Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401200.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_435.0, 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: 19114
ACGTcount: A:0.26, C:0.09, G:0.08, T:0.26
Warning! 5902 characters in sequence are not A, C, G, or T
Found at i:2378 original size:171 final size:168
Alignment explanation
Indices: 1887--2752 Score: 656
Period size: 171 Copynumber: 5.1 Consensus size: 168
1877 NNNNNNNNNN
* * *
1887 ATTGATTTTATGTTGAATTTTTTTACATTTTT-AGTTAAAACAGACAATAATTGACTG-TCTACC
1 ATTGATTTTAAGCTGAATTTTTTTACATTTTTCA-TTAAAACAGACAATAATTGAATGCT-TACC
* * * *
1950 TCGAGAAATGTAAAGAAAAACGCATTCA-TAGATTAAAAAAGTTTATTTATAGTCACCCATTCTT
64 TCAAGAAATGTAAAGAAAAAC-CATTCATTA-A-AAAAAAAGTTCATTTATAGTCACCCATTCCT
********** *
2014 TCAAAAGCCTTATTACNNNNNNNNNNTGGTTTTATAATCTCATA
126 TC-AAAGCCTTATTACTCGCTTTAAATTGTTTTATAATCTCATA
* * * * * * * *
2058 ATTGATTTTAAGCTGAATTTTTTTACCTTTTTCATTAGAATAGTCTATAACTGAATGCTTGCCTT
1 ATTGATTTTAAGCTGAATTTTTTTACATTTTTCATTAAAACAGACAATAATTGAATGCTTACCTC
* ** **
2123 AAGAAATATGTAGAAAAATCCATTCATTAAAAAAAAAG-TCTATTTATAGTCGTCCATTCCTTCA
66 AAGAAATGTAAAGAAAAA-CCATTCATTAAAAAAAAAGTTC-ATTTATAGTCACCCATTCCTTC-
* *********
2187 AAAACCTTATTACTCGCTTTAAATTGTTTTATNNNNNNNNN
128 AAAGCCTTATTACTCGCTTTAAATTGTTTTATAATCTCATA
* * **
2228 NTTGATTTTAAGTTG-ATTTTGTTTACATTTTTTGTTAAAACAGACAATAATTGAATG-TCTACC
1 ATTGATTTTAAGCTGAATTTT-TTTACATTTTTCATTAAAACAGACAATAATTGAATGCT-TACC
* * *
2291 TCAAGAAATGTAAAGAAAAACACATTCATTGATAAAAAAAGTTCATATATAGTCACCCATTTCTT
64 TCAAGAAATGTAAAGAAAAAC-CATTCATT-AAAAAAAAAGTTCATTTATAGTCACCCATTCCTT
*
2356 CAAAGTCCTTATTACTCGCTTTAAA-TGATTTTAGAATCTCATA
127 CAAAG-CCTTATTACTCGCTTTAAATTG-TTTTATAATCTCATA
* *
2399 ATTGATTTTAAGCTGAATTTTTTTACATTTTTCATTAAAACAGTCTATAATTGAATGCTTACCTC
1 ATTGATTTTAAGCTGAATTTTTTTACATTTTTCATTAAAACAGACAATAATTGAATGCTTACCTC
* ** * *
2464 GAGAAACATGTAAA-AAAAGTCATTCATTAAAAAGAAAAGTCCATTTATAGTGACCCATTCCTTC
66 AAG-AA-ATGTAAAGAAAAACCATTCATTAAAAA-AAAAGTTCATTTATAGTCACCCATTCCTTC
* * **********
2528 ACAAGCCTTATTACTCACTTTAAATTATNNNNNNNNNNCATA
128 A-AAGCCTTATTACTCGCTTTAAATTGTTTTATAATCTCATA
* * * ** *
2570 ATTGATTTTAAGTTGAATTTTTTTAAATTTTTGAAGAAAATAGACAATAATTGAATG-TCTA-CT
1 ATTGATTTTAAGCTGAATTTTTTTACATTTTTCATTAAAACAGACAATAATTGAATGCT-TACCT
** * **** * *
2633 -ATGAGAAACATGAAGAAAAACGCATTCACGGGCAAGAAAAGTTTATTTATAGTCACCCATTCCT
65 CA--AGAAATGTAAAGAAAAAC-CATTCA-TTAAAAAAAAAGTTCATTTATAGTCACCCATTCC-
* **
2697 TTGAAAGTTTTATTACTCGCTTTAAATTGTTTTATAATCTCATA
125 TTCAAAGCCTTATTACTCGCTTTAAATTGTTTTATAATCTCATA
2741 ATTGATTTTAAG
1 ATTGATTTTAAG
2753 TNNNNNNNNN
Statistics
Matches: 534, Mismatches: 135, Indels: 52
0.74 0.19 0.07
Matches are distributed among these distances:
169 12 0.02
170 133 0.25
171 354 0.66
172 28 0.05
173 7 0.01
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.37
Consensus pattern (168 bp):
ATTGATTTTAAGCTGAATTTTTTTACATTTTTCATTAAAACAGACAATAATTGAATGCTTACCTC
AAGAAATGTAAAGAAAAACCATTCATTAAAAAAAAAGTTCATTTATAGTCACCCATTCCTTCAAA
GCCTTATTACTCGCTTTAAATTGTTTTATAATCTCATA
Found at i:2675 original size:342 final size:336
Alignment explanation
Indices: 1887--2752 Score: 829
Period size: 341 Copynumber: 2.5 Consensus size: 336
1877 NNNNNNNNNN
* *
1887 ATTGATTTTATGTTGAATTTT-TTTAC-ATTTTT-AGTTAAAACAGACAATAATTGACTGTCTAC
1 ATTGATTTTAAGTTG-ATTTTGTTTACAATTTTTGAG--AAAACAGACAATAATTGAATGTCTAC
* ** * ** ** * *
1949 CTCGAGAAATGTAAAGAAAAACGCATTCATAGATTAAAAAAGTTTATTTATAGTCACCCATT-CT
63 CTCAAGAAACATAAAGAAAAACACATTCACGGACAAAAAAAGTTCATATATAGTCACCCATTCCT
* ********** *
2013 TTCAAAAGCCTTATTACNNNNNNNNNNTGGTTTTATAATCTCATAATTGATTTTAAGCTGAATTT
128 TTC-AAAGTCTTATTACTCGCTTTAAATTGTTTTATAATCTCATAATTGATTTTAAGCTGAATTT
* * * * * * *
2078 TTTTACCTTTTTCATTAGAATAGTCTATAACTGAATGCTTGCCTTAAGAAATATGTAGAAAAATC
192 TTTTACATTTTTCATTAAAACAGTCTATAACTGAATGCTTACCTCAAGAAACATGTAAAAAAATC
* * *
2143 CATTCATTAAAAAAAAAGTCTATTTATAGTCGTCCATTCCTTCAAAAACCTTATTACTCGCTTTA
257 CATTCATTAAAAAAAAAGTCCATTTATAGTCGCCCATTCCTTCAAAAACCTTATTACTCACTTTA
* ****
2208 AATTGTTTTATNNNNNNNNN
322 AATTATTTTAT-----CATA
* * **
2228 NTTGATTTTAAGTTGATTTTGTTTACATTTTTTGTTAAAACAGACAATAATTGAATGTCTACCTC
1 ATTGATTTTAAGTTGATTTTGTTTACAATTTTTGAGAAAACAGACAATAATTGAATGTCTACCTC
** ** * *
2293 AAGAAATGTAAAGAAAAACACATTCATTGATAAAAAAAGTTCATATATAGTCACCCATTTC-TTC
66 AAGAAACATAAAGAAAAACACATTCACGGACAAAAAAAGTTCATATATAGTCACCCATTCCTTTC
*
2357 AAAGTCCTTATTACTCGCTTTAAA-TGATTTTAGAATCTCATAATTGATTTTAAGCTGAATTTTT
131 AAAGT-CTTATTACTCGCTTTAAATTG-TTTTATAATCTCATAATTGATTTTAAGCTGAATTTTT
* *
2421 TTACATTTTTCATTAAAACAGTCTATAATTGAATGCTTACCTCGAGAAACATGTAAAAAAAGT-C
194 TTACATTTTTCATTAAAACAGTCTATAACTGAATGCTTACCTCAAGAAACATGTAAAAAAA-TCC
* *
2485 ATTCATTAAAAAGAAAAGTCCATTTATAGT-GACCCATTCCTTCACAAGCCTTATTACTCACTTT
258 ATTCATTAAAAA-AAAAGTCCATTTATAGTCG-CCCATTCCTTCAAAAACCTTATTACTCACTTT
*****
2549 AAATTATNNNNNNNNNNCATA
321 AAATTAT-----TTTATCATA
*
2570 ATTGATTTTAAGTTGAATTTT-TTTA-AATTTTTGAAGAAAATAGACAATAATTGAATGTCTA-C
1 ATTGATTTTAAGTTG-ATTTTGTTTACAATTTTTG-AGAAAACAGACAATAATTGAATGTCTACC
* * * * * *
2632 T-ATGAGAAACATGAAGAAAAACGCATTCACGGGCAAGAAAAGTTTATTTATAGTCACCCATTCC
64 TCA--AGAAACATAAAGAAAAACACATTCACGGACAAAAAAAGTTCATATATAGTCACCCATTCC
* *
2696 TTTGAAAGTTTTATTACTCGCTTTAAATTGTTTTATAATCTCATAATTGATTTTAAG
127 TTTCAAAGTCTTATTACTCGCTTTAAATTGTTTTATAATCTCATAATTGATTTTAAG
2753 TNNNNNNNNN
Statistics
Matches: 436, Mismatches: 69, Indels: 39
0.80 0.13 0.07
Matches are distributed among these distances:
340 11 0.03
341 221 0.51
342 190 0.44
343 14 0.03
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.37
Consensus pattern (336 bp):
ATTGATTTTAAGTTGATTTTGTTTACAATTTTTGAGAAAACAGACAATAATTGAATGTCTACCTC
AAGAAACATAAAGAAAAACACATTCACGGACAAAAAAAGTTCATATATAGTCACCCATTCCTTTC
AAAGTCTTATTACTCGCTTTAAATTGTTTTATAATCTCATAATTGATTTTAAGCTGAATTTTTTT
ACATTTTTCATTAAAACAGTCTATAACTGAATGCTTACCTCAAGAAACATGTAAAAAAATCCATT
CATTAAAAAAAAAGTCCATTTATAGTCGCCCATTCCTTCAAAAACCTTATTACTCACTTTAAATT
ATTTTATCATA
Found at i:3242 original size:171 final size:172
Alignment explanation
Indices: 2937--3660 Score: 570
Period size: 171 Copynumber: 4.2 Consensus size: 172
2927 NNNNNNNNNN
* * * * *
2937 ACTCGCTTTAAATTATTTTATAATCTCATAATTGATTTTAAGTTGCATTTTTTTACATTTTTAGA
1 ACTCTCTTTAAATTGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTATTACATTTTTGGA
* * * * *
3002 TAAAACAGACTACAATTGAATGTCTATCAT-GAGAAACGTGAAGAAAAAAACATTCATT-AGCAA
66 TAAAACAGACAATAATTGAATGTCTACCATCGAGAAACGTAAAGAAAAACACATTCATTGA-CAA
3065 GAAAAGTCCATTTATTGTCACCCATTCCTTCAAAAGCATTATT
130 GAAAAGTCCATTTATTGTCACCCATTCCTTCAAAAGCATTATT
* * * *
3108 ACTCTCTTTATATTGTTTTATAATCCCATAATTGATTTTAAGTTGAATTTTATTATATTTTTGGT
1 ACTCTCTTTAAATTGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTATTACATTTTTGGA
* * * * * *
3173 TAAAATAGACAATAATTGATTGTCTACCAT-GAGATATGTAAAGAAAAACGCATTCATTGACAGG
66 TAAAACAGACAATAATTGAATGTCTACCATCGAGAAACGTAAAGAAAAACACATTCATTGACAAG
* ** * **
3237 AAAAGTCTAATTATATTG--ACGTATTGCTTCAAAAATATTATT
131 AAAAGTC-CATT-TATTGTCACCCATTCCTTCAAAAGCATTATT
* ********** **
3279 ACT-TGCTTTAAATTATTTNNNNNNNNNNTAATTGATTTTAAGTTGAATTTTATTGTATTTTTGG
1 ACTCT-CTTTAAATTGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTATTACATTTTTGG
* * ********** * *
3343 TTAAAATAGACAATAATTGAATGTCTACC-TCNNNNNNNNNNAAGAAAAACACATTCAATGGCAA
65 ATAAAACAGACAATAATTGAATGTCTACCATCGAGAAACGTAAAGAAAAACACATTCATTGACAA
* * * *
3407 GAAAAGTCCATTTCTGGTCACCCATTCCTTTAAAAGCCTTATT
130 GAAAAGTCCATTTATTGTCACCCATTCCTTCAAAAGCATTATT
* * ********* * *
3450 CCTCACTTTAAATTGTTTTATAATCTCATANNNNNNNNNNAA-TTGAATTTTTTTACATTTTTGA
1 ACTCTCTTTAAATTGTTTTATAATCTCATA-ATTGATTTTAAGTTGAATTTTATTACATTTTTGG
* ** * **
3514 ATAAGACAGGTAATAATTGAATATCTA-CATCGAGAAACG-AGAAGAAAAACACATTCATTGGTA
65 ATAAAACAGACAATAATTGAATGTCTACCATCGAGAAACGTA-AAGAAAAACACATTCATTGACA
* * * * *
3577 AGAAAAGTCCACTTATAGTCACCCATCCCATCAAAAGCCTTATT
129 AGAAAAGTCCATTTATTGTCACCCATTCCTTCAAAAGCATTATT
*
3621 ACT-TCCTTTAAATAGTTTTATAATCTCATAATTGATTTTA
1 ACTCT-CTTTAAATTGTTTTATAATCTCATAATTGATTTTA
3661 NNNNNNNNNN
Statistics
Matches: 416, Mismatches: 125, Indels: 25
0.73 0.22 0.04
Matches are distributed among these distances:
169 3 0.01
170 7 0.02
171 395 0.95
172 6 0.01
173 5 0.01
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.37
Consensus pattern (172 bp):
ACTCTCTTTAAATTGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTATTACATTTTTGGA
TAAAACAGACAATAATTGAATGTCTACCATCGAGAAACGTAAAGAAAAACACATTCATTGACAAG
AAAAGTCCATTTATTGTCACCCATTCCTTCAAAAGCATTATT
Found at i:5599 original size:171 final size:170
Alignment explanation
Indices: 5041--6541 Score: 850
Period size: 171 Copynumber: 8.9 Consensus size: 170
5031 NNNNNNNNNN
* *
5041 CTTCAAAAGTCTTATTACTCGCTTTAAATTGTTTTATAATCTCATAATTTA-TTTAAGTTGAATT
1 CTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAATCTCATAATTGATTTTAAGTTGAATT
** * ** * * * *
5105 TTTTTACATTTTTGCTTAAAACAGAGTACAATTGAATGTCTGCCTCAAGAAACAT-ATAGAAAAA
66 TTTTTACATTTTTGAATAAAATAGACAATAATTGAATGTCTACCTCGAGAAACGTGA-AGAAAAA
*********** *
5169 GCNNNNNNNNNNGAAGAAAAGTCCATTTATAGTTA-CCATTC
130 G-AATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTC
* ********** * *
5210 ATTCAAAAGCCTTATTACTCGCTTTNNNNNNNNNNATATTCTCATAATTGATTTTAAGTTAAATT
1 CTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAATCTCATAATTGATTTTAAGTTGAATT
** * * * * * * ** * * *
5275 TTTAAATATTTTT-AGTTAAAACAAACTATAAGTGAATG-CTTGTCTTGAAAAACGTGTAGAAAA
66 TTTTTACATTTTTGA-ATAAAATAGACAATAATTGAATGTC-TACCTCGAGAAACGTGAAGAAAA
* * * * *
5338 AGCCATTCATTGAGAAGAAAAGTCCGTTTATAGTTACCCGTTC
129 AG-AATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTC
* * ********** * * *
5381 TTTCAAAAGCCTTATTACTAGCTTNNNNNNNNNNTATAATATCATAATTGATTTTAAATTGTATT
1 CTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAATCTCATAATTGATTTTAAGTTGAATT
* * *
5446 TTTTTAAATTTTTGAATAACATAGACAATAATTGAATGTCTACCTCAAGAAACGTGAAGAAAAAT
66 TTTTTACATTTTTGAATAAAATAGACAATAATTGAATGTCTACCTCGAGAAACGTGAAGAAAAA-
* *
5511 GAATTCGTTGACAAGAAAAGTCCATTTATAGTCACCCCTTC
130 GAATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTC
* * *
5552 ATTCAAAAGCCTTATTACTCACTTTGAATTGTTTTATAATCTCATAATTGA-TTTACA-TT---T
1 CTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAATCTCATAATTGATTTTA-AGTTGAAT
* * * *
5612 TTTATTA-A------AATAAAAT--AC---AATTGAATGACTGA-CTCAAGAAACAT-ATAGAAA
65 TTTTTTACATTTTTGAATAAAATAGACAATAATTGAATGTCT-ACCTCGAGAAACGTGA-AGAAA
* ** * * * *
5663 AAGCCATTCATTGTGAAAAAAAGTTCATTTGTAGTCACGCATTC
128 AAG-AATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTC
* **********
5707 CTTCAAAAGCCTTATTACTTGCTTTAAATTGTNNNNNNNNNNCATAATTGATTTTAAGTTGAATT
1 CTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAATCTCATAATTGATTTTAAGTTGAATT
* * * * *
5772 TTTGTACATTTTTTAATAAAACAGAAAATAATTGAATGTTTACCTCGAGAAA-GATGAAGAAAAA
66 TTTTTACATTTTTGAATAAAATAGACAATAATTGAATGTCTACCTCGAGAAACG-TGAAGAAAAA
* * * *
5836 CACATTCATTGGCAAGAAAAGTCCATTTATAGACACCTATTC
130 GA-ATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTC
* * * * * *
5878 CTTTAAAAGCCTCATTACTCACTTTAAATTGTTTTATAATCTTATAAATAATTTTAAGTTGAA-T
1 CTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAATCTCATAATTGATTTTAAGTTGAATT
* ********** * ** *
5942 TTTTTACATTTTTGATTNNNNNNNNNNATAATTGAATGTCTACCTTGAGAAATATGAAAAAAAAA
66 TTTTTACATTTTTGAATAAAATAGACAATAATTGAATGTCTACCTCGAGAAACGTG-AAGAAAAA
* * * *
6007 GCATTCATTGAGAAGAAAAGAT-AATTTATAGTCAACCATTC
130 GAATTCATTGACAAGAAAAG-TCCATTTATAGTCACCCATTC
* * ********** ** *
6048 ATTCAAAAGCCTTATTACTCTCTTNNNNNNNNNNTATAATCTCATAATTGATTTTAAACTGTATT
1 CTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAATCTCATAATTGATTTTAAGTTGAATT
* * * * *
6113 TTTTTACATTTTTTTATTAAAACAGACAATAATTGAATGTCTACCTCAAGAAACTTGAAGAAAAA
66 TTTTTACA-TTTTTGAATAAAATAGACAATAATTGAATGTCTACCTCGAGAAACGTGAAGAAAAA
* * ** * *
6178 CACATTCGTTGACAAGAAAAGTATATTTATAGTCACTCGTTC
130 GA-ATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTC
* **********
6220 CTTCAAAAGCCTTATTACTCGCTTTGAATTGTTTTANNNNNNNNNNATTGATTTTAAGTTGAATT
1 CTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAATCTCATAATTGATTTTAAGTTGAATT
* * * * * *
6285 TCTTTACATTTTTGGATAAAATAGACTACAATTGAATGTTTACAAT-GAGAAACGTGAAGAAAAA
66 TTTTTACATTTTTGAATAAAATAGACAATAATTGAATGTCTAC-CTCGAGAAACGTGAAGAAAAA
* * * * *
6349 TGCATTTACT-AGTAAGAAAAGTTCATTTATAGTCACCCATTC
130 -GAATTCATTGA-CAAGAAAAGTCCATTTATAGTCACCCATTC
* * * * *
6391 CTTCAAAAGCATTATTAGTCGCTTTAAATTGTTTTATAATCTAATAATTGATTTTAGGTTAAATT
1 CTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAATCTCATAATTGATTTTAAGTTGAATT
* * * * *
6456 TCTTTACATTTTTGGATAAAACT-GACTACAAATGAATGTCTACCAT-GAGAAACGTGAAGAAAA
66 TTTTTACATTTTTGAATAAAA-TAGACAATAATTGAATGTCTACC-TCGAGAAACGTGAAGAAAA
* *
6519 ATGCATTCATTGGCAAGAAAAGT
129 A-GAATTCATTGACAAGAAAAGT
6542 TTATTTATNN
Statistics
Matches: 1002, Mismatches: 284, Indels: 90
0.73 0.21 0.07
Matches are distributed among these distances:
154 2 0.00
155 98 0.10
156 7 0.01
158 2 0.00
159 6 0.01
160 8 0.01
166 8 0.01
167 7 0.01
168 1 0.00
169 38 0.04
170 204 0.20
171 504 0.50
172 117 0.12
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.36
Consensus pattern (170 bp):
CTTCAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAATCTCATAATTGATTTTAAGTTGAATT
TTTTTACATTTTTGAATAAAATAGACAATAATTGAATGTCTACCTCGAGAAACGTGAAGAAAAAG
AATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTC
Found at i:6381 original size:20 final size:21
Alignment explanation
Indices: 6341--6381 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6331 GAGAAACGTG
6341 AAGAAAAATGCATTTACTAGT
1 AAGAAAAATGCATTTACTAGT
* *
6362 AAGAAAAGTTCATTTA-TAGT
1 AAGAAAAATGCATTTACTAGT
6382 CACCCATTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.46, C:0.07, G:0.15, T:0.32
Consensus pattern (21 bp):
AAGAAAAATGCATTTACTAGT
Found at i:8229 original size:171 final size:171
Alignment explanation
Indices: 7917--8256 Score: 416
Period size: 171 Copynumber: 2.0 Consensus size: 171
7907 NNNNAATTAT
* * * *
7917 TTTATAATCTCATAATTGATTTTAAGTTGCATTTTTTTACGTTTTTAGATAAAACAAACTACAAT
1 TTTATAATCTCATAATTGATTTTAAGTTGAATTTTATTACATTTTTAGATAAAACAAACAACAAT
* * * * *
7982 AGAATGTCTACCATGAGAAACGTGAAGAAAAAAGCATTCATTAGCAAGAAAAGTTTATTTATTGT
66 AGAATGTCTACCATAAGAAACGTAAAGAAAAAAGCATTCATTAGCAAGAAAAGTCTAATTATAGT
*
8047 TACCCATTCCTTCA-AAAGCATTATTACTC-TCTTTAAATTGC
131 GACCCATTCCTTCATAAA-CATTATTACTCGT-TTTAAATTGC
* * * * * *
8088 TTTATAATCTCTTAATTGATTTTAAGTTGAATTTTATTACATTTTTTGTTGAAACAGACAATAAT
1 TTTATAATCTCATAATTGATTTTAAGTTGAATTTTATTACATTTTTAGATAAAACAAACAACAAT
* * * * * *
8153 TGAATGTCTACCATAAGAAATGTAAATAAAAACGTATTCATT-GACAAGACAAGTCTAATTATAG
66 AGAATGTCTACCATAAGAAACGTAAAGAAAAAAGCATTCATTAG-CAAGAAAAGTCTAATTATAG
* *
8217 TGACCTATTCCTTCATATACATTATTACTCGTTTTAAATT
130 TGACCCATTCCTTCATAAACATTATTACTCGTTTTAAATT
8257 ATTTNNNNNN
Statistics
Matches: 142, Mismatches: 24, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
170 1 0.01
171 138 0.97
172 3 0.02
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.39
Consensus pattern (171 bp):
TTTATAATCTCATAATTGATTTTAAGTTGAATTTTATTACATTTTTAGATAAAACAAACAACAAT
AGAATGTCTACCATAAGAAACGTAAAGAAAAAAGCATTCATTAGCAAGAAAAGTCTAATTATAGT
GACCCATTCCTTCATAAACATTATTACTCGTTTTAAATTGC
Found at i:10101 original size:171 final size:160
Alignment explanation
Indices: 9924--10249 Score: 330
Period size: 170 Copynumber: 2.0 Consensus size: 160
9914 NNNNTCACCC
* * *
9924 ATTCCTTCAAAAGCATTATTACTCGT-TTTAAATTGTTTTGTGATCTCATAATTGATTTTAAGTT
1 ATTCCTTAAAAAGCATTATTACTC-TCTTTAAATTG-TTTATAATCTCATAATTGATTTTAAGTT
********** *
9988 GAANNNNNNNNNNTTTTTAGTTAAAACAGACAATAATTGAATGTTTACCATGAGAAATGTAAAGA
64 GAATTTTATTACATTTTTAGTTAAAACAGACAATAATTGAATGTCTACCATGAGAAATGTAAAGA
* *
10053 AAAACGCATTCATTGACAAGAAAAGTCTAATT
129 AAAACACATTCAATGACAAGAAAAGTCTAATT
**
10085 NNNNNNNNNNATTCCTTAAAAAGCATTATTACTCTCTTTAAATTGTTTATAATCTTGTAATTGAT
1 ----------ATTCCTTAAAAAGCATTATTACTCTCTTTAAATTGTTTATAATCTCATAATTGAT
* *
10150 TTTAAGTTGAATTTTATTACATTTTTTGTTAAAACAGACAATAATTGAATGTCTACCTTGAGAAA
56 TTTAAGTTGAATTTTATTACATTTTTAGTTAAAACAGACAATAATTGAATGTCTACCATGAGAAA
* * *
10215 TTTAAAGAAAAACACATTCAATGGCAAGCAAAGTC
121 TGTAAAGAAAAACACATTCAATGACAAGAAAAGTC
10250 CATTTATAGT
Statistics
Matches: 131, Mismatches: 23, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
170 99 0.76
171 32 0.24
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.36
Consensus pattern (160 bp):
ATTCCTTAAAAAGCATTATTACTCTCTTTAAATTGTTTATAATCTCATAATTGATTTTAAGTTGA
ATTTTATTACATTTTTAGTTAAAACAGACAATAATTGAATGTCTACCATGAGAAATGTAAAGAAA
AACACATTCAATGACAAGAAAAGTCTAATT
Found at i:10367 original size:171 final size:160
Alignment explanation
Indices: 10130--10440 Score: 342
Period size: 171 Copynumber: 1.9 Consensus size: 160
10120 CTTTAAATTG
** * *
10130 TTTATAATCTTGTAATTGATTTTAAGTTGAATTTTATTACATTTTTTGTTAAAACAGACAATAAT
1 TTTATAATCTCATAATTGATTTTAAGGTGAATTTTATTACATTTTTCGTTAAAACAGACAATAAT
* * *
10195 TGAATGTCTACCT-TGAGAAATTTAAAGAAAAACACATTCAATG-GCAAGCAAAGTCCATTTATA
66 TGAATGCCTACCTAT-A-AAATGTAAAGAAAAACACATTCAATGAG-AAGAAAAGTCCATTTATA
10258 GTCA-CCTATTCCTTTAAAAGCCTTATTACTTGC
128 GTCATCC-ATTCCTTTAAAAGCCTTATTACTTGC
10291 NNNNNNNNNNTTTATAATCTCATAATTGATTTTAAGGTGAATTTGT-TTACATTTTTCGTTAAAA
1 ----------TTTATAATCTCATAATTGATTTTAAGGTGAATTT-TATTACATTTTTCGTTAAAA
* * ** *
10355 CAGACTATAATTGAATGCCTACCTCATAAAATGTATAGAAAAAGGCATTCATTGAGAAGAAAAGT
55 CAGACAATAATTGAATGCCTACCT-ATAAAATGTAAAGAAAAACACATTCAATGAGAAGAAAAGT
10420 CCATTTATAGTCATCCATTCC
119 CCATTTATAGTCATCCATTCC
10441 NNNNNNNNNN
Statistics
Matches: 123, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
171 117 0.95
172 5 0.04
173 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.36
Consensus pattern (160 bp):
TTTATAATCTCATAATTGATTTTAAGGTGAATTTTATTACATTTTTCGTTAAAACAGACAATAAT
TGAATGCCTACCTATAAAATGTAAAGAAAAACACATTCAATGAGAAGAAAAGTCCATTTATAGTC
ATCCATTCCTTTAAAAGCCTTATTACTTGC
Found at i:13345 original size:171 final size:163
Alignment explanation
Indices: 13026--13386 Score: 355
Period size: 171 Copynumber: 2.1 Consensus size: 163
13016 NNNNNNNNNN
* ** *
13026 TCTCATAATTGATTTTAAGTTAAATTTTTTTAAATTTTTGGATAAAATACACTACAATTGAATGT
1 TCTCATAATTGATTTTAAGATAAATTTTTTTAAATTTTTAAATAAAACACACTACAATTGAATGT
* * * * **
13091 CTACCAATAGAAACATGAAGAAAAATGCATTCGTTGGCAAGAAAAGTCCNNNNNNNNNNACCCAT
66 CTACCAATAGAAACATAAAGAAAAAAGCATTCATTAGCAAGAAAAGTCC--------TCACCCAT
* *
13156 TCCTTTAAAAGCATTATTACTTACTTTAAATTGTTTTATAA
123 TCCTTCAAAAGCATTATTACTCACTTTAAATTGTTTTATAA
* * *
13197 TCTCATAATTAATTTTAAGATACATTTTTTTAAATTTTTAAATAAAACAGACTACAATTGAATGT
1 TCTCATAATTGATTTTAAGATAAATTTTTTTAAATTTTTAAATAAAACACACTACAATTGAATGT
* **
13262 CTACC-ATAAGAAACGTAAAGAAAAAAGCATTCATTAGCAAGAAAAGTNNNNNNNNNNTCACCCA
66 CTACCAAT-AGAAACATAAAGAAAAAAGCATTCATTAGCAAGAAAAGT--------CCTCACCCA
* * * * *
13326 TTCCTTCAAAAGTATTATTACTCGCTTTAAATTTTTTTGTGA
122 TTCCTTCAAAAGCATTATTACTCACTTTAAATTGTTTTATAA
13368 TCTCATAATTGATTTTAAG
1 TCTCATAATTGATTTTAAG
13387 TTGAANNNNN
Statistics
Matches: 157, Mismatches: 24, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
170 2 0.01
171 155 0.99
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.35
Consensus pattern (163 bp):
TCTCATAATTGATTTTAAGATAAATTTTTTTAAATTTTTAAATAAAACACACTACAATTGAATGT
CTACCAATAGAAACATAAAGAAAAAAGCATTCATTAGCAAGAAAAGTCCTCACCCATTCCTTCAA
AAGCATTATTACTCACTTTAAATTGTTTTATAA
Found at i:15558 original size:171 final size:161
Alignment explanation
Indices: 15290--15948 Score: 366
Period size: 171 Copynumber: 4.0 Consensus size: 161
15280 AGTTTTATAA
* * ** *
15290 TCTCATAATTGATTTTAATTTGAATTTTTTTACATTTTTGCTTAAAACAGACTACAATTGAATGT
1 TCTCATAATTGATTTTAAGTTAAATTTTTAAACATTTTTGCTTAAAACAGACTACAAGTGAATGT
* *
15355 CTACCTCAAGAAACATATAGAAAAAGCCATTCATAT-TGAAGAAAAGTCCGTTTATAGTTACCCA
66 CTACCTCAAGAAACATATAGAAAAAGCCATTCAT-TGAGAAGAAAAGTCCGTTTATAGTCACCCA
15419 TTCATTCAAAAACCTTATTACTCA-CTTTAAAT
130 TTCATTCAAAAACCTTATTACT-AGCTTTAAAT
*
15451 TNNNNNNNNNNCTCATAATTGATTTTAAGTTAAATTTTTAAATATTTTTAG-TTAAAACAGACTA
1 T----------CTCATAATTGATTTTAAGTTAAATTTTTAAACATTTTT-GCTTAAAACAGACTA
* * * * *
15515 TAAGTGAATG-CTTGTCTTGAA-AAACATGTAG-AAAAGACCATTCATTGAGAAGAAAAGTCCGT
55 CAAGTGAATGTC-T-ACCTCAAGAAACATATAGAAAAAG-CCATTCATTGAGAAGAAAAGTCCGT
* *
15577 TTATAGTCACCCATTCTTTCAAAAGCCTTATTACTAGCTTTAAATT
117 TTATAGTCACCCATTCATTCAAAAACCTTATTACTAGCTTTAAA-T
* ** ** * * *
15623 ATTTNNNNNNNNNNTAATTGATTTTAAGTTAAATTTTTTAAA-ATTTTTGGATAACACAGACAAT
1 -TCT--------CATAATTGATTTTAAGTTAAA-TTTTTAAACATTTTTGCTTAAAACAGACTAC
* * * * * * * *
15687 AATTGAATGTCTACCTGAAGAAACGTGA-AGGAAAA-CGAATTCGTTGACAAGAAACA-TCCATT
56 AAGTGAATGTCTACCTCAAGAAACAT-ATAGAAAAAGC-CATTCATTGAGAAGAAA-AGTCCGTT
* * * * *
15749 TATAGTCACCTATTCCTTCAAAAGCCTTATTAGTCA-CTTTGAAT
118 TATAGTCACCCATTCATTCAAAAACCTTATTACT-AGCTTTAAAT
* * * * * * * * ** * * *
15793 TGT-TTTA-TAATCTCATGATT-GA--TTT--ACATTTTTTATTAAAATAGAATACAATTGAATG
1 TCTCATAATTGATTTTAAG-TTAAATTTTTAAACATTTTTGCTTAAAACAGACTACAAGTGAATG
* * * * *
15851 ACTGA-CTCAAGACACATATAGAAAACGCCATTCATTGAGAAGAAAAGTCCATTTATAGTCACGC
65 TCT-ACCTCAAGAAACATATAGAAAAAGCCATTCATTGAGAAGAAAAGTCCGTTTATAGTCACCC
** * *
15915 ATTTTTTCAAAAGCCTTATTACTTGCTTTAAAT
129 ATTCATTCAAAAACCTTATTACTAGCTTTAAAT
15948 T
1 T
15949 ATTTTATAAT
Statistics
Matches: 390, Mismatches: 66, Indels: 90
0.71 0.12 0.16
Matches are distributed among these distances:
154 3 0.01
155 96 0.25
156 5 0.01
159 7 0.02
160 4 0.01
161 1 0.00
163 1 0.00
169 2 0.01
170 16 0.04
171 233 0.60
172 21 0.05
173 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.36
Consensus pattern (161 bp):
TCTCATAATTGATTTTAAGTTAAATTTTTAAACATTTTTGCTTAAAACAGACTACAAGTGAATGT
CTACCTCAAGAAACATATAGAAAAAGCCATTCATTGAGAAGAAAAGTCCGTTTATAGTCACCCAT
TCATTCAAAAACCTTATTACTAGCTTTAAAT
Found at i:17960 original size:314 final size:314
Alignment explanation
Indices: 17391--17972 Score: 720
Period size: 314 Copynumber: 1.9 Consensus size: 314
17381 TTAAAATTAT
*
17391 TTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTTTTAAAGAAATAGGTGTCTAAAAAT
1 TTATGAGATTATAAAATAATTCAAAGCGAGTAATAAGGCTTTTAAAGAAATAGGTGTCTAAAAAT
* * *
17456 GGACTTTTCTTCCCAATGAATGTGTTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTCTTTTA
66 AGACTTTTCTTCCCAATGAATGTGTTTTTCTTCATGTTTCTCGAAGTAGACATTCAATTATTTTA
* *
17521 TGTTTTATTAAAAAATATAAAAAAATTCAACTCAAAATCAATTATGAGATTATCAAACAATTTAA
131 TGTTTTATCAAAAAATATAAAAAAATTCAACTCAAAATCAATTATGAGATTATAAAACAATTTAA
* * ********** *
17586 AGCAAGTAATAAGACTTTTGAAGGAATGCGTGACTATAAANNNNNNNNNNTTCTCAATGAATGGC
196 AGCAAGTAATAAGACTTGTGAAGGAATGCGCGACTATAAATGTATTTTTTTTCTCAATGAATAGC
17651 TTTTTCTATATGTTTATTCAATTGTATTTTGTTTTAACAAGAAATGTAAATCAA
261 TTTTTCTATATGTTTATTCAATTGTATTTTGTTTTAACAAGAAATGTAAATCAA
* * * *
17705 TTATGAGATTATAAAATAATTCAAAGTGAGTAATAAGGCTTTTGAAGGAAT-GAGTGGT-TATAA
1 TTATGAGATTATAAAATAATTCAAAGCGAGTAATAAGGCTTTTAAAGAAATAG-GT-GTCTAAAA
** *
17768 ATAGACTTTTCTTGTCAATGAAT-TCGTTTTTCTTCATGTTTCTTGAAGTAGACATTCAATTATT
64 ATAGACTTTTCTTCCCAATGAATGT-GTTTTTCTTCATGTTTCTCGAAGTAGACATTCAATTATT
* * * ********** *
17832 TTCTGTTTTATCCAAAAATATAAAAAAATTCAACTTANNNNNNNNNNTGAGATTATAAAACGATT
128 TTATGTTTTATCAAAAAATATAAAAAAATTCAACTCAAAATCAATTATGAGATTATAAAACAATT
* * * *
17897 TAAAGCTAGTAATAAGGCTTGTGAAGGAGTGGGCGACTATAAATGTATTTTTTTTCTCAATGAAT
193 TAAAGCAAGTAATAAGACTTGTGAAGGAATGCGCGACTATAAATGTATTTTTTTTCTCAATGAAT
17962 AGCTTTTTCTA
258 AGCTTTTTCTA
17973 CACGTTTCTC
Statistics
Matches: 221, Mismatches: 44, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
313 2 0.01
314 217 0.98
315 2 0.01
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.37
Consensus pattern (314 bp):
TTATGAGATTATAAAATAATTCAAAGCGAGTAATAAGGCTTTTAAAGAAATAGGTGTCTAAAAAT
AGACTTTTCTTCCCAATGAATGTGTTTTTCTTCATGTTTCTCGAAGTAGACATTCAATTATTTTA
TGTTTTATCAAAAAATATAAAAAAATTCAACTCAAAATCAATTATGAGATTATAAAACAATTTAA
AGCAAGTAATAAGACTTGTGAAGGAATGCGCGACTATAAATGTATTTTTTTTCTCAATGAATAGC
TTTTTCTATATGTTTATTCAATTGTATTTTGTTTTAACAAGAAATGTAAATCAA
Found at i:18056 original size:171 final size:171
Alignment explanation
Indices: 17698--18857 Score: 513
Period size: 171 Copynumber: 6.8 Consensus size: 171
17688 CAAGAAATGT
* * * * *
17698 AAATCAATTATGAGATTATAAAATAATTCAAAG-TGAGTAATAAGGCTTTTGAAGGAATGAGTGG
1 AAATCAATTATGAGATTATAAAACAATTTAAAGCT-AGTAATAAGGCTTGTGAAGGAATGAGCGA
* * * * * *
17762 TTATAAATAGACTTTTCTTGTCAATGAATTCGTTTTTCTTCATGTTTCTTGAAGTAGACATTCAA
65 CTATAAATAGACTTTTCTTCTCAATGAATGCGTTTTTCTACACGTTTCTTCAAGTAGACATTCAA
** *
17827 TTATTTTCTGTTTTATCCAAAAATATAAAAAAATTCAACTTA
130 TTATAGTCTGTTTTAACCAAAAATATAAAAAAATTCAACTTA
********** * * *
17869 NNNNNNNNNNTGAGATTATAAAACGATTTAAAGCTAGTAATAAGGCTTGTGAAGGAGTGGGCGAC
1 AAATCAATTATGAGATTATAAAACAATTTAAAGCTAGTAATAAGGCTTGTGAAGGAATGAGCGAC
* *
17934 TATAAAT-GTATTTTTTTTCTCAATGAATAGC-TTTTTCTACACGTTTC-TCAAGATAGACATTC
66 TATAAATAG-ACTTTTCTTCTCAATGAAT-GCGTTTTTCTACACGTTTCTTCAAG-TAGACATTC
* ***
17996 ACTTATAGTCTGTTTTAACCAAAAATATTTGAAAATTCAACTTA
128 AATTATAGTCTGTTTTAACCAAAAATATAAAAAAATTCAACTTA
* ************************
18040 AAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAANNNNNNNNNNNNNNNNNNNNNNNNC
1 AAATCAATTATGAGATTATAAAACAATTTAAAGCTAGTAATAAGGCTTGTGAAGGAATGAGCGAC
* * * * * * *
18105 TATAAATGGACTTTTCTTC-AATATGAATG-GCTTTTTCTATATGTTTCTTGAGGTTGACATTCA
66 TATAAATAGACTTTTCTTCTCA-ATGAATGCG-TTTTTCTACACGTTTCTTCAAGTAGACATTCA
* * * *
18168 ATTGTAGTCTGTTTTAAGCAAAAATGTAAAGAAATTCAACTTA
129 ATTATAGTCTGTTTTAACCAAAAATATAAAAAAATTCAACTTA
* * * * * *
18211 AAATTAATTATGAGATTAT-AAATAATTTAAAG-TGACTAATAATGCTT-TTAACGAAAT-AG-G
1 AAATCAATTATGAGATTATAAAACAATTTAAAGCT-AGTAATAAGGCTTGTGAA-GGAATGAGCG
** * * * * * *
18271 TAACTATAAAT-GAACTTTTCTGGTTAGTGAATACATTTTTCTTCACGTTT-TTCATTGTAGACA
64 --ACTATAAATAG-ACTTTTCTTCTCAATGAATGCGTTTTTCTACACGTTTCTTCA-AGTAGACA
* * * *
18334 TTCAATTGTAGTCTGTTTTATCAAAAAATGTAAAGAAAATT-AACTTA
125 TTCAATTATAGTCTGTTTTAACCAAAAATATAAA-AAAATTCAACTTA
********** * ** * *
18381 AAATCAATTATNNNNNNNNNNAATAATTTAAAG-TGAGTAATAAAACTT-TTAAGGAATTG-GTG
1 AAATCAATTATGAGATTATAAAACAATTTAAAGCT-AGTAATAAGGCTTGTGAAGGAA-TGAGCG
* * * * * * *
18443 ACTATAAATGGACTTTTCTTGGT-AGTGAATGCATTTTTCTTCACATTT-GTCATCA-TAGACAT
64 ACTATAAATAGACTTTTCTT-CTCAATGAATGCGTTTTTCTACACGTTTCTTCA--AGTAGACAT
* *
18505 TCAATTATTA-TCTGTTTTATCCAAAAATGT-AAAAAATTCAACTTA
126 TCAATTA-TAGTCTGTTTTAACCAAAAATATAAAAAAATTCAACTTA
*********** * * * * *
18550 AAATCAATTATGAGATTANNNNNNNNNNNAAAGCGAGTAATAAGACTTTTGAAGGAATGGGTGAC
1 AAATCAATTATGAGATTATAAAACAATTTAAAGCTAGTAATAAGGCTTGTGAAGGAATGAGCGAC
* * * * * * * *
18615 TATAAATGGACTTTTATTCTTAATGAATG-GCTTTGTCTACACGTTTCTTGAGGCA-AGTATTCA
66 TATAAATAGACTTTTCTTCTCAATGAATGCG-TTTTTCTACACGTTTCTTCAAGTAGA-CATTCA
* * **
18678 ATTATAGTCTGTTTTAACTAAAAATGTGGAAAAATTCAACTTA
129 ATTATAGTCTGTTTTAACCAAAAATATAAAAAAATTCAACTTA
* ** * * * *
18721 AAATCAATTATGAGATTATGAAACTCTTTAAATG-GAGTAATAAGGCTT-TCTAAGGAATGGGTG
1 AAATCAATTATGAGATTATAAAACAATTTAAA-GCTAGTAATAAGGCTTGT-GAAGGAATGAGCG
* * * * * * * * *
18784 ACTAT-AATGGACTTTTCTTAC-AAATAAATGTGTTTTTCTTCATGTTTCTTGAGGTAAACATTC
64 ACTATAAATAGACTTTTCTT-CTCAATGAATGCGTTTTTCTACACGTTTCTTCAAGTAGACATTC
18847 AATTATAGTCT
128 AATTATAGTCT
18858 ATNNNNNNNN
Statistics
Matches: 745, Mismatches: 202, Indels: 85
0.72 0.20 0.08
Matches are distributed among these distances:
168 6 0.01
169 48 0.06
170 319 0.43
171 364 0.49
172 8 0.01
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.36
Consensus pattern (171 bp):
AAATCAATTATGAGATTATAAAACAATTTAAAGCTAGTAATAAGGCTTGTGAAGGAATGAGCGAC
TATAAATAGACTTTTCTTCTCAATGAATGCGTTTTTCTACACGTTTCTTCAAGTAGACATTCAAT
TATAGTCTGTTTTAACCAAAAATATAAAAAAATTCAACTTA
Found at i:18346 original size:170 final size:169
Alignment explanation
Indices: 18160--18567 Score: 500
Period size: 170 Copynumber: 2.4 Consensus size: 169
18150 TCTTGAGGTT
* *
18160 GACATTCAATTGTAGTCTGTTTTAAGCAAAAATGTAAAGAAATTCAACTTAAAATTAATTATGAG
1 GACATTCAATTGTAGTCTGTTTTAACCAAAAATGTAAAGAAATTCAACTTAAAATCAATTATGAG
**
18225 ATTATAAATAATTTAAAGTGACTAATAATGCTTTTAACGAAATAGGTAACTATAAATGAACTTTT
66 ATTATAAATAATTTAAAGTGACTAATAAAACTTTTAA-GAAATAGGTAACTATAAATGAACTTTT
* * **
18290 C-TGGTTAGTGAATACATTTTTCTTCACGTTTTTCATTGTA
130 CTTGG-TAGTGAATACATTTTTCTTCACATTTGTCATCATA
* * *
18330 GACATTCAATTGTAGTCTGTTTTATCAAAAAATGTAAAGAAAATT-AACTTAAAATCAATTATNN
1 GACATTCAATTGTAGTCTGTTTTAACCAAAAATGTAAAG-AAATTCAACTTAAAATCAATTAT-G
******** * * * * *
18394 NNNNNNNNAATAATTTAAAGTGAGTAATAAAACTTTTAAGGAATTGGTGACTATAAATGGACTTT
64 AGATTATAAATAATTTAAAGTGACTAATAAAACTTTTAAGAAATAGGTAACTATAAATGAACTTT
*
18459 TCTTGGTAGTGAATGCATTTTTCTTCACATTTGTCATCATA
129 TCTTGGTAGTGAATACATTTTTCTTCACATTTGTCATCATA
* *
18500 GACATTCAATTATTA-TCTGTTTTATCCAAAAATGTAAA-AAATTCAACTTAAAATCAATTATGA
1 GACATTCAATT-GTAGTCTGTTTTAACCAAAAATGTAAAGAAATTCAACTTAAAATCAATTATGA
18563 GATTA
65 GATTA
18568 NNNNNNNNNN
Statistics
Matches: 199, Mismatches: 34, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
168 5 0.03
169 17 0.09
170 139 0.70
171 38 0.19
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.37
Consensus pattern (169 bp):
GACATTCAATTGTAGTCTGTTTTAACCAAAAATGTAAAGAAATTCAACTTAAAATCAATTATGAG
ATTATAAATAATTTAAAGTGACTAATAAAACTTTTAAGAAATAGGTAACTATAAATGAACTTTTC
TTGGTAGTGAATACATTTTTCTTCACATTTGTCATCATA
Found at i:18607 original size:170 final size:159
Alignment explanation
Indices: 18410--18738 Score: 326
Period size: 170 Copynumber: 2.0 Consensus size: 159
18400 NNAATAATTT
* * * * *
18410 AAAGTGAGTAATAAAACTTTTAAGGAATTGGTGACTATAAATGGACTTTTCTTGGTAGTGAAT-G
1 AAAGCGAGTAATAAAACTTTTAAGGAATGGGTGACTATAAATGGACTTTTATTCGTAATGAATGG
* * * *
18474 CATTTTTCTTCACATTT-GTCA-TCATAGACATTCAATTATTA-TCTGTTTTATCCAAAAATGT-
66 C-TTTGTCTACACATTTCGTCAGGCA-AG-CATTCAATTA-TAGTCTGTTTTAACCAAAAATGTG
18535 AAAAAATTCAACTTAAAATCAATTATGAGATTA
127 AAAAAATTCAACTTAAAATCAATTATGAGATTA
*
18568 NNNNNNNNNNNAAAGCGAGTAATAAGACTTTTGAAGGAATGGGTGACTATAAATGGACTTTTATT
1 -----------AAAGCGAGTAATAAAACTTTT-AAGGAATGGGTGACTATAAATGGACTTTTATT
* * * * * *
18633 CTTAATGAATGGCTTTGTCTACACGTTTCTTGAGGCAAGTATTCAATTATAGTCTGTTTTAACTA
54 CGTAATGAATGGCTTTGTCTACACATTTCGTCAGGCAAGCATTCAATTATAGTCTGTTTTAACCA
*
18698 AAAATGTGGAAAAATTCAACTTAAAATCAATTATGAGATTA
119 AAAATGTGAAAAAATTCAACTTAAAATCAATTATGAGATTA
18739 TGAAACTCTT
Statistics
Matches: 137, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
169 21 0.15
170 76 0.55
171 38 0.28
172 2 0.01
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.35
Consensus pattern (159 bp):
AAAGCGAGTAATAAAACTTTTAAGGAATGGGTGACTATAAATGGACTTTTATTCGTAATGAATGG
CTTTGTCTACACATTTCGTCAGGCAAGCATTCAATTATAGTCTGTTTTAACCAAAAATGTGAAAA
AATTCAACTTAAAATCAATTATGAGATTA
Done.