Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401185.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4336.0, 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: 4732
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.33
Warning! 280 characters in sequence are not A, C, G, or T
Found at i:417 original size:173 final size:171
Alignment explanation
Indices: 238--602 Score: 460
Period size: 171 Copynumber: 2.1 Consensus size: 171
228 NNNNNNNNNN
* *
238 CAATGAATGGCTTTTTCTTCACATTTCTCAAGATAAACATTCAATTACTATCTGTTTTACACAAA
1 CAATGAATGGCTTTTTCTTCACATTTCTCAAGACAAACATTCAATTACTATCTATTTTACACAAA
*
303 AATGTAAAAAAAAAAAAAACTTAAAATCATTTATGATATTATAAAACCATTTAAAGCGAGTAATA
66 AATGT--AAAAAAAAAAAACTTAAAATCATTTATGAGATTATAAAACCATTTAAAGCGAGTAATA
* * *
368 AGGGTCTTGAAGGCATTGGTGACTATAAGTAGACTTTTCTGGC
129 AGCGTCTTGAAGGCATGGGTGACTACAAGTAGACTTTTCTGGC
* * ** *
411 CAATGAATGGCTTTTTCTTCACGTTTGTTGAGACAAACATTCAATTACTATCTATTTTACCCAAA
1 CAATGAATGGCTTTTTCTTCACATTTCTCAAGACAAACATTCAATTACTATCTATTTTACACAAA
* *** ********** *
476 CATGTAAAAAAATTCAACTTAANNNNNNNNNNGAGATTATAAAACCATTTAAAGTGAGTAATAAG
66 AATGTAAAAAAAAAAAACTTAAAATCATTTATGAGATTATAAAACCATTTAAAGCGAGTAATAAG
*
541 CGTCTTGAAGGCATGGGTGACTACAAGTAGACTTTTCTTGC
131 CGTCTTGAAGGCATGGGTGACTACAAGTAGACTTTTCTGGC
*
582 CAATGAATGGCTTTTCCTTCA
1 CAATGAATGGCTTTTTCTTCA
603 GGTTTCGCTA
Statistics
Matches: 164, Mismatches: 28, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
171 102 0.62
173 62 0.38
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.32
Consensus pattern (171 bp):
CAATGAATGGCTTTTTCTTCACATTTCTCAAGACAAACATTCAATTACTATCTATTTTACACAAA
AATGTAAAAAAAAAAAACTTAAAATCATTTATGAGATTATAAAACCATTTAAAGCGAGTAATAAG
CGTCTTGAAGGCATGGGTGACTACAAGTAGACTTTTCTGGC
Found at i:685 original size:171 final size:170
Alignment explanation
Indices: 238--690 Score: 437
Period size: 171 Copynumber: 2.6 Consensus size: 170
228 NNNNNNNNNN
* * * * * *
238 CAATGAATGGCTTTTTCTTCACATTT-CTCAAGATAAACATTCAATTACTATCTGT-TTTACACA
1 CAATGAATGGCTTTTCCTTCACGTTTGCT-GAGACAAACATTCAATTACTATCTATGTTAAC-CA
*** * *
301 AAAATGTAAAAAAAAAAAAAACTTAAAATCATTTATGATATTATAAAACCATTTAAAGCGAGTAA
64 AAAATGT--AAAAAAATTCAACTT-AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAA
* * *
366 TAAGGGTCTTGAAGGCATTGGTGACTATAAGTAGACTTTTCTGGC
126 TAAGCGTCTTGAAGGCATGGGTGACTACAAGTAGACTTTTCTGGC
* * * *
411 CAATGAATGGCTTTTTCTTCACGTTTGTTGAGACAAACATTCAATTACTATCTATTTTACCCAAA
1 CAATGAATGGCTTTTCCTTCACGTTTGCTGAGACAAACATTCAATTACTATCTATGTTAACCAAA
* ********* *
476 CATGTAAAAAAATTCAACTTAANNNNNNNNNNGAGATTATAAAACCATTTAAAGTGAGTAATAAG
66 AATGTAAAAAAATTCAACTTAA-ATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAG
*
541 CGTCTTGAAGGCATGGGTGACTACAAGTAGACTTTTCTTGC
130 CGTCTTGAAGGCATGGGTGACTACAAGTAGACTTTTCTGGC
* * * * * * **
582 CAATGAATGGCTTTTCCTTCAGGTTTCGCT-AGGCAAACATTCAGTTATTATTTGTGTTAATTAA
1 CAATGAATGGCTTTTCCTTCACGTTT-GCTGAGACAAACATTCAATTACTATCTATGTTAACCAA
* *
646 AAATGTAAAAAACTT-AGGCTTGAAATCAATTATGAGATTATAAAA
65 AAATGTAAAAAAATTCA-ACTT-AAATCAATTATGAGATTATAAAA
691 ANNNNNNNNN
Statistics
Matches: 224, Mismatches: 50, Indels: 14
0.78 0.17 0.05
Matches are distributed among these distances:
170 3 0.01
171 157 0.70
172 4 0.02
173 56 0.25
174 4 0.02
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.33
Consensus pattern (170 bp):
CAATGAATGGCTTTTCCTTCACGTTTGCTGAGACAAACATTCAATTACTATCTATGTTAACCAAA
AATGTAAAAAAATTCAACTTAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGC
GTCTTGAAGGCATGGGTGACTACAAGTAGACTTTTCTGGC
Found at i:1647 original size:170 final size:167
Alignment explanation
Indices: 1182--2477 Score: 659
Period size: 171 Copynumber: 7.6 Consensus size: 167
1172 NNNNAGCTTG
* * * * *
1182 AAATCAATTATGAGATTATAAAAAT-ATTTAAAACGAGTAATAAGGCTTTC-AAAAGCATCGA-T
1 AAATCAATTATGAGGTTAT-AAAATCATTTAGAGC-A-AAATAAGGCTTTCGAAGA-CAT-GAGT
* * * * *
1244 GACTACAAATGGGCTTTTCTTGCCAATGGATAACTCTTTCATCATG-TTCCTTGAGGTAGACATT
61 GACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTCC-TGAGGTAGACATT
*
1308 CAATTATAAT-TTTTTTAATAAAAATATAAAAAAATTCAACTTA
125 CAATTATAATCTATTTTAATAAAAATAT-AAAAAATTCAACTTA
* * * * *
1351 AAATCAATTATGAGGTTATCAAATCATTTAGAGCAAAACAAGGCTTTCGAAGGCATGGGTGGCTA
1 AAATCAATTATGAGGTTATAAAATCATTTAGAGCAAAATAAGGCTTTCGAAGACATGAGTGACTA
* * * * * ** *
1416 TAAATGGAATTCTCTTACCAATGGATATCTTTTTCTTGATATTTTTTGAGGTAGCCATTCAATTA
66 TAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTCCTGAGGTAGACATTCAATTA
*
1481 TAATCTATTTTAATAAAAATATAAAACAATTTAACTTA
131 TAATCTATTTTAATAAAAATATAAAA-AATTCAACTTA
* ********
1519 AAATCAATTATGAGGTTATAAAATTATTTANNNNNNNNNNTAAGGCTTTCGAAGACATGAGTGAC
1 AAATCAATTATGAGGTTATAAAATCATTTA--GAGCAAAATAAGGCTTTCGAAGACATGAGTGAC
* * **
1584 TATAAATGGACTTTTCTTGTCAATAGATATCTTTTTCTTCATGTTTCCCAAGGTAGACATTCAAT
64 TATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTCCTGAGGTAGACATTCAAT
* * * * **
1649 TATTATCTGTTTTAACCAAAAATGTACAAAAATTCATGTTA
129 TATAATCTATTTTAA-TAAAAATATA-AAAAATTCAACTTA
* ** * * * * *
1690 AAATCAATTACGA-AATACTAATAA-CATTTTAG-GCACGTAATAAGACTTTTGAAGGCATGGGT
1 AAATCAATTATGAGGTTA-TAA-AATCA-TTTAGAGCA--AAATAAGGCTTTCGAAGACATGAGT
* * * ** * * * *
1752 AACTATAAATGTACTTCTT-TT-CCAATGAATGGCTTTTTCTTCAGGTTTTCCT-AGGAAAAGAT
61 GACTATAAATGGACTT-TTCTTGCCAATGGATATCTTTTTCTTCATG-TTTCCTGAGGTAGACAT
* * * * *
1814 TCAATTATTATTTGTTTTAATCAAAAA-ATAAAAAAATTCAGCTTG
124 TCAATTATAATCTATTTTAAT-AAAAATAT-AAAAAATTCAACTTA
* * * ** * * *
1859 AAATCAATTATGAGATTATAAAAACATTTAAAGCGGGTAATAAGGCTTCCAAAGGCATCG-GTGA
1 AAATCAATTATGAGGTTATAAAATCATTTAGAGC--AAAATAAGGCTTTCGAAGACAT-GAGTGA
* * * ********** *
1923 CTACAAATGGGCTTTTCTTGCCAATGAATATCTTTNNNNNNNNNNTT-CTCAAGGTAGACATTCA
63 CTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTCCT-GAGGTAGACATTCA
** * ** *
1987 ATTATTTTCTGTTTTGACCAAAAATATAAAAAATTTTAACTTA
127 ATTATAATCTATTTT-AATAAAAATATAAAAAA-TTCAACTTA
* * ******** * * *
2030 AAATCAATTATGAGATTATAAAAACATTTANNNNNNNNNNTAAGGCTTTCGAAGGCGTGGGTGAC
1 AAATCAATTATGAGGTTATAAAATCATTTA--GAGCAAAATAAGGCTTTCGAAGACATGAGTGAC
* **
2095 TATAAATGGACTGTTT-TTGCCAATGAATATCTTTGTT-TTCATGTTTCCCAAGGTAGACATTCA
64 TATAAATGGACT-TTTCTTGCCAATGGATATCTTT-TTCTTCATGTTTCCTGAGGTAGACATTCA
* * * * *
2158 CTTGTAATATGTTTTAATAATAAA-AGTAAAAACAATTCAACTTG
127 ATTATAATCTATTTTAATAA-AAATA-T-AAAA-AATTCAACTTA
* * * ** * * * * *
2202 AGATCAATTATGAGATTATAAAACCATGAAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGAG
1 AAATCAATTATGAGGTTATAAAATCATTTAGAGC-A-AAATAAGGCTTTCGAAGACATGAGTGAC
* ********** * ** *
2267 TATAAATGAACTTTTNNNNNNNNNNGATATATTTTTCTTCACATTTCTTGAGGTAGACATTCAAT
64 TATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTCCTGAGGTAGACATTCAAT
* * * *
2332 TATAATCTGTTTCAATAAAAAATGTAAAAACATTCATCTTA
129 TATAATCTATTTTAAT-AAAAATATAAAAA-ATTCAACTTA
* * * * * * * *
2373 AAATCGATTATGACGTTATAAAATCATTTAAATCGAGTAATAAGAACTTT-GAA-ATGCATGGGA
1 AAATCAATTATGAGGTTATAAAATCATTTAGAGC-A-AAATAAG-GCTTTCGAAGA--CATGAGT
* * **
2436 GACTATAAATGAACTTTTCTTGCCAATGAATGGCTTTTTCTT
61 GACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTT
2478 NNNNNNNNNN
Statistics
Matches: 854, Mismatches: 221, Indels: 101
0.73 0.19 0.09
Matches are distributed among these distances:
166 1 0.00
167 76 0.09
168 73 0.09
169 91 0.11
170 196 0.23
171 244 0.29
172 169 0.20
173 4 0.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.34
Consensus pattern (167 bp):
AAATCAATTATGAGGTTATAAAATCATTTAGAGCAAAATAAGGCTTTCGAAGACATGAGTGACTA
TAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTCCTGAGGTAGACATTCAATTA
TAATCTATTTTAATAAAAATATAAAAAATTCAACTTA
Found at i:1905 original size:340 final size:334
Alignment explanation
Indices: 1061--2281 Score: 922
Period size: 340 Copynumber: 3.6 Consensus size: 334
1051 TAATGGTCTT
* * * * * *
1061 GAAGGCATGGCTGACTATAAGTAGACTT-TTCTTGTCAATGAATGGCTTTTTCTTCTGGTTTTCC
1 GAAGGCATGGGTGACTATAAATGGACTTCTT-TT-CCAATGAATAGCTTTTTCTTCAGGTTTTCC
* * * * ********** *
1125 TAGGCAAACATTTAGTTATTATTTGTTTTAATTAAAAATATNNNNNNNNNNAGCTTGAAATCAAT
64 TAGGTAAACATTCAATTATAATTTGTTTTAA-TAAAAATATAAAAAAATTCAACTTGAAATCAAT
* * *
1190 TATGAGATTATAAAAATATTTAAAACGAGTAATAAGGCTTTC-AAAAGCATCGA-TGACTACAAA
128 TATGAGATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTCGAAGA-CATCGAGTGACTACAAA
* * * ** *
1253 TGGGCTTTTCTTGCCAATGGATAACTCTTTCATCATGTTCCTTGAGGTAGACATTCAATTATAAT
192 TGGACTTTTCTTGCCAAT-GATATCTTTTTCATCATGTTCC-CAAGGTAGACATTCAATTATTAT
* * * *
1318 -TTTTTTAA-TAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGGTTATCAAATCATTTA
255 CTGTTTTAACCAAAAATAT-AAAAAATTCAACTTAAAATCAATTATGAGATTAT-AAAACATTTA
*
1381 GAGCAAAACAAGGCTTTC
318 G-GCAAAATAAGGCTTTC
* * * * * * ** *
1399 GAAGGCATGGGTGGCTATAAATGGAATTCTCTTACCAATGGATATCTTTTTCTTGATATTTT-TT
1 GAAGGCATGGGTGACTATAAATGGACTTCT-TTTCCAATGAATAGCTTTTTCTTCAGGTTTTCCT
** * * * * *
1463 GAGGTAGCCATTCAATTATAATCTATTTTAATAAAAATATAAAACAATTTAACTTAAAATCAATT
65 -AGGTAAACATTCAATTATAATTTGTTTTAATAAAAATATAAAAAAATTCAACTTGAAATCAATT
* ** ********** *
1528 ATGAGGTTATAAAATTATTTANNNNNNNNNNTAAGGCTTTCGAAGACAT-GAGTGACTATAAATG
129 ATGAGATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTCGAAGACATCGAGTGACTACAAATG
* *
1592 GACTTTTCTTGTCAATAGATATCTTTTTCTTCATGTTTCCCAAGGTAGACATTCAATTATTATCT
194 GACTTTTCTTGCCAAT-GATATCTTTTTCATCATG-TTCCCAAGGTAGACATTCAATTATTATCT
* ** * *
1657 GTTTTAACCAAAAATGTACAAAAATTCATGTTAAAATCAATTACGA-AATACTAATAACATTTTA
257 GTTTTAACCAAAAATATA-AAAAATTCAACTTAAAATCAATTATGAGATTA-TAA-AACA-TTTA
* * *
1721 GGCACGTAATAAGACTTTT
318 GGCA--AAATAAGGCTTTC
* * *
1740 GAAGGCATGGGTAACTATAAATGTACTTCTTTTCCAATGAATGGCTTTTTCTTCAGGTTTTCCTA
1 GAAGGCATGGGTGACTATAAATGGACTTCTTTTCCAATGAATAGCTTTTTCTTCAGGTTTTCCTA
* * * *
1805 GGAAAAGATTCAATTATTATTTGTTTTAATCAAAAA-ATAAAAAAATTCAGCTTGAAATCAATTA
66 GGTAAACATTCAATTATAATTTGTTTTAAT-AAAAATATAAAAAAATTCAACTTGAAATCAATTA
* * * *
1869 TGAGATTATAAAAACATTTAAAGCGGGTAATAAGGCTTCCAAAGGCATCG-GTGACTACAAATGG
130 TGAGATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTCGAAGACATCGAGTGACTACAAATGG
* ********* * *
1933 GCTTTTCTTGCCAATGAATATCTTTNNNNNNNNNNTTCTCAAGGTAGACATTCAATTATTTTCTG
195 ACTTTTCTTGCCAATG-ATATCTTT-TTCATCATGTTCCCAAGGTAGACATTCAATTATTATCTG
* *
1998 TTTTGACCAAAAATATAAAAAATTTTAACTTAAAATCAATTATGAGATTATAAAAACATTTANNN
258 TTTTAACCAAAAATATAAAAAA-TTCAACTTAAAATCAATTATGAGATTAT-AAAACATTTA---
*******
2063 NNNNNNNTAAGGCTTTC
318 GGCAAAATAAGGCTTTC
* * * *
2080 GAAGGCGTGGGTGACTATAAATGGACTGT-TTTTGCCAATGAATATCTTTGTT-TTCATGTTTCC
1 GAAGGCATGGGTGACTATAAATGGACT-TCTTTT-CCAATGAATAGCTTT-TTCTTCAGGTTTTC
* * * * * *
2143 CAAGGTAGACATTCACTTGTAATATGTTTTAATAATAAA-AGTAAAAACAATTCAACTTGAGATC
63 CTAGGTAAACATTCAATTATAATTTGTTTTAATAA-AAATA-TAAAAA-AATTCAACTTGAAATC
* ** * * * *
2207 AATTATGAGATTATAAAACCATGAAAAGCGAGTAATAAGGCTTTCGAAGGCAT-GGGTGAGTATA
125 AATTATGAGATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTCGAAGACATCGAGTGACTACA
*
2271 AATGAACTTTT
190 AATGGACTTTT
2282 NNNNNNNNNN
Statistics
Matches: 684, Mismatches: 167, Indels: 59
0.75 0.18 0.06
Matches are distributed among these distances:
336 2 0.00
337 115 0.17
338 84 0.12
339 50 0.07
340 248 0.36
341 99 0.14
342 9 0.01
343 77 0.11
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.35
Consensus pattern (334 bp):
GAAGGCATGGGTGACTATAAATGGACTTCTTTTCCAATGAATAGCTTTTTCTTCAGGTTTTCCTA
GGTAAACATTCAATTATAATTTGTTTTAATAAAAATATAAAAAAATTCAACTTGAAATCAATTAT
GAGATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTCGAAGACATCGAGTGACTACAAATGGA
CTTTTCTTGCCAATGATATCTTTTTCATCATGTTCCCAAGGTAGACATTCAATTATTATCTGTTT
TAACCAAAAATATAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACATTTAGGCAAAAT
AAGGCTTTC
Found at i:2095 original size:171 final size:160
Alignment explanation
Indices: 1968--2274 Score: 159
Period size: 172 Copynumber: 1.8 Consensus size: 160
1958 NNNNNNNNNN
* * *
1968 TTCTCAAGGTAGACATTCAATTATT-TTCTGTTTTGACCAAAAATATAAAAAATTTTAACTTAAA
1 TTCTCAAGGTAGACATTCAATTATTATT-TGTTTTAACCAAAAA-ATAAAAAAATTCAACTTAAA
********** * * * *
2032 ATCAATTATGAGATTATAAAAACATTTANNNNNNNNNNTAAGGCTTTCGAAGGCGTGGGTGACTA
64 ATCAATTATGAGATTATAAAAACATTTAAAGCGGGTAATAAGGCTTCCAAAGGCATCGGTGACTA
*
2097 TAAATGGACTGTTTTTGCCAATGAATATCTTTGTT
129 CAAATGGACTGTTTTTGCCAATGAATATC--T-TT
* * * * *
2132 TTCATGTTTCCCAAGGTAGACATTCACTTGTAATATGTTTTAA-TAATAAAAGTAAAAACAATTC
1 TTC-----T--CAAGGTAGACATTCAATTATTATTTGTTTTAACCAA-AAAA-TAAAAA-AATTC
* * * ** * * * *
2196 AACTTGAGATCAATTATGAGATTATAAAACCATGAAAAGCGAGTAATAAGGCTTTCGAAGGCATG
56 AACTTAAAATCAATTATGAGATTATAAAAACATTTAAAGCGGGTAATAAGGCTTCCAAAGGCATC
* *
2261 GGTGAGTATAAATG
121 GGTGACTACAAATG
2275 AACTTTTNNN
Statistics
Matches: 107, Mismatches: 25, Indels: 14
0.73 0.17 0.10
Matches are distributed among these distances:
164 3 0.03
169 1 0.01
170 3 0.03
171 34 0.32
172 66 0.62
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.33
Consensus pattern (160 bp):
TTCTCAAGGTAGACATTCAATTATTATTTGTTTTAACCAAAAAATAAAAAAATTCAACTTAAAAT
CAATTATGAGATTATAAAAACATTTAAAGCGGGTAATAAGGCTTCCAAAGGCATCGGTGACTACA
AATGGACTGTTTTTGCCAATGAATATCTTT
Found at i:2917 original size:171 final size:169
Alignment explanation
Indices: 2588--4515 Score: 1174
Period size: 171 Copynumber: 11.3 Consensus size: 169
2578 NNNNNNNNNN
* * * *
2588 ACTTAAAATCATTTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGGTCTTAAACGCATGT
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAA-GGTCTTGAAGGCATGG
* * * ** *
2653 GTGACTATAAGTAGACTTTTCTTGCCAATGAATGGCTTTTTCTTTACGTTTGCTGAGACAAACAT
65 GTGACTATAAAT-GACTTTTCTTGCCAATGAATGGCTTTTTCTTCACGTTTTCCAAGGCAAACAT
* * ** ***
2718 TCAATTACTATCTACTTTACCAAAAAATGTAAAAAAATTCA
129 TCAATTATTATTTGTTTTAATTAAAAATGTAAAAAAATTCA
*
2759 ACCTAAAATC-ATTCATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCGTCTTGAAGGCATG
1 ACTTAAAATCAATT-ATGAGATTATAAAACCATTTAAAGCGAGTAATAAG-GTCTTGAAGGCATG
* * * * *
2823 GGTGACTATAAGTAGATTTTTCTTGCCAATGAATGGCTTTTTCTTCAGGTTTCCCAAGGCAAACC
64 GGTGACTATAAAT-GACTTTTCTTGCCAATGAATGGCTTTTTCTTCACGTTTTCCAAGGCAAACA
* * *
2888 TTCAGTTATTATTTGTGTGAATTAAAAATGTAAAAAAATTCA
128 TTCAATTATTATTTGTTTTAATTAAAAATGTAAAAAAATTCA
* ** ********** * *
2930 GCTCGAAATCAATTATGAGATTATAAANNNNNNNNNNGCGAGTAATAAGG-CTTTCCAAGGCATC
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGTC-TT-GAAGGCATG
* * * * ** * ** * * *
2994 GGTGACTATAAATGGGCTTTTTTTGTCAATGGATATCTTTTTCTTCATGTTTTTGAAAGTAGACA
64 GGTGACTATAAAT-GACTTTTCTTGCCAATGAATGGCTTTTTCTTCACGTTTTCCAAGGCAAACA
* * * * *
3059 TTCAATTATAATCTATTTTAATAAAAAATATAAAAAAAATTC-
128 TTCAATTATTATTTGTTTTAATTAAAAATGT-AAAAAAATTCA
* * * *
3101 ACTTAAAATCAATTATGAGTTTATAAAATCATTTAAACCGAGTAATAAGG-CTTTGAAATGCATG
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGTC-TTG-AAGGCATG
** * * * *
3165 GAAGACTATAAATGAACTTTTCTTTCCAATGAATGGATTTTTCTTCAAGTTTGT-CAAGACAAAC
64 GGTGACTATAAATG-ACTTTTCTTGCCAATGAATGGCTTTTTCTTCACGTTT-TCCAAGGCAAAC
* * * ***
3229 ATTCAATTACTATCTGCTTTACCCAAAAATGTAAAAAAAAATT-A
127 ATTCAATTATTATTTGTTTTAATTAAAAATGT--AAAAAAATTCA
* * * * *
3273 AGTCAAAATCATTTATGAGATTATAAAACCATTTAAAGCGAGTAATAACAGT-TCTGAAGGCATT
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAA-GGTCT-TGAAGGCATG
* * * * * *
3337 GGTGGCTATAAGTAGACTTTTCTTGCCAATGAATGGCTTTTGCTTTAGGTTTTCCTAGGCAAACA
64 GGTGACTATAAAT-GACTTTTCTTGCCAATGAATGGCTTTTTCTTCACGTTTTCCAAGGCAAACA
* * *
3402 TTTAGTTATTATTTGTTTGAATTAAAAATGTAAAAACAATTCA
128 TTCAATTATTATTTGTTTTAATTAAAAATGTAAAAA-AATTCA
* * ********* * * *
3445 GCTTGAAATCAATTATNNNNNNNNNNAAA-CATTTAAAGCGAGTAATAAGGT-TTCAAAAGCATC
1 ACTTAAAATCAATTAT-GAGATTATAAAACCATTTAAAGCGAGTAATAAGGTCTT-GAAGGCATG
* * * * * ** * * * *
3508 GATGACTACAAATGGGCTTTTCTTGTCAATGGATATCTTTTTCATCACG-TTTCTAGAGGTAGAC
64 GGTGACTATAAAT-GACTTTTCTTGCCAATGAATGGCTTTTTCTTCACGTTTTCCA-AGGCAAAC
* *
3572 ATTCAATTATAATTTTTTTTAA-TAAAAA-GTATAAAAACATTCA
127 ATTCAATTATTATTTGTTTTAATTAAAAATGTA-AAAAA-ATTCA
* * * * * * *
3615 ACTCAAAATCAATTATGAGGTTATAAAATCATTTAGAGCAAGTAACAAGG-CTTTCGAAGGTATG
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGTC-TT-GAAGGCATG
* ** * ** * * *** * *
3679 GGTGACTATAAATGAAATTTTCTTATCAATGGATATCTTTTTCTTGACATTTTTTGAGGTAGACA
64 GGTGACTATAAATG-ACTTTTCTTGCCAATGAATGGCTTTTTCTTCACGTTTTCCAAGGCAAACA
* * * * ** *
3744 TTCAATTATAATCTATTTTAA-TAAAAATATAAATTAATTTA
128 TTCAATTATTATTTGTTTTAATTAAAAATGTAAAAAAATTCA
* **
3785 ACTTAAAATCAATTATGAGGTTATAAAATTATTTAAAGCGAG-AATAAGG-CTTTCGAAGGCATG
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGTC-TT-GAAGGCATG
* * * * *
3848 GGTAACTATAAATGGACTTTTCTTGTCAATAGATAT--CTTTTTCTTTACGTTTCCCAAGGTAGA
64 GGTGACTATAAAT-GACTTTTCTTGCCAAT-GA-ATGGCTTTTTCTTCACGTTTTCCAAGGCA-A
* * *
3911 A-ATTCAATTATTATCTGTTTTAA-TCAAAATGTATAAAAATTCA
125 ACATTCAATTATTATTTGTTTTAATTAAAAATGTAAAAAAATTCA
** * * * * *
3954 TGTTAAAATCAATTACGAGATTCTAAAAACATTTTAAGC-ACGTAATAAGGCTTTTGAAGGCATG
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGA-GTAATAAGG-TCTTGAAGGCATG
* * * * *
4018 GGTAACTATAAATGTACTTCT-TTGCCAATGAATGGCTTTTTCTTCAGGTTTTCCTAGGCAAAGA
64 GGTGACTATAAATG-ACTTTTCTTGCCAATGAATGGCTTTTTCTTCACGTTTTCCAAGGCAAACA
* * * *
4082 TTCAGTTATTATTTGTTTTAATCATAAAT-TAAAAAAATTTA
128 TTCAATTATTATTTGTTTTAATTAAAAATGTAAAAAAATTCA
* * * * * * *
4123 GCTTGAAATCAATTATGAGATTATAAAAACATTTAAAACGGGTAATAAGG-CTTCCAAAGGCATC
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGTCTT--GAAGGCATG
** * ** **********
4187 GGTGACTGCAAATGGGCTTTTCTTGCCAATGAATATC-TTNNNNNNNNNNTTTCTCAAGGCAAAC
64 GGTGACTATAAAT-GACTTTTCTTGCCAATGAATGGCTTTTTCTTCACGTTTTC-CAAGGCAAAC
* * * * * *
4251 ATTCAATTATTATCTATTTTGACTAAAAATGTAAAAACATTTA
127 ATTCAATTATTATTTGTTTTAATTAAAAATGTAAAAAAATTCA
* ********** *
4294 ACTTAAAATCAATTATGAGAATANNNNNNNNNNTAAACCGAGTAATAAGG-CTTTCGAAGG-AGT
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGTC-TT-GAAGGCA-T
* * *** ** * * * *
4357 GGGTGACTATAAATGGACTGTTCTTGACAATGAAAATCTTGGTCTTCATGTTTCCCAAGGTAGAC
63 GGGTGACTATAAAT-GACTTTTCTTGCCAATGAATGGCTTTTTCTTCACGTTTTCCAAGGCAAAC
* * * * * * *
4422 ATTCACTTGTAATCTGTTTTAATAAAAAATATAAAAAAAATTTA
127 ATTCAATTATTATTTGTTTTAATTAAAAATGT-AAAAAAATTCA
* * * *
4466 ACTTAAGACCAATTATGAGATTATAAAACCATTAAAAGTGAGTAATAAGG
1 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGG
4516 CTTTCGAAGN
Statistics
Matches: 1345, Mismatches: 359, Indels: 105
0.74 0.20 0.06
Matches are distributed among these distances:
167 4 0.00
168 5 0.00
169 263 0.20
170 193 0.14
171 641 0.48
172 232 0.17
173 7 0.01
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.34
Consensus pattern (169 bp):
ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGTCTTGAAGGCATGGG
TGACTATAAATGACTTTTCTTGCCAATGAATGGCTTTTTCTTCACGTTTTCCAAGGCAAACATTC
AATTATTATTTGTTTTAATTAAAAATGTAAAAAAATTCA
Found at i:3572 original size:514 final size:511
Alignment explanation
Indices: 2588--4220 Score: 1457
Period size: 514 Copynumber: 3.2 Consensus size: 511
2578 NNNNNNNNNN
* * *
2588 ACTTAAAATCATTTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGGTCTT-AAACGCATG
1 ACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCT-TTGAAACGCATG
* * * * *
2652 TGTGACTATAAGT-AGACTTTTCTTGCCAATGAATGGCTTTTTCTTTACGTTTGCTGAGACAAAC
65 -GTGACTATAAATGA-ACTTTTCTTGCCAATGAATGGATTTTTCTTCAAGTTTGCTAAGACAAAC
2716 ATTCAATTACTATCTACTTTACCAAAAAATGTAAAAAAATTCAACCTAAAATCATTCATGAGATT
128 ATTCAATTACTATCTACTTTACCAAAAAATGTAAAAAAATTCAACCTAAAATCATTCATGAGATT
*
2781 ATAAAACCATTTAAAGCGAGTAATAAGCGTCTTGAAGGCATGGGTGACTATAAGTAGATTTTTCT
193 ATAAAACCATTTAAAGCGAGTAATAAGCGTCTTGAAGGCATGGGTGACTATAAGTAGACTTTTCT
* *
2846 TGCCAATGAATGGCTTTTTCTTCAGGTTTCCCAAGGCAAACCTTCAGTTATTATTTGTGTGAATT
258 TGCCAATGAATGGCTTTTGCTTCAGGTTTCCCAAGGCAAACATTCAGTTATTATTTGTGTGAATT
*********
2911 AAAAATGTAAAAAAATTCAGCTCGAAATCAATTATGAGATTATAAANNNNNNNNNNGCGAGTAAT
323 AAAAATGTAAAAAAATTCAGCTCGAAATCAATTATGAGATTATAAA-ACATTTAAAGCGAGTAAT
* * * * * *
2976 AAGGCTTTCCAAGGCATCGGTGACTATAAATGGGCTTTTTTTGTCAATGGATATCTTTTTCTTCA
387 AAGGCTTTCAAAAGCATCGATGACTACAAATGGGCTTTTCTTGTCAATGGATATCTTTTTCATCA
* *
3041 TGTTTTTGAAAGTAGACATTCAATTATAATCTATTTTAATAAAAAATATAAAAAAAATTC-
452 CGTTTTAGAAAGTAGACATTCAATTATAATCTATTTTAATAAAAAATAT-AAAAAAATTCA
* * *
3101 ACTTAAAATCAATTATGAGTTTATAAAATCATTTAAACCGAGTAATAAGGCTTTGAAATGCATGG
1 ACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTGAAACGCATGG
* *
3166 AAGACTATAAATGAACTTTTCTTTCCAATGAATGGATTTTTCTTCAAGTTTG-TCAAGACAAACA
66 -TGACTATAAATGAACTTTTCTTGCCAATGAATGGATTTTTCTTCAAGTTTGCT-AAGACAAACA
* * * *
3230 TTCAATTACTATCTGCTTTACCCAAAAATGTAAAAAAAAATT-AA-GTCAAAATCATTTATGAGA
129 TTCAATTACTATCTACTTTACCAAAAAATGT--AAAAAAATTCAACCT-AAAATCATTCATGAGA
* *
3293 TTATAAAACCATTTAAAGCGAGTAATAA-CAGT-TCTGAAGGCATTGGTGGCTATAAGTAGACTT
191 TTATAAAACCATTTAAAGCGAGTAATAAGC-GTCT-TGAAGGCATGGGTGACTATAAGTAGACTT
* * * * *
3356 TTCTTGCCAATGAATGGCTTTTGCTTTAGGTTTTCCTAGGCAAACATTTAGTTATTATTTGTTTG
254 TTCTTGCCAATGAATGGCTTTTGCTTCAGGTTTCCCAAGGCAAACATTCAGTTATTATTTGTGTG
* *********
3421 AATTAAAAATGTAAAAACAATTCAGCTTGAAATCAATTATNNNNNNNNNNAAACATTTAAAGCGA
319 AATTAAAAATGTAAAAA-AATTCAGCTCGAAATCAATTAT-GAGATTATAAAACATTTAAAGCGA
3486 GTAATAAGG-TTTCAAAAGCATCGATGACTACAAATGGGCTTTTCTTGTCAATGGATATCTTTTT
382 GTAATAAGGCTTTCAAAAGCATCGATGACTACAAATGGGCTTTTCTTGTCAATGGATATCTTTTT
* * * * *
3550 CATCACGTTTCTAG-AGGTAGACATTCAATTATAATTTTTTTTAATAAAAAGTATAAAAACATTC
447 CATCACGTTT-TAGAAAGTAGACATTCAATTATAATCTATTTTAATAAAAAATATAAAAAAATTC
3614 A
511 A
* * * * * * *
3615 ACTCAAAATCAATTATGAGGTTATAAAATCATTTAGAGCAAGTAACAAGGCTTTCG-AAGGTATG
1 ACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTT-GAAACGCAT-
* ** * *** * ** * ** *
3679 GGTGACTATAAATGAAATTTTCTTATCAATGGATATCTTTTTCTTGACA-TTTTTTGAGGTAGAC
64 GGTGACTATAAATGAACTTTTCTTGCCAATGAATGGATTTTTCTTCA-AGTTTGCTAAGACAAAC
* * ** * *
3743 ATTCAATTA-TAATCTATTTTA--ATAAAAATATAAATTAATTTAACTTAAAATCAATT-ATGAG
128 ATTCAATTACT-ATCTACTTTACCA-AAAAATGTAAAAAAATTCAACCTAAAATC-ATTCATGAG
* ** * * *
3804 GTTATAAAATTATTTAAAGCGAG-AATAAG-G-CTTTCGAAGGCATGGGTAACTATAAATGGACT
190 ATTATAAAACCATTTAAAGCGAGTAATAAGCGTC-TT-GAAGGCATGGGTGACTATAAGTAGACT
* * * * * * *
3866 TTTCTTGTCAATAGATAT--CTTTTTCTTTACGTTTCCCAAGGTAGAA-ATTCAATTATTATCTG
253 TTTCTTGCCAAT-GA-ATGGCTTTTGCTTCAGGTTTCCCAAGGCA-AACATTCAGTTATTATTTG
* * * * ** * * *
3928 TTTTAA-TCAAAATGTATAAAAATTCATG-TTAAAATCAATTACGAGATTCTAAAAACATTTTAA
315 TGTGAATTAAAAATGTAAAAAAATTCA-GCTCGAAATCAATTATGAGATTAT-AAAACATTTAAA
** * * * * * ** * * * **
3991 GC-ACGTAATAAGGCTTTTGAAGGCATGGGTAACTATAAATGTACTTCT-TTGCCAATGAATGGC
378 GCGA-GTAATAAGGCTTTCAAAAGCATCGATGACTACAAATGGGCTTTTCTTGTCAATGGATATC
* * *** * * * * * * * * * *
4054 TTTTTCTTCAGGTTTTCCTAGGCAAAGATTCAGTTATTATTTGTTTTAATCATAAAT-TAAAAAA
442 TTTTTCATCACGTTTTAGAAAGTAGACATTCAATTATAATCTATTTTAATAAAAAATATAAAAAA
*
4118 ATTTA
507 ATTCA
* * * * * ** *
4123 GCTTGAAATCAATTATGAGATTATAAAAACATTTAAAACGGGTAATAAGGCTTCCAAAGGCATCG
1 ACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTGAAACGCAT-G
** **
4188 GTGACTGCAAATGGGCTTTTCTTGCCAATGAAT
65 GTGACTATAAATGAACTTTTCTTGCCAATGAAT
4221 ATCTTNNNNN
Statistics
Matches: 914, Mismatches: 171, Indels: 75
0.79 0.15 0.06
Matches are distributed among these distances:
508 87 0.10
509 92 0.10
510 39 0.04
511 84 0.09
512 41 0.04
513 162 0.18
514 357 0.39
515 50 0.05
516 2 0.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.35
Consensus pattern (511 bp):
ACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTGAAACGCATGG
TGACTATAAATGAACTTTTCTTGCCAATGAATGGATTTTTCTTCAAGTTTGCTAAGACAAACATT
CAATTACTATCTACTTTACCAAAAAATGTAAAAAAATTCAACCTAAAATCATTCATGAGATTATA
AAACCATTTAAAGCGAGTAATAAGCGTCTTGAAGGCATGGGTGACTATAAGTAGACTTTTCTTGC
CAATGAATGGCTTTTGCTTCAGGTTTCCCAAGGCAAACATTCAGTTATTATTTGTGTGAATTAAA
AATGTAAAAAAATTCAGCTCGAAATCAATTATGAGATTATAAAACATTTAAAGCGAGTAATAAGG
CTTTCAAAAGCATCGATGACTACAAATGGGCTTTTCTTGTCAATGGATATCTTTTTCATCACGTT
TTAGAAAGTAGACATTCAATTATAATCTATTTTAATAAAAAATATAAAAAAATTCA
Done.