Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397403.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_833.0, 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: 23435
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.28
Warning! 5508 characters in sequence are not A, C, G, or T
Found at i:516 original size:171 final size:169
Alignment explanation
Indices: 9--1284 Score: 900
Period size: 171 Copynumber: 7.5 Consensus size: 169
1 TATAAAAT
* * * * * *
9 CATTTAAAGTGTGTAATAAGGCTTTTAAAGGAATGGGTGACTAT-AATAGACTTTTCTTACCAAC
1 CATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAAT
** * * * ** * * * **
73 GAATGCCATTCTCTTCACATTTCTCAA-GCTAGACGTTCAATTATAATCTGTTTTAATAAAAAAT
66 GAATATCTTTTTCTTTATGTATC-CAAGGC-AGACATTCAATTATAATATGTTTTAA-CCAAAA-
* ** * * *
137 ATGCAAGGAATTCAAACTAAAATCAATT-TGAAAATTATAAAAC
127 ATGTAAAAAATTCAATCTAAAATCAATTATG-AGATTATAAAGC
* * * * * *
180 CATTGAAAGTGAGGAATAAGGCTTTTGAAGGAATGGGTGACTATTAATGGACTTGTCCTGCCAAT
1 CATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAAT
* * * * * * * *
245 GAATACCTTTTTCTTCATGTTTCTTAGGGCAGACATTCAATTATAATATGTTCTAACCAAAACTA
66 GAATATCTTTTTCTTTATGTATC-CAAGGCAGACATTCAATTATAATATGTTTTAACCAAAAATG
********** *
310 TAAAAAAATTCANNNNNNNNNNATTTATGAGATTATAAAGC
130 T-AAAAAATTCAATCTAAAATCAATTATGAGATTATAAAGC
* * * * *
351 CATTTAATGTGAGTAACAAAGCTTTTGAAGGAATGAGTGACTACAAATGGGCTTTTCTTGCCAAT
1 CATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAAT
* * * * *
416 GAATATCTTTTTCTTTGTGTATGCCAAGGCAGACATTTAATTATAATCTTTTTTAACTAAAAATG
66 GAATATCTTTTTCTTTATGTAT-CCAAGGCAGACATTCAATTATAATATGTTTTAACCAAAAATG
* * * * * *
481 TAAAAAACTTTAGTGTAAAATCAATGATAAGATTATAAAAC
130 TAAAAAA-TTCAATCTAAAATCAATTATGAGATTATAAAGC
** * * * * ** * **
522 CATTTAAAACGAGTAGTAACGCTTTT-AATGGAATAAGTGAATATAAATAAACTTTTCTAGTAAA
1 CATTTAAAGTGAGTAATAAGGCTTTTGAA-GGAATGAGTGACTATAAATGGACTTTTCTTGCCAA
** * * * * *
586 TGAATGCCTTTCTCTTCACGTATCTCAAGGTTA-ACATTCAATTAGAATATGTTTTAACCAAAAA
65 TGAATATCTTTTTCTTTATGTATC-CAAGG-CAGACATTCAATTATAATATGTTTTAACCAAAAA
* * * *
650 TGTACAAAAAATTCAAACTAAAATCAATTTTGAGATTACAAAAC
128 TGT--AAAAAATTCAATCTAAAATCAATTATGAGATTATAAAGC
* *
694 CATTTAAAGTGAGTAATAAGGCTTTTAAAGG-ATGAGTGACTGTAAATGGACTTTTCTTGCCAAT
1 CATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAAT
* * * * * ** * *
758 GAATGTATTTTTCTTTCTATTTCTTGAGGTAGACATTCAATTATAATCTGTTTTAACC-AAAATG
66 GAATATCTTTTTCTTTATGTATC-CAAGGCAGACATTCAATTATAATATGTTTTAACCAAAAAT-
* * * *****
822 GATAAAGAATTCAA-ATAAAATCAATTTTGAGATTATNNNNN
129 G-TAAAAAATTCAATCTAAAATCAATTATGAGATTATAAAGC
***** * * * *
863 NNNNNAAAGTGAGTAATAAGGATTTTGAAGGAATGGGT-AATGATAAATGGAATTTTCTTGCCAA
1 CATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACT-ATAAATGGACTTTTCTTGCCAA
* * * * * * *
927 TTAAAACCTTTTTCTTCATGTATCCTAGGACAGACATTCAATTATAATATGTTCTAACCACAAAT
65 TGAATATCTTTTTCTTTATGTATCCAAGG-CAGACATTCAATTATAATATGTTTTAACCAAAAAT
* *
992 GTAAGAAAATTCAATCTAAAATCAATTACT-AGATTGTTAAGC
129 GTAA-AAAATTCAATCTAAAATCAATTA-TGAGATTATAAAGC
* * * * * *
1034 TATTTAATGTGAGTAATAAGGTTTTTGAAGGAATGAGTGACTATAAAGGGGCTTTTTCTTGCCAG
1 CATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGAC-TTTTCTTGCCAA
* * * * *
1099 TGAATATCTTTTTCTTTATGTTTCCAAAGCAAACATTCAATTATAATATGTTCTAACCACAAATG
65 TGAATATCTTTTTCTTTATGTATCCAAGGCAGACATTCAATTATAATATGTTTTAACCAAAAATG
**********
1164 TTAAAAAATTCAATCTAAANNNNNNNNNNAGATTATAAAGC
130 -TAAAAAATTCAATCTAAAATCAATTATGAGATTATAAAGC
* * * *
1205 CATTTAATA-TGATTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATCGACTTTTCTTACAAA
1 CATTTAA-AGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAA
* *
1269 TGAATGTGTTTTTCTT
65 TGAATATCTTTTTCTT
1285 CACGTTTCTA
Statistics
Matches: 854, Mismatches: 224, Indels: 55
0.75 0.20 0.05
Matches are distributed among these distances:
169 52 0.06
170 125 0.15
171 516 0.60
172 151 0.18
173 10 0.01
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.34
Consensus pattern (169 bp):
CATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAAT
GAATATCTTTTTCTTTATGTATCCAAGGCAGACATTCAATTATAATATGTTTTAACCAAAAATGT
AAAAAATTCAATCTAAAATCAATTATGAGATTATAAAGC
Found at i:1790 original size:170 final size:171
Alignment explanation
Indices: 1460--1866 Score: 412
Period size: 170 Copynumber: 2.4 Consensus size: 171
1450 TTATAATATA
* ** * * *
1460 TTTTAACAAAAAATGTAAAAAGTTTTAAACTTAAAATCAATTTTGAA-ATGATAAAATTATTTAA
1 TTTTAAC-AAAAATATAAAAAAATTTGAACTTAAAATCAATTTT-AAGATTATAAAACTATTTAA
* * * * * * *
1524 AATGAGTAATAAGGCTTTTGAAGGAATGGGTGACAATGAATAGACCTTTCTTACTAGTGAATGCC
64 AACGAGTAATAAGGCTTTTGAAGAAATGGGTGACAATCAATAGACATTTCTTACAAATAAATGCC
*
1589 TTTTTCTTCACCTTTCTCAAGATAAACATTTAAATATAACCTAT
129 TTTTTCTTCACCTTTCTCAAGATAAACATTTAAATATAACCT-G
* *
1633 TTTTAA-AAAAATATAAAAAAA-TTGAACTTAAAATCAATTATAAGATTATAAAACCT-TTTACA
1 TTTTAACAAAAATATAAAAAAATTTGAACTTAAAATCAATTTTAAGATTATAAAA-CTATTTAAA
* * * *
1695 ACGATTAATAAGGCTTTTGAAGAAATGGGTGACTATCAATGGACATTTAC-TGCAAATAAAT-CT
65 ACGAGTAATAAGGCTTTTGAAGAAATGGGTGACAATCAATAGACATTT-CTTACAAATAAATGC-
** * * ** ** *
1758 CTTTTTCTTCAGGTTTCTCGAGGTTGACATTTATTTATAATCTG
128 CTTTTTCTTCACCTTTCTCAAGATAAACATTTAAATATAACCTG
* * * *
1802 TTTTAACTAAAAATGTAAAAAAATTTGAACATAAAATCAATTTTGAGATTATAAAATTATTTAAA
1 TTTTAAC-AAAAATATAAAAAAATTTGAACTTAAAATCAATTTTAAGATTATAAAACTATTTAAA
1867 NNNNNNNNNN
Statistics
Matches: 191, Mismatches: 35, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
169 9 0.05
170 113 0.59
171 29 0.15
172 34 0.18
173 6 0.03
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (171 bp):
TTTTAACAAAAATATAAAAAAATTTGAACTTAAAATCAATTTTAAGATTATAAAACTATTTAAAA
CGAGTAATAAGGCTTTTGAAGAAATGGGTGACAATCAATAGACATTTCTTACAAATAAATGCCTT
TTTCTTCACCTTTCTCAAGATAAACATTTAAATATAACCTG
Found at i:2085 original size:171 final size:170
Alignment explanation
Indices: 1444--3098 Score: 895
Period size: 171 Copynumber: 9.7 Consensus size: 170
1434 CTCAGCACGT
* * * *** * * *
1444 ATTCAATTATAATATATTTTAACAAAAAATGTAAAAAGTTTTAAACTTAAAATCAATTTTGAAAT
1 ATTCAATTATAATCTGTTTTAACCAAAAATG-AAAAAAAATTCAATTTAAAATCAATTTTGAGAT
* ** * * * * * *
1509 GATAAAATTATTTAAAATGAGTAATAAGGCTTTTGAAGGAATGGGTGACAATGAATAGACCTTTC
65 TATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATAGACTTTTC
* * * * *
1574 TTA-CTAGTGAATGCCTTTTTCTTCACCTTTCTCAAGATAAAC
130 TTATC-AATGAATGCCTTTTTCTTCACGTTTCT-GAGGTAGAC
* * * * * * * *
1616 ATTTAAATATAACCTATTTTTAA--AAAAAT-ATAAAAAAATTGAACTTAAAATCAATTATAAGA
1 ATTCAATTATAATCT-GTTTTAACCAAAAATGA-AAAAAAATTCAATTTAAAATCAATTTTGAGA
* * * * * * * *
1678 TTATAAAACCTTTTACAA-CGATTAATAAGGCTTTTGAAGAAATGGGTGACTATCAATGGACATT
64 TTATAAAACCATTTA-AAGTGAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATAGAC-TT
* * * * *
1742 TAC-T-GCAAATAAAT-CTCTTTTTCTTCAGGTTTCTCGAGGTTGAC
127 TTCTTATC-AATGAATGC-CTTTTTCTTCACGTTTCT-GAGGTAGAC
* * * * * **
1786 ATTTATTTATAATCTGTTTTAACTAAAAATGTAAAAAAATTTGAACATAAAATCAATTTTGAGAT
1 ATTCAATTATAATCTGTTTTAACCAAAAATG-AAAAAAAATTCAATTTAAAATCAATTTTGAGAT
** ******************** * * *
1851 TATAAAATTATTTAAANNNNNNNNNNNNNNNNNNNNAGGTATGGGTGACTATAAATGGACTTTTC
65 TATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATAGACTTTTC
* * * * *
1916 TTGTCAATGAATGTCTTATTCTTCATGTTTCATGAGGTAGGC
130 TTATCAATGAATGCCTTTTTCTTCACGTTTC-TGAGGTAGAC
* **
1958 ATTCAATTATAATCTGTTTTAGCCAAAAATGTTAAAAAATTCAATTTAAAATC-ATTTCTGAGAT
1 ATTCAATTATAATCTGTTTTAACCAAAAATGAAAAAAAATTCAATTTAAAATCAATTT-TGAGAT
* *
2022 TATAAAACCATTCAAAGTGAGTAATAAGGCTTCTAAAGGAATGAGTGACTATAAATAGACTTTTC
65 TATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATAGACTTTTC
* * *
2087 TTCTCAAT-AAGTGTCTTTTTCTTCATGTTTGTCTG-GGTAGAC
130 TTATCAATGAA-TGCCTTTTTCTTCACG-TT-TCTGAGGTAGAC
* * ** *
2129 ATTCAATTATAATCTGTTTTAACTAAAAATGTAAAAAAAAAATTGAGCTTAAAATCGATTTTGAG
1 ATTCAATTATAATCTGTTTTAACCAAAAATG---AAAAAAAATTCAATTTAAAATCAATTTTGAG
* * * *
2194 ATTATAAAATCATTTAAATTCAGTAATAAGGCTTTTGAAGGAAT-AGGTGACTATAAATAGACTT
63 ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGA-GTGACTATAAATAGACTT
* * * * *
2258 TT-TATACCAATGAATACATTTCTCTTCACGTTTCTCAAGGTAGAC
127 TTCT-TATCAATGAATGCCTTTTTCTTCACGTTTCT-GAGGTAGAC
* * * *
2303 ATTCAATTATAATATTTTTTAACCAAAAAT-AAAAACAAATTCAACTTAGAATCAATTTTGAGAT
1 ATTCAATTATAATCTGTTTTAACCAAAAATGAAAAA-AAATTCAATTTAAAATCAATTTTGAGAT
********** * * * *
2367 TATNNNNNNNNNNAAAGTGAGTAATAAGTCTTTTGAAA-GAATGGGTTACTATAAATGGACTTTT
65 TATAAAACCATTTAAAGTGAGTAATAAGGCTTTT-AAAGGAATGAGTGACTATAAATAGACTTTT
* * * * *
2431 TTTATAAATGAATACCTTTTTCTTCACGTTTCCT-AGATTAAAC
129 CTTATCAATGAATGCCTTTTTCTTCACGTTT-CTGAG-GTAGAC
* * * *
2474 ATTCAAATTATAATATGTTCTAATCAAAAAT-ACAAAAAAATTCAATCTT-AAATAAATTATT-A
1 ATTC-AATTATAATCTGTTTTAACCAAAAATGA-AAAAAAATTCAAT-TTAAAATCAATT-TTGA
* * * * * * * * *
2536 GTTTATAAAATCATTTAAAGTGAGAAATAAGACTTTTGAAGAAATGAGTGACTGTAAATGGGCTT
62 GATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATAGACTT
* * * * * *
2601 TTCTTACCAATGAATACCTTTTTCTTCACATTTCTCAAGGCAAAC
127 TTCTTATCAATGAATGCCTTTTTCTTCACGTTTCT-GAGGTAGAC
* * * ** * * * *
2646 ATTCATTTATAATTTGTTCTAATAAAAAAT-ATAAAAGAATTAAATCTAAAATCAATTATGAGAT
1 ATTCAATTATAATCTGTTTTAACCAAAAATGA-AAAAAAATTCAATTTAAAATCAATTTTGAGAT
* * * * *
2710 TATAAAAACCATTTAGA-TAGAGTAATAAGGCTTTTAAAAGAATGGGTGACTTTAAATAGAGTTT
65 TAT-AAAACCATTTAAAGT-GAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATAGACTTT
* * * **
2774 T-TCTATCAATGAATGGCTTTTTCTTCATGTTTTTTGAACTAGAC
128 TCT-TATCAATGAATGCCTTTTTCTTCACG-TTTCTGAGGTAGAC
* * * *
2818 ATTCAATTATAATCTG-TTTAACC-AAAATGTACAAAGAATTTAA-ATAAAATCAATTTTGAGAT
1 ATTCAATTATAATCTGTTTTAACCAAAAATG-AAAAAAAATTCAATTTAAAATCAATTTTGAGAT
********** * * * * *
2880 TATAAAACCATTTANNNNNNNNNNTAAGGGTTTTGAAGGAATGGGTGA-TGATAAATGGAATTTT
65 TATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAGTGACT-ATAAATAGACTTTT
** * ** * * *
2944 CTTGCCAATTAAAACCTTTTTCTTTAAGTTTCCT-AGGACAGAC
129 CTTATCAATGAATGCCTTTTTCTTCACGTTT-CTGAGG-TAGAC
* * * *
2987 ATTCAATTATAATCTATTCTAACCATAAAT-ATAAAAAAATTCAATCTAAAATCAATTATT-AGA
1 ATTCAATTATAATCTGTTTTAACCAAAAATGA-AAAAAAATTCAATTTAAAATCAATT-TTGAGA
* *** * * *
3050 TTGTAAAGTGATTTAATA-TGAGTAATAAGACTTTTGAAGGAATGGGTGA
64 TTATAAAACCATTTAA-AGTGAGTAATAAGGCTTTTAAAGGAATGAGTGA
3099 NNNNNNNNNN
Statistics
Matches: 1137, Mismatches: 286, Indels: 121
0.74 0.19 0.08
Matches are distributed among these distances:
168 5 0.00
169 90 0.08
170 169 0.15
171 361 0.32
172 348 0.31
173 29 0.03
174 129 0.11
175 6 0.01
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.36
Consensus pattern (170 bp):
ATTCAATTATAATCTGTTTTAACCAAAAATGAAAAAAAATTCAATTTAAAATCAATTTTGAGATT
ATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATAGACTTTTCT
TATCAATGAATGCCTTTTTCTTCACGTTTCTGAGGTAGAC
Found at i:2828 original size:343 final size:340
Alignment explanation
Indices: 1957--2893 Score: 853
Period size: 343 Copynumber: 2.7 Consensus size: 340
1947 ATGAGGTAGG
* * * * * * *
1957 CATTCAATTATAATCTGTTT-TAGCCAAAAATGTTAAAAAATTCAATTTAAAATCATTTCTGAGA
1 CATTCAATTATAATAT-TTTCTAACAAAAAAT-ATAAAAAATTCAATCTAAAATCAATTATGAGA
* * * *
2021 TTATAAAACCATTCAAAGTGAGTAATAAGGCTTCTAAAGGAATGAGTGACTATAAATAGACTTTT
64 TTATAAAACCATTCAAAGTGAGTAATAAGGCTTTTAAAAGAATGGGTGACTATAAATAGATTTTT
* * **
2086 CTTCTCAAT-AAGTGTCTTTTTCTTCATGTTTGTCTG-GGTAGACATTCAATTATAATCTGTTTT
129 C-TATCAATGAA-TGCCTTTTTCTTCATGTTT-TCTGAACTAGACATTCAATTATAATCTG-TTT
* ** *
2149 AACTAAAAATGTAAAAAAAAAATTGAGCTTAAAATCGATTTTGAGATTATAAAATCATTTAAATT
190 AAC-AAAAA-GTAAAAAAAAAATTAAGCTTAAAATAAATTTTGAGATTATAAAATCATTTAAAGT
* * *
2214 CAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATAGACTTTTTATACCAATGAATACATTT
253 CAGAAATAAGACTTTTGAAGAAATAGGTGACTATAAATAGACTTTTTATACCAATGAATACATTT
* * *
2279 CTCTTCACGTTTCTCAAGGTAGA
318 CTCTTCACATTTCTCAAGGCAAA
* * * * *
2302 CATTCAATTATAATATTTTTTAACCAAAAATAAAAACAAATTCAA-CTTAGAATCAATTTTGAGA
1 CATTCAATTATAATATTTTCTAACAAAAAATATAAA-AAATTCAATC-TAAAATCAATTATGAGA
********** * * * *
2366 TTATNNNNNNNNNNAAAGTGAGTAATAAGTCTTTTGAAAGAATGGGTTACTATAAATGGACTTTT
64 TTATAAAACCATTCAAAGTGAGTAATAAGGCTTTTAAAAGAATGGGTGACTATAAATAGA-TTTT
* * * * * * * *
2431 TTTATAAATGAATACCTTTTTCTTCACGTTTCCT-AGATTAAACATTCAAATTATAATATGTTCT
128 TCTATCAATGAATGCCTTTTTCTTCATGTTTTCTGA-ACTAGACATTC-AATTATAATCTGTT-T
* * *
2495 AATCAAAAA-T-ACAAAAAAATTCAATCTT-AAATAAATTATT-AGTTTATAAAATCATTTAAAG
190 AA-CAAAAAGTAAAAAAAAAATT-AAGCTTAAAATAAATT-TTGAGATTATAAAATCATTTAAAG
* * * * *
2556 TGAGAAATAAGACTTTTGAAGAAAT-GAGTGACTGTAAATGGGCTTTTCT-TACCAATGAATACC
252 TCAGAAATAAGACTTTTGAAGAAATAG-GTGACTATAAATAGACTTTT-TATACCAATGAATACA
*
2619 TTTTTCTTCACATTTCTCAAGGCAAA
315 TTTCTCTTCACATTTCTCAAGGCAAA
* * *
2645 CATTCATTTATAAT-TTGTTCTAATAAAAAATATAAAAGAATTAAATCTAAAATCAATTATGAGA
1 CATTCAATTATAATATT-TTCTAACAAAAAATATAAAA-AATTCAATCTAAAATCAATTATGAGA
* * *
2709 TTATAAAAACCATTTAGA-TAGAGTAATAAGGCTTTTAAAAGAATGGGTGACTTTAAATAGAGTT
64 TTAT-AAAACCATTCAAAGT-GAGTAATAAGGCTTTTAAAAGAATGGGTGACTATAAATAGA-TT
* *
2773 TTTCTATCAATGAATGGCTTTTTCTTCATGTTTTTTGAACTAGACATTCAATTATAATCTGTTTA
126 TTTCTATCAATGAATGCCTTTTTCTTCATGTTTTCTGAACTAGACATTCAATTATAATCTGTTTA
* * * * * * *
2838 ACCAAAATGT-ACAAAGAATTTAA--ATAAAATCAATTTTGAGATTATAAAACCATTTA
191 A-CAAAAAGTAAAAAAAAAATTAAGCTTAAAATAAATTTTGAGATTATAAAATCATTTA
2894 NNNNNNNNNN
Statistics
Matches: 470, Mismatches: 99, Indels: 50
0.76 0.16 0.08
Matches are distributed among these distances:
340 3 0.01
341 24 0.05
342 14 0.03
343 186 0.40
344 95 0.20
345 122 0.26
346 25 0.05
347 1 0.00
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.36
Consensus pattern (340 bp):
CATTCAATTATAATATTTTCTAACAAAAAATATAAAAAATTCAATCTAAAATCAATTATGAGATT
ATAAAACCATTCAAAGTGAGTAATAAGGCTTTTAAAAGAATGGGTGACTATAAATAGATTTTTCT
ATCAATGAATGCCTTTTTCTTCATGTTTTCTGAACTAGACATTCAATTATAATCTGTTTAACAAA
AAGTAAAAAAAAAATTAAGCTTAAAATAAATTTTGAGATTATAAAATCATTTAAAGTCAGAAATA
AGACTTTTGAAGAAATAGGTGACTATAAATAGACTTTTTATACCAATGAATACATTTCTCTTCAC
ATTTCTCAAGGCAAA
Found at i:3650 original size:171 final size:168
Alignment explanation
Indices: 3350--4245 Score: 696
Period size: 171 Copynumber: 5.2 Consensus size: 168
3340 ATCTATTTTA
* * ** * **
3350 AAATCAATTATT-CGATTATAAAACCATTTAAAACGAGTAATAAGGATTTTGAAGGAATGGGAAA
1 AAATCAATT-TTGAGATTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGA
* * * * * * * * * *
3414 CCACAAATGGACTTTTCTTCCCAATAAATGAC-TTTTACTAC-TCGTTTCCCTCGGCACG-TATT
65 CTATAAATAGACTTTTCTTGCCAATGAAT-ACATTTTTCTTCAT-GTTT-CATAGGCA-GACATT
*
3476 CAATTATAATCTGTTTTAACCAAAAATGTAAAAAATTTTAAACTT
126 CAATTATAATATGTTTTAACCAAAAATGTAAAAAA--TTAAACTT
* * * * ** *
3521 AAATAAATTTTGAGATTATAAAATTATTTAAAGCGAGTAACAAGGCTTTTGAAGGTGTGGGTGAT
1 AAATCAATTTTGAGATTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
* * * *
3586 TATAAATAGACTATTCTTGCCAATGAATGTC-TTATTCTTCATGTTTCATGAGGTAGACATTCAA
66 TATAAATAGACTTTTCTTGCCAATGAAT-ACATTTTTCTTCATGTTTCAT-AGGCAGACATTCAA
* * * *
3650 TTATAATCTGTTTTAGCCAAAAATGTTAAAAAATTCAATTT
129 TTATAATATGTTTTAACCAAAAATG-TAAAAAATTAAACTT
* *
3691 AAAATCAATTTTGAGATTATAAAATCATTCAAAGTGAGTAGTAAGGCTTTTGAAGGAATGGGTGA
1 -AAATCAATTTTGAGATTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGA
* *** * ** ***
3756 CTATAAATAGACTTTTCTTGTCAATGAATGTTTTTTTCTTCATTTTTGTTAAATTAGACATTCAA
65 CTATAAATAGACTTTTCTTGCCAATGAATACATTTTTCTTCATGTTTCAT-AGGCAGACATTCAA
* * * * *
3821 TTATAATATATTTTGACTAGAAATGTAAAAAAATTCAACTT
129 TTATAATATGTTTTAACCAAAAATGT-AAAAAATTAAACTT
********* * * *
3862 AAANNNNNNNNNNAGATTATAAAATTATTTAAAGTGTGTAATATGGCTTTTGAAGGAAT-GGTGA
1 AAA-TCAATTTTGAGATTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGA
** * * * * * * *
3926 CTATAAATAGACTTTTCTTGGTAGTGAATACTTTTTTCTTTACGTTCCCTAGGGCATACATTCAA
65 CTATAAATAGACTTTTCTTGCCAATGAATACATTTTTCTTCATGTTTCATA-GGCAGACATTCAA
* * **
3991 TTTTAATATGTTCTAACCAAAAATGTAAAAAAACACAATCTT
129 TTATAATATGTTTTAACCAAAAATGTAAAAAATTA-AA-CTT
* * *
4033 AAATCAATTATT-AGTTTATAAAACCATTTAAAGTGAGAAATAAGGCTTTTGAAGGAATGGGTGA
1 AAATCAATT-TTGAGATTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGA
* * *
4097 CTGTAAAT-GAGCTTTTCTTGCCAGTGAATACATTTTTCTTCACAT-TTTCCA-AGGCAAACATT
65 CTATAAATAGA-CTTTTCTTGCCAATGAATACATTTTTCTT--CATGTTT-CATAGGCAGACATT
* * * * *
4159 CACTTATAATTTGTTCTAACCAAAAATATTAAAAAATTAAACCTA
126 CAATTATAATATGTTTTAACCAAAAAT-GTAAAAAATTAAA-CTT
* * * *
4204 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGCAATA
1 AAATCAATTTTGAGATTATAAAATCATTTAAAGTGAGTAATA
4246 NNNNNNNNNN
Statistics
Matches: 576, Mismatches: 129, Indels: 40
0.77 0.17 0.05
Matches are distributed among these distances:
169 7 0.01
170 133 0.23
171 415 0.72
172 19 0.03
173 2 0.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (168 bp):
AAATCAATTTTGAGATTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
TATAAATAGACTTTTCTTGCCAATGAATACATTTTTCTTCATGTTTCATAGGCAGACATTCAATT
ATAATATGTTTTAACCAAAAATGTAAAAAATTAAACTT
Found at i:3989 original size:170 final size:161
Alignment explanation
Indices: 3704--4206 Score: 357
Period size: 170 Copynumber: 3.0 Consensus size: 161
3694 ATCAATTTTG
*
3704 AGATTATAAAATCATTCAAAGTGAGTAGTAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACT
1 AGATTATAAAATCATTCAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACT
** ** *** ** *
3769 TTTCTTGTCAATGAATGTTTTTTTCTTCATTTTTGTTAAATTAGACATTCAATTATAATATATTT
66 TTTCTTGTCAATGAATACTTTTTTCTTCACGTTCCCTAAAGCAGACATTCAATTATAATATATTC
* * *
3834 TGACTAGAAATGTAAAAAAATTCAACTTAAA
131 TAACCAAAAATGTAAAAAAATTCAACTTAAA
* * * *
3865 NNNNNNNNNNAGATTATAAAATTATTTAAAGTGTGTAATATGGCTTTTGAAGGAAT-GGTGACTA
1 ----------AGATTATAAAATCATTCAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTA
* * ** *
3929 TAAATAGACTTTTCTTGGT-AGTGAATACTTTTTTCTTTACGTTCCCTAGGGCATACATTCAATT
56 TAAATAGACTTTTCTT-GTCAATGAATACTTTTTTCTTCACGTTCCCTAAAGCAGACATTCAATT
* * **
3993 TTAATATGTTCTAACCAAAAATGTAAAAAAACACAATCTTAAATCAATTA
120 ATAATATATTCTAACCAAAAATGTAAAAAAATTCAA-C-T---T-AA--A
* * * * *
4043 TTAGTTTATAAAACCATTTAAAGTGAGAAATAAGGCTTTTGAAGGAATGGGTGACTGTAAAT-GA
1 --AGATTATAAAATCATTCAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGA
* * * * * * * * *
4107 GCTTTTCTTGCCAGTGAATACATTTTTCTTCACATTTTCC-AAGGCAAACATTCACTTATAATTT
64 -CTTTTCTTGTCAATGAATACTTTTTTCTTCAC-GTTCCCTAAAGCAGACATTCAATTATAATAT
* * * * *
4171 GTTCTAACCAAAAATATTAAAAAATTAAACCTAAA
127 ATTCTAACCAAAAATGTAAAAAAATTCAACTTAAA
4206 A
1 A
4207 TCAATTATGA
Statistics
Matches: 267, Mismatches: 52, Indels: 36
0.75 0.15 0.10
Matches are distributed among these distances:
161 1 0.00
163 1 0.00
165 2 0.01
166 1 0.00
170 127 0.48
171 126 0.47
172 5 0.02
175 1 0.00
176 2 0.01
178 1 0.00
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.36
Consensus pattern (161 bp):
AGATTATAAAATCATTCAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACT
TTTCTTGTCAATGAATACTTTTTTCTTCACGTTCCCTAAAGCAGACATTCAATTATAATATATTC
TAACCAAAAATGTAAAAAAATTCAACTTAAA
Found at i:4222 original size:341 final size:341
Alignment explanation
Indices: 3473--4240 Score: 751
Period size: 341 Copynumber: 2.2 Consensus size: 341
3463 CTCGGCACGT
* * * *
3473 ATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAATTTTAAA-CTTAAATAAATTTTGAGAT
1 ATTCAATTATAATATGTTTTAACCAAAAATTTAAAAAA--TTAAACCTAAAATAAATTATGAGAT
** *
3537 TATAAAATTATTTAAAGCGAGTAACAAGGCTTTTGAAGGTGTGGGTGATTATAAATAGACTATTC
64 TATAAAATTATTTAAAGCGAGTAACAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTATTC
* * * * * * *
3602 TTGCCAATGAATGTCTTATTCTTCATGTTTCATGAGGTAGACATTCAATTATAATCTGTTTTAGC
129 TTGCCAATGAATCTCTTATTCTTCACGTTCCATGAGGCAGACATTCAATTATAATATGTTCTAAC
* ** * * *
3667 CAAAAATGTTAAAAAATTCAATTTAAAATCAATTTTGAGATTATAAAATCATTCAAAGTGAGTAG
194 CAAAAATGTAAAAAAACACAATTTAAAATCAATTTTGAGATTATAAAACCATTCAAAGTGAGAAA
* ***
3732 TAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGTCAATGAATGTTTTTTTCTTC
259 TAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATACATTTTTCTTC
* ** ** *
3797 ATTTTTGTTAAATTAGAC
324 AATTTTGCCAAAGCAAAC
* * * * * * * **********
3815 ATTCAATTATAATATATTTTGACTAGAAATGTAAAAAAATTCAACTTAAANNNNNNNNNNAGATT
1 ATTCAATTATAATATGTTTTAACCAAAAAT-TTAAAAAATTAAACCTAAAATAAATTATGAGATT
* * * * *
3880 ATAAAATTATTTAAAGTGTGTAATATGGCTTTTGAAGGAAT-GGTGACTATAAATAGACTTTTCT
65 ATAAAATTATTTAAAGCGAGTAACAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTATTCT
** * * * * * *
3944 TGGTAGTGAATACT-TTTTTCTTTACGTTCCCT-AGGGCATACATTCAATTTTAATATGTTCTAA
130 TGCCAATGAAT-CTCTTATTCTTCACGTTCCATGA-GGCAGACATTCAATTATAATATGTTCTAA
* *
4007 CCAAAAATGTAAAAAAACACAATCTT-AAATCAATTATT-AGTTTATAAAACCATTTAAAGTGAG
193 CCAAAAATGTAAAAAAACACAAT-TTAAAATCAATT-TTGAGATTATAAAACCATTCAAAGTGAG
* *
4070 AAATAAGGCTTTTGAAGGAATGGGTGACTGTAAAT-GAGCTTTTCTTGCCAGTGAATACATTTTT
256 AAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGA-CTTTTCTTGCCAATGAATACATTTTT
*
4134 CTTCACATTTT-CCAAGGCAAAC
320 CTTCA-ATTTTGCCAAAGCAAAC
* * * *
4156 ATTCACTTATAATTTGTTCTAACCAAAAATATTAAAAAATTAAACCTAAAATCAATTATGAGATT
1 ATTCAATTATAATATGTTTTAACCAAAAAT-TTAAAAAATTAAACCTAAAATAAATTATGAGATT
**
4221 ATAAAACCATTTAAAGCGAG
65 ATAAAATTATTTAAAGCGAG
4241 CAATANNNNN
Statistics
Matches: 329, Mismatches: 89, Indels: 17
0.76 0.20 0.04
Matches are distributed among these distances:
340 3 0.01
341 243 0.74
342 77 0.23
343 6 0.02
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.36
Consensus pattern (341 bp):
ATTCAATTATAATATGTTTTAACCAAAAATTTAAAAAATTAAACCTAAAATAAATTATGAGATTA
TAAAATTATTTAAAGCGAGTAACAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTATTCTT
GCCAATGAATCTCTTATTCTTCACGTTCCATGAGGCAGACATTCAATTATAATATGTTCTAACCA
AAAATGTAAAAAAACACAATTTAAAATCAATTTTGAGATTATAAAACCATTCAAAGTGAGAAATA
AGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATACATTTTTCTTCAA
TTTTGCCAAAGCAAAC
Found at i:4936 original size:170 final size:171
Alignment explanation
Indices: 4756--5129 Score: 460
Period size: 169 Copynumber: 2.2 Consensus size: 171
4746 GTTTACGTAC
*
4756 AAAG-AATTCAA-GTAAAATCAATT-TTGAGATTATAAAACCATGAAAAGTGAGTAATAAACATT
1 AAAGAAATTCAATCTAAAATCAATTATT-AGATTATAAAACCATGAAAAGTGAGTAATAAA-ATT
* * *
4818 TTGAAGGAATGTGTGA-TGATAAATG-GAATTTTTTTGCCAATTAAAACCTTTTT-TTTCATATT
64 TTGAAGGAATGGGTGACT-ATAAATGAG-ATTTTCTTGCCAATGAAAACCTTTTTCTTT-ATATT
* * * * *
4880 TCCTAGGGCAAACATTCAATTATAATCTGTTTTAACCACAAATG-T
126 TCCCAAGGCAAACATTCAATTATAATATGTTCTAACCAAAAATGTT
* * ** * * *
4925 AAAGAAATTCAATCTAAAATCAATTATTAGATTGT-AAGCCATTTAATGTGAGTAATAGAGTTTT
1 AAAGAAATTCAATCTAAAATCAATTATTAGATTATAAAACCATGAAAAGTGAGTAATAAAATTTT
* * *
4989 GAAGGAATGGGTGACTATAAATGAGCTTTTCTTGCCAATGAATACCTTTTTCTTTATGTTTCCCA
66 GAAGGAATGGGTGACTATAAATGAGATTTTCTTGCCAATGAAAACCTTTTTCTTTATATTTCCCA
*
5054 AGGCGAACATTCAATTATAATATGTTCTAACCAAAAATGTT
131 AGGCAAACATTCAATTATAATATGTTCTAACCAAAAATGTT
5095 AAA-AAATTCAATCTAAAATCAATTATTAGATTATA
1 AAAGAAATTCAATCTAAAATCAATTATTAGATTATA
5130 NNNNNNNNNN
Statistics
Matches: 176, Mismatches: 21, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
169 122 0.69
170 35 0.20
171 17 0.10
172 2 0.01
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (171 bp):
AAAGAAATTCAATCTAAAATCAATTATTAGATTATAAAACCATGAAAAGTGAGTAATAAAATTTT
GAAGGAATGGGTGACTATAAATGAGATTTTCTTGCCAATGAAAACCTTTTTCTTTATATTTCCCA
AGGCAAACATTCAATTATAATATGTTCTAACCAAAAATGTT
Found at i:5243 original size:171 final size:169
Alignment explanation
Indices: 4756--5202 Score: 410
Period size: 169 Copynumber: 2.6 Consensus size: 169
4746 GTTTACGTAC
* * * * * *
4756 AAAG-AATTCAA-GTAAAATCAATT-TTGAGATTATAAAACCA-TGAAAAGTGAGTAATAAACAT
1 AAAGAAATTCAATCTAAAATCAATTATT-AGATTAT-AAGCCATTTAATA-TGAGTAATAGA-GT
* * * * * *
4817 TTTGAAGGAATGTGTGA-TGATAAATGGAA-TTTTTTTGCCAATTAAAACCTTTTT-TTTCATAT
62 TTTGAAGGAATGAGTGACT-ATAAAT-CAACTTTTCTTGCCAATGAATACCTTTTTCTTT-ACAT
* * * * *
4879 TTCCTAGGGCA-AACATTCAATTATAATCTGTTTTAACCACAAATGT
124 TTCCCAAGG-AGAACATTCAATTATAATATGTTCTAACCAAAAATGT
* *
4925 AAAGAAATTCAATCTAAAATCAATTATTAGATTGTAAGCCATTTAATGTGAGTAATAGAGTTTTG
1 AAAGAAATTCAATCTAAAATCAATTATTAGATTATAAGCCATTTAATATGAGTAATAGAGTTTTG
* * * **
4990 AAGGAATGGGTGACTATAAATGAGCTTTTCTTGCCAATGAATACCTTTTTCTTTATGTTTCCCAA
66 AAGGAATGAGTGACTATAAATCAACTTTTCTTGCCAATGAATACCTTTTTCTTTACATTTCCCAA
*
5055 GGCGAACATTCAATTATAATATGTTCTAACCAAAAATGTT
131 GGAGAACATTCAATTATAATATGTTCTAACCAAAAATG-T
*********
5095 AAA-AAATTCAATCTAAAATCAATTATTAGATTATANNNNNNNNNNATATGAGTAATA-AGGCTT
1 AAAGAAATTCAATCTAAAATCAATTATTAGATTATA-AGCCATTTAATATGAGTAATAGA-G-TT
5158 TTGAAGGAATGAGTGACTATAAATCAACTTTTCTTGCCAATGAAT
63 TTGAAGGAATGAGTGACTATAAATCAACTTTTCTTGCCAATGAAT
5203 GTGTTTTTTT
Statistics
Matches: 232, Mismatches: 34, Indels: 22
0.81 0.12 0.08
Matches are distributed among these distances:
168 2 0.01
169 122 0.53
170 42 0.18
171 64 0.28
172 2 0.01
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.34
Consensus pattern (169 bp):
AAAGAAATTCAATCTAAAATCAATTATTAGATTATAAGCCATTTAATATGAGTAATAGAGTTTTG
AAGGAATGAGTGACTATAAATCAACTTTTCTTGCCAATGAATACCTTTTTCTTTACATTTCCCAA
GGAGAACATTCAATTATAATATGTTCTAACCAAAAATGT
Found at i:5847 original size:171 final size:169
Alignment explanation
Indices: 5666--6167 Score: 535
Period size: 173 Copynumber: 2.9 Consensus size: 169
5656 NNNNNNNNNN
* * *
5666 TTAACCAAAAATGTAAAAAAATTAAATTTAAAATCAATTATAAGATTATAAAACCTTTTACAGCG
1 TTAACCAAAAATATAAAAAAATTAAATTTAAAATCAATTATGAGATTATAAAACCTTTTAAAGCG
* * * * *
5731 AGTAATAAGACTTTTGAAAGAATAGGTGACTATAAAT-GAACATTTATTGCAAATGAATGTCTTT
66 AGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATAGAA-TTTTCTTTC-AATGAATGTCTTT
* *
5795 TTCTTTATGTTTCTCGAGGTAGACATTCAATTATTAT-CTCTT
129 TTCTTCATGTTT-TCGAGGTAGACATTCAATTATAATCCT-TT
* * * * *
5837 TTAACCAAAAATATAAAAAAAAACTGAACTTAAAATCAATTTTGAGATTATAAAA-TTATTTAAA
1 TTAACCAAAAATAT--AAAAAAATTAAATTTAAAATCAATTATGAGATTATAAAACCT-TTTAAA
* * * *
5901 GCGAGTAAGAAGGCTTTTGAAAGTATGGGTGACTATAAATAGAATTTTCTTTCCAATAAATATCT
63 GCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATAGAATTTTCTTT-CAATGAATGTCT
* * * * *
5966 TATTCTTCACGTTTTATGTGGTAGACATTTAATTATAATCCTTT
127 TTTTCTTCATGTTTT-CGAGGTAGACATTCAATTATAATCCTTT
* * * * * * * * *
6010 TTAGCTAAAAATTTTAAAAAATTCAATTTAAAATCAATTCTGAGATTATAAAACCATTCAAAGTG
1 TTAACCAAAAATATAAAAAAATTAAATTTAAAATCAATTATGAGATTATAAAACCTTTTAAAGCG
* *
6075 AGTCATAAGGCTTCT-AAATGAATGGGTGACTATAAATAGAATTTTCTTATCAATGAATGTCTTT
66 AGTAATAAGGCTTTTGAAA-GAATGGGTGACTATAAATAGAATTTTCTT-TCAATGAATGTCTTT
* *
6139 TTCTTCATGTTTGTCTAGGTAGATATTCA
129 TTCTTCATGTTT-TCGAGGTAGACATTCA
6168 NNNNNNNNNN
Statistics
Matches: 271, Mismatches: 49, Indels: 22
0.79 0.14 0.06
Matches are distributed among these distances:
170 3 0.01
171 126 0.46
172 4 0.01
173 132 0.49
174 6 0.02
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.37
Consensus pattern (169 bp):
TTAACCAAAAATATAAAAAAATTAAATTTAAAATCAATTATGAGATTATAAAACCTTTTAAAGCG
AGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATAGAATTTTCTTTCAATGAATGTCTTTTT
CTTCATGTTTTCGAGGTAGACATTCAATTATAATCCTTT
Found at i:5920 original size:173 final size:169
Alignment explanation
Indices: 5666--6271 Score: 572
Period size: 171 Copynumber: 3.5 Consensus size: 169
5656 NNNNNNNNNN
* * * * * *
5666 TTAACCAAAAATGT-AAAAAAATTAAATTTAAAATCAATTATAAGATTATAAAACCTTTTACAGC
1 TTAACCAAAAATGTAAAAAAAATTGAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGC
* * * * *
5730 GAGTAATAAGACTTTTGAAAGAATAGGTGACTATAAAT-GAACATTTATTGCAAATGAATGTCTT
66 GAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATAGAA-TTTTCTTTC-AATGAATGTCTT
* *
5794 TTTCTTTATGTTTCTCGAGGTAGACATTCAATTATTATCTCTT
129 TTTCTTCATGTTT-TCGAGGTAGACATTCAATTATAATC-CTT
* * **
5837 TTAACCAAAAATATAAAAAAAAACTGAACTTAAAATCAATTTTGAGATTATAAAATTATTTAAAG
1 TTAACCAAAAATGT-AAAAAAAATTGAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAG
* * * *
5902 CGAGTAAGAAGGCTTTTGAAAGTATGGGTGACTATAAATAGAATTTTCTTTCCAATAAATATCTT
65 CGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATAGAATTTTCTTT-CAATGAATGTCTT
* * * * *
5967 ATTCTTCACGTTTTATGTGGTAGACATTTAATTATAATCCTTT
129 TTTCTTCATGTTTT-CGAGGTAGACATTCAATTATAATCC-TT
* * ** * * * * *
6010 TTAGCTAAAAAT-TTTAAAAAATTCAATTTAAAATCAATTCTGAGATTATAAAACCATTCAAAGT
1 TTAACCAAAAATGTAAAAAAAATTGAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGC
* *
6074 GAGTCATAAGGCTTCT-AAATGAATGGGTGACTATAAATAGAATTTTCTTATCAATGAATGTCTT
66 GAGTAATAAGGCTTTTGAAA-GAATGGGTGACTATAAATAGAATTTTCTT-TCAATGAATGTCTT
* * **********
6138 TTTCTTCATGTTTGTCTAGGTAGATATTCANNNNNNNNNNGTT
129 TTTCTTCATGTTT-TCGAGGTAGACATTCA-ATTATAATCCTT
* * * *
6181 TTAACCAAAAATGTAAAAAAAAAAGTGAGCTTAAAACCAATTTTGAGATTATAAAATCATTTAAA
1 TTAACCAAAAATGT--AAAAAAAATTGAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAA
*
6246 GTGAGTAATAAGGCTTTTGAAAGAAT
64 GCGAGTAATAAGGCTTTTGAAAGAAT
6272 NNNNNNNNNN
Statistics
Matches: 346, Mismatches: 75, Indels: 25
0.78 0.17 0.06
Matches are distributed among these distances:
170 3 0.01
171 139 0.40
172 6 0.02
173 132 0.38
174 63 0.18
175 3 0.01
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.35
Consensus pattern (169 bp):
TTAACCAAAAATGTAAAAAAAATTGAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGC
GAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATAGAATTTTCTTTCAATGAATGTCTTTT
TCTTCATGTTTTCGAGGTAGACATTCAATTATAATCCTT
Found at i:7914 original size:172 final size:172
Alignment explanation
Indices: 7250--7930 Score: 548
Period size: 172 Copynumber: 4.0 Consensus size: 172
7240 NNNNNNCTCG
* * * *
7250 AAATTGATTTCACTTTGAATTCTTTGTACACTTTTAGTTAAAACAGATTAGAATTGAATGTCTAC
1 AAATTGATTTCACTTTGAATTCTTTGTACATTTTTTGTTAAAACAGATTATAATTGAATGTTTAC
* * * *
7315 CTTGAGAAACATTAAGAAAAAGATATTCATTGATAAGAAAAGTGCATTTACAGTCACCCATTTCT
66 CTTGAGAAACATGAAGAAAAAGACATTCATTGACAAGAAAAGTCCATTTACAGTCACCCATTTCT
* *** *
7380 TTATAAGCCTTATTACTTGTTTTAAATGGTTTTATAATATCA
131 TTAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCA
* * * ********
7422 AAATTGATTTTAGTTTGAATTCTTTGTACATTTTTTGTTAAAACATATTATAATTGANNNNNNNN
1 AAATTGATTTCACTTTGAATTCTTTGTACATTTTTTGTTAAAACAGATTATAATTGAATGTTTAC
**** * * * *
7487 NNCAAGAAACATAAAGAAAAAGTCATTCATTGACAAGAAAAGTCCATTTAAAGTCATCCA-TTCT
66 CTTGAGAAACATGAAGAAAAAGACATTCATTGACAAGAAAAGTCCATTTACAGTCACCCATTTC-
* **********
7551 TTTAAAAGCCCTATTACTCNNNNNNNNNNGTTTTATAATCTCA
130 TTTAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCA
* *** * * * * *
7594 TAATTGATTTTTGGTTT-AATGT-TTT-TATA-TTTTT-TTAGAACAAATTATAAGTGAATTTTT
1 AAATTGA-TTTCACTTTGAAT-TCTTTGTACATTTTTTGTTAAAACAGATTATAATTGAATGTTT
* * ** ** * *
7654 GCCTTGGGAAATGTGAAGAAAAAGGTATTCATTGACAAGAAAAGCCCATTTACAGTCACCCATTC
64 ACCTTGAGAAACATGAAGAAAAAGACATTCATTGACAAGAAAAGTCCATTTACAGTCACCCATTT
* ********** *
7719 CTTCAANNNNNNNNNNACTCACTTTAAATGGTTTTATAATCTTA
129 CTTTAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCA
* *
7763 AAATTGATTTCACTTTGAATTCTTTGTACATTTTTTCTTAAAGCAGATTATAATTGAATGTTTAC
1 AAATTGATTTCACTTTGAATTCTTTGTACATTTTTTGTTAAAACAGATTATAATTGAATGTTTAC
* * * * *
7828 CTTGAGAAATATGAAGAAAAAGACATTCATTGATAAGAAATGTCCATTCGA-AGACACCCATTTC
66 CTTGAGAAACATGAAGAAAAAGACATTCATTGACAAGAAAAGTCCATT-TACAGTCACCCATTTC
* *
7892 TTTAAAAGCCTTATTGCTCACTTTAAATAGTTTTATAAT
130 TTTAAAAGCCTTATTACTCACTTTAAATGGTTTTATAAT
7931 TNNNNNNNNN
Statistics
Matches: 376, Mismatches: 123, Indels: 20
0.72 0.24 0.04
Matches are distributed among these distances:
168 7 0.02
169 97 0.26
170 10 0.03
171 11 0.03
172 241 0.64
173 10 0.03
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.37
Consensus pattern (172 bp):
AAATTGATTTCACTTTGAATTCTTTGTACATTTTTTGTTAAAACAGATTATAATTGAATGTTTAC
CTTGAGAAACATGAAGAAAAAGACATTCATTGACAAGAAAAGTCCATTTACAGTCACCCATTTCT
TTAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCA
Found at i:8581 original size:171 final size:171
Alignment explanation
Indices: 8296--8802 Score: 437
Period size: 171 Copynumber: 3.0 Consensus size: 171
8286 NNNNNNNNNN
* * *
8296 ATAAGGCTTTTGAAGGAATGGGTGATTATAAATGGACTTTTTTTGTAAATGAATGCTATTTTCTT
1 ATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGTAAATGAATGCTATTTTCTT
* *********** * *
8361 CACGTTTCTCAAGGNNNNNNNNNNATTATAGTCTATTTTAACCAAAAGTGCCAAA-CAATTCAAC
66 CACATTTCTCAAGATAGACATTCAATTATAGCCTATTTTAACCAAAAGTG-CAAAGAAATTCAAC
* ****
8425 TTAAAATCAATTATGACTTTATAAAACTATTTAAAGTGTGTA
130 TTAAAATCAATTATGACTTTATAAAACCATTTAAAGCAAATA
* ** *
8467 ATAAGGCTTTTAAAGGAATAGGTGACTATAAATGGACTTTTCTTGTCCATGAATGCTTTTTTCTT
1 ATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGTAAATGAATGCTATTTTCTT
* * * *
8532 CACATTTCTCAAGATAGACATTCAATTATAGCCTGTTTTGACCAAAAGTGTAAAGAAATTGAACT
66 CACATTTCTCAAGATAGACATTCAATTATAGCCTATTTTAACCAAAAGTGCAAAGAAATTCAACT
* *
8597 TAAAATCAATTATTATTTTATAAAACCATTTAAAGCAAATA
131 TAAAATCAATTATGACTTTATAAAACCATTTAAAGCAAATA
* ** * * * ** **
8638 ATAAGGCTTTCGAAGGCTTAAGTGACTATAAATGGACTTTTCATGCT-AGTGGTTGGCT-TTCAC
1 ATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTG-TAAATGAAT-GCTATTTTC
* ** * * * * * ** *
8701 TTTATGTTTCCCAAGACAGACATTCAATTGTAGCCTTTTTTATCCAAAAACGTAAA-AAGATTCA
64 TTCACATTTCTCAAGATAGACATTCAATTATAGCCTATTTTAACCAAAAGTGCAAAGAA-ATTCA
* ** *
8765 ACTTAAAATCAATTTTGAGATTATAAAATCATTTAAAG
128 ACTTAAAATCAATTATGACTTTATAAAACCATTTAAAG
8803 TGANNNNNNN
Statistics
Matches: 271, Mismatches: 61, Indels: 8
0.80 0.18 0.02
Matches are distributed among these distances:
170 5 0.02
171 262 0.97
172 4 0.01
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.36
Consensus pattern (171 bp):
ATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGTAAATGAATGCTATTTTCTT
CACATTTCTCAAGATAGACATTCAATTATAGCCTATTTTAACCAAAAGTGCAAAGAAATTCAACT
TAAAATCAATTATGACTTTATAAAACCATTTAAAGCAAATA
Found at i:9758 original size:172 final size:172
Alignment explanation
Indices: 9035--9805 Score: 715
Period size: 172 Copynumber: 4.5 Consensus size: 172
9025 NNNNNNNNNN
* ** * * *
9035 TGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCATTTTTCTTCACATTTTTCGAGGTAAA
1 TGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGA
* * * * * * *
9100 CATTCGATTATAATCTGTTTTAACTAAAAATATATAAATAATTCAAATTGAAATCAATTTTGAGA
66 CATTCAATTATAATCTGTTCTAACTAAAAATGTATAAAAAATTCAAACTAAAATCAATTATGAGA
********** * *
9165 TTATAAAACCATTTAANNNNNNNNNNAAAGATTTTGAAGGAA
131 TTATAAAACCATTTAAAGTGAGTAATAAAGCTTTTAAAGGAA
* * ** * * * *
9207 TGGGTGACTATAAATGGACTTTTCTTACTAATGAATATCTCTTTCTTCATGTTTCCCCAGGCAGA
1 TGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGA
* * * * ******
9272 CATTCAATTATAATCTGTTCTAACTAAAAATGTATGAAGAATTCAAATTGAAATCAATTNNNNNN
66 CATTCAATTATAATCTGTTCTAACTAAAAATGTATAAAAAATTCAAACTAAAATCAATTATGAGA
**** ** *
9337 NNNNAAAACCATTTAAAGTGAGTAATAAAGCTTTTGCAGTAA
131 TTATAAAACCATTTAAAGTGAGTAATAAAGCTTTTAAAGGAA
* * * * * * * * *
9379 TTGGTGACTATAAATGGGCTTTTCTTGTCAATGAATACCTTTTTCTTTATGTTTCTTAGGGCAAA
1 TGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGA
* *
9444 CATTCAATTATAATCTGTTCTAACTAAAAATGTAAAAAAAATT-AACCTAAAATCAATTATGAGA
66 CATTCAATTATAATCTGTTCTAACTAAAAATGTATAAAAAATTCAAACTAAAATCAATTATGAGA
*
9508 TTATAAAA-CAGTTTACAGTGAGTAATAAAGCTTTTAAAGGAA
131 TTATAAAACCA-TTTAAAGTGAGTAATAAAGCTTTTAAAGGAA
* * ** * *
9550 TGAGTGACAATAAAT-GACATTTTCTTG-CATATGAATGTATTTTTCTTCATATTTCTCAAGGTT
1 TGGGTGACTATAAATGGAC-TTTTCTTGCCA-ATGAATGCCTTTTTCTTCATGTTTCTCAAGGTA
* * * * *
9613 GGCATTCAATTATTATCTGTTTTAACTAAAAATGTACAAAAAATTCAAACTAAAATCAAATT-TA
64 GACATTCAATTATAATCTGTTCTAACTAAAAATGTATAAAAAATTCAAACTAAAATC-AATTATG
* ** * * * * *
9677 AGATAAGGAAACTATTTAAAGCGATTTATAAGGCTTTTAAAGGAA
128 AGATTATAAAACCATTTAAAGTGAGTAATAAAGCTTTTAAAGGAA
* *
9722 TGGGTGACTATAAATGAACTTTTCTTGCCCATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGA
1 TGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGA
*
9787 CATTCAATTATAATATGTT
66 CATTCAATTATAATCTGTT
9806 NNNNNNNNNN
Statistics
Matches: 477, Mismatches: 114, Indels: 16
0.79 0.19 0.03
Matches are distributed among these distances:
170 6 0.01
171 127 0.27
172 336 0.70
173 8 0.02
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.36
Consensus pattern (172 bp):
TGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGA
CATTCAATTATAATCTGTTCTAACTAAAAATGTATAAAAAATTCAAACTAAAATCAATTATGAGA
TTATAAAACCATTTAAAGTGAGTAATAAAGCTTTTAAAGGAA
Found at i:10658 original size:171 final size:171
Alignment explanation
Indices: 10407--10962 Score: 584
Period size: 171 Copynumber: 3.2 Consensus size: 171
10397 CAAACTTTTA
* * * *
10407 AGATTATAAAACCATTTAAAGTTAGGAATAAGGCTTCTAAAGGAATGGGTGACTATAAATGGACT
1 AGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGGTGACTACAAATGGACT
** * * * * *
10472 GGTCTTGCCAATGAATATCTTTTTCTTCACGTTTCTCT-AGACAGACATTCAATTATAATATGTT
66 TTTCTTGCTAATGAATAACTTTTTCTTCACGTATCTCTAAGGCAGACATTCAATTATAATCTGTT
* * *
10536 CTAACCAAAACTGTAAAAAAATTCAATCTAAAATTATTTATG
131 TTAA-CAAAAATGTAAAAAAATTCAAGCTAAAATTATTTATG
* * * * * *
10578 AGATTATAAAGCCATTGAATGTGAGTAACAAGGCTTTTGAAGGAATGGGTGACTACAAATGGGCT
1 AGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGGTGACTACAAATGGACT
* * *
10643 TTTCTTGCTAATGAATAAATTTTTCTTTACGTATC-CTAAGGCAGGCATTCAATTATAATCTGTT
66 TTTCTTGCTAATGAATAACTTTTTCTTCACGTATCTCTAAGGCAGACATTCAATTATAATCTGTT
* *********
10707 TTAATAAAAAATGTAAAAAAATTCAANNNNNNNNNNA-TTATG
131 TTAA-CAAAAATGTAAAAAAATTCAA-GCTAAAATTATTTATG
* * * * * **
10749 AGATTATAAAACTATTTAAAGTGAGTAGTAAGGTTTTTAATGGAATGAGTGACTACAAATAAACT
1 AGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGGTGACTACAAATGGACT
** * *
10814 TTTCTTG-TCAATGAATGCCTTTTTCTTCACGTATCT-TAAGGTAAACATTCAATTATAATCTGT
66 TTTCTTGCT-AATGAATAACTTTTTCTTCACGTATCTCTAAGGCAGACATTCAATTATAATCTGT
* *
10877 TTTAACTAAAGATGTACAAAGAATTCAAGCTAAAATTAATTT-TG
130 TTTAAC-AAAAATGTA-AAAAAATTCAAGCTAAAATT-ATTTATG
*
10921 AGATTACAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAG
1 AGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAG
10963 NNNNNNNNNN
Statistics
Matches: 307, Mismatches: 70, Indels: 15
0.78 0.18 0.04
Matches are distributed among these distances:
170 3 0.01
171 251 0.82
172 51 0.17
173 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.34
Consensus pattern (171 bp):
AGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGGTGACTACAAATGGACT
TTTCTTGCTAATGAATAACTTTTTCTTCACGTATCTCTAAGGCAGACATTCAATTATAATCTGTT
TTAACAAAAATGTAAAAAAATTCAAGCTAAAATTATTTATG
Found at i:11526 original size:171 final size:161
Alignment explanation
Indices: 11236--11549 Score: 378
Period size: 171 Copynumber: 1.9 Consensus size: 161
11226 NNNNNNNNNA
* * ** *
11236 TTTTCTTGCCAATTAAAACCTTTTTCTTCATGTTTCCCAAGTTAGACATTCAATTATAATATGTT
1 TTTTCTTGCCAATGAAAACCTTTTTCTTCATCTTTCCCAAGCCAAACATTCAATTATAATATGTT
* * * *
11301 CTAATCATAAATGTAAAGAAATTCAATCTAAAATCAATTATTAAATTGTAAAGCCATTTAATGTG
66 CTAACCATAAATGTAAAGAAAATCAATCTAAAATCAATTATTAAATTATAAAGCCATTTAATATG
11366 AGTAATAAGGCTTNNNNNNNNNNGGGTGACTATAAATGGGC
131 AGTAATAAGGCTT----------GGGTGACTATAAATGGGC
* * * * *
11407 TTTTCTTGCTAATGAATACCTTTTTCTTTATCTTTCTCAAGCCAAACATTCAATTATAATCTGTT
1 TTTTCTTGCCAATGAAAACCTTTTTCTTCATCTTTCCCAAGCCAAACATTCAATTATAATATGTT
* *
11472 CTAACCATAAATGTTAAA-AAAATCAATCTAAAGTCAATTATTAGATTATAAAGCCATTTAATAT
66 CTAACCATAAATG-TAAAGAAAATCAATCTAAAATCAATTATTAAATTATAAAGCCATTTAATAT
11536 GAGTAATAAGGCTT
130 GAGTAATAAGGCTT
11550 TTGAAGGAAN
Statistics
Matches: 126, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
171 122 0.97
172 4 0.03
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.37
Consensus pattern (161 bp):
TTTTCTTGCCAATGAAAACCTTTTTCTTCATCTTTCCCAAGCCAAACATTCAATTATAATATGTT
CTAACCATAAATGTAAAGAAAATCAATCTAAAATCAATTATTAAATTATAAAGCCATTTAATATG
AGTAATAAGGCTTGGGTGACTATAAATGGGC
Found at i:13352 original size:171 final size:169
Alignment explanation
Indices: 12394--13625 Score: 714
Period size: 171 Copynumber: 7.3 Consensus size: 169
12384 NNNNNNNNNN
* * *
12394 GACTATAAATAGACTTGTC-TGCCAATGAATATCTTTTGCTTTACAT-T-TCTTAAGGTAGACAT
1 GACTATAAATAGACTTTTCTTGCCAATGAATACCTTTTTC-TT-CATGTATCTTAAGGTAGACAT
* * * * * *
12456 TTAATTATAATCTGTTATAACCAAAAATGTA-AAAAAATTCAATCTAAAATCAATTCTGAGATTA
64 TCAATTATAATCTGTTTTAACC-AAAATATACAAAGAATTCAA-ATAAAATCAATTTTGAGATTA
* * *
12520 T-AAAGTCATTTAATGTGAGTAATAAGGCTTTTGAAGGAAAGGGT
127 TAAAACT-ATTTAAAGTGAGTAATAAGGCTTTT-AAGGAATGGGT
* * * *** * * * * * * *
12564 GGCTATAAATGGGCTTTTCTTATGAATGAATGCCTTTTTCTTCAAGTTTCCTAAGGGAAACATTG
1 GACTATAAATAGACTTTTCTTGCCAATGAATACCTTTTTCTTCATGTATCTTAAGGTAGACATTC
** * ** *
12629 AATTATAATCTGTTCGAACCAAAAATATA-AAAAAATTCAGCCTAAAATCAAATTTGAGATTATA
66 AATTATAATCTGTTTTAACC-AAAATATACAAAGAATTCA-AATAAAATCAATTTTGAGATTATA
* ********** *
12693 AAACCATTTAAAGTNNNNNNNNNNGCTTTTAAAGGAATGAGT
129 AAACTATTTAAAGTGAGTAATAAGGCTTTT-AAGGAATGGGT
* * * * * * *
12735 GACTATAAATGGACTTTT-TATGCCAACGAATACCGTTTTCTTCATATTTCTT-GGGCTATACAT
1 GACTATAAATAGACTTTTCT-TGCCAATGAATACCTTTTTCTTCATGTATCTTAAGG-TAGACAT
* *
12798 TCAATTATAATCTGTTTTAACTAAAAATATGCAAAGAATTC-----AAA-C--TTTTGAGATTAT
64 TCAATTATAATCTGTTTTAAC-CAAAATATACAAAGAATTCAAATAAAATCAATTTTGAGATTAT
* * ***
12855 AAAACCATTTAAAGTGAGAAATAAGGCTTTTGAAGGAATGANN
128 AAAACTATTTAAAGTGAGTAATAAGGCTTTT-AAGGAATGGGT
******** * * * * * * *
12898 NNNNNNNNATGGACTTGTCTTGCCAATGAATACCTTCTTCTGCACGTTTCTCT-TGGTAGACATT
1 GACTATAAATAGACTTTTCTTGCCAATGAATACCTTTTTCTTCATGTATCT-TAAGGTAGACATT
* * * * * *
12962 CAATTATAATATGTTCTCACCAAAACTATA-AAAAAATTCAATCTAAAAT-TATTTATGAGATTA
65 CAATTATAATCTGTTTTAACCAAAA-TATACAAAGAATTCAA-ATAAAATCAATTT-TGAGATTA
* * * * *
13025 TAAAGCCATTTAATGTGAGTAATAAGGCTTTTGAAGAAATGGGN
127 TAAAACTATTTAAAGTGAGTAATAAGGCTTTT-AAGGAATGGGT
************************ * * *
13069 NNNNNNNNNNNNNNNNNNNNNNNAAATGAATACCTTTTT-TTCATGTATCCTAAGGCAGGCATTC
1 GACTATAAATAGACTTTTCTTGCCAATGAATACCTTTTTCTTCATGTATCTTAAGGTAGACATTC
* * * * * *
13133 AATTATAATCTGTTCTAACCAAAAATGTA-AAAAAATTTAATGTAAAATCAATTATGAGATTATA
66 AATTATAATCTGTTTTAACC-AAAATATACAAAGAATTCAA-ATAAAATCAATTTTGAGATTATA
** * * *
13197 AAACTATTTAAAACGAGTAGTAAGGCTCTTAATGAAATGGGT
129 AAACTATTTAAAGTGAGTAATAAGGCTTTTAA-GGAATGGGT
* * *
13239 GACTATTAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTATCTTAAGGTAAACATTC
1 GACTATAAATAGACTTTTCTTGCCAATGAATACCTTTTTCTTCATGTATCTTAAGGTAGACATTC
*
13304 AATTATAATCTGTTTTAACCAAAATATACAAAGAATTCAAACTAAAATCAATTTTGAGATTACAA
66 AATTATAATCTGTTTTAACCAAAATATACAAAGAATTCAAA-TAAAATCAATTTTGAGATTATAA
********** *
13369 AACTATTTAAAGTGNNNNNNNNNNCTTTTAAAGGAATAGGT
130 AACTATTTAAAGTGAGTAATAAGGCTTTT-AAGGAATGGGT
* * * * *
13410 AACTATAAATAGACTTTTCCTGCCAATGAATACATTTTTGTTTCTAT-T-TCTCAAGGTAGACAT
1 GACTATAAATAGACTTTTCTTGCCAATGAATACCTTTTT-CTTC-ATGTATCTTAAGGTAGACAT
*
13473 TCAATTATAATCTGTTTT-ACCAAAATTTACAAAGAATTCAAATAAAATCAATTTTGAGATTATA
64 TCAATTATAATCTGTTTTAACCAAAATATACAAAGAATTCAAATAAAATCAATTTTGAGATTATA
* * *
13537 AAACCATTTAAGGTGAGTAATAAGGATTTTGAAGGAATGGGT
129 AAACTATTTAAAGTGAGTAATAAGGCTTTT-AAGGAATGGGT
* * *
13579 GA-TAATAAATAGAATTTTCTTGCCAATTAAAACCTTTTTCTTCATGT
1 GACT-ATAAATAGACTTTTCTTGCCAATGAATACCTTTTTCTTCATGT
13626 TTCCTAGGGT
Statistics
Matches: 806, Mismatches: 222, Indels: 70
0.73 0.20 0.06
Matches are distributed among these distances:
162 12 0.01
163 102 0.13
164 4 0.00
165 1 0.00
166 3 0.00
167 2 0.00
168 8 0.01
169 84 0.10
170 163 0.20
171 408 0.51
172 17 0.02
173 2 0.00
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.34
Consensus pattern (169 bp):
GACTATAAATAGACTTTTCTTGCCAATGAATACCTTTTTCTTCATGTATCTTAAGGTAGACATTC
AATTATAATCTGTTTTAACCAAAATATACAAAGAATTCAAATAAAATCAATTTTGAGATTATAAA
ACTATTTAAAGTGAGTAATAAGGCTTTTAAGGAATGGGT
Found at i:14599 original size:168 final size:167
Alignment explanation
Indices: 14200--14613 Score: 388
Period size: 168 Copynumber: 2.4 Consensus size: 167
14190 NNTTCCTTGT
* * * * * *
14200 GTATCCCAAGATAGACATTCAAATATAATTTGTTCTAACTAAAAATATAAAAAAATTCAATGTAA
1 GTATCTCAAGGTAGACATTCAATTATAATATGTTTTAAC-AAAAATATAAAAAAATTCAA-ATAA
* *
14265 AATCAATTATAAGATTATAAAACCATTTAAAGCGAGTAGTAAGGCTTTTAATAGAATGGGTGACT
64 AATCAATTTTAAGATTATAAAACCATTT-AA-CGAGTAATAAGGCTTTTAATAGAATGGGTGACT
** *
14330 ATAAATAGACTTTTTTAGTCAATGAATGACTTTTTCTTCAC
127 ATAAATAGACTTTTCCAGCCAATGAATGACTTTTTCTTCAC
* *********
14371 GTATCTCAAGGTAAACATTCAATTATAATATGTTTTAACTAAAANNNNNNNNNNAATTCAAACTA
1 GTATCTCAAGGTAGACATTCAATTATAATATGTTTTAAC-AAAA-ATATAAAAAAATTCAAA-TA
* *
14436 AAATCAATTTTGAGATTATAAAACCATTT-A-GAGTAATAAGGCTTTTAA-AGGAATGTGTGACT
63 AAATCAATTTTAAGATTATAAAACCATTTAACGAGTAATAAGGCTTTTAATA-GAATGGGTGACT
* *
14498 ATAAATGGACTTTTCCCGCCAATGAATG-CATTTTTCTTTCTA-
127 ATAAATAGACTTTTCCAGCCAATGAATGAC-TTTTTC-TTC-AC
* * * * * * * *
14540 TTTTCTTAAGGTCGACATTCAATTATAATCTGTTTTAACCAAAATGTACAAAGAATTCAAATAAA
1 GTATCTCAAGGTAGACATTCAATTATAATATGTTTTAACAAAAATATA-AAAAAATTCAAATAAA
14605 ATCAATTTT
65 ATCAATTTT
14614 NNNNNNNNNN
Statistics
Matches: 195, Mismatches: 41, Indels: 18
0.77 0.16 0.07
Matches are distributed among these distances:
167 15 0.08
168 68 0.35
169 36 0.18
170 2 0.01
171 38 0.19
172 36 0.18
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.35
Consensus pattern (167 bp):
GTATCTCAAGGTAGACATTCAATTATAATATGTTTTAACAAAAATATAAAAAAATTCAAATAAAA
TCAATTTTAAGATTATAAAACCATTTAACGAGTAATAAGGCTTTTAATAGAATGGGTGACTATAA
ATAGACTTTTCCAGCCAATGAATGACTTTTTCTTCAC
Found at i:15347 original size:20 final size:20
Alignment explanation
Indices: 15322--15360 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
15312 AAGGAATGAG
15322 TTACTA-TAAATAGCCTTTTC
1 TTACTAGTAAAT-GCCTTTTC
*
15342 TTACTAGTGAATGCCTTTT
1 TTACTAGTAAATGCCTTTT
15361 TCTTCACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.26, C:0.18, G:0.10, T:0.46
Consensus pattern (20 bp):
TTACTAGTAAATGCCTTTTC
Found at i:15843 original size:171 final size:171
Alignment explanation
Indices: 15258--16005 Score: 655
Period size: 171 Copynumber: 4.4 Consensus size: 171
15248 NNNNNNNNNN
* * * * *
15258 TTAAAATCAATTTTGAGATAATATAACCATTTAAAGTAAGTAATAAGGTTTTTGAAGGAATGAGT
1 TTAAAATCAATTTTGAGATTATAAAACCATTCAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGT
* * * * * * ** *
15323 TACTATAAATAGCCTTTTCTT-ACTAGTGAATGCCTTTTTCTTCACCTTTCTCAAGGTAGACATT
66 GACTATAAATGGACTTTTCTTGTC-AATGAATGTCTTTTTCTTCAAGTTTCT-GAGGTAGACATT
* ********* *
15387 TAATTATAATNNNNNNNNNNC-AAAAATGT-AAAAATATTGAAC
129 CAATTATAAT-CTATTTTAACTAAAAATGTAAAAAAAATTGAAC
* * ** * * *
15429 TTAAAATCAATTATAAGATTATAAAACTTTTTACAGCGAGTAATAAGGCTTTTGAAGGAATGAGT
1 TTAAAATCAATTTTGAGATTATAAAACCATTCAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGT
* * * * *
15494 GAGTATAAATGGACTTTTTTTGTCAACGAATGTTTTTTTCTTCATA-TTTCTTGAGGTAAACATT
66 GACTATAAATGGACTTTTCTTGTCAATGAATGTCTTTTTCTTCA-AGTTTC-TGAGGTAGACATT
* **********
15558 CAATTATAATCTGTTNNNNNNNNNNATGTAAAAACAAATTGAAC
129 CAATTATAATCTATTTTAACTAAAAATGTAAAAA-AAATTGAAC
** * * * *
15602 TTAAAATCAATTTTGAGATTATAAAATTATCCAAAGTGAGTAACAAGGCTTTCGAAGGTATGAGT
1 TTAAAATCAATTTTGAGATTATAAAACCATTCAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGT
* *
15667 GACTATAAATGGACTTTTCTTGCCAATGAATGTCTTATTCTTCAAGTTTCATGAGGTAGACATTC
66 GACTATAAATGGACTTTTCTTGTCAATGAATGTCTTTTTCTTCAAGTTTC-TGAGGTAGACATTC
* * * * * *
15732 AATTATAATCTATTTTAGCTAAGAATAT-TAAAAAATTCAAT
130 AATTATAATCTATTTTAACTAAAAATGTAAAAAAAATTGAAC
* * * *
15773 TTAAAATCAATTCTGATATTATAAAACCATTCAAAGTGAGTAATAAGGCTTATAAAGGAATG-GA
1 TTAAAATCAATTTTGAGATTATAAAACCATTCAAAGTGAGTAATAAGGCTTTTGAAGGAATGAG-
* * * *
15837 TGACTATAAATAGACTTTTCTTATCAGTGAATGTCTTTTTCTTCATGTTTGTCT-AGGTAGACAT
65 TGACTATAAATGGACTTTTCTTGTCAATGAATGTCTTTTTCTTCAAG-TT-TCTGAGGTAGACAT
* * * *
15901 TTAATTATAATTTCTTTTAACTAAAAATGTAAAAAAAATTGACC
128 TCAATTATAATCTATTTTAACTAAAAATGTAAAAAAAATTGAAC
* * * *
15945 TTAAAACCAATTTTGAGATCATAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAAT
1 TTAAAATCAATTTTGAGATTATAAAACCATTCAAAGTGAGTAATAAGGCTTTTGAAGGAAT
16006 NNNNNNNNNN
Statistics
Matches: 463, Mismatches: 103, Indels: 21
0.79 0.18 0.04
Matches are distributed among these distances:
170 5 0.01
171 248 0.54
172 75 0.16
173 135 0.29
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.36
Consensus pattern (171 bp):
TTAAAATCAATTTTGAGATTATAAAACCATTCAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGT
GACTATAAATGGACTTTTCTTGTCAATGAATGTCTTTTTCTTCAAGTTTCTGAGGTAGACATTCA
ATTATAATCTATTTTAACTAAAAATGTAAAAAAAATTGAAC
Found at i:17026 original size:171 final size:170
Alignment explanation
Indices: 16697--17026 Score: 358
Period size: 170 Copynumber: 1.9 Consensus size: 170
16687 GCTTTCAAAG
* *
16697 GAATTGGTGACTATAAATGGACTTTTCTTGACAATGAATACCTTTTTCTTCATGTTTCCTAGGAC
1 GAATGGGTGACTATAAATGGACTTTTCTTGACAATGAATACCTTTTTCTTCATGTTTCCAAGGAC
* * * * **
16762 AGACATTCAATTATATTGTGTTCTAACTAAAAATGTAAAAAAATTTAATATAAAATCAATTATGA
66 AGACATTAAATTATAATCTATTCTAACTAAAAATGTAAAAAAATAAAATATAAAATCAATTATGA
********** **
16827 GATTATANNNNNNNNNNAAGTGAGTAATAAGACTTTTGCA
131 GATTATAAAACCATTTAAAGCAAGTAATAAGACTTTTGCA
* * * * *
16867 GAATGGGTGACTGTAAATGGACTTTTTTTGCCAATGAATGCCTTTTTCTTCATGTTTTTCAAGG-
1 GAATGGGTGACTATAAATGGACTTTTCTTGACAATGAATACCTTTTTCTTCATG-TTTCCAAGGA
* * * *
16931 TAGACATTAAATTATAATCTATTTTAACTGAAAATGTAAAAAAAATAAAACT-TAAAATCAATTT
65 CAGACATTAAATTATAATCTATTCTAACTAAAAATGT-AAAAAAATAAAA-TATAAAATCAATTA
16995 TGAGATTATAAAACCATTTAAAGCAAGTAATA
128 TGAGATTATAAAACCATTTAAAGCAAGTAATA
17027 NNNNNNNNNN
Statistics
Matches: 128, Mismatches: 29, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
170 79 0.62
171 48 0.38
172 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.35
Consensus pattern (170 bp):
GAATGGGTGACTATAAATGGACTTTTCTTGACAATGAATACCTTTTTCTTCATGTTTCCAAGGAC
AGACATTAAATTATAATCTATTCTAACTAAAAATGTAAAAAAATAAAATATAAAATCAATTATGA
GATTATAAAACCATTTAAAGCAAGTAATAAGACTTTTGCA
Found at i:19160 original size:172 final size:171
Alignment explanation
Indices: 18874--19262 Score: 421
Period size: 172 Copynumber: 2.3 Consensus size: 171
18864 CAATTCAATC
* * * **
18874 TAAAATCAATTATGAGATTATAAAACTATTTAAAGA-AAATAATAAGGTTTTTGAAGGAATGGGT
1 TAAAATCAATTATGAGATTATAAAACAATTTAAA-ACGAGTAATAAGACTTTTGAAGGAATGGGT
* * * *
18938 GACTATATATGGACATTTCTTGCCAATGAATATATTTTTCCTCATGTTTCTCAA-GGTAGACATT
65 GACTATAAATGGAAATTTCTTGCCAATGAATAGATTTTTCCTCATGTTTCTCAAGGGAAG-CATT
* *
19002 CAATTATAATCTGTTTTAACAAAAAATTTAAAAAACATTG-AATT
129 CAATTATAATCTGTTTTAACAAAAAATGT-AAAAACA-TGCAAAT
* * *
19046 TAAAATC-ATATATTATATTATAAAATAATTTAAAACGAGTAATAAGACTTTTGAAGGAATGGGT
1 TAAAATCAAT-TATGAGATTATAAAACAATTTAAAACGAGTAATAAGACTTTTGAAGGAATGGGT
* * * * * * *
19110 GGCTATAAAT-TAAATTTTTTTCTCAATGAATGGCTTTTT-CTACATGTTTCTCGAGGGAAGCAT
65 GACTATAAATGGAAATTTCTTGC-CAATGAATAGATTTTTCCT-CATGTTTCTCAAGGGAAGCAT
* * ***
19173 TCAATTATAGTGTGTTTTAGTGAAAAATGTAAAAACATGCAAAT
128 TCAATTATAATCTGTTTTAACAAAAAATGTAAAAACATGCAAAT
* *
19217 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAG
1 TAAAATCAATTATGAGATTATAAAACAATTTAAAACGAGTAATAAG
19263 CCTNNNNNNN
Statistics
Matches: 179, Mismatches: 31, Indels: 15
0.80 0.14 0.07
Matches are distributed among these distances:
170 2 0.01
171 61 0.34
172 112 0.63
173 4 0.02
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (171 bp):
TAAAATCAATTATGAGATTATAAAACAATTTAAAACGAGTAATAAGACTTTTGAAGGAATGGGTG
ACTATAAATGGAAATTTCTTGCCAATGAATAGATTTTTCCTCATGTTTCTCAAGGGAAGCATTCA
ATTATAATCTGTTTTAACAAAAAATGTAAAAACATGCAAAT
Found at i:20092 original size:173 final size:171
Alignment explanation
Indices: 19707--20205 Score: 492
Period size: 171 Copynumber: 2.9 Consensus size: 171
19697 NNNNNNNNNN
* *
19707 TTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTAACTATAATGGACTTTTCTGACCAATGAAT
1 TTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAATAGACTTTTCTGACCAATGAAT
* * * * *
19772 CTCTTTTTCTTCACGTTTCTTAAGCTAGATATTCAATTATAATATGTTTTAACTAATAATGTAAA
66 CTCTTTTTCTTCACATTTCTTAAGCTAGACATTCAATTATAATATGTTATAACCAAAAATGTAAA
* * *
19837 AACAATTGAACCTCAAATCAATTATGAGATTATAAAAGCAT
131 AAAAATTGAACCTCAAATCAATTATAAGATTATAAAACCAT
* * * * *
19878 TTAAAGCTACTAATAAGGCTTTTGAAGGAATGGGTGACTATAATAGACTTTTC-GTACTAATGGA
1 TTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAATAGACTTTTCTG-ACCAATGAA
* * * ** *
19942 TGC-CTTTTTCTTCACATTTCTTGAGGTTGACATTCAATTATTGTCTGTTATAACCAAAAATGTA
65 T-CTCTTTTTCTTCACATTTCTTAAGCTAGACATTCAATTATAATATGTTATAACCAAAAATGT-
*
20006 AAAAAAAAATTGAACC-CAAAATCAATTTTAAGATTATAAAACCAT
128 -AAAAAAAATTGAACCTC-AAATCAATTATAAGATTATAAAACCAT
* * * *
20051 TTAAAGCGAGTAAGAAGGCTTTTGAAGGTATACGG-GACTATAAATAGACATTTCTTG-CAAATG
1 TTAAAGCGAGTAATAAGGCTTTTGAAGGAATA-GGTGACTAT-AATAGACTTTTC-TGACCAATG
* ** * * * * * * * *
20114 AAT-TTTTTTATCTTCATGTTTC-TAGAGGTAAACAATCAATTATAGTCTATTTTAACCAAAGAT
63 AATCTCTTTT-TCTTCACATTTCTTA-AGCTAGACATTCAATTATAATATGTTATAACCAAAAAT
* * *
20177 G-AAAAAAAATTCAACTTAAAATCAATTAT
126 GTAAAAAAAATTGAACCTCAAATCAATTAT
20206 TAGNNNNNNN
Statistics
Matches: 270, Mismatches: 45, Indels: 26
0.79 0.13 0.08
Matches are distributed among these distances:
170 1 0.00
171 128 0.47
172 2 0.01
173 76 0.28
174 62 0.23
176 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (171 bp):
TTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAATAGACTTTTCTGACCAATGAAT
CTCTTTTTCTTCACATTTCTTAAGCTAGACATTCAATTATAATATGTTATAACCAAAAATGTAAA
AAAAATTGAACCTCAAATCAATTATAAGATTATAAAACCAT
Found at i:21202 original size:171 final size:170
Alignment explanation
Indices: 20880--21227 Score: 434
Period size: 171 Copynumber: 2.0 Consensus size: 170
20870 NNNNNNNNTA
* * * *
20880 TTTTGACAAAAAATACAAAAAAATTCAACTTAAAATCAATTATGAGATTACACAATAATTTAAAG
1 TTTTAACAAAAAATACAAAAAAATTCAACTTAAAATCAATTATGAGATTACAAAACAACTTAAAG
* * * ** *
20945 CGAGAAATAAGGCTTTTGAAAAATGGGTGACTATAAATGGACTTGTCTTGCCAATGAAATCCTTT
66 CAAGAAATAAGGCCTTTGAAAAATAGGAAACTATAAATGGACTTGTCTTACCAATGAAATCCTTT
21010 TCCTTCATGTTTCCAAAGGTAGACATTCAATTATA-TCCTG
131 TCCTTCATGTTTCCAAAGGTAGACATTCAATTATAGT-CTG
** * * * *
21050 TTTTAACAAAAAATGTAAAAATATTCAA-TTGAAAATCAATTATGAGATTATAAAACCACTTCAA
1 TTTTAACAAAAAATACAAAAAAATTCAACTT-AAAATCAATTATGAGATTACAAAACAACTTAAA
* * * *
21114 GCAAGTAATAAGGCCTTTGAAGGAATAGGAAACTATAAATGGACTTTTCTTACCAATGAAA-GCT
65 GCAAGAAATAAGGCCTTTGAA-AAATAGGAAACTATAAATGGACTTGTCTTACCAATGAAATCCT
*
21178 TGTTTCTTCATGTTTCTC-AAGGTAGACATTCAATTATAGTCTG
129 T-TTCCTTCATGTTTC-CAAAGGTAGACATTCAATTATAGTCTG
21221 TTTTAAC
1 TTTTAAC
21228 TNNNNNNNNN
Statistics
Matches: 152, Mismatches: 21, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
169 2 0.01
170 72 0.47
171 76 0.50
172 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (170 bp):
TTTTAACAAAAAATACAAAAAAATTCAACTTAAAATCAATTATGAGATTACAAAACAACTTAAAG
CAAGAAATAAGGCCTTTGAAAAATAGGAAACTATAAATGGACTTGTCTTACCAATGAAATCCTTT
TCCTTCATGTTTCCAAAGGTAGACATTCAATTATAGTCTG
Done.