Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003306.1 Hibiscus syriacus cultivar Beakdansim tig00006952_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: 66351
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:29 original size:21 final size:21
Alignment explanation
Indices: 1--75 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
1 GCCTCTTGAACGGTGGGAGGG
1 GCCTCTTGAACGGTGGGAGGG
* * **
22 GACTCTTG-AGGGATGATAGGG
1 GCCTCTTGAACGG-TGGGAGGG
* * *
43 GCCTCTTGAACGATAGGAGAG
1 GCCTCTTGAACGGTGGGAGGG
64 GCCTCTTGAACG
1 GCCTCTTGAACG
76 ATGACAGGTG
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
20 3 0.07
21 36 0.88
22 2 0.05
ACGTcount: A:0.21, C:0.19, G:0.39, T:0.21
Consensus pattern (21 bp):
GCCTCTTGAACGGTGGGAGGG
Found at i:624 original size:20 final size:22
Alignment explanation
Indices: 599--647 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
589 GAAACTTAAA
599 ATCGCAACGTG-GAA-ATGACT
1 ATCGCAACGTGCGAATATGACT
*
619 ATCGCAA--TGCGAATTTGACT
1 ATCGCAACGTGCGAATATGACT
639 ATCGCAACG
1 ATCGCAACG
648 GGATAATCGC
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 2 0.08
19 3 0.12
20 19 0.79
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (22 bp):
ATCGCAACGTGCGAATATGACT
Found at i:676 original size:19 final size:20
Alignment explanation
Indices: 652--690 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
642 GCAACGGGAT
*
652 AATCGCAATGCGAAA-TAAA
1 AATCGCAACGCGAAACTAAA
671 AATCGCAACGCGAAACTAAA
1 AATCGCAACGCGAAACTAAA
691 TTCGTGTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.51, C:0.21, G:0.15, T:0.13
Consensus pattern (20 bp):
AATCGCAACGCGAAACTAAA
Found at i:1552 original size:127 final size:127
Alignment explanation
Indices: 1394--1647 Score: 449
Period size: 127 Copynumber: 2.0 Consensus size: 127
1384 AAGGGGGGAA
1394 TCGGTACCCCTGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTC-AGAGCCAAACCATT
1 TCGGTACCCCTGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGA-AGCCAAACCATT
* * *
1458 TAG-GGGGAATCGGTATCCCCTGGGGGGGAATCGGTTCCCTCTGAGCAATCTGAAATTTTTGG
65 CAGAGGGGAATCGGTACCCCCTGGGGGAGAATCGGTTCCCTCTGAGCAATCTGAAATTTTTGG
1520 TCGGTACCCCCTGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGAAGCCAAACCATT
1 TCGGTA-CCCCTGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGAAGCCAAACCATT
1585 CAGAGGGGAATCGGTACCCCCTGGGGGAGAATCGGTTCCCTCTGAGCAATCTGAAATTTTTGG
65 CAGAGGGGAATCGGTACCCCCTGGGGGAGAATCGGTTCCCTCTGAGCAATCTGAAATTTTTGG
1648 CTTTGAAATG
Statistics
Matches: 122, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
126 6 0.05
127 58 0.48
128 58 0.48
ACGTcount: A:0.21, C:0.26, G:0.30, T:0.24
Consensus pattern (127 bp):
TCGGTACCCCTGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGAAGCCAAACCATTC
AGAGGGGAATCGGTACCCCCTGGGGGAGAATCGGTTCCCTCTGAGCAATCTGAAATTTTTGG
Found at i:4232 original size:22 final size:22
Alignment explanation
Indices: 4191--4253 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 22
4181 CCAGAACCCC
* *
4191 AGGGGGGTATCGATTTCCCTGT
1 AGGGGGGAATCGATTCCCCTGT
*
4213 AGGGGGGAATCGGTTCCCCT-T
1 AGGGGGGAATCGATTCCCCTGT
4234 CAAAGGGGGG-ATCGATTCCC
1 ---AGGGGGGAATCGATTCCC
4254 TCTACACCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
21 1 0.03
22 17 0.50
23 9 0.26
24 7 0.21
ACGTcount: A:0.17, C:0.22, G:0.37, T:0.24
Consensus pattern (22 bp):
AGGGGGGAATCGATTCCCCTGT
Found at i:10137 original size:128 final size:127
Alignment explanation
Indices: 9973--10223 Score: 425
Period size: 128 Copynumber: 2.0 Consensus size: 127
9963 GGGGAATCGA
*
9973 TACCCCCTGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCTGAGCCAAACCATTCAGGG
1 TACCCCCTGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAGCCAAACCATTCAGGG
*
10038 GGGAATCGGTA-CCCCTGGGGGGGAATCGGTTCCCTCTGAGCAATTTGAAATTTTTGGTCGG
66 GGGAATCGGTACCCCCTGGGGGGGAATCGGTTCCCTCTGAGCAATCTGAAATTTTTGGTCGG
**
10099 TACCCCCTGGGGGGGGAAT-GGTTTGGCTCCGAGCATACTGGAATTCTCGGAGCCAAACCATTCA
1 TACCCCCT--GGGGGGAATCGG-TTCCCTCCGAGCATACTGGAATTCTCGGAGCCAAACCATTCA
10163 GGGGGGAATCGGTACCCCCTGGGGGGGAATCGGTTCCCTCTGAGCAATCTGAAATTTTTGG
63 GGGGGGAATCGGTACCCCCTGGGGGGGAATCGGTTCCCTCTGAGCAATCTGAAATTTTTGG
10224 CTTTGAAATG
Statistics
Matches: 117, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
126 8 0.07
127 2 0.02
128 62 0.53
129 45 0.38
ACGTcount: A:0.20, C:0.25, G:0.31, T:0.24
Consensus pattern (127 bp):
TACCCCCTGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAGCCAAACCATTCAGGG
GGGAATCGGTACCCCCTGGGGGGGAATCGGTTCCCTCTGAGCAATCTGAAATTTTTGGTCGG
Found at i:12939 original size:22 final size:22
Alignment explanation
Indices: 12914--12960 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
12904 GATGGAGATA
12914 GACGGATTTCGCCGAAGATGGG
1 GACGGATTTCGCCGAAGATGGG
* *
12936 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGAAGATGGG
12958 GAC
1 GAC
12961 AGATGTCGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.21, C:0.17, G:0.43, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGCCGAAGATGGG
Found at i:12969 original size:22 final size:22
Alignment explanation
Indices: 12929--12971 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
12919 ATTTCGCCGA
* *
12929 AGATGGGGACGGATTTCGTCGG
1 AGATGGGGACAGATGTCGTCGG
12951 AGATGGGGACAGATGTCGTCG
1 AGATGGGGACAGATGTCGTCG
12972 TAGAGAGTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.14, G:0.44, T:0.21
Consensus pattern (22 bp):
AGATGGGGACAGATGTCGTCGG
Found at i:13160 original size:20 final size:20
Alignment explanation
Indices: 13137--13200 Score: 78
Period size: 20 Copynumber: 3.1 Consensus size: 20
13127 ATTATCGCAA
13137 TGCGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
*
13157 TGCGATTAAGT-A-ATATCACGT
1 TGCGA-T-AGTCAGA-ATCGCGT
13178 TGCGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
13198 TGC
1 TGC
13201 TATTTACATA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
19 3 0.08
20 17 0.46
21 14 0.38
22 3 0.08
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.28
Consensus pattern (20 bp):
TGCGATAGTCAGAATCGCGT
Found at i:13313 original size:19 final size:19
Alignment explanation
Indices: 13289--13325 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
13279 TGTGATACTG
*
13289 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
13308 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
13326 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:18629 original size:2 final size:2
Alignment explanation
Indices: 18622--18655 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
18612 AAAAGAAATT
18622 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
18656 CTAAACTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:27135 original size:34 final size:34
Alignment explanation
Indices: 27096--27180 Score: 161
Period size: 34 Copynumber: 2.5 Consensus size: 34
27086 CGATTATATA
27096 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
27130 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
*
27164 TATATATAAAATATTTT
1 TATATATATAATATTTT
27181 CGGGTTCGGG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (34 bp):
TATATATATAATATTTTATATTTTTTATATTAAT
Found at i:32012 original size:2 final size:2
Alignment explanation
Indices: 32005--32061 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
31995 CGTACATACA
*
32005 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32047 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
32062 GTAACACGTA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:32458 original size:2 final size:2
Alignment explanation
Indices: 32451--32486 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
32441 CACTTTTACC
32451 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32487 TTCTTCTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34859 original size:33 final size:33
Alignment explanation
Indices: 34822--34884 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
34812 AAATCCACCA
* *
34822 CCTCCACGACCACCACCTCTACCGCCACCTCTG
1 CCTCCACCACCACCACCTCTACCACCACCTCTG
* * *
34855 CCTCCTCCACGACCACCTCTTCCACCACCT
1 CCTCCACCACCACCACCTCTACCACCACCT
34885 TGTACCAGCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.17, C:0.59, G:0.06, T:0.17
Consensus pattern (33 bp):
CCTCCACCACCACCACCTCTACCACCACCTCTG
Found at i:39339 original size:2 final size:2
Alignment explanation
Indices: 39332--39359 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39322 TTAGTATTAG
39332 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39360 TAAATCTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44916 original size:47 final size:50
Alignment explanation
Indices: 44833--44940 Score: 125
Period size: 47 Copynumber: 2.2 Consensus size: 50
44823 GCGCTCTCTG
* ** * *
44833 TCCGTGCTATATGCTGATTTGACGTCACGTGAGGTAT-A-GCGCCCCTTA
1 TCCGCGCTATATGCTGACATGACGTCACGTGAGGTATAACACGCCCCTGA
*
44881 -CCGCGCTATATGCTGACATGACTTACACGTG-GGTATAACACGCCCCTGA
1 TCCGCGCTATATGCTGACATGACGT-CACGTGAGGTATAACACGCCCCTGA
44930 TCCGCGCTATA
1 TCCGCGCTATA
44941 CGTCACGTAG
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
47 25 0.50
48 7 0.14
49 8 0.16
50 10 0.20
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.27
Consensus pattern (50 bp):
TCCGCGCTATATGCTGACATGACGTCACGTGAGGTATAACACGCCCCTGA
Found at i:45894 original size:35 final size:34
Alignment explanation
Indices: 45809--45895 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
45799 AATATAATTT
*
45809 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
45843 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
45881 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
45896 ATTGAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:45999 original size:16 final size:17
Alignment explanation
Indices: 45980--46012 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
45970 TTACAATTTA
*
45980 ACAAA-ATAAAATAAAT
1 ACAAATATAAAAAAAAT
45996 ACAAATATAAAAAAAAT
1 ACAAATATAAAAAAAAT
46013 CTATCGATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (17 bp):
ACAAATATAAAAAAAAT
Found at i:46863 original size:22 final size:22
Alignment explanation
Indices: 46836--46907 Score: 135
Period size: 22 Copynumber: 3.3 Consensus size: 22
46826 TTTGTCTTGC
46836 CGCGTCTATCTGTGCTATGCAA
1 CGCGTCTATCTGTGCTATGCAA
46858 CGCGTCTATCTGTGCTATGCAA
1 CGCGTCTATCTGTGCTATGCAA
46880 CGCGTCTATCTGTGCTATGCAA
1 CGCGTCTATCTGTGCTATGCAA
*
46902 CTCGTC
1 CGCGTC
46908 CATATTGCGA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.17, C:0.29, G:0.22, T:0.32
Consensus pattern (22 bp):
CGCGTCTATCTGTGCTATGCAA
Found at i:48273 original size:17 final size:18
Alignment explanation
Indices: 48253--48293 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
48243 AAATTATATT
48253 AGTAAAAT-ATTAAATAA
1 AGTAAAATGATTAAATAA
*
48270 AGTAAAATGCTTAAATAA
1 AGTAAAATGATTAAATAA
*
48288 ATTAAA
1 AGTAAA
48294 TACATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.29
Consensus pattern (18 bp):
AGTAAAATGATTAAATAA
Found at i:48577 original size:51 final size:51
Alignment explanation
Indices: 48446--48586 Score: 135
Period size: 51 Copynumber: 2.8 Consensus size: 51
48436 CCCTCTGTAC
* ** * * *
48446 CGCGCTATACCCCACGTGTCAGATAAA-CATC-TATAGCGTGGATCAGGGGG
1 CGCGCTATA-CCCACGTGTAAGCCAAATCAGCATATAGTGCGGATCAGGGGG
* ** *
48496 CGCGCTATACCCACGTGTAAGCTATGTCAGCGTATAGTGCGGATCAGGGGG
1 CGCGCTATACCCACGTGTAAGCCAAATCAGCATATAGTGCGGATCAGGGGG
**
48547 CGCGCTATACCTCACGTG-GCGCCAAATCAGCATATAGTGC
1 CGCGCTATACC-CACGTGTAAGCCAAATCAGCATATAGTGC
48587 CGGGTAAGGA
Statistics
Matches: 75, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
49 13 0.17
50 12 0.16
51 44 0.59
52 6 0.08
ACGTcount: A:0.24, C:0.27, G:0.28, T:0.21
Consensus pattern (51 bp):
CGCGCTATACCCACGTGTAAGCCAAATCAGCATATAGTGCGGATCAGGGGG
Found at i:56306 original size:22 final size:23
Alignment explanation
Indices: 56234--56295 Score: 115
Period size: 23 Copynumber: 2.7 Consensus size: 23
56224 TCCCCTGTGG
*
56234 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGAAATCGGTTCCCCTTCAAA
56257 GGGGAAATCGGTTCCCCTTCAAA
1 GGGGAAATCGGTTCCCCTTCAAA
56280 GGGGAAATCGGTTCCC
1 GGGGAAATCGGTTCCC
56296 TCAAGGGGGG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.23, C:0.26, G:0.31, T:0.21
Consensus pattern (23 bp):
GGGGAAATCGGTTCCCCTTCAAA
Done.