattern (17 bp):
TGCATCAGAATAGCTGG
Found at i:20221 original size:27 final size:27
Alignment explanation
Indices: 20190--20246 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
20180 ACCTCTTAGC
20190 GAACTGTCTTACTAATGATAACGAATT
1 GAACTGTCTTACTAATGATAACGAATT
20217 GAACTGTCTTACTAATGATAACGAATT
1 GAACTGTCTTACTAATGATAACGAATT
20244 GAA
1 GAA
20247 TACATTCTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (27 bp):
GAACTGTCTTACTAATGATAACGAATT
Found at i:20495 original size:43 final size:43
Alignment explanation
Indices: 20447--20543 Score: 185
Period size: 43 Copynumber: 2.3 Consensus size: 43
20437 GATCCTTCCC
20447 TACAAAATGCCTATCAACCTATCAAGGTTCCTCAATTTTTACT
1 TACAAAATGCCTATCAACCTATCAAGGTTCCTCAATTTTTACT
*
20490 TACAAAATGCCTATCAACCTATCAGGGTTCCTCAATTTTTACT
1 TACAAAATGCCTATCAACCTATCAAGGTTCCTCAATTTTTACT
20533 TACAAAATGCC
1 TACAAAATGCC
20544 GTAAGATATT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 53 1.00
ACGTcount: A:0.33, C:0.26, G:0.08, T:0.33
Consensus pattern (43 bp):
TACAAAATGCCTATCAACCTATCAAGGTTCCTCAATTTTTACT
Found at i:20622 original size:41 final size:41
Alignment explanation
Indices: 20577--20657 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
20567 AGAATGAAAT
20577 CAGAAAATCAACCTATCAGGTTTCAAGTAATATATAGTAAA
1 CAGAAAATCAACCTATCAGGTTTCAAGTAATATATAGTAAA
20618 CAGAAAATCAACCTATCAGGTTTCAAGTAATATATAGTAA
1 CAGAAAATCAACCTATCAGGTTTCAAGTAATATATAGTAA
20658 TAAAGAGGGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (41 bp):
CAGAAAATCAACCTATCAGGTTTCAAGTAATATATAGTAAA
Found at i:33516 original size:26 final size:26
Alignment explanation
Indices: 33482--33533 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
33472 TGCATACATG
* *
33482 AAAAGATTGAAGCATGAAAATGATGA
1 AAAAAATTGAAACATGAAAATGATGA
33508 AAAAAATTGAAACATGAAAATGATGA
1 AAAAAATTGAAACATGAAAATGATGA
33534 TAGGTGACTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.58, C:0.04, G:0.19, T:0.19
Consensus pattern (26 bp):
AAAAAATTGAAACATGAAAATGATGA
Found at i:36881 original size:113 final size:110
Alignment explanation
Indices: 36635--36844 Score: 314
Period size: 113 Copynumber: 1.9 Consensus size: 110
36625 CTCTTTGCTC
* *
36635 TTAAATGCATCATTTATGCATGATAACATATTAGCCTTACATCATAAATCACATAAACCACAACA
1 TTAAATGCATCATTCATGCATGATAACAGATTAGCCTTACATCATAAATCACATAAACCACAACA
* * *
36700 GAAATTTCAGTACCTATTAATCGAAAAACAGTTAACTCTTTGCTG
66 GAAATTCCAGTACCTATTAATCGAAAAACAGTTAACACTTTGATG
*
36745 TTAAATGCATCATTGATGCATGATAACAGATTAGCC-TACATCATAAATCACATGAATGAACCAC
1 TTAAATGCATCATTCATGCATGATAACAGATTAGCCTTACATCATAAATCACAT--A--AACCAC
*
36809 AACAGAAATTCCATTACCTATTAATCGAAAAACAGT
62 AACAGAAATTCCAGTACCTATTAATCGAAAAACAGT
36845 AAACTTGAAT
Statistics
Matches: 92, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
109 17 0.18
110 34 0.37
111 1 0.01
113 40 0.43
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (110 bp):
TTAAATGCATCATTCATGCATGATAACAGATTAGCCTTACATCATAAATCACATAAACCACAACA
GAAATTCCAGTACCTATTAATCGAAAAACAGTTAACACTTTGATG
Found at i:46892 original size:3 final size:3
Alignment explanation
Indices: 46886--46911 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
46876 ATCCGAACTA
46886 CTG CTG CTG CTG CTG CTG CTG CTG CT
1 CTG CTG CTG CTG CTG CTG CTG CTG CT
46912 AGAGCTCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.31, T:0.35
Consensus pattern (3 bp):
CTG
Found at i:48367 original size:16 final size:16
Alignment explanation
Indices: 48335--48364 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
48325 AGTGTCATCT
48335 TTTAATTATGTCATTA
1 TTTAATTATGTCATTA
48351 TTTAATTAT-TCATT
1 TTTAATTATGTCATT
48365 TATGCCCACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (16 bp):
TTTAATTATGTCATTA
Found at i:50416 original size:50 final size:50
Alignment explanation
Indices: 50340--50440 Score: 157
Period size: 50 Copynumber: 2.0 Consensus size: 50
50330 GTCATGTGAT
50340 TTAGTATTATTAAGGACAGCCAGCATGTTCAATGTTAATATATCTAATAA
1 TTAGTATTATTAAGGACAGCCAGCATGTTCAATGTTAATATATCTAATAA
** * * *
50390 TTAGTATTATTAAGGATGGTCGGCATGTTCAATGTTAATATATCTAGTAA
1 TTAGTATTATTAAGGACAGCCAGCATGTTCAATGTTAATATATCTAATAA
50440 T
1 T
50441 AAACTTCAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.39
Consensus pattern (50 bp):
TTAGTATTATTAAGGACAGCCAGCATGTTCAATGTTAATATATCTAATAA
Found at i:55680 original size:13 final size:14
Alignment explanation
Indices: 55646--55678 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
55636 ATTTTTTTTT
55646 AAAAAAA-AAAAAG
1 AAAAAAAGAAAAAG
55659 AAAAAAAGAAAAAG
1 AAAAAAAGAAAAAG
55673 AAAAAA
1 AAAAAA
55679 GATTACCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Found at i:63656 original size:1 final size:1
Alignment explanation
Indices: 63612--63639 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
63602 AATCAGCCAC
63612 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
63640 GCTGTTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.