Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001893.1 Hibiscus syriacus cultivar Beakdansim tig00003839_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: 52762
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1017 original size:13 final size:14
Alignment explanation
Indices: 991--1021 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
981 GTTTAATTGA
991 TTGTAAAAGATGAT
1 TTGTAAAAGATGAT
1005 TTGTAAAAG-TGAT
1 TTGTAAAAGATGAT
1018 TTGT
1 TTGT
1022 GTAATTGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (14 bp):
TTGTAAAAGATGAT
Found at i:1144 original size:19 final size:19
Alignment explanation
Indices: 1128--1229 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
1118 AAAAATGACT
1128 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1147 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1166 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1180 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1199 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1219 ATCGCAATGCG
1 ATCGCAATGCG
1230 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1282 original size:19 final size:19
Alignment explanation
Indices: 1258--1531 Score: 354
Period size: 19 Copynumber: 15.4 Consensus size: 19
1248 GATTATCTCG
1258 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1277 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1296 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
1310 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1329 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1348 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1367 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1386 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1405 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
*
1419 TTGCAATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1438 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1457 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1471 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1491 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
1505 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
1524 TTGCGATT
1 TTGCGATT
1532 GTATTTTCCG
Statistics
Matches: 226, Mismatches: 8, Indels: 42
0.82 0.03 0.15
Matches are distributed among these distances:
14 28 0.12
16 24 0.11
17 21 0.09
18 3 0.01
19 138 0.61
20 12 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1298 original size:52 final size:52
Alignment explanation
Indices: 1236--1503 Score: 437
Period size: 52 Copynumber: 5.0 Consensus size: 52
1226 TGCGTTTATA
*
1236 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
1288 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
1340 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
* *
1397 ATTTCGCATTGCGATTCTGTCGTTGCAATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1449 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
1502 AT
1 AT
1504 GTTGGGATTT
Statistics
Matches: 204, Mismatches: 6, Indels: 11
0.92 0.03 0.05
Matches are distributed among these distances:
52 128 0.63
53 17 0.08
54 7 0.03
55 8 0.04
57 44 0.22
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:1387 original size:109 final size:102
Alignment explanation
Indices: 1258--1498 Score: 176
Period size: 109 Copynumber: 2.3 Consensus size: 102
1248 GATTATCTCG
1258 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TTTCG-TTGCGATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--TTGCGATTTCATTTCGATTGCGATTTT
*
1320 CATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
61 CATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* *
1367 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TGTCG-TTGCAATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--TTGCGATTTCATTTCGATTGCGATTTT
* * * * *
1429 CATTTCGCATTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
61 CATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1471 TTGCGATTTTCATTTCCGCATTGCGATT
1 TTGCGATTTTCATTT-CGCATTGCGATT
1499 TTCATGTTGG
Statistics
Matches: 121, Mismatches: 7, Indels: 14
0.85 0.05 0.10
Matches are distributed among these distances:
102 7 0.06
103 6 0.05
104 20 0.17
105 11 0.09
107 2 0.02
109 75 0.62
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (102 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTCATTTCGATTGCGATTTTCATTT
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:3827 original size:12 final size:12
Alignment explanation
Indices: 3810--3834 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3800 TCTTCGGGGA
3810 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3822 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3834 C
1 C
3835 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:4043 original size:24 final size:24
Alignment explanation
Indices: 4009--4055 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3999 CTGAAACATC
4009 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
4033 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
4056 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:4766 original size:20 final size:20
Alignment explanation
Indices: 4738--5106 Score: 442
Period size: 20 Copynumber: 18.4 Consensus size: 20
4728 AAATTTAAGT
* * * *
4738 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
4758 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
4778 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
4798 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
4818 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
4838 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
*
4858 GTTGCAATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
4878 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
4898 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
4918 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
4938 GTTGC-AGTTTACGGATACGC
1 GTTGCGA-TTTACGGATACGC
4958 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
4978 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
4998 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
5018 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
5038 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
5058 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
5078 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
5098 GTTGCGATT
1 GTTGCGATT
5107 ATGGAAAATC
Statistics
Matches: 307, Mismatches: 32, Indels: 20
0.86 0.09 0.06
Matches are distributed among these distances:
19 6 0.02
20 295 0.96
21 6 0.02
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:14013 original size:56 final size:57
Alignment explanation
Indices: 13902--14028 Score: 156
Period size: 56 Copynumber: 2.2 Consensus size: 57
13892 ATTCTTGGGT
*
13902 AAAGTATAC-AAATGGTCCCGACTATAGAGTGTTACTTTGTTGAGTTCTTCGACTATTA
1 AAAGT-TACAAAATGGTCCCGACTATAGAGTGTTA-TTTGTTGAGTTCTTCAACTATTA
*
13960 GAAGTTACAAAATGGTCCCCGACTATAG-GATG-T-TTTGTTGAG-TCTTTCAACTATTA
1 AAAGTTACAAAATGGT-CCCGACTATAGAG-TGTTATTTGTTGAGTTC-TTCAACTATTA
14016 AAAGTTACAAAAT
1 AAAGTTACAAAAT
14029 AATCATTAGA
Statistics
Matches: 62, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
55 2 0.03
56 31 0.50
57 3 0.05
58 13 0.21
59 13 0.21
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (57 bp):
AAAGTTACAAAATGGTCCCGACTATAGAGTGTTATTTGTTGAGTTCTTCAACTATTA
Found at i:34971 original size:2 final size:2
Alignment explanation
Indices: 34924--34954 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
34914 ACACGTGTGT
34924 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
34955 GGGTACATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:35271 original size:2 final size:2
Alignment explanation
Indices: 35264--35296 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
35254 TTAAGTAAAT
35264 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35297 TAAGTTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36108 original size:28 final size:27
Alignment explanation
Indices: 36077--36133 Score: 78
Period size: 28 Copynumber: 2.1 Consensus size: 27
36067 ATAAAAAAAC
36077 AAACTTATTAATCTAATAATACATAATT
1 AAACTTATTAATCTAATAAT-CATAATT
* * *
36105 AAACTTATTATTCTGATGATCATAATT
1 AAACTTATTAATCTAATAATCATAATT
36132 AA
1 AA
36134 CAATTCGGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 9 0.35
28 17 0.65
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.40
Consensus pattern (27 bp):
AAACTTATTAATCTAATAATCATAATT
Found at i:36405 original size:28 final size:28
Alignment explanation
Indices: 36374--36436 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
36364 AACCAAATGT
* *
36374 AACTCGACTTTATATCAATACCAATTCA
1 AACTCAACTTCATATCAATACCAATTCA
*
36402 AACTCAACTTCATATCAATATCAATTCA
1 AACTCAACTTCATATCAATACCAATTCA
36430 AACTCAA
1 AACTCAA
36437 ATTAATTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.43, C:0.25, G:0.02, T:0.30
Consensus pattern (28 bp):
AACTCAACTTCATATCAATACCAATTCA
Found at i:37148 original size:18 final size:17
Alignment explanation
Indices: 37127--37160 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
37117 AGGGAATCAG
37127 AATCTGTGAAGGAATTGA
1 AATCTGT-AAGGAATTGA
*
37145 AATCTGTCAGGAATTG
1 AATCTGTAAGGAATTG
37161 GAATTCAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.09, G:0.26, T:0.29
Consensus pattern (17 bp):
AATCTGTAAGGAATTGA
Found at i:37775 original size:37 final size:37
Alignment explanation
Indices: 37725--37819 Score: 172
Period size: 37 Copynumber: 2.6 Consensus size: 37
37715 CCTAAACTCG
37725 AACCCGACCCGACCCGAATATCACACTTAAAAAACCC
1 AACCCGACCCGACCCGAATATCACACTTAAAAAACCC
*
37762 AACCCGACTCGACCCGAATATCACACTTAAAAAACCC
1 AACCCGACCCGACCCGAATATCACACTTAAAAAACCC
*
37799 GACCCGACCCGACCCGAATAT
1 AACCCGACCCGACCCGAATAT
37820 ATGAATTAGA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.38, C:0.40, G:0.11, T:0.12
Consensus pattern (37 bp):
AACCCGACCCGACCCGAATATCACACTTAAAAAACCC
Found at i:40950 original size:29 final size:29
Alignment explanation
Indices: 40881--40936 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
40871 AAATTTTAAA
40881 TTGAA-CCTCAAACTTTAAAACATTCTAC
1 TTGAATCCTCAAACTTTAAAACATTCTAC
*
40909 TTGAATTCTCAAACTTTAAAACATTCTA
1 TTGAATCCTCAAACTTTAAAACATTCTA
40937 GTTACCTCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.36
Consensus pattern (29 bp):
TTGAATCCTCAAACTTTAAAACATTCTAC
Found at i:46083 original size:16 final size:16
Alignment explanation
Indices: 46062--46122 Score: 95
Period size: 16 Copynumber: 3.8 Consensus size: 16
46052 TAATAAATAA
46062 ACGAACATAAACAAAC
1 ACGAACATAAACAAAC
*
46078 ACGAACATAAACGAAC
1 ACGAACATAAACAAAC
**
46094 ACGAACATAAATGAAC
1 ACGAACATAAACAAAC
46110 ACGAACATAAACA
1 ACGAACATAAACA
46123 TTATAGACAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.59, C:0.23, G:0.10, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACAAAC
Found at i:46909 original size:24 final size:25
Alignment explanation
Indices: 46855--46922 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 25
46845 TTAAACATAA
*
46855 ATGAATGAACATAAACGAACATTAC
1 ATGAACGAACATAAACGAACATTAC
* *
46880 A-AAACGAACATAACCGAACATT-C
1 ATGAACGAACATAAACGAACATTAC
*
46903 ATGAACGTAA-ATGAACGAAC
1 ATGAACG-AACATAAACGAAC
46923 GAGACTTATG
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
23 2 0.06
24 30 0.86
25 3 0.09
ACGTcount: A:0.51, C:0.19, G:0.13, T:0.16
Consensus pattern (25 bp):
ATGAACGAACATAAACGAACATTAC
Found at i:47835 original size:14 final size:15
Alignment explanation
Indices: 47818--47852 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
47808 GGTTTTTTCT
47818 TTTAAAAA-TTATAA
1 TTTAAAAATTTATAA
*
47832 TTTAAAAATTTCTAA
1 TTTAAAAATTTATAA
47847 TTTAAA
1 TTTAAA
47853 TAAAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (15 bp):
TTTAAAAATTTATAA
Found at i:51283 original size:74 final size:75
Alignment explanation
Indices: 51194--51359 Score: 194
Period size: 74 Copynumber: 2.2 Consensus size: 75
51184 CTTTGTTTAG
* *
51194 TGCTATGTTGATTAAACTT-ATAAAAAATACCATTGTCTGCTTGTATGCTACTAA-ATGAATTGT
1 TGCTATGTTGATTAAACTTCATAAAAAATACCATTGTATACTTGTATGCTACTAATATGAATTGT
51257 TTTGTTTAATA
66 TTTG-TTAATA
* * * * * * *
51268 TGCTATGTTGATTAAA-TTCATAGAATATATCATTGTATATTTGTATGCTACTAATTTTAATTTT
1 TGCTATGTTGATTAAACTTCATAAAAAATACCATTGTATACTTGTATGCTACTAATATGAATTGT
**
51332 TTTGTTCGTA
66 TTTGTTAATA
*
51342 TGCTATGTTGATTTAACT
1 TGCTATGTTGATTAAACT
51360 ATTAGAAAGT
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
73 2 0.03
74 64 0.83
75 11 0.14
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.48
Consensus pattern (75 bp):
TGCTATGTTGATTAAACTTCATAAAAAATACCATTGTATACTTGTATGCTACTAATATGAATTGT
TTTGTTAATA
Done.