Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401196.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4347.0, 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: 2574
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.32
Warning! 302 characters in sequence are not A, C, G, or T
Found at i:1063 original size:171 final size:171
Alignment explanation
Indices: 746--2562 Score: 1595
Period size: 171 Copynumber: 10.7 Consensus size: 171
736 NNNNNNNNNN
* * *
746 AAAGTGAGTAATAAGGCTTTTAAAGTAATGGGTGACTATAAATAGACTTTTCTTTCCAATGAATG
1 AAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATG
* * * *
811 CC-TTTCCTT--TACTTTTCTCAA-ACTAGACATTCAATTATAATCTGTTTTAACCAAAAATATA
66 CCTTTTTCTTCATA-GTTTCT-AAGGC-AGACATTCAATTATAATCTGTTTTAACCAAAAATGTA
* *
872 AAAAAGTCTGAACTTAAAATCAATTTTGGGATTATAAAACCATTT
128 AAAAAGT-TCAACTTAAAATCAATTTTGAGATTATAAAACCATTT
**
917 AAAGTGAGTAATAAGGCTTTTGAAGGTTTGGGTGACTATAAAT-GAACTTTTCTTGCCAATGAAT
1 AAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAG-ACTTTTCTTGCCAATGAAT
* * * ** *
981 ACCTTTTTCTTCATAGTTTCTAAGGCAGACATTCAATAATAATCTGTTCTAACCAAAAACCTCAA
65 GCCTTTTTCTTCATAGTTTCTAAGGCAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAA
* ** * *
1046 AAAGTTCAACCTAAAATC-ATTTATGAGACAATAGAACTATTT
130 AAAGTTCAACTTAAAATCAATTT-TGAGATTATAAAACCATTT
* * * *
1088 AAACTGAGTAATAAGG-TATTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTGCCGATGAAT
1 AAAGTGAGTAATAAGGCT-TTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAAT
* * * * * * * * *
1152 GTCTTTGTCTTCACT--TTTCT-CGAGCTAAACATACAATTATAATTTATTTTAATCAGAAATGT
65 GCCTTTTTCTTCA-TAGTTTCTAAG-GC-AGACATTCAATTATAATCTGTTTTAACCAAAAATGT
* * * *
1214 AAAAACATTTGAACTTAAAATCAATTTTGAGATTATAAAATCATTG
127 AAAAA-AGTTCAACTTAAAATCAATTTTGAGATTATAAAACCATTT
* **
1260 AAAGTGAGTAATAAGGCTTTTAAAGCTAT-GGTGACTATAAATAGACTTTTCTTGCCAATGAATG
1 AAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATG
* * * *
1324 CCTTTTTCTTTACA-TTTCTCAA-GCTAGACATTCAATTATAATCAGTTTTAACTAAAAATGTTA
66 CCTTTTTCTTCATAGTTTCT-AAGGC-AGACATTCAATTATAATCTGTTTTAACCAAAAATG-TA
* *
1387 AAAAA-TCTTAACTTAAAATCAATTTTGAGATTATAAAATCATTT
128 AAAAAGT-TCAACTTAAAATCAATTTTGAGATTATAAAACCATTT
* *
1431 AAAGTGAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAAT-GAACTTTTCTTACCAATGAAT
1 AAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAG-ACTTTTCTTGCCAATGAAT
* * * * *
1495 ACCTTTTTCTTCAT-GTTTCCCAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAACGTTA
65 GCCTTTTTCTTCATAGTTT-CTAAGGCAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAA
* * * * *
1559 AAAAGTTCAACCTAAAATGAATTATGAGACTATAAAACTATTT
129 AAAAGTTCAACTTAAAATCAATTTTGAGATTATAAAACCATTT
* * * * * * *
1602 AAAGTGAGTAATAAAGCCTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGTCGATGAATA
1 AAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATG
* * * * * * * *
1667 CCTTTTTCTTCACA-TTTACTAAGGAAAACTTTCAATTAGAATCTGTTCTAACTAAAAACGTAAA
66 CCTTTTTCTTCATAGTTT-CTAAGGCAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAA
* ** *
1731 AAAATTCAACCGAAAATCAATTATGAGATTATAAAACCATTT
130 AAAGTTCAACTTAAAATCAATTTTGAGATTATAAAACCATTT
* * * * *
1773 AAAGTTAGTAATAAGGCTTTTGAATGAATGAGTAACTATAAATAGACTTTTCTTGCAAATGAATG
1 AAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATG
* * * *
1838 CCTTTTTATT-A-ACG-TTCGTCGAGGTAGACATTCAATTACT-ATCTGTTTTAACTAAAAATGT
66 CCTTTTTCTTCATA-GTTTC-T-AAGGCAGACATTCAATTA-TAATCTGTTTTAACCAAAAATGT
* * * * * * *
1899 ACGAAGAA-TTCAAATTTAAATTAATTTTGAGAATATAAAATCATTG
127 A--AAAAAGTTCAACTTAAAATCAATTTTGAGATTATAAAACCATTT
* * * * *
1945 AAAGTGAGCAATAAGGCTTTTAAAGGATTGTGTGACTATAAATAGATTTTTCTTGCCAATGAATG
1 AAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATG
* *
2010 CCTTTTTCTTCAT-GTTTCT-TGAGCTAG--A--C-ATTA-AA----TTATAACCAAAAATGT--
66 CCTTTTTCTTCATAGTTTCTAAG-GC-AGACATTCAATTATAATCTGTTTTAACCAAAAATGTAA
2061 AAAA----AA--T----T-AATTTTGAGATTATAAAACCATTT
129 AAAAGTTCAACTTAAAATCAATTTTGAGATTATAAAACCATTT
* * * * *
2093 AAAGT-ATGTAGTAGGGCTTTTGATGGAATGGGTGAC-AGTACATAGACTTTTCTTGCCAAGGAA
1 AAAGTGA-GTAATAAGGCTTTTGAAGGAATGGGTGACTA-TAAATAGACTTTTCTTGCCAATGAA
* * * * * * * *
2156 TACCTTTTTCTTCA-GGTTTCCTACGGTAGACATTCAATTATAATTTGTTCTAACTAAAAATGTC
64 TGCCTTTTTCTTCATAGTTT-CTAAGGCAGACATTCAATTATAATCTGTTTTAACCAAAAATGTA
*
2220 AAAAAGTTCAACTTAAAATCCATTATT-AGATTATAAAACCATTT
128 AAAAAGTTCAACTTAAAATCAATT-TTGAGATTATAAAACCATTT
* * * * * **
2264 AAAGTGAGCAATATGGCTTTTGACGGAATGGATGACTATAAATAGACATTT-TTGCTGATGAATG
1 AAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATG
* ** *
2328 TCC-TTTTCTTCATA-TTTCTTGAGGTTGACATTCAATTATAATCTGTTTTGAAACAAAAATGTA
66 -CCTTTTTCTTCATAGTTTC-TAAGGCAGACATTCAATTATAATCTGTTTT-AACCAAAAATGTA
* * * *
2391 CAAAGAA-TTCAAATTTAAATCGATTTCGAGATTATAAAACCATTT
128 -AAA-AAGTTCAACTTAAAATCAATTTTGAGATTATAAAACCATTT
* * * ** * * ** *
2436 AAAGTGAGTAATATGGCCTTTAAAGGAATGCATGACTGTAAATGGACTTTTCTTATCAATGAACG
1 AAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATG
* * * * * *
2501 CTTTTTTCTTCAT-GTTTCTCAAGGTAGACATTCAATTCTAGTCTGGTTTAACTAAAAATGTA
66 CCTTTTTCTTCATAGTTTCT-AAGGCAGACATTCAATTATAATCTGTTTTAACCAAAAATGTA
2563 TAAAGAATTC
Statistics
Matches: 1342, Mismatches: 222, Indels: 163
0.78 0.13 0.09
Matches are distributed among these distances:
147 2 0.00
148 89 0.07
149 4 0.00
150 2 0.00
152 1 0.00
153 5 0.00
154 2 0.00
155 2 0.00
158 17 0.01
160 4 0.00
162 14 0.01
164 2 0.00
166 2 0.00
167 4 0.00
168 1 0.00
169 4 0.00
170 67 0.05
171 672 0.50
172 377 0.28
173 69 0.05
174 2 0.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (171 bp):
AAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATG
CCTTTTTCTTCATAGTTTCTAAGGCAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAA
AAGTTCAACTTAAAATCAATTTTGAGATTATAAAACCATTT
Found at i:1445 original size:343 final size:339
Alignment explanation
Indices: 746--2562 Score: 1679
Period size: 343 Copynumber: 5.4 Consensus size: 339
736 NNNNNNNNNN
*
746 AAAGTGAGTAATAAGGCTTTT-AAAGTAATGGGTGACTATAAATAGACTTTTCTTTCCAATGAAT
1 AAAGTGAGTAATAAGGCTTTTGAAAG-AATGGGTGACTATAAATAGACTTTTCTTGCCAATGAAT
* * * * *
810 GCC-TTTCCTTTACTTTTCTCAAACTAGACATTCAATTATAATCTGTTTTAACCAAAAATATAAA
65 GCCTTTTTCTTCACTTTTCTCGAGCTAGACATTCAATTATAATCTGTTTTAA-CAAAAATGTAAA
* *
874 AAAGTCTGAACTTAAAATCAATTTTGGGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
129 AAAGT-TCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
** *
939 AAGGTTTGGGTGACTATAAAT-GAACTTTTCTTGCCAATGAATACCTTTTTCTTCATAGTTTCTA
193 AAGGAAT-GGTGACTATAAATAG-ACTTTTCTTGCCAATGAATGCCTTTTTCTTCATA-TTTCTA
* ** * *
1003 AGGC-AGACATTCAATAATAATCTGTTCTAACCAAAAACCTCAAAAAGTTCAACCTAAAATC-AT
255 A-GCTAGACATTCAATTATAATCTGTTCTAACCAAAAATGTTAAAAAATTCAACCTAAAATCAAT
** * *
1066 TTATGAGACAATAGAACTATTT
319 TT-TGAGATTATAAAACCATTT
* * *
1088 AAACTGAGTAATAAGG-TATTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTGCCGATGAAT
1 AAAGTGAGTAATAAGGCT-TTTGAAAGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAAT
* * * * * * *
1152 GTCTTTGTCTTCACTTTTCTCGAGCTAAACATACAATTATAATTTATTTTAATCAGAAATGTAAA
65 GCCTTTTTCTTCACTTTTCTCGAGCTAGACATTCAATTATAATCTGTTTTAA-CAAAAATGTAAA
* * * * *
1217 AACATTTGAACTTAAAATCAATTTTGAGATTATAAAATCATTGAAAGTGAGTAATAAGGCTTTTA
129 AA-AGTTCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
** * *
1282 AAGCTATGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTTACATTTCTCAAG
193 AAGGAATGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATATTTCT-AAG
* * * * *
1347 CTAGACATTCAATTATAATCAGTTTTAACTAAAAATGTTAAAAAATCTTAACTTAAAATCAATTT
257 CTAGACATTCAATTATAATCTGTTCTAACCAAAAATGTTAAAAAAT-TCAACCTAAAATCAATTT
*
1412 TGAGATTATAAAATCATTT
321 TGAGATTATAAAACCATTT
* * *
1431 AAAGTGAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAAT-GAACTTTTCTTACCAATGAAT
1 AAAGTGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATAG-ACTTTTCTTGCCAATGAAT
* * * * * *
1495 ACCTTTTTCTTCA-TGTTTCCCAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAACGTTA
65 GCCTTTTTCTTCACT-TTTCTCGAGCTAGACATTCAATTATAATCTGTTTTAA-CAAAAATGTAA
* * * * * * *
1559 AAAAGTTCAACCTAAAATGAATTATGAGACTATAAAACTATTTAAAGTGAGTAATAAAGCCTTTG
128 AAAAGTTCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
* * * * *
1624 AAGGAATAGGTGACTATAAATGGACTTTTCTTGTCGATGAATACCTTTTTCTTCACATTTACTAA
193 AAGGAAT-GGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATATTT-CTAA
** * * * * * * * *
1689 GGAAAACTTTCAATTAGAATCTGTTCTAACTAAAAACGTAAAAAAATTCAACCGAAAATCAATTA
256 GCTAGACATTCAATTATAATCTGTTCTAACCAAAAATGTTAAAAAATTCAACCTAAAATCAATTT
1754 TGAGATTATAAAACCATTT
321 TGAGATTATAAAACCATTT
* * * * *
1773 AAAGTTAGTAATAAGGCTTTTGAATGAATGAGTAACTATAAATAGACTTTTCTTGCAAATGAATG
1 AAAGTGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATG
* * * *
1838 CCTTTTTATTAAC-GTTCGTCGAGGTAGACATTCAATTACT-ATCTGTTTTAACTAAAAATGTAC
66 CCTTTTTCTTCACTTTTC-TCGAGCTAGACATTCAATTA-TAATCTGTTTTAAC-AAAAATGTA-
* * * * * * * *
1901 GAAGAA-TTCAAATTTAAATTAATTTTGAGAATATAAAATCATTGAAAGTGAGCAATAAGGCTTT
127 -AAAAAGTTCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTT
* * * *
1965 TAAAGGATTGTGTGACTATAAATAGATTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTT
191 TGAAGGAATG-GTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATATTTC-T
* *
2030 GAGCTAG--A--C-ATTA-AA----TTATAACCAAAAATG-T--AAAA---AA--T----T-AAT
254 AAGCTAGACATTCAATTATAATCTGTTCTAACCAAAAATGTTAAAAAATTCAACCTAAAATCAAT
2072 TTTGAGATTATAAAACCATTT
319 TTTGAGATTATAAAACCATTT
* * ** * *
2093 AAAGT-ATGTAGTAGGGCTTTTGATGGAATGGGTGAC-AGTACATAGACTTTTCTTGCCAAGGAA
1 AAAGTGA-GTAATAAGGCTTTTGAAAGAATGGGTGACTA-TAAATAGACTTTTCTTGCCAATGAA
* * * * *
2156 TACCTTTTTCTTCAGGTTTCCTACG-G-TAGACATTCAATTATAATTTGTTCTAACTAAAAATGT
64 TGCCTTTTTCTTCA-CTTTTCT-CGAGCTAGACATTCAATTATAATCTGTTTTAAC-AAAAATGT
* * * *
2219 CAAAAAGTTCAACTTAAAATCCATTATT-AGATTATAAAACCATTTAAAGTGAGCAATATGGCTT
126 AAAAAAGTTCAACTTAAAATCAATT-TTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTT
* * **
2283 TTGACGGAATGGATGACTATAAATAGACATTT-TTGCTGATGAATGTCC-TTTTCTTCATATTTC
190 TTGAAGGAATGG-TGACTATAAATAGACTTTTCTTGCCAATGAATG-CCTTTTTCTTCATATTTC
* * * * * ** *
2346 TTGAGGTTGACATTCAATTATAATCTGTTTTGAAACAAAAATG-TACAAAGAATTCAAATTTAAA
253 -TAAGCTAGACATTCAATTATAATCTGTTCT-AACCAAAAATGTTA-AAA-AATTCAACCTAAAA
* *
2410 TCGATTTCGAGATTATAAAACCATTT
314 TCAATTTTGAGATTATAAAACCATTT
* * ** * * ** *
2436 AAAGTGAGTAATATGGCCTTT-AAAGGAATGCATGACTGTAAATGGACTTTTCTTATCAATGAAC
1 AAAGTGAGTAATAAGGCTTTTGAAA-GAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAAT
* * * * * *
2500 GCTTTTTTCTTCA-TGTTTCTCAAGGTAGACATTCAATTCTAGTCTGGTTTAACTAAAAATGTA
65 GCCTTTTTCTTCACT-TTTCTCGAGCTAGACATTCAATTATAATCTGTTTTAAC-AAAAATGTA
2563 TAAAGAATTC
Statistics
Matches: 1204, Mismatches: 207, Indels: 127
0.78 0.13 0.08
Matches are distributed among these distances:
318 37 0.03
319 76 0.06
320 120 0.10
321 3 0.00
322 5 0.00
323 4 0.00
324 2 0.00
327 2 0.00
328 3 0.00
329 11 0.01
330 4 0.00
332 2 0.00
333 14 0.01
336 2 0.00
337 2 0.00
338 5 0.00
339 1 0.00
341 14 0.01
342 336 0.28
343 547 0.45
344 14 0.01
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (339 bp):
AAAGTGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATG
CCTTTTTCTTCACTTTTCTCGAGCTAGACATTCAATTATAATCTGTTTTAACAAAAATGTAAAAA
AGTTCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAG
GAATGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATATTTCTAAGCTAG
ACATTCAATTATAATCTGTTCTAACCAAAAATGTTAAAAAATTCAACCTAAAATCAATTTTGAGA
TTATAAAACCATTT
Found at i:1732 original size:514 final size:508
Alignment explanation
Indices: 746--2558 Score: 1898
Period size: 514 Copynumber: 3.6 Consensus size: 508
736 NNNNNNNNNN
*
746 AAAGTGAGTAATAAGGCTTTTAAAGTAATGGGTGACTATAAATAGACTTTTCTTTCCAATGAATG
1 AAAGTGAGTAATAAGGCTTTTAAAG-AAT-GGTGACTATAAATAGACTTTTCTTGCCAATGAATG
* * * * *
811 CCTTTCCTTTACTTTTCTCAAACTAGACATTCAATTATAATCTGTTTTAACCAAAAATATA-AAA
64 CCTTTTCTTTACATTTCTCAAGCTAGACATTCAATTATAATCTGTTTTAACTAAAAATGTACAAA
* * * *
875 AAGTCTGAACTTAAAATCAATTTTGGGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGA
129 AA-T-TCAAATTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAA
* * *
940 AGGTTTGGGTGACTATAAATGAACTTTTCTTGCCAATGAATACCTTTTTCTTCATAGTTT-CTAA
192 AGGTATGGGTGACTATAAATGAACTTTTCTTACCAATGAATACCTTTTTCTTCAT-GTTTCCCAA
* * * * *
1004 GGCAGACATTCAATAATAATCTGTTCTAACCAAAAACCTCAAAAAGTTCAACCTAAAATCATTTA
256 GGTAGACATTCAATTATAATCTGTTTTAACCAAAAA-CTTAAAAAGTTCAACCTAAAATCAATTA
* * * * *
1069 TGAGACAATAGAACTATTTAAACTGAGTAATAAGGTATTTGAAAGAATGGGTGACTATAAATGGA
320 TGAGACTATAAAACTATTTAAAGTGAGTAATAAGGCATTTGAAGGAATGGGTGACTATAAATGGA
** * * * * * *
1134 CTTTTCTTGCCGATGAATGTCTTTGTCTTCACTTTTCTCGAGCTAAACATACAATTATAATTTAT
385 CTTTTCTTGCCGATGAATACCTTTTTCTTCACTTTACT-AAGGTAAACATTCAATTATAATTTGT
* * * * * *
1199 TTTAA-TCAGAAATGTAAAAACATTTGAACTTAAAATCAATTTTGAGATTATAAAATCATTG
449 TCTAACT-AAAAATGTAAAAA-AATTCAACTTAAAATCAATTTTGAGATTATAAAACCATTT
*
1260 AAAGTGAGTAATAAGGCTTTTAAAGCTATGGTGACTATAAATAGACTTTTCTTGCCAATGAATGC
1 AAAGTGAGTAATAAGGCTTTTAAAG-AATGGTGACTATAAATAGACTTTTCTTGCCAATGAATGC
*
1325 CTTTTTCTTTACATTTCTCAAGCTAGACATTCAATTATAATCAGTTTTAACTAAAAATGTTA-AA
65 C-TTTTCTTTACATTTCTCAAGCTAGACATTCAATTATAATCTGTTTTAACTAAAAATG-TACAA
* * * *
1389 AAATCTTAACTTAAAATCAATTTTGAGATTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTGA
128 AAAT-TCAAATTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAA
1454 AGGTATGGGTGACTATAAATGAACTTTTCTTACCAATGAATACCTTTTTCTTCATGTTTCCCAAG
192 AGGTATGGGTGACTATAAATGAACTTTTCTTACCAATGAATACCTTTTTCTTCATGTTTCCCAAG
*
1519 GTAGACATTCAATTATAATCTGTTTTAACCAAAAACGTTAAAAAGTTCAACCTAAAATGAATTAT
257 GTAGACATTCAATTATAATCTGTTTTAACCAAAAAC-TTAAAAAGTTCAACCTAAAATCAATTAT
* * *
1584 GAGACTATAAAACTATTTAAAGTGAGTAATAAAGCCTTTGAAGGAATAGGTGACTATAAATGGAC
321 GAGACTATAAAACTATTTAAAGTGAGTAATAAGGCATTTGAAGGAATGGGTGACTATAAATGGAC
* * * * *
1649 TTTTCTTGTCGATGAATACCTTTTTCTTCACATTTACTAAGGAAAACTTTCAATTAGAATCTGTT
386 TTTTCTTGCCGATGAATACCTTTTTCTTCAC-TTTACTAAGGTAAACATTCAATTATAATTTGTT
* ** *
1714 CTAACTAAAAACGTAAAAAAATTCAACCGAAAATCAATTATGAGATTATAAAACCATTT
450 CTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTTTGAGATTATAAAACCATTT
* * * *
1773 AAAGTTAGTAATAAGGCTTTTGAATGAATGAGTAACTATAAATAGACTTTTCTTGCAAATGAATG
1 AAAGTGAGTAATAAGGCTTTT-AAAGAATG-GTGACTATAAATAGACTTTTCTTGCCAATGAATG
* * *
1838 CCTTTT-TATTA-ACGTTCGTCGAGGTAGACATTCAATTACT-ATCTGTTTTAACTAAAAATGTA
64 CCTTTTCT-TTACA-TTTC-TCAAGCTAGACATTCAATTA-TAATCTGTTTTAACTAAAAATGTA
* * * * * * *
1900 CGAAGAATTCAAATTTAAATTAATTTTGAGAATATAAAATCATTGAAAGTGAGCAATAAGGCTTT
125 C-AAAAATTCAAATTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTT
* * * *
1965 TAAAGG-ATTGTGTGACTATAAAT-AGATTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTC
189 TAAAGGTA-TGGGTGACTATAAATGA-ACTTTTCTTACCAATGAATACCTTTTTCTTCATGTTTC
*** * * *
2028 TTGAGCTAG--A--C-ATTA-AA----TTATAACCAAAAA--T-----G-T-AA---AAAATTAA
252 CCAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAACTTAAAAAGTTCAACCTAAAATCAA
* * * * * * * *
2071 TTTTGAGATTATAAAACCATTTAAAGT-ATGTAGTAGGGCTTTTGATGGAATGGGTGAC-AGTAC
317 TTATGAGACTATAAAACTATTTAAAGTGA-GTAATAAGGCATTTGAAGGAATGGGTGACTA-TAA
* * * * * * *
2134 ATAGACTTTTCTTGCCAAGGAATACCTTTTTCTTCAGGTTTCCTACGGTAGACATTCAATTATAA
380 ATGGACTTTTCTTGCCGATGAATACCTTTTTCTTCA-CTTTACTAAGGTAAACATTCAATTATAA
* * *
2199 TTTGTTCTAACTAAAAATGTCAAAAAGTTCAACTTAAAATCCATTATT-AGATTATAAAACCATT
444 TTTGTTCTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATT-TTGAGATTATAAAACCATT
2263 T
508 T
* * ** * **
2264 AAAGTGAGCAATATGGCTTTTGACGGAATGGATGACTATAAATAGACATTT-TTGCTGATGAATG
1 AAAGTGAGTAATAAGGCTTTT-AAAGAATGG-TGACTATAAATAGACTTTTCTTGCCAATGAATG
* * ** * *
2328 TCCTTTTCTTCATATTTCTTGAGGTTGACATTCAATTATAATCTGTTTTGAAAC-AAAAATGTAC
64 -CCTTTTCTTTACATTTCTCAAGCTAGACATTCAATTATAATCTGTTTT--AACTAAAAATGTAC
* * * * *
2392 AAAGAATTCAAATTTAAATCGATTTCGAGATTATAAAACCATTTAAAGTGAGTAATATGGCCTTT
126 AAA-AATTCAAATTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTT
* ** * * * ** * *
2457 AAAGGAATGCATGACTGTAAATGGACTTTTCTTATCAATGAACGCTTTTTTCTTCATGTTTCTCA
190 AAAGGTATGGGTGACTATAAATGAACTTTTCTTACCAATGAATACCTTTTTCTTCATGTTTCCCA
* * * *
2522 AGGTAGACATTCAATTCTAGTCTGGTTTAACTAAAAA
255 AGGTAGACATTCAATTATAATCTGTTTTAACCAAAAA
2559 TGTATAAAGA
Statistics
Matches: 1110, Mismatches: 149, Indels: 93
0.82 0.11 0.07
Matches are distributed among these distances:
489 1 0.00
490 43 0.04
491 335 0.30
492 7 0.01
493 1 0.00
494 2 0.00
495 2 0.00
496 4 0.00
497 1 0.00
501 11 0.01
504 12 0.01
508 2 0.00
509 4 0.00
510 1 0.00
512 3 0.00
513 111 0.10
514 551 0.50
515 19 0.02
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (508 bp):
AAAGTGAGTAATAAGGCTTTTAAAGAATGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCC
TTTTCTTTACATTTCTCAAGCTAGACATTCAATTATAATCTGTTTTAACTAAAAATGTACAAAAA
TTCAAATTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGT
ATGGGTGACTATAAATGAACTTTTCTTACCAATGAATACCTTTTTCTTCATGTTTCCCAAGGTAG
ACATTCAATTATAATCTGTTTTAACCAAAAACTTAAAAAGTTCAACCTAAAATCAATTATGAGAC
TATAAAACTATTTAAAGTGAGTAATAAGGCATTTGAAGGAATGGGTGACTATAAATGGACTTTTC
TTGCCGATGAATACCTTTTTCTTCACTTTACTAAGGTAAACATTCAATTATAATTTGTTCTAACT
AAAAATGTAAAAAAATTCAACTTAAAATCAATTTTGAGATTATAAAACCATTT
Found at i:2186 original size:148 final size:148
Alignment explanation
Indices: 1916--2198 Score: 356
Period size: 148 Copynumber: 1.9 Consensus size: 148
1906 ATTCAAATTT
* * *
1916 AAATTAATTTTGAGAATATAAAATCATTGAAAGTGAGCAATAAGGCTTTTAAAGGATTGTGTGAC
1 AAATTAATTTTGAGAATATAAAACCATTGAAAGTGAGCAATAAGGCTTTTAAAGGAATGGGTGAC
* * * * *
1981 TATAAATAGATTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTTGAGCTAGACATTAAAT
66 TATAAATAGACTTTTCTTGCCAAGGAATACCTTTTTCTTCAGGTTTCCTGAGCTAGACATTAAAT
2046 TATAACCAAAAATGTAAA
131 TATAACCAAAAATGTAAA
* * * * * * *
2064 AAATTAATTTTGAGATTATAAAACCATTTAAAGT-ATGTAGTAGGGCTTTTGATGGAATGGGTGA
1 AAATTAATTTTGAGAATATAAAACCATTGAAAGTGA-GCAATAAGGCTTTTAAAGGAATGGGTGA
* * *
2128 C-AGTACATAGACTTTTCTTGCCAAGGAATACCTTTTTCTTCAGGTTTCCT-ACGGTAGACATTC
65 CTA-TAAATAGACTTTTCTTGCCAAGGAATACCTTTTTCTTCAGGTTTCCTGA-GCTAGACATTA
2191 AATTATAA
128 AATTATAA
2199 TTTGTTCTAA
Statistics
Matches: 114, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
147 3 0.03
148 111 0.97
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (148 bp):
AAATTAATTTTGAGAATATAAAACCATTGAAAGTGAGCAATAAGGCTTTTAAAGGAATGGGTGAC
TATAAATAGACTTTTCTTGCCAAGGAATACCTTTTTCTTCAGGTTTCCTGAGCTAGACATTAAAT
TATAACCAAAAATGTAAA
Found at i:2443 original size:172 final size:169
Alignment explanation
Indices: 2072--2574 Score: 502
Period size: 172 Copynumber: 2.9 Consensus size: 169
2062 AAAAATTAAT
* * * * *
2072 TTTGAGATTATAAAACCATTTAAAGT-ATGTAGTAGGGCTTTTGATGGAATGGGTGAC-AGTACA
1 TTTGAGATTATAAAACCATTTAAAGTGA-GTAATATGGCTTTTGAAGGAATGGATGACTA-TAAA
* * * *
2135 TAGACTTTTCTTGCCAAGGAAT-ACCTTTTTCTTCAGGTTTCCTACGGTAGACATTCAATTATAA
64 TAGAC-TTT-TTGCTAATGAATGACCTTTTTCTTCATGTTTCTTA-GGTAGACATTCAATTATAA
* * *
2199 TTTGTTCTAACTAAAAATGT-CAAA-AAGTTCAACTTAAAATCCA
126 TCTGTTTTAACTAAAAATGTACAAAGAA-TTCAAATTAAAATCCA
* * *
2242 TTATTAGATTATAAAACCATTTAAAGTGAGCAATATGGCTTTTGACGGAATGGATGACTATAAAT
1 TT-TGAGATTATAAAACCATTTAAAGTGAGTAATATGGCTTTTGAAGGAATGGATGACTATAAAT
* * * *
2307 AGACATTTTTGCTGATGAATGTCC-TTTTCTTCATATTTCTTGAGGTTGACATTCAATTATAATC
65 AGAC-TTTTTGCTAATGAATGACCTTTTTCTTCATGTTTCTT-AGGTAGACATTCAATTATAATC
* *
2371 TGTTTTGAAAC-AAAAATGTACAAAGAATTCAAATTTAAATCGA
128 TGTTTT--AACTAAAAATGTACAAAGAATTCAAATTAAAATCCA
* * * *
2414 TTTCGAGATTATAAAACCATTTAAAGTGAGTAATATGGCCTTTAAAGGAATGCATGACTGTAAAT
1 TTT-GAGATTATAAAACCATTTAAAGTGAGTAATATGGCTTTTGAAGGAATGGATGACTATAAAT
* * * * * *
2479 GGAC-TTTT-CTTATCAATGAACGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTCTAG
65 AGACTTTTTGCTAATGAATG-AC-C-TTTTTCTTCATGTTTCT-TAGGTAGACATTCAATTATAA
* *
2542 TCTGGTTTAACTAAAAATGTATAAAGAATTCAA
126 TCTGTTTTAACTAAAAATGTACAAAGAATTCAA
Statistics
Matches: 278, Mismatches: 39, Indels: 30
0.80 0.11 0.09
Matches are distributed among these distances:
169 8 0.03
170 54 0.19
171 74 0.27
172 101 0.36
173 41 0.15
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (169 bp):
TTTGAGATTATAAAACCATTTAAAGTGAGTAATATGGCTTTTGAAGGAATGGATGACTATAAATA
GACTTTTTGCTAATGAATGACCTTTTTCTTCATGTTTCTTAGGTAGACATTCAATTATAATCTGT
TTTAACTAAAAATGTACAAAGAATTCAAATTAAAATCCA
Done.