Multiple sequence alignment - TraesCS5D01G334500

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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 TraesCS5D01G334500 chr5D 100.000 5093 0 0 1 5093 424044998 424039906 0.000000e+00 9406.0
1 TraesCS5D01G334500 chr5A 88.419 3264 211 99 169 3346 537636406 537633224 0.000000e+00 3779.0
2 TraesCS5D01G334500 chr5A 89.913 1715 86 33 3372 5041 537633112 537631440 0.000000e+00 2128.0
3 TraesCS5D01G334500 chr5A 90.534 412 31 5 4423 4832 37995822 37995417 5.800000e-149 538.0
4 TraesCS5D01G334500 chr5A 94.372 231 12 1 4863 5093 37995422 37995193 2.260000e-93 353.0
5 TraesCS5D01G334500 chr5A 79.941 339 49 10 4682 5009 537630081 537629751 1.100000e-56 231.0
6 TraesCS5D01G334500 chr5A 88.112 143 8 4 4175 4317 37995966 37995833 1.470000e-35 161.0
7 TraesCS5D01G334500 chr5A 95.122 41 2 0 144 184 537636466 537636426 1.180000e-06 65.8
8 TraesCS5D01G334500 chr5B 88.802 2438 103 78 150 2462 512248526 512246134 0.000000e+00 2833.0
9 TraesCS5D01G334500 chr5B 89.557 1762 86 29 3351 5064 512245234 512243523 0.000000e+00 2145.0
10 TraesCS5D01G334500 chr5B 91.505 412 27 4 4423 4832 588652754 588653159 1.240000e-155 560.0
11 TraesCS5D01G334500 chr5B 85.349 587 27 26 2805 3343 512245893 512245318 2.070000e-153 553.0
12 TraesCS5D01G334500 chr5B 93.074 231 15 1 4863 5093 588653154 588653383 2.270000e-88 337.0
13 TraesCS5D01G334500 chr5B 83.333 120 7 7 2531 2640 512246133 512246017 1.170000e-16 99.0
14 TraesCS5D01G334500 chr2B 92.500 400 22 4 4423 4820 539374082 539374475 2.660000e-157 566.0
15 TraesCS5D01G334500 chr2B 94.805 231 11 1 4863 5093 539374482 539374711 4.850000e-95 359.0
16 TraesCS5D01G334500 chr6B 91.771 401 26 3 4433 4832 279574413 279574807 7.450000e-153 551.0
17 TraesCS5D01G334500 chr6B 91.019 412 29 5 4423 4832 581866019 581865614 2.680000e-152 549.0
18 TraesCS5D01G334500 chr6B 93.074 231 14 2 4863 5093 581865619 581865391 2.270000e-88 337.0
19 TraesCS5D01G334500 chr6B 93.722 223 13 1 4863 5085 279574802 279575023 2.940000e-87 333.0
20 TraesCS5D01G334500 chr6B 88.112 143 8 4 4175 4317 581866163 581866030 1.470000e-35 161.0
21 TraesCS5D01G334500 chr6B 87.857 140 8 4 4175 4314 279574258 279574388 6.830000e-34 156.0
22 TraesCS5D01G334500 chr6B 90.741 54 5 0 4406 4459 119842750 119842697 7.070000e-09 73.1
23 TraesCS5D01G334500 chr1B 96.629 178 6 0 4916 5093 60968465 60968288 3.860000e-76 296.0


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 TraesCS5D01G334500 chr5D 424039906 424044998 5092 True 9406.000000 9406 100.000000 1 5093 1 chr5D.!!$R1 5092
1 TraesCS5D01G334500 chr5A 537629751 537636466 6715 True 1550.950000 3779 88.348750 144 5041 4 chr5A.!!$R2 4897
2 TraesCS5D01G334500 chr5A 37995193 37995966 773 True 350.666667 538 91.006000 4175 5093 3 chr5A.!!$R1 918
3 TraesCS5D01G334500 chr5B 512243523 512248526 5003 True 1407.500000 2833 86.760250 150 5064 4 chr5B.!!$R1 4914
4 TraesCS5D01G334500 chr5B 588652754 588653383 629 False 448.500000 560 92.289500 4423 5093 2 chr5B.!!$F1 670
5 TraesCS5D01G334500 chr2B 539374082 539374711 629 False 462.500000 566 93.652500 4423 5093 2 chr2B.!!$F1 670
6 TraesCS5D01G334500 chr6B 581865391 581866163 772 True 349.000000 549 90.735000 4175 5093 3 chr6B.!!$R2 918
7 TraesCS5D01G334500 chr6B 279574258 279575023 765 False 346.666667 551 91.116667 4175 5085 3 chr6B.!!$F1 910

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
976 1078 0.036875 AAAGGGAAAGAGGAGCCGTG 59.963 55.0 0.0 0.0 0.0 4.94 F
984 1086 0.333993 AGAGGAGCCGTGGTAGGTAA 59.666 55.0 0.0 0.0 0.0 2.85 F
985 1087 0.459078 GAGGAGCCGTGGTAGGTAAC 59.541 60.0 0.0 0.0 0.0 2.50 F
2725 2912 0.953960 AAAGACATTCACCGACGCCC 60.954 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2632 2819 0.108585 AGGCCTCTTTCGACTTTGCA 59.891 50.0 0.0 0.0 0.00 4.08 R
2786 2977 0.604243 ACGCCCACGACTTGCAAATA 60.604 50.0 0.0 0.0 43.93 1.40 R
2839 3050 1.164411 CGCCCACTTTTGTATGCTCA 58.836 50.0 0.0 0.0 0.00 4.26 R
4519 5006 0.034059 AGACAGACAGGCGACCAAAG 59.966 55.0 0.0 0.0 0.00 2.77 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
29 30 9.740710 ATATCATTAACTCTAAGCCATAAACCC 57.259 33.333 0.00 0.00 0.00 4.11
30 31 6.964464 TCATTAACTCTAAGCCATAAACCCA 58.036 36.000 0.00 0.00 0.00 4.51
31 32 6.826741 TCATTAACTCTAAGCCATAAACCCAC 59.173 38.462 0.00 0.00 0.00 4.61
32 33 3.261981 ACTCTAAGCCATAAACCCACG 57.738 47.619 0.00 0.00 0.00 4.94
33 34 1.940613 CTCTAAGCCATAAACCCACGC 59.059 52.381 0.00 0.00 0.00 5.34
34 35 1.021968 CTAAGCCATAAACCCACGCC 58.978 55.000 0.00 0.00 0.00 5.68
35 36 0.745128 TAAGCCATAAACCCACGCCG 60.745 55.000 0.00 0.00 0.00 6.46
36 37 2.748647 GCCATAAACCCACGCCGT 60.749 61.111 0.00 0.00 0.00 5.68
37 38 2.337246 GCCATAAACCCACGCCGTT 61.337 57.895 0.00 0.00 0.00 4.44
38 39 1.504446 CCATAAACCCACGCCGTTG 59.496 57.895 0.00 0.00 0.00 4.10
39 40 1.504446 CATAAACCCACGCCGTTGG 59.496 57.895 5.72 5.72 36.26 3.77
40 41 2.337246 ATAAACCCACGCCGTTGGC 61.337 57.895 7.35 0.00 46.75 4.52
111 112 8.603898 TCTGTTAATAAACTACTCCTCATCCA 57.396 34.615 0.00 0.00 36.51 3.41
112 113 9.042450 TCTGTTAATAAACTACTCCTCATCCAA 57.958 33.333 0.00 0.00 36.51 3.53
113 114 9.667107 CTGTTAATAAACTACTCCTCATCCAAA 57.333 33.333 0.00 0.00 36.51 3.28
114 115 9.667107 TGTTAATAAACTACTCCTCATCCAAAG 57.333 33.333 0.00 0.00 36.51 2.77
115 116 9.668497 GTTAATAAACTACTCCTCATCCAAAGT 57.332 33.333 0.00 0.00 32.54 2.66
116 117 9.667107 TTAATAAACTACTCCTCATCCAAAGTG 57.333 33.333 0.00 0.00 0.00 3.16
117 118 3.618690 ACTACTCCTCATCCAAAGTGC 57.381 47.619 0.00 0.00 0.00 4.40
118 119 2.906389 ACTACTCCTCATCCAAAGTGCA 59.094 45.455 0.00 0.00 0.00 4.57
119 120 2.957402 ACTCCTCATCCAAAGTGCAA 57.043 45.000 0.00 0.00 0.00 4.08
120 121 2.787994 ACTCCTCATCCAAAGTGCAAG 58.212 47.619 0.00 0.00 0.00 4.01
121 122 2.107204 ACTCCTCATCCAAAGTGCAAGT 59.893 45.455 0.00 0.00 0.00 3.16
122 123 3.327757 ACTCCTCATCCAAAGTGCAAGTA 59.672 43.478 0.00 0.00 0.00 2.24
123 124 4.018960 ACTCCTCATCCAAAGTGCAAGTAT 60.019 41.667 0.00 0.00 0.00 2.12
124 125 4.517285 TCCTCATCCAAAGTGCAAGTATC 58.483 43.478 0.00 0.00 0.00 2.24
125 126 4.225942 TCCTCATCCAAAGTGCAAGTATCT 59.774 41.667 0.00 0.00 0.00 1.98
126 127 4.946157 CCTCATCCAAAGTGCAAGTATCTT 59.054 41.667 0.00 0.00 0.00 2.40
127 128 5.416952 CCTCATCCAAAGTGCAAGTATCTTT 59.583 40.000 0.00 0.00 32.60 2.52
128 129 6.404074 CCTCATCCAAAGTGCAAGTATCTTTC 60.404 42.308 0.00 0.00 30.41 2.62
129 130 5.415701 TCATCCAAAGTGCAAGTATCTTTCC 59.584 40.000 0.00 0.00 30.41 3.13
130 131 4.724399 TCCAAAGTGCAAGTATCTTTCCA 58.276 39.130 0.00 0.00 30.41 3.53
131 132 5.136828 TCCAAAGTGCAAGTATCTTTCCAA 58.863 37.500 0.00 0.00 30.41 3.53
132 133 5.009610 TCCAAAGTGCAAGTATCTTTCCAAC 59.990 40.000 0.00 0.00 30.41 3.77
133 134 5.221224 CCAAAGTGCAAGTATCTTTCCAACA 60.221 40.000 0.00 0.00 30.41 3.33
134 135 6.449698 CAAAGTGCAAGTATCTTTCCAACAT 58.550 36.000 0.00 0.00 30.41 2.71
135 136 5.886960 AGTGCAAGTATCTTTCCAACATC 57.113 39.130 0.00 0.00 0.00 3.06
136 137 5.316167 AGTGCAAGTATCTTTCCAACATCA 58.684 37.500 0.00 0.00 0.00 3.07
137 138 5.769662 AGTGCAAGTATCTTTCCAACATCAA 59.230 36.000 0.00 0.00 0.00 2.57
138 139 6.265196 AGTGCAAGTATCTTTCCAACATCAAA 59.735 34.615 0.00 0.00 0.00 2.69
139 140 7.039504 AGTGCAAGTATCTTTCCAACATCAAAT 60.040 33.333 0.00 0.00 0.00 2.32
140 141 7.062605 GTGCAAGTATCTTTCCAACATCAAATG 59.937 37.037 0.00 0.00 0.00 2.32
141 142 7.039853 TGCAAGTATCTTTCCAACATCAAATGA 60.040 33.333 0.00 0.00 0.00 2.57
142 143 7.977853 GCAAGTATCTTTCCAACATCAAATGAT 59.022 33.333 0.00 0.00 34.56 2.45
209 252 7.928307 ACCCATGATAGATACAAATATGCAC 57.072 36.000 0.00 0.00 0.00 4.57
210 253 7.460910 ACCCATGATAGATACAAATATGCACA 58.539 34.615 0.00 0.00 0.00 4.57
229 272 5.714333 TGCACAATGTACAATGACCCTAAAT 59.286 36.000 17.74 0.00 0.00 1.40
232 275 9.062524 GCACAATGTACAATGACCCTAAATATA 57.937 33.333 17.74 0.00 0.00 0.86
263 306 2.954318 TGGTAACCAGTCTCGGTATAGC 59.046 50.000 0.00 0.00 38.76 2.97
294 338 5.648960 GTCAACCCAAGTTATTCCCGATAAA 59.351 40.000 0.00 0.00 33.27 1.40
297 341 5.434408 ACCCAAGTTATTCCCGATAAAGAC 58.566 41.667 0.00 0.00 32.20 3.01
310 354 7.152645 TCCCGATAAAGACTGAGTATATTTGC 58.847 38.462 0.00 0.00 0.00 3.68
312 356 6.929049 CCGATAAAGACTGAGTATATTTGCCA 59.071 38.462 0.00 0.00 0.00 4.92
313 357 7.604164 CCGATAAAGACTGAGTATATTTGCCAT 59.396 37.037 0.00 0.00 0.00 4.40
314 358 9.639601 CGATAAAGACTGAGTATATTTGCCATA 57.360 33.333 0.00 0.00 0.00 2.74
321 365 9.494271 GACTGAGTATATTTGCCATATTTCTCA 57.506 33.333 13.55 13.55 0.00 3.27
347 391 2.489329 CTGTGACCAACATCCAACCATC 59.511 50.000 0.00 0.00 38.39 3.51
361 405 1.000896 CCATCTTCGGCCCAACCTT 60.001 57.895 0.00 0.00 35.61 3.50
364 408 0.255033 ATCTTCGGCCCAACCTTACC 59.745 55.000 0.00 0.00 35.61 2.85
379 423 5.930209 ACCTTACCCCATCATTCATGTAT 57.070 39.130 0.00 0.00 0.00 2.29
449 502 0.591170 CAACCGACAATCCGCAAACT 59.409 50.000 0.00 0.00 0.00 2.66
450 503 0.872388 AACCGACAATCCGCAAACTC 59.128 50.000 0.00 0.00 0.00 3.01
462 515 3.380004 TCCGCAAACTCAAAAACTGATGT 59.620 39.130 0.00 0.00 32.14 3.06
470 523 7.801716 AACTCAAAAACTGATGTAACAGCTA 57.198 32.000 0.00 0.00 41.06 3.32
471 524 7.986085 ACTCAAAAACTGATGTAACAGCTAT 57.014 32.000 0.00 0.00 41.06 2.97
474 527 9.979270 CTCAAAAACTGATGTAACAGCTATTAG 57.021 33.333 0.00 0.00 41.06 1.73
478 531 7.849804 AACTGATGTAACAGCTATTAGGTTG 57.150 36.000 0.00 0.00 41.06 3.77
479 532 7.182817 ACTGATGTAACAGCTATTAGGTTGA 57.817 36.000 0.00 0.00 41.06 3.18
481 534 7.549488 ACTGATGTAACAGCTATTAGGTTGAAC 59.451 37.037 0.00 0.00 41.06 3.18
563 646 0.248417 CAGAGTCTCGCCGTGATGAG 60.248 60.000 0.00 0.00 0.00 2.90
600 683 1.286501 GCCGCGATTCACTGTCAATA 58.713 50.000 8.23 0.00 0.00 1.90
601 684 1.258982 GCCGCGATTCACTGTCAATAG 59.741 52.381 8.23 0.00 0.00 1.73
602 685 2.540515 CCGCGATTCACTGTCAATAGT 58.459 47.619 8.23 0.00 0.00 2.12
603 686 2.930040 CCGCGATTCACTGTCAATAGTT 59.070 45.455 8.23 0.00 0.00 2.24
604 687 3.000322 CCGCGATTCACTGTCAATAGTTC 60.000 47.826 8.23 0.00 0.00 3.01
605 688 3.612423 CGCGATTCACTGTCAATAGTTCA 59.388 43.478 0.00 0.00 0.00 3.18
625 708 1.161843 CACTCCAAAATTACCGCCGT 58.838 50.000 0.00 0.00 0.00 5.68
627 710 0.730840 CTCCAAAATTACCGCCGTCC 59.269 55.000 0.00 0.00 0.00 4.79
648 731 2.622962 CGTCCGGAAAGGGCCAAAC 61.623 63.158 5.23 0.00 43.19 2.93
649 732 2.116556 TCCGGAAAGGGCCAAACC 59.883 61.111 0.00 4.44 41.52 3.27
650 733 2.203567 CCGGAAAGGGCCAAACCA 60.204 61.111 6.18 0.00 42.05 3.67
651 734 1.834822 CCGGAAAGGGCCAAACCAA 60.835 57.895 6.18 0.00 42.05 3.67
652 735 1.403687 CCGGAAAGGGCCAAACCAAA 61.404 55.000 6.18 0.00 42.05 3.28
678 762 2.126071 ACAGAATCACCGCCGTCG 60.126 61.111 0.00 0.00 0.00 5.12
681 765 1.065928 AGAATCACCGCCGTCGATC 59.934 57.895 0.00 0.00 38.10 3.69
723 807 0.108424 CAAGACTCCAAGAGCCCGAG 60.108 60.000 0.00 0.00 32.04 4.63
725 809 1.682684 GACTCCAAGAGCCCGAGGA 60.683 63.158 0.00 0.00 32.04 3.71
728 812 0.543749 CTCCAAGAGCCCGAGGAAAT 59.456 55.000 0.00 0.00 0.00 2.17
731 815 1.474143 CCAAGAGCCCGAGGAAATCTC 60.474 57.143 0.00 0.00 39.10 2.75
735 819 2.822399 CCCGAGGAAATCTCCCGG 59.178 66.667 7.75 7.75 46.78 5.73
785 874 0.931005 CGCCATCTTCCTCGCTAAAC 59.069 55.000 0.00 0.00 0.00 2.01
815 911 4.135153 CGTGACCTCCCAGGCGAG 62.135 72.222 0.00 0.00 39.63 5.03
817 913 2.680352 TGACCTCCCAGGCGAGAC 60.680 66.667 6.53 2.44 39.63 3.36
818 914 3.827898 GACCTCCCAGGCGAGACG 61.828 72.222 6.53 0.00 39.63 4.18
819 915 4.361971 ACCTCCCAGGCGAGACGA 62.362 66.667 6.53 0.00 39.63 4.20
820 916 3.068691 CCTCCCAGGCGAGACGAA 61.069 66.667 6.53 0.00 30.97 3.85
821 917 2.646175 CCTCCCAGGCGAGACGAAA 61.646 63.158 6.53 0.00 30.97 3.46
822 918 1.292223 CTCCCAGGCGAGACGAAAA 59.708 57.895 0.00 0.00 30.97 2.29
824 920 2.033194 CCCAGGCGAGACGAAAACC 61.033 63.158 0.00 0.00 0.00 3.27
833 932 4.960866 ACGAAAACCCCCACCCGC 62.961 66.667 0.00 0.00 0.00 6.13
976 1078 0.036875 AAAGGGAAAGAGGAGCCGTG 59.963 55.000 0.00 0.00 0.00 4.94
984 1086 0.333993 AGAGGAGCCGTGGTAGGTAA 59.666 55.000 0.00 0.00 0.00 2.85
985 1087 0.459078 GAGGAGCCGTGGTAGGTAAC 59.541 60.000 0.00 0.00 0.00 2.50
986 1088 1.140375 GGAGCCGTGGTAGGTAACG 59.860 63.158 0.00 0.00 46.39 3.18
994 1110 2.102438 GGTAGGTAACGTTGGCCGC 61.102 63.158 11.99 10.91 46.39 6.53
1314 1430 1.289800 GGCTCGTCGTCTCCAAAACC 61.290 60.000 0.00 0.00 0.00 3.27
1317 1433 2.673043 GCTCGTCGTCTCCAAAACCATA 60.673 50.000 0.00 0.00 0.00 2.74
1749 1865 2.202453 GTCTCCGCCGTCTTCGTC 60.202 66.667 0.00 0.00 35.01 4.20
1758 1874 3.470567 GTCTTCGTCGCCGTGCTG 61.471 66.667 0.00 0.00 35.01 4.41
1893 2009 2.266055 GACTCCAAGGAGGCGGTG 59.734 66.667 19.62 0.00 45.88 4.94
1894 2010 3.316573 GACTCCAAGGAGGCGGTGG 62.317 68.421 19.62 0.00 45.88 4.61
1895 2011 3.003173 CTCCAAGGAGGCGGTGGA 61.003 66.667 8.28 0.00 39.14 4.02
1896 2012 3.003173 TCCAAGGAGGCGGTGGAG 61.003 66.667 0.00 0.00 36.51 3.86
2085 2225 1.518572 CATGGGCTACACCGACGTC 60.519 63.158 5.18 5.18 40.62 4.34
2088 2228 2.099831 GGCTACACCGACGTCTCG 59.900 66.667 14.70 5.97 39.83 4.04
2175 2315 4.243270 AGCACTTCATCAAGTACGTTACC 58.757 43.478 0.00 0.00 41.24 2.85
2178 2318 4.863131 CACTTCATCAAGTACGTTACCTCC 59.137 45.833 0.00 0.00 41.24 4.30
2181 2321 3.194116 TCATCAAGTACGTTACCTCCACC 59.806 47.826 0.00 0.00 0.00 4.61
2182 2322 2.880443 TCAAGTACGTTACCTCCACCT 58.120 47.619 0.00 0.00 0.00 4.00
2184 2324 3.642848 TCAAGTACGTTACCTCCACCTTT 59.357 43.478 0.00 0.00 0.00 3.11
2186 2326 5.304101 TCAAGTACGTTACCTCCACCTTTTA 59.696 40.000 0.00 0.00 0.00 1.52
2197 2353 5.491078 ACCTCCACCTTTTACTCCATGATTA 59.509 40.000 0.00 0.00 0.00 1.75
2221 2377 1.754201 GCCGCCATTAATTCCCTTCCT 60.754 52.381 0.00 0.00 0.00 3.36
2222 2378 1.956477 CCGCCATTAATTCCCTTCCTG 59.044 52.381 0.00 0.00 0.00 3.86
2223 2379 1.338020 CGCCATTAATTCCCTTCCTGC 59.662 52.381 0.00 0.00 0.00 4.85
2224 2380 2.670939 GCCATTAATTCCCTTCCTGCT 58.329 47.619 0.00 0.00 0.00 4.24
2225 2381 2.363359 GCCATTAATTCCCTTCCTGCTG 59.637 50.000 0.00 0.00 0.00 4.41
2226 2382 2.363359 CCATTAATTCCCTTCCTGCTGC 59.637 50.000 0.00 0.00 0.00 5.25
2391 2562 1.447838 GGCGCAGAGATTTCGTGGA 60.448 57.895 10.83 0.00 0.00 4.02
2417 2589 4.445453 TGCTTTCAGATGAGATAATGCGT 58.555 39.130 0.00 0.00 0.00 5.24
2442 2618 1.611977 TGGGTCGTGTGAGAAGTACAG 59.388 52.381 0.00 0.00 0.00 2.74
2444 2620 2.095161 GGGTCGTGTGAGAAGTACAGAG 60.095 54.545 0.00 0.00 0.00 3.35
2480 2657 4.626081 GCCGGCGCCTCCATACAT 62.626 66.667 26.68 0.00 34.01 2.29
2483 2660 2.828868 GGCGCCTCCATACATCCA 59.171 61.111 22.15 0.00 34.01 3.41
2529 2706 7.979786 TTGGGATCTTTCTAGATGTAGAAGT 57.020 36.000 11.73 3.81 44.42 3.01
2589 2776 9.410556 CATATTTTGGTTAAAAGAACTGGACTG 57.589 33.333 0.00 0.00 39.01 3.51
2632 2819 4.202070 GCTATCTTAAGCACGAAGGAGACT 60.202 45.833 0.00 0.00 42.41 3.24
2640 2827 1.795286 CACGAAGGAGACTGCAAAGTC 59.205 52.381 0.00 0.00 42.68 3.01
2641 2828 1.063806 CGAAGGAGACTGCAAAGTCG 58.936 55.000 0.00 0.00 42.68 4.18
2642 2829 1.335964 CGAAGGAGACTGCAAAGTCGA 60.336 52.381 0.00 0.00 42.68 4.20
2643 2830 2.755650 GAAGGAGACTGCAAAGTCGAA 58.244 47.619 0.00 0.00 42.68 3.71
2644 2831 2.910688 AGGAGACTGCAAAGTCGAAA 57.089 45.000 0.00 0.00 43.15 3.46
2645 2832 2.760374 AGGAGACTGCAAAGTCGAAAG 58.240 47.619 0.00 0.00 43.15 2.62
2646 2833 2.365617 AGGAGACTGCAAAGTCGAAAGA 59.634 45.455 0.00 0.00 43.15 2.52
2653 2840 1.732809 GCAAAGTCGAAAGAGGCCTAC 59.267 52.381 4.42 0.00 43.49 3.18
2679 2866 3.323403 AGAAGAGTAAAGTGAGCAGCAGT 59.677 43.478 0.00 0.00 0.00 4.40
2725 2912 0.953960 AAAGACATTCACCGACGCCC 60.954 55.000 0.00 0.00 0.00 6.13
2773 2964 6.266168 TCAACAAAGTGATGCCGATAAAAT 57.734 33.333 0.00 0.00 0.00 1.82
2774 2965 6.092092 TCAACAAAGTGATGCCGATAAAATG 58.908 36.000 0.00 0.00 0.00 2.32
2777 2968 6.551736 ACAAAGTGATGCCGATAAAATGTAC 58.448 36.000 0.00 0.00 0.00 2.90
2780 2971 5.428253 AGTGATGCCGATAAAATGTACAGT 58.572 37.500 0.33 0.00 0.00 3.55
2785 2976 8.731605 TGATGCCGATAAAATGTACAGTAAAAA 58.268 29.630 0.33 0.00 0.00 1.94
2786 2977 9.730420 GATGCCGATAAAATGTACAGTAAAAAT 57.270 29.630 0.33 0.00 0.00 1.82
2798 2989 8.942669 TGTACAGTAAAAATATTTGCAAGTCG 57.057 30.769 0.39 0.00 34.02 4.18
2799 2990 8.561212 TGTACAGTAAAAATATTTGCAAGTCGT 58.439 29.630 0.39 0.00 34.02 4.34
2800 2991 7.851822 ACAGTAAAAATATTTGCAAGTCGTG 57.148 32.000 0.39 0.00 34.02 4.35
2801 2992 6.861055 ACAGTAAAAATATTTGCAAGTCGTGG 59.139 34.615 0.39 0.00 34.02 4.94
2803 2994 2.939460 AATATTTGCAAGTCGTGGGC 57.061 45.000 0.00 0.00 0.00 5.36
2839 3050 1.859302 TGGACAAAACAAAGCCCTGT 58.141 45.000 0.00 0.00 0.00 4.00
2847 3058 1.826385 ACAAAGCCCTGTGAGCATAC 58.174 50.000 0.00 0.00 0.00 2.39
2922 3139 4.756084 AGAAGTGTCAACTTTATGCAGC 57.244 40.909 0.00 0.00 46.84 5.25
2932 3149 1.002468 CTTTATGCAGCGTATGGGCAC 60.002 52.381 0.00 0.00 40.83 5.01
2939 3156 3.264897 CGTATGGGCACGCAGCTC 61.265 66.667 0.27 0.00 46.89 4.09
2963 3188 1.302671 CCTTTTACCGGTGGGCGAA 60.303 57.895 19.93 0.00 36.48 4.70
2997 3226 3.883489 ACGCTTTTTGGTAGAAAGAAGCT 59.117 39.130 9.58 0.00 36.45 3.74
3020 3259 9.118300 AGCTGATATTTTATTATGCCTGATAGC 57.882 33.333 0.00 0.00 0.00 2.97
3021 3260 9.118300 GCTGATATTTTATTATGCCTGATAGCT 57.882 33.333 0.00 0.00 0.00 3.32
3026 3265 8.757982 ATTTTATTATGCCTGATAGCTATGGG 57.242 34.615 11.94 13.67 0.00 4.00
3027 3266 3.634397 TTATGCCTGATAGCTATGGGC 57.366 47.619 27.48 27.48 42.73 5.36
3097 3342 2.824341 AGTAGTAGGTGGTGGTTTCTCG 59.176 50.000 0.00 0.00 0.00 4.04
3165 3414 8.395633 ACCTGTATAATGAACTGTTATTTTCGC 58.604 33.333 0.00 0.00 0.00 4.70
3167 3416 9.425893 CTGTATAATGAACTGTTATTTTCGCTG 57.574 33.333 0.00 0.00 0.00 5.18
3250 3505 2.802247 TCAGCGTGTCACATTCTGAAAG 59.198 45.455 13.82 0.00 31.62 2.62
3260 3515 3.187227 CACATTCTGAAAGGAACTCGTGG 59.813 47.826 0.00 0.00 38.49 4.94
3262 3517 4.256920 CATTCTGAAAGGAACTCGTGGAT 58.743 43.478 0.00 0.00 38.49 3.41
3328 3595 5.335504 GGTGTAGTAGTACTGTCCAAGTCAC 60.336 48.000 13.29 8.44 40.56 3.67
3340 3607 7.099764 ACTGTCCAAGTCACTCATTATGTAAG 58.900 38.462 0.00 0.00 31.64 2.34
3343 3610 6.313905 GTCCAAGTCACTCATTATGTAAGTGG 59.686 42.308 12.19 4.32 40.60 4.00
3346 3613 6.859112 AGTCACTCATTATGTAAGTGGAGT 57.141 37.500 12.19 0.00 40.60 3.85
3347 3614 7.956328 AGTCACTCATTATGTAAGTGGAGTA 57.044 36.000 12.19 0.00 40.60 2.59
3349 3692 7.396339 AGTCACTCATTATGTAAGTGGAGTACA 59.604 37.037 12.19 0.00 40.60 2.90
3370 3713 6.287107 ACAATTTTCTGACACTGTCTAACG 57.713 37.500 10.54 0.00 33.15 3.18
3373 3716 7.226720 ACAATTTTCTGACACTGTCTAACGATT 59.773 33.333 10.54 3.59 33.15 3.34
3391 3789 3.481951 CGATTCGAAACAACGATCACTGG 60.482 47.826 0.00 0.00 41.82 4.00
3420 3818 4.023739 TCTTGCTTTTCGATCATGCATG 57.976 40.909 21.07 21.07 33.50 4.06
3451 3849 4.929211 TCGAAACATCGATCACTGTCAATT 59.071 37.500 0.00 0.00 37.20 2.32
3503 3903 2.477825 TGCTCTCATTATTGCTCGCTC 58.522 47.619 0.00 0.00 0.00 5.03
3551 3988 6.092807 ACCTAATCTCTTCATTTCTGTTTCGC 59.907 38.462 0.00 0.00 0.00 4.70
3555 3992 5.510671 TCTCTTCATTTCTGTTTCGCAAAC 58.489 37.500 5.22 5.22 41.73 2.93
3562 3999 9.684448 TTCATTTCTGTTTCGCAAACATAAATA 57.316 25.926 22.35 13.96 46.95 1.40
3564 4001 9.726034 CATTTCTGTTTCGCAAACATAAATAAC 57.274 29.630 22.35 0.00 46.95 1.89
3565 4002 9.469807 ATTTCTGTTTCGCAAACATAAATAACA 57.530 25.926 21.94 8.52 46.88 2.41
3720 4157 3.812019 TCGCTCTTCGTCGGCTCC 61.812 66.667 0.00 0.00 39.67 4.70
3729 4166 4.736896 GTCGGCTCCGTGGTGGTC 62.737 72.222 8.28 0.00 40.74 4.02
3864 4301 1.519719 CTTCCTCTTCTCGGGCCTG 59.480 63.158 4.71 4.71 0.00 4.85
4116 4564 2.103934 CGCCGCTCTTCTCAGAGG 59.896 66.667 0.00 0.00 46.24 3.69
4217 4696 4.247781 CGCAGCAATGAAGGGGAT 57.752 55.556 0.00 0.00 0.00 3.85
4218 4697 3.402186 CGCAGCAATGAAGGGGATA 57.598 52.632 0.00 0.00 0.00 2.59
4219 4698 0.947244 CGCAGCAATGAAGGGGATAC 59.053 55.000 0.00 0.00 0.00 2.24
4220 4699 1.746861 CGCAGCAATGAAGGGGATACA 60.747 52.381 0.00 0.00 39.74 2.29
4221 4700 2.590821 GCAGCAATGAAGGGGATACAT 58.409 47.619 0.00 0.00 39.74 2.29
4222 4701 3.754965 GCAGCAATGAAGGGGATACATA 58.245 45.455 0.00 0.00 39.74 2.29
4223 4702 3.503748 GCAGCAATGAAGGGGATACATAC 59.496 47.826 0.00 0.00 39.74 2.39
4224 4703 4.717877 CAGCAATGAAGGGGATACATACA 58.282 43.478 0.00 0.00 39.74 2.29
4225 4704 5.319453 CAGCAATGAAGGGGATACATACAT 58.681 41.667 0.00 0.00 39.74 2.29
4226 4705 6.475504 CAGCAATGAAGGGGATACATACATA 58.524 40.000 0.00 0.00 39.74 2.29
4227 4706 6.372659 CAGCAATGAAGGGGATACATACATAC 59.627 42.308 0.00 0.00 39.74 2.39
4228 4707 6.044287 AGCAATGAAGGGGATACATACATACA 59.956 38.462 0.00 0.00 39.74 2.29
4229 4708 6.372659 GCAATGAAGGGGATACATACATACAG 59.627 42.308 0.00 0.00 39.74 2.74
4271 4750 9.515226 TTTTGGGCAAAGATGGATAGTATATAC 57.485 33.333 4.60 4.60 0.00 1.47
4272 4751 6.873997 TGGGCAAAGATGGATAGTATATACG 58.126 40.000 7.23 0.00 0.00 3.06
4273 4752 5.753921 GGGCAAAGATGGATAGTATATACGC 59.246 44.000 7.23 1.72 0.00 4.42
4293 4775 8.988064 ATACGCAGATTCAATTGGTATACTAG 57.012 34.615 5.42 0.00 0.00 2.57
4294 4776 7.050970 ACGCAGATTCAATTGGTATACTAGA 57.949 36.000 5.42 0.00 0.00 2.43
4295 4777 7.671302 ACGCAGATTCAATTGGTATACTAGAT 58.329 34.615 5.42 0.00 0.00 1.98
4296 4778 7.600375 ACGCAGATTCAATTGGTATACTAGATG 59.400 37.037 5.42 0.35 0.00 2.90
4297 4779 7.600375 CGCAGATTCAATTGGTATACTAGATGT 59.400 37.037 5.42 0.00 0.00 3.06
4332 4819 3.070018 GCTACTATGGCTGTGCAATAGG 58.930 50.000 15.74 3.42 44.42 2.57
4445 4932 1.006832 CCACGCCAAGTATTTCCGAG 58.993 55.000 0.00 0.00 0.00 4.63
4497 4984 2.029838 CCTGTTCGGCATAAGAGCTT 57.970 50.000 0.00 0.00 34.17 3.74
4519 5006 4.247258 TGCATCAATTCAAGTGCATTTCC 58.753 39.130 0.00 0.00 42.13 3.13
4523 5010 6.619874 GCATCAATTCAAGTGCATTTCCTTTG 60.620 38.462 0.00 0.00 37.52 2.77
4551 5042 5.521735 GCCTGTCTGTCTGTCTGTTATTATG 59.478 44.000 0.00 0.00 0.00 1.90
4579 5070 4.693283 TCGGCTCAGTACATGGAATTAAG 58.307 43.478 0.00 0.00 0.00 1.85
4601 5092 5.809001 AGAAGTGCTTTCAGGATCACATAA 58.191 37.500 0.00 0.00 38.31 1.90
4613 5105 5.008415 CAGGATCACATAACTGATTCCAAGC 59.992 44.000 0.00 0.00 30.62 4.01
4808 5305 1.679311 CAGCAGCCTGAGGTTGGTA 59.321 57.895 19.47 0.00 42.35 3.25
4820 5318 5.398353 CCTGAGGTTGGTATGATCTGGAAAT 60.398 44.000 0.00 0.00 32.45 2.17
4826 5324 6.833933 GGTTGGTATGATCTGGAAATTTACCT 59.166 38.462 0.00 0.00 0.00 3.08
4856 5361 3.594134 GTCTCAGGTGAAGTGATTGAGG 58.406 50.000 0.56 0.00 36.72 3.86
4861 5366 6.096987 TCTCAGGTGAAGTGATTGAGGTATAC 59.903 42.308 0.00 0.00 36.72 1.47
4883 5388 6.715347 ACTTGATGCTTAACCTGACTTTTT 57.285 33.333 0.00 0.00 0.00 1.94
4906 5411 7.540474 TTCTCCACTATTAACACTTCAGTCT 57.460 36.000 0.00 0.00 0.00 3.24
4941 5447 5.713025 CTGTGAGGTTTCATATGGTTTTGG 58.287 41.667 2.13 0.00 35.39 3.28
4946 5452 4.772100 AGGTTTCATATGGTTTTGGGACAG 59.228 41.667 2.13 0.00 42.39 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.740710 GGGTTTATGGCTTAGAGTTAATGATAT 57.259 33.333 0.00 0.00 0.00 1.63
4 5 8.719596 TGGGTTTATGGCTTAGAGTTAATGATA 58.280 33.333 0.00 0.00 0.00 2.15
5 6 7.502561 GTGGGTTTATGGCTTAGAGTTAATGAT 59.497 37.037 0.00 0.00 0.00 2.45
6 7 6.826741 GTGGGTTTATGGCTTAGAGTTAATGA 59.173 38.462 0.00 0.00 0.00 2.57
7 8 6.238374 CGTGGGTTTATGGCTTAGAGTTAATG 60.238 42.308 0.00 0.00 0.00 1.90
8 9 5.820947 CGTGGGTTTATGGCTTAGAGTTAAT 59.179 40.000 0.00 0.00 0.00 1.40
9 10 5.180271 CGTGGGTTTATGGCTTAGAGTTAA 58.820 41.667 0.00 0.00 0.00 2.01
10 11 4.761975 CGTGGGTTTATGGCTTAGAGTTA 58.238 43.478 0.00 0.00 0.00 2.24
11 12 3.606687 CGTGGGTTTATGGCTTAGAGTT 58.393 45.455 0.00 0.00 0.00 3.01
12 13 2.679930 GCGTGGGTTTATGGCTTAGAGT 60.680 50.000 0.00 0.00 0.00 3.24
13 14 1.940613 GCGTGGGTTTATGGCTTAGAG 59.059 52.381 0.00 0.00 0.00 2.43
14 15 1.407712 GGCGTGGGTTTATGGCTTAGA 60.408 52.381 0.00 0.00 0.00 2.10
15 16 1.021968 GGCGTGGGTTTATGGCTTAG 58.978 55.000 0.00 0.00 0.00 2.18
16 17 0.745128 CGGCGTGGGTTTATGGCTTA 60.745 55.000 0.00 0.00 0.00 3.09
17 18 2.043980 CGGCGTGGGTTTATGGCTT 61.044 57.895 0.00 0.00 0.00 4.35
18 19 2.437716 CGGCGTGGGTTTATGGCT 60.438 61.111 0.00 0.00 0.00 4.75
19 20 2.337246 AACGGCGTGGGTTTATGGC 61.337 57.895 15.70 0.00 0.00 4.40
20 21 1.504446 CAACGGCGTGGGTTTATGG 59.496 57.895 15.70 0.00 0.00 2.74
21 22 1.504446 CCAACGGCGTGGGTTTATG 59.496 57.895 25.42 11.88 34.77 1.90
22 23 2.337246 GCCAACGGCGTGGGTTTAT 61.337 57.895 32.43 3.49 39.62 1.40
23 24 2.979120 GCCAACGGCGTGGGTTTA 60.979 61.111 32.43 0.00 39.62 2.01
85 86 9.213777 TGGATGAGGAGTAGTTTATTAACAGAT 57.786 33.333 0.00 0.00 36.70 2.90
86 87 8.603898 TGGATGAGGAGTAGTTTATTAACAGA 57.396 34.615 0.00 0.00 36.70 3.41
87 88 9.667107 TTTGGATGAGGAGTAGTTTATTAACAG 57.333 33.333 0.00 0.00 36.70 3.16
88 89 9.667107 CTTTGGATGAGGAGTAGTTTATTAACA 57.333 33.333 0.00 0.00 36.70 2.41
89 90 9.668497 ACTTTGGATGAGGAGTAGTTTATTAAC 57.332 33.333 0.00 0.00 34.36 2.01
90 91 9.667107 CACTTTGGATGAGGAGTAGTTTATTAA 57.333 33.333 0.00 0.00 0.00 1.40
91 92 7.769044 GCACTTTGGATGAGGAGTAGTTTATTA 59.231 37.037 0.00 0.00 0.00 0.98
92 93 6.599638 GCACTTTGGATGAGGAGTAGTTTATT 59.400 38.462 0.00 0.00 0.00 1.40
93 94 6.116126 GCACTTTGGATGAGGAGTAGTTTAT 58.884 40.000 0.00 0.00 0.00 1.40
94 95 5.012664 TGCACTTTGGATGAGGAGTAGTTTA 59.987 40.000 0.00 0.00 0.00 2.01
95 96 4.202461 TGCACTTTGGATGAGGAGTAGTTT 60.202 41.667 0.00 0.00 0.00 2.66
96 97 3.327757 TGCACTTTGGATGAGGAGTAGTT 59.672 43.478 0.00 0.00 0.00 2.24
97 98 2.906389 TGCACTTTGGATGAGGAGTAGT 59.094 45.455 0.00 0.00 0.00 2.73
98 99 3.616956 TGCACTTTGGATGAGGAGTAG 57.383 47.619 0.00 0.00 0.00 2.57
99 100 3.327757 ACTTGCACTTTGGATGAGGAGTA 59.672 43.478 0.00 0.00 0.00 2.59
100 101 2.107204 ACTTGCACTTTGGATGAGGAGT 59.893 45.455 0.00 0.00 0.00 3.85
101 102 2.787994 ACTTGCACTTTGGATGAGGAG 58.212 47.619 0.00 0.00 0.00 3.69
102 103 2.957402 ACTTGCACTTTGGATGAGGA 57.043 45.000 0.00 0.00 0.00 3.71
103 104 4.521146 AGATACTTGCACTTTGGATGAGG 58.479 43.478 0.00 0.00 0.00 3.86
104 105 6.404074 GGAAAGATACTTGCACTTTGGATGAG 60.404 42.308 4.16 0.00 34.63 2.90
105 106 5.415701 GGAAAGATACTTGCACTTTGGATGA 59.584 40.000 4.16 0.00 34.63 2.92
106 107 5.183713 TGGAAAGATACTTGCACTTTGGATG 59.816 40.000 4.16 0.00 34.63 3.51
107 108 5.324409 TGGAAAGATACTTGCACTTTGGAT 58.676 37.500 4.16 0.00 34.63 3.41
108 109 4.724399 TGGAAAGATACTTGCACTTTGGA 58.276 39.130 4.16 0.00 34.63 3.53
109 110 5.221224 TGTTGGAAAGATACTTGCACTTTGG 60.221 40.000 4.16 0.00 34.63 3.28
110 111 5.830912 TGTTGGAAAGATACTTGCACTTTG 58.169 37.500 4.16 0.00 34.63 2.77
111 112 6.265196 TGATGTTGGAAAGATACTTGCACTTT 59.735 34.615 0.00 0.00 36.71 2.66
112 113 5.769662 TGATGTTGGAAAGATACTTGCACTT 59.230 36.000 0.00 0.00 25.38 3.16
113 114 5.316167 TGATGTTGGAAAGATACTTGCACT 58.684 37.500 0.00 0.00 25.38 4.40
114 115 5.627499 TGATGTTGGAAAGATACTTGCAC 57.373 39.130 0.00 0.00 25.38 4.57
115 116 6.647334 TTTGATGTTGGAAAGATACTTGCA 57.353 33.333 0.00 0.00 25.38 4.08
116 117 7.315142 TCATTTGATGTTGGAAAGATACTTGC 58.685 34.615 0.00 0.00 25.38 4.01
152 153 7.812648 TGCATTTATGTAACAAGTACTTGGAC 58.187 34.615 33.11 28.65 44.45 4.02
204 247 3.700538 AGGGTCATTGTACATTGTGCAT 58.299 40.909 15.41 0.00 0.00 3.96
232 275 6.433404 CCGAGACTGGTTACCATGTAGTATAT 59.567 42.308 3.88 0.00 30.82 0.86
233 276 5.766670 CCGAGACTGGTTACCATGTAGTATA 59.233 44.000 3.88 0.00 30.82 1.47
234 277 4.583489 CCGAGACTGGTTACCATGTAGTAT 59.417 45.833 3.88 0.00 30.82 2.12
235 278 3.949754 CCGAGACTGGTTACCATGTAGTA 59.050 47.826 3.88 0.00 30.82 1.82
236 279 2.758979 CCGAGACTGGTTACCATGTAGT 59.241 50.000 3.88 0.00 30.82 2.73
237 280 2.758979 ACCGAGACTGGTTACCATGTAG 59.241 50.000 3.88 0.00 39.99 2.74
238 281 2.811410 ACCGAGACTGGTTACCATGTA 58.189 47.619 3.88 0.00 39.99 2.29
243 286 2.954318 TGCTATACCGAGACTGGTTACC 59.046 50.000 0.00 0.00 43.56 2.85
250 293 5.077564 TGACCATATTGCTATACCGAGACT 58.922 41.667 0.00 0.00 0.00 3.24
294 338 9.717942 GAGAAATATGGCAAATATACTCAGTCT 57.282 33.333 0.00 0.00 0.00 3.24
310 354 6.356556 TGGTCACAGGTATTGAGAAATATGG 58.643 40.000 0.00 0.00 0.00 2.74
312 356 7.402054 TGTTGGTCACAGGTATTGAGAAATAT 58.598 34.615 0.00 0.00 0.00 1.28
313 357 6.774673 TGTTGGTCACAGGTATTGAGAAATA 58.225 36.000 0.00 0.00 0.00 1.40
314 358 5.630121 TGTTGGTCACAGGTATTGAGAAAT 58.370 37.500 0.00 0.00 0.00 2.17
315 359 5.042463 TGTTGGTCACAGGTATTGAGAAA 57.958 39.130 0.00 0.00 0.00 2.52
318 362 3.941483 GGATGTTGGTCACAGGTATTGAG 59.059 47.826 0.00 0.00 39.40 3.02
319 363 3.329225 TGGATGTTGGTCACAGGTATTGA 59.671 43.478 0.00 0.00 39.40 2.57
321 365 4.079253 GTTGGATGTTGGTCACAGGTATT 58.921 43.478 0.00 0.00 39.40 1.89
323 367 2.224670 GGTTGGATGTTGGTCACAGGTA 60.225 50.000 0.00 0.00 39.40 3.08
324 368 1.478654 GGTTGGATGTTGGTCACAGGT 60.479 52.381 0.00 0.00 39.40 4.00
347 391 1.378119 GGGTAAGGTTGGGCCGAAG 60.378 63.158 0.00 0.00 43.70 3.79
361 405 5.789521 CGTACATACATGAATGATGGGGTA 58.210 41.667 0.00 0.00 36.23 3.69
364 408 4.318332 AGCGTACATACATGAATGATGGG 58.682 43.478 0.00 0.00 36.23 4.00
449 502 8.946085 CCTAATAGCTGTTACATCAGTTTTTGA 58.054 33.333 0.00 0.00 40.85 2.69
450 503 8.730680 ACCTAATAGCTGTTACATCAGTTTTTG 58.269 33.333 0.00 0.00 37.70 2.44
462 515 8.911918 TTTCTTGTTCAACCTAATAGCTGTTA 57.088 30.769 0.00 0.00 0.00 2.41
470 523 4.339814 TGCCGTTTTCTTGTTCAACCTAAT 59.660 37.500 0.00 0.00 0.00 1.73
471 524 3.695060 TGCCGTTTTCTTGTTCAACCTAA 59.305 39.130 0.00 0.00 0.00 2.69
474 527 2.159296 ACTGCCGTTTTCTTGTTCAACC 60.159 45.455 0.00 0.00 0.00 3.77
478 531 3.263602 GGTACTGCCGTTTTCTTGTTC 57.736 47.619 0.00 0.00 0.00 3.18
563 646 0.096454 GCGACTATTTTGGCACGGAC 59.904 55.000 0.00 0.00 0.00 4.79
600 683 3.252458 GCGGTAATTTTGGAGTGTGAACT 59.748 43.478 0.00 0.00 0.00 3.01
601 684 3.561503 GCGGTAATTTTGGAGTGTGAAC 58.438 45.455 0.00 0.00 0.00 3.18
602 685 2.554893 GGCGGTAATTTTGGAGTGTGAA 59.445 45.455 0.00 0.00 0.00 3.18
603 686 2.156098 GGCGGTAATTTTGGAGTGTGA 58.844 47.619 0.00 0.00 0.00 3.58
604 687 1.135803 CGGCGGTAATTTTGGAGTGTG 60.136 52.381 0.00 0.00 0.00 3.82
605 688 1.161843 CGGCGGTAATTTTGGAGTGT 58.838 50.000 0.00 0.00 0.00 3.55
627 710 4.468689 GGCCCTTTCCGGACGAGG 62.469 72.222 21.29 21.29 33.16 4.63
648 731 4.990426 GGTGATTCTGTGGATTTTGTTTGG 59.010 41.667 0.00 0.00 0.00 3.28
649 732 4.681025 CGGTGATTCTGTGGATTTTGTTTG 59.319 41.667 0.00 0.00 0.00 2.93
650 733 4.795962 GCGGTGATTCTGTGGATTTTGTTT 60.796 41.667 0.00 0.00 0.00 2.83
651 734 3.305335 GCGGTGATTCTGTGGATTTTGTT 60.305 43.478 0.00 0.00 0.00 2.83
652 735 2.228822 GCGGTGATTCTGTGGATTTTGT 59.771 45.455 0.00 0.00 0.00 2.83
678 762 1.887707 GGCGGGACATTGTCGGATC 60.888 63.158 10.56 0.00 32.65 3.36
681 765 2.819595 CAGGCGGGACATTGTCGG 60.820 66.667 10.56 6.44 32.65 4.79
723 807 3.793888 ACGGGCCGGGAGATTTCC 61.794 66.667 31.78 0.00 43.23 3.13
725 809 3.325201 GACACGGGCCGGGAGATTT 62.325 63.158 38.35 12.75 32.98 2.17
785 874 0.463833 GGTCACGCTAAGATTGGGGG 60.464 60.000 0.00 0.00 0.00 5.40
815 911 2.670592 CGGGTGGGGGTTTTCGTC 60.671 66.667 0.00 0.00 0.00 4.20
976 1078 2.102438 GCGGCCAACGTTACCTACC 61.102 63.158 15.35 6.17 46.52 3.18
1314 1430 1.738099 GTAGGGCAGCGGCGATATG 60.738 63.158 12.98 6.98 42.47 1.78
1317 1433 4.227134 CAGTAGGGCAGCGGCGAT 62.227 66.667 12.98 0.00 42.47 4.58
1671 1787 3.850095 GAGGTAGAGCGCGATGGCC 62.850 68.421 12.10 5.14 35.02 5.36
1867 1983 1.004560 CCTTGGAGTCGAGCAGCAA 60.005 57.895 0.00 0.00 0.00 3.91
1891 2007 3.117171 CTGCAGCTGCGTCTCCAC 61.117 66.667 32.11 5.47 45.83 4.02
1892 2008 4.383861 CCTGCAGCTGCGTCTCCA 62.384 66.667 32.11 13.90 45.83 3.86
1941 2081 3.432051 GATCGTGTGCTCCTCCCCG 62.432 68.421 0.00 0.00 0.00 5.73
1974 2114 1.293498 CACCCAGAAGTCCACCGAG 59.707 63.158 0.00 0.00 0.00 4.63
2085 2225 0.735471 TCATGGAGACGAAGAGCGAG 59.265 55.000 0.00 0.00 44.57 5.03
2175 2315 6.653989 AGTAATCATGGAGTAAAAGGTGGAG 58.346 40.000 0.00 0.00 0.00 3.86
2178 2318 5.006746 GCGAGTAATCATGGAGTAAAAGGTG 59.993 44.000 0.00 0.00 0.00 4.00
2181 2321 4.209288 CGGCGAGTAATCATGGAGTAAAAG 59.791 45.833 0.00 0.00 0.00 2.27
2182 2322 4.116961 CGGCGAGTAATCATGGAGTAAAA 58.883 43.478 0.00 0.00 0.00 1.52
2184 2324 2.545113 GCGGCGAGTAATCATGGAGTAA 60.545 50.000 12.98 0.00 0.00 2.24
2186 2326 0.249489 GCGGCGAGTAATCATGGAGT 60.249 55.000 12.98 0.00 0.00 3.85
2197 2353 0.818040 GGGAATTAATGGCGGCGAGT 60.818 55.000 12.98 0.00 0.00 4.18
2221 2377 2.260434 GGAGTTCGTACCGCAGCA 59.740 61.111 0.00 0.00 0.00 4.41
2222 2378 2.879462 CGGAGTTCGTACCGCAGC 60.879 66.667 0.00 0.00 42.55 5.25
2355 2519 2.601804 GCCGTCCATGCGTTTTTATTT 58.398 42.857 0.00 0.00 0.00 1.40
2391 2562 6.512903 CGCATTATCTCATCTGAAAGCAACAT 60.513 38.462 0.00 0.00 0.00 2.71
2417 2589 3.625897 CTCACACGACCCAGGCCA 61.626 66.667 5.01 0.00 0.00 5.36
2442 2618 3.306919 GCCCATTCATCTCAGATCTCCTC 60.307 52.174 0.00 0.00 0.00 3.71
2444 2620 2.290197 GGCCCATTCATCTCAGATCTCC 60.290 54.545 0.00 0.00 0.00 3.71
2480 2657 2.717044 CCGCGGACACCACTATGGA 61.717 63.158 24.07 0.00 40.96 3.41
2483 2660 2.363276 TCCCGCGGACACCACTAT 60.363 61.111 30.73 0.00 0.00 2.12
2538 2715 6.148480 GGTGGTGCTTAAGATAGAATATGCAG 59.852 42.308 6.67 0.00 34.21 4.41
2581 2767 1.675641 GCGGCCATTTCAGTCCAGT 60.676 57.895 2.24 0.00 0.00 4.00
2589 2776 4.114997 CACCACCGCGGCCATTTC 62.115 66.667 28.58 0.00 39.03 2.17
2610 2797 5.277825 CAGTCTCCTTCGTGCTTAAGATAG 58.722 45.833 6.67 0.00 0.00 2.08
2632 2819 0.108585 AGGCCTCTTTCGACTTTGCA 59.891 50.000 0.00 0.00 0.00 4.08
2659 2846 3.760580 ACTGCTGCTCACTTTACTCTT 57.239 42.857 0.00 0.00 0.00 2.85
2725 2912 9.765795 GAATATATCTGGGGTTTCTATAATCCG 57.234 37.037 0.00 0.00 0.00 4.18
2732 2923 9.627123 CTTTGTTGAATATATCTGGGGTTTCTA 57.373 33.333 0.00 0.00 0.00 2.10
2773 2964 8.561212 ACGACTTGCAAATATTTTTACTGTACA 58.439 29.630 0.00 0.00 0.00 2.90
2774 2965 8.837059 CACGACTTGCAAATATTTTTACTGTAC 58.163 33.333 0.00 0.00 0.00 2.90
2777 2968 6.307800 CCCACGACTTGCAAATATTTTTACTG 59.692 38.462 0.00 0.00 0.00 2.74
2780 2971 5.164954 GCCCACGACTTGCAAATATTTTTA 58.835 37.500 0.00 0.00 0.00 1.52
2785 2976 0.732571 CGCCCACGACTTGCAAATAT 59.267 50.000 0.00 0.00 43.93 1.28
2786 2977 0.604243 ACGCCCACGACTTGCAAATA 60.604 50.000 0.00 0.00 43.93 1.40
2787 2978 1.896660 ACGCCCACGACTTGCAAAT 60.897 52.632 0.00 0.00 43.93 2.32
2789 2980 3.276091 CACGCCCACGACTTGCAA 61.276 61.111 0.00 0.00 43.93 4.08
2811 3013 6.198687 GGCTTTGTTTTGTCCATTAAAAAGC 58.801 36.000 7.99 7.99 32.06 3.51
2820 3022 1.480137 CACAGGGCTTTGTTTTGTCCA 59.520 47.619 0.00 0.00 0.00 4.02
2839 3050 1.164411 CGCCCACTTTTGTATGCTCA 58.836 50.000 0.00 0.00 0.00 4.26
2847 3058 1.596954 CGAAGTTGACGCCCACTTTTG 60.597 52.381 0.00 0.00 0.00 2.44
2892 3106 8.799091 CATAAAGTTGACACTTCTATACTCGTG 58.201 37.037 0.00 0.00 42.89 4.35
2922 3139 3.264897 GAGCTGCGTGCCCATACG 61.265 66.667 0.00 0.00 46.28 3.06
2936 3153 3.506096 GGTAAAAGGCGCCCGAGC 61.506 66.667 26.15 11.96 0.00 5.03
2937 3154 3.192922 CGGTAAAAGGCGCCCGAG 61.193 66.667 26.15 3.85 43.01 4.63
2938 3155 4.763646 CCGGTAAAAGGCGCCCGA 62.764 66.667 26.15 2.27 43.01 5.14
3009 3238 0.622665 GGCCCATAGCTATCAGGCAT 59.377 55.000 31.42 2.27 45.72 4.40
3027 3266 4.806640 AACAAACAGAATTGGCCATAGG 57.193 40.909 6.09 0.00 34.56 2.57
3097 3342 2.156504 CGATTCATGCGATCTTAGTGCC 59.843 50.000 0.00 0.00 0.00 5.01
3165 3414 6.351796 CCCCCTTCCCATTAATAAAAACACAG 60.352 42.308 0.00 0.00 0.00 3.66
3167 3416 5.486063 ACCCCCTTCCCATTAATAAAAACAC 59.514 40.000 0.00 0.00 0.00 3.32
3250 3505 3.181506 GCAATCTGAAATCCACGAGTTCC 60.182 47.826 0.00 0.00 36.05 3.62
3260 3515 6.529125 ACGATTGTTCATTGCAATCTGAAATC 59.471 34.615 15.26 16.25 45.86 2.17
3262 3517 5.630264 CACGATTGTTCATTGCAATCTGAAA 59.370 36.000 15.26 6.78 45.86 2.69
3340 3607 5.527582 ACAGTGTCAGAAAATTGTACTCCAC 59.472 40.000 0.00 0.00 0.00 4.02
3343 3610 8.488764 GTTAGACAGTGTCAGAAAATTGTACTC 58.511 37.037 24.73 0.98 34.60 2.59
3346 3613 7.204604 TCGTTAGACAGTGTCAGAAAATTGTA 58.795 34.615 24.73 2.73 34.60 2.41
3347 3614 6.046593 TCGTTAGACAGTGTCAGAAAATTGT 58.953 36.000 24.73 3.71 34.60 2.71
3349 3692 7.359264 CGAATCGTTAGACAGTGTCAGAAAATT 60.359 37.037 24.73 16.75 34.60 1.82
3370 3713 3.725010 GCCAGTGATCGTTGTTTCGAATC 60.725 47.826 0.00 0.00 42.99 2.52
3373 3716 1.144969 GCCAGTGATCGTTGTTTCGA 58.855 50.000 0.00 0.00 43.86 3.71
3391 3789 5.156355 TGATCGAAAAGCAAGAAAATCAGC 58.844 37.500 0.00 0.00 0.00 4.26
3451 3849 7.507277 AGTTTCTGGATCTCTATGCACATACTA 59.493 37.037 0.00 0.00 29.41 1.82
3503 3903 7.869937 AGGTTGAGTACATAATGATGATCGAAG 59.130 37.037 0.00 0.00 36.48 3.79
3573 4010 8.399425 TCATGTTTCACAACGTTATACACTTTT 58.601 29.630 0.00 0.00 35.40 2.27
3575 4012 7.225931 AGTCATGTTTCACAACGTTATACACTT 59.774 33.333 0.00 0.00 35.40 3.16
3593 4030 3.753272 CGTCCTGGAAATTCAGTCATGTT 59.247 43.478 0.00 0.00 33.14 2.71
3783 4220 1.202268 CCGTAGTACTTGAGGCCGAAG 60.202 57.143 14.22 14.22 0.00 3.79
3843 4280 1.518302 GCCCGAGAAGAGGAAGGAC 59.482 63.158 0.00 0.00 0.00 3.85
4116 4564 1.575576 CTGTGCAGCCAGCTGAGTTC 61.576 60.000 23.40 5.97 46.30 3.01
4210 4689 7.527196 GCATGTACTGTATGTATGTATCCCCTT 60.527 40.741 0.00 0.00 33.23 3.95
4211 4690 6.070767 GCATGTACTGTATGTATGTATCCCCT 60.071 42.308 0.00 0.00 33.23 4.79
4212 4691 6.106673 GCATGTACTGTATGTATGTATCCCC 58.893 44.000 0.00 0.00 33.23 4.81
4213 4692 6.070767 AGGCATGTACTGTATGTATGTATCCC 60.071 42.308 0.00 0.00 33.23 3.85
4214 4693 6.936279 AGGCATGTACTGTATGTATGTATCC 58.064 40.000 0.00 0.00 33.23 2.59
4215 4694 8.088365 TCAAGGCATGTACTGTATGTATGTATC 58.912 37.037 0.00 0.00 33.23 2.24
4216 4695 7.962441 TCAAGGCATGTACTGTATGTATGTAT 58.038 34.615 0.00 0.00 33.23 2.29
4217 4696 7.354751 TCAAGGCATGTACTGTATGTATGTA 57.645 36.000 0.00 0.00 33.23 2.29
4218 4697 6.233905 TCAAGGCATGTACTGTATGTATGT 57.766 37.500 0.00 0.00 33.23 2.29
4219 4698 7.658982 AGAATCAAGGCATGTACTGTATGTATG 59.341 37.037 0.00 0.00 33.23 2.39
4220 4699 7.739825 AGAATCAAGGCATGTACTGTATGTAT 58.260 34.615 0.00 0.00 33.23 2.29
4221 4700 7.124573 AGAATCAAGGCATGTACTGTATGTA 57.875 36.000 0.00 0.00 0.00 2.29
4222 4701 5.994250 AGAATCAAGGCATGTACTGTATGT 58.006 37.500 0.00 0.00 0.00 2.29
4223 4702 6.932356 AAGAATCAAGGCATGTACTGTATG 57.068 37.500 0.00 0.00 0.00 2.39
4224 4703 7.148018 CCAAAAGAATCAAGGCATGTACTGTAT 60.148 37.037 0.00 0.00 0.00 2.29
4225 4704 6.150976 CCAAAAGAATCAAGGCATGTACTGTA 59.849 38.462 0.00 0.00 0.00 2.74
4226 4705 5.047802 CCAAAAGAATCAAGGCATGTACTGT 60.048 40.000 0.00 0.00 0.00 3.55
4227 4706 5.404946 CCAAAAGAATCAAGGCATGTACTG 58.595 41.667 0.00 0.00 0.00 2.74
4228 4707 4.463891 CCCAAAAGAATCAAGGCATGTACT 59.536 41.667 0.00 0.00 0.00 2.73
4229 4708 4.747810 CCCAAAAGAATCAAGGCATGTAC 58.252 43.478 0.00 0.00 0.00 2.90
4271 4750 7.600375 ACATCTAGTATACCAATTGAATCTGCG 59.400 37.037 7.12 0.00 0.00 5.18
4272 4751 8.715998 CACATCTAGTATACCAATTGAATCTGC 58.284 37.037 7.12 0.00 0.00 4.26
4273 4752 9.212641 CCACATCTAGTATACCAATTGAATCTG 57.787 37.037 7.12 0.00 0.00 2.90
4295 4777 8.588472 GCCATAGTAGCATATATATCATCCACA 58.412 37.037 0.00 0.00 0.00 4.17
4296 4778 8.811017 AGCCATAGTAGCATATATATCATCCAC 58.189 37.037 0.00 0.00 0.00 4.02
4297 4779 8.810041 CAGCCATAGTAGCATATATATCATCCA 58.190 37.037 0.00 0.00 0.00 3.41
4332 4819 2.045926 ACCGGCCTCTGCATCAAC 60.046 61.111 0.00 0.00 40.13 3.18
4421 4908 3.551250 CGGAAATACTTGGCGTGGTTTTT 60.551 43.478 0.00 0.00 0.00 1.94
4445 4932 1.955080 ACATACTACTACTGCCTCCGC 59.045 52.381 0.00 0.00 0.00 5.54
4519 5006 0.034059 AGACAGACAGGCGACCAAAG 59.966 55.000 0.00 0.00 0.00 2.77
4523 5010 1.080434 GACAGACAGACAGGCGACC 60.080 63.158 0.00 0.00 0.00 4.79
4551 5042 0.108615 ATGTACTGAGCCGAGCACAC 60.109 55.000 0.00 0.00 0.00 3.82
4579 5070 5.645497 AGTTATGTGATCCTGAAAGCACTTC 59.355 40.000 0.00 0.00 32.69 3.01
4613 5105 1.862815 GCAGCTCACAAACAGCACTTG 60.863 52.381 0.00 0.00 39.56 3.16
4808 5305 8.827832 TTCATCAAGGTAAATTTCCAGATCAT 57.172 30.769 0.00 0.00 0.00 2.45
4826 5324 3.648067 ACTTCACCTGAGACCTTCATCAA 59.352 43.478 0.00 0.00 34.68 2.57
4841 5339 6.640518 TCAAGTATACCTCAATCACTTCACC 58.359 40.000 0.00 0.00 0.00 4.02
4856 5361 8.494016 AAAGTCAGGTTAAGCATCAAGTATAC 57.506 34.615 7.52 0.00 0.00 1.47
4861 5366 6.974965 AGAAAAAGTCAGGTTAAGCATCAAG 58.025 36.000 7.52 0.00 0.00 3.02
4883 5388 7.232737 TCAAGACTGAAGTGTTAATAGTGGAGA 59.767 37.037 0.00 0.00 29.85 3.71
4906 5411 5.126869 TGAAACCTCACAGCAAAAATCTCAA 59.873 36.000 0.00 0.00 0.00 3.02
4946 5452 1.471684 CAGCAGAAAATGGGACTCAGC 59.528 52.381 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.