Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398481.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1777.0, 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: 7922
ACGTcount: A:0.30, C:0.09, G:0.10, T:0.28
Warning! 1822 characters in sequence are not A, C, G, or T
Found at i:380 original size:170 final size:171
Alignment explanation
Indices: 4--848 Score: 779
Period size: 170 Copynumber: 5.0 Consensus size: 171
1 TCA
* * * * *
4 ATTATGAGATTATAAAATTATTTAAAGCGAGTAATAAGGCTTTCGAAGATATAGGTAACTATAAG
1 ATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTCGAAGACATGGGTGACTATAAA
* * * * * *
69 TAGATTTTTCTTACCAGTAGATATCTTTTTCTTCATG-TTTCCAGAGGTAAACATTAAATTATAA
66 TGGACTTTTCTTACCAATGGATATCTTTTTCTTCATGTTTTCTA-AGGTAAACATTCAATTATAA
* * **
133 TTTGTTTGAATAAAAAATGTAAAAAATTTCAGTTTAAAATCT
130 TTTGTTTTAATAAAAAATGTAAAAAAATTCAACTTAAAATCT
* * * *
175 ATTATGAGATTTTAAAAATATTTAAAGCAAGTAATAAGGCTTTCGAAGACATGGGTGGCTATAAA
1 ATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTCGAAGACATGGGTGACTATAAA
* ** *
240 TAGACTTTTCTTGTCAATGGATATC-TTTTCTTCATGTTTTCTAAGGAAAACATTCAATTATAAT
66 TGGACTTTTCTTACCAATGGATATCTTTTTCTTCATGTTTTCTAAGGTAAACATTCAATTATAAT
* * *
304 TTGTTTTAATGAAAAATATAAAAAAATTCAACTTAAAATAT
131 TTGTTTTAATAAAAAATGTAAAAAAATTCAACTTAAAATCT
* * ** * * ** *
345 ATTTTGAGATTGTAAAACTATTCGAAGTGAGTAATAAGGCTTTCGAAGGCATGACTGATTATAAA
1 ATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTCGAAGACATGGGTGACTATAAA
* * * * * * *
410 TGGACTTTTCTTACTAATGGATATCTTTTTCTTTACGTTTTCTGAGGTAGACATTCAATTCTTAT
66 TGGACTTTTCTTACCAATGGATATCTTTTTCTTCATGTTTTCTAAGGTAAACATTCAATTATAAT
* * ***
475 CTGTTTTAATGAAAAATGTAAAAAAATTCAACTTAAAANNN
131 TTGTTTTAATAAAAAATGTAAAAAAATTCAACTTAAAATCT
******* *
516 NNNNNNNGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTC-AA-ACGTATGGGTGACTATA
1 ATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTCGAAGAC--ATGGGTGACTATA
* * * * * *
579 AGTGGATTTTTTTTACCAATAGATATCTTTTTCTTCATG-TTTCTAGAGGTAGA-ATTAAATTAT
64 AATGGACTTTTCTTACCAATGGATATCTTTTTCTTCATGTTTTCTA-AGGTAAACATTCAATTAT
* * * * * *
642 AACTTGTTTGAATAAAAAATGTAAAAATATTTAGCTGAAAATCT
128 AATTTGTTTTAATAAAAAATGTAAAAAAATTCAACTTAAAATCT
* * * ********** *
686 ATTATAAGATTTTAAAAAC-ATTTAAAGCGAGTAATAAGGTTTTNNNNNNNNNNGGTGACTACAA
1 ATTATGAGATTAT-AAAACTATTTAAAGCGAGTAATAAGGCTTTCGAAGACATGGGTGACTATAA
*** * * *
750 ATGGACTTTTCTTGGTAATGAATATC-TTTTCTTCATGTTTTCCAAGGAAAACATTCAATTATAA
65 ATGGACTTTTCTTACCAATGGATATCTTTTTCTTCATGTTTTCTAAGGTAAACATTCAATTATAA
* * *
814 TATGTTTTAATAAAAAATATAAAAACATTCAACTT
130 TTTGTTTTAATAAAAAATGTAAAAAAATTCAACTT
849 NNNNNNNNNN
Statistics
Matches: 537, Mismatches: 127, Indels: 21
0.78 0.19 0.03
Matches are distributed among these distances:
169 17 0.03
170 284 0.53
171 236 0.44
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.37
Consensus pattern (171 bp):
ATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTCGAAGACATGGGTGACTATAAA
TGGACTTTTCTTACCAATGGATATCTTTTTCTTCATGTTTTCTAAGGTAAACATTCAATTATAAT
TTGTTTTAATAAAAAATGTAAAAAAATTCAACTTAAAATCT
Found at i:1671 original size:171 final size:171
Alignment explanation
Indices: 1324--1923 Score: 553
Period size: 171 Copynumber: 3.5 Consensus size: 171
1314 NNNNNNNNNN
** * * *
1324 ATTATAATTTGTTTCAATAAAAAATGTAAAAAAATTCAACTTAAAATCAATTTTGTGATTATAAA
1 ATTATAACCTGTTTTAATAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
* * * * * * * *
1389 ACCATTTAAAGCAAATAATAAGACTTTCGAAGGCATGGGAGACTATAAATGGACTTTTCTTGTCA
66 ACTATTTAAAACTAGTAATAAGGCTTTCGAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCA
* ** *
1454 ATGGATATCTTTTTTTTCACACTTCTTGAGGTAGGCATTTA
131 ATGGATATCTTTTTTTTCACACTTCTCGAGGTAAACATTCA
* * * *
1495 ATTATAGCCTGTTTTAATAAAAAATGTAAAACAATTCAACCTAAAATCGATTATGAGATTATAAA
1 ATTATAACCTGTTTTAATAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
* *
1560 ACTATTTAAAACTAGTAATAAGGC-TTCTGAATGTATGAGTGACTATAAATGGACTTTTCTTGCC
66 ACTATTTAAAACTAGTAATAAGGCTTTC-GAAGGTATGGGTGACTATAAATGGACTTTTCTTGCC
* ********** *
1624 AATGGATATCGTTTTNNNNNNNNNNCTCGAGGTAAATATTCA
130 AATGGATATCTTTTTTTTCACACTTCTCGAGGTAAACATTCA
* * * *
1666 ATTATAATCTGTTTTAATAAAAAAATATAAAAAAATT-AA-TTAAAAATTAATTATAAGATTATA
1 ATTATAACCTGTTTTAAT-AAAAAATGTAAAAAAATTCAACTT-AAAATCAATTATGAGATTATA
* * ** *
1729 AAA-TAATTT-AAAGTGAGTAATAAGGCTTTCGAAGGTACGGGTGACTATAGGTGGATTTTTCTT
64 AAACT-ATTTAAAACT-AGTAATAAGGCTTTCGAAGGTATGGGTGACTATAAATGGACTTTTCTT
* * *** * * * *
1792 ACCAATGGATATCTTTTTCTTCATGTTTCTAGAGGTATATATTAA
127 GCCAATGGATATCTTTTTTTTCACACTTCTCGAGGTAAACATTCA
** * * * **
1837 ATTATAATTTGTTTGAATAACAAATGTAAAAAAATTCAGCTTAAAATCAATTATGAGATTGCAAA
1 ATTATAACCTGTTTTAATAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
* * *
1902 ACTATTCAAAGCAAGTAATAAG
66 ACTATTTAAAACTAGTAATAAG
1924 NNNNNNNNNN
Statistics
Matches: 341, Mismatches: 78, Indels: 20
0.78 0.18 0.05
Matches are distributed among these distances:
170 25 0.07
171 292 0.86
172 24 0.07
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.35
Consensus pattern (171 bp):
ATTATAACCTGTTTTAATAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
ACTATTTAAAACTAGTAATAAGGCTTTCGAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCA
ATGGATATCTTTTTTTTCACACTTCTCGAGGTAAACATTCA
Found at i:3805 original size:341 final size:339
Alignment explanation
Indices: 2922--3821 Score: 817
Period size: 340 Copynumber: 2.6 Consensus size: 339
2912 NNNNNNNACC
* * * * * * *
2922 TAAAATCAAATATGAGATTATAAAGCCATTTAAAGTAAGTAATAAGGCTTTTC-AATGCATGGGT
1 TAAAATCAATTATGAGAGTATAAAACTATTTAAAGCAAGTAATAAGGC-TTTCGAAGGCATGAGT
* * * * * ********
2986 GACTATAAATGGACTTTTCTTACCAATGGATATCT-TTTTCTTGACATTTAC-CGAGNNNNNNNN
65 AACTATAAATGGACTTCTCCTACCAAGGGATAT-TGTTTTCTTTACATTT-CTCGAGGCAGACAA
** * *
3049 NNAATTATAATATGTTTTAATAAAAAGTATAAAAAAATCAATTTAAAATCAATTATGAAATTATA
128 TCAATTATAATCTGTTTTAATAAAAAGTATAAAAAAATCAAATTAAAATCAATTATGAAATTATA
* * * *
3114 AAAATATTTAAAGTCAGTAACAAGGGTTTCGAAGGCATGGGTGACTATAAATAGACTTTTCTTGC
193 AAAATATTTAAAG-AAGTAATAAGGCTTCCGAAGGCATGGGTGACTATAAATAGACTTTTCTTGC
* * * * *
3179 CAATGAATATCTTTTCTTCATATTTCTCGAGGAAAATATTTAATTATAATATGTTTTAATAAAAA
257 CAATGAATATCTTTTCTTCATATTTCTCAAGGAAAACATTCAATTATAATATATTTAAATAAAAA
*********
3244 ATATAAAAANNNNNNNNN
322 ATATAAAAAAATTTAACT
* * * *
3262 NAAAATCAATTATGATATTATAAAGCTATTTAAAGCAAGTAATAAGGCTTTCGAAGGCATGAGTA
1 TAAAATCAATTATGAGAGTATAAAACTATTTAAAGCAAGTAATAAGGCTTTCGAAGGCATGAGTA
* * * * * * * * * *
3327 ACTGTAAATGGACTTCTCTTGCCAATGGATATTTTTTTCTTTGCATTTCTCTAGGTAGACATTTA
66 ACTATAAATGGACTTCTCCTACCAAGGGATATTGTTTTCTTTACATTTCTCGAGGCAGACAATCA
* **********
3392 ATTATAATCTGTTTTAATAAAAAGTAT-AAAAAATCAACTTAAAATCAATTATGNNNNNNNNNNA
131 ATTATAATCTGTTTTAATAAAAAGTATAAAAAAATCAAATTAAAATCAATTATGAAATTATAAAA
** * *
3456 CCATTTAAAGAGAGTAATAAGGCTTCCGAAGGTATGGGTGACTATAAATGGACTTTTTCTTGCCA
196 ATATTTAAAGA-AGTAATAAGGCTTCCGAAGGCATGGGTGACTATAAATAGAC-TTTTCTTGCCA
** * * * * ** * *
3521 ATGGGTGTCTTTTTCTTCATGTTTCTTAAGGTAGGCATTCAATTATTATCTATTTAAATAAAAAA
259 ATGAATATC-TTTTCTTCATATTTCTCAAGGAAAACATTCAATTATAATATATTTAAATAAAAAA
*
3586 TGTAAAAAAATTTAACT
323 TATAAAAAAATTTAACT
* * *
3603 TAAAATCAATTATGAGAGTATAAATAC-ATTTAAAGCGAGTAATAAGGCTTTTGAAGGTAT-AGG
1 TAAAATCAATTATGAGAGTATAAA-ACTATTTAAAGCAAGTAATAAGGCTTTCGAAGGCATGA-G
* * *
3666 TTAGTATAAATGGACTTTTCCTACCAAGGGATA-TGTTTTCTTTACATTTCTCGAGGCAGACAAT
64 TAACTATAAATGGACTTCTCCTACCAAGGGATATTGTTTTCTTTACATTTCTCGAGGCAGACAAT
* * * *
3730 CAATTATTATCTGTTTGAATCAAAAA-TATAAAAAAATCAAATTAAAATTAATTATGAGATTATA
129 CAATTATAATCTGTTTTAAT-AAAAAGTATAAAAAAATCAAATTAAAATCAATTATGAAATTATA
3794 AAAATATTTAAAGCAAGTAATAAGGCTT
193 AAAATATTTAAAG-AAGTAATAAGGCTT
3822 TTGAAGNNNN
Statistics
Matches: 444, Mismatches: 105, Indels: 21
0.78 0.18 0.04
Matches are distributed among these distances:
339 76 0.17
340 187 0.42
341 179 0.40
342 2 0.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.35
Consensus pattern (339 bp):
TAAAATCAATTATGAGAGTATAAAACTATTTAAAGCAAGTAATAAGGCTTTCGAAGGCATGAGTA
ACTATAAATGGACTTCTCCTACCAAGGGATATTGTTTTCTTTACATTTCTCGAGGCAGACAATCA
ATTATAATCTGTTTTAATAAAAAGTATAAAAAAATCAAATTAAAATCAATTATGAAATTATAAAA
ATATTTAAAGAAGTAATAAGGCTTCCGAAGGCATGGGTGACTATAAATAGACTTTTCTTGCCAAT
GAATATCTTTTCTTCATATTTCTCAAGGAAAACATTCAATTATAATATATTTAAATAAAAAATAT
AAAAAAATTTAACT
Found at i:3819 original size:169 final size:168
Alignment explanation
Indices: 2922--3827 Score: 726
Period size: 170 Copynumber: 5.3 Consensus size: 168
2912 NNNNNNNACC
* *** * *
2922 TAAAATCAAATATGAGATTATAAAGCCATTTAAAGTAAGTAATAAGGCTTTTC-AATGCATGGGT
1 TAAAATCAATTATGAGATTATAAAAATATTTAAAGCAAGTAATAAGGC-TTTCGAAGGCATGGGT
* * * *********
2986 GACTATAAATGGACTTTTCTTACCAATGGATATCTTTTTCTTGACATTTAC-CGAGNNNNNNNNN
65 GACTATAAATGGACTTTTCTTGCCAAGGGATAT-TTTTTCTTCACATTT-CTCGAGGTAGACATT
* * *
3050 NAATTATAATATGTTTTAATAAAAAGTATAAAAAAATCAATT
128 CAATTATAATCTGTTTTAATAAAAA-TATAAAAAAATCAACT
* * *
3092 TAAAATCAATTATGAAATTATAAAAATATTTAAAGTC-AGTAACAAGGGTTTCGAAGGCATGGGT
1 TAAAATCAATTATGAGATTATAAAAATATTTAAAG-CAAGTAATAAGGCTTTCGAAGGCATGGGT
* * * * * * * * *
3156 GACTATAAATAGACTTTTCTTGCCAATGAATATCTTTTCTTCATATTTCTCGAGGAAAATATTTA
65 GACTATAAATGGACTTTTCTTGCCAAGGGATATTTTTTCTTCACATTTCTCGAGGTAGACATTCA
* ********
3221 ATTATAATATGTTTTAATAAAAAATATAAAAANNNNNNNNN
130 ATTATAATCTGTTTTAAT-AAAAATATAAAAA-AATCAACT
* * ** * *
3262 NAAAATCAATTATGATATTATAAAGCTATTTAAAGCAAGTAATAAGGCTTTCGAAGGCATGAGTA
1 TAAAATCAATTATGAGATTATAAAAATATTTAAAGCAAGTAATAAGGCTTTCGAAGGCATGGGTG
* * * ** * *
3327 ACTGTAAATGGACTTCTCTTGCCAATGGATATTTTTTTCTTTGCATTTCTCTAGGTAGACATTTA
66 ACTATAAATGGACTTTTCTTGCCAAGGGATA-TTTTTTCTTCACATTTCTCGAGGTAGACATTCA
3392 ATTATAATCTGTTTTAATAAAAAGTAT-AAAAAATCAACT
130 ATTATAATCTGTTTTAATAAAAA-TATAAAAAAATCAACT
********** ** * *
3431 TAAAATCAATTATGNNNNNNNNNNACCATTTAAAG-AGAGTAATAAGGCTTCCGAAGGTATGGGT
1 TAAAATCAATTATGAGATTATAAAAATATTTAAAGCA-AGTAATAAGGCTTTCGAAGGCATGGGT
* ** ** *
3495 GACTATAAATGGACTTTTTCTTGCCAATGGG-TGTCTTTTTCTTCATGTTTCTTAAGGTAGGCAT
65 GACTATAAATGGAC-TTTTCTTGCCAA-GGGATAT-TTTTTCTTCACATTTCTCGAGGTAGACAT
* * * * *
3559 TCAATTATTATCTATTTAAATAAAAAATGTAAAAAAATTTAACT
127 TCAATTATAATCTGTTTTAAT-AAAAATATAAAAAAA-TCAACT
* * * * * * * *
3603 TAAAATCAATTATGAGAGTATAAATACATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATAGGTT
1 TAAAATCAATTATGAGATTATAAAAATATTTAAAGCAAGTAATAAGGCTTTCGAAGGCATGGGTG
* * * * * * *
3668 AGTATAAATGGACTTTTCCTACCAAGGGATATGTTTTCTTTACATTTCTCGAGGCAGACAATCAA
66 ACTATAAATGGACTTTTCTTGCCAAGGGATATTTTTTCTTCACATTTCTCGAGGTAGACATTCAA
* * *
3733 TTATTATCTGTTTGAATCAAAAATATAAAAAAATCAAAT
131 TTATAATCTGTTTTAAT-AAAAATATAAAAAAATCAACT
* *
3772 TAAAATTAATTATGAGATTATAAAAATATTTAAAGCAAGTAATAAGGCTTTTGAAG
1 TAAAATCAATTATGAGATTATAAAAATATTTAAAGCAAGTAATAAGGCTTTCGAAG
3828 NNNNNNNNNN
Statistics
Matches: 582, Mismatches: 137, Indels: 35
0.77 0.18 0.05
Matches are distributed among these distances:
168 2 0.00
169 162 0.28
170 284 0.49
171 70 0.12
172 64 0.11
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.35
Consensus pattern (168 bp):
TAAAATCAATTATGAGATTATAAAAATATTTAAAGCAAGTAATAAGGCTTTCGAAGGCATGGGTG
ACTATAAATGGACTTTTCTTGCCAAGGGATATTTTTTCTTCACATTTCTCGAGGTAGACATTCAA
TTATAATCTGTTTTAATAAAAATATAAAAAAATCAACT
Found at i:4231 original size:171 final size:161
Alignment explanation
Indices: 3989--4802 Score: 364
Period size: 171 Copynumber: 4.8 Consensus size: 161
3979 ACCAATAATG
* * * * *
3989 AGATTATAAAACCATTTAAAGGGAGTAATGAGGTTTTTGAAGGTATGGGTTACTATAAATAGACC
1 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATAGACC
* * * *
4054 TTTCTTGCCAATGGATA-CATTTTTTTTCACATTTCTCGAGGTAGACATTCAACTATAATCTGTT
66 TTTCTTGCCAATGGATATC-TTTTTTGTCACATTTCTCAAGGTAGACATTCAAATATAATCTATT
4118 TTAATAAAAAATATAAAACANNNNNNNNNNAAATCAATTATA
130 TTAATAAAAAATATAAAACA----------AAATCAATTATA
* ** * * * *
4160 AGATTATAAAACTATTTAACTCGAGTAATAAGGCTTTTGAATGCATGGGTGACTATCAATGGACT
1 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATAGACC
* *
4225 TTTCTTGTCAATGGATATCTTTTTTGTCACGTTTCTCAAGGTAGACATTCAAATATAATCTATTT
66 TTTCTTGCCAATGGATATCTTTTTTGTCACATTTCTCAAGGTAGACATTCAAATATAATCTATTT
* * * *
4290 TAGTAAAAAATGTAAAA-AAATTCAACTNNNNNNNNNNTATG
131 TAATAAAAAATATAAAACAAAATCAA-T----------TATA
* * * * * * * * * *
4331 AGATTATAAAACCATTTAACGCGAGTAATAATGCGTTCGACGGCATGGATGACTATATATGGGCT
1 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATAGACC
* * * ** * * *
4396 TTTCTTGCTAATGAATATCTTTTTCT-TTACATTTCTTGAGGTAAACATTCAATTATAAT-TTTT
66 TTTCTTGCCAATGGATATCTTTTT-TGTCACATTTCTCAAGGTAGACATTCAAATATAATCTATT
* * * *
4459 TTAAACAAAAAACATGAAAAAAATTCAACCTAAATCAAATATT
130 TT-AA-TAAAAA-AT--ATAAAA--C-A---AAATCAATTATA
********** * * * * * * *
4502 AGATTATAAANNNNNNNNNNGCAAGTAATAAGGCTTTCGAAGGCGTGAGTGACAATAAATGGACT
1 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATAGACC
* * ** * *
4567 TTTCTTGTCAATGGATATCTTTCTTT-TTACATTTCTTGAGGTAGACATTGAATTATAATTTGCC
66 TTTCTTGCCAATGGATATCTTT-TTTGTCACATTTCTCAAGGTAGACATTCAAATATAA--T--C
*** * ** * *
4631 TGAATAAAAATACAAAAAAATTTAACTTAAAATTAATTATG
126 T--ATTTTAATA-AAAAATATAAAAC--AAAATCAATTATA
* * * * * * *
4672 AGATTATAAAATCATTTAACGCGAGTTATAAGGCTTCTGAAGGTATGGGTGAATATAAATGGACC
1 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATAGACC
* * ** * * *
4737 TTTTTTGCCAA-GAAATATCTTTTTCT-TCATGTTTCTTAAGGTAGACATTCAATTATAATCTGT
66 TTTCTTGCCAATG-GATATCTTTTT-TGTCACATTTCTCAAGGTAGACATTCAAATATAATCTAT
4800 TTT
129 TTT
4803 NNNNNNNNNN
Statistics
Matches: 486, Mismatches: 120, Indels: 81
0.71 0.17 0.12
Matches are distributed among these distances:
160 6 0.01
161 1 0.00
164 1 0.00
166 2 0.00
168 1 0.00
169 3 0.01
170 105 0.22
171 329 0.68
172 10 0.02
173 4 0.01
174 3 0.01
175 4 0.01
176 3 0.01
177 6 0.01
178 1 0.00
179 1 0.00
182 6 0.01
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.35
Consensus pattern (161 bp):
AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGGGTGACTATAAATAGACC
TTTCTTGCCAATGGATATCTTTTTTGTCACATTTCTCAAGGTAGACATTCAAATATAATCTATTT
TAATAAAAAATATAAAACAAAATCAATTATA
Found at i:5591 original size:172 final size:170
Alignment explanation
Indices: 4858--5901 Score: 1084
Period size: 171 Copynumber: 6.1 Consensus size: 170
4848 NNNNNNNNNN
* * * * *
4858 GATTATAAAA-CTATTTAAAGTGAGTAATAAGTCTTTTGAA-GGCATGTGTGCCTATAAATGGAC
1 GATTATAAAATC-ATTTAAAGCGAGTAATAAGGCTTTT-AAGGGCATGGGTGACTATAAATAGAC
* * * * * * * * *
4921 TTTTCTTGCCAATGAATATCTTCTT-TCTCATGTTTTTTGAGGCAAACATTCAATTATTATCTGT
64 TTTTCTTGTCAATGGATACCTT-TTCT-TCATGTTTCTCGAGGTAGACATTCAATTATAATCTAT
* *
4985 TTTAACTAAAAATAT-T-AAAAAATTTAACTAAAAATCAATTATGA
127 TTTAA-TAAAAA-ATGTAAAAAAATTCAACTTAAAATCAATTATGA
* * *
5029 GATTATAAAATCATTTAAAGCGAGTATTAAGGCTTTTAAGGGCGTAGGTGACTATAAATAGACTT
1 GATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTAAGGGCATGGGTGACTATAAATAGACTT
* * * * * *
5094 TTTTTG-CTAATGGATACCTTTTTCTTTATGTTTCTCAAGGTAGATAATCAATTATAATCTGTTT
66 TTCTTGTC-AATGGATACC-TTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAATCTATTT
* * *
5158 TAATAAAAAATGTAAAACAATTCAAGTTAAAATCAACTATGA
129 TAATAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGA
* * * * * * *
5200 GATTATTAAACCATTTAAAGCGAGTATTAGGGC-TTTAAGGGCGTTGGTGACTATAAATGGACTT
1 GATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTAAGGGCATGGGTGACTATAAATAGACTT
* * *
5264 TTCTT-TCTAATGGATACCTTTTTCTTCATATTTCTCGAGCTAGACATTTAATTATAATCTATTT
66 TTCTTGTC-AATGGATACC-TTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAATCTATTT
* * * *
5328 TAATAAAAAAATGTGAAACAATTCAAGTAAAAATCAATTATGA
129 TAAT-AAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGA
* * * * * *
5371 GATTATAAAATCATTTAAAGTGAGTAATCAGGCTTTCAAAGACATGGGTGACTATAAATAGATTT
1 GATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTAAGGGCATGGGTGACTATAAATAGACTT
* * * * * *
5436 TTTTTGTCAATGGATACCTTTATCTTCACGTTTCTCGA-GTAGATATTTAATTATTATTTATTTT
66 TTCTTGTCAATGGATACCTTT-TCTTCATGTTTCTCGAGGTAGACATTCAATTATAATCTATTTT
* *
5500 AACT-AAAAATTTAAAAAAAATTCAACTTAAAATCAATAATGA
130 AA-TAAAAAATGT-AAAAAAATTCAACTTAAAATCAATTATGA
* * * * ** * *
5542 GATTATAAAACCATTTAAAAGCAAGTAATGAGGCTTTCGAA-GGCATGGGTGGTTATAAATGGAT
1 GATTATAAAATCATTT-AAAGCGAGTAATAAGGCTTT-TAAGGGCATGGGTGACTATAAATAGAC
* * * * *
5606 TTTTCTTGCCAATGGAAATCTTTTCATTCATGTTTCTCAAGGTAGACATTCAATTATAATCTGTT
64 TTTTCTTGTCAATGGATACCTTTTC-TTCATGTTTCTCGAGGTAGACATTCAATTATAATCTATT
* * * * * *
5671 TTTATAAAAAATGTAAAAAATTTCAAGTTAAAATTAACTGTGA
128 TTAATAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGA
* *
5714 GATTGTAAAATCATTTAAAGCGAGTATTAAGGCTTTTAAGGGCATGGGTGACTATAAATAGACTT
1 GATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTAAGGGCATGGGTGACTATAAATAGACTT
** * *
5779 TTCTTGTCAATGGATATATTTCCTTTATGTTTCTCGAGGTAGACATTCAATTATAATCTATTTTA
66 TTCTTGTCAATGGATACCTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAATCTATTTTA
* *
5844 ATAAAAAAATGTAAAACAATTCAACTTAAAATTAATTATGA
131 AT-AAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGA
* *
5885 GATTAGAAAATTATTTA
1 GATTATAAAATCATTTA
5902 NNNNNNNNNN
Statistics
Matches: 730, Mismatches: 122, Indels: 42
0.82 0.14 0.05
Matches are distributed among these distances:
169 2 0.00
170 146 0.20
171 387 0.53
172 162 0.22
173 33 0.05
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (170 bp):
GATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTAAGGGCATGGGTGACTATAAATAGACTT
TTCTTGTCAATGGATACCTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAATCTATTTTA
ATAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGA
Found at i:5700 original size:514 final size:512
Alignment explanation
Indices: 4972--5901 Score: 1336
Period size: 514 Copynumber: 1.8 Consensus size: 512
4962 GCAAACATTC
* * *
4972 AATTATTATCTGTTTTAACTAAAAATATTAAAAAATTTAACTAAAAATCAATTATGAGATTATAA
1 AATTATTATCTATTTTAACTAAAAATATTAAAAAATTCAACTAAAAATCAATAATGAGATTATAA
* * * * * *
5037 AATCATTTAAAGCGAGTATTAAGGCTTTTAAGGGCGTAGGTGACTATAAATAGACTTTTTTTGCT
66 AACCATTTAAAGCAAGTAATAAGGCTTTGAAGGGCATAGGTGACTATAAATAGACTTTTTTTGCC
* * *
5102 AATGGATACCTTTTTCTTTATGTTTCTCAAGGTAGATAATCAATTATAATCTGTTTTAATAAAAA
131 AATGGAAACCTTTTTCTTCATGTTTCTCAAGGTAGACAATCAATTATAATCTGTTTTAATAAAAA
* *
5167 ATGTAAAACAATTCAAGTTAAAATCAACTATGAGATTATTAAACCATTTAAAGCGAGTATTAGGG
196 ATGTAAAACAATTCAAGTTAAAATCAACTATGAGATTATAAAACCATTTAAAGCGAGTATTAAGG
* * * *
5232 C-TTTAAGGGCGTTGGTGACTATAAATGGACTTTTCTT-TCTAATGGATACCT-TTTTCTTCATA
261 CTTTTAAGGGCATGGGTGACTATAAATAGACTTTTCTTGTC-AATGGATA--TATTTCCTTCATA
* * *
5294 TTTCTCGAGCTAGACATTTAATTATAATCTATTTTAATAAAAAAATGTGAAACAATTCAAGTAAA
323 TTTCTCGAGCTAGACATTCAATTATAATCTATTTTAATAAAAAAATGTAAAACAATTCAACTAAA
*
5359 AATCAATTATGAGATTATAAAATCATTTAAAGTGAGTAATCAGGCTTTCAAAGACATGGGTGACT
388 AATCAATTATGAGATTAGAAAATCATTTAAAGTGAGTAATCAGGCTTTCAAAGACATGGGTGACT
5424 ATAAATAGATTTTTTTTGTCAATGGATACCTTTATCTTCACGTTTCTCGAGTAGATATTT
453 ATAAATAGATTTTTTTTGTCAATGGATACCTTTATCTTCACGTTTCTCGAGTAGATATTT
* *
5484 AATTATTATTTATTTTAACTAAAAAT-TTAAAAAAAATTCAACTTAAAATCAATAATGAGATTAT
1 AATTATTATCTATTTTAACTAAAAATATT--AAAAAATTCAACTAAAAATCAATAATGAGATTAT
* * ** *
5548 AAAACCATTTAAAAGCAAGTAATGAGGCTTTCGAA-GGCATGGGTGGTTATAAATGGA-TTTTTC
64 AAAACCATTT-AAAGCAAGTAATAAGGCTTT-GAAGGGCATAGGTGACTATAAATAGACTTTTT-
* * *
5611 TTGCCAATGGAAATC-TTTTCATTCATGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTTA
126 TTGCCAATGGAAACCTTTTTC-TTCATGTTTCTCAAGGTAGACAATCAATTATAATCTGTTTTAA
* * * *
5675 TAAAAAATGTAAAA-AATTTCAAGTTAAAATTAACTGTGAGATTGTAAAATCATTTAAAGCGAGT
190 TAAAAAATGTAAAACAA-TTCAAGTTAAAATCAACTATGAGATTATAAAACCATTTAAAGCGAGT
5739 ATTAAGGCTTTTAAGGGCATGGGTGACTATAAATAGACTTTTCTTGTCAATGGATATATTTCCTT
254 ATTAAGGCTTTTAAGGGCATGGGTGACTATAAATAGACTTTTCTTGTCAATGGATATATTTCCTT
* * *
5804 TATGTTTCTCGAGGTAGACATTCAATTATAATCTATTTTAATAAAAAAATGTAAAACAATTCAAC
319 CATATTTCTCGAGCTAGACATTCAATTATAATCTATTTTAATAAAAAAATGTAAAACAATTCAAC
* * *
5869 TTAAAATTAATTATGAGATTAGAAAATTATTTA
384 TAAAAATCAATTATGAGATTAGAAAATCATTTA
5902 NNNNNNNNNN
Statistics
Matches: 366, Mismatches: 42, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
511 2 0.01
512 24 0.07
513 53 0.14
514 242 0.66
515 43 0.12
516 2 0.01
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (512 bp):
AATTATTATCTATTTTAACTAAAAATATTAAAAAATTCAACTAAAAATCAATAATGAGATTATAA
AACCATTTAAAGCAAGTAATAAGGCTTTGAAGGGCATAGGTGACTATAAATAGACTTTTTTTGCC
AATGGAAACCTTTTTCTTCATGTTTCTCAAGGTAGACAATCAATTATAATCTGTTTTAATAAAAA
ATGTAAAACAATTCAAGTTAAAATCAACTATGAGATTATAAAACCATTTAAAGCGAGTATTAAGG
CTTTTAAGGGCATGGGTGACTATAAATAGACTTTTCTTGTCAATGGATATATTTCCTTCATATTT
CTCGAGCTAGACATTCAATTATAATCTATTTTAATAAAAAAATGTAAAACAATTCAACTAAAAAT
CAATTATGAGATTAGAAAATCATTTAAAGTGAGTAATCAGGCTTTCAAAGACATGGGTGACTATA
AATAGATTTTTTTTGTCAATGGATACCTTTATCTTCACGTTTCTCGAGTAGATATTT
Found at i:7392 original size:170 final size:169
Alignment explanation
Indices: 7098--7411 Score: 387
Period size: 170 Copynumber: 1.9 Consensus size: 169
7088 CTAAAAATCA
* * * ** * *
7098 ATTATGAGATTATAAAACCTTTTAAAACGAGTAATATGTCTTTCGAAGGCATGGGTGGCAATAAA
1 ATTATGAGATTATAAAAACTTTTAAAACGAGTAATAAGGCTTTCGAAGAAATGGGTGACAACAAA
* ** * *
7163 TGGACTTTTCTTGCCAATAGATATCATTTTCTTCACGTCTCCTAAGGCAGACATTCAATTATTAT
66 TAGACTTTTCTTAACAATAGATATCATTTTCTCCACGTCTCCTAAGGCAAACATTCAATTATTAT
* *
7228 TTGTTTTAACTAAAAATGTTCAAAATTCGTCTTAAAATTG
131 CTGTGTTAAC-AAAAATGTTCAAAATTCGTCTTAAAATTG
* ** * *
7268 ATTATGAGATTATAAAAATTTTTAAATTGAGTAATAAGGCTTTTGAAGAAATGGGTGACTACAAA
1 ATTATGAGATTATAAAAACTTTTAAAACGAGTAATAAGGCTTTCGAAGAAATGGGTGACAACAAA
* * * * *
7333 TAGACTTTTCTTAACAATGGATATC-TTCTTCTCCATGTTTCCTGAGGCAAACTTTCAATTATTA
66 TAGACTTTTCTTAACAATAGATATCATT-TTCTCCACGTCTCCTAAGGCAAACATTCAATTATTA
7397 TCTGTGTTAACAAAA
130 TCTGTGTTAACAAAA
7412 TATATAAAAA
Statistics
Matches: 119, Mismatches: 24, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
169 6 0.05
170 113 0.95
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (169 bp):
ATTATGAGATTATAAAAACTTTTAAAACGAGTAATAAGGCTTTCGAAGAAATGGGTGACAACAAA
TAGACTTTTCTTAACAATAGATATCATTTTCTCCACGTCTCCTAAGGCAAACATTCAATTATTAT
CTGTGTTAACAAAAATGTTCAAAATTCGTCTTAAAATTG
Found at i:7856 original size:171 final size:170
Alignment explanation
Indices: 7084--7918 Score: 660
Period size: 171 Copynumber: 4.9 Consensus size: 170
7074 NNNNNNNNAT
* * * * * * *
7084 TCAACTAAAAATCAATTATGAGATTATAAAACCTTTTAAAACGAGTAATATGTCTTTCGAAGGCA
1 TCAACTTAAAATCAATTATGAGATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTCGAAAGCA
* * * * * * * *
7149 TGGGTGGCAATAAATGGACTTTTCTTGCCAATAGATATCATTTTCTTCACGTCTCCTAAGGCAGA
66 TGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACATTTTCTGAGGCAGA
* * * * ** *
7214 CATTCAATTATTATTTGTTTTAACT-AAAAATGTTCAAAAT
131 CATTCAATTATAATCTATTTTAA-TAAAAAATATAAAAAAA
** ** ** ** * *
7254 TCGTCTTAAAATTGATTATGAGATTATAAAAATTTTTAAATTGAGTAATAAGGCTTTTG-AAGAA
1 TCAACTTAAAATCAATTATGAGATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTCGAAAG-C
* * ** *
7318 ATGGGTGACTACAAATAGACTTTTCTTAACAATGGATATCTTCTTC-TC-CATGTTTCCTGAGGC
65 ATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACAT-TTT-CTGAGGC
* * * * * * *
7381 AAACTTTCAATTATTATCTGTGTTAACAAAATATATAAAAAAA
128 AGACATTCAATTATAATCTATTTTAATAAAAAATATAAAAAAA
** * * **********
7424 TTCAACTCGAAATCAATTATAAGATTATAAAACCATTTAAAGCGAGTANNNNNNNNNNC-AAAGG
1 -TCAACTTAAAATCAATTATGAGATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTCGAAA-G
* * * *
7488 CATGGATGACTATAAATGGACTTTTCTTGTCAATGGATA-CATTTTGCTTCATA-TTTCTCGAGG
64 CATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATC-TTTTTCTTCACATTTTCT-GAGG
* * * *
7551 TAGACATTCAATTATAATATTTTTTAATAAAAAAATATAAAACAAT
127 CAGACATTCAATTATAATCTATTTTAAT-AAAAAATATAAAA-AAA
* * * **********
7597 TTAACTAAAAATCAGTTATGAGANNNNNNNNNNATTTAAAGCGAGTAATAAGGCTTTC-AAAGAC
1 TCAACTTAAAATCAATTATGAGATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTCGAAAG-C
* * * *
7661 ATGGGTGACTATAAATGAACTTTTCTTGCCAGTGGATATCTTTTTTTTCACATTTTCTGAGGTAG
65 ATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACATTTTCTGAGGCAG
7726 ACATTCAATTATAATCTATTTTAATAAAAAATATAAAAGAAA
130 ACATTCAATTATAATCTATTTTAATAAAAAATATAAAA-AAA
* * * *
7768 TCAAGTTAACATTAATTATGAGATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTCGAAAGTA
1 TCAACTTAAAATCAATTATGAGATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTCGAAAGCA
* * * * * *
7833 TTGGTAACTATAAATGGACTTTTCCTACCAATGGATATCTTTTTCTTCACTTTTTCTCGAGGCAA
66 TGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACATTTTCT-GAGGCAG
7898 ACATTCAATTATAATCTATTT
130 ACATTCAATTATAATCTATTT
7919 CAAT
Statistics
Matches: 505, Mismatches: 142, Indels: 34
0.74 0.21 0.05
Matches are distributed among these distances:
168 2 0.00
169 5 0.01
170 125 0.25
171 209 0.41
172 155 0.31
173 9 0.02
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.35
Consensus pattern (170 bp):
TCAACTTAAAATCAATTATGAGATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTCGAAAGCA
TGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACATTTTCTGAGGCAGA
CATTCAATTATAATCTATTTTAATAAAAAATATAAAAAAA
Done.