Multiple sequence alignment - TraesCS4D01G133000

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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 TraesCS4D01G133000 chr4D 100.000 1907 0 0 1 1907 119801570 119803476 0.000000e+00 3522.0
1 TraesCS4D01G133000 chr4D 100.000 1754 0 0 2184 3937 119803753 119805506 0.000000e+00 3240.0
2 TraesCS4D01G133000 chr4D 96.450 169 4 2 3323 3490 119804853 119805020 1.080000e-70 278.0
3 TraesCS4D01G133000 chr4D 96.450 169 4 2 3284 3451 119804892 119805059 1.080000e-70 278.0
4 TraesCS4D01G133000 chr4D 96.124 129 4 1 3363 3490 119804853 119804981 3.990000e-50 209.0
5 TraesCS4D01G133000 chr4D 96.124 129 4 1 3284 3412 119804932 119805059 3.990000e-50 209.0
6 TraesCS4D01G133000 chr4D 98.851 87 0 1 3402 3487 119804853 119804939 1.890000e-33 154.0
7 TraesCS4D01G133000 chr4D 98.851 87 0 1 3284 3370 119804971 119805056 1.890000e-33 154.0
8 TraesCS4D01G133000 chr4D 100.000 50 0 0 3441 3490 119804853 119804902 4.190000e-15 93.5
9 TraesCS4D01G133000 chr4D 100.000 50 0 0 3284 3333 119805010 119805059 4.190000e-15 93.5
10 TraesCS4D01G133000 chr4B 93.849 1138 47 3 2197 3333 182258672 182259787 0.000000e+00 1692.0
11 TraesCS4D01G133000 chr4B 95.532 649 24 5 893 1540 182257488 182258132 0.000000e+00 1033.0
12 TraesCS4D01G133000 chr4B 88.066 662 68 10 1 655 182256366 182257023 0.000000e+00 774.0
13 TraesCS4D01G133000 chr4B 87.574 507 18 14 3441 3937 182259738 182260209 2.680000e-151 545.0
14 TraesCS4D01G133000 chr4B 84.884 430 25 13 1500 1907 182258252 182258663 7.930000e-107 398.0
15 TraesCS4D01G133000 chr4A 90.807 1153 44 7 2197 3333 450763253 450764359 0.000000e+00 1485.0
16 TraesCS4D01G133000 chr4A 92.444 622 21 11 1295 1907 450762640 450763244 0.000000e+00 865.0
17 TraesCS4D01G133000 chr4A 88.138 666 55 10 1 660 450761461 450762108 0.000000e+00 771.0
18 TraesCS4D01G133000 chr4A 90.891 505 24 10 3441 3937 450764310 450764800 0.000000e+00 658.0
19 TraesCS4D01G133000 chr4A 94.321 405 13 6 837 1239 450762230 450762626 2.600000e-171 612.0
20 TraesCS4D01G133000 chrUn 88.710 124 9 5 690 808 32514115 32514238 3.170000e-31 147.0
21 TraesCS4D01G133000 chrUn 88.710 124 9 5 690 808 262107372 262107495 3.170000e-31 147.0
22 TraesCS4D01G133000 chrUn 88.710 124 9 5 690 808 282923735 282923612 3.170000e-31 147.0
23 TraesCS4D01G133000 chrUn 88.710 124 9 5 690 808 343828100 343828223 3.170000e-31 147.0
24 TraesCS4D01G133000 chr6D 89.076 119 7 5 690 802 57855589 57855707 4.100000e-30 143.0
25 TraesCS4D01G133000 chr5B 79.397 199 41 0 3733 3931 288176222 288176420 1.470000e-29 141.0
26 TraesCS4D01G133000 chr5A 79.592 196 40 0 3742 3937 337943192 337942997 1.470000e-29 141.0
27 TraesCS4D01G133000 chr5A 84.615 104 16 0 1358 1461 338231758 338231655 1.940000e-18 104.0
28 TraesCS4D01G133000 chr3A 87.200 125 10 6 690 808 55574269 55574145 1.910000e-28 137.0
29 TraesCS4D01G133000 chr3A 87.200 125 10 6 690 808 55618038 55617914 1.910000e-28 137.0
30 TraesCS4D01G133000 chr5D 79.474 190 39 0 3742 3931 254588540 254588351 6.860000e-28 135.0
31 TraesCS4D01G133000 chr3B 86.400 125 12 4 691 810 780862826 780862950 8.880000e-27 132.0
32 TraesCS4D01G133000 chr2B 85.385 130 13 4 687 810 206726572 206726701 3.190000e-26 130.0
33 TraesCS4D01G133000 chr2B 89.552 67 6 1 99 164 12946865 12946931 2.520000e-12 84.2
34 TraesCS4D01G133000 chr2A 78.443 167 27 9 2 164 8717641 8717802 2.500000e-17 100.0
35 TraesCS4D01G133000 chr1B 77.711 166 33 4 2 166 688075627 688075789 9.000000e-17 99.0
36 TraesCS4D01G133000 chr7B 77.576 165 34 3 2 165 85135621 85135783 3.240000e-16 97.1
37 TraesCS4D01G133000 chr7B 77.576 165 34 3 2 165 724480978 724480816 3.240000e-16 97.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G133000 chr4D 119801570 119805506 3936 False 823.1 3522 98.2850 1 3937 10 chr4D.!!$F1 3936
1 TraesCS4D01G133000 chr4B 182256366 182260209 3843 False 888.4 1692 89.9810 1 3937 5 chr4B.!!$F1 3936
2 TraesCS4D01G133000 chr4A 450761461 450764800 3339 False 878.2 1485 91.3202 1 3937 5 chr4A.!!$F1 3936

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
809 833 0.462937 CTTGACACCAACACCCGTCA 60.463 55.0 0.0 0.0 36.63 4.35 F
815 839 0.467290 ACCAACACCCGTCAGCATTT 60.467 50.0 0.0 0.0 0.00 2.32 F
1213 1473 0.556380 TTCCTCCTCCTCCTCCTCCT 60.556 60.0 0.0 0.0 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2305 2765 0.456221 TAAGAGCAGCTACGGCAGAC 59.544 55.0 0.0 0.0 41.70 3.51 R
2558 3023 0.627451 AGCCAATTCAGCTCCCATCA 59.373 50.0 0.0 0.0 34.91 3.07 R
3066 3531 0.322546 AACACGCTCCCCTCCATTTC 60.323 55.0 0.0 0.0 0.00 2.17 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
97 98 6.081356 ACTAGCCCTTAAAGAGAGAGCATAT 58.919 40.000 0.00 0.00 0.00 1.78
154 156 9.023962 TCCTAAACTCATGACTAAAAATGCAAT 57.976 29.630 0.00 0.00 0.00 3.56
183 186 4.778534 AAAACTGGACTGCTCATTGATG 57.221 40.909 0.00 0.00 0.00 3.07
190 193 4.063689 GGACTGCTCATTGATGTATCTGG 58.936 47.826 0.00 0.00 0.00 3.86
268 271 3.365666 GCAATCTAATGCCACATGGATCG 60.366 47.826 0.87 0.00 40.49 3.69
276 279 4.241555 ACATGGATCGGCCGCTCC 62.242 66.667 35.54 35.54 40.66 4.70
298 302 2.088104 AGATCATCCGCCAGGTCTAA 57.912 50.000 0.00 0.00 39.05 2.10
323 327 1.203994 TCCGTAACTGCTAGTGCTTCC 59.796 52.381 0.00 0.00 40.48 3.46
324 328 1.641577 CGTAACTGCTAGTGCTTCCC 58.358 55.000 0.00 0.00 40.48 3.97
326 330 1.067071 GTAACTGCTAGTGCTTCCCGT 60.067 52.381 0.00 0.00 40.48 5.28
338 342 1.503818 CTTCCCGTGTTGTTGGGTCG 61.504 60.000 0.00 0.00 46.13 4.79
339 343 2.944409 TTCCCGTGTTGTTGGGTCGG 62.944 60.000 0.00 0.00 46.13 4.79
341 345 1.959226 CCGTGTTGTTGGGTCGGAG 60.959 63.158 0.00 0.00 43.22 4.63
373 378 7.872993 TCCGAAAATAATTACAAATGCACCAAA 59.127 29.630 0.00 0.00 0.00 3.28
397 402 2.475155 AGACCCAAGATGATCTCTGCA 58.525 47.619 0.00 0.00 33.29 4.41
418 423 4.680440 GCAACAACTCCAATTGAACCACTT 60.680 41.667 7.12 0.00 33.57 3.16
425 430 5.160607 TCCAATTGAACCACTTCTCGTAT 57.839 39.130 7.12 0.00 0.00 3.06
442 447 4.425520 TCGTATGTGTCGCATCAACATAA 58.574 39.130 1.19 0.00 38.94 1.90
453 458 6.901887 GTCGCATCAACATAAATCTTACACAG 59.098 38.462 0.00 0.00 0.00 3.66
468 473 6.591935 TCTTACACAGATTTTCAGAAGGTGT 58.408 36.000 0.00 0.00 40.65 4.16
496 501 8.982723 AGCTAATGATTTAGTCTTACTCTCCAA 58.017 33.333 0.00 0.00 37.68 3.53
525 537 0.899720 TTTGGTCTAACCGGAGCGAT 59.100 50.000 9.46 0.00 42.58 4.58
546 558 1.271926 ACTGGTGGTTGTATTGGAGGC 60.272 52.381 0.00 0.00 0.00 4.70
547 559 1.004745 CTGGTGGTTGTATTGGAGGCT 59.995 52.381 0.00 0.00 0.00 4.58
569 581 5.415701 GCTTTGTCCACAATCTAAAGATCCA 59.584 40.000 0.00 0.00 35.55 3.41
591 603 7.995289 TCCAATATAAATGCGTTGATGAAACT 58.005 30.769 0.00 0.00 36.56 2.66
655 668 0.687757 TCCTCCTTGCGCTCCATACT 60.688 55.000 9.73 0.00 0.00 2.12
681 705 6.155737 GTCCAACCTTCCTCCTAAACTATACA 59.844 42.308 0.00 0.00 0.00 2.29
685 709 5.071923 ACCTTCCTCCTAAACTATACATGCC 59.928 44.000 0.00 0.00 0.00 4.40
686 710 5.071788 CCTTCCTCCTAAACTATACATGCCA 59.928 44.000 0.00 0.00 0.00 4.92
688 712 7.038302 CCTTCCTCCTAAACTATACATGCCATA 60.038 40.741 0.00 0.00 0.00 2.74
692 716 9.520515 CCTCCTAAACTATACATGCCATATTTT 57.479 33.333 0.00 1.12 0.00 1.82
720 744 9.546428 TTTCATGATAATACGTGTCTCATTCAT 57.454 29.630 0.00 0.00 0.00 2.57
753 777 8.779354 AGATCAAAGTACAAGTCTTAATGACC 57.221 34.615 0.00 0.00 46.46 4.02
754 778 7.545965 AGATCAAAGTACAAGTCTTAATGACCG 59.454 37.037 0.00 0.00 46.46 4.79
755 779 6.751157 TCAAAGTACAAGTCTTAATGACCGA 58.249 36.000 0.00 0.00 46.46 4.69
756 780 6.643770 TCAAAGTACAAGTCTTAATGACCGAC 59.356 38.462 0.00 0.00 46.46 4.79
757 781 5.717078 AGTACAAGTCTTAATGACCGACA 57.283 39.130 0.00 0.00 46.46 4.35
758 782 6.282199 AGTACAAGTCTTAATGACCGACAT 57.718 37.500 0.00 0.00 46.46 3.06
759 783 6.100004 AGTACAAGTCTTAATGACCGACATG 58.900 40.000 0.00 0.00 46.46 3.21
760 784 5.147330 ACAAGTCTTAATGACCGACATGA 57.853 39.130 0.00 0.00 46.46 3.07
763 787 5.147330 AGTCTTAATGACCGACATGACAA 57.853 39.130 0.00 0.00 46.46 3.18
764 788 5.547465 AGTCTTAATGACCGACATGACAAA 58.453 37.500 0.00 0.00 46.46 2.83
765 789 5.995282 AGTCTTAATGACCGACATGACAAAA 59.005 36.000 0.00 0.00 46.46 2.44
766 790 6.073222 AGTCTTAATGACCGACATGACAAAAC 60.073 38.462 0.00 0.00 46.46 2.43
767 791 5.995282 TCTTAATGACCGACATGACAAAACT 59.005 36.000 0.00 0.00 39.39 2.66
768 792 7.117236 GTCTTAATGACCGACATGACAAAACTA 59.883 37.037 0.00 0.00 39.69 2.24
769 793 7.658167 TCTTAATGACCGACATGACAAAACTAA 59.342 33.333 0.00 0.00 39.39 2.24
770 794 6.627395 AATGACCGACATGACAAAACTAAA 57.373 33.333 0.00 0.00 39.39 1.85
771 795 6.627395 ATGACCGACATGACAAAACTAAAA 57.373 33.333 0.00 0.00 37.87 1.52
774 798 8.155821 TGACCGACATGACAAAACTAAAATAA 57.844 30.769 0.00 0.00 0.00 1.40
775 799 8.071368 TGACCGACATGACAAAACTAAAATAAC 58.929 33.333 0.00 0.00 0.00 1.89
776 800 7.073265 ACCGACATGACAAAACTAAAATAACG 58.927 34.615 0.00 0.00 0.00 3.18
777 801 7.041916 ACCGACATGACAAAACTAAAATAACGA 60.042 33.333 0.00 0.00 0.00 3.85
779 803 9.160576 CGACATGACAAAACTAAAATAACGAAA 57.839 29.630 0.00 0.00 0.00 3.46
781 805 9.790389 ACATGACAAAACTAAAATAACGAAACA 57.210 25.926 0.00 0.00 0.00 2.83
791 815 9.654663 ACTAAAATAACGAAACATCTCTAAGCT 57.345 29.630 0.00 0.00 0.00 3.74
794 818 8.547967 AAATAACGAAACATCTCTAAGCTTGA 57.452 30.769 9.86 3.84 0.00 3.02
795 819 5.847670 AACGAAACATCTCTAAGCTTGAC 57.152 39.130 9.86 0.00 0.00 3.18
796 820 4.883083 ACGAAACATCTCTAAGCTTGACA 58.117 39.130 9.86 0.00 0.00 3.58
797 821 4.686554 ACGAAACATCTCTAAGCTTGACAC 59.313 41.667 9.86 0.00 0.00 3.67
798 822 4.092091 CGAAACATCTCTAAGCTTGACACC 59.908 45.833 9.86 0.00 0.00 4.16
799 823 4.623932 AACATCTCTAAGCTTGACACCA 57.376 40.909 9.86 0.00 0.00 4.17
801 825 4.319177 ACATCTCTAAGCTTGACACCAAC 58.681 43.478 9.86 0.00 0.00 3.77
802 826 4.202357 ACATCTCTAAGCTTGACACCAACA 60.202 41.667 9.86 0.00 0.00 3.33
803 827 3.728845 TCTCTAAGCTTGACACCAACAC 58.271 45.455 9.86 0.00 0.00 3.32
805 829 1.880027 CTAAGCTTGACACCAACACCC 59.120 52.381 9.86 0.00 0.00 4.61
806 830 1.101049 AAGCTTGACACCAACACCCG 61.101 55.000 0.00 0.00 0.00 5.28
807 831 1.822186 GCTTGACACCAACACCCGT 60.822 57.895 0.00 0.00 0.00 5.28
808 832 1.782028 GCTTGACACCAACACCCGTC 61.782 60.000 0.00 0.00 0.00 4.79
809 833 0.462937 CTTGACACCAACACCCGTCA 60.463 55.000 0.00 0.00 36.63 4.35
810 834 0.462937 TTGACACCAACACCCGTCAG 60.463 55.000 0.00 0.00 39.39 3.51
811 835 2.203153 ACACCAACACCCGTCAGC 60.203 61.111 0.00 0.00 0.00 4.26
812 836 2.203139 CACCAACACCCGTCAGCA 60.203 61.111 0.00 0.00 0.00 4.41
814 838 1.150536 ACCAACACCCGTCAGCATT 59.849 52.632 0.00 0.00 0.00 3.56
815 839 0.467290 ACCAACACCCGTCAGCATTT 60.467 50.000 0.00 0.00 0.00 2.32
816 840 0.673437 CCAACACCCGTCAGCATTTT 59.327 50.000 0.00 0.00 0.00 1.82
817 841 1.335872 CCAACACCCGTCAGCATTTTC 60.336 52.381 0.00 0.00 0.00 2.29
818 842 0.591170 AACACCCGTCAGCATTTTCG 59.409 50.000 0.00 0.00 0.00 3.46
821 845 3.187058 CCGTCAGCATTTTCGGGG 58.813 61.111 0.00 0.00 39.41 5.73
823 847 1.501741 CGTCAGCATTTTCGGGGTG 59.498 57.895 0.00 0.00 0.00 4.61
824 848 0.953471 CGTCAGCATTTTCGGGGTGA 60.953 55.000 0.00 0.00 39.03 4.02
825 849 1.463674 GTCAGCATTTTCGGGGTGAT 58.536 50.000 0.00 0.00 42.67 3.06
826 850 1.818674 GTCAGCATTTTCGGGGTGATT 59.181 47.619 0.00 0.00 42.67 2.57
827 851 2.091541 TCAGCATTTTCGGGGTGATTC 58.908 47.619 0.00 0.00 36.68 2.52
828 852 1.818060 CAGCATTTTCGGGGTGATTCA 59.182 47.619 0.00 0.00 34.58 2.57
829 853 2.428171 CAGCATTTTCGGGGTGATTCAT 59.572 45.455 0.00 0.00 34.58 2.57
830 854 3.099141 AGCATTTTCGGGGTGATTCATT 58.901 40.909 0.00 0.00 0.00 2.57
831 855 3.131046 AGCATTTTCGGGGTGATTCATTC 59.869 43.478 0.00 0.00 0.00 2.67
833 857 4.675510 CATTTTCGGGGTGATTCATTCAG 58.324 43.478 0.00 0.00 34.17 3.02
834 858 2.418368 TTCGGGGTGATTCATTCAGG 57.582 50.000 0.00 0.00 34.17 3.86
853 1111 2.946947 CTGAACAATCGGCCCAACT 58.053 52.632 0.00 0.00 0.00 3.16
874 1132 2.193536 GCCCGCCACAAACTTCACT 61.194 57.895 0.00 0.00 0.00 3.41
875 1133 1.734388 GCCCGCCACAAACTTCACTT 61.734 55.000 0.00 0.00 0.00 3.16
996 1256 1.589196 GCGAATCTCGAGGGTTCGG 60.589 63.158 33.67 23.46 46.67 4.30
1191 1451 2.606519 AGCCTCCCGCAACAGGTA 60.607 61.111 0.00 0.00 41.38 3.08
1195 1455 1.202770 GCCTCCCGCAACAGGTATATT 60.203 52.381 0.00 0.00 37.47 1.28
1196 1456 2.767505 CCTCCCGCAACAGGTATATTC 58.232 52.381 0.00 0.00 0.00 1.75
1197 1457 2.550208 CCTCCCGCAACAGGTATATTCC 60.550 54.545 0.00 0.00 0.00 3.01
1213 1473 0.556380 TTCCTCCTCCTCCTCCTCCT 60.556 60.000 0.00 0.00 0.00 3.69
1216 1476 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
1280 1540 1.227999 TGCCAGCGAGCAAAGTACAC 61.228 55.000 0.83 0.00 40.56 2.90
1293 1553 1.185618 AGTACACTGCCAGCCTCGAA 61.186 55.000 0.00 0.00 0.00 3.71
1335 1601 1.810755 CTCTCGTGTGTAGCACAGGTA 59.189 52.381 17.60 9.39 45.43 3.08
1555 1982 2.163818 TGCTGTCCCTAACAAACTCG 57.836 50.000 0.00 0.00 37.45 4.18
1557 1984 1.876416 GCTGTCCCTAACAAACTCGCA 60.876 52.381 0.00 0.00 37.45 5.10
1610 2038 2.661675 CGTAGGTAATTCATCATCCGCG 59.338 50.000 0.00 0.00 0.00 6.46
1733 2184 3.452474 GCTGTTAGCTACCATCTGTCAG 58.548 50.000 0.00 0.00 38.45 3.51
1741 2192 0.612229 ACCATCTGTCAGTGCTGAGG 59.388 55.000 1.65 2.88 40.75 3.86
1755 2207 7.934120 GTCAGTGCTGAGGGTTATTTATCTTAT 59.066 37.037 1.65 0.00 40.75 1.73
1771 2223 2.305635 TCTTATGCCTTCAGAGCAACCA 59.694 45.455 0.00 0.00 44.83 3.67
1784 2236 3.259625 AGAGCAACCACTAACTTCTCTCC 59.740 47.826 0.00 0.00 0.00 3.71
1891 2343 5.289595 CAGCGCTACTCCATTAACTATGAA 58.710 41.667 10.99 0.00 36.26 2.57
2200 2652 4.054085 CCTGGCTCACACACACAG 57.946 61.111 0.00 0.00 0.00 3.66
2208 2660 1.064505 CTCACACACACAGGCACTTTG 59.935 52.381 0.00 0.00 42.66 2.77
2296 2756 4.518970 GGAACTGCAGAGGTTGTATTTTCA 59.481 41.667 23.35 0.00 0.00 2.69
2305 2765 5.352569 AGAGGTTGTATTTTCAGCAAGATCG 59.647 40.000 0.00 0.00 0.00 3.69
2615 3080 8.939929 CAGCCATAGGTAGTTATCATTATGTTG 58.060 37.037 0.00 0.00 0.00 3.33
2797 3262 4.322385 GTTTGGTGGTCGTGGCGC 62.322 66.667 0.00 0.00 0.00 6.53
3023 3488 9.091784 CTGACCTATATTAATTGGATGACGATG 57.908 37.037 0.00 0.00 32.84 3.84
3066 3531 2.092212 AGAAGGTAGCATTGGGTGATGG 60.092 50.000 0.00 0.00 0.00 3.51
3081 3546 0.536006 GATGGAAATGGAGGGGAGCG 60.536 60.000 0.00 0.00 0.00 5.03
3091 3556 1.507141 GAGGGGAGCGTGTTTGTGTG 61.507 60.000 0.00 0.00 0.00 3.82
3124 3589 0.025001 CCTTCATTTGCGACGTAGCG 59.975 55.000 15.98 4.09 40.67 4.26
3146 3611 2.640332 GGAGGGAGGGAATTGGTCTATC 59.360 54.545 0.00 0.00 0.00 2.08
3208 3674 3.243704 TGTTTGGCTGGTTTATGTCTTGC 60.244 43.478 0.00 0.00 0.00 4.01
3209 3675 2.284754 TGGCTGGTTTATGTCTTGCA 57.715 45.000 0.00 0.00 0.00 4.08
3210 3676 1.885887 TGGCTGGTTTATGTCTTGCAC 59.114 47.619 0.00 0.00 0.00 4.57
3211 3677 2.162681 GGCTGGTTTATGTCTTGCACT 58.837 47.619 0.00 0.00 0.00 4.40
3212 3678 2.162408 GGCTGGTTTATGTCTTGCACTC 59.838 50.000 0.00 0.00 0.00 3.51
3213 3679 3.077359 GCTGGTTTATGTCTTGCACTCT 58.923 45.455 0.00 0.00 0.00 3.24
3214 3680 3.503748 GCTGGTTTATGTCTTGCACTCTT 59.496 43.478 0.00 0.00 0.00 2.85
3215 3681 4.614535 GCTGGTTTATGTCTTGCACTCTTG 60.615 45.833 0.00 0.00 0.00 3.02
3256 3722 0.743688 TTTGTGGCATGTTGCTTCGT 59.256 45.000 0.00 0.00 44.28 3.85
3308 3777 2.409948 GCTGTAGCCTTTGGTGATCT 57.590 50.000 0.00 0.00 34.31 2.75
3309 3778 2.284190 GCTGTAGCCTTTGGTGATCTC 58.716 52.381 0.00 0.00 34.31 2.75
3310 3779 2.911484 CTGTAGCCTTTGGTGATCTCC 58.089 52.381 6.88 6.88 0.00 3.71
3311 3780 2.237143 CTGTAGCCTTTGGTGATCTCCA 59.763 50.000 12.50 12.50 35.49 3.86
3312 3781 2.027192 TGTAGCCTTTGGTGATCTCCAC 60.027 50.000 16.01 5.14 44.95 4.02
3347 3816 2.409948 GCTGTAGCCTTTGGTGATCT 57.590 50.000 0.00 0.00 34.31 2.75
3348 3817 2.284190 GCTGTAGCCTTTGGTGATCTC 58.716 52.381 0.00 0.00 34.31 2.75
3349 3818 2.911484 CTGTAGCCTTTGGTGATCTCC 58.089 52.381 6.88 6.88 0.00 3.71
3350 3819 2.237143 CTGTAGCCTTTGGTGATCTCCA 59.763 50.000 12.50 12.50 35.49 3.86
3351 3820 2.027192 TGTAGCCTTTGGTGATCTCCAC 60.027 50.000 16.01 5.14 44.95 4.02
3385 3854 4.637771 GCCGTAGCCTTTGGTGAT 57.362 55.556 0.00 0.00 0.00 3.06
3386 3855 2.394604 GCCGTAGCCTTTGGTGATC 58.605 57.895 0.00 0.00 0.00 2.92
3387 3856 0.107654 GCCGTAGCCTTTGGTGATCT 60.108 55.000 0.00 0.00 0.00 2.75
3388 3857 1.941325 CCGTAGCCTTTGGTGATCTC 58.059 55.000 0.00 0.00 0.00 2.75
3389 3858 1.473434 CCGTAGCCTTTGGTGATCTCC 60.473 57.143 6.88 6.88 0.00 3.71
3390 3859 1.207089 CGTAGCCTTTGGTGATCTCCA 59.793 52.381 12.50 12.50 35.49 3.86
3391 3860 2.633488 GTAGCCTTTGGTGATCTCCAC 58.367 52.381 16.01 5.14 44.95 4.02
3406 3875 3.081554 CACCAGGGAAGTGGGGAG 58.918 66.667 0.00 0.00 44.81 4.30
3407 3876 2.204151 ACCAGGGAAGTGGGGAGG 60.204 66.667 0.00 0.00 42.54 4.30
3408 3877 3.732849 CCAGGGAAGTGGGGAGGC 61.733 72.222 0.00 0.00 33.46 4.70
3409 3878 2.612115 CAGGGAAGTGGGGAGGCT 60.612 66.667 0.00 0.00 0.00 4.58
3410 3879 2.612115 AGGGAAGTGGGGAGGCTG 60.612 66.667 0.00 0.00 0.00 4.85
3411 3880 2.936032 GGGAAGTGGGGAGGCTGT 60.936 66.667 0.00 0.00 0.00 4.40
3412 3881 1.615424 GGGAAGTGGGGAGGCTGTA 60.615 63.158 0.00 0.00 0.00 2.74
3413 3882 1.627297 GGGAAGTGGGGAGGCTGTAG 61.627 65.000 0.00 0.00 0.00 2.74
3414 3883 1.222113 GAAGTGGGGAGGCTGTAGC 59.778 63.158 0.00 0.00 41.14 3.58
3426 3895 2.409948 GCTGTAGCCTTTGGTGATCT 57.590 50.000 0.00 0.00 34.31 2.75
3427 3896 2.284190 GCTGTAGCCTTTGGTGATCTC 58.716 52.381 0.00 0.00 34.31 2.75
3428 3897 2.911484 CTGTAGCCTTTGGTGATCTCC 58.089 52.381 6.88 6.88 0.00 3.71
3429 3898 2.237143 CTGTAGCCTTTGGTGATCTCCA 59.763 50.000 12.50 12.50 35.49 3.86
3430 3899 2.027192 TGTAGCCTTTGGTGATCTCCAC 60.027 50.000 16.01 5.14 44.95 4.02
3517 3988 4.142730 GGCAATGCTGAGAAACTAGAGTTG 60.143 45.833 4.82 0.00 38.44 3.16
3600 4082 6.885952 AGTATGTATAGCTGGAGTGTACAG 57.114 41.667 0.00 0.00 38.95 2.74
3633 4115 6.609237 ATTAATGTTCATGGATCACTGTCG 57.391 37.500 0.00 0.00 0.00 4.35
3682 4169 2.887152 GTTCTATGGATGATGGGTTGCC 59.113 50.000 0.00 0.00 0.00 4.52
3706 4193 3.063084 GAGGCGTCAGTCGTCCCT 61.063 66.667 0.52 0.00 46.16 4.20
3707 4194 3.053849 GAGGCGTCAGTCGTCCCTC 62.054 68.421 0.52 0.00 46.16 4.30
3708 4195 3.063084 GGCGTCAGTCGTCCCTCT 61.063 66.667 0.00 0.00 42.13 3.69
3709 4196 2.486042 GCGTCAGTCGTCCCTCTC 59.514 66.667 0.00 0.00 42.13 3.20
3710 4197 2.785921 CGTCAGTCGTCCCTCTCG 59.214 66.667 0.00 0.00 34.52 4.04
3711 4198 2.751913 CGTCAGTCGTCCCTCTCGG 61.752 68.421 0.00 0.00 34.52 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 9.653287 TCATTCTCTTGTAAAAGTTATGACGAT 57.347 29.630 0.00 0.00 0.00 3.73
30 31 4.631813 AGCACGGTGATCTTACTTTCATTC 59.368 41.667 13.29 0.00 0.00 2.67
31 32 4.393062 CAGCACGGTGATCTTACTTTCATT 59.607 41.667 13.29 0.00 0.00 2.57
97 98 2.415168 CGAGGCTCACAATTTAGCGAAA 59.585 45.455 15.95 0.00 39.71 3.46
183 186 8.361139 ACAGTCTATTGTGCTATTACCAGATAC 58.639 37.037 0.00 0.00 0.00 2.24
190 193 5.728255 CGCAACAGTCTATTGTGCTATTAC 58.272 41.667 0.00 0.00 31.37 1.89
268 271 0.107945 GGATGATCTATGGAGCGGCC 60.108 60.000 0.00 0.00 37.10 6.13
276 279 1.898472 AGACCTGGCGGATGATCTATG 59.102 52.381 0.00 0.00 0.00 2.23
298 302 2.612221 GCACTAGCAGTTACGGAGGTTT 60.612 50.000 0.00 0.00 41.58 3.27
304 308 1.641577 GGAAGCACTAGCAGTTACGG 58.358 55.000 0.00 0.00 45.49 4.02
323 327 1.959226 CTCCGACCCAACAACACGG 60.959 63.158 0.00 0.00 44.09 4.94
324 328 0.320421 ATCTCCGACCCAACAACACG 60.320 55.000 0.00 0.00 0.00 4.49
326 330 0.323629 GGATCTCCGACCCAACAACA 59.676 55.000 0.00 0.00 0.00 3.33
339 343 8.446599 TTTGTAATTATTTTCGGAGGGATCTC 57.553 34.615 0.00 0.00 39.25 2.75
341 345 7.595130 GCATTTGTAATTATTTTCGGAGGGATC 59.405 37.037 0.00 0.00 0.00 3.36
373 378 5.131642 TGCAGAGATCATCTTGGGTCTTATT 59.868 40.000 0.00 0.00 35.47 1.40
397 402 4.956075 AGAAGTGGTTCAATTGGAGTTGTT 59.044 37.500 5.42 0.00 34.82 2.83
418 423 2.094957 TGTTGATGCGACACATACGAGA 60.095 45.455 0.00 0.00 39.84 4.04
425 430 5.878332 AAGATTTATGTTGATGCGACACA 57.122 34.783 0.00 0.00 29.85 3.72
453 458 8.268850 TCATTAGCTTACACCTTCTGAAAATC 57.731 34.615 0.00 0.00 0.00 2.17
463 468 9.819267 GTAAGACTAAATCATTAGCTTACACCT 57.181 33.333 21.62 0.00 44.80 4.00
517 529 0.806102 CAACCACCAGTATCGCTCCG 60.806 60.000 0.00 0.00 0.00 4.63
525 537 2.026636 GCCTCCAATACAACCACCAGTA 60.027 50.000 0.00 0.00 0.00 2.74
531 543 3.153919 GACAAAGCCTCCAATACAACCA 58.846 45.455 0.00 0.00 0.00 3.67
546 558 7.452880 TTGGATCTTTAGATTGTGGACAAAG 57.547 36.000 0.00 0.00 39.55 2.77
547 559 9.699410 ATATTGGATCTTTAGATTGTGGACAAA 57.301 29.630 0.00 0.00 39.55 2.83
591 603 3.717392 TCAAACCCCGATATCCACCAATA 59.283 43.478 0.00 0.00 0.00 1.90
655 668 3.323775 AGTTTAGGAGGAAGGTTGGACA 58.676 45.455 0.00 0.00 0.00 4.02
693 717 9.377312 TGAATGAGACACGTATTATCATGAAAA 57.623 29.630 0.00 0.00 31.24 2.29
727 751 9.220767 GGTCATTAAGACTTGTACTTTGATCTT 57.779 33.333 0.00 0.00 46.72 2.40
728 752 7.545965 CGGTCATTAAGACTTGTACTTTGATCT 59.454 37.037 0.00 0.00 46.72 2.75
729 753 7.544566 TCGGTCATTAAGACTTGTACTTTGATC 59.455 37.037 0.00 0.00 46.72 2.92
731 755 6.643770 GTCGGTCATTAAGACTTGTACTTTGA 59.356 38.462 0.00 0.00 46.72 2.69
732 756 6.422701 TGTCGGTCATTAAGACTTGTACTTTG 59.577 38.462 0.00 0.00 46.72 2.77
734 758 6.092955 TGTCGGTCATTAAGACTTGTACTT 57.907 37.500 0.00 0.00 46.72 2.24
735 759 5.717078 TGTCGGTCATTAAGACTTGTACT 57.283 39.130 0.00 0.00 46.72 2.73
736 760 6.034683 GTCATGTCGGTCATTAAGACTTGTAC 59.965 42.308 0.00 0.00 46.72 2.90
738 762 4.929808 GTCATGTCGGTCATTAAGACTTGT 59.070 41.667 0.00 0.00 46.72 3.16
740 764 5.147330 TGTCATGTCGGTCATTAAGACTT 57.853 39.130 0.00 0.00 46.72 3.01
741 765 4.801330 TGTCATGTCGGTCATTAAGACT 57.199 40.909 0.00 0.00 46.72 3.24
743 767 5.995282 AGTTTTGTCATGTCGGTCATTAAGA 59.005 36.000 0.00 0.00 34.09 2.10
744 768 6.241207 AGTTTTGTCATGTCGGTCATTAAG 57.759 37.500 0.00 0.00 34.09 1.85
745 769 7.731882 TTAGTTTTGTCATGTCGGTCATTAA 57.268 32.000 0.00 0.00 34.09 1.40
746 770 7.731882 TTTAGTTTTGTCATGTCGGTCATTA 57.268 32.000 0.00 0.00 34.09 1.90
747 771 6.627395 TTTAGTTTTGTCATGTCGGTCATT 57.373 33.333 0.00 0.00 34.09 2.57
750 774 7.267600 CGTTATTTTAGTTTTGTCATGTCGGTC 59.732 37.037 0.00 0.00 0.00 4.79
751 775 7.041916 TCGTTATTTTAGTTTTGTCATGTCGGT 60.042 33.333 0.00 0.00 0.00 4.69
753 777 8.702408 TTCGTTATTTTAGTTTTGTCATGTCG 57.298 30.769 0.00 0.00 0.00 4.35
755 779 9.790389 TGTTTCGTTATTTTAGTTTTGTCATGT 57.210 25.926 0.00 0.00 0.00 3.21
765 789 9.654663 AGCTTAGAGATGTTTCGTTATTTTAGT 57.345 29.630 0.00 0.00 0.00 2.24
768 792 8.999431 TCAAGCTTAGAGATGTTTCGTTATTTT 58.001 29.630 0.00 0.00 0.00 1.82
769 793 8.443937 GTCAAGCTTAGAGATGTTTCGTTATTT 58.556 33.333 0.00 0.00 0.00 1.40
770 794 7.602644 TGTCAAGCTTAGAGATGTTTCGTTATT 59.397 33.333 0.00 0.00 0.00 1.40
771 795 7.063544 GTGTCAAGCTTAGAGATGTTTCGTTAT 59.936 37.037 0.00 0.00 0.00 1.89
774 798 4.686554 GTGTCAAGCTTAGAGATGTTTCGT 59.313 41.667 0.00 0.00 0.00 3.85
775 799 4.092091 GGTGTCAAGCTTAGAGATGTTTCG 59.908 45.833 0.00 0.00 0.00 3.46
776 800 4.997395 TGGTGTCAAGCTTAGAGATGTTTC 59.003 41.667 0.00 0.00 0.00 2.78
777 801 4.973168 TGGTGTCAAGCTTAGAGATGTTT 58.027 39.130 0.00 0.00 0.00 2.83
779 803 4.202357 TGTTGGTGTCAAGCTTAGAGATGT 60.202 41.667 0.00 0.00 32.92 3.06
780 804 4.153117 GTGTTGGTGTCAAGCTTAGAGATG 59.847 45.833 0.00 0.00 32.92 2.90
781 805 4.319177 GTGTTGGTGTCAAGCTTAGAGAT 58.681 43.478 0.00 0.00 32.92 2.75
782 806 3.494398 GGTGTTGGTGTCAAGCTTAGAGA 60.494 47.826 0.00 0.00 32.92 3.10
783 807 2.808543 GGTGTTGGTGTCAAGCTTAGAG 59.191 50.000 0.00 0.00 32.92 2.43
784 808 2.486548 GGGTGTTGGTGTCAAGCTTAGA 60.487 50.000 0.00 0.00 32.92 2.10
786 810 1.812324 CGGGTGTTGGTGTCAAGCTTA 60.812 52.381 0.00 0.00 32.92 3.09
787 811 1.101049 CGGGTGTTGGTGTCAAGCTT 61.101 55.000 0.00 0.00 32.92 3.74
789 813 1.782028 GACGGGTGTTGGTGTCAAGC 61.782 60.000 0.00 0.00 32.92 4.01
790 814 0.462937 TGACGGGTGTTGGTGTCAAG 60.463 55.000 0.00 0.00 38.32 3.02
791 815 0.462937 CTGACGGGTGTTGGTGTCAA 60.463 55.000 0.00 0.00 40.50 3.18
793 817 2.251642 GCTGACGGGTGTTGGTGTC 61.252 63.158 0.00 0.00 0.00 3.67
794 818 2.203153 GCTGACGGGTGTTGGTGT 60.203 61.111 0.00 0.00 0.00 4.16
795 819 1.172180 AATGCTGACGGGTGTTGGTG 61.172 55.000 0.00 0.00 0.00 4.17
796 820 0.467290 AAATGCTGACGGGTGTTGGT 60.467 50.000 0.00 0.00 0.00 3.67
797 821 0.673437 AAAATGCTGACGGGTGTTGG 59.327 50.000 0.00 0.00 0.00 3.77
798 822 1.662876 CGAAAATGCTGACGGGTGTTG 60.663 52.381 0.00 0.00 0.00 3.33
799 823 0.591170 CGAAAATGCTGACGGGTGTT 59.409 50.000 0.00 0.00 0.00 3.32
801 825 1.501741 CCGAAAATGCTGACGGGTG 59.498 57.895 0.00 0.00 41.41 4.61
802 826 3.981308 CCGAAAATGCTGACGGGT 58.019 55.556 0.00 0.00 41.41 5.28
805 829 0.953471 TCACCCCGAAAATGCTGACG 60.953 55.000 0.00 0.00 0.00 4.35
806 830 1.463674 ATCACCCCGAAAATGCTGAC 58.536 50.000 0.00 0.00 0.00 3.51
807 831 2.091541 GAATCACCCCGAAAATGCTGA 58.908 47.619 0.00 0.00 0.00 4.26
808 832 1.818060 TGAATCACCCCGAAAATGCTG 59.182 47.619 0.00 0.00 0.00 4.41
809 833 2.214376 TGAATCACCCCGAAAATGCT 57.786 45.000 0.00 0.00 0.00 3.79
810 834 3.119173 TGAATGAATCACCCCGAAAATGC 60.119 43.478 0.00 0.00 31.50 3.56
811 835 4.440525 CCTGAATGAATCACCCCGAAAATG 60.441 45.833 0.00 0.00 33.47 2.32
812 836 3.701040 CCTGAATGAATCACCCCGAAAAT 59.299 43.478 0.00 0.00 33.47 1.82
814 838 2.722094 CCTGAATGAATCACCCCGAAA 58.278 47.619 0.00 0.00 33.47 3.46
815 839 1.681780 GCCTGAATGAATCACCCCGAA 60.682 52.381 0.00 0.00 33.47 4.30
816 840 0.107214 GCCTGAATGAATCACCCCGA 60.107 55.000 0.00 0.00 33.47 5.14
817 841 0.107017 AGCCTGAATGAATCACCCCG 60.107 55.000 0.00 0.00 33.47 5.73
818 842 1.064463 TCAGCCTGAATGAATCACCCC 60.064 52.381 0.00 0.00 33.47 4.95
820 844 3.084039 TGTTCAGCCTGAATGAATCACC 58.916 45.455 10.87 0.00 38.79 4.02
821 845 4.771590 TTGTTCAGCCTGAATGAATCAC 57.228 40.909 10.87 0.00 38.79 3.06
823 847 4.497006 CCGATTGTTCAGCCTGAATGAATC 60.497 45.833 21.22 21.22 38.79 2.52
824 848 3.379372 CCGATTGTTCAGCCTGAATGAAT 59.621 43.478 10.87 11.64 38.79 2.57
825 849 2.749076 CCGATTGTTCAGCCTGAATGAA 59.251 45.455 10.87 7.31 38.79 2.57
826 850 2.358957 CCGATTGTTCAGCCTGAATGA 58.641 47.619 10.87 2.88 38.79 2.57
827 851 1.202222 GCCGATTGTTCAGCCTGAATG 60.202 52.381 10.87 0.00 38.79 2.67
828 852 1.098050 GCCGATTGTTCAGCCTGAAT 58.902 50.000 10.87 0.00 38.79 2.57
829 853 0.960364 GGCCGATTGTTCAGCCTGAA 60.960 55.000 2.24 2.24 41.49 3.02
830 854 1.377202 GGCCGATTGTTCAGCCTGA 60.377 57.895 0.00 0.00 41.49 3.86
831 855 2.409870 GGGCCGATTGTTCAGCCTG 61.410 63.158 0.00 0.00 43.79 4.85
833 857 1.976474 TTGGGCCGATTGTTCAGCC 60.976 57.895 0.00 0.00 43.61 4.85
834 858 1.212751 GTTGGGCCGATTGTTCAGC 59.787 57.895 0.00 0.00 0.00 4.26
853 1111 1.896660 GAAGTTTGTGGCGGGCTGA 60.897 57.895 0.00 0.00 0.00 4.26
861 1119 5.819901 AGAGAGAGAAAAGTGAAGTTTGTGG 59.180 40.000 0.00 0.00 0.00 4.17
874 1132 6.352222 GGAGAGAGAGAGAGAGAGAGAGAAAA 60.352 46.154 0.00 0.00 0.00 2.29
875 1133 5.129485 GGAGAGAGAGAGAGAGAGAGAGAAA 59.871 48.000 0.00 0.00 0.00 2.52
986 1246 4.856801 CCATGCCCCGAACCCTCG 62.857 72.222 0.00 0.00 45.02 4.63
1191 1451 2.385417 GGAGGAGGAGGAGGAGGAATAT 59.615 54.545 0.00 0.00 0.00 1.28
1195 1455 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
1196 1456 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
1197 1457 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
1213 1473 5.017490 ACTTAATCACGAGGAAGAAGAGGA 58.983 41.667 0.00 0.00 0.00 3.71
1216 1476 6.183360 CGTCTACTTAATCACGAGGAAGAAGA 60.183 42.308 0.00 0.00 34.06 2.87
1280 1540 1.739562 GTGAGTTCGAGGCTGGCAG 60.740 63.158 10.94 10.94 0.00 4.85
1293 1553 6.269769 AGAGAGGAAAGAAGATTTGAGTGAGT 59.730 38.462 0.00 0.00 0.00 3.41
1555 1982 8.239314 TGAAATCTCTTGAGTTGAATGTATTGC 58.761 33.333 0.00 0.00 30.06 3.56
1623 2070 7.009999 GTGTCAGTGAAGAATGTAAGCTATCAG 59.990 40.741 0.00 0.00 0.00 2.90
1625 2072 6.813649 TGTGTCAGTGAAGAATGTAAGCTATC 59.186 38.462 0.00 0.00 0.00 2.08
1628 2075 4.960938 TGTGTCAGTGAAGAATGTAAGCT 58.039 39.130 0.00 0.00 0.00 3.74
1633 2080 5.335426 GCATGATTGTGTCAGTGAAGAATGT 60.335 40.000 0.00 0.00 40.92 2.71
1725 2176 1.356124 AACCCTCAGCACTGACAGAT 58.644 50.000 10.08 0.00 35.46 2.90
1727 2178 3.340814 AATAACCCTCAGCACTGACAG 57.659 47.619 0.00 0.00 35.46 3.51
1728 2179 3.788227 AAATAACCCTCAGCACTGACA 57.212 42.857 0.00 0.00 35.46 3.58
1733 2184 6.072452 GGCATAAGATAAATAACCCTCAGCAC 60.072 42.308 0.00 0.00 0.00 4.40
1741 2192 7.445402 TGCTCTGAAGGCATAAGATAAATAACC 59.555 37.037 0.00 0.00 34.56 2.85
1755 2207 1.055849 TAGTGGTTGCTCTGAAGGCA 58.944 50.000 0.00 0.00 37.97 4.75
2183 2635 1.598962 CCTGTGTGTGTGAGCCAGG 60.599 63.158 0.00 0.00 37.00 4.45
2184 2636 2.256591 GCCTGTGTGTGTGAGCCAG 61.257 63.158 0.00 0.00 0.00 4.85
2185 2637 2.203195 GCCTGTGTGTGTGAGCCA 60.203 61.111 0.00 0.00 0.00 4.75
2186 2638 2.203195 TGCCTGTGTGTGTGAGCC 60.203 61.111 0.00 0.00 0.00 4.70
2187 2639 1.097547 AAGTGCCTGTGTGTGTGAGC 61.098 55.000 0.00 0.00 0.00 4.26
2188 2640 1.064505 CAAAGTGCCTGTGTGTGTGAG 59.935 52.381 0.00 0.00 0.00 3.51
2189 2641 1.093972 CAAAGTGCCTGTGTGTGTGA 58.906 50.000 0.00 0.00 0.00 3.58
2190 2642 0.810648 ACAAAGTGCCTGTGTGTGTG 59.189 50.000 0.00 0.00 29.74 3.82
2191 2643 1.472480 GAACAAAGTGCCTGTGTGTGT 59.528 47.619 0.00 0.00 31.55 3.72
2192 2644 1.472082 TGAACAAAGTGCCTGTGTGTG 59.528 47.619 0.00 0.00 31.55 3.82
2193 2645 1.472480 GTGAACAAAGTGCCTGTGTGT 59.528 47.619 0.00 0.00 31.55 3.72
2194 2646 1.202290 GGTGAACAAAGTGCCTGTGTG 60.202 52.381 0.00 0.00 31.55 3.82
2195 2647 1.102978 GGTGAACAAAGTGCCTGTGT 58.897 50.000 0.00 0.00 32.64 3.72
2200 2652 4.584327 AATACAAGGTGAACAAAGTGCC 57.416 40.909 0.00 0.00 0.00 5.01
2208 2660 7.494298 ACCATTCAAACAAAATACAAGGTGAAC 59.506 33.333 0.00 0.00 0.00 3.18
2305 2765 0.456221 TAAGAGCAGCTACGGCAGAC 59.544 55.000 0.00 0.00 41.70 3.51
2558 3023 0.627451 AGCCAATTCAGCTCCCATCA 59.373 50.000 0.00 0.00 34.91 3.07
2615 3080 8.181573 TCTTGATTTATACGGCAATGAAGTTTC 58.818 33.333 0.00 0.00 28.91 2.78
2774 3239 2.975799 CGACCACCAAACCCACCG 60.976 66.667 0.00 0.00 0.00 4.94
2797 3262 2.032071 GACCACCGAACCCACCTG 59.968 66.667 0.00 0.00 0.00 4.00
3066 3531 0.322546 AACACGCTCCCCTCCATTTC 60.323 55.000 0.00 0.00 0.00 2.17
3081 3546 1.001378 GGCACCTCATCACACAAACAC 60.001 52.381 0.00 0.00 0.00 3.32
3091 3556 2.425143 TGAAGGAATGGCACCTCATC 57.575 50.000 0.00 0.00 36.67 2.92
3124 3589 0.624795 AGACCAATTCCCTCCCTCCC 60.625 60.000 0.00 0.00 0.00 4.30
3146 3611 4.260294 GCGCTTCAGAAAATCTCATCTCAG 60.260 45.833 0.00 0.00 0.00 3.35
3208 3674 4.361451 ACAACAAGAAGCAACAAGAGTG 57.639 40.909 0.00 0.00 0.00 3.51
3209 3675 5.449177 GCTAACAACAAGAAGCAACAAGAGT 60.449 40.000 0.00 0.00 35.05 3.24
3210 3676 4.972440 GCTAACAACAAGAAGCAACAAGAG 59.028 41.667 0.00 0.00 35.05 2.85
3211 3677 4.640201 AGCTAACAACAAGAAGCAACAAGA 59.360 37.500 0.00 0.00 37.44 3.02
3212 3678 4.736793 CAGCTAACAACAAGAAGCAACAAG 59.263 41.667 0.00 0.00 37.44 3.16
3213 3679 4.397730 TCAGCTAACAACAAGAAGCAACAA 59.602 37.500 0.00 0.00 37.44 2.83
3214 3680 3.944650 TCAGCTAACAACAAGAAGCAACA 59.055 39.130 0.00 0.00 37.44 3.33
3215 3681 4.552166 TCAGCTAACAACAAGAAGCAAC 57.448 40.909 0.00 0.00 37.44 4.17
3302 3771 0.543749 CCTTCCCTGGTGGAGATCAC 59.456 60.000 0.00 0.00 46.24 3.06
3303 3772 0.621571 CCCTTCCCTGGTGGAGATCA 60.622 60.000 0.00 0.00 46.24 2.92
3304 3773 1.348775 CCCCTTCCCTGGTGGAGATC 61.349 65.000 0.00 0.00 46.24 2.75
3305 3774 1.308216 CCCCTTCCCTGGTGGAGAT 60.308 63.158 0.00 0.00 46.24 2.75
3306 3775 2.124996 CCCCTTCCCTGGTGGAGA 59.875 66.667 0.00 0.00 46.24 3.71
3307 3776 3.017581 CCCCCTTCCCTGGTGGAG 61.018 72.222 0.00 0.00 46.24 3.86
3328 3797 2.284190 GAGATCACCAAAGGCTACAGC 58.716 52.381 0.00 0.00 41.14 4.40
3329 3798 2.237143 TGGAGATCACCAAAGGCTACAG 59.763 50.000 9.69 0.00 36.96 2.74
3330 3799 2.027192 GTGGAGATCACCAAAGGCTACA 60.027 50.000 13.92 0.00 41.87 2.74
3331 3800 2.633488 GTGGAGATCACCAAAGGCTAC 58.367 52.381 13.92 0.00 41.87 3.58
3333 3802 3.965888 GTGGAGATCACCAAAGGCT 57.034 52.632 13.92 0.00 41.87 4.58
3341 3810 0.543749 CCTTCCCTGGTGGAGATCAC 59.456 60.000 0.00 0.00 46.24 3.06
3342 3811 0.621571 CCCTTCCCTGGTGGAGATCA 60.622 60.000 0.00 0.00 46.24 2.92
3343 3812 1.348775 CCCCTTCCCTGGTGGAGATC 61.349 65.000 0.00 0.00 46.24 2.75
3344 3813 1.308216 CCCCTTCCCTGGTGGAGAT 60.308 63.158 0.00 0.00 46.24 2.75
3345 3814 2.124996 CCCCTTCCCTGGTGGAGA 59.875 66.667 0.00 0.00 46.24 3.71
3346 3815 3.017581 CCCCCTTCCCTGGTGGAG 61.018 72.222 0.00 0.00 46.24 3.86
3368 3837 0.107654 AGATCACCAAAGGCTACGGC 60.108 55.000 0.00 0.00 37.82 5.68
3369 3838 1.473434 GGAGATCACCAAAGGCTACGG 60.473 57.143 4.05 0.72 0.00 4.02
3370 3839 1.207089 TGGAGATCACCAAAGGCTACG 59.793 52.381 9.69 0.00 36.96 3.51
3371 3840 2.633488 GTGGAGATCACCAAAGGCTAC 58.367 52.381 13.92 0.00 41.87 3.58
3373 3842 3.965888 GTGGAGATCACCAAAGGCT 57.034 52.632 13.92 0.00 41.87 4.58
3381 3850 1.065854 CACTTCCCTGGTGGAGATCAC 60.066 57.143 0.00 0.00 46.24 3.06
3382 3851 1.279496 CACTTCCCTGGTGGAGATCA 58.721 55.000 0.00 0.00 46.24 2.92
3389 3858 2.606587 CCTCCCCACTTCCCTGGTG 61.607 68.421 0.00 0.00 34.78 4.17
3390 3859 2.204151 CCTCCCCACTTCCCTGGT 60.204 66.667 0.00 0.00 0.00 4.00
3391 3860 3.732849 GCCTCCCCACTTCCCTGG 61.733 72.222 0.00 0.00 0.00 4.45
3392 3861 2.612115 AGCCTCCCCACTTCCCTG 60.612 66.667 0.00 0.00 0.00 4.45
3393 3862 2.119847 TACAGCCTCCCCACTTCCCT 62.120 60.000 0.00 0.00 0.00 4.20
3394 3863 1.615424 TACAGCCTCCCCACTTCCC 60.615 63.158 0.00 0.00 0.00 3.97
3395 3864 1.908483 CTACAGCCTCCCCACTTCC 59.092 63.158 0.00 0.00 0.00 3.46
3396 3865 1.222113 GCTACAGCCTCCCCACTTC 59.778 63.158 0.00 0.00 34.31 3.01
3397 3866 3.404773 GCTACAGCCTCCCCACTT 58.595 61.111 0.00 0.00 34.31 3.16
3407 3876 2.284190 GAGATCACCAAAGGCTACAGC 58.716 52.381 0.00 0.00 41.14 4.40
3408 3877 2.237143 TGGAGATCACCAAAGGCTACAG 59.763 50.000 9.69 0.00 36.96 2.74
3409 3878 2.027192 GTGGAGATCACCAAAGGCTACA 60.027 50.000 13.92 0.00 41.87 2.74
3410 3879 2.633488 GTGGAGATCACCAAAGGCTAC 58.367 52.381 13.92 0.00 41.87 3.58
3412 3881 3.965888 GTGGAGATCACCAAAGGCT 57.034 52.632 13.92 0.00 41.87 4.58
3420 3889 0.543749 CCTTCCCTGGTGGAGATCAC 59.456 60.000 0.00 0.00 46.24 3.06
3421 3890 0.621571 CCCTTCCCTGGTGGAGATCA 60.622 60.000 0.00 0.00 46.24 2.92
3422 3891 1.348775 CCCCTTCCCTGGTGGAGATC 61.349 65.000 0.00 0.00 46.24 2.75
3423 3892 1.308216 CCCCTTCCCTGGTGGAGAT 60.308 63.158 0.00 0.00 46.24 2.75
3424 3893 2.124996 CCCCTTCCCTGGTGGAGA 59.875 66.667 0.00 0.00 46.24 3.71
3425 3894 3.017581 CCCCCTTCCCTGGTGGAG 61.018 72.222 0.00 0.00 46.24 3.86
3446 3915 2.284190 GAGATCACCAAAGGCTACAGC 58.716 52.381 0.00 0.00 41.14 4.40
3447 3916 2.237143 TGGAGATCACCAAAGGCTACAG 59.763 50.000 9.69 0.00 36.96 2.74
3448 3917 2.027192 GTGGAGATCACCAAAGGCTACA 60.027 50.000 13.92 0.00 41.87 2.74
3449 3918 2.633488 GTGGAGATCACCAAAGGCTAC 58.367 52.381 13.92 0.00 41.87 3.58
3451 3920 3.965888 GTGGAGATCACCAAAGGCT 57.034 52.632 13.92 0.00 41.87 4.58
3517 3988 6.178239 ACGTGGAATGAGTTAATTTACTGC 57.822 37.500 1.04 0.00 0.00 4.40
3587 4069 8.438676 AATTATCAATTACTGTACACTCCAGC 57.561 34.615 0.00 0.00 33.09 4.85
3688 4175 3.371063 GGGACGACTGACGCCTCA 61.371 66.667 0.00 0.00 46.94 3.86
3758 4251 3.131223 ACATCGACAAGGTCTTCATCGAT 59.869 43.478 17.02 17.02 43.23 3.59
3763 4256 3.574396 AGAGAACATCGACAAGGTCTTCA 59.426 43.478 3.74 0.00 0.00 3.02
3821 4314 1.142097 GACGCTCAAGCTCTACCCC 59.858 63.158 0.00 0.00 39.32 4.95


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

AutoCloner maintained by Alex Coulton.