Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397751.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1048.0, 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: 8052
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.22
Warning! 3142 characters in sequence are not A, C, G, or T
Found at i:931 original size:171 final size:170
Alignment explanation
Indices: 2--3429 Score: 1121
Period size: 171 Copynumber: 20.2 Consensus size: 170
1 G
* ** *
2 CTTAACATCAATTATCTGATTATAAAACCATTTAAAGAGAGTAATAAGGCTTT-GAAAGGAATGA
1 CTTAAAATCAATTATGAGATTATAAAACTATTTAAAGAGAGTAATAAGGCTTTCG-AAGGAATG-
* * ** * * * *
66 GTGACTATAAAT-AGACTTTTCTTACTAATAAATGGTTTTTTCTACACGTTTCTCAAGGCAAACA
64 GTGACTATAAATGA-ACTTTTCTTACCAATGAATACTTTTTTCTTCATGTTTCTCGAGGTAAACA
* * *
130 TTCAATTATAGTTTATTTTAACTAAAAACGTAAAAAAATTCAA
128 TTCAATTATAGTATATTTTAACCAAAAATGTAAAAAAATTCAA
* * ***********************
173 CTTAAAATCAATTATGAGGTTATAAAA-TCATTTAAAGCGANNNNNNNNNNNNNNNNNNNNNNNN
1 CTTAAAATCAATTATGAGATTATAAAACT-ATTTAAAGAGA-GTAATAAGGCTTTCGAAGGAATG
***** ** * * * * **
237 NNNNNTATAAAT-AGACTTTTCTTGTCAATGAATGCTATTTTCTTCATGTTTCTCTAAGTTGACA
64 GTGACTATAAATGA-ACTTTTCTTACCAATGAATACTTTTTTCTTCATGTTTCTCGAGGTAAACA
* * * * * *
301 TTCAATTATAGTTTGTTTCAACTAAAAATATAAAAAAATTTAA
128 TTCAATTATAGTATATTTTAACCAAAAATGTAAAAAAATTCAA
* * ********** *
344 CTTAAAATCAATTATGAGATTATTAAACCATTTAAAGNNNNNNNNNNGGCTTTTGAAGGAATGGG
1 CTTAAAATCAATTATGAGATTATAAAACTATTTAAAGAGAGTAATAAGGCTTTCGAAGGAAT-GG
* * * ** * * * *
409 TGACAATAAATGGACTTTTCTTGCCAATGAAGGCTTATTTCTTCACGTTTCTCAAGGTAAAAATT
65 TGACTATAAATGAACTTTTCTTACCAATGAATACTTTTTTCTTCATGTTTCTCGAGGTAAACATT
* * * * *
474 CAATTGTAGTCTGTATTAACCAAAAATGTAAAAAAATTTAA
130 CAATTATAGTATATTTTAACCAAAAATGTAAAAAAATTCAA
* ****************** *
515 CTTAAAATTAATTATGAGATTATAAAACNNNNNNNNNNNNNNNNNNAGGCTTTTGAAGGAATGGG
1 CTTAAAATCAATTATGAGATTATAAAACTATTTAAAGAGAGTAATAAGGCTTTCGAAGGAAT-GG
* * * ** * ** * * *
580 TGACTATAAATGGACTTTTCTTACTAATGAATGCCATTTTCTTTATGTAGCTTGAGCTAGACATT
65 TGACTATAAATGAACTTTTCTTACCAATGAATACTTTTTTCTTCATGTTTCTCGAGGTAAACATT
* * * ** *
645 CAATTATATTATATTTTAATCAATAATCCAAAAGAAATTGAA
130 CAATTATAGTATATTTTAACCAAAAATGTAAAA-AAATTCAA
* * * * * * * *
687 CCTAAAATCAATTTTGAGATTACAAAACCATTTAAAGTGAGTAATCAGGCTTTTGAGGGAATAGG
1 CTTAAAATCAATTATGAGATTATAAAACTATTTAAAGAGAGTAATAAGGCTTTCGAAGGAAT-GG
* * * * *
752 AGACTATAAATGAAATTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCGAGGTACACCTT
65 TGACTATAAATGAACTTTTCTTACCAATGAATACTTTTTTCTTCATGTTTCTCGAGGTAAACATT
* * *
817 CATTTATAGTATGTTTTAACCAAAAATATAAAAAAATTCAA
130 CAATTATAGTATATTTTAACCAAAAATGTAAAAAAATTCAA
* * * * * *
858 CTAAAAATCAATTAGGAGATTATAAAACTAATTAAAGCGAGTAATTAGACTTTCGAAGGAATGGT
1 CTTAAAATCAATTATGAGATTATAAAACTATTTAAAGAGAGTAATAAGGCTTTCGAAGGAATGG-
* * * * * * * *
923 TGACTATAAATTAAGTTTTCTTGCCAATGAAT-GTCTTTTTCTTCTTTTTTCTTGAGGTATACAT
65 TGACTATAAATGAACTTTTCTTACCAATGAATACT-TTTTTCTTCATGTTTCTCGAGGTAAACAT
* * * * *
987 TCAATTATTGTCTGTTTAAACCAAAAATGTAAAAAAATTCAG
129 TCAATTATAGTATATTTTAACCAAAAATGTAAAAAAATTCAA
* * * *
1029 CTTAACATCAATTATAAGATTATAAAACTATTTAAAAAGAGTAATAAGGC-TTCTAAAGGAATGA
1 CTTAAAATCAATTATGAGATTATAAAACTATTTAAAGAGAGTAATAAGGCTTTC-GAAGGAATG-
* * * * *
1093 GTGACTATAAATGGACTTTTCTTACCAATGAATGAC-TTTTTCTACACGTTTCTCAAGGCAAACA
64 GTGACTATAAATGAACTTTTCTTACCAATGAAT-ACTTTTTTCTTCATGTTTCTCGAGGTAAACA
* * *
1157 TTTAATTATAGTATATTTTAACCAAAAACGTAAAAAAATTTAA
128 TTCAATTATAGTATATTTTAACCAAAAATGTAAAAAAATTCAA
*********** * * *
1200 CTTAAAATCGNNNNNNNNNNTATAAAACCATTTAAAGAGAGTAATGAGGCTTT----TGAA--G-
1 CTTAAAATCAATTATGAGATTATAAAACTATTTAAAGAGAGTAATAAGGCTTTCGAAGGAATGGT
* * * * * * * *
1258 GA--AT---TG-ACTTTTCTTATCAATAAAT-GTATTTTTCTTTAAGTTTCT-TAGGGTAGATAT
66 GACTATAAATGAACTTTTCTTACCAATGAATACT-TTTTTCTTCATGTTTCTCGA-GGTAAACAT
* * * * * *
1315 TAAATTAT-GATCTGTTTTAACCAATAACGTAAAATAAATT-GA
129 TCAATTATAG-TATATTTTAACCAAAAATGTAAAA-AAATTCAA
* * * *
1357 CTTAAAATCAATTATTAGATTATAAAA-TAATTTAAAGAGAGTAATAAGACTTTTGAAGGAATNN
1 CTTAAAATCAATTATGAGATTATAAAACT-ATTTAAAGAGAGTAATAAGGCTTTCGAAGGAAT-G
******** * * * * * * *
1421 NNNNNNNNAAATAAACTTTTCTTGCCAATGAAT-GTTTGTTTCTTTACGTTTCTCAAGGTAGACA
64 GTGACTATAAATGAACTTTTCTTACCAATGAATACTTT-TTTCTTCATGTTTCTCGAGGTAAACA
* * * *
1485 TTTAATTATAGTTTGTTTTAA-CAAAAATGCAAAAAAATTC-A
128 TTCAATTATAGTATATTTTAACCAAAAATGTAAAAAAATTCAA
* * * * *
1526 TTTTAAATCAATTATGAGATTATAAAACTATTTAGAGCGAGTAATACA-GCTTTTGAAGGAATGG
1 CTTAAAATCAATTATGAGATTATAAAACTATTTAAAGAGAGTAATA-AGGCTTTCGAAGGAAT-G
* ** * * * * **
1590 GTGAGTATAAAT-AGACTTTTCTT-CTCAATGAAT-GGTTTTTCTACATATTTTCTTGAGGCATG
64 GTGACTATAAATGA-ACTTTTCTTAC-CAATGAATACTTTTTTCTTCAT-GTTTCTCGAGGTAAA
* * **********
1652 CATTCAATTATAGTCTGTNNNNNNNNNNAATGTAAAAAAATTCAA
126 CATTCAATTATAGTATATTTTAACCAAAAATGTAAAAAAATTCAA
* * * * *
1697 CTAAAAATCATTTATGAGATTAT-AAACTATTTAAAGCGAGTAATAAGGCCTTT-GAAGAAATAA
1 CTTAAAATCAATTATGAGATTATAAAACTATTTAAAGAGAGTAATAAGG-CTTTCGAAGGAAT-G
* ** * * * * *
1760 GTGGCTATAAATGAACTTTTCTTGTCAATGAATGCTTGTTTCTTTATGTTTCTTGAGGCT-AATA
64 GTGACTATAAATGAACTTTTCTTACCAATGAATACTTTTTTCTTCATGTTTCTCGAGG-TAAACA
* * * *
1824 TTGAATTATAGTTTGTTTTAACTAAAAATGTAAAAAAAAATT-AA
128 TTCAATTATAGTATATTTTAACCAAAAATGT--AAAAAAATTCAA
********** * * *
1868 CTTAAAATNNNNNNNNNNATTATAAAACAATTTAGAA-TGAGTAATAAGGCTTTTGAAGGAATGG
1 CTTAAAATCAATTATGAGATTATAAAACTATTTA-AAGAGAGTAATAAGGCTTTCGAAGGAAT-G
* * * * **
1932 GTGACTATAAATTG--TTTTGTCTT-CTCAATGAATGGCTTTTTTCTACACGTTTCTTAAGG-AA
64 GTGACTATAAA-TGAACTTT-TCTTAC-CAATGAAT-ACTTTTTTCTTCATGTTTCTCGAGGTAA
* * * *
1993 GGCATTCAATTATAGTCTATTTTAACTAAAAATGCAAAAAAAATTCAA
125 -ACATTCAATTATAGTATATTTTAACCAAAAATG-TAAAAAAATTCAA
***********************
2041 CTTAAAATCAATTATGAGATTATACAAAC-ATTT--A-A-A-NNNNNNNNNNNNNNNNNNNNNNN
1 CTTAAAATCAATTATGAGATTATA-AAACTATTTAAAGAGAGTAATAAGGCTTTCGAAGGAATGG
** * * * * * * * * *
2100 NNACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTTACGTTTCTTGAGCTAGACATT
65 TGACTATAAATGAACTTTTCTTACCAATGAATACTTTTTTCTTCATGTTTCTCGAGGTAAACATT
* * * * * *
2165 CAATTATAATCTGTTTTAACCAATAATGCATAAAAAATTGAA
130 CAATTATAGTATATTTTAACCAAAAATGTA-AAAAAATTCAA
* * * * *
2207 CCTAAAATCAATT-TCGAGATTATAAAACTATTTGATGCGAGTAATAAGGCTTTTG-AGAGAATA
1 CTTAAAATCAATTAT-GAGATTATAAAACTATTTAAAGAGAGTAATAAGGCTTTCGAAG-GAAT-
* * * * * * * * * **
2270 AGAGACTATAAAT-AGACTTTTCTTACCAATGAATGCTTATTTCTTTACGTCTCTTGGGGTTTAC
63 GGTGACTATAAATGA-ACTTTTCTTACCAATGAATACTTTTTTCTTCATGTTTCTCGAGGTAAAC
* * * *
2334 ATTCAATTATAGTCTGTTTTAACTAAAATTGTAAAAAAATTCAA
127 ATTCAATTATAGTATATTTTAACCAAAAATGTAAAAAAATTCAA
* * * * * * *
2378 CTTAAAATTAGTTATGAGATTATAAAACCATTTTAAGAGAGTAATTAGGCTTTTGAAAGAATGGG
1 CTTAAAATCAATTATGAGATTATAAAACTATTTAAAGAGAGTAATAAGGCTTTCGAAGGAAT-GG
* * * * ** *** * * **
2443 TGACTATAAATGGACTTTTCTT-CTCAATGACTGGC-TTGTTCCACACAATTCTCAAGGCAAGTA
65 TGACTATAAATGAACTTTTCTTAC-CAATGAAT-ACTTTTTTCTTCATGTTTCTCGAGGTAAACA
* * * ***
2506 TTCAATTATAGT-TTTTTTAACTAAAAATATAAAAAAATTNNN
128 TTCAATTATAGTATATTTTAACCAAAAATGTAAAAAAATTCAA
******* * * ** *
2548 NNNNNNNTCAATTATGAGATTATAAAA-TAATTTAACGGGAGTAATAAGGCTTTTAAAAGAATAG
1 CTTAAAATCAATTATGAGATTATAAAACT-ATTTAAAGAGAGTAATAAGGCTTTCGAAGGAAT-G
* * * * * * ** * * *
2612 ATGACTATAAATGGACTTTTTTTGCCAATGAATGCATTTTTCTTCACATTTCTTGAGATAGACAT
64 GTGACTATAAATGAACTTTTCTTACCAATGAATACTTTTTTCTTCATGTTTCTCGAGGTAAACAT
** ** * * *
2677 TCAATTATAGCCTATTTTAACTGATAATGTAAAGCAAATT-GA
129 TCAATTATAGTATATTTTAACCAAAAATGTAAA-AAAATTCAA
* * * * * * *
2719 CTTAAAATCAATTATGAGATTATACAACAATTTACAGCGAGTAATAAGGCTTTTGGAGGAATCCG
1 CTTAAAATCAATTATGAGATTATAAAACTATTTAAAGAGAGTAATAAGGCTTTCGAAGGAAT-GG
* * * * * * ** *
2784 TGACCATAAATGAGCTTTTCTT-CTAAATGAA-AGGC-TTTTTCTACACGTTTTTTAAGG-AAGG
65 TGACTATAAATGAACTTTTCTTAC-CAATGAATA--CTTTTTTCTTCATGTTTCTCGAGGTAA-A
* * *
2845 CATTCAATTATAGTCTATTTTAACCAAAAATGTAAAAACACTCAA
126 CATTCAATTATAGTATATTTTAACCAAAAATGTAAAAAAATTCAA
********** * * *
2890 CTTAAAATCAATTATGAGANNNNNNNNNNATTTAAAGTGAGTAATAAGGCTTTTTGAA-TAATGC
1 CTTAAAATCAATTATGAGATTATAAAACTATTTAAAGAGAGTAATAAGGC-TTTCGAAGGAATG-
*********** * * * **
2954 GTGACTATAAAT-AGACTTTTCTTGNNNNNNNNNNCTATTTTCTTCATGTTTCTCTAAGTCGACA
64 GTGACTATAAATGA-ACTTTTCTTACCAATGAATACTTTTTTCTTCATGTTTCTCGAGGTAAACA
* * * * *
3018 TTGAATTATAGTTTGTTTCAACCAAAAATGTAAAAAAATTTAA
128 TTCAATTATAGTATATTTTAACCAAAAATGTAAAAAAATTCAA
************************ *
3061 CTTAAAATCAATTATGAGATTATNNNNNNNNNNNNNNNNNNNNNNNNGGCTTTTGAAGGAATGGG
1 CTTAAAATCAATTATGAGATTATAAAACTATTTAAAGAGAGTAATAAGGCTTTCGAAGGAAT-GG
* ** ** * * *
3126 TGACTATAAATGGACTTTTCTTGTCAATGAAGGCTTGTTTCTTCACGTTTCTCAAGGTAAACATT
65 TGACTATAAATGAACTTTTCTTACCAATGAATACTTTTTTCTTCATGTTTCTCGAGGTAAACATT
* * * * * *
3191 CAATTGTAGTCTGTTTCAACTAAAAATATAAAAACAATTCAA
130 CAATTATAGTATATTTTAACCAAAAATGTAAAAA-AATTCAA
* * * * * * ********
3233 CTTAAAATCAATTATGGGATTATAAAACCATTTAGAGCGAGTAATAAAGCTTTTGANNNNNNNNN
1 CTTAAAATCAATTATGAGATTATAAAACTATTTAAAGAGAGTAATAAGGCTTTCGA-AGGAATGG
* * * * ** * * * * **
3298 NGACTATAAATGGACTTTT-TTTCTGAATGAATGGTTTTTTCTACACGTTTCTTGAGGCATGCAT
65 TGACTATAAATGAACTTTTCTTAC-CAATGAATACTTTTTTCTTCATGTTTCTCGAGGTAAACAT
* * * *
3362 TCAATTATAGTTTGTTTTAACCAAAAAAGTAAAAAAATTCAC
129 TCAATTATAGTATATTTTAACCAAAAATGTAAAAAAATTCAA
3404 CTTAAAATCAATTATGAGATTATAAA
1 CTTAAAATCAATTATGAGATTATAAA
3430 NNNNNNNNNN
Statistics
Matches: 2395, Mismatches: 753, Indels: 218
0.71 0.22 0.06
Matches are distributed among these distances:
156 2 0.00
157 104 0.04
158 7 0.00
161 5 0.00
163 2 0.00
164 1 0.00
165 6 0.00
166 85 0.04
167 24 0.01
168 12 0.01
169 111 0.05
170 272 0.11
171 1283 0.54
172 405 0.17
173 72 0.03
174 4 0.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.35
Consensus pattern (170 bp):
CTTAAAATCAATTATGAGATTATAAAACTATTTAAAGAGAGTAATAAGGCTTTCGAAGGAATGGT
GACTATAAATGAACTTTTCTTACCAATGAATACTTTTTTCTTCATGTTTCTCGAGGTAAACATTC
AATTATAGTATATTTTAACCAAAAATGTAAAAAAATTCAA
Found at i:1193 original size:342 final size:340
Alignment explanation
Indices: 2--3429 Score: 1803
Period size: 342 Copynumber: 10.1 Consensus size: 340
1 G
* **
2 CTTAACATCAATTATCTGATTATAAAACCATTTAAAGAGAGTAATAAGGC-TTTGAAAGGAATGA
1 CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTG-AAGGAATGA
* * * * * *
66 GTGACTATAAATAGACTTTTCTTACTAATAAATGGTTTTTTCTACACGTTTCTCAAGGCAAACAT
65 GTGACTATAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCACGTTTCTCAAGGCAAACAT
* * * * *
131 TCAATTATAGTTTATTTTAACTAAAAACGTAAAAAAATTCAACTTAAAATCAATTATGAGGTTAT
130 TCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
*****************************
196 AAAA-TCATTTAAAGCGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNTATAAATAGACTTTTCTT
195 AAAACT-ATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATA-ACTTTTCTT
** * * * *
260 GTCAATGAATGCTATTTTCTTCAT-GTTTCTCT-AAGTTGACATTCAATTATAGTTTGTTTCAAC
258 ACCAATGAATGCT-TTTTCTTC-TCGTTTCT-TGAGGTAGACATTCAATTATAGTCTGTTTTAAC
* *
323 TAAAAATATAAAAAAATTTAA
320 TAAAAATGTAAAAAAATTCAA
* ********** *
344 CTTAAAATCAATTATGAGATTATTAAACCATTTAAAGNNNNNNNNNNGGCTTTTGAAGGAATGGG
1 CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGAATGAG
* * *
409 TGACAATAAATGGACTTTTCTTGCCAATGAA-GGCTTATTTCTTCACGTTTCTCAAGGTAAAAAT
66 TGACTATAAATGGACTTTTCTTGCCAATGAATGGCTT-TTTCTTCACGTTTCTCAAGGCAAACAT
* * * *
473 TCAATTGTAGTCTGTATTAACCAAAAATGTAAAAAAATTTAACTTAAAATTAATTATGAGATTAT
130 TCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
****************** *
538 AAAACNNNNNNNNNNNNNNNNNNAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTA
195 AAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT-AACTTTTCTTA
* * * ** * * * *
603 CTAATGAATGCCATTTTCTT-TATGTAGCTTGAGCTAGACATTCAATTATATTATATTTTAA-TC
259 CCAATGAATG-CTTTTTCTTCT-CGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACT-
* ** *
666 AATAATCCAAAAGAAATTGAA
321 AAAAATGTAAAA-AAATTCAA
* * * * * *
687 CCTAAAATCAATTTTGAGATTACAAAACCATTTAAAGTGAGTAATCAGGCTTTTGAGGGAAT-AG
1 CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGAATGA-
* * * * * * * * *
751 GAGACTATAAATGAAATTTTCTTGCCAATGAAT-ACTTTTTTCTTCATGTTTCTCGAGGTACACC
65 GTGACTATAAATGGACTTTTCTTGCCAATGAATGGC-TTTTTCTTCACGTTTCTCAAGGCAAACA
* * * * *
815 TTCATTTATAGTATGTTTTAACCAAAAATATAAAAAAATTCAACTAAAAATCAATTAGGAGATTA
129 TTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTA
* * * * * *
880 TAAAACTAATTAAAGCGAGTAATTAGACTTTCGAAGGAATGGTTGACTATAAATTAAGTTTTCTT
194 TAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAA-TAACTTTTCTT
* ** * * * *
945 GCCAATGAATGTCTTTTTCTTCTTTTTTCTTGAGGTATACATTCAATTATTGTCTGTTTAAACCA
258 ACCAATGAATG-CTTTTTCTTCTCGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACTA
*
1010 AAAATGTAAAAAAATTCAG
322 AAAATGTAAAAAAATTCAA
* * * * * *
1029 CTTAACATCAATTATAAGATTATAAAACTATTTAAAAAGAGTAATAAGGCTTCTAAAGGAATGAG
1 CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGAATGAG
* * *
1094 TGACTATAAATGGACTTTTCTTACCAATGAATGACTTTTTCTACACGTTTCTCAAGGCAAACATT
66 TGACTATAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCACGTTTCTCAAGGCAAACATT
* * * * * ***********
1159 TAATTATAGTATATTTTAACCAAAAACGTAAAAAAATTTAACTTAAAATCGNNNNNNNNNNTATA
131 CAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATA
* * * *
1224 AAACCATTTAAAGAGAGTAATGAGGCTTTTGAAGGAAT---TG----------ACTTTTCTTATC
196 AAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAACTTTTCTTACC
* * * * * *
1276 AATAAATGTATTTTTCTT-TAAGTTTCTT-AGGGTAGATATTAAATTAT-GATCTGTTTTAACCA
261 AATGAATG-CTTTTTCTTCT-CGTTTCTTGA-GGTAGACATTCAATTATAG-TCTGTTTTAACTA
* * *
1338 ATAACGTAAAATAAATT-GA
322 AAAATGTAAAA-AAATTCAA
* ** * ***
1357 CTTAAAATCAATTATTAGATTATAAAATAATTTAAAGAGAGTAATAAGACTTTTGAAGGAATNNN
1 CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGAATGAG
******* ** * * * *
1422 NNNNNNNAAATAAACTTTTCTTGCCAATGAAT-GTTTGTTTCTTTACGTTTCTCAAGGTAGACAT
66 TGACTATAAATGGACTTTTCTTGCCAATGAATGGCTT-TTTCTTCACGTTTCTCAAGGCAAACAT
* * * * *
1486 TTAATTATAGTTTGTTTTAA-CAAAAATGCAAAAAAATTC-ATTTTAAATCAATTATGAGATTAT
130 TCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* *
1549 AAAACTATTTAGAGCGAGTAATACA-GCTTTTGAAGGAATGGGTGAGTATAAATAGACTTTTCTT
195 AAAACTATTTAAAGCGAGTAATA-AGGCTTTTGAAGGAATGGGTGACTATAAATA-ACTTTTCTT
* * ** * ******
1613 -CTCAATGAATGGTTTTTCTACATATTTTCTTGAGGCATG-CATTCAATTATAGTCTGTNNNNNN
258 AC-CAATGAATGCTTTTTCTTC-TCGTTTCTTGAGGTA-GACATTCAATTATAGTCTGTTTTAAC
****
1676 NNNNAATGTAAAAAAATTCAA
320 TAAAAATGTAAAAAAATTCAA
* * * * * * *
1697 CTAAAAATCATTTATGAGATTAT-AAACTATTTAAAGCGAGTAATAAGGCCTTTGAAGAAATAAG
1 CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGAATGAG
* * * * * ** * *
1761 TGGCTATAAATGAACTTTTCTTGTCAATGAAT-GCTTGTTTCTTTATGTTTCTTGAGGCTAATAT
66 TGACTATAAATGGACTTTTCTTGCCAATGAATGGCTT-TTTCTTCACGTTTCTCAAGGCAAACAT
* * * **********
1825 TGAATTATAGTTTGTTTTAACTAAAAATGTAAAAAAAAATT-AACTTAAAATNNNNNNNNNNATT
130 TCAATTATAGTCTGTTTTAACCAAAAATGT--AAAAAAATTCAACTTAAAATCAATTATGAGATT
* * ***
1889 ATAAAACAATTTAGAA-TGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATTGTTTTGTC
193 ATAAAACTATTTA-AAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAACTTT-TC
* * * * * *
1953 TT-CTCAATGAATGGCTTTTTTCTACACGTTTCTTAAGGAAGGCATTCAATTATAGTCTATTTTA
256 TTAC-CAATGAAT-GC-TTTTTCTTCTCGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTA
*
2017 ACTAAAAATGCAAAAAAAATTCAA
318 ACTAAAAATG-TAAAAAAATTCAA
**********************
2041 CTTAAAATCAATTATGAGATTATACAAA-CATTT--A-A-A--NNNNNNNNNNNNNNNNNNNNNN
1 CTTAAAATCAATTATGAGATTATA-AAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGAATGA
*** * * ** *
2099 NNNACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTTACGTTTCTTGA-GCTAGACA
65 GTGACTATAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCACGTTTCTCAAGGC-AAACA
* * * * *
2163 TTCAATTATAATCTGTTTTAACCAATAATGCATAAAAAATTGAACCTAAAATCAATT-TCGAGAT
129 TTCAATTATAGTCTGTTTTAACCAAAAATGTA-AAAAAATTCAACTTAAAATCAATTAT-GAGAT
* * ** *
2227 TATAAAACTATTTGATGCGAGTAATAAGGCTTTTG-AGAGAATAAGAGACTATAAATAGACTTTT
192 TATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAG-GAATGGGTGACTATAAATA-ACTTTT
* * **
2291 CTTACCAATGAATGCTTATTTCTT-TACGTCTCTTGGGGTTTACATTCAATTATAGTCTGTTTTA
255 CTTACCAATGAATGCTT-TTTCTTCT-CGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTA
*
2355 ACTAAAATTGTAAAAAAATTCAA
318 ACTAAAAATGTAAAAAAATTCAA
* * * * * *
2378 CTTAAAATTAGTTATGAGATTATAAAACCATTTTAAGAGAGTAATTAGGCTTTTGAAAGAATGGG
1 CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGAATGAG
* * ** ** **
2443 TGACTATAAATGGACTTTTCTT-CTCAATGACTGGCTTGTTCCACACAATTCTCAAGGCAAGTAT
66 TGACTATAAATGGACTTTTCTTGC-CAATGAATGGCTTTTTCTTCACGTTTCTCAAGGCAAACAT
* * * **********
2507 TCAATTATAGT-TTTTTTAACTAAAAATATAAAAAAATTNNNNNNNNNNTCAATTATGAGATTAT
130 TCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* * * * * * * *
2571 AAAA-TAATTTAACGGGAGTAATAAGGCTTTTAAAAGAATAGATGACTATAAATGGACTTTTTTT
195 AAAACT-ATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT-AACTTTTCTT
* * * * * * *
2635 GCCAATGAATGCATTTTTCTTCACATTTCTTGAGATAGACATTCAATTATAGCCTATTTTAACTG
258 ACCAATGAATGC-TTTTTCTTCTCGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACTA
* * *
2700 ATAATGTAAAGCAAATT-GA
322 AAAATGTAAA-AAAATTCAA
* * * * * **
2719 CTTAAAATCAATTATGAGATTATACAACAATTTACAGCGAGTAATAAGGCTTTTGGAGGAATCCG
1 CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGAATGAG
* * * * * * *
2784 TGACCATAAAT-GAGCTTTTCTT-CTAAATGAAAGGCTTTTTCTACACGTTTTTTAAGG-AAGGC
66 TGACTATAAATGGA-CTTTTCTTGC-CAATGAATGGCTTTTTCTTCACGTTTCTCAAGGCAA-AC
* * * **
2846 ATTCAATTATAGTCTATTTTAACCAAAAATGTAAAAACACTCAACTTAAAATCAATTATGAGANN
128 ATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATT
******** * * *
2911 NNNNNNNNATTTAAAGTGAGTAATAAGGCTTTTTGAA-TAATGCGTGACTATAAATAGACTTTTC
193 ATAAAACTATTTAAAGCGAGTAATAAGGC-TTTTGAAGGAATGGGTGACTATAAATA-ACTTTTC
*********** * * * * *
2975 TTGNNNNNNNNNNCTATTTTCTTCAT-GTTTCTCT-AAGTCGACATTGAATTATAGTTTGTTTCA
256 TTACCAATGAATGCT-TTTTCTTC-TCGTTTCT-TGAGGTAGACATTCAATTATAGTCTGTTTTA
* *
3038 ACCAAAAATGTAAAAAAATTTAA
318 ACTAAAAATGTAAAAAAATTCAA
************************ *
3061 CTTAAAATCAATTATGAGATTATNNNNNNNNNNNNNNNNNNNNNNNNGGCTTTTGAAGGAATGGG
1 CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGAATGAG
* *
3126 TGACTATAAATGGACTTTTCTTGTCAATGAA-GGCTTGTTTCTTCACGTTTCTCAAGGTAAACAT
66 TGACTATAAATGGACTTTTCTTGCCAATGAATGGCTT-TTTCTTCACGTTTCTCAAGGCAAACAT
* * * * *
3190 TCAATTGTAGTCTGTTTCAACTAAAAATATAAAAACAATTCAACTTAAAATCAATTATGGGATTA
130 TCAATTATAGTCTGTTTTAACCAAAAATGTAAAAA-AATTCAACTTAAAATCAATTATGAGATTA
* * * ********** *
3255 TAAAACCATTTAGAGCGAGTAATAAAGCTTTTGANNNNNNNNNNGACTATAAATGGACTTTT-TT
194 TAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT-AACTTTTCTT
* * * * * * *
3319 TCTGAATGAATGGTTTTTTCTACACGTTTCTTGAGGCATG-CATTCAATTATAGTTTGTTTTAAC
258 AC-CAATGAAT-GCTTTTTCTTCTCGTTTCTTGAGGTA-GACATTCAATTATAGTCTGTTTTAAC
* * *
3383 CAAAAAAGTAAAAAAATTCAC
320 TAAAAATGTAAAAAAATTCAA
3404 CTTAAAATCAATTATGAGATTATAAA
1 CTTAAAATCAATTATGAGATTATAAA
3430 NNNNNNNNNN
Statistics
Matches: 2289, Mismatches: 690, Indels: 213
0.72 0.22 0.07
Matches are distributed among these distances:
326 44 0.02
327 22 0.01
328 183 0.08
329 7 0.00
336 3 0.00
337 42 0.02
338 59 0.03
339 251 0.11
340 91 0.04
341 268 0.12
342 765 0.33
343 497 0.22
344 50 0.02
345 4 0.00
346 3 0.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.35
Consensus pattern (340 bp):
CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGAATGAG
TGACTATAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCACGTTTCTCAAGGCAAACATT
CAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATA
AAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAACTTTTCTTACC
AATGAATGCTTTTTCTTCTCGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAA
TGTAAAAAAATTCAA
Found at i:1570 original size:169 final size:161
Alignment explanation
Indices: 1220--1587 Score: 326
Period size: 169 Copynumber: 2.3 Consensus size: 161
1210 NNNNNNNNNN
** * * *
1220 TATAAAACCATTTAAAGAGAGTAATGA-GGCTTTTGAAGGAAT---T-GACTTTTCTTATCAATA
1 TATAAAATAATTTAAAGAGAGTAAT-ACAGCTTTTGAAGGAATAAATAAACTTTTCTTACCAATA
* * * * *
1280 AATGTATTTTTCTTTAAGTTTCTTAGGGTAGATATTAAATTATGATCTGTTTTAACCAATAACGT
65 AATGTATTTTTCTTTAAGTTTCTCAAGGTAGACATTAAATTATGATCTGTTTTAACCAAAAACGC
* *
1345 AAAATAAATTGACTTAAAATCAATTATTAGAT
130 AAAATAAATTCACTTAAAATCAATTATGAGAT
1377 TATAAAATAATTTAAAGAGAGTAATA-AGACTTTTGAAGGAATNNNNNNNNNNAAATAAACTTTT
1 TATAAAATAATTTAAAGAGAGTAATACAG-CTTTTGAAGGAAT----------AAATAAACTTTT
* * * * *
1441 CTTGCCAATGAATGT-TTGTTTCTTTACGTTTCTCAAGGTAGACATTTAATTAT-AGTTTGTTTT
55 CTTACCAATAAATGTATT-TTTCTTTAAGTTTCTCAAGGTAGACATTAAATTATGA-TCTGTTTT
* * *
1504 AA-CAAAAATGCAAAA-AAATTCATTTTAAATCAATTATGAGAT
118 AACCAAAAACGCAAAATAAATTCACTTAAAATCAATTATGAGAT
* *
1546 TATAAAACT-ATTTAGAGCGAGTAATACAGCTTTTGAAGGAAT
1 TATAAAA-TAATTTAAAGAGAGTAATACAGCTTTTGAAGGAAT
1588 GGGTGAGTAT
Statistics
Matches: 170, Mismatches: 22, Indels: 26
0.78 0.10 0.12
Matches are distributed among these distances:
156 2 0.01
157 36 0.21
169 58 0.34
170 17 0.10
171 57 0.34
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.37
Consensus pattern (161 bp):
TATAAAATAATTTAAAGAGAGTAATACAGCTTTTGAAGGAATAAATAAACTTTTCTTACCAATAA
ATGTATTTTTCTTTAAGTTTCTCAAGGTAGACATTAAATTATGATCTGTTTTAACCAAAAACGCA
AAATAAATTCACTTAAAATCAATTATGAGAT
Found at i:2601 original size:341 final size:332
Alignment explanation
Indices: 2214--2882 Score: 701
Period size: 341 Copynumber: 2.0 Consensus size: 332
2204 GAACCTAAAA
* * * *
2214 TCAATTTCGAGATTATAAAACTATTTGATGCGAGTAATAAGGCTTTTGAGAGAATAAGA-GACTA
1 TCAATTTCGAGATTATAAAACTATTTAACGCGAGTAATAAGGCTTTTAAAAGAAT-AGATGACTA
* * * * **
2278 TAAATAGACTTTTCTTACCAATGAATGC-TTATTTCTTTACGTCTCTTGGGGTTTACATTCAATT
65 TAAATAGACTTTTCTTACCAATGAATGCATT-TTTCTTCACATCTCTTGAGATAGACATTCAATT
* * * *
2342 ATAGTCTGTTTTAACT-AAAATTGTAAA-AAAATTCAACTTAAAATTAGTTATGAGATTATAAAA
129 ATAGCCTATTTTAACTGAAAA-TGTAAAGAAAATT-AACTTAAAATCAATTATGAGATTATAAAA
* * ** * *
2405 CCATTTTA-AGAGAGTAATTAGGCTTTTGAAAGAATGGGTGACTATAAATG-GACTTTTCTTCTC
192 -CAATTTACAGAGAGTAATAAGGCTTTTGAAAGAATCCGTGACCATAAATGAG-CTTTTCTTCTA
** * * *
2468 AATGACTGGCTTGTTCCACACAATTCTCAAGGCAA-GTATTCAATTATAGT-TTTTTTAACTAAA
255 AATGAAAGGCTTGTTCCACACAATTCTCAAGG-AAGGCATTCAATTATAGTCTATTTTAACCAAA
2531 AATATAAAAAAATT
319 AATATAAAAAAATT
*
2545 NNNNNNNNNNTCAATTAT-GAGATTATAAAA-TAATTTAACGGGAGTAATAAGGCTTTTAAAAGA
1 ----------TCAATT-TCGAGATTATAAAACT-ATTTAACGCGAGTAATAAGGCTTTTAAAAGA
* * * *
2608 ATAGATGACTATAAATGGACTTTTTTTGCCAATGAATGCATTTTTCTTCACATTTCTTGAGATAG
54 ATAGATGACTATAAATAGACTTTTCTTACCAATGAATGCATTTTTCTTCACATCTCTTGAGATAG
* * *
2673 ACATTCAATTATAGCCTATTTTAACTGATAATGTAAAGCAAATTGACTTAAAATCAATTATGAGA
119 ACATTCAATTATAGCCTATTTTAACTGAAAATGTAAAGAAAATTAACTTAAAATCAATTATGAGA
* * * *
2738 TTATACAACAATTTACAGCGAGTAATAAGGCTTTTGGAGGAATCCGTGACCATAAATGAGCTTTT
184 TTATAAAACAATTTACAGAGAGTAATAAGGCTTTTGAAAGAATCCGTGACCATAAATGAGCTTTT
* * ** * *
2803 CTTCTAAATGAAAGGCTTTTTCTACACGTTTTTTAAGGAAGGCATTCAATTATAGTCTATTTTAA
249 CTTCTAAATGAAAGGCTTGTTCCACACAATTCTCAAGGAAGGCATTCAATTATAGTCTATTTTAA
*
2868 CCAAAAATGTAAAAA
314 CCAAAAATATAAAAA
2883 CACTCAACTT
Statistics
Matches: 274, Mismatches: 44, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
340 12 0.04
341 230 0.84
342 32 0.12
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.35
Consensus pattern (332 bp):
TCAATTTCGAGATTATAAAACTATTTAACGCGAGTAATAAGGCTTTTAAAAGAATAGATGACTAT
AAATAGACTTTTCTTACCAATGAATGCATTTTTCTTCACATCTCTTGAGATAGACATTCAATTAT
AGCCTATTTTAACTGAAAATGTAAAGAAAATTAACTTAAAATCAATTATGAGATTATAAAACAAT
TTACAGAGAGTAATAAGGCTTTTGAAAGAATCCGTGACCATAAATGAGCTTTTCTTCTAAATGAA
AGGCTTGTTCCACACAATTCTCAAGGAAGGCATTCAATTATAGTCTATTTTAACCAAAAATATAA
AAAAATT
Found at i:6862 original size:171 final size:170
Alignment explanation
Indices: 6466--6892 Score: 439
Period size: 171 Copynumber: 2.5 Consensus size: 170
6456 NNNNNNNNNN
* * * * * *
6466 CGTTTCTCCACGCAGACATTCAATTATAGTCTGTTTTAACAAAAACAGTAAAAACATTTAACTTA
1 CGTTTCTCAAGGCAGACATTCAATTATAGTCTGTTCTAACAAAAATA-TAAAAAAATTCAACTTA
* * * *
6531 AAATCAATTATGAGATTATTAAACAATTTAAAGTGAATAATAAGACTTTTGAAGGATTGAGTGAC
65 AAATCAATTATGAGATTATAAAACAATTTAAAGCGAATAATAAGACTTTTCAAGGATAGAGTGAC
* * **
6596 TATAAATAGACTTTTCTTACAAATGAATATCTTTTTCTTCA
130 TATAAATAGACTTTTCTTACAAATGAATAGCTTGTTCCACA
* * * * ********* * *
6637 CATTTCTCGAGGTAGACATTCAATTATAGCCTGTNNNNNNNNNNAATGTAAAAAAAATCAACTTA
1 CGTTTCTCAAGGCAGACATTCAATTATAGTCTGT-TCTAACAAAAATATAAAAAAATTCAACTTA
* * * *
6702 AAATCAATTATGAGACTATAAAACAATTTAACGCGAGTAATAAGTCTTTTCAAGGAATAG-GTGA
65 AAATCAATTATGAGATTATAAAACAATTTAAAGCGAATAATAAGACTTTTCAAGG-ATAGAGTGA
* *
6766 TTATAAAT-GAACTTTTCTT-CTTAATGAA-AGGCTTGTTCCACA
129 CTATAAATAG-ACTTTTCTTAC-AAATGAATA-GCTTGTTCCACA
*
6808 CGTTTCTCAAGGCAGGCATTCAATTATAGTCTGTTCTAATCAAAAATATAAAAAAATTCAACTTA
1 CGTTTCTCAAGGCAGACATTCAATTATAGTCTGTTCTAA-CAAAAATATAAAAAAATTCAACTTA
6873 AAATCAATTATGAGATTATA
65 AAATCAATTATGAGATTATA
6893 NNNNNNNNNN
Statistics
Matches: 200, Mismatches: 50, Indels: 12
0.76 0.19 0.05
Matches are distributed among these distances:
170 3 0.01
171 192 0.96
172 5 0.03
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.33
Consensus pattern (170 bp):
CGTTTCTCAAGGCAGACATTCAATTATAGTCTGTTCTAACAAAAATATAAAAAAATTCAACTTAA
AATCAATTATGAGATTATAAAACAATTTAAAGCGAATAATAAGACTTTTCAAGGATAGAGTGACT
ATAAATAGACTTTTCTTACAAATGAATAGCTTGTTCCACA
Done.