Multiple sequence alignment - TraesCS3B01G559400

Loading Multiple Alignment...

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 TraesCS3B01G559400 chr3B 100.000 4264 0 0 1 4264 793262736 793266999 0.000000e+00 7875.0
1 TraesCS3B01G559400 chr3B 88.760 258 11 6 984 1229 793168571 793168822 2.490000e-77 300.0
2 TraesCS3B01G559400 chr3B 82.589 224 23 9 1513 1736 509969724 509969517 2.620000e-42 183.0
3 TraesCS3B01G559400 chr3B 94.595 37 2 0 2041 2077 658489579 658489615 1.660000e-04 58.4
4 TraesCS3B01G559400 chr3A 93.978 3371 123 38 950 4264 721584235 721580889 0.000000e+00 5027.0
5 TraesCS3B01G559400 chr3A 76.639 244 39 13 3165 3407 89387 89161 7.490000e-23 119.0
6 TraesCS3B01G559400 chr3D 84.465 1944 210 56 2123 4013 591240962 591239058 0.000000e+00 1832.0
7 TraesCS3B01G559400 chr3D 89.237 799 42 18 948 1736 591242198 591241434 0.000000e+00 959.0
8 TraesCS3B01G559400 chr3D 82.486 708 106 15 1 701 87333247 87332551 4.720000e-169 604.0
9 TraesCS3B01G559400 chr3D 90.213 235 20 3 1802 2033 591241299 591241065 1.930000e-78 303.0
10 TraesCS3B01G559400 chr3D 83.691 233 22 8 4012 4231 591238986 591238757 5.590000e-49 206.0
11 TraesCS3B01G559400 chr3D 77.049 244 38 13 3165 3407 562543289 562543063 1.610000e-24 124.0
12 TraesCS3B01G559400 chr3D 100.000 31 0 0 2047 2077 311663328 311663298 1.660000e-04 58.4
13 TraesCS3B01G559400 chr5D 82.934 709 103 15 1 701 21300800 21301498 1.300000e-174 623.0
14 TraesCS3B01G559400 chr7A 81.392 704 118 12 1 701 237748114 237747421 2.880000e-156 562.0
15 TraesCS3B01G559400 chr7A 79.681 251 35 6 2659 2896 26873464 26873711 2.640000e-37 167.0
16 TraesCS3B01G559400 chr7A 79.283 251 35 7 2659 2896 24773973 24773727 4.410000e-35 159.0
17 TraesCS3B01G559400 chr7A 97.297 37 1 0 2041 2077 596662074 596662038 3.560000e-06 63.9
18 TraesCS3B01G559400 chr6B 87.852 461 56 0 1 461 64010348 64009888 3.750000e-150 542.0
19 TraesCS3B01G559400 chr6B 87.692 65 5 3 638 701 618671072 618671010 5.910000e-09 73.1
20 TraesCS3B01G559400 chr6A 80.463 691 120 13 1 687 446798273 446798952 8.180000e-142 514.0
21 TraesCS3B01G559400 chr6A 84.241 514 78 3 7 518 76595803 76595291 8.230000e-137 497.0
22 TraesCS3B01G559400 chr6A 85.561 374 37 10 1363 1736 437702447 437702091 4.030000e-100 375.0
23 TraesCS3B01G559400 chr6A 94.595 37 2 0 2041 2077 92848745 92848709 1.660000e-04 58.4
24 TraesCS3B01G559400 chr7B 79.468 789 102 34 2531 3272 14874188 14873413 4.920000e-139 505.0
25 TraesCS3B01G559400 chr7B 83.300 497 81 2 23 518 530181390 530180895 1.400000e-124 457.0
26 TraesCS3B01G559400 chr7B 85.146 377 39 9 1357 1733 153181117 153181476 1.870000e-98 370.0
27 TraesCS3B01G559400 chr7B 84.759 374 37 11 1363 1736 42361071 42360718 1.460000e-94 357.0
28 TraesCS3B01G559400 chr7B 91.342 231 20 0 1376 1606 14875433 14875203 2.470000e-82 316.0
29 TraesCS3B01G559400 chr7B 77.995 409 48 26 3299 3688 285917368 285917753 7.180000e-53 219.0
30 TraesCS3B01G559400 chr7B 83.929 224 20 10 1513 1736 707545242 707545035 2.600000e-47 200.0
31 TraesCS3B01G559400 chr7B 81.500 200 18 7 1039 1220 14875799 14875601 3.440000e-31 147.0
32 TraesCS3B01G559400 chr7B 94.595 37 2 0 2041 2077 589467130 589467094 1.660000e-04 58.4
33 TraesCS3B01G559400 chr7D 81.481 594 77 22 2706 3272 73130051 73130638 1.400000e-124 457.0
34 TraesCS3B01G559400 chr7D 80.987 547 70 24 1069 1606 73128587 73129108 1.850000e-108 403.0
35 TraesCS3B01G559400 chr5B 83.824 476 75 1 23 498 586469424 586468951 6.500000e-123 451.0
36 TraesCS3B01G559400 chr5B 81.055 512 95 2 8 518 711570443 711570953 1.430000e-109 407.0
37 TraesCS3B01G559400 chr5B 78.973 409 44 22 3299 3688 390011904 390012289 1.530000e-59 241.0
38 TraesCS3B01G559400 chr5B 92.308 39 3 0 2041 2079 687803410 687803372 5.960000e-04 56.5
39 TraesCS3B01G559400 chr4A 84.777 381 38 12 1357 1736 670379711 670379350 8.710000e-97 364.0
40 TraesCS3B01G559400 chr2B 78.912 441 64 19 2658 3080 16303283 16302854 5.430000e-69 272.0
41 TraesCS3B01G559400 chr5A 80.400 250 32 9 2661 2896 595011095 595010849 1.580000e-39 174.0
42 TraesCS3B01G559400 chr5A 83.648 159 22 2 2738 2896 84158838 84158992 3.440000e-31 147.0
43 TraesCS3B01G559400 chr2A 79.762 252 34 7 2659 2896 690920334 690920582 2.640000e-37 167.0
44 TraesCS3B01G559400 chrUn 97.297 37 1 0 2041 2077 321270873 321270837 3.560000e-06 63.9
45 TraesCS3B01G559400 chr6D 92.500 40 3 0 2039 2078 426154403 426154364 1.660000e-04 58.4


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 TraesCS3B01G559400 chr3B 793262736 793266999 4263 False 7875.000000 7875 100.000000 1 4264 1 chr3B.!!$F3 4263
1 TraesCS3B01G559400 chr3A 721580889 721584235 3346 True 5027.000000 5027 93.978000 950 4264 1 chr3A.!!$R2 3314
2 TraesCS3B01G559400 chr3D 591238757 591242198 3441 True 825.000000 1832 86.901500 948 4231 4 chr3D.!!$R4 3283
3 TraesCS3B01G559400 chr3D 87332551 87333247 696 True 604.000000 604 82.486000 1 701 1 chr3D.!!$R1 700
4 TraesCS3B01G559400 chr5D 21300800 21301498 698 False 623.000000 623 82.934000 1 701 1 chr5D.!!$F1 700
5 TraesCS3B01G559400 chr7A 237747421 237748114 693 True 562.000000 562 81.392000 1 701 1 chr7A.!!$R2 700
6 TraesCS3B01G559400 chr6A 446798273 446798952 679 False 514.000000 514 80.463000 1 687 1 chr6A.!!$F1 686
7 TraesCS3B01G559400 chr6A 76595291 76595803 512 True 497.000000 497 84.241000 7 518 1 chr6A.!!$R1 511
8 TraesCS3B01G559400 chr7B 14873413 14875799 2386 True 322.666667 505 84.103333 1039 3272 3 chr7B.!!$R5 2233
9 TraesCS3B01G559400 chr7D 73128587 73130638 2051 False 430.000000 457 81.234000 1069 3272 2 chr7D.!!$F1 2203
10 TraesCS3B01G559400 chr5B 711570443 711570953 510 False 407.000000 407 81.055000 8 518 1 chr5B.!!$F2 510

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
802 810 0.032615 ATCGGCCCAAAAATAGCCCA 60.033 50.0 0.00 0.0 44.13 5.36 F
831 839 0.034896 AAAGCACCTGGGACTACGTG 59.965 55.0 0.00 0.0 0.00 4.49 F
2372 2986 0.037326 TAGGCTGAAGCAACTGACCG 60.037 55.0 4.43 0.0 44.36 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1695 1840 1.047002 CAATTCAGTTGCCCACCCAA 58.953 50.000 0.0 0.0 0.00 4.12 R
2813 3473 1.073722 CTTGCCAGCCTTCACCTCA 59.926 57.895 0.0 0.0 0.00 3.86 R
4240 5042 2.286950 GCGACTTGCTGTTCATTGTTCA 60.287 45.455 0.0 0.0 41.73 3.18 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
51 52 1.084370 CCTTCACCGCCGACTCAATC 61.084 60.000 0.00 0.00 0.00 2.67
55 56 0.179100 CACCGCCGACTCAATCAGAT 60.179 55.000 0.00 0.00 0.00 2.90
57 58 1.338337 ACCGCCGACTCAATCAGATAG 59.662 52.381 0.00 0.00 0.00 2.08
60 61 3.004419 CCGCCGACTCAATCAGATAGTTA 59.996 47.826 0.00 0.00 0.00 2.24
146 147 4.137116 TGAAACCGTCATATTCCTCCAG 57.863 45.455 0.00 0.00 0.00 3.86
177 178 1.215173 TGATCCCTAAACAGCCATGGG 59.785 52.381 15.13 0.00 39.22 4.00
195 196 4.249638 TGGGCCTTCATACATAGCTTTT 57.750 40.909 4.53 0.00 0.00 2.27
241 242 1.595794 GCGTCGAAAACAAGTTCTCCA 59.404 47.619 0.00 0.00 0.00 3.86
253 254 4.782156 ACAAGTTCTCCATGATCTTCCTCT 59.218 41.667 0.00 0.00 33.73 3.69
303 304 1.182667 CCCTCATGTCACCGTACAGA 58.817 55.000 0.00 0.00 31.70 3.41
339 340 1.136110 GTTTTTGGTGTGTGGACCCTG 59.864 52.381 0.00 0.00 34.79 4.45
361 363 2.629050 GATCGCTAGCCACTTCGCCA 62.629 60.000 9.66 0.00 0.00 5.69
464 466 2.726351 CCGCTGTCTCCTTCCCCTC 61.726 68.421 0.00 0.00 0.00 4.30
476 478 1.156322 TTCCCCTCCTCCCTCTGAGT 61.156 60.000 3.66 0.00 39.65 3.41
479 481 0.930726 CCCTCCTCCCTCTGAGTACT 59.069 60.000 0.00 0.00 39.65 2.73
517 519 1.832411 CGCGATCCGATCTGACGAGA 61.832 60.000 0.00 0.00 40.02 4.04
518 520 0.308068 GCGATCCGATCTGACGAGAA 59.692 55.000 6.81 0.00 35.09 2.87
519 521 1.268589 GCGATCCGATCTGACGAGAAA 60.269 52.381 6.81 0.00 35.09 2.52
520 522 2.645163 CGATCCGATCTGACGAGAAAG 58.355 52.381 6.81 0.00 35.09 2.62
537 539 0.690762 AAGAAAACTAGCGCTCCCCA 59.309 50.000 16.34 0.00 0.00 4.96
542 544 2.215942 AACTAGCGCTCCCCAAAAAT 57.784 45.000 16.34 0.00 0.00 1.82
546 548 1.560505 AGCGCTCCCCAAAAATCAAT 58.439 45.000 2.64 0.00 0.00 2.57
556 558 3.444029 CCAAAAATCAATCAGACCCCCT 58.556 45.455 0.00 0.00 0.00 4.79
558 560 3.833559 AAAATCAATCAGACCCCCTGT 57.166 42.857 0.00 0.00 43.38 4.00
581 583 1.497309 AAGGCCGGGAAGGATCACAA 61.497 55.000 2.18 0.00 45.00 3.33
601 603 2.003548 GATCCCCCTTGGTCAGCCT 61.004 63.158 0.00 0.00 35.27 4.58
608 610 1.536073 CCTTGGTCAGCCTGAGTCGA 61.536 60.000 0.00 0.00 35.27 4.20
611 613 2.716017 GGTCAGCCTGAGTCGAGGG 61.716 68.421 0.00 2.41 33.17 4.30
614 616 3.999285 AGCCTGAGTCGAGGGGGT 61.999 66.667 9.72 1.67 33.17 4.95
617 620 2.711922 CCTGAGTCGAGGGGGTTCG 61.712 68.421 0.00 0.00 41.79 3.95
627 630 2.202892 GGGGTTCGATCGTGCTCC 60.203 66.667 15.94 14.25 0.00 4.70
630 633 2.582498 GTTCGATCGTGCTCCGGG 60.582 66.667 15.94 0.00 37.11 5.73
660 667 3.453559 GGAAGATTCCCGCGAAGAA 57.546 52.632 8.23 11.21 41.62 2.52
688 695 4.321230 GGAAGACGTCGAAACCCTAGTTTA 60.321 45.833 10.46 0.00 46.25 2.01
701 709 3.442076 CCTAGTTTATCGCCTAGGGGAT 58.558 50.000 35.55 35.55 44.40 3.85
702 710 4.607239 CCTAGTTTATCGCCTAGGGGATA 58.393 47.826 33.69 33.69 44.40 2.59
703 711 4.645588 CCTAGTTTATCGCCTAGGGGATAG 59.354 50.000 34.40 27.58 45.98 2.08
704 712 2.832733 AGTTTATCGCCTAGGGGATAGC 59.167 50.000 34.40 30.33 45.98 2.97
705 713 1.861982 TTATCGCCTAGGGGATAGCC 58.138 55.000 34.40 9.02 45.98 3.93
706 714 1.008403 TATCGCCTAGGGGATAGCCT 58.992 55.000 33.69 20.32 44.29 4.58
707 715 1.008403 ATCGCCTAGGGGATAGCCTA 58.992 55.000 33.65 11.18 44.29 3.93
708 716 0.781920 TCGCCTAGGGGATAGCCTAA 59.218 55.000 23.87 0.00 33.58 2.69
709 717 1.148446 TCGCCTAGGGGATAGCCTAAA 59.852 52.381 23.87 0.00 33.58 1.85
710 718 1.975680 CGCCTAGGGGATAGCCTAAAA 59.024 52.381 20.99 0.00 33.58 1.52
711 719 2.370849 CGCCTAGGGGATAGCCTAAAAA 59.629 50.000 20.99 0.00 33.58 1.94
736 744 4.250080 CGAGCAGCGCTATATGCA 57.750 55.556 19.79 0.00 45.01 3.96
737 745 2.746997 CGAGCAGCGCTATATGCAT 58.253 52.632 19.79 3.79 45.01 3.96
738 746 1.073964 CGAGCAGCGCTATATGCATT 58.926 50.000 19.79 1.74 45.01 3.56
739 747 1.462283 CGAGCAGCGCTATATGCATTT 59.538 47.619 19.79 0.00 45.01 2.32
740 748 2.096069 CGAGCAGCGCTATATGCATTTT 60.096 45.455 19.79 0.69 45.01 1.82
741 749 3.607775 CGAGCAGCGCTATATGCATTTTT 60.608 43.478 19.79 0.33 45.01 1.94
742 750 3.635331 AGCAGCGCTATATGCATTTTTG 58.365 40.909 19.79 1.29 45.01 2.44
743 751 3.316029 AGCAGCGCTATATGCATTTTTGA 59.684 39.130 19.79 0.00 45.01 2.69
744 752 4.022589 AGCAGCGCTATATGCATTTTTGAT 60.023 37.500 19.79 0.00 45.01 2.57
745 753 4.682860 GCAGCGCTATATGCATTTTTGATT 59.317 37.500 10.99 0.00 42.11 2.57
746 754 5.388061 GCAGCGCTATATGCATTTTTGATTG 60.388 40.000 10.99 0.00 42.11 2.67
747 755 5.916320 CAGCGCTATATGCATTTTTGATTGA 59.084 36.000 10.99 0.00 43.06 2.57
748 756 6.584942 CAGCGCTATATGCATTTTTGATTGAT 59.415 34.615 10.99 0.00 43.06 2.57
749 757 7.115805 CAGCGCTATATGCATTTTTGATTGATT 59.884 33.333 10.99 0.00 43.06 2.57
750 758 8.298854 AGCGCTATATGCATTTTTGATTGATTA 58.701 29.630 8.99 0.00 43.06 1.75
751 759 9.079833 GCGCTATATGCATTTTTGATTGATTAT 57.920 29.630 3.54 0.00 43.06 1.28
777 785 5.687166 TGACCTATAAACAACCCAGTAGG 57.313 43.478 0.00 0.00 43.78 3.18
789 797 2.294979 CCCAGTAGGTTAAAATCGGCC 58.705 52.381 0.00 0.00 0.00 6.13
790 798 2.294979 CCAGTAGGTTAAAATCGGCCC 58.705 52.381 0.00 0.00 0.00 5.80
791 799 2.356330 CCAGTAGGTTAAAATCGGCCCA 60.356 50.000 0.00 0.00 0.00 5.36
792 800 3.349022 CAGTAGGTTAAAATCGGCCCAA 58.651 45.455 0.00 0.00 0.00 4.12
793 801 3.759618 CAGTAGGTTAAAATCGGCCCAAA 59.240 43.478 0.00 0.00 0.00 3.28
794 802 4.218852 CAGTAGGTTAAAATCGGCCCAAAA 59.781 41.667 0.00 0.00 0.00 2.44
795 803 4.833938 AGTAGGTTAAAATCGGCCCAAAAA 59.166 37.500 0.00 0.00 0.00 1.94
796 804 4.901197 AGGTTAAAATCGGCCCAAAAAT 57.099 36.364 0.00 0.00 0.00 1.82
797 805 6.664384 AGTAGGTTAAAATCGGCCCAAAAATA 59.336 34.615 0.00 0.00 0.00 1.40
798 806 5.972935 AGGTTAAAATCGGCCCAAAAATAG 58.027 37.500 0.00 0.00 0.00 1.73
799 807 4.569162 GGTTAAAATCGGCCCAAAAATAGC 59.431 41.667 0.00 0.00 0.00 2.97
800 808 2.979814 AAATCGGCCCAAAAATAGCC 57.020 45.000 0.00 0.00 43.53 3.93
801 809 1.119684 AATCGGCCCAAAAATAGCCC 58.880 50.000 0.00 0.00 44.13 5.19
802 810 0.032615 ATCGGCCCAAAAATAGCCCA 60.033 50.000 0.00 0.00 44.13 5.36
803 811 0.251832 TCGGCCCAAAAATAGCCCAA 60.252 50.000 0.00 0.00 44.13 4.12
804 812 0.108377 CGGCCCAAAAATAGCCCAAC 60.108 55.000 0.00 0.00 44.13 3.77
805 813 0.980423 GGCCCAAAAATAGCCCAACA 59.020 50.000 0.00 0.00 41.00 3.33
806 814 1.066215 GGCCCAAAAATAGCCCAACAG 60.066 52.381 0.00 0.00 41.00 3.16
807 815 1.066215 GCCCAAAAATAGCCCAACAGG 60.066 52.381 0.00 0.00 39.47 4.00
816 824 4.777384 CCCAACAGGCCAAAAAGC 57.223 55.556 5.01 0.00 0.00 3.51
817 825 1.828768 CCCAACAGGCCAAAAAGCA 59.171 52.632 5.01 0.00 0.00 3.91
818 826 0.532640 CCCAACAGGCCAAAAAGCAC 60.533 55.000 5.01 0.00 0.00 4.40
819 827 0.532640 CCAACAGGCCAAAAAGCACC 60.533 55.000 5.01 0.00 0.00 5.01
820 828 0.465287 CAACAGGCCAAAAAGCACCT 59.535 50.000 5.01 0.00 0.00 4.00
822 830 1.368579 CAGGCCAAAAAGCACCTGG 59.631 57.895 5.01 0.00 44.90 4.45
823 831 1.838396 AGGCCAAAAAGCACCTGGG 60.838 57.895 5.01 0.00 0.00 4.45
824 832 1.836604 GGCCAAAAAGCACCTGGGA 60.837 57.895 0.00 0.00 0.00 4.37
825 833 1.367471 GCCAAAAAGCACCTGGGAC 59.633 57.895 0.00 0.00 0.00 4.46
826 834 1.115326 GCCAAAAAGCACCTGGGACT 61.115 55.000 0.00 0.00 0.00 3.85
827 835 1.821666 GCCAAAAAGCACCTGGGACTA 60.822 52.381 0.00 0.00 0.00 2.59
828 836 1.886542 CCAAAAAGCACCTGGGACTAC 59.113 52.381 0.00 0.00 0.00 2.73
829 837 1.535462 CAAAAAGCACCTGGGACTACG 59.465 52.381 0.00 0.00 0.00 3.51
830 838 0.763035 AAAAGCACCTGGGACTACGT 59.237 50.000 0.00 0.00 0.00 3.57
831 839 0.034896 AAAGCACCTGGGACTACGTG 59.965 55.000 0.00 0.00 0.00 4.49
832 840 2.434359 GCACCTGGGACTACGTGC 60.434 66.667 0.00 0.00 44.17 5.34
833 841 2.264794 CACCTGGGACTACGTGCC 59.735 66.667 0.00 0.00 44.48 5.01
834 842 3.001406 ACCTGGGACTACGTGCCC 61.001 66.667 14.08 14.08 43.57 5.36
839 847 4.157120 GGACTACGTGCCCGGCAT 62.157 66.667 16.96 2.56 41.91 4.40
864 872 3.625099 GGCTGGCCCGACTAGTAA 58.375 61.111 0.00 0.00 0.00 2.24
865 873 1.902556 GGCTGGCCCGACTAGTAAA 59.097 57.895 0.00 0.00 0.00 2.01
866 874 0.179081 GGCTGGCCCGACTAGTAAAG 60.179 60.000 0.00 0.00 0.00 1.85
867 875 0.822164 GCTGGCCCGACTAGTAAAGA 59.178 55.000 0.00 0.00 0.00 2.52
868 876 1.202428 GCTGGCCCGACTAGTAAAGAG 60.202 57.143 0.00 0.00 0.00 2.85
869 877 1.409427 CTGGCCCGACTAGTAAAGAGG 59.591 57.143 0.00 0.00 0.00 3.69
870 878 1.006281 TGGCCCGACTAGTAAAGAGGA 59.994 52.381 0.00 0.00 0.00 3.71
871 879 1.408340 GGCCCGACTAGTAAAGAGGAC 59.592 57.143 0.00 0.00 0.00 3.85
872 880 1.408340 GCCCGACTAGTAAAGAGGACC 59.592 57.143 0.00 0.00 0.00 4.46
873 881 2.731572 CCCGACTAGTAAAGAGGACCA 58.268 52.381 0.00 0.00 0.00 4.02
874 882 2.688958 CCCGACTAGTAAAGAGGACCAG 59.311 54.545 0.00 0.00 0.00 4.00
875 883 2.688958 CCGACTAGTAAAGAGGACCAGG 59.311 54.545 0.00 0.00 0.00 4.45
876 884 2.099427 CGACTAGTAAAGAGGACCAGGC 59.901 54.545 0.00 0.00 0.00 4.85
877 885 2.431419 GACTAGTAAAGAGGACCAGGCC 59.569 54.545 0.00 0.00 0.00 5.19
878 886 2.044630 ACTAGTAAAGAGGACCAGGCCT 59.955 50.000 0.00 0.00 42.17 5.19
879 887 1.280457 AGTAAAGAGGACCAGGCCTG 58.720 55.000 26.87 26.87 38.73 4.85
880 888 1.203313 AGTAAAGAGGACCAGGCCTGA 60.203 52.381 34.91 7.71 38.73 3.86
881 889 1.208293 GTAAAGAGGACCAGGCCTGAG 59.792 57.143 34.91 24.76 38.73 3.35
882 890 1.204113 AAAGAGGACCAGGCCTGAGG 61.204 60.000 34.91 21.20 38.73 3.86
883 891 3.086600 GAGGACCAGGCCTGAGGG 61.087 72.222 34.91 20.39 38.73 4.30
906 914 2.677524 CACACCATGCCCCAGTGG 60.678 66.667 0.63 0.63 41.35 4.00
925 933 2.744709 CCGTACTGGCCCGTTTGG 60.745 66.667 4.69 4.06 37.09 3.28
934 942 2.747855 CCCGTTTGGCCAGCTCTC 60.748 66.667 5.11 0.00 0.00 3.20
935 943 3.121030 CCGTTTGGCCAGCTCTCG 61.121 66.667 5.11 7.77 0.00 4.04
936 944 3.121030 CGTTTGGCCAGCTCTCGG 61.121 66.667 5.11 0.00 0.00 4.63
937 945 2.347490 GTTTGGCCAGCTCTCGGA 59.653 61.111 5.11 0.00 0.00 4.55
938 946 1.743252 GTTTGGCCAGCTCTCGGAG 60.743 63.158 5.11 0.00 0.00 4.63
939 947 2.959484 TTTGGCCAGCTCTCGGAGG 61.959 63.158 5.11 0.00 0.00 4.30
942 950 3.535962 GCCAGCTCTCGGAGGGAG 61.536 72.222 9.59 0.00 44.58 4.30
943 951 2.837291 CCAGCTCTCGGAGGGAGG 60.837 72.222 9.59 5.72 43.34 4.30
944 952 2.277072 CAGCTCTCGGAGGGAGGA 59.723 66.667 9.59 0.00 43.34 3.71
945 953 1.827789 CAGCTCTCGGAGGGAGGAG 60.828 68.421 9.59 0.00 43.34 3.69
946 954 2.277404 GCTCTCGGAGGGAGGAGT 59.723 66.667 9.59 0.00 43.34 3.85
962 970 4.806247 GGAGGAGTATCATTCTGTTCGTTG 59.194 45.833 0.00 0.00 36.25 4.10
1247 1275 2.936032 GCTCCCCACTCCCCACTT 60.936 66.667 0.00 0.00 0.00 3.16
1248 1276 2.972819 GCTCCCCACTCCCCACTTC 61.973 68.421 0.00 0.00 0.00 3.01
1249 1277 2.606519 TCCCCACTCCCCACTTCG 60.607 66.667 0.00 0.00 0.00 3.79
1250 1278 4.410400 CCCCACTCCCCACTTCGC 62.410 72.222 0.00 0.00 0.00 4.70
1256 1284 3.665675 CTCCCCACTTCGCCTTCCG 62.666 68.421 0.00 0.00 38.61 4.30
1293 1340 2.514824 GCATCCGGGCTGGTTCTC 60.515 66.667 13.14 0.00 39.52 2.87
1303 1350 1.213013 CTGGTTCTCGTCTGTCGGG 59.787 63.158 0.00 0.00 42.07 5.14
1412 1527 2.575993 CACGGAGGTGCAGGAGAG 59.424 66.667 0.00 0.00 37.35 3.20
1627 1770 3.914426 TGCTTCTCCCCTTCTAATGAC 57.086 47.619 0.00 0.00 0.00 3.06
1631 1774 4.102367 GCTTCTCCCCTTCTAATGACAGAT 59.898 45.833 0.00 0.00 0.00 2.90
1640 1783 6.481644 CCCTTCTAATGACAGATACTCTTTGC 59.518 42.308 0.00 0.00 0.00 3.68
1652 1797 7.387948 ACAGATACTCTTTGCGTTGTTTATCTT 59.612 33.333 0.00 0.00 0.00 2.40
1683 1828 2.618241 TGATGTGTCAAGCTTTGTCACC 59.382 45.455 17.18 8.05 45.10 4.02
1692 1837 2.565841 AGCTTTGTCACCTGTCAGTTC 58.434 47.619 0.00 0.00 0.00 3.01
1693 1838 2.092968 AGCTTTGTCACCTGTCAGTTCA 60.093 45.455 0.00 0.00 0.00 3.18
1694 1839 2.289002 GCTTTGTCACCTGTCAGTTCAG 59.711 50.000 0.00 0.00 35.45 3.02
1695 1840 3.535561 CTTTGTCACCTGTCAGTTCAGT 58.464 45.455 0.00 0.00 34.02 3.41
1696 1841 3.627395 TTGTCACCTGTCAGTTCAGTT 57.373 42.857 0.00 0.00 34.02 3.16
1697 1842 2.905075 TGTCACCTGTCAGTTCAGTTG 58.095 47.619 0.00 0.00 34.02 3.16
1736 1882 4.515191 TGCTGGTTCAGTTTAACATGACTC 59.485 41.667 0.00 0.00 33.43 3.36
1841 2057 2.489938 TGTGGTTGCTACAATCTCCC 57.510 50.000 0.00 0.00 0.00 4.30
1977 2437 5.765182 ACTAATATATGCTGCCCAAGACAAC 59.235 40.000 0.00 0.00 0.00 3.32
2029 2536 5.529791 CCATGTTCTTATGTACTACTCCCG 58.470 45.833 0.00 0.00 0.00 5.14
2036 2543 0.107066 TGTACTACTCCCGCCGATCA 60.107 55.000 0.00 0.00 0.00 2.92
2372 2986 0.037326 TAGGCTGAAGCAACTGACCG 60.037 55.000 4.43 0.00 44.36 4.79
2392 3006 5.983540 ACCGCTCAAGAGAAGATAAAATCT 58.016 37.500 0.32 0.00 42.61 2.40
2404 3018 8.438676 AGAAGATAAAATCTACCATTTGGACG 57.561 34.615 3.01 0.00 39.08 4.79
2666 3300 2.031012 CTTGGCCTCACTGCACGA 59.969 61.111 3.32 0.00 0.00 4.35
2905 3565 9.899226 AGAATTATTGTTTTAGAACTTCTGTGC 57.101 29.630 1.17 0.00 36.70 4.57
3342 4044 4.141846 TGCAAAAGCTGGAATTGTGGTTAA 60.142 37.500 0.00 0.00 0.00 2.01
3389 4091 1.608055 TGCTGTGTCTGATTTGGTGG 58.392 50.000 0.00 0.00 0.00 4.61
3416 4118 6.204301 AGCAAGCTACTGCATATACTTCAATG 59.796 38.462 12.73 0.00 45.18 2.82
3423 4125 6.893583 ACTGCATATACTTCAATGAAGACCT 58.106 36.000 27.63 14.03 41.71 3.85
3437 4139 6.940430 ATGAAGACCTTCCCATCAAATTTT 57.060 33.333 7.24 0.00 38.77 1.82
3439 4141 7.847711 TGAAGACCTTCCCATCAAATTTTAA 57.152 32.000 7.24 0.00 38.77 1.52
3446 4148 5.798125 TCCCATCAAATTTTAAGTGTGCA 57.202 34.783 0.00 0.00 0.00 4.57
3530 4236 9.976511 TGATATACCTTAGGTATTTGAAGAACG 57.023 33.333 26.57 0.00 45.54 3.95
3539 4245 5.128827 AGGTATTTGAAGAACGCCTATCTCA 59.871 40.000 0.00 0.00 0.00 3.27
3546 4252 5.826208 TGAAGAACGCCTATCTCATACTGTA 59.174 40.000 0.00 0.00 0.00 2.74
3550 4256 8.405418 AGAACGCCTATCTCATACTGTATTTA 57.595 34.615 0.00 0.00 0.00 1.40
3575 4281 4.195225 ACTGTTAGCTAAGGAGACAAGC 57.805 45.455 6.38 0.00 40.72 4.01
3577 4283 4.040461 ACTGTTAGCTAAGGAGACAAGCAA 59.960 41.667 6.38 0.00 42.29 3.91
3632 4341 9.952341 GAACTTAAAACTGAACAAAACATTGTC 57.048 29.630 0.00 0.00 33.35 3.18
3657 4366 5.246883 AGCCAAAATTTAGCAGACCTGAAAT 59.753 36.000 13.77 0.00 0.00 2.17
3726 4435 6.200878 ACCCTAGTTCTTTGGAATTCTTGA 57.799 37.500 5.23 0.00 33.71 3.02
3780 4489 0.685458 ATGGGCCCTGCTGTTTCATC 60.685 55.000 25.70 0.00 0.00 2.92
3816 4526 5.733620 AAGTGAAAATGACATGCAGGAAT 57.266 34.783 4.84 0.00 0.00 3.01
3859 4570 2.603075 TTTGCCCACCAGCTAGAATT 57.397 45.000 0.00 0.00 0.00 2.17
3872 4583 8.715998 CACCAGCTAGAATTAATATCATCACAC 58.284 37.037 0.00 0.00 0.00 3.82
3978 4694 7.448469 TCTCCAATCTTACAAAGAAAGGAAAGG 59.552 37.037 11.94 4.66 41.21 3.11
3998 4714 4.482990 AGGAAAAGGAGGAAAGCATGAAA 58.517 39.130 0.00 0.00 0.00 2.69
4145 4936 7.124147 CCACACATCCCTCAAATATTTACCTTT 59.876 37.037 0.00 0.00 0.00 3.11
4162 4964 2.031120 CTTTTGTCCACAAAGGCCTCA 58.969 47.619 5.23 0.00 45.34 3.86
4210 5012 6.183360 GCTGTTTCTGCATCCAAAAAGAAAAA 60.183 34.615 7.11 0.00 39.60 1.94
4221 5023 9.362539 CATCCAAAAAGAAAAAGATTGATCGAT 57.637 29.630 0.00 0.00 0.00 3.59
4236 5038 4.625028 TGATCGATCCAGCTCAGTATTTG 58.375 43.478 22.31 0.00 0.00 2.32
4240 5042 3.181471 CGATCCAGCTCAGTATTTGGACT 60.181 47.826 0.00 0.00 42.12 3.85
4253 5055 7.206981 AGTATTTGGACTGAACAATGAACAG 57.793 36.000 9.00 9.00 37.62 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 6.239543 CCTGCCTGATAACTATCTGATTGAGT 60.240 42.308 6.11 0.00 34.68 3.41
51 52 2.297315 TCGCCTGCCTGATAACTATCTG 59.703 50.000 0.00 0.00 33.88 2.90
55 56 1.344438 CCATCGCCTGCCTGATAACTA 59.656 52.381 0.00 0.00 0.00 2.24
57 58 0.106708 TCCATCGCCTGCCTGATAAC 59.893 55.000 0.00 0.00 0.00 1.89
60 61 1.126329 AGATCCATCGCCTGCCTGAT 61.126 55.000 0.00 0.00 0.00 2.90
195 196 3.295093 TGGTTGTCTTGCAGATTGGAAA 58.705 40.909 0.00 0.00 0.00 3.13
219 220 2.031191 GGAGAACTTGTTTTCGACGCAA 59.969 45.455 0.00 0.00 0.00 4.85
241 242 5.310451 GACGGTAGTCTAGAGGAAGATCAT 58.690 45.833 0.00 0.00 43.80 2.45
297 298 3.445857 CTTTAGCCCTAACGCTCTGTAC 58.554 50.000 0.00 0.00 40.39 2.90
303 304 2.873094 AAACCTTTAGCCCTAACGCT 57.127 45.000 0.00 0.00 43.09 5.07
339 340 1.951631 GAAGTGGCTAGCGATCGCC 60.952 63.158 34.89 20.58 46.46 5.54
361 363 2.043227 GCTACCAGACCTAATGGAGCT 58.957 52.381 0.00 0.00 40.51 4.09
435 437 0.605589 AGACAGCGGAGGAACTTCTG 59.394 55.000 0.00 0.00 41.55 3.02
438 440 0.543174 AGGAGACAGCGGAGGAACTT 60.543 55.000 0.00 0.00 41.55 2.66
476 478 1.043116 CATGGAGGACGGCAGGAGTA 61.043 60.000 0.00 0.00 0.00 2.59
479 481 3.083349 CCATGGAGGACGGCAGGA 61.083 66.667 5.56 0.00 41.22 3.86
517 519 1.073284 TGGGGAGCGCTAGTTTTCTTT 59.927 47.619 11.50 0.00 0.00 2.52
518 520 0.690762 TGGGGAGCGCTAGTTTTCTT 59.309 50.000 11.50 0.00 0.00 2.52
519 521 0.690762 TTGGGGAGCGCTAGTTTTCT 59.309 50.000 11.50 0.00 0.00 2.52
520 522 1.530323 TTTGGGGAGCGCTAGTTTTC 58.470 50.000 11.50 0.00 0.00 2.29
537 539 4.132122 ACAGGGGGTCTGATTGATTTTT 57.868 40.909 0.00 0.00 46.18 1.94
542 544 0.991920 GGAACAGGGGGTCTGATTGA 59.008 55.000 0.00 0.00 46.18 2.57
546 548 2.463441 CTTGGAACAGGGGGTCTGA 58.537 57.895 0.00 0.00 46.18 3.27
556 558 2.434331 CTTCCCGGCCTTGGAACA 59.566 61.111 17.19 1.74 36.97 3.18
558 560 1.921869 GATCCTTCCCGGCCTTGGAA 61.922 60.000 19.26 19.26 39.54 3.53
601 603 2.437449 TCGAACCCCCTCGACTCA 59.563 61.111 0.00 0.00 42.69 3.41
608 610 2.683933 AGCACGATCGAACCCCCT 60.684 61.111 24.34 5.22 0.00 4.79
643 646 0.645868 CGTTCTTCGCGGGAATCTTC 59.354 55.000 15.86 6.15 0.00 2.87
688 695 4.463043 GGCTATCCCCTAGGCGAT 57.537 61.111 13.46 13.46 42.46 4.58
751 759 9.096823 CCTACTGGGTTGTTTATAGGTCATATA 57.903 37.037 0.00 0.00 0.00 0.86
752 760 7.974504 CCTACTGGGTTGTTTATAGGTCATAT 58.025 38.462 0.00 0.00 0.00 1.78
753 761 7.369551 CCTACTGGGTTGTTTATAGGTCATA 57.630 40.000 0.00 0.00 0.00 2.15
754 762 6.248569 CCTACTGGGTTGTTTATAGGTCAT 57.751 41.667 0.00 0.00 0.00 3.06
755 763 5.687166 CCTACTGGGTTGTTTATAGGTCA 57.313 43.478 0.00 0.00 0.00 4.02
769 777 2.294979 GGCCGATTTTAACCTACTGGG 58.705 52.381 0.00 0.00 41.89 4.45
770 778 2.294979 GGGCCGATTTTAACCTACTGG 58.705 52.381 0.00 0.00 39.83 4.00
771 779 2.993937 TGGGCCGATTTTAACCTACTG 58.006 47.619 0.00 0.00 0.00 2.74
772 780 3.724732 TTGGGCCGATTTTAACCTACT 57.275 42.857 0.00 0.00 0.00 2.57
773 781 4.787260 TTTTGGGCCGATTTTAACCTAC 57.213 40.909 0.00 0.00 0.00 3.18
774 782 6.406065 GCTATTTTTGGGCCGATTTTAACCTA 60.406 38.462 0.00 0.00 0.00 3.08
775 783 4.901197 ATTTTTGGGCCGATTTTAACCT 57.099 36.364 0.00 0.00 0.00 3.50
776 784 4.569162 GCTATTTTTGGGCCGATTTTAACC 59.431 41.667 0.00 0.00 0.00 2.85
777 785 4.569162 GGCTATTTTTGGGCCGATTTTAAC 59.431 41.667 0.00 0.00 36.37 2.01
778 786 4.383226 GGGCTATTTTTGGGCCGATTTTAA 60.383 41.667 0.00 0.00 46.10 1.52
779 787 3.133183 GGGCTATTTTTGGGCCGATTTTA 59.867 43.478 0.00 0.00 46.10 1.52
780 788 2.093181 GGGCTATTTTTGGGCCGATTTT 60.093 45.455 0.00 0.00 46.10 1.82
781 789 1.484653 GGGCTATTTTTGGGCCGATTT 59.515 47.619 0.00 0.00 46.10 2.17
782 790 1.119684 GGGCTATTTTTGGGCCGATT 58.880 50.000 0.00 0.00 46.10 3.34
783 791 2.820845 GGGCTATTTTTGGGCCGAT 58.179 52.632 0.00 0.00 46.10 4.18
784 792 4.347865 GGGCTATTTTTGGGCCGA 57.652 55.556 0.00 0.00 46.10 5.54
786 794 0.980423 TGTTGGGCTATTTTTGGGCC 59.020 50.000 0.00 0.00 46.56 5.80
787 795 1.066215 CCTGTTGGGCTATTTTTGGGC 60.066 52.381 0.00 0.00 0.00 5.36
799 807 0.532640 GTGCTTTTTGGCCTGTTGGG 60.533 55.000 3.32 0.00 38.36 4.12
800 808 0.532640 GGTGCTTTTTGGCCTGTTGG 60.533 55.000 3.32 0.00 0.00 3.77
801 809 0.465287 AGGTGCTTTTTGGCCTGTTG 59.535 50.000 3.32 0.00 0.00 3.33
802 810 0.465287 CAGGTGCTTTTTGGCCTGTT 59.535 50.000 3.32 0.00 42.47 3.16
803 811 1.402107 CCAGGTGCTTTTTGGCCTGT 61.402 55.000 3.32 0.00 45.08 4.00
804 812 1.368579 CCAGGTGCTTTTTGGCCTG 59.631 57.895 3.32 0.00 45.86 4.85
805 813 1.838396 CCCAGGTGCTTTTTGGCCT 60.838 57.895 3.32 0.00 0.00 5.19
806 814 1.836604 TCCCAGGTGCTTTTTGGCC 60.837 57.895 0.00 0.00 0.00 5.36
807 815 1.115326 AGTCCCAGGTGCTTTTTGGC 61.115 55.000 0.00 0.00 0.00 4.52
808 816 1.886542 GTAGTCCCAGGTGCTTTTTGG 59.113 52.381 0.00 0.00 0.00 3.28
809 817 1.535462 CGTAGTCCCAGGTGCTTTTTG 59.465 52.381 0.00 0.00 0.00 2.44
810 818 1.142262 ACGTAGTCCCAGGTGCTTTTT 59.858 47.619 0.00 0.00 29.74 1.94
811 819 0.763035 ACGTAGTCCCAGGTGCTTTT 59.237 50.000 0.00 0.00 29.74 2.27
812 820 0.034896 CACGTAGTCCCAGGTGCTTT 59.965 55.000 0.00 0.00 41.61 3.51
813 821 1.671742 CACGTAGTCCCAGGTGCTT 59.328 57.895 0.00 0.00 41.61 3.91
814 822 3.377656 CACGTAGTCCCAGGTGCT 58.622 61.111 0.00 0.00 41.61 4.40
816 824 2.264794 GGCACGTAGTCCCAGGTG 59.735 66.667 0.00 0.00 41.61 4.00
817 825 3.001406 GGGCACGTAGTCCCAGGT 61.001 66.667 13.12 0.00 43.92 4.00
818 826 4.143333 CGGGCACGTAGTCCCAGG 62.143 72.222 16.80 1.76 44.44 4.45
819 827 4.143333 CCGGGCACGTAGTCCCAG 62.143 72.222 7.97 10.65 44.44 4.45
822 830 4.157120 ATGCCGGGCACGTAGTCC 62.157 66.667 26.48 0.00 43.04 3.85
823 831 2.890474 CATGCCGGGCACGTAGTC 60.890 66.667 26.48 0.00 43.04 2.59
825 833 4.838152 AGCATGCCGGGCACGTAG 62.838 66.667 26.48 15.41 43.04 3.51
847 855 0.179081 CTTTACTAGTCGGGCCAGCC 60.179 60.000 4.39 0.00 0.00 4.85
848 856 0.822164 TCTTTACTAGTCGGGCCAGC 59.178 55.000 4.39 0.00 0.00 4.85
849 857 1.409427 CCTCTTTACTAGTCGGGCCAG 59.591 57.143 4.39 0.00 0.00 4.85
850 858 1.006281 TCCTCTTTACTAGTCGGGCCA 59.994 52.381 4.39 0.00 0.00 5.36
851 859 1.408340 GTCCTCTTTACTAGTCGGGCC 59.592 57.143 0.00 0.00 0.00 5.80
852 860 1.408340 GGTCCTCTTTACTAGTCGGGC 59.592 57.143 0.00 0.00 0.00 6.13
853 861 2.688958 CTGGTCCTCTTTACTAGTCGGG 59.311 54.545 0.00 0.00 0.00 5.14
854 862 2.688958 CCTGGTCCTCTTTACTAGTCGG 59.311 54.545 0.00 0.00 0.00 4.79
855 863 2.099427 GCCTGGTCCTCTTTACTAGTCG 59.901 54.545 0.00 0.00 0.00 4.18
856 864 2.431419 GGCCTGGTCCTCTTTACTAGTC 59.569 54.545 0.00 0.00 0.00 2.59
857 865 2.044630 AGGCCTGGTCCTCTTTACTAGT 59.955 50.000 3.11 0.00 0.00 2.57
858 866 2.432510 CAGGCCTGGTCCTCTTTACTAG 59.567 54.545 26.14 0.00 33.25 2.57
859 867 2.043939 TCAGGCCTGGTCCTCTTTACTA 59.956 50.000 32.23 5.30 33.25 1.82
860 868 1.203313 TCAGGCCTGGTCCTCTTTACT 60.203 52.381 32.23 0.00 33.25 2.24
861 869 1.208293 CTCAGGCCTGGTCCTCTTTAC 59.792 57.143 32.23 0.00 33.25 2.01
862 870 1.573108 CTCAGGCCTGGTCCTCTTTA 58.427 55.000 32.23 8.89 33.25 1.85
863 871 1.204113 CCTCAGGCCTGGTCCTCTTT 61.204 60.000 32.23 0.00 33.25 2.52
864 872 1.614824 CCTCAGGCCTGGTCCTCTT 60.615 63.158 32.23 0.00 33.25 2.85
865 873 2.040278 CCTCAGGCCTGGTCCTCT 59.960 66.667 32.23 0.00 33.25 3.69
866 874 3.086600 CCCTCAGGCCTGGTCCTC 61.087 72.222 32.23 0.00 33.25 3.71
876 884 2.125512 GTGTGCTACGCCCTCAGG 60.126 66.667 0.00 0.00 0.00 3.86
877 885 2.125512 GGTGTGCTACGCCCTCAG 60.126 66.667 7.42 0.00 42.80 3.35
889 897 2.677524 CCACTGGGGCATGGTGTG 60.678 66.667 0.00 0.00 0.00 3.82
908 916 2.744709 CCAAACGGGCCAGTACGG 60.745 66.667 9.60 9.16 38.11 4.02
917 925 2.747855 GAGAGCTGGCCAAACGGG 60.748 66.667 7.01 0.00 40.85 5.28
918 926 3.121030 CGAGAGCTGGCCAAACGG 61.121 66.667 7.01 0.00 0.00 4.44
919 927 3.121030 CCGAGAGCTGGCCAAACG 61.121 66.667 7.01 8.23 0.00 3.60
920 928 1.743252 CTCCGAGAGCTGGCCAAAC 60.743 63.158 7.01 1.16 0.00 2.93
921 929 2.665000 CTCCGAGAGCTGGCCAAA 59.335 61.111 7.01 0.00 0.00 3.28
922 930 3.393970 CCTCCGAGAGCTGGCCAA 61.394 66.667 7.01 0.00 0.00 4.52
925 933 3.535962 CTCCCTCCGAGAGCTGGC 61.536 72.222 0.00 0.00 41.63 4.85
926 934 2.837291 CCTCCCTCCGAGAGCTGG 60.837 72.222 0.00 0.00 41.63 4.85
927 935 1.827789 CTCCTCCCTCCGAGAGCTG 60.828 68.421 0.00 0.00 41.63 4.24
928 936 0.989212 TACTCCTCCCTCCGAGAGCT 60.989 60.000 0.00 0.00 41.63 4.09
929 937 0.111639 ATACTCCTCCCTCCGAGAGC 59.888 60.000 0.00 0.00 41.63 4.09
930 938 1.422024 TGATACTCCTCCCTCCGAGAG 59.578 57.143 0.00 0.00 41.63 3.20
931 939 1.519498 TGATACTCCTCCCTCCGAGA 58.481 55.000 0.00 0.00 41.63 4.04
932 940 2.595750 ATGATACTCCTCCCTCCGAG 57.404 55.000 0.00 0.00 38.46 4.63
933 941 2.447429 AGAATGATACTCCTCCCTCCGA 59.553 50.000 0.00 0.00 0.00 4.55
934 942 2.560542 CAGAATGATACTCCTCCCTCCG 59.439 54.545 0.00 0.00 39.69 4.63
935 943 3.582164 ACAGAATGATACTCCTCCCTCC 58.418 50.000 0.00 0.00 39.69 4.30
936 944 4.261825 CGAACAGAATGATACTCCTCCCTC 60.262 50.000 0.00 0.00 39.69 4.30
937 945 3.639094 CGAACAGAATGATACTCCTCCCT 59.361 47.826 0.00 0.00 39.69 4.20
938 946 3.385111 ACGAACAGAATGATACTCCTCCC 59.615 47.826 0.00 0.00 39.69 4.30
939 947 4.657436 ACGAACAGAATGATACTCCTCC 57.343 45.455 0.00 0.00 39.69 4.30
940 948 4.806247 CCAACGAACAGAATGATACTCCTC 59.194 45.833 0.00 0.00 39.69 3.71
941 949 4.759782 CCAACGAACAGAATGATACTCCT 58.240 43.478 0.00 0.00 39.69 3.69
942 950 3.309954 GCCAACGAACAGAATGATACTCC 59.690 47.826 0.00 0.00 39.69 3.85
943 951 3.932710 TGCCAACGAACAGAATGATACTC 59.067 43.478 0.00 0.00 39.69 2.59
944 952 3.935203 CTGCCAACGAACAGAATGATACT 59.065 43.478 0.00 0.00 39.69 2.12
945 953 3.485877 GCTGCCAACGAACAGAATGATAC 60.486 47.826 0.00 0.00 39.69 2.24
946 954 2.677836 GCTGCCAACGAACAGAATGATA 59.322 45.455 0.00 0.00 39.69 2.15
1023 1034 0.743097 GGATGATTGCTCCACCAAGC 59.257 55.000 0.00 0.00 42.82 4.01
1026 1037 1.224315 CCGGATGATTGCTCCACCA 59.776 57.895 0.00 0.00 32.72 4.17
1120 1142 2.472059 CGTCCACCGATGCCATTGG 61.472 63.158 9.57 9.57 39.56 3.16
1237 1265 2.593956 GGAAGGCGAAGTGGGGAGT 61.594 63.158 0.00 0.00 0.00 3.85
1238 1266 2.269241 GGAAGGCGAAGTGGGGAG 59.731 66.667 0.00 0.00 0.00 4.30
1239 1267 3.702048 CGGAAGGCGAAGTGGGGA 61.702 66.667 0.00 0.00 0.00 4.81
1240 1268 3.952628 GACGGAAGGCGAAGTGGGG 62.953 68.421 0.00 0.00 0.00 4.96
1241 1269 2.434359 GACGGAAGGCGAAGTGGG 60.434 66.667 0.00 0.00 0.00 4.61
1249 1277 4.083862 AGGGAAGCGACGGAAGGC 62.084 66.667 0.00 0.00 0.00 4.35
1250 1278 2.184579 GAGGGAAGCGACGGAAGG 59.815 66.667 0.00 0.00 0.00 3.46
1256 1284 1.281899 CAAGAATCGAGGGAAGCGAC 58.718 55.000 0.00 0.00 40.94 5.19
1293 1340 0.734253 CAAGAAGCTCCCGACAGACG 60.734 60.000 0.00 0.00 42.18 4.18
1303 1350 0.254178 TCCAGCCATCCAAGAAGCTC 59.746 55.000 0.00 0.00 31.93 4.09
1412 1527 2.728817 CGTACCTCGCCAGGATCC 59.271 66.667 3.62 2.48 43.65 3.36
1609 1752 5.885449 ATCTGTCATTAGAAGGGGAGAAG 57.115 43.478 0.00 0.00 0.00 2.85
1631 1774 7.724305 AGAAAGATAAACAACGCAAAGAGTA 57.276 32.000 0.00 0.00 0.00 2.59
1652 1797 8.506437 CAAAGCTTGACACATCAGTTATTAGAA 58.494 33.333 0.00 0.00 35.83 2.10
1683 1828 1.597742 CCACCCAACTGAACTGACAG 58.402 55.000 0.00 0.00 42.78 3.51
1694 1839 1.047801 AATTCAGTTGCCCACCCAAC 58.952 50.000 0.00 0.00 44.12 3.77
1695 1840 1.047002 CAATTCAGTTGCCCACCCAA 58.953 50.000 0.00 0.00 0.00 4.12
1696 1841 2.744062 CAATTCAGTTGCCCACCCA 58.256 52.632 0.00 0.00 0.00 4.51
1716 1862 4.951254 TCGAGTCATGTTAAACTGAACCA 58.049 39.130 0.00 0.00 0.00 3.67
1721 1867 8.412608 ACAGATTATCGAGTCATGTTAAACTG 57.587 34.615 7.85 7.85 32.31 3.16
1736 1882 7.801716 TTTTTCCCCATCTAACAGATTATCG 57.198 36.000 0.00 0.00 31.32 2.92
1841 2057 7.549134 TCTGCCATGTGACATTAAACTAGTAAG 59.451 37.037 0.00 0.00 0.00 2.34
2215 2820 3.409851 TCAATCAATGATTGCGTCTGC 57.590 42.857 26.32 0.00 46.14 4.26
2288 2896 3.421741 CACAAGTTTTGCGTTTTCTCGA 58.578 40.909 0.00 0.00 0.00 4.04
2350 2964 2.233922 GGTCAGTTGCTTCAGCCTAGTA 59.766 50.000 0.00 0.00 41.18 1.82
2372 2986 8.900983 ATGGTAGATTTTATCTTCTCTTGAGC 57.099 34.615 0.00 0.00 40.76 4.26
2392 3006 7.394923 AGGAAAATAAATGACGTCCAAATGGTA 59.605 33.333 14.12 0.00 36.34 3.25
2404 3018 7.617041 AGCAGTGAGTAGGAAAATAAATGAC 57.383 36.000 0.00 0.00 0.00 3.06
2452 3067 8.862550 AAACAGCTCAAATAAACAAGAAAGAG 57.137 30.769 0.00 0.00 0.00 2.85
2666 3300 5.757850 AAGAACAAAGAGCAACGAAGAAT 57.242 34.783 0.00 0.00 0.00 2.40
2813 3473 1.073722 CTTGCCAGCCTTCACCTCA 59.926 57.895 0.00 0.00 0.00 3.86
2904 3564 3.338249 TGTTCTGAAGGACATAGCAAGC 58.662 45.455 0.00 0.00 0.00 4.01
2905 3565 5.413833 ACAATGTTCTGAAGGACATAGCAAG 59.586 40.000 4.65 0.00 0.00 4.01
3360 4062 3.141398 TCAGACACAGCAAGAATGTTCC 58.859 45.455 0.00 0.00 0.00 3.62
3389 4091 6.216569 TGAAGTATATGCAGTAGCTTGCTAC 58.783 40.000 21.24 21.24 44.38 3.58
3416 4118 7.814587 CACTTAAAATTTGATGGGAAGGTCTTC 59.185 37.037 2.29 2.29 38.80 2.87
3423 4125 6.166984 TGCACACTTAAAATTTGATGGGAA 57.833 33.333 0.00 0.00 0.00 3.97
3546 4252 9.032624 TGTCTCCTTAGCTAACAGTAAGTAAAT 57.967 33.333 0.86 0.00 0.00 1.40
3550 4256 6.572703 GCTTGTCTCCTTAGCTAACAGTAAGT 60.573 42.308 0.86 0.00 32.26 2.24
3575 4281 4.027572 ACATGGACAACACGAAACTTTG 57.972 40.909 0.00 0.00 0.00 2.77
3577 4283 3.312421 CAGACATGGACAACACGAAACTT 59.688 43.478 0.00 0.00 0.00 2.66
3632 4341 3.507233 TCAGGTCTGCTAAATTTTGGCTG 59.493 43.478 16.94 16.04 38.08 4.85
3657 4366 2.570135 TCACACACTTATGCTGCAACA 58.430 42.857 6.36 0.00 0.00 3.33
3738 4447 7.972277 CCATGCTGCATAATATTCACCTTATTC 59.028 37.037 15.78 0.00 0.00 1.75
3816 4526 8.884124 AATGATGTTTATTTCTCCTTTCCTCA 57.116 30.769 0.00 0.00 0.00 3.86
3872 4583 8.246180 ACAATTTCAGCAATAAACCTGTGATAG 58.754 33.333 0.00 0.00 0.00 2.08
3878 4589 6.029346 AGGACAATTTCAGCAATAAACCTG 57.971 37.500 0.00 0.00 0.00 4.00
3943 4659 5.705609 TGTAAGATTGGAGAGGTTTTTGC 57.294 39.130 0.00 0.00 0.00 3.68
3978 4694 5.459536 AGTTTCATGCTTTCCTCCTTTTC 57.540 39.130 0.00 0.00 0.00 2.29
3983 4699 5.003804 TCTACAAGTTTCATGCTTTCCTCC 58.996 41.667 0.00 0.00 0.00 4.30
3998 4714 9.482175 AGGACTAAGATCTAATGTTCTACAAGT 57.518 33.333 0.00 0.00 0.00 3.16
4162 4964 3.356529 AATCGGATCAGTTCAAAGGCT 57.643 42.857 0.00 0.00 0.00 4.58
4210 5012 2.964464 ACTGAGCTGGATCGATCAATCT 59.036 45.455 25.93 16.46 0.00 2.40
4236 5038 3.316308 ACTTGCTGTTCATTGTTCAGTCC 59.684 43.478 10.56 0.41 0.00 3.85
4240 5042 2.286950 GCGACTTGCTGTTCATTGTTCA 60.287 45.455 0.00 0.00 41.73 3.18
4244 5046 2.404265 TTGCGACTTGCTGTTCATTG 57.596 45.000 0.00 0.00 46.63 2.82


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

AutoCloner maintained by Alex Coulton.