Multiple sequence alignment - TraesCS1B01G164800

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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 TraesCS1B01G164800 chr1B 100.000 3911 0 0 1 3911 287840086 287843996 0.000000e+00 7223.0
1 TraesCS1B01G164800 chr1B 91.956 547 34 8 3371 3911 38012948 38012406 0.000000e+00 758.0
2 TraesCS1B01G164800 chr1B 91.758 546 36 8 3371 3911 1466014 1465473 0.000000e+00 750.0
3 TraesCS1B01G164800 chr1B 75.855 994 198 34 1495 2478 671225467 671226428 5.920000e-128 468.0
4 TraesCS1B01G164800 chr1B 87.115 357 39 3 2971 3327 1469325 1468976 7.870000e-107 398.0
5 TraesCS1B01G164800 chr1B 82.796 93 16 0 1367 1459 671225365 671225457 2.500000e-12 84.2
6 TraesCS1B01G164800 chr1D 94.690 2354 85 12 634 2970 200095539 200093209 0.000000e+00 3618.0
7 TraesCS1B01G164800 chr1D 87.838 222 22 5 3587 3805 422834455 422834674 5.010000e-64 255.0
8 TraesCS1B01G164800 chr1A 93.949 2099 118 3 843 2941 253037163 253035074 0.000000e+00 3164.0
9 TraesCS1B01G164800 chr1A 78.431 510 91 13 1512 2016 579288548 579288053 8.160000e-82 315.0
10 TraesCS1B01G164800 chr1A 91.018 167 8 2 635 801 253037330 253037171 6.580000e-53 219.0
11 TraesCS1B01G164800 chr4A 91.971 548 32 9 3371 3911 633746467 633747009 0.000000e+00 758.0
12 TraesCS1B01G164800 chr4A 83.835 266 41 2 2971 3235 732372432 732372696 6.490000e-63 252.0
13 TraesCS1B01G164800 chr4A 83.835 266 38 5 2971 3235 731586097 731585836 8.390000e-62 248.0
14 TraesCS1B01G164800 chr4A 82.642 265 40 6 2971 3234 633747523 633747264 3.040000e-56 230.0
15 TraesCS1B01G164800 chr3B 87.789 606 69 5 1 603 690481015 690480412 0.000000e+00 704.0
16 TraesCS1B01G164800 chr3B 89.541 545 29 10 3371 3911 661746931 661747451 0.000000e+00 665.0
17 TraesCS1B01G164800 chr6D 86.689 601 76 4 6 604 318366163 318366761 0.000000e+00 664.0
18 TraesCS1B01G164800 chr4B 75.575 1392 276 52 1370 2719 637724104 637722735 2.560000e-176 628.0
19 TraesCS1B01G164800 chr4D 75.054 1391 285 50 1370 2719 497152448 497151079 1.210000e-164 590.0
20 TraesCS1B01G164800 chr4D 73.475 1180 245 54 1389 2540 497158385 497157246 2.200000e-102 383.0
21 TraesCS1B01G164800 chr5A 74.874 1385 274 51 1382 2719 676951001 676949644 2.640000e-156 562.0
22 TraesCS1B01G164800 chr6B 92.135 356 19 7 3559 3911 42679996 42679647 9.760000e-136 494.0
23 TraesCS1B01G164800 chr7B 73.837 1376 284 61 1367 2710 575388039 575386708 9.830000e-131 477.0
24 TraesCS1B01G164800 chr7B 74.342 912 171 37 1376 2275 577142844 577141984 2.910000e-86 329.0
25 TraesCS1B01G164800 chr7B 82.900 269 40 6 2969 3235 412813861 412813597 1.820000e-58 237.0
26 TraesCS1B01G164800 chr7B 84.100 239 32 4 2999 3237 412812134 412812366 3.930000e-55 226.0
27 TraesCS1B01G164800 chr7A 76.840 924 166 31 1367 2275 615376101 615375211 9.830000e-131 477.0
28 TraesCS1B01G164800 chr2A 73.680 1364 301 43 1366 2691 602652760 602651417 9.830000e-131 477.0
29 TraesCS1B01G164800 chr2A 89.655 203 16 5 3605 3805 535215570 535215371 1.800000e-63 254.0
30 TraesCS1B01G164800 chr2D 73.768 1319 286 45 1412 2691 459334857 459333560 7.650000e-127 464.0
31 TraesCS1B01G164800 chr2D 82.403 233 34 7 2971 3199 536927820 536927591 3.080000e-46 196.0
32 TraesCS1B01G164800 chr2D 100.000 29 0 0 3628 3656 134477135 134477107 2.000000e-03 54.7
33 TraesCS1B01G164800 chr2B 94.191 241 9 4 3675 3911 579527120 579526881 2.870000e-96 363.0
34 TraesCS1B01G164800 chr2B 89.591 269 19 7 3371 3636 579527380 579527118 2.250000e-87 333.0
35 TraesCS1B01G164800 chr2B 73.678 813 165 39 1485 2268 709992115 709992907 1.790000e-68 270.0
36 TraesCS1B01G164800 chr2B 81.648 267 45 3 2971 3237 18524840 18525102 6.580000e-53 219.0
37 TraesCS1B01G164800 chr5B 83.019 265 40 5 2960 3223 311521224 311520964 6.530000e-58 235.0
38 TraesCS1B01G164800 chr5B 91.228 57 3 2 3474 3529 711050962 711050907 4.190000e-10 76.8
39 TraesCS1B01G164800 chr7D 88.889 45 4 1 3464 3508 603727100 603727057 2.000000e-03 54.7


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 TraesCS1B01G164800 chr1B 287840086 287843996 3910 False 7223.0 7223 100.0000 1 3911 1 chr1B.!!$F1 3910
1 TraesCS1B01G164800 chr1B 38012406 38012948 542 True 758.0 758 91.9560 3371 3911 1 chr1B.!!$R1 540
2 TraesCS1B01G164800 chr1B 1465473 1469325 3852 True 574.0 750 89.4365 2971 3911 2 chr1B.!!$R2 940
3 TraesCS1B01G164800 chr1B 671225365 671226428 1063 False 276.1 468 79.3255 1367 2478 2 chr1B.!!$F2 1111
4 TraesCS1B01G164800 chr1D 200093209 200095539 2330 True 3618.0 3618 94.6900 634 2970 1 chr1D.!!$R1 2336
5 TraesCS1B01G164800 chr1A 253035074 253037330 2256 True 1691.5 3164 92.4835 635 2941 2 chr1A.!!$R2 2306
6 TraesCS1B01G164800 chr4A 633746467 633747009 542 False 758.0 758 91.9710 3371 3911 1 chr4A.!!$F1 540
7 TraesCS1B01G164800 chr3B 690480412 690481015 603 True 704.0 704 87.7890 1 603 1 chr3B.!!$R1 602
8 TraesCS1B01G164800 chr3B 661746931 661747451 520 False 665.0 665 89.5410 3371 3911 1 chr3B.!!$F1 540
9 TraesCS1B01G164800 chr6D 318366163 318366761 598 False 664.0 664 86.6890 6 604 1 chr6D.!!$F1 598
10 TraesCS1B01G164800 chr4B 637722735 637724104 1369 True 628.0 628 75.5750 1370 2719 1 chr4B.!!$R1 1349
11 TraesCS1B01G164800 chr4D 497151079 497152448 1369 True 590.0 590 75.0540 1370 2719 1 chr4D.!!$R1 1349
12 TraesCS1B01G164800 chr4D 497157246 497158385 1139 True 383.0 383 73.4750 1389 2540 1 chr4D.!!$R2 1151
13 TraesCS1B01G164800 chr5A 676949644 676951001 1357 True 562.0 562 74.8740 1382 2719 1 chr5A.!!$R1 1337
14 TraesCS1B01G164800 chr7B 575386708 575388039 1331 True 477.0 477 73.8370 1367 2710 1 chr7B.!!$R2 1343
15 TraesCS1B01G164800 chr7B 577141984 577142844 860 True 329.0 329 74.3420 1376 2275 1 chr7B.!!$R3 899
16 TraesCS1B01G164800 chr7A 615375211 615376101 890 True 477.0 477 76.8400 1367 2275 1 chr7A.!!$R1 908
17 TraesCS1B01G164800 chr2A 602651417 602652760 1343 True 477.0 477 73.6800 1366 2691 1 chr2A.!!$R2 1325
18 TraesCS1B01G164800 chr2D 459333560 459334857 1297 True 464.0 464 73.7680 1412 2691 1 chr2D.!!$R2 1279
19 TraesCS1B01G164800 chr2B 709992115 709992907 792 False 270.0 270 73.6780 1485 2268 1 chr2B.!!$F2 783

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
516 520 0.106167 CGTATCCTCTCTCACCCCCA 60.106 60.000 0.00 0.0 0.00 4.96 F
625 629 0.446222 CGCGTTTCACCATTCGGAAT 59.554 50.000 0.00 0.0 35.59 3.01 F
719 723 0.611896 CGGTCAAAAGAAGGGGGCAT 60.612 55.000 0.00 0.0 0.00 4.40 F
722 726 0.783206 TCAAAAGAAGGGGGCATCCA 59.217 50.000 0.00 0.0 37.22 3.41 F
834 848 1.272313 ACTCATCTGCAGCAACCCATT 60.272 47.619 9.47 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2162 2254 1.066858 CGTTGATGTGGCTCCTGTAGT 60.067 52.381 0.00 0.0 0.00 2.73 R
2296 2391 1.134075 CGCAGCTGACTTGCATCAC 59.866 57.895 20.43 0.0 41.59 3.06 R
2568 2666 1.641577 GGGACAACTCTACGCACATC 58.358 55.000 0.00 0.0 0.00 3.06 R
2808 2906 1.227645 CATGTCCATCATCGCCGGT 60.228 57.895 1.90 0.0 34.09 5.28 R
2917 3015 4.219115 GTCAATCCTGATCCTCTACCTCA 58.781 47.826 0.00 0.0 33.05 3.86 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
22 23 1.673920 TCCGGCTCTTCAAACACAAAC 59.326 47.619 0.00 0.00 0.00 2.93
28 29 3.490933 GCTCTTCAAACACAAACCCTTCC 60.491 47.826 0.00 0.00 0.00 3.46
45 46 3.397482 CTTCCGCTTCCTTATCCATCAG 58.603 50.000 0.00 0.00 0.00 2.90
59 61 0.552848 CATCAGTACCATGCCCCCTT 59.447 55.000 0.00 0.00 0.00 3.95
60 62 0.552848 ATCAGTACCATGCCCCCTTG 59.447 55.000 0.00 0.00 0.00 3.61
65 67 0.548926 TACCATGCCCCCTTGTCTCA 60.549 55.000 0.00 0.00 0.00 3.27
89 91 0.323542 AAGACTCGACGTGGGATCCT 60.324 55.000 12.58 0.00 0.00 3.24
92 94 1.753078 CTCGACGTGGGATCCTGGA 60.753 63.158 12.58 0.00 0.00 3.86
101 103 3.631250 GTGGGATCCTGGATTTTGCTTA 58.369 45.455 12.58 0.00 0.00 3.09
169 171 1.739929 CATCGGCGTAACCACTGCA 60.740 57.895 6.85 0.00 39.03 4.41
252 254 1.415672 TTCCTCTGGTTTGCCGTCCT 61.416 55.000 0.00 0.00 37.67 3.85
275 277 1.529948 CCGGATGCATGGCTGGATT 60.530 57.895 2.46 0.00 32.99 3.01
307 309 0.516001 TCTTCTGGTTCGTCTCGTCG 59.484 55.000 0.00 0.00 0.00 5.12
337 339 3.621715 CCGGTATACTGCTTTGTTTCCTC 59.378 47.826 6.15 0.00 0.00 3.71
395 399 2.510918 GCCCGAAACCCTAGTCGC 60.511 66.667 0.00 0.00 35.93 5.19
473 477 1.980232 TCGGTTTAGAGGGCTGCGA 60.980 57.895 0.00 0.00 0.00 5.10
516 520 0.106167 CGTATCCTCTCTCACCCCCA 60.106 60.000 0.00 0.00 0.00 4.96
591 595 1.975680 TCGCCCTTAGAGTTTTCCTGT 59.024 47.619 0.00 0.00 0.00 4.00
594 598 3.075148 GCCCTTAGAGTTTTCCTGTGTC 58.925 50.000 0.00 0.00 0.00 3.67
604 608 4.016706 CCTGTGTCGTGGACCCCC 62.017 72.222 0.00 0.00 0.00 5.40
605 609 4.373116 CTGTGTCGTGGACCCCCG 62.373 72.222 0.00 0.00 34.29 5.73
619 623 3.732892 CCCGCGCGTTTCACCATT 61.733 61.111 29.95 0.00 0.00 3.16
620 624 2.202298 CCGCGCGTTTCACCATTC 60.202 61.111 29.95 0.00 0.00 2.67
621 625 2.570581 CGCGCGTTTCACCATTCG 60.571 61.111 24.19 0.00 0.00 3.34
622 626 2.202298 GCGCGTTTCACCATTCGG 60.202 61.111 8.43 0.00 38.77 4.30
623 627 2.673114 GCGCGTTTCACCATTCGGA 61.673 57.895 8.43 0.00 35.59 4.55
624 628 1.863491 CGCGTTTCACCATTCGGAA 59.137 52.632 0.00 0.00 35.59 4.30
625 629 0.446222 CGCGTTTCACCATTCGGAAT 59.554 50.000 0.00 0.00 35.59 3.01
626 630 1.661617 CGCGTTTCACCATTCGGAATA 59.338 47.619 2.35 0.00 35.59 1.75
627 631 2.286833 CGCGTTTCACCATTCGGAATAT 59.713 45.455 2.35 0.00 35.59 1.28
628 632 3.617669 GCGTTTCACCATTCGGAATATG 58.382 45.455 2.35 5.49 35.59 1.78
629 633 3.548014 GCGTTTCACCATTCGGAATATGG 60.548 47.826 2.35 5.89 46.48 2.74
630 634 3.874543 CGTTTCACCATTCGGAATATGGA 59.125 43.478 15.47 4.59 44.36 3.41
631 635 4.334203 CGTTTCACCATTCGGAATATGGAA 59.666 41.667 15.47 9.70 44.36 3.53
632 636 5.008613 CGTTTCACCATTCGGAATATGGAAT 59.991 40.000 15.47 0.00 44.36 3.01
668 672 7.182361 TCTGTTAGTACTACGATATCGGTTG 57.818 40.000 27.58 18.42 44.95 3.77
672 676 4.070716 AGTACTACGATATCGGTTGAGGG 58.929 47.826 27.58 11.85 44.95 4.30
718 722 1.228429 CGGTCAAAAGAAGGGGGCA 60.228 57.895 0.00 0.00 0.00 5.36
719 723 0.611896 CGGTCAAAAGAAGGGGGCAT 60.612 55.000 0.00 0.00 0.00 4.40
720 724 1.186200 GGTCAAAAGAAGGGGGCATC 58.814 55.000 0.00 0.00 0.00 3.91
721 725 1.186200 GTCAAAAGAAGGGGGCATCC 58.814 55.000 0.00 0.00 0.00 3.51
722 726 0.783206 TCAAAAGAAGGGGGCATCCA 59.217 50.000 0.00 0.00 37.22 3.41
752 756 5.426504 CTGAGCTGATTCAGAACCACTTAT 58.573 41.667 17.87 0.00 45.95 1.73
753 757 6.544928 TGAGCTGATTCAGAACCACTTATA 57.455 37.500 17.87 0.00 32.44 0.98
770 774 4.560035 ACTTATACCACGTCAACGAAATCG 59.440 41.667 9.88 0.48 43.02 3.34
790 794 2.936498 CGGCACTGGAATTCTTATTCGT 59.064 45.455 5.23 0.00 40.91 3.85
815 829 7.062722 GTCGGTGGATTGTTCTAAACTAGTAAC 59.937 40.741 0.00 0.00 0.00 2.50
817 831 7.275123 CGGTGGATTGTTCTAAACTAGTAACTC 59.725 40.741 0.00 0.00 0.00 3.01
831 845 1.740025 GTAACTCATCTGCAGCAACCC 59.260 52.381 9.47 0.00 0.00 4.11
834 848 1.272313 ACTCATCTGCAGCAACCCATT 60.272 47.619 9.47 0.00 0.00 3.16
848 862 6.808212 CAGCAACCCATTACTTGTTTATGAAG 59.192 38.462 0.00 0.00 0.00 3.02
895 916 2.939460 GGGAACGCAATAACAGCAAT 57.061 45.000 0.00 0.00 0.00 3.56
897 918 4.364415 GGGAACGCAATAACAGCAATAA 57.636 40.909 0.00 0.00 0.00 1.40
898 919 4.932146 GGGAACGCAATAACAGCAATAAT 58.068 39.130 0.00 0.00 0.00 1.28
899 920 4.739716 GGGAACGCAATAACAGCAATAATG 59.260 41.667 0.00 0.00 0.00 1.90
925 946 6.408858 TTTTCTAATCGCTGTCATCTTGTC 57.591 37.500 0.00 0.00 0.00 3.18
926 947 4.991153 TCTAATCGCTGTCATCTTGTCT 57.009 40.909 0.00 0.00 0.00 3.41
1107 1128 1.375523 CCACCAGTTCCACTACCGC 60.376 63.158 0.00 0.00 0.00 5.68
1336 1357 4.460683 GCGACCGGCACCATGGTA 62.461 66.667 19.28 0.00 42.87 3.25
1587 1617 2.357836 CTGAAGCAGGCCATGGGT 59.642 61.111 15.13 0.00 0.00 4.51
2296 2391 2.434185 CCACGGATGTCACCCACG 60.434 66.667 0.00 0.00 0.00 4.94
2723 2821 4.819761 GATGTCTGGCGCCAGCGA 62.820 66.667 44.77 33.95 46.35 4.93
2772 2870 2.132762 CTTGGCACGACGGTAATATCC 58.867 52.381 0.00 0.00 0.00 2.59
2917 3015 0.033504 CGCACACTACTGAACCCACT 59.966 55.000 0.00 0.00 0.00 4.00
2975 3080 7.857569 TGGTTTTCAAGTTTGTATAAGAGTCG 58.142 34.615 0.00 0.00 0.00 4.18
2982 3087 9.917129 TCAAGTTTGTATAAGAGTCGATTACAA 57.083 29.630 9.40 9.40 0.00 2.41
2986 3091 9.136952 GTTTGTATAAGAGTCGATTACAACACT 57.863 33.333 11.77 0.00 0.00 3.55
2988 3093 7.823665 TGTATAAGAGTCGATTACAACACTGT 58.176 34.615 0.00 0.00 39.75 3.55
3001 3106 5.385509 ACAACACTGTTGCTTAAACTTGT 57.614 34.783 19.86 0.00 39.70 3.16
3010 3115 6.255215 TGTTGCTTAAACTTGTCGAGAAAAG 58.745 36.000 0.00 1.67 39.70 2.27
3021 3126 6.255887 ACTTGTCGAGAAAAGTCACTTTAGTG 59.744 38.462 2.38 3.47 46.91 2.74
3023 3128 4.056050 TCGAGAAAAGTCACTTTAGTGCC 58.944 43.478 2.38 0.00 45.25 5.01
3035 3140 0.107831 TTAGTGCCAGAACTTGCGGT 59.892 50.000 0.00 0.00 0.00 5.68
3079 3184 0.319986 TGGCTCGTCGTGCAAATACA 60.320 50.000 19.74 6.38 0.00 2.29
3108 3213 3.444916 ACTCGTTTGTATACTCATGCGG 58.555 45.455 4.17 0.00 0.00 5.69
3110 3215 1.071502 CGTTTGTATACTCATGCGGCG 60.072 52.381 0.51 0.51 0.00 6.46
3115 3220 2.029380 TGTATACTCATGCGGCGCTAAT 60.029 45.455 33.26 16.58 0.00 1.73
3120 3225 2.974698 ATGCGGCGCTAATGAGGC 60.975 61.111 33.26 0.10 35.36 4.70
3128 3233 1.756375 CGCTAATGAGGCGTGACAGC 61.756 60.000 0.00 0.00 46.37 4.40
3154 3259 2.283101 TGGGCCCATTGTCAGTGC 60.283 61.111 24.45 0.00 0.00 4.40
3158 3263 2.350895 CCCATTGTCAGTGCCCGA 59.649 61.111 0.00 0.00 0.00 5.14
3177 3282 1.681793 GAGCGGTGTAGAAGAGGCATA 59.318 52.381 0.00 0.00 0.00 3.14
3182 3287 2.408050 GTGTAGAAGAGGCATATGGCG 58.592 52.381 22.17 0.00 46.16 5.69
3187 3292 1.668419 AAGAGGCATATGGCGTGTTC 58.332 50.000 22.17 14.58 39.34 3.18
3190 3295 2.017049 GAGGCATATGGCGTGTTCTTT 58.983 47.619 22.17 3.40 46.16 2.52
3214 3319 8.710835 TTTTTCAAAAACTAGCCTCGAATTTT 57.289 26.923 0.00 0.00 0.00 1.82
3215 3320 9.804758 TTTTTCAAAAACTAGCCTCGAATTTTA 57.195 25.926 0.00 0.00 0.00 1.52
3216 3321 9.974980 TTTTCAAAAACTAGCCTCGAATTTTAT 57.025 25.926 0.00 0.00 0.00 1.40
3260 3365 3.045142 GGACCGACTTGTCCGTCA 58.955 61.111 18.51 0.00 44.98 4.35
3287 3392 1.673665 CTCTCTGTGCCAGCCAACC 60.674 63.158 0.00 0.00 0.00 3.77
3299 3404 3.803082 CCAACCGATGTGCGCAGG 61.803 66.667 12.22 11.82 39.11 4.85
3333 3448 4.022242 ACCAGGATAACGATTCAGGATACG 60.022 45.833 0.00 0.00 46.39 3.06
3336 3451 3.921021 GGATAACGATTCAGGATACGCAG 59.079 47.826 0.00 0.00 46.39 5.18
3338 3453 2.961526 ACGATTCAGGATACGCAGTT 57.038 45.000 0.00 0.00 37.78 3.16
3347 3462 8.858003 ATTCAGGATACGCAGTTATTATATCG 57.142 34.615 0.00 0.00 37.78 2.92
3350 3465 8.301720 TCAGGATACGCAGTTATTATATCGTTT 58.698 33.333 0.00 0.00 37.78 3.60
3368 3483 6.825944 TCGTTTTAAATGATCCAACATCCA 57.174 33.333 0.00 0.00 0.00 3.41
3369 3484 6.616947 TCGTTTTAAATGATCCAACATCCAC 58.383 36.000 0.00 0.00 0.00 4.02
3373 6396 6.528537 TTAAATGATCCAACATCCACCAAG 57.471 37.500 0.00 0.00 0.00 3.61
3389 6412 6.472887 TCCACCAAGATAACCTCTACAAAAG 58.527 40.000 0.00 0.00 32.41 2.27
3390 6413 6.271391 TCCACCAAGATAACCTCTACAAAAGA 59.729 38.462 0.00 0.00 32.41 2.52
3395 6418 9.899226 CCAAGATAACCTCTACAAAAGAAAAAG 57.101 33.333 0.00 0.00 32.46 2.27
3442 6466 4.405358 TCAAAAGTGGCAAAAGTGAAGGAT 59.595 37.500 0.00 0.00 0.00 3.24
3450 6474 2.807967 CAAAAGTGAAGGATGACGCTGA 59.192 45.455 0.00 0.00 0.00 4.26
3529 6553 0.454620 GACACCTGACTCGTAGCACG 60.455 60.000 2.79 2.79 44.19 5.34
3538 6563 0.456312 CTCGTAGCACGTCCCTTGTC 60.456 60.000 8.22 0.00 43.14 3.18
3719 6747 5.550290 AGGTTGGCATTTTTGGAATTACAG 58.450 37.500 0.00 0.00 0.00 2.74
3859 6889 9.744468 GTGTGTTAGTGACAAAAAGGATAAAAT 57.256 29.630 0.00 0.00 40.65 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 0.837272 TGGATAAGGAAGCGGAAGGG 59.163 55.000 0.00 0.00 0.00 3.95
28 29 3.069586 TGGTACTGATGGATAAGGAAGCG 59.930 47.826 0.00 0.00 0.00 4.68
45 46 0.107165 GAGACAAGGGGGCATGGTAC 60.107 60.000 0.00 0.00 0.00 3.34
89 91 1.889829 CCCGGTTGTAAGCAAAATCCA 59.110 47.619 0.00 0.00 36.22 3.41
92 94 1.890489 GTCCCCGGTTGTAAGCAAAAT 59.110 47.619 0.00 0.00 36.22 1.82
101 103 0.841289 TCTTCAAAGTCCCCGGTTGT 59.159 50.000 0.00 0.00 0.00 3.32
183 185 1.134367 CGAGCAGGAAGAATACCACGA 59.866 52.381 0.00 0.00 0.00 4.35
252 254 4.916293 GCCATGCATCCGGCTCGA 62.916 66.667 18.43 0.00 45.29 4.04
307 309 4.857509 AAGCAGTATACCGGAGAAGATC 57.142 45.455 9.46 0.00 0.00 2.75
395 399 2.689034 AGGAGGCGGGAGGAAAGG 60.689 66.667 0.00 0.00 0.00 3.11
418 422 4.154347 GCTGGAGGTGGAGCGGAG 62.154 72.222 0.00 0.00 0.00 4.63
427 431 3.382832 CCCGTCTTCGCTGGAGGT 61.383 66.667 0.00 0.00 35.54 3.85
461 465 3.138798 GACGGTCGCAGCCCTCTA 61.139 66.667 0.00 0.00 0.00 2.43
490 494 1.320507 GAGAGAGGATACGGTGGTCC 58.679 60.000 6.35 6.35 46.39 4.46
516 520 1.446016 AGGGTTAGGGTTTGAGCTGT 58.554 50.000 0.00 0.00 0.00 4.40
604 608 2.570581 CGAATGGTGAAACGCGCG 60.571 61.111 30.96 30.96 38.12 6.86
605 609 2.177654 TTCCGAATGGTGAAACGCGC 62.178 55.000 5.73 0.00 38.12 6.86
606 610 0.446222 ATTCCGAATGGTGAAACGCG 59.554 50.000 3.53 3.53 38.12 6.01
607 611 3.548014 CCATATTCCGAATGGTGAAACGC 60.548 47.826 3.73 0.00 39.30 4.84
608 612 3.874543 TCCATATTCCGAATGGTGAAACG 59.125 43.478 3.73 0.00 43.72 3.60
609 613 5.828299 TTCCATATTCCGAATGGTGAAAC 57.172 39.130 3.73 0.00 43.72 2.78
610 614 6.183360 CCAATTCCATATTCCGAATGGTGAAA 60.183 38.462 3.73 0.00 43.72 2.69
611 615 5.301551 CCAATTCCATATTCCGAATGGTGAA 59.698 40.000 3.73 4.20 43.72 3.18
612 616 4.826733 CCAATTCCATATTCCGAATGGTGA 59.173 41.667 3.73 0.00 43.72 4.02
613 617 4.584325 ACCAATTCCATATTCCGAATGGTG 59.416 41.667 3.73 3.18 43.72 4.17
614 618 4.803452 ACCAATTCCATATTCCGAATGGT 58.197 39.130 3.73 0.00 43.72 3.55
615 619 5.789643 AACCAATTCCATATTCCGAATGG 57.210 39.130 3.73 0.00 44.51 3.16
616 620 5.984926 CCAAACCAATTCCATATTCCGAATG 59.015 40.000 3.73 0.00 0.00 2.67
617 621 5.660864 ACCAAACCAATTCCATATTCCGAAT 59.339 36.000 0.00 0.00 0.00 3.34
618 622 5.020132 ACCAAACCAATTCCATATTCCGAA 58.980 37.500 0.00 0.00 0.00 4.30
619 623 4.605183 ACCAAACCAATTCCATATTCCGA 58.395 39.130 0.00 0.00 0.00 4.55
620 624 4.644685 AGACCAAACCAATTCCATATTCCG 59.355 41.667 0.00 0.00 0.00 4.30
621 625 6.381133 AGAAGACCAAACCAATTCCATATTCC 59.619 38.462 0.00 0.00 0.00 3.01
622 626 7.093771 ACAGAAGACCAAACCAATTCCATATTC 60.094 37.037 0.00 0.00 0.00 1.75
623 627 6.725834 ACAGAAGACCAAACCAATTCCATATT 59.274 34.615 0.00 0.00 0.00 1.28
624 628 6.256053 ACAGAAGACCAAACCAATTCCATAT 58.744 36.000 0.00 0.00 0.00 1.78
625 629 5.640147 ACAGAAGACCAAACCAATTCCATA 58.360 37.500 0.00 0.00 0.00 2.74
626 630 4.482990 ACAGAAGACCAAACCAATTCCAT 58.517 39.130 0.00 0.00 0.00 3.41
627 631 3.909732 ACAGAAGACCAAACCAATTCCA 58.090 40.909 0.00 0.00 0.00 3.53
628 632 4.937201 AACAGAAGACCAAACCAATTCC 57.063 40.909 0.00 0.00 0.00 3.01
629 633 6.635030 ACTAACAGAAGACCAAACCAATTC 57.365 37.500 0.00 0.00 0.00 2.17
630 634 7.287810 AGTACTAACAGAAGACCAAACCAATT 58.712 34.615 0.00 0.00 0.00 2.32
631 635 6.838382 AGTACTAACAGAAGACCAAACCAAT 58.162 36.000 0.00 0.00 0.00 3.16
632 636 6.243216 AGTACTAACAGAAGACCAAACCAA 57.757 37.500 0.00 0.00 0.00 3.67
752 756 1.700523 CCGATTTCGTTGACGTGGTA 58.299 50.000 0.00 0.00 40.80 3.25
753 757 1.562575 GCCGATTTCGTTGACGTGGT 61.563 55.000 0.00 0.00 40.80 4.16
770 774 3.001330 CGACGAATAAGAATTCCAGTGCC 59.999 47.826 0.65 0.00 38.66 5.01
790 794 5.733620 ACTAGTTTAGAACAATCCACCGA 57.266 39.130 0.00 0.00 0.00 4.69
815 829 1.471119 AATGGGTTGCTGCAGATGAG 58.529 50.000 20.43 0.00 0.00 2.90
817 831 2.372264 AGTAATGGGTTGCTGCAGATG 58.628 47.619 20.43 0.00 0.00 2.90
892 913 7.644945 TGACAGCGATTAGAAAATGCATTATTG 59.355 33.333 13.39 7.15 0.00 1.90
893 914 7.706159 TGACAGCGATTAGAAAATGCATTATT 58.294 30.769 13.39 9.26 0.00 1.40
894 915 7.263100 TGACAGCGATTAGAAAATGCATTAT 57.737 32.000 13.39 1.37 0.00 1.28
895 916 6.676237 TGACAGCGATTAGAAAATGCATTA 57.324 33.333 13.39 0.00 0.00 1.90
896 917 5.565592 TGACAGCGATTAGAAAATGCATT 57.434 34.783 5.99 5.99 0.00 3.56
897 918 5.530171 AGATGACAGCGATTAGAAAATGCAT 59.470 36.000 0.00 0.00 0.00 3.96
898 919 4.877823 AGATGACAGCGATTAGAAAATGCA 59.122 37.500 0.00 0.00 0.00 3.96
899 920 5.415415 AGATGACAGCGATTAGAAAATGC 57.585 39.130 0.00 0.00 0.00 3.56
900 921 6.779117 ACAAGATGACAGCGATTAGAAAATG 58.221 36.000 0.00 0.00 0.00 2.32
901 922 6.820656 AGACAAGATGACAGCGATTAGAAAAT 59.179 34.615 0.00 0.00 0.00 1.82
902 923 6.166279 AGACAAGATGACAGCGATTAGAAAA 58.834 36.000 0.00 0.00 0.00 2.29
903 924 5.724328 AGACAAGATGACAGCGATTAGAAA 58.276 37.500 0.00 0.00 0.00 2.52
904 925 5.330455 AGACAAGATGACAGCGATTAGAA 57.670 39.130 0.00 0.00 0.00 2.10
905 926 4.991153 AGACAAGATGACAGCGATTAGA 57.009 40.909 0.00 0.00 0.00 2.10
906 927 7.706281 AATAAGACAAGATGACAGCGATTAG 57.294 36.000 0.00 0.00 0.00 1.73
907 928 7.549134 ACAAATAAGACAAGATGACAGCGATTA 59.451 33.333 0.00 0.00 0.00 1.75
925 946 5.997746 TGGTGAGAGAGGTTTGACAAATAAG 59.002 40.000 3.49 0.00 0.00 1.73
926 947 5.763204 GTGGTGAGAGAGGTTTGACAAATAA 59.237 40.000 3.49 0.00 0.00 1.40
1329 1350 2.890474 GCACTCGCGGTACCATGG 60.890 66.667 11.19 11.19 0.00 3.66
1764 1797 3.249189 ACCTTGGCGGCCTTGAGA 61.249 61.111 21.46 0.00 35.61 3.27
2162 2254 1.066858 CGTTGATGTGGCTCCTGTAGT 60.067 52.381 0.00 0.00 0.00 2.73
2296 2391 1.134075 CGCAGCTGACTTGCATCAC 59.866 57.895 20.43 0.00 41.59 3.06
2568 2666 1.641577 GGGACAACTCTACGCACATC 58.358 55.000 0.00 0.00 0.00 3.06
2808 2906 1.227645 CATGTCCATCATCGCCGGT 60.228 57.895 1.90 0.00 34.09 5.28
2917 3015 4.219115 GTCAATCCTGATCCTCTACCTCA 58.781 47.826 0.00 0.00 33.05 3.86
2975 3080 7.700656 ACAAGTTTAAGCAACAGTGTTGTAATC 59.299 33.333 31.12 21.36 37.93 1.75
2982 3087 3.936453 TCGACAAGTTTAAGCAACAGTGT 59.064 39.130 0.00 0.00 38.15 3.55
2986 3091 5.804692 TTTCTCGACAAGTTTAAGCAACA 57.195 34.783 0.00 0.00 37.93 3.33
2988 3093 6.092944 TGACTTTTCTCGACAAGTTTAAGCAA 59.907 34.615 0.57 0.00 33.22 3.91
3021 3126 2.018542 TGTATACCGCAAGTTCTGGC 57.981 50.000 0.00 0.00 0.00 4.85
3023 3128 5.351465 AGTTCAATGTATACCGCAAGTTCTG 59.649 40.000 0.00 0.00 0.00 3.02
3035 3140 4.293662 TGTGGCACCAGTTCAATGTATA 57.706 40.909 16.26 0.00 0.00 1.47
3090 3195 1.071502 CGCCGCATGAGTATACAAACG 60.072 52.381 5.50 1.65 0.00 3.60
3101 3206 1.595109 CCTCATTAGCGCCGCATGA 60.595 57.895 13.36 11.95 0.00 3.07
3110 3215 1.756375 CGCTGTCACGCCTCATTAGC 61.756 60.000 0.00 0.00 0.00 3.09
3115 3220 4.662961 CCACGCTGTCACGCCTCA 62.663 66.667 0.00 0.00 36.19 3.86
3136 3241 2.639327 GCACTGACAATGGGCCCAC 61.639 63.158 31.51 15.89 0.00 4.61
3137 3242 2.283101 GCACTGACAATGGGCCCA 60.283 61.111 30.92 30.92 0.00 5.36
3154 3259 1.433879 CTCTTCTACACCGCTCGGG 59.566 63.158 13.31 4.45 43.62 5.14
3158 3263 1.776662 TATGCCTCTTCTACACCGCT 58.223 50.000 0.00 0.00 0.00 5.52
3190 3295 9.974980 ATAAAATTCGAGGCTAGTTTTTGAAAA 57.025 25.926 15.42 0.00 0.00 2.29
3193 3298 9.974980 AAAATAAAATTCGAGGCTAGTTTTTGA 57.025 25.926 15.42 4.11 0.00 2.69
3201 3306 9.862371 TGCAAAATAAAATAAAATTCGAGGCTA 57.138 25.926 0.00 0.00 0.00 3.93
3202 3307 8.655970 GTGCAAAATAAAATAAAATTCGAGGCT 58.344 29.630 0.00 0.00 0.00 4.58
3203 3308 8.439286 TGTGCAAAATAAAATAAAATTCGAGGC 58.561 29.630 0.00 0.00 0.00 4.70
3237 3342 4.353437 ACAAGTCGGTCCCGCGAC 62.353 66.667 8.23 0.00 39.59 5.19
3238 3343 4.047059 GACAAGTCGGTCCCGCGA 62.047 66.667 8.23 0.00 39.59 5.87
3257 3362 2.246719 ACAGAGAGTGTGCCTTTGAC 57.753 50.000 0.00 0.00 38.28 3.18
3278 3383 3.803082 CGCACATCGGTTGGCTGG 61.803 66.667 0.00 0.00 33.78 4.85
3287 3392 3.264897 GGCTACCTGCGCACATCG 61.265 66.667 5.66 0.00 44.05 3.84
3299 3404 1.209621 TATCCTGGTGGGTTGGCTAC 58.790 55.000 0.00 0.00 36.25 3.58
3308 3413 2.434336 TCCTGAATCGTTATCCTGGTGG 59.566 50.000 0.00 0.00 0.00 4.61
3347 3462 6.696411 TGGTGGATGTTGGATCATTTAAAAC 58.304 36.000 0.00 0.00 0.00 2.43
3350 3465 6.252233 TCTTGGTGGATGTTGGATCATTTAA 58.748 36.000 0.00 0.00 0.00 1.52
3353 3468 4.320546 TCTTGGTGGATGTTGGATCATT 57.679 40.909 0.00 0.00 0.00 2.57
3354 3469 4.531357 ATCTTGGTGGATGTTGGATCAT 57.469 40.909 0.00 0.00 0.00 2.45
3356 3471 4.580580 GGTTATCTTGGTGGATGTTGGATC 59.419 45.833 0.00 0.00 0.00 3.36
3358 3473 3.591527 AGGTTATCTTGGTGGATGTTGGA 59.408 43.478 0.00 0.00 0.00 3.53
3360 3475 4.848357 AGAGGTTATCTTGGTGGATGTTG 58.152 43.478 0.00 0.00 32.99 3.33
3361 3476 5.487488 TGTAGAGGTTATCTTGGTGGATGTT 59.513 40.000 0.00 0.00 39.64 2.71
3363 3478 5.614324 TGTAGAGGTTATCTTGGTGGATG 57.386 43.478 0.00 0.00 39.64 3.51
3365 3480 6.271391 TCTTTTGTAGAGGTTATCTTGGTGGA 59.729 38.462 0.00 0.00 39.64 4.02
3366 3481 6.472887 TCTTTTGTAGAGGTTATCTTGGTGG 58.527 40.000 0.00 0.00 39.64 4.61
3367 3482 7.979444 TTCTTTTGTAGAGGTTATCTTGGTG 57.021 36.000 0.00 0.00 39.64 4.17
3368 3483 8.990163 TTTTCTTTTGTAGAGGTTATCTTGGT 57.010 30.769 0.00 0.00 39.64 3.67
3369 3484 9.899226 CTTTTTCTTTTGTAGAGGTTATCTTGG 57.101 33.333 0.00 0.00 39.64 3.61
3389 6412 2.882324 TGTGTTGCGGGTTTCTTTTTC 58.118 42.857 0.00 0.00 0.00 2.29
3390 6413 2.997303 GTTGTGTTGCGGGTTTCTTTTT 59.003 40.909 0.00 0.00 0.00 1.94
3395 6418 1.310904 TAGGTTGTGTTGCGGGTTTC 58.689 50.000 0.00 0.00 0.00 2.78
3396 6419 1.611491 CATAGGTTGTGTTGCGGGTTT 59.389 47.619 0.00 0.00 0.00 3.27
3442 6466 2.995939 CAAAATCTAGTGCTCAGCGTCA 59.004 45.455 0.00 0.00 0.00 4.35
3513 6537 1.584380 GGACGTGCTACGAGTCAGGT 61.584 60.000 14.18 0.00 46.05 4.00
3514 6538 1.136984 GGACGTGCTACGAGTCAGG 59.863 63.158 14.18 0.00 46.05 3.86
3692 6719 7.605691 TGTAATTCCAAAAATGCCAACCTATTG 59.394 33.333 0.00 0.00 35.40 1.90
3865 6897 5.479375 GCATCCACATTCATTTGATCCCTAT 59.521 40.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.