Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005727.1 Hibiscus syriacus cultivar Beakdansim tig00013385_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: 69692
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:652 original size:14 final size:14
Alignment explanation
Indices: 633--666 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
623 TAACAATTTC
*
633 TTTTGTTTATCTTA
1 TTTTGTCTATCTTA
647 TTTTGTCTATCTTA
1 TTTTGTCTATCTTA
661 TGTTTG
1 T-TTTG
667 CATTTGCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.12, C:0.09, G:0.12, T:0.68
Consensus pattern (14 bp):
TTTTGTCTATCTTA
Found at i:3488 original size:54 final size:54
Alignment explanation
Indices: 3332--3493 Score: 195
Period size: 54 Copynumber: 3.0 Consensus size: 54
3322 AATACATATG
* *
3332 TTATAATTACTATATCGACACTATGTGTGC-AACCCACATAATTCATAATGAGT
1 TTATGATTACCATATCGACACTATGTGTGCAAACCCACATAATTCATAATGAGT
* * * *
3385 TTGTGAATTACCTTATCGAC-GT-TGTGTGTACAACCCACATAATTCATAATGAGT
1 TTATG-ATTACCATATCGACACTATGTGTGCA-AACCCACATAATTCATAATGAGT
* ** *
3439 TTATGATTACCATATCGACACTATGTGTGCAAAACCACGGAATTTATAATGAGT
1 TTATGATTACCATATCGACACTATGTGTGCAAACCCACATAATTCATAATGAGT
3493 T
1 T
3494 GTAATATTCA
Statistics
Matches: 90, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
52 6 0.07
53 17 0.19
54 60 0.67
55 7 0.08
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (54 bp):
TTATGATTACCATATCGACACTATGTGTGCAAACCCACATAATTCATAATGAGT
Found at i:9666 original size:54 final size:54
Alignment explanation
Indices: 9524--9698 Score: 235
Period size: 54 Copynumber: 3.3 Consensus size: 54
9514 ACAGTATCAA
* * * *
9524 CACTATGTGTGCAACCTACATAATTCATAGTGAGTTTGTGAATTACCATATCAG
1 CACTATGTGTGCAACCAACGTAATTCATAATGAGTTTGTGAATTACCATATCGG
* * * *
9578 -ACTTTGTTTGCAACCCATGTAATTCATAATGAGTTTGTGAATTACCATATCGG
1 CACTATGTGTGCAACCAACGTAATTCATAATGAGTTTGTGAATTACCATATCGG
* * * *
9631 CACTATGTGTACAACCAACGTAATTCATAATGAGTTTGTGAATTACCGTATTGA
1 CACTATGTGTGCAACCAACGTAATTCATAATGAGTTTGTGAATTACCATATCGG
9685 CACTATGTGTGCAA
1 CACTATGTGTGCAA
9699 AACCACATAA
Statistics
Matches: 104, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
53 46 0.44
54 58 0.56
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (54 bp):
CACTATGTGTGCAACCAACGTAATTCATAATGAGTTTGTGAATTACCATATCGG
Found at i:11142 original size:31 final size:30
Alignment explanation
Indices: 11107--11164 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
11097 GACTTCGAAT
11107 AACCAAGAATAAAAAAG-AGAAAAAAAATCTG
1 AACCAA-AA-AAAAAAGAAGAAAAAAAATCTG
*
11138 AACCAAAAAAAAAAGAAGAAGAAAAAT
1 AACCAAAAAAAAAAGAAGAAAAAAAAT
11165 ATACAAGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 7 0.28
30 12 0.48
31 6 0.24
ACGTcount: A:0.72, C:0.09, G:0.12, T:0.07
Consensus pattern (30 bp):
AACCAAAAAAAAAAGAAGAAAAAAAATCTG
Found at i:19569 original size:8 final size:8
Alignment explanation
Indices: 19556--19587 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
19546 GTCACATGAA
19556 TTTGCATC
1 TTTGCATC
19564 TTTGCATC
1 TTTGCATC
19572 TTTGCATC
1 TTTGCATC
19580 TTTGCATC
1 TTTGCATC
19588 ATACATTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.12, C:0.25, G:0.12, T:0.50
Consensus pattern (8 bp):
TTTGCATC
Found at i:20188 original size:37 final size:37
Alignment explanation
Indices: 20114--20190 Score: 102
Period size: 38 Copynumber: 2.1 Consensus size: 37
20104 GTTTTTCTCC
* *
20114 AAACAAATTTTGTCTCGCTTGGGACAATTTTCACTTG
1 AAACAAATTTTGTCTCGCTTGAGACAATGTTCACTTG
* *
20151 AAACAAAATTTTGTCTTGCTTGAGACAA-GTTCTCTTG
1 AAAC-AAATTTTGTCTCGCTTGAGACAATGTTCACTTG
20188 AAA
1 AAA
20191 TACAAATCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.40
38 21 0.60
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (37 bp):
AAACAAATTTTGTCTCGCTTGAGACAATGTTCACTTG
Found at i:20582 original size:16 final size:16
Alignment explanation
Indices: 20561--20603 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
20551 AAGTTTCGTC
20561 TCGCTTGAGATAGTTT
1 TCGCTTGAGATAGTTT
20577 TCGCTTGAGATAGTTT
1 TCGCTTGAGATAGTTT
*
20593 TCCCTTGAGAT
1 TCGCTTGAGAT
20604 GAAAATTTTG
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:0.19, C:0.16, G:0.23, T:0.42
Consensus pattern (16 bp):
TCGCTTGAGATAGTTT
Found at i:21101 original size:103 final size:102
Alignment explanation
Indices: 20994--21264 Score: 321
Period size: 104 Copynumber: 2.6 Consensus size: 102
20984 GAATGTTCTC
* * * * * *
20994 AAAACAAAATTCGTCTCACTTGAGATAGTTTTTCTTCAAAACACAAATTCTGAATTTTTTTTATT
1 AAAACAAATTTCGTCTCGCTTGAGATAGTTTTTCTTCAAAACACAAATT-TGAAATTGTTTCACT
*
21059 TGAAAAAAAATTGATAACAATTGAGATTGTGTTTCTTA
65 AGAAAAAAAATTGATAACAATTGAGATTGTGTTTCTTA
* * *
21097 AAAACAAATTTCATCTCGCTTGAGATAG-TTTTCCTCAAAACTCAAAAATTTGGAAATTGTTTCA
1 AAAACAAATTTCGTCTCGCTTGAGATAGTTTTTCTTCAAAA--CACAAATTT-GAAATTGTTTCA
* * *
21161 CTAGAAACAAAATTGATAACATTTGAGATTGTTTTTCTTA
63 CTAGAAAAAAAATTGATAACAATTGAGATTGTGTTTCTTA
* * * **
21201 AAAACAAATTTTGTCTCGCTTGAGATAATTTTCCTTTGAAACACAAATTTTGAAA-TGTTTCACT
1 AAAACAAATTTCGTCTCGCTTGAGATAGTTTTTCTTCAAAACACAAA-TTTGAAATTGTTTCACT
21265 CAAAACAGGA
Statistics
Matches: 142, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
102 20 0.14
103 35 0.25
104 79 0.56
105 8 0.06
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (102 bp):
AAAACAAATTTCGTCTCGCTTGAGATAGTTTTTCTTCAAAACACAAATTTGAAATTGTTTCACTA
GAAAAAAAATTGATAACAATTGAGATTGTGTTTCTTA
Found at i:21658 original size:139 final size:137
Alignment explanation
Indices: 21395--22058 Score: 526
Period size: 139 Copynumber: 4.8 Consensus size: 137
21385 CCTCACACGA
* * * * ** ** * *
21395 AGGAACAATGTCGTTCACCGATCAGATCTCCTCAACGCGAAAGAGTAGTGTCATCCTCAGATAAT
1 AGGAACAATGTCGTCCACCGACCAGATCTCCTCAACGCGTAGGAACAACGTCATCCTAAGATAAC
* * ** * * * *
21460 CAAACTTTCTCAATGCA-AAAGAATCGTGTTGTATCCAAATTATCTCCTACAATGACTAGACGTC
66 CAGACTTCCTC-AT-CACGTAGAACCGTGTTGTCTCCAAATTATC-CCTAAAATGGCTAGACGTC
*
21524 TTCATCACAT
128 CTCATCACAT
* * *
21534 AGGTACAATATCGACCACCGACCAGATCTCCTCAACGCGTAGGAACAACGTCATCCTAAGATAAC
1 AGGAACAATGTCGTCCACCGACCAGATCTCCTCAACGCGTAGGAACAACGTCATCCTAAGATAAC
* * *
21599 CAGACTTCCTCATCACGTATGAACTGTGTTATCTCCAAATTATCCTTAAACATGGCTAGACGTCC
66 CAGACTTCCTCATCACGTA-GAACCGTGTTGTCTCCAAATTATCCCTAAA-ATGGCTAGACGTCC
*
21664 TCATCACGT
129 TCATCACAT
* ** * * * * * * * *
21673 AGGAATAATGTATTCCATCGACTATATCTCCTCAATGTGTAAGAGTAGAA--TCATCCTCAAG-C
1 AGGAACAATGTCGTCCACCGACCAGATCTCCTCAACGCGT-AG-GAACAACGTCATCCT-AAGAT
* * * * * *
21735 AATCAAACTTCCTCATCACGTAGGAACCATTTTGTCTCCAAATTATCCCTAAAGACGGCTAAACG
63 AACCAGACTTCCTCATCACGTA-GAACCGTGTTGTCTCCAAATTATCCCTAAA-ATGGCTAGACG
21800 TCCTCATCACAT
126 TCCTCATCACAT
* * * * *
21812 AGGAACAATGTCGTCCACCGACCAGATCTCCTCAACTCGTAGGACCAGCGTTATCCTTAGATAAC
1 AGGAACAATGTCGTCCACCGACCAGATCTCCTCAACGCGTAGGAACAACGTCATCCTAAGATAAC
* * * * *
21877 CAGACTTCCTCATCATGTAGAAACCGTGTTGTCTCCAAATTATCCTTAAAACGGCTATACGCCCT
66 CAGACTTCCTCATCACGTAG-AACCGTGTTGTCTCCAAATTATCCCTAAAATGGCTAGACGTCCT
* *
21942 AATCATAT
130 CATCACAT
* * * * * * ** * * ** * ** * *
21950 AGGAACAATGTCATCCACTGAACAAATCTCTTCAATGCAAAAGAGCAGTGTCACCCTCGGACAAT
1 AGGAACAATGTCGTCCACCGACCAGATCTCCTCAACGCGTAGGAACAACGTCATCCTAAGATAAC
* *
22015 CAGACTTCCTCATCATGTAGGAACCGTGTTGTCACCAAATTATC
66 CAGACTTCCTCATCACGTA-GAACCGTGTTGTCTCCAAATTATC
22059 TTAAAATTGA
Statistics
Matches: 417, Mismatches: 97, Indels: 23
0.78 0.18 0.04
Matches are distributed among these distances:
137 4 0.01
138 119 0.29
139 285 0.68
140 5 0.01
141 4 0.01
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.26
Consensus pattern (137 bp):
AGGAACAATGTCGTCCACCGACCAGATCTCCTCAACGCGTAGGAACAACGTCATCCTAAGATAAC
CAGACTTCCTCATCACGTAGAACCGTGTTGTCTCCAAATTATCCCTAAAATGGCTAGACGTCCTC
ATCACAT
Found at i:27533 original size:18 final size:18
Alignment explanation
Indices: 27493--27542 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
27483 TACATTGGAC
27493 TATGAATCTGAAGATGAGT
1 TATGAATCTGAA-ATGAGT
27512 TATGAATCTGAAAT-AGGT
1 TATGAATCTGAAATGA-GT
*
27530 TATGAATATGAAA
1 TATGAATCTGAAA
27543 ATAAAAAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 1 0.03
18 16 0.55
19 12 0.41
ACGTcount: A:0.42, C:0.04, G:0.22, T:0.32
Consensus pattern (18 bp):
TATGAATCTGAAATGAGT
Found at i:27985 original size:20 final size:20
Alignment explanation
Indices: 27960--28002 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
27950 TTTAAGAGCT
*
27960 CATTTAGGACCATGTAGATG
1 CATTTAGAACCATGTAGATG
* *
27980 CATTTAGAAGCATTTAGATG
1 CATTTAGAACCATGTAGATG
28000 CAT
1 CAT
28003 GTGGTAGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.33
Consensus pattern (20 bp):
CATTTAGAACCATGTAGATG
Found at i:33079 original size:9 final size:9
Alignment explanation
Indices: 33060--33095 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
33050 AAAACCCACT
33060 AAAAATG-A
1 AAAAATGAA
33068 AAAAATGAAA
1 AAAAATG-AA
33078 AAAAATGAA
1 AAAAATGAA
33087 AAAAATGAA
1 AAAAATGAA
33096 GTTGTGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 7 0.27
9 11 0.42
10 8 0.31
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (9 bp):
AAAAATGAA
Found at i:33081 original size:18 final size:19
Alignment explanation
Indices: 33060--33095 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
33050 AAAACCCACT
33060 AAAAATG-AAAAAATGAAA
1 AAAAATGAAAAAAATGAAA
33078 AAAAATGAAAAAAATGAA
1 AAAAATGAAAAAAATGAA
33096 GTTGTGAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (19 bp):
AAAAATGAAAAAAATGAAA
Found at i:33387 original size:10 final size:10
Alignment explanation
Indices: 33374--33424 Score: 59
Period size: 10 Copynumber: 4.9 Consensus size: 10
33364 AAAACCCACT
33374 AAAAATG-AA
1 AAAAATGAAA
33383 AAAAATGAAAAA
1 AAAAATG--AAA
33395 AAAAATTGAAA
1 AAAAA-TGAAA
*
33406 AAAAAAGAAA
1 AAAAATGAAA
33416 AAAAATGAA
1 AAAAATGAA
33425 GTTGTGAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
9 7 0.19
10 12 0.33
11 8 0.22
12 7 0.19
13 2 0.06
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (10 bp):
AAAAATGAAA
Found at i:33396 original size:314 final size:314
Alignment explanation
Indices: 32827--33397 Score: 1088
Period size: 314 Copynumber: 1.8 Consensus size: 314
32817 CATGAGTAAA
32827 GGTTTGAATAGTTTTCGGGAATTAGTTAAGGATGCCCAATGATGATGAATCTTGATGGCTAGGAT
1 GGTTTGAATAGTTTTCGGGAATTAGTTAAGGATGCCCAATGATGATGAATCTTGATGGCTAGGAT
32892 AGAATGTACATGACTGGTTGAGGATGATAGAACTAACTTTAGGACTTGCTTATTTGAAATCCTTG
66 AGAATGTACATGACTGGTTGAGGATGATAGAACTAACTTTAGGACTTGCTTATTTGAAATCCTTG
32957 AGCACACGATTGTATGTTTTCCATGCTTGAGAAACTTAGAAATATTTTATAAGAGAATTCTTAAA
131 AGCACACGATTGTATGTTTTCCATGCTTGAGAAACTTAGAAATATTTTATAAGAGAATTCTTAAA
*
33022 ATGCCGTGGCATAAAATTTTGAATAATGAAAACCCACTAAAAATGAAAAAATGAAAAAAAATGAA
196 ATGCCATGGCATAAAATTTTGAATAATGAAAACCCACTAAAAATGAAAAAATGAAAAAAAATGAA
33087 AAAAATGAAGTTGTGAATAAATTCCTTGGCATGTCTGTAGAGGGACACTCCGTT
261 AAAAATGAAGTTGTGAATAAATTCCTTGGCATGTCTGTAGAGGGACACTCCGTT
*
33141 GGTTTGAATAGTTTTCTGGAATTAGTTAAGGATGCCCAATGATGATGAATCTTGATGGCTAGGAT
1 GGTTTGAATAGTTTTCGGGAATTAGTTAAGGATGCCCAATGATGATGAATCTTGATGGCTAGGAT
33206 AGAATGTACATGACTGGTTGAGGATGATAGAACTAACTTTAGGACTTGCTTATTTGAAATCCTTG
66 AGAATGTACATGACTGGTTGAGGATGATAGAACTAACTTTAGGACTTGCTTATTTGAAATCCTTG
* *
33271 AGCACACGGTTGTATGTTTTCCATGCTTGAGAAACTTAGAAATTTTTTATAAGAGAATTCTTAAA
131 AGCACACGATTGTATGTTTTCCATGCTTGAGAAACTTAGAAATATTTTATAAGAGAATTCTTAAA
*
33336 ATGCCATGGCATAAAATTTTGAATGATGAAAACCCACTAAAAATGAAAAAAATGAAAAAAAA
196 ATGCCATGGCATAAAATTTTGAATAATGAAAACCCACTAAAAATG-AAAAAATGAAAAAAAA
33398 AATTGAAAAA
Statistics
Matches: 251, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
314 235 0.94
315 16 0.06
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.31
Consensus pattern (314 bp):
GGTTTGAATAGTTTTCGGGAATTAGTTAAGGATGCCCAATGATGATGAATCTTGATGGCTAGGAT
AGAATGTACATGACTGGTTGAGGATGATAGAACTAACTTTAGGACTTGCTTATTTGAAATCCTTG
AGCACACGATTGTATGTTTTCCATGCTTGAGAAACTTAGAAATATTTTATAAGAGAATTCTTAAA
ATGCCATGGCATAAAATTTTGAATAATGAAAACCCACTAAAAATGAAAAAATGAAAAAAAATGAA
AAAAATGAAGTTGTGAATAAATTCCTTGGCATGTCTGTAGAGGGACACTCCGTT
Found at i:33398 original size:12 final size:12
Alignment explanation
Indices: 33381--33420 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
33371 ACTAAAAATG
33381 AAAAAAATGAAA
1 AAAAAAATGAAA
33393 AAAAAAATTG-AA
1 AAAAAAA-TGAAA
33405 AAAAAAA-GAAA
1 AAAAAAATGAAA
33416 AAAAA
1 AAAAA
33421 TGAAGTTGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 1 0.04
11 7 0.27
12 16 0.62
13 2 0.08
ACGTcount: A:0.85, C:0.00, G:0.07, T:0.07
Consensus pattern (12 bp):
AAAAAAATGAAA
Found at i:33399 original size:13 final size:13
Alignment explanation
Indices: 33381--33411 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
33371 ACTAAAAATG
33381 AAAAAAATGAAAA
1 AAAAAAATGAAAA
*
33394 AAAAAATTGAAAA
1 AAAAAAATGAAAA
33407 AAAAA
1 AAAAA
33412 GAAAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.84, C:0.00, G:0.06, T:0.10
Consensus pattern (13 bp):
AAAAAAATGAAAA
Found at i:33404 original size:22 final size:22
Alignment explanation
Indices: 33374--33420 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
33364 AAAACCCACT
*
33374 AAAAATG-AAAAAAATGAAAAA
1 AAAAATGAAAAAAAAAGAAAAA
33395 AAAAATTGAAAAAAAAAGAAAAA
1 AAAAA-TGAAAAAAAAAGAAAAA
33418 AAA
1 AAA
33421 TGAAGTTGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.22
22 2 0.09
23 16 0.70
ACGTcount: A:0.83, C:0.00, G:0.09, T:0.09
Consensus pattern (22 bp):
AAAAATGAAAAAAAAAGAAAAA
Found at i:40517 original size:14 final size:14
Alignment explanation
Indices: 40500--40552 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
40490 AAATTTAACA
40500 TTTTTTTTTTACTT
1 TTTTTTTTTTACTT
* *
40514 TTTTTGTGTTACTT
1 TTTTTTTTTTACTT
* *
40528 TTTTTATTTCA-TT
1 TTTTTTTTTTACTT
40541 TTTTTCTTTTTA
1 TTTTT-TTTTTA
40553 TTATGTTTCT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
13 7 0.23
14 24 0.77
ACGTcount: A:0.09, C:0.08, G:0.04, T:0.79
Consensus pattern (14 bp):
TTTTTTTTTTACTT
Found at i:40784 original size:6 final size:6
Alignment explanation
Indices: 40773--40799 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
40763 AATCAAATGT
40773 TTTAAA TTTAAA TTTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT
40800 TTGAAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:45136 original size:14 final size:14
Alignment explanation
Indices: 45117--45145 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
45107 AGATTTGACT
45117 GAATATAAATGAAC
1 GAATATAAATGAAC
45131 GAATATAAATGAAC
1 GAATATAAATGAAC
45145 G
1 G
45146 GACATAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.07, G:0.17, T:0.21
Consensus pattern (14 bp):
GAATATAAATGAAC
Found at i:48293 original size:22 final size:22
Alignment explanation
Indices: 48262--48307 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
48252 ATTTGTGTTT
48262 ATTTCAATTTCTCTAAAACACA
1 ATTTCAATTTCTCTAAAACACA
*
48284 ATTTCTATTTCTCTAAAACACA
1 ATTTCAATTTCTCTAAAACACA
48306 AT
1 AT
48308 CCTTTCTCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.39, C:0.22, G:0.00, T:0.39
Consensus pattern (22 bp):
ATTTCAATTTCTCTAAAACACA
Found at i:54211 original size:31 final size:29
Alignment explanation
Indices: 54157--54223 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 29
54147 TCAGATTATA
54157 TAACTTTTTAAAATTACACTTTAGTC-CT
1 TAACTTTTTAAAATTACACTTTAGTCACT
* *
54185 TAAACTTTTCTAAAGTTTATACTTTAGTCACT
1 T-AACTTTT-TAAA-ATTACACTTTAGTCACT
54217 TAACTTT
1 TAACTTT
54224 CAAAATTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 1 0.03
29 7 0.21
30 4 0.12
31 18 0.55
32 3 0.09
ACGTcount: A:0.31, C:0.16, G:0.04, T:0.48
Consensus pattern (29 bp):
TAACTTTTTAAAATTACACTTTAGTCACT
Found at i:60153 original size:14 final size:12
Alignment explanation
Indices: 60125--60153 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
60115 TATCTTTGGT
60125 GAAGAATATGAA
1 GAAGAATATGAA
60137 GAAGAATATG-A
1 GAAGAATATGAA
60148 GAAGAA
1 GAAGAA
60154 AAGAGGAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.59, C:0.00, G:0.28, T:0.14
Consensus pattern (12 bp):
GAAGAATATGAA
Found at i:65491 original size:43 final size:43
Alignment explanation
Indices: 65443--65538 Score: 108
Period size: 43 Copynumber: 2.2 Consensus size: 43
65433 TTGGGCTAAG
*
65443 AGTATCGATATTCAGGTTCATTG-TATCAAT-CTTACTTCACAAT
1 AGTATCGATATTCAGGTTCA-CGATATCAATAC-TACTTCACAAT
* * *
65486 AGTATCCG-TATTCGGGTTCACGATATCAATACTACTTCGCAGT
1 AGTAT-CGATATTCAGGTTCACGATATCAATACTACTTCACAAT
65529 AGTATCGATA
1 AGTATCGATA
65539 CTCTTAAGAG
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
42 3 0.07
43 39 0.87
44 3 0.07
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (43 bp):
AGTATCGATATTCAGGTTCACGATATCAATACTACTTCACAAT
Found at i:66368 original size:20 final size:20
Alignment explanation
Indices: 66277--66410 Score: 137
Period size: 20 Copynumber: 6.7 Consensus size: 20
66267 CGATTTTTCC
*
66277 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCGATTAT
* *
66297 GTA-AATCGCAATGCGAGTAT
1 G-ACTATCGCAATGCGATTAT
* *
66317 GACTATCGCAACGCGAATAT
1 GACTATCGCAATGCGATTAT
*
66337 GTA-AATCGCAATGCGATTAT
1 G-ACTATCGCAATGCGATTAT
*
66357 GACTATCACAATGCGATTAT
1 GACTATCGCAATGCGATTAT
* *
66377 GACTATCGCAACGCGATTCT
1 GACTATCGCAATGCGATTAT
* *
66397 AACTGTCGCAATGC
1 GACTATCGCAATGC
66411 TGAATTTCAA
Statistics
Matches: 94, Mismatches: 16, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
19 2 0.02
20 90 0.96
21 2 0.02
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (20 bp):
GACTATCGCAATGCGATTAT
Found at i:66385 original size:40 final size:40
Alignment explanation
Indices: 66277--66415 Score: 172
Period size: 40 Copynumber: 3.5 Consensus size: 40
66267 CGATTTTTCC
*
66277 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTAT
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATTAT
*
66317 GACTATCGCAACGCGAATATGTAAATCGCAATGCGATTAT
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATTAT
* * * * *
66357 GACTATCACAATGCGATTATG-ACTATCGCAACGCGATTCT
1 GACTATCGCAATGCGAATATGTA-AATCGCAATGCGATTAT
* *
66397 AACTGTCGCAATGCTGAAT
1 GACTATCGCAATGC-GAAT
66416 TTCAAATTCG
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
39 1 0.01
40 81 0.95
41 3 0.04
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (40 bp):
GACTATCGCAATGCGAATATGTAAATCGCAATGCGATTAT
Found at i:67245 original size:24 final size:24
Alignment explanation
Indices: 67213--67266 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
67203 GTATTCGAAA
*
67213 TTTGATCTTGTTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
67237 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
67261 TTTGAT
1 TTTGAT
67267 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:67449 original size:3 final size:3
Alignment explanation
Indices: 67441--67467 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
67431 ATATAACCCT
67441 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
67468 ATCCCCGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:67488 original size:14 final size:14
Alignment explanation
Indices: 67459--67495 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
67449 AGAAGAAGAA
67459 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
67474 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
67488 GAAGAAAA
1 GAAGAAAA
67496 TGCCAATGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:69519 original size:18 final size:17
Alignment explanation
Indices: 69488--69521 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
69478 AAGCAAAGGC
*
69488 AATCAAATCGCAATCAA
1 AATCAAATCCCAATCAA
69505 AATCAAAATCCCAATCA
1 AATC-AAATCCCAATCA
69522 CAACCGGCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.53, C:0.26, G:0.03, T:0.18
Consensus pattern (17 bp):
AATCAAATCCCAATCAA
Done.