Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400198.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3411.0, 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: 8644
ACGTcount: A:0.28, C:0.10, G:0.09, T:0.27
Warning! 2268 characters in sequence are not A, C, G, or T
Found at i:2033 original size:169 final size:169
Alignment explanation
Indices: 1747--2731 Score: 940
Period size: 169 Copynumber: 5.8 Consensus size: 169
1737 ATTATTAGAT
* * ** * *
1747 TATAATTGAATGTCTACATCAAGAAAC-GTGAAGAAAAAGGCATTCA-TTGGCAAGAAAAGTCTA
1 TATAATTGAATGCCTACTTCAAGAAACTGT-AA-AAAAACCCATTTATTTGG-AAGAAAAGTCCA
* * * * * * *
1810 TTTCTAGCCACGCATTCATTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAAT
63 TTTATAGTCTCCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCATAAT
* * *
1875 TGA-TTGAAGTTAAATTTTTTACATTTCTCAATAAAGCAGAC
128 TGATTTTAAGTTAAATTTTTTACATTTCTCATTAAAACAGAC
* * * * *
1916 TATAATTGAATACCTGCTTGAAGAAACCTGTAGAAAAACCCATTTATTTGGAAGAAAAGTCCAAT
1 TATAATTGAATGCCTACTTCAAGAAA-CTGTAAAAAAACCCATTTATTTGGAAGAAAAGTCCATT
* * * *
1981 TATATTCTCCCACTCCTTCGAAAGCCTTATTACTCGCTTTAAAT-GCTTTTATAATCTCATAATT
65 TATAGTCTCCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATAG-TTTTATAATCTCATAATT
* * *
2045 GGTTTTAAGTTAAATTTTTTATATTT-TCATTAAAATAGAC
129 GATTTTAAGTTAAATTTTTTACATTTCTCATTAAAACAGAC
* * * *
2085 TATAATTCAATACC--CGTCTCGAA-AAA-TGTATAGAAAACCCAGTTATTTGGAAGAAAAGTCC
1 TATAATTGAATGCCTAC-T-TC-AAGAAACTGTA-AAAAAACCCATTTATTTGGAAGAAAAGTCC
* * *
2146 ATTTATAGTCTTCCATTCCTTCAAAAGCCTTATTAGTCACTTTAAATGGTTTTATAATCTCATAA
62 ATTTATAGTCTCCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCATAA
* ** *
2211 TTGATTTTAAGTTAAATTTTTTACATTTTTTGTTAAAACAAAC
127 TTGATTTTAAGTTAAATTTTTTACATTTCTCATTAAAACAGAC
* * * * *
2254 TTTAATTGAATGCCTACCTCTAGAAA-TGTATAAAAAACCTATTTATTTAGAAGAAAAGTCCATT
1 TATAATTGAATGCCTACTTCAAGAAACTGTA-AAAAAACCCATTTATTTGGAAGAAAAGTCCATT
* * * * * *
2318 TATAGTCTCCTATTCCTTCATAAGCCTTATTGCTCGCTTTAAATAGTTTTATAAACTTATAATTG
65 TATAGTCTCCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCATAATTG
* * * *
2383 ATTTTAAGTTAATTGTTTTTACATTTTTGATTAAAATAGAC
130 ATTTTAAGTTAAAT-TTTTTACATTTCTCATTAAAACAGAC
* * * * *** * * *
2424 TATAAATGAATGTCTACCTT-TAGAAACGTGAAAAAAAATAAATTCATTTGCAAGAAAAGTCTAT
1 TATAATTGAATGCCTA-CTTCAAGAAAC-TGTAAAAAAACCCATTTATTTGGAAGAAAAGTCCAT
* * *
2488 TTATAGTCAT-GCATTCCTTTAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCAAAAT
64 TTATAGTC-TCCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCATAAT
* **
2552 TGATTTTAAGTTCAAATTTTTTTAC-TTTCTTGATTAAAACAGGT
128 TGATTTTAAGTT-AAA-TTTTTTACATTTC-TCATTAAAACAGAC
* * * ** * * * *
2596 TATAATTGAATGTCTACATCAAGAAACAT-AAAGAAAAAGGCATTCA-TTGATAAGAAAAATTCA
1 TATAATTGAATGCCTACTTCAAGAAAC-TGTAA-AAAAACCCATTTATTTG-GAAGAAAAGTCCA
* *
2659 TTTATAGTCTCTCATTCCTTCAAAAG-CTTAATTACTCACTTTAAATAGTTTAATAATCTCATAA
63 TTTATAGTCTCCCATTCCTTCAAAAGCCTT-ATTACTCACTTTAAATAGTTTTATAATCTCATAA
2723 TTGATTTTA
127 TTGATTTTA
2732 TGTTCAGGTT
Statistics
Matches: 682, Mismatches: 107, Indels: 51
0.81 0.13 0.06
Matches are distributed among these distances:
167 5 0.01
168 112 0.16
169 256 0.38
170 70 0.10
171 110 0.16
172 128 0.19
173 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (169 bp):
TATAATTGAATGCCTACTTCAAGAAACTGTAAAAAAACCCATTTATTTGGAAGAAAAGTCCATTT
ATAGTCTCCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCATAATTGA
TTTTAAGTTAAATTTTTTACATTTCTCATTAAAACAGAC
Found at i:3153 original size:172 final size:154
Alignment explanation
Indices: 2941--3254 Score: 254
Period size: 172 Copynumber: 1.9 Consensus size: 154
2931 AGAAATGGTA
* * * * *
2941 GACTATAAATAGATTTTTCTTACCAATGAATGCCTTTTTTTTCATGTTTCTTG-ATGTAGACATT
1 GACTATAAATAGACTTTTCTTACAAATGAATGCATTTTTTTTCACGTTTC-TGAAGGTAGACATT
* * * * *
3005 CAATTATAACCCATTTTAATGAAGAAA-CTAAAAAAATTTGAACTTAAAATCAATTTTGAGATTA
65 CAATTATAACCCATTTTAATCAA-AAATCTAAAAAAA-ATCAACTTAAAATCAATTATAAGATTA
3069 TAAAACCATTTAAAGTGANNNNNNNNNNNNNNNNNGGAATGAGT
128 TAAAACCATTTAAAGTGA-----------------GGAATGAGT
* * *
3113 GACTATAAATAGACTTTTCTTGCAAATGAGTTCATTTTTTTTCACGTTTCTGAAGGTAGACATTC
1 GACTATAAATAGACTTTTCTTACAAATGAATGCATTTTTTTTCACGTTTCTGAAGGTAGACATTC
* * * * *
3178 ATTTATAATCTATTTTAATCAAAAATGTAAAAAAAATCAACTTAAAATCAATTATAAGTTTATAA
66 AATTATAACCCATTTTAATCAAAAATCTAAAAAAAATCAACTTAAAATCAATTATAAGATTATAA
**
3243 AACTGTTTAAAG
131 AACCATTTAAAG
3255 CGAGTAATAA
Statistics
Matches: 120, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
171 40 0.33
172 80 0.67
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.36
Consensus pattern (154 bp):
GACTATAAATAGACTTTTCTTACAAATGAATGCATTTTTTTTCACGTTTCTGAAGGTAGACATTC
AATTATAACCCATTTTAATCAAAAATCTAAAAAAAATCAACTTAAAATCAATTATAAGATTATAA
AACCATTTAAAGTGAGGAATGAGT
Found at i:3617 original size:338 final size:338
Alignment explanation
Indices: 3173--4722 Score: 1404
Period size: 338 Copynumber: 4.6 Consensus size: 338
3163 TGAAGGTAGA
* * * * * *
3173 CATTCATTTATAATCTATTTTAATCAAAAATGTAAAAAAAATCAACTTAAAATCAATTATAAGTT
1 CATTCAATTATAATCTGTTTTAAT-AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGAT
* * *
3238 TATAAAACTGTTTAAAGCGAGTAATAAGGCTTATGAAGGAATGGGAGACTATAAATGGATTTTTC
65 TATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTC
* * * *
3303 TTCTAAACAAAT-AGGTTTTTTTATACGCTTCCAGAGGCAAGCATTCAATTAAAGTCTGTTTTGA
130 TTCTAAATAAATGA-GTTTTTTTACACGTTTCCAGAGGCAAGCATTCAATTATAGTCTGTTTT-A
*
3367 CAAAAAATGTAAAAAAGTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGACTAA
193 CAAAAAATGTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGACTAA
* * * *
3432 TAAGACTTTTGAAGGAATAAAAGACTATAAATGGACTTTTCTTCCAAATAACTGGGTTTTCTACA
258 TAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTTCCAAATAAATGGGTTTTCTACA
* * *
3497 TATTTTTTGAGGTAGG
323 TGTTTCTTGAGGCAGG
* * * * *
3513 TATTGAATTATAGTCTATTTTAATGAAAATAT-AAAAAATTCAACTTAAAATCAATTATGAGATT
1 CATTCAATTATAATCTGTTTTAATAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATT
** * * * * * *
3577 ATAAAACTATTTAAAGCGAGTAATAAGGCTTTCAAAGGAATAGAAGAATATAATTAGAATTTTCT
66 ATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTCT
* ** * * * * * *
3642 TCCAAATAAATGAGTTTTCCTACAGGTTTCTCA-AGGCAGGCCTTCAATTATAGTTTGCTTTATT
131 TCTAAATAAATGAGTTTTTTTACACGTTTC-CAGAGGCAAGCATTCAATTATAGTCTGTTTTA-C
* * * *
3706 GAGAAATGTAAAAAATTCAACTT-CAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
194 AAAAAATGTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGACTAAT
* * * * * *** *
3770 AAGGCTTTTGAAAGAACGCGTAG-CTAGAAATGGACTTTTCTTACC-AATGAATTCTTTTTTCTT
259 AAGGCTTTTGAAGGAATGAG-AGACTATAAATGGACTTTTCTT-CCAAAT-AAATGGGTTTTCTA
* * *
3833 CATGTTTCTTGATGTAGA
321 CATGTTTCTTGAGGCAGG
* * * *
3851 CATTCAATTATAATCTGTTTTAATCAAAAA-AGTAAAAATAACTGAACTTAGAATCAGTTATGAG
1 CATTCAATTATAATCTGTTTTAAT-AAAAATA-TAAAAA-AATTCAACTTAAAATCAATTATGAG
* ** * * * *
3915 ACTATAAAACTATTTAAAATGAGTAATAAGTCTTTTGAAAGAACGGGTG-CATATAAATGGACTT
63 ATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGAC-TATAAATGGACTT
* * * ** * * * * *
3979 TTCTTGTTAGTGTAT-ACTTTCTTCTT-CACGTTT-CATTAGG-TAGACATTTAATTATATTCTG
127 TTCTTCTAAATAAATGAGTTT-TT-TTACACGTTTCCA-GAGGCAAG-CATTCAATTATAGTCTG
* * * *
4040 TTTTCTTCAAAAATAT-AAAAAAATTCAATTTAAAATCAATTGTGAGATTATAAAACCATTTAAA
188 -TTT-TACAAAAA-ATGTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA
* * *
4104 GCGAGTAATAAGGCTTTTGAAGGAATGTGAGACTATAAATGGA-TGTTGT-TTCAAAATAAATGG
250 GCGACTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACT-TT-TCTTCCAAATAAATGG
* ** * *
4167 GTTTCTCTGCATGTTTCTCAAGACATG
313 GTTT-TCTACATGTTTCTTGAGGCAGG
* * * *
4194 CATTCAATTATAATCTGTTTTAACAAAAA-ATAAAAAAAGTACATCTTAAAATCAATTATCAGAT
1 CATTCAATTATAATCTGTTTTAATAAAAATATAAAAAAA-TTCAACTTAAAATCAATTATGAGAT
* * * * * ** *
4258 TATGAAACCATTAAAAGCAAGTAGTAAGGCTTTTGAAGGAATAAGAGACTATAAATAGACTTTTC
65 TATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTC
* * * * * * *
4323 TTTTAAATAAATGAGTTTTTGTATATGTTTCCTGAGGCAAGCGTTCAATTATAGTCTCTTTTA-A
130 TTCTAAATAAATGAGTTTTTTTACACGTTTCCAGAGGCAAGCATTCAATTATAGTCTGTTTTACA
* * *
4387 TGAAAAATGTAAAAATTTCAACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGGGACTAA
195 --AAAAATGTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGACTAA
* * * * *
4452 TAAGGCTTTTGAAGGAACGAGAGACTATAAATGAACTTTTCTTTCAAATAAATGGCTTTT-TCCA
258 TAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTTCCAAATAAATGGGTTTTCTACA
* * * *
4516 CGTCTCCCT-AGGCAAG
323 TGT-TTCTTGAGGCAGG
* * * *
4532 CATTTAATTATAGTCTGTTTTAACAAAAAATATAAAAAAATT-TACTT-AAATCAATTATGAGAT
1 CATTCAATTATAATCTGTTTTAA-TAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGAT
* * * *
4595 TAAAAAAGC-ATTTAAAGCGAGTAATAGGGCTTTTGAAGGAATGAGAGACTATAAATGGAGTTTT
65 TATAAAA-CTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTT
* * * ** * *
4659 CTT-TCAAATAAATG-GCTTTTTCTACATGTTTTTCA-AGATAGGCATTCAATTATAGTTTGTTT
129 CTTCT-AAATAAATGAG-TTTTTTTACACG-TTTCCAGAGGCAAGCATTCAATTATAGTCTGTTT
4721 TA
191 TA
4723 ATATGANNNN
Statistics
Matches: 962, Mismatches: 205, Indels: 89
0.77 0.16 0.07
Matches are distributed among these distances:
336 2 0.00
337 188 0.20
338 236 0.25
339 29 0.03
340 146 0.15
341 204 0.21
342 43 0.04
343 113 0.12
344 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.35
Consensus pattern (338 bp):
CATTCAATTATAATCTGTTTTAATAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATT
ATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTCT
TCTAAATAAATGAGTTTTTTTACACGTTTCCAGAGGCAAGCATTCAATTATAGTCTGTTTTACAA
AAAATGTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGACTAATAA
GGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTTCCAAATAAATGGGTTTTCTACATGT
TTCTTGAGGCAGG
Found at i:3762 original size:169 final size:170
Alignment explanation
Indices: 2877--4725 Score: 1326
Period size: 170 Copynumber: 10.9 Consensus size: 170
2867 AAACTGAACG
* * * * *
2877 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCTAGTAATTAGGCTTTTGAAGAAATGGTAG
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGAAG
* * * ** * * ** * * *
2942 ACTATAAATAGATTTTTCTTACC-AATGAATGCCTTTTTTTTCATGTTTCTTGATGTAGACATTC
66 ACTATAAATGGACTTTTCTT-CCAAATAAATGAGTTTTTCTACATGTTTCTCAAGGCAGGCATTC
** ** * * *
3006 AATTATAACCCATTTTAATGAAGAAACT-AAAAAAATTTGAACT
130 AATTATAGTCTGTTTTAAT-AA-AAAATGTAAAAAA-TTCAACT
* * ***************** *
3049 TAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGANNNNNNNNNNNNNNNNNGGAAT-GAGT
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGA-A
* * ** * * * * * * *
3113 GACTATAAATAGACTTTTCTTGCAAATGAGTTCA-TTTTTTTTCACGTTTCTGAAGGTAGACATT
65 GACTATAAATGGACTTTTCTTCCAAAT-AAATGAGTTTTTCTACATGTTTCTCAAGGCAGGCATT
* * * * *
3177 CATTTATAATCTATTTTAATCAAAAATGTAAAAAAAATCAACT
129 CAATTATAGTCTGTTTTAATAAAAAATGT-AAAAAATTCAACT
* * ** * * *
3220 TAAAATCAATTATAAGTTTATAAAACTGTTTAAAGCGAGTAATAAGGCTTATGAAGGAATGGGAG
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGAAG
* * * * * * * *
3285 ACTATAAATGGATTTTTCTTCTAAACAAAT-AGGTTTTTTTATACGCTTC-CAGAGGCAAGCATT
66 ACTATAAATGGACTTTTCTTCCAAATAAATGA-GTTTTTCTACATGTTTCTCA-AGGCAGGCATT
* * * *
3348 CAATTAAAGTCTGTTTTGACAAAAAATGTAAAAAAGTCAACT
129 CAATTATAGTCTGTTTTAATAAAAAATGTAAAAAATTCAACT
* * *
3390 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGACTAATAAGACTTTTGAAGGAATAAAAG
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGAAG
* * * * ** * * *
3455 ACTATAAATGGACTTTTCTTCCAAATAACTG-GGTTTTCTACATATTTTTTGAGGTAGGTATTGA
66 ACTATAAATGGACTTTTCTTCCAAATAAATGAGTTTTTCTACATGTTTCTCAAGGCAGGCATTCA
* * *
3519 ATTATAGTCTATTTTAAT-GAAAATATAAAAAATTCAACT
131 ATTATAGTCTGTTTTAATAAAAAATGTAAAAAATTCAACT
* **
3558 TAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTCAAAGGAATAGAAG
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGAAG
* * * * * * *
3623 AATATAATTAGAATTTTCTTCCAAATAAATGAGTTTTCCTACAGGTTTCTCAAGGCAGGCCTTCA
66 ACTATAAATGGACTTTTCTTCCAAATAAATGAGTTTTTCTACATGTTTCTCAAGGCAGGCATTCA
* * * * *
3688 ATTATAGTTTGCTTTATTGAGAAATGTAAAAAATTCAACT
131 ATTATAGTCTGTTTTAATAAAAAATGTAAAAAATTCAACT
* * ** *
3728 T-CAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAACGCGTA
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAA-TAGAA
* * *** * ** * * *
3792 G-CTAGAAATGGACTTTTCTTACC-AATGAATTCTTTTTTCTTCATGTTTCTTGATGTAGACATT
65 GACTATAAATGGACTTTTCTT-CCAAATAAATGAGTTTTTCTACATGTTTCTCAAGGCAGGCATT
* * *
3855 CAATTATAATCTGTTTTAATCAAAAAA-GTAAAAATAACTGAACT
129 CAATTATAGTCTGTTTTAAT-AAAAAATGT-AAAA-AATTCAACT
* * * * ** * * ** **
3899 TAGAATCAGTTATGAGACTATAAAACTATTTAAAATGAGTAATAAGTCTTTTGAAAGAACGGGTG
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGAAG
*** * ** * * * * * *
3964 -CATATAAATGGACTTTTCTTGTTAGTGTAT-ACTTTCTTCTTCACGTTTCAT-TAGGTAGACAT
66 AC-TATAAATGGACTTTTCTTCCAAATAAATGAGTTT-TTCTACATGTTTC-TCAAGGCAGGCAT
* * ** * * *
4026 TTAATTATATTCTGTTTTCTTCAAAAATATAAAAAAATTCAATT
128 TCAATTATAGTCTGTTTTAATAAAAAATGT-AAAAAATTCAACT
* *
4070 TAAAATCAATTGTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT-GTGA
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAG-AA
* * * * * *
4134 GACTATAAATGGA-TGTTGT-TTCAAAATAAATGGGTTTCTCTGCATGTTTCTCAAGACATGCAT
65 GACTATAAATGGACT-TT-TCTTCCAAATAAATGAGTTTTTCTACATGTTTCTCAAGGCAGGCAT
* * * * *
4197 TCAATTATAATCTGTTTTAACAAAAAAT-AAAAAAAGTACATCT
128 TCAATTATAGTCTGTTTTAATAAAAAATGTAAAAAA-TTCAACT
* * * * *
4240 TAAAATCAATTATCAGATTATGAAACCATTAAAAGCAAGTAGTAAGGCTTTTGAAGGAATA-AGA
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGA-A
* ** * * * * *
4304 GACTATAAATAGACTTTTCTTTTAAATAAATGAGTTTTTGTATATGTTTC-CTGAGGCAAGCGTT
65 GACTATAAATGGACTTTTCTTCCAAATAAATGAGTTTTTCTACATGTTTCTC-AAGGCAGGCATT
* * *
4368 CAATTATAGTCTCTTTTAATGAAAAATGTAAAAATTTCAACT
129 CAATTATAGTCTGTTTTAATAAAAAATGTAAAAAATTCAACT
* * * *
4410 TAAAATCAATTATGAGATTATAAAATCATTTAAAGGGACTAATAAGGCTTTTGAAGGAA-CGAGA
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGA-A
* * * * * * *
4474 GACTATAAATGAACTTTTCTTTCAAATAAATG-GCTTTTTC--CACGTCTCCCTAGGCAAGCATT
65 GACTATAAATGGACTTTTCTTCCAAATAAATGAG-TTTTTCTACATGTTTCTCAAGGCAGGCATT
* * * *
4536 TAATTATAGTCTGTTTTAACAAAAAATATAAAAAAATT-TACT
129 CAATTATAGTCTGTTTTAATAAAAAATGT-AAAAAATTCAACT
* * *
4578 T-AAATCAATTATGAGATTAAAAAAGCATTTAAAGCGAGTAATAGGGCTTTTGAAGGAAT-GAGA
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGA-A
* * * **
4641 GACTATAAATGGAGTTTTCTTTCAAATAAATG-GCTTTTTCTACATGTTTTTCAAGATAGGCATT
65 GACTATAAATGGACTTTTCTTCCAAATAAATGAG-TTTTTCTACATGTTTCTCAAGGCAGGCATT
*
4705 CAATTATAGTTTGTTTTAATA
129 CAATTATAGTCTGTTTTAATA
4726 TGANNNNNNN
Statistics
Matches: 1310, Mismatches: 323, Indels: 91
0.76 0.19 0.05
Matches are distributed among these distances:
167 94 0.07
168 146 0.11
169 230 0.18
170 356 0.27
171 249 0.19
172 233 0.18
173 2 0.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.35
Consensus pattern (170 bp):
TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGAAG
ACTATAAATGGACTTTTCTTCCAAATAAATGAGTTTTTCTACATGTTTCTCAAGGCAGGCATTCA
ATTATAGTCTGTTTTAATAAAAAATGTAAAAAATTCAACT
Found at i:4543 original size:850 final size:850
Alignment explanation
Indices: 2879--4724 Score: 2057
Period size: 850 Copynumber: 2.2 Consensus size: 850
2869 ACTGAACGTA
* *
2879 AAATCAATTATGAGATTATAAAACCATTTAAAGCTAGTAATTAGGCTTTTG-AAGAAATGGTAGA
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAG-AATGGTAGA
* *
2943 CTATAAATAGATTTTTCTTACCAATGAATGCCTTTTTT-TTCATGTTTCTTGATGTAGACATTCA
65 CTATAAATGGACTTTTCTTACCAATGAATGCCTTTTTTCTTCATGTTTCTTGATGTAGACATTCA
* ** * * * * *
3007 ATTATAACCCATTTTAATGAAGAAACTAAAAAAATTTGAACTTAAAATCAATTTTGAGATTATAA
130 ATTATAATCTGTTTTAATCAAAAAACTAAAAAAATCTGAACTTAAAATCAATTATGAGACTATAA
* ****************** *
3072 AACCATTTAAAGTGANNNNNNNNNNNNNNNNNGGAATGAGTGACTATAAATAGACTTTTCTTGCA
195 AACCATTTAAAATGAGTAATAAGTCTTTTGAAAGAACGAGTGACTATAAATAGACTTTTCTTGCA
* * *
3137 AATGAGTTCATTTTTTTTCACGTTTCTGAAGGTAGACATTCATTTATAATCTATTTTAATCAAAA
260 AATGAGTACATTTTTCTTCACGTTTCTGAAGGTAGACATTCAATTATAATCTATTTTAATCAAAA
* * **
3202 ATGTAAAAAAAATCAACTTAAAATCAATTATAAGTTTATAAAACTGTTTAAAGCGAGTAATAAGG
325 ATATAAAAAAAATCAACTTAAAATCAATTATAAGATTATAAAACCATTTAAAGCGAGTAATAAGG
* * * * *
3267 CTTATGAAGGAATGGGAGACTATAAATGGATTTTTCTTCTAAACAAATAGGTTTTTTTATACGCT
390 CTTATGAAGGAATGGGAGACTATAAATGGATTTGTCTTCAAAACAAATAGGTTTCTCTACACGCT
* * *
3332 TCCAGAGGCAAGCATTCAATTAAAGTCTGTTTTGACAAAAAATGTAAAAAAGTCAACTTAAAATC
455 TCCAGAGACAAGCATTCAATTAAAGTCTGTTTTAACAAAAAATGAAAAAAAGTCAACTTAAAATC
* * *
3397 AATTATGAGATTATAAAACCATTTAAAGCGACTAATAAGACTTTTGAAGGAATAAAAGACTATAA
520 AATTATCAGATTATAAAACCATTAAAAGCAACTAATAAGACTTTTGAAGGAATAAAAGACTATAA
* * * * * * * *
3462 ATGGACTTTTCTTCCAAATAACTGGGTTTTCTACATATTTTTTGAGGTAGGTATTGAATTATAGT
585 ATAGACTTTTCTTCCAAATAAATGAGTTTTCTACATATTTTCTGAGGCAAGCATTCAATTATAGT
3527 CTATTTTAATGAAAATATAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAA
650 CTATTTTAATGAAAATATAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAA
* * *
3592 GCGAGTAATAAGGCTTTCAAAGGAATAGAAGAATATAATTAGAATTTTCTTCCAAATAAATGAGT
715 GCGACTAATAAGGCTTTCAAAGGAAGAGAAGAATATAAATAGAATTTTCTTCCAAATAAATGAGT
* * * * * *** * *
3657 TTTCCTACAGGTTTCTCAAGGCAGGCCTTCAATTATAGTTTGCTTTATTGAGAAATGT-AAAAAA
780 TTTCCTACA-GTCTCCCAAGGCAAGCATTCAATTATAGTCTGCTTTAACAAAAAATATAAAAAAA
3721 TTCAACTT
844 TT-AACTT
* *
3729 CAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAACGCGTAG-
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATG-GTAGA
* *
3793 CTAGAAATGGACTTTTCTTACCAATGAAT-TCTTTTTTCTTCATGTTTCTTGATGTAGACATTCA
65 CTATAAATGGACTTTTCTTACCAATGAATGCCTTTTTTCTTCATGTTTCTTGATGTAGACATTCA
* * *
3857 ATTATAATCTGTTTTAATCAAAAAAGTAAAAATAA-CTGAACTTAGAATCAGTTATGAGACTATA
130 ATTATAATCTGTTTTAATCAAAAAACTAAAAA-AATCTGAACTTAAAATCAATTATGAGACTATA
* * *
3921 AAACTATTTAAAATGAGTAATAAGTCTTTTGAAAGAACGGGTG-CATATAAATGGACTTTTCTTG
194 AAACCATTTAAAATGAGTAATAAGTCTTTTGAAAGAACGAGTGAC-TATAAATAGACTTTTCTTG
** * * * * * **
3985 TTAGTGTA-TAC-TTTCTTCTTCACGTTTCAT-TAGGTAGACATTTAATTATATTCTGTTTTCTT
258 CAAATG-AGTACATTT-TTCTTCACGTTTC-TGAAGGTAGACATTCAATTATAATCTATTTTAAT
* * * *
4047 CAAAAATATAAAAAAATTCAATTTAAAATCAATTGTGAGATTATAAAACCATTTAAAGCGAGTAA
320 CAAAAATATAAAAAAAATCAACTTAAAATCAATTATAAGATTATAAAACCATTTAAAGCGAGTAA
* * * * *
4112 TAAGGCTTTTGAAGGAATGTGAGACTATAAATGGATGTTGT-TTCAAAATAAATGGGTTTCTCTG
385 TAAGGCTTATGAAGGAATGGGAGACTATAAATGGAT-TTGTCTTCAAAACAAATAGGTTTCTCTA
* * * *
4176 CATGTTTCTCA-AGACATGCATTCAATTATAA-TCTGTTTTAACAAAAAAT-AAAAAAAGTACAT
449 CACGCTTC-CAGAGACAAGCATTCAATTA-AAGTCTGTTTTAACAAAAAATGAAAAAAAGT-CAA
* * * * *
4238 CTTAAAATCAATTATCAGATTATGAAACCATTAAAAGCAAGTAGTAAGGCTTTTGAAGGAATAAG
511 CTTAAAATCAATTATCAGATTATAAAACCATTAAAAGCAACTAATAAGACTTTTGAAGGAATAAA
** ** *
4303 AGACTATAAATAGACTTTTCTTTTAAATAAATGAGTTTT-TGTATATGTTTCCTGAGGCAAGCGT
576 AGACTATAAATAGACTTTTCTTCCAAATAAATGAGTTTTCTACATAT-TTT-CTGAGGCAAGCAT
* * *
4367 TCAATTATAGTCTCTTTTAATGAAAAATGTAAAAATTTCAACTTAAAATCAATTATGAGATTATA
639 TCAATTATAGTCTATTTTAATG-AAAATATAAAAAATTCAACTTAAAATCAATTATGAGATTATA
* ** *
4432 AAA-TCATTTAAAGGGACTAATAAGGCTTTTGAAGGAACGAG-AGACTATAAAT-GAACTTTTCT
703 AAACT-ATTTAAAGCGACTAATAAGGCTTTCAAAGGAA-GAGAAGAATATAAATAGAA-TTTTCT
* * * *
4494 TTCAAATAAATG-GCTTTTTCC-AC-GTCTCCCTAGGCAAGCATTTAATTATAGTCTGTTTTAAC
765 TCCAAATAAATGAG--TTTTCCTACAGTCTCCCAAGGCAAGCATTCAATTATAGTCTGCTTTAAC
*
4556 AAAAAATATAAAAAAATTTACTT
828 AAAAAATATAAAAAAATTAACTT
* * * *
4579 AAATCAATTATGAGATTAAAAAAGCATTTAAAGCGAGTAATAGGGCTTTTGAAGGAATGAG-AGA
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATG-GTAGA
* * * * * * * * *
4643 CTATAAATGGAGTTTTCTTTCAAATAAATGGC-TTTTTCTACATGTTT-TTCAAGATAGGCATTC
65 CTATAAATGGACTTTTCTTACCAATGAATGCCTTTTTTCTTCATGTTTCTTGATG-TAGACATTC
* *
4706 AATTATAGTTTGTTTTAAT
129 AATTATAATCTGTTTTAAT
4725 ATGANNNNNN
Statistics
Matches: 828, Mismatches: 144, Indels: 48
0.81 0.14 0.05
Matches are distributed among these distances:
849 30 0.04
850 631 0.76
851 60 0.07
852 99 0.12
853 8 0.01
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.35
Consensus pattern (850 bp):
AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGTAGAC
TATAAATGGACTTTTCTTACCAATGAATGCCTTTTTTCTTCATGTTTCTTGATGTAGACATTCAA
TTATAATCTGTTTTAATCAAAAAACTAAAAAAATCTGAACTTAAAATCAATTATGAGACTATAAA
ACCATTTAAAATGAGTAATAAGTCTTTTGAAAGAACGAGTGACTATAAATAGACTTTTCTTGCAA
ATGAGTACATTTTTCTTCACGTTTCTGAAGGTAGACATTCAATTATAATCTATTTTAATCAAAAA
TATAAAAAAAATCAACTTAAAATCAATTATAAGATTATAAAACCATTTAAAGCGAGTAATAAGGC
TTATGAAGGAATGGGAGACTATAAATGGATTTGTCTTCAAAACAAATAGGTTTCTCTACACGCTT
CCAGAGACAAGCATTCAATTAAAGTCTGTTTTAACAAAAAATGAAAAAAAGTCAACTTAAAATCA
ATTATCAGATTATAAAACCATTAAAAGCAACTAATAAGACTTTTGAAGGAATAAAAGACTATAAA
TAGACTTTTCTTCCAAATAAATGAGTTTTCTACATATTTTCTGAGGCAAGCATTCAATTATAGTC
TATTTTAATGAAAATATAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAG
CGACTAATAAGGCTTTCAAAGGAAGAGAAGAATATAAATAGAATTTTCTTCCAAATAAATGAGTT
TTCCTACAGTCTCCCAAGGCAAGCATTCAATTATAGTCTGCTTTAACAAAAAATATAAAAAAATT
AACTT
Done.