Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005922.1 Hibiscus syriacus cultivar Beakdansim tig00013901_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: 73124
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2108 original size:43 final size:43
Alignment explanation
Indices: 2038--2124 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 43
2028 AGTCCAGGAA
* * *
2038 CTTGTGTGAACCCTTTTACAATAAATCGAGCCTTGTACTTATG
1 CTTGTGTAAACCCTTTTACAACAAATCGAGCCTTGTACCTATG
** *
2081 CTTGTGTAAACCCTTTTGTAACCAATCGAGCCTTGTACCTATG
1 CTTGTGTAAACCCTTTTACAACAAATCGAGCCTTGTACCTATG
2124 C
1 C
2125 ACAGACATGT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (43 bp):
CTTGTGTAAACCCTTTTACAACAAATCGAGCCTTGTACCTATG
Found at i:6591 original size:158 final size:159
Alignment explanation
Indices: 6294--6613 Score: 516
Period size: 158 Copynumber: 2.0 Consensus size: 159
6284 GAAACACTTT
* * *
6294 ATATTAATGTATTCATATATAAGAACTCTTAACGTGACGTAAATGTTTTTCTAAGACATCAAAAT
1 ATATTAATGTATTCATATATAAAAACTCTCAACGTGACGAAAATGTTTTTCTAAGACATCAAAAT
6359 ACTTAATTGATCGATTCATTTATCCTTGGATATCTTTCTGTTATAAATTCATTCGCCCATAGATG
66 ACTTAATTGATCGATTCATTTATCCTTGGATATCTTTCTGTTATAAATTCATTCGCCCATAGATG
*
6424 TCTTCTCACTGTGAATGTTTTTCAAAAGC
131 TCGTCTCACTGTGAATGTTTTTCAAAAGC
* * * * **
6453 ATATTAAT-TATTCATATCTAAAAACTCTCAACGTGAGGAAAATGTTTTTCTAATATATCGGAAT
1 ATATTAATGTATTCATATATAAAAACTCTCAACGTGACGAAAATGTTTTTCTAAGACATCAAAAT
* * *
6517 ACTTAATTGATTGATTCATTTGTCCTTGGATATCTTTCTGTTATAAATTCATTCGCCCTTAGATG
66 ACTTAATTGATCGATTCATTTATCCTTGGATATCTTTCTGTTATAAATTCATTCGCCCATAGATG
6582 TCGTCTCACTGTGAATGTTTTTCAAAAGC
131 TCGTCTCACTGTGAATGTTTTTCAAAAGC
6611 ATA
1 ATA
6614 AGAGTTTTCT
Statistics
Matches: 148, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
158 140 0.95
159 8 0.05
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (159 bp):
ATATTAATGTATTCATATATAAAAACTCTCAACGTGACGAAAATGTTTTTCTAAGACATCAAAAT
ACTTAATTGATCGATTCATTTATCCTTGGATATCTTTCTGTTATAAATTCATTCGCCCATAGATG
TCGTCTCACTGTGAATGTTTTTCAAAAGC
Found at i:13929 original size:22 final size:21
Alignment explanation
Indices: 13902--13981 Score: 74
Period size: 23 Copynumber: 3.7 Consensus size: 21
13892 TTTAGTGTAG
13902 AGGGAATCGATACCCCCTTGA
1 AGGGAATCGATACCCCCTTGA
* *
13923 AGGGGAACCGATTCCCCCTTTGA
1 A-GGGAATCGATACCCCC-TTGA
*
13946 ATGGGAA-CTGATTCCCTCCTTG-
1 A-GGGAATC-GATACCC-CCTTGA
13968 AGGGAATCGATACC
1 AGGGAATCGATACC
13982 TCCCACGGGT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
21 11 0.22
22 17 0.34
23 20 0.40
24 2 0.04
ACGTcount: A:0.25, C:0.28, G:0.25, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCCTTGA
Found at i:13968 original size:23 final size:22
Alignment explanation
Indices: 13903--13968 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 22
13893 TTAGTGTAGA
* *
13903 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCCTTGAAG
*
13925 GGGAACCGATTCCCCCTTTGAAT
1 GGGAACCGATTCCCCC-TTGAAG
*
13948 GGGAACTGATTCCCTCCTTGA
1 GGGAACCGATTCCC-CCTTGA
13969 GGGAATCGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 14 0.37
23 22 0.58
24 2 0.05
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.24
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTGAAG
Found at i:23478 original size:11 final size:11
Alignment explanation
Indices: 23462--23503 Score: 75
Period size: 11 Copynumber: 3.8 Consensus size: 11
23452 CTAGAAGCAT
23462 GTTGACTGGAC
1 GTTGACTGGAC
23473 GTTGACTGGAC
1 GTTGACTGGAC
*
23484 GTTGACTGGAT
1 GTTGACTGGAC
23495 GTTGACTGG
1 GTTGACTGG
23504 GCACTTGTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.17, C:0.14, G:0.38, T:0.31
Consensus pattern (11 bp):
GTTGACTGGAC
Found at i:23992 original size:61 final size:65
Alignment explanation
Indices: 23918--24038 Score: 164
Period size: 67 Copynumber: 1.9 Consensus size: 65
23908 TTTATATTTT
*
23918 AAAAATATTTTTAA-AT-T-A-AG-AATAAAATATTTTTAAATATATA-TTTAATAAAATAAAAA
1 AAAAATATTTTTAATATATAATAGTAATAAAATATTTTTAAAT-TA-AGTTAAATAAAATAAAAA
23977 TA
64 TA
23979 AAAAATATTTTTAATATAATAATAGTAATAAAATATTTTTAAATTAAGTTAAATAAAATA
1 AAAAATATTTTTAATAT-ATAATAGTAATAAAATATTTTTAAATTAAGTTAAATAAAATA
24039 TGTTTTTAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
61 14 0.27
62 2 0.04
64 1 0.02
65 2 0.04
66 15 0.29
67 18 0.35
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (65 bp):
AAAAATATTTTTAATATATAATAGTAATAAAATATTTTTAAATTAAGTTAAATAAAATAAAAATA
Found at i:24018 original size:29 final size:28
Alignment explanation
Indices: 23952--24018 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 28
23942 AAATATTTTT
*
23952 AAATATATATTTAATAAAATAAAAATAAA
1 AAATAT-TTTTTAATAAAATAAAAATAAA
* * *
23981 AAATA-TTTTTAATATAATAATAGTAATA
1 AAATATTTTTTAATAAAATAAAAATAA-A
24009 AAATATTTTT
1 AAATATTTTT
24019 AAATTAAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 17 0.53
28 6 0.19
29 9 0.28
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (28 bp):
AAATATTTTTTAATAAAATAAAAATAAA
Found at i:24322 original size:16 final size:16
Alignment explanation
Indices: 24298--24336 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
24288 ATGGATACCC
* *
24298 ATTTAATATTTATTTT
1 ATTTTATATTTAATTT
24314 ATTTTATATTTAATTT
1 ATTTTATATTTAATTT
*
24330 ATATTAT
1 ATTTTAT
24337 TTTTTAGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTTTATATTTAATTT
Found at i:24532 original size:21 final size:20
Alignment explanation
Indices: 24490--24534 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
24480 ACTCAATTTA
* *
24490 AAATAATTTAAGATTAAAAT
1 AAATAATTTAAAAATAAAAT
*
24510 AAATAATTTTAAAAATAATAT
1 AAATAA-TTTAAAAATAAAAT
24531 AAAT
1 AAAT
24535 GTTAAGGTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
AAATAATTTAAAAATAAAAT
Found at i:25257 original size:2 final size:2
Alignment explanation
Indices: 25252--25278 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
25242 CCCTCTCTCC
25252 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 T
25279 GTTCACCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:32186 original size:14 final size:15
Alignment explanation
Indices: 32149--32186 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
32139 ATAAATTAAT
*
32149 TAAAAAATTTAAAAG
1 TAAAATATTTAAAAG
*
32164 TAAATTATTTAAAA-
1 TAAAATATTTAAAAG
32178 TAAAATATT
1 TAAAATATT
32187 AATTACATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (15 bp):
TAAAATATTTAAAAG
Found at i:32256 original size:19 final size:17
Alignment explanation
Indices: 32218--32279 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 17
32208 TTTAGCAATA
*
32218 AAAATTATAAAATACCTTT
1 AAAATTATAAAA-A-ATTT
*
32237 AAAATTATCTAAAATATTT
1 AAAATTA--TAAAAAATTT
32256 AAAGGATTATAAAAAATTT
1 AAA--ATTATAAAAAATTT
32275 AAAAT
1 AAAAT
32280 AATATAATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
17 2 0.06
19 25 0.69
21 9 0.25
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.35
Consensus pattern (17 bp):
AAAATTATAAAAAATTT
Found at i:32285 original size:19 final size:19
Alignment explanation
Indices: 32234--32286 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 19
32224 ATAAAATACC
* * *
32234 TTTAAAATTATCTAAAATA
1 TTTAAAATAATATAAAAAA
** *
32253 TTTAAAGGATTATAAAAAA
1 TTTAAAATAATATAAAAAA
32272 TTTAAAATAATATAA
1 TTTAAAATAATATAA
32287 TTAATATTTT
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (19 bp):
TTTAAAATAATATAAAAAA
Found at i:36587 original size:16 final size:16
Alignment explanation
Indices: 36555--36611 Score: 89
Period size: 16 Copynumber: 3.6 Consensus size: 16
36545 GTTTATTTCA
*
36555 GAATGATT-AAGTGCT
1 GAATGATTCAAATGCT
*
36570 GAGTGATTCAAATGCT
1 GAATGATTCAAATGCT
36586 GAATGATTCAAATGCT
1 GAATGATTCAAATGCT
36602 GAATGATTCA
1 GAATGATTCA
36612 GAGGCTCAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
15 7 0.18
16 31 0.82
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.32
Consensus pattern (16 bp):
GAATGATTCAAATGCT
Found at i:42761 original size:33 final size:35
Alignment explanation
Indices: 42689--42892 Score: 182
Period size: 41 Copynumber: 5.4 Consensus size: 35
42679 GTTTATGTAT
*
42689 CATGTCTCTATGCTTTTGTCCAAATTAAAA--TCTC
1 CATGTCTCTATGCTGTTGTCC-AATTAAAACCTCTC
*
42723 TATGTCTCTATGCTGTTGTCCAATTAAAACCTCCATGTCTC
1 CATGTCTCTATGCTGTTGTCCAATTAAAA---CC---TCTC
42764 CATGTCTCTATGCTGTTGTCCAATTAAAACCTCCATGTCTC
1 CATGTCTCTATGCTGTTGTCCAATTAAAA---CC---TCTC
42805 CATGTCTCTATGCTGTTGTCCAATTAAAACCTCCATGTCTC
1 CATGTCTCTATGCTGTTGTCCAATTAAAA---CC---TCTC
*
42846 CATGTCTCTATGCTGTTGTCCAATTAAAA-C-CTA
1 CATGTCTCTATGCTGTTGTCCAATTAAAACCTCTC
42879 CATGTCTCTATGCT
1 CATGTCTCTATGCT
42893 ACACTTGTAA
Statistics
Matches: 158, Mismatches: 4, Indels: 17
0.88 0.02 0.09
Matches are distributed among these distances:
33 24 0.15
34 19 0.12
37 1 0.01
41 114 0.72
ACGTcount: A:0.23, C:0.27, G:0.12, T:0.38
Consensus pattern (35 bp):
CATGTCTCTATGCTGTTGTCCAATTAAAACCTCTC
Found at i:42781 original size:41 final size:41
Alignment explanation
Indices: 42719--42886 Score: 318
Period size: 41 Copynumber: 4.1 Consensus size: 41
42709 CAAATTAAAA
*
42719 TCTCTATGTCTCTATGCTGTTGTCCAATTAAAACCTCCATG
1 TCTCCATGTCTCTATGCTGTTGTCCAATTAAAACCTCCATG
42760 TCTCCATGTCTCTATGCTGTTGTCCAATTAAAACCTCCATG
1 TCTCCATGTCTCTATGCTGTTGTCCAATTAAAACCTCCATG
42801 TCTCCATGTCTCTATGCTGTTGTCCAATTAAAACCTCCATG
1 TCTCCATGTCTCTATGCTGTTGTCCAATTAAAACCTCCATG
*
42842 TCTCCATGTCTCTATGCTGTTGTCCAATTAAAACCTACATG
1 TCTCCATGTCTCTATGCTGTTGTCCAATTAAAACCTCCATG
42883 TCTC
1 TCTC
42887 TATGCTACAC
Statistics
Matches: 125, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 125 1.00
ACGTcount: A:0.22, C:0.29, G:0.12, T:0.38
Consensus pattern (41 bp):
TCTCCATGTCTCTATGCTGTTGTCCAATTAAAACCTCCATG
Found at i:43849 original size:3 final size:3
Alignment explanation
Indices: 43841--43867 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
43831 GAACCCATGG
43841 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
43868 TTGTTAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:60209 original size:3 final size:3
Alignment explanation
Indices: 60201--60230 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
60191 ACCGTAAAAC
*
60201 ATA ATA ATA ATA ATA ATA ATA ATC ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
60231 TGATTTTAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:68986 original size:30 final size:29
Alignment explanation
Indices: 68952--69080 Score: 168
Period size: 30 Copynumber: 4.3 Consensus size: 29
68942 CAGGAGCCAA
**
68952 CTGAGGAGGGGTTCGACGAACTAGAGCCGC
1 CTGAGGAGGGGTT-GACGAACCGGAGCCGC
*
68982 CTGAGGAGGGGTTTGACGAGCCGGAGCCGC
1 CTGAGGAGGGG-TTGACGAACCGGAGCCGC
*
69012 CTGAGGAGGCGGTTGACGAGCCGGAGCCGC
1 CTGAGGAGG-GGTTGACGAACCGGAGCCGC
* *
69042 CTGAGGATGTGGTTGGCGAACCGGAGCCGC
1 CTGAGGA-GGGGTTGACGAACCGGAGCCGC
69072 CTGAGGAGG
1 CTGAGGAGG
69081 AGGCGGGGTA
Statistics
Matches: 89, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.01
30 83 0.93
31 5 0.06
ACGTcount: A:0.19, C:0.23, G:0.45, T:0.13
Consensus pattern (29 bp):
CTGAGGAGGGGTTGACGAACCGGAGCCGC
Found at i:71766 original size:26 final size:28
Alignment explanation
Indices: 71706--71767 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 28
71696 GAGTATTGCT
*
71706 GAGCTCGACTCGACTCGAAAACTCTGAAATT
1 GAGCTCGACTCGACTCGAAAACTCTG--A-C
71737 GAGCTCGACTCGACTCGAAAACTC-G-C
1 GAGCTCGACTCGACTCGAAAACTCTGAC
71763 GAGCT
1 GAGCT
71768 TAAAATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.17
30 1 0.03
31 24 0.80
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.19
Consensus pattern (28 bp):
GAGCTCGACTCGACTCGAAAACTCTGAC
Done.