Multiple sequence alignment - TraesCS3D01G311900

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 TraesCS3D01G311900 chr3D 100.000 2969 0 0 1 2969 426492614 426489646 0 5483
1 TraesCS3D01G311900 chr3B 85.473 2905 382 17 90 2969 638122932 638125821 0 2990
2 TraesCS3D01G311900 chr3B 84.941 2902 397 18 93 2969 22531028 22528142 0 2902
3 TraesCS3D01G311900 chr1A 85.439 2905 382 18 90 2969 154692996 154695884 0 2983
4 TraesCS3D01G311900 chr4A 85.291 2903 385 19 93 2969 311087703 311084817 0 2957
5 TraesCS3D01G311900 chr3A 85.257 2903 386 19 93 2969 744002534 743999648 0 2952
6 TraesCS3D01G311900 chr7B 85.155 2910 385 22 90 2969 623968835 623971727 0 2937
7 TraesCS3D01G311900 chr7B 84.981 2903 393 19 93 2969 323827733 323824848 0 2905
8 TraesCS3D01G311900 chr5B 85.034 2900 385 18 93 2969 572907760 572904887 0 2905
9 TraesCS3D01G311900 chr1B 84.726 2920 389 29 90 2969 252757109 252760011 0 2868
10 TraesCS3D01G311900 chr6A 88.171 1471 173 1 1499 2969 426133171 426134640 0 1751


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 TraesCS3D01G311900 chr3D 426489646 426492614 2968 True 5483 5483 100.000 1 2969 1 chr3D.!!$R1 2968
1 TraesCS3D01G311900 chr3B 638122932 638125821 2889 False 2990 2990 85.473 90 2969 1 chr3B.!!$F1 2879
2 TraesCS3D01G311900 chr3B 22528142 22531028 2886 True 2902 2902 84.941 93 2969 1 chr3B.!!$R1 2876
3 TraesCS3D01G311900 chr1A 154692996 154695884 2888 False 2983 2983 85.439 90 2969 1 chr1A.!!$F1 2879
4 TraesCS3D01G311900 chr4A 311084817 311087703 2886 True 2957 2957 85.291 93 2969 1 chr4A.!!$R1 2876
5 TraesCS3D01G311900 chr3A 743999648 744002534 2886 True 2952 2952 85.257 93 2969 1 chr3A.!!$R1 2876
6 TraesCS3D01G311900 chr7B 623968835 623971727 2892 False 2937 2937 85.155 90 2969 1 chr7B.!!$F1 2879
7 TraesCS3D01G311900 chr7B 323824848 323827733 2885 True 2905 2905 84.981 93 2969 1 chr7B.!!$R1 2876
8 TraesCS3D01G311900 chr5B 572904887 572907760 2873 True 2905 2905 85.034 93 2969 1 chr5B.!!$R1 2876
9 TraesCS3D01G311900 chr1B 252757109 252760011 2902 False 2868 2868 84.726 90 2969 1 chr1B.!!$F1 2879
10 TraesCS3D01G311900 chr6A 426133171 426134640 1469 False 1751 1751 88.171 1499 2969 1 chr6A.!!$F1 1470

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
803 818 0.106167 CGAGGTGGATAGGGAGGTCA 60.106 60.0 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
2360 2413 0.252103 AGTTTGTCGGCCTCCTCCTA 60.252 55.0 0.0 0.0 0.0 2.94 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
17 18 4.988065 TCGAAGAGAAGGGCGTTG 57.012 55.556 0.00 0.00 0.00 4.10
18 19 1.374252 TCGAAGAGAAGGGCGTTGC 60.374 57.895 0.00 0.00 0.00 4.17
28 29 2.331451 GGCGTTGCCTGTGTTCAC 59.669 61.111 0.00 0.00 46.69 3.18
29 30 2.052237 GCGTTGCCTGTGTTCACG 60.052 61.111 0.00 0.00 0.00 4.35
30 31 2.631428 CGTTGCCTGTGTTCACGG 59.369 61.111 4.93 4.93 0.00 4.94
31 32 2.177580 CGTTGCCTGTGTTCACGGT 61.178 57.895 10.31 0.00 0.00 4.83
32 33 1.355210 GTTGCCTGTGTTCACGGTG 59.645 57.895 0.56 0.56 0.00 4.94
33 34 2.477176 TTGCCTGTGTTCACGGTGC 61.477 57.895 2.51 12.40 0.00 5.01
34 35 2.899838 GCCTGTGTTCACGGTGCA 60.900 61.111 2.51 0.00 0.00 4.57
35 36 2.260869 GCCTGTGTTCACGGTGCAT 61.261 57.895 2.51 0.00 0.00 3.96
36 37 1.795170 GCCTGTGTTCACGGTGCATT 61.795 55.000 2.51 0.00 0.00 3.56
37 38 0.667993 CCTGTGTTCACGGTGCATTT 59.332 50.000 2.51 0.00 0.00 2.32
38 39 1.066908 CCTGTGTTCACGGTGCATTTT 59.933 47.619 2.51 0.00 0.00 1.82
39 40 2.118683 CTGTGTTCACGGTGCATTTTG 58.881 47.619 2.51 0.00 0.00 2.44
40 41 1.745653 TGTGTTCACGGTGCATTTTGA 59.254 42.857 2.51 0.00 0.00 2.69
41 42 2.116366 GTGTTCACGGTGCATTTTGAC 58.884 47.619 2.51 0.00 0.00 3.18
42 43 1.066303 TGTTCACGGTGCATTTTGACC 59.934 47.619 2.51 0.00 0.00 4.02
43 44 1.336755 GTTCACGGTGCATTTTGACCT 59.663 47.619 2.51 0.00 0.00 3.85
44 45 1.686355 TCACGGTGCATTTTGACCTT 58.314 45.000 2.51 0.00 0.00 3.50
45 46 1.606668 TCACGGTGCATTTTGACCTTC 59.393 47.619 2.51 0.00 0.00 3.46
46 47 1.608590 CACGGTGCATTTTGACCTTCT 59.391 47.619 0.00 0.00 0.00 2.85
47 48 1.608590 ACGGTGCATTTTGACCTTCTG 59.391 47.619 0.00 0.00 0.00 3.02
48 49 1.068333 CGGTGCATTTTGACCTTCTGG 60.068 52.381 0.00 0.00 39.83 3.86
49 50 2.238521 GGTGCATTTTGACCTTCTGGA 58.761 47.619 0.00 0.00 37.04 3.86
50 51 2.229784 GGTGCATTTTGACCTTCTGGAG 59.770 50.000 0.00 0.00 37.04 3.86
58 59 3.710722 CCTTCTGGAGGGCACGCT 61.711 66.667 0.00 0.00 42.26 5.07
59 60 2.435586 CTTCTGGAGGGCACGCTG 60.436 66.667 0.00 0.00 0.00 5.18
60 61 4.704833 TTCTGGAGGGCACGCTGC 62.705 66.667 0.00 0.00 44.08 5.25
85 86 3.157252 GGAGCTGGAGCCGATGGA 61.157 66.667 0.00 0.00 43.38 3.41
86 87 2.735772 GGAGCTGGAGCCGATGGAA 61.736 63.158 0.00 0.00 43.38 3.53
87 88 1.227497 GAGCTGGAGCCGATGGAAG 60.227 63.158 0.00 0.00 43.38 3.46
88 89 1.965754 GAGCTGGAGCCGATGGAAGT 61.966 60.000 0.00 0.00 43.38 3.01
89 90 1.817099 GCTGGAGCCGATGGAAGTG 60.817 63.158 0.00 0.00 34.31 3.16
90 91 1.900351 CTGGAGCCGATGGAAGTGA 59.100 57.895 0.00 0.00 0.00 3.41
91 92 0.460987 CTGGAGCCGATGGAAGTGAC 60.461 60.000 0.00 0.00 0.00 3.67
166 168 4.561155 ACCAGACCTTCGGTGGAT 57.439 55.556 1.76 0.00 35.25 3.41
232 234 1.019673 CAGCGGAGATGTCCATTTGG 58.980 55.000 9.94 0.00 44.18 3.28
235 237 1.729881 GGAGATGTCCATTTGGCGC 59.270 57.895 3.49 0.00 43.31 6.53
241 243 2.018542 TGTCCATTTGGCGCTACTAC 57.981 50.000 7.64 0.00 34.44 2.73
253 255 2.158943 GCGCTACTACCCAGAGGATTTT 60.159 50.000 0.00 0.00 36.73 1.82
254 256 3.718815 CGCTACTACCCAGAGGATTTTC 58.281 50.000 0.00 0.00 36.73 2.29
268 270 2.027837 GGATTTTCTGGTGCTTTGCCAT 60.028 45.455 0.00 0.00 35.19 4.40
273 275 1.228094 TGGTGCTTTGCCATGACGA 60.228 52.632 0.00 0.00 0.00 4.20
276 278 0.799534 GTGCTTTGCCATGACGATGC 60.800 55.000 0.00 0.00 0.00 3.91
300 302 3.272334 GGATCGGATGGTGCGTGC 61.272 66.667 0.00 0.00 31.47 5.34
301 303 3.630148 GATCGGATGGTGCGTGCG 61.630 66.667 0.00 0.00 35.61 5.34
319 321 2.517166 GGCAAGGCGGATTCCTCC 60.517 66.667 3.32 3.32 34.82 4.30
325 327 1.208165 AGGCGGATTCCTCCTGGTTT 61.208 55.000 13.57 0.00 39.65 3.27
352 354 3.976701 CTTGCGGCCCTGGATTCGT 62.977 63.158 0.00 0.00 0.00 3.85
404 406 0.179043 CCTCGTCCCGATCTCTCTGA 60.179 60.000 0.00 0.00 34.61 3.27
406 408 0.179043 TCGTCCCGATCTCTCTGAGG 60.179 60.000 4.59 0.00 0.00 3.86
407 409 0.179043 CGTCCCGATCTCTCTGAGGA 60.179 60.000 4.59 1.70 0.00 3.71
482 484 3.315949 GCTACGTGGTGGGGGTGA 61.316 66.667 0.00 0.00 0.00 4.02
487 489 2.032071 GTGGTGGGGGTGAACGAG 59.968 66.667 0.00 0.00 0.00 4.18
502 504 4.373116 GAGGACACCGCGAGCCAA 62.373 66.667 8.23 0.00 0.00 4.52
532 534 1.227853 GGACTTCCGTGTGTGGCTT 60.228 57.895 0.00 0.00 0.00 4.35
544 546 4.680237 TGGCTTCGCACAGACCGG 62.680 66.667 0.00 0.00 0.00 5.28
564 566 3.064079 CGCATCGGATTCCAAGACA 57.936 52.632 3.09 0.00 0.00 3.41
570 585 0.179073 CGGATTCCAAGACAGCGGAT 60.179 55.000 3.09 0.00 0.00 4.18
594 609 2.358737 CGGCGAACTCTTTGGGCT 60.359 61.111 0.00 0.00 34.28 5.19
595 610 2.680913 CGGCGAACTCTTTGGGCTG 61.681 63.158 0.00 0.00 34.28 4.85
596 611 1.302511 GGCGAACTCTTTGGGCTGA 60.303 57.895 0.00 0.00 33.73 4.26
597 612 0.889186 GGCGAACTCTTTGGGCTGAA 60.889 55.000 0.00 0.00 33.73 3.02
611 626 1.900351 CTGAAGAGGATGGACGGCA 59.100 57.895 0.00 0.00 0.00 5.69
612 627 0.467384 CTGAAGAGGATGGACGGCAT 59.533 55.000 0.00 0.00 0.00 4.40
613 628 0.911769 TGAAGAGGATGGACGGCATT 59.088 50.000 0.00 0.00 0.00 3.56
621 636 1.812571 GATGGACGGCATTTGACTGTT 59.187 47.619 0.00 0.00 0.00 3.16
624 639 0.951558 GACGGCATTTGACTGTTGGT 59.048 50.000 0.00 0.00 0.00 3.67
625 640 2.147958 GACGGCATTTGACTGTTGGTA 58.852 47.619 0.00 0.00 0.00 3.25
644 659 3.181967 GTGCACTACGGCGCTCTG 61.182 66.667 10.32 0.00 40.99 3.35
656 671 0.171455 GCGCTCTGGTATCCTATCGG 59.829 60.000 0.00 0.00 0.00 4.18
683 698 4.090588 GTTGGCGGACCCGATGGA 62.091 66.667 13.24 0.00 42.83 3.41
687 702 3.234730 GCGGACCCGATGGAGGAT 61.235 66.667 13.24 0.00 42.83 3.24
689 704 2.872388 CGGACCCGATGGAGGATGG 61.872 68.421 1.54 0.00 42.83 3.51
694 709 1.152247 CCGATGGAGGATGGGGAGA 60.152 63.158 0.00 0.00 0.00 3.71
696 711 0.760567 CGATGGAGGATGGGGAGACA 60.761 60.000 0.00 0.00 0.00 3.41
738 753 3.716195 CCGCCACCACCTCCATCA 61.716 66.667 0.00 0.00 0.00 3.07
741 756 2.268920 CCACCACCTCCATCACCG 59.731 66.667 0.00 0.00 0.00 4.94
762 777 1.888215 CCACTGGGAATGATGATCCG 58.112 55.000 0.00 0.00 37.87 4.18
763 778 1.417517 CCACTGGGAATGATGATCCGA 59.582 52.381 0.00 0.00 37.87 4.55
767 782 0.249868 GGGAATGATGATCCGACGCA 60.250 55.000 0.00 0.00 37.87 5.24
771 786 0.952497 ATGATGATCCGACGCATGGC 60.952 55.000 0.00 0.00 0.00 4.40
793 808 2.764128 ATGGCGGTCGAGGTGGAT 60.764 61.111 0.00 0.00 0.00 3.41
798 813 1.152819 CGGTCGAGGTGGATAGGGA 60.153 63.158 0.00 0.00 0.00 4.20
803 818 0.106167 CGAGGTGGATAGGGAGGTCA 60.106 60.000 0.00 0.00 0.00 4.02
807 822 1.760875 TGGATAGGGAGGTCACGCC 60.761 63.158 0.00 0.00 35.57 5.68
839 854 3.712907 CCACGGTGGGGATTCGGT 61.713 66.667 19.63 0.00 32.67 4.69
846 861 2.220586 TGGGGATTCGGTGAGCACA 61.221 57.895 2.75 0.00 0.00 4.57
923 947 2.668550 GTCGGTGGCTGTTGGGTC 60.669 66.667 0.00 0.00 0.00 4.46
932 956 1.003355 CTGTTGGGTCGGTCAGCAT 60.003 57.895 0.00 0.00 0.00 3.79
988 1027 2.885644 CGGTCGTGGAGCCAATCG 60.886 66.667 0.00 0.00 0.00 3.34
1000 1039 2.046023 CAATCGTGGAGCCAGGCA 60.046 61.111 15.80 0.00 0.00 4.75
1001 1040 1.452651 CAATCGTGGAGCCAGGCAT 60.453 57.895 15.80 0.00 0.00 4.40
1003 1042 4.783621 TCGTGGAGCCAGGCATGC 62.784 66.667 15.80 9.90 0.00 4.06
1020 1059 3.067091 CTGGGTGTCAGCTGCTCT 58.933 61.111 9.47 0.00 36.60 4.09
1077 1116 4.048470 GTGGGGCCCAGGAAGACC 62.048 72.222 29.66 8.70 32.34 3.85
1080 1119 3.647771 GGGCCCAGGAAGACCGTT 61.648 66.667 19.95 0.00 41.83 4.44
1083 1122 1.228154 GCCCAGGAAGACCGTTTGT 60.228 57.895 0.00 0.00 41.83 2.83
1106 1145 4.617875 ACCATCGGTGCAGCTAAC 57.382 55.556 14.92 0.00 32.98 2.34
1131 1170 1.216710 GCGACAGAAGGAGGTGGAG 59.783 63.158 0.00 0.00 0.00 3.86
1142 1181 2.749441 GGTGGAGGAAGCTGCTGC 60.749 66.667 1.35 7.62 40.05 5.25
1163 1202 4.847367 GCAGGGGATTGGGGCCAG 62.847 72.222 4.39 0.00 0.00 4.85
1201 1240 1.380785 AATGGAGGGCTGCATGTGG 60.381 57.895 0.50 0.00 40.85 4.17
1203 1242 2.439156 GGAGGGCTGCATGTGGAC 60.439 66.667 0.50 0.00 0.00 4.02
1209 1248 1.450134 GCTGCATGTGGACGGATCA 60.450 57.895 0.00 0.00 0.00 2.92
1213 1252 0.391661 GCATGTGGACGGATCAGTGT 60.392 55.000 2.27 0.00 0.00 3.55
1214 1253 1.362768 CATGTGGACGGATCAGTGTG 58.637 55.000 2.27 0.00 0.00 3.82
1227 1266 1.207089 TCAGTGTGGATCGGATTGGTC 59.793 52.381 0.00 0.00 0.00 4.02
1237 1276 3.223946 GGATTGGTCCAAATCCCCC 57.776 57.895 8.75 1.89 46.81 5.40
1241 1280 1.514864 TTGGTCCAAATCCCCCTCCC 61.515 60.000 0.40 0.00 0.00 4.30
1242 1281 1.622752 GGTCCAAATCCCCCTCCCT 60.623 63.158 0.00 0.00 0.00 4.20
1257 1296 2.323599 CTCCCTCTGCAGGATATGACA 58.676 52.381 15.13 0.00 43.65 3.58
1270 1309 5.050499 CAGGATATGACAGACGAAGATTTGC 60.050 44.000 0.00 0.00 0.00 3.68
1275 1314 2.808543 GACAGACGAAGATTTGCCAAGT 59.191 45.455 0.00 0.00 0.00 3.16
1276 1315 2.549754 ACAGACGAAGATTTGCCAAGTG 59.450 45.455 0.00 0.00 0.00 3.16
1278 1317 3.003689 CAGACGAAGATTTGCCAAGTGTT 59.996 43.478 0.00 0.00 0.00 3.32
1290 1329 2.770164 CAAGTGTTGGGACTAGGGAG 57.230 55.000 0.00 0.00 0.00 4.30
1296 1335 3.263425 GTGTTGGGACTAGGGAGAATCAA 59.737 47.826 0.00 0.00 36.25 2.57
1309 1348 3.193691 GGAGAATCAAGAACTCCTGTCGA 59.806 47.826 14.88 0.00 44.54 4.20
1314 1353 1.998315 CAAGAACTCCTGTCGATGCAG 59.002 52.381 0.00 0.00 36.31 4.41
1326 1365 0.745486 CGATGCAGCAGGATGTGGAA 60.745 55.000 1.53 0.00 39.31 3.53
1329 1368 0.321919 TGCAGCAGGATGTGGAAGAC 60.322 55.000 0.00 0.00 39.31 3.01
1356 1395 3.406200 CAGGTGGAGCCCTGGGAG 61.406 72.222 19.27 0.00 46.89 4.30
1374 1413 2.180276 GAGACTTTCCAGGTCAGCCTA 58.820 52.381 0.00 0.00 44.97 3.93
1380 1419 0.937441 TCCAGGTCAGCCTATCCTCT 59.063 55.000 0.00 0.00 44.97 3.69
1400 1439 2.583520 GGAGACCAGCCAGCTGAG 59.416 66.667 21.01 12.90 46.30 3.35
1404 1443 2.285969 ACCAGCCAGCTGAGGGAT 60.286 61.111 21.01 0.00 46.30 3.85
1413 1452 2.444706 CTGAGGGATCCGAGGCCA 60.445 66.667 5.01 0.00 0.00 5.36
1414 1453 1.840650 CTGAGGGATCCGAGGCCAT 60.841 63.158 5.01 0.00 0.00 4.40
1416 1455 3.543536 GAGGGATCCGAGGCCATGC 62.544 68.421 5.01 0.00 0.00 4.06
1420 1459 1.071987 GATCCGAGGCCATGCATGA 59.928 57.895 28.31 6.34 0.00 3.07
1422 1461 0.322277 ATCCGAGGCCATGCATGATC 60.322 55.000 28.31 19.53 0.00 2.92
1423 1462 1.228033 CCGAGGCCATGCATGATCA 60.228 57.895 28.31 0.00 0.00 2.92
1458 1497 4.554036 GGCCAGCCCGAGGATGAC 62.554 72.222 9.41 0.00 42.34 3.06
1460 1499 4.899239 CCAGCCCGAGGATGACGC 62.899 72.222 9.41 0.00 42.34 5.19
1468 1507 4.552365 AGGATGACGCGGGCCATG 62.552 66.667 12.47 0.00 0.00 3.66
1490 1529 1.514087 CCAACCAGATGGCATGCAC 59.486 57.895 21.36 9.64 39.32 4.57
1493 1532 3.135457 CCAGATGGCATGCACGCA 61.135 61.111 21.36 8.94 0.00 5.24
1496 1535 2.103538 GATGGCATGCACGCAAGG 59.896 61.111 21.36 0.00 46.39 3.61
1515 1554 1.952102 GCAGTCCGACGAATGGGGTA 61.952 60.000 0.00 0.00 34.63 3.69
1542 1581 2.063378 CCCACCTGAGGAGGAGCTC 61.063 68.421 17.10 4.71 42.93 4.09
1572 1611 2.507944 GATCCGAGGCCATGCAGT 59.492 61.111 5.01 0.00 0.00 4.40
1590 1629 0.035056 GTACTGTTCCCATGCAGGCT 60.035 55.000 0.00 0.00 37.07 4.58
1592 1631 2.677524 TGTTCCCATGCAGGCTGC 60.678 61.111 31.91 31.91 45.29 5.25
1626 1665 1.933021 TTCACGTAGATGTGGGGACT 58.067 50.000 2.15 0.00 40.31 3.85
1676 1716 0.745845 CCGATCCTGCCAAGACCAAG 60.746 60.000 0.00 0.00 0.00 3.61
1677 1717 1.372087 CGATCCTGCCAAGACCAAGC 61.372 60.000 0.00 0.00 0.00 4.01
1683 1723 2.618816 CCTGCCAAGACCAAGCAATAGA 60.619 50.000 0.00 0.00 35.79 1.98
1695 1735 1.176527 GCAATAGAACTGCTGCCCAA 58.823 50.000 0.00 0.00 36.84 4.12
1836 1876 0.326238 ACGAGGGGGAGGCTATTTCA 60.326 55.000 0.00 0.00 0.00 2.69
1841 1881 0.767998 GGGGAGGCTATTTCAGAGGG 59.232 60.000 0.00 0.00 0.00 4.30
1842 1882 0.109532 GGGAGGCTATTTCAGAGGGC 59.890 60.000 0.00 0.00 0.00 5.19
1868 1908 4.935205 TCTTCGGATGTATGTTGACCTTTG 59.065 41.667 0.00 0.00 0.00 2.77
1972 2012 1.120530 CCCTATCGTGGCCTAGTTGT 58.879 55.000 3.32 0.00 0.00 3.32
1991 2031 2.123683 CGCTCAGCTAGGAGGGGA 60.124 66.667 9.54 0.00 42.34 4.81
2016 2056 2.038689 TGTGGGCATTGCAAATGAATGT 59.961 40.909 11.39 0.00 33.96 2.71
2050 2090 0.470341 TGTTGGTGTGGAATGTCCGA 59.530 50.000 0.00 0.00 40.17 4.55
2152 2192 6.212235 AGAGACTAAACTGCATGATGTATCG 58.788 40.000 0.00 0.00 0.00 2.92
2155 2195 1.220529 AACTGCATGATGTATCGGCG 58.779 50.000 0.00 0.00 33.91 6.46
2179 2232 2.126346 GTGCGTCAATGCCTTGGC 60.126 61.111 4.43 4.43 33.51 4.52
2191 2244 6.421801 GTCAATGCCTTGGCAATAAATATGAC 59.578 38.462 18.76 17.08 36.95 3.06
2246 2299 1.139498 TGGGATCTTGGTGGCTTGGA 61.139 55.000 0.00 0.00 0.00 3.53
2294 2347 2.284150 CCGCACTACACAAATCATACGG 59.716 50.000 0.00 0.00 0.00 4.02
2317 2370 4.284550 GCCCTGGTCAAGTGCCCA 62.285 66.667 0.00 0.00 0.00 5.36
2353 2406 1.908619 TGGTGGCTGATGTGTGTCTAT 59.091 47.619 0.00 0.00 0.00 1.98
2360 2413 1.915489 TGATGTGTGTCTATGGCCCTT 59.085 47.619 0.00 0.00 0.00 3.95
2387 2440 1.141053 AGGCCGACAAACTTGAGTTCT 59.859 47.619 0.00 0.00 37.25 3.01
2464 2517 4.024670 GAGACTTTAACCTCCTAGCTGGA 58.975 47.826 0.00 1.40 43.86 3.86
2531 2584 3.556365 GCGGTTTAGATCTAAGCTGAACC 59.444 47.826 31.25 24.51 44.23 3.62
2560 2613 9.699703 CTAGAATTGAAGGAGCTATACCTAAAC 57.300 37.037 0.00 0.00 36.67 2.01
2602 2655 3.062763 CAACGAGAGACAGAATGCAACT 58.937 45.455 0.00 0.00 42.53 3.16
2619 2672 3.000724 GCAACTCTGGAGAAAATCGATCG 59.999 47.826 9.36 9.36 0.00 3.69
2623 2676 4.177026 CTCTGGAGAAAATCGATCGTGTT 58.823 43.478 15.94 8.75 0.00 3.32
2705 2758 1.345741 CAGTATCGGATCACTGCCCAT 59.654 52.381 11.79 0.00 36.09 4.00
2744 2797 5.360591 ACATGGAGATTATGACGAGGAAAC 58.639 41.667 0.00 0.00 0.00 2.78
2746 2799 3.697542 TGGAGATTATGACGAGGAAACGA 59.302 43.478 0.00 0.00 37.03 3.85
2822 2875 0.617820 GGCTTGGGACTCCACTCCTA 60.618 60.000 0.00 0.00 43.94 2.94
2824 2877 1.840635 GCTTGGGACTCCACTCCTAAT 59.159 52.381 0.00 0.00 43.94 1.73
2830 2883 2.111384 GACTCCACTCCTAATGCCTCA 58.889 52.381 0.00 0.00 0.00 3.86
2954 3007 2.423538 GCGTTGGAGGTGATAAAGCAAT 59.576 45.455 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.374252 GCAACGCCCTTCTCTTCGA 60.374 57.895 0.00 0.00 0.00 3.71
1 2 2.391389 GGCAACGCCCTTCTCTTCG 61.391 63.158 0.00 0.00 44.06 3.79
2 3 3.579685 GGCAACGCCCTTCTCTTC 58.420 61.111 0.00 0.00 44.06 2.87
12 13 2.052237 CGTGAACACAGGCAACGC 60.052 61.111 5.80 0.00 46.39 4.84
13 14 2.177580 ACCGTGAACACAGGCAACG 61.178 57.895 12.78 0.00 46.39 4.10
14 15 1.355210 CACCGTGAACACAGGCAAC 59.645 57.895 12.78 0.00 0.00 4.17
15 16 2.477176 GCACCGTGAACACAGGCAA 61.477 57.895 1.65 0.00 0.00 4.52
16 17 2.899838 GCACCGTGAACACAGGCA 60.900 61.111 1.65 0.00 0.00 4.75
17 18 1.795170 AATGCACCGTGAACACAGGC 61.795 55.000 1.65 9.41 0.00 4.85
18 19 0.667993 AAATGCACCGTGAACACAGG 59.332 50.000 1.65 9.30 0.00 4.00
19 20 2.118683 CAAAATGCACCGTGAACACAG 58.881 47.619 1.65 0.00 0.00 3.66
20 21 1.745653 TCAAAATGCACCGTGAACACA 59.254 42.857 1.65 0.00 0.00 3.72
21 22 2.116366 GTCAAAATGCACCGTGAACAC 58.884 47.619 1.65 0.00 0.00 3.32
22 23 1.066303 GGTCAAAATGCACCGTGAACA 59.934 47.619 1.65 0.00 0.00 3.18
23 24 1.336755 AGGTCAAAATGCACCGTGAAC 59.663 47.619 1.65 0.00 37.79 3.18
24 25 1.686355 AGGTCAAAATGCACCGTGAA 58.314 45.000 1.65 0.00 37.79 3.18
25 26 1.606668 GAAGGTCAAAATGCACCGTGA 59.393 47.619 1.65 0.00 37.79 4.35
26 27 1.608590 AGAAGGTCAAAATGCACCGTG 59.391 47.619 0.00 0.00 37.79 4.94
27 28 1.608590 CAGAAGGTCAAAATGCACCGT 59.391 47.619 0.00 0.00 37.79 4.83
28 29 1.068333 CCAGAAGGTCAAAATGCACCG 60.068 52.381 0.00 0.00 37.79 4.94
29 30 2.229784 CTCCAGAAGGTCAAAATGCACC 59.770 50.000 0.00 0.00 35.89 5.01
30 31 2.229784 CCTCCAGAAGGTCAAAATGCAC 59.770 50.000 0.00 0.00 40.67 4.57
31 32 2.517959 CCTCCAGAAGGTCAAAATGCA 58.482 47.619 0.00 0.00 40.67 3.96
32 33 1.821136 CCCTCCAGAAGGTCAAAATGC 59.179 52.381 0.00 0.00 44.56 3.56
33 34 1.821136 GCCCTCCAGAAGGTCAAAATG 59.179 52.381 0.00 0.00 44.56 2.32
34 35 1.428912 TGCCCTCCAGAAGGTCAAAAT 59.571 47.619 0.00 0.00 44.56 1.82
35 36 0.850100 TGCCCTCCAGAAGGTCAAAA 59.150 50.000 0.00 0.00 44.56 2.44
36 37 0.110486 GTGCCCTCCAGAAGGTCAAA 59.890 55.000 0.00 0.00 44.56 2.69
37 38 1.761174 GTGCCCTCCAGAAGGTCAA 59.239 57.895 0.00 0.00 44.56 3.18
38 39 2.583441 CGTGCCCTCCAGAAGGTCA 61.583 63.158 0.00 0.00 44.56 4.02
39 40 2.266055 CGTGCCCTCCAGAAGGTC 59.734 66.667 0.00 0.00 44.56 3.85
40 41 4.021925 GCGTGCCCTCCAGAAGGT 62.022 66.667 0.00 0.00 44.56 3.50
41 42 3.710722 AGCGTGCCCTCCAGAAGG 61.711 66.667 0.00 0.00 45.77 3.46
42 43 2.435586 CAGCGTGCCCTCCAGAAG 60.436 66.667 0.00 0.00 0.00 2.85
43 44 4.704833 GCAGCGTGCCCTCCAGAA 62.705 66.667 0.00 0.00 37.42 3.02
66 67 4.598894 CATCGGCTCCAGCTCCGG 62.599 72.222 11.27 0.00 45.31 5.14
67 68 4.598894 CCATCGGCTCCAGCTCCG 62.599 72.222 5.25 5.25 46.52 4.63
68 69 2.657102 CTTCCATCGGCTCCAGCTCC 62.657 65.000 0.00 0.00 41.70 4.70
69 70 1.227497 CTTCCATCGGCTCCAGCTC 60.227 63.158 0.00 0.00 41.70 4.09
70 71 1.992277 ACTTCCATCGGCTCCAGCT 60.992 57.895 0.00 0.00 41.70 4.24
71 72 1.817099 CACTTCCATCGGCTCCAGC 60.817 63.158 0.00 0.00 41.14 4.85
72 73 0.460987 GTCACTTCCATCGGCTCCAG 60.461 60.000 0.00 0.00 0.00 3.86
73 74 1.596934 GTCACTTCCATCGGCTCCA 59.403 57.895 0.00 0.00 0.00 3.86
74 75 1.519455 CGTCACTTCCATCGGCTCC 60.519 63.158 0.00 0.00 0.00 4.70
75 76 0.802607 GTCGTCACTTCCATCGGCTC 60.803 60.000 0.00 0.00 0.00 4.70
76 77 1.215647 GTCGTCACTTCCATCGGCT 59.784 57.895 0.00 0.00 0.00 5.52
77 78 1.080093 TGTCGTCACTTCCATCGGC 60.080 57.895 0.00 0.00 0.00 5.54
78 79 1.071019 CGTGTCGTCACTTCCATCGG 61.071 60.000 10.95 0.00 41.89 4.18
79 80 1.674611 GCGTGTCGTCACTTCCATCG 61.675 60.000 10.95 0.00 41.89 3.84
80 81 1.674611 CGCGTGTCGTCACTTCCATC 61.675 60.000 10.95 0.00 41.89 3.51
81 82 1.733041 CGCGTGTCGTCACTTCCAT 60.733 57.895 10.95 0.00 41.89 3.41
82 83 2.354188 CGCGTGTCGTCACTTCCA 60.354 61.111 10.95 0.00 41.89 3.53
83 84 3.103911 CCGCGTGTCGTCACTTCC 61.104 66.667 4.92 0.00 41.89 3.46
84 85 3.764049 GCCGCGTGTCGTCACTTC 61.764 66.667 4.92 2.22 41.89 3.01
116 117 1.962822 CAAGCACAGCTCTCGCCAA 60.963 57.895 0.00 0.00 38.25 4.52
139 141 1.056700 AAGGTCTGGTGCCAGTCACT 61.057 55.000 16.85 10.95 44.98 3.41
212 214 1.407299 CCAAATGGACATCTCCGCTGA 60.407 52.381 0.00 0.00 39.88 4.26
214 216 0.749454 GCCAAATGGACATCTCCGCT 60.749 55.000 2.98 0.00 39.88 5.52
220 222 1.668419 AGTAGCGCCAAATGGACATC 58.332 50.000 2.29 0.00 37.39 3.06
230 232 1.756950 CCTCTGGGTAGTAGCGCCA 60.757 63.158 2.29 0.00 0.00 5.69
232 234 1.041437 AATCCTCTGGGTAGTAGCGC 58.959 55.000 0.00 0.00 0.00 5.92
253 255 1.236616 CGTCATGGCAAAGCACCAGA 61.237 55.000 0.00 0.00 41.46 3.86
254 256 1.210931 CGTCATGGCAAAGCACCAG 59.789 57.895 0.00 0.00 41.46 4.00
262 264 0.462581 GGAGAGCATCGTCATGGCAA 60.463 55.000 0.00 0.00 42.67 4.52
268 270 1.455773 ATCCCGGAGAGCATCGTCA 60.456 57.895 0.73 0.00 42.67 4.35
300 302 4.489771 AGGAATCCGCCTTGCCCG 62.490 66.667 0.00 0.00 33.46 6.13
301 303 2.517166 GAGGAATCCGCCTTGCCC 60.517 66.667 0.00 0.00 38.73 5.36
311 313 2.238395 AGAGCTCAAACCAGGAGGAATC 59.762 50.000 17.77 0.00 38.69 2.52
312 314 2.238395 GAGAGCTCAAACCAGGAGGAAT 59.762 50.000 17.77 0.00 38.69 3.01
319 321 1.163554 GCAAGGAGAGCTCAAACCAG 58.836 55.000 17.77 12.95 0.00 4.00
418 420 1.127567 TCCTCTGGTTCCAGGTGTGG 61.128 60.000 17.37 13.95 46.63 4.17
422 424 1.913762 CCGTCCTCTGGTTCCAGGT 60.914 63.158 17.37 0.00 35.01 4.00
461 463 4.096003 CCCCACCACGTAGCCCAG 62.096 72.222 0.00 0.00 0.00 4.45
472 474 2.926242 TCCTCGTTCACCCCCACC 60.926 66.667 0.00 0.00 0.00 4.61
482 484 4.719369 GCTCGCGGTGTCCTCGTT 62.719 66.667 6.13 0.00 0.00 3.85
499 501 4.776322 TCCGCCATGTCCGCTTGG 62.776 66.667 0.00 0.00 41.38 3.61
502 504 3.665675 GAAGTCCGCCATGTCCGCT 62.666 63.158 0.00 0.00 0.00 5.52
550 552 1.218047 CCGCTGTCTTGGAATCCGA 59.782 57.895 0.00 0.00 0.00 4.55
559 561 1.299976 GGGGTTCATCCGCTGTCTT 59.700 57.895 0.00 0.00 44.48 3.01
562 564 4.096003 CCGGGGTTCATCCGCTGT 62.096 66.667 0.00 0.00 45.60 4.40
570 585 2.047213 AAAGAGTTCGCCGGGGTTCA 62.047 55.000 19.13 0.86 0.00 3.18
594 609 0.911769 AATGCCGTCCATCCTCTTCA 59.088 50.000 0.00 0.00 31.43 3.02
595 610 1.672881 CAAATGCCGTCCATCCTCTTC 59.327 52.381 0.00 0.00 31.43 2.87
596 611 1.281867 TCAAATGCCGTCCATCCTCTT 59.718 47.619 0.00 0.00 31.43 2.85
597 612 0.911769 TCAAATGCCGTCCATCCTCT 59.088 50.000 0.00 0.00 31.43 3.69
603 618 0.950836 CAACAGTCAAATGCCGTCCA 59.049 50.000 0.00 0.00 0.00 4.02
611 626 2.884639 GTGCACCTACCAACAGTCAAAT 59.115 45.455 5.22 0.00 0.00 2.32
612 627 2.092646 AGTGCACCTACCAACAGTCAAA 60.093 45.455 14.63 0.00 0.00 2.69
613 628 1.488812 AGTGCACCTACCAACAGTCAA 59.511 47.619 14.63 0.00 0.00 3.18
621 636 2.975536 GCCGTAGTGCACCTACCA 59.024 61.111 14.63 0.00 42.69 3.25
656 671 3.499737 CCGCCAACACCTCGATGC 61.500 66.667 0.00 0.00 0.00 3.91
666 681 4.090588 TCCATCGGGTCCGCCAAC 62.091 66.667 4.27 0.00 39.59 3.77
679 694 1.779092 CATTGTCTCCCCATCCTCCAT 59.221 52.381 0.00 0.00 0.00 3.41
683 698 1.516110 CTCCATTGTCTCCCCATCCT 58.484 55.000 0.00 0.00 0.00 3.24
687 702 1.619363 CCCCTCCATTGTCTCCCCA 60.619 63.158 0.00 0.00 0.00 4.96
689 704 2.597903 GCCCCTCCATTGTCTCCC 59.402 66.667 0.00 0.00 0.00 4.30
690 705 2.190578 CGCCCCTCCATTGTCTCC 59.809 66.667 0.00 0.00 0.00 3.71
726 741 3.717294 GGCGGTGATGGAGGTGGT 61.717 66.667 0.00 0.00 0.00 4.16
727 742 4.489771 GGGCGGTGATGGAGGTGG 62.490 72.222 0.00 0.00 0.00 4.61
728 743 3.716195 TGGGCGGTGATGGAGGTG 61.716 66.667 0.00 0.00 0.00 4.00
729 744 3.717294 GTGGGCGGTGATGGAGGT 61.717 66.667 0.00 0.00 0.00 3.85
730 745 3.402681 AGTGGGCGGTGATGGAGG 61.403 66.667 0.00 0.00 0.00 4.30
731 746 2.124983 CAGTGGGCGGTGATGGAG 60.125 66.667 0.00 0.00 0.00 3.86
738 753 2.308722 ATCATTCCCAGTGGGCGGT 61.309 57.895 24.75 7.72 43.94 5.68
741 756 1.613836 GATCATCATTCCCAGTGGGC 58.386 55.000 24.75 1.75 43.94 5.36
767 782 4.856801 GACCGCCATGACCGCCAT 62.857 66.667 0.00 0.00 35.44 4.40
771 786 4.873129 CCTCGACCGCCATGACCG 62.873 72.222 0.00 0.00 0.00 4.79
774 789 3.770040 CCACCTCGACCGCCATGA 61.770 66.667 0.00 0.00 0.00 3.07
780 795 1.152819 TCCCTATCCACCTCGACCG 60.153 63.158 0.00 0.00 0.00 4.79
785 800 1.415200 GTGACCTCCCTATCCACCTC 58.585 60.000 0.00 0.00 0.00 3.85
819 834 4.041762 GAATCCCCACCGTGGCCA 62.042 66.667 12.54 0.00 35.79 5.36
825 840 2.186903 CTCACCGAATCCCCACCG 59.813 66.667 0.00 0.00 0.00 4.94
831 846 2.109126 GGCTGTGCTCACCGAATCC 61.109 63.158 0.00 0.00 0.00 3.01
896 920 2.968156 CCACCGACGCCGTTTGAA 60.968 61.111 0.00 0.00 0.00 2.69
905 929 4.619227 ACCCAACAGCCACCGACG 62.619 66.667 0.00 0.00 0.00 5.12
907 931 4.308458 CGACCCAACAGCCACCGA 62.308 66.667 0.00 0.00 0.00 4.69
910 934 2.668550 GACCGACCCAACAGCCAC 60.669 66.667 0.00 0.00 0.00 5.01
914 938 1.003355 ATGCTGACCGACCCAACAG 60.003 57.895 0.00 0.00 0.00 3.16
917 941 1.296392 CTGATGCTGACCGACCCAA 59.704 57.895 0.00 0.00 0.00 4.12
953 992 3.443925 GGCCCGCAGAAAAGCCTC 61.444 66.667 0.00 0.00 42.34 4.70
978 1017 2.514824 GGCTCCACGATTGGCTCC 60.515 66.667 0.00 0.00 43.56 4.70
979 1018 1.817099 CTGGCTCCACGATTGGCTC 60.817 63.158 0.00 0.00 43.56 4.70
988 1027 3.138798 CAGCATGCCTGGCTCCAC 61.139 66.667 21.03 6.84 40.23 4.02
996 1035 2.353958 CTGACACCCAGCATGCCT 59.646 61.111 15.66 0.00 35.89 4.75
1003 1042 1.079266 GAGAGCAGCTGACACCCAG 60.079 63.158 20.43 0.00 45.67 4.45
1008 1047 0.316522 GTGACAGAGAGCAGCTGACA 59.683 55.000 20.43 4.89 36.11 3.58
1010 1049 1.583477 CGTGACAGAGAGCAGCTGA 59.417 57.895 20.43 0.00 36.86 4.26
1017 1056 2.202544 GCCTCGCGTGACAGAGAG 60.203 66.667 10.21 4.41 36.65 3.20
1058 1097 2.935481 TCTTCCTGGGCCCCACTG 60.935 66.667 22.27 6.77 0.00 3.66
1059 1098 2.936032 GTCTTCCTGGGCCCCACT 60.936 66.667 22.27 0.00 0.00 4.00
1060 1099 4.048470 GGTCTTCCTGGGCCCCAC 62.048 72.222 22.27 5.92 0.00 4.61
1066 1105 1.235724 GAACAAACGGTCTTCCTGGG 58.764 55.000 0.00 0.00 0.00 4.45
1070 1109 1.332686 GTGGTGAACAAACGGTCTTCC 59.667 52.381 0.00 0.00 0.00 3.46
1077 1116 0.237235 CCGATGGTGGTGAACAAACG 59.763 55.000 0.00 0.00 0.00 3.60
1079 1118 3.811031 ACCGATGGTGGTGAACAAA 57.189 47.368 0.00 0.00 41.85 2.83
1106 1145 2.046892 CCTTCTGTCGCCACCTGG 60.047 66.667 0.00 0.00 38.53 4.45
1142 1181 2.510906 CCCCAATCCCCTGCGTAG 59.489 66.667 0.00 0.00 0.00 3.51
1143 1182 3.804329 GCCCCAATCCCCTGCGTA 61.804 66.667 0.00 0.00 0.00 4.42
1162 1201 4.845580 CATCAAGGCCGAGGCGCT 62.846 66.667 7.64 3.78 43.06 5.92
1172 1211 0.757935 CCCTCCATTGGGCATCAAGG 60.758 60.000 2.09 0.82 40.84 3.61
1184 1223 2.277737 CCACATGCAGCCCTCCAT 59.722 61.111 0.00 0.00 0.00 3.41
1191 1230 1.434622 CTGATCCGTCCACATGCAGC 61.435 60.000 0.00 0.00 0.00 5.25
1193 1232 0.391528 CACTGATCCGTCCACATGCA 60.392 55.000 0.00 0.00 0.00 3.96
1195 1234 1.362768 CACACTGATCCGTCCACATG 58.637 55.000 0.00 0.00 0.00 3.21
1201 1240 0.249073 CCGATCCACACTGATCCGTC 60.249 60.000 0.00 0.00 38.32 4.79
1203 1242 0.676184 ATCCGATCCACACTGATCCG 59.324 55.000 0.00 0.00 38.32 4.18
1209 1248 0.541863 GGACCAATCCGATCCACACT 59.458 55.000 0.00 0.00 34.48 3.55
1227 1266 1.925888 CAGAGGGAGGGGGATTTGG 59.074 63.158 0.00 0.00 0.00 3.28
1237 1276 2.299582 CTGTCATATCCTGCAGAGGGAG 59.700 54.545 17.39 1.98 40.25 4.30
1241 1280 2.620585 TCGTCTGTCATATCCTGCAGAG 59.379 50.000 17.39 5.49 38.12 3.35
1242 1281 2.654863 TCGTCTGTCATATCCTGCAGA 58.345 47.619 17.39 1.21 36.39 4.26
1257 1296 2.851195 ACACTTGGCAAATCTTCGTCT 58.149 42.857 0.00 0.00 0.00 4.18
1275 1314 3.199442 TGATTCTCCCTAGTCCCAACA 57.801 47.619 0.00 0.00 0.00 3.33
1276 1315 3.775316 TCTTGATTCTCCCTAGTCCCAAC 59.225 47.826 0.00 0.00 0.00 3.77
1278 1317 3.775316 GTTCTTGATTCTCCCTAGTCCCA 59.225 47.826 0.00 0.00 0.00 4.37
1285 1324 3.517500 GACAGGAGTTCTTGATTCTCCCT 59.482 47.826 14.20 0.00 46.15 4.20
1290 1329 3.308323 GCATCGACAGGAGTTCTTGATTC 59.692 47.826 0.00 0.00 0.00 2.52
1296 1335 0.108424 GCTGCATCGACAGGAGTTCT 60.108 55.000 9.42 0.00 38.16 3.01
1309 1348 0.622136 TCTTCCACATCCTGCTGCAT 59.378 50.000 1.31 0.00 0.00 3.96
1314 1353 1.364626 CGCAGTCTTCCACATCCTGC 61.365 60.000 0.00 0.00 43.84 4.85
1380 1419 4.664267 AGCTGGCTGGTCTCCCCA 62.664 66.667 0.00 0.00 42.51 4.96
1386 1425 2.322638 GATCCCTCAGCTGGCTGGTC 62.323 65.000 20.41 4.36 43.75 4.02
1389 1428 2.509916 GGATCCCTCAGCTGGCTG 59.490 66.667 15.13 15.58 44.86 4.85
1394 1433 2.841988 GCCTCGGATCCCTCAGCT 60.842 66.667 6.06 0.00 0.00 4.24
1399 1438 3.564218 GCATGGCCTCGGATCCCT 61.564 66.667 6.06 0.00 0.00 4.20
1400 1439 3.201707 ATGCATGGCCTCGGATCCC 62.202 63.158 6.06 0.00 0.00 3.85
1404 1443 1.071987 GATCATGCATGGCCTCGGA 59.928 57.895 25.97 5.63 0.00 4.55
1479 1518 2.103538 CCTTGCGTGCATGCCATC 59.896 61.111 27.43 4.90 0.00 3.51
1480 1519 4.137872 GCCTTGCGTGCATGCCAT 62.138 61.111 27.43 0.00 0.00 4.40
1490 1529 4.717629 TCGTCGGACTGCCTTGCG 62.718 66.667 6.57 0.00 0.00 4.85
1493 1532 1.079127 CCATTCGTCGGACTGCCTT 60.079 57.895 6.57 0.00 0.00 4.35
1495 1534 2.511600 CCCATTCGTCGGACTGCC 60.512 66.667 6.57 0.00 0.00 4.85
1496 1535 1.952102 TACCCCATTCGTCGGACTGC 61.952 60.000 6.57 0.00 0.00 4.40
1498 1537 0.033796 TCTACCCCATTCGTCGGACT 60.034 55.000 6.57 0.00 0.00 3.85
1515 1554 2.284625 TCAGGTGGGTCCGCATCT 60.285 61.111 2.81 0.00 41.99 2.90
1592 1631 3.116531 GAAACTCGTTCCCCGCCG 61.117 66.667 0.00 0.00 36.19 6.46
1595 1634 0.039256 TACGTGAAACTCGTTCCCCG 60.039 55.000 0.00 0.00 41.72 5.73
1626 1665 1.518133 GCGCACACCAGCACAAAAA 60.518 52.632 0.30 0.00 0.00 1.94
1647 1686 1.144936 CAGGATCGGAGACAAGGGC 59.855 63.158 0.00 0.00 42.51 5.19
1676 1716 1.176527 TTGGGCAGCAGTTCTATTGC 58.823 50.000 0.00 0.00 41.83 3.56
1677 1717 2.094545 GGTTTGGGCAGCAGTTCTATTG 60.095 50.000 0.00 0.00 0.00 1.90
1683 1723 2.501602 GCAGGTTTGGGCAGCAGTT 61.502 57.895 0.00 0.00 0.00 3.16
1695 1735 3.297620 CTTGCTTGGCGGCAGGTT 61.298 61.111 22.00 0.00 43.39 3.50
1704 1744 0.606401 TCGGCTTCTTCCTTGCTTGG 60.606 55.000 0.00 0.00 0.00 3.61
1728 1768 3.141488 CTCCTAGGCGTGGCGTCT 61.141 66.667 2.96 0.45 46.06 4.18
1733 1773 3.211288 CACTCCTCCTAGGCGTGG 58.789 66.667 2.96 6.43 45.01 4.94
1818 1858 0.394565 CTGAAATAGCCTCCCCCTCG 59.605 60.000 0.00 0.00 0.00 4.63
1841 1881 1.258982 CAACATACATCCGAAGAGCGC 59.741 52.381 0.00 0.00 39.11 5.92
1842 1882 2.535984 GTCAACATACATCCGAAGAGCG 59.464 50.000 0.00 0.00 40.47 5.03
1972 2012 2.123683 CCCTCCTAGCTGAGCGGA 60.124 66.667 0.00 0.00 0.00 5.54
1991 2031 0.392336 ATTTGCAATGCCCACAACGT 59.608 45.000 1.53 0.00 0.00 3.99
2016 2056 5.069251 CACACCAACATTTTAAGGGGTTGTA 59.931 40.000 11.67 0.00 35.06 2.41
2138 2178 1.066136 CTCGCCGATACATCATGCAG 58.934 55.000 0.00 0.00 0.00 4.41
2152 2192 2.257286 ATTGACGCACAATGCTCGCC 62.257 55.000 7.47 0.00 45.99 5.54
2191 2244 4.557205 ACGCTGGTAAGTAGAAGAACTTG 58.443 43.478 0.00 0.00 39.95 3.16
2209 2262 2.357034 CCACGTGTGCCTAACGCT 60.357 61.111 15.65 0.00 44.80 5.07
2246 2299 9.911788 ATTGGACAAGTGAGTAATAGATTCATT 57.088 29.630 0.00 0.00 0.00 2.57
2294 2347 2.358737 CTTGACCAGGGCCGTCAC 60.359 66.667 13.01 0.84 39.89 3.67
2317 2370 0.913451 ACCAGGCTTGCTCATCCTCT 60.913 55.000 0.00 0.00 0.00 3.69
2343 2396 1.837439 CCTAAGGGCCATAGACACACA 59.163 52.381 17.11 0.00 0.00 3.72
2344 2397 2.103263 CTCCTAAGGGCCATAGACACAC 59.897 54.545 17.11 0.00 0.00 3.82
2353 2406 2.366972 GCCTCCTCCTAAGGGCCA 60.367 66.667 6.18 0.00 43.56 5.36
2360 2413 0.252103 AGTTTGTCGGCCTCCTCCTA 60.252 55.000 0.00 0.00 0.00 2.94
2387 2440 3.431626 CGTATATCCACCAGGTCTTGCAA 60.432 47.826 0.00 0.00 35.89 4.08
2432 2485 5.512576 GGAGGTTAAAGTCTCCAGCAACTAA 60.513 44.000 13.02 0.00 46.54 2.24
2464 2517 1.980765 TCATTGCTCTTGTCCTCCTGT 59.019 47.619 0.00 0.00 0.00 4.00
2531 2584 6.014669 AGGTATAGCTCCTTCAATTCTAGCAG 60.015 42.308 0.00 0.00 35.63 4.24
2602 2655 3.868757 ACACGATCGATTTTCTCCAGA 57.131 42.857 24.34 0.00 0.00 3.86
2650 2703 3.372206 CAGAGACGAAACATGATGGGAAC 59.628 47.826 0.00 0.00 0.00 3.62
2705 2758 6.358991 TCTCCATGTTCATATCAAGCATCAA 58.641 36.000 0.00 0.00 0.00 2.57
2744 2797 4.470462 CAGAAAGCCTCAAACTTGAATCG 58.530 43.478 0.00 0.00 36.64 3.34
2746 2799 4.473444 TCCAGAAAGCCTCAAACTTGAAT 58.527 39.130 0.00 0.00 36.64 2.57
2822 2875 4.265073 GTGAGGTAGTCATTTGAGGCATT 58.735 43.478 0.00 0.00 37.56 3.56
2824 2877 2.353704 CGTGAGGTAGTCATTTGAGGCA 60.354 50.000 0.00 0.00 37.56 4.75
2830 2883 1.899814 TGGAGCGTGAGGTAGTCATTT 59.100 47.619 0.00 0.00 45.11 2.32


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

AutoCloner maintained by Alex Coulton.