Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006527.1 Hibiscus syriacus cultivar Beakdansim tig00015907_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: 65567
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:10521 original size:24 final size:24
Alignment explanation
Indices: 10478--10526 Score: 57
Period size: 24 Copynumber: 2.0 Consensus size: 24
10468 AGATCATCAA
*
10478 TATTTATTGTTTTTTCTTT-ATTT
1 TATTTATTGTTATTTCTTTAATTT
10501 TATTATATTGTATATTT-TTTAATTT
1 TATT-TATTGT-TATTTCTTTAATTT
10526 T
1 T
10527 TAATAGTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 4 0.18
24 9 0.41
25 9 0.41
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.73
Consensus pattern (24 bp):
TATTTATTGTTATTTCTTTAATTT
Found at i:15134 original size:19 final size:19
Alignment explanation
Indices: 15110--15148 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
15100 ACGAATATTT
*
15110 TCTCTGATTTCTGTTCTGA
1 TCTCTGATCTCTGTTCTGA
15129 TCTCTGATCTCTGTTCTGA
1 TCTCTGATCTCTGTTCTGA
15148 T
1 T
15149 TTCTAATATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.10, C:0.23, G:0.15, T:0.51
Consensus pattern (19 bp):
TCTCTGATCTCTGTTCTGA
Found at i:20164 original size:31 final size:32
Alignment explanation
Indices: 20129--20197 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 32
20119 CTTAAAATTT
*
20129 ATTCAGAGGACTAAATTG-AAATTTAAATTAA
1 ATTCAGAGGACTAAAGTGAAAATTTAAATTAA
* * *
20160 ATTCAG-GGGCTATAGTGAAAATTTTAATTAA
1 ATTCAGAGGACTAAAGTGAAAATTTAAATTAA
20191 ATTCAGA
1 ATTCAGA
20198 TCCAAACTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 8 0.25
31 24 0.75
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.33
Consensus pattern (32 bp):
ATTCAGAGGACTAAAGTGAAAATTTAAATTAA
Found at i:20788 original size:18 final size:18
Alignment explanation
Indices: 20767--20809 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
20757 TCGTTGACCA
20767 TTGACCGACCATTGA-TCG
1 TTGACCGACCATTGACT-G
*
20785 TTGACCGACCTTTGACTG
1 TTGACCGACCATTGACTG
20803 TTGACCG
1 TTGACCG
20810 TCGTTGACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.19, C:0.28, G:0.23, T:0.30
Consensus pattern (18 bp):
TTGACCGACCATTGACTG
Found at i:22110 original size:29 final size:30
Alignment explanation
Indices: 22077--22150 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 30
22067 AATATTCCAT
22077 ACTCAGAAATCATATACAG-AA-ATACAGTA
1 ACTCA-AAATCATATACAGAAATATACAGTA
*
22106 ACTCAAGATCATAT-CAGAAATATACAGTA
1 ACTCAAAATCATATACAGAAATATACAGTA
* *
22135 AATCATATATCATATA
1 ACTCA-AAATCATATA
22151 AACAATATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
27 3 0.08
28 10 0.26
29 17 0.45
30 8 0.21
ACGTcount: A:0.50, C:0.16, G:0.08, T:0.26
Consensus pattern (30 bp):
ACTCAAAATCATATACAGAAATATACAGTA
Found at i:22158 original size:30 final size:28
Alignment explanation
Indices: 22085--22158 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 28
22075 ATACTCAGAA
* *
22085 ATCATATACAGAA-ATACAGTAACTCAAG
1 ATCATATA-AAAATATACAGTAAATCAAG
* *
22113 ATCATATCAGAAATATACAGTAAATCATAT
1 ATCATAT-AAAAATATACAGTAAATCA-AG
22143 ATCATATAAACAATAT
1 ATCATATAAA-AATAT
22159 TAAGAAAATC
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
28 9 0.24
29 15 0.41
30 13 0.35
ACGTcount: A:0.51, C:0.15, G:0.07, T:0.27
Consensus pattern (28 bp):
ATCATATAAAAATATACAGTAAATCAAG
Found at i:30547 original size:21 final size:21
Alignment explanation
Indices: 30494--30547 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
30484 TCGAATGTTT
* *
30494 TACGAGGTCCTTCGGGACATG
1 TACGAGGTCCTTCAGGACATC
* *
30515 TATGTGGTCCTTCAGGACATC
1 TACGAGGTCCTTCAGGACATC
*
30536 TACGAGGACCTT
1 TACGAGGTCCTT
30548 TGAGACAATT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.28
Consensus pattern (21 bp):
TACGAGGTCCTTCAGGACATC
Found at i:32424 original size:28 final size:28
Alignment explanation
Indices: 32384--32469 Score: 172
Period size: 28 Copynumber: 3.1 Consensus size: 28
32374 GCGGAGGAGT
32384 TTGTCTTGGAATTGGGTGGCAACATACC
1 TTGTCTTGGAATTGGGTGGCAACATACC
32412 TTGTCTTGGAATTGGGTGGCAACATACC
1 TTGTCTTGGAATTGGGTGGCAACATACC
32440 TTGTCTTGGAATTGGGTGGCAACATACC
1 TTGTCTTGGAATTGGGTGGCAACATACC
32468 TT
1 TT
32470 AGGAGATGGC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 58 1.00
ACGTcount: A:0.21, C:0.17, G:0.28, T:0.34
Consensus pattern (28 bp):
TTGTCTTGGAATTGGGTGGCAACATACC
Found at i:36733 original size:19 final size:19
Alignment explanation
Indices: 36709--36755 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
36699 TTCACCGTTA
36709 AAAACTTGAAAGAACGGTT
1 AAAACTTGAAAGAACGGTT
*
36728 AAAACTTGAAGGAACGGTT
1 AAAACTTGAAAGAACGGTT
36747 AAAACTTGA
1 AAAACTTGA
36756 CATATTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.47, C:0.11, G:0.21, T:0.21
Consensus pattern (19 bp):
AAAACTTGAAAGAACGGTT
Found at i:40006 original size:13 final size:13
Alignment explanation
Indices: 39988--40012 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39978 GTTAATATTT
39988 TTTACTATTTTTC
1 TTTACTATTTTTC
40001 TTTACTATTTTT
1 TTTACTATTTTT
40013 TATATCACGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTACTATTTTTC
Found at i:42266 original size:25 final size:25
Alignment explanation
Indices: 42237--42322 Score: 136
Period size: 25 Copynumber: 3.4 Consensus size: 25
42227 CGGGATAACA
*
42237 TTAAGACAATCAATCACAATATAAT
1 TTAAGACAATCAATTACAATATAAT
*
42262 TTAAGACAATCAATTACAGTATAAT
1 TTAAGACAATCAATTACAATATAAT
42287 TTAAGACAATCAATTACAATATAAT
1 TTAAGACAATCAATTACAATATAAT
*
42312 TCAAGAACAAT
1 TTAAG-ACAAT
42323 GTGGTTTAAG
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
25 51 0.91
26 5 0.09
ACGTcount: A:0.51, C:0.14, G:0.06, T:0.29
Consensus pattern (25 bp):
TTAAGACAATCAATTACAATATAAT
Found at i:42331 original size:41 final size:41
Alignment explanation
Indices: 42286--42403 Score: 211
Period size: 41 Copynumber: 2.9 Consensus size: 41
42276 TACAGTATAA
*
42286 TTTAAGACAATCAATTACAATATAATTCAAGAACAATGTGG
1 TTTAAGACAATCAATCACAATATAATTCAAGAACAATGTGG
42327 TTTAAGACAATCAATCACAATATAATTCAAGAACAATGTGG
1 TTTAAGACAATCAATCACAATATAATTCAAGAACAATGTGG
*
42368 TTTAAGACAATCAATCACAATATAATTTAAG-ACAAT
1 TTTAAGACAATCAATCACAATATAATTCAAGAACAAT
42404 TAATTACAGT
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
40 5 0.07
41 70 0.93
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (41 bp):
TTTAAGACAATCAATCACAATATAATTCAAGAACAATGTGG
Found at i:42388 original size:66 final size:64
Alignment explanation
Indices: 42237--42403 Score: 172
Period size: 66 Copynumber: 2.5 Consensus size: 64
42227 CGGGATAACA
* * *
42237 TTAAGACAATCAATCACAATATAATTTAAGACAATCAATTACAGTATAATTTAAGACAATCAAT
1 TTAAGACAATCAATCACAATATAATTTAAGACAATCAATCACAATATAATTCAAGACAATCAAT
* * * ** * ** *
42301 TACAATATAATTCAAGAACAATGTGGTTTAAGACAATCAATCACAATATAATTCAAGAACAATGT
1 T-TAAGACAA-TCAATCACAATATAATTTAAGACAATCAATCACAATATAATTCAAG-ACAAT-C
**
42366 GGT
62 AAT
42369 TTAAGACAATCAATCACAATATAATTTAAGACAAT
1 TTAAGACAATCAATCACAATATAATTTAAGACAAT
42404 TAATTACAGT
Statistics
Matches: 77, Mismatches: 22, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
64 1 0.01
65 5 0.06
66 59 0.77
67 10 0.13
68 2 0.03
ACGTcount: A:0.49, C:0.14, G:0.09, T:0.29
Consensus pattern (64 bp):
TTAAGACAATCAATCACAATATAATTTAAGACAATCAATCACAATATAATTCAAGACAATCAAT
Found at i:45193 original size:2 final size:2
Alignment explanation
Indices: 45186--45218 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
45176 TAATTCATAA
45186 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
45219 ACTTTTTTAT
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:58597 original size:54 final size:54
Alignment explanation
Indices: 58472--59029 Score: 745
Period size: 54 Copynumber: 10.6 Consensus size: 54
58462 GTTTAATGTA
*
58472 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTA-CGTATTGACAC
1 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATTGGCAC
* *
58525 TATGTGTGCAACCTACGTAATTCATAATGAGTTTGTGAATTACCGTATTGGTAC
1 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATTGGCAC
* * *
58579 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTA-CATACT---AA
1 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATTGGCAC
*
58629 TACT-TGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATTGTCAC
1 TA-TGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATTGGCAC
* *
58683 TATGTGTGCAACTCACGTAATTCATAATGAGTTTGTGAATTACAGTATTGGCAC
1 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATTGGCAC
*
58737 TATGTGTGCAACCTACGTAATTCATAATGA-TTTGTGAA-T---G---TGGCAC
1 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATTGGCAC
*
58783 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACAGTATTGGCAC
1 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATTGGCAC
* * *
58837 TATGTG-GCAACTCACGTAATTCATAATGAGTTTGTTAATTATCGTATTGGCAC
1 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATTGGCAC
* * * *
58890 TATGTGTGCAACCCACGTAATTAATAATTAGTTTTTGAATTA-CGTA-TGACAC
1 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATTGGCAC
* * * * *
58942 TATGTATGTAACCCACATAATTCATAATGAGTTTGTGAATTACCGTATCGGTAC
1 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATTGGCAC
* * *
58996 TATGTGTGCAAAACCACGGAATTTATAATGAGTT
1 TATGTGTGC-AACCCACGTAATTCATAATGAGTT
59030 GAAATAATCA
Statistics
Matches: 445, Mismatches: 41, Indels: 36
0.85 0.08 0.07
Matches are distributed among these distances:
46 35 0.08
47 8 0.02
48 1 0.00
49 1 0.00
50 41 0.09
51 6 0.01
52 42 0.09
53 111 0.25
54 180 0.40
55 20 0.04
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (54 bp):
TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATTGGCAC
Found at i:59013 original size:107 final size:105
Alignment explanation
Indices: 58472--59029 Score: 740
Period size: 107 Copynumber: 5.3 Consensus size: 105
58462 GTTTAATGTA
58472 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACGTATTGACACTATGTGTGCAAC
1 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACGTATTGACACTATGT-TGCAAC
*
58537 CTACGTAATTCATAATGAGTTTGTGAATTACCGTATTGGTAC
65 CCACGTAATTCATAATGAGTTTGTGAATTACCGTA-TGGTAC
* * * *
58579 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACATACTAATACT-TG-TGCAACC
1 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACGTATTGACACTATGTTGCAACC
*
58642 CACGTAATTCATAATGAGTTTGTGAATTACCGTATTGTCAC
66 CACGTAATTCATAATGAGTTTGTGAATTACCGTATGGT-AC
* *
58683 TATGTGTGCAACTCACGTAATTCATAATGAGTTTGTGAATTACAGTATTGGCACTATGTGTGCAA
1 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTAC-GTATTGACACTATGT-TGCAA
* *
58748 CCTACGTAATTCATAATGA-TTTGTGAA-T---G--TGGCAC
64 CCCACGTAATTCATAATGAGTTTGTGAATTACCGTATGGTAC
* *
58783 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACAGTATTGGCACTATGTGGCAAC
1 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTAC-GTATTGACACTATGTTGCAAC
* * * *
58848 TCACGTAATTCATAATGAGTTTGTTAATTATCGTATTGGCAC
65 CCACGTAATTCATAATGAGTTTGTGAATTACCGTA-TGGTAC
* * * *
58890 TATGTGTGCAACCCACGTAATTAATAATTAGTTTTTGAATTACGTA-TGACACTATGTATGTAAC
1 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACGTATTGACACTATGT-TGCAAC
*
58954 CCACATAATTCATAATGAGTTTGTGAATTACCGTATCGGTAC
65 CCACGTAATTCATAATGAGTTTGTGAATTACCGTAT-GGTAC
* * *
58996 TATGTGTGCAAAACCACGGAATTTATAATGAGTT
1 TATGTGTGC-AACCCACGTAATTCATAATGAGTT
59030 GAAATAATCA
Statistics
Matches: 400, Mismatches: 35, Indels: 32
0.86 0.07 0.07
Matches are distributed among these distances:
99 21 0.05
100 67 0.17
101 3 0.01
103 4 0.01
104 85 0.21
105 17 0.04
106 56 0.14
107 124 0.31
108 23 0.06
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (105 bp):
TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACGTATTGACACTATGTTGCAACC
CACGTAATTCATAATGAGTTTGTGAATTACCGTATGGTAC
Found at i:62079 original size:17 final size:17
Alignment explanation
Indices: 62057--62109 Score: 106
Period size: 17 Copynumber: 3.1 Consensus size: 17
62047 TAGAGCCATA
62057 TATTATTAGATGATTGG
1 TATTATTAGATGATTGG
62074 TATTATTAGATGATTGG
1 TATTATTAGATGATTGG
62091 TATTATTAGATGATTGG
1 TATTATTAGATGATTGG
62108 TA
1 TA
62110 ACACTCTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (17 bp):
TATTATTAGATGATTGG
Found at i:65208 original size:22 final size:23
Alignment explanation
Indices: 65182--65232 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
65172 AAAAGAATGT
*
65182 AAAGATATTAATCT-AAGTAA-TA
1 AAAGATAGTAA-CTAAAGTAAGTA
*
65204 AAAGAAAGTAACTAAAGTAAGTA
1 AAAGATAGTAACTAAAGTAAGTA
65227 AAAGAT
1 AAAGAT
65233 GAAAAGAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 2 0.08
22 15 0.62
23 7 0.29
ACGTcount: A:0.59, C:0.04, G:0.14, T:0.24
Consensus pattern (23 bp):
AAAGATAGTAACTAAAGTAAGTA
Done.