Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397395.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1097.0, 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: 26056
ACGTcount: A:0.25, C:0.08, G:0.09, T:0.25
Warning! 8630 characters in sequence are not A, C, G, or T
Found at i:3867 original size:171 final size:171
Alignment explanation
Indices: 3545--4023 Score: 370
Period size: 171 Copynumber: 2.8 Consensus size: 171
3535 NNNNNGGGTA
* * * ** ** *** * * *
3545 ACTATAAATAGACTTTTCTTGCCAATGGATATCTTTTTTTTCACGTTTCTCGAGGTAAATAATCA
1 ACTATAAATTGACATTTCTTCCCAATGGATATCTTTTCCTTCACGTTTCTTAAACCAGACATTCA
* * * * * ** *
3610 ATTATAATCTATTTTAATAGAAAATATAAAAAAATTGAAATTAAAATCAATTACGATGTTATAAN
66 ATTATAATTTATTTTAATAAAAAATATAAAAAAATTCAAATTAAAATAAATTATGGGGTTATAAA
********* ** * * *
3675 NNNNNNNNNTGCGACTAATAAGGCTTTTGAAGGTATAGGTG
131 ATTATTTAATGCGGGTAATAAGGCTTTCGAAAGCATAGGTG
* * * **
3716 ACTATAAATTGACTTTTCTTCCCAATGGATA-CATTTTTCTTCACGTTTCTTCAAGTAGACATTC
1 ACTATAAATTGACATTTCTTCCCAATGGATATC-TTTTCCTTCACGTTTCTTAAACCAGACATTC
* **
3780 AATTATAATTT-TTTTAATAAACAACATA-AAAAAAATTCAATTTAAAATAAATTATGTTGTTAT
65 AATTATAATTTATTTTAATAAA-AA-ATATAAAAAAATTCAAATTAAAATAAATTATGGGGTTAT
*
3843 AAAATTATTTAATGCGGGTAATAAGGCTTTCGAAAGCATGGGTG
128 AAAATTATTTAATGCGGGTAATAAGGCTTTCGAAAGCATAGGTG
********** * * *
3887 ACTNNNNNNNNNNATTTCTTGCCAATGGATATCTTTTCCTTCATGTTTCTTAAACCAGACATTTA
1 ACTATAAATTGACATTTCTTCCCAATGGATATCTTTTCCTTCACGTTTCTTAAACCAGACATTCA
* * *
3952 ATTATAATTTATTTTATTTAAAAATATAAAAAAATTCAAATTAAAATCAATTATGGGGTTATAAA
66 ATTATAATTTATTTTAATAAAAAATATAAAAAAATTCAAATTAAAATAAATTATGGGGTTATAAA
4017 ATTATTT
131 ATTATTT
4024 NNNNNNNNNN
Statistics
Matches: 246, Mismatches: 56, Indels: 12
0.78 0.18 0.04
Matches are distributed among these distances:
170 13 0.05
171 221 0.90
172 12 0.05
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.38
Consensus pattern (171 bp):
ACTATAAATTGACATTTCTTCCCAATGGATATCTTTTCCTTCACGTTTCTTAAACCAGACATTCA
ATTATAATTTATTTTAATAAAAAATATAAAAAAATTCAAATTAAAATAAATTATGGGGTTATAAA
ATTATTTAATGCGGGTAATAAGGCTTTCGAAAGCATAGGTG
Found at i:7855 original size:104 final size:94
Alignment explanation
Indices: 7742--7941 Score: 206
Period size: 104 Copynumber: 2.0 Consensus size: 94
7732 TTCTTAAAGT
* * *
7742 AGACATTCAATTGTAATTT-TTTTA-ATAAAGAATATAAAAAAAATTCAATTTAAAATTAATTAT
1 AGACATTCAATTATAATTTATTTTATATAAA-AATAT-AAAAAAATTCAAATTAAAATCAATTAT
* *
7805 GTGGTTATAAAATTATTTAATGCGAGTAATA
64 GGGGTTATAAAATTATTTAATGAGAGTAATA
* * *
7836 AGNNNNNNNNNNACATTCAATTATAATTTATTTTATTTAAAAATATAAAAATATTTAAATTAAAA
1 AG----------ACATTCAATTATAATTTATTTTATATAAAAATATAAAAAAATTCAAATTAAAA
7901 TCAATTATGGGGTTATAAAATTATTTAATGAGAGTAATA
56 TCAATTATGGGGTTATAAAATTATTTAATGAGAGTAATA
7940 AG
1 AG
7942 GCTTTCGAAG
Statistics
Matches: 86, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
94 2 0.02
104 70 0.81
105 10 0.12
106 4 0.05
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.38
Consensus pattern (94 bp):
AGACATTCAATTATAATTTATTTTATATAAAAATATAAAAAAATTCAAATTAAAATCAATTATGG
GGTTATAAAATTATTTAATGAGAGTAATA
Found at i:11444 original size:170 final size:170
Alignment explanation
Indices: 10695--11514 Score: 673
Period size: 171 Copynumber: 4.8 Consensus size: 170
10685 NNNNNNNNNN
* * * * * * *
10695 AAATCAATTATGAGGTTATAAAATCATTAAAAGGGAGTGATAAGGC-TTCTGAAGGCGTGGATGA
1 AAATCAATTATGAGGTTATAAAAACATTTAATGCGAGTAATAAGGCTTTC-GAAGGCATGGGTGA
********** * * * *
10759 CTATAAATGGACTTTTCTNNNNNNNNNNTATC-TTTTTCTTCACGTTTCTTAAGGTAAACAATCA
65 CTATAAATGGACTTTTCTTGCCAATGGATA-CATTTTTCTTCACGTTTCTCAAAGTAGACATTCA
* **
10823 ATTATAATTTGTTTTAATAGCAAATATA-AAAAAATTCAAATTA
129 ATTATAATCTG-TTTAATAAAAAATA-AGAAAAAATTCAAATTA
* * * * *
10866 AAATCAATTATGAGATTATAAAAAC--TTAATGCGACTAATAACGCTTTCAAAGGCATGAGTGAC
1 AAATCAATTATGAGGTTATAAAAACATTTAATGCGAGTAATAAGGCTTTCGAAGGCATGGGTGAC
* * * * * *
10929 TATAAATTGACTTTTCTTGCCAGTGGATACATTTTTGTTCATGTTTCTTAAAGTAGATATTCAAT
66 TATAAATGGACTTTTCTTGCCAATGGATACATTTTTCTTCACGTTTCTCAAAGTAGACATTCAAT
* * ********** *
10994 TATAATTTTTTTAATAAAAAATATANNNNNNNNNNAATTTA
131 TATAATCTGTTTAATAAAAAATA-AGAAAAAATTCAAATTA
* * ** * * *
11035 AAATCAATTATGTGGTTGTAAAATTATTTAATGCGAGTAATAAGGCTTCCTAAAGCATGGGTGAC
1 AAATCAATTATGAGGTTATAAAAACATTTAATGCGAGTAATAAGGCTTTCGAAGGCATGGGTGAC
* * * * * *
11100 TCTAAATGGACTTATCTTGCCAATGGATATC-TTTTCCTTCACATTTCTCAAGGTAGACATTTAA
66 TATAAATGGACTTTTCTTGCCAATGGATA-CATTTTTCTTCACGTTTCTCAAAGTAGACATTCAA
* * *
11164 TTATAATCTTTTTTAATAAAAAATATGAAAAAATTTAAATTA
130 TTATAATC-TGTTTAATAAAAAATAAGAAAAAATTCAAATTA
* **********
11206 AAATCGATTATGAGGTTATAAAAACATTTAATGNNNNNNNNNNGGCTTTCGAAGGCATGGGTGAC
1 AAATCAATTATGAGGTTATAAAAACATTTAATGCGAGTAATAAGGCTTTCGAAGGCATGGGTGAC
*
11271 TATAAATGGACTCTTCTTGCCAATGGATACATTTTTCTTCACGTTTCTCAAAGTAGACATTCAAT
66 TATAAATGGACTTTTCTTGCCAATGGATACATTTTTCTTCACGTTTCTCAAAGTAGACATTCAAT
**********
11336 TATAATCTGTTTAATAAAAAATANNNNNNNNNNCAAATTA
131 TATAATCTGTTTAATAAAAAATAAGAAAAAATTCAAATTA
* * * * *
11376 AAATCAATTATAAGGTTATAAAAACAATTAATGCGAGTTAA-AAGGCTTTCGTAGGCATAGGCGA
1 AAATCAATTATGAGGTTATAAAAACATTTAATGCGAG-TAATAAGGCTTTCGAAGGCATGGGTGA
* * *
11440 CTATAAATGGACTTTTCTTGTCAATGGATACATTTTTCTTCACGTTTCTTAAGGTAGACATTCAA
65 CTATAAATGGACTTTTCTTGCCAATGGATACATTTTTCTTCACGTTTCTCAAAGTAGACATTCAA
11505 TTATAATCTG
130 TTATAATCTG
11515 NNNNNNNNNN
Statistics
Matches: 506, Mismatches: 134, Indels: 19
0.77 0.20 0.03
Matches are distributed among these distances:
168 15 0.03
169 103 0.20
170 144 0.28
171 227 0.45
172 17 0.03
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.35
Consensus pattern (170 bp):
AAATCAATTATGAGGTTATAAAAACATTTAATGCGAGTAATAAGGCTTTCGAAGGCATGGGTGAC
TATAAATGGACTTTTCTTGCCAATGGATACATTTTTCTTCACGTTTCTCAAAGTAGACATTCAAT
TATAATCTGTTTAATAAAAAATAAGAAAAAATTCAAATTA
Found at i:12908 original size:171 final size:169
Alignment explanation
Indices: 12551--13440 Score: 815
Period size: 171 Copynumber: 5.2 Consensus size: 169
12541 NNNNNNNNNN
* * *
12551 AGGCATGGGTGACTACT-AATGGACCTGTT-TTACCCATGGATATCTTTTTCTTCACGTTTCTCA
1 AGGCATGGGTGACTA-TAAATGGA-CTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCTC-
* * * *
12614 AGATAGACATTCAATTATAATATGTTTTAATAAAAGTATAAAAAAATTCAAATCAAAATCAATTA
63 AGGTAGACATTCAATTATAATCTGTTTTAATAAAAATATAAAAAAATTCAAATTAAAATCAATTA
* * * * *
12679 TGAGGTTAT-TAAATCATTAAAAGTGAGTGATAAGGC-TTCTGA
128 TGAGGTTATAAAAAT-ATTTAAAGCGAGTAATAAGGCTTTC-AA
* * *
12721 AGGCGTGGGCGACTATAAATAGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCTCGAG
1 AGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCTC-AG
* * * *
12786 GCAAACAATCAATTATAATCTGTTTTAATAGAAAATATAAAAAAATTCAAATTAAAATCAAGTAT
65 GTAGACATTCAATTATAATCTGTTTTAATA-AAAATATAAAAAAATTCAAATTAAAATCAATTAT
* * * *
12851 GAGGTTATAAAAATATTTAATGCAACTAATAAGGCTTTCGA
129 GAGGTTATAAAAATATTTAAAGCGAGTAATAAGGCTTTCAA
********** *
12892 AGGCATGGGTGACTATAAANNNNNNNNNNTTGCCAATGGATA-CATTTTTCTTCACATTTCTTAC
1 AGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATC-TTTTTCTTCACGTTTC-T-C
* * *
12956 A-GTAGACATTCAATTATAAT-TTTTTTAAAAAAATATATAAAAAAAGTTCAATTTAAAATCAAT
63 AGGTAGACATTCAATTATAATCTGTTTTAATAAAA-ATATAAAAAAA-TTCAAATTAAAATCAAT
* * * *
13019 TATGTGGTTATAAAATTATTTAATGTGAGTAATAAGGCTTTCAA
126 TATGAGGTTATAAAAATATTTAAAGCGAGTAATAAGGCTTTCAA
* * * * * *
13063 AAGTATGGGTGACTCTAAATGGACATTTCTTGCCAATGGATATCTTTTCCTTTACGTTTCTCAAG
1 AGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCTC-AG
* * * * *
13128 CTAGACATTCAATTATAATCTATTTTATTTAAAAATATAAAAAAATTTAAATTAAATTCAATTAT
65 GTAGACATTCAATTATAATCTGTTTTA-ATAAAAATATAAAAAAATTCAAATTAAAATCAATTAT
* * **********
13193 GGGGTTATAAAATTATTTNNNNNNNNNNATAAGGCTTTCAA
129 GAGGTTATAAAAATATTTAAAGCGAGTAATAAGGCTTTCAA
* * * * *
13234 AGGTATGGGTGACTGTAAATGGACTTTTCTTGTCAATGGATA-CATTTTTCTTCATGTTTCTTAA
1 AGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATC-TTTTTCTTCACGTTTC-TCA
* ********* *
13298 GGTAAACATTCAATTATAATCTGTTNNNNNNNNNNATATAAAAAAATTCAACTTAAAATCAATTA
64 GGTAGACATTCAATTATAATCTGTT-TTAATAAAAATATAAAAAAATTCAAATTAAAATCAATTA
* *
13363 TGAGGTTATAAAAAAAATTTAAACCGAGTAATAAGGCTTTCAA
128 TGAGGTTAT-AAAAATATTTAAAGCGAGTAATAAGGCTTTCAA
*
13406 AGGCATGGGTTACTATAAATGGACTTTTCTTGCCA
1 AGGCATGGGTGACTATAAATGGACTTTTCTTGCCA
13441 NNNNNNNNNN
Statistics
Matches: 579, Mismatches: 122, Indels: 36
0.79 0.17 0.05
Matches are distributed among these distances:
169 9 0.02
170 99 0.17
171 386 0.67
172 80 0.14
173 5 0.01
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.35
Consensus pattern (169 bp):
AGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCTCAGG
TAGACATTCAATTATAATCTGTTTTAATAAAAATATAAAAAAATTCAAATTAAAATCAATTATGA
GGTTATAAAAATATTTAAAGCGAGTAATAAGGCTTTCAA
Found at i:13273 original size:342 final size:340
Alignment explanation
Indices: 12551--13440 Score: 912
Period size: 342 Copynumber: 2.6 Consensus size: 340
12541 NNNNNNNNNN
* * * *
12551 AGGCATGGGTGACTACT-AATGGACCTGTT-TTACCCATGGATATC-TTTTTCTTCACGTTTCTC
1 AGGCATGGGTGACTA-TAAATGGA-CTTTTCTTGCCAATGGATA-CATTTTTCTTCACGTTTCTT
* * *
12613 AAGATAGACATTCAATTATAATATGTTTTAATAAAAGTATAAAAAAATTCAAATCAAAATCAATT
63 AAG-TAGACATTCAATTATAATATGTTTTAAAAAAAATATAAAAAAATTCAAATTAAAATCAATT
* * * * * * * *
12678 ATGAGGTTATTAAATCATTAAAAGTGAGTGATAAGGC-TTCTGAAGGCGTGGGCGACTATAAATA
127 ATGAGGTTATAAAATAATTTAAAGTGAGTAATAAGGCTTTC-AAAGGCATGGGTGACTATAAATG
* *
12742 GACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCTCGAGGCAAACAATCAATTATAATCT
191 GACTTTTCTTGCCAATGGATATCTTTTCCTTCACGTTTCTCGAAGCAAACAATCAATTATAATCT
*
12807 GTTTTAATAGAAAATATAAAAAAATTCAAATTAAAATCAAGTATGAGGTTATAAAAATATTTAAT
256 ATTTTAATAGAAAATATAAAAAAATTCAAATTAAAATCAAGTATGAGGTTATAAAAATATTTAAT
*
12872 GCAACTAATAAGGCTTTCGA
321 GCAACTAATAAGGCTTTCAA
********** *
12892 AGGCATGGGTGACTATAAANNNNNNNNNNTTGCCAATGGATACATTTTTCTTCACATTTCTTACA
1 AGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATACATTTTTCTTCACGTTTCTTA-A
* *
12957 GTAGACATTCAATTATAAT-TTTTTTAAAAAAATATATAAAAAAAGTTCAATTTAAAATCAATTA
65 GTAGACATTCAATTATAATATGTTTTAAAAAAA-ATATAAAAAAA-TTCAAATTAAAATCAATTA
* * * * * *
13021 TGTGGTTATAAAATTATTTAATGTGAGTAATAAGGCTTTCAAAAGTATGGGTGACTCTAAATGGA
128 TGAGGTTATAAAATAATTTAAAGTGAGTAATAAGGCTTTCAAAGGCATGGGTGACTATAAATGGA
* * * *
13086 CATTTCTTGCCAATGGATATCTTTTCCTTTACGTTTCTC-AAGCTAGACATTCAATTATAATCTA
193 CTTTTCTTGCCAATGGATATCTTTTCCTTCACGTTTCTCGAAGC-AAACAATCAATTATAATCTA
* * * * * * ***
13150 TTTTATTTA-AAAATATAAAAAAATTTAAATTAAATTCAATTATGGGGTTATAAAATTATTTNNN
257 TTTTA-ATAGAAAATATAAAAAAATTCAAATTAAAATCAAGTATGAGGTTATAAAAATATTTAAT
*******
13214 NNNNNNNATAAGGCTTTCAA
321 GCAACTAATAAGGCTTTCAA
* * * *
13234 AGGTATGGGTGACTGTAAATGGACTTTTCTTGTCAATGGATACATTTTTCTTCATGTTTCTTAAG
1 AGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATACATTTTTCTTCACGTTTCTTAA-
* * ********* *
13299 GTAAACATTCAATTATAATCTGTTNNNNNNNNNNATATAAAAAAATTCAACTTAAAATCAATTAT
65 GTAGACATTCAATTATAATATGTT-TTAAAAAAAATATAAAAAAATTCAAATTAAAATCAATTAT
* ** *
13364 GAGGTTATAAAAAAAATTTAAACCGAGTAATAAGGCTTTCAAAGGCATGGGTTACTATAAATGGA
129 GAGGTTAT-AAAATAATTTAAAGTGAGTAATAAGGCTTTCAAAGGCATGGGTGACTATAAATGGA
13429 CTTTTCTTGCCA
193 CTTTTCTTGCCA
13441 NNNNNNNNNN
Statistics
Matches: 443, Mismatches: 93, Indels: 24
0.79 0.17 0.04
Matches are distributed among these distances:
340 13 0.03
341 77 0.17
342 276 0.62
343 77 0.17
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.35
Consensus pattern (340 bp):
AGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATACATTTTTCTTCACGTTTCTTAAG
TAGACATTCAATTATAATATGTTTTAAAAAAAATATAAAAAAATTCAAATTAAAATCAATTATGA
GGTTATAAAATAATTTAAAGTGAGTAATAAGGCTTTCAAAGGCATGGGTGACTATAAATGGACTT
TTCTTGCCAATGGATATCTTTTCCTTCACGTTTCTCGAAGCAAACAATCAATTATAATCTATTTT
AATAGAAAATATAAAAAAATTCAAATTAAAATCAAGTATGAGGTTATAAAAATATTTAATGCAAC
TAATAAGGCTTTCAA
Found at i:14090 original size:170 final size:160
Alignment explanation
Indices: 13818--14149 Score: 348
Period size: 171 Copynumber: 2.0 Consensus size: 160
13808 TAATAAAGCT
* ** *
13818 TTTGAAGGCATAGGTGGCTATAAATGGACTTCTCTTGCCAATGGCTATCTTTTTTTCACGTTTCT
1 TTTGAAGGCATAGGTGACTATAAATGGACTTCTCTTGCCAATGAATATCTTTTTTTCAAGTTTCT
* * *
13883 CGAGGTAAACTTTCAATTATAATTTGATTTATTAAAAAATATAAAAAAATTCGAA-TTAAAA-TC
66 CGAGGCAAACGTTCAATTATAATTT-ATTTATTAAAAAATATAAAAAAAATCGAAGTTAAAACT-
*
13946 AATTATGAGTTTATAAAATCATTTAAAGCGAG
129 AATTATGAGGTTATAAAATCATTTAAAGCGAG
*
13978 NNNNNNNNNNTTTGAAGGCATTA-GTGACTATAAATGGACTTTTCTTGCCAATGAATATCTTTTT
1 ----------TTTGAAGGCA-TAGGTGACTATAAATGGACTTCTCTTGCCAATGAATATCTTTTT
* * * * * * *
14042 GTTCAAGTTTCTTGAGGCACACGTTCAATTGTAATTT-TTTCTTTAAAAATTGTAAAAAAAATCT
55 -TTCAAGTTTCTCGAGGCAAACGTTCAATTATAATTTATTT-ATTAAAAAATATAAAAAAAATCG
*
14106 AAGTTAAAACTAATTATGAGGTTATACAATCATTTAAAGCGAG
118 AAGTTAAAACTAATTATGAGGTTATAAAATCATTTAAAGCGAG
14149 T
1 T
14150 AATCAGGCTT
Statistics
Matches: 140, Mismatches: 17, Indels: 19
0.80 0.10 0.11
Matches are distributed among these distances:
161 1 0.01
169 3 0.02
170 67 0.48
171 68 0.49
172 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.37
Consensus pattern (160 bp):
TTTGAAGGCATAGGTGACTATAAATGGACTTCTCTTGCCAATGAATATCTTTTTTTCAAGTTTCT
CGAGGCAAACGTTCAATTATAATTTATTTATTAAAAAATATAAAAAAAATCGAAGTTAAAACTAA
TTATGAGGTTATAAAATCATTTAAAGCGAG
Found at i:16798 original size:171 final size:170
Alignment explanation
Indices: 16210--17151 Score: 690
Period size: 171 Copynumber: 5.5 Consensus size: 170
16200 TTTTATCTCT
* * * * *
16210 AGAAACGTGAAGAAAAAGATATTCATTGGCAAG-TAAGTCCATTAATAGTCACCCATACCTTCGA
1 AGAAACGTGAAGAAAAATATATCCATTGGCAAGAAAAGTCCATTTATAGTCACCCATGCCTTCGA
* * * * *
16274 AAGCCTTATTACTCACTTTAAATGATTGTATAACTTCATAATTGGTTTTAAGTTGAATTTTATTA
66 AAGCCTTATTACTCGCTTTAAATGATTTTATAACCTCATAATTGATTTT-AGTTGAATTTTTTTA
* * * * * * *
16339 CAATTTTTA-TAGAAAAAAATTATAATTGAATGTCTGCCTCA
130 TATTTTTTATTA-AAACAGATTATAATTGAAAGTCTACCTCG
* * * ** *
16380 AAAAACCTGAACAAAAATATATCCATTGGCAAGAAAAGTCCATTTAT-GATCACTGATGCCTTCA
1 AGAAACGTGAAGAAAAATATATCCATTGGCAAGAAAAGTCCATTTATAG-TCACCCATGCCTTCG
*********** *
16444 AAAGCCTTATTACTCGCTTTAAATGATTTTATAAANNNNNNNNNNATTTTAATTTGAATTTTTTT
65 AAAGCCTTATTACTCGCTTTAAATGATTTTATAACCTCATAATTGATTTT-AGTTGAATTTTTTT
* * * *
16509 ATATTTTTTAATAAAACAGATTATAATTGCAAGTTTTCCTCG
129 ATATTTTTTATTAAAACAGATTATAATTGAAAGTCTACCTCG
* * * * *****
16551 AGAAACGTGAAGAACAAGATATCCATTGGTAAGAAAAGTCCATTTATAGTCACCTATGCCNNNNN
1 AGAAACGTGAAGAAAAATATATCCATTGGCAAGAAAAGTCCATTTATAGTCACCCATGCCTTCGA
***** * **
16616 NNNNNTTATTACTCGCTTTAAATGATTTTGTAACCTCATAATTGATTTTAGTTTGGGTTTTTTTA
66 AAGCCTTATTACTCGCTTTAAATGATTTTATAACCTCATAATTGATTTTAG-TTGAATTTTTTTA
* *
16681 TATTTTTTATTAAAACAGATTATAATTGAAAATCCACCTCG
130 TATTTTTTATTAAAACAGATTATAATTGAAAGTCTACCTCG
* * * * * *
16722 AGAAACGTGAAGAAAGATACATCCATTGGCATGAAAAGTCCATTTATAGTCACCCACGCTTTTGA
1 AGAAACGTGAAGAAAAATATATCCATTGGCAAGAAAAGTCCATTTATAGTCACCCATGCCTTCGA
********** * * **
16787 AAGCCTTATTACTCGCTTTAANNNNNNNNNNAATCTCATAA-TAAGTTTTAAGTTGACCTTTTTT
66 AAGCCTTATTACTCGCTTTAAATGATTTTATAACCTCATAATTGA-TTTT-AGTTGAATTTTTTT
* *
16851 ATATTTTTTACTAAAACAGATAATAATT-AAATGTCTACCTCG
129 ATATTTTTTATTAAAACAGATTATAATTGAAA-GTCTACCTCG
********* * * *
16893 AGAAACGT-AANNNNNNNNNNATCCATTGGCAAGAAAAGTCCATTTATAGTAACCTATGCCTCCG
1 AGAAACGTGAA-GAAAAATATATCCATTGGCAAGAAAAGTCCATTTATAGTCACCCATGCCTTCG
** **
16957 AAAGCCTTATTACTCGCTTTAAATTTTTTTATAACCTCATAATTGATATGAAGTTGAATTTTTTT
65 AAAGCCTTATTACTCGCTTTAAATGATTTTATAACCTCATAATTGAT-TTTAGTTGAA-TTTTTT
* * * **
17022 TATATTTTATGTTAAAACAGATTATAATTGAATGTCTACCTNN
128 TATATTTTTTATTAAAACAGATTATAATTGAAAGTCTACCTCG
******** ** * * * * *
17065 NNNNNNNNGAAGAAAAAGGTATTCATTGACAAGAAAAGTCCAATTACAGTCACCCATACCTTCGA
1 AGAAACGTGAAGAAAAATATATCCATTGGCAAGAAAAGTCCATTTATAGTCACCCATGCCTTCGA
*
17130 AAGCCTTATTACTCGCATTAAA
66 AAGCCTTATTACTCGCTTTAAA
17152 NNNNNNNNNN
Statistics
Matches: 580, Mismatches: 178, Indels: 26
0.74 0.23 0.03
Matches are distributed among these distances:
170 37 0.06
171 435 0.75
172 104 0.18
173 4 0.01
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.34
Consensus pattern (170 bp):
AGAAACGTGAAGAAAAATATATCCATTGGCAAGAAAAGTCCATTTATAGTCACCCATGCCTTCGA
AAGCCTTATTACTCGCTTTAAATGATTTTATAACCTCATAATTGATTTTAGTTGAATTTTTTTAT
ATTTTTTATTAAAACAGATTATAATTGAAAGTCTACCTCG
Found at i:19515 original size:170 final size:171
Alignment explanation
Indices: 19222--19548 Score: 399
Period size: 170 Copynumber: 1.9 Consensus size: 171
19212 NNNNNNNNNN
*
19222 AATTATAATCTGTTTTAATAGAAAATATAAAAAAATTCAAATTAAAATCAATTACGAGGTTATAA
1 AATTATAATCTGTTTTAATAAAAAATATAAAAAAATTCAAATTAAAATCAATTACGAGGTTATAA
* * ********** *
19287 AAATATTTAATGCGACTAATAAGGCTTTCGANNNNNNNNNNGACTATAAATTGACTTTTCTTGCC
66 AAATATTTAATGCGACTAATAAGACTTTCAAAAGCATAGGTGACTATAAATGGACTTTTCTTGCC
* *
19352 AATTGATA-CATTTTTCTTCACGTTTCTTAAAGTAGACATTC
131 AATGGATATC-TTTTCCTTCACGTTTCTTAAAGTAGACATTC
* * * *
19393 AATTATAAT-T-TTTTAATAAAAAATATAAAAAAAATTTAATTTAAAATCAATTATGTGGTTATA
1 AATTATAATCTGTTTTAATAAAAAATAT-AAAAAAATTCAAATTAAAATCAATTACGAGGTTATA
* * * *
19456 ATATTATTTAATGCGAGTAATAAGACTTTCAAAAGCATAGGTGACTCTAAATGGACTTTTCTTGC
65 AAAATATTTAATGCGACTAATAAGACTTTCAAAAGCATAGGTGACTATAAATGGACTTTTCTTGC
19521 CAATGGATATCTTTTCCTTCACGTTTCT
130 CAATGGATATCTTTTCCTTCACGTTTCT
19549 NNNNNNNNNN
Statistics
Matches: 130, Mismatches: 24, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
169 15 0.12
170 105 0.81
171 10 0.08
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.37
Consensus pattern (171 bp):
AATTATAATCTGTTTTAATAAAAAATATAAAAAAATTCAAATTAAAATCAATTACGAGGTTATAA
AAATATTTAATGCGACTAATAAGACTTTCAAAAGCATAGGTGACTATAAATGGACTTTTCTTGCC
AATGGATATCTTTTCCTTCACGTTTCTTAAAGTAGACATTC
Found at i:21816 original size:170 final size:161
Alignment explanation
Indices: 21634--21958 Score: 325
Period size: 170 Copynumber: 2.0 Consensus size: 161
21624 TAAAATTATT
* * * * * *
21634 TAATTCGAGTAATAAGGCTTTCGAAAGCATGGGTGTCTCTAAATAGACTTTTCTTGCCAATGGAT
1 TAATGCGAGTAATAAGGCTTTCGAAAGCATGGGCGACTATAAATAGACTTTTCTTACCAAAGGAT
** * *
21699 A-TCTCTTCCTTCAC-TTTCCTCAGGGCAGACATTTAATTATAATCCGTGTTAAT-AAAAGTATA
66 ACT-TCTTCCTTCACGTTT-CTCAAAGCAGACATTCAATTATAATCCGTGTTAATAAAAAATATA
*
21761 GAAAAAA-TCAAATTAAAATCAATTATGAGGTTA
129 -AAAAAATTCAAATCAAAATCAATTATGAGGTTA
* * *
21794 NNNNNNNNNNTAATGCGAGTAATAAGGCTTTCGAAGGTATGGGCGACTATAAATGGACTTTTCTT
1 ----------TAATGCGAGTAATAAGGCTTTCGAAAGCATGGGCGACTATAAATAGACTTTTCTT
* * * * * *
21859 ACCAAAGGATACTTTTTTCTTCACGTTTCTCAAAGTAGACATTCAGTTATAATCTGTTTTAATAA
56 ACCAAAGGATACTTCTTCCTTCACGTTTCTCAAAGCAGACATTCAATTATAATCCGTGTTAATAA
21924 AAAATATAAAAAAATTCAAATCAAAATCAATTATG
121 AAAATATAAAAAAATTCAAATCAAAATCAATTATG
21959 NNNNNNNNNN
Statistics
Matches: 131, Mismatches: 20, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
170 100 0.76
171 31 0.24
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.33
Consensus pattern (161 bp):
TAATGCGAGTAATAAGGCTTTCGAAAGCATGGGCGACTATAAATAGACTTTTCTTACCAAAGGAT
ACTTCTTCCTTCACGTTTCTCAAAGCAGACATTCAATTATAATCCGTGTTAATAAAAAATATAAA
AAAATTCAAATCAAAATCAATTATGAGGTTA
Found at i:23731 original size:343 final size:331
Alignment explanation
Indices: 23365--23991 Score: 696
Period size: 343 Copynumber: 1.9 Consensus size: 331
23355 NNNNNNNNNN
* * * * * **
23365 AAAATTCAACTTAAAACCAATTATGATGTTATACGATCATTTAAAGCGAGTAATAAGGCTTTCGA
1 AAAATTTAAATTAAAACCAATTATAAGGCTATAAAATCATTTAAAGCGAGTAATAAGGCTTTCGA
* * ********** * * *
23430 ATGTATGGGTGACTATAAANNNNNNNNNNTTGCCAATGGATATCTTTTTCTTCACGTTTTTCAAG
66 AAGCATGGGTGACTATAAATGGACTTTTCTTGCCAATAGATATCTTTTTCTTCACATTTCTCAAG
*
23495 GTAGAAATTCAATTATAATCTGTTTGAATAAAAACTATAAAAAAATTTAAAATTAAAATCAATTA
131 GTAGAAATTCAATTATAATATGTTTGAATAAAAA-TATAAAAAAA-TTAAAATTAAAATCAATTA
* * **
23560 TGAGGTTATAAAATCATTTAAAGCAAGTAATAAGGCTTTTGAAGGTATGAGTGATTATAAATGGA
194 TGAGGTTATAAAATCATTAAAAGCAAGTAATAAGGCTTTTGAAGGCATGAGTGAGCATAAATGGA
*
23625 CTTTTTTTGCCAATGGATATCTTTTTCTACACTTTTCTCTAGACAAACATTCGATTATAATCTAT
259 CTTTTCTTGCCAATGGATATCTTTTTCTACACTTTTCTCTAGACAAACATTCGATTATAATCTAT
23690 TTTAATAA
324 TTTAATAA
* *
23698 AAAANNNNNNNNNNTTTAAATTAAAATCAATTATAAGGCTATAAAATCATTTAAAGTGAGTAATA
1 AAAA----------TTTAAATTAAAACCAATTATAAGGCTATAAAATCATTTAAAGCGAGTAATA
*
23763 AGGCTTTCTAAAGCATGGGTGACTATAAATGGACTTTTCTTGCCAATAGATATCTTTTTCTTCAC
56 AGGCTTTCGAAAGCATGGGTGACTATAAATGGACTTTTCTTGCCAATAGATATCTTTTTCTTCAC
* * * * * *****
23828 ATTTCTCGAGGTAGACATTCAATTATAATATGTTTTAATAAAAATATAAAAATATTCAAANNNNN
121 ATTTCTCAAGGTAGAAATTCAATTATAATATGTTTGAATAAAAATATAAAAAAATTAAAATTAAA
***** ** * *
23893 NNNNNTTATGAGGTTATAAAATCATTAAAAGTGAGTGATAAGGCTTTTGAAGGCGTGAGTGAGCA
186 ATCAATTATGAGGTTATAAAATCATTAAAAGCAAGTAATAAGGCTTTTGAAGGCATGAGTGAGCA
23958 TAAATGGACTTTTCTTGCCAATGGATATCTTTTT
251 TAAATGGACTTTTCTTGCCAATGGATATCTTTTT
23992 GTTCAGGTTT
Statistics
Matches: 234, Mismatches: 50, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
333 4 0.02
341 90 0.38
342 9 0.04
343 131 0.56
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.35
Consensus pattern (331 bp):
AAAATTTAAATTAAAACCAATTATAAGGCTATAAAATCATTTAAAGCGAGTAATAAGGCTTTCGA
AAGCATGGGTGACTATAAATGGACTTTTCTTGCCAATAGATATCTTTTTCTTCACATTTCTCAAG
GTAGAAATTCAATTATAATATGTTTGAATAAAAATATAAAAAAATTAAAATTAAAATCAATTATG
AGGTTATAAAATCATTAAAAGCAAGTAATAAGGCTTTTGAAGGCATGAGTGAGCATAAATGGACT
TTTCTTGCCAATGGATATCTTTTTCTACACTTTTCTCTAGACAAACATTCGATTATAATCTATTT
TAATAA
Found at i:23792 original size:171 final size:161
Alignment explanation
Indices: 23534--23871 Score: 390
Period size: 171 Copynumber: 2.0 Consensus size: 161
23524 AAAAACTATA
* *
23534 AAAAAATTTAAAATTAAAATCAATTATGAGGTTATAAAATCATTTAAAGCAAGTAATAAGGCTTT
1 AAAAAATTT-AAATTAAAATCAATTATAAGGCTATAAAATCATTTAAAGCAAGTAATAAGGCTTT
* * * * * *
23599 TGAAGGTATGAGTGATTATAAATGGACTTTTTTTGCCAATGGATATCTTTTTCTACACTTTTCTC
65 TGAAAGCATGAGTGACTATAAATGGACTTTTCTTGCCAATAGATATCTTTTTCTACACATTTCTC
* * *
23664 TAGACAAACATTCGATTATAATCTATTTTAAT
130 GAGACAAACATTCAATTATAATATATTTTAAT
**
23696 AAAAAANNNNNNNNNNTTTAAATTAAAATCAATTATAAGGCTATAAAATCATTTAAAGTGAGTAA
1 AAAAAA----------TTTAAATTAAAATCAATTATAAGGCTATAAAATCATTTAAAGCAAGTAA
* *
23761 TAAGGCTTTCT-AAAGCATGGGTGACTATAAATGGACTTTTCTTGCCAATAGATATCTTTTTCTT
56 TAAGGCTTT-TGAAAGCATGAGTGACTATAAATGGACTTTTCTTGCCAATAGATATCTTTTTCTA
** * *
23825 CACATTTCTCGAGGTAGACATTCAATTATAATATGTTTTAAT
120 CACATTTCTCGAGACAAACATTCAATTATAATATATTTTAAT
23867 AAAAA
1 AAAAA
23872 TATAAAAATA
Statistics
Matches: 146, Mismatches: 19, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
162 6 0.04
171 136 0.93
172 4 0.03
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.36
Consensus pattern (161 bp):
AAAAAATTTAAATTAAAATCAATTATAAGGCTATAAAATCATTTAAAGCAAGTAATAAGGCTTTT
GAAAGCATGAGTGACTATAAATGGACTTTTCTTGCCAATAGATATCTTTTTCTACACATTTCTCG
AGACAAACATTCAATTATAATATATTTTAAT
Found at i:24495 original size:171 final size:172
Alignment explanation
Indices: 24186--24496 Score: 412
Period size: 171 Copynumber: 1.8 Consensus size: 172
24176 NNNNNNNNNN
*
24186 CTGTTTTAATAAAAAATATAAAAAAAATTTAACTTAAAATCAATTATGAGATTACAAAAGCATTT
1 CTGTTTTAATAAAAAATATAAAAAAAATTCAACTTAAAATCAATTATGAGATTACAAAAGCATTT
* * * * *
24251 AAAGTGACTAATAAGGCTTTCGAAGGCATTGGTGTCAATAAATGAACTTTTTTTGCCAATGAATA
66 AAAGCGACTAATAAGACTTTCGAAGGCATAGGTGACAATAAATGAACTTTTCTTGCCAATGAATA
*
24316 TTTTTTTCTTCACGTTTCTCGAAGAAAACATTTAATTATAAT
131 TCTTTTTCTTCACGTTTCTCGAAGAAAACATTTAATTATAAT
* * *
24358 CTGTTTTAATAAAAAATAT-AAAAAAGTTCAACTTCAAA-CTAATTATGGGATTTA-AAAAGCAT
1 CTGTTTTAATAAAAAATATAAAAAAAATTCAACTTAAAATC-AATTATGAGA-TTACAAAAGCAT
* * * * * * * * *
24420 TTAAAGCGAGTAGTACGACTTTTGAAGTCATAGGTGACTATAAATGGACTTTTCTTGCTAATGGA
64 TTAAAGCGACTAATAAGACTTTCGAAGGCATAGGTGACAATAAATGAACTTTTCTTGCCAATGAA
24485 TATCTTTTTCTT
129 TATCTTTTTCTT
24497 GACATTTNNN
Statistics
Matches: 118, Mismatches: 19, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
170 1 0.01
171 95 0.81
172 22 0.19
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (172 bp):
CTGTTTTAATAAAAAATATAAAAAAAATTCAACTTAAAATCAATTATGAGATTACAAAAGCATTT
AAAGCGACTAATAAGACTTTCGAAGGCATAGGTGACAATAAATGAACTTTTCTTGCCAATGAATA
TCTTTTTCTTCACGTTTCTCGAAGAAAACATTTAATTATAAT
Found at i:25506 original size:170 final size:170
Alignment explanation
Indices: 24604--26056 Score: 650
Period size: 170 Copynumber: 8.5 Consensus size: 170
24594 NNNNNNNNNN
* * ** *
24604 CCAATGGATATCTTTTTCTTCACGTTTCTCGAGGTAAACTTTCAATTATAATCTAATTTATTAAA
1 CCAATGGATATCTTTTTCTTCACGTTTCTCAAGG-AAAATTTCAATTATAATCTGTTTTAATAAA
********** * * *
24669 AAATATAAAAAAATTCAAATTAAAATCAANNNNNNNNNNATAAAATCATTTAAAGCGAGTGATAA
65 AAATATAAAAAAATTCAAATTAAAATCAATTATGAGCTTATAAAATTATTTAATGCGAGTAATAA
* ** *
24734 GGCTTT-TGAAGGCATCAGTGACTATAAATGGACTTTTCTAG
130 GGCTTTCGGAA-GCATGGGTGACTATAAATGGACTTTTCTTG
* * ** * ** * * **
24775 CCAATGAATATCTTTTTATTCACGTTTCTTGAGTTAAACGTTCAACTGTAAT-T-TTTTCCTTTA
1 CCAATGGATATCTTTTTCTTCACGTTTCTCAAG-GAAAATTTCAATTATAATCTGTTTT--AATA
* * * * * *********** *
24838 AAAATTGTAAAAACATTTAACTTAAAA-CTAATTATGAGGNNNNNNNNNNATTTAAAGCGAGTAA
63 AAAAATATAAAAAAATTCAAATTAAAATC-AATTATGAGCTTATAAAATTATTTAATGCGAGTAA
* * * ** ** * *
24902 TAAGGCTTTCGTAGGAATGGAAGACCCCT-AATGGATCTGTT-TTA
127 TAAGGCTTTCGGAAGCATGGGTGA-CTATAAATGGA-CTTTTCTTG
* * * * *
24946 CCCATGGATATATTTTTCTTCACGTTTCTCGA-GATAGACA-TTGAATTATAATATGTTTTAAT-
1 CCAATGGATATCTTTTTCTTCACGTTTCTCAAGGA-A-A-ATTTCAATTATAATCTGTTTTAATA
* ********** * * * ** *
25008 AAAAGTATAAAAAAATTCAAANNNNNNNNNNTTATGAGGTTATAAAATCATTAAAAACGAGTGAT
63 AAAAATATAAAAAAATTCAAATTAAAATCAATTATGAGCTTATAAAATTATTTAATGCGAGTAAT
* *
25073 AAGGC-TTCTGAAGGCGTGGGTGACTATAAATGGACTTTTCTTG
128 AAGGCTTTCGGAA-GCATGGGTGACTATAAATGGACTTTTCTTG
* ********** * ** * ** *
25116 GCAATGGATNNNNNNNNNNTCATGTTTCTCAAGGAAAACAATCAATTATAATATGTAATAATAGA
1 CCAATGGATATCTTTTTCTTCACGTTTCTCAAGGAAAA-TTTCAATTATAATCTGTTTTAATAAA
* *********** *
25181 AAATATAAAAAAATTTAAATTAAAATCAATTATGAGNNNNNNNNNNCATTTAATGCGACTAATAA
65 AAATATAAAAAAATTCAAATTAAAATCAATTATGAGCTTATAAAATTATTTAATGCGAGTAATAA
* * *
25246 GGCTTTC-GAAGGCATGAGAGACTATAAATTGACTTTTCTTG
130 GGCTTTCGGAA-GCATGGGTGACTATAAATGGACTTTTCTTG
******* * *
25287 CCAATGGATA-CATTTTTCTTCACGTTNNNNNNNNNNG-ACA-TTCAATTATAAT-TTTTTTAAT
1 CCAATGGATATC-TTTTTCTTCACGTT---TCTCAAGGAAAATTTCAATTATAATCTGTTTTAAT
* * * *
25348 AAAAAATATAAAAAAATACAATTTAAAATCAATTATGTGGTTATAAAATTATTTAATGCGAGTAA
62 AAAAAATATAAAAAAATTCAAATTAAAATCAATTATGAGCTTATAAAATTATTTAATGCGAGTAA
* * * *
25413 TGAGGCTTTCGGAAGCATGGGTGACTTTAATTGGACTTTTCATG
127 TAAGGCTTTCGGAAGCATGGGTGACTATAAATGGACTTTTCTTG
* * *
25457 CCAATGGATATCTTTTCCTTCACGTTTCTCAAGGCAAAATTTTAATTATAATATGTTTTAATAAA
1 CCAATGGATATCTTTTTCTTCACGTTTCTCAAGG-AAAATTTCAATTATAATCTGTTTTAATAAA
********** ** *
25522 AAATAT-AAAAAATTCAAATTAAAATCAATNNNNNNNNNNTAAAAACATTTAATGCAAGTAATAA
65 AAATATAAAAAAATTCAAATTAAAATCAATTATGAGCTTATAAAATTATTTAATGCGAGTAATAA
*
25586 GGCTTTC-GAAGGCATGGGTGACTATAACTGGACTTTTCTTG
130 GGCTTTCGGAA-GCATGGGTGACTATAAATGGACTTTTCTTG
* * * *
25627 TCAATGGATA-CTTTTTTCTTTACGTTTCTCATAGTAGACA-TTCAATTATAATCTGTTTTAA-A
1 CCAATGGATATC-TTTTTCTTCACGTTTCTCA-AGGA-AAATTTCAATTATAATCTGTTTTAATA
* * ***
25689 AAATATATAAAAAAATTCAAATCAAAAT-ATATTATGAGCTTATAAAATTATTTAATGCGAGNNN
63 AAAAATATAAAAAAATTCAAATTAAAATCA-ATTATGAGCTTATAAAATTATTTAATGCGAGTAA
******* * * * *
25753 NNNNNNNTTCGAAAGCATGGGTGACTCTAAATAGACTTTCCTTG
127 TAAGGCTTTCGGAAGCATGGGTGACTATAAATGGACTTTTCTTG
* * * *
25797 CCAATGGATATCTTTTTCTTCACGTTTCCCAAGGTAGATATTCAATTATAATCTGTTTTAATATA
1 CCAATGGATATCTTTTTCTTCACGTTTCTCAAGGAAAAT-TTCAATTATAATCTGTTTTAATAAA
********** ** *
25862 AAATATAAAAAAAATTCAAATTAAAATCNNNNNNNNNNTTATAAAAACATTGAATGCGAGTTAA-
65 AAATAT-AAAAAAATTCAAATTAAAATCAATTATGAGCTTATAAAATTATTTAATGCGAG-TAAT
* ** * * * *
25926 AAGGCTTTCGAAAATATAGGCGACTATAAATTGACTTTTGTTG
128 AAGGCTTTCGGAAGCATGGGTGACTATAAATGGACTTTTCTTG
* * * ** * * *
25969 CCAATGGATATTTTTTTCTTCACATTTCTTAAACTAGACATTT-AATTATAATTTATTTTAATAA
1 CCAATGGATATCTTTTTCTTCACGTTTC-TCAAGGA-AAATTTCAATTATAATCTGTTTTAATAA
26033 AAAATAT-AAAAAATTCAAATTAAA
64 AAAATATAAAAAAATTCAAATTAAA
Statistics
Matches: 927, Mismatches: 308, Indels: 95
0.70 0.23 0.07
Matches are distributed among these distances:
167 1 0.00
168 3 0.00
169 32 0.03
170 468 0.50
171 280 0.30
172 129 0.14
173 10 0.01
174 4 0.00
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.34
Consensus pattern (170 bp):
CCAATGGATATCTTTTTCTTCACGTTTCTCAAGGAAAATTTCAATTATAATCTGTTTTAATAAAA
AATATAAAAAAATTCAAATTAAAATCAATTATGAGCTTATAAAATTATTTAATGCGAGTAATAAG
GCTTTCGGAAGCATGGGTGACTATAAATGGACTTTTCTTG
Found at i:25669 original size:340 final size:335
Alignment explanation
Indices: 25227--26045 Score: 813
Period size: 340 Copynumber: 2.4 Consensus size: 335
25217 NNNNNNNNNN
* *
25227 CATTTAATGCGACTAATAAGGCTTTCGAAGGCATGAGAGACTATAAATTGACTTTTCTTGCCAAT
1 CATTTAATGCGAGTAATAAGGCTTTCGAAGGCATGGGAGACTATAAATTGACTTTTCTTGCCAAT
* **********
25292 GGATACATTTTTCTTCACGTTNNNNNNNNNNGACATTCAATTATAATTTTTTTAATAAAAAATAT
66 GGATACTTTTTTCTTCACGTTTCTCAAACTAGACATTCAATTATAATTTTTTTAATAAAAAATAT
* * * *
25357 AAAAAAATACAATTTAAAATCA-ATTATGTGGTTATAAAATTATTTAATGCGAGTAATGAGGCTT
131 AAAAAAATACAAATCAAAAT-ATATTATGAGCTTATAAAATTATTTAATGCGAGTAATGAGGCTT
* * * * * *
25421 TCGGAAGCATGGGTGACTTTAATTGGACTTTTCATGCCAATGGATATCTTTTCCTTCACGTTTCT
195 TCGAAAGCATGGGTGACTCTAAATAGACTTTCCATGCCAATGGATATCTTTTCCTTCACGTTTCC
* *
25486 CAAGGCAAAAT-TTTAATTATAATATGTTTTAATA-AAAA-ATATAAAAAATTCAAATTAAAATC
260 CAAGG-AAAATATTCAATTATAATATGTTTTAATATAAAATATAAAAAAAATTCAAATTAAAATC
***
25548 AATNNNNNNNNNNTAAAAA
324 AAT-------TTATAAAAA
* * * * *
25567 CATTTAATGCAAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAACTGGACTTTTCTTGTCAAT
1 CATTTAATGCGAGTAATAAGGCTTTCGAAGGCATGGGAGACTATAAATTGACTTTTCTTGCCAAT
* * * * *
25632 GGATACTTTTTTCTTTACGTTTCTCATAGTAGACATTCAATTATAATCTGTTTTAA-AAAATATA
66 GGATACTTTTTTCTTCACGTTTCTCAAACTAGACATTCAATTATAAT-TTTTTTAATAAAAAATA
* **********
25696 TAAAAAAATTCAAATCAAAATATATTATGAGCTTATAAAATTATTTAATGCGAGNNNNNNNNNNT
130 TAAAAAAATACAAATCAAAATATATTATGAGCTTATAAAATTATTTAATGCGAGTAATGAGGCTT
* *
25761 TCGAAAGCATGGGTGACTCTAAATAGACTTTCCTTGCCAATGGATATCTTTTTCTTCACGTTTCC
195 TCGAAAGCATGGGTGACTCTAAATAGACTTTCCATGCCAATGGATATCTTTTCCTTCACGTTTCC
* * *
25826 CAAGGTAGATATTCAATTATAATCTGTTTTAATATAAAATATAAAAAAAATTCAAATTAAAATCN
260 CAAGGAAAATATTCAATTATAATATGTTTTAATATAAAATATAAAAAAAATTCAAATTAAAATC-
***
25891 NNNNNNNNNTTATAAAAA
324 ------AATTTATAAAAA
* *** * * *
25909 CATTGAATGCGAGTTAA-AAGGCTTTCGAAAATATAGGCGACTATAAATTGACTTTTGTTGCCAA
1 CATTTAATGCGAG-TAATAAGGCTTTCGAAGGCATGGGAGACTATAAATTGACTTTTCTTGCCAA
* * * *
25973 TGGATATTTTTTTCTTCACATTTCTTAAACTAGACATTTAATTATAATTTATTTTAATAAAAAAT
65 TGGATACTTTTTTCTTCACGTTTCTCAAACTAGACATTCAATTATAATTT-TTTTAATAAAAAAT
26038 ATAAAAAA
129 ATAAAAAA
26046 TTCAAATTAA
Statistics
Matches: 389, Mismatches: 75, Indels: 27
0.79 0.15 0.05
Matches are distributed among these distances:
339 4 0.01
340 231 0.59
341 12 0.03
342 125 0.32
343 17 0.04
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.35
Consensus pattern (335 bp):
CATTTAATGCGAGTAATAAGGCTTTCGAAGGCATGGGAGACTATAAATTGACTTTTCTTGCCAAT
GGATACTTTTTTCTTCACGTTTCTCAAACTAGACATTCAATTATAATTTTTTTAATAAAAAATAT
AAAAAAATACAAATCAAAATATATTATGAGCTTATAAAATTATTTAATGCGAGTAATGAGGCTTT
CGAAAGCATGGGTGACTCTAAATAGACTTTCCATGCCAATGGATATCTTTTCCTTCACGTTTCCC
AAGGAAAATATTCAATTATAATATGTTTTAATATAAAATATAAAAAAAATTCAAATTAAAATCAA
TTTATAAAAA
Done.