Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399905.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3139.0, 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: 8312
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.33
Warning! 967 characters in sequence are not A, C, G, or T
Found at i:300 original size:170 final size:170
Alignment explanation
Indices: 1--2052 Score: 1302
Period size: 172 Copynumber: 12.0 Consensus size: 170
* * * *
1 AAAATCAATTATGAGATTATAAAACTATTTATAGTGAGTAATAAGGCTTTTGAAAGAATAAGTGA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGA
* * * **
66 GTATAAATGGACTTTTCTTGCCAATGAATG-CGTTCTTCTTCACGTTTTTCAAGACA-AGCATTC
66 CTATAAATGGACTTTTCTTGCCAATGAATGTC-TTTTTCTTCACGTTTCTCAAGGTAGA-CATTC
*
129 AATTATAGTTTTTTTTTAA-GAAAATGTAAAAAAATTCAACTT
129 AATTATAG-TTTTTTTTAACAAAAATGTAAAAAAATTCAACTT
* * * * * * * *
171 ATAATCAGTTATGAGATTACAAAGCCATTTATAGCAAGTAATAAGACTTTTGAAGGAATGAGTGA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGA
* * * * *
236 CAATAAATAGGA-TTTTTTTGCCAATGAATGCCTTTTTCTTCACGTTTCCCAATGTAGACATTCA
66 CTATAAAT-GGACTTTTCTTGCCAATGAATGTCTTTTTCTTCACGTTTCTCAAGGTAGACATTCA
* * * *
300 ATTATAATTTGTTTTAACCAAAATAGTAAGAAAAATTGAACTT
130 ATTATAGTTTTTTTTAACAAAAAT-GTAA-AAAAATTCAACTT
* * ********** * **
343 AAAATCAATTTTGAGATTATAAAACCATTTAAATCGAGNNNNNNNNNNTTTGAAGGAATGAAAGA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGA
* * * *
408 CTATAAATGGACTTTTCTTGCCAATGAATG-CTTCTTCCTTCATGTTTCTCAAGTTAGACATTTA
66 CTATAAATGGACTTTTCTTGCCAATGAATGTCTT-TTTCTTCACGTTTCTCAAGGTAGACATTCA
* * * *
472 ATTATAGTATGTTTTAATGAAAAATGTAAACAAATTCAACTT
130 ATTATAGTTTTTTTTAA-CAAAAATGTAAAAAAATTCAACTT
**************** *
514 AAAATCAATTANNNNNNNNNNNNNNNNTTTAAAGCGAGTAATAAGGCTTTTGAAGGAATTG-GTG
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAA-TGAGTG
* * * * * * * *
578 ACTATAAATAGATTTTTCTTGCTAATGAAAG-CTTTTTCTTAATGTTTCTCAACGTAGGCATTCA
65 ACTATAAATGGACTTTTCTTGCCAATGAATGTCTTTTTCTTCACGTTTCTCAAGGTAGACATTCA
*** * * *
642 GCAATAGTCTATTTTAACCAAAA-GTATAAAAGAATTCAACTT
130 ATTATAGTTTTTTTTAACAAAAATGTA-AAAA-AATTCAACTT
* * *
684 AAAATCAATTATGAGAATATAAAACCATTTAAAGCGAGCAATAAGGCTTTAGAAAGAATGAGTGA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGA
* * * * ** * *
749 CTATGACTGAACTTTTCTTGCCAATGAATGTCTTTTTCTGCTGGTTTCTCGAGGTAGACGTTCAA
66 CTATAAATGGACTTTTCTTGCCAATGAATGTCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAA
* * * * * *
814 TTATAATCTATTTTAAATAAAAATATAAAAAAATACAACTT
131 TTATAGT-TTTTTTTAACAAAAATGTAAAAAAATTCAACTT
** * * *
855 ---A--AA--ATGAGATTATAAAAGTATTTAAAGTGAGCAATAAGGCTTTTGAAAGAATGAGTGT
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGA
* * * * **
913 CTATAAATGAACTTTTCTTGCTAATAAATGTGTTTTTCTTCTA-GTTTCTTGAGGTAGACATTCA
66 CTATAAATGGACTTTTCTTGCCAATGAATGTCTTTTTCTTC-ACGTTTCTCAAGGTAGACATTCA
* * *
977 ATTATAGTTTGTTTAAACCAAAAATATAAAAAACAATTCAACTT
130 ATTATAGTTTTTTTTAA-CAAAAATGT-AAAAA-AATTCAACTT
* ********** * *
1021 AAAATCAATTATGAGATTATAAACCCATTNNNNNNNNNNAATAAGGCTTTTGAAGGAATAAGTGA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGA
* * * *
1086 CTATAAATGGACTTTTATTGCCAATGAATGTCTTTTTCTTCATGTTTTTCGAGGTAGACATTCAA
66 CTATAAATGGACTTTTCTTGCCAATGAATGTCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAA
* * * *
1151 TTATAGCTTGTTTTATCCAAAAA-GATAAATAAAATTCTACTT
131 TTATAGTTTTTTTTA-ACAAAAATG-TAAA-AAAATTCAACTT
* * * * *
1193 AAAATCAATTTTGAGATTATAAAATCATTGAAAGCGCGTAATAAGGCTTTTGAAAGAATAAGTGA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGA
** * * * * ** *
1258 CTATAAATGGACTTTTCTTGCCCGTGAATATTTTTTTCTTCACATTTGTTGAGGTAGACTTTCAA
66 CTATAAATGGACTTTTCTTGCCAATGAATGTCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAA
* * * * * **
1323 TTATA-ATCTGTTTAACCAAAAATATAAACAAATTTGACTT
131 TTATAGTTTTTTTTAA-CAAAAATGTAAAAAAATTCAACTT
* * ** * **
1363 AAAATGAATTATGAGATTATAAAACTATTTAAAGTAAGTACTAATACTTTTGAAAGAATTG-GT-
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAA-TGAGTG
* * * * * * * * *
1426 ATCTATAACTAGACTTTT-TTTCTCAATAAATGGCATTCTCTAT-ACGTTT-TCCAAGCTAGATA
65 A-CTATAAATGGACTTTTCTTGC-CAATGAATGTCTTTTTCT-TCACGTTTCT-CAAGGTAGACA
* * * *
1488 TTCAATTAAAGTCTGTTTTAA-AGACAAATGTAAAAAAATTTAACTT
126 TTCAATTATAGTTTTTTTTAACA-A-AAATGTAAAAAAATTCAACTT
* * * * * ********** *
1534 ATAATCAATTATGCGATTACAAAATCATTTAAAGTGAGTAATAAGGCNNNNNNNNNNATGGGTGA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGA
* * * ** * * *
1599 CAACAAATAGACTTTTCTTATCAATGAATGCCTTTTTCTTCACGTTTCTCAATGTAGATATTCAA
66 CTATAAATGGACTTTTCTTGCCAATGAATGTCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAA
* * * * * *
1664 TTATAATCTGTTTTAATCAAAAAAGT--TAAAATTTAACTT
131 TTATAGTTTTTTTTAA-CAAAAATGTAAAAAAATTCAACTT
* * * * * *
1703 AAAATCAATTTTGAGACTATAAAACCATTTAAAGTGAGCAATAAGGCTTTTGAAGGAATGGGT-A
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGA
* * ** * ** * *
1767 ATAATAAATGGTCTTTT-TATGGTAATGAATGTATTTTTCTTCATATTTCTTAACGTAGACATTC
66 CT-ATAAATGGACTTTTCT-TGCCAATGAATGTCTTTTTCTTCACGTTTCTCAAGGTAGACATTC
* * * * * * *
1831 AGTTATAATATGTTTTAACCAAAAAAGGAAAAAAAATTAAACTT
129 AATTATAGTTTTTTTTAA-C-AAAAATGTAAAAAAATTCAACTT
* ********** * * *
1875 AAAATCAATTTTGAGATTATNNNNNNNNNNAAATCGAGTAATAAGGCTTTTGAAGGAATGAGAGA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGA
* * * * * * * * * * *
1940 GTATAAGTGGGCTTTTCTTACCAATGAATAAT-TTTTTCTTCGCATCTCTTAAGATAGACATTTA
66 CTATAAATGGACTTTTCTTGCCAATGAAT-GTCTTTTTCTTCACGTTTCTCAAGGTAGACATTCA
* * *
2004 ATTATAGTATGTTTTAATGAAAAATGT-AAAAAATTCAACTT
130 ATTATAGTTTTTTTTAA-CAAAAATGTAAAAAAATTCAACTT
2045 AAAATCAA
1 AAAATCAA
2053 NNNNNNNNNN
Statistics
Matches: 1446, Mismatches: 380, Indels: 112
0.75 0.20 0.06
Matches are distributed among these distances:
163 7 0.00
164 118 0.08
165 5 0.00
166 11 0.01
168 6 0.00
169 146 0.10
170 358 0.25
171 279 0.19
172 387 0.27
173 129 0.09
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.35
Consensus pattern (170 bp):
AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGA
CTATAAATGGACTTTTCTTGCCAATGAATGTCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAA
TTATAGTTTTTTTTAACAAAAATGTAAAAAAATTCAACTT
Found at i:911 original size:164 final size:166
Alignment explanation
Indices: 694--1350 Score: 511
Period size: 173 Copynumber: 3.9 Consensus size: 166
684 AAAATCAATT
* *
694 ATGAGAATATAAAACCATTTAAAGCGAGCAATAAGGCTTTAGAAAGAATGAGTGACTATGACTGA
1 ATGAGAATATAAAACCATTTAAAGCGAGCAATAAGGCTTTAGAAAGAATGAGTGACTATAAATGA
* * *
759 ACTTTTCTTGCCAATGAATGTCTTTTTCTGCTGGTTTCTCGAGGTAGACGTTCAATTATAATCTA
66 ACTTTTCTTGCCAATAAATGTCTTTTTCTGCTAGTTTCTCGAGGTAGACATTCAATTATAAT-T-
*
824 T-TTTAAA-TAAAAATAT-AAAAA-AATACAACTTAAA
129 TGTTTAAACCAAAAATATAAAAAACAATACAACTTAAA
* ** * * *
858 ATGAGATTATAAAAGTATTTAAAGTGAGCAATAAGGCTTTTGAAAGAATGAGTGTCTATAAATGA
1 ATGAGAATATAAAACCATTTAAAGCGAGCAATAAGGCTTTAGAAAGAATGAGTGACTATAAATGA
* * * * *
923 ACTTTTCTTGCTAATAAATGTGTTTTTCTTCTAGTTTCTTGAGGTAGACATTCAATTATAGTTTG
66 ACTTTTCTTGCCAATAAATGTCTTTTTCTGCTAGTTTCTCGAGGTAGACATTCAATTATAATTTG
*
988 TTTAAACCAAAAATATAAAAAACAATTCAACTTAAAATCAA
131 TTTAAACCAAAAATATAAAAAACAATACAACTT---A--AA
* * ********** * * *
1029 TTATGAGATTATAAACCCATTNNNNNNNNNNAATAAGGCTTTTGAAGGAATAAGTGACTATAAAT
1 --ATGAGAATATAAAACCATTTAAAGCGAGCAATAAGGCTTTAGAAAGAATGAGTGACTATAAAT
* * * * * **
1094 GGACTTTTATTGCCAATGAATGTCTTTTTCTTC-ATGTTTTTCGAGGTAGACATTCAATTATAGC
64 GAACTTTTCTTGCCAATAAATGTCTTTTTCTGCTA-GTTTCTCGAGGTAGACATTCAATTATAAT
* * * * * *
1158 TTGTTTTATCCAAAAAGATAAATAA-AATTCTACTTAAAATCA
128 TTGTTTAAACCAAAAATATAAAAAACAATACAACTT--AA--A
* * * * * * *
1200 ATTTTGAGATTATAAAATCATTGAAAGCGCGTAATAAGGCTTTTGAAAGAATAAGTGACTATAAA
1 A---TGAGAATATAAAACCATTTAAAGCGAGCAATAAGGCTTTAGAAAGAATGAGTGACTATAAA
* ** * * * * * * * *
1265 TGGACTTTTCTTGCCCGTGAATATTTTTTTCTTC-ACATTTGTTGAGGTAGACTTTCAATTATAA
63 TGAACTTTTCTTGCCAATAAATGTCTTTTTCTGCTA-GTTTCTCGAGGTAGACATTCAATTATAA
*
1329 TCTGTTT-AACCAAAAATATAAA
127 TTTGTTTAAACCAAAAATATAAA
1351 CAAATTTGAC
Statistics
Matches: 401, Mismatches: 75, Indels: 27
0.80 0.15 0.05
Matches are distributed among these distances:
162 1 0.00
163 7 0.02
164 119 0.30
165 5 0.01
166 9 0.02
169 3 0.01
171 19 0.05
172 116 0.29
173 122 0.30
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.35
Consensus pattern (166 bp):
ATGAGAATATAAAACCATTTAAAGCGAGCAATAAGGCTTTAGAAAGAATGAGTGACTATAAATGA
ACTTTTCTTGCCAATAAATGTCTTTTTCTGCTAGTTTCTCGAGGTAGACATTCAATTATAATTTG
TTTAAACCAAAAATATAAAAAACAATACAACTTAAA
Found at i:3283 original size:171 final size:171
Alignment explanation
Indices: 2372--5447 Score: 1898
Period size: 171 Copynumber: 18.0 Consensus size: 171
2362 NNNNNNNNNN
* * *
2372 AAAATCATTTAAAGCGCGTAATAAGGCTTTTGAAAGAATAAGTGACTATAAATGGACTTTTCTCG
1 AAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAATGGACTTTTCTTG
* * * * * * * * *
2437 CCCATGAATATTTTTTTCTTTACGTTTCTTGAGATAGACATTCAATTATTA-TTTG-TTTAACAA
66 CCAATGAATGTCTTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTA-TAGTCTGTTTTAACTA
* * *
2500 AAAATATAAAAAAATTCAACTTAAAATGAATTATGAGATTAT
130 AAAATGTAAAAAAATACAACTTAAAATCAATTATGAGATTAT
****************** * * * *
2542 AAAANNNNNNNNNNNNNNNNNNAATGCTTTTGAAAGAATGGGTGTCTATAAATAGACTTTTCTT-
1 AAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAATGGACTTTTCTTG
* * * * ** * * * *
2606 CTCAATAAATGGT-ATTTTCTACATGTTTC-CTAAGCCAAATATTCAATTAAATTCTGTTTTAA-
66 C-CAATGAAT-GTCTTTTTCTTCATGTTTCTC-GAGGTAGACATTCAATTATAGTCTGTTTTAAC
* * * * *
2668 TGAAAAATATAAAAAAATTCAATTTATAATCAATTATGAGATTAC
128 T-AAAAATGTAAAAAAATACAACTTAAAATCAATTATGAGATTAT
* * * * * * * * **
2713 AAAACCATTTAAAGCGAGGACTAAGCCTTTTGAAGGAATGTGTGGCAATAAATAAACTTTTTCTA
1 AAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAATGGAC-TTTTCT-
* * * * * * * * *
2778 T--CAATGAATGGCTTTTTCTTCACGTTTCTCAATGTAAAGATTCAATTATAATATGTTTTAACC
64 TGCCAATGAATGTCTTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAACT
********* ** *
2841 ANNNNNNNNNNAAAAATTGAACTTAAAATCAATT-TAAAGATTAT
129 A-AAAATGTAAAAAAATACAACTTAAAATCAATTAT-GAGATTAT
* * ********* * *
2885 AAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGGACT-ANNNNNNNNNNAATAGATTTTTCTT
1 AAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGA-GTGACTATAAATGGACTTTTCTT
* * * * * * * * *
2949 ACTAATGAAT-ACATTTTTCTTCATGTTT-TCCAATGTAGACGTTCAGTTATAATATGTTTTAA-
65 GCCAATGAATGTC-TTTTTCTTCATGTTTCT-CGAGGTAGACATTCAATTATAGTCTGTTTTAAC
* * *
3011 TCAAAAAAGTAAAAAAGAATTA-AACTTGAAATCAATTTTGAGATTAT
128 T-AAAAATGT-AAAAA-AA-TACAACTTAAAATCAATTATGAGATTAT
* * * *
3058 AAAA-CTATTTAAATCTAGTAATAAGGTTTTTG-AAGAAATGAGAGACTATAAATGGACTTTTCT
1 AAAATC-ATTTAAAGCGAGTAATAAGGCTTTTGAAAG-AATGAGTGACTATAAATGGACTTTTCT
* * * * * *
3121 AGCCAATGAATATATTTTTCTTCAGGTTTCTCGAGGTAGACATTCAATTATAGTCTATTTTAACG
64 TGCCAATGAATGTCTTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAACT
* * *
3186 AAAAATGTAAAAAAATACGACTTAAAATTAATCATGAGATTAT
129 AAAAATGTAAAAAAATACAACTTAAAATCAATTATGAGATTAT
** * * * * * *
3229 AAAATCATTTGCAGCGAGTAATAAAGTTTTTCAAAGAATGAGTGAATGTAAATGGACTTTTCTTA
1 AAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAATGGACTTTTCTTG
* ** * * * * * * *
3294 TCAATGAATACCTTCTTT-TTCATGTTTTTTGAGGCAGGCATTCAATTATACTCTATTTTAACAA
66 CCAATGAATGTCTT-TTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAACTA
* * * * * * *
3358 AAAATGTAAACAAATTCAAGTTAAAATTAACTATAAGATTAC
130 AAAATGTAAAAAAATACAACTTAAAATCAATTATGAGATTAT
* * *** * **
3400 AAAATTAGTTAAAATAAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGA-TTTGTCCC
1 AAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAATGGACTTT-TCTT
* * ** * * ** *
3464 GCCAATGAATG-CCTTTTCTTCACGTTTCTTAATGTAGGCATTCAACAATAGTTTGTTTTAA-TG
65 GCCAATGAATGTCTTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAACT-
* * * * *
3527 AAAAATATAAAAAAATATAACTCAAAATTAATTATTAGATTAT
129 AAAAATGTAAAAAAATACAACTTAAAATCAATTATGAGATTAT
* ** * ** *
3570 AAAACCATTTACAA-TAAGTAATATGGCTTTTGAAAGAATGAGTGGGTATAAATAGACTTTTCTT
1 AAAATCATTTA-AAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAATGGACTTTTCTT
* * * * * * *
3634 ACCAATGAATGTCTTTTTCTTAAGGTTTTTTGAGGCAGACATTCGATTATAGTCTGTTTTAACTA
65 GCCAATGAATGTCTTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAACTA
*
3699 AAACTGTAAAAAAATACAACTTAAAATCAATTATGAGATTAT
130 AAAATGTAAAAAAATACAACTTAAAATCAATTATGAGATTAT
* * * * *
3741 AACA-CTATTTACAGCGAGTAATAATGG-TTTTGAAAAAATGAGTGAGTATAAATGCACTTTTCT
1 AAAATC-ATTTAAAGCGAGTAATAA-GGCTTTTGAAAGAATGAGTGACTATAAATGGACTTTTCT
* * ** * ** * * *
3804 TACTAATGAATGTCTTTTTCTTCACATTTTTTAAGGTAGAAATTCAATTATAGTCAGTTTTAACA
64 TGCCAATGAATGTCTTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAACT
* * * * *
3869 AAAAATATGAACAAATTCAACTTAAAATCATTTATGAGATTAT
129 AAAAATGTAAAAAAATACAACTTAAAATCAATTATGAGATTAT
* * * * *
3912 AAAATCATTTAAAGCCAATAATAAGGCTTTT-AAAGGAATG-GATAACTATAAATGGATTTTTTT
1 AAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAA-GAATGAG-TGACTATAAATGGACTTTTCT
* * ** *
3975 TGTCAATGAATG-CCTTTTCTTCATGTTTCTCGAGGTA-AGCATTCAACAATAGTCTCTTTTAAC
64 TGCCAATGAATGTCTTTTTCTTCATGTTTCTCGAGGTAGA-CATTCAATTATAGTCTGTTTTAAC
* ** * *
4038 TAAAAATAT-AAAAAATTTAACTCAAAATCAATTATGAGATCAT
128 TAAAAATGTAAAAAAATACAACTTAAAATCAATTATGAGATTAT
* * * * * * *
4081 AAAA-CAATTTACAGCAAGCAATAAGGCTTTTGAAAGATTGAGTGAGTATAAATAGACTTTTTTT
1 AAAATC-ATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAATGGACTTTTCTT
* * * * *
4145 GCTAATAAATGTCTTTTTCTTCATGTTTTTTGAGGTA-AGTATTCAATTATAGTCTGTTTTAAC-
65 GCCAATGAATGTCTTTTTCTTCATGTTTCTCGAGGTAGA-CATTCAATTATAGTCTGTTTTAACT
* * * *
4208 AAAAAGGTAAAAAAATTCAACCTAAAATCAATTATGAAATTAT
129 AAAAATGTAAAAAAATACAACTTAAAATCAATTATGAGATTAT
* * * *********** *
4251 AAAATCATTTAAAGTGTGTAATAAAGCTTTANNNNNNNNNNGTGACTATAAATGGATTTTTCTTG
1 AAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAATGGACTTTTCTTG
* * * * *
4316 CCAATGAATATCTTTTTCTTCATGTTTTTTC-AGGTAAACATACAATTATAATCTGTTTTAACTA
66 CCAATGAATGTCTTTTTCTTCATG-TTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAACTA
* * **********
4380 AAAATGTAAACAAATTCAACTTAAAATCNNNNNNNNNNTTAT
130 AAAATGTAAAAAAATACAACTTAAAATCAATTATGAGATTAT
* * * * *
4422 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAATGAATGGGTGAATATAAATAGACTTTTCTTG
1 AAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAATGGACTTTTCTTG
* * * * * * * * *
4487 CCAATGAATCTCTTTTTCTTCATATTTCTCAAGGCAGACATTCAATTATATTCTATTTTGACCAC
66 CCAATGAATGTCTTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAACTAA
** * *
4552 AAATGTAAAAAAAAAATTGAACTTAAAATCAATTTTAAGATTAT
131 AAATGT---AAAAAAATACAACTTAAAATCAATTATGAGATTAT
* * * *
4596 AAAA-CTATTTAAAGTGAGTAATATGCCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTT
1 AAAATC-ATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAATGGACTTTTCTT
* * * *
4660 GCCAATGACTGTCTTTTTCTTCATATTTCTCGAGGTAGACATTCAATTACAGTCTGTTTTAACCA
65 GCCAATGAATGTCTTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAACTA
* * **
4725 AAAATGT-GAAATATTTAACTTAAAATCAATTATGAGATTAT
130 AAAATGTAAAAAAATACAACTTAAAATCAATTATGAGATTAT
**************************
4766 AAAA-CTATTT-AA---AG---NNNNNNNNNNNNNNNNNNNNNNNNNNATAAATGGACTTTTCTT
1 AAAATC-ATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAATGGACTTTTCTT
* * * * *
4823 GCCAATGAATG-CTTTTTTCTTCATGTTTCTTGAGTTAAACATTCAATTATAGTTTGTTTTAACC
65 GCCAATGAATGTC-TTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAACT
* * ** *
4887 CAAAATAT-AAAAAATTTAACTTAAAATCAGTTATGAGATTAT
129 AAAAATGTAAAAAAATACAACTTAAAATCAATTATGAGATTAT
* * * * * *
4929 AAAACCATTTAAAGCGAGAAATAATGCTTTTGAAAGAATTG-GTGACTAGAAATAGATCTTTTTT
1 AAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAA-TGAGTGACTATAAATGGA-CTTTTCT
* * * * *
4993 TGTCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGAC-TGTCAATTATAGTCTATTTTAAG
64 TGCCAATGAATGTCTTTTTCTTCATGTTTCTCGAGGTAGACAT-TCAATTATAGTCTGTTTTAAC
* * * * *
5057 TAAAACTATAAAACAATTCAACTTAAAATCAATTATGAGCTTAT
128 TAAAAATGTAAAAAAATACAACTTAAAATCAATTATGAGATTAT
* * * ********** * * *
5101 AAAATCATTTGAAGTGACTANNNNNNNNNNTGAAGGAATGAGTGACTATAAATATGACTTTTTTT
1 AAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAAT-GGACTTTTCTT
* * * * *
5166 GCCAATGAATGTCTTTTTATTCAAGTTTCTAGAGGTAGACATTCAATTATAGTTTATTTTAA-TC
65 GCCAATGAATGTCTTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAACT-
* *
5230 AAAAATGCAAAAAAAATACAACTTGAAATCAATTATGAGATTAT
129 AAAAATG-TAAAAAAATACAACTTAAAATCAATTATGAGATTAT
* * *
5274 AAAA-CTATTTACAA-TGAGTAATAAGGCTTTTGAAAGAATGAGTGTGC-ATAAATAGACTTTTC
1 AAAATC-ATTTA-AAGCGAGTAATAAGGCTTTTGAAAGAATGAGTG-ACTATAAATGGACTTTTC
* * * * * * * * *
5336 -TGATCAATGAATGCCTTTTTCTTCACGTTTTTAGAGGTAGGCATTCAATTATAGTTTATTTTAT
63 TTG-CCAATGAATGTCTTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAA
* * **
5400 CCAAAAATGTAAACAAATTGAACTTAAAATCAATTATGAGATTAT
127 CTAAAAATGTAAAAAAATACAACTTAAAATCAATTATGAGATTAT
5445 AAA
1 AAA
5448 NNNNNNNNNN
Statistics
Matches: 2229, Mismatches: 591, Indels: 171
0.75 0.20 0.06
Matches are distributed among these distances:
162 1 0.00
163 117 0.05
164 3 0.00
166 2 0.00
167 2 0.00
168 1 0.00
169 98 0.04
170 479 0.21
171 849 0.38
172 343 0.15
173 185 0.08
174 149 0.07
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.36
Consensus pattern (171 bp):
AAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAATGGACTTTTCTTG
CCAATGAATGTCTTTTTCTTCATGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAACTAA
AAATGTAAAAAAATACAACTTAAAATCAATTATGAGATTAT
Found at i:3995 original size:341 final size:339
Alignment explanation
Indices: 2378--4779 Score: 1645
Period size: 341 Copynumber: 7.0 Consensus size: 339
2368 NNNNAAAATC
** * * *
2378 ATTTAAAGCGCGTAATAAGGCTTTTGAAAGAATAAGTGACTATAAATGGACTTTTCTCGCCCATG
1 ATTTAAAGCAAGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAAT-GACTTTTCTTGCCAATG
* * * * * **
2443 AATATTTTTTTCTTTACGTTTCTTGAGATAGACATTCAATTATTA-TTTG-TTTAACAAAAAATA
65 AATGTCTTTTTCTTCACGTTTCTTAAGGTAGACATTCAATTA-TAGTCAGTTTTAACAAAAAATA
* ****************** *
2506 TAAAAAAATTCAACTTAAAATGAATTATGAGATTATAAAANNNNNNNNNNNNNNNNNNAATGCTT
129 TAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTT
* * * * * * *
2571 TTGAAAGAATGGGTGTCTATAAATAGACTTTTCTT-CTCAATAAATGGTATTTTCTACATGTTTC
194 TTGAAAGAAT-GATGACTATAAATGGACTTTTCTTGC-CAATGAATGCT-TTTTCTTCATGTTTT
* * ** * * * * * * *
2635 CTAAGCCAAATATTCAATTAAATTCTGTTTTAA-TGAAAAATATAAAAAAATTCAATTTATAATC
256 TTGAGGTAGACATTCAATTATAGTCTGTTTTAACT-AAAAATGTAAAAAAATTCAACTTAAAATC
* *
2699 AATTATGAGATTACAAAACC
320 AATTATGAGATTATAAAACT
* * * * * * * * *
2719 ATTTAAAGCGAGGACTAAGCCTTTTGAAGGAATGTGTGGCAATAAATAAACTTTTTCTAT--CAA
1 ATTTAAAGCAAGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAAT-GAC-TTTTCT-TGCCAA
* * * * * * ****
2782 TGAATGGCTTTTTCTTCACGTTTCTCAATGTAAAGATTCAATTATAAT-ATGTTTTAACCANNNN
63 TGAATGTCTTTTTCTTCACGTTTCTTAAGGTAGACATTCAATTATAGTCA-GTTTTAA-CAAAAA
****** * *
2846 NNNNNNAAAAATTGAACTTAAAATCAATT-TAAAGATTATAAAATCATTTAAAGCGAGTAATAAG
126 ATATAAAAAAATTCAACTTAAAATCAATTAT-GAGATTATAAAATCATTTAAAGCGAGTAATAAG
* * ******** * * * * *
2910 GCTTTTGAAGGACT-ANNNNNNNNNNAATAGATTTTTCTTACTAATGAATACATTTTTCTTCATG
190 GCTTTTGAAAGAATGA--TGACTATAAATGGACTTTTCTTGCCAATGAATGC-TTTTTCTTCATG
*** * * * * * * *
2974 TTTTCCAATGTAGACGTTCAGTTATAATATGTTTTAA-TCAAAAAAGTAAAAAAGAATTAAACTT
252 TTTTTTGAGGTAGACATTCAATTATAGTCTGTTTTAACT-AAAAATGT-AAAAA-AATTCAACTT
* *
3038 GAAATCAATTTTGAGATTATAAAACT
314 AAAATCAATTATGAGATTATAAAACT
* * * * *
3064 ATTTAAATCTAGTAATAAGGTTTTTG-AAGAAATGAGAGACTATAAATGGACTTTTCTAGCCAAT
1 ATTTAAAGCAAGTAATAAGGCTTTTGAAAG-AATGAGTGACTATAAAT-GACTTTTCTTGCCAAT
* * * ** *
3128 GAATATATTTTTCTTCAGGTTTCTCGAGGTAGACATTCAATTATAGTCTA-TTTTAACGAAAAAT
64 GAATGTCTTTTTCTTCACGTTTCTTAAGGTAGACATTCAATTATAGTC-AGTTTTAACAAAAAAT
* * * * * ** * *
3192 GTAAAAAAATACGACTTAAAATTAATCATGAGATTATAAAATCATTTGCAGCGAGTAATAAAGTT
128 ATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCT
* * * ** *
3257 TTTCAAAGAATGAGTGAATGTAAATGGACTTTTCTTATCAATGAATACCTTCTTT-TTCATGTTT
193 TTTGAAAGAATGA-TGACTATAAATGGACTTTTCTTGCCAATGAAT-GCTT-TTTCTTCATGTTT
* * * * * * * *
3321 TTTGAGGCAGGCATTCAATTATACTCTATTTTAACAAAAAATGTAAACAAATTCAAGTTAAAATT
255 TTTGAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATC
* * * *
3386 AACTATAAGATTACAAAATT
320 AATTATGAGATTATAAAACT
* ** * **
3406 AGTTAAAATAAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGA-TTTGTCCCGCCAAT
1 ATTTAAAGCAAGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAAT-GACTTT-TCTTGCCAAT
* * * ** ** **
3470 GAATG-CCTTTTCTTCACGTTTCTTAATGTAGGCATTCAACAATAGTTTGTTTTAATGAAAAATA
64 GAATGTCTTTTTCTTCACGTTTCTTAAGGTAGACATTCAATTATAGTCAGTTTTAACAAAAAATA
* * * * ** *
3534 TAAAAAAATAT-AACTCAAAATTAATTATTAGATTATAAAACCATTTACAA-TAAGTAATATGGC
129 TAAAAAAAT-TCAACTTAAAATCAATTATGAGATTATAAAATCATTTA-AAGCGAGTAATAAGGC
** * * * *
3597 TTTTGAAAGAATGAGTGGGTATAAATAGACTTTTCTTACCAATGAATGTCTTTTTCTTAAGGTTT
192 TTTTGAAAGAATGA-TGACTATAAATGGACTTTTCTTGCCAATGAATG-CTTTTTCTTCATGTTT
* * * *
3662 TTTGAGGCAGACATTCGATTATAGTCTGTTTTAACTAAAACTGTAAAAAAATACAACTTAAAATC
255 TTTGAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATC
*
3727 AATTATGAGATTATAACACT
320 AATTATGAGATTATAAAACT
* * * * * *
3747 ATTTACAGCGAGTAATAATGG-TTTTGAAAAAATGAGTGAGTATAAATGCACTTTTCTTACTAAT
1 ATTTAAAGCAAGTAATAA-GGCTTTTGAAAGAATGAGTGACTATAAATG-ACTTTTCTTGCCAAT
* * *
3811 GAATGTCTTTTTCTTCACATTTTTTAAGGTAGAAATTCAATTATAGTCAGTTTTAACAAAAAATA
64 GAATGTCTTTTTCTTCACGTTTCTTAAGGTAGACATTCAATTATAGTCAGTTTTAACAAAAAATA
* * * * *
3876 TGAACAAATTCAACTTAAAATCATTTATGAGATTATAAAATCATTTAAAGCCAATAATAAGGCTT
129 TAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTT
* * * * * *
3941 TT-AAAGGAATGGATAACTATAAATGGATTTTTTTTGTCAATGAATGCCTTTTCTTCATGTTTCT
194 TTGAAA-GAAT-GATGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTCTTCATGTTTTT
* ** * * * *
4005 CGAGGTA-AGCATTCAACAATAGTCTCTTTTAACTAAAAATAT-AAAAAATTTAACTCAAAATCA
257 TGAGGTAGA-CATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCA
* *
4068 ATTATGAGATCATAAAACA
321 ATTATGAGATTATAAAACT
* * * * * * *
4087 ATTTACAGCAAGCAATAAGGCTTTTGAAAGATTGAGTGAGTATAAATAGACTTTTTTTGCTAATA
1 ATTTAAAGCAAGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAAT-GACTTTTCTTGCCAATG
* * * * * **
4152 AATGTCTTTTTCTTCATGTTTTTTGAGGTA-AGTATTCAATTATAGTCTGTTTTAAC-AAAAAGG
65 AATGTCTTTTTCTTCACGTTTCTTAAGGTAGA-CATTCAATTATAGTCAGTTTTAACAAAAAATA
* * * * *
4215 TAAAAAAATTCAACCTAAAATCAATTATGAAATTATAAAATCATTTAAAGTGTGTAATAAAGCTT
129 TAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTT
********* * *
4280 TANNNNNNNNNNG-TGACTATAAATGGATTTTTCTTGCCAATGAATATCTTTTTCTTCATGTTTT
194 T--TGAAAGAATGATGACTATAAATGGACTTTTCTTGCCAATGAAT-GCTTTTTCTTCATGTTTT
* * * * * *
4344 TTCAGGTAAACATACAATTATAATCTGTTTTAACTAAAAATGTAAACAAATTCAACTTAAAATCN
256 TTGAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCA
********* *
4409 NNNNNNNNNTTATAAAACC
321 ATTATGAGATTATAAAACT
* * * *
4428 ATTTAAAGCGAGTAATAAGGCTTTTGAATGAATGGGTGAATATAAATAGACTTTTCTTGCCAATG
1 ATTTAAAGCAAGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAAT-GACTTTTCTTGCCAATG
* ** * * * * **
4493 AATCTCTTTTTCTTCATATTTCTCAAGGCAGACATTCAATTATATTCTA-TTTTGACCACAAATG
65 AATGTCTTTTTCTTCACGTTTCTTAAGGTAGACATTCAATTATAGTC-AGTTTT-AACA-AAAAA
* * * * * *
4557 TAAAAAAAAAATTGAACTTAAAATCAATTTTAAGATTATAAAA-CTATTTAAAGTGAGTAATATG
127 T-ATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATC-ATTTAAAGCGAGTAATAAG
* * * *
4621 CCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGACTGTCTTTTTCTTCATAT
190 GCTTTTGAAAGAAT-GATGACTATAAATGGACTTTTCTTGCCAATGAATG-CTTTTTCTTCATGT
* * * * * * *
4686 TTCTCGAGGTAGACATTCAATTACAGTCTGTTTTAACCAAAAATGT-GAAATATTTAACTTAAAA
253 TTTTTGAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAA
4750 TCAATTATGAGATTATAAAACT
318 TCAATTATGAGATTATAAAACT
4772 ATTTAAAG
1 ATTTAAAG
4780 NNNNNNNNNN
Statistics
Matches: 1572, Mismatches: 431, Indels: 113
0.74 0.20 0.05
Matches are distributed among these distances:
339 93 0.06
340 192 0.12
341 517 0.33
342 226 0.14
343 118 0.08
344 172 0.11
345 253 0.16
347 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.36
Consensus pattern (339 bp):
ATTTAAAGCAAGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAATGACTTTTCTTGCCAATGA
ATGTCTTTTTCTTCACGTTTCTTAAGGTAGACATTCAATTATAGTCAGTTTTAACAAAAAATATA
AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTT
GAAAGAATGATGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTCTTCATGTTTTTTGAG
GTAGACATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTAT
GAGATTATAAAACT
Found at i:6432 original size:165 final size:165
Alignment explanation
Indices: 6212--6519 Score: 363
Period size: 165 Copynumber: 1.9 Consensus size: 165
6202 TTATAATCCC
* * * *
6212 AAAATTAATTTTAAGTTAAACTTTTTTACATTTTTGGTTAAAACAGATAATAATTGACCATCTAC
1 AAAATTAATTTTAAGTTAAACTTTTTTACATTTGTAGTCAAAACAGATAATAATTGAACATCTAC
* * * * *
6277 CTAGAGAAACGTTAAGAAAAA-TACATTCATCGGCAAGAAAAGTCTA-TTATAGTCAC-CAATTC
66 CTAGAGAAACGTGAAGAAAAAGGA-ATTCATCAGCAAAAAAAGTCCATTTATAGTCACTC-ATTC
*
6339 CTTCAAAAGCTTTATTACTCTCTTTAATTGTAATCTA
129 CTTCAAAAGCCTTATTACTCTCTTTAATTGTAATCTA
* ** * ** *
6376 AAAATTGATTTTAAGTTTAATTTTTTTTACATTTGTAGTCAAAATAGA-ATATAATTGAATGTTT
1 AAAATTAATTTTAAG-TTAAACTTTTTTACATTTGTAGTCAAAACAGATA-ATAATTGAACATCT
** * *
6440 ACCTTTAGAAACGTGAAGAAAAAGGAATTCATTAGCAAAAAAAGTCCATTTATAGTCGCTCATTC
64 ACCTAGAGAAACGTGAAGAAAAAGGAATTCATCAGCAAAAAAAGTCCATTTATAGTCACTCATTC
6505 CTTCAAAAGCCTTAT
129 CTTCAAAAGCCTTAT
6520 NNNNNNNNNN
Statistics
Matches: 118, Mismatches: 21, Indels: 8
0.80 0.14 0.05
Matches are distributed among these distances:
164 15 0.13
165 74 0.63
166 28 0.24
167 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (165 bp):
AAAATTAATTTTAAGTTAAACTTTTTTACATTTGTAGTCAAAACAGATAATAATTGAACATCTAC
CTAGAGAAACGTGAAGAAAAAGGAATTCATCAGCAAAAAAAGTCCATTTATAGTCACTCATTCCT
TCAAAAGCCTTATTACTCTCTTTAATTGTAATCTA
Found at i:7530 original size:171 final size:170
Alignment explanation
Indices: 7123--8304 Score: 939
Period size: 171 Copynumber: 6.9 Consensus size: 170
7113 NNNNNNNNNN
* * * ** ** * * *
7123 TTAAAACA-AACTATAATTAAATGCCTACCTCAGGAAACGTGTTGAAAAA-ATATTTATTCGAAA
1 TTAAAACAGAA-TATAATTGAATGTCTACCTCAAGAAACGTGAAGAAAAAGGCATTCATTGGCAA
* ** * * * *
7186 GAAAAGTCTATTTATAGTTTCCCATTCCTTCAAAAGCCATGTTACTCGCTTTAAATAGTTTTATA
65 GAAAAGTCCATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACT-GCTTTAAATGGTTTTATA
* * * *
7251 ATCTCATAATT-AATTTAAGTT-AAATTTGTTTACATTTTTAG
129 ATCTCATAATTGATTTTAAGTTGAATTTTTTTTACA-TTTTGG
**** * * *
7292 TTAAAACAG-ATAATAATTGCCCATCTA-CTAAGAGAAACGTAAAGAAAAATGCATTCATTGGCA
1 TTAAAACAGAAT-ATAATTGAATGTCTACCTCA-AGAAACGTGAAGAAAAAGGCATTCATTGGCA
* * *
7355 AGAAAAGTTCA-TTATAGTCACTCATTCCTTCAAAAGCCTTATTACTGACTTTAATTAGTTTTAT
64 AGAAAAGTCCATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACTG-CTTTAAATGGTTTTAT
* * *
7419 AATATCAAAATTGATTTTAAGTTCAATTTTTTTTACATTTGTGG
128 AATCTCATAATTGATTTTAAGTTGAATTTTTTTTACATTT-TGG
* * * * * * *
7463 TTAAAATAGAATATAATTTAATGTCTACCTCAAGAAATGTAAAGAAAAAGGGATTCCTTAGCAAG
1 TTAAAACAGAATATAATTGAATGTCTACCTCAAGAAACGTGAAGAAAAAGGCATTCATTGGCAAG
* * * * * ***
7528 AAAAGTTCATTTATCGTCGCCCATTCCTTCAAAAGCATTATTACTGGCTTTAAATGGTTTTANNN
66 AAAAGTCCATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACT-GCTTTAAATGGTTTTATAA
******* * *
7593 NNNNNNNATTGATTTTAAGTTGAATTTGTTTATA-ATTTTGA
130 TCTCATAATTGATTTTAAGTTGAATTT-TTTTTACATTTTGG
* * * **
7634 TTAAAACA-AACTATAATTGAATGTCTGCCTC-AGAAAATGTGAAGAAAAATGCATTCATTGATA
1 TTAAAACAGAA-TATAATTGAATGTCTACCTCAAG-AAACGTGAAGAAAAAGGCATTCATTGGCA
* ********* *
7697 AGAAAAGTCCATTTATAGTCACTCATTCTTTCAAAAGCCTTNNNNNNNNNNTTAAGTGGTTTTAT
64 AGAAAAGTCCATTTATAGTCACTCATTCCTTCAAAAGCCTT-ATTACTGCTTTAAATGGTTTTAT
* *
7762 AATCTCATAGTTGATTTTAAGTT-AAATTTTTTTACATTTTGG
128 AATCTCATAATTGATTTTAAGTTGAATTTTTTTTACATTTTGG
* * * * *
7804 TTAAAACAGACTATAATTGAATGTCTACCTTAAAAAACCTGAAGAAAAAGACATGT-ATTGGCAA
1 TTAAAACAGAATATAATTGAATGTCTACCTCAAGAAACGTGAAGAAAAAGGCAT-TCATTGGCAA
** * * * * * * *
7868 GAAAAGTTTATTTATAGCCACTTATTCTTTTAAAAGCCTTATTGCTCGCATTAAATAGTTTTATA
65 GAAAAGTCCATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACT-GCTTTAAATGGTTTTATA
* * * * *
7933 ATCTCATAATTGATTATAAGTTTAATTCTTTTATA-TTTTTGA
129 ATCTCATAATTGATTTTAAGTTGAATT-TTTTTTACATTTTGG
* ** ** *
7975 TTAAAACAGACTATTGTTGAATG-CTTACCTTGAGAAACGTGAAG-AAAAGGAATTCATT-G-AT
1 TTAAAACAGAATATAATTGAATGTC-TACCTCAAGAAACGTGAAGAAAAAGGCATTCATTGGCA-
* * * * *
8036 AGAAAAATCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTTACATTGAATGGTTTTAT
64 AGAAAAGTCCATTTATAGTCACTCATTCCTTCAAAAGCCTTATTAC-TGCTTTAAATGGTTTTAT
* * *
8101 AACCTCATAATTGATTTTAAGTTGAA-TTTATTTACACTTTTAG
128 AATCTCATAATTGATTTTAAGTTGAATTTTTTTTACA-TTTTGG
* * * * *
8144 TTAAAACAGACTATAATTGAATG-CTTGCATC-AGAAAACGTGAAGAAAATGGCATTCCTTGGCA
1 TTAAAACAGAATATAATTGAATGTC-TACCTCAAG-AAACGTGAAGAAAAAGGCATTCATTGGCA
* * * * *
8207 AGAAAAGTCCATTTATACG-CACTCATTCTTTCAAAAGCGTTAATATTCGCTGTAAATGGTTTTA
64 AGAAAAGTCCATTTATA-GTCACTCATTCCTTCAAAAGCCTTATTACT-GCTTTAAATGGTTTTA
8271 TAATCTCATAATTGATTTTAAGTTGAATTTTTTT
127 TAATCTCATAATTGATTTTAAGTTGAATTTTTTT
8305 ACTTTTTT
Statistics
Matches: 797, Mismatches: 180, Indels: 69
0.76 0.17 0.07
Matches are distributed among these distances:
167 5 0.01
168 9 0.01
169 207 0.26
170 183 0.23
171 302 0.38
172 85 0.11
173 6 0.01
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.37
Consensus pattern (170 bp):
TTAAAACAGAATATAATTGAATGTCTACCTCAAGAAACGTGAAGAAAAAGGCATTCATTGGCAAG
AAAAGTCCATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACTGCTTTAAATGGTTTTATAAT
CTCATAATTGATTTTAAGTTGAATTTTTTTTACATTTTGG
Found at i:8269 original size:510 final size:512
Alignment explanation
Indices: 7123--8311 Score: 1196
Period size: 510 Copynumber: 2.3 Consensus size: 512
7113 NNNNNNNNNN
* * * * * ** *
7123 TTAAAACAAACTATAATTAAATGCCTACCTCAGGAAACGTGTTGAAAAAAT--ATTTATTCGA-A
1 TTAAAACAAACTATAATTGAATGTCTGCATCAGAAAACGTGAAG-AAAAATGCATTCATT-GACA
* ** * * * ** * *
7185 AGAAAAGTCTATTTATAGTTTCCCATTCCTTCAAAAGCCAT-GTTACTCGCTTTAAATAGTTTTA
64 AGAAAAGTCCATTTATAGTCACTCATTCTTTCAAAAGCCTTAAATATTCGC-TTAAATGGTTTTA
* * **
7249 TAATCTCATAATT-AATTTAAGTTAAATTTGTTTACATTTTTAGTTAAAACAGATAATAATTGCC
128 TAATCTCATAATTGATTTTAAGTTAAATTTTTTTACA-TTTTAGTTAAAACAGATAATAATTGAA
* *
7313 CATCTACTAAGAGAAACGTAAAGAAAAATGCATTCATTGGCAAGAAAAGTTCATTATAGTCACTC
192 CATCTACTAAGAGAAACCTAAAGAAAAATGCATTCATTGGCAAGAAAAGTTCATTATAGCCACTC
* * *
7378 ATTCCTTCAAAAGCCTTATTACTGACTTTAATTAGTTTTATAATATCAAAATTGATTTTAAGTTC
257 ATTCCTTCAAAAGCCTTATTACTGACATTAAATAGTTTTATAATATCAAAATTGATTATAAGTTC
* * * * *
7443 AATTTTTTTTACATTTGTGGTTAAAATAGAATATAATTTAATGTCTACCTCAAGAAATGTAAAGA
322 AATTTCTTTTACATTTGTGATTAAAACAGAATATAATTGAATGTCTACCTCAAGAAACGTAAAGA
* * * * * *
7508 AAAAGGGATTCCTTAGCAAGAAAAGTTCATTTATCGTCGCCCATTCCTTCAAAAGCATTATTACT
387 AAAAGGAATTCATTAGCAAGAAAAATCCATTTATAGTCACCCATTCCTTCAAAAGCATTATTACT
* * ********** * *
7573 GGCTTTAAATGGTTTTANNNNNNNNNNATTGATTTTAAGTTGAATTTGTTTATAATTTTGA
452 GACATTAAATGGTTTTATAACCTCATAATTGATTTTAAGTTGAATTTATTTACAATTTTGA
* * *
7634 TTAAAACAAACTATAATTGAATGTCTGCCTCAGAAAATGTGAAGAAAAATGCATTCATTGATAAG
1 TTAAAACAAACTATAATTGAATGTCTGCATCAGAAAACGTGAAGAAAAATGCATTCATTGACAAG
********** *
7699 AAAAGTCCATTTATAGTCACTCATTCTTTCAAAAGCCTTNNNNNNNNNNTTAAGTGGTTTTATAA
66 AAAAGTCCATTTATAGTCACTCATTCTTTCAAAAGCCTTAAATATTCGCTTAAATGGTTTTATAA
* * **
7764 TCTCATAGTTGATTTTAAGTTAAATTTTTTTACATTTTGGTTAAAACAGACT-ATAATTGAATGT
131 TCTCATAATTGATTTTAAGTTAAATTTTTTTACATTTTAGTTAAAACAGA-TAATAATTGAACAT
* *
7828 CTACCTTAA-A-AAACCTGAAGAAAAA-GACATGT-ATTGGCAAGAAAAGTTTATTTATAGCCAC
195 CTA-C-TAAGAGAAACCTAAAGAAAAATG-CAT-TCATTGGCAAGAAAAGTTCA-TTATAGCCAC
* * * * * *
7889 TTATTCTTTTAAAAGCCTTATTGCTCG-CATTAAATAGTTTTATAATCTCATAATTGATTATAAG
255 TCATTCCTTCAAAAGCCTTATTACT-GACATTAAATAGTTTTATAATATCAAAATTGATTATAAG
* * * * ** ** *
7953 TTTAA-TTCTTTTATATTTTTGATTAAAACAGACTATTGTTGAATG-CTTACCTTGAGAAACGTG
319 TTCAATTTCTTTTACATTTGTGATTAAAACAGAATATAATTGAATGTC-TACCTCAAGAAACGTA
*
8016 AAG-AAAAGGAATTCATT-G-ATAGAAAAATCCATTTATAGTCACCCATTCCTTCAAAAGCCTTA
383 AAGAAAAAGGAATTCATTAGCA-AGAAAAATCCATTTATAGTCACCCATTCCTTCAAAAGCATTA
* * *
8078 TTACTTACATTGAATGGTTTTATAACCTCATAATTGATTTTAAGTTGAATTTATTTACACTTTT-
447 TTACTGACATTAAATGGTTTTATAACCTCATAATTGATTTTAAGTTGAATTTATTTACAATTTTG
8142 A
512 A
* * *
8143 GTTAAAACAGACTATAATTGAATG-CTTGCATCAGAAAACGTGAAG-AAAATGGCATTCCTTGGC
1 -TTAAAACAAACTATAATTGAATGTC-TGCATCAGAAAACGTGAAGAAAAAT-GCATTCATTGAC
*
8206 AAGAAAAGTCCATTTATACG-CACTCATTCTTTCAAAAGCGTT-AATATTCGCTGTAAATGGTTT
63 AAGAAAAGTCCATTTATA-GTCACTCATTCTTTCAAAAGCCTTAAATATTCGCT-TAAATGGTTT
* *
8269 TATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACTTTTT
126 TATAATCTCATAATTGATTTTAAGTTAAATTTTTTTACATTTT
8312 T
Statistics
Matches: 555, Mismatches: 104, Indels: 39
0.80 0.15 0.06
Matches are distributed among these distances:
509 9 0.02
510 227 0.41
511 54 0.10
512 170 0.31
513 91 0.16
514 4 0.01
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.37
Consensus pattern (512 bp):
TTAAAACAAACTATAATTGAATGTCTGCATCAGAAAACGTGAAGAAAAATGCATTCATTGACAAG
AAAAGTCCATTTATAGTCACTCATTCTTTCAAAAGCCTTAAATATTCGCTTAAATGGTTTTATAA
TCTCATAATTGATTTTAAGTTAAATTTTTTTACATTTTAGTTAAAACAGATAATAATTGAACATC
TACTAAGAGAAACCTAAAGAAAAATGCATTCATTGGCAAGAAAAGTTCATTATAGCCACTCATTC
CTTCAAAAGCCTTATTACTGACATTAAATAGTTTTATAATATCAAAATTGATTATAAGTTCAATT
TCTTTTACATTTGTGATTAAAACAGAATATAATTGAATGTCTACCTCAAGAAACGTAAAGAAAAA
GGAATTCATTAGCAAGAAAAATCCATTTATAGTCACCCATTCCTTCAAAAGCATTATTACTGACA
TTAAATGGTTTTATAACCTCATAATTGATTTTAAGTTGAATTTATTTACAATTTTGA
Done.