Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003964.1 Hibiscus syriacus cultivar Beakdansim tig00008589_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: 89567
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4444 original size:13 final size:13
Alignment explanation
Indices: 4406--4444 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
4396 CAAATGAGAG
4406 AAAAAAACGAAATT
1 AAAAAAA-GAAATT
* *
4420 AAATAAATAAATT
1 AAAAAAAGAAATT
4433 AAAAAAAGAAAT
1 AAAAAAAGAAAT
4445 AATAATAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (13 bp):
AAAAAAAGAAATT
Found at i:4572 original size:30 final size:29
Alignment explanation
Indices: 4533--4597 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
4523 AACTATATAT
*
4533 TATATAGTTTCCAAAATGATTTAAAAAAA
1 TATATAGTTTCCAAAAAGATTTAAAAAAA
* * * *
4562 TATATGAGTTTTCAAAAAGTTTTTATAAAA
1 TATAT-AGTTTCCAAAAAGATTTAAAAAAA
4592 TATATA
1 TATATA
4598 TTATATATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 6 0.20
30 24 0.80
ACGTcount: A:0.48, C:0.05, G:0.08, T:0.40
Consensus pattern (29 bp):
TATATAGTTTCCAAAAAGATTTAAAAAAA
Found at i:4604 original size:39 final size:37
Alignment explanation
Indices: 4561--4724 Score: 133
Period size: 39 Copynumber: 4.2 Consensus size: 37
4551 ATTTAAAAAA
4561 ATATATGAGTTTTCAAAAAGTTTTTATAAAA-TATATATT
1 ATATAT-A-TTTTCAAAAAGTTTTTA-AAAACTATATATT
*
4600 ATATAT-TTTTCAAAAATTCTTTTTATTTAAAAGC-ATATATT
1 ATATATATTTTCAAAAA--GTTTTTA---AAAA-CTATATATT
* *
4641 ATATA-ATTTTTCAAAATG-TTTTAAGAACTATATATT
1 ATATATA-TTTTCAAAAAGTTTTTAAAAACTATATATT
*
4677 ATATATTTATTTTCAAAATGTTTTTAAAAACTATA-ATAT
1 ATATA--TATTTTCAAAAAGTTTTTAAAAACTATATAT-T
4716 ATATATATT
1 ATATATATT
4725 ATATATATCT
Statistics
Matches: 106, Mismatches: 5, Indels: 30
0.75 0.04 0.21
Matches are distributed among these distances:
35 1 0.01
36 25 0.24
37 4 0.04
38 19 0.18
39 31 0.29
40 5 0.05
41 12 0.11
42 9 0.08
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (37 bp):
ATATATATTTTCAAAAAGTTTTTAAAAACTATATATT
Found at i:4691 original size:38 final size:38
Alignment explanation
Indices: 4570--4724 Score: 142
Period size: 41 Copynumber: 4.0 Consensus size: 38
4560 AATATATGAG
*
4570 TTTTCAAAAAGTTTTTATAAAA-TATATATTATATA--T
1 TTTTCAAAATGTTTTTA-AAAACTATATATTATATATTT
* *
4606 TTTTCAAAAATTCTTTTTATTTAAAAGC-ATATATTATATA-AT
1 TTTTC-AAAA-TGTTTTTA---AAAA-CTATATATTATATATTT
*
4648 TTTTCAAAATG-TTTTAAGAACTATATATTATATATTT
1 TTTTCAAAATGTTTTTAAAAACTATATATTATATATTT
4685 ATTTTCAAAATGTTTTTAAAAACTATAATATATATATATT
1 -TTTTCAAAATGTTTTTAAAAACTAT-ATAT-TATATATT
4725 ATATATATCT
Statistics
Matches: 100, Mismatches: 6, Indels: 21
0.79 0.05 0.17
Matches are distributed among these distances:
35 1 0.01
36 20 0.20
37 5 0.05
38 17 0.17
39 17 0.17
40 10 0.10
41 24 0.24
42 6 0.06
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (38 bp):
TTTTCAAAATGTTTTTAAAAACTATATATTATATATTT
Found at i:4719 original size:2 final size:2
Alignment explanation
Indices: 4708--4744 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
4698 TTTTAAAAAC
*
4708 TA TA -A TA TA TA TA TA T- TA TA TA TA TC TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4745 TTCCAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5631 original size:81 final size:81
Alignment explanation
Indices: 5434--6471 Score: 535
Period size: 81 Copynumber: 12.8 Consensus size: 81
5424 ATTTTATTGA
* * * * * * * * * * *
5434 CAGATAGCCCTTCTTGCCTTGAGCTATGCTGTAAATGATATACCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATACCGCAAATGATGTCCCTT-GAGTTGAGTGTAATCGAA
* *
5499 CTCGAAGGT-TTTTTTG
65 CTCAAAGGTCTTTTTGG
** * * *
5515 CAG--AACCCTTCTAGCCTTGAGCCATACCGTAAATGATAT-CGTTGAGTTGAGTGTAATC-AGA
1 CAGATAACCCTTCTAGCCTTGAGTTATACCGCAAATGATGTCCCTTGAGTTGAGTGTAATCGA-A
5576 CTCAAAGGTCTTTGTTGG
65 CTCAAAGGTCTTT-TTGG
* * * ** * *
5594 CAGATAACTCTTATAGCCTTGAGTTATACTGCAAATGATGTGCCCTCAAAGCTGAGTGTAATCAA
1 CAGATAACCCTTCTAGCCTTGAGTTATACCGCAAATGATGT-CCCT-TGAGTTGAGTGTAATCGA
** *
5659 ACTTGAGGGTC---TTGG
64 ACTCAAAGGTCTTTTTGG
* * * *
5674 CAGATAGCCCTTCTAGCCTTGAGCTATACCGCAAATGATATGCCGTTGAGTTGAGTGTAATCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATACCGCAAATGATGT-CCCTTGAGTTGAGTGTAATCGAA
*
5739 CTCAAAGGTCTTTATTAG
65 CTCAAAGGTCTTT-TTGG
* * ** * *
5757 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCAAAGCTGAGTGTAATTGA
1 CAGATAACCCTTCTAGCCTTGAGTTATACCGCAAATGATGT-CCCT-TGAGTTGAGTGTAATCGA
* *
5822 ACTCGAGGGTC--TTTGG
64 ACTCAAAGGTCTTTTTGG
* * * *
5838 CAGATAGCCCTTCTAGCCTTGAGTTATACCACAAATGATGTGCCATTGAATTGAGTGTAATCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATACCGCAAATGATGT-CCCTTGAGTTGAGTGTAATCGAA
5903 CTC-AAGGTCTTTGTT-G
65 CTCAAAGGTCTTT-TTGG
* * **
5919 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTACCCTCAAAGTTGAGTGTAATCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATACCGCAAATGATGT-CCCT-TGAGTTGAGTGTAATCGA
*
5984 ACTC-GAGTGTC--TTTGG
64 ACTCAAAG-GTCTTTTTGG
* * * * * * * * * * * * * *
6000 CAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATAATGTGCCTTTAAGCTGAGCGTAGTTGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATACCGCAAATGATGT-CCCTTGAGTTGAGTGTAATCGAA
**
6065 CTCGCAGGTC--TTTGG
65 CTCAAAGGTCTTTTTGG
* * * * * * * * * * ** *
6080 CAGATAGCCCTTTTCGACTTAAGTTATACTGTAAATGA--T-CTTTAAGCTGAGCATAGTCGAAC
1 CAGATAACCCTTCTAGCCTTGAGTTATACCGCAAATGATGTCCCTTGAGTTGAGTGTAATCGAAC
* *
6142 TCGAAGGTCTTTTAGTGA
66 TCAAAGGTCTTTT--TGG
* * * * * * *
6160 CAG-TAACCCTTCTAGCCTTGAGTTATGCTGTAAATGA--TACCTCTGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATACCGCAAATGATGTCCCT-TGAGTTGAGTGTAATCGAA
6222 CTCAAAGGTC-TTTTGG
65 CTCAAAGGTCTTTTTGG
* * * * * ** * * *
6238 TCACATATAACCCTTCTAGCCTTGGGTTATGCTGTAAATGATGTTCCCACGAAGCTGAGTTTTAT
1 ---CAGATAACCCTTCTAGCCTTGAGTTATACCGCAAATGATG-TCCCTTG-AGTTGAGTGTAAT
** *
6303 CGAACTTGAGGGTC--TTTGG
61 CGAACTCAAAGGTCTTTTTGG
* * * * * *** * * * *
6322 CAGATAGCCCTTCTCGACTTAAGCTATGTTGCAAATGATGTACCTGGAGTTGAGCGTAGTCGAAC
1 CAGATAACCCTTCTAGCCTTGAGTTATACCGCAAATGATGTCCCTTGAGTTGAGTGTAATCGAAC
*
6387 TCGAAGGTCTTTGGTTGG
66 TCAAAGGTCTTT--TTGG
* * * * * * * * ** *
6405 CAAATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATATGCCCTCAAGCTGAGTGTAATCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATACCGCAAATGATGT-CCCTTGAGTTGAGTGTAATCGAA
6470 CT
65 CT
6472 TGAGGGATTT
Statistics
Matches: 765, Mismatches: 152, Indels: 77
0.77 0.15 0.08
Matches are distributed among these distances:
76 30 0.04
77 21 0.03
78 11 0.01
79 113 0.15
80 134 0.18
81 219 0.29
82 57 0.07
83 87 0.11
84 69 0.09
85 24 0.03
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (81 bp):
CAGATAACCCTTCTAGCCTTGAGTTATACCGCAAATGATGTCCCTTGAGTTGAGTGTAATCGAAC
TCAAAGGTCTTTTTGG
Found at i:5751 original size:163 final size:163
Alignment explanation
Indices: 5434--6770 Score: 1154
Period size: 164 Copynumber: 8.2 Consensus size: 163
5424 ATTTTATTGA
* * * * * * *** * *
5434 CAGATAGCCCTTCTTGCCTTGAGCTATGCTGTAAATGATAT-ACCTTGGAGCTGAGCGTAGTCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCAAAGCTGAGTGTAATCGA
* * * * * * * * * * *
5498 ACTCGAAGGTTTTTTTGCAGA-A-CCCTTCTAGCCTTGAGCCATACCGTAAATGATAT-CGTTGA
66 ACTTG-AGGGTCTTTGGCAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGATATGCCTTGA
* * * *
5560 GTTGAGTGTAATC-AGACTCAAAGGTCTTTGTTGG
130 GCTGAGCGTAGTCGA-ACTCGAAGGTCTTTGTTGG
* * * *
5594 CAGATAACTCTTATAGCCTTGAGTTATACTGCAAATGATGTGCCCTCAAAGCTGAGTGTAATCAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCAAAGCTGAGTGTAATCGA
* * * *
5659 ACTTGAGGGTC-TTGGCAGATAGCCCTTCTAGCCTTGAGCTATACCGCAAATGATATGCCGTTGA
66 ACTTGAGGGTCTTTGGCAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGATATGCC-TTGA
* * * * * *
5723 GTTGAGTGTAATCGAACTCAAAGGTCTTTATTAG
130 GCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGG
*
5757 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCAAAGCTGAGTGTAATTGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCAAAGCTGAGTGTAATCGA
* * * * * ** *
5822 ACTCGAGGGTCTTTGGCAGATAGCCCTTCTAGCCTTGAGTTATACCACAAATGATGTGCCATTGA
66 ACTTGAGGGTCTTTGGCAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGATATGCC-TTGA
** * *
5887 ATTGAGTGTAATCGAACTC-AAGGTCTTTGTT-G
130 GCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGG
* *
5919 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTACCCTCAAAGTTGAGTGTAATCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCAAAGCTGAGTGTAATCGA
* * * * * * *
5984 ACTCGAGTGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATAATGTGCCTTTAA
66 ACTTGAGGGTCTTTGGCAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGATATGCC-TTGA
* *
6049 GCTGAGCGTAGTTGAACTCGCAGGTC--T-TTGG
130 GCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGG
* * * * * * * ** ** *
6080 CAGATAGCCCTTTTCGACTTAAGTTATACTGTAAATGA--T---CTTTAAGCTGAGCATAGTCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCAAAGCTGAGTGTAATCGA
* * * * * * *
6140 ACTCGAAGGTCTTTTAGTGACAG-TAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATA--CCT
66 ACTTGAGGGTC-TTT-G-G-CAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGATATGCCT
* * **
6202 CTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCA
127 -TGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGTTGG
* * * * * * * *
6241 CATATAACCCTTCTAGCCTTGGGTTATGCTGTAAATGATGTTCCCACGAAGCTGAGTTTTATCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCAAAGCTGAGTGTAATCGA
* * * * *
6306 ACTTGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGTTGCAAATGATGTACCTGGAG
66 ACTTGAGGGTCTTTGGCAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGATATGCCTTGAG
*
6371 TTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGG
131 CTGAGCGTAGTCGAACTCGAAGGTCTTT-GTTGG
* * * * * *
6405 CAAATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATATGCCCTC-AAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCAAAGCTGAGTGTAATCGA
* *** * *
6469 ACTTGAGGGATTTTTTTATATATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGA-AGTGCCTT
66 ACTTGAGGG--TCTTTGGCAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGATA-TGCCTT
* * * *
6533 GGAGCTGAGCGTAGTCAAACTCGAAGGTATTTTGGTGA
128 -GAGCTGAGCGTAGTCGAACTCGAAGGT-CTTTGTTGG
* ** * *
6571 CAAATAA-CCTTCTAGCCTTGAGTTATGCTATAAATGATGTGCCCTCGAAGCTGAGTATAATCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCAAAGCTGAGTGTAATCGA
* * * * * *
6635 ACTTGAGGGTCTTTGGCATATAGACCTTCTCGACATAAGTTATGCTGCAAATGATGTGCCTTGGA
66 ACTTGAGGGTCTTTGGCAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGATATGCCTT-GA
*
6700 GCTGAGCATAGTCGAACTCGAAGGT-TTTGGTTGG
130 GCTGAGCGTAGTCGAACTCGAAGGTCTTT-GTTGG
* * *
6734 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
6771 TTATCTTAAA
Statistics
Matches: 975, Mismatches: 166, Indels: 68
0.81 0.14 0.06
Matches are distributed among these distances:
156 25 0.03
157 30 0.03
158 1 0.00
159 36 0.04
160 44 0.05
161 116 0.12
162 138 0.14
163 186 0.19
164 230 0.24
165 83 0.09
166 83 0.09
167 3 0.00
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (163 bp):
CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCAAAGCTGAGTGTAATCGA
ACTTGAGGGTCTTTGGCAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGATATGCCTTGAG
CTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGG
Found at i:6687 original size:81 final size:80
Alignment explanation
Indices: 5590--6770 Score: 687
Period size: 81 Copynumber: 14.5 Consensus size: 80
5580 AAGGTCTTTG
* * * * *
5590 TTGGCAGATAACTCTTATAGCCTTGAGTTATACTGCAAATGATGTGCCCTCAAAGCTGAGTGTAA
1 TTGGCAGATAAC-CTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
* *
5655 TCAAACTTGAGGGTC-
65 TCGAACTCGAGGGTCT
* * * * * * * * * *
5670 TTGGCAGATAGCCCTTCTAGCCTTGAGCTATACCGCAAATGATATGCCGTTG-AGTTGAGTGTAA
1 TTGGCAGATA-ACCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
* *
5734 TCGAACTCAAAGGTCTTT
65 TCGAACTCGAGGGTC--T
* * * *
5752 ATTAGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCAAAGCTGAGTGTA
1 -TTGGCAGATAA-CCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTA
*
5817 ATTGAACTCGAGGGTCT
64 ATCGAACTCGAGGGTCT
* * * * ** * * *
5834 TTGGCAGATAGCCCTTCTAGCCTTGAGTTATACCACAAATGATGTGCCATTGAA-TTGAGTGTAA
1 TTGGCAGATA-ACCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
*
5898 TCGAACTC-AAGGTCT
65 TCGAACTCGAGGGTCT
* * * * *
5913 TTGTTGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTACCCTCAAAGTTGAGTGT
1 TTG--GCAGATAA-CCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGT
*
5978 AATCGAACTCGAGTGTCT
63 AATCGAACTCGAGGGTCT
* * * * * ** * *
5996 TTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATAATGTG-CCTTTAAGCTGAGCGTAG
1 TTGGCAGATA-ACCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
*
6060 TTGAACTCGCA-GGTCT
65 TCGAACTCG-AGGGTCT
* * * * * ** ** *
6076 TTGGCAGATAGCCCTTTTCGACTTAAGTTATACTGTAAATGA--T---CTTTAAGCTGAGCATAG
1 TTGGCAGATA-ACCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
*
6136 TCGAACTCGAAGGTCTT
65 TCGAACTCGAGGGTC-T
* * * * *
6153 TTAGTGACAG-TAACCCTTCTAGCCTTGAGTTATGCTGTAAATGA--T-ACCTCTG-AGCTGAGC
1 TT-G-G-CAGATAA-CCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTC-GAAGCTGAGT
* * *
6213 GTAGTCGAACTCAAAGGTCTT
61 GTAATCGAACTCGAGGGTC-T
* * ** * * * *
6234 TTGGTCACATATAACCCTTCTAGCCTTGGGTTATGCTGTAAATGATGTTCCCACGAAGCTGAGTT
1 TTGG---CAGATAA-CCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTG
* *
6299 TTATCGAACTTGAGGGTCT
62 TAATCGAACTCGAGGGTCT
* * * * * * * * *
6318 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGTTGCAAATGATGT-ACCT-GGAGTTGAGCGTAG
1 TTGGCAGATA-ACCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
*
6381 TCGAACTCGAAGGTCTTT
65 TCGAACTCGAGGGTC--T
* * * *
6399 GGTTGGCAAATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATATGCCCTC-AAGCTGAGTGT
1 --TTGGCAGATAA-CCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGT
*
6463 AATCGAACTTGAGGGAT-T
63 AATCGAACTCGAGGG-TCT
*** * * * * * * *
6481 TTTTTATATATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGAAGTG-CCTTGGAGCTGAGCGT
1 TTGGCAGATA-A--CCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGT
* * * *
6545 AGTCAAACTCGAAGGTATT
63 AATCGAACTCGAGGGT-CT
* * * ** *
6564 TTGGTGACAAATAACCTTCTAGCCTTGAGTTATGCTATAAATGATGTGCCCTCGAAGCTGAGTAT
1 TT-G-G-CAGATAACCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGT
*
6629 AATCGAACTTGAGGGTCT
63 AATCGAACTCGAGGGTCT
* * * * * ** *
6647 TTGGCATATAGACCTTCTCGACATAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCATAG
1 TTGGCAGATA-ACCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
* *
6711 TCGAACTCGAAGGTTTT
65 TCGAACTCG-AGGGTCT
*
6728 GGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
1 --TTGGCAGATAA-CCTTCTAGACTTAAGTTATGCTGCAAATG
6771 TTATCTTAAA
Statistics
Matches: 874, Mismatches: 173, Indels: 105
0.76 0.15 0.09
Matches are distributed among these distances:
75 1 0.00
76 28 0.03
77 3 0.00
78 2 0.00
79 82 0.09
80 159 0.18
81 229 0.26
82 106 0.12
83 158 0.18
84 77 0.09
85 25 0.03
86 4 0.00
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (80 bp):
TTGGCAGATAACCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAAT
CGAACTCGAGGGTCT
Found at i:10881 original size:21 final size:21
Alignment explanation
Indices: 10854--10904 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
10844 ATGAAAATGA
*
10854 AAAAAATATTAAGAAAAAAT-
1 AAAAAATATTAACAAAAAATC
10874 AAATAAATATTAACAAAGAAATC
1 AAA-AAATATTAACAAA-AAATC
10897 AAAAAATA
1 AAAAAATA
10905 AGTAAAAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 3 0.11
21 12 0.44
22 9 0.33
23 3 0.11
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.20
Consensus pattern (21 bp):
AAAAAATATTAACAAAAAATC
Found at i:12060 original size:3 final size:3
Alignment explanation
Indices: 12052--12098 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
12042 ATAAATAAAA
**
12052 AAT AAT AAT AAT AAT AAT AAAT ACC AAT AAT -AT AAT AAT ATAT AAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT A-AT AAT
12098 A
1 A
12099 CATTTCAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
2 2 0.05
3 29 0.78
4 6 0.16
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:12073 original size:30 final size:33
Alignment explanation
Indices: 12037--12098 Score: 85
Period size: 30 Copynumber: 1.9 Consensus size: 33
12027 AATGAAATTA
12037 AATAAATA-AATAA-AAAATAATA-ATAATAAT
1 AATAAATACAATAATAAAATAATATATAATAAT
*
12067 AATAAATACCAATAATATAATAATATATAATA
1 AATAAATA-CAATAATAAAATAATATATAATA
12099 CATTTCAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 8 0.30
32 5 0.19
33 8 0.30
34 6 0.22
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (33 bp):
AATAAATACAATAATAAAATAATATATAATAAT
Found at i:12208 original size:33 final size:33
Alignment explanation
Indices: 12156--12229 Score: 107
Period size: 33 Copynumber: 2.3 Consensus size: 33
12146 CAAAAACTAT
12156 ATATTATATAGTTTCCAAAAATG-ATTTAAAAA
1 ATATTATATAGTTTCCAAAAATGTATTTAAAAA
* *
12188 ATATTATATGAGTTTTCAAAAATGTTTTTAAAAA
1 ATATTATAT-AGTTTCCAAAAATGTATTTAAAAA
12222 ATA-TATAT
1 ATATTATAT
12230 TATATAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
32 9 0.24
33 18 0.47
34 11 0.29
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (33 bp):
ATATTATATAGTTTCCAAAAATGTATTTAAAAA
Found at i:12242 original size:38 final size:37
Alignment explanation
Indices: 12122--12354 Score: 192
Period size: 38 Copynumber: 6.2 Consensus size: 37
12112 TTTTTTAACT
* * *
12122 TTATATTATTTTTCTAAAAT-TTTCCAAAAACTATATA
1 TTATATAATTTTTCAAAAATGTTT-TAAAAACTATATA
* * *
12159 TTATAT-AGTTTCCAAAAATGATTT-AAAA--A-ATA
1 TTATATAATTTTTCAAAAATGTTTTAAAAACTATATA
* * *
12191 TTATATGAGTTTTCAAAAATGTTTTTAAAAAATATATA
1 TTATATAATTTTTCAAAAATG-TTTTAAAAACTATATA
*
12229 TTATATAATTTTTCAAAAATGTTTTTTATTTAAAACCATATA
1 TTATATAATTTTTCAAAAATG--TTTTA---AAAACTATATA
* *
12271 TTATATAATTTTTCAAAACTGTTTTAAAAACTATTTA
1 TTATATAATTTTTCAAAAATGTTTTAAAAACTATATA
* *
12308 TTATATATTTATTTTC-AAAGTGTTTTAAAAACTATAATA
1 TTATATA-AT-TTTTCAAAAATGTTTTAAAAACTAT-ATA
12347 TATATATA
1 T-TATATA
12355 TATATATATA
Statistics
Matches: 164, Mismatches: 17, Indels: 27
0.79 0.08 0.13
Matches are distributed among these distances:
32 9 0.05
33 14 0.09
34 3 0.02
35 8 0.05
36 10 0.06
37 25 0.15
38 41 0.25
39 14 0.09
40 11 0.07
42 29 0.18
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (37 bp):
TTATATAATTTTTCAAAAATGTTTTAAAAACTATATA
Found at i:12282 original size:42 final size:39
Alignment explanation
Indices: 12188--12295 Score: 137
Period size: 42 Copynumber: 2.7 Consensus size: 39
12178 GATTTAAAAA
* * *
12188 ATATTATATGAGTTTTCAAAAATG-TTTTTAAAAAATAT
1 ATATTATATAATTTTTCAAAAATGTTTTTTAAAAAACAT
*
12226 ATATTATATAATTTTTCAAAAATGTTTTTTATTTAAAACCAT
1 ATATTATATAATTTTTCAAAAATGTTTTTTA---AAAAACAT
*
12268 ATATTATATAATTTTTCAAAACTGTTTT
1 ATATTATATAATTTTTCAAAAATGTTTT
12296 AAAAACTATT
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
38 22 0.36
39 6 0.10
42 33 0.54
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.49
Consensus pattern (39 bp):
ATATTATATAATTTTTCAAAAATGTTTTTTAAAAAACAT
Found at i:12351 original size:2 final size:2
Alignment explanation
Indices: 12340--12373 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
12330 TTTTAAAAAC
12340 TA TA -A 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 TA T
12374 TTCCAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15300 original size:28 final size:30
Alignment explanation
Indices: 15259--15342 Score: 84
Period size: 28 Copynumber: 2.8 Consensus size: 30
15249 GGTTGTATAG
15259 TTTAAGTACATATTTTGACATAAAAT-ACT
1 TTTAAGTACATATTTTGACATAAAATAACT
* * *
15288 TTT-AGTACCTATTCTGACTAAAAATATAACT
1 TTTAAGTACATATTTTGAC-ATAAA-ATAACT
**
15319 TTTAAGTATTTATTTTGAC-TAAAA
1 TTTAAGTACATATTTTGACATAAAA
15343 AATAATTTAG
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
28 13 0.30
29 8 0.18
30 5 0.11
31 6 0.14
32 12 0.27
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (30 bp):
TTTAAGTACATATTTTGACATAAAATAACT
Found at i:15341 original size:32 final size:31
Alignment explanation
Indices: 15259--15347 Score: 103
Period size: 32 Copynumber: 2.9 Consensus size: 31
15249 GGTTGTATAG
*
15259 TTTAAGTACATATTTTGAC-ATAAAAT-ACT
1 TTTAAGTACATATTTTGACTAAAAAATAACT
* *
15288 TTT-AGTACCTATTCTGACTAAAAATATAACT
1 TTTAAGTACATATTTTGACTAAAAA-ATAACT
**
15319 TTTAAGTATTTATTTTGACTAAAAAATAA
1 TTTAAGTACATATTTTGACTAAAAAATAA
15348 TTTAGGTACT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
28 13 0.26
29 7 0.14
30 2 0.04
31 10 0.20
32 18 0.36
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.42
Consensus pattern (31 bp):
TTTAAGTACATATTTTGACTAAAAAATAACT
Found at i:21830 original size:334 final size:338
Alignment explanation
Indices: 21203--21882 Score: 1058
Period size: 334 Copynumber: 2.0 Consensus size: 338
21193 ATAGGAGTGA
* * *
21203 GAACATAGTTGAGTGATGAATGATGTAATTTATCCATAAAATGGTAGTTTCGTTAAGTTTCTATC
1 GAACATAGTTGAATGATGAATGATGTAATTTATCCATAAAATGGAAGTTTCGTTAAGTTTCTAGC
* *
21268 TATGAGTACTAAAATGAAACAAAAAGTAAACATTAGATATAATTTTGGGGAAAAAATAAAAGGTT
66 TATGAGTACTAAAATGAAACAAAAAGTAAACATTAGACATAATTTT-GGGAAAAAATAAAAGATT
*
21333 AAATACTAAAACGGAACAAAAGTGATAGTTTAGATGCTAAATGTAGAGTTTATCCATAAAATACT
130 AAATACTAAAACGGAACAAAAGTGATAG-TTAGATACTAAATGTAGAGTTTATCCATAAAATACT
* *
21398 TAAGGCTTTTTTTTAAACTTTAAGTAGTAATTCAATATGTTTTAACATAGGTAAAATAATAATAA
194 TAACGCTTTTTCTTAAACTTTAAGTAGTAATTCAATATGTTTTAACATAGGTAAAATAATAATAA
*
21463 TAATAATAATTTATTGTAGTGAAACTTAAAAAAAATGGCAGTTAAATC-TTAATGAACCATTGAT
259 TAATAATAATTTATTGTAGTGAAACTTAAAAAAAATAGCAGTTAAATCGTTAATG-ACCATTGAT
21527 GATGAAGATAAAATAT
323 GATGAAGATAAAATAT
* *
21543 GAACATAGTTGAATGATGAATGATGTAATTTATCCGT-AAATGGAAGTTTCGTTTAGTTTCTAGC
1 GAACATAGTTGAATGATGAATGATGTAATTTATCCATAAAATGGAAGTTTCGTTAAGTTTCTAGC
* *
21607 TATGGGTACT-AAATGAAAC-AAAAGTAAACATTAGACATAGTTTT-GGAAAAAATAAAAGATTA
66 TATGAGTACTAAAATGAAACAAAAAGTAAACATTAGACATAATTTTGGGAAAAAATAAAAGATTA
*
21669 AATACTAAAACGGAACAAAAGTGATCA-TTAGATACTAAATGTATAGTTTATCCATAAAATACTT
131 AATACTAAAACGGAACAAAAGTGAT-AGTTAGATACTAAATGTAGAGTTTATCCATAAAATACTT
21733 AACGC-TTTTCTTAAATCTTTAAGTAGTAATTCAATATGTTTTAACAT-GG-ATAAATAATAA-A
195 AACGCTTTTTCTTAAA-CTTTAAGTAGTAATTCAATATGTTTTAACATAGGTA-AAATAATAATA
*
21794 A-AATAATAATTTGTTGTAGTGAAACTTAAAAAAAAAATTAGCAGTTAAATCGTTAATGACCATT
258 ATAATAATAATTTATTGTAGTGAAACTT--AAAAAAAA-TAGCAGTTAAATCGTTAATGACCATT
21858 GATGATGAAGATAAAATAT
320 GATGATGAAGATAAAATAT
*
21877 CAACAT
1 GAACAT
21883 TATAAATCTT
Statistics
Matches: 317, Mismatches: 16, Indels: 20
0.90 0.05 0.06
Matches are distributed among these distances:
331 25 0.08
332 3 0.01
333 28 0.09
334 112 0.35
335 48 0.15
336 1 0.00
337 23 0.07
338 9 0.03
339 33 0.10
340 35 0.11
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (338 bp):
GAACATAGTTGAATGATGAATGATGTAATTTATCCATAAAATGGAAGTTTCGTTAAGTTTCTAGC
TATGAGTACTAAAATGAAACAAAAAGTAAACATTAGACATAATTTTGGGAAAAAATAAAAGATTA
AATACTAAAACGGAACAAAAGTGATAGTTAGATACTAAATGTAGAGTTTATCCATAAAATACTTA
ACGCTTTTTCTTAAACTTTAAGTAGTAATTCAATATGTTTTAACATAGGTAAAATAATAATAATA
ATAATAATTTATTGTAGTGAAACTTAAAAAAAATAGCAGTTAAATCGTTAATGACCATTGATGAT
GAAGATAAAATAT
Found at i:26808 original size:23 final size:21
Alignment explanation
Indices: 26754--26836 Score: 78
Period size: 21 Copynumber: 3.9 Consensus size: 21
26744 AGCAGAACCC
* *
26754 CAAGGGGGTATCGATTCCCCT
1 CAAGGGGGAATCGGTTCCCCT
***
26775 GTGGGGGGAATCGGTTCCCCTT
1 CAAGGGGGAATCGGTTCCCC-T
26797 CAAAGGGGGAATCGGTT-CCCT
1 C-AAGGGGGAATCGGTTCCCCT
* *
26818 CAGGGGGGAATCGATTCCC
1 CAAGGGGGAATCGGTTCCC
26837 TCTGCACCAA
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
20 13 0.27
21 19 0.39
22 4 0.08
23 13 0.27
ACGTcount: A:0.18, C:0.25, G:0.35, T:0.22
Consensus pattern (21 bp):
CAAGGGGGAATCGGTTCCCCT
Found at i:26826 original size:20 final size:21
Alignment explanation
Indices: 26777--26838 Score: 81
Period size: 20 Copynumber: 2.9 Consensus size: 21
26767 ATTCCCCTGT
26777 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTT-CCC-TCAA
*
26800 AGGGGGAATCGGTTCCCTC-A
1 GGGGGGAATCGGTTCCCTCAA
*
26820 GGGGGGAATCGATTCCCTC
1 GGGGGGAATCGGTTCCCTC
26839 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.35, T:0.21
Consensus pattern (21 bp):
GGGGGGAATCGGTTCCCTCAA
Found at i:39618 original size:24 final size:24
Alignment explanation
Indices: 39591--39693 Score: 85
Period size: 24 Copynumber: 4.5 Consensus size: 24
39581 ATTCACTACT
*
39591 ACAAATTCCATCCCACTCACCTTC
1 ACAAATTCCATCTCACTCACCTTC
*
39615 AC-AATTGCAT-TCACT-A-C-T-
1 ACAAATTCCATCTCACTCACCTTC
39633 ACAAATTCCATCTCACTCACCTTC
1 ACAAATTCCATCTCACTCACCTTC
* * **
39657 ACAGAA-TCCATCACATTCATTTTC
1 ACA-AATTCCATCTCACTCACCTTC
*
39681 ACAAATTTCATCT
1 ACAAATTCCATCT
39694 TCACAAAGTC
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
18 2 0.03
19 8 0.13
20 6 0.10
21 2 0.03
22 5 0.08
23 10 0.16
24 27 0.44
25 2 0.03
ACGTcount: A:0.32, C:0.35, G:0.02, T:0.31
Consensus pattern (24 bp):
ACAAATTCCATCTCACTCACCTTC
Found at i:39630 original size:42 final size:42
Alignment explanation
Indices: 39571--39659 Score: 169
Period size: 42 Copynumber: 2.1 Consensus size: 42
39561 TCAAAATCCA
39571 TCACAATTGCATTCACTACTACAAATTCCATCCCACTCACCT
1 TCACAATTGCATTCACTACTACAAATTCCATCCCACTCACCT
*
39613 TCACAATTGCATTCACTACTACAAATTCCATCTCACTCACCT
1 TCACAATTGCATTCACTACTACAAATTCCATCCCACTCACCT
39655 TCACA
1 TCACA
39660 GAATCCATCA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.29
Consensus pattern (42 bp):
TCACAATTGCATTCACTACTACAAATTCCATCCCACTCACCT
Found at i:39636 original size:18 final size:18
Alignment explanation
Indices: 39573--39636 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 18
39563 AAAATCCATC
39573 ACAATTGCATTCACTACT
1 ACAATTGCATTCACTACT
* *
39591 ACAAATTCCATCCCACTCACCTT
1 AC-AATTGCAT-TCACT-A-C-T
39614 CACAATTGCATTCACTACT
1 -ACAATTGCATTCACTACT
39633 ACAA
1 ACAA
39637 ATTCCATCTC
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
18 6 0.17
19 8 0.22
20 5 0.14
21 2 0.06
22 5 0.14
23 8 0.22
24 2 0.06
ACGTcount: A:0.34, C:0.34, G:0.03, T:0.28
Consensus pattern (18 bp):
ACAATTGCATTCACTACT
Found at i:39696 original size:15 final size:15
Alignment explanation
Indices: 39672--39711 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
39662 ATCCATCACA
* *
39672 TTCATTTTCACAAAT
1 TTCATCTTCACAAAG
39687 TTCATCTTCACAAAG
1 TTCATCTTCACAAAG
*
39702 TCCATCTTCA
1 TTCATCTTCA
39712 TCTCATTCTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.30, C:0.28, G:0.03, T:0.40
Consensus pattern (15 bp):
TTCATCTTCACAAAG
Found at i:39848 original size:24 final size:24
Alignment explanation
Indices: 39821--39876 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
39811 TACCACAGGT
*
39821 TCCATCTCACTCACCTTCACAAAA
1 TCCATCTCACTCACCATCACAAAA
* * *
39845 TCCATCACACTTACCATCACAAAT
1 TCCATCTCACTCACCATCACAAAA
*
39869 TTCATCTC
1 TCCATCTC
39877 CATAAATACC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.32, C:0.39, G:0.00, T:0.29
Consensus pattern (24 bp):
TCCATCTCACTCACCATCACAAAA
Found at i:39925 original size:15 final size:15
Alignment explanation
Indices: 39907--39936 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39897 TCCTTTACAA
*
39907 TCATAGATTCTATCT
1 TCATAAATTCTATCT
39922 TCATAAATTCTATCT
1 TCATAAATTCTATCT
39937 CCGTGTACTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.20, G:0.03, T:0.47
Consensus pattern (15 bp):
TCATAAATTCTATCT
Found at i:42986 original size:2 final size:2
Alignment explanation
Indices: 42979--43004 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42969 TTTTGTAAAA
42979 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
43005 TTTGAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43448 original size:22 final size:21
Alignment explanation
Indices: 43400--43441 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
43390 TTTTTGTTTA
* *
43400 AATTTTTTAAGTATTATTAAT
1 AATTTTTTAAGAATAATTAAT
43421 AATTTTTTAA-AATAATTAAT
1 AATTTTTTAAGAATAATTAAT
43441 A
1 A
43442 TCATTTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
AATTTTTTAAGAATAATTAAT
Found at i:44838 original size:25 final size:25
Alignment explanation
Indices: 44802--44856 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
44792 TCATATTGGA
* *
44802 AGTACTATAAGATTGTCCTCACTTC
1 AGTACTAGAAGATTGTCATCACTTC
44827 AGTACTAGAAGATTGTCATCACTTC
1 AGTACTAGAAGATTGTCATCACTTC
44852 AGTAC
1 AGTAC
44857 AGATTTCCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.33
Consensus pattern (25 bp):
AGTACTAGAAGATTGTCATCACTTC
Found at i:47949 original size:11 final size:11
Alignment explanation
Indices: 47933--47967 Score: 70
Period size: 11 Copynumber: 3.2 Consensus size: 11
47923 AAAAATAGTA
47933 AATTAAATAAT
1 AATTAAATAAT
47944 AATTAAATAAT
1 AATTAAATAAT
47955 AATTAAATAAT
1 AATTAAATAAT
47966 AA
1 AA
47968 ACTATTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AATTAAATAAT
Found at i:50580 original size:22 final size:22
Alignment explanation
Indices: 50537--50580 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
50527 TTAGTAAAAA
* *
50537 TTATCTAAAATATTATTATTTT
1 TTATCTAAAACATAATTATTTT
50559 TTATCTAAAACATCAATT-TTTT
1 TTATCTAAAACAT-AATTATTTT
50581 AATATATCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (22 bp):
TTATCTAAAACATAATTATTTT
Found at i:55131 original size:14 final size:14
Alignment explanation
Indices: 55089--55131 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
55079 GATCTTATAG
55089 ATTTAAATAATATATT
1 ATTTAAAT-ATA-ATT
*
55105 TTTATAAATATAATT
1 ATT-TAAATATAATT
55120 ATTTAAATATAA
1 ATTTAAATATAA
55132 CTTTTGCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 9 0.38
15 5 0.21
16 5 0.21
17 5 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATTTAAATATAATT
Found at i:62285 original size:13 final size:13
Alignment explanation
Indices: 62267--62298 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
62257 GATTAATTAA
62267 ACAAGAAAACAAT
1 ACAAGAAAACAAT
62280 ACAAGAAAACAAT
1 ACAAGAAAACAAT
62293 A-AAGAA
1 ACAAGAA
62299 TAACCATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.72, C:0.12, G:0.09, T:0.06
Consensus pattern (13 bp):
ACAAGAAAACAAT
Found at i:66018 original size:16 final size:16
Alignment explanation
Indices: 65997--66027 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
65987 ATAAATAAAT
65997 GAACATAAACGAACAC
1 GAACATAAACGAACAC
66013 GAACATAAACGAACA
1 GAACATAAACGAACA
66028 AATTTTTTTT
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:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:66108 original size:10 final size:10
Alignment explanation
Indices: 66093--66167 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
66083 CATTTAATAA
66093 ATAAACGAAC
1 ATAAACGAAC
66103 ATAAACGAAC
1 ATAAACGAAC
*
66113 ----GCGAAC
1 ATAAACGAAC
66119 ATAAACGAAC
1 ATAAACGAAC
** *
66129 ACGAAC-ATAA
1 ATAAACGA-AC
66139 ATGAACACGAAC
1 AT-AA-ACGAAC
66151 ATAAACGAAC
1 ATAAACGAAC
66161 ATAAACG
1 ATAAACG
66168 TTGGAGACCC
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
6 5 0.10
9 1 0.02
10 34 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.56, C:0.21, G:0.13, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:66119 original size:16 final size:16
Alignment explanation
Indices: 66097--66161 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
66087 TAATAAATAA
66097 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
66113 GCGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
66129 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
66145 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
66161 A
1 A
66162 TAAACGTTGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.55, C:0.23, G:0.14, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:66923 original size:10 final size:10
Alignment explanation
Indices: 66908--66955 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
66898 ATAAATGAAT
66908 GAACATAAAC
1 GAACATAAAC
66918 GAACATAACCGAAC
1 GAACAT-A---AAC
66932 GAACATAAAC
1 GAACATAAAC
*
66942 GAACATAACC
1 GAACATAAAC
66952 GAAC
1 GAAC
66956 GTTCACGAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.08
Consensus pattern (10 bp):
GAACATAAAC
Found at i:66932 original size:14 final size:14
Alignment explanation
Indices: 66915--66956 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
66905 AATGAACATA
66915 AACGAACATAACCG
1 AACGAACATAACCG
66929 AACGAACAT-A---
1 AACGAACATAACCG
66939 AACGAACATAACCG
1 AACGAACATAACCG
66953 AACG
1 AACG
66957 TTCACGAACG
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
10 9 0.38
11 1 0.04
13 1 0.04
14 13 0.54
ACGTcount: A:0.52, C:0.26, G:0.14, T:0.07
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:66935 original size:24 final size:24
Alignment explanation
Indices: 66908--66956 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
66898 ATAAATGAAT
66908 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
66932 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
66956 G
1 G
66957 TTCACGAACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.53, C:0.24, G:0.14, T:0.08
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:67709 original size:77 final size:79
Alignment explanation
Indices: 67592--67756 Score: 262
Period size: 77 Copynumber: 2.1 Consensus size: 79
67582 TATTGACACC
* * *
67592 TTAAATCTTAATTTTATTTTTATTTAAAATCACCTAAAATTTTATAAATATAATATTGAATACTT
1 TTAAATCTTAATTTTATTTTTATTGAAAAGCACCTAAAATTTTATAAATATAATATTAAATACTT
67657 TAAATTTTTATTAT
66 TAAATTTTTATTAT
*
67671 TTAAATCTTAA-TTT-TTTTTATTGAAAAGCACCTCAAATTTTATAAATATAATATTAAATACTT
1 TTAAATCTTAATTTTATTTTTATTGAAAAGCACCTAAAATTTTATAAATATAATATTAAATACTT
*
67734 TAATTTTTTATTAT
66 TAAATTTTTATTAT
67748 TTAATATCT
1 TTAA-ATCT
67757 ATCATCTGTT
Statistics
Matches: 80, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
77 62 0.77
78 7 0.09
79 11 0.14
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (79 bp):
TTAAATCTTAATTTTATTTTTATTGAAAAGCACCTAAAATTTTATAAATATAATATTAAATACTT
TAAATTTTTATTAT
Found at i:72045 original size:10 final size:10
Alignment explanation
Indices: 72030--72104 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
72020 CATTTAATAA
72030 ATAAACGAAC
1 ATAAACGAAC
72040 ATAAACGAAC
1 ATAAACGAAC
72050 ----ACGAAC
1 ATAAACGAAC
72056 ATAAACGAAC
1 ATAAACGAAC
** *
72066 ACGAAC-ATAA
1 ATAAACGA-AC
72076 ATGAACACGAAC
1 AT-AA-ACGAAC
72088 ATAAACGAAC
1 ATAAACGAAC
*
72098 ATCAACG
1 ATAAACG
72105 TTAGAGATCC
Statistics
Matches: 50, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 34 0.68
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.56, C:0.23, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:72055 original size:16 final size:16
Alignment explanation
Indices: 72034--72098 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
72024 TAATAAATAA
72034 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
72050 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
72066 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
72082 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
72098 A
1 A
72099 TCAACGTTAG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:73113 original size:24 final size:24
Alignment explanation
Indices: 73085--73135 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
73075 GATTGGGTTA
73085 AACATAAAT-GAAAGAACATAAACG
1 AACAT-AATCGAAAGAACATAAACG
* *
73109 AACATAATCGAACGAACATAACCG
1 AACATAATCGAAAGAACATAAACG
73133 AAC
1 AAC
73136 GAACATAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.57, C:0.20, G:0.12, T:0.12
Consensus pattern (24 bp):
AACATAATCGAAAGAACATAAACG
Found at i:73122 original size:14 final size:14
Alignment explanation
Indices: 73105--73150 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
73095 AAAGAACATA
*
73105 AACGAACATAATCG
1 AACGAACATAACCG
73119 AACGAACATAACCG
1 AACGAACATAACCG
73133 AACGAACATAACCG
1 AACGAACATAACCG
73147 AACG
1 AACG
73151 TTCACGAACG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.50, C:0.26, G:0.15, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:75886 original size:36 final size:34
Alignment explanation
Indices: 75831--75909 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
75821 TTTAAATAGT
*
75831 TATTATTTTTTATATT--AAT-ATATTTATGTAAA
1 TATTATTTTTT-TATTAAAATAATATTTATATAAA
*
75863 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATTAAAATAATATTTATATAAA
*
75897 TATTATTTATTTA
1 TATTATTTTTTTA
75910 GAATTATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
31 4 0.10
32 11 0.27
33 3 0.07
34 23 0.56
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (34 bp):
TATTATTTTTTTATTAAAATAATATTTATATAAA
Found at i:77662 original size:21 final size:21
Alignment explanation
Indices: 77632--77679 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
77622 GCAGGGGTAC
* *
77632 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
77653 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
77674 ATGCCA
1 ATGCCA
77680 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:77709 original size:21 final size:21
Alignment explanation
Indices: 77683--77776 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
77673 TATGCCATCT
* *
77683 CCGCAGGGTTACATTCCAAGC
1 CCGCAGGGTTACATGCCTAGC
*
77704 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
77725 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
77746 CCGTCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
77767 CCGCAGGGTT
1 CCGCAGGGTT
77777 TTATACCATA
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
20 2 0.03
21 64 0.94
22 2 0.03
ACGTcount: A:0.19, C:0.34, G:0.26, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:80735 original size:12 final size:13
Alignment explanation
Indices: 80702--80739 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
80692 AAATACATAA
80702 ATATATTTAATAT
1 ATATATTTAATAT
*
80715 ATTTATTTAATAT
1 ATATATTTAATAT
80728 A-ATATTTAATAT
1 ATATATTTAATAT
80740 TATTAGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATATATTTAATAT
Done.