Multiple sequence alignment - TraesCS2D01G551100

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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 TraesCS2D01G551100 chr2D 100.000 2968 0 0 1 2968 626601190 626598223 0.000000e+00 5481.0
1 TraesCS2D01G551100 chr2D 92.932 1726 97 14 889 2611 626606891 626608594 0.000000e+00 2488.0
2 TraesCS2D01G551100 chr2D 84.774 1064 119 19 953 2003 626713058 626712025 0.000000e+00 1027.0
3 TraesCS2D01G551100 chr2D 84.843 1049 122 15 953 1993 626749831 626748812 0.000000e+00 1022.0
4 TraesCS2D01G551100 chr2D 76.894 1043 187 35 974 2002 625587080 625588082 2.600000e-150 542.0
5 TraesCS2D01G551100 chr2D 96.721 122 4 0 545 666 626606772 626606893 1.390000e-48 204.0
6 TraesCS2D01G551100 chr2D 85.567 194 26 1 147 340 19647297 19647488 5.020000e-48 202.0
7 TraesCS2D01G551100 chr2A 92.472 1687 88 13 1255 2930 757563757 757562099 0.000000e+00 2375.0
8 TraesCS2D01G551100 chr2A 76.195 1067 198 42 974 2030 756543024 756544044 2.040000e-141 512.0
9 TraesCS2D01G551100 chr2A 91.553 367 20 3 889 1248 757564177 757563815 2.050000e-136 496.0
10 TraesCS2D01G551100 chr2A 86.207 203 26 1 664 864 424445821 424445619 4.980000e-53 219.0
11 TraesCS2D01G551100 chr2A 84.951 206 31 0 664 869 652011683 652011478 3.000000e-50 209.0
12 TraesCS2D01G551100 chr2A 96.721 122 4 0 545 666 757564296 757564175 1.390000e-48 204.0
13 TraesCS2D01G551100 chr2B 86.253 1644 171 21 1298 2930 768064173 768062574 0.000000e+00 1733.0
14 TraesCS2D01G551100 chr2B 86.406 1611 173 16 1324 2930 768074905 768073337 0.000000e+00 1720.0
15 TraesCS2D01G551100 chr2B 82.633 1071 146 18 965 2022 768081644 768080601 0.000000e+00 911.0
16 TraesCS2D01G551100 chr2B 82.032 1063 152 18 965 2014 768070851 768069815 0.000000e+00 869.0
17 TraesCS2D01G551100 chr2B 85.036 274 39 2 976 1248 768075302 768075030 8.100000e-71 278.0
18 TraesCS2D01G551100 chr2B 83.755 277 42 3 974 1248 768064559 768064284 2.930000e-65 259.0
19 TraesCS2D01G551100 chr2B 97.778 45 1 0 1253 1297 779319929 779319973 8.820000e-11 78.7
20 TraesCS2D01G551100 chr2B 81.188 101 13 4 1324 1421 185761717 185761620 3.170000e-10 76.8
21 TraesCS2D01G551100 chr2B 97.619 42 1 0 1253 1294 69007290 69007331 4.100000e-09 73.1
22 TraesCS2D01G551100 chr6D 99.630 541 2 0 1 541 28664702 28664162 0.000000e+00 989.0
23 TraesCS2D01G551100 chr6D 87.500 200 23 1 147 346 384279842 384280039 2.300000e-56 230.0
24 TraesCS2D01G551100 chr6D 95.455 44 1 1 2926 2968 262785772 262785729 5.310000e-08 69.4
25 TraesCS2D01G551100 chr6D 97.500 40 1 0 2929 2968 436676079 436676040 5.310000e-08 69.4
26 TraesCS2D01G551100 chr6D 93.478 46 2 1 2924 2968 383334853 383334898 1.910000e-07 67.6
27 TraesCS2D01G551100 chr7A 92.939 524 32 3 14 537 688747193 688747711 0.000000e+00 758.0
28 TraesCS2D01G551100 chr7A 89.423 208 22 0 662 869 57702418 57702211 2.270000e-66 263.0
29 TraesCS2D01G551100 chr7A 89.950 199 20 0 668 866 554556505 554556703 1.060000e-64 257.0
30 TraesCS2D01G551100 chr7A 87.000 200 24 1 147 346 511469958 511470155 1.070000e-54 224.0
31 TraesCS2D01G551100 chr7A 85.644 202 27 2 666 866 518506459 518506259 8.330000e-51 211.0
32 TraesCS2D01G551100 chr4A 88.973 526 47 6 14 538 618170611 618170096 8.970000e-180 640.0
33 TraesCS2D01G551100 chr5A 90.148 203 20 0 664 866 529164325 529164527 6.310000e-67 265.0
34 TraesCS2D01G551100 chr1A 88.942 208 21 2 663 869 304488404 304488198 3.800000e-64 255.0
35 TraesCS2D01G551100 chr1A 88.889 207 23 0 663 869 304649983 304649777 3.800000e-64 255.0
36 TraesCS2D01G551100 chr1A 97.500 40 1 0 2929 2968 240878497 240878536 5.310000e-08 69.4
37 TraesCS2D01G551100 chr1A 95.455 44 1 1 1251 1294 385890134 385890176 5.310000e-08 69.4
38 TraesCS2D01G551100 chr1A 97.436 39 1 0 2930 2968 381813767 381813729 1.910000e-07 67.6
39 TraesCS2D01G551100 chr1A 93.478 46 2 1 2923 2968 527154848 527154892 1.910000e-07 67.6
40 TraesCS2D01G551100 chr7D 87.895 190 21 2 655 844 114590638 114590825 3.850000e-54 222.0
41 TraesCS2D01G551100 chr7D 97.561 41 1 0 2928 2968 500950962 500951002 1.480000e-08 71.3
42 TraesCS2D01G551100 chr5B 95.652 46 1 1 1251 1296 689931109 689931065 4.100000e-09 73.1
43 TraesCS2D01G551100 chr3D 97.619 42 1 0 2927 2968 495216514 495216473 4.100000e-09 73.1
44 TraesCS2D01G551100 chr3D 97.619 42 1 0 2927 2968 597625485 597625444 4.100000e-09 73.1
45 TraesCS2D01G551100 chr3B 97.619 42 1 0 1253 1294 554699793 554699834 4.100000e-09 73.1
46 TraesCS2D01G551100 chr3B 93.750 48 2 1 1255 1301 812729363 812729410 1.480000e-08 71.3
47 TraesCS2D01G551100 chr7B 97.561 41 1 0 2928 2968 656418331 656418371 1.480000e-08 71.3
48 TraesCS2D01G551100 chr1D 97.561 41 1 0 2928 2968 467989612 467989652 1.480000e-08 71.3
49 TraesCS2D01G551100 chr1D 97.500 40 1 0 2929 2968 23987689 23987650 5.310000e-08 69.4
50 TraesCS2D01G551100 chr1D 97.436 39 1 0 2930 2968 171331779 171331817 1.910000e-07 67.6
51 TraesCS2D01G551100 chr1D 97.436 39 1 0 2930 2968 181698813 181698775 1.910000e-07 67.6
52 TraesCS2D01G551100 chr1D 97.436 39 1 0 2930 2968 253382992 253382954 1.910000e-07 67.6
53 TraesCS2D01G551100 chr1D 97.368 38 1 0 2931 2968 134562332 134562295 6.870000e-07 65.8
54 TraesCS2D01G551100 chr1D 94.872 39 2 0 2930 2968 119004828 119004866 8.880000e-06 62.1
55 TraesCS2D01G551100 chr1D 97.222 36 1 0 2930 2965 362791460 362791495 8.880000e-06 62.1
56 TraesCS2D01G551100 chr6B 97.500 40 1 0 2929 2968 712317393 712317354 5.310000e-08 69.4
57 TraesCS2D01G551100 chr5D 93.617 47 2 1 1251 1297 524638484 524638439 5.310000e-08 69.4
58 TraesCS2D01G551100 chr4D 97.500 40 1 0 2929 2968 472132312 472132273 5.310000e-08 69.4
59 TraesCS2D01G551100 chr4D 97.436 39 1 0 2930 2968 463430363 463430325 1.910000e-07 67.6
60 TraesCS2D01G551100 chr1B 93.617 47 2 1 2922 2968 626297599 626297554 5.310000e-08 69.4
61 TraesCS2D01G551100 chr4B 95.238 42 2 0 2927 2968 51547618 51547577 1.910000e-07 67.6
62 TraesCS2D01G551100 chr4B 97.436 39 1 0 2930 2968 167197824 167197786 1.910000e-07 67.6
63 TraesCS2D01G551100 chr4B 97.368 38 1 0 2930 2967 5333310 5333273 6.870000e-07 65.8
64 TraesCS2D01G551100 chr4B 95.122 41 2 0 2928 2968 51190784 51190744 6.870000e-07 65.8
65 TraesCS2D01G551100 chr4B 87.500 56 5 2 1247 1301 123448094 123448148 2.470000e-06 63.9


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 TraesCS2D01G551100 chr2D 626598223 626601190 2967 True 5481.000000 5481 100.000000 1 2968 1 chr2D.!!$R1 2967
1 TraesCS2D01G551100 chr2D 626606772 626608594 1822 False 1346.000000 2488 94.826500 545 2611 2 chr2D.!!$F3 2066
2 TraesCS2D01G551100 chr2D 626712025 626713058 1033 True 1027.000000 1027 84.774000 953 2003 1 chr2D.!!$R2 1050
3 TraesCS2D01G551100 chr2D 626748812 626749831 1019 True 1022.000000 1022 84.843000 953 1993 1 chr2D.!!$R3 1040
4 TraesCS2D01G551100 chr2D 625587080 625588082 1002 False 542.000000 542 76.894000 974 2002 1 chr2D.!!$F2 1028
5 TraesCS2D01G551100 chr2A 757562099 757564296 2197 True 1025.000000 2375 93.582000 545 2930 3 chr2A.!!$R3 2385
6 TraesCS2D01G551100 chr2A 756543024 756544044 1020 False 512.000000 512 76.195000 974 2030 1 chr2A.!!$F1 1056
7 TraesCS2D01G551100 chr2B 768062574 768064559 1985 True 996.000000 1733 85.004000 974 2930 2 chr2B.!!$R3 1956
8 TraesCS2D01G551100 chr2B 768069815 768075302 5487 True 955.666667 1720 84.491333 965 2930 3 chr2B.!!$R4 1965
9 TraesCS2D01G551100 chr2B 768080601 768081644 1043 True 911.000000 911 82.633000 965 2022 1 chr2B.!!$R2 1057
10 TraesCS2D01G551100 chr6D 28664162 28664702 540 True 989.000000 989 99.630000 1 541 1 chr6D.!!$R1 540
11 TraesCS2D01G551100 chr7A 688747193 688747711 518 False 758.000000 758 92.939000 14 537 1 chr7A.!!$F3 523
12 TraesCS2D01G551100 chr4A 618170096 618170611 515 True 640.000000 640 88.973000 14 538 1 chr4A.!!$R1 524

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
52 53 0.037326 AATCAAGCTTCTCGCCGACA 60.037 50.0 0.00 0.0 40.39 4.35 F
777 778 0.103208 ATAGCGCTTCCCGAGACAAG 59.897 55.0 18.68 0.0 40.02 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1659 6227 0.247736 GACTCATCAGCGTCTTGGGT 59.752 55.0 0.0 0.0 0.0 4.51 R
2765 7361 0.179015 ACGTATGCAACCACCAACCA 60.179 50.0 0.0 0.0 0.0 3.67 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
52 53 0.037326 AATCAAGCTTCTCGCCGACA 60.037 50.000 0.00 0.00 40.39 4.35
541 542 4.271776 GGGTCGTATAAGATTGTTTTCCCG 59.728 45.833 0.00 0.00 0.00 5.14
542 543 5.111293 GGTCGTATAAGATTGTTTTCCCGA 58.889 41.667 0.00 0.00 0.00 5.14
543 544 5.233689 GGTCGTATAAGATTGTTTTCCCGAG 59.766 44.000 0.00 0.00 0.00 4.63
627 628 3.255149 TCGAAGACCTGAGTGAGTAAACC 59.745 47.826 0.00 0.00 0.00 3.27
631 632 1.000955 ACCTGAGTGAGTAAACCTGCG 59.999 52.381 0.00 0.00 0.00 5.18
666 667 8.511604 TCTGGGATTTTTGCTTCTCTTATTAG 57.488 34.615 0.00 0.00 0.00 1.73
667 668 7.557719 TCTGGGATTTTTGCTTCTCTTATTAGG 59.442 37.037 0.00 0.00 0.00 2.69
668 669 6.096846 TGGGATTTTTGCTTCTCTTATTAGGC 59.903 38.462 0.00 0.00 0.00 3.93
669 670 6.322456 GGGATTTTTGCTTCTCTTATTAGGCT 59.678 38.462 0.00 0.00 0.00 4.58
670 671 7.502561 GGGATTTTTGCTTCTCTTATTAGGCTA 59.497 37.037 0.00 0.00 0.00 3.93
671 672 8.563732 GGATTTTTGCTTCTCTTATTAGGCTAG 58.436 37.037 0.00 0.00 0.00 3.42
672 673 9.114952 GATTTTTGCTTCTCTTATTAGGCTAGT 57.885 33.333 0.00 0.00 0.00 2.57
673 674 8.494016 TTTTTGCTTCTCTTATTAGGCTAGTC 57.506 34.615 0.00 0.00 0.00 2.59
674 675 6.791867 TTGCTTCTCTTATTAGGCTAGTCA 57.208 37.500 0.00 0.00 0.00 3.41
675 676 6.985653 TGCTTCTCTTATTAGGCTAGTCAT 57.014 37.500 0.00 0.00 0.00 3.06
676 677 8.478775 TTGCTTCTCTTATTAGGCTAGTCATA 57.521 34.615 0.00 0.00 0.00 2.15
677 678 8.116651 TGCTTCTCTTATTAGGCTAGTCATAG 57.883 38.462 0.00 0.00 0.00 2.23
678 679 7.726291 TGCTTCTCTTATTAGGCTAGTCATAGT 59.274 37.037 0.00 0.00 0.00 2.12
679 680 8.026607 GCTTCTCTTATTAGGCTAGTCATAGTG 58.973 40.741 0.00 0.00 0.00 2.74
680 681 8.410673 TTCTCTTATTAGGCTAGTCATAGTGG 57.589 38.462 0.00 0.00 0.00 4.00
681 682 6.948886 TCTCTTATTAGGCTAGTCATAGTGGG 59.051 42.308 0.00 0.00 0.00 4.61
682 683 6.860034 TCTTATTAGGCTAGTCATAGTGGGA 58.140 40.000 0.00 0.00 0.00 4.37
683 684 6.948886 TCTTATTAGGCTAGTCATAGTGGGAG 59.051 42.308 0.00 0.00 0.00 4.30
684 685 4.537945 TTAGGCTAGTCATAGTGGGAGT 57.462 45.455 0.00 0.00 0.00 3.85
685 686 5.658198 TTAGGCTAGTCATAGTGGGAGTA 57.342 43.478 0.00 0.00 0.00 2.59
686 687 4.537945 AGGCTAGTCATAGTGGGAGTAA 57.462 45.455 0.00 0.00 0.00 2.24
687 688 4.216708 AGGCTAGTCATAGTGGGAGTAAC 58.783 47.826 0.00 0.00 0.00 2.50
688 689 4.079096 AGGCTAGTCATAGTGGGAGTAACT 60.079 45.833 0.00 0.00 0.00 2.24
689 690 4.650131 GGCTAGTCATAGTGGGAGTAACTT 59.350 45.833 0.00 0.00 0.00 2.66
690 691 5.832060 GGCTAGTCATAGTGGGAGTAACTTA 59.168 44.000 0.00 0.00 0.00 2.24
691 692 6.016108 GGCTAGTCATAGTGGGAGTAACTTAG 60.016 46.154 0.00 0.00 0.00 2.18
692 693 6.016108 GCTAGTCATAGTGGGAGTAACTTAGG 60.016 46.154 0.00 0.00 0.00 2.69
693 694 5.840081 AGTCATAGTGGGAGTAACTTAGGT 58.160 41.667 0.00 0.00 0.00 3.08
694 695 6.978261 AGTCATAGTGGGAGTAACTTAGGTA 58.022 40.000 0.00 0.00 0.00 3.08
695 696 7.061688 AGTCATAGTGGGAGTAACTTAGGTAG 58.938 42.308 0.00 0.00 0.00 3.18
696 697 6.832900 GTCATAGTGGGAGTAACTTAGGTAGT 59.167 42.308 0.00 0.00 39.32 2.73
697 698 7.995488 GTCATAGTGGGAGTAACTTAGGTAGTA 59.005 40.741 0.00 0.00 35.54 1.82
698 699 8.560039 TCATAGTGGGAGTAACTTAGGTAGTAA 58.440 37.037 0.00 0.00 35.54 2.24
699 700 8.628280 CATAGTGGGAGTAACTTAGGTAGTAAC 58.372 40.741 0.00 0.00 35.54 2.50
700 701 6.555711 AGTGGGAGTAACTTAGGTAGTAACA 58.444 40.000 0.00 0.00 35.54 2.41
701 702 7.187676 AGTGGGAGTAACTTAGGTAGTAACAT 58.812 38.462 0.00 0.00 35.54 2.71
702 703 8.339247 AGTGGGAGTAACTTAGGTAGTAACATA 58.661 37.037 0.00 0.00 35.54 2.29
703 704 8.628280 GTGGGAGTAACTTAGGTAGTAACATAG 58.372 40.741 0.00 0.00 35.54 2.23
704 705 7.286316 TGGGAGTAACTTAGGTAGTAACATAGC 59.714 40.741 0.00 0.00 35.54 2.97
705 706 7.358830 GGAGTAACTTAGGTAGTAACATAGCG 58.641 42.308 0.00 0.00 35.54 4.26
706 707 6.733145 AGTAACTTAGGTAGTAACATAGCGC 58.267 40.000 0.00 0.00 35.54 5.92
707 708 5.587388 AACTTAGGTAGTAACATAGCGCA 57.413 39.130 11.47 0.00 35.54 6.09
708 709 4.929781 ACTTAGGTAGTAACATAGCGCAC 58.070 43.478 11.47 0.00 34.56 5.34
709 710 4.643784 ACTTAGGTAGTAACATAGCGCACT 59.356 41.667 11.47 5.48 34.56 4.40
710 711 3.712091 AGGTAGTAACATAGCGCACTC 57.288 47.619 11.47 0.00 0.00 3.51
711 712 3.288964 AGGTAGTAACATAGCGCACTCT 58.711 45.455 11.47 0.26 0.00 3.24
712 713 4.458397 AGGTAGTAACATAGCGCACTCTA 58.542 43.478 11.47 0.00 0.00 2.43
713 714 4.885907 AGGTAGTAACATAGCGCACTCTAA 59.114 41.667 11.47 0.00 0.00 2.10
714 715 5.008811 AGGTAGTAACATAGCGCACTCTAAG 59.991 44.000 11.47 0.00 0.00 2.18
715 716 5.008415 GGTAGTAACATAGCGCACTCTAAGA 59.992 44.000 11.47 0.00 0.00 2.10
716 717 5.578005 AGTAACATAGCGCACTCTAAGAA 57.422 39.130 11.47 0.00 0.00 2.52
717 718 5.962433 AGTAACATAGCGCACTCTAAGAAA 58.038 37.500 11.47 0.00 0.00 2.52
718 719 6.395629 AGTAACATAGCGCACTCTAAGAAAA 58.604 36.000 11.47 0.00 0.00 2.29
719 720 7.042335 AGTAACATAGCGCACTCTAAGAAAAT 58.958 34.615 11.47 0.00 0.00 1.82
720 721 6.743575 AACATAGCGCACTCTAAGAAAATT 57.256 33.333 11.47 0.00 0.00 1.82
721 722 6.743575 ACATAGCGCACTCTAAGAAAATTT 57.256 33.333 11.47 0.00 0.00 1.82
722 723 7.145932 ACATAGCGCACTCTAAGAAAATTTT 57.854 32.000 11.47 2.28 0.00 1.82
723 724 7.023575 ACATAGCGCACTCTAAGAAAATTTTG 58.976 34.615 11.47 0.00 0.00 2.44
724 725 4.229876 AGCGCACTCTAAGAAAATTTTGC 58.770 39.130 11.47 2.64 0.00 3.68
725 726 4.022849 AGCGCACTCTAAGAAAATTTTGCT 60.023 37.500 11.47 3.82 0.00 3.91
726 727 4.681483 GCGCACTCTAAGAAAATTTTGCTT 59.319 37.500 8.47 13.00 0.00 3.91
727 728 5.856455 GCGCACTCTAAGAAAATTTTGCTTA 59.144 36.000 8.47 13.38 0.00 3.09
728 729 6.528072 GCGCACTCTAAGAAAATTTTGCTTAT 59.472 34.615 8.47 0.05 0.00 1.73
729 730 7.461938 GCGCACTCTAAGAAAATTTTGCTTATG 60.462 37.037 8.47 11.12 0.00 1.90
730 731 7.538678 CGCACTCTAAGAAAATTTTGCTTATGT 59.461 33.333 8.47 12.66 0.00 2.29
731 732 8.642020 GCACTCTAAGAAAATTTTGCTTATGTG 58.358 33.333 22.84 22.84 34.86 3.21
732 733 9.132521 CACTCTAAGAAAATTTTGCTTATGTGG 57.867 33.333 21.23 9.55 31.93 4.17
733 734 7.814587 ACTCTAAGAAAATTTTGCTTATGTGGC 59.185 33.333 8.47 0.00 0.00 5.01
734 735 7.665690 TCTAAGAAAATTTTGCTTATGTGGCA 58.334 30.769 8.47 0.00 37.97 4.92
735 736 8.147058 TCTAAGAAAATTTTGCTTATGTGGCAA 58.853 29.630 8.47 0.00 46.12 4.52
746 747 7.637631 TGCTTATGTGGCAAGTAATTAATGA 57.362 32.000 0.00 0.00 36.71 2.57
747 748 7.706159 TGCTTATGTGGCAAGTAATTAATGAG 58.294 34.615 0.00 0.00 36.71 2.90
748 749 7.555914 TGCTTATGTGGCAAGTAATTAATGAGA 59.444 33.333 0.00 0.00 36.71 3.27
749 750 8.405531 GCTTATGTGGCAAGTAATTAATGAGAA 58.594 33.333 0.00 0.00 0.00 2.87
750 751 9.941664 CTTATGTGGCAAGTAATTAATGAGAAG 57.058 33.333 0.00 0.00 0.00 2.85
751 752 7.944729 ATGTGGCAAGTAATTAATGAGAAGT 57.055 32.000 0.00 0.00 0.00 3.01
752 753 7.144722 TGTGGCAAGTAATTAATGAGAAGTG 57.855 36.000 0.00 0.00 0.00 3.16
753 754 6.150976 TGTGGCAAGTAATTAATGAGAAGTGG 59.849 38.462 0.00 0.00 0.00 4.00
754 755 6.151144 GTGGCAAGTAATTAATGAGAAGTGGT 59.849 38.462 0.00 0.00 0.00 4.16
755 756 7.335924 GTGGCAAGTAATTAATGAGAAGTGGTA 59.664 37.037 0.00 0.00 0.00 3.25
756 757 7.885922 TGGCAAGTAATTAATGAGAAGTGGTAA 59.114 33.333 4.19 0.00 0.00 2.85
757 758 8.182227 GGCAAGTAATTAATGAGAAGTGGTAAC 58.818 37.037 4.19 0.00 0.00 2.50
769 770 3.772619 TGGTAACATAGCGCTTCCC 57.227 52.632 18.68 7.49 46.17 3.97
770 771 0.179094 TGGTAACATAGCGCTTCCCG 60.179 55.000 18.68 4.15 46.17 5.14
771 772 0.103572 GGTAACATAGCGCTTCCCGA 59.896 55.000 18.68 0.00 40.02 5.14
772 773 1.488527 GTAACATAGCGCTTCCCGAG 58.511 55.000 18.68 1.79 40.02 4.63
773 774 1.066605 GTAACATAGCGCTTCCCGAGA 59.933 52.381 18.68 0.00 40.02 4.04
774 775 0.179108 AACATAGCGCTTCCCGAGAC 60.179 55.000 18.68 0.00 40.02 3.36
775 776 1.320344 ACATAGCGCTTCCCGAGACA 61.320 55.000 18.68 0.00 40.02 3.41
776 777 0.179111 CATAGCGCTTCCCGAGACAA 60.179 55.000 18.68 0.00 40.02 3.18
777 778 0.103208 ATAGCGCTTCCCGAGACAAG 59.897 55.000 18.68 0.00 40.02 3.16
778 779 0.963856 TAGCGCTTCCCGAGACAAGA 60.964 55.000 18.68 0.00 40.02 3.02
779 780 1.153549 GCGCTTCCCGAGACAAGAT 60.154 57.895 0.00 0.00 40.02 2.40
780 781 1.424493 GCGCTTCCCGAGACAAGATG 61.424 60.000 0.00 0.00 40.02 2.90
781 782 0.173481 CGCTTCCCGAGACAAGATGA 59.827 55.000 0.00 0.00 40.02 2.92
782 783 1.800655 CGCTTCCCGAGACAAGATGAG 60.801 57.143 0.00 0.00 40.02 2.90
783 784 1.205893 GCTTCCCGAGACAAGATGAGT 59.794 52.381 0.00 0.00 0.00 3.41
784 785 2.737039 GCTTCCCGAGACAAGATGAGTC 60.737 54.545 0.00 0.00 36.26 3.36
786 787 3.646736 TCCCGAGACAAGATGAGTCTA 57.353 47.619 0.00 0.00 45.79 2.59
787 788 3.546724 TCCCGAGACAAGATGAGTCTAG 58.453 50.000 0.00 0.00 45.79 2.43
788 789 3.200165 TCCCGAGACAAGATGAGTCTAGA 59.800 47.826 5.25 0.00 45.79 2.43
789 790 3.948473 CCCGAGACAAGATGAGTCTAGAA 59.052 47.826 0.00 0.00 45.79 2.10
790 791 4.036262 CCCGAGACAAGATGAGTCTAGAAG 59.964 50.000 0.00 0.00 45.79 2.85
791 792 4.638421 CCGAGACAAGATGAGTCTAGAAGT 59.362 45.833 0.00 0.00 45.79 3.01
792 793 5.124776 CCGAGACAAGATGAGTCTAGAAGTT 59.875 44.000 0.00 0.00 45.79 2.66
793 794 6.316640 CCGAGACAAGATGAGTCTAGAAGTTA 59.683 42.308 0.00 0.00 45.79 2.24
794 795 7.148222 CCGAGACAAGATGAGTCTAGAAGTTAA 60.148 40.741 0.00 0.00 45.79 2.01
795 796 8.402472 CGAGACAAGATGAGTCTAGAAGTTAAT 58.598 37.037 0.00 0.00 45.79 1.40
805 806 9.601217 TGAGTCTAGAAGTTAATAAATGAAGCC 57.399 33.333 0.00 0.00 0.00 4.35
806 807 9.601217 GAGTCTAGAAGTTAATAAATGAAGCCA 57.399 33.333 0.00 0.00 0.00 4.75
848 849 6.266168 TGTTACTTTGCATTATGAAGGTGG 57.734 37.500 0.00 0.00 0.00 4.61
849 850 5.772672 TGTTACTTTGCATTATGAAGGTGGT 59.227 36.000 0.00 0.00 0.00 4.16
850 851 6.943146 TGTTACTTTGCATTATGAAGGTGGTA 59.057 34.615 0.00 0.00 0.00 3.25
851 852 7.448777 TGTTACTTTGCATTATGAAGGTGGTAA 59.551 33.333 0.00 0.00 0.00 2.85
852 853 6.267496 ACTTTGCATTATGAAGGTGGTAAC 57.733 37.500 0.00 0.00 0.00 2.50
880 881 7.254227 GACTAGTGTCTTACTCCTCACTATG 57.746 44.000 0.00 0.00 40.81 2.23
881 882 6.959904 ACTAGTGTCTTACTCCTCACTATGA 58.040 40.000 0.00 0.00 40.81 2.15
882 883 6.824704 ACTAGTGTCTTACTCCTCACTATGAC 59.175 42.308 0.00 0.00 40.81 3.06
883 884 5.822204 AGTGTCTTACTCCTCACTATGACT 58.178 41.667 0.00 0.00 39.01 3.41
884 885 6.959904 AGTGTCTTACTCCTCACTATGACTA 58.040 40.000 0.00 0.00 39.01 2.59
885 886 7.051623 AGTGTCTTACTCCTCACTATGACTAG 58.948 42.308 0.00 0.00 39.01 2.57
886 887 5.823570 TGTCTTACTCCTCACTATGACTAGC 59.176 44.000 0.00 0.00 0.00 3.42
887 888 5.239963 GTCTTACTCCTCACTATGACTAGCC 59.760 48.000 0.00 0.00 0.00 3.93
888 889 3.963476 ACTCCTCACTATGACTAGCCT 57.037 47.619 0.00 0.00 0.00 4.58
889 890 4.258457 ACTCCTCACTATGACTAGCCTT 57.742 45.455 0.00 0.00 0.00 4.35
890 891 5.390087 ACTCCTCACTATGACTAGCCTTA 57.610 43.478 0.00 0.00 0.00 2.69
970 981 9.280174 CACAAATTAACTTCCCTACTTAACTGA 57.720 33.333 0.00 0.00 0.00 3.41
1021 1034 1.217882 GCTCTTTACACACTGCACGT 58.782 50.000 0.00 0.00 0.00 4.49
1026 1039 2.018727 TTACACACTGCACGTCGGGT 62.019 55.000 0.00 0.00 0.00 5.28
1145 1162 2.268920 GGTTGCTGCCCGAGATGA 59.731 61.111 0.00 0.00 0.00 2.92
1222 1239 6.605471 TCCTCAATGAAGCGGTATGTATAT 57.395 37.500 0.00 0.00 0.00 0.86
1253 1320 9.377312 ACTATTCTTCTTCTTATTCTTGCAGTC 57.623 33.333 0.00 0.00 0.00 3.51
1265 1389 6.734104 ATTCTTGCAGTCAGTGATCTAAAC 57.266 37.500 0.00 0.00 0.00 2.01
1326 1467 3.057876 GCAAATACGACCATGGTGTTTGA 60.058 43.478 28.23 14.11 44.34 2.69
1374 1515 0.951558 AGTTCGTGCAATTGTGTCCC 59.048 50.000 7.40 0.00 0.00 4.46
1383 1524 0.482446 AATTGTGTCCCAGAAGCCCA 59.518 50.000 0.00 0.00 0.00 5.36
1444 1585 2.502295 CTCCCAAGATAGAGCATTGGC 58.498 52.381 0.00 0.00 41.79 4.52
1450 1591 2.928334 AGATAGAGCATTGGCCAGTTG 58.072 47.619 5.11 9.59 42.56 3.16
1486 1636 6.968131 TGATGGCGATTATTATGAAGCTAC 57.032 37.500 0.00 0.00 0.00 3.58
1627 6177 0.391661 TTTGAGCATGGAGTCCGAGC 60.392 55.000 15.75 15.75 0.00 5.03
1659 6227 1.135286 CACTATCTCAGCAGCACGACA 60.135 52.381 0.00 0.00 0.00 4.35
1662 6230 2.513026 ATCTCAGCAGCACGACACCC 62.513 60.000 0.00 0.00 0.00 4.61
1663 6231 3.519973 CTCAGCAGCACGACACCCA 62.520 63.158 0.00 0.00 0.00 4.51
1664 6232 2.591429 CAGCAGCACGACACCCAA 60.591 61.111 0.00 0.00 0.00 4.12
1665 6233 2.281070 AGCAGCACGACACCCAAG 60.281 61.111 0.00 0.00 0.00 3.61
1666 6234 2.280797 GCAGCACGACACCCAAGA 60.281 61.111 0.00 0.00 0.00 3.02
1667 6235 2.607892 GCAGCACGACACCCAAGAC 61.608 63.158 0.00 0.00 0.00 3.01
1668 6236 2.029073 AGCACGACACCCAAGACG 59.971 61.111 0.00 0.00 0.00 4.18
1669 6237 3.712881 GCACGACACCCAAGACGC 61.713 66.667 0.00 0.00 0.00 5.19
1670 6238 2.029073 CACGACACCCAAGACGCT 59.971 61.111 0.00 0.00 0.00 5.07
1706 6274 3.996150 ATGGAAGTTGTGTTGCTTGAG 57.004 42.857 0.00 0.00 0.00 3.02
1720 6288 2.612212 TGCTTGAGTCGAAAGTTGGAAC 59.388 45.455 0.00 0.00 0.00 3.62
1932 6516 2.369532 AGGTGGAGTTTACCGTTGCTTA 59.630 45.455 0.00 0.00 43.06 3.09
2065 6652 5.011329 ACCGACAAAGGTAGTACAGAAATGA 59.989 40.000 2.06 0.00 43.89 2.57
2068 6655 6.089551 CGACAAAGGTAGTACAGAAATGACAG 59.910 42.308 2.06 0.00 0.00 3.51
2095 6682 6.359804 TCCTGATCATCCTTTTATCAAGGTG 58.640 40.000 0.00 0.06 38.55 4.00
2117 6704 5.357878 GTGAATGTGGATGCTTCTTTCCATA 59.642 40.000 0.00 0.00 43.61 2.74
2179 6766 1.210155 CAAGGGCACTTTGCTACGC 59.790 57.895 0.00 0.00 44.28 4.42
2296 6883 3.244422 TGCGGAAGGTGATAGTTGAAACT 60.244 43.478 0.71 0.71 42.91 2.66
2357 6944 4.855715 TTCGATCATTCCGAGATAGCTT 57.144 40.909 0.00 0.00 37.35 3.74
2389 6976 4.265904 TGAAATACGAGAGCTTTGTGGA 57.734 40.909 0.00 0.00 0.00 4.02
2664 7253 0.821517 CACCTCTGTATACCACCGCA 59.178 55.000 0.00 0.00 0.00 5.69
2770 7366 9.965824 AAGAATAACACAACTTAATTCTGGTTG 57.034 29.630 13.12 13.12 43.84 3.77
2771 7367 8.576442 AGAATAACACAACTTAATTCTGGTTGG 58.424 33.333 16.74 10.94 42.93 3.77
2841 7439 3.879912 CGTTCCCGTACAGTGAAGT 57.120 52.632 0.00 0.00 0.00 3.01
2864 7462 3.639445 AGATGCGTCTCATGGCCT 58.361 55.556 3.32 0.00 35.05 5.19
2865 7463 1.445095 AGATGCGTCTCATGGCCTC 59.555 57.895 3.32 0.00 35.05 4.70
2866 7464 1.144716 GATGCGTCTCATGGCCTCA 59.855 57.895 3.32 0.00 35.05 3.86
2867 7465 0.250209 GATGCGTCTCATGGCCTCAT 60.250 55.000 3.32 0.00 35.05 2.90
2887 7485 3.842869 GGGACCTACACAAGCAGAG 57.157 57.895 0.00 0.00 0.00 3.35
2930 7529 2.333069 AGCATAGGAGCTGATTGGCTA 58.667 47.619 0.00 0.00 44.66 3.93
2931 7530 2.707791 AGCATAGGAGCTGATTGGCTAA 59.292 45.455 0.00 0.00 44.66 3.09
2932 7531 3.072944 GCATAGGAGCTGATTGGCTAAG 58.927 50.000 0.00 0.00 43.20 2.18
2933 7532 3.672808 CATAGGAGCTGATTGGCTAAGG 58.327 50.000 0.00 0.00 43.20 2.69
2934 7533 1.885049 AGGAGCTGATTGGCTAAGGA 58.115 50.000 0.00 0.00 43.20 3.36
2935 7534 2.416638 AGGAGCTGATTGGCTAAGGAT 58.583 47.619 0.00 0.00 43.20 3.24
2936 7535 3.591789 AGGAGCTGATTGGCTAAGGATA 58.408 45.455 0.00 0.00 43.20 2.59
2937 7536 3.582208 AGGAGCTGATTGGCTAAGGATAG 59.418 47.826 0.00 0.00 43.20 2.08
2952 7551 7.219484 CTAAGGATAGCAATTTTACCCATGG 57.781 40.000 4.14 4.14 0.00 3.66
2953 7552 4.482990 AGGATAGCAATTTTACCCATGGG 58.517 43.478 30.23 30.23 42.03 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 0.109342 AGCCAGCTTAGCAACACACT 59.891 50.000 7.07 0.00 0.00 3.55
541 542 2.131067 CGAAGGCCTCCTCCTCCTC 61.131 68.421 5.23 0.00 34.82 3.71
542 543 2.042435 CGAAGGCCTCCTCCTCCT 60.042 66.667 5.23 0.00 34.82 3.69
543 544 3.855853 GCGAAGGCCTCCTCCTCC 61.856 72.222 5.23 0.00 34.82 4.30
627 628 3.526931 TCCCAGAAGATTTAGACGCAG 57.473 47.619 0.00 0.00 0.00 5.18
631 632 7.163001 AGCAAAAATCCCAGAAGATTTAGAC 57.837 36.000 0.29 0.00 43.90 2.59
666 667 4.216708 AGTTACTCCCACTATGACTAGCC 58.783 47.826 0.00 0.00 0.00 3.93
667 668 5.855740 AAGTTACTCCCACTATGACTAGC 57.144 43.478 0.00 0.00 0.00 3.42
668 669 7.061688 ACCTAAGTTACTCCCACTATGACTAG 58.938 42.308 0.00 0.00 0.00 2.57
669 670 6.978261 ACCTAAGTTACTCCCACTATGACTA 58.022 40.000 0.00 0.00 0.00 2.59
670 671 5.840081 ACCTAAGTTACTCCCACTATGACT 58.160 41.667 0.00 0.00 0.00 3.41
671 672 6.832900 ACTACCTAAGTTACTCCCACTATGAC 59.167 42.308 0.00 0.00 33.35 3.06
672 673 6.978261 ACTACCTAAGTTACTCCCACTATGA 58.022 40.000 0.00 0.00 33.35 2.15
673 674 8.628280 GTTACTACCTAAGTTACTCCCACTATG 58.372 40.741 0.00 0.00 39.80 2.23
674 675 8.339247 TGTTACTACCTAAGTTACTCCCACTAT 58.661 37.037 0.00 0.00 38.33 2.12
675 676 7.698912 TGTTACTACCTAAGTTACTCCCACTA 58.301 38.462 0.00 0.00 38.33 2.74
676 677 6.555711 TGTTACTACCTAAGTTACTCCCACT 58.444 40.000 0.00 0.00 38.33 4.00
677 678 6.840780 TGTTACTACCTAAGTTACTCCCAC 57.159 41.667 0.00 0.00 38.33 4.61
678 679 7.286316 GCTATGTTACTACCTAAGTTACTCCCA 59.714 40.741 0.00 0.00 38.33 4.37
679 680 7.521261 CGCTATGTTACTACCTAAGTTACTCCC 60.521 44.444 0.00 0.00 38.33 4.30
680 681 7.358830 CGCTATGTTACTACCTAAGTTACTCC 58.641 42.308 0.00 0.00 38.33 3.85
681 682 6.855403 GCGCTATGTTACTACCTAAGTTACTC 59.145 42.308 0.00 0.00 38.33 2.59
682 683 6.319658 TGCGCTATGTTACTACCTAAGTTACT 59.680 38.462 9.73 0.00 38.33 2.24
683 684 6.416161 GTGCGCTATGTTACTACCTAAGTTAC 59.584 42.308 9.73 0.00 39.80 2.50
684 685 6.319658 AGTGCGCTATGTTACTACCTAAGTTA 59.680 38.462 9.73 0.00 39.80 2.24
685 686 5.126707 AGTGCGCTATGTTACTACCTAAGTT 59.873 40.000 9.73 0.00 39.80 2.66
686 687 4.643784 AGTGCGCTATGTTACTACCTAAGT 59.356 41.667 9.73 0.00 42.62 2.24
687 688 5.008811 AGAGTGCGCTATGTTACTACCTAAG 59.991 44.000 9.73 0.00 0.00 2.18
688 689 4.885907 AGAGTGCGCTATGTTACTACCTAA 59.114 41.667 9.73 0.00 0.00 2.69
689 690 4.458397 AGAGTGCGCTATGTTACTACCTA 58.542 43.478 9.73 0.00 0.00 3.08
690 691 3.288964 AGAGTGCGCTATGTTACTACCT 58.711 45.455 9.73 0.00 0.00 3.08
691 692 3.712091 AGAGTGCGCTATGTTACTACC 57.288 47.619 9.73 0.00 0.00 3.18
692 693 6.057627 TCTTAGAGTGCGCTATGTTACTAC 57.942 41.667 9.73 0.00 0.00 2.73
693 694 6.688637 TTCTTAGAGTGCGCTATGTTACTA 57.311 37.500 9.73 0.00 0.00 1.82
694 695 5.578005 TTCTTAGAGTGCGCTATGTTACT 57.422 39.130 9.73 1.27 0.00 2.24
695 696 6.642683 TTTTCTTAGAGTGCGCTATGTTAC 57.357 37.500 9.73 0.00 0.00 2.50
696 697 7.843490 AATTTTCTTAGAGTGCGCTATGTTA 57.157 32.000 9.73 0.00 0.00 2.41
697 698 6.743575 AATTTTCTTAGAGTGCGCTATGTT 57.256 33.333 9.73 0.00 0.00 2.71
698 699 6.743575 AAATTTTCTTAGAGTGCGCTATGT 57.256 33.333 9.73 0.00 0.00 2.29
699 700 6.021153 GCAAAATTTTCTTAGAGTGCGCTATG 60.021 38.462 9.73 0.00 0.00 2.23
700 701 6.030228 GCAAAATTTTCTTAGAGTGCGCTAT 58.970 36.000 9.73 0.00 0.00 2.97
701 702 5.181245 AGCAAAATTTTCTTAGAGTGCGCTA 59.819 36.000 9.73 0.00 35.92 4.26
702 703 4.022849 AGCAAAATTTTCTTAGAGTGCGCT 60.023 37.500 9.73 0.00 35.92 5.92
703 704 4.229876 AGCAAAATTTTCTTAGAGTGCGC 58.770 39.130 0.00 0.00 35.92 6.09
704 705 7.538678 ACATAAGCAAAATTTTCTTAGAGTGCG 59.461 33.333 18.83 10.82 35.92 5.34
705 706 8.642020 CACATAAGCAAAATTTTCTTAGAGTGC 58.358 33.333 23.19 15.61 31.74 4.40
706 707 9.132521 CCACATAAGCAAAATTTTCTTAGAGTG 57.867 33.333 24.90 24.90 35.00 3.51
707 708 7.814587 GCCACATAAGCAAAATTTTCTTAGAGT 59.185 33.333 18.83 17.05 0.00 3.24
708 709 7.814107 TGCCACATAAGCAAAATTTTCTTAGAG 59.186 33.333 18.83 16.68 37.28 2.43
709 710 7.665690 TGCCACATAAGCAAAATTTTCTTAGA 58.334 30.769 18.83 7.75 37.28 2.10
710 711 7.887996 TGCCACATAAGCAAAATTTTCTTAG 57.112 32.000 18.83 15.10 37.28 2.18
722 723 7.555914 TCTCATTAATTACTTGCCACATAAGCA 59.444 33.333 0.00 0.00 38.81 3.91
723 724 7.930217 TCTCATTAATTACTTGCCACATAAGC 58.070 34.615 0.00 0.00 0.00 3.09
724 725 9.941664 CTTCTCATTAATTACTTGCCACATAAG 57.058 33.333 0.00 0.00 0.00 1.73
725 726 9.461312 ACTTCTCATTAATTACTTGCCACATAA 57.539 29.630 0.00 0.00 0.00 1.90
726 727 8.892723 CACTTCTCATTAATTACTTGCCACATA 58.107 33.333 0.00 0.00 0.00 2.29
727 728 7.148018 CCACTTCTCATTAATTACTTGCCACAT 60.148 37.037 0.00 0.00 0.00 3.21
728 729 6.150976 CCACTTCTCATTAATTACTTGCCACA 59.849 38.462 0.00 0.00 0.00 4.17
729 730 6.151144 ACCACTTCTCATTAATTACTTGCCAC 59.849 38.462 0.00 0.00 0.00 5.01
730 731 6.245408 ACCACTTCTCATTAATTACTTGCCA 58.755 36.000 0.00 0.00 0.00 4.92
731 732 6.759497 ACCACTTCTCATTAATTACTTGCC 57.241 37.500 0.00 0.00 0.00 4.52
732 733 8.726988 TGTTACCACTTCTCATTAATTACTTGC 58.273 33.333 0.00 0.00 0.00 4.01
737 738 9.256477 CGCTATGTTACCACTTCTCATTAATTA 57.744 33.333 0.00 0.00 0.00 1.40
738 739 7.254795 GCGCTATGTTACCACTTCTCATTAATT 60.255 37.037 0.00 0.00 0.00 1.40
739 740 6.202954 GCGCTATGTTACCACTTCTCATTAAT 59.797 38.462 0.00 0.00 0.00 1.40
740 741 5.522460 GCGCTATGTTACCACTTCTCATTAA 59.478 40.000 0.00 0.00 0.00 1.40
741 742 5.047847 GCGCTATGTTACCACTTCTCATTA 58.952 41.667 0.00 0.00 0.00 1.90
742 743 3.871594 GCGCTATGTTACCACTTCTCATT 59.128 43.478 0.00 0.00 0.00 2.57
743 744 3.133003 AGCGCTATGTTACCACTTCTCAT 59.867 43.478 8.99 0.00 0.00 2.90
744 745 2.496070 AGCGCTATGTTACCACTTCTCA 59.504 45.455 8.99 0.00 0.00 3.27
745 746 3.166489 AGCGCTATGTTACCACTTCTC 57.834 47.619 8.99 0.00 0.00 2.87
746 747 3.522553 GAAGCGCTATGTTACCACTTCT 58.477 45.455 12.05 0.00 31.58 2.85
747 748 2.608090 GGAAGCGCTATGTTACCACTTC 59.392 50.000 12.05 0.00 33.08 3.01
748 749 2.629051 GGAAGCGCTATGTTACCACTT 58.371 47.619 12.05 0.00 0.00 3.16
749 750 1.134491 GGGAAGCGCTATGTTACCACT 60.134 52.381 12.05 0.00 0.00 4.00
750 751 1.296727 GGGAAGCGCTATGTTACCAC 58.703 55.000 12.05 0.00 0.00 4.16
751 752 0.179094 CGGGAAGCGCTATGTTACCA 60.179 55.000 12.05 0.00 0.00 3.25
752 753 0.103572 TCGGGAAGCGCTATGTTACC 59.896 55.000 12.05 3.57 0.00 2.85
753 754 1.066605 TCTCGGGAAGCGCTATGTTAC 59.933 52.381 12.05 0.00 0.00 2.50
754 755 1.066605 GTCTCGGGAAGCGCTATGTTA 59.933 52.381 12.05 0.00 0.00 2.41
755 756 0.179108 GTCTCGGGAAGCGCTATGTT 60.179 55.000 12.05 0.00 0.00 2.71
756 757 1.320344 TGTCTCGGGAAGCGCTATGT 61.320 55.000 12.05 0.00 0.00 2.29
757 758 0.179111 TTGTCTCGGGAAGCGCTATG 60.179 55.000 12.05 0.24 0.00 2.23
758 759 0.103208 CTTGTCTCGGGAAGCGCTAT 59.897 55.000 12.05 0.00 0.00 2.97
759 760 0.963856 TCTTGTCTCGGGAAGCGCTA 60.964 55.000 12.05 0.00 0.00 4.26
760 761 1.608717 ATCTTGTCTCGGGAAGCGCT 61.609 55.000 2.64 2.64 0.00 5.92
761 762 1.153549 ATCTTGTCTCGGGAAGCGC 60.154 57.895 0.00 0.00 0.00 5.92
762 763 0.173481 TCATCTTGTCTCGGGAAGCG 59.827 55.000 0.00 0.00 0.00 4.68
763 764 1.205893 ACTCATCTTGTCTCGGGAAGC 59.794 52.381 0.00 0.00 0.00 3.86
764 765 2.757868 AGACTCATCTTGTCTCGGGAAG 59.242 50.000 0.00 0.00 40.35 3.46
765 766 2.808919 AGACTCATCTTGTCTCGGGAA 58.191 47.619 0.00 0.00 40.35 3.97
766 767 2.516227 AGACTCATCTTGTCTCGGGA 57.484 50.000 0.00 0.00 40.35 5.14
767 768 3.546724 TCTAGACTCATCTTGTCTCGGG 58.453 50.000 0.00 0.00 42.95 5.14
768 769 4.638421 ACTTCTAGACTCATCTTGTCTCGG 59.362 45.833 0.00 0.00 42.95 4.63
769 770 5.811399 ACTTCTAGACTCATCTTGTCTCG 57.189 43.478 0.00 0.00 42.95 4.04
779 780 9.601217 GGCTTCATTTATTAACTTCTAGACTCA 57.399 33.333 0.00 0.00 0.00 3.41
780 781 9.601217 TGGCTTCATTTATTAACTTCTAGACTC 57.399 33.333 0.00 0.00 0.00 3.36
822 823 8.465999 CCACCTTCATAATGCAAAGTAACATAA 58.534 33.333 0.00 0.00 0.00 1.90
823 824 7.613801 ACCACCTTCATAATGCAAAGTAACATA 59.386 33.333 0.00 0.00 0.00 2.29
824 825 6.437162 ACCACCTTCATAATGCAAAGTAACAT 59.563 34.615 0.00 0.00 0.00 2.71
825 826 5.772672 ACCACCTTCATAATGCAAAGTAACA 59.227 36.000 0.00 0.00 0.00 2.41
826 827 6.267496 ACCACCTTCATAATGCAAAGTAAC 57.733 37.500 0.00 0.00 0.00 2.50
827 828 7.448777 TGTTACCACCTTCATAATGCAAAGTAA 59.551 33.333 0.00 0.00 0.00 2.24
828 829 6.943146 TGTTACCACCTTCATAATGCAAAGTA 59.057 34.615 0.00 0.00 0.00 2.24
829 830 5.772672 TGTTACCACCTTCATAATGCAAAGT 59.227 36.000 0.00 0.00 0.00 2.66
830 831 6.266168 TGTTACCACCTTCATAATGCAAAG 57.734 37.500 0.00 0.00 0.00 2.77
831 832 6.849085 ATGTTACCACCTTCATAATGCAAA 57.151 33.333 0.00 0.00 0.00 3.68
832 833 7.282224 GTCTATGTTACCACCTTCATAATGCAA 59.718 37.037 0.00 0.00 0.00 4.08
833 834 6.765989 GTCTATGTTACCACCTTCATAATGCA 59.234 38.462 0.00 0.00 0.00 3.96
834 835 6.992715 AGTCTATGTTACCACCTTCATAATGC 59.007 38.462 0.00 0.00 0.00 3.56
835 836 9.698309 CTAGTCTATGTTACCACCTTCATAATG 57.302 37.037 0.00 0.00 0.00 1.90
836 837 9.435570 ACTAGTCTATGTTACCACCTTCATAAT 57.564 33.333 0.00 0.00 0.00 1.28
837 838 8.692710 CACTAGTCTATGTTACCACCTTCATAA 58.307 37.037 0.00 0.00 0.00 1.90
838 839 7.837689 ACACTAGTCTATGTTACCACCTTCATA 59.162 37.037 0.00 0.00 0.00 2.15
839 840 6.668283 ACACTAGTCTATGTTACCACCTTCAT 59.332 38.462 0.00 0.00 0.00 2.57
840 841 6.014647 ACACTAGTCTATGTTACCACCTTCA 58.985 40.000 0.00 0.00 0.00 3.02
841 842 6.527057 ACACTAGTCTATGTTACCACCTTC 57.473 41.667 0.00 0.00 0.00 3.46
842 843 6.527057 GACACTAGTCTATGTTACCACCTT 57.473 41.667 0.00 0.00 41.64 3.50
856 857 7.011669 GTCATAGTGAGGAGTAAGACACTAGTC 59.988 44.444 0.00 0.00 44.91 2.59
857 858 6.824704 GTCATAGTGAGGAGTAAGACACTAGT 59.175 42.308 0.00 0.00 44.91 2.57
858 859 7.051623 AGTCATAGTGAGGAGTAAGACACTAG 58.948 42.308 0.00 0.00 44.91 2.57
859 860 6.959904 AGTCATAGTGAGGAGTAAGACACTA 58.040 40.000 0.00 0.00 45.46 2.74
860 861 5.822204 AGTCATAGTGAGGAGTAAGACACT 58.178 41.667 0.00 0.00 44.17 3.55
861 862 6.238538 GCTAGTCATAGTGAGGAGTAAGACAC 60.239 46.154 0.00 0.00 30.99 3.67
862 863 5.823570 GCTAGTCATAGTGAGGAGTAAGACA 59.176 44.000 0.00 0.00 30.99 3.41
863 864 5.239963 GGCTAGTCATAGTGAGGAGTAAGAC 59.760 48.000 0.00 0.00 0.00 3.01
864 865 5.132985 AGGCTAGTCATAGTGAGGAGTAAGA 59.867 44.000 0.00 0.00 0.00 2.10
865 866 5.381757 AGGCTAGTCATAGTGAGGAGTAAG 58.618 45.833 0.00 0.00 0.00 2.34
866 867 5.390087 AGGCTAGTCATAGTGAGGAGTAA 57.610 43.478 0.00 0.00 0.00 2.24
867 868 5.390087 AAGGCTAGTCATAGTGAGGAGTA 57.610 43.478 0.00 0.00 0.00 2.59
868 869 3.963476 AGGCTAGTCATAGTGAGGAGT 57.037 47.619 0.00 0.00 0.00 3.85
869 870 5.381757 AGTAAGGCTAGTCATAGTGAGGAG 58.618 45.833 0.00 0.00 0.00 3.69
870 871 5.378332 GAGTAAGGCTAGTCATAGTGAGGA 58.622 45.833 0.00 0.00 0.00 3.71
871 872 4.214545 CGAGTAAGGCTAGTCATAGTGAGG 59.785 50.000 0.00 0.00 0.00 3.86
872 873 4.817464 ACGAGTAAGGCTAGTCATAGTGAG 59.183 45.833 0.00 0.00 0.00 3.51
873 874 4.778579 ACGAGTAAGGCTAGTCATAGTGA 58.221 43.478 0.00 0.00 0.00 3.41
874 875 5.098218 GACGAGTAAGGCTAGTCATAGTG 57.902 47.826 0.00 0.00 45.39 2.74
880 881 1.760192 TGGGACGAGTAAGGCTAGTC 58.240 55.000 0.00 0.00 45.36 2.59
881 882 2.226962 TTGGGACGAGTAAGGCTAGT 57.773 50.000 0.00 0.00 35.73 2.57
882 883 2.224066 CCATTGGGACGAGTAAGGCTAG 60.224 54.545 0.00 0.00 35.59 3.42
883 884 1.760613 CCATTGGGACGAGTAAGGCTA 59.239 52.381 0.00 0.00 35.59 3.93
884 885 0.541863 CCATTGGGACGAGTAAGGCT 59.458 55.000 0.00 0.00 35.59 4.58
885 886 0.252197 ACCATTGGGACGAGTAAGGC 59.748 55.000 7.78 0.00 38.05 4.35
886 887 2.781681 AACCATTGGGACGAGTAAGG 57.218 50.000 7.78 0.00 38.05 2.69
887 888 4.814771 GGATTAACCATTGGGACGAGTAAG 59.185 45.833 7.78 0.00 38.79 2.34
888 889 4.225492 TGGATTAACCATTGGGACGAGTAA 59.775 41.667 7.78 0.00 44.64 2.24
889 890 3.775866 TGGATTAACCATTGGGACGAGTA 59.224 43.478 7.78 0.00 44.64 2.59
890 891 2.574369 TGGATTAACCATTGGGACGAGT 59.426 45.455 7.78 0.00 44.64 4.18
911 917 1.471119 TAAAGAGCGACCGGACAGAT 58.529 50.000 9.46 0.00 0.00 2.90
937 943 9.856162 AGTAGGGAAGTTAATTTGTGTTAGAAA 57.144 29.630 0.00 0.00 0.00 2.52
938 944 9.856162 AAGTAGGGAAGTTAATTTGTGTTAGAA 57.144 29.630 0.00 0.00 0.00 2.10
1021 1034 1.002624 GGACTGGCATGAAACCCGA 60.003 57.895 0.00 0.00 0.00 5.14
1026 1039 1.971167 GGCGTGGACTGGCATGAAA 60.971 57.895 0.00 0.00 0.00 2.69
1145 1162 1.002257 TTGCGGTGCTCATCCACAT 60.002 52.632 0.00 0.00 37.46 3.21
1242 1309 5.349817 CGTTTAGATCACTGACTGCAAGAAT 59.650 40.000 0.00 0.00 37.43 2.40
1253 1320 9.900710 AGTAATATAAGAGCGTTTAGATCACTG 57.099 33.333 0.00 0.00 37.82 3.66
1265 1389 7.358066 TCACTCCGTAAAGTAATATAAGAGCG 58.642 38.462 0.00 0.00 0.00 5.03
1326 1467 7.569240 CCAGTCAAGTATAGAAAAGGATCCTT 58.431 38.462 21.89 21.89 37.98 3.36
1374 1515 2.028420 TCGATGTCAATGGGCTTCTG 57.972 50.000 0.00 0.00 0.00 3.02
1383 1524 6.207417 ACTTTGAGTTGGATTTCGATGTCAAT 59.793 34.615 0.00 0.00 0.00 2.57
1444 1585 6.974622 GCCATCATAATAAAAGACACAACTGG 59.025 38.462 0.00 0.00 0.00 4.00
1486 1636 7.427606 GCTTTTCAATGATGATCGTACTTGAAG 59.572 37.037 17.32 11.83 34.99 3.02
1524 1674 2.627945 CTGTTGGGCGCATAACTCTAA 58.372 47.619 21.41 1.33 0.00 2.10
1627 6177 1.606668 GAGATAGTGAGGAGCAGACCG 59.393 57.143 0.00 0.00 34.73 4.79
1659 6227 0.247736 GACTCATCAGCGTCTTGGGT 59.752 55.000 0.00 0.00 0.00 4.51
1662 6230 0.460987 GGGGACTCATCAGCGTCTTG 60.461 60.000 0.00 0.00 30.34 3.02
1663 6231 0.904865 TGGGGACTCATCAGCGTCTT 60.905 55.000 0.00 0.00 30.34 3.01
1664 6232 0.689080 ATGGGGACTCATCAGCGTCT 60.689 55.000 0.00 0.00 30.34 4.18
1665 6233 0.249657 GATGGGGACTCATCAGCGTC 60.250 60.000 7.29 0.00 42.16 5.19
1666 6234 0.689080 AGATGGGGACTCATCAGCGT 60.689 55.000 14.15 0.00 44.30 5.07
1667 6235 1.332195 TAGATGGGGACTCATCAGCG 58.668 55.000 14.15 0.00 44.30 5.18
1668 6236 2.027377 CCATAGATGGGGACTCATCAGC 60.027 54.545 14.15 0.00 44.30 4.26
1669 6237 3.977134 CCATAGATGGGGACTCATCAG 57.023 52.381 14.15 4.12 44.30 2.90
1706 6274 3.414549 TGCTTTGTTCCAACTTTCGAC 57.585 42.857 0.00 0.00 0.00 4.20
1720 6288 1.782569 CACGTTTCACTGCATGCTTTG 59.217 47.619 20.33 15.36 0.00 2.77
1789 6357 5.376854 TGCTTGAATGAGAACTTTAAGCC 57.623 39.130 9.22 0.00 38.52 4.35
1848 6432 3.387374 TGTTTTGGGCATGACAAAGACAT 59.613 39.130 7.96 0.00 38.84 3.06
1849 6433 2.762887 TGTTTTGGGCATGACAAAGACA 59.237 40.909 7.96 7.96 38.84 3.41
2065 6652 1.890552 AAGGATGATCAGGAGGCTGT 58.109 50.000 0.09 0.00 0.00 4.40
2068 6655 4.978099 TGATAAAAGGATGATCAGGAGGC 58.022 43.478 0.09 0.00 0.00 4.70
2117 6704 1.470805 GCCGCCTTGTTGTGTTTCTTT 60.471 47.619 0.00 0.00 0.00 2.52
2179 6766 4.469552 CATCATACCATATTGCTTGTGCG 58.530 43.478 0.00 0.00 43.34 5.34
2357 6944 4.574892 TCTCGTATTTCATGCAAAGTGGA 58.425 39.130 0.00 0.00 0.00 4.02
2389 6976 6.532988 ACTAAGCGAAACTCCTCTAGATTT 57.467 37.500 0.00 0.00 0.00 2.17
2459 7046 5.141182 CCTTCTCCTAGAGGCACTACATTA 58.859 45.833 0.00 0.00 41.55 1.90
2664 7253 8.710749 ACAATATATCATGCTACCAAAACCAT 57.289 30.769 0.00 0.00 0.00 3.55
2707 7301 4.755123 AGTTGAAAGTGGTGTTATTCGGAG 59.245 41.667 0.00 0.00 0.00 4.63
2765 7361 0.179015 ACGTATGCAACCACCAACCA 60.179 50.000 0.00 0.00 0.00 3.67
2766 7362 0.519961 GACGTATGCAACCACCAACC 59.480 55.000 0.00 0.00 0.00 3.77
2767 7363 1.231221 TGACGTATGCAACCACCAAC 58.769 50.000 0.00 0.00 0.00 3.77
2768 7364 1.968704 TTGACGTATGCAACCACCAA 58.031 45.000 0.00 0.00 0.00 3.67
2769 7365 1.968704 TTTGACGTATGCAACCACCA 58.031 45.000 0.00 0.00 0.00 4.17
2770 7366 3.003897 TCTTTTTGACGTATGCAACCACC 59.996 43.478 0.00 0.00 0.00 4.61
2771 7367 4.217754 TCTTTTTGACGTATGCAACCAC 57.782 40.909 0.00 0.00 0.00 4.16
2834 7430 3.056250 AGACGCATCTCAATCACTTCACT 60.056 43.478 0.00 0.00 0.00 3.41
2861 7459 1.271840 TGTGTAGGTCCCCATGAGGC 61.272 60.000 0.00 0.00 0.00 4.70
2862 7460 1.210478 CTTGTGTAGGTCCCCATGAGG 59.790 57.143 0.00 0.00 0.00 3.86
2863 7461 1.407437 GCTTGTGTAGGTCCCCATGAG 60.407 57.143 0.00 0.00 0.00 2.90
2864 7462 0.618458 GCTTGTGTAGGTCCCCATGA 59.382 55.000 0.00 0.00 0.00 3.07
2865 7463 0.327924 TGCTTGTGTAGGTCCCCATG 59.672 55.000 0.00 0.00 0.00 3.66
2866 7464 0.620556 CTGCTTGTGTAGGTCCCCAT 59.379 55.000 0.00 0.00 0.00 4.00
2867 7465 0.472925 TCTGCTTGTGTAGGTCCCCA 60.473 55.000 0.00 0.00 0.00 4.96
2868 7466 0.250513 CTCTGCTTGTGTAGGTCCCC 59.749 60.000 0.00 0.00 0.00 4.81
2930 7529 4.901250 CCCATGGGTAAAATTGCTATCCTT 59.099 41.667 23.93 0.00 0.00 3.36
2931 7530 4.482990 CCCATGGGTAAAATTGCTATCCT 58.517 43.478 23.93 0.00 0.00 3.24
2932 7531 4.871933 CCCATGGGTAAAATTGCTATCC 57.128 45.455 23.93 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.