Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002967.1 Hibiscus syriacus cultivar Beakdansim tig00006136_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: 82049
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:111 original size:24 final size:24
Alignment explanation
Indices: 81--136 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
71 CGAACGGTTA
*
81 AGCGGTTCTGGCCGGTTCACTAAT
1 AGCGGTTCTGGCCAGTTCACTAAT
105 AGCGGTTCTGGCCAGTTCACTAAT
1 AGCGGTTCTGGCCAGTTCACTAAT
129 AGCGGTTC
1 AGCGGTTC
137 AACCGGTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.18, C:0.25, G:0.29, T:0.29
Consensus pattern (24 bp):
AGCGGTTCTGGCCAGTTCACTAAT
Found at i:2604 original size:2 final size:2
Alignment explanation
Indices: 2597--2655 Score: 93
Period size: 2 Copynumber: 30.0 Consensus size: 2
2587 GCATGCATGC
**
2597 AT AT AT AT AT AT AT AT A- AT AT AT AT GC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2638 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
2656 GAGATTAAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2734 original size:16 final size:16
Alignment explanation
Indices: 2713--2747 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2703 TAAAATACTG
* *
2713 AAAAATGAAAGAGAAA
1 AAAAATAAAAGACAAA
2729 AAAAATAAAAGACAAA
1 AAAAATAAAAGACAAA
2745 AAA
1 AAA
2748 TTAAAATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.80, C:0.03, G:0.11, T:0.06
Consensus pattern (16 bp):
AAAAATAAAAGACAAA
Found at i:4172 original size:10 final size:10
Alignment explanation
Indices: 4159--4185 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
4149 GTGGAGTTGG
4159 GCTGCTGGCA
1 GCTGCTGGCA
4169 GCTGCTGGCA
1 GCTGCTGGCA
4179 GCTGCTG
1 GCTGCTG
4186 TATGGAGCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.07, C:0.30, G:0.41, T:0.22
Consensus pattern (10 bp):
GCTGCTGGCA
Found at i:15080 original size:2 final size:2
Alignment explanation
Indices: 15073--15151 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
15063 TTCTTATAAG
15073 TA TA TA TA TA TA TA TA TA TA TA TA TA 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
15115 TA TA TA 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 TA TA TA T
15152 GACATTTTAT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29943 original size:2 final size:2
Alignment explanation
Indices: 29938--29971 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
29928 ATATATATAT
29938 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
29972 CCCATGCCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:33358 original size:11 final size:11
Alignment explanation
Indices: 33330--33359 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
33320 GAGGAGAAGT
*
33330 ATCCGCACCTA
1 ATCCGCCCCTA
33341 ATCCGCCCCTA
1 ATCCGCCCCTA
33352 ATCCGCCC
1 ATCCGCCC
33360 GTACCCGCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.20, C:0.53, G:0.10, T:0.17
Consensus pattern (11 bp):
ATCCGCCCCTA
Found at i:42275 original size:24 final size:24
Alignment explanation
Indices: 42243--42290 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
42233 CCATCTAACC
42243 ATTAAAAGTTACAAAATGATCACT
1 ATTAAAAGTTACAAAATGATCACT
42267 ATTAAAAGTTACAAAATGATCACT
1 ATTAAAAGTTACAAAATGATCACT
42291 CAACTATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.12, G:0.08, T:0.29
Consensus pattern (24 bp):
ATTAAAAGTTACAAAATGATCACT
Found at i:43062 original size:60 final size:60
Alignment explanation
Indices: 42981--43125 Score: 184
Period size: 60 Copynumber: 2.4 Consensus size: 60
42971 AACTGTAATG
** *
42981 TTCAAAAAGTTTGGGGATTAATTTAGAATGA-AGGTCATAGTTTGGGGATGAAATTAAAATA
1 TTCAAAAA-TTTAAGGATTAATTTAGAATGATA-GTCATAGTTTAGGGATGAAATTAAAATA
* **
43042 TTCAAAAATTTAAGGATTAATTTAGCATGATAGTCATAGTTTAGGGATGAAATTGGAATA
1 TTCAAAAATTTAAGGATTAATTTAGAATGATAGTCATAGTTTAGGGATGAAATTAAAATA
* * *
43102 TTTAAAAGTTTAAGGATCAATTTA
1 TTCAAAAATTTAAGGATTAATTTA
43126 ATATAAGGGA
Statistics
Matches: 74, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
60 65 0.88
61 9 0.12
ACGTcount: A:0.40, C:0.04, G:0.21, T:0.35
Consensus pattern (60 bp):
TTCAAAAATTTAAGGATTAATTTAGAATGATAGTCATAGTTTAGGGATGAAATTAAAATA
Found at i:46108 original size:23 final size:23
Alignment explanation
Indices: 46064--46118 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
46054 AAGTTATTAA
*
46064 AAATTATTATTTTTAAATATATT
1 AAATTATAATTTTTAAATATATT
*
46087 AAATTATAATTATTTGAA-ATATT
1 AAATTATAATT-TTTAAATATATT
46110 AAATATATA
1 AAAT-TATA
46119 TGTATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 19 0.68
24 9 0.32
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
AAATTATAATTTTTAAATATATT
Found at i:46131 original size:23 final size:23
Alignment explanation
Indices: 46080--46134 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
46070 TTATTTTTAA
*
46080 ATATATTAAATTATAATTATTTG
1 ATATATTAAATTATAATTATATG
*
46103 AAATATTAAA-TATATATGTATAT-
1 ATATATTAAATTATA-AT-TATATG
46126 ATATATTAA
1 ATATATTAA
46135 CAGTTTGTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 4 0.15
23 19 0.70
24 4 0.15
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (23 bp):
ATATATTAAATTATAATTATATG
Found at i:49250 original size:17 final size:18
Alignment explanation
Indices: 49207--49247 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
49197 GAATTATATT
49207 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
49224 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
49242 ATTAAA
1 AGTAAA
49248 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:57894 original size:3 final size:3
Alignment explanation
Indices: 57886--57910 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
57876 GATCAATTTA
57886 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
57911 GTTTATCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:58479 original size:23 final size:23
Alignment explanation
Indices: 58461--58505 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
58451 ATGAAAATCG
*
58461 TACTACAAAGACATAGAAAAACA
1 TACTACAAAGACAGAGAAAAACA
* *
58484 TATTATAAAGACAGAGAAAAAC
1 TACTACAAAGACAGAGAAAAAC
58506 GTGTCACAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.60, C:0.13, G:0.11, T:0.16
Consensus pattern (23 bp):
TACTACAAAGACAGAGAAAAACA
Found at i:58850 original size:11 final size:11
Alignment explanation
Indices: 58821--58853 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
58811 TTGCTTTTAC
*
58821 ATTATAAAATA
1 ATTATAAATTA
58832 ATTA-AAATTA
1 ATTATAAATTA
58842 ATTATAAATTA
1 ATTATAAATTA
58853 A
1 A
58854 GTGAAAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
ATTATAAATTA
Found at i:65815 original size:28 final size:27
Alignment explanation
Indices: 65789--65869 Score: 63
Period size: 28 Copynumber: 2.9 Consensus size: 27
65779 AAAGTTATAG
*
65789 TAAAATATATTATTATAACTATTTATAA
1 TAAAATATATTATTATAAATATTTAT-A
* * * *
65817 TATAATAAATAATTATAAATATATTGTTA
1 TAAAATATATTATTATAAATAT-TT-ATA
* * *
65846 AAAAATATATTATTTTAATTATTT
1 TAAAATATATTATTATAAATATTT
65870 TAAAATATTA
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
28 20 0.50
29 19 0.47
30 1 0.03
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (27 bp):
TAAAATATATTATTATAAATATTTATA
Found at i:66207 original size:78 final size:77
Alignment explanation
Indices: 66097--66250 Score: 218
Period size: 78 Copynumber: 2.0 Consensus size: 77
66087 AGTTGGGCTA
* * * *
66097 CGAGTCATATTAATGGGCTTAAAGAGGGTTTTACCCGCTAAAATCGTAAATTAGGGTTTATGCTC
1 CGAGTCATATTAATGGGCTTAAACAAGCTTTTACCCGCTAAAATCGCAAATTAGGGTTTATGCTC
*
66162 CGCATATATATC
66 CGCAGATATATC
* * *
66174 CGAGTCATGTTAATTGGGCTTAAACAAGCTTTTACCCGCTAAAATGGCATATTAGGGTTTATGCT
1 CGAGTCATATTAA-TGGGCTTAAACAAGCTTTTACCCGCTAAAATCGCAAATTAGGGTTTATGCT
*
66239 CCTCAGATATAT
65 CCGCAGATATAT
66251 ATACCCCGCG
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
77 12 0.18
78 55 0.82
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (77 bp):
CGAGTCATATTAATGGGCTTAAACAAGCTTTTACCCGCTAAAATCGCAAATTAGGGTTTATGCTC
CGCAGATATATC
Found at i:69499 original size:2 final size:2
Alignment explanation
Indices: 69492--69537 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
69482 TTGTATTTTC
69492 TA TA TA TA TA TA TA TA TA TA TA TA TA 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
69534 TA TA
1 TA TA
69538 AATTCATTGC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:70511 original size:3 final size:3
Alignment explanation
Indices: 70505--70539 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
70495 GTCGTTTGTT
70505 AAG AAG AA- AGAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG A-AG AAG AAG AAG AAG AAG AAG AAG AA
70540 TAAGTTAACC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 1 0.03
3 28 0.93
4 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:75317 original size:2 final size:2
Alignment explanation
Indices: 75310--75338 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
75300 TTACAAGGTA
75310 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
75339 ATTTCCTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:79097 original size:12 final size:12
Alignment explanation
Indices: 79080--79104 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
79070 GTTAATTAGT
79080 TACCAAAAAATA
1 TACCAAAAAATA
79092 TACCAAAAAATA
1 TACCAAAAAATA
79104 T
1 T
79105 TTTTATTTAA
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:0.64, C:0.16, G:0.00, T:0.20
Consensus pattern (12 bp):
TACCAAAAAATA
Done.