Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008108.1 Hibiscus syriacus cultivar Beakdansim tig00110644_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: 71186
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:1635 original size:13 final size:14
Alignment explanation
Indices: 1619--1654 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
1609 ATGAATTAGG
1619 TATAAGAATATG-A
1 TATAAGAATATGCA
1632 TATAA-AATATGCA
1 TATAAGAATATGCA
1645 -ATAAGAATAT
1 TATAAGAATAT
1655 ATGTGTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.56, C:0.03, G:0.11, T:0.31
Consensus pattern (14 bp):
TATAAGAATATGCA
Found at i:2376 original size:21 final size:20
Alignment explanation
Indices: 2339--2377 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2329 TATTGCTTGA
*
2339 TTAAATGAATCATATGAGGC
1 TTAAATGAATAATATGAGGC
2359 TTAAATGAATGAATATGAG
1 TTAAATGAAT-AATATGAG
2378 TATATGATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.31
Consensus pattern (20 bp):
TTAAATGAATAATATGAGGC
Found at i:7245 original size:16 final size:16
Alignment explanation
Indices: 7220--7262 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
7210 ATATGCTCTG
*
7220 ATTTGGTTGTAAAATA
1 ATTTGATTGTAAAATA
7236 ATTTGATTGTAAAATA
1 ATTTGATTGTAAAATA
7252 ATTTGATTGTA
1 ATTTGATTGTA
7263 TTTATTACTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (16 bp):
ATTTGATTGTAAAATA
Found at i:13589 original size:18 final size:18
Alignment explanation
Indices: 13568--13637 Score: 70
Period size: 18 Copynumber: 3.8 Consensus size: 18
13558 AAACAAATTT
13568 GGTATCAATACCCATGGG
1 GGTATCAATACCCATGGG
* *
13586 GGTATCGATACCTA-GGG
1 GGTATCAATACCCATGGG
13603 TAGAGTATCAATACCCATGGG
1 --G-GTATCAATACCCATGGG
* *
13624 AGTATCGATACCCA
1 GGTATCAATACCCA
13638 AGCATTTTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
17 3 0.07
18 24 0.57
19 1 0.02
20 11 0.26
21 3 0.07
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (18 bp):
GGTATCAATACCCATGGG
Found at i:15761 original size:2 final size:2
Alignment explanation
Indices: 15756--15789 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
15746 CACACATTTA
15756 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
15790 TAATAACTAA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25256 original size:28 final size:28
Alignment explanation
Indices: 25225--25279 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
25215 ACATATATTT
25225 CTTTATACTTATTCCATAATATTAAAAG
1 CTTTATACTTATTCCATAATATTAAAAG
25253 CTTTATACTTATTCCATAATATTAAAA
1 CTTTATACTTATTCCATAATATTAAAA
25280 AAATCTGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.40, C:0.15, G:0.02, T:0.44
Consensus pattern (28 bp):
CTTTATACTTATTCCATAATATTAAAAG
Found at i:43120 original size:16 final size:16
Alignment explanation
Indices: 43099--43136 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
43089 CTATTAACAA
*
43099 CTAACTTTTATAATTT
1 CTAACTTTTATAACTT
*
43115 CTAACTTTTCTAACTT
1 CTAACTTTTATAACTT
43131 CTAACT
1 CTAACT
43137 GCTAACCACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (16 bp):
CTAACTTTTATAACTT
Found at i:43375 original size:14 final size:14
Alignment explanation
Indices: 43356--43391 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
43346 AATTTTTTTA
*
43356 TTTAATTTCAGTCC
1 TTTAATTTCAGTAC
*
43370 TTTAATTTCATTAC
1 TTTAATTTCAGTAC
43384 TTTAATTT
1 TTTAATTT
43392 ACTATTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.25, C:0.14, G:0.03, T:0.58
Consensus pattern (14 bp):
TTTAATTTCAGTAC
Found at i:43458 original size:18 final size:17
Alignment explanation
Indices: 43435--43487 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 17
43425 TTTTACTTTA
43435 ATTTTAATCCTTTTATAT
1 ATTTTAATCCTTTTA-AT
43453 ATTTTAATTGCC-TTTAAT
1 ATTTTAA-T-CCTTTTAAT
43471 ATTTGT-ATCCTTTTAAT
1 ATTT-TAATCCTTTTAAT
43488 TTAGTCCTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
16 2 0.06
17 7 0.23
18 14 0.45
19 6 0.19
20 2 0.06
ACGTcount: A:0.26, C:0.11, G:0.04, T:0.58
Consensus pattern (17 bp):
ATTTTAATCCTTTTAAT
Found at i:48631 original size:98 final size:96
Alignment explanation
Indices: 48322--48710 Score: 351
Period size: 98 Copynumber: 3.9 Consensus size: 96
48312 AGACAAAAGC
* * *
48322 TGATCTTACTTGAGATTGTTTTCTTAAAATAAATTTCGTCTTGCTGGAGACAGTTTCCCTTGAAA
1 TGATCTCACTTGAGATTGTTTT-TTAAAATAAATTTCGTCTTGCTTGAGACAATTTCCCTTGAAA
*
48387 CACAA-TTTGAAATTGTTTCACTCGAAAAA-AT
65 CATAATTTTGAAATTGTTTCACTC-AAAAACAT
* ** *
48418 TGATCTCATTTGAGATTGTTTTTCTCAAAACCAATTTCAT-TTCGCTTGAGACAATTTTCCCTTG
1 TGATCTCACTTGAGATTGTTTTT-T-AAAATAAATTTCGTCTT-GCTTGAGACAA-TTTCCCTTG
* * * *
48482 AAATATAAAATTTGGAATTTGTTTCACCTGAAACCAA-AT
62 AAACAT--AATTTTGAAATTGTTTCA-CTCAAA--AACAT
* *
48521 TGATCTCACTTGAGATTGTTTTTT-AAATAAATTTCGTCTTGCTTGAGATAATTTCCCTCGAAAC
1 TGATCTCACTTGAGATTGTTTTTTAAAATAAATTTCGTCTTGCTTGAGACAATTTCCCTTGAAAC
*
48585 GTAATTTTTGAAATTGTTTCACTCAAAAACTTTAT
66 ATAA-TTTTGAAATTGTTTCACTCAAAAAC---AT
* ** * * *
48620 T-ATCTCACTTGAGA-TGAATTCTTTTAAAATCAATTTCGTCTTTTTTAAAGGCAGTTTCCCTTG
1 TGATCTCACTTGAGATTG--TT-TTTTAAAATAAATTTCGTCTTGCTT-GAGACAATTTCCCTTG
*
48683 AAACACAAATTTTGAAATTGTTTCACTC
62 AAACA-TAATTTTGAAATTGTTTCACTC
48711 GAAACAAAAA
Statistics
Matches: 238, Mismatches: 33, Indels: 38
0.77 0.11 0.12
Matches are distributed among these distances:
95 3 0.01
96 23 0.10
97 29 0.12
98 40 0.17
99 17 0.07
100 26 0.11
101 35 0.15
102 37 0.16
103 28 0.12
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.41
Consensus pattern (96 bp):
TGATCTCACTTGAGATTGTTTTTTAAAATAAATTTCGTCTTGCTTGAGACAATTTCCCTTGAAAC
ATAATTTTGAAATTGTTTCACTCAAAAACAT
Found at i:49312 original size:138 final size:139
Alignment explanation
Indices: 49120--49457 Score: 554
Period size: 138 Copynumber: 2.4 Consensus size: 139
49110 ATTCATATTG
* *
49120 AGAAATCATTCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATT
1 AGAACTCATTCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTAAACCTTAGCTCGATT
* *
49185 CATCACATATGGAGTTGAATTAACAACACCTCACTCGA-GGATCAACAATTCCAGTAGAGAGTTC
66 CATCACATATAGAGTTGAATCAACAACACCTCACTCGAGGGATCAACAATTCCAGTAGAGAGTTC
49249 ATAATGAGA
131 ATAATGAGA
* *
49258 AGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTG-TATAACCTTAGCTTGAT
1 AGAACTCATTCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTA-AACCTTAGCTCGAT
* * *
49322 TCATCACATATAGAGTTGAATCAGCAGCATCTCACTCGAGGGATCAACAATTCCAGTAGAGAGTT
65 TCATCACATATAGAGTTGAATCAACAACACCTCACTCGAGGGATCAACAATTCCAGTAGAGAGTT
49387 CATAATGAGA
130 CATAATGAGA
* *
49397 AGAACTCGTTCGATGAGAGAGAAGAAGTTCATAATGAGAAGAACTTGTTAAACCTTAGCTC
1 AGAACTCATTCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTAAACCTTAGCTC
49458 TTTTCCTTCA
Statistics
Matches: 184, Mismatches: 13, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
137 1 0.01
138 92 0.50
139 89 0.48
140 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (139 bp):
AGAACTCATTCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTAAACCTTAGCTCGATT
CATCACATATAGAGTTGAATCAACAACACCTCACTCGAGGGATCAACAATTCCAGTAGAGAGTTC
ATAATGAGA
Found at i:51331 original size:14 final size:14
Alignment explanation
Indices: 51312--51347 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
51302 TTTTTATTTA
*
51312 TTTAATTTCAGTCC
1 TTTAATTTCAGTAC
*
51326 TTTAATTTCATTAC
1 TTTAATTTCAGTAC
51340 TTTAATTT
1 TTTAATTT
51348 AATATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.25, C:0.14, G:0.03, T:0.58
Consensus pattern (14 bp):
TTTAATTTCAGTAC
Found at i:51414 original size:18 final size:16
Alignment explanation
Indices: 51391--51443 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 16
51381 TTGTACTTTA
51391 ATTTTAGTCCTTTTATAT
1 ATTTTA-TCCTTTTA-AT
*
51409 ATTTTAATTGCTTTTAAT
1 ATTTT-A-TCCTTTTAAT
51427 ATTTGTATCCTTTTAAT
1 ATTT-TATCCTTTTAAT
51444 TTAGTCCTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 9 0.30
18 12 0.40
19 9 0.30
ACGTcount: A:0.25, C:0.09, G:0.06, T:0.60
Consensus pattern (16 bp):
ATTTTATCCTTTTAAT
Found at i:57597 original size:108 final size:108
Alignment explanation
Indices: 57404--57775 Score: 480
Period size: 108 Copynumber: 3.4 Consensus size: 108
57394 CTATGTGTAC
* * *
57404 TATAGGCACTAAGTGTGCAACCCATGTAATTCATCATATGTTGATAAACAACCGTATAGGCACTA
1 TATAGGCACTAAGTGTGCAACCCATGAAATTCATCATATGTTGATGAATAACCGTATAGGCACTA
* *
57469 AGTGTGCAACCCACGTAATTCATAATGTGTTTATTAATGACCA
66 AGTGTGCAACCCACGAAATTCATAATGTGTTTATGAATGACCA
* *
57512 TATAGGCACTAAGTGTGAAACCCAT-AGAATTCATCATACGTTGATGAATAACCGTATAGGCACT
1 TATAGGCACTAAGTGTGCAACCCATGA-AATTCATCATATGTTGATGAATAACCGTATAGGCACT
* *
57576 AAGTGTGCAACCCACAAAATTCATAATGTGTTTATGAATGACCG
65 AAGTGTGCAACCCACGAAATTCATAATGTGTTTATGAATGACCA
* * * *
57620 TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGATTGACTGTATAGGCACTA
1 TATAGGCACTAAGTGTGCAACCCATGAAATTCATCATATGTTGATGAATAACCGTATAGGCACTA
* * * * ***
57685 ACTGTGCAACCCACGGAATTCATAATGTGTTTTTG-ATCAAGTG
66 AGTGTGCAACCCACGAAATTCATAATGTGTTTATGAAT-GACCA
* * * *
57728 TATAGGCACTAAATGTGCAA-CCATCGAAATTCATAATGTGTTTATGAA
1 TATAGGCACTAAGTGTGCAACCCAT-GAAATTCATCATATGTTGATGAA
57776 CGACAGTATC
Statistics
Matches: 232, Mismatches: 28, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
107 5 0.02
108 226 0.97
109 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (108 bp):
TATAGGCACTAAGTGTGCAACCCATGAAATTCATCATATGTTGATGAATAACCGTATAGGCACTA
AGTGTGCAACCCACGAAATTCATAATGTGTTTATGAATGACCA
Found at i:57680 original size:162 final size:162
Alignment explanation
Indices: 57404--57784 Score: 460
Period size: 162 Copynumber: 2.4 Consensus size: 162
57394 CTATGTGTAC
* * * * * * *
57404 TATAGGCACTAAGTGTGCAACCCATGTAATTCATCATATGTTGATAAACAACCGTATAGGCACTA
1 TATAGGCACTAAGTGTGCAACCCACGAAATTCATAATGTGTTTATGAACGACCGTATAGGCACTA
* * * * *
57469 AGTGTGCAACCCACGTAATTCATAATGTGTTTATTAATGACCATATAGGCACTAAGTGTGAAACC
66 AGTGTGCAACCCACGAAATTCATAATATGTTGATGAATGACCATATAGGCACTAACTGTGAAACC
* *
57534 CATAGAATTCATCATACGTTGATGAAT-AACCG
131 CACAGAATTCATAATACGTTGATG-ATCAACCG
* *
57566 TATAGGCACTAAGTGTGCAACCCACAAAATTCATAATGTGTTTATGAATGACCGTATAGGCACTA
1 TATAGGCACTAAGTGTGCAACCCACGAAATTCATAATGTGTTTATGAACGACCGTATAGGCACTA
* * ** *
57631 AGTGTGCAACCCACGAAATTCATCATATGTTGATGATTGACTGTATAGGCACTAACTGTGCAACC
66 AGTGTGCAACCCACGAAATTCATAATATGTTGATGAATGACCATATAGGCACTAACTGTGAAACC
* ** ** **
57696 CACGGAATTCATAATGTGTTTTTGATCAAGTG
131 CACAGAATTCATAATACGTTGATGATCAACCG
* *
57728 TATAGGCACTAAATGTGCAA-CCATCGAAATTCATAATGTGTTTATGAACGACAGTAT
1 TATAGGCACTAAGTGTGCAACCCA-CGAAATTCATAATGTGTTTATGAACGACCGTAT
57785 CGACACTACA
Statistics
Matches: 185, Mismatches: 32, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
161 5 0.03
162 180 0.97
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (162 bp):
TATAGGCACTAAGTGTGCAACCCACGAAATTCATAATGTGTTTATGAACGACCGTATAGGCACTA
AGTGTGCAACCCACGAAATTCATAATATGTTGATGAATGACCATATAGGCACTAACTGTGAAACC
CACAGAATTCATAATACGTTGATGATCAACCG
Found at i:57792 original size:54 final size:54
Alignment explanation
Indices: 57404--57784 Score: 417
Period size: 54 Copynumber: 7.1 Consensus size: 54
57394 CTATGTGTAC
* * * * * * **
57404 TATAGGCACTAAGTGTGCAACCCATGTAATTCATCATATGTTGATAAACAACCG
1 TATAGGCACTAAGTGTGCAACCCACGAAATTCATAATGTGTTTATGAATGACCG
* * *
57458 TATAGGCACTAAGTGTGCAACCCACGTAATTCATAATGTGTTTATTAATGACCA
1 TATAGGCACTAAGTGTGCAACCCACGAAATTCATAATGTGTTTATGAATGACCG
* * * ** * *
57512 TATAGGCACTAAGTGTGAAACCCA-TAGAATTCATCATACGTTGATGAATAACCG
1 TATAGGCACTAAGTGTGCAACCCACGA-AATTCATAATGTGTTTATGAATGACCG
*
57566 TATAGGCACTAAGTGTGCAACCCACAAAATTCATAATGTGTTTATGAATGACCG
1 TATAGGCACTAAGTGTGCAACCCACGAAATTCATAATGTGTTTATGAATGACCG
* * * * *
57620 TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGATTGACTG
1 TATAGGCACTAAGTGTGCAACCCACGAAATTCATAATGTGTTTATGAATGACCG
* * * * **
57674 TATAGGCACTAACTGTGCAACCCACGGAATTCATAATGTGTTTTTG-ATCAAGTG
1 TATAGGCACTAAGTGTGCAACCCACGAAATTCATAATGTGTTTATGAAT-GACCG
* * *
57728 TATAGGCACTAAATGTGCAA-CCATCGAAATTCATAATGTGTTTATGAACGACAG
1 TATAGGCACTAAGTGTGCAACCCA-CGAAATTCATAATGTGTTTATGAATGACCG
57782 TAT
1 TAT
57785 CGACACTACA
Statistics
Matches: 275, Mismatches: 47, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
53 4 0.01
54 269 0.98
55 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (54 bp):
TATAGGCACTAAGTGTGCAACCCACGAAATTCATAATGTGTTTATGAATGACCG
Found at i:61022 original size:30 final size:31
Alignment explanation
Indices: 60959--61037 Score: 115
Period size: 32 Copynumber: 2.5 Consensus size: 31
60949 AAAAAAATTG
*
60959 AATACTTTAGGTACCTATCTTGACCAAAAAAA
1 AATACTTTAGGTACTTATCTTGACC-AAAAAA
* *
60991 AATACTTTAGATACTTATTTTGACC-AAAAA
1 AATACTTTAGGTACTTATCTTGACCAAAAAA
61021 AATACTTTAGGTACTTA
1 AATACTTTAGGTACTTA
61038 AATGAAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
30 21 0.49
32 22 0.51
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.34
Consensus pattern (31 bp):
AATACTTTAGGTACTTATCTTGACCAAAAAA
Found at i:62754 original size:10 final size:10
Alignment explanation
Indices: 62739--62797 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
62729 GGGTCTCCAA
62739 CGTTTATGTT
1 CGTTTATGTT
62749 CGTTTATGTT
1 CGTTTATGTT
62759 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
62770 ATGTTCGTGTT
1 -CGTTTATGTT
62781 CGTTTATGTT
1 CGTTTATGTT
62791 CGTTTAT
1 CGTTTAT
62798 TTATTAAATG
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
10 28 0.72
11 7 0.18
12 4 0.10
ACGTcount: A:0.10, C:0.12, G:0.20, T:0.58
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:62770 original size:16 final size:16
Alignment explanation
Indices: 62745--62801 Score: 82
Period size: 16 Copynumber: 3.7 Consensus size: 16
62735 CCAACGTTTA
*
62745 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
62761 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
62777 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
62793 T-TT-ATTTAT
1 TGTTCATTTAT
62802 TAAATGAACG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
14 5 0.13
15 2 0.05
16 31 0.82
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.60
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Done.