Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001713.1 Hibiscus syriacus cultivar Beakdansim tig00003465_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: 59279
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:7567 original size:16 final size:16
Alignment explanation
Indices: 7546--7576 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
7536 ACCTCACATT
*
7546 TGTGTGTGTGTGTATA
1 TGTGTGTGTATGTATA
7562 TGTGTGTGTATGTAT
1 TGTGTGTGTATGTAT
7577 GTATATGTCG
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:0.13, C:0.00, G:0.35, T:0.52
Consensus pattern (16 bp):
TGTGTGTGTATGTATA
Found at i:10372 original size:58 final size:59
Alignment explanation
Indices: 10299--10412 Score: 142
Period size: 58 Copynumber: 1.9 Consensus size: 59
10289 AGGAGGAATG
* * **
10299 TGTTGAGTGGGCCTGTTAAAGGCTTTAT-TGTAG-TCTTTTGGTTCTATCCACTTTTATT
1 TGTTGAGCGAGCCTGTTAAAGGCTTT-TCCCTAGTTCTTTTGGTTCTATCCACTTTTATT
** *
10357 TGTTGAGCGAGCCTGTTAAATTCTTTTCCCTAGTTTTTTTGGTTCTATCCACTTTT
1 TGTTGAGCGAGCCTGTTAAAGGCTTTTCCCTAGTTCTTTTGGTTCTATCCACTTTT
10413 TTGCTCCTGT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
57 1 0.02
58 25 0.53
59 21 0.45
ACGTcount: A:0.15, C:0.17, G:0.19, T:0.49
Consensus pattern (59 bp):
TGTTGAGCGAGCCTGTTAAAGGCTTTTCCCTAGTTCTTTTGGTTCTATCCACTTTTATT
Found at i:13770 original size:53 final size:53
Alignment explanation
Indices: 13634--13772 Score: 251
Period size: 53 Copynumber: 2.6 Consensus size: 53
13624 CGGATATGAT
* * *
13634 ATTATTCTGCCATTAGAAGCTTAGATTAGTCTCTTTACCATTTTCATGCTTGA
1 ATTATTCTGCCATTAGAAGGTTAGTTTAGTTTCTTTACCATTTTCATGCTTGA
13687 ATTATTCTGCCATTAGAAGGTTAGTTTAGTTTCTTTACCATTTTCATGCTTGA
1 ATTATTCTGCCATTAGAAGGTTAGTTTAGTTTCTTTACCATTTTCATGCTTGA
13740 ATTATTCTGCCATTAGAAGGTTAGTTTAGTTTC
1 ATTATTCTGCCATTAGAAGGTTAGTTTAGTTTC
13773 AATAAACATC
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
53 83 1.00
ACGTcount: A:0.24, C:0.16, G:0.15, T:0.45
Consensus pattern (53 bp):
ATTATTCTGCCATTAGAAGGTTAGTTTAGTTTCTTTACCATTTTCATGCTTGA
Found at i:23192 original size:21 final size:21
Alignment explanation
Indices: 23168--23212 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
23158 TCTTAACATG
*
23168 TTTAGTCCCTAAACTATCAAT
1 TTTAGTACCTAAACTATCAAT
* *
23189 TTTAGTACCTAAACTTTCATT
1 TTTAGTACCTAAACTATCAAT
23210 TTT
1 TTT
23213 TCCAGTAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.20, G:0.04, T:0.47
Consensus pattern (21 bp):
TTTAGTACCTAAACTATCAAT
Found at i:31333 original size:56 final size:59
Alignment explanation
Indices: 31246--31404 Score: 168
Period size: 59 Copynumber: 2.8 Consensus size: 59
31236 TAAATCTGGA
* *
31246 GATAAAATT-GAA-GATGCAAAAGTTTAGGGACTAATTTAG-AT-AT-CCATAGTTTGGG
1 GATAAAATTAGAATG-TTCAAAAGTTTAAGGACTAATTTAGAATGATACCATAGTTTGGG
** *
31301 GATAAAATTAGAATGTTCAAAAGTTTAAGGACTAATTTAGAATGATAGTTATAGTTTTGG
1 GATAAAATTAGAATGTTCAAAAGTTTAAGGACTAATTTAGAATGATA-CCATAGTTTGGG
* * * * *
31361 GATGAAA-TAGAATGTTAAAAAATTTAAGGATTAATTTAAAATGA
1 GATAAAATTAGAATGTTCAAAAGTTTAAGGACTAATTTAGAATGA
31405 GGGTCATAGT
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
55 9 0.10
56 26 0.30
57 3 0.03
58 2 0.02
59 33 0.38
60 15 0.17
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.33
Consensus pattern (59 bp):
GATAAAATTAGAATGTTCAAAAGTTTAAGGACTAATTTAGAATGATACCATAGTTTGGG
Found at i:31387 original size:59 final size:60
Alignment explanation
Indices: 31290--31418 Score: 170
Period size: 59 Copynumber: 2.2 Consensus size: 60
31280 TTTAGATATC
* * * * *
31290 CATAGTTTGGGGATAAAATTAGAATGTTCAAAAGTTTAAGGACTAATTTAGAATGATAGT
1 CATAGTTTTGGGATAAAATTAGAATGTTAAAAAATTTAAGGACTAATTTAAAATGAGAGT
* * * *
31350 TATAGTTTTGGGATGAAA-TAGAATGTTAAAAAATTTAAGGATTAATTTAAAATGAGGGT
1 CATAGTTTTGGGATAAAATTAGAATGTTAAAAAATTTAAGGACTAATTTAAAATGAGAGT
31409 CATAGTTTTG
1 CATAGTTTTG
31419 AGACATATAA
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
59 44 0.75
60 15 0.25
ACGTcount: A:0.40, C:0.03, G:0.22, T:0.36
Consensus pattern (60 bp):
CATAGTTTTGGGATAAAATTAGAATGTTAAAAAATTTAAGGACTAATTTAAAATGAGAGT
Found at i:31679 original size:25 final size:25
Alignment explanation
Indices: 31642--31697 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
31632 TAAATAAATT
31642 TATATAAACTAAAATTT-ATACTATA
1 TATATAAACTAAAATTTCATA-TATA
*
31667 TATATCAAA-TAAATTTTCATATATA
1 TATAT-AAACTAAAATTTCATATATA
31692 TATATA
1 TATATA
31698 TTTTTTTTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 1 0.04
25 21 0.75
26 6 0.21
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (25 bp):
TATATAAACTAAAATTTCATATATA
Found at i:35889 original size:16 final size:17
Alignment explanation
Indices: 35855--35895 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
35845 TTATATGAAA
*
35855 TGATATGTGCTTATATG
1 TGATATGTGATTATATG
*
35872 TGCTATGTGATT-TATG
1 TGATATGTGATTATATG
35888 TGATATGT
1 TGATATGT
35896 CATATGGGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.22, C:0.05, G:0.24, T:0.49
Consensus pattern (17 bp):
TGATATGTGATTATATG
Found at i:36490 original size:23 final size:23
Alignment explanation
Indices: 36456--36542 Score: 79
Period size: 23 Copynumber: 3.7 Consensus size: 23
36446 GGACATATTA
36456 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
36479 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
36502 CGGTC-CTTCGG-GACAAAATTCTACG
1 TGG-CACTACGGTG-C--AATTCTACG
*
36527 TGGCACTACAGTGCAA
1 TGGCACTACGGTGCAA
36543 ATTTATACGA
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
22 1 0.02
23 32 0.63
24 2 0.04
25 15 0.29
26 1 0.02
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:37550 original size:22 final size:22
Alignment explanation
Indices: 37525--37566 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
37515 AAAGACATAG
*
37525 ATAAACGTGTCACAAAAACAAA
1 ATAAACATGTCACAAAAACAAA
*
37547 ATAAACATGTCATAAAAACA
1 ATAAACATGTCACAAAAACA
37567 TAATTATTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.17, G:0.07, T:0.17
Consensus pattern (22 bp):
ATAAACATGTCACAAAAACAAA
Found at i:38221 original size:21 final size:19
Alignment explanation
Indices: 38197--38291 Score: 91
Period size: 21 Copynumber: 4.6 Consensus size: 19
38187 CATATTCGCA
38197 TTGCGATAGTCCAAGTTCGAG
1 TTGCGATAGTCCAAGTTC--G
*
38218 TTGCGATTTATTCCAAGTTCG
1 TTGCGA--TAGTCCAAGTTCG
*
38239 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
*
38260 TTGCGATTTATTCCAAGTTCG
1 TTGCGA--TAGTCCAAGTTCG
38281 TTGCGATAGTC
1 TTGCGATAGTC
38292 TAAAATCGCA
Statistics
Matches: 62, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
19 13 0.21
21 29 0.47
23 20 0.32
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (19 bp):
TTGCGATAGTCCAAGTTCG
Found at i:38236 original size:23 final size:21
Alignment explanation
Indices: 38206--38287 Score: 96
Period size: 21 Copynumber: 3.8 Consensus size: 21
38196 ATTGCGATAG
38206 TCCAAGTTCGAGTTGCGATTTAT
1 TCCAAGTTC--GTTGCGATTTAT
*
38229 TCCAAGTTCGTTGCGA--TAG
1 TCCAAGTTCGTTGCGATTTAT
*
38248 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGATTTAT
38271 TCCAAGTTCGTTGCGAT
1 TCCAAGTTCGTTGCGAT
38288 AGTCTAAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
19 9 0.18
21 24 0.47
23 18 0.35
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.37
Consensus pattern (21 bp):
TCCAAGTTCGTTGCGATTTAT
Found at i:38248 original size:42 final size:42
Alignment explanation
Indices: 38197--38291 Score: 172
Period size: 42 Copynumber: 2.3 Consensus size: 42
38187 CATATTCGCA
38197 TTGCGATAGTCCAAGTTCGAGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGAGTTGCGATTTATTCCAAGTTCG
* *
38239 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGAGTTGCGATTTATTCCAAGTTCG
38281 TTGCGATAGTC
1 TTGCGATAGTC
38292 TAAAATCGCA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGAGTTGCGATTTATTCCAAGTTCG
Found at i:38478 original size:21 final size:21
Alignment explanation
Indices: 38413--38479 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
38403 GATCACGACC
* * *
38413 GCGATAGTCTAAATTCGCATT
1 GCGATAGTCGAAGTTCGCGTT
*
38434 GCAATAGTCGAAGTTCGCGTT
1 GCGATAGTCGAAGTTCGCGTT
38455 GCGATAGTCGAAGTTCGCGTT
1 GCGATAGTCGAAGTTCGCGTT
38476 GCGA
1 GCGA
38480 ATTTAGAAAC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.28
Consensus pattern (21 bp):
GCGATAGTCGAAGTTCGCGTT
Found at i:42473 original size:37 final size:37
Alignment explanation
Indices: 42397--42473 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
42387 TTTTTATATT
*
42397 TTTAATTTTATAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTATAAAAAAAATTATATAAATATTATCAA
* * *
42434 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTATAAAAAAAATTATATAAATATTAT-CAA
42471 TTT
1 TTT
42474 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (37 bp):
TTTAATTTTATAAAAAAAATTATATAAATATTATCAA
Found at i:42875 original size:19 final size:21
Alignment explanation
Indices: 42839--42880 Score: 70
Period size: 19 Copynumber: 2.1 Consensus size: 21
42829 GTATGAATCG
42839 ATCATCTAAAACATTGAATAA
1 ATCATCTAAAACATTGAATAA
42860 ATCA-CTAAAA-ATTGAATAA
1 ATCATCTAAAACATTGAATAA
42879 AT
1 AT
42881 ATAAATACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 11 0.52
20 6 0.29
21 4 0.19
ACGTcount: A:0.55, C:0.12, G:0.05, T:0.29
Consensus pattern (21 bp):
ATCATCTAAAACATTGAATAA
Found at i:46536 original size:123 final size:123
Alignment explanation
Indices: 46317--46564 Score: 329
Period size: 123 Copynumber: 2.0 Consensus size: 123
46307 ACCACCCATG
*
46317 TCTTCAAGTATGTACCGTTTGAATCTGTCCGGCACGTCGGGTGTTGGGATTGGAGAAGAGGGTTT
1 TCTTCAAGTATGTACCGTTTGAAACTGTCCGGCACGTCGGGTGTTGGGATTGGAGAAGAGGGTTT
* * * ** *
46382 CTGTTTCTTGCTTCTCTTCAACTTGGATTTCAGTTCACTTCCTCGTTCTCGATCACCA
66 CTGTTTCTTGCGTCTCTTCAACTTGGATTTCAGTCCACTTCCCCAATCTCCATCACCA
* * * * *
46440 TCTTCAAGTATGTGCCGTTTGAAAGTGTCCGGCATGTCGGGTGTTGTGATT-GAGGATTG-GGGT
1 TCTTCAAGTATGTACCGTTTGAAACTGTCCGGCACGTCGGGTGTTGGGATTGGA-GA-AGAGGGT
* * *
46503 TTCTGTTTTTTGCGTCTTTTCAACTTGGGTTTCAGTCCACTTCCCCAATCTCCATCACCA
64 TTCTGTTTCTTGCGTCTCTTCAACTTGGATTTCAGTCCACTTCCCCAATCTCCATCACCA
46563 TC
1 TC
46565 ACCATCTTCT
Statistics
Matches: 108, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
122 2 0.02
123 105 0.97
124 1 0.01
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.38
Consensus pattern (123 bp):
TCTTCAAGTATGTACCGTTTGAAACTGTCCGGCACGTCGGGTGTTGGGATTGGAGAAGAGGGTTT
CTGTTTCTTGCGTCTCTTCAACTTGGATTTCAGTCCACTTCCCCAATCTCCATCACCA
Found at i:53201 original size:13 final size:13
Alignment explanation
Indices: 53183--53209 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
53173 TTACAGAAGC
53183 GCATATGAAGACT
1 GCATATGAAGACT
53196 GCATATGAAGACT
1 GCATATGAAGACT
53209 G
1 G
53210 TTCAACTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:54631 original size:20 final size:20
Alignment explanation
Indices: 54605--54671 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
54595 CAAAACAATG
* *
54605 AAGGGATTGATACTTTTGAA
1 AAGGGATCGATACTTTTAAA
* *
54625 GAGGGATCGATCCTTTTAAA
1 AAGGGATCGATACTTTTAAA
54645 AAGGGATCGAT-CATTTTAAA
1 AAGGGATCGATAC-TTTTAAA
54665 AAGGGAT
1 AAGGGAT
54672 AGATCCATTG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
19 1 0.02
20 40 0.98
ACGTcount: A:0.36, C:0.09, G:0.25, T:0.30
Consensus pattern (20 bp):
AAGGGATCGATACTTTTAAA
Found at i:54676 original size:20 final size:20
Alignment explanation
Indices: 54626--54676 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
54616 ACTTTTGAAG
*
54626 AGGGATCGATCCTTTTAAAA
1 AGGGATCGATCATTTTAAAA
54646 AGGGATCGATCATTTTAAAA
1 AGGGATCGATCATTTTAAAA
*
54666 AGGGATAGATC
1 AGGGATCGATC
54677 CATTGCACAA
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:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (20 bp):
AGGGATCGATCATTTTAAAA
Found at i:55990 original size:4 final size:4
Alignment explanation
Indices: 55981--56005 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
55971 AACTCAAAAG
55981 TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA T
56006 GCGTACATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (4 bp):
TACA
Done.