Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005889.1 Hibiscus syriacus cultivar Beakdansim tig00013829_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: 93020
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:10310 original size:71 final size:71
Alignment explanation
Indices: 10131--10623 Score: 493
Period size: 71 Copynumber: 7.0 Consensus size: 71
10121 AGGGTGCTAG
* * * * *
10131 ATTCACTTATTAAAAGATCATAAAAACACA-G-GTGTTACGACAACTTAAAAAGATCATCATATG
1 ATTCACTTCTTAAAAGATCATAAAAGCACATGAGTGTTACGACAACATAGAAAGATAATCATATG
10194 ATCCTA
66 ATCCTA
10200 ATTCA--T-TTAAAAGATCATAAAAGCACATGAGTGTTACGACAACATAGAAAGATTAAT-ATAT
1 ATTCACTTCTTAAAAGATCATAAAAGCACATGAGTGTTACGACAACATAGAAAGA-TAATCATAT
10261 GATCCTA
65 GATCCTA
* * * * * *
10268 TTTCACTTCTTAAAAGATCATAAAAGAACAGGAGGGTTACGACAACATAGAAAGATCATCGTATG
1 ATTCACTTCTTAAAAGATCATAAAAGCACATGAGTGTTACGACAACATAGAAAGATAATCATATG
10333 ATCCTA
66 ATCCTA
* * * * * ** *
10339 ATTTACTTCTTAAAGGATCATCAAATCACATAAGCATTACCACAACATAGAAAGA-ACATCATAT
1 ATTCACTTCTTAAAAGATCATAAAAGCACATGAGTGTTACGACAACATAGAAAGATA-ATCATAT
10403 GATCCTA
65 GATCCTA
* * ** *
10410 ATTCACTTCTTATAAGATCATAAAAGCACATGAGTGTTACGACAACTTAGAAAGATCGTCATATA
1 ATTCACTTCTTAAAAGATCATAAAAGCACATGAGTGTTACGACAACATAGAAAGATAATCATATG
10475 ATCCTA
66 ATCCTA
* ** * * * * * *
10481 ATTAACGCCTCAAAAGATCATTAAAGCACAT-ACGTGTTACAAAAACTTAGAAAGATCATCATAT
1 ATTCACTTCTTAAAAGATCATAAAAGCACATGA-GTGTTACGACAACATAGAAAGATAATCATAT
*
10545 AATCCTA
65 GATCCTA
* * * * * * *
10552 ATCCACTTCTTAAAAGATCACCAAAA-CATAT-AGGCGTTACGAAAACTTAGAAAGATCATCATA
1 ATTCACTTCTTAAAAGATCA-TAAAAGCACATGA-GTGTTACGACAACATAGAAAGATAATCATA
*
10615 TGAACCTA
64 TGATCCTA
10623 A
1 A
10624 ACTTCTAAAA
Statistics
Matches: 355, Mismatches: 58, Indels: 20
0.82 0.13 0.05
Matches are distributed among these distances:
66 20 0.06
67 2 0.01
68 35 0.10
69 8 0.02
70 5 0.01
71 282 0.79
72 3 0.01
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.27
Consensus pattern (71 bp):
ATTCACTTCTTAAAAGATCATAAAAGCACATGAGTGTTACGACAACATAGAAAGATAATCATATG
ATCCTA
Found at i:10403 original size:142 final size:141
Alignment explanation
Indices: 10131--10623 Score: 543
Period size: 142 Copynumber: 3.5 Consensus size: 141
10121 AGGGTGCTAG
* *
10131 ATTCACTTATTAAAAGATCATAAAA-ACACAGGTGTTACGACAACTTAAAAAGATCATCATATGA
1 ATTCACTTCTTAAAAGATCATAAAAGACACAGGTGTTACGACAACTTAGAAAGATCATCATATGA
* *
10195 TCCTAA-TT-CAT-TTAAAAGATCATAAAAGCACATGAGTGTTACGACAACATAGAAAGATTA-A
66 TCCTAATTTACATCTTAAAAGATCATAAAAGCACATAAGTGTTACAACAACATAGAAAGA--ACA
10256 T-ATATGATCCTA
129 TCATATGATCCTA
* * * *
10268 TTTCACTTCTTAAAAGATCATAAAAGA-ACAGGAGGGTTACGACAACATAGAAAGATCATCGTAT
1 ATTCACTTCTTAAAAGATCATAAAAGACACA-G-GTGTTACGACAACTTAGAAAGATCATCATAT
* * * * ** *
10332 GATCCTAATTTACTTCTTAAAGGATCATCAAATCACATAAGCATTACCACAACATAGAAAGAACA
64 GATCCTAATTTACATCTTAAAAGATCATAAAAGCACATAAGTGTTACAACAACATAGAAAGAACA
10397 TCATATGATCCTA
129 TCATATGATCCTA
* *
10410 ATTCACTTCTTATAAGATCATAAAAG-CACATGAGTGTTACGACAACTTAGAAAGATCGTCATAT
1 ATTCACTTCTTAAAAGATCATAAAAGACACA-G-GTGTTACGACAACTTAGAAAGATCATCATAT
* * ** * * * * * *
10474 AATCCTAATTAACGCCTCAAAAGATCATTAAAGCACATACGTGTTACAAAAACTTAGAAAGATCA
64 GATCCTAATTTACATCTTAAAAGATCATAAAAGCACATAAGTGTTACAACAACATAGAAAGAACA
*
10539 TCATATAATCCTA
129 TCATATGATCCTA
* * * * * * *
10552 ATCCACTTCTTAAAAGATCACCAAAACATATAGGCGTTACGAAAACTTAGAAAGATCATCATATG
1 ATTCACTTCTTAAAAGATCA-TAAAAGACACAGGTGTTACGACAACTTAGAAAGATCATCATATG
*
10617 AACCTAA
65 ATCCTAA
10624 ACTTCTAAAA
Statistics
Matches: 297, Mismatches: 48, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
137 26 0.09
138 2 0.01
139 35 0.12
140 3 0.01
141 4 0.01
142 220 0.74
143 5 0.02
144 2 0.01
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.27
Consensus pattern (141 bp):
ATTCACTTCTTAAAAGATCATAAAAGACACAGGTGTTACGACAACTTAGAAAGATCATCATATGA
TCCTAATTTACATCTTAAAAGATCATAAAAGCACATAAGTGTTACAACAACATAGAAAGAACATC
ATATGATCCTA
Found at i:10605 original size:213 final size:208
Alignment explanation
Indices: 10134--10623 Score: 572
Period size: 213 Copynumber: 2.3 Consensus size: 208
10124 GTGCTAGATT
* * * * *
10134 CACTTATTAAAAGATCATAAAA-ACACAGGTGTTACGACAACTTAAAAAGATCATCATATGATCC
1 CACTTCTTAAAAGATCACAAAACACATAGGCGTTACGACAACTTAGAAAGATCATCATATGATCC
10198 TAATTCATTTAAAAGATCATAAAAGCACATGAGTGTTACGACAACATAGAAAGATTAATATATGA
66 TAATTCATTTAAAAGATCATAAAAGCACATGAGTGTTACGACAACATAGAAAGATTAATATA-GA
* * ** * * *
10263 TCCTATTTCACTTCTTAAAAGATCATAAAAGAACAGGAGGGTTACGACAACATAGAAAGATCATC
130 TCCTAATTAACGCCTCAAAAGATCATAAAAGAACAGGAGGGTTACAAAAACATAGAAAGATCATC
* * *
10328 GTATGATCCTAATT
195 ATATAATCCTAATC
* * * * * * * *
10342 TACTTCTTAAAGGATCATCAAATCACATAAGCATTACCACAACATAGAAAGAACATCATATGATC
1 CACTTCTTAAAAGATCA-CAAAACACATAGGCGTTACGACAACTTAGAAAGATCATCATATGATC
* * *
10407 CTAATTCACTTCTTATAAGATCATAAAAGCACATGAGTGTTACGACAACTTAGAAAGATCGTCAT
65 CTAATTCA--T-TTAAAAGATCATAAAAGCACATGAGTGTTACGACAACATAGAAAGAT--TAAT
* * * * *
10472 ATA-ATCCTAATTAACGCCTCAAAAGATCATTAAAGCACA-TACGTGTTACAAAAACTTAGAAAG
125 ATAGATCCTAATTAACGCCTCAAAAGATCATAAAAGAACAGGA-GGGTTACAAAAACATAGAAAG
10535 ATCATCATATAATCCTAATC
189 ATCATCATATAATCCTAATC
* * *
10555 CACTTCTTAAAAGATCACCAAAACATATAGGCGTTACGAAAACTTAGAAAGATCATCATATGAAC
1 CACTTCTTAAAAGATCA-CAAAACACATAGGCGTTACGACAACTTAGAAAGATCATCATATGATC
10620 CTAA
65 CTAA
10624 ACTTCTAAAA
Statistics
Matches: 231, Mismatches: 43, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
208 14 0.06
209 3 0.01
210 41 0.18
212 2 0.01
213 165 0.71
215 6 0.03
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.26
Consensus pattern (208 bp):
CACTTCTTAAAAGATCACAAAACACATAGGCGTTACGACAACTTAGAAAGATCATCATATGATCC
TAATTCATTTAAAAGATCATAAAAGCACATGAGTGTTACGACAACATAGAAAGATTAATATAGAT
CCTAATTAACGCCTCAAAAGATCATAAAAGAACAGGAGGGTTACAAAAACATAGAAAGATCATCA
TATAATCCTAATC
Found at i:10766 original size:20 final size:22
Alignment explanation
Indices: 10741--10780 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
10731 AATAATTGAT
10741 TGAAGCT-TCATAT-TCTTAGG
1 TGAAGCTGTCATATCTCTTAGG
10761 TGAAGCTGTCATATCTCTTA
1 TGAAGCTGTCATATCTCTTA
10781 TTAGCTGCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 6 0.33
22 5 0.28
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.40
Consensus pattern (22 bp):
TGAAGCTGTCATATCTCTTAGG
Found at i:17343 original size:2 final size:2
Alignment explanation
Indices: 17336--17369 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
17326 AAAGCTTCAA
17336 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
17370 TCTTTGTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17751 original size:40 final size:39
Alignment explanation
Indices: 17653--17756 Score: 145
Period size: 39 Copynumber: 2.6 Consensus size: 39
17643 AGTTTGAATG
17653 GTACTAAAATGAAACAAAAACTAAAGTTTTTAACGACGA
1 GTACTAAAATGAAACAAAAACTAAAGTTTTTAACGACGA
* * ** *
17692 GTACTAAAATGAATCAAAAACTGAAGTTTTTAACGGTGG
1 GTACTAAAATGAAACAAAAACTAAAGTTTTTAACGACGA
*
17731 GATATTAAAATGAAACAAAAACTAAA
1 G-TACTAAAATGAAACAAAAACTAAA
17757 CTTCTGGTAT
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 35 0.62
40 21 0.38
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.24
Consensus pattern (39 bp):
GTACTAAAATGAAACAAAAACTAAAGTTTTTAACGACGA
Found at i:25400 original size:21 final size:21
Alignment explanation
Indices: 25376--25416 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
25366 TATGGTATCG
* *
25376 ATGTGATAATTTATGATGTTA
1 ATGTGACAATTCATGATGTTA
25397 ATGTGACAATTCATGATGTT
1 ATGTGACAATTCATGATGTT
25417 GACATAGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.44
Consensus pattern (21 bp):
ATGTGACAATTCATGATGTTA
Found at i:36643 original size:16 final size:16
Alignment explanation
Indices: 36619--36651 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
36609 TATCGCCGAC
*
36619 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
36635 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
36651 C
1 C
36652 ATGAATAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.33
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:40608 original size:14 final size:16
Alignment explanation
Indices: 40589--40620 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
40579 CTGCATTGAA
40589 TTCATTG-TTTTC-TT
1 TTCATTGATTTTCATT
40603 TTCATTGATTTTCATT
1 TTCATTGATTTTCATT
40619 TT
1 TT
40621 TTATGTCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 5 0.31
16 4 0.25
ACGTcount: A:0.12, C:0.12, G:0.06, T:0.69
Consensus pattern (16 bp):
TTCATTGATTTTCATT
Found at i:47060 original size:2 final size:2
Alignment explanation
Indices: 47053--47078 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
47043 TGCCCTCTTT
47053 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
47079 AGCAAACTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:54309 original size:23 final size:23
Alignment explanation
Indices: 54279--54322 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
54269 CAAGCATGGT
*
54279 ATATAATATCTTGTCTAATTGGC
1 ATATAATATATTGTCTAATTGGC
54302 ATATAATATATTGTCTAATTG
1 ATATAATATATTGTCTAATTG
54323 AGAAAACAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.45
Consensus pattern (23 bp):
ATATAATATATTGTCTAATTGGC
Found at i:63013 original size:20 final size:20
Alignment explanation
Indices: 62988--63032 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
62978 AAATAAAAAT
* *
62988 AAATATTTTTGTATTGTAAA
1 AAATATTTGTGTAGTGTAAA
63008 AAATATTTGTGTAGTGTAAA
1 AAATATTTGTGTAGTGTAAA
63028 AAATA
1 AAATA
63033 AGTTATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.42
Consensus pattern (20 bp):
AAATATTTGTGTAGTGTAAA
Found at i:72656 original size:2 final size:2
Alignment explanation
Indices: 72651--72683 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
72641 TCTCAACATA
72651 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
72684 GGTAAGATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:72909 original size:2 final size:2
Alignment explanation
Indices: 72902--72929 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
72892 ATTATAACTC
72902 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
72930 TAACATCTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:74486 original size:38 final size:35
Alignment explanation
Indices: 74441--74530 Score: 103
Period size: 38 Copynumber: 2.5 Consensus size: 35
74431 TTTTTGGGCC
74441 ACCCGACCCGACCCGA-GAAGA-AAGGGTTTTCACCCGTG
1 ACCCGACCCGACCCGACGAA-ATAA-GG-TTTCACCC--G
74479 ACCCGACCCGACCCGACGAAATTAAGGTTTCACCCG
1 ACCCGACCCGACCCGACGAAA-TAAGGTTTCACCCG
*
74515 ACCGGACCCGACCCGA
1 ACCCGACCCGACCCGA
74531 ATATATGACT
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
36 16 0.33
38 25 0.52
39 5 0.10
40 2 0.04
ACGTcount: A:0.27, C:0.39, G:0.23, T:0.11
Consensus pattern (35 bp):
ACCCGACCCGACCCGACGAAATAAGGTTTCACCCG
Found at i:74791 original size:34 final size:36
Alignment explanation
Indices: 74730--74811 Score: 89
Period size: 34 Copynumber: 2.3 Consensus size: 36
74720 CCTAAACCCG
* *
74730 ACCCGACCCGACCTGAACAGTACA-TTTTT-AAAAA
1 ACCCGACCCGACCCGAACAGTAAATTTTTTAAAAAA
*
74764 ACCCGACCCGACCCGAACCCG-AAATTTTTTTAAAAAA
1 ACCCGACCCGACCCGAA-CAGTAAA-TTTTTTAAAAAA
*
74801 ATCCGACCCGA
1 ACCCGACCCGA
74812 TCGGGTCGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
34 18 0.45
35 2 0.05
36 5 0.12
37 15 0.38
ACGTcount: A:0.37, C:0.33, G:0.12, T:0.18
Consensus pattern (36 bp):
ACCCGACCCGACCCGAACAGTAAATTTTTTAAAAAA
Found at i:75692 original size:23 final size:22
Alignment explanation
Indices: 75651--75697 Score: 53
Period size: 21 Copynumber: 2.1 Consensus size: 22
75641 TTTTAAATTA
75651 TTATATATTTTAAATATTT-TT
1 TTATATATTTTAAATATTTATT
75672 TTATAT-TTTTATTAATAATTTATT
1 TTATATATTTTA--AAT-ATTTATT
75696 TT
1 TT
75698 CACCTCTAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
20 5 0.23
21 6 0.27
22 3 0.14
23 4 0.18
24 4 0.18
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTATATATTTTAAATATTTATT
Done.