Multiple sequence alignment - TraesCS1D01G016700

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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 TraesCS1D01G016700 chr1D 100.000 3341 0 0 1 3341 7509095 7512435 0.000000e+00 6170.0
1 TraesCS1D01G016700 chr1D 84.073 879 91 27 2300 3139 7761538 7762406 0.000000e+00 802.0
2 TraesCS1D01G016700 chr1D 83.959 879 92 27 2300 3139 7731581 7732449 0.000000e+00 797.0
3 TraesCS1D01G016700 chr1D 93.367 196 6 4 942 1130 7037800 7037605 1.960000e-72 283.0
4 TraesCS1D01G016700 chr1B 90.611 2407 161 33 803 3187 9712830 9710467 0.000000e+00 3133.0
5 TraesCS1D01G016700 chr1B 87.331 592 43 12 89 667 664387376 664386804 0.000000e+00 649.0
6 TraesCS1D01G016700 chr1B 90.640 406 28 5 2738 3139 9923993 9924392 6.350000e-147 531.0
7 TraesCS1D01G016700 chr1B 93.333 360 15 2 2837 3187 9706397 9706038 1.060000e-144 523.0
8 TraesCS1D01G016700 chr1B 93.056 360 16 2 2837 3187 9708610 9708251 4.940000e-143 518.0
9 TraesCS1D01G016700 chr1B 87.390 341 38 4 337 674 373111405 373111067 1.450000e-103 387.0
10 TraesCS1D01G016700 chr1B 90.948 232 13 3 102 332 684286554 684286778 4.190000e-79 305.0
11 TraesCS1D01G016700 chr1B 100.000 48 0 0 3140 3187 9924428 9924475 4.590000e-14 89.8
12 TraesCS1D01G016700 chr2B 86.378 1615 173 33 948 2533 72589215 72587619 0.000000e+00 1720.0
13 TraesCS1D01G016700 chr2D 85.970 1618 174 25 948 2533 45547954 45546358 0.000000e+00 1681.0
14 TraesCS1D01G016700 chr2D 88.305 590 42 12 89 667 376948416 376947843 0.000000e+00 682.0
15 TraesCS1D01G016700 chr2D 81.722 569 51 29 102 667 571746160 571746678 3.080000e-115 425.0
16 TraesCS1D01G016700 chr1A 97.612 670 11 4 1 667 14809088 14809755 0.000000e+00 1144.0
17 TraesCS1D01G016700 chr1A 84.000 875 94 24 2300 3139 9197142 9198005 0.000000e+00 798.0
18 TraesCS1D01G016700 chr1A 83.808 877 94 24 2303 3139 9158319 9159187 0.000000e+00 789.0
19 TraesCS1D01G016700 chr1A 91.964 112 8 1 3231 3341 9123291 9123402 4.460000e-34 156.0
20 TraesCS1D01G016700 chr3B 95.301 681 16 7 1 668 215888926 215889603 0.000000e+00 1066.0
21 TraesCS1D01G016700 chr4A 85.876 885 120 5 942 1824 727127646 727128527 0.000000e+00 937.0
22 TraesCS1D01G016700 chr4A 85.792 549 75 3 945 1493 727190770 727190225 2.230000e-161 579.0
23 TraesCS1D01G016700 chr4A 82.456 570 47 26 102 668 729509489 729508970 1.830000e-122 449.0
24 TraesCS1D01G016700 chr4A 90.031 321 29 3 1888 2208 727128630 727128947 2.400000e-111 412.0
25 TraesCS1D01G016700 chrUn 84.429 867 88 20 2309 3139 276777778 276776923 0.000000e+00 809.0
26 TraesCS1D01G016700 chrUn 84.429 867 88 20 2309 3139 278891098 278890243 0.000000e+00 809.0
27 TraesCS1D01G016700 chr7D 88.364 593 41 13 89 670 177093471 177092896 0.000000e+00 688.0
28 TraesCS1D01G016700 chr5B 81.913 575 51 28 102 673 15120392 15119868 1.420000e-118 436.0
29 TraesCS1D01G016700 chr5B 81.787 582 50 27 89 667 605327091 605326563 1.420000e-118 436.0
30 TraesCS1D01G016700 chr5B 88.623 334 31 7 337 667 341579174 341578845 1.870000e-107 399.0
31 TraesCS1D01G016700 chr6A 81.293 588 53 28 86 669 50197595 50198129 1.110000e-114 424.0
32 TraesCS1D01G016700 chr6A 81.371 569 52 27 102 667 106803993 106804510 6.670000e-112 414.0
33 TraesCS1D01G016700 chr2A 89.254 335 30 5 337 668 3767033 3766702 6.670000e-112 414.0
34 TraesCS1D01G016700 chr2A 88.024 334 34 5 337 667 766842545 766842875 1.120000e-104 390.0
35 TraesCS1D01G016700 chr6B 73.671 771 163 25 1056 1818 712331924 712332662 2.560000e-66 263.0
36 TraesCS1D01G016700 chr5D 93.103 58 4 0 696 753 20209446 20209503 5.940000e-13 86.1


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 TraesCS1D01G016700 chr1D 7509095 7512435 3340 False 6170.000000 6170 100.000000 1 3341 1 chr1D.!!$F1 3340
1 TraesCS1D01G016700 chr1D 7761538 7762406 868 False 802.000000 802 84.073000 2300 3139 1 chr1D.!!$F3 839
2 TraesCS1D01G016700 chr1D 7731581 7732449 868 False 797.000000 797 83.959000 2300 3139 1 chr1D.!!$F2 839
3 TraesCS1D01G016700 chr1B 9706038 9712830 6792 True 1391.333333 3133 92.333333 803 3187 3 chr1B.!!$R3 2384
4 TraesCS1D01G016700 chr1B 664386804 664387376 572 True 649.000000 649 87.331000 89 667 1 chr1B.!!$R2 578
5 TraesCS1D01G016700 chr2B 72587619 72589215 1596 True 1720.000000 1720 86.378000 948 2533 1 chr2B.!!$R1 1585
6 TraesCS1D01G016700 chr2D 45546358 45547954 1596 True 1681.000000 1681 85.970000 948 2533 1 chr2D.!!$R1 1585
7 TraesCS1D01G016700 chr2D 376947843 376948416 573 True 682.000000 682 88.305000 89 667 1 chr2D.!!$R2 578
8 TraesCS1D01G016700 chr2D 571746160 571746678 518 False 425.000000 425 81.722000 102 667 1 chr2D.!!$F1 565
9 TraesCS1D01G016700 chr1A 14809088 14809755 667 False 1144.000000 1144 97.612000 1 667 1 chr1A.!!$F4 666
10 TraesCS1D01G016700 chr1A 9197142 9198005 863 False 798.000000 798 84.000000 2300 3139 1 chr1A.!!$F3 839
11 TraesCS1D01G016700 chr1A 9158319 9159187 868 False 789.000000 789 83.808000 2303 3139 1 chr1A.!!$F2 836
12 TraesCS1D01G016700 chr3B 215888926 215889603 677 False 1066.000000 1066 95.301000 1 668 1 chr3B.!!$F1 667
13 TraesCS1D01G016700 chr4A 727127646 727128947 1301 False 674.500000 937 87.953500 942 2208 2 chr4A.!!$F1 1266
14 TraesCS1D01G016700 chr4A 727190225 727190770 545 True 579.000000 579 85.792000 945 1493 1 chr4A.!!$R1 548
15 TraesCS1D01G016700 chr4A 729508970 729509489 519 True 449.000000 449 82.456000 102 668 1 chr4A.!!$R2 566
16 TraesCS1D01G016700 chrUn 276776923 276777778 855 True 809.000000 809 84.429000 2309 3139 1 chrUn.!!$R1 830
17 TraesCS1D01G016700 chrUn 278890243 278891098 855 True 809.000000 809 84.429000 2309 3139 1 chrUn.!!$R2 830
18 TraesCS1D01G016700 chr7D 177092896 177093471 575 True 688.000000 688 88.364000 89 670 1 chr7D.!!$R1 581
19 TraesCS1D01G016700 chr5B 15119868 15120392 524 True 436.000000 436 81.913000 102 673 1 chr5B.!!$R1 571
20 TraesCS1D01G016700 chr5B 605326563 605327091 528 True 436.000000 436 81.787000 89 667 1 chr5B.!!$R3 578
21 TraesCS1D01G016700 chr6A 50197595 50198129 534 False 424.000000 424 81.293000 86 669 1 chr6A.!!$F1 583
22 TraesCS1D01G016700 chr6A 106803993 106804510 517 False 414.000000 414 81.371000 102 667 1 chr6A.!!$F2 565
23 TraesCS1D01G016700 chr6B 712331924 712332662 738 False 263.000000 263 73.671000 1056 1818 1 chr6B.!!$F1 762

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
740 798 0.110056 GCATGCACGGTCAAGTCTTG 60.11 55.0 14.21 6.21 0.00 3.02 F
2042 2172 0.110486 AGCAGGAAACCGTGTCCAAT 59.89 50.0 10.55 0.00 37.65 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2076 2206 0.456824 CGCTGGATCCCGTCGATATG 60.457 60.0 9.9 0.0 0.00 1.78 R
3234 7832 1.358152 AATCGTCCCAGGTTTCTCCA 58.642 50.0 0.0 0.0 39.02 3.86 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
297 338 8.424274 AAAGGATCACTTGACAAAATTTTCAC 57.576 30.769 0.00 0.00 39.96 3.18
298 339 7.111247 AGGATCACTTGACAAAATTTTCACA 57.889 32.000 0.00 1.69 0.00 3.58
299 340 7.555087 AGGATCACTTGACAAAATTTTCACAA 58.445 30.769 0.00 9.26 0.00 3.33
300 341 8.040132 AGGATCACTTGACAAAATTTTCACAAA 58.960 29.630 15.42 6.44 0.00 2.83
301 342 8.829612 GGATCACTTGACAAAATTTTCACAAAT 58.170 29.630 15.42 7.38 33.72 2.32
302 343 9.853921 GATCACTTGACAAAATTTTCACAAATC 57.146 29.630 15.42 12.77 30.80 2.17
303 344 8.768957 TCACTTGACAAAATTTTCACAAATCA 57.231 26.923 15.42 5.93 30.80 2.57
335 377 6.899892 AGTTCTTCTAAAGATCCCCTGATT 57.100 37.500 0.00 0.00 37.38 2.57
420 475 8.415950 TGAAGCCTACATTCAAATTTAGGAAA 57.584 30.769 15.86 0.00 39.93 3.13
574 631 6.645003 TGCTATGTACTGGATATTACTTTGCG 59.355 38.462 0.00 0.00 31.38 4.85
676 734 2.279451 CGGCGCTGCACATAGCTA 60.279 61.111 7.64 0.00 45.94 3.32
677 735 2.305853 CGGCGCTGCACATAGCTAG 61.306 63.158 7.64 0.00 45.94 3.42
678 736 2.602322 GGCGCTGCACATAGCTAGC 61.602 63.158 6.62 6.62 45.94 3.42
679 737 1.593750 GCGCTGCACATAGCTAGCT 60.594 57.895 23.12 23.12 45.94 3.32
680 738 1.156645 GCGCTGCACATAGCTAGCTT 61.157 55.000 24.88 8.10 45.94 3.74
681 739 1.869754 GCGCTGCACATAGCTAGCTTA 60.870 52.381 24.88 9.42 45.94 3.09
682 740 2.681706 CGCTGCACATAGCTAGCTTAT 58.318 47.619 24.88 11.38 45.94 1.73
683 741 2.665537 CGCTGCACATAGCTAGCTTATC 59.334 50.000 24.88 8.69 45.94 1.75
684 742 2.999355 GCTGCACATAGCTAGCTTATCC 59.001 50.000 24.88 8.69 45.94 2.59
685 743 3.555795 GCTGCACATAGCTAGCTTATCCA 60.556 47.826 24.88 12.71 45.94 3.41
686 744 4.829968 CTGCACATAGCTAGCTTATCCAT 58.170 43.478 24.88 6.86 45.94 3.41
687 745 4.572909 TGCACATAGCTAGCTTATCCATG 58.427 43.478 24.88 21.10 45.94 3.66
688 746 4.040829 TGCACATAGCTAGCTTATCCATGT 59.959 41.667 24.88 21.77 45.94 3.21
689 747 5.245977 TGCACATAGCTAGCTTATCCATGTA 59.754 40.000 24.88 9.03 45.94 2.29
690 748 6.166279 GCACATAGCTAGCTTATCCATGTAA 58.834 40.000 24.88 0.00 41.15 2.41
691 749 6.091441 GCACATAGCTAGCTTATCCATGTAAC 59.909 42.308 24.88 16.01 41.15 2.50
692 750 7.154656 CACATAGCTAGCTTATCCATGTAACA 58.845 38.462 24.88 0.00 0.00 2.41
693 751 7.116948 CACATAGCTAGCTTATCCATGTAACAC 59.883 40.741 24.88 0.00 0.00 3.32
694 752 5.614324 AGCTAGCTTATCCATGTAACACA 57.386 39.130 12.68 0.00 0.00 3.72
695 753 5.360591 AGCTAGCTTATCCATGTAACACAC 58.639 41.667 12.68 0.00 0.00 3.82
696 754 5.104941 AGCTAGCTTATCCATGTAACACACA 60.105 40.000 12.68 0.00 42.69 3.72
697 755 5.235186 GCTAGCTTATCCATGTAACACACAG 59.765 44.000 7.70 0.00 41.51 3.66
698 756 3.941483 AGCTTATCCATGTAACACACAGC 59.059 43.478 0.00 0.00 41.51 4.40
699 757 3.941483 GCTTATCCATGTAACACACAGCT 59.059 43.478 0.00 0.00 41.51 4.24
700 758 5.104941 AGCTTATCCATGTAACACACAGCTA 60.105 40.000 0.00 0.00 41.51 3.32
701 759 5.235186 GCTTATCCATGTAACACACAGCTAG 59.765 44.000 0.00 0.00 41.51 3.42
702 760 2.972625 TCCATGTAACACACAGCTAGC 58.027 47.619 6.62 6.62 41.51 3.42
703 761 2.567169 TCCATGTAACACACAGCTAGCT 59.433 45.455 12.68 12.68 41.51 3.32
704 762 3.007940 TCCATGTAACACACAGCTAGCTT 59.992 43.478 16.46 1.38 41.51 3.74
705 763 4.221924 TCCATGTAACACACAGCTAGCTTA 59.778 41.667 16.46 0.23 41.51 3.09
706 764 5.104941 TCCATGTAACACACAGCTAGCTTAT 60.105 40.000 16.46 3.00 41.51 1.73
707 765 5.235186 CCATGTAACACACAGCTAGCTTATC 59.765 44.000 16.46 0.89 41.51 1.75
708 766 4.755411 TGTAACACACAGCTAGCTTATCC 58.245 43.478 16.46 0.00 31.89 2.59
709 767 3.981071 AACACACAGCTAGCTTATCCA 57.019 42.857 16.46 0.00 0.00 3.41
710 768 3.252974 ACACACAGCTAGCTTATCCAC 57.747 47.619 16.46 0.00 0.00 4.02
711 769 2.567169 ACACACAGCTAGCTTATCCACA 59.433 45.455 16.46 0.00 0.00 4.17
712 770 2.932614 CACACAGCTAGCTTATCCACAC 59.067 50.000 16.46 0.00 0.00 3.82
713 771 2.567169 ACACAGCTAGCTTATCCACACA 59.433 45.455 16.46 0.00 0.00 3.72
714 772 3.007940 ACACAGCTAGCTTATCCACACAA 59.992 43.478 16.46 0.00 0.00 3.33
715 773 3.372206 CACAGCTAGCTTATCCACACAAC 59.628 47.826 16.46 0.00 0.00 3.32
716 774 2.939103 CAGCTAGCTTATCCACACAACC 59.061 50.000 16.46 0.00 0.00 3.77
717 775 2.571653 AGCTAGCTTATCCACACAACCA 59.428 45.455 12.68 0.00 0.00 3.67
718 776 3.200825 AGCTAGCTTATCCACACAACCAT 59.799 43.478 12.68 0.00 0.00 3.55
719 777 3.313526 GCTAGCTTATCCACACAACCATG 59.686 47.826 7.70 0.00 0.00 3.66
720 778 3.439857 AGCTTATCCACACAACCATGT 57.560 42.857 0.00 0.00 41.61 3.21
736 794 3.343972 GTGCATGCACGGTCAAGT 58.656 55.556 33.20 0.00 37.19 3.16
737 795 1.207593 GTGCATGCACGGTCAAGTC 59.792 57.895 33.20 9.23 37.19 3.01
738 796 1.071299 TGCATGCACGGTCAAGTCT 59.929 52.632 18.46 0.00 0.00 3.24
739 797 0.534877 TGCATGCACGGTCAAGTCTT 60.535 50.000 18.46 0.00 0.00 3.01
740 798 0.110056 GCATGCACGGTCAAGTCTTG 60.110 55.000 14.21 6.21 0.00 3.02
741 799 1.511850 CATGCACGGTCAAGTCTTGA 58.488 50.000 11.36 11.36 37.33 3.02
742 800 2.079158 CATGCACGGTCAAGTCTTGAT 58.921 47.619 18.08 0.00 42.47 2.57
743 801 2.254546 TGCACGGTCAAGTCTTGATT 57.745 45.000 18.08 3.83 42.47 2.57
744 802 3.394674 TGCACGGTCAAGTCTTGATTA 57.605 42.857 18.08 0.00 42.47 1.75
745 803 3.937814 TGCACGGTCAAGTCTTGATTAT 58.062 40.909 18.08 4.36 42.47 1.28
746 804 3.932710 TGCACGGTCAAGTCTTGATTATC 59.067 43.478 18.08 5.56 42.47 1.75
747 805 3.309954 GCACGGTCAAGTCTTGATTATCC 59.690 47.826 18.08 13.03 42.47 2.59
748 806 4.759782 CACGGTCAAGTCTTGATTATCCT 58.240 43.478 18.08 3.19 42.47 3.24
749 807 5.681437 GCACGGTCAAGTCTTGATTATCCTA 60.681 44.000 18.08 0.00 42.47 2.94
750 808 6.338146 CACGGTCAAGTCTTGATTATCCTAA 58.662 40.000 18.08 0.00 42.47 2.69
751 809 6.255887 CACGGTCAAGTCTTGATTATCCTAAC 59.744 42.308 18.08 3.02 42.47 2.34
752 810 6.070995 ACGGTCAAGTCTTGATTATCCTAACA 60.071 38.462 18.08 0.00 42.47 2.41
753 811 6.986817 CGGTCAAGTCTTGATTATCCTAACAT 59.013 38.462 18.08 0.00 42.47 2.71
754 812 7.495934 CGGTCAAGTCTTGATTATCCTAACATT 59.504 37.037 18.08 0.00 42.47 2.71
755 813 8.831550 GGTCAAGTCTTGATTATCCTAACATTC 58.168 37.037 18.08 0.71 42.47 2.67
756 814 9.606631 GTCAAGTCTTGATTATCCTAACATTCT 57.393 33.333 18.08 0.00 42.47 2.40
769 827 7.348080 TCCTAACATTCTACACTATCACTGG 57.652 40.000 0.00 0.00 0.00 4.00
770 828 7.123383 TCCTAACATTCTACACTATCACTGGA 58.877 38.462 0.00 0.00 0.00 3.86
771 829 7.285629 TCCTAACATTCTACACTATCACTGGAG 59.714 40.741 0.00 0.00 0.00 3.86
772 830 6.859112 AACATTCTACACTATCACTGGAGT 57.141 37.500 0.00 0.00 0.00 3.85
773 831 6.859112 ACATTCTACACTATCACTGGAGTT 57.141 37.500 0.00 0.00 0.00 3.01
774 832 6.634805 ACATTCTACACTATCACTGGAGTTG 58.365 40.000 0.00 0.00 0.00 3.16
775 833 6.437477 ACATTCTACACTATCACTGGAGTTGA 59.563 38.462 0.00 0.00 0.00 3.18
776 834 6.911250 TTCTACACTATCACTGGAGTTGAA 57.089 37.500 0.00 0.00 0.00 2.69
777 835 6.516739 TCTACACTATCACTGGAGTTGAAG 57.483 41.667 0.00 0.00 0.00 3.02
778 836 4.543590 ACACTATCACTGGAGTTGAAGG 57.456 45.455 0.00 0.00 0.00 3.46
779 837 4.160329 ACACTATCACTGGAGTTGAAGGA 58.840 43.478 0.00 0.00 0.00 3.36
780 838 4.780021 ACACTATCACTGGAGTTGAAGGAT 59.220 41.667 0.00 0.00 0.00 3.24
781 839 5.958380 ACACTATCACTGGAGTTGAAGGATA 59.042 40.000 0.00 0.00 0.00 2.59
782 840 6.613271 ACACTATCACTGGAGTTGAAGGATAT 59.387 38.462 0.00 0.00 0.00 1.63
783 841 7.126421 ACACTATCACTGGAGTTGAAGGATATT 59.874 37.037 0.00 0.00 0.00 1.28
784 842 7.989741 CACTATCACTGGAGTTGAAGGATATTT 59.010 37.037 0.00 0.00 0.00 1.40
785 843 8.207545 ACTATCACTGGAGTTGAAGGATATTTC 58.792 37.037 0.00 0.00 0.00 2.17
786 844 6.627087 TCACTGGAGTTGAAGGATATTTCT 57.373 37.500 0.00 0.00 0.00 2.52
787 845 7.020827 TCACTGGAGTTGAAGGATATTTCTT 57.979 36.000 0.00 0.00 0.00 2.52
788 846 7.461749 TCACTGGAGTTGAAGGATATTTCTTT 58.538 34.615 0.00 0.00 0.00 2.52
789 847 8.602424 TCACTGGAGTTGAAGGATATTTCTTTA 58.398 33.333 0.00 0.00 0.00 1.85
790 848 9.401058 CACTGGAGTTGAAGGATATTTCTTTAT 57.599 33.333 0.00 0.00 0.00 1.40
791 849 9.981460 ACTGGAGTTGAAGGATATTTCTTTATT 57.019 29.630 0.00 0.00 0.00 1.40
800 858 9.931210 GAAGGATATTTCTTTATTTACACGTGG 57.069 33.333 21.57 1.66 0.00 4.94
801 859 8.446599 AGGATATTTCTTTATTTACACGTGGG 57.553 34.615 21.57 0.00 0.00 4.61
818 876 4.261801 CGTGGGTGATTTAGGAAATCTGT 58.738 43.478 11.97 0.00 45.85 3.41
819 877 4.700213 CGTGGGTGATTTAGGAAATCTGTT 59.300 41.667 11.97 0.00 45.85 3.16
821 879 6.542370 CGTGGGTGATTTAGGAAATCTGTTAT 59.458 38.462 11.97 0.00 45.85 1.89
882 940 1.814394 GCCTGATTGCAAGTCACATCA 59.186 47.619 4.94 1.36 0.00 3.07
906 964 3.073678 TCACATCCAATGACTTTCCGTG 58.926 45.455 0.00 0.00 0.00 4.94
915 973 5.401550 CAATGACTTTCCGTGCATTATGTT 58.598 37.500 0.00 0.00 30.45 2.71
924 982 2.284798 CGTGCATTATGTTACGTCACGG 60.285 50.000 0.35 0.00 41.14 4.94
925 983 1.661617 TGCATTATGTTACGTCACGGC 59.338 47.619 0.35 0.00 0.00 5.68
930 988 0.179119 ATGTTACGTCACGGCTAGCC 60.179 55.000 24.75 24.75 0.00 3.93
940 998 2.829458 GGCTAGCCGTCGGAGAGT 60.829 66.667 20.16 0.00 36.95 3.24
941 999 1.525535 GGCTAGCCGTCGGAGAGTA 60.526 63.158 20.16 0.00 36.95 2.59
1008 1081 3.084039 CCTAGCATTCAACACACCATGT 58.916 45.455 0.00 0.00 46.42 3.21
1022 1095 1.446099 CATGTCGTCCCACGTCCAG 60.446 63.158 0.00 0.00 43.14 3.86
1163 1242 2.070039 CGCCATCCACCTTAGGGGA 61.070 63.158 0.04 6.51 38.76 4.81
1194 1273 1.372087 CTTGTCTGATCTTGCCGCCC 61.372 60.000 0.00 0.00 0.00 6.13
1233 1312 0.903454 GAAGTTCTCCCACCTCCGGA 60.903 60.000 2.93 2.93 0.00 5.14
1334 1416 1.545706 GGGTCTCTCGCCTCCTTGTT 61.546 60.000 0.00 0.00 0.00 2.83
1337 1419 0.832135 TCTCTCGCCTCCTTGTTGGT 60.832 55.000 0.00 0.00 37.07 3.67
1343 1425 1.151450 CCTCCTTGTTGGTGCTGGT 59.849 57.895 0.00 0.00 37.07 4.00
1376 1458 3.680786 CGCCGTGACCTGTCTCCA 61.681 66.667 0.00 0.00 0.00 3.86
1382 1467 1.270839 CGTGACCTGTCTCCAATGGTT 60.271 52.381 0.00 0.00 32.30 3.67
1410 1495 4.444838 TCAACCCGGTCGCCATCG 62.445 66.667 0.00 0.00 0.00 3.84
1451 1536 1.259770 GAGTGGTTCACCGACGAAAAC 59.740 52.381 0.00 0.00 39.43 2.43
1464 1549 2.672996 AAAACAGCGCCGCCTCAT 60.673 55.556 4.98 0.00 0.00 2.90
1479 1564 2.556257 CCTCATCGTCTCTCTTCGAGA 58.444 52.381 0.00 0.00 46.32 4.04
1490 1575 1.522355 CTTCGAGATGGCGCATGGT 60.522 57.895 10.83 0.00 0.00 3.55
1619 1704 1.735376 GCAGCGTCTTCGGATCCCTA 61.735 60.000 6.06 0.00 37.56 3.53
1820 1905 4.625028 ACACCGTTCTACTCAAGGTAAAC 58.375 43.478 0.00 0.00 33.30 2.01
1829 1954 7.549147 TCTACTCAAGGTAAACATACAACCT 57.451 36.000 0.00 0.00 45.62 3.50
1856 1986 8.840321 GCATAGTCCATTTCACTATAACAACAT 58.160 33.333 0.00 0.00 35.28 2.71
1955 2085 3.033184 CGCCAGTGCAAGAAAGCA 58.967 55.556 0.00 0.00 43.35 3.91
2013 2143 2.248248 TGGATATGGTGGTCGGATCTC 58.752 52.381 0.00 0.00 0.00 2.75
2014 2144 2.248248 GGATATGGTGGTCGGATCTCA 58.752 52.381 0.00 0.00 0.00 3.27
2020 2150 1.306141 TGGTCGGATCTCAAGGGCT 60.306 57.895 0.00 0.00 0.00 5.19
2042 2172 0.110486 AGCAGGAAACCGTGTCCAAT 59.890 50.000 10.55 0.00 37.65 3.16
2072 2202 5.642063 GGAGGTTTTGTTCGATGTCTTCATA 59.358 40.000 0.00 0.00 34.06 2.15
2076 2206 6.251376 GGTTTTGTTCGATGTCTTCATAATGC 59.749 38.462 0.00 0.00 34.06 3.56
2078 2208 6.682423 TTGTTCGATGTCTTCATAATGCAT 57.318 33.333 0.00 0.00 34.06 3.96
2159 2289 3.119245 TCAGCGACTACAAGATTACACCC 60.119 47.826 0.00 0.00 0.00 4.61
2307 2442 4.938226 AGTAAAATGAGTGCTAGCTTGACC 59.062 41.667 17.23 1.52 0.00 4.02
2392 2530 7.095271 CGTTGCAAAATCACCATCCTTTTAAAT 60.095 33.333 0.00 0.00 0.00 1.40
2412 2551 2.223745 TGATAGACGCGTATGCCACTA 58.776 47.619 18.06 11.08 38.08 2.74
2416 2555 1.136305 AGACGCGTATGCCACTAACAT 59.864 47.619 13.97 0.00 38.08 2.71
2446 2586 5.883328 TGTCGATATTCATGCGTAACTTC 57.117 39.130 0.00 0.00 0.00 3.01
2465 2610 7.526142 AACTTCCTTTCTTAGTCCCAAAATC 57.474 36.000 0.00 0.00 0.00 2.17
2471 2616 8.933653 TCCTTTCTTAGTCCCAAAATCAAAATT 58.066 29.630 0.00 0.00 0.00 1.82
2635 2818 8.699749 GTTGTCAAATAAAAAGCACATACTTCC 58.300 33.333 0.00 0.00 0.00 3.46
2673 2857 5.552178 AGAGTACTTTTCTGCGAGGAAAAT 58.448 37.500 13.51 8.66 42.07 1.82
2680 2864 5.560966 TTTCTGCGAGGAAAATAATGGAC 57.439 39.130 0.00 0.00 33.04 4.02
2689 2875 6.370442 CGAGGAAAATAATGGACACAACACTA 59.630 38.462 0.00 0.00 0.00 2.74
2690 2876 7.065803 CGAGGAAAATAATGGACACAACACTAT 59.934 37.037 0.00 0.00 0.00 2.12
2932 5310 8.828644 TCAATTTACAAAGAAGTTAGCACGTAA 58.171 29.630 0.00 0.00 0.00 3.18
2943 5321 5.548406 AGTTAGCACGTAAGAAAAGTGGAT 58.452 37.500 0.00 0.00 37.96 3.41
3083 7675 9.442047 ACTGTAGATCACAAAAATAGAGAAAGG 57.558 33.333 0.00 0.00 36.48 3.11
3187 7785 6.023435 CACGATCAAATCACTAACCACATTG 58.977 40.000 0.00 0.00 0.00 2.82
3188 7786 5.123820 ACGATCAAATCACTAACCACATTGG 59.876 40.000 0.00 0.00 45.02 3.16
3189 7787 4.782019 TCAAATCACTAACCACATTGGC 57.218 40.909 0.00 0.00 42.67 4.52
3190 7788 3.190327 TCAAATCACTAACCACATTGGCG 59.810 43.478 0.00 0.00 42.67 5.69
3191 7789 2.779755 ATCACTAACCACATTGGCGA 57.220 45.000 0.00 0.00 42.67 5.54
3192 7790 2.093306 TCACTAACCACATTGGCGAG 57.907 50.000 0.00 0.00 42.67 5.03
3193 7791 1.086696 CACTAACCACATTGGCGAGG 58.913 55.000 0.00 0.00 42.67 4.63
3194 7792 0.035439 ACTAACCACATTGGCGAGGG 60.035 55.000 0.00 0.00 42.67 4.30
3195 7793 1.376609 CTAACCACATTGGCGAGGGC 61.377 60.000 0.00 0.00 42.67 5.19
3206 7804 2.978010 CGAGGGCGGCAACAGTTT 60.978 61.111 12.47 0.00 0.00 2.66
3207 7805 2.551912 CGAGGGCGGCAACAGTTTT 61.552 57.895 12.47 0.00 0.00 2.43
3208 7806 1.739667 GAGGGCGGCAACAGTTTTT 59.260 52.632 12.47 0.00 0.00 1.94
3246 7844 8.539117 AAAAAGGAATATATGGAGAAACCTGG 57.461 34.615 0.00 0.00 39.86 4.45
3247 7845 5.850046 AGGAATATATGGAGAAACCTGGG 57.150 43.478 0.00 0.00 39.86 4.45
3248 7846 5.486332 AGGAATATATGGAGAAACCTGGGA 58.514 41.667 0.00 0.00 39.86 4.37
3249 7847 5.310857 AGGAATATATGGAGAAACCTGGGAC 59.689 44.000 0.00 0.00 39.86 4.46
3250 7848 4.891992 ATATATGGAGAAACCTGGGACG 57.108 45.455 0.00 0.00 39.86 4.79
3251 7849 2.241281 TATGGAGAAACCTGGGACGA 57.759 50.000 0.00 0.00 39.86 4.20
3252 7850 1.584724 ATGGAGAAACCTGGGACGAT 58.415 50.000 0.00 0.00 39.86 3.73
3253 7851 1.358152 TGGAGAAACCTGGGACGATT 58.642 50.000 0.00 0.00 39.86 3.34
3254 7852 1.702957 TGGAGAAACCTGGGACGATTT 59.297 47.619 0.00 0.00 39.86 2.17
3255 7853 2.107552 TGGAGAAACCTGGGACGATTTT 59.892 45.455 0.00 0.00 39.86 1.82
3256 7854 2.488153 GGAGAAACCTGGGACGATTTTG 59.512 50.000 0.00 0.00 35.41 2.44
3257 7855 3.408634 GAGAAACCTGGGACGATTTTGA 58.591 45.455 0.00 0.00 0.00 2.69
3258 7856 4.010349 GAGAAACCTGGGACGATTTTGAT 58.990 43.478 0.00 0.00 0.00 2.57
3259 7857 4.010349 AGAAACCTGGGACGATTTTGATC 58.990 43.478 0.00 0.00 0.00 2.92
3260 7858 3.433306 AACCTGGGACGATTTTGATCA 57.567 42.857 0.00 0.00 0.00 2.92
3261 7859 3.433306 ACCTGGGACGATTTTGATCAA 57.567 42.857 3.38 3.38 0.00 2.57
3262 7860 3.081804 ACCTGGGACGATTTTGATCAAC 58.918 45.455 7.89 0.00 0.00 3.18
3263 7861 3.081061 CCTGGGACGATTTTGATCAACA 58.919 45.455 7.89 1.31 0.00 3.33
3264 7862 3.505680 CCTGGGACGATTTTGATCAACAA 59.494 43.478 7.89 6.58 36.65 2.83
3265 7863 4.379813 CCTGGGACGATTTTGATCAACAAG 60.380 45.833 7.89 3.43 39.77 3.16
3266 7864 3.505680 TGGGACGATTTTGATCAACAAGG 59.494 43.478 7.89 0.83 39.77 3.61
3267 7865 3.506067 GGGACGATTTTGATCAACAAGGT 59.494 43.478 7.89 4.19 39.77 3.50
3268 7866 4.698304 GGGACGATTTTGATCAACAAGGTA 59.302 41.667 7.89 0.00 39.77 3.08
3269 7867 5.182380 GGGACGATTTTGATCAACAAGGTAA 59.818 40.000 7.89 0.00 39.77 2.85
3270 7868 6.294286 GGGACGATTTTGATCAACAAGGTAAA 60.294 38.462 7.89 0.00 39.77 2.01
3271 7869 7.142680 GGACGATTTTGATCAACAAGGTAAAA 58.857 34.615 7.89 0.00 39.77 1.52
3272 7870 7.812669 GGACGATTTTGATCAACAAGGTAAAAT 59.187 33.333 7.89 2.50 39.77 1.82
3273 7871 9.834628 GACGATTTTGATCAACAAGGTAAAATA 57.165 29.630 7.89 0.00 39.77 1.40
3281 7879 8.956426 TGATCAACAAGGTAAAATAAGATGACC 58.044 33.333 0.00 0.00 0.00 4.02
3282 7880 8.877864 ATCAACAAGGTAAAATAAGATGACCA 57.122 30.769 0.00 0.00 32.28 4.02
3283 7881 8.877864 TCAACAAGGTAAAATAAGATGACCAT 57.122 30.769 0.00 0.00 32.28 3.55
3284 7882 9.967451 TCAACAAGGTAAAATAAGATGACCATA 57.033 29.630 0.00 0.00 32.28 2.74
3286 7884 9.975218 AACAAGGTAAAATAAGATGACCATACT 57.025 29.630 0.00 0.00 32.28 2.12
3287 7885 9.614792 ACAAGGTAAAATAAGATGACCATACTC 57.385 33.333 0.00 0.00 32.28 2.59
3288 7886 9.613428 CAAGGTAAAATAAGATGACCATACTCA 57.387 33.333 0.00 0.00 32.28 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
244 271 8.560903 AGGGATTTTACCTCTTCATCTATTTGT 58.439 33.333 0.00 0.00 31.01 2.83
302 343 9.575783 GGATCTTTAGAAGAACTACTAGTTGTG 57.424 37.037 10.78 0.10 38.80 3.33
303 344 8.751242 GGGATCTTTAGAAGAACTACTAGTTGT 58.249 37.037 6.17 1.41 38.80 3.32
335 377 7.446769 TGGTTGCTACTTAGATCTTTTGTGTA 58.553 34.615 0.00 0.00 0.00 2.90
420 475 2.825861 CTTTCCACAAAAGCCTGCAT 57.174 45.000 0.00 0.00 38.11 3.96
670 728 7.155328 GTGTGTTACATGGATAAGCTAGCTAT 58.845 38.462 19.70 11.72 0.00 2.97
673 731 5.116180 TGTGTGTTACATGGATAAGCTAGC 58.884 41.667 6.62 6.62 33.42 3.42
674 732 5.235186 GCTGTGTGTTACATGGATAAGCTAG 59.765 44.000 0.00 0.00 38.92 3.42
675 733 5.104941 AGCTGTGTGTTACATGGATAAGCTA 60.105 40.000 0.00 0.00 38.92 3.32
676 734 3.941483 GCTGTGTGTTACATGGATAAGCT 59.059 43.478 0.00 0.00 38.92 3.74
677 735 3.941483 AGCTGTGTGTTACATGGATAAGC 59.059 43.478 0.00 0.00 38.92 3.09
678 736 5.235186 GCTAGCTGTGTGTTACATGGATAAG 59.765 44.000 7.70 0.00 38.92 1.73
679 737 5.104941 AGCTAGCTGTGTGTTACATGGATAA 60.105 40.000 18.57 0.00 38.92 1.75
680 738 4.405680 AGCTAGCTGTGTGTTACATGGATA 59.594 41.667 18.57 0.00 38.92 2.59
681 739 3.198635 AGCTAGCTGTGTGTTACATGGAT 59.801 43.478 18.57 0.00 38.92 3.41
682 740 2.567169 AGCTAGCTGTGTGTTACATGGA 59.433 45.455 18.57 0.00 38.92 3.41
683 741 2.977914 AGCTAGCTGTGTGTTACATGG 58.022 47.619 18.57 0.00 38.92 3.66
684 742 5.235186 GGATAAGCTAGCTGTGTGTTACATG 59.765 44.000 20.16 0.00 38.92 3.21
685 743 5.104941 TGGATAAGCTAGCTGTGTGTTACAT 60.105 40.000 20.16 0.11 38.92 2.29
686 744 4.221924 TGGATAAGCTAGCTGTGTGTTACA 59.778 41.667 20.16 7.03 37.78 2.41
687 745 4.567159 GTGGATAAGCTAGCTGTGTGTTAC 59.433 45.833 20.16 8.36 0.00 2.50
688 746 4.221924 TGTGGATAAGCTAGCTGTGTGTTA 59.778 41.667 20.16 5.97 0.00 2.41
689 747 3.007940 TGTGGATAAGCTAGCTGTGTGTT 59.992 43.478 20.16 3.46 0.00 3.32
690 748 2.567169 TGTGGATAAGCTAGCTGTGTGT 59.433 45.455 20.16 4.30 0.00 3.72
691 749 2.932614 GTGTGGATAAGCTAGCTGTGTG 59.067 50.000 20.16 0.00 0.00 3.82
692 750 2.567169 TGTGTGGATAAGCTAGCTGTGT 59.433 45.455 20.16 7.28 0.00 3.72
693 751 3.251479 TGTGTGGATAAGCTAGCTGTG 57.749 47.619 20.16 0.00 0.00 3.66
694 752 3.600388 GTTGTGTGGATAAGCTAGCTGT 58.400 45.455 20.16 10.54 0.00 4.40
695 753 2.939103 GGTTGTGTGGATAAGCTAGCTG 59.061 50.000 20.16 0.00 0.00 4.24
696 754 2.571653 TGGTTGTGTGGATAAGCTAGCT 59.428 45.455 12.68 12.68 0.00 3.32
697 755 2.985896 TGGTTGTGTGGATAAGCTAGC 58.014 47.619 6.62 6.62 0.00 3.42
698 756 4.333649 CACATGGTTGTGTGGATAAGCTAG 59.666 45.833 0.00 0.00 46.68 3.42
699 757 4.260985 CACATGGTTGTGTGGATAAGCTA 58.739 43.478 0.00 0.00 46.68 3.32
700 758 3.084039 CACATGGTTGTGTGGATAAGCT 58.916 45.455 0.00 0.00 46.68 3.74
701 759 3.492421 CACATGGTTGTGTGGATAAGC 57.508 47.619 0.00 0.00 46.68 3.09
711 769 1.286570 CGTGCATGCACATGGTTGT 59.713 52.632 40.95 0.00 46.47 3.32
712 770 1.444724 CCGTGCATGCACATGGTTG 60.445 57.895 40.95 26.92 46.47 3.77
713 771 2.964174 CCGTGCATGCACATGGTT 59.036 55.556 40.95 0.00 46.47 3.67
716 774 0.455464 CTTGACCGTGCATGCACATG 60.455 55.000 40.95 33.64 46.47 3.21
717 775 0.890542 ACTTGACCGTGCATGCACAT 60.891 50.000 40.95 31.49 46.47 3.21
718 776 1.506309 GACTTGACCGTGCATGCACA 61.506 55.000 40.95 24.84 46.47 4.57
719 777 1.207593 GACTTGACCGTGCATGCAC 59.792 57.895 35.76 35.76 43.01 4.57
720 778 0.534877 AAGACTTGACCGTGCATGCA 60.535 50.000 18.46 18.46 0.00 3.96
721 779 0.110056 CAAGACTTGACCGTGCATGC 60.110 55.000 11.82 11.82 0.00 4.06
722 780 1.511850 TCAAGACTTGACCGTGCATG 58.488 50.000 13.99 0.00 34.08 4.06
723 781 2.479566 ATCAAGACTTGACCGTGCAT 57.520 45.000 19.96 0.00 43.48 3.96
724 782 2.254546 AATCAAGACTTGACCGTGCA 57.745 45.000 19.96 0.00 43.48 4.57
725 783 3.309954 GGATAATCAAGACTTGACCGTGC 59.690 47.826 19.96 10.01 43.48 5.34
726 784 4.759782 AGGATAATCAAGACTTGACCGTG 58.240 43.478 19.96 0.00 43.48 4.94
727 785 6.070995 TGTTAGGATAATCAAGACTTGACCGT 60.071 38.462 19.96 10.85 43.48 4.83
728 786 6.338146 TGTTAGGATAATCAAGACTTGACCG 58.662 40.000 19.96 0.00 43.48 4.79
729 787 8.738645 AATGTTAGGATAATCAAGACTTGACC 57.261 34.615 19.96 15.74 43.48 4.02
730 788 9.606631 AGAATGTTAGGATAATCAAGACTTGAC 57.393 33.333 19.96 7.44 43.48 3.18
743 801 9.078990 CCAGTGATAGTGTAGAATGTTAGGATA 57.921 37.037 0.00 0.00 0.00 2.59
744 802 7.785028 TCCAGTGATAGTGTAGAATGTTAGGAT 59.215 37.037 0.00 0.00 0.00 3.24
745 803 7.123383 TCCAGTGATAGTGTAGAATGTTAGGA 58.877 38.462 0.00 0.00 0.00 2.94
746 804 7.068839 ACTCCAGTGATAGTGTAGAATGTTAGG 59.931 40.741 0.00 0.00 0.00 2.69
747 805 8.001881 ACTCCAGTGATAGTGTAGAATGTTAG 57.998 38.462 0.00 0.00 0.00 2.34
748 806 7.956328 ACTCCAGTGATAGTGTAGAATGTTA 57.044 36.000 0.00 0.00 0.00 2.41
749 807 6.859112 ACTCCAGTGATAGTGTAGAATGTT 57.141 37.500 0.00 0.00 0.00 2.71
750 808 6.437477 TCAACTCCAGTGATAGTGTAGAATGT 59.563 38.462 0.00 0.00 0.00 2.71
751 809 6.867550 TCAACTCCAGTGATAGTGTAGAATG 58.132 40.000 0.00 0.00 0.00 2.67
752 810 7.364232 CCTTCAACTCCAGTGATAGTGTAGAAT 60.364 40.741 0.00 0.00 0.00 2.40
753 811 6.071334 CCTTCAACTCCAGTGATAGTGTAGAA 60.071 42.308 0.00 1.08 0.00 2.10
754 812 5.419155 CCTTCAACTCCAGTGATAGTGTAGA 59.581 44.000 0.00 0.00 0.00 2.59
755 813 5.419155 TCCTTCAACTCCAGTGATAGTGTAG 59.581 44.000 0.00 0.00 0.00 2.74
756 814 5.330233 TCCTTCAACTCCAGTGATAGTGTA 58.670 41.667 0.00 0.00 0.00 2.90
757 815 4.160329 TCCTTCAACTCCAGTGATAGTGT 58.840 43.478 0.00 0.00 0.00 3.55
758 816 4.808414 TCCTTCAACTCCAGTGATAGTG 57.192 45.455 0.00 0.00 0.00 2.74
759 817 7.682787 AATATCCTTCAACTCCAGTGATAGT 57.317 36.000 0.00 0.00 0.00 2.12
760 818 8.428063 AGAAATATCCTTCAACTCCAGTGATAG 58.572 37.037 0.00 0.00 0.00 2.08
761 819 8.324191 AGAAATATCCTTCAACTCCAGTGATA 57.676 34.615 0.00 0.00 0.00 2.15
762 820 7.205515 AGAAATATCCTTCAACTCCAGTGAT 57.794 36.000 0.00 0.00 0.00 3.06
763 821 6.627087 AGAAATATCCTTCAACTCCAGTGA 57.373 37.500 0.00 0.00 0.00 3.41
764 822 7.693969 AAAGAAATATCCTTCAACTCCAGTG 57.306 36.000 0.00 0.00 0.00 3.66
765 823 9.981460 AATAAAGAAATATCCTTCAACTCCAGT 57.019 29.630 0.00 0.00 0.00 4.00
774 832 9.931210 CCACGTGTAAATAAAGAAATATCCTTC 57.069 33.333 15.65 0.00 0.00 3.46
775 833 8.899771 CCCACGTGTAAATAAAGAAATATCCTT 58.100 33.333 15.65 0.00 0.00 3.36
776 834 8.050930 ACCCACGTGTAAATAAAGAAATATCCT 58.949 33.333 15.65 0.00 0.00 3.24
777 835 8.126700 CACCCACGTGTAAATAAAGAAATATCC 58.873 37.037 15.65 0.00 35.10 2.59
778 836 8.885722 TCACCCACGTGTAAATAAAGAAATATC 58.114 33.333 15.65 0.00 41.09 1.63
779 837 8.795842 TCACCCACGTGTAAATAAAGAAATAT 57.204 30.769 15.65 0.00 41.09 1.28
780 838 8.795842 ATCACCCACGTGTAAATAAAGAAATA 57.204 30.769 15.65 0.00 41.09 1.40
781 839 7.696992 ATCACCCACGTGTAAATAAAGAAAT 57.303 32.000 15.65 0.00 41.09 2.17
782 840 7.513371 AATCACCCACGTGTAAATAAAGAAA 57.487 32.000 15.65 0.00 41.09 2.52
783 841 7.513371 AAATCACCCACGTGTAAATAAAGAA 57.487 32.000 15.65 0.00 41.09 2.52
784 842 7.334921 CCTAAATCACCCACGTGTAAATAAAGA 59.665 37.037 15.65 1.32 41.09 2.52
785 843 7.334921 TCCTAAATCACCCACGTGTAAATAAAG 59.665 37.037 15.65 2.99 41.09 1.85
786 844 7.166851 TCCTAAATCACCCACGTGTAAATAAA 58.833 34.615 15.65 0.00 41.09 1.40
787 845 6.709281 TCCTAAATCACCCACGTGTAAATAA 58.291 36.000 15.65 0.00 41.09 1.40
788 846 6.297080 TCCTAAATCACCCACGTGTAAATA 57.703 37.500 15.65 0.00 41.09 1.40
789 847 5.168647 TCCTAAATCACCCACGTGTAAAT 57.831 39.130 15.65 0.00 41.09 1.40
790 848 4.620589 TCCTAAATCACCCACGTGTAAA 57.379 40.909 15.65 0.00 41.09 2.01
791 849 4.620589 TTCCTAAATCACCCACGTGTAA 57.379 40.909 15.65 0.00 41.09 2.41
792 850 4.620589 TTTCCTAAATCACCCACGTGTA 57.379 40.909 15.65 0.00 41.09 2.90
793 851 3.495434 TTTCCTAAATCACCCACGTGT 57.505 42.857 15.65 0.00 41.09 4.49
794 852 4.616181 GATTTCCTAAATCACCCACGTG 57.384 45.455 9.08 9.08 45.18 4.49
810 868 9.612620 CTCCCGCAATTTAATATAACAGATTTC 57.387 33.333 0.00 0.00 0.00 2.17
832 890 2.553172 GCAAGATGATGATTGCTCTCCC 59.447 50.000 2.80 0.00 46.49 4.30
882 940 5.528690 CACGGAAAGTCATTGGATGTGATAT 59.471 40.000 0.00 0.00 0.00 1.63
906 964 1.931172 AGCCGTGACGTAACATAATGC 59.069 47.619 3.64 0.00 0.00 3.56
924 982 0.029167 GTTACTCTCCGACGGCTAGC 59.971 60.000 9.66 6.04 0.00 3.42
925 983 1.331138 CTGTTACTCTCCGACGGCTAG 59.669 57.143 9.66 11.25 0.00 3.42
930 988 0.803117 TGAGCTGTTACTCTCCGACG 59.197 55.000 0.00 0.00 37.58 5.12
940 998 1.414919 AGGTGAACGGTTGAGCTGTTA 59.585 47.619 11.16 0.00 45.99 2.41
1008 1081 2.203523 TTCCTGGACGTGGGACGA 60.204 61.111 2.62 0.00 46.05 4.20
1022 1095 0.105593 TCATGGCGAGCTCATCTTCC 59.894 55.000 15.40 6.76 0.00 3.46
1289 1368 1.006571 CTTGTACACGGTGTCGCCT 60.007 57.895 18.43 0.00 40.63 5.52
1334 1416 4.007644 CTCTCGCCACCAGCACCA 62.008 66.667 0.00 0.00 44.04 4.17
1337 1419 4.074526 GAGCTCTCGCCACCAGCA 62.075 66.667 6.43 0.00 44.04 4.41
1376 1458 1.107114 TGACAAACACGCCAACCATT 58.893 45.000 0.00 0.00 0.00 3.16
1382 1467 3.515611 GGGTTGACAAACACGCCA 58.484 55.556 5.42 0.00 38.10 5.69
1479 1564 1.643868 CGTGTACAACCATGCGCCAT 61.644 55.000 4.18 0.00 0.00 4.40
1490 1575 1.634960 TCATCTCCCACCGTGTACAA 58.365 50.000 0.00 0.00 0.00 2.41
1529 1614 2.175811 GCATTGAACACGCGACCC 59.824 61.111 15.93 0.00 0.00 4.46
1532 1617 3.418913 CCGGCATTGAACACGCGA 61.419 61.111 15.93 0.00 0.00 5.87
1591 1676 0.948141 GAAGACGCTGCTGCACTCTT 60.948 55.000 19.43 19.43 38.08 2.85
1619 1704 1.986757 ATCGACCAGTGAGCTGCCT 60.987 57.895 0.00 0.00 41.26 4.75
1673 1758 1.907807 GTGTGGGAATGCCTTGGCA 60.908 57.895 17.19 17.19 0.00 4.92
1743 1828 4.036380 GGGGACGAAGGTTAAATTAGCATG 59.964 45.833 0.00 0.00 0.00 4.06
1820 1905 5.589855 TGAAATGGACTATGCAGGTTGTATG 59.410 40.000 0.00 0.00 0.00 2.39
1829 1954 7.826744 TGTTGTTATAGTGAAATGGACTATGCA 59.173 33.333 0.00 0.00 37.25 3.96
1973 2103 3.395607 CCATGATTATCACCTTCCCTCCA 59.604 47.826 0.00 0.00 0.00 3.86
2013 2143 1.904865 TTTCCTGCTGCAGCCCTTG 60.905 57.895 34.64 20.89 41.18 3.61
2014 2144 1.905354 GTTTCCTGCTGCAGCCCTT 60.905 57.895 34.64 0.00 41.18 3.95
2020 2150 1.891919 GACACGGTTTCCTGCTGCA 60.892 57.895 0.88 0.88 0.00 4.41
2042 2172 0.882927 CGAACAAAACCTCCGCCTCA 60.883 55.000 0.00 0.00 0.00 3.86
2072 2202 1.623311 TGGATCCCGTCGATATGCATT 59.377 47.619 9.90 0.00 0.00 3.56
2076 2206 0.456824 CGCTGGATCCCGTCGATATG 60.457 60.000 9.90 0.00 0.00 1.78
2078 2208 1.228033 TCGCTGGATCCCGTCGATA 60.228 57.895 9.90 0.00 0.00 2.92
2159 2289 1.011968 TTGAGCGAATTCCCGTCACG 61.012 55.000 0.00 0.00 0.00 4.35
2280 2415 8.669243 GTCAAGCTAGCACTCATTTTACTTAAT 58.331 33.333 18.83 0.00 0.00 1.40
2307 2442 1.270826 TGCGAGACAGAGGAAGAGTTG 59.729 52.381 0.00 0.00 0.00 3.16
2348 2484 4.597079 CAACGTACTGTTTGACTGCAAAT 58.403 39.130 0.00 0.00 45.01 2.32
2351 2487 1.329292 GCAACGTACTGTTTGACTGCA 59.671 47.619 0.00 0.00 39.29 4.41
2352 2488 1.329292 TGCAACGTACTGTTTGACTGC 59.671 47.619 0.00 0.00 39.29 4.40
2392 2530 1.029681 AGTGGCATACGCGTCTATCA 58.970 50.000 18.63 8.19 39.92 2.15
2399 2537 4.725556 AAATATGTTAGTGGCATACGCG 57.274 40.909 3.53 3.53 39.92 6.01
2416 2555 7.883229 ACGCATGAATATCGACATGTAAATA 57.117 32.000 13.38 0.00 43.67 1.40
2593 2773 3.194755 TGACAACTATACAGTGCGGTGAT 59.805 43.478 0.00 0.00 34.36 3.06
2598 2778 8.942669 TTTTTATTTGACAACTATACAGTGCG 57.057 30.769 0.00 0.00 34.36 5.34
2635 2818 7.611213 AAAGTACTCTATCCATTTTGAACCG 57.389 36.000 0.00 0.00 0.00 4.44
2673 2857 9.325198 GTGATATCAATAGTGTTGTGTCCATTA 57.675 33.333 7.07 0.00 0.00 1.90
2680 2864 8.204160 TCTAAGGGTGATATCAATAGTGTTGTG 58.796 37.037 7.07 0.00 0.00 3.33
2932 5310 4.261801 CGGGATTGTACATCCACTTTTCT 58.738 43.478 19.53 0.00 39.93 2.52
2943 5321 2.125310 CGCTGGCGGGATTGTACA 60.125 61.111 7.12 0.00 35.56 2.90
3083 7675 7.115520 CACCAATCATCTTGTCGTGATAGATAC 59.884 40.741 0.00 0.00 34.14 2.24
3087 7679 5.351458 TCACCAATCATCTTGTCGTGATAG 58.649 41.667 0.00 0.00 34.14 2.08
3165 7763 5.572211 CCAATGTGGTTAGTGATTTGATCG 58.428 41.667 0.00 0.00 31.35 3.69
3189 7787 2.070654 AAAAACTGTTGCCGCCCTCG 62.071 55.000 0.00 0.00 0.00 4.63
3190 7788 1.739667 AAAAACTGTTGCCGCCCTC 59.260 52.632 0.00 0.00 0.00 4.30
3191 7789 3.948702 AAAAACTGTTGCCGCCCT 58.051 50.000 0.00 0.00 0.00 5.19
3221 7819 7.565029 CCCAGGTTTCTCCATATATTCCTTTTT 59.435 37.037 0.00 0.00 39.02 1.94
3222 7820 7.069344 CCCAGGTTTCTCCATATATTCCTTTT 58.931 38.462 0.00 0.00 39.02 2.27
3223 7821 6.392842 TCCCAGGTTTCTCCATATATTCCTTT 59.607 38.462 0.00 0.00 39.02 3.11
3224 7822 5.917087 TCCCAGGTTTCTCCATATATTCCTT 59.083 40.000 0.00 0.00 39.02 3.36
3225 7823 5.310857 GTCCCAGGTTTCTCCATATATTCCT 59.689 44.000 0.00 0.00 39.02 3.36
3226 7824 5.561679 GTCCCAGGTTTCTCCATATATTCC 58.438 45.833 0.00 0.00 39.02 3.01
3227 7825 5.011738 TCGTCCCAGGTTTCTCCATATATTC 59.988 44.000 0.00 0.00 39.02 1.75
3228 7826 4.905456 TCGTCCCAGGTTTCTCCATATATT 59.095 41.667 0.00 0.00 39.02 1.28
3229 7827 4.489737 TCGTCCCAGGTTTCTCCATATAT 58.510 43.478 0.00 0.00 39.02 0.86
3230 7828 3.918566 TCGTCCCAGGTTTCTCCATATA 58.081 45.455 0.00 0.00 39.02 0.86
3231 7829 2.759355 TCGTCCCAGGTTTCTCCATAT 58.241 47.619 0.00 0.00 39.02 1.78
3232 7830 2.241281 TCGTCCCAGGTTTCTCCATA 57.759 50.000 0.00 0.00 39.02 2.74
3233 7831 1.584724 ATCGTCCCAGGTTTCTCCAT 58.415 50.000 0.00 0.00 39.02 3.41
3234 7832 1.358152 AATCGTCCCAGGTTTCTCCA 58.642 50.000 0.00 0.00 39.02 3.86
3235 7833 2.488153 CAAAATCGTCCCAGGTTTCTCC 59.512 50.000 0.00 0.00 0.00 3.71
3236 7834 3.408634 TCAAAATCGTCCCAGGTTTCTC 58.591 45.455 0.00 0.00 0.00 2.87
3237 7835 3.502123 TCAAAATCGTCCCAGGTTTCT 57.498 42.857 0.00 0.00 0.00 2.52
3238 7836 3.756434 TGATCAAAATCGTCCCAGGTTTC 59.244 43.478 0.00 0.00 34.39 2.78
3239 7837 3.761897 TGATCAAAATCGTCCCAGGTTT 58.238 40.909 0.00 0.00 34.39 3.27
3240 7838 3.433306 TGATCAAAATCGTCCCAGGTT 57.567 42.857 0.00 0.00 34.39 3.50
3241 7839 3.081804 GTTGATCAAAATCGTCCCAGGT 58.918 45.455 10.35 0.00 34.39 4.00
3242 7840 3.081061 TGTTGATCAAAATCGTCCCAGG 58.919 45.455 10.35 0.00 34.39 4.45
3243 7841 4.379813 CCTTGTTGATCAAAATCGTCCCAG 60.380 45.833 10.35 0.00 35.48 4.45
3244 7842 3.505680 CCTTGTTGATCAAAATCGTCCCA 59.494 43.478 10.35 0.00 35.48 4.37
3245 7843 3.506067 ACCTTGTTGATCAAAATCGTCCC 59.494 43.478 10.35 0.00 35.48 4.46
3246 7844 4.766404 ACCTTGTTGATCAAAATCGTCC 57.234 40.909 10.35 0.00 35.48 4.79
3247 7845 8.742554 ATTTTACCTTGTTGATCAAAATCGTC 57.257 30.769 10.35 0.00 35.48 4.20
3255 7853 8.956426 GGTCATCTTATTTTACCTTGTTGATCA 58.044 33.333 0.00 0.00 0.00 2.92
3256 7854 8.956426 TGGTCATCTTATTTTACCTTGTTGATC 58.044 33.333 0.00 0.00 0.00 2.92
3257 7855 8.877864 TGGTCATCTTATTTTACCTTGTTGAT 57.122 30.769 0.00 0.00 0.00 2.57
3258 7856 8.877864 ATGGTCATCTTATTTTACCTTGTTGA 57.122 30.769 0.00 0.00 0.00 3.18
3260 7858 9.975218 AGTATGGTCATCTTATTTTACCTTGTT 57.025 29.630 0.00 0.00 0.00 2.83
3261 7859 9.614792 GAGTATGGTCATCTTATTTTACCTTGT 57.385 33.333 0.00 0.00 0.00 3.16
3262 7860 9.613428 TGAGTATGGTCATCTTATTTTACCTTG 57.387 33.333 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.