Multiple sequence alignment - TraesCS5A01G451100

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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 TraesCS5A01G451100 chr5A 100.000 3370 0 0 1 3370 632902750 632906119 0.000000e+00 6224.0
1 TraesCS5A01G451100 chr5A 83.701 1270 161 28 982 2226 632992970 632994218 0.000000e+00 1157.0
2 TraesCS5A01G451100 chr5A 77.860 813 128 27 1446 2212 632886582 632887388 1.100000e-124 457.0
3 TraesCS5A01G451100 chr5A 87.556 225 27 1 982 1206 632886120 632886343 3.340000e-65 259.0
4 TraesCS5A01G451100 chr5A 86.784 227 25 2 2281 2502 632994657 632994883 7.220000e-62 248.0
5 TraesCS5A01G451100 chr5A 94.702 151 5 2 816 963 448627540 448627390 7.270000e-57 231.0
6 TraesCS5A01G451100 chr5D 90.352 1337 70 34 961 2250 505420629 505421953 0.000000e+00 1700.0
7 TraesCS5A01G451100 chr5D 83.888 1291 162 29 958 2226 505429013 505430279 0.000000e+00 1190.0
8 TraesCS5A01G451100 chr5D 87.308 780 78 11 963 1735 505410026 505410791 0.000000e+00 872.0
9 TraesCS5A01G451100 chr5D 96.372 441 16 0 2281 2721 505422021 505422461 0.000000e+00 726.0
10 TraesCS5A01G451100 chr5D 78.171 875 142 29 1261 2103 505347809 505348666 2.320000e-141 512.0
11 TraesCS5A01G451100 chr5D 79.677 743 104 18 1421 2130 505405726 505406454 3.020000e-135 492.0
12 TraesCS5A01G451100 chr5D 86.761 355 34 9 2959 3311 505422830 505423173 1.900000e-102 383.0
13 TraesCS5A01G451100 chr5D 88.444 225 25 1 982 1206 505405249 505405472 1.540000e-68 270.0
14 TraesCS5A01G451100 chr5D 87.143 210 25 2 2747 2955 505412028 505412236 1.560000e-58 237.0
15 TraesCS5A01G451100 chr5D 84.167 240 16 13 2281 2500 505430430 505430667 2.630000e-51 213.0
16 TraesCS5A01G451100 chr5D 86.755 151 18 1 2806 2956 505422647 505422795 2.080000e-37 167.0
17 TraesCS5A01G451100 chr5D 93.939 66 4 0 3305 3370 505423235 505423300 2.140000e-17 100.0
18 TraesCS5A01G451100 chr5B 89.450 1346 71 23 961 2253 635515165 635516492 0.000000e+00 1633.0
19 TraesCS5A01G451100 chr5B 83.103 1302 168 31 958 2226 635533319 635534601 0.000000e+00 1138.0
20 TraesCS5A01G451100 chr5B 87.421 787 75 13 958 1735 635510495 635511266 0.000000e+00 883.0
21 TraesCS5A01G451100 chr5B 91.068 571 45 5 2743 3311 635517212 635517778 0.000000e+00 767.0
22 TraesCS5A01G451100 chr5B 83.510 849 71 36 1 817 635509699 635510510 0.000000e+00 728.0
23 TraesCS5A01G451100 chr5B 95.575 452 19 1 2281 2732 635516557 635517007 0.000000e+00 723.0
24 TraesCS5A01G451100 chr5B 77.788 1058 172 33 1043 2067 635346288 635347315 8.050000e-166 593.0
25 TraesCS5A01G451100 chr5B 78.293 820 117 30 1359 2130 635467270 635468076 3.940000e-129 472.0
26 TraesCS5A01G451100 chr5B 79.937 638 106 16 1446 2066 635463319 635463951 1.840000e-122 449.0
27 TraesCS5A01G451100 chr5B 89.381 113 12 0 2281 2393 635534724 635534836 3.510000e-30 143.0
28 TraesCS5A01G451100 chr5B 100.000 29 0 0 1299 1327 676017825 676017797 2.000000e-03 54.7
29 TraesCS5A01G451100 chr7A 97.279 147 1 2 818 961 602095154 602095008 2.600000e-61 246.0
30 TraesCS5A01G451100 chr4B 95.484 155 2 3 814 963 500347859 500347705 3.360000e-60 243.0
31 TraesCS5A01G451100 chr1B 94.595 148 5 2 816 960 573047533 573047680 3.380000e-55 226.0
32 TraesCS5A01G451100 chr6D 92.568 148 7 3 816 960 59341377 59341523 3.410000e-50 209.0
33 TraesCS5A01G451100 chr2A 92.414 145 8 2 816 957 58373299 58373155 1.590000e-48 204.0
34 TraesCS5A01G451100 chr2A 89.189 148 13 2 816 960 82060768 82060621 7.430000e-42 182.0
35 TraesCS5A01G451100 chr2B 91.724 145 9 2 816 957 786236685 786236829 7.380000e-47 198.0
36 TraesCS5A01G451100 chr7B 94.175 103 3 2 816 915 501763451 501763349 1.620000e-33 154.0
37 TraesCS5A01G451100 chr3D 84.768 151 7 5 816 963 478649449 478649312 1.630000e-28 137.0


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 TraesCS5A01G451100 chr5A 632902750 632906119 3369 False 6224.00 6224 100.0000 1 3370 1 chr5A.!!$F1 3369
1 TraesCS5A01G451100 chr5A 632992970 632994883 1913 False 702.50 1157 85.2425 982 2502 2 chr5A.!!$F3 1520
2 TraesCS5A01G451100 chr5A 632886120 632887388 1268 False 358.00 457 82.7080 982 2212 2 chr5A.!!$F2 1230
3 TraesCS5A01G451100 chr5D 505429013 505430667 1654 False 701.50 1190 84.0275 958 2500 2 chr5D.!!$F4 1542
4 TraesCS5A01G451100 chr5D 505420629 505423300 2671 False 615.20 1700 90.8358 961 3370 5 chr5D.!!$F3 2409
5 TraesCS5A01G451100 chr5D 505347809 505348666 857 False 512.00 512 78.1710 1261 2103 1 chr5D.!!$F1 842
6 TraesCS5A01G451100 chr5D 505405249 505412236 6987 False 467.75 872 85.6430 963 2955 4 chr5D.!!$F2 1992
7 TraesCS5A01G451100 chr5B 635509699 635517778 8079 False 946.80 1633 89.4048 1 3311 5 chr5B.!!$F3 3310
8 TraesCS5A01G451100 chr5B 635533319 635534836 1517 False 640.50 1138 86.2420 958 2393 2 chr5B.!!$F4 1435
9 TraesCS5A01G451100 chr5B 635346288 635347315 1027 False 593.00 593 77.7880 1043 2067 1 chr5B.!!$F1 1024
10 TraesCS5A01G451100 chr5B 635463319 635468076 4757 False 460.50 472 79.1150 1359 2130 2 chr5B.!!$F2 771

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
822 854 0.031616 TTTCCCACCCCAAAACTGCT 60.032 50.0 0.0 0.0 0.0 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2792 13301 0.328258 CGAAGGGGGTGAAAGATGGT 59.672 55.0 0.0 0.0 0.0 3.55 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
125 126 3.081061 TGGCTTTGGCACTACAACATAG 58.919 45.455 0.00 0.00 40.87 2.23
147 148 4.223923 AGGGAAGTCTCAGTTATTGTCCAG 59.776 45.833 0.00 0.00 0.00 3.86
150 151 5.279506 GGAAGTCTCAGTTATTGTCCAGTCA 60.280 44.000 0.00 0.00 0.00 3.41
166 167 3.114616 CAGACTCAGGCGTTGGCG 61.115 66.667 0.00 0.00 41.24 5.69
177 178 0.736325 GCGTTGGCGACACTCTACAT 60.736 55.000 5.58 0.00 42.67 2.29
232 233 3.826729 TCGTTCTGAGATCCAGTTCTTGA 59.173 43.478 9.98 2.66 43.38 3.02
235 236 4.750021 TCTGAGATCCAGTTCTTGATGG 57.250 45.455 9.98 0.00 43.38 3.51
245 246 6.364701 TCCAGTTCTTGATGGAAAAGAGAAA 58.635 36.000 0.00 0.00 42.61 2.52
297 298 9.959721 GGATAAAATAGGGTAGCAGATCAATTA 57.040 33.333 0.00 0.00 0.00 1.40
300 301 8.682936 AAAATAGGGTAGCAGATCAATTAGTG 57.317 34.615 0.00 0.00 0.00 2.74
301 302 4.078639 AGGGTAGCAGATCAATTAGTGC 57.921 45.455 0.00 0.00 36.10 4.40
302 303 3.142174 GGGTAGCAGATCAATTAGTGCC 58.858 50.000 0.00 0.00 36.54 5.01
307 308 3.118775 AGCAGATCAATTAGTGCCGTACA 60.119 43.478 0.00 0.00 36.54 2.90
368 369 6.951971 AGGACCATATAATGTATCAAGGAGC 58.048 40.000 0.00 0.00 0.00 4.70
369 370 6.732862 AGGACCATATAATGTATCAAGGAGCT 59.267 38.462 0.00 0.00 0.00 4.09
370 371 7.238514 AGGACCATATAATGTATCAAGGAGCTT 59.761 37.037 0.00 0.00 0.00 3.74
371 372 7.550906 GGACCATATAATGTATCAAGGAGCTTC 59.449 40.741 0.00 0.00 0.00 3.86
390 391 3.340814 TCTGCCTCTCAACTGAAATCC 57.659 47.619 0.00 0.00 0.00 3.01
391 392 2.909006 TCTGCCTCTCAACTGAAATCCT 59.091 45.455 0.00 0.00 0.00 3.24
394 395 5.190528 TCTGCCTCTCAACTGAAATCCTATT 59.809 40.000 0.00 0.00 0.00 1.73
397 398 8.262601 TGCCTCTCAACTGAAATCCTATTATA 57.737 34.615 0.00 0.00 0.00 0.98
398 399 8.150945 TGCCTCTCAACTGAAATCCTATTATAC 58.849 37.037 0.00 0.00 0.00 1.47
454 455 7.218614 TCACGAAGTAAATTTCTTTCACCCTA 58.781 34.615 12.42 0.00 41.61 3.53
455 456 7.716123 TCACGAAGTAAATTTCTTTCACCCTAA 59.284 33.333 12.42 0.00 41.61 2.69
456 457 8.347035 CACGAAGTAAATTTCTTTCACCCTAAA 58.653 33.333 12.42 0.00 41.61 1.85
457 458 8.905850 ACGAAGTAAATTTCTTTCACCCTAAAA 58.094 29.630 12.42 0.00 41.94 1.52
508 514 1.758440 AAGAGCCAAGGCACGACAGA 61.758 55.000 14.40 0.00 44.88 3.41
509 515 2.029844 GAGCCAAGGCACGACAGAC 61.030 63.158 14.40 0.00 44.88 3.51
519 525 1.633561 CACGACAGACTATGGCTGTG 58.366 55.000 11.09 6.19 45.94 3.66
523 529 2.350522 GACAGACTATGGCTGTGGTTG 58.649 52.381 11.09 0.00 45.94 3.77
533 539 0.813184 GCTGTGGTTGGATGGTCATG 59.187 55.000 0.00 0.00 0.00 3.07
535 541 2.947243 GCTGTGGTTGGATGGTCATGAT 60.947 50.000 0.00 0.00 0.00 2.45
553 566 6.375455 GTCATGATGACAGTGGTATCCTTTTT 59.625 38.462 19.96 0.00 46.22 1.94
579 592 2.457366 GAGTTCAACTCCGGTGATGT 57.543 50.000 11.17 0.00 39.28 3.06
580 593 2.767505 GAGTTCAACTCCGGTGATGTT 58.232 47.619 11.17 4.90 39.28 2.71
582 595 4.504858 GAGTTCAACTCCGGTGATGTTAT 58.495 43.478 11.17 0.00 39.28 1.89
583 596 4.253685 AGTTCAACTCCGGTGATGTTATG 58.746 43.478 11.17 0.03 0.00 1.90
595 608 4.764823 GGTGATGTTATGTGGGAGAAAACA 59.235 41.667 0.00 0.00 34.81 2.83
600 613 8.106462 TGATGTTATGTGGGAGAAAACATTCTA 58.894 33.333 0.00 0.00 40.02 2.10
606 619 4.626172 GTGGGAGAAAACATTCTAGTCGAC 59.374 45.833 7.70 7.70 0.00 4.20
608 621 5.713389 TGGGAGAAAACATTCTAGTCGACTA 59.287 40.000 23.34 23.34 0.00 2.59
610 623 7.095270 GGGAGAAAACATTCTAGTCGACTAAA 58.905 38.462 24.66 20.15 0.00 1.85
611 624 7.275999 GGGAGAAAACATTCTAGTCGACTAAAG 59.724 40.741 24.66 16.73 0.00 1.85
615 628 9.408069 GAAAACATTCTAGTCGACTAAAGAAGA 57.592 33.333 26.51 19.47 0.00 2.87
616 629 8.745464 AAACATTCTAGTCGACTAAAGAAGAC 57.255 34.615 26.51 0.00 0.00 3.01
619 632 5.776519 TCTAGTCGACTAAAGAAGACGTC 57.223 43.478 24.66 7.70 42.78 4.34
620 633 5.477510 TCTAGTCGACTAAAGAAGACGTCT 58.522 41.667 24.66 13.58 42.78 4.18
632 645 1.499049 AGACGTCTTTGGCGACTTTC 58.501 50.000 13.58 0.00 31.22 2.62
647 660 4.815269 CGACTTTCTCAATCTCAAGGACT 58.185 43.478 0.00 0.00 0.00 3.85
648 661 4.624882 CGACTTTCTCAATCTCAAGGACTG 59.375 45.833 0.00 0.00 0.00 3.51
649 662 4.322567 ACTTTCTCAATCTCAAGGACTGC 58.677 43.478 0.00 0.00 0.00 4.40
658 683 0.601558 TCAAGGACTGCGTCTGTACC 59.398 55.000 8.26 0.00 32.47 3.34
665 690 0.506932 CTGCGTCTGTACCGTGTTTG 59.493 55.000 0.00 0.00 0.00 2.93
668 693 2.030096 TGCGTCTGTACCGTGTTTGATA 60.030 45.455 0.00 0.00 0.00 2.15
669 694 2.988493 GCGTCTGTACCGTGTTTGATAA 59.012 45.455 0.00 0.00 0.00 1.75
744 776 6.985188 AAAAGAAAGAAAAGAAAACTGGCC 57.015 33.333 0.00 0.00 0.00 5.36
779 811 0.391130 GTAGCCATCCAACGAGCACA 60.391 55.000 0.00 0.00 0.00 4.57
809 841 0.840722 GGAGTCTCCACCCTTTCCCA 60.841 60.000 14.46 0.00 36.28 4.37
810 842 0.325272 GAGTCTCCACCCTTTCCCAC 59.675 60.000 0.00 0.00 0.00 4.61
811 843 1.134438 AGTCTCCACCCTTTCCCACC 61.134 60.000 0.00 0.00 0.00 4.61
813 845 2.861974 TCCACCCTTTCCCACCCC 60.862 66.667 0.00 0.00 0.00 4.95
815 847 2.784654 CCACCCTTTCCCACCCCAA 61.785 63.158 0.00 0.00 0.00 4.12
816 848 1.234529 CACCCTTTCCCACCCCAAA 59.765 57.895 0.00 0.00 0.00 3.28
817 849 0.399233 CACCCTTTCCCACCCCAAAA 60.399 55.000 0.00 0.00 0.00 2.44
818 850 0.399376 ACCCTTTCCCACCCCAAAAC 60.399 55.000 0.00 0.00 0.00 2.43
819 851 0.105194 CCCTTTCCCACCCCAAAACT 60.105 55.000 0.00 0.00 0.00 2.66
820 852 1.047801 CCTTTCCCACCCCAAAACTG 58.952 55.000 0.00 0.00 0.00 3.16
821 853 0.392706 CTTTCCCACCCCAAAACTGC 59.607 55.000 0.00 0.00 0.00 4.40
822 854 0.031616 TTTCCCACCCCAAAACTGCT 60.032 50.000 0.00 0.00 0.00 4.24
825 857 1.152567 CCACCCCAAAACTGCTGGA 60.153 57.895 0.00 0.00 35.85 3.86
828 860 0.032615 ACCCCAAAACTGCTGGACAA 60.033 50.000 0.00 0.00 35.85 3.18
829 861 1.118838 CCCCAAAACTGCTGGACAAA 58.881 50.000 0.00 0.00 35.85 2.83
830 862 1.202521 CCCCAAAACTGCTGGACAAAC 60.203 52.381 0.00 0.00 35.85 2.93
832 864 2.539476 CCAAAACTGCTGGACAAACAC 58.461 47.619 0.00 0.00 35.85 3.32
833 865 2.166254 CCAAAACTGCTGGACAAACACT 59.834 45.455 0.00 0.00 35.85 3.55
834 866 3.380004 CCAAAACTGCTGGACAAACACTA 59.620 43.478 0.00 0.00 35.85 2.74
836 868 1.884235 ACTGCTGGACAAACACTAGC 58.116 50.000 0.00 0.00 41.14 3.42
839 871 1.160137 GCTGGACAAACACTAGCTGG 58.840 55.000 0.00 0.00 38.49 4.85
840 872 1.160137 CTGGACAAACACTAGCTGGC 58.840 55.000 0.00 0.00 0.00 4.85
841 873 0.250727 TGGACAAACACTAGCTGGCC 60.251 55.000 0.00 0.00 38.88 5.36
842 874 1.298859 GGACAAACACTAGCTGGCCG 61.299 60.000 0.00 0.00 0.00 6.13
844 876 0.107831 ACAAACACTAGCTGGCCGAA 59.892 50.000 0.00 0.00 0.00 4.30
845 877 0.517316 CAAACACTAGCTGGCCGAAC 59.483 55.000 0.00 0.00 0.00 3.95
846 878 0.605589 AAACACTAGCTGGCCGAACC 60.606 55.000 0.00 0.00 39.84 3.62
847 879 2.125106 CACTAGCTGGCCGAACCC 60.125 66.667 0.00 0.00 37.83 4.11
848 880 3.400054 ACTAGCTGGCCGAACCCC 61.400 66.667 0.00 0.00 37.83 4.95
849 881 3.399181 CTAGCTGGCCGAACCCCA 61.399 66.667 0.00 0.00 37.83 4.96
850 882 3.682292 CTAGCTGGCCGAACCCCAC 62.682 68.421 0.00 0.00 37.83 4.61
855 887 4.404098 GGCCGAACCCCACACGAT 62.404 66.667 0.00 0.00 0.00 3.73
856 888 3.124921 GCCGAACCCCACACGATG 61.125 66.667 0.00 0.00 0.00 3.84
857 889 3.124921 CCGAACCCCACACGATGC 61.125 66.667 0.00 0.00 0.00 3.91
858 890 2.358125 CGAACCCCACACGATGCA 60.358 61.111 0.00 0.00 0.00 3.96
859 891 2.390599 CGAACCCCACACGATGCAG 61.391 63.158 0.00 0.00 0.00 4.41
860 892 2.034066 AACCCCACACGATGCAGG 59.966 61.111 0.00 0.00 0.00 4.85
861 893 2.463589 GAACCCCACACGATGCAGGA 62.464 60.000 0.00 0.00 0.00 3.86
862 894 2.063015 AACCCCACACGATGCAGGAA 62.063 55.000 0.00 0.00 0.00 3.36
865 897 1.378882 CCCACACGATGCAGGAATGG 61.379 60.000 0.00 0.00 0.00 3.16
866 898 0.392863 CCACACGATGCAGGAATGGA 60.393 55.000 0.00 0.00 0.00 3.41
867 899 0.729116 CACACGATGCAGGAATGGAC 59.271 55.000 0.00 0.00 0.00 4.02
869 901 1.153369 ACGATGCAGGAATGGACGG 60.153 57.895 0.00 0.00 0.00 4.79
870 902 1.153369 CGATGCAGGAATGGACGGT 60.153 57.895 0.00 0.00 0.00 4.83
871 903 1.431488 CGATGCAGGAATGGACGGTG 61.431 60.000 0.00 0.00 0.00 4.94
872 904 0.392998 GATGCAGGAATGGACGGTGT 60.393 55.000 0.00 0.00 0.00 4.16
873 905 0.038166 ATGCAGGAATGGACGGTGTT 59.962 50.000 0.00 0.00 0.00 3.32
876 908 1.156736 CAGGAATGGACGGTGTTGTC 58.843 55.000 0.00 0.00 38.17 3.18
877 909 1.056660 AGGAATGGACGGTGTTGTCT 58.943 50.000 0.00 0.00 38.91 3.41
879 911 0.517316 GAATGGACGGTGTTGTCTGC 59.483 55.000 0.00 0.00 38.91 4.26
880 912 0.108585 AATGGACGGTGTTGTCTGCT 59.891 50.000 0.00 0.00 38.91 4.24
881 913 0.108585 ATGGACGGTGTTGTCTGCTT 59.891 50.000 0.00 0.00 38.91 3.91
882 914 0.107410 TGGACGGTGTTGTCTGCTTT 60.107 50.000 0.00 0.00 38.91 3.51
883 915 1.021968 GGACGGTGTTGTCTGCTTTT 58.978 50.000 0.00 0.00 38.91 2.27
900 932 4.398247 GCTTTTGCTCTAACTCATCAACG 58.602 43.478 0.00 0.00 43.35 4.10
901 933 4.670221 GCTTTTGCTCTAACTCATCAACGG 60.670 45.833 0.00 0.00 43.35 4.44
902 934 2.010145 TGCTCTAACTCATCAACGGC 57.990 50.000 0.00 0.00 0.00 5.68
903 935 1.550524 TGCTCTAACTCATCAACGGCT 59.449 47.619 0.00 0.00 0.00 5.52
904 936 2.028112 TGCTCTAACTCATCAACGGCTT 60.028 45.455 0.00 0.00 0.00 4.35
905 937 2.349886 GCTCTAACTCATCAACGGCTTG 59.650 50.000 0.00 0.00 0.00 4.01
906 938 3.849911 CTCTAACTCATCAACGGCTTGA 58.150 45.455 2.63 2.63 40.77 3.02
907 939 4.437239 CTCTAACTCATCAACGGCTTGAT 58.563 43.478 6.42 6.42 46.36 2.57
914 946 2.831685 TCAACGGCTTGATGTGTAGT 57.168 45.000 0.00 0.00 31.00 2.73
915 947 2.412870 TCAACGGCTTGATGTGTAGTG 58.587 47.619 0.00 0.00 31.00 2.74
918 950 0.992072 CGGCTTGATGTGTAGTGTCG 59.008 55.000 0.00 0.00 0.00 4.35
919 951 1.668919 CGGCTTGATGTGTAGTGTCGT 60.669 52.381 0.00 0.00 0.00 4.34
921 953 1.993370 GCTTGATGTGTAGTGTCGTCC 59.007 52.381 0.00 0.00 0.00 4.79
922 954 2.251040 CTTGATGTGTAGTGTCGTCCG 58.749 52.381 0.00 0.00 0.00 4.79
926 958 1.167781 TGTGTAGTGTCGTCCGCTGA 61.168 55.000 1.99 0.00 35.05 4.26
927 959 0.170561 GTGTAGTGTCGTCCGCTGAT 59.829 55.000 1.99 0.00 35.05 2.90
928 960 0.450583 TGTAGTGTCGTCCGCTGATC 59.549 55.000 1.99 0.00 35.05 2.92
930 962 1.022982 TAGTGTCGTCCGCTGATCGT 61.023 55.000 1.99 0.00 35.05 3.73
931 963 1.868251 GTGTCGTCCGCTGATCGTC 60.868 63.158 0.00 0.00 36.19 4.20
932 964 2.278013 GTCGTCCGCTGATCGTCC 60.278 66.667 0.00 0.00 36.19 4.79
934 966 2.180769 CGTCCGCTGATCGTCCAA 59.819 61.111 0.00 0.00 36.19 3.53
935 967 1.445410 CGTCCGCTGATCGTCCAAA 60.445 57.895 0.00 0.00 36.19 3.28
936 968 0.806102 CGTCCGCTGATCGTCCAAAT 60.806 55.000 0.00 0.00 36.19 2.32
940 972 1.645034 CGCTGATCGTCCAAATCTGT 58.355 50.000 0.00 0.00 0.00 3.41
941 973 1.590238 CGCTGATCGTCCAAATCTGTC 59.410 52.381 0.00 0.00 0.00 3.51
944 976 2.854777 CTGATCGTCCAAATCTGTCGTC 59.145 50.000 0.00 0.00 0.00 4.20
945 977 2.492088 TGATCGTCCAAATCTGTCGTCT 59.508 45.455 0.00 0.00 0.00 4.18
946 978 2.347697 TCGTCCAAATCTGTCGTCTG 57.652 50.000 0.00 0.00 0.00 3.51
948 980 1.721389 CGTCCAAATCTGTCGTCTGTG 59.279 52.381 0.00 0.00 0.00 3.66
950 982 3.610821 CGTCCAAATCTGTCGTCTGTGTA 60.611 47.826 0.00 0.00 0.00 2.90
952 984 2.668457 CCAAATCTGTCGTCTGTGTAGC 59.332 50.000 0.00 0.00 0.00 3.58
953 985 3.317150 CAAATCTGTCGTCTGTGTAGCA 58.683 45.455 0.00 0.00 0.00 3.49
954 986 2.929531 ATCTGTCGTCTGTGTAGCAG 57.070 50.000 0.00 0.00 46.34 4.24
955 987 0.241213 TCTGTCGTCTGTGTAGCAGC 59.759 55.000 0.00 0.00 44.66 5.25
956 988 1.067743 CTGTCGTCTGTGTAGCAGCG 61.068 60.000 0.00 0.00 44.66 5.18
957 989 2.126463 TCGTCTGTGTAGCAGCGC 60.126 61.111 0.00 0.00 44.66 5.92
958 990 2.126307 CGTCTGTGTAGCAGCGCT 60.126 61.111 2.64 2.64 44.66 5.92
959 991 2.155194 CGTCTGTGTAGCAGCGCTC 61.155 63.158 7.13 2.24 44.66 5.03
960 992 1.214062 GTCTGTGTAGCAGCGCTCT 59.786 57.895 7.13 10.92 44.66 4.09
961 993 0.389166 GTCTGTGTAGCAGCGCTCTT 60.389 55.000 7.13 0.00 44.66 2.85
963 995 1.079819 TGTGTAGCAGCGCTCTTCC 60.080 57.895 7.13 3.40 40.44 3.46
964 996 1.811679 GTGTAGCAGCGCTCTTCCC 60.812 63.158 7.13 0.00 40.44 3.97
1119 5957 2.669569 GCCTCCGCTGTCTGCAAA 60.670 61.111 2.42 0.00 43.06 3.68
1294 10821 1.160329 CGACCATCCCGATTGGCTTC 61.160 60.000 0.00 0.00 0.00 3.86
1343 10870 4.308458 CGACCGCACCTGGGACAA 62.308 66.667 0.00 0.00 38.70 3.18
1344 10871 2.112297 GACCGCACCTGGGACAAA 59.888 61.111 0.00 0.00 38.70 2.83
1411 11013 2.091222 GTGTCCTCCCCCTATACTCACT 60.091 54.545 0.00 0.00 0.00 3.41
1439 11043 3.716006 CAGTGCGGCGGTGTTCTG 61.716 66.667 9.78 0.00 0.00 3.02
1485 11095 2.113139 CACGGTTGCCAAGGAGGT 59.887 61.111 0.00 0.00 40.61 3.85
1600 11210 2.507471 ACCTCTCTTCATCACCCCAATC 59.493 50.000 0.00 0.00 0.00 2.67
1660 11279 3.003480 GGTGATGCACTCTACTTCAACC 58.997 50.000 0.00 0.00 34.40 3.77
1699 11318 1.523758 CCAACTTGGTACACTCTGCC 58.476 55.000 0.00 0.00 39.29 4.85
1886 11544 4.704833 GGCGCTGCTCCCTGTTGA 62.705 66.667 7.64 0.00 0.00 3.18
1932 11641 1.445095 GAGGATCAGTGGCATCGCT 59.555 57.895 0.00 0.00 33.17 4.93
2067 11790 3.630769 TGAGCTTCTACATACCAGGTACG 59.369 47.826 0.00 0.00 0.00 3.67
2068 11791 3.629087 AGCTTCTACATACCAGGTACGT 58.371 45.455 3.33 3.33 0.00 3.57
2069 11792 3.380637 AGCTTCTACATACCAGGTACGTG 59.619 47.826 8.67 8.61 0.00 4.49
2070 11793 3.703420 CTTCTACATACCAGGTACGTGC 58.297 50.000 8.67 0.00 0.00 5.34
2073 11796 3.879295 TCTACATACCAGGTACGTGCTAC 59.121 47.826 8.67 0.00 0.00 3.58
2134 11887 3.998341 TGTTACGATCTTTTAGTGGCACC 59.002 43.478 15.27 0.00 0.00 5.01
2173 11926 8.177119 TGAAAATATGTTTCTTGGCAAGTAGT 57.823 30.769 25.39 7.92 0.00 2.73
2174 11927 9.290988 TGAAAATATGTTTCTTGGCAAGTAGTA 57.709 29.630 25.39 12.20 0.00 1.82
2266 12430 5.414789 TTTATTCTCGGTCCTTGTGATCA 57.585 39.130 0.00 0.00 0.00 2.92
2690 12929 0.035458 ACTGGTACTCCACAAGCTGC 59.965 55.000 0.00 0.00 39.03 5.25
2707 12946 6.821665 ACAAGCTGCTCTTCCGTTAATATTTA 59.178 34.615 1.00 0.00 31.27 1.40
2721 12960 7.758528 CCGTTAATATTTATTAGCTCGCCTACT 59.241 37.037 0.00 0.00 30.25 2.57
2722 12961 9.136952 CGTTAATATTTATTAGCTCGCCTACTT 57.863 33.333 0.00 0.00 30.25 2.24
2732 12971 2.152699 CGCCTACTTGCTGACGACG 61.153 63.158 0.00 0.00 0.00 5.12
2735 12974 0.458543 CCTACTTGCTGACGACGCAT 60.459 55.000 0.00 0.00 37.22 4.73
2736 12975 1.202256 CCTACTTGCTGACGACGCATA 60.202 52.381 0.00 0.00 37.22 3.14
2738 12977 1.280982 ACTTGCTGACGACGCATATG 58.719 50.000 0.00 0.00 37.22 1.78
2740 12979 1.428370 TTGCTGACGACGCATATGGC 61.428 55.000 4.56 0.00 37.22 4.40
2741 12980 1.882625 GCTGACGACGCATATGGCA 60.883 57.895 4.56 0.00 45.17 4.92
2791 13300 4.674362 GCATATGGCGTGTCGTCTGATATA 60.674 45.833 4.56 0.00 30.55 0.86
2792 13301 5.399013 CATATGGCGTGTCGTCTGATATAA 58.601 41.667 0.00 0.00 30.55 0.98
2796 13305 3.552273 GGCGTGTCGTCTGATATAACCAT 60.552 47.826 0.00 0.00 0.00 3.55
2827 13336 2.121564 TTCGACGACGTCTGGACCAC 62.122 60.000 24.36 0.00 40.69 4.16
2828 13337 2.257676 GACGACGTCTGGACCACC 59.742 66.667 20.52 0.00 0.00 4.61
2904 13413 6.268387 TCTTCTCTGGAAAATTTTGGATGCTT 59.732 34.615 8.47 0.00 0.00 3.91
2983 13522 3.155093 ACAAGCTGAAAGTGTGCAAAG 57.845 42.857 0.00 0.00 35.30 2.77
3061 13601 9.151471 CCTCGAATCAAGAAGTATTTTCACTAA 57.849 33.333 0.00 0.00 0.00 2.24
3110 13650 5.869753 ATGTTGTTCACTATTGCAGAGAC 57.130 39.130 4.81 0.00 0.00 3.36
3120 13660 0.400213 TTGCAGAGACCGTGGGAAAT 59.600 50.000 0.00 0.00 0.00 2.17
3129 13669 0.881118 CCGTGGGAAATTGGTGACTG 59.119 55.000 0.00 0.00 0.00 3.51
3156 13697 1.073125 TCCTTTGGACGATTTGGCTCA 59.927 47.619 0.00 0.00 0.00 4.26
3191 13732 3.245797 AGTGTTCGACGACATCTCAATG 58.754 45.455 0.00 0.00 38.93 2.82
3195 13736 1.482621 CGACGACATCTCAATGCCCG 61.483 60.000 0.00 0.00 37.89 6.13
3198 13739 1.769098 CGACATCTCAATGCCCGCTG 61.769 60.000 0.00 0.00 36.26 5.18
3256 13797 0.249868 CTGGTCTCACAGCCAAACGA 60.250 55.000 0.00 0.00 33.93 3.85
3270 13811 2.356125 CCAAACGATCAGAGTTGGGGAT 60.356 50.000 0.00 0.00 38.67 3.85
3344 13953 7.172703 GTGTAAGACTGTTTGTATGCTTACCTT 59.827 37.037 7.25 4.46 37.79 3.50
3356 13965 4.464069 TGCTTACCTTGTTTGCTGTTTT 57.536 36.364 0.00 0.00 0.00 2.43
3366 13975 6.852345 CCTTGTTTGCTGTTTTTATGAAATGC 59.148 34.615 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 9.352163 CAATACAACAACGCATTTTTAGAAAAC 57.648 29.630 0.00 0.00 0.00 2.43
125 126 4.020128 ACTGGACAATAACTGAGACTTCCC 60.020 45.833 0.00 0.00 0.00 3.97
147 148 2.029844 GCCAACGCCTGAGTCTGAC 61.030 63.158 0.00 0.00 0.00 3.51
150 151 3.303135 TCGCCAACGCCTGAGTCT 61.303 61.111 0.00 0.00 39.84 3.24
166 167 1.410882 GAGCCCTCCATGTAGAGTGTC 59.589 57.143 0.00 0.00 31.53 3.67
177 178 2.421952 GCAGAATACAATGAGCCCTCCA 60.422 50.000 0.00 0.00 0.00 3.86
245 246 9.606631 CAGGTCTAAGCTTCATAGAAATAAACT 57.393 33.333 0.00 0.00 31.52 2.66
262 263 7.016268 TGCTACCCTATTTTATCCAGGTCTAAG 59.984 40.741 0.00 0.00 0.00 2.18
307 308 3.181495 GCAGTGCTATCTTCAGTACGACT 60.181 47.826 8.18 0.00 36.39 4.18
344 345 6.732862 AGCTCCTTGATACATTATATGGTCCT 59.267 38.462 0.00 0.00 33.60 3.85
346 347 8.317679 AGAAGCTCCTTGATACATTATATGGTC 58.682 37.037 0.00 0.00 33.60 4.02
347 348 8.099537 CAGAAGCTCCTTGATACATTATATGGT 58.900 37.037 0.00 0.00 33.60 3.55
349 350 7.065563 GGCAGAAGCTCCTTGATACATTATATG 59.934 40.741 0.00 0.00 41.70 1.78
351 352 6.270927 AGGCAGAAGCTCCTTGATACATTATA 59.729 38.462 0.00 0.00 41.70 0.98
355 356 2.776536 AGGCAGAAGCTCCTTGATACAT 59.223 45.455 0.00 0.00 41.70 2.29
356 357 2.169352 GAGGCAGAAGCTCCTTGATACA 59.831 50.000 0.00 0.00 41.70 2.29
357 358 2.433970 AGAGGCAGAAGCTCCTTGATAC 59.566 50.000 0.00 0.00 41.70 2.24
358 359 2.697751 GAGAGGCAGAAGCTCCTTGATA 59.302 50.000 0.00 0.00 41.70 2.15
359 360 1.485895 GAGAGGCAGAAGCTCCTTGAT 59.514 52.381 0.00 0.00 41.70 2.57
360 361 0.901124 GAGAGGCAGAAGCTCCTTGA 59.099 55.000 0.00 0.00 41.70 3.02
363 364 0.612744 GTTGAGAGGCAGAAGCTCCT 59.387 55.000 0.00 0.00 41.70 3.69
364 365 0.612744 AGTTGAGAGGCAGAAGCTCC 59.387 55.000 0.00 0.00 41.70 4.70
365 366 1.274728 TCAGTTGAGAGGCAGAAGCTC 59.725 52.381 0.00 0.00 41.70 4.09
366 367 1.346062 TCAGTTGAGAGGCAGAAGCT 58.654 50.000 0.00 0.00 41.70 3.74
368 369 3.688673 GGATTTCAGTTGAGAGGCAGAAG 59.311 47.826 0.00 0.00 0.00 2.85
369 370 3.328931 AGGATTTCAGTTGAGAGGCAGAA 59.671 43.478 0.00 0.00 0.00 3.02
370 371 2.909006 AGGATTTCAGTTGAGAGGCAGA 59.091 45.455 0.00 0.00 0.00 4.26
371 372 3.347077 AGGATTTCAGTTGAGAGGCAG 57.653 47.619 0.00 0.00 0.00 4.85
508 514 1.064463 CCATCCAACCACAGCCATAGT 60.064 52.381 0.00 0.00 0.00 2.12
509 515 1.064463 ACCATCCAACCACAGCCATAG 60.064 52.381 0.00 0.00 0.00 2.23
519 525 2.947652 CTGTCATCATGACCATCCAACC 59.052 50.000 15.44 0.00 46.40 3.77
523 529 2.092753 ACCACTGTCATCATGACCATCC 60.093 50.000 15.44 0.00 46.40 3.51
568 581 1.484653 TCCCACATAACATCACCGGAG 59.515 52.381 9.46 0.00 0.00 4.63
573 586 5.957842 TGTTTTCTCCCACATAACATCAC 57.042 39.130 0.00 0.00 0.00 3.06
575 588 7.396540 AGAATGTTTTCTCCCACATAACATC 57.603 36.000 0.00 0.00 37.69 3.06
576 589 8.109634 ACTAGAATGTTTTCTCCCACATAACAT 58.890 33.333 0.00 0.00 41.36 2.71
579 592 6.816640 CGACTAGAATGTTTTCTCCCACATAA 59.183 38.462 0.00 0.00 41.36 1.90
580 593 6.153851 TCGACTAGAATGTTTTCTCCCACATA 59.846 38.462 0.00 0.00 41.36 2.29
582 595 4.282449 TCGACTAGAATGTTTTCTCCCACA 59.718 41.667 0.00 0.00 41.36 4.17
583 596 4.626172 GTCGACTAGAATGTTTTCTCCCAC 59.374 45.833 8.70 0.00 41.36 4.61
595 608 6.594937 AGACGTCTTCTTTAGTCGACTAGAAT 59.405 38.462 24.18 13.78 38.21 2.40
610 623 0.674534 AGTCGCCAAAGACGTCTTCT 59.325 50.000 29.82 18.46 45.26 2.85
611 624 1.499049 AAGTCGCCAAAGACGTCTTC 58.501 50.000 29.82 17.01 45.26 2.87
615 628 1.202486 TGAGAAAGTCGCCAAAGACGT 60.202 47.619 0.00 0.00 45.26 4.34
616 629 1.497991 TGAGAAAGTCGCCAAAGACG 58.502 50.000 0.00 0.00 45.26 4.18
619 632 3.748048 TGAGATTGAGAAAGTCGCCAAAG 59.252 43.478 0.00 0.00 0.00 2.77
620 633 3.738982 TGAGATTGAGAAAGTCGCCAAA 58.261 40.909 0.00 0.00 0.00 3.28
624 637 3.369451 GTCCTTGAGATTGAGAAAGTCGC 59.631 47.826 0.00 0.00 0.00 5.19
625 638 4.624882 CAGTCCTTGAGATTGAGAAAGTCG 59.375 45.833 0.00 0.00 34.18 4.18
632 645 2.376808 ACGCAGTCCTTGAGATTGAG 57.623 50.000 0.00 0.00 29.74 3.02
647 660 0.102663 TCAAACACGGTACAGACGCA 59.897 50.000 0.00 0.00 34.00 5.24
648 661 1.425412 ATCAAACACGGTACAGACGC 58.575 50.000 0.00 0.00 34.00 5.19
649 662 5.579384 TTTTATCAAACACGGTACAGACG 57.421 39.130 0.00 0.00 37.36 4.18
744 776 1.723003 GCTACTACACGGTTCGGTTTG 59.277 52.381 0.00 0.00 0.00 2.93
779 811 1.979693 GAGACTCCACGGAGCAGGT 60.980 63.158 13.16 0.00 45.54 4.00
801 833 1.047801 CAGTTTTGGGGTGGGAAAGG 58.952 55.000 0.00 0.00 0.00 3.11
805 837 1.152567 CAGCAGTTTTGGGGTGGGA 60.153 57.895 0.00 0.00 0.00 4.37
809 841 0.032615 TTGTCCAGCAGTTTTGGGGT 60.033 50.000 0.00 0.00 36.34 4.95
810 842 1.118838 TTTGTCCAGCAGTTTTGGGG 58.881 50.000 0.00 0.00 36.34 4.96
811 843 1.480137 TGTTTGTCCAGCAGTTTTGGG 59.520 47.619 0.00 0.00 36.34 4.12
813 845 3.508744 AGTGTTTGTCCAGCAGTTTTG 57.491 42.857 0.00 0.00 0.00 2.44
815 847 2.618709 GCTAGTGTTTGTCCAGCAGTTT 59.381 45.455 0.00 0.00 32.46 2.66
816 848 2.158755 AGCTAGTGTTTGTCCAGCAGTT 60.159 45.455 0.00 0.00 34.65 3.16
817 849 1.417890 AGCTAGTGTTTGTCCAGCAGT 59.582 47.619 0.00 0.00 34.65 4.40
818 850 1.802960 CAGCTAGTGTTTGTCCAGCAG 59.197 52.381 0.00 0.00 34.65 4.24
819 851 1.543208 CCAGCTAGTGTTTGTCCAGCA 60.543 52.381 0.00 0.00 34.65 4.41
820 852 1.160137 CCAGCTAGTGTTTGTCCAGC 58.840 55.000 0.00 0.00 0.00 4.85
821 853 1.160137 GCCAGCTAGTGTTTGTCCAG 58.840 55.000 0.00 0.00 0.00 3.86
822 854 0.250727 GGCCAGCTAGTGTTTGTCCA 60.251 55.000 0.00 0.00 0.00 4.02
825 857 0.107831 TTCGGCCAGCTAGTGTTTGT 59.892 50.000 2.24 0.00 0.00 2.83
828 860 1.003718 GGTTCGGCCAGCTAGTGTT 60.004 57.895 2.24 0.00 37.17 3.32
829 861 2.663196 GGTTCGGCCAGCTAGTGT 59.337 61.111 2.24 0.00 37.17 3.55
830 862 2.125106 GGGTTCGGCCAGCTAGTG 60.125 66.667 2.24 0.00 39.65 2.74
832 864 3.399181 TGGGGTTCGGCCAGCTAG 61.399 66.667 2.24 0.00 39.65 3.42
833 865 3.712907 GTGGGGTTCGGCCAGCTA 61.713 66.667 2.24 0.00 39.65 3.32
839 871 3.124921 CATCGTGTGGGGTTCGGC 61.125 66.667 0.00 0.00 0.00 5.54
840 872 3.124921 GCATCGTGTGGGGTTCGG 61.125 66.667 0.00 0.00 0.00 4.30
841 873 2.358125 TGCATCGTGTGGGGTTCG 60.358 61.111 0.00 0.00 0.00 3.95
842 874 2.040544 CCTGCATCGTGTGGGGTTC 61.041 63.158 0.00 0.00 0.00 3.62
844 876 1.852157 ATTCCTGCATCGTGTGGGGT 61.852 55.000 0.00 0.00 0.00 4.95
845 877 1.077501 ATTCCTGCATCGTGTGGGG 60.078 57.895 0.00 0.00 0.00 4.96
846 878 1.378882 CCATTCCTGCATCGTGTGGG 61.379 60.000 0.00 0.00 0.00 4.61
847 879 0.392863 TCCATTCCTGCATCGTGTGG 60.393 55.000 0.00 0.00 0.00 4.17
848 880 0.729116 GTCCATTCCTGCATCGTGTG 59.271 55.000 0.00 0.00 0.00 3.82
849 881 0.740868 CGTCCATTCCTGCATCGTGT 60.741 55.000 0.00 0.00 0.00 4.49
850 882 1.431488 CCGTCCATTCCTGCATCGTG 61.431 60.000 0.00 0.00 0.00 4.35
851 883 1.153369 CCGTCCATTCCTGCATCGT 60.153 57.895 0.00 0.00 0.00 3.73
853 885 0.392998 ACACCGTCCATTCCTGCATC 60.393 55.000 0.00 0.00 0.00 3.91
855 887 0.888736 CAACACCGTCCATTCCTGCA 60.889 55.000 0.00 0.00 0.00 4.41
856 888 0.889186 ACAACACCGTCCATTCCTGC 60.889 55.000 0.00 0.00 0.00 4.85
857 889 1.156736 GACAACACCGTCCATTCCTG 58.843 55.000 0.00 0.00 0.00 3.86
858 890 1.056660 AGACAACACCGTCCATTCCT 58.943 50.000 0.00 0.00 36.52 3.36
859 891 1.156736 CAGACAACACCGTCCATTCC 58.843 55.000 0.00 0.00 36.52 3.01
860 892 0.517316 GCAGACAACACCGTCCATTC 59.483 55.000 0.00 0.00 36.52 2.67
861 893 0.108585 AGCAGACAACACCGTCCATT 59.891 50.000 0.00 0.00 36.52 3.16
862 894 0.108585 AAGCAGACAACACCGTCCAT 59.891 50.000 0.00 0.00 36.52 3.41
865 897 1.859998 GCAAAAGCAGACAACACCGTC 60.860 52.381 0.00 0.00 36.08 4.79
866 898 0.100503 GCAAAAGCAGACAACACCGT 59.899 50.000 0.00 0.00 0.00 4.83
867 899 0.381801 AGCAAAAGCAGACAACACCG 59.618 50.000 0.00 0.00 0.00 4.94
869 901 4.035675 AGTTAGAGCAAAAGCAGACAACAC 59.964 41.667 0.00 0.00 0.00 3.32
870 902 4.199310 AGTTAGAGCAAAAGCAGACAACA 58.801 39.130 0.00 0.00 0.00 3.33
871 903 4.273480 TGAGTTAGAGCAAAAGCAGACAAC 59.727 41.667 0.00 0.00 0.00 3.32
872 904 4.450976 TGAGTTAGAGCAAAAGCAGACAA 58.549 39.130 0.00 0.00 0.00 3.18
873 905 4.071961 TGAGTTAGAGCAAAAGCAGACA 57.928 40.909 0.00 0.00 0.00 3.41
876 908 5.388944 GTTGATGAGTTAGAGCAAAAGCAG 58.611 41.667 0.00 0.00 0.00 4.24
877 909 4.083855 CGTTGATGAGTTAGAGCAAAAGCA 60.084 41.667 0.00 0.00 0.00 3.91
879 911 4.670221 GCCGTTGATGAGTTAGAGCAAAAG 60.670 45.833 0.00 0.00 0.00 2.27
880 912 3.188460 GCCGTTGATGAGTTAGAGCAAAA 59.812 43.478 0.00 0.00 0.00 2.44
881 913 2.742053 GCCGTTGATGAGTTAGAGCAAA 59.258 45.455 0.00 0.00 0.00 3.68
882 914 2.028112 AGCCGTTGATGAGTTAGAGCAA 60.028 45.455 0.00 0.00 0.00 3.91
883 915 1.550524 AGCCGTTGATGAGTTAGAGCA 59.449 47.619 0.00 0.00 0.00 4.26
885 917 3.849911 TCAAGCCGTTGATGAGTTAGAG 58.150 45.455 0.00 0.00 37.79 2.43
886 918 3.953712 TCAAGCCGTTGATGAGTTAGA 57.046 42.857 0.00 0.00 37.79 2.10
895 927 2.224185 ACACTACACATCAAGCCGTTGA 60.224 45.455 0.00 0.00 46.81 3.18
896 928 2.143122 ACACTACACATCAAGCCGTTG 58.857 47.619 0.00 0.00 34.67 4.10
897 929 2.413837 GACACTACACATCAAGCCGTT 58.586 47.619 0.00 0.00 0.00 4.44
898 930 1.668919 CGACACTACACATCAAGCCGT 60.669 52.381 0.00 0.00 0.00 5.68
899 931 0.992072 CGACACTACACATCAAGCCG 59.008 55.000 0.00 0.00 0.00 5.52
900 932 1.993370 GACGACACTACACATCAAGCC 59.007 52.381 0.00 0.00 0.00 4.35
901 933 1.993370 GGACGACACTACACATCAAGC 59.007 52.381 0.00 0.00 0.00 4.01
902 934 2.251040 CGGACGACACTACACATCAAG 58.749 52.381 0.00 0.00 0.00 3.02
903 935 1.667756 GCGGACGACACTACACATCAA 60.668 52.381 0.00 0.00 0.00 2.57
904 936 0.109458 GCGGACGACACTACACATCA 60.109 55.000 0.00 0.00 0.00 3.07
905 937 0.170561 AGCGGACGACACTACACATC 59.829 55.000 0.00 0.00 0.00 3.06
906 938 0.109272 CAGCGGACGACACTACACAT 60.109 55.000 0.00 0.00 0.00 3.21
907 939 1.167781 TCAGCGGACGACACTACACA 61.168 55.000 0.00 0.00 0.00 3.72
908 940 0.170561 ATCAGCGGACGACACTACAC 59.829 55.000 0.00 0.00 0.00 2.90
909 941 0.450583 GATCAGCGGACGACACTACA 59.549 55.000 0.00 0.00 0.00 2.74
910 942 0.589229 CGATCAGCGGACGACACTAC 60.589 60.000 0.00 0.00 36.03 2.73
911 943 1.022982 ACGATCAGCGGACGACACTA 61.023 55.000 13.53 0.00 46.49 2.74
912 944 2.254703 GACGATCAGCGGACGACACT 62.255 60.000 13.53 0.00 46.49 3.55
914 946 2.483745 GACGATCAGCGGACGACA 59.516 61.111 13.53 0.00 46.49 4.35
915 947 2.278013 GGACGATCAGCGGACGAC 60.278 66.667 13.53 8.56 46.49 4.34
918 950 0.931005 GATTTGGACGATCAGCGGAC 59.069 55.000 0.00 0.00 46.49 4.79
919 951 0.824109 AGATTTGGACGATCAGCGGA 59.176 50.000 0.00 0.00 46.49 5.54
922 954 1.590238 CGACAGATTTGGACGATCAGC 59.410 52.381 0.00 0.00 32.75 4.26
926 958 2.231478 ACAGACGACAGATTTGGACGAT 59.769 45.455 10.80 0.00 34.26 3.73
927 959 1.611977 ACAGACGACAGATTTGGACGA 59.388 47.619 10.80 0.00 34.26 4.20
928 960 1.721389 CACAGACGACAGATTTGGACG 59.279 52.381 0.00 4.22 35.49 4.79
930 962 3.614150 GCTACACAGACGACAGATTTGGA 60.614 47.826 0.00 0.00 0.00 3.53
931 963 2.668457 GCTACACAGACGACAGATTTGG 59.332 50.000 0.00 0.00 0.00 3.28
932 964 3.317150 TGCTACACAGACGACAGATTTG 58.683 45.455 0.00 0.00 0.00 2.32
945 977 1.079819 GGAAGAGCGCTGCTACACA 60.080 57.895 18.48 0.00 39.88 3.72
946 978 1.811679 GGGAAGAGCGCTGCTACAC 60.812 63.158 18.48 0.00 39.88 2.90
948 980 1.811679 GTGGGAAGAGCGCTGCTAC 60.812 63.158 18.48 0.61 39.88 3.58
950 982 4.400961 GGTGGGAAGAGCGCTGCT 62.401 66.667 18.48 9.38 43.88 4.24
952 984 3.551496 TTGGGTGGGAAGAGCGCTG 62.551 63.158 18.48 0.00 0.00 5.18
953 985 2.829384 TTTGGGTGGGAAGAGCGCT 61.829 57.895 11.27 11.27 0.00 5.92
954 986 2.282180 TTTGGGTGGGAAGAGCGC 60.282 61.111 0.00 0.00 0.00 5.92
955 987 1.971695 GGTTTGGGTGGGAAGAGCG 60.972 63.158 0.00 0.00 0.00 5.03
956 988 1.606601 GGGTTTGGGTGGGAAGAGC 60.607 63.158 0.00 0.00 0.00 4.09
957 989 0.038310 GAGGGTTTGGGTGGGAAGAG 59.962 60.000 0.00 0.00 0.00 2.85
958 990 1.774894 CGAGGGTTTGGGTGGGAAGA 61.775 60.000 0.00 0.00 0.00 2.87
959 991 1.303317 CGAGGGTTTGGGTGGGAAG 60.303 63.158 0.00 0.00 0.00 3.46
960 992 2.840576 CGAGGGTTTGGGTGGGAA 59.159 61.111 0.00 0.00 0.00 3.97
961 993 3.961414 GCGAGGGTTTGGGTGGGA 61.961 66.667 0.00 0.00 0.00 4.37
963 995 3.920093 GAGGCGAGGGTTTGGGTGG 62.920 68.421 0.00 0.00 0.00 4.61
964 996 2.359975 GAGGCGAGGGTTTGGGTG 60.360 66.667 0.00 0.00 0.00 4.61
1197 10718 2.602267 TCGCCCCGTTGGAAGAGA 60.602 61.111 0.00 0.00 35.39 3.10
1328 10855 1.303317 GATTTGTCCCAGGTGCGGT 60.303 57.895 0.00 0.00 0.00 5.68
1343 10870 1.210478 CCAAGACCATGAGGACGGATT 59.790 52.381 0.00 0.00 38.69 3.01
1344 10871 0.833287 CCAAGACCATGAGGACGGAT 59.167 55.000 0.00 0.00 38.69 4.18
1411 11013 2.049156 CGCACTGAAGCTGACCGA 60.049 61.111 0.00 0.00 0.00 4.69
1575 11185 1.484240 GGGTGATGAAGAGAGGTGAGG 59.516 57.143 0.00 0.00 0.00 3.86
1600 11210 4.427312 GCAGCCAAATTGGTAAATCTGAG 58.573 43.478 14.17 0.00 40.46 3.35
1660 11279 1.012086 CACTCGATGATGCCACCAAG 58.988 55.000 0.00 0.00 0.00 3.61
1699 11318 1.391485 CGGCTTCTCGAACATTGACAG 59.609 52.381 0.00 0.00 0.00 3.51
1731 11350 1.305297 TGTCGCCATGAGAGTCCCT 60.305 57.895 0.00 0.00 0.00 4.20
1754 11412 2.892425 CGAATCCCAGCAGTCCGC 60.892 66.667 0.00 0.00 42.91 5.54
1758 11416 2.437359 GCAGCGAATCCCAGCAGT 60.437 61.111 0.00 0.00 35.48 4.40
1932 11641 2.323999 AAATGATTTGGGTGCCCTCA 57.676 45.000 8.91 4.59 36.94 3.86
2125 11878 0.608856 CATGTTGCCAGGTGCCACTA 60.609 55.000 0.00 0.00 40.16 2.74
2134 11887 7.837202 ACATATTTTCATTTCATGTTGCCAG 57.163 32.000 0.00 0.00 0.00 4.85
2266 12430 2.711547 ACCAGGCTTTTCCTTACTCACT 59.288 45.455 0.00 0.00 44.75 3.41
2393 12585 4.655963 AGCTTGCTCCATTAACTTGAGAA 58.344 39.130 2.74 0.00 0.00 2.87
2394 12586 4.019860 AGAGCTTGCTCCATTAACTTGAGA 60.020 41.667 17.78 0.00 0.00 3.27
2690 12929 8.373992 GCGAGCTAATAAATATTAACGGAAGAG 58.626 37.037 0.00 0.00 0.00 2.85
2707 12946 1.757118 TCAGCAAGTAGGCGAGCTAAT 59.243 47.619 0.00 0.00 39.27 1.73
2732 12971 3.056607 ACAGGTGAAAAACTGCCATATGC 60.057 43.478 0.00 0.00 38.25 3.14
2735 12974 3.561143 ACACAGGTGAAAAACTGCCATA 58.439 40.909 6.40 0.00 38.25 2.74
2736 12975 2.387757 ACACAGGTGAAAAACTGCCAT 58.612 42.857 6.40 0.00 38.25 4.40
2738 12977 2.539476 CAACACAGGTGAAAAACTGCC 58.461 47.619 6.40 0.00 38.25 4.85
2740 12979 3.508744 AGCAACACAGGTGAAAAACTG 57.491 42.857 6.40 0.00 40.48 3.16
2741 12980 4.535526 AAAGCAACACAGGTGAAAAACT 57.464 36.364 6.40 0.00 0.00 2.66
2791 13300 1.271926 CGAAGGGGGTGAAAGATGGTT 60.272 52.381 0.00 0.00 0.00 3.67
2792 13301 0.328258 CGAAGGGGGTGAAAGATGGT 59.672 55.000 0.00 0.00 0.00 3.55
2796 13305 0.828762 TCGTCGAAGGGGGTGAAAGA 60.829 55.000 0.00 0.00 0.00 2.52
2904 13413 3.066064 TGAAGAGCAAAGCGTTTTAAGCA 59.934 39.130 9.19 0.00 37.01 3.91
3029 13569 9.449719 AAAATACTTCTTGATTCGAGGTAACAT 57.550 29.630 1.00 0.00 41.41 2.71
3061 13601 8.477419 TTCACTCCATTGGTTTTTATTCTTCT 57.523 30.769 1.86 0.00 0.00 2.85
3074 13614 5.463061 GTGAACAACATTTTCACTCCATTGG 59.537 40.000 7.77 0.00 46.29 3.16
3110 13650 0.881118 CAGTCACCAATTTCCCACGG 59.119 55.000 0.00 0.00 0.00 4.94
3145 13686 3.504863 CAATTTCTGGTGAGCCAAATCG 58.495 45.455 0.00 0.00 45.51 3.34
3156 13697 4.036380 GTCGAACACTTTCCAATTTCTGGT 59.964 41.667 0.00 0.00 46.51 4.00
3165 13706 2.035449 AGATGTCGTCGAACACTTTCCA 59.965 45.455 0.00 0.00 30.55 3.53
3173 13714 1.324736 GGCATTGAGATGTCGTCGAAC 59.675 52.381 0.00 0.00 35.63 3.95
3195 13736 2.912624 GCCTTGGCACTGTCACAGC 61.913 63.158 4.13 0.00 34.37 4.40
3198 13739 0.675633 ATTTGCCTTGGCACTGTCAC 59.324 50.000 14.52 0.00 0.00 3.67
3214 13755 3.009916 AGCCTCACCATCTCTGAACATTT 59.990 43.478 0.00 0.00 0.00 2.32
3279 13820 0.176680 TTCAGCCTTCGATCCAGCTC 59.823 55.000 0.00 0.00 31.93 4.09
3344 13953 6.915544 TGCATTTCATAAAAACAGCAAACA 57.084 29.167 0.00 0.00 31.85 2.83


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

AutoCloner maintained by Alex Coulton.