Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397381.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_589.0, 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: 32778
ACGTcount: A:0.25, C:0.09, G:0.09, T:0.25
Warning! 10753 characters in sequence are not A, C, G, or T
Found at i:6920 original size:170 final size:170
Alignment explanation
Indices: 6428--7413 Score: 792
Period size: 171 Copynumber: 5.8 Consensus size: 170
6418 NNNNNNNNNN
* * * * * * * * * *
6428 AAATGGACTCTTCTTCTCAATGAATGGCTTTTTCTTTACGTTTCTTAAGGTAGATATTCAATTGT
1 AAATAGACTTTTCTTGTCAATGAATAGCTTTTCCTTCACATTTCTTAAGGCAGACATTCAATTAT
* * * * * * **
6493 AATATGTTTTAACTAAAAATGTAAAATTATTCAACTTAAAATCAATTATAAGATTACGAAACCAT
66 AATCTATTTTAACCAAAAATATAAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAACCAT
* * * * ** *
6558 TTAAAG-AAATAATAAGGCTTTCGAAGGGTTG-GATGACCAT
130 TTAAAGTGAGTAATAAGGCTTTTGAAAGAATGAG-TGACTAT
* * * * * * * *
6598 AAATGGACTTTT-TGTATCAAT-AGATGGCTTTTGCTTCACGTTTCTCCAA-GAAAACATTCAAT
1 AAATAGACTTTTCT-TGTCAATGA-ATAGCTTTTCCTTCACATTTCT-TAAGGCAGACATTCAAT
* ** * * *
6660 TATAATATATTTTAGTCAAAAATGTAAAAAAAATTCAACTTAAAATCAGTTAAG-GTATTATAAA
63 TATAATCTATTTTAACCAAAAA--TATAAAAAATTCAACTTAAAATCAATTATGAG-ATTATAAA
* * * * *
6724 ACTATTTAAAATGAGTCATGAGGCTTTTG-AAGAAATGAGTCACTAT
125 ACCATTTAAAGTGAGTAATAAGGCTTTTGAAAG-AATGAGTGACTAT
* * * * * * *
6770 AAATGGACTTTTCTTGTCAATGACTACCTTTTCCTTCACATTTTTTGAGGCAGACGTTCAATCAT
1 AAATAGACTTTTCTTGTCAATGAATAGCTTTTCCTTCACATTTCTTAAGGCAGACATTCAATTAT
* * * *
6835 AATCTGTTTTAACAAAAAATATGAAAAAATTCAACCTAAAATCAATTATGAGA-TATAAAATCAT
66 AATCTATTTTAACCAAAAATAT-AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCAT
* * * * * *
6899 TTAAAGTGAGTAATAAGGCTTTTGAAGGTATAAATGGCTAG
130 TTAAAGTGAGTAATAAGGCTTTTGAAAGAATGAGTGACTAT
** * * *
6940 AAATAGACTTTTCTCATCAATGAAT-GGTTGTTCCTTCAAATTTCTTAAGGCAGACAATCAATTA
1 AAATAGACTTTTCTTGTCAATGAATAGCTT-TTCCTTCACATTTCTTAAGGCAGACATTCAATTA
* * * *
7004 TAATCTATTTTAACCAAAAATACAAAAAAACTCAACTTAAAATCAATTATGAGATAATAAAGCCA
65 TAATCTATTTTAACCAAAAATA-TAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCA
* *
7069 TTTAAAGTGAGTAATAAGGCATTTGAAAGAATCAGTGACTAT
129 TTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGAGTGACTAT
* * * * * * * ** * *
7111 AAATAGACTCTTCCTCTGAATGAATAGCTTTTTCTAT-GCGTTTCCAAAGGTAGACATTCAATTG
1 AAATAGACTTTTCTTGTCAATGAATAGCTTTTCCT-TCACATTTCTTAAGGCAGACATTCAATTA
* * * *
7175 TAATCTATTTTAACCAAAAATGTAAAATTATTCAACTTAAAATAAATTATAAGATTATAAAACCA
65 TAATCTATTTTAACCAAAAATATAAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAACCA
** * **
7240 TTTAAAGCAATTAATAAGGCTTTTGAAAGGTTGAGTGACTAT
129 TTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGAGTGACTAT
* * * * * * *
7282 AAATGGACTTTTTTTGTCAAT-AGATAGCTTTTGCTTTACGTTTCCCTAA-GCAAACATTCAATT
1 AAATAGACTTTTCTTGTCAATGA-ATAGCTTTTCCTTCACATTT-CTTAAGGCAGACATTCAATT
* * ** *
7345 ACAATATATTTTAGTC-AAAATATAAAAAAATTCAATTTAAAATCAATTATGAGATTATAAAACC
64 ATAATCTATTTTAACCAAAAATAT-AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACC
7409 ATTTA
128 ATTTA
7414 NNNNNNNNNN
Statistics
Matches: 646, Mismatches: 145, Indels: 50
0.77 0.17 0.06
Matches are distributed among these distances:
169 4 0.01
170 250 0.39
171 296 0.46
172 93 0.14
173 3 0.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (170 bp):
AAATAGACTTTTCTTGTCAATGAATAGCTTTTCCTTCACATTTCTTAAGGCAGACATTCAATTAT
AATCTATTTTAACCAAAAATATAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATT
TAAAGTGAGTAATAAGGCTTTTGAAAGAATGAGTGACTAT
Found at i:7244 original size:342 final size:340
Alignment explanation
Indices: 6428--7413 Score: 920
Period size: 342 Copynumber: 2.9 Consensus size: 340
6418 NNNNNNNNNN
* *
6428 AAATGGACTCTTCTTCTCAATGAATGGCTTTTTCTTTACGTTTCTTAAGGTAGATATTCAATTGT
1 AAATGGACTCTTCTTCTCAATGAATAGCTTTTTC-TTACGTTTCTTAAGGTAGACATTCAATTGT
* * **
6493 AATATGTTTTAACTAAAAATGTAAAATTATTCAACTTAAAATCAATTATAAGATTACGAAACCAT
65 AATCTGTTTTAACAAAAAATGTAAAATTATTCAACTTAAAATCAATTATAAGATTATAAAACCAT
* ** * * *
6558 TTAAAGAAATAATAAGGCTTTCGAAGGGTTGGATGACCATAAATGGACTTTTTGTATCAATAGAT
130 TTAAAGAAATAATAAGGCTTTTGAAGGGTTAAATGACCAGAAATAGACTTTTTGCATCAATAGAT
* ** * **
6623 GGCTTTTGCTTCACGTTTCTCCAAGAAAACATTCAATTATAATATATTTTAGTCAAAAATGTAAA
195 GGCTTTTCCTTCAAATTTCTCCAAGAAAACAATCAATTATAATATATTTTAACCAAAAA-GTAAA
* * * * * * *
6688 AAAAATTCAACTTAAAATCAGTTAAGGTATTATAAAACTATTTAAAATGAGTCATGAGGCTTTTG
259 AAAAACTCAACTTAAAATCAATTAAGGTATAATAAAACCATTTAAAATGAGTAATAAGGCATTTG
*
6753 AAGAAATGAGTCACTAT
324 AAGAAATCAGTCACTAT
* * * * * * * * * * **
6770 AAATGGACTTTTCTTGTCAATGACTACCTTTTCCTTCACATTTTTTGAGGCAGACGTTCAATCAT
1 AAATGGACTCTTCTTCTCAATGAATAGCTTTTTCTT-ACGTTTCTTAAGGTAGACATTCAATTGT
* * * * *
6835 AATCTGTTTTAACAAAAAATATGAAAA-AATTCAACCTAAAATCAATTATGAGA-TATAAAATCA
65 AATCTGTTTTAACAAAAAATGT-AAAATTATTCAACTTAAAATCAATTATAAGATTATAAAACCA
* * * *
6898 TTTAAAGTGAGTAATAAGGCTTTTGAA-GGTATAAATGGCTAGAAATAGACTTTTCT-CATCAAT
129 TTTAAAG-AAATAATAAGGCTTTTGAAGGGT-TAAATGACCAGAAATAGACTTTT-TGCATCAAT
* * * *
6961 -GAATGG-TTGTTCCTTCAAATTTCT-TAAGGCAGACAATCAATTATAATCTATTTTAACCAAAA
191 AG-ATGGCTT-TTCCTTCAAATTTCTCCAA-GAAAACAATCAATTATAATATATTTTAACCAAAA
* * *
7023 A-TACAAAAAAACTCAACTTAAAATCAATTATGAG-ATAATAAAGCCATTTAAAGTGAGTAATAA
253 AGTA-AAAAAAACTCAACTTAAAATCAATTAAG-GTATAATAAAACCATTTAAAATGAGTAATAA
*
7086 GGCATTTGAA-AGAATCAGTGACTAT
316 GGCATTTGAAGA-AATCAGTCACTAT
* * * * **
7111 AAATAGACTCTTCCTCTGAATGAATAGCTTTTTCTATGCGTTTCCAAAGGTAGACATTCAATTGT
1 AAATGGACTCTTCTTCTCAATGAATAGCTTTTTCT-TACGTTTCTTAAGGTAGACATTCAATTGT
* * *
7176 AATCTATTTTAACCAAAAATGTAAAATTATTCAACTTAAAATAAATTATAAGATTATAAAACCAT
65 AATCTGTTTTAACAAAAAATGTAAAATTATTCAACTTAAAATCAATTATAAGATTATAAAACCAT
* * * * * * * ***
7241 TTAAAGCAATTAATAAGGCTTTTGAAAGGTTGAGTGACTATAAATGGACTTTTTTTGTCAATAGA
130 TTAAAG-AAATAATAAGGCTTTTGAAGGGTTAAATGACCAGAAATAGACTTTTTGCATCAATAGA
* * * ** * * * **
7306 TAGCTTTTGCTTTACGTTTC-CCTAAGCAAACATTCAATTACAATATATTTTAGTC-AAAA-TAT
194 TGGCTTTTCCTTCAAATTTCTCC-AAGAAAACAATCAATTATAATATATTTTAACCAAAAAGTA-
* * * *
7368 AAAAAAATTCAATTTAAAATCAATTATGAG-ATTATAAAACCATTTA
257 AAAAAAACTCAACTTAAAATCAATTAAG-GTATAATAAAACCATTTA
7414 NNNNNNNNNN
Statistics
Matches: 516, Mismatches: 108, Indels: 41
0.78 0.16 0.06
Matches are distributed among these distances:
340 7 0.01
341 227 0.44
342 269 0.52
343 13 0.03
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (340 bp):
AAATGGACTCTTCTTCTCAATGAATAGCTTTTTCTTACGTTTCTTAAGGTAGACATTCAATTGTA
ATCTGTTTTAACAAAAAATGTAAAATTATTCAACTTAAAATCAATTATAAGATTATAAAACCATT
TAAAGAAATAATAAGGCTTTTGAAGGGTTAAATGACCAGAAATAGACTTTTTGCATCAATAGATG
GCTTTTCCTTCAAATTTCTCCAAGAAAACAATCAATTATAATATATTTTAACCAAAAAGTAAAAA
AAACTCAACTTAAAATCAATTAAGGTATAATAAAACCATTTAAAATGAGTAATAAGGCATTTGAA
GAAATCAGTCACTAT
Found at i:16438 original size:170 final size:160
Alignment explanation
Indices: 16262--16569 Score: 296
Period size: 170 Copynumber: 1.9 Consensus size: 160
16252 NNNNNNNNNN
** * *
16262 AGGCTTTTAAAAGAATGGGTGACTCTAAAT-GAACTTTTCTTACTAATGAAT-CCTTTATTCTCA
1 AGGCTTTTAAAAGAATAAGTGACTATAAATAG-ACTTTT-TTACCAATGAATGCCTTTATTCTCA
* * * *
16325 CGTTTCTTGAGGTAGATATTCAATTACAGTCTGTTTCAACTAAAAACATAAAAATATTCAACTTA
64 CGTTTCTCGAGATAGACATTCAATTACAATCTGTTTCAACTAAAAACATAAAAATATTCAACTTA
16390 AAATCAATTATGAGATTANNNNNNNNNNTGAAGTGAGTAGTA
129 AAATCAATTATGAGATTA----------TGAAGTGAGTAGTA
* * * * * * *
16432 AGGCTTTTGAAGGAATAAGTGACTATGAATAGACTTTTTTGCCAATGAATGTCTTTTTTCTTACG
1 AGGCTTTTAAAAGAATAAGTGACTATAAATAGACTTTTTTACCAATGAATGCCTTTATTCTCACG
* * * * * * *
16497 TTTCTCGATATAGACATTTAATTATAATCTGTTTTAACTAAAAATATAAATATATTTAACTTAAA
66 TTTCTCGAGATAGACATTCAATTACAATCTGTTTCAACTAAAAACATAAAAATATTCAACTTAAA
16562 ATCAATTA
131 ATCAATTA
16570 NNNNNNNNNN
Statistics
Matches: 114, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
169 10 0.09
170 103 0.90
171 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.37
Consensus pattern (160 bp):
AGGCTTTTAAAAGAATAAGTGACTATAAATAGACTTTTTTACCAATGAATGCCTTTATTCTCACG
TTTCTCGAGATAGACATTCAATTACAATCTGTTTCAACTAAAAACATAAAAATATTCAACTTAAA
ATCAATTATGAGATTATGAAGTGAGTAGTA
Found at i:20309 original size:171 final size:161
Alignment explanation
Indices: 20206--20536 Score: 191
Period size: 171 Copynumber: 2.0 Consensus size: 161
20196 NNNNNNNNNN
* *
20206 TAATCTCATAATTGATTTTAAATTGAATTTTTTTA-ATTTTTTTGTTAAAACATATTTTAATTGA
1 TAATCTCATAATTGATTTTAAATTGAATTTTTTTATA-TTTTTTGTTAAAACAAATTATAATTGA
* * * * * *
20270 ATGTTTTCTTCGAGAAACGTGAAGAAAATGAAATTCATTGACAAAAAAAGTCCATTTATAGTCAC
65 ATGTCTACCTCGAGAAACATGAAGAAAAAGAAATTCATTGACAAAAAAAGTCCACTTATAGTCAC
* * * * *
20335 TTATGCTTTCACAAGCCTTGTTACTCACTTTAAATTGTTTTA
130 CTATGCCTTCAAAACCCTTATTACTCAC----------TTTA
* * * ** * * * * *
20377 TAATCTCATCATTTATTTTCAGCTGAATTGTTTTGTATTTTTAGTTAAAATAGATTATAATTGAA
1 TAATCTCATAATTGATTTTAAATTGAATTTTTTTATATTTTTTGTTAAAACAAATTATAATTGAA
* * ** * * * * *
20442 TGTTTGCCT-GAGAAAACATGAAGAAAAAGTCATTCATTGACTATAAAA-CCCATTTATAATCAC
66 TGTCTACCTCGAG-AAACATGAAGAAAAAGAAATTCATTGACAAAAAAAGTCCACTTATAGTCAC
* ** * * *
20505 CCATATCTTCGAAAGCCTTATTACTCGCTTTA
130 CTATGCCTTCAAAACCCTTATTACTCACTTTA
20537 AATAGTTTTA
Statistics
Matches: 128, Mismatches: 30, Indels: 15
0.74 0.17 0.09
Matches are distributed among these distances:
160 4 0.03
170 35 0.27
171 88 0.69
172 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (161 bp):
TAATCTCATAATTGATTTTAAATTGAATTTTTTTATATTTTTTGTTAAAACAAATTATAATTGAA
TGTCTACCTCGAGAAACATGAAGAAAAAGAAATTCATTGACAAAAAAAGTCCACTTATAGTCACC
TATGCCTTCAAAACCCTTATTACTCACTTTA
Found at i:21882 original size:341 final size:341
Alignment explanation
Indices: 20945--22095 Score: 836
Period size: 342 Copynumber: 3.4 Consensus size: 341
20935 NNAAGAAAAG
* * * * * * *
20945 GGCATTTATTGGCGAGAAAACTCCATTTGTAGTCACCCATTCCTTCTAAAA-CCTTA-TCCTCAC
1 GGCATTCATTAGCAAGAAAAGTCCATTTATAGTCACACATTCCTT-TAAAAGCCTTACTACTCAC
* ** * * * * *
21008 TGTAAACAGTTTTATAATATAATAATTAATTTTAAGTTAA-ATTTTATTATATTTTTAGTTAACA
65 TTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAATA-TTT-TTACATTTTTAGTTAAAA
* * * * * * * * * * *
21072 CATATTATAATTGAATGTCTATATCAAGAAACGTGAAGAAAAAGCCATTCATTGACTAGAAAAGC
128 CAGATTAAAATTGAATGTCTACATCAAAAAATGTAAAGGAAAAGCTACTCATTGACAAGAAAAGT
** * *********** * * * ** * *
21137 CCATTTATNNNNNNNNNNGCCGTCGAAAGCCTTATTACTTGCTTTAAA-TGATTTTGTAATCTCA
193 ATATTCATAATCACTGATTCCTTCAAAAGCCTTACTACTAACTTCAAACTG-TTTTATAATCTCA
* * * * * * * * **
21201 TTATTGATTTTAAGTTGAAT-TTTTTAAAATTTTTGATTAAAACGGGCTATAATTGCATGTCTGT
257 TAAATGATTTTAAGTTGAATATTTTT-ATATTTTTGATGAAAACAGACTATAATTGGATATCTAC
** **
21265 CTTGAGAAACGTGAAGAA-AAA
321 CTCAAGAAACAAG-AGAAGAAA
** * ** * * *
21286 GTTATTCATT-GACATGAAAAGTCCACATATAGTCACTCATTCCTTTAAATGCCTTACTACTGAC
1 GGCATTCATTAG-CAAGAAAAGTCCATTTATAGTCACACATTCCTTTAAAAGCCTTACTACTCAC
* *
21350 TTTAAATGGTTTTATAATCTAATAATTAATTTTAAGTTCAATATTTTTACATTTTTAGTTAAAAC
65 TTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTT-AATATTTTTACATTTTTAGTTAAAAC
** * **
21415 AGATTACGATTGAATGTTTACATCAGGAAATGTAAAGGAAAAGCTACTCATTGACAAGAAAAGTA
129 AGATTAAAATTGAATGTCTACATCAAAAAATGTAAAGGAAAAGCTACTCATTGACAAGAAAAGTA
* * * **********
21480 TATTTATAATCACTGATTCCTTCAAAAGCCTTATTACTCANNNNNNNNNNTTTTATAATCTCATA
194 TATTCATAATCACTGATTCCTTCAAAAGCCTTACTACTAACTTCAAACTGTTTTATAATCTCATA
* * * * * * *
21545 AATGATTTTAAGTTGATTTTTTTTTATATTTTTGATGAGAATAGACTATAATT-GATTATTTGCT
259 AATGATTTTAAGTTGA-ATATTTTTATATTTTTGATGAAAACAGACTATAATTGGA-TATCTACC
*
21609 TCAAGAAAC-A-TGAAGAAA
322 TCAAGAAACAAGAGAAGAAA
* * * * * * *
21627 GGCATTCATTGGTAA-AAAAGTCCATTTATAGTCTCCCATTCCTTCAAAACCCTTGCTACTCACT
1 GGCATTCATTAGCAAGAAAAGTCCATTTATAGTCACACATTCCTTTAAAAGCCTTACTACTCACT
* *
21691 TTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATATATTTTACATTTTTTGTTAGAAC
66 TTAAATGGTTTTATAATCTCATAATTGATTTTAAGTT-AATAT-TTTTACATTTTTAGTTAAAAC
* * * *
21756 AGATTAAAATTGAATGTCTATC-TCAAAAAATGT-GAGAGAAAAGAC-ATTCATTGGCAAGAAAT
129 AGATTAAAATTGAATGTCTA-CATCAAAAAATGTAAAG-GAAAAG-CTACTCATTGACAAGAAAA
* * * * * * *
21818 GTCTATTCATAGTCATTTATTTCTTCAAAAGCTTTACTACTAACTTCAAACTGTTTTGTAATCTC
191 GTATATTCATAATCACTGATTCCTTCAAAAGCCTTACTACTAACTTCAAACTGTTTTATAATCTC
* * * * * * * *
21883 ATAATTGATTTTGAGTTGAATATTTTTATGTTTTTGGTTAAAACAGATTGTAATTGGATGTCTAC
256 ATAAATGATTTTAAGTTGAATATTTTTATATTTTTGATGAAAACAGACTATAATTGGATATCTAC
*
21948 CTCAAGAAACAAGAGAATAAA
321 CTCAAGAAACAAGAGAAGAAA
* * * *
21969 GTCATTCATTAGCAAGAAAAGTTCATTTAAAGTCACACATTCCTTTAAAAGCCTTATTACTCACT
1 GGCATTCATTAGCAAGAAAAGTCCATTTATAGTCACACATTCCTTTAAAAGCCTTACTACTCACT
* * * * * *
22034 TTAAATGATTTTATCATCTCATAACTGATTTTAAGTTAAAATTTTTTGCATTTTTGGTTAAA
66 TTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAATA-TTTTTACATTTTTAGTTAAA
22096 NNNNNNNNNN
Statistics
Matches: 631, Mismatches: 159, Indels: 39
0.76 0.19 0.05
Matches are distributed among these distances:
340 130 0.21
341 180 0.29
342 200 0.32
343 115 0.18
344 6 0.01
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.38
Consensus pattern (341 bp):
GGCATTCATTAGCAAGAAAAGTCCATTTATAGTCACACATTCCTTTAAAAGCCTTACTACTCACT
TTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAATATTTTTACATTTTTAGTTAAAACAG
ATTAAAATTGAATGTCTACATCAAAAAATGTAAAGGAAAAGCTACTCATTGACAAGAAAAGTATA
TTCATAATCACTGATTCCTTCAAAAGCCTTACTACTAACTTCAAACTGTTTTATAATCTCATAAA
TGATTTTAAGTTGAATATTTTTATATTTTTGATGAAAACAGACTATAATTGGATATCTACCTCAA
GAAACAAGAGAAGAAA
Found at i:22055 original size:171 final size:169
Alignment explanation
Indices: 20959--22095 Score: 700
Period size: 171 Copynumber: 6.7 Consensus size: 169
20949 TTTATTGGCG
* * * * * * *
20959 AGAAAACTCCATTTGTAGTCACCCATTCCTTCTAAAA-CCTTA-TCCTCACTGTAAA-CAGTTTT
1 AGAAAAGTTCATTTATAGTCACTCATTCCTTC-AAAAGCCTTACTACTCACTTTAAATGA-TTTT
* * * * * * *
21021 ATAATATAATAATTAATTTTAAGTTAAAT-TTTATTATATTTTTAGTTAACACATATTATAATTG
64 ATAATCTCATAATTGATTTTAAGTTGAATATTT-TTATATTTTTGGTTAAAACAGATTATAATTG
** ** * *
21085 AATGTCTATATCAAGAAACGTGAAGAAAAAGCCATTCATTGACT
128 AATGTCTACCTCAAGAAACAAG-AGAAAAAGTCATTCATTG-CA
** *********** * * * ** *
21129 AGAAAAGCCCATTTATNNNNNNNNNNGCCGTCGAAAGCCTTATTACTTGCTTTAAATGATTTTGT
1 AGAAAAGTTCATTTATAGTCACTCATTCCTTCAAAAGCCTTACTACTCACTTTAAATGATTTTAT
* * * * ** *
21194 AATCTCATTATTGATTTTAAGTTGAAT-TTTTTAAAATTTTTGATTAAAACGGGCTATAATTGCA
66 AATCTCATAATTGATTTTAAGTTGAATATTTTT-ATATTTTTGGTTAAAACAGATTATAATTGAA
** ** ** *
21258 TGTCTGTCTTGAGAAACGTGAAGAAAAAGTTATTCATTGACA
130 TGTCTACCTCAAGAAACAAG-AGAAAAAGTCATTCATTG-CA
* * ** * * * *
21300 TGAAAAGTCCACATATAGTCACTCATTCCTTTAAATGCCTTACTACTGACTTTAAATGGTTTTAT
1 AGAAAAGTTCATTTATAGTCACTCATTCCTTCAAAAGCCTTACTACTCACTTTAAATGATTTTAT
* * * * * **
21365 AATCTAATAATTAATTTTAAGTTCAATATTTTTACATTTTTAGTTAAAACAGATTACGATTGAAT
66 AATCTCATAATTGATTTTAAGTTGAATATTTTTATATTTTTGGTTAAAACAGATTATAATTGAAT
* * * * * *
21430 GTTTACATCAGGAAATGTAA-AGGAAAAG-CTACTCATTGACA
131 GTCTACCTCAAGAAA--CAAGAGAAAAAGTC-ATTCATTG-CA
* * * **********
21471 AGAAAAGTAT-ATTTATAATCACTGATTCCTTCAAAAGCCTTATTACTCANNNNNNNNNNTTTTA
1 AGAAAAGT-TCATTTATAGTCACTCATTCCTTCAAAAGCCTTACTACTCACTTTAAATGATTTTA
* * * * * * * *
21535 TAATCTCATAAATGATTTTAAGTTGATTTTTTTTTATATTTTTGATGAGAATAGACTATAATTGA
65 TAATCTCATAATTGATTTTAAGTTGA-ATATTTTTATATTTTTGGTTAAAACAGATTATAATTGA
* * * * * * * * *
21600 TTATTTGCTTCAAGAAACATGA-AGAAAGGCATTCATTGGTA
129 ATGTCTACCTCAAGAAACAAGAGAAAAAGTCATTCATT-GCA
* * * * * *
21641 A-AAAAGTCCATTTATAGTCTCCCATTCCTTCAAAACCCTTGCTACTCACTTTAAATGGTTTTAT
1 AGAAAAGTTCATTTATAGTCACTCATTCCTTCAAAAGCCTTACTACTCACTTTAAATGATTTTAT
* * * *
21705 AATCTCATAATTGATTTTAAGTTGAATATATTTTACATTTTTTGTTAGAACAGATTAAAATTGAA
66 AATCTCATAATTGATTTTAAGTTGAATAT-TTTTATATTTTTGGTTAAAACAGATTATAATTGAA
* * *** *
21770 TGTCTATCTCAAAAAATGTGAGAGAAAAGACATTCATTGGCA
130 TGTCTACCTCAAGAAACAAGAGA-AAAAGTCATTCATT-GCA
* * * * * * * *
21812 AGAAATG-TCTATTCATAGTCATTTATTTCTTCAAAAGCTTTACTACTAACTTCAAACTG-TTTT
1 AGAAAAGTTC-ATTTATAGTCACTCATTCCTTCAAAAGCCTTACTACTCACTTTAAA-TGATTTT
* * * * *
21875 GTAATCTCATAATTGATTTTGAGTTGAATATTTTTATGTTTTTGGTTAAAACAGATTGTAATTGG
64 ATAATCTCATAATTGATTTTAAGTTGAATATTTTTATATTTTTGGTTAAAACAGATTATAATTGA
21940 ATGTCTACCTCAAGAAACAAGAGAATAAAGTCATTCATTAGCA
129 ATGTCTACCTCAAGAAACAAGAGAA-AAAGTCATTCATT-GCA
* * * *
21983 AGAAAAGTTCATTTAAAGTCACACATTCCTTTAAAAGCCTTATTACTCACTTTAAATGATTTTAT
1 AGAAAAGTTCATTTATAGTCACTCATTCCTTCAAAAGCCTTACTACTCACTTTAAATGATTTTAT
* * *
22048 CATCTCATAACTGATTTTAAGTT-AAAATTTTT-TGCATTTTTGGTTAAA
66 AATCTCATAATTGATTTTAAGTTGAATATTTTTAT--ATTTTTGGTTAAA
22096 NNNNNNNNNN
Statistics
Matches: 716, Mismatches: 226, Indels: 49
0.72 0.23 0.05
Matches are distributed among these distances:
168 2 0.00
169 112 0.16
170 49 0.07
171 432 0.60
172 119 0.17
173 2 0.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.38
Consensus pattern (169 bp):
AGAAAAGTTCATTTATAGTCACTCATTCCTTCAAAAGCCTTACTACTCACTTTAAATGATTTTAT
AATCTCATAATTGATTTTAAGTTGAATATTTTTATATTTTTGGTTAAAACAGATTATAATTGAAT
GTCTACCTCAAGAAACAAGAGAAAAAGTCATTCATTGCA
Found at i:25112 original size:170 final size:169
Alignment explanation
Indices: 24817--25750 Score: 920
Period size: 170 Copynumber: 5.5 Consensus size: 169
24807 NNNNNTAACT
* * * * * *
24817 AGAAAAGGCCATTTATAGTCACTC-TTGCTTTCGAAAGTCTTATTACTCGTTTTAAATGGTTTTA
1 AGAAAAGTCCATTTATAGTCACCCATT-CTTT-AAAAGCCTTATTACTCGCTTTAAATAGTTTTA
* *
24881 TAATCTCGTAATTGATTTTAAGTT-ACATTTTTTTACATTTTTAGTTTAAACA-ATCTATAATTG
64 TAATCTCATAATTGATTTTAAGTTGA-A-TTTTTTACATTTTTAGTTAAAACAGAT-TATAATTG
* * * * *
24944 AATTTGTACCTCAAAAAACAT-ACAGAAAAAGTTATTCATTGGCA
126 AATTTCTGCCTCAAGAAACATGA-AGAAAAAGTCATTCATTGACA
* * * * *
24988 AAAAAAGTCTA-TTATAGTCACCCATTCTTTTAAAAACCTTATTACTTGCTTTAAATGGTTTTAT
1 AGAAAAGTCCATTTATAGTCACCCATTC-TTTAAAAGCCTTATTACTCGCTTTAAATAGTTTTAT
*
25052 AATCTCATAATTGATTTTAAGTTGAATTCTTTTACATTTTTGGTTAAAACAGATTATAATTGAAT
65 AATCTCATAATTGATTTTAAGTTGAATT-TTTTACATTTTTAGTTAAAACAGATTATAATTGAAT
* *
25117 GTCTGCCTCAAGAAACATGAAGAAAAAGTCATTCATTGACT
129 TTCTGCCTCAAGAAACATGAAGAAAAAGTCATTCATTGACA
** * * * *
25158 AGAAAACCCCATTTATAGTCACCCATGCCTTTGAAAGGCTTATTACTCTCTTTAAATAGTTTTAT
1 AGAAAAGTCCATTTATAGTCACCCAT-TCTTTAAAAGCCTTATTACTCGCTTTAAATAGTTTTAT
* * * * *
25223 AATCTCGTAATTGATTTTAAGTTGAATTTTTTTAAATTTTTGGTTAAAATAAATTATAATTG-AT
65 AATCTCATAATTGATTTTAAGTTGAA-TTTTTTACATTTTTAGTTAAAACAGATTATAATTGAAT
* * * *
25287 TGTCTACCTCCAGAAACATGAAGAAAAAGTCGTTCATTGGCA
129 T-TCTGCCTCAAGAAACATGAAGAAAAAGTCATTCATTGACA
* * * * * * *
25329 AGAAAAGTCTACTTATAGTCACCTATTCTTTCAAACCCTTATTACTCGCTTTAAAT-GACTTTGT
1 AGAAAAGTCCATTTATAGTCACCCATTCTTTAAAAGCCTTATTACTCGCTTTAAATAG-TTTTAT
* * * *
25393 AATCTCATAATTGATTTTAAATTGAATTTTGTTACATTTTTTGTTAAAACATATTTTAATTG-AT
65 AATCTCATAATTGATTTTAAGTTGAATTTT-TTACATTTTTAGTTAAAACAGATTATAATTGAAT
* * * * * ** *
25457 TGTTTGCTTCGAGAAACGTGAAGAAAATGAAATTCATTGATA
129 T-TCTGCCTCAAGAAACATGAAGAAAAAGTCATTCATTGACA
** * * * *
25499 AGAAAAGTCCATTTATAGTCACTTATGCTTTCAAAATCCTTGTTACTCACTTTAAATAGTTTTAT
1 AGAAAAGTCCATTTATAGTCACCCATTCTTT-AAAAGCCTTATTACTCGCTTTAAATAGTTTTAT
* * * * ** * *
25564 AATCTGATAATTTATTTTCAGCTGAATGTTTTTGTATTTTTAGTTAAAATAGATTATAATTAAAT
65 AATCTCATAATTGATTTTAAGTTGAAT-TTTTTACATTTTTAGTTAAAACAGATTATAATTGAAT
* *
25629 GTT-TGCCT-TAGAAAACATGAAAAAAAAGTCATTCATTGACTA
129 -TTCTGCCTCAAG-AAACATGAAGAAAAAGTCATTCATTGAC-A
* * * *
25671 CGAAAA-CCCATTTATAG-CACCCATATCTTCAAAAGCCTTATTACTCGCTTTAAATAGTTTTAC
1 AGAAAAGTCCATTTATAGTCACCCAT-TCTTTAAAAGCCTTATTACTCGCTTTAAATAGTTTTAT
*
25734 AATCTCGTAATTGATTT
65 AATCTCATAATTGATTT
25751 NNNNNNNNNN
Statistics
Matches: 630, Mismatches: 113, Indels: 41
0.80 0.14 0.05
Matches are distributed among these distances:
169 7 0.01
170 324 0.51
171 282 0.45
172 16 0.03
173 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.40
Consensus pattern (169 bp):
AGAAAAGTCCATTTATAGTCACCCATTCTTTAAAAGCCTTATTACTCGCTTTAAATAGTTTTATA
ATCTCATAATTGATTTTAAGTTGAATTTTTTACATTTTTAGTTAAAACAGATTATAATTGAATTT
CTGCCTCAAGAAACATGAAGAAAAAGTCATTCATTGACA
Found at i:25441 original size:341 final size:339
Alignment explanation
Indices: 24814--25750 Score: 1056
Period size: 341 Copynumber: 2.7 Consensus size: 339
24804 NNNNNNNNTA
* * * *
24814 ACTAGAAAAGGCCATTTATAGTCACTCTTGCTTTCGAAAGTCTTATTACTCGT-TTTAAATGGTT
1 ACTAGAAAAGCCCATTTATAGTCACTCATGCTTTCGAAAGCCTTATTACTC-TCTTTAAATAGTT
* * *
24878 TTATAATCTCGTAATTGATTTTAAGTT-ACATTTTTTTACATTTTTAGTTTAAA-CAATCTATAA
65 TTATAATCTCGTAATTGATTTTAAGTTGA-ATTTTTTTAAATTTTTAGTTAAAATAAAT-TATAA
* * * *
24941 TTGAATT-TGTACCTCAAAAAACAT-ACAGAAAAAGTTATTCATTGGCAAAAAAAGTCTATTATA
128 TTG-ATTGTCTACCTCAAGAAACATGA-AGAAAAAGTCATTCATTGGCAAGAAAAGTCTATTATA
* * **
25004 GTCACCCATTCTTTTAAAAACCTTATTACTTGCTTTAAATGGTTTTATAATCTCATAATTGATTT
191 GTCACCCATTC-TTTCAAAACCTTATTACTCGCTTTAAATGACTTT-TAATCTCATAATTGATTT
*
25069 TAAGTTGAATTCTTTTACATTTTTGGTTAAAACAGATTATAATTGAATGTCTGCCTCAAGAAACA
254 TAAATTGAATTCTTTTACATTTTTGGTTAAAACAGATTATAATTGAATGTCTGCCTCAAGAAACA
**
25134 TGAAGAAAAAGTCATTCATTG
319 TGAAGAAAAAGAAATTCATTG
* * *
25155 ACTAGAAAACCCCATTTATAGTCACCCATGCCTTT-GAAAGGCTTATTACTCTCTTTAAATAGTT
1 ACTAGAAAAGCCCATTTATAGTCACTCATG-CTTTCGAAAGCCTTATTACTCTCTTTAAATAGTT
*
25219 TTATAATCTCGTAATTGATTTTAAGTTGAATTTTTTTAAATTTTTGGTTAAAATAAATTATAATT
65 TTATAATCTCGTAATTGATTTTAAGTTGAATTTTTTTAAATTTTTAGTTAAAATAAATTATAATT
* *
25284 GATTGTCTACCTCCAGAAACATGAAGAAAAAGTCGTTCATTGGCAAGAAAAGTCTACTTATAGTC
130 GATTGTCTACCTCAAGAAACATGAAGAAAAAGTCATTCATTGGCAAGAAAAGTCTA-TTATAGTC
* *
25349 ACCTATTCTTTCAAACCCTTATTACTCGCTTTAAATGACTTTGTAATCTCATAATTGATTTTAAA
194 ACCCATTCTTTCAAAACCTTATTACTCGCTTTAAATGACTTT-TAATCTCATAATTGATTTTAAA
* * * * * * * *
25414 TTGAATT-TTGTTACATTTTTTGTTAAAACATATTTTAATTGATTGTTTGCTTCGAGAAACGTGA
258 TTGAATTCTT-TTACATTTTTGGTTAAAACAGATTATAATTGAATGTCTGCCTCAAGAAACATGA
*
25478 AGAAAATGAAATTCATTG
322 AGAAAAAGAAATTCATTG
* * * * * *
25496 A-TAAGAAAAGTCCATTTATAGTCACTTATGCTTTCAAAATCCTTGTTACTCACTTTAAATAGTT
1 ACT-AGAAAAGCCCATTTATAGTCACTCATGCTTTCGAAAGCCTTATTACTCTCTTTAAATAGTT
* * * * ** *
25560 TTATAATCT-GATAATTTATTTTCAGCTGAATGTTTTTGTATTTTTAGTTAAAATAGATTATAAT
65 TTATAATCTCG-TAATTGATTTTAAGTTGAATTTTTTTAAATTTTTAGTTAAAATAAATTATAAT
* * * * * * * * * *
25624 TAAATGTTTGCCT-TAGAAAACATGAAAAAAAAGTCATTCATTGACTACGAAAA-CCCATTTATA
129 TGATTGTCTACCTCAAG-AAACATGAAGAAAAAGTCATTCATTGGC-AAGAAAAGTCTA-TTATA
* *
25687 G-CACCCATATC-TTCAAAAGCCTTATTACTCGCTTTAAAT-AGTTTTACAATCTCGTAATTGAT
191 GTCACCCAT-TCTTTCAAAA-CCTTATTACTCGCTTTAAATGACTTTT--AATCTCATAATTGAT
25749 TT
252 TT
25751 NNNNNNNNNN
Statistics
Matches: 511, Mismatches: 68, Indels: 34
0.83 0.11 0.06
Matches are distributed among these distances:
339 1 0.00
340 30 0.06
341 450 0.88
342 30 0.06
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.40
Consensus pattern (339 bp):
ACTAGAAAAGCCCATTTATAGTCACTCATGCTTTCGAAAGCCTTATTACTCTCTTTAAATAGTTT
TATAATCTCGTAATTGATTTTAAGTTGAATTTTTTTAAATTTTTAGTTAAAATAAATTATAATTG
ATTGTCTACCTCAAGAAACATGAAGAAAAAGTCATTCATTGGCAAGAAAAGTCTATTATAGTCAC
CCATTCTTTCAAAACCTTATTACTCGCTTTAAATGACTTTTAATCTCATAATTGATTTTAAATTG
AATTCTTTTACATTTTTGGTTAAAACAGATTATAATTGAATGTCTGCCTCAAGAAACATGAAGAA
AAAGAAATTCATTG
Found at i:26437 original size:170 final size:169
Alignment explanation
Indices: 26144--26453 Score: 433
Period size: 170 Copynumber: 1.8 Consensus size: 169
26134 NNNNNNNNGA
*
26144 CATTCAATTACAATCTGTTTCAACCAAAAACATAAAATATTCAACTTAAAATTAATTATGACATT
1 CATTCAATTACAATCTGTTTCAACCAAAAACATAAAATATTCAACTTAAAATCAATTATGACATT
* * * * * *
26209 ATAAAACCTTTTGAAGTGAGTAGTAAGATTTTTGAAGGAATAAATGATTATGAATAGACTTTTTT
66 ATAAAACCATTTAAAGTGAGTAGCAAGAGTTTTGAAGGAATAAATGACTATAAATAGAC-TTTTT
26274 TGCCAATAAATACTTTTTTTCTCACGTTTCCTGAGGTAGG
130 TGCCAATAAATACTTTTTTTCTCACGTTTCCTGAGGTAGG
* * * * *
26314 CATTCAATTATAATCTGTTTTAA-TAAAAATATAAATATATTCAACTTAAAATCAATTATGAGAT
1 CATTCAATTACAATCTGTTTCAACCAAAAACATAAA-ATATTCAACTTAAAATCAATTATGACAT
* * ***
26378 TATAAAATCATTTAAAGTGAGTAGCAAGGGTTTTGAAGGAATGGGTGACTATAAATAGACTTTTT
65 TATAAAACCATTTAAAGTGAGTAGCAAGAGTTTTGAAGGAATAAATGACTATAAATAGACTTTTT
*
26443 TGTCAATAAAT
130 TGCCAATAAAT
26454 GCCTCTTTCT
Statistics
Matches: 121, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
169 25 0.21
170 96 0.79
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.37
Consensus pattern (169 bp):
CATTCAATTACAATCTGTTTCAACCAAAAACATAAAATATTCAACTTAAAATCAATTATGACATT
ATAAAACCATTTAAAGTGAGTAGCAAGAGTTTTGAAGGAATAAATGACTATAAATAGACTTTTTT
GCCAATAAATACTTTTTTTCTCACGTTTCCTGAGGTAGG
Found at i:27646 original size:171 final size:170
Alignment explanation
Indices: 26823--29304 Score: 1576
Period size: 171 Copynumber: 14.5 Consensus size: 170
26813 NNNNNNNNNN
* * *
26823 TGAGATTATAAAACCATTTAAAGTGAGTAGT-AGGACTTTTGAAGGAATGGGTGACTATAAA-CG
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGG-CTTTTGAAGGAATGGGTGACTATAAATAG
* * * * * * **
26886 GACTTTTGTTGTCAATGAAT-AGCTTTTTATTCACGTTT-TCCAAGACAAACATTCAATTATAGC
65 G-CTTTTCTAGTCAATGAATGA-CTTTTTCTTCAC-TTTCT-TAAGGCAGACATTCAATTATAAT
* * *
26949 CTATTTTAACAAAAAATTTAAAAAAATTCAACTTAAAATCAATTA
126 CTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTA
* * ********** ** *
26994 TAAGATTACAAAACCATNNNNNNNNNNTAATAAGGCTTTCAAAGGCATGGGTGACTATAAATAGG
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGG
* * *
27059 CTTTTCTAGTCAATGAATGACTTTTTCTTCACATTTCCTAAGGTAGACATTCAATTATAATCTAT
66 CTTTTCTAGTCAATGAATGACTTTTTCTTCAC-TTTCTTAAGGCAGACATTCAATTATAATCTGT
* * * * **********
27124 GTTAACTAAAAATGTAATAAAATTTAACTTANNNNNNNNNN
130 TTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTA
*** *
27165 NNNGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTGGAAGGAATGGGTGAC--TAAATATG
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATA-G
* ** * * * * * * * * * *
27228 GAGTTTTC-ACACCAATAAATGTCCTTTTCTTTACATGTC-CAGAGACTGACATTCTATTATAGT
65 G-CTTTTCTA-GTCAATGAATGACTTTTTCTTCAC-TTTCTTA-AGGCAGACATTCAATTATAAT
* ********** *
27291 CTATTTTAACCAAAAATGTANNNNNNNNNNACTTAAAATGAATTA
126 CTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTA
* * * *
27336 TG-GATTATAAAACCATTTAAATCAAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGA
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGG
* * * * * * * *
27400 CTTTTTTTTTGTCAATGAATGGCTTTTTCTTTACGCTTT-TCATGGCAGAAATTCAATTAT-AGC
66 C--TTTTCTAGTCAATGAATGACTTTTTC-TT-CACTTTCTTAAGGCAGACATTCAATTATAATC
*
27463 TTGTTTTAACCAAAAATGTAAAAAAAATCAACTTAAAATCAATTA
127 -TGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTA
* * * * * * *
27508 CGAGATTGTAAAACTATTTAAAACGAGTAATAAGGCTTTCGAAGGTATAGGTGACTATAAATAGG
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGG
* * * * *
27573 CTTTTCTAGTCAATAAATGGCTTTTTCTTCATCTTTTTTGAGGCAGACATTCAATTATAATCTAT
66 CTTTTCTAGTCAATGAATGACTTTTTCTTCA-CTTTCTTAAGGCAGACATTCAATTATAATCTGT
* *
27638 TTTAACCAAAATTGTAAAAAAATTCAACTTAAAATGAATTA
130 TTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTA
** * * * *
27679 TGAGATTATAAAATTATTTAAAGTGAATAAT-AGGCTTTTGAAAGCATGGGTGACTATAAAT-GG
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGG
* * * * * *
27742 ACTTTTCTTGCCAATGAAT-TCTTTTTTCTTCAAGTTTCTTAAGGCA-ACCATTCAATTAAAATA
66 -CTTTTCTAGTCAATGAATGAC-TTTTTCTTC-ACTTTCTTAAGGCAGA-CATTCAATTATAATC
*
27805 TGTTTTAACAAAAAATGTAAAAAGAATTCAACTTAAAATCAATTA
127 TGTTTTAACCAAAAATGTAAAAA-AATTCAACTTAAAATCAATTA
* * * * * *
27850 TGAGATTACAAAGCCATTTAAAGCGAGGAATAAGGGTTTTGAAGGAATGGGTGACTATAAGTAGA
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGG
* * * * * * *
27915 CTTTTCTTG-CTAATGAATGGCTTTTTCTTCATGTTTCCTAAGGTAGACAATCAATTATAATTTG
66 CTTTTCTAGTC-AATGAATGACTTTTTCTTCA-CTTTCTTAAGGCAGACATTCAATTATAATCTG
* * *
27979 TTTTAAGCAAAAATATAAAAAAAATCAACTTAAAATCAATTA
129 TTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTA
* * * * * * *
28021 CGAGATTATAAAACTATTTAAAACCAGTAATAAGGC-TTTCAA-AAATGTTAGTGACTATAAAT-
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATG--GGTGACTATAAATA
* * * * *
28083 GGACTTTTCTCGTCAATGAATTACTTTTTCTTTACGTTTCTCAAGGGAGACATTCAATTATAATC
64 GG-CTTTTCTAGTCAATGAATGACTTTTTCTTCAC-TTTCTTAAGGCAGACATTCAATTATAATC
* * *
28148 TGTTTTATCCAAAAAAGTAAAAAAATTCAATTTAAAATCAATTA
127 TGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTA
* ** * *
28192 --AGATTATAAAACCATTTAAAGCAAGTAATAAGATTTTTAAAGGAATGGGTGATTATAAAT-GG
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGG
* * * * * * * * * *
28254 ACTTTTTTTGCCAATGAATCACCTTTTCTTTACATTT-TTGGAGACAAAAATTCAATTATAGAT-
66 -CTTTTCTAGTCAATGAATGACTTTTTCTTCAC-TTTCTT-AAGGCAGACATTCAATTATA-ATC
* *
28317 TGTTTGAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTA
127 TGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTA
* * *
28361 CGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAAGCAA-GGGTGACTATAAAT-G
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG-AAGGAATGGGTGACTATAAATAG
* * * * * * * *
28424 GTCTTTTTTAGTTAGTGAATGACTTTTTCTTCA-TGTCGCCTAAGGTAAACATTCAATTATAACC
65 G-CTTTTCTAGTCAATGAATGACTTTTTCTTCACT-T-TCTTAAGGCAGACATTCAATTATAATC
*
28488 TGTTTTAA-CTAAAATGTAAAAAAATTCAACTTAAAATCAATTA
127 TGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTA
* * * * * * * ** *
28531 TGAGACTATAAAACTATTTAGAGTGAATAATGAGACTTTTGAACAAATGGGTGACTATATAT-GA
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAG-
* * * * * * *
28595 ACTTTTCTTACT-TATGAAT-AGCTTTCT-TTCACGTTT-TT-CGTGCCTGACATTCAATTATAG
65 GCTTTTC-TAGTCAATGAATGA-CTTTTTCTTCAC-TTTCTTAAG-G-CAGACATTCAATTATAA
* * * * *
28655 CCTATTTTAGA--GAAAATATAAAAAAAGTT-AACCTAAAATCAATTA
125 TCTGTTTTA-ACCAAAAATGTAAAAAAA-TTCAACTTAAAATCAATTA
* * * * * * *
28700 TAAGATTACAAAACTATTTAAAGCAAGTAATAAGGCTTTTGAAAGAATGGGT-AGCTATAGACAG
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGA-CTATAAATAG
** * * * ** * * * *
28764 AATTTTCTTGGCAATGAATGACTTTTTCTTCATGTTTCCCAAGGTA-AGCAATCAATTCTAATAT
65 GCTTTTCTAGTCAATGAATGACTTTTTCTTCA-CTTTCTTAAGGCAGA-CATTCAATTATAATCT
* * * * *
28828 CTTTTATCCAAAAATATAAAAACAAATTCAATTTGAAATCAATTA
128 GTTTTAACCAAAAATGT-AAAA-AAATTCAACTTAAAATCAATTA
* * * *
28873 CGAGATTATAAAACCATTTAATGCAAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAAT-GA
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAG-
* * * ************************** * * * *
28937 ACTTTTCTTGCCAANNNNNNNNNNNNNNNNNNNNNNNNNNNAGACAAATATTCAATTAT-ATATG
65 GCTTTTCTAGTCAA-TGAATGACTTTTTCTTCACTTTCTTAAGGCAGACATTCAATTATAATCTG
** *
29001 TTTTAACTTAAAATGTAAAAAAATTCAACATAAAATCAATTA
129 TTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTA
* * ** * * * * *
29043 TGAGATTAAAAAACTATTTAAAGTAAGTAATAAGGCTTTTGAATGAATCGGTAACTATAAGTAGA
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGG
* *** * * * * * *
29108 CTTTTTTTCCCAATGAACGACTTTTTCTTAACATTTGC-CAAGGTAGACAATCAATTATAATTTG
66 CTTTTCTAGTCAATGAATGACTTTTTCTTCAC-TTT-CTTAAGGCAGACATTCAATTATAATCTG
*
29172 TTTTAACCAAAAATGTAAAAAAATTTAACTTAAAATCAATTA
129 TTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTA
* * * * ** *
29214 GGATATTAGAAAACCATTTAAAGTGAGTAATAAGGCTTTCAAAGGTATGGGTGACTATAAAT-GG
1 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGG
* *
29278 ACTTTTCTAGTTAATGAATAACTTTTT
66 -CTTTTCTAGTCAATGAATGACTTTTT
29305 TTTACGTTTC
Statistics
Matches: 1770, Mismatches: 460, Indels: 162
0.74 0.19 0.07
Matches are distributed among these distances:
167 1 0.00
168 5 0.00
169 266 0.15
170 387 0.22
171 750 0.42
172 203 0.11
173 155 0.09
174 3 0.00
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.34
Consensus pattern (170 bp):
TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGG
CTTTTCTAGTCAATGAATGACTTTTTCTTCACTTTCTTAAGGCAGACATTCAATTATAATCTGTT
TTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTA
Found at i:28350 original size:340 final size:337
Alignment explanation
Indices: 26824--29285 Score: 1619
Period size: 343 Copynumber: 7.2 Consensus size: 337
26814 NNNNNNNNNT
** * * *
26824 GAGATTATAAAACCATTTAAAGTGAGTAGTAGGACTTTTGAAGGAATGGGTGACTATAAACGGAC
1 GAGATTATAAAACCATTTAAAGCAAGTAATAAGACTTTTGAAGGAATGGGTGACTATAAATGGAC
* * * * *** **
26889 TTTTGTTGTCAATGAAT-AGCTTTT-TATTCACGTTTTCCAAGACA-AACATTCAATTATAGCCT
66 TTTTCTTGCCAATGAATGACCTTTTCT-TT-ACATTTTTGGAGACAGAA-ATTCAATTATA-ATT
* * * * *****
26951 ATTTTAACAAAAAATTTAAAAAAATTCAACTTAAAATCAATTATAAGATTACAAAACCATNNNNN
127 ATTTTAAC-AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAA
***** * * *
27016 NNNNNTAATAAGGC-TTTCAAAGGCATGGGTGACTATAAATAGG-CTTTTCTAGTCAATGAATGA
191 GCAAGTAATAAGGCTTTTGAAA-GAATGGGTGACTATAAAT-GGACTTTTCTTGTCAATGAATGA
* * * * * * *
27079 CTTTTTCTTCACATTTC-CTAAGGTAGACATTCAATTATAATCTATGTTAACTAAAAATGTAATA
254 CTTTTTCTTCACGTTTCTC-AAGGCA-ACATTCAATTATAATCTGT-TTTACCAAAAAAGTAAAA
* **********
27143 AAATTTAACTTANNNNNNNNNNN
316 AAATTCAACTTA-AAATCAATTA
** * * *
27166 NNGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTGGAAGGAATGGGTGACTA-AATATGGA
1 GAGATTATAAAACCATTTAAAGCAAGTAATAAGACTTTTGAAGGAATGGGTGACTATAA-ATGGA
* *** * * * *** * * * *
27230 GTTTTCACACCAATAAATGTCCTTTTCTTTACATGTCCAGAGACTGACATTCTATTATAGTCTAT
65 CTTTTCTTGCCAATGAATGACCTTTTCTTTACATTTTTGGAGACAGAAATTCAATTATAAT-TAT
* ********** * * *
27295 TTTAACCAAAAATGTANNNNNNNNNNACTTAAAATGAATTATG-GATTATAAAACCATTTAAATC
129 TTTAA-CAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGC
* * * * *
27359 AAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTTTTTTTGTCAATGAATGGCT
193 AAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGAC--TTTTCTTGTCAATGAATGACT
* * * * *
27424 TTTTCTTTACGCTTT-TCATGGCAGAAATTCAATTAT-AGCTTGTTTTAACCAAAAATGTAAAAA
256 TTTTCTTCACG-TTTCTCAAGGCA-ACATTCAATTATAATC-TGTTTT-ACCAAAAAAGTAAAAA
*
27487 AAATCAACTTAAAATCAATTA
317 AATTCAACTTAAAATCAATTA
* * * * * * * *
27508 CGAGATTGTAAAACTATTTAAAACGAGTAATAAGGCTTTCGAAGGTATAGGTGACTATAAATAGG
1 -GAGATTATAAAACCATTTAAAGCAAGTAATAAGACTTTTGAAGGAATGGGTGACTATAAAT-GG
* * * * * * * * *
27573 -CTTTTCTAGTCAATAAATGGCTTTTTCTTCATC-TTTTTTGAGGCAGACATTCAATTATAATCT
64 ACTTTTCTTGCCAATGAATGACCTTTTCTTTA-CATTTTTGGAGACAGAAATTCAATTATAAT-T
* * * *
27636 ATTTTAACCAAAATTGTAAAAAAATTCAACTTAAAATGAATTATGAGATTATAAAATTATTTAAA
127 ATTTTAA-CAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAA
* * * *
27701 GTGAA-TAAT-AGGCTTTTGAAAGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAT-TC
191 G-CAAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGAC
* * * * *
27763 TTTTTTCTTCAAGTTTCTTAAGGCAACCATTCAATTAAAATATGTTTTAACAAAAAATGTAAAAA
255 -TTTTTCTTCACGTTTCTCAAGGCAA-CATTCAATTATAATCTGTTTTACCAAAAAA-GTAAAAA
27828 GAATTCAACTTAAAATCAATTA
317 -AATTCAACTTAAAATCAATTA
* * * * ** * *
27850 TGAGATTACAAAGCCATTTAAAGCGAGGAATAAGGGTTTTGAAGGAATGGGTGACTATAAGTAGA
1 -GAGATTATAAAACCATTTAAAGCAAGTAATAAGACTTTTGAAGGAATGGGTGACTATAAATGGA
* * * * **
27915 CTTTTCTTGCTAATGAATGGCTTTTTC-TT-CATGTTTCCT-AAGGTAGACAA-TCAATTATAAT
65 CTTTTCTTGCCAATGAATGACCTTTTCTTTACAT-TTT--TGGAGACAGA-AATTCAATTATAA-
* * *
27976 TTGTTTTAAGCAAAAATATAAAAAAAATCAACTTAAAATCAATTACGAGATTATAAAACTATTTA
125 TTATTTTAA-CAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTA
* * * * *
28041 AAACCAGTAATAAGGC-TTTCAAA-AATGTTAGTGACTATAAATGGACTTTTCTCGTCAATGAAT
189 AAGCAAGTAATAAGGCTTTTGAAAGAATG--GGTGACTATAAATGGACTTTTCTTGTCAATGAAT
* * *
28104 TACTTTTTCTTTACGTTTCTCAAGGGAGACATTCAATTATAATCTGTTTTATCCAAAAAAGTAAA
252 GACTTTTTCTTCACGTTTCTCAAGGCA-ACATTCAATTATAATCTGTTTTA-CCAAAAAAGTAAA
*
28169 AAAATTCAATTTAAAATCAATTA
315 AAAATTCAACTTAAAATCAATTA
* * *
28192 -AGATTATAAAACCATTTAAAGCAAGTAATAAGATTTTTAAAGGAATGGGTGATTATAAATGGAC
1 GAGATTATAAAACCATTTAAAGCAAGTAATAAGACTTTTGAAGGAATGGGTGACTATAAATGGAC
* * * *
28256 TTTTTTTGCCAATGAATCACCTTTTCTTTACATTTTTGGAGACAAAAATTCAATTATAGATTGTT
66 TTTTCTTGCCAATGAATGACCTTTTCTTTACATTTTTGGAGACAGAAATTCAATTATA-ATTATT
* * * * *
28321 TGAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTACGAGATTATAAAACCATTTAAAGCG
130 TTAAC-AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCA
* * * *
28386 AGTAATAAGGCTTTCGAAAGCAA-GGGTGACTATAAATGGTCTTTT-TTAGTTAGTGAATGACTT
194 AGTAATAAGGCTTTTGAAAG-AATGGGTGACTATAAATGGACTTTTCTT-GTCAATGAATGACTT
* ** * * * * *
28449 TTTCTTCATGTCGC-CTAAGGTAAACATTCAATTATAACCTGTTTTAACTAAAATGTAAAAAAAT
257 TTTCTTCACGTTTCTC-AAGG-CAACATTCAATTATAATCTGTTTTACCAAAAAAGTAAAAAAAT
28513 TCAACTTAAAATCAATTA
320 TCAACTTAAAATCAATTA
* * * * * ** * *
28531 TGAGACTATAAAACTATTTAGAGTGAA-TAATGAGACTTTTGAACAAATGGGTGACTATATATGA
1 -GAGATTATAAAACCATTTAAAG-CAAGTAATAAGACTTTTGAAGGAATGGGTGACTATAAATGG
* ** * * * * * * * **
28595 ACTTTTCTTACTTATGAAT-AGC-TTTCTTTCACGTTTTTCGTGCCTGACATTCAATTATAGCCT
64 ACTTTTCTTGCCAATGAATGACCTTTTCTTT-ACATTTTTGGAGACAGAAATTCAATTATA-ATT
* * * *
28658 ATTTTAGA-GAAAATATAAAAAAAGTT-AACCTAAAATCAATTATAAGATTACAAAACTATTTAA
127 ATTTTA-ACAAAAATATAAAAAAA-TTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAA
* ** * *
28721 AGCAAGTAATAAGGCTTTTGAAAGAATGGGT-AGCTATAGACAGAATTTTCTTGGCAATGAATGA
190 AGCAAGTAATAAGGCTTTTGAAAGAATGGGTGA-CTATAAATGGACTTTTCTTGTCAATGAATGA
* * * * * * *
28785 CTTTTTCTTCATGTTTCCCAAGGTAAGCAATCAATTCTAATATCTTTTATCCAAAAATA-TAAAA
254 CTTTTTCTTCACGTTTCTCAAGGCAA-CATTCAATTATAATCTGTTTTA-CCAAAAA-AGT-AAA
* *
28849 ACAAATTCAATTTGAAATCAATTA
315 A-AAATTCAACTTAAAATCAATTA
* * * *
28873 CGAGATTATAAAACCATTTAATGCAAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGAA
1 -GAGATTATAAAACCATTTAAAGCAAGTAATAAGACTTTTGAAGGAATGGGTGACTATAAATGGA
*************************** *
28938 CTTTTCTTGCCAANNNNNNNNNNNNNNNNNNNNNNNNNNNAGACA-AATATTCAATTAT-ATATG
65 CTTTTCTTGCCAATGAATGACCTTTTCTTTACATTTTTGGAGACAGAA-ATTCAATTATAAT-TA
* * * *
29001 TTTTAACTTAAAATGTAAAAAAATTCAACATAAAATCAATTATGAGATTAAAAAACTATTTAAAG
128 TTTTAAC-AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAG
* * * * * * * ** *
29066 TAAGTAATAAGGCTTTTGAATGAATCGGTAACTATAAGTAGACTTTTTTTCCCAATGAACGACTT
192 CAAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGACTT
* * * * * *
29131 TTTCTTAACATTTGC-CAAGGTAGACAATCAATTATAATTTGTTTTAACCAAAAATGTAAAAAAA
257 TTTCTTCACGTTT-CTCAAGGCA-ACATTCAATTATAATCTGTTTT-ACCAAAAAAGTAAAAAAA
*
29195 TTTAACTTAAAATCAATTA
319 TTCAACTTAAAATCAATTA
* * ** * ** *
29214 GGATATTAGAAAACCATTTAAAGTGAGTAATAAGGCTTTCAAAGGTATGGGTGACTATAAATGGA
1 -GAGATTATAAAACCATTTAAAGCAAGTAATAAGACTTTTGAAGGAATGGGTGACTATAAATGGA
29279 CTTTTCT
65 CTTTTCT
29286 AGTTAATGAA
Statistics
Matches: 1672, Mismatches: 368, Indels: 161
0.76 0.17 0.07
Matches are distributed among these distances:
338 5 0.00
339 173 0.10
340 283 0.17
341 265 0.16
342 421 0.25
343 479 0.29
344 44 0.03
345 2 0.00
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.34
Consensus pattern (337 bp):
GAGATTATAAAACCATTTAAAGCAAGTAATAAGACTTTTGAAGGAATGGGTGACTATAAATGGAC
TTTTCTTGCCAATGAATGACCTTTTCTTTACATTTTTGGAGACAGAAATTCAATTATAATTATTT
TAACAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCAAG
TAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGACTTTTTC
TTCACGTTTCTCAAGGCAACATTCAATTATAATCTGTTTTACCAAAAAAGTAAAAAAATTCAACT
TAAAATCAATTA
Found at i:29064 original size:853 final size:852
Alignment explanation
Indices: 26823--29304 Score: 2159
Period size: 853 Copynumber: 2.9 Consensus size: 852
26813 NNNNNNNNNN
* * * * * * *
26823 TGAGATTATAAAACCATTTAAAGTGAGTAGTAGGACTTTTGAAGGAATGGGTGACTATAAACGGA
1 TGAGACTATAAAACTATTTAAAGTGAATAATA-GACTTTTGAAAGAATGGGTGACTATAAATGAA
* ** * * * * * * * *
26888 CTTTTGTTGTCAATGAATAGCTTTT-TATTCACGTTT-TCCAAGACAAACATTCAATTATAGCCT
65 CTTTTCTTACCAATGAAT-GCTTTTCTCTTCAAGTTTCT-TAAGGCAACCATTCAATTAAAACAT
* * ****
26951 ATTTTAACAAAAAATTTAAAAA-AATTCAACTTAAAATCAATTATAAGATTACAAAACCATNNNN
128 ATTTTAACAAAAAATATAAAAAGAATTCAACCTAAAATCAATTATAAGATTACAAAACCATTTAA
******* * * ** ** *
27015 NNNNNNTAATAAGGC-TTTCAAAGGCATGGGTGACTATAAATAGGCTTTTCTAG-TCAATGAATG
193 AGCAAGGAATAAGGCTTTTGAAA-GAATGGGTGACTATAAGCAGAATTTTCTTGCT-AATGAATG
** * * * * * * * *
27078 ACTTTTTCTTCACATTTCCTAAGGTAGACATTCAATTATAATCTATGTTAACTAAAAATGTAATA
256 ACTTTTTCTTCATGTTTCCCAAGGTAGACAATCAATTATAATATCTTTTAACCAAAAATATAAAA
* * ************* * * *
27143 AAATTTAACTTANNNNNNNNNNNNNGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTGGAA
321 AAAATCAACTTAAAATCAATTACGAGATTATAAAACCATTTAAAACAAGTAATAAGGCTTT-CAA
* * * * * * * * * *
27208 GGAATG-GGTGACTA-AATATGGAGTTTTCACACCAATAAATGT-CCTTTTCTTTACATGTC-CA
385 -AAATGTAGTGACTATAA-ATGAACTTTTCTCGCCAATGAAT-TACTTTTTCTTTACGTTTCTCA
** * * * * * ********** * *
27269 GAGACTGACATTCTATTATAGTCTATTTTAACCAAAAATGTANNNNNNNNNNACTTAAAATGAAT
447 -AGACAAACATTCAATTATAATATGTTTTAACCAAAAAAGTAAAAAAATTCAACATAAAATCAAT
* *
27334 TATG-GATTATAAAACCATTTAAATCAAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATA
511 TATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATA
* ** * * * * *
27398 GACTTTTTTTTTGTCAATGAATGGCTTTTTCTTTACGCTTTTCATGGCAGAAATTCAATTATAGC
576 GAC--TTTTTTTGCCAATGAATCACTTTTTCTTTAC-ATTTTTAAGGCAAAAATTCAATTATAGA
* * *
27463 TTGTTTTAACCAAAAATGTAAAAAAAATCAACTTAAAATCAATTACGAGATTGTAAAACTATTTA
638 TTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTACGAGATTATAAAACCATTTA
* * * *
27528 AAACGAGTAATAAGGCTTTCGAAGGTATA-GGTGACTATAAATAGGCTTTTCTAGTCAATAAATG
703 AAGCGAGTAATAAGGCTTTCGAAAGTA-AGGGTGACTATAAAT-GGCTTTTCTAGTTAATGAATG
* **** * * *
27592 GCTTTTTCTTCATCTTTTTTGAGGCAGACATTCAATTATAATCTATTTTAACCAAAATTGTAAAA
766 ACTTTTTCTTCATCTCGCCTAAGGCAAACATTCAATTATAACCTATTTTAACCAAAATTGTAAAA
*
27657 AAATTCAACTTAAAATGAATTA
831 AAATTCAACTTAAAATCAATTA
* * * * *
27679 TGAGATTATAAAATTATTTAAAGTGAATAATAGGCTTTTGAAAGCATGGGTGACTATAAATGGAC
1 TGAGACTATAAAACTATTTAAAGTGAATAATAGACTTTTGAAAGAATGGGTGACTATAAATGAAC
* * * * *
27744 TTTTCTTGCCAATGAATTCTTTTTTCTTCAAGTTTCTTAAGGCAACCATTCAATTAAAATATGTT
66 TTTTCTTACCAATGAATGCTTTTCTCTTCAAGTTTCTTAAGGCAACCATTCAATTAAAACATATT
* * * *
27809 TTAACAAAAAATGTAAAAAGAATTCAACTTAAAATCAATTATGAGATTACAAAGCCATTTAAAGC
131 TTAACAAAAAATATAAAAAGAATTCAACCTAAAATCAATTATAAGATTACAAAACCATTTAAAGC
* * * * * *
27874 GAGGAATAAGGGTTTTGAAGGAATGGGTGACTATAAGTAGACTTTTCTTGCTAATGAATGGCTTT
196 AAGGAATAAGGCTTTTGAAAGAATGGGTGACTATAAGCAGAATTTTCTTGCTAATGAATGACTTT
* * * *
27939 TTCTTCATGTTTCCTAAGGTAGACAATCAATTATAATTTGTTTTAAGCAAAAATATAAAAAAAAT
261 TTCTTCATGTTTCCCAAGGTAGACAATCAATTATAATATCTTTTAACCAAAAATATAAAAAAAAT
* *
28004 CAACTTAAAATCAATTACGAGATTATAAAACTATTTAAAACCAGTAATAAGGCTTTCAAAAATGT
326 CAACTTAAAATCAATTACGAGATTATAAAACCATTTAAAACAAGTAATAAGGCTTTCAAAAATG-
* * ** *
28069 TAGTGACTATAAATGGACTTTTCTCGTCAATGAATTACTTTTTCTTTACGTTTCTCAAGGGAGAC
390 TAGTGACTATAAATGAACTTTTCTCGCCAATGAATTACTTTTTCTTTACGTTTCTCAAGACAAAC
* * **
28134 ATTCAATTATAATCTGTTTTATCCAAAAAAGTAAAAAAATTCAATTTAAAATCAATTA--AGATT
455 ATTCAATTATAATATGTTTTAACCAAAAAAGTAAAAAAATTCAACATAAAATCAATTATGAGATT
** * * *
28197 ATAAAACCATTTAAAGCAAGTAATAAGATTTTTAAAGGAATGGGTGATTATAAATGGACTTTTTT
520 ATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTTT
* * * * *
28262 TGCCAATGAATCACCTTTTCTTTACATTTTTGGAGACAAAAATTCAATTATAGATTGTTTGAACT
585 TGCCAATGAATCACTTTTTCTTTACATTTTT-AAGGCAAAAATTCAATTATAGATTGTTTTAACC
28327 AAAAATGTAAAAAAATTCAACTTAAAATCAATTACGAGATTATAAAACCATTTAAAGCGAGTAAT
649 AAAAATGTAAAAAAATTCAACTTAAAATCAATTACGAGATTATAAAACCATTTAAAGCGAGTAAT
* * *
28392 AAGGCTTTCGAAAGCAAGGGTGACTATAAATGGTCTTTTTTAGTTAGTGAATGACTTTTTCTTCA
714 AAGGCTTTCGAAAGTAAGGGTGACTATAAATGG-CTTTTCTAGTTAATGAATGACTTTTTCTTCA
* * * *
28457 TGTCGCCTAAGGTAAACATTCAATTATAACCTGTTTTAACTAAAA-TGTAAAAAAATTCAACTTA
778 TCTCGCCTAAGGCAAACATTCAATTATAACCTATTTTAACCAAAATTGTAAAAAAATTCAACTTA
28521 AAATCAATTA
843 AAATCAATTA
* *
28531 TGAGACTATAAAACTATTTAGAGTGAATAATGAGACTTTTGAACA-AATGGGTGACTATATATGA
1 TGAGACTATAAAACTATTTAAAGTGAATAAT-AGACTTTTGAA-AGAATGGGTGACTATAAATGA
** * * * * *
28595 ACTTTTCTTACTTATGAATAGC-TTTCT-TTCACGTTT-TT-CGTGCCTGA-CATTCAATTATAG
64 ACTTTTCTTACCAATGAAT-GCTTTTCTCTTCAAGTTTCTTAAG-G-C-AACCATTCAATTAAAA
* * * *
28655 CCTATTTT-AGAGAAAATATAAAAA-AAGTT-AACCTAAAATCAATTATAAGATTACAAAACTAT
125 CATATTTTAACAAAAAATATAAAAAGAA-TTCAACCTAAAATCAATTATAAGATTACAAAACCAT
*
28717 TTAAAGCAAGTAATAAGGCTTTTGAAAGAATGGGT-AGCTAT-AGACAGAATTTTCTTGGC-AAT
189 TTAAAGCAAGGAATAAGGCTTTTGAAAGAATGGGTGA-CTATAAG-CAGAATTTTCTT-GCTAAT
* *
28779 GAATGACTTTTTCTTCATGTTTCCCAAGGTA-AGCAATCAATTCTAATATCTTTTATCCAAAAAT
251 GAATGACTTTTTCTTCATGTTTCCCAAGGTAGA-CAATCAATTATAATATCTTTTAACCAAAAAT
* * **
28843 ATAAAAACAAATTCAATTTGAAATCAATTACGAGATTATAAAACCATTTAATGCAAGTAATAAGG
315 ATAAAAA-AAA-TCAACTTAAAATCAATTACGAGATTATAAAACCATTTAAAACAAGTAATAAGG
* * * *********************
28908 CTTTTGAAAGAATG-GGTGACTATAAATGAACTTTTCTTGCCAANNNNNNNNNNNNNNNNNNNNN
378 C-TTTCAAA-AATGTAGTGACTATAAATGAACTTTTCTCGCCAATGAATTACTTTTTCTTTACGT
****** * ** *
28972 NNNNNNAGACAAATATTCAATTAT-ATATGTTTTAACTTAAAATGTAAAAAAATTCAACATAAAA
441 TTCTCAAGACAAACATTCAATTATAATATGTTTTAACCAAAAAAGTAAAAAAATTCAACATAAAA
* * * * * *
29036 TCAATTATGAGATTAAAAAACTATTTAAAGTAAGTAATAAGGCTTTTGAATGAATCGGTAACTAT
506 TCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGGGTGACTAT
* * * ** * *
29101 AAGTAGACTTTTTTTCCCAATGAA-CGACTTTTTCTTAACATTTGCCAAGGTAGACAA-TCAATT
571 AAATAGACTTTTTTTGCCAATGAATC-ACTTTTTCTTTACATTT-TTAAGGCA-AAAATTCAATT
* * * *
29164 ATA-ATTTGTTTTAACCAAAAATGTAAAAAAATTTAACTTAAAATCAATTAGGATATTAGAAAAC
633 ATAGA-TTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTACGAGATTATAAAAC
* *
29228 CATTTAAAGTGAGTAATAAGGCTTTC-AAAGGTATGGGTGACTATAAATGGACTTTTCTAGTTAA
697 CATTTAAAGCGAGTAATAAGGCTTTCGAAA-GTAAGGGTGACTATAAATGG-CTTTTCTAGTTAA
*
29292 TGAATAACTTTTT
760 TGAATGACTTTTT
29305 TTTACGTTTC
Statistics
Matches: 1322, Mismatches: 268, Indels: 75
0.79 0.16 0.05
Matches are distributed among these distances:
849 4 0.00
850 142 0.11
851 63 0.05
852 180 0.14
853 467 0.35
854 18 0.01
855 150 0.11
856 288 0.22
857 10 0.01
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.34
Consensus pattern (852 bp):
TGAGACTATAAAACTATTTAAAGTGAATAATAGACTTTTGAAAGAATGGGTGACTATAAATGAAC
TTTTCTTACCAATGAATGCTTTTCTCTTCAAGTTTCTTAAGGCAACCATTCAATTAAAACATATT
TTAACAAAAAATATAAAAAGAATTCAACCTAAAATCAATTATAAGATTACAAAACCATTTAAAGC
AAGGAATAAGGCTTTTGAAAGAATGGGTGACTATAAGCAGAATTTTCTTGCTAATGAATGACTTT
TTCTTCATGTTTCCCAAGGTAGACAATCAATTATAATATCTTTTAACCAAAAATATAAAAAAAAT
CAACTTAAAATCAATTACGAGATTATAAAACCATTTAAAACAAGTAATAAGGCTTTCAAAAATGT
AGTGACTATAAATGAACTTTTCTCGCCAATGAATTACTTTTTCTTTACGTTTCTCAAGACAAACA
TTCAATTATAATATGTTTTAACCAAAAAAGTAAAAAAATTCAACATAAAATCAATTATGAGATTA
TAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTTTT
GCCAATGAATCACTTTTTCTTTACATTTTTAAGGCAAAAATTCAATTATAGATTGTTTTAACCAA
AAATGTAAAAAAATTCAACTTAAAATCAATTACGAGATTATAAAACCATTTAAAGCGAGTAATAA
GGCTTTCGAAAGTAAGGGTGACTATAAATGGCTTTTCTAGTTAATGAATGACTTTTTCTTCATCT
CGCCTAAGGCAAACATTCAATTATAACCTATTTTAACCAAAATTGTAAAAAAATTCAACTTAAAA
TCAATTA
Found at i:29654 original size:171 final size:170
Alignment explanation
Indices: 29352--30727 Score: 1174
Period size: 171 Copynumber: 8.0 Consensus size: 170
29342 NNTTAAAGCG
* * ** * * *
29352 AGTAATAAGGC-TTTGAAAGGAATGGGTGACTACAAATGGGGTTTTCTCG-TCAATCAATGACTT
1 AGTAATAAGGCTTTTGAAA-GAATGAGTGACTATAAATGGACTTTTCTAGCT-AATGAATGGCTT
* * * * * * *
29415 TTTGTTTAC-ATCTTCAGAGACTA-ACATTCTATTATAG-TCTGTTTTAACTAAAAATATGAAAA
64 TTTCTTTACGTTTTTCAG-G-C-AGACATTCAATTATAGCT-TGTTTTAACCAAAAATGTAAAAA
* * **
29477 AATTCAACTTAAAATGAATTATGAGATTATAAAACTATTTAAAACA
125 AATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTA
* * * * * *
29523 AGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTTTTTGCTAATGAAAGGCTTTC
1 AGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAATGGACTTTTCTAGCTAATGAATGGCTTTT
* * ** *
29588 TCTTTACGTTTTTCATGGCAGAAATTCAATTATAGCTTGTTTAAATAAAAAATTTAAAAAAATTC
66 TCTTTACGTTTTTCA-GGCAGACATTCAATTATAGCTTGTTTTAACCAAAAATGTAAAAAAATTC
* * * *
29653 AACTTAAACTCAATTACGAGATTATAAAACCATTTAAAATG
130 AACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTA
* * * * *
29694 AGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAATGGGCTTTTCTAGTTAATGAATGGCTTTT
1 AGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAATGGACTTTTCTAGCTAATGAATGGCTTTT
* * * **
29759 T-TTTCATGTTTCTTGAGGTA-ACCATTCAATTATAATTTGTTTTAACCAAAAATGTAAAAAAAT
66 TCTTT-ACGTTT-TTCAGGCAGA-CATTCAATTATAGCTTGTTTTAACCAAAAATGTAAAAAAAT
* * * * *
29822 TCAATTTAAAATGAATTATGAGATTAGACAACCATTTAAAGTG
128 TCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTA
* * * * * *
29865 AGTAATAAGG-TTTTGAAAGGAAT-AGGAGACTACAAATGGAGTTTTCTCGCTAATAAATGCCTT
1 AGTAATAAGGCTTTTGAAA-GAATGA-GTGACTATAAATGGACTTTTCTAGCTAATGAATGGCTT
* * * * *
29928 TTTCTTTACATTTGT-AGGAACTGACATTCTATTATAG-TCTGTTTTTACCAAAAATGTAAAAAA
64 TTTCTTTACGTTTTTCAGG--CAGACATTCAATTATAGCT-TGTTTTAACCAAAAATGTAAAAAA
* * * *
29991 ATTCAACTTAAAATGAATTATGACATTATAAAACTATTTAAATTA
126 ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTA
* * * * * * * * *
30036 AGTAACAAGGCTTTTGAAAAAATGGGTGGCTATAAATAGACTTTTTTTTGTTAATGAATTGCTTT
1 AGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAATGGAC-TTTTCTAGCTAATGAATGGCTTT
* * * *
30101 TTCTTTACGTTTTTCATGGCAGAAATTCAATTATAACTTGTTTTAACAAAAAATGTAAAACAATT
65 TTCTTTACGTTTTTCA-GGCAGACATTCAATTATAGCTTGTTTTAACCAAAAATGTAAAAAAATT
* * * * * **
30166 TAATTTCAAATCAATTACGAGATTGTAAAACCATTTAAAGCG
129 CAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTA
* * ** *
30208 AGTAATAACGCTTTTAAAATTAT-AGGTGACTATAAATGGACTTTTCTAG-TCAATGAATGACTT
1 AGTAATAAGGCTTTTGAAAGAATGA-GTGACTATAAATGGACTTTTCTAGCT-AATGAATGGCTT
** * * *
30271 TTTCTTTATATTTCTCGAGGCAGACATTCAATTACA-ATATGTTTTAACCAAAAATGTAAAACAA
64 TTTCTTTACGTTTTTC-AGGCAGACATTCAATTATAGCT-TGTTTTAACCAAAAATGTAAAA-AA
* *
30335 A-TCAACTTGAAATCAATTATGAGATTATAAAATCATTTAAAGCT-
126 ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG-TA
* * ** **
30379 AGCAATAAGGCTTTTGAAAGCATGAGTGACTATAAATAAACTTTTCTAG-TCAATGAATAACTTT
1 AGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAATGGACTTTTCTAGCT-AATGAATGGCTTT
* ** *** * * * *
30443 TTCTTCA-AATTTTCAAAAATTGACTTTCTATCATAGCCTGTTTTAACCAAAAATGTAAAAAAAT
65 TTCTTTACGTTTTTCAGGCA--GACATTCAATTATAGCTTGTTTTAACCAAAAATGTAAAAAAAT
* * *
30507 TCAGCTTAAAATGAATCATGAGATTATAAAACCATTTAAAGTA
128 TCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTA
* * * *
30550 AGTAATAAGGCTTTTGAAAAAAT-ATGTGACTATAAATGGACTTTTTTTGCCAATGAATGGCTTC
1 AGTAATAAGGCTTTTGAAAGAATGA-GTGACTATAAATGGACTTTTCTAGCTAATGAATGGCTT-
** * * * * * *
30614 TTT-TTTACGTTTTTTTGACAAAAATTCCATTACAGCTTGTTTTAACAAAAAATGTAAAAAAATT
64 TTTCTTTACGTTTTTCAGGCAGACATTCAATTATAGCTTGTTTTAACCAAAAATGTAAAAAAATT
* * **
30678 CAACTTAAAATCAATT-TCGAGATTGTAAAACTATTTAAAGGG
129 CAACTTAAAATCAATTAT-GAGATTATAAAACCATTTAAAGTA
30720 AGTAATAA
1 AGTAATAA
30728 CACTTNNNNN
Statistics
Matches: 968, Mismatches: 198, Indels: 79
0.78 0.16 0.06
Matches are distributed among these distances:
169 6 0.01
170 103 0.11
171 683 0.71
172 171 0.18
173 3 0.00
174 2 0.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (170 bp):
AGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAATGGACTTTTCTAGCTAATGAATGGCTTTT
TCTTTACGTTTTTCAGGCAGACATTCAATTATAGCTTGTTTTAACCAAAAATGTAAAAAAATTCA
ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTA
Found at i:30317 original size:514 final size:509
Alignment explanation
Indices: 29344--30728 Score: 1762
Period size: 514 Copynumber: 2.7 Consensus size: 509
29334 NNNNNNNNNN
* * * *
29344 TTAAAGCGAGTAATAAGGCTTTGAAAGGAATGGGTGACTACAAATGGGGTTTTCTCGTCAATCAA
1 TTAAAGTGAGTAATAAGGTTTTGAAAGGAAT-GGTGACTACAAATGGAGTTTTCTCGTCAATAAA
* * * * * *
29409 TGACTTTTTGTTTACATCTTCAGAGACTAACATTCTATTATAGTCTGTTTTAACTAAAAATATGA
65 TGACTTTTTCTTTACAT-TTTAGA-ACTGACATTCTATTATAGTCTGTTTTAACCAAAAATGTAA
*
29474 AAAAATTCAACTTAAAATGAATTATGAGATTATAAAACTATTTAAAACAAGTAATAAGGCTTTTG
128 AAAAATTCAACTTAAAATGAATTATGAGATTATAAAACTATTTAAAATAAGTAATAAGGCTTTTG
** * *
29539 AAGGAATGAGTGACTATAAATAGACTTTTTTTGCTAATGAAAGGCTTTCTCTTTACGTTTTTCAT
193 AAAAAATGAGTGACTATAAATAGACTTTTTTTGCTAATGAATGGCTTTTTCTTTACGTTTTTCAT
* * *
29604 GGCAGAAATTCAATTATAGCTTGTTTAAATAAAAAATTTAAAAAAATTCAACTTAAACTCAATTA
258 GGCAGAAATTCAATTATAGCTTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAA-TCAATTA
* ** * * * * *
29669 CGAGATTATAAAACCATTTAAAATGAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAATGGG
322 CGAGATTGTAAAACCATTTAAAGCGAGTAATAACGCTTTTAAAAGTATAGGTGACTATAAATGGA
* * * * * * *
29734 CTTTTCTAGTTAATGAATGGCTTTTTTTTCATGTTTCTTGAGGTAACCATTCAATTATAATTTGT
387 CTTTTCTAGTCAATGAATGACTTTTTTTTCATATTTCTCGAGGCAACCATTCAATTACAATATGT
* * *
29799 TTTAACCAAAAATGTAAAA-AAATTCAATTTAAAATGAATTATGAGATTAGACAACCAT
452 TTTAACCAAAAATGTAAAACAAA-TCAACTTAAAATCAATTATGAGATTAGAAAACCAT
*
29857 TTAAAGTGAGTAATAAGGTTTTGAAAGGAATAGGAGACTACAAATGGAGTTTTCTCG-CTAATAA
1 TTAAAGTGAGTAATAAGGTTTTGAAAGGAAT-GGTGACTACAAATGGAGTTTTCTCGTC-AATAA
* *
29921 ATGCCTTTTTCTTTACATTTGTAGGAACTGACATTCTATTATAGTCTGTTTTTACCAAAAATGTA
64 ATGACTTTTTCTTTACATTT-TA-GAACTGACATTCTATTATAGTCTGTTTTAACCAAAAATGTA
* * *
29986 AAAAAATTCAACTTAAAATGAATTATGACATTATAAAACTATTTAAATTAAGTAACAAGGCTTTT
127 AAAAAATTCAACTTAAAATGAATTATGAGATTATAAAACTATTTAAAATAAGTAATAAGGCTTTT
* * * *
30051 GAAAAAATGGGTGGCTATAAATAGACTTTTTTTTGTTAATGAATTGCTTTTTCTTTACGTTTTTC
192 GAAAAAATGAGTGACTATAAATAGAC-TTTTTTTGCTAATGAATGGCTTTTTCTTTACGTTTTTC
* * * *
30116 ATGGCAGAAATTCAATTATAACTTGTTTTAACAAAAAATGTAAAACAATTTAATTTCAAATCAAT
256 ATGGCAGAAATTCAATTATAGCTTGTTTTAACAAAAAATGTAAAAAAATTCAACTT-AAATCAAT
*
30181 TACGAGATTGTAAAACCATTTAAAGCGAGTAATAACGCTTTTAAAATTATAGGTGACTATAAATG
320 TACGAGATTGTAAAACCATTTAAAGCGAGTAATAACGCTTTTAAAAGTATAGGTGACTATAAATG
30246 GACTTTTCTAGTCAATGAATGACTTTTTCTTT-ATATTTCTCGAGGCAGA-CATTCAATTACAAT
385 GACTTTTCTAGTCAATGAATGACTTTTT-TTTCATATTTCTCGAGGCA-ACCATTCAATTACAAT
* * *
30309 ATGTTTTAACCAAAAATGTAAAACAAATCAACTTGAAATCAATTATGAGATTATAAAATCAT
448 ATGTTTTAACCAAAAATGTAAAACAAATCAACTTAAAATCAATTATGAGATTAGAAAACCAT
* * * ** * * *
30371 TTAAAGCT-AGCAATAAGGCTTTTGAAA-GCATGAGTGACTATAAATAAACTTTTCTAGTCAATG
1 TTAAAG-TGAGTAATAAGG-TTTTGAAAGGAATG-GTGACTACAAATGGAGTTTTCTCGTCAATA
* * * * * * * *
30434 AATAACTTTTTCTTCAAATTTTCAAAAATTGACTTTCTATCATAGCCTGTTTTAACCAAAAATGT
63 AATGACTTTTTCTTTACATTTT--AGAACTGACATTCTATTATAGTCTGTTTTAACCAAAAATGT
* * * *
30499 AAAAAAATTCAGCTTAAAATGAATCATGAGATTATAAAACCATTTAAAGTAAGTAATAAGGCTTT
126 AAAAAAATTCAACTTAAAATGAATTATGAGATTATAAAACTATTTAAAATAAGTAATAAGGCTTT
* *
30564 TGAAAAAAT-ATGTGACTATAAATGGACTTTTTTTGCCAATGAATGGCTTCTTT-TTTACGTTTT
191 TGAAAAAATGA-GTGACTATAAATAGACTTTTTTTGCTAATGAATGGCTT-TTTCTTTACGTTTT
* * * * *
30627 T-TTGACAAAAATTCCATTACAGCTTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATCA
254 TCATGGCAGAAATTCAATTATAGCTTGTTTTAACAAAAAATGTAAAAAAATTCAACTT-AAATCA
* * *
30691 ATTTCGAGATTGTAAAACTATTTAAAGGGAGTAATAAC
318 ATTACGAGATTGTAAAACCATTTAAAGCGAGTAATAAC
30729 ACTTNNNNNN
Statistics
Matches: 757, Mismatches: 99, Indels: 33
0.85 0.11 0.04
Matches are distributed among these distances:
512 91 0.12
513 222 0.29
514 423 0.56
515 21 0.03
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (509 bp):
TTAAAGTGAGTAATAAGGTTTTGAAAGGAATGGTGACTACAAATGGAGTTTTCTCGTCAATAAAT
GACTTTTTCTTTACATTTTAGAACTGACATTCTATTATAGTCTGTTTTAACCAAAAATGTAAAAA
AATTCAACTTAAAATGAATTATGAGATTATAAAACTATTTAAAATAAGTAATAAGGCTTTTGAAA
AAATGAGTGACTATAAATAGACTTTTTTTGCTAATGAATGGCTTTTTCTTTACGTTTTTCATGGC
AGAAATTCAATTATAGCTTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAATCAATTACGAG
ATTGTAAAACCATTTAAAGCGAGTAATAACGCTTTTAAAAGTATAGGTGACTATAAATGGACTTT
TCTAGTCAATGAATGACTTTTTTTTCATATTTCTCGAGGCAACCATTCAATTACAATATGTTTTA
ACCAAAAATGTAAAACAAATCAACTTAAAATCAATTATGAGATTAGAAAACCAT
Found at i:31150 original size:171 final size:170
Alignment explanation
Indices: 30862--32764 Score: 1260
Period size: 171 Copynumber: 11.2 Consensus size: 170
30852 NNNNNNNNNN
* * * *
30862 AAGGCAGACATTCAATTATAATCTGTTTTAACTAAAAATATAAAAAA-ACAACTTAAAATTAATA
1 AAGGCAGACATTCAATTATAATCTGTTTTGACTAAAAATGTAAAAAATTCAACTTAAAATTAATT
* ** * ** *
30926 ATGAGATAATAAAACCATTTAAAGTAACTAATAAGGCTTTCAAAGGCATGGGTGACTATAAATGA
66 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGA
* * * *
30991 GCCTTTCTAATCATTGAATGATTTTTTTTTCACGTTTCCC
131 GCCTTTCTTATCAATGAATGACTTTTTCTTCACGTTTCCC
* * *
31031 AAGGCAGAAATTCAATTATAATCTGTTTTGACCAAAAATGTAAAATAATTCAACTTAAAATGAAT
1 AAGGCAGACATTCAATTATAATCTGTTTTGACTAAAAATGTAAAA-AATTCAACTTAAAATTAAT
* * * * * *
31096 TATGAGATTGTAAAACTATTTAAAGTGAGTAATAAAGCTTTTGCAA-GTATGGGTGACTTTAAAT
65 TATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG-AAGGAATGGGTGACTATAAAT
* * * ** * * *
31160 -AGACATTTCTTACCAATAAATTCCGTTTTCTTCAAGTTTCTC
129 GAG-CCTTTCTTATCAATGAATGACTTTTTCTTCACGTTTCCC
* * * * *
31202 GAGGCAAACATTCAATTAAAATATGTTTT-AGCTAAAAAT-TATCAAAAATTCAACTTAAAATCA
1 AAGGCAGACATTCAATTATAATCTGTTTTGA-CTAAAAATGTA--AAAAATTCAACTTAAAATTA
* * * * * *
31265 ATTATGAGATTACAAAGCCATGTCAAGCGAGTAATAAGGGTTTTGAAGGAATGGGTGACTATAAC
63 ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAA
* ** ** *
31330 T-AGACTTATCTTGCCAATGAA-CCCTATTTTCTTCACGCTT-CC
128 TGAGCCTT-TCTTATCAATGAATGACT-TTTTCTTCACGTTTCCC
* * * * *
31372 AGAGGTAGAGATTCAATTATAATCTGTTTTGACCAAAAATGTAAAAAAATTCAACTTACAATTTA
1 A-AGGCAGACATTCAATTATAATCTGTTTTGACTAAAAATGT-AAAAAATTCAACTTAAAATTAA
* * * * ** * * *
31437 TTACGAGATTATAAAACCATTTAAAGCGAGTAATAAAGCTTTCGAAAGCTTGAGTAAGTATAAAT
64 TTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT
* *
31502 AGAG-TTTTC-TAGTCAATGAATGACTTTTTCTTCACGTTTCCA
129 -GAGCCTTTCTTA-TCAATGAATGACTTTTTCTTCACGTTTCCC
* * * * *
31544 AAGGCACACATTCAATTATAATCT-ATTTGAATTAAAAATATAAAAAAATTCAACTTAAAATGAA
1 AAGGCAGACATTCAATTATAATCTGTTTTG-ACTAAAAATGT-AAAAAATTCAACTTAAAATTAA
* * *
31608 TTATGAGATTATAAAACCATTTAATGCAAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAAT
64 TTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT
* * * * * ***
31673 G-GACTTTTTTTTGTCAATGAATGGCTTTTTCTTTACGTTTTTT
129 GAG-C-CTTTCTTATCAATGAATGACTTTTTCTTCACGTTTCCC
* * * * *
31716 AAAGTAGAAATTCAATTATAA-CT-TGTTTGAAC-AAAATATGCAAAAACATTCAACTGAAAATT
1 AAGGCAGACATTCAATTATAATCTGT-TTTG-ACTAAAA-ATGTAAAAA-ATTCAACTTAAAATT
** ** *** * * *
31778 AATTACAAGATTATAAAACCATTTAAAGTAAGTAATAAGGCTTCCAAAAGCATAGGTGACTATAA
62 AATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAA
** * *
31843 AT-AAACTTTTTTAATCAATGAATGACTTTTTTTTCACGTTTCCC
127 ATGAGCCTTTCTT-ATCAATGAATGACTTTTTCTTCACGTTTCCC
*** * * * *
31887 AAAATAGACATTCAATTATAA-CT-TATTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCA
1 AAGGCAGACATTCAATTATAATCTGT-TTTGACT-AAAAATGT-AAAAAATTCAACTTAAAATTA
********** * * *
31950 ATTATGA-NNNNNNNNNNCATTTAAAGAGAGTAATAAGGCTTTTGAAGGAATGAGTGACTGTAAA
63 ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAA
** * ** * ***
32014 TG-GATTTTTTTTATGTATGAATGACTTTTTCTTCATGTTTTTT
128 TGAG-CCTTTCTTATCAATGAATGACTTTTTCTTCACGTTTCCC
* * ** * * * *
32057 GAGACAGACATTCAATTATAGCCTATTTT-AGCAAAAAATGTAAAACAATTTAACCTAAAATTAA
1 AAGGCAGACATTCAATTATAATCTGTTTTGA-CTAAAAATGTAAAA-AATTCAACTTAAAATTAA
* * ** * *
32121 TTTTTAGATTACCAAACCATTTAAAGCGAGTAATAATGCTTTTGAAGGAATGGGTGACTAAAAAT
64 TTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT
* * * * *
32186 -AGACTTTGCTTGTCAAGGAACGAC-TTTTCTTCATGTTTCCC
129 GAGCCTTT-CTTATCAATGAATGACTTTTTCTTCACGTTTCCC
* * * * * *
32227 GAGGCAGACAATT-AATTATAATATATTTT-ATCTAAAAATATTAAAAAATTTAACTTAAAATCA
1 AAGGCAGAC-ATTCAATTATAATCTGTTTTGA-CTAAAAAT-GTAAAAAATTCAACTTAAAATTA
* * *
32290 ATTACGAGATTATAAAACCATTTAAAGTGAGTAATAAGGTTTTTGAAGGAATGGGTGACTATAAA
63 ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAA
* * * ** * *
32355 T-AGACTTT-TCATGCCAATGAATG-CTTTTTATAAATG-TTCTTC
128 TGAGCCTTTCTTAT--CAATGAATGACTTTTTCTTCACGTTTC-CC
* * **
32397 AAGACAGACATTCAATTAT-ATCTGTTTTAACTAAAAATGTAAAAAAGTTTGACTTAAAATTAAT
1 AAGGCAGACATTCAATTATAATCTGTTTTGACTAAAAATGTAAAAAA-TTCAACTTAAAATTAAT
* * * * * *
32461 TATGAGATTACAAAACTACTTAAAGCAAGTAATAAGGTTTTTGAAGGCATGGGTGACTATAAATG
65 TATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATG
********** * ** * *
32526 ANNNNNNNNNNTCAATAAATGGTTTTTTCTTCATGTTTCTC
130 AGCCTTTCTTATCAATGAATGACTTTTTCTTCACGTTTCCC
** * * * * * * * * *
32567 GTGGTAGACATTCAATTATAATATATTTGGACCAAAAATATGAAAAAATTCCACCTAAAATCAAT
1 AAGGCAGACATTCAATTATAATCTGTTTTGACTAAAAATGT-AAAAAATTCAACTTAAAATTAAT
* ***********
32632 TATGAGATTATAAAATCATTTNNNNNNNNNNGTAAGGCTTTTGAAGGAATGGGTGACTATAAAT-
65 TATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATG
** ** **
32696 AGATTTTTCTTATCAATGAATG-CTTTTTTCTTCGTGTTTCTT
130 AG-CCTTTCTTATCAATGAATGAC-TTTTTCTTCACGTTTCCC
* *
32738 AAGGTAGACATTCAATTATAATTTGTT
1 AAGGCAGACATTCAATTATAATCTGTT
32765 CTAACTGAAA
Statistics
Matches: 1347, Mismatches: 329, Indels: 114
0.75 0.18 0.06
Matches are distributed among these distances:
168 9 0.01
169 148 0.11
170 316 0.23
171 718 0.53
172 152 0.11
173 4 0.00
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.35
Consensus pattern (170 bp):
AAGGCAGACATTCAATTATAATCTGTTTTGACTAAAAATGTAAAAAATTCAACTTAAAATTAATT
ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGA
GCCTTTCTTATCAATGAATGACTTTTTCTTCACGTTTCCC
Found at i:31535 original size:342 final size:339
Alignment explanation
Indices: 30862--32764 Score: 1503
Period size: 342 Copynumber: 5.6 Consensus size: 339
30852 NNNNNNNNNN
* * * * *
30862 AAGGCAGACATTCAATTATAATCTGTTTTAACTAAAAATATAAAAAA-ACAACTTAAAATTAATA
1 AAGGCAGACATTCAATTATAATATATTTTAACTAAAAATATAAAAAATTCAACTTAAAATCAATT
* ** * ** *
30926 ATGAGATAATAAAACCATTTAAAGTAACTAATAAGGCTTTCAAAGGCATGGGTGACTATAAAT-G
66 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAG
* ** * ** *
30990 AGCCTTTCTAATCATTGAATGATTTTTTTTTCACGTTTCCCAAGGCAGAAATTCAATTATAATCT
131 A-CTTTTCTTGTCAATGAA-GGCTTTTTCTTCACGTTT-CCAAGGCAGAAATTCAATTATAATCT
* * * *
31055 GTTTTGACCAAAAATGTAAAATAATTCAACTTAAAATGAATTATGAGATTGTAAAACTATTTAAA
193 GTTTTGACCAAAAATGTAAAAAAATTCAACTTAAAATTAATTATGAGATTATAAAACCATTTAAA
* * * * * * * * * **
31120 GTGAGTAATAAAGCTTTTGCAAGTATGGGTGACTTTAAATAGACATTTCTTA-CCAATAAATTCC
258 GCGAGTAATAAAGCTTTCGAAAGCATGAGTGACTATAAATAGACTTTTC-TAGTCAATGAATGAC
* * *
31184 GTTTTCTTCAAGTTTCTC
322 TTTTTCTTCACGTTTCCC
* * * * * *
31202 GAGGCAAACATTCAATTAAAATATGTTTTAGCTAAAAATTATCAAAAATTCAACTTAAAATCAAT
1 AAGGCAGACATTCAATTATAATATATTTTAACTAAAAA-TATAAAAAATTCAACTTAAAATCAAT
* * * * * *
31267 TATGAGATTACAAAGCCATGTCAAGCGAGTAATAAGGGTTTTGAAGGAATGGGTGACTATAACTA
65 TATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATA
* * ** * * *
31332 GACTTATCTTGCCAATGAACCCTATTTTCTTCACGCTTCCAGAGGTAGAGATTCAATTATAATCT
130 GACTTTTCTTGTCAATGAAGGCT-TTTTCTTCACGTTTCCA-AGGCAGAAATTCAATTATAATCT
* * *
31397 GTTTTGACCAAAAATGTAAAAAAATTCAACTTACAATTTATTACGAGATTATAAAACCATTTAAA
193 GTTTTGACCAAAAATGTAAAAAAATTCAACTTAAAATTAATTATGAGATTATAAAACCATTTAAA
* * * *
31462 GCGAGTAATAAAGCTTTCGAAAGCTTGAGTAAGTATAAATAGAGTTTTCTAGTCAATGAATGACT
258 GCGAGTAATAAAGCTTTCGAAAGCATGAGTGACTATAAATAGACTTTTCTAGTCAATGAATGACT
*
31527 TTTTCTTCACGTTTCCA
323 TTTTCTTCACGTTTCCC
* * * * *
31544 AAGGCACACATTCAATTATAATCTATTTGAATTAAAAATATAAAAAAATTCAACTTAAAATGAAT
1 AAGGCAGACATTCAATTATAATATATTTTAACTAAAAATAT-AAAAAATTCAACTTAAAATCAAT
* * * *
31609 TATGAGATTATAAAACCATTTAATGCAAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATG
65 TATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATA
* * ** * *
31674 GACTTTTTTTTGTCAATGAATGGCTTTTTCTTTACGTTTTTTAAAGTAGAAATTCAATTATAA-C
130 GAC-TTTTCTTGTCAATGAA-GGCTTTTTCTTCACG-TTTCCAAGGCAGAAATTCAATTATAATC
* * * * **
31738 T-TGTTTGAACAAAATATGCAAAAACATTCAACTGAAAATTAATTACAAGATTATAAAACCATTT
192 TGT-TTTGACCAAAA-ATGTAAAAAAATTCAACTTAAAATTAATTATGAGATTATAAAACCATTT
** * * * * * *
31802 AAAGTAAGTAATAAGGCTTCCAAAAGCAT-AGGTGACTATAAATAAACTTTTTTAATCAATGAAT
255 AAAGCGAGTAATAAAGCTTTCGAAAGCATGA-GTGACTATAAATAGACTTTTCTAGTCAATGAAT
*
31866 GACTTTTTTTTCACGTTTCCC
319 GACTTTTTCTTCACGTTTCCC
***
31887 AAAATAGACATTCAATTATAACT-TATTTTAA-TAAAAAATATAAAAAAATTCAACTTAAAATCA
1 AAGGCAGACATTCAATTATAA-TATATTTTAACT-AAAAATAT-AAAAAATTCAACTTAAAATCA
********** * * *
31950 ATTATGA-NNNNNNNNNNCATTTAAAGAGAGTAATAAGGCTTTTGAAGGAATGAGTGACTGTAAA
63 ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAA
* * * * ** * * *** * * **
32014 TGGATTTTTTTTATGTATGAATGACTTTTTCTTCATGTTTTTTGAGACAGACATTCAATTATAGC
128 TAGACTTTTCTTGTCAATGAA-GGCTTTTTCTTCACG-TTTCCAAGGCAGAAATTCAATTATAAT
* * * * * * * **
32079 CTATTTT-AGCAAAAAATGTAAAACAATTTAACCTAAAATTAATTTTTAGATTACCAAACCATTT
191 CTGTTTTGA-CCAAAAATGTAAAAAAATTCAACTTAAAATTAATTATGAGATTATAAAACCATTT
* * * * * * * * * *
32143 AAAGCGAGTAATAATGCTTTTGAAGGAATGGGTGACTAAAAATAGACTTTGCTTGTCAAGGAACG
255 AAAGCGAGTAATAAAGCTTTCGAAAGCATGAGTGACTATAAATAGACTTTTCTAGTCAATGAATG
*
32208 AC-TTTTCTTCATGTTTCCC
320 ACTTTTTCTTCACGTTTCCC
* * *
32227 GAGGCAGACAATT-AATTATAATATATTTTATCTAAAAATATTAAAAAATTTAACTTAAAATCAA
1 AAGGCAGAC-ATTCAATTATAATATATTTTAACTAAAAATA-TAAAAAATTCAACTTAAAATCAA
* * *
32291 TTACGAGATTATAAAACCATTTAAAGTGAGTAATAAGGTTTTTGAAGGAATGGGTGACTATAAAT
64 TTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT
* * * * ** * * * *
32356 AGACTTTTCATGCCAATGAATGCTTTTTATAAATGTTCTTCAAGACAGACATTCAATTAT-ATCT
129 AGACTTTTCTTGTCAATGAAGGCTTTTTCTTCACGTT-TCCAAGGCAGAAATTCAATTATAATCT
* * * ** * * *
32420 GTTTTAACTAAAAATGTAAAAAAGTTTGACTTAAAATTAATTATGAGATTACAAAACTACTTAAA
193 GTTTTGACCAAAAATGTAAAAAAATTCAACTTAAAATTAATTATGAGATTATAAAACCATTTAAA
* * * * * * ********* * **
32485 GCAAGTAATAAGGTTTTTGAAGGCATGGGTGACTATAAAT-GANNNNNNNNNNTCAATAAATGGT
258 GCGAGTAATAAAGCTTTCGAAAGCATGAGTGACTATAAATAGA-CTTTTCTAGTCAATGAATGAC
* *
32549 TTTTTCTTCATGTTTCTC
322 TTTTTCTTCACGTTTCCC
** * ** * * *
32567 GTGGTAGACATTCAATTATAATATATTTGGACCAAAAATATGAAAAAATTCCACCTAAAATCAAT
1 AAGGCAGACATTCAATTATAATATATTTTAACTAAAAATAT-AAAAAATTCAACTTAAAATCAAT
* ***********
32632 TATGAGATTATAAAATCATTTNNNNNNNNNNGTAAGGCTTTTGAAGGAATGGGTGACTATAAATA
65 TATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATA
* * * ** * * * *
32697 GATTTTTCTTATCAATGAATGCTTTTTTCTTCGTGTTTCTTAAGGTAGACATTCAATTATAATTT
130 GACTTTTCTTGTCAATGAAGGC-TTTTTCTTCACGTTTC-CAAGGCAGAAATTCAATTATAATCT
32762 GTT
193 GTT
32765 CTAACTGAAA
Statistics
Matches: 1245, Mismatches: 285, Indels: 64
0.78 0.18 0.04
Matches are distributed among these distances:
338 2 0.00
339 103 0.08
340 268 0.22
341 241 0.19
342 409 0.33
343 216 0.17
344 6 0.00
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.35
Consensus pattern (339 bp):
AAGGCAGACATTCAATTATAATATATTTTAACTAAAAATATAAAAAATTCAACTTAAAATCAATT
ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAG
ACTTTTCTTGTCAATGAAGGCTTTTTCTTCACGTTTCCAAGGCAGAAATTCAATTATAATCTGTT
TTGACCAAAAATGTAAAAAAATTCAACTTAAAATTAATTATGAGATTATAAAACCATTTAAAGCG
AGTAATAAAGCTTTCGAAAGCATGAGTGACTATAAATAGACTTTTCTAGTCAATGAATGACTTTT
TCTTCACGTTTCCC
Done.