Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006428.1 Hibiscus syriacus cultivar Beakdansim tig00015517_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: 61266
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:602 original size:20 final size:20
Alignment explanation
Indices: 577--652 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
567 AAACCGAAAA
*
577 TCGCGTTGCGAATTTGGCTT
1 TCGCGTTGCGAATTTGACTT
597 TCGCGTTGCGAATTTGACTT
1 TCGCGTTGCGAATTTGACTT
** *
617 TCGCGTTATGAATTTAACTT
1 TCGCGTTGCGAATTTGACTT
637 TCGCGTTGCGAATTTG
1 TCGCGTTGCGAATTTG
653 TACCTTCAAC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.16, C:0.18, G:0.25, T:0.41
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTT
Found at i:816 original size:60 final size:62
Alignment explanation
Indices: 691--821 Score: 185
Period size: 61 Copynumber: 2.1 Consensus size: 62
681 GAATTGCTCA
*
691 AACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAAATTAAACAAATC
1 AACTTTTACAAATCAATT--A-AAGCAAAAAATAAATCTTATTTACACATCAAATTAAACAAATC
* * *
756 AACTTTTACAAATCAATT-AATCAAAAAATAAATCTTATTTCCTCATC-AATTAAACAAATC
1 AACTTTTACAAATCAATTAAAGCAAAAAATAAATCTTATTTACACATCAAATTAAACAAATC
816 AACTTT
1 AACTTT
822 CAATGTAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
60 19 0.31
61 25 0.40
65 18 0.29
ACGTcount: A:0.50, C:0.18, G:0.01, T:0.32
Consensus pattern (62 bp):
AACTTTTACAAATCAATTAAAGCAAAAAATAAATCTTATTTACACATCAAATTAAACAAATC
Found at i:2216 original size:21 final size:21
Alignment explanation
Indices: 2192--2290 Score: 85
Period size: 21 Copynumber: 4.7 Consensus size: 21
2182 GCAGGCAGGA
*
2192 CCTCTTGAACGATGACAGGGG
1 CCTCTTGAACGATGAGAGGGG
* *
2213 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGAGAGGGG
* * *
2234 CTTC-TGCGATGATGAGAGGGG
1 CCTCTTG-AACGATGAGAGGGG
* *
2255 CCTCTTGAACGAT-AGGAAGTG
1 CCTCTTGAACGATGA-GAGGGG
*
2276 CCTCTTGAATGATGA
1 CCTCTTGAACGATGA
2291 TAGGTGCATC
Statistics
Matches: 60, Mismatches: 14, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
20 3 0.05
21 54 0.90
22 3 0.05
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.23
Consensus pattern (21 bp):
CCTCTTGAACGATGAGAGGGG
Found at i:2288 original size:42 final size:42
Alignment explanation
Indices: 2172--2290 Score: 114
Period size: 42 Copynumber: 2.8 Consensus size: 42
2162 GTGAATCAGG
** * * *
2172 CTCTTGAACGGCAGGCAGGACCTCTTGAACGATGACAGGGGC
1 CTCTTGAACGATAGGAAGGGCCTCTTGAATGATGACAGGGGC
* * * * * *
2214 CTCTTGAACGGTGGGAGGGGCTTC-TGCGATGATGAGAGGGGC
1 CTCTTGAACGATAGGAAGGGCCTCTTG-AATGATGACAGGGGC
*
2256 CTCTTGAACGATAGGAAGTGCCTCTTGAATGATGA
1 CTCTTGAACGATAGGAAGGGCCTCTTGAATGATGA
2291 TAGGTGCATC
Statistics
Matches: 60, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
41 2 0.03
42 56 0.93
43 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.35, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGATAGGAAGGGCCTCTTGAATGATGACAGGGGC
Found at i:2297 original size:21 final size:20
Alignment explanation
Indices: 2242--2297 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 20
2232 GGCTTCTGCG
*
2242 ATGATGAGAGGGGCCTCTTGA
1 ATGATGA-AGGTGCCTCTTGA
*
2263 ACGATAGGAA-GTGCCTCTTGA
1 ATGAT--GAAGGTGCCTCTTGA
2284 ATGATGATAGGTGC
1 ATGATGA-AGGTGC
2298 ATCGGGCTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
19 2 0.07
20 1 0.04
21 22 0.79
22 1 0.04
23 2 0.07
ACGTcount: A:0.27, C:0.14, G:0.34, T:0.25
Consensus pattern (20 bp):
ATGATGAAGGTGCCTCTTGA
Found at i:4438 original size:20 final size:20
Alignment explanation
Indices: 4428--4478 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
4418 ACTTAAATTT
* *
4428 GCAACGCGAAAAAGAAAATC
1 GCAACGCGAAAATGAAAATA
4448 GCAACGCGAAAATGAAAATA
1 GCAACGCGAAAATGAAAATA
4468 GCAACGCGAAA
1 GCAACGCGAAA
4479 CTAAAATCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.53, C:0.20, G:0.22, T:0.06
Consensus pattern (20 bp):
GCAACGCGAAAATGAAAATA
Found at i:4880 original size:43 final size:43
Alignment explanation
Indices: 4832--4924 Score: 177
Period size: 43 Copynumber: 2.2 Consensus size: 43
4822 GTAGAGAGTG
4832 AGAGATGGAGATGAGACTGAGTTGCGATTTAGGGTTTTAGGTT
1 AGAGATGGAGATGAGACTGAGTTGCGATTTAGGGTTTTAGGTT
*
4875 AGAGATGGAGATGAGACTGAGTTGTGATTTAGGGTTTTAGGTT
1 AGAGATGGAGATGAGACTGAGTTGCGATTTAGGGTTTTAGGTT
4918 AGAGATG
1 AGAGATG
4925 ATTTGCGATA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.27, C:0.03, G:0.38, T:0.32
Consensus pattern (43 bp):
AGAGATGGAGATGAGACTGAGTTGCGATTTAGGGTTTTAGGTT
Found at i:5013 original size:20 final size:20
Alignment explanation
Indices: 4986--5153 Score: 171
Period size: 20 Copynumber: 8.4 Consensus size: 20
4976 GCGTAAAAAC
4986 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* * * *
5006 AATTGACTATCGTGTTACGA
1 ATTTGACTTTCGCGTTGCGA
*
5026 ATTTGAC-TTCTGTGTTGCG-
1 ATTTGACTTTC-GCGTTGCGA
* **
5045 ATTTATAAATTCGCGTTGCGA
1 ATTT-GACTTTCGCGTTGCGA
* *
5066 ATTTGACTTTTGTGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
5086 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
5106 ATTTGACTTT-GTGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
5125 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
5145 ATTTAACTT
1 ATTTGACTT
5154 ATGTGTTGCG
Statistics
Matches: 119, Mismatches: 24, Indels: 10
0.78 0.16 0.07
Matches are distributed among these distances:
19 23 0.19
20 89 0.75
21 7 0.06
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.42
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:5043 original size:40 final size:39
Alignment explanation
Indices: 4986--5164 Score: 234
Period size: 40 Copynumber: 4.5 Consensus size: 39
4976 GCGTAAAAAC
* * * *
4986 ATTTGACTTTCGCGTTGCGAAATTGACTATCGTGTTACGA
1 ATTTGACTTT-GTGTTGCGAATTTGACTATCGCGTTGCGA
* * *
5026 ATTTGACTTCTGTGTTGCGATTTATAAAT-TCGCGTTGCGA
1 ATTTGACTT-TGTGTTGCGAATT-TGACTATCGCGTTGCGA
5066 ATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGA
1 ATTTGAC-TTTGTGTTGCGAATTTGACTATCGCGTTGCGA
5106 ATTTGACTTTGTGTTGCGAATTTGACTATCGCGTTGCGA
1 ATTTGACTTTGTGTTGCGAATTTGACTATCGCGTTGCGA
*
5145 ATTTAACTTATGTGTTGCGA
1 ATTTGACTT-TGTGTTGCGA
5165 TTTACAAATT
Statistics
Matches: 123, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
39 43 0.35
40 74 0.60
41 6 0.05
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.41
Consensus pattern (39 bp):
ATTTGACTTTGTGTTGCGAATTTGACTATCGCGTTGCGA
Found at i:5159 original size:79 final size:80
Alignment explanation
Indices: 4999--5164 Score: 237
Period size: 79 Copynumber: 2.1 Consensus size: 80
4989 TGACTTTCGC
* *
4999 GTTGCGAAATTGACTATCGTGTTACGAATTTGACTTCTGTGTTGCGATTTATAAATTCGCGTTGC
1 GTTGCGAAATTGACTATCGCGTTACGAATTTGACTTCTGTGTTGCGAATTATAAATTCGCGTTGC
* *
5064 GAATTTGACTTTTGT
66 GAATTTAACTTATGT
* * * *
5079 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTT-TGTGTTGCGAATT-TGACTATCGCGTTG
1 GTTGCGAAATTGACTATCGCGTTACGAATTTGACTTCTGTGTTGCGAATTATAAAT-TCGCGTTG
5142 CGAATTTAACTTATGT
65 CGAATTTAACTTATGT
5158 GTTGCGA
1 GTTGCGA
5165 TTTACAAATT
Statistics
Matches: 77, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
78 3 0.04
79 41 0.53
80 33 0.43
ACGTcount: A:0.20, C:0.14, G:0.24, T:0.41
Consensus pattern (80 bp):
GTTGCGAAATTGACTATCGCGTTACGAATTTGACTTCTGTGTTGCGAATTATAAATTCGCGTTGC
GAATTTAACTTATGT
Found at i:5178 original size:40 final size:39
Alignment explanation
Indices: 4986--5184 Score: 217
Period size: 40 Copynumber: 5.0 Consensus size: 39
4976 GCGTAAAAAC
* * * * *
4986 ATTTGACTTTCGCGTTGCGAAATTGACTATCGTGTTACGA
1 ATTTGACTTT-GTGTTGCGAATTTGACAATCGCGTTGCGA
*
5026 ATTTGACTTCTGTGTTGCG-ATTT-ATAAATTCGCGTTGCGA
1 ATTTGACTT-TGTGTTGCGAATTTGA-CAA-TCGCGTTGCGA
*
5066 ATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGA
1 ATTTGAC-TTTGTGTTGCGAATTTGACAATCGCGTTGCGA
*
5106 ATTTGACTTTGTGTTGCGAATTTGACTATCGCGTTGCGA
1 ATTTGACTTTGTGTTGCGAATTTGACAATCGCGTTGCGA
*
5145 ATTTAACTTATGTGTTGCG-ATTT-ACAAATTCGCGTTGCGA
1 ATTTGACTT-TGTGTTGCGAATTTGAC-AA-TCGCGTTGCGA
5185 TTTATAGATT
Statistics
Matches: 140, Mismatches: 10, Indels: 18
0.83 0.06 0.11
Matches are distributed among these distances:
38 3 0.02
39 49 0.35
40 79 0.56
41 8 0.06
42 1 0.01
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.41
Consensus pattern (39 bp):
ATTTGACTTTGTGTTGCGAATTTGACAATCGCGTTGCGA
Found at i:5178 original size:79 final size:80
Alignment explanation
Indices: 4999--5184 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 80
4989 TGACTTTCGC
* * * * *
4999 GTTGCGAAATTGACTATCGTGTTACGAATTTGACTTCTGTGTTGCGATTTATAAATTCGCGTTGC
1 GTTGCGAATTTGACAATCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTATAAATTCGCGTTGC
* *
5064 GAATTTGACTTTTGT
66 GAATTTAACTTATGT
* * *
5079 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTT-TGTGTTGCGAATT-TGACTATCGCGTTG
1 GTTGCGAATTTGACAATCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTATAAAT-TCGCGTTG
5142 CGAATTTAACTTATGT
65 CGAATTTAACTTATGT
5158 GTTGCG-ATTT-ACAAATTCGCGTTGCGA
1 GTTGCGAATTTGAC-AA-TCGCGTTGCGA
5185 TTTATAGATT
Statistics
Matches: 94, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
77 2 0.02
78 8 0.09
79 51 0.54
80 33 0.35
ACGTcount: A:0.21, C:0.15, G:0.24, T:0.40
Consensus pattern (80 bp):
GTTGCGAATTTGACAATCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTATAAATTCGCGTTGC
GAATTTAACTTATGT
Found at i:5201 original size:20 final size:20
Alignment explanation
Indices: 5158--5204 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
5148 TAACTTATGT
**
5158 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCAA
* *
5178 GTTGCGATTTATAGATTCAA
1 GTTGCGATTTACAAATTCAA
5198 GTTGCGA
1 GTTGCGA
5205 AATTGTAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCAA
Found at i:5299 original size:20 final size:19
Alignment explanation
Indices: 5250--5303 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
5240 AATGCGACAT
5250 ATTCGCGTTGCGAAATTGG
1 ATTCGCGTTGCGAAATTGG
** *
5269 AAACTGGGTTGCGAAATTGG
1 ATTC-GCGTTGCGAAATTGG
5289 AGTTCGCGTTGCGAA
1 A-TTCGCGTTGCGAA
5304 TTTATTGGTC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 24 0.89
21 1 0.04
ACGTcount: A:0.24, C:0.15, G:0.33, T:0.28
Consensus pattern (19 bp):
ATTCGCGTTGCGAAATTGG
Found at i:15696 original size:29 final size:29
Alignment explanation
Indices: 15663--15720 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
15653 GAGAGAGAAG
* *
15663 AAAGTTGACTGGTGAATTATGTAATTTAC
1 AAAGTTGACAGGTGAATTATGTAAATTAC
*
15692 AAAGTTGACAGGTGATTTATGTAAATTAC
1 AAAGTTGACAGGTGAATTATGTAAATTAC
15721 CTTTTCTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (29 bp):
AAAGTTGACAGGTGAATTATGTAAATTAC
Found at i:19946 original size:29 final size:29
Alignment explanation
Indices: 19910--19968 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
19900 ATGTATTCCG
19910 TAATTATTTTAAGATCAATCTATTACGTA
1 TAATTATTTTAAGATCAATCTATTACGTA
*
19939 TAATTATTTTAAGATCGATCTATTACGTA
1 TAATTATTTTAAGATCAATCTATTACGTA
19968 T
1 T
19969 GTTCAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46
Consensus pattern (29 bp):
TAATTATTTTAAGATCAATCTATTACGTA
Found at i:24320 original size:8 final size:8
Alignment explanation
Indices: 24307--24382 Score: 56
Period size: 8 Copynumber: 9.8 Consensus size: 8
24297 CCATATGGTC
24307 TTATTATA
1 TTATTATA
24315 TTATTAGT-
1 TTATTA-TA
24323 TTATTATAA
1 TTATTAT-A
24332 TTATTA-A
1 TTATTATA
*
24339 -CA-TATAA
1 TTATTAT-A
24346 TTATTATA
1 TTATTATA
24354 TTA-TATA
1 TTATTATA
*
24361 TCATTATA
1 TTATTATA
24369 TTAATTAT-
1 TT-ATTATA
24377 TTATTA
1 TTATTA
24383 ACTATAATTC
Statistics
Matches: 55, Mismatches: 4, Indels: 19
0.71 0.05 0.24
Matches are distributed among these distances:
5 2 0.04
6 1 0.02
7 13 0.24
8 24 0.44
9 15 0.27
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (8 bp):
TTATTATA
Found at i:24353 original size:23 final size:22
Alignment explanation
Indices: 24323--24391 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 22
24313 TATTATTAGT
24323 TTATTATAATTATTAACATATAA
1 TTATTAT-ATTATTAACATATAA
*
24346 TTATTATATTATATATCAT-TATA
1 TTATTATATTAT-TAACATATA-A
24369 TTAATTAT-TTATTAAC-TATAA
1 TT-ATTATATTATTAACATATAA
24390 TT
1 TT
24392 CAATCTGTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
21 4 0.10
22 12 0.30
23 19 0.47
24 5 0.12
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (22 bp):
TTATTATATTATTAACATATAA
Found at i:27548 original size:22 final size:22
Alignment explanation
Indices: 27523--27571 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
27513 TACTATTTTA
27523 TTAGGGATAGTAGACCTAATTC
1 TTAGGGATAGTAGACCTAATTC
27545 TTAGGGATAGTAGACCTAATTC
1 TTAGGGATAGTAGACCTAATTC
*
27567 CTAGG
1 TTAGG
27572 AGTGTGCTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (22 bp):
TTAGGGATAGTAGACCTAATTC
Found at i:28926 original size:2 final size:2
Alignment explanation
Indices: 28919--28950 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
28909 TAAACTTTAC
28919 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28951 AATAATAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34494 original size:2 final size:2
Alignment explanation
Indices: 34487--34537 Score: 52
Period size: 2 Copynumber: 26.5 Consensus size: 2
34477 TTTAAATTAA
* * *
34487 AT AT AT AT AT AT AT AT AT AT A- AT AT CT AT AT AT TT A- AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
34527 AA AT AT AT AT A
1 AT AT AT AT AT A
34538 CCCGGCCCGA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35821 original size:7 final size:7
Alignment explanation
Indices: 35809--35837 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
35799 ACTCACTCAC
35809 TTCTTCT
1 TTCTTCT
35816 TTCTTCT
1 TTCTTCT
35823 TTCTTCT
1 TTCTTCT
35830 TTCTTCT
1 TTCTTCT
35837 T
1 T
35838 CATTCGGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (7 bp):
TTCTTCT
Done.