Multiple sequence alignment - TraesCS3A01G282200

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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 TraesCS3A01G282200 chr3A 100.000 3847 0 0 1 3847 510718760 510722606 0.000000e+00 7105
1 TraesCS3A01G282200 chr3A 94.167 120 5 2 3267 3385 658713043 658713161 8.490000e-42 182
2 TraesCS3A01G282200 chr3D 94.662 2529 94 18 767 3271 390198089 390200600 0.000000e+00 3884
3 TraesCS3A01G282200 chr3D 93.735 431 26 1 3367 3796 390200705 390201135 0.000000e+00 645
4 TraesCS3A01G282200 chr3B 94.215 2472 104 11 767 3212 507386480 507388938 0.000000e+00 3736
5 TraesCS3A01G282200 chr7D 91.186 590 43 5 150 730 483283127 483283716 0.000000e+00 793
6 TraesCS3A01G282200 chr1D 82.933 750 98 20 2 727 470517938 470517195 0.000000e+00 649
7 TraesCS3A01G282200 chr1D 94.958 119 4 2 3268 3385 100826375 100826492 6.560000e-43 185
8 TraesCS3A01G282200 chr5A 83.796 685 83 14 52 727 486990017 486990682 3.260000e-175 625
9 TraesCS3A01G282200 chr5A 97.297 111 3 0 3277 3387 601257307 601257417 5.070000e-44 189
10 TraesCS3A01G282200 chr5A 95.652 115 5 0 3271 3385 363850784 363850898 6.560000e-43 185
11 TraesCS3A01G282200 chr5A 93.277 119 8 0 3267 3385 69844776 69844894 3.950000e-40 176
12 TraesCS3A01G282200 chr4D 81.184 760 90 16 2 727 222193476 222194216 2.590000e-156 562
13 TraesCS3A01G282200 chr7B 86.364 352 27 13 1 331 327399400 327399751 7.850000e-97 364
14 TraesCS3A01G282200 chr5B 82.785 395 49 14 2 381 587898887 587899277 6.160000e-88 335
15 TraesCS3A01G282200 chr2D 93.506 154 9 1 1 153 405401893 405401740 1.080000e-55 228
16 TraesCS3A01G282200 chr2D 82.288 271 38 6 420 685 463876848 463876583 3.870000e-55 226
17 TraesCS3A01G282200 chr2B 87.640 178 18 4 3467 3642 154289845 154290020 1.810000e-48 204
18 TraesCS3A01G282200 chr2B 86.982 169 20 2 3475 3642 154350992 154351159 5.070000e-44 189
19 TraesCS3A01G282200 chr2A 95.652 115 5 0 3273 3387 209894160 209894274 6.560000e-43 185
20 TraesCS3A01G282200 chr2A 92.126 127 8 2 3269 3395 753463787 753463663 1.100000e-40 178
21 TraesCS3A01G282200 chr6A 94.915 118 4 2 3271 3387 477910764 477910880 2.360000e-42 183
22 TraesCS3A01G282200 chr6A 90.909 132 10 2 3268 3399 576393133 576393262 3.950000e-40 176


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 TraesCS3A01G282200 chr3A 510718760 510722606 3846 False 7105.0 7105 100.0000 1 3847 1 chr3A.!!$F1 3846
1 TraesCS3A01G282200 chr3D 390198089 390201135 3046 False 2264.5 3884 94.1985 767 3796 2 chr3D.!!$F1 3029
2 TraesCS3A01G282200 chr3B 507386480 507388938 2458 False 3736.0 3736 94.2150 767 3212 1 chr3B.!!$F1 2445
3 TraesCS3A01G282200 chr7D 483283127 483283716 589 False 793.0 793 91.1860 150 730 1 chr7D.!!$F1 580
4 TraesCS3A01G282200 chr1D 470517195 470517938 743 True 649.0 649 82.9330 2 727 1 chr1D.!!$R1 725
5 TraesCS3A01G282200 chr5A 486990017 486990682 665 False 625.0 625 83.7960 52 727 1 chr5A.!!$F3 675
6 TraesCS3A01G282200 chr4D 222193476 222194216 740 False 562.0 562 81.1840 2 727 1 chr4D.!!$F1 725

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
239 288 0.104409 ACCTCACCCCAGACTCCTTT 60.104 55.0 0.00 0.0 0.00 3.11 F
685 740 0.322008 CCAGAACTGGCTCTTGGGAC 60.322 60.0 7.95 0.0 44.73 4.46 F
1579 1685 0.600255 GATGTACGGGCAGGGATTCG 60.600 60.0 0.00 0.0 0.00 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1413 1519 0.727398 GGTACTGATCAAACAGGCGC 59.273 55.000 0.00 0.00 41.59 6.53 R
2628 2734 0.653636 CAGTAGAGCTCGACGACCTC 59.346 60.000 19.51 11.47 0.00 3.85 R
3450 3568 1.258982 CGCCCTGATTCGATCGAAAAG 59.741 52.381 32.11 28.30 37.69 2.27 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
28 30 7.432869 CCAAATACAAAAGTCTGGATCAACAA 58.567 34.615 0.00 0.00 0.00 2.83
39 42 1.000843 GGATCAACAAAGCCACCCAAC 59.999 52.381 0.00 0.00 0.00 3.77
68 71 5.295152 CCTTGCTGCTTCATTTCTTTTTCT 58.705 37.500 0.00 0.00 0.00 2.52
79 82 7.707624 TCATTTCTTTTTCTATCATGTGGCT 57.292 32.000 0.00 0.00 0.00 4.75
115 118 3.152341 CATGTTGCTCCTCCAGTTCTTT 58.848 45.455 0.00 0.00 0.00 2.52
230 279 3.311110 GAGACGCACCTCACCCCA 61.311 66.667 0.00 0.00 33.50 4.96
239 288 0.104409 ACCTCACCCCAGACTCCTTT 60.104 55.000 0.00 0.00 0.00 3.11
252 301 1.208293 ACTCCTTTCGCCAGATCCTTC 59.792 52.381 0.00 0.00 0.00 3.46
261 310 0.752009 CCAGATCCTTCGTCGAGGGA 60.752 60.000 26.19 26.19 41.92 4.20
268 317 2.372504 TCCTTCGTCGAGGGAGAGATAT 59.627 50.000 21.17 0.00 32.81 1.63
435 484 4.021925 GGGTGCAGCGGAGGAAGT 62.022 66.667 10.24 0.00 0.00 3.01
443 492 2.593956 GCGGAGGAAGTGAAGGGGT 61.594 63.158 0.00 0.00 0.00 4.95
480 529 1.753078 CCACGACCATCGAGGGAGA 60.753 63.158 25.24 0.00 44.94 3.71
481 530 1.729470 CCACGACCATCGAGGGAGAG 61.729 65.000 25.24 15.12 44.94 3.20
482 531 0.748367 CACGACCATCGAGGGAGAGA 60.748 60.000 25.24 0.00 43.74 3.10
557 612 0.800012 GAGAAGAGACACGAGCGAGT 59.200 55.000 0.00 0.00 0.00 4.18
589 644 1.134491 GTCCGGTCGATTTGGAGGAAT 60.134 52.381 0.00 0.00 31.04 3.01
610 665 1.271102 GCCCAAGTTCGGCATAAACAA 59.729 47.619 6.63 0.00 46.27 2.83
629 684 1.507140 AGGAATATGCCGTTCCCTGA 58.493 50.000 7.90 0.00 45.00 3.86
673 728 3.074412 CCGCAATCTAAACACCAGAACT 58.926 45.455 0.00 0.00 0.00 3.01
685 740 0.322008 CCAGAACTGGCTCTTGGGAC 60.322 60.000 7.95 0.00 44.73 4.46
688 743 3.553095 AACTGGCTCTTGGGACGGC 62.553 63.158 0.00 0.00 0.00 5.68
691 746 3.766691 GGCTCTTGGGACGGCGTA 61.767 66.667 14.74 0.00 0.00 4.42
692 747 2.508663 GCTCTTGGGACGGCGTAC 60.509 66.667 15.37 15.37 0.00 3.67
693 748 2.183555 CTCTTGGGACGGCGTACC 59.816 66.667 34.09 34.09 36.98 3.34
704 759 2.224428 GGCGTACCGTTTCGTTTCA 58.776 52.632 0.00 0.00 0.00 2.69
705 760 0.792031 GGCGTACCGTTTCGTTTCAT 59.208 50.000 0.00 0.00 0.00 2.57
706 761 1.462869 GGCGTACCGTTTCGTTTCATG 60.463 52.381 0.00 0.00 0.00 3.07
707 762 1.456544 GCGTACCGTTTCGTTTCATGA 59.543 47.619 0.00 0.00 0.00 3.07
708 763 2.719688 GCGTACCGTTTCGTTTCATGAC 60.720 50.000 0.00 0.00 0.00 3.06
709 764 2.472115 CGTACCGTTTCGTTTCATGACA 59.528 45.455 0.00 0.00 0.00 3.58
710 765 3.421312 CGTACCGTTTCGTTTCATGACAG 60.421 47.826 0.00 0.00 0.00 3.51
711 766 2.828877 ACCGTTTCGTTTCATGACAGA 58.171 42.857 0.00 0.00 0.00 3.41
712 767 3.199677 ACCGTTTCGTTTCATGACAGAA 58.800 40.909 0.00 0.00 0.00 3.02
713 768 3.623960 ACCGTTTCGTTTCATGACAGAAA 59.376 39.130 12.62 12.62 35.28 2.52
722 777 5.651387 TTTCATGACAGAAACCAAACACA 57.349 34.783 0.00 0.00 32.88 3.72
723 778 4.630894 TCATGACAGAAACCAAACACAC 57.369 40.909 0.00 0.00 0.00 3.82
724 779 3.380004 TCATGACAGAAACCAAACACACC 59.620 43.478 0.00 0.00 0.00 4.16
725 780 2.096248 TGACAGAAACCAAACACACCC 58.904 47.619 0.00 0.00 0.00 4.61
726 781 2.291282 TGACAGAAACCAAACACACCCT 60.291 45.455 0.00 0.00 0.00 4.34
727 782 2.758423 GACAGAAACCAAACACACCCTT 59.242 45.455 0.00 0.00 0.00 3.95
728 783 3.949113 GACAGAAACCAAACACACCCTTA 59.051 43.478 0.00 0.00 0.00 2.69
729 784 3.951680 ACAGAAACCAAACACACCCTTAG 59.048 43.478 0.00 0.00 0.00 2.18
730 785 3.951680 CAGAAACCAAACACACCCTTAGT 59.048 43.478 0.00 0.00 0.00 2.24
731 786 4.036380 CAGAAACCAAACACACCCTTAGTC 59.964 45.833 0.00 0.00 0.00 2.59
732 787 3.945640 AACCAAACACACCCTTAGTCT 57.054 42.857 0.00 0.00 0.00 3.24
733 788 3.208747 ACCAAACACACCCTTAGTCTG 57.791 47.619 0.00 0.00 0.00 3.51
734 789 1.880027 CCAAACACACCCTTAGTCTGC 59.120 52.381 0.00 0.00 0.00 4.26
735 790 2.571212 CAAACACACCCTTAGTCTGCA 58.429 47.619 0.00 0.00 0.00 4.41
736 791 2.549754 CAAACACACCCTTAGTCTGCAG 59.450 50.000 7.63 7.63 0.00 4.41
737 792 1.424638 ACACACCCTTAGTCTGCAGT 58.575 50.000 14.67 0.00 0.00 4.40
738 793 1.768870 ACACACCCTTAGTCTGCAGTT 59.231 47.619 14.67 6.17 0.00 3.16
739 794 2.224305 ACACACCCTTAGTCTGCAGTTC 60.224 50.000 14.67 8.51 0.00 3.01
740 795 1.000955 ACACCCTTAGTCTGCAGTTCG 59.999 52.381 14.67 0.00 0.00 3.95
741 796 0.608640 ACCCTTAGTCTGCAGTTCGG 59.391 55.000 14.67 8.33 0.00 4.30
742 797 0.608640 CCCTTAGTCTGCAGTTCGGT 59.391 55.000 14.67 0.00 0.00 4.69
743 798 1.673033 CCCTTAGTCTGCAGTTCGGTG 60.673 57.143 14.67 0.00 0.00 4.94
744 799 1.272490 CCTTAGTCTGCAGTTCGGTGA 59.728 52.381 14.67 0.00 0.00 4.02
745 800 2.093973 CCTTAGTCTGCAGTTCGGTGAT 60.094 50.000 14.67 0.00 0.00 3.06
746 801 2.654749 TAGTCTGCAGTTCGGTGATG 57.345 50.000 14.67 0.00 0.00 3.07
747 802 0.969149 AGTCTGCAGTTCGGTGATGA 59.031 50.000 14.67 0.00 0.00 2.92
748 803 1.552337 AGTCTGCAGTTCGGTGATGAT 59.448 47.619 14.67 0.00 0.00 2.45
749 804 1.929836 GTCTGCAGTTCGGTGATGATC 59.070 52.381 14.67 0.00 0.00 2.92
750 805 1.134699 TCTGCAGTTCGGTGATGATCC 60.135 52.381 14.67 0.00 0.00 3.36
751 806 0.612744 TGCAGTTCGGTGATGATCCA 59.387 50.000 0.00 0.00 0.00 3.41
752 807 1.293924 GCAGTTCGGTGATGATCCAG 58.706 55.000 0.00 0.00 0.00 3.86
753 808 1.945387 CAGTTCGGTGATGATCCAGG 58.055 55.000 0.00 0.00 0.00 4.45
754 809 0.833287 AGTTCGGTGATGATCCAGGG 59.167 55.000 0.00 0.00 0.00 4.45
755 810 0.830648 GTTCGGTGATGATCCAGGGA 59.169 55.000 0.00 0.00 0.00 4.20
756 811 1.209504 GTTCGGTGATGATCCAGGGAA 59.790 52.381 0.00 0.00 0.00 3.97
757 812 1.806496 TCGGTGATGATCCAGGGAAT 58.194 50.000 0.00 0.00 0.00 3.01
758 813 1.694150 TCGGTGATGATCCAGGGAATC 59.306 52.381 0.00 0.00 0.00 2.52
759 814 1.696336 CGGTGATGATCCAGGGAATCT 59.304 52.381 0.00 0.00 0.00 2.40
760 815 2.549563 CGGTGATGATCCAGGGAATCTG 60.550 54.545 0.00 0.00 43.00 2.90
761 816 2.441001 GGTGATGATCCAGGGAATCTGT 59.559 50.000 0.00 0.00 41.83 3.41
762 817 3.648067 GGTGATGATCCAGGGAATCTGTA 59.352 47.826 0.00 0.00 41.83 2.74
763 818 4.503991 GGTGATGATCCAGGGAATCTGTAC 60.504 50.000 0.00 0.00 41.83 2.90
764 819 3.321968 TGATGATCCAGGGAATCTGTACG 59.678 47.826 0.00 0.00 41.83 3.67
765 820 2.747177 TGATCCAGGGAATCTGTACGT 58.253 47.619 0.00 0.00 41.83 3.57
806 861 4.400961 GCGGCTGCCTCCACTTCT 62.401 66.667 17.92 0.00 33.98 2.85
847 902 2.097038 GCCACAGCTGTGCGACTAG 61.097 63.158 36.38 23.91 44.34 2.57
856 911 2.797792 GCTGTGCGACTAGAAGATCCAG 60.798 54.545 0.00 0.00 0.00 3.86
1075 1163 2.376231 GATCGTGTCGTCGGATCGCT 62.376 60.000 0.00 0.00 0.00 4.93
1131 1219 2.586357 GAGGGATTCGACGGCAGC 60.586 66.667 0.00 0.00 0.00 5.25
1233 1333 1.012486 ACGCTGACGGGAAATTCGAC 61.012 55.000 0.00 0.00 46.04 4.20
1437 1543 3.866651 CCTGTTTGATCAGTACCTCCTG 58.133 50.000 0.00 0.00 34.02 3.86
1509 1615 4.423022 TTCATCCGCGCCGTCGAA 62.423 61.111 0.00 0.06 38.10 3.71
1566 1672 0.645868 GCTTCCGCTTCGTGATGTAC 59.354 55.000 0.00 0.00 0.00 2.90
1579 1685 0.600255 GATGTACGGGCAGGGATTCG 60.600 60.000 0.00 0.00 0.00 3.34
1670 1776 4.612033 CGTCGACATGTTGTACACAGTCTA 60.612 45.833 17.16 0.00 39.40 2.59
1671 1777 5.399858 GTCGACATGTTGTACACAGTCTAT 58.600 41.667 11.55 0.00 39.40 1.98
1740 1846 2.417924 CCTAAGAGTGTGCTTCTGCGAT 60.418 50.000 0.00 0.00 43.34 4.58
1746 1852 0.737367 TGTGCTTCTGCGATCTTCCG 60.737 55.000 0.00 0.00 43.34 4.30
1815 1921 1.305930 GCCTGTCCAATGTCCGAACC 61.306 60.000 0.00 0.00 0.00 3.62
1854 1960 1.065273 GATGCTTGCTCATTGCCCG 59.935 57.895 0.00 0.00 42.00 6.13
1926 2032 2.046892 CGGTCCAAGAGCCTGGTG 60.047 66.667 0.00 0.00 37.74 4.17
2067 2173 3.573229 AAGCTGCAGGTGCTGGGA 61.573 61.111 20.97 0.00 41.03 4.37
2137 2243 5.537188 TCGATGTAAATGCTTTGCCTTTTT 58.463 33.333 0.00 0.00 30.02 1.94
2140 2246 6.806249 CGATGTAAATGCTTTGCCTTTTTCTA 59.194 34.615 0.00 0.00 30.02 2.10
2172 2278 5.368145 TGCAGCTAAAACTCGGATGATATT 58.632 37.500 0.00 0.00 0.00 1.28
2432 2538 5.249163 AGCTCTACCATCATACCATGCATTA 59.751 40.000 0.00 0.00 0.00 1.90
2480 2586 3.002791 GGCAGACAGTCGATCAATTTCA 58.997 45.455 0.00 0.00 0.00 2.69
2524 2630 2.418334 GGGACACGACAACTTCTATCCC 60.418 54.545 0.00 0.00 37.96 3.85
2628 2734 4.456911 TGCTTGAGATGGCTAAAACTCTTG 59.543 41.667 0.00 0.00 0.00 3.02
2684 2790 6.631962 AGACTGTGCCAGTAGACTAATAAAC 58.368 40.000 7.69 0.00 45.44 2.01
2871 2977 4.773674 AGGTGATTGCAATCTGAAAATCCA 59.226 37.500 33.23 13.15 36.39 3.41
2890 2996 4.191485 GTTGTCGTCGGATGCGCG 62.191 66.667 14.93 14.93 0.00 6.86
2922 3028 3.914312 TCTTGTGTCAGAATCCGAGAAC 58.086 45.455 0.00 0.00 0.00 3.01
3010 3116 4.559153 CTGGTTGGCTGGAACTATTTTTG 58.441 43.478 0.00 0.00 0.00 2.44
3011 3117 3.964031 TGGTTGGCTGGAACTATTTTTGT 59.036 39.130 0.00 0.00 0.00 2.83
3102 3208 7.846066 AGCATAATGGTTTAGCATTTTGGTAA 58.154 30.769 20.23 2.77 38.40 2.85
3236 3344 1.305201 TTTGTCCCTCAACTTGTCGC 58.695 50.000 0.00 0.00 35.61 5.19
3251 3359 1.202188 TGTCGCGTTGCACAAATTTGA 60.202 42.857 24.64 0.00 0.00 2.69
3256 3364 2.865670 GCGTTGCACAAATTTGATCCCA 60.866 45.455 24.64 11.80 0.00 4.37
3271 3379 9.699410 AATTTGATCCCAGACTTTGATTATGTA 57.301 29.630 0.00 0.00 0.00 2.29
3272 3380 8.737168 TTTGATCCCAGACTTTGATTATGTAG 57.263 34.615 0.00 0.00 0.00 2.74
3273 3381 7.437713 TGATCCCAGACTTTGATTATGTAGT 57.562 36.000 0.00 0.00 0.00 2.73
3274 3382 8.547481 TGATCCCAGACTTTGATTATGTAGTA 57.453 34.615 0.00 0.00 0.00 1.82
3278 3386 9.656323 TCCCAGACTTTGATTATGTAGTATACT 57.344 33.333 10.87 10.87 43.54 2.12
3288 3396 8.045507 TGATTATGTAGTATACTACTCCCTCCG 58.954 40.741 32.68 0.00 46.74 4.63
3289 3397 5.839517 ATGTAGTATACTACTCCCTCCGT 57.160 43.478 32.68 12.18 46.74 4.69
3291 3399 5.615289 TGTAGTATACTACTCCCTCCGTTC 58.385 45.833 32.68 11.56 46.74 3.95
3292 3400 5.367937 TGTAGTATACTACTCCCTCCGTTCT 59.632 44.000 32.68 0.83 46.74 3.01
3294 3402 6.506538 AGTATACTACTCCCTCCGTTCTAA 57.493 41.667 2.75 0.00 32.47 2.10
3295 3403 6.904626 AGTATACTACTCCCTCCGTTCTAAA 58.095 40.000 2.75 0.00 32.47 1.85
3296 3404 7.525165 AGTATACTACTCCCTCCGTTCTAAAT 58.475 38.462 2.75 0.00 32.47 1.40
3297 3405 8.003629 AGTATACTACTCCCTCCGTTCTAAATT 58.996 37.037 2.75 0.00 32.47 1.82
3298 3406 9.289782 GTATACTACTCCCTCCGTTCTAAATTA 57.710 37.037 0.00 0.00 0.00 1.40
3299 3407 6.462552 ACTACTCCCTCCGTTCTAAATTAC 57.537 41.667 0.00 0.00 0.00 1.89
3300 3408 6.193504 ACTACTCCCTCCGTTCTAAATTACT 58.806 40.000 0.00 0.00 0.00 2.24
3302 3410 5.731591 ACTCCCTCCGTTCTAAATTACTTG 58.268 41.667 0.00 0.00 0.00 3.16
3303 3411 5.247792 ACTCCCTCCGTTCTAAATTACTTGT 59.752 40.000 0.00 0.00 0.00 3.16
3304 3412 5.727434 TCCCTCCGTTCTAAATTACTTGTC 58.273 41.667 0.00 0.00 0.00 3.18
3305 3413 4.565564 CCCTCCGTTCTAAATTACTTGTCG 59.434 45.833 0.00 0.00 0.00 4.35
3306 3414 4.032558 CCTCCGTTCTAAATTACTTGTCGC 59.967 45.833 0.00 0.00 0.00 5.19
3307 3415 4.558178 TCCGTTCTAAATTACTTGTCGCA 58.442 39.130 0.00 0.00 0.00 5.10
3308 3416 4.624024 TCCGTTCTAAATTACTTGTCGCAG 59.376 41.667 0.00 0.00 0.00 5.18
3309 3417 4.201685 CCGTTCTAAATTACTTGTCGCAGG 60.202 45.833 0.00 0.00 0.00 4.85
3310 3418 4.387862 CGTTCTAAATTACTTGTCGCAGGT 59.612 41.667 0.91 0.91 0.00 4.00
3311 3419 5.574055 CGTTCTAAATTACTTGTCGCAGGTA 59.426 40.000 0.00 0.00 0.00 3.08
3312 3420 6.255020 CGTTCTAAATTACTTGTCGCAGGTAT 59.745 38.462 3.46 0.00 0.00 2.73
3313 3421 7.399523 GTTCTAAATTACTTGTCGCAGGTATG 58.600 38.462 3.46 0.00 0.00 2.39
3314 3422 6.046593 TCTAAATTACTTGTCGCAGGTATGG 58.953 40.000 3.46 0.00 0.00 2.74
3315 3423 4.481368 AATTACTTGTCGCAGGTATGGA 57.519 40.909 3.46 0.00 0.00 3.41
3316 3424 4.689612 ATTACTTGTCGCAGGTATGGAT 57.310 40.909 3.46 0.00 0.00 3.41
3317 3425 2.315925 ACTTGTCGCAGGTATGGATG 57.684 50.000 0.00 0.00 0.00 3.51
3319 3427 2.764010 ACTTGTCGCAGGTATGGATGTA 59.236 45.455 0.00 0.00 0.00 2.29
3321 3429 3.660501 TGTCGCAGGTATGGATGTATC 57.339 47.619 0.00 0.00 0.00 2.24
3323 3431 4.403734 TGTCGCAGGTATGGATGTATCTA 58.596 43.478 0.00 0.00 0.00 1.98
3324 3432 4.459337 TGTCGCAGGTATGGATGTATCTAG 59.541 45.833 0.00 0.00 0.00 2.43
3325 3433 4.700692 GTCGCAGGTATGGATGTATCTAGA 59.299 45.833 0.00 0.00 0.00 2.43
3326 3434 5.358442 GTCGCAGGTATGGATGTATCTAGAT 59.642 44.000 10.73 10.73 0.00 1.98
3327 3435 5.358160 TCGCAGGTATGGATGTATCTAGATG 59.642 44.000 15.79 0.00 0.00 2.90
3328 3436 5.126222 CGCAGGTATGGATGTATCTAGATGT 59.874 44.000 15.79 1.25 0.00 3.06
3331 3439 8.700051 GCAGGTATGGATGTATCTAGATGTATT 58.300 37.037 15.79 0.00 0.00 1.89
3360 3468 9.167311 AGTTTTAGATACATCCATTTCTGTGAC 57.833 33.333 0.00 0.00 0.00 3.67
3361 3469 7.770801 TTTAGATACATCCATTTCTGTGACG 57.229 36.000 0.00 0.00 0.00 4.35
3363 3471 5.595885 AGATACATCCATTTCTGTGACGAG 58.404 41.667 0.00 0.00 0.00 4.18
3364 3472 3.685139 ACATCCATTTCTGTGACGAGT 57.315 42.857 0.00 0.00 0.00 4.18
3367 3475 5.734720 ACATCCATTTCTGTGACGAGTAAT 58.265 37.500 0.00 0.00 0.00 1.89
3368 3476 6.173339 ACATCCATTTCTGTGACGAGTAATT 58.827 36.000 0.00 0.00 0.00 1.40
3370 3478 6.480524 TCCATTTCTGTGACGAGTAATTTG 57.519 37.500 0.00 0.00 0.00 2.32
3371 3479 6.227522 TCCATTTCTGTGACGAGTAATTTGA 58.772 36.000 0.00 0.00 0.00 2.69
3391 3509 3.637229 TGAAACGGAGGGAGTAGATGATC 59.363 47.826 0.00 0.00 0.00 2.92
3393 3511 3.534357 ACGGAGGGAGTAGATGATCAT 57.466 47.619 8.25 8.25 0.00 2.45
3394 3512 3.161067 ACGGAGGGAGTAGATGATCATG 58.839 50.000 14.30 0.00 0.00 3.07
3402 3520 0.600057 TAGATGATCATGCGCGCTCT 59.400 50.000 33.29 25.07 0.00 4.09
3403 3521 0.944788 AGATGATCATGCGCGCTCTG 60.945 55.000 33.29 27.22 0.00 3.35
3434 3552 3.118519 GGGACATGTACGTTTGATACCCT 60.119 47.826 0.92 0.00 0.00 4.34
3441 3559 5.503927 TGTACGTTTGATACCCTCTAGTCT 58.496 41.667 0.00 0.00 0.00 3.24
3446 3564 5.462405 GTTTGATACCCTCTAGTCTATGCG 58.538 45.833 0.00 0.00 0.00 4.73
3547 3665 6.992715 ACAGTTATTCTATCTATGTTGTGCCC 59.007 38.462 0.00 0.00 0.00 5.36
3571 3689 2.518949 GTGTTATTGCCTGAACATGCG 58.481 47.619 0.00 0.00 37.84 4.73
3614 3732 6.037610 AGGATAATTTCTTCTTTGCTAGCGTG 59.962 38.462 10.77 2.61 0.00 5.34
3637 3755 2.417516 CCAGCGCGTGGTAGCTAT 59.582 61.111 8.43 0.00 42.52 2.97
3692 3810 1.696884 CCCTGGGGAGATTCTAGCTTC 59.303 57.143 4.27 0.00 37.50 3.86
3717 3835 2.292292 GGATTACGGCTGTTGTGTTGTT 59.708 45.455 1.99 0.00 0.00 2.83
3802 3920 8.634475 TGTCTTATCTCGTTTGACAGATAATG 57.366 34.615 3.33 0.34 39.68 1.90
3803 3921 7.706607 TGTCTTATCTCGTTTGACAGATAATGG 59.293 37.037 3.33 0.00 39.68 3.16
3804 3922 7.921214 GTCTTATCTCGTTTGACAGATAATGGA 59.079 37.037 3.33 0.00 39.68 3.41
3805 3923 8.642432 TCTTATCTCGTTTGACAGATAATGGAT 58.358 33.333 3.33 0.00 39.68 3.41
3806 3924 9.914131 CTTATCTCGTTTGACAGATAATGGATA 57.086 33.333 3.33 0.00 39.68 2.59
3809 3927 8.818141 TCTCGTTTGACAGATAATGGATATTC 57.182 34.615 0.00 0.00 0.00 1.75
3810 3928 8.642432 TCTCGTTTGACAGATAATGGATATTCT 58.358 33.333 0.00 0.00 0.00 2.40
3811 3929 9.914131 CTCGTTTGACAGATAATGGATATTCTA 57.086 33.333 0.00 0.00 0.00 2.10
3812 3930 9.692749 TCGTTTGACAGATAATGGATATTCTAC 57.307 33.333 0.00 0.00 0.00 2.59
3813 3931 9.476202 CGTTTGACAGATAATGGATATTCTACA 57.524 33.333 0.00 0.00 0.00 2.74
3836 3954 8.877864 ACACTAAAAAGACAATGGGATAATCA 57.122 30.769 0.00 0.00 0.00 2.57
3837 3955 9.308000 ACACTAAAAAGACAATGGGATAATCAA 57.692 29.630 0.00 0.00 0.00 2.57
3841 3959 8.831715 AAAAAGACAATGGGATAATCAAACAC 57.168 30.769 0.00 0.00 0.00 3.32
3842 3960 5.818136 AGACAATGGGATAATCAAACACG 57.182 39.130 0.00 0.00 0.00 4.49
3843 3961 5.496556 AGACAATGGGATAATCAAACACGA 58.503 37.500 0.00 0.00 0.00 4.35
3844 3962 5.943416 AGACAATGGGATAATCAAACACGAA 59.057 36.000 0.00 0.00 0.00 3.85
3845 3963 6.432783 AGACAATGGGATAATCAAACACGAAA 59.567 34.615 0.00 0.00 0.00 3.46
3846 3964 6.620678 ACAATGGGATAATCAAACACGAAAG 58.379 36.000 0.00 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.476599 TGATCCAGACTTTTGTATTTGGGTG 59.523 40.000 0.00 0.00 32.60 4.61
15 16 1.541588 GGTGGCTTTGTTGATCCAGAC 59.458 52.381 0.00 0.00 0.00 3.51
68 71 0.980754 ACCCCGTCAGCCACATGATA 60.981 55.000 0.00 0.00 0.00 2.15
79 82 0.251121 ACATGCAATTCACCCCGTCA 60.251 50.000 0.00 0.00 0.00 4.35
194 239 1.878088 TCTGTGTACGTGAGGAGACAC 59.122 52.381 9.55 9.55 44.18 3.67
230 279 0.827368 GGATCTGGCGAAAGGAGTCT 59.173 55.000 0.00 0.00 0.00 3.24
239 288 1.715862 CTCGACGAAGGATCTGGCGA 61.716 60.000 0.00 7.00 37.31 5.54
252 301 2.080693 CCTCATATCTCTCCCTCGACG 58.919 57.143 0.00 0.00 0.00 5.12
261 310 1.792026 TCTCCTGCCCCTCATATCTCT 59.208 52.381 0.00 0.00 0.00 3.10
343 392 2.185350 CTCATCGAAGGTGCGGCT 59.815 61.111 0.00 0.00 0.00 5.52
435 484 2.349755 GCTGCCGTAACCCCTTCA 59.650 61.111 0.00 0.00 0.00 3.02
480 529 1.077625 ACGACCTCTGCCCTCTTCT 59.922 57.895 0.00 0.00 0.00 2.85
481 530 1.216710 CACGACCTCTGCCCTCTTC 59.783 63.158 0.00 0.00 0.00 2.87
482 531 2.286523 CCACGACCTCTGCCCTCTT 61.287 63.158 0.00 0.00 0.00 2.85
519 572 4.608774 TCGACTCACCCACCCCGT 62.609 66.667 0.00 0.00 0.00 5.28
575 630 0.623194 TGGGCATTCCTCCAAATCGA 59.377 50.000 0.00 0.00 36.20 3.59
610 665 1.507140 TCAGGGAACGGCATATTCCT 58.493 50.000 11.39 0.00 44.43 3.36
676 731 2.183555 GGTACGCCGTCCCAAGAG 59.816 66.667 0.00 0.00 0.00 2.85
688 743 8.395510 TTTCTGTCATGAAACGAAACGGTACG 62.396 42.308 0.00 6.20 43.64 3.67
689 744 3.737266 TCTGTCATGAAACGAAACGGTAC 59.263 43.478 0.00 0.00 0.00 3.34
690 745 3.979948 TCTGTCATGAAACGAAACGGTA 58.020 40.909 0.00 0.00 0.00 4.02
691 746 2.828877 TCTGTCATGAAACGAAACGGT 58.171 42.857 0.00 0.00 0.00 4.83
692 747 3.870723 TTCTGTCATGAAACGAAACGG 57.129 42.857 0.00 0.00 0.00 4.44
700 755 5.406649 GTGTGTTTGGTTTCTGTCATGAAA 58.593 37.500 0.00 0.00 34.05 2.69
701 756 4.142271 GGTGTGTTTGGTTTCTGTCATGAA 60.142 41.667 0.00 0.00 0.00 2.57
702 757 3.380004 GGTGTGTTTGGTTTCTGTCATGA 59.620 43.478 0.00 0.00 0.00 3.07
703 758 3.490761 GGGTGTGTTTGGTTTCTGTCATG 60.491 47.826 0.00 0.00 0.00 3.07
704 759 2.693074 GGGTGTGTTTGGTTTCTGTCAT 59.307 45.455 0.00 0.00 0.00 3.06
705 760 2.096248 GGGTGTGTTTGGTTTCTGTCA 58.904 47.619 0.00 0.00 0.00 3.58
706 761 2.375146 AGGGTGTGTTTGGTTTCTGTC 58.625 47.619 0.00 0.00 0.00 3.51
707 762 2.525105 AGGGTGTGTTTGGTTTCTGT 57.475 45.000 0.00 0.00 0.00 3.41
708 763 3.951680 ACTAAGGGTGTGTTTGGTTTCTG 59.048 43.478 0.00 0.00 0.00 3.02
709 764 4.079958 AGACTAAGGGTGTGTTTGGTTTCT 60.080 41.667 0.00 0.00 0.00 2.52
710 765 4.036380 CAGACTAAGGGTGTGTTTGGTTTC 59.964 45.833 0.00 0.00 34.91 2.78
711 766 3.951680 CAGACTAAGGGTGTGTTTGGTTT 59.048 43.478 0.00 0.00 34.91 3.27
712 767 3.551846 CAGACTAAGGGTGTGTTTGGTT 58.448 45.455 0.00 0.00 34.91 3.67
713 768 2.748465 GCAGACTAAGGGTGTGTTTGGT 60.748 50.000 0.00 0.00 40.76 3.67
714 769 1.880027 GCAGACTAAGGGTGTGTTTGG 59.120 52.381 0.00 0.00 40.76 3.28
715 770 2.549754 CTGCAGACTAAGGGTGTGTTTG 59.450 50.000 8.42 0.00 40.76 2.93
716 771 2.172717 ACTGCAGACTAAGGGTGTGTTT 59.827 45.455 23.35 0.00 40.76 2.83
717 772 1.768870 ACTGCAGACTAAGGGTGTGTT 59.231 47.619 23.35 0.00 40.76 3.32
718 773 1.424638 ACTGCAGACTAAGGGTGTGT 58.575 50.000 23.35 0.00 40.76 3.72
719 774 2.417719 GAACTGCAGACTAAGGGTGTG 58.582 52.381 23.35 0.00 41.47 3.82
720 775 1.000955 CGAACTGCAGACTAAGGGTGT 59.999 52.381 23.35 0.00 0.00 4.16
721 776 1.673033 CCGAACTGCAGACTAAGGGTG 60.673 57.143 23.35 0.00 0.00 4.61
722 777 0.608640 CCGAACTGCAGACTAAGGGT 59.391 55.000 23.35 0.00 0.00 4.34
723 778 0.608640 ACCGAACTGCAGACTAAGGG 59.391 55.000 23.35 14.10 0.00 3.95
724 779 1.272490 TCACCGAACTGCAGACTAAGG 59.728 52.381 23.35 17.22 0.00 2.69
725 780 2.724977 TCACCGAACTGCAGACTAAG 57.275 50.000 23.35 7.33 0.00 2.18
726 781 2.560981 TCATCACCGAACTGCAGACTAA 59.439 45.455 23.35 0.00 0.00 2.24
727 782 2.167662 TCATCACCGAACTGCAGACTA 58.832 47.619 23.35 0.00 0.00 2.59
728 783 0.969149 TCATCACCGAACTGCAGACT 59.031 50.000 23.35 6.77 0.00 3.24
729 784 1.929836 GATCATCACCGAACTGCAGAC 59.070 52.381 23.35 12.87 0.00 3.51
730 785 1.134699 GGATCATCACCGAACTGCAGA 60.135 52.381 23.35 0.00 0.00 4.26
731 786 1.293924 GGATCATCACCGAACTGCAG 58.706 55.000 13.48 13.48 0.00 4.41
732 787 0.612744 TGGATCATCACCGAACTGCA 59.387 50.000 0.00 0.00 0.00 4.41
733 788 1.293924 CTGGATCATCACCGAACTGC 58.706 55.000 0.00 0.00 0.00 4.40
734 789 1.473965 CCCTGGATCATCACCGAACTG 60.474 57.143 0.00 0.00 0.00 3.16
735 790 0.833287 CCCTGGATCATCACCGAACT 59.167 55.000 0.00 0.00 0.00 3.01
736 791 0.830648 TCCCTGGATCATCACCGAAC 59.169 55.000 0.00 0.00 0.00 3.95
737 792 1.578897 TTCCCTGGATCATCACCGAA 58.421 50.000 0.00 0.00 0.00 4.30
738 793 1.694150 GATTCCCTGGATCATCACCGA 59.306 52.381 0.00 0.00 0.00 4.69
739 794 1.696336 AGATTCCCTGGATCATCACCG 59.304 52.381 0.00 0.00 0.00 4.94
740 795 3.137446 CAGATTCCCTGGATCATCACC 57.863 52.381 0.00 0.00 39.23 4.02
751 806 1.749634 CTTCCGACGTACAGATTCCCT 59.250 52.381 0.00 0.00 0.00 4.20
752 807 1.202382 CCTTCCGACGTACAGATTCCC 60.202 57.143 0.00 0.00 0.00 3.97
753 808 1.475682 ACCTTCCGACGTACAGATTCC 59.524 52.381 0.00 0.00 0.00 3.01
754 809 2.527100 CACCTTCCGACGTACAGATTC 58.473 52.381 0.00 0.00 0.00 2.52
755 810 1.203994 CCACCTTCCGACGTACAGATT 59.796 52.381 0.00 0.00 0.00 2.40
756 811 0.815734 CCACCTTCCGACGTACAGAT 59.184 55.000 0.00 0.00 0.00 2.90
757 812 0.538057 ACCACCTTCCGACGTACAGA 60.538 55.000 0.00 0.00 0.00 3.41
758 813 0.316204 AACCACCTTCCGACGTACAG 59.684 55.000 0.00 0.00 0.00 2.74
759 814 0.314935 GAACCACCTTCCGACGTACA 59.685 55.000 0.00 0.00 0.00 2.90
760 815 0.730494 CGAACCACCTTCCGACGTAC 60.730 60.000 0.00 0.00 0.00 3.67
761 816 1.580942 CGAACCACCTTCCGACGTA 59.419 57.895 0.00 0.00 0.00 3.57
762 817 2.337532 CGAACCACCTTCCGACGT 59.662 61.111 0.00 0.00 0.00 4.34
763 818 2.431942 CCGAACCACCTTCCGACG 60.432 66.667 0.00 0.00 0.00 5.12
764 819 2.741211 GCCGAACCACCTTCCGAC 60.741 66.667 0.00 0.00 0.00 4.79
765 820 2.920912 AGCCGAACCACCTTCCGA 60.921 61.111 0.00 0.00 0.00 4.55
806 861 3.697747 CCTACCCACGCCGTCCAA 61.698 66.667 0.00 0.00 0.00 3.53
856 911 0.521735 GTCCATCTGAAACCAACGGC 59.478 55.000 0.00 0.00 0.00 5.68
1218 1318 1.738830 GCCGTCGAATTTCCCGTCA 60.739 57.895 0.00 0.00 0.00 4.35
1413 1519 0.727398 GGTACTGATCAAACAGGCGC 59.273 55.000 0.00 0.00 41.59 6.53
1422 1528 3.245622 TGAAGTCCAGGAGGTACTGATCA 60.246 47.826 0.00 0.00 41.55 2.92
1425 1531 2.897969 GTTGAAGTCCAGGAGGTACTGA 59.102 50.000 0.00 0.00 41.55 3.41
1437 1543 2.954753 CTGGCACGCGTTGAAGTCC 61.955 63.158 10.22 4.94 0.00 3.85
1566 1672 1.153168 ATTGACGAATCCCTGCCCG 60.153 57.895 0.00 0.00 0.00 6.13
1670 1776 4.936081 CGGGGAGGGTCGGCCTAT 62.936 72.222 5.77 0.00 34.45 2.57
1746 1852 1.079057 GTCCACCTCCGCTTCCTTC 60.079 63.158 0.00 0.00 0.00 3.46
1854 1960 2.281484 TTTGCGCACTCCAGGGAC 60.281 61.111 11.12 0.00 0.00 4.46
1974 2080 2.525124 TTCTTCAAGGCTCGGGGCA 61.525 57.895 13.05 0.00 44.01 5.36
2016 2122 1.781025 TTTTCACCGTTGCTCTGCCG 61.781 55.000 0.00 0.00 0.00 5.69
2025 2131 2.465855 GCGGAAACAATTTTCACCGTT 58.534 42.857 0.00 0.00 42.72 4.44
2067 2173 1.206371 CCGACGTTCTTCCCCAAGTAT 59.794 52.381 0.00 0.00 0.00 2.12
2137 2243 5.588648 AGTTTTAGCTGCAACAAACAGTAGA 59.411 36.000 17.85 0.00 37.47 2.59
2140 2246 4.672409 GAGTTTTAGCTGCAACAAACAGT 58.328 39.130 17.85 4.42 37.47 3.55
2184 2290 7.281774 ACATGTCATAGGAAGCAAAGATACTTG 59.718 37.037 0.00 0.00 0.00 3.16
2304 2410 1.270147 ACTGAGCAACGAAGGTGGTAC 60.270 52.381 0.00 0.00 0.00 3.34
2432 2538 5.873179 AACGTCGACCATGATTAACAAAT 57.127 34.783 10.58 0.00 0.00 2.32
2480 2586 1.207329 GATTCAGGAGTAACCCGCTGT 59.793 52.381 0.00 0.00 40.05 4.40
2628 2734 0.653636 CAGTAGAGCTCGACGACCTC 59.346 60.000 19.51 11.47 0.00 3.85
2684 2790 8.710551 CAGACTCTATTTATGCTGCTTAGAATG 58.289 37.037 0.00 0.00 0.00 2.67
2871 2977 2.452813 GCGCATCCGACGACAACAT 61.453 57.895 0.30 0.00 36.29 2.71
2890 2996 6.844696 TTCTGACACAAGATCACAACTTAC 57.155 37.500 0.00 0.00 0.00 2.34
3010 3116 6.651225 AGAAGTCCAGCTAATTGTGTTCTAAC 59.349 38.462 0.00 0.00 0.00 2.34
3011 3117 6.769512 AGAAGTCCAGCTAATTGTGTTCTAA 58.230 36.000 0.00 0.00 0.00 2.10
3078 3184 7.763985 AGTTACCAAAATGCTAAACCATTATGC 59.236 33.333 0.00 0.00 34.50 3.14
3102 3208 2.914059 ACTTGAACTACGGTGCAAAGT 58.086 42.857 0.00 0.00 40.17 2.66
3236 3344 2.988493 CTGGGATCAAATTTGTGCAACG 59.012 45.455 17.47 1.32 42.39 4.10
3272 3380 7.757941 ATTTAGAACGGAGGGAGTAGTATAC 57.242 40.000 0.00 0.00 43.47 1.47
3273 3381 9.289782 GTAATTTAGAACGGAGGGAGTAGTATA 57.710 37.037 0.00 0.00 0.00 1.47
3274 3382 8.003629 AGTAATTTAGAACGGAGGGAGTAGTAT 58.996 37.037 0.00 0.00 0.00 2.12
3277 3385 6.712179 AGTAATTTAGAACGGAGGGAGTAG 57.288 41.667 0.00 0.00 0.00 2.57
3278 3386 6.438425 ACAAGTAATTTAGAACGGAGGGAGTA 59.562 38.462 0.00 0.00 0.00 2.59
3279 3387 5.247792 ACAAGTAATTTAGAACGGAGGGAGT 59.752 40.000 0.00 0.00 0.00 3.85
3280 3388 5.731591 ACAAGTAATTTAGAACGGAGGGAG 58.268 41.667 0.00 0.00 0.00 4.30
3283 3391 4.032558 GCGACAAGTAATTTAGAACGGAGG 59.967 45.833 0.00 0.00 0.00 4.30
3284 3392 4.624024 TGCGACAAGTAATTTAGAACGGAG 59.376 41.667 0.00 0.00 0.00 4.63
3285 3393 4.558178 TGCGACAAGTAATTTAGAACGGA 58.442 39.130 0.00 0.00 0.00 4.69
3286 3394 4.201685 CCTGCGACAAGTAATTTAGAACGG 60.202 45.833 0.00 0.00 0.00 4.44
3288 3396 5.857822 ACCTGCGACAAGTAATTTAGAAC 57.142 39.130 0.00 0.00 0.00 3.01
3289 3397 6.537301 CCATACCTGCGACAAGTAATTTAGAA 59.463 38.462 0.00 0.00 0.00 2.10
3291 3399 6.046593 TCCATACCTGCGACAAGTAATTTAG 58.953 40.000 0.00 0.00 0.00 1.85
3292 3400 5.979993 TCCATACCTGCGACAAGTAATTTA 58.020 37.500 0.00 0.00 0.00 1.40
3294 3402 4.481368 TCCATACCTGCGACAAGTAATT 57.519 40.909 0.00 0.00 0.00 1.40
3295 3403 4.141711 ACATCCATACCTGCGACAAGTAAT 60.142 41.667 0.00 0.00 0.00 1.89
3296 3404 3.196901 ACATCCATACCTGCGACAAGTAA 59.803 43.478 0.00 0.00 0.00 2.24
3297 3405 2.764010 ACATCCATACCTGCGACAAGTA 59.236 45.455 0.00 0.00 0.00 2.24
3298 3406 1.555075 ACATCCATACCTGCGACAAGT 59.445 47.619 0.00 0.00 0.00 3.16
3299 3407 2.315925 ACATCCATACCTGCGACAAG 57.684 50.000 0.00 0.00 0.00 3.16
3300 3408 3.641436 AGATACATCCATACCTGCGACAA 59.359 43.478 0.00 0.00 0.00 3.18
3302 3410 3.944055 AGATACATCCATACCTGCGAC 57.056 47.619 0.00 0.00 0.00 5.19
3303 3411 4.918588 TCTAGATACATCCATACCTGCGA 58.081 43.478 0.00 0.00 0.00 5.10
3304 3412 5.126222 ACATCTAGATACATCCATACCTGCG 59.874 44.000 4.54 0.00 0.00 5.18
3305 3413 6.537453 ACATCTAGATACATCCATACCTGC 57.463 41.667 4.54 0.00 0.00 4.85
3335 3443 8.116753 CGTCACAGAAATGGATGTATCTAAAAC 58.883 37.037 0.00 0.00 0.00 2.43
3336 3444 8.038351 TCGTCACAGAAATGGATGTATCTAAAA 58.962 33.333 0.00 0.00 0.00 1.52
3337 3445 7.552459 TCGTCACAGAAATGGATGTATCTAAA 58.448 34.615 0.00 0.00 0.00 1.85
3338 3446 7.107639 TCGTCACAGAAATGGATGTATCTAA 57.892 36.000 0.00 0.00 0.00 2.10
3340 3448 5.127845 ACTCGTCACAGAAATGGATGTATCT 59.872 40.000 0.00 0.00 0.00 1.98
3341 3449 5.352284 ACTCGTCACAGAAATGGATGTATC 58.648 41.667 0.00 0.00 0.00 2.24
3342 3450 5.344743 ACTCGTCACAGAAATGGATGTAT 57.655 39.130 0.00 0.00 0.00 2.29
3344 3452 3.685139 ACTCGTCACAGAAATGGATGT 57.315 42.857 0.00 0.00 0.00 3.06
3345 3453 6.668541 AATTACTCGTCACAGAAATGGATG 57.331 37.500 0.00 0.00 0.00 3.51
3347 3455 6.227522 TCAAATTACTCGTCACAGAAATGGA 58.772 36.000 0.00 0.00 0.00 3.41
3348 3456 6.480524 TCAAATTACTCGTCACAGAAATGG 57.519 37.500 0.00 0.00 0.00 3.16
3350 3458 7.069569 CGTTTCAAATTACTCGTCACAGAAAT 58.930 34.615 0.00 0.00 0.00 2.17
3351 3459 6.415702 CGTTTCAAATTACTCGTCACAGAAA 58.584 36.000 0.00 0.00 0.00 2.52
3352 3460 5.050634 CCGTTTCAAATTACTCGTCACAGAA 60.051 40.000 0.00 0.00 0.00 3.02
3353 3461 4.446385 CCGTTTCAAATTACTCGTCACAGA 59.554 41.667 0.00 0.00 0.00 3.41
3356 3464 4.143179 CCTCCGTTTCAAATTACTCGTCAC 60.143 45.833 0.00 0.00 0.00 3.67
3357 3465 3.991773 CCTCCGTTTCAAATTACTCGTCA 59.008 43.478 0.00 0.00 0.00 4.35
3359 3467 3.007182 TCCCTCCGTTTCAAATTACTCGT 59.993 43.478 0.00 0.00 0.00 4.18
3360 3468 3.592059 TCCCTCCGTTTCAAATTACTCG 58.408 45.455 0.00 0.00 0.00 4.18
3361 3469 4.576879 ACTCCCTCCGTTTCAAATTACTC 58.423 43.478 0.00 0.00 0.00 2.59
3363 3471 5.727434 TCTACTCCCTCCGTTTCAAATTAC 58.273 41.667 0.00 0.00 0.00 1.89
3364 3472 6.155565 TCATCTACTCCCTCCGTTTCAAATTA 59.844 38.462 0.00 0.00 0.00 1.40
3367 3475 3.835978 TCATCTACTCCCTCCGTTTCAAA 59.164 43.478 0.00 0.00 0.00 2.69
3368 3476 3.437213 TCATCTACTCCCTCCGTTTCAA 58.563 45.455 0.00 0.00 0.00 2.69
3370 3478 3.637229 TGATCATCTACTCCCTCCGTTTC 59.363 47.826 0.00 0.00 0.00 2.78
3371 3479 3.643237 TGATCATCTACTCCCTCCGTTT 58.357 45.455 0.00 0.00 0.00 3.60
3402 3520 4.758251 CATGTCCCTCGTGCGGCA 62.758 66.667 0.00 0.00 0.00 5.69
3403 3521 3.365291 TACATGTCCCTCGTGCGGC 62.365 63.158 0.00 0.00 36.60 6.53
3408 3526 1.614903 TCAAACGTACATGTCCCTCGT 59.385 47.619 0.00 7.04 36.31 4.18
3412 3530 3.118519 AGGGTATCAAACGTACATGTCCC 60.119 47.826 0.00 2.29 0.00 4.46
3414 3532 5.007385 AGAGGGTATCAAACGTACATGTC 57.993 43.478 0.00 0.00 0.00 3.06
3434 3552 4.573607 TCGAAAAGCTACGCATAGACTAGA 59.426 41.667 0.00 0.00 0.00 2.43
3441 3559 3.343380 TCGATCGAAAAGCTACGCATA 57.657 42.857 16.99 0.00 0.00 3.14
3446 3564 3.491267 CCCTGATTCGATCGAAAAGCTAC 59.509 47.826 32.11 18.70 37.69 3.58
3450 3568 1.258982 CGCCCTGATTCGATCGAAAAG 59.741 52.381 32.11 28.30 37.69 2.27
3494 3612 4.814234 ACATATCACACGCGAATAACCAAT 59.186 37.500 15.93 0.00 0.00 3.16
3547 3665 1.876799 TGTTCAGGCAATAACACCACG 59.123 47.619 0.00 0.00 30.88 4.94
3571 3689 2.630098 TCCTGCTGACATGTATAGGAGC 59.370 50.000 19.49 13.13 31.19 4.70
3626 3744 3.187227 GCAATCCATTCATAGCTACCACG 59.813 47.826 0.00 0.00 0.00 4.94
3633 3751 2.626743 AGGCAAGCAATCCATTCATAGC 59.373 45.455 0.00 0.00 0.00 2.97
3637 3755 1.551430 CCAAGGCAAGCAATCCATTCA 59.449 47.619 0.00 0.00 0.00 2.57
3692 3810 1.401552 CACAACAGCCGTAATCCATGG 59.598 52.381 4.97 4.97 36.25 3.66
3777 3895 7.706607 CCATTATCTGTCAAACGAGATAAGACA 59.293 37.037 0.00 0.00 41.96 3.41
3810 3928 9.967451 TGATTATCCCATTGTCTTTTTAGTGTA 57.033 29.630 0.00 0.00 0.00 2.90
3811 3929 8.877864 TGATTATCCCATTGTCTTTTTAGTGT 57.122 30.769 0.00 0.00 0.00 3.55
3815 3933 9.921637 GTGTTTGATTATCCCATTGTCTTTTTA 57.078 29.630 0.00 0.00 0.00 1.52
3816 3934 7.598493 CGTGTTTGATTATCCCATTGTCTTTTT 59.402 33.333 0.00 0.00 0.00 1.94
3817 3935 7.040062 TCGTGTTTGATTATCCCATTGTCTTTT 60.040 33.333 0.00 0.00 0.00 2.27
3818 3936 6.432783 TCGTGTTTGATTATCCCATTGTCTTT 59.567 34.615 0.00 0.00 0.00 2.52
3819 3937 5.943416 TCGTGTTTGATTATCCCATTGTCTT 59.057 36.000 0.00 0.00 0.00 3.01
3820 3938 5.496556 TCGTGTTTGATTATCCCATTGTCT 58.503 37.500 0.00 0.00 0.00 3.41
3821 3939 5.811399 TCGTGTTTGATTATCCCATTGTC 57.189 39.130 0.00 0.00 0.00 3.18
3822 3940 6.582677 TTTCGTGTTTGATTATCCCATTGT 57.417 33.333 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.