Multiple sequence alignment - TraesCS3A01G502900

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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 TraesCS3A01G502900 chr3A 100.000 2648 0 0 1 2648 725841411 725844058 0.000000e+00 4891.0
1 TraesCS3A01G502900 chr3A 86.792 424 48 5 1067 1490 726716275 726715860 1.440000e-127 466.0
2 TraesCS3A01G502900 chr3A 86.765 408 38 5 1307 1706 725911624 725912023 8.700000e-120 440.0
3 TraesCS3A01G502900 chr3A 84.327 453 44 19 858 1305 725904435 725904865 4.080000e-113 418.0
4 TraesCS3A01G502900 chr3A 93.304 224 6 3 1490 1706 725905324 725905545 3.290000e-84 322.0
5 TraesCS3A01G502900 chr3A 96.450 169 6 0 1481 1649 726714175 726714007 2.010000e-71 279.0
6 TraesCS3A01G502900 chr3A 89.796 196 18 2 1307 1501 725904977 725905171 1.570000e-62 250.0
7 TraesCS3A01G502900 chr3A 86.555 119 12 4 1189 1305 725911405 725911521 7.690000e-26 128.0
8 TraesCS3A01G502900 chr3A 90.909 88 6 1 998 1083 726716512 726716425 1.670000e-22 117.0
9 TraesCS3A01G502900 chr3A 94.915 59 1 1 2392 2450 456910780 456910836 1.010000e-14 91.6
10 TraesCS3A01G502900 chr3A 100.000 40 0 0 1863 1902 587393367 587393406 1.020000e-09 75.0
11 TraesCS3A01G502900 chr3D 88.688 1715 83 41 758 2394 594892796 594894477 0.000000e+00 1989.0
12 TraesCS3A01G502900 chr3D 90.394 406 29 5 1307 1704 594955602 594956005 2.330000e-145 525.0
13 TraesCS3A01G502900 chr3D 86.283 452 45 12 858 1305 594955062 594955500 2.390000e-130 475.0
14 TraesCS3A01G502900 chr3D 91.930 285 18 4 1 284 594892026 594892306 6.870000e-106 394.0
15 TraesCS3A01G502900 chr3D 82.311 424 44 21 305 712 594892379 594892787 3.260000e-89 339.0
16 TraesCS3A01G502900 chr3B 86.801 1341 70 41 744 2020 798397015 798398312 0.000000e+00 1397.0
17 TraesCS3A01G502900 chr3B 91.241 411 25 5 1307 1706 798404132 798404542 1.390000e-152 549.0
18 TraesCS3A01G502900 chr3B 88.496 452 35 13 858 1305 798403607 798404045 5.020000e-147 531.0
19 TraesCS3A01G502900 chr3B 89.789 284 24 4 1 284 798395766 798396044 2.510000e-95 359.0
20 TraesCS3A01G502900 chr3B 84.979 233 17 5 286 516 798396080 798396296 1.230000e-53 220.0
21 TraesCS3A01G502900 chr4A 100.000 53 0 0 2398 2450 10642055 10642003 6.030000e-17 99.0
22 TraesCS3A01G502900 chr4A 90.625 64 6 0 2387 2450 572708398 572708461 4.700000e-13 86.1
23 TraesCS3A01G502900 chr7A 87.059 85 11 0 1522 1606 146951390 146951474 2.170000e-16 97.1
24 TraesCS3A01G502900 chr7A 90.909 66 3 3 2385 2450 709594262 709594200 4.700000e-13 86.1
25 TraesCS3A01G502900 chr2B 96.491 57 2 0 2394 2450 597223430 597223374 7.800000e-16 95.3
26 TraesCS3A01G502900 chr2B 95.000 40 2 0 1866 1905 45729753 45729714 2.200000e-06 63.9
27 TraesCS3A01G502900 chr1B 92.424 66 3 2 2387 2450 675768797 675768862 2.810000e-15 93.5
28 TraesCS3A01G502900 chr7D 85.882 85 12 0 1522 1606 146106565 146106649 1.010000e-14 91.6
29 TraesCS3A01G502900 chr7D 93.023 43 3 0 1859 1901 613635600 613635558 2.200000e-06 63.9
30 TraesCS3A01G502900 chr5B 93.548 62 2 2 2390 2450 703506600 703506540 1.010000e-14 91.6
31 TraesCS3A01G502900 chr6A 90.909 66 3 2 2385 2447 103953289 103953354 4.700000e-13 86.1
32 TraesCS3A01G502900 chr6A 90.909 44 4 0 1859 1902 583130283 583130326 2.850000e-05 60.2
33 TraesCS3A01G502900 chr4B 90.909 66 3 3 2385 2450 421735345 421735283 4.700000e-13 86.1
34 TraesCS3A01G502900 chr4D 95.349 43 1 1 1863 1904 504595401 504595443 1.700000e-07 67.6
35 TraesCS3A01G502900 chr2A 97.436 39 1 0 1863 1901 13014867 13014905 1.700000e-07 67.6
36 TraesCS3A01G502900 chr5D 97.297 37 1 0 1866 1902 327480376 327480412 2.200000e-06 63.9


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 TraesCS3A01G502900 chr3A 725841411 725844058 2647 False 4891.000000 4891 100.000000 1 2648 1 chr3A.!!$F3 2647
1 TraesCS3A01G502900 chr3A 725904435 725905545 1110 False 330.000000 418 89.142333 858 1706 3 chr3A.!!$F4 848
2 TraesCS3A01G502900 chr3A 726714007 726716512 2505 True 287.333333 466 91.383667 998 1649 3 chr3A.!!$R1 651
3 TraesCS3A01G502900 chr3A 725911405 725912023 618 False 284.000000 440 86.660000 1189 1706 2 chr3A.!!$F5 517
4 TraesCS3A01G502900 chr3D 594892026 594894477 2451 False 907.333333 1989 87.643000 1 2394 3 chr3D.!!$F1 2393
5 TraesCS3A01G502900 chr3D 594955062 594956005 943 False 500.000000 525 88.338500 858 1704 2 chr3D.!!$F2 846
6 TraesCS3A01G502900 chr3B 798395766 798398312 2546 False 658.666667 1397 87.189667 1 2020 3 chr3B.!!$F1 2019
7 TraesCS3A01G502900 chr3B 798403607 798404542 935 False 540.000000 549 89.868500 858 1706 2 chr3B.!!$F2 848

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
499 551 0.037303 AGTAGTGTGCCAAGCTGCAT 59.963 50.0 1.02 0.0 44.3 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2428 5410 0.159554 CGCGTGTATATGAGCGCTTG 59.84 55.0 13.26 0.0 46.56 4.01 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
51 52 2.553602 CACTTGAGCAGTTGTATTGCCA 59.446 45.455 0.00 0.00 42.48 4.92
86 87 3.055602 AGCCCGTTTCGAGTAATTAAGGT 60.056 43.478 0.00 0.00 0.00 3.50
112 113 4.691326 TGTGTGTGTAAATGTAGGGTCA 57.309 40.909 0.00 0.00 0.00 4.02
150 151 4.462483 CAGCTATGGGGAAAAAGTTAGCAA 59.538 41.667 0.00 0.00 0.00 3.91
261 262 8.709646 GGAAACATAATCTACGTATCCAACATC 58.290 37.037 0.00 0.00 0.00 3.06
275 276 5.152623 TCCAACATCATCTCTTTTCGACT 57.847 39.130 0.00 0.00 0.00 4.18
284 285 4.193826 TCTCTTTTCGACTGAGGGATTG 57.806 45.455 8.15 0.00 0.00 2.67
287 288 4.315803 TCTTTTCGACTGAGGGATTGTTC 58.684 43.478 0.00 0.00 0.00 3.18
288 289 3.762407 TTTCGACTGAGGGATTGTTCA 57.238 42.857 0.00 0.00 0.00 3.18
290 291 1.066858 TCGACTGAGGGATTGTTCAGC 60.067 52.381 1.66 0.00 43.59 4.26
291 292 1.066573 CGACTGAGGGATTGTTCAGCT 60.067 52.381 1.66 0.00 43.59 4.24
292 293 2.613977 CGACTGAGGGATTGTTCAGCTT 60.614 50.000 1.66 0.00 43.59 3.74
303 349 0.310854 GTTCAGCTTTTCACCCACCG 59.689 55.000 0.00 0.00 0.00 4.94
323 374 6.872020 CCACCGTCTTTCTTTCTTACATCTTA 59.128 38.462 0.00 0.00 0.00 2.10
336 387 9.719355 TTTCTTACATCTTATAGTGTCTTGCAA 57.281 29.630 0.00 0.00 0.00 4.08
356 407 9.357652 CTTGCAATGCTAGTAACAAATGTTTAT 57.642 29.630 6.82 0.00 39.31 1.40
357 408 8.909708 TGCAATGCTAGTAACAAATGTTTATC 57.090 30.769 6.82 0.00 39.31 1.75
358 409 8.739039 TGCAATGCTAGTAACAAATGTTTATCT 58.261 29.630 6.82 4.35 39.31 1.98
359 410 9.573133 GCAATGCTAGTAACAAATGTTTATCTT 57.427 29.630 3.85 0.00 39.31 2.40
368 419 9.968743 GTAACAAATGTTTATCTTCTTCCTACG 57.031 33.333 3.85 0.00 39.31 3.51
394 445 2.885676 CGCAATCCTCCATTCGGCG 61.886 63.158 0.00 0.00 32.46 6.46
414 465 3.396560 CGAGCATGAATGAGCAGGATTA 58.603 45.455 0.00 0.00 0.00 1.75
424 475 2.766263 TGAGCAGGATTATTCCAGTCGT 59.234 45.455 6.44 0.00 45.30 4.34
434 485 3.490759 CCAGTCGTGCATCGCCAC 61.491 66.667 0.00 0.00 39.67 5.01
499 551 0.037303 AGTAGTGTGCCAAGCTGCAT 59.963 50.000 1.02 0.00 44.30 3.96
517 570 1.739466 CATACAGCGTGCAGAAACCAT 59.261 47.619 0.00 0.00 0.00 3.55
547 600 3.933155 AATAGCGCGATATAGCATTGC 57.067 42.857 18.33 0.00 36.85 3.56
548 601 2.654749 TAGCGCGATATAGCATTGCT 57.345 45.000 16.63 16.63 43.41 3.91
549 602 1.800805 AGCGCGATATAGCATTGCTT 58.199 45.000 17.71 7.45 40.44 3.91
550 603 2.146342 AGCGCGATATAGCATTGCTTT 58.854 42.857 17.71 11.72 40.44 3.51
551 604 2.549754 AGCGCGATATAGCATTGCTTTT 59.450 40.909 17.71 7.70 40.44 2.27
552 605 3.003689 AGCGCGATATAGCATTGCTTTTT 59.996 39.130 17.71 4.03 40.44 1.94
605 658 1.261480 ATAGCATACTCTCAGGGGCG 58.739 55.000 0.00 0.00 0.00 6.13
607 660 2.435693 GCATACTCTCAGGGGCGGT 61.436 63.158 0.00 0.00 0.00 5.68
697 807 5.728637 AACTTCATGGGGAAACAAATCTC 57.271 39.130 0.00 0.00 34.44 2.75
713 823 1.981256 TCTCCAAAGGAAAGCGCTTT 58.019 45.000 34.16 34.16 35.14 3.51
714 824 2.306847 TCTCCAAAGGAAAGCGCTTTT 58.693 42.857 34.01 18.50 32.11 2.27
716 826 1.068434 TCCAAAGGAAAGCGCTTTTGG 59.932 47.619 31.87 31.87 46.88 3.28
719 829 1.115326 AAGGAAAGCGCTTTTGGCCT 61.115 50.000 34.01 30.25 37.74 5.19
720 830 1.373371 GGAAAGCGCTTTTGGCCTG 60.373 57.895 34.01 0.00 37.74 4.85
721 831 2.023771 GAAAGCGCTTTTGGCCTGC 61.024 57.895 34.01 17.08 37.74 4.85
722 832 2.426122 GAAAGCGCTTTTGGCCTGCT 62.426 55.000 34.01 10.99 38.83 4.24
723 833 2.704342 AAAGCGCTTTTGGCCTGCTG 62.704 55.000 29.11 1.82 37.61 4.41
725 835 3.677648 CGCTTTTGGCCTGCTGCT 61.678 61.111 3.32 0.00 40.92 4.24
727 837 2.654877 CTTTTGGCCTGCTGCTGG 59.345 61.111 19.96 19.96 40.92 4.85
729 839 1.874345 CTTTTGGCCTGCTGCTGGAG 61.874 60.000 27.16 12.36 40.92 3.86
730 840 2.356173 TTTTGGCCTGCTGCTGGAGA 62.356 55.000 27.16 10.76 40.92 3.71
731 841 2.356173 TTTGGCCTGCTGCTGGAGAA 62.356 55.000 27.16 15.62 40.92 2.87
733 843 1.379576 GGCCTGCTGCTGGAGAATT 60.380 57.895 27.16 0.00 40.92 2.17
735 845 1.382692 GCCTGCTGCTGGAGAATTCC 61.383 60.000 27.16 5.64 44.31 3.01
779 1508 7.791590 TGAATTTTGAATTTGAATTCGTTTCGC 59.208 29.630 10.81 2.28 46.01 4.70
784 1513 2.961522 TTGAATTCGTTTCGCACTCC 57.038 45.000 0.04 0.00 37.13 3.85
910 1659 2.349590 CCGTCATCAAACTCATCTGCA 58.650 47.619 0.00 0.00 0.00 4.41
932 1682 3.097830 AAACCCCACACCGACCCA 61.098 61.111 0.00 0.00 0.00 4.51
942 1692 0.101399 CACCGACCCAAGATCTCGAG 59.899 60.000 5.93 5.93 0.00 4.04
1431 2486 1.810030 GACCGTGATCAAGGGCGAC 60.810 63.158 28.13 14.32 37.32 5.19
1575 4488 0.031857 CGAGCGAGGAGATGCAGAAT 59.968 55.000 0.00 0.00 0.00 2.40
1652 4565 6.548993 GGGATGAAGATGCCTTCTTAAGATTT 59.451 38.462 5.89 0.00 44.88 2.17
1706 4632 5.684704 TGCGGAAGATTTTAGATGGAGAAT 58.315 37.500 0.00 0.00 0.00 2.40
1783 4739 0.536724 TGATGGTCACTGTATGCGCT 59.463 50.000 9.73 0.00 0.00 5.92
1791 4747 1.190984 CACTGTATGCGCTATGCTTCG 59.809 52.381 9.73 0.96 46.63 3.79
1850 4806 5.293569 TCAGACTTTCTCGGTTCTTTCAAAC 59.706 40.000 0.00 0.00 0.00 2.93
1852 4808 5.294552 AGACTTTCTCGGTTCTTTCAAACAG 59.705 40.000 0.00 0.00 0.00 3.16
1857 4813 6.693315 TCTCGGTTCTTTCAAACAGAAAAT 57.307 33.333 0.00 0.00 45.11 1.82
1927 4883 2.099141 TCTTCCGTTTGGCTCATGAG 57.901 50.000 18.84 18.84 34.14 2.90
2006 4962 6.564709 TTGATCTCAAAGGTTCAGACATTG 57.435 37.500 0.00 0.00 32.11 2.82
2023 4979 4.270008 ACATTGGGGATGTACAGTTTAGC 58.730 43.478 0.33 0.00 47.00 3.09
2027 4983 2.289565 GGGATGTACAGTTTAGCCAGC 58.710 52.381 0.33 0.00 0.00 4.85
2046 5002 4.237724 CAGCTTCTTGTCGACTGAATACA 58.762 43.478 17.92 0.00 0.00 2.29
2048 5004 5.005203 CAGCTTCTTGTCGACTGAATACATC 59.995 44.000 17.92 8.04 0.00 3.06
2051 5007 4.998788 TCTTGTCGACTGAATACATCCTG 58.001 43.478 17.92 0.00 0.00 3.86
2060 5016 6.227298 ACTGAATACATCCTGTCTAACCAG 57.773 41.667 0.00 0.00 0.00 4.00
2071 5027 4.081420 CCTGTCTAACCAGAACTATGCACT 60.081 45.833 0.00 0.00 34.23 4.40
2072 5028 4.820897 TGTCTAACCAGAACTATGCACTG 58.179 43.478 0.00 0.00 30.85 3.66
2073 5029 4.526650 TGTCTAACCAGAACTATGCACTGA 59.473 41.667 2.98 0.00 34.07 3.41
2079 5035 4.122776 CCAGAACTATGCACTGATGGTAC 58.877 47.826 2.98 0.00 34.07 3.34
2098 5054 6.448852 TGGTACGATATGCACGTATTTATGT 58.551 36.000 10.71 0.00 45.42 2.29
2099 5055 6.924612 TGGTACGATATGCACGTATTTATGTT 59.075 34.615 10.71 0.00 45.42 2.71
2151 5118 1.638467 GCGATGCCGAACTTGCTAG 59.362 57.895 0.00 0.00 38.22 3.42
2157 5124 1.078848 CCGAACTTGCTAGCAGCCT 60.079 57.895 18.45 5.86 41.51 4.58
2178 5145 3.066380 TGACCAAACGTCATGATGTCTG 58.934 45.455 20.61 16.90 46.80 3.51
2179 5146 3.244044 TGACCAAACGTCATGATGTCTGA 60.244 43.478 20.67 0.54 46.80 3.27
2180 5147 3.738982 ACCAAACGTCATGATGTCTGAA 58.261 40.909 20.67 0.00 0.00 3.02
2181 5148 4.326826 ACCAAACGTCATGATGTCTGAAT 58.673 39.130 20.67 7.46 0.00 2.57
2182 5149 4.761739 ACCAAACGTCATGATGTCTGAATT 59.238 37.500 20.67 9.15 0.00 2.17
2183 5150 5.241506 ACCAAACGTCATGATGTCTGAATTT 59.758 36.000 20.67 8.48 0.00 1.82
2184 5151 5.570206 CCAAACGTCATGATGTCTGAATTTG 59.430 40.000 20.67 18.08 34.18 2.32
2185 5152 6.372981 CAAACGTCATGATGTCTGAATTTGA 58.627 36.000 20.61 0.00 35.25 2.69
2186 5153 5.791367 ACGTCATGATGTCTGAATTTGAG 57.209 39.130 14.99 0.00 0.00 3.02
2190 5157 4.638865 TCATGATGTCTGAATTTGAGGCTG 59.361 41.667 0.00 0.00 0.00 4.85
2191 5158 2.751259 TGATGTCTGAATTTGAGGCTGC 59.249 45.455 0.00 0.00 0.00 5.25
2192 5159 2.574006 TGTCTGAATTTGAGGCTGCT 57.426 45.000 0.00 0.00 0.00 4.24
2195 5162 3.638160 TGTCTGAATTTGAGGCTGCTTTT 59.362 39.130 0.00 0.00 0.00 2.27
2196 5163 4.233005 GTCTGAATTTGAGGCTGCTTTTC 58.767 43.478 0.00 0.00 0.00 2.29
2204 5181 1.474478 GAGGCTGCTTTTCCCTTAAGC 59.526 52.381 0.00 0.00 46.33 3.09
2275 5254 5.565592 AATTGTTGCTGCTTCGATCATAA 57.434 34.783 0.00 0.00 0.00 1.90
2281 5260 6.260714 TGTTGCTGCTTCGATCATAAACATAT 59.739 34.615 0.00 0.00 0.00 1.78
2317 5298 9.850198 TGATATTCATGATGATAACTTGGTTGA 57.150 29.630 0.00 0.00 0.00 3.18
2330 5311 3.381272 ACTTGGTTGATGTTTCTGTGTGG 59.619 43.478 0.00 0.00 0.00 4.17
2344 5325 0.385390 GTGTGGCCTTTGGAGTGTTG 59.615 55.000 3.32 0.00 0.00 3.33
2350 5331 1.609072 GCCTTTGGAGTGTTGTTCCTC 59.391 52.381 0.00 0.00 35.67 3.71
2351 5332 1.873591 CCTTTGGAGTGTTGTTCCTCG 59.126 52.381 0.00 0.00 35.67 4.63
2352 5333 1.873591 CTTTGGAGTGTTGTTCCTCGG 59.126 52.381 0.00 0.00 35.67 4.63
2353 5334 0.834612 TTGGAGTGTTGTTCCTCGGT 59.165 50.000 0.00 0.00 35.67 4.69
2354 5335 0.391597 TGGAGTGTTGTTCCTCGGTC 59.608 55.000 0.00 0.00 35.67 4.79
2388 5370 5.435557 GTGCGCAGATGTTCTGTTATATTC 58.564 41.667 12.22 0.00 45.94 1.75
2393 5375 7.698130 GCGCAGATGTTCTGTTATATTCTTTTT 59.302 33.333 0.30 0.00 45.94 1.94
2431 5413 3.917988 TGAGCATCAGTACAGACACAAG 58.082 45.455 0.00 0.00 42.56 3.16
2432 5414 2.670414 GAGCATCAGTACAGACACAAGC 59.330 50.000 0.00 0.00 33.17 4.01
2433 5415 1.391485 GCATCAGTACAGACACAAGCG 59.609 52.381 0.00 0.00 0.00 4.68
2434 5416 1.391485 CATCAGTACAGACACAAGCGC 59.609 52.381 0.00 0.00 0.00 5.92
2435 5417 0.673985 TCAGTACAGACACAAGCGCT 59.326 50.000 2.64 2.64 0.00 5.92
2436 5418 1.063806 CAGTACAGACACAAGCGCTC 58.936 55.000 12.06 0.00 0.00 5.03
2437 5419 0.673985 AGTACAGACACAAGCGCTCA 59.326 50.000 12.06 0.00 0.00 4.26
2438 5420 1.273606 AGTACAGACACAAGCGCTCAT 59.726 47.619 12.06 0.00 0.00 2.90
2439 5421 2.492088 AGTACAGACACAAGCGCTCATA 59.508 45.455 12.06 0.00 0.00 2.15
2440 5422 2.680312 ACAGACACAAGCGCTCATAT 57.320 45.000 12.06 0.00 0.00 1.78
2441 5423 3.801114 ACAGACACAAGCGCTCATATA 57.199 42.857 12.06 0.00 0.00 0.86
2442 5424 3.448686 ACAGACACAAGCGCTCATATAC 58.551 45.455 12.06 1.00 0.00 1.47
2443 5425 3.119137 ACAGACACAAGCGCTCATATACA 60.119 43.478 12.06 0.00 0.00 2.29
2444 5426 3.243877 CAGACACAAGCGCTCATATACAC 59.756 47.826 12.06 0.00 0.00 2.90
2445 5427 2.193447 ACACAAGCGCTCATATACACG 58.807 47.619 12.06 0.00 0.00 4.49
2449 5431 3.916439 CGCTCATATACACGCGCA 58.084 55.556 5.73 0.00 39.11 6.09
2450 5432 1.482955 CGCTCATATACACGCGCAC 59.517 57.895 5.73 0.00 39.11 5.34
2451 5433 0.934901 CGCTCATATACACGCGCACT 60.935 55.000 5.73 0.00 39.11 4.40
2452 5434 1.209128 GCTCATATACACGCGCACTT 58.791 50.000 5.73 0.00 0.00 3.16
2453 5435 1.593006 GCTCATATACACGCGCACTTT 59.407 47.619 5.73 0.00 0.00 2.66
2454 5436 2.030457 GCTCATATACACGCGCACTTTT 59.970 45.455 5.73 0.00 0.00 2.27
2455 5437 3.485216 GCTCATATACACGCGCACTTTTT 60.485 43.478 5.73 0.00 0.00 1.94
2473 5455 4.552166 TTTTTCTTGAGCTGAAGTTCGG 57.448 40.909 12.87 7.38 0.00 4.30
2474 5456 2.910688 TTCTTGAGCTGAAGTTCGGT 57.089 45.000 12.87 6.37 0.00 4.69
2475 5457 4.330944 TTTCTTGAGCTGAAGTTCGGTA 57.669 40.909 12.87 0.00 0.00 4.02
2476 5458 4.330944 TTCTTGAGCTGAAGTTCGGTAA 57.669 40.909 12.87 5.94 0.00 2.85
2477 5459 4.537135 TCTTGAGCTGAAGTTCGGTAAT 57.463 40.909 12.87 0.17 0.00 1.89
2478 5460 4.894784 TCTTGAGCTGAAGTTCGGTAATT 58.105 39.130 12.87 0.00 0.00 1.40
2479 5461 5.305585 TCTTGAGCTGAAGTTCGGTAATTT 58.694 37.500 12.87 0.00 0.00 1.82
2480 5462 6.460781 TCTTGAGCTGAAGTTCGGTAATTTA 58.539 36.000 12.87 0.00 0.00 1.40
2481 5463 6.367969 TCTTGAGCTGAAGTTCGGTAATTTAC 59.632 38.462 12.87 0.00 0.00 2.01
2482 5464 5.790593 TGAGCTGAAGTTCGGTAATTTACT 58.209 37.500 13.23 0.00 0.00 2.24
2483 5465 6.927416 TGAGCTGAAGTTCGGTAATTTACTA 58.073 36.000 13.23 0.00 0.00 1.82
2484 5466 7.033791 TGAGCTGAAGTTCGGTAATTTACTAG 58.966 38.462 13.23 0.00 0.00 2.57
2485 5467 6.932947 AGCTGAAGTTCGGTAATTTACTAGT 58.067 36.000 13.23 0.00 0.00 2.57
2486 5468 7.034397 AGCTGAAGTTCGGTAATTTACTAGTC 58.966 38.462 13.23 0.00 0.00 2.59
2487 5469 6.810182 GCTGAAGTTCGGTAATTTACTAGTCA 59.190 38.462 13.23 0.00 0.00 3.41
2488 5470 7.201418 GCTGAAGTTCGGTAATTTACTAGTCAC 60.201 40.741 13.23 0.00 0.00 3.67
2489 5471 7.660112 TGAAGTTCGGTAATTTACTAGTCACA 58.340 34.615 0.00 0.00 0.00 3.58
2490 5472 7.811236 TGAAGTTCGGTAATTTACTAGTCACAG 59.189 37.037 0.00 0.00 0.00 3.66
2491 5473 6.098017 AGTTCGGTAATTTACTAGTCACAGC 58.902 40.000 0.00 0.00 0.00 4.40
2492 5474 5.909621 TCGGTAATTTACTAGTCACAGCT 57.090 39.130 0.00 0.00 0.00 4.24
2493 5475 6.276832 TCGGTAATTTACTAGTCACAGCTT 57.723 37.500 0.00 0.00 0.00 3.74
2494 5476 6.327934 TCGGTAATTTACTAGTCACAGCTTC 58.672 40.000 0.00 0.00 0.00 3.86
2495 5477 6.152323 TCGGTAATTTACTAGTCACAGCTTCT 59.848 38.462 0.00 0.00 0.00 2.85
2496 5478 6.812160 CGGTAATTTACTAGTCACAGCTTCTT 59.188 38.462 0.00 0.00 0.00 2.52
2497 5479 7.331193 CGGTAATTTACTAGTCACAGCTTCTTT 59.669 37.037 0.00 0.00 0.00 2.52
2498 5480 9.000486 GGTAATTTACTAGTCACAGCTTCTTTT 58.000 33.333 0.00 0.00 0.00 2.27
2500 5482 8.677148 AATTTACTAGTCACAGCTTCTTTTCA 57.323 30.769 0.00 0.00 0.00 2.69
2501 5483 7.715265 TTTACTAGTCACAGCTTCTTTTCAG 57.285 36.000 0.00 0.00 0.00 3.02
2502 5484 4.061596 ACTAGTCACAGCTTCTTTTCAGC 58.938 43.478 0.00 0.00 37.56 4.26
2503 5485 2.923121 AGTCACAGCTTCTTTTCAGCA 58.077 42.857 0.00 0.00 39.99 4.41
2504 5486 3.484407 AGTCACAGCTTCTTTTCAGCAT 58.516 40.909 0.00 0.00 39.99 3.79
2505 5487 3.501445 AGTCACAGCTTCTTTTCAGCATC 59.499 43.478 0.00 0.00 39.99 3.91
2506 5488 2.816087 TCACAGCTTCTTTTCAGCATCC 59.184 45.455 0.00 0.00 39.99 3.51
2507 5489 2.555325 CACAGCTTCTTTTCAGCATCCA 59.445 45.455 0.00 0.00 39.99 3.41
2508 5490 3.192844 CACAGCTTCTTTTCAGCATCCAT 59.807 43.478 0.00 0.00 39.99 3.41
2509 5491 3.830755 ACAGCTTCTTTTCAGCATCCATT 59.169 39.130 0.00 0.00 39.99 3.16
2510 5492 5.012239 ACAGCTTCTTTTCAGCATCCATTA 58.988 37.500 0.00 0.00 39.99 1.90
2511 5493 5.125097 ACAGCTTCTTTTCAGCATCCATTAG 59.875 40.000 0.00 0.00 39.99 1.73
2512 5494 4.097589 AGCTTCTTTTCAGCATCCATTAGC 59.902 41.667 0.00 0.00 39.99 3.09
2513 5495 4.735873 GCTTCTTTTCAGCATCCATTAGCC 60.736 45.833 0.00 0.00 37.22 3.93
2514 5496 3.290710 TCTTTTCAGCATCCATTAGCCC 58.709 45.455 0.00 0.00 0.00 5.19
2515 5497 2.071778 TTTCAGCATCCATTAGCCCC 57.928 50.000 0.00 0.00 0.00 5.80
2516 5498 1.225373 TTCAGCATCCATTAGCCCCT 58.775 50.000 0.00 0.00 0.00 4.79
2517 5499 0.475475 TCAGCATCCATTAGCCCCTG 59.525 55.000 0.00 0.00 0.00 4.45
2518 5500 1.152368 AGCATCCATTAGCCCCTGC 59.848 57.895 0.00 0.00 37.95 4.85
2557 5539 7.765695 TTTTTGAGCAACTGGAGAATCTTAT 57.234 32.000 0.00 0.00 33.73 1.73
2558 5540 7.765695 TTTTGAGCAACTGGAGAATCTTATT 57.234 32.000 0.00 0.00 33.73 1.40
2559 5541 6.748333 TTGAGCAACTGGAGAATCTTATTG 57.252 37.500 0.00 0.00 33.73 1.90
2560 5542 6.053632 TGAGCAACTGGAGAATCTTATTGA 57.946 37.500 0.00 0.00 33.73 2.57
2561 5543 6.656902 TGAGCAACTGGAGAATCTTATTGAT 58.343 36.000 0.00 0.00 36.89 2.57
2563 5545 8.267183 TGAGCAACTGGAGAATCTTATTGATTA 58.733 33.333 0.00 0.00 44.70 1.75
2564 5546 9.113838 GAGCAACTGGAGAATCTTATTGATTAA 57.886 33.333 0.00 0.00 44.70 1.40
2565 5547 9.638176 AGCAACTGGAGAATCTTATTGATTAAT 57.362 29.630 0.00 0.00 44.70 1.40
2566 5548 9.674824 GCAACTGGAGAATCTTATTGATTAATG 57.325 33.333 0.00 0.00 44.70 1.90
2583 5565 9.747898 TTGATTAATGTTTACAGGGATACAAGT 57.252 29.630 0.00 0.00 39.74 3.16
2587 5569 7.933215 AATGTTTACAGGGATACAAGTAACC 57.067 36.000 0.00 0.00 37.17 2.85
2588 5570 5.807909 TGTTTACAGGGATACAAGTAACCC 58.192 41.667 15.58 15.58 45.52 4.11
2592 5574 2.904697 GGGATACAAGTAACCCTCCG 57.095 55.000 15.96 0.00 42.84 4.63
2593 5575 1.415289 GGGATACAAGTAACCCTCCGG 59.585 57.143 15.96 0.00 42.84 5.14
2594 5576 3.871737 GGGATACAAGTAACCCTCCGGG 61.872 59.091 15.96 0.00 42.84 5.73
2605 5587 2.683475 CTCCGGGGGAGCCAAAAT 59.317 61.111 0.00 0.00 43.29 1.82
2606 5588 1.754234 CTCCGGGGGAGCCAAAATG 60.754 63.158 0.00 0.00 43.29 2.32
2607 5589 3.460868 CCGGGGGAGCCAAAATGC 61.461 66.667 0.00 0.00 0.00 3.56
2608 5590 2.679642 CGGGGGAGCCAAAATGCA 60.680 61.111 0.00 0.00 0.00 3.96
2609 5591 2.282039 CGGGGGAGCCAAAATGCAA 61.282 57.895 0.00 0.00 0.00 4.08
2610 5592 1.825281 CGGGGGAGCCAAAATGCAAA 61.825 55.000 0.00 0.00 0.00 3.68
2611 5593 0.620030 GGGGGAGCCAAAATGCAAAT 59.380 50.000 0.00 0.00 0.00 2.32
2612 5594 1.836802 GGGGGAGCCAAAATGCAAATA 59.163 47.619 0.00 0.00 0.00 1.40
2613 5595 2.439135 GGGGGAGCCAAAATGCAAATAT 59.561 45.455 0.00 0.00 0.00 1.28
2614 5596 3.469739 GGGGAGCCAAAATGCAAATATG 58.530 45.455 0.00 0.00 0.00 1.78
2615 5597 3.118298 GGGGAGCCAAAATGCAAATATGT 60.118 43.478 0.00 0.00 0.00 2.29
2616 5598 4.100808 GGGGAGCCAAAATGCAAATATGTA 59.899 41.667 0.00 0.00 0.00 2.29
2617 5599 5.221702 GGGGAGCCAAAATGCAAATATGTAT 60.222 40.000 0.00 0.00 32.80 2.29
2618 5600 5.697633 GGGAGCCAAAATGCAAATATGTATG 59.302 40.000 0.00 0.00 31.74 2.39
2619 5601 6.282930 GGAGCCAAAATGCAAATATGTATGT 58.717 36.000 0.00 0.00 31.74 2.29
2620 5602 6.421801 GGAGCCAAAATGCAAATATGTATGTC 59.578 38.462 0.00 0.00 31.74 3.06
2621 5603 7.116075 AGCCAAAATGCAAATATGTATGTCT 57.884 32.000 0.00 0.00 31.74 3.41
2622 5604 8.236585 AGCCAAAATGCAAATATGTATGTCTA 57.763 30.769 0.00 0.00 31.74 2.59
2623 5605 8.137437 AGCCAAAATGCAAATATGTATGTCTAC 58.863 33.333 0.00 0.00 31.74 2.59
2624 5606 7.382218 GCCAAAATGCAAATATGTATGTCTACC 59.618 37.037 0.00 0.00 31.74 3.18
2625 5607 7.867403 CCAAAATGCAAATATGTATGTCTACCC 59.133 37.037 0.00 0.00 31.74 3.69
2626 5608 8.412456 CAAAATGCAAATATGTATGTCTACCCA 58.588 33.333 0.00 0.00 31.74 4.51
2627 5609 7.510549 AATGCAAATATGTATGTCTACCCAC 57.489 36.000 0.00 0.00 31.74 4.61
2628 5610 5.995446 TGCAAATATGTATGTCTACCCACA 58.005 37.500 0.00 0.00 0.00 4.17
2629 5611 6.600388 TGCAAATATGTATGTCTACCCACAT 58.400 36.000 0.00 0.00 40.28 3.21
2630 5612 6.710295 TGCAAATATGTATGTCTACCCACATC 59.290 38.462 0.00 0.00 38.07 3.06
2631 5613 6.710295 GCAAATATGTATGTCTACCCACATCA 59.290 38.462 0.00 0.00 38.07 3.07
2632 5614 7.228507 GCAAATATGTATGTCTACCCACATCAA 59.771 37.037 0.00 0.00 38.07 2.57
2633 5615 8.777413 CAAATATGTATGTCTACCCACATCAAG 58.223 37.037 0.00 0.00 38.07 3.02
2634 5616 5.957771 ATGTATGTCTACCCACATCAAGT 57.042 39.130 0.00 0.00 38.07 3.16
2635 5617 8.721133 ATATGTATGTCTACCCACATCAAGTA 57.279 34.615 0.00 0.00 38.07 2.24
2636 5618 6.216801 TGTATGTCTACCCACATCAAGTAC 57.783 41.667 0.00 0.00 38.07 2.73
2637 5619 5.717654 TGTATGTCTACCCACATCAAGTACA 59.282 40.000 0.00 0.00 38.07 2.90
2638 5620 4.801330 TGTCTACCCACATCAAGTACAG 57.199 45.455 0.00 0.00 0.00 2.74
2639 5621 4.157246 TGTCTACCCACATCAAGTACAGT 58.843 43.478 0.00 0.00 0.00 3.55
2640 5622 4.021456 TGTCTACCCACATCAAGTACAGTG 60.021 45.833 0.00 0.00 0.00 3.66
2643 5625 2.479566 CCACATCAAGTACAGTGGCT 57.520 50.000 0.00 0.00 44.25 4.75
2644 5626 2.079158 CCACATCAAGTACAGTGGCTG 58.921 52.381 0.00 0.00 44.25 4.85
2645 5627 1.466167 CACATCAAGTACAGTGGCTGC 59.534 52.381 0.00 0.00 34.37 5.25
2646 5628 1.089920 CATCAAGTACAGTGGCTGCC 58.910 55.000 12.87 12.87 34.37 4.85
2647 5629 0.987294 ATCAAGTACAGTGGCTGCCT 59.013 50.000 21.03 1.26 34.37 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.180276 ACGGAGCTTCAGTCTAACCAT 58.820 47.619 0.00 0.00 0.00 3.55
21 22 1.078497 TGCTCAAGTGCCCATACGG 60.078 57.895 0.00 0.00 0.00 4.02
91 92 4.345547 TCTGACCCTACATTTACACACACA 59.654 41.667 0.00 0.00 0.00 3.72
92 93 4.890088 TCTGACCCTACATTTACACACAC 58.110 43.478 0.00 0.00 0.00 3.82
93 94 5.302360 GTTCTGACCCTACATTTACACACA 58.698 41.667 0.00 0.00 0.00 3.72
94 95 4.694037 GGTTCTGACCCTACATTTACACAC 59.306 45.833 0.00 0.00 40.25 3.82
112 113 1.073897 GCTGAAGTGGGCTGGTTCT 59.926 57.895 0.00 0.00 0.00 3.01
150 151 4.853007 AGCCAGCTCTTCAATACATTTCT 58.147 39.130 0.00 0.00 0.00 2.52
215 216 7.762615 TGTTTCCTGAATATGTTAGGTAGAACG 59.237 37.037 0.00 0.00 33.30 3.95
249 250 5.748630 TCGAAAAGAGATGATGTTGGATACG 59.251 40.000 0.00 0.00 42.51 3.06
261 262 3.876274 TCCCTCAGTCGAAAAGAGATG 57.124 47.619 10.57 3.54 0.00 2.90
275 276 3.569701 GTGAAAAGCTGAACAATCCCTCA 59.430 43.478 0.00 0.00 0.00 3.86
284 285 0.310854 CGGTGGGTGAAAAGCTGAAC 59.689 55.000 0.00 0.00 0.00 3.18
287 288 0.535102 AGACGGTGGGTGAAAAGCTG 60.535 55.000 0.00 0.00 0.00 4.24
288 289 0.182775 AAGACGGTGGGTGAAAAGCT 59.817 50.000 0.00 0.00 0.00 3.74
290 291 2.572290 AGAAAGACGGTGGGTGAAAAG 58.428 47.619 0.00 0.00 0.00 2.27
291 292 2.721425 AGAAAGACGGTGGGTGAAAA 57.279 45.000 0.00 0.00 0.00 2.29
292 293 2.721425 AAGAAAGACGGTGGGTGAAA 57.279 45.000 0.00 0.00 0.00 2.69
323 374 6.406370 TGTTACTAGCATTGCAAGACACTAT 58.594 36.000 11.91 0.00 0.00 2.12
332 383 8.739039 AGATAAACATTTGTTACTAGCATTGCA 58.261 29.630 11.91 0.00 37.25 4.08
356 407 2.163010 CGTTGGTAGCGTAGGAAGAAGA 59.837 50.000 0.00 0.00 0.00 2.87
357 408 2.527100 CGTTGGTAGCGTAGGAAGAAG 58.473 52.381 0.00 0.00 0.00 2.85
358 409 1.403249 GCGTTGGTAGCGTAGGAAGAA 60.403 52.381 0.00 0.00 0.00 2.52
359 410 0.171903 GCGTTGGTAGCGTAGGAAGA 59.828 55.000 0.00 0.00 0.00 2.87
363 414 0.928229 GATTGCGTTGGTAGCGTAGG 59.072 55.000 0.00 0.00 37.44 3.18
368 419 0.392461 TGGAGGATTGCGTTGGTAGC 60.392 55.000 0.00 0.00 0.00 3.58
394 445 5.106237 GGAATAATCCTGCTCATTCATGCTC 60.106 44.000 0.00 0.00 42.93 4.26
414 465 3.799753 GCGATGCACGACTGGAAT 58.200 55.556 11.94 0.00 45.77 3.01
424 475 2.891941 GAATCCCCAGTGGCGATGCA 62.892 60.000 10.13 0.00 0.00 3.96
434 485 6.772605 TCACAATACTATGATGAATCCCCAG 58.227 40.000 0.00 0.00 0.00 4.45
499 551 1.535028 CAATGGTTTCTGCACGCTGTA 59.465 47.619 0.00 0.00 0.00 2.74
527 580 3.525537 AGCAATGCTATATCGCGCTATT 58.474 40.909 5.69 0.00 36.99 1.73
529 582 2.654749 AGCAATGCTATATCGCGCTA 57.345 45.000 5.69 0.00 36.99 4.26
530 583 1.800805 AAGCAATGCTATATCGCGCT 58.199 45.000 8.68 0.00 38.25 5.92
531 584 2.601481 AAAGCAATGCTATATCGCGC 57.399 45.000 8.68 0.00 38.25 6.86
556 609 9.806203 CAATGCTATATTGTTGGATCTCAAAAA 57.194 29.630 0.00 0.00 37.03 1.94
557 610 7.922278 GCAATGCTATATTGTTGGATCTCAAAA 59.078 33.333 0.00 0.00 37.08 2.44
558 611 7.286087 AGCAATGCTATATTGTTGGATCTCAAA 59.714 33.333 5.69 0.00 36.99 2.69
559 612 6.774170 AGCAATGCTATATTGTTGGATCTCAA 59.226 34.615 5.69 0.00 36.99 3.02
560 613 6.301486 AGCAATGCTATATTGTTGGATCTCA 58.699 36.000 5.69 0.00 36.99 3.27
561 614 6.814506 AGCAATGCTATATTGTTGGATCTC 57.185 37.500 5.69 0.00 36.99 2.75
562 615 8.874744 ATTAGCAATGCTATATTGTTGGATCT 57.125 30.769 16.35 0.00 41.01 2.75
564 617 8.680903 GCTATTAGCAATGCTATATTGTTGGAT 58.319 33.333 16.35 5.74 41.01 3.41
565 618 8.044060 GCTATTAGCAATGCTATATTGTTGGA 57.956 34.615 16.35 0.00 41.01 3.53
594 647 1.690219 AATAGCACCGCCCCTGAGAG 61.690 60.000 0.00 0.00 0.00 3.20
596 649 0.394352 AAAATAGCACCGCCCCTGAG 60.394 55.000 0.00 0.00 0.00 3.35
633 741 2.038557 GTGGAGTAGGTTTCTGCAAGGA 59.961 50.000 0.00 0.00 35.27 3.36
635 743 2.808543 GTGTGGAGTAGGTTTCTGCAAG 59.191 50.000 0.00 0.00 35.27 4.01
668 778 1.923356 TCCCCATGAAGTTTCTTGCC 58.077 50.000 0.00 0.00 32.70 4.52
669 779 3.069443 TGTTTCCCCATGAAGTTTCTTGC 59.931 43.478 0.00 0.00 33.63 4.01
697 807 1.501169 CCAAAAGCGCTTTCCTTTGG 58.499 50.000 33.69 30.37 33.14 3.28
713 823 2.146146 ATTCTCCAGCAGCAGGCCAA 62.146 55.000 5.01 0.00 46.50 4.52
714 824 2.146146 AATTCTCCAGCAGCAGGCCA 62.146 55.000 5.01 0.00 46.50 5.36
716 826 1.382692 GGAATTCTCCAGCAGCAGGC 61.383 60.000 5.23 0.00 41.96 4.85
719 829 0.324614 TTCGGAATTCTCCAGCAGCA 59.675 50.000 5.23 0.00 42.58 4.41
720 830 0.729690 GTTCGGAATTCTCCAGCAGC 59.270 55.000 5.23 0.00 42.58 5.25
721 831 2.275318 GAGTTCGGAATTCTCCAGCAG 58.725 52.381 5.23 0.00 42.58 4.24
722 832 1.623311 TGAGTTCGGAATTCTCCAGCA 59.377 47.619 13.42 0.00 42.58 4.41
723 833 2.386661 TGAGTTCGGAATTCTCCAGC 57.613 50.000 13.42 0.00 42.58 4.85
725 835 5.677319 ATAGTTGAGTTCGGAATTCTCCA 57.323 39.130 13.42 0.00 42.58 3.86
756 1262 7.042791 AGTGCGAAACGAATTCAAATTCAAAAT 60.043 29.630 14.11 0.00 43.85 1.82
776 1400 0.249868 CTTGGTCAGTTGGAGTGCGA 60.250 55.000 0.00 0.00 0.00 5.10
779 1508 3.808728 TCTTTCTTGGTCAGTTGGAGTG 58.191 45.455 0.00 0.00 0.00 3.51
784 1513 5.818136 TGAGTTTCTTTCTTGGTCAGTTG 57.182 39.130 0.00 0.00 0.00 3.16
851 1598 5.182570 GTCCCGTTTATTTATATTGGGCTCC 59.817 44.000 0.00 0.00 35.09 4.70
892 1641 4.330894 TCGATTGCAGATGAGTTTGATGAC 59.669 41.667 0.00 0.00 0.00 3.06
910 1659 0.604511 GTCGGTGTGGGGTTTCGATT 60.605 55.000 0.00 0.00 32.46 3.34
951 1701 1.957695 GGTTTCGGTCGGCTTTCGT 60.958 57.895 0.00 0.00 40.32 3.85
952 1702 2.674084 GGGTTTCGGTCGGCTTTCG 61.674 63.158 0.00 0.00 40.90 3.46
953 1703 0.037046 TAGGGTTTCGGTCGGCTTTC 60.037 55.000 0.00 0.00 0.00 2.62
954 1704 0.036671 CTAGGGTTTCGGTCGGCTTT 60.037 55.000 0.00 0.00 0.00 3.51
1431 2486 2.758327 TGGGTGTCGATCTCCGGG 60.758 66.667 0.00 0.00 39.14 5.73
1575 4488 3.071457 TGAGTTTCTTGAGCATGTCCTGA 59.929 43.478 0.00 0.00 0.00 3.86
1706 4632 5.761234 ACAAGACACCGAAATAGCAAAGTAA 59.239 36.000 0.00 0.00 0.00 2.24
1828 4784 5.183228 TGTTTGAAAGAACCGAGAAAGTCT 58.817 37.500 0.00 0.00 0.00 3.24
1894 4850 7.422399 CCAAACGGAAGATTCAAGTTTTTCTA 58.578 34.615 12.59 0.00 37.42 2.10
1902 4858 2.813754 TGAGCCAAACGGAAGATTCAAG 59.186 45.455 0.00 0.00 0.00 3.02
1906 4862 3.012518 CTCATGAGCCAAACGGAAGATT 58.987 45.455 10.38 0.00 0.00 2.40
1927 4883 4.511826 CGAAGGCCTAATTTCTCATACACC 59.488 45.833 5.16 0.00 0.00 4.16
2006 4962 2.919228 CTGGCTAAACTGTACATCCCC 58.081 52.381 0.00 0.00 0.00 4.81
2023 4979 2.154854 TTCAGTCGACAAGAAGCTGG 57.845 50.000 19.50 0.00 0.00 4.85
2027 4983 5.518128 CAGGATGTATTCAGTCGACAAGAAG 59.482 44.000 19.50 2.04 0.00 2.85
2046 5002 4.716784 TGCATAGTTCTGGTTAGACAGGAT 59.283 41.667 0.00 0.00 38.98 3.24
2048 5004 4.081420 AGTGCATAGTTCTGGTTAGACAGG 60.081 45.833 0.00 0.00 38.98 4.00
2051 5007 5.073311 TCAGTGCATAGTTCTGGTTAGAC 57.927 43.478 0.00 0.00 31.21 2.59
2060 5016 4.041740 TCGTACCATCAGTGCATAGTTC 57.958 45.455 0.00 0.00 0.00 3.01
2071 5027 4.776795 ATACGTGCATATCGTACCATCA 57.223 40.909 9.86 0.00 44.44 3.07
2072 5028 7.274904 ACATAAATACGTGCATATCGTACCATC 59.725 37.037 9.86 0.00 44.44 3.51
2073 5029 7.094631 ACATAAATACGTGCATATCGTACCAT 58.905 34.615 9.86 3.34 44.44 3.55
2079 5035 8.760703 TGAAAAACATAAATACGTGCATATCG 57.239 30.769 0.00 0.00 0.00 2.92
2098 5054 7.335673 GGAAAGAAACCACCAAAATCTGAAAAA 59.664 33.333 0.00 0.00 0.00 1.94
2099 5055 6.821160 GGAAAGAAACCACCAAAATCTGAAAA 59.179 34.615 0.00 0.00 0.00 2.29
2116 5072 2.925724 TCGCCAACTTCAGGAAAGAAA 58.074 42.857 0.00 0.00 38.44 2.52
2147 5110 1.639298 CGTTTGGTCAGGCTGCTAGC 61.639 60.000 10.34 8.10 41.46 3.42
2151 5118 2.946762 GACGTTTGGTCAGGCTGC 59.053 61.111 10.34 4.94 45.36 5.25
2178 5145 2.564504 AGGGAAAAGCAGCCTCAAATTC 59.435 45.455 0.00 0.00 0.00 2.17
2179 5146 2.613129 AGGGAAAAGCAGCCTCAAATT 58.387 42.857 0.00 0.00 0.00 1.82
2180 5147 2.315720 AGGGAAAAGCAGCCTCAAAT 57.684 45.000 0.00 0.00 0.00 2.32
2181 5148 2.086610 AAGGGAAAAGCAGCCTCAAA 57.913 45.000 0.00 0.00 0.00 2.69
2182 5149 2.969821 TAAGGGAAAAGCAGCCTCAA 57.030 45.000 0.00 0.00 0.00 3.02
2183 5150 2.795329 CTTAAGGGAAAAGCAGCCTCA 58.205 47.619 0.00 0.00 0.00 3.86
2184 5151 1.474478 GCTTAAGGGAAAAGCAGCCTC 59.526 52.381 4.29 0.00 46.85 4.70
2185 5152 1.550327 GCTTAAGGGAAAAGCAGCCT 58.450 50.000 4.29 0.00 46.85 4.58
2190 5157 1.738350 GAGACCGCTTAAGGGAAAAGC 59.262 52.381 20.33 0.00 44.72 3.51
2191 5158 3.003480 CAGAGACCGCTTAAGGGAAAAG 58.997 50.000 20.33 6.55 35.02 2.27
2192 5159 2.635915 TCAGAGACCGCTTAAGGGAAAA 59.364 45.455 20.33 0.00 35.02 2.29
2195 5162 1.933021 TTCAGAGACCGCTTAAGGGA 58.067 50.000 20.33 0.00 35.02 4.20
2196 5163 2.990066 ATTCAGAGACCGCTTAAGGG 57.010 50.000 12.42 12.42 35.02 3.95
2204 5181 8.994429 ATAGAGCAATATTAATTCAGAGACCG 57.006 34.615 0.00 0.00 0.00 4.79
2317 5298 1.688197 CCAAAGGCCACACAGAAACAT 59.312 47.619 5.01 0.00 0.00 2.71
2330 5311 1.609072 GAGGAACAACACTCCAAAGGC 59.391 52.381 0.00 0.00 35.20 4.35
2352 5333 1.282875 GCGCACCTTGGTTTCTGAC 59.717 57.895 0.30 0.00 0.00 3.51
2353 5334 1.153066 TGCGCACCTTGGTTTCTGA 60.153 52.632 5.66 0.00 0.00 3.27
2354 5335 1.165907 TCTGCGCACCTTGGTTTCTG 61.166 55.000 5.66 0.00 0.00 3.02
2362 5344 2.548178 CAGAACATCTGCGCACCTT 58.452 52.632 5.66 0.00 37.72 3.50
2406 5388 5.122519 TGTGTCTGTACTGATGCTCAAAAA 58.877 37.500 5.69 0.00 0.00 1.94
2407 5389 4.702831 TGTGTCTGTACTGATGCTCAAAA 58.297 39.130 5.69 0.00 0.00 2.44
2408 5390 4.335400 TGTGTCTGTACTGATGCTCAAA 57.665 40.909 5.69 0.00 0.00 2.69
2409 5391 4.309933 CTTGTGTCTGTACTGATGCTCAA 58.690 43.478 5.69 6.69 0.00 3.02
2410 5392 3.862264 GCTTGTGTCTGTACTGATGCTCA 60.862 47.826 5.69 0.00 0.00 4.26
2411 5393 2.670414 GCTTGTGTCTGTACTGATGCTC 59.330 50.000 5.69 0.00 0.00 4.26
2412 5394 2.693069 GCTTGTGTCTGTACTGATGCT 58.307 47.619 5.69 0.00 0.00 3.79
2413 5395 1.391485 CGCTTGTGTCTGTACTGATGC 59.609 52.381 5.69 3.20 0.00 3.91
2414 5396 1.391485 GCGCTTGTGTCTGTACTGATG 59.609 52.381 0.00 0.00 0.00 3.07
2415 5397 1.273606 AGCGCTTGTGTCTGTACTGAT 59.726 47.619 2.64 0.00 0.00 2.90
2416 5398 0.673985 AGCGCTTGTGTCTGTACTGA 59.326 50.000 2.64 0.00 0.00 3.41
2417 5399 1.063806 GAGCGCTTGTGTCTGTACTG 58.936 55.000 13.26 0.00 0.00 2.74
2418 5400 0.673985 TGAGCGCTTGTGTCTGTACT 59.326 50.000 13.26 0.00 0.00 2.73
2419 5401 1.714794 ATGAGCGCTTGTGTCTGTAC 58.285 50.000 13.26 0.00 0.00 2.90
2420 5402 3.801114 ATATGAGCGCTTGTGTCTGTA 57.199 42.857 13.26 0.00 0.00 2.74
2421 5403 2.680312 ATATGAGCGCTTGTGTCTGT 57.320 45.000 13.26 0.00 0.00 3.41
2422 5404 3.243877 GTGTATATGAGCGCTTGTGTCTG 59.756 47.826 13.26 0.00 0.00 3.51
2423 5405 3.448686 GTGTATATGAGCGCTTGTGTCT 58.551 45.455 13.26 0.00 0.00 3.41
2424 5406 2.216488 CGTGTATATGAGCGCTTGTGTC 59.784 50.000 13.26 0.00 0.00 3.67
2425 5407 2.193447 CGTGTATATGAGCGCTTGTGT 58.807 47.619 13.26 4.27 0.00 3.72
2426 5408 1.071239 GCGTGTATATGAGCGCTTGTG 60.071 52.381 13.26 0.00 45.48 3.33
2427 5409 1.209128 GCGTGTATATGAGCGCTTGT 58.791 50.000 13.26 5.98 45.48 3.16
2428 5410 0.159554 CGCGTGTATATGAGCGCTTG 59.840 55.000 13.26 0.00 46.56 4.01
2429 5411 2.506544 CGCGTGTATATGAGCGCTT 58.493 52.632 13.26 0.00 46.56 4.68
2430 5412 4.228451 CGCGTGTATATGAGCGCT 57.772 55.556 11.27 11.27 46.56 5.92
2433 5415 1.209128 AAGTGCGCGTGTATATGAGC 58.791 50.000 8.43 0.41 38.85 4.26
2434 5416 3.925688 AAAAGTGCGCGTGTATATGAG 57.074 42.857 8.43 0.00 0.00 2.90
2452 5434 3.945285 ACCGAACTTCAGCTCAAGAAAAA 59.055 39.130 3.60 0.00 0.00 1.94
2453 5435 3.541632 ACCGAACTTCAGCTCAAGAAAA 58.458 40.909 3.60 0.00 0.00 2.29
2454 5436 3.194005 ACCGAACTTCAGCTCAAGAAA 57.806 42.857 3.60 0.00 0.00 2.52
2455 5437 2.910688 ACCGAACTTCAGCTCAAGAA 57.089 45.000 3.60 0.00 0.00 2.52
2456 5438 4.537135 ATTACCGAACTTCAGCTCAAGA 57.463 40.909 3.60 0.00 0.00 3.02
2457 5439 5.613358 AAATTACCGAACTTCAGCTCAAG 57.387 39.130 0.00 0.00 0.00 3.02
2458 5440 6.228258 AGTAAATTACCGAACTTCAGCTCAA 58.772 36.000 0.00 0.00 0.00 3.02
2459 5441 5.790593 AGTAAATTACCGAACTTCAGCTCA 58.209 37.500 0.00 0.00 0.00 4.26
2460 5442 7.034397 ACTAGTAAATTACCGAACTTCAGCTC 58.966 38.462 0.00 0.00 0.00 4.09
2461 5443 6.932947 ACTAGTAAATTACCGAACTTCAGCT 58.067 36.000 0.00 0.00 0.00 4.24
2462 5444 6.810182 TGACTAGTAAATTACCGAACTTCAGC 59.190 38.462 0.00 0.00 0.00 4.26
2463 5445 7.811236 TGTGACTAGTAAATTACCGAACTTCAG 59.189 37.037 0.00 0.00 0.00 3.02
2464 5446 7.660112 TGTGACTAGTAAATTACCGAACTTCA 58.340 34.615 0.00 0.00 0.00 3.02
2465 5447 7.201418 GCTGTGACTAGTAAATTACCGAACTTC 60.201 40.741 0.00 0.00 0.00 3.01
2466 5448 6.589139 GCTGTGACTAGTAAATTACCGAACTT 59.411 38.462 0.00 0.00 0.00 2.66
2467 5449 6.071503 AGCTGTGACTAGTAAATTACCGAACT 60.072 38.462 0.00 0.00 0.00 3.01
2468 5450 6.098017 AGCTGTGACTAGTAAATTACCGAAC 58.902 40.000 0.00 0.00 0.00 3.95
2469 5451 6.276832 AGCTGTGACTAGTAAATTACCGAA 57.723 37.500 0.00 0.00 0.00 4.30
2470 5452 5.909621 AGCTGTGACTAGTAAATTACCGA 57.090 39.130 0.00 0.00 0.00 4.69
2471 5453 6.331061 AGAAGCTGTGACTAGTAAATTACCG 58.669 40.000 0.00 0.00 0.00 4.02
2472 5454 8.549338 AAAGAAGCTGTGACTAGTAAATTACC 57.451 34.615 0.00 0.00 0.00 2.85
2474 5456 9.772973 TGAAAAGAAGCTGTGACTAGTAAATTA 57.227 29.630 0.00 0.00 0.00 1.40
2475 5457 8.677148 TGAAAAGAAGCTGTGACTAGTAAATT 57.323 30.769 0.00 0.00 0.00 1.82
2476 5458 7.095017 GCTGAAAAGAAGCTGTGACTAGTAAAT 60.095 37.037 0.00 0.00 37.69 1.40
2477 5459 6.202954 GCTGAAAAGAAGCTGTGACTAGTAAA 59.797 38.462 0.00 0.00 37.69 2.01
2478 5460 5.696724 GCTGAAAAGAAGCTGTGACTAGTAA 59.303 40.000 0.00 0.00 37.69 2.24
2479 5461 5.221441 TGCTGAAAAGAAGCTGTGACTAGTA 60.221 40.000 0.00 0.00 41.42 1.82
2480 5462 4.061596 GCTGAAAAGAAGCTGTGACTAGT 58.938 43.478 0.00 0.00 37.69 2.57
2481 5463 4.060900 TGCTGAAAAGAAGCTGTGACTAG 58.939 43.478 0.00 0.00 41.42 2.57
2482 5464 4.071961 TGCTGAAAAGAAGCTGTGACTA 57.928 40.909 0.00 0.00 41.42 2.59
2483 5465 2.923121 TGCTGAAAAGAAGCTGTGACT 58.077 42.857 0.00 0.00 41.42 3.41
2484 5466 3.365767 GGATGCTGAAAAGAAGCTGTGAC 60.366 47.826 0.00 0.00 41.42 3.67
2485 5467 2.816087 GGATGCTGAAAAGAAGCTGTGA 59.184 45.455 0.00 0.00 41.42 3.58
2486 5468 2.555325 TGGATGCTGAAAAGAAGCTGTG 59.445 45.455 0.00 0.00 41.42 3.66
2487 5469 2.867624 TGGATGCTGAAAAGAAGCTGT 58.132 42.857 0.00 0.00 41.42 4.40
2488 5470 4.451629 AATGGATGCTGAAAAGAAGCTG 57.548 40.909 0.00 0.00 41.42 4.24
2489 5471 4.097589 GCTAATGGATGCTGAAAAGAAGCT 59.902 41.667 0.00 0.00 41.42 3.74
2490 5472 4.357996 GCTAATGGATGCTGAAAAGAAGC 58.642 43.478 0.00 0.00 41.22 3.86
2491 5473 4.202090 GGGCTAATGGATGCTGAAAAGAAG 60.202 45.833 0.00 0.00 0.00 2.85
2492 5474 3.701040 GGGCTAATGGATGCTGAAAAGAA 59.299 43.478 0.00 0.00 0.00 2.52
2493 5475 3.290710 GGGCTAATGGATGCTGAAAAGA 58.709 45.455 0.00 0.00 0.00 2.52
2494 5476 2.363359 GGGGCTAATGGATGCTGAAAAG 59.637 50.000 0.00 0.00 0.00 2.27
2495 5477 2.024080 AGGGGCTAATGGATGCTGAAAA 60.024 45.455 0.00 0.00 0.00 2.29
2496 5478 1.570501 AGGGGCTAATGGATGCTGAAA 59.429 47.619 0.00 0.00 0.00 2.69
2497 5479 1.133699 CAGGGGCTAATGGATGCTGAA 60.134 52.381 0.00 0.00 0.00 3.02
2498 5480 0.475475 CAGGGGCTAATGGATGCTGA 59.525 55.000 0.00 0.00 0.00 4.26
2499 5481 1.177256 GCAGGGGCTAATGGATGCTG 61.177 60.000 0.00 0.00 36.96 4.41
2500 5482 1.152368 GCAGGGGCTAATGGATGCT 59.848 57.895 0.00 0.00 36.96 3.79
2501 5483 3.769201 GCAGGGGCTAATGGATGC 58.231 61.111 0.00 0.00 36.96 3.91
2533 5515 7.765695 ATAAGATTCTCCAGTTGCTCAAAAA 57.234 32.000 0.00 0.00 0.00 1.94
2534 5516 7.448161 TCAATAAGATTCTCCAGTTGCTCAAAA 59.552 33.333 0.00 0.00 0.00 2.44
2535 5517 6.942005 TCAATAAGATTCTCCAGTTGCTCAAA 59.058 34.615 0.00 0.00 0.00 2.69
2536 5518 6.475504 TCAATAAGATTCTCCAGTTGCTCAA 58.524 36.000 0.00 0.00 0.00 3.02
2537 5519 6.053632 TCAATAAGATTCTCCAGTTGCTCA 57.946 37.500 0.00 0.00 0.00 4.26
2538 5520 7.565323 AATCAATAAGATTCTCCAGTTGCTC 57.435 36.000 0.00 0.00 43.42 4.26
2539 5521 9.638176 ATTAATCAATAAGATTCTCCAGTTGCT 57.362 29.630 0.00 0.00 43.42 3.91
2540 5522 9.674824 CATTAATCAATAAGATTCTCCAGTTGC 57.325 33.333 0.00 0.00 43.42 4.17
2557 5539 9.747898 ACTTGTATCCCTGTAAACATTAATCAA 57.252 29.630 0.00 0.00 0.00 2.57
2561 5543 9.452287 GGTTACTTGTATCCCTGTAAACATTAA 57.548 33.333 0.00 0.00 34.03 1.40
2562 5544 8.048514 GGGTTACTTGTATCCCTGTAAACATTA 58.951 37.037 15.95 0.00 35.13 1.90
2563 5545 6.888088 GGGTTACTTGTATCCCTGTAAACATT 59.112 38.462 15.95 0.00 35.13 2.71
2564 5546 6.420638 GGGTTACTTGTATCCCTGTAAACAT 58.579 40.000 15.95 0.00 35.13 2.71
2565 5547 5.807909 GGGTTACTTGTATCCCTGTAAACA 58.192 41.667 15.95 0.00 35.13 2.83
2573 5555 2.904697 CGGAGGGTTACTTGTATCCC 57.095 55.000 15.61 15.61 40.16 3.85
2589 5571 2.358619 CATTTTGGCTCCCCCGGA 59.641 61.111 0.73 0.00 35.87 5.14
2590 5572 3.460868 GCATTTTGGCTCCCCCGG 61.461 66.667 0.00 0.00 35.87 5.73
2591 5573 1.825281 TTTGCATTTTGGCTCCCCCG 61.825 55.000 0.00 0.00 35.87 5.73
2592 5574 0.620030 ATTTGCATTTTGGCTCCCCC 59.380 50.000 0.00 0.00 34.04 5.40
2593 5575 3.118298 ACATATTTGCATTTTGGCTCCCC 60.118 43.478 0.00 0.00 34.04 4.81
2594 5576 4.141233 ACATATTTGCATTTTGGCTCCC 57.859 40.909 0.00 0.00 34.04 4.30
2595 5577 6.282930 ACATACATATTTGCATTTTGGCTCC 58.717 36.000 0.00 0.00 34.04 4.70
2596 5578 7.205297 AGACATACATATTTGCATTTTGGCTC 58.795 34.615 0.00 0.00 34.04 4.70
2597 5579 7.116075 AGACATACATATTTGCATTTTGGCT 57.884 32.000 0.00 0.00 34.04 4.75
2598 5580 7.382218 GGTAGACATACATATTTGCATTTTGGC 59.618 37.037 0.00 0.00 33.21 4.52
2599 5581 7.867403 GGGTAGACATACATATTTGCATTTTGG 59.133 37.037 0.00 0.00 33.21 3.28
2600 5582 8.412456 TGGGTAGACATACATATTTGCATTTTG 58.588 33.333 0.00 0.00 33.21 2.44
2601 5583 8.413229 GTGGGTAGACATACATATTTGCATTTT 58.587 33.333 0.00 0.00 33.21 1.82
2602 5584 7.559533 TGTGGGTAGACATACATATTTGCATTT 59.440 33.333 0.00 0.00 33.21 2.32
2603 5585 7.059788 TGTGGGTAGACATACATATTTGCATT 58.940 34.615 0.00 0.00 33.21 3.56
2604 5586 6.600388 TGTGGGTAGACATACATATTTGCAT 58.400 36.000 0.00 0.00 33.21 3.96
2605 5587 5.995446 TGTGGGTAGACATACATATTTGCA 58.005 37.500 0.00 0.00 33.21 4.08
2606 5588 6.710295 TGATGTGGGTAGACATACATATTTGC 59.290 38.462 0.00 0.00 36.67 3.68
2607 5589 8.675705 TTGATGTGGGTAGACATACATATTTG 57.324 34.615 0.00 0.00 36.67 2.32
2608 5590 8.494433 ACTTGATGTGGGTAGACATACATATTT 58.506 33.333 0.00 0.00 36.67 1.40
2609 5591 8.034313 ACTTGATGTGGGTAGACATACATATT 57.966 34.615 0.00 0.00 36.67 1.28
2610 5592 7.618019 ACTTGATGTGGGTAGACATACATAT 57.382 36.000 0.00 0.00 36.67 1.78
2611 5593 7.562088 TGTACTTGATGTGGGTAGACATACATA 59.438 37.037 0.00 0.00 36.67 2.29
2612 5594 5.957771 ACTTGATGTGGGTAGACATACAT 57.042 39.130 0.00 0.00 36.67 2.29
2613 5595 5.717654 TGTACTTGATGTGGGTAGACATACA 59.282 40.000 0.00 0.00 36.67 2.29
2614 5596 6.127423 ACTGTACTTGATGTGGGTAGACATAC 60.127 42.308 0.00 0.00 36.67 2.39
2615 5597 5.955959 ACTGTACTTGATGTGGGTAGACATA 59.044 40.000 0.00 0.00 36.67 2.29
2616 5598 4.777896 ACTGTACTTGATGTGGGTAGACAT 59.222 41.667 0.00 0.00 39.34 3.06
2617 5599 4.021456 CACTGTACTTGATGTGGGTAGACA 60.021 45.833 0.00 0.00 0.00 3.41
2618 5600 4.495422 CACTGTACTTGATGTGGGTAGAC 58.505 47.826 0.00 0.00 0.00 2.59
2619 5601 3.513912 CCACTGTACTTGATGTGGGTAGA 59.486 47.826 0.00 0.00 44.33 2.59
2620 5602 3.861840 CCACTGTACTTGATGTGGGTAG 58.138 50.000 0.00 0.00 44.33 3.18
2621 5603 3.973206 CCACTGTACTTGATGTGGGTA 57.027 47.619 0.00 0.00 44.33 3.69
2622 5604 2.859165 CCACTGTACTTGATGTGGGT 57.141 50.000 0.00 0.00 44.33 4.51
2625 5607 1.466167 GCAGCCACTGTACTTGATGTG 59.534 52.381 0.00 0.00 33.43 3.21
2626 5608 1.611673 GGCAGCCACTGTACTTGATGT 60.612 52.381 6.55 0.00 33.43 3.06
2627 5609 1.089920 GGCAGCCACTGTACTTGATG 58.910 55.000 6.55 0.00 33.43 3.07
2628 5610 0.987294 AGGCAGCCACTGTACTTGAT 59.013 50.000 15.80 0.00 33.43 2.57
2629 5611 2.452116 AGGCAGCCACTGTACTTGA 58.548 52.632 15.80 0.00 33.43 3.02


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

AutoCloner maintained by Alex Coulton.