Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006740.1 Hibiscus syriacus cultivar Beakdansim tig00016917_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: 57437
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:526 original size:101 final size:103
Alignment explanation
Indices: 349--564 Score: 373
Period size: 101 Copynumber: 2.1 Consensus size: 103
339 GTAGAGGGTC
* *
349 TATGTGGTCCTTCGGGACATGTATGTATTCTTTGGAACAGGTGTGAGGTCTGTTAAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGGTAAGACACATAC
*
414 TTGATCTTTGGCATAT-TATATGATTCTTAA-GAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* *
450 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGGTAAGACACATAC
515 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
553 TATGTGGTCCTT
1 TATGTGGTCCTT
565 ATAGACATTA
Statistics
Matches: 108, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
101 76 0.70
102 14 0.13
103 18 0.17
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGGTAAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:9131 original size:17 final size:17
Alignment explanation
Indices: 9109--9153 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
9099 TGTGTAAAGT
*
9109 AGTATCGGTGCCCCTTG
1 AGTATCGGTACCCCTTG
9126 AGTATCGGTACCCCTTG
1 AGTATCGGTACCCCTTG
9143 AGTATCGGTAC
1 AGTATCGGTAC
9154 TTATTATGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.29
Consensus pattern (17 bp):
AGTATCGGTACCCCTTG
Found at i:11519 original size:31 final size:31
Alignment explanation
Indices: 11464--11523 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
11454 AATACAGTCT
**
11464 CCCAACATTTAGTTTGTTTGCAATATGGTAC
1 CCCAACATTTAGTCCGTTTGCAATATGGTAC
*
11495 CCCAACATTTAGTCCGTTTTCAATATGGT
1 CCCAACATTTAGTCCGTTTGCAATATGGT
11524 CCCTACGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (31 bp):
CCCAACATTTAGTCCGTTTGCAATATGGTAC
Found at i:13343 original size:31 final size:31
Alignment explanation
Indices: 13289--13364 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
13279 CTTTTAAAAC
* *
13289 TTGCAAAATGGT-CCCCAATATTTAGTCCGT
1 TTGCAATATGGTCCCCCAACATTTAGTCCGT
*
13319 TTGCAATATGGTCCCCCAACATTTATTCCGT
1 TTGCAATATGGTCCCCCAACATTTAGTCCGT
*
13350 TTACAATATGGTCCC
1 TTGCAATATGGTCCC
13365 AACGTAACTG
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 11 0.27
31 30 0.73
ACGTcount: A:0.25, C:0.26, G:0.14, T:0.34
Consensus pattern (31 bp):
TTGCAATATGGTCCCCCAACATTTAGTCCGT
Found at i:16911 original size:23 final size:23
Alignment explanation
Indices: 16885--16932 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
16875 ATTTATCTTT
*
16885 TAAATTTTATAAAAAATTATATA
1 TAAATTTTATAAAAAATCATATA
*
16908 TAAATTTTATTAAAAATCATATA
1 TAAATTTTATAAAAAATCATATA
16931 TA
1 TA
16933 TATATTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
TAAATTTTATAAAAAATCATATA
Found at i:16957 original size:20 final size:20
Alignment explanation
Indices: 16915--16960 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
16905 ATATAAATTT
* *
16915 TATTAAAAATCATATATATA
1 TATTAAAAATAATAAATATA
16935 TATTAAAAATAATAAAGTAATA
1 TATTAAAAATAATAAA-T-ATA
16957 TATT
1 TATT
16961 TTTGAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 14 0.64
21 1 0.05
22 7 0.32
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (20 bp):
TATTAAAAATAATAAATATA
Found at i:16972 original size:23 final size:23
Alignment explanation
Indices: 16942--16993 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
16932 ATATATTAAA
16942 AATAATAAAGTAATATATTTTTG
1 AATAATAAAGTAATATATTTTTG
16965 AATAATAAAGTAATATATTTTTG
1 AATAATAAAGTAATATATTTTTG
16988 AATAAT
1 AATAAT
16994 TTTTATATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (23 bp):
AATAATAAAGTAATATATTTTTG
Found at i:17169 original size:17 final size:17
Alignment explanation
Indices: 17147--17305 Score: 264
Period size: 17 Copynumber: 9.4 Consensus size: 17
17137 CCAAACACAA
*
17147 TAATGTAACATTCTCAG
1 TAATGTAACATTCCCAG
*
17164 TAATGTAACATTCTCAG
1 TAATGTAACATTCCCAG
*
17181 TAATGTAACATTTCCAG
1 TAATGTAACATTCCCAG
*
17198 TAATGTAACATTCACAG
1 TAATGTAACATTCCCAG
17215 TAATGTAACATTCCCAG
1 TAATGTAACATTCCCAG
17232 TAATGTAACATTCCCAG
1 TAATGTAACATTCCCAG
17249 TAATGTAACATTCCCAG
1 TAATGTAACATTCCCAG
*
17266 TAATGTAACATTCACAG
1 TAATGTAACATTCCCAG
*
17283 TAATGTAACATTCCCAA
1 TAATGTAACATTCCCAG
17300 TAATGT
1 TAATGT
17306 GTTAGGTAAT
Statistics
Matches: 134, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 134 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.32
Consensus pattern (17 bp):
TAATGTAACATTCCCAG
Found at i:31228 original size:145 final size:145
Alignment explanation
Indices: 30974--31234 Score: 380
Period size: 145 Copynumber: 1.8 Consensus size: 145
30964 GACAATAAAT
* *
30974 ACTCATTCACCCCTACAAAAGTTATAATCAAACTCGAGACATAAAAAAATAACAATGATTAACAC
1 ACTCATTCACCCCTACAAAAGTTATAATCAAACTCGAAACATAAAAAAATAACAATAATTAACAC
31039 ATAGATACAAAGACAATAGATAGAAACAATAAAGAATCTTCCTAGTTTAACTGCTTTTATCACTA
66 ATAGATACAAAGACAATAGATAGAAACAATAAAGAATCTTCCTAGTTTAACTGCTTTTATCACTA
31104 TTGTTCACAATCAGC
131 TTGTTCACAATCAGC
* * * * * *
31119 ACTCCTTCACCCCTACAAATGTTATACTCAAACTCGAAATATAAGAAAATAATAATAATTAACAC
1 ACTCATTCACCCCTACAAAAGTTATAATCAAACTCGAAACATAAAAAAATAACAATAATTAACAC
* * * * **
31184 ATAGGTGCATAGA-AAGTAGATAGATACAATTGAGAATCTTCCTAGTTTAAC
66 ATAGATACAAAGACAA-TAGATAGAAACAATAAAGAATCTTCCTAGTTTAAC
31235 ATCGCATAGC
Statistics
Matches: 101, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
144 2 0.02
145 99 0.98
ACGTcount: A:0.44, C:0.19, G:0.10, T:0.27
Consensus pattern (145 bp):
ACTCATTCACCCCTACAAAAGTTATAATCAAACTCGAAACATAAAAAAATAACAATAATTAACAC
ATAGATACAAAGACAATAGATAGAAACAATAAAGAATCTTCCTAGTTTAACTGCTTTTATCACTA
TTGTTCACAATCAGC
Found at i:32244 original size:6 final size:6
Alignment explanation
Indices: 32225--32273 Score: 66
Period size: 6 Copynumber: 8.5 Consensus size: 6
32215 TTACCTTAAA
* *
32225 AATTAC AATT-T AATTAT AATTAT AATTAT AATTAT AATTA- AATTTT
1 AATTAT AATTAT AATTAT AATTAT AATTAT AATTAT AATTAT AATTAT
32271 AAT
1 AAT
32274 AAATGATTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
5 8 0.21
6 31 0.79
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (6 bp):
AATTAT
Found at i:32601 original size:3 final size:3
Alignment explanation
Indices: 32593--32620 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
32583 GTAATACCCT
32593 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
32621 CCTCCTCCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:33047 original size:16 final size:16
Alignment explanation
Indices: 33023--33054 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
33013 TGCCTCCTTG
*
33023 CCGTTGTCCCTTCTCC
1 CCGTCGTCCCTTCTCC
33039 CCGTCGTCCCTTCTCC
1 CCGTCGTCCCTTCTCC
33055 GTCTGTGGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.53, G:0.12, T:0.34
Consensus pattern (16 bp):
CCGTCGTCCCTTCTCC
Found at i:34838 original size:33 final size:33
Alignment explanation
Indices: 34801--34868 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
34791 GGTTAATATA
* **
34801 TATATATATATTATTTTTAA-TTAATTTATTTTT
1 TATATATATA-TATTTTGAATTTAAAATATTTTT
*
34834 TATATTTATATATTTTGAATTTAAAATATTTTT
1 TATATATATATATTTTGAATTTAAAATATTTTT
34867 TA
1 TA
34869 AAATCAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 8 0.27
33 22 0.73
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.63
Consensus pattern (33 bp):
TATATATATATATTTTGAATTTAAAATATTTTT
Found at i:41681 original size:18 final size:18
Alignment explanation
Indices: 41658--41700 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
41648 CCACTTGCAT
41658 TGCTTCATCATAGCACTC
1 TGCTTCATCATAGCACTC
*
41676 TGCTTCATCATAGCATTC
1 TGCTTCATCATAGCACTC
*
41694 TGGTTCA
1 TGCTTCA
41701 CCATTGTCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.28, G:0.14, T:0.37
Consensus pattern (18 bp):
TGCTTCATCATAGCACTC
Found at i:44109 original size:16 final size:16
Alignment explanation
Indices: 44088--44119 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
44078 ATTCGACAAA
44088 AAATTTACTATTCACG
1 AAATTTACTATTCACG
44104 AAATTTACTATTCACG
1 AAATTTACTATTCACG
44120 TGAATAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.38
Consensus pattern (16 bp):
AAATTTACTATTCACG
Found at i:52862 original size:5 final size:5
Alignment explanation
Indices: 52852--52882 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
52842 TCAATCCAAA
52852 CCATG CCATG CCATG CCATG CCATG CCATG C
1 CCATG CCATG CCATG CCATG CCATG CCATG C
52883 ATATGCTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.42, G:0.19, T:0.19
Consensus pattern (5 bp):
CCATG
Found at i:56681 original size:31 final size:30
Alignment explanation
Indices: 56616--56685 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
56606 TAATTTTATT
* *
56616 AATTTTTGATTAATTACATTTAGATCCCTG
1 AATTTTTGAATAATTACATTTAGATCCCTA
* *
56646 AATTTTTGAATATTTATATTTTAG-TCCCTA
1 AATTTTTGAATAATTACA-TTTAGATCCCTA
*
56676 AAATTTTGAA
1 AATTTTTGAA
56686 AAGTTATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 29 0.85
31 5 0.15
ACGTcount: A:0.33, C:0.10, G:0.09, T:0.49
Consensus pattern (30 bp):
AATTTTTGAATAATTACATTTAGATCCCTA
Found at i:56693 original size:30 final size:31
Alignment explanation
Indices: 56634--56693 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
56624 ATTAATTACA
* * * *
56634 TTTAGATCCCTGAATTTTTGAATATTTATAT
1 TTTAGATCCCTAAAATTTTGAAAAGTTATAT
56665 TTTAG-TCCCTAAAATTTTGAAAAGTTATA
1 TTTAGATCCCTAAAATTTTGAAAAGTTATA
56694 AATTGATATG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.47
Consensus pattern (31 bp):
TTTAGATCCCTAAAATTTTGAAAAGTTATAT
Found at i:56925 original size:17 final size:17
Alignment explanation
Indices: 56902--56944 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
56892 TTTAATTATT
*
56902 TTATATTTTTATAATAATA
1 TTAT-TTTTTA-AAAAATA
56921 TTATTTTTTAAAAAATA
1 TTATTTTTTAAAAAATA
56938 TTATTTT
1 TTATTTT
56945 AATTTATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 13 0.57
18 6 0.26
19 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTATTTTTTAAAAAATA
Found at i:57265 original size:19 final size:19
Alignment explanation
Indices: 57241--57282 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
57231 CTTAGGGACG
*
57241 AAAATGAAATGAAA-GAAAA
1 AAAATGAAA-AAAATGAAAA
57260 AAAATGAAAAAAATGAAAA
1 AAAATGAAAAAAATGAAAA
57279 AAAA
1 AAAA
57283 AATGAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.10
Consensus pattern (19 bp):
AAAATGAAAAAAATGAAAA
Found at i:57281 original size:12 final size:12
Alignment explanation
Indices: 57266--57291 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
57256 AAAAAAAATG
57266 AAAAAAATGAAA
1 AAAAAAATGAAA
57278 AAAAAAATGAAA
1 AAAAAAATGAAA
57290 AA
1 AA
57292 TAATTGGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.08, T:0.08
Consensus pattern (12 bp):
AAAAAAATGAAA
Found at i:57282 original size:21 final size:23
Alignment explanation
Indices: 57247--57291 Score: 76
Period size: 21 Copynumber: 2.0 Consensus size: 23
57237 GACGAAAATG
57247 AAATGAAAGAAAAAAAATGAAAA
1 AAATGAAAGAAAAAAAATGAAAA
57270 AAATG-AA-AAAAAAAATGAAAA
1 AAATGAAAGAAAAAAAATGAAAA
57291 A
1 A
57292 TAATTGGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 15 0.68
22 2 0.09
23 5 0.23
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (23 bp):
AAATGAAAGAAAAAAAATGAAAA
Found at i:57291 original size:10 final size:10
Alignment explanation
Indices: 57241--57282 Score: 52
Period size: 9 Copynumber: 4.4 Consensus size: 10
57231 CTTAGGGACG
*
57241 AAAATGAAAT
1 AAAATGAAAA
*
57251 GAAA-GAAAA
1 AAAATGAAAA
57260 AAAATG-AAA
1 AAAATGAAAA
57269 AAAATGAAAA
1 AAAATGAAAA
57279 AAAA
1 AAAA
57283 AATGAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
9 16 0.59
10 11 0.41
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.10
Consensus pattern (10 bp):
AAAATGAAAA
Done.