Multiple sequence alignment - TraesCS2A01G436600

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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 TraesCS2A01G436600 chr2A 100.000 4767 0 0 1 4767 688615703 688620469 0.000000e+00 8804.0
1 TraesCS2A01G436600 chr2A 82.149 605 100 8 4 602 46321270 46320668 3.290000e-141 512.0
2 TraesCS2A01G436600 chr2A 81.910 597 97 11 1 589 500706580 500707173 1.190000e-135 494.0
3 TraesCS2A01G436600 chr2D 95.287 3331 136 8 1032 4344 544888327 544885000 0.000000e+00 5262.0
4 TraesCS2A01G436600 chr2D 95.765 307 9 3 4462 4767 544884819 544884516 4.290000e-135 492.0
5 TraesCS2A01G436600 chr2D 94.382 89 5 0 810 898 544888420 544888332 2.310000e-28 137.0
6 TraesCS2A01G436600 chr2B 94.100 3339 134 17 1015 4302 651365900 651362574 0.000000e+00 5016.0
7 TraesCS2A01G436600 chr2B 85.282 727 77 21 1 716 651367146 651366439 0.000000e+00 723.0
8 TraesCS2A01G436600 chr2B 95.745 423 13 4 4350 4767 651362486 651362064 0.000000e+00 676.0
9 TraesCS2A01G436600 chr2B 96.000 100 4 0 799 898 651365991 651365892 3.820000e-36 163.0
10 TraesCS2A01G436600 chr1D 82.833 600 97 6 3 597 468039619 468039021 2.530000e-147 532.0
11 TraesCS2A01G436600 chr5B 80.791 708 107 21 1 691 25261037 25261732 1.180000e-145 527.0
12 TraesCS2A01G436600 chr5B 95.726 117 4 1 899 1014 550918214 550918330 2.270000e-43 187.0
13 TraesCS2A01G436600 chr3A 82.401 608 99 8 1 602 87386445 87385840 1.520000e-144 523.0
14 TraesCS2A01G436600 chr3A 94.215 121 6 1 895 1015 439913216 439913335 2.930000e-42 183.0
15 TraesCS2A01G436600 chr3D 82.483 588 95 8 3 584 74368046 74367461 4.260000e-140 508.0
16 TraesCS2A01G436600 chr1B 79.745 706 127 13 1 694 646481475 646482176 9.210000e-137 497.0
17 TraesCS2A01G436600 chr6D 78.824 680 128 12 21 691 438516970 438516298 1.220000e-120 444.0
18 TraesCS2A01G436600 chr3B 79.276 608 112 10 1 601 556060877 556061477 3.430000e-111 412.0
19 TraesCS2A01G436600 chr3B 77.577 388 76 8 218 602 662516153 662515774 1.730000e-54 224.0
20 TraesCS2A01G436600 chr4A 76.447 501 98 17 110 598 19522869 19522377 2.200000e-63 254.0
21 TraesCS2A01G436600 chr4A 96.183 131 3 2 891 1020 356606056 356605927 3.740000e-51 213.0
22 TraesCS2A01G436600 chr4A 98.276 116 2 0 899 1014 715296487 715296602 2.250000e-48 204.0
23 TraesCS2A01G436600 chr1A 98.305 118 2 0 897 1014 371408223 371408340 1.740000e-49 207.0
24 TraesCS2A01G436600 chr6B 98.261 115 2 0 899 1013 204112994 204113108 8.090000e-48 202.0
25 TraesCS2A01G436600 chr6B 94.872 117 5 1 899 1014 712178734 712178618 1.050000e-41 182.0
26 TraesCS2A01G436600 chr7A 92.537 134 5 5 891 1021 736354355 736354224 2.270000e-43 187.0
27 TraesCS2A01G436600 chr7A 92.500 40 3 0 4305 4344 121396105 121396066 1.850000e-04 58.4
28 TraesCS2A01G436600 chr4B 94.872 117 6 0 899 1015 620055591 620055707 2.930000e-42 183.0
29 TraesCS2A01G436600 chrUn 92.857 42 3 0 4302 4343 216303041 216303000 1.430000e-05 62.1
30 TraesCS2A01G436600 chr7B 91.304 46 3 1 647 691 634159343 634159388 1.430000e-05 62.1
31 TraesCS2A01G436600 chr5A 86.207 58 6 2 4302 4359 585092713 585092658 1.430000e-05 62.1
32 TraesCS2A01G436600 chr4D 92.857 42 3 0 4302 4343 131330674 131330633 1.430000e-05 62.1
33 TraesCS2A01G436600 chr7D 92.308 39 2 1 711 749 565471771 565471734 2.000000e-03 54.7


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 TraesCS2A01G436600 chr2A 688615703 688620469 4766 False 8804.000000 8804 100.000000 1 4767 1 chr2A.!!$F2 4766
1 TraesCS2A01G436600 chr2A 46320668 46321270 602 True 512.000000 512 82.149000 4 602 1 chr2A.!!$R1 598
2 TraesCS2A01G436600 chr2A 500706580 500707173 593 False 494.000000 494 81.910000 1 589 1 chr2A.!!$F1 588
3 TraesCS2A01G436600 chr2D 544884516 544888420 3904 True 1963.666667 5262 95.144667 810 4767 3 chr2D.!!$R1 3957
4 TraesCS2A01G436600 chr2B 651362064 651367146 5082 True 1644.500000 5016 92.781750 1 4767 4 chr2B.!!$R1 4766
5 TraesCS2A01G436600 chr1D 468039021 468039619 598 True 532.000000 532 82.833000 3 597 1 chr1D.!!$R1 594
6 TraesCS2A01G436600 chr5B 25261037 25261732 695 False 527.000000 527 80.791000 1 691 1 chr5B.!!$F1 690
7 TraesCS2A01G436600 chr3A 87385840 87386445 605 True 523.000000 523 82.401000 1 602 1 chr3A.!!$R1 601
8 TraesCS2A01G436600 chr3D 74367461 74368046 585 True 508.000000 508 82.483000 3 584 1 chr3D.!!$R1 581
9 TraesCS2A01G436600 chr1B 646481475 646482176 701 False 497.000000 497 79.745000 1 694 1 chr1B.!!$F1 693
10 TraesCS2A01G436600 chr6D 438516298 438516970 672 True 444.000000 444 78.824000 21 691 1 chr6D.!!$R1 670
11 TraesCS2A01G436600 chr3B 556060877 556061477 600 False 412.000000 412 79.276000 1 601 1 chr3B.!!$F1 600

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
924 1318 0.108329 AATCCTGTACGACCCGCTTG 60.108 55.0 0.00 0.0 0.00 4.01 F
943 1337 0.172352 GTGAGAGAGCTCTTCGTGGG 59.828 60.0 19.36 0.0 40.61 4.61 F
2658 3073 0.179009 TTGCTTCAGTGCTTCCTGCT 60.179 50.0 0.00 0.0 43.37 4.24 F
2721 3136 0.318955 ATTGTTTTGCTCTGCGCCAC 60.319 50.0 4.18 0.0 38.05 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2828 3243 0.031585 TGTCGTGTAGGTGACAGTGC 59.968 55.000 0.00 0.0 40.02 4.40 R
2906 3321 1.271856 TAACCCCTTGTCTCGCATCA 58.728 50.000 0.00 0.0 0.00 3.07 R
3690 4115 0.251742 CTCCCCTTTTCACCATGGCA 60.252 55.000 13.04 0.0 0.00 4.92 R
4231 4684 1.077787 TGCTTTGGCGTATCCCTGG 60.078 57.895 0.00 0.0 42.25 4.45 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
85 87 1.136565 GCACATTGCGCCGTACAAT 59.863 52.632 4.18 0.00 38.25 2.71
163 166 2.213499 CAGACCACAGTCACCAAGTTC 58.787 52.381 0.00 0.00 46.15 3.01
258 263 6.293626 GCTTCTTCTTGCTCAACTTGTTGATA 60.294 38.462 15.35 6.58 0.00 2.15
260 265 5.702670 TCTTCTTGCTCAACTTGTTGATAGG 59.297 40.000 15.35 9.24 0.00 2.57
283 292 7.673180 AGGTTCATTCATTCATTCAATGTTGT 58.327 30.769 0.00 0.00 42.47 3.32
357 366 3.498397 GGGATGGTCATTTACGCACATAG 59.502 47.826 0.00 0.00 0.00 2.23
375 384 6.678900 GCACATAGACTGTTGGATGAAATTCC 60.679 42.308 0.00 0.00 35.29 3.01
397 407 0.460284 GGGCAGTATGTGTGAGACGG 60.460 60.000 0.00 0.00 39.31 4.79
405 415 0.607620 TGTGTGAGACGGCATGATCA 59.392 50.000 0.00 0.00 0.00 2.92
432 444 5.710613 TGAAAAACTTTTGAACATTCGGC 57.289 34.783 0.00 0.00 0.00 5.54
436 449 7.708752 TGAAAAACTTTTGAACATTCGGCTATT 59.291 29.630 0.00 0.00 0.00 1.73
438 451 8.432110 AAAACTTTTGAACATTCGGCTATTTT 57.568 26.923 0.00 0.00 0.00 1.82
486 507 7.697691 ACTTGACTTATTTGCATGCTATGTAC 58.302 34.615 20.33 4.54 0.00 2.90
494 515 6.480524 TTTGCATGCTATGTACGGATAATC 57.519 37.500 20.33 0.00 0.00 1.75
529 550 6.924913 TTATCCAAACATTGATGAAACCCA 57.075 33.333 0.00 0.00 0.00 4.51
553 576 3.067320 TGTGTTTGCATGAATTTCGTCCA 59.933 39.130 0.00 0.00 0.00 4.02
579 603 3.573967 AGTTGAATCCGGCTTGAAATGTT 59.426 39.130 0.00 0.00 0.00 2.71
602 626 2.896854 GCAGCATTCGATGGCCGA 60.897 61.111 0.00 0.00 46.94 5.54
636 660 0.956633 GTGTCCGTGTACTGGTCTCA 59.043 55.000 0.00 0.00 0.00 3.27
640 665 2.029290 GTCCGTGTACTGGTCTCATGTT 60.029 50.000 0.00 0.00 0.00 2.71
656 681 0.321210 TGTTCGTGAACGGATGCCAT 60.321 50.000 8.11 0.00 43.94 4.40
666 691 8.586550 CGTGAACGGATGCCATAGCAAATTTA 62.587 42.308 0.00 0.00 43.92 1.40
674 699 5.181690 GCCATAGCAAATTTACGGATCAA 57.818 39.130 0.00 0.00 39.53 2.57
688 713 2.947652 CGGATCAACATTGAAGATGCCT 59.052 45.455 0.00 0.00 41.13 4.75
723 752 7.996758 AAGAAGGAAAGAATATACTCCCTCA 57.003 36.000 0.00 0.00 0.00 3.86
725 754 7.136203 AGAAGGAAAGAATATACTCCCTCAGT 58.864 38.462 0.00 0.00 39.41 3.41
726 755 6.987403 AGGAAAGAATATACTCCCTCAGTC 57.013 41.667 0.00 0.00 36.43 3.51
727 756 5.841783 AGGAAAGAATATACTCCCTCAGTCC 59.158 44.000 0.00 0.00 36.43 3.85
728 757 5.012251 GGAAAGAATATACTCCCTCAGTCCC 59.988 48.000 0.00 0.00 36.43 4.46
729 758 4.834406 AGAATATACTCCCTCAGTCCCA 57.166 45.455 0.00 0.00 36.43 4.37
730 759 5.361630 AGAATATACTCCCTCAGTCCCAT 57.638 43.478 0.00 0.00 36.43 4.00
731 760 6.485388 AGAATATACTCCCTCAGTCCCATA 57.515 41.667 0.00 0.00 36.43 2.74
735 764 3.136641 ACTCCCTCAGTCCCATAATGT 57.863 47.619 0.00 0.00 0.00 2.71
736 765 4.280789 ACTCCCTCAGTCCCATAATGTA 57.719 45.455 0.00 0.00 0.00 2.29
737 766 4.631234 ACTCCCTCAGTCCCATAATGTAA 58.369 43.478 0.00 0.00 0.00 2.41
740 769 6.160459 ACTCCCTCAGTCCCATAATGTAAAAT 59.840 38.462 0.00 0.00 0.00 1.82
742 771 6.389869 TCCCTCAGTCCCATAATGTAAAATCT 59.610 38.462 0.00 0.00 0.00 2.40
743 772 7.062957 CCCTCAGTCCCATAATGTAAAATCTT 58.937 38.462 0.00 0.00 0.00 2.40
744 773 7.561356 CCCTCAGTCCCATAATGTAAAATCTTT 59.439 37.037 0.00 0.00 0.00 2.52
745 774 8.971073 CCTCAGTCCCATAATGTAAAATCTTTT 58.029 33.333 0.00 0.00 0.00 2.27
777 806 4.483476 AAAACGCCTTACATCTTGTGAC 57.517 40.909 0.00 0.00 0.00 3.67
779 808 0.999406 CGCCTTACATCTTGTGACGG 59.001 55.000 0.00 0.00 0.00 4.79
781 810 2.271800 GCCTTACATCTTGTGACGGAG 58.728 52.381 0.00 0.00 0.00 4.63
784 813 2.225382 TACATCTTGTGACGGAGGGA 57.775 50.000 0.00 0.00 0.00 4.20
785 814 0.898320 ACATCTTGTGACGGAGGGAG 59.102 55.000 0.00 0.00 0.00 4.30
787 816 0.904865 ATCTTGTGACGGAGGGAGCA 60.905 55.000 0.00 0.00 0.00 4.26
789 818 1.533033 TTGTGACGGAGGGAGCAGA 60.533 57.895 0.00 0.00 0.00 4.26
790 819 0.904865 TTGTGACGGAGGGAGCAGAT 60.905 55.000 0.00 0.00 0.00 2.90
791 820 1.142748 GTGACGGAGGGAGCAGATG 59.857 63.158 0.00 0.00 0.00 2.90
792 821 2.107953 GACGGAGGGAGCAGATGC 59.892 66.667 0.00 0.00 42.49 3.91
793 822 2.685017 ACGGAGGGAGCAGATGCA 60.685 61.111 7.68 0.00 45.16 3.96
794 823 2.202987 CGGAGGGAGCAGATGCAC 60.203 66.667 7.68 0.06 45.16 4.57
834 1228 3.891056 AAAGAAAGCGGGTTTTACGAG 57.109 42.857 6.62 0.00 0.00 4.18
866 1260 3.190849 CGATGCGTCTGTGGCTGG 61.191 66.667 4.05 0.00 0.00 4.85
906 1300 4.069232 CACGAGGCAGGAGGCGAA 62.069 66.667 0.00 0.00 46.16 4.70
907 1301 3.077556 ACGAGGCAGGAGGCGAAT 61.078 61.111 0.00 0.00 46.16 3.34
908 1302 2.279784 CGAGGCAGGAGGCGAATC 60.280 66.667 0.00 0.00 46.16 2.52
909 1303 2.110006 GAGGCAGGAGGCGAATCC 59.890 66.667 0.00 0.00 46.16 3.01
918 1312 1.814527 AGGCGAATCCTGTACGACC 59.185 57.895 0.00 0.00 45.54 4.79
919 1313 1.227176 GGCGAATCCTGTACGACCC 60.227 63.158 0.00 0.00 0.00 4.46
920 1314 1.588139 GCGAATCCTGTACGACCCG 60.588 63.158 0.00 0.00 0.00 5.28
921 1315 1.588139 CGAATCCTGTACGACCCGC 60.588 63.158 0.00 0.00 0.00 6.13
922 1316 1.814527 GAATCCTGTACGACCCGCT 59.185 57.895 0.00 0.00 0.00 5.52
923 1317 0.175073 GAATCCTGTACGACCCGCTT 59.825 55.000 0.00 0.00 0.00 4.68
924 1318 0.108329 AATCCTGTACGACCCGCTTG 60.108 55.000 0.00 0.00 0.00 4.01
925 1319 1.255667 ATCCTGTACGACCCGCTTGT 61.256 55.000 0.00 0.00 0.00 3.16
926 1320 1.736645 CCTGTACGACCCGCTTGTG 60.737 63.158 0.00 0.00 0.00 3.33
927 1321 1.287815 CTGTACGACCCGCTTGTGA 59.712 57.895 0.00 0.00 0.00 3.58
928 1322 0.732880 CTGTACGACCCGCTTGTGAG 60.733 60.000 0.00 0.00 0.00 3.51
929 1323 1.174078 TGTACGACCCGCTTGTGAGA 61.174 55.000 0.00 0.00 0.00 3.27
930 1324 0.456312 GTACGACCCGCTTGTGAGAG 60.456 60.000 0.00 0.00 0.00 3.20
931 1325 0.607217 TACGACCCGCTTGTGAGAGA 60.607 55.000 0.00 0.00 0.00 3.10
932 1326 1.153939 CGACCCGCTTGTGAGAGAG 60.154 63.158 0.00 0.00 0.00 3.20
933 1327 1.446966 GACCCGCTTGTGAGAGAGC 60.447 63.158 0.00 0.00 35.58 4.09
934 1328 1.882989 GACCCGCTTGTGAGAGAGCT 61.883 60.000 0.00 0.00 36.76 4.09
935 1329 1.153667 CCCGCTTGTGAGAGAGCTC 60.154 63.158 5.27 5.27 41.67 4.09
936 1330 1.603236 CCCGCTTGTGAGAGAGCTCT 61.603 60.000 18.28 18.28 43.78 4.09
937 1331 0.246086 CCGCTTGTGAGAGAGCTCTT 59.754 55.000 19.36 7.93 40.61 2.85
938 1332 1.627879 CGCTTGTGAGAGAGCTCTTC 58.372 55.000 19.36 16.68 40.61 2.87
939 1333 1.627879 GCTTGTGAGAGAGCTCTTCG 58.372 55.000 19.36 6.05 40.61 3.79
940 1334 1.067915 GCTTGTGAGAGAGCTCTTCGT 60.068 52.381 19.36 5.75 40.61 3.85
941 1335 2.594321 CTTGTGAGAGAGCTCTTCGTG 58.406 52.381 19.36 1.42 40.61 4.35
942 1336 0.884514 TGTGAGAGAGCTCTTCGTGG 59.115 55.000 19.36 0.00 40.61 4.94
943 1337 0.172352 GTGAGAGAGCTCTTCGTGGG 59.828 60.000 19.36 0.00 40.61 4.61
944 1338 0.967887 TGAGAGAGCTCTTCGTGGGG 60.968 60.000 19.36 0.00 40.61 4.96
945 1339 0.968393 GAGAGAGCTCTTCGTGGGGT 60.968 60.000 19.36 0.00 40.61 4.95
946 1340 1.216710 GAGAGCTCTTCGTGGGGTG 59.783 63.158 19.36 0.00 0.00 4.61
947 1341 2.232298 GAGAGCTCTTCGTGGGGTGG 62.232 65.000 19.36 0.00 0.00 4.61
948 1342 3.959991 GAGCTCTTCGTGGGGTGGC 62.960 68.421 6.43 0.00 0.00 5.01
950 1344 4.410400 CTCTTCGTGGGGTGGCCC 62.410 72.222 0.00 0.00 44.51 5.80
969 1363 4.517934 CCTGCCAGCCTCCCCATG 62.518 72.222 0.00 0.00 0.00 3.66
1005 1399 3.930504 GACCCGGTCGTACAGGAT 58.069 61.111 0.65 0.00 35.32 3.24
1006 1400 2.196319 GACCCGGTCGTACAGGATT 58.804 57.895 0.65 0.00 35.32 3.01
1007 1401 1.392589 GACCCGGTCGTACAGGATTA 58.607 55.000 0.65 0.00 35.32 1.75
1008 1402 1.959282 GACCCGGTCGTACAGGATTAT 59.041 52.381 0.65 0.00 35.32 1.28
1009 1403 2.363359 GACCCGGTCGTACAGGATTATT 59.637 50.000 0.65 0.00 35.32 1.40
1010 1404 2.767960 ACCCGGTCGTACAGGATTATTT 59.232 45.455 0.00 0.00 35.32 1.40
1011 1405 3.198417 ACCCGGTCGTACAGGATTATTTT 59.802 43.478 0.00 0.00 35.32 1.82
1012 1406 3.558418 CCCGGTCGTACAGGATTATTTTG 59.442 47.826 0.00 0.00 35.32 2.44
1013 1407 3.001939 CCGGTCGTACAGGATTATTTTGC 59.998 47.826 0.00 0.00 35.32 3.68
1014 1408 3.001939 CGGTCGTACAGGATTATTTTGCC 59.998 47.826 0.00 0.00 0.00 4.52
1015 1409 3.942748 GGTCGTACAGGATTATTTTGCCA 59.057 43.478 0.00 0.00 0.00 4.92
1016 1410 4.201881 GGTCGTACAGGATTATTTTGCCAC 60.202 45.833 0.00 0.00 0.00 5.01
1017 1411 3.619483 TCGTACAGGATTATTTTGCCACG 59.381 43.478 0.00 0.00 0.00 4.94
1018 1412 3.619483 CGTACAGGATTATTTTGCCACGA 59.381 43.478 0.00 0.00 0.00 4.35
1019 1413 4.260212 CGTACAGGATTATTTTGCCACGAG 60.260 45.833 0.00 0.00 0.00 4.18
1020 1414 3.016736 ACAGGATTATTTTGCCACGAGG 58.983 45.455 0.00 0.00 38.23 4.63
1030 1424 2.433838 CCACGAGGCACAGCTCAG 60.434 66.667 0.00 0.00 0.00 3.35
1091 1491 4.083862 GGAGGAGCGACACCACCC 62.084 72.222 0.00 0.00 33.19 4.61
1596 2011 2.480555 CTGTTCGACGCAATGCCC 59.519 61.111 0.00 0.00 0.00 5.36
1678 2093 0.620556 TGAAGCCCTGGAGATGTTCC 59.379 55.000 0.00 0.00 46.98 3.62
1695 2110 2.203167 CTGCGCATGCTGGAGGAT 60.203 61.111 12.24 0.00 43.34 3.24
1701 2116 1.452651 CATGCTGGAGGATGGCGTT 60.453 57.895 0.35 0.00 39.75 4.84
1824 2239 6.352516 GGTGGAGTATGTCAATGATCTCTTT 58.647 40.000 0.00 0.00 0.00 2.52
1836 2251 3.320626 TGATCTCTTTGTTGTCAGCTCG 58.679 45.455 0.00 0.00 0.00 5.03
2016 2431 2.158943 GGGGTCTAAAGAGGTTCCATCG 60.159 54.545 0.00 0.00 0.00 3.84
2074 2489 1.606480 CGCAGTCACAAGATGTCAGGT 60.606 52.381 0.00 0.00 0.00 4.00
2199 2614 4.818534 TCAGACTGCATTTGAACTGTTC 57.181 40.909 13.49 13.49 0.00 3.18
2412 2827 2.297315 GTCGCATGGGTATCTCATCAGA 59.703 50.000 9.86 0.00 0.00 3.27
2430 2845 1.442526 GACATGGCATTGAGGGCGAG 61.443 60.000 0.00 0.00 35.84 5.03
2559 2974 2.154854 CCATGATAGCAGGGTACACG 57.845 55.000 2.88 0.00 40.98 4.49
2563 2978 0.744874 GATAGCAGGGTACACGCAGA 59.255 55.000 13.11 2.83 0.00 4.26
2658 3073 0.179009 TTGCTTCAGTGCTTCCTGCT 60.179 50.000 0.00 0.00 43.37 4.24
2704 3119 2.025981 TGTGCAGGGAAGCAGATACATT 60.026 45.455 0.00 0.00 46.69 2.71
2712 3127 4.082026 GGGAAGCAGATACATTGTTTTGCT 60.082 41.667 13.36 13.36 43.13 3.91
2721 3136 0.318955 ATTGTTTTGCTCTGCGCCAC 60.319 50.000 4.18 0.00 38.05 5.01
2724 3139 2.260869 TTTTGCTCTGCGCCACTCC 61.261 57.895 4.18 0.00 38.05 3.85
2725 3140 2.680974 TTTTGCTCTGCGCCACTCCT 62.681 55.000 4.18 0.00 38.05 3.69
2763 3178 2.038952 TGTAGGCACAGCTCTTGTTGAT 59.961 45.455 0.00 0.00 38.16 2.57
2778 3193 5.874810 TCTTGTTGATATGTACTCCAAGTGC 59.125 40.000 0.00 0.00 31.97 4.40
2793 3208 1.377202 GTGCGGGGAGATTTCTGCA 60.377 57.895 1.43 0.00 35.89 4.41
2823 3238 1.537202 GTCTTTGGTGGCATGACTGAC 59.463 52.381 0.00 0.00 0.00 3.51
2828 3243 1.271001 TGGTGGCATGACTGACAAGAG 60.271 52.381 0.00 0.00 43.72 2.85
2841 3256 2.035961 TGACAAGAGCACTGTCACCTAC 59.964 50.000 10.45 0.00 37.61 3.18
2906 3321 5.103686 AGAGAGCACTATCCCTCTTCTACTT 60.104 44.000 0.00 0.00 38.48 2.24
2952 3367 4.329545 GCCGTGACCTTCCTGGCA 62.330 66.667 0.00 0.00 45.06 4.92
2953 3368 2.429930 CCGTGACCTTCCTGGCAA 59.570 61.111 0.00 0.00 40.22 4.52
2988 3403 4.880120 TGTAATTACTCTGGACTCGTCGAT 59.120 41.667 16.33 0.00 0.00 3.59
3122 3537 1.464997 CGACTTTGTAGAAAGCCTGGC 59.535 52.381 11.65 11.65 42.19 4.85
3444 3859 4.824479 AAATTTCCCCGAAAATGAGCAT 57.176 36.364 0.00 0.00 35.11 3.79
3481 3899 3.118038 GGATGGGGATACTTGCAGTACAA 60.118 47.826 0.00 0.00 32.84 2.41
3559 3977 1.958288 ACCTGGAGATTAGCAGGTGT 58.042 50.000 0.00 0.00 45.38 4.16
3560 3978 1.834263 ACCTGGAGATTAGCAGGTGTC 59.166 52.381 0.00 0.00 45.38 3.67
3568 3986 2.596904 TTAGCAGGTGTCGATTAGCC 57.403 50.000 0.00 0.00 0.00 3.93
3579 3997 3.181479 TGTCGATTAGCCCATACTGTCAC 60.181 47.826 0.00 0.00 0.00 3.67
3596 4015 0.803768 CACGGATCGAACTCCTGCTG 60.804 60.000 3.65 0.00 32.77 4.41
3602 4021 3.123620 GAACTCCTGCTGCCTGCG 61.124 66.667 0.00 0.00 46.63 5.18
3634 4055 4.380843 TTTGCCTTCTCCCAGAATACAA 57.619 40.909 0.00 0.00 33.13 2.41
3706 4131 1.593265 GCTGCCATGGTGAAAAGGG 59.407 57.895 14.67 0.00 0.00 3.95
3716 4141 1.692411 GTGAAAAGGGGAGCAAGTGT 58.308 50.000 0.00 0.00 0.00 3.55
3825 4252 0.391661 CGAGACCATGAACCACTGGG 60.392 60.000 0.00 0.00 36.82 4.45
3932 4359 8.587952 AATTTTTGTTCATACTTGTTGCTACC 57.412 30.769 0.00 0.00 0.00 3.18
4231 4684 2.119457 CCAGCAAAAGAACTGAAACGC 58.881 47.619 0.00 0.00 35.90 4.84
4235 4688 2.731217 CAAAAGAACTGAAACGCCAGG 58.269 47.619 0.00 0.00 38.44 4.45
4241 4694 0.108329 ACTGAAACGCCAGGGATACG 60.108 55.000 0.00 0.00 38.44 3.06
4303 4756 4.265073 ACCCAGCAGTGAAAGAATCATAC 58.735 43.478 0.00 0.00 40.97 2.39
4310 4763 5.396213 GCAGTGAAAGAATCATACTCCCTCT 60.396 44.000 0.00 0.00 40.97 3.69
4326 4779 6.538263 ACTCCCTCTATTCCATAATTCTTGC 58.462 40.000 0.00 0.00 0.00 4.01
4328 4781 4.697352 CCCTCTATTCCATAATTCTTGCCG 59.303 45.833 0.00 0.00 0.00 5.69
4340 4793 3.701532 TTCTTGCCGTGGTTTTAGTTG 57.298 42.857 0.00 0.00 0.00 3.16
4391 4930 9.031537 TGAGAATAAAGGTGATCACTGTAGTTA 57.968 33.333 24.50 14.97 0.00 2.24
4453 4992 0.179113 CCGGGTGGCAAATTACATGC 60.179 55.000 0.00 0.00 43.08 4.06
4541 5080 7.912250 GTGACATTATCTATTGGTTTGCTCAAG 59.088 37.037 0.00 0.00 0.00 3.02
4560 5099 5.793817 TCAAGTATGCTTCAGCTGACTTTA 58.206 37.500 18.03 4.74 41.38 1.85
4624 5165 1.100510 CCAGCCTGTGATTGGTGATG 58.899 55.000 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 81 6.806388 TCATGGATGATGTGCATATTGTAC 57.194 37.500 0.00 0.00 36.66 2.90
85 87 3.004862 GCGATCATGGATGATGTGCATA 58.995 45.455 6.85 0.00 46.84 3.14
163 166 6.481313 CCTCCAACATATCAACTGTGTCATAG 59.519 42.308 0.00 0.00 0.00 2.23
258 263 7.673180 ACAACATTGAATGAATGAATGAACCT 58.327 30.769 12.80 0.00 43.87 3.50
260 265 9.199982 AGAACAACATTGAATGAATGAATGAAC 57.800 29.630 12.80 0.00 43.87 3.18
283 292 2.560504 CGGGCTGCACAATATGTAGAA 58.439 47.619 1.50 0.00 43.37 2.10
317 326 5.306937 CCATCCCTGTATCCTGTTGTACATA 59.693 44.000 0.00 0.00 31.06 2.29
375 384 0.904649 TCTCACACATACTGCCCCTG 59.095 55.000 0.00 0.00 0.00 4.45
405 415 8.550376 CCGAATGTTCAAAAGTTTTTCATGAAT 58.450 29.630 9.40 0.00 0.00 2.57
459 473 8.279970 ACATAGCATGCAAATAAGTCAAGTAA 57.720 30.769 21.98 0.00 0.00 2.24
464 482 5.236263 CCGTACATAGCATGCAAATAAGTCA 59.764 40.000 21.98 0.00 0.00 3.41
516 537 4.740334 GCAAACACAGTGGGTTTCATCAAT 60.740 41.667 20.64 0.00 36.38 2.57
526 547 3.389925 AATTCATGCAAACACAGTGGG 57.610 42.857 5.31 0.00 0.00 4.61
529 550 4.290155 GACGAAATTCATGCAAACACAGT 58.710 39.130 0.00 0.00 0.00 3.55
553 576 3.695830 TCAAGCCGGATTCAACTAACT 57.304 42.857 5.05 0.00 0.00 2.24
602 626 3.790437 CACGAGGGAGCTGGCCAT 61.790 66.667 5.51 0.00 0.00 4.40
604 628 4.459089 GACACGAGGGAGCTGGCC 62.459 72.222 0.00 0.00 0.00 5.36
607 631 3.374402 ACGGACACGAGGGAGCTG 61.374 66.667 0.00 0.00 44.60 4.24
609 633 2.338015 TACACGGACACGAGGGAGC 61.338 63.158 0.00 0.00 44.60 4.70
613 637 1.211969 CCAGTACACGGACACGAGG 59.788 63.158 0.00 0.00 44.60 4.63
614 638 0.109873 GACCAGTACACGGACACGAG 60.110 60.000 8.25 0.00 44.60 4.18
636 660 0.321210 TGGCATCCGTTCACGAACAT 60.321 50.000 10.35 0.00 43.02 2.71
640 665 0.529773 GCTATGGCATCCGTTCACGA 60.530 55.000 1.65 0.00 38.98 4.35
656 681 7.384439 TCAATGTTGATCCGTAAATTTGCTA 57.616 32.000 0.00 0.00 31.01 3.49
666 691 2.684881 GGCATCTTCAATGTTGATCCGT 59.315 45.455 0.00 0.00 37.00 4.69
670 695 7.649533 TTCATTAGGCATCTTCAATGTTGAT 57.350 32.000 0.00 0.00 37.00 2.57
716 745 5.630415 TTTACATTATGGGACTGAGGGAG 57.370 43.478 0.00 0.00 0.00 4.30
717 746 6.389869 AGATTTTACATTATGGGACTGAGGGA 59.610 38.462 0.00 0.00 0.00 4.20
718 747 6.605119 AGATTTTACATTATGGGACTGAGGG 58.395 40.000 0.00 0.00 0.00 4.30
719 748 8.525290 AAAGATTTTACATTATGGGACTGAGG 57.475 34.615 0.00 0.00 0.00 3.86
755 784 4.553938 CGTCACAAGATGTAAGGCGTTTTT 60.554 41.667 0.00 0.00 0.00 1.94
756 785 3.059188 CGTCACAAGATGTAAGGCGTTTT 60.059 43.478 0.00 0.00 0.00 2.43
757 786 2.478894 CGTCACAAGATGTAAGGCGTTT 59.521 45.455 0.00 0.00 0.00 3.60
758 787 2.066262 CGTCACAAGATGTAAGGCGTT 58.934 47.619 0.00 0.00 0.00 4.84
759 788 1.671850 CCGTCACAAGATGTAAGGCGT 60.672 52.381 0.00 0.00 0.00 5.68
760 789 0.999406 CCGTCACAAGATGTAAGGCG 59.001 55.000 0.00 0.00 0.00 5.52
762 791 2.418746 CCCTCCGTCACAAGATGTAAGG 60.419 54.545 0.00 0.00 34.19 2.69
764 793 2.496070 CTCCCTCCGTCACAAGATGTAA 59.504 50.000 0.00 0.00 0.00 2.41
765 794 2.100197 CTCCCTCCGTCACAAGATGTA 58.900 52.381 0.00 0.00 0.00 2.29
766 795 0.898320 CTCCCTCCGTCACAAGATGT 59.102 55.000 0.00 0.00 0.00 3.06
767 796 0.460987 GCTCCCTCCGTCACAAGATG 60.461 60.000 0.00 0.00 0.00 2.90
768 797 0.904865 TGCTCCCTCCGTCACAAGAT 60.905 55.000 0.00 0.00 0.00 2.40
769 798 1.533033 TGCTCCCTCCGTCACAAGA 60.533 57.895 0.00 0.00 0.00 3.02
770 799 1.079543 CTGCTCCCTCCGTCACAAG 60.080 63.158 0.00 0.00 0.00 3.16
771 800 0.904865 ATCTGCTCCCTCCGTCACAA 60.905 55.000 0.00 0.00 0.00 3.33
772 801 1.305297 ATCTGCTCCCTCCGTCACA 60.305 57.895 0.00 0.00 0.00 3.58
773 802 1.142748 CATCTGCTCCCTCCGTCAC 59.857 63.158 0.00 0.00 0.00 3.67
774 803 2.725312 GCATCTGCTCCCTCCGTCA 61.725 63.158 0.00 0.00 38.21 4.35
777 806 2.202987 GTGCATCTGCTCCCTCCG 60.203 66.667 3.53 0.00 42.66 4.63
830 1224 2.178521 CGGCAGAAGCGTACTCGT 59.821 61.111 0.00 0.00 43.41 4.18
834 1228 1.226603 ATCGACGGCAGAAGCGTAC 60.227 57.895 0.00 0.00 43.41 3.67
898 1292 0.248949 GTCGTACAGGATTCGCCTCC 60.249 60.000 0.00 0.00 46.97 4.30
901 1295 1.227176 GGGTCGTACAGGATTCGCC 60.227 63.158 0.00 0.00 0.00 5.54
902 1296 1.588139 CGGGTCGTACAGGATTCGC 60.588 63.158 0.00 0.00 0.00 4.70
903 1297 1.588139 GCGGGTCGTACAGGATTCG 60.588 63.158 0.00 0.00 0.00 3.34
904 1298 0.175073 AAGCGGGTCGTACAGGATTC 59.825 55.000 0.00 0.00 0.00 2.52
905 1299 0.108329 CAAGCGGGTCGTACAGGATT 60.108 55.000 0.00 0.00 0.00 3.01
906 1300 1.255667 ACAAGCGGGTCGTACAGGAT 61.256 55.000 0.00 0.00 0.00 3.24
907 1301 1.904865 ACAAGCGGGTCGTACAGGA 60.905 57.895 0.00 0.00 0.00 3.86
908 1302 1.736645 CACAAGCGGGTCGTACAGG 60.737 63.158 0.00 0.00 0.00 4.00
909 1303 0.732880 CTCACAAGCGGGTCGTACAG 60.733 60.000 0.00 0.00 0.00 2.74
910 1304 1.174078 TCTCACAAGCGGGTCGTACA 61.174 55.000 0.00 0.00 0.00 2.90
911 1305 0.456312 CTCTCACAAGCGGGTCGTAC 60.456 60.000 0.00 0.00 0.00 3.67
912 1306 0.607217 TCTCTCACAAGCGGGTCGTA 60.607 55.000 0.00 0.00 0.00 3.43
913 1307 1.867919 CTCTCTCACAAGCGGGTCGT 61.868 60.000 0.00 0.00 0.00 4.34
914 1308 1.153939 CTCTCTCACAAGCGGGTCG 60.154 63.158 0.00 0.00 0.00 4.79
915 1309 1.446966 GCTCTCTCACAAGCGGGTC 60.447 63.158 0.00 0.00 0.00 4.46
916 1310 1.882989 GAGCTCTCTCACAAGCGGGT 61.883 60.000 6.43 0.00 43.37 5.28
917 1311 1.153667 GAGCTCTCTCACAAGCGGG 60.154 63.158 6.43 0.00 43.37 6.13
918 1312 0.246086 AAGAGCTCTCTCACAAGCGG 59.754 55.000 18.55 0.00 43.37 5.52
919 1313 1.627879 GAAGAGCTCTCTCACAAGCG 58.372 55.000 18.55 0.00 43.37 4.68
920 1314 1.067915 ACGAAGAGCTCTCTCACAAGC 60.068 52.381 18.55 0.00 41.81 4.01
921 1315 2.594321 CACGAAGAGCTCTCTCACAAG 58.406 52.381 18.55 6.13 41.81 3.16
922 1316 1.270826 CCACGAAGAGCTCTCTCACAA 59.729 52.381 18.55 0.00 41.81 3.33
923 1317 0.884514 CCACGAAGAGCTCTCTCACA 59.115 55.000 18.55 0.00 41.81 3.58
924 1318 0.172352 CCCACGAAGAGCTCTCTCAC 59.828 60.000 18.55 8.26 41.81 3.51
925 1319 0.967887 CCCCACGAAGAGCTCTCTCA 60.968 60.000 18.55 0.00 41.81 3.27
926 1320 0.968393 ACCCCACGAAGAGCTCTCTC 60.968 60.000 18.55 15.06 39.39 3.20
927 1321 1.077625 ACCCCACGAAGAGCTCTCT 59.922 57.895 18.55 7.43 42.75 3.10
928 1322 1.216710 CACCCCACGAAGAGCTCTC 59.783 63.158 18.55 9.76 0.00 3.20
929 1323 2.286523 CCACCCCACGAAGAGCTCT 61.287 63.158 11.45 11.45 0.00 4.09
930 1324 2.266055 CCACCCCACGAAGAGCTC 59.734 66.667 5.27 5.27 0.00 4.09
931 1325 4.021925 GCCACCCCACGAAGAGCT 62.022 66.667 0.00 0.00 0.00 4.09
952 1346 4.517934 CATGGGGAGGCTGGCAGG 62.518 72.222 17.64 0.00 0.00 4.85
988 1382 1.392589 TAATCCTGTACGACCGGGTC 58.607 55.000 17.38 17.38 0.00 4.46
989 1383 2.077687 ATAATCCTGTACGACCGGGT 57.922 50.000 6.32 0.00 0.00 5.28
990 1384 3.464111 AAATAATCCTGTACGACCGGG 57.536 47.619 6.32 0.00 0.00 5.73
991 1385 3.001939 GCAAAATAATCCTGTACGACCGG 59.998 47.826 0.00 0.00 0.00 5.28
992 1386 3.001939 GGCAAAATAATCCTGTACGACCG 59.998 47.826 0.00 0.00 0.00 4.79
993 1387 3.942748 TGGCAAAATAATCCTGTACGACC 59.057 43.478 0.00 0.00 0.00 4.79
994 1388 4.493545 CGTGGCAAAATAATCCTGTACGAC 60.494 45.833 0.00 0.00 0.00 4.34
995 1389 3.619483 CGTGGCAAAATAATCCTGTACGA 59.381 43.478 0.00 0.00 0.00 3.43
996 1390 3.619483 TCGTGGCAAAATAATCCTGTACG 59.381 43.478 0.00 0.00 0.00 3.67
997 1391 4.035208 CCTCGTGGCAAAATAATCCTGTAC 59.965 45.833 0.00 0.00 0.00 2.90
998 1392 4.196193 CCTCGTGGCAAAATAATCCTGTA 58.804 43.478 0.00 0.00 0.00 2.74
999 1393 3.016736 CCTCGTGGCAAAATAATCCTGT 58.983 45.455 0.00 0.00 0.00 4.00
1000 1394 3.698029 CCTCGTGGCAAAATAATCCTG 57.302 47.619 0.00 0.00 0.00 3.86
1013 1407 2.433838 CTGAGCTGTGCCTCGTGG 60.434 66.667 0.00 0.00 34.56 4.94
1014 1408 1.735920 GACTGAGCTGTGCCTCGTG 60.736 63.158 0.00 0.00 34.56 4.35
1015 1409 2.203082 TGACTGAGCTGTGCCTCGT 61.203 57.895 0.00 0.00 34.56 4.18
1016 1410 1.735920 GTGACTGAGCTGTGCCTCG 60.736 63.158 0.00 0.00 34.56 4.63
1017 1411 0.669932 CTGTGACTGAGCTGTGCCTC 60.670 60.000 0.00 0.00 0.00 4.70
1018 1412 1.370437 CTGTGACTGAGCTGTGCCT 59.630 57.895 0.00 0.00 0.00 4.75
1019 1413 0.948141 GACTGTGACTGAGCTGTGCC 60.948 60.000 0.00 0.00 0.00 5.01
1020 1414 0.249615 TGACTGTGACTGAGCTGTGC 60.250 55.000 0.00 0.00 0.00 4.57
1021 1415 1.202452 TGTGACTGTGACTGAGCTGTG 60.202 52.381 0.00 0.00 0.00 3.66
1022 1416 1.068281 CTGTGACTGTGACTGAGCTGT 59.932 52.381 0.00 0.00 0.00 4.40
1023 1417 1.604947 CCTGTGACTGTGACTGAGCTG 60.605 57.143 5.90 0.00 0.00 4.24
1024 1418 0.678395 CCTGTGACTGTGACTGAGCT 59.322 55.000 5.90 0.00 0.00 4.09
1025 1419 0.320247 CCCTGTGACTGTGACTGAGC 60.320 60.000 5.90 0.00 0.00 4.26
1026 1420 0.319728 CCCCTGTGACTGTGACTGAG 59.680 60.000 5.90 0.00 0.00 3.35
1027 1421 0.105709 TCCCCTGTGACTGTGACTGA 60.106 55.000 5.90 0.00 0.00 3.41
1028 1422 0.979665 ATCCCCTGTGACTGTGACTG 59.020 55.000 0.00 0.00 0.00 3.51
1029 1423 0.979665 CATCCCCTGTGACTGTGACT 59.020 55.000 0.00 0.00 0.00 3.41
1030 1424 0.976641 TCATCCCCTGTGACTGTGAC 59.023 55.000 0.00 0.00 0.00 3.67
1071 1471 2.680352 TGGTGTCGCTCCTCCTCC 60.680 66.667 0.90 0.00 0.00 4.30
1072 1472 2.574399 GTGGTGTCGCTCCTCCTC 59.426 66.667 0.90 0.00 0.00 3.71
1073 1473 2.997897 GGTGGTGTCGCTCCTCCT 60.998 66.667 10.03 0.00 36.17 3.69
1091 1491 1.525923 CACTGAGGAGGAGCCATGG 59.474 63.158 7.63 7.63 40.02 3.66
1596 2011 2.347292 CCACGAAACGACGTTCTTCTTG 60.347 50.000 14.58 12.00 44.76 3.02
1653 2068 2.040442 TCCAGGGCTTCATCGGGA 59.960 61.111 0.00 0.00 0.00 5.14
1678 2093 2.203167 ATCCTCCAGCATGCGCAG 60.203 61.111 18.32 9.45 42.27 5.18
1824 2239 1.446099 GATCGCCGAGCTGACAACA 60.446 57.895 0.00 0.00 0.00 3.33
1836 2251 1.227380 AGAGAACATGCCGATCGCC 60.227 57.895 10.32 0.00 36.24 5.54
1871 2286 0.687354 AAACACCATCCGAGCTGTCT 59.313 50.000 0.00 0.00 0.00 3.41
2001 2416 4.019681 ACAACATCCGATGGAACCTCTTTA 60.020 41.667 13.00 0.00 34.34 1.85
2016 2431 4.555511 GCTGACAAGAAAGTCACAACATCC 60.556 45.833 0.00 0.00 43.18 3.51
2074 2489 1.180456 CCATGCAGTTGCTGACCCAA 61.180 55.000 5.62 0.00 42.66 4.12
2199 2614 0.807667 CCTTCTCTGGCAACCGATCG 60.808 60.000 8.51 8.51 0.00 3.69
2412 2827 1.452651 CTCGCCCTCAATGCCATGT 60.453 57.895 0.00 0.00 0.00 3.21
2553 2968 1.738099 CTGGCCACTCTGCGTGTAC 60.738 63.158 0.00 0.00 42.20 2.90
2559 2974 3.557903 TTCAGGCTGGCCACTCTGC 62.558 63.158 20.30 14.41 38.92 4.26
2563 2978 2.433446 CTGTTCAGGCTGGCCACT 59.567 61.111 15.73 0.00 38.92 4.00
2658 3073 2.824880 CCCTCCAACGGGGTCACAA 61.825 63.158 0.00 0.00 40.75 3.33
2733 3148 3.490348 AGCTGTGCCTACAAAGACATTT 58.510 40.909 0.00 0.00 36.14 2.32
2748 3163 5.521735 GGAGTACATATCAACAAGAGCTGTG 59.478 44.000 0.00 0.00 38.67 3.66
2763 3178 0.828022 CCCCGCACTTGGAGTACATA 59.172 55.000 0.00 0.00 0.00 2.29
2778 3193 1.078214 TGCTGCAGAAATCTCCCCG 60.078 57.895 20.43 0.00 0.00 5.73
2793 3208 2.787994 CCACCAAAGACATTCTCTGCT 58.212 47.619 0.00 0.00 0.00 4.24
2823 3238 2.408050 GTGTAGGTGACAGTGCTCTTG 58.592 52.381 0.00 0.00 39.29 3.02
2828 3243 0.031585 TGTCGTGTAGGTGACAGTGC 59.968 55.000 0.00 0.00 40.02 4.40
2841 3256 3.516981 AGACCAGAGATCATTGTCGTG 57.483 47.619 0.00 0.00 0.00 4.35
2906 3321 1.271856 TAACCCCTTGTCTCGCATCA 58.728 50.000 0.00 0.00 0.00 3.07
2952 3367 7.148018 CCAGAGTAATTACATGCTGAAATGGTT 60.148 37.037 23.46 0.87 31.46 3.67
2953 3368 6.319658 CCAGAGTAATTACATGCTGAAATGGT 59.680 38.462 23.46 1.23 31.46 3.55
2988 3403 5.104693 TGACCTGTACAAAGAAAGACCTTCA 60.105 40.000 0.00 0.00 36.40 3.02
3093 3508 5.120208 GCTTTCTACAAAGTCGTATGCTTCA 59.880 40.000 0.00 0.00 41.18 3.02
3122 3537 2.831333 CGATGAAGTTCCCATCCTCAG 58.169 52.381 0.00 0.00 37.67 3.35
3341 3756 0.977395 AGAACCCACCTCTTTCCTCG 59.023 55.000 0.00 0.00 0.00 4.63
3444 3859 1.405933 CCATCCAGCATCGAGAACACA 60.406 52.381 0.00 0.00 0.00 3.72
3481 3899 9.389570 GTACTTAAACTGTTAAATGATTGCGTT 57.610 29.630 0.00 0.00 0.00 4.84
3559 3977 2.034179 CGTGACAGTATGGGCTAATCGA 59.966 50.000 0.00 0.00 43.62 3.59
3560 3978 2.394708 CGTGACAGTATGGGCTAATCG 58.605 52.381 0.00 0.00 43.62 3.34
3568 3986 2.099263 AGTTCGATCCGTGACAGTATGG 59.901 50.000 0.00 0.00 43.62 2.74
3579 3997 1.880340 GCAGCAGGAGTTCGATCCG 60.880 63.158 0.00 0.00 44.65 4.18
3602 4021 3.119352 GGAGAAGGCAAATCATGACAACC 60.119 47.826 0.00 0.00 40.75 3.77
3687 4112 1.593265 CCTTTTCACCATGGCAGCC 59.407 57.895 13.04 3.66 0.00 4.85
3690 4115 0.251742 CTCCCCTTTTCACCATGGCA 60.252 55.000 13.04 0.00 0.00 4.92
3716 4141 1.079197 ATGCGATGTTGTCTCGGCA 60.079 52.632 0.00 0.00 36.65 5.69
3772 4197 3.548770 TGTTTCATCTCTGATGGATGCC 58.451 45.455 7.58 0.00 40.02 4.40
3825 4252 1.578423 GCTGCAGCTGGTTCTTCAC 59.422 57.895 31.33 0.00 38.21 3.18
3846 4273 6.481644 GTCAGGTCTCAGAATTAATGATGTCC 59.518 42.308 0.00 0.00 0.00 4.02
3851 4278 6.820152 CACATGTCAGGTCTCAGAATTAATGA 59.180 38.462 0.00 0.00 0.00 2.57
3932 4359 3.367932 ACATGAATGTTTACAGCGTCTCG 59.632 43.478 0.00 0.00 37.90 4.04
4231 4684 1.077787 TGCTTTGGCGTATCCCTGG 60.078 57.895 0.00 0.00 42.25 4.45
4235 4688 3.007635 ACTTTAGTGCTTTGGCGTATCC 58.992 45.455 0.00 0.00 42.25 2.59
4241 4694 5.288804 TCATTTGAACTTTAGTGCTTTGGC 58.711 37.500 0.00 0.00 39.26 4.52
4303 4756 5.942826 GGCAAGAATTATGGAATAGAGGGAG 59.057 44.000 0.00 0.00 0.00 4.30
4310 4763 4.787551 ACCACGGCAAGAATTATGGAATA 58.212 39.130 0.00 0.00 0.00 1.75
4340 4793 9.061610 CATATTGTTAATTCTTGTCGTGGTTTC 57.938 33.333 0.00 0.00 0.00 2.78
4521 5060 7.775093 AGCATACTTGAGCAAACCAATAGATAA 59.225 33.333 0.00 0.00 0.00 1.75
4541 5080 6.814146 ACTAAGTAAAGTCAGCTGAAGCATAC 59.186 38.462 20.19 17.78 45.16 2.39
4560 5099 3.046374 AGGACAACCACTCCAACTAAGT 58.954 45.455 0.00 0.00 38.94 2.24
4624 5165 3.548818 GCTACACCATTGGCGAATTCATC 60.549 47.826 6.22 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.