Multiple sequence alignment - TraesCS4D01G316700

Loading Multiple Alignment...

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 TraesCS4D01G316700 chr4D 100.000 3260 0 0 1 3260 481894337 481891078 0.000000e+00 6021.0
1 TraesCS4D01G316700 chr4B 93.480 1457 79 9 999 2449 611426640 611425194 0.000000e+00 2150.0
2 TraesCS4D01G316700 chr4B 85.885 836 56 22 2453 3255 611425071 611424265 0.000000e+00 833.0
3 TraesCS4D01G316700 chr4B 84.130 586 62 17 261 821 646813949 646813370 3.700000e-149 538.0
4 TraesCS4D01G316700 chr5A 85.314 1464 123 41 1850 3260 660831263 660832687 0.000000e+00 1428.0
5 TraesCS4D01G316700 chr5A 94.040 453 26 1 999 1451 660830301 660830752 0.000000e+00 686.0
6 TraesCS4D01G316700 chr5A 97.135 349 9 1 1481 1828 660830751 660831099 3.620000e-164 588.0
7 TraesCS4D01G316700 chr5A 83.246 573 62 20 275 818 259074756 259074189 2.260000e-136 496.0
8 TraesCS4D01G316700 chr7B 82.506 806 99 22 42 810 592717468 592718268 0.000000e+00 669.0
9 TraesCS4D01G316700 chr7B 79.865 740 118 26 84 809 708859291 708858569 2.240000e-141 512.0
10 TraesCS4D01G316700 chr7B 83.601 561 71 19 267 816 189711616 189711066 1.040000e-139 507.0
11 TraesCS4D01G316700 chr7B 84.501 471 57 16 353 816 113134294 113133833 4.960000e-123 451.0
12 TraesCS4D01G316700 chr2A 82.637 766 101 25 61 810 653045673 653044924 0.000000e+00 649.0
13 TraesCS4D01G316700 chr2A 85.714 364 41 10 60 415 10040895 10040535 1.100000e-99 374.0
14 TraesCS4D01G316700 chr2A 84.426 366 41 10 60 415 10003443 10003084 2.410000e-91 346.0
15 TraesCS4D01G316700 chr5D 84.591 636 66 15 198 809 495141891 495141264 1.290000e-168 603.0
16 TraesCS4D01G316700 chr5D 84.050 558 71 17 261 810 388771410 388771957 3.730000e-144 521.0
17 TraesCS4D01G316700 chr5D 83.248 585 63 21 261 817 450616260 450616837 3.750000e-139 505.0
18 TraesCS4D01G316700 chr2B 86.703 549 63 9 268 810 676940205 676939661 4.650000e-168 601.0
19 TraesCS4D01G316700 chr2B 84.183 569 66 15 261 823 788241934 788241384 6.190000e-147 531.0
20 TraesCS4D01G316700 chr2B 86.207 348 42 4 67 411 146713554 146713898 3.970000e-99 372.0
21 TraesCS4D01G316700 chr3B 81.987 755 86 26 67 810 160833281 160832566 2.170000e-166 595.0
22 TraesCS4D01G316700 chr3B 85.996 557 64 13 261 810 776862583 776862034 4.690000e-163 584.0
23 TraesCS4D01G316700 chr7D 86.282 554 63 10 261 809 619013420 619012875 1.010000e-164 590.0
24 TraesCS4D01G316700 chr7D 85.971 556 62 14 261 810 551833806 551833261 6.060000e-162 580.0
25 TraesCS4D01G316700 chr1D 85.996 557 58 16 261 810 490549444 490549987 2.180000e-161 579.0
26 TraesCS4D01G316700 chr6D 83.562 584 58 22 261 816 422220714 422221287 2.240000e-141 512.0
27 TraesCS4D01G316700 chr7A 85.564 381 42 11 41 411 521949004 521949381 1.420000e-103 387.0
28 TraesCS4D01G316700 chr6A 85.635 362 44 6 61 415 543525030 543525390 1.100000e-99 374.0
29 TraesCS4D01G316700 chr6B 84.636 371 46 8 61 423 82550417 82550784 3.090000e-95 359.0
30 TraesCS4D01G316700 chr5B 82.143 112 14 5 1 106 606883609 606883498 1.250000e-14 91.6


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 TraesCS4D01G316700 chr4D 481891078 481894337 3259 True 6021.000000 6021 100.0000 1 3260 1 chr4D.!!$R1 3259
1 TraesCS4D01G316700 chr4B 611424265 611426640 2375 True 1491.500000 2150 89.6825 999 3255 2 chr4B.!!$R2 2256
2 TraesCS4D01G316700 chr4B 646813370 646813949 579 True 538.000000 538 84.1300 261 821 1 chr4B.!!$R1 560
3 TraesCS4D01G316700 chr5A 660830301 660832687 2386 False 900.666667 1428 92.1630 999 3260 3 chr5A.!!$F1 2261
4 TraesCS4D01G316700 chr5A 259074189 259074756 567 True 496.000000 496 83.2460 275 818 1 chr5A.!!$R1 543
5 TraesCS4D01G316700 chr7B 592717468 592718268 800 False 669.000000 669 82.5060 42 810 1 chr7B.!!$F1 768
6 TraesCS4D01G316700 chr7B 708858569 708859291 722 True 512.000000 512 79.8650 84 809 1 chr7B.!!$R3 725
7 TraesCS4D01G316700 chr7B 189711066 189711616 550 True 507.000000 507 83.6010 267 816 1 chr7B.!!$R2 549
8 TraesCS4D01G316700 chr2A 653044924 653045673 749 True 649.000000 649 82.6370 61 810 1 chr2A.!!$R3 749
9 TraesCS4D01G316700 chr5D 495141264 495141891 627 True 603.000000 603 84.5910 198 809 1 chr5D.!!$R1 611
10 TraesCS4D01G316700 chr5D 388771410 388771957 547 False 521.000000 521 84.0500 261 810 1 chr5D.!!$F1 549
11 TraesCS4D01G316700 chr5D 450616260 450616837 577 False 505.000000 505 83.2480 261 817 1 chr5D.!!$F2 556
12 TraesCS4D01G316700 chr2B 676939661 676940205 544 True 601.000000 601 86.7030 268 810 1 chr2B.!!$R1 542
13 TraesCS4D01G316700 chr2B 788241384 788241934 550 True 531.000000 531 84.1830 261 823 1 chr2B.!!$R2 562
14 TraesCS4D01G316700 chr3B 160832566 160833281 715 True 595.000000 595 81.9870 67 810 1 chr3B.!!$R1 743
15 TraesCS4D01G316700 chr3B 776862034 776862583 549 True 584.000000 584 85.9960 261 810 1 chr3B.!!$R2 549
16 TraesCS4D01G316700 chr7D 619012875 619013420 545 True 590.000000 590 86.2820 261 809 1 chr7D.!!$R2 548
17 TraesCS4D01G316700 chr7D 551833261 551833806 545 True 580.000000 580 85.9710 261 810 1 chr7D.!!$R1 549
18 TraesCS4D01G316700 chr1D 490549444 490549987 543 False 579.000000 579 85.9960 261 810 1 chr1D.!!$F1 549
19 TraesCS4D01G316700 chr6D 422220714 422221287 573 False 512.000000 512 83.5620 261 816 1 chr6D.!!$F1 555

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
946 1246 0.029834 GCCCATGTAATTGCTGCGAG 59.97 55.0 0.0 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2496 3110 0.611896 AGTTTGAAATGCCCTCCCCG 60.612 55.0 0.0 0.0 0.0 5.73 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
21 22 3.483421 ACCGGTCTTCCTTAGTTTTTGG 58.517 45.455 0.00 0.00 0.00 3.28
22 23 3.136992 ACCGGTCTTCCTTAGTTTTTGGA 59.863 43.478 0.00 0.00 0.00 3.53
23 24 4.139038 CCGGTCTTCCTTAGTTTTTGGAA 58.861 43.478 0.00 0.00 38.10 3.53
24 25 4.023450 CCGGTCTTCCTTAGTTTTTGGAAC 60.023 45.833 0.00 0.00 36.11 3.62
25 26 4.577283 CGGTCTTCCTTAGTTTTTGGAACA 59.423 41.667 0.00 0.00 36.11 3.18
81 82 1.176619 TTCCTTCCGCGAGAGTCACA 61.177 55.000 8.23 0.00 0.00 3.58
167 173 3.626680 TTCTTCCGCGAGAGGCACG 62.627 63.158 8.23 0.00 43.84 5.34
183 189 2.173382 CGGTTTTGCTTCCGCGAG 59.827 61.111 8.23 0.00 40.28 5.03
186 192 1.497722 GTTTTGCTTCCGCGAGAGG 59.502 57.895 8.23 4.88 39.65 3.69
190 196 3.267860 GCTTCCGCGAGAGGCATG 61.268 66.667 20.89 0.00 46.54 4.06
191 197 2.587194 CTTCCGCGAGAGGCATGG 60.587 66.667 8.23 0.00 43.84 3.66
192 198 3.376935 CTTCCGCGAGAGGCATGGT 62.377 63.158 8.23 0.00 43.84 3.55
193 199 2.859273 CTTCCGCGAGAGGCATGGTT 62.859 60.000 8.23 0.00 43.84 3.67
194 200 3.197790 CCGCGAGAGGCATGGTTG 61.198 66.667 8.23 0.00 43.84 3.77
195 201 2.434884 CGCGAGAGGCATGGTTGT 60.435 61.111 0.00 0.00 43.84 3.32
196 202 2.743752 CGCGAGAGGCATGGTTGTG 61.744 63.158 0.00 0.00 43.84 3.33
214 220 0.243636 TGCTTTCGCGAGAGTCATGA 59.756 50.000 25.34 0.00 43.69 3.07
217 223 0.601057 TTTCGCGAGAGTCATGACCA 59.399 50.000 22.21 0.00 43.69 4.02
265 290 9.413048 ACGTGTTTTCTATTTTTGTTTCTTTCA 57.587 25.926 0.00 0.00 0.00 2.69
357 459 0.949105 GGTTTTGCTTCCGCGAGAGA 60.949 55.000 8.23 0.00 39.65 3.10
360 462 0.037326 TTTGCTTCCGCGAGAGACAT 60.037 50.000 8.23 0.00 39.65 3.06
381 484 1.069090 TTGTGCTTTCGCGAGAGGT 59.931 52.632 25.84 0.00 43.69 3.85
382 485 0.944311 TTGTGCTTTCGCGAGAGGTC 60.944 55.000 25.84 12.23 43.69 3.85
411 517 2.229062 GCCTCCTCGGAAAAGGAAAAAG 59.771 50.000 9.01 0.00 44.81 2.27
416 703 4.337274 TCCTCGGAAAAGGAAAAAGAACAC 59.663 41.667 0.00 0.00 42.56 3.32
427 714 6.552629 AGGAAAAAGAACACGTTTTCTCTTC 58.447 36.000 16.80 19.10 39.76 2.87
428 715 6.374613 AGGAAAAAGAACACGTTTTCTCTTCT 59.625 34.615 24.12 13.47 39.76 2.85
429 716 7.027760 GGAAAAAGAACACGTTTTCTCTTCTT 58.972 34.615 24.12 12.96 39.76 2.52
430 717 7.218393 GGAAAAAGAACACGTTTTCTCTTCTTC 59.782 37.037 24.12 19.04 39.76 2.87
491 778 2.433664 CGCGGGCGTACCTCTTTT 60.434 61.111 4.64 0.00 36.97 2.27
620 916 2.969628 AAAGATCTTGACGCGAGGAT 57.030 45.000 15.93 10.28 0.00 3.24
776 1075 1.261238 CCTGAGGAGGTGGGAGTGAC 61.261 65.000 0.00 0.00 34.16 3.67
777 1076 0.542938 CTGAGGAGGTGGGAGTGACA 60.543 60.000 0.00 0.00 0.00 3.58
831 1131 9.918630 ATTTCAATAAATATATGAGTGGCTTGC 57.081 29.630 0.00 0.00 33.45 4.01
832 1132 8.462589 TTCAATAAATATATGAGTGGCTTGCA 57.537 30.769 0.00 0.00 0.00 4.08
833 1133 8.102800 TCAATAAATATATGAGTGGCTTGCAG 57.897 34.615 0.00 0.00 0.00 4.41
834 1134 7.175467 TCAATAAATATATGAGTGGCTTGCAGG 59.825 37.037 0.00 0.00 0.00 4.85
835 1135 2.260844 TATATGAGTGGCTTGCAGGC 57.739 50.000 13.24 13.24 41.77 4.85
836 1136 0.549950 ATATGAGTGGCTTGCAGGCT 59.450 50.000 21.07 0.00 41.96 4.58
837 1137 0.329261 TATGAGTGGCTTGCAGGCTT 59.671 50.000 21.07 6.74 41.96 4.35
838 1138 0.541296 ATGAGTGGCTTGCAGGCTTT 60.541 50.000 21.07 6.37 41.96 3.51
839 1139 1.288127 GAGTGGCTTGCAGGCTTTG 59.712 57.895 21.07 0.00 41.96 2.77
840 1140 1.152694 AGTGGCTTGCAGGCTTTGA 60.153 52.632 21.07 0.00 41.96 2.69
841 1141 0.756442 AGTGGCTTGCAGGCTTTGAA 60.756 50.000 21.07 0.00 41.96 2.69
842 1142 0.104671 GTGGCTTGCAGGCTTTGAAA 59.895 50.000 21.07 0.00 41.96 2.69
843 1143 0.829333 TGGCTTGCAGGCTTTGAAAA 59.171 45.000 21.07 0.00 41.96 2.29
844 1144 1.209019 TGGCTTGCAGGCTTTGAAAAA 59.791 42.857 21.07 0.00 41.96 1.94
845 1145 2.158784 TGGCTTGCAGGCTTTGAAAAAT 60.159 40.909 21.07 0.00 41.96 1.82
846 1146 2.880268 GGCTTGCAGGCTTTGAAAAATT 59.120 40.909 21.07 0.00 37.85 1.82
847 1147 3.058708 GGCTTGCAGGCTTTGAAAAATTC 60.059 43.478 21.07 0.00 37.85 2.17
848 1148 3.058708 GCTTGCAGGCTTTGAAAAATTCC 60.059 43.478 14.45 0.00 0.00 3.01
849 1149 3.124578 TGCAGGCTTTGAAAAATTCCC 57.875 42.857 0.00 0.00 0.00 3.97
850 1150 2.705127 TGCAGGCTTTGAAAAATTCCCT 59.295 40.909 0.00 0.00 0.00 4.20
851 1151 3.244181 TGCAGGCTTTGAAAAATTCCCTC 60.244 43.478 0.00 0.00 0.00 4.30
852 1152 3.244181 GCAGGCTTTGAAAAATTCCCTCA 60.244 43.478 0.00 0.00 0.00 3.86
853 1153 4.564199 GCAGGCTTTGAAAAATTCCCTCAT 60.564 41.667 0.00 0.00 0.00 2.90
854 1154 4.933400 CAGGCTTTGAAAAATTCCCTCATG 59.067 41.667 0.00 0.00 0.00 3.07
855 1155 4.019950 AGGCTTTGAAAAATTCCCTCATGG 60.020 41.667 0.00 0.00 0.00 3.66
870 1170 5.983333 CCTCATGGGCTATATTCCCTATT 57.017 43.478 12.38 0.00 44.23 1.73
871 1171 5.688807 CCTCATGGGCTATATTCCCTATTG 58.311 45.833 12.38 8.47 44.23 1.90
872 1172 5.429762 CCTCATGGGCTATATTCCCTATTGA 59.570 44.000 12.38 11.17 44.23 2.57
873 1173 6.069440 CCTCATGGGCTATATTCCCTATTGAA 60.069 42.308 12.38 0.00 44.23 2.69
874 1174 7.367186 CCTCATGGGCTATATTCCCTATTGAAT 60.367 40.741 12.38 0.00 44.23 2.57
875 1175 7.348815 TCATGGGCTATATTCCCTATTGAATG 58.651 38.462 12.38 7.71 44.23 2.67
876 1176 6.718593 TGGGCTATATTCCCTATTGAATGT 57.281 37.500 12.38 0.00 44.23 2.71
877 1177 6.721318 TGGGCTATATTCCCTATTGAATGTC 58.279 40.000 12.38 0.00 44.23 3.06
878 1178 6.122964 GGGCTATATTCCCTATTGAATGTCC 58.877 44.000 5.69 0.00 40.66 4.02
879 1179 6.069381 GGGCTATATTCCCTATTGAATGTCCT 60.069 42.308 5.69 0.00 40.66 3.85
880 1180 7.127339 GGGCTATATTCCCTATTGAATGTCCTA 59.873 40.741 5.69 0.00 40.66 2.94
881 1181 8.718656 GGCTATATTCCCTATTGAATGTCCTAT 58.281 37.037 0.00 0.00 35.77 2.57
885 1185 6.959639 TTCCCTATTGAATGTCCTATTTGC 57.040 37.500 0.00 0.00 0.00 3.68
886 1186 5.063204 TCCCTATTGAATGTCCTATTTGCG 58.937 41.667 0.00 0.00 0.00 4.85
887 1187 4.320494 CCCTATTGAATGTCCTATTTGCGC 60.320 45.833 0.00 0.00 0.00 6.09
888 1188 4.516698 CCTATTGAATGTCCTATTTGCGCT 59.483 41.667 9.73 0.00 0.00 5.92
889 1189 3.763097 TTGAATGTCCTATTTGCGCTG 57.237 42.857 9.73 0.00 0.00 5.18
890 1190 2.710377 TGAATGTCCTATTTGCGCTGT 58.290 42.857 9.73 0.00 0.00 4.40
891 1191 2.419673 TGAATGTCCTATTTGCGCTGTG 59.580 45.455 9.73 0.00 0.00 3.66
892 1192 2.113860 ATGTCCTATTTGCGCTGTGT 57.886 45.000 9.73 0.00 0.00 3.72
893 1193 2.753055 TGTCCTATTTGCGCTGTGTA 57.247 45.000 9.73 0.00 0.00 2.90
894 1194 2.343101 TGTCCTATTTGCGCTGTGTAC 58.657 47.619 9.73 0.00 0.00 2.90
895 1195 1.323534 GTCCTATTTGCGCTGTGTACG 59.676 52.381 9.73 0.00 0.00 3.67
896 1196 1.202817 TCCTATTTGCGCTGTGTACGA 59.797 47.619 9.73 0.00 0.00 3.43
897 1197 1.588404 CCTATTTGCGCTGTGTACGAG 59.412 52.381 9.73 0.00 0.00 4.18
898 1198 2.526077 CTATTTGCGCTGTGTACGAGA 58.474 47.619 9.73 0.00 0.00 4.04
899 1199 2.010145 ATTTGCGCTGTGTACGAGAT 57.990 45.000 9.73 0.00 0.00 2.75
900 1200 1.067693 TTTGCGCTGTGTACGAGATG 58.932 50.000 9.73 0.00 0.00 2.90
901 1201 0.735978 TTGCGCTGTGTACGAGATGG 60.736 55.000 9.73 0.00 0.00 3.51
902 1202 1.878522 GCGCTGTGTACGAGATGGG 60.879 63.158 0.00 0.00 0.00 4.00
903 1203 1.878522 CGCTGTGTACGAGATGGGC 60.879 63.158 0.00 0.00 0.00 5.36
904 1204 1.218047 GCTGTGTACGAGATGGGCA 59.782 57.895 0.00 0.00 0.00 5.36
905 1205 0.391130 GCTGTGTACGAGATGGGCAA 60.391 55.000 0.00 0.00 0.00 4.52
906 1206 1.359848 CTGTGTACGAGATGGGCAAC 58.640 55.000 0.00 0.00 0.00 4.17
907 1207 0.389296 TGTGTACGAGATGGGCAACG 60.389 55.000 0.00 0.00 37.60 4.10
908 1208 0.389426 GTGTACGAGATGGGCAACGT 60.389 55.000 0.00 0.00 41.66 3.99
909 1209 1.135315 GTGTACGAGATGGGCAACGTA 60.135 52.381 0.00 0.00 39.59 3.57
910 1210 4.904466 ACGAGATGGGCAACGTAC 57.096 55.556 0.00 0.00 37.22 3.67
911 1211 1.466856 TACGAGATGGGCAACGTACT 58.533 50.000 0.00 0.00 39.59 2.73
912 1212 1.466856 ACGAGATGGGCAACGTACTA 58.533 50.000 0.00 0.00 37.22 1.82
913 1213 1.820519 ACGAGATGGGCAACGTACTAA 59.179 47.619 0.00 0.00 37.22 2.24
914 1214 2.231964 ACGAGATGGGCAACGTACTAAA 59.768 45.455 0.00 0.00 37.22 1.85
915 1215 2.601763 CGAGATGGGCAACGTACTAAAC 59.398 50.000 0.00 0.00 37.60 2.01
916 1216 3.675228 CGAGATGGGCAACGTACTAAACT 60.675 47.826 0.00 0.00 37.60 2.66
917 1217 3.858247 AGATGGGCAACGTACTAAACTC 58.142 45.455 0.00 0.00 37.60 3.01
918 1218 2.460757 TGGGCAACGTACTAAACTCC 57.539 50.000 0.00 0.00 37.60 3.85
919 1219 1.337074 TGGGCAACGTACTAAACTCCG 60.337 52.381 0.00 0.00 37.60 4.63
920 1220 1.353076 GGCAACGTACTAAACTCCGG 58.647 55.000 0.00 0.00 0.00 5.14
921 1221 0.717784 GCAACGTACTAAACTCCGGC 59.282 55.000 0.00 0.00 0.00 6.13
922 1222 1.353076 CAACGTACTAAACTCCGGCC 58.647 55.000 0.00 0.00 0.00 6.13
923 1223 0.968405 AACGTACTAAACTCCGGCCA 59.032 50.000 2.24 0.00 0.00 5.36
924 1224 0.968405 ACGTACTAAACTCCGGCCAA 59.032 50.000 2.24 0.00 0.00 4.52
925 1225 1.551883 ACGTACTAAACTCCGGCCAAT 59.448 47.619 2.24 0.00 0.00 3.16
926 1226 2.760092 ACGTACTAAACTCCGGCCAATA 59.240 45.455 2.24 0.00 0.00 1.90
927 1227 3.181483 ACGTACTAAACTCCGGCCAATAG 60.181 47.826 2.24 0.00 0.00 1.73
928 1228 2.327200 ACTAAACTCCGGCCAATAGC 57.673 50.000 2.24 0.00 42.60 2.97
940 1240 3.030668 GCCAATAGCCCATGTAATTGC 57.969 47.619 0.00 0.00 34.35 3.56
941 1241 2.629617 GCCAATAGCCCATGTAATTGCT 59.370 45.455 0.00 0.00 36.06 3.91
942 1242 3.553508 GCCAATAGCCCATGTAATTGCTG 60.554 47.826 0.00 0.00 34.12 4.41
943 1243 3.553508 CCAATAGCCCATGTAATTGCTGC 60.554 47.826 0.00 0.00 34.12 5.25
944 1244 1.308047 TAGCCCATGTAATTGCTGCG 58.692 50.000 0.00 0.00 34.12 5.18
945 1245 0.394216 AGCCCATGTAATTGCTGCGA 60.394 50.000 0.00 0.00 31.23 5.10
946 1246 0.029834 GCCCATGTAATTGCTGCGAG 59.970 55.000 0.00 0.00 0.00 5.03
947 1247 1.667236 CCCATGTAATTGCTGCGAGA 58.333 50.000 0.00 0.00 0.00 4.04
948 1248 2.016318 CCCATGTAATTGCTGCGAGAA 58.984 47.619 0.00 0.00 0.00 2.87
949 1249 2.032550 CCCATGTAATTGCTGCGAGAAG 59.967 50.000 0.00 0.00 0.00 2.85
950 1250 2.032550 CCATGTAATTGCTGCGAGAAGG 59.967 50.000 0.00 0.00 0.00 3.46
951 1251 1.086696 TGTAATTGCTGCGAGAAGGC 58.913 50.000 0.00 0.00 0.00 4.35
952 1252 0.378610 GTAATTGCTGCGAGAAGGCC 59.621 55.000 0.00 0.00 0.00 5.19
953 1253 0.253044 TAATTGCTGCGAGAAGGCCT 59.747 50.000 0.00 0.00 0.00 5.19
954 1254 1.310933 AATTGCTGCGAGAAGGCCTG 61.311 55.000 5.69 0.00 0.00 4.85
955 1255 3.907260 TTGCTGCGAGAAGGCCTGG 62.907 63.158 5.69 0.00 0.00 4.45
956 1256 4.400961 GCTGCGAGAAGGCCTGGT 62.401 66.667 5.69 0.00 0.00 4.00
957 1257 2.125350 CTGCGAGAAGGCCTGGTC 60.125 66.667 5.69 5.09 0.00 4.02
958 1258 3.997064 CTGCGAGAAGGCCTGGTCG 62.997 68.421 25.74 25.74 35.51 4.79
961 1261 4.070552 GAGAAGGCCTGGTCGCGT 62.071 66.667 5.69 0.00 0.00 6.01
962 1262 3.591254 GAGAAGGCCTGGTCGCGTT 62.591 63.158 5.69 0.00 39.42 4.84
963 1263 2.221906 GAGAAGGCCTGGTCGCGTTA 62.222 60.000 5.69 0.00 37.00 3.18
964 1264 1.810030 GAAGGCCTGGTCGCGTTAG 60.810 63.158 5.69 2.88 37.00 2.34
965 1265 2.221906 GAAGGCCTGGTCGCGTTAGA 62.222 60.000 5.69 0.00 37.00 2.10
966 1266 1.823169 AAGGCCTGGTCGCGTTAGAA 61.823 55.000 5.69 0.00 35.22 2.10
967 1267 2.098831 GGCCTGGTCGCGTTAGAAC 61.099 63.158 5.77 0.00 0.00 3.01
989 1289 8.398665 AGAACGATTGAAATGTTTAGATAAGCC 58.601 33.333 0.00 0.00 0.00 4.35
990 1290 7.865706 ACGATTGAAATGTTTAGATAAGCCT 57.134 32.000 0.00 0.00 0.00 4.58
991 1291 8.281212 ACGATTGAAATGTTTAGATAAGCCTT 57.719 30.769 0.00 0.00 0.00 4.35
992 1292 8.184192 ACGATTGAAATGTTTAGATAAGCCTTG 58.816 33.333 0.00 0.00 0.00 3.61
993 1293 8.184192 CGATTGAAATGTTTAGATAAGCCTTGT 58.816 33.333 0.00 0.00 0.00 3.16
994 1294 9.294030 GATTGAAATGTTTAGATAAGCCTTGTG 57.706 33.333 0.00 0.00 0.00 3.33
995 1295 7.156876 TGAAATGTTTAGATAAGCCTTGTGG 57.843 36.000 0.00 0.00 0.00 4.17
996 1296 6.152661 TGAAATGTTTAGATAAGCCTTGTGGG 59.847 38.462 0.00 0.00 38.36 4.61
1199 1499 1.578206 GCCAAGTTCTTCGCTCCCAC 61.578 60.000 0.00 0.00 0.00 4.61
1227 1527 2.424684 ACCAACCCTCTCTCCTTTCT 57.575 50.000 0.00 0.00 0.00 2.52
1266 1566 4.504132 GCCTTACCTGCGAGTCTG 57.496 61.111 0.00 0.00 0.00 3.51
1267 1567 1.811679 GCCTTACCTGCGAGTCTGC 60.812 63.158 0.00 0.77 0.00 4.26
1330 1637 2.358957 TGAATCTCCGAAATGGCTGTG 58.641 47.619 0.00 0.00 37.80 3.66
1367 1674 2.228103 AGCGAATTCGATAGCGGATGTA 59.772 45.455 31.01 0.00 43.02 2.29
1408 1716 4.245660 TGGTAGAAGCAAGACTGAATTCG 58.754 43.478 0.04 0.00 0.00 3.34
1467 1775 4.840680 TCCCTGTCTCTCAAGAAATGAAGA 59.159 41.667 0.00 0.00 37.67 2.87
1468 1776 5.046735 TCCCTGTCTCTCAAGAAATGAAGAG 60.047 44.000 0.00 0.00 37.67 2.85
1480 1788 7.387122 TCAAGAAATGAAGAGAACACTCATCAG 59.613 37.037 10.09 0.00 40.17 2.90
1539 1848 4.079253 GGATCAGCACTTAAAGGGTTCAA 58.921 43.478 0.00 0.00 0.00 2.69
1612 1925 1.071471 CCTGCTTCGGAACACAGGT 59.929 57.895 19.87 0.00 43.86 4.00
1648 1961 4.569966 GTCACTGACTATGATCTTGCCTTG 59.430 45.833 1.58 0.00 0.00 3.61
1659 1972 0.039437 CTTGCCTTGCTCAGTTGCTG 60.039 55.000 0.00 0.00 0.00 4.41
1925 2389 3.319755 TCGTTGGTTTGTTATCTCCGTC 58.680 45.455 0.00 0.00 0.00 4.79
1936 2400 7.624360 TTGTTATCTCCGTCAAAATTAGCAT 57.376 32.000 0.00 0.00 0.00 3.79
1940 2404 9.010366 GTTATCTCCGTCAAAATTAGCATTTTC 57.990 33.333 0.00 0.00 40.09 2.29
1941 2405 6.817765 TCTCCGTCAAAATTAGCATTTTCT 57.182 33.333 0.00 0.00 40.09 2.52
1942 2406 7.214467 TCTCCGTCAAAATTAGCATTTTCTT 57.786 32.000 0.00 0.00 40.09 2.52
1997 2461 5.678955 AGGAGTTAGGAGTTCCATAACAC 57.321 43.478 16.07 12.14 38.12 3.32
2012 2476 6.454795 TCCATAACACAAAGAAAAATCCAGC 58.545 36.000 0.00 0.00 0.00 4.85
2274 2739 4.019411 TCTGATTGATTGGGAGTTGCTACA 60.019 41.667 0.13 0.00 0.00 2.74
2290 2755 2.678190 GCTACAAGTCTGTTAGCTGGGG 60.678 54.545 0.00 0.00 36.96 4.96
2301 2766 5.483583 TCTGTTAGCTGGGGCATAAATTTTT 59.516 36.000 0.00 0.00 41.70 1.94
2310 2776 6.347696 TGGGGCATAAATTTTTGAGCTTATG 58.652 36.000 12.18 1.53 35.68 1.90
2313 2779 6.907206 GCATAAATTTTTGAGCTTATGCCA 57.093 33.333 12.18 0.00 45.58 4.92
2399 2865 3.037851 TGGTCTCAGCTCATCCACTAT 57.962 47.619 0.00 0.00 0.00 2.12
2428 2923 4.158025 ACACTAGTACGGTTTGAGATCCAG 59.842 45.833 0.00 0.00 0.00 3.86
2449 2944 5.868801 CCAGCACCCAATTTGTAATTTGTAG 59.131 40.000 0.00 0.00 0.00 2.74
2450 2945 5.868801 CAGCACCCAATTTGTAATTTGTAGG 59.131 40.000 0.00 0.00 0.00 3.18
2451 2946 5.542251 AGCACCCAATTTGTAATTTGTAGGT 59.458 36.000 0.00 0.00 0.00 3.08
2463 3077 5.941948 AATTTGTAGGTAAGTGAGCACAC 57.058 39.130 6.11 6.11 46.24 3.82
2486 3100 1.608590 TGTAGGAGTTGCTTGCTTTGC 59.391 47.619 0.00 0.00 0.00 3.68
2490 3104 2.169144 AGGAGTTGCTTGCTTTGCTTTT 59.831 40.909 0.00 0.00 0.00 2.27
2491 3105 2.938451 GGAGTTGCTTGCTTTGCTTTTT 59.062 40.909 0.00 0.00 0.00 1.94
2505 3119 2.116556 TTTTTCCACGGGGAGGGC 59.883 61.111 6.46 0.00 46.01 5.19
2506 3120 2.769120 TTTTTCCACGGGGAGGGCA 61.769 57.895 6.46 0.00 46.01 5.36
2507 3121 2.087857 TTTTTCCACGGGGAGGGCAT 62.088 55.000 6.46 0.00 46.01 4.40
2517 3131 0.247460 GGGAGGGCATTTCAAACTGC 59.753 55.000 0.00 0.00 37.66 4.40
2539 3153 3.028130 TGTAGCATTGTCGGTGGATCTA 58.972 45.455 0.00 0.00 0.00 1.98
2541 3155 4.830600 TGTAGCATTGTCGGTGGATCTATA 59.169 41.667 0.00 0.00 0.00 1.31
2555 3174 7.173907 CGGTGGATCTATATTTTGCATTTCTCT 59.826 37.037 0.00 0.00 0.00 3.10
2593 3212 5.939296 TGACATCACAATTAAGCTGATCACA 59.061 36.000 0.00 0.00 0.00 3.58
2627 3246 5.533482 AGTTTATCTATTGTCTAGCTGGCG 58.467 41.667 0.00 0.00 0.00 5.69
2628 3247 2.447244 ATCTATTGTCTAGCTGGCGC 57.553 50.000 0.00 0.00 0.00 6.53
2629 3248 0.389391 TCTATTGTCTAGCTGGCGCC 59.611 55.000 22.73 22.73 36.60 6.53
2630 3249 0.941463 CTATTGTCTAGCTGGCGCCG 60.941 60.000 23.90 17.75 36.60 6.46
2632 3251 2.907897 ATTGTCTAGCTGGCGCCGTC 62.908 60.000 23.90 16.04 36.60 4.79
2633 3252 4.129737 GTCTAGCTGGCGCCGTCA 62.130 66.667 23.90 2.68 36.60 4.35
2634 3253 4.129737 TCTAGCTGGCGCCGTCAC 62.130 66.667 23.90 10.97 36.60 3.67
2635 3254 4.435436 CTAGCTGGCGCCGTCACA 62.435 66.667 23.90 1.77 36.60 3.58
2672 3291 7.671819 TGTAGGGTTTTCCATGATGAAACAATA 59.328 33.333 10.60 2.39 42.91 1.90
2693 3312 7.812669 ACAATACAAGTTTATGGTAAAAGCAGC 59.187 33.333 0.00 0.00 0.00 5.25
2739 3364 1.141657 GTCCTGATCAGCCATAGCCAA 59.858 52.381 17.76 0.00 41.25 4.52
2742 3367 3.008375 TCCTGATCAGCCATAGCCAATAC 59.992 47.826 17.76 0.00 41.25 1.89
2752 3377 3.312421 CCATAGCCAATACGAACAACAGG 59.688 47.826 0.00 0.00 0.00 4.00
2793 3418 6.916360 TGCTATTTCAAATCTGGGAAAACT 57.084 33.333 0.00 0.00 36.67 2.66
2794 3419 6.690530 TGCTATTTCAAATCTGGGAAAACTG 58.309 36.000 0.00 0.00 36.67 3.16
2795 3420 5.578336 GCTATTTCAAATCTGGGAAAACTGC 59.422 40.000 0.00 0.00 36.67 4.40
2796 3421 5.813513 ATTTCAAATCTGGGAAAACTGCT 57.186 34.783 0.00 0.00 36.67 4.24
2797 3422 4.589216 TTCAAATCTGGGAAAACTGCTG 57.411 40.909 0.00 0.00 0.00 4.41
2798 3423 3.565307 TCAAATCTGGGAAAACTGCTGT 58.435 40.909 0.00 0.00 0.00 4.40
2799 3424 4.724399 TCAAATCTGGGAAAACTGCTGTA 58.276 39.130 0.00 0.00 0.00 2.74
2800 3425 4.761739 TCAAATCTGGGAAAACTGCTGTAG 59.238 41.667 0.00 0.00 0.00 2.74
2801 3426 2.859165 TCTGGGAAAACTGCTGTAGG 57.141 50.000 0.00 0.00 0.00 3.18
2802 3427 2.054799 TCTGGGAAAACTGCTGTAGGT 58.945 47.619 0.00 0.00 0.00 3.08
2803 3428 3.244582 TCTGGGAAAACTGCTGTAGGTA 58.755 45.455 0.00 0.00 0.00 3.08
2804 3429 3.007614 TCTGGGAAAACTGCTGTAGGTAC 59.992 47.826 0.00 0.00 0.00 3.34
2813 3450 4.188247 CTGCTGTAGGTACTGCTGTAAA 57.812 45.455 16.88 0.04 46.94 2.01
2817 3454 4.321750 GCTGTAGGTACTGCTGTAAAGACA 60.322 45.833 4.88 8.41 44.53 3.41
2969 3606 1.601419 ATGGCAGCTTTGCATTCGCT 61.601 50.000 0.00 0.00 39.64 4.93
2991 3628 1.376553 GCCTCCCTGAGACAGCAAC 60.377 63.158 0.00 0.00 0.00 4.17
2996 3633 3.643320 CCTCCCTGAGACAGCAACATATA 59.357 47.826 0.00 0.00 0.00 0.86
2997 3634 4.285517 CCTCCCTGAGACAGCAACATATAT 59.714 45.833 0.00 0.00 0.00 0.86
2998 3635 5.221803 CCTCCCTGAGACAGCAACATATATT 60.222 44.000 0.00 0.00 0.00 1.28
3088 3725 5.507985 GCAGTTTGCTGATAGGTGAAGTTTT 60.508 40.000 0.00 0.00 45.28 2.43
3175 3840 1.419012 TGGCATTGGTCAAAATTGGCA 59.581 42.857 7.60 7.60 33.59 4.92
3176 3841 2.078392 GGCATTGGTCAAAATTGGCAG 58.922 47.619 0.00 0.00 33.59 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.746940 TCCAAAAACTAAGGAAGACCGG 58.253 45.455 0.00 0.00 41.83 5.28
2 3 4.577283 TGTTCCAAAAACTAAGGAAGACCG 59.423 41.667 0.00 0.00 41.74 4.79
3 4 6.459670 TTGTTCCAAAAACTAAGGAAGACC 57.540 37.500 0.00 0.00 41.74 3.85
4 5 8.766000 TTTTTGTTCCAAAAACTAAGGAAGAC 57.234 30.769 10.02 0.00 41.74 3.01
64 65 1.153939 CTGTGACTCTCGCGGAAGG 60.154 63.158 6.13 0.00 35.34 3.46
250 256 5.163561 TGCCTCTCGTGAAAGAAACAAAAAT 60.164 36.000 0.00 0.00 0.00 1.82
256 262 1.192534 CGTGCCTCTCGTGAAAGAAAC 59.807 52.381 0.00 0.00 0.00 2.78
475 762 0.952010 TTCAAAAGAGGTACGCCCGC 60.952 55.000 0.00 0.00 38.74 6.13
570 866 9.217278 CTAGATCCCATGTTGATAGATTTTGAG 57.783 37.037 0.00 0.00 0.00 3.02
601 897 2.969628 ATCCTCGCGTCAAGATCTTT 57.030 45.000 4.86 0.00 0.00 2.52
620 916 1.401199 GAACCGTTTTCACCGTTGGAA 59.599 47.619 0.00 0.00 0.00 3.53
711 1008 1.592400 GCCACTTGTTGCAACCTGC 60.592 57.895 26.14 16.52 45.29 4.85
810 1110 6.071728 GCCTGCAAGCCACTCATATATTTATT 60.072 38.462 0.00 0.00 0.00 1.40
818 1118 0.329261 AAGCCTGCAAGCCACTCATA 59.671 50.000 3.00 0.00 0.00 2.15
823 1123 0.104671 TTTCAAAGCCTGCAAGCCAC 59.895 50.000 3.00 0.00 0.00 5.01
824 1124 0.829333 TTTTCAAAGCCTGCAAGCCA 59.171 45.000 3.00 0.00 0.00 4.75
825 1125 1.952193 TTTTTCAAAGCCTGCAAGCC 58.048 45.000 3.00 0.00 0.00 4.35
826 1126 3.058708 GGAATTTTTCAAAGCCTGCAAGC 60.059 43.478 0.00 0.00 0.00 4.01
827 1127 3.499537 GGGAATTTTTCAAAGCCTGCAAG 59.500 43.478 0.00 0.00 0.00 4.01
828 1128 3.136260 AGGGAATTTTTCAAAGCCTGCAA 59.864 39.130 0.00 0.00 0.00 4.08
829 1129 2.705127 AGGGAATTTTTCAAAGCCTGCA 59.295 40.909 0.00 0.00 0.00 4.41
830 1130 3.244181 TGAGGGAATTTTTCAAAGCCTGC 60.244 43.478 0.00 0.00 0.00 4.85
831 1131 4.605640 TGAGGGAATTTTTCAAAGCCTG 57.394 40.909 0.00 0.00 0.00 4.85
832 1132 4.019950 CCATGAGGGAATTTTTCAAAGCCT 60.020 41.667 0.00 0.00 40.01 4.58
833 1133 4.256110 CCATGAGGGAATTTTTCAAAGCC 58.744 43.478 0.00 0.00 40.01 4.35
854 1154 6.069381 AGGACATTCAATAGGGAATATAGCCC 60.069 42.308 5.60 5.60 46.40 5.19
855 1155 6.963322 AGGACATTCAATAGGGAATATAGCC 58.037 40.000 0.00 0.00 35.79 3.93
859 1159 9.247861 GCAAATAGGACATTCAATAGGGAATAT 57.752 33.333 0.00 0.00 35.79 1.28
860 1160 7.390440 CGCAAATAGGACATTCAATAGGGAATA 59.610 37.037 0.00 0.00 35.79 1.75
861 1161 6.207417 CGCAAATAGGACATTCAATAGGGAAT 59.793 38.462 0.00 0.00 37.99 3.01
862 1162 5.530915 CGCAAATAGGACATTCAATAGGGAA 59.469 40.000 0.00 0.00 0.00 3.97
863 1163 5.063204 CGCAAATAGGACATTCAATAGGGA 58.937 41.667 0.00 0.00 0.00 4.20
864 1164 4.320494 GCGCAAATAGGACATTCAATAGGG 60.320 45.833 0.30 0.00 0.00 3.53
865 1165 4.516698 AGCGCAAATAGGACATTCAATAGG 59.483 41.667 11.47 0.00 0.00 2.57
866 1166 5.008019 ACAGCGCAAATAGGACATTCAATAG 59.992 40.000 11.47 0.00 0.00 1.73
867 1167 4.881273 ACAGCGCAAATAGGACATTCAATA 59.119 37.500 11.47 0.00 0.00 1.90
868 1168 3.696051 ACAGCGCAAATAGGACATTCAAT 59.304 39.130 11.47 0.00 0.00 2.57
869 1169 3.081061 ACAGCGCAAATAGGACATTCAA 58.919 40.909 11.47 0.00 0.00 2.69
870 1170 2.419673 CACAGCGCAAATAGGACATTCA 59.580 45.455 11.47 0.00 0.00 2.57
871 1171 2.420022 ACACAGCGCAAATAGGACATTC 59.580 45.455 11.47 0.00 0.00 2.67
872 1172 2.436417 ACACAGCGCAAATAGGACATT 58.564 42.857 11.47 0.00 0.00 2.71
873 1173 2.113860 ACACAGCGCAAATAGGACAT 57.886 45.000 11.47 0.00 0.00 3.06
874 1174 2.343101 GTACACAGCGCAAATAGGACA 58.657 47.619 11.47 0.00 0.00 4.02
875 1175 1.323534 CGTACACAGCGCAAATAGGAC 59.676 52.381 11.47 0.00 0.00 3.85
876 1176 1.202817 TCGTACACAGCGCAAATAGGA 59.797 47.619 11.47 4.77 0.00 2.94
877 1177 1.588404 CTCGTACACAGCGCAAATAGG 59.412 52.381 11.47 2.25 0.00 2.57
878 1178 2.526077 TCTCGTACACAGCGCAAATAG 58.474 47.619 11.47 0.00 0.00 1.73
879 1179 2.640346 TCTCGTACACAGCGCAAATA 57.360 45.000 11.47 0.00 0.00 1.40
880 1180 1.660607 CATCTCGTACACAGCGCAAAT 59.339 47.619 11.47 0.00 0.00 2.32
881 1181 1.067693 CATCTCGTACACAGCGCAAA 58.932 50.000 11.47 0.00 0.00 3.68
882 1182 0.735978 CCATCTCGTACACAGCGCAA 60.736 55.000 11.47 0.00 0.00 4.85
883 1183 1.153842 CCATCTCGTACACAGCGCA 60.154 57.895 11.47 0.00 0.00 6.09
884 1184 1.878522 CCCATCTCGTACACAGCGC 60.879 63.158 0.00 0.00 0.00 5.92
885 1185 1.878522 GCCCATCTCGTACACAGCG 60.879 63.158 0.00 0.00 0.00 5.18
886 1186 0.391130 TTGCCCATCTCGTACACAGC 60.391 55.000 0.00 0.00 0.00 4.40
887 1187 1.359848 GTTGCCCATCTCGTACACAG 58.640 55.000 0.00 0.00 0.00 3.66
888 1188 0.389296 CGTTGCCCATCTCGTACACA 60.389 55.000 0.00 0.00 0.00 3.72
889 1189 0.389426 ACGTTGCCCATCTCGTACAC 60.389 55.000 0.00 0.00 34.78 2.90
890 1190 1.175654 TACGTTGCCCATCTCGTACA 58.824 50.000 0.00 0.00 37.66 2.90
891 1191 1.553308 GTACGTTGCCCATCTCGTAC 58.447 55.000 10.08 10.08 46.66 3.67
892 1192 1.466856 AGTACGTTGCCCATCTCGTA 58.533 50.000 0.00 0.00 37.66 3.43
893 1193 1.466856 TAGTACGTTGCCCATCTCGT 58.533 50.000 0.00 0.00 39.74 4.18
894 1194 2.572191 TTAGTACGTTGCCCATCTCG 57.428 50.000 0.00 0.00 0.00 4.04
895 1195 3.858247 AGTTTAGTACGTTGCCCATCTC 58.142 45.455 0.00 0.00 0.00 2.75
896 1196 3.369157 GGAGTTTAGTACGTTGCCCATCT 60.369 47.826 0.00 0.00 0.00 2.90
897 1197 2.934553 GGAGTTTAGTACGTTGCCCATC 59.065 50.000 0.00 0.00 0.00 3.51
898 1198 2.675889 CGGAGTTTAGTACGTTGCCCAT 60.676 50.000 0.00 0.00 0.00 4.00
899 1199 1.337074 CGGAGTTTAGTACGTTGCCCA 60.337 52.381 0.00 0.00 0.00 5.36
900 1200 1.353076 CGGAGTTTAGTACGTTGCCC 58.647 55.000 0.00 0.00 0.00 5.36
901 1201 1.353076 CCGGAGTTTAGTACGTTGCC 58.647 55.000 0.00 0.00 0.00 4.52
902 1202 0.717784 GCCGGAGTTTAGTACGTTGC 59.282 55.000 5.05 0.00 0.00 4.17
903 1203 1.337074 TGGCCGGAGTTTAGTACGTTG 60.337 52.381 5.05 0.00 0.00 4.10
904 1204 0.968405 TGGCCGGAGTTTAGTACGTT 59.032 50.000 5.05 0.00 0.00 3.99
905 1205 0.968405 TTGGCCGGAGTTTAGTACGT 59.032 50.000 5.05 0.00 0.00 3.57
906 1206 2.304751 ATTGGCCGGAGTTTAGTACG 57.695 50.000 5.05 0.00 0.00 3.67
907 1207 3.129109 GCTATTGGCCGGAGTTTAGTAC 58.871 50.000 5.05 0.00 34.27 2.73
908 1208 3.464111 GCTATTGGCCGGAGTTTAGTA 57.536 47.619 5.05 0.00 34.27 1.82
909 1209 2.327200 GCTATTGGCCGGAGTTTAGT 57.673 50.000 5.05 0.00 34.27 2.24
920 1220 2.629617 AGCAATTACATGGGCTATTGGC 59.370 45.455 0.00 0.00 40.90 4.52
921 1221 3.553508 GCAGCAATTACATGGGCTATTGG 60.554 47.826 0.00 0.00 34.25 3.16
922 1222 3.645884 GCAGCAATTACATGGGCTATTG 58.354 45.455 0.00 2.66 34.25 1.90
923 1223 2.294233 CGCAGCAATTACATGGGCTATT 59.706 45.455 0.00 0.00 34.25 1.73
924 1224 1.881973 CGCAGCAATTACATGGGCTAT 59.118 47.619 0.00 0.00 34.25 2.97
925 1225 1.134250 TCGCAGCAATTACATGGGCTA 60.134 47.619 0.00 0.00 34.25 3.93
926 1226 0.394216 TCGCAGCAATTACATGGGCT 60.394 50.000 0.00 0.00 36.99 5.19
927 1227 0.029834 CTCGCAGCAATTACATGGGC 59.970 55.000 0.00 0.00 0.00 5.36
928 1228 1.667236 TCTCGCAGCAATTACATGGG 58.333 50.000 0.00 0.00 0.00 4.00
929 1229 2.032550 CCTTCTCGCAGCAATTACATGG 59.967 50.000 0.00 0.00 0.00 3.66
930 1230 2.540361 GCCTTCTCGCAGCAATTACATG 60.540 50.000 0.00 0.00 0.00 3.21
931 1231 1.672881 GCCTTCTCGCAGCAATTACAT 59.327 47.619 0.00 0.00 0.00 2.29
932 1232 1.086696 GCCTTCTCGCAGCAATTACA 58.913 50.000 0.00 0.00 0.00 2.41
933 1233 0.378610 GGCCTTCTCGCAGCAATTAC 59.621 55.000 0.00 0.00 0.00 1.89
934 1234 0.253044 AGGCCTTCTCGCAGCAATTA 59.747 50.000 0.00 0.00 0.00 1.40
935 1235 1.001641 AGGCCTTCTCGCAGCAATT 60.002 52.632 0.00 0.00 0.00 2.32
936 1236 1.748122 CAGGCCTTCTCGCAGCAAT 60.748 57.895 0.00 0.00 0.00 3.56
937 1237 2.359107 CAGGCCTTCTCGCAGCAA 60.359 61.111 0.00 0.00 0.00 3.91
938 1238 4.399395 CCAGGCCTTCTCGCAGCA 62.399 66.667 0.00 0.00 0.00 4.41
939 1239 4.400961 ACCAGGCCTTCTCGCAGC 62.401 66.667 0.00 0.00 0.00 5.25
940 1240 2.125350 GACCAGGCCTTCTCGCAG 60.125 66.667 0.00 0.00 0.00 5.18
941 1241 4.069232 CGACCAGGCCTTCTCGCA 62.069 66.667 14.41 0.00 0.00 5.10
944 1244 2.221906 TAACGCGACCAGGCCTTCTC 62.222 60.000 15.93 0.00 0.00 2.87
945 1245 2.227089 CTAACGCGACCAGGCCTTCT 62.227 60.000 15.93 0.00 0.00 2.85
946 1246 1.810030 CTAACGCGACCAGGCCTTC 60.810 63.158 15.93 0.00 0.00 3.46
947 1247 1.823169 TTCTAACGCGACCAGGCCTT 61.823 55.000 15.93 0.00 0.00 4.35
948 1248 2.280552 TTCTAACGCGACCAGGCCT 61.281 57.895 15.93 0.00 0.00 5.19
949 1249 2.098831 GTTCTAACGCGACCAGGCC 61.099 63.158 15.93 0.00 0.00 5.19
950 1250 2.442188 CGTTCTAACGCGACCAGGC 61.442 63.158 15.93 0.00 46.06 4.85
951 1251 3.763319 CGTTCTAACGCGACCAGG 58.237 61.111 15.93 0.00 46.06 4.45
963 1263 8.398665 GGCTTATCTAAACATTTCAATCGTTCT 58.601 33.333 0.00 0.00 0.00 3.01
964 1264 8.398665 AGGCTTATCTAAACATTTCAATCGTTC 58.601 33.333 0.00 0.00 0.00 3.95
965 1265 8.281212 AGGCTTATCTAAACATTTCAATCGTT 57.719 30.769 0.00 0.00 0.00 3.85
966 1266 7.865706 AGGCTTATCTAAACATTTCAATCGT 57.134 32.000 0.00 0.00 0.00 3.73
967 1267 8.184192 ACAAGGCTTATCTAAACATTTCAATCG 58.816 33.333 0.00 0.00 0.00 3.34
968 1268 9.294030 CACAAGGCTTATCTAAACATTTCAATC 57.706 33.333 0.00 0.00 0.00 2.67
969 1269 8.253113 CCACAAGGCTTATCTAAACATTTCAAT 58.747 33.333 0.00 0.00 0.00 2.57
970 1270 7.309744 CCCACAAGGCTTATCTAAACATTTCAA 60.310 37.037 0.00 0.00 0.00 2.69
971 1271 6.152661 CCCACAAGGCTTATCTAAACATTTCA 59.847 38.462 0.00 0.00 0.00 2.69
972 1272 6.564328 CCCACAAGGCTTATCTAAACATTTC 58.436 40.000 0.00 0.00 0.00 2.17
973 1273 6.530019 CCCACAAGGCTTATCTAAACATTT 57.470 37.500 0.00 0.00 0.00 2.32
988 1288 3.384532 GCACATGGGCCCACAAGG 61.385 66.667 31.51 19.62 39.47 3.61
989 1289 2.601067 TGCACATGGGCCCACAAG 60.601 61.111 31.51 22.72 0.00 3.16
990 1290 2.916703 GTGCACATGGGCCCACAA 60.917 61.111 31.51 4.00 0.00 3.33
995 1295 3.434319 CTGACGTGCACATGGGCC 61.434 66.667 19.33 7.98 0.00 5.80
996 1296 3.434319 CCTGACGTGCACATGGGC 61.434 66.667 14.67 14.67 0.00 5.36
997 1297 2.747460 CCCTGACGTGCACATGGG 60.747 66.667 18.64 16.92 0.00 4.00
1002 1302 3.349006 CACAGCCCTGACGTGCAC 61.349 66.667 6.82 6.82 0.00 4.57
1063 1363 4.320456 ACTCCCCACGCTGCAGTG 62.320 66.667 25.37 25.37 41.53 3.66
1227 1527 3.375610 CGAGAAGAAGTTCAGATCGGAGA 59.624 47.826 5.50 0.00 36.43 3.71
1260 1560 0.548510 ATTAAGGGGGCTGCAGACTC 59.451 55.000 21.42 17.35 0.00 3.36
1261 1561 1.002857 AATTAAGGGGGCTGCAGACT 58.997 50.000 21.42 7.18 0.00 3.24
1262 1562 1.852633 AAATTAAGGGGGCTGCAGAC 58.147 50.000 20.43 16.66 0.00 3.51
1263 1563 2.091885 CCTAAATTAAGGGGGCTGCAGA 60.092 50.000 20.43 0.00 32.55 4.26
1264 1564 2.310538 CCTAAATTAAGGGGGCTGCAG 58.689 52.381 10.11 10.11 32.55 4.41
1265 1565 1.643811 ACCTAAATTAAGGGGGCTGCA 59.356 47.619 0.50 0.00 41.32 4.41
1266 1566 2.430694 CAACCTAAATTAAGGGGGCTGC 59.569 50.000 0.00 0.00 41.32 5.25
1267 1567 2.430694 GCAACCTAAATTAAGGGGGCTG 59.569 50.000 0.00 0.00 41.32 4.85
1324 1631 3.488090 GAGTAACGCGGCACAGCC 61.488 66.667 12.47 0.00 46.75 4.85
1330 1637 1.740043 CGCTAACTGAGTAACGCGGC 61.740 60.000 12.47 0.00 37.25 6.53
1334 1641 4.093514 TCGAATTCGCTAACTGAGTAACG 58.906 43.478 22.90 0.00 39.60 3.18
1340 1647 3.297472 CGCTATCGAATTCGCTAACTGA 58.703 45.455 22.90 4.23 39.60 3.41
1367 1674 2.505819 CCAGTTATAAGGTCACAGGCCT 59.494 50.000 0.00 0.00 38.11 5.19
1480 1788 5.065218 CCCTTCATGTTATGCTAGTCAACAC 59.935 44.000 7.72 1.95 35.17 3.32
1539 1848 6.327104 AGCACTGATCTCAATCTAGGAGAAAT 59.673 38.462 1.90 0.00 44.01 2.17
1648 1961 1.202076 GCCGTATTTCAGCAACTGAGC 60.202 52.381 0.00 0.00 41.75 4.26
1659 1972 5.751243 AAAGTATCACCATGCCGTATTTC 57.249 39.130 0.00 0.00 0.00 2.17
1936 2400 8.491950 GCAAGTTGTTCAACAAACTTAAGAAAA 58.508 29.630 10.09 0.00 40.15 2.29
1940 2404 7.542130 AGAAGCAAGTTGTTCAACAAACTTAAG 59.458 33.333 4.02 0.00 40.15 1.85
1941 2405 7.375053 AGAAGCAAGTTGTTCAACAAACTTAA 58.625 30.769 4.02 0.00 40.15 1.85
1942 2406 6.919721 AGAAGCAAGTTGTTCAACAAACTTA 58.080 32.000 4.02 0.00 40.15 2.24
1997 2461 5.117592 GTCATCAACGCTGGATTTTTCTTTG 59.882 40.000 0.00 0.00 0.00 2.77
2012 2476 5.698832 TGAAGCAAAATTAGGTCATCAACG 58.301 37.500 0.00 0.00 0.00 4.10
2120 2584 5.273944 GGTGCAGTTAAGTGAGAAAACAAG 58.726 41.667 14.64 0.00 0.00 3.16
2274 2739 0.995024 ATGCCCCAGCTAACAGACTT 59.005 50.000 0.00 0.00 40.80 3.01
2301 2766 4.080356 ACTGGAAATAGTGGCATAAGCTCA 60.080 41.667 0.00 0.00 41.70 4.26
2313 2779 4.666512 AGCAAACATCCACTGGAAATAGT 58.333 39.130 0.66 0.00 34.34 2.12
2399 2865 5.706833 TCTCAAACCGTACTAGTGTACATGA 59.293 40.000 5.39 2.66 46.88 3.07
2425 2920 4.640364 ACAAATTACAAATTGGGTGCTGG 58.360 39.130 0.00 0.00 0.00 4.85
2428 2923 5.789521 ACCTACAAATTACAAATTGGGTGC 58.210 37.500 0.00 0.00 0.00 5.01
2449 2944 2.080286 ACATCGTGTGCTCACTTACC 57.920 50.000 16.23 0.00 41.89 2.85
2450 2945 3.119602 TCCTACATCGTGTGCTCACTTAC 60.120 47.826 16.23 0.00 41.89 2.34
2451 2946 3.086282 TCCTACATCGTGTGCTCACTTA 58.914 45.455 16.23 5.46 41.89 2.24
2463 3077 2.015736 AGCAAGCAACTCCTACATCG 57.984 50.000 0.00 0.00 0.00 3.84
2467 3081 1.882623 AGCAAAGCAAGCAACTCCTAC 59.117 47.619 0.00 0.00 0.00 3.18
2470 3084 2.229675 AAAGCAAAGCAAGCAACTCC 57.770 45.000 0.00 0.00 0.00 3.85
2490 3104 2.087857 AAATGCCCTCCCCGTGGAAA 62.088 55.000 0.00 0.00 41.17 3.13
2491 3105 2.493273 GAAATGCCCTCCCCGTGGAA 62.493 60.000 0.00 0.00 41.17 3.53
2492 3106 2.938798 AAATGCCCTCCCCGTGGA 60.939 61.111 0.00 0.00 38.75 4.02
2494 3108 0.897863 TTTGAAATGCCCTCCCCGTG 60.898 55.000 0.00 0.00 0.00 4.94
2496 3110 0.611896 AGTTTGAAATGCCCTCCCCG 60.612 55.000 0.00 0.00 0.00 5.73
2497 3111 0.897621 CAGTTTGAAATGCCCTCCCC 59.102 55.000 0.00 0.00 0.00 4.81
2517 3131 2.159043 AGATCCACCGACAATGCTACAG 60.159 50.000 0.00 0.00 0.00 2.74
2527 3141 6.560253 AATGCAAAATATAGATCCACCGAC 57.440 37.500 0.00 0.00 0.00 4.79
2609 3228 1.001406 GGCGCCAGCTAGACAATAGAT 59.999 52.381 24.80 0.00 44.37 1.98
2622 3241 2.913054 ATCAGATGTGACGGCGCCAG 62.913 60.000 28.98 21.29 34.75 4.85
2623 3242 3.017771 ATCAGATGTGACGGCGCCA 62.018 57.895 28.98 6.55 34.75 5.69
2624 3243 2.202932 ATCAGATGTGACGGCGCC 60.203 61.111 19.07 19.07 34.75 6.53
2627 3246 0.742281 ACAGCATCAGATGTGACGGC 60.742 55.000 12.18 9.56 43.89 5.68
2628 3247 3.448267 ACAGCATCAGATGTGACGG 57.552 52.632 12.18 0.00 43.89 4.79
2634 3253 2.996249 ACCCTACACAGCATCAGATG 57.004 50.000 5.98 5.98 37.14 2.90
2635 3254 4.265073 GAAAACCCTACACAGCATCAGAT 58.735 43.478 0.00 0.00 0.00 2.90
2672 3291 4.586841 TGGCTGCTTTTACCATAAACTTGT 59.413 37.500 0.00 0.00 0.00 3.16
2686 3305 1.063492 TGATGGATGGATGGCTGCTTT 60.063 47.619 0.00 0.00 0.00 3.51
2693 3312 3.762288 CCTAGCAAATGATGGATGGATGG 59.238 47.826 0.00 0.00 0.00 3.51
2739 3364 9.477484 GAATATCTATCAACCTGTTGTTCGTAT 57.523 33.333 9.65 0.00 41.16 3.06
2742 3367 7.042456 CCAGAATATCTATCAACCTGTTGTTCG 60.042 40.741 9.65 0.00 41.16 3.95
2793 3418 3.830178 TCTTTACAGCAGTACCTACAGCA 59.170 43.478 3.07 0.00 40.63 4.41
2794 3419 4.174762 GTCTTTACAGCAGTACCTACAGC 58.825 47.826 0.00 0.00 38.77 4.40
2795 3420 5.386958 TGTCTTTACAGCAGTACCTACAG 57.613 43.478 0.00 0.00 0.00 2.74
2796 3421 5.794726 TTGTCTTTACAGCAGTACCTACA 57.205 39.130 0.00 0.00 36.83 2.74
2797 3422 7.010275 GCTAATTGTCTTTACAGCAGTACCTAC 59.990 40.741 0.00 0.00 36.83 3.18
2798 3423 7.039882 GCTAATTGTCTTTACAGCAGTACCTA 58.960 38.462 0.00 0.00 36.83 3.08
2799 3424 5.875359 GCTAATTGTCTTTACAGCAGTACCT 59.125 40.000 0.00 0.00 36.83 3.08
2800 3425 5.875359 AGCTAATTGTCTTTACAGCAGTACC 59.125 40.000 0.00 0.00 36.83 3.34
2801 3426 6.969828 AGCTAATTGTCTTTACAGCAGTAC 57.030 37.500 0.00 0.00 36.83 2.73
2802 3427 7.979444 AAAGCTAATTGTCTTTACAGCAGTA 57.021 32.000 5.34 0.00 36.83 2.74
2803 3428 6.884280 AAAGCTAATTGTCTTTACAGCAGT 57.116 33.333 5.34 0.00 36.83 4.40
2804 3429 7.362662 TGAAAAGCTAATTGTCTTTACAGCAG 58.637 34.615 7.04 0.00 36.83 4.24
2813 3450 5.300286 ACAGCAACTGAAAAGCTAATTGTCT 59.700 36.000 0.78 0.00 36.73 3.41
2817 3454 4.301628 GCACAGCAACTGAAAAGCTAATT 58.698 39.130 0.78 0.00 36.73 1.40
3019 3656 1.219646 GGAACGGCTAAACGAACACA 58.780 50.000 0.00 0.00 37.61 3.72
3088 3725 1.130561 CTGTCGCTCGTACTGATGACA 59.869 52.381 15.22 15.22 38.68 3.58


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

AutoCloner maintained by Alex Coulton.