Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399652.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_290.0, 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: 21956
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.28
Warning! 5228 characters in sequence are not A, C, G, or T
Found at i:1546 original size:10 final size:10
Alignment explanation
Indices: 1531--1557 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1521 TTGTTTTAAT
1531 AAAAAATATA
1 AAAAAATATA
1541 AAAAAATATA
1 AAAAAATATA
1551 AAAAAAT
1 AAAAAAT
1558 TCAACTTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (10 bp):
AAAAAATATA
Found at i:3182 original size:172 final size:171
Alignment explanation
Indices: 2894--3360 Score: 522
Period size: 172 Copynumber: 2.7 Consensus size: 171
2884 NNNNATTACA
* * * * * *
2894 AGATTATAAAACCATTTAAAACGAGTAATAAGGCTTTCAAAGGCATGGATGACTATAAATGGGCT
1 AGATTATAAAAACATTTCAACCGAGCAATAAGGCTTTCGAAGGCATGGATGACTATAAATGGACT
* * * * **
2959 TTTCTTGTCGATGAATATCTTTTTCCTCATGTTTCTCAAGGCAGACATTCAATTATTATTTGTTT
66 TTTCTTGGCGATGAATATCTTTTTCTTCACGTTTCTCGAGGCAGACATTCAATTATTATCAGTTT
* *
3024 TAACCAAAAA-AGTAAAAAAAATGCAACTTGAAATTAATTATG
131 TAACCAAAAATA-TAAAAAAAAT-CAACTTAAAATCAATTATG
* ** * *
3066 ATATTATAAAAACATTTCAGGCTAGCAATAAGGTTTTCGAAGGCATGGATGACTATAAATGGACT
1 AGATTATAAAAACATTTCAACCGAGCAATAAGGCTTTCGAAGGCATGGATGACTATAAATGGACT
* * *
3131 TTTCTTGGCGATGGATATCTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAATCAGTTT
66 TTTCTTGGCGATGAATATCTTTTTCTTCACGTTTCTCGAGGCAGACATTCAATTATTATCAGTTT
** *
3196 TAATTAAAAATATAAAAAAACTCAACTTAAAATCAATTATG
131 TAACCAAAAATATAAAAAAAATCAACTTAAAATCAATTATG
* * * * * * * * *
3237 AGGTTATAAAATCATTTGAACCGAGTACTAAGGCTTTCGAATGTATGGGTGACTATAAATGAACT
1 AGATTATAAAAACATTTCAACCGAGCAATAAGGCTTTCGAAGGCATGGATGACTATAAATGGACT
* * ** * * * * *
3302 TTTCTTAGCAATGAATGGCTTTTTCTTCACATTTGTGGCGACAGACATTCAATTATTAT
66 TTTCTTGGCGATGAATATCTTTTTCTTCACGTTTCTCGAGGCAGACATTCAATTATTAT
3361 GTATCTTNNN
Statistics
Matches: 244, Mismatches: 50, Indels: 3
0.82 0.17 0.01
Matches are distributed among these distances:
171 115 0.47
172 128 0.52
173 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.35
Consensus pattern (171 bp):
AGATTATAAAAACATTTCAACCGAGCAATAAGGCTTTCGAAGGCATGGATGACTATAAATGGACT
TTTCTTGGCGATGAATATCTTTTTCTTCACGTTTCTCGAGGCAGACATTCAATTATTATCAGTTT
TAACCAAAAATATAAAAAAAATCAACTTAAAATCAATTATG
Found at i:3810 original size:171 final size:172
Alignment explanation
Indices: 3575--3970 Score: 449
Period size: 171 Copynumber: 2.3 Consensus size: 172
3565 TATTATGATA
** *
3575 TTATAAAAAT-ATTTAAAGCGTGTAATAAGGCTTTTAAAGGCATGGGTGACTATAAATAGACTTT
1 TTAT-AAAATCATTTAAAGCGTGTAATAAGGCTTTCGAAGGCATAGGTGACTATAAATAGACTTT
* * *
3639 TCGTGCCAATGGATATCTTCTTCTTCACGTTTCTTGAGGTAGATATTCAATTATAATCTATTGTA
65 TCGTACCAATGGATATCTTCTTCTTCACGTTACTCGAGGTAGATATTCAATTATAATCTATTGTA
* * *
3704 ATAAAAAATGTAAAAAAATTCAACTTAAATTCAA-T-TGAGAGC
130 ATAAAAAATATAAAAAAACTCAACTTAAAATCAATTCTGAG-GC
* * * * *
3746 TTATAAAATCATTTAAAGCGTGTTATAAGGCTTTCGAAGGTATAGGTTAGTATAAATGGACTTTT
1 TTATAAAATCATTTAAAGCGTGTAATAAGGCTTTCGAAGGCATAGGTGACTATAAATAGACTTTT
* * ********** *
3811 CTTACCAATGGATATCTTTTTCTTCACGTTACTCGAGNNNNNNNNNNAATTATAATCTATTTTAA
66 CGTACCAATGGATATCTTCTTCTTCACGTTACTCGAGGTAGATATTCAATTATAATCTATTGTAA
3876 TAAAAAATATAAAAAAACTCAACTTAAAATCAATTCTGAGGC
131 TAAAAAATATAAAAAAACTCAACTTAAAATCAATTCTGAGGC
* * ** * *
3918 -TATAAAATCATATAAACCGAATAATAAGGCTTTCGAATGCATGGGTGACTATA
1 TTATAAAATCATTTAAAGCGTGTAATAAGGCTTTCGAAGGCATAGGTGACTATA
3971 TNNNNNNNNN
Statistics
Matches: 185, Mismatches: 37, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
170 5 0.03
171 173 0.94
172 3 0.02
173 4 0.02
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.34
Consensus pattern (172 bp):
TTATAAAATCATTTAAAGCGTGTAATAAGGCTTTCGAAGGCATAGGTGACTATAAATAGACTTTT
CGTACCAATGGATATCTTCTTCTTCACGTTACTCGAGGTAGATATTCAATTATAATCTATTGTAA
TAAAAAATATAAAAAAACTCAACTTAAAATCAATTCTGAGGC
Found at i:7269 original size:171 final size:172
Alignment explanation
Indices: 7024--7746 Score: 445
Period size: 171 Copynumber: 4.3 Consensus size: 172
7014 TCGTTTTTAT
* * * *
7024 GTTGAGTTTTTTTATATTTTTTTATTAAAACAGATTATAATTGAATGTCTACCTCGAGTAACGTG
1 GTTGAATTTTTTTACATTTTTTTATTAAAACAGATTATAATTGAATATCTACCTCGAGAAACGTG
** * ** *
7089 AAGAAAAAGATATTTATTAGCAAGAAAAGTCCATTTATAGTCA-TCTATACCTTCGGAAGCTTTA
66 AAGAAAAAGATATCCATTAGCAAGAAAAGTCCATTTATAGTCACTC-ACACCTTCAAAAGCCTTA
7153 TTACACGCTTTAAATAAATTTATAACCTCCTAATTATGTTTGA
130 TTACACGCTTTAAATAAATTTATAACCTCCTAATTATGTTTGA
** * *
7196 GTTGAATTTTTTTACA-TTTTTTATTGCAATAGATTA-ATATTGAATATCTACCTCGAGAAATGT
1 GTTGAATTTTTTTACATTTTTTTATTAAAACAGATTATA-ATTGAATATCTACCTCGAGAAACGT
* * * * *
7259 GAAGAAAAAGATATCCATTGGTATGAAAAGTCCATTTATAGTCACTCACGCCTTTAAAAGCCTTA
65 GAAGAAAAAGATATCCATTAGCAAGAAAAGTCCATTTATAGTCACTCACACCTTCAAAAGCCTTA
*** * *****
7324 TTACACGCTTTAAATGTTTTTATAA--T-C---TCAT-NNNNN
130 TTACACGCTTTAAATAAATTTATAACCTCCTAATTATGTTTGA
***** * * * ** * * *
7360 NNNNNATTTTTTTAC-CTTTTTTATTAAAACAGATTACAATTGAGTGCCTACCTTGGGAAACATG
1 GTTGAATTTTTTTACATTTTTTTATTAAAACAGATTATAATTGAATATCTACCTCGAGAAACGTG
* * * * * * ** *
7424 AAGAAAACA-ATATTCATTGGTACGAAAAGTCTACTTATAGTCACTCATGCCTTCAAACGCCTTA
66 AAGAAAA-AGATATCCATTAGCAAGAAAAGTCCATTTATAGTCACTCACACCTTCAAAAGCCTTA
* ** *** * * * *
7488 TTGCTTGCTTTAAATGGTTTTATAATCTCATAAATGAT-TTTAA
130 TTACACGCTTTAAATAAATTTATAACCTCCT-AATTATGTTTGA
* * *** * * * ** * *
7531 GTTGAATATTTTAACA-TTTTTGGGTAAAATAGATAATAATTGAATGTCTGTCTCGACAAATGTG
1 GTTGAATTTTTTTACATTTTTTTATTAAAACAGATTATAATTGAATATCTACCTCGAGAAACGTG
** * * * * ** * *
7595 AAGAAAAAGCCATTCATT-GCTAGAAAAAGTCCATTTATAATCACCCATGCATTCGAAAGCCTTA
66 AAGAAAAAGATATCCATTAGCAAG-AAAAGTCCATTTATAGTCACTCACACCTTCAAAAGCCTTA
*** * * * *
7659 TTATTTGGTTTAAATAATTTTATAACCTCATAATTGAT-TTTAA
130 TTACACGCTTTAAATAAATTTATAACCTCCTAATT-ATGTTTGA
* * *
7702 GTTGAGTTTTTTTATA-TTCTTTATTAAAACAGATTATAATTGAAT
1 GTTGAATTTTTTTACATTTTTTTATTAAAACAGATTATAATTGAAT
7747 NNNNNNNNNN
Statistics
Matches: 423, Mismatches: 112, Indels: 33
0.74 0.20 0.06
Matches are distributed among these distances:
164 122 0.29
165 5 0.01
166 1 0.00
168 1 0.00
169 1 0.00
170 7 0.02
171 270 0.64
172 16 0.04
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.39
Consensus pattern (172 bp):
GTTGAATTTTTTTACATTTTTTTATTAAAACAGATTATAATTGAATATCTACCTCGAGAAACGTG
AAGAAAAAGATATCCATTAGCAAGAAAAGTCCATTTATAGTCACTCACACCTTCAAAAGCCTTAT
TACACGCTTTAAATAAATTTATAACCTCCTAATTATGTTTGA
Found at i:7673 original size:335 final size:338
Alignment explanation
Indices: 6822--7844 Score: 875
Period size: 335 Copynumber: 3.0 Consensus size: 338
6812 NNNNNNNNNN
* * *
6822 AATGGTTTTATAATCTCATAAATGATTTTAAGTTGAATTTTTTCACATGTTTGACTAAAACTCG-
1 AATGGTTTTATAATCTCATAAATGATTTTAAGTTGAATTTTTTAACATTTTTGACTAAAA-TAGA
* * * **
6886 TAATAATTAAATGTCTGTCTCGATAAATGTAAAGAAAAAGCCATTCATTATTAGGAAAAA-TCCA
65 TAATAATTGAATGTCTGTCTCGACAAATGTGAAGAAAAAGCCATTCATTGCTAGGAAAAAGTCCA
* *
6950 TTTATAGTTACCCATGCATTTGAAAGCCTTATTATTCGGTTTATATGATTTTATAACCTCATAAT
130 TTTATAGTCACCCATGCATTTGAAAGCCTTATTATTCGGTTTAAATGATTTTATAA--TC----T
* * * *
7015 CGTTTTTATGTTGAGTTTTTTTATATTTTTTTATTAAAACAGATTATAATTGAATGTCTACCTCG
189 CATTTTTATGTTGAGTTTTTTTATACTTTTTTATTAAAACAGATTACAATTGAATGCCTACCTCG
* * * * *
7080 AGTAACGTGAAGAAAAAGATATTTATTAGCAAGAAAAGTCCATTTATAGTCATCTATACCTTCGG
254 AGAAACATGAAGAAAAAGATATTCATTAGCAAGAAAAGTCCACTTATAGTCATCTATACCTTCGA
*
7145 AAGCTTTATTACACGCTTTA
319 AAGCCTTATTACACGCTTTA
*** * * * * * * * **
7165 AATAAATTTATAACCTCCT-AATTATGTTTGAGTTGAATTTTTTTACATTTTTTATTGCAATAGA
1 AATGGTTTTATAATCTCATAAATGAT-TTTAAGTTGAATTTTTTAACATTTTTGACTAAAATAGA
* ** * ** * * *
7229 TTAAT-ATTGAATATCTACCTCGAGAAATGTGAAGAAAAAGATATCCATTGGTATG-AAAAGTCC
65 -TAATAATTGAATGTCTGTCTCGACAAATGTGAAGAAAAAGCCATTCATTGCTAGGAAAAAGTCC
* * * * ** * * **
7292 ATTTATAGTCACTCACGCCTTTAAAAGCCTTATTACACGCTTTAAATGTTTTTATAATCTCATNN
129 ATTTATAGTCACCCATGCATTTGAAAGCCTTATTATTCGGTTTAAATGATTTTATAATCTCATTT
******** * * * *
7357 NNNNNNNNA-TTTTTTTA-CCTTTTTTATTAAAACAGATTACAATTGAGTGCCTACCTTGGGAAA
194 TTATGTTGAGTTTTTTTATACTTTTTTATTAAAACAGATTACAATTGAATGCCTACCTCGAGAAA
* * * * *
7420 CATGAAGAAAACA-ATATTCATTGGTACGAAAAGTCTACTTATAGTCA-CTCATGCCTTC-AAAC
259 CATGAAGAAAA-AGATATTCATTAGCAAGAAAAGTCCACTTATAGTCATCT-ATACCTTCGAAA-
* **
7482 GCCTTATTGCTTGCTTTA
321 GCCTTATTACACGCTTTA
* **
7500 AATGGTTTTATAATCTCATAAATGATTTTAAGTTGAATATTTTAACATTTTTGGGTAAAATAGAT
1 AATGGTTTTATAATCTCATAAATGATTTTAAGTTGAATTTTTTAACATTTTTGACTAAAATAGAT
7565 AATAATTGAATGTCTGTCTCGACAAATGTGAAGAAAAAGCCATTCATTGCTA-GAAAAAGTCCAT
66 AATAATTGAATGTCTGTCTCGACAAATGTGAAGAAAAAGCCATTCATTGCTAGGAAAAAGTCCAT
* * * * *
7629 TTATAATCACCCATGCATTCGAAAGCCTTATTATTTGGTTTAAATAATTTTATAACCTCATAATT
131 TTATAGTCACCCATGCATTTGAAAGCCTTATTATTCGGTTTAAATGATTTTATAA--TC-TCA-T
* * * **********
7694 GATTTTAAGTTGAGTTTTTTTATA-TTCTTTATTAAAACAGATTATAATTGAATNNNNNNNNNNA
192 --TTTTATGTTGAGTTTTTTTATACTTTTTTATTAAAACAGATTACAATTGAATGCCTACCTCGA
* * * * *
7758 GAAACATGATGAAAAAGATATCCA-TCGTCAAGAAAAGTCCATTTATAGTCACCTATACCTTCGA
255 GAAACATGAAGAAAAAGATATTCATTAG-CAAGAAAAGTCCACTTATAGTCATCTATACCTTCGA
** * *
7822 AAATCTTATTACTCGCCTTA
319 AAGCCTTATTACACGCTTTA
7842 AAT
1 AAT
7845 NNNNNNNNNN
Statistics
Matches: 517, Mismatches: 141, Indels: 45
0.74 0.20 0.06
Matches are distributed among these distances:
334 9 0.02
335 234 0.45
336 14 0.03
337 6 0.01
338 2 0.00
339 1 0.00
341 6 0.01
342 107 0.21
343 134 0.26
344 4 0.01
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.38
Consensus pattern (338 bp):
AATGGTTTTATAATCTCATAAATGATTTTAAGTTGAATTTTTTAACATTTTTGACTAAAATAGAT
AATAATTGAATGTCTGTCTCGACAAATGTGAAGAAAAAGCCATTCATTGCTAGGAAAAAGTCCAT
TTATAGTCACCCATGCATTTGAAAGCCTTATTATTCGGTTTAAATGATTTTATAATCTCATTTTT
ATGTTGAGTTTTTTTATACTTTTTTATTAAAACAGATTACAATTGAATGCCTACCTCGAGAAACA
TGAAGAAAAAGATATTCATTAGCAAGAAAAGTCCACTTATAGTCATCTATACCTTCGAAAGCCTT
ATTACACGCTTTA
Found at i:11396 original size:171 final size:168
Alignment explanation
Indices: 10998--12655 Score: 816
Period size: 171 Copynumber: 9.7 Consensus size: 168
10988 NNNNNNNNTG
* * * * *
10998 TAAAAAAATTCAGCTTGAAATCAATTATAAGTTTATAAAATCAGTTAAAGCGAGTAATAAGGCTT
1 TAAAAAAATTCAACTTAAAAT-AATTATGAG-TTATAAAATCATTTAAAGCGTGTAATAAGGCTT
** ********** * *
11063 TCAAAGGCATGGGTGACNNNNNNNNNNCTTTTCTTGTCGATGAATATCTTTTTCTTCACGTTTCT
64 TTGAAGGCATGGGTGACTATAAATGGACTTTTCTT-ACAATGAATATCTTTTTCTTCACGTTTCT
* * * * * * *
11128 CAAGGCAGATATACAATTATTATTTGTTTTAACAAAAAA-A
128 CAAGGTAGACATTCAATTATAATCTATTTTAATAAAAAATA
* * ******* * * *
11168 GTAAAAAACTACAACTTAAAATTAATTATGA--TANNNNNNNNNNATTTAAGGCGAGTAATAAGA
1 -TAAAAAAATTCAACTTAAAA-TAATTATGAGTTA---TAAAATCATTTAAAGCGTGTAATAAGG
* * * *
11231 TTTTTGAAGGTATGGGTGACTATAAATGGACTTTTCTTGACGATGGATATCTTTTTCTTCACGTT
61 CTTTTGAAGGCATGGGTGACTATAAATGGACTTTTCTT-ACAATGAATATCTTTTTCTTCACGTT
* * *
11296 TCTCAACGTAGACATTCAATTATAATCTGTTTTAATAAAGAATA
125 TCTCAAGGTAGACATTCAATTATAATCTATTTTAATAAAAAATA
* * * * * *
11340 TAAAAAAACTCAACTTGAAATCAATTATGATGTTACAAAATTATTTAAACCGAGTAATAAGGCTT
1 TAAAAAAATTCAACTTAAAAT-AATTATGA-GTTATAAAATCATTTAAAGCGTGTAATAAGGCTT
* * * * * * *
11405 TCGAATGCATGGGTGACTATAAATGGACTTTTCCTAGTAATGAATGGT-TTTTTCTTCACATTTG
64 TTGAAGGCATGGGTGACTATAAATGGACTTTTCTTA-CAATGAAT-ATCTTTTTCTTCACGTTTC
* ** * *** * *
11469 TCGAGACAGACATTCAATTATTATCTATTTTACCCAACAATG
127 TCAAGGTAGACATTCAATTATAATCTATTTTAATAAAAAATA
* * * * * *
11511 TGAAAATATTCAACTTAAAATCATTTATGAGATTATAAAACCATTTAAAGCGTGCAATAAGGCGT
1 TAAAAAAATTCAACTTAAAAT-AATTATGAG-TTATAAAATCATTTAAAGCGTGTAATAAGGCTT
* * * * *
11576 TTGAAGGCATGGGTGACTATAAGTAGACTTTTCGTACCAATGAATATCGTTTTCTTCATGTTTC-
64 TTGAAGGCATGGGTGACTATAAATGGACTTTTCTTA-CAATGAATATCTTTTTCTTCACGTTTCT
* * * * * **
11640 CTGAGGTAGGCACTCAATTGTAATCTGTTTTAATAAAAAAGG
128 C-AAGGTAGACATTCAATTATAATCTATTTTAATAAAAAATA
* * * *
11682 TAAAGAAATTCTAC-T----T-ATTATGAGATTATAAAAACATTTAAGGCGTGTAATAAGGCTTT
1 TAAAAAAATTCAACTTAAAATAATTATGAG-TTATAAAATCATTTAAAGCGTGTAATAAGGCTTT
* * * * *******
11741 TAAAGGCGTGGGTGACTATAAATGGACTTTTCGTACCAATGGATATCTTTTTCTTCACNNNNNNN
65 TGAAGGCATGGGTGACTATAAATGGACTTTTCTTA-CAATGAATATCTTTTTCTTCACGTTTCTC
*** * *
11806 NNNGTAGATATTCAATTATAATCTATTGTAATAAAAAATA
129 AAGGTAGACATTCAATTATAATCTATTTTAATAAAAAATA
*
11846 TAAAAAAATTCAACTTAAACATAATTAGGAGGTTATAAAATCATTTAAAGCGTGTAATAAGGCTT
1 TAAAAAAATTCAACTTAAA-ATAATTATGA-GTTATAAAATCATTTAAAGCGTGTAATAAGGCTT
** ** * * * *
11911 CCGAAGGTGTAGGTGACTATAAATGGACTTTTCTTGCCAAT-AGATATCTTTTTCTTCATGTTAC
64 TTGAAGGCATGGGTGACTATAAATGGACTTTTCTT-ACAATGA-ATATCTTTTTCTTCACGTTTC
* ***
11975 TCGAGGTAGACATTCAATTATAATCTATTTTAATAAAAANNN
127 TCAAGGTAGACATTCAATTATAATCTATTTTAATAAAAAATA
******* * *
12017 NNNNNNNACTCAACTTAAAATCAATTATGAGGTTATAAAATCATATAAA-C-TGAATAATAAGG-
1 TAAAAAAATTCAACTTAAAAT-AATTATGA-GTTATAAAATCATTTAAAGCGTG--TAATAAGGC
** ** ** * * ** * *
12079 TTTCAAATTCATGGGTGACTATAAATGGGTTTTTCTTAATAATAAATGGCTTTTTCTTTACATTT
62 TTTTGAAGGCATGGGTGACTATAAATGGACTTTTCTT-ACAATGAATATCTTTTTCTTCACGTTT
* * ** * * * * * *
12144 GTCGAGACAGACATTCAATTATTAT-GAGTTTTACTCAAACATG
126 CTCAAGGTAGACATTCAATTATAATCTA-TTTTAATAAAAAATA
* * * ** ********
12187 T-GAAAAATTCAACTTAAAATCATTTATGAGATTATAAAACCATTTAAAGCAAGTAANNNNNNNN
1 TAAAAAAATTCAACTTAAAAT-AATTATGAG-TTATAAAATCATTTAAAGCGTGTAATAAGGCTT
********** * * * * * * *
12251 NNNNNNNNNNGGATGACTATAAGTAGACTTTTGTTGCCAATGAATATCTTGTTCTTAACGTTTCT
64 TTGAAGGCATGGGTGACTATAAATGGACTTTTCTT-ACAATGAATATCTTTTTCTTCACGTTTCT
* * * *
12316 TAAGGTAGGCATTCAATTATAATCTGTTTTAATAAAAAATG
128 CAAGGTAGACATTCAATTATAATCTATTTTAATAAAAAATA
* * * ** *
12357 TAAAAAAAATCAA-TAAAAAATTAATTATGAGATTATAAAACCATTTAAATTGAGTAATAAGGCT
1 TAAAAAAATTCAACT-TAAAA-TAATTATGAG-TTATAAAATCATTTAAAGCGTGTAATAAGGCT
** * * * * * * *
12421 TTCAAAGGCATGGGTGACTATACATGGGCTTTTCTTGGCATTGAATATCTTTTCCTTCATGGTTC
63 TTTGAAGGCATGGGTGACTATAAATGGACTTTTCTT-ACAATGAATATCTTTTTCTTCACGTTTC
* * * * * * *
12486 CCAAGGCATACATTCAATTATTATCTGTTTCAACAAAAAATA
127 TCAAGGTAGACATTCAATTATAATCTATTTTAATAAAAAATA
* * ** * * * * ****
12528 TACAAAAATTCAAGTTAAAATCAATTACAAGATTTTAAAAACATTTTAGGCACAAAATAAGGCTT
1 TAAAAAAATTCAACTTAAAAT-AATTATGAG-TTATAAAATCATTTAAAGCGTGTAATAAGGCTT
* ** * * *
12593 TTGAAGGTATGGGTGTTTATAAATGGACTTTTCTTGCCAATGAATGGT-TTTTTCTTCAGGTTT
64 TTGAAGGCATGGGTGACTATAAATGGACTTTTCTT-ACAATGAAT-ATCTTTTTCTTCACGTTT
12656 TCCTAGGCAA
Statistics
Matches: 1104, Mismatches: 342, Indels: 82
0.72 0.22 0.05
Matches are distributed among these distances:
164 130 0.12
165 1 0.00
166 1 0.00
168 3 0.00
169 42 0.04
170 157 0.14
171 761 0.69
172 7 0.01
174 2 0.00
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.34
Consensus pattern (168 bp):
TAAAAAAATTCAACTTAAAATAATTATGAGTTATAAAATCATTTAAAGCGTGTAATAAGGCTTTT
GAAGGCATGGGTGACTATAAATGGACTTTTCTTACAATGAATATCTTTTTCTTCACGTTTCTCAA
GGTAGACATTCAATTATAATCTATTTTAATAAAAAATA
Found at i:13505 original size:164 final size:152
Alignment explanation
Indices: 13272--13585 Score: 292
Period size: 164 Copynumber: 2.0 Consensus size: 152
13262 AAATCATTTT
* * * *
13272 TGAGATTATAAAACCATTTAAAGCGAGCAATAAGGCGTTTGAAGGCATGGATGACTATAAGTAGA
1 TGAGATTATAAAAACATTTAAAACGAGCAATAAGGCGTTTAAAGGCATGGATGACTATAAATAGA
* * * *
13337 CTTTTCGTACCAATGAGTATCGTTTTCTTCATGTTTCCCGAGGTAG-TCACTCAATTGTAA-CTT
66 CTTTTCGTACCAATGAATATCGTTTTCTTCACGTTTCCCAAGGTAGAT-ACTCAATTATAATC-T
*
13400 ATTTTAATAAAAAAGGTAAAAAAATNNNNNNNNNNA
129 ATTGTAATAAAAAA--TAAAAAAAT----------A
* * * * * *
13436 TGAGATTATAAAAACATTTAAAAC-ATGTAATAAGGCTTTTAAAGGCCTGGGTGGCTATAAATGG
1 TGAGATTATAAAAACATTTAAAACGA-GCAATAAGGCGTTTAAAGGCATGGATGACTATAAATAG
** * * *
13500 ACTTTTCGTGTCAATGAATATCTTTTTCTTCACGTTTCTCAAGGTAGATATTCAATTATAATCTA
65 ACTTTTCGTACCAATGAATATCGTTTTCTTCACGTTTCCCAAGGTAGATACTCAATTATAATCTA
13565 TTGTAATAAAAAATAAAAAAA
130 TTGTAATAAAAAATAAAAAAA
13586 ATTCAACTTA
Statistics
Matches: 127, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
162 8 0.06
163 1 0.01
164 116 0.91
165 2 0.02
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.32
Consensus pattern (152 bp):
TGAGATTATAAAAACATTTAAAACGAGCAATAAGGCGTTTAAAGGCATGGATGACTATAAATAGA
CTTTTCGTACCAATGAATATCGTTTTCTTCACGTTTCCCAAGGTAGATACTCAATTATAATCTAT
TGTAATAAAAAATAAAAAAATA
Found at i:14067 original size:171 final size:171
Alignment explanation
Indices: 13887--14276 Score: 446
Period size: 171 Copynumber: 2.3 Consensus size: 171
13877 TTGTCGAGAC
* * * * * ** * *
13887 AGACATTCAATTATTATAAGTTTTACTCAAACATGTGAAATAATTCAACTTAAAATTATTTATGA
1 AGACATTCAATTATTATAAGTTTTAATAAAAAATGTAAAAAAATTCAACAAAAAATTAATTATAA
*
13952 GATTATAAAACCATTTAAAGT-AAGTAATAATGCTTTT-GAAGGCATGGATGACTATA-AGTAGA
66 GATTATAAAACCATTTAAA-TCAAGTAATAA-GCTTTTCAAAGGCATGGATGACTATACA-TAGA
* *
14014 CTTTTGTTGCAAATGAATATCTTGTT-CTTAATGTTTCCTAAGGT
128 CTTTTCTTGCAAATGAATATCTT-TTCCTTAATGTTTCCCAAGGT
* * **
14058 AGGCATTCAATTATAATCTGTTTTAATAAAAAATGTAAAAAAATTCAACAAAAAATTAATTATAA
1 AGACATTCAATTATTATAAGTTTTAATAAAAAATGTAAAAAAATTCAACAAAAAATTAATTATAA
* * * * **
14123 GATTATAAAACCATTTAAATCGAGTAATAAGGTTTTCAAAGGCATGGGTGACTATACATGGGTTT
66 GATTATAAAACCATTTAAATCAAGTAATAAGCTTTTCAAAGGCATGGATGACTATACATAGACTT
* * *
14188 TTCTTGCCAATGGATATCTTTTCCTTCATGTTTCCCAAGGT
131 TTCTTGCAAATGAATATCTTTTCCTTAATGTTTCCCAAGGT
** * * *
14229 AGACATTCAATTATTATTTGTTTGAACAAAAAATATAAAAAAATTCAA
1 AGACATTCAATTATTATAAGTTTTAATAAAAAATGTAAAAAAATTCAA
14277 GTTAAAATCA
Statistics
Matches: 184, Mismatches: 31, Indels: 8
0.83 0.14 0.04
Matches are distributed among these distances:
170 8 0.04
171 175 0.95
172 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.36
Consensus pattern (171 bp):
AGACATTCAATTATTATAAGTTTTAATAAAAAATGTAAAAAAATTCAACAAAAAATTAATTATAA
GATTATAAAACCATTTAAATCAAGTAATAAGCTTTTCAAAGGCATGGATGACTATACATAGACTT
TTCTTGCAAATGAATATCTTTTCCTTAATGTTTCCCAAGGT
Found at i:16416 original size:170 final size:171
Alignment explanation
Indices: 15803--16422 Score: 685
Period size: 171 Copynumber: 3.6 Consensus size: 171
15793 NNNNNNNNNN
* * *
15803 AGGCTTTCGAAGGCATGGGTGACTATAAATGGAATTTTCTTGCTAATGGATATCATTTTCTTCAT
1 AGGCTTTCGAAGGCATGGGTGACTATAAATAGACTTTTCTTGCTAATGGATATCTTTTTCTTCAT
* * *
15868 GTTTCCCAAGGCAGACATTCAATTATTATTTGTTTTAATAAAAATTATAAAAAAATTCAACTTAA
66 GTTTCCCAAGGCAGACAATCAATTATTATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAA
* * * * *
15933 AATCAATTAGGAGGTTATAAAACCATTTAAAGCAATTAACA
131 AATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
* * * *
15974 ACGCTTTCGAAGGCATGAGTGACTATAAATGGATTTTTCTTGCTAATGGATATCTTTTTCTTCAT
1 AGGCTTTCGAAGGCATGGGTGACTATAAATAGACTTTTCTTGCTAATGGATATCTTTTTCTTCAT
* ** * *
16039 ATTTTTCAAGGCAGA-TATACAATTATTATCTGTTTT-ATCCAAAAATATAAAAAAATTCAACTT
66 GTTTCCCAAGGCAGACAAT-CAATTATTATCTGTTTTAAT-AAAAAATATAAAAAAATTCAACTT
* * * *
16102 AAAATCAATTATGAGACTATAAAAACATTTAAAGTGAGTAATG
129 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
* * **********
16145 AGGCATTT-AAAGGCATGGGTGACTATAAATAGACTATTCTTNNNNNNNNNNATCTTTTTCTTCA
1 AGGC-TTTCGAAGGCATGGGTGACTATAAATAGACTTTTCTTGCTAATGGATATCTTTTTCTTCA
* * *
16209 TGTTTCCCAAGGTAGACATTCAATTAAATT-T-TGTTTTAATAAAAAATGTAAAAAAATTCAACT
65 TGTTTCCCAAGGCAGACAATCAATT--ATTATCTGTTTTAATAAAAAATATAAAAAAATTCAACT
* * * * *
16272 TAAATTTAATTTTTAGATTATAAAACCATTTAAAACGAGTAATA
128 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
* * *
16316 AGGC-TTCGAAGGCATGGGTGACAATAAATATACTTTTCTTGCCAATGGATATCTTTTTCTTCAT
1 AGGCTTTCGAAGGCATGGGTGACTATAAATAGACTTTTCTTGCTAATGGATATCTTTTTCTTCAT
*** **
16380 GTTTCTTGAGATAGACAATCAATTATTATCTGTTTTAATAAAA
66 GTTTCCCAAGGCAGACAATCAATTATTATCTGTTTTAATAAAA
16423 NNNNNNNNNN
Statistics
Matches: 366, Mismatches: 73, Indels: 21
0.80 0.16 0.05
Matches are distributed among these distances:
168 3 0.01
169 3 0.01
170 78 0.21
171 272 0.74
172 7 0.02
173 3 0.01
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.36
Consensus pattern (171 bp):
AGGCTTTCGAAGGCATGGGTGACTATAAATAGACTTTTCTTGCTAATGGATATCTTTTTCTTCAT
GTTTCCCAAGGCAGACAATCAATTATTATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAA
AATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
Found at i:16938 original size:170 final size:160
Alignment explanation
Indices: 16629--16946 Score: 361
Period size: 170 Copynumber: 1.9 Consensus size: 160
16619 NNNNNNNNNN
* * * * *
16629 TGACTATAAATGGACTTTTCTTGCTAATGAATATCTTTTTCTTCATGTTTCCTAAGGTAGACATT
1 TGACTATAAATGGACTTTTCATGCCAATGAATATCTTTTTCTTCATGCTTCCCAAGGCAGACATT
* *
16694 CAATTAATATCTCTTTTAACCAAAAACGTAAAAAAATTCAATTCAAAATCAATTATGAGATTATA
66 CAATTAATATCTATTTTAACCAAAAACGTAAAAAAATTCAATTCAAAATCAATTATGAGATAATA
* *
16759 AAGCATTTAAAGCGAGTACTAAGGCTTNNNNNNNNNNGGG
131 AAACATTTAAAGCAAGTACTAAGGCTT----------GGG
* * * *
16799 TGACTATAAATGGACTTTTCATGCCAGTGGATATCTTTTTCTTCATGCTTCCCGAGGCAGATATT
1 TGACTATAAATGGACTTTTCATGCCAATGAATATCTTTTTCTTCATGCTTCCCAAGGCAGACATT
* * * *
16864 CAATTATTATCTATTTTAGCC-CAAATGTAAAAAAATTCAACTT-AAAATCAATTATGAGATAAT
66 CAATTAATATCTATTTTAACCAAAAACGTAAAAAAATTCAA-TTCAAAATCAATTATGAGATAAT
16927 AAAAACATTTAAAGCAAGTA
130 -AAAACATTTAAAGCAAGTA
16947 ATGAGGTTTT
Statistics
Matches: 129, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
169 36 0.28
170 93 0.72
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.34
Consensus pattern (160 bp):
TGACTATAAATGGACTTTTCATGCCAATGAATATCTTTTTCTTCATGCTTCCCAAGGCAGACATT
CAATTAATATCTATTTTAACCAAAAACGTAAAAAAATTCAATTCAAAATCAATTATGAGATAATA
AAACATTTAAAGCAAGTACTAAGGCTTGGG
Found at i:17553 original size:171 final size:169
Alignment explanation
Indices: 16629--17574 Score: 557
Period size: 171 Copynumber: 5.5 Consensus size: 169
16619 NNNNNNNNNN
* * ** *
16629 TGACTATAAATGGACTTTTCTTG-CTAATGAATATCTTTTTCTTCATGTTTC-CTAAGGT-AGAC
1 TGACTATAAATAGACTTTTCTTGTC-AATGGATATCTTTTTCTTCACATTTCTC-GAGGTAAG-C
* * * * *
16691 ATTCAATTA-ATATCTCTTTTAACCAAAAACGTA-AAAAAATTC-AATTCAAAATCAATTATGAG
63 ATTCAATTATA-ATCTATTTTAA-TAAAAA-ATATAAAAAATTCTACTT-AAAGTCAATTATGAG
* * **********
16753 ATTAT-AAAGCATTTAAAGCGAGTACTAAGGCTTNNNNNNNNNNGGG
124 ATTATAAAAACATTTAAAGCGAGTAATAAGGCTT-TGAAGGCATAGG
* * * * *** * * *
16799 TGACTATAAATGGACTTTTCATGCCAGTGGATATCTTTTTCTTCATGCTTCCCGAGG-CAGATAT
1 TGACTATAAATAGACTTTTCTTGTCAATGGATATCTTTTTCTTCACATTTCTCGAGGTAAG-CAT
* **** * * * *
16863 TCAATTATTATCTATTTT-AGCCCAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATAAT
65 TCAATTATAATCTATTTTAATAAAAAATAT-AAAAAATTCTACTTAAAGTCAATTATGAGATTAT
* * * * ********
16927 AAAAACATTTAAAGCAAGTAATGAGGTTTTTAAANNNNNNNN
129 AAAAACATTTAAAGCGAGTAATAAGG-CTTTGAAGGCATAGG
** * * ** *** ** *
16969 NNACTATGAATCGACAATTCTTG-CTAAAAAATATCTTTTTCTTCATGTTTCTCGAGGTAGGCAT
1 TGACTATAAATAGACTTTTCTTGTC-AATGGATATCTTTTTCTTCACATTTCTCGAGGTAAGCAT
* * * *
17033 TTAATTACAATTTATTTTAATAAAAAAATATAAAAAAATTCTACTGAAAGTCAATTATGAGATTA
65 TCAATTATAATCTATTTTAAT-AAAAAATAT-AAAAAATTCTACTTAAAGTCAATTATGAGATTA
* *
17098 TAAAAACATTTAAAGTGAGTAATAAGGCTTTTAGAGGCATAGG
128 TAAAAACATTTAAAGCGAGTAATAAGGCTTTGA-AGGCATAGG
* * ** * * * * *
17141 TGACTATAAGTAGATTTTTCTTGTCAATAAATATATTTTTTTTCACATTGCCCGAGGTAAGCACT
1 TGACTATAAATAGACTTTTCTTGTCAATGGATATCTTTTTCTTCACATTTCTCGAGGTAAGCATT
* * ** *
17206 CAATTATAATATGTTTTAATAAAAAAGGTAAAAACATTCTACTTAAAGTTAATTATGAGATTATA
66 CAATTATAATCTATTTTAATAAAAAATATAAAAA-ATTCTACTTAAAGTCAATTATGAGATTATA
* * ** *
17271 AAAACATTTAAAGCGAGCAATAAGGTTTTTGAAGGTGTGGG
130 AAAACATTTAAAGCGAGTAATAAGG-CTTTGAAGGCATAGG
* * * * * **********
17312 TGACTGTAAATTGACTTTTCGTGCCAATGGATATCTTTTTCTTCATATTTCTCGNNNNNNNNNNT
1 TGACTATAAATAGACTTTTCTTGTCAATGGATATCTTTTTCTTCACATTTCTCGAGGTAAGCATT
* * * *
17377 CAATTATAATCTGTTTTAATAAAAAATATAACATAAA-TCAACTTAAAATCAATTA-GAAGTTTA
66 CAATTATAATCTATTTTAATAAAAAATATAA-A-AAATTCTACTTAAAGTCAATTATG-AGATTA
* *
17440 TAAAATCATTTAAAGCGAGTAATAAGGCTTCTGAAGACATAGG
128 TAAAAACATTTAAAGCGAGTAATAAGGCTT-TGAAGGCATAGG
* * * * * * *
17483 TGACTATAAATGGACTATTCTTATCAATGGATATCTTATTCTTCACGTTTCTCAAGGTAAACATT
1 TGACTATAAATAGACTTTTCTTGTCAATGGATATCTTTTTCTTCACATTTCTCGAGGTAAGCATT
17548 CAATTATAATCTATTTTAATAAAAAAT
66 CAATTATAATCTATTTTAATAAAAAAT
17575 NNNNNNNNNN
Statistics
Matches: 595, Mismatches: 160, Indels: 41
0.75 0.20 0.05
Matches are distributed among these distances:
167 1 0.00
168 2 0.00
169 30 0.05
170 163 0.27
171 268 0.45
172 128 0.22
173 3 0.01
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.35
Consensus pattern (169 bp):
TGACTATAAATAGACTTTTCTTGTCAATGGATATCTTTTTCTTCACATTTCTCGAGGTAAGCATT
CAATTATAATCTATTTTAATAAAAAATATAAAAAATTCTACTTAAAGTCAATTATGAGATTATAA
AAACATTTAAAGCGAGTAATAAGGCTTTGAAGGCATAGG
Found at i:19006 original size:171 final size:171
Alignment explanation
Indices: 18163--19160 Score: 542
Period size: 171 Copynumber: 5.8 Consensus size: 171
18153 NNNNNNNNNN
* * * * ** *
18163 TAATAAAAAATATAAAAACATTCTACTTAAAGTCAATTATGATATTATAAAAAT-ATTTAAAGTG
1 TAATAAAAAATATAAAAAGATTCAACTTAAAATCAATTAGGAGGTTAT-AAAATCATTTAAAG-C
** * * * ** *
18227 AA-TAATAAGGCTTTTGAAGGCGTGAGTGACTATAAATGGACTTTTAGTGTCAATGGATATCTTT
64 AAGTAATAAGGCTTTCAAAGGCATGAGTGACTATCAATGGACTTCTCTTGCCAATGGATATCTTT
* ** * * *********** *
18291 TTCTTTACATTTCTCGAGGTAGATATTCANNNNNNNNNNATTT
129 TTCTTCATGTTTCTCGAGGAAGACATTCAATTATAATCTGTCT
* * *
18334 TAATAAAAAATATAAAAACATTCAACTTAAAATCAATTAAGAGGTTATAAAATCATTTAAAGCTA
1 TAATAAAAAATATAAAAAGATTCAACTTAAAATCAATTAGGAGGTTATAAAATCATTTAAAGCAA
* ********** * * * * * *
18399 GTAAGAANNNNNNNNNNGGCATGGGTGACTATAAATAGACTTTTCTTGACAATGGATTTCTTTTT
66 GTAATAAGGCTTTCAAAGGCATGAGTGACTATCAATGGACTTCTCTTGCCAATGGATATCTTTTT
* * * * *
18464 CTTCACGTTTCTCAAGGTAG-CATTCTATTATAATCTGTTT
131 CTTCATGTTTCTCGAGGAAGACATTCAATTATAATCTGTCT
* * * * * * *
18504 TAATAAAAATTGTAAAAAAAAACTCAACTTAAAATCAATTATGAGCTTATAAAATCATTTAAACC
1 TAATAAAAA--ATATAAAAAGATTCAACTTAAAATCAATTAGGAGGTTATAAAATCATTTAAAGC
********* * * * * ** **
18569 AAGTAATAAGGCTTTNNNNNNNNNNG-GTGATTATAAATGGACTTTTCCTAACAAT-GAGTGGCT
64 AAGTAATAAGGCTTT-CAAAGGCATGAGTGACTATCAATGGACTTCTCTTGCCAATGGA-TATCT
* ** * * *
18632 TTTTCTTAACATTTATCGA-GACAGACATTCAATTATTAGCTG-CTT
127 TTTTCTTCATGTTTCTCGAGGA-AGACATTCAATTATAATCTGTC-T
*** * * * * * * *
18677 TACCCAAAAATATGAAAAA-ATTTAACTTAAAATCATTTATGAGATTGTAAAACCATTTAAAGCG
1 TAATAAAAAATAT-AAAAAGATTCAACTTAAAATCAATTAGGAGGTTATAAAATCATTTAAAGCA
* * * * ***********
18741 AG-AATAAAGCTTTCGAAGGCATGGGTGACTATAAATGNNNNNNNNNNACCAATGGATATCTTTT
65 AGTAATAAGGCTTTCAAAGGCATGAGTGACTATCAATGGACTTCTCTTGCCAATGGATATCTTTT
18805 TCTTCATGTTTCTCGAGGAAGACATTCAATTATAATCTGTCT
130 TCTTCATGTTTCTCGAGGAAGACATTCAATTATAATCTGTCT
* * **
18847 TAATAAAAAATATAAAACA-ATTTAGCTTAAAATCAATTAGGAGGTTATAAAATCATTTAAAGTG
1 TAATAAAAAATATAAAA-AGATTCAACTTAAAATCAATTAGGAGGTTATAAAATCATTTAAAGCA
* ** * * * *
18911 ATTAATAAGGCTTTTGAAGGCATGCGTGATTA-CAAATGGACTTTTCTTGCTAATGGATATCTTT
65 AGTAATAAGGCTTTCAAAGGCATGAGTGACTATC-AATGGACTTCTCTTGCCAATGGATATCTTT
* * ** * *
18975 TTCTTCATTTTTCTTGAGGTTGACATTCAATTATAATTTGTTT
129 TTCTTCATGTTTCTCGAGGAAGACATTCAATTATAATCTGTCT
* ********** *
19018 TAATAAAGAATATAAAAAGATTCAACTTNNNNNNNNNNATGAGGTTATAAAATCATTTAAAGCAA
1 TAATAAAAAATATAAAAAGATTCAACTTAAAATCAATTAGGAGGTTATAAAATCATTTAAAGCAA
*
19083 GTAATAAGGCTTTCAAAGGTATGAGTGACTATCAATGGACTTCTCTTGCCAATGGATATCTTTTT
66 GTAATAAGGCTTTCAAAGGCATGAGTGACTATCAATGGACTTCTCTTGCCAATGGATATCTTTTT
19148 CTTCATGTTTCTC
131 CTTCATGTTTCTC
19161 TAGGTAGGCA
Statistics
Matches: 629, Mismatches: 179, Indels: 38
0.74 0.21 0.04
Matches are distributed among these distances:
169 5 0.01
170 137 0.22
171 356 0.57
172 105 0.17
173 26 0.04
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.34
Consensus pattern (171 bp):
TAATAAAAAATATAAAAAGATTCAACTTAAAATCAATTAGGAGGTTATAAAATCATTTAAAGCAA
GTAATAAGGCTTTCAAAGGCATGAGTGACTATCAATGGACTTCTCTTGCCAATGGATATCTTTTT
CTTCATGTTTCTCGAGGAAGACATTCAATTATAATCTGTCT
Found at i:19608 original size:171 final size:171
Alignment explanation
Indices: 19421--19772 Score: 383
Period size: 171 Copynumber: 2.1 Consensus size: 171
19411 NNNNNNNNNN
* * * * *
19421 CATAATTGACTTTAAG-TAGAATGTTTTT-ATATTTTTTATTAAAATAGATTATAACTGAATGCC
1 CATAATTGATTTTAAGTTA-AAT-TTTTTCACATTTTTGAGTAAAATAGATAATAACTGAATGCC
*
19484 TACCTCAGA-AAACATGAAGAAAAAGAT-ATTCGTTGGAAAGAAAAG-TCTACTTATAGTAACCC
64 TACCTCA-ACAAACATGAAGAAAAAG-TCATTCATTGGAAAGAAAAGTTC-ACTTATAGTAACCC
* ** ** *
19546 ATGCCTTCAAAAGCCTTATTACTCGCTTTAAAT-AGTTCTATAATCT
126 ACGCAGTCAAAAGCCTTATTACTCAATTTAAATGA-TTCTATAACCT
* * * * *
19592 CATAAATGATTTTAAGTTAAATTTTTTCACATTTTTGGGTAAAATAGATAATAATTGAATGTCTG
1 CATAATTGATTTTAAGTTAAATTTTTTCACATTTTTGAGTAAAATAGATAATAACTGAATGCCTA
* ** ** * *
19657 TCTCAACAAATGTGAAGAAAAAGTCATTCATTGTTAAGAAAAGTTCATTTATAGTCACCCACGCA
66 CCTCAACAAACATGAAGAAAAAGTCATTCATTGGAAAGAAAAGTTCACTTATAGTAACCCACGCA
*
19722 GTCAAAAGCCTTATTACTCAATTTAAATGATTTTATAACCT
131 GTCAAAAGCCTTATTACTCAATTTAAATGATTCTATAACCT
19763 CATAATTGAT
1 CATAATTGAT
19773 NNNNNNNNNN
Statistics
Matches: 149, Mismatches: 26, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
170 7 0.05
171 137 0.92
172 5 0.03
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (171 bp):
CATAATTGATTTTAAGTTAAATTTTTTCACATTTTTGAGTAAAATAGATAATAACTGAATGCCTA
CCTCAACAAACATGAAGAAAAAGTCATTCATTGGAAAGAAAAGTTCACTTATAGTAACCCACGCA
GTCAAAAGCCTTATTACTCAATTTAAATGATTCTATAACCT
Found at i:21038 original size:171 final size:171
Alignment explanation
Indices: 20838--21158 Score: 466
Period size: 171 Copynumber: 1.9 Consensus size: 171
20828 AAAACCTCAT
* * * *
20838 TACTTGCTTCAAATGTTTTTATTATCTCATAATTGATTTT-AAGTTTAATTTTTTTACATTTTGG
1 TACTCGCTTCAAATGCTTTTATAATCTCATAATTGATTTTGAA-TTGAATTTTTTTACATTTTGG
* * *
20902 GCTAAAACAGATAATAATTGAATATCTACCTT-GAGAAGCATGAAGAAAAAGATATCCACTGGCA
65 GCTAAAACAGATAATAATTGAATATATACCTTAG-GAAACATGAAAAAAAAGATATCCACTGGCA
*
20966 TGAAAAGTCCATTTATAGTCACCGATGCCTTCAAAAGCCTTAG
129 AGAAAAGTCCATTTATAGTCACCGATGCCTTCAAAAGCCTTAG
* * * *
21009 TACTCGCTTTAAATGCTTTTATAATCTCATAATTGTTTTTGAATTGAATTTTTTTACGTTTTTGG
1 TACTCGCTTCAAATGCTTTTATAATCTCATAATTGATTTTGAATTGAATTTTTTTACATTTTGGG
* * * *
21074 TTAAAAGAGATAATAATTGAATGTATACCTTAGGAAACATGAAAAAAAAGATATCCATTGGCAAG
66 CTAAAACAGATAATAATTGAATATATACCTTAGGAAACATGAAAAAAAAGATATCCACTGGCAAG
21139 AAAAGTCCATTTATAGTCAC
131 AAAAGTCCATTTATAGTCAC
21159 NNNNNNNNNN
Statistics
Matches: 132, Mismatches: 16, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
171 129 0.98
172 3 0.02
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (171 bp):
TACTCGCTTCAAATGCTTTTATAATCTCATAATTGATTTTGAATTGAATTTTTTTACATTTTGGG
CTAAAACAGATAATAATTGAATATATACCTTAGGAAACATGAAAAAAAAGATATCCACTGGCAAG
AAAAGTCCATTTATAGTCACCGATGCCTTCAAAAGCCTTAG
Found at i:21803 original size:171 final size:162
Alignment explanation
Indices: 21626--21954 Score: 328
Period size: 172 Copynumber: 2.0 Consensus size: 162
21616 AGAATAGTCT
* * * **
21626 ATTTATAGTCACCCATGCCTT-TAAA-TGCCTTATTACTCACTTTAAATGTTTTTATGGTCC-CA
1 ATTTATAGTCACCCATGCCTTCGAAAGTG--TTATTAATCACTTTAAATGGTTTTAT-AACCTCA
* * *
21688 TAATTGATTTTAAGTTGAA-TTTTTTTAT-ATTTCTGGA-TAAAACAGATAATAATTGTATATCT
63 TAACTGATTTTAAGTTGAATTTTTTTTATAATTT-T-GATTAAAAAAGATAATAATTGAATATCT
21750 GCCTCGAAAAACATGAAGAAAAAGATATCCATTAGCNNNNNNNNNNC
126 GCCTCGAAAAACATGAAGAAAAAGATATCCATTAGC----------C
* ** *
21797 ATTTATAGTCACTCATGCCTTCGAAAGTGTTATTAATCGTTTTAAATGGTTTTATAACCTCCTAA
1 ATTTATAGTCACCCATGCCTTCGAAAGTGTTATTAATCACTTTAAATGGTTTTATAACCTCATAA
* * *
21862 CTGATTTTAAGTTGAATTTTTTTTATAATTTTTATTAAAAAAGATAATAATTGAATGTCTGCCTT
66 CTGATTTTAAGTTGAATTTTTTTTATAATTTTGATTAAAAAAGATAATAATTGAATATCTGCCTC
* *
21927 GGAAAACATGAAGAAAATGATATCCATT
131 GAAAAACATGAAGAAAAAGATATCCATT
21955 GG
Statistics
Matches: 135, Mismatches: 17, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
170 2 0.01
171 62 0.46
172 65 0.48
173 6 0.04
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.39
Consensus pattern (162 bp):
ATTTATAGTCACCCATGCCTTCGAAAGTGTTATTAATCACTTTAAATGGTTTTATAACCTCATAA
CTGATTTTAAGTTGAATTTTTTTTATAATTTTGATTAAAAAAGATAATAATTGAATATCTGCCTC
GAAAAACATGAAGAAAAAGATATCCATTAGCC
Done.