Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004390.1 Hibiscus syriacus cultivar Beakdansim tig00009633_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: 67157
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:472 original size:21 final size:22
Alignment explanation
Indices: 446--500 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
436 GGTAAACATG
446 ATGTAA-AGGTAGCCCTTATAT
1 ATGTAATAGGTAGCCCTTATAT
* **
467 ATGTAATAGGTATCGTTTATAT
1 ATGTAATAGGTAGCCCTTATAT
489 A-GTAATAGGTAG
1 ATGTAATAGGTAG
501 TGGTTATATG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 16 0.55
22 13 0.45
ACGTcount: A:0.35, C:0.07, G:0.22, T:0.36
Consensus pattern (22 bp):
ATGTAATAGGTAGCCCTTATAT
Found at i:507 original size:21 final size:21
Alignment explanation
Indices: 461--513 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
451 AAGGTAGCCC
*
461 TTATATATGTAATAGGTATCGT
1 TTATATA-GTAATAGGTATCGG
483 TTATATAGTAATAGGTAGT-GG
1 TTATATAGTAATAGGTA-TCGG
504 TTATAT-GTAA
1 TTATATAGTAA
514 AGTGTCTATC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 4 0.14
21 17 0.59
22 8 0.28
ACGTcount: A:0.34, C:0.02, G:0.21, T:0.43
Consensus pattern (21 bp):
TTATATAGTAATAGGTATCGG
Found at i:545 original size:18 final size:18
Alignment explanation
Indices: 512--546 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
502 GGTTATATGT
* *
512 AAAGTGTCTATCCTTTTA
1 AAAGTGTCCATACTTTTA
530 AAAGTGTCCATACTTTT
1 AAAGTGTCCATACTTTT
547 TTCACTGTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.43
Consensus pattern (18 bp):
AAAGTGTCCATACTTTTA
Found at i:880 original size:21 final size:21
Alignment explanation
Indices: 851--905 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 21
841 ATAGGTAAAC
*
851 ATATGATGTAAGGTAGCCCTT
1 ATATAATGTAAGGTAGCCCTT
* **
872 ATATAATGTAATAGGTATCGTTT
1 ATATAATGT-A-AGGTAGCCCTT
895 ATATAATGTAA
1 ATATAATGTAA
906 TAGGTAGTGG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 9 0.32
22 2 0.07
23 17 0.61
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.38
Consensus pattern (21 bp):
ATATAATGTAAGGTAGCCCTT
Found at i:919 original size:23 final size:23
Alignment explanation
Indices: 870--919 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
860 AAGGTAGCCC
*
870 TTATATAATGTAATAGGTATCGT
1 TTATATAATGTAATAGGTATCGG
893 TTATATAATGTAATAGGTAGT-GG
1 TTATATAATGTAATAGGTA-TCGG
916 TTAT
1 TTAT
920 TGTAAAGTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 24 0.96
24 1 0.04
ACGTcount: A:0.34, C:0.02, G:0.20, T:0.44
Consensus pattern (23 bp):
TTATATAATGTAATAGGTATCGG
Found at i:1212 original size:24 final size:25
Alignment explanation
Indices: 1180--1229 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
1170 ACAACAAATC
*
1180 AATTAAACA-TGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
1204 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
1229 A
1 A
1230 TTTGGATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.38
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:1806 original size:39 final size:39
Alignment explanation
Indices: 1763--1887 Score: 225
Period size: 39 Copynumber: 3.2 Consensus size: 39
1753 TTCGATGCTC
* *
1763 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1802 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1841 ATCAAAATCCAAATCTCATATGATGCCAAGC-AAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1879 ATCAAAATC
1 ATCAAAATC
1888 TACAACTTGA
Statistics
Matches: 84, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
38 16 0.19
39 68 0.81
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
Found at i:2316 original size:23 final size:23
Alignment explanation
Indices: 2285--2348 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
2275 ATAGGTAAAC
*
2285 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
2308 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
2331 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
2349 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:2355 original size:23 final size:23
Alignment explanation
Indices: 2285--2357 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
2275 ATAGGTAAAC
* **
2285 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
2308 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
2331 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
2354 ATAT
1 ATAT
2358 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:17616 original size:13 final size:13
Alignment explanation
Indices: 17600--17630 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
17590 AAAAAAATTG
17600 AAAAAAATTAAAA
1 AAAAAAATTAAAA
17613 AAAAAAATTAAAA
1 AAAAAAATTAAAA
17626 AAAAA
1 AAAAA
17631 TGTACCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (13 bp):
AAAAAAATTAAAA
Found at i:17628 original size:9 final size:10
Alignment explanation
Indices: 17586--17615 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
17576 CAGTTAAACG
17586 ATTGAAAAAA
1 ATTGAAAAAA
17596 ATTGAAAAAA
1 ATTGAAAAAA
17606 ATT-AAAAAA
1 ATTGAAAAAA
17615 A
1 A
17616 AAAATTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 7 0.35
10 13 0.65
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (10 bp):
ATTGAAAAAA
Found at i:30517 original size:47 final size:47
Alignment explanation
Indices: 30459--30558 Score: 137
Period size: 47 Copynumber: 2.1 Consensus size: 47
30449 ACGATTTTTC
*
30459 TATATACAAATAAATTTTTCTAATCGTCTTCTATCAATTCATTAATT
1 TATATACAAATAAATTTGTCTAATCGTCTTCTATCAATTCATTAATT
* ** * * *
30506 TATATAGAAATAAATTTGTCTTGTCGTTTTTTATCAATTCATTGATT
1 TATATACAAATAAATTTGTCTAATCGTCTTCTATCAATTCATTAATT
30553 TATATA
1 TATATA
30559 TTTTCTAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.34, C:0.11, G:0.06, T:0.49
Consensus pattern (47 bp):
TATATACAAATAAATTTGTCTAATCGTCTTCTATCAATTCATTAATT
Found at i:39139 original size:3 final size:3
Alignment explanation
Indices: 39131--39191 Score: 50
Period size: 3 Copynumber: 20.3 Consensus size: 3
39121 GCAGCGGCAG
* ** * * * *
39131 CAA CAA CAA CTA CTG CAA CAA CAG CAG CTA CAA CAA CAA CTA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
*
39179 CAA CTA CAA CAA C
1 CAA CAA CAA CAA C
39192 CACCACCACC
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.52, C:0.34, G:0.05, T:0.08
Consensus pattern (3 bp):
CAA
Found at i:39150 original size:15 final size:15
Alignment explanation
Indices: 39130--39185 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
39120 TGCAGCGGCA
39130 GCAACAACAACTACT
1 GCAACAACAACTACT
*
39145 GCAACAACAGC-AGCT
1 GCAACAACAACTA-CT
*
39160 ACAACAACAACTA--
1 GCAACAACAACTACT
39173 -CAACAACAACTAC
1 GCAACAACAACTAC
39186 AACAACCACC
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
12 12 0.34
14 1 0.03
15 21 0.60
16 1 0.03
ACGTcount: A:0.50, C:0.34, G:0.07, T:0.09
Consensus pattern (15 bp):
GCAACAACAACTACT
Found at i:39163 original size:12 final size:12
Alignment explanation
Indices: 39133--39191 Score: 73
Period size: 12 Copynumber: 4.7 Consensus size: 12
39123 AGCGGCAGCA
*
39133 ACAACAACTACT
1 ACAACAACAACT
*
39145 GCAACAACAGCAGCT
1 ACAACAACA--A-CT
39160 ACAACAACAACT
1 ACAACAACAACT
39172 ACAACAACAACT
1 ACAACAACAACT
39184 ACAACAAC
1 ACAACAAC
39192 CACCACCACC
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
12 29 0.71
13 1 0.02
14 1 0.02
15 10 0.24
ACGTcount: A:0.53, C:0.34, G:0.05, T:0.08
Consensus pattern (12 bp):
ACAACAACAACT
Found at i:43465 original size:25 final size:24
Alignment explanation
Indices: 43412--43466 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
43402 TGTAAATACA
* *
43412 ATTATAAGTATAATTAACACATTC
1 ATTATAACTATAATTAACACAATC
43436 A-TATAACTATAATTAGA-ACAGATC
1 ATTATAACTATAATTA-ACACA-ATC
43460 ATTATAA
1 ATTATAA
43467 AACACAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 16 0.62
24 5 0.19
25 5 0.19
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.35
Consensus pattern (24 bp):
ATTATAACTATAATTAACACAATC
Found at i:55612 original size:19 final size:18
Alignment explanation
Indices: 55571--55613 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
55561 ATTTTATCAA
*
55571 AAAATAAAATGAAACATT
1 AAAATAAAATCAAACATT
*
55589 AAAATCAAAATCATACATT
1 AAAAT-AAAATCAAACATT
55608 AAAATA
1 AAAATA
55614 TTAACAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.65, C:0.09, G:0.02, T:0.23
Consensus pattern (18 bp):
AAAATAAAATCAAACATT
Found at i:55712 original size:5 final size:5
Alignment explanation
Indices: 55702--55727 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
55692 GAGTATTCTT
55702 CCGAC CCGAC CCGAC CCGAC CCGAC C
1 CCGAC CCGAC CCGAC CCGAC CCGAC C
55728 GAATAAATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.62, G:0.19, T:0.00
Consensus pattern (5 bp):
CCGAC
Found at i:62238 original size:60 final size:60
Alignment explanation
Indices: 62128--62240 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 60
62118 TATAGGACAC
* *
62128 TACTTTATTAAGTCCTCCAACTATTAAAAGTTACAAAATGATTCTCTGACTATAAGGTGT
1 TACTTTATTAAGTCCTCCAACTATTAAAAATTACAAAATGATACTCTGACTATAAGGTGT
* * * *
62188 TACTTTGTTGAGTCCTTCGACTATTAAAAATTACAAAATGATCACT-TGACTAT
1 TACTTTATTAAGTCCTCCAACTATTAAAAATTACAAAATGAT-ACTCTGACTAT
62241 TCATATGTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
60 44 0.96
61 2 0.04
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.37
Consensus pattern (60 bp):
TACTTTATTAAGTCCTCCAACTATTAAAAATTACAAAATGATACTCTGACTATAAGGTGT
Done.