Multiple sequence alignment - TraesCS2A01G034900

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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 TraesCS2A01G034900 chr2A 100.000 2975 0 0 1 2975 15231920 15228946 0.000000e+00 5494.0
1 TraesCS2A01G034900 chr2A 76.943 386 62 20 1050 1418 15402139 15401764 8.410000e-46 195.0
2 TraesCS2A01G034900 chr2D 95.696 1185 49 2 937 2119 13200839 13199655 0.000000e+00 1905.0
3 TraesCS2A01G034900 chr2D 84.603 604 61 13 1 578 13202319 13201722 3.330000e-159 571.0
4 TraesCS2A01G034900 chr2D 85.451 543 52 18 2457 2974 13193588 13193048 9.380000e-150 540.0
5 TraesCS2A01G034900 chr2D 85.350 314 31 4 2133 2436 13195625 13195317 8.010000e-81 311.0
6 TraesCS2A01G034900 chr2D 77.713 341 62 10 1118 1451 13431305 13430972 2.340000e-46 196.0
7 TraesCS2A01G034900 chr2D 76.261 337 65 11 1122 1452 13426418 13426091 6.600000e-37 165.0
8 TraesCS2A01G034900 chr2D 91.398 93 7 1 2884 2975 13195752 13195660 3.110000e-25 126.0
9 TraesCS2A01G034900 chr2D 89.796 49 5 0 2926 2974 12554277 12554325 2.480000e-06 63.9
10 TraesCS2A01G034900 chr2B 92.918 1172 78 4 895 2066 23737180 23736014 0.000000e+00 1700.0
11 TraesCS2A01G034900 chr2B 78.233 317 56 10 1122 1431 24093893 24093583 1.090000e-44 191.0
12 TraesCS2A01G034900 chr2B 86.705 173 7 8 2805 2975 23717380 23717222 8.470000e-41 178.0
13 TraesCS2A01G034900 chr7A 85.227 88 13 0 2508 2595 518806087 518806000 1.140000e-14 91.6
14 TraesCS2A01G034900 chr5D 93.182 44 3 0 540 583 339071049 339071006 6.880000e-07 65.8
15 TraesCS2A01G034900 chr4B 90.244 41 4 0 539 579 104441894 104441854 1.000000e-03 54.7


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 TraesCS2A01G034900 chr2A 15228946 15231920 2974 True 5494.0 5494 100.0000 1 2975 1 chr2A.!!$R1 2974
1 TraesCS2A01G034900 chr2D 13193048 13202319 9271 True 690.6 1905 88.4996 1 2975 5 chr2D.!!$R3 2974
2 TraesCS2A01G034900 chr2B 23736014 23737180 1166 True 1700.0 1700 92.9180 895 2066 1 chr2B.!!$R2 1171

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
875 918 0.174845 TTAGCCGTTGGATCCACTCG 59.825 55.0 23.56 23.56 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2449 8896 0.030235 TCGTCACTGTCACAACCGAG 59.97 55.0 0.0 0.0 0.0 4.63 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
60 61 7.176589 AGCATTTATATAGTACTCCCTCTGC 57.823 40.000 0.00 1.78 0.00 4.26
62 63 6.155393 GCATTTATATAGTACTCCCTCTGCCT 59.845 42.308 0.00 0.00 0.00 4.75
76 77 4.326826 CCTCTGCCTTGAATTACTTGTCA 58.673 43.478 0.00 0.00 0.00 3.58
78 79 4.072131 TCTGCCTTGAATTACTTGTCACC 58.928 43.478 0.00 0.00 0.00 4.02
83 84 5.506649 GCCTTGAATTACTTGTCACCGAAAA 60.507 40.000 0.00 0.00 0.00 2.29
117 118 7.766219 TGGATGTTTCTAGTCTAAAATACGC 57.234 36.000 0.00 0.00 0.00 4.42
149 150 4.304110 TCCATATCCGCGACAAGTAATTC 58.696 43.478 8.23 0.00 0.00 2.17
153 154 1.347221 CGCGACAAGTAATTCGGGC 59.653 57.895 0.00 0.00 40.63 6.13
154 155 1.719709 GCGACAAGTAATTCGGGCC 59.280 57.895 0.00 0.00 35.73 5.80
160 161 0.906775 AAGTAATTCGGGCCGGAGAA 59.093 50.000 27.98 14.04 0.00 2.87
171 172 1.202336 GGCCGGAGAAAGCATTGATTG 60.202 52.381 5.05 0.00 0.00 2.67
193 197 5.862845 TGTGTTGCATTTTTCCAATATGGT 58.137 33.333 0.00 0.00 39.03 3.55
194 198 5.699915 TGTGTTGCATTTTTCCAATATGGTG 59.300 36.000 0.00 0.00 39.03 4.17
209 213 6.037391 CCAATATGGTGCAAATGATTTTGTCC 59.963 38.462 0.00 4.75 37.66 4.02
225 229 7.982354 TGATTTTGTCCCAAAACTTTTATCGTT 59.018 29.630 4.41 0.00 0.00 3.85
311 315 8.570068 AAATTTTAATTCAGGTACGCCTAGAA 57.430 30.769 0.00 0.00 44.97 2.10
323 327 5.221382 GGTACGCCTAGAATAAGATTCCACA 60.221 44.000 0.00 0.00 0.00 4.17
340 344 2.092646 CCACAGGGTATTTTCCGATGGA 60.093 50.000 0.00 0.00 36.74 3.41
351 355 0.817013 TCCGATGGAATGCCTTTTGC 59.183 50.000 0.00 0.00 41.77 3.68
367 371 3.591196 TTTGCAAAGTCCCATATGTGC 57.409 42.857 8.05 4.46 0.00 4.57
380 384 5.874261 TCCCATATGTGCGTATGATTACATG 59.126 40.000 11.73 0.00 37.87 3.21
413 417 4.399004 TGCTGGTATTTTGCAAGTTTGT 57.601 36.364 0.00 0.00 33.48 2.83
425 429 0.758123 AAGTTTGTTGGCCCCATGTG 59.242 50.000 0.00 0.00 0.00 3.21
427 431 0.467804 GTTTGTTGGCCCCATGTGTT 59.532 50.000 0.00 0.00 0.00 3.32
428 432 1.689273 GTTTGTTGGCCCCATGTGTTA 59.311 47.619 0.00 0.00 0.00 2.41
431 435 3.011566 TGTTGGCCCCATGTGTTATAG 57.988 47.619 0.00 0.00 0.00 1.31
437 462 6.517013 TGGCCCCATGTGTTATAGTATTAA 57.483 37.500 0.00 0.00 0.00 1.40
471 496 3.287222 AGTAGCTGGAGAGAGTAAGCTG 58.713 50.000 6.29 0.00 45.33 4.24
481 506 5.297569 AGAGAGTAAGCTGACCTTTGTTT 57.702 39.130 0.00 0.00 34.95 2.83
491 516 7.260558 AGCTGACCTTTGTTTTTACTCTAAC 57.739 36.000 0.00 0.00 0.00 2.34
514 539 7.712204 ACTAAAAGAAAAGAAAACCACTCCA 57.288 32.000 0.00 0.00 0.00 3.86
521 546 6.327365 AGAAAAGAAAACCACTCCATCCATTT 59.673 34.615 0.00 0.00 0.00 2.32
523 548 4.739793 AGAAAACCACTCCATCCATTTCA 58.260 39.130 0.00 0.00 0.00 2.69
527 552 4.860802 ACCACTCCATCCATTTCACATA 57.139 40.909 0.00 0.00 0.00 2.29
532 557 6.982141 CCACTCCATCCATTTCACATAAATTG 59.018 38.462 0.00 0.00 0.00 2.32
533 558 7.364056 CCACTCCATCCATTTCACATAAATTGT 60.364 37.037 0.00 0.00 39.91 2.71
631 674 9.638239 TTAAAAATCAAATGTTATCTGGAGCAC 57.362 29.630 0.00 0.00 0.00 4.40
632 675 6.839124 AAATCAAATGTTATCTGGAGCACA 57.161 33.333 0.00 0.00 0.00 4.57
633 676 7.414222 AAATCAAATGTTATCTGGAGCACAT 57.586 32.000 0.00 0.00 0.00 3.21
634 677 5.823209 TCAAATGTTATCTGGAGCACATG 57.177 39.130 0.00 0.00 30.15 3.21
635 678 4.096833 TCAAATGTTATCTGGAGCACATGC 59.903 41.667 0.00 0.00 42.49 4.06
648 691 2.300433 GCACATGCTCCCATATGTTCA 58.700 47.619 1.24 0.00 35.46 3.18
649 692 2.689471 GCACATGCTCCCATATGTTCAA 59.311 45.455 1.24 0.00 35.46 2.69
650 693 3.319972 GCACATGCTCCCATATGTTCAAT 59.680 43.478 1.24 0.00 35.46 2.57
651 694 4.520111 GCACATGCTCCCATATGTTCAATA 59.480 41.667 1.24 0.00 35.46 1.90
652 695 5.563475 GCACATGCTCCCATATGTTCAATAC 60.563 44.000 1.24 0.00 35.46 1.89
653 696 4.756642 ACATGCTCCCATATGTTCAATACG 59.243 41.667 1.24 0.00 34.00 3.06
654 697 4.415881 TGCTCCCATATGTTCAATACGT 57.584 40.909 1.24 0.00 0.00 3.57
655 698 5.538849 TGCTCCCATATGTTCAATACGTA 57.461 39.130 0.00 0.00 32.93 3.57
656 699 5.919755 TGCTCCCATATGTTCAATACGTAA 58.080 37.500 0.00 0.00 32.18 3.18
657 700 6.530120 TGCTCCCATATGTTCAATACGTAAT 58.470 36.000 0.00 0.00 32.18 1.89
658 701 6.995686 TGCTCCCATATGTTCAATACGTAATT 59.004 34.615 0.00 0.00 32.18 1.40
659 702 8.151596 TGCTCCCATATGTTCAATACGTAATTA 58.848 33.333 0.00 0.00 32.18 1.40
660 703 9.162764 GCTCCCATATGTTCAATACGTAATTAT 57.837 33.333 0.00 0.00 32.18 1.28
662 705 9.361315 TCCCATATGTTCAATACGTAATTATCG 57.639 33.333 0.00 6.08 32.18 2.92
663 706 8.600625 CCCATATGTTCAATACGTAATTATCGG 58.399 37.037 0.00 0.00 32.18 4.18
664 707 9.146984 CCATATGTTCAATACGTAATTATCGGT 57.853 33.333 0.00 3.30 32.18 4.69
665 708 9.952341 CATATGTTCAATACGTAATTATCGGTG 57.048 33.333 0.00 6.89 32.18 4.94
666 709 9.917129 ATATGTTCAATACGTAATTATCGGTGA 57.083 29.630 0.00 8.43 32.18 4.02
667 710 7.453980 TGTTCAATACGTAATTATCGGTGAC 57.546 36.000 0.00 0.00 0.00 3.67
668 711 7.034397 TGTTCAATACGTAATTATCGGTGACA 58.966 34.615 0.00 0.00 0.00 3.58
669 712 7.544915 TGTTCAATACGTAATTATCGGTGACAA 59.455 33.333 0.00 2.73 0.00 3.18
670 713 8.382130 GTTCAATACGTAATTATCGGTGACAAA 58.618 33.333 0.00 0.00 0.00 2.83
671 714 8.122306 TCAATACGTAATTATCGGTGACAAAG 57.878 34.615 0.00 0.00 0.00 2.77
672 715 7.760794 TCAATACGTAATTATCGGTGACAAAGT 59.239 33.333 0.00 0.00 0.00 2.66
673 716 7.689953 ATACGTAATTATCGGTGACAAAGTC 57.310 36.000 0.00 0.00 0.00 3.01
674 717 4.866486 ACGTAATTATCGGTGACAAAGTCC 59.134 41.667 10.67 0.00 0.00 3.85
675 718 5.107133 CGTAATTATCGGTGACAAAGTCCT 58.893 41.667 0.00 0.00 0.00 3.85
676 719 6.127647 ACGTAATTATCGGTGACAAAGTCCTA 60.128 38.462 10.67 0.00 0.00 2.94
677 720 6.197842 CGTAATTATCGGTGACAAAGTCCTAC 59.802 42.308 0.00 0.00 0.00 3.18
678 721 5.934402 ATTATCGGTGACAAAGTCCTACT 57.066 39.130 0.00 0.00 0.00 2.57
679 722 3.870633 ATCGGTGACAAAGTCCTACTC 57.129 47.619 0.00 0.00 0.00 2.59
680 723 2.872732 TCGGTGACAAAGTCCTACTCT 58.127 47.619 0.00 0.00 0.00 3.24
681 724 4.025040 TCGGTGACAAAGTCCTACTCTA 57.975 45.455 0.00 0.00 0.00 2.43
682 725 4.008330 TCGGTGACAAAGTCCTACTCTAG 58.992 47.826 0.00 0.00 0.00 2.43
683 726 3.757493 CGGTGACAAAGTCCTACTCTAGT 59.243 47.826 0.00 0.00 0.00 2.57
684 727 4.217983 CGGTGACAAAGTCCTACTCTAGTT 59.782 45.833 0.00 0.00 0.00 2.24
685 728 5.278858 CGGTGACAAAGTCCTACTCTAGTTT 60.279 44.000 0.00 0.00 0.00 2.66
686 729 6.157904 GGTGACAAAGTCCTACTCTAGTTTC 58.842 44.000 0.00 0.00 0.00 2.78
687 730 6.015265 GGTGACAAAGTCCTACTCTAGTTTCT 60.015 42.308 0.00 0.00 0.00 2.52
688 731 7.435305 GTGACAAAGTCCTACTCTAGTTTCTT 58.565 38.462 0.00 0.00 0.00 2.52
689 732 7.927092 GTGACAAAGTCCTACTCTAGTTTCTTT 59.073 37.037 0.00 0.00 0.00 2.52
690 733 8.142551 TGACAAAGTCCTACTCTAGTTTCTTTC 58.857 37.037 0.00 0.00 0.00 2.62
691 734 7.146648 ACAAAGTCCTACTCTAGTTTCTTTCG 58.853 38.462 0.00 0.00 0.00 3.46
692 735 5.313520 AGTCCTACTCTAGTTTCTTTCGC 57.686 43.478 0.00 0.00 0.00 4.70
693 736 4.765856 AGTCCTACTCTAGTTTCTTTCGCA 59.234 41.667 0.00 0.00 0.00 5.10
694 737 5.243283 AGTCCTACTCTAGTTTCTTTCGCAA 59.757 40.000 0.00 0.00 0.00 4.85
695 738 5.924825 GTCCTACTCTAGTTTCTTTCGCAAA 59.075 40.000 0.00 0.00 0.00 3.68
696 739 6.423001 GTCCTACTCTAGTTTCTTTCGCAAAA 59.577 38.462 0.00 0.00 0.00 2.44
697 740 6.987992 TCCTACTCTAGTTTCTTTCGCAAAAA 59.012 34.615 0.00 0.00 0.00 1.94
722 765 8.890124 AAAAGTCCTACTCTAGTTTTCTTGTC 57.110 34.615 0.00 0.00 0.00 3.18
723 766 7.598759 AAGTCCTACTCTAGTTTTCTTGTCA 57.401 36.000 0.00 0.00 0.00 3.58
724 767 7.598759 AGTCCTACTCTAGTTTTCTTGTCAA 57.401 36.000 0.00 0.00 0.00 3.18
725 768 8.196378 AGTCCTACTCTAGTTTTCTTGTCAAT 57.804 34.615 0.00 0.00 0.00 2.57
726 769 8.652290 AGTCCTACTCTAGTTTTCTTGTCAATT 58.348 33.333 0.00 0.00 0.00 2.32
727 770 9.274206 GTCCTACTCTAGTTTTCTTGTCAATTT 57.726 33.333 0.00 0.00 0.00 1.82
728 771 9.273016 TCCTACTCTAGTTTTCTTGTCAATTTG 57.727 33.333 0.00 0.00 0.00 2.32
729 772 8.507249 CCTACTCTAGTTTTCTTGTCAATTTGG 58.493 37.037 0.00 0.00 0.00 3.28
730 773 9.273016 CTACTCTAGTTTTCTTGTCAATTTGGA 57.727 33.333 0.00 0.00 0.00 3.53
731 774 8.519799 ACTCTAGTTTTCTTGTCAATTTGGAA 57.480 30.769 0.00 0.00 0.00 3.53
732 775 9.136323 ACTCTAGTTTTCTTGTCAATTTGGAAT 57.864 29.630 0.00 0.00 0.00 3.01
733 776 9.617975 CTCTAGTTTTCTTGTCAATTTGGAATC 57.382 33.333 0.00 0.00 0.00 2.52
734 777 9.130661 TCTAGTTTTCTTGTCAATTTGGAATCA 57.869 29.630 0.00 0.00 0.00 2.57
735 778 9.748708 CTAGTTTTCTTGTCAATTTGGAATCAA 57.251 29.630 0.00 0.00 0.00 2.57
752 795 8.741101 TGGAATCAAATTTTACAAATCAGACG 57.259 30.769 0.00 0.00 0.00 4.18
753 796 8.356657 TGGAATCAAATTTTACAAATCAGACGT 58.643 29.630 0.00 0.00 0.00 4.34
754 797 9.191995 GGAATCAAATTTTACAAATCAGACGTT 57.808 29.630 0.00 0.00 0.00 3.99
771 814 5.409520 CAGACGTTGATTTTGAATGGAGAGA 59.590 40.000 0.00 0.00 0.00 3.10
772 815 5.997746 AGACGTTGATTTTGAATGGAGAGAA 59.002 36.000 0.00 0.00 0.00 2.87
773 816 6.002062 ACGTTGATTTTGAATGGAGAGAAC 57.998 37.500 0.00 0.00 0.00 3.01
774 817 5.530915 ACGTTGATTTTGAATGGAGAGAACA 59.469 36.000 0.00 0.00 0.00 3.18
775 818 6.207417 ACGTTGATTTTGAATGGAGAGAACAT 59.793 34.615 0.00 0.00 0.00 2.71
776 819 6.525628 CGTTGATTTTGAATGGAGAGAACATG 59.474 38.462 0.00 0.00 0.00 3.21
777 820 5.957798 TGATTTTGAATGGAGAGAACATGC 58.042 37.500 0.00 0.00 0.00 4.06
778 821 5.713389 TGATTTTGAATGGAGAGAACATGCT 59.287 36.000 0.00 0.00 0.00 3.79
779 822 5.633830 TTTTGAATGGAGAGAACATGCTC 57.366 39.130 0.00 0.00 35.11 4.26
783 826 3.776616 GGAGAGAACATGCTCCCAG 57.223 57.895 5.95 0.00 43.91 4.45
795 838 0.886490 GCTCCCAGATGCCCAATACG 60.886 60.000 0.00 0.00 0.00 3.06
802 845 4.133820 CCAGATGCCCAATACGAAATACA 58.866 43.478 0.00 0.00 0.00 2.29
803 846 4.214119 CCAGATGCCCAATACGAAATACAG 59.786 45.833 0.00 0.00 0.00 2.74
818 861 8.018677 ACGAAATACAGTAATCAGTGACAAAG 57.981 34.615 0.00 0.00 0.00 2.77
822 865 5.552870 ACAGTAATCAGTGACAAAGTCCT 57.447 39.130 0.00 0.00 0.00 3.85
824 867 6.692486 ACAGTAATCAGTGACAAAGTCCTAG 58.308 40.000 0.00 0.00 0.00 3.02
830 873 6.235231 TCAGTGACAAAGTCCTAGTTTTCT 57.765 37.500 0.00 0.00 0.00 2.52
835 878 7.494952 AGTGACAAAGTCCTAGTTTTCTTGTAC 59.505 37.037 0.00 0.00 0.00 2.90
837 880 7.990886 TGACAAAGTCCTAGTTTTCTTGTACAT 59.009 33.333 0.00 0.00 0.00 2.29
866 909 4.160594 GGAAAAATACGTTTAGCCGTTGG 58.839 43.478 0.00 0.00 42.00 3.77
875 918 0.174845 TTAGCCGTTGGATCCACTCG 59.825 55.000 23.56 23.56 0.00 4.18
881 924 1.087501 GTTGGATCCACTCGGCTTTC 58.912 55.000 15.91 0.00 0.00 2.62
919 995 6.554419 CATTCTTTATCGCAACAGAAATGGA 58.446 36.000 0.00 0.00 0.00 3.41
923 999 1.428448 TCGCAACAGAAATGGAGTCG 58.572 50.000 0.00 0.00 0.00 4.18
924 1000 0.443869 CGCAACAGAAATGGAGTCGG 59.556 55.000 0.00 0.00 0.00 4.79
925 1001 1.523758 GCAACAGAAATGGAGTCGGT 58.476 50.000 0.00 0.00 0.00 4.69
927 1003 2.095718 GCAACAGAAATGGAGTCGGTTC 60.096 50.000 0.00 0.00 32.13 3.62
931 1007 3.581332 ACAGAAATGGAGTCGGTTCCTAA 59.419 43.478 7.48 0.00 38.12 2.69
933 1009 3.581332 AGAAATGGAGTCGGTTCCTAACA 59.419 43.478 7.48 0.00 38.12 2.41
935 1011 0.606604 TGGAGTCGGTTCCTAACAGC 59.393 55.000 7.48 0.00 38.12 4.40
959 1670 2.168106 CTGCAGCTCCAGATCAACTACT 59.832 50.000 0.00 0.00 34.77 2.57
962 1673 3.529533 CAGCTCCAGATCAACTACTTGG 58.470 50.000 0.00 0.00 0.00 3.61
969 1680 1.562672 ATCAACTACTTGGCCGCCCT 61.563 55.000 7.03 0.00 0.00 5.19
1212 1923 2.666098 GGCTTTCCTGGACGCCCTA 61.666 63.158 20.32 0.00 36.56 3.53
1258 1969 2.203337 GTGCAGGCCTGAACCACA 60.203 61.111 37.21 20.95 32.90 4.17
1332 2043 3.152937 CTACTCCTCGGACGTCGCG 62.153 68.421 17.01 17.01 39.05 5.87
1549 2260 2.043248 TCTCCTACCACTCCCGCC 60.043 66.667 0.00 0.00 0.00 6.13
1652 2363 3.998672 GTTGACGGCCGAGACCCA 61.999 66.667 35.90 17.56 0.00 4.51
1653 2364 3.000819 TTGACGGCCGAGACCCAT 61.001 61.111 35.90 7.12 0.00 4.00
1662 2373 1.226323 CGAGACCCATCACGTCGTC 60.226 63.158 0.00 0.00 34.62 4.20
1908 2619 3.745803 GACCTCGACCGCCTCGTT 61.746 66.667 1.28 0.00 43.45 3.85
1995 2706 2.668457 AGCACAAAGAATGTCGATCGTC 59.332 45.455 15.94 10.48 41.46 4.20
2034 2747 7.370383 TCTTCACAAAGAATAAAACTGGCATC 58.630 34.615 0.00 0.00 38.58 3.91
2090 2803 0.538057 TTGTCCCTCCAAAGCAGCAG 60.538 55.000 0.00 0.00 0.00 4.24
2109 2822 1.137086 AGGTACGATGAGACCATGCAC 59.863 52.381 0.00 0.00 38.27 4.57
2119 2832 6.403527 CGATGAGACCATGCACAAATCTAAAA 60.404 38.462 0.00 0.00 32.09 1.52
2121 2834 5.064441 AGACCATGCACAAATCTAAAAGC 57.936 39.130 0.00 0.00 0.00 3.51
2122 2835 4.523943 AGACCATGCACAAATCTAAAAGCA 59.476 37.500 0.00 0.00 36.34 3.91
2124 2837 3.615496 CCATGCACAAATCTAAAAGCAGC 59.385 43.478 0.00 0.00 35.26 5.25
2125 2838 4.239304 CATGCACAAATCTAAAAGCAGCA 58.761 39.130 0.00 0.00 35.26 4.41
2127 2840 3.248266 GCACAAATCTAAAAGCAGCAGG 58.752 45.455 0.00 0.00 0.00 4.85
2129 2842 4.479619 CACAAATCTAAAAGCAGCAGGTC 58.520 43.478 0.00 0.00 0.00 3.85
2130 2843 3.507622 ACAAATCTAAAAGCAGCAGGTCC 59.492 43.478 0.00 0.00 0.00 4.46
2131 2844 2.426842 ATCTAAAAGCAGCAGGTCCC 57.573 50.000 0.00 0.00 0.00 4.46
2157 6886 2.254651 GTCTTGGTCGTCGACGCT 59.745 61.111 32.19 0.00 39.60 5.07
2161 6890 0.732880 CTTGGTCGTCGACGCTGATT 60.733 55.000 32.19 0.00 39.60 2.57
2168 6897 0.862283 GTCGACGCTGATTCCTCGAC 60.862 60.000 0.00 5.39 45.73 4.20
2172 6901 0.681564 ACGCTGATTCCTCGACCTCT 60.682 55.000 2.36 0.00 0.00 3.69
2180 6909 2.470362 CCTCGACCTCTAGCGCGAA 61.470 63.158 12.10 0.00 31.89 4.70
2187 6916 1.226717 CTCTAGCGCGAACCAGACC 60.227 63.158 12.10 0.00 0.00 3.85
2192 6921 4.796231 CGCGAACCAGACCTCCCG 62.796 72.222 0.00 0.00 0.00 5.14
2197 6926 2.465055 GAACCAGACCTCCCGGTTGG 62.465 65.000 0.00 4.32 45.73 3.77
2198 6927 4.410400 CCAGACCTCCCGGTTGGC 62.410 72.222 9.58 3.75 45.73 4.52
2199 6928 4.410400 CAGACCTCCCGGTTGGCC 62.410 72.222 9.58 0.00 45.73 5.36
2254 6983 1.728502 GCTCCGACGTCAGTAACTCAC 60.729 57.143 17.16 0.00 0.00 3.51
2262 6991 1.466167 GTCAGTAACTCACGGCGTCTA 59.534 52.381 10.85 0.00 0.00 2.59
2315 7054 1.063469 GACATTGAAATACGGTGCGGG 59.937 52.381 0.00 0.00 0.00 6.13
2320 7059 1.078708 AAATACGGTGCGGGTCCAG 60.079 57.895 0.00 0.00 0.00 3.86
2346 7085 0.105760 ACAATGGGGCAGGTTGACAA 60.106 50.000 2.66 0.00 0.00 3.18
2349 7088 0.540365 ATGGGGCAGGTTGACAACTG 60.540 55.000 17.52 13.91 37.76 3.16
2377 7116 2.440796 CGGCTACCGGTACTCCCA 60.441 66.667 11.16 0.00 44.15 4.37
2408 7147 1.815408 GCCTGTTGCATCGGGATGTAT 60.815 52.381 24.21 0.00 40.80 2.29
2470 8917 1.213094 CGGTTGTGACAGTGACGACC 61.213 60.000 17.61 17.61 42.49 4.79
2472 8919 0.878961 GTTGTGACAGTGACGACCCC 60.879 60.000 0.00 0.00 0.00 4.95
2473 8920 2.049433 GTGACAGTGACGACCCCG 60.049 66.667 0.00 0.00 42.50 5.73
2476 8923 4.608774 ACAGTGACGACCCCGGGA 62.609 66.667 26.32 0.00 40.78 5.14
2477 8924 4.065281 CAGTGACGACCCCGGGAC 62.065 72.222 26.32 15.08 40.78 4.46
2502 8950 2.677979 GCGCCGGGTCAGAACTTTC 61.678 63.158 2.18 0.00 0.00 2.62
2522 8970 0.038801 GCTTGCCCTTGCTGAAGAAC 60.039 55.000 0.00 0.00 38.71 3.01
2534 8982 2.044946 AAGAACCCCATGGCGAGC 60.045 61.111 6.09 0.00 33.59 5.03
2545 8993 1.032114 ATGGCGAGCTAGGTTTTGCC 61.032 55.000 20.49 20.49 43.04 4.52
2588 9036 0.545787 TGGTTAGATGTGGACGGGGT 60.546 55.000 0.00 0.00 0.00 4.95
2602 9050 1.532238 GGGGTAGGGAAGTGGATGC 59.468 63.158 0.00 0.00 0.00 3.91
2607 9055 0.616395 TAGGGAAGTGGATGCGGTCA 60.616 55.000 0.00 0.00 0.00 4.02
2668 9116 2.593436 CCGAGGTGGTTTTGCCGT 60.593 61.111 0.00 0.00 41.21 5.68
2669 9117 2.613506 CCGAGGTGGTTTTGCCGTC 61.614 63.158 0.00 0.00 41.21 4.79
2670 9118 1.597027 CGAGGTGGTTTTGCCGTCT 60.597 57.895 0.00 0.00 41.21 4.18
2672 9120 1.674817 CGAGGTGGTTTTGCCGTCTAT 60.675 52.381 0.00 0.00 41.21 1.98
2673 9121 2.433436 GAGGTGGTTTTGCCGTCTATT 58.567 47.619 0.00 0.00 41.21 1.73
2675 9123 2.817844 AGGTGGTTTTGCCGTCTATTTC 59.182 45.455 0.00 0.00 41.21 2.17
2676 9124 2.554893 GGTGGTTTTGCCGTCTATTTCA 59.445 45.455 0.00 0.00 41.21 2.69
2677 9125 3.192633 GGTGGTTTTGCCGTCTATTTCAT 59.807 43.478 0.00 0.00 41.21 2.57
2678 9126 4.165779 GTGGTTTTGCCGTCTATTTCATG 58.834 43.478 0.00 0.00 41.21 3.07
2679 9127 3.823873 TGGTTTTGCCGTCTATTTCATGT 59.176 39.130 0.00 0.00 41.21 3.21
2680 9128 4.279671 TGGTTTTGCCGTCTATTTCATGTT 59.720 37.500 0.00 0.00 41.21 2.71
2682 9130 5.457140 GTTTTGCCGTCTATTTCATGTTCA 58.543 37.500 0.00 0.00 0.00 3.18
2684 9132 4.880886 TGCCGTCTATTTCATGTTCATG 57.119 40.909 6.46 6.46 0.00 3.07
2685 9133 4.260985 TGCCGTCTATTTCATGTTCATGT 58.739 39.130 11.73 0.00 0.00 3.21
2686 9134 4.094739 TGCCGTCTATTTCATGTTCATGTG 59.905 41.667 11.73 0.00 0.00 3.21
2687 9135 4.332543 GCCGTCTATTTCATGTTCATGTGA 59.667 41.667 11.73 3.77 0.00 3.58
2695 9158 7.915293 ATTTCATGTTCATGTGAATGCAAAT 57.085 28.000 11.73 6.61 36.33 2.32
2699 9162 7.036829 TCATGTTCATGTGAATGCAAATAAGG 58.963 34.615 11.73 0.00 36.33 2.69
2724 9187 6.245710 GTGTAAATTTGCGTCTGAAATACGTC 59.754 38.462 0.00 0.00 42.26 4.34
2725 9188 5.607119 AAATTTGCGTCTGAAATACGTCT 57.393 34.783 0.00 0.00 42.26 4.18
2726 9189 6.715344 AAATTTGCGTCTGAAATACGTCTA 57.285 33.333 0.00 0.00 42.26 2.59
2728 9191 4.690184 TTGCGTCTGAAATACGTCTAGA 57.310 40.909 0.00 0.00 42.26 2.43
2729 9192 4.012319 TGCGTCTGAAATACGTCTAGAC 57.988 45.455 13.18 13.18 42.26 2.59
2745 9208 4.979197 GTCTAGACGGACATTGATGACATC 59.021 45.833 7.22 8.59 36.35 3.06
2746 9209 2.814269 AGACGGACATTGATGACATCG 58.186 47.619 10.79 0.26 0.00 3.84
2748 9211 0.230515 CGGACATTGATGACATCGCG 59.769 55.000 10.79 0.00 0.00 5.87
2749 9212 1.570813 GGACATTGATGACATCGCGA 58.429 50.000 13.09 13.09 0.00 5.87
2764 9229 2.184836 CGATTGGTCCGCGGGTTA 59.815 61.111 27.83 8.82 0.00 2.85
2766 9231 1.523032 GATTGGTCCGCGGGTTAGG 60.523 63.158 27.83 0.00 0.00 2.69
2801 9266 4.487948 CGTATCGGTTGGAGTTGTTCTTA 58.512 43.478 0.00 0.00 0.00 2.10
2812 9277 5.191722 TGGAGTTGTTCTTAGGAATAGCCAT 59.808 40.000 0.00 0.00 40.02 4.40
2824 9289 4.082125 GGAATAGCCATATTTGGTCCAGG 58.918 47.826 4.00 0.00 45.57 4.45
2834 9299 0.323629 TTGGTCCAGGAACCGATGTC 59.676 55.000 0.61 0.00 42.62 3.06
2871 9337 0.959372 CTGTCCTCCAAAGCAGCAGG 60.959 60.000 0.00 0.00 0.00 4.85
2872 9338 1.073897 GTCCTCCAAAGCAGCAGGT 59.926 57.895 0.00 0.00 0.00 4.00
2873 9339 0.324943 GTCCTCCAAAGCAGCAGGTA 59.675 55.000 0.00 0.00 0.00 3.08
2874 9340 0.324943 TCCTCCAAAGCAGCAGGTAC 59.675 55.000 0.00 0.00 0.00 3.34
2876 9342 1.677217 CCTCCAAAGCAGCAGGTACTC 60.677 57.143 0.00 0.00 34.60 2.59
2877 9343 0.324943 TCCAAAGCAGCAGGTACTCC 59.675 55.000 0.00 0.00 34.60 3.85
2878 9344 1.021390 CCAAAGCAGCAGGTACTCCG 61.021 60.000 0.00 0.00 34.60 4.63
2921 9392 2.044352 TCCACGGAGCGATGGAGA 60.044 61.111 0.00 0.00 40.17 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 2.811431 CGGTGACAAGTAATTCAAGGCA 59.189 45.455 0.00 0.00 0.00 4.75
60 61 5.682943 TTTCGGTGACAAGTAATTCAAGG 57.317 39.130 0.00 0.00 0.00 3.61
94 95 6.985059 AGGCGTATTTTAGACTAGAAACATCC 59.015 38.462 0.00 0.00 0.00 3.51
117 118 5.705905 TGTCGCGGATATGGATATATCTAGG 59.294 44.000 6.13 0.00 43.07 3.02
125 126 5.654603 ATTACTTGTCGCGGATATGGATA 57.345 39.130 6.13 0.00 0.00 2.59
132 133 1.567504 CCGAATTACTTGTCGCGGAT 58.432 50.000 6.13 0.00 41.11 4.18
134 135 2.003672 CCCGAATTACTTGTCGCGG 58.996 57.895 6.13 0.00 35.93 6.46
149 150 2.438434 AATGCTTTCTCCGGCCCG 60.438 61.111 0.00 0.00 0.00 6.13
153 154 2.489329 ACACAATCAATGCTTTCTCCGG 59.511 45.455 0.00 0.00 0.00 5.14
154 155 3.837213 ACACAATCAATGCTTTCTCCG 57.163 42.857 0.00 0.00 0.00 4.63
160 161 6.380095 AAAAATGCAACACAATCAATGCTT 57.620 29.167 0.00 0.00 39.49 3.91
171 172 5.390779 GCACCATATTGGAAAAATGCAACAC 60.391 40.000 0.00 0.00 40.96 3.32
280 284 8.931775 GGCGTACCTGAATTAAAATTTTGAATT 58.068 29.630 13.76 13.59 0.00 2.17
281 285 8.474006 GGCGTACCTGAATTAAAATTTTGAAT 57.526 30.769 13.76 0.00 0.00 2.57
300 304 5.839621 TGTGGAATCTTATTCTAGGCGTAC 58.160 41.667 0.00 0.00 0.00 3.67
311 315 6.062095 CGGAAAATACCCTGTGGAATCTTAT 58.938 40.000 0.00 0.00 34.81 1.73
323 327 3.222603 GCATTCCATCGGAAAATACCCT 58.777 45.455 0.00 0.00 45.41 4.34
351 355 4.126437 TCATACGCACATATGGGACTTTG 58.874 43.478 9.80 0.66 41.24 2.77
380 384 8.930760 TGCAAAATACCAGCAATAAATAAACAC 58.069 29.630 0.00 0.00 34.97 3.32
391 395 4.764172 ACAAACTTGCAAAATACCAGCAA 58.236 34.783 0.00 0.00 45.07 3.91
412 416 3.012934 ACTATAACACATGGGGCCAAC 57.987 47.619 4.39 0.00 0.00 3.77
413 417 5.396057 AATACTATAACACATGGGGCCAA 57.604 39.130 4.39 0.00 0.00 4.52
491 516 7.867909 GGATGGAGTGGTTTTCTTTTCTTTTAG 59.132 37.037 0.00 0.00 0.00 1.85
496 521 4.803452 TGGATGGAGTGGTTTTCTTTTCT 58.197 39.130 0.00 0.00 0.00 2.52
497 522 5.728637 ATGGATGGAGTGGTTTTCTTTTC 57.271 39.130 0.00 0.00 0.00 2.29
502 527 4.280677 TGTGAAATGGATGGAGTGGTTTTC 59.719 41.667 0.00 0.00 0.00 2.29
503 528 4.222336 TGTGAAATGGATGGAGTGGTTTT 58.778 39.130 0.00 0.00 0.00 2.43
504 529 3.843422 TGTGAAATGGATGGAGTGGTTT 58.157 40.909 0.00 0.00 0.00 3.27
505 530 3.524095 TGTGAAATGGATGGAGTGGTT 57.476 42.857 0.00 0.00 0.00 3.67
506 531 3.744940 ATGTGAAATGGATGGAGTGGT 57.255 42.857 0.00 0.00 0.00 4.16
507 532 6.720112 ATTTATGTGAAATGGATGGAGTGG 57.280 37.500 0.00 0.00 0.00 4.00
508 533 7.549839 ACAATTTATGTGAAATGGATGGAGTG 58.450 34.615 0.00 0.00 41.93 3.51
532 557 9.257651 ACGTTTAGATACATCTATTTTAGGCAC 57.742 33.333 0.00 0.00 39.02 5.01
578 607 6.301687 TCGTCAAAACATCCATTTTAACGA 57.698 33.333 5.49 5.49 45.44 3.85
608 651 7.230849 TGTGCTCCAGATAACATTTGATTTT 57.769 32.000 0.00 0.00 0.00 1.82
628 671 2.300433 TGAACATATGGGAGCATGTGC 58.700 47.619 7.80 0.00 35.59 4.57
629 672 5.334337 CGTATTGAACATATGGGAGCATGTG 60.334 44.000 7.80 0.00 35.59 3.21
630 673 4.756642 CGTATTGAACATATGGGAGCATGT 59.243 41.667 7.80 0.00 36.96 3.21
631 674 4.756642 ACGTATTGAACATATGGGAGCATG 59.243 41.667 7.80 0.00 0.00 4.06
632 675 4.973168 ACGTATTGAACATATGGGAGCAT 58.027 39.130 7.80 0.00 0.00 3.79
633 676 4.415881 ACGTATTGAACATATGGGAGCA 57.584 40.909 7.80 0.00 0.00 4.26
634 677 7.435068 AATTACGTATTGAACATATGGGAGC 57.565 36.000 7.80 0.00 0.00 4.70
636 679 9.361315 CGATAATTACGTATTGAACATATGGGA 57.639 33.333 7.80 0.00 0.00 4.37
637 680 8.600625 CCGATAATTACGTATTGAACATATGGG 58.399 37.037 7.80 0.00 0.00 4.00
638 681 9.146984 ACCGATAATTACGTATTGAACATATGG 57.853 33.333 7.80 0.00 0.00 2.74
639 682 9.952341 CACCGATAATTACGTATTGAACATATG 57.048 33.333 0.00 0.00 0.00 1.78
640 683 9.917129 TCACCGATAATTACGTATTGAACATAT 57.083 29.630 0.00 0.00 0.00 1.78
641 684 9.184062 GTCACCGATAATTACGTATTGAACATA 57.816 33.333 0.00 0.00 0.00 2.29
642 685 7.707464 TGTCACCGATAATTACGTATTGAACAT 59.293 33.333 0.00 0.00 0.00 2.71
643 686 7.034397 TGTCACCGATAATTACGTATTGAACA 58.966 34.615 0.00 0.00 0.00 3.18
644 687 7.453980 TGTCACCGATAATTACGTATTGAAC 57.546 36.000 0.00 0.00 0.00 3.18
645 688 8.476657 TTTGTCACCGATAATTACGTATTGAA 57.523 30.769 0.00 0.00 0.00 2.69
646 689 7.760794 ACTTTGTCACCGATAATTACGTATTGA 59.239 33.333 0.00 0.00 0.00 2.57
647 690 7.902032 ACTTTGTCACCGATAATTACGTATTG 58.098 34.615 0.00 0.00 0.00 1.90
648 691 7.223387 GGACTTTGTCACCGATAATTACGTATT 59.777 37.037 0.00 0.00 33.68 1.89
649 692 6.698766 GGACTTTGTCACCGATAATTACGTAT 59.301 38.462 0.00 0.00 33.68 3.06
650 693 6.035843 GGACTTTGTCACCGATAATTACGTA 58.964 40.000 0.00 0.00 33.68 3.57
651 694 4.866486 GGACTTTGTCACCGATAATTACGT 59.134 41.667 0.00 0.00 33.68 3.57
652 695 5.107133 AGGACTTTGTCACCGATAATTACG 58.893 41.667 0.07 0.00 33.68 3.18
653 696 7.263496 AGTAGGACTTTGTCACCGATAATTAC 58.737 38.462 0.07 0.00 33.68 1.89
654 697 7.341256 AGAGTAGGACTTTGTCACCGATAATTA 59.659 37.037 0.07 0.00 33.68 1.40
655 698 6.154706 AGAGTAGGACTTTGTCACCGATAATT 59.845 38.462 0.07 0.00 33.68 1.40
656 699 5.657302 AGAGTAGGACTTTGTCACCGATAAT 59.343 40.000 0.07 0.00 33.68 1.28
657 700 5.014858 AGAGTAGGACTTTGTCACCGATAA 58.985 41.667 0.07 0.00 33.68 1.75
658 701 4.597004 AGAGTAGGACTTTGTCACCGATA 58.403 43.478 0.07 0.00 33.68 2.92
659 702 3.432378 AGAGTAGGACTTTGTCACCGAT 58.568 45.455 0.07 0.00 33.68 4.18
660 703 2.872732 AGAGTAGGACTTTGTCACCGA 58.127 47.619 0.07 0.00 33.68 4.69
661 704 3.757493 ACTAGAGTAGGACTTTGTCACCG 59.243 47.826 0.00 0.00 33.68 4.94
662 705 5.725325 AACTAGAGTAGGACTTTGTCACC 57.275 43.478 0.00 0.00 33.68 4.02
663 706 6.983984 AGAAACTAGAGTAGGACTTTGTCAC 58.016 40.000 0.00 0.00 33.68 3.67
664 707 7.598759 AAGAAACTAGAGTAGGACTTTGTCA 57.401 36.000 0.00 0.00 33.68 3.58
665 708 7.326547 CGAAAGAAACTAGAGTAGGACTTTGTC 59.673 40.741 0.00 0.00 31.90 3.18
666 709 7.146648 CGAAAGAAACTAGAGTAGGACTTTGT 58.853 38.462 0.00 0.00 31.90 2.83
667 710 6.089685 GCGAAAGAAACTAGAGTAGGACTTTG 59.910 42.308 0.00 0.00 31.90 2.77
668 711 6.157904 GCGAAAGAAACTAGAGTAGGACTTT 58.842 40.000 0.00 0.00 33.19 2.66
669 712 5.243283 TGCGAAAGAAACTAGAGTAGGACTT 59.757 40.000 0.00 0.00 0.00 3.01
670 713 4.765856 TGCGAAAGAAACTAGAGTAGGACT 59.234 41.667 0.00 0.00 0.00 3.85
671 714 5.056894 TGCGAAAGAAACTAGAGTAGGAC 57.943 43.478 0.00 0.00 0.00 3.85
672 715 5.717078 TTGCGAAAGAAACTAGAGTAGGA 57.283 39.130 0.00 0.00 0.00 2.94
673 716 6.780706 TTTTGCGAAAGAAACTAGAGTAGG 57.219 37.500 0.00 0.00 0.00 3.18
696 739 9.327628 GACAAGAAAACTAGAGTAGGACTTTTT 57.672 33.333 0.00 0.00 0.00 1.94
697 740 8.483758 TGACAAGAAAACTAGAGTAGGACTTTT 58.516 33.333 0.00 0.00 0.00 2.27
698 741 8.019656 TGACAAGAAAACTAGAGTAGGACTTT 57.980 34.615 0.00 0.00 0.00 2.66
699 742 7.598759 TGACAAGAAAACTAGAGTAGGACTT 57.401 36.000 0.00 0.00 0.00 3.01
700 743 7.598759 TTGACAAGAAAACTAGAGTAGGACT 57.401 36.000 0.00 0.00 0.00 3.85
701 744 8.834749 AATTGACAAGAAAACTAGAGTAGGAC 57.165 34.615 0.00 0.00 0.00 3.85
702 745 9.273016 CAAATTGACAAGAAAACTAGAGTAGGA 57.727 33.333 0.00 0.00 0.00 2.94
703 746 8.507249 CCAAATTGACAAGAAAACTAGAGTAGG 58.493 37.037 0.00 0.00 0.00 3.18
704 747 9.273016 TCCAAATTGACAAGAAAACTAGAGTAG 57.727 33.333 0.00 0.00 0.00 2.57
705 748 9.621629 TTCCAAATTGACAAGAAAACTAGAGTA 57.378 29.630 0.00 0.00 0.00 2.59
706 749 8.519799 TTCCAAATTGACAAGAAAACTAGAGT 57.480 30.769 0.00 0.00 0.00 3.24
707 750 9.617975 GATTCCAAATTGACAAGAAAACTAGAG 57.382 33.333 0.00 0.00 0.00 2.43
708 751 9.130661 TGATTCCAAATTGACAAGAAAACTAGA 57.869 29.630 0.00 0.00 0.00 2.43
709 752 9.748708 TTGATTCCAAATTGACAAGAAAACTAG 57.251 29.630 0.00 0.00 0.00 2.57
726 769 9.190858 CGTCTGATTTGTAAAATTTGATTCCAA 57.809 29.630 0.00 0.00 0.00 3.53
727 770 8.356657 ACGTCTGATTTGTAAAATTTGATTCCA 58.643 29.630 0.00 0.00 0.00 3.53
728 771 8.742554 ACGTCTGATTTGTAAAATTTGATTCC 57.257 30.769 0.00 0.00 0.00 3.01
729 772 9.993881 CAACGTCTGATTTGTAAAATTTGATTC 57.006 29.630 0.00 0.00 0.00 2.52
730 773 9.743057 TCAACGTCTGATTTGTAAAATTTGATT 57.257 25.926 0.00 0.00 0.00 2.57
731 774 9.912634 ATCAACGTCTGATTTGTAAAATTTGAT 57.087 25.926 7.22 0.00 42.46 2.57
746 789 5.304778 TCTCCATTCAAAATCAACGTCTGA 58.695 37.500 0.00 0.00 38.81 3.27
747 790 5.409520 TCTCTCCATTCAAAATCAACGTCTG 59.590 40.000 0.00 0.00 0.00 3.51
748 791 5.551233 TCTCTCCATTCAAAATCAACGTCT 58.449 37.500 0.00 0.00 0.00 4.18
749 792 5.862924 TCTCTCCATTCAAAATCAACGTC 57.137 39.130 0.00 0.00 0.00 4.34
750 793 5.530915 TGTTCTCTCCATTCAAAATCAACGT 59.469 36.000 0.00 0.00 0.00 3.99
751 794 6.000891 TGTTCTCTCCATTCAAAATCAACG 57.999 37.500 0.00 0.00 0.00 4.10
752 795 6.309737 GCATGTTCTCTCCATTCAAAATCAAC 59.690 38.462 0.00 0.00 0.00 3.18
753 796 6.209986 AGCATGTTCTCTCCATTCAAAATCAA 59.790 34.615 0.00 0.00 0.00 2.57
754 797 5.713389 AGCATGTTCTCTCCATTCAAAATCA 59.287 36.000 0.00 0.00 0.00 2.57
765 808 1.198713 TCTGGGAGCATGTTCTCTCC 58.801 55.000 11.03 9.49 46.25 3.71
767 810 1.134159 GCATCTGGGAGCATGTTCTCT 60.134 52.381 11.03 0.00 33.70 3.10
771 814 1.076485 GGGCATCTGGGAGCATGTT 60.076 57.895 0.00 0.00 0.00 2.71
772 815 1.866483 TTGGGCATCTGGGAGCATGT 61.866 55.000 0.00 0.00 0.00 3.21
773 816 0.469331 ATTGGGCATCTGGGAGCATG 60.469 55.000 0.00 0.00 0.00 4.06
774 817 1.151760 TATTGGGCATCTGGGAGCAT 58.848 50.000 0.00 0.00 0.00 3.79
775 818 0.183492 GTATTGGGCATCTGGGAGCA 59.817 55.000 0.00 0.00 0.00 4.26
776 819 0.886490 CGTATTGGGCATCTGGGAGC 60.886 60.000 0.00 0.00 0.00 4.70
777 820 0.758734 TCGTATTGGGCATCTGGGAG 59.241 55.000 0.00 0.00 0.00 4.30
778 821 1.208706 TTCGTATTGGGCATCTGGGA 58.791 50.000 0.00 0.00 0.00 4.37
779 822 2.051334 TTTCGTATTGGGCATCTGGG 57.949 50.000 0.00 0.00 0.00 4.45
780 823 4.133820 TGTATTTCGTATTGGGCATCTGG 58.866 43.478 0.00 0.00 0.00 3.86
783 826 6.854496 TTACTGTATTTCGTATTGGGCATC 57.146 37.500 0.00 0.00 0.00 3.91
795 838 8.443937 GGACTTTGTCACTGATTACTGTATTTC 58.556 37.037 0.07 0.00 33.68 2.17
802 845 6.919775 ACTAGGACTTTGTCACTGATTACT 57.080 37.500 0.00 0.00 33.68 2.24
803 846 7.964604 AAACTAGGACTTTGTCACTGATTAC 57.035 36.000 0.00 0.00 33.68 1.89
837 880 8.081025 ACGGCTAAACGTATTTTTCCAAATTTA 58.919 29.630 0.00 0.00 46.58 1.40
840 883 6.016213 ACGGCTAAACGTATTTTTCCAAAT 57.984 33.333 0.00 0.00 46.58 2.32
841 884 5.435820 ACGGCTAAACGTATTTTTCCAAA 57.564 34.783 0.00 0.00 46.58 3.28
853 896 0.725117 GTGGATCCAACGGCTAAACG 59.275 55.000 18.20 0.00 40.31 3.60
854 897 2.007608 GAGTGGATCCAACGGCTAAAC 58.992 52.381 18.20 0.00 0.00 2.01
860 903 2.511600 GCCGAGTGGATCCAACGG 60.512 66.667 36.57 36.57 44.54 4.44
866 909 0.528684 CGAGGAAAGCCGAGTGGATC 60.529 60.000 0.00 0.00 39.96 3.36
875 918 0.727398 CGGAAATGACGAGGAAAGCC 59.273 55.000 0.00 0.00 0.00 4.35
881 924 1.656652 AGAATGCGGAAATGACGAGG 58.343 50.000 0.00 0.00 0.00 4.63
919 995 1.692519 AGTTGCTGTTAGGAACCGACT 59.307 47.619 9.19 0.00 46.08 4.18
923 999 1.537202 CTGCAGTTGCTGTTAGGAACC 59.463 52.381 5.25 0.00 46.08 3.62
924 1000 1.068954 GCTGCAGTTGCTGTTAGGAAC 60.069 52.381 16.64 5.24 45.40 3.62
925 1001 1.202806 AGCTGCAGTTGCTGTTAGGAA 60.203 47.619 16.64 0.00 42.66 3.36
927 1003 0.801251 GAGCTGCAGTTGCTGTTAGG 59.199 55.000 16.64 0.00 41.30 2.69
931 1007 1.600076 CTGGAGCTGCAGTTGCTGT 60.600 57.895 25.76 0.00 41.30 4.40
933 1009 0.392729 GATCTGGAGCTGCAGTTGCT 60.393 55.000 31.17 16.41 44.24 3.91
935 1011 1.467734 GTTGATCTGGAGCTGCAGTTG 59.532 52.381 31.17 10.75 0.00 3.16
969 1680 2.261671 GCGAGAAGAGGGCGTGAA 59.738 61.111 0.00 0.00 0.00 3.18
1230 1941 2.734723 CCTGCACTGACCGTGACG 60.735 66.667 0.00 0.00 46.81 4.35
1233 1944 4.320456 AGGCCTGCACTGACCGTG 62.320 66.667 3.11 0.00 46.58 4.94
1236 1947 1.968540 GTTCAGGCCTGCACTGACC 60.969 63.158 28.91 0.36 44.07 4.02
1258 1969 3.148279 GCACTCGGGGAGGTCGAT 61.148 66.667 0.00 0.00 36.01 3.59
1518 2229 2.202623 GAGACGACGCAGCCGAAT 60.203 61.111 0.00 0.00 38.29 3.34
1636 2347 3.000819 ATGGGTCTCGGCCGTCAA 61.001 61.111 27.15 9.03 0.00 3.18
1652 2363 2.178521 GCCTGTCGACGACGTGAT 59.821 61.111 22.06 0.00 40.69 3.06
1653 2364 4.379143 CGCCTGTCGACGACGTGA 62.379 66.667 22.06 4.97 41.67 4.35
1970 2681 1.800586 TCGACATTCTTTGTGCTCAGC 59.199 47.619 0.00 0.00 39.18 4.26
1995 2706 1.803519 GAAGAGCTCGCGGTCAGTG 60.804 63.158 6.13 0.00 40.07 3.66
2034 2747 1.734163 GGTTGGTGGTGGACTAATCG 58.266 55.000 0.00 0.00 0.00 3.34
2090 2803 1.134818 TGTGCATGGTCTCATCGTACC 60.135 52.381 0.00 0.00 36.24 3.34
2109 2822 3.119352 GGGACCTGCTGCTTTTAGATTTG 60.119 47.826 0.00 0.00 0.00 2.32
2131 2844 1.443872 CGACCAAGACGAACCGGAG 60.444 63.158 9.46 0.76 0.00 4.63
2157 6886 1.309950 CGCTAGAGGTCGAGGAATCA 58.690 55.000 0.00 0.00 0.00 2.57
2161 6890 2.864378 TTCGCGCTAGAGGTCGAGGA 62.864 60.000 5.56 0.00 32.31 3.71
2168 6897 1.226717 GTCTGGTTCGCGCTAGAGG 60.227 63.158 5.56 0.00 0.00 3.69
2172 6901 2.707849 GGAGGTCTGGTTCGCGCTA 61.708 63.158 5.56 0.00 0.00 4.26
2231 6960 1.071567 GTTACTGACGTCGGAGCAGC 61.072 60.000 30.55 12.83 33.03 5.25
2240 6969 1.081641 CGCCGTGAGTTACTGACGT 60.082 57.895 21.20 0.00 39.27 4.34
2290 7029 0.303493 CCGTATTTCAATGTCGGCGG 59.697 55.000 7.21 0.00 33.33 6.13
2299 7038 0.674269 GGACCCGCACCGTATTTCAA 60.674 55.000 0.00 0.00 0.00 2.69
2300 7039 1.078988 GGACCCGCACCGTATTTCA 60.079 57.895 0.00 0.00 0.00 2.69
2315 7054 0.819582 CCCATTGTTGGCATCTGGAC 59.180 55.000 5.63 0.00 42.15 4.02
2334 7073 2.359900 CTATCCAGTTGTCAACCTGCC 58.640 52.381 12.17 0.00 0.00 4.85
2359 7098 3.909285 GGGAGTACCGGTAGCCGC 61.909 72.222 16.41 13.90 46.86 6.53
2367 7106 2.264794 GTGGCACTGGGAGTACCG 59.735 66.667 11.13 0.00 44.64 4.02
2368 7107 2.669240 GGTGGCACTGGGAGTACC 59.331 66.667 18.45 0.00 40.81 3.34
2389 7128 2.260844 ATACATCCCGATGCAACAGG 57.739 50.000 4.58 0.00 42.39 4.00
2393 7132 1.939381 GCGCTATACATCCCGATGCAA 60.939 52.381 0.00 0.00 42.39 4.08
2398 7137 2.257371 GCGCGCTATACATCCCGA 59.743 61.111 26.67 0.00 0.00 5.14
2440 8887 2.030562 ACAACCGAGTCCTTGGCG 59.969 61.111 0.16 0.00 37.67 5.69
2444 8891 1.120530 ACTGTCACAACCGAGTCCTT 58.879 50.000 0.00 0.00 0.00 3.36
2449 8896 0.030235 TCGTCACTGTCACAACCGAG 59.970 55.000 0.00 0.00 0.00 4.63
2451 8898 1.213094 GGTCGTCACTGTCACAACCG 61.213 60.000 0.00 0.00 0.00 4.44
2452 8899 0.878961 GGGTCGTCACTGTCACAACC 60.879 60.000 0.00 0.00 0.00 3.77
2455 8902 2.852180 CGGGGTCGTCACTGTCACA 61.852 63.158 0.00 0.00 0.00 3.58
2476 8923 4.295119 GACCCGGCGCCATATCGT 62.295 66.667 28.98 13.89 0.00 3.73
2477 8924 4.293648 TGACCCGGCGCCATATCG 62.294 66.667 28.98 11.99 0.00 2.92
2478 8925 2.357517 CTGACCCGGCGCCATATC 60.358 66.667 28.98 19.75 0.00 1.63
2479 8926 2.439960 TTCTGACCCGGCGCCATAT 61.440 57.895 28.98 10.60 0.00 1.78
2480 8927 3.078196 TTCTGACCCGGCGCCATA 61.078 61.111 28.98 6.07 0.00 2.74
2487 8935 0.602905 AAGCGAAAGTTCTGACCCGG 60.603 55.000 0.00 0.00 0.00 5.73
2490 8938 0.238553 GGCAAGCGAAAGTTCTGACC 59.761 55.000 0.00 0.00 0.00 4.02
2502 8950 1.518056 TTCTTCAGCAAGGGCAAGCG 61.518 55.000 0.00 0.00 44.61 4.68
2522 8970 2.270874 AAACCTAGCTCGCCATGGGG 62.271 60.000 22.46 22.46 37.18 4.96
2588 9036 0.616395 TGACCGCATCCACTTCCCTA 60.616 55.000 0.00 0.00 0.00 3.53
2660 9108 5.697473 TGAACATGAAATAGACGGCAAAA 57.303 34.783 0.00 0.00 0.00 2.44
2661 9109 5.182950 ACATGAACATGAAATAGACGGCAAA 59.817 36.000 19.56 0.00 41.20 3.68
2662 9110 4.699735 ACATGAACATGAAATAGACGGCAA 59.300 37.500 19.56 0.00 41.20 4.52
2663 9111 4.094739 CACATGAACATGAAATAGACGGCA 59.905 41.667 19.56 0.00 41.20 5.69
2664 9112 4.332543 TCACATGAACATGAAATAGACGGC 59.667 41.667 19.56 0.00 41.20 5.68
2665 9113 6.421377 TTCACATGAACATGAAATAGACGG 57.579 37.500 19.56 0.92 41.20 4.79
2666 9114 6.412943 GCATTCACATGAACATGAAATAGACG 59.587 38.462 19.56 8.89 41.20 4.18
2668 9116 7.393841 TGCATTCACATGAACATGAAATAGA 57.606 32.000 19.56 7.75 41.20 1.98
2669 9117 8.468720 TTTGCATTCACATGAACATGAAATAG 57.531 30.769 19.56 13.04 41.20 1.73
2672 9120 8.828688 TTATTTGCATTCACATGAACATGAAA 57.171 26.923 19.56 13.38 41.20 2.69
2673 9121 7.546316 CCTTATTTGCATTCACATGAACATGAA 59.454 33.333 19.56 7.41 41.20 2.57
2675 9123 6.814644 ACCTTATTTGCATTCACATGAACATG 59.185 34.615 12.43 12.43 44.15 3.21
2676 9124 6.814644 CACCTTATTTGCATTCACATGAACAT 59.185 34.615 0.00 0.00 36.80 2.71
2677 9125 6.157904 CACCTTATTTGCATTCACATGAACA 58.842 36.000 0.00 0.00 36.80 3.18
2678 9126 6.158598 ACACCTTATTTGCATTCACATGAAC 58.841 36.000 0.00 0.00 36.80 3.18
2679 9127 6.343716 ACACCTTATTTGCATTCACATGAA 57.656 33.333 0.00 0.00 38.56 2.57
2680 9128 5.981088 ACACCTTATTTGCATTCACATGA 57.019 34.783 0.00 0.00 31.07 3.07
2682 9130 9.723601 AAATTTACACCTTATTTGCATTCACAT 57.276 25.926 0.00 0.00 0.00 3.21
2695 9158 6.621316 TTTCAGACGCAAATTTACACCTTA 57.379 33.333 0.00 0.00 0.00 2.69
2699 9162 6.075280 ACGTATTTCAGACGCAAATTTACAC 58.925 36.000 0.00 0.00 44.14 2.90
2724 9187 3.977579 CGATGTCATCAATGTCCGTCTAG 59.022 47.826 13.22 0.00 0.00 2.43
2725 9188 3.795488 GCGATGTCATCAATGTCCGTCTA 60.795 47.826 13.22 0.00 0.00 2.59
2726 9189 2.814269 CGATGTCATCAATGTCCGTCT 58.186 47.619 13.22 0.00 0.00 4.18
2728 9191 1.290203 GCGATGTCATCAATGTCCGT 58.710 50.000 13.22 0.00 0.00 4.69
2729 9192 0.230515 CGCGATGTCATCAATGTCCG 59.769 55.000 13.22 0.00 0.00 4.79
2731 9194 3.538780 CAATCGCGATGTCATCAATGTC 58.461 45.455 24.47 0.00 0.00 3.06
2732 9195 2.288729 CCAATCGCGATGTCATCAATGT 59.711 45.455 24.47 0.00 0.00 2.71
2733 9196 2.288729 ACCAATCGCGATGTCATCAATG 59.711 45.455 24.47 14.00 0.00 2.82
2734 9197 2.545526 GACCAATCGCGATGTCATCAAT 59.454 45.455 26.02 7.19 0.00 2.57
2735 9198 1.933181 GACCAATCGCGATGTCATCAA 59.067 47.619 26.02 0.00 0.00 2.57
2736 9199 1.570813 GACCAATCGCGATGTCATCA 58.429 50.000 26.02 0.00 0.00 3.07
2737 9200 0.861837 GGACCAATCGCGATGTCATC 59.138 55.000 29.53 21.26 0.00 2.92
2739 9202 1.518352 CGGACCAATCGCGATGTCA 60.518 57.895 29.53 4.51 0.00 3.58
2741 9204 2.890474 GCGGACCAATCGCGATGT 60.890 61.111 24.47 17.34 43.71 3.06
2748 9211 1.523032 CCTAACCCGCGGACCAATC 60.523 63.158 30.73 0.00 0.00 2.67
2749 9212 2.587889 CCTAACCCGCGGACCAAT 59.412 61.111 30.73 10.07 0.00 3.16
2812 9277 2.574369 ACATCGGTTCCTGGACCAAATA 59.426 45.455 13.40 0.00 39.78 1.40
2824 9289 1.021390 CCACCAGCAGACATCGGTTC 61.021 60.000 0.00 0.00 0.00 3.62
2871 9337 1.521580 AGCTATCGCCTACGGAGTAC 58.478 55.000 0.00 0.00 39.29 2.73
2872 9338 2.267174 AAGCTATCGCCTACGGAGTA 57.733 50.000 0.00 0.00 42.66 2.59
2873 9339 1.878734 GTAAGCTATCGCCTACGGAGT 59.121 52.381 0.00 0.00 40.62 3.85
2874 9340 1.199558 GGTAAGCTATCGCCTACGGAG 59.800 57.143 0.00 0.00 40.63 4.63
2876 9342 0.956633 TGGTAAGCTATCGCCTACGG 59.043 55.000 0.00 0.00 40.63 4.02
2877 9343 3.243336 GAATGGTAAGCTATCGCCTACG 58.757 50.000 0.00 0.00 34.57 3.51
2878 9344 3.586892 GGAATGGTAAGCTATCGCCTAC 58.413 50.000 0.00 0.00 36.60 3.18
2890 9360 1.200519 CGTGGAGGAGGGAATGGTAA 58.799 55.000 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.