Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008523.1 Hibiscus syriacus cultivar Beakdansim tig00111392_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: 4657139
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 18
Found at i:4616320 original size:14 final size:14
Alignment explanation
Indices: 4616301--4616337 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
4616291 CATCAATTAA
4616301 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
4616315 ACAAATCACCTTTT
1 ACAAATCAACTTTT
4616329 ACAAATCAA
1 ACAAATCAA
4616338 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:4617756 original size:21 final size:21
Alignment explanation
Indices: 4617690--4617756 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
4617680 GTGAATCGGG
*
4617690 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
4617710 TCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
4617732 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
4617753 CTCT
1 CTCT
4617757 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.19, G:0.36, T:0.25
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:4617775 original size:42 final size:41
Alignment explanation
Indices: 4617690--4617812 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
4617680 GTGAATCGGG
* * * *
4617690 CTCTTGAATGGTGGGA-GGGATCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
4617732 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
4617774 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
4617813 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:4619892 original size:19 final size:19
Alignment explanation
Indices: 4619868--4619956 Score: 142
Period size: 19 Copynumber: 4.7 Consensus size: 19
4619858 GCGACGAGAG
*
4619868 AATCGCAACACGAAATGAA
1 AATCGCAACGCGAAATGAA
* *
4619887 AATCGCAACGCGGAATAAA
1 AATCGCAACGCGAAATGAA
4619906 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
4619925 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
4619944 AATCGCAATGCGA
1 AATCGCAACGCGA
4619957 TTTTTGTTTC
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 64 1.00
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:4619988 original size:19 final size:19
Alignment explanation
Indices: 4619952--4619996 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
4619942 AAAATCGCAA
*
4619952 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
4619971 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
4619990 TGCGATT
1 TGCGATT
4619997 CTCATTGCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.07, C:0.16, G:0.24, T:0.53
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:4620569 original size:20 final size:20
Alignment explanation
Indices: 4620544--4620596 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
4620534 GCGCTATGTA
4620544 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
4620564 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
4620584 TATCTCGTTGCGA
1 AATCGCGTTGCGA
4620597 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:4620630 original size:20 final size:20
Alignment explanation
Indices: 4620605--4620658 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
4620595 GATTTTGTAT
4620605 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
4620625 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
4620645 TATCGCATTGCGAT
1 TATCGCATTGCGAT
4620659 TTTTCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:4620643 original size:61 final size:61
Alignment explanation
Indices: 4620545--4620661 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
4620535 CGCTATGTAA
* * * * *
4620545 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
4620606 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
4620662 TCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:4620677 original size:61 final size:61
Alignment explanation
Indices: 4620540--4620679 Score: 160
Period size: 61 Copynumber: 2.3 Consensus size: 61
4620530 AATGGCGCTA
* * * * *
4620540 TGTAA-ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTT
1 TGTAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTT
* * * *
4620600 TGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTT
1 TGTAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTT
4620661 T-TCCAAT-TCGCGTTGCGAT
1 TGT--AATATCGCGTTGCGAT
4620680 TTACTTATTC
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
60 5 0.08
61 59 0.89
62 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (61 bp):
TGTAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTT
Found at i:4620769 original size:21 final size:21
Alignment explanation
Indices: 4620729--4620769 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4620719 ACTGTAGACC
**
4620729 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
4620750 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
4620770 ACGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:4628896 original size:2 final size:2
Alignment explanation
Indices: 4628885--4628918 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
4628875 CTTCAAACCA
4628885 AT AT AT -T AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4628919 TAAATAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4636805 original size:36 final size:34
Alignment explanation
Indices: 4636765--4636848 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 34
4636755 GAAGTTAAAA
* *
4636765 TAAATATTTTAAAAAATAATTTTGGAATGTTATGAT
1 TAAATAATTTAAAAAATAA--TTAGAATGTTATGAT
*
4636801 TAAATAATTT--AAGA-AATTAGAATGTTATGAT
1 TAAATAATTTAAAAAATAATTAGAATGTTATGAT
*
4636832 GAAATAATTTAAAAAAT
1 TAAATAATTTAAAAAAT
4636849 TATGAATTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
31 23 0.57
33 5 0.12
34 3 0.08
36 9 0.22
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (34 bp):
TAAATAATTTAAAAAATAATTAGAATGTTATGAT
Found at i:4636824 original size:31 final size:32
Alignment explanation
Indices: 4636789--4636855 Score: 109
Period size: 31 Copynumber: 2.1 Consensus size: 32
4636779 AATAATTTTG
* *
4636789 GAATGTTATGATTAAATAATTTAAGAAATTA-
1 GAATGTTATGATGAAATAATTTAAAAAATTAT
4636820 GAATGTTATGATGAAATAATTTAAAAAATTAT
1 GAATGTTATGATGAAATAATTTAAAAAATTAT
4636852 GAAT
1 GAAT
4636856 TTAAAATGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
31 29 0.88
32 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.37
Consensus pattern (32 bp):
GAATGTTATGATGAAATAATTTAAAAAATTAT
Found at i:4640572 original size:20 final size:21
Alignment explanation
Indices: 4640527--4640572 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
4640517 TCCTAAAAAT
4640527 TTAAAATTATAATATATTTTA
1 TTAAAATTATAATATATTTTA
* *
4640548 -AAAAATT-TAATATTTTTTA
1 TTAAAATTATAATATATTTTA
4640567 TTAAAA
1 TTAAAA
4640573 AATTATTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTAAAATTATAATATATTTTA
Found at i:4645761 original size:17 final size:17
Alignment explanation
Indices: 4645741--4645773 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4645731 TTTAGGGAAG
4645741 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
*
4645758 TAGTTCATTTATTAAA
1 TAGTTCATTAATTAAA
4645774 TTAACTCTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:4648701 original size:242 final size:243
Alignment explanation
Indices: 4648274--4649007 Score: 1418
Period size: 244 Copynumber: 3.0 Consensus size: 243
4648264 TTTCTCCGAA
4648274 CTCCGCCTCCATTTGGAAACCGATCATAGACAAATTTAAAAATCGCCTTGATGGTTGGAAAAGTA
1 CTCCGCCTCCATTTGGAAACCGATCATAGACAAATTTAAAAATCGCCTTGATGGTTGGAAAAGTA
4648339 GGATGCTCTCTTTTGGGGGACGCATAACCTTAGCCAAGTCCGTCCTATCAAGCTTACCGGTGTAC
66 GGATGC-CTCTTTTGGGGGACGCATAACCTTAGCCAAGTCCGTCCTATCAAGCTTACCGGTGTAC
4648404 TTCTTGTCCATTTTCCAAATGCCGTGTTCGTCAGCATCGACGCTTAATAAAATAATAGCCAGGTT
130 TTCTTGTCCATTTTCCAAATGCCGTGTTCGTCAGCATCGACGCTTAATAAAATAATAGCCAGGTT
4648469 TATCTGGGGTTCCACTAATTCTAGAGCCATTCACTGGGTTAGTTGGAAT
195 TATCTGGGGTTCCACTAATTCTAGAGCCATTCACTGGGTTAGTTGGAAT
4648518 CTCCGCCTCCATTTGGAAACCGATCATAGACAAATTTAAAAATCGCCTTGATGGTTGGAAAAGTA
1 CTCCGCCTCCATTTGGAAACCGATCATAGACAAATTTAAAAATCGCCTTGATGGTTGGAAAAGTA
4648583 GGATG-CTCTTTTGGGGGACGCATAACCTTAGCCAAAGTCCGT-CTATCAAGCTTACCGGTGTAC
66 GGATGCCTCTTTTGGGGGACGCATAACCTTAGCC-AAGTCCGTCCTATCAAGCTTACCGGTGTAC
4648646 TTCTTGTCCATTTTCCAAATGCCGTGTTCGTCAGCATCGACGCTTAATAAAATAATAGCCAGGTT
130 TTCTTGTCCATTTTCCAAATGCCGTGTTCGTCAGCATCGACGCTTAATAAAATAATAGCCAGGTT
4648711 TATCTGGGGTTCCACTAATTCTAGAGCCATTCACTGGGTTAGTTGGAAT
195 TATCTGGGGTTCCACTAATTCTAGAGCCATTCACTGGGTTAGTTGGAAT
4648760 CTCCGCCTCCATTTGGAAACCGATCATAGACAAATTTAAAAATCGCCTTGATGGTTGGAAAAGTA
1 CTCCGCCTCCATTTGGAAACCGATCATAGACAAATTTAAAAATCGCCTTGATGGTTGGAAAAGTA
4648825 GGATGCTCTCTTTTGGGGGACGCATAACCTTAGCCAAGTCCGTCCTATCAAGCTTACCGGTGTAC
66 GGATGC-CTCTTTTGGGGGACGCATAACCTTAGCCAAGTCCGTCCTATCAAGCTTACCGGTGTAC
4648890 TTCTTGTCCATTTTCCAAATGCCGTGTTCGTCAGCATCGACGCTTAATAAAATAATAGCCAGGTT
130 TTCTTGTCCATTTTCCAAATGCCGTGTTCGTCAGCATCGACGCTTAATAAAATAATAGCCAGGTT
*
4648955 TATCTGGGGTTCCACTTATTCTAGAGCCATTCACTGGGTTAGTTGGAAT
195 TATCTGGGGTTCCACTAATTCTAGAGCCATTCACTGGGTTAGTTGGAAT
4649004 CTCC
1 CTCC
4649008 TAAGCAGATC
Statistics
Matches: 485, Mismatches: 1, Indels: 8
0.98 0.00 0.02
Matches are distributed among these distances:
242 233 0.48
243 16 0.03
244 236 0.49
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (243 bp):
CTCCGCCTCCATTTGGAAACCGATCATAGACAAATTTAAAAATCGCCTTGATGGTTGGAAAAGTA
GGATGCCTCTTTTGGGGGACGCATAACCTTAGCCAAGTCCGTCCTATCAAGCTTACCGGTGTACT
TCTTGTCCATTTTCCAAATGCCGTGTTCGTCAGCATCGACGCTTAATAAAATAATAGCCAGGTTT
ATCTGGGGTTCCACTAATTCTAGAGCCATTCACTGGGTTAGTTGGAAT
Found at i:4652443 original size:23 final size:25
Alignment explanation
Indices: 4652399--4652445 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
4652389 CCTATAGTTG
4652399 AGATATCATTTTATAACTTTAAAAT
1 AGATATCATTTTATAACTTTAAAAT
4652424 AGATA-CATTATTA-AA-TTTAAAA
1 AGATATCATT-TTATAACTTTAAAA
4652446 CAATCAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 7 0.33
24 6 0.29
25 8 0.38
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.40
Consensus pattern (25 bp):
AGATATCATTTTATAACTTTAAAAT
Found at i:4653180 original size:25 final size:25
Alignment explanation
Indices: 4653140--4653190 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
4653130 CGATGAAGCA
*
4653140 CAAATCTTAAACCCACATCATCTCT
1 CAAATCTTAAACCCACACCATCTCT
** *
4653165 CAAATCTTAATTCCACGCCATCTCT
1 CAAATCTTAAACCCACACCATCTCT
4653190 C
1 C
4653191 GTTATCGTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.29
Consensus pattern (25 bp):
CAAATCTTAAACCCACACCATCTCT
Found at i:4654738 original size:173 final size:174
Alignment explanation
Indices: 4654461--4654806 Score: 502
Period size: 173 Copynumber: 2.0 Consensus size: 174
4654451 GTAAGATTTT
* * * * *
4654461 TTTTTTCATTAAACTAATGTGAATTACAAAGTAGTATCAATTCTAAGTAATCTAAATCATTTAAC
1 TTTTTTCATGAAACTAATGTGAATTACAAAGTAATATCAAGTCTAAATAATCTAAACCATTTAAC
4654526 AATAAACGTTTAATCATCTATGCTGTTGATGGTGTCTGAACTCATGACCTCTAGAAACAATAATA
66 AATAAACGTTTAATCATCTATGCTGTTGATGGTGTCTGAACTCATGACCTCTAGAAACAA-AATA
* *
4654591 -ATTTTTAACCGCTGAAATAAGTTGATTATGAAATATTAAAGTAAA
130 CATTTTTAACCACCGAAATAAG-TGATTATGAAATATTAAAGTAAA
* *
4654636 TTTTTTCATGAAACTAATGTG-ATTACAAAGTAATATC-AGTCTAAATACTCTAAACCATTTGAC
1 TTTTTTCATGAAACTAATGTGAATTACAAAGTAATATCAAGTCTAAATAATCTAAACCATTTAAC
* * * * *
4654699 AATGAACGTTTAATCATCTTTG-TAGTTGCTGGTGTCTGAACTCATGACCTCTATAAACAAATTA
66 AATAAACGTTTAATCATCTATGCT-GTTGATGGTGTCTGAACTCATGACCTCTAGAAACAAAATA
*
4654763 CTTTTTTAACCACCGAAATAAGTGATTATGAAATATTAAAGTAA
130 CATTTTTAACCACCGAAATAAGTGATTATGAAATATTAAAGTAA
4654807 GAACTAAATT
Statistics
Matches: 154, Mismatches: 15, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
172 26 0.17
173 93 0.60
174 15 0.10
175 20 0.13
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (174 bp):
TTTTTTCATGAAACTAATGTGAATTACAAAGTAATATCAAGTCTAAATAATCTAAACCATTTAAC
AATAAACGTTTAATCATCTATGCTGTTGATGGTGTCTGAACTCATGACCTCTAGAAACAAAATAC
ATTTTTAACCACCGAAATAAGTGATTATGAAATATTAAAGTAAA
Found at i:4655153 original size:29 final size:26
Alignment explanation
Indices: 4655113--4655172 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
4655103 AAGGAAATTA
*
4655113 AAATTATGATTAAATTCATAAAATATAT
1 AAATTAAGATTAAA-T-ATAAAATATAT
*
4655141 AAATTAAGAATTAAATATATAATATAT
1 AAATTAAG-ATTAAATATAAAATATAT
*
4655168 CAATT
1 AAATT
4655173 TTTTTAACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 14 0.50
28 8 0.29
29 6 0.21
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (26 bp):
AAATTAAGATTAAATATAAAATATAT
Done.