Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003719.1 Hibiscus syriacus cultivar Beakdansim tig00007952_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: 341516
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 2 of 2
Found at i:275216 original size:18 final size:19
Alignment explanation
Indices: 275161--275217 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
275151 CACGGAATGT
275161 AAGATTACCG-GTAGGAATAA
1 AAGATTACCGAG--GGAATAA
*
275181 AAGATTACCGGTGGGAATAA
1 AAGATTACC-GAGGGAATAA
275201 AAGATTACC-AGGGAATA
1 AAGATTACCGAGGGAATA
275218 TGATTACTGG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
18 7 0.21
20 25 0.74
21 1 0.03
22 1 0.03
ACGTcount: A:0.44, C:0.11, G:0.26, T:0.19
Consensus pattern (19 bp):
AAGATTACCGAGGGAATAA
Found at i:275799 original size:14 final size:14
Alignment explanation
Indices: 275780--275807 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
275770 TTCCATTCCC
275780 ATGAGAATCTCACA
1 ATGAGAATCTCACA
275794 ATGAGAATCTCACA
1 ATGAGAATCTCACA
275808 TTCCCCCAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.21
Consensus pattern (14 bp):
ATGAGAATCTCACA
Found at i:276317 original size:26 final size:27
Alignment explanation
Indices: 276257--276318 Score: 72
Period size: 31 Copynumber: 2.2 Consensus size: 27
276247 GAGTATTGCT
*
276257 GAGCTCGACTCGACTCGAAAACTCTGAAATT
1 GAGCTCGACTCGACTCGAAAACTC----ATC
276288 GAGCTCGACTCGACTCGAAAACTC-TC
1 GAGCTCGACTCGACTCGAAAACTCATC
276314 GAGCT
1 GAGCT
276319 TAAAATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 6 0.20
31 24 0.80
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (27 bp):
GAGCTCGACTCGACTCGAAAACTCATC
Found at i:277173 original size:60 final size:59
Alignment explanation
Indices: 277061--277200 Score: 183
Period size: 60 Copynumber: 2.4 Consensus size: 59
277051 GTCTCTTCTG
* * *
277061 ACAATCAAAAGTTACAAAATGATCCCCGATTATAGGGTGTTGCTTTGTTGAGTCCCCTA
1 ACAATCAAAAGTTACAAAATGATCCCCGACTATAGGATGTTGCCTTGTTGAGTCCCCTA
* **
277120 ACAAT-AAGAAGTTATAAAATGATCCTCCGACTATAGGATGTTGCCTTGTTGAGTCCCCCG
1 ACAATCAA-AAGTTACAAAATGATCC-CCGACTATAGGATGTTGCCTTGTTGAGTCCCCTA
* *
277180 ACTATTAAAAGTTACAAAATG
1 ACAATCAAAAGTTACAAAATG
277201 GTCACCTGAC
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
58 2 0.03
59 21 0.30
60 45 0.64
61 2 0.03
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (59 bp):
ACAATCAAAAGTTACAAAATGATCCCCGACTATAGGATGTTGCCTTGTTGAGTCCCCTA
Found at i:286463 original size:69 final size:69
Alignment explanation
Indices: 286347--286493 Score: 249
Period size: 69 Copynumber: 2.1 Consensus size: 69
286337 AAAAAAATAA
* *
286347 TACAACGGTAAAAGTAAATGCACTGGTGTAAGTAAATAAAATAAACAAGTGTAACACTTAACACA
1 TACACCGGTAAAAGTAAATGCACCGGTGTAAGTAAATAAAATAAACAAGTGTAACACTTAACACA
286412 TACT
66 TACT
* * *
286416 TACACCGGTATAAGTAAATGCACCGGTGTAAGTGAATAAAATAAACAAGTGTAGCACTTAACACA
1 TACACCGGTAAAAGTAAATGCACCGGTGTAAGTAAATAAAATAAACAAGTGTAACACTTAACACA
286481 TACT
66 TACT
286485 TACACCGGT
1 TACACCGGT
286494 GTAAATGAAT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 73 1.00
ACGTcount: A:0.44, C:0.17, G:0.16, T:0.23
Consensus pattern (69 bp):
TACACCGGTAAAAGTAAATGCACCGGTGTAAGTAAATAAAATAAACAAGTGTAACACTTAACACA
TACT
Found at i:286496 original size:51 final size:51
Alignment explanation
Indices: 286436--286601 Score: 278
Period size: 51 Copynumber: 3.3 Consensus size: 51
286426 TAAGTAAATG
*
286436 CACCGGTGTAAGTGAATAAAATAAACAAGTGTAGCACTTAACACATACTTA
1 CACCGGTGTAAGTGAATAAAATAAAAAAGTGTAGCACTTAACACATACTTA
*
286487 CACCGGTGTAAATGAATAAAATAAAAAAGTGTAGCACTTAACACATACTTA
1 CACCGGTGTAAGTGAATAAAATAAAAAAGTGTAGCACTTAACACATACTTA
** *
286538 CAAAGGTGTAAGTAAATAAAATAAAAAAGTGTAGCACTTAACACATACTTA
1 CACCGGTGTAAGTGAATAAAATAAAAAAGTGTAGCACTTAACACATACTTA
*
286589 CACCGATGTAAGT
1 CACCGGTGTAAGT
286602 ATCTACATCT
Statistics
Matches: 106, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 106 1.00
ACGTcount: A:0.46, C:0.16, G:0.15, T:0.23
Consensus pattern (51 bp):
CACCGGTGTAAGTGAATAAAATAAAAAAGTGTAGCACTTAACACATACTTA
Found at i:290773 original size:54 final size:54
Alignment explanation
Indices: 290713--290888 Score: 140
Period size: 54 Copynumber: 3.1 Consensus size: 54
290703 AAATATTTTA
* *
290713 TATTAATCTCCAACCTATCAATATCGTTCCATTTTGACCCTTTTGTTAACATTT
1 TATTAATCTCCAACCTATCAATATCATTCCATTTTGACCCTTTTGATAACATTT
* * * * ** ** * *
290767 TATTAATCCCCAAACTAT-GATATTCACTATAAATTGATCCATAAACTTTT-AAAATATTTT
1 TATTAATCTCCAACCTATCAATA-TCATTCCATTTTGA-CC-----CTTTTGATAACA-TTT
*
290827 ATATTAATCTCCAACCTATCAATATCATTCCATTTTGACCCTTTTGGTAACATTT
1 -TATTAATCTCCAACCTATCAATATCATTCCATTTTGACCCTTTTGATAACATTT
290882 TATTAAT
1 TATTAAT
290889 TCTGCTGGTT
Statistics
Matches: 88, Mismatches: 23, Indels: 22
0.66 0.17 0.17
Matches are distributed among these distances:
53 3 0.03
54 31 0.35
55 10 0.11
56 3 0.03
59 3 0.03
60 10 0.11
61 25 0.28
62 3 0.03
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (54 bp):
TATTAATCTCCAACCTATCAATATCATTCCATTTTGACCCTTTTGATAACATTT
Found at i:290858 original size:115 final size:115
Alignment explanation
Indices: 290652--290888 Score: 456
Period size: 115 Copynumber: 2.1 Consensus size: 115
290642 AATCATTCTG
290652 TATTAATCCCCAAACTATGATATTCACTATAAATTGATCCATAAACTTTTAAAATATTTTATATT
1 TATTAATCCCCAAACTATGATATTCACTATAAATTGATCCATAAACTTTTAAAATATTTTATATT
* *
290717 AATCTCCAACCTATCAATATCGTTCCATTTTGACCCTTTTGTTAACATTT
66 AATCTCCAACCTATCAATATCATTCCATTTTGACCCTTTTGGTAACATTT
290767 TATTAATCCCCAAACTATGATATTCACTATAAATTGATCCATAAACTTTTAAAATATTTTATATT
1 TATTAATCCCCAAACTATGATATTCACTATAAATTGATCCATAAACTTTTAAAATATTTTATATT
290832 AATCTCCAACCTATCAATATCATTCCATTTTGACCCTTTTGGTAACATTT
66 AATCTCCAACCTATCAATATCATTCCATTTTGACCCTTTTGGTAACATTT
290882 TATTAAT
1 TATTAAT
290889 TCTGCTGGTT
Statistics
Matches: 120, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
115 120 1.00
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.42
Consensus pattern (115 bp):
TATTAATCCCCAAACTATGATATTCACTATAAATTGATCCATAAACTTTTAAAATATTTTATATT
AATCTCCAACCTATCAATATCATTCCATTTTGACCCTTTTGGTAACATTT
Found at i:292248 original size:2 final size:2
Alignment explanation
Indices: 292241--292267 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
292231 AAATTGTCTT
292241 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
292268 TTAACAAGTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:292719 original size:14 final size:14
Alignment explanation
Indices: 292700--292727 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
292690 TTCCATTCCC
292700 ATGAGAATCTCACA
1 ATGAGAATCTCACA
292714 ATGAGAATCTCACA
1 ATGAGAATCTCACA
292728 TTCCCCCAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.21
Consensus pattern (14 bp):
ATGAGAATCTCACA
Found at i:294114 original size:60 final size:59
Alignment explanation
Indices: 293987--294154 Score: 194
Period size: 60 Copynumber: 2.8 Consensus size: 59
293977 TCGTTTTGTT
** * * * * * *
293987 TTGTTGAGTCATCTGACAATCAAAAGTTACAAAATGATCCCCAACTATAGGGTGTTGCT
1 TTGTTGAGTCCCCTAACAATTAAAAGTTACAAAATGATCACCGACTATAGGATGTTGCC
* *
294046 TTGTTGAGTCCCCTAACAATTAGAAGTTATAAAATGATCATCCGACTATAGGATGTTGCC
1 TTGTTGAGTCCCCTAACAATTAAAAGTTACAAAATGATCA-CCGACTATAGGATGTTGCC
* *
294106 TTGTTGAGTCCCC-AGACTATTAAAAGTTACAAAATGGTCACCTGACTAT
1 TTGTTGAGTCCCCTA-ACAATTAAAAGTTACAAAATGATCACC-GACTAT
294155 TCATTATATT
Statistics
Matches: 92, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
59 36 0.39
60 56 0.61
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (59 bp):
TTGTTGAGTCCCCTAACAATTAAAAGTTACAAAATGATCACCGACTATAGGATGTTGCC
Found at i:306832 original size:20 final size:19
Alignment explanation
Indices: 306782--306837 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
306772 AACCAATAAT
306782 AATAAACATAAAAT-AATTG
1 AATAAA-ATAAAATAAATTG
*
306801 GATGAAAA-AAAATGAAATTG
1 AAT-AAAATAAAAT-AAATTG
306821 AATAAAATAAAATAAAT
1 AATAAAATAAAATAAAT
306838 GAAGATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 5 0.16
19 11 0.35
20 15 0.48
ACGTcount: A:0.66, C:0.02, G:0.09, T:0.23
Consensus pattern (19 bp):
AATAAAATAAAATAAATTG
Found at i:306986 original size:21 final size:22
Alignment explanation
Indices: 306937--307013 Score: 75
Period size: 22 Copynumber: 3.3 Consensus size: 22
306927 ATATAATGAA
*
306937 AATAAATAAATAGTATAAATAAAAT
1 AATAAA-AAATA-TATATAT-AAAT
306962 AATAAAAAATATATATATAAA-
1 AATAAAAAATATATATATAAAT
* *
306983 AATATAAAAATGTATGTATAATAT
1 AATA-AAAAATATATATATAA-AT
307007 AATAAAA
1 AATAAAA
307014 TACTAAATAG
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
21 4 0.09
22 17 0.37
23 10 0.22
24 9 0.20
25 6 0.13
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (22 bp):
AATAAAAAATATATATATAAAT
Found at i:307002 original size:22 final size:21
Alignment explanation
Indices: 306923--307013 Score: 69
Period size: 22 Copynumber: 4.1 Consensus size: 21
306913 CAAAGAAATT
*
306923 AAAA-ATATA-ATGAAAATAA
1 AAAATATATATATAAAAATAA
*
306942 ATAAATAGTATAAATAAAATAATAA
1 A-AAATA-TATATAT-AAA-AATAA
306967 AAAATATATATATAAAAATATA
1 AAAATATATATATAAAAATA-A
* *
306989 AAAATGTATGTATAATATAATAA
1 AAAATATATATATAA-A-AATAA
307012 AA
1 AA
307014 TACTAAATAG
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
19 1 0.02
20 3 0.05
21 5 0.08
22 21 0.36
23 12 0.20
24 11 0.19
25 6 0.10
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (21 bp):
AAAATATATATATAAAAATAA
Found at i:307772 original size:37 final size:37
Alignment explanation
Indices: 307697--307794 Score: 115
Period size: 37 Copynumber: 2.6 Consensus size: 37
307687 ATGCTTGTAG
* * * ** *
307697 ATCCTATCTTTAGGAGTTTAAATAATAGTATAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAACAAAACTCT
*
307734 ATCCTATTTTTAGGAGTTTGAATCATAACAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAACAAAACTCT
* *
307771 ATCATATTTTTAAGAGTTTGAATC
1 ATCCTATTTTTAGGAGTTTGAATC
307795 CTAGTAGGAC
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAACAAAACTCT
Found at i:313969 original size:23 final size:24
Alignment explanation
Indices: 313928--313984 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
313918 AAACAGTATA
*
313928 ATAAAAAATAAGGATAAAATAAAT
1 ATAAAAAATTAGGATAAAATAAAT
* *
313952 ATAAAAAATTAGTA-AAAATAATT
1 ATAAAAAATTAGGATAAAATAAAT
*
313975 TTAAAAAATT
1 ATAAAAAATT
313985 TATCTTCCCA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 17 0.59
24 12 0.41
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (24 bp):
ATAAAAAATTAGGATAAAATAAAT
Found at i:327555 original size:15 final size:15
Alignment explanation
Indices: 327527--327569 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
327517 ACCGCCACAA
327527 GGATACCCTCCTCAG
1 GGATACCCTCCTCAG
* *
327542 GGATATCCTGCTCAG
1 GGATACCCTCCTCAG
327557 GGATACCCTCCTC
1 GGATACCCTCCTC
327570 CCTATGCCCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.19, C:0.37, G:0.21, T:0.23
Consensus pattern (15 bp):
GGATACCCTCCTCAG
Found at i:333698 original size:33 final size:33
Alignment explanation
Indices: 333661--333724 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
333651 CAAGAAAACA
*
333661 AAGAGTACAAATACATGATATCGGATGTATCCC
1 AAGAGTACAAATACATGATATCAGATGTATCCC
*
333694 AAGAGTACAAATACGTGATATCAGATGTATC
1 AAGAGTACAAATACATGATATCAGATGTATC
333725 TCAAAACAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.25
Consensus pattern (33 bp):
AAGAGTACAAATACATGATATCAGATGTATCCC
Found at i:335574 original size:13 final size:14
Alignment explanation
Indices: 335543--335585 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
335533 CTTTCATATT
*
335543 TAAAGGAAAAAAGA
1 TAAAAGAAAAAAGA
335557 TAAAAGAAAAAAGA
1 TAAAAGAAAAAAGA
*
335571 -AAAAGAAAAATGA
1 TAAAAGAAAAAAGA
335584 TA
1 TA
335586 TAGATGACAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 12 0.46
14 14 0.54
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.09
Consensus pattern (14 bp):
TAAAAGAAAAAAGA
Found at i:337967 original size:14 final size:14
Alignment explanation
Indices: 337948--337974 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
337938 AAACTTGACT
337948 CGAACCCGATTACC
1 CGAACCCGATTACC
337962 CGAACCCGATTAC
1 CGAACCCGATTAC
337975 GAATCGATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.41, G:0.15, T:0.15
Consensus pattern (14 bp):
CGAACCCGATTACC
Found at i:338113 original size:16 final size:16
Alignment explanation
Indices: 338094--338124 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
338084 AACCATAATC
*
338094 GAAATTAACCTGAACT
1 GAAATTAACCCGAACT
338110 GAAATTAACCCGAAC
1 GAAATTAACCCGAAC
338125 GAAGCAATCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.23, G:0.13, T:0.19
Consensus pattern (16 bp):
GAAATTAACCCGAACT
Found at i:338294 original size:17 final size:18
Alignment explanation
Indices: 338256--338310 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 18
338246 TAATAAATTA
* *
338256 ATTTAAATAAAATTGATA-
1 ATTTATATAAAA-TAATAG
*
338274 ATTTAT-TAAAATATTAG
1 ATTTATATAAAATAATAG
338291 ATTTATAATAAAATAATAG
1 ATTTAT-ATAAAATAATAG
338310 A
1 A
338311 AAGTTTAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
16 3 0.10
17 11 0.37
18 5 0.17
19 11 0.37
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (18 bp):
ATTTATATAAAATAATAG
Found at i:339178 original size:14 final size:14
Alignment explanation
Indices: 339159--339185 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
339149 TCTAGACCCA
339159 AAATTACTCGACCG
1 AAATTACTCGACCG
339173 AAATTACTCGACC
1 AAATTACTCGACC
339186 CAAACTCGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.30, G:0.11, T:0.22
Consensus pattern (14 bp):
AAATTACTCGACCG
Found at i:340894 original size:29 final size:30
Alignment explanation
Indices: 340860--340928 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
340850 TATATTTTAC
340860 ATAGT-ATTTATATTA-TATTATTAATATTT
1 ATAGTAATTTATATTATTATTA-TAATATTT
*
340889 ATAGTAATTGTATATTATTATTATATTATTT
1 ATAGTAATT-TATATTATTATTATAATATTT
*
340920 -TAGTGATTT
1 ATAGTAATTT
340929 TAATTGTGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 6 0.17
30 10 0.29
31 14 0.40
32 5 0.14
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (30 bp):
ATAGTAATTTATATTATTATTATAATATTT
Done.