Multiple sequence alignment - TraesCS5D01G160200

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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 TraesCS5D01G160200 chr5D 100.000 2705 0 0 1 2705 249979964 249982668 0.000000e+00 4996
1 TraesCS5D01G160200 chr5D 93.435 655 42 1 1 655 93630749 93630096 0.000000e+00 970
2 TraesCS5D01G160200 chr5D 97.917 96 2 0 2610 2705 249993800 249993895 1.670000e-37 167
3 TraesCS5D01G160200 chr5A 94.565 1711 54 12 914 2610 332719308 332720993 0.000000e+00 2608
4 TraesCS5D01G160200 chr5A 97.917 96 2 0 2610 2705 241286812 241286907 1.670000e-37 167
5 TraesCS5D01G160200 chr5A 95.146 103 3 2 2601 2703 616402922 616402822 7.750000e-36 161
6 TraesCS5D01G160200 chr5B 95.536 1456 53 8 882 2328 282847126 282848578 0.000000e+00 2318
7 TraesCS5D01G160200 chr5B 88.931 262 8 5 2370 2610 282848580 282848841 1.220000e-78 303
8 TraesCS5D01G160200 chr3A 94.198 655 38 0 1 655 420322385 420321731 0.000000e+00 1000
9 TraesCS5D01G160200 chr4D 94.046 655 39 0 1 655 85333427 85334081 0.000000e+00 994
10 TraesCS5D01G160200 chr4D 86.792 371 33 6 1089 1453 116153753 116153393 1.510000e-107 399
11 TraesCS5D01G160200 chr6D 93.598 656 41 1 1 655 87445472 87444817 0.000000e+00 977
12 TraesCS5D01G160200 chr3D 93.140 656 44 1 1 655 402137594 402136939 0.000000e+00 961
13 TraesCS5D01G160200 chr2D 93.130 655 45 0 1 655 135154777 135154123 0.000000e+00 961
14 TraesCS5D01G160200 chr2D 92.988 656 45 1 1 655 121161309 121161964 0.000000e+00 955
15 TraesCS5D01G160200 chr2D 92.977 655 45 1 1 655 248856879 248857532 0.000000e+00 953
16 TraesCS5D01G160200 chr1D 93.140 656 44 1 1 655 71010803 71011458 0.000000e+00 961
17 TraesCS5D01G160200 chr1D 97.895 95 2 0 2611 2705 31324600 31324694 5.990000e-37 165
18 TraesCS5D01G160200 chr4B 86.472 377 34 7 1084 1453 177861919 177861553 5.430000e-107 398
19 TraesCS5D01G160200 chr4A 86.364 374 35 9 1086 1453 460448872 460449235 7.020000e-106 394
20 TraesCS5D01G160200 chr7D 97.917 96 2 0 2610 2705 140762399 140762494 1.670000e-37 167
21 TraesCS5D01G160200 chr7D 97.917 96 2 0 2610 2705 186399176 186399081 1.670000e-37 167
22 TraesCS5D01G160200 chr7D 97.895 95 2 0 2611 2705 140749873 140749967 5.990000e-37 165
23 TraesCS5D01G160200 chr6A 97.917 96 2 0 2610 2705 100315947 100316042 1.670000e-37 167
24 TraesCS5D01G160200 chr3B 96.000 100 3 1 2606 2705 541524030 541524128 7.750000e-36 161


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 TraesCS5D01G160200 chr5D 249979964 249982668 2704 False 4996.0 4996 100.0000 1 2705 1 chr5D.!!$F1 2704
1 TraesCS5D01G160200 chr5D 93630096 93630749 653 True 970.0 970 93.4350 1 655 1 chr5D.!!$R1 654
2 TraesCS5D01G160200 chr5A 332719308 332720993 1685 False 2608.0 2608 94.5650 914 2610 1 chr5A.!!$F2 1696
3 TraesCS5D01G160200 chr5B 282847126 282848841 1715 False 1310.5 2318 92.2335 882 2610 2 chr5B.!!$F1 1728
4 TraesCS5D01G160200 chr3A 420321731 420322385 654 True 1000.0 1000 94.1980 1 655 1 chr3A.!!$R1 654
5 TraesCS5D01G160200 chr4D 85333427 85334081 654 False 994.0 994 94.0460 1 655 1 chr4D.!!$F1 654
6 TraesCS5D01G160200 chr6D 87444817 87445472 655 True 977.0 977 93.5980 1 655 1 chr6D.!!$R1 654
7 TraesCS5D01G160200 chr3D 402136939 402137594 655 True 961.0 961 93.1400 1 655 1 chr3D.!!$R1 654
8 TraesCS5D01G160200 chr2D 135154123 135154777 654 True 961.0 961 93.1300 1 655 1 chr2D.!!$R1 654
9 TraesCS5D01G160200 chr2D 121161309 121161964 655 False 955.0 955 92.9880 1 655 1 chr2D.!!$F1 654
10 TraesCS5D01G160200 chr2D 248856879 248857532 653 False 953.0 953 92.9770 1 655 1 chr2D.!!$F2 654
11 TraesCS5D01G160200 chr1D 71010803 71011458 655 False 961.0 961 93.1400 1 655 1 chr1D.!!$F2 654

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
631 633 0.036952 CTCCATGGACTCACGCAACT 60.037 55.0 11.44 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2619 2657 0.107165 CAGTGGGCCTAGCTAAACCC 60.107 60.0 19.66 19.66 43.14 4.11 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
183 185 1.039785 TCGTGGAGAGAGCCATCAGG 61.040 60.000 0.00 0.00 40.68 3.86
259 261 6.947733 TGTGTTGAGACCAAGATATTCCAATT 59.052 34.615 0.00 0.00 32.06 2.32
316 318 5.796424 AGTTGCTTTCCACTCAAATCATT 57.204 34.783 0.00 0.00 0.00 2.57
342 344 4.728772 TCACCAAATCCAAATCTGTGAGT 58.271 39.130 0.00 0.00 0.00 3.41
355 357 2.035193 TCTGTGAGTGAGAGTTGAGTGC 59.965 50.000 0.00 0.00 0.00 4.40
411 413 4.460382 GGAGTTCATCATCAACACACCATT 59.540 41.667 0.00 0.00 0.00 3.16
424 426 8.239038 TCAACACACCATTTATTACCTTTTGA 57.761 30.769 0.00 0.00 0.00 2.69
503 505 3.066760 GGAGTTGAACCAAGGAGTTTGTG 59.933 47.826 0.00 0.00 34.87 3.33
624 626 0.343018 TGGATCCCTCCATGGACTCA 59.657 55.000 11.44 0.00 46.95 3.41
631 633 0.036952 CTCCATGGACTCACGCAACT 60.037 55.000 11.44 0.00 0.00 3.16
655 657 2.928416 CCTTCGTGGGTTGAAGTCC 58.072 57.895 2.47 0.00 40.96 3.85
656 658 0.605589 CCTTCGTGGGTTGAAGTCCC 60.606 60.000 2.47 0.00 40.96 4.46
657 659 0.396811 CTTCGTGGGTTGAAGTCCCT 59.603 55.000 2.65 0.00 44.84 4.20
658 660 0.841289 TTCGTGGGTTGAAGTCCCTT 59.159 50.000 2.65 0.00 44.84 3.95
659 661 1.719529 TCGTGGGTTGAAGTCCCTTA 58.280 50.000 2.65 0.00 44.84 2.69
660 662 1.345415 TCGTGGGTTGAAGTCCCTTAC 59.655 52.381 2.65 0.00 44.84 2.34
661 663 1.346722 CGTGGGTTGAAGTCCCTTACT 59.653 52.381 2.65 0.00 44.84 2.24
662 664 2.779506 GTGGGTTGAAGTCCCTTACTG 58.220 52.381 2.65 0.00 44.84 2.74
663 665 2.370849 GTGGGTTGAAGTCCCTTACTGA 59.629 50.000 2.65 0.00 44.84 3.41
664 666 2.370849 TGGGTTGAAGTCCCTTACTGAC 59.629 50.000 2.65 0.00 44.84 3.51
665 667 2.638363 GGGTTGAAGTCCCTTACTGACT 59.362 50.000 0.00 0.00 44.75 3.41
666 668 3.557264 GGGTTGAAGTCCCTTACTGACTG 60.557 52.174 0.00 0.00 42.10 3.51
667 669 3.071167 GGTTGAAGTCCCTTACTGACTGT 59.929 47.826 0.00 0.00 42.10 3.55
668 670 4.444449 GGTTGAAGTCCCTTACTGACTGTT 60.444 45.833 0.00 0.00 42.10 3.16
669 671 4.602340 TGAAGTCCCTTACTGACTGTTC 57.398 45.455 0.00 0.00 42.10 3.18
670 672 3.964688 TGAAGTCCCTTACTGACTGTTCA 59.035 43.478 0.00 0.00 42.10 3.18
671 673 4.202223 TGAAGTCCCTTACTGACTGTTCAC 60.202 45.833 0.00 0.00 42.10 3.18
672 674 2.633481 AGTCCCTTACTGACTGTTCACC 59.367 50.000 0.00 0.00 41.40 4.02
673 675 1.616865 TCCCTTACTGACTGTTCACCG 59.383 52.381 0.00 0.00 0.00 4.94
674 676 1.343465 CCCTTACTGACTGTTCACCGT 59.657 52.381 0.00 0.00 0.00 4.83
675 677 2.559668 CCCTTACTGACTGTTCACCGTA 59.440 50.000 0.00 0.00 0.00 4.02
676 678 3.006110 CCCTTACTGACTGTTCACCGTAA 59.994 47.826 0.00 0.00 0.00 3.18
677 679 4.235360 CCTTACTGACTGTTCACCGTAAG 58.765 47.826 0.00 0.00 38.77 2.34
678 680 4.022589 CCTTACTGACTGTTCACCGTAAGA 60.023 45.833 12.17 0.00 40.09 2.10
679 681 5.508489 CCTTACTGACTGTTCACCGTAAGAA 60.508 44.000 12.17 0.00 40.09 2.52
680 682 3.978687 ACTGACTGTTCACCGTAAGAAG 58.021 45.455 0.00 0.00 43.02 2.85
681 683 3.635373 ACTGACTGTTCACCGTAAGAAGA 59.365 43.478 0.00 0.00 43.02 2.87
682 684 4.281182 ACTGACTGTTCACCGTAAGAAGAT 59.719 41.667 0.00 0.00 43.02 2.40
683 685 5.209818 TGACTGTTCACCGTAAGAAGATT 57.790 39.130 0.00 0.00 43.02 2.40
684 686 5.607477 TGACTGTTCACCGTAAGAAGATTT 58.393 37.500 0.00 0.00 43.02 2.17
685 687 5.465390 TGACTGTTCACCGTAAGAAGATTTG 59.535 40.000 0.00 0.00 43.02 2.32
686 688 5.607477 ACTGTTCACCGTAAGAAGATTTGA 58.393 37.500 0.00 0.00 43.02 2.69
687 689 5.465724 ACTGTTCACCGTAAGAAGATTTGAC 59.534 40.000 0.00 0.00 43.02 3.18
688 690 4.753107 TGTTCACCGTAAGAAGATTTGACC 59.247 41.667 0.00 0.00 43.02 4.02
689 691 4.610605 TCACCGTAAGAAGATTTGACCA 57.389 40.909 0.00 0.00 43.02 4.02
690 692 5.160607 TCACCGTAAGAAGATTTGACCAT 57.839 39.130 0.00 0.00 43.02 3.55
691 693 5.175859 TCACCGTAAGAAGATTTGACCATC 58.824 41.667 0.00 0.00 43.02 3.51
692 694 5.046591 TCACCGTAAGAAGATTTGACCATCT 60.047 40.000 0.00 0.00 43.02 2.90
693 695 5.292101 CACCGTAAGAAGATTTGACCATCTC 59.708 44.000 0.00 0.00 43.02 2.75
694 696 5.187967 ACCGTAAGAAGATTTGACCATCTCT 59.812 40.000 0.00 0.00 43.02 3.10
695 697 5.521735 CCGTAAGAAGATTTGACCATCTCTG 59.478 44.000 0.00 0.00 43.02 3.35
696 698 5.521735 CGTAAGAAGATTTGACCATCTCTGG 59.478 44.000 0.00 0.00 45.27 3.86
706 708 2.276732 CCATCTCTGGTTTGTGTGGT 57.723 50.000 0.00 0.00 37.79 4.16
707 709 2.586425 CCATCTCTGGTTTGTGTGGTT 58.414 47.619 0.00 0.00 37.79 3.67
708 710 2.958355 CCATCTCTGGTTTGTGTGGTTT 59.042 45.455 0.00 0.00 37.79 3.27
709 711 3.243501 CCATCTCTGGTTTGTGTGGTTTG 60.244 47.826 0.00 0.00 37.79 2.93
710 712 2.374184 TCTCTGGTTTGTGTGGTTTGG 58.626 47.619 0.00 0.00 0.00 3.28
711 713 1.408702 CTCTGGTTTGTGTGGTTTGGG 59.591 52.381 0.00 0.00 0.00 4.12
712 714 1.006043 TCTGGTTTGTGTGGTTTGGGA 59.994 47.619 0.00 0.00 0.00 4.37
713 715 1.408702 CTGGTTTGTGTGGTTTGGGAG 59.591 52.381 0.00 0.00 0.00 4.30
714 716 0.750249 GGTTTGTGTGGTTTGGGAGG 59.250 55.000 0.00 0.00 0.00 4.30
715 717 0.750249 GTTTGTGTGGTTTGGGAGGG 59.250 55.000 0.00 0.00 0.00 4.30
716 718 0.397816 TTTGTGTGGTTTGGGAGGGG 60.398 55.000 0.00 0.00 0.00 4.79
717 719 2.117423 GTGTGGTTTGGGAGGGGG 59.883 66.667 0.00 0.00 0.00 5.40
718 720 2.038221 TGTGGTTTGGGAGGGGGA 60.038 61.111 0.00 0.00 0.00 4.81
719 721 2.160171 TGTGGTTTGGGAGGGGGAG 61.160 63.158 0.00 0.00 0.00 4.30
720 722 2.534272 TGGTTTGGGAGGGGGAGG 60.534 66.667 0.00 0.00 0.00 4.30
721 723 4.062032 GGTTTGGGAGGGGGAGGC 62.062 72.222 0.00 0.00 0.00 4.70
722 724 4.426313 GTTTGGGAGGGGGAGGCG 62.426 72.222 0.00 0.00 0.00 5.52
723 725 4.995058 TTTGGGAGGGGGAGGCGT 62.995 66.667 0.00 0.00 0.00 5.68
733 735 4.353437 GGAGGCGTCGACGTTGGT 62.353 66.667 35.48 19.44 42.22 3.67
734 736 2.562912 GAGGCGTCGACGTTGGTA 59.437 61.111 35.48 0.00 42.22 3.25
735 737 1.799121 GAGGCGTCGACGTTGGTAC 60.799 63.158 35.48 19.44 42.22 3.34
736 738 2.050168 GGCGTCGACGTTGGTACA 60.050 61.111 35.48 0.00 42.22 2.90
737 739 1.444895 GGCGTCGACGTTGGTACAT 60.445 57.895 35.48 0.00 42.22 2.29
738 740 1.408474 GGCGTCGACGTTGGTACATC 61.408 60.000 35.48 17.34 42.22 3.06
739 741 0.455633 GCGTCGACGTTGGTACATCT 60.456 55.000 35.48 0.00 42.22 2.90
740 742 1.973138 CGTCGACGTTGGTACATCTT 58.027 50.000 29.08 0.00 39.30 2.40
741 743 1.909532 CGTCGACGTTGGTACATCTTC 59.090 52.381 29.08 0.00 39.30 2.87
742 744 2.257034 GTCGACGTTGGTACATCTTCC 58.743 52.381 0.00 0.00 39.30 3.46
743 745 1.887854 TCGACGTTGGTACATCTTCCA 59.112 47.619 2.20 0.00 39.30 3.53
744 746 1.990563 CGACGTTGGTACATCTTCCAC 59.009 52.381 0.00 0.00 39.30 4.02
745 747 2.352421 CGACGTTGGTACATCTTCCACT 60.352 50.000 0.00 0.00 39.30 4.00
746 748 3.251571 GACGTTGGTACATCTTCCACTC 58.748 50.000 0.00 0.00 39.30 3.51
747 749 2.631062 ACGTTGGTACATCTTCCACTCA 59.369 45.455 0.00 0.00 39.30 3.41
748 750 2.993899 CGTTGGTACATCTTCCACTCAC 59.006 50.000 0.00 0.00 39.30 3.51
749 751 3.306088 CGTTGGTACATCTTCCACTCACT 60.306 47.826 0.00 0.00 39.30 3.41
750 752 4.246458 GTTGGTACATCTTCCACTCACTC 58.754 47.826 0.00 0.00 39.30 3.51
751 753 3.779444 TGGTACATCTTCCACTCACTCT 58.221 45.455 0.00 0.00 0.00 3.24
752 754 4.930696 TGGTACATCTTCCACTCACTCTA 58.069 43.478 0.00 0.00 0.00 2.43
753 755 4.705507 TGGTACATCTTCCACTCACTCTAC 59.294 45.833 0.00 0.00 0.00 2.59
754 756 4.951094 GGTACATCTTCCACTCACTCTACT 59.049 45.833 0.00 0.00 0.00 2.57
755 757 5.163602 GGTACATCTTCCACTCACTCTACTG 60.164 48.000 0.00 0.00 0.00 2.74
756 758 4.667573 ACATCTTCCACTCACTCTACTGA 58.332 43.478 0.00 0.00 0.00 3.41
757 759 5.268387 ACATCTTCCACTCACTCTACTGAT 58.732 41.667 0.00 0.00 0.00 2.90
758 760 5.359576 ACATCTTCCACTCACTCTACTGATC 59.640 44.000 0.00 0.00 0.00 2.92
759 761 4.923415 TCTTCCACTCACTCTACTGATCA 58.077 43.478 0.00 0.00 0.00 2.92
760 762 5.514169 TCTTCCACTCACTCTACTGATCAT 58.486 41.667 0.00 0.00 0.00 2.45
761 763 6.663734 TCTTCCACTCACTCTACTGATCATA 58.336 40.000 0.00 0.00 0.00 2.15
762 764 6.770303 TCTTCCACTCACTCTACTGATCATAG 59.230 42.308 0.00 1.02 0.00 2.23
763 765 6.007485 TCCACTCACTCTACTGATCATAGT 57.993 41.667 0.00 0.00 34.71 2.12
764 766 6.427441 TCCACTCACTCTACTGATCATAGTT 58.573 40.000 0.00 0.00 32.19 2.24
765 767 7.574607 TCCACTCACTCTACTGATCATAGTTA 58.425 38.462 0.00 0.00 32.19 2.24
766 768 8.221251 TCCACTCACTCTACTGATCATAGTTAT 58.779 37.037 0.00 0.00 32.19 1.89
767 769 8.511321 CCACTCACTCTACTGATCATAGTTATC 58.489 40.741 0.00 0.00 32.19 1.75
768 770 9.061435 CACTCACTCTACTGATCATAGTTATCA 57.939 37.037 0.00 0.00 32.19 2.15
769 771 9.062524 ACTCACTCTACTGATCATAGTTATCAC 57.937 37.037 0.00 0.00 32.19 3.06
770 772 9.283768 CTCACTCTACTGATCATAGTTATCACT 57.716 37.037 0.00 0.00 36.99 3.41
773 775 9.733556 ACTCTACTGATCATAGTTATCACTAGG 57.266 37.037 0.00 0.00 38.96 3.02
774 776 9.733556 CTCTACTGATCATAGTTATCACTAGGT 57.266 37.037 0.00 0.00 38.96 3.08
775 777 9.508642 TCTACTGATCATAGTTATCACTAGGTG 57.491 37.037 0.00 0.00 38.96 4.00
776 778 7.531857 ACTGATCATAGTTATCACTAGGTGG 57.468 40.000 0.00 0.00 38.96 4.61
777 779 6.015010 ACTGATCATAGTTATCACTAGGTGGC 60.015 42.308 0.00 0.00 38.96 5.01
778 780 5.246203 TGATCATAGTTATCACTAGGTGGCC 59.754 44.000 0.00 0.00 38.96 5.36
779 781 4.816126 TCATAGTTATCACTAGGTGGCCT 58.184 43.478 3.32 0.00 38.96 5.19
780 782 5.960704 TCATAGTTATCACTAGGTGGCCTA 58.039 41.667 3.32 0.00 38.96 3.93
781 783 6.562228 TCATAGTTATCACTAGGTGGCCTAT 58.438 40.000 3.32 0.00 38.96 2.57
782 784 7.705700 TCATAGTTATCACTAGGTGGCCTATA 58.294 38.462 3.32 0.00 38.96 1.31
783 785 8.174757 TCATAGTTATCACTAGGTGGCCTATAA 58.825 37.037 3.32 0.00 38.96 0.98
784 786 8.812972 CATAGTTATCACTAGGTGGCCTATAAA 58.187 37.037 3.32 0.00 38.96 1.40
785 787 7.063934 AGTTATCACTAGGTGGCCTATAAAC 57.936 40.000 3.32 0.00 35.36 2.01
786 788 4.976540 ATCACTAGGTGGCCTATAAACC 57.023 45.455 3.32 1.87 35.36 3.27
787 789 4.003584 TCACTAGGTGGCCTATAAACCT 57.996 45.455 15.52 15.52 46.14 3.50
788 790 3.709653 TCACTAGGTGGCCTATAAACCTG 59.290 47.826 19.52 12.50 44.13 4.00
789 791 3.709653 CACTAGGTGGCCTATAAACCTGA 59.290 47.826 19.52 5.43 44.13 3.86
790 792 4.348168 CACTAGGTGGCCTATAAACCTGAT 59.652 45.833 19.52 6.59 44.13 2.90
791 793 4.975794 ACTAGGTGGCCTATAAACCTGATT 59.024 41.667 19.52 3.27 44.13 2.57
792 794 4.170468 AGGTGGCCTATAAACCTGATTG 57.830 45.455 10.83 0.00 42.78 2.67
793 795 3.527665 AGGTGGCCTATAAACCTGATTGT 59.472 43.478 10.83 0.00 42.78 2.71
794 796 4.724798 AGGTGGCCTATAAACCTGATTGTA 59.275 41.667 10.83 0.00 42.78 2.41
795 797 5.192923 AGGTGGCCTATAAACCTGATTGTAA 59.807 40.000 10.83 0.00 42.78 2.41
796 798 5.298527 GGTGGCCTATAAACCTGATTGTAAC 59.701 44.000 3.32 0.00 0.00 2.50
797 799 6.120220 GTGGCCTATAAACCTGATTGTAACT 58.880 40.000 3.32 0.00 0.00 2.24
798 800 6.038271 GTGGCCTATAAACCTGATTGTAACTG 59.962 42.308 3.32 0.00 0.00 3.16
799 801 5.008712 GGCCTATAAACCTGATTGTAACTGC 59.991 44.000 0.00 0.00 0.00 4.40
800 802 5.588648 GCCTATAAACCTGATTGTAACTGCA 59.411 40.000 0.00 0.00 0.00 4.41
801 803 6.263168 GCCTATAAACCTGATTGTAACTGCAT 59.737 38.462 0.00 0.00 0.00 3.96
802 804 7.444183 GCCTATAAACCTGATTGTAACTGCATA 59.556 37.037 0.00 0.00 0.00 3.14
803 805 9.507329 CCTATAAACCTGATTGTAACTGCATAT 57.493 33.333 0.00 0.00 0.00 1.78
807 809 7.466746 AACCTGATTGTAACTGCATATTTGT 57.533 32.000 0.00 0.00 0.00 2.83
808 810 7.466746 ACCTGATTGTAACTGCATATTTGTT 57.533 32.000 0.00 0.00 0.00 2.83
809 811 7.895759 ACCTGATTGTAACTGCATATTTGTTT 58.104 30.769 0.00 0.00 0.00 2.83
810 812 8.367156 ACCTGATTGTAACTGCATATTTGTTTT 58.633 29.630 0.00 0.00 0.00 2.43
811 813 9.206870 CCTGATTGTAACTGCATATTTGTTTTT 57.793 29.630 0.00 0.00 0.00 1.94
835 837 7.758613 TTTATTTTGCTATCACGACATACGA 57.241 32.000 0.00 0.00 45.77 3.43
836 838 7.940178 TTATTTTGCTATCACGACATACGAT 57.060 32.000 0.00 0.00 45.77 3.73
837 839 5.635549 TTTTGCTATCACGACATACGATG 57.364 39.130 0.00 0.00 45.77 3.84
838 840 4.561735 TTGCTATCACGACATACGATGA 57.438 40.909 0.00 0.00 45.77 2.92
839 841 4.561735 TGCTATCACGACATACGATGAA 57.438 40.909 0.00 0.00 45.77 2.57
840 842 5.121221 TGCTATCACGACATACGATGAAT 57.879 39.130 0.00 0.00 45.77 2.57
841 843 6.249035 TGCTATCACGACATACGATGAATA 57.751 37.500 0.00 0.00 45.77 1.75
842 844 6.314784 TGCTATCACGACATACGATGAATAG 58.685 40.000 0.00 0.00 45.77 1.73
843 845 6.148811 TGCTATCACGACATACGATGAATAGA 59.851 38.462 0.00 0.00 45.77 1.98
844 846 7.148239 TGCTATCACGACATACGATGAATAGAT 60.148 37.037 0.00 0.00 45.77 1.98
845 847 7.698550 GCTATCACGACATACGATGAATAGATT 59.301 37.037 0.00 0.00 45.77 2.40
846 848 7.803079 ATCACGACATACGATGAATAGATTG 57.197 36.000 0.00 0.00 45.77 2.67
847 849 6.966021 TCACGACATACGATGAATAGATTGA 58.034 36.000 0.00 0.00 45.77 2.57
848 850 7.422399 TCACGACATACGATGAATAGATTGAA 58.578 34.615 0.00 0.00 45.77 2.69
849 851 7.378728 TCACGACATACGATGAATAGATTGAAC 59.621 37.037 0.00 0.00 45.77 3.18
850 852 6.359883 ACGACATACGATGAATAGATTGAACG 59.640 38.462 0.00 0.00 45.77 3.95
851 853 6.359883 CGACATACGATGAATAGATTGAACGT 59.640 38.462 2.99 2.99 45.77 3.99
852 854 7.096599 CGACATACGATGAATAGATTGAACGTT 60.097 37.037 0.00 0.00 45.77 3.99
853 855 8.420374 ACATACGATGAATAGATTGAACGTTT 57.580 30.769 0.46 0.00 34.70 3.60
854 856 8.879759 ACATACGATGAATAGATTGAACGTTTT 58.120 29.630 0.46 0.00 34.70 2.43
855 857 9.702726 CATACGATGAATAGATTGAACGTTTTT 57.297 29.630 0.46 0.00 34.70 1.94
875 877 6.864360 TTTTTGGAAAGAAAATGATGCAGG 57.136 33.333 0.00 0.00 0.00 4.85
876 878 4.540359 TTGGAAAGAAAATGATGCAGGG 57.460 40.909 0.00 0.00 0.00 4.45
877 879 2.833338 TGGAAAGAAAATGATGCAGGGG 59.167 45.455 0.00 0.00 0.00 4.79
878 880 2.419159 GGAAAGAAAATGATGCAGGGGC 60.419 50.000 0.00 0.00 41.68 5.80
879 881 1.197812 AAGAAAATGATGCAGGGGCC 58.802 50.000 0.00 0.00 40.13 5.80
880 882 1.039233 AGAAAATGATGCAGGGGCCG 61.039 55.000 0.00 0.00 40.13 6.13
1321 1328 1.139095 CTTCTACACCGACGAGGCC 59.861 63.158 0.00 0.00 46.52 5.19
1668 1675 2.421424 CACTTAGATCTGCCAAGCAACC 59.579 50.000 5.18 0.00 38.41 3.77
1678 1685 3.408634 TGCCAAGCAACCTTACTAGTTC 58.591 45.455 0.00 0.00 34.76 3.01
1703 1710 4.919774 TTATGGTGCCCTTCTGTTTCTA 57.080 40.909 0.00 0.00 0.00 2.10
1705 1712 3.806949 TGGTGCCCTTCTGTTTCTATT 57.193 42.857 0.00 0.00 0.00 1.73
1819 1832 2.457366 ACTTGTTCTGCCGACTTAGG 57.543 50.000 0.00 0.00 0.00 2.69
1937 1950 4.036027 CCGTTTCGAAGTATAGCTCACCTA 59.964 45.833 0.00 0.00 0.00 3.08
2017 2030 7.140048 TGTTATTTGTTTGGTGAATACGTTCC 58.860 34.615 0.00 0.00 33.26 3.62
2030 2043 2.258286 GTTCCACGCCCACATTGC 59.742 61.111 0.00 0.00 0.00 3.56
2084 2097 0.805711 GCGCACCAAGTTTGTTTGCT 60.806 50.000 0.30 0.00 34.73 3.91
2162 2175 4.400251 TGCCAGGCTCAAGAAATTTATCAG 59.600 41.667 14.15 0.00 0.00 2.90
2180 2193 2.378547 TCAGTTTACCAAATGCCTCCCT 59.621 45.455 0.00 0.00 0.00 4.20
2246 2263 3.947834 CACCCTGAGTGTTTCTTTCTGTT 59.052 43.478 0.00 0.00 41.93 3.16
2247 2264 4.399303 CACCCTGAGTGTTTCTTTCTGTTT 59.601 41.667 0.00 0.00 41.93 2.83
2279 2296 3.274288 GCTGGAGCTTTGCAATAGTACT 58.726 45.455 0.00 0.00 38.21 2.73
2287 2304 7.306866 GGAGCTTTGCAATAGTACTAGAATTCG 60.307 40.741 8.85 0.00 0.00 3.34
2291 2308 8.942338 TTTGCAATAGTACTAGAATTCGACAT 57.058 30.769 8.85 0.00 0.00 3.06
2319 2336 4.085876 GCACTGGCAAGATGGTGT 57.914 55.556 0.00 0.00 40.72 4.16
2525 2551 2.708861 TGTTAGAACCAAGAAGGCCTGA 59.291 45.455 5.69 0.00 43.14 3.86
2551 2589 4.202315 TGACTATGTGCACAAACTACAGGT 60.202 41.667 25.72 12.83 0.00 4.00
2555 2593 2.680841 TGTGCACAAACTACAGGTTGAC 59.319 45.455 19.28 6.03 38.29 3.18
2584 2622 4.642437 GGCCTCTTAGGATTTTTCTCAAGG 59.358 45.833 0.00 0.00 37.67 3.61
2587 2625 5.124617 CCTCTTAGGATTTTTCTCAAGGTGC 59.875 44.000 0.00 0.00 37.67 5.01
2610 2648 9.423061 GTGCATTTAAGTTTTGAAGGATATTGT 57.577 29.630 0.00 0.00 0.00 2.71
2611 2649 9.421806 TGCATTTAAGTTTTGAAGGATATTGTG 57.578 29.630 0.00 0.00 0.00 3.33
2612 2650 9.423061 GCATTTAAGTTTTGAAGGATATTGTGT 57.577 29.630 0.00 0.00 0.00 3.72
2618 2656 7.547227 AGTTTTGAAGGATATTGTGTTATGGC 58.453 34.615 0.00 0.00 0.00 4.40
2619 2657 5.749596 TTGAAGGATATTGTGTTATGGCG 57.250 39.130 0.00 0.00 0.00 5.69
2620 2658 4.133820 TGAAGGATATTGTGTTATGGCGG 58.866 43.478 0.00 0.00 0.00 6.13
2621 2659 3.140325 AGGATATTGTGTTATGGCGGG 57.860 47.619 0.00 0.00 0.00 6.13
2622 2660 2.441750 AGGATATTGTGTTATGGCGGGT 59.558 45.455 0.00 0.00 0.00 5.28
2623 2661 3.117663 AGGATATTGTGTTATGGCGGGTT 60.118 43.478 0.00 0.00 0.00 4.11
2624 2662 3.634910 GGATATTGTGTTATGGCGGGTTT 59.365 43.478 0.00 0.00 0.00 3.27
2625 2663 4.822896 GGATATTGTGTTATGGCGGGTTTA 59.177 41.667 0.00 0.00 0.00 2.01
2626 2664 5.048991 GGATATTGTGTTATGGCGGGTTTAG 60.049 44.000 0.00 0.00 0.00 1.85
2627 2665 1.455248 TGTGTTATGGCGGGTTTAGC 58.545 50.000 0.00 0.00 0.00 3.09
2628 2666 1.003812 TGTGTTATGGCGGGTTTAGCT 59.996 47.619 0.00 0.00 34.52 3.32
2629 2667 2.236644 TGTGTTATGGCGGGTTTAGCTA 59.763 45.455 0.00 0.00 34.52 3.32
2630 2668 2.870411 GTGTTATGGCGGGTTTAGCTAG 59.130 50.000 0.00 0.00 34.52 3.42
2631 2669 2.158871 TGTTATGGCGGGTTTAGCTAGG 60.159 50.000 0.00 0.00 34.52 3.02
2632 2670 0.395312 TATGGCGGGTTTAGCTAGGC 59.605 55.000 0.00 0.00 34.52 3.93
2633 2671 2.203167 GGCGGGTTTAGCTAGGCC 60.203 66.667 0.00 0.00 34.52 5.19
2634 2672 2.203167 GCGGGTTTAGCTAGGCCC 60.203 66.667 19.33 19.33 37.79 5.80
2635 2673 3.038945 GCGGGTTTAGCTAGGCCCA 62.039 63.158 25.18 0.00 41.11 5.36
2636 2674 1.153229 CGGGTTTAGCTAGGCCCAC 60.153 63.158 25.18 7.64 41.11 4.61
2637 2675 1.623542 CGGGTTTAGCTAGGCCCACT 61.624 60.000 25.18 0.00 41.11 4.00
2638 2676 0.107165 GGGTTTAGCTAGGCCCACTG 60.107 60.000 22.56 0.00 40.76 3.66
2639 2677 0.107165 GGTTTAGCTAGGCCCACTGG 60.107 60.000 0.00 0.00 0.00 4.00
2641 2679 0.549169 TTTAGCTAGGCCCACTGGGT 60.549 55.000 16.03 0.00 46.51 4.51
2642 2680 0.340558 TTAGCTAGGCCCACTGGGTA 59.659 55.000 16.03 0.19 46.51 3.69
2643 2681 0.340558 TAGCTAGGCCCACTGGGTAA 59.659 55.000 16.03 0.84 46.51 2.85
2644 2682 0.327576 AGCTAGGCCCACTGGGTAAT 60.328 55.000 16.03 4.70 46.51 1.89
2645 2683 0.108774 GCTAGGCCCACTGGGTAATC 59.891 60.000 16.03 3.74 46.51 1.75
2646 2684 1.807814 CTAGGCCCACTGGGTAATCT 58.192 55.000 16.03 10.43 46.51 2.40
2647 2685 2.127708 CTAGGCCCACTGGGTAATCTT 58.872 52.381 16.03 0.00 46.51 2.40
2648 2686 2.280308 AGGCCCACTGGGTAATCTTA 57.720 50.000 16.03 0.00 46.51 2.10
2649 2687 2.127708 AGGCCCACTGGGTAATCTTAG 58.872 52.381 16.03 0.00 46.51 2.18
2650 2688 1.477014 GGCCCACTGGGTAATCTTAGC 60.477 57.143 16.03 0.00 46.51 3.09
2651 2689 1.477014 GCCCACTGGGTAATCTTAGCC 60.477 57.143 16.03 10.55 46.51 3.93
2658 2696 3.646736 GGGTAATCTTAGCCCACAAGT 57.353 47.619 6.88 0.00 43.70 3.16
2659 2697 3.964411 GGGTAATCTTAGCCCACAAGTT 58.036 45.455 6.88 0.00 43.70 2.66
2660 2698 5.106876 GGGTAATCTTAGCCCACAAGTTA 57.893 43.478 6.88 0.00 43.70 2.24
2661 2699 5.691896 GGGTAATCTTAGCCCACAAGTTAT 58.308 41.667 6.88 0.00 43.70 1.89
2662 2700 5.763698 GGGTAATCTTAGCCCACAAGTTATC 59.236 44.000 6.88 0.00 43.70 1.75
2663 2701 6.409349 GGGTAATCTTAGCCCACAAGTTATCT 60.409 42.308 6.88 0.00 43.70 1.98
2664 2702 7.054751 GGTAATCTTAGCCCACAAGTTATCTT 58.945 38.462 0.00 0.00 0.00 2.40
2665 2703 8.208903 GGTAATCTTAGCCCACAAGTTATCTTA 58.791 37.037 0.00 0.00 32.07 2.10
2666 2704 9.262358 GTAATCTTAGCCCACAAGTTATCTTAG 57.738 37.037 0.00 0.00 32.07 2.18
2667 2705 6.235231 TCTTAGCCCACAAGTTATCTTAGG 57.765 41.667 0.00 0.00 32.07 2.69
2668 2706 5.724854 TCTTAGCCCACAAGTTATCTTAGGT 59.275 40.000 4.43 0.00 32.07 3.08
2669 2707 4.929146 AGCCCACAAGTTATCTTAGGTT 57.071 40.909 4.43 0.00 32.07 3.50
2670 2708 7.400915 TCTTAGCCCACAAGTTATCTTAGGTTA 59.599 37.037 4.43 0.00 32.07 2.85
2671 2709 6.382919 AGCCCACAAGTTATCTTAGGTTAA 57.617 37.500 4.43 0.00 32.07 2.01
2672 2710 6.970191 AGCCCACAAGTTATCTTAGGTTAAT 58.030 36.000 4.43 0.00 32.07 1.40
2673 2711 7.410991 AGCCCACAAGTTATCTTAGGTTAATT 58.589 34.615 4.43 0.00 32.07 1.40
2674 2712 7.556635 AGCCCACAAGTTATCTTAGGTTAATTC 59.443 37.037 0.00 0.00 32.07 2.17
2675 2713 7.556635 GCCCACAAGTTATCTTAGGTTAATTCT 59.443 37.037 0.00 0.00 32.07 2.40
2676 2714 9.462606 CCCACAAGTTATCTTAGGTTAATTCTT 57.537 33.333 0.00 0.00 32.07 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.386661 GGTGAGACCGACATGTCAAT 57.613 50.000 24.93 12.35 37.73 2.57
22 24 5.309638 TGTGAATGTTAGGATTTTCGGTGA 58.690 37.500 0.00 0.00 0.00 4.02
98 100 8.611654 AATCTAACCGTTACACACAATTTACT 57.388 30.769 0.00 0.00 0.00 2.24
259 261 6.119240 AGAGATCAAGATTCTTGTGGTTGA 57.881 37.500 22.44 6.18 0.00 3.18
316 318 6.882656 TCACAGATTTGGATTTGGTGAAAAA 58.117 32.000 0.00 0.00 0.00 1.94
320 322 4.520111 CACTCACAGATTTGGATTTGGTGA 59.480 41.667 0.00 0.00 0.00 4.02
342 344 0.471780 TCCCCAGCACTCAACTCTCA 60.472 55.000 0.00 0.00 0.00 3.27
355 357 5.529060 GTGCTTCAAATAATAGTCTCCCCAG 59.471 44.000 0.00 0.00 0.00 4.45
411 413 7.514721 AGACACCACTCTTCAAAAGGTAATAA 58.485 34.615 0.00 0.00 0.00 1.40
424 426 3.772025 CCAATCTAGGAGACACCACTCTT 59.228 47.826 0.00 0.00 42.04 2.85
578 580 4.021016 ACGAAGAAGCAACCTTGTCTATCT 60.021 41.667 0.00 0.00 0.00 1.98
616 618 2.413837 GTAACAGTTGCGTGAGTCCAT 58.586 47.619 0.00 0.00 0.00 3.41
624 626 0.105408 ACGAAGGGTAACAGTTGCGT 59.895 50.000 0.00 0.00 39.74 5.24
655 657 2.814280 ACGGTGAACAGTCAGTAAGG 57.186 50.000 0.00 0.00 33.27 2.69
656 658 5.117355 TCTTACGGTGAACAGTCAGTAAG 57.883 43.478 6.79 6.79 40.52 2.34
657 659 5.300034 TCTTCTTACGGTGAACAGTCAGTAA 59.700 40.000 0.00 0.00 33.27 2.24
658 660 4.823442 TCTTCTTACGGTGAACAGTCAGTA 59.177 41.667 0.00 0.00 33.27 2.74
659 661 3.635373 TCTTCTTACGGTGAACAGTCAGT 59.365 43.478 0.00 0.00 33.27 3.41
660 662 4.238761 TCTTCTTACGGTGAACAGTCAG 57.761 45.455 0.00 0.00 33.27 3.51
661 663 4.866508 ATCTTCTTACGGTGAACAGTCA 57.133 40.909 0.00 0.00 0.00 3.41
662 664 5.694910 TCAAATCTTCTTACGGTGAACAGTC 59.305 40.000 0.00 0.00 0.00 3.51
663 665 5.465724 GTCAAATCTTCTTACGGTGAACAGT 59.534 40.000 0.00 0.00 0.00 3.55
664 666 5.107065 GGTCAAATCTTCTTACGGTGAACAG 60.107 44.000 0.00 0.00 0.00 3.16
665 667 4.753107 GGTCAAATCTTCTTACGGTGAACA 59.247 41.667 0.00 0.00 0.00 3.18
666 668 4.753107 TGGTCAAATCTTCTTACGGTGAAC 59.247 41.667 0.00 0.00 0.00 3.18
667 669 4.963373 TGGTCAAATCTTCTTACGGTGAA 58.037 39.130 0.00 0.00 0.00 3.18
668 670 4.610605 TGGTCAAATCTTCTTACGGTGA 57.389 40.909 0.00 0.00 0.00 4.02
669 671 5.178797 AGATGGTCAAATCTTCTTACGGTG 58.821 41.667 0.00 0.00 32.88 4.94
670 672 5.187967 AGAGATGGTCAAATCTTCTTACGGT 59.812 40.000 0.00 0.00 37.03 4.83
671 673 5.521735 CAGAGATGGTCAAATCTTCTTACGG 59.478 44.000 0.00 0.00 37.03 4.02
672 674 5.521735 CCAGAGATGGTCAAATCTTCTTACG 59.478 44.000 0.00 0.00 37.03 3.18
673 675 6.410540 ACCAGAGATGGTCAAATCTTCTTAC 58.589 40.000 0.00 0.00 37.74 2.34
674 676 6.627087 ACCAGAGATGGTCAAATCTTCTTA 57.373 37.500 0.00 0.00 37.74 2.10
675 677 5.511386 ACCAGAGATGGTCAAATCTTCTT 57.489 39.130 0.00 0.00 37.74 2.52
676 678 5.511386 AACCAGAGATGGTCAAATCTTCT 57.489 39.130 0.00 0.00 42.20 2.85
677 679 5.474876 ACAAACCAGAGATGGTCAAATCTTC 59.525 40.000 0.00 0.00 42.20 2.87
678 680 5.242393 CACAAACCAGAGATGGTCAAATCTT 59.758 40.000 0.00 0.00 42.20 2.40
679 681 4.763793 CACAAACCAGAGATGGTCAAATCT 59.236 41.667 0.00 0.00 42.20 2.40
680 682 4.520492 ACACAAACCAGAGATGGTCAAATC 59.480 41.667 0.00 0.00 42.20 2.17
681 683 4.279169 CACACAAACCAGAGATGGTCAAAT 59.721 41.667 0.00 0.00 42.20 2.32
682 684 3.631686 CACACAAACCAGAGATGGTCAAA 59.368 43.478 0.00 0.00 42.20 2.69
683 685 3.213506 CACACAAACCAGAGATGGTCAA 58.786 45.455 0.00 0.00 42.20 3.18
684 686 2.487086 CCACACAAACCAGAGATGGTCA 60.487 50.000 0.00 0.00 42.20 4.02
685 687 2.154462 CCACACAAACCAGAGATGGTC 58.846 52.381 0.00 0.00 42.20 4.02
686 688 1.494721 ACCACACAAACCAGAGATGGT 59.505 47.619 0.00 0.00 45.55 3.55
687 689 2.276732 ACCACACAAACCAGAGATGG 57.723 50.000 0.00 0.00 0.00 3.51
688 690 3.243501 CCAAACCACACAAACCAGAGATG 60.244 47.826 0.00 0.00 0.00 2.90
689 691 2.958355 CCAAACCACACAAACCAGAGAT 59.042 45.455 0.00 0.00 0.00 2.75
690 692 2.374184 CCAAACCACACAAACCAGAGA 58.626 47.619 0.00 0.00 0.00 3.10
691 693 1.408702 CCCAAACCACACAAACCAGAG 59.591 52.381 0.00 0.00 0.00 3.35
692 694 1.006043 TCCCAAACCACACAAACCAGA 59.994 47.619 0.00 0.00 0.00 3.86
693 695 1.408702 CTCCCAAACCACACAAACCAG 59.591 52.381 0.00 0.00 0.00 4.00
694 696 1.479709 CTCCCAAACCACACAAACCA 58.520 50.000 0.00 0.00 0.00 3.67
695 697 0.750249 CCTCCCAAACCACACAAACC 59.250 55.000 0.00 0.00 0.00 3.27
696 698 0.750249 CCCTCCCAAACCACACAAAC 59.250 55.000 0.00 0.00 0.00 2.93
697 699 0.397816 CCCCTCCCAAACCACACAAA 60.398 55.000 0.00 0.00 0.00 2.83
698 700 1.231641 CCCCTCCCAAACCACACAA 59.768 57.895 0.00 0.00 0.00 3.33
699 701 2.773527 CCCCCTCCCAAACCACACA 61.774 63.158 0.00 0.00 0.00 3.72
700 702 2.117423 CCCCCTCCCAAACCACAC 59.883 66.667 0.00 0.00 0.00 3.82
701 703 2.038221 TCCCCCTCCCAAACCACA 60.038 61.111 0.00 0.00 0.00 4.17
702 704 2.763902 CTCCCCCTCCCAAACCAC 59.236 66.667 0.00 0.00 0.00 4.16
703 705 2.534272 CCTCCCCCTCCCAAACCA 60.534 66.667 0.00 0.00 0.00 3.67
704 706 4.062032 GCCTCCCCCTCCCAAACC 62.062 72.222 0.00 0.00 0.00 3.27
705 707 4.426313 CGCCTCCCCCTCCCAAAC 62.426 72.222 0.00 0.00 0.00 2.93
706 708 4.995058 ACGCCTCCCCCTCCCAAA 62.995 66.667 0.00 0.00 0.00 3.28
716 718 2.981560 TACCAACGTCGACGCCTCC 61.982 63.158 35.92 0.00 44.43 4.30
717 719 1.799121 GTACCAACGTCGACGCCTC 60.799 63.158 35.92 17.09 44.43 4.70
718 720 1.870055 ATGTACCAACGTCGACGCCT 61.870 55.000 35.92 21.67 44.43 5.52
719 721 1.408474 GATGTACCAACGTCGACGCC 61.408 60.000 35.92 17.45 44.43 5.68
720 722 0.455633 AGATGTACCAACGTCGACGC 60.456 55.000 35.92 19.63 44.88 5.19
721 723 1.909532 GAAGATGTACCAACGTCGACG 59.090 52.381 34.58 34.58 44.88 5.12
722 724 2.257034 GGAAGATGTACCAACGTCGAC 58.743 52.381 5.18 5.18 44.88 4.20
723 725 1.887854 TGGAAGATGTACCAACGTCGA 59.112 47.619 0.00 0.00 44.88 4.20
724 726 1.990563 GTGGAAGATGTACCAACGTCG 59.009 52.381 0.00 0.00 44.88 5.12
725 727 3.251571 GAGTGGAAGATGTACCAACGTC 58.748 50.000 0.00 0.00 41.25 4.34
726 728 2.631062 TGAGTGGAAGATGTACCAACGT 59.369 45.455 0.00 0.00 37.94 3.99
727 729 2.993899 GTGAGTGGAAGATGTACCAACG 59.006 50.000 0.00 0.00 37.94 4.10
728 730 4.021016 AGAGTGAGTGGAAGATGTACCAAC 60.021 45.833 0.00 0.00 37.94 3.77
729 731 4.160329 AGAGTGAGTGGAAGATGTACCAA 58.840 43.478 0.00 0.00 37.94 3.67
730 732 3.779444 AGAGTGAGTGGAAGATGTACCA 58.221 45.455 0.00 0.00 0.00 3.25
731 733 4.951094 AGTAGAGTGAGTGGAAGATGTACC 59.049 45.833 0.00 0.00 0.00 3.34
732 734 5.648526 TCAGTAGAGTGAGTGGAAGATGTAC 59.351 44.000 0.00 0.00 0.00 2.90
733 735 5.816682 TCAGTAGAGTGAGTGGAAGATGTA 58.183 41.667 0.00 0.00 0.00 2.29
734 736 4.667573 TCAGTAGAGTGAGTGGAAGATGT 58.332 43.478 0.00 0.00 0.00 3.06
735 737 5.359292 TGATCAGTAGAGTGAGTGGAAGATG 59.641 44.000 0.00 0.00 0.00 2.90
736 738 5.514169 TGATCAGTAGAGTGAGTGGAAGAT 58.486 41.667 0.00 0.00 0.00 2.40
737 739 4.923415 TGATCAGTAGAGTGAGTGGAAGA 58.077 43.478 0.00 0.00 0.00 2.87
738 740 5.850557 ATGATCAGTAGAGTGAGTGGAAG 57.149 43.478 0.09 0.00 0.00 3.46
739 741 6.427441 ACTATGATCAGTAGAGTGAGTGGAA 58.573 40.000 15.02 0.00 0.00 3.53
740 742 6.007485 ACTATGATCAGTAGAGTGAGTGGA 57.993 41.667 15.02 0.00 0.00 4.02
741 743 6.707440 AACTATGATCAGTAGAGTGAGTGG 57.293 41.667 15.02 0.00 0.00 4.00
742 744 9.061435 TGATAACTATGATCAGTAGAGTGAGTG 57.939 37.037 15.02 0.00 0.00 3.51
743 745 9.062524 GTGATAACTATGATCAGTAGAGTGAGT 57.937 37.037 15.02 1.70 34.02 3.41
744 746 9.283768 AGTGATAACTATGATCAGTAGAGTGAG 57.716 37.037 15.02 1.22 35.62 3.51
751 753 7.176865 GCCACCTAGTGATAACTATGATCAGTA 59.823 40.741 0.09 0.00 37.92 2.74
752 754 6.015010 GCCACCTAGTGATAACTATGATCAGT 60.015 42.308 0.09 0.00 39.68 3.41
753 755 6.393990 GCCACCTAGTGATAACTATGATCAG 58.606 44.000 0.09 0.00 35.23 2.90
754 756 5.246203 GGCCACCTAGTGATAACTATGATCA 59.754 44.000 0.00 0.00 35.23 2.92
755 757 5.482175 AGGCCACCTAGTGATAACTATGATC 59.518 44.000 5.01 0.00 35.23 2.92
756 758 5.407049 AGGCCACCTAGTGATAACTATGAT 58.593 41.667 5.01 0.00 35.23 2.45
757 759 4.816126 AGGCCACCTAGTGATAACTATGA 58.184 43.478 5.01 0.00 35.23 2.15
758 760 6.859112 ATAGGCCACCTAGTGATAACTATG 57.141 41.667 5.01 0.00 39.70 2.23
759 761 8.813951 GTTTATAGGCCACCTAGTGATAACTAT 58.186 37.037 5.01 0.00 39.70 2.12
760 762 7.234166 GGTTTATAGGCCACCTAGTGATAACTA 59.766 40.741 5.01 0.00 39.70 2.24
761 763 6.042897 GGTTTATAGGCCACCTAGTGATAACT 59.957 42.308 5.01 0.00 39.70 2.24
762 764 6.042897 AGGTTTATAGGCCACCTAGTGATAAC 59.957 42.308 9.94 0.00 39.70 1.89
763 765 6.042781 CAGGTTTATAGGCCACCTAGTGATAA 59.957 42.308 11.21 0.00 39.70 1.75
764 766 5.542635 CAGGTTTATAGGCCACCTAGTGATA 59.457 44.000 11.21 0.00 39.70 2.15
765 767 4.348168 CAGGTTTATAGGCCACCTAGTGAT 59.652 45.833 11.21 0.00 39.70 3.06
766 768 3.709653 CAGGTTTATAGGCCACCTAGTGA 59.290 47.826 11.21 0.00 39.70 3.41
767 769 3.709653 TCAGGTTTATAGGCCACCTAGTG 59.290 47.826 11.21 1.56 39.70 2.74
768 770 4.003584 TCAGGTTTATAGGCCACCTAGT 57.996 45.455 11.21 0.00 39.70 2.57
769 771 5.163195 ACAATCAGGTTTATAGGCCACCTAG 60.163 44.000 11.21 6.80 39.70 3.02
770 772 4.724798 ACAATCAGGTTTATAGGCCACCTA 59.275 41.667 11.21 0.00 39.01 3.08
771 773 3.527665 ACAATCAGGTTTATAGGCCACCT 59.472 43.478 5.01 5.53 41.97 4.00
772 774 3.898482 ACAATCAGGTTTATAGGCCACC 58.102 45.455 5.01 2.56 0.00 4.61
773 775 6.038271 CAGTTACAATCAGGTTTATAGGCCAC 59.962 42.308 5.01 0.00 0.00 5.01
774 776 6.119536 CAGTTACAATCAGGTTTATAGGCCA 58.880 40.000 5.01 0.00 0.00 5.36
775 777 5.008712 GCAGTTACAATCAGGTTTATAGGCC 59.991 44.000 0.00 0.00 0.00 5.19
776 778 5.588648 TGCAGTTACAATCAGGTTTATAGGC 59.411 40.000 0.00 0.00 0.00 3.93
777 779 7.807977 ATGCAGTTACAATCAGGTTTATAGG 57.192 36.000 0.00 0.00 0.00 2.57
781 783 9.019656 ACAAATATGCAGTTACAATCAGGTTTA 57.980 29.630 0.00 0.00 0.00 2.01
782 784 7.895759 ACAAATATGCAGTTACAATCAGGTTT 58.104 30.769 0.00 0.00 0.00 3.27
783 785 7.466746 ACAAATATGCAGTTACAATCAGGTT 57.533 32.000 0.00 0.00 0.00 3.50
784 786 7.466746 AACAAATATGCAGTTACAATCAGGT 57.533 32.000 0.00 0.00 0.00 4.00
785 787 8.761575 AAAACAAATATGCAGTTACAATCAGG 57.238 30.769 0.00 0.00 0.00 3.86
809 811 8.657729 TCGTATGTCGTGATAGCAAAATAAAAA 58.342 29.630 0.00 0.00 40.80 1.94
810 812 8.187354 TCGTATGTCGTGATAGCAAAATAAAA 57.813 30.769 0.00 0.00 40.80 1.52
811 813 7.758613 TCGTATGTCGTGATAGCAAAATAAA 57.241 32.000 0.00 0.00 40.80 1.40
812 814 7.650104 TCATCGTATGTCGTGATAGCAAAATAA 59.350 33.333 0.00 0.00 40.80 1.40
813 815 7.142680 TCATCGTATGTCGTGATAGCAAAATA 58.857 34.615 0.00 0.00 40.80 1.40
814 816 5.983118 TCATCGTATGTCGTGATAGCAAAAT 59.017 36.000 0.00 0.00 40.80 1.82
815 817 5.344884 TCATCGTATGTCGTGATAGCAAAA 58.655 37.500 0.00 0.00 40.80 2.44
816 818 4.927422 TCATCGTATGTCGTGATAGCAAA 58.073 39.130 0.00 0.00 40.80 3.68
817 819 4.561735 TCATCGTATGTCGTGATAGCAA 57.438 40.909 0.00 0.00 40.80 3.91
818 820 4.561735 TTCATCGTATGTCGTGATAGCA 57.438 40.909 0.00 0.00 40.80 3.49
819 821 6.543736 TCTATTCATCGTATGTCGTGATAGC 58.456 40.000 0.00 0.00 40.80 2.97
820 822 9.004146 CAATCTATTCATCGTATGTCGTGATAG 57.996 37.037 0.00 0.00 40.80 2.08
821 823 8.726988 TCAATCTATTCATCGTATGTCGTGATA 58.273 33.333 0.00 0.00 40.80 2.15
822 824 7.593825 TCAATCTATTCATCGTATGTCGTGAT 58.406 34.615 0.00 0.00 40.80 3.06
823 825 6.966021 TCAATCTATTCATCGTATGTCGTGA 58.034 36.000 0.00 0.00 40.80 4.35
824 826 7.494130 GTTCAATCTATTCATCGTATGTCGTG 58.506 38.462 0.00 0.00 40.80 4.35
825 827 6.359883 CGTTCAATCTATTCATCGTATGTCGT 59.640 38.462 0.00 0.00 40.80 4.34
826 828 6.359883 ACGTTCAATCTATTCATCGTATGTCG 59.640 38.462 0.00 0.00 41.41 4.35
827 829 7.624706 ACGTTCAATCTATTCATCGTATGTC 57.375 36.000 0.00 0.00 0.00 3.06
828 830 8.420374 AAACGTTCAATCTATTCATCGTATGT 57.580 30.769 0.00 0.00 0.00 2.29
829 831 9.702726 AAAAACGTTCAATCTATTCATCGTATG 57.297 29.630 0.00 0.00 0.00 2.39
852 854 5.764192 CCCTGCATCATTTTCTTTCCAAAAA 59.236 36.000 0.00 0.00 0.00 1.94
853 855 5.307204 CCCTGCATCATTTTCTTTCCAAAA 58.693 37.500 0.00 0.00 0.00 2.44
854 856 4.262981 CCCCTGCATCATTTTCTTTCCAAA 60.263 41.667 0.00 0.00 0.00 3.28
855 857 3.261390 CCCCTGCATCATTTTCTTTCCAA 59.739 43.478 0.00 0.00 0.00 3.53
856 858 2.833338 CCCCTGCATCATTTTCTTTCCA 59.167 45.455 0.00 0.00 0.00 3.53
857 859 2.419159 GCCCCTGCATCATTTTCTTTCC 60.419 50.000 0.00 0.00 37.47 3.13
858 860 2.419159 GGCCCCTGCATCATTTTCTTTC 60.419 50.000 0.00 0.00 40.13 2.62
859 861 1.556451 GGCCCCTGCATCATTTTCTTT 59.444 47.619 0.00 0.00 40.13 2.52
860 862 1.197812 GGCCCCTGCATCATTTTCTT 58.802 50.000 0.00 0.00 40.13 2.52
861 863 1.039233 CGGCCCCTGCATCATTTTCT 61.039 55.000 0.00 0.00 40.13 2.52
862 864 1.438814 CGGCCCCTGCATCATTTTC 59.561 57.895 0.00 0.00 40.13 2.29
863 865 2.059786 CCGGCCCCTGCATCATTTT 61.060 57.895 0.00 0.00 40.13 1.82
864 866 2.442643 CCGGCCCCTGCATCATTT 60.443 61.111 0.00 0.00 40.13 2.32
865 867 4.528039 CCCGGCCCCTGCATCATT 62.528 66.667 0.00 0.00 40.13 2.57
868 870 2.829384 TAATCCCGGCCCCTGCATC 61.829 63.158 0.00 0.00 40.13 3.91
869 871 2.776526 TAATCCCGGCCCCTGCAT 60.777 61.111 0.00 0.00 40.13 3.96
870 872 3.804329 GTAATCCCGGCCCCTGCA 61.804 66.667 0.00 0.00 40.13 4.41
871 873 4.581093 GGTAATCCCGGCCCCTGC 62.581 72.222 0.00 0.00 0.00 4.85
872 874 3.886001 GGGTAATCCCGGCCCCTG 61.886 72.222 0.00 0.00 44.74 4.45
910 913 5.054390 ACTCTTCTTCGACTTGAGATGTC 57.946 43.478 9.81 0.00 0.00 3.06
911 914 6.576662 TTACTCTTCTTCGACTTGAGATGT 57.423 37.500 9.81 2.54 0.00 3.06
912 915 9.574458 TTAATTACTCTTCTTCGACTTGAGATG 57.426 33.333 9.81 2.26 0.00 2.90
977 981 2.185608 GGAGGAGAAGCAGCGGAC 59.814 66.667 0.00 0.00 0.00 4.79
1108 1112 4.101448 GAGGTGCGAGCCATGGGT 62.101 66.667 18.33 18.33 0.00 4.51
1703 1710 5.863397 CACAATTCATCGCAACAAGGTAAAT 59.137 36.000 0.00 0.00 0.00 1.40
1705 1712 4.320861 CCACAATTCATCGCAACAAGGTAA 60.321 41.667 0.00 0.00 0.00 2.85
1886 1899 4.933400 TCGGTTCTCTAAAATGCAGTAACC 59.067 41.667 4.55 4.55 33.41 2.85
1937 1950 4.479158 CTCTACTTTCTCCTAGATGGGCT 58.521 47.826 0.00 0.00 36.20 5.19
1939 1952 4.479158 AGCTCTACTTTCTCCTAGATGGG 58.521 47.826 0.00 0.00 36.20 4.00
2030 2043 2.515290 TGCCCATGAGATGCTGCG 60.515 61.111 0.00 0.00 31.62 5.18
2044 2057 0.320421 TGCTAAGGACACGAACTGCC 60.320 55.000 0.00 0.00 0.00 4.85
2084 2097 2.356125 GGTTAGGAGAGCCAAATCAGCA 60.356 50.000 0.00 0.00 36.29 4.41
2162 2175 3.864540 GCAAAGGGAGGCATTTGGTAAAC 60.865 47.826 0.00 0.00 36.99 2.01
2180 2193 6.481643 AGAAGTTATAACCTAGCTTGGCAAA 58.518 36.000 14.60 0.07 0.00 3.68
2260 2277 5.932619 TCTAGTACTATTGCAAAGCTCCA 57.067 39.130 1.71 0.00 0.00 3.86
2261 2278 7.306866 CGAATTCTAGTACTATTGCAAAGCTCC 60.307 40.741 1.71 0.00 0.00 4.70
2279 2296 3.065786 ACGGCGTAGAATGTCGAATTCTA 59.934 43.478 12.58 18.20 39.01 2.10
2287 2304 0.736325 AGTGCACGGCGTAGAATGTC 60.736 55.000 14.22 0.00 0.00 3.06
2291 2308 2.048597 CCAGTGCACGGCGTAGAA 60.049 61.111 14.22 0.00 0.00 2.10
2319 2336 9.725206 AGATAGTAGGAGTATTTGGTAAGGAAA 57.275 33.333 0.00 0.00 0.00 3.13
2492 2511 8.314143 TCTTGGTTCTAACAATAAGTAAACCG 57.686 34.615 0.00 0.00 38.92 4.44
2504 2523 2.708861 TCAGGCCTTCTTGGTTCTAACA 59.291 45.455 0.00 0.00 38.35 2.41
2525 2551 5.304778 TGTAGTTTGTGCACATAGTCACAT 58.695 37.500 22.39 3.90 42.07 3.21
2551 2589 2.708861 TCCTAAGAGGCCTTGTTGTCAA 59.291 45.455 6.77 0.00 34.61 3.18
2555 2593 5.478332 AGAAAAATCCTAAGAGGCCTTGTTG 59.522 40.000 6.77 0.00 34.61 3.33
2584 2622 9.423061 ACAATATCCTTCAAAACTTAAATGCAC 57.577 29.630 0.00 0.00 0.00 4.57
2610 2648 2.158871 CCTAGCTAAACCCGCCATAACA 60.159 50.000 0.00 0.00 0.00 2.41
2611 2649 2.490991 CCTAGCTAAACCCGCCATAAC 58.509 52.381 0.00 0.00 0.00 1.89
2612 2650 1.202722 GCCTAGCTAAACCCGCCATAA 60.203 52.381 0.00 0.00 0.00 1.90
2613 2651 0.395312 GCCTAGCTAAACCCGCCATA 59.605 55.000 0.00 0.00 0.00 2.74
2614 2652 1.148498 GCCTAGCTAAACCCGCCAT 59.852 57.895 0.00 0.00 0.00 4.40
2615 2653 2.587889 GCCTAGCTAAACCCGCCA 59.412 61.111 0.00 0.00 0.00 5.69
2616 2654 2.203167 GGCCTAGCTAAACCCGCC 60.203 66.667 0.00 0.00 0.00 6.13
2617 2655 2.203167 GGGCCTAGCTAAACCCGC 60.203 66.667 13.59 2.28 31.32 6.13
2618 2656 1.153229 GTGGGCCTAGCTAAACCCG 60.153 63.158 20.59 0.00 46.02 5.28
2619 2657 0.107165 CAGTGGGCCTAGCTAAACCC 60.107 60.000 19.66 19.66 43.14 4.11
2620 2658 0.107165 CCAGTGGGCCTAGCTAAACC 60.107 60.000 4.53 0.00 0.00 3.27
2621 2659 0.107165 CCCAGTGGGCCTAGCTAAAC 60.107 60.000 17.33 0.00 35.35 2.01
2622 2660 2.307153 CCCAGTGGGCCTAGCTAAA 58.693 57.895 17.33 0.00 35.35 1.85
2623 2661 4.066614 CCCAGTGGGCCTAGCTAA 57.933 61.111 17.33 0.00 35.35 3.09
2633 2671 2.640316 GGGCTAAGATTACCCAGTGG 57.360 55.000 0.63 0.63 43.64 4.00
2638 2676 3.646736 ACTTGTGGGCTAAGATTACCC 57.353 47.619 0.00 0.00 44.52 3.69
2639 2677 6.592870 AGATAACTTGTGGGCTAAGATTACC 58.407 40.000 0.00 0.00 0.00 2.85
2640 2678 9.262358 CTAAGATAACTTGTGGGCTAAGATTAC 57.738 37.037 0.00 0.00 37.53 1.89
2641 2679 8.429641 CCTAAGATAACTTGTGGGCTAAGATTA 58.570 37.037 0.00 0.00 37.53 1.75
2642 2680 7.092399 ACCTAAGATAACTTGTGGGCTAAGATT 60.092 37.037 9.98 0.00 37.53 2.40
2643 2681 6.387220 ACCTAAGATAACTTGTGGGCTAAGAT 59.613 38.462 9.98 0.00 37.53 2.40
2644 2682 5.724854 ACCTAAGATAACTTGTGGGCTAAGA 59.275 40.000 9.98 0.00 37.53 2.10
2645 2683 5.990668 ACCTAAGATAACTTGTGGGCTAAG 58.009 41.667 9.98 0.00 37.53 2.18
2646 2684 6.382919 AACCTAAGATAACTTGTGGGCTAA 57.617 37.500 9.98 0.00 37.53 3.09
2647 2685 7.499200 TTAACCTAAGATAACTTGTGGGCTA 57.501 36.000 9.98 1.68 37.53 3.93
2648 2686 4.929146 AACCTAAGATAACTTGTGGGCT 57.071 40.909 9.98 0.00 37.53 5.19
2649 2687 7.556635 AGAATTAACCTAAGATAACTTGTGGGC 59.443 37.037 9.98 0.00 37.53 5.36
2650 2688 9.462606 AAGAATTAACCTAAGATAACTTGTGGG 57.537 33.333 9.98 5.92 37.53 4.61


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

AutoCloner maintained by Alex Coulton.