Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000856.1 Hibiscus syriacus cultivar Beakdansim tig00001659_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: 63307
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:15937 original size:559 final size:561
Alignment explanation
Indices: 15191--16253 Score: 1706
Period size: 559 Copynumber: 1.9 Consensus size: 561
15181 CATTTAATAA
15191 TTTCCTTAATCATATAAATTTATAAAATACTGTTTGATCATTGAAAACTAATTTGATTTCAGTCA
1 TTTCCTTAATCATATAAATTTATAAAATACTGTTTGATCATTGAAAACTAATTTGATTTCAGTCA
* * * * *
15256 GTAATTAGGCAGTTAGTGTTGTTTCATATCCAAATACAACTGCCTAATACTGCTTGATTTTAAAT
66 GTAATTAGACAGTTAATGTTGTTTCATACCCAAATACAACTGCCCAATACTGCTTGATTTTAAAC
15321 CATTTAAAATATAACATTTATACTATTCACTCATAAATAAGATTAATACTAAAATTAGACAAAAC
131 CATTTAAAATATAACATTTATACTATTCACTCATAAATAAGATTAATACTAAAATTAGACAAAAC
* *
15386 TAAAGAAAATAACCATAATTATTATTACAAACCCTTTTAAAATAAATCTGATAAAGCAACCTAAC
196 TAAAGAAAATAACCATAATTACTATTACAAACCCTTTTAAAATAAATCTGATAAAGCAACCCAAC
* * * *
15451 -ATATATAATGTACATGCCACAAATAATTCAAAGTTAGGATGTCTTATTGATATTG-TCGGTAGG
261 AAAATATAATGTACATGCCACAAATAAGTCAAAGTTAGGATGTCTTACTGATATTGTTC-GTAAG
* * *
15514 TTTGATTTTTACATGAGATGTTGGCAAGCTCCTCACTCCACGACCTCTATTTTATTCAAATCTAC
325 TTTGATTTTTACATAAGATGTTGGCAAGCTCCTCACTCCACAACCTCTATTTTATTCAAACCTAC
* *
15579 GCATGAAAATCATCACG-AACTAAGTAAAATTTAGTGAGGTAAAAATATAACTAAAGTGATAT-A
390 GCACGAAAATCATCACGCAA-TAAGTAAAACTTAGTGAGGTAAAAATATAACTAAAGTGATATAA
* * *
15642 AATCATAAATTTCATAAAATATAATAAATAAATTGTAATTTAAATAAAAACTATTCGATCACTCA
454 AACCATAAATTTCATAAAATATAAGAAATAAAGTGTAATTTAAATAAAAACTATTCGATCACTCA
15707 TAAATTTTGTTTCATTTAATAATTTCCTTTTGAACTTAAATTT
519 TAAATTTTGTTTCATTTAATAATTTCCTTTTGAACTTAAATTT
*
15750 TTTCCTTAATCATATAAATTTATAAAATATTGTTTGATCATTG-AAACTAATTTGATTTCAGAT-
1 TTTCCTTAATCATATAAATTTATAAAATACTGTTTGATCATTGAAAACTAATTTGATTTCAG-TC
*
15813 AGTAATTAGACAGTTCAATGTTGTTTCATACCCAAATACAACTGCCCAATACTGTTTGATTTTAA
65 AGTAATTAGACAGTT-AATGTTGTTTCATACCCAAATACAACTGCCCAATACTGCTTGATTTTAA
* *
15878 ACCATTTAAAATATAACATTTATACTATTCACTCATAAATAATATTAATACTCAAATTAGACAAA
129 ACCATTTAAAATATAACATTTATACTATTCACTCATAAATAAGATTAATACTAAAATTAGACAAA
* * *
15943 ACTAAAGAAAATAACCATAATTACTATTATAAACCCTTTTCAAATGAATCTGATAAAGCAACCCA
194 ACTAAAGAAAATAACCATAATTACTATTACAAACCCTTTTAAAATAAATCTGATAAAGCAACCCA
* *
16008 ACAAAATATAATGTACTTGCCACTAATAAGTCAAAGTTAGGATGTCTTACTGATATTGTTCGTAA
259 ACAAAATATAATGTACATGCCACAAATAAGTCAAAGTTAGGATGTCTTACTGATATTGTTCGTAA
* * * **
16073 GTTTGATTTTTGCATAAGATGTTGGCAAGTTCCTCACTTCACAACCTCTATTTTATTTGAACCTA
324 GTTTGATTTTTACATAAGATGTTGGCAAGCTCCTCACTCCACAACCTCTATTTTATTCAAACCTA
* * **
16138 CGTACGAAAATCATCACGCGATAAGTAAAACTTAGTGAGGTAGGAATATAACTAAAGTGATATAA
389 CGCACGAAAATCATCACGCAATAAGTAAAACTTAGTGAGGTAAAAATATAACTAAAGTGATATAA
*
16203 AACCATAAATTTCATAAAATATAAGCAATAAAGTGTAATTTAAATAAAAAC
454 AACCATAAATTTCATAAAATATAAGAAATAAAGTGTAATTTAAATAAAAAC
16254 ATTAAACTTC
Statistics
Matches: 460, Mismatches: 38, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
558 32 0.07
559 212 0.46
560 165 0.36
561 51 0.11
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (561 bp):
TTTCCTTAATCATATAAATTTATAAAATACTGTTTGATCATTGAAAACTAATTTGATTTCAGTCA
GTAATTAGACAGTTAATGTTGTTTCATACCCAAATACAACTGCCCAATACTGCTTGATTTTAAAC
CATTTAAAATATAACATTTATACTATTCACTCATAAATAAGATTAATACTAAAATTAGACAAAAC
TAAAGAAAATAACCATAATTACTATTACAAACCCTTTTAAAATAAATCTGATAAAGCAACCCAAC
AAAATATAATGTACATGCCACAAATAAGTCAAAGTTAGGATGTCTTACTGATATTGTTCGTAAGT
TTGATTTTTACATAAGATGTTGGCAAGCTCCTCACTCCACAACCTCTATTTTATTCAAACCTACG
CACGAAAATCATCACGCAATAAGTAAAACTTAGTGAGGTAAAAATATAACTAAAGTGATATAAAA
CCATAAATTTCATAAAATATAAGAAATAAAGTGTAATTTAAATAAAAACTATTCGATCACTCATA
AATTTTGTTTCATTTAATAATTTCCTTTTGAACTTAAATTT
Found at i:16632 original size:29 final size:29
Alignment explanation
Indices: 16598--16691 Score: 143
Period size: 29 Copynumber: 3.2 Consensus size: 29
16588 TACCAGCGAT
* *
16598 GTTGAACATTGGTACACGAATGTACCAAA
1 GTTGAACATTAGTACACTAATGTACCAAA
*
16627 GTTGAACATTAGTACACTAATGTACTAAA
1 GTTGAACATTAGTACACTAATGTACCAAA
*
16656 GTTGAATATTAGTACACTAATGTACCAAA
1 GTTGAACATTAGTACACTAATGTACCAAA
*
16685 GCTGAAC
1 GTTGAAC
16692 TTAAATGCTT
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (29 bp):
GTTGAACATTAGTACACTAATGTACCAAA
Found at i:20051 original size:29 final size:29
Alignment explanation
Indices: 20009--20073 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
19999 TACCAACAAT
*
20009 GTTGAACATTGGTACACGAATATACTAAA
1 GTTGAACATTGGTACACGAATATACCAAA
* *
20038 GTTGAACATTGGTACACTAATGTACCAAA
1 GTTGAACATTGGTACACGAATATACCAAA
20067 GTTGAAC
1 GTTGAAC
20074 TTAAATTCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (29 bp):
GTTGAACATTGGTACACGAATATACCAAA
Found at i:21169 original size:17 final size:17
Alignment explanation
Indices: 21127--21191 Score: 69
Period size: 17 Copynumber: 3.8 Consensus size: 17
21117 AATATGTGTT
* *
21127 TGATAACTGTAAAATATA
1 TGATATCTGT-AAATATC
21145 TG-TATCTGTAAATATC
1 TGATATCTGTAAATATC
* *
21161 TGATGTCTGTAAATATT
1 TGATATCTGTAAATATC
*
21178 TGATAACTGTAAAT
1 TGATATCTGTAAAT
21192 GTTTAGAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
16 8 0.20
17 30 0.75
18 2 0.05
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (17 bp):
TGATATCTGTAAATATC
Found at i:25755 original size:23 final size:23
Alignment explanation
Indices: 25729--25778 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
25719 ACTTAAAAAG
*
25729 GGCTCTCCTTTTTATTACTCCAT
1 GGCTCTCCATTTTATTACTCCAT
25752 GGCTCTCCATTTTATTACTCCAT
1 GGCTCTCCATTTTATTACTCCAT
25775 GGCT
1 GGCT
25779 TTCTATGCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.14, C:0.30, G:0.12, T:0.44
Consensus pattern (23 bp):
GGCTCTCCATTTTATTACTCCAT
Found at i:39073 original size:60 final size:59
Alignment explanation
Indices: 39005--39165 Score: 191
Period size: 60 Copynumber: 2.7 Consensus size: 59
38995 GATGAATTTG
* *
39005 GGGATGAAATTGGAAGATTCAAAAGTGTGGGGACCAATTTAGAAAGAGAGTCATAGTTT
1 GGGATGAAATTGGAAGATTCAAAAGTTTAGGGACCAATTTAGAAAGAGAGTCATAGTTT
* * * *
39064 AGGGATGAAATT-AAATTG-TTTAAAAGTTTAGGGACTAATTTAGAATGAGAGTCATAGTTT
1 -GGGATGAAATTGGAA--GATTCAAAAGTTTAGGGACCAATTTAGAAAGAGAGTCATAGTTT
* * *
39124 GAGGATGAAACTGGAATATTCAAAAGTTTAAGGACCAATTTA
1 G-GGATGAAATTGGAAGATTCAAAAGTTTAGGGACCAATTTA
39166 AAATGACGGT
Statistics
Matches: 84, Mismatches: 12, Indels: 10
0.79 0.11 0.09
Matches are distributed among these distances:
59 3 0.04
60 78 0.93
61 3 0.04
ACGTcount: A:0.39, C:0.06, G:0.25, T:0.29
Consensus pattern (59 bp):
GGGATGAAATTGGAAGATTCAAAAGTTTAGGGACCAATTTAGAAAGAGAGTCATAGTTT
Found at i:39171 original size:60 final size:59
Alignment explanation
Indices: 39001--39187 Score: 184
Period size: 60 Copynumber: 3.1 Consensus size: 59
38991 TTTGGATGAA
* * * *
39001 TTTGGGGATGAAATTGGAAGATTCAAAAGTGTGGGGACCAATTTAGAAA-GAGAGTCATAG
1 TTTGAGGATGAAA-TGGAATATTCAAAAGTTTAGGGACCAATTTA-AAATGAGAGTCATAG
** * * * *
39061 TTT-AGGGATGAAATTAAATTGTTTAAAAGTTTAGGGACTAATTTAGAATGAGAGTCATAG
1 TTTGA-GGATGAAATGGAA-TATTCAAAAGTTTAGGGACCAATTTAAAATGAGAGTCATAG
* *
39121 TTTGAGGATGAAACTGGAATATTCAAAAGTTTAAGGACCAATTTAAAATGACG-GTTATAG
1 TTTGAGGATGAAA-TGGAATATTCAAAAGTTTAGGGACCAATTTAAAATGA-GAGTCATAG
39181 -TTGAGGA
1 TTTGAGGA
39188 CATATGATGA
Statistics
Matches: 103, Mismatches: 18, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
59 12 0.12
60 86 0.83
61 5 0.05
ACGTcount: A:0.38, C:0.06, G:0.26, T:0.30
Consensus pattern (59 bp):
TTTGAGGATGAAATGGAATATTCAAAAGTTTAGGGACCAATTTAAAATGAGAGTCATAG
Found at i:40875 original size:21 final size:21
Alignment explanation
Indices: 40849--40893 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
40839 GATTTCTGGG
* *
40849 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
40870 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
40891 CAA
1 CAA
40894 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:42658 original size:22 final size:22
Alignment explanation
Indices: 42585--42651 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
42575 TATGGACATC
*
42585 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
42607 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
42629 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
42652 TTATACGAGC
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:45185 original size:19 final size:19
Alignment explanation
Indices: 45161--45199 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
45151 GTTACTGCAG
45161 TTCATTTGATTAACATGCT
1 TTCATTTGATTAACATGCT
45180 TTCATTTGATTAACATGCT
1 TTCATTTGATTAACATGCT
45199 T
1 T
45200 CCCACAAGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (19 bp):
TTCATTTGATTAACATGCT
Found at i:47604 original size:27 final size:27
Alignment explanation
Indices: 47574--47635 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
47564 TGTTAAAACT
47574 GTTGTGCAGTTAGTTACAGCCAGCTTA
1 GTTGTGCAGTTAGTTACAGCCAGCTTA
*
47601 GTTGTGCATTTAGTTACAGCCAGCTTA
1 GTTGTGCAGTTAGTTACAGCCAGCTTA
47628 GTTGTGCA
1 GTTGTGCA
47636 AACTTGTATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (27 bp):
GTTGTGCAGTTAGTTACAGCCAGCTTA
Found at i:50779 original size:24 final size:24
Alignment explanation
Indices: 50752--50806 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
50742 TGGAGATTTG
50752 AAATTTTAATATTAT-ATTTTTTAT
1 AAATTTT-ATATTATAATTTTTTAT
* * *
50776 AAATTTTGTTTTCTAATTTTTTAT
1 AAATTTTATATTATAATTTTTTAT
50800 AAATTTT
1 AAATTTT
50807 TAATGAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 4 0.15
24 23 0.85
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (24 bp):
AAATTTTATATTATAATTTTTTAT
Found at i:50818 original size:24 final size:25
Alignment explanation
Indices: 50765--50818 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
50755 TTTTAATATT
** *
50765 ATATTTTTTATAAATTTTGTTTTCT
1 ATATTTTTTATAAATTTTGTAATCA
*
50790 A-ATTTTTTATAAATTTT-TAATGA
1 ATATTTTTTATAAATTTTGTAATCA
50813 ATATTT
1 ATATTT
50819 ATAACTTTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
23 3 0.12
24 20 0.83
25 1 0.04
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (25 bp):
ATATTTTTTATAAATTTTGTAATCA
Found at i:52914 original size:25 final size:25
Alignment explanation
Indices: 52886--52943 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 25
52876 AATATTATAT
52886 ATATAAT-TAATATAAAAAATATAAA
1 ATATAATAT-ATATAAAAAATATAAA
* **
52911 ATATTATATATATAATTAATATAAA
1 ATATAATATATATAAAAAATATAAA
52936 A-A-AATATA
1 ATATAATATA
52944 AAATATTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 5 0.18
24 1 0.04
25 21 0.75
26 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
ATATAATATATATAAAAAATATAAA
Found at i:52917 original size:34 final size:35
Alignment explanation
Indices: 52874--52959 Score: 165
Period size: 35 Copynumber: 2.5 Consensus size: 35
52864 CCCGAACCCG
52874 AAAATATTATATATATAATTAATAT-AAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAAATAT
52908 AAAATATTATATATATAATTAATATAAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAAATAT
52943 AAAATATTATATATATA
1 AAAATATTATATATATA
52960 TATAATCGGG
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
34 25 0.49
35 26 0.51
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (35 bp):
AAAATATTATATATATAATTAATATAAAAAAATAT
Done.