Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402979.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_644.0, 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: 49972
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.21
Warning! 21591 characters in sequence are not A, C, G, or T
Found at i:3908 original size:170 final size:172
Alignment explanation
Indices: 3575--3958 Score: 433
Period size: 170 Copynumber: 2.2 Consensus size: 172
3565 NNNNNNNNAT
* * *
3575 TCCTTCAAAAGCTTTATTACTAGCTTTAAA-TATTTTTCTAATCTCATAATTATTTTTAAGTTGA
1 TCCTTCAAAAGCCTTATTACTAGCTTTAAATTA-TTTTATAATCTAATAATTATTTTTAAGTTGA
* * * *** *
3639 ATTTGTTTTTTATATTTTTCATTAAAACAGACTATAATTGAATGTCTATTGGAAAAATGTGAATA
65 AATTG-TTTTTACATTTTTCATTAAAACAGACTATAATTGAATGTCTATTGCAAAAACACGAAGA
* * *
3704 AAAGAACATTCATTAGCAAGAAAAGTCTATTTATAGTCTCCGAG
129 AAAGAACATTCATTAGCAAGAAAAGTCCATTTATAGTCACCCAG
* * *
3748 TCCTTCAAAAGCCTTATTACTAGTTTTAAATTATTTTATATTCTAATAATTGTTTTTAAGTT-AA
1 TCCTTCAAAAGCCTTATTACTAGCTTTAAATTATTTTATAATCTAATAATTATTTTTAAGTTGAA
* * *
3812 ATTG-TTTTACATTTTTTATTAAAATAGA-TAATAATTGATTGTCTATCT-CAAGAAACACGAAG
66 ATTGTTTTTACATTTTTCATTAAAACAGACT-ATAATTGAATGTCTAT-TGCAA-AAACACGAAG
* * *
3874 AAAA-AACATTGATTGGCAAGAAAAGTCCATTTATAGTCACCCAT
128 AAAAGAACATTCATTAGCAAGAAAAGTCCATTTATAGTCACCCAG
* *
3918 TCCATT-AAAA-CCATTATTACTCGCTTTAAATCATTTTATAA
1 TCC-TTCAAAAGCC-TTATTACTAGCTTTAAATTATTTTATAA
3959 NNNNNNNNNN
Statistics
Matches: 179, Mismatches: 26, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
169 3 0.02
170 103 0.58
171 13 0.07
172 5 0.03
173 53 0.30
174 2 0.01
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.41
Consensus pattern (172 bp):
TCCTTCAAAAGCCTTATTACTAGCTTTAAATTATTTTATAATCTAATAATTATTTTTAAGTTGAA
ATTGTTTTTACATTTTTCATTAAAACAGACTATAATTGAATGTCTATTGCAAAAACACGAAGAAA
AGAACATTCATTAGCAAGAAAAGTCCATTTATAGTCACCCAG
Found at i:10833 original size:171 final size:170
Alignment explanation
Indices: 10656--11122 Score: 477
Period size: 171 Copynumber: 2.7 Consensus size: 170
10646 NNNNNNNNNN
* * * * *
10656 AAGTTGATTTTTTTTACATTTTTGATTAAAACAGACTATAATTGAATGTCTACCACAAGAAACGT
1 AAGTTGATTTTTTTTACATTTTTCATTAAAACAGACTATAATTAAATGTCTGCCTCAAGAAACAT
* * *
10721 GAATAAAAGAGCATTCGTGGGTAAAAAAAGTCCATTTATAGTCTCCCAATCCTTCAAAAGCCTTA
66 GAAGAAAA-AGCATTCAT-GGTAAAAAAAGTCCATTTATAGTCTCCCATTCCTTCAAAAGCCTTA
* *
10786 TTACTCG-CATTAAATGGTTTTATAATCTCATGATTGATTTT
129 TTACTCGTCATAAAATGGTTTTATAATCTCATGATTAATTTT
** * **********
10827 AAGTTGAAGTTTTTTACATTTTTCATTAAAACAGGCTNNNNNNNNNNGTCTGCCTCAAGAAACAT
1 AAGTTGATTTTTTTTACATTTTTCATTAAAACAGACTATAATTAAATGTCTGCCTCAAGAAACAT
* *** * *
10892 GAAGAAAAAAGCATTCACTGATAAAAATTTTCCATTTATAGTCTCCCATTCCTTCAACAGCCTTT
66 GAAG-AAAAAGCATTCA-TGGTAAAAAAAGTCCATTTATAGTCTCCCATTCCTTCAAAAGCCTTA
* *
10957 TTACTCGTCCTAAAATGGTTTTATAATCTCATTATTAATTTT
129 TTACTCGTCATAAAATGGTTTTATAATCTCATGATTAATTTT
* * * * * * * *
10999 AATTTTAATTTTTTTTATATTTTTTATTAAAAAAGACTATAATTAAATGTTTGCCTTAAGAAGCA
1 AA-GTTGATTTTTTTTACATTTTTCATTAAAACAGACTATAATTAAATGTCTGCCTCAAGAAACA
* ** * *
11064 TGAAGAAAAAGCATTCATTGGCAAAAAAAGTGTATTTACAGCCTCCCATTCCTTCAAAA
65 TGAAGAAAAAGCATTCA-TGGTAAAAAAAGTCCATTTATAGTCTCCCATTCCTTCAAAA
11123 NNNNNNNNNN
Statistics
Matches: 230, Mismatches: 62, Indels: 7
0.77 0.21 0.02
Matches are distributed among these distances:
171 104 0.45
172 80 0.35
173 46 0.20
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.36
Consensus pattern (170 bp):
AAGTTGATTTTTTTTACATTTTTCATTAAAACAGACTATAATTAAATGTCTGCCTCAAGAAACAT
GAAGAAAAAGCATTCATGGTAAAAAAAGTCCATTTATAGTCTCCCATTCCTTCAAAAGCCTTATT
ACTCGTCATAAAATGGTTTTATAATCTCATGATTAATTTT
Found at i:20894 original size:171 final size:170
Alignment explanation
Indices: 20584--21391 Score: 683
Period size: 171 Copynumber: 4.7 Consensus size: 170
20574 NNNNNNNNNT
* * * ** * *
20584 GACTATAAATGGATTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTTAAGACAGAAAATC
1 GACTATAAATGGACTTTTCTTGCCAATGAATGCTCTTTTCTTCATGTTTCTTATGGTAGACATTC
* ** ** * * * *
20649 AATTATTGTCTGTTTTAATCAAAAATGTAAACTAATTTAACTTAAAATCAATTATTAGTTTATAA
66 AATTA-TATCAATTTTAATCAAAAATGTAAAAAAAATCAACTTAAAATCAATTATGAGATTATAA
* *
20714 AATTATTTAAAGCTAGTAATAAGGCTTTTAAAGGACTCG-GA
130 AACTATTTAAAGCTAGTAATAAGGCTTTTGAAGGACT-GAGA
* ** * *
20755 GACTATAAATGGACTTTTCTTACCAATGAATGCTCTTTTCTTCACATTTCTTACGGTAGACATTT
1 GACTATAAATGGACTTTTCTTGCCAATGAATGCTCTTTTCTTCATGTTTCTTATGGTAGACATTC
* * * * *
20820 AATTATCATCAATTTTAATGAAATATGTAAAAAAAATCAACTTAAAATTAATTCTGAGATTAGAA
66 AATTAT-ATCAATTTTAATCAAAAATGTAAAAAAAATCAACTTAAAATCAATTATGAGATTATAA
* * ***
20885 AACTATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGNNN
130 AACTATTTAAAGCTAGTAATAAGGCTTTTGAAGGACTGAGA
******* * * *
20926 NNNNNNNAATAGACTTTTCTTGCCAATGAATACT-TTTCTCTTCATGTTTCTTATGGTAGATATT
1 GACTATAAATGGACTTTTCTTGCCAATGAATGCTCTTT-TCTTCATGTTTCTTATGGTAGACATT
* ** **********
20990 CAATTATAGTC--TGTTTAATGAAAAATGTAAAAAACTTCAACTTANNNNNNNNNNTGAGATTAT
65 CAATTATA-TCAAT-TTTAATCAAAAATGTAAAAAAAATCAACTTAAAATCAATTATGAGATTAT
* * * *
21053 AAAGCCATTTAAAGCGAGTAATAAGGCTTTTGAAGGATTGAGA
128 AAAACTATTTAAAGCTAGTAATAAGGCTTTTGAAGGACTGAGA
* * * *
21096 GACTATAAATAGACTTTTCTTGCCTATGAATGCTCTTTTATTCATGTTTCTTGA-GGTAGATATT
1 GACTATAAATGGACTTTTCTTGCCAATGAATGCTCTTTTCTTCATGTTTCTT-ATGGTAGACATT
* ********** * *
21160 CAATCATAGTCTAA-TTTAATCAAAAATGTAAAAANNNNNNNNNNAAAATCAGTTATTAGATTAT
65 CAATTATA-TC-AATTTTAATCAAAAATGTAAAAAAAATCAACTTAAAATCAATTATGAGATTAT
* *
21224 AAAACTGTTTAAAGCTAGTAATAAGCCTTTTGAAGGACTGAGA
128 AAAACTATTTAAAGCTAGTAATAAGGCTTTTGAAGGACTGAGA
* * ** * *
21267 GACTATAAATGGACTTTTCTTGTCAATGAATGCACTTTTCTTCACATTTCTTGTGGTAGACATTG
1 GACTATAAATGGACTTTTCTTGCCAATGAATGCTCTTTTCTTCATGTTTCTTATGGTAGACATTC
* * * *
21332 AATTACCATTAGTTTTAATTAAAAATGTAAAAAAAATCAACTTAAAATCAATTATGAGAT
66 AATTA-TATCAATTTTAATCAAAAATGTAAAAAAAATCAACTTAAAATCAATTATGAGAT
21392 NNNNNNNNNN
Statistics
Matches: 491, Mismatches: 133, Indels: 26
0.76 0.20 0.04
Matches are distributed among these distances:
169 1 0.00
170 137 0.28
171 352 0.72
172 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.36
Consensus pattern (170 bp):
GACTATAAATGGACTTTTCTTGCCAATGAATGCTCTTTTCTTCATGTTTCTTATGGTAGACATTC
AATTATATCAATTTTAATCAAAAATGTAAAAAAAATCAACTTAAAATCAATTATGAGATTATAAA
ACTATTTAAAGCTAGTAATAAGGCTTTTGAAGGACTGAGA
Found at i:21787 original size:171 final size:162
Alignment explanation
Indices: 21492--21815 Score: 309
Period size: 171 Copynumber: 1.9 Consensus size: 162
21482 NNNNNNNNNN
* * * *
21492 CATTTAAAGCGAGTAATAAGGCTTTTGAAGGACTAGGAGACTATAAATGGACTTCTCTTGCCCAT
1 CATTTAAAGCGAGTAATAAGACTTTTGAAGGAATAGGAGACTATAAATAGACTTCTCTTGCCAAT
* * * *
21557 TAATGCTCTTTTATTCACTTTTCTTGTAGTAGATATTCAATTATAGTCTGTTGTAATGAAAAATA
66 GAATGCTCTTTTATTCACGTTTCTTGTAGTAAACATTCAATTATAGTCTGTTGTAATGAAAAATA
*
21622 T-AAAAAAATTTAACTTAAAATCNNNNNNNNNNTTATAAAAT
131 TAAAAAAAAATTAACTTAAAATC----------TTATAAAAT
* * * *
21663 CATTTAAAGCGAGTACTAAGACTTTTGAAGGAATGGGTGAAC-ATAAATAGACTTTTCTTGCCAA
1 CATTTAAAGCGAGTAATAAGACTTTTGAAGGAATAGGAG-ACTATAAATAGACTTCTCTTGCCAA
* * * *
21727 TGAATAG-T-TTTGTCTTCACGTTTCTTG-AGATAAACATTC-ATATATTGTTTGTTTTAATGAA
65 TGAAT-GCTCTTT-TATTCACGTTTCTTGTAG-TAAACATTCAAT-TATAGTCTGTTGTAATGAA
*
21788 AAATGTAAAAAAAAATTAACTTAAAATC
126 AAATATAAAAAAAAATTAACTTAAAATC
21816 AATTATGTGA
Statistics
Matches: 129, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
170 7 0.05
171 99 0.77
172 23 0.18
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.35
Consensus pattern (162 bp):
CATTTAAAGCGAGTAATAAGACTTTTGAAGGAATAGGAGACTATAAATAGACTTCTCTTGCCAAT
GAATGCTCTTTTATTCACGTTTCTTGTAGTAAACATTCAATTATAGTCTGTTGTAATGAAAAATA
TAAAAAAAAATTAACTTAAAATCTTATAAAAT
Found at i:22761 original size:171 final size:169
Alignment explanation
Indices: 22313--22835 Score: 446
Period size: 171 Copynumber: 3.1 Consensus size: 169
22303 NNNNNNNNNN
* * * *
22313 TTATGAGATTATAAAACGATTTAAAGTGAGTAATAAGGGTTTTGAAGGAATGGGCGATTATAAAT
1 TTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAAT-GGAGACTATAAAT
* * **
22378 GGACTTTTTTTACCAATGAATGCTTTTTTCTTCATGTTTCTTGAGAGAGACAATCAATTATTATC
65 GGACTTTTCTT-CCAATGAATGCTTTTGTCTTCATGTTTCTCAAGAGAGACAATCAATTATTATC
*
22443 AGTTTTAATCAAAAATATAAAAAAATTTAACTTAAAATCAA
129 AGTTTTAATCAAAAATATAAAAAAATTCAACTTAAAATCAA
* * * * * *
22484 TTATTACATTATAAAATCATTTAAAGCT-AGTAATAAGGCTTTTGAAGGACTAAGAGGCTATAAA
1 TTATGAGATTATAAAACCATTTAAAG-TGAGTAATAAGGCTTTTGAAGGAAT-GGAGACTATAAA
********* * * *
22548 TGGACTTTTCTNNNNNNNNNNTGC-TTTGTTCTTCACGTTTCTCAAG-GTAGACATTTAATTA-T
64 TGGACTTTTCT-TCCAATGAATGCTTTTG-TCTTCATGTTTCTCAAGAG-AGACAATCAATTATT
* * * ********** *
22610 AGTCTA-TTTTAATGAAAAATGTAAAACAATTCANNNNNNNNNNAG
126 A-TC-AGTTTTAATCAAAAATATAAAAAAATTCAACTTAAAATCAA
* *
22655 TTATGAGATTATAAAACCATTCAAAGTGAGTAATAAGGCTTTTGAAGGAATGGATGACCATAAAT
1 TTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGA-GACTATAAAT
* * * *
22720 GGACTTTTCTTCCAAATGAATGCTTTTGTCTTCATGTTTCTCGAGATAAACACTC-ATATATTAT
65 GGACTTTTCTTCC-AATGAATGCTTTTGTCTTCATGTTTCTCAAGAGAGACAATCAAT-TATTAT
* *
22784 CTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAA
128 CAGTTTTAATCAAAAATATAAAAAAATTCAACTTAAAATCAA
*
22826 TTATGTGATT
1 TTATGAGATT
22836 NNNNNNNNNN
Statistics
Matches: 257, Mismatches: 81, Indels: 28
0.70 0.22 0.08
Matches are distributed among these distances:
170 11 0.04
171 238 0.93
172 8 0.03
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.35
Consensus pattern (169 bp):
TTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGAGACTATAAATG
GACTTTTCTTCCAATGAATGCTTTTGTCTTCATGTTTCTCAAGAGAGACAATCAATTATTATCAG
TTTTAATCAAAAATATAAAAAAATTCAACTTAAAATCAA
Found at i:30859 original size:15 final size:15
Alignment explanation
Indices: 30835--30865 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
30825 TATAATCTCA
30835 TAATTGTTTTTAAAT
1 TAATTGTTTTTAAAT
*
30850 TAATTTTTTTTAAAT
1 TAATTGTTTTTAAAT
30865 T
1 T
30866 TTTCACTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (15 bp):
TAATTGTTTTTAAAT
Found at i:32629 original size:19 final size:19
Alignment explanation
Indices: 32605--32648 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
32595 GCCTATTTAT
*
32605 AGCCTTCCATTCCTTTAGA
1 AGCCTTCCATTCCTTCAGA
32624 AGCCTTCCATTCCTTCAGA
1 AGCCTTCCATTCCTTCAGA
32643 AGCCTT
1 AGCCTT
32649 ATTACTCGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.20, C:0.34, G:0.11, T:0.34
Consensus pattern (19 bp):
AGCCTTCCATTCCTTCAGA
Found at i:39110 original size:171 final size:170
Alignment explanation
Indices: 38933--39287 Score: 408
Period size: 171 Copynumber: 2.1 Consensus size: 170
38923 TATGACCATG
*
38933 CATTCCTTCAA-AAGACTTATTACTCGCTTTAAATGGTCTTATAATCTCATAATTGATTTTAAGT
1 CATTCCTTCAACAA-ACTTATTACTCGCTTTAAATGGTCTTATAATCTCATAATTAATTTTAAGT
* * * *
38997 TGAAGTTATTTACATTTTTCTTTAAAACAGACTATAATTGAATGTCTGCCTCAAGAAAAAACAAT
65 T-AAGTTATTTACATTTTTCATTAAAACAGACTATAATTGAAGGTCTACCTCAAGAAAAAACAAG
*
39062 ATAAAAGTATTCACTAATAAGAAAAGTCCATATATAACCT-T
129 AAAAAAGTATTCACTAATAAGAAAAGTCCATATATAACCTCT
* * * * * ********
39103 CCATTCCTTTAACAACCTTTTTACTCGTTTTAAATGGTTTTATAATCTCATAATTANNNNNNNNN
1 -CATTCCTTCAACAAACTTATTACTCGCTTTAAATGGTCTTATAATCTCATAATTA-ATTTTAAG
* * * * **
39168 NTAATTTTTTTACATTTTTCATTAAAACAGACTATAATTGAAGGTCTACCTCAAGAAACATGAAG
64 TTAAGTTATTTACATTTTTCATTAAAACAGACTATAATTGAAGGTCTACCTCAAGAAAAAACAAG
* * *
39233 AAAAAAGTATTCACTTATAAGAAAAGTCCATTTATAGCCTCT
129 AAAAAAGTATTCACTAATAAGAAAAGTCCATATATAACCTCT
39275 CATTCCTTCAACA
1 CATTCCTTCAACA
39288 GCCTTTTTGC
Statistics
Matches: 152, Mismatches: 29, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
171 148 0.97
172 4 0.03
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.36
Consensus pattern (170 bp):
CATTCCTTCAACAAACTTATTACTCGCTTTAAATGGTCTTATAATCTCATAATTAATTTTAAGTT
AAGTTATTTACATTTTTCATTAAAACAGACTATAATTGAAGGTCTACCTCAAGAAAAAACAAGAA
AAAAGTATTCACTAATAAGAAAAGTCCATATATAACCTCT
Found at i:46461 original size:171 final size:170
Alignment explanation
Indices: 46201--46889 Score: 564
Period size: 171 Copynumber: 4.0 Consensus size: 170
46191 NNNNNNNNNN
* * ** * *
46201 TAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGTCATTGAATACTCTTTTCTTA
1 TAAGGCTTTTGAAGGAATGAGAGACTATAAATGCACTTTTCTTACCAATGAATACTCTTTTCTTC
* ** * *
46266 ATAGTTCTTGAGATAGATATTCAATTATAGTCTATTTTAATAAAAAATGTAAAAACATTTAACTT
66 ATATTTCTTGAGGCAGACATTCAATTATAGTCTATTTTAATAAAAAATGTAAAAACATTCAACTT
* *
46331 AAAATCGATTATTAGATTATAAAACCTTTTAAAGTATGTAA
131 AAAATCAATTATGAGATTATAAAACCTTTTAAAGTA-GTAA
* * * * * *
46372 TAAGACTTTTAAAGGAATGAGAGGCTATAAATACACTTTTCTTACCAATGAATACTTTTTTCTTT
1 TAAGGCTTTTGAAGGAATGAGAGACTATAAATGCACTTTTCTTACCAATGAATACTCTTTTCTTC
* * * * * *
46437 ATACTTCTTAAGGCAGACATTCAATTATAGTCTATTTTATTAAAAAATGTAAAAAAATTGAAATT
66 ATATTTCTTGAGGCAGACATTCAATTATAGTCTATTTTAATAAAAAATGTAAAAACATTCAACTT
**********
46502 ANNNNNNNNNNTGAGATTATAAAA-CTATTTAGAA-TGAGTAA
131 AAAATCAATTATGAGATTATAAAACCT-TTTA-AAGT-AGTAA
* ** * * * * *
46543 -AATGGCTATTGAAGGAATTTGAGGCTATAAATGGC-CTTTTTTTTATCAGTGAATGCT-TTTTC
1 TAA-GGCTTTTGAAGGAATGAGAGACTATAAAT-GCAC-TTTTCTTACCAATGAATACTCTTTT-
* * * * ***********
46605 CTTCATGTTTCTTGAGGCAGACATTCAATTATAGTTTGTTTTAATGAAAAATGTNNNNNNNNNNN
62 CTTCATATTTCTTGAGGCAGACATTCAATTATAGTCTATTTTAATAAAAAATGTAAAAACATTCA
* *
46670 ACTTAAAATCAATTATGAGATTATAAATCCATTTAAAGTAAGTAA
127 ACTTAAAATCAATTATGAGATTATAAAACCTTTTAAAGT-AGTAA
* * * *
46715 TAAGGCTTTTGAA-GAATTGAGAGACTATAAATGGACTTTTCTTGCCCATGAATACTCTTTTATT
1 TAAGGCTTTTGAAGGAA-TGAGAGACTATAAATGCACTTTTCTTACCAATGAATACTCTTTTCTT
* * * * * * *
46779 CATGTTTCTTGTGGTAGATATTCAATTATAGT-TTTTTTGAATCAAAAATATAAAAACATTCAAC
65 CATATTTCTTGAGGCAGACATTCAATTATAGTCTATTTT-AATAAAAAATGTAAAAACATTCAAC
* *
46843 TTAAAATCAATTATTAGATTATAAAACCGTTTAAAGCTAGTAA
129 TTAAAATCAATTATGAGATTATAAAACCTTTTAAAG-TAGTAA
46886 TAAG
1 TAAG
46890 NNNNNNNNNN
Statistics
Matches: 397, Mismatches: 106, Indels: 30
0.74 0.20 0.06
Matches are distributed among these distances:
170 9 0.02
171 266 0.67
172 119 0.30
173 3 0.01
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.38
Consensus pattern (170 bp):
TAAGGCTTTTGAAGGAATGAGAGACTATAAATGCACTTTTCTTACCAATGAATACTCTTTTCTTC
ATATTTCTTGAGGCAGACATTCAATTATAGTCTATTTTAATAAAAAATGTAAAAACATTCAACTT
AAAATCAATTATGAGATTATAAAACCTTTTAAAGTAGTAA
Found at i:47269 original size:171 final size:171
Alignment explanation
Indices: 46964--47468 Score: 444
Period size: 171 Copynumber: 3.0 Consensus size: 171
46954 NNNNTATCAA
* * * *
46964 TGAATGCTTTTGTCTTCACGTTTCTCGAGATAGACAGTCAATTGTTGTATATTGTAATCAAAAAT
1 TGAATACTTTTGCCTTCACGTTTCTCGAGATAGACAGTAAATTATTGTATATTGTAATCAAAAAT
* ** * *
47029 GTAAAAAAATATAACTTAAAATCAATTATTATATTAGAAAATCATTTAAAATGAGTAATAAGGCT
66 GTAAAAAAATATAACTTAAAATCAATTATTAGATTAGAAAATCATTTAAAACAAGAAAAAAGGCT
* * *
47094 TTTGAATGAATAAAAGGCTATAAATAGATTTTTCTTGCCAT
131 TTTGAAGGAATAAAAGGCTACAAATAGACTTTTCTTGCCAT
* * * *
47135 TGAATACTTTTGCCTTCA-GTTTTCTCGAGATAGATAGTAAATTATTGTCTATTTTAATCAAATA
1 TGAATACTTTTGCCTTCACG-TTTCTCGAGATAGACAGTAAATTATTGTATATTGTAATCAAAAA
* * * *
47199 TGTTAAAAAATTTAACTTAAAATCAATTATTAGATTATAAAA-CTATTTAAAGCAAGAAAAAAGG
65 TGTAAAAAAATATAACTTAAAATCAATTATTAGATTAGAAAATC-ATTTAAAACAAGAAAAAAGG
* * * * *
47263 CTTTTGAAGGAATGAGAGGCTACAAATAGACTTTTCTCGTCAA
129 CTTTTGAAGGAATAAAAGGCTACAAATAGACTTTTCTTGCCAT
* ** * * ** ** * ** * * *
47306 TGAATGCTTTTTTCTTCACTTTTTTTAAGGCAGACATTCTATTATAG-ACTATTTTAATGAAAAA
1 TGAATACTTTTGCCTTCACGTTTCTCGAGATAGACAGTAAATTATTGTA-TATTGTAATCAAAAA
* * ** * * * ** *
47370 TGTAAAAAAAT-TACCGTTAAAATTAATTACGAGATTATAAAACCATTTAGAATGAGTAAAAAGG
65 TGTAAAAAAATATAAC-TTAAAATCAATTATTAGATTAGAAAATCATTTAAAACAAGAAAAAAGG
* * * *
47434 CTGTTGAAGGACTAGGAA-GCTAGAAATAGACTTTT
129 CTTTTGAAGGAATA-AAAGGCTACAAATAGACTTTT
47469 GTTATCAATG
Statistics
Matches: 269, Mismatches: 58, Indels: 14
0.79 0.17 0.04
Matches are distributed among these distances:
170 5 0.02
171 262 0.97
172 2 0.01
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (171 bp):
TGAATACTTTTGCCTTCACGTTTCTCGAGATAGACAGTAAATTATTGTATATTGTAATCAAAAAT
GTAAAAAAATATAACTTAAAATCAATTATTAGATTAGAAAATCATTTAAAACAAGAAAAAAGGCT
TTTGAAGGAATAAAAGGCTACAAATAGACTTTTCTTGCCAT
Found at i:47479 original size:171 final size:169
Alignment explanation
Indices: 46959--47563 Score: 430
Period size: 171 Copynumber: 3.5 Consensus size: 169
46949 NNNNNNNNNT
* * * ** * * * * * *
46959 ATCAATGAATGCTTTTGTCTTCACGTTTCTCGAGATAGACAGTCAATTGTTGTA-TATTGTAATC
1 ATCAATGAATGCTTTTTTCTTCACGGTTCTCAAGGCAAACATTCAATTATAG-ACTATTTTAATA
** * * * *
47023 AAAAATGTAAAAAAATATAACTTAAAATCAATTATTATATTAGAAAATCATTTAAA-ATGAGTAA
65 AAAAATGTAAAAAAAT-TAACTTAAAATCAATTACGAGATTATAAAACCATTTAAAGA--AGAAA
* * * * * * *
47087 TAAGGCTTTTGAATGAAT-AAAAGGCTATAAATAGATTTTTCTT
127 AAAGGCTGTTGAAGGAATGAGAA-GCTACAAATAGACTTTTCTC
** * * ** * * ** * * * * * * *
47130 GCCATTGAATACTTTTGCCTTCA-GTTTTCTCGAGATAGATAGTAAATTATTGTCTATTTTAATC
1 ATCAATGAATGCTTTTTTCTTCACG-GTTCTCAAGGCAAACATTCAATTATAGACTATTTTAATA
* * ** *
47194 AAATATGTTAAAAAATTTAACTTAAAATCAATTATTAGATTATAAAACTATTTAAAGCAAGAAAA
65 AAAAATG-TAAAAAAATTAACTTAAAATCAATTACGAGATTATAAAACCATTTAAAG-AAGAAAA
* *
47259 AAGGCTTTTGAAGGAATGAGAGGCTACAAATAGACTTTTCTC
128 AAGGCTGTTGAAGGAATGAGAAGCTACAAATAGACTTTTCTC
* ** * * * * *
47301 GTCAATGAATGCTTTTTTCTTCACTTTTTTTAAGGCAGACATTCTATTATAGACTATTTTAATGA
1 ATCAATGAATGCTTTTTTCTTCACGGTTCTCAAGGCAAACATTCAATTATAGACTATTTTAATAA
* * *
47366 AAAATGTAAAAAAATTACCGTTAAAATTAATTACGAGATTATAAAACCATTTAGAATG-AGTAAA
66 AAAATGTAAAAAAATTAAC-TTAAAATCAATTACGAGATTATAAAACCATTTA-AA-GAAGAAAA
* * * *
47430 AAGGCTGTTGAAGGACT-AGGAAGCTAGAAATAGACTTTTGTT
128 AAGGCTGTTGAAGGAATGA-GAAGCTACAAATAGACTTTTCTC
* * * * *
47472 ATCAATGAATGCTTTTTTTTTCACGGTTCTCGAGGCAAACATTCAATTATAGTCTTTTTTAACAA
1 ATCAATGAATGCTTTTTTCTTCACGGTTCTCAAGGCAAACATTCAATTATAGACTATTTTAATAA
*
47537 AAAAAGTAAAAAAATTCAACTTAAAAT
66 AAAATGTAAAAAAATT-AACTTAAAAT
47564 NNNNNNNNNN
Statistics
Matches: 351, Mismatches: 71, Indels: 24
0.79 0.16 0.05
Matches are distributed among these distances:
170 13 0.04
171 322 0.92
172 14 0.04
173 2 0.01
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (169 bp):
ATCAATGAATGCTTTTTTCTTCACGGTTCTCAAGGCAAACATTCAATTATAGACTATTTTAATAA
AAAATGTAAAAAAATTAACTTAAAATCAATTACGAGATTATAAAACCATTTAAAGAAGAAAAAAG
GCTGTTGAAGGAATGAGAAGCTACAAATAGACTTTTCTC
Found at i:49099 original size:19 final size:21
Alignment explanation
Indices: 49075--49114 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
49065 GCCTATTTAT
49075 AGCCTT-TT-ATTCCTTTAAA
1 AGCCTTATTAATTCCTTTAAA
*
49094 AGCCTTATTAATTGCTTTAAA
1 AGCCTTATTAATTCCTTTAAA
49115 TAGTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 2 0.11
21 10 0.56
ACGTcount: A:0.30, C:0.17, G:0.07, T:0.45
Consensus pattern (21 bp):
AGCCTTATTAATTCCTTTAAA
Done.