Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398057.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1365.0, 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: 12677
ACGTcount: A:0.23, C:0.07, G:0.08, T:0.23
Warning! 4846 characters in sequence are not A, C, G, or T
Found at i:387 original size:173 final size:171
Alignment explanation
Indices: 1--1079 Score: 925
Period size: 173 Copynumber: 6.3 Consensus size: 171
* * *
1 GAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTGGAAGGAATGAGAGACTATAAATGGAC
1 GAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGAAC
* * * *
66 ATTTCTTGCCAATGAATGCCTTTTTCTACATGTTT-TCTAA-CTAGACATTCAATTATAATCTTG
66 TTTTC-TGCCAATGAATGCCTTTTTCTTCATGTTTCT-TAAGGTAGACATTCAATTATAATCGT-
* * ** *
129 TTTAACTAAAAATATAAAAAAAATTTGATGATAAAATCAATTTT
128 TTTAACCAAAAATATAAAAAAAAATTGATCTTAAAATCAATTAT
* * * * * *
173 GATATTGTAATACCATTTAAAGTGAGTAATAAGGTTTTTGAAGGAATGAGTGACTAGAAATGAAC
1 GAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGAAC
* * * * *
238 TTTTTCTGTCAATGAATGCCTTTCTCTTCATGTTTTTTAAGGTAAACATTCAATTATAATCCATT
66 -TTTTCTGCCAATGAATGCCTTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTATAAT-CGTT
* *
303 TTAACTAAAAATGTAAAAAAAAATTGATCTTAAAATCAATTAT
129 TTAACCAAAAATATAAAAAAAAATTGATCTTAAAATCAATTAT
* * * * * * *
346 GAGATGATAAAACCATTGAAACTGAGTAACAAGGGTTTTGAAGGAATGGGAGACTATAAATGGAC
1 GAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGAAC
** *
411 TTTTCTTGCCAATGAAT---TTTTT-TT-ATGTTTCTCGAGGTAGACATTCAATTATAGAT-TTT
66 TTTTC-TGCCAATGAATGCCTTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTATA-ATCGTT
* * * *
470 GTTAACCAAAAATAT--AAAATAATTCAACTTAAAATTAATTAT
129 -TTAACCAAAAATATAAAAAAAAATTGATCTTAAAATCAATTAT
* * * * * *
512 GAGATTATAAAACCATGTAAAGCGAGTAACAGGGCTTTTTAAGGAATGAGAGACTATAAATGGAC
1 GAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGAAC
* * * * * *
577 TTTTGTTGTCAATGAATGCTTTTTTCTTCATGTATCTCGAA-GTAGACATTCAATTATAGTC-TG
66 TTTT-CTGCCAATGAATGCCTTTTTCTTCATGTTTCT-TAAGGTAGACATTCAATTATAATCGT-
* * * *
640 TTTAACAAAAAATGT-AAAAATATTTGAGT-TTAAAATCAATTAT
128 TTTAACCAAAAATATAAAAAAAAATTGA-TCTTAAAATCAATTAT
* * ** ********
683 GGGATTATAAAACCATTTAAAGTTAGTAATAAGGCTTTTGAAAAAATGAGANNNNNNNNNNA-G-
1 GAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGA--GACTATAAATGA
* ** * *
746 ACTTTTCTTGCTAATGAATGCCTTTTTCTTCACATTTCTTAAGGTA-AGCTTTCAATTATAATAT
64 ACTTTTC-TGCCAATGAATGCCTTTTTCTTCATGTTTCTTAAGGTAGA-CATTCAATTATAAT-C
* * *
810 GTTTTAACCAAAAATATAAAAGAAAAATTGAACTTAAAAACAATAAT
126 GTTTTAACCAAAAATATAAAA-AAAAATTGATCTTAAAATCAATTAT
* ********** * *
857 GATATTATAAAACCATTTAAAGCT-AGTANNNNNNNNNNTGAAGGAATGGGAGACTATAAATGAG
1 GAGATTATAAAACCATTTAAAG-TGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGAA
* * * * * * *
921 CTTTTTTTGCCAATGAATGCTTTTTTCTTCATATTTCTTGAGGTAGACAATCAATTATAGTTTGT
65 C-TTTTCTGCCAATGAATGCCTTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTATA-ATCGT
* * ** *
986 TTTAACCAAAAATATATAAAAAAATTGAGCCGAAAATCAATTGT
128 TTTAACCAAAAATATAAAAAAAAATTGATCTTAAAATCAATTAT
* *
1030 GAGATTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTCAAGGAATGAG
1 GAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAG
1080 NNNNNNNNNN
Statistics
Matches: 717, Mismatches: 155, Indels: 69
0.76 0.16 0.07
Matches are distributed among these distances:
166 93 0.13
167 2 0.00
168 37 0.05
169 9 0.01
170 23 0.03
171 135 0.19
172 107 0.15
173 183 0.26
174 121 0.17
175 7 0.01
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.35
Consensus pattern (171 bp):
GAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGAAC
TTTTCTGCCAATGAATGCCTTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTATAATCGTTTT
AACCAAAAATATAAAAAAAAATTGATCTTAAAATCAATTAT
Found at i:1896 original size:170 final size:170
Alignment explanation
Indices: 1577--2420 Score: 623
Period size: 170 Copynumber: 4.9 Consensus size: 170
1567 NNNNATGGGT
* * * * * *
1577 GACTATAAATAGATTTTTTTTGTCAATGAATGCCTTTTT-TCTCACGTTTCTTGAA-GTAGACAT
1 GACTATAAATGGACTTTTCTTGCCAATGAATG-CTTTTTCT-TCATGTTTC-TCAAGGTAGACAT
* * *****
1640 TCAATTATAATCTGTTTTAACTAACAATGTAAAAAAATTGAACTTAAAATCAATTATGGGNNNNN
63 TCAATTATAATCTGTTTTAACTAAAAATGTAAAAAAATTGAACTTAAAATCAATTATGAGATTAT
***** *
1705 NNNNNCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGA
128 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGA
* * * * *
1748 AACTATAAATGAACTTTTCTTGCCAATGAATGCCTTTTCTTCACGTTTCACAAGGTAGACATTCA
1 GACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTCTTCATGTTTCTCAAGGTAGACATTCA
* * * *
1813 ATTATAATCTGTTTTAACTAAAAATATAAAAAAATTGAACTTAAATTTAATTTTGAGATTATAAA
66 ATTATAATCTGTTTTAACTAAAAATGTAAAAAAATTGAACTTAAAATCAATTATGAGATTATAAA
* * ********** *
1878 ACCATTGAAAGTGAGTAATANNNNNNNNNNAGGAAT-AGGT
131 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGA-GA
* * * * *
1918 GATTATAAATGGACTTTTCTTGCTAATGAATGGCTTTTTCTTCTTGTTTCTTAAGGTATACATTC
1 GACTATAAATGGACTTTTCTTGCCAATGAAT-GCTTTTTCTTCATGTTTCTCAAGGTAGACATTC
* * *****
1983 AATTATAATCTATTTTAACTAAAAATGTAAAAACAAATTGAACATAAAATCAATTAT-ANNNNNN
65 AATTATAATCTGTTTTAACTAAAAATGT-AAAA-AAATTGAACTTAAAATCAATTATGA-GATTA
**** * ** *
2047 NNNNATCATTTAGCGTGAGTAATAAGGCTTTTGAAGGAATGAGA
127 TAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGA
* * ** * * * *
2091 GAGTATAAATGGACTTTT-TCTACCAATGAATATTTTTGTGTTAATATTTCTCGAGGTAGACATT
1 GACTATAAATGGACTTTTCT-TGCCAATGAATGCTTTT-TCTTCATGTTTCTCAAGGTAGACATT
** *
2155 CAATTATTGTCTGTTTTAACCAAAAATGTAAAAAAA-T-AACTTAAAATCAATTATGAGATTATA
64 CAATTATAATCTGTTTTAACTAAAAATGTAAAAAAATTGAACTTAAAATCAATTATGAGATTATA
********** * *
2218 AAACCATTNNNNNNNNNNAATAAGACTTTTGAAGGAATGGGA
129 AAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGA
* *
2260 GACTATAAATGGTCTTTTCTT-CTCAATGAATGGCTTTTTCTAT-ATGTTT-TCTAAGGTAGGCA
1 GACTATAAATGGACTTTTCTTGC-CAATGAAT-GCTTTTTCT-TCATGTTTCTC-AAGGTAGACA
* * * * * * *
2322 TTCAATTGTAGTATATTTTAA-TAAAAAATATAAAAAAATTCAACTT-AAATCAATTATAAGATT
62 TTCAATTATAATCTGTTTTAACT-AAAAATGTAAAAAAATTGAACTTAAAATCAATTATGAGATT
*
2385 ATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAA
126 ATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAA
2421 AAANNNNNNN
Statistics
Matches: 510, Mismatches: 144, Indels: 39
0.74 0.21 0.06
Matches are distributed among these distances:
168 3 0.01
169 117 0.23
170 175 0.34
171 88 0.17
172 14 0.03
173 112 0.22
174 1 0.00
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.35
Consensus pattern (170 bp):
GACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTCTTCATGTTTCTCAAGGTAGACATTCA
ATTATAATCTGTTTTAACTAAAAATGTAAAAAAATTGAACTTAAAATCAATTATGAGATTATAAA
ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGA
Found at i:2289 original size:169 final size:160
Alignment explanation
Indices: 2066--2395 Score: 312
Period size: 169 Copynumber: 2.0 Consensus size: 160
2056 TTAGCGTGAG
* * *
2066 TAATAAGGCTTTTGAAGGAATGAGAGAGTATAAATGGACTTTTTCTACCAATGAAT-ATTTTTGT
1 TAATAAGACTTTTGAAGGAATGAGAGACTATAAATGGACTTTTTCTACCAATGAATGACTTTT-T
* * * * * * *
2130 GTTAATAT-TTCTC-GAGGTAGACATTCAATTATTGTCTGTTTTAACCAAAAATGTAAAAAAA-T
65 -CT-ATATGTTCTCTAAGGTAGACATTCAATTATAGTATATTTTAACAAAAAATATAAAAAAATT
*
2192 -AACTTAAAATCAATTATGAGATTATAAAACCAT
128 CAACTT-AAATCAATTATAAGATTATAAAACCAT
* * *
2225 TNNNNNNNNNNAATAAGACTTTTGAAGGAATGGGAGACTATAAATGGTC-TTTTCTTCTCAATGA
1 T----------AATAAGACTTTTGAAGGAATGAGAGACTATAAATGGACTTTTTCTAC-CAATGA
* * * * *
2289 ATGGCTTTTTCTATATGTTTTCTAAGGTAGGCATTCAATTGTAGTATATTTTAATAAAAAATATA
55 ATGACTTTTTCTATATGTTCTCTAAGGTAGACATTCAATTATAGTATATTTTAACAAAAAATATA
2354 AAAAAATTCAACTTAAATCAATTATAAGATTATAAAACCAT
120 AAAAAATTCAACTTAAATCAATTATAAGATTATAAAACCAT
2395 T
1 T
2396 TAAAGCAAGT
Statistics
Matches: 136, Mismatches: 19, Indels: 21
0.77 0.11 0.12
Matches are distributed among these distances:
159 1 0.01
167 4 0.03
168 12 0.09
169 82 0.60
170 32 0.24
171 5 0.04
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.36
Consensus pattern (160 bp):
TAATAAGACTTTTGAAGGAATGAGAGACTATAAATGGACTTTTTCTACCAATGAATGACTTTTTC
TATATGTTCTCTAAGGTAGACATTCAATTATAGTATATTTTAACAAAAAATATAAAAAAATTCAA
CTTAAATCAATTATAAGATTATAAAACCAT
Found at i:3240 original size:171 final size:170
Alignment explanation
Indices: 2942--4321 Score: 1029
Period size: 171 Copynumber: 8.0 Consensus size: 170
2932 NNNNNNNNNN
* * * * * *
2942 TTTTTCTTCTTATTTCTTGAGGTAGACATTCAATTATAGTGTGTTTGAACCAAAAATGCAAAAAC
1 TTTTTCTTCATCTTTCTTGAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAA-
* * * **********
3007 AATCGAATTTAAAATCAATTATGAGATTATGAAACCATTTAAAGCGNNNNNNNNNNCTTTTGAAG
65 AATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAG
*
3072 GAATGAGAGACTATAAATAGACGTTTCTTAGCAATGAATACC
130 GAATGAGAGACTATAAATAGAC-TTTCTTAGCAATGAATGCC
* * *
3114 TTTTTCTTCATCTTTCTTGAGGTAGACTTTCAATTATAATCTGTTTTAGCCACAAATGTAAAAAA
1 TTTTTCTTCATCTTTCTTGAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAA
* ** * *
3179 ATTGAACTTAAAATCAATTATAAGATTATAAAATTATTTAAAGTGAGTAACAAGGCTTTTGAAGG
66 ATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGG
* * * ** * *
3244 AATGGGTGAATATAAACGGACTTT-TCACGTCAATGAATG-T
131 AATGAGAGACTATAAATAGACTTTCTTA-G-CAATGAATGCC
** * * *
3284 TTTTTCTTTTTATTT-TTGAGGTAGACATTCAATTATAATATGTTTTAACCAAAAATGCAAAAAC
1 TTTTTCTTCATCTTTCTTGAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAA-
******************
3348 AATTGAACTTAAAATCAATTATGAGATTNNNNNNNNNNNNNNNNNNAGTAATAAGGCTTTTGAAG
65 AATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAG
* *
3413 GAATGAGAGACTATAAATAGACTTTTCTTAGCAATAAATGTC
130 GAATGAGAGACTATAAATAGAC-TTTCTTAGCAATGAATGCC
* * ** *
3455 TTTTTCTTCATGTTTCTTGAGGTAGACTTTCAATTATAATCTGTTTTAGTCAAAAATATAAAAAA
1 TTTTTCTTCATCTTTCTTGAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAA
* * * *
3520 ATTGAACTTAGAATGAATTATGAGATTATAAGACCATTTAAAGCGAGTAATAAGGCTCTTGAAGG
66 ATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGG
* * *
3585 AATGAGAGACTATAAATAGACTTTTTCTACCAATGAATGCT
131 AATGAGAGACTATAAATAGACTTTCT-TAGCAATGAATGCC
* * * ** *
3626 TTTTTTTCTCATGTTTCTTAAGGTAGACATTCAATTATAATCTGTTTTAATGAAAAATATAAAAC
1 TTTTTCT-TCATCTTTCTTGAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAA-
********** *
3691 AAATTGAACTTAAAATCAATTATGAGANNNNNNNNNNATTTAAAGCCAGTAATAAGGCTTTTGAA
64 AAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAA
* * * *
3756 GGAATGGGAGACTATAAATGGACTTTCTTTGCCAATGAAAG-C
129 GGAATGAGAGACTATAAATAGACTTTCTTAG-CAATGAATGCC
** * * *
3798 TTTTTCTTCATGCTTT-TCAAGGTAGACATTCAATTATACTCTATTTTAATCAAAAAATGTAAAA
1 TTTTTCTTCAT-CTTTCTTGAGGTAGACATTCAATTATAATCTGTTTTAA-CCAAAAATGTAAAA
* * ***********
3862 AAAATAAACTTAAAATCAATTATTNNNNNNNNNNACCATTTAAAGCGAGTAATAAGGCTTTTGAA
64 AAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAA
* * * **
3927 AGAATG-GTTA-ACTATAAAT-GAACTTTTTTTATCAATGAATATC
129 GGAATGAG--AGACTATAAATAG-AC-TTTCTTAGCAATGAATGCC
* ********** *
3970 TTTTTCTTCA-CGTTTCTCGAGGTAGACATTCAATTANNNNNNNNNNTAACTAAAAATGTAAAAA
1 TTTTTCTTCATC-TTTCTTGAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAA
* * * * * *
4034 AATTTAACTTAAAATTAATTTTGAGATTATAAAACCATTTAAAGTGTGTAATAAAGCTTTTGAAG
65 AATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAG
* ** * * *
4099 GAATGGGTCACTATAAATAGACTTTTTTTGCTAATGAATGCT
130 GAATGAGAGACTATAAATAGACTTTCTTAGC-AATGAATGCC
* * * * ** *
4141 TTTTTCTTCA-CATTT-TATGAGGTAAACATTTAATTATAATCTATTTTAACTACGAATTTAAAA
1 TTTTTCTTCATC-TTTCT-TGAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGT-AAA
* * * * * * * *
4204 AAATATTGACCTTAAAATTAATTTTTAGATTATAAAATCATTGAAAGTGAGTAATAAAGCTTTTG
63 AAA-ATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
* * * *
4269 AAGGAAT-AGGTGACTATAAATAGAGTTTTCTTACCAATGAATGTC
127 AAGGAATGA-GAGACTATAAATAGA-CTTTCTTAGCAATGAATGCC
4314 TTTTTCTT
1 TTTTTCTT
4322 TNNNNNNNNN
Statistics
Matches: 956, Mismatches: 223, Indels: 57
0.77 0.18 0.05
Matches are distributed among these distances:
169 45 0.05
170 101 0.11
171 409 0.43
172 219 0.23
173 176 0.18
174 6 0.01
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.35
Consensus pattern (170 bp):
TTTTTCTTCATCTTTCTTGAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAA
ATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGG
AATGAGAGACTATAAATAGACTTTCTTAGCAATGAATGCC
Found at i:3863 original size:344 final size:331
Alignment explanation
Indices: 2942--3884 Score: 875
Period size: 341 Copynumber: 2.7 Consensus size: 331
2932 NNNNNNNNNN
* * * *
2942 TTTTTCTTCT-TATTTCTTGAGGTAGACATTCAATTATAGTGTGTTTGAACCAAAAATGCAAAAA
1 TTTTTCTT-TATATTT-TTAAGGTAGACATTCAATTATAATATGTTTTAACCAAAAAT-CAAAAA
* * * * *
3006 CAATCGAATTTAAAATCAATTATGAGATTA-TGAAA-CCATTTA-AAGCGNNNNNNNNNNCTTTT
63 CAATTGAACTTAAAATCAATTATGAGATTATTTAAAGCCAGTAATAAG-G----------CTTTT
*
3068 GAAGGAATGAGAGACTATAAATAGACGTTTCTTAGCAATGAATACCTTTTTCTTCAT-CTTTCTT
117 GAAGGAATGAGAGACTATAAATAGACGTTTCTTAGCAATGAA-AGCTTTTTCTTCATGCTTTCTT
** *
3132 GAGGTAGACTTTCAATTATAATCTGTTTTAGCCACAAATGTAAAAAAATTGAACTTAAAATCAAT
181 GAGGTAGACTTTCAATTATAATCTGTTTTAATCAAAAATGTAAAAAAATTGAACTTAAAATCAAT
** * * * * *
3197 TATAAGATTATAAAATTATTTAAAGTGAGTAACAAGGCTTTTGAAGGAATGGGTGAATATAAACG
246 TATAAGATTATAAAACCATTTAAAGCGAGTAACAAGGCTCTTGAAGGAATGAGAGAATATAAACA
3262 GACTTTTCACGTCAATGAATGT
311 GACTTTTCACG-CAATGAATGT
* *
3284 TTTTTCTTTTTATTTTTGAGGTAGACATTCAATTATAATATGTTTTAACCAAAAATGCAAAAACA
1 TTTTTCTTTATATTTTTAAGGTAGACATTCAATTATAATATGTTTTAACCAAAAAT-CAAAAACA
**********
3349 ATTGAACTTAAAATCAATTATGAGATTNNNNNNNNNNNNNNNNNNAGTAATAAGGCTTTTGAAGG
65 ATTGAACTTAAAATCAATTATGAGATT--------ATTTAAAGCCAGTAATAAGGCTTTTGAAGG
*
3414 AATGAGAGACTATAAATAGACTTTTCTTAGCAAT-AAATGTCTTTTTCTTCATG-TTTCTTGAGG
122 AATGAGAGACTATAAATAGACGTTTCTTAGCAATGAAA-G-CTTTTTCTTCATGCTTTCTTGAGG
* * * * *
3477 TAGACTTTCAATTATAATCTGTTTTAGTCAAAAATATAAAAAAATTGAACTTAGAATGAATTATG
185 TAGACTTTCAATTATAATCTGTTTTAATCAAAAATGTAAAAAAATTGAACTTAAAATCAATTATA
* * * *
3542 AGATTATAAGACCATTTAAAGCGAGTAATAAGGCTCTTGAAGGAATGAGAGACTATAAATAGACT
250 AGATTATAAAACCATTTAAAGCGAGTAACAAGGCTCTTGAAGGAATGAGAGAATATAAACAGAC-
3607 TTTTCTAC-CAATGAATGCT
314 TTTTC-ACGCAATGAATG-T
* * **
3626 TTTTT-TTCTCATGTTTCTTAAGGTAGACATTCAATTATAATCTGTTTTAATGAAAAAT-ATAAA
1 TTTTTCTT-T-ATATTT-TTAAGGTAGACATTCAATTATAATATGTTTTAACCAAAAATCA-AAA
**
3689 ACAAATTGAACTTAAAATCAATTATGAGANNNNNNNNNNATTTAAAGCCAGTAATAAGGCTTTTG
62 AC-AATTGAACTTAAAATCAATTATGAGA--------TTATTTAAAGCCAGTAATAAGGCTTTTG
* * * **
3754 AAGGAATGGGAGACTATAAATGGAC-TTTCTTTGCCAATGAAAGCTTTTTCTTCATGCTTT-TCA
118 AAGGAATGAGAGACTATAAATAGACGTTTCTTAG-CAATGAAAGCTTTTTCTTCATGCTTTCTTG
* * * * *
3817 AGGTAGACATTCAATTATACTCTATTTTAATCAAAAAATGTAAAAAAAATAAACTTAAAATCAAT
182 AGGTAGACTTTCAATTATAATCTGTTTTAATC-AAAAATGTAAAAAAATTGAACTTAAAATCAAT
3882 TAT
246 TAT
3885 TNNNNNNNNN
Statistics
Matches: 500, Mismatches: 66, Indels: 68
0.79 0.10 0.11
Matches are distributed among these distances:
339 1 0.00
340 2 0.00
341 261 0.52
342 26 0.05
343 60 0.12
344 140 0.28
345 3 0.01
351 4 0.01
352 3 0.01
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.35
Consensus pattern (331 bp):
TTTTTCTTTATATTTTTAAGGTAGACATTCAATTATAATATGTTTTAACCAAAAATCAAAAACAA
TTGAACTTAAAATCAATTATGAGATTATTTAAAGCCAGTAATAAGGCTTTTGAAGGAATGAGAGA
CTATAAATAGACGTTTCTTAGCAATGAAAGCTTTTTCTTCATGCTTTCTTGAGGTAGACTTTCAA
TTATAATCTGTTTTAATCAAAAATGTAAAAAAATTGAACTTAAAATCAATTATAAGATTATAAAA
CCATTTAAAGCGAGTAACAAGGCTCTTGAAGGAATGAGAGAATATAAACAGACTTTTCACGCAAT
GAATGT
Found at i:4854 original size:194 final size:193
Alignment explanation
Indices: 4494--4863 Score: 422
Period size: 194 Copynumber: 1.9 Consensus size: 193
4484 ATAAATAGAC
* * *
4494 ATTTCTTGCCAATGAATGATTTTTTCTTCATGTTTCTCAAAGTAAACATTCAATTATAGTCTGTT
1 ATTTCTTGCCAATGAATGATTTTTTCTTCACGTTTCTCAAAGTAAACATTCAATTATAATATGTT
** * * * *
4559 TTAATGAAAAATATAAAATACATTGAGCTTAAAATCAATTATGTGATTATAAAACTATTTAAAGA
66 TTAACCAAAAATATAAAAAAAATTGAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGA
* **********
4624 GAGTAATAAGGCTTTTGAAANNNNNNNNNNCTATAAATAGACTTTTTTTGTCAATGAATACAT
131 GAGTAATAAGGCTTATGAAAGAATGGGAGACTATAAATAGACTTTTTTTGTCAATGAATACAT
* ** * *
4687 ATTTGTTGCCAATGAATGCA-TTTTTCTTCACGTTTCAT-AGGGTAAACTTTTAATTATAATATG
1 ATTTCTTGCCAATGAATG-ATTTTTTCTTCACGTTTC-TCAAAGTAAACATTCAATTATAATATG
*
4750 TTTTAACCAAAAATGTAAAAAAAAATTGAACTTAAAAAT-AATTATGAGATTATAAAACTATTTA
64 TTTTAACCAAAAATAT-AAAAAAAATTGAACTT-AAAATCAATTATGAGATTATAAAACTATTTA
* * *
4814 AAGCGAGTAATAAGGCTTATGAATGAATGGGAGACTATAAATGGACTTTT
127 AAGAGAGTAATAAGGCTTATGAAAGAATGGGAGACTATAAATAGACTTTT
4864 CTTGCCGATG
Statistics
Matches: 144, Mismatches: 29, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
193 64 0.44
194 75 0.52
195 5 0.03
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.36
Consensus pattern (193 bp):
ATTTCTTGCCAATGAATGATTTTTTCTTCACGTTTCTCAAAGTAAACATTCAATTATAATATGTT
TTAACCAAAAATATAAAAAAAATTGAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGA
GAGTAATAAGGCTTATGAAAGAATGGGAGACTATAAATAGACTTTTTTTGTCAATGAATACAT
Found at i:5498 original size:171 final size:170
Alignment explanation
Indices: 5075--5581 Score: 503
Period size: 171 Copynumber: 3.0 Consensus size: 170
5065 NNNNNNNNNN
* * *
5075 ACCATTTAAAGCGAGTAATAAGGCTTTGGAAGGAATGGAAGACTATAAATGGACCTTTCTTATCA
1 ACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGAAGACTATAAAT-GAACTTTCTTATCA
* * *
5140 ATGAATGTTTTTTTCTTCACATTTCTTGAGATAGACATTGAATTATAGTCTGTTTTAACTAAAAA
65 ATGAATGATTTTTTCTTCACATTTCTTGAGATAGACATTCAATTATAATCTGTTTTAAC-AAAAA
* * **********
5205 TGTAAAAAAAATTGAACATAAAATCAATTNNNNNNNNNNAAA
129 TGTAAAAAAAATTAAACTTAAAATCAATTATGAGGTTAGAAA
* * * ** * * * *
5247 ACAATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATAGTTGATTGTAAATGGACTTTCCTTACCA
1 ACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGAAGACTATAAATGAACTTT-CTTATCA
* * * * * * *
5312 ATGAATAATTTTTTCTTCACGTTTTTTGAGGTAGACATTTAGTTATAATCTGTTTTAGTCAAAAA
65 ATGAATGATTTTTTCTTCACATTTCTTGAGATAGACATTCAATTATAATCTGTTTTA-ACAAAAA
* ** *
5377 AGTAAAAAAAATT-AACTTGGAATCAATTTTGAGGTTAGAAA
129 TGTAAAAAAAATTAAACTTAAAATCAATTATGAGGTTAGAAA
* ** * * *
5418 ACCATTGAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGCGACTATAAATAAAATATTCTTGTCA
1 ACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGAAGACTATAAATGAACT-TTCTTATCA
** * ** *
5483 ATGAATGCCTTTTTCTTTACATTTCTCAAGATAGACATTCAATTATAATCTGTTTTAACCACAAA
65 ATGAATGATTTTTTCTTCACATTTCTTGAGATAGACATTCAATTATAATCTGTTTTAA-CAAAAA
5548 TGTAAAAAAAATTAAACTTAAAATCAATTATGAG
129 TGTAAAAAAAATTAAACTTAAAATCAATTATGAG
5582 ATTATAANNN
Statistics
Matches: 265, Mismatches: 65, Indels: 10
0.78 0.19 0.03
Matches are distributed among these distances:
171 132 0.50
172 132 0.50
173 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.34
Consensus pattern (170 bp):
ACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGAAGACTATAAATGAACTTTCTTATCAA
TGAATGATTTTTTCTTCACATTTCTTGAGATAGACATTCAATTATAATCTGTTTTAACAAAAATG
TAAAAAAAATTAAACTTAAAATCAATTATGAGGTTAGAAA
Done.