Multiple sequence alignment - TraesCS1A01G303800

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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 TraesCS1A01G303800 chr1A 100.000 4835 0 0 1 4835 497244621 497239787 0.000000e+00 8929.0
1 TraesCS1A01G303800 chr1A 93.794 564 32 3 122 684 521625882 521626443 0.000000e+00 845.0
2 TraesCS1A01G303800 chr1A 92.683 123 9 0 1 123 521625181 521625303 1.380000e-40 178.0
3 TraesCS1A01G303800 chr1D 93.809 4022 161 32 845 4835 401135239 401131275 0.000000e+00 5967.0
4 TraesCS1A01G303800 chr1B 95.449 3296 93 25 835 4099 538868682 538865413 0.000000e+00 5203.0
5 TraesCS1A01G303800 chr1B 87.348 656 63 7 4183 4835 538865172 538864534 0.000000e+00 734.0
6 TraesCS1A01G303800 chr1B 80.070 572 96 13 122 688 625926865 625926307 4.500000e-110 409.0
7 TraesCS1A01G303800 chr1B 89.855 69 4 1 785 853 538868759 538868694 8.620000e-13 86.1
8 TraesCS1A01G303800 chr2D 85.757 1004 139 4 1355 2356 612365325 612366326 0.000000e+00 1059.0
9 TraesCS1A01G303800 chr2D 78.382 1397 234 57 2446 3790 612366320 612367700 0.000000e+00 845.0
10 TraesCS1A01G303800 chr2D 87.097 186 18 2 1098 1277 612365140 612365325 6.340000e-49 206.0
11 TraesCS1A01G303800 chr2B 85.757 1004 139 4 1355 2356 747237628 747238629 0.000000e+00 1059.0
12 TraesCS1A01G303800 chr2B 78.959 1307 206 58 2446 3703 747238623 747239909 0.000000e+00 826.0
13 TraesCS1A01G303800 chr2B 86.022 186 20 3 1098 1277 747237443 747237628 1.370000e-45 195.0
14 TraesCS1A01G303800 chr2A 85.501 1007 136 9 1355 2356 744492303 744493304 0.000000e+00 1042.0
15 TraesCS1A01G303800 chr2A 78.939 1301 204 49 2446 3703 744493298 744494571 0.000000e+00 821.0
16 TraesCS1A01G303800 chr2A 81.229 586 83 19 122 690 673029998 673029423 9.550000e-122 448.0
17 TraesCS1A01G303800 chr2A 86.559 186 19 3 1098 1277 744492118 744492303 2.950000e-47 200.0
18 TraesCS1A01G303800 chr3A 84.861 1004 146 5 1355 2355 587636058 587637058 0.000000e+00 1007.0
19 TraesCS1A01G303800 chr3A 93.509 570 36 1 122 691 701636120 701636688 0.000000e+00 846.0
20 TraesCS1A01G303800 chr3A 78.947 1292 215 49 2448 3703 587637139 587638409 0.000000e+00 826.0
21 TraesCS1A01G303800 chr3A 93.939 528 29 2 122 647 732486667 732486141 0.000000e+00 795.0
22 TraesCS1A01G303800 chr3A 84.979 699 87 14 4142 4835 594672364 594673049 0.000000e+00 693.0
23 TraesCS1A01G303800 chr3A 91.620 179 15 0 1099 1277 587635880 587636058 1.040000e-61 248.0
24 TraesCS1A01G303800 chr3B 84.776 1005 145 6 1355 2355 584811684 584812684 0.000000e+00 1002.0
25 TraesCS1A01G303800 chr3B 78.605 1290 228 41 2448 3703 584812778 584814053 0.000000e+00 809.0
26 TraesCS1A01G303800 chr3B 91.620 179 15 0 1099 1277 584811506 584811684 1.040000e-61 248.0
27 TraesCS1A01G303800 chr3D 85.079 945 139 2 1412 2355 445858536 445859479 0.000000e+00 963.0
28 TraesCS1A01G303800 chr3D 78.809 1293 215 52 2448 3703 445859573 445860843 0.000000e+00 815.0
29 TraesCS1A01G303800 chr3D 91.620 179 15 0 1099 1277 445858301 445858479 1.040000e-61 248.0
30 TraesCS1A01G303800 chr7A 94.035 570 34 0 122 691 678158834 678159403 0.000000e+00 865.0
31 TraesCS1A01G303800 chr7A 91.549 568 33 3 122 688 685094010 685094563 0.000000e+00 769.0
32 TraesCS1A01G303800 chr7A 96.364 110 4 0 1 110 678158117 678158226 1.070000e-41 182.0
33 TraesCS1A01G303800 chr4A 92.644 571 34 4 122 692 456751771 456751209 0.000000e+00 815.0
34 TraesCS1A01G303800 chr4A 96.114 386 14 1 122 507 456939286 456938902 3.180000e-176 628.0
35 TraesCS1A01G303800 chr4A 96.748 123 4 0 1 123 456847171 456847049 6.340000e-49 206.0
36 TraesCS1A01G303800 chr4A 95.935 123 5 0 1 123 456752489 456752367 2.950000e-47 200.0
37 TraesCS1A01G303800 chr4A 95.935 123 5 0 1 123 456940005 456939883 2.950000e-47 200.0
38 TraesCS1A01G303800 chr5A 92.058 277 21 1 415 691 4954435 4954160 5.870000e-104 388.0
39 TraesCS1A01G303800 chr5A 92.664 259 18 1 122 380 4955014 4954757 5.910000e-99 372.0
40 TraesCS1A01G303800 chr5A 95.122 123 6 0 1 123 4955734 4955612 1.370000e-45 195.0
41 TraesCS1A01G303800 chr5B 72.690 963 219 32 1410 2347 35146953 35147896 1.020000e-71 281.0
42 TraesCS1A01G303800 chr5B 81.212 165 21 8 3127 3283 35148496 35148658 1.830000e-24 124.0
43 TraesCS1A01G303800 chrUn 95.041 121 6 0 3 123 312405654 312405534 1.780000e-44 191.0
44 TraesCS1A01G303800 chrUn 95.041 121 6 0 3 123 351212598 351212478 1.780000e-44 191.0
45 TraesCS1A01G303800 chr6A 93.388 121 8 0 3 123 202508188 202508308 3.840000e-41 180.0
46 TraesCS1A01G303800 chr6A 80.357 112 16 5 3589 3697 546929510 546929618 4.010000e-11 80.5
47 TraesCS1A01G303800 chr6D 74.138 290 61 9 2963 3242 400701400 400701685 1.840000e-19 108.0
48 TraesCS1A01G303800 chr6D 81.633 98 12 5 3603 3697 400701998 400702092 5.190000e-10 76.8
49 TraesCS1A01G303800 chr5D 83.186 113 19 0 4721 4833 217752498 217752610 2.380000e-18 104.0
50 TraesCS1A01G303800 chr6B 81.633 98 12 5 3603 3697 599758758 599758852 5.190000e-10 76.8


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 TraesCS1A01G303800 chr1A 497239787 497244621 4834 True 8929.000000 8929 100.000000 1 4835 1 chr1A.!!$R1 4834
1 TraesCS1A01G303800 chr1A 521625181 521626443 1262 False 511.500000 845 93.238500 1 684 2 chr1A.!!$F1 683
2 TraesCS1A01G303800 chr1D 401131275 401135239 3964 True 5967.000000 5967 93.809000 845 4835 1 chr1D.!!$R1 3990
3 TraesCS1A01G303800 chr1B 538864534 538868759 4225 True 2007.700000 5203 90.884000 785 4835 3 chr1B.!!$R2 4050
4 TraesCS1A01G303800 chr1B 625926307 625926865 558 True 409.000000 409 80.070000 122 688 1 chr1B.!!$R1 566
5 TraesCS1A01G303800 chr2D 612365140 612367700 2560 False 703.333333 1059 83.745333 1098 3790 3 chr2D.!!$F1 2692
6 TraesCS1A01G303800 chr2B 747237443 747239909 2466 False 693.333333 1059 83.579333 1098 3703 3 chr2B.!!$F1 2605
7 TraesCS1A01G303800 chr2A 744492118 744494571 2453 False 687.666667 1042 83.666333 1098 3703 3 chr2A.!!$F1 2605
8 TraesCS1A01G303800 chr2A 673029423 673029998 575 True 448.000000 448 81.229000 122 690 1 chr2A.!!$R1 568
9 TraesCS1A01G303800 chr3A 701636120 701636688 568 False 846.000000 846 93.509000 122 691 1 chr3A.!!$F2 569
10 TraesCS1A01G303800 chr3A 732486141 732486667 526 True 795.000000 795 93.939000 122 647 1 chr3A.!!$R1 525
11 TraesCS1A01G303800 chr3A 587635880 587638409 2529 False 693.666667 1007 85.142667 1099 3703 3 chr3A.!!$F3 2604
12 TraesCS1A01G303800 chr3A 594672364 594673049 685 False 693.000000 693 84.979000 4142 4835 1 chr3A.!!$F1 693
13 TraesCS1A01G303800 chr3B 584811506 584814053 2547 False 686.333333 1002 85.000333 1099 3703 3 chr3B.!!$F1 2604
14 TraesCS1A01G303800 chr3D 445858301 445860843 2542 False 675.333333 963 85.169333 1099 3703 3 chr3D.!!$F1 2604
15 TraesCS1A01G303800 chr7A 685094010 685094563 553 False 769.000000 769 91.549000 122 688 1 chr7A.!!$F1 566
16 TraesCS1A01G303800 chr7A 678158117 678159403 1286 False 523.500000 865 95.199500 1 691 2 chr7A.!!$F2 690
17 TraesCS1A01G303800 chr4A 456751209 456752489 1280 True 507.500000 815 94.289500 1 692 2 chr4A.!!$R2 691
18 TraesCS1A01G303800 chr4A 456938902 456940005 1103 True 414.000000 628 96.024500 1 507 2 chr4A.!!$R3 506
19 TraesCS1A01G303800 chr5A 4954160 4955734 1574 True 318.333333 388 93.281333 1 691 3 chr5A.!!$R1 690
20 TraesCS1A01G303800 chr5B 35146953 35148658 1705 False 202.500000 281 76.951000 1410 3283 2 chr5B.!!$F1 1873

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
783 1700 0.034756 TCCGTGTGTGTAGCATTGCT 59.965 50.0 16.63 16.63 43.41 3.91 F
899 1850 0.036858 GAACCAGCCACACTCCTCTC 60.037 60.0 0.00 0.00 0.00 3.20 F
2388 3379 0.096976 CTCGCGCGGATTTGAACAAT 59.903 50.0 31.69 0.00 0.00 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2365 3355 0.179111 TTCAAATCCGCGCGAGAGAT 60.179 50.0 34.63 22.54 0.0 2.75 R
2427 3422 0.524604 GCAACCACAACAACACCGAC 60.525 55.0 0.00 0.00 0.0 4.79 R
4324 5856 1.100510 TACCCGACGTCTCTTCATGG 58.899 55.0 14.70 5.19 0.0 3.66 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
94 95 1.132817 AGACCCCTTATATGCGGACCT 60.133 52.381 0.00 0.00 0.00 3.85
110 111 4.330894 GCGGACCTTTATAGTGTGTTTACC 59.669 45.833 0.00 0.00 0.00 2.85
117 118 7.039784 ACCTTTATAGTGTGTTTACCGTGTCTA 60.040 37.037 0.00 0.00 0.00 2.59
127 729 4.465632 TTACCGTGTCTATTCAGTGCAT 57.534 40.909 0.00 0.00 0.00 3.96
302 918 1.064357 CAACAACGGTGGTGTGGTTAC 59.936 52.381 11.27 0.00 37.70 2.50
504 1413 1.877637 TACATGCACAACGCTTCAGT 58.122 45.000 0.00 0.00 43.06 3.41
507 1416 1.198408 CATGCACAACGCTTCAGTCAT 59.802 47.619 0.00 0.00 43.06 3.06
524 1433 2.929964 ATTGACAATGGGCCCCGGT 61.930 57.895 22.27 15.12 0.00 5.28
649 1565 5.771469 CAAGTTTATGCATCAAACTGACCA 58.229 37.500 23.22 0.00 43.62 4.02
692 1609 6.890293 ACTCCTGATGTATTTACCTCTTTCC 58.110 40.000 0.00 0.00 0.00 3.13
693 1610 6.443849 ACTCCTGATGTATTTACCTCTTTCCA 59.556 38.462 0.00 0.00 0.00 3.53
694 1611 7.127955 ACTCCTGATGTATTTACCTCTTTCCAT 59.872 37.037 0.00 0.00 0.00 3.41
695 1612 8.561536 TCCTGATGTATTTACCTCTTTCCATA 57.438 34.615 0.00 0.00 0.00 2.74
696 1613 8.429641 TCCTGATGTATTTACCTCTTTCCATAC 58.570 37.037 0.00 0.00 0.00 2.39
697 1614 8.432805 CCTGATGTATTTACCTCTTTCCATACT 58.567 37.037 0.00 0.00 0.00 2.12
705 1622 7.613551 TTACCTCTTTCCATACTAATCTCCC 57.386 40.000 0.00 0.00 0.00 4.30
706 1623 4.908481 ACCTCTTTCCATACTAATCTCCCC 59.092 45.833 0.00 0.00 0.00 4.81
707 1624 4.287326 CCTCTTTCCATACTAATCTCCCCC 59.713 50.000 0.00 0.00 0.00 5.40
721 1638 3.200565 CCCCCACCCCCTTGATTT 58.799 61.111 0.00 0.00 0.00 2.17
722 1639 1.473844 CCCCCACCCCCTTGATTTT 59.526 57.895 0.00 0.00 0.00 1.82
723 1640 0.617535 CCCCCACCCCCTTGATTTTC 60.618 60.000 0.00 0.00 0.00 2.29
724 1641 0.116143 CCCCACCCCCTTGATTTTCA 59.884 55.000 0.00 0.00 0.00 2.69
725 1642 1.560505 CCCACCCCCTTGATTTTCAG 58.439 55.000 0.00 0.00 0.00 3.02
726 1643 1.203174 CCCACCCCCTTGATTTTCAGT 60.203 52.381 0.00 0.00 0.00 3.41
727 1644 1.895131 CCACCCCCTTGATTTTCAGTG 59.105 52.381 0.00 0.00 0.00 3.66
728 1645 1.895131 CACCCCCTTGATTTTCAGTGG 59.105 52.381 0.00 0.00 0.00 4.00
729 1646 1.203174 ACCCCCTTGATTTTCAGTGGG 60.203 52.381 9.40 9.40 39.84 4.61
730 1647 1.077005 CCCCCTTGATTTTCAGTGGGA 59.923 52.381 15.06 0.00 41.45 4.37
731 1648 2.292455 CCCCCTTGATTTTCAGTGGGAT 60.292 50.000 15.06 0.00 41.45 3.85
732 1649 2.762327 CCCCTTGATTTTCAGTGGGATG 59.238 50.000 15.06 1.68 41.45 3.51
733 1650 3.434309 CCCTTGATTTTCAGTGGGATGT 58.566 45.455 10.37 0.00 41.45 3.06
734 1651 3.194116 CCCTTGATTTTCAGTGGGATGTG 59.806 47.826 10.37 0.00 41.45 3.21
735 1652 3.828451 CCTTGATTTTCAGTGGGATGTGT 59.172 43.478 0.00 0.00 0.00 3.72
736 1653 4.321452 CCTTGATTTTCAGTGGGATGTGTG 60.321 45.833 0.00 0.00 0.00 3.82
737 1654 2.557924 TGATTTTCAGTGGGATGTGTGC 59.442 45.455 0.00 0.00 0.00 4.57
738 1655 1.327303 TTTTCAGTGGGATGTGTGCC 58.673 50.000 0.00 0.00 36.16 5.01
739 1656 0.184692 TTTCAGTGGGATGTGTGCCA 59.815 50.000 0.00 0.00 44.40 4.92
743 1660 4.762016 TGGGATGTGTGCCAATCC 57.238 55.556 0.00 0.00 43.55 3.01
744 1661 1.378382 TGGGATGTGTGCCAATCCG 60.378 57.895 0.00 0.00 43.55 4.18
745 1662 1.378514 GGGATGTGTGCCAATCCGT 60.379 57.895 0.00 0.00 35.58 4.69
746 1663 0.965363 GGGATGTGTGCCAATCCGTT 60.965 55.000 0.00 0.00 35.58 4.44
747 1664 0.171007 GGATGTGTGCCAATCCGTTG 59.829 55.000 0.00 0.00 35.05 4.10
748 1665 1.164411 GATGTGTGCCAATCCGTTGA 58.836 50.000 0.00 0.00 37.53 3.18
749 1666 1.745087 GATGTGTGCCAATCCGTTGAT 59.255 47.619 0.00 0.00 37.53 2.57
750 1667 1.614996 TGTGTGCCAATCCGTTGATT 58.385 45.000 0.00 0.00 41.96 2.57
751 1668 1.539388 TGTGTGCCAATCCGTTGATTC 59.461 47.619 0.00 0.00 39.20 2.52
752 1669 1.135402 GTGTGCCAATCCGTTGATTCC 60.135 52.381 0.00 0.00 39.20 3.01
753 1670 0.455815 GTGCCAATCCGTTGATTCCC 59.544 55.000 0.00 0.00 39.20 3.97
754 1671 0.331278 TGCCAATCCGTTGATTCCCT 59.669 50.000 0.00 0.00 39.20 4.20
755 1672 1.562008 TGCCAATCCGTTGATTCCCTA 59.438 47.619 0.00 0.00 39.20 3.53
756 1673 2.025793 TGCCAATCCGTTGATTCCCTAA 60.026 45.455 0.00 0.00 39.20 2.69
757 1674 3.020984 GCCAATCCGTTGATTCCCTAAA 58.979 45.455 0.00 0.00 39.20 1.85
758 1675 3.445805 GCCAATCCGTTGATTCCCTAAAA 59.554 43.478 0.00 0.00 39.20 1.52
759 1676 4.081917 GCCAATCCGTTGATTCCCTAAAAA 60.082 41.667 0.00 0.00 39.20 1.94
760 1677 5.395214 GCCAATCCGTTGATTCCCTAAAAAT 60.395 40.000 0.00 0.00 39.20 1.82
761 1678 6.273071 CCAATCCGTTGATTCCCTAAAAATC 58.727 40.000 0.00 0.00 39.20 2.17
762 1679 6.127479 CCAATCCGTTGATTCCCTAAAAATCA 60.127 38.462 0.00 0.00 39.20 2.57
763 1680 6.699575 ATCCGTTGATTCCCTAAAAATCAG 57.300 37.500 0.00 0.00 42.40 2.90
764 1681 5.566469 TCCGTTGATTCCCTAAAAATCAGT 58.434 37.500 0.00 0.00 42.40 3.41
765 1682 5.646360 TCCGTTGATTCCCTAAAAATCAGTC 59.354 40.000 0.00 0.00 42.40 3.51
766 1683 5.163652 CCGTTGATTCCCTAAAAATCAGTCC 60.164 44.000 0.00 0.00 42.40 3.85
767 1684 5.447279 CGTTGATTCCCTAAAAATCAGTCCG 60.447 44.000 0.00 0.00 42.40 4.79
768 1685 5.174037 TGATTCCCTAAAAATCAGTCCGT 57.826 39.130 0.00 0.00 38.02 4.69
769 1686 4.941263 TGATTCCCTAAAAATCAGTCCGTG 59.059 41.667 0.00 0.00 38.02 4.94
770 1687 4.360951 TTCCCTAAAAATCAGTCCGTGT 57.639 40.909 0.00 0.00 0.00 4.49
771 1688 3.670625 TCCCTAAAAATCAGTCCGTGTG 58.329 45.455 0.00 0.00 0.00 3.82
772 1689 3.071892 TCCCTAAAAATCAGTCCGTGTGT 59.928 43.478 0.00 0.00 0.00 3.72
773 1690 3.188460 CCCTAAAAATCAGTCCGTGTGTG 59.812 47.826 0.00 0.00 0.00 3.82
774 1691 3.813166 CCTAAAAATCAGTCCGTGTGTGT 59.187 43.478 0.00 0.00 0.00 3.72
775 1692 4.992319 CCTAAAAATCAGTCCGTGTGTGTA 59.008 41.667 0.00 0.00 0.00 2.90
776 1693 5.120208 CCTAAAAATCAGTCCGTGTGTGTAG 59.880 44.000 0.00 0.00 0.00 2.74
777 1694 2.080286 AATCAGTCCGTGTGTGTAGC 57.920 50.000 0.00 0.00 0.00 3.58
778 1695 0.966179 ATCAGTCCGTGTGTGTAGCA 59.034 50.000 0.00 0.00 0.00 3.49
779 1696 0.966179 TCAGTCCGTGTGTGTAGCAT 59.034 50.000 0.00 0.00 0.00 3.79
780 1697 1.343142 TCAGTCCGTGTGTGTAGCATT 59.657 47.619 0.00 0.00 0.00 3.56
781 1698 1.460743 CAGTCCGTGTGTGTAGCATTG 59.539 52.381 0.00 0.00 0.00 2.82
782 1699 0.165944 GTCCGTGTGTGTAGCATTGC 59.834 55.000 0.00 0.00 0.00 3.56
783 1700 0.034756 TCCGTGTGTGTAGCATTGCT 59.965 50.000 16.63 16.63 43.41 3.91
803 1720 1.643832 CGGCCGAAATTAGCAGCTC 59.356 57.895 24.07 0.00 0.00 4.09
804 1721 1.776034 CGGCCGAAATTAGCAGCTCC 61.776 60.000 24.07 0.00 0.00 4.70
805 1722 0.464554 GGCCGAAATTAGCAGCTCCT 60.465 55.000 0.00 0.00 0.00 3.69
806 1723 0.940833 GCCGAAATTAGCAGCTCCTC 59.059 55.000 0.00 0.00 0.00 3.71
899 1850 0.036858 GAACCAGCCACACTCCTCTC 60.037 60.000 0.00 0.00 0.00 3.20
900 1851 0.472734 AACCAGCCACACTCCTCTCT 60.473 55.000 0.00 0.00 0.00 3.10
1285 2254 1.359475 GAGATCCTCGTACGTGCCC 59.641 63.158 16.05 4.67 0.00 5.36
1300 2269 1.410153 GTGCCCTGCCTCCATTAATTG 59.590 52.381 0.00 0.00 0.00 2.32
1304 2273 3.902218 CCCTGCCTCCATTAATTGAGAA 58.098 45.455 16.22 5.30 0.00 2.87
1305 2274 3.633986 CCCTGCCTCCATTAATTGAGAAC 59.366 47.826 16.22 9.43 0.00 3.01
1306 2275 4.272489 CCTGCCTCCATTAATTGAGAACA 58.728 43.478 16.22 12.70 0.00 3.18
1307 2276 4.891756 CCTGCCTCCATTAATTGAGAACAT 59.108 41.667 16.22 0.00 0.00 2.71
1334 2315 0.662374 CTTGCTTGCTTGCTCAACGG 60.662 55.000 3.47 0.00 0.00 4.44
2357 3347 0.606673 GGAAGGGACAAGCAGGTGAC 60.607 60.000 0.00 0.00 0.00 3.67
2358 3348 0.606673 GAAGGGACAAGCAGGTGACC 60.607 60.000 0.00 0.00 33.21 4.02
2359 3349 1.352622 AAGGGACAAGCAGGTGACCA 61.353 55.000 3.63 0.00 35.35 4.02
2360 3350 1.136329 AGGGACAAGCAGGTGACCAT 61.136 55.000 3.63 0.00 35.35 3.55
2361 3351 0.678048 GGGACAAGCAGGTGACCATC 60.678 60.000 3.63 0.00 35.35 3.51
2363 3353 1.271597 GGACAAGCAGGTGACCATCTT 60.272 52.381 3.63 3.30 34.03 2.40
2364 3354 2.079925 GACAAGCAGGTGACCATCTTC 58.920 52.381 3.63 0.00 0.00 2.87
2365 3355 1.421268 ACAAGCAGGTGACCATCTTCA 59.579 47.619 3.63 0.00 0.00 3.02
2374 3365 1.066152 TGACCATCTTCATCTCTCGCG 59.934 52.381 0.00 0.00 0.00 5.87
2376 3367 1.274126 CCATCTTCATCTCTCGCGCG 61.274 60.000 26.76 26.76 0.00 6.86
2381 3372 0.179111 TTCATCTCTCGCGCGGATTT 60.179 50.000 31.69 12.69 0.00 2.17
2382 3373 0.871592 TCATCTCTCGCGCGGATTTG 60.872 55.000 31.69 22.05 0.00 2.32
2384 3375 0.179111 ATCTCTCGCGCGGATTTGAA 60.179 50.000 31.69 7.55 0.00 2.69
2385 3376 1.076533 TCTCTCGCGCGGATTTGAAC 61.077 55.000 31.69 0.00 0.00 3.18
2386 3377 1.351430 CTCTCGCGCGGATTTGAACA 61.351 55.000 31.69 5.83 0.00 3.18
2387 3378 0.946700 TCTCGCGCGGATTTGAACAA 60.947 50.000 31.69 4.97 0.00 2.83
2388 3379 0.096976 CTCGCGCGGATTTGAACAAT 59.903 50.000 31.69 0.00 0.00 2.71
2389 3380 0.519519 TCGCGCGGATTTGAACAATT 59.480 45.000 31.69 0.00 0.00 2.32
2390 3381 1.068885 TCGCGCGGATTTGAACAATTT 60.069 42.857 31.69 0.00 0.00 1.82
2392 3383 2.323959 GCGCGGATTTGAACAATTTCA 58.676 42.857 8.83 0.00 40.14 2.69
2405 3396 7.176285 TGAACAATTTCAATTTGCAACTAGC 57.824 32.000 0.00 0.00 38.87 3.42
2406 3397 6.985645 TGAACAATTTCAATTTGCAACTAGCT 59.014 30.769 0.00 0.00 40.58 3.32
2407 3398 8.140628 TGAACAATTTCAATTTGCAACTAGCTA 58.859 29.630 0.00 0.00 40.58 3.32
2411 3402 2.677836 TCAATTTGCAACTAGCTAGCGG 59.322 45.455 20.91 13.63 45.94 5.52
2412 3403 1.668419 ATTTGCAACTAGCTAGCGGG 58.332 50.000 20.91 11.14 45.94 6.13
2414 3405 2.962253 GCAACTAGCTAGCGGGCG 60.962 66.667 20.91 5.95 41.15 6.13
2427 3422 3.124921 GGGCGAACGTGACATGGG 61.125 66.667 0.00 0.00 0.00 4.00
2859 4115 1.714414 CGTCGGTCAGTAGTCCTCG 59.286 63.158 0.00 0.00 0.00 4.63
2863 4119 2.287373 GTCGGTCAGTAGTCCTCGTATG 59.713 54.545 0.00 0.00 0.00 2.39
2865 4121 1.337387 GGTCAGTAGTCCTCGTATGCC 59.663 57.143 0.00 0.00 0.00 4.40
3122 4431 2.932622 GCTTCAACGAGAGCATCCTCAA 60.933 50.000 0.00 0.00 40.68 3.02
3713 5058 2.815647 GCAGTACCAGCTCACCGC 60.816 66.667 0.93 0.00 39.57 5.68
3714 5059 2.507102 CAGTACCAGCTCACCGCG 60.507 66.667 0.00 0.00 45.59 6.46
3858 5209 5.760253 ACACGATAGCTCTTGATTAATTGGG 59.240 40.000 0.00 0.00 42.67 4.12
3862 5213 6.146837 CGATAGCTCTTGATTAATTGGGTCTG 59.853 42.308 0.00 0.00 0.00 3.51
3983 5334 5.700832 TGTTTTCTGCTATGTAGACCTTGTG 59.299 40.000 0.00 0.00 0.00 3.33
4020 5371 6.084326 TGGTTTTTGTAATGAGAAGAAGGC 57.916 37.500 0.00 0.00 0.00 4.35
4101 5630 6.942532 TGGTGTCCTGCATAGAAATTTATC 57.057 37.500 0.00 0.00 0.00 1.75
4106 5635 7.712639 GTGTCCTGCATAGAAATTTATCTCTCA 59.287 37.037 0.00 0.00 0.00 3.27
4107 5636 8.435187 TGTCCTGCATAGAAATTTATCTCTCAT 58.565 33.333 0.00 0.00 0.00 2.90
4109 5638 9.857656 TCCTGCATAGAAATTTATCTCTCATTT 57.142 29.630 0.00 0.00 0.00 2.32
4171 5702 6.038271 GCGGGTGAGAAAATTGTATTACTCAT 59.962 38.462 0.00 0.00 36.89 2.90
4192 5723 6.653020 TCATGAGTAGCAAGGTTACAATCAT 58.347 36.000 0.00 0.00 0.00 2.45
4194 5725 5.428253 TGAGTAGCAAGGTTACAATCATCC 58.572 41.667 0.00 0.00 0.00 3.51
4232 5764 2.269241 GGAGGGCGAGAACCAAGG 59.731 66.667 0.00 0.00 0.00 3.61
4257 5789 1.626321 TCATGGTTCTGCCTTCCGTTA 59.374 47.619 0.00 0.00 38.35 3.18
4258 5790 2.238646 TCATGGTTCTGCCTTCCGTTAT 59.761 45.455 0.00 0.00 38.35 1.89
4291 5823 7.464830 TTTGCTAGATCATCGCTAACTTTAC 57.535 36.000 0.00 0.00 0.00 2.01
4324 5856 6.195983 CCGACTTACATGAGTAATACGACAAC 59.804 42.308 0.00 0.00 39.36 3.32
4327 5859 7.553334 ACTTACATGAGTAATACGACAACCAT 58.447 34.615 0.00 0.00 39.36 3.55
4328 5860 7.491372 ACTTACATGAGTAATACGACAACCATG 59.509 37.037 0.00 0.00 39.36 3.66
4336 5868 2.065993 ACGACAACCATGAAGAGACG 57.934 50.000 0.00 0.00 0.00 4.18
4339 5871 1.986378 GACAACCATGAAGAGACGTCG 59.014 52.381 10.46 0.00 0.00 5.12
4363 5895 7.284034 TCGGGTACTTAATCTCCTTAACTACAG 59.716 40.741 0.00 0.00 0.00 2.74
4368 5912 6.898521 ACTTAATCTCCTTAACTACAGAGGCT 59.101 38.462 0.00 0.00 0.00 4.58
4386 5930 2.887783 GGCTTAGATCGATCTGTCCAGA 59.112 50.000 33.22 13.18 42.37 3.86
4422 5966 5.651387 TCAACTTCACAACAACAATGGAA 57.349 34.783 0.00 0.00 0.00 3.53
4453 5997 1.557443 GATATTTGGGGCGTCGCTCG 61.557 60.000 18.11 0.00 43.12 5.03
4472 6016 4.574828 GCTCGGTTGGATAGCAAAAGATAA 59.425 41.667 0.00 0.00 36.26 1.75
4489 6033 8.522830 CAAAAGATAAACCTTCCATACACACAT 58.477 33.333 0.00 0.00 0.00 3.21
4491 6035 8.732746 AAGATAAACCTTCCATACACACATAC 57.267 34.615 0.00 0.00 0.00 2.39
4502 6046 1.897133 ACACACATACAGTTCCGCCTA 59.103 47.619 0.00 0.00 0.00 3.93
4577 6122 3.119849 CCACAATCATTCCGAAGAACCAC 60.120 47.826 0.00 0.00 33.97 4.16
4691 6237 4.111198 GTGTCATCAGTCTATGTGAGCTG 58.889 47.826 0.00 0.00 0.00 4.24
4692 6238 3.122297 GTCATCAGTCTATGTGAGCTGC 58.878 50.000 0.00 0.00 0.00 5.25
4693 6239 3.029570 TCATCAGTCTATGTGAGCTGCT 58.970 45.455 0.00 0.00 0.00 4.24
4694 6240 3.450096 TCATCAGTCTATGTGAGCTGCTT 59.550 43.478 2.53 0.00 0.00 3.91
4695 6241 3.242549 TCAGTCTATGTGAGCTGCTTG 57.757 47.619 2.53 0.00 0.00 4.01
4696 6242 1.664659 CAGTCTATGTGAGCTGCTTGC 59.335 52.381 2.53 0.16 43.29 4.01
4724 6270 7.521099 GCTTGCTGCAACATTATACATCACTAT 60.521 37.037 11.69 0.00 42.31 2.12
4767 6313 7.714377 GGATCATCACATAGATCAAGTTTCAGT 59.286 37.037 0.00 0.00 41.84 3.41
4819 6365 6.705381 AAGAAATCTCTTAGATGCTTCCATCG 59.295 38.462 0.00 0.00 42.11 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 95 9.357652 GAATAGACACGGTAAACACACTATAAA 57.642 33.333 0.00 0.00 0.00 1.40
110 111 6.588348 TTCATTATGCACTGAATAGACACG 57.412 37.500 0.00 0.00 0.00 4.49
117 118 6.971726 ATGGACATTCATTATGCACTGAAT 57.028 33.333 12.75 12.75 41.56 2.57
267 874 3.798337 CGTTGTTGTTTACACGGACTACT 59.202 43.478 0.00 0.00 36.21 2.57
458 1364 3.857157 TTTGTAGAAGCACCCTCAAGT 57.143 42.857 0.00 0.00 0.00 3.16
504 1413 1.379710 CGGGGCCCATTGTCAATGA 60.380 57.895 26.86 0.00 41.46 2.57
507 1416 3.577334 GACCGGGGCCCATTGTCAA 62.577 63.158 26.86 0.00 0.00 3.18
541 1450 3.388024 ACACGGATGTATTCACTGCCTAT 59.612 43.478 0.00 0.00 37.26 2.57
567 1482 3.602062 CGTGCAAATACGGTCACATTTTC 59.398 43.478 0.00 0.00 40.22 2.29
568 1483 3.560503 CGTGCAAATACGGTCACATTTT 58.439 40.909 0.00 0.00 40.22 1.82
609 1525 9.388346 CATAAACTTGCAAAATACGTGTTTCTA 57.612 29.630 10.88 0.00 0.00 2.10
649 1565 4.177026 GAGTCATAGAACTTGCACGTGAT 58.823 43.478 22.23 0.00 0.00 3.06
704 1621 0.617535 GAAAATCAAGGGGGTGGGGG 60.618 60.000 0.00 0.00 0.00 5.40
705 1622 0.116143 TGAAAATCAAGGGGGTGGGG 59.884 55.000 0.00 0.00 0.00 4.96
706 1623 1.203174 ACTGAAAATCAAGGGGGTGGG 60.203 52.381 0.00 0.00 0.00 4.61
707 1624 1.895131 CACTGAAAATCAAGGGGGTGG 59.105 52.381 0.00 0.00 0.00 4.61
708 1625 1.895131 CCACTGAAAATCAAGGGGGTG 59.105 52.381 0.00 0.00 0.00 4.61
709 1626 1.203174 CCCACTGAAAATCAAGGGGGT 60.203 52.381 1.57 0.00 37.84 4.95
710 1627 1.077005 TCCCACTGAAAATCAAGGGGG 59.923 52.381 3.43 3.43 40.36 5.40
711 1628 2.603075 TCCCACTGAAAATCAAGGGG 57.397 50.000 14.21 11.63 40.36 4.79
712 1629 3.194116 CACATCCCACTGAAAATCAAGGG 59.806 47.826 9.98 9.98 40.95 3.95
713 1630 3.828451 ACACATCCCACTGAAAATCAAGG 59.172 43.478 0.00 0.00 0.00 3.61
714 1631 4.801891 CACACATCCCACTGAAAATCAAG 58.198 43.478 0.00 0.00 0.00 3.02
715 1632 3.005684 GCACACATCCCACTGAAAATCAA 59.994 43.478 0.00 0.00 0.00 2.57
716 1633 2.557924 GCACACATCCCACTGAAAATCA 59.442 45.455 0.00 0.00 0.00 2.57
717 1634 2.094545 GGCACACATCCCACTGAAAATC 60.095 50.000 0.00 0.00 0.00 2.17
718 1635 1.895131 GGCACACATCCCACTGAAAAT 59.105 47.619 0.00 0.00 0.00 1.82
719 1636 1.327303 GGCACACATCCCACTGAAAA 58.673 50.000 0.00 0.00 0.00 2.29
720 1637 0.184692 TGGCACACATCCCACTGAAA 59.815 50.000 0.00 0.00 0.00 2.69
721 1638 0.184692 TTGGCACACATCCCACTGAA 59.815 50.000 0.00 0.00 39.29 3.02
722 1639 0.405198 ATTGGCACACATCCCACTGA 59.595 50.000 0.00 0.00 39.29 3.41
723 1640 0.813184 GATTGGCACACATCCCACTG 59.187 55.000 0.00 0.00 39.29 3.66
724 1641 0.323725 GGATTGGCACACATCCCACT 60.324 55.000 5.53 0.00 39.29 4.00
725 1642 1.656818 CGGATTGGCACACATCCCAC 61.657 60.000 10.37 0.00 40.43 4.61
726 1643 1.378382 CGGATTGGCACACATCCCA 60.378 57.895 10.37 0.00 40.43 4.37
727 1644 0.965363 AACGGATTGGCACACATCCC 60.965 55.000 10.37 0.00 40.43 3.85
728 1645 0.171007 CAACGGATTGGCACACATCC 59.829 55.000 6.62 6.62 39.29 3.51
729 1646 1.164411 TCAACGGATTGGCACACATC 58.836 50.000 0.00 0.00 39.29 3.06
730 1647 1.838112 ATCAACGGATTGGCACACAT 58.162 45.000 0.00 0.00 39.29 3.21
731 1648 1.539388 GAATCAACGGATTGGCACACA 59.461 47.619 0.00 0.00 43.69 3.72
732 1649 1.135402 GGAATCAACGGATTGGCACAC 60.135 52.381 0.00 0.00 43.69 3.82
733 1650 1.173043 GGAATCAACGGATTGGCACA 58.827 50.000 0.00 0.00 43.69 4.57
734 1651 0.455815 GGGAATCAACGGATTGGCAC 59.544 55.000 0.00 0.00 43.69 5.01
735 1652 0.331278 AGGGAATCAACGGATTGGCA 59.669 50.000 0.00 0.00 43.69 4.92
736 1653 2.341846 TAGGGAATCAACGGATTGGC 57.658 50.000 0.00 0.00 43.69 4.52
737 1654 5.652994 TTTTTAGGGAATCAACGGATTGG 57.347 39.130 0.00 0.00 43.69 3.16
738 1655 6.862209 TGATTTTTAGGGAATCAACGGATTG 58.138 36.000 0.00 0.00 43.69 2.67
739 1656 6.663523 ACTGATTTTTAGGGAATCAACGGATT 59.336 34.615 1.77 0.00 46.27 3.01
740 1657 6.187682 ACTGATTTTTAGGGAATCAACGGAT 58.812 36.000 1.77 0.00 41.49 4.18
741 1658 5.566469 ACTGATTTTTAGGGAATCAACGGA 58.434 37.500 1.77 0.00 41.49 4.69
742 1659 5.163652 GGACTGATTTTTAGGGAATCAACGG 60.164 44.000 1.77 0.00 41.49 4.44
743 1660 5.447279 CGGACTGATTTTTAGGGAATCAACG 60.447 44.000 1.77 3.56 41.49 4.10
744 1661 5.414765 ACGGACTGATTTTTAGGGAATCAAC 59.585 40.000 1.77 0.23 41.49 3.18
745 1662 5.414454 CACGGACTGATTTTTAGGGAATCAA 59.586 40.000 1.77 0.00 41.49 2.57
746 1663 4.941263 CACGGACTGATTTTTAGGGAATCA 59.059 41.667 0.00 0.00 40.24 2.57
747 1664 4.941873 ACACGGACTGATTTTTAGGGAATC 59.058 41.667 0.00 0.00 34.78 2.52
748 1665 4.700213 CACACGGACTGATTTTTAGGGAAT 59.300 41.667 0.00 0.00 0.00 3.01
749 1666 4.069304 CACACGGACTGATTTTTAGGGAA 58.931 43.478 0.00 0.00 0.00 3.97
750 1667 3.071892 ACACACGGACTGATTTTTAGGGA 59.928 43.478 0.00 0.00 0.00 4.20
751 1668 3.188460 CACACACGGACTGATTTTTAGGG 59.812 47.826 0.00 0.00 0.00 3.53
752 1669 3.813166 ACACACACGGACTGATTTTTAGG 59.187 43.478 0.00 0.00 0.00 2.69
753 1670 5.389516 GCTACACACACGGACTGATTTTTAG 60.390 44.000 0.00 0.00 0.00 1.85
754 1671 4.449743 GCTACACACACGGACTGATTTTTA 59.550 41.667 0.00 0.00 0.00 1.52
755 1672 3.250040 GCTACACACACGGACTGATTTTT 59.750 43.478 0.00 0.00 0.00 1.94
756 1673 2.806244 GCTACACACACGGACTGATTTT 59.194 45.455 0.00 0.00 0.00 1.82
757 1674 2.224185 TGCTACACACACGGACTGATTT 60.224 45.455 0.00 0.00 0.00 2.17
758 1675 1.343142 TGCTACACACACGGACTGATT 59.657 47.619 0.00 0.00 0.00 2.57
759 1676 0.966179 TGCTACACACACGGACTGAT 59.034 50.000 0.00 0.00 0.00 2.90
760 1677 0.966179 ATGCTACACACACGGACTGA 59.034 50.000 0.00 0.00 0.00 3.41
761 1678 1.460743 CAATGCTACACACACGGACTG 59.539 52.381 0.00 0.00 0.00 3.51
762 1679 1.795768 CAATGCTACACACACGGACT 58.204 50.000 0.00 0.00 0.00 3.85
763 1680 0.165944 GCAATGCTACACACACGGAC 59.834 55.000 0.00 0.00 0.00 4.79
764 1681 0.034756 AGCAATGCTACACACACGGA 59.965 50.000 5.69 0.00 36.99 4.69
765 1682 0.443869 GAGCAATGCTACACACACGG 59.556 55.000 8.12 0.00 39.88 4.94
766 1683 0.443869 GGAGCAATGCTACACACACG 59.556 55.000 13.46 0.00 39.71 4.49
767 1684 0.443869 CGGAGCAATGCTACACACAC 59.556 55.000 18.59 0.00 39.98 3.82
768 1685 0.673333 CCGGAGCAATGCTACACACA 60.673 55.000 18.59 0.00 39.98 3.72
769 1686 1.982073 GCCGGAGCAATGCTACACAC 61.982 60.000 18.59 1.79 39.98 3.82
770 1687 1.745115 GCCGGAGCAATGCTACACA 60.745 57.895 18.59 0.00 39.98 3.72
771 1688 2.472909 GGCCGGAGCAATGCTACAC 61.473 63.158 18.59 8.59 39.98 2.90
772 1689 2.124736 GGCCGGAGCAATGCTACA 60.125 61.111 18.59 0.00 39.98 2.74
773 1690 3.272334 CGGCCGGAGCAATGCTAC 61.272 66.667 20.10 7.82 39.88 3.58
774 1691 2.529454 TTTCGGCCGGAGCAATGCTA 62.529 55.000 27.83 0.00 39.88 3.49
775 1692 3.918253 TTTCGGCCGGAGCAATGCT 62.918 57.895 27.83 7.79 43.88 3.79
776 1693 2.283472 AATTTCGGCCGGAGCAATGC 62.283 55.000 27.83 0.00 42.56 3.56
777 1694 1.002468 CTAATTTCGGCCGGAGCAATG 60.002 52.381 27.83 6.88 42.56 2.82
778 1695 1.308998 CTAATTTCGGCCGGAGCAAT 58.691 50.000 27.83 15.37 42.56 3.56
779 1696 1.373590 GCTAATTTCGGCCGGAGCAA 61.374 55.000 27.83 9.47 42.56 3.91
780 1697 1.817941 GCTAATTTCGGCCGGAGCA 60.818 57.895 27.83 1.56 42.56 4.26
781 1698 1.776034 CTGCTAATTTCGGCCGGAGC 61.776 60.000 27.83 23.98 38.76 4.70
782 1699 1.776034 GCTGCTAATTTCGGCCGGAG 61.776 60.000 27.83 15.50 0.00 4.63
783 1700 1.817941 GCTGCTAATTTCGGCCGGA 60.818 57.895 27.83 16.16 0.00 5.14
803 1720 3.775654 GGCGGTGAGTGGGAGAGG 61.776 72.222 0.00 0.00 0.00 3.69
804 1721 4.135153 CGGCGGTGAGTGGGAGAG 62.135 72.222 0.00 0.00 0.00 3.20
835 1752 2.092429 TGAAGAGAGAGAGAGAGGGAGC 60.092 54.545 0.00 0.00 0.00 4.70
839 1756 5.009631 TCAAAGTGAAGAGAGAGAGAGAGG 58.990 45.833 0.00 0.00 0.00 3.69
1285 2254 5.591472 TCATGTTCTCAATTAATGGAGGCAG 59.409 40.000 18.07 11.51 0.00 4.85
1300 2269 4.413087 CAAGCAAGCAGAATCATGTTCTC 58.587 43.478 7.35 4.53 0.00 2.87
1304 2273 2.168496 AGCAAGCAAGCAGAATCATGT 58.832 42.857 3.19 0.00 36.85 3.21
1305 2274 2.923655 CAAGCAAGCAAGCAGAATCATG 59.076 45.455 3.19 0.00 36.85 3.07
1306 2275 2.674177 GCAAGCAAGCAAGCAGAATCAT 60.674 45.455 3.19 0.00 36.85 2.45
1307 2276 1.336517 GCAAGCAAGCAAGCAGAATCA 60.337 47.619 3.19 0.00 36.85 2.57
1334 2315 0.914551 CTGCAGCACATACGTACGTC 59.085 55.000 26.53 10.24 0.00 4.34
1464 2445 3.622704 CGACCAGGAAGAGGAAGTAGAGA 60.623 52.174 0.00 0.00 0.00 3.10
2357 3347 1.274126 CGCGCGAGAGATGAAGATGG 61.274 60.000 28.94 0.00 0.00 3.51
2358 3348 1.274126 CCGCGCGAGAGATGAAGATG 61.274 60.000 34.63 5.25 0.00 2.90
2359 3349 1.007964 CCGCGCGAGAGATGAAGAT 60.008 57.895 34.63 0.00 0.00 2.40
2360 3350 1.448119 ATCCGCGCGAGAGATGAAGA 61.448 55.000 34.63 17.01 0.00 2.87
2361 3351 0.596083 AATCCGCGCGAGAGATGAAG 60.596 55.000 34.63 11.36 0.00 3.02
2363 3353 0.871592 CAAATCCGCGCGAGAGATGA 60.872 55.000 34.63 19.47 0.00 2.92
2364 3354 0.871592 TCAAATCCGCGCGAGAGATG 60.872 55.000 34.63 24.93 0.00 2.90
2365 3355 0.179111 TTCAAATCCGCGCGAGAGAT 60.179 50.000 34.63 22.54 0.00 2.75
2381 3372 6.985645 AGCTAGTTGCAAATTGAAATTGTTCA 59.014 30.769 12.38 0.00 45.94 3.18
2382 3373 7.412137 AGCTAGTTGCAAATTGAAATTGTTC 57.588 32.000 12.38 0.00 45.94 3.18
2384 3375 6.587608 GCTAGCTAGTTGCAAATTGAAATTGT 59.412 34.615 21.62 0.00 45.94 2.71
2385 3376 6.237384 CGCTAGCTAGTTGCAAATTGAAATTG 60.237 38.462 21.62 0.45 45.94 2.32
2386 3377 5.801947 CGCTAGCTAGTTGCAAATTGAAATT 59.198 36.000 21.62 0.00 45.94 1.82
2387 3378 5.335127 CGCTAGCTAGTTGCAAATTGAAAT 58.665 37.500 21.62 0.30 45.94 2.17
2388 3379 4.379394 CCGCTAGCTAGTTGCAAATTGAAA 60.379 41.667 21.62 0.00 45.94 2.69
2389 3380 3.126858 CCGCTAGCTAGTTGCAAATTGAA 59.873 43.478 21.62 0.00 45.94 2.69
2390 3381 2.677836 CCGCTAGCTAGTTGCAAATTGA 59.322 45.455 21.62 0.00 45.94 2.57
2392 3383 2.017049 CCCGCTAGCTAGTTGCAAATT 58.983 47.619 21.62 0.00 45.94 1.82
2393 3384 1.668419 CCCGCTAGCTAGTTGCAAAT 58.332 50.000 21.62 4.23 45.94 2.32
2394 3385 1.024579 GCCCGCTAGCTAGTTGCAAA 61.025 55.000 21.62 0.00 45.94 3.68
2395 3386 1.449601 GCCCGCTAGCTAGTTGCAA 60.450 57.895 21.62 0.00 45.94 4.08
2396 3387 2.186903 GCCCGCTAGCTAGTTGCA 59.813 61.111 21.62 0.00 45.94 4.08
2397 3388 2.901051 TTCGCCCGCTAGCTAGTTGC 62.901 60.000 21.62 18.65 43.29 4.17
2398 3389 1.141019 TTCGCCCGCTAGCTAGTTG 59.859 57.895 21.62 14.16 0.00 3.16
2399 3390 1.141234 GTTCGCCCGCTAGCTAGTT 59.859 57.895 21.62 0.00 0.00 2.24
2400 3391 2.806237 GTTCGCCCGCTAGCTAGT 59.194 61.111 21.62 0.00 0.00 2.57
2401 3392 2.353607 CGTTCGCCCGCTAGCTAG 60.354 66.667 16.84 16.84 0.00 3.42
2402 3393 3.136123 ACGTTCGCCCGCTAGCTA 61.136 61.111 13.93 0.00 0.00 3.32
2403 3394 4.796231 CACGTTCGCCCGCTAGCT 62.796 66.667 13.93 0.00 0.00 3.32
2404 3395 4.789075 TCACGTTCGCCCGCTAGC 62.789 66.667 4.06 4.06 0.00 3.42
2405 3396 2.879462 GTCACGTTCGCCCGCTAG 60.879 66.667 0.00 0.00 0.00 3.42
2406 3397 2.997075 ATGTCACGTTCGCCCGCTA 61.997 57.895 0.00 0.00 0.00 4.26
2407 3398 4.373116 ATGTCACGTTCGCCCGCT 62.373 61.111 0.00 0.00 0.00 5.52
2411 3402 2.358247 ACCCATGTCACGTTCGCC 60.358 61.111 0.00 0.00 0.00 5.54
2412 3403 2.726691 CGACCCATGTCACGTTCGC 61.727 63.158 0.00 0.00 41.85 4.70
2414 3405 1.005394 ACCGACCCATGTCACGTTC 60.005 57.895 0.00 0.00 41.85 3.95
2427 3422 0.524604 GCAACCACAACAACACCGAC 60.525 55.000 0.00 0.00 0.00 4.79
2432 3427 0.529833 CACCTGCAACCACAACAACA 59.470 50.000 0.00 0.00 0.00 3.33
2433 3428 0.805711 GCACCTGCAACCACAACAAC 60.806 55.000 0.00 0.00 41.59 3.32
2434 3429 0.969917 AGCACCTGCAACCACAACAA 60.970 50.000 0.00 0.00 45.16 2.83
2859 4115 3.560902 TCGATCGATCTCAAGGCATAC 57.439 47.619 22.43 0.00 0.00 2.39
2863 4119 1.066914 GCATCGATCGATCTCAAGGC 58.933 55.000 27.20 21.32 31.62 4.35
2865 4121 3.423253 GCATTGCATCGATCGATCTCAAG 60.423 47.826 29.81 24.53 32.00 3.02
3202 4511 1.142748 CGAAGAAGAGGAGCGCCAT 59.857 57.895 9.88 0.00 36.29 4.40
3291 4606 1.658114 CGGGATGAAGCGGACGATA 59.342 57.895 0.00 0.00 0.00 2.92
3472 4814 1.374252 CCACCTGCTCCACGTACAC 60.374 63.158 0.00 0.00 0.00 2.90
3822 5173 2.025155 CTATCGTGTCAGTAGCCACCT 58.975 52.381 0.00 0.00 0.00 4.00
3830 5181 4.727507 AATCAAGAGCTATCGTGTCAGT 57.272 40.909 0.00 0.00 36.44 3.41
4020 5371 7.876068 TGAATTTACACTAGGGTTCAACTACAG 59.124 37.037 1.15 0.00 0.00 2.74
4171 5702 5.045942 TGGATGATTGTAACCTTGCTACTCA 60.046 40.000 0.00 0.00 0.00 3.41
4192 5723 3.443925 CCGTCGAGCTGCTCTGGA 61.444 66.667 25.59 14.60 0.00 3.86
4194 5725 3.921767 TTGCCGTCGAGCTGCTCTG 62.922 63.158 25.59 18.75 0.00 3.35
4214 5746 2.269241 CTTGGTTCTCGCCCTCCC 59.731 66.667 0.00 0.00 0.00 4.30
4222 5754 1.815003 CCATGACTTGCCTTGGTTCTC 59.185 52.381 0.00 0.00 0.00 2.87
4232 5764 1.251251 AAGGCAGAACCATGACTTGC 58.749 50.000 0.00 0.00 46.94 4.01
4276 5808 5.410439 GGAACCAAAGTAAAGTTAGCGATGA 59.590 40.000 0.00 0.00 0.00 2.92
4277 5809 5.628134 GGAACCAAAGTAAAGTTAGCGATG 58.372 41.667 0.00 0.00 0.00 3.84
4291 5823 4.315803 ACTCATGTAAGTCGGAACCAAAG 58.684 43.478 0.00 0.00 0.00 2.77
4324 5856 1.100510 TACCCGACGTCTCTTCATGG 58.899 55.000 14.70 5.19 0.00 3.66
4327 5859 1.901591 AAGTACCCGACGTCTCTTCA 58.098 50.000 14.70 0.00 0.00 3.02
4328 5860 4.335037 AGATTAAGTACCCGACGTCTCTTC 59.665 45.833 14.70 0.55 0.00 2.87
4336 5868 6.462552 AGTTAAGGAGATTAAGTACCCGAC 57.537 41.667 0.00 0.00 35.64 4.79
4363 5895 2.887783 TGGACAGATCGATCTAAGCCTC 59.112 50.000 26.87 15.16 34.85 4.70
4386 5930 3.265791 GAAGTTGATCCAAGCTCGTGAT 58.734 45.455 0.00 0.00 0.00 3.06
4422 5966 5.184479 CGCCCCAAATATCATTGAGATGAAT 59.816 40.000 0.00 0.00 44.96 2.57
4453 5997 6.775594 AGGTTTATCTTTTGCTATCCAACC 57.224 37.500 0.00 0.00 31.97 3.77
4455 5999 6.951198 TGGAAGGTTTATCTTTTGCTATCCAA 59.049 34.615 0.00 0.00 0.00 3.53
4472 6016 5.499004 ACTGTATGTGTGTATGGAAGGTT 57.501 39.130 0.00 0.00 0.00 3.50
4489 6033 1.345089 TGCTTTGTAGGCGGAACTGTA 59.655 47.619 0.00 0.00 0.00 2.74
4491 6035 1.398390 GATGCTTTGTAGGCGGAACTG 59.602 52.381 0.00 0.00 0.00 3.16
4502 6046 2.146342 CCTCTTGTCGTGATGCTTTGT 58.854 47.619 0.00 0.00 0.00 2.83
4590 6135 1.078918 CTTGTCTCCTGATGGCGCA 60.079 57.895 10.83 0.00 0.00 6.09
4716 6262 3.629398 GGAAGGGCAAGTCAATAGTGATG 59.371 47.826 0.00 0.00 35.80 3.07
4724 6270 1.125093 TCCTCGGAAGGGCAAGTCAA 61.125 55.000 0.00 0.00 43.56 3.18
4767 6313 4.079253 GCTACTTGGAATCTTTGGTTGGA 58.921 43.478 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.