Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009312.1 Hibiscus syriacus cultivar Beakdansim tig00113056_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: 50814
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:2781 original size:14 final size:13
Alignment explanation
Indices: 2762--2809 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
2752 GTGCAAAAAG
2762 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
2776 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
*
2789 AGAAGAAAAAAAGAA
1 A-AAGAAAAAGA-AA
2804 AAAGAA
1 AAAGAA
2810 TTCAAAAGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 3 0.10
14 23 0.79
15 3 0.10
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:2800 original size:11 final size:11
Alignment explanation
Indices: 2759--2803 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
2749 GGAGTGCAAA
*
2759 AAGAAAGAAA-
1 AAGAAAAAAAG
*
2769 AAGACAAAAAG
1 AAGAAAAAAAG
*
2780 AAGAAGAAAAG
1 AAGAAAAAAAG
2791 AAGAAAAAAAG
1 AAGAAAAAAAG
2802 AA
1 AA
2804 AAAGAATTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 8 0.28
11 21 0.72
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAG
Found at i:8057 original size:19 final size:20
Alignment explanation
Indices: 8016--8066 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
8006 GAAACCCCTT
*
8016 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTTAA
8036 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
8055 TGAAGATACATG
1 TGAAAATACATG
8067 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:8963 original size:30 final size:31
Alignment explanation
Indices: 8924--8983 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
8914 ACATGCTGCC
** *
8924 ATGATATCTAAATGATATGTAAATATAATAA
1 ATGATATCTAAAACATATGTAAACATAATAA
8955 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGTAAACATAATA
8984 TAAAGCTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.07, G:0.08, T:0.32
Consensus pattern (31 bp):
ATGATATCTAAAACATATGTAAACATAATAA
Found at i:23089 original size:22 final size:24
Alignment explanation
Indices: 23062--23114 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
23052 AAAATTAACA
23062 AAGAAATTG-AAGCACTC-AAAAG
1 AAGAAATTGCAAGCACTCAAAAAG
23084 AAGAAAATTGCAAGCACTCAAAAAG
1 AAG-AAATTGCAAGCACTCAAAAAG
23109 AAGAAA
1 AAGAAA
23115 AAGAAAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 3 0.11
23 6 0.21
24 11 0.39
25 8 0.29
ACGTcount: A:0.58, C:0.13, G:0.17, T:0.11
Consensus pattern (24 bp):
AAGAAATTGCAAGCACTCAAAAAG
Found at i:23093 original size:23 final size:25
Alignment explanation
Indices: 23065--23115 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
23055 ATTAACAAAG
23065 AAATTG-AAGCACTC-AAAAGAAGA
1 AAATTGCAAGCACTCAAAAAGAAGA
23088 AAATTGCAAGCACTCAAAAAGAAGA
1 AAATTGCAAGCACTCAAAAAGAAGA
23113 AAA
1 AAA
23116 AGAAAGAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 6 0.23
24 8 0.31
25 12 0.46
ACGTcount: A:0.59, C:0.14, G:0.16, T:0.12
Consensus pattern (25 bp):
AAATTGCAAGCACTCAAAAAGAAGA
Found at i:23423 original size:17 final size:17
Alignment explanation
Indices: 23403--23461 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
23393 TTTAGGGAAG
23403 TAGTTCATTTATGCATC
1 TAGTTCATTTATGCATC
* *
23420 TAGTT-ATTTAAT-AAAC
1 TAGTTCATTT-ATGCATC
* * *
23436 TAATTCATTCATGCATT
1 TAGTTCATTTATGCATC
23453 TAGTTCATT
1 TAGTTCATT
23462 GAATAATGTT
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (17 bp):
TAGTTCATTTATGCATC
Found at i:30305 original size:17 final size:17
Alignment explanation
Indices: 30280--30319 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
30270 GTATGTTGTT
*
30280 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
30297 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
30314 CATTTA
1 CATTTA
30320 GGGAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:30398 original size:18 final size:18
Alignment explanation
Indices: 30375--30422 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
30365 ATTCATGCAT
30375 TTAGTTCATTAAATAAAG
1 TTAGTTCATTAAATAAAG
* *
30393 TTAGTTCATTGAATAATG
1 TTAGTTCATTAAATAAAG
*
30411 TTATTTCATTAA
1 TTAGTTCATTAA
30423 TCAAACTAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (18 bp):
TTAGTTCATTAAATAAAG
Found at i:33227 original size:17 final size:17
Alignment explanation
Indices: 33202--33241 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
33192 GTATGTTGTT
*
33202 CATTGAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
33219 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
33236 CATTTA
1 CATTTA
33242 GGGAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:33320 original size:18 final size:18
Alignment explanation
Indices: 33297--33344 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
33287 ATTCATGCAT
33297 TTAGTTCATTAAATAAAG
1 TTAGTTCATTAAATAAAG
* *
33315 TTAGTTCATTGAATAATG
1 TTAGTTCATTAAATAAAG
*
33333 TTATTTCATTAA
1 TTAGTTCATTAA
33345 TCAAACTAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (18 bp):
TTAGTTCATTAAATAAAG
Found at i:44673 original size:17 final size:17
Alignment explanation
Indices: 44648--44687 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
44638 GTATGTTGTT
*
44648 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
44665 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
44682 CATTTA
1 CATTTA
44688 GGGAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:44769 original size:17 final size:18
Alignment explanation
Indices: 44744--44788 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
44734 ATTCATGCAT
44744 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
*
44762 TTAG-TCATTGAATAATG
1 TTAGTTCATTGAATAAAG
*
44779 TTAATTCATT
1 TTAGTTCATT
44789 AATCAACTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:47524 original size:17 final size:17
Alignment explanation
Indices: 47499--47538 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
47489 GTATGTTGTT
*
47499 CATTGAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
47516 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
47533 CATTTA
1 CATTTA
47539 GGGAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:50289 original size:17 final size:17
Alignment explanation
Indices: 50264--50303 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
50254 GTATGTTGTT
*
50264 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
50281 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
50298 CATTTA
1 CATTTA
50304 GGGAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:50400 original size:18 final size:16
Alignment explanation
Indices: 50358--50388 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
50348 TTCATGCATT
50358 TAGTTCATTGAATAAG
1 TAGTTCATTGAATAAG
50374 TAGTTCATTGAATAA
1 TAGTTCATTGAATAA
50389 TGTTATTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (16 bp):
TAGTTCATTGAATAAG
Done.