Multiple sequence alignment - TraesCS2B01G536200

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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 TraesCS2B01G536200 chr2B 100.000 4341 0 0 725 5065 731899238 731894898 0.000000e+00 8017.0
1 TraesCS2B01G536200 chr2B 87.160 1472 161 18 2856 4323 732013644 732012197 0.000000e+00 1646.0
2 TraesCS2B01G536200 chr2B 86.965 1473 163 19 2856 4323 732018411 732016963 0.000000e+00 1629.0
3 TraesCS2B01G536200 chr2B 100.000 490 0 0 1 490 731899962 731899473 0.000000e+00 905.0
4 TraesCS2B01G536200 chr2B 84.314 153 24 0 1101 1253 733179112 733179264 3.160000e-32 150.0
5 TraesCS2B01G536200 chr2D 93.953 3853 159 21 1265 5065 601605064 601601234 0.000000e+00 5757.0
6 TraesCS2B01G536200 chr2D 89.048 1324 134 9 2853 4165 601964258 601962935 0.000000e+00 1631.0
7 TraesCS2B01G536200 chr2D 85.325 1615 175 34 2853 4436 601709501 601707918 0.000000e+00 1613.0
8 TraesCS2B01G536200 chr2D 89.444 1260 130 3 2853 4110 602773851 602775109 0.000000e+00 1587.0
9 TraesCS2B01G536200 chr2D 88.333 480 36 6 9 481 601607322 601606856 4.430000e-155 558.0
10 TraesCS2B01G536200 chr2D 89.431 369 35 4 909 1276 601606723 601606358 3.570000e-126 462.0
11 TraesCS2B01G536200 chr2D 88.652 141 12 4 725 864 601606863 601606726 8.720000e-38 169.0
12 TraesCS2B01G536200 chr2D 80.392 204 40 0 1101 1304 602766511 602766714 6.790000e-34 156.0
13 TraesCS2B01G536200 chr2A 93.317 2095 119 10 2856 4944 734893907 734891828 0.000000e+00 3073.0
14 TraesCS2B01G536200 chr2A 89.872 1254 124 3 2853 4104 735397084 735398336 0.000000e+00 1609.0
15 TraesCS2B01G536200 chr2A 88.370 1264 141 6 2850 4110 735560596 735561856 0.000000e+00 1515.0
16 TraesCS2B01G536200 chr2A 87.500 128 16 0 1101 1228 735388823 735388950 1.140000e-31 148.0
17 TraesCS2B01G536200 chr2A 93.056 72 2 1 4994 5065 734891826 734891758 8.970000e-18 102.0
18 TraesCS2B01G536200 chr7D 82.555 321 52 3 4329 4649 596241337 596241021 3.860000e-71 279.0
19 TraesCS2B01G536200 chr7B 82.099 324 51 6 4329 4650 674310338 674310020 2.320000e-68 270.0
20 TraesCS2B01G536200 chrUn 81.731 104 12 4 4196 4298 15279997 15280094 4.200000e-11 80.5
21 TraesCS2B01G536200 chrUn 81.731 104 12 4 4196 4298 258625770 258625867 4.200000e-11 80.5
22 TraesCS2B01G536200 chrUn 81.731 104 12 4 4196 4298 388793386 388793483 4.200000e-11 80.5
23 TraesCS2B01G536200 chrUn 81.731 104 12 4 4196 4298 428013337 428013434 4.200000e-11 80.5


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G536200 chr2B 731894898 731899962 5064 True 4461.0 8017 100.00000 1 5065 2 chr2B.!!$R1 5064
1 TraesCS2B01G536200 chr2B 732012197 732018411 6214 True 1637.5 1646 87.06250 2856 4323 2 chr2B.!!$R2 1467
2 TraesCS2B01G536200 chr2D 601601234 601607322 6088 True 1736.5 5757 90.09225 9 5065 4 chr2D.!!$R3 5056
3 TraesCS2B01G536200 chr2D 601962935 601964258 1323 True 1631.0 1631 89.04800 2853 4165 1 chr2D.!!$R2 1312
4 TraesCS2B01G536200 chr2D 601707918 601709501 1583 True 1613.0 1613 85.32500 2853 4436 1 chr2D.!!$R1 1583
5 TraesCS2B01G536200 chr2D 602773851 602775109 1258 False 1587.0 1587 89.44400 2853 4110 1 chr2D.!!$F2 1257
6 TraesCS2B01G536200 chr2A 735397084 735398336 1252 False 1609.0 1609 89.87200 2853 4104 1 chr2A.!!$F2 1251
7 TraesCS2B01G536200 chr2A 734891758 734893907 2149 True 1587.5 3073 93.18650 2856 5065 2 chr2A.!!$R1 2209
8 TraesCS2B01G536200 chr2A 735560596 735561856 1260 False 1515.0 1515 88.37000 2850 4110 1 chr2A.!!$F3 1260

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
909 917 0.029567 CGAGAGCGATGTACAGGACC 59.970 60.0 0.33 0.0 40.82 4.46 F
915 923 0.100682 CGATGTACAGGACCCAGTCG 59.899 60.0 0.33 0.0 32.65 4.18 F
1573 2885 0.106116 AGGTCTCCCGTCCTATGACC 60.106 60.0 0.00 0.0 45.31 4.02 F
1768 3080 0.325203 TCATGTGGGAGATGACGGGA 60.325 55.0 0.00 0.0 0.00 5.14 F
2501 3856 0.605319 TCATTCAACCAGCCCGACAC 60.605 55.0 0.00 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2345 3700 0.031716 CATGTCTGGAGGGGAGGAGA 60.032 60.000 0.00 0.0 0.00 3.71 R
2478 3833 0.321564 CGGGCTGGTTGAATGAGTGA 60.322 55.000 0.00 0.0 0.00 3.41 R
2631 3987 1.001974 CCGAACAGAACCCATGAGACA 59.998 52.381 0.00 0.0 0.00 3.41 R
2755 4111 1.423921 ACTGGTGAAAACTGTAGGGGG 59.576 52.381 0.00 0.0 0.00 5.40 R
4406 10569 5.243507 TGCATTGCCTTCTCATTAGTGAAAA 59.756 36.000 6.12 0.0 33.05 2.29 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
69 70 2.657237 GGTCGTGTGCTAGCAGGT 59.343 61.111 20.03 0.00 0.00 4.00
82 83 2.948720 GCAGGTCAGTCCGCCTCTT 61.949 63.158 0.00 0.00 41.99 2.85
147 148 2.996249 ATCAATGGTGAGCGACTCAT 57.004 45.000 11.73 0.00 42.73 2.90
148 149 2.768253 TCAATGGTGAGCGACTCATT 57.232 45.000 11.73 1.82 42.73 2.57
149 150 3.885724 TCAATGGTGAGCGACTCATTA 57.114 42.857 11.73 5.89 42.73 1.90
150 151 4.200838 TCAATGGTGAGCGACTCATTAA 57.799 40.909 11.73 3.29 42.73 1.40
151 152 4.769688 TCAATGGTGAGCGACTCATTAAT 58.230 39.130 11.73 5.05 42.73 1.40
152 153 5.185454 TCAATGGTGAGCGACTCATTAATT 58.815 37.500 11.73 9.44 42.73 1.40
153 154 6.345298 TCAATGGTGAGCGACTCATTAATTA 58.655 36.000 11.73 0.00 42.73 1.40
154 155 6.821160 TCAATGGTGAGCGACTCATTAATTAA 59.179 34.615 11.73 0.00 42.73 1.40
172 173 1.038280 AAGGACTCGACGTTTCTGGT 58.962 50.000 0.00 0.00 0.00 4.00
178 179 4.421948 GACTCGACGTTTCTGGTGAATAT 58.578 43.478 0.00 0.00 31.56 1.28
181 182 6.570692 ACTCGACGTTTCTGGTGAATATATT 58.429 36.000 0.00 0.00 31.56 1.28
188 189 6.481976 CGTTTCTGGTGAATATATTACAGCCA 59.518 38.462 17.06 12.99 31.56 4.75
198 199 9.905713 TGAATATATTACAGCCAAGAGTTCTTT 57.094 29.630 0.00 0.00 33.11 2.52
209 210 6.147985 AGCCAAGAGTTCTTTAGTTCGATTTC 59.852 38.462 0.00 0.00 33.11 2.17
210 211 6.620949 GCCAAGAGTTCTTTAGTTCGATTTCC 60.621 42.308 0.00 0.00 33.11 3.13
211 212 6.426937 CCAAGAGTTCTTTAGTTCGATTTCCA 59.573 38.462 0.00 0.00 33.11 3.53
214 215 7.893658 AGAGTTCTTTAGTTCGATTTCCAGTA 58.106 34.615 0.00 0.00 0.00 2.74
217 218 9.503399 AGTTCTTTAGTTCGATTTCCAGTATTT 57.497 29.630 0.00 0.00 0.00 1.40
220 221 4.600012 AGTTCGATTTCCAGTATTTGCG 57.400 40.909 0.00 0.00 0.00 4.85
249 250 3.316253 GAGCTGTTCGATGAAATGCTC 57.684 47.619 14.64 14.64 39.69 4.26
261 262 2.224597 TGAAATGCTCAAGTCAGCTCCA 60.225 45.455 0.00 0.00 40.39 3.86
269 270 0.990374 AAGTCAGCTCCAGCCAAGAT 59.010 50.000 0.00 0.00 43.38 2.40
281 282 3.321682 CCAGCCAAGATTCTTGGTTCAAA 59.678 43.478 34.78 0.00 41.53 2.69
285 286 4.800582 GCCAAGATTCTTGGTTCAAAAGGG 60.801 45.833 34.78 14.86 41.53 3.95
326 328 3.217626 GGCTAGCAGCATTGAGGTAAAT 58.782 45.455 18.24 0.00 44.75 1.40
331 333 5.077134 AGCAGCATTGAGGTAAATTTTCC 57.923 39.130 5.74 5.74 0.00 3.13
337 339 7.874528 CAGCATTGAGGTAAATTTTCCTTTCTT 59.125 33.333 16.56 1.83 33.83 2.52
374 376 1.696063 CCATTATCTGGTTGCCTGGG 58.304 55.000 0.00 0.00 40.49 4.45
434 442 1.961277 CCAACGCACTCTGTCCACC 60.961 63.158 0.00 0.00 0.00 4.61
444 452 0.245539 TCTGTCCACCGAATCCGTTC 59.754 55.000 0.00 0.00 0.00 3.95
463 471 1.454847 GCGGGCAATGGGGTTATCA 60.455 57.895 0.00 0.00 0.00 2.15
465 473 0.395036 CGGGCAATGGGGTTATCACA 60.395 55.000 0.00 0.00 0.00 3.58
466 474 1.859302 GGGCAATGGGGTTATCACAA 58.141 50.000 0.00 0.00 0.00 3.33
467 475 1.756538 GGGCAATGGGGTTATCACAAG 59.243 52.381 0.00 0.00 0.00 3.16
468 476 1.136891 GGCAATGGGGTTATCACAAGC 59.863 52.381 0.00 0.00 0.00 4.01
469 477 2.102578 GCAATGGGGTTATCACAAGCT 58.897 47.619 0.00 0.00 0.00 3.74
470 478 2.497273 GCAATGGGGTTATCACAAGCTT 59.503 45.455 0.00 0.00 0.00 3.74
471 479 3.676873 GCAATGGGGTTATCACAAGCTTG 60.677 47.826 24.84 24.84 0.00 4.01
472 480 1.544724 TGGGGTTATCACAAGCTTGC 58.455 50.000 26.27 8.60 0.00 4.01
473 481 0.817654 GGGGTTATCACAAGCTTGCC 59.182 55.000 26.27 16.98 0.00 4.52
474 482 0.817654 GGGTTATCACAAGCTTGCCC 59.182 55.000 26.27 21.72 0.00 5.36
475 483 0.817654 GGTTATCACAAGCTTGCCCC 59.182 55.000 26.27 12.62 0.00 5.80
476 484 0.451783 GTTATCACAAGCTTGCCCCG 59.548 55.000 26.27 12.31 0.00 5.73
477 485 0.679640 TTATCACAAGCTTGCCCCGG 60.680 55.000 26.27 10.81 0.00 5.73
478 486 1.558167 TATCACAAGCTTGCCCCGGA 61.558 55.000 26.27 15.48 0.00 5.14
479 487 2.215451 ATCACAAGCTTGCCCCGGAT 62.215 55.000 26.27 16.90 0.00 4.18
480 488 2.361610 ACAAGCTTGCCCCGGATG 60.362 61.111 26.27 0.00 0.00 3.51
481 489 2.045045 CAAGCTTGCCCCGGATGA 60.045 61.111 14.65 0.00 0.00 2.92
482 490 1.678635 CAAGCTTGCCCCGGATGAA 60.679 57.895 14.65 0.00 0.00 2.57
483 491 1.039233 CAAGCTTGCCCCGGATGAAT 61.039 55.000 14.65 0.00 0.00 2.57
484 492 0.753111 AAGCTTGCCCCGGATGAATC 60.753 55.000 0.73 0.00 0.00 2.52
485 493 1.152881 GCTTGCCCCGGATGAATCT 60.153 57.895 0.73 0.00 0.00 2.40
486 494 1.169034 GCTTGCCCCGGATGAATCTC 61.169 60.000 0.73 0.00 0.00 2.75
487 495 0.181114 CTTGCCCCGGATGAATCTCA 59.819 55.000 0.73 0.00 0.00 3.27
488 496 0.623194 TTGCCCCGGATGAATCTCAA 59.377 50.000 0.73 0.00 0.00 3.02
489 497 0.623194 TGCCCCGGATGAATCTCAAA 59.377 50.000 0.73 0.00 0.00 2.69
757 765 0.880441 TGCGACCAATGACCAACATG 59.120 50.000 0.00 0.00 39.39 3.21
768 776 0.881118 ACCAACATGTTGACCGATGC 59.119 50.000 34.76 0.00 42.93 3.91
781 789 2.187946 GATGCCCTCCAGTCCACG 59.812 66.667 0.00 0.00 0.00 4.94
789 797 0.038159 CTCCAGTCCACGAAGGTCAC 60.038 60.000 0.00 0.00 39.02 3.67
791 799 1.202964 TCCAGTCCACGAAGGTCACTA 60.203 52.381 0.00 0.00 39.02 2.74
804 812 5.428253 GAAGGTCACTATTGGCATAGACAA 58.572 41.667 9.84 0.00 36.58 3.18
813 821 3.719268 TGGCATAGACAAGTTGGACAT 57.281 42.857 7.96 0.00 0.00 3.06
828 836 4.724074 TGGACATGATTTCCAAATCTGC 57.276 40.909 12.22 0.49 43.97 4.26
829 837 4.087907 TGGACATGATTTCCAAATCTGCA 58.912 39.130 12.22 2.74 43.97 4.41
830 838 4.712829 TGGACATGATTTCCAAATCTGCAT 59.287 37.500 12.22 0.00 43.97 3.96
832 840 6.040054 TGGACATGATTTCCAAATCTGCATAG 59.960 38.462 12.22 1.16 43.97 2.23
845 853 7.201758 CCAAATCTGCATAGAAGATTAGCACAA 60.202 37.037 0.82 0.00 42.26 3.33
846 854 6.857777 ATCTGCATAGAAGATTAGCACAAC 57.142 37.500 0.00 0.00 36.32 3.32
851 859 5.582269 GCATAGAAGATTAGCACAACACTCA 59.418 40.000 0.00 0.00 0.00 3.41
864 872 4.761739 CACAACACTCATTAACATCCACCT 59.238 41.667 0.00 0.00 0.00 4.00
865 873 5.241506 CACAACACTCATTAACATCCACCTT 59.758 40.000 0.00 0.00 0.00 3.50
867 875 5.505181 ACACTCATTAACATCCACCTTCT 57.495 39.130 0.00 0.00 0.00 2.85
868 876 5.880901 ACACTCATTAACATCCACCTTCTT 58.119 37.500 0.00 0.00 0.00 2.52
869 877 6.306987 ACACTCATTAACATCCACCTTCTTT 58.693 36.000 0.00 0.00 0.00 2.52
870 878 6.777580 ACACTCATTAACATCCACCTTCTTTT 59.222 34.615 0.00 0.00 0.00 2.27
872 880 6.434340 ACTCATTAACATCCACCTTCTTTTCC 59.566 38.462 0.00 0.00 0.00 3.13
873 881 5.714806 TCATTAACATCCACCTTCTTTTCCC 59.285 40.000 0.00 0.00 0.00 3.97
874 882 2.604912 ACATCCACCTTCTTTTCCCC 57.395 50.000 0.00 0.00 0.00 4.81
876 884 2.450886 ACATCCACCTTCTTTTCCCCTT 59.549 45.455 0.00 0.00 0.00 3.95
877 885 2.971901 TCCACCTTCTTTTCCCCTTC 57.028 50.000 0.00 0.00 0.00 3.46
878 886 1.073284 TCCACCTTCTTTTCCCCTTCG 59.927 52.381 0.00 0.00 0.00 3.79
879 887 1.534729 CACCTTCTTTTCCCCTTCGG 58.465 55.000 0.00 0.00 0.00 4.30
880 888 1.146452 ACCTTCTTTTCCCCTTCGGT 58.854 50.000 0.00 0.00 0.00 4.69
881 889 1.497716 ACCTTCTTTTCCCCTTCGGTT 59.502 47.619 0.00 0.00 0.00 4.44
882 890 2.091499 ACCTTCTTTTCCCCTTCGGTTT 60.091 45.455 0.00 0.00 0.00 3.27
883 891 2.963101 CCTTCTTTTCCCCTTCGGTTTT 59.037 45.455 0.00 0.00 0.00 2.43
884 892 4.146564 CCTTCTTTTCCCCTTCGGTTTTA 58.853 43.478 0.00 0.00 0.00 1.52
885 893 4.585581 CCTTCTTTTCCCCTTCGGTTTTAA 59.414 41.667 0.00 0.00 0.00 1.52
886 894 5.245301 CCTTCTTTTCCCCTTCGGTTTTAAT 59.755 40.000 0.00 0.00 0.00 1.40
887 895 5.970317 TCTTTTCCCCTTCGGTTTTAATC 57.030 39.130 0.00 0.00 0.00 1.75
888 896 5.386924 TCTTTTCCCCTTCGGTTTTAATCA 58.613 37.500 0.00 0.00 0.00 2.57
889 897 5.475564 TCTTTTCCCCTTCGGTTTTAATCAG 59.524 40.000 0.00 0.00 0.00 2.90
890 898 2.718563 TCCCCTTCGGTTTTAATCAGC 58.281 47.619 0.00 0.00 0.00 4.26
891 899 1.400494 CCCCTTCGGTTTTAATCAGCG 59.600 52.381 1.37 1.37 36.47 5.18
892 900 2.352388 CCCTTCGGTTTTAATCAGCGA 58.648 47.619 5.59 5.59 42.12 4.93
893 901 2.351726 CCCTTCGGTTTTAATCAGCGAG 59.648 50.000 8.82 5.15 44.32 5.03
894 902 3.259064 CCTTCGGTTTTAATCAGCGAGA 58.741 45.455 8.82 0.00 44.32 4.04
895 903 3.307242 CCTTCGGTTTTAATCAGCGAGAG 59.693 47.826 8.82 9.20 44.32 3.20
908 916 3.535691 CGAGAGCGATGTACAGGAC 57.464 57.895 0.33 0.00 40.82 3.85
909 917 0.029567 CGAGAGCGATGTACAGGACC 59.970 60.000 0.33 0.00 40.82 4.46
910 918 0.386113 GAGAGCGATGTACAGGACCC 59.614 60.000 0.33 0.00 0.00 4.46
911 919 0.324368 AGAGCGATGTACAGGACCCA 60.324 55.000 0.33 0.00 0.00 4.51
912 920 0.103208 GAGCGATGTACAGGACCCAG 59.897 60.000 0.33 0.00 0.00 4.45
913 921 0.614979 AGCGATGTACAGGACCCAGT 60.615 55.000 0.33 0.00 0.00 4.00
914 922 0.179108 GCGATGTACAGGACCCAGTC 60.179 60.000 0.33 0.00 0.00 3.51
915 923 0.100682 CGATGTACAGGACCCAGTCG 59.899 60.000 0.33 0.00 32.65 4.18
916 924 1.183549 GATGTACAGGACCCAGTCGT 58.816 55.000 0.33 0.00 32.65 4.34
917 925 1.549170 GATGTACAGGACCCAGTCGTT 59.451 52.381 0.33 0.00 32.65 3.85
918 926 1.416243 TGTACAGGACCCAGTCGTTT 58.584 50.000 0.00 0.00 32.65 3.60
919 927 2.596346 TGTACAGGACCCAGTCGTTTA 58.404 47.619 0.00 0.00 32.65 2.01
920 928 2.297033 TGTACAGGACCCAGTCGTTTAC 59.703 50.000 0.00 6.74 35.51 2.01
921 929 1.416243 ACAGGACCCAGTCGTTTACA 58.584 50.000 0.00 0.00 32.65 2.41
922 930 1.343465 ACAGGACCCAGTCGTTTACAG 59.657 52.381 0.00 0.00 32.65 2.74
925 933 1.145803 GACCCAGTCGTTTACAGTGC 58.854 55.000 0.00 0.00 0.00 4.40
932 940 4.242475 CAGTCGTTTACAGTGCCATAGAA 58.758 43.478 0.00 0.00 0.00 2.10
934 942 4.870426 AGTCGTTTACAGTGCCATAGAATG 59.130 41.667 0.00 0.00 0.00 2.67
936 944 5.121768 GTCGTTTACAGTGCCATAGAATGTT 59.878 40.000 0.00 0.00 0.00 2.71
946 954 5.877012 GTGCCATAGAATGTTCAGAGAAGAA 59.123 40.000 0.00 0.00 0.00 2.52
953 961 1.336795 TGTTCAGAGAAGAATGCGCGA 60.337 47.619 12.10 0.00 0.00 5.87
963 971 2.766313 AGAATGCGCGATAAATAGGCA 58.234 42.857 12.10 0.00 38.09 4.75
966 974 0.882927 TGCGCGATAAATAGGCACCC 60.883 55.000 12.10 0.00 0.00 4.61
968 976 1.878953 CGCGATAAATAGGCACCCTT 58.121 50.000 0.00 0.00 34.61 3.95
970 978 2.616842 CGCGATAAATAGGCACCCTTTT 59.383 45.455 0.00 0.00 34.61 2.27
971 979 3.066203 CGCGATAAATAGGCACCCTTTTT 59.934 43.478 0.00 5.31 38.14 1.94
990 998 4.637483 TTTTCTTGCACCAAAGAGACAG 57.363 40.909 0.00 0.00 37.48 3.51
995 1003 2.297701 TGCACCAAAGAGACAGGTTTC 58.702 47.619 0.00 0.00 32.15 2.78
998 1006 2.880890 CACCAAAGAGACAGGTTTCCAG 59.119 50.000 0.00 0.00 32.15 3.86
1018 1026 1.457346 GATGGTGCTGGTTTCCTCTG 58.543 55.000 0.00 0.00 0.00 3.35
1020 1028 1.973812 GGTGCTGGTTTCCTCTGCC 60.974 63.158 0.00 0.00 0.00 4.85
1025 1033 0.322906 CTGGTTTCCTCTGCCCCTTC 60.323 60.000 0.00 0.00 0.00 3.46
1027 1035 1.767692 GTTTCCTCTGCCCCTTCCA 59.232 57.895 0.00 0.00 0.00 3.53
1028 1036 0.609406 GTTTCCTCTGCCCCTTCCAC 60.609 60.000 0.00 0.00 0.00 4.02
1072 1080 2.566833 TGCAGCATTAACACTCCAGT 57.433 45.000 0.00 0.00 0.00 4.00
1155 1163 0.252835 TAGCCGTCCCCTACCCTTTT 60.253 55.000 0.00 0.00 0.00 2.27
1159 1167 1.848886 CGTCCCCTACCCTTTTGGCT 61.849 60.000 0.00 0.00 37.83 4.75
1191 1199 2.033448 TTCCGCACGGGCTTCAAT 59.967 55.556 8.62 0.00 38.10 2.57
1206 1214 0.454452 TCAATCTCACGTGCGACGAG 60.454 55.000 10.96 2.35 46.05 4.18
1243 1251 4.720902 TGCTGGTGGGTGATGGCG 62.721 66.667 0.00 0.00 0.00 5.69
1266 1274 4.034510 GCGGAAGTGGTTGATATTTCTCTG 59.965 45.833 0.00 0.00 0.00 3.35
1323 2635 3.578282 TGAGTATCTGGCTGAACACAAGA 59.422 43.478 0.00 0.00 34.92 3.02
1342 2654 6.711194 CACAAGATCTAATCAATCAGATGGCT 59.289 38.462 0.00 0.00 36.96 4.75
1391 2703 1.704641 CCCCTGATAGTGTCCATCGA 58.295 55.000 0.00 0.00 0.00 3.59
1416 2728 2.469516 CCGGTTCGTTGCTATGGGC 61.470 63.158 0.00 0.00 42.22 5.36
1438 2750 1.679944 GCAATGTCTTAGCCAGCCTCA 60.680 52.381 0.00 0.00 0.00 3.86
1448 2760 1.382692 GCCAGCCTCATTGCCTCTTC 61.383 60.000 0.00 0.00 0.00 2.87
1459 2771 3.280920 GCCTCTTCTGGCGACTATG 57.719 57.895 0.00 0.00 43.74 2.23
1471 2783 3.257375 TGGCGACTATGTTAGTGTCTGTT 59.743 43.478 0.00 0.00 39.59 3.16
1483 2795 3.650139 AGTGTCTGTTCCGTGTATTGTC 58.350 45.455 0.00 0.00 0.00 3.18
1489 2801 2.365941 TGTTCCGTGTATTGTCCTGACA 59.634 45.455 0.00 0.00 39.98 3.58
1495 2807 2.029290 GTGTATTGTCCTGACAGACCGT 60.029 50.000 3.32 0.00 42.94 4.83
1558 2870 2.279517 CCATCGCACGGCTAGGTC 60.280 66.667 0.00 0.00 0.00 3.85
1571 2883 1.202903 GCTAGGTCTCCCGTCCTATGA 60.203 57.143 0.00 0.00 36.00 2.15
1573 2885 0.106116 AGGTCTCCCGTCCTATGACC 60.106 60.000 0.00 0.00 45.31 4.02
1579 2891 1.742768 CCGTCCTATGACCTCCAGC 59.257 63.158 0.00 0.00 38.32 4.85
1615 2927 2.304470 TGGAGAACCGGTGATTCATTGA 59.696 45.455 8.52 0.00 39.42 2.57
1660 2972 1.228124 CAAGAGTGGTTGGCCCGAA 60.228 57.895 0.00 0.00 35.15 4.30
1699 3011 6.738453 GCAGTTGAATTACTTTGACAACCCAT 60.738 38.462 0.00 0.00 40.77 4.00
1719 3031 6.486657 ACCCATATAAGATTGTTGATTCCACG 59.513 38.462 0.00 0.00 0.00 4.94
1759 3071 2.795231 ATGGTCACTTCATGTGGGAG 57.205 50.000 0.00 0.00 46.20 4.30
1768 3080 0.325203 TCATGTGGGAGATGACGGGA 60.325 55.000 0.00 0.00 0.00 5.14
1783 3095 1.003928 ACGGGAAATTGTACTGGGGAC 59.996 52.381 0.00 0.00 0.00 4.46
1790 3102 1.268992 TTGTACTGGGGACGGGATGG 61.269 60.000 0.00 0.00 42.76 3.51
1797 3109 1.227383 GGGACGGGATGGCTTTGAT 59.773 57.895 0.00 0.00 0.00 2.57
1819 3131 4.617253 TTATATGAACACAGGGGATCCG 57.383 45.455 5.45 0.00 38.33 4.18
1934 3270 4.022068 CGCAAATGGATGCCAAGGTATATT 60.022 41.667 0.00 0.00 43.47 1.28
1990 3326 1.194781 AGGGACCATGTTGCTCGTCT 61.195 55.000 0.00 0.00 0.00 4.18
2039 3392 7.826690 ACCGCACTTTGAACATATTAGATTTT 58.173 30.769 0.00 0.00 0.00 1.82
2075 3430 3.181496 TGTGAGCAAAATGTGTTTACGCA 60.181 39.130 0.00 0.00 40.98 5.24
2189 3544 1.378382 CATCAATGTGCCGGGGACA 60.378 57.895 23.96 23.96 0.00 4.02
2301 3656 8.667592 AGTTAAGGTCCTTAGAAGTATCTGTT 57.332 34.615 11.23 0.00 37.10 3.16
2302 3657 9.102453 AGTTAAGGTCCTTAGAAGTATCTGTTT 57.898 33.333 11.23 0.00 37.10 2.83
2303 3658 9.152595 GTTAAGGTCCTTAGAAGTATCTGTTTG 57.847 37.037 11.23 0.00 37.10 2.93
2304 3659 6.936968 AGGTCCTTAGAAGTATCTGTTTGT 57.063 37.500 0.00 0.00 37.10 2.83
2305 3660 8.431910 AAGGTCCTTAGAAGTATCTGTTTGTA 57.568 34.615 0.93 0.00 37.10 2.41
2306 3661 8.611051 AGGTCCTTAGAAGTATCTGTTTGTAT 57.389 34.615 0.00 0.00 37.10 2.29
2345 3700 1.283613 TGGCGAGGTTGGTCCATTAAT 59.716 47.619 0.00 0.00 39.02 1.40
2352 3707 3.459969 AGGTTGGTCCATTAATCTCCTCC 59.540 47.826 0.00 0.00 39.02 4.30
2357 3712 2.640332 GTCCATTAATCTCCTCCCCTCC 59.360 54.545 0.00 0.00 0.00 4.30
2363 3718 0.948050 ATCTCCTCCCCTCCAGACAT 59.052 55.000 0.00 0.00 0.00 3.06
2373 3728 2.022195 CCTCCAGACATGAGCCATTTG 58.978 52.381 0.00 0.00 0.00 2.32
2379 3734 4.321008 CCAGACATGAGCCATTTGATATGC 60.321 45.833 0.00 0.00 0.00 3.14
2380 3735 3.825014 AGACATGAGCCATTTGATATGCC 59.175 43.478 0.00 0.00 0.00 4.40
2382 3737 3.962063 ACATGAGCCATTTGATATGCCAA 59.038 39.130 0.00 0.00 0.00 4.52
2388 3743 4.114794 GCCATTTGATATGCCAAACAGTC 58.885 43.478 0.00 0.00 38.65 3.51
2501 3856 0.605319 TCATTCAACCAGCCCGACAC 60.605 55.000 0.00 0.00 0.00 3.67
2502 3857 0.606401 CATTCAACCAGCCCGACACT 60.606 55.000 0.00 0.00 0.00 3.55
2631 3987 1.538687 GGCATTGTTCCTTGCTGCCT 61.539 55.000 4.67 0.00 46.97 4.75
2771 4127 1.144298 ACCACCCCCTACAGTTTTCAC 59.856 52.381 0.00 0.00 0.00 3.18
3170 9294 6.707608 GCATCTTATCTGATCAACATGTGGTA 59.292 38.462 0.00 0.00 0.00 3.25
3305 9429 2.163412 CCTCGAGACAGAAGTTCCTCTG 59.837 54.545 15.71 0.00 46.94 3.35
3392 9516 7.872138 ACCCTTTGTCATGGAAAGATAGATTA 58.128 34.615 15.74 0.00 33.01 1.75
3420 9544 1.345415 CATTGGAAACTGCAAGGGCTT 59.655 47.619 0.00 0.00 41.91 4.35
3549 9673 5.336690 GGAGCTTCAAGGTCAATTGCAATAA 60.337 40.000 18.19 0.95 44.10 1.40
3584 9708 0.320073 TTACAGCCGTCCAAGGAACG 60.320 55.000 0.00 0.00 0.00 3.95
3638 9762 1.158434 GTCGACTCACGGAGAAGAGT 58.842 55.000 8.70 0.00 45.35 3.24
3687 9811 1.686355 AGAGCTACTGACGAGGATGG 58.314 55.000 0.00 0.00 0.00 3.51
3725 9849 3.466836 TCATTCGTCAGAAAGCACAAGT 58.533 40.909 0.00 0.00 40.15 3.16
3741 9865 4.508861 GCACAAGTCTTGCATCACATTTTT 59.491 37.500 12.66 0.00 39.93 1.94
3913 10037 3.812053 GAGACAACACTTGAAGATGTGCT 59.188 43.478 0.00 1.77 37.68 4.40
3951 10075 5.384063 TCTCAGTTCTCAGATCACAAGAC 57.616 43.478 0.00 0.00 0.00 3.01
3963 10087 5.704515 CAGATCACAAGACTGAACCAGAATT 59.295 40.000 0.45 0.00 35.18 2.17
3964 10088 5.704515 AGATCACAAGACTGAACCAGAATTG 59.295 40.000 0.45 7.44 36.92 2.32
4040 10164 5.192327 ACAGCTTGGAAAAAGAGTTCATG 57.808 39.130 0.00 0.00 0.00 3.07
4048 10172 6.761312 TGGAAAAAGAGTTCATGCATTCATT 58.239 32.000 0.00 0.00 0.00 2.57
4080 10207 6.889177 TCCAAGATGATTTTGCTTACATGGTA 59.111 34.615 0.00 0.00 0.00 3.25
4081 10208 6.974622 CCAAGATGATTTTGCTTACATGGTAC 59.025 38.462 0.00 0.00 0.00 3.34
4406 10569 2.224329 TGAAATGCTTTGTTGCAGGCAT 60.224 40.909 0.00 0.00 46.71 4.40
4414 10577 4.619973 CTTTGTTGCAGGCATTTTCACTA 58.380 39.130 0.00 0.00 0.00 2.74
4436 10607 5.873179 AATGAGAAGGCAATGCAAATTTG 57.127 34.783 14.03 14.03 0.00 2.32
4571 10742 0.179129 CCGGCCTGAAATGATTGTGC 60.179 55.000 0.00 0.00 0.00 4.57
4664 10838 6.038714 GGAGAGAAAAAGGTATTGCCACATAG 59.961 42.308 0.00 0.00 40.61 2.23
4770 10947 3.995636 ACCTCTAGGCCATGTTTCTCTA 58.004 45.455 5.01 0.00 39.32 2.43
4775 10952 5.918608 TCTAGGCCATGTTTCTCTATTGAC 58.081 41.667 5.01 0.00 0.00 3.18
4861 11038 6.203530 AGGAAAATATGTATGATGCGTCAGTG 59.796 38.462 15.04 0.00 37.87 3.66
4862 11039 6.202762 GGAAAATATGTATGATGCGTCAGTGA 59.797 38.462 15.04 0.45 37.87 3.41
4863 11040 7.254761 GGAAAATATGTATGATGCGTCAGTGAA 60.255 37.037 15.04 0.49 37.87 3.18
4864 11041 7.552458 AAATATGTATGATGCGTCAGTGAAA 57.448 32.000 15.04 0.35 37.87 2.69
4865 11042 7.552458 AATATGTATGATGCGTCAGTGAAAA 57.448 32.000 15.04 0.00 37.87 2.29
4866 11043 7.734924 ATATGTATGATGCGTCAGTGAAAAT 57.265 32.000 15.04 3.50 37.87 1.82
4867 11044 8.831715 ATATGTATGATGCGTCAGTGAAAATA 57.168 30.769 15.04 5.46 37.87 1.40
4868 11045 7.734924 ATGTATGATGCGTCAGTGAAAATAT 57.265 32.000 15.04 0.00 37.87 1.28
4869 11046 7.552458 TGTATGATGCGTCAGTGAAAATATT 57.448 32.000 15.04 0.00 37.87 1.28
4880 11057 9.658475 CGTCAGTGAAAATATTGAAAACACTAA 57.342 29.630 0.00 0.00 35.77 2.24
4896 11073 8.947055 AAAACACTAAATTTCAGACAAGCATT 57.053 26.923 0.00 0.00 0.00 3.56
4953 11130 6.351456 GCCTGATCTAACACTTCCTTAGTTCT 60.351 42.308 0.00 0.00 33.85 3.01
4958 11135 9.791820 GATCTAACACTTCCTTAGTTCTAACTC 57.208 37.037 0.00 0.00 40.37 3.01
4964 11141 4.820894 TCCTTAGTTCTAACTCCCAAGC 57.179 45.455 0.00 0.00 40.37 4.01
5026 11203 5.611374 TGCTTTCAGCTACTTGTAGAAAGT 58.389 37.500 17.01 0.00 44.18 2.66
5027 11204 6.055588 TGCTTTCAGCTACTTGTAGAAAGTT 58.944 36.000 17.01 0.00 44.18 2.66
5028 11205 7.214381 TGCTTTCAGCTACTTGTAGAAAGTTA 58.786 34.615 17.01 8.09 44.18 2.24
5029 11206 7.385205 TGCTTTCAGCTACTTGTAGAAAGTTAG 59.615 37.037 17.01 3.08 44.18 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 4.279145 AGTTATTAGAAGAGGCGGACTGA 58.721 43.478 0.00 0.00 0.00 3.41
120 121 2.564771 GCTCACCATTGATTCCGATCA 58.435 47.619 0.00 0.00 40.46 2.92
147 148 5.865552 CCAGAAACGTCGAGTCCTTAATTAA 59.134 40.000 0.00 0.00 0.00 1.40
148 149 5.047802 ACCAGAAACGTCGAGTCCTTAATTA 60.048 40.000 0.00 0.00 0.00 1.40
149 150 4.243270 CCAGAAACGTCGAGTCCTTAATT 58.757 43.478 0.00 0.00 0.00 1.40
150 151 3.257624 ACCAGAAACGTCGAGTCCTTAAT 59.742 43.478 0.00 0.00 0.00 1.40
151 152 2.624838 ACCAGAAACGTCGAGTCCTTAA 59.375 45.455 0.00 0.00 0.00 1.85
152 153 2.030540 CACCAGAAACGTCGAGTCCTTA 60.031 50.000 0.00 0.00 0.00 2.69
153 154 1.038280 ACCAGAAACGTCGAGTCCTT 58.962 50.000 0.00 0.00 0.00 3.36
154 155 0.314302 CACCAGAAACGTCGAGTCCT 59.686 55.000 0.00 0.00 0.00 3.85
172 173 9.905713 AAAGAACTCTTGGCTGTAATATATTCA 57.094 29.630 0.00 0.00 36.12 2.57
178 179 7.544566 CGAACTAAAGAACTCTTGGCTGTAATA 59.455 37.037 0.00 0.00 36.12 0.98
181 182 5.010314 TCGAACTAAAGAACTCTTGGCTGTA 59.990 40.000 0.00 0.00 36.12 2.74
188 189 7.217906 ACTGGAAATCGAACTAAAGAACTCTT 58.782 34.615 0.00 0.00 37.91 2.85
198 199 4.033587 GCGCAAATACTGGAAATCGAACTA 59.966 41.667 0.30 0.00 0.00 2.24
209 210 1.430632 CCTGCAGCGCAAATACTGG 59.569 57.895 11.47 3.41 38.41 4.00
210 211 1.226491 GCCTGCAGCGCAAATACTG 60.226 57.895 18.68 0.00 38.41 2.74
211 212 3.190878 GCCTGCAGCGCAAATACT 58.809 55.556 18.68 0.00 38.41 2.12
220 221 3.797546 GAACAGCTCGCCTGCAGC 61.798 66.667 8.66 2.87 45.78 5.25
249 250 0.035881 TCTTGGCTGGAGCTGACTTG 59.964 55.000 0.00 0.00 41.70 3.16
261 262 4.039609 CCTTTTGAACCAAGAATCTTGGCT 59.960 41.667 34.77 26.61 43.23 4.75
269 270 2.763448 CCACACCCTTTTGAACCAAGAA 59.237 45.455 0.00 0.00 0.00 2.52
281 282 4.740822 GGCGCCATCCACACCCTT 62.741 66.667 24.80 0.00 0.00 3.95
308 309 5.951747 AGGAAAATTTACCTCAATGCTGCTA 59.048 36.000 0.00 0.00 0.00 3.49
326 328 4.951094 TCGAAAACAGGGAAGAAAGGAAAA 59.049 37.500 0.00 0.00 0.00 2.29
331 333 5.175673 GCAATTTCGAAAACAGGGAAGAAAG 59.824 40.000 15.66 0.00 32.24 2.62
337 339 2.311463 TGGCAATTTCGAAAACAGGGA 58.689 42.857 15.66 0.00 0.00 4.20
444 452 2.518349 ATAACCCCATTGCCCGCG 60.518 61.111 0.00 0.00 0.00 6.46
446 454 0.395036 TGTGATAACCCCATTGCCCG 60.395 55.000 0.00 0.00 0.00 6.13
456 464 0.817654 GGGGCAAGCTTGTGATAACC 59.182 55.000 26.55 17.44 0.00 2.85
457 465 0.451783 CGGGGCAAGCTTGTGATAAC 59.548 55.000 26.55 9.43 0.00 1.89
458 466 0.679640 CCGGGGCAAGCTTGTGATAA 60.680 55.000 26.55 0.00 0.00 1.75
463 471 2.361610 CATCCGGGGCAAGCTTGT 60.362 61.111 26.55 2.87 0.00 3.16
465 473 0.753111 GATTCATCCGGGGCAAGCTT 60.753 55.000 0.00 0.00 0.00 3.74
466 474 1.152881 GATTCATCCGGGGCAAGCT 60.153 57.895 0.00 0.00 0.00 3.74
467 475 1.152881 AGATTCATCCGGGGCAAGC 60.153 57.895 0.00 0.00 0.00 4.01
468 476 0.181114 TGAGATTCATCCGGGGCAAG 59.819 55.000 0.00 0.00 0.00 4.01
469 477 0.623194 TTGAGATTCATCCGGGGCAA 59.377 50.000 0.00 0.00 0.00 4.52
470 478 0.623194 TTTGAGATTCATCCGGGGCA 59.377 50.000 0.00 0.00 0.00 5.36
471 479 3.494850 TTTGAGATTCATCCGGGGC 57.505 52.632 0.00 0.00 0.00 5.80
757 765 1.450312 CTGGAGGGCATCGGTCAAC 60.450 63.158 0.00 0.00 0.00 3.18
768 776 1.889530 GACCTTCGTGGACTGGAGGG 61.890 65.000 4.38 0.00 39.71 4.30
781 789 5.023533 TGTCTATGCCAATAGTGACCTTC 57.976 43.478 0.00 0.00 37.60 3.46
789 797 5.185454 TGTCCAACTTGTCTATGCCAATAG 58.815 41.667 0.00 0.00 37.68 1.73
791 799 4.032960 TGTCCAACTTGTCTATGCCAAT 57.967 40.909 0.00 0.00 0.00 3.16
813 821 8.529424 AATCTTCTATGCAGATTTGGAAATCA 57.471 30.769 13.30 0.00 45.59 2.57
825 833 5.583854 AGTGTTGTGCTAATCTTCTATGCAG 59.416 40.000 0.00 0.00 34.15 4.41
826 834 5.491070 AGTGTTGTGCTAATCTTCTATGCA 58.509 37.500 0.00 0.00 0.00 3.96
827 835 5.582269 TGAGTGTTGTGCTAATCTTCTATGC 59.418 40.000 0.00 0.00 0.00 3.14
828 836 7.783090 ATGAGTGTTGTGCTAATCTTCTATG 57.217 36.000 0.00 0.00 0.00 2.23
829 837 9.890629 TTAATGAGTGTTGTGCTAATCTTCTAT 57.109 29.630 0.00 0.00 0.00 1.98
830 838 9.151471 GTTAATGAGTGTTGTGCTAATCTTCTA 57.849 33.333 0.00 0.00 0.00 2.10
832 840 7.806690 TGTTAATGAGTGTTGTGCTAATCTTC 58.193 34.615 0.00 0.00 0.00 2.87
840 848 4.475944 GTGGATGTTAATGAGTGTTGTGC 58.524 43.478 0.00 0.00 0.00 4.57
845 853 5.505181 AGAAGGTGGATGTTAATGAGTGT 57.495 39.130 0.00 0.00 0.00 3.55
846 854 6.824305 AAAGAAGGTGGATGTTAATGAGTG 57.176 37.500 0.00 0.00 0.00 3.51
851 859 5.023452 GGGGAAAAGAAGGTGGATGTTAAT 58.977 41.667 0.00 0.00 0.00 1.40
874 882 3.242123 GCTCTCGCTGATTAAAACCGAAG 60.242 47.826 0.00 0.00 0.00 3.79
876 884 2.268298 GCTCTCGCTGATTAAAACCGA 58.732 47.619 0.00 0.00 0.00 4.69
877 885 1.005975 CGCTCTCGCTGATTAAAACCG 60.006 52.381 0.00 0.00 0.00 4.44
878 886 2.268298 TCGCTCTCGCTGATTAAAACC 58.732 47.619 0.00 0.00 35.26 3.27
879 887 3.307242 ACATCGCTCTCGCTGATTAAAAC 59.693 43.478 0.00 0.00 35.59 2.43
880 888 3.521560 ACATCGCTCTCGCTGATTAAAA 58.478 40.909 0.00 0.00 35.59 1.52
881 889 3.165058 ACATCGCTCTCGCTGATTAAA 57.835 42.857 0.00 0.00 35.59 1.52
882 890 2.871182 ACATCGCTCTCGCTGATTAA 57.129 45.000 0.00 0.00 35.59 1.40
883 891 2.616842 TGTACATCGCTCTCGCTGATTA 59.383 45.455 0.00 0.00 35.59 1.75
884 892 1.405463 TGTACATCGCTCTCGCTGATT 59.595 47.619 0.00 0.00 35.59 2.57
885 893 1.001924 CTGTACATCGCTCTCGCTGAT 60.002 52.381 0.00 0.00 35.59 2.90
886 894 0.378610 CTGTACATCGCTCTCGCTGA 59.621 55.000 0.00 0.00 35.59 4.26
887 895 0.593518 CCTGTACATCGCTCTCGCTG 60.594 60.000 0.00 0.00 37.78 5.18
888 896 0.748367 TCCTGTACATCGCTCTCGCT 60.748 55.000 0.00 0.00 35.26 4.93
889 897 0.592754 GTCCTGTACATCGCTCTCGC 60.593 60.000 0.00 0.00 35.26 5.03
890 898 0.029567 GGTCCTGTACATCGCTCTCG 59.970 60.000 0.00 0.00 0.00 4.04
891 899 0.386113 GGGTCCTGTACATCGCTCTC 59.614 60.000 0.00 0.00 0.00 3.20
892 900 0.324368 TGGGTCCTGTACATCGCTCT 60.324 55.000 0.00 0.00 0.00 4.09
893 901 0.103208 CTGGGTCCTGTACATCGCTC 59.897 60.000 0.00 0.00 0.00 5.03
894 902 0.614979 ACTGGGTCCTGTACATCGCT 60.615 55.000 0.00 0.00 0.00 4.93
895 903 0.179108 GACTGGGTCCTGTACATCGC 60.179 60.000 0.00 0.00 0.00 4.58
896 904 0.100682 CGACTGGGTCCTGTACATCG 59.899 60.000 0.00 0.00 0.00 3.84
897 905 1.183549 ACGACTGGGTCCTGTACATC 58.816 55.000 0.00 0.00 0.00 3.06
898 906 1.640917 AACGACTGGGTCCTGTACAT 58.359 50.000 0.00 0.00 0.00 2.29
899 907 1.416243 AAACGACTGGGTCCTGTACA 58.584 50.000 0.00 0.00 0.00 2.90
900 908 2.297033 TGTAAACGACTGGGTCCTGTAC 59.703 50.000 0.00 0.00 0.00 2.90
901 909 2.559668 CTGTAAACGACTGGGTCCTGTA 59.440 50.000 0.00 0.00 0.00 2.74
902 910 1.343465 CTGTAAACGACTGGGTCCTGT 59.657 52.381 0.00 0.00 0.00 4.00
903 911 1.343465 ACTGTAAACGACTGGGTCCTG 59.657 52.381 0.00 0.00 0.00 3.86
904 912 1.343465 CACTGTAAACGACTGGGTCCT 59.657 52.381 0.00 0.00 0.00 3.85
905 913 1.792006 CACTGTAAACGACTGGGTCC 58.208 55.000 0.00 0.00 0.00 4.46
906 914 1.145803 GCACTGTAAACGACTGGGTC 58.854 55.000 0.00 0.00 33.08 4.46
907 915 0.250166 GGCACTGTAAACGACTGGGT 60.250 55.000 0.00 0.00 33.08 4.51
908 916 0.250124 TGGCACTGTAAACGACTGGG 60.250 55.000 0.00 0.00 33.64 4.45
909 917 1.808411 ATGGCACTGTAAACGACTGG 58.192 50.000 0.00 0.00 0.00 4.00
910 918 3.845178 TCTATGGCACTGTAAACGACTG 58.155 45.455 0.00 0.00 0.00 3.51
911 919 4.530710 TTCTATGGCACTGTAAACGACT 57.469 40.909 0.00 0.00 0.00 4.18
912 920 4.630069 ACATTCTATGGCACTGTAAACGAC 59.370 41.667 0.00 0.00 33.60 4.34
913 921 4.827692 ACATTCTATGGCACTGTAAACGA 58.172 39.130 0.00 0.00 33.60 3.85
914 922 5.121611 TGAACATTCTATGGCACTGTAAACG 59.878 40.000 0.00 0.00 33.60 3.60
915 923 6.371548 TCTGAACATTCTATGGCACTGTAAAC 59.628 38.462 0.00 0.00 33.60 2.01
916 924 6.472016 TCTGAACATTCTATGGCACTGTAAA 58.528 36.000 0.00 0.00 33.60 2.01
917 925 6.048732 TCTGAACATTCTATGGCACTGTAA 57.951 37.500 0.00 0.00 33.60 2.41
918 926 5.422012 TCTCTGAACATTCTATGGCACTGTA 59.578 40.000 0.00 0.00 33.60 2.74
919 927 4.223700 TCTCTGAACATTCTATGGCACTGT 59.776 41.667 0.00 0.00 33.60 3.55
920 928 4.763073 TCTCTGAACATTCTATGGCACTG 58.237 43.478 0.00 0.00 33.60 3.66
921 929 5.188555 TCTTCTCTGAACATTCTATGGCACT 59.811 40.000 0.00 0.00 33.60 4.40
922 930 5.423015 TCTTCTCTGAACATTCTATGGCAC 58.577 41.667 0.00 0.00 33.60 5.01
925 933 6.292757 CGCATTCTTCTCTGAACATTCTATGG 60.293 42.308 0.00 0.00 33.60 2.74
932 940 1.662629 CGCGCATTCTTCTCTGAACAT 59.337 47.619 8.75 0.00 0.00 2.71
934 942 1.350193 TCGCGCATTCTTCTCTGAAC 58.650 50.000 8.75 0.00 0.00 3.18
936 944 3.436700 TTATCGCGCATTCTTCTCTGA 57.563 42.857 8.75 0.00 0.00 3.27
946 954 1.156736 GGTGCCTATTTATCGCGCAT 58.843 50.000 8.75 2.59 34.71 4.73
968 976 4.142182 CCTGTCTCTTTGGTGCAAGAAAAA 60.142 41.667 0.00 0.00 0.00 1.94
970 978 2.951642 CCTGTCTCTTTGGTGCAAGAAA 59.048 45.455 0.00 0.00 0.00 2.52
971 979 2.092429 ACCTGTCTCTTTGGTGCAAGAA 60.092 45.455 0.00 0.00 32.16 2.52
972 980 1.490490 ACCTGTCTCTTTGGTGCAAGA 59.510 47.619 0.00 0.00 32.16 3.02
990 998 2.571548 CAGCACCATCCTGGAAACC 58.428 57.895 0.00 0.00 40.96 3.27
998 1006 0.329596 AGAGGAAACCAGCACCATCC 59.670 55.000 0.00 0.00 0.00 3.51
1004 1012 2.436109 GGGCAGAGGAAACCAGCA 59.564 61.111 0.00 0.00 0.00 4.41
1009 1017 0.609406 GTGGAAGGGGCAGAGGAAAC 60.609 60.000 0.00 0.00 0.00 2.78
1011 1019 1.065410 TTGTGGAAGGGGCAGAGGAA 61.065 55.000 0.00 0.00 0.00 3.36
1018 1026 0.467804 TTTGCTTTTGTGGAAGGGGC 59.532 50.000 0.00 0.00 0.00 5.80
1020 1028 3.541996 AACTTTGCTTTTGTGGAAGGG 57.458 42.857 0.00 0.00 0.00 3.95
1025 1033 3.494251 GGTGCATAACTTTGCTTTTGTGG 59.506 43.478 0.00 0.00 43.18 4.17
1027 1035 4.141959 ACTGGTGCATAACTTTGCTTTTGT 60.142 37.500 0.00 0.00 43.18 2.83
1028 1036 4.370917 ACTGGTGCATAACTTTGCTTTTG 58.629 39.130 0.00 0.00 43.18 2.44
1072 1080 3.876914 GCTGCTAATGTTGCCACTATACA 59.123 43.478 0.00 0.00 0.00 2.29
1073 1081 4.130118 AGCTGCTAATGTTGCCACTATAC 58.870 43.478 0.00 0.00 0.00 1.47
1140 1148 1.378119 GCCAAAAGGGTAGGGGACG 60.378 63.158 0.00 0.00 39.65 4.79
1155 1163 4.659172 CACCCTTGCCGGAAGCCA 62.659 66.667 5.05 0.00 42.71 4.75
1180 1188 0.670546 CACGTGAGATTGAAGCCCGT 60.671 55.000 10.90 0.00 0.00 5.28
1191 1199 2.554775 GTCTCGTCGCACGTGAGA 59.445 61.111 22.23 20.24 43.41 3.27
1243 1251 4.034510 CAGAGAAATATCAACCACTTCCGC 59.965 45.833 0.00 0.00 0.00 5.54
1244 1252 5.292101 GTCAGAGAAATATCAACCACTTCCG 59.708 44.000 0.00 0.00 0.00 4.30
1266 1274 2.162754 CCGCAACGTACCATCCGTC 61.163 63.158 0.00 0.00 37.61 4.79
1279 2591 0.035152 ATCTTGCTGTGGATCCGCAA 60.035 50.000 27.33 23.36 42.28 4.85
1323 2635 5.768662 CCACAAGCCATCTGATTGATTAGAT 59.231 40.000 0.00 0.00 33.92 1.98
1342 2654 4.641645 CAGGCCAGCGGACCACAA 62.642 66.667 5.01 0.00 0.00 3.33
1379 2691 2.159296 CGGTTGTGATCGATGGACACTA 60.159 50.000 0.54 0.00 35.83 2.74
1391 2703 0.534203 AGCAACGAACCGGTTGTGAT 60.534 50.000 27.87 15.62 46.93 3.06
1416 2728 0.737219 GGCTGGCTAAGACATTGCAG 59.263 55.000 0.00 0.00 32.10 4.41
1448 2760 3.119459 ACAGACACTAACATAGTCGCCAG 60.119 47.826 0.00 0.00 36.76 4.85
1459 2771 4.986659 ACAATACACGGAACAGACACTAAC 59.013 41.667 0.00 0.00 0.00 2.34
1471 2783 2.230508 GTCTGTCAGGACAATACACGGA 59.769 50.000 3.45 0.00 41.33 4.69
1483 2795 2.159819 CTCACCCACGGTCTGTCAGG 62.160 65.000 0.00 0.00 31.02 3.86
1489 2801 3.681835 GTCGCTCACCCACGGTCT 61.682 66.667 0.00 0.00 31.02 3.85
1556 2868 1.320507 GAGGTCATAGGACGGGAGAC 58.679 60.000 0.77 0.00 45.28 3.36
1558 2870 0.106167 TGGAGGTCATAGGACGGGAG 60.106 60.000 0.77 0.00 45.28 4.30
1579 2891 2.575532 TCTCCAGTTCAAAGCACCAAG 58.424 47.619 0.00 0.00 0.00 3.61
1594 2906 2.304470 TCAATGAATCACCGGTTCTCCA 59.696 45.455 2.97 0.95 0.00 3.86
1595 2907 2.939103 CTCAATGAATCACCGGTTCTCC 59.061 50.000 2.97 0.00 0.00 3.71
1611 2923 3.134623 TGAACACCGCTCCATATCTCAAT 59.865 43.478 0.00 0.00 0.00 2.57
1615 2927 3.306364 GCTATGAACACCGCTCCATATCT 60.306 47.826 0.00 0.00 0.00 1.98
1664 2976 0.892755 ATTCAACTGCAGCATGGGTG 59.107 50.000 15.27 0.00 35.86 4.61
1699 3011 8.731275 ATCAACGTGGAATCAACAATCTTATA 57.269 30.769 0.00 0.00 0.00 0.98
1732 3044 5.241403 ACATGAAGTGACCATTCTACCAA 57.759 39.130 0.00 0.00 0.00 3.67
1759 3071 2.943033 CCCAGTACAATTTCCCGTCATC 59.057 50.000 0.00 0.00 0.00 2.92
1768 3080 1.364269 TCCCGTCCCCAGTACAATTT 58.636 50.000 0.00 0.00 0.00 1.82
1783 3095 6.016360 TGTTCATATAAATCAAAGCCATCCCG 60.016 38.462 0.00 0.00 0.00 5.14
1790 3102 6.321181 TCCCCTGTGTTCATATAAATCAAAGC 59.679 38.462 0.00 0.00 0.00 3.51
1797 3109 4.410883 ACGGATCCCCTGTGTTCATATAAA 59.589 41.667 6.06 0.00 0.00 1.40
1819 3131 6.453922 GCGACTATGAAGCAGTTTACACTTAC 60.454 42.308 0.00 0.00 0.00 2.34
1934 3270 9.116067 AGTGCAAGAAAACAACAAGTAGTAATA 57.884 29.630 0.00 0.00 0.00 0.98
1950 3286 4.458989 CCTGGCTATAACAAGTGCAAGAAA 59.541 41.667 0.00 0.00 0.00 2.52
2016 3369 8.798153 GGAAAAATCTAATATGTTCAAAGTGCG 58.202 33.333 0.00 0.00 0.00 5.34
2039 3392 3.286353 TGCTCACAAAGTTGACATGGAA 58.714 40.909 0.00 0.00 0.00 3.53
2046 3399 5.070770 ACACATTTTGCTCACAAAGTTGA 57.929 34.783 0.00 0.00 46.08 3.18
2048 3401 6.034470 CGTAAACACATTTTGCTCACAAAGTT 59.966 34.615 0.00 0.00 46.08 2.66
2107 3462 8.045507 ACTCATCAATATCTGAAAAGAGAGCAA 58.954 33.333 0.00 0.00 37.67 3.91
2189 3544 2.418368 TCTTTGCAAGGCATCGGTAT 57.582 45.000 3.19 0.00 38.76 2.73
2267 3622 9.411189 CTTCTAAGGACCTTAACTATCACTAGT 57.589 37.037 14.90 0.00 39.97 2.57
2302 3657 9.944376 GCCAACTCATATCTTTATAGGAATACA 57.056 33.333 0.00 0.00 28.56 2.29
2303 3658 9.088512 CGCCAACTCATATCTTTATAGGAATAC 57.911 37.037 0.00 0.00 28.56 1.89
2304 3659 9.031537 TCGCCAACTCATATCTTTATAGGAATA 57.968 33.333 0.00 0.00 28.56 1.75
2305 3660 7.907389 TCGCCAACTCATATCTTTATAGGAAT 58.093 34.615 0.00 0.00 28.56 3.01
2306 3661 7.297936 TCGCCAACTCATATCTTTATAGGAA 57.702 36.000 0.00 0.00 28.56 3.36
2345 3700 0.031716 CATGTCTGGAGGGGAGGAGA 60.032 60.000 0.00 0.00 0.00 3.71
2352 3707 0.549950 AATGGCTCATGTCTGGAGGG 59.450 55.000 0.00 0.00 32.96 4.30
2357 3712 4.321008 GGCATATCAAATGGCTCATGTCTG 60.321 45.833 4.46 0.00 40.85 3.51
2363 3718 3.768215 TGTTTGGCATATCAAATGGCTCA 59.232 39.130 12.05 6.77 43.89 4.26
2373 3728 5.858381 TCCATCTAGACTGTTTGGCATATC 58.142 41.667 4.67 0.00 0.00 1.63
2379 3734 3.686726 GTGCTTCCATCTAGACTGTTTGG 59.313 47.826 0.00 0.00 0.00 3.28
2380 3735 4.318332 TGTGCTTCCATCTAGACTGTTTG 58.682 43.478 0.00 0.00 0.00 2.93
2382 3737 4.040952 AGTTGTGCTTCCATCTAGACTGTT 59.959 41.667 0.00 0.00 0.00 3.16
2388 3743 3.265791 GTGGAGTTGTGCTTCCATCTAG 58.734 50.000 0.00 0.00 34.50 2.43
2478 3833 0.321564 CGGGCTGGTTGAATGAGTGA 60.322 55.000 0.00 0.00 0.00 3.41
2501 3856 4.134379 ACAAGTCATCAGGTGCTCATAG 57.866 45.455 0.00 0.00 0.00 2.23
2502 3857 4.100035 CCTACAAGTCATCAGGTGCTCATA 59.900 45.833 0.00 0.00 0.00 2.15
2540 3895 2.197792 TACACGTGCGTTGCTATAGG 57.802 50.000 17.22 0.00 0.00 2.57
2542 3897 4.207635 GCTAAATACACGTGCGTTGCTATA 59.792 41.667 17.22 0.00 0.00 1.31
2543 3898 3.000925 GCTAAATACACGTGCGTTGCTAT 59.999 43.478 17.22 1.55 0.00 2.97
2544 3899 2.346244 GCTAAATACACGTGCGTTGCTA 59.654 45.455 17.22 0.00 0.00 3.49
2545 3900 1.127951 GCTAAATACACGTGCGTTGCT 59.872 47.619 17.22 0.00 0.00 3.91
2546 3901 1.127951 AGCTAAATACACGTGCGTTGC 59.872 47.619 17.22 12.57 0.00 4.17
2547 3902 2.410392 TCAGCTAAATACACGTGCGTTG 59.590 45.455 17.22 5.85 0.00 4.10
2548 3903 2.410730 GTCAGCTAAATACACGTGCGTT 59.589 45.455 17.22 7.89 0.00 4.84
2550 3905 1.323534 GGTCAGCTAAATACACGTGCG 59.676 52.381 17.22 0.00 0.00 5.34
2631 3987 1.001974 CCGAACAGAACCCATGAGACA 59.998 52.381 0.00 0.00 0.00 3.41
2755 4111 1.423921 ACTGGTGAAAACTGTAGGGGG 59.576 52.381 0.00 0.00 0.00 5.40
2836 4192 8.607459 TGCACAAAATGTAATGTTTTAACCAAG 58.393 29.630 0.00 0.00 0.00 3.61
3036 4392 7.820648 TGAAAATCCTTGTTCTTTCTGCTATC 58.179 34.615 0.00 0.00 0.00 2.08
3305 9429 8.651588 CCATTCGATATGAACTCATAAACTAGC 58.348 37.037 3.61 0.00 41.60 3.42
3549 9673 5.675538 GGCTGTAAGTATTCCTGTCTCATT 58.324 41.667 0.00 0.00 35.30 2.57
3584 9708 7.736893 AGTATTCAGGATCAAGGTAACCATAC 58.263 38.462 0.00 0.00 37.17 2.39
3638 9762 6.072175 GGATAACACCAAAGCTGTAAACATCA 60.072 38.462 0.00 0.00 0.00 3.07
3913 10037 7.509546 AGAACTGAGATTGACCTTTAAGTTCA 58.490 34.615 13.01 0.00 35.70 3.18
3963 10087 8.933653 TCCCTTGTATGACTGATCATTTATACA 58.066 33.333 20.11 20.11 43.40 2.29
3964 10088 9.778741 TTCCCTTGTATGACTGATCATTTATAC 57.221 33.333 16.51 16.51 43.40 1.47
4040 10164 7.837202 TCATCTTGGAATTTCAAATGAATGC 57.163 32.000 15.92 0.00 33.54 3.56
4048 10172 9.206870 GTAAGCAAAATCATCTTGGAATTTCAA 57.793 29.630 0.00 0.00 0.00 2.69
4080 10207 9.720769 AAGTAATAATAGTAACTGCAACACTGT 57.279 29.630 5.09 0.00 0.00 3.55
4104 10237 6.317140 ACTTGATATGCAGTATGACACCAAAG 59.683 38.462 0.00 0.00 39.69 2.77
4406 10569 5.243507 TGCATTGCCTTCTCATTAGTGAAAA 59.756 36.000 6.12 0.00 33.05 2.29
4414 10577 5.410439 GTCAAATTTGCATTGCCTTCTCATT 59.590 36.000 13.54 0.00 0.00 2.57
4436 10607 7.042725 CCATTTTGATCATCTGATTGCAATGTC 60.043 37.037 18.59 4.68 34.37 3.06
4532 10703 2.084546 GACTGCCTGTATTTGACCACC 58.915 52.381 0.00 0.00 0.00 4.61
4695 10869 8.807667 ATCTCTAGTTCACATTTTGCAAAAAG 57.192 30.769 27.10 24.37 0.00 2.27
4775 10952 5.884792 AGCATTCCTCATTGACCTAAAGAAG 59.115 40.000 0.00 0.00 0.00 2.85
4867 11044 9.034544 GCTTGTCTGAAATTTAGTGTTTTCAAT 57.965 29.630 0.00 0.00 40.31 2.57
4868 11045 8.031864 TGCTTGTCTGAAATTTAGTGTTTTCAA 58.968 29.630 0.00 0.00 40.31 2.69
4869 11046 7.542890 TGCTTGTCTGAAATTTAGTGTTTTCA 58.457 30.769 0.00 0.00 39.00 2.69
4953 11130 2.708861 TCAGTTTCCTGCTTGGGAGTTA 59.291 45.455 0.00 0.00 38.66 2.24
4958 11135 0.251077 AGCTCAGTTTCCTGCTTGGG 60.251 55.000 0.00 0.00 38.66 4.12
4964 11141 4.083590 GCTTTGTAAGAGCTCAGTTTCCTG 60.084 45.833 17.77 0.81 40.25 3.86
5026 11203 3.580895 TGGATGCACCTCAGTGTTACTAA 59.419 43.478 0.00 0.00 46.35 2.24
5027 11204 3.169908 TGGATGCACCTCAGTGTTACTA 58.830 45.455 0.00 0.00 46.35 1.82
5028 11205 1.977854 TGGATGCACCTCAGTGTTACT 59.022 47.619 0.00 0.00 46.35 2.24
5029 11206 2.472695 TGGATGCACCTCAGTGTTAC 57.527 50.000 0.00 0.00 46.35 2.50


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

AutoCloner maintained by Alex Coulton.