Multiple sequence alignment - TraesCS3A01G347600

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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 TraesCS3A01G347600 chr3A 100.000 6243 0 0 1 6243 596739518 596745760 0.000000e+00 11529.0
1 TraesCS3A01G347600 chr3A 97.318 261 7 0 5545 5805 596750076 596750336 1.600000e-120 444.0
2 TraesCS3A01G347600 chr3D 92.647 3971 184 53 1642 5551 454671376 454675299 0.000000e+00 5616.0
3 TraesCS3A01G347600 chr3D 89.577 662 55 4 1 648 454665013 454665674 0.000000e+00 828.0
4 TraesCS3A01G347600 chr3D 87.931 696 65 16 5552 6243 123665910 123666590 0.000000e+00 802.0
5 TraesCS3A01G347600 chr3D 87.101 752 33 23 837 1562 454670215 454670928 0.000000e+00 793.0
6 TraesCS3A01G347600 chr3D 97.059 34 1 0 1555 1588 454671332 454671365 2.430000e-04 58.4
7 TraesCS3A01G347600 chr3B 92.650 3755 194 40 1843 5549 597451244 597454964 0.000000e+00 5330.0
8 TraesCS3A01G347600 chr3B 87.029 1087 53 36 780 1855 597450192 597451201 0.000000e+00 1146.0
9 TraesCS3A01G347600 chr3B 86.036 666 66 11 1 648 597449401 597450057 0.000000e+00 689.0
10 TraesCS3A01G347600 chr2D 93.669 695 41 3 5552 6243 534289840 534289146 0.000000e+00 1037.0
11 TraesCS3A01G347600 chr2D 91.985 262 17 2 5545 5805 534284842 534284584 1.280000e-96 364.0
12 TraesCS3A01G347600 chr5A 93.516 694 43 2 5552 6243 638790164 638789471 0.000000e+00 1031.0
13 TraesCS3A01G347600 chr2A 90.374 696 62 5 5552 6243 9354118 9354812 0.000000e+00 909.0
14 TraesCS3A01G347600 chr2A 89.872 701 56 11 5552 6243 12254060 12254754 0.000000e+00 887.0
15 TraesCS3A01G347600 chr4B 89.802 706 54 11 5552 6243 394639698 394638997 0.000000e+00 889.0
16 TraesCS3A01G347600 chr4B 93.333 225 13 2 5545 5768 394626008 394625785 1.300000e-86 331.0
17 TraesCS3A01G347600 chr1D 89.542 698 59 12 5550 6243 486447730 486448417 0.000000e+00 872.0
18 TraesCS3A01G347600 chr1A 88.953 697 59 12 5552 6243 568458749 568458066 0.000000e+00 845.0
19 TraesCS3A01G347600 chr6D 88.379 697 63 12 5552 6243 470087869 470088552 0.000000e+00 822.0
20 TraesCS3A01G347600 chr5D 84.900 702 79 23 5552 6243 390710147 390710831 0.000000e+00 684.0
21 TraesCS3A01G347600 chr7A 91.985 262 17 1 5545 5806 80495640 80495897 1.280000e-96 364.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G347600 chr3A 596739518 596745760 6242 False 11529.000000 11529 100.000000 1 6243 1 chr3A.!!$F1 6242
1 TraesCS3A01G347600 chr3D 454670215 454675299 5084 False 2155.800000 5616 92.269000 837 5551 3 chr3D.!!$F3 4714
2 TraesCS3A01G347600 chr3D 454665013 454665674 661 False 828.000000 828 89.577000 1 648 1 chr3D.!!$F2 647
3 TraesCS3A01G347600 chr3D 123665910 123666590 680 False 802.000000 802 87.931000 5552 6243 1 chr3D.!!$F1 691
4 TraesCS3A01G347600 chr3B 597449401 597454964 5563 False 2388.333333 5330 88.571667 1 5549 3 chr3B.!!$F1 5548
5 TraesCS3A01G347600 chr2D 534289146 534289840 694 True 1037.000000 1037 93.669000 5552 6243 1 chr2D.!!$R2 691
6 TraesCS3A01G347600 chr5A 638789471 638790164 693 True 1031.000000 1031 93.516000 5552 6243 1 chr5A.!!$R1 691
7 TraesCS3A01G347600 chr2A 9354118 9354812 694 False 909.000000 909 90.374000 5552 6243 1 chr2A.!!$F1 691
8 TraesCS3A01G347600 chr2A 12254060 12254754 694 False 887.000000 887 89.872000 5552 6243 1 chr2A.!!$F2 691
9 TraesCS3A01G347600 chr4B 394638997 394639698 701 True 889.000000 889 89.802000 5552 6243 1 chr4B.!!$R2 691
10 TraesCS3A01G347600 chr1D 486447730 486448417 687 False 872.000000 872 89.542000 5550 6243 1 chr1D.!!$F1 693
11 TraesCS3A01G347600 chr1A 568458066 568458749 683 True 845.000000 845 88.953000 5552 6243 1 chr1A.!!$R1 691
12 TraesCS3A01G347600 chr6D 470087869 470088552 683 False 822.000000 822 88.379000 5552 6243 1 chr6D.!!$F1 691
13 TraesCS3A01G347600 chr5D 390710147 390710831 684 False 684.000000 684 84.900000 5552 6243 1 chr5D.!!$F1 691

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
771 815 0.180406 ATATCCCCACAAGGACACGC 59.820 55.000 0.00 0.00 39.24 5.34 F
1487 1562 0.178953 AAGGTTGGCAGTTGGCTGAT 60.179 50.000 7.23 0.00 45.28 2.90 F
1594 2080 0.182537 TTTCAGGTGGTGGACTGGTG 59.817 55.000 0.00 0.00 35.47 4.17 F
1633 2119 1.202568 TGAAGGATGAGATTGCGCGAT 60.203 47.619 12.10 10.69 0.00 4.58 F
2121 2673 1.276421 CCAACGAGTGGGAAGAGTCAT 59.724 52.381 0.00 0.00 44.64 3.06 F
3255 3825 1.508632 TCTTGCGCAACCTTCTACAC 58.491 50.000 21.02 0.00 0.00 2.90 F
4153 4727 0.534877 TCCTTTCTGCAGAAGCGCAA 60.535 50.000 27.02 12.83 46.23 4.85 F
4413 4987 0.765510 ACCAGGTTGTCAAGGTCCTC 59.234 55.000 0.00 0.00 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1916 2462 1.227556 GACTGTGTGGGAGCAACGT 60.228 57.895 0.00 0.00 0.00 3.99 R
2634 3195 1.405821 AGGCTTGAGGATAGTCGAACG 59.594 52.381 0.00 0.00 0.00 3.95 R
3589 4159 1.003112 ACGTCAATTTGGGCGCCTA 60.003 52.632 28.56 19.98 0.00 3.93 R
3603 4173 3.056749 ACAGAAAGTGACCATAGGACGTC 60.057 47.826 7.13 7.13 0.00 4.34 R
3694 4265 0.710567 CTGTCACAAGCTTCGCTACG 59.289 55.000 0.00 0.00 38.25 3.51 R
4693 5267 0.247460 TCTCTGTGCCTGTTCATCGG 59.753 55.000 0.00 0.00 0.00 4.18 R
5061 5644 0.942962 CCAGAGCCTGCGATCAAATC 59.057 55.000 0.00 0.00 0.00 2.17 R
5890 6516 1.131638 ACTCTCAAGACCAGGTTGCA 58.868 50.000 0.00 0.00 0.00 4.08 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
158 170 9.292195 CTAATTTAGAACAAAGTCCACCCTTAA 57.708 33.333 0.00 0.00 0.00 1.85
272 285 0.459237 CTCTTGTCACCAGCTAGCCG 60.459 60.000 12.13 0.00 0.00 5.52
338 351 2.349886 GAGTGACAGGACGATCAATTGC 59.650 50.000 0.00 0.00 0.00 3.56
435 448 0.250467 ATAGCATCACCATCACCGGC 60.250 55.000 0.00 0.00 0.00 6.13
444 457 3.861797 ATCACCGGCCGGGCTTAG 61.862 66.667 44.99 28.32 40.62 2.18
470 488 0.249120 CACTTCCACTCGGCATACCA 59.751 55.000 0.00 0.00 34.57 3.25
479 497 2.092646 ACTCGGCATACCAAGGCAAATA 60.093 45.455 0.00 0.00 32.88 1.40
512 531 3.960755 TCAAACTCACTCCTCAGACTCAA 59.039 43.478 0.00 0.00 0.00 3.02
526 545 4.101585 TCAGACTCAAGGTCAACATCAGTT 59.898 41.667 0.00 0.00 46.72 3.16
527 546 5.304357 TCAGACTCAAGGTCAACATCAGTTA 59.696 40.000 0.00 0.00 46.72 2.24
535 554 3.055819 GGTCAACATCAGTTAGCTCCAGA 60.056 47.826 0.00 0.00 35.85 3.86
609 628 4.324874 CCTTGGGAAGATCTCATCAAGGTT 60.325 45.833 26.43 1.25 44.11 3.50
634 653 0.794981 CTTCTCCTTGCTCGTCGACG 60.795 60.000 31.30 31.30 41.45 5.12
648 668 2.281276 GACGGGGTGCCGTTCTTT 60.281 61.111 0.00 0.00 46.81 2.52
649 669 1.004679 GACGGGGTGCCGTTCTTTA 60.005 57.895 0.00 0.00 46.81 1.85
658 697 4.505191 GGGTGCCGTTCTTTAAAAGTTTTC 59.495 41.667 3.60 0.00 0.00 2.29
660 699 5.457799 GGTGCCGTTCTTTAAAAGTTTTCTC 59.542 40.000 3.60 0.00 0.00 2.87
662 701 6.750501 GTGCCGTTCTTTAAAAGTTTTCTCTT 59.249 34.615 3.60 0.00 0.00 2.85
663 702 7.274904 GTGCCGTTCTTTAAAAGTTTTCTCTTT 59.725 33.333 3.60 0.00 39.00 2.52
673 712 4.695217 AGTTTTCTCTTTCGTTGCAACA 57.305 36.364 28.01 13.24 0.00 3.33
676 715 4.630894 TTTCTCTTTCGTTGCAACACAT 57.369 36.364 28.01 0.00 0.00 3.21
678 717 3.202097 TCTCTTTCGTTGCAACACATGA 58.798 40.909 28.01 18.27 0.00 3.07
679 718 3.625313 TCTCTTTCGTTGCAACACATGAA 59.375 39.130 28.01 19.38 0.00 2.57
680 719 4.275689 TCTCTTTCGTTGCAACACATGAAT 59.724 37.500 28.01 0.00 0.00 2.57
691 730 5.234116 TGCAACACATGAATATACGTGCTAG 59.766 40.000 0.00 0.00 32.53 3.42
692 731 5.333339 GCAACACATGAATATACGTGCTAGG 60.333 44.000 0.00 0.00 32.53 3.02
693 732 5.784578 ACACATGAATATACGTGCTAGGA 57.215 39.130 0.00 0.00 32.53 2.94
694 733 6.156748 ACACATGAATATACGTGCTAGGAA 57.843 37.500 0.00 0.00 32.53 3.36
696 735 7.045416 ACACATGAATATACGTGCTAGGAAAA 58.955 34.615 0.00 0.00 32.53 2.29
697 736 7.224753 ACACATGAATATACGTGCTAGGAAAAG 59.775 37.037 0.00 0.00 32.53 2.27
698 737 6.706270 ACATGAATATACGTGCTAGGAAAAGG 59.294 38.462 0.00 0.00 0.00 3.11
701 740 6.984474 TGAATATACGTGCTAGGAAAAGGAAG 59.016 38.462 0.00 0.00 0.00 3.46
703 742 3.764237 ACGTGCTAGGAAAAGGAAGAA 57.236 42.857 0.00 0.00 0.00 2.52
706 745 4.515567 ACGTGCTAGGAAAAGGAAGAAAAG 59.484 41.667 0.00 0.00 0.00 2.27
708 747 5.238650 CGTGCTAGGAAAAGGAAGAAAAGAA 59.761 40.000 0.00 0.00 0.00 2.52
710 749 5.241728 TGCTAGGAAAAGGAAGAAAAGAAGC 59.758 40.000 0.00 0.00 0.00 3.86
711 750 5.241728 GCTAGGAAAAGGAAGAAAAGAAGCA 59.758 40.000 0.00 0.00 0.00 3.91
712 751 5.781210 AGGAAAAGGAAGAAAAGAAGCAG 57.219 39.130 0.00 0.00 0.00 4.24
742 786 5.818136 AAATGTGTGAACGATATCTTGGG 57.182 39.130 0.34 0.00 0.00 4.12
743 787 2.627945 TGTGTGAACGATATCTTGGGC 58.372 47.619 0.34 0.00 0.00 5.36
744 788 2.236146 TGTGTGAACGATATCTTGGGCT 59.764 45.455 0.34 0.00 0.00 5.19
745 789 3.449377 TGTGTGAACGATATCTTGGGCTA 59.551 43.478 0.34 0.00 0.00 3.93
746 790 4.051922 GTGTGAACGATATCTTGGGCTAG 58.948 47.826 0.34 0.00 0.00 3.42
747 791 3.060602 GTGAACGATATCTTGGGCTAGC 58.939 50.000 6.04 6.04 0.00 3.42
748 792 2.965831 TGAACGATATCTTGGGCTAGCT 59.034 45.455 15.72 0.00 0.00 3.32
749 793 3.243873 TGAACGATATCTTGGGCTAGCTG 60.244 47.826 15.72 3.11 0.00 4.24
750 794 1.620819 ACGATATCTTGGGCTAGCTGG 59.379 52.381 15.72 0.00 0.00 4.85
751 795 1.066573 CGATATCTTGGGCTAGCTGGG 60.067 57.143 15.72 3.11 0.00 4.45
752 796 2.260822 GATATCTTGGGCTAGCTGGGA 58.739 52.381 15.72 8.49 0.00 4.37
755 799 2.422939 TCTTGGGCTAGCTGGGATAT 57.577 50.000 15.72 0.00 0.00 1.63
756 800 2.260822 TCTTGGGCTAGCTGGGATATC 58.739 52.381 15.72 0.00 0.00 1.63
757 801 1.280421 CTTGGGCTAGCTGGGATATCC 59.720 57.143 15.72 13.87 0.00 2.59
769 813 2.640316 GGATATCCCCACAAGGACAC 57.360 55.000 11.02 0.00 39.24 3.67
770 814 1.202651 GGATATCCCCACAAGGACACG 60.203 57.143 11.02 0.00 39.24 4.49
771 815 0.180406 ATATCCCCACAAGGACACGC 59.820 55.000 0.00 0.00 39.24 5.34
772 816 2.233605 TATCCCCACAAGGACACGCG 62.234 60.000 3.53 3.53 39.24 6.01
776 820 3.716006 CACAAGGACACGCGGCAG 61.716 66.667 12.47 1.86 0.00 4.85
777 821 4.235762 ACAAGGACACGCGGCAGT 62.236 61.111 12.47 5.84 0.00 4.40
778 822 2.972505 CAAGGACACGCGGCAGTT 60.973 61.111 12.47 0.00 0.00 3.16
785 829 3.706373 ACGCGGCAGTTGGAGGAT 61.706 61.111 12.47 0.00 0.00 3.24
835 879 6.033966 CAGAGTTGGTGGTTTGTTAAAGTTC 58.966 40.000 0.00 0.00 0.00 3.01
913 968 5.889853 TCAGCGGAGACCTTACTTAAATCTA 59.110 40.000 0.00 0.00 0.00 1.98
915 970 5.892686 AGCGGAGACCTTACTTAAATCTACT 59.107 40.000 0.00 0.00 0.00 2.57
916 971 6.039605 AGCGGAGACCTTACTTAAATCTACTC 59.960 42.308 0.00 0.00 0.00 2.59
918 973 6.737118 GGAGACCTTACTTAAATCTACTCCG 58.263 44.000 0.00 0.00 32.55 4.63
919 974 6.545298 GGAGACCTTACTTAAATCTACTCCGA 59.455 42.308 0.00 0.00 32.55 4.55
920 975 7.332213 AGACCTTACTTAAATCTACTCCGAC 57.668 40.000 0.00 0.00 0.00 4.79
921 976 6.038050 AGACCTTACTTAAATCTACTCCGACG 59.962 42.308 0.00 0.00 0.00 5.12
940 997 3.426615 ACGAACACAGGATCTTCTCTCT 58.573 45.455 0.00 0.00 0.00 3.10
941 998 3.442273 ACGAACACAGGATCTTCTCTCTC 59.558 47.826 0.00 0.00 0.00 3.20
997 1057 2.197324 CCCCCTCTCTCTCTCCCG 59.803 72.222 0.00 0.00 0.00 5.14
998 1058 2.197324 CCCCTCTCTCTCTCCCGG 59.803 72.222 0.00 0.00 0.00 5.73
999 1059 2.695970 CCCCTCTCTCTCTCCCGGT 61.696 68.421 0.00 0.00 0.00 5.28
1097 1160 0.553862 TCTCCACCTCCTCCTCCTCT 60.554 60.000 0.00 0.00 0.00 3.69
1178 1244 3.855853 GAGAAGGAGGAGGCGGCC 61.856 72.222 12.11 12.11 0.00 6.13
1223 1289 2.273557 TGGTACGCCGATTTCTTTAGC 58.726 47.619 0.00 0.00 37.67 3.09
1287 1362 4.008074 TGAGTTGAGATTGAGACCAACC 57.992 45.455 0.00 0.00 39.57 3.77
1304 1379 3.507597 CCAAATGGTCTCGTCGTCA 57.492 52.632 0.00 0.00 0.00 4.35
1329 1404 3.772060 AAAAAGAATCAGATGGCGAGC 57.228 42.857 0.00 0.00 0.00 5.03
1330 1405 1.293924 AAAGAATCAGATGGCGAGCG 58.706 50.000 0.00 0.00 0.00 5.03
1331 1406 1.156645 AAGAATCAGATGGCGAGCGC 61.157 55.000 6.27 6.27 41.06 5.92
1361 1436 3.209410 CCCATTGATAGACCAGCAAGTC 58.791 50.000 0.00 0.00 35.66 3.01
1403 1478 1.939974 TGCTCAGCGATTTAGCGAAT 58.060 45.000 0.00 0.00 43.00 3.34
1420 1495 1.594862 GAATTGCGTACTAGGCTGCTG 59.405 52.381 0.00 0.00 0.00 4.41
1465 1540 0.320683 TCATGTCGTGACCTTGCCTG 60.321 55.000 0.00 0.00 0.00 4.85
1468 1543 1.069090 GTCGTGACCTTGCCTGTCA 59.931 57.895 0.00 0.00 40.28 3.58
1469 1544 0.531974 GTCGTGACCTTGCCTGTCAA 60.532 55.000 2.11 0.00 43.82 3.18
1476 1551 1.662044 CTTGCCTGTCAAGGTTGGC 59.338 57.895 0.00 0.00 46.50 4.52
1482 1557 2.805897 TGTCAAGGTTGGCAGTTGG 58.194 52.632 0.00 0.00 37.97 3.77
1483 1558 1.363807 GTCAAGGTTGGCAGTTGGC 59.636 57.895 0.00 0.00 43.74 4.52
1484 1559 1.109323 GTCAAGGTTGGCAGTTGGCT 61.109 55.000 7.23 0.00 44.01 4.75
1485 1560 1.108727 TCAAGGTTGGCAGTTGGCTG 61.109 55.000 7.23 0.00 45.23 4.85
1486 1561 1.108727 CAAGGTTGGCAGTTGGCTGA 61.109 55.000 7.23 0.00 45.28 4.26
1487 1562 0.178953 AAGGTTGGCAGTTGGCTGAT 60.179 50.000 7.23 0.00 45.28 2.90
1488 1563 0.896940 AGGTTGGCAGTTGGCTGATG 60.897 55.000 7.23 0.00 45.28 3.07
1489 1564 1.588082 GTTGGCAGTTGGCTGATGG 59.412 57.895 7.23 0.00 45.28 3.51
1490 1565 2.277591 TTGGCAGTTGGCTGATGGC 61.278 57.895 7.23 3.66 45.28 4.40
1491 1566 2.677524 GGCAGTTGGCTGATGGCA 60.678 61.111 0.00 0.00 45.28 4.92
1519 1594 3.050275 GGCACCAGCGAACTGTCC 61.050 66.667 0.00 0.00 42.81 4.02
1590 2076 3.662759 TTTTCTTTCAGGTGGTGGACT 57.337 42.857 0.00 0.00 0.00 3.85
1591 2077 2.638480 TTCTTTCAGGTGGTGGACTG 57.362 50.000 0.00 0.00 36.07 3.51
1592 2078 0.764890 TCTTTCAGGTGGTGGACTGG 59.235 55.000 0.00 0.00 35.47 4.00
1593 2079 0.474184 CTTTCAGGTGGTGGACTGGT 59.526 55.000 0.00 0.00 35.47 4.00
1594 2080 0.182537 TTTCAGGTGGTGGACTGGTG 59.817 55.000 0.00 0.00 35.47 4.17
1595 2081 1.705002 TTCAGGTGGTGGACTGGTGG 61.705 60.000 0.00 0.00 35.47 4.61
1617 2103 1.632422 GTGCCAAATTGCCGATGAAG 58.368 50.000 0.00 0.00 0.00 3.02
1633 2119 1.202568 TGAAGGATGAGATTGCGCGAT 60.203 47.619 12.10 10.69 0.00 4.58
1635 2121 2.820059 AGGATGAGATTGCGCGATAA 57.180 45.000 12.10 4.08 0.00 1.75
1640 2126 3.165058 TGAGATTGCGCGATAAGAACT 57.835 42.857 12.10 2.45 0.00 3.01
1670 2156 7.499438 TTGTTGTAGTGTTTTTGACATTTCG 57.501 32.000 0.00 0.00 41.10 3.46
1849 2339 5.203060 AGTTTCTGACTACAGGTGTTCTC 57.797 43.478 0.00 0.00 43.60 2.87
1860 2405 5.825593 ACAGGTGTTCTCTTGAGGATAAA 57.174 39.130 0.00 0.00 0.00 1.40
1869 2414 8.378565 TGTTCTCTTGAGGATAAAAAGTGATCT 58.621 33.333 0.00 0.00 0.00 2.75
1882 2427 9.927668 ATAAAAAGTGATCTGGTTTAATGGTTG 57.072 29.630 0.00 0.00 0.00 3.77
1883 2428 6.976934 AAAGTGATCTGGTTTAATGGTTGT 57.023 33.333 0.00 0.00 0.00 3.32
1884 2429 8.472007 AAAAGTGATCTGGTTTAATGGTTGTA 57.528 30.769 0.00 0.00 0.00 2.41
1885 2430 7.448748 AAGTGATCTGGTTTAATGGTTGTAC 57.551 36.000 0.00 0.00 0.00 2.90
1886 2431 6.539173 AGTGATCTGGTTTAATGGTTGTACA 58.461 36.000 0.00 0.00 0.00 2.90
1887 2432 7.175104 AGTGATCTGGTTTAATGGTTGTACAT 58.825 34.615 0.00 0.00 0.00 2.29
1888 2433 7.121168 AGTGATCTGGTTTAATGGTTGTACATG 59.879 37.037 0.00 0.00 0.00 3.21
1889 2434 5.637006 TCTGGTTTAATGGTTGTACATGC 57.363 39.130 0.00 0.00 0.00 4.06
1898 2443 3.009026 TGGTTGTACATGCTACATGCTG 58.991 45.455 7.46 0.00 43.37 4.41
1916 2462 4.270008 TGCTGCATGACACTACTACTAGA 58.730 43.478 0.00 0.00 0.00 2.43
1983 2531 7.496529 TTTTCTTCTAAATGTCTGGTGTCTG 57.503 36.000 0.00 0.00 0.00 3.51
2061 2613 8.670135 TGGTTTATTATATTGTGGAAACAGACG 58.330 33.333 0.00 0.00 44.46 4.18
2068 2620 3.047877 GGAAACAGACGTGGGCCG 61.048 66.667 0.00 0.00 44.03 6.13
2095 2647 2.418471 CCACCAAAATGCGCATGGTTAT 60.418 45.455 27.31 8.56 44.92 1.89
2121 2673 1.276421 CCAACGAGTGGGAAGAGTCAT 59.724 52.381 0.00 0.00 44.64 3.06
2130 2682 6.426646 AGTGGGAAGAGTCATTCATATACC 57.573 41.667 0.00 0.00 0.00 2.73
2264 2816 3.126831 CAGGACACGAAGGATGCTATTC 58.873 50.000 0.00 0.00 0.00 1.75
2404 2958 5.392380 CCTTAGTTTTCATGTCCTGATGTGC 60.392 44.000 0.00 0.00 32.72 4.57
2533 3088 5.927281 ATGTGCCTGCATTTAGAGAAAAT 57.073 34.783 0.00 0.00 38.36 1.82
2551 3106 3.366052 AATCGAAGGTTGGTGGCTATT 57.634 42.857 0.00 0.00 0.00 1.73
2579 3134 2.019984 GTGGATTGCATGACCCTTCTC 58.980 52.381 0.00 0.00 0.00 2.87
2591 3146 4.345854 TGACCCTTCTCTTCTAGTCTTCC 58.654 47.826 0.00 0.00 0.00 3.46
2599 3154 6.384258 TCTCTTCTAGTCTTCCAATCATCG 57.616 41.667 0.00 0.00 0.00 3.84
2634 3195 3.879892 AGCAAAGTCAAGGAGAGTGAAAC 59.120 43.478 0.00 0.00 0.00 2.78
2651 3212 4.323868 GTGAAACGTTCGACTATCCTCAAG 59.676 45.833 0.00 0.00 0.00 3.02
2661 3222 4.704540 CGACTATCCTCAAGCCTCTATGAT 59.295 45.833 0.00 0.00 0.00 2.45
2674 3235 3.127895 CCTCTATGATACAGCGTCCTAGC 59.872 52.174 0.00 0.00 37.41 3.42
2683 3244 2.133553 CAGCGTCCTAGCAATGATGAG 58.866 52.381 0.00 0.00 40.15 2.90
2754 3315 9.253832 ACATTGGTTATGGACTTCAAATGAATA 57.746 29.630 0.00 0.00 38.64 1.75
2797 3358 4.885907 CCATGTCAGATAATTGAGCTTGGT 59.114 41.667 0.00 0.00 0.00 3.67
3026 3590 9.448438 ACATACACTGAAGATTTAGCATACAAA 57.552 29.630 0.00 0.00 0.00 2.83
3082 3646 6.388619 AGGAAAATACCTTGGTATGTGACT 57.611 37.500 12.51 6.90 36.86 3.41
3099 3663 9.029243 GTATGTGACTATGTGAGAAATCTTCTG 57.971 37.037 0.00 0.00 40.87 3.02
3163 3727 5.797934 TGTTTCATCGATAACATTTTTCGGC 59.202 36.000 9.22 0.00 33.82 5.54
3209 3773 6.874278 TGATTCTCACTTTATTGAGGAGGA 57.126 37.500 0.46 0.00 42.95 3.71
3234 3798 6.094603 AGTGGAACAAAATGATGATCAGTAGC 59.905 38.462 0.09 0.00 44.16 3.58
3250 3820 4.465413 GCATCTTGCGCAACCTTC 57.535 55.556 21.02 5.34 31.71 3.46
3255 3825 1.508632 TCTTGCGCAACCTTCTACAC 58.491 50.000 21.02 0.00 0.00 2.90
3342 3912 6.149129 TCCAGTGTCAGTACTATGCTAATG 57.851 41.667 0.00 0.00 0.00 1.90
3428 3998 8.437360 TGAAAGATATAATTGCAGTACCACAG 57.563 34.615 0.00 0.00 0.00 3.66
3533 4103 4.253685 TCTCCTGCAGCATAGTGTTTAAC 58.746 43.478 8.66 0.00 0.00 2.01
3589 4159 2.057922 CCCCTGCCCTACAGTATGAAT 58.942 52.381 0.00 0.00 45.68 2.57
3603 4173 3.569701 AGTATGAATAGGCGCCCAAATTG 59.430 43.478 26.15 0.00 0.00 2.32
3619 4189 4.253685 CAAATTGACGTCCTATGGTCACT 58.746 43.478 14.12 0.00 42.43 3.41
3679 4250 7.673641 ATCATCCTTCTACAGATTGAAGTCT 57.326 36.000 0.00 0.00 38.30 3.24
3805 4376 2.825836 GGTTCATCAGCAGGGCCG 60.826 66.667 0.00 0.00 0.00 6.13
3858 4429 6.412362 AAACATATTTGCACCTGTAACCAA 57.588 33.333 0.00 0.00 0.00 3.67
3929 4501 2.103941 GGTTCCCTTTGCAATTGGTTCA 59.896 45.455 7.72 0.00 0.00 3.18
4044 4616 2.829120 AGCCTTTCTGAGAGTCTGGTAC 59.171 50.000 0.00 0.00 0.00 3.34
4047 4619 3.119779 CCTTTCTGAGAGTCTGGTACGTC 60.120 52.174 0.00 0.00 0.00 4.34
4069 4641 6.291743 CGTCCATGCAAATTATTCATTTTCCG 60.292 38.462 0.00 0.00 32.24 4.30
4070 4642 6.534793 GTCCATGCAAATTATTCATTTTCCGT 59.465 34.615 0.00 0.00 32.24 4.69
4086 4660 2.632377 TCCGTTCAGATTGGATTCAGC 58.368 47.619 0.00 0.00 0.00 4.26
4092 4666 3.349927 TCAGATTGGATTCAGCCTTGTG 58.650 45.455 0.00 0.00 0.00 3.33
4153 4727 0.534877 TCCTTTCTGCAGAAGCGCAA 60.535 50.000 27.02 12.83 46.23 4.85
4245 4819 4.706962 GCTTTAGAGGACCCATTTCATGTT 59.293 41.667 0.00 0.00 0.00 2.71
4258 4832 6.651643 CCCATTTCATGTTGACATCACAAAAT 59.348 34.615 0.00 0.00 33.61 1.82
4355 4929 3.855689 AATGAAATTGCTCGTTCCTGG 57.144 42.857 0.00 0.00 33.44 4.45
4413 4987 0.765510 ACCAGGTTGTCAAGGTCCTC 59.234 55.000 0.00 0.00 0.00 3.71
4467 5041 2.251869 TGAACTACACCGTCGAATCG 57.748 50.000 0.00 0.00 0.00 3.34
4524 5098 5.517411 CGATATGCTTGCACATTTTGACAAT 59.483 36.000 0.00 0.00 0.00 2.71
4551 5125 1.134530 GCGAAGGACACGACGATGAG 61.135 60.000 0.00 0.00 0.00 2.90
4629 5203 4.602006 CAGTCGACTATGTACAGGTGATG 58.398 47.826 19.57 0.00 0.00 3.07
4650 5224 4.730966 TGTACCAACCATACCAAACACAT 58.269 39.130 0.00 0.00 0.00 3.21
4660 5234 6.719370 ACCATACCAAACACATTGACAATACT 59.281 34.615 0.00 0.00 41.85 2.12
4670 5244 8.044060 ACACATTGACAATACTTATTCACTGG 57.956 34.615 0.00 0.00 0.00 4.00
4676 5250 5.611374 ACAATACTTATTCACTGGATCCGG 58.389 41.667 19.66 19.66 0.00 5.14
4677 5251 5.130477 ACAATACTTATTCACTGGATCCGGT 59.870 40.000 21.21 21.21 35.66 5.28
4679 5253 3.375699 ACTTATTCACTGGATCCGGTCT 58.624 45.455 24.03 13.37 32.44 3.85
4680 5254 3.775316 ACTTATTCACTGGATCCGGTCTT 59.225 43.478 24.03 13.18 32.44 3.01
4681 5255 4.960469 ACTTATTCACTGGATCCGGTCTTA 59.040 41.667 24.03 11.87 32.44 2.10
4682 5256 5.602978 ACTTATTCACTGGATCCGGTCTTAT 59.397 40.000 24.03 17.60 32.44 1.73
4685 5259 4.837093 TCACTGGATCCGGTCTTATTTT 57.163 40.909 24.03 0.00 32.44 1.82
4686 5260 5.174037 TCACTGGATCCGGTCTTATTTTT 57.826 39.130 24.03 0.00 32.44 1.94
4687 5261 6.302535 TCACTGGATCCGGTCTTATTTTTA 57.697 37.500 24.03 0.00 32.44 1.52
4688 5262 6.110707 TCACTGGATCCGGTCTTATTTTTAC 58.889 40.000 24.03 0.00 32.44 2.01
4691 5265 7.931948 CACTGGATCCGGTCTTATTTTTACTAT 59.068 37.037 24.03 0.00 32.44 2.12
4693 5267 8.897872 TGGATCCGGTCTTATTTTTACTATTC 57.102 34.615 7.39 0.00 0.00 1.75
4694 5268 7.935210 TGGATCCGGTCTTATTTTTACTATTCC 59.065 37.037 7.39 0.00 0.00 3.01
4695 5269 7.117379 GGATCCGGTCTTATTTTTACTATTCCG 59.883 40.741 0.00 0.00 35.02 4.30
4696 5270 7.111247 TCCGGTCTTATTTTTACTATTCCGA 57.889 36.000 0.00 0.00 36.97 4.55
4697 5271 7.729116 TCCGGTCTTATTTTTACTATTCCGAT 58.271 34.615 0.00 0.00 36.97 4.18
4808 5391 2.427506 GAGCTCGTTTGTCTGGGAAAT 58.572 47.619 0.00 0.00 0.00 2.17
4947 5530 4.218417 ACCATGACCACATTGTAAGCTTTC 59.782 41.667 3.20 0.00 31.94 2.62
4989 5572 0.887387 TTACCTTGAGCAACGGCACC 60.887 55.000 0.00 0.00 44.61 5.01
5006 5589 2.681706 CACCACTAGAGTTCACAGCAG 58.318 52.381 0.00 0.00 0.00 4.24
5061 5644 3.854666 TGACCATGTTTGTGTGTTTTGG 58.145 40.909 0.00 0.00 0.00 3.28
5079 5662 0.942962 GGATTTGATCGCAGGCTCTG 59.057 55.000 0.00 0.00 34.12 3.35
5153 5736 5.799936 CACCGATTGACGCAAATTAGAAAAT 59.200 36.000 0.00 0.00 41.07 1.82
5154 5737 5.799936 ACCGATTGACGCAAATTAGAAAATG 59.200 36.000 0.00 0.00 41.07 2.32
5155 5738 5.275881 CCGATTGACGCAAATTAGAAAATGC 60.276 40.000 0.00 0.00 41.07 3.56
5182 5765 3.393089 AGTAATTAGCCGGCTGATGAG 57.607 47.619 38.98 0.00 0.00 2.90
5225 5808 2.508526 GTGTGCTGTTTCCCTTGAGAT 58.491 47.619 0.00 0.00 0.00 2.75
5286 5872 2.244510 AGTTACATTGGGGGATGCATGA 59.755 45.455 2.46 0.00 0.00 3.07
5376 5962 4.202441 GCAAATCAGTGGAGTGATGGTAT 58.798 43.478 0.00 0.00 37.24 2.73
5387 5973 6.313905 GTGGAGTGATGGTATTTCTTGTGTAG 59.686 42.308 0.00 0.00 0.00 2.74
5388 5974 6.212589 TGGAGTGATGGTATTTCTTGTGTAGA 59.787 38.462 0.00 0.00 0.00 2.59
5418 6027 6.740411 TTTGAAAAATGCAAGCAAACTCTT 57.260 29.167 0.00 0.00 0.00 2.85
5423 6032 4.389890 AATGCAAGCAAACTCTTGTGAA 57.610 36.364 0.00 0.00 43.92 3.18
5425 6034 3.510719 TGCAAGCAAACTCTTGTGAAAC 58.489 40.909 0.00 0.00 43.92 2.78
5644 6258 3.058777 CCAAATACGCGTACAGGTTGTTT 60.059 43.478 23.19 13.21 0.00 2.83
5687 6302 7.816300 AAGGAAGAAAACTAGGGATAAGAGT 57.184 36.000 0.00 0.00 0.00 3.24
5768 6385 5.113383 CCTTCATGTATACGCCTTGTACAA 58.887 41.667 8.28 8.28 35.44 2.41
5777 6394 1.983605 CGCCTTGTACAAGTCTACACG 59.016 52.381 29.05 19.18 36.72 4.49
5801 6426 4.033472 CACGCAACCATATCATCACGTTTA 59.967 41.667 0.00 0.00 0.00 2.01
5923 6557 6.036191 GGTCTTGAGAGTGAATAAACCGAATC 59.964 42.308 0.00 0.00 0.00 2.52
5980 6614 6.734104 AAGTGAAAGTCTATCTCAATGTGC 57.266 37.500 0.00 0.00 0.00 4.57
6054 6691 4.632327 TGTCACACCATAAACATGGAGA 57.368 40.909 10.57 3.11 44.39 3.71
6077 6715 8.312669 AGATCTAGTGCTTTCATACCTAGTTT 57.687 34.615 0.00 0.00 0.00 2.66
6224 6862 4.646945 TCCAAAGAATACTGCAAAACCACA 59.353 37.500 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
165 177 1.872773 GAGGGACACTCTCCAAGGAT 58.127 55.000 0.00 0.00 43.14 3.24
192 204 5.176590 GCTAAGATAGAAAGAGAACATGCCG 59.823 44.000 0.00 0.00 0.00 5.69
196 208 9.950496 TTCTTTGCTAAGATAGAAAGAGAACAT 57.050 29.630 11.41 0.00 40.01 2.71
306 319 2.143925 CCTGTCACTCGGTTTTCCTTC 58.856 52.381 0.00 0.00 37.95 3.46
338 351 6.017109 TGACTCTTTTCCCTTTGAATCTTTCG 60.017 38.462 0.00 0.00 31.67 3.46
416 429 0.250467 GCCGGTGATGGTGATGCTAT 60.250 55.000 1.90 0.00 0.00 2.97
435 448 2.484742 AGTGTAAAACCTAAGCCCGG 57.515 50.000 0.00 0.00 0.00 5.73
439 452 4.151867 CGAGTGGAAGTGTAAAACCTAAGC 59.848 45.833 0.00 0.00 0.00 3.09
444 457 1.534163 GCCGAGTGGAAGTGTAAAACC 59.466 52.381 0.00 0.00 37.49 3.27
470 488 9.830975 AGTTTGAAAAACAGTTATATTTGCCTT 57.169 25.926 5.72 0.00 0.00 4.35
479 497 7.556275 TGAGGAGTGAGTTTGAAAAACAGTTAT 59.444 33.333 5.72 0.00 0.00 1.89
512 531 2.906389 TGGAGCTAACTGATGTTGACCT 59.094 45.455 0.00 0.00 37.59 3.85
526 545 3.840666 ACTTGGATGACTTTCTGGAGCTA 59.159 43.478 0.00 0.00 0.00 3.32
527 546 2.641815 ACTTGGATGACTTTCTGGAGCT 59.358 45.455 0.00 0.00 0.00 4.09
535 554 3.318017 CTTCGTCGACTTGGATGACTTT 58.682 45.455 14.70 0.00 31.92 2.66
578 597 4.006319 GAGATCTTCCCAAGGTTTCACTG 58.994 47.826 0.00 0.00 0.00 3.66
609 628 0.891373 CGAGCAAGGAGAAGAGGTGA 59.109 55.000 0.00 0.00 0.00 4.02
634 653 1.958579 ACTTTTAAAGAACGGCACCCC 59.041 47.619 12.02 0.00 0.00 4.95
648 668 7.061326 GTGTTGCAACGAAAGAGAAAACTTTTA 59.939 33.333 23.79 0.00 39.71 1.52
649 669 5.923684 TGTTGCAACGAAAGAGAAAACTTTT 59.076 32.000 23.79 0.00 39.71 2.27
658 697 3.607422 TCATGTGTTGCAACGAAAGAG 57.393 42.857 23.79 11.73 0.00 2.85
660 699 6.192682 CGTATATTCATGTGTTGCAACGAAAG 59.807 38.462 23.79 14.06 0.00 2.62
662 701 5.120986 ACGTATATTCATGTGTTGCAACGAA 59.879 36.000 23.79 19.75 0.00 3.85
663 702 4.627900 ACGTATATTCATGTGTTGCAACGA 59.372 37.500 23.79 13.78 0.00 3.85
673 712 6.706270 CCTTTTCCTAGCACGTATATTCATGT 59.294 38.462 0.00 0.00 0.00 3.21
676 715 6.474140 TCCTTTTCCTAGCACGTATATTCA 57.526 37.500 0.00 0.00 0.00 2.57
678 717 7.120923 TCTTCCTTTTCCTAGCACGTATATT 57.879 36.000 0.00 0.00 0.00 1.28
679 718 6.726490 TCTTCCTTTTCCTAGCACGTATAT 57.274 37.500 0.00 0.00 0.00 0.86
680 719 6.534475 TTCTTCCTTTTCCTAGCACGTATA 57.466 37.500 0.00 0.00 0.00 1.47
691 730 4.584743 TCCTGCTTCTTTTCTTCCTTTTCC 59.415 41.667 0.00 0.00 0.00 3.13
692 731 5.774498 TCCTGCTTCTTTTCTTCCTTTTC 57.226 39.130 0.00 0.00 0.00 2.29
693 732 5.893824 TCTTCCTGCTTCTTTTCTTCCTTTT 59.106 36.000 0.00 0.00 0.00 2.27
694 733 5.449553 TCTTCCTGCTTCTTTTCTTCCTTT 58.550 37.500 0.00 0.00 0.00 3.11
696 735 4.713792 TCTTCCTGCTTCTTTTCTTCCT 57.286 40.909 0.00 0.00 0.00 3.36
697 736 5.774498 TTTCTTCCTGCTTCTTTTCTTCC 57.226 39.130 0.00 0.00 0.00 3.46
733 777 2.422939 TCCCAGCTAGCCCAAGATAT 57.577 50.000 12.13 0.00 0.00 1.63
735 779 2.422939 TATCCCAGCTAGCCCAAGAT 57.577 50.000 12.13 11.26 0.00 2.40
750 794 1.202651 CGTGTCCTTGTGGGGATATCC 60.203 57.143 13.87 13.87 37.73 2.59
751 795 1.810412 GCGTGTCCTTGTGGGGATATC 60.810 57.143 0.00 0.00 37.73 1.63
752 796 0.180406 GCGTGTCCTTGTGGGGATAT 59.820 55.000 0.00 0.00 37.73 1.63
755 799 4.308458 CGCGTGTCCTTGTGGGGA 62.308 66.667 0.00 0.00 35.33 4.81
759 803 3.716006 CTGCCGCGTGTCCTTGTG 61.716 66.667 4.92 0.00 0.00 3.33
760 804 3.750373 AACTGCCGCGTGTCCTTGT 62.750 57.895 4.92 0.00 0.00 3.16
761 805 2.972505 AACTGCCGCGTGTCCTTG 60.973 61.111 4.92 0.00 0.00 3.61
762 806 2.972505 CAACTGCCGCGTGTCCTT 60.973 61.111 4.92 0.00 0.00 3.36
763 807 4.988598 CCAACTGCCGCGTGTCCT 62.989 66.667 4.92 0.00 0.00 3.85
764 808 4.980805 TCCAACTGCCGCGTGTCC 62.981 66.667 4.92 0.00 0.00 4.02
765 809 3.414700 CTCCAACTGCCGCGTGTC 61.415 66.667 4.92 0.00 0.00 3.67
766 810 4.988598 CCTCCAACTGCCGCGTGT 62.989 66.667 4.92 0.00 0.00 4.49
767 811 3.958147 ATCCTCCAACTGCCGCGTG 62.958 63.158 4.92 0.00 0.00 5.34
768 812 3.706373 ATCCTCCAACTGCCGCGT 61.706 61.111 4.92 0.00 0.00 6.01
769 813 3.197790 CATCCTCCAACTGCCGCG 61.198 66.667 0.00 0.00 0.00 6.46
770 814 3.512516 GCATCCTCCAACTGCCGC 61.513 66.667 0.00 0.00 0.00 6.53
771 815 3.197790 CGCATCCTCCAACTGCCG 61.198 66.667 0.00 0.00 32.24 5.69
772 816 2.825836 CCGCATCCTCCAACTGCC 60.826 66.667 0.00 0.00 32.24 4.85
773 817 3.512516 GCCGCATCCTCCAACTGC 61.513 66.667 0.00 0.00 0.00 4.40
774 818 2.825836 GGCCGCATCCTCCAACTG 60.826 66.667 0.00 0.00 0.00 3.16
775 819 4.473520 CGGCCGCATCCTCCAACT 62.474 66.667 14.67 0.00 0.00 3.16
776 820 3.969250 TTCGGCCGCATCCTCCAAC 62.969 63.158 23.51 0.00 0.00 3.77
777 821 3.680620 CTTCGGCCGCATCCTCCAA 62.681 63.158 23.51 5.79 0.00 3.53
778 822 4.161295 CTTCGGCCGCATCCTCCA 62.161 66.667 23.51 0.00 0.00 3.86
801 845 1.199327 CACCAACTCTGCTGATTGCTG 59.801 52.381 0.00 0.00 43.37 4.41
809 853 2.143876 AACAAACCACCAACTCTGCT 57.856 45.000 0.00 0.00 0.00 4.24
812 856 5.126545 GGAACTTTAACAAACCACCAACTCT 59.873 40.000 0.00 0.00 0.00 3.24
813 857 5.345702 GGAACTTTAACAAACCACCAACTC 58.654 41.667 0.00 0.00 0.00 3.01
835 879 4.038402 GCCAGTGATGATTAAATGAAGGGG 59.962 45.833 0.00 0.00 0.00 4.79
913 968 0.526662 GATCCTGTGTTCGTCGGAGT 59.473 55.000 0.00 0.00 0.00 3.85
915 970 1.201647 GAAGATCCTGTGTTCGTCGGA 59.798 52.381 0.00 0.00 0.00 4.55
916 971 1.202582 AGAAGATCCTGTGTTCGTCGG 59.797 52.381 0.00 0.00 35.38 4.79
918 973 3.442273 AGAGAGAAGATCCTGTGTTCGTC 59.558 47.826 0.00 0.00 35.38 4.20
919 974 3.426615 AGAGAGAAGATCCTGTGTTCGT 58.573 45.455 0.00 0.00 35.38 3.85
920 975 3.694072 AGAGAGAGAAGATCCTGTGTTCG 59.306 47.826 0.00 0.00 35.38 3.95
921 976 4.704540 TGAGAGAGAGAAGATCCTGTGTTC 59.295 45.833 0.00 0.00 0.00 3.18
940 997 2.058593 TCTCTATCCGCTGCTTGAGA 57.941 50.000 0.00 0.00 0.00 3.27
941 998 2.352617 GGATCTCTATCCGCTGCTTGAG 60.353 54.545 0.00 0.00 42.41 3.02
1097 1160 2.358247 GAAACAGAGGGCGGCGAA 60.358 61.111 12.98 0.00 0.00 4.70
1223 1289 2.223203 GCTGCTGAATCGAATGGAAGTG 60.223 50.000 0.00 0.00 0.00 3.16
1287 1362 5.524511 TTAATTGACGACGAGACCATTTG 57.475 39.130 0.00 0.00 0.00 2.32
1330 1405 2.715532 TATCAATGGGCTCGCTCGGC 62.716 60.000 0.00 0.00 0.00 5.54
1331 1406 0.668706 CTATCAATGGGCTCGCTCGG 60.669 60.000 0.00 0.00 0.00 4.63
1341 1416 2.868583 CGACTTGCTGGTCTATCAATGG 59.131 50.000 7.73 0.00 34.38 3.16
1378 1453 2.286654 GCTAAATCGCTGAGCAATCACC 60.287 50.000 4.88 0.00 36.20 4.02
1396 1471 1.679680 AGCCTAGTACGCAATTCGCTA 59.320 47.619 0.00 0.00 43.23 4.26
1403 1478 1.218047 CCAGCAGCCTAGTACGCAA 59.782 57.895 0.00 0.00 0.00 4.85
1428 1503 5.822278 ACATGAACAGTAGCATAGTACGAG 58.178 41.667 0.00 0.00 0.00 4.18
1465 1540 1.109323 AGCCAACTGCCAACCTTGAC 61.109 55.000 0.00 0.00 42.71 3.18
1468 1543 0.178953 ATCAGCCAACTGCCAACCTT 60.179 50.000 0.00 0.00 44.10 3.50
1469 1544 0.896940 CATCAGCCAACTGCCAACCT 60.897 55.000 0.00 0.00 44.10 3.50
1471 1546 1.588082 CCATCAGCCAACTGCCAAC 59.412 57.895 0.00 0.00 44.10 3.77
1472 1547 2.277591 GCCATCAGCCAACTGCCAA 61.278 57.895 0.00 0.00 44.10 4.52
1473 1548 2.677524 GCCATCAGCCAACTGCCA 60.678 61.111 0.00 0.00 44.10 4.92
1474 1549 2.677524 TGCCATCAGCCAACTGCC 60.678 61.111 0.00 0.00 44.10 4.85
1475 1550 1.530013 AAGTGCCATCAGCCAACTGC 61.530 55.000 0.00 0.00 44.10 4.40
1476 1551 0.242825 CAAGTGCCATCAGCCAACTG 59.757 55.000 0.00 0.00 45.95 3.16
1477 1552 0.896940 CCAAGTGCCATCAGCCAACT 60.897 55.000 0.00 0.00 42.71 3.16
1478 1553 1.588082 CCAAGTGCCATCAGCCAAC 59.412 57.895 0.00 0.00 42.71 3.77
1479 1554 2.277591 GCCAAGTGCCATCAGCCAA 61.278 57.895 0.00 0.00 42.71 4.52
1480 1555 2.677524 GCCAAGTGCCATCAGCCA 60.678 61.111 0.00 0.00 42.71 4.75
1481 1556 2.677524 TGCCAAGTGCCATCAGCC 60.678 61.111 0.00 0.00 42.71 4.85
1482 1557 1.530013 AAGTGCCAAGTGCCATCAGC 61.530 55.000 0.00 0.00 40.16 4.26
1483 1558 0.242825 CAAGTGCCAAGTGCCATCAG 59.757 55.000 0.00 0.00 40.16 2.90
1484 1559 1.180456 CCAAGTGCCAAGTGCCATCA 61.180 55.000 0.00 0.00 40.16 3.07
1485 1560 1.588082 CCAAGTGCCAAGTGCCATC 59.412 57.895 0.00 0.00 40.16 3.51
1486 1561 2.576832 GCCAAGTGCCAAGTGCCAT 61.577 57.895 0.00 0.00 40.16 4.40
1487 1562 3.225798 GCCAAGTGCCAAGTGCCA 61.226 61.111 0.00 0.00 40.16 4.92
1488 1563 3.225798 TGCCAAGTGCCAAGTGCC 61.226 61.111 0.00 0.00 40.16 5.01
1489 1564 2.028043 GTGCCAAGTGCCAAGTGC 59.972 61.111 0.00 0.00 40.16 4.40
1490 1565 2.079020 CTGGTGCCAAGTGCCAAGTG 62.079 60.000 0.00 0.00 40.16 3.16
1491 1566 1.829533 CTGGTGCCAAGTGCCAAGT 60.830 57.895 0.00 0.00 40.16 3.16
1492 1567 3.045142 CTGGTGCCAAGTGCCAAG 58.955 61.111 0.00 0.00 40.16 3.61
1499 1574 2.949106 CAGTTCGCTGGTGCCAAG 59.051 61.111 0.00 0.00 41.40 3.61
1519 1594 2.359169 TAGGGCACTCCAGGAAGCG 61.359 63.158 0.00 0.00 38.24 4.68
1588 2074 2.325101 AATTTGGCACCCCCACCAGT 62.325 55.000 0.00 0.00 45.34 4.00
1589 2075 1.536174 AATTTGGCACCCCCACCAG 60.536 57.895 0.00 0.00 45.34 4.00
1590 2076 1.840650 CAATTTGGCACCCCCACCA 60.841 57.895 0.00 0.00 45.34 4.17
1591 2077 3.067985 CAATTTGGCACCCCCACC 58.932 61.111 0.00 0.00 45.34 4.61
1592 2078 2.347114 GCAATTTGGCACCCCCAC 59.653 61.111 0.00 0.00 45.34 4.61
1593 2079 2.927317 GGCAATTTGGCACCCCCA 60.927 61.111 17.26 0.00 43.14 4.96
1594 2080 4.081185 CGGCAATTTGGCACCCCC 62.081 66.667 21.18 1.63 43.94 5.40
1595 2081 2.358372 ATCGGCAATTTGGCACCCC 61.358 57.895 21.18 2.30 43.94 4.95
1617 2103 2.677199 TCTTATCGCGCAATCTCATCC 58.323 47.619 8.75 0.00 0.00 3.51
1633 2119 5.813672 ACACTACAACAAAAGCGAGTTCTTA 59.186 36.000 0.00 0.00 0.00 2.10
1635 2121 4.189231 ACACTACAACAAAAGCGAGTTCT 58.811 39.130 0.00 0.00 0.00 3.01
1640 2126 5.569823 GTCAAAAACACTACAACAAAAGCGA 59.430 36.000 0.00 0.00 0.00 4.93
1644 2130 8.428536 CGAAATGTCAAAAACACTACAACAAAA 58.571 29.630 0.00 0.00 41.75 2.44
1670 2156 2.290093 GTGATAAGCAGGAATCAGCTGC 59.710 50.000 9.47 0.00 41.70 5.25
1726 2215 5.623956 TCCAACAGAACCACGGATATTAT 57.376 39.130 0.00 0.00 0.00 1.28
1737 2226 4.037923 ACATTGTCACATTCCAACAGAACC 59.962 41.667 0.00 0.00 37.29 3.62
1828 2318 5.203060 AGAGAACACCTGTAGTCAGAAAC 57.797 43.478 0.00 0.00 43.76 2.78
1849 2339 7.693969 AACCAGATCACTTTTTATCCTCAAG 57.306 36.000 0.00 0.00 0.00 3.02
1860 2405 6.976934 ACAACCATTAAACCAGATCACTTT 57.023 33.333 0.00 0.00 0.00 2.66
1869 2414 6.004574 TGTAGCATGTACAACCATTAAACCA 58.995 36.000 0.00 0.00 0.00 3.67
1888 2433 1.376543 AGTGTCATGCAGCATGTAGC 58.623 50.000 30.38 21.98 41.98 3.58
1889 2434 3.790091 AGTAGTGTCATGCAGCATGTAG 58.210 45.455 30.38 9.85 41.98 2.74
1898 2443 4.879104 ACGTCTAGTAGTAGTGTCATGC 57.121 45.455 4.51 0.00 0.00 4.06
1903 2448 3.688673 GGAGCAACGTCTAGTAGTAGTGT 59.311 47.826 4.51 2.58 0.00 3.55
1916 2462 1.227556 GACTGTGTGGGAGCAACGT 60.228 57.895 0.00 0.00 0.00 3.99
2005 2556 5.675538 AGCTTTCCTAAGAGCGAATTACAT 58.324 37.500 0.00 0.00 43.53 2.29
2007 2558 6.314152 AGAAAGCTTTCCTAAGAGCGAATTAC 59.686 38.462 30.83 5.18 43.53 1.89
2008 2559 6.407202 AGAAAGCTTTCCTAAGAGCGAATTA 58.593 36.000 30.83 0.00 43.53 1.40
2068 2620 2.738139 GCATTTTGGTGGCCACGC 60.738 61.111 29.08 21.18 30.78 5.34
2095 2647 1.701031 TTCCCACTCGTTGGCAAGGA 61.701 55.000 20.18 20.18 45.37 3.36
2102 2654 2.751166 ATGACTCTTCCCACTCGTTG 57.249 50.000 0.00 0.00 0.00 4.10
2264 2816 7.530010 TCTTTTCTCGAAATATCTTTTGCAGG 58.470 34.615 0.00 0.00 0.00 4.85
2353 2905 7.989416 ACCCTTCGTAATTACTTTTGAATCA 57.011 32.000 13.56 0.00 0.00 2.57
2457 3012 3.272031 GGCAGAACCAAGCAGAGC 58.728 61.111 0.00 0.00 38.86 4.09
2533 3088 3.370103 CCTTAATAGCCACCAACCTTCGA 60.370 47.826 0.00 0.00 0.00 3.71
2551 3106 3.554934 GTCATGCAATCCACCATCCTTA 58.445 45.455 0.00 0.00 0.00 2.69
2579 3134 5.046529 CCACGATGATTGGAAGACTAGAAG 58.953 45.833 0.00 0.00 36.02 2.85
2591 3146 4.728882 GCTTTTGCTACTCCACGATGATTG 60.729 45.833 0.00 0.00 43.35 2.67
2634 3195 1.405821 AGGCTTGAGGATAGTCGAACG 59.594 52.381 0.00 0.00 0.00 3.95
2651 3212 1.889829 AGGACGCTGTATCATAGAGGC 59.110 52.381 0.00 0.00 0.00 4.70
2661 3222 2.693074 TCATCATTGCTAGGACGCTGTA 59.307 45.455 0.00 0.00 0.00 2.74
2674 3235 8.118976 ACATAAAGGCAATATCCTCATCATTG 57.881 34.615 0.00 0.00 34.82 2.82
2683 3244 4.385825 TGACCGACATAAAGGCAATATCC 58.614 43.478 0.00 0.00 0.00 2.59
2754 3315 9.118300 GACATGGAGATTACTGAATCAAAAGAT 57.882 33.333 0.00 0.00 43.51 2.40
2766 3327 7.877097 GCTCAATTATCTGACATGGAGATTACT 59.123 37.037 13.10 0.00 32.32 2.24
2767 3328 7.877097 AGCTCAATTATCTGACATGGAGATTAC 59.123 37.037 13.10 0.00 32.32 1.89
2768 3329 7.971201 AGCTCAATTATCTGACATGGAGATTA 58.029 34.615 13.10 6.51 32.32 1.75
3026 3590 2.555757 GTCATCTGCCTCTTTTGCTTGT 59.444 45.455 0.00 0.00 0.00 3.16
3075 3639 7.046652 CCAGAAGATTTCTCACATAGTCACAT 58.953 38.462 0.00 0.00 38.11 3.21
3076 3640 6.401394 CCAGAAGATTTCTCACATAGTCACA 58.599 40.000 0.00 0.00 38.11 3.58
3077 3641 5.814705 CCCAGAAGATTTCTCACATAGTCAC 59.185 44.000 0.00 0.00 38.11 3.67
3078 3642 5.721480 TCCCAGAAGATTTCTCACATAGTCA 59.279 40.000 0.00 0.00 38.11 3.41
3079 3643 6.227298 TCCCAGAAGATTTCTCACATAGTC 57.773 41.667 0.00 0.00 38.11 2.59
3080 3644 6.627087 TTCCCAGAAGATTTCTCACATAGT 57.373 37.500 0.00 0.00 38.11 2.12
3081 3645 9.790344 ATAATTCCCAGAAGATTTCTCACATAG 57.210 33.333 0.00 0.00 38.11 2.23
3163 3727 8.893219 TCAATCTTAACAGGAAGCTATGTATG 57.107 34.615 0.00 0.00 0.00 2.39
3209 3773 6.094603 GCTACTGATCATCATTTTGTTCCACT 59.905 38.462 0.00 0.00 0.00 4.00
3234 3798 2.076100 TGTAGAAGGTTGCGCAAGATG 58.924 47.619 25.78 0.00 43.02 2.90
3250 3820 5.640218 TCGGAGTTTTAAAACACGTGTAG 57.360 39.130 29.97 17.26 41.30 2.74
3255 3825 3.304190 CCCCTTCGGAGTTTTAAAACACG 60.304 47.826 28.03 27.89 41.30 4.49
3287 3857 7.600960 TGCTTGCAACTAATTTCACATAATCA 58.399 30.769 0.00 0.00 0.00 2.57
3428 3998 3.681593 TGAGCCCCAAGTTGTATTGTAC 58.318 45.455 1.45 0.00 0.00 2.90
3502 4072 1.066358 TGCTGCAGGAGAGATGAACAG 60.066 52.381 17.12 0.00 0.00 3.16
3510 4080 2.687700 AACACTATGCTGCAGGAGAG 57.312 50.000 25.96 25.96 0.00 3.20
3574 4144 2.931320 GCGCCTATTCATACTGTAGGGC 60.931 54.545 0.00 0.00 36.36 5.19
3575 4145 2.353803 GGCGCCTATTCATACTGTAGGG 60.354 54.545 22.15 0.00 36.36 3.53
3576 4146 2.353803 GGGCGCCTATTCATACTGTAGG 60.354 54.545 28.56 0.00 38.39 3.18
3577 4147 2.299013 TGGGCGCCTATTCATACTGTAG 59.701 50.000 28.56 0.00 0.00 2.74
3578 4148 2.321719 TGGGCGCCTATTCATACTGTA 58.678 47.619 28.56 0.00 0.00 2.74
3589 4159 1.003112 ACGTCAATTTGGGCGCCTA 60.003 52.632 28.56 19.98 0.00 3.93
3603 4173 3.056749 ACAGAAAGTGACCATAGGACGTC 60.057 47.826 7.13 7.13 0.00 4.34
3619 4189 5.645929 TCAGAACACTGCTTAAACACAGAAA 59.354 36.000 6.77 0.00 37.35 2.52
3694 4265 0.710567 CTGTCACAAGCTTCGCTACG 59.289 55.000 0.00 0.00 38.25 3.51
3929 4501 2.238646 TGTTATGGATCCTGCCGTTTCT 59.761 45.455 14.23 0.00 0.00 2.52
4044 4616 6.291743 CGGAAAATGAATAATTTGCATGGACG 60.292 38.462 0.00 0.00 38.52 4.79
4047 4619 6.907206 ACGGAAAATGAATAATTTGCATGG 57.093 33.333 0.00 0.00 38.52 3.66
4069 4641 3.760684 ACAAGGCTGAATCCAATCTGAAC 59.239 43.478 0.00 0.00 0.00 3.18
4070 4642 3.760151 CACAAGGCTGAATCCAATCTGAA 59.240 43.478 0.00 0.00 0.00 3.02
4086 4660 8.830580 ACGATAATAAACTCATCATTCACAAGG 58.169 33.333 0.00 0.00 0.00 3.61
4153 4727 6.703607 GCATCTAATACAATAGCACAGTCTGT 59.296 38.462 0.00 0.00 0.00 3.41
4245 4819 5.359292 TCCAACAGTGAATTTTGTGATGTCA 59.641 36.000 0.00 0.00 0.00 3.58
4258 4832 4.937620 GCTGTCAAGATATCCAACAGTGAA 59.062 41.667 21.46 0.00 39.56 3.18
4304 4878 1.737793 GACTGCCGAACACATTTAGGG 59.262 52.381 0.00 0.00 0.00 3.53
4355 4929 2.494073 AGAGTTTGTCCGAGGATCAGAC 59.506 50.000 0.00 1.91 42.79 3.51
4413 4987 1.450312 CTTAGCACCCTTGGCGGAG 60.450 63.158 0.00 0.00 36.08 4.63
4467 5041 5.163854 CGTGATGTTTAGAATGGACTGAACC 60.164 44.000 0.00 0.00 36.16 3.62
4524 5098 2.203084 TGTCCTTCGCGTTGCCAA 60.203 55.556 5.77 0.00 0.00 4.52
4551 5125 3.265791 CCACTGGTCTTGAGCTTCATAC 58.734 50.000 0.00 0.00 0.00 2.39
4629 5203 5.241949 TCAATGTGTTTGGTATGGTTGGTAC 59.758 40.000 0.00 0.00 35.92 3.34
4636 5210 7.156876 AGTATTGTCAATGTGTTTGGTATGG 57.843 36.000 8.39 0.00 35.92 2.74
4650 5224 6.761242 CGGATCCAGTGAATAAGTATTGTCAA 59.239 38.462 13.41 0.00 0.00 3.18
4660 5234 6.494666 AATAAGACCGGATCCAGTGAATAA 57.505 37.500 9.46 0.00 0.00 1.40
4670 5244 7.869429 TCGGAATAGTAAAAATAAGACCGGATC 59.131 37.037 9.46 1.42 37.69 3.36
4679 5253 8.617809 GCCTGTTCATCGGAATAGTAAAAATAA 58.382 33.333 0.00 0.00 39.75 1.40
4680 5254 7.771361 TGCCTGTTCATCGGAATAGTAAAAATA 59.229 33.333 0.00 0.00 39.75 1.40
4681 5255 6.601613 TGCCTGTTCATCGGAATAGTAAAAAT 59.398 34.615 0.00 0.00 39.75 1.82
4682 5256 5.941058 TGCCTGTTCATCGGAATAGTAAAAA 59.059 36.000 0.00 0.00 39.75 1.94
4685 5259 4.081365 TGTGCCTGTTCATCGGAATAGTAA 60.081 41.667 0.00 0.00 39.75 2.24
4686 5260 3.449377 TGTGCCTGTTCATCGGAATAGTA 59.551 43.478 0.00 0.00 39.75 1.82
4687 5261 2.236146 TGTGCCTGTTCATCGGAATAGT 59.764 45.455 0.00 0.00 39.75 2.12
4688 5262 2.868583 CTGTGCCTGTTCATCGGAATAG 59.131 50.000 0.00 0.00 40.71 1.73
4691 5265 0.684535 TCTGTGCCTGTTCATCGGAA 59.315 50.000 0.00 0.00 0.00 4.30
4693 5267 0.247460 TCTCTGTGCCTGTTCATCGG 59.753 55.000 0.00 0.00 0.00 4.18
4694 5268 1.638133 CTCTCTGTGCCTGTTCATCG 58.362 55.000 0.00 0.00 0.00 3.84
4695 5269 1.367659 GCTCTCTGTGCCTGTTCATC 58.632 55.000 0.00 0.00 0.00 2.92
4696 5270 0.390866 CGCTCTCTGTGCCTGTTCAT 60.391 55.000 0.00 0.00 0.00 2.57
4697 5271 1.005748 CGCTCTCTGTGCCTGTTCA 60.006 57.895 0.00 0.00 0.00 3.18
4859 5442 1.227527 GTTGCCTTTTGGTGGGTGC 60.228 57.895 0.00 0.00 42.99 5.01
4973 5556 2.594303 TGGTGCCGTTGCTCAAGG 60.594 61.111 0.00 0.00 38.71 3.61
4989 5572 3.667497 TTCCTGCTGTGAACTCTAGTG 57.333 47.619 0.00 0.00 0.00 2.74
5006 5589 4.554723 CGTTCCTCATGTCAACAAGTTTCC 60.555 45.833 0.00 0.00 0.00 3.13
5061 5644 0.942962 CCAGAGCCTGCGATCAAATC 59.057 55.000 0.00 0.00 0.00 2.17
5153 5736 3.527533 CCGGCTAATTACTTGTGTAGCA 58.472 45.455 0.00 0.00 40.61 3.49
5154 5737 2.287103 GCCGGCTAATTACTTGTGTAGC 59.713 50.000 22.15 0.00 38.58 3.58
5155 5738 3.555956 CAGCCGGCTAATTACTTGTGTAG 59.444 47.826 32.30 7.54 0.00 2.74
5182 5765 5.875359 ACGGAGTTTTCTTCTCAATACCATC 59.125 40.000 0.00 0.00 37.78 3.51
5225 5808 6.457355 TGCCGCCGTAGAAATATCTTATTTA 58.543 36.000 0.00 0.00 37.10 1.40
5387 5973 7.642071 TGCTTGCATTTTTCAAATCTACTTC 57.358 32.000 0.00 0.00 0.00 3.01
5388 5974 8.337532 GTTTGCTTGCATTTTTCAAATCTACTT 58.662 29.630 0.00 0.00 0.00 2.24
5418 6027 5.336849 CCCACCAAAGTTTACAAGTTTCACA 60.337 40.000 0.00 0.00 31.88 3.58
5423 6032 3.035363 CCCCCACCAAAGTTTACAAGTT 58.965 45.455 0.00 0.00 0.00 2.66
5425 6034 1.343142 GCCCCCACCAAAGTTTACAAG 59.657 52.381 0.00 0.00 0.00 3.16
5529 6140 7.309377 GCACATGGTATATGAATTGTGGCTAAT 60.309 37.037 0.00 0.00 36.01 1.73
5598 6210 4.335594 GCTCGCAACCCTTCTATTTAACAT 59.664 41.667 0.00 0.00 0.00 2.71
5706 6322 6.493978 CGGAGGAGTAGTTAGTTAGCTAAAC 58.506 44.000 7.99 3.08 38.74 2.01
5768 6385 1.663702 GGTTGCGTGCGTGTAGACT 60.664 57.895 0.00 0.00 0.00 3.24
5777 6394 1.333169 CGTGATGATATGGTTGCGTGC 60.333 52.381 0.00 0.00 0.00 5.34
5801 6426 4.741928 AGTTTGATTAAGGGAGGGTGTT 57.258 40.909 0.00 0.00 0.00 3.32
5889 6515 1.490490 ACTCTCAAGACCAGGTTGCAA 59.510 47.619 0.00 0.00 0.00 4.08
5890 6516 1.131638 ACTCTCAAGACCAGGTTGCA 58.868 50.000 0.00 0.00 0.00 4.08
6054 6691 8.312669 AGAAACTAGGTATGAAAGCACTAGAT 57.687 34.615 0.00 0.00 36.06 1.98
6077 6715 7.395772 TCATATGGGTGCAGTCAATTTTAAAGA 59.604 33.333 2.13 0.00 0.00 2.52
6123 6761 4.941263 ACGGAAGCAGAATACAAAGCATTA 59.059 37.500 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.