Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005112.1 Hibiscus syriacus cultivar Beakdansim tig00011491_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: 41874
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:169 original size:16 final size:16
Alignment explanation
Indices: 144--178 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
134 ATTCATACAG
144 AGCATCTGAACCATTC
1 AGCATCTGAACCATTC
* *
160 AGCATTTGAATCATTC
1 AGCATCTGAACCATTC
176 AGC
1 AGC
179 GCTTAATCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (16 bp):
AGCATCTGAACCATTC
Found at i:4289 original size:11 final size:11
Alignment explanation
Indices: 4254--4315 Score: 76
Period size: 11 Copynumber: 5.7 Consensus size: 11
4244 AATTTATTTT
4254 TATAAT-ATAA
1 TATAATAATAA
4264 TAT-ATATATATA
1 TATAATA-ATA-A
4276 TATAATAATAA
1 TATAATAATAA
*
4287 TATAATAATAT
1 TATAATAATAA
4298 TATAATAATAA
1 TATAATAATAA
4309 -ATAATAA
1 TATAATAA
4316 GTAAAATGGG
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
9 2 0.04
10 10 0.22
11 24 0.52
12 7 0.15
13 3 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TATAATAATAA
Found at i:4895 original size:115 final size:112
Alignment explanation
Indices: 4662--5138 Score: 374
Period size: 115 Copynumber: 4.2 Consensus size: 112
4652 TAGAATTATG
* ** *
4662 CAAAATGTTGAACAAGCTCTTCTCATTGTGAA--CTTC-TTCTTCTTCAGATGAGTTCTTCTCA-
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
* * * *
4723 T-TGAACT-TTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTAG
66 TATGAACTCTACTCTGGAAAAGCTGATCCATCAAATGATGAATTAAA
4768 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGACGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTTCTTTCTTCTTCAGAT---GAGTTCTTC
* *
4833 TCATTATGAACTCTAC-CTGGCAATG-TCGATCCATCAAATGATGAATTCAAA
62 TCATTATGAACTCTACTCTGGAAAAGCT-GATCCATCAAATGATGAATT-AAA
*
4884 C-AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC-TCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTTCTTTCTTCTTCAGATGAGTTCTTCTCA
* * * * *** *
4947 TTATGAACTCGA-ACTGGAAATGTTAATGCTAATCTATCTTCTTCTGTGATAGAATTAAG
65 TTATGAACTCTACTCTGG-AA----AA-GCTGATC---CATC--AAATGAT-GAATTAAA
** ** *
5006 CAAAAAAATTGAACAAGCTCTTCTCATTATGAACTTCTTCTTTC-TCTTCAGATAAGTTCTTCTC
1 C-AAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTTCTTTCTTCTTCAGATGAGTTCTTCTC
* * ** * *
5070 ATTATGAAC-CT--TCTGGCAACGCTGATCCATTGAATGATGAATTTGAG
64 ATTATGAACTCTACTCTGGAAAAGCTGATCCATCAAATGATGAA-TTAAA
5117 C-AAAGGTTGAACAAATTCTTCT
1 CAAAAGGTTGAACAAATTCTTCT
5139 TTCTTCAGAT
Statistics
Matches: 299, Mismatches: 42, Indels: 57
0.75 0.11 0.14
Matches are distributed among these distances:
106 28 0.09
109 21 0.07
110 16 0.05
111 29 0.10
112 7 0.02
113 14 0.05
114 2 0.01
115 81 0.27
116 11 0.04
117 5 0.02
118 1 0.00
120 3 0.01
121 1 0.00
122 11 0.04
123 20 0.07
124 49 0.16
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (112 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAATTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTCTACTCTGGAAAAGCTGATCCATCAAATGATGAATTAAA
Found at i:6128 original size:115 final size:114
Alignment explanation
Indices: 5904--6349 Score: 724
Period size: 115 Copynumber: 3.9 Consensus size: 114
5894 GATCATGCAG
* * * * * *
5904 TCATCTTTCAATTCTAATGATTGG-TTCTGTGGTTCCTACCGAACCAGATCAGATAACTCAAGAA
1 TCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAGAA
*
5968 CACTTCCAG-A-A-GCTATTGGGTC--CTTATTTCTACTATGAGCAAAT
66 CACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAAT
* * *
6012 TCATCTTTTAAATCTAATGATTGGTTTTTGGGGTTCATACCAAACCATATCAGATAACTCAAAGA
1 TCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTC-AAGA
6077 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAAT
65 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAAT
*
6127 TCATATTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTC-AAGA
*
6192 ACACTTCCAGAAGCTGCTATTGAGTCTTCTTATTTCTACTATGAGCAAAT
65 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAAT
6242 TCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAGAA
1 TCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAGAA
6307 CACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGA
66 CACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGA
6350 TAACGTGGTA
Statistics
Matches: 316, Mismatches: 15, Indels: 8
0.93 0.04 0.02
Matches are distributed among these distances:
108 22 0.07
109 30 0.09
110 14 0.04
111 1 0.00
112 1 0.00
113 10 0.03
114 47 0.15
115 191 0.60
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (114 bp):
TCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAGAA
CACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAAT
Found at i:6663 original size:19 final size:17
Alignment explanation
Indices: 6635--6683 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
6625 CAAAAAAAAG
*
6635 AATAAGTTGAATTTTCGAA
1 AATAAATTGAATTTTC--A
*
6654 AATAAATTGAA-TCTCA
1 AATAAATTGAATTTTCA
6670 AATAAATTGAATTT
1 AATAAATTGAATTT
6684 AGAGAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 12 0.46
17 1 0.04
18 3 0.12
19 10 0.38
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (17 bp):
AATAAATTGAATTTTCA
Found at i:7050 original size:10 final size:10
Alignment explanation
Indices: 7031--7094 Score: 76
Period size: 10 Copynumber: 6.5 Consensus size: 10
7021 TGACCCCCTC
7031 TTTTTC-TTT
1 TTTTTCTTTT
7040 TTTTTCTTTT
1 TTTTTCTTTT
** *
7050 TTCCTCATTT
1 TTTTTCTTTT
7060 TTTTTCTTTT
1 TTTTTCTTTT
*
7070 TTGTTCTTTT
1 TTTTTCTTTT
*
7080 TTGTTCTTTT
1 TTTTTCTTTT
7090 TTTTT
1 TTTTT
7095 TCTTCAAGCA
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
9 6 0.13
10 40 0.87
ACGTcount: A:0.02, C:0.12, G:0.03, T:0.83
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:14413 original size:15 final size:15
Alignment explanation
Indices: 14390--14421 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
14380 TGCAATAAAT
14390 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
14405 AATGCATGTATGCAA
1 AATGAATGTATGCAA
14420 AA
1 AA
14422 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:17735 original size:36 final size:34
Alignment explanation
Indices: 17665--17743 Score: 86
Period size: 36 Copynumber: 2.3 Consensus size: 34
17655 GACAGACAAT
* *
17665 AAATAATGAAATAAAATACTTAAAAATAAAATGA
1 AAATAATAAAATAAAATACATAAAAATAAAATGA
* * **
17699 AACATTAATAAAATAATATACATATAAATATTATGA
1 AA-A-TAATAAAATAAAATACATAAAAATAAAATGA
17735 AAATAATAA
1 AAATAATAA
17744 GTATATATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
34 8 0.22
35 2 0.05
36 27 0.73
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.28
Consensus pattern (34 bp):
AAATAATAAAATAAAATACATAAAAATAAAATGA
Found at i:17763 original size:28 final size:26
Alignment explanation
Indices: 17708--17765 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
17698 AAACATTAAT
*
17708 AAAATAATATACATATAAATATTATG
1 AAAATAATATACATATAAAAATTATG
* *
17734 AAAATAATAAGTATATATAAAAATTTTG
1 AAAATAAT-A-TACATATAAAAATTATG
17762 AAAA
1 AAAA
17766 GAAAGAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 8 0.30
27 1 0.04
28 18 0.67
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (26 bp):
AAAATAATATACATATAAAAATTATG
Found at i:20804 original size:18 final size:21
Alignment explanation
Indices: 20781--20822 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
20771 GATGATATCT
20781 AAAATATT-T-AA-AAATAAA
1 AAAATATTATAAACAAATAAA
20799 AAAATATTATAAACAAATAAA
1 AAAATATTATAAACAAATAAA
20820 AAA
1 AAA
20823 TAAATAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 1 0.05
20 2 0.10
21 10 0.48
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAATATTATAAACAAATAAA
Found at i:22805 original size:2 final size:2
Alignment explanation
Indices: 22794--22823 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
22784 CCTCTGCAAA
22794 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
22824 GATTTTCCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:23259 original size:2 final size:2
Alignment explanation
Indices: 23252--23278 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
23242 CCATTTCACA
23252 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 A
23279 GTTTTCCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26334 original size:19 final size:19
Alignment explanation
Indices: 26305--26353 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
26295 AATAATGACA
*
26305 CTAATTTTTTTGTAATTTTT
1 CTAA-TTTTTTATAATTTTT
* *
26325 CTGATTTTTTATATTTTTT
1 CTAATTTTTTATAATTTTT
26344 CTAATTTTTT
1 CTAATTTTTT
26354 TAAATTTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 22 0.88
20 3 0.12
ACGTcount: A:0.18, C:0.06, G:0.04, T:0.71
Consensus pattern (19 bp):
CTAATTTTTTATAATTTTT
Found at i:40490 original size:25 final size:25
Alignment explanation
Indices: 40456--40513 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
40446 GATATAGCTC
40456 ATGCACTCGCATACCAGCATGACCA
1 ATGCACTCGCATACCAGCATGACCA
40481 ATGCACTCGCATACCAGCATGACCA
1 ATGCACTCGCATACCAGCATGACCA
40506 ATGCACTC
1 ATGCACTC
40514 CAAAGGTTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.31, C:0.36, G:0.16, T:0.17
Consensus pattern (25 bp):
ATGCACTCGCATACCAGCATGACCA
Done.