Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003815.1 Hibiscus syriacus cultivar Beakdansim tig00008177_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: 76570
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:446 original size:41 final size:42
Alignment explanation
Indices: 366--466 Score: 141
Period size: 41 Copynumber: 2.4 Consensus size: 42
356 CCCGAATTTG
* * *
366 TAAATCTTTCGGGTCATCAATAAGTCTTTCGAGCCTGATGCT
1 TAAATCCTTCGGGTCATCAAGAAGTCTTTCGAGCATGATGCT
* * *
408 TAAATCCTTCGGGTCATC-AGAAGTCTTTTGAGTATGATGGT
1 TAAATCCTTCGGGTCATCAAGAAGTCTTTCGAGCATGATGCT
449 TAAATCCTTCGGGTCATC
1 TAAATCCTTCGGGTCATC
467 TGTAAGCCTT
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 36 0.68
42 17 0.32
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.36
Consensus pattern (42 bp):
TAAATCCTTCGGGTCATCAAGAAGTCTTTCGAGCATGATGCT
Found at i:696 original size:22 final size:21
Alignment explanation
Indices: 668--737 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 21
658 CATCAGTAAG
668 TCTTTCGAGCATGATGTTTAAA
1 TCTTTCGAGCATGATG-TTAAA
* * *
690 TCTTTCGGGTC-TCA-G-TAAG
1 TCTTTCGAG-CATGATGTTAAA
709 TCTTTCGAGCATGATGCTTAAA
1 TCTTTCGAGCATGATG-TTAAA
*
731 TCCTTCG
1 TCTTTCG
738 GGTCATCTGT
Statistics
Matches: 36, Mismatches: 7, Indels: 10
0.68 0.13 0.19
Matches are distributed among these distances:
18 1 0.03
19 13 0.36
20 1 0.03
21 1 0.03
22 19 0.53
23 1 0.03
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (21 bp):
TCTTTCGAGCATGATGTTAAA
Found at i:706 original size:41 final size:42
Alignment explanation
Indices: 649--759 Score: 172
Period size: 41 Copynumber: 2.7 Consensus size: 42
639 ATTTGTAGGT
*
649 TCTTT-GGGTCATCAGTAAGTCTTTCGAGCATGATGTTTAAA
1 TCTTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAA
690 TCTTTCGGGTC-TCAGTAAGTCTTTCGAGCATGATGCTTAAA
1 TCTTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAA
* * *
731 TCCTTCGGGTCATCTGTAAGCCTTTCGAG
1 TCTTTCGGGTCATCAGTAAGTCTTTCGAG
760 TAATATGATA
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
41 44 0.69
42 20 0.31
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.37
Consensus pattern (42 bp):
TCTTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAA
Found at i:932 original size:300 final size:302
Alignment explanation
Indices: 489--1324 Score: 1264
Period size: 300 Copynumber: 2.8 Consensus size: 302
479 AAGAAATATA
*
489 ATAAGACCTTCAGTGCAGG-TGTTTTCAAATGAGA-TTTAAAAATTAAGCCTATTTTAGGGGTTT
1 ATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAAAAACTAAGCCTATTTTAGGGGTTT
* * *
552 CTTAATTATCTCAAAAGAGTTGTT-AAGGAAGCTA-GCCTTTTAAGGGGTTTCTTAACAACTAAT
66 CTTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTATGCCTTTTAAGGGGTTCCTTGACAACTAAA
* * *
615 AACTAAGTTTTCGAGGGTTTCTTGATTTGTAGGTTCTTTGGGTCATCAGTAAGTCTTTCGAGCAT
131 AACTAAGCTTTCGAGGGTTTCTTGATTTGTAAGTTCTTCGGG-CATCAGTAAGTCTTTCGAGCAT
680 GATGTTTAAATCTTTCGGGTC-TCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCAT
195 GATGTTTAAATCTTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAAT-CTTCGGGTCAT
* *
744 CTGTAAGCCTTTC-GAGTAATATGAT-AAGACCTTCGGGCCATCC
259 CTGTAAGCCTTTCAGAGCAAGATGATAAAG-CCTTCGGGCCATCC
*
787 ATAAGACCTTCAGCGCAGGATGTTTTCAAATGAGATTTTAAAAACTAAGCCTATTTTAGGGGTTT
1 ATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAAAAACTAAGCCTATTTTAGGGGTTT
*
852 CTTAATTATCTC-AAAGAGTTATTAAAGGAAGCTATGCCTTTTAAGGGGTTCCTTGAC-ACTAAA
66 CTTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTATGCCTTTTAAGGGGTTCCTTGACAACTAAA
*
915 AACTAAGCTTTCGAGGGTTTCTTGATTTGTAAGTTCTTCGGGCTATCTGTAAGTCTTTCGAGCAT
131 AACTAAGCTTTCGAGGGTTTCTTGATTTGTAAGTTCTTCGGGC-ATCAGTAAGTCTTTCGAGCAT
* * * * *
980 GATATTTAAATCCTTT-GGGTCATTAGTAAGTCTTTCAAGCATGATGCTTAAATTTTCGGGTTAT
195 GATGTTTAAAT-CTTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCTTCGGGTCAT
*
1044 CTGTAAGCCTTTCGAGAGCAAGATGATAAAGCCTTCGGGTCATCC
259 CTGTAAGCCTTTC-AGAGCAAGATGATAAAGCCTTCGGGCCATCC
* *
1089 ATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAAAAACTAAGTCTGTTTTAGGGGTTT
1 ATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAAAAACTAAGCCTATTTTAGGGGTTT
*
1154 CTTAATTATCTCAAAAGAGTTGTTAAAGGAAGC-ATAGCCTTTTAAGGGGTTCCTTGACAATTAA
66 CTTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAT-GCCTTTTAAGGGGTTCCTTGACAACTAA
* * *
1218 GAAACTAAGCTTTCGAGGG-TTCTTGATTTGTAAATCCGTCGGGACATCAGTAAGTCTTTCGAGC
130 -AAACTAAGCTTTCGAGGGTTTCTTGATTTGTAAGTTCTTCGGG-CATCAGTAAGTCTTTCGAGC
* * *
1282 ATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCA
193 ATGATGTTTAAATCTTTCGGGTCATCAGTAAGTCTTTCGAGCA
1325 AGATAAGTCC
Statistics
Matches: 489, Mismatches: 33, Indels: 26
0.89 0.06 0.05
Matches are distributed among these distances:
298 18 0.04
299 26 0.05
300 151 0.31
301 53 0.11
302 99 0.20
303 47 0.10
304 76 0.16
305 19 0.04
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (302 bp):
ATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAAAAACTAAGCCTATTTTAGGGGTTT
CTTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTATGCCTTTTAAGGGGTTCCTTGACAACTAAA
AACTAAGCTTTCGAGGGTTTCTTGATTTGTAAGTTCTTCGGGCATCAGTAAGTCTTTCGAGCATG
ATGTTTAAATCTTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCTTCGGGTCATCT
GTAAGCCTTTCAGAGCAAGATGATAAAGCCTTCGGGCCATCC
Found at i:1816 original size:3 final size:3
Alignment explanation
Indices: 1808--1856 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
1798 CATTTTTTAT
*
1808 TTA TTA TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1854 TTA
1 TTA
1857 ATAAACTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 4 0.10
3 38 0.90
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:10430 original size:2 final size:2
Alignment explanation
Indices: 10423--10470 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
10413 TTTTCAAATG
10423 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10465 TA TA TA
1 TA TA TA
10471 GTTTGCTCCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15741 original size:20 final size:20
Alignment explanation
Indices: 15703--15741 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
15693 ATTTGTGTGC
* **
15703 TTTTTATTAAAATTTATTAG
1 TTTTTAATAAAATAAATTAG
15723 TTTTTAATAAAATAAATTA
1 TTTTTAATAAAATAAATTA
15742 TAATAGATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (20 bp):
TTTTTAATAAAATAAATTAG
Found at i:19127 original size:18 final size:19
Alignment explanation
Indices: 19090--19129 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
19080 TTGTTAAAAT
*
19090 TTATAAAATAAATTTTTTA
1 TTATAAAATAAATGTTTTA
*
19109 TTATAGAAT-AATGTTTTA
1 TTATAAAATAAATGTTTTA
19127 TTA
1 TTA
19130 AGTCCTACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (19 bp):
TTATAAAATAAATGTTTTA
Found at i:20630 original size:26 final size:26
Alignment explanation
Indices: 20600--20661 Score: 124
Period size: 26 Copynumber: 2.4 Consensus size: 26
20590 GTTCAAGCCT
20600 TTTCGAGTTCAAGTTTCAATATTATA
1 TTTCGAGTTCAAGTTTCAATATTATA
20626 TTTCGAGTTCAAGTTTCAATATTATA
1 TTTCGAGTTCAAGTTTCAATATTATA
20652 TTTCGAGTTC
1 TTTCGAGTTC
20662 GATTTGAACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (26 bp):
TTTCGAGTTCAAGTTTCAATATTATA
Found at i:20854 original size:10 final size:10
Alignment explanation
Indices: 20822--20855 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
20812 AATTGGCGGT
20822 TTTTTTCCGG
1 TTTTTTCCGG
* *
20832 TTTTTCCCAG
1 TTTTTTCCGG
20842 TTTTTTCCGG
1 TTTTTTCCGG
20852 TTTT
1 TTTT
20856 CAGCCGGTCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.03, C:0.21, G:0.15, T:0.62
Consensus pattern (10 bp):
TTTTTTCCGG
Found at i:25621 original size:10 final size:10
Alignment explanation
Indices: 25606--25634 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
25596 TCCTTTACCA
25606 TTTATTTATT
1 TTTATTTATT
25616 TTTATTTATT
1 TTTATTTATT
25626 TTTATTTAT
1 TTTATTTAT
25635 CTCTATCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTATTTATT
Found at i:35115 original size:8 final size:8
Alignment explanation
Indices: 35070--35107 Score: 60
Period size: 8 Copynumber: 4.9 Consensus size: 8
35060 TCCTAAGTTG
35070 AAAAAAA-
1 AAAAAAAC
*
35077 AAACAAAC
1 AAAAAAAC
35085 AAAAAAAC
1 AAAAAAAC
35093 AAAAAAAC
1 AAAAAAAC
35101 AAAAAAA
1 AAAAAAA
35108 ATCAAAAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:35925 original size:105 final size:105
Alignment explanation
Indices: 35743--36410 Score: 1237
Period size: 105 Copynumber: 6.4 Consensus size: 105
35733 AAAAAATCAT
35743 CAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
1 CAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
35808 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
66 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
*
35848 CAAACATCTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
1 CAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
35913 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
66 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
*
35953 CAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAAC
1 CAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
36018 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
66 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
*
36058 CAAACATTTCTCAAATCCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
1 CAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
36123 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
66 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
*
36163 CAAACATTTCTCAAATTCAGAGCCGATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
1 CAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
36228 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
66 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
*
36268 CAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAAC
1 CAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
* *
36333 GCAAGTTCAACTTCACGGCGAAAGGACCGCTGGTTGTCAA
66 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
* * *
36373 CAAACAATTTCCCAATTTCGGAGCCAATTTCAACTTCA
1 CAAAC-ATTTCTCAAATTCAGAGCCAATTTCAACTTCA
36411 TAGCGAAAGA
Statistics
Matches: 548, Mismatches: 14, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
105 519 0.95
106 29 0.05
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
CAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
Found at i:39174 original size:34 final size:32
Alignment explanation
Indices: 39110--39176 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 32
39100 ACTACAGTAT
*
39110 ATCATAAGCACACACAATGCTATCACATCGAA
1 ATCATAAGCACACACAATGCAATCACATCGAA
*
39142 ATCATATATGCACACA-AAGTGCAATCATATCGAA
1 ATCATA-A-GCACACACAA-TGCAATCACATCGAA
39176 A
1 A
39177 ATATACTAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 6 0.20
33 3 0.10
34 21 0.70
ACGTcount: A:0.45, C:0.24, G:0.10, T:0.21
Consensus pattern (32 bp):
ATCATAAGCACACACAATGCAATCACATCGAA
Found at i:39190 original size:102 final size:103
Alignment explanation
Indices: 39013--39215 Score: 288
Period size: 102 Copynumber: 2.0 Consensus size: 103
39003 AGAACATATT
* * * * *
39013 AGCACACACAGTGCTATCATATCAGAATCATAATATGGATACAAAGTGCAATCACATCTGAATTA
1 AGCACACACAATGCTATCACATCAGAATCATAATATGCACACAAAGTGCAATCACATCTGAAATA
*
39078 TACTAGTGTACCTACCGGTAACA-CTACAGTATATCATA
66 TACTAGTGTACCCACCGGTAACATC-ACAGTATATCATA
*
39116 AGCACACACAATGCTATCACATC-GAAATCAT-ATATGCACACAAAGTGCAATCATATC-GAAAA
1 AGCACACACAATGCTATCACATCAG-AATCATAATATGCACACAAAGTGCAATCACATCTG-AAA
39178 TATACTAGTGTACCCACCGGTAACATCACAGTATATCA
64 TATACTAGTGTACCCACCGGTAACATCACAGTATATCA
39216 ATCACTCAAC
Statistics
Matches: 90, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
101 1 0.01
102 61 0.68
103 28 0.31
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.24
Consensus pattern (103 bp):
AGCACACACAATGCTATCACATCAGAATCATAATATGCACACAAAGTGCAATCACATCTGAAATA
TACTAGTGTACCCACCGGTAACATCACAGTATATCATA
Found at i:41673 original size:5 final size:5
Alignment explanation
Indices: 41665--41695 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
41655 TATTATTATT
41665 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG T
41696 TTCTAAGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:42490 original size:23 final size:23
Alignment explanation
Indices: 42460--42536 Score: 100
Period size: 23 Copynumber: 3.3 Consensus size: 23
42450 AAATGTAACA
42460 AAGTGCCACGTAGAATTGCACCG
1 AAGTGCCACGTAGAATTGCACCG
*
42483 AAGTGCCACGTAGAATTACACCG
1 AAGTGCCACGTAGAATTGCACCG
* * * *
42506 TAGTGTCGCGTAGAATTGCACTG
1 AAGTGCCACGTAGAATTGCACCG
*
42529 TAGTGCCA
1 AAGTGCCA
42537 TATAATAATA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.22
Consensus pattern (23 bp):
AAGTGCCACGTAGAATTGCACCG
Found at i:43544 original size:21 final size:21
Alignment explanation
Indices: 43512--43554 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
43502 TGTTTATTTA
43512 ATTGAGAGTGCATCGATGCAC
1 ATTGAGAGTGCATCGATGCAC
43533 ATTGA-AGATGCATCGATGCAC
1 ATTGAGAG-TGCATCGATGCAC
43554 A
1 A
43555 CAACCCAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (21 bp):
ATTGAGAGTGCATCGATGCAC
Found at i:45380 original size:2 final size:2
Alignment explanation
Indices: 45373--45420 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
45363 ATCATCTGAG
* * *
45373 AT AT AT AT AT AT AT AT CT AT AT CT AT AT CT 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
45415 AT AT AT
1 AT AT AT
45421 TTCTAATCCT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47015 original size:23 final size:23
Alignment explanation
Indices: 46985--47038 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
46975 AAATGTAACA
46985 AAGTGCCACGTAGAATTGCACCG
1 AAGTGCCACGTAGAATTGCACCG
47008 AAGTGCCACGTAGAATTGCACCG
1 AAGTGCCACGTAGAATTGCACCG
*
47031 TAGTGCCA
1 AAGTGCCA
47039 TATAATAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.19
Consensus pattern (23 bp):
AAGTGCCACGTAGAATTGCACCG
Found at i:49329 original size:23 final size:24
Alignment explanation
Indices: 49303--49363 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
49293 GTTCTATGAT
* *
49303 GTCCTTCGGGATAAAA-TTATGTG
1 GTCCTTCGGGACAAAACCTATGTG
49326 GTCCTTCGGGACAAAACCTATGTG
1 GTCCTTCGGGACAAAACCTATGTG
49350 GTCCTTCGGGACAA
1 GTCCTTCGGGACAA
49364 TTATGTGGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
23 15 0.43
24 20 0.57
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (24 bp):
GTCCTTCGGGACAAAACCTATGTG
Found at i:56121 original size:24 final size:23
Alignment explanation
Indices: 56064--56153 Score: 110
Period size: 23 Copynumber: 3.9 Consensus size: 23
56054 GTCGAGGGTT
* *
56064 TTATGTGGTTCTTCGAGACAAAA
1 TTATGTGGTCCTTCGGGACAAAA
*
56087 TTATGTAGTCCTTCGGGACAAAA
1 TTATGTGGTCCTTCGGGACAAAA
*
56110 CCTATGTGGTCCTTCGGGAC-AAA
1 -TTATGTGGTCCTTCGGGACAAAA
* *
56133 TTATGTGGTCATTTGGGACAA
1 TTATGTGGTCCTTCGGGACAA
56154 TAATGTGATA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
22 16 0.28
23 24 0.42
24 17 0.30
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (23 bp):
TTATGTGGTCCTTCGGGACAAAA
Found at i:58476 original size:26 final size:26
Alignment explanation
Indices: 58440--58490 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
58430 AAAGATGAAG
*
58440 AAATTACTTTTGCATGTCTTTCTCTA
1 AAATTACTTTTGCATGTATTTCTCTA
*
58466 AAATTACTTTTTCATGTATTTCTCT
1 AAATTACTTTTGCATGTATTTCTCT
58491 CATTCTCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.53
Consensus pattern (26 bp):
AAATTACTTTTGCATGTATTTCTCTA
Found at i:64776 original size:30 final size:30
Alignment explanation
Indices: 64740--64821 Score: 80
Period size: 30 Copynumber: 2.7 Consensus size: 30
64730 TAAAATATAT
64740 AACTTTTCAAAATTACATTTTTAGACCCT-A
1 AACTTTTCAAAATTACATTTTTA-ACCCTCA
** *
64770 AACTTTT-ATAAATTTTATACTTTAACCCTCA
1 AACTTTTCA-AAATTACAT-TTTTAACCCTCA
64801 AAC-TTTCAAAACTTACATTTT
1 AACTTTTCAAAA-TTACATTTT
64822 AGTCACTAGC
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
29 1 0.02
30 27 0.66
31 13 0.32
ACGTcount: A:0.37, C:0.20, G:0.01, T:0.43
Consensus pattern (30 bp):
AACTTTTCAAAATTACATTTTTAACCCTCA
Done.