Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398437.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1737.0, 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: 13149
ACGTcount: A:0.32, C:0.10, G:0.11, T:0.29
Warning! 2340 characters in sequence are not A, C, G, or T
Found at i:308 original size:170 final size:170
Alignment explanation
Indices: 1--308 Score: 390
Period size: 170 Copynumber: 1.8 Consensus size: 170
* *
1 CAATTATGAGATTATAAAACCTTTTAAAATGAGTAATAAGGCTTTTAAAGGAATCAGTGACTATA
1 CAATTATGAGATTATAAAACCATTTAAAATGAGTAATAAGACTTTTAAAGGAATCAGTGACTATA
* * * * * *
66 AATAAACTTTTCTTGCTAATGAATGCCTTTTTCTTCACATTTTTCAACATAGACATTCGATTATA
66 AATAAACGTTTATTGCCAATGAATGCATTTCTCTTCACATTTTTCAACATAGACATTCAATTATA
131 ATCTGTTTTAATCAAAAAAGAAAAAAATTAAACTTAAAAT
131 ATCTGTTTTAATCAAAAAAGAAAAAAATTAAACTTAAAAT
* * * * * **
171 CAATTTTGAGATTATAAAACCATTTACAGTGAGTAATAAGACTTTTGAAGTAAT-AGATGGTTAT
1 CAATTATGAGATTATAAAACCATTTAAAATGAGTAATAAGACTTTTAAAGGAATCAG-TGACTAT
* *
235 AAATAGACGTTTATTGCCAATGAATGCATTTCTCTTCACGTTTCTT-AAGGCA-A-ACATTCAAT
65 AAATAAACGTTTATTGCCAATGAATGCATTTCTCTTCACATTT-TTCAA--CATAGACATTCAAT
*
297 TATAGTCTGTTT
127 TATAATCTGTTT
309 NNNNNNNNNN
Statistics
Matches: 116, Mismatches: 18, Indels: 8
0.82 0.13 0.06
Matches are distributed among these distances:
169 2 0.02
170 109 0.94
171 3 0.03
172 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (170 bp):
CAATTATGAGATTATAAAACCATTTAAAATGAGTAATAAGACTTTTAAAGGAATCAGTGACTATA
AATAAACGTTTATTGCCAATGAATGCATTTCTCTTCACATTTTTCAACATAGACATTCAATTATA
ATCTGTTTTAATCAAAAAAGAAAAAAATTAAACTTAAAAT
Found at i:1039 original size:18 final size:20
Alignment explanation
Indices: 1001--1039 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
991 NNNNNNNAAC
*
1001 ATAAAATCAATTTTGAGATA
1 ATAAAATCAATTTTAAGATA
1021 ATAAAATC-A-TTTAAGATA
1 ATAAAATCAATTTTAAGATA
1039 A
1 A
1040 GTAATAAGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 1 0.06
20 8 0.44
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.33
Consensus pattern (20 bp):
ATAAAATCAATTTTAAGATA
Found at i:1239 original size:170 final size:171
Alignment explanation
Indices: 754--2105 Score: 1121
Period size: 171 Copynumber: 7.9 Consensus size: 171
744 TATAAATAGA
* * * *
754 CTTTTTCTTCACGTTTCATGAGGTAGACATTCAATTATAATCTGTTTTAACTCG--CAATGTTAC
1 CTTTTTCTTCATGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAA-T-GAAAAATG-TA-
** * * * ** * **
817 ACGAAATTGAAC-TCAAAATCAATTATAAGATTATAAAGCGGTTTAAAGTGAGTAATAACACTTT
62 AAAAAATTCAACAT-AAAATCAATTATGAGATTATAAAACCATTTAAAGTAAGTAATAAGGCTTT
* *
881 TGAAGGAATGAGAGACTATAAATGAACTTTTCTTGCTAATGAATGC
126 TGAAGGAATGGGAGACTATAAATGAACTTTTCTTGCCAATGAATGC
* * * * ** ***
927 TTTTTTCTTCAAGTTTCTTTAGTTAGACATTCAATTATAGTCTGTTTTAACAAAAAATGTANNNN
1 CTTTTTCTTCATGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAATGAAAAATGTA-AAA
****** * * *
992 NNNNNNAACATAAAATCAATTTTGAGATAATAAAATCATTT-AAGATAAGTAATAAGGCTTTTGA
65 AAATTCAACATAAAATCAATTATGAGATTATAAAACCATTTAAAG-TAAGTAATAAGGCTTTTGA
* * *
1056 TA-GAATAGGTGACTATAAATGAACTTTTCTTGCCAATGAATAC
129 -AGGAATGGGAGACTATAAATGAACTTTTCTTGCCAATGAATGC
* * * * * * * *
1099 CTCTTTCTTC-TGTTTCTCGAGGTTGAGATTCAATTATAATCTCTTTTAATGAAAAATATAAAAG
1 CTTTTTCTTCATGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAATGAAAAATGTAAAAA
** * *
1163 AATTCAAGTTAAAATCAATTATGAGGTTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAG
66 AATTCAACATAAAATCAATTATGAGATTATAAAACCATTTAAAGTAAGTAATAAGGCTTTTGAAG
* * *
1228 GAATGGGTGACTATAAATGGACCTTTCTTGCCAATGAATGC
131 GAATGGGAGACTATAAATGAACTTTTCTTGCCAATGAATGC
* * * * * * * *
1269 TTTTTTGTTAACGTTTCTTGAGGTAAACAATCAATTATAATCTGTTTTAACT-AAAAATGTAAAT
1 CTTTTTCTTCATGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAA-TGAAAAATGTAAAA
* * *
1333 AAATTCAACTTAAAATCAATTTTGAGATTAT-AAACCATTTAAAGCAAGTAATAAGGCTTTTGAA
65 AAATTCAACATAAAATCAATTATGAGATTATAAAACCATTTAAAGTAAGTAATAAGGCTTTTGAA
* * *
1397 GGAATGGGAGACTAT-ACT-TA-TTTTC-T--CAATTG-ATGG
130 GGAATGGGAGACTATAAATGAACTTTTCTTGCCAA-TGAATGC
** * * * * * *
1433 CTTTTAT-AACATGTTTCCTAAGGCAGGCATTCAATTATAGTCTATTTTAATGAAAAATGTAGAA
1 CTTTT-TCTTCATGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAATGAAAAATGTAAAA
* ** * * *
1497 AAATTTAAGTTAAAATCAATTAGGAGATTATAAAACTATTTAAAGCAAGTAATAAGGCTTTTGAA
65 AAATTCAACATAAAATCAATTATGAGATTATAAAACCATTTAAAGTAAGTAATAAGGCTTTTGAA
* * *
1562 GGAATGGGTGACTATACAT-AGACTTTTCTTGCCAAAGAATGC
130 GGAATGGGAGACTATAAATGA-ACTTTTCTTGCCAATGAATGC
** **
1604 CTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAACCTGTTTT-ATGCAAAAATGTAAAA
1 CTTTTTCTTCATGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAATG-AAAAATGT-AAA
* ** * * * * ** *
1668 ACAAATTGAACATAATTTCAATTTTGAGATAATAAAACCATTTAACGTGAGTGCTAAGG-TGTTA
64 A-AAATTCAACATAAAATCAATTATGAGATTATAAAACCATTTAAAGTAAGTAATAAGGCT-TTT
* * ** *
1732 GAAGGAATGGGTGACTATAAAT-AGACTTTTATTTTCAATGAATAC
127 GAAGGAATGGGAGACTATAAATGA-ACTTTTCTTGCCAATGAATGC
* ** * * * ** *
1777 ATTTTTCTTCACATTTTTTGA-GCAGATATTCAATTATAGTCTGTTTTAACCAAAAATATAAAAA
1 CTTTTTCTTCATGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAATGAAAAATGTAAAAA
* * * ** * *
1841 AATTCAACCTAAAATCAATTATGAGATTATAAAGCTATTTAAAACAAGTAATAAGGTTTTTAAAG
66 AATTCAACATAAAATCAATTATGAGATTATAAAACCATTTAAAGTAAGTAATAAGGCTTTTGAAG
* * * ** *
1906 GAATGGGAGACTAGAAATGCACTTTTGTTATCAATTAATGC
131 GAATGGGAGACTATAAATGAACTTTTCTTGCCAATGAATGC
* * * * * *
1947 TTTTTTCTTTACGATTCTTGAGGTAGACATTCAATTATAGTATGTTTTAATCG-AAAATATAAAA
1 CTTTTTCTTCATGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAAT-GAAAAATGTAAAA
* * * * * * *
2011 AAACTGAACATAAAATCAATTTTGAGGTAATAAAACTATTT-AAGATGAGTAATAAGGCTTTTGA
65 AAATTCAACATAAAATCAATTATGAGATTATAAAACCATTTAAAG-TAAGTAATAAGGCTTTTGA
* *
2075 AGGAATGGAAGACTATAAATGGACTTTTCTT
129 AGGAATGGGAGACTATAAATGAACTTTTCTT
2106 CTAAGTAAAT
Statistics
Matches: 938, Mismatches: 210, Indels: 64
0.77 0.17 0.05
Matches are distributed among these distances:
163 1 0.00
164 78 0.08
165 49 0.05
166 2 0.00
167 5 0.01
168 6 0.01
169 4 0.00
170 239 0.25
171 282 0.30
172 122 0.13
173 150 0.16
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (171 bp):
CTTTTTCTTCATGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAATGAAAAATGTAAAAA
AATTCAACATAAAATCAATTATGAGATTATAAAACCATTTAAAGTAAGTAATAAGGCTTTTGAAG
GAATGGGAGACTATAAATGAACTTTTCTTGCCAATGAATGC
Found at i:1873 original size:678 final size:668
Alignment explanation
Indices: 492--2091 Score: 1604
Period size: 678 Copynumber: 2.4 Consensus size: 668
482 ATGAAAATGT
* *** *
492 AAAAAATTCAACTTAAAATCAATTACGAGATTATAAAATGTTTTAAAGCGGGTAATAAGGCTTTT
1 AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT
* * * * * * * *
557 GAAGGAATGGATGACGATAAATGTG-CTTTTCTTGCCAATAAATGCCTTTTCCTTCATGCTTCAT
66 GAAGGAATGGGTGACTATAAATG-GACTTTTCTTGCCAATAAATGCTTTTTTCTTAACGATTCTT
** * * * * *
621 GAGGTAGTTATTCAATTGTAATTTCTTTTCACCAAAAATGTAAAATAAATTGAACATAAAATCAA
130 GAGGTAGACATTCAATTATAATATGTTTTAACTAAAAATGT-AAATAAATTGAACATAAAATCAA
* *
686 TTTTGAGATAATAAAACTATTTAAA-CTGAGTAATAAGGCTTTTAAAGGAAT-GGATGAC--TAT
194 TTTTGAGATAATAAAACTATTTAAAGC-AAGTAATAAGGCTTTTGAAGGAATGGGA-GACTATAT
** * * * *
747 AAATAGACTTTTTCTTCACGTTTCATGAGGTAGACATTCAATTATAATCTGTTTTAACTCGCAAT
257 AAATAGACTTTTTCAACACGTTTCATAAGGCAGACATTCAATTATAATCTATTTTAACTCGAAAT
* * * * **
812 GTTACACGAAATTGAACTCAAAATCAATTATAAGATTATAAAGCGGTTTAAAGTGAGTAATAACA
322 GTTACACAAAATTGAACTCAAAATCAATTAGAAGATTATAAAACGATTTAAAGCAAGTAATAACA
* * *
877 CTTTTGAAGGAATGAGAGACTATAAATGAACTTTTCTTGCTAATGAATGCTTTTTTCTTCAAGTT
387 CTTTTGAAGGAATGAGAGACTATAAATGAACTTTTCTTGCCAAAGAATGCCTTTTTCTTCAAGTT
** * ** **********
942 TCTTTAGTTAGACATTCAATTATAGTCTGTTTTAACAAAAAATGTANNNNNNNNNNAACATAAAA
452 TCTCAAGGTAGACATTCAATTATAACCTGTTTTAACAAAAAATGTAAAACAAATTGAACATAAAA
* *
1007 TCAATTTTGAGATAATAAAATCATTTAAGATAAGTAATAAGGCTTTTGATAGAATAGGTGACTAT
517 TCAATTTTGAGATAATAAAACCATTTAAGATAAGTAATAAGGCTTTAGATAGAATAGGTGACTAT
* * ** **
1072 AAATGAACTTTTCTTGCCAATGAATACCTCTTTCTTCTGTTTCTCGAGGTTGAGATTCAATTATA
582 AAATGAACTTTTATTGCCAATGAATACATCTTTCTTCCATTTCTCGAGGCAGAGATTCAATTATA
**
1137 ATCTCTTTTAATGAAAAATATA
647 ATCTCTTTTAACCAAAAATATA
* * * *
1159 AAAGAATTCAAGTTAAAATCAATTATGAGGTTATAAAACCATTTAAAGTGAGTAATAAGGCTTTT
1 AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT
* * * *
1224 GAAGGAATGGGTGACTATAAATGGACCTTTCTTGCCAATGAATGCTTTTTTGTTAACGTTTCTTG
66 GAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATGCTTTTTTCTTAACGATTCTTG
* * * * *
1289 AGGTAAACAATCAATTATAATCTGTTTTAACTAAAAATGTAAATAAATTCAACTTAAAATCAATT
131 AGGTAGACATTCAATTATAATATGTTTTAACTAAAAATGTAAATAAATTGAACATAAAATCAATT
* *
1354 TTGAGATTAT-AAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGGGAGACTATACTTAT
196 TTGAGATAATAAAACTATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGGGAGACTATA--TA-
* * * * *
1418 TTTCTCAATTGATGGCTTTTAT-AACATGTTTCCTAAGGCAGGCATTCAATTATAGTCTATTTTA
258 ------AA-T-A-GACTTTT-TCAACACGTTTCATAAGGCAGACATTCAATTATAATCTATTTTA
* * * * * *
1482 A-T-GAAAAATG-TAGA-AAAATTTAAGTTAAAATCAATTAGGAGATTATAAAACTATTTAAAGC
313 ACTCG--AAATGTTACACAAAATTGAACTCAAAATCAATTAGAAGATTATAAAACGATTTAAAGC
** * * *
1543 AAGTAATAAGGCTTTTGAAGGAATGGGTGACTATACAT-AGACTTTTCTTGCCAAAGAATGCCTT
376 AAGTAATAACACTTTTGAAGGAATGAGAGACTATAAATGA-ACTTTTCTTGCCAAAGAATGCCTT
* *
1607 TTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAACCTGTTTTATGC-AAAAATGTAAAAACA
440 TTTCTTCAAGTTTCTCAAGGTAGACATTCAATTATAACCTGTTTTA-ACAAAAAATGT-AAAACA
** * **
1671 AATTGAACATAATTTCAATTTTGAGATAATAAAACCATTTAACG-TGAGTGCTAAGG-TGTTAGA
503 AATTGAACATAAAATCAATTTTGAGATAATAAAACCATTTAA-GATAAGTAATAAGGCT-TTAGA
* ** * * *
1734 -AGGAATGGGTGACTATAAAT-AGACTTTTATTTTCAATGAATACATTTTTCTTCACATTTTTTG
566 TA-GAATAGGTGACTATAAATGA-ACTTTTATTGCCAATGAATACATCTTTCTTC-CATTTCTCG
* * *
1797 A-GCAGATATTCAATTATAGTCTGTTTTAACCAAAAATATA
628 AGGCAGAGATTCAATTATAATCTCTTTTAACCAAAAATATA
* * * * * *
1837 AAAAAATTCAACCTAAAATCAATTATGAGATTATAAAGCTATTTAAAACAAGTAATAAGGTTTTT
1 AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT
* * * * * ** * *
1902 AAAGGAATGGGAGACTAGAAATGCACTTTTGTTATCAATTAATGCTTTTTTCTTTACGATTCTTG
66 GAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATGCTTTTTTCTTAACGATTCTTG
* * * * *
1967 AGGTAGACATTCAATTATAGTATGTTTTAA-TCGAAAATATAAAAAAACTGAACATAAAATCAAT
131 AGGTAGACATTCAATTATAATATGTTTTAACT-AAAAATGTAAATAAATTGAACATAAAATCAAT
* *
2031 TTTGAGGTAATAAAACTATTT-AAG-ATGAGTAATAAGGCTTTTGAAGGAATGGAAGACTATA
195 TTTGAGATAATAAAACTATTTAAAGCA--AGTAATAAGGCTTTTGAAGGAATGGGAGACTATA
2092 AATGGACTTT
Statistics
Matches: 758, Mismatches: 143, Indels: 52
0.80 0.15 0.05
Matches are distributed among these distances:
665 36 0.05
666 37 0.05
667 141 0.19
669 2 0.00
676 3 0.00
677 145 0.19
678 301 0.40
679 92 0.12
680 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.35
Consensus pattern (668 bp):
AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT
GAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATGCTTTTTTCTTAACGATTCTTG
AGGTAGACATTCAATTATAATATGTTTTAACTAAAAATGTAAATAAATTGAACATAAAATCAATT
TTGAGATAATAAAACTATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGGGAGACTATATAAAT
AGACTTTTTCAACACGTTTCATAAGGCAGACATTCAATTATAATCTATTTTAACTCGAAATGTTA
CACAAAATTGAACTCAAAATCAATTAGAAGATTATAAAACGATTTAAAGCAAGTAATAACACTTT
TGAAGGAATGAGAGACTATAAATGAACTTTTCTTGCCAAAGAATGCCTTTTTCTTCAAGTTTCTC
AAGGTAGACATTCAATTATAACCTGTTTTAACAAAAAATGTAAAACAAATTGAACATAAAATCAA
TTTTGAGATAATAAAACCATTTAAGATAAGTAATAAGGCTTTAGATAGAATAGGTGACTATAAAT
GAACTTTTATTGCCAATGAATACATCTTTCTTCCATTTCTCGAGGCAGAGATTCAATTATAATCT
CTTTTAACCAAAAATATA
Found at i:3301 original size:171 final size:170
Alignment explanation
Indices: 2872--3322 Score: 476
Period size: 170 Copynumber: 2.6 Consensus size: 170
2862 NNNNNNNNNG
* * * *
2872 GACTTTTCTTGCCAATGAATACCTTTTTCTTCATGTTTCTTAAGGTAGACATTGAATTATAAAT-
1 GACTTTTATTGCCAATGAATGCATTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTAT-AATC
** * *
2936 TGTTTTATGCAAAAATGTAAAAAAAAATGAACATAATATCAAATTTGAGATAATAAAACTATTTA
65 TGTTTTAACCAAAAATGT-AAAAAAAATCAACATAATAT-AAATTTGAGATAATAAAACCATTTA
* *** * * * *
3001 AAGTGAGTGCTAAGGCTTTAGAAGGAGTGAGTGACTATAAATA
128 AAGTAAGAAATAAAGCTTTAGAAAGAATGAGAGACTATAAATA
* * * *
3044 GACTTTTATTGCCAATAAATGCATTTTTCTTCATGTTTCTTGA-GCAGACATGCAATTATAATCT
1 GACTTTTATTGCCAATGAATGCATTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTATAATCT
* * * * * *
3108 GTTTTAACGAAAAATGTAAAAAAATTCAACCTAA-ATATAATTATGTGATTATTAAACCATTTAA
66 GTTTTAACCAAAAATGTAAAAAAAATCAACATAATATA-AATT-TGAGATAATAAAACCATTTAA
*
3172 AGTAAGAAATAAAGCTTTTGAAAGAATGAGAGACTATAAATA
129 AGTAAGAAATAAAGCTTTAGAAAGAATGAGAGACTATAAATA
* * * * * * **
3214 GACTTTTTTTGCCAATGAATGCTTTTTTCTTTACGTTACTCAAGGTAGACATTCAATTATTGTCT
1 GACTTTTATTGCCAATGAATGCATTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTATAATCT
* * * *
3279 GTTTTAACCATAAATGTAAAAAAAATTGAACATAAAATCAATTT
66 GTTTTAACCAAAAATGTAAAAAAAA-TCAACATAATATAAATTT
3323 NNNNNNNNNN
Statistics
Matches: 228, Mismatches: 45, Indels: 13
0.80 0.16 0.05
Matches are distributed among these distances:
168 1 0.00
169 6 0.03
170 102 0.45
171 68 0.30
172 49 0.21
173 2 0.01
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.36
Consensus pattern (170 bp):
GACTTTTATTGCCAATGAATGCATTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTATAATCT
GTTTTAACCAAAAATGTAAAAAAAATCAACATAATATAAATTTGAGATAATAAAACCATTTAAAG
TAAGAAATAAAGCTTTAGAAAGAATGAGAGACTATAAATA
Found at i:4147 original size:172 final size:170
Alignment explanation
Indices: 3657--4533 Score: 676
Period size: 172 Copynumber: 5.1 Consensus size: 170
3647 NNNNNNNNNN
* ** * * * * **
3657 AAAAAAATTGAACACAATATCAATTTTGAGAAAATAAAACCATTTAAAGTGAGTGCTAAGGCTTT
1 AAAAAAATTCAACTTAAAATCAATTATGAGATAATAAAACCATTTAAAGCGAGTAATAAGGCTTT
* * * * * * *
3722 AGAAGGAAT-AGATGACTATAAATAGACTTTTATTGCCAATAAATATATTTTTCTTCACGTTTCT
66 TGAAGGAATGGGA-GACTATAAATGGACTTTTCTTGCCAATGAATACATTTTTCTTCATG-TTCT
* * * * * ** * * ** * *
3786 TCA-GCAAATATTGAATTATAGTCTGTTTTTACCAAATATGT
129 TGAGGTAGACATTCAATTATAACCTATTTTAATGAAAAATAT
* * *
3827 AAAAAAATTCAACCTGAAATCAATTATGAGATTAT-AAACCATTTAAAGCGAGTAATAAGGCTTT
1 AAAAAAATTCAACTTAAAATCAATTATGAGATAATAAAACCATTTAAAGCGAGTAATAAGGCTTT
** * * ** * *
3891 TGAAGGAATGCAAGACTATAAATGGACTTCTCTT-CTCAATCG-GT-GGTGTTTATTACATGTAT
66 TGAAGGAATGGGAGACTATAAATGGACTTTTCTTGC-CAAT-GAATACATTTTTCTT-CATGT-T
* ** **
3953 CCTGAGGTAGGTAGTT-AATTATAATATATTTTAATGAAAAATAT
127 CTTGAGGTAGACA-TTCAATTATAACCTATTTTAATGAAAAATAT
* * * * *
3997 AAAAATAGTTCAACTTAAAATCAATTAGGAGATTATAAAACTATTTAAACCGAGTAATAAGGCTT
1 AAAAA-AATTCAACTTAAAATCAATTATGAGATAATAAAACCATTTAAAGCGAGTAATAAGGCTT
* * * * * *
4062 TTGAAGGAATGGGTGACTATAAATGGACTTGTCTTGACAATGAATGCCTTTTTCTTCATGCTTTT
65 TTGAAGGAATGGGAGACTATAAATGGACTTTTCTTGCCAATGAATACATTTTTCTTCATG-TTCT
* * *
4127 TAAGGTAGACATTCAATTATAACCTGTTTT-ATGCAAAAATGT
129 TGAGGTAGACATTCAATTATAACCTATTTTAATG-AAAAATAT
** * * * * * * **
4169 AAAAAAAATAGAACATAATATCAATTTTGAGATAACAAAATCATTTAAAGTGAGTGCTAAGGCTT
1 -AAAAAAATTCAACTTAAAATCAATTATGAGATAATAAAACCATTTAAAGCGAGTAATAAGGCTT
* * * * * * *
4234 TAGAAGGAATGGGTGACTATAAATAGACTTTTATTGCCAATAAATATATTTTTCTTCACGCTTCT
65 TTGAAGGAATGGGAGACTATAAATGGACTTTTCTTGCCAATGAATACATTTTTCTTCATG-TTCT
* * * * * * * ** * *
4299 TCA-GAAAATATTGAATTATAGCCTATTTTTACCAAATATGT
129 TGAGGTAGACATTCAATTATAACCTATTTTAATGAAAAATAT
* *
4340 AAAAAAATTCAACTTGAAATCAATTATGAGATAATAAAACCATTTAAAGCGAGTAAAAAGGCTTT
1 AAAAAAATTCAACTTAAAATCAATTATGAGATAATAAAACCATTTAAAGCGAGTAATAAGGCTTT
* * * * ** *
4405 TGAGGGAATGAGAGACTACAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTTGTGTTTCTC
66 TGAAGGAATGGGAGACTATAAATGGACTTTTCTTGCCAATGAATACATTTTTCTTCATG-TTCTT
**
4470 GAGGTAGACATTCAATTATAGTCTATTTTAATG-AAAATAT
130 GAGGTAGACATTCAATTATAACCTATTTTAATGAAAAATAT
*
4510 AAAACAATTCAACTTAAAATCAAT
1 AAAAAAATTCAACTTAAAATCAAT
4534 NNNNNNNNNN
Statistics
Matches: 551, Mismatches: 138, Indels: 36
0.76 0.19 0.05
Matches are distributed among these distances:
168 8 0.01
169 64 0.12
170 188 0.34
171 83 0.15
172 196 0.36
173 12 0.02
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (170 bp):
AAAAAAATTCAACTTAAAATCAATTATGAGATAATAAAACCATTTAAAGCGAGTAATAAGGCTTT
TGAAGGAATGGGAGACTATAAATGGACTTTTCTTGCCAATGAATACATTTTTCTTCATGTTCTTG
AGGTAGACATTCAATTATAACCTATTTTAATGAAAAATAT
Found at i:7342 original size:515 final size:509
Alignment explanation
Indices: 6357--7836 Score: 1762
Period size: 515 Copynumber: 2.9 Consensus size: 509
6347 NNNNNNNNNN
* * ** *
6357 AGGAATTGGTGACTATAAATAGA-CTTTTCTTATCAATGAATTACTTTT--TTATATATTTTTTA
1 AGGAATGGGTGACTATAAATA-ATCTTTTCTTATCAATGAATT-CTTTTCCTT-TATGTTTCATG
* * * *
6419 AGGTAGACATTCAATTATAACCTGTTTT-ACGCAAAAA-AGTAAAAAAATATAGAACATAATATC
63 AGGTAGTCATTCAATTATAATCTGTTTTAAC-TAAAAATA-TAAAAAAAT-TA-AACATAAAATC
* * ** * * * *
6482 AATGTTGAGATAATAAAACTATTTAAAGTGAGTGCTAAGACTTTAGAAGGAATGAGTGGCTATAA
124 AATTTTGAGATAATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAA
* * *** * * * * * **
6547 ATACACTTTTATTGGCAATGAATAAATTTTTCTTCATGTTTCTCGA-GCAGATATTCAACTGTTG
189 ATAGACTTTTATTGCCAATGAATGCCTTTTTCTTCATGTTTCACAAGGTAGACATTCAATTGTAA
* * * * *
6611 TCTGTTTTAGC-ACAAAATAT-TAAAAAATTCAACTTAAAGTCGATTACGAGATTATAAAACTAT
254 TCTGTTTTAACTA-AAAATGTGAAAAAAATTGAACTTAAAGTCGATTACGAGATTATAAAACCAT
* *
6674 TTAATGC-AGTAATAAGGCTTTTGAAGAAATGAGAGGCTATAAAAAGAATTTTCTTCCAAATAAA
318 TTAAAGCGAGTAATAAGGCTTTTAAAG-AATGAGAGGCTATAAAAAGAATTTTCTTCCAAATAAA
* * * * *
6738 TAGATTTTTCTATATATTTCCCAAGGCAGGCATTCAACTCTAGTTTGTTTTAATGAAAAATATAA
382 T-GATTTTT-TACATATTTTCTAAGGCAGGCATTCAACTATAGTTTGTTTTAATGAAAAATGTAA
*
6803 AAAATTAAACTTTAAATTAATTACGAGATTATAAAAAGTTTTCAAGCGAGTAGTAAAGG-TTTTA
445 AAAATTAAACTTTAAATCAATTACGAGATTATAAAAAGTTTTCAAGCGAGTAGT-AAGGCTTTTA
6867 A
509 A
* * *
6868 AGGAATGGGCGACTATAAATATTCTTTTCTTACCAATGAATATCTTTTCCTTTATGTTTCATGAG
1 AGGAATGGGTGACTATAAATAATCTTTTCTTATCAATGAAT-TCTTTTCCTTTATGTTTCATGAG
* *
6933 GTAGTCATTCAACTATAATCTATTTTAACTAAAAATATAAAAATAATTAAACATAAAATCAATTT
65 GTAGTCATTCAATTATAATCTGTTTTAACTAAAAATATAAAAA-AATTAAACATAAAATCAATTT
* * *
6998 TGAGATAAGAAAACCATTTAGAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGA
129 TGAGATAATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGA
* *
7063 CTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCACAAGGTAGACATTCAATTATAATCTGT
194 CTTTTATTGCCAATGAATGCCTTTTTCTTCATGTTTCACAAGGTAGACATTCAATTGTAATCTGT
7128 TTTAACTAAAAATGTCGAAAAAAATTGAACTTAAAGTCGATTACGAGATTATAAAACCATTTAAA
259 TTTAACTAAAAATGT-GAAAAAAATTGAACTTAAAGTCGATTACGAGATTATAAAACCATTTAAA
*
7193 GCGAGTAATAAGGCTTTTAAAAGAATGAGAGGCTATAAAAAGAATTTTCTTCCAAATAAATGGGT
323 GCGAGTAATAAGGCTTTT-AAAGAATGAGAGGCTATAAAAAGAATTTTCTTCCAAATAAAT-GAT
7258 TTTTATACATATTTTCTAAGGCAGGCATTCAACTATAGTTTGTTTTAATGAAAAATGTAAAAAAT
386 TTTT-TACATATTTTCTAAGGCAGGCATTCAACTATAGTTTGTTTTAATGAAAAATGTAAAAAAT
* * * * *
7323 TCAGCTTTAAATCAATTACGATATTATAAAAATTTTTGAAGCGAGTAGTAAGGCTTTTAA
450 TAAACTTTAAATCAATTACGAGATTATAAAAAGTTTTCAAGCGAGTAGTAAGGCTTTTAA
* * *
7383 AGGAATGGGTGACTATATATAGAT-TTTTCTTATCAATGAATGCCTTTTCCTTCATGTTTCATGA
1 AGGAATGGGTGACTATAAATA-ATCTTTTCTTATCAATGAAT-TCTTTTCCTTTATGTTTCATGA
* * * *
7447 GGTAATCATTCAATTATAATCTGTTTTAACTAAAAATGTAAAAAAAATTGAACATAAACTCAATT
64 GGTAGTCATTCAATTATAATCTGTTTTAACTAAAAATAT-AAAAAAATTAAACATAAAATCAATT
* * *
7512 TTGAGATAATAAAACCATTTACAGTGTGTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATAG
128 TTGAGATAATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAG
* *
7577 ACTTTTATTGCCAATGAATGCCTTTTTCTTCAAGTTTCACAAGGTAAACATTCAATTGTAATCTG
193 ACTTTTATTGCCAATGAATGCCTTTTTCTTCATGTTTCACAAGGTAGACATTCAATTGTAATCTG
* * * ** * *
7642 TTTTAAGTAAAAATGTTGAAAGAAATTGAACTTAAAATCGATTATAAGATTATAAAGCCGTTTAA
258 TTTTAACTAAAAATG-TGAAAAAAATTGAACTTAAAGTCGATTACGAGATTATAAAACCATTTAA
* ** * * * * * * * * *
7707 AGTGAGTAATAATACTTTTGAAGGAATGGGGGGCTACAAATAGACTTCTCTTACC-AATGAATGC
322 AGCGAGTAATAAGGCTTTT-AAAGAATGAGAGGCTATAAAAAGAATTTTCTT-CCAAATAAATGA
* * * * * * *
7771 TTTTTT-CTTTACGTTTCTCAAGGTAGACATTCAAATATAGTCTGTTTTAATCAAAAATGTAAAA
385 TTTTTTAC-ATA-TTTTCT-AAGGCAGGCATTCAACTATAGTTTGTTTTAATGAAAAATGTAAAA
7835 AA
447 AA
7837 AAATTGAACA
Statistics
Matches: 839, Mismatches: 109, Indels: 38
0.85 0.11 0.04
Matches are distributed among these distances:
511 143 0.17
512 74 0.09
513 12 0.01
514 61 0.07
515 537 0.64
516 12 0.01
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (509 bp):
AGGAATGGGTGACTATAAATAATCTTTTCTTATCAATGAATTCTTTTCCTTTATGTTTCATGAGG
TAGTCATTCAATTATAATCTGTTTTAACTAAAAATATAAAAAAATTAAACATAAAATCAATTTTG
AGATAATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACT
TTTATTGCCAATGAATGCCTTTTTCTTCATGTTTCACAAGGTAGACATTCAATTGTAATCTGTTT
TAACTAAAAATGTGAAAAAAATTGAACTTAAAGTCGATTACGAGATTATAAAACCATTTAAAGCG
AGTAATAAGGCTTTTAAAGAATGAGAGGCTATAAAAAGAATTTTCTTCCAAATAAATGATTTTTT
ACATATTTTCTAAGGCAGGCATTCAACTATAGTTTGTTTTAATGAAAAATGTAAAAAATTAAACT
TTAAATCAATTACGAGATTATAAAAAGTTTTCAAGCGAGTAGTAAGGCTTTTAA
Found at i:7769 original size:173 final size:172
Alignment explanation
Indices: 6123--7845 Score: 1136
Period size: 172 Copynumber: 10.1 Consensus size: 172
6113 NAATACAAAT
* *** *
6123 AAATTCAACTTAAAATCAATTATGAGATTAT-AAACCATTTAAAACAAGTAATAAGGCTTTTGAA
1 AAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAA
**** * * * **
6187 GGAATAAAAGACTATAAATGGACTTCTCTT-CTCAATTG-ATGGCTTTTAT-TAT-ATGTTTCTT
66 GGAATGGGTGACTATAAATAGACTTTTCTTAC-CAA-TGAATGCCTTTT-TCT-TCATGTTTCAC
* * * * ** * * * *
6248 GAGGCAGGCATTCAATTCTACCCT-ATTTCAGTGAAAAAT-ATAAAA
127 AAGGTAGACATTCAATTATAATCTGTTTTAACT-AAAAATGTTAAAA
* * * * * * **********
6293 CAATTCAATTTAAAATCAATTAGGAGATTATAAAACCATTTAAGGCGAGTAATANNNNNNNNNNA
1 AAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAA
* * ** * ***
6358 GGAATTGGTGACTATAAATAGACTTTTCTTATCAATGAATTACTTTTT-TAT-ATATTTTTTAAG
66 GGAATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGCCTTTTTCT-TCATGTTTCACAAG
* * *
6421 GTAGACATTCAATTATAACCTGTTTT-ACGCAAAAAAG-TAAAA
130 GTAGACATTCAATTATAATCTGTTTTAAC-TAAAAATGTTAAAA
* * * * ** *
6463 AAATATAGAACATAATATCAATGT-TGAGATAATAAAACTATTTAAAGTGAGTGCTAAGAC-TTT
1 AAAT-T-GAACTTAAAATCAAT-TATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTT
* * * * ** *** *
6526 AGAAGGAATGAGTGGCTATAAATACACTTTTATTGGCAATGAATAAATTTTTCTTCATGTTTCTC
63 A-AAGGAATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGCCTTTTTCTTCATGTTTCAC
* * * * * ** * *
6591 GA-GCAGATATTCAACTGTTGTCTGTTTTAGC-ACAAAATATT-AAA
127 AAGGTAGACATTCAATTATAATCTGTTTTAACTA-AAAATGTTAAAA
* * * * * *
6635 AAATTCAACTTAAAGTCGATTACGAGATTATAAAACTATTT-AA-TGCAGTAATAAGGCTTTTGA
1 AAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTG-AGTAATAAGGCTTTTAA
* * * * * * * * * *
6698 AGAAATGAGAGGCTATAAAAAGAATTTTCTT-CCAAATAAATAG-ATTTTTCTAT-ATATTTCCC
65 AGGAATGGGTGACTATAAATAGACTTTTCTTACC-AATGAAT-GCCTTTTTCT-TCATGTTTCAC
* * * * * * *
6760 AAGGCAGGCATTCAACTCTAGTTTGTTTTAA-TGAAAAAT-AT-AAA
127 AAGGTAGACATTCAATTATAATCTGTTTTAACT-AAAAATGTTAAAA
* * * * *** * * *
6804 AAATTAAACTTTAAATTAATTACGAGATTATAAAAAGTTTTCAAGCGAGTAGTAAAGG-TTTTAA
1 AAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAAT-AAGGCTTTTAA
* ** ** * * **
6868 AGGAATGGGCGACTATAAATATTCTTTTCTTACCAATGAATATCTTTTCCTTTATGTTTCATGAG
65 AGGAATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGCCTTTTTCTTCATGTTTCACAAG
* * * *
6933 GTAGTCATTCAACTATAATCTATTTTAACTAAAAAT-ATAAAA
130 GTAGACATTCAATTATAATCTGTTTTAACTAAAAATGTTAAAA
* * * * * * *
6975 ATAATTAAACATAAAATCAATTTTGAGATAAGAAAACCATTTAGAGTGAGTAATAAGGCTTTTGA
1 A-AATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAA
* *
7040 AGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCACAAG
65 AGGAATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGCCTTTTTCTTCATGTTTCACAAG
*
7105 GTAGACATTCAATTATAATCTGTTTTAACTAAAAATGTCGAAAA
130 GTAGACATTCAATTATAATCTGTTTTAACTAAAAATGT-TAAAA
* * * *
7149 AAATTGAACTTAAAGTCGATTACGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAA
1 AAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAA
* * * * * * * ** * * * *
7214 AGAATGAGAGGCTATAAAAAGAATTTTCTT-CCAAATAAATGGGTTTTTATACATATTTTC-TAA
66 GGAATGGGTGACTATAAATAGACTTTTCTTACC-AATGAATGCCTTTTTCTTCAT-GTTTCACAA
* * * * *
7277 GGCAGGCATTCAACTATAGTTTGTTTTAA-TGAAAAATG-T-AAA
129 GGTAGACATTCAATTATAATCTGTTTTAACT-AAAAATGTTAAAA
* * * * * *** * * *
7319 AAATTCAGCTTTAAATCAATTACGATATTATAAAAATTTTTGAAGCGAGTAGTAAGGCTTTTAAA
1 AAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAA
* * * * **
7384 GGAATGGGTGACTATATATAGATTTTTCTTATCAATGAATGCCTTTTCCTTCATGTTTCATGAGG
66 GGAATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGCCTTTTTCTTCATGTTTCACAAGG
*
7449 TA-ATCATTCAATTATAATCTGTTTTAACTAAAAATGTAAAAA
131 TAGA-CATTCAATTATAATCTGTTTTAACTAAAAATGTTAAAA
* * * * * *
7491 AAATTGAACATAAACTCAATTTTGAGATAATAAAACCATTTACAGTGTGTAATAAGGCTTTTAAA
1 AAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAA
* * *
7556 GGAATGGGTGACTATAAATAGACTTTTATTGCCAATGAATGCCTTTTTCTTCAAGTTTCACAAGG
66 GGAATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGCCTTTTTCTTCATGTTTCACAAGG
* * * *
7621 TAAACATTCAATTGTAATCTGTTTTAAGTAAAAATGTTGAAAG
131 TAGACATTCAATTATAATCTGTTTTAACTAAAAATGTT-AAAA
* * * * ** *
7664 AAATTGAACTTAAAATCGATTATAAGATTATAAAGCCGTTTAAAGTGAGTAATAATACTTTTGAA
1 AAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAA
* * * * * * * *
7729 GGAATGGGGGGCTACAAATAGACTTCTCTTACCAATGAATGCTTTTTTCTTTACGTTTCTCAAGG
66 GGAATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGCCTTTTTCTTCATGTTTCACAAGG
* * *
7794 TAGACATTCAAATATAGTCTGTTTTAA-TCAAAAATGTAAAAAA
131 TAGACATTCAATTATAATCTGTTTTAACT-AAAAATGT-TAAAA
7837 AAATTGAAC
1 AAATTGAAC
7846 ATAANNNNNN
Statistics
Matches: 1207, Mismatches: 297, Indels: 95
0.75 0.19 0.06
Matches are distributed among these distances:
168 3 0.00
169 101 0.08
170 344 0.29
171 79 0.07
172 381 0.32
173 290 0.24
174 9 0.01
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.35
Consensus pattern (172 bp):
AAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAA
GGAATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGCCTTTTTCTTCATGTTTCACAAGG
TAGACATTCAATTATAATCTGTTTTAACTAAAAATGTTAAAA
Found at i:9859 original size:172 final size:171
Alignment explanation
Indices: 9567--10659 Score: 776
Period size: 172 Copynumber: 6.4 Consensus size: 171
9557 CAAGGTAGAT
* * * *
9567 ATTCAATTATAATCTGTTTTAACTAAAAATGTTGAAAGAATTTGAACTTAAAATCAATTATAAGA
1 ATTCAATTATAATCTGTTTTAACTAAAAATG-T-AAAAAAATTCAACTTAAAATCAATTATGAGA
* * * *
9632 TTATAAAGCCCTTTAAGGTGAGTAATAATACTTTTAAAGGAATGAAG-GACTATAAATGGACTTT
64 TTATAAAACCATTTAAAGTGAGTAATAAGACTTTTAAAGGAATG-AGTGACTATAAATGGACTTT
* * * * * * * *
9696 TCTTGCTAATGAATGCTTTTTTTTTTCAGGTTTCTGGATGTAGAC
128 TCTTGCCAATAAATGC-CTTTTTCTTCATGTTTCTCGAGGTAAAC
* * * *
9741 ATTCAATTATAATCTGTTTTAACTAAAAATGTAAAAAAATTGAACATAAAATCAATTTTGAGATA
1 ATTCAATTATAATCTGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATT
* * * * * *
9806 ATAAAACCATTTAAGGTGAGTAACAAGGCTTTTAAAGGAATGGGTGGCTATAAATGGACTTTTTT
66 ATAAAACCATTTAAAGTGAGTAATAAGACTTTTAAAGGAATGAGTGACTATAAATGGACTTTTCT
* *
9871 TGCTAATAAATGCCTTTTTCTTCATGTTTCTCAAGGTAAAC
131 TGCCAATAAATGCCTTTTTCTTCATGTTTCTCGAGGTAAAC
* * * * * **********
9912 ATTCAATTATAATTTATTTTAA-TGAAAATTGTAAAAGAATTCAAGTTAAAATCANNNNNNNNNN
1 ATTCAATTATAATCTGTTTTAACT-AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGAT
* * *
9976 TATAAAACCATTTAAAGTGAGTAATTAGTCTTTTGAAA-GAATGAGTGACTATAAATGGACCTTT
65 TATAAAACCATTTAAAGTGAGTAATAAGACTTTT-AAAGGAATGAGTGACTATAAATGGACTTTT
* * * * * *
10040 CTTACCAATGAATGCTTTTTTCTTAACGTTCCT-GAGGTAAAC
129 CTTGCCAATAAATGCCTTTTTCTTCATGTTTCTCGAGGTAAAC
* * * * *
10082 ATTCAGTTATAGTCTGCTTTAA-TAAAAA-ATACAAATAAATTCAGCTTAAAATCAATTATGAGA
1 ATTCAATTATAATCTGTTTTAACTAAAAATGTA-AAA-AAATTCAACTTAAAATCAATTATGAGA
* * * * *
10145 TTAT-AAACCTTTTAAA-TCGAGTAATAAGACTTTTGAAGAAATAAAAT-ACTATAAATGGACTT
64 TTATAAAACCATTTAAAGT-GAGTAATAAGACTTTTAAAGGAAT-GAGTGACTATAAATGGACTT
** * * * *
10207 TTCTT-CTCAATTGATGGCTTTTAT-TACATGTTTCTTGAGGTAAGC
127 TTCTTGC-CAATAAATGCCTTTT-TCTTCATGTTTCTCGAGGTAAAC
* * * * *
10252 ATTCAATTCTATTCTATTTTAA-TGAAAAATGTAAAACAAATTCAATTTAAAATCAATTAGGAGA
1 ATTCAATTATAATCTGTTTTAACT-AAAAATGTAAAA-AAATTCAACTTAAAATCAATTATGAGA
* * ********** * * * *
10316 TTATAAAACTATTTAAAGCGAGTNNNNNNNNNNTTGAAGGAATGGGTGACTATAAATAGATTTTT
64 TTATAAAACCATTTAAAGTGAGTAATAAGACTTTTAAAGGAATGAGTGACTATAAATGGACTTTT
* **
10381 CTTGCCAATAAATGCCTTTTTCTTCATGATTCTTAAGGTAAAC
129 CTTGCCAATAAATGCCTTTTTCTTCATGTTTCTCGAGGTAAAC
* * * * ** ** * *
10424 TTTCAATTGTAACCTGTTTTAAGC-AAAAATATAAAAAAACATAGAACACAATATCAATTTTGAG
1 ATTCAATTATAATCTGTTTTAA-CTAAAAATGT-AAAAAA-ATTCAACTTAAAATCAATTATGAG
* * * ** * * * * * *
10488 ATAATAAAATCATTTAAAATGAGTGCTAAGGC-TTTAGATGAAATGGGTGACTATAACTAGACTT
63 ATTATAAAACCATTTAAAGTGAGTAATAAGACTTTTA-AAGGAATGAGTGACTATAAATGGACTT
* * * ** * * * *
10552 TTATTGCCAATAAATACATTTTTCTTCACATTTCCCTA-GCAGAC
127 TTCTTGCCAATAAATGCCTTTTTCTTCATGTTTCTCGAGGTAAAC
* * * * *
10596 ATTCAATTATAGTTTGTTTTAACTAAAAATGTAAAAATATTTAACCTAAAATCAATTATGAGAT
1 ATTCAATTATAATCTGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGAT
10660 NNNNNNNNNN
Statistics
Matches: 709, Mismatches: 186, Indels: 52
0.75 0.20 0.05
Matches are distributed among these distances:
168 6 0.01
169 72 0.10
170 94 0.13
171 188 0.27
172 225 0.32
173 93 0.13
174 31 0.04
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.36
Consensus pattern (171 bp):
ATTCAATTATAATCTGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATT
ATAAAACCATTTAAAGTGAGTAATAAGACTTTTAAAGGAATGAGTGACTATAAATGGACTTTTCT
TGCCAATAAATGCCTTTTTCTTCATGTTTCTCGAGGTAAAC
Found at i:10198 original size:169 final size:172
Alignment explanation
Indices: 9976--10338 Score: 386
Period size: 169 Copynumber: 2.1 Consensus size: 172
9966 NNNNNNNNNN
* * * * * *
9976 TATAAAACCATTTAAAGTGAGTAATTAGTCTTTTGAA-AGAAT-GAGTGACTATAAATGGACCTT
1 TATAAAACTATTTAAAGCGAGTAATAAGACTTTTGAAGA-AATAAAAT-ACTATAAATGGACCTT
* * *
10039 TCTTAC-CAA-TGAAT-GCTTTTTTCTTA-ACG-TTCCTGAGGTAAACATTCAGTTATAGTCTGC
64 TCTT-CTCAATTG-ATGGC--TTTTATTACACGTTTCCTGAGGTAAACATTCAATTATAGTCTAC
* * *
10099 TTTAAT-AAAAA-ATACAAATAAATTCAGCTTAAAATCAATTATGAGAT
125 TTTAATGAAAAATATA-AAACAAATTCAACTTAAAATCAATTAGGAGAT
* * *
10146 TATAAACCT-TTTAAATCGAGTAATAAGACTTTTGAAGAAATAAAATACTATAAATGGACTTTTC
1 TATAAAACTATTTAAAGCGAGTAATAAGACTTTTGAAGAAATAAAATACTATAAATGGACCTTTC
* * * * * *
10210 TTCTCAATTGATGGCTTTTATTACATGTTTCTTGAGGTAAGCATTCAATTCTATTCTATTTTAAT
66 TTCTCAATTGATGGCTTTTATTACACGTTTCCTGAGGTAAACATTCAATTATAGTCTACTTTAAT
* *
10275 GAAAAATGTAAAACAAATTCAATTTAAAATCAATTAGGAGAT
131 GAAAAATATAAAACAAATTCAACTTAAAATCAATTAGGAGAT
10317 TATAAAACTATTTAAAGCGAGT
1 TATAAAACTATTTAAAGCGAGT
10339 NNNNNNNNNN
Statistics
Matches: 158, Mismatches: 25, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
168 8 0.05
169 52 0.33
170 44 0.28
171 41 0.26
172 13 0.08
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (172 bp):
TATAAAACTATTTAAAGCGAGTAATAAGACTTTTGAAGAAATAAAATACTATAAATGGACCTTTC
TTCTCAATTGATGGCTTTTATTACACGTTTCCTGAGGTAAACATTCAATTATAGTCTACTTTAAT
GAAAAATATAAAACAAATTCAACTTAAAATCAATTAGGAGAT
Found at i:12152 original size:170 final size:171
Alignment explanation
Indices: 11555--13147 Score: 1369
Period size: 170 Copynumber: 9.3 Consensus size: 171
11545 NNNNNNNNNN
* * * ** *
11555 ATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGTCTTTTTCTTCATGTTCCTTGAGGTAA
1 ATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTAATGTTTCTCAAGGTAG
* * * * * * * *
11620 ACATTCAATTATAATTTGTTTTAGTGAAAAATGTAAAAGAATTCAAGTTAAAATTAATTATGAGG
66 ACATTCAATTATAGTCTGTTTTAATGAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGA
* * *
11685 TTATAAAACTATTTAAAGTGAGTAATAAGACTTTTGAAGGA
131 TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGA
** * * * * ** *
11726 ATATGTGATTATAAAT-GACCTTTTCTTTCCAATGAATGCTTTTTTGTTAACATTTCTTAAGGTA
1 ATGGGTGACTATAAATAGA-CTTTTCTTGCCAATGAATGCCTTTTTCTTAATGTTTCTCAAGGTA
* * ** * * *
11790 GATATTCAATTTTAGTCTGTTTTAACCAAAAATATAAATAAATTTAATTTAAAATCAATTATGAG
65 GACATTCAATTATAGTCTGTTTTAATGAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAG
* * *
11855 ATTAT-AAACCATTTGAAGCGAGTAAAAAGGCTTTTAAAGGA
130 ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGA
* * * * * * *
11896 ATGCGAGACTATAAATGGAGTTCTCCT-CTCAATTG-ATAG--TTTTTATTACATGTTTC-CTAA
1 ATGGGTGACTATAAATAGACTTTTCTTGC-CAA-TGAAT-GCCTTTTTCTTA-ATGTTTCTC-AA
* * *
11956 GGGAGGCATTCAATTATAGTCTATTTTAATGAAAAATATAAAAAAATTCAACTTAAAATCAATTA
61 GGTAGACATTCAATTATAGTCTGTTTTAATGAAAAATATAAAAAAATTCAACTTAAAATCAATTA
*
12021 -GAAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGGA
126 TG-AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGA
* * * * *
12067 ATGGGTGACTATAAAT-GGCATTTCTTACCAATGAATGCCGTTTTCTTAATGTTCCTCAAGGTAG
1 ATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTAATGTTTCTCAAGGTAG
* * ** * * * * * * *
12131 ACATTTAATTTTAACCTATTTT-ATGCAAAATTTTTAAAAAATAAATTGAACATAATATCAATTT
66 ACATTCAATTATAGTCTGTTTTAATG-AAAA---ATATAAAA-AAATTCAACTTAAAATCAATTA
* * * ** *
12195 TGACATAATAAAACCATTTAAAGTGAGTGCTAGGGCTTTTGAAGGA
126 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGA
* * * * * * * ** *
12241 ATAGGTAACTATAAATAGACTTTTATTGTCAATGAATACAC-TTTTCTTTACGTTTCTTGA-GCA
1 ATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGC-CTTTTTCTTAATGTTTCTCAAGGTA
* * *
12304 GACATTCAATTATAGTCTGTTTTAACT-AAAAATGTAAAAAATTTCAA-TCTAAAATCAGTTATG
65 GACATTCAATTATAGTCTGTTTTAA-TGAAAAATATAAAAAAATTCAACT-TAAAATCAATTATG
* * *
12367 AGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTCGAAAGA
128 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGA
* * * * * * *
12411 ATGTGAGACTATAAAT-GAACTTTTCTTACCAATGAATACTTTTTTCTTCATGTTTCTCGAGGTA
1 ATGGGTGACTATAAATAG-ACTTTTCTTGCCAATGAATGCCTTTTTCTTAATGTTTCTCAAGGTA
* * *
12475 AACATTCAAGTATAGTCTGTTTTAATG-AAAATGTAAAAGAAA-TCAACTTAAAATCAATTATGA
65 GACATTCAATTATAGTCTGTTTTAATGAAAAATATAAAA-AAATTCAACTTAAAATCAATTATGA
* *
12538 GATTACAAAACCTTTTAAAGCGAGTAATAAGGCTTTTGAAGGA
129 GATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGA
* * * * *
12581 ATGGGTGACTATACATAAACTTTTCTTACCAATGAATGCCTTTTTCTTCATGTTTCTCAATGTAG
1 ATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTAATGTTTCTCAAGGTAG
* * * * ** *
12646 ATATTCAATTATAATTTGTGTTAACCAAAAA-AGTAAAAAAAATT-AGACTTAAAATCAATTTTG
66 ACATTCAATTATAGTCTGTTTTAATGAAAAATA-T-AAAAAAATTCA-ACTTAAAATCAATTATG
* * * *
12709 AGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTCAAGCA
128 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGA
* * * * ** * * *
12753 ATAGGTGGCTATAAATAGACTTTTATTGCCAATGAATGCATTTCACTTCATGTTTCTTATGGCTA
1 ATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTAATGTTTCTCAAGG-TA
* * * * * * * *
12818 -ACATCCAATTATAGTTTTTTTTAATCAAAAAATATAAAGAACTTCAACTTAAAATCGATTACGA
65 GACATTCAATTATAGTCTGTTTTAAT-GAAAAATATAAAAAAATTCAACTTAAAATCAATTATGA
* * *
12882 GATTATAAAATCATTTAAAGCTAGTAATAAGGCTTTTGAAGAA
129 GATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGA
** * * * ** * *
12925 ATAAGAGACTATAAATCGACTTTTCTT-CCAAATAAATGGGTTTTTC-TACATGTTTCTCAATGC
1 ATGGGTGACTATAAATAGACTTTTCTTGCC-AATGAATGCCTTTTTCTTA-ATGTTTCTCAAGGT
* * * * * *
12988 AAACATTCAATTATAATCTGTTTCAACTAGGAAAGTAA-AAAAAAAAATTGAACTTAATATCAAT
64 AGACATTCAATTATAGTCTGTTTTAA-T--GAAA--AATATAAAAAAATTCAACTTAAAATCAAT
* * * * *
13052 TTTAAGATTATAAAACCATTAAAAGTGAGTAATAACGCTTTTGAAGGA
124 TATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGA
* *
13100 ATGGCTGACTATAAATAGACTTTTCTTGCCAATGAATGCATTTTTCTT
1 ATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTT
13148 CA
Statistics
Matches: 1128, Mismatches: 244, Indels: 95
0.77 0.17 0.06
Matches are distributed among these distances:
169 17 0.02
170 406 0.36
171 210 0.19
172 249 0.22
173 16 0.01
174 97 0.09
175 126 0.11
176 7 0.01
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (171 bp):
ATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTAATGTTTCTCAAGGTAG
ACATTCAATTATAGTCTGTTTTAATGAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGA
TTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGA
Found at i:12322 original size:514 final size:509
Alignment explanation
Indices: 11555--13147 Score: 1598
Period size: 514 Copynumber: 3.1 Consensus size: 509
11545 NNNNNNNNNN
* * * ** *
11555 ATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGTCTTTTTCTTCATGTTCCTTGAGGTAA
1 ATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGCCTTTTTCTTAATGTTCCTCAAGGTAG
** * * *** * * ** * *
11620 ACATTCAATTATAATTTGTTTTAGTGAAAAATGT-AAAAGAATTCA-AGTTAAAATTAATTATGA
66 ACATTCAATTATAACCTATGTTAACCAAAAAAGTAAAAAAAATT-AGACATAAAATCAATTTTGA
** * * * *
11683 GGTTATAAAACTATTTAAAGTGAGTAATAAGACTTTTGAAGGAATATGTGATTATAAAT-GACCT
130 CATAATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATAGA-CT
* * * * * * *
11747 TTTCTT-TCCAATGAATGCTTTTTTGTTAACATTTCTTAAGGTAGATATTCAATTTTAGTCTGTT
194 TTTATTGT-CAATGAATGC-ATTTTCTTAACGTTTCTT-AGGCAGACATTCAATTATAGTCTGTT
* *
11811 TTAACCAAAAATATAAATAAATTTAATTTAAAATCAATTATGAGATTAT-AAACCATTTGAAGCG
256 TTAACAAAAAATATAAA-AAATTTAATTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCG
* * * * *
11875 AGTAAAAAGGCTTTTAAAGGAATGCGAGACTATAAATGGAGTTCTCCTCTCAATTGATAGTTTTT
320 AGTAATAAGGCTTTTAAAGGAATGAGAGACTATAAATGGACTTTTCTTC-CAATTGATAGTTTTT
* ** *
11940 ATTACATGTTTC-CTAAGGGAGGCATTCAATTATAGTCTATTTTAATGAAAAATATAAAAAAATT
384 -TTACATGTTTCTC-AAGGCAAACATTCAATTATAGTCTGTTTTAATGAAAAATATAAAAAAATT
*
12004 CAACTTAAAATCAATTAGAAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGGA
447 CAACTTAAAATCAATTAGAAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGA
* * *
12067 ATGGGTGACTATAAAT-GGCATTTCTTACCAATGAATGCCGTTTTCTTAATGTTCCTCAAGGTAG
1 ATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGCCTTTTTCTTAATGTTCCTCAAGGTAG
* * * ** *** *
12131 ACATTTAATTTTAACCTATTTTATGCAAAATTTTTAAAAAATAAATT-GAACATAATATCAATTT
66 ACATTCAATTATAACCTATGTTAACCAAAA-AAGT-AAAAA-AAATTAG-ACATAAAATCAATTT
* ** * *
12195 TGACATAATAAAACCATTTAAAGTGAGTGCTAGGGCTTTTGAAGGAATAGGTAACTATAAATAGA
127 TGACATAATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATAGA
* *
12260 CTTTTATTGTCAATGAATACACTTTTCTTTACGTTTCTT-GAGCAGACATTCAATTATAGTCTGT
192 CTTTTATTGTCAATGAATGCA-TTTTCTTAACGTTTCTTAG-GCAGACATTCAATTATAGTCTGT
* * * * *
12324 TTTAACTAAAAATGTAAAAAATTTCAATCTAAAATCAGTTATGAGATTATAAAACTATTTAAAGC
255 TTTAACAAAAAATATAAAAAATTT-AATTTAAAATCAATTATGAGATTATAAAACCATTTAAAGC
* * * *
12389 GAGTAATAAGGCTTTCGAAA-GAATGTGAGACTATAAATGAACTTTTCTTACCAA-TGAATACTT
319 GAGTAATAAGGCTTT-TAAAGGAATGAGAGACTATAAATGGACTTTTCTT-CCAATTG-ATAGTT
* * * * *
12452 TTTTCTTCATGTTTCTCGAGGTAAACATTCAAGTATAGTCTGTTTTAATG-AAAATGTAAAAGAA
381 TTTT-TACATGTTTCTCAAGGCAAACATTCAATTATAGTCTGTTTTAATGAAAAATATAAAA-AA
* *
12516 A-TCAACTTAAAATCAATTATG-AGATTACAAAACCTTTTAAAGCGAGTAATAAGGCTTTTGAAG
444 ATTCAACTTAAAATCAATTA-GAAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAG
12579 GA
508 GA
* * * * *
12581 ATGGGTGACTATACATAAACTTTTCTTACCAATGAATGCCTTTTTCTTCATGTTTCTCAATGTAG
1 ATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGCCTTTTTCTTAATGTTCCTCAAGGTAG
* ** * * *
12646 ATATTCAATTATAATTTGTGTTAACCAAAAAAGTAAAAAAAATTAGACTTAAAATCAATTTTGAG
66 ACATTCAATTATAACCTATGTTAACCAAAAAAGTAAAAAAAATTAGACATAAAATCAATTTTGAC
* * * *
12711 ATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTCAAGCAATAGGTGGCTATAAATAGACTTT
131 ATAATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATAGACTTT
* * * * * * *
12776 TATTGCCAATGAATGCATTTCACTTCATGTTTCTTATGGCTA-ACATCCAATTATAGTTTTTTTT
196 TATTGTCAATGAATGCATTT-TCTTAACGTTTCTTA-GGC-AGACATTCAATTATAGTCTGTTTT
* * * * * * *
12840 AATCAAAAAATATAAAGAACTTCAACTTAAAATCGATTACGAGATTATAAAATCATTTAAAGCTA
258 AA-CAAAAAATATAAA-AAATTTAATTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGA
* * * * ** *
12905 GTAATAAGGCTTTTGAAGAAATAAGAGACTATAAATCGACTTTTCTTCCAAATAAATGGGTTTTT
321 GTAATAAGGCTTTTAAAGGAATGAGAGACTATAAATGGACTTTTCTTCC-AATTGAT-AGTTTTT
* * * * *
12970 CTACATGTTTCTCAATGCAAACATTCAATTATAATCTGTTTCAACTAGGAAAGTAA-AAAAAAAA
384 TTACATGTTTCTCAAGGCAAACATTCAATTATAGTCTGTTTTAA-T--GAAA--AATATAAAAAA
* * ** * * *
13034 ATTGAACTTAATATCAATTTTAAGATTATAAAACCATTAAAAGTGAGTAATAACGCTTTTGAAGG
444 ATTCAACTTAAAATCAATTAGAAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGG
13099 A
509 A
* * *
13100 ATGGCTGACTATAAATAGACTTTTCTTGCCAATGAATGCATTTTTCTT
1 ATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGCCTTTTTCTT
13148 CA
Statistics
Matches: 885, Mismatches: 157, Indels: 71
0.80 0.14 0.06
Matches are distributed among these distances:
511 64 0.07
512 121 0.14
513 40 0.05
514 275 0.31
515 268 0.30
516 8 0.01
517 1 0.00
518 5 0.01
519 101 0.11
520 2 0.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (509 bp):
ATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGCCTTTTTCTTAATGTTCCTCAAGGTAG
ACATTCAATTATAACCTATGTTAACCAAAAAAGTAAAAAAAATTAGACATAAAATCAATTTTGAC
ATAATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATAGACTTT
TATTGTCAATGAATGCATTTTCTTAACGTTTCTTAGGCAGACATTCAATTATAGTCTGTTTTAAC
AAAAAATATAAAAAATTTAATTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
AAGGCTTTTAAAGGAATGAGAGACTATAAATGGACTTTTCTTCCAATTGATAGTTTTTTTACATG
TTTCTCAAGGCAAACATTCAATTATAGTCTGTTTTAATGAAAAATATAAAAAAATTCAACTTAAA
ATCAATTAGAAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGA
Found at i:12360 original size:344 final size:339
Alignment explanation
Indices: 11562--13147 Score: 1047
Period size: 344 Copynumber: 4.6 Consensus size: 339
11552 NNNATGGGTG
* * * ** * * ** * * *
11562 ACTATAAATAGACTTTTCTTGCCAATGAATGTCTTTTTCTTCATGTTCCTTGAGGTAAACATTCA
1 ACTATAAATAAACTTTTATTACCAATGAATACCTTTTTCTTCACGTTTCTCAATGCAGACATTCA
* * * * * * *
11627 ATTATAATTTGTTTT-AGTGAAAAATGTAAAAGAATTCAAGTTAAAATTAATTATGAGGTTATAA
66 ATTATAGTCTGTTTTAACT-AAAAATGTAAAAAAATTCAACTTAAAATCAATTA-GAGATTATAA
* * ** * *
11691 AACTATTTAAAGTGAGTAATAAGACTTTTGAAGGAATATGTGATTATAAATGACCTTTTCTTTCC
129 AACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGA-CTTTTCTTACC
** * ** * * * * * * ** * **
11756 AATGAATGCTTTTTTGTTAACATTTCTTAAGGTAGATATTCAATTTTAGTCTGTTTTAACCAAAA
193 AATGAATGCCGTTTTCTTAATGTTCCTCAAGGTAAACATTCAAGTATAACCTATTTTAA-TGAAA
* * * ** * * * * *
11821 ATATAAATA-AATTTAATTTAAAATCAATTATGAGATTA-TAAACCATTTGAAGCGAGTAAAAAG
257 ATGTAAA-AGAAATCAACATAAAATCAATTATGACATAACAAAACCATTTAAAGCGAGTAATAAG
*
11884 GCTTTTAAAGGAAT-GCG-A
321 GCTTTTGAAGGAATAG-GTA
** * * ** * * * * * *
11902 GACTATAAATGGAGTTCTCCT-CTCAATTG-ATA-GTTTTTATTACATGTTTC-CTAAGGGAGGC
1 -ACTATAAATAAACTTTTATTAC-CAA-TGAATACCTTTTTCTT-CACGTTTCTC-AATGCAGAC
* *
11963 ATTCAATTATAGTCTATTTTAA-TGAAAAATATAAAAAAATTCAACTTAAAATCAATTAGAAGAT
61 ATTCAATTATAGTCTGTTTTAACT-AAAAATGTAAAAAAATTCAACTTAAAATCAATTAG-AGAT
* *
12027 TATAAAA-TCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGCATTTC
124 TATAAAACT-ATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGACTTTTC
* * * *
12091 TTACCAATGAATGCCGTTTTCTTAATGTTCCTCAAGGTAGACATTTAATTTTAACCTATTTT-AT
188 TTACCAATGAATGCCGTTTTCTTAATGTTCCTCAAGGTAAACATTCAAGTATAACCTATTTTAAT
* * * * * * *
12155 GCAAAATTTTTAAAAAATAAATTGAACATAATATCAATTTTGACATAATAAAACCATTTAAAGTG
253 G-AAAA--TGT--AAAAGAAA-TCAACATAAAATCAATTATGACATAACAAAACCATTTAAAGCG
** *
12220 AGTGCTAGGGCTTTTGAAGGAATAGGTA
312 AGTAATAAGGCTTTTGAAGGAATAGGTA
* ** * **
12248 ACTATAAATAGACTTTTATTGTCAATGAATACAC-TTTTCTTTACGTTTCTTGA-GCAGACATTC
1 ACTATAAATAAACTTTTATTACCAATGAATAC-CTTTTTCTTCACGTTTCTCAATGCAGACATTC
* *
12311 AATTATAGTCTGTTTTAACTAAAAATGTAAAAAATTTCAA-TCTAAAATCAGTTATGAGATTATA
65 AATTATAGTCTGTTTTAACTAAAAATGTAAAAAAATTCAACT-TAAAATCAATTA-GAGATTATA
* * * *
12375 AAACTATTTAAAGCGAGTAATAAGGCTTTCGAAAGAATGTGAGACTATAAATGAACTTTTCTTAC
128 AAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATG-ACTTTTCTTAC
* ** * * * ** *
12440 CAATGAATACTTTTTTCTTCATGTTTCTCGAGGTAAACATTCAAGTATAGTCTGTTTTAATGAAA
192 CAATGAATGCCGTTTTCTTAATGTTCCTCAAGGTAAACATTCAAGTATAACCTATTTTAATGAAA
* * * *
12505 ATGTAAAAGAAATCAACTTAAAATCAATTATGAGATTACAAAACCTTTTAAAGCGAGTAATAAGG
257 ATGTAAAAGAAATCAACATAAAATCAATTATGACATAACAAAACCATTTAAAGCGAGTAATAAGG
* *
12570 CTTTTGAAGGAATGGGTG
322 CTTTTGAAGGAATAGGTA
* * * * * *
12588 ACTATACATAAACTTTTCTTACCAATGAATGCCTTTTTCTTCATGTTTCTCAATGTAGATATTCA
1 ACTATAAATAAACTTTTATTACCAATGAATACCTTTTTCTTCACGTTTCTCAATGCAGACATTCA
* * * * * *
12653 ATTATAATTTGTGTTAACCAAAAAAGTAAAAAAAATT-AGACTTAAAATCAATTTTGAGATTATA
66 ATTATAGTCTGTTTTAACTAAAAATGT-AAAAAAATTCA-ACTTAAAATCAA-TTAGAGATTATA
* * * * * * *
12717 AAACTATTTAAAGTGAGTAATAAGGCTTTTCAAGCAATAGGTGGCTATAAATAGACTTTTATTGC
128 AAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT-GACTTTTCTTAC
* * * * * * * * *** * *
12782 CAATGAATG-CATTTCACTTCATGTTTCTTATGGCT-AACATCCAATTATAGTTTTTTTTAATCA
192 CAATGAATGCCGTTT-TCTTAATGTTCCTCAAGG-TAAACATTCAAGTATAACCTATTTTAATGA
** * * * * * * * * *
12845 AAAAATATAAAGAACTTCAACTTAAAATCGATTACGAGATTATAAAATCATTTAAAGCTAGTAAT
255 AAATGTA-AAAGAA-ATCAACATAAAATCAATTATGACATAACAAAACCATTTAAAGCGAGTAAT
* *
12910 AAGGCTTTTGAAGAAATAAG-A
318 AAGGCTTTTGAAGGAATAGGTA
** * * *** * * *
12931 GACTATAAATCGACTTTTCTT-CCAAATAAATGGGTTTTTCTACATGTTTCTCAATGCAAACATT
1 -ACTATAAATAAACTTTTATTACC-AATGAATACCTTTTTCTTCACGTTTCTCAATGCAGACATT
* * * * *
12995 CAATTATAATCTGTTTCAACTAGGAAA-GTAAAAAAAAAAATTGAACTTAATATCAATTTTA-AG
64 CAATTATAGTCTGTTTTAACTA-AAAATGT----AAAAAAATTCAACTTAAAATCAA--TTAGAG
* * * * *
13058 ATTATAAAACCATTAAAAGTGAGTAATAACGCTTTTGAAGGAATGGCTGACTATAAATAGACTTT
122 ATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT-GACTTT
* **
13123 TCTTGCCAATGAATGCATTTTTCTT
186 TCTTACCAATGAATGCCGTTTTCTT
13148 CA
Statistics
Matches: 999, Mismatches: 198, Indels: 90
0.78 0.15 0.07
Matches are distributed among these distances:
339 6 0.01
340 162 0.16
341 179 0.18
342 132 0.13
343 21 0.02
344 260 0.26
345 124 0.12
346 11 0.01
347 97 0.10
348 7 0.01
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (339 bp):
ACTATAAATAAACTTTTATTACCAATGAATACCTTTTTCTTCACGTTTCTCAATGCAGACATTCA
ATTATAGTCTGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTAGAGATTATAAAA
CTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGACTTTTCTTACCAAT
GAATGCCGTTTTCTTAATGTTCCTCAAGGTAAACATTCAAGTATAACCTATTTTAATGAAAATGT
AAAAGAAATCAACATAAAATCAATTATGACATAACAAAACCATTTAAAGCGAGTAATAAGGCTTT
TGAAGGAATAGGTA
Found at i:12996 original size:685 final size:684
Alignment explanation
Indices: 11561--13149 Score: 1549
Period size: 685 Copynumber: 2.3 Consensus size: 684
11551 NNNNATGGGT
* *
11561 GACTATAAATAGACTTTTCTTGCCAATGAATGTC-TTTTTCTTCATGTTCCTTGAGGTAAACATT
1 GACTATAAATAGACTTTTCTTGCCAATGAATG-CATTTTTCTTCATGTTTCTTGA-GCAAACATT
* * * *
11625 CAATTATAATTTGTTTT-AGTGAAAAATGTAAAAGAATTCAAGT-TAAAATTAATTATGAGGTTA
64 CAATTATAATCTGTTTTAACT-AAAAATGTAAAA-AATTCAA-TCTAAAATCAATTATGAGATTA
* * * *
11688 TAAAACTATTTAAAGTGAGTAATAAGACTTTTGAAGGAATATGTGATTATAAATGACCTTTTCTT
126 TAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGTGTGACTATAAATGAACTTTTCTT
* * * * * * * *
11753 TCCAATGAATGCTTTTTTGTTAACATTTCTTAAGGTAGATATTCAATTTTAGTCTGTTTTAACCA
191 ACCAATGAATGCTTTTTTCTTCACATTTCTCAAGGTAAACATTCAAGTATAGTCTGTTTTAACCA
* * * * *
11818 AAAATATAAATAAATTTAATTTAAAATCAATTATGAGATTATAAACCATTTGAAGCGAGTAAAAA
256 AAAATATAAATAAAATCAACTTAAAATCAATTATGAGATTAAAAACCATTTAAAGCGAGTAAAAA
** *
11883 GGCTTTTAAAGGAATGCGAGACTATAAATGGAGTTCTCCTCTCAATTGATAGTTTTTATTACATG
321 GGCTTTTAAAGGAATGCGAGACTATAAATAAACTTCTCCTCTCAATTGATAGTTTTTATTACATG
* * * **
11948 TTTCCTAAGGGAGGCATTCAATTATAGTCTATTTTAATGAAAAATATAAAAAAATTCAACTTAAA
386 TTTCCTAAGGGAGACATTCAATTATAATCTATGTTAACAAAAAATATAAAAAAATTCAACTTAAA
* * *
12013 ATCAATTAGAAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTA
451 ATCAATTAGAAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTCAAGCAATAGGTGACTA
* * * * ** *
12078 TAAATGGCATTTCTTACCAATGAATGCCGTTTTCTTAATGTTCCTCAAGGTAGACATTTAATTTT
516 TAAATGACATTTATTACCAATGAATGCCATTTACTTAATGTTCCTCAAGGTAGACATCCAATTAT
** * * * **
12143 AACCTATTTTATGCAAAATTTTTAAAAAATAAATTGAACATAATATCAATTTTGACATAATAAAA
581 AACCTATTTTATGCAAAA-TAATAAAAAAGAAATTCAACATAAAATCAATTACGACATAATAAAA
** * * *
12208 CCATTTAAAGTGAGTGCTAGGGCTTTTGAAGGAATAGGTA
645 CCATTTAAAGTGAGTAATAAGGCTTTTGAAGAAATAAGTA
* * * * * * *
12248 -ACTATAAATAGACTTTTATTGTCAATGAATACACTTTTCTTTACGTTTCTTGAGCAGACATTCA
1 GACTATAAATAGACTTTTCTTGCCAATGAATGCATTTTTCTTCATGTTTCTTGAGCAAACATTCA
* *
12312 ATTATAGTCTGTTTTAACTAAAAATGTAAAAAATTTCAATCTAAAATCAGTTATGAGATTATAAA
66 ATTATAATCTGTTTTAACTAAAAATGTAAAAAA-TTCAATCTAAAATCAATTATGAGATTATAAA
* * * *
12377 ACTATTTAAAGCGAGTAATAAGGCTTTCGAAAGAATGTGAGACTATAAATGAACTTTTCTTACCA
130 ACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGTGTGACTATAAATGAACTTTTCTTACCA
* ** * **
12442 ATGAATACTTTTTTCTTCATGTTTCTCGAGGTAAACATTCAAGTATAGTCTGTTTTAA-TGAAAA
195 ATGAATGCTTTTTTCTTCACATTTCTCAAGGTAAACATTCAAGTATAGTCTGTTTTAACCAAAAA
* * *
12506 TGTAAA-AGAAATCAACTTAAAATCAATTATGAGATTACAAAACCTTTTAAAGCGAGTAATAAGG
260 TATAAATA-AAATCAACTTAAAATCAATTATGAGATTA-AAAACCATTTAAAGCGAGTAAAAAGG
* * * * * * *
12570 CTTTTGAAGGAATGGGTGACTATACATAAACTTTTCTTAC-CAA-TGA-ATGCCTTTTTCTT-CA
323 CTTTTAAAGGAATGCGAGACTATAAATAAACTTCTCCT-CTCAATTGATA-G--TTTTTATTACA
* * * * *
12631 TGTTT-CTCAATGTAGATATTCAATTATAATTTGTGTTAACCAAAAAAGTA-AAAAAAATT-AGA
384 TGTTTCCT-AAGGGAGACATTCAATTATAATCTATGTTAA-CAAAAAA-TATAAAAAAATTCA-A
* *
12693 CTTAAAATCAATTTTG-AGATTATAAAA-CTATTTAAAGTGAGTAATAAGGCTTTTCAAGCAATA
445 CTTAAAATCAA-TTAGAAGATTATAAAATC-ATTTAAAGCGAGTAATAAGGCTTTTCAAGCAATA
* * * * * * *
12756 GGTGGCTATAAATAGACTTTTATTGCCAATGAATG-CATTTCACTTCATGTTTCTTATGGCTA-A
508 GGTGACTATAAAT-GACATTTATTACCAATGAATGCCATTT-ACTTAATGTTCCTCAAGG-TAGA
*** * * * * *
12819 CATCCAATTATAGTTTTTTTTAAT-CAAAA-AAT-ATAAAGAACTTCAACTTAAAATCGATTACG
570 CATCCAATTATAACCTATTTT-ATGCAAAATAATAAAAAAGAAATTCAACATAAAATCAATTACG
* * *
12881 AGATTATAAAATCATTTAAAGCT-AGTAATAAGGCTTTTGAAGAAATAAG-A
634 ACATAATAAAACCATTTAAAG-TGAGTAATAAGGCTTTTGAAGAAATAAGTA
* * ** * **
12931 GACTATAAATCGACTTTTCTT-CCAAATAAATGGGTTTTTCTACATGTTTCTCAATGCAAACATT
1 GACTATAAATAGACTTTTCTTGCC-AATGAATGCATTTTTCTTCATGTTTCTTGA-GCAAACATT
* * * * * *
12995 CAATTATAATCTGTTTCAACTAGGAAA-GTAAAAAAAAAAATTGAA-CTTAATATCAATTTTAAG
64 CAATTATAATCTGTTTTAACTA-AAAATGT-----AAAAAATTCAATC-TAAAATCAATTATGAG
* * *
13058 ATTATAAAACCATTAAAAGTGAGTAATAACGCTTTTGAAGGAATG-GCTGACTATAAAT-AGACT
122 ATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGTG-TGACTATAAATGA-ACT
* *
13121 TTTCTTGCCAATGAATGCATTTTTCTTCA
185 TTTCTTACCAATGAATGCTTTTTTCTTCA
Statistics
Matches: 730, Mismatches: 139, Indels: 64
0.78 0.15 0.07
Matches are distributed among these distances:
683 4 0.01
684 142 0.19
685 282 0.39
686 140 0.19
687 55 0.08
688 7 0.01
689 94 0.13
690 6 0.01
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (684 bp):
GACTATAAATAGACTTTTCTTGCCAATGAATGCATTTTTCTTCATGTTTCTTGAGCAAACATTCA
ATTATAATCTGTTTTAACTAAAAATGTAAAAAATTCAATCTAAAATCAATTATGAGATTATAAAA
CTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGTGTGACTATAAATGAACTTTTCTTACCAA
TGAATGCTTTTTTCTTCACATTTCTCAAGGTAAACATTCAAGTATAGTCTGTTTTAACCAAAAAT
ATAAATAAAATCAACTTAAAATCAATTATGAGATTAAAAACCATTTAAAGCGAGTAAAAAGGCTT
TTAAAGGAATGCGAGACTATAAATAAACTTCTCCTCTCAATTGATAGTTTTTATTACATGTTTCC
TAAGGGAGACATTCAATTATAATCTATGTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAA
TTAGAAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTCAAGCAATAGGTGACTATAAAT
GACATTTATTACCAATGAATGCCATTTACTTAATGTTCCTCAAGGTAGACATCCAATTATAACCT
ATTTTATGCAAAATAATAAAAAAGAAATTCAACATAAAATCAATTACGACATAATAAAACCATTT
AAAGTGAGTAATAAGGCTTTTGAAGAAATAAGTA
Done.