Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005754.1 Hibiscus syriacus cultivar Beakdansim tig00013462_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: 84718
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:10209 original size:2 final size:2
Alignment explanation
Indices: 10202--10254 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
10192 GATCCCATCT
10202 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10243 TA TA TA TA TA TA
1 TA TA TA TA TA TA
10255 GCTTAATTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:18319 original size:12 final size:12
Alignment explanation
Indices: 18302--18326 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18292 TTGAGACTTT
18302 AAACCGAACCGA
1 AAACCGAACCGA
18314 AAACCGAACCGA
1 AAACCGAACCGA
18326 A
1 A
18327 CCATTTTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.32, G:0.16, T:0.00
Consensus pattern (12 bp):
AAACCGAACCGA
Found at i:18527 original size:2 final size:2
Alignment explanation
Indices: 18520--18549 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
18510 TGCATGTAAG
18520 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18550 CACAATGTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19836 original size:4 final size:4
Alignment explanation
Indices: 19829--19859 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
19819 AATACTTATA
*
19829 TATG TATG TATG TATG TATG TATG TAGG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
19860 ATATTGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (4 bp):
TATG
Found at i:22940 original size:42 final size:42
Alignment explanation
Indices: 22894--23016 Score: 124
Period size: 42 Copynumber: 2.9 Consensus size: 42
22884 TGAAATTCAG
* *
22894 TATCTGGTTTGTCCTTCAAGAGCCTCGGTGATAGAAATGAAC
1 TATCTGGTTTGTCCTTCAAGAGCCTTGGTGATTGAAATGAAC
* * * * ***
22936 TATCTGATTTGCTCAC-T-AGGAGCCTTGGGGATTGAACTCCCC
1 TATCTGGTTTG-TC-CTTCAAGAGCCTTGGTGATTGAAATGAAC
*
22978 AATCTGGTTTGTCCTTCAAGAGCCTTGGTGATTGAAATG
1 TATCTGGTTTGTCCTTCAAGAGCCTTGGTGATTGAAATG
23017 CATTTTCTGA
Statistics
Matches: 62, Mismatches: 15, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
40 1 0.02
41 3 0.05
42 54 0.87
43 3 0.05
44 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (42 bp):
TATCTGGTTTGTCCTTCAAGAGCCTTGGTGATTGAAATGAAC
Found at i:23057 original size:84 final size:83
Alignment explanation
Indices: 22895--23109 Score: 227
Period size: 84 Copynumber: 2.6 Consensus size: 83
22885 GAAATTCAGT
* * * *
22895 ATCTGGTTTGTCCTTCAAGAGCCTCGGTGATAGAAATGAACTATCTGATTTGCTCACTAGGAGCC
1 ATCTGGTTTGTCCTTCAAGAGCCTTGGTGATTGAAATGCACTATCTGATATGCTCACTAGGAGCC
** *
22960 TTGGGGATTGAACTCCCCA
66 -TGGAAATAGAACTCCCCA
* * * *
22979 ATCTGGTTTGTCCTTCAAGAGCCTTGGTGATTGAAATGCATTTTCTGATATGTTCACTAGGGGAC
1 ATCTGGTTTGTCCTTCAAGAGCCTTGGTGATTGAAATGCACTATCTGATATGCTCACTAGGAG-C
*
23044 C-GGAAAATAGAACTCCCCT
65 CTGG-AAATAGAACTCCCCA
* * * * *
23063 ATCTGATTT-TGCCTTCGAGAACCTTGGTGTTTGAACTGCACTATCTG
1 ATCTGGTTTGT-CCTTCAAGAGCCTTGGTGATTGAAATGCACTATCTG
23110 GTTTGTTCCC
Statistics
Matches: 109, Mismatches: 19, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
83 3 0.03
84 104 0.95
85 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (83 bp):
ATCTGGTTTGTCCTTCAAGAGCCTTGGTGATTGAAATGCACTATCTGATATGCTCACTAGGAGCC
TGGAAATAGAACTCCCCA
Found at i:28993 original size:23 final size:23
Alignment explanation
Indices: 28941--28994 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
28931 TCTAAATGTT
*
28941 ATTTTTAAATTGTATTTAAACAA
1 ATTTTTAAATTATATTTAAACAA
** * *
28964 ACATTTATATTATATTTAAATAA
1 ATTTTTAAATTATATTTAAACAA
28987 ATTTTTAA
1 ATTTTTAA
28995 TTGTTATAAA
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (23 bp):
ATTTTTAAATTATATTTAAACAA
Found at i:30289 original size:40 final size:40
Alignment explanation
Indices: 30234--30313 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
30224 TACATGCTAC
30234 ATGGGACAGGCATAAGATGGTTTACCATTTTCGTTGATCA
1 ATGGGACAGGCATAAGATGGTTTACCATTTTCGTTGATCA
*
30274 ATGGGACAAGG-ATAAGATGGTTTCCCATTTTCGTTGATCA
1 ATGGGAC-AGGCATAAGATGGTTTACCATTTTCGTTGATCA
30314 GTAAATAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 35 0.92
41 3 0.08
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.33
Consensus pattern (40 bp):
ATGGGACAGGCATAAGATGGTTTACCATTTTCGTTGATCA
Found at i:33515 original size:11 final size:10
Alignment explanation
Indices: 33499--33532 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
33489 AATTGAACAT
33499 ATAAACGAAC
1 ATAAACGAAC
33509 GATAAACGAAC
1 -ATAAACGAAC
33520 ACTAAACGAAC
1 A-TAAACGAAC
33531 AT
1 AT
33533 GCTCGTGAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.09
11 20 0.91
ACGTcount: A:0.56, C:0.21, G:0.12, T:0.12
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:33542 original size:23 final size:23
Alignment explanation
Indices: 33516--33595 Score: 81
Period size: 23 Copynumber: 3.4 Consensus size: 23
33506 AACGATAAAC
* *
33516 GAACACTAAACGAACATGCTCGT
1 GAACAATAAACGAACATGTTCGT
** * *
33539 GAACGCTAAATGAACACT-TTCAT
1 GAACAATAAACGAACA-TGTTCGT
33562 GAACATATAAACGAACATGTTCGT
1 GAACA-ATAAACGAACATGTTCGT
33586 GAACAATAAA
1 GAACAATAAA
33596 TAAACGAACA
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
23 27 0.59
24 19 0.41
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.21
Consensus pattern (23 bp):
GAACAATAAACGAACATGTTCGT
Found at i:33577 original size:24 final size:27
Alignment explanation
Indices: 33545--33606 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 27
33535 TCGTGAACGC
*
33545 TAAATGAACACT-TTCATGAAC-AT-A
1 TAAACGAACACTGTTCATGAACAATAA
*
33569 TAAACGAACA-TGTTCGTGAACAATAAA
1 TAAACGAACACTGTTCATGAACAAT-AA
33596 TAAACGAACAC
1 TAAACGAACAC
33607 GAATATCTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
23 1 0.03
24 17 0.55
25 2 0.06
27 11 0.35
ACGTcount: A:0.48, C:0.18, G:0.11, T:0.23
Consensus pattern (27 bp):
TAAACGAACACTGTTCATGAACAATAA
Found at i:36012 original size:25 final size:25
Alignment explanation
Indices: 35984--36046 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
35974 AATATTTTAT
35984 ATATAAT-TAATATAAAAAATATAAA
1 ATATAATAT-ATATAAAAAATATAAA
* **
36009 ATATTATATATATAATTAATATAAA
1 ATATAATATATATAAAAAATATAAA
* *
36034 AAATATTATATAT
1 ATATAATATATAT
36047 TATATATATA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
25 30 0.97
26 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
ATATAATATATATAAAAAATATAAA
Found at i:36019 original size:34 final size:34
Alignment explanation
Indices: 35972--36056 Score: 143
Period size: 34 Copynumber: 2.5 Consensus size: 34
35962 CCCGAACCCG
*
35972 AAAATATTTTATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
36006 AAAATATTATATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
* *
36040 TATATATTATATATATA
1 AAAATATTATATATATA
36057 TATATATATA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAT
Found at i:38379 original size:2 final size:2
Alignment explanation
Indices: 38372--38396 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38362 AATCTTTTAT
38372 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 T
38397 CGTAATATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39411 original size:15 final size:15
Alignment explanation
Indices: 39393--39424 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
39383 CGACGAGGAA
39393 GAGGGAGAGGAAAGT
1 GAGGGAGAGGAAAGT
39408 GAGGGAGAGGAAAGT
1 GAGGGAGAGGAAAGT
39423 GA
1 GA
39425 AGGTGAAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.53, T:0.06
Consensus pattern (15 bp):
GAGGGAGAGGAAAGT
Found at i:39430 original size:21 final size:21
Alignment explanation
Indices: 39401--39448 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
39391 AAGAGGGAGA
* *
39401 GGAAAGTGAGGGAGAGGAAAG
1 GGAAGGTGAAGGAGAGGAAAG
* *
39422 TGAAGGTGAAGGAGAGGAGAG
1 GGAAGGTGAAGGAGAGGAAAG
39443 GGAAGG
1 GGAAGG
39449 GATGAAGAGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.54, T:0.06
Consensus pattern (21 bp):
GGAAGGTGAAGGAGAGGAAAG
Found at i:39818 original size:16 final size:16
Alignment explanation
Indices: 39797--39829 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
39787 CAAAGATACC
39797 TCTCAATCATTTGTTA
1 TCTCAATCATTTGTTA
39813 TCTCAATCATTTGTTA
1 TCTCAATCATTTGTTA
39829 T
1 T
39830 TGAACGTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.52
Consensus pattern (16 bp):
TCTCAATCATTTGTTA
Found at i:41017 original size:22 final size:22
Alignment explanation
Indices: 40992--41038 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
40982 TTATCTGTTC
*
40992 GTCTAAATTATTTTCTTGGCGT
1 GTCTAAATTATTTTCTTGGCAT
41014 GTCTAAATTATTTTCTTGGCAT
1 GTCTAAATTATTTTCTTGGCAT
41036 GTC
1 GTC
41039 GGCATAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.19, C:0.15, G:0.17, T:0.49
Consensus pattern (22 bp):
GTCTAAATTATTTTCTTGGCAT
Found at i:48870 original size:99 final size:97
Alignment explanation
Indices: 48701--48893 Score: 341
Period size: 99 Copynumber: 2.0 Consensus size: 97
48691 CAGTTACGAG
*
48701 GATGAAGTGAAGAATGTGAGGTTGAAGATACGACAAAGGTGGTTGCATTATGGGGCTAGTGTCCC
1 GATGAAGTGAAGAATGTGAGGCTGAAGATACGACAAAGGTGGTTGCATTATGGGGCTAGTGTCCC
48766 TCTAATAAGACACTTAAATTGTGGGTTTCGAT
66 TCTAATAAGACACTTAAATTGTGGGTTTCGAT
* *
48798 GATGAAGTGAAGAATGTGAGGCTGAAGATACACGGCAAAGGTTGTTGCATTATGGGGCTAGTGTC
1 GATGAAGTGAAGAATGTGAGGCTGAAGAT--ACGACAAAGGTGGTTGCATTATGGGGCTAGTGTC
48863 CCTCTAATAAGACACTTAAATTGTGGGTTTC
64 CCTCTAATAAGACACTTAAATTGTGGGTTTC
48894 ATAGGAGGGT
Statistics
Matches: 91, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
97 28 0.31
99 63 0.69
ACGTcount: A:0.30, C:0.12, G:0.30, T:0.28
Consensus pattern (97 bp):
GATGAAGTGAAGAATGTGAGGCTGAAGATACGACAAAGGTGGTTGCATTATGGGGCTAGTGTCCC
TCTAATAAGACACTTAAATTGTGGGTTTCGAT
Found at i:53656 original size:240 final size:240
Alignment explanation
Indices: 53233--53688 Score: 675
Period size: 240 Copynumber: 1.9 Consensus size: 240
53223 AATGCCTGCA
* ** * ** *
53233 GTTACAGATGATAATGTAGTTCATCATCTATCTATGGTTGAATCCTCTGCCTCATCCAATATTAT
1 GTTACAGATGATAATGCAGACCATCATCCATCTATAATTGAATCCTCTGCCTCATCCAATATCAT
* *
53298 TTCTAGCAATGGAATCTCCACGAGTTTACCTGATCCATATCCCTCACAGAATCCTCCCATTGAAC
66 TTCTAGCAATGGAATCTCCACGAGTTTACCTGAACCATATCCCTCACAGAATCCTCCCACTGAAC
*
53363 AGATGTTGCAACTCTCGGGGAAATCTTCTGATCCTGACAATTTACCCAGTACAGATTTATACACG
131 AGATGTTGCAACTCTCAGGGAAATCTTCTGATCCTGACAATTTACCCAGTACAGATTTATACACG
53428 AGTGATGAAATTCATAATATTCACCCAGTACAGATGTTGCCTAAG
196 AGTGATGAAATTCATAATATTCACCCAGTACAGATGTTGCCTAAG
*
53473 GTTACAGATGATAATGCAGACCATCATCCAT-TAATAATTGATTCCTCTGCCTCATCCAATATCA
1 GTTACAGATGATAATGCAGACCATCATCCATCT-ATAATTGAATCCTCTGCCTCATCCAATATCA
* * * * * * *
53537 TTTC-AGGCATTGGGATCTCCACGAGTTTACCTGAACTATCTCCCTCAGAGAAAT-TTTCCACTG
65 TTTCTA-GCAATGGAATCTCCACGAGTTTACCTGAACCATATCCCTCACAG-AATCCTCCCACTG
** *
53600 AACAGATGTTGCAGTTCTCAGGGAAATCTTCTGATCCTGACAATTTACCCAGTACAGATTTATGC
128 AACAGATGTTGCAACTCTCAGGGAAATCTTCTGATCCTGACAATTTACCCAGTACAGATTTATAC
53665 ACGAGTGATGAAATTCATAATATT
193 ACGAGTGATGAAATTCATAATATT
53689 TCACTAGTGG
Statistics
Matches: 192, Mismatches: 21, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
239 2 0.01
240 187 0.97
241 3 0.02
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (240 bp):
GTTACAGATGATAATGCAGACCATCATCCATCTATAATTGAATCCTCTGCCTCATCCAATATCAT
TTCTAGCAATGGAATCTCCACGAGTTTACCTGAACCATATCCCTCACAGAATCCTCCCACTGAAC
AGATGTTGCAACTCTCAGGGAAATCTTCTGATCCTGACAATTTACCCAGTACAGATTTATACACG
AGTGATGAAATTCATAATATTCACCCAGTACAGATGTTGCCTAAG
Found at i:68027 original size:33 final size:33
Alignment explanation
Indices: 67985--68048 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
67975 AATCTAAATG
*
67985 ATGCTAAAGCACACCGGTTGGTCCATAAAATTA
1 ATGCTAAAGCACACCGGTTGGACCATAAAATTA
*
68018 ATGCTAAAGCACACCGGTTGGACCATGAAAT
1 ATGCTAAAGCACACCGGTTGGACCATAAAAT
68049 CGGTGCATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (33 bp):
ATGCTAAAGCACACCGGTTGGACCATAAAATTA
Found at i:69873 original size:39 final size:39
Alignment explanation
Indices: 69786--69873 Score: 92
Period size: 39 Copynumber: 2.3 Consensus size: 39
69776 ACCCTTTTAT
* **
69786 TAAATATTTTTATATTTTCAATTTTGTAAAAAACAATTA
1 TAAATATTTTTAAATTTAAAATTTTGTAAAAAACAATTA
*
69825 TATAA-ATTTTATAAATTTAAAATTTT-TAAAAAA-TATATA
1 TA-AATATTTT-TAAATTTAAAATTTTGTAAAAAACAAT-TA
69864 TAAATATTTT
1 TAAATATTTT
69874 CCAACTTGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
38 4 0.10
39 23 0.56
40 14 0.34
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (39 bp):
TAAATATTTTTAAATTTAAAATTTTGTAAAAAACAATTA
Found at i:70060 original size:20 final size:20
Alignment explanation
Indices: 70024--70061 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
70014 ATCCTATTTT
**
70024 CTGATAATCTTTTATTCCCA
1 CTGATAATCTTACATTCCCA
70044 CTGATAATCTTACATTCC
1 CTGATAATCTTACATTCC
70062 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.42
Consensus pattern (20 bp):
CTGATAATCTTACATTCCCA
Found at i:78014 original size:13 final size:13
Alignment explanation
Indices: 77996--78029 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
77986 TATCGTATAT
77996 TTTATATTTTTTC
1 TTTATATTTTTTC
78009 TTTATATTTTTTC
1 TTTATATTTTTTC
*
78022 TTGATATT
1 TTTATATT
78030 CTCTTTCCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.74
Consensus pattern (13 bp):
TTTATATTTTTTC
Done.