Multiple sequence alignment - TraesCS2B01G214200

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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 TraesCS2B01G214200 chr2B 100.000 2531 0 0 1 2531 199022040 199019510 0.000000e+00 4674.0
1 TraesCS2B01G214200 chr2D 89.134 2089 124 36 1 2024 141474354 141476404 0.000000e+00 2505.0
2 TraesCS2B01G214200 chr2D 87.546 538 39 9 1481 1993 553366191 553365657 4.660000e-167 597.0
3 TraesCS2B01G214200 chr2D 95.973 149 4 1 2385 2531 141476499 141476647 9.050000e-60 241.0
4 TraesCS2B01G214200 chr2A 90.726 1790 97 27 3 1758 159879629 159877875 0.000000e+00 2322.0
5 TraesCS2B01G214200 chr2A 93.878 147 9 0 2385 2531 159877389 159877243 3.280000e-54 222.0
6 TraesCS2B01G214200 chr2A 100.000 28 0 0 2130 2157 733522269 733522242 5.000000e-03 52.8
7 TraesCS2B01G214200 chrUn 88.462 546 34 9 1481 2000 22375513 22376055 1.280000e-177 632.0
8 TraesCS2B01G214200 chr1A 88.257 545 34 10 1481 2000 451521516 451522055 2.140000e-175 625.0
9 TraesCS2B01G214200 chr1A 87.523 545 38 12 1481 2000 552087274 552086735 1.000000e-168 603.0
10 TraesCS2B01G214200 chr6D 87.339 545 39 11 1481 2000 19564535 19565074 4.660000e-167 597.0
11 TraesCS2B01G214200 chr5A 86.472 547 43 14 1481 2000 19264853 19264311 2.820000e-159 571.0
12 TraesCS2B01G214200 chr7A 86.264 546 46 11 1481 2000 606317396 606317938 1.310000e-157 566.0
13 TraesCS2B01G214200 chr7A 86.055 545 43 14 1481 2000 110399076 110398540 2.840000e-154 555.0
14 TraesCS2B01G214200 chr4B 85.662 544 50 8 1481 2000 279320433 279320972 4.760000e-152 547.0
15 TraesCS2B01G214200 chr4D 87.465 359 25 7 1658 2000 346188487 346188841 1.820000e-106 396.0
16 TraesCS2B01G214200 chr4D 92.857 98 7 0 1481 1578 346158952 346159049 2.620000e-30 143.0
17 TraesCS2B01G214200 chr5D 90.637 267 16 2 1501 1758 485907524 485907258 1.860000e-91 346.0
18 TraesCS2B01G214200 chr5D 87.727 220 22 3 1783 2000 485907186 485906970 4.180000e-63 252.0


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 TraesCS2B01G214200 chr2B 199019510 199022040 2530 True 4674 4674 100.0000 1 2531 1 chr2B.!!$R1 2530
1 TraesCS2B01G214200 chr2D 141474354 141476647 2293 False 1373 2505 92.5535 1 2531 2 chr2D.!!$F1 2530
2 TraesCS2B01G214200 chr2D 553365657 553366191 534 True 597 597 87.5460 1481 1993 1 chr2D.!!$R1 512
3 TraesCS2B01G214200 chr2A 159877243 159879629 2386 True 1272 2322 92.3020 3 2531 2 chr2A.!!$R2 2528
4 TraesCS2B01G214200 chrUn 22375513 22376055 542 False 632 632 88.4620 1481 2000 1 chrUn.!!$F1 519
5 TraesCS2B01G214200 chr1A 451521516 451522055 539 False 625 625 88.2570 1481 2000 1 chr1A.!!$F1 519
6 TraesCS2B01G214200 chr1A 552086735 552087274 539 True 603 603 87.5230 1481 2000 1 chr1A.!!$R1 519
7 TraesCS2B01G214200 chr6D 19564535 19565074 539 False 597 597 87.3390 1481 2000 1 chr6D.!!$F1 519
8 TraesCS2B01G214200 chr5A 19264311 19264853 542 True 571 571 86.4720 1481 2000 1 chr5A.!!$R1 519
9 TraesCS2B01G214200 chr7A 606317396 606317938 542 False 566 566 86.2640 1481 2000 1 chr7A.!!$F1 519
10 TraesCS2B01G214200 chr7A 110398540 110399076 536 True 555 555 86.0550 1481 2000 1 chr7A.!!$R1 519
11 TraesCS2B01G214200 chr4B 279320433 279320972 539 False 547 547 85.6620 1481 2000 1 chr4B.!!$F1 519
12 TraesCS2B01G214200 chr5D 485906970 485907524 554 True 299 346 89.1820 1501 2000 2 chr5D.!!$R1 499

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
207 208 0.460987 GAGGCCAAGGATGTCAGACG 60.461 60.0 5.01 0.0 0.0 4.18 F
892 956 0.802222 CACGTGTCATGCGGGTAGAG 60.802 60.0 7.58 0.0 0.0 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1152 1231 0.031616 GGATGGAGGAGGAGACCAGT 60.032 60.0 0.00 0.0 37.12 4.0 R
2300 2573 0.036022 GGACAGCTTCAGCAGAACCT 59.964 55.0 0.75 0.0 45.16 3.5 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
78 79 4.037923 GGAGAAGCTCCTACAGAAGATGAG 59.962 50.000 6.23 0.00 46.41 2.90
150 151 4.431416 TGGAAGAAAGTGGTTTGAGCTA 57.569 40.909 0.00 0.00 0.00 3.32
207 208 0.460987 GAGGCCAAGGATGTCAGACG 60.461 60.000 5.01 0.00 0.00 4.18
427 428 1.135315 GCAAGAATCAGCCAATCGCAA 60.135 47.619 0.00 0.00 41.38 4.85
464 465 2.541588 CGTTGCACAAAGGTCAAAGAGG 60.542 50.000 0.00 0.00 0.00 3.69
504 505 6.313411 CGCCATCCATCAAATAAAAACATTGT 59.687 34.615 0.00 0.00 0.00 2.71
546 547 7.846107 GTGTGTTGTAATAGCATTTCTGATACG 59.154 37.037 0.00 0.00 0.00 3.06
556 557 7.156876 AGCATTTCTGATACGGATTTTGAAA 57.843 32.000 6.24 6.24 0.00 2.69
559 560 9.515020 GCATTTCTGATACGGATTTTGAAATTA 57.485 29.630 11.31 0.00 32.53 1.40
563 564 9.443323 TTCTGATACGGATTTTGAAATTACTGA 57.557 29.630 0.00 0.00 0.00 3.41
663 668 5.766150 AACTGTGTTGATGAAATTTCGGA 57.234 34.783 13.34 0.00 0.00 4.55
664 669 5.362556 ACTGTGTTGATGAAATTTCGGAG 57.637 39.130 13.34 3.24 0.00 4.63
665 670 4.159377 TGTGTTGATGAAATTTCGGAGC 57.841 40.909 13.34 0.50 0.00 4.70
679 695 3.981071 TCGGAGCTATGGATAATTGGG 57.019 47.619 0.00 0.00 0.00 4.12
682 698 4.841813 TCGGAGCTATGGATAATTGGGTTA 59.158 41.667 0.00 0.00 0.00 2.85
708 724 6.028146 TGATGGAATGTTGGAGAACAATTG 57.972 37.500 3.24 3.24 45.23 2.32
733 751 1.768684 GCCTGTGACCACCCTCTGAA 61.769 60.000 0.00 0.00 0.00 3.02
741 759 5.116882 GTGACCACCCTCTGAACATTATAC 58.883 45.833 0.00 0.00 0.00 1.47
751 783 6.701841 CCTCTGAACATTATACGCACTAACAT 59.298 38.462 0.00 0.00 0.00 2.71
796 860 7.607607 TGCACATTACTTCATCTTTATCTGTGT 59.392 33.333 0.00 0.00 34.33 3.72
797 861 7.907045 GCACATTACTTCATCTTTATCTGTGTG 59.093 37.037 0.00 0.00 34.33 3.82
799 863 7.607607 ACATTACTTCATCTTTATCTGTGTGCA 59.392 33.333 0.00 0.00 0.00 4.57
800 864 5.869753 ACTTCATCTTTATCTGTGTGCAC 57.130 39.130 10.75 10.75 0.00 4.57
801 865 5.308014 ACTTCATCTTTATCTGTGTGCACA 58.692 37.500 17.42 17.42 39.32 4.57
802 866 5.180117 ACTTCATCTTTATCTGTGTGCACAC 59.820 40.000 37.28 37.28 46.59 3.82
803 867 4.002982 TCATCTTTATCTGTGTGCACACC 58.997 43.478 39.34 24.98 45.88 4.16
804 868 3.483808 TCTTTATCTGTGTGCACACCA 57.516 42.857 39.34 28.75 45.88 4.17
805 869 3.138304 TCTTTATCTGTGTGCACACCAC 58.862 45.455 39.34 21.25 45.88 4.16
817 881 5.818136 GTGCACACCACATATACAAATCT 57.182 39.130 13.17 0.00 44.06 2.40
818 882 5.810525 GTGCACACCACATATACAAATCTC 58.189 41.667 13.17 0.00 44.06 2.75
819 883 5.586243 GTGCACACCACATATACAAATCTCT 59.414 40.000 13.17 0.00 44.06 3.10
820 884 5.585844 TGCACACCACATATACAAATCTCTG 59.414 40.000 0.00 0.00 0.00 3.35
821 885 5.586243 GCACACCACATATACAAATCTCTGT 59.414 40.000 0.00 0.00 0.00 3.41
822 886 6.761242 GCACACCACATATACAAATCTCTGTA 59.239 38.462 0.00 0.00 36.27 2.74
823 887 7.279981 GCACACCACATATACAAATCTCTGTAA 59.720 37.037 0.00 0.00 35.48 2.41
824 888 9.161629 CACACCACATATACAAATCTCTGTAAA 57.838 33.333 0.00 0.00 35.48 2.01
825 889 9.905713 ACACCACATATACAAATCTCTGTAAAT 57.094 29.630 0.00 0.00 35.48 1.40
827 891 9.905713 ACCACATATACAAATCTCTGTAAATGT 57.094 29.630 0.00 0.00 35.48 2.71
855 919 5.423886 AGAAAGCAGAGCAATTACCTCTAC 58.576 41.667 7.31 3.38 37.57 2.59
863 927 3.684788 AGCAATTACCTCTACAACTTGCG 59.315 43.478 0.00 0.00 41.64 4.85
865 929 2.754946 TTACCTCTACAACTTGCGGG 57.245 50.000 0.00 0.00 0.00 6.13
870 934 0.895530 TCTACAACTTGCGGGGAGAG 59.104 55.000 0.00 0.00 0.00 3.20
892 956 0.802222 CACGTGTCATGCGGGTAGAG 60.802 60.000 7.58 0.00 0.00 2.43
984 1048 4.316823 ACCCTCCACCTCCGCTCA 62.317 66.667 0.00 0.00 0.00 4.26
1082 1146 1.822613 CCTTCGCCATCAGCTGCAT 60.823 57.895 9.47 0.43 40.39 3.96
1168 1247 1.000771 CGACTGGTCTCCTCCTCCA 60.001 63.158 0.00 0.00 0.00 3.86
1176 1255 4.137615 TCCTCCTCCATCCGCCGA 62.138 66.667 0.00 0.00 0.00 5.54
1546 1626 3.996363 GCACTGATTGATTTTGTTTCCCC 59.004 43.478 0.00 0.00 0.00 4.81
1559 1639 3.215975 TGTTTCCCCGTTCGATTTCTTT 58.784 40.909 0.00 0.00 0.00 2.52
1562 1642 3.967332 TCCCCGTTCGATTTCTTTAGT 57.033 42.857 0.00 0.00 0.00 2.24
1642 1738 5.593909 TGTTCCTCAACTGTTGATGTGATTT 59.406 36.000 22.28 0.00 39.30 2.17
1664 1762 0.250295 TTGCGGCTGCTGTTCTACTT 60.250 50.000 20.27 0.00 43.34 2.24
1666 1764 1.639298 GCGGCTGCTGTTCTACTTGG 61.639 60.000 11.21 0.00 38.39 3.61
1695 1794 1.079503 GTTGGCGTCCTGATGAACTC 58.920 55.000 0.00 0.00 0.00 3.01
1737 1836 1.021968 GTTCGTCTGGTTTTGCTGGT 58.978 50.000 0.00 0.00 0.00 4.00
1776 1917 3.432933 ACGAATTCATTTGTTGCAATGGC 59.567 39.130 0.59 0.00 41.68 4.40
1817 2075 1.200020 GTTCAGTTATTTGCTGCCGCT 59.800 47.619 0.70 0.00 36.97 5.52
1820 2078 2.418628 TCAGTTATTTGCTGCCGCTAAC 59.581 45.455 0.70 2.40 33.90 2.34
1840 2098 4.357947 GCGGACGTGCTCTCACCA 62.358 66.667 5.27 0.00 40.04 4.17
1846 2104 2.547218 GGACGTGCTCTCACCAAGTTTA 60.547 50.000 0.00 0.00 40.04 2.01
1851 2109 2.972713 TGCTCTCACCAAGTTTAGAGGT 59.027 45.455 0.00 0.00 36.74 3.85
1852 2110 3.391296 TGCTCTCACCAAGTTTAGAGGTT 59.609 43.478 0.00 0.00 36.74 3.50
1853 2111 4.141482 TGCTCTCACCAAGTTTAGAGGTTT 60.141 41.667 0.00 0.00 36.74 3.27
1856 2114 6.513556 GCTCTCACCAAGTTTAGAGGTTTTTC 60.514 42.308 0.00 0.00 36.74 2.29
1890 2148 6.475504 TCAACTCTAGATCTTGGCAATTTGA 58.524 36.000 0.00 0.00 0.00 2.69
1891 2149 6.596888 TCAACTCTAGATCTTGGCAATTTGAG 59.403 38.462 0.00 5.92 0.00 3.02
1896 2154 3.767673 AGATCTTGGCAATTTGAGTGCAT 59.232 39.130 0.00 0.00 44.07 3.96
1966 2230 5.522641 ACCGAAATAGGACCCTCTTAGTTA 58.477 41.667 0.00 0.00 34.73 2.24
1980 2245 5.220739 CCTCTTAGTTAGCGAACGTTAGCTA 60.221 44.000 31.17 31.17 44.15 3.32
2017 2282 3.438216 TGGCATTTCCAACTGAGATGA 57.562 42.857 0.00 0.00 43.21 2.92
2018 2283 3.084039 TGGCATTTCCAACTGAGATGAC 58.916 45.455 0.00 0.00 42.63 3.06
2030 2295 3.574396 ACTGAGATGACAACTTCTTCGGA 59.426 43.478 0.00 0.00 34.28 4.55
2039 2304 5.818336 TGACAACTTCTTCGGAACAACATTA 59.182 36.000 0.00 0.00 0.00 1.90
2043 2308 6.877611 ACTTCTTCGGAACAACATTAACAT 57.122 33.333 0.00 0.00 0.00 2.71
2051 2316 7.142680 TCGGAACAACATTAACATTTTCTTCC 58.857 34.615 0.00 0.00 0.00 3.46
2115 2383 2.035066 AGCAACTAAAACAGCCAGCAAG 59.965 45.455 0.00 0.00 0.00 4.01
2119 2392 1.881973 CTAAAACAGCCAGCAAGAGCA 59.118 47.619 0.00 0.00 45.49 4.26
2125 2398 0.886563 AGCCAGCAAGAGCATTTGAC 59.113 50.000 4.58 0.00 45.49 3.18
2130 2403 2.161808 CAGCAAGAGCATTTGACCTCAG 59.838 50.000 4.58 0.00 45.49 3.35
2131 2404 2.039480 AGCAAGAGCATTTGACCTCAGA 59.961 45.455 4.58 0.00 45.49 3.27
2132 2405 2.419324 GCAAGAGCATTTGACCTCAGAG 59.581 50.000 4.58 0.00 41.58 3.35
2133 2406 2.399916 AGAGCATTTGACCTCAGAGC 57.600 50.000 0.00 0.00 0.00 4.09
2134 2407 1.627329 AGAGCATTTGACCTCAGAGCA 59.373 47.619 0.00 0.00 0.00 4.26
2135 2408 2.239150 AGAGCATTTGACCTCAGAGCAT 59.761 45.455 0.00 0.00 0.00 3.79
2136 2409 2.613133 GAGCATTTGACCTCAGAGCATC 59.387 50.000 0.00 0.00 0.00 3.91
2148 2421 2.378028 GAGCATCTCCAACAGACGC 58.622 57.895 0.00 0.00 40.90 5.19
2150 2423 0.671781 AGCATCTCCAACAGACGCAC 60.672 55.000 0.00 0.00 43.19 5.34
2151 2424 0.950555 GCATCTCCAACAGACGCACA 60.951 55.000 0.00 0.00 40.27 4.57
2153 2426 1.872952 CATCTCCAACAGACGCACAAA 59.127 47.619 0.00 0.00 32.26 2.83
2154 2427 2.031258 TCTCCAACAGACGCACAAAA 57.969 45.000 0.00 0.00 0.00 2.44
2155 2428 2.360844 TCTCCAACAGACGCACAAAAA 58.639 42.857 0.00 0.00 0.00 1.94
2156 2429 2.096819 TCTCCAACAGACGCACAAAAAC 59.903 45.455 0.00 0.00 0.00 2.43
2157 2430 1.813178 TCCAACAGACGCACAAAAACA 59.187 42.857 0.00 0.00 0.00 2.83
2158 2431 1.917303 CCAACAGACGCACAAAAACAC 59.083 47.619 0.00 0.00 0.00 3.32
2159 2432 1.577134 CAACAGACGCACAAAAACACG 59.423 47.619 0.00 0.00 0.00 4.49
2160 2433 0.522495 ACAGACGCACAAAAACACGC 60.522 50.000 0.00 0.00 0.00 5.34
2161 2434 0.522286 CAGACGCACAAAAACACGCA 60.522 50.000 0.00 0.00 0.00 5.24
2162 2435 0.169230 AGACGCACAAAAACACGCAA 59.831 45.000 0.00 0.00 0.00 4.85
2163 2436 1.196200 GACGCACAAAAACACGCAAT 58.804 45.000 0.00 0.00 0.00 3.56
2164 2437 0.919981 ACGCACAAAAACACGCAATG 59.080 45.000 0.00 0.00 0.00 2.82
2165 2438 0.381668 CGCACAAAAACACGCAATGC 60.382 50.000 0.00 0.00 0.00 3.56
2166 2439 0.649475 GCACAAAAACACGCAATGCA 59.351 45.000 5.91 0.00 0.00 3.96
2167 2440 1.061711 GCACAAAAACACGCAATGCAA 59.938 42.857 5.91 0.00 0.00 4.08
2168 2441 2.475187 GCACAAAAACACGCAATGCAAA 60.475 40.909 5.91 0.00 0.00 3.68
2169 2442 3.788135 GCACAAAAACACGCAATGCAAAT 60.788 39.130 5.91 0.00 0.00 2.32
2170 2443 4.341099 CACAAAAACACGCAATGCAAATT 58.659 34.783 5.91 0.00 0.00 1.82
2171 2444 4.202558 CACAAAAACACGCAATGCAAATTG 59.797 37.500 5.91 4.10 34.79 2.32
2172 2445 4.142730 ACAAAAACACGCAATGCAAATTGT 60.143 33.333 5.91 4.71 34.21 2.71
2173 2446 3.589061 AAACACGCAATGCAAATTGTG 57.411 38.095 5.91 11.16 44.89 3.33
2174 2447 2.505628 ACACGCAATGCAAATTGTGA 57.494 40.000 18.00 0.00 42.78 3.58
2175 2448 3.029320 ACACGCAATGCAAATTGTGAT 57.971 38.095 18.00 5.31 42.78 3.06
2176 2449 2.732500 ACACGCAATGCAAATTGTGATG 59.267 40.909 18.00 14.13 42.78 3.07
2177 2450 1.727880 ACGCAATGCAAATTGTGATGC 59.272 42.857 18.00 7.73 42.78 3.91
2178 2451 1.266647 CGCAATGCAAATTGTGATGCG 60.267 47.619 19.93 19.93 45.47 4.73
2179 2452 1.528198 GCAATGCAAATTGTGATGCGC 60.528 47.619 0.00 0.00 45.47 6.09
2180 2453 0.993532 AATGCAAATTGTGATGCGCG 59.006 45.000 0.00 0.00 45.47 6.86
2181 2454 1.415288 ATGCAAATTGTGATGCGCGC 61.415 50.000 27.26 27.26 45.47 6.86
2182 2455 2.087593 GCAAATTGTGATGCGCGCA 61.088 52.632 38.27 38.27 32.17 6.09
2183 2456 1.415288 GCAAATTGTGATGCGCGCAT 61.415 50.000 43.91 43.91 36.78 4.73
2184 2457 1.825077 CAAATTGTGATGCGCGCATA 58.175 45.000 43.27 29.58 36.78 3.14
2185 2458 2.183636 CAAATTGTGATGCGCGCATAA 58.816 42.857 43.27 35.68 36.78 1.90
2186 2459 2.780065 AATTGTGATGCGCGCATAAT 57.220 40.000 43.27 34.00 36.78 1.28
2187 2460 2.320805 ATTGTGATGCGCGCATAATC 57.679 45.000 43.27 32.47 36.78 1.75
2188 2461 0.307453 TTGTGATGCGCGCATAATCC 59.693 50.000 43.27 30.82 36.78 3.01
2189 2462 0.813210 TGTGATGCGCGCATAATCCA 60.813 50.000 43.27 32.93 36.70 3.41
2190 2463 0.110509 GTGATGCGCGCATAATCCAG 60.111 55.000 43.27 0.00 36.70 3.86
2191 2464 1.154338 GATGCGCGCATAATCCAGC 60.154 57.895 43.27 26.32 36.70 4.85
2192 2465 1.844771 GATGCGCGCATAATCCAGCA 61.845 55.000 43.27 15.19 36.70 4.41
2193 2466 2.051882 GCGCGCATAATCCAGCAC 60.052 61.111 29.10 0.00 0.00 4.40
2194 2467 2.633657 CGCGCATAATCCAGCACC 59.366 61.111 8.75 0.00 0.00 5.01
2195 2468 2.896801 CGCGCATAATCCAGCACCC 61.897 63.158 8.75 0.00 0.00 4.61
2196 2469 2.555547 GCGCATAATCCAGCACCCC 61.556 63.158 0.30 0.00 0.00 4.95
2197 2470 1.152984 CGCATAATCCAGCACCCCA 60.153 57.895 0.00 0.00 0.00 4.96
2198 2471 0.751277 CGCATAATCCAGCACCCCAA 60.751 55.000 0.00 0.00 0.00 4.12
2199 2472 0.746659 GCATAATCCAGCACCCCAAC 59.253 55.000 0.00 0.00 0.00 3.77
2200 2473 1.402787 CATAATCCAGCACCCCAACC 58.597 55.000 0.00 0.00 0.00 3.77
2201 2474 1.006813 ATAATCCAGCACCCCAACCA 58.993 50.000 0.00 0.00 0.00 3.67
2202 2475 0.780637 TAATCCAGCACCCCAACCAA 59.219 50.000 0.00 0.00 0.00 3.67
2203 2476 0.105246 AATCCAGCACCCCAACCAAA 60.105 50.000 0.00 0.00 0.00 3.28
2204 2477 0.116940 ATCCAGCACCCCAACCAAAT 59.883 50.000 0.00 0.00 0.00 2.32
2205 2478 0.105246 TCCAGCACCCCAACCAAATT 60.105 50.000 0.00 0.00 0.00 1.82
2206 2479 0.764271 CCAGCACCCCAACCAAATTT 59.236 50.000 0.00 0.00 0.00 1.82
2207 2480 1.974236 CCAGCACCCCAACCAAATTTA 59.026 47.619 0.00 0.00 0.00 1.40
2208 2481 2.289382 CCAGCACCCCAACCAAATTTAC 60.289 50.000 0.00 0.00 0.00 2.01
2209 2482 2.366916 CAGCACCCCAACCAAATTTACA 59.633 45.455 0.00 0.00 0.00 2.41
2210 2483 2.632512 AGCACCCCAACCAAATTTACAG 59.367 45.455 0.00 0.00 0.00 2.74
2211 2484 2.870035 GCACCCCAACCAAATTTACAGC 60.870 50.000 0.00 0.00 0.00 4.40
2212 2485 2.366916 CACCCCAACCAAATTTACAGCA 59.633 45.455 0.00 0.00 0.00 4.41
2213 2486 3.007831 CACCCCAACCAAATTTACAGCAT 59.992 43.478 0.00 0.00 0.00 3.79
2214 2487 3.007831 ACCCCAACCAAATTTACAGCATG 59.992 43.478 0.00 0.00 46.00 4.06
2215 2488 3.002102 CCCAACCAAATTTACAGCATGC 58.998 45.455 10.51 10.51 42.53 4.06
2216 2489 3.556633 CCCAACCAAATTTACAGCATGCA 60.557 43.478 21.98 0.00 42.53 3.96
2217 2490 4.255301 CCAACCAAATTTACAGCATGCAT 58.745 39.130 21.98 10.24 42.53 3.96
2218 2491 4.696402 CCAACCAAATTTACAGCATGCATT 59.304 37.500 21.98 7.45 42.53 3.56
2219 2492 5.873712 CCAACCAAATTTACAGCATGCATTA 59.126 36.000 21.98 7.35 42.53 1.90
2220 2493 6.036300 CCAACCAAATTTACAGCATGCATTAG 59.964 38.462 21.98 9.13 42.53 1.73
2221 2494 5.111293 ACCAAATTTACAGCATGCATTAGC 58.889 37.500 21.98 0.00 42.53 3.09
2222 2495 4.207635 CCAAATTTACAGCATGCATTAGCG 59.792 41.667 21.98 3.15 46.23 4.26
2223 2496 2.473530 TTTACAGCATGCATTAGCGC 57.526 45.000 21.98 0.00 46.23 5.92
2224 2497 1.667236 TTACAGCATGCATTAGCGCT 58.333 45.000 21.98 17.26 46.23 5.92
2225 2498 1.667236 TACAGCATGCATTAGCGCTT 58.333 45.000 18.68 0.00 46.23 4.68
2226 2499 0.813184 ACAGCATGCATTAGCGCTTT 59.187 45.000 18.68 0.00 46.23 3.51
2227 2500 1.203052 ACAGCATGCATTAGCGCTTTT 59.797 42.857 18.68 0.00 46.23 2.27
2228 2501 2.264813 CAGCATGCATTAGCGCTTTTT 58.735 42.857 18.68 0.00 46.23 1.94
2229 2502 2.280708 CAGCATGCATTAGCGCTTTTTC 59.719 45.455 18.68 3.63 46.23 2.29
2230 2503 2.094597 AGCATGCATTAGCGCTTTTTCA 60.095 40.909 18.68 10.01 46.23 2.69
2231 2504 2.028404 GCATGCATTAGCGCTTTTTCAC 59.972 45.455 18.68 1.05 46.23 3.18
2232 2505 3.504863 CATGCATTAGCGCTTTTTCACT 58.495 40.909 18.68 0.00 46.23 3.41
2233 2506 3.641437 TGCATTAGCGCTTTTTCACTT 57.359 38.095 18.68 0.00 46.23 3.16
2234 2507 3.307674 TGCATTAGCGCTTTTTCACTTG 58.692 40.909 18.68 3.30 46.23 3.16
2235 2508 3.243367 TGCATTAGCGCTTTTTCACTTGT 60.243 39.130 18.68 0.00 46.23 3.16
2236 2509 4.023622 TGCATTAGCGCTTTTTCACTTGTA 60.024 37.500 18.68 0.00 46.23 2.41
2237 2510 5.095490 GCATTAGCGCTTTTTCACTTGTAT 58.905 37.500 18.68 0.00 0.00 2.29
2238 2511 5.228012 GCATTAGCGCTTTTTCACTTGTATC 59.772 40.000 18.68 0.00 0.00 2.24
2239 2512 3.831715 AGCGCTTTTTCACTTGTATCC 57.168 42.857 2.64 0.00 0.00 2.59
2240 2513 3.146066 AGCGCTTTTTCACTTGTATCCA 58.854 40.909 2.64 0.00 0.00 3.41
2241 2514 3.568007 AGCGCTTTTTCACTTGTATCCAA 59.432 39.130 2.64 0.00 0.00 3.53
2242 2515 3.668656 GCGCTTTTTCACTTGTATCCAAC 59.331 43.478 0.00 0.00 0.00 3.77
2243 2516 4.226761 CGCTTTTTCACTTGTATCCAACC 58.773 43.478 0.00 0.00 0.00 3.77
2244 2517 4.023193 CGCTTTTTCACTTGTATCCAACCT 60.023 41.667 0.00 0.00 0.00 3.50
2245 2518 5.507315 CGCTTTTTCACTTGTATCCAACCTT 60.507 40.000 0.00 0.00 0.00 3.50
2246 2519 6.280643 GCTTTTTCACTTGTATCCAACCTTT 58.719 36.000 0.00 0.00 0.00 3.11
2247 2520 6.761242 GCTTTTTCACTTGTATCCAACCTTTT 59.239 34.615 0.00 0.00 0.00 2.27
2248 2521 7.279981 GCTTTTTCACTTGTATCCAACCTTTTT 59.720 33.333 0.00 0.00 0.00 1.94
2249 2522 8.710835 TTTTTCACTTGTATCCAACCTTTTTC 57.289 30.769 0.00 0.00 0.00 2.29
2250 2523 7.411486 TTTCACTTGTATCCAACCTTTTTCA 57.589 32.000 0.00 0.00 0.00 2.69
2251 2524 6.385649 TCACTTGTATCCAACCTTTTTCAC 57.614 37.500 0.00 0.00 0.00 3.18
2252 2525 5.300792 TCACTTGTATCCAACCTTTTTCACC 59.699 40.000 0.00 0.00 0.00 4.02
2253 2526 5.301805 CACTTGTATCCAACCTTTTTCACCT 59.698 40.000 0.00 0.00 0.00 4.00
2254 2527 5.897250 ACTTGTATCCAACCTTTTTCACCTT 59.103 36.000 0.00 0.00 0.00 3.50
2255 2528 6.382859 ACTTGTATCCAACCTTTTTCACCTTT 59.617 34.615 0.00 0.00 0.00 3.11
2256 2529 6.800072 TGTATCCAACCTTTTTCACCTTTT 57.200 33.333 0.00 0.00 0.00 2.27
2257 2530 7.189079 TGTATCCAACCTTTTTCACCTTTTT 57.811 32.000 0.00 0.00 0.00 1.94
2278 2551 6.375830 TTTTTACCCAACCTTTTTCACCTT 57.624 33.333 0.00 0.00 0.00 3.50
2279 2552 6.375830 TTTTACCCAACCTTTTTCACCTTT 57.624 33.333 0.00 0.00 0.00 3.11
2280 2553 6.375830 TTTACCCAACCTTTTTCACCTTTT 57.624 33.333 0.00 0.00 0.00 2.27
2281 2554 4.919774 ACCCAACCTTTTTCACCTTTTT 57.080 36.364 0.00 0.00 0.00 1.94
2303 2576 7.733402 TTTTAACACGAGCTATTTTACAGGT 57.267 32.000 0.00 0.00 0.00 4.00
2304 2577 7.733402 TTTAACACGAGCTATTTTACAGGTT 57.267 32.000 0.00 0.00 0.00 3.50
2305 2578 5.857822 AACACGAGCTATTTTACAGGTTC 57.142 39.130 0.00 0.00 0.00 3.62
2306 2579 5.148651 ACACGAGCTATTTTACAGGTTCT 57.851 39.130 0.00 0.00 0.00 3.01
2307 2580 4.929808 ACACGAGCTATTTTACAGGTTCTG 59.070 41.667 0.00 0.00 37.52 3.02
2308 2581 3.933332 ACGAGCTATTTTACAGGTTCTGC 59.067 43.478 0.00 0.00 34.37 4.26
2309 2582 4.184629 CGAGCTATTTTACAGGTTCTGCT 58.815 43.478 0.00 0.00 34.37 4.24
2310 2583 4.033358 CGAGCTATTTTACAGGTTCTGCTG 59.967 45.833 0.00 0.00 34.37 4.41
2311 2584 5.165961 AGCTATTTTACAGGTTCTGCTGA 57.834 39.130 0.00 0.00 34.37 4.26
2312 2585 5.560724 AGCTATTTTACAGGTTCTGCTGAA 58.439 37.500 1.33 1.33 34.37 3.02
2313 2586 5.645497 AGCTATTTTACAGGTTCTGCTGAAG 59.355 40.000 6.24 0.00 34.37 3.02
2319 2592 2.549332 GGTTCTGCTGAAGCTGTCC 58.451 57.895 23.39 10.38 44.58 4.02
2320 2593 0.250467 GGTTCTGCTGAAGCTGTCCA 60.250 55.000 23.39 0.00 44.58 4.02
2321 2594 1.155042 GTTCTGCTGAAGCTGTCCAG 58.845 55.000 6.24 6.65 42.66 3.86
2350 2623 4.657436 AAAACCCGAATTTTAGCACACA 57.343 36.364 0.00 0.00 29.93 3.72
2351 2624 4.657436 AAACCCGAATTTTAGCACACAA 57.343 36.364 0.00 0.00 0.00 3.33
2352 2625 3.915437 ACCCGAATTTTAGCACACAAG 57.085 42.857 0.00 0.00 0.00 3.16
2353 2626 2.556622 ACCCGAATTTTAGCACACAAGG 59.443 45.455 0.00 0.00 0.00 3.61
2354 2627 2.595386 CCGAATTTTAGCACACAAGGC 58.405 47.619 0.00 0.00 0.00 4.35
2355 2628 2.030363 CCGAATTTTAGCACACAAGGCA 60.030 45.455 0.00 0.00 0.00 4.75
2356 2629 3.236816 CGAATTTTAGCACACAAGGCAG 58.763 45.455 0.00 0.00 0.00 4.85
2357 2630 3.304659 CGAATTTTAGCACACAAGGCAGT 60.305 43.478 0.00 0.00 0.00 4.40
2358 2631 4.620982 GAATTTTAGCACACAAGGCAGTT 58.379 39.130 0.00 0.00 0.00 3.16
2359 2632 4.670896 ATTTTAGCACACAAGGCAGTTT 57.329 36.364 0.00 0.00 0.00 2.66
2360 2633 4.464069 TTTTAGCACACAAGGCAGTTTT 57.536 36.364 0.00 0.00 0.00 2.43
2361 2634 4.464069 TTTAGCACACAAGGCAGTTTTT 57.536 36.364 0.00 0.00 0.00 1.94
2362 2635 2.298411 AGCACACAAGGCAGTTTTTG 57.702 45.000 0.00 0.00 0.00 2.44
2363 2636 1.134729 AGCACACAAGGCAGTTTTTGG 60.135 47.619 0.00 0.00 0.00 3.28
2364 2637 1.938625 CACACAAGGCAGTTTTTGGG 58.061 50.000 0.00 0.00 33.94 4.12
2365 2638 0.177836 ACACAAGGCAGTTTTTGGGC 59.822 50.000 0.00 0.00 30.85 5.36
2366 2639 0.875474 CACAAGGCAGTTTTTGGGCG 60.875 55.000 0.00 0.00 34.32 6.13
2367 2640 1.955663 CAAGGCAGTTTTTGGGCGC 60.956 57.895 0.00 0.00 34.32 6.53
2368 2641 2.430610 AAGGCAGTTTTTGGGCGCA 61.431 52.632 10.83 0.00 34.32 6.09
2369 2642 1.757423 AAGGCAGTTTTTGGGCGCAT 61.757 50.000 10.83 0.00 34.32 4.73
2370 2643 0.897863 AGGCAGTTTTTGGGCGCATA 60.898 50.000 10.83 0.00 34.32 3.14
2371 2644 0.175531 GGCAGTTTTTGGGCGCATAT 59.824 50.000 10.83 0.00 0.00 1.78
2372 2645 1.405391 GGCAGTTTTTGGGCGCATATT 60.405 47.619 10.83 0.00 0.00 1.28
2373 2646 1.660104 GCAGTTTTTGGGCGCATATTG 59.340 47.619 10.83 2.04 0.00 1.90
2374 2647 2.673610 GCAGTTTTTGGGCGCATATTGA 60.674 45.455 10.83 0.00 0.00 2.57
2375 2648 3.583806 CAGTTTTTGGGCGCATATTGAA 58.416 40.909 10.83 0.00 0.00 2.69
2376 2649 3.993081 CAGTTTTTGGGCGCATATTGAAA 59.007 39.130 10.83 0.00 0.00 2.69
2377 2650 4.091800 CAGTTTTTGGGCGCATATTGAAAG 59.908 41.667 10.83 0.00 0.00 2.62
2378 2651 4.021544 AGTTTTTGGGCGCATATTGAAAGA 60.022 37.500 10.83 0.00 0.00 2.52
2379 2652 4.527509 TTTTGGGCGCATATTGAAAGAA 57.472 36.364 10.83 0.00 0.00 2.52
2380 2653 4.527509 TTTGGGCGCATATTGAAAGAAA 57.472 36.364 10.83 0.00 0.00 2.52
2381 2654 4.527509 TTGGGCGCATATTGAAAGAAAA 57.472 36.364 10.83 0.00 0.00 2.29
2382 2655 4.527509 TGGGCGCATATTGAAAGAAAAA 57.472 36.364 10.83 0.00 0.00 1.94
2450 2725 9.994432 ATACAGAAAGAAGAGCAAAAATTATCG 57.006 29.630 0.00 0.00 0.00 2.92
2481 2756 4.024048 TCCTTCGCAGAGAAACACAATTTC 60.024 41.667 0.00 0.00 38.57 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.877097 TTGCTGTGATGGCTCCTTTA 57.123 45.000 0.00 0.00 0.00 1.85
17 18 1.959282 CTTCCAAGCTGTTCCTTTGCT 59.041 47.619 0.00 0.00 38.87 3.91
78 79 1.915141 CATGGGAGGTTCCATATGCC 58.085 55.000 0.00 0.00 45.08 4.40
150 151 2.555757 GGCTGATTTCTGTGCTTTGAGT 59.444 45.455 0.00 0.00 0.00 3.41
207 208 0.703466 CGTCGTCGTTTGCTTCTCTC 59.297 55.000 0.00 0.00 0.00 3.20
310 311 1.630878 ACCAGTGACCTCAATTCCTCC 59.369 52.381 0.00 0.00 0.00 4.30
427 428 1.066573 CAACGCACATCTCTTCCTCCT 60.067 52.381 0.00 0.00 0.00 3.69
504 505 2.108075 ACACACAACAGGATCAATGGGA 59.892 45.455 0.00 0.00 0.00 4.37
577 578 6.815089 ACATGAACAGCAAATCAAAACCTTA 58.185 32.000 0.00 0.00 0.00 2.69
583 584 7.547019 TGTTTACAACATGAACAGCAAATCAAA 59.453 29.630 0.00 0.00 36.25 2.69
628 629 7.552687 TCATCAACACAGTTACACTTTCTTCTT 59.447 33.333 0.00 0.00 0.00 2.52
630 631 7.246674 TCATCAACACAGTTACACTTTCTTC 57.753 36.000 0.00 0.00 0.00 2.87
632 633 7.624360 TTTCATCAACACAGTTACACTTTCT 57.376 32.000 0.00 0.00 0.00 2.52
644 645 3.820467 AGCTCCGAAATTTCATCAACACA 59.180 39.130 17.99 0.00 0.00 3.72
645 646 4.425577 AGCTCCGAAATTTCATCAACAC 57.574 40.909 17.99 1.04 0.00 3.32
660 665 3.703001 ACCCAATTATCCATAGCTCCG 57.297 47.619 0.00 0.00 0.00 4.63
663 668 5.310594 TCAGCTAACCCAATTATCCATAGCT 59.689 40.000 0.00 0.00 43.81 3.32
664 669 5.560724 TCAGCTAACCCAATTATCCATAGC 58.439 41.667 0.00 0.00 35.65 2.97
665 670 6.600822 CCATCAGCTAACCCAATTATCCATAG 59.399 42.308 0.00 0.00 0.00 2.23
679 695 4.517285 TCTCCAACATTCCATCAGCTAAC 58.483 43.478 0.00 0.00 0.00 2.34
682 698 3.245016 TGTTCTCCAACATTCCATCAGCT 60.245 43.478 0.00 0.00 37.61 4.24
708 724 1.600916 GGTGGTCACAGGCAGAACC 60.601 63.158 3.40 0.00 39.61 3.62
733 751 8.888716 TCAAAATCATGTTAGTGCGTATAATGT 58.111 29.630 0.00 0.00 0.00 2.71
741 759 4.346734 AGCTCAAAATCATGTTAGTGCG 57.653 40.909 0.00 0.00 0.00 5.34
751 783 8.681486 ATGTGCATAGTATAAGCTCAAAATCA 57.319 30.769 0.00 0.00 41.19 2.57
779 843 5.625251 GTGTGCACACAGATAAAGATGAAG 58.375 41.667 38.42 0.00 45.75 3.02
793 857 4.757799 TTTGTATATGTGGTGTGCACAC 57.242 40.909 36.56 36.56 45.72 3.82
796 860 5.585844 CAGAGATTTGTATATGTGGTGTGCA 59.414 40.000 0.00 0.00 0.00 4.57
797 861 5.586243 ACAGAGATTTGTATATGTGGTGTGC 59.414 40.000 0.00 0.00 0.00 4.57
799 863 9.905713 ATTTACAGAGATTTGTATATGTGGTGT 57.094 29.630 0.00 0.00 33.81 4.16
801 865 9.905713 ACATTTACAGAGATTTGTATATGTGGT 57.094 29.630 16.13 0.00 45.73 4.16
810 874 9.778741 TTTCTCTACACATTTACAGAGATTTGT 57.221 29.630 1.31 0.00 42.23 2.83
812 876 8.940952 GCTTTCTCTACACATTTACAGAGATTT 58.059 33.333 1.31 0.00 42.23 2.17
813 877 8.097038 TGCTTTCTCTACACATTTACAGAGATT 58.903 33.333 1.31 0.00 42.23 2.40
814 878 7.615403 TGCTTTCTCTACACATTTACAGAGAT 58.385 34.615 1.31 0.00 42.23 2.75
815 879 6.993079 TGCTTTCTCTACACATTTACAGAGA 58.007 36.000 0.00 0.00 41.28 3.10
816 880 7.093354 TCTGCTTTCTCTACACATTTACAGAG 58.907 38.462 0.00 0.00 36.64 3.35
817 881 6.993079 TCTGCTTTCTCTACACATTTACAGA 58.007 36.000 0.00 0.00 0.00 3.41
818 882 6.183360 GCTCTGCTTTCTCTACACATTTACAG 60.183 42.308 0.00 0.00 0.00 2.74
819 883 5.639506 GCTCTGCTTTCTCTACACATTTACA 59.360 40.000 0.00 0.00 0.00 2.41
820 884 5.639506 TGCTCTGCTTTCTCTACACATTTAC 59.360 40.000 0.00 0.00 0.00 2.01
821 885 5.793817 TGCTCTGCTTTCTCTACACATTTA 58.206 37.500 0.00 0.00 0.00 1.40
822 886 4.645535 TGCTCTGCTTTCTCTACACATTT 58.354 39.130 0.00 0.00 0.00 2.32
823 887 4.277515 TGCTCTGCTTTCTCTACACATT 57.722 40.909 0.00 0.00 0.00 2.71
824 888 3.969287 TGCTCTGCTTTCTCTACACAT 57.031 42.857 0.00 0.00 0.00 3.21
825 889 3.751479 TTGCTCTGCTTTCTCTACACA 57.249 42.857 0.00 0.00 0.00 3.72
826 890 5.064071 GGTAATTGCTCTGCTTTCTCTACAC 59.936 44.000 0.00 0.00 0.00 2.90
827 891 5.046304 AGGTAATTGCTCTGCTTTCTCTACA 60.046 40.000 0.00 0.00 0.00 2.74
828 892 5.423886 AGGTAATTGCTCTGCTTTCTCTAC 58.576 41.667 0.00 0.00 0.00 2.59
829 893 5.423610 AGAGGTAATTGCTCTGCTTTCTCTA 59.576 40.000 0.00 0.00 0.00 2.43
830 894 4.224818 AGAGGTAATTGCTCTGCTTTCTCT 59.775 41.667 0.00 0.00 0.00 3.10
831 895 4.512484 AGAGGTAATTGCTCTGCTTTCTC 58.488 43.478 0.00 0.00 0.00 2.87
832 896 4.566426 AGAGGTAATTGCTCTGCTTTCT 57.434 40.909 0.00 0.00 0.00 2.52
833 897 5.178797 TGTAGAGGTAATTGCTCTGCTTTC 58.821 41.667 0.00 0.00 32.39 2.62
834 898 5.165961 TGTAGAGGTAATTGCTCTGCTTT 57.834 39.130 0.00 0.00 32.39 3.51
855 919 2.032528 TGCTCTCCCCGCAAGTTG 59.967 61.111 0.00 0.00 33.87 3.16
863 927 2.048127 GACACGTGTGCTCTCCCC 60.048 66.667 28.82 4.79 0.00 4.81
865 929 1.630244 GCATGACACGTGTGCTCTCC 61.630 60.000 28.82 11.09 36.02 3.71
870 934 4.088762 CCCGCATGACACGTGTGC 62.089 66.667 28.82 21.96 35.59 4.57
974 1038 4.070552 GCGGAGTTGAGCGGAGGT 62.071 66.667 0.00 0.00 46.54 3.85
984 1048 0.249489 GCATAGTGATCCGCGGAGTT 60.249 55.000 33.87 18.58 0.00 3.01
1152 1231 0.031616 GGATGGAGGAGGAGACCAGT 60.032 60.000 0.00 0.00 37.12 4.00
1368 1447 2.131067 CCTCTTCCTCCTCCTCGCC 61.131 68.421 0.00 0.00 0.00 5.54
1546 1626 7.304849 GCAAATGCATACTAAAGAAATCGAACG 60.305 37.037 0.00 0.00 41.59 3.95
1559 1639 2.353269 CGTTTCGGGCAAATGCATACTA 59.647 45.455 0.00 0.00 44.36 1.82
1562 1642 0.453793 CCGTTTCGGGCAAATGCATA 59.546 50.000 0.00 0.00 44.15 3.14
1584 1680 4.278419 GCACAAGGAAACCTACAATTCTGT 59.722 41.667 0.00 0.00 39.75 3.41
1642 1738 0.533978 TAGAACAGCAGCCGCAACAA 60.534 50.000 0.00 0.00 42.27 2.83
1664 1762 1.675310 CGCCAACAGAATGCCTCCA 60.675 57.895 0.00 0.00 42.53 3.86
1666 1764 1.648467 GGACGCCAACAGAATGCCTC 61.648 60.000 0.00 0.00 42.53 4.70
1695 1794 3.005554 AGATGCTCCAAATCAACAGTCG 58.994 45.455 0.00 0.00 0.00 4.18
1737 1836 3.333029 TCGTTGATGCTTCCATCTCAA 57.667 42.857 5.41 0.00 46.43 3.02
1772 1913 3.131577 CCATTTCAGCAACACATAGCCAT 59.868 43.478 0.00 0.00 0.00 4.40
1776 1917 6.149308 TGAACTACCATTTCAGCAACACATAG 59.851 38.462 0.00 0.00 0.00 2.23
1817 2075 0.731417 GAGAGCACGTCCGCTAGTTA 59.269 55.000 0.00 0.00 44.01 2.24
1820 2078 1.226435 GTGAGAGCACGTCCGCTAG 60.226 63.158 0.00 0.00 44.01 3.42
1846 2104 9.278978 GAGTTGATTCTAAGAAGAAAAACCTCT 57.721 33.333 10.82 0.00 44.75 3.69
1856 2114 9.748708 CCAAGATCTAGAGTTGATTCTAAGAAG 57.251 37.037 15.94 0.00 0.00 2.85
1966 2230 0.739561 CCTCCTAGCTAACGTTCGCT 59.260 55.000 27.48 27.48 40.15 4.93
2006 2271 4.151335 CCGAAGAAGTTGTCATCTCAGTTG 59.849 45.833 0.00 0.00 0.00 3.16
2010 2275 4.202212 TGTTCCGAAGAAGTTGTCATCTCA 60.202 41.667 0.00 0.00 30.91 3.27
2011 2276 4.307432 TGTTCCGAAGAAGTTGTCATCTC 58.693 43.478 0.00 0.00 30.91 2.75
2012 2277 4.336889 TGTTCCGAAGAAGTTGTCATCT 57.663 40.909 0.00 0.00 30.91 2.90
2013 2278 4.272504 TGTTGTTCCGAAGAAGTTGTCATC 59.727 41.667 0.00 0.00 30.91 2.92
2014 2279 4.196193 TGTTGTTCCGAAGAAGTTGTCAT 58.804 39.130 0.00 0.00 30.91 3.06
2015 2280 3.601435 TGTTGTTCCGAAGAAGTTGTCA 58.399 40.909 0.00 0.00 30.91 3.58
2016 2281 4.813296 ATGTTGTTCCGAAGAAGTTGTC 57.187 40.909 0.00 0.00 30.91 3.18
2017 2282 6.094325 TGTTAATGTTGTTCCGAAGAAGTTGT 59.906 34.615 0.00 0.00 30.91 3.32
2018 2283 6.491394 TGTTAATGTTGTTCCGAAGAAGTTG 58.509 36.000 0.00 0.00 30.91 3.16
2030 2295 9.883142 TTCTTGGAAGAAAATGTTAATGTTGTT 57.117 25.926 0.00 0.00 41.75 2.83
2066 2331 4.344679 AGATCAAATGGTGGCAGTTTTCAA 59.655 37.500 0.00 0.00 0.00 2.69
2067 2332 3.896888 AGATCAAATGGTGGCAGTTTTCA 59.103 39.130 0.00 0.00 0.00 2.69
2068 2333 4.022068 TGAGATCAAATGGTGGCAGTTTTC 60.022 41.667 0.00 0.00 0.00 2.29
2115 2383 2.105006 TGCTCTGAGGTCAAATGCTC 57.895 50.000 6.83 0.00 0.00 4.26
2119 2392 2.842496 TGGAGATGCTCTGAGGTCAAAT 59.158 45.455 6.83 0.00 0.00 2.32
2125 2398 1.829849 TCTGTTGGAGATGCTCTGAGG 59.170 52.381 6.83 0.00 0.00 3.86
2133 2406 1.511850 TTGTGCGTCTGTTGGAGATG 58.488 50.000 0.00 0.00 40.33 2.90
2134 2407 2.254546 TTTGTGCGTCTGTTGGAGAT 57.745 45.000 0.00 0.00 31.63 2.75
2135 2408 2.031258 TTTTGTGCGTCTGTTGGAGA 57.969 45.000 0.00 0.00 0.00 3.71
2136 2409 2.159448 TGTTTTTGTGCGTCTGTTGGAG 60.159 45.455 0.00 0.00 0.00 3.86
2137 2410 1.813178 TGTTTTTGTGCGTCTGTTGGA 59.187 42.857 0.00 0.00 0.00 3.53
2138 2411 1.917303 GTGTTTTTGTGCGTCTGTTGG 59.083 47.619 0.00 0.00 0.00 3.77
2139 2412 1.577134 CGTGTTTTTGTGCGTCTGTTG 59.423 47.619 0.00 0.00 0.00 3.33
2140 2413 1.889891 CGTGTTTTTGTGCGTCTGTT 58.110 45.000 0.00 0.00 0.00 3.16
2141 2414 0.522495 GCGTGTTTTTGTGCGTCTGT 60.522 50.000 0.00 0.00 0.00 3.41
2142 2415 0.522286 TGCGTGTTTTTGTGCGTCTG 60.522 50.000 0.00 0.00 0.00 3.51
2146 2419 0.381668 GCATTGCGTGTTTTTGTGCG 60.382 50.000 0.00 0.00 0.00 5.34
2147 2420 0.649475 TGCATTGCGTGTTTTTGTGC 59.351 45.000 3.84 0.00 0.00 4.57
2148 2421 3.380486 TTTGCATTGCGTGTTTTTGTG 57.620 38.095 3.84 0.00 0.00 3.33
2150 2423 4.202558 CACAATTTGCATTGCGTGTTTTTG 59.797 37.500 3.84 4.92 43.39 2.44
2151 2424 4.093998 TCACAATTTGCATTGCGTGTTTTT 59.906 33.333 3.84 0.00 43.39 1.94
2153 2426 3.193263 TCACAATTTGCATTGCGTGTTT 58.807 36.364 3.84 0.00 43.39 2.83
2154 2427 2.819115 TCACAATTTGCATTGCGTGTT 58.181 38.095 3.84 0.00 43.39 3.32
2155 2428 2.505628 TCACAATTTGCATTGCGTGT 57.494 40.000 3.84 2.99 43.39 4.49
2156 2429 2.473212 GCATCACAATTTGCATTGCGTG 60.473 45.455 3.84 5.78 43.39 5.34
2157 2430 1.727880 GCATCACAATTTGCATTGCGT 59.272 42.857 3.84 0.00 43.39 5.24
2158 2431 1.266647 CGCATCACAATTTGCATTGCG 60.267 47.619 19.14 19.14 43.39 4.85
2159 2432 1.528198 GCGCATCACAATTTGCATTGC 60.528 47.619 0.30 0.46 43.39 3.56
2160 2433 1.266647 CGCGCATCACAATTTGCATTG 60.267 47.619 8.75 0.00 44.90 2.82
2161 2434 0.993532 CGCGCATCACAATTTGCATT 59.006 45.000 8.75 0.00 38.80 3.56
2162 2435 1.415288 GCGCGCATCACAATTTGCAT 61.415 50.000 29.10 0.00 38.80 3.96
2163 2436 2.087593 GCGCGCATCACAATTTGCA 61.088 52.632 29.10 0.00 38.80 4.08
2164 2437 1.415288 ATGCGCGCATCACAATTTGC 61.415 50.000 39.13 2.13 35.50 3.68
2165 2438 1.825077 TATGCGCGCATCACAATTTG 58.175 45.000 46.16 0.00 37.82 2.32
2166 2439 2.558265 TTATGCGCGCATCACAATTT 57.442 40.000 46.16 26.07 37.82 1.82
2167 2440 2.605338 GGATTATGCGCGCATCACAATT 60.605 45.455 46.16 26.84 37.82 2.32
2168 2441 1.069022 GGATTATGCGCGCATCACAAT 60.069 47.619 46.16 37.34 37.82 2.71
2169 2442 0.307453 GGATTATGCGCGCATCACAA 59.693 50.000 46.16 34.76 37.82 3.33
2170 2443 0.813210 TGGATTATGCGCGCATCACA 60.813 50.000 46.16 34.12 37.82 3.58
2171 2444 0.110509 CTGGATTATGCGCGCATCAC 60.111 55.000 46.16 34.10 37.82 3.06
2172 2445 1.844771 GCTGGATTATGCGCGCATCA 61.845 55.000 46.16 37.07 37.82 3.07
2173 2446 1.154338 GCTGGATTATGCGCGCATC 60.154 57.895 46.16 33.45 37.82 3.91
2174 2447 1.893335 TGCTGGATTATGCGCGCAT 60.893 52.632 43.68 43.68 40.19 4.73
2175 2448 2.513435 TGCTGGATTATGCGCGCA 60.513 55.556 38.27 38.27 0.00 6.09
2176 2449 2.051882 GTGCTGGATTATGCGCGC 60.052 61.111 27.26 27.26 0.00 6.86
2177 2450 2.633657 GGTGCTGGATTATGCGCG 59.366 61.111 0.00 0.00 40.21 6.86
2178 2451 2.555547 GGGGTGCTGGATTATGCGC 61.556 63.158 0.00 0.00 38.78 6.09
2179 2452 0.751277 TTGGGGTGCTGGATTATGCG 60.751 55.000 0.00 0.00 0.00 4.73
2180 2453 0.746659 GTTGGGGTGCTGGATTATGC 59.253 55.000 0.00 0.00 0.00 3.14
2181 2454 1.341877 TGGTTGGGGTGCTGGATTATG 60.342 52.381 0.00 0.00 0.00 1.90
2182 2455 1.006813 TGGTTGGGGTGCTGGATTAT 58.993 50.000 0.00 0.00 0.00 1.28
2183 2456 0.780637 TTGGTTGGGGTGCTGGATTA 59.219 50.000 0.00 0.00 0.00 1.75
2184 2457 0.105246 TTTGGTTGGGGTGCTGGATT 60.105 50.000 0.00 0.00 0.00 3.01
2185 2458 0.116940 ATTTGGTTGGGGTGCTGGAT 59.883 50.000 0.00 0.00 0.00 3.41
2186 2459 0.105246 AATTTGGTTGGGGTGCTGGA 60.105 50.000 0.00 0.00 0.00 3.86
2187 2460 0.764271 AAATTTGGTTGGGGTGCTGG 59.236 50.000 0.00 0.00 0.00 4.85
2188 2461 2.366916 TGTAAATTTGGTTGGGGTGCTG 59.633 45.455 0.00 0.00 0.00 4.41
2189 2462 2.632512 CTGTAAATTTGGTTGGGGTGCT 59.367 45.455 0.00 0.00 0.00 4.40
2190 2463 2.870035 GCTGTAAATTTGGTTGGGGTGC 60.870 50.000 0.00 0.00 0.00 5.01
2191 2464 2.366916 TGCTGTAAATTTGGTTGGGGTG 59.633 45.455 0.00 0.00 0.00 4.61
2192 2465 2.683768 TGCTGTAAATTTGGTTGGGGT 58.316 42.857 0.00 0.00 0.00 4.95
2193 2466 3.598299 CATGCTGTAAATTTGGTTGGGG 58.402 45.455 0.00 0.00 0.00 4.96
2194 2467 3.002102 GCATGCTGTAAATTTGGTTGGG 58.998 45.455 11.37 0.00 0.00 4.12
2195 2468 3.661944 TGCATGCTGTAAATTTGGTTGG 58.338 40.909 20.33 0.00 0.00 3.77
2196 2469 5.866335 AATGCATGCTGTAAATTTGGTTG 57.134 34.783 20.33 0.00 0.00 3.77
2197 2470 5.581874 GCTAATGCATGCTGTAAATTTGGTT 59.418 36.000 20.33 0.00 39.41 3.67
2198 2471 5.111293 GCTAATGCATGCTGTAAATTTGGT 58.889 37.500 20.33 0.00 39.41 3.67
2199 2472 4.207635 CGCTAATGCATGCTGTAAATTTGG 59.792 41.667 20.33 7.43 39.64 3.28
2200 2473 4.317558 GCGCTAATGCATGCTGTAAATTTG 60.318 41.667 20.33 11.35 39.64 2.32
2201 2474 3.798337 GCGCTAATGCATGCTGTAAATTT 59.202 39.130 20.33 0.00 39.64 1.82
2202 2475 3.067180 AGCGCTAATGCATGCTGTAAATT 59.933 39.130 20.33 12.02 39.64 1.82
2203 2476 2.620115 AGCGCTAATGCATGCTGTAAAT 59.380 40.909 20.33 0.00 39.64 1.40
2204 2477 2.016318 AGCGCTAATGCATGCTGTAAA 58.984 42.857 20.33 0.00 39.64 2.01
2205 2478 1.667236 AGCGCTAATGCATGCTGTAA 58.333 45.000 20.33 0.00 39.64 2.41
2206 2479 1.667236 AAGCGCTAATGCATGCTGTA 58.333 45.000 20.33 9.80 36.33 2.74
2207 2480 0.813184 AAAGCGCTAATGCATGCTGT 59.187 45.000 20.33 9.10 36.33 4.40
2208 2481 1.917273 AAAAGCGCTAATGCATGCTG 58.083 45.000 20.33 7.65 36.33 4.41
2209 2482 2.094597 TGAAAAAGCGCTAATGCATGCT 60.095 40.909 20.33 0.77 37.46 3.79
2210 2483 2.028404 GTGAAAAAGCGCTAATGCATGC 59.972 45.455 12.05 11.82 39.64 4.06
2211 2484 3.504863 AGTGAAAAAGCGCTAATGCATG 58.495 40.909 12.05 0.00 39.64 4.06
2212 2485 3.855689 AGTGAAAAAGCGCTAATGCAT 57.144 38.095 12.05 0.00 39.64 3.96
2213 2486 3.243367 ACAAGTGAAAAAGCGCTAATGCA 60.243 39.130 12.05 4.28 39.64 3.96
2214 2487 3.308530 ACAAGTGAAAAAGCGCTAATGC 58.691 40.909 12.05 0.93 0.00 3.56
2215 2488 5.739161 GGATACAAGTGAAAAAGCGCTAATG 59.261 40.000 12.05 3.77 0.00 1.90
2216 2489 5.880341 GGATACAAGTGAAAAAGCGCTAAT 58.120 37.500 12.05 0.00 0.00 1.73
2217 2490 5.291293 GGATACAAGTGAAAAAGCGCTAA 57.709 39.130 12.05 0.00 0.00 3.09
2218 2491 4.939509 GGATACAAGTGAAAAAGCGCTA 57.060 40.909 12.05 0.00 0.00 4.26
2219 2492 3.831715 GGATACAAGTGAAAAAGCGCT 57.168 42.857 2.64 2.64 0.00 5.92
2255 2528 6.375830 AAGGTGAAAAAGGTTGGGTAAAAA 57.624 33.333 0.00 0.00 0.00 1.94
2256 2529 6.375830 AAAGGTGAAAAAGGTTGGGTAAAA 57.624 33.333 0.00 0.00 0.00 1.52
2257 2530 6.375830 AAAAGGTGAAAAAGGTTGGGTAAA 57.624 33.333 0.00 0.00 0.00 2.01
2258 2531 6.375830 AAAAAGGTGAAAAAGGTTGGGTAA 57.624 33.333 0.00 0.00 0.00 2.85
2260 2533 4.919774 AAAAAGGTGAAAAAGGTTGGGT 57.080 36.364 0.00 0.00 0.00 4.51
2278 2551 8.156994 ACCTGTAAAATAGCTCGTGTTAAAAA 57.843 30.769 0.00 0.00 0.00 1.94
2279 2552 7.733402 ACCTGTAAAATAGCTCGTGTTAAAA 57.267 32.000 0.00 0.00 0.00 1.52
2280 2553 7.658575 AGAACCTGTAAAATAGCTCGTGTTAAA 59.341 33.333 0.00 0.00 0.00 1.52
2281 2554 7.117236 CAGAACCTGTAAAATAGCTCGTGTTAA 59.883 37.037 0.00 0.00 0.00 2.01
2282 2555 6.588756 CAGAACCTGTAAAATAGCTCGTGTTA 59.411 38.462 0.00 0.00 0.00 2.41
2283 2556 5.408604 CAGAACCTGTAAAATAGCTCGTGTT 59.591 40.000 0.00 0.00 0.00 3.32
2284 2557 4.929808 CAGAACCTGTAAAATAGCTCGTGT 59.070 41.667 0.00 0.00 0.00 4.49
2285 2558 4.201724 GCAGAACCTGTAAAATAGCTCGTG 60.202 45.833 0.00 0.00 33.43 4.35
2286 2559 3.933332 GCAGAACCTGTAAAATAGCTCGT 59.067 43.478 0.00 0.00 33.43 4.18
2287 2560 4.033358 CAGCAGAACCTGTAAAATAGCTCG 59.967 45.833 0.00 0.00 33.43 5.03
2288 2561 5.178797 TCAGCAGAACCTGTAAAATAGCTC 58.821 41.667 0.00 0.00 33.43 4.09
2289 2562 5.165961 TCAGCAGAACCTGTAAAATAGCT 57.834 39.130 0.00 0.00 33.43 3.32
2290 2563 5.674820 GCTTCAGCAGAACCTGTAAAATAGC 60.675 44.000 0.00 0.00 41.59 2.97
2291 2564 5.645497 AGCTTCAGCAGAACCTGTAAAATAG 59.355 40.000 0.75 0.00 45.16 1.73
2292 2565 5.412594 CAGCTTCAGCAGAACCTGTAAAATA 59.587 40.000 6.11 0.00 45.16 1.40
2293 2566 4.217118 CAGCTTCAGCAGAACCTGTAAAAT 59.783 41.667 6.11 0.00 45.16 1.82
2294 2567 3.565482 CAGCTTCAGCAGAACCTGTAAAA 59.435 43.478 6.11 0.00 45.16 1.52
2295 2568 3.141398 CAGCTTCAGCAGAACCTGTAAA 58.859 45.455 6.11 0.00 45.16 2.01
2296 2569 2.104792 ACAGCTTCAGCAGAACCTGTAA 59.895 45.455 15.81 0.00 44.71 2.41
2297 2570 1.694150 ACAGCTTCAGCAGAACCTGTA 59.306 47.619 15.81 0.00 44.71 2.74
2298 2571 0.471617 ACAGCTTCAGCAGAACCTGT 59.528 50.000 12.59 12.59 42.83 4.00
2299 2572 1.155042 GACAGCTTCAGCAGAACCTG 58.845 55.000 11.45 11.45 45.16 4.00
2300 2573 0.036022 GGACAGCTTCAGCAGAACCT 59.964 55.000 0.75 0.00 45.16 3.50
2301 2574 0.250467 TGGACAGCTTCAGCAGAACC 60.250 55.000 0.75 3.88 45.16 3.62
2302 2575 1.155042 CTGGACAGCTTCAGCAGAAC 58.845 55.000 0.75 0.00 45.16 3.01
2303 2576 3.620061 CTGGACAGCTTCAGCAGAA 57.380 52.632 0.75 0.00 45.16 3.02
2328 2601 5.012328 TGTGTGCTAAAATTCGGGTTTTT 57.988 34.783 4.46 1.40 33.62 1.94
2329 2602 4.657436 TGTGTGCTAAAATTCGGGTTTT 57.343 36.364 4.54 4.54 35.60 2.43
2330 2603 4.500716 CCTTGTGTGCTAAAATTCGGGTTT 60.501 41.667 0.00 0.00 0.00 3.27
2331 2604 3.005367 CCTTGTGTGCTAAAATTCGGGTT 59.995 43.478 0.00 0.00 0.00 4.11
2332 2605 2.556622 CCTTGTGTGCTAAAATTCGGGT 59.443 45.455 0.00 0.00 0.00 5.28
2333 2606 2.671070 GCCTTGTGTGCTAAAATTCGGG 60.671 50.000 0.00 0.00 0.00 5.14
2334 2607 2.030363 TGCCTTGTGTGCTAAAATTCGG 60.030 45.455 0.00 0.00 0.00 4.30
2335 2608 3.236816 CTGCCTTGTGTGCTAAAATTCG 58.763 45.455 0.00 0.00 0.00 3.34
2336 2609 4.243007 ACTGCCTTGTGTGCTAAAATTC 57.757 40.909 0.00 0.00 0.00 2.17
2337 2610 4.670896 AACTGCCTTGTGTGCTAAAATT 57.329 36.364 0.00 0.00 0.00 1.82
2338 2611 4.670896 AAACTGCCTTGTGTGCTAAAAT 57.329 36.364 0.00 0.00 0.00 1.82
2339 2612 4.464069 AAAACTGCCTTGTGTGCTAAAA 57.536 36.364 0.00 0.00 0.00 1.52
2340 2613 4.180057 CAAAAACTGCCTTGTGTGCTAAA 58.820 39.130 0.00 0.00 0.00 1.85
2341 2614 3.430098 CCAAAAACTGCCTTGTGTGCTAA 60.430 43.478 0.00 0.00 0.00 3.09
2342 2615 2.100584 CCAAAAACTGCCTTGTGTGCTA 59.899 45.455 0.00 0.00 0.00 3.49
2343 2616 1.134729 CCAAAAACTGCCTTGTGTGCT 60.135 47.619 0.00 0.00 0.00 4.40
2344 2617 1.289276 CCAAAAACTGCCTTGTGTGC 58.711 50.000 0.00 0.00 0.00 4.57
2345 2618 1.938625 CCCAAAAACTGCCTTGTGTG 58.061 50.000 0.00 0.00 0.00 3.82
2346 2619 0.177836 GCCCAAAAACTGCCTTGTGT 59.822 50.000 0.00 0.00 0.00 3.72
2347 2620 0.875474 CGCCCAAAAACTGCCTTGTG 60.875 55.000 0.00 0.00 0.00 3.33
2348 2621 1.441311 CGCCCAAAAACTGCCTTGT 59.559 52.632 0.00 0.00 0.00 3.16
2349 2622 1.955663 GCGCCCAAAAACTGCCTTG 60.956 57.895 0.00 0.00 0.00 3.61
2350 2623 1.757423 ATGCGCCCAAAAACTGCCTT 61.757 50.000 4.18 0.00 0.00 4.35
2351 2624 0.897863 TATGCGCCCAAAAACTGCCT 60.898 50.000 4.18 0.00 0.00 4.75
2352 2625 0.175531 ATATGCGCCCAAAAACTGCC 59.824 50.000 4.18 0.00 0.00 4.85
2353 2626 1.660104 CAATATGCGCCCAAAAACTGC 59.340 47.619 4.18 0.00 0.00 4.40
2354 2627 3.229276 TCAATATGCGCCCAAAAACTG 57.771 42.857 4.18 0.00 0.00 3.16
2355 2628 3.951775 TTCAATATGCGCCCAAAAACT 57.048 38.095 4.18 0.00 0.00 2.66
2356 2629 4.241681 TCTTTCAATATGCGCCCAAAAAC 58.758 39.130 4.18 0.00 0.00 2.43
2357 2630 4.527509 TCTTTCAATATGCGCCCAAAAA 57.472 36.364 4.18 0.00 0.00 1.94
2358 2631 4.527509 TTCTTTCAATATGCGCCCAAAA 57.472 36.364 4.18 0.00 0.00 2.44
2359 2632 4.527509 TTTCTTTCAATATGCGCCCAAA 57.472 36.364 4.18 0.00 0.00 3.28
2360 2633 4.527509 TTTTCTTTCAATATGCGCCCAA 57.472 36.364 4.18 0.00 0.00 4.12
2361 2634 4.527509 TTTTTCTTTCAATATGCGCCCA 57.472 36.364 4.18 0.00 0.00 5.36
2379 2652 0.537371 CGTCAGCTGGGAGGGTTTTT 60.537 55.000 15.13 0.00 0.00 1.94
2380 2653 1.073199 CGTCAGCTGGGAGGGTTTT 59.927 57.895 15.13 0.00 0.00 2.43
2381 2654 1.705997 AACGTCAGCTGGGAGGGTTT 61.706 55.000 15.13 0.00 0.00 3.27
2382 2655 2.113243 GAACGTCAGCTGGGAGGGTT 62.113 60.000 15.13 10.70 0.00 4.11
2383 2656 2.526873 AACGTCAGCTGGGAGGGT 60.527 61.111 15.13 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.