Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002171.1 Hibiscus syriacus cultivar Beakdansim tig00004427_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: 71790
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:3335 original size:24 final size:24
Alignment explanation
Indices: 3308--3357 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
3298 ATAAAGAACC
3308 AAAATAAA-CTTAAACATACCATTA
1 AAAATAAAGCTTAAACAT-CCATTA
*
3332 AAAATAAAGTTTAAACATCCATTA
1 AAAATAAAGCTTAAACATCCATTA
3356 AA
1 AA
3358 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAAGCTTAAACATCCATTA
Found at i:8169 original size:30 final size:30
Alignment explanation
Indices: 8129--8190 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
8119 AATTCGACAT
**
8129 GACTCAAATTTTATAAACTTGACTCAACTC
1 GACTCAAATTTTATAAACCCGACTCAACTC
*
8159 GACTCGAATTTTATAAACCCGACTCAACTC
1 GACTCAAATTTTATAAACCCGACTCAACTC
8189 GA
1 GA
8191 AAAAATTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.35, C:0.26, G:0.10, T:0.29
Consensus pattern (30 bp):
GACTCAAATTTTATAAACCCGACTCAACTC
Found at i:21830 original size:25 final size:25
Alignment explanation
Indices: 21802--21850 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
21792 ATTTCTTTCT
21802 ATTATTTATATT-AGATCTTATTTTG
1 ATTATTT-TATTAAGATCTTATTTTG
* *
21827 ATTATTTTCTTAAGATTTTATTTT
1 ATTATTTTATTAAGATCTTATTTT
21851 ATTTAGTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 3 0.14
25 18 0.86
ACGTcount: A:0.27, C:0.04, G:0.06, T:0.63
Consensus pattern (25 bp):
ATTATTTTATTAAGATCTTATTTTG
Found at i:29195 original size:37 final size:36
Alignment explanation
Indices: 29120--29195 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
29110 TTTTTATATT
*
29120 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
29156 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
29193 TTT
1 TTT
29196 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:45158 original size:14 final size:15
Alignment explanation
Indices: 45139--45169 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
45129 AAAAGATTGA
45139 AATAAAG-AAAAATT
1 AATAAAGAAAAAATT
45153 AATAAAGAAAAAATT
1 AATAAAGAAAAAATT
45168 AA
1 AA
45170 ATGATACTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (15 bp):
AATAAAGAAAAAATT
Found at i:50283 original size:13 final size:13
Alignment explanation
Indices: 50265--50292 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
50255 AACACGTATC
50265 ATCATTCGATTGG
1 ATCATTCGATTGG
50278 ATCATTCGATTGG
1 ATCATTCGATTGG
50291 AT
1 AT
50293 GACTAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.39
Consensus pattern (13 bp):
ATCATTCGATTGG
Found at i:50597 original size:35 final size:30
Alignment explanation
Indices: 50522--50625 Score: 122
Period size: 30 Copynumber: 3.4 Consensus size: 30
50512 TTAAATTTTA
*
50522 AAAATATATTTTGTTTTTGTTTTAACTTAT
1 AAAATATATTTTATTTTTGTTTTAACTTAT
50552 AAAATATATTTTATTTTT-TTCTTAACTTAT
1 AAAATATATTTTATTTTTGTT-TTAACTTAT
* * * *
50582 TAAATATAATTTATTTTTATTTTAA-TGTAA
1 AAAATATATTTTATTTTTGTTTTAACT-TAT
50612 AAATATATATTTTA
1 AAA-ATATATTTTA
50626 GATTTATCAT
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
29 3 0.05
30 50 0.78
31 11 0.17
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (30 bp):
AAAATATATTTTATTTTTGTTTTAACTTAT
Found at i:50721 original size:30 final size:29
Alignment explanation
Indices: 50685--50780 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 29
50675 ATATATTTAA
50685 ATATTTTATTAATAA-TTT-AATATAAAATAT
1 ATATTTTATT-ATAATTTTAAAT-TAAAA-AT
*
50715 ATATTTTATTCTAATTTTAAATTAAAAAT
1 ATATTTTATTATAATTTTAAATTAAAAAT
* * *
50744 ATATTTTAATATTATCTTTAACTTTTAAAAAT
1 ATATTTTATTATAAT-TTTAA--ATTAAAAAT
50776 ATATT
1 ATATT
50781 AAAATATCTT
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
29 17 0.30
30 23 0.41
31 3 0.05
32 13 0.23
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (29 bp):
ATATTTTATTATAATTTTAAATTAAAAAT
Found at i:50865 original size:25 final size:25
Alignment explanation
Indices: 50837--50887 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
50827 ATTTTAAATT
50837 TTTTTAAAGTT-AAGATAAGAATAAA
1 TTTTTAAA-TTAAAGATAAGAATAAA
* *
50862 TTTTTTAATTAAATATAAGAATAAA
1 TTTTTAAATTAAAGATAAGAATAAA
50887 T
1 T
50888 ATATGTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 2 0.09
25 21 0.91
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (25 bp):
TTTTTAAATTAAAGATAAGAATAAA
Found at i:50956 original size:14 final size:14
Alignment explanation
Indices: 50921--50963 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
50911 TAAAATATTT
*
50921 AAATATATTTTAAGT
1 AAATATATTTTAA-A
*
50936 TAATATATTTTAAA
1 AAATATATTTTAAA
50950 AAATATATTTTAAA
1 AAATATATTTTAAA
50964 TGATGATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (14 bp):
AAATATATTTTAAA
Found at i:51067 original size:30 final size:29
Alignment explanation
Indices: 51002--51079 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 29
50992 ACATTAAAAT
* *
51002 AAAAATAAATTATATTTAATAAGTTAAGA
1 AAAAATAAAATATATTTTATAAGTTAAGA
51031 AGAAAATAAAATATATTTTATAAGTTACA-A
1 A-AAAATAAAATATATTTTATAAGTTA-AGA
*
51061 CAAAAATAAAAGATATTTT
1 -AAAAATAAAATATATTTT
51080 CAAAATTTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
29 1 0.02
30 40 0.93
31 2 0.05
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (29 bp):
AAAAATAAAATATATTTTATAAGTTAAGA
Found at i:53247 original size:19 final size:19
Alignment explanation
Indices: 53223--53267 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
53213 TACAATTTAG
53223 GTTATGAAATGCCCATCAT
1 GTTATGAAATGCCCATCAT
*
53242 GTTATGAAATGCCTATCAT
1 GTTATGAAATGCCCATCAT
53261 GTTATGA
1 GTTATGA
53268 TATGTAAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.36
Consensus pattern (19 bp):
GTTATGAAATGCCCATCAT
Found at i:53618 original size:18 final size:19
Alignment explanation
Indices: 53578--53628 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
53568 TATGAACTTG
*
53578 AAAATAAGCTATGAATCTA
1 AAAATAAGTTATGAATCTA
53597 AAAATAAGTTATGAATCT-
1 AAAATAAGTTATGAATCTA
53615 AAAATAAGTTATGA
1 AAAATAAGTTATGA
53629 GTCCGGAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 14 0.45
19 17 0.55
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.29
Consensus pattern (19 bp):
AAAATAAGTTATGAATCTA
Found at i:53795 original size:18 final size:18
Alignment explanation
Indices: 53772--53836 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 18
53762 TTAAAAAGAA
53772 TATGATATGATTATTATG
1 TATGATATGATTATTATG
* *
53790 TATGATATTGTTTATCATGG
1 TATGATA-TGATTATTAT-G
* *
53810 CTTTGATATGACTATTATG
1 -TATGATATGATTATTATG
53829 TATGATAT
1 TATGATAT
53837 TGTTTATCAT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
18 14 0.38
19 9 0.24
20 8 0.22
21 6 0.16
ACGTcount: A:0.29, C:0.05, G:0.17, T:0.49
Consensus pattern (18 bp):
TATGATATGATTATTATG
Found at i:53826 original size:39 final size:39
Alignment explanation
Indices: 53774--53848 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
53764 AAAAAGAATA
*
53774 TGATATGATTATTATGTATGATATTGTTTATCATGGCTT
1 TGATATGACTATTATGTATGATATTGTTTATCATGGCTT
53813 TGATATGACTATTATGTATGATATTGTTTATCATGG
1 TGATATGACTATTATGTATGATATTGTTTATCATGG
53849 TTTTTATAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.27, C:0.05, G:0.19, T:0.49
Consensus pattern (39 bp):
TGATATGACTATTATGTATGATATTGTTTATCATGGCTT
Found at i:55663 original size:23 final size:23
Alignment explanation
Indices: 55630--55727 Score: 99
Period size: 23 Copynumber: 4.3 Consensus size: 23
55620 GAGTCGAGGG
55630 TCTACGCGGTCCTTCGGGACAAT
1 TCTACGCGGTCCTTCGGGACAAT
* * * *
55653 TCTACGGGGTCATTCAGGACATT
1 TCTACGCGGTCCTTCGGGACAAT
55676 TCTACGCGGTCCTTCGGGACATAT
1 TCTACGCGGTCCTTCGGGACA-AT
* * * * *
55700 T-TATGTGGTACTTCGAGACATT
1 TCTACGCGGTCCTTCGGGACAAT
55722 TCTACG
1 TCTACG
55728 TGGCACATCA
Statistics
Matches: 59, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
22 2 0.03
23 55 0.93
24 2 0.03
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.32
Consensus pattern (23 bp):
TCTACGCGGTCCTTCGGGACAAT
Found at i:57187 original size:18 final size:17
Alignment explanation
Indices: 57152--57195 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
57142 CTCAAAATTA
*
57152 AATATTATTTTAAGTAAT
1 AATATT-TTTTAAATAAT
*
57170 TATATTTTTTATAATAAT
1 AATATTTTTTA-AATAAT
57188 AATATTTT
1 AATATTTT
57196 CACCCCATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
AATATTTTTTAAATAAT
Found at i:58034 original size:17 final size:17
Alignment explanation
Indices: 58002--58044 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
57992 AATATTTTTC
*
58002 AAAAAATATAAGAAAA-A
1 AAAAAAT-TTAGAAAATA
58019 AATAAAATTTAGAAAATA
1 AA-AAAATTTAGAAAATA
58037 AAAAAATT
1 AAAAAATT
58045 CAAGGTGACG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (17 bp):
AAAAAATTTAGAAAATA
Done.