Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402019.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5114.0, 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: 6098
ACGTcount: A:0.32, C:0.10, G:0.11, T:0.29
Warning! 1114 characters in sequence are not A, C, G, or T
Found at i:1203 original size:173 final size:172
Alignment explanation
Indices: 1024--1787 Score: 604
Period size: 173 Copynumber: 4.5 Consensus size: 172
1014 NNNNNNNNNN
* * * *
1024 TTTAACTAAAAATGTAAAAAAAAATTGAACTAAAAATTAATT-TGGAGATTATAATACCATATAA
1 TTTAACTAAAAAT-TAAAAAAAAATTGAACTTAAAATCAATTATGGAGATTATAAAACCATTTAA
* * * * *
1088 AGCGAGTAATAAGGCTTTTAAAAAAATAAGTGACTATAAATAGACTTTACTTGCCAATGAATGTC
65 AGCGAGTAATAAGGCTTTTAAAGAAATAAGAGACTACAAATTGACTTTTCTTGCCAATGAATGTC
1153 TTTTTCTTCACGTTTCTTGAGGTGAACATTTAATTATAATCTGT
130 TTTTTCTTCACGTTTCTTGAGGT-AACATTTAATTATAATCTGT
* * * *
1197 TTTAACTAAAAA-TATAAAAAAATTTAACTTGAAATCAATTATGG-GATTATAAAACAATTTAAA
1 TTTAACTAAAAATTAAAAAAAAATTGAACTTAAAATCAATTATGGAGATTATAAAACCATTTAAA
** * *
1260 GCGAGTAATAAAACTTTTAAAGGAATAGGAGACTACAAATTGACTTTTCTTGCCAATGAATG-CT
66 GCGAGTAATAAGGCTTTTAAAGAAATAAGAGACTACAAATTGACTTTTCTTGCCAATGAATGTC-
* * *
1324 TTTTTCTTCACGTTTCTTAAGGTAGACATTAAATTATTATCTGT
130 TTTTTCTTCACGTTTCTTGAGGTA-ACATTTAATTATAATCTGT
********* *
1368 TTTAACTAANNNNNNNNNNAAAAATTGAACTTAAAATCAATTAT-GAGAGTATAAAACCATTTAA
1 TTTAACTAA-AAATTAAAAAAAAATTGAACTTAAAATCAATTATGGAGATTATAAAACCATTTAA
* * * * *
1432 A-CTGAGTAATAAGGCTTTTGAAGAAATGAGAGACTACAAATTGACTTTTCTTCCCAATAAATAT
65 AGC-GAGTAATAAGGCTTTTAAAGAAATAAGAGACTACAAATTGACTTTTCTTGCCAATGAATGT
* ** * * * * *
1496 TTTTTTCAACATGTTTCTTGAGATAAGCATTTAATTATAGTGTAT
129 CTTTTTCTTCACGTTTCTTGAGGTAA-CATTTAATTATAATCTGT
* * * ****
1541 TTTAA-TGAAAAA-T-ATAAAAAATTCAACTTAAAATCAATTAT-GAGTTTATAAAACCATNNNN
1 TTTAACT-AAAAATTAAAAAAAAATTGAACTTAAAATCAATTATGGAGATTATAAAACCATTTAA
****** * * * ** * * * * * *
1602 NNNNNNTAATAGGGCTTTTGAAGGAATGGGTGACTATAAATAGATTTTTCTTACCAATGAAT-CC
65 AGCGAGTAATAAGGCTTTTAAAGAAATAAGAGACTACAAATTGACTTTTCTTGCCAATGAATGTC
** ** *
1666 TTTTTTCTTCACGTTTCTCAAGGTAA-ATATTCAATTATGTTCTAT
130 -TTTTTCTTCACGTTTCTTGAGGTAACAT-TT-AATTATAATCTGT
** ** *
1711 TTT-ACTAACAAATGT-AAAAAATCTTGAACTTAAAATCAATT-TTAAGATTATAAAACTATTTA
1 TTTAACTAA-AAAT-TAAAAAAAAATTGAACTTAAAATCAATTATGGAGATTATAAAACCATTTA
*
1773 AAGTGAGTAATAAGG
64 AAGCGAGTAATAAGG
1788 NNNNNNNNNN
Statistics
Matches: 463, Mismatches: 109, Indels: 39
0.76 0.18 0.06
Matches are distributed among these distances:
168 2 0.00
169 5 0.01
170 123 0.27
171 141 0.30
172 50 0.11
173 142 0.31
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.35
Consensus pattern (172 bp):
TTTAACTAAAAATTAAAAAAAAATTGAACTTAAAATCAATTATGGAGATTATAAAACCATTTAAA
GCGAGTAATAAGGCTTTTAAAGAAATAAGAGACTACAAATTGACTTTTCTTGCCAATGAATGTCT
TTTTCTTCACGTTTCTTGAGGTAACATTTAATTATAATCTGT
Found at i:1318 original size:171 final size:170
Alignment explanation
Indices: 1024--1787 Score: 637
Period size: 171 Copynumber: 4.4 Consensus size: 170
1014 NNNNNNNNNN
* * * * *
1024 TTTAACTAAAAATGTAAAAAAAAATTGAACTAAAAATTAATT-TGGAGATTATAATACCATATAA
1 TTTAACTAAAAA--TATAAAAAAATTGAACTTAAAATCAATTAT-GAGATTATAAAACCATTTAA
* * * * * *
1088 AGCGAGTAATAAGGCTTTTAAAAAAATAAGTGACTATAAATAGACTTTACTTGCCAATGAATGTC
63 AGCGAGTAATAAGGCTTTTAAAGAAATAGGAGACTACAAATTGACTTTTCTTGCCAATGAATGTC
1153 TTTTTCTTCACGTTTCTTGAGGTGAACATTTAATTATAATCTGT
128 TTTTTCTTCACGTTTCTTGAGGT-AACATTTAATTATAATCTGT
* * * *
1197 TTTAACTAAAAATATAAAAAAATTTAACTTGAAATCAATTATGGGATTATAAAACAATTTAAAGC
1 TTTAACTAAAAATATAAAAAAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGC
** *
1262 GAGTAATAAAACTTTTAAAGGAATAGGAGACTACAAATTGACTTTTCTTGCCAATGAATG-CTTT
66 GAGTAATAAGGCTTTTAAAGAAATAGGAGACTACAAATTGACTTTTCTTGCCAATGAATGTC-TT
* * *
1326 TTTCTTCACGTTTCTTAAGGTAGACATTAAATTATTATCTGT
130 TTTCTTCACGTTTCTTGAGGTA-ACATTTAATTATAATCTGT
******** *
1368 TTTAACTAANNNNNNNNNNAAAAATTGAACTTAAAATCAATTATGAGAGTATAAAACCATTTAAA
1 TTTAACTAA--AAATATAAAAAAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA
* * * *
1433 -CTGAGTAATAAGGCTTTTGAAGAAAT-GAGAGACTACAAATTGACTTTTCTTCCCAATAAATAT
64 GC-GAGTAATAAGGCTTTTAAAGAAATAG-GAGACTACAAATTGACTTTTCTTGCCAATGAATGT
* ** * * * * *
1496 TTTTTTCAACATGTTTCTTGAGATAAGCATTTAATTATAGTGTAT
127 CTTTTTCTTCACGTTTCTTGAGGTAA-CATTTAATTATAATCTGT
* * ******
1541 TTTAA-TGAAAAATAT-AAAAAATTCAACTTAAAATCAATTATGAGTTTATAAAACCATNNNNNN
1 TTTAACT-AAAAATATAAAAAAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
**** * * * * * * * * * *
1604 NNNNTAATAGGGCTTTTGAAGGAATGGGTGACTATAAATAGATTTTTCTTACCAATGAAT-CCTT
65 CGAGTAATAAGGCTTTTAAAGAAATAGGAGACTACAAATTGACTTTTCTTGCCAATGAATGTC-T
** ** *
1668 TTTTCTTCACGTTTCTCAAGGTAA-ATATTCAATTATGTTCTAT
129 TTTTCTTCACGTTTCTTGAGGTAACAT-TT-AATTATAATCTGT
* * * * *
1711 TTT-ACTAACAAATGTAAAAAATCTTGAACTTAAAATCAATTTTAAGATTATAAAACTATTTAAA
1 TTTAACTAA-AAATATAAAAAA-ATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA
*
1775 GTGAGTAATAAGG
64 GCGAGTAATAAGG
1788 NNNNNNNNNN
Statistics
Matches: 464, Mismatches: 108, Indels: 39
0.76 0.18 0.06
Matches are distributed among these distances:
168 2 0.00
169 5 0.01
170 124 0.27
171 147 0.32
172 43 0.09
173 143 0.31
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.35
Consensus pattern (170 bp):
TTTAACTAAAAATATAAAAAAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGC
GAGTAATAAGGCTTTTAAAGAAATAGGAGACTACAAATTGACTTTTCTTGCCAATGAATGTCTTT
TTCTTCACGTTTCTTGAGGTAACATTTAATTATAATCTGT
Found at i:2312 original size:169 final size:167
Alignment explanation
Indices: 2004--2884 Score: 575
Period size: 169 Copynumber: 5.2 Consensus size: 167
1994 NNNNNNNNNG
* * ** *
2004 GACTTTTCTTGTCAATGAATG-TCTTTTTCTTCATGTTTCTTGAGGTAAACATTTAATTATAATC
1 GACTTTT-TTGACAATGAATGCT-TTTTTCTTCACGTTTCTCAAGGTAAACATTCAATTATAATC
* * * ********** *
2068 TGTTTTAACCAAAAATATAAAAACAATTGAACTTAAAATCAATTTTGNNNNNNNNNNATCATTTA
64 TG-TTTAACAAAAAATAT-AAAA-AA-TAAACTTAAAATCAATTATGAGATGATAAAACCATTTA
* * *
2133 AAGTGAGTAATAAGGCTTTTGAAAGAATGGGAGACTACAAATA
125 AAGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATA
* * * * *
2176 GACTTTTTTGACAATGAATGCTTTTTTCTTCACGTTTTTCAAAGTAGACATTCCATTATTATCTG
1 GACTTTTTTGACAATGAATGCTTTTTTCTTCACGTTTCTCAAGGTAAACATTCAATTATAATCTG
* * * *
2241 CTTTAATAAAAAATATAAAAATATAAACTTAAAATCAATTATTAGATGACAAAACCATTTAAAGT
66 -TTTAACAAAAAATATAAAAA-ATAAACTTAAAATCAATTATGAGATGATAAAACCATTTAAAGC
* ***********
2306 GAGTAATAAGGCTTTTGAACGAATGGGTNNNNNNNNNNG
129 GAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATA
* * * * * *
2345 GACTTTTCTTGCCAATGAAT-ATCTTTTCTTCATGTTTCTCAAGGTAAACGTTTAATTATAATCT
1 GACTTTT-TTGACAATGAATGCTTTTTTCTTCACGTTTCTCAAGGTAAACATTCAATTATAATCT
* * * * *
2409 GTTTCAACAGAAAACT-TAAAAAAATTGAAC-TAAAATCAATT-TCGAGATTATAATACCATATA
65 GTTT-AACA-AAAAATAT-AAAAAA-TAAACTTAAAATCAATTAT-GAGATGATAAAACCATTTA
* * *
2471 AACCGAGTAATAAGGTTTTTGAAAGAATGGGTGACTATAAAGA
125 AAGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATA
* * * * *
2514 GACTTTTCTT-ACCAATGAATGCCTATTTCTTCATGTTT-TCTAAGGCAAACATTCAATTATAGT
1 GACTTTT-TTGA-CAATGAATGCTTTTTTCTTCACGTTTCTC-AAGGTAAACATTCAATTATAAT
******** * *
2577 CTGTTTTAATC-AAAAATATANNNNNNNNNNACTTAAAATCAATTATAAGATTG-TAAAATCATT
63 CTG-TTTAA-CAAAAAATATA--AAAAATAAACTTAAAATCAATTATGAGA-TGATAAAACCATT
* * * * * *
2640 TAAAGCAAGTAATAAGCCATTTGAAGGAATGTGTGACTATAAATT
123 TAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATA
* *
2685 GACTTTTTTTG-CAAATGAAT-CTCTATTTCTTCACGTTTCTCAAGGTACACAATT-AATTATAA
1 GAC-TTTTTTGAC-AATGAATGCT-TTTTTCTTCACGTTTCTCAAGGTAAAC-ATTCAATTATAA
* * * * * * *
2747 TTTGGTTTAACCAAAAATAT-AAAAA-AAACTTAAAATTAATTATGAGGTTATAAAATCATTTAC
62 TCT-GTTTAACAAAAAATATAAAAAATAAACTTAAAATCAATTATGAGATGATAAAACCATTTAA
* * *
2810 AGCGAGTAATAAGGCTTCTGAAAGAATGAGTGACTATAAATG
126 AGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATA
* * *
2852 GACATTTCTTGCCAATGAATGCCTTTTTCTTCA
1 GAC-TTTTTTGACAATGAATGCTTTTTTCTTCA
2885 TGTTCTCCGA
Statistics
Matches: 544, Mismatches: 135, Indels: 65
0.73 0.18 0.09
Matches are distributed among these distances:
166 1 0.00
167 89 0.16
168 6 0.01
169 181 0.33
170 72 0.13
171 175 0.32
172 20 0.04
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.35
Consensus pattern (167 bp):
GACTTTTTTGACAATGAATGCTTTTTTCTTCACGTTTCTCAAGGTAAACATTCAATTATAATCTG
TTTAACAAAAAATATAAAAAATAAACTTAAAATCAATTATGAGATGATAAAACCATTTAAAGCGA
GTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATA
Found at i:2912 original size:167 final size:164
Alignment explanation
Indices: 2003--2939 Score: 528
Period size: 171 Copynumber: 5.5 Consensus size: 164
1993 NNNNNNNNNN
* * * ** * * *
2003 GGACTTTTCTTGTCAATGAATGTCTTTTTCTTCATGTTTCTTGAGGTAAACATTTAATTATAATC
1 GGACTTTTCTTGCCAATGAATGCCTATTTCTTCATGTTTC-CAAGGCAAACATTCAATTATAATA
* ***********
2068 TGTTTTAACCAAAAATATAAAAACAATTGAACTTAAAATCAATTTTGNNNNNNNNNNATCATTTA
65 TG-TTTAACCAAAAATAT-AAAA-AA---AACTTAAAATCAATTATAAGATTATAAAATCATTTA
* * * *
2133 AAGTGAGTAATAAGGCTTTTGAAAGAATGGGAGACTACAAAT
124 AAGCGAGTAATAAGGC-TTTGAAAGAATGAGTGACTATAAAT
* * * * * * * * * * * *
2175 AGACTTTT-TTGACAATGAATGCTTTTTTCTTCACGTTTTTCAAAGTAGACATTCCATTATTATC
1 GGACTTTTCTTGCCAATGAATGCCTATTTCTTCATG-TTTCCAAGGCAAACATTCAATTATAATA
** * * * *
2239 TGCTTTAATAAAAAATATAAAAATATAAACTTAAAATCAATTATTAGATGACAAAACCATTTAAA
65 TG-TTTAACCAAAAATAT-AAAA-A-AAACTTAAAATCAATTATAAGATTATAAAATCATTTAAA
* * * **********
2304 GTGAGTAATAAGGCTTTTGAACGAATGGGTNNNNNNNNNN
126 GCGAGTAATAAGGC-TTTGAAAGAATGAGTGACTATAAAT
** * * * *
2344 GGACTTTTCTTGCCAATGAATATCT-TTTCTTCATGTTTCTCAAGGTAAACGTTTAATTATAATC
1 GGACTTTTCTTGCCAATGAATGCCTATTTCTTCATGTTTC-CAAGGCAAACATTCAATTATAATA
* * * *
2408 TGTTTCAA-CAGAAAACT-TAAAAAAATTGAAC-TAAAATCAATT-TCGAGATTATAATACCATA
65 TGTTT-AACCA-AAAA-TAT-AAAAAA---AACTTAAAATCAATTAT-AAGATTATAAAATCATT
* * *
2469 TAAACCGAGTAATAAGGTTTTTGAAAGAATGGGTGACTATAAA-
122 TAAAGCGAGTAATAAGG-CTTTGAAAGAATGAGTGACTATAAAT
* * *
2512 GAGACTTTTCTTACCAATGAATGCCTATTTCTTCATGTTTTCTAAGGCAAACATTCAATTATAGT
1 G-GACTTTTCTTGCCAATGAATGCCTATTTCTTCATG-TTTCCAAGGCAAACATTCAATTATAAT
* * ****** *
2577 CTGTTTTAATCAAAAATATANNNNNNNNNNACTTAAAATCAATTATAAGATTGTAAAATCATTTA
64 ATG-TTTAACCAAAAATATA----AAAAAAACTTAAAATCAATTATAAGATTATAAAATCATTTA
* * * *
2642 AAGCAAGTAATAAGCCATTTGAAGGAATGTGTGACTATAAAT
124 AAGCGAGTAATAAGGC-TTTGAAAGAATGAGTGACTATAAAT
* * * * * *
2684 TGACTTTTTTTGCAAATGAAT-CTCTATTTCTTCACGTTTCTCAAGGTACACAATT-AATTATAA
1 GGACTTTTCTTGCCAATGAATGC-CTATTTCTTCATGTTTC-CAAGGCAAAC-ATTCAATTATAA
* * * * *
2747 TTTGGTTTAACCAAAAATATAAAAAAAACTTAAAATTAATTATGAGGTTATAAAATCATTTACAG
63 TAT-GTTTAACCAAAAATATAAAAAAAACTTAAAATCAATTATAAGATTATAAAATCATTTAAAG
2812 CGAGTAATAAGGCTTCTGAAAGAATGAGTGACTATAAAT
127 CGAGTAATAAGGCTT-TGAAAGAATGAGTGACTATAAAT
* * **
2851 GGACATTTCTTGCCAATGAATGCCTTTTTCTTCATGTTCTCCGAA-GCAGGCATTCAATTATACA
1 GGACTTTTCTTGCCAATGAATGCCTATTTCTTCATGTT-TCC-AAGGCAAACATTCAATTATA-A
*
2915 CTAT-TTTAACCAAAAACATAAAAAA
63 -TATGTTTAACCAAAAATATAAAAAA
2940 TTTAACTTAA
Statistics
Matches: 592, Mismatches: 136, Indels: 79
0.73 0.17 0.10
Matches are distributed among these distances:
166 5 0.01
167 127 0.21
168 16 0.03
169 178 0.30
170 61 0.10
171 189 0.32
172 16 0.03
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.34
Consensus pattern (164 bp):
GGACTTTTCTTGCCAATGAATGCCTATTTCTTCATGTTTCCAAGGCAAACATTCAATTATAATAT
GTTTAACCAAAAATATAAAAAAAACTTAAAATCAATTATAAGATTATAAAATCATTTAAAGCGAG
TAATAAGGCTTTGAAAGAATGAGTGACTATAAAT
Found at i:3271 original size:171 final size:170
Alignment explanation
Indices: 2981--3996 Score: 742
Period size: 168 Copynumber: 6.0 Consensus size: 170
2971 NNNNNNNNNN
* * * * * * * *
2981 GTGACTATAAATGGACTTTTCTTGCCAATGAATGCGTTTTTTTTCATGTTTCTCGAGGTAGACAT
1 GTGACTATAAATGCACTTTTCTTACCAATGAATACATTTTTCTTAACGTTTCTCAAGGTAGACAT
* * * *
3046 TCAACTGTAGTCTGTTTTAACCAAAAATGTAAAAAACCTCAACTTAAAATGAATTATGAGAGTAC
66 TCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAA-TTCAACTTAAAATGAATTATGAGATTAC
3111 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATTG
130 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATTG
* * * * ********** *
3152 GTGAATATAAATGGACTTTTCTTGCCAATGAATGTC-TTTTTCTTNNNNNNNNNNAAGGTAAACA
1 GTGACTATAAATGCACTTTTCTTACCAATGAAT-ACATTTTTCTTAACGTTTCTCAAGGTAGACA
* * * *
3216 TTCAATTATAGTCTGTTTTAACCAAAAATATAAGAAAATTTAAATTAAAATGAATTATAAGATTA
65 TTCAATTATAGTCTGTTTTAACCAAAAATGTAA-AAAATTCAACTTAAAATGAATTATGAGATTA
* * *
3281 CAGAACCGTTTAAAGCGAGTAATAAGGCTTTTCAAAGAA-TG
129 CAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATTG
* * * * *
3322 AGTGACTATAAATGCACTTTTTTTACCCATGAATACATTTTTCTTAACGTTTCTCGAGATAGACT
1 -GTGACTATAAATGCACTTTTCTTACCAATGAATACATTTTTCTTAACGTTTCTCAAGGTAGACA
* * * * * *
3387 TTTAGTTATAGTCTGTTTTAACCAAAAATGTAAAAAATTCAACCTACAATCAATTATGAGATTAT
65 TTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAATTCAACTTAAAATGAATTATGAGATTAC
* * *
3452 AAAACCATTTAAAGCGATTAATTAGGCTTTTGAAAGAATGG
130 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATTG
* * * * *
3493 GAGACTATAAATGCACTTTTTTTACCCATAGAA-GC-TTTTT-TTTACGTTTCTCAAGGTAGACA
1 GTGACTATAAATGCACTTTTCTTACCAAT-GAATACATTTTTCTTAACGTTTCTCAAGGTAGACA
* ** ********** * *
3555 TTCAACTATAGTCTGTTTTAAGTAAAAATGTAAAAAATNNNNNNNNNNATCAATTATGAGATTAT
65 TTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAATTCAACTTAAAATGAATTATGAGATTAC
* * * * *
3620 AAAACCATTTAAAGCAATTAATTAGTCTTTTGAAAGAATGG
130 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATTG
* * * * * * * *
3661 GTGACTATAAATGGATTTTTTTTACCCAT-AAAAGC-TTTTTTTTATA--TTTCTCGAGGTAGAT
1 GTGACTATAAATGCACTTTTCTTACCAATGAATA-CATTTTTCTTA-ACGTTTCTCAAGGTAGAC
* ** ********** *
3722 ATTCAACTATAGTCTGTTTTAAGTAAAAATGTAAAAAATNNNNNNNNNNATCAATTATGAGATTA
64 ATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAATTCAACTTAAAATGAATTATGAGATTA
* * * * *
3787 TAAAACCATTTAAAGCGATTAATCAGGCTTTTAAAAGAATGG
129 CAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATTG
* ** * * * * * *
3829 GTGACTATAAATAG-AATTTTCTTTTCAATGAATGCCTTTCTCTTCATA-ATTTTTCTAGGTAGA
1 GTGACTATAAAT-GCACTTTTCTTACCAATGAATACATTTTTCTT-A-ACGTTTCTCAAGGTAGA
* * * * * * * * *
3892 CATCCAATTATAATCTGTTTTAACCAATAACGTAAAAACAAATTGAACCTAAAATCAATTTTAAG
63 CATTCAATTATAGTCTGTTTTAACCAAAAATGT--AAA-AAATTCAACTTAAAATGAATTATGAG
* * *
3957 ATTATAAAACAATTTCAAGCGAGTAATAAGGCTTTT-AAAG
125 ATTACAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAG
3997 GAATAAAGGA
Statistics
Matches: 696, Mismatches: 131, Indels: 34
0.81 0.15 0.04
Matches are distributed among these distances:
166 2 0.00
168 278 0.40
169 16 0.02
170 94 0.14
171 248 0.36
172 5 0.01
173 7 0.01
174 46 0.07
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.35
Consensus pattern (170 bp):
GTGACTATAAATGCACTTTTCTTACCAATGAATACATTTTTCTTAACGTTTCTCAAGGTAGACAT
TCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAATTCAACTTAAAATGAATTATGAGATTACA
AAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATTG
Found at i:3616 original size:168 final size:168
Alignment explanation
Indices: 2981--3840 Score: 772
Period size: 168 Copynumber: 5.1 Consensus size: 168
2971 NNNNNNNNNN
* * * * *
2981 GTGACTATAAATGGACTTTTCTTGCCAAT-GAATGCGTTTTTTTTCATGTTTCTCGAGGTAGACA
1 GTGACTATAAATGCACTTTTTTTACCCATAGAA-GC-TTTTTTTT-ACGTTTCTCGAGGTAGACA
* ** * * * * *
3045 TTCAACTGTAGTCTGTTTTAACCAAAAATGTAAAAAACCTCAACTTAAAATGAATTATGAGAGTA
63 TTCAACTATAGTCTGTTTTAAGTAAAAATGTAAAAAA-TTCAACCTACAATCAATTATGAGATTA
* * * *
3110 CAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATTG
127 TAAAACCATTTAAAGCGATTAATTAGGCTTTTGAAAGAATGG
* * * * * *********** *
3152 GTGAATATAAATGGACTTTTCTTGCCAAT-GAATGTCTTTTTCTTNNNNNNNNNNAAGGTAAACA
1 GTGACTATAAATGCACTTTTTTTACCCATAGAA-G-CTTTTT-TTTACGTTTCTCGAGGTAGACA
* ** * * ** * * *
3216 TTCAATTATAGTCTGTTTTAACCAAAAATATAAGAAAATTTAAATTAAAATGAATTATAAGATTA
63 TTCAACTATAGTCTGTTTTAAGTAAAAATGTAA-AAAATTCAACCTACAATCAATTATGAGATTA
* * * * * * *
3281 CAGAACCGTTTAAAGCGAGTAATAAGGCTTTTCAAAGAATGA
127 TAAAACCATTTAAAGCGATTAATTAGGCTTTTGAAAGAATGG
* * * *
3323 GTGACTATAAATGCACTTTTTTTACCCAT-GAATACATTTTTCTTAACGTTTCTCGAGATAGACT
1 GTGACTATAAATGCACTTTTTTTACCCATAGAA-GC-TTTTT-TTTACGTTTCTCGAGGTAGACA
* ** **
3387 TTTAGTTATAGTCTGTTTTAACCAAAAATGTAAAAAATTCAACCTACAATCAATTATGAGATTAT
63 TTCAACTATAGTCTGTTTTAAGTAAAAATGTAAAAAATTCAACCTACAATCAATTATGAGATTAT
3452 AAAACCATTTAAAGCGATTAATTAGGCTTTTGAAAGAATGG
128 AAAACCATTTAAAGCGATTAATTAGGCTTTTGAAAGAATGG
* *
3493 GAGACTATAAATGCACTTTTTTTACCCATAGAAGCTTTTTTTTACGTTTCTCAAGGTAGACATTC
1 GTGACTATAAATGCACTTTTTTTACCCATAGAAGCTTTTTTTTACGTTTCTCGAGGTAGACATTC
**********
3558 AACTATAGTCTGTTTTAAGTAAAAATGTAAAAAATNNNNNNNNNNATCAATTATGAGATTATAAA
66 AACTATAGTCTGTTTTAAGTAAAAATGTAAAAAATTCAACCTACAATCAATTATGAGATTATAAA
* *
3623 ACCATTTAAAGCAATTAATTAGTCTTTTGAAAGAATGG
131 ACCATTTAAAGCGATTAATTAGGCTTTTGAAAGAATGG
* * * ** *
3661 GTGACTATAAATGGATTTTTTTTACCCATAAAAGCTTTTTTTTATATTTCTCGAGGTAGATATTC
1 GTGACTATAAATGCACTTTTTTTACCCATAGAAGCTTTTTTTTACGTTTCTCGAGGTAGACATTC
**********
3726 AACTATAGTCTGTTTTAAGTAAAAATGTAAAAAATNNNNNNNNNNATCAATTATGAGATTATAAA
66 AACTATAGTCTGTTTTAAGTAAAAATGTAAAAAATTCAACCTACAATCAATTATGAGATTATAAA
* *
3791 ACCATTTAAAGCGATTAATCAGGCTTTTAAAAGAATGG
131 ACCATTTAAAGCGATTAATTAGGCTTTTGAAAGAATGG
3829 GTGACTATAAAT
1 GTGACTATAAAT
3841 AGAATTTTCT
Statistics
Matches: 587, Mismatches: 97, Indels: 13
0.84 0.14 0.02
Matches are distributed among these distances:
168 275 0.47
169 5 0.01
170 90 0.15
171 210 0.36
172 7 0.01
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.34
Consensus pattern (168 bp):
GTGACTATAAATGCACTTTTTTTACCCATAGAAGCTTTTTTTTACGTTTCTCGAGGTAGACATTC
AACTATAGTCTGTTTTAAGTAAAAATGTAAAAAATTCAACCTACAATCAATTATGAGATTATAAA
ACCATTTAAAGCGATTAATTAGGCTTTTGAAAGAATGG
Found at i:4039 original size:125 final size:121
Alignment explanation
Indices: 3885--4113 Score: 280
Period size: 121 Copynumber: 1.9 Consensus size: 121
3875 TAATTTTTCT
* ** *
3885 AGGTAGACATCCAATTATAATCTGTTTTAACCAATAACGTAAAAACAAATTGAACCT-AAAATCA
1 AGGTAGACATCCAATTATAATCTATTTT-A--AATAAAATAAAAA-AAATTCAA-CTGAAAATCA
* * *
3949 ATTTTAAGATTATAAAACAATTTCAAGCGAGTAATAAGGCTTTTAAAGGAATAAAGGAATA
61 ATTATAACATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATAAAGGAATA
* * * *
4010 AGGTAGACATTCAATTATAGTCTATTTTAAATAAAATATAAAAAATTCAATTGAAAATCAATTAT
1 AGGTAGACATCCAATTATAATCTATTTTAAATAAAATAAAAAAAATTCAACTGAAAATCAATTAT
* * *
4075 GACATTATAAAACCATTTAAAGCTAGTAATAAGGCTTTT
66 AACATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTT
4114 TTAGGAATTG
Statistics
Matches: 89, Mismatches: 14, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
120 1 0.01
121 52 0.58
122 10 0.11
124 1 0.01
125 25 0.28
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.31
Consensus pattern (121 bp):
AGGTAGACATCCAATTATAATCTATTTTAAATAAAATAAAAAAAATTCAACTGAAAATCAATTAT
AACATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTAAAGGAATAAAGGAATA
Found at i:6006 original size:170 final size:172
Alignment explanation
Indices: 5684--6096 Score: 482
Period size: 170 Copynumber: 2.4 Consensus size: 172
5674 ATTTAAAGCA
* * * *
5684 AGTAATAAGGCTTTTGAATGAAT-AGGTTACTATAAAAGGACTTTTC-TACCAATGAATGCCTTT
1 AGTAATAAGGCTTTTGAAAGAATGA-GTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTT
* * *
5747 TTCTTCAAGTTTTTCAAGAAACACATTTAATTATAGTCTGTCTTAACCAAAAATGTAAAAAAAAA
65 TTCTTCAAGTTTCTCAAGAAACACATTCAATTATAGTCTATCTTAACCAAAAATG-AAAAAAAAA
* * * *
5812 TACAACTTAAAATTAATTATGAGATTATAAAA-TCAATTACAGCG
129 TACAACTTAAAATCAATTATGAGATTAAAAAACT-AATTAAAACG
* * *
5856 AGTAATAAGGCTTTTGAAAGAATGAGTGAGTATAAATGGACATTCCTTGCCAATGAATGCCTTTT
1 AGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTT
* * * * *
5921 TCTTCACG-TTCTCTAAGACAA-GCATTCAATTATTGTCTAT-TTGAACTAAAAA-G-ATAAAAA
66 TCTTCAAGTTTCTC-AAGA-AACACATTCAATTATAGTCTATCTT-AACCAAAAATGAAAAAAAA
* *
5981 ATTCAACTTAAAATCAATTATGAGATTAAAAAACTATTTAAAACG
128 ATACAACTTAAAATCAATTATGAGATTAAAAAACTAATTAAAACG
* * * **
6026 AGTAATAAGGATTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTGCTAATGAATATCTTTT
1 AGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTT
6091 TCTTCA
66 TCTTCA
6097 TG
Statistics
Matches: 206, Mismatches: 29, Indels: 14
0.83 0.12 0.06
Matches are distributed among these distances:
170 106 0.51
171 1 0.00
172 45 0.22
173 52 0.25
174 2 0.01
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.34
Consensus pattern (172 bp):
AGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTT
TCTTCAAGTTTCTCAAGAAACACATTCAATTATAGTCTATCTTAACCAAAAATGAAAAAAAAATA
CAACTTAAAATCAATTATGAGATTAAAAAACTAATTAAAACG
Done.