Multiple sequence alignment - TraesCS3A01G456300

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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 TraesCS3A01G456300 chr3A 100.000 2976 0 0 1 2976 693465452 693468427 0.000000e+00 5496
1 TraesCS3A01G456300 chr3A 92.211 398 28 1 986 1383 693450428 693450034 7.200000e-156 560
2 TraesCS3A01G456300 chr3A 91.457 398 31 2 988 1385 693444170 693443776 7.250000e-151 544
3 TraesCS3A01G456300 chr3A 81.734 323 49 7 1662 1980 693449755 693449439 8.180000e-66 261
4 TraesCS3A01G456300 chr3D 88.248 1353 84 41 650 1985 557710775 557712069 0.000000e+00 1548
5 TraesCS3A01G456300 chr3D 93.170 937 60 4 2041 2976 338497016 338497949 0.000000e+00 1373
6 TraesCS3A01G456300 chr3D 93.590 390 22 1 988 1377 557699874 557699488 1.990000e-161 579
7 TraesCS3A01G456300 chr3D 91.980 399 29 1 988 1386 557652588 557652193 9.320000e-155 556
8 TraesCS3A01G456300 chr3D 86.895 351 41 4 261 609 557710422 557710769 3.600000e-104 388
9 TraesCS3A01G456300 chr3D 86.335 322 43 1 1659 1980 557699206 557698886 1.700000e-92 350
10 TraesCS3A01G456300 chr3D 87.591 274 16 10 1 258 557708767 557709038 4.820000e-78 302
11 TraesCS3A01G456300 chr3D 86.667 255 18 4 19 258 557710093 557710346 4.890000e-68 268
12 TraesCS3A01G456300 chr3D 77.817 284 57 5 1688 1968 557523448 557523168 1.420000e-38 171
13 TraesCS3A01G456300 chr5D 93.555 931 54 5 2047 2976 428663060 428663985 0.000000e+00 1382
14 TraesCS3A01G456300 chr5D 92.193 935 64 5 2043 2976 546898075 546899001 0.000000e+00 1314
15 TraesCS3A01G456300 chr5D 91.649 934 68 6 2045 2976 531902151 531903076 0.000000e+00 1284
16 TraesCS3A01G456300 chr3B 90.619 1066 57 15 928 1985 739989239 739990269 0.000000e+00 1375
17 TraesCS3A01G456300 chr3B 84.360 633 73 16 261 880 739988014 739988633 5.490000e-167 597
18 TraesCS3A01G456300 chr3B 91.980 399 29 1 988 1386 739951485 739951090 9.320000e-155 556
19 TraesCS3A01G456300 chr3B 91.457 398 31 1 986 1383 739932969 739932575 7.250000e-151 544
20 TraesCS3A01G456300 chr3B 91.228 399 30 2 988 1386 739926145 739925752 3.380000e-149 538
21 TraesCS3A01G456300 chr3B 87.097 310 40 0 1659 1968 739957279 739956970 4.720000e-93 351
22 TraesCS3A01G456300 chr3B 85.266 319 46 1 1662 1980 739932280 739931963 7.950000e-86 327
23 TraesCS3A01G456300 chr3B 85.866 283 24 6 1 268 739985698 739985979 1.350000e-73 287
24 TraesCS3A01G456300 chr3B 86.194 268 21 6 6 258 739986386 739986652 2.920000e-70 276
25 TraesCS3A01G456300 chr3B 85.874 269 21 6 6 258 739987032 739987299 1.360000e-68 270
26 TraesCS3A01G456300 chr3B 85.200 250 22 11 19 258 739987694 739987938 2.960000e-60 243
27 TraesCS3A01G456300 chr1D 92.763 912 63 3 2064 2974 364716465 364717374 0.000000e+00 1315
28 TraesCS3A01G456300 chr6D 91.944 931 66 4 2047 2976 23079561 23078639 0.000000e+00 1295
29 TraesCS3A01G456300 chr2D 91.738 932 72 5 2047 2976 649655089 649654161 0.000000e+00 1290
30 TraesCS3A01G456300 chr6A 91.640 933 69 8 2047 2976 604103911 604102985 0.000000e+00 1282
31 TraesCS3A01G456300 chr4D 91.323 945 70 7 2035 2976 59071180 59072115 0.000000e+00 1280
32 TraesCS3A01G456300 chrUn 78.169 284 56 5 1688 1968 395273510 395273230 3.050000e-40 176
33 TraesCS3A01G456300 chrUn 77.385 283 60 3 1688 1968 252805925 252805645 6.600000e-37 165


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 TraesCS3A01G456300 chr3A 693465452 693468427 2975 False 5496.0 5496 100.000000 1 2976 1 chr3A.!!$F1 2975
1 TraesCS3A01G456300 chr3A 693449439 693450428 989 True 410.5 560 86.972500 986 1980 2 chr3A.!!$R2 994
2 TraesCS3A01G456300 chr3D 338497016 338497949 933 False 1373.0 1373 93.170000 2041 2976 1 chr3D.!!$F1 935
3 TraesCS3A01G456300 chr3D 557708767 557712069 3302 False 626.5 1548 87.350250 1 1985 4 chr3D.!!$F2 1984
4 TraesCS3A01G456300 chr3D 557698886 557699874 988 True 464.5 579 89.962500 988 1980 2 chr3D.!!$R3 992
5 TraesCS3A01G456300 chr5D 428663060 428663985 925 False 1382.0 1382 93.555000 2047 2976 1 chr5D.!!$F1 929
6 TraesCS3A01G456300 chr5D 546898075 546899001 926 False 1314.0 1314 92.193000 2043 2976 1 chr5D.!!$F3 933
7 TraesCS3A01G456300 chr5D 531902151 531903076 925 False 1284.0 1284 91.649000 2045 2976 1 chr5D.!!$F2 931
8 TraesCS3A01G456300 chr3B 739985698 739990269 4571 False 508.0 1375 86.352167 1 1985 6 chr3B.!!$F1 1984
9 TraesCS3A01G456300 chr3B 739931963 739932969 1006 True 435.5 544 88.361500 986 1980 2 chr3B.!!$R4 994
10 TraesCS3A01G456300 chr1D 364716465 364717374 909 False 1315.0 1315 92.763000 2064 2974 1 chr1D.!!$F1 910
11 TraesCS3A01G456300 chr6D 23078639 23079561 922 True 1295.0 1295 91.944000 2047 2976 1 chr6D.!!$R1 929
12 TraesCS3A01G456300 chr2D 649654161 649655089 928 True 1290.0 1290 91.738000 2047 2976 1 chr2D.!!$R1 929
13 TraesCS3A01G456300 chr6A 604102985 604103911 926 True 1282.0 1282 91.640000 2047 2976 1 chr6A.!!$R1 929
14 TraesCS3A01G456300 chr4D 59071180 59072115 935 False 1280.0 1280 91.323000 2035 2976 1 chr4D.!!$F1 941

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
859 2986 0.036732 TCACTCAGGTTGGCATGGTC 59.963 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2041 4819 0.036875 GGTGGAGTTGGACCTCAAGG 59.963 60.0 0.0 0.0 42.17 3.61 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
123 139 7.951565 GCATGATGCATGTTTTAACTAAACAAC 59.048 33.333 13.36 4.18 46.39 3.32
207 224 2.774809 TCACCCGATATCCAACATCCAA 59.225 45.455 0.00 0.00 0.00 3.53
208 225 3.394274 TCACCCGATATCCAACATCCAAT 59.606 43.478 0.00 0.00 0.00 3.16
229 246 6.750039 CCAATATGTTGAAACCAAACCGATAC 59.250 38.462 3.41 0.00 37.53 2.24
242 259 3.002038 ACCGATACGAACCTTCTCTCT 57.998 47.619 0.00 0.00 0.00 3.10
254 271 8.043710 ACGAACCTTCTCTCTGATATTTTGAAT 58.956 33.333 0.00 0.00 0.00 2.57
256 273 8.744568 AACCTTCTCTCTGATATTTTGAATCC 57.255 34.615 0.00 0.00 0.00 3.01
259 276 7.041235 CCTTCTCTCTGATATTTTGAATCCTGC 60.041 40.741 0.00 0.00 0.00 4.85
272 360 3.265221 TGAATCCTGCAGTGATCTTCCTT 59.735 43.478 13.81 0.09 0.00 3.36
323 411 2.115291 GCTTGGATTCCGTGGGCTC 61.115 63.158 0.00 0.00 0.00 4.70
393 482 2.355837 CCTCGGTGGTGTGTGTCG 60.356 66.667 0.00 0.00 0.00 4.35
397 486 1.227147 CGGTGGTGTGTGTCGACTT 60.227 57.895 17.92 0.00 0.00 3.01
406 495 1.933853 GTGTGTCGACTTTGTCTTGCT 59.066 47.619 17.92 0.00 0.00 3.91
407 496 1.933181 TGTGTCGACTTTGTCTTGCTG 59.067 47.619 17.92 0.00 0.00 4.41
433 522 3.784701 ATATGTCGAGTGAGTGGTGTC 57.215 47.619 0.00 0.00 0.00 3.67
439 528 1.230324 GAGTGAGTGGTGTCTTTGGC 58.770 55.000 0.00 0.00 0.00 4.52
462 551 4.444056 CGTTCGGTTGCAATCTTCATTTTT 59.556 37.500 8.32 0.00 0.00 1.94
492 581 7.410485 AGTCTTTCTTCTAAGTTTTTGCTTCG 58.590 34.615 0.00 0.00 0.00 3.79
533 2615 2.704725 TTGGCAAGACAAATCGCTTC 57.295 45.000 0.00 0.00 0.00 3.86
534 2616 1.896220 TGGCAAGACAAATCGCTTCT 58.104 45.000 0.00 0.00 0.00 2.85
609 2692 5.923684 GCATTTGGTCGAAAATACCTCAAAA 59.076 36.000 0.00 0.00 37.91 2.44
612 2695 5.890424 TGGTCGAAAATACCTCAAAATCC 57.110 39.130 0.00 0.00 37.91 3.01
613 2696 5.317808 TGGTCGAAAATACCTCAAAATCCA 58.682 37.500 0.00 0.00 37.91 3.41
614 2697 5.182380 TGGTCGAAAATACCTCAAAATCCAC 59.818 40.000 0.00 0.00 37.91 4.02
615 2698 5.182380 GGTCGAAAATACCTCAAAATCCACA 59.818 40.000 0.00 0.00 33.97 4.17
616 2699 6.127730 GGTCGAAAATACCTCAAAATCCACAT 60.128 38.462 0.00 0.00 33.97 3.21
617 2700 6.747280 GTCGAAAATACCTCAAAATCCACATG 59.253 38.462 0.00 0.00 0.00 3.21
618 2701 6.432783 TCGAAAATACCTCAAAATCCACATGT 59.567 34.615 0.00 0.00 0.00 3.21
619 2702 7.040062 TCGAAAATACCTCAAAATCCACATGTT 60.040 33.333 0.00 0.00 0.00 2.71
620 2703 7.598493 CGAAAATACCTCAAAATCCACATGTTT 59.402 33.333 0.00 0.00 0.00 2.83
621 2704 9.921637 GAAAATACCTCAAAATCCACATGTTTA 57.078 29.630 0.00 0.00 0.00 2.01
622 2705 9.927668 AAAATACCTCAAAATCCACATGTTTAG 57.072 29.630 0.00 0.00 0.00 1.85
623 2706 5.391312 ACCTCAAAATCCACATGTTTAGC 57.609 39.130 0.00 0.00 0.00 3.09
624 2707 4.832266 ACCTCAAAATCCACATGTTTAGCA 59.168 37.500 0.00 0.00 0.00 3.49
625 2708 5.481473 ACCTCAAAATCCACATGTTTAGCAT 59.519 36.000 0.00 0.00 38.60 3.79
626 2709 6.663093 ACCTCAAAATCCACATGTTTAGCATA 59.337 34.615 0.00 0.00 35.74 3.14
627 2710 7.178274 ACCTCAAAATCCACATGTTTAGCATAA 59.822 33.333 0.00 0.00 35.74 1.90
628 2711 8.034215 CCTCAAAATCCACATGTTTAGCATAAA 58.966 33.333 0.00 0.00 35.74 1.40
629 2712 9.590451 CTCAAAATCCACATGTTTAGCATAAAT 57.410 29.630 0.00 0.00 35.74 1.40
630 2713 9.941325 TCAAAATCCACATGTTTAGCATAAATT 57.059 25.926 0.00 0.00 35.74 1.82
634 2717 9.941325 AATCCACATGTTTAGCATAAATTTTCA 57.059 25.926 0.00 0.00 35.74 2.69
635 2718 8.984891 TCCACATGTTTAGCATAAATTTTCAG 57.015 30.769 0.00 0.00 35.74 3.02
636 2719 8.801299 TCCACATGTTTAGCATAAATTTTCAGA 58.199 29.630 0.00 0.00 35.74 3.27
637 2720 9.421806 CCACATGTTTAGCATAAATTTTCAGAA 57.578 29.630 0.00 0.00 35.74 3.02
648 2731 9.750882 GCATAAATTTTCAGAATTTTCTTCAGC 57.249 29.630 0.00 0.00 34.74 4.26
669 2794 3.979495 GCAAAGCATCACAAGAAGACAAG 59.021 43.478 0.00 0.00 0.00 3.16
692 2817 7.488187 AGTGCATTATCATGTGTCAATCTAC 57.512 36.000 0.00 0.00 32.28 2.59
727 2852 8.672823 AATACTCCGTATTTTTCAAGGGATAC 57.327 34.615 0.00 0.00 35.50 2.24
747 2872 3.486383 ACGATCAAAATTGTGAGGTGGT 58.514 40.909 4.31 0.00 0.00 4.16
748 2873 4.647611 ACGATCAAAATTGTGAGGTGGTA 58.352 39.130 4.31 0.00 0.00 3.25
750 2875 5.181245 ACGATCAAAATTGTGAGGTGGTAAG 59.819 40.000 4.31 0.00 0.00 2.34
751 2876 5.411361 CGATCAAAATTGTGAGGTGGTAAGA 59.589 40.000 4.31 0.00 0.00 2.10
752 2877 6.575162 ATCAAAATTGTGAGGTGGTAAGAC 57.425 37.500 4.31 0.00 0.00 3.01
754 2879 4.345859 AAATTGTGAGGTGGTAAGACGA 57.654 40.909 0.00 0.00 0.00 4.20
755 2880 2.806608 TTGTGAGGTGGTAAGACGAC 57.193 50.000 0.00 0.00 0.00 4.34
756 2881 0.594602 TGTGAGGTGGTAAGACGACG 59.405 55.000 0.00 0.00 0.00 5.12
757 2882 0.731855 GTGAGGTGGTAAGACGACGC 60.732 60.000 0.00 0.00 0.00 5.19
758 2883 0.892358 TGAGGTGGTAAGACGACGCT 60.892 55.000 0.00 0.00 0.00 5.07
759 2884 0.243095 GAGGTGGTAAGACGACGCTT 59.757 55.000 9.02 9.02 0.00 4.68
760 2885 0.038526 AGGTGGTAAGACGACGCTTG 60.039 55.000 12.72 0.00 0.00 4.01
761 2886 0.319297 GGTGGTAAGACGACGCTTGT 60.319 55.000 12.72 0.00 0.00 3.16
762 2887 1.058404 GTGGTAAGACGACGCTTGTC 58.942 55.000 12.72 7.30 39.33 3.18
763 2888 0.669619 TGGTAAGACGACGCTTGTCA 59.330 50.000 12.72 8.81 43.03 3.58
764 2889 1.271379 TGGTAAGACGACGCTTGTCAT 59.729 47.619 12.72 0.00 43.03 3.06
765 2890 2.488937 TGGTAAGACGACGCTTGTCATA 59.511 45.455 12.72 0.00 43.03 2.15
794 2919 3.056536 GCTCACTGATGTCCACTACTCAA 60.057 47.826 0.00 0.00 0.00 3.02
795 2920 4.742417 CTCACTGATGTCCACTACTCAAG 58.258 47.826 0.00 0.00 0.00 3.02
797 2922 2.834549 ACTGATGTCCACTACTCAAGGG 59.165 50.000 0.00 0.00 0.00 3.95
798 2923 3.099905 CTGATGTCCACTACTCAAGGGA 58.900 50.000 0.00 0.00 0.00 4.20
799 2924 3.708631 CTGATGTCCACTACTCAAGGGAT 59.291 47.826 0.00 0.00 30.26 3.85
800 2925 4.878968 TGATGTCCACTACTCAAGGGATA 58.121 43.478 0.00 0.00 30.26 2.59
802 2927 4.055710 TGTCCACTACTCAAGGGATACA 57.944 45.455 0.00 0.00 39.74 2.29
804 2929 5.030147 TGTCCACTACTCAAGGGATACAAT 58.970 41.667 0.00 0.00 39.74 2.71
805 2930 5.128827 TGTCCACTACTCAAGGGATACAATC 59.871 44.000 0.00 0.00 39.74 2.67
806 2931 5.128827 GTCCACTACTCAAGGGATACAATCA 59.871 44.000 0.00 0.00 39.74 2.57
857 2984 1.171308 CTTCACTCAGGTTGGCATGG 58.829 55.000 0.00 0.00 0.00 3.66
858 2985 0.478072 TTCACTCAGGTTGGCATGGT 59.522 50.000 0.00 0.00 0.00 3.55
859 2986 0.036732 TCACTCAGGTTGGCATGGTC 59.963 55.000 0.00 0.00 0.00 4.02
861 2988 1.379916 CTCAGGTTGGCATGGTCCA 59.620 57.895 0.00 0.00 0.00 4.02
866 2993 1.047801 GGTTGGCATGGTCCAAAACT 58.952 50.000 6.39 0.00 46.63 2.66
880 3007 4.214758 GTCCAAAACTACTATTGGCACGTT 59.785 41.667 0.00 0.00 44.63 3.99
882 3009 4.214545 CCAAAACTACTATTGGCACGTTCA 59.785 41.667 0.00 0.00 39.64 3.18
884 3011 3.671008 ACTACTATTGGCACGTTCACA 57.329 42.857 0.00 0.00 0.00 3.58
900 3605 3.531934 TCACATGCCAGTGAGATACAG 57.468 47.619 4.39 0.00 43.18 2.74
901 3606 2.833943 TCACATGCCAGTGAGATACAGT 59.166 45.455 4.39 0.00 43.18 3.55
902 3607 4.023291 TCACATGCCAGTGAGATACAGTA 58.977 43.478 4.39 0.00 43.18 2.74
903 3608 4.115516 CACATGCCAGTGAGATACAGTAC 58.884 47.826 0.00 0.00 42.05 2.73
904 3609 4.026744 ACATGCCAGTGAGATACAGTACT 58.973 43.478 0.00 0.00 0.00 2.73
905 3610 4.142071 ACATGCCAGTGAGATACAGTACTG 60.142 45.833 21.44 21.44 40.06 2.74
907 3612 2.428890 GCCAGTGAGATACAGTACTGCT 59.571 50.000 22.90 11.81 39.27 4.24
908 3613 3.490078 GCCAGTGAGATACAGTACTGCTC 60.490 52.174 22.90 19.64 39.27 4.26
909 3614 3.951037 CCAGTGAGATACAGTACTGCTCT 59.049 47.826 22.90 22.45 39.27 4.09
910 3615 4.036262 CCAGTGAGATACAGTACTGCTCTC 59.964 50.000 30.89 30.89 40.35 3.20
911 3616 4.881273 CAGTGAGATACAGTACTGCTCTCT 59.119 45.833 33.78 27.06 40.47 3.10
912 3617 5.007626 CAGTGAGATACAGTACTGCTCTCTC 59.992 48.000 33.78 31.41 40.47 3.20
913 3618 4.025229 GTGAGATACAGTACTGCTCTCTCG 60.025 50.000 33.78 12.27 40.47 4.04
914 3619 3.472652 AGATACAGTACTGCTCTCTCGG 58.527 50.000 22.90 0.00 0.00 4.63
915 3620 1.380524 TACAGTACTGCTCTCTCGGC 58.619 55.000 22.90 0.00 0.00 5.54
916 3621 0.609406 ACAGTACTGCTCTCTCGGCA 60.609 55.000 22.90 0.00 38.10 5.69
917 3622 0.528017 CAGTACTGCTCTCTCGGCAA 59.472 55.000 10.54 0.00 39.30 4.52
918 3623 1.067565 CAGTACTGCTCTCTCGGCAAA 60.068 52.381 10.54 0.00 39.30 3.68
919 3624 1.203523 AGTACTGCTCTCTCGGCAAAG 59.796 52.381 0.00 0.00 39.30 2.77
920 3625 1.202582 GTACTGCTCTCTCGGCAAAGA 59.797 52.381 0.00 0.00 39.30 2.52
921 3626 0.246086 ACTGCTCTCTCGGCAAAGAG 59.754 55.000 8.00 8.00 43.50 2.85
926 3631 0.741326 TCTCTCGGCAAAGAGATCCG 59.259 55.000 11.99 0.00 45.31 4.18
973 3685 4.752879 GGCAACGTAGCGCCCTCA 62.753 66.667 2.29 0.00 42.80 3.86
978 3690 3.812019 CGTAGCGCCCTCACTCGT 61.812 66.667 2.29 0.00 0.00 4.18
1050 3766 2.125326 CATCCTCGTCCACGGCCTA 61.125 63.158 0.00 0.00 40.29 3.93
1399 4116 5.357742 AAGCAAACCTCAAGTTTTCCATT 57.642 34.783 0.00 0.00 46.79 3.16
1406 4123 3.304659 CCTCAAGTTTTCCATTGACACCG 60.305 47.826 0.00 0.00 32.25 4.94
1415 4179 2.956333 TCCATTGACACCGATCGATACT 59.044 45.455 18.66 0.00 0.00 2.12
1466 4233 1.301401 CAGAAGAACCACGCCGGAA 60.301 57.895 5.05 0.00 38.63 4.30
1591 4358 2.427506 CCCAGCTGAGGTAACAAGAAC 58.572 52.381 17.39 0.00 41.41 3.01
1620 4391 4.884668 TTTTCGTCCCAGATGTTCTAGT 57.115 40.909 0.00 0.00 0.00 2.57
1622 4393 2.376109 TCGTCCCAGATGTTCTAGTCC 58.624 52.381 0.00 0.00 0.00 3.85
1624 4395 2.359531 CGTCCCAGATGTTCTAGTCCTC 59.640 54.545 0.00 0.00 0.00 3.71
1625 4396 2.359531 GTCCCAGATGTTCTAGTCCTCG 59.640 54.545 0.00 0.00 0.00 4.63
1627 4398 3.117474 TCCCAGATGTTCTAGTCCTCGAT 60.117 47.826 0.00 0.00 0.00 3.59
1628 4399 3.005261 CCCAGATGTTCTAGTCCTCGATG 59.995 52.174 0.00 0.00 0.00 3.84
1629 4400 3.551863 CCAGATGTTCTAGTCCTCGATGC 60.552 52.174 0.00 0.00 0.00 3.91
1630 4401 3.317711 CAGATGTTCTAGTCCTCGATGCT 59.682 47.826 0.00 0.00 0.00 3.79
1631 4402 3.317711 AGATGTTCTAGTCCTCGATGCTG 59.682 47.826 0.00 0.00 0.00 4.41
1632 4403 2.723273 TGTTCTAGTCCTCGATGCTGA 58.277 47.619 0.00 0.00 0.00 4.26
1633 4404 2.423892 TGTTCTAGTCCTCGATGCTGAC 59.576 50.000 0.00 0.00 0.00 3.51
1634 4405 2.420058 TCTAGTCCTCGATGCTGACA 57.580 50.000 7.12 0.00 0.00 3.58
1635 4406 2.937519 TCTAGTCCTCGATGCTGACAT 58.062 47.619 7.12 0.00 39.98 3.06
1636 4407 2.620585 TCTAGTCCTCGATGCTGACATG 59.379 50.000 0.00 0.00 36.35 3.21
1637 4408 0.463204 AGTCCTCGATGCTGACATGG 59.537 55.000 0.00 0.00 36.35 3.66
1638 4409 0.531532 GTCCTCGATGCTGACATGGG 60.532 60.000 0.00 0.00 36.35 4.00
1639 4410 0.977627 TCCTCGATGCTGACATGGGT 60.978 55.000 0.00 0.00 36.35 4.51
1640 4411 0.107508 CCTCGATGCTGACATGGGTT 60.108 55.000 0.00 0.00 36.35 4.11
1641 4412 1.679944 CCTCGATGCTGACATGGGTTT 60.680 52.381 0.00 0.00 36.35 3.27
1642 4413 2.086869 CTCGATGCTGACATGGGTTTT 58.913 47.619 0.00 0.00 36.35 2.43
1643 4414 3.270027 CTCGATGCTGACATGGGTTTTA 58.730 45.455 0.00 0.00 36.35 1.52
1644 4415 3.006940 TCGATGCTGACATGGGTTTTAC 58.993 45.455 0.00 0.00 36.35 2.01
1645 4416 2.097466 CGATGCTGACATGGGTTTTACC 59.903 50.000 0.00 0.00 36.35 2.85
1646 4417 2.969821 TGCTGACATGGGTTTTACCT 57.030 45.000 0.00 0.00 38.64 3.08
1647 4418 4.523083 GATGCTGACATGGGTTTTACCTA 58.477 43.478 0.00 0.00 35.93 3.08
1648 4419 3.681593 TGCTGACATGGGTTTTACCTAC 58.318 45.455 0.00 0.00 38.64 3.18
1649 4420 2.676342 GCTGACATGGGTTTTACCTACG 59.324 50.000 0.00 0.00 38.64 3.51
1650 4421 3.267483 CTGACATGGGTTTTACCTACGG 58.733 50.000 0.00 0.00 38.64 4.02
1651 4422 2.011947 GACATGGGTTTTACCTACGGC 58.988 52.381 0.00 0.00 38.64 5.68
1652 4423 1.351683 ACATGGGTTTTACCTACGGCA 59.648 47.619 0.00 0.00 38.64 5.69
1653 4424 2.025699 ACATGGGTTTTACCTACGGCAT 60.026 45.455 0.00 0.00 38.64 4.40
1654 4425 3.200385 ACATGGGTTTTACCTACGGCATA 59.800 43.478 0.00 0.00 38.64 3.14
1655 4426 3.264998 TGGGTTTTACCTACGGCATAC 57.735 47.619 0.00 0.00 38.64 2.39
1656 4427 2.570752 TGGGTTTTACCTACGGCATACA 59.429 45.455 0.00 0.00 38.64 2.29
1657 4428 3.008813 TGGGTTTTACCTACGGCATACAA 59.991 43.478 0.00 0.00 38.64 2.41
1753 4528 2.486504 GTGGACGACGCGATGGTA 59.513 61.111 15.93 0.00 0.00 3.25
1774 4549 2.872001 GACGAGACGCTGCTCACG 60.872 66.667 13.71 13.71 34.56 4.35
1788 4563 3.475774 CACGGACGCCAACTACGC 61.476 66.667 0.00 0.00 0.00 4.42
1861 4636 2.827190 ATGCAGCGCTGGATGGTG 60.827 61.111 38.81 14.81 40.21 4.17
1867 4645 2.187946 CGCTGGATGGTGGACCTC 59.812 66.667 0.00 0.00 36.82 3.85
1928 4706 2.133281 CATGGCCATGTTCTCCAAGA 57.867 50.000 33.68 0.00 34.23 3.02
1969 4747 2.125147 CTCAGGATCGCCGGCAAA 60.125 61.111 28.98 14.85 39.96 3.68
1985 4763 2.098770 GGCAAAGCATGACTGAGAATCC 59.901 50.000 0.00 0.00 32.61 3.01
1986 4764 3.015327 GCAAAGCATGACTGAGAATCCT 58.985 45.455 0.00 0.00 0.00 3.24
1987 4765 3.442977 GCAAAGCATGACTGAGAATCCTT 59.557 43.478 0.00 0.00 0.00 3.36
1988 4766 4.674623 GCAAAGCATGACTGAGAATCCTTG 60.675 45.833 0.00 0.00 0.00 3.61
1989 4767 3.996921 AGCATGACTGAGAATCCTTGT 57.003 42.857 0.00 0.00 0.00 3.16
1990 4768 3.871485 AGCATGACTGAGAATCCTTGTC 58.129 45.455 0.00 0.00 0.00 3.18
1991 4769 2.606725 GCATGACTGAGAATCCTTGTCG 59.393 50.000 0.00 0.00 32.58 4.35
1992 4770 2.370281 TGACTGAGAATCCTTGTCGC 57.630 50.000 0.00 0.00 32.58 5.19
1993 4771 1.272781 GACTGAGAATCCTTGTCGCG 58.727 55.000 0.00 0.00 0.00 5.87
1994 4772 0.108615 ACTGAGAATCCTTGTCGCGG 60.109 55.000 6.13 0.00 0.00 6.46
1995 4773 0.108615 CTGAGAATCCTTGTCGCGGT 60.109 55.000 6.13 0.00 0.00 5.68
1996 4774 0.389817 TGAGAATCCTTGTCGCGGTG 60.390 55.000 6.13 0.00 0.00 4.94
1997 4775 0.108804 GAGAATCCTTGTCGCGGTGA 60.109 55.000 6.13 0.00 0.00 4.02
2011 4789 2.908817 GGTGACGGACAATTCGTGT 58.091 52.632 0.00 0.00 45.74 4.49
2012 4790 2.068837 GGTGACGGACAATTCGTGTA 57.931 50.000 0.00 0.00 41.96 2.90
2013 4791 2.613691 GGTGACGGACAATTCGTGTAT 58.386 47.619 0.00 0.00 41.96 2.29
2014 4792 2.997986 GGTGACGGACAATTCGTGTATT 59.002 45.455 0.00 0.00 41.96 1.89
2015 4793 3.181524 GGTGACGGACAATTCGTGTATTG 60.182 47.826 0.00 0.00 41.96 1.90
2017 4795 3.430556 TGACGGACAATTCGTGTATTGTG 59.569 43.478 14.65 7.08 45.98 3.33
2018 4796 2.739913 ACGGACAATTCGTGTATTGTGG 59.260 45.455 14.65 10.27 45.98 4.17
2019 4797 2.739913 CGGACAATTCGTGTATTGTGGT 59.260 45.455 14.65 0.00 45.98 4.16
2020 4798 3.187637 CGGACAATTCGTGTATTGTGGTT 59.812 43.478 14.65 0.00 45.98 3.67
2021 4799 4.472286 GGACAATTCGTGTATTGTGGTTG 58.528 43.478 14.65 0.00 45.98 3.77
2022 4800 4.023536 GGACAATTCGTGTATTGTGGTTGT 60.024 41.667 14.65 0.00 45.98 3.32
2023 4801 4.854399 ACAATTCGTGTATTGTGGTTGTG 58.146 39.130 10.80 0.00 44.71 3.33
2024 4802 4.336993 ACAATTCGTGTATTGTGGTTGTGT 59.663 37.500 10.80 0.00 44.71 3.72
2025 4803 5.527951 ACAATTCGTGTATTGTGGTTGTGTA 59.472 36.000 10.80 0.00 44.71 2.90
2026 4804 6.205853 ACAATTCGTGTATTGTGGTTGTGTAT 59.794 34.615 10.80 0.00 44.71 2.29
2027 4805 7.388224 ACAATTCGTGTATTGTGGTTGTGTATA 59.612 33.333 10.80 0.00 44.71 1.47
2028 4806 7.908827 ATTCGTGTATTGTGGTTGTGTATAA 57.091 32.000 0.00 0.00 0.00 0.98
2029 4807 6.709145 TCGTGTATTGTGGTTGTGTATAAC 57.291 37.500 0.00 0.00 0.00 1.89
2030 4808 6.457355 TCGTGTATTGTGGTTGTGTATAACT 58.543 36.000 0.00 0.00 0.00 2.24
2031 4809 6.366604 TCGTGTATTGTGGTTGTGTATAACTG 59.633 38.462 0.00 0.00 0.00 3.16
2032 4810 6.146510 CGTGTATTGTGGTTGTGTATAACTGT 59.853 38.462 0.00 0.00 0.00 3.55
2033 4811 7.328982 CGTGTATTGTGGTTGTGTATAACTGTA 59.671 37.037 0.00 0.00 0.00 2.74
2034 4812 8.437742 GTGTATTGTGGTTGTGTATAACTGTAC 58.562 37.037 0.00 0.00 0.00 2.90
2035 4813 6.715344 ATTGTGGTTGTGTATAACTGTACG 57.285 37.500 0.00 0.00 0.00 3.67
2036 4814 5.199024 TGTGGTTGTGTATAACTGTACGT 57.801 39.130 0.00 0.00 0.00 3.57
2037 4815 5.221880 TGTGGTTGTGTATAACTGTACGTC 58.778 41.667 0.00 0.00 0.00 4.34
2038 4816 4.622740 GTGGTTGTGTATAACTGTACGTCC 59.377 45.833 0.00 0.00 0.00 4.79
2039 4817 3.853671 GGTTGTGTATAACTGTACGTCCG 59.146 47.826 0.00 0.00 0.00 4.79
2040 4818 3.763097 TGTGTATAACTGTACGTCCGG 57.237 47.619 0.00 0.00 0.00 5.14
2041 4819 2.159393 TGTGTATAACTGTACGTCCGGC 60.159 50.000 0.00 0.00 0.00 6.13
2042 4820 1.405105 TGTATAACTGTACGTCCGGCC 59.595 52.381 0.00 0.00 0.00 6.13
2043 4821 1.678101 GTATAACTGTACGTCCGGCCT 59.322 52.381 0.00 0.00 0.00 5.19
2049 4827 2.283388 TACGTCCGGCCTTGAGGT 60.283 61.111 17.85 17.85 37.57 3.85
2061 4839 0.764890 CTTGAGGTCCAACTCCACCA 59.235 55.000 0.00 0.00 36.66 4.17
2065 4843 1.074775 GGTCCAACTCCACCATGCA 59.925 57.895 0.00 0.00 32.33 3.96
2111 4889 4.737353 GTTTGAGGTAAAACGGACGAAT 57.263 40.909 0.00 0.00 30.90 3.34
2176 4954 1.218316 GTCCGCTTTCGACCCATCT 59.782 57.895 0.00 0.00 38.10 2.90
2216 4994 1.960689 CTTTTGGGGTGAAACGGACAT 59.039 47.619 0.00 0.00 38.12 3.06
2220 4998 0.250553 GGGGTGAAACGGACATCACA 60.251 55.000 8.04 0.00 46.07 3.58
2298 5079 0.656259 GCGTCTTTTTCTATCCGCCC 59.344 55.000 0.00 0.00 35.45 6.13
2299 5080 1.296727 CGTCTTTTTCTATCCGCCCC 58.703 55.000 0.00 0.00 0.00 5.80
2347 5129 2.843113 CCATTCTTCTCCACTCTTCCCT 59.157 50.000 0.00 0.00 0.00 4.20
2668 5457 0.810031 GCCGGCAGATACACGAATGT 60.810 55.000 24.80 0.00 43.30 2.71
2707 5496 1.202268 GCTAGCCTAAAAGCTCGTCGA 60.202 52.381 2.29 0.00 43.67 4.20
2732 5521 0.796312 CGTTGCCGCTCATTAAGTGT 59.204 50.000 0.00 0.00 33.38 3.55
2785 5576 0.892755 TCTACAACGCCGGAACATCT 59.107 50.000 5.05 0.00 0.00 2.90
2920 5713 5.512232 GGATGCAAGTTTTGGTATTGGGAAA 60.512 40.000 0.00 0.00 0.00 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 8.950210 TGCAGAAAATTCTTACTCTTAGATTGG 58.050 33.333 0.00 0.00 34.74 3.16
207 224 5.875910 TCGTATCGGTTTGGTTTCAACATAT 59.124 36.000 0.00 0.00 31.78 1.78
208 225 5.236282 TCGTATCGGTTTGGTTTCAACATA 58.764 37.500 0.00 0.00 31.78 2.29
229 246 7.834068 TTCAAAATATCAGAGAGAAGGTTCG 57.166 36.000 0.00 0.00 0.00 3.95
242 259 7.058525 AGATCACTGCAGGATTCAAAATATCA 58.941 34.615 19.93 0.00 0.00 2.15
254 271 2.544721 AGAAGGAAGATCACTGCAGGA 58.455 47.619 19.93 12.85 0.00 3.86
256 273 2.419324 GCAAGAAGGAAGATCACTGCAG 59.581 50.000 13.48 13.48 31.76 4.41
259 276 6.373774 ACTTTATGCAAGAAGGAAGATCACTG 59.626 38.462 14.58 0.00 36.21 3.66
298 386 2.409870 CGGAATCCAAGCCAGCCAC 61.410 63.158 0.00 0.00 0.00 5.01
337 425 1.202639 TCCACATGTGCCATCGGTATC 60.203 52.381 20.81 0.00 0.00 2.24
341 429 1.371337 CTGTCCACATGTGCCATCGG 61.371 60.000 20.81 5.79 0.00 4.18
342 430 1.985447 GCTGTCCACATGTGCCATCG 61.985 60.000 20.81 6.51 0.00 3.84
368 456 0.182775 ACACCACCGAGGAAAAGCTT 59.817 50.000 0.00 0.00 41.22 3.74
371 460 0.944386 CACACACCACCGAGGAAAAG 59.056 55.000 0.00 0.00 41.22 2.27
376 465 2.355837 CGACACACACCACCGAGG 60.356 66.667 0.00 0.00 45.67 4.63
379 468 0.808453 AAAGTCGACACACACCACCG 60.808 55.000 19.50 0.00 0.00 4.94
393 482 4.574599 ATTTCCACAGCAAGACAAAGTC 57.425 40.909 0.00 0.00 0.00 3.01
397 486 4.154015 CGACATATTTCCACAGCAAGACAA 59.846 41.667 0.00 0.00 0.00 3.18
406 495 4.494484 CACTCACTCGACATATTTCCACA 58.506 43.478 0.00 0.00 0.00 4.17
407 496 3.865745 CCACTCACTCGACATATTTCCAC 59.134 47.826 0.00 0.00 0.00 4.02
433 522 0.318614 ATTGCAACCGAACGCCAAAG 60.319 50.000 0.00 0.00 0.00 2.77
439 528 2.900122 ATGAAGATTGCAACCGAACG 57.100 45.000 0.00 0.00 0.00 3.95
470 559 6.495706 ACCGAAGCAAAAACTTAGAAGAAAG 58.504 36.000 0.00 0.00 0.00 2.62
486 575 5.142061 TCTATTGTCAACTAACCGAAGCA 57.858 39.130 0.00 0.00 0.00 3.91
487 576 6.663944 AATCTATTGTCAACTAACCGAAGC 57.336 37.500 0.00 0.00 0.00 3.86
492 581 9.516314 GCCAATTAAATCTATTGTCAACTAACC 57.484 33.333 0.00 0.00 32.38 2.85
553 2636 4.802039 TGAATGTTTAACTCTATCCGTCGC 59.198 41.667 0.00 0.00 0.00 5.19
569 2652 9.033481 CGACCAAATGCAATAAATATGAATGTT 57.967 29.630 0.00 0.00 0.00 2.71
582 2665 5.184864 TGAGGTATTTTCGACCAAATGCAAT 59.815 36.000 11.23 1.85 39.65 3.56
588 2671 6.265649 TGGATTTTGAGGTATTTTCGACCAAA 59.734 34.615 0.00 0.00 39.65 3.28
594 2677 6.620678 ACATGTGGATTTTGAGGTATTTTCG 58.379 36.000 0.00 0.00 0.00 3.46
609 2692 9.590451 CTGAAAATTTATGCTAAACATGTGGAT 57.410 29.630 0.00 0.00 40.06 3.41
622 2705 9.750882 GCTGAAGAAAATTCTGAAAATTTATGC 57.249 29.630 0.00 0.00 37.65 3.14
627 2710 8.340443 GCTTTGCTGAAGAAAATTCTGAAAATT 58.660 29.630 0.00 0.00 37.65 1.82
628 2711 7.496591 TGCTTTGCTGAAGAAAATTCTGAAAAT 59.503 29.630 0.00 0.00 37.65 1.82
629 2712 6.817641 TGCTTTGCTGAAGAAAATTCTGAAAA 59.182 30.769 0.00 0.89 37.65 2.29
630 2713 6.339730 TGCTTTGCTGAAGAAAATTCTGAAA 58.660 32.000 0.00 0.00 37.65 2.69
631 2714 5.904941 TGCTTTGCTGAAGAAAATTCTGAA 58.095 33.333 0.00 0.00 37.65 3.02
632 2715 5.518848 TGCTTTGCTGAAGAAAATTCTGA 57.481 34.783 0.00 0.00 37.65 3.27
633 2716 5.924254 TGATGCTTTGCTGAAGAAAATTCTG 59.076 36.000 0.00 0.00 37.65 3.02
634 2717 5.924825 GTGATGCTTTGCTGAAGAAAATTCT 59.075 36.000 4.84 0.00 37.57 2.40
635 2718 5.693104 TGTGATGCTTTGCTGAAGAAAATTC 59.307 36.000 4.84 0.00 37.57 2.17
636 2719 5.603596 TGTGATGCTTTGCTGAAGAAAATT 58.396 33.333 4.84 0.00 37.57 1.82
637 2720 5.204409 TGTGATGCTTTGCTGAAGAAAAT 57.796 34.783 4.84 0.00 37.57 1.82
638 2721 4.652421 TGTGATGCTTTGCTGAAGAAAA 57.348 36.364 4.84 0.00 37.57 2.29
639 2722 4.338964 TCTTGTGATGCTTTGCTGAAGAAA 59.661 37.500 4.84 0.00 37.57 2.52
640 2723 3.884693 TCTTGTGATGCTTTGCTGAAGAA 59.115 39.130 4.84 0.00 37.57 2.52
641 2724 3.479489 TCTTGTGATGCTTTGCTGAAGA 58.521 40.909 4.84 0.00 37.57 2.87
642 2725 3.909776 TCTTGTGATGCTTTGCTGAAG 57.090 42.857 0.00 0.00 38.45 3.02
643 2726 3.884693 TCTTCTTGTGATGCTTTGCTGAA 59.115 39.130 0.00 0.00 0.00 3.02
644 2727 3.251729 GTCTTCTTGTGATGCTTTGCTGA 59.748 43.478 0.00 0.00 0.00 4.26
645 2728 3.004002 TGTCTTCTTGTGATGCTTTGCTG 59.996 43.478 0.00 0.00 0.00 4.41
646 2729 3.216800 TGTCTTCTTGTGATGCTTTGCT 58.783 40.909 0.00 0.00 0.00 3.91
647 2730 3.631145 TGTCTTCTTGTGATGCTTTGC 57.369 42.857 0.00 0.00 0.00 3.68
648 2731 4.974275 CACTTGTCTTCTTGTGATGCTTTG 59.026 41.667 0.00 0.00 32.72 2.77
652 2777 2.291465 TGCACTTGTCTTCTTGTGATGC 59.709 45.455 0.00 0.00 32.72 3.91
669 2794 7.250445 TGTAGATTGACACATGATAATGCAC 57.750 36.000 0.00 0.00 0.00 4.57
727 2852 5.411361 TCTTACCACCTCACAATTTTGATCG 59.589 40.000 0.00 0.00 0.00 3.69
747 2872 2.098607 CCCTATGACAAGCGTCGTCTTA 59.901 50.000 0.00 2.93 45.80 2.10
748 2873 1.135083 CCCTATGACAAGCGTCGTCTT 60.135 52.381 0.00 0.00 45.80 3.01
750 2875 0.454600 TCCCTATGACAAGCGTCGTC 59.545 55.000 0.00 0.00 45.80 4.20
751 2876 0.172803 GTCCCTATGACAAGCGTCGT 59.827 55.000 0.00 0.00 45.80 4.34
752 2877 2.959275 GTCCCTATGACAAGCGTCG 58.041 57.895 0.00 0.00 45.80 5.12
760 2885 2.103373 TCAGTGAGCAGTCCCTATGAC 58.897 52.381 0.00 0.00 44.82 3.06
761 2886 2.532250 TCAGTGAGCAGTCCCTATGA 57.468 50.000 0.00 0.00 0.00 2.15
762 2887 2.433604 ACATCAGTGAGCAGTCCCTATG 59.566 50.000 0.00 0.00 0.00 2.23
763 2888 2.697751 GACATCAGTGAGCAGTCCCTAT 59.302 50.000 10.48 0.00 0.00 2.57
764 2889 2.103373 GACATCAGTGAGCAGTCCCTA 58.897 52.381 10.48 0.00 0.00 3.53
765 2890 0.901124 GACATCAGTGAGCAGTCCCT 59.099 55.000 10.48 0.00 0.00 4.20
773 2898 4.381398 CCTTGAGTAGTGGACATCAGTGAG 60.381 50.000 0.00 0.00 0.00 3.51
774 2899 3.511540 CCTTGAGTAGTGGACATCAGTGA 59.488 47.826 0.00 0.00 0.00 3.41
794 2919 4.322057 AGCAGGTTTTGATTGTATCCCT 57.678 40.909 0.00 0.00 0.00 4.20
795 2920 5.047377 TCAAAGCAGGTTTTGATTGTATCCC 60.047 40.000 7.14 0.00 40.95 3.85
797 2922 6.681777 AGTCAAAGCAGGTTTTGATTGTATC 58.318 36.000 13.18 1.83 45.67 2.24
798 2923 6.655078 AGTCAAAGCAGGTTTTGATTGTAT 57.345 33.333 13.18 0.00 45.67 2.29
799 2924 6.463995 AAGTCAAAGCAGGTTTTGATTGTA 57.536 33.333 13.18 0.00 45.67 2.41
800 2925 5.343307 AAGTCAAAGCAGGTTTTGATTGT 57.657 34.783 13.18 1.39 45.67 2.71
802 2927 6.461509 CCAGTAAGTCAAAGCAGGTTTTGATT 60.462 38.462 13.18 7.50 45.67 2.57
804 2929 4.338118 CCAGTAAGTCAAAGCAGGTTTTGA 59.662 41.667 7.14 7.14 42.93 2.69
805 2930 4.338118 TCCAGTAAGTCAAAGCAGGTTTTG 59.662 41.667 0.00 2.63 38.97 2.44
806 2931 4.532834 TCCAGTAAGTCAAAGCAGGTTTT 58.467 39.130 0.00 0.00 0.00 2.43
857 2984 3.749609 ACGTGCCAATAGTAGTTTTGGAC 59.250 43.478 20.33 14.35 44.23 4.02
858 2985 4.010667 ACGTGCCAATAGTAGTTTTGGA 57.989 40.909 20.33 6.06 44.23 3.53
859 2986 4.214545 TGAACGTGCCAATAGTAGTTTTGG 59.785 41.667 13.76 13.76 44.29 3.28
861 2988 4.817464 TGTGAACGTGCCAATAGTAGTTTT 59.183 37.500 0.00 0.00 0.00 2.43
880 3007 2.833943 ACTGTATCTCACTGGCATGTGA 59.166 45.455 15.61 15.61 43.72 3.58
882 3009 4.026744 AGTACTGTATCTCACTGGCATGT 58.973 43.478 0.00 0.00 0.00 3.21
884 3011 3.181471 GCAGTACTGTATCTCACTGGCAT 60.181 47.826 23.44 0.00 39.02 4.40
899 3604 1.203523 CTTTGCCGAGAGAGCAGTACT 59.796 52.381 0.00 0.00 42.17 2.73
900 3605 1.202582 TCTTTGCCGAGAGAGCAGTAC 59.797 52.381 0.00 0.00 42.17 2.73
901 3606 1.474478 CTCTTTGCCGAGAGAGCAGTA 59.526 52.381 7.48 0.00 44.78 2.74
902 3607 0.246086 CTCTTTGCCGAGAGAGCAGT 59.754 55.000 7.48 0.00 44.78 4.40
903 3608 0.529833 TCTCTTTGCCGAGAGAGCAG 59.470 55.000 11.01 0.00 45.39 4.24
904 3609 2.658548 TCTCTTTGCCGAGAGAGCA 58.341 52.632 11.01 0.00 45.39 4.26
912 3617 1.432270 GCTTCCGGATCTCTTTGCCG 61.432 60.000 4.15 0.00 44.42 5.69
913 3618 1.098129 GGCTTCCGGATCTCTTTGCC 61.098 60.000 4.15 7.23 0.00 4.52
914 3619 1.432270 CGGCTTCCGGATCTCTTTGC 61.432 60.000 4.15 1.38 44.15 3.68
915 3620 2.682893 CGGCTTCCGGATCTCTTTG 58.317 57.895 4.15 0.00 44.15 2.77
968 3680 0.101399 CCGATGAGAACGAGTGAGGG 59.899 60.000 0.00 0.00 0.00 4.30
969 3681 1.064803 CTCCGATGAGAACGAGTGAGG 59.935 57.143 0.00 0.00 41.42 3.86
973 3685 0.811915 CACCTCCGATGAGAACGAGT 59.188 55.000 0.00 0.00 41.42 4.18
978 3690 3.543680 GGATTTCACCTCCGATGAGAA 57.456 47.619 0.00 0.00 41.42 2.87
1110 3826 4.002506 ATGTCCAGCGCGGTGACA 62.003 61.111 37.48 33.36 42.65 3.58
1395 4111 3.371102 AGTATCGATCGGTGTCAATGG 57.629 47.619 16.41 0.00 0.00 3.16
1399 4116 1.202371 GCCAAGTATCGATCGGTGTCA 60.202 52.381 16.41 0.00 0.00 3.58
1406 4123 5.992217 ACCAGAAATTAGCCAAGTATCGATC 59.008 40.000 0.00 0.00 0.00 3.69
1415 4179 4.640771 AGAGTCACCAGAAATTAGCCAA 57.359 40.909 0.00 0.00 0.00 4.52
1466 4233 3.012518 CCTCTCGCTGTCCATGAAAAAT 58.987 45.455 0.00 0.00 0.00 1.82
1523 4290 2.119484 ATTTGGGGCCGAACACGAGA 62.119 55.000 0.00 0.00 0.00 4.04
1591 4358 4.697352 ACATCTGGGACGAAAAAGATTGAG 59.303 41.667 0.00 0.00 0.00 3.02
1620 4391 0.977627 ACCCATGTCAGCATCGAGGA 60.978 55.000 0.00 0.00 31.99 3.71
1622 4393 1.742761 AAACCCATGTCAGCATCGAG 58.257 50.000 0.00 0.00 31.99 4.04
1624 4395 2.097466 GGTAAAACCCATGTCAGCATCG 59.903 50.000 0.00 0.00 31.99 3.84
1625 4396 3.356290 AGGTAAAACCCATGTCAGCATC 58.644 45.455 0.00 0.00 39.75 3.91
1627 4398 2.969821 AGGTAAAACCCATGTCAGCA 57.030 45.000 0.00 0.00 39.75 4.41
1628 4399 2.676342 CGTAGGTAAAACCCATGTCAGC 59.324 50.000 0.00 0.00 39.75 4.26
1645 4416 2.797156 GTCAGCATCTTGTATGCCGTAG 59.203 50.000 6.36 0.00 45.59 3.51
1646 4417 2.167487 TGTCAGCATCTTGTATGCCGTA 59.833 45.455 6.36 0.00 45.59 4.02
1647 4418 1.066215 TGTCAGCATCTTGTATGCCGT 60.066 47.619 6.36 0.00 45.59 5.68
1648 4419 1.655484 TGTCAGCATCTTGTATGCCG 58.345 50.000 6.36 0.00 45.59 5.69
1649 4420 3.243301 CCAATGTCAGCATCTTGTATGCC 60.243 47.826 6.36 0.00 45.59 4.40
1650 4421 3.379372 ACCAATGTCAGCATCTTGTATGC 59.621 43.478 1.74 1.74 44.85 3.14
1651 4422 5.571784 AACCAATGTCAGCATCTTGTATG 57.428 39.130 0.00 0.00 33.50 2.39
1652 4423 6.015180 ACAAAACCAATGTCAGCATCTTGTAT 60.015 34.615 0.00 0.00 33.50 2.29
1653 4424 5.301551 ACAAAACCAATGTCAGCATCTTGTA 59.698 36.000 0.00 0.00 33.50 2.41
1654 4425 4.099881 ACAAAACCAATGTCAGCATCTTGT 59.900 37.500 0.00 0.00 33.50 3.16
1655 4426 4.446385 CACAAAACCAATGTCAGCATCTTG 59.554 41.667 0.00 0.00 33.50 3.02
1656 4427 4.501915 CCACAAAACCAATGTCAGCATCTT 60.502 41.667 0.00 0.00 33.50 2.40
1657 4428 3.006110 CCACAAAACCAATGTCAGCATCT 59.994 43.478 0.00 0.00 33.50 2.90
1668 4439 2.759973 TGCCGGCCACAAAACCAA 60.760 55.556 26.77 0.00 0.00 3.67
1753 4528 1.080434 GAGCAGCGTCTCGTCCTTT 60.080 57.895 0.00 0.00 0.00 3.11
1788 4563 1.694639 GTACACCTTCTTCACCGACG 58.305 55.000 0.00 0.00 0.00 5.12
1928 4706 2.364842 ATCGCAGAGCTCCCTGGT 60.365 61.111 10.93 0.00 43.63 4.00
1969 4747 3.678252 CGACAAGGATTCTCAGTCATGCT 60.678 47.826 7.19 0.00 31.99 3.79
1985 4763 3.103911 GTCCGTCACCGCGACAAG 61.104 66.667 8.23 0.00 45.70 3.16
1986 4764 3.427598 TTGTCCGTCACCGCGACAA 62.428 57.895 8.23 5.27 45.70 3.18
1987 4765 2.702751 AATTGTCCGTCACCGCGACA 62.703 55.000 8.23 0.00 45.70 4.35
1988 4766 1.952266 GAATTGTCCGTCACCGCGAC 61.952 60.000 8.23 0.00 41.62 5.19
1989 4767 1.735198 GAATTGTCCGTCACCGCGA 60.735 57.895 8.23 0.00 0.00 5.87
1990 4768 2.776072 GAATTGTCCGTCACCGCG 59.224 61.111 0.00 0.00 0.00 6.46
1991 4769 2.025418 ACGAATTGTCCGTCACCGC 61.025 57.895 0.00 0.00 34.97 5.68
1992 4770 0.942410 ACACGAATTGTCCGTCACCG 60.942 55.000 0.00 0.00 38.29 4.94
1993 4771 2.068837 TACACGAATTGTCCGTCACC 57.931 50.000 0.00 0.00 39.91 4.02
1994 4772 3.430895 ACAATACACGAATTGTCCGTCAC 59.569 43.478 8.89 0.00 44.79 3.67
1995 4773 3.430556 CACAATACACGAATTGTCCGTCA 59.569 43.478 10.94 0.00 44.79 4.35
1996 4774 3.181524 CCACAATACACGAATTGTCCGTC 60.182 47.826 10.94 0.00 44.79 4.79
1997 4775 2.739913 CCACAATACACGAATTGTCCGT 59.260 45.455 10.94 0.00 44.79 4.69
1998 4776 2.739913 ACCACAATACACGAATTGTCCG 59.260 45.455 10.94 8.04 44.79 4.79
1999 4777 4.023536 ACAACCACAATACACGAATTGTCC 60.024 41.667 10.94 0.00 44.79 4.02
2000 4778 4.909305 CACAACCACAATACACGAATTGTC 59.091 41.667 10.94 0.00 44.79 3.18
2002 4780 4.854399 ACACAACCACAATACACGAATTG 58.146 39.130 0.00 0.00 41.65 2.32
2003 4781 6.811253 ATACACAACCACAATACACGAATT 57.189 33.333 0.00 0.00 0.00 2.17
2004 4782 7.604927 AGTTATACACAACCACAATACACGAAT 59.395 33.333 0.00 0.00 0.00 3.34
2005 4783 6.930164 AGTTATACACAACCACAATACACGAA 59.070 34.615 0.00 0.00 0.00 3.85
2006 4784 6.366604 CAGTTATACACAACCACAATACACGA 59.633 38.462 0.00 0.00 0.00 4.35
2007 4785 6.146510 ACAGTTATACACAACCACAATACACG 59.853 38.462 0.00 0.00 0.00 4.49
2008 4786 7.429636 ACAGTTATACACAACCACAATACAC 57.570 36.000 0.00 0.00 0.00 2.90
2009 4787 7.328982 CGTACAGTTATACACAACCACAATACA 59.671 37.037 0.00 0.00 0.00 2.29
2010 4788 7.329226 ACGTACAGTTATACACAACCACAATAC 59.671 37.037 0.00 0.00 0.00 1.89
2011 4789 7.377398 ACGTACAGTTATACACAACCACAATA 58.623 34.615 0.00 0.00 0.00 1.90
2012 4790 6.225318 ACGTACAGTTATACACAACCACAAT 58.775 36.000 0.00 0.00 0.00 2.71
2013 4791 5.599732 ACGTACAGTTATACACAACCACAA 58.400 37.500 0.00 0.00 0.00 3.33
2014 4792 5.199024 ACGTACAGTTATACACAACCACA 57.801 39.130 0.00 0.00 0.00 4.17
2015 4793 4.622740 GGACGTACAGTTATACACAACCAC 59.377 45.833 0.00 0.00 0.00 4.16
2016 4794 4.615682 CGGACGTACAGTTATACACAACCA 60.616 45.833 0.00 0.00 0.00 3.67
2017 4795 3.853671 CGGACGTACAGTTATACACAACC 59.146 47.826 0.00 0.00 0.00 3.77
2018 4796 3.853671 CCGGACGTACAGTTATACACAAC 59.146 47.826 0.00 0.00 0.00 3.32
2019 4797 3.673052 GCCGGACGTACAGTTATACACAA 60.673 47.826 5.05 0.00 0.00 3.33
2020 4798 2.159393 GCCGGACGTACAGTTATACACA 60.159 50.000 5.05 0.00 0.00 3.72
2021 4799 2.454055 GCCGGACGTACAGTTATACAC 58.546 52.381 5.05 0.00 0.00 2.90
2022 4800 1.405105 GGCCGGACGTACAGTTATACA 59.595 52.381 5.05 0.00 0.00 2.29
2023 4801 1.678101 AGGCCGGACGTACAGTTATAC 59.322 52.381 5.05 0.00 0.00 1.47
2024 4802 2.057137 AGGCCGGACGTACAGTTATA 57.943 50.000 5.05 0.00 0.00 0.98
2025 4803 1.134907 CAAGGCCGGACGTACAGTTAT 60.135 52.381 5.05 0.00 0.00 1.89
2026 4804 0.244450 CAAGGCCGGACGTACAGTTA 59.756 55.000 5.05 0.00 0.00 2.24
2027 4805 1.005394 CAAGGCCGGACGTACAGTT 60.005 57.895 5.05 0.00 0.00 3.16
2028 4806 1.874345 CTCAAGGCCGGACGTACAGT 61.874 60.000 5.05 0.00 0.00 3.55
2029 4807 1.153823 CTCAAGGCCGGACGTACAG 60.154 63.158 5.05 0.00 0.00 2.74
2030 4808 2.642254 CCTCAAGGCCGGACGTACA 61.642 63.158 5.05 0.00 0.00 2.90
2031 4809 2.183555 CCTCAAGGCCGGACGTAC 59.816 66.667 5.05 0.00 0.00 3.67
2032 4810 2.283388 ACCTCAAGGCCGGACGTA 60.283 61.111 5.05 0.00 39.32 3.57
2033 4811 3.692406 GACCTCAAGGCCGGACGT 61.692 66.667 5.05 0.00 39.32 4.34
2034 4812 4.452733 GGACCTCAAGGCCGGACG 62.453 72.222 5.05 0.00 39.32 4.79
2035 4813 2.890766 TTGGACCTCAAGGCCGGAC 61.891 63.158 5.05 0.00 39.32 4.79
2036 4814 2.528127 TTGGACCTCAAGGCCGGA 60.528 61.111 5.05 0.00 39.32 5.14
2037 4815 2.359975 GTTGGACCTCAAGGCCGG 60.360 66.667 0.00 0.00 39.32 6.13
2038 4816 1.376037 GAGTTGGACCTCAAGGCCG 60.376 63.158 0.00 0.00 39.32 6.13
2039 4817 1.002011 GGAGTTGGACCTCAAGGCC 60.002 63.158 0.00 0.00 39.32 5.19
2040 4818 0.606673 GTGGAGTTGGACCTCAAGGC 60.607 60.000 0.00 0.00 39.32 4.35
2041 4819 0.036875 GGTGGAGTTGGACCTCAAGG 59.963 60.000 0.00 0.00 42.17 3.61
2042 4820 0.764890 TGGTGGAGTTGGACCTCAAG 59.235 55.000 0.00 0.00 35.80 3.02
2043 4821 1.073763 CATGGTGGAGTTGGACCTCAA 59.926 52.381 0.00 0.00 32.91 3.02
2049 4827 0.539438 GGTTGCATGGTGGAGTTGGA 60.539 55.000 0.00 0.00 0.00 3.53
2061 4839 1.742761 CGGACAAGATGAGGTTGCAT 58.257 50.000 0.00 0.00 0.00 3.96
2065 4843 1.741770 GCGCGGACAAGATGAGGTT 60.742 57.895 8.83 0.00 0.00 3.50
2127 4905 1.586123 CAAAAGTCCGTTTGCGTTTGG 59.414 47.619 0.00 0.00 36.15 3.28
2129 4907 2.521996 GACAAAAGTCCGTTTGCGTTT 58.478 42.857 5.75 0.00 41.33 3.60
2130 4908 1.202211 GGACAAAAGTCCGTTTGCGTT 60.202 47.619 5.75 0.00 41.33 4.84
2131 4909 0.379316 GGACAAAAGTCCGTTTGCGT 59.621 50.000 5.75 0.00 41.33 5.24
2151 4929 1.265905 GGTCGAAAGCGGACACAAAAT 59.734 47.619 0.00 0.00 38.28 1.82
2195 4973 1.341187 TGTCCGTTTCACCCCAAAAGT 60.341 47.619 0.00 0.00 0.00 2.66
2321 5103 2.192263 GAGTGGAGAAGAATGGAGGGT 58.808 52.381 0.00 0.00 0.00 4.34
2347 5129 2.890371 GGCGGCGAGGAAAGAGTA 59.110 61.111 12.98 0.00 0.00 2.59
2371 5159 0.458669 GCTACAATGGCAGCAGCAAT 59.541 50.000 2.65 0.00 44.61 3.56
2372 5160 0.609957 AGCTACAATGGCAGCAGCAA 60.610 50.000 2.65 0.00 44.61 3.91
2555 5344 3.636231 CCTTCTGGCCCGGTGTCA 61.636 66.667 0.00 0.00 0.00 3.58
2694 5483 1.005294 GGTGCGTCGACGAGCTTTTA 61.005 55.000 39.74 13.76 43.02 1.52
2732 5521 1.414919 ACCTTCTTTACGCAGTGGTCA 59.585 47.619 0.00 0.00 45.73 4.02
2785 5576 1.628340 ACTTGATGAACACCCATCCGA 59.372 47.619 0.00 0.00 41.60 4.55
2839 5632 4.973168 AGTCAAATCTAGAGCACAAACCA 58.027 39.130 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.