Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003026.1 Hibiscus syriacus cultivar Beakdansim tig00006296_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: 64969
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:5619 original size:2 final size:2
Alignment explanation
Indices: 5612--5666 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
5602 CATGGCTGCA
5612 AT AT AT 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 AT AT AT
*
5654 AT AT AT AC AT AT A
1 AT AT AT AT AT AT A
5667 AGCAAATTTG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:14560 original size:24 final size:24
Alignment explanation
Indices: 14533--14579 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
14523 GGGACCTGCT
14533 AAAGAAGAAAAGAAGGACGACAAA
1 AAAGAAGAAAAGAAGGACGACAAA
* *
14557 AAAGATGAAAAGAAGGATGACAA
1 AAAGAAGAAAAGAAGGACGACAA
14580 GAAATGATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.64, C:0.06, G:0.26, T:0.04
Consensus pattern (24 bp):
AAAGAAGAAAAGAAGGACGACAAA
Found at i:16527 original size:22 final size:19
Alignment explanation
Indices: 16492--16534 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 19
16482 GGACTTTTGG
16492 ATTTTTAAAAATTAAATAAAT
1 ATTTTTAAAAATT--ATAAAT
*
16513 ATTTTTATAATATTATAAAT
1 ATTTTTA-AAAATTATAAAT
16533 AT
1 AT
16535 ACTTTTTCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 8 0.40
21 7 0.35
22 5 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTTTAAAAATTATAAAT
Found at i:17166 original size:5 final size:5
Alignment explanation
Indices: 17156--17281 Score: 216
Period size: 5 Copynumber: 25.2 Consensus size: 5
17146 TTTTCTTCTC
* * *
17156 CATAT CATAT CATAT CATAT CATAT CATAC CATAT CATAC CATAC CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
*
17206 CATAC CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
17256 CATAT CATAT CATAT CATAT CATAT C
1 CATAT CATAT CATAT CATAT CATAT C
17282 TTTATTTTAT
Statistics
Matches: 115, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 115 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.37
Consensus pattern (5 bp):
CATAT
Found at i:18783 original size:23 final size:23
Alignment explanation
Indices: 18757--18881 Score: 133
Period size: 23 Copynumber: 5.3 Consensus size: 23
18747 CACCACAGCT
*
18757 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGGAGTGCCA
*
18780 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGGAGTGCCA
* * *
18803 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGGAGTGCCA
* *
18826 TATAATAATTGCACCGGAGTGCCG
1 CAT-ATAATTGCACCGGAGTGCCA
* * *
18850 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGGAGTGCCA
*
18873 TATAATAAT
1 CAT-ATAAT
18882 GTCCATAAGG
Statistics
Matches: 81, Mismatches: 19, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
23 59 0.73
24 22 0.27
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGGAGTGCCA
Found at i:18846 original size:47 final size:47
Alignment explanation
Indices: 18762--18881 Score: 215
Period size: 47 Copynumber: 2.6 Consensus size: 47
18752 CAGCTCATAT
* *
18762 AATTGCACCGAAGTGCCACAT-ATAATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGTAGTGCCATATAATAATTGCACCGGAGTGCCGCGTAG
18808 AATTGCACCGTAGTGCCATATAATAATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGTAGTGCCATATAATAATTGCACCGGAGTGCCGCGTAG
18855 AATTGCACCGTAGTGCCATATAATAAT
1 AATTGCACCGTAGTGCCATATAATAAT
18882 GTCCATAAGG
Statistics
Matches: 71, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
46 19 0.27
47 52 0.73
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (47 bp):
AATTGCACCGTAGTGCCATATAATAATTGCACCGGAGTGCCGCGTAG
Found at i:19059 original size:103 final size:103
Alignment explanation
Indices: 18888--19105 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
18878 TAATGTCCAT
* *
18888 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
18953 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
18991 AAGGACTACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
19056 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
19094 AAGGACCACATA
1 AAGGACCACATA
19106 GACCCTCGAC
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:24115 original size:17 final size:17
Alignment explanation
Indices: 24093--24125 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
24083 CTAAAATGAA
24093 ATAAAA-GTGATAATTTT
1 ATAAAACGTG-TAATTTT
24110 ATAAAACGTGTAATTT
1 ATAAAACGTGTAATTT
24126 ACCCTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.45, C:0.03, G:0.12, T:0.39
Consensus pattern (17 bp):
ATAAAACGTGTAATTTT
Found at i:26066 original size:51 final size:51
Alignment explanation
Indices: 25964--26067 Score: 129
Period size: 51 Copynumber: 2.0 Consensus size: 51
25954 CATTTAATTG
** * * *
25964 AAGGCGCGTCCCCGGGGATACGTTTTCCACACGTGGCAGTCGAGCTGGCGA
1 AAGGCGCGTCCCCGGGGATACGCCTTCCACACGTGGCAGTCCAACTAGCGA
* *
26015 AAGGCGCGTCCCCGGGGATGCGCCTTCCATACGTGGCA-TCCAACTCAGCGA
1 AAGGCGCGTCCCCGGGGATACGCCTTCCACACGTGGCAGTCCAACT-AGCGA
26066 AA
1 AA
26068 ACACGGGTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
50 5 0.11
51 40 0.89
ACGTcount: A:0.20, C:0.32, G:0.32, T:0.16
Consensus pattern (51 bp):
AAGGCGCGTCCCCGGGGATACGCCTTCCACACGTGGCAGTCCAACTAGCGA
Found at i:26431 original size:19 final size:20
Alignment explanation
Indices: 26391--26435 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
26381 TAGTTAATTT
*
26391 AATTTATATTTTTCTTCATA
1 AATTTATATTTTTCATCATA
26411 AATTATATATTTTT-ATC-TA
1 AATT-TATATTTTTCATCATA
26430 AATTTA
1 AATTTA
26436 AAGTGTATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 2 0.09
19 6 0.26
20 6 0.26
21 9 0.39
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.58
Consensus pattern (20 bp):
AATTTATATTTTTCATCATA
Found at i:26654 original size:2 final size:2
Alignment explanation
Indices: 26649--26736 Score: 176
Period size: 2 Copynumber: 44.0 Consensus size: 2
26639 ATAATAATTC
26649 AT AT AT 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 AT AT AT
26691 AT AT AT 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 AT AT AT
26733 AT AT
1 AT AT
26737 CTCGACTTAA
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 86 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31155 original size:19 final size:17
Alignment explanation
Indices: 31122--31165 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
31112 AATTTCAATA
31122 ATTA-TTTTTTAAAAAC
1 ATTATTTTTTTAAAAAC
31138 ATTATTTTTTTATGAAAAC
1 ATTATTTTTTTA--AAAAC
*
31157 GTTATTTTT
1 ATTATTTTT
31166 AAATTATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 4 0.17
17 7 0.29
19 13 0.54
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.57
Consensus pattern (17 bp):
ATTATTTTTTTAAAAAC
Found at i:31567 original size:24 final size:24
Alignment explanation
Indices: 31530--31581 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
31520 GTCTTTCAAT
* *
31530 TTTATCAATTAGATCACTTAACTA
1 TTTATAAATCAGATCACTTAACTA
31554 TTTATAAATCAGATCACTTAACTA
1 TTTATAAATCAGATCACTTAACTA
31578 TTTA
1 TTTA
31582 ATTATTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.04, T:0.42
Consensus pattern (24 bp):
TTTATAAATCAGATCACTTAACTA
Found at i:31682 original size:5 final size:5
Alignment explanation
Indices: 31672--31730 Score: 57
Period size: 6 Copynumber: 11.0 Consensus size: 5
31662 ATACATTCTA
31672 TTAAT TTAATT TTAATT TTAATT TTAATT TTAATT TTAAT TTAAT TTAA-
1 TTAAT TTAA-T TTAA-T TTAA-T TTAA-T TTAA-T TTAAT TTAAT TTAAT
*
31721 TAAAT TTAAT
1 TTAAT TTAAT
31731 CCTTCAATCA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
4 3 0.06
5 18 0.36
6 29 0.58
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTAAT
Found at i:31685 original size:6 final size:6
Alignment explanation
Indices: 31672--31718 Score: 80
Period size: 6 Copynumber: 8.2 Consensus size: 6
31662 ATACATTCTA
31672 TTAA-T TTAATT TTAATT TTAATT TTAATT TTAATT TTAA-T TTAATT
1 TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT
31718 T
1 T
31719 AATAAATTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
5 9 0.22
6 31 0.77
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TTAATT
Found at i:38471 original size:12 final size:11
Alignment explanation
Indices: 38442--38471 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
38432 TATTTTTAAT
38442 AAAATTAATAA
1 AAAATTAATAA
38453 AAAATTAATAA
1 AAAATTAATAA
38464 AAATATTA
1 AAA-ATTA
38472 TTATTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AAAATTAATAA
Found at i:45172 original size:15 final size:16
Alignment explanation
Indices: 45141--45174 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
45131 TATTTTTGTT
*
45141 TAAATTAACTGATAAA
1 TAAATTAAATGATAAA
45157 TAAATTAAAT-ATAAA
1 TAAATTAAATGATAAA
45172 TAA
1 TAA
45175 TTATATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (16 bp):
TAAATTAAATGATAAA
Found at i:46541 original size:6 final size:6
Alignment explanation
Indices: 46530--46555 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
46520 AGCCCTAAAT
46530 CCTAAC CCTAAC CCTAAC CCTAAC CC
1 CCTAAC CCTAAC CCTAAC CCTAAC CC
46556 ATTGTCGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.54, G:0.00, T:0.15
Consensus pattern (6 bp):
CCTAAC
Found at i:50721 original size:70 final size:70
Alignment explanation
Indices: 50507--50749 Score: 251
Period size: 70 Copynumber: 3.4 Consensus size: 70
50497 AAAAAAATAT
* *
50507 TTATCTCTTT-AATTT-ATATATTAATAAGATAATTATATTCTTTTGAATATTTAAAATTAAAAG
1 TTATCTATTTAAATTTGA-ATATTAA-AAGATAATCATA-TCTTTTGAATATTTAAAATTAAAAG
* *
50570 ATTTTTTTG
63 A-TATTTTA
* * * * * *
50579 TTATTTATTTAACTTTGAATATTAAAATATAATTATATCGTTTTGAATACTTCAAATTAAAAGAT
1 TTATCTATTTAAATTTGAATATTAAAAGATAATCATATC-TTTTGAATATTTAAAATTAAAAGAT
*
50644 A-TCTA
65 ATTTTA
* * * * * *
50649 TTATCTCTTTAAGTTTGAATATTCAAAGGT-ATCCATATCTTTTAAATATTTTAAATTAAAAGAT
1 TTATCTATTTAAATTTGAATATTAAAAGATAAT-CATATCTTTTGAATATTTAAAATTAAAAGAT
50713 ATTTTA
65 ATTTTA
50719 TTATCTATTTAAATTTGAATATTAAAAGATA
1 TTATCTATTTAAATTTGAATATTAAAAGATA
50750 TTTATTTTAA
Statistics
Matches: 141, Mismatches: 24, Indels: 13
0.79 0.13 0.07
Matches are distributed among these distances:
69 25 0.18
70 60 0.43
71 3 0.02
72 41 0.29
73 11 0.08
74 1 0.01
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (70 bp):
TTATCTATTTAAATTTGAATATTAAAAGATAATCATATCTTTTGAATATTTAAAATTAAAAGATA
TTTTA
Found at i:50724 original size:36 final size:36
Alignment explanation
Indices: 50562--50752 Score: 121
Period size: 35 Copynumber: 5.4 Consensus size: 36
50552 AATATTTAAA
* * * *
50562 ATTAAAAGATTTTTTTGTTATTTATTTAACTTTGAAT
1 ATTAAAAGA-TATTTTATTATCTATTTAAATTTGAAT
* * * *
50599 ATTAAAATATA-ATTA-TATCGT-TTTGAATACTTCAA-
1 ATTAAAAGATATTTTATTATC-TATTT-AA-ATTTGAAT
* * *
50634 ATTAAAAGATA-TCTATTATCTCTTTAAGTTTGAAT
1 ATTAAAAGATATTTTATTATCTATTTAAATTTGAAT
* * ** *
50669 ATTCAAAGGTA-TCCA-TATCT-TTTAAATATTTTAA-
1 ATTAAAAGATATTTTATTATCTATTT-AA-ATTTGAAT
50703 ATTAAAAGATATTTTATTATCTATTTAAATTTGAAT
1 ATTAAAAGATATTTTATTATCTATTTAAATTTGAAT
50739 ATTAAAAGATATTT
1 ATTAAAAGATATTT
50753 ATTTTAAGTA
Statistics
Matches: 118, Mismatches: 24, Indels: 25
0.71 0.14 0.15
Matches are distributed among these distances:
33 3 0.03
34 26 0.22
35 45 0.38
36 33 0.28
37 11 0.09
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.48
Consensus pattern (36 bp):
ATTAAAAGATATTTTATTATCTATTTAAATTTGAAT
Found at i:55128 original size:17 final size:17
Alignment explanation
Indices: 55103--55140 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
55093 CAAAAAAATT
*
55103 CAAAGTCAAACAATCCA
1 CAAATTCAAACAATCCA
*
55120 CAAATTCAAACATTCCA
1 CAAATTCAAACAATCCA
55137 -AAAT
1 CAAAT
55141 ATCCAAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.53, C:0.26, G:0.03, T:0.18
Consensus pattern (17 bp):
CAAATTCAAACAATCCA
Found at i:55426 original size:18 final size:18
Alignment explanation
Indices: 55405--55443 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
55395 GCATTTGATA
*
55405 CTCTGGACGAGGTTGTTC
1 CTCTGGACGAGCTTGTTC
* *
55423 CTCTGGAGGTGCTTGTTC
1 CTCTGGACGAGCTTGTTC
55441 CTC
1 CTC
55444 GTGCTGCTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.26, G:0.31, T:0.36
Consensus pattern (18 bp):
CTCTGGACGAGCTTGTTC
Found at i:57078 original size:22 final size:23
Alignment explanation
Indices: 57020--57079 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 23
57010 ACAGAACCCC
57020 AGGGGGTATCGATTCCCCTACAT
1 AGGGGGTATCGATTCCCCTACAT
* * *
57043 A--GGGAATCGGTTCCCCTTCA-
1 AGGGGGTATCGATTCCCCTACAT
57063 AGGGGGTATCGATTCCC
1 AGGGGGTATCGATTCCC
57080 TTTGCACCAA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
20 1 0.03
21 16 0.53
22 12 0.40
23 1 0.03
ACGTcount: A:0.20, C:0.27, G:0.28, T:0.25
Consensus pattern (23 bp):
AGGGGGTATCGATTCCCCTACAT
Done.