Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023805.1 Corchorus olitorius cultivar O-4 contig23838, 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: 18157
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Found at i:363 original size:9 final size:9
Alignment explanation
Indices: 349--373 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
339 TACATGCCCG
349 GCCATCCGT
1 GCCATCCGT
358 GCCATCCGT
1 GCCATCCGT
367 GCCATCC
1 GCCATCC
374 TCCGCGCCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.48, G:0.20, T:0.20
Consensus pattern (9 bp):
GCCATCCGT
Found at i:743 original size:21 final size:21
Alignment explanation
Indices: 719--766 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
709 ACCCATTACT
*
719 GTGCCACCATCGG-TCAAGCCC
1 GTGCCACCACCGGCT-AAGCCC
*
740 GTGCCACCACCGGCTATGCCC
1 GTGCCACCACCGGCTAAGCCC
761 GTGCCA
1 GTGCCA
767 TCGCCATTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.17, C:0.44, G:0.25, T:0.15
Consensus pattern (21 bp):
GTGCCACCACCGGCTAAGCCC
Found at i:1144 original size:15 final size:14
Alignment explanation
Indices: 1124--1153 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1114 ATCTCTTTAA
1124 TTTTCCTTGCATTAT
1 TTTTCCTTG-ATTAT
1139 TTTTCCTTGATTAT
1 TTTTCCTTGATTAT
1153 T
1 T
1154 GCTTTAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTTCCTTGATTAT
Found at i:4001 original size:16 final size:15
Alignment explanation
Indices: 3980--4023 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
3970 TTACTCTGCT
3980 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
3996 TTGTTTTTTCTGTTTAA
1 TTG--TTTTCTGTTTAA
*
4013 TTGCTTTCTGT
1 TTGTTTTCTGT
4024 CAACCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 7 0.28
16 3 0.12
17 9 0.36
18 6 0.24
ACGTcount: A:0.11, C:0.09, G:0.14, T:0.66
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:11011 original size:22 final size:23
Alignment explanation
Indices: 10986--11032 Score: 87
Period size: 22 Copynumber: 2.1 Consensus size: 23
10976 ACAAGGGCTT
10986 AAGCTATATGATCAAAGTGC-AA
1 AAGCTATATGATCAAAGTGCGAA
11008 AAGCTATATGATCAAAGTGCGAA
1 AAGCTATATGATCAAAGTGCGAA
11031 AA
1 AA
11033 TATTAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.47, C:0.13, G:0.19, T:0.21
Consensus pattern (23 bp):
AAGCTATATGATCAAAGTGCGAA
Found at i:16929 original size:16 final size:17
Alignment explanation
Indices: 16908--16940 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
16898 AAAAGGGTTG
*
16908 TTAAAAA-AATTGTTTT
1 TTAAAAAGAAGTGTTTT
16924 TTAAAAAGAAGTGTTTT
1 TTAAAAAGAAGTGTTTT
16941 CATGCAAGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.45
Consensus pattern (17 bp):
TTAAAAAGAAGTGTTTT
Found at i:17373 original size:43 final size:42
Alignment explanation
Indices: 17185--17512 Score: 366
Period size: 41 Copynumber: 7.8 Consensus size: 42
17175 CAATAACCAA
*
17185 AAAGTCCCCAAACACATATATAACACATG-GGCAATTCTAT-TCC
1 AAAGTCCCCAAACACATATATAACACA-GAGGC-A-TCTATATAC
* * *
17228 AAAAGTCCTCAAACACATATATAACATAGAGGCACCTATAT-C
1 -AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATAC
* * ** *
17270 CAAGTCCCCAAACAC--ATATAACACAGGGGCGCCTTTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATA-TAC
* *
17311 AAAGTCCTCAAACACATATATAACATAGAGGCATCTATAT-C
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATAC
*
17352 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTAT-TAC
1 AAAGTCCCCAAACACATATATAACACAGAGGC-A-TCTATATAC
* *
17395 AAAGTCCTCAAACACATATATAACACAGAGGCATTTATAT-C
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATAC
* * *
17436 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAG
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATA-TAC
*
17479 AAAGTCCTCAAACACATATATAACACAGAGGCAT
1 AAAGTCCCCAAACACATATATAACACAGAGGCAT
17513 TTCTCCTTAT
Statistics
Matches: 243, Mismatches: 29, Indels: 25
0.82 0.10 0.08
Matches are distributed among these distances:
39 18 0.07
40 1 0.00
41 97 0.40
42 11 0.05
43 88 0.36
44 28 0.12
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21
Consensus pattern (42 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATAC
Found at i:17399 original size:84 final size:84
Alignment explanation
Indices: 17185--17512 Score: 516
Period size: 84 Copynumber: 3.9 Consensus size: 84
17175 CAATAACCAA
* * *
17185 AAAGTCCCCAAACACATATATAACACATGGGCAATTCTATTCCAAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC-AAAGTCCTCAAACACATATAT
* *
17250 AACATAGAGGCACCTATATC
65 AACACAGAGGCATCTATATC
* ** *
17270 CAAGTCCCCAAACAC--ATATAACACAGGGGCGCCTTTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
*
17333 ACATAGAGGCATCTATATC
66 ACACAGAGGCATCTATATC
17352 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
*
17417 ACACAGAGGCATTTATATC
66 ACACAGAGGCATCTATATC
* *
17436 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAGAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
17501 ACACAGAGGCAT
66 ACACAGAGGCAT
17513 TTCTCCTTAT
Statistics
Matches: 225, Mismatches: 16, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
82 54 0.24
83 20 0.09
84 137 0.61
85 14 0.06
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATC
Done.