Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001354.1 Hibiscus syriacus cultivar Beakdansim tig00002637_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: 71038
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:592 original size:25 final size:28
Alignment explanation
Indices: 536--592 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 28
526 ATTAACAGTT
**
536 AAATCTAATAATTATATTTTTATGCATG
1 AAATCTAATAATTATATTTTTATGCAAA
*
564 AAATCT-A-AATTA-ATTTTTATTCAAA
1 AAATCTAATAATTATATTTTTATGCAAA
589 AAAT
1 AAAT
593 ATATGTATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 14 0.54
26 5 0.19
27 1 0.04
28 6 0.23
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.44
Consensus pattern (28 bp):
AAATCTAATAATTATATTTTTATGCAAA
Found at i:5624 original size:21 final size:21
Alignment explanation
Indices: 5600--5645 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
5590 AGACAAATGA
* *
5600 TGTTCTCTCATCTCAAAATTC
1 TGTTATCTCATCTCAAAACTC
* *
5621 TGTTATTTCATCTGAAAACTC
1 TGTTATCTCATCTCAAAACTC
5642 TGTT
1 TGTT
5646 GAGTTTTCAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.46
Consensus pattern (21 bp):
TGTTATCTCATCTCAAAACTC
Found at i:12093 original size:232 final size:231
Alignment explanation
Indices: 11366--12766 Score: 2511
Period size: 232 Copynumber: 6.0 Consensus size: 231
11356 AAGGGGCAAA
*
11366 AACAATTTTTAATAGAAAATACAAAGAAAATATCTAAAATATATAGAAATTTCACCCTAAAATGA
1 AACAATTTTCAATAGAAAATACAAAGAAAATATCTAAAATATATAGAAATTTCACCCTAAAATGA
11431 CACGAGTATAGAAGGTTATGCAAACAATAAAGTTAGGTGAATATCAACGAACTG--AAAAAAAAC
66 CACGAGTATAGAAGGTTATGCAAACAATAAAGTTAGGTGAATATCAACGAACTGAAAAAAAAAAC
*
11494 CTTCTTTTCCTTGAAGAAAAGGAGTAATATCCAACCGGATAGTGGTGTAACGACTGTTATATTGC
131 CTTCTTTTCCTTGAAGAAAAGGAGTAATATCCAACCGGATAGTGGTGTAACGACTGTTATATAGC
* *
11559 AAAGCAGCACAATCTAAAATTATTATTGTCAAAAAT
196 AGAGCGGCACAATCTAAAATTATTATTGTCAAAAAT
11595 AACAATTTTCAATAGAAAATACAAAGAAAATATCTAAAATATATAGAAATTTCACCCTAAAATGA
1 AACAATTTTCAATAGAAAATACAAAGAAAATATCTAAAATATATAGAAATTTCACCCTAAAATGA
* * * *
11660 CACGAGTATAGAAGGTTATACAAACAATAAAGTTTGGCGAATATCAACGAATTGAAAAAAAAAAC
66 CACGAGTATAGAAGGTTATGCAAACAATAAAGTTAGGTGAATATCAACGAACTGAAAAAAAAAAC
11725 CTTCTTTTCCTTGAAGAAAAGGAGTAATATCCAACCGGATAGTGGTGTAACGACTGTTATATAGC
131 CTTCTTTTCCTTGAAGAAAAGGAGTAATATCCAACCGGATAGTGGTGTAACGACTGTTATATAGC
11790 AGAGCGGCACAATCTAAAATTATTATTGTCAAAAAT
196 AGAGCGGCACAATCTAAAATTATTATTGTCAAAAAT
11826 AACAATTTTCAATAGAAAATACAAAGAAAATATCTAAAATATATAGAAATTTCACCCTAAAATGA
1 AACAATTTTCAATAGAAAATACAAAGAAAATATCTAAAATATATAGAAATTTCACCCTAAAATGA
*
11891 CACGAGTATAGAAGGTTATGCAAATAATAAAGTTAGGTGAATATCAACGAACTGAAAAAAAAAAA
66 CACGAGTATAGAAGGTTATGCAAACAATAAAGTTAGGTGAATATCAACGAACTG-AAAAAAAAAA
11956 CCTTCTTTTCCTTGAAGAAAAGGAGTAATATCCAACCGGATAGTGGTGTAACGACTGTTATATAG
130 CCTTCTTTTCCTTGAAGAAAAGGAGTAATATCCAACCGGATAGTGGTGTAACGACTGTTATATAG
12021 CAGAGCGGCACAATCTAAAATTATTATTGTCAAAAAT
195 CAGAGCGGCACAATCTAAAATTATTATTGTCAAAAAT
*
12058 AACAATTTTCAATAGAAAATACAAAGAAAATATCTAAAATATATAGAAATTTCACCCCTAAACTG
1 AACAATTTTCAATAGAAAATACAAAGAAAATATCTAAAATATATAGAAATTTCA-CCCTAAAATG
12123 ACACGAGTATAGAAGGTTATGCAAACAATAAAGTTAGGTGAATATCAACGAACTGAAAAAAAAAA
65 ACACGAGTATAGAAGGTTATGCAAACAATAAAGTTAGGTGAATATCAACGAACTGAAAAAAAAAA
12188 CCTTCTTTTCCTTGAAGAAAAGGAGTAATATCCAACCGGATAGTGGTGTAACGACTGTTATATAG
130 CCTTCTTTTCCTTGAAGAAAAGGAGTAATATCCAACCGGATAGTGGTGTAACGACTGTTATATAG
12253 CAGAGCGGCACAATCTAAAATTATTATTGTCAAAAAT
195 CAGAGCGGCACAATCTAAAATTATTATTGTCAAAAAT
12290 AACAATTTTCAATAGAAAATACAAAGAAAATATCTAAAATATATAGAAATTTCACCCTAAAATGA
1 AACAATTTTCAATAGAAAATACAAAGAAAATATCTAAAATATATAGAAATTTCACCCTAAAATGA
* *
12355 CATGAGTATAGAAGGTTATGCAAACAATAAAGTTAGGTGAATATCAACGAACTGGGAAAAAAAAA
66 CACGAGTATAGAAGGTTATGCAAACAATAAAGTTAGGTGAATATCAACGAACT-GAAAAAAAAAA
12420 CCTTCTTTTCCTTGAAGAAAAGGAGTAATATCCAACCGGATAGTGGTGTAACGACTGTTATATAG
130 CCTTCTTTTCCTTGAAGAAAAGGAGTAATATCCAACCGGATAGTGGTGTAACGACTGTTATATAG
*
12485 TAGAGCGGCACAATCTAAAATTATTATTGTCAAAAAT
195 CAGAGCGGCACAATCTAAAATTATTATTGTCAAAAAT
12522 AACAATTTTCAATAGAAAATACAAAGAAAATACAAAGAAAATATCTAAAATATATAGAAATTTCA
1 AACAATTTTC-------AAT----AGAAAATACAAAGAAAATATCTAAAATATATAGAAATTTCA
*
12587 CCCTAAACTGACACGAGTATAGAAGGTTATGCAAACAATAAAGTTAGGTGAATATCAACGAACTG
55 CCCTAAAATGACACGAGTATAGAAGGTTATGCAAACAATAAAGTTAGGTGAATATCAACGAACTG
12652 -AAAAAAAAACCTTCTTTTCCTTGAAGAAAAGGAGTAATATCCAACCGGATAGTGGTGTAACGAC
120 AAAAAAAAAACCTTCTTTTCCTTGAAGAAAAGGAGTAATATCCAACCGGATAGTGGTGTAACGAC
* *
12716 TGTTATATAGCAGAGTGGCACAATCTAAAATTACTATTGTCAAAAAT
185 TGTTATATAGCAGAGCGGCACAATCTAAAATTATTATTGTCAAAAAT
12763 AACA
1 AACA
12767 GTGGATAATA
Statistics
Matches: 1132, Mismatches: 24, Indels: 20
0.96 0.02 0.02
Matches are distributed among these distances:
229 114 0.10
231 283 0.25
232 453 0.40
233 63 0.06
239 3 0.00
241 112 0.10
242 1 0.00
243 103 0.09
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (231 bp):
AACAATTTTCAATAGAAAATACAAAGAAAATATCTAAAATATATAGAAATTTCACCCTAAAATGA
CACGAGTATAGAAGGTTATGCAAACAATAAAGTTAGGTGAATATCAACGAACTGAAAAAAAAAAC
CTTCTTTTCCTTGAAGAAAAGGAGTAATATCCAACCGGATAGTGGTGTAACGACTGTTATATAGC
AGAGCGGCACAATCTAAAATTATTATTGTCAAAAAT
Found at i:12551 original size:11 final size:11
Alignment explanation
Indices: 12535--12564 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
12525 AATTTTCAAT
12535 AGAAAATACAA
1 AGAAAATACAA
12546 AGAAAATACAA
1 AGAAAATACAA
12557 AGAAAATA
1 AGAAAATA
12565 TCTAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.73, C:0.07, G:0.10, T:0.10
Consensus pattern (11 bp):
AGAAAATACAA
Found at i:14042 original size:60 final size:60
Alignment explanation
Indices: 13929--14043 Score: 164
Period size: 60 Copynumber: 1.9 Consensus size: 60
13919 ATAGTCGGGT
* *
13929 GATCATTTTGTAACTTTTAATAGTCGATGGACTCAATAAAATAGTTCTTTATAGTTGAAG
1 GATCATTTTGTAACTTTTAATAGTCGATGGACTCAATAAAATAATTCTCTATAGTTGAAG
13989 GATCATTTTGTAACTTTTAATAGTC-A-GGTAACTCAATAAAATAATAT-TCTATAGT
1 GATCATTTTGTAACTTTTAATAGTCGATGG--ACTCAATAAAATAAT-TCTCTATAGT
14044 GGGGGGCCAT
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
58 2 0.04
59 1 0.02
60 46 0.92
61 1 0.02
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (60 bp):
GATCATTTTGTAACTTTTAATAGTCGATGGACTCAATAAAATAATTCTCTATAGTTGAAG
Found at i:17498 original size:129 final size:130
Alignment explanation
Indices: 17328--17561 Score: 326
Period size: 129 Copynumber: 1.8 Consensus size: 130
17318 CTGTTGACTA
* * * * * * *
17328 TTGACTTTGACCAAAAAGTTAAATTTTTTCGACATGTCATATTTTATGTTTTTTGACGTACTAAA
1 TTGACTTTGACCAAAAAGTCAAATATTTTCAAAAAGCCATATTTTATGTTTTTCGACGTACTAAA
*
17393 TCCGATTCCGAAGTCCAATTTGCCAAATTCGAACCCGAAAGCCTCAAAATCGCCAGTAAAACCCG
66 TCCGATTCCGAAGTCCAATTTGCCAAATTAGAACCCGAAAGCCTCAAAATCGCCAGTAAAACCCG
* * *
17458 TTGACTTTGACCAAAAAGTCAAA-ATTTTCAAAAAGCCATATTTTATGTTTTTCGATGTCCTGAA
1 TTGACTTTGACCAAAAAGTCAAATATTTTCAAAAAGCCATATTTTATGTTTTTCGACGTACTAAA
* ** *
17522 TCTGATTCCGAAGTCCGTTTTGCCAAATTATAACCCGAAA
66 TCCGATTCCGAAGTCCAATTTGCCAAATTAGAACCCGAAA
17562 ACCCCGAATT
Statistics
Matches: 89, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
129 67 0.75
130 22 0.25
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (130 bp):
TTGACTTTGACCAAAAAGTCAAATATTTTCAAAAAGCCATATTTTATGTTTTTCGACGTACTAAA
TCCGATTCCGAAGTCCAATTTGCCAAATTAGAACCCGAAAGCCTCAAAATCGCCAGTAAAACCCG
Found at i:19465 original size:21 final size:20
Alignment explanation
Indices: 19441--19489 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
19431 CTCAAAATCA
* *
19441 TTTTTCAAAATTTCATTTTG
1 TTTTTCAAAATCTAATTTTG
19461 TTTTTCAAAATCTAATTTTG
1 TTTTTCAAAATCTAATTTTG
*
19481 CTTTT-AAAA
1 TTTTTCAAAA
19490 GAAAATCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.31, C:0.10, G:0.04, T:0.55
Consensus pattern (20 bp):
TTTTTCAAAATCTAATTTTG
Found at i:21683 original size:35 final size:35
Alignment explanation
Indices: 21637--21704 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 35
21627 ATGTGCAGGG
21637 GAACAGATTCCCCCCT-GGGGGCATCGATTCCCCGA
1 GAACAGATT-CCCCCTGGGGGGCATCGATTCCCCGA
*
21672 GAACAGATTCCCCCTGGGGGGTATCGATTCCCC
1 GAACAGATTCCCCCTGGGGGGCATCGATTCCCC
21705 CCTAAATGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 6 0.19
35 25 0.81
ACGTcount: A:0.19, C:0.35, G:0.26, T:0.19
Consensus pattern (35 bp):
GAACAGATTCCCCCTGGGGGGCATCGATTCCCCGA
Found at i:22606 original size:38 final size:38
Alignment explanation
Indices: 22551--22648 Score: 124
Period size: 38 Copynumber: 2.6 Consensus size: 38
22541 TATAAGACAT
* * * * *
22551 ATGATAGGTCCTACGGGACACATATTACATCTTTCGAG
1 ATGACAGGTCCTTCGGGACACAGATGACATCCTTCGAG
* *
22589 ATGACAGGTCTTTCGGGACACAGATGACATCCTTCGGG
1 ATGACAGGTCCTTCGGGACACAGATGACATCCTTCGAG
*
22627 ATGATAGGTCCTTCGGGACACA
1 ATGACAGGTCCTTCGGGACACA
22649 ATTTATACGA
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 51 1.00
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.26
Consensus pattern (38 bp):
ATGACAGGTCCTTCGGGACACAGATGACATCCTTCGAG
Found at i:40810 original size:25 final size:25
Alignment explanation
Indices: 40781--40832 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
40771 TAAGTATGAT
*
40781 CTAATTCATACTTAGCTAAACTCCA
1 CTAATCCATACTTAGCTAAACTCCA
*
40806 CTAATCCATGCTTAGCTAAACTCCA
1 CTAATCCATACTTAGCTAAACTCCA
40831 CT
1 CT
40833 TAGCCTAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.33, C:0.31, G:0.06, T:0.31
Consensus pattern (25 bp):
CTAATCCATACTTAGCTAAACTCCA
Found at i:51415 original size:62 final size:63
Alignment explanation
Indices: 51227--51424 Score: 380
Period size: 63 Copynumber: 3.2 Consensus size: 63
51217 AGATTTCCTT
51227 ACCAGCAAAAATCTGAGGTGGAAAGCCAAAATAATAGAATTGTTGGCTGCATCGGTGATTAAG
1 ACCAGCAAAAATCTGAGGTGGAAAGCCAAAATAATAGAATTGTTGGCTGCATCGGTGATTAAG
51290 ACCAGCAAAAATCTGAGGTGGAAAGCCAAAATAATAGAATTGTTGGCTGCATCGGTGATTAAG
1 ACCAGCAAAAATCTGAGGTGGAAAGCCAAAATAATAGAATTGTTGGCTGCATCGGTGATTAAG
*
51353 ACCAGCAAAAATCTGAGGTGGAAAGCC-AAATAATAGAATTGTTGGCTGCATCAGTGATTAAG
1 ACCAGCAAAAATCTGAGGTGGAAAGCCAAAATAATAGAATTGTTGGCTGCATCGGTGATTAAG
51415 ACCAGCAAAA
1 ACCAGCAAAA
51425 GTCCCTCTGT
Statistics
Matches: 134, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
62 44 0.33
63 90 0.67
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.21
Consensus pattern (63 bp):
ACCAGCAAAAATCTGAGGTGGAAAGCCAAAATAATAGAATTGTTGGCTGCATCGGTGATTAAG
Found at i:56281 original size:19 final size:20
Alignment explanation
Indices: 56237--56281 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
56227 ATTTGTTTTT
56237 AATAAATTTTTATCTATTAA
1 AATAAATTTTTATCTATTAA
*
56257 ATTAAATTTTTAT-T-TTCAA
1 AATAAATTTTTATCTATT-AA
56276 AATAAA
1 AATAAA
56282 ATATTAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 8 0.36
20 12 0.55
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (20 bp):
AATAAATTTTTATCTATTAA
Found at i:56310 original size:14 final size:13
Alignment explanation
Indices: 56282--56317 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
56272 TCAAAATAAA
56282 ATATTAAAATAGT
1 ATATTAAAATAGT
*
56295 ATATTAATATTAGT
1 ATATTAA-AATAGT
56309 ATATTAAAA
1 ATATTAAAA
56318 GATAACTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.42
Consensus pattern (13 bp):
ATATTAAAATAGT
Found at i:60702 original size:60 final size:58
Alignment explanation
Indices: 60607--60737 Score: 149
Period size: 60 Copynumber: 2.2 Consensus size: 58
60597 ATATTAGGGT
* *
60607 AAAGTATAC-AAATGGTCTCCCGATTATAGGTTGTTGCTTTATTGAGTCTTCAAACTATTA
1 AAAGT-TACAAAATGGTCTCCCGACTATAGGATGTTGCTTTATTGAGTC--CAAACTATTA
* * * **
60667 AAAGTTACAAAATGGTC-CCTCGACTATATGATGTTGTTTTGTTGAGTCCCGACTATTA
1 AAAGTTACAAAATGGTCTCC-CGACTATAGGATGTTGCTTTATTGAGTCCAAACTATTA
60725 AAAGTTACAAAAT
1 AAAGTTACAAAAT
60738 AATCATCTAA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
58 21 0.34
59 5 0.08
60 36 0.58
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (58 bp):
AAAGTTACAAAATGGTCTCCCGACTATAGGATGTTGCTTTATTGAGTCCAAACTATTA
Found at i:63878 original size:30 final size:30
Alignment explanation
Indices: 63812--63898 Score: 97
Period size: 30 Copynumber: 2.9 Consensus size: 30
63802 AGGCTTGAGA
63812 GCCTACCCAAGAAAGTTCTCAGGGCCACGGG
1 GCCTACCCAAGAAAGTTCTCAGGGCCAC-GG
* *
63843 GCCTACCCAAGAAAGATT-TCGGGGCGCA-TG
1 GCCTACCCAAGAAAG-TTCTCAGGGC-CACGG
* *
63873 GCCTACCCAAGAATGATCTCAGGGCC
1 GCCTACCCAAGAAAGTTCTCAGGGCC
63899 GTAGAGCCTA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
29 2 0.04
30 21 0.44
31 21 0.44
32 4 0.08
ACGTcount: A:0.26, C:0.31, G:0.28, T:0.15
Consensus pattern (30 bp):
GCCTACCCAAGAAAGTTCTCAGGGCCACGG
Found at i:68178 original size:31 final size:31
Alignment explanation
Indices: 68143--68257 Score: 110
Period size: 31 Copynumber: 3.7 Consensus size: 31
68133 GAGCATCTTG
*
68143 GGGCCTAAGAGCCTACCCAAGAAAGTTCTCA
1 GGGCCTAAGAGCCTACCCAAGAAAGATCTCA
* * *
68174 GGGCC-ACGAGGCCTACCCAAGAAAAATCCCA
1 GGGCCTAAGA-GCCTACCCAAGAAAGATCTCA
* *
68205 GGG-CTGCAAG-GCCTACACAAGAATGATCTCA
1 GGGCCT--AAGAGCCTACCCAAGAAAGATCTCA
**
68236 GGGCCGCAGAGCCTACCCAAGA
1 GGGCCTAAGAGCCTACCCAAGA
68258 GTCACATTAG
Statistics
Matches: 66, Mismatches: 12, Indels: 12
0.73 0.13 0.13
Matches are distributed among these distances:
30 6 0.09
31 57 0.86
32 1 0.02
33 2 0.03
ACGTcount: A:0.32, C:0.31, G:0.25, T:0.11
Consensus pattern (31 bp):
GGGCCTAAGAGCCTACCCAAGAAAGATCTCA
Done.