Multiple sequence alignment - TraesCS1A01G376300

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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 TraesCS1A01G376300 chr1A 100.000 3182 0 0 1 3182 550594766 550591585 0.000000e+00 5877
1 TraesCS1A01G376300 chr1D 87.178 2137 121 72 919 3013 458132903 458134928 0.000000e+00 2287
2 TraesCS1A01G376300 chr1D 79.603 353 33 17 20 346 458132066 458132405 1.920000e-52 217
3 TraesCS1A01G376300 chr1B 88.287 1827 103 44 628 2411 628500090 628498332 0.000000e+00 2085
4 TraesCS1A01G376300 chr1B 80.628 764 74 40 2418 3163 628494709 628494002 1.010000e-144 523
5 TraesCS1A01G376300 chr1B 86.082 194 7 5 140 322 628500637 628500453 1.170000e-44 191
6 TraesCS1A01G376300 chr1B 91.176 136 8 3 1 132 628500874 628500739 7.010000e-42 182
7 TraesCS1A01G376300 chr3D 80.139 861 150 15 1214 2068 365054436 365053591 9.690000e-175 623
8 TraesCS1A01G376300 chr3B 80.208 864 144 22 1214 2068 475385384 475384539 9.690000e-175 623
9 TraesCS1A01G376300 chr3A 79.954 863 148 19 1214 2068 486929713 486928868 2.100000e-171 612


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 TraesCS1A01G376300 chr1A 550591585 550594766 3181 True 5877.00 5877 100.00000 1 3182 1 chr1A.!!$R1 3181
1 TraesCS1A01G376300 chr1D 458132066 458134928 2862 False 1252.00 2287 83.39050 20 3013 2 chr1D.!!$F1 2993
2 TraesCS1A01G376300 chr1B 628494002 628500874 6872 True 745.25 2085 86.54325 1 3163 4 chr1B.!!$R1 3162
3 TraesCS1A01G376300 chr3D 365053591 365054436 845 True 623.00 623 80.13900 1214 2068 1 chr3D.!!$R1 854
4 TraesCS1A01G376300 chr3B 475384539 475385384 845 True 623.00 623 80.20800 1214 2068 1 chr3B.!!$R1 854
5 TraesCS1A01G376300 chr3A 486928868 486929713 845 True 612.00 612 79.95400 1214 2068 1 chr3A.!!$R1 854

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
519 807 0.036875 CCCGAAGCAAAACTCTCCCT 59.963 55.0 0.0 0.0 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2211 2569 0.456995 CGTCTCTCTCGCCCAGAAAC 60.457 60.0 0.0 0.0 0.0 2.78 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 90 2.356553 TTGGGCTCGAACCGAACG 60.357 61.111 0.00 0.00 34.74 3.95
96 108 2.435410 AAATTCCGTCGGGACCGC 60.435 61.111 12.29 0.52 43.74 5.68
136 152 4.953868 CGACACGACGCCACCCAA 62.954 66.667 0.00 0.00 0.00 4.12
138 154 3.802418 GACACGACGCCACCCAAGT 62.802 63.158 0.00 0.00 0.00 3.16
145 255 3.357079 GCCACCCAAGTCACGCAG 61.357 66.667 0.00 0.00 0.00 5.18
273 394 0.604511 AGGCCGGTTAAACAACTCCG 60.605 55.000 1.90 0.00 42.22 4.63
276 397 1.871077 CGGTTAAACAACTCCGGCC 59.129 57.895 0.00 0.00 39.41 6.13
346 484 6.203808 GGAATGTTCCCGCTTATTTTAACT 57.796 37.500 0.09 0.00 41.62 2.24
348 486 5.576447 ATGTTCCCGCTTATTTTAACTGG 57.424 39.130 0.00 0.00 0.00 4.00
349 487 4.400120 TGTTCCCGCTTATTTTAACTGGT 58.600 39.130 0.00 0.00 0.00 4.00
350 488 4.216687 TGTTCCCGCTTATTTTAACTGGTG 59.783 41.667 0.00 0.00 0.00 4.17
351 489 2.750712 TCCCGCTTATTTTAACTGGTGC 59.249 45.455 0.00 0.00 0.00 5.01
354 492 2.477189 CGCTTATTTTAACTGGTGCCCG 60.477 50.000 0.00 0.00 0.00 6.13
356 494 2.201921 TATTTTAACTGGTGCCCGCA 57.798 45.000 0.00 0.00 0.00 5.69
357 495 1.555967 ATTTTAACTGGTGCCCGCAT 58.444 45.000 0.00 0.00 0.00 4.73
358 496 0.600557 TTTTAACTGGTGCCCGCATG 59.399 50.000 0.00 0.00 0.00 4.06
359 497 1.247419 TTTAACTGGTGCCCGCATGG 61.247 55.000 0.00 0.00 37.09 3.66
414 687 1.360192 GCCCGGCTGCAATCATAAC 59.640 57.895 0.71 0.00 0.00 1.89
423 696 4.330620 GGCTGCAATCATAACCAAAACATG 59.669 41.667 0.50 0.00 0.00 3.21
447 720 4.562394 ACAGAGCGATGTGTTTTTGTTTTG 59.438 37.500 0.00 0.00 30.46 2.44
452 725 6.303370 AGCGATGTGTTTTTGTTTTGTTTTC 58.697 32.000 0.00 0.00 0.00 2.29
455 728 7.630606 GCGATGTGTTTTTGTTTTGTTTTCTAG 59.369 33.333 0.00 0.00 0.00 2.43
456 729 8.107564 CGATGTGTTTTTGTTTTGTTTTCTAGG 58.892 33.333 0.00 0.00 0.00 3.02
470 743 5.427481 TGTTTTCTAGGTTAAGATCCCCGAT 59.573 40.000 0.00 0.00 0.00 4.18
472 745 2.897969 TCTAGGTTAAGATCCCCGATGC 59.102 50.000 0.00 0.00 0.00 3.91
475 748 1.342174 GGTTAAGATCCCCGATGCGTA 59.658 52.381 0.00 0.00 0.00 4.42
480 753 2.088674 GATCCCCGATGCGTACTGCT 62.089 60.000 10.27 0.00 46.63 4.24
481 754 2.369257 ATCCCCGATGCGTACTGCTG 62.369 60.000 10.27 0.00 46.63 4.41
482 755 2.586079 CCCGATGCGTACTGCTGG 60.586 66.667 10.27 9.10 46.63 4.85
483 756 3.264897 CCGATGCGTACTGCTGGC 61.265 66.667 10.27 0.00 46.63 4.85
487 775 1.003355 ATGCGTACTGCTGGCTTGT 60.003 52.632 10.27 0.00 46.63 3.16
494 782 2.661537 TGCTGGCTTGTCACGACG 60.662 61.111 0.00 0.00 0.00 5.12
511 799 2.258013 CGCTGTCCCCGAAGCAAAA 61.258 57.895 0.00 0.00 39.47 2.44
512 800 1.285950 GCTGTCCCCGAAGCAAAAC 59.714 57.895 0.00 0.00 39.31 2.43
513 801 1.172812 GCTGTCCCCGAAGCAAAACT 61.173 55.000 0.00 0.00 39.31 2.66
514 802 0.875059 CTGTCCCCGAAGCAAAACTC 59.125 55.000 0.00 0.00 0.00 3.01
515 803 0.472471 TGTCCCCGAAGCAAAACTCT 59.528 50.000 0.00 0.00 0.00 3.24
518 806 0.960861 CCCCGAAGCAAAACTCTCCC 60.961 60.000 0.00 0.00 0.00 4.30
519 807 0.036875 CCCGAAGCAAAACTCTCCCT 59.963 55.000 0.00 0.00 0.00 4.20
523 811 3.399330 CGAAGCAAAACTCTCCCTAACA 58.601 45.455 0.00 0.00 0.00 2.41
526 814 3.744660 AGCAAAACTCTCCCTAACACTG 58.255 45.455 0.00 0.00 0.00 3.66
530 818 1.939980 ACTCTCCCTAACACTGTCCC 58.060 55.000 0.00 0.00 0.00 4.46
535 823 0.546747 CCCTAACACTGTCCCCTCCA 60.547 60.000 0.00 0.00 0.00 3.86
539 827 0.475632 AACACTGTCCCCTCCATCCA 60.476 55.000 0.00 0.00 0.00 3.41
542 830 0.695803 ACTGTCCCCTCCATCCATCC 60.696 60.000 0.00 0.00 0.00 3.51
548 836 0.477202 CCCTCCATCCATCCATCCCT 60.477 60.000 0.00 0.00 0.00 4.20
550 838 1.785208 CCTCCATCCATCCATCCCTTT 59.215 52.381 0.00 0.00 0.00 3.11
551 839 2.490351 CCTCCATCCATCCATCCCTTTG 60.490 54.545 0.00 0.00 0.00 2.77
552 840 2.176364 CTCCATCCATCCATCCCTTTGT 59.824 50.000 0.00 0.00 0.00 2.83
556 844 2.561187 TCCATCCATCCCTTTGTCTGA 58.439 47.619 0.00 0.00 0.00 3.27
558 846 2.025981 CCATCCATCCCTTTGTCTGACA 60.026 50.000 6.36 6.36 0.00 3.58
561 849 1.442769 CATCCCTTTGTCTGACACCG 58.557 55.000 10.56 4.35 0.00 4.94
564 852 2.317609 CCTTTGTCTGACACCGCCG 61.318 63.158 10.56 0.00 0.00 6.46
565 853 2.954753 CTTTGTCTGACACCGCCGC 61.955 63.158 10.56 0.00 0.00 6.53
583 871 4.379243 CGGCCGCTGTCCAGTCTT 62.379 66.667 14.67 0.00 0.00 3.01
584 872 2.032681 GGCCGCTGTCCAGTCTTT 59.967 61.111 0.00 0.00 0.00 2.52
585 873 1.600916 GGCCGCTGTCCAGTCTTTT 60.601 57.895 0.00 0.00 0.00 2.27
586 874 1.172812 GGCCGCTGTCCAGTCTTTTT 61.173 55.000 0.00 0.00 0.00 1.94
608 896 7.740519 TTTTCTTTTCTTTTTCTGAAGCTCG 57.259 32.000 0.00 0.00 0.00 5.03
609 897 4.848757 TCTTTTCTTTTTCTGAAGCTCGC 58.151 39.130 0.00 0.00 0.00 5.03
610 898 4.576463 TCTTTTCTTTTTCTGAAGCTCGCT 59.424 37.500 0.00 0.00 0.00 4.93
611 899 3.885484 TTCTTTTTCTGAAGCTCGCTG 57.115 42.857 0.00 0.00 0.00 5.18
612 900 2.838736 TCTTTTTCTGAAGCTCGCTGT 58.161 42.857 0.00 0.00 0.00 4.40
613 901 2.802816 TCTTTTTCTGAAGCTCGCTGTC 59.197 45.455 0.00 0.00 0.00 3.51
614 902 1.512926 TTTTCTGAAGCTCGCTGTCC 58.487 50.000 0.00 0.00 0.00 4.02
615 903 0.392706 TTTCTGAAGCTCGCTGTCCA 59.607 50.000 0.00 0.00 0.00 4.02
616 904 0.037882 TTCTGAAGCTCGCTGTCCAG 60.038 55.000 0.00 1.50 0.00 3.86
617 905 1.181741 TCTGAAGCTCGCTGTCCAGT 61.182 55.000 12.60 0.00 0.00 4.00
618 906 0.735632 CTGAAGCTCGCTGTCCAGTC 60.736 60.000 0.00 0.00 0.00 3.51
619 907 1.181741 TGAAGCTCGCTGTCCAGTCT 61.182 55.000 0.00 0.00 0.00 3.24
620 908 0.037790 GAAGCTCGCTGTCCAGTCTT 60.038 55.000 0.00 0.00 0.00 3.01
621 909 0.394565 AAGCTCGCTGTCCAGTCTTT 59.605 50.000 0.00 0.00 0.00 2.52
622 910 0.037790 AGCTCGCTGTCCAGTCTTTC 60.038 55.000 0.00 0.00 0.00 2.62
623 911 1.347817 GCTCGCTGTCCAGTCTTTCG 61.348 60.000 0.00 0.00 0.00 3.46
624 912 0.734253 CTCGCTGTCCAGTCTTTCGG 60.734 60.000 0.00 0.00 0.00 4.30
625 913 1.006102 CGCTGTCCAGTCTTTCGGT 60.006 57.895 0.00 0.00 0.00 4.69
648 936 3.902261 ATATATACACGGACGCACGAA 57.098 42.857 6.34 0.00 37.61 3.85
649 937 1.831343 ATATACACGGACGCACGAAC 58.169 50.000 6.34 0.00 37.61 3.95
650 938 0.520847 TATACACGGACGCACGAACA 59.479 50.000 6.34 0.00 37.61 3.18
651 939 1.005294 ATACACGGACGCACGAACAC 61.005 55.000 6.34 0.00 37.61 3.32
674 966 4.349503 AGCAGCCGTGGCATCCAA 62.350 61.111 14.29 0.00 44.88 3.53
675 967 3.142838 GCAGCCGTGGCATCCAAT 61.143 61.111 14.29 0.00 44.88 3.16
683 975 3.761896 TGGCATCCAATCCACAACA 57.238 47.368 0.00 0.00 0.00 3.33
684 976 1.548081 TGGCATCCAATCCACAACAG 58.452 50.000 0.00 0.00 0.00 3.16
711 1003 0.477202 CCATCCCATCCATCTCCCCT 60.477 60.000 0.00 0.00 0.00 4.79
718 1010 1.753073 CATCCATCTCCCCTGCAAAAC 59.247 52.381 0.00 0.00 0.00 2.43
735 1027 1.265454 AACCCCCAAAACCAAACGCA 61.265 50.000 0.00 0.00 0.00 5.24
736 1028 1.265454 ACCCCCAAAACCAAACGCAA 61.265 50.000 0.00 0.00 0.00 4.85
738 1030 1.148759 CCCCAAAACCAAACGCAACG 61.149 55.000 0.00 0.00 0.00 4.10
739 1031 1.633697 CCAAAACCAAACGCAACGC 59.366 52.632 0.00 0.00 0.00 4.84
740 1032 1.633697 CAAAACCAAACGCAACGCC 59.366 52.632 0.00 0.00 0.00 5.68
741 1033 1.519676 AAAACCAAACGCAACGCCC 60.520 52.632 0.00 0.00 0.00 6.13
841 1145 2.106074 CCAGGTGCGCGCTAAATCA 61.106 57.895 33.29 7.72 0.00 2.57
844 1148 0.168128 AGGTGCGCGCTAAATCAAAC 59.832 50.000 33.29 18.72 0.00 2.93
863 1167 1.301009 CCGGAAGCGGAGATTAGGC 60.301 63.158 0.00 0.00 34.67 3.93
898 1220 4.457496 CGCGTCCAGGGCTGTGAT 62.457 66.667 0.00 0.00 0.00 3.06
899 1221 2.045926 GCGTCCAGGGCTGTGATT 60.046 61.111 0.00 0.00 0.00 2.57
900 1222 1.675641 GCGTCCAGGGCTGTGATTT 60.676 57.895 0.00 0.00 0.00 2.17
901 1223 0.392461 GCGTCCAGGGCTGTGATTTA 60.392 55.000 0.00 0.00 0.00 1.40
902 1224 1.747206 GCGTCCAGGGCTGTGATTTAT 60.747 52.381 0.00 0.00 0.00 1.40
903 1225 2.484770 GCGTCCAGGGCTGTGATTTATA 60.485 50.000 0.00 0.00 0.00 0.98
905 1227 3.744660 GTCCAGGGCTGTGATTTATAGG 58.255 50.000 0.00 0.00 0.00 2.57
906 1228 2.711009 TCCAGGGCTGTGATTTATAGGG 59.289 50.000 0.00 0.00 0.00 3.53
907 1229 2.443255 CCAGGGCTGTGATTTATAGGGT 59.557 50.000 0.00 0.00 0.00 4.34
908 1230 3.496870 CCAGGGCTGTGATTTATAGGGTC 60.497 52.174 0.00 0.00 0.00 4.46
909 1231 2.711547 AGGGCTGTGATTTATAGGGTCC 59.288 50.000 0.00 0.00 0.00 4.46
910 1232 2.441750 GGGCTGTGATTTATAGGGTCCA 59.558 50.000 0.00 0.00 0.00 4.02
911 1233 3.496870 GGGCTGTGATTTATAGGGTCCAG 60.497 52.174 0.00 0.00 0.00 3.86
912 1234 3.496870 GGCTGTGATTTATAGGGTCCAGG 60.497 52.174 0.00 0.00 0.00 4.45
913 1235 3.496870 GCTGTGATTTATAGGGTCCAGGG 60.497 52.174 0.00 0.00 0.00 4.45
914 1236 2.441750 TGTGATTTATAGGGTCCAGGGC 59.558 50.000 0.00 0.00 0.00 5.19
915 1237 2.711547 GTGATTTATAGGGTCCAGGGCT 59.288 50.000 0.00 0.00 0.00 5.19
916 1238 2.979678 TGATTTATAGGGTCCAGGGCTC 59.020 50.000 0.00 0.00 0.00 4.70
917 1239 1.815757 TTTATAGGGTCCAGGGCTCC 58.184 55.000 0.00 0.00 0.00 4.70
974 1299 0.959553 GGCTAATCAGGATCCGTCGA 59.040 55.000 5.98 5.02 0.00 4.20
975 1300 1.336056 GGCTAATCAGGATCCGTCGAC 60.336 57.143 5.18 5.18 0.00 4.20
977 1302 0.309922 TAATCAGGATCCGTCGACGC 59.690 55.000 31.73 18.21 38.18 5.19
1036 1361 0.536260 TCGGGTTATTACCACCACCG 59.464 55.000 2.85 0.00 46.96 4.94
1046 1371 4.230002 CACCACCGTCACCACCGT 62.230 66.667 0.00 0.00 0.00 4.83
1131 1468 2.817423 CGCGGCAATGAGCTCTTCC 61.817 63.158 16.19 9.34 44.79 3.46
1140 1486 2.317371 TGAGCTCTTCCTCCTCTTGT 57.683 50.000 16.19 0.00 0.00 3.16
1143 1489 1.548269 AGCTCTTCCTCCTCTTGTTCG 59.452 52.381 0.00 0.00 0.00 3.95
1159 1505 1.215679 TTCGTCCTCCTCCTCCTCCT 61.216 60.000 0.00 0.00 0.00 3.69
1160 1506 1.152839 CGTCCTCCTCCTCCTCCTC 60.153 68.421 0.00 0.00 0.00 3.71
1161 1507 1.231928 GTCCTCCTCCTCCTCCTCC 59.768 68.421 0.00 0.00 0.00 4.30
1162 1508 1.230650 TCCTCCTCCTCCTCCTCCA 60.231 63.158 0.00 0.00 0.00 3.86
1199 1545 4.179599 GGGGGAGGAGGGGGAGAG 62.180 77.778 0.00 0.00 0.00 3.20
1200 1546 4.179599 GGGGAGGAGGGGGAGAGG 62.180 77.778 0.00 0.00 0.00 3.69
1201 1547 4.179599 GGGAGGAGGGGGAGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
1202 1548 4.890306 GGAGGAGGGGGAGAGGGC 62.890 77.778 0.00 0.00 0.00 5.19
1327 1673 1.751351 CCGACAAGATCCAGCTCTACA 59.249 52.381 0.00 0.00 0.00 2.74
1722 2071 2.124403 GGCATGGTGGAGGAGCTG 60.124 66.667 0.00 0.00 0.00 4.24
1728 2077 4.459089 GTGGAGGAGCTGCGGGAC 62.459 72.222 0.00 0.00 0.00 4.46
2072 2421 2.725203 TTCCTCGCCGACCAAACCTG 62.725 60.000 0.00 0.00 0.00 4.00
2074 2423 3.883744 CTCGCCGACCAAACCTGCT 62.884 63.158 0.00 0.00 0.00 4.24
2075 2424 3.423154 CGCCGACCAAACCTGCTC 61.423 66.667 0.00 0.00 0.00 4.26
2076 2425 3.423154 GCCGACCAAACCTGCTCG 61.423 66.667 0.00 0.00 0.00 5.03
2100 2452 3.272334 GATGACGCCACCGCCATC 61.272 66.667 0.00 0.00 44.73 3.51
2182 2540 1.293963 CTGCGACATGGTGGTGTGAG 61.294 60.000 0.00 0.00 31.16 3.51
2183 2541 2.680913 GCGACATGGTGGTGTGAGC 61.681 63.158 0.00 0.00 31.16 4.26
2184 2542 2.034879 CGACATGGTGGTGTGAGCC 61.035 63.158 0.00 0.00 31.16 4.70
2185 2543 2.032528 ACATGGTGGTGTGAGCCG 59.967 61.111 0.00 0.00 0.00 5.52
2186 2544 3.434319 CATGGTGGTGTGAGCCGC 61.434 66.667 0.00 0.00 38.26 6.53
2187 2545 3.640407 ATGGTGGTGTGAGCCGCT 61.640 61.111 0.00 0.00 38.94 5.52
2188 2546 3.907260 ATGGTGGTGTGAGCCGCTG 62.907 63.158 0.00 0.00 38.94 5.18
2222 2580 4.243008 TGGTGCGTTTCTGGGCGA 62.243 61.111 0.00 0.00 0.00 5.54
2241 2599 2.362632 AGAGACGGACGGAAGGGG 60.363 66.667 0.00 0.00 0.00 4.79
2353 2712 1.069568 CCGAGAATCCGAGATCGACAG 60.070 57.143 3.31 0.00 43.02 3.51
2358 2717 0.950836 ATCCGAGATCGACAGCAGAG 59.049 55.000 3.31 0.00 43.02 3.35
2367 2726 1.016627 CGACAGCAGAGAGAGAGAGG 58.983 60.000 0.00 0.00 0.00 3.69
2368 2727 1.406751 CGACAGCAGAGAGAGAGAGGA 60.407 57.143 0.00 0.00 0.00 3.71
2369 2728 2.292267 GACAGCAGAGAGAGAGAGGAG 58.708 57.143 0.00 0.00 0.00 3.69
2370 2729 1.915489 ACAGCAGAGAGAGAGAGGAGA 59.085 52.381 0.00 0.00 0.00 3.71
2411 2772 3.251004 GTGTAAAAAGTGACAGCAGGAGG 59.749 47.826 0.00 0.00 0.00 4.30
2416 6393 3.005539 TGACAGCAGGAGGAGGGC 61.006 66.667 0.00 0.00 0.00 5.19
2430 6407 2.976882 AGGAGGGCTTGTGTGTAAGTTA 59.023 45.455 0.00 0.00 0.00 2.24
2488 6473 5.946486 AGGGTGAGTGAATTCTTTTCTTCT 58.054 37.500 7.05 0.00 0.00 2.85
2489 6474 6.368805 AGGGTGAGTGAATTCTTTTCTTCTT 58.631 36.000 7.05 0.00 0.00 2.52
2490 6475 6.488344 AGGGTGAGTGAATTCTTTTCTTCTTC 59.512 38.462 7.05 0.00 0.00 2.87
2491 6476 6.488344 GGGTGAGTGAATTCTTTTCTTCTTCT 59.512 38.462 7.05 0.00 0.00 2.85
2492 6477 7.013750 GGGTGAGTGAATTCTTTTCTTCTTCTT 59.986 37.037 7.05 0.00 0.00 2.52
2493 6478 7.859875 GGTGAGTGAATTCTTTTCTTCTTCTTG 59.140 37.037 7.05 0.00 0.00 3.02
2494 6479 8.616076 GTGAGTGAATTCTTTTCTTCTTCTTGA 58.384 33.333 7.05 0.00 0.00 3.02
2502 6487 9.924650 ATTCTTTTCTTCTTCTTGATTGATTGG 57.075 29.630 0.00 0.00 0.00 3.16
2534 6523 5.163943 GGAGTATTTGTTTCGTCTGCTTCTC 60.164 44.000 0.00 0.00 0.00 2.87
2550 6539 0.032952 TCTCAACCGCACCACTGTAC 59.967 55.000 0.00 0.00 0.00 2.90
2556 6545 1.418342 CCGCACCACTGTACGTATGC 61.418 60.000 0.00 2.25 34.94 3.14
2560 6549 2.616960 CACCACTGTACGTATGCATGT 58.383 47.619 10.16 1.67 0.00 3.21
2562 6551 4.368315 CACCACTGTACGTATGCATGTAT 58.632 43.478 10.16 0.82 0.00 2.29
2563 6552 4.209080 CACCACTGTACGTATGCATGTATG 59.791 45.833 10.16 0.00 0.00 2.39
2564 6553 4.142026 ACCACTGTACGTATGCATGTATGT 60.142 41.667 10.16 4.41 0.00 2.29
2565 6554 5.068067 ACCACTGTACGTATGCATGTATGTA 59.932 40.000 10.16 3.33 0.00 2.29
2566 6555 5.980715 CCACTGTACGTATGCATGTATGTAA 59.019 40.000 10.16 0.00 30.24 2.41
2567 6556 6.645003 CCACTGTACGTATGCATGTATGTAAT 59.355 38.462 10.16 0.00 30.24 1.89
2568 6557 7.359181 CCACTGTACGTATGCATGTATGTAATG 60.359 40.741 10.16 5.91 30.24 1.90
2569 6558 7.169140 CACTGTACGTATGCATGTATGTAATGT 59.831 37.037 10.16 1.28 30.24 2.71
2591 6580 1.475280 TGTAGGCAGTCGTCATGTACC 59.525 52.381 0.00 0.00 0.00 3.34
2652 6652 8.485392 CAAATTTTGAAACATATATGGGACCCT 58.515 33.333 16.96 0.00 0.00 4.34
2653 6653 9.722317 AAATTTTGAAACATATATGGGACCCTA 57.278 29.630 16.96 2.01 0.00 3.53
2654 6654 8.940397 ATTTTGAAACATATATGGGACCCTAG 57.060 34.615 16.96 0.00 0.00 3.02
2656 6656 4.288626 TGAAACATATATGGGACCCTAGCC 59.711 45.833 16.96 0.00 0.00 3.93
2659 6659 2.337359 TATATGGGACCCTAGCCACC 57.663 55.000 13.00 0.00 0.00 4.61
2679 6679 1.154016 CACACGCGGGTAGAGTCTG 60.154 63.158 16.65 0.00 0.00 3.51
2723 6728 2.180204 CGCACCGGAACCATCCATC 61.180 63.158 9.46 0.00 46.97 3.51
2724 6729 1.823899 GCACCGGAACCATCCATCC 60.824 63.158 9.46 0.00 46.97 3.51
2785 6790 1.205064 GCGTATGATGTGGCGATGC 59.795 57.895 0.00 0.00 0.00 3.91
2801 6806 1.267574 ATGCGCTTTGAGGAGGAGGA 61.268 55.000 9.73 0.00 0.00 3.71
2806 6811 1.958288 CTTTGAGGAGGAGGAGGGAA 58.042 55.000 0.00 0.00 0.00 3.97
2809 6814 1.958288 TGAGGAGGAGGAGGGAAAAG 58.042 55.000 0.00 0.00 0.00 2.27
2811 6816 2.115427 GAGGAGGAGGAGGGAAAAGAG 58.885 57.143 0.00 0.00 0.00 2.85
2812 6817 0.544223 GGAGGAGGAGGGAAAAGAGC 59.456 60.000 0.00 0.00 0.00 4.09
2814 6819 0.545548 AGGAGGAGGGAAAAGAGCGT 60.546 55.000 0.00 0.00 0.00 5.07
2815 6820 0.391793 GGAGGAGGGAAAAGAGCGTG 60.392 60.000 0.00 0.00 0.00 5.34
2854 6859 1.843368 CATGCCATGGTGGACTCTTT 58.157 50.000 14.67 0.00 40.96 2.52
2914 6919 0.804989 GCCATGCTTACTGTGTGACC 59.195 55.000 0.00 0.00 0.00 4.02
2928 6933 1.278985 TGTGACCCACTGCTGATTAGG 59.721 52.381 0.00 0.00 35.11 2.69
2946 6951 3.090532 GGGGAGGAGGGAATGCGT 61.091 66.667 0.00 0.00 0.00 5.24
2958 6965 1.570347 GAATGCGTTGGCCGTGTGTA 61.570 55.000 0.00 0.00 38.85 2.90
2970 6977 1.338294 CCGTGTGTATTGGTAGGTGCA 60.338 52.381 0.00 0.00 0.00 4.57
3016 7029 1.069227 GTTGCCAGCTAGGAAAACACG 60.069 52.381 6.40 0.00 36.38 4.49
3033 7046 4.660938 GCAGGCCAAACCCGGTCT 62.661 66.667 5.01 0.00 43.61 3.85
3034 7047 2.115266 CAGGCCAAACCCGGTCTT 59.885 61.111 5.01 0.00 37.95 3.01
3035 7048 1.971695 CAGGCCAAACCCGGTCTTC 60.972 63.158 5.01 0.00 37.95 2.87
3036 7049 2.154074 AGGCCAAACCCGGTCTTCT 61.154 57.895 5.01 0.00 37.95 2.85
3037 7050 1.674651 GGCCAAACCCGGTCTTCTC 60.675 63.158 0.00 0.00 0.00 2.87
3038 7051 1.375326 GCCAAACCCGGTCTTCTCT 59.625 57.895 0.00 0.00 0.00 3.10
3039 7052 0.673956 GCCAAACCCGGTCTTCTCTC 60.674 60.000 0.00 0.00 0.00 3.20
3040 7053 0.977395 CCAAACCCGGTCTTCTCTCT 59.023 55.000 0.00 0.00 0.00 3.10
3041 7054 1.066787 CCAAACCCGGTCTTCTCTCTC 60.067 57.143 0.00 0.00 0.00 3.20
3042 7055 1.896465 CAAACCCGGTCTTCTCTCTCT 59.104 52.381 0.00 0.00 0.00 3.10
3043 7056 1.842052 AACCCGGTCTTCTCTCTCTC 58.158 55.000 0.00 0.00 0.00 3.20
3046 7059 1.350319 CGGTCTTCTCTCTCTCGCG 59.650 63.158 0.00 0.00 0.00 5.87
3049 7062 2.650602 CTTCTCTCTCTCGCGCGC 60.651 66.667 27.95 23.91 0.00 6.86
3050 7063 4.522421 TTCTCTCTCTCGCGCGCG 62.522 66.667 44.84 44.84 41.35 6.86
3074 7087 1.004080 CTGGTGACTGACTGGCTGG 60.004 63.158 0.00 0.00 0.00 4.85
3075 7088 2.359230 GGTGACTGACTGGCTGGC 60.359 66.667 0.00 0.00 0.00 4.85
3078 7091 2.046507 GACTGACTGGCTGGCTGG 60.047 66.667 12.46 3.50 0.00 4.85
3081 7094 4.340246 TGACTGGCTGGCTGGCTG 62.340 66.667 19.64 19.64 43.88 4.85
3084 7097 4.124943 CTGGCTGGCTGGCTGGAT 62.125 66.667 18.27 0.00 42.34 3.41
3085 7098 4.435970 TGGCTGGCTGGCTGGATG 62.436 66.667 18.27 0.00 42.34 3.51
3121 7141 1.151908 CCGGTCAGGAACCCCAAAA 59.848 57.895 0.00 0.00 46.27 2.44
3124 7144 0.469144 GGTCAGGAACCCCAAAAGCA 60.469 55.000 0.00 0.00 42.85 3.91
3128 7148 0.471591 AGGAACCCCAAAAGCATGCA 60.472 50.000 21.98 0.00 33.88 3.96
3175 7195 2.808315 CGAGGACACGGGAGATGG 59.192 66.667 0.00 0.00 0.00 3.51
3176 7196 2.052690 CGAGGACACGGGAGATGGT 61.053 63.158 0.00 0.00 0.00 3.55
3177 7197 1.605058 CGAGGACACGGGAGATGGTT 61.605 60.000 0.00 0.00 0.00 3.67
3178 7198 0.175989 GAGGACACGGGAGATGGTTC 59.824 60.000 0.00 0.00 0.00 3.62
3179 7199 0.252284 AGGACACGGGAGATGGTTCT 60.252 55.000 0.00 0.00 33.88 3.01
3180 7200 0.175989 GGACACGGGAGATGGTTCTC 59.824 60.000 0.00 0.00 46.52 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 90 2.458610 GCGGTCCCGACGGAATTTC 61.459 63.158 17.49 0.43 40.92 2.17
128 144 3.357079 CTGCGTGACTTGGGTGGC 61.357 66.667 0.00 0.00 0.00 5.01
132 148 3.357079 GTGCCTGCGTGACTTGGG 61.357 66.667 0.00 0.00 0.00 4.12
133 149 3.716006 CGTGCCTGCGTGACTTGG 61.716 66.667 0.00 0.00 0.00 3.61
134 150 4.374702 GCGTGCCTGCGTGACTTG 62.375 66.667 0.00 0.00 0.00 3.16
155 265 1.590792 GGATTCGGCGAACCTACGG 60.591 63.158 26.22 0.00 0.00 4.02
364 502 4.742201 CTGTGCTCGTGACCCGGG 62.742 72.222 22.25 22.25 41.15 5.73
367 599 2.029844 GCTTCTGTGCTCGTGACCC 61.030 63.158 0.00 0.00 0.00 4.46
373 605 3.123620 GGGCAGCTTCTGTGCTCG 61.124 66.667 0.00 0.00 41.98 5.03
403 651 6.015603 TCTGTCATGTTTTGGTTATGATTGCA 60.016 34.615 0.00 0.00 33.82 4.08
414 687 2.485426 ACATCGCTCTGTCATGTTTTGG 59.515 45.455 0.00 0.00 0.00 3.28
423 696 3.609103 ACAAAAACACATCGCTCTGTC 57.391 42.857 0.00 0.00 0.00 3.51
447 720 5.349061 TCGGGGATCTTAACCTAGAAAAC 57.651 43.478 0.00 0.00 0.00 2.43
452 725 2.352814 CGCATCGGGGATCTTAACCTAG 60.353 54.545 0.00 0.00 0.00 3.02
455 728 0.106149 ACGCATCGGGGATCTTAACC 59.894 55.000 0.00 0.00 0.00 2.85
456 729 2.035576 AGTACGCATCGGGGATCTTAAC 59.964 50.000 0.00 0.00 0.00 2.01
470 743 1.667830 GACAAGCCAGCAGTACGCA 60.668 57.895 11.30 0.00 46.13 5.24
472 745 1.617755 CGTGACAAGCCAGCAGTACG 61.618 60.000 0.00 0.00 0.00 3.67
475 748 1.595382 GTCGTGACAAGCCAGCAGT 60.595 57.895 0.00 0.00 0.00 4.40
480 753 2.661537 CAGCGTCGTGACAAGCCA 60.662 61.111 0.41 0.00 0.00 4.75
481 754 2.658707 GACAGCGTCGTGACAAGCC 61.659 63.158 0.41 0.00 0.00 4.35
482 755 2.658707 GGACAGCGTCGTGACAAGC 61.659 63.158 0.41 0.00 32.65 4.01
483 756 2.022129 GGGACAGCGTCGTGACAAG 61.022 63.158 0.41 0.00 32.65 3.16
494 782 1.172812 AGTTTTGCTTCGGGGACAGC 61.173 55.000 0.00 0.00 0.00 4.40
503 791 4.214332 CAGTGTTAGGGAGAGTTTTGCTTC 59.786 45.833 0.00 0.00 0.00 3.86
511 799 1.552719 GGGGACAGTGTTAGGGAGAGT 60.553 57.143 0.00 0.00 0.00 3.24
512 800 1.196012 GGGGACAGTGTTAGGGAGAG 58.804 60.000 0.00 0.00 0.00 3.20
513 801 0.790993 AGGGGACAGTGTTAGGGAGA 59.209 55.000 0.00 0.00 0.00 3.71
514 802 1.196012 GAGGGGACAGTGTTAGGGAG 58.804 60.000 0.00 0.00 0.00 4.30
515 803 0.252558 GGAGGGGACAGTGTTAGGGA 60.253 60.000 0.00 0.00 0.00 4.20
518 806 1.486726 GGATGGAGGGGACAGTGTTAG 59.513 57.143 0.00 0.00 0.00 2.34
519 807 1.203376 TGGATGGAGGGGACAGTGTTA 60.203 52.381 0.00 0.00 0.00 2.41
523 811 0.695803 GGATGGATGGAGGGGACAGT 60.696 60.000 0.00 0.00 0.00 3.55
526 814 0.695347 GATGGATGGATGGAGGGGAC 59.305 60.000 0.00 0.00 0.00 4.46
530 818 1.453633 AAGGGATGGATGGATGGAGG 58.546 55.000 0.00 0.00 0.00 4.30
535 823 3.117738 GTCAGACAAAGGGATGGATGGAT 60.118 47.826 0.00 0.00 0.00 3.41
539 827 2.025887 GGTGTCAGACAAAGGGATGGAT 60.026 50.000 4.32 0.00 0.00 3.41
542 830 1.442769 CGGTGTCAGACAAAGGGATG 58.557 55.000 4.32 0.00 0.00 3.51
548 836 2.970324 GCGGCGGTGTCAGACAAA 60.970 61.111 9.78 0.00 0.00 2.83
583 871 7.201435 GCGAGCTTCAGAAAAAGAAAAGAAAAA 60.201 33.333 0.00 0.00 0.00 1.94
584 872 6.253512 GCGAGCTTCAGAAAAAGAAAAGAAAA 59.746 34.615 0.00 0.00 0.00 2.29
585 873 5.743872 GCGAGCTTCAGAAAAAGAAAAGAAA 59.256 36.000 0.00 0.00 0.00 2.52
586 874 5.066505 AGCGAGCTTCAGAAAAAGAAAAGAA 59.933 36.000 0.00 0.00 0.00 2.52
587 875 4.576463 AGCGAGCTTCAGAAAAAGAAAAGA 59.424 37.500 0.00 0.00 0.00 2.52
588 876 4.674211 CAGCGAGCTTCAGAAAAAGAAAAG 59.326 41.667 0.00 0.00 0.00 2.27
589 877 4.096382 ACAGCGAGCTTCAGAAAAAGAAAA 59.904 37.500 0.00 0.00 0.00 2.29
590 878 3.627577 ACAGCGAGCTTCAGAAAAAGAAA 59.372 39.130 0.00 0.00 0.00 2.52
591 879 3.206150 ACAGCGAGCTTCAGAAAAAGAA 58.794 40.909 0.00 0.00 0.00 2.52
592 880 2.802816 GACAGCGAGCTTCAGAAAAAGA 59.197 45.455 0.00 0.00 0.00 2.52
593 881 2.096019 GGACAGCGAGCTTCAGAAAAAG 60.096 50.000 0.00 0.00 0.00 2.27
594 882 1.873591 GGACAGCGAGCTTCAGAAAAA 59.126 47.619 0.00 0.00 0.00 1.94
595 883 1.202639 TGGACAGCGAGCTTCAGAAAA 60.203 47.619 0.00 0.00 0.00 2.29
596 884 0.392706 TGGACAGCGAGCTTCAGAAA 59.607 50.000 0.00 0.00 0.00 2.52
597 885 0.037882 CTGGACAGCGAGCTTCAGAA 60.038 55.000 11.76 0.00 0.00 3.02
598 886 1.181741 ACTGGACAGCGAGCTTCAGA 61.182 55.000 19.41 3.92 0.00 3.27
599 887 0.735632 GACTGGACAGCGAGCTTCAG 60.736 60.000 14.16 14.16 0.00 3.02
600 888 1.181741 AGACTGGACAGCGAGCTTCA 61.182 55.000 0.00 0.00 0.00 3.02
601 889 0.037790 AAGACTGGACAGCGAGCTTC 60.038 55.000 0.00 0.00 0.00 3.86
602 890 0.394565 AAAGACTGGACAGCGAGCTT 59.605 50.000 0.00 0.00 0.00 3.74
603 891 0.037790 GAAAGACTGGACAGCGAGCT 60.038 55.000 0.00 0.00 0.00 4.09
604 892 1.347817 CGAAAGACTGGACAGCGAGC 61.348 60.000 0.00 0.00 0.00 5.03
605 893 0.734253 CCGAAAGACTGGACAGCGAG 60.734 60.000 0.00 0.00 0.00 5.03
606 894 1.289066 CCGAAAGACTGGACAGCGA 59.711 57.895 0.00 0.00 0.00 4.93
607 895 1.006102 ACCGAAAGACTGGACAGCG 60.006 57.895 0.00 0.00 0.00 5.18
608 896 0.249911 ACACCGAAAGACTGGACAGC 60.250 55.000 0.00 0.00 0.00 4.40
609 897 3.594603 ATACACCGAAAGACTGGACAG 57.405 47.619 0.00 0.00 0.00 3.51
610 898 6.971726 ATATATACACCGAAAGACTGGACA 57.028 37.500 0.00 0.00 0.00 4.02
611 899 7.879070 TGTATATATACACCGAAAGACTGGAC 58.121 38.462 19.51 0.00 38.28 4.02
625 913 3.745458 TCGTGCGTCCGTGTATATATACA 59.255 43.478 19.51 19.51 40.69 2.29
640 928 4.210093 TGGGTCGTGTTCGTGCGT 62.210 61.111 0.00 0.00 38.33 5.24
643 931 2.279851 TGCTGGGTCGTGTTCGTG 60.280 61.111 0.00 0.00 38.33 4.35
644 932 2.029073 CTGCTGGGTCGTGTTCGT 59.971 61.111 0.00 0.00 38.33 3.85
645 933 3.414700 GCTGCTGGGTCGTGTTCG 61.415 66.667 0.00 0.00 38.55 3.95
670 962 1.076549 GGGGCTGTTGTGGATTGGA 59.923 57.895 0.00 0.00 0.00 3.53
671 963 0.615544 ATGGGGCTGTTGTGGATTGG 60.616 55.000 0.00 0.00 0.00 3.16
674 966 1.307647 GGATGGGGCTGTTGTGGAT 59.692 57.895 0.00 0.00 0.00 3.41
675 967 2.763215 GGATGGGGCTGTTGTGGA 59.237 61.111 0.00 0.00 0.00 4.02
681 973 3.105928 GGGATGGGATGGGGCTGT 61.106 66.667 0.00 0.00 0.00 4.40
682 974 2.436596 GATGGGATGGGATGGGGCTG 62.437 65.000 0.00 0.00 0.00 4.85
683 975 2.036908 ATGGGATGGGATGGGGCT 60.037 61.111 0.00 0.00 0.00 5.19
684 976 2.442413 GATGGGATGGGATGGGGC 59.558 66.667 0.00 0.00 0.00 5.80
711 1003 0.991920 TTGGTTTTGGGGGTTTTGCA 59.008 45.000 0.00 0.00 0.00 4.08
718 1010 0.812014 GTTGCGTTTGGTTTTGGGGG 60.812 55.000 0.00 0.00 0.00 5.40
825 1129 0.168128 GTTTGATTTAGCGCGCACCT 59.832 50.000 35.10 16.01 0.00 4.00
863 1167 1.792506 CGCAGATCGAAACTCGCTCG 61.793 60.000 0.00 0.00 39.67 5.03
898 1220 1.010294 TGGAGCCCTGGACCCTATAAA 59.990 52.381 0.00 0.00 0.00 1.40
899 1221 0.645496 TGGAGCCCTGGACCCTATAA 59.355 55.000 0.00 0.00 0.00 0.98
900 1222 0.191064 CTGGAGCCCTGGACCCTATA 59.809 60.000 0.00 0.00 0.00 1.31
901 1223 1.074167 CTGGAGCCCTGGACCCTAT 60.074 63.158 0.00 0.00 0.00 2.57
902 1224 2.368594 CTGGAGCCCTGGACCCTA 59.631 66.667 0.00 0.00 0.00 3.53
903 1225 4.748798 CCTGGAGCCCTGGACCCT 62.749 72.222 10.45 0.00 44.09 4.34
907 1229 3.696518 ATACGCCTGGAGCCCTGGA 62.697 63.158 17.59 1.78 44.09 3.86
908 1230 2.270874 AAATACGCCTGGAGCCCTGG 62.271 60.000 0.00 11.33 44.16 4.45
909 1231 0.468226 TAAATACGCCTGGAGCCCTG 59.532 55.000 0.00 0.00 38.78 4.45
910 1232 0.759346 CTAAATACGCCTGGAGCCCT 59.241 55.000 0.00 0.00 38.78 5.19
911 1233 0.885150 GCTAAATACGCCTGGAGCCC 60.885 60.000 0.00 0.00 38.78 5.19
912 1234 0.179056 TGCTAAATACGCCTGGAGCC 60.179 55.000 0.00 0.00 38.78 4.70
913 1235 1.663695 TTGCTAAATACGCCTGGAGC 58.336 50.000 0.00 0.00 38.52 4.70
914 1236 2.614057 CCTTTGCTAAATACGCCTGGAG 59.386 50.000 0.00 0.00 0.00 3.86
915 1237 2.237643 TCCTTTGCTAAATACGCCTGGA 59.762 45.455 0.00 0.00 0.00 3.86
916 1238 2.354821 GTCCTTTGCTAAATACGCCTGG 59.645 50.000 0.00 0.00 0.00 4.45
917 1239 3.006940 TGTCCTTTGCTAAATACGCCTG 58.993 45.455 0.00 0.00 0.00 4.85
977 1302 4.504596 TAATGCGGCAGCCAGGGG 62.505 66.667 13.30 0.00 44.33 4.79
1064 1389 4.681978 AAGTGGCAGGCGGTCGTC 62.682 66.667 0.00 0.00 0.00 4.20
1065 1390 4.681978 GAAGTGGCAGGCGGTCGT 62.682 66.667 0.00 0.00 0.00 4.34
1124 1458 1.273886 ACGAACAAGAGGAGGAAGAGC 59.726 52.381 0.00 0.00 0.00 4.09
1131 1468 1.474879 GAGGAGGACGAACAAGAGGAG 59.525 57.143 0.00 0.00 0.00 3.69
1140 1486 1.215679 AGGAGGAGGAGGAGGACGAA 61.216 60.000 0.00 0.00 0.00 3.85
1143 1489 1.231928 GGAGGAGGAGGAGGAGGAC 59.768 68.421 0.00 0.00 0.00 3.85
1193 1539 4.816984 TCGTCCTCGCCCTCTCCC 62.817 72.222 0.00 0.00 36.96 4.30
1194 1540 3.213402 CTCGTCCTCGCCCTCTCC 61.213 72.222 0.00 0.00 36.96 3.71
1195 1541 3.213402 CCTCGTCCTCGCCCTCTC 61.213 72.222 0.00 0.00 36.96 3.20
1196 1542 3.729489 TCCTCGTCCTCGCCCTCT 61.729 66.667 0.00 0.00 36.96 3.69
1197 1543 3.519930 GTCCTCGTCCTCGCCCTC 61.520 72.222 0.00 0.00 36.96 4.30
1327 1673 2.342648 GGTGACGTCGAGGCCTTT 59.657 61.111 6.77 0.00 0.00 3.11
1728 2077 2.813908 GTGGTGGCGGCGAAGTAG 60.814 66.667 12.98 0.00 0.00 2.57
2192 2550 3.506096 CACCAGCGGCATCAGCAG 61.506 66.667 1.45 0.00 44.61 4.24
2211 2569 0.456995 CGTCTCTCTCGCCCAGAAAC 60.457 60.000 0.00 0.00 0.00 2.78
2222 2580 1.378778 CCCTTCCGTCCGTCTCTCT 60.379 63.158 0.00 0.00 0.00 3.10
2241 2599 3.744155 CCTCCTCCCCCAAAGCCC 61.744 72.222 0.00 0.00 0.00 5.19
2253 2612 2.434774 GGCGGTCAAAACCCTCCT 59.565 61.111 0.00 0.00 43.21 3.69
2353 2712 3.118261 TCTCTTCTCCTCTCTCTCTCTGC 60.118 52.174 0.00 0.00 0.00 4.26
2358 2717 4.651503 TCTCTCTCTCTTCTCCTCTCTCTC 59.348 50.000 0.00 0.00 0.00 3.20
2367 2726 5.934625 CACTAGCCTATCTCTCTCTCTTCTC 59.065 48.000 0.00 0.00 0.00 2.87
2368 2727 5.369699 ACACTAGCCTATCTCTCTCTCTTCT 59.630 44.000 0.00 0.00 0.00 2.85
2369 2728 5.621193 ACACTAGCCTATCTCTCTCTCTTC 58.379 45.833 0.00 0.00 0.00 2.87
2370 2729 5.646692 ACACTAGCCTATCTCTCTCTCTT 57.353 43.478 0.00 0.00 0.00 2.85
2411 2772 5.959618 AATTAACTTACACACAAGCCCTC 57.040 39.130 0.00 0.00 0.00 4.30
2488 6473 5.012239 CCAACTCTCCCAATCAATCAAGAA 58.988 41.667 0.00 0.00 0.00 2.52
2489 6474 4.289410 TCCAACTCTCCCAATCAATCAAGA 59.711 41.667 0.00 0.00 0.00 3.02
2490 6475 4.592942 TCCAACTCTCCCAATCAATCAAG 58.407 43.478 0.00 0.00 0.00 3.02
2491 6476 4.043310 ACTCCAACTCTCCCAATCAATCAA 59.957 41.667 0.00 0.00 0.00 2.57
2492 6477 3.588842 ACTCCAACTCTCCCAATCAATCA 59.411 43.478 0.00 0.00 0.00 2.57
2493 6478 4.227864 ACTCCAACTCTCCCAATCAATC 57.772 45.455 0.00 0.00 0.00 2.67
2494 6479 5.983333 ATACTCCAACTCTCCCAATCAAT 57.017 39.130 0.00 0.00 0.00 2.57
2502 6487 4.995487 ACGAAACAAATACTCCAACTCTCC 59.005 41.667 0.00 0.00 0.00 3.71
2550 6539 8.807581 CCTACATACATTACATACATGCATACG 58.192 37.037 0.00 0.00 0.00 3.06
2556 6545 7.062255 CGACTGCCTACATACATTACATACATG 59.938 40.741 0.00 0.00 0.00 3.21
2560 6549 6.263617 TGACGACTGCCTACATACATTACATA 59.736 38.462 0.00 0.00 0.00 2.29
2562 6551 4.399934 TGACGACTGCCTACATACATTACA 59.600 41.667 0.00 0.00 0.00 2.41
2563 6552 4.928601 TGACGACTGCCTACATACATTAC 58.071 43.478 0.00 0.00 0.00 1.89
2564 6553 5.068591 ACATGACGACTGCCTACATACATTA 59.931 40.000 0.00 0.00 0.00 1.90
2565 6554 4.141937 ACATGACGACTGCCTACATACATT 60.142 41.667 0.00 0.00 0.00 2.71
2566 6555 3.384789 ACATGACGACTGCCTACATACAT 59.615 43.478 0.00 0.00 0.00 2.29
2567 6556 2.758423 ACATGACGACTGCCTACATACA 59.242 45.455 0.00 0.00 0.00 2.29
2568 6557 3.438297 ACATGACGACTGCCTACATAC 57.562 47.619 0.00 0.00 0.00 2.39
2569 6558 3.317149 GGTACATGACGACTGCCTACATA 59.683 47.826 0.00 0.00 0.00 2.29
2591 6580 2.205074 GATTAGTGATGAGTGGTGGCG 58.795 52.381 0.00 0.00 0.00 5.69
2673 6673 1.003696 CCTTTGGGAGGTTCCAGACTC 59.996 57.143 0.00 0.00 40.95 3.36
2706 6711 1.823899 GGATGGATGGTTCCGGTGC 60.824 63.158 0.00 0.00 45.89 5.01
2714 6719 2.001803 CAGGTGGTGGATGGATGGT 58.998 57.895 0.00 0.00 0.00 3.55
2723 6728 0.033796 AATGATGGAGCAGGTGGTGG 60.034 55.000 0.00 0.00 0.00 4.61
2724 6729 1.475280 CAAATGATGGAGCAGGTGGTG 59.525 52.381 0.00 0.00 0.00 4.17
2785 6790 1.519719 CCTCCTCCTCCTCAAAGCG 59.480 63.158 0.00 0.00 0.00 4.68
2801 6806 2.358737 CGCCACGCTCTTTTCCCT 60.359 61.111 0.00 0.00 0.00 4.20
2928 6933 3.878667 CGCATTCCCTCCTCCCCC 61.879 72.222 0.00 0.00 0.00 5.40
2946 6951 1.339247 CCTACCAATACACACGGCCAA 60.339 52.381 2.24 0.00 0.00 4.52
3016 7029 4.660938 AGACCGGGTTTGGCCTGC 62.661 66.667 6.32 0.00 42.42 4.85
3029 7042 1.063488 GCGCGAGAGAGAGAAGACC 59.937 63.158 12.10 0.00 0.00 3.85
3031 7044 3.094154 CGCGCGAGAGAGAGAAGA 58.906 61.111 28.94 0.00 31.43 2.87
3055 7068 1.750930 CAGCCAGTCAGTCACCAGT 59.249 57.895 0.00 0.00 0.00 4.00
3059 7072 1.670406 CAGCCAGCCAGTCAGTCAC 60.670 63.158 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.