Multiple sequence alignment - TraesCS2D01G231300

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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 TraesCS2D01G231300 chr2D 100.000 3143 0 0 1 3143 202571100 202567958 0.000000e+00 5805.0
1 TraesCS2D01G231300 chr2D 89.116 147 13 3 789 932 474662605 474662751 2.490000e-41 180.0
2 TraesCS2D01G231300 chr2B 95.837 2042 62 10 978 3005 256329931 256327899 0.000000e+00 3278.0
3 TraesCS2D01G231300 chr2B 89.110 652 50 5 1 643 256331271 256330632 0.000000e+00 791.0
4 TraesCS2D01G231300 chr2B 92.308 130 10 0 790 919 687383155 687383026 5.350000e-43 185.0
5 TraesCS2D01G231300 chr2B 92.308 130 8 2 781 909 370528304 370528176 1.930000e-42 183.0
6 TraesCS2D01G231300 chr2B 90.647 139 11 2 782 919 778694799 778694936 1.930000e-42 183.0
7 TraesCS2D01G231300 chr2B 89.286 140 13 2 781 919 188392089 188392227 1.160000e-39 174.0
8 TraesCS2D01G231300 chr2A 92.660 2030 81 24 978 2958 229675599 229673589 0.000000e+00 2861.0
9 TraesCS2D01G231300 chr2A 85.868 651 83 3 1 643 229716825 229716176 0.000000e+00 684.0
10 TraesCS2D01G231300 chr7D 83.062 307 45 7 325 627 517593706 517593403 3.990000e-69 272.0
11 TraesCS2D01G231300 chr7D 89.286 140 12 3 781 919 81308045 81308182 4.170000e-39 172.0
12 TraesCS2D01G231300 chr7D 95.918 49 1 1 2971 3018 627197209 627197161 9.350000e-11 78.7
13 TraesCS2D01G231300 chr7B 80.323 371 58 12 237 596 550672004 550671638 1.860000e-67 267.0
14 TraesCS2D01G231300 chr7A 83.566 286 39 7 346 627 592305066 592304785 8.650000e-66 261.0
15 TraesCS2D01G231300 chr3A 81.699 306 51 5 325 628 131456553 131456855 1.870000e-62 250.0
16 TraesCS2D01G231300 chr3D 99.231 130 1 0 3014 3143 29412509 29412638 5.240000e-58 235.0
17 TraesCS2D01G231300 chr3D 93.023 129 7 2 791 919 51673711 51673585 1.490000e-43 187.0
18 TraesCS2D01G231300 chr3D 90.000 50 4 1 2977 3026 550208038 550208086 2.620000e-06 63.9
19 TraesCS2D01G231300 chr5D 99.206 126 1 0 3018 3143 561495204 561495079 8.770000e-56 228.0
20 TraesCS2D01G231300 chr5D 93.893 131 7 1 791 920 521487806 521487936 2.470000e-46 196.0
21 TraesCS2D01G231300 chr3B 96.825 126 4 0 3018 3143 560594756 560594631 8.830000e-51 211.0
22 TraesCS2D01G231300 chr3B 92.308 130 9 1 790 919 749582459 749582331 1.930000e-42 183.0
23 TraesCS2D01G231300 chr3B 90.071 141 12 2 781 920 193090848 193090709 6.920000e-42 182.0
24 TraesCS2D01G231300 chr3B 84.962 133 14 5 3013 3143 20358914 20359042 2.540000e-26 130.0
25 TraesCS2D01G231300 chr4A 78.006 341 56 12 293 628 109446923 109446597 2.470000e-46 196.0
26 TraesCS2D01G231300 chr1A 77.219 338 68 9 258 589 256917749 256918083 4.140000e-44 189.0
27 TraesCS2D01G231300 chr6A 90.580 138 11 2 790 925 60495174 60495037 6.920000e-42 182.0
28 TraesCS2D01G231300 chr4B 90.000 140 12 2 781 919 87102314 87102176 2.490000e-41 180.0
29 TraesCS2D01G231300 chr4B 89.286 140 13 2 781 919 405589346 405589208 1.160000e-39 174.0
30 TraesCS2D01G231300 chr4B 75.521 384 68 21 258 628 439046940 439047310 6.970000e-37 165.0
31 TraesCS2D01G231300 chr6B 89.362 141 14 1 781 920 121669239 121669379 3.220000e-40 176.0
32 TraesCS2D01G231300 chr6B 89.286 140 12 3 781 919 503085620 503085483 4.170000e-39 172.0
33 TraesCS2D01G231300 chr6B 91.176 68 6 0 3017 3084 683233905 683233972 3.340000e-15 93.5
34 TraesCS2D01G231300 chr1D 89.091 110 7 2 3034 3143 468157712 468157816 7.070000e-27 132.0
35 TraesCS2D01G231300 chr6D 91.026 78 4 3 3009 3084 95346893 95346969 5.550000e-18 102.0


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 TraesCS2D01G231300 chr2D 202567958 202571100 3142 True 5805.0 5805 100.0000 1 3143 1 chr2D.!!$R1 3142
1 TraesCS2D01G231300 chr2B 256327899 256331271 3372 True 2034.5 3278 92.4735 1 3005 2 chr2B.!!$R3 3004
2 TraesCS2D01G231300 chr2A 229673589 229675599 2010 True 2861.0 2861 92.6600 978 2958 1 chr2A.!!$R1 1980
3 TraesCS2D01G231300 chr2A 229716176 229716825 649 True 684.0 684 85.8680 1 643 1 chr2A.!!$R2 642

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
695 799 0.025898 GGAGCGCCGAAAAATACGTC 59.974 55.0 2.29 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2271 2822 0.320421 TGAACCAACTCAGCCTACGC 60.32 55.0 0.0 0.0 0.0 4.42 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
30 31 2.892425 CAGTGGCGAATCCGAGGC 60.892 66.667 0.00 0.00 38.22 4.70
46 47 1.553704 GAGGCGAAAGGGGAAGAACTA 59.446 52.381 0.00 0.00 0.00 2.24
47 48 1.278413 AGGCGAAAGGGGAAGAACTAC 59.722 52.381 0.00 0.00 0.00 2.73
53 54 1.482954 AGGGGAAGAACTACGTAGGC 58.517 55.000 25.63 16.85 0.00 3.93
148 149 3.560251 CGATCCCCGGCCAAGGAT 61.560 66.667 20.90 20.90 45.76 3.24
159 160 2.499205 CAAGGATGCGCTCGGGTA 59.501 61.111 9.73 0.00 0.00 3.69
200 201 1.677966 CGAGGAAGACGACAGGGGA 60.678 63.158 0.00 0.00 0.00 4.81
210 213 1.550130 CGACAGGGGAAGTTGGGCTA 61.550 60.000 0.00 0.00 0.00 3.93
230 233 4.141688 GCTAGGCCTTTACTGTGGACTTAT 60.142 45.833 12.58 0.00 38.91 1.73
235 238 4.323562 GCCTTTACTGTGGACTTATGGTCT 60.324 45.833 0.00 0.00 43.97 3.85
245 248 3.430929 GGACTTATGGTCTAGTGGCACAG 60.431 52.174 21.41 14.68 41.75 3.66
342 352 5.479716 ACGCAACTTAGCACATAAATACC 57.520 39.130 0.00 0.00 0.00 2.73
344 354 5.588648 ACGCAACTTAGCACATAAATACCAT 59.411 36.000 0.00 0.00 0.00 3.55
364 374 4.430007 CATGCAATGTTTTGAGCTAGCAT 58.570 39.130 18.83 1.44 40.20 3.79
366 376 3.184541 GCAATGTTTTGAGCTAGCATGG 58.815 45.455 18.83 0.00 34.60 3.66
496 506 9.993454 TTCAAATGATGTTGGATTTTACATGAA 57.007 25.926 0.00 0.00 35.24 2.57
536 546 4.487714 TGCAACCCAACCAACATTTTTA 57.512 36.364 0.00 0.00 0.00 1.52
589 599 9.947669 TGACTTGCAATTTAAATTTGAATTTGG 57.052 25.926 15.97 9.00 38.90 3.28
623 633 8.519799 TTTATCAAGGGACAATTTAGCTTAGG 57.480 34.615 0.00 0.00 0.00 2.69
650 754 1.331756 GTCATTAGCATGGAACGGCAG 59.668 52.381 0.00 0.00 33.60 4.85
652 756 0.394216 ATTAGCATGGAACGGCAGCA 60.394 50.000 0.00 0.00 33.60 4.41
653 757 1.026182 TTAGCATGGAACGGCAGCAG 61.026 55.000 0.00 0.00 33.60 4.24
692 796 2.450160 CAATGGAGCGCCGAAAAATAC 58.550 47.619 2.29 0.00 36.79 1.89
694 798 0.671163 TGGAGCGCCGAAAAATACGT 60.671 50.000 2.29 0.00 36.79 3.57
695 799 0.025898 GGAGCGCCGAAAAATACGTC 59.974 55.000 2.29 0.00 0.00 4.34
696 800 0.025898 GAGCGCCGAAAAATACGTCC 59.974 55.000 2.29 0.00 0.00 4.79
699 803 0.714994 CGCCGAAAAATACGTCCGAA 59.285 50.000 0.00 0.00 0.00 4.30
700 804 1.325338 CGCCGAAAAATACGTCCGAAT 59.675 47.619 0.00 0.00 0.00 3.34
702 806 2.595881 GCCGAAAAATACGTCCGAATCG 60.596 50.000 0.00 0.00 0.00 3.34
713 817 3.607987 CGAATCGCGACGTGCCTC 61.608 66.667 12.93 0.31 44.57 4.70
714 818 2.202623 GAATCGCGACGTGCCTCT 60.203 61.111 12.93 0.00 42.08 3.69
715 819 1.063649 GAATCGCGACGTGCCTCTA 59.936 57.895 12.93 0.00 42.08 2.43
717 821 1.374343 AATCGCGACGTGCCTCTAGA 61.374 55.000 12.93 0.00 42.08 2.43
718 822 1.167155 ATCGCGACGTGCCTCTAGAT 61.167 55.000 12.93 0.00 42.08 1.98
719 823 0.531311 TCGCGACGTGCCTCTAGATA 60.531 55.000 3.71 0.00 42.08 1.98
720 824 0.110599 CGCGACGTGCCTCTAGATAG 60.111 60.000 0.00 0.00 42.08 2.08
723 827 2.033049 GCGACGTGCCTCTAGATAGAAA 59.967 50.000 0.00 0.00 37.76 2.52
724 828 3.304794 GCGACGTGCCTCTAGATAGAAAT 60.305 47.826 0.00 0.00 37.76 2.17
725 829 4.468643 CGACGTGCCTCTAGATAGAAATC 58.531 47.826 0.00 0.00 0.00 2.17
726 830 4.214545 CGACGTGCCTCTAGATAGAAATCT 59.785 45.833 0.00 0.00 44.80 2.40
727 831 5.278071 CGACGTGCCTCTAGATAGAAATCTT 60.278 44.000 0.00 0.00 39.55 2.40
728 832 6.472686 ACGTGCCTCTAGATAGAAATCTTT 57.527 37.500 0.00 0.00 39.55 2.52
729 833 6.508777 ACGTGCCTCTAGATAGAAATCTTTC 58.491 40.000 0.00 0.00 39.55 2.62
730 834 6.096987 ACGTGCCTCTAGATAGAAATCTTTCA 59.903 38.462 5.53 0.00 39.55 2.69
731 835 7.151308 CGTGCCTCTAGATAGAAATCTTTCAT 58.849 38.462 5.53 0.00 39.55 2.57
732 836 7.655328 CGTGCCTCTAGATAGAAATCTTTCATT 59.345 37.037 5.53 0.00 39.55 2.57
733 837 8.772705 GTGCCTCTAGATAGAAATCTTTCATTG 58.227 37.037 5.53 0.00 39.55 2.82
735 839 8.153550 GCCTCTAGATAGAAATCTTTCATTGGA 58.846 37.037 5.53 0.00 39.55 3.53
736 840 9.709495 CCTCTAGATAGAAATCTTTCATTGGAG 57.291 37.037 5.53 4.61 39.55 3.86
742 1251 6.696441 AGAAATCTTTCATTGGAGATGCTC 57.304 37.500 5.53 0.00 39.61 4.26
745 1254 8.051535 AGAAATCTTTCATTGGAGATGCTCTTA 58.948 33.333 5.53 0.00 39.61 2.10
757 1266 7.857456 TGGAGATGCTCTTATAACCACTTTTA 58.143 34.615 0.00 0.00 0.00 1.52
777 1286 6.484818 TTTACGGGAAAAGATTTTACGAGG 57.515 37.500 16.54 3.53 35.74 4.63
781 1290 3.128764 GGGAAAAGATTTTACGAGGGCTG 59.871 47.826 0.00 0.00 31.63 4.85
782 1291 3.756963 GGAAAAGATTTTACGAGGGCTGT 59.243 43.478 0.00 0.00 0.00 4.40
783 1292 4.217767 GGAAAAGATTTTACGAGGGCTGTT 59.782 41.667 0.00 0.00 0.00 3.16
784 1293 4.766404 AAAGATTTTACGAGGGCTGTTG 57.234 40.909 0.00 0.00 0.00 3.33
785 1294 2.711542 AGATTTTACGAGGGCTGTTGG 58.288 47.619 0.00 0.00 0.00 3.77
786 1295 2.304761 AGATTTTACGAGGGCTGTTGGA 59.695 45.455 0.00 0.00 0.00 3.53
787 1296 2.642154 TTTTACGAGGGCTGTTGGAA 57.358 45.000 0.00 0.00 0.00 3.53
788 1297 2.871096 TTTACGAGGGCTGTTGGAAT 57.129 45.000 0.00 0.00 0.00 3.01
789 1298 2.871096 TTACGAGGGCTGTTGGAATT 57.129 45.000 0.00 0.00 0.00 2.17
790 1299 2.396590 TACGAGGGCTGTTGGAATTC 57.603 50.000 0.00 0.00 0.00 2.17
791 1300 0.400213 ACGAGGGCTGTTGGAATTCA 59.600 50.000 7.93 0.00 0.00 2.57
792 1301 1.089920 CGAGGGCTGTTGGAATTCAG 58.910 55.000 7.93 0.00 35.12 3.02
793 1302 1.611673 CGAGGGCTGTTGGAATTCAGT 60.612 52.381 7.93 0.00 34.57 3.41
794 1303 2.519013 GAGGGCTGTTGGAATTCAGTT 58.481 47.619 7.93 0.00 34.57 3.16
795 1304 2.893489 GAGGGCTGTTGGAATTCAGTTT 59.107 45.455 7.93 0.00 34.57 2.66
796 1305 2.629617 AGGGCTGTTGGAATTCAGTTTG 59.370 45.455 7.93 0.00 34.57 2.93
797 1306 2.365293 GGGCTGTTGGAATTCAGTTTGT 59.635 45.455 7.93 0.00 34.57 2.83
798 1307 3.552890 GGGCTGTTGGAATTCAGTTTGTC 60.553 47.826 7.93 0.00 34.57 3.18
799 1308 3.319122 GGCTGTTGGAATTCAGTTTGTCT 59.681 43.478 7.93 0.00 34.57 3.41
800 1309 4.518970 GGCTGTTGGAATTCAGTTTGTCTA 59.481 41.667 7.93 0.00 34.57 2.59
801 1310 5.009610 GGCTGTTGGAATTCAGTTTGTCTAA 59.990 40.000 7.93 0.00 34.57 2.10
802 1311 6.294731 GGCTGTTGGAATTCAGTTTGTCTAAT 60.295 38.462 7.93 0.00 34.57 1.73
803 1312 7.147976 GCTGTTGGAATTCAGTTTGTCTAATT 58.852 34.615 7.93 0.00 34.57 1.40
804 1313 7.327032 GCTGTTGGAATTCAGTTTGTCTAATTC 59.673 37.037 7.93 0.00 37.52 2.17
805 1314 8.231692 TGTTGGAATTCAGTTTGTCTAATTCA 57.768 30.769 7.93 0.00 39.16 2.57
806 1315 8.134895 TGTTGGAATTCAGTTTGTCTAATTCAC 58.865 33.333 7.93 0.00 39.16 3.18
807 1316 7.815840 TGGAATTCAGTTTGTCTAATTCACA 57.184 32.000 7.93 0.00 39.16 3.58
808 1317 8.408043 TGGAATTCAGTTTGTCTAATTCACAT 57.592 30.769 7.93 0.00 39.16 3.21
809 1318 8.514594 TGGAATTCAGTTTGTCTAATTCACATC 58.485 33.333 7.93 0.00 39.16 3.06
810 1319 8.734386 GGAATTCAGTTTGTCTAATTCACATCT 58.266 33.333 7.93 0.00 39.16 2.90
815 1324 9.591792 TCAGTTTGTCTAATTCACATCTAGATG 57.408 33.333 27.63 27.63 44.15 2.90
842 1351 7.849804 TTTTAAGGATGTCACATCTAAGCTC 57.150 36.000 17.46 0.00 0.00 4.09
843 1352 6.798427 TTAAGGATGTCACATCTAAGCTCT 57.202 37.500 17.46 2.09 0.00 4.09
844 1353 4.935352 AGGATGTCACATCTAAGCTCTC 57.065 45.455 17.46 0.00 0.00 3.20
845 1354 4.285020 AGGATGTCACATCTAAGCTCTCA 58.715 43.478 17.46 0.00 0.00 3.27
846 1355 4.099266 AGGATGTCACATCTAAGCTCTCAC 59.901 45.833 17.46 0.00 0.00 3.51
847 1356 4.142071 GGATGTCACATCTAAGCTCTCACA 60.142 45.833 17.46 0.00 0.00 3.58
848 1357 4.871933 TGTCACATCTAAGCTCTCACAA 57.128 40.909 0.00 0.00 0.00 3.33
849 1358 5.213891 TGTCACATCTAAGCTCTCACAAA 57.786 39.130 0.00 0.00 0.00 2.83
850 1359 5.798132 TGTCACATCTAAGCTCTCACAAAT 58.202 37.500 0.00 0.00 0.00 2.32
851 1360 6.935167 TGTCACATCTAAGCTCTCACAAATA 58.065 36.000 0.00 0.00 0.00 1.40
852 1361 7.559486 TGTCACATCTAAGCTCTCACAAATAT 58.441 34.615 0.00 0.00 0.00 1.28
853 1362 8.695456 TGTCACATCTAAGCTCTCACAAATATA 58.305 33.333 0.00 0.00 0.00 0.86
854 1363 9.703892 GTCACATCTAAGCTCTCACAAATATAT 57.296 33.333 0.00 0.00 0.00 0.86
921 1430 9.859427 ATAGACCATAAACAAAATGAACATGTG 57.141 29.630 0.00 0.00 0.00 3.21
922 1431 7.725251 AGACCATAAACAAAATGAACATGTGT 58.275 30.769 0.00 0.00 0.00 3.72
923 1432 7.867403 AGACCATAAACAAAATGAACATGTGTC 59.133 33.333 0.00 0.00 0.00 3.67
924 1433 6.928492 ACCATAAACAAAATGAACATGTGTCC 59.072 34.615 0.00 0.00 0.00 4.02
925 1434 6.089283 CCATAAACAAAATGAACATGTGTCCG 59.911 38.462 0.00 0.00 0.00 4.79
926 1435 4.647424 AACAAAATGAACATGTGTCCGT 57.353 36.364 0.00 0.00 0.00 4.69
927 1436 4.223320 ACAAAATGAACATGTGTCCGTC 57.777 40.909 0.00 0.00 0.00 4.79
928 1437 3.882888 ACAAAATGAACATGTGTCCGTCT 59.117 39.130 0.00 0.00 0.00 4.18
929 1438 5.060506 ACAAAATGAACATGTGTCCGTCTA 58.939 37.500 0.00 0.00 0.00 2.59
930 1439 5.179368 ACAAAATGAACATGTGTCCGTCTAG 59.821 40.000 0.00 0.00 0.00 2.43
931 1440 4.801330 AATGAACATGTGTCCGTCTAGA 57.199 40.909 0.00 0.00 0.00 2.43
932 1441 3.570926 TGAACATGTGTCCGTCTAGAC 57.429 47.619 13.18 13.18 37.28 2.59
933 1442 2.230508 TGAACATGTGTCCGTCTAGACC 59.769 50.000 17.23 4.06 35.83 3.85
934 1443 1.183549 ACATGTGTCCGTCTAGACCC 58.816 55.000 17.23 6.15 35.83 4.46
937 1446 0.538057 TGTGTCCGTCTAGACCCGTT 60.538 55.000 17.23 0.00 35.83 4.44
953 1462 2.351738 CCCGTTGGAATTGCTCTCAAAC 60.352 50.000 0.00 0.00 35.56 2.93
960 1469 3.380142 GAATTGCTCTCAAACGGCAAAA 58.620 40.909 3.79 0.00 46.59 2.44
961 1470 2.490328 TTGCTCTCAAACGGCAAAAG 57.510 45.000 0.00 0.00 41.96 2.27
962 1471 1.388547 TGCTCTCAAACGGCAAAAGT 58.611 45.000 0.00 0.00 32.79 2.66
963 1472 1.333619 TGCTCTCAAACGGCAAAAGTC 59.666 47.619 0.00 0.00 32.79 3.01
964 1473 1.660333 GCTCTCAAACGGCAAAAGTCG 60.660 52.381 0.00 0.00 0.00 4.18
965 1474 1.864711 CTCTCAAACGGCAAAAGTCGA 59.135 47.619 0.00 0.00 0.00 4.20
966 1475 2.281517 TCTCAAACGGCAAAAGTCGAA 58.718 42.857 0.00 0.00 0.00 3.71
967 1476 2.031191 TCTCAAACGGCAAAAGTCGAAC 59.969 45.455 0.00 0.00 0.00 3.95
968 1477 1.738350 TCAAACGGCAAAAGTCGAACA 59.262 42.857 0.00 0.00 0.00 3.18
969 1478 2.161808 TCAAACGGCAAAAGTCGAACAA 59.838 40.909 0.00 0.00 0.00 2.83
970 1479 2.182904 AACGGCAAAAGTCGAACAAC 57.817 45.000 0.00 0.00 0.00 3.32
972 1481 1.673920 ACGGCAAAAGTCGAACAACAT 59.326 42.857 0.00 0.00 0.00 2.71
973 1482 2.286772 ACGGCAAAAGTCGAACAACATC 60.287 45.455 0.00 0.00 0.00 3.06
974 1483 2.286713 CGGCAAAAGTCGAACAACATCA 60.287 45.455 0.00 0.00 0.00 3.07
975 1484 3.042887 GGCAAAAGTCGAACAACATCAC 58.957 45.455 0.00 0.00 0.00 3.06
976 1485 2.713976 GCAAAAGTCGAACAACATCACG 59.286 45.455 0.00 0.00 0.00 4.35
1056 1586 4.856607 GCCTTCTCCGCCTCGTCG 62.857 72.222 0.00 0.00 0.00 5.12
1378 1923 3.144506 CCTGCTCGATCAAATGCCTAAT 58.855 45.455 0.00 0.00 0.00 1.73
1409 1954 4.184629 ACGAATGGAATCTTCTTTCTCCG 58.815 43.478 0.00 0.00 0.00 4.63
1453 2003 1.064758 CCATGGAGACCGAATTCCCAA 60.065 52.381 5.56 0.00 32.29 4.12
1485 2035 2.487775 TGTGTGGCTAACATCCCCTAT 58.512 47.619 0.00 0.00 41.97 2.57
1721 2271 1.152943 CCTCCCTCGTCGAGATCCA 60.153 63.158 23.74 3.34 0.00 3.41
1730 2280 3.610669 CGAGATCCAGCCGAGGGG 61.611 72.222 0.00 0.00 0.00 4.79
1773 2323 2.431683 GAGTGGCTGGGCTTCACA 59.568 61.111 0.00 0.00 34.17 3.58
2165 2715 0.528466 TTGTCAGCGCATCGGATCTC 60.528 55.000 11.47 0.00 0.00 2.75
2271 2822 5.011090 TGTATGTTTAGCAGCTGTCTAGG 57.989 43.478 16.64 0.00 0.00 3.02
2276 2827 1.309950 TAGCAGCTGTCTAGGCGTAG 58.690 55.000 16.64 7.12 34.52 3.51
2343 2894 4.130286 ACCTTAAGCCGAAGATCTCAAG 57.870 45.455 0.00 0.00 0.00 3.02
2490 3041 3.790091 CTGGTAGACAGGACATGACATG 58.210 50.000 14.02 14.02 43.70 3.21
2566 3142 9.161629 ACTGATAATCATGATTTACGAACAACA 57.838 29.630 25.26 9.92 32.50 3.33
2593 3169 3.450457 CCATAGGATCAGGATGCTACTCC 59.550 52.174 11.94 6.23 43.02 3.85
2604 3180 0.690762 TGCTACTCCAGACCAAACCC 59.309 55.000 0.00 0.00 0.00 4.11
2681 3260 5.538849 TGGAAAAATCCTTAACCAACACC 57.461 39.130 0.00 0.00 0.00 4.16
2809 3392 1.074405 TGATGGCAGGAAAGAGTGCTT 59.926 47.619 0.00 0.00 39.76 3.91
2820 3403 7.031975 CAGGAAAGAGTGCTTCATTTTTATCC 58.968 38.462 0.00 0.00 31.82 2.59
2934 3517 4.515567 GTGGGAGAAAAGAAGTAACCTGTG 59.484 45.833 0.00 0.00 0.00 3.66
3001 3584 7.184862 ACTCCCTCCATTTCATAATTCTTGTT 58.815 34.615 0.00 0.00 0.00 2.83
3005 3588 7.546667 CCCTCCATTTCATAATTCTTGTTGTTG 59.453 37.037 0.00 0.00 0.00 3.33
3006 3589 8.090214 CCTCCATTTCATAATTCTTGTTGTTGT 58.910 33.333 0.00 0.00 0.00 3.32
3007 3590 9.480053 CTCCATTTCATAATTCTTGTTGTTGTT 57.520 29.630 0.00 0.00 0.00 2.83
3008 3591 9.829507 TCCATTTCATAATTCTTGTTGTTGTTT 57.170 25.926 0.00 0.00 0.00 2.83
3019 3602 9.705290 ATTCTTGTTGTTGTTTTAGTTCAAACT 57.295 25.926 0.46 0.46 42.91 2.66
3021 3604 9.834628 TCTTGTTGTTGTTTTAGTTCAAACTAG 57.165 29.630 3.08 0.00 42.04 2.57
3022 3605 9.620660 CTTGTTGTTGTTTTAGTTCAAACTAGT 57.379 29.630 3.08 0.00 42.04 2.57
3023 3606 9.968870 TTGTTGTTGTTTTAGTTCAAACTAGTT 57.031 25.926 1.12 1.12 42.04 2.24
3029 3612 9.777575 TTGTTTTAGTTCAAACTAGTTAACTGC 57.222 29.630 24.59 15.70 42.04 4.40
3030 3613 8.400186 TGTTTTAGTTCAAACTAGTTAACTGCC 58.600 33.333 24.59 14.18 42.04 4.85
3031 3614 7.500720 TTTAGTTCAAACTAGTTAACTGCCC 57.499 36.000 24.59 9.09 42.04 5.36
3032 3615 5.043737 AGTTCAAACTAGTTAACTGCCCA 57.956 39.130 18.68 0.00 37.52 5.36
3033 3616 5.631119 AGTTCAAACTAGTTAACTGCCCAT 58.369 37.500 18.68 0.00 37.52 4.00
3034 3617 5.473504 AGTTCAAACTAGTTAACTGCCCATG 59.526 40.000 18.68 10.35 37.52 3.66
3035 3618 3.756434 TCAAACTAGTTAACTGCCCATGC 59.244 43.478 18.56 0.00 38.26 4.06
3036 3619 2.024176 ACTAGTTAACTGCCCATGCG 57.976 50.000 18.56 0.00 41.78 4.73
3037 3620 1.278127 ACTAGTTAACTGCCCATGCGT 59.722 47.619 18.56 0.19 41.78 5.24
3038 3621 2.290071 ACTAGTTAACTGCCCATGCGTT 60.290 45.455 18.56 0.00 41.78 4.84
3039 3622 0.881118 AGTTAACTGCCCATGCGTTG 59.119 50.000 7.48 0.00 41.78 4.10
3040 3623 0.732538 GTTAACTGCCCATGCGTTGC 60.733 55.000 0.00 0.00 41.78 4.17
3041 3624 1.175347 TTAACTGCCCATGCGTTGCA 61.175 50.000 0.00 0.00 44.86 4.08
3050 3633 2.046411 TGCGTTGCATCGGGACAT 60.046 55.556 18.16 0.00 31.71 3.06
3051 3634 1.219393 TGCGTTGCATCGGGACATA 59.781 52.632 18.16 0.00 31.71 2.29
3052 3635 0.391793 TGCGTTGCATCGGGACATAA 60.392 50.000 18.16 0.00 31.71 1.90
3053 3636 0.304705 GCGTTGCATCGGGACATAAG 59.695 55.000 18.16 0.00 0.00 1.73
3054 3637 1.934589 CGTTGCATCGGGACATAAGA 58.065 50.000 9.33 0.00 0.00 2.10
3055 3638 2.276201 CGTTGCATCGGGACATAAGAA 58.724 47.619 9.33 0.00 0.00 2.52
3056 3639 2.675844 CGTTGCATCGGGACATAAGAAA 59.324 45.455 9.33 0.00 0.00 2.52
3057 3640 3.312421 CGTTGCATCGGGACATAAGAAAT 59.688 43.478 9.33 0.00 0.00 2.17
3058 3641 4.552767 CGTTGCATCGGGACATAAGAAATC 60.553 45.833 9.33 0.00 0.00 2.17
3059 3642 4.149511 TGCATCGGGACATAAGAAATCA 57.850 40.909 0.00 0.00 0.00 2.57
3060 3643 4.717877 TGCATCGGGACATAAGAAATCAT 58.282 39.130 0.00 0.00 0.00 2.45
3061 3644 4.516321 TGCATCGGGACATAAGAAATCATG 59.484 41.667 0.00 0.00 0.00 3.07
3062 3645 4.516698 GCATCGGGACATAAGAAATCATGT 59.483 41.667 0.00 0.00 38.08 3.21
3063 3646 5.561532 GCATCGGGACATAAGAAATCATGTG 60.562 44.000 0.00 0.00 35.55 3.21
3064 3647 5.351948 TCGGGACATAAGAAATCATGTGA 57.648 39.130 0.00 0.00 35.55 3.58
3065 3648 5.739959 TCGGGACATAAGAAATCATGTGAA 58.260 37.500 0.00 0.00 35.55 3.18
3066 3649 6.176896 TCGGGACATAAGAAATCATGTGAAA 58.823 36.000 0.00 0.00 35.55 2.69
3067 3650 6.093495 TCGGGACATAAGAAATCATGTGAAAC 59.907 38.462 0.00 0.00 35.55 2.78
3089 3672 9.781834 GAAACATGTATATCTCTAAGATCCTCG 57.218 37.037 0.00 0.00 36.20 4.63
3090 3673 8.871629 AACATGTATATCTCTAAGATCCTCGT 57.128 34.615 0.00 0.00 36.20 4.18
3091 3674 8.275015 ACATGTATATCTCTAAGATCCTCGTG 57.725 38.462 0.00 0.91 36.20 4.35
3092 3675 6.745159 TGTATATCTCTAAGATCCTCGTGC 57.255 41.667 0.00 0.00 36.20 5.34
3093 3676 6.238648 TGTATATCTCTAAGATCCTCGTGCA 58.761 40.000 0.00 0.00 36.20 4.57
3094 3677 5.637006 ATATCTCTAAGATCCTCGTGCAC 57.363 43.478 6.82 6.82 36.20 4.57
3095 3678 2.723273 TCTCTAAGATCCTCGTGCACA 58.277 47.619 18.64 3.15 0.00 4.57
3096 3679 3.291584 TCTCTAAGATCCTCGTGCACAT 58.708 45.455 18.64 1.81 0.00 3.21
3097 3680 3.701542 TCTCTAAGATCCTCGTGCACATT 59.298 43.478 18.64 2.16 0.00 2.71
3098 3681 4.887655 TCTCTAAGATCCTCGTGCACATTA 59.112 41.667 18.64 0.08 0.00 1.90
3099 3682 5.359860 TCTCTAAGATCCTCGTGCACATTAA 59.640 40.000 18.64 0.00 0.00 1.40
3100 3683 5.972935 TCTAAGATCCTCGTGCACATTAAA 58.027 37.500 18.64 0.00 0.00 1.52
3101 3684 4.946784 AAGATCCTCGTGCACATTAAAC 57.053 40.909 18.64 3.88 0.00 2.01
3102 3685 3.937814 AGATCCTCGTGCACATTAAACA 58.062 40.909 18.64 0.00 0.00 2.83
3103 3686 4.323417 AGATCCTCGTGCACATTAAACAA 58.677 39.130 18.64 0.00 0.00 2.83
3104 3687 4.943705 AGATCCTCGTGCACATTAAACAAT 59.056 37.500 18.64 0.00 0.00 2.71
3105 3688 6.112734 AGATCCTCGTGCACATTAAACAATA 58.887 36.000 18.64 0.00 0.00 1.90
3106 3689 6.767902 AGATCCTCGTGCACATTAAACAATAT 59.232 34.615 18.64 0.00 0.00 1.28
3107 3690 6.751514 TCCTCGTGCACATTAAACAATATT 57.248 33.333 18.64 0.00 0.00 1.28
3108 3691 6.550843 TCCTCGTGCACATTAAACAATATTG 58.449 36.000 18.64 14.01 0.00 1.90
3109 3692 6.150307 TCCTCGTGCACATTAAACAATATTGT 59.850 34.615 18.64 15.47 44.72 2.71
3110 3693 6.468956 CCTCGTGCACATTAAACAATATTGTC 59.531 38.462 21.02 7.07 41.31 3.18
3111 3694 6.903419 TCGTGCACATTAAACAATATTGTCA 58.097 32.000 21.02 9.79 41.31 3.58
3112 3695 7.363431 TCGTGCACATTAAACAATATTGTCAA 58.637 30.769 21.02 17.23 41.31 3.18
3113 3696 7.324856 TCGTGCACATTAAACAATATTGTCAAC 59.675 33.333 21.02 7.60 41.31 3.18
3114 3697 7.114106 CGTGCACATTAAACAATATTGTCAACA 59.886 33.333 21.02 9.69 41.31 3.33
3115 3698 8.924691 GTGCACATTAAACAATATTGTCAACAT 58.075 29.630 21.02 8.70 41.31 2.71
3116 3699 9.486497 TGCACATTAAACAATATTGTCAACATT 57.514 25.926 21.02 13.41 41.31 2.71
3125 3708 8.761575 ACAATATTGTCAACATTTGATTCACC 57.238 30.769 15.47 0.00 42.47 4.02
3126 3709 8.366401 ACAATATTGTCAACATTTGATTCACCA 58.634 29.630 15.47 0.00 42.47 4.17
3127 3710 9.373603 CAATATTGTCAACATTTGATTCACCAT 57.626 29.630 7.32 0.00 42.47 3.55
3128 3711 8.936070 ATATTGTCAACATTTGATTCACCATG 57.064 30.769 4.22 4.22 42.47 3.66
3129 3712 5.787953 TGTCAACATTTGATTCACCATGT 57.212 34.783 5.25 5.25 42.47 3.21
3130 3713 6.159299 TGTCAACATTTGATTCACCATGTT 57.841 33.333 13.94 13.94 42.47 2.71
3131 3714 7.282332 TGTCAACATTTGATTCACCATGTTA 57.718 32.000 17.26 5.82 42.47 2.41
3132 3715 7.894708 TGTCAACATTTGATTCACCATGTTAT 58.105 30.769 17.26 1.78 42.47 1.89
3133 3716 9.018582 TGTCAACATTTGATTCACCATGTTATA 57.981 29.630 17.26 9.96 42.47 0.98
3134 3717 9.853555 GTCAACATTTGATTCACCATGTTATAA 57.146 29.630 17.26 8.31 42.47 0.98
3141 3724 7.581213 TGATTCACCATGTTATAAATCACCC 57.419 36.000 0.00 0.00 30.47 4.61
3142 3725 7.353525 TGATTCACCATGTTATAAATCACCCT 58.646 34.615 0.00 0.00 30.47 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 4.508128 TCGCCTCGGATTCGCCAC 62.508 66.667 0.00 0.00 35.94 5.01
16 17 3.303761 TTTCGCCTCGGATTCGCCA 62.304 57.895 0.00 0.00 35.94 5.69
19 20 1.883084 CCCTTTCGCCTCGGATTCG 60.883 63.158 0.00 0.00 37.82 3.34
25 26 1.019805 GTTCTTCCCCTTTCGCCTCG 61.020 60.000 0.00 0.00 0.00 4.63
30 31 2.738013 ACGTAGTTCTTCCCCTTTCG 57.262 50.000 0.00 0.00 37.78 3.46
46 47 1.734137 CGCATCCACTAGCCTACGT 59.266 57.895 0.00 0.00 0.00 3.57
47 48 1.007271 CCGCATCCACTAGCCTACG 60.007 63.158 0.00 0.00 0.00 3.51
53 54 1.278238 GTTTCGTCCGCATCCACTAG 58.722 55.000 0.00 0.00 0.00 2.57
104 105 1.692042 CAGTCATCCAGGCCTCCCT 60.692 63.158 0.00 0.00 44.25 4.20
112 113 1.742880 CCACACGCCAGTCATCCAG 60.743 63.158 0.00 0.00 0.00 3.86
144 145 2.442272 AGTACCCGAGCGCATCCT 60.442 61.111 11.47 0.00 0.00 3.24
148 149 3.755628 GTGGAGTACCCGAGCGCA 61.756 66.667 11.47 0.00 37.93 6.09
174 175 0.313043 TCGTCTTCCTCGTGTTCACC 59.687 55.000 0.00 0.00 0.00 4.02
210 213 3.054361 CCATAAGTCCACAGTAAAGGCCT 60.054 47.826 0.00 0.00 0.00 5.19
230 233 0.679505 GACACTGTGCCACTAGACCA 59.320 55.000 7.90 0.00 0.00 4.02
235 238 3.118408 ACAAAAGAGACACTGTGCCACTA 60.118 43.478 7.90 0.00 0.00 2.74
320 330 4.938832 TGGTATTTATGTGCTAAGTTGCGT 59.061 37.500 0.00 0.00 35.36 5.24
321 331 5.478233 TGGTATTTATGTGCTAAGTTGCG 57.522 39.130 0.00 0.00 35.36 4.85
342 352 3.840468 TGCTAGCTCAAAACATTGCATG 58.160 40.909 17.23 0.00 0.00 4.06
344 354 3.367600 CCATGCTAGCTCAAAACATTGCA 60.368 43.478 17.23 0.00 0.00 4.08
364 374 6.707440 TTCAAAATAAGTTGAGACTTGCCA 57.293 33.333 2.25 0.00 45.46 4.92
366 376 9.899226 AACTATTCAAAATAAGTTGAGACTTGC 57.101 29.630 2.25 0.00 45.46 4.01
496 506 9.869757 GGGTTGCAAATATTCACTAAGTAATTT 57.130 29.630 0.00 0.00 0.00 1.82
584 594 9.671279 GTCCCTTGATAAAAATCAAATCCAAAT 57.329 29.630 2.74 0.00 39.73 2.32
623 633 5.095490 CGTTCCATGCTAATGACCTTTTTC 58.905 41.667 0.00 0.00 35.67 2.29
673 777 1.063469 CGTATTTTTCGGCGCTCCATT 59.937 47.619 7.64 0.00 0.00 3.16
682 786 2.595881 GCGATTCGGACGTATTTTTCGG 60.596 50.000 8.34 0.00 0.00 4.30
683 787 2.611070 GCGATTCGGACGTATTTTTCG 58.389 47.619 8.34 0.00 0.00 3.46
685 789 2.028404 GTCGCGATTCGGACGTATTTTT 59.972 45.455 14.06 0.00 39.05 1.94
692 796 3.594827 CACGTCGCGATTCGGACG 61.595 66.667 30.50 30.50 42.72 4.79
696 800 2.642249 TAGAGGCACGTCGCGATTCG 62.642 60.000 14.06 15.47 43.84 3.34
699 803 1.167155 ATCTAGAGGCACGTCGCGAT 61.167 55.000 14.06 0.00 43.84 4.58
700 804 0.531311 TATCTAGAGGCACGTCGCGA 60.531 55.000 3.71 3.71 43.84 5.87
702 806 1.227639 TCTATCTAGAGGCACGTCGC 58.772 55.000 0.00 0.00 41.28 5.19
714 818 9.499479 GCATCTCCAATGAAAGATTTCTATCTA 57.501 33.333 6.84 0.00 40.26 1.98
715 819 8.219178 AGCATCTCCAATGAAAGATTTCTATCT 58.781 33.333 6.84 0.00 43.01 1.98
717 821 8.393671 GAGCATCTCCAATGAAAGATTTCTAT 57.606 34.615 6.84 0.00 38.02 1.98
718 822 7.798596 GAGCATCTCCAATGAAAGATTTCTA 57.201 36.000 6.84 0.00 38.02 2.10
719 823 6.696441 GAGCATCTCCAATGAAAGATTTCT 57.304 37.500 6.84 0.00 38.02 2.52
736 840 6.018180 CCCGTAAAAGTGGTTATAAGAGCATC 60.018 42.308 0.00 0.00 0.00 3.91
757 1266 3.340928 CCCTCGTAAAATCTTTTCCCGT 58.659 45.455 0.00 0.00 0.00 5.28
767 1276 2.871096 TCCAACAGCCCTCGTAAAAT 57.129 45.000 0.00 0.00 0.00 1.82
768 1277 2.642154 TTCCAACAGCCCTCGTAAAA 57.358 45.000 0.00 0.00 0.00 1.52
776 1285 2.365293 ACAAACTGAATTCCAACAGCCC 59.635 45.455 2.27 0.00 37.61 5.19
777 1286 3.319122 AGACAAACTGAATTCCAACAGCC 59.681 43.478 2.27 0.00 37.61 4.85
781 1290 8.134895 TGTGAATTAGACAAACTGAATTCCAAC 58.865 33.333 2.27 0.00 37.45 3.77
782 1291 8.231692 TGTGAATTAGACAAACTGAATTCCAA 57.768 30.769 2.27 0.00 37.45 3.53
783 1292 7.815840 TGTGAATTAGACAAACTGAATTCCA 57.184 32.000 2.27 0.00 37.45 3.53
784 1293 8.734386 AGATGTGAATTAGACAAACTGAATTCC 58.266 33.333 2.27 0.00 37.45 3.01
789 1298 9.591792 CATCTAGATGTGAATTAGACAAACTGA 57.408 33.333 22.42 0.00 34.23 3.41
817 1326 8.103305 AGAGCTTAGATGTGACATCCTTAAAAA 58.897 33.333 21.05 6.46 0.00 1.94
818 1327 7.624549 AGAGCTTAGATGTGACATCCTTAAAA 58.375 34.615 21.05 8.00 0.00 1.52
819 1328 7.093333 TGAGAGCTTAGATGTGACATCCTTAAA 60.093 37.037 21.05 10.18 0.00 1.52
820 1329 6.381133 TGAGAGCTTAGATGTGACATCCTTAA 59.619 38.462 21.05 13.11 0.00 1.85
821 1330 5.893824 TGAGAGCTTAGATGTGACATCCTTA 59.106 40.000 21.05 6.22 0.00 2.69
822 1331 4.713814 TGAGAGCTTAGATGTGACATCCTT 59.286 41.667 21.05 7.22 0.00 3.36
823 1332 4.099266 GTGAGAGCTTAGATGTGACATCCT 59.901 45.833 21.05 11.37 0.00 3.24
824 1333 4.142071 TGTGAGAGCTTAGATGTGACATCC 60.142 45.833 21.05 6.69 0.00 3.51
825 1334 5.003692 TGTGAGAGCTTAGATGTGACATC 57.996 43.478 17.46 17.46 0.00 3.06
826 1335 5.411831 TTGTGAGAGCTTAGATGTGACAT 57.588 39.130 0.00 0.00 0.00 3.06
827 1336 4.871933 TTGTGAGAGCTTAGATGTGACA 57.128 40.909 0.00 0.00 0.00 3.58
828 1337 9.703892 ATATATTTGTGAGAGCTTAGATGTGAC 57.296 33.333 0.00 0.00 0.00 3.67
895 1404 9.859427 CACATGTTCATTTTGTTTATGGTCTAT 57.141 29.630 0.00 0.00 0.00 1.98
896 1405 8.855110 ACACATGTTCATTTTGTTTATGGTCTA 58.145 29.630 0.00 0.00 0.00 2.59
897 1406 7.725251 ACACATGTTCATTTTGTTTATGGTCT 58.275 30.769 0.00 0.00 0.00 3.85
898 1407 7.116233 GGACACATGTTCATTTTGTTTATGGTC 59.884 37.037 0.00 0.00 0.00 4.02
899 1408 6.928492 GGACACATGTTCATTTTGTTTATGGT 59.072 34.615 0.00 0.00 0.00 3.55
900 1409 6.089283 CGGACACATGTTCATTTTGTTTATGG 59.911 38.462 0.00 0.00 0.00 2.74
901 1410 6.640499 ACGGACACATGTTCATTTTGTTTATG 59.360 34.615 0.00 0.00 0.00 1.90
902 1411 6.744112 ACGGACACATGTTCATTTTGTTTAT 58.256 32.000 0.00 0.00 0.00 1.40
903 1412 6.038825 AGACGGACACATGTTCATTTTGTTTA 59.961 34.615 0.00 0.00 0.00 2.01
904 1413 5.004922 ACGGACACATGTTCATTTTGTTT 57.995 34.783 0.00 0.00 0.00 2.83
905 1414 4.338118 AGACGGACACATGTTCATTTTGTT 59.662 37.500 0.00 0.00 0.00 2.83
906 1415 3.882888 AGACGGACACATGTTCATTTTGT 59.117 39.130 0.00 0.00 0.00 2.83
907 1416 4.488126 AGACGGACACATGTTCATTTTG 57.512 40.909 0.00 0.00 0.00 2.44
908 1417 5.408604 GTCTAGACGGACACATGTTCATTTT 59.591 40.000 7.22 0.00 36.35 1.82
909 1418 4.929808 GTCTAGACGGACACATGTTCATTT 59.070 41.667 7.22 0.00 36.35 2.32
910 1419 4.495422 GTCTAGACGGACACATGTTCATT 58.505 43.478 7.22 0.00 36.35 2.57
911 1420 3.119101 GGTCTAGACGGACACATGTTCAT 60.119 47.826 16.56 0.00 37.91 2.57
912 1421 2.230508 GGTCTAGACGGACACATGTTCA 59.769 50.000 16.56 0.00 37.91 3.18
913 1422 2.416972 GGGTCTAGACGGACACATGTTC 60.417 54.545 16.56 0.00 39.26 3.18
914 1423 1.549170 GGGTCTAGACGGACACATGTT 59.451 52.381 16.56 0.00 39.26 2.71
915 1424 1.183549 GGGTCTAGACGGACACATGT 58.816 55.000 16.56 0.00 39.26 3.21
916 1425 0.100682 CGGGTCTAGACGGACACATG 59.899 60.000 16.56 0.00 39.40 3.21
917 1426 0.323178 ACGGGTCTAGACGGACACAT 60.323 55.000 16.56 0.00 39.40 3.21
918 1427 0.538057 AACGGGTCTAGACGGACACA 60.538 55.000 16.56 0.00 39.40 3.72
919 1428 0.109412 CAACGGGTCTAGACGGACAC 60.109 60.000 16.56 2.28 37.91 3.67
920 1429 1.246056 CCAACGGGTCTAGACGGACA 61.246 60.000 16.56 0.00 37.91 4.02
921 1430 0.962356 TCCAACGGGTCTAGACGGAC 60.962 60.000 16.56 8.53 34.93 4.79
922 1431 0.251297 TTCCAACGGGTCTAGACGGA 60.251 55.000 16.56 13.62 34.93 4.69
923 1432 0.822164 ATTCCAACGGGTCTAGACGG 59.178 55.000 16.56 13.03 34.93 4.79
924 1433 2.268298 CAATTCCAACGGGTCTAGACG 58.732 52.381 16.56 8.91 34.93 4.18
925 1434 2.007608 GCAATTCCAACGGGTCTAGAC 58.992 52.381 14.87 14.87 34.93 2.59
926 1435 1.906574 AGCAATTCCAACGGGTCTAGA 59.093 47.619 0.00 0.00 34.93 2.43
927 1436 2.093447 AGAGCAATTCCAACGGGTCTAG 60.093 50.000 0.00 0.00 36.44 2.43
928 1437 1.906574 AGAGCAATTCCAACGGGTCTA 59.093 47.619 0.00 0.00 36.44 2.59
929 1438 0.693049 AGAGCAATTCCAACGGGTCT 59.307 50.000 0.00 0.00 33.62 3.85
930 1439 1.087501 GAGAGCAATTCCAACGGGTC 58.912 55.000 0.00 0.00 34.93 4.46
931 1440 0.400213 TGAGAGCAATTCCAACGGGT 59.600 50.000 0.00 0.00 34.93 5.28
932 1441 1.533625 TTGAGAGCAATTCCAACGGG 58.466 50.000 0.00 0.00 0.00 5.28
933 1442 2.665519 CGTTTGAGAGCAATTCCAACGG 60.666 50.000 11.19 0.00 33.25 4.44
934 1443 2.574322 CGTTTGAGAGCAATTCCAACG 58.426 47.619 6.94 6.94 33.25 4.10
937 1446 0.881118 GCCGTTTGAGAGCAATTCCA 59.119 50.000 0.00 0.00 33.25 3.53
953 1462 2.286713 TGATGTTGTTCGACTTTTGCCG 60.287 45.455 0.00 0.00 0.00 5.69
960 1469 1.935300 GCTCCGTGATGTTGTTCGACT 60.935 52.381 0.00 0.00 0.00 4.18
961 1470 0.438830 GCTCCGTGATGTTGTTCGAC 59.561 55.000 0.00 0.00 0.00 4.20
962 1471 1.006825 CGCTCCGTGATGTTGTTCGA 61.007 55.000 0.00 0.00 0.00 3.71
963 1472 1.006825 TCGCTCCGTGATGTTGTTCG 61.007 55.000 0.00 0.00 0.00 3.95
964 1473 1.136336 GTTCGCTCCGTGATGTTGTTC 60.136 52.381 0.00 0.00 0.00 3.18
965 1474 0.865769 GTTCGCTCCGTGATGTTGTT 59.134 50.000 0.00 0.00 0.00 2.83
966 1475 0.949105 GGTTCGCTCCGTGATGTTGT 60.949 55.000 0.00 0.00 0.00 3.32
967 1476 1.787847 GGTTCGCTCCGTGATGTTG 59.212 57.895 0.00 0.00 0.00 3.33
968 1477 1.736645 CGGTTCGCTCCGTGATGTT 60.737 57.895 9.35 0.00 44.77 2.71
969 1478 2.126071 CGGTTCGCTCCGTGATGT 60.126 61.111 9.35 0.00 44.77 3.06
976 1485 2.358247 TTTGGCTCGGTTCGCTCC 60.358 61.111 0.00 0.00 0.00 4.70
1110 1655 1.302832 GTTGGTGAGGAGGTGCTGG 60.303 63.158 0.00 0.00 0.00 4.85
1119 1664 4.619227 ACGCGTGGGTTGGTGAGG 62.619 66.667 12.93 0.00 0.00 3.86
1378 1923 5.939883 AGAAGATTCCATTCGTCATTTGACA 59.060 36.000 11.02 0.00 44.99 3.58
1409 1954 4.326255 CCTGGATCACCTGGCAAC 57.674 61.111 0.00 0.00 45.65 4.17
1453 2003 0.375803 GCCACACAAACGTCGAACTT 59.624 50.000 0.00 0.00 0.00 2.66
1485 2035 4.841617 AGCGGCGAGGAGATCCCA 62.842 66.667 12.98 0.00 37.41 4.37
1894 2444 1.077212 GGATGATGCCACTGCCAGT 60.077 57.895 0.00 0.00 36.33 4.00
1956 2506 4.717629 CCGCTGTCGCCGTCTTCA 62.718 66.667 0.00 0.00 0.00 3.02
2165 2715 1.089112 TTGCATCGGTGAGCAATCAG 58.911 50.000 0.00 0.00 44.98 2.90
2219 2769 3.370978 GCAAATTCGCTTCTGTGCTACTA 59.629 43.478 0.00 0.00 0.00 1.82
2220 2770 2.160417 GCAAATTCGCTTCTGTGCTACT 59.840 45.455 0.00 0.00 0.00 2.57
2221 2771 2.509870 GCAAATTCGCTTCTGTGCTAC 58.490 47.619 0.00 0.00 0.00 3.58
2271 2822 0.320421 TGAACCAACTCAGCCTACGC 60.320 55.000 0.00 0.00 0.00 4.42
2276 2827 1.876156 CAACTCTGAACCAACTCAGCC 59.124 52.381 0.00 0.00 42.25 4.85
2343 2894 8.860128 CATAATCATTTCATGAATAGCACATGC 58.140 33.333 9.40 0.00 43.50 4.06
2380 2931 8.718102 ATTGTGTATGTGTGAATCCTAGTAAC 57.282 34.615 0.00 0.00 0.00 2.50
2459 3010 5.601313 TGTCCTGTCTACCAGTAGTTTTCTT 59.399 40.000 4.81 0.00 39.74 2.52
2513 3064 7.402811 TTGTTGAACAGTCGAAACATAGTAG 57.597 36.000 0.00 0.00 0.00 2.57
2514 3065 7.707464 TCTTTGTTGAACAGTCGAAACATAGTA 59.293 33.333 12.48 2.31 0.00 1.82
2515 3066 6.537301 TCTTTGTTGAACAGTCGAAACATAGT 59.463 34.615 12.48 0.00 0.00 2.12
2516 3067 6.846283 GTCTTTGTTGAACAGTCGAAACATAG 59.154 38.462 0.00 8.63 0.00 2.23
2558 3134 2.773487 TCCTATGGTGGTTGTTGTTCG 58.227 47.619 0.00 0.00 0.00 3.95
2566 3142 2.107204 GCATCCTGATCCTATGGTGGTT 59.893 50.000 0.00 0.00 0.00 3.67
2593 3169 1.681264 GTTCTGGTTGGGTTTGGTCTG 59.319 52.381 0.00 0.00 0.00 3.51
2604 3180 1.608055 TGCATCACCTGTTCTGGTTG 58.392 50.000 0.00 0.00 38.45 3.77
2746 3325 4.815308 GCTGCAGATGTTGAATCTCTGTAT 59.185 41.667 20.43 0.00 38.88 2.29
2809 3392 5.652014 ACTCTTTGCATCCGGATAAAAATGA 59.348 36.000 18.63 16.25 0.00 2.57
2966 3549 7.947782 TGAAATGGAGGGAGTAATTATACCT 57.052 36.000 5.55 5.55 32.08 3.08
2979 3562 7.174107 ACAACAAGAATTATGAAATGGAGGG 57.826 36.000 0.00 0.00 0.00 4.30
3005 3588 7.859377 GGGCAGTTAACTAGTTTGAACTAAAAC 59.141 37.037 18.86 12.47 40.70 2.43
3006 3589 7.556996 TGGGCAGTTAACTAGTTTGAACTAAAA 59.443 33.333 18.86 2.07 40.70 1.52
3007 3590 7.055378 TGGGCAGTTAACTAGTTTGAACTAAA 58.945 34.615 18.86 2.71 40.70 1.85
3008 3591 6.593807 TGGGCAGTTAACTAGTTTGAACTAA 58.406 36.000 18.86 3.35 40.70 2.24
3009 3592 6.177310 TGGGCAGTTAACTAGTTTGAACTA 57.823 37.500 18.86 5.72 40.37 2.24
3010 3593 5.043737 TGGGCAGTTAACTAGTTTGAACT 57.956 39.130 14.49 14.90 42.91 3.01
3011 3594 5.699839 CATGGGCAGTTAACTAGTTTGAAC 58.300 41.667 14.49 12.82 0.00 3.18
3012 3595 4.217550 GCATGGGCAGTTAACTAGTTTGAA 59.782 41.667 14.49 0.00 40.72 2.69
3013 3596 3.756434 GCATGGGCAGTTAACTAGTTTGA 59.244 43.478 14.49 0.06 40.72 2.69
3014 3597 3.426159 CGCATGGGCAGTTAACTAGTTTG 60.426 47.826 14.49 7.43 41.24 2.93
3015 3598 2.747446 CGCATGGGCAGTTAACTAGTTT 59.253 45.455 14.49 0.00 41.24 2.66
3016 3599 2.290071 ACGCATGGGCAGTTAACTAGTT 60.290 45.455 13.68 13.68 41.24 2.24
3017 3600 1.278127 ACGCATGGGCAGTTAACTAGT 59.722 47.619 8.04 0.00 41.24 2.57
3018 3601 2.024176 ACGCATGGGCAGTTAACTAG 57.976 50.000 8.04 4.36 41.24 2.57
3019 3602 2.080693 CAACGCATGGGCAGTTAACTA 58.919 47.619 8.04 0.00 41.24 2.24
3020 3603 0.881118 CAACGCATGGGCAGTTAACT 59.119 50.000 10.10 1.12 41.24 2.24
3021 3604 0.732538 GCAACGCATGGGCAGTTAAC 60.733 55.000 10.10 0.00 41.24 2.01
3022 3605 1.175347 TGCAACGCATGGGCAGTTAA 61.175 50.000 10.10 0.00 41.24 2.01
3023 3606 1.602041 TGCAACGCATGGGCAGTTA 60.602 52.632 10.10 0.00 41.24 2.24
3024 3607 2.911509 TGCAACGCATGGGCAGTT 60.912 55.556 10.10 0.00 41.24 3.16
3033 3616 0.391793 TTATGTCCCGATGCAACGCA 60.392 50.000 11.32 4.22 44.86 5.24
3034 3617 0.304705 CTTATGTCCCGATGCAACGC 59.695 55.000 11.32 0.00 0.00 4.84
3035 3618 1.934589 TCTTATGTCCCGATGCAACG 58.065 50.000 9.71 9.71 0.00 4.10
3036 3619 4.335315 TGATTTCTTATGTCCCGATGCAAC 59.665 41.667 0.00 0.00 0.00 4.17
3037 3620 4.522114 TGATTTCTTATGTCCCGATGCAA 58.478 39.130 0.00 0.00 0.00 4.08
3038 3621 4.149511 TGATTTCTTATGTCCCGATGCA 57.850 40.909 0.00 0.00 0.00 3.96
3039 3622 4.516698 ACATGATTTCTTATGTCCCGATGC 59.483 41.667 0.00 0.00 32.32 3.91
3040 3623 5.759763 TCACATGATTTCTTATGTCCCGATG 59.240 40.000 0.00 0.00 35.46 3.84
3041 3624 5.928976 TCACATGATTTCTTATGTCCCGAT 58.071 37.500 0.00 0.00 35.46 4.18
3042 3625 5.351948 TCACATGATTTCTTATGTCCCGA 57.648 39.130 0.00 0.00 35.46 5.14
3043 3626 6.128035 TGTTTCACATGATTTCTTATGTCCCG 60.128 38.462 0.00 0.00 35.46 5.14
3044 3627 7.156876 TGTTTCACATGATTTCTTATGTCCC 57.843 36.000 0.00 0.00 35.46 4.46
3063 3646 9.781834 CGAGGATCTTAGAGATATACATGTTTC 57.218 37.037 2.30 0.00 34.53 2.78
3064 3647 9.303116 ACGAGGATCTTAGAGATATACATGTTT 57.697 33.333 2.30 0.00 34.53 2.83
3065 3648 8.735315 CACGAGGATCTTAGAGATATACATGTT 58.265 37.037 2.30 0.00 34.53 2.71
3066 3649 7.148154 GCACGAGGATCTTAGAGATATACATGT 60.148 40.741 2.69 2.69 34.53 3.21
3067 3650 7.148171 TGCACGAGGATCTTAGAGATATACATG 60.148 40.741 0.00 0.00 34.53 3.21
3068 3651 6.887002 TGCACGAGGATCTTAGAGATATACAT 59.113 38.462 0.00 0.00 34.53 2.29
3069 3652 6.149640 GTGCACGAGGATCTTAGAGATATACA 59.850 42.308 0.00 0.00 34.53 2.29
3070 3653 6.149640 TGTGCACGAGGATCTTAGAGATATAC 59.850 42.308 13.13 0.00 34.53 1.47
3071 3654 6.238648 TGTGCACGAGGATCTTAGAGATATA 58.761 40.000 13.13 0.00 34.53 0.86
3072 3655 5.073428 TGTGCACGAGGATCTTAGAGATAT 58.927 41.667 13.13 0.00 34.53 1.63
3073 3656 4.461198 TGTGCACGAGGATCTTAGAGATA 58.539 43.478 13.13 0.00 34.53 1.98
3074 3657 3.291584 TGTGCACGAGGATCTTAGAGAT 58.708 45.455 13.13 0.00 37.73 2.75
3075 3658 2.723273 TGTGCACGAGGATCTTAGAGA 58.277 47.619 13.13 0.00 0.00 3.10
3076 3659 3.724508 ATGTGCACGAGGATCTTAGAG 57.275 47.619 13.13 0.00 0.00 2.43
3077 3660 5.592104 TTAATGTGCACGAGGATCTTAGA 57.408 39.130 13.13 0.00 0.00 2.10
3078 3661 5.580691 TGTTTAATGTGCACGAGGATCTTAG 59.419 40.000 13.13 0.00 0.00 2.18
3079 3662 5.483811 TGTTTAATGTGCACGAGGATCTTA 58.516 37.500 13.13 0.00 0.00 2.10
3080 3663 4.323417 TGTTTAATGTGCACGAGGATCTT 58.677 39.130 13.13 0.00 0.00 2.40
3081 3664 3.937814 TGTTTAATGTGCACGAGGATCT 58.062 40.909 13.13 0.00 0.00 2.75
3082 3665 4.678509 TTGTTTAATGTGCACGAGGATC 57.321 40.909 13.13 2.30 0.00 3.36
3083 3666 6.942532 ATATTGTTTAATGTGCACGAGGAT 57.057 33.333 13.13 0.00 0.00 3.24
3084 3667 6.150307 ACAATATTGTTTAATGTGCACGAGGA 59.850 34.615 15.47 0.00 38.47 3.71
3085 3668 6.321717 ACAATATTGTTTAATGTGCACGAGG 58.678 36.000 15.47 0.00 38.47 4.63
3086 3669 7.020602 TGACAATATTGTTTAATGTGCACGAG 58.979 34.615 21.63 0.00 42.43 4.18
3087 3670 6.903419 TGACAATATTGTTTAATGTGCACGA 58.097 32.000 21.63 1.58 42.43 4.35
3088 3671 7.114106 TGTTGACAATATTGTTTAATGTGCACG 59.886 33.333 21.63 0.00 42.43 5.34
3089 3672 8.291888 TGTTGACAATATTGTTTAATGTGCAC 57.708 30.769 21.63 10.75 42.43 4.57
3090 3673 9.486497 AATGTTGACAATATTGTTTAATGTGCA 57.514 25.926 21.63 9.92 42.43 4.57
3099 3682 9.206870 GGTGAATCAAATGTTGACAATATTGTT 57.793 29.630 21.63 6.41 43.48 2.83
3100 3683 8.366401 TGGTGAATCAAATGTTGACAATATTGT 58.634 29.630 20.93 20.93 43.48 2.71
3101 3684 8.760103 TGGTGAATCAAATGTTGACAATATTG 57.240 30.769 14.01 14.01 43.48 1.90
3102 3685 9.373603 CATGGTGAATCAAATGTTGACAATATT 57.626 29.630 4.47 4.47 43.48 1.28
3103 3686 8.533657 ACATGGTGAATCAAATGTTGACAATAT 58.466 29.630 6.92 0.00 43.48 1.28
3104 3687 7.894708 ACATGGTGAATCAAATGTTGACAATA 58.105 30.769 6.92 0.00 43.48 1.90
3105 3688 6.761312 ACATGGTGAATCAAATGTTGACAAT 58.239 32.000 6.92 0.00 43.48 2.71
3106 3689 6.159299 ACATGGTGAATCAAATGTTGACAA 57.841 33.333 6.92 0.00 43.48 3.18
3107 3690 5.787953 ACATGGTGAATCAAATGTTGACA 57.212 34.783 6.92 0.00 43.48 3.58
3108 3691 9.853555 TTATAACATGGTGAATCAAATGTTGAC 57.146 29.630 24.28 0.00 43.48 3.18
3115 3698 8.474025 GGGTGATTTATAACATGGTGAATCAAA 58.526 33.333 15.95 1.66 35.88 2.69
3116 3699 7.838696 AGGGTGATTTATAACATGGTGAATCAA 59.161 33.333 15.95 3.92 35.88 2.57
3117 3700 7.353525 AGGGTGATTTATAACATGGTGAATCA 58.646 34.615 12.30 12.30 32.79 2.57
3118 3701 7.823745 AGGGTGATTTATAACATGGTGAATC 57.176 36.000 0.00 1.55 0.00 2.52


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

AutoCloner maintained by Alex Coulton.