Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004139.1 Hibiscus syriacus cultivar Beakdansim tig00009053_pilon, 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: 65448
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:18645 original size:18 final size:18
Alignment explanation
Indices: 18624--18670 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
18614 GGTTGTGGAG
*
18624 TTGGTTTCGGTTTCGGCT
1 TTGGCTTCGGTTTCGGCT
18642 TTGGCTTCGGTTTCGGCT
1 TTGGCTTCGGTTTCGGCT
*
18660 TCGGCTTCGGT
1 TTGGCTTCGGT
18671 GTTGGAGGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.00, C:0.21, G:0.34, T:0.45
Consensus pattern (18 bp):
TTGGCTTCGGTTTCGGCT
Found at i:18659 original size:12 final size:12
Alignment explanation
Indices: 18626--18669 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
18616 TTGTGGAGTT
*
18626 GGTTTCGGTTTC
1 GGTTTCGGCTTC
18638 GGCTTT-GGCTTC
1 GG-TTTCGGCTTC
18650 GGTTTCGGCTTC
1 GGTTTCGGCTTC
*
18662 GGCTTCGG
1 GGTTTCGG
18670 TGTTGGAGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 3 0.11
12 22 0.79
13 3 0.11
ACGTcount: A:0.00, C:0.23, G:0.36, T:0.41
Consensus pattern (12 bp):
GGTTTCGGCTTC
Found at i:24148 original size:5 final size:5
Alignment explanation
Indices: 24135--24165 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
24125 TAGTACTGAA
*
24135 GTTCC GTTCT GTTCT GTTCT GTTCT GTTCT G
1 GTTCT GTTCT GTTCT GTTCT GTTCT GTTCT G
24166 CTTTTCAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.23, G:0.23, T:0.55
Consensus pattern (5 bp):
GTTCT
Found at i:28003 original size:6 final size:6
Alignment explanation
Indices: 27992--28027 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
27982 AAAAAGGGAC
27992 AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG
1 AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG
28028 CCGCTAGAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (6 bp):
AGAGGG
Found at i:34289 original size:31 final size:30
Alignment explanation
Indices: 34215--34281 Score: 93
Period size: 31 Copynumber: 2.3 Consensus size: 30
34205 TAATTTTTGA
*
34215 AAATTTAAAAATTTAGGTATTAAAATAAAT
1 AAATTTAATAATTTAGGTATTAAAATAAAT
*
34245 CAAATTTAATAATTTAGGTATT-AAATACAT
1 -AAATTTAATAATTTAGGTATTAAAATAAAT
34275 -AATTTAA
1 AAATTTAA
34282 CCTTAATTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 7 0.21
30 7 0.21
31 20 0.59
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (30 bp):
AAATTTAATAATTTAGGTATTAAAATAAAT
Found at i:34788 original size:3 final size:3
Alignment explanation
Indices: 34780--34805 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
34770 CCAATGGCTC
34780 TGG TGG TGG TGG TGG TGG TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TG
34806 CTTGGAGACG
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:0.00, G:0.65, T:0.35
Consensus pattern (3 bp):
TGG
Found at i:35398 original size:21 final size:22
Alignment explanation
Indices: 35355--35403 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
35345 CGTCGAATAC
*
35355 TTTAA-ATATGTAAATATATAA
1 TTTAATATATGTAAAAATATAA
35376 TTTAATATATGTAAAAATA-AA
1 TTTAATATATGTAAAAATATAA
35397 TTTAATA
1 TTTAATA
35404 ATTAAATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (22 bp):
TTTAATATATGTAAAAATATAA
Found at i:43215 original size:21 final size:21
Alignment explanation
Indices: 43189--43245 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
43179 AAGGGGGTTA
43189 ACTGAAATCAATGGCTAAGGG
1 ACTGAAATCAATGGCTAAGGG
43210 ACTGAAATCAATGGCTAAGGG
1 ACTGAAATCAATGGCTAAGGG
*
43231 ACTAAAATCGAATGG
1 ACTGAAATC-AATGG
43246 ATCAATAAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 29 0.85
22 5 0.15
ACGTcount: A:0.40, C:0.14, G:0.26, T:0.19
Consensus pattern (21 bp):
ACTGAAATCAATGGCTAAGGG
Found at i:44386 original size:76 final size:76
Alignment explanation
Indices: 44251--44398 Score: 176
Period size: 76 Copynumber: 1.9 Consensus size: 76
44241 TTTAATTTCA
* * *
44251 TCCTTAAATTATGATTATCATTTTAAATTAGTCCTCAAACTTTTGAACATTTTAGTTTCATCCCC
1 TCCTGAAACTATGATTATCATTTTAAATTAGTCCTCAAACTTTTGAACATTTTAATTTCATCCCC
44316 AAACTATACCC
66 AAACTATACCC
** *
44327 TCCTGAAACTATGATTATTGTTTTAAATTGGTCC-CTAAACTTTT-AA-ATGGTTTAATTTCATC
1 TCCTGAAACTATGATTATCATTTTAAATTAGTCCTC-AAACTTTTGAACAT--TTTAATTTCATC
**
44389 CTTAAACTAT
63 CCCAAACTAT
44399 GATTATCATT
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
74 2 0.03
75 3 0.05
76 56 0.92
ACGTcount: A:0.31, C:0.19, G:0.07, T:0.43
Consensus pattern (76 bp):
TCCTGAAACTATGATTATCATTTTAAATTAGTCCTCAAACTTTTGAACATTTTAATTTCATCCCC
AAACTATACCC
Found at i:44456 original size:60 final size:59
Alignment explanation
Indices: 44332--44458 Score: 132
Period size: 60 Copynumber: 2.1 Consensus size: 59
44322 TACCCTCCTG
** * * **
44332 AAACTATGATTATTGTTTTAAATTGGTCCCTAAACTTTTAAATGGTTTAATTTCATCCTT
1 AAACTATGATTATCATTTTAAATTAGTCCCTAAACTTTTAAAT-GTTTAATTTAATCCCC
* *
44392 AAACTATGATTATCATTTTAAATTAGT-CATCAAACTTTTGAACAT-TTTAGTTTAATCCCC
1 AAACTATGATTATCATTTTAAATTAGTCCCT-AAACTTTT-AA-ATGTTTAATTTAATCCCC
44452 AAACTAT
1 AAACTAT
44459 ACCCTTCATT
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
59 2 0.04
60 50 0.89
61 2 0.04
62 2 0.04
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.43
Consensus pattern (59 bp):
AAACTATGATTATCATTTTAAATTAGTCCCTAAACTTTTAAATGTTTAATTTAATCCCC
Found at i:44717 original size:33 final size:32
Alignment explanation
Indices: 44649--44716 Score: 111
Period size: 32 Copynumber: 2.1 Consensus size: 32
44639 TTTGATTCGG
*
44649 CCCCTCATTTTCTATGGTTAATTATACTTTGC
1 CCCCTCATTTTCTATGATTAATTATACTTTGC
44681 CCCCTCAATTTT-TATGATTAATTATACTTTGC
1 CCCCTC-ATTTTCTATGATTAATTATACTTTGC
44713 CCCC
1 CCCC
44717 CCCTTAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 29 0.85
33 5 0.15
ACGTcount: A:0.21, C:0.28, G:0.07, T:0.44
Consensus pattern (32 bp):
CCCCTCATTTTCTATGATTAATTATACTTTGC
Found at i:44942 original size:60 final size:60
Alignment explanation
Indices: 44869--45026 Score: 199
Period size: 60 Copynumber: 2.6 Consensus size: 60
44859 ATGAAATTGG
* * * *
44869 AAAGTTTAGGGACTAATTTAGAATAAGTGTCATAGTTTAAGGATGAAATTGGAATGTTTA
1 AAAGTTTAGGGACTAATTTAGAATGAGTGTCATAGTTTAAGGATGAAATTAGAATATTAA
* * * * * * *
44929 AAAGTTTAAGGACTAATTTATAATGAGTATTACAGTTTGAGGATGAAATTATAATATTAA
1 AAAGTTTAGGGACTAATTTAGAATGAGTGTCATAGTTTAAGGATGAAATTAGAATATTAA
* *
44989 AAAATTTAGGGACTAATTTAGAATGAGAGTCATAGTTT
1 AAAGTTTAGGGACTAATTTAGAATGAGTGTCATAGTTT
45027 GGGGAAATTT
Statistics
Matches: 80, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 80 1.00
ACGTcount: A:0.41, C:0.04, G:0.20, T:0.35
Consensus pattern (60 bp):
AAAGTTTAGGGACTAATTTAGAATGAGTGTCATAGTTTAAGGATGAAATTAGAATATTAA
Found at i:46034 original size:2 final size:2
Alignment explanation
Indices: 46027--46057 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
46017 ATTCTTTGAT
46027 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
46058 TGTTATCCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:59081 original size:10 final size:9
Alignment explanation
Indices: 59053--59080 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
59043 ATAGTTTATT
59053 ATTAAAAAA
1 ATTAAAAAA
59062 ATTAAAAAA
1 ATTAAAAAA
59071 ATTAAAAAA
1 ATTAAAAAA
59080 A
1 A
59081 ACGATAGACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
ATTAAAAAA
Found at i:62184 original size:14 final size:15
Alignment explanation
Indices: 62165--62197 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
62155 TTAGATATCC
*
62165 TTTTTCTT-TTGATA
1 TTTTTCTTATTAATA
62179 TTTTTCTTATTAATA
1 TTTTTCTTATTAATA
62194 TTTT
1 TTTT
62198 CTTCTGCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.73
Consensus pattern (15 bp):
TTTTTCTTATTAATA
Found at i:65219 original size:23 final size:23
Alignment explanation
Indices: 65192--65238 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
65182 TTAAAATTTA
65192 ATTTAATAAAAA-ATATATTATAT
1 ATTTAATAAAAATATATA-TATAT
**
65215 ATTTAATTTAAATATATATATAT
1 ATTTAATAAAAATATATATATAT
65238 A
1 A
65239 CCCGACCCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTTAATAAAAATATATATATAT
Found at i:65235 original size:28 final size:26
Alignment explanation
Indices: 65170--65237 Score: 73
Period size: 28 Copynumber: 2.5 Consensus size: 26
65160 ATATATATAT
65170 ATATATATAATATTAAAATTTAATTTA
1 ATATATAT-ATATTAAAATTTAATTTA
* * *
65197 ATAAAAAATATATTATATATTTAATTTAA
1 AT-ATATATATATTA-AAATTTAATTT-A
65226 ATATATATATAT
1 ATATATATATAT
65238 ACCCGACCCG
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
27 8 0.24
28 22 0.67
29 3 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
ATATATATATATTAAAATTTAATTTA
Found at i:65268 original size:24 final size:24
Alignment explanation
Indices: 65236--65290 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
65226 ATATATATAT
* * *
65236 ATACCCGACCCGATTCTCGGCCCA
1 ATACCCGACCCAATACCCGGCCCA
65260 ATACCCGACCCAATACCCGGCCCA
1 ATACCCGACCCAATACCCGGCCCA
65284 ATACCCG
1 ATACCCG
65291 TTTAAATAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.25, C:0.47, G:0.15, T:0.13
Consensus pattern (24 bp):
ATACCCGACCCAATACCCGGCCCA
Found at i:65273 original size:12 final size:12
Alignment explanation
Indices: 65236--65290 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
65226 ATATATATAT
*
65236 ATACCCGACCCG
1 ATACCCGACCCA
* * *
65248 ATTCTCGGCCCA
1 ATACCCGACCCA
65260 ATACCCGACCCA
1 ATACCCGACCCA
*
65272 ATACCCGGCCCA
1 ATACCCGACCCA
65284 ATACCCG
1 ATACCCG
65291 TTTAAATAAC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.25, C:0.47, G:0.15, T:0.13
Consensus pattern (12 bp):
ATACCCGACCCA
Done.