Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009289.1 Hibiscus syriacus cultivar Beakdansim tig00112988_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: 1661737
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 8
Found at i:1591551 original size:21 final size:20
Alignment explanation
Indices: 1591504--1591552 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
1591494 GTTACAGTAT
* **
1591504 TGGCGTGCTAGTCACGGTGT
1 TGGCGTGATAGTCACGGTAC
*
1591524 TGACGTGATAGTCCACGGTAC
1 TGGCGTGATAGT-CACGGTAC
1591545 TGGCGTGA
1 TGGCGTGA
1591553 CAATCCATCT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.16, C:0.20, G:0.37, T:0.27
Consensus pattern (20 bp):
TGGCGTGATAGTCACGGTAC
Found at i:1595214 original size:93 final size:93
Alignment explanation
Indices: 1595088--1595380 Score: 392
Period size: 93 Copynumber: 3.2 Consensus size: 93
1595078 TCTGAAACTC
* * *
1595088 CATCTTCCCTCTCAACAATCTTGGTTTGCTTACTTCTCGGAATTCTCTGAGGTTGCTGAAGAGAA
1 CATCTTCCCTCTCAGCAATCTTGGTTTGCTTACTTCTCGGAATTCTCCGAGGCTGCTGAAGAGAA
*
1595153 CTGTCATCCGGAGAATCAGATGAAACTG
66 CTGTCATCCGGAGAATCAGATGAAACAG
* * *
1595181 CATCTTCCCTCTCGGCAATCTTGGTTTGCTTACTTCTCGGAATTCTCCGAGGCTGCTGAACAGAG
1 CATCTTCCCTCTCAGCAATCTTGGTTTGCTTACTTCTCGGAATTCTCCGAGGCTGCTGAAGAGAA
1595246 CTGTCATCCGGAGAATCAGATGAAACAG
66 CTGTCATCCGGAGAATCAGATGAAACAG
* * * * * *
1595274 CATCTTCCCTCCCAAG-AAT-TTCAGTCTGCTTACTTCTCGGAATCCTCCGAGGCTGCCGTAGAG
1 CATCTTCCCTCTC-AGCAATCTT-GGTTTGCTTACTTCTCGGAATTCTCCGAGGCTGCTGAAGAG
* * * *
1595337 GACTATAATCTGGAGAATCAGATGAAACAG
64 AACTGTCATCCGGAGAATCAGATGAAACAG
*
1595367 CCTCTTCCCTCTCA
1 CATCTTCCCTCTCA
1595381 ATAAGCTCAG
Statistics
Matches: 176, Mismatches: 22, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
92 3 0.02
93 172 0.98
94 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (93 bp):
CATCTTCCCTCTCAGCAATCTTGGTTTGCTTACTTCTCGGAATTCTCCGAGGCTGCTGAAGAGAA
CTGTCATCCGGAGAATCAGATGAAACAG
Found at i:1608400 original size:20 final size:20
Alignment explanation
Indices: 1608375--1608420 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1608365 ATATGTTTTG
1608375 AAAAATAAATTTTATAG-AA
1 AAAAATAAATTTTATAGTAA
* *
1608394 TAAAAATTAATTTTTTAGTAA
1 -AAAAATAAATTTTATAGTAA
1608415 AAAAAT
1 AAAAAT
1608421 CAGACATTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (20 bp):
AAAAATAAATTTTATAGTAA
Found at i:1608846 original size:58 final size:57
Alignment explanation
Indices: 1608739--1608853 Score: 135
Period size: 58 Copynumber: 2.0 Consensus size: 57
1608729 AATGGGAGTC
* * * * *
1608739 ATAGTTTGAGGATGAAATTGGAATTTTTAAAATTTAGTATTAATTTAGAATGAGAATT
1 ATAGTTTGAGGATGAAATTGAAATATTCAAAATTTAGTACTAA-TTAGAATAAGAATT
1608797 ATAGTTTGAGGATGAAATTGAAATATTCAAAAGTTTACAG-ACTAA-TAGAATAAGAAT
1 ATAGTTTGAGGATGAAATTGAAATATTCAAAA-TTT--AGTACTAATTAGAATAAGAAT
1608854 CATAATTTAG
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
58 40 0.82
59 3 0.06
60 4 0.08
61 2 0.04
ACGTcount: A:0.43, C:0.03, G:0.18, T:0.36
Consensus pattern (57 bp):
ATAGTTTGAGGATGAAATTGAAATATTCAAAATTTAGTACTAATTAGAATAAGAATT
Found at i:1609248 original size:42 final size:43
Alignment explanation
Indices: 1609201--1609290 Score: 121
Period size: 42 Copynumber: 2.1 Consensus size: 43
1609191 ATATTTTATT
* *
1609201 AAAATAAAAATATTA-TAATTATATTAAATATTTATTAAAATA
1 AAAATAAAAATATTATTAAGTATATTAAATACTTATTAAAATA
* *
1609243 AAAAT-AATATATTATTAAGTATATTAATTACTTATTAAAATA
1 AAAATAAAAATATTATTAAGTATATTAAATACTTATTAAAATA
*
1609285 ATAATA
1 AAAATA
1609291 TTATTAAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
41 8 0.20
42 33 0.80
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (43 bp):
AAAATAAAAATATTATTAAGTATATTAAATACTTATTAAAATA
Found at i:1609254 original size:30 final size:32
Alignment explanation
Indices: 1609169--1609325 Score: 104
Period size: 36 Copynumber: 4.7 Consensus size: 32
1609159 ACTACATTTT
* *
1609169 AAATAAAAATACTAATATTATTATATTTTATTA
1 AAATAAAAATAAT-ATATTATAATATTTTATTA
* *
1609202 AAATAAAAATATTATAATTATATTAAATATTTATTA
1 AAATAAAAATAATAT-ATTATA--ATAT-TTTATTA
*
1609238 AAATAAAAATAATATATTATTAAGTATATTAATTA
1 AAATAAAAATAATATATTA-TAA-TAT-TTTATTA
** * *
1609273 CTTATTAAAATAATAATATTATTAA-A--ATATTA
1 -AAATAAAAATAAT-ATATTA-TAATATTTTATTA
*
1609305 AAATAAAAATATTATATTATA
1 AAATAAAAATAATATATTATA
1609326 TTTTAAAAAG
Statistics
Matches: 101, Mismatches: 15, Indels: 20
0.74 0.11 0.15
Matches are distributed among these distances:
29 2 0.02
30 6 0.06
31 9 0.09
32 6 0.06
33 17 0.17
34 1 0.01
35 17 0.17
36 33 0.33
37 10 0.10
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (32 bp):
AAATAAAAATAATATATTATAATATTTTATTA
Found at i:1609292 original size:25 final size:25
Alignment explanation
Indices: 1609263--1609333 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 25
1609253 ATTATTAAGT
** *
1609263 ATATTAATTACTTATTAAAATAATA
1 ATATTAATTAAATATTAAAATAAAA
1609288 ATATT-ATTAAAATATTAAAATAAAA
1 ATATTAATT-AAATATTAAAATAAAA
* *
1609313 ATATTATATTATATTTTAAAA
1 ATATTA-ATTAAATATTAAAA
1609334 AGTATATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
24 3 0.08
25 23 0.61
26 9 0.24
27 3 0.08
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (25 bp):
ATATTAATTAAATATTAAAATAAAA
Found at i:1609296 original size:17 final size:17
Alignment explanation
Indices: 1609243--1609301 Score: 66
Period size: 17 Copynumber: 3.4 Consensus size: 17
1609233 TATTAAAATA
1609243 AAAATAAT-ATATTATT
1 AAAATAATAATATTATT
* *
1609259 AAGTATATTAATTACTTATT
1 AA-AATAATAA-TA-TTATT
1609279 AAAATAATAATATTATT
1 AAAATAATAATATTATT
1609296 AAAATA
1 AAAATA
1609302 TTAAAATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
16 2 0.06
17 15 0.43
18 3 0.09
19 8 0.23
20 7 0.20
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
AAAATAATAATATTATT
Found at i:1613316 original size:3 final size:3
Alignment explanation
Indices: 1613308--1613336 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1613298 TCTCAAAACC
1613308 TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1613337 GGTGCCCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:1617265 original size:25 final size:25
Alignment explanation
Indices: 1617237--1617297 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
1617227 TTTAAATATC
* *
1617237 ACTTTTAAAAGTTCTTTTGTAC-AA
1 ACTTTTAAAAGTTATTTTCTACGAA
*
1617261 TACTTTTAAAAGTTATTTTCTACGGA
1 -ACTTTTAAAAGTTATTTTCTACGAA
1617287 ACTTTTAAAAG
1 ACTTTTAAAAG
1617298 ACACTTTCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
25 31 0.97
26 1 0.03
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.44
Consensus pattern (25 bp):
ACTTTTAAAAGTTATTTTCTACGAA
Found at i:1619863 original size:24 final size:23
Alignment explanation
Indices: 1619831--1619879 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
1619821 CTAATTTTTT
1619831 TTAAAATGAACATTTTTT-ATTTAA
1 TTAAAATG-A-ATTTTTTAATTTAA
* *
1619855 TTAATATGATTTTTTTAATTTAA
1 TTAAAATGAATTTTTTAATTTAA
1619878 TT
1 TT
1619880 CGACTTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 6 0.27
23 9 0.41
24 7 0.32
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (23 bp):
TTAAAATGAATTTTTTAATTTAA
Found at i:1626417 original size:52 final size:53
Alignment explanation
Indices: 1626334--1626433 Score: 175
Period size: 52 Copynumber: 1.9 Consensus size: 53
1626324 ATTTTGAAAT
*
1626334 TCAGTTTTTCGAATTGGTAAAATCTGACCTCGAGTTGAACTCGAAAACAAAAC
1 TCAGTTTTTCGAATTGATAAAATCTGACCTCGAGTTGAACTCGAAAACAAAAC
*
1626387 TCAG-TTTTCGAATTGATAAAATCTGGCCTCGAGTTGAACTCGAAAAC
1 TCAGTTTTTCGAATTGATAAAATCTGACCTCGAGTTGAACTCGAAAAC
1626434 CGACTCACTA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 41 0.91
53 4 0.09
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (53 bp):
TCAGTTTTTCGAATTGATAAAATCTGACCTCGAGTTGAACTCGAAAACAAAAC
Found at i:1631180 original size:123 final size:124
Alignment explanation
Indices: 1630885--1631256 Score: 714
Period size: 123 Copynumber: 3.0 Consensus size: 124
1630875 TTTGTTGTTG
1630885 TTTTAGTGAAATTTTTATGGTAAAAGCTTGAATTATAAGGAAAACCTGCTTGTATACTGTGGGGT
1 TTTTAGTGAAATTTTTATGGTAAAAGCTTGAATTATAAGGAAAACCTGCTTGTATACTGTGGGGT
1630950 ACTCATAATAT-GGGAGTGAATCAACATATTGTGCAATTTGATC-TTGTTGTGCTGGTC
66 ACTCATAATATGGGGAGTGAATCAACATATTGTGCAATTTGATCTTTGTTGTGCTGGTC
1631007 TTTTAGTGAAATTTTTATGGTAAAAGCTTGAATTATAAGGAAAACCTGCTTGTATACTGTGGGGT
1 TTTTAGTGAAATTTTTATGGTAAAAGCTTGAATTATAAGGAAAACCTGCTTGTATACTGTGGGGT
*
1631072 ACTCATAATATGGGGAGTGAATCAACATATTGTGCAATTTGATCTTTGTTGTGCTGGCC
66 ACTCATAATATGGGGAGTGAATCAACATATTGTGCAATTTGATCTTTGTTGTGCTGGTC
1631131 TTTTAGTGAAA-TTTTATGGTAAAAGCTTGAATTATAAGGAAAACCTGCTTGTATACTGTGGGGT
1 TTTTAGTGAAATTTTTATGGTAAAAGCTTGAATTATAAGGAAAACCTGCTTGTATACTGTGGGGT
1631195 ACTCATAATATGGGGAGTGAATCAACATATTGTGCAATTTGATCTTTGTTGTGCTGGTC
66 ACTCATAATATGGGGAGTGAATCAACATATTGTGCAATTTGATCTTTGTTGTGCTGGTC
1631254 TTT
1 TTT
1631257 CAAGAAGGTT
Statistics
Matches: 246, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
122 76 0.31
123 146 0.59
124 24 0.10
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.38
Consensus pattern (124 bp):
TTTTAGTGAAATTTTTATGGTAAAAGCTTGAATTATAAGGAAAACCTGCTTGTATACTGTGGGGT
ACTCATAATATGGGGAGTGAATCAACATATTGTGCAATTTGATCTTTGTTGTGCTGGTC
Found at i:1645893 original size:16 final size:17
Alignment explanation
Indices: 1645872--1645904 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1645862 GAGGCTCACT
1645872 TATTTTC-AAAAAAAAA
1 TATTTTCGAAAAAAAAA
1645888 TATTTTCGAAAAAAAAA
1 TATTTTCGAAAAAAAAA
1645905 CTCACTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.30
Consensus pattern (17 bp):
TATTTTCGAAAAAAAAA
Found at i:1655741 original size:2 final size:2
Alignment explanation
Indices: 1655734--1655793 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
1655724 GTAGGTATTA
1655734 AT AT AT AT AT AT 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 AT AT AT AT AT AT
1655776 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
1655794 GCAAACAATT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.