Multiple sequence alignment - TraesCS2A01G275600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2A01G275600 chr2A 100.000 4544 0 0 1 4544 454689307 454693850 0.000000e+00 8392.0
1 TraesCS2A01G275600 chr2B 92.761 2072 91 24 1 2031 408723034 408725087 0.000000e+00 2940.0
2 TraesCS2A01G275600 chr2B 91.232 1631 73 28 2350 3958 408725325 408726907 0.000000e+00 2156.0
3 TraesCS2A01G275600 chr2B 87.742 465 18 11 3975 4401 408727036 408727499 1.460000e-139 507.0
4 TraesCS2A01G275600 chr2B 99.248 133 1 0 4399 4531 408727844 408727976 1.630000e-59 241.0
5 TraesCS2A01G275600 chr2B 92.262 168 5 3 2029 2194 408725168 408725329 9.830000e-57 231.0
6 TraesCS2A01G275600 chr2B 82.424 165 25 2 2191 2352 710988971 710988808 1.700000e-29 141.0
7 TraesCS2A01G275600 chr2B 81.609 174 26 4 2191 2360 778844709 778844880 6.130000e-29 139.0
8 TraesCS2A01G275600 chr2D 95.458 1365 39 10 845 2194 343555134 343556490 0.000000e+00 2156.0
9 TraesCS2A01G275600 chr2D 92.661 1308 55 19 2617 3900 343557044 343558334 0.000000e+00 1845.0
10 TraesCS2A01G275600 chr2D 95.503 378 8 6 4155 4531 343559045 343559414 3.030000e-166 595.0
11 TraesCS2A01G275600 chr2D 87.417 302 28 5 1 294 343540104 343540403 5.630000e-89 339.0
12 TraesCS2A01G275600 chr2D 79.856 417 73 9 296 705 16233715 16233303 1.240000e-75 294.0
13 TraesCS2A01G275600 chr2D 87.547 265 15 10 2358 2622 343556494 343556740 1.600000e-74 291.0
14 TraesCS2A01G275600 chr2D 79.087 416 60 12 296 704 605567730 605568125 1.250000e-65 261.0
15 TraesCS2A01G275600 chr2D 93.023 129 8 1 707 834 343540392 343540520 2.160000e-43 187.0
16 TraesCS2A01G275600 chr2D 83.133 166 23 2 2191 2352 615978349 615978185 3.660000e-31 147.0
17 TraesCS2A01G275600 chr4D 85.060 415 49 9 296 704 441081529 441081122 1.180000e-110 411.0
18 TraesCS2A01G275600 chr7A 80.861 418 65 8 290 704 105519744 105520149 9.490000e-82 315.0
19 TraesCS2A01G275600 chr1D 80.714 420 65 13 294 704 79803010 79802598 3.410000e-81 313.0
20 TraesCS2A01G275600 chr3D 80.191 419 70 11 292 704 394627690 394628101 7.390000e-78 302.0
21 TraesCS2A01G275600 chr3D 79.097 421 65 12 296 704 499000661 499001070 7.490000e-68 268.0
22 TraesCS2A01G275600 chr3D 78.774 424 72 12 296 706 602717721 602718139 7.490000e-68 268.0
23 TraesCS2A01G275600 chr5B 86.145 166 18 3 2190 2351 355618186 355618350 1.680000e-39 174.0
24 TraesCS2A01G275600 chr5B 82.530 166 24 4 2191 2352 394012738 394012574 1.700000e-29 141.0
25 TraesCS2A01G275600 chr4B 84.940 166 19 3 2191 2352 369937898 369937735 3.640000e-36 163.0
26 TraesCS2A01G275600 chr4B 82.941 170 23 3 2190 2355 428023552 428023385 1.020000e-31 148.0
27 TraesCS2A01G275600 chr7B 84.024 169 21 3 2191 2355 64695459 64695625 1.690000e-34 158.0
28 TraesCS2A01G275600 chr6A 84.568 162 22 3 2191 2350 104411374 104411214 1.690000e-34 158.0
29 TraesCS2A01G275600 chr6A 88.462 78 8 1 2983 3059 499406954 499406877 4.840000e-15 93.5
30 TraesCS2A01G275600 chr6D 88.462 78 8 1 2983 3059 357012990 357012913 4.840000e-15 93.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G275600 chr2A 454689307 454693850 4543 False 8392.00 8392 100.00000 1 4544 1 chr2A.!!$F1 4543
1 TraesCS2A01G275600 chr2B 408723034 408727976 4942 False 1215.00 2940 92.64900 1 4531 5 chr2B.!!$F2 4530
2 TraesCS2A01G275600 chr2D 343555134 343559414 4280 False 1221.75 2156 92.79225 845 4531 4 chr2D.!!$F3 3686

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
922 955 0.324091 TCAACTACCTCCTCGTCCCC 60.324 60.0 0.00 0.0 0.00 4.81 F
2196 2327 0.036875 AGCTGCAACAAGGTACTCCC 59.963 55.0 1.02 0.0 38.49 4.30 F
2353 2484 0.115745 TTGGGAACGGAGGGAGTACT 59.884 55.0 0.00 0.0 0.00 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2334 2465 0.115745 AGTACTCCCTCCGTTCCCAA 59.884 55.0 0.0 0.0 0.00 4.12 R
3519 4005 0.394352 CGCCATAGAAAGCTTGGGGT 60.394 55.0 0.0 0.0 38.33 4.95 R
3598 4086 0.807496 GCAACCTCAGCACAGAATCC 59.193 55.0 0.0 0.0 0.00 3.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 8.986477 AGATGTTGTTTAATTTGCAGGAATAC 57.014 30.769 0.00 0.00 0.00 1.89
60 61 4.637483 ATTTGCAGGAATACAATCCGTG 57.363 40.909 0.00 0.00 44.60 4.94
66 67 4.745478 GCAGGAATACAATCCGTGGGAATA 60.745 45.833 0.00 0.00 44.60 1.75
74 75 9.635404 AATACAATCCGTGGGAATAATTCTTAA 57.365 29.630 0.00 0.00 34.34 1.85
79 80 6.354130 TCCGTGGGAATAATTCTTAAGGAAG 58.646 40.000 1.85 0.00 37.36 3.46
117 118 7.804843 TTTCATTGGAAATTTTGCATGAAGT 57.195 28.000 18.21 0.00 38.07 3.01
130 131 2.931325 GCATGAAGTCTGAGCTCTTGAG 59.069 50.000 16.19 4.09 0.00 3.02
213 215 2.110578 GGTTCAAATAGGCAGGGCATT 58.889 47.619 0.00 0.00 0.00 3.56
318 321 8.769891 CCAAAAATACAAAGGTTAACATGGTTC 58.230 33.333 8.10 0.00 0.00 3.62
319 322 8.769891 CAAAAATACAAAGGTTAACATGGTTCC 58.230 33.333 8.10 0.00 0.00 3.62
343 346 2.287915 GCGCACCCACATGAATAGTAAG 59.712 50.000 0.30 0.00 0.00 2.34
417 421 4.223700 ACTTGATCAGCCATTCTACTCACA 59.776 41.667 0.00 0.00 0.00 3.58
485 491 8.164733 TGAACAATACAATTGGGACCTTACTAA 58.835 33.333 10.83 0.00 0.00 2.24
488 494 8.333235 ACAATACAATTGGGACCTTACTAATCA 58.667 33.333 10.83 0.00 0.00 2.57
528 534 5.927030 TCAATATTGCTTCGACTTTGTCAC 58.073 37.500 10.76 0.00 32.09 3.67
551 557 2.818751 TGCCCCGAATAACAAGGATT 57.181 45.000 0.00 0.00 0.00 3.01
558 564 6.700081 GCCCCGAATAACAAGGATTTAAATTC 59.300 38.462 1.43 0.00 0.00 2.17
605 611 7.862873 GGTATACCGGTTGACTAAGTATGTTAC 59.137 40.741 15.04 0.00 0.00 2.50
681 688 2.095213 TCATAAAAGATGCGCGTGGAAC 59.905 45.455 6.97 0.00 0.00 3.62
698 705 2.033801 GGAACCATGCTCATCAAATCCG 59.966 50.000 0.00 0.00 0.00 4.18
711 720 3.973657 TCAAATCCGCGTCCTAGTATTC 58.026 45.455 4.92 0.00 0.00 1.75
724 733 7.308229 GCGTCCTAGTATTCTTTTCCTATCGTA 60.308 40.741 0.00 0.00 0.00 3.43
747 757 8.397906 CGTATGAATTAAATCAAAGAGCCTGAA 58.602 33.333 0.00 0.00 32.06 3.02
748 758 9.727627 GTATGAATTAAATCAAAGAGCCTGAAG 57.272 33.333 0.00 0.00 32.06 3.02
750 760 7.820648 TGAATTAAATCAAAGAGCCTGAAGAC 58.179 34.615 0.00 0.00 0.00 3.01
761 771 4.534103 AGAGCCTGAAGACTATGTTTCCTT 59.466 41.667 0.00 0.00 0.00 3.36
762 772 4.583871 AGCCTGAAGACTATGTTTCCTTG 58.416 43.478 0.00 0.00 0.00 3.61
822 835 5.184864 AGAACATAGAGAACAGAGTGACCAG 59.815 44.000 0.00 0.00 0.00 4.00
823 836 4.411927 ACATAGAGAACAGAGTGACCAGT 58.588 43.478 0.00 0.00 0.00 4.00
833 846 2.830923 AGAGTGACCAGTGATCAGAAGG 59.169 50.000 0.00 0.53 0.00 3.46
834 847 1.277557 AGTGACCAGTGATCAGAAGGC 59.722 52.381 0.00 0.00 0.00 4.35
836 849 0.460987 GACCAGTGATCAGAAGGCGG 60.461 60.000 0.00 0.00 0.00 6.13
837 850 0.904865 ACCAGTGATCAGAAGGCGGA 60.905 55.000 0.00 0.00 0.00 5.54
838 851 0.467384 CCAGTGATCAGAAGGCGGAT 59.533 55.000 0.00 0.00 0.00 4.18
840 853 1.134580 CAGTGATCAGAAGGCGGATGT 60.135 52.381 0.00 0.00 0.00 3.06
842 855 2.766263 AGTGATCAGAAGGCGGATGTAA 59.234 45.455 0.00 0.00 0.00 2.41
922 955 0.324091 TCAACTACCTCCTCGTCCCC 60.324 60.000 0.00 0.00 0.00 4.81
1033 1066 2.294132 CTTCTTCCCCGGCGAGTACC 62.294 65.000 9.30 0.00 0.00 3.34
1044 1077 1.602327 GCGAGTACCTTTCCTCCGGT 61.602 60.000 0.00 0.00 37.31 5.28
1047 1080 2.681976 CGAGTACCTTTCCTCCGGTCTA 60.682 54.545 0.00 0.00 34.76 2.59
1086 1119 4.752879 TCTTACGTGCAGCCGCCC 62.753 66.667 0.00 0.00 37.32 6.13
1197 1233 1.373497 CTTTGACTCCGCGCTCAGT 60.373 57.895 5.56 6.85 0.00 3.41
1249 1285 2.584608 GCGGAGGCTTAGGCTTCA 59.415 61.111 14.60 0.00 44.87 3.02
1419 1455 3.763356 ATCGCTGCGCTGGAGACA 61.763 61.111 18.65 0.00 39.59 3.41
1502 1538 1.819208 CGGCGCCATTGGATCAGAA 60.819 57.895 28.98 0.00 0.00 3.02
1554 1596 3.515286 CAGCCCGCAATGCAGGAG 61.515 66.667 12.35 0.00 0.00 3.69
1980 2025 2.911636 CCGACCTCCTACCTATCCTAGA 59.088 54.545 0.00 0.00 0.00 2.43
1982 2028 4.720773 CCGACCTCCTACCTATCCTAGATA 59.279 50.000 0.00 0.00 0.00 1.98
1983 2029 5.396660 CCGACCTCCTACCTATCCTAGATAC 60.397 52.000 0.00 0.00 0.00 2.24
2031 2077 5.933187 AATGCACGTCACTGTAATTTACA 57.067 34.783 8.86 8.86 37.13 2.41
2054 2183 7.640852 ACATACTAATCACTTGAGCGTACTAG 58.359 38.462 0.00 0.00 0.00 2.57
2055 2184 7.282675 ACATACTAATCACTTGAGCGTACTAGT 59.717 37.037 0.00 0.00 0.00 2.57
2056 2185 8.771766 CATACTAATCACTTGAGCGTACTAGTA 58.228 37.037 0.00 0.00 0.00 1.82
2057 2186 7.014092 ACTAATCACTTGAGCGTACTAGTAC 57.986 40.000 21.06 21.06 0.00 2.73
2058 2187 6.822676 ACTAATCACTTGAGCGTACTAGTACT 59.177 38.462 26.36 12.22 34.04 2.73
2059 2188 7.984050 ACTAATCACTTGAGCGTACTAGTACTA 59.016 37.037 26.36 10.66 34.04 1.82
2060 2189 6.847956 ATCACTTGAGCGTACTAGTACTAG 57.152 41.667 26.36 25.30 39.04 2.57
2194 2325 1.537202 CCAAGCTGCAACAAGGTACTC 59.463 52.381 1.02 0.00 38.49 2.59
2195 2326 1.537202 CAAGCTGCAACAAGGTACTCC 59.463 52.381 1.02 0.00 38.49 3.85
2196 2327 0.036875 AGCTGCAACAAGGTACTCCC 59.963 55.000 1.02 0.00 38.49 4.30
2198 2329 1.946283 GCTGCAACAAGGTACTCCCTC 60.946 57.143 0.00 0.00 45.47 4.30
2199 2330 0.690762 TGCAACAAGGTACTCCCTCC 59.309 55.000 0.00 0.00 45.47 4.30
2200 2331 0.391263 GCAACAAGGTACTCCCTCCG 60.391 60.000 0.00 0.00 45.47 4.63
2201 2332 0.974383 CAACAAGGTACTCCCTCCGT 59.026 55.000 0.00 0.00 45.47 4.69
2202 2333 1.346722 CAACAAGGTACTCCCTCCGTT 59.653 52.381 0.00 0.00 45.47 4.44
2203 2334 1.264295 ACAAGGTACTCCCTCCGTTC 58.736 55.000 0.00 0.00 45.47 3.95
2204 2335 0.535797 CAAGGTACTCCCTCCGTTCC 59.464 60.000 0.00 0.00 45.47 3.62
2205 2336 0.412640 AAGGTACTCCCTCCGTTCCT 59.587 55.000 0.00 0.00 45.47 3.36
2206 2337 1.302907 AGGTACTCCCTCCGTTCCTA 58.697 55.000 0.00 0.00 40.71 2.94
2207 2338 1.642762 AGGTACTCCCTCCGTTCCTAA 59.357 52.381 0.00 0.00 40.71 2.69
2208 2339 2.030371 GGTACTCCCTCCGTTCCTAAG 58.970 57.143 0.00 0.00 0.00 2.18
2209 2340 2.622714 GGTACTCCCTCCGTTCCTAAGT 60.623 54.545 0.00 0.00 0.00 2.24
2210 2341 3.372025 GGTACTCCCTCCGTTCCTAAGTA 60.372 52.174 0.00 0.00 0.00 2.24
2211 2342 3.684408 ACTCCCTCCGTTCCTAAGTAT 57.316 47.619 0.00 0.00 0.00 2.12
2212 2343 4.803329 ACTCCCTCCGTTCCTAAGTATA 57.197 45.455 0.00 0.00 0.00 1.47
2213 2344 5.134725 ACTCCCTCCGTTCCTAAGTATAA 57.865 43.478 0.00 0.00 0.00 0.98
2214 2345 5.139001 ACTCCCTCCGTTCCTAAGTATAAG 58.861 45.833 0.00 0.00 0.00 1.73
2215 2346 5.134725 TCCCTCCGTTCCTAAGTATAAGT 57.865 43.478 0.00 0.00 0.00 2.24
2216 2347 5.136105 TCCCTCCGTTCCTAAGTATAAGTC 58.864 45.833 0.00 0.00 0.00 3.01
2217 2348 5.103771 TCCCTCCGTTCCTAAGTATAAGTCT 60.104 44.000 0.00 0.00 0.00 3.24
2218 2349 5.009811 CCCTCCGTTCCTAAGTATAAGTCTG 59.990 48.000 0.00 0.00 0.00 3.51
2219 2350 5.826737 CCTCCGTTCCTAAGTATAAGTCTGA 59.173 44.000 0.00 0.00 0.00 3.27
2220 2351 6.016943 CCTCCGTTCCTAAGTATAAGTCTGAG 60.017 46.154 0.00 0.00 0.00 3.35
2221 2352 6.421485 TCCGTTCCTAAGTATAAGTCTGAGT 58.579 40.000 0.00 0.00 0.00 3.41
2222 2353 7.568349 TCCGTTCCTAAGTATAAGTCTGAGTA 58.432 38.462 0.00 0.00 0.00 2.59
2223 2354 8.216423 TCCGTTCCTAAGTATAAGTCTGAGTAT 58.784 37.037 0.00 0.00 0.00 2.12
2224 2355 9.499479 CCGTTCCTAAGTATAAGTCTGAGTATA 57.501 37.037 0.00 0.00 0.00 1.47
2326 2457 8.889717 AGTCGTTTGTTGAAATCTCTAAAAAGA 58.110 29.630 0.00 0.00 0.00 2.52
2327 2458 8.944927 GTCGTTTGTTGAAATCTCTAAAAAGAC 58.055 33.333 0.00 0.00 31.18 3.01
2328 2459 8.889717 TCGTTTGTTGAAATCTCTAAAAAGACT 58.110 29.630 0.00 0.00 0.00 3.24
2329 2460 9.159470 CGTTTGTTGAAATCTCTAAAAAGACTC 57.841 33.333 0.00 0.00 0.00 3.36
2330 2461 9.159470 GTTTGTTGAAATCTCTAAAAAGACTCG 57.841 33.333 0.00 0.00 0.00 4.18
2331 2462 8.433421 TTGTTGAAATCTCTAAAAAGACTCGT 57.567 30.769 0.00 0.00 0.00 4.18
2332 2463 9.537192 TTGTTGAAATCTCTAAAAAGACTCGTA 57.463 29.630 0.00 0.00 0.00 3.43
2333 2464 9.706691 TGTTGAAATCTCTAAAAAGACTCGTAT 57.293 29.630 0.00 0.00 0.00 3.06
2337 2468 9.974750 GAAATCTCTAAAAAGACTCGTATTTGG 57.025 33.333 0.00 0.00 0.00 3.28
2338 2469 8.494016 AATCTCTAAAAAGACTCGTATTTGGG 57.506 34.615 0.00 0.00 0.00 4.12
2339 2470 7.235935 TCTCTAAAAAGACTCGTATTTGGGA 57.764 36.000 0.00 0.00 0.00 4.37
2340 2471 7.673180 TCTCTAAAAAGACTCGTATTTGGGAA 58.327 34.615 0.00 0.00 0.00 3.97
2341 2472 7.601508 TCTCTAAAAAGACTCGTATTTGGGAAC 59.398 37.037 0.00 0.00 0.00 3.62
2342 2473 5.352643 AAAAAGACTCGTATTTGGGAACG 57.647 39.130 0.00 0.00 40.40 3.95
2343 2474 2.667473 AGACTCGTATTTGGGAACGG 57.333 50.000 0.00 0.00 39.52 4.44
2344 2475 2.173519 AGACTCGTATTTGGGAACGGA 58.826 47.619 0.00 0.00 39.52 4.69
2345 2476 2.165845 AGACTCGTATTTGGGAACGGAG 59.834 50.000 0.00 0.00 39.52 4.63
2346 2477 1.206371 ACTCGTATTTGGGAACGGAGG 59.794 52.381 0.00 0.00 39.52 4.30
2347 2478 0.538118 TCGTATTTGGGAACGGAGGG 59.462 55.000 0.00 0.00 39.52 4.30
2348 2479 0.538118 CGTATTTGGGAACGGAGGGA 59.462 55.000 0.00 0.00 35.51 4.20
2349 2480 1.472728 CGTATTTGGGAACGGAGGGAG 60.473 57.143 0.00 0.00 35.51 4.30
2350 2481 1.558294 GTATTTGGGAACGGAGGGAGT 59.442 52.381 0.00 0.00 0.00 3.85
2351 2482 1.961133 ATTTGGGAACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
2352 2483 0.978907 TTTGGGAACGGAGGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73
2353 2484 0.115745 TTGGGAACGGAGGGAGTACT 59.884 55.000 0.00 0.00 0.00 2.73
2381 2512 7.405769 TGTATGTGTTTATGCATGTATGAACG 58.594 34.615 20.87 0.00 31.37 3.95
2386 2517 1.024271 ATGCATGTATGAACGCACCC 58.976 50.000 0.00 0.00 37.17 4.61
2403 2534 0.746563 CCCGAGCCGCAATTTCCTTA 60.747 55.000 0.00 0.00 0.00 2.69
2416 2547 6.308766 CGCAATTTCCTTAAGGTCAAATTCTG 59.691 38.462 22.20 16.95 32.54 3.02
2428 2561 7.654022 AGGTCAAATTCTGTTTAACTTGGAA 57.346 32.000 0.00 0.00 0.00 3.53
2482 2615 2.902705 TAGCGTTTTGGAGACTGTGT 57.097 45.000 0.00 0.00 0.00 3.72
2483 2616 1.583054 AGCGTTTTGGAGACTGTGTC 58.417 50.000 0.00 0.00 0.00 3.67
2484 2617 0.586802 GCGTTTTGGAGACTGTGTCC 59.413 55.000 16.54 16.54 32.18 4.02
2485 2618 1.948104 CGTTTTGGAGACTGTGTCCA 58.052 50.000 21.50 21.50 42.62 4.02
2546 2683 5.897050 AGTACTGCTTACTACTGCTTGATC 58.103 41.667 0.00 0.00 39.45 2.92
2563 2700 3.664107 TGATCTTGTTGTCAGCTACCAC 58.336 45.455 0.00 0.00 0.00 4.16
2577 2714 4.331168 CAGCTACCACTTGTTCATTAGCTC 59.669 45.833 0.00 0.00 40.17 4.09
2581 2718 6.072452 GCTACCACTTGTTCATTAGCTCTTTT 60.072 38.462 0.00 0.00 31.23 2.27
2744 3191 7.891183 TGGAGGCAGTAATTTAGTAATTTGGAA 59.109 33.333 1.18 0.00 35.61 3.53
2909 3356 2.202427 CGGCGGCGGTCAAATTTC 60.202 61.111 25.36 0.00 0.00 2.17
2923 3370 6.291374 CGGTCAAATTTCGGTTTGTTTAAGTG 60.291 38.462 0.00 0.00 39.50 3.16
3060 3507 1.306148 CAGCGTCAGGTCGAGGTATA 58.694 55.000 0.00 0.00 0.00 1.47
3061 3508 1.002684 CAGCGTCAGGTCGAGGTATAC 60.003 57.143 0.00 0.00 0.00 1.47
3062 3509 1.134159 AGCGTCAGGTCGAGGTATACT 60.134 52.381 2.25 0.00 0.00 2.12
3063 3510 1.674962 GCGTCAGGTCGAGGTATACTT 59.325 52.381 2.25 0.00 0.00 2.24
3064 3511 2.098770 GCGTCAGGTCGAGGTATACTTT 59.901 50.000 2.25 0.00 0.00 2.66
3075 3522 6.319911 GTCGAGGTATACTTTAGTAACCACCT 59.680 42.308 15.48 15.48 40.68 4.00
3084 3531 6.407202 ACTTTAGTAACCACCTAAGATGCAG 58.593 40.000 0.00 0.00 0.00 4.41
3161 3637 6.899393 ATTTGTGCATTCCTTCAGTTTCTA 57.101 33.333 0.00 0.00 0.00 2.10
3244 3720 6.385176 TCCAAAGAGGTGAGAGTTCATATGAT 59.615 38.462 6.17 0.00 39.02 2.45
3246 3722 8.373981 CCAAAGAGGTGAGAGTTCATATGATAT 58.626 37.037 6.17 0.00 35.39 1.63
3248 3724 8.718158 AAGAGGTGAGAGTTCATATGATATGA 57.282 34.615 10.93 10.93 35.39 2.15
3249 3725 8.121305 AGAGGTGAGAGTTCATATGATATGAC 57.879 38.462 14.33 9.93 35.39 3.06
3250 3726 7.727634 AGAGGTGAGAGTTCATATGATATGACA 59.272 37.037 14.33 6.62 35.39 3.58
3251 3727 7.665690 AGGTGAGAGTTCATATGATATGACAC 58.334 38.462 14.33 16.43 35.39 3.67
3252 3728 6.584184 GGTGAGAGTTCATATGATATGACACG 59.416 42.308 14.33 0.00 35.39 4.49
3254 3730 8.290325 GTGAGAGTTCATATGATATGACACGTA 58.710 37.037 14.33 0.00 35.39 3.57
3255 3731 9.014297 TGAGAGTTCATATGATATGACACGTAT 57.986 33.333 14.33 7.84 0.00 3.06
3513 3999 3.593794 GCCAGCAGCAGCCATAGC 61.594 66.667 0.00 0.00 43.56 2.97
3517 4003 3.593794 GCAGCAGCCATAGCCAGC 61.594 66.667 0.00 0.00 41.25 4.85
3519 4005 1.751544 CAGCAGCCATAGCCAGCAA 60.752 57.895 1.46 0.00 41.59 3.91
3534 4020 2.450476 CAGCAACCCCAAGCTTTCTAT 58.550 47.619 0.00 0.00 39.50 1.98
3545 4031 3.334583 AGCTTTCTATGGCGAGTGAAA 57.665 42.857 0.00 0.00 0.00 2.69
3569 4057 2.040412 ACCAGATCACCTTTCCTTGGTC 59.960 50.000 0.00 0.00 35.28 4.02
3598 4086 1.574428 CTGAAAACGGCCGGTTCTG 59.426 57.895 31.74 27.61 38.08 3.02
3739 4227 2.106332 GTACATACGCCAGCCGCT 59.894 61.111 0.00 0.00 41.76 5.52
3740 4228 1.949631 GTACATACGCCAGCCGCTC 60.950 63.158 0.00 0.00 41.76 5.03
3741 4229 3.146726 TACATACGCCAGCCGCTCC 62.147 63.158 0.00 0.00 41.76 4.70
3833 4321 0.316204 CCAGCAGGTTTCAGGCTTTG 59.684 55.000 0.00 0.00 35.27 2.77
3875 4366 2.456577 GCAGGGTATGAATTTGGGTGT 58.543 47.619 0.00 0.00 0.00 4.16
3876 4367 3.626222 GGCAGGGTATGAATTTGGGTGTA 60.626 47.826 0.00 0.00 0.00 2.90
3877 4368 4.020543 GCAGGGTATGAATTTGGGTGTAA 58.979 43.478 0.00 0.00 0.00 2.41
3894 4385 7.429633 TGGGTGTAATATGTGTGTTGAAAAAG 58.570 34.615 0.00 0.00 0.00 2.27
3898 4389 5.543507 AATATGTGTGTTGAAAAAGGGCA 57.456 34.783 0.00 0.00 0.00 5.36
3899 4390 3.902881 ATGTGTGTTGAAAAAGGGCAA 57.097 38.095 0.00 0.00 0.00 4.52
3932 4423 2.421424 GGATTGTGTGATGAACTCCTGC 59.579 50.000 0.00 0.00 0.00 4.85
3944 4440 2.361992 TCCTGCTTGCATGCCCTG 60.362 61.111 20.65 11.17 0.00 4.45
3965 4544 6.037098 CCTGACTGTAGAAAGTATGTAGTGC 58.963 44.000 0.00 0.00 0.00 4.40
3979 4587 7.540299 AGTATGTAGTGCTAGTTTCTCAACTC 58.460 38.462 0.00 0.00 42.66 3.01
3995 4603 4.326826 TCAACTCGGAAAGCATGAGAATT 58.673 39.130 0.00 0.00 33.93 2.17
4003 4611 5.220624 CGGAAAGCATGAGAATTCAGAGAAG 60.221 44.000 8.44 0.00 36.61 2.85
4007 4615 6.740411 AGCATGAGAATTCAGAGAAGAAAC 57.260 37.500 8.44 0.00 36.61 2.78
4025 4633 6.465439 AGAAACAAAGTTACCTTCCCTTTG 57.535 37.500 9.19 9.19 46.55 2.77
4032 4640 2.889045 GTTACCTTCCCTTTGGGTGTTC 59.111 50.000 2.25 0.00 44.74 3.18
4035 4643 2.292587 ACCTTCCCTTTGGGTGTTCAAA 60.293 45.455 2.25 0.00 44.74 2.69
4040 4648 5.993748 TCCCTTTGGGTGTTCAAATTATC 57.006 39.130 2.25 0.00 44.74 1.75
4053 4661 9.606631 GTGTTCAAATTATCTCCTAGATCAACT 57.393 33.333 0.00 0.00 36.20 3.16
4094 4702 6.313519 TCTGTTTTGGATGCCTCTAGTATT 57.686 37.500 0.00 0.00 0.00 1.89
4103 4711 6.042093 TGGATGCCTCTAGTATTTTACTCCAG 59.958 42.308 0.00 0.00 40.14 3.86
4358 5430 1.477553 TACAGCCGTTGGGTAGGTAG 58.522 55.000 0.00 0.00 34.97 3.18
4360 5432 0.108329 CAGCCGTTGGGTAGGTAGTG 60.108 60.000 0.00 0.00 34.97 2.74
4447 5875 3.668141 TGCAATGATTGGTAGATGGGT 57.332 42.857 7.35 0.00 0.00 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 6.002062 ACAACATCTACTTTGCTTAGTTGC 57.998 37.500 0.00 0.00 38.82 4.17
13 14 9.944663 TTAAACAACATCTACTTTGCTTAGTTG 57.055 29.630 0.00 0.00 40.48 3.16
44 45 3.275617 TTCCCACGGATTGTATTCCTG 57.724 47.619 0.00 0.00 33.30 3.86
52 53 6.770785 TCCTTAAGAATTATTCCCACGGATTG 59.229 38.462 3.36 0.00 0.00 2.67
117 118 5.735285 TGATCTTTTCTCAAGAGCTCAGA 57.265 39.130 17.77 12.39 34.09 3.27
308 311 1.301795 TGCGCGTGGAACCATGTTA 60.302 52.632 8.43 0.00 35.52 2.41
309 312 2.593148 TGCGCGTGGAACCATGTT 60.593 55.556 8.43 0.00 35.52 2.71
311 314 4.101790 GGTGCGCGTGGAACCATG 62.102 66.667 8.43 8.53 33.94 3.66
319 322 1.365368 TATTCATGTGGGTGCGCGTG 61.365 55.000 8.43 0.00 0.00 5.34
380 384 5.938125 GCTGATCAAGTTTGTTACCCTAGAA 59.062 40.000 0.00 0.00 0.00 2.10
382 386 4.636206 GGCTGATCAAGTTTGTTACCCTAG 59.364 45.833 0.00 0.00 0.00 3.02
384 388 3.181434 TGGCTGATCAAGTTTGTTACCCT 60.181 43.478 0.00 0.00 0.00 4.34
399 403 4.162888 TCACATGTGAGTAGAATGGCTGAT 59.837 41.667 24.56 0.00 34.14 2.90
417 421 8.292448 GTGTCAATACTTCATGAAACTTCACAT 58.708 33.333 9.88 0.00 40.49 3.21
504 510 6.017933 GTGACAAAGTCGAAGCAATATTGAG 58.982 40.000 19.73 6.93 34.95 3.02
506 512 5.931532 AGTGACAAAGTCGAAGCAATATTG 58.068 37.500 11.27 11.27 34.95 1.90
528 534 2.823154 TCCTTGTTATTCGGGGCAAAAG 59.177 45.455 0.00 0.00 0.00 2.27
558 564 4.082787 ACCCGCATATGAAGTTTCACAAAG 60.083 41.667 6.97 0.00 40.49 2.77
649 656 7.475565 CGCGCATCTTTTATGAATAGTACATTC 59.524 37.037 8.75 3.58 0.00 2.67
653 660 6.065153 CACGCGCATCTTTTATGAATAGTAC 58.935 40.000 5.73 0.00 0.00 2.73
669 676 3.814268 GCATGGTTCCACGCGCAT 61.814 61.111 5.73 0.00 0.00 4.73
681 688 0.040692 CGCGGATTTGATGAGCATGG 60.041 55.000 0.00 0.00 0.00 3.66
688 695 2.225068 ACTAGGACGCGGATTTGATG 57.775 50.000 12.47 0.00 0.00 3.07
690 697 3.635373 AGAATACTAGGACGCGGATTTGA 59.365 43.478 12.47 0.00 0.00 2.69
698 705 5.857517 CGATAGGAAAAGAATACTAGGACGC 59.142 44.000 0.00 0.00 0.00 5.19
724 733 8.465201 GTCTTCAGGCTCTTTGATTTAATTCAT 58.535 33.333 1.11 0.00 0.00 2.57
783 793 8.467598 TCTCTATGTTCTCCTACAAACATACAC 58.532 37.037 4.32 0.00 42.67 2.90
788 798 7.232737 TCTGTTCTCTATGTTCTCCTACAAACA 59.767 37.037 0.00 0.00 39.52 2.83
789 799 7.603651 TCTGTTCTCTATGTTCTCCTACAAAC 58.396 38.462 0.00 0.00 0.00 2.93
790 800 7.451877 ACTCTGTTCTCTATGTTCTCCTACAAA 59.548 37.037 0.00 0.00 0.00 2.83
792 802 6.375736 CACTCTGTTCTCTATGTTCTCCTACA 59.624 42.308 0.00 0.00 0.00 2.74
793 803 6.600032 TCACTCTGTTCTCTATGTTCTCCTAC 59.400 42.308 0.00 0.00 0.00 3.18
822 835 2.890808 TACATCCGCCTTCTGATCAC 57.109 50.000 0.00 0.00 0.00 3.06
823 836 2.766263 ACTTACATCCGCCTTCTGATCA 59.234 45.455 0.00 0.00 0.00 2.92
833 846 1.802365 ACGGTGAAAACTTACATCCGC 59.198 47.619 0.00 0.00 40.05 5.54
834 847 2.412325 GCACGGTGAAAACTTACATCCG 60.412 50.000 13.29 0.00 41.77 4.18
836 849 2.550606 TGGCACGGTGAAAACTTACATC 59.449 45.455 13.29 0.00 0.00 3.06
837 850 2.292292 GTGGCACGGTGAAAACTTACAT 59.708 45.455 13.29 0.00 0.00 2.29
838 851 1.671845 GTGGCACGGTGAAAACTTACA 59.328 47.619 13.29 0.00 0.00 2.41
840 853 1.671845 GTGTGGCACGGTGAAAACTTA 59.328 47.619 13.29 0.00 0.00 2.24
842 855 1.381165 GGTGTGGCACGGTGAAAACT 61.381 55.000 13.29 0.00 34.83 2.66
922 955 0.322008 GAGGAAGGCTGTGGAGGTTG 60.322 60.000 0.00 0.00 0.00 3.77
1086 1119 2.033194 GGCTTCGAACCCTGAACGG 61.033 63.158 2.03 0.00 0.00 4.44
1136 1169 1.833630 CTACTGGAAGATGCTGGTCCA 59.166 52.381 0.00 0.00 39.14 4.02
1176 1212 1.664965 GAGCGCGGAGTCAAAGTGT 60.665 57.895 8.83 0.00 0.00 3.55
1197 1233 1.827681 CAGGAGACGAGACCAGAGAA 58.172 55.000 0.00 0.00 0.00 2.87
1407 1443 4.383861 CTGCCTGTCTCCAGCGCA 62.384 66.667 11.47 0.00 40.36 6.09
1419 1455 4.499116 ACCCGGGATAGCCTGCCT 62.499 66.667 32.02 0.00 39.39 4.75
1502 1538 1.599047 CTCATCTCCAGTTGGGCGT 59.401 57.895 0.00 0.00 36.21 5.68
1554 1596 4.050934 CCCTTTTTCGTGGGCGGC 62.051 66.667 0.00 0.00 36.61 6.53
1790 1832 1.949631 CTTCGGCGGGCTCGTATTC 60.950 63.158 8.30 0.00 38.89 1.75
1963 2008 8.927411 GTAGTAGTATCTAGGATAGGTAGGAGG 58.073 44.444 0.00 0.00 34.34 4.30
1982 2028 8.333235 TGGATTTGGGAATTAATGTGTAGTAGT 58.667 33.333 0.00 0.00 0.00 2.73
1983 2029 8.746052 TGGATTTGGGAATTAATGTGTAGTAG 57.254 34.615 0.00 0.00 0.00 2.57
2031 2077 7.804843 ACTAGTACGCTCAAGTGATTAGTAT 57.195 36.000 0.00 0.00 0.00 2.12
2054 2183 9.480053 TGAATAACAACAACAAGGTACTAGTAC 57.520 33.333 22.53 22.53 38.49 2.73
2056 2185 8.967664 TTGAATAACAACAACAAGGTACTAGT 57.032 30.769 0.00 0.00 32.37 2.57
2084 2213 5.643379 AGCAAAGTCTTCACACTTGAAAA 57.357 34.783 0.00 0.00 41.34 2.29
2085 2214 5.048083 ACAAGCAAAGTCTTCACACTTGAAA 60.048 36.000 17.10 0.00 41.34 2.69
2090 2221 4.265073 AGAACAAGCAAAGTCTTCACACT 58.735 39.130 0.00 0.00 0.00 3.55
2194 2325 5.009811 CAGACTTATACTTAGGAACGGAGGG 59.990 48.000 0.00 0.00 0.00 4.30
2195 2326 5.826737 TCAGACTTATACTTAGGAACGGAGG 59.173 44.000 0.00 0.00 0.00 4.30
2196 2327 6.543100 ACTCAGACTTATACTTAGGAACGGAG 59.457 42.308 0.00 0.00 0.00 4.63
2197 2328 6.421485 ACTCAGACTTATACTTAGGAACGGA 58.579 40.000 0.00 0.00 0.00 4.69
2198 2329 6.696441 ACTCAGACTTATACTTAGGAACGG 57.304 41.667 0.00 0.00 0.00 4.44
2300 2431 8.889717 TCTTTTTAGAGATTTCAACAAACGACT 58.110 29.630 0.00 0.00 0.00 4.18
2301 2432 8.944927 GTCTTTTTAGAGATTTCAACAAACGAC 58.055 33.333 0.00 0.00 0.00 4.34
2302 2433 8.889717 AGTCTTTTTAGAGATTTCAACAAACGA 58.110 29.630 0.00 0.00 0.00 3.85
2303 2434 9.159470 GAGTCTTTTTAGAGATTTCAACAAACG 57.841 33.333 0.00 0.00 0.00 3.60
2304 2435 9.159470 CGAGTCTTTTTAGAGATTTCAACAAAC 57.841 33.333 0.00 0.00 0.00 2.93
2305 2436 8.889717 ACGAGTCTTTTTAGAGATTTCAACAAA 58.110 29.630 0.00 0.00 0.00 2.83
2306 2437 8.433421 ACGAGTCTTTTTAGAGATTTCAACAA 57.567 30.769 0.00 0.00 0.00 2.83
2307 2438 9.706691 ATACGAGTCTTTTTAGAGATTTCAACA 57.293 29.630 0.00 0.00 0.00 3.33
2311 2442 9.974750 CCAAATACGAGTCTTTTTAGAGATTTC 57.025 33.333 0.00 0.00 0.00 2.17
2312 2443 8.947115 CCCAAATACGAGTCTTTTTAGAGATTT 58.053 33.333 0.00 0.00 0.00 2.17
2313 2444 8.319146 TCCCAAATACGAGTCTTTTTAGAGATT 58.681 33.333 0.00 0.00 0.00 2.40
2314 2445 7.848128 TCCCAAATACGAGTCTTTTTAGAGAT 58.152 34.615 0.00 0.00 0.00 2.75
2315 2446 7.235935 TCCCAAATACGAGTCTTTTTAGAGA 57.764 36.000 0.00 0.00 0.00 3.10
2316 2447 7.411588 CGTTCCCAAATACGAGTCTTTTTAGAG 60.412 40.741 0.00 0.00 40.03 2.43
2317 2448 6.366877 CGTTCCCAAATACGAGTCTTTTTAGA 59.633 38.462 0.00 0.00 40.03 2.10
2318 2449 6.401796 CCGTTCCCAAATACGAGTCTTTTTAG 60.402 42.308 0.00 0.00 40.03 1.85
2319 2450 5.409214 CCGTTCCCAAATACGAGTCTTTTTA 59.591 40.000 0.00 0.00 40.03 1.52
2320 2451 4.214758 CCGTTCCCAAATACGAGTCTTTTT 59.785 41.667 0.00 0.00 40.03 1.94
2321 2452 3.749609 CCGTTCCCAAATACGAGTCTTTT 59.250 43.478 0.00 0.00 40.03 2.27
2322 2453 3.007182 TCCGTTCCCAAATACGAGTCTTT 59.993 43.478 0.00 0.00 40.03 2.52
2323 2454 2.564062 TCCGTTCCCAAATACGAGTCTT 59.436 45.455 0.00 0.00 40.03 3.01
2324 2455 2.165845 CTCCGTTCCCAAATACGAGTCT 59.834 50.000 0.00 0.00 40.03 3.24
2325 2456 2.537401 CTCCGTTCCCAAATACGAGTC 58.463 52.381 0.00 0.00 40.03 3.36
2326 2457 1.206371 CCTCCGTTCCCAAATACGAGT 59.794 52.381 0.00 0.00 40.03 4.18
2327 2458 1.472728 CCCTCCGTTCCCAAATACGAG 60.473 57.143 0.00 0.00 40.03 4.18
2328 2459 0.538118 CCCTCCGTTCCCAAATACGA 59.462 55.000 0.00 0.00 40.03 3.43
2329 2460 0.538118 TCCCTCCGTTCCCAAATACG 59.462 55.000 0.00 0.00 37.50 3.06
2330 2461 1.558294 ACTCCCTCCGTTCCCAAATAC 59.442 52.381 0.00 0.00 0.00 1.89
2331 2462 1.961133 ACTCCCTCCGTTCCCAAATA 58.039 50.000 0.00 0.00 0.00 1.40
2332 2463 1.558294 GTACTCCCTCCGTTCCCAAAT 59.442 52.381 0.00 0.00 0.00 2.32
2333 2464 0.978907 GTACTCCCTCCGTTCCCAAA 59.021 55.000 0.00 0.00 0.00 3.28
2334 2465 0.115745 AGTACTCCCTCCGTTCCCAA 59.884 55.000 0.00 0.00 0.00 4.12
2335 2466 1.002069 TAGTACTCCCTCCGTTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
2336 2467 1.064091 AGTAGTACTCCCTCCGTTCCC 60.064 57.143 0.00 0.00 0.00 3.97
2337 2468 2.022934 CAGTAGTACTCCCTCCGTTCC 58.977 57.143 0.00 0.00 0.00 3.62
2338 2469 2.720915 ACAGTAGTACTCCCTCCGTTC 58.279 52.381 0.00 0.00 0.00 3.95
2339 2470 2.895242 ACAGTAGTACTCCCTCCGTT 57.105 50.000 0.00 0.00 0.00 4.44
2340 2471 3.201708 ACATACAGTAGTACTCCCTCCGT 59.798 47.826 0.00 0.00 31.96 4.69
2341 2472 3.564644 CACATACAGTAGTACTCCCTCCG 59.435 52.174 0.00 0.00 31.96 4.63
2342 2473 4.534797 ACACATACAGTAGTACTCCCTCC 58.465 47.826 0.00 0.00 31.96 4.30
2343 2474 6.527057 AAACACATACAGTAGTACTCCCTC 57.473 41.667 0.00 0.00 31.96 4.30
2344 2475 7.417570 GCATAAACACATACAGTAGTACTCCCT 60.418 40.741 0.00 0.00 31.96 4.20
2345 2476 6.700520 GCATAAACACATACAGTAGTACTCCC 59.299 42.308 0.00 0.00 31.96 4.30
2346 2477 7.262772 TGCATAAACACATACAGTAGTACTCC 58.737 38.462 0.00 0.00 31.96 3.85
2347 2478 8.755941 CATGCATAAACACATACAGTAGTACTC 58.244 37.037 0.00 0.00 31.96 2.59
2348 2479 8.258007 ACATGCATAAACACATACAGTAGTACT 58.742 33.333 0.00 0.00 31.96 2.73
2349 2480 8.420374 ACATGCATAAACACATACAGTAGTAC 57.580 34.615 0.00 0.00 31.96 2.73
2351 2482 9.045223 CATACATGCATAAACACATACAGTAGT 57.955 33.333 0.00 0.00 0.00 2.73
2352 2483 9.260002 TCATACATGCATAAACACATACAGTAG 57.740 33.333 0.00 0.00 0.00 2.57
2353 2484 9.606631 TTCATACATGCATAAACACATACAGTA 57.393 29.630 0.00 0.00 0.00 2.74
2381 2512 3.683587 GAAATTGCGGCTCGGGTGC 62.684 63.158 0.00 0.00 0.00 5.01
2386 2517 1.064060 CCTTAAGGAAATTGCGGCTCG 59.936 52.381 17.21 0.00 37.39 5.03
2403 2534 7.654022 TCCAAGTTAAACAGAATTTGACCTT 57.346 32.000 0.00 0.00 29.93 3.50
2416 2547 5.161358 GCATGCTAACCTTCCAAGTTAAAC 58.839 41.667 11.37 0.00 29.68 2.01
2428 2561 2.372264 CCTTCACATGCATGCTAACCT 58.628 47.619 26.53 2.71 0.00 3.50
2482 2615 9.473007 TTCAAATGTATTTTAGACATGGATGGA 57.527 29.630 0.00 0.00 37.59 3.41
2483 2616 9.520204 GTTCAAATGTATTTTAGACATGGATGG 57.480 33.333 0.00 0.00 37.59 3.51
2524 2661 5.897050 AGATCAAGCAGTAGTAAGCAGTAC 58.103 41.667 0.00 0.00 0.00 2.73
2529 2666 5.409826 ACAACAAGATCAAGCAGTAGTAAGC 59.590 40.000 0.00 0.00 0.00 3.09
2531 2668 6.521162 TGACAACAAGATCAAGCAGTAGTAA 58.479 36.000 0.00 0.00 0.00 2.24
2536 2673 2.551459 GCTGACAACAAGATCAAGCAGT 59.449 45.455 0.00 0.00 0.00 4.40
2537 2674 2.812591 AGCTGACAACAAGATCAAGCAG 59.187 45.455 0.00 0.00 0.00 4.24
2538 2675 2.854963 AGCTGACAACAAGATCAAGCA 58.145 42.857 0.00 0.00 0.00 3.91
2539 2676 3.126000 GGTAGCTGACAACAAGATCAAGC 59.874 47.826 0.00 0.00 0.00 4.01
2540 2677 4.153117 GTGGTAGCTGACAACAAGATCAAG 59.847 45.833 0.00 0.00 31.46 3.02
2541 2678 4.065088 GTGGTAGCTGACAACAAGATCAA 58.935 43.478 0.00 0.00 31.46 2.57
2542 2679 3.324846 AGTGGTAGCTGACAACAAGATCA 59.675 43.478 0.00 0.00 33.92 2.92
2546 2683 3.206150 ACAAGTGGTAGCTGACAACAAG 58.794 45.455 0.00 0.00 33.92 3.16
2581 2718 8.154856 AGTAGCTAGTAATGAACTTGTCCAAAA 58.845 33.333 0.00 0.00 39.80 2.44
2585 2722 9.465985 GATTAGTAGCTAGTAATGAACTTGTCC 57.534 37.037 30.03 13.91 39.80 4.02
2597 2734 6.014755 TCCTCAGTAGCGATTAGTAGCTAGTA 60.015 42.308 4.07 4.07 44.92 1.82
2598 2735 4.998672 CCTCAGTAGCGATTAGTAGCTAGT 59.001 45.833 6.29 6.29 46.90 2.57
2599 2736 5.239351 TCCTCAGTAGCGATTAGTAGCTAG 58.761 45.833 0.26 0.00 45.32 3.42
2744 3191 2.093106 CTAGCTCTTGGACCACTACGT 58.907 52.381 0.00 0.00 0.00 3.57
2778 3225 5.039333 ACGTCGCAACTAATTATGACTACC 58.961 41.667 0.00 0.00 0.00 3.18
2779 3226 6.291479 GGAACGTCGCAACTAATTATGACTAC 60.291 42.308 0.00 0.00 0.00 2.73
2882 3329 2.407210 CGCCGCCGCAATAATTGT 59.593 55.556 0.00 0.00 34.03 2.71
2909 3356 5.494632 AGGAGAAACACTTAAACAAACCG 57.505 39.130 0.00 0.00 0.00 4.44
3060 3507 6.368779 TGCATCTTAGGTGGTTACTAAAGT 57.631 37.500 0.00 0.00 30.68 2.66
3061 3508 5.294552 GCTGCATCTTAGGTGGTTACTAAAG 59.705 44.000 0.00 0.00 30.68 1.85
3062 3509 5.183228 GCTGCATCTTAGGTGGTTACTAAA 58.817 41.667 0.00 0.00 30.68 1.85
3063 3510 4.224147 TGCTGCATCTTAGGTGGTTACTAA 59.776 41.667 0.00 0.00 0.00 2.24
3064 3511 3.772572 TGCTGCATCTTAGGTGGTTACTA 59.227 43.478 0.00 0.00 0.00 1.82
3131 3601 7.260603 ACTGAAGGAATGCACAAATTATTAGC 58.739 34.615 0.00 0.00 0.00 3.09
3161 3637 4.525996 TCATGGTCGACAATTTCATGGAT 58.474 39.130 23.01 0.00 36.72 3.41
3210 3686 1.553248 CACCTCTTTGGACGGGATGTA 59.447 52.381 0.00 0.00 39.71 2.29
3513 3999 0.829182 AGAAAGCTTGGGGTTGCTGG 60.829 55.000 0.00 0.00 37.43 4.85
3517 4003 1.478105 GCCATAGAAAGCTTGGGGTTG 59.522 52.381 0.00 0.00 33.11 3.77
3519 4005 0.394352 CGCCATAGAAAGCTTGGGGT 60.394 55.000 0.00 0.00 38.33 4.95
3534 4020 3.055458 TGATCTGGTATTTTCACTCGCCA 60.055 43.478 0.00 0.00 0.00 5.69
3545 4031 4.292306 ACCAAGGAAAGGTGATCTGGTATT 59.708 41.667 0.00 0.00 38.13 1.89
3598 4086 0.807496 GCAACCTCAGCACAGAATCC 59.193 55.000 0.00 0.00 0.00 3.01
3670 4158 4.819630 TCAACCTTCATGTGGTTTACTGTC 59.180 41.667 18.39 0.00 44.54 3.51
3679 4167 5.720371 TTTATGGTTCAACCTTCATGTGG 57.280 39.130 8.40 6.07 39.58 4.17
3747 4235 3.480470 CTGTGCAGGGAGAAGAGAAAAA 58.520 45.455 0.00 0.00 0.00 1.94
3859 4347 8.134895 CACACATATTACACCCAAATTCATACC 58.865 37.037 0.00 0.00 0.00 2.73
3875 4366 6.656632 TGCCCTTTTTCAACACACATATTA 57.343 33.333 0.00 0.00 0.00 0.98
3876 4367 5.543507 TGCCCTTTTTCAACACACATATT 57.456 34.783 0.00 0.00 0.00 1.28
3877 4368 5.543507 TTGCCCTTTTTCAACACACATAT 57.456 34.783 0.00 0.00 0.00 1.78
3898 4389 1.149133 ACAATCCCTGGCCCCTCTTT 61.149 55.000 0.00 0.00 0.00 2.52
3899 4390 1.544917 ACAATCCCTGGCCCCTCTT 60.545 57.895 0.00 0.00 0.00 2.85
3932 4423 1.065926 TCTACAGTCAGGGCATGCAAG 60.066 52.381 21.36 8.50 0.00 4.01
3944 4440 7.987649 ACTAGCACTACATACTTTCTACAGTC 58.012 38.462 0.00 0.00 0.00 3.51
3965 4544 4.307432 TGCTTTCCGAGTTGAGAAACTAG 58.693 43.478 0.00 0.00 32.22 2.57
3979 4587 4.186926 TCTCTGAATTCTCATGCTTTCCG 58.813 43.478 7.05 0.00 0.00 4.30
4025 4633 7.509546 TGATCTAGGAGATAATTTGAACACCC 58.490 38.462 0.00 0.00 34.53 4.61
4053 4661 9.734620 CAAAACAGAAACAAGATCAAAGACATA 57.265 29.630 0.00 0.00 0.00 2.29
4067 4675 3.565307 AGAGGCATCCAAAACAGAAACA 58.435 40.909 0.00 0.00 0.00 2.83
4072 4680 7.396540 AAAATACTAGAGGCATCCAAAACAG 57.603 36.000 0.00 0.00 0.00 3.16
4103 4711 2.965572 ACATGTATGTTGCCATTGGC 57.034 45.000 21.12 21.12 40.64 4.52
4121 4729 8.417884 GGGCTCATAATGATATACTAGAGGAAC 58.582 40.741 0.00 0.00 0.00 3.62
4126 4734 8.844865 ATGTGGGCTCATAATGATATACTAGA 57.155 34.615 0.00 0.00 0.00 2.43
4129 4737 7.746243 AGATGTGGGCTCATAATGATATACT 57.254 36.000 0.00 0.00 0.00 2.12
4358 5430 3.067833 GGTCTTGGTTCTAAGCACTCAC 58.932 50.000 0.00 0.00 35.94 3.51
4360 5432 2.038557 TGGGTCTTGGTTCTAAGCACTC 59.961 50.000 0.00 0.00 35.94 3.51


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.