Multiple sequence alignment - TraesCS5D01G115100

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 TraesCS5D01G115100 chr5D 100.000 2882 0 0 1 2882 134797875 134794994 0.000000e+00 5323.0
1 TraesCS5D01G115100 chr5D 100.000 32 0 0 447 478 134797400 134797369 3.100000e-05 60.2
2 TraesCS5D01G115100 chr5D 100.000 32 0 0 476 507 134797429 134797398 3.100000e-05 60.2
3 TraesCS5D01G115100 chr5B 95.508 1603 22 18 900 2500 146279231 146277677 0.000000e+00 2516.0
4 TraesCS5D01G115100 chr5B 94.788 307 15 1 2576 2882 146277386 146277081 7.220000e-131 477.0
5 TraesCS5D01G115100 chr5B 90.099 303 30 0 476 778 146279771 146279469 7.480000e-106 394.0
6 TraesCS5D01G115100 chr5B 84.912 285 19 4 202 478 146280008 146279740 1.700000e-67 267.0
7 TraesCS5D01G115100 chr5B 94.000 150 9 0 1449 1598 511468851 511468702 8.030000e-56 228.0
8 TraesCS5D01G115100 chr5B 96.460 113 4 0 1483 1595 50654056 50654168 1.360000e-43 187.0
9 TraesCS5D01G115100 chr5B 92.982 114 8 0 123 236 146280122 146280009 1.780000e-37 167.0
10 TraesCS5D01G115100 chr5B 90.833 120 11 0 1 120 146280545 146280426 8.260000e-36 161.0
11 TraesCS5D01G115100 chr5A 93.344 1202 47 14 1005 2192 158967956 158966774 0.000000e+00 1746.0
12 TraesCS5D01G115100 chr5A 88.244 706 61 16 2181 2879 158950696 158950006 0.000000e+00 824.0
13 TraesCS5D01G115100 chr2B 95.973 149 4 1 1449 1595 526519593 526519741 1.030000e-59 241.0
14 TraesCS5D01G115100 chr2B 85.043 234 33 2 617 850 215072149 215071918 1.330000e-58 237.0
15 TraesCS5D01G115100 chr6A 94.521 146 8 0 1449 1594 52323655 52323510 2.890000e-55 226.0
16 TraesCS5D01G115100 chr6A 94.521 146 8 0 1449 1594 52328972 52328827 2.890000e-55 226.0
17 TraesCS5D01G115100 chr6A 93.919 148 8 1 1449 1595 16649396 16649249 3.740000e-54 222.0
18 TraesCS5D01G115100 chr4D 91.667 156 4 1 1449 1595 503795907 503795752 1.050000e-49 207.0
19 TraesCS5D01G115100 chr4B 100.000 29 0 0 2255 2283 311352744 311352716 1.000000e-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 TraesCS5D01G115100 chr5D 134794994 134797875 2881 True 1814.466667 5323 100.000000 1 2882 3 chr5D.!!$R1 2881
1 TraesCS5D01G115100 chr5B 146277081 146280545 3464 True 663.666667 2516 91.520333 1 2882 6 chr5B.!!$R2 2881
2 TraesCS5D01G115100 chr5A 158966774 158967956 1182 True 1746.000000 1746 93.344000 1005 2192 1 chr5A.!!$R2 1187
3 TraesCS5D01G115100 chr5A 158950006 158950696 690 True 824.000000 824 88.244000 2181 2879 1 chr5A.!!$R1 698

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
841 1209 0.030504 TGCCGTTGACGTACTTTCGA 59.969 50.0 2.63 0.0 37.74 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2541 3077 0.03601 GTGAAGAAGCTAGCCCTGCA 60.036 55.0 12.13 11.15 0.0 4.41 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
34 35 3.871006 GACATCGCACCACTGATTCATTA 59.129 43.478 0.00 0.00 0.00 1.90
37 38 6.233434 ACATCGCACCACTGATTCATTATAT 58.767 36.000 0.00 0.00 0.00 0.86
49 50 6.223120 TGATTCATTATATGGTGGACACTCG 58.777 40.000 2.13 0.00 0.00 4.18
61 62 1.402984 GGACACTCGCACTAGGAACAG 60.403 57.143 0.00 0.00 0.00 3.16
68 69 0.245539 GCACTAGGAACAGGCGTACA 59.754 55.000 0.00 0.00 0.00 2.90
69 70 1.337447 GCACTAGGAACAGGCGTACAA 60.337 52.381 0.00 0.00 0.00 2.41
72 73 2.829720 ACTAGGAACAGGCGTACAATCA 59.170 45.455 0.00 0.00 0.00 2.57
78 79 1.893137 ACAGGCGTACAATCAGTGAGA 59.107 47.619 0.00 0.00 0.00 3.27
84 85 3.838120 CGTACAATCAGTGAGAGCTTGA 58.162 45.455 10.44 0.00 0.00 3.02
93 94 2.072298 GTGAGAGCTTGAAGAATGCGT 58.928 47.619 0.00 0.00 0.00 5.24
115 116 0.255604 TGGCTACATGATGTGGGTGG 59.744 55.000 8.61 0.00 28.80 4.61
120 121 0.620556 ACATGATGTGGGTGGAGACC 59.379 55.000 0.00 0.00 42.27 3.85
121 122 0.914644 CATGATGTGGGTGGAGACCT 59.085 55.000 0.00 0.00 42.66 3.85
148 450 2.199291 GTGAGGTCCACGTATAACCG 57.801 55.000 7.34 0.00 38.14 4.44
168 470 2.688507 GCTTGTGTCTCGAAATCCAGA 58.311 47.619 0.00 0.00 0.00 3.86
175 477 3.637229 TGTCTCGAAATCCAGAGGGTATC 59.363 47.826 0.00 0.00 35.34 2.24
176 478 3.637229 GTCTCGAAATCCAGAGGGTATCA 59.363 47.826 0.00 0.00 35.34 2.15
209 511 2.260844 TTTGGAAGAGCTGGACACTG 57.739 50.000 0.00 0.00 0.00 3.66
210 512 1.131638 TTGGAAGAGCTGGACACTGT 58.868 50.000 0.00 0.00 0.00 3.55
248 585 2.908428 TGGTTGGCAGTGCAGCAG 60.908 61.111 18.61 0.00 35.83 4.24
249 586 3.677648 GGTTGGCAGTGCAGCAGG 61.678 66.667 18.61 0.00 35.83 4.85
250 587 2.595463 GTTGGCAGTGCAGCAGGA 60.595 61.111 18.61 0.00 35.83 3.86
251 588 2.595463 TTGGCAGTGCAGCAGGAC 60.595 61.111 18.61 0.00 35.83 3.85
252 589 4.994471 TGGCAGTGCAGCAGGACG 62.994 66.667 18.61 0.00 41.52 4.79
258 603 3.381983 TGCAGCAGGACGTCGGAT 61.382 61.111 9.92 0.00 0.00 4.18
287 632 1.659098 GAAACACGGGCTACAAGATCG 59.341 52.381 0.00 0.00 0.00 3.69
297 642 0.395311 TACAAGATCGGCCGTCTCCT 60.395 55.000 27.15 14.66 0.00 3.69
316 661 1.457823 TTGCTTCACTTGCCTGCAGG 61.458 55.000 29.34 29.34 35.02 4.85
334 679 1.696832 GGATGAAGACAACGCCGAGC 61.697 60.000 0.00 0.00 0.00 5.03
335 680 1.005037 ATGAAGACAACGCCGAGCA 60.005 52.632 0.00 0.00 0.00 4.26
336 681 1.291877 ATGAAGACAACGCCGAGCAC 61.292 55.000 0.00 0.00 0.00 4.40
337 682 1.954146 GAAGACAACGCCGAGCACA 60.954 57.895 0.00 0.00 0.00 4.57
338 683 1.291877 GAAGACAACGCCGAGCACAT 61.292 55.000 0.00 0.00 0.00 3.21
339 684 0.037697 AAGACAACGCCGAGCACATA 60.038 50.000 0.00 0.00 0.00 2.29
340 685 0.175760 AGACAACGCCGAGCACATAT 59.824 50.000 0.00 0.00 0.00 1.78
341 686 1.006832 GACAACGCCGAGCACATATT 58.993 50.000 0.00 0.00 0.00 1.28
342 687 0.726827 ACAACGCCGAGCACATATTG 59.273 50.000 0.00 0.00 0.00 1.90
343 688 1.006086 CAACGCCGAGCACATATTGA 58.994 50.000 0.00 0.00 0.00 2.57
344 689 1.396648 CAACGCCGAGCACATATTGAA 59.603 47.619 0.00 0.00 0.00 2.69
345 690 1.006832 ACGCCGAGCACATATTGAAC 58.993 50.000 0.00 0.00 0.00 3.18
346 691 0.304705 CGCCGAGCACATATTGAACC 59.695 55.000 0.00 0.00 0.00 3.62
347 692 1.378531 GCCGAGCACATATTGAACCA 58.621 50.000 0.00 0.00 0.00 3.67
373 718 3.341857 TTTGGTTCAATGTGTGTACGC 57.658 42.857 0.00 0.00 0.00 4.42
375 720 1.141645 GGTTCAATGTGTGTACGCGA 58.858 50.000 15.93 0.00 0.00 5.87
376 721 1.527736 GGTTCAATGTGTGTACGCGAA 59.472 47.619 15.93 0.00 0.00 4.70
377 722 2.411031 GGTTCAATGTGTGTACGCGAAG 60.411 50.000 15.93 0.00 0.00 3.79
378 723 2.425578 TCAATGTGTGTACGCGAAGA 57.574 45.000 15.93 0.00 0.00 2.87
383 728 3.352554 TGTGTGTACGCGAAGAAAGTA 57.647 42.857 15.93 0.00 0.00 2.24
385 730 3.671459 TGTGTGTACGCGAAGAAAGTATG 59.329 43.478 15.93 0.00 0.00 2.39
391 736 1.933181 CGCGAAGAAAGTATGGCATGA 59.067 47.619 10.98 0.00 0.00 3.07
396 741 5.505286 CGAAGAAAGTATGGCATGAATGTC 58.495 41.667 10.98 0.44 0.00 3.06
401 746 6.318144 AGAAAGTATGGCATGAATGTCTTCAG 59.682 38.462 10.98 0.00 44.32 3.02
420 765 7.857885 GTCTTCAGAAACTTAACTTGAACATGG 59.142 37.037 0.00 0.00 0.00 3.66
422 767 7.496529 TCAGAAACTTAACTTGAACATGGAG 57.503 36.000 0.00 0.00 0.00 3.86
424 769 7.773224 TCAGAAACTTAACTTGAACATGGAGAA 59.227 33.333 0.00 0.00 0.00 2.87
465 810 1.894466 TGTTGGATTGGTGGCTCAATG 59.106 47.619 10.42 0.00 37.47 2.82
466 811 0.896923 TTGGATTGGTGGCTCAATGC 59.103 50.000 14.73 14.73 43.02 3.56
475 820 3.930504 GCTCAATGCCAGAAGGGG 58.069 61.111 0.00 0.00 37.04 4.79
476 821 1.000396 GCTCAATGCCAGAAGGGGT 60.000 57.895 0.00 0.00 37.04 4.95
477 822 0.613012 GCTCAATGCCAGAAGGGGTT 60.613 55.000 0.00 0.00 37.04 4.11
478 823 1.180029 CTCAATGCCAGAAGGGGTTG 58.820 55.000 0.00 0.00 37.04 3.77
479 824 0.251742 TCAATGCCAGAAGGGGTTGG 60.252 55.000 0.00 0.00 37.04 3.77
480 825 0.251742 CAATGCCAGAAGGGGTTGGA 60.252 55.000 0.00 0.00 36.55 3.53
481 826 0.712380 AATGCCAGAAGGGGTTGGAT 59.288 50.000 0.00 0.00 36.55 3.41
482 827 0.712380 ATGCCAGAAGGGGTTGGATT 59.288 50.000 0.00 0.00 36.55 3.01
483 828 0.251742 TGCCAGAAGGGGTTGGATTG 60.252 55.000 0.00 0.00 36.55 2.67
484 829 0.972471 GCCAGAAGGGGTTGGATTGG 60.972 60.000 0.00 0.00 36.55 3.16
485 830 0.409484 CCAGAAGGGGTTGGATTGGT 59.591 55.000 0.00 0.00 36.55 3.67
486 831 1.549203 CAGAAGGGGTTGGATTGGTG 58.451 55.000 0.00 0.00 0.00 4.17
487 832 0.409484 AGAAGGGGTTGGATTGGTGG 59.591 55.000 0.00 0.00 0.00 4.61
488 833 1.229177 AAGGGGTTGGATTGGTGGC 60.229 57.895 0.00 0.00 0.00 5.01
489 834 1.739608 AAGGGGTTGGATTGGTGGCT 61.740 55.000 0.00 0.00 0.00 4.75
490 835 1.682344 GGGGTTGGATTGGTGGCTC 60.682 63.158 0.00 0.00 0.00 4.70
491 836 1.076549 GGGTTGGATTGGTGGCTCA 59.923 57.895 0.00 0.00 0.00 4.26
492 837 0.541764 GGGTTGGATTGGTGGCTCAA 60.542 55.000 0.00 0.00 0.00 3.02
493 838 1.560505 GGTTGGATTGGTGGCTCAAT 58.439 50.000 6.40 6.40 39.76 2.57
508 853 1.821136 CTCAATGCCAGAAGGGGTTTC 59.179 52.381 0.00 0.00 37.04 2.78
515 860 1.339727 CCAGAAGGGGTTTCGGTAAGG 60.340 57.143 0.00 0.00 40.86 2.69
520 865 5.739366 AGAAGGGGTTTCGGTAAGGAACTT 61.739 45.833 0.00 0.00 45.95 2.66
549 894 5.067273 TGGGTTCGACATCTTTGTTATTGT 58.933 37.500 0.00 0.00 35.79 2.71
550 895 6.231951 TGGGTTCGACATCTTTGTTATTGTA 58.768 36.000 0.00 0.00 35.79 2.41
560 905 7.174946 ACATCTTTGTTATTGTAGTGACTTGGG 59.825 37.037 0.00 0.00 29.55 4.12
561 906 6.597562 TCTTTGTTATTGTAGTGACTTGGGT 58.402 36.000 0.00 0.00 0.00 4.51
565 910 6.828788 TGTTATTGTAGTGACTTGGGTGTTA 58.171 36.000 0.00 0.00 0.00 2.41
568 913 5.554437 TTGTAGTGACTTGGGTGTTATGA 57.446 39.130 0.00 0.00 0.00 2.15
575 920 4.037446 TGACTTGGGTGTTATGAAAACAGC 59.963 41.667 10.71 10.71 45.07 4.40
580 925 3.376540 GGTGTTATGAAAACAGCGCAAA 58.623 40.909 11.47 0.00 38.61 3.68
623 968 0.598065 GCAACAAAGGTCGGCTCATT 59.402 50.000 0.00 0.00 0.00 2.57
632 977 2.431057 AGGTCGGCTCATTAACTAGTGG 59.569 50.000 0.00 0.00 0.00 4.00
643 988 7.201920 GCTCATTAACTAGTGGAGTTCATCCTA 60.202 40.741 0.00 0.00 45.81 2.94
656 1001 6.024563 AGTTCATCCTAAGAGAGATCCAGA 57.975 41.667 0.00 0.00 0.00 3.86
661 1006 5.458451 TCCTAAGAGAGATCCAGAACTGA 57.542 43.478 3.19 0.00 0.00 3.41
677 1022 0.532573 CTGAAGAGAGGCTGGCGTAA 59.467 55.000 0.00 0.00 0.00 3.18
687 1032 0.386113 GCTGGCGTAAGAGTAGGAGG 59.614 60.000 0.00 0.00 43.02 4.30
690 1035 1.272872 TGGCGTAAGAGTAGGAGGGTT 60.273 52.381 0.00 0.00 43.02 4.11
701 1046 4.398319 AGTAGGAGGGTTGTCACATTTTG 58.602 43.478 0.00 0.00 0.00 2.44
724 1069 6.482524 TGTGAGAGAGTAGGCTTTAGTCTAA 58.517 40.000 0.00 0.00 33.56 2.10
732 1077 3.257578 AGGCTTTAGTCTAAAGTGGGGT 58.742 45.455 26.03 9.83 45.30 4.95
752 1097 1.696884 TGTAATGTGGTGTGGCTGAGA 59.303 47.619 0.00 0.00 0.00 3.27
783 1151 3.505293 GTGCATCTTCTTCTTGGCTTCTT 59.495 43.478 0.00 0.00 0.00 2.52
796 1164 8.419076 TTCTTGGCTTCTTTTGTAAATTGTTC 57.581 30.769 0.00 0.00 0.00 3.18
797 1165 6.983890 TCTTGGCTTCTTTTGTAAATTGTTCC 59.016 34.615 0.00 0.00 0.00 3.62
801 1169 5.926542 GCTTCTTTTGTAAATTGTTCCTCCC 59.073 40.000 0.00 0.00 0.00 4.30
806 1174 7.563556 TCTTTTGTAAATTGTTCCTCCCTCTTT 59.436 33.333 0.00 0.00 0.00 2.52
833 1201 4.119442 AGATAAGTTATGCCGTTGACGT 57.881 40.909 0.00 0.00 37.74 4.34
837 1205 3.308438 AGTTATGCCGTTGACGTACTT 57.692 42.857 2.63 0.00 37.74 2.24
838 1206 3.656559 AGTTATGCCGTTGACGTACTTT 58.343 40.909 2.63 0.00 37.74 2.66
839 1207 3.676646 AGTTATGCCGTTGACGTACTTTC 59.323 43.478 2.63 0.00 37.74 2.62
840 1208 1.065358 ATGCCGTTGACGTACTTTCG 58.935 50.000 2.63 0.00 37.74 3.46
841 1209 0.030504 TGCCGTTGACGTACTTTCGA 59.969 50.000 2.63 0.00 37.74 3.71
842 1210 1.130955 GCCGTTGACGTACTTTCGAA 58.869 50.000 0.00 0.00 37.74 3.71
843 1211 1.522258 GCCGTTGACGTACTTTCGAAA 59.478 47.619 10.71 10.71 37.74 3.46
844 1212 2.033832 GCCGTTGACGTACTTTCGAAAA 60.034 45.455 12.41 0.00 37.74 2.29
845 1213 3.543852 GCCGTTGACGTACTTTCGAAAAA 60.544 43.478 12.41 0.09 37.74 1.94
937 1443 3.992643 TCAAGCCATTGTTTTCATGTGG 58.007 40.909 0.00 0.00 38.30 4.17
938 1444 3.387374 TCAAGCCATTGTTTTCATGTGGT 59.613 39.130 0.00 0.00 37.87 4.16
939 1445 4.128643 CAAGCCATTGTTTTCATGTGGTT 58.871 39.130 0.00 0.00 37.87 3.67
940 1446 4.420522 AGCCATTGTTTTCATGTGGTTT 57.579 36.364 0.00 0.00 37.87 3.27
941 1447 4.779696 AGCCATTGTTTTCATGTGGTTTT 58.220 34.783 0.00 0.00 37.87 2.43
944 1450 6.997476 AGCCATTGTTTTCATGTGGTTTTATT 59.003 30.769 0.00 0.00 37.87 1.40
945 1451 7.041235 AGCCATTGTTTTCATGTGGTTTTATTG 60.041 33.333 0.00 0.00 37.87 1.90
946 1452 7.041508 GCCATTGTTTTCATGTGGTTTTATTGA 60.042 33.333 0.00 0.00 37.87 2.57
947 1453 9.001542 CCATTGTTTTCATGTGGTTTTATTGAT 57.998 29.630 0.00 0.00 33.84 2.57
951 1457 9.605275 TGTTTTCATGTGGTTTTATTGATTTCA 57.395 25.926 0.00 0.00 0.00 2.69
955 1461 9.434420 TTCATGTGGTTTTATTGATTTCAATCC 57.566 29.630 8.99 5.63 44.67 3.01
956 1462 8.591940 TCATGTGGTTTTATTGATTTCAATCCA 58.408 29.630 8.99 7.92 44.67 3.41
957 1463 9.217278 CATGTGGTTTTATTGATTTCAATCCAA 57.783 29.630 8.99 2.23 44.67 3.53
958 1464 8.600449 TGTGGTTTTATTGATTTCAATCCAAC 57.400 30.769 8.99 12.03 44.67 3.77
959 1465 7.383572 TGTGGTTTTATTGATTTCAATCCAACG 59.616 33.333 8.99 0.00 44.67 4.10
960 1466 7.383843 GTGGTTTTATTGATTTCAATCCAACGT 59.616 33.333 8.99 0.00 44.67 3.99
961 1467 7.596995 TGGTTTTATTGATTTCAATCCAACGTC 59.403 33.333 8.99 4.03 44.67 4.34
973 1479 1.600013 TCCAACGTCGGTTTTCATGTG 59.400 47.619 0.00 0.00 32.98 3.21
987 1493 7.095060 CGGTTTTCATGTGATATTCTCCCATAG 60.095 40.741 0.00 0.00 0.00 2.23
1069 1575 0.672401 TACTACCGGCTTGTTGCTGC 60.672 55.000 0.00 0.00 46.34 5.25
1946 2470 4.180946 AGAGCAGAGTACGGCGCG 62.181 66.667 6.90 0.00 40.96 6.86
2068 2592 0.603569 GTGTCGGATCAGGTGTGACT 59.396 55.000 0.00 0.00 34.75 3.41
2071 2595 1.139734 CGGATCAGGTGTGACTCCG 59.860 63.158 0.00 10.01 42.32 4.63
2525 3061 2.511452 CCCAGGGCTCGGATGGTAG 61.511 68.421 0.00 0.00 31.85 3.18
2542 3078 2.174349 GCTCGCCAAAAGCTCGTG 59.826 61.111 0.00 0.00 40.39 4.35
2547 3083 2.956987 CCAAAAGCTCGTGCAGGG 59.043 61.111 12.58 3.52 42.74 4.45
2553 3089 4.154347 GCTCGTGCAGGGCTAGCT 62.154 66.667 15.72 0.00 44.82 3.32
2554 3090 2.581354 CTCGTGCAGGGCTAGCTT 59.419 61.111 15.72 0.00 0.00 3.74
2556 3092 1.954362 CTCGTGCAGGGCTAGCTTCT 61.954 60.000 15.72 9.88 0.00 2.85
2557 3093 1.078848 CGTGCAGGGCTAGCTTCTT 60.079 57.895 15.72 0.00 0.00 2.52
2558 3094 1.086634 CGTGCAGGGCTAGCTTCTTC 61.087 60.000 15.72 7.87 0.00 2.87
2559 3095 0.036010 GTGCAGGGCTAGCTTCTTCA 60.036 55.000 15.72 10.35 0.00 3.02
2560 3096 0.036010 TGCAGGGCTAGCTTCTTCAC 60.036 55.000 15.72 5.61 0.00 3.18
2562 3098 0.107459 CAGGGCTAGCTTCTTCACCC 60.107 60.000 15.72 4.39 37.63 4.61
2564 3100 1.275421 GGGCTAGCTTCTTCACCCCT 61.275 60.000 15.72 0.00 0.00 4.79
2567 3103 0.833949 CTAGCTTCTTCACCCCTCCC 59.166 60.000 0.00 0.00 0.00 4.30
2568 3104 0.620700 TAGCTTCTTCACCCCTCCCC 60.621 60.000 0.00 0.00 0.00 4.81
2619 3367 2.436646 CTTTGCCCACGCGGATCT 60.437 61.111 12.47 0.00 38.08 2.75
2666 3414 1.332375 CGGTGGTGCTTTTTCGAGAAA 59.668 47.619 0.78 0.78 0.00 2.52
2716 3464 0.172578 TTCTCCACGCGTGTCATAGG 59.827 55.000 34.81 20.52 0.00 2.57
2823 3571 1.330655 TGGCACGATCTCCTTCTCCC 61.331 60.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 1.195115 AGTGCGAGTGTCCACCATAT 58.805 50.000 0.00 0.00 32.48 1.78
37 38 1.532604 CCTAGTGCGAGTGTCCACCA 61.533 60.000 0.00 0.00 32.48 4.17
49 50 0.245539 TGTACGCCTGTTCCTAGTGC 59.754 55.000 0.00 0.00 0.00 4.40
61 62 1.134965 AGCTCTCACTGATTGTACGCC 60.135 52.381 0.00 0.00 0.00 5.68
68 69 4.395542 GCATTCTTCAAGCTCTCACTGATT 59.604 41.667 0.00 0.00 0.00 2.57
69 70 3.940221 GCATTCTTCAAGCTCTCACTGAT 59.060 43.478 0.00 0.00 0.00 2.90
72 73 2.289320 ACGCATTCTTCAAGCTCTCACT 60.289 45.455 0.00 0.00 0.00 3.41
78 79 1.741706 CCATCACGCATTCTTCAAGCT 59.258 47.619 0.00 0.00 0.00 3.74
84 85 2.401583 TGTAGCCATCACGCATTCTT 57.598 45.000 0.00 0.00 0.00 2.52
93 94 1.845791 ACCCACATCATGTAGCCATCA 59.154 47.619 0.00 0.00 0.00 3.07
148 450 2.670414 CTCTGGATTTCGAGACACAAGC 59.330 50.000 0.00 0.00 0.00 4.01
209 511 8.587952 ACCAGACAAATATTTTGCACTTAAAC 57.412 30.769 0.00 0.00 0.00 2.01
210 512 9.039870 CAACCAGACAAATATTTTGCACTTAAA 57.960 29.630 0.00 0.00 0.00 1.52
229 566 2.595463 GCTGCACTGCCAACCAGA 60.595 61.111 0.00 0.00 44.64 3.86
231 568 2.908428 CTGCTGCACTGCCAACCA 60.908 61.111 0.00 0.00 0.00 3.67
248 585 3.023950 CTCTCCGATCCGACGTCC 58.976 66.667 10.58 0.00 0.00 4.79
249 586 2.328639 GCTCTCCGATCCGACGTC 59.671 66.667 5.18 5.18 0.00 4.34
250 587 3.574445 CGCTCTCCGATCCGACGT 61.574 66.667 0.00 0.00 40.02 4.34
251 588 2.319011 TTTCGCTCTCCGATCCGACG 62.319 60.000 0.00 0.00 46.81 5.12
252 589 0.866483 GTTTCGCTCTCCGATCCGAC 60.866 60.000 0.00 0.00 46.81 4.79
258 603 2.257371 CCGTGTTTCGCTCTCCGA 59.743 61.111 0.00 0.00 45.77 4.55
287 632 2.035442 GTGAAGCAAGGAGACGGCC 61.035 63.158 0.00 0.00 36.36 6.13
297 642 1.457823 CCTGCAGGCAAGTGAAGCAA 61.458 55.000 22.33 0.00 34.45 3.91
316 661 1.014044 TGCTCGGCGTTGTCTTCATC 61.014 55.000 6.85 0.00 0.00 2.92
334 679 6.709145 CCAAAATGTGTGGTTCAATATGTG 57.291 37.500 0.00 0.00 0.00 3.21
373 718 5.295292 AGACATTCATGCCATACTTTCTTCG 59.705 40.000 0.00 0.00 0.00 3.79
375 720 6.660521 TGAAGACATTCATGCCATACTTTCTT 59.339 34.615 0.00 0.00 40.54 2.52
376 721 6.182627 TGAAGACATTCATGCCATACTTTCT 58.817 36.000 0.00 0.00 40.54 2.52
377 722 6.317140 TCTGAAGACATTCATGCCATACTTTC 59.683 38.462 0.00 0.00 44.32 2.62
378 723 6.182627 TCTGAAGACATTCATGCCATACTTT 58.817 36.000 0.00 0.00 44.32 2.66
383 728 5.014858 AGTTTCTGAAGACATTCATGCCAT 58.985 37.500 0.00 0.00 44.32 4.40
385 730 5.382618 AAGTTTCTGAAGACATTCATGCC 57.617 39.130 0.00 0.00 44.32 4.40
391 736 8.956426 TGTTCAAGTTAAGTTTCTGAAGACATT 58.044 29.630 0.00 0.00 0.00 2.71
396 741 7.930217 TCCATGTTCAAGTTAAGTTTCTGAAG 58.070 34.615 0.00 0.00 0.00 3.02
401 746 7.648112 GGTTTCTCCATGTTCAAGTTAAGTTTC 59.352 37.037 0.00 0.00 35.97 2.78
420 765 7.384932 CAGGTTGTTATCCATTTTTGGTTTCTC 59.615 37.037 0.00 0.00 0.00 2.87
422 767 6.989759 ACAGGTTGTTATCCATTTTTGGTTTC 59.010 34.615 0.00 0.00 0.00 2.78
424 769 6.493189 ACAGGTTGTTATCCATTTTTGGTT 57.507 33.333 0.00 0.00 0.00 3.67
465 810 0.972471 CCAATCCAACCCCTTCTGGC 60.972 60.000 0.00 0.00 32.33 4.85
466 811 0.409484 ACCAATCCAACCCCTTCTGG 59.591 55.000 0.00 0.00 0.00 3.86
467 812 1.549203 CACCAATCCAACCCCTTCTG 58.451 55.000 0.00 0.00 0.00 3.02
468 813 0.409484 CCACCAATCCAACCCCTTCT 59.591 55.000 0.00 0.00 0.00 2.85
469 814 1.257750 GCCACCAATCCAACCCCTTC 61.258 60.000 0.00 0.00 0.00 3.46
470 815 1.229177 GCCACCAATCCAACCCCTT 60.229 57.895 0.00 0.00 0.00 3.95
471 816 2.155197 GAGCCACCAATCCAACCCCT 62.155 60.000 0.00 0.00 0.00 4.79
472 817 1.682344 GAGCCACCAATCCAACCCC 60.682 63.158 0.00 0.00 0.00 4.95
473 818 0.541764 TTGAGCCACCAATCCAACCC 60.542 55.000 0.00 0.00 0.00 4.11
474 819 1.205417 CATTGAGCCACCAATCCAACC 59.795 52.381 0.00 0.00 34.77 3.77
475 820 1.404583 GCATTGAGCCACCAATCCAAC 60.405 52.381 0.00 0.00 34.77 3.77
476 821 0.896923 GCATTGAGCCACCAATCCAA 59.103 50.000 0.00 0.00 34.77 3.53
477 822 2.582272 GCATTGAGCCACCAATCCA 58.418 52.632 0.00 0.00 34.77 3.41
487 832 0.613012 AACCCCTTCTGGCATTGAGC 60.613 55.000 0.00 0.00 44.65 4.26
488 833 1.821136 GAAACCCCTTCTGGCATTGAG 59.179 52.381 0.00 0.00 0.00 3.02
489 834 1.886222 CGAAACCCCTTCTGGCATTGA 60.886 52.381 0.00 0.00 31.20 2.57
490 835 0.527565 CGAAACCCCTTCTGGCATTG 59.472 55.000 0.00 0.00 31.20 2.82
491 836 0.611896 CCGAAACCCCTTCTGGCATT 60.612 55.000 0.00 0.00 31.20 3.56
492 837 1.000896 CCGAAACCCCTTCTGGCAT 60.001 57.895 0.00 0.00 31.20 4.40
493 838 1.128809 TACCGAAACCCCTTCTGGCA 61.129 55.000 0.00 0.00 33.54 4.92
508 853 4.329392 ACCCATGTTTAAGTTCCTTACCG 58.671 43.478 0.00 0.00 0.00 4.02
515 860 5.411669 AGATGTCGAACCCATGTTTAAGTTC 59.588 40.000 0.00 0.00 33.97 3.01
520 865 5.067273 ACAAAGATGTCGAACCCATGTTTA 58.933 37.500 8.63 0.00 34.63 2.01
525 870 5.710099 ACAATAACAAAGATGTCGAACCCAT 59.290 36.000 0.00 0.00 39.40 4.00
549 894 6.358178 TGTTTTCATAACACCCAAGTCACTA 58.642 36.000 0.00 0.00 0.00 2.74
550 895 5.197451 TGTTTTCATAACACCCAAGTCACT 58.803 37.500 0.00 0.00 0.00 3.41
560 905 3.121362 GCTTTGCGCTGTTTTCATAACAC 60.121 43.478 9.73 0.00 35.14 3.32
561 906 3.049206 GCTTTGCGCTGTTTTCATAACA 58.951 40.909 9.73 0.00 35.14 2.41
580 925 2.622436 GTCTTGTTGAAGATAGGCGCT 58.378 47.619 7.64 0.00 40.40 5.92
585 930 1.324736 GCGCCGTCTTGTTGAAGATAG 59.675 52.381 0.00 0.00 40.40 2.08
587 932 0.602638 TGCGCCGTCTTGTTGAAGAT 60.603 50.000 4.18 0.00 40.40 2.40
632 977 6.068010 TCTGGATCTCTCTTAGGATGAACTC 58.932 44.000 0.00 0.00 0.00 3.01
643 988 5.579047 TCTCTTCAGTTCTGGATCTCTCTT 58.421 41.667 0.00 0.00 0.00 2.85
656 1001 1.294780 CGCCAGCCTCTCTTCAGTT 59.705 57.895 0.00 0.00 0.00 3.16
661 1006 0.820871 CTCTTACGCCAGCCTCTCTT 59.179 55.000 0.00 0.00 0.00 2.85
677 1022 2.696526 TGTGACAACCCTCCTACTCT 57.303 50.000 0.00 0.00 0.00 3.24
701 1046 7.121611 ACTTTAGACTAAAGCCTACTCTCTCAC 59.878 40.741 27.56 0.00 46.97 3.51
703 1048 7.415877 CCACTTTAGACTAAAGCCTACTCTCTC 60.416 44.444 27.56 0.00 46.97 3.20
705 1050 6.406065 CCCACTTTAGACTAAAGCCTACTCTC 60.406 46.154 27.56 0.00 46.97 3.20
712 1057 3.244805 ACACCCCACTTTAGACTAAAGCC 60.245 47.826 27.56 0.00 46.97 4.35
724 1069 1.497286 ACACCACATTACACCCCACTT 59.503 47.619 0.00 0.00 0.00 3.16
732 1077 1.696884 TCTCAGCCACACCACATTACA 59.303 47.619 0.00 0.00 0.00 2.41
771 1139 7.494298 GGAACAATTTACAAAAGAAGCCAAGAA 59.506 33.333 0.00 0.00 0.00 2.52
783 1151 7.669089 AAAAGAGGGAGGAACAATTTACAAA 57.331 32.000 0.00 0.00 0.00 2.83
806 1174 8.757789 CGTCAACGGCATAACTTATCTTTATAA 58.242 33.333 0.00 0.00 35.37 0.98
819 1187 2.662637 CGAAAGTACGTCAACGGCATAA 59.337 45.455 7.53 0.00 44.95 1.90
863 1231 9.529823 AGATCGGGTGATGTTCTATTACTATAA 57.470 33.333 0.00 0.00 34.09 0.98
864 1232 9.175312 GAGATCGGGTGATGTTCTATTACTATA 57.825 37.037 0.00 0.00 34.09 1.31
865 1233 7.670140 TGAGATCGGGTGATGTTCTATTACTAT 59.330 37.037 0.00 0.00 34.09 2.12
866 1234 7.002276 TGAGATCGGGTGATGTTCTATTACTA 58.998 38.462 0.00 0.00 34.09 1.82
867 1235 5.833667 TGAGATCGGGTGATGTTCTATTACT 59.166 40.000 0.00 0.00 34.09 2.24
868 1236 6.085555 TGAGATCGGGTGATGTTCTATTAC 57.914 41.667 0.00 0.00 34.09 1.89
869 1237 6.918067 ATGAGATCGGGTGATGTTCTATTA 57.082 37.500 0.00 0.00 34.09 0.98
870 1238 5.815233 ATGAGATCGGGTGATGTTCTATT 57.185 39.130 0.00 0.00 34.09 1.73
871 1239 7.487822 AATATGAGATCGGGTGATGTTCTAT 57.512 36.000 0.00 0.00 34.09 1.98
872 1240 6.918067 AATATGAGATCGGGTGATGTTCTA 57.082 37.500 0.00 0.00 34.09 2.10
873 1241 5.815233 AATATGAGATCGGGTGATGTTCT 57.185 39.130 0.00 0.00 34.09 3.01
874 1242 6.867662 AAAATATGAGATCGGGTGATGTTC 57.132 37.500 0.00 0.00 34.09 3.18
937 1443 7.201316 CCGACGTTGGATTGAAATCAATAAAAC 60.201 37.037 17.67 13.35 45.72 2.43
938 1444 6.804295 CCGACGTTGGATTGAAATCAATAAAA 59.196 34.615 17.67 4.26 45.72 1.52
939 1445 6.072397 ACCGACGTTGGATTGAAATCAATAAA 60.072 34.615 29.00 4.57 45.72 1.40
940 1446 5.413213 ACCGACGTTGGATTGAAATCAATAA 59.587 36.000 29.00 0.00 45.72 1.40
941 1447 4.938832 ACCGACGTTGGATTGAAATCAATA 59.061 37.500 29.00 0.00 45.72 1.90
944 1450 2.773487 ACCGACGTTGGATTGAAATCA 58.227 42.857 29.00 0.00 37.15 2.57
945 1451 3.824414 AACCGACGTTGGATTGAAATC 57.176 42.857 29.00 0.00 34.66 2.17
946 1452 4.036971 TGAAAACCGACGTTGGATTGAAAT 59.963 37.500 29.00 7.64 30.72 2.17
947 1453 3.377485 TGAAAACCGACGTTGGATTGAAA 59.623 39.130 29.00 9.24 30.72 2.69
948 1454 2.943690 TGAAAACCGACGTTGGATTGAA 59.056 40.909 29.00 11.67 30.72 2.69
949 1455 2.562635 TGAAAACCGACGTTGGATTGA 58.437 42.857 29.00 13.65 30.72 2.57
950 1456 3.233578 CATGAAAACCGACGTTGGATTG 58.766 45.455 29.00 7.94 30.72 2.67
951 1457 2.882137 ACATGAAAACCGACGTTGGATT 59.118 40.909 29.00 20.06 30.72 3.01
952 1458 2.225491 CACATGAAAACCGACGTTGGAT 59.775 45.455 29.00 14.51 30.72 3.41
953 1459 1.600013 CACATGAAAACCGACGTTGGA 59.400 47.619 29.00 5.66 30.72 3.53
954 1460 1.600013 TCACATGAAAACCGACGTTGG 59.400 47.619 20.86 20.86 30.72 3.77
955 1461 3.536158 ATCACATGAAAACCGACGTTG 57.464 42.857 0.00 0.00 30.72 4.10
956 1462 5.642063 AGAATATCACATGAAAACCGACGTT 59.358 36.000 0.00 0.00 0.00 3.99
957 1463 5.175859 AGAATATCACATGAAAACCGACGT 58.824 37.500 0.00 0.00 0.00 4.34
958 1464 5.276868 GGAGAATATCACATGAAAACCGACG 60.277 44.000 0.00 0.00 0.00 5.12
959 1465 5.007724 GGGAGAATATCACATGAAAACCGAC 59.992 44.000 0.00 0.00 0.00 4.79
960 1466 5.123227 GGGAGAATATCACATGAAAACCGA 58.877 41.667 0.00 0.00 0.00 4.69
961 1467 4.881273 TGGGAGAATATCACATGAAAACCG 59.119 41.667 0.00 0.00 36.00 4.44
1069 1575 1.002366 GTGGCAGCGTCAGAGTAATG 58.998 55.000 0.00 0.00 0.00 1.90
2068 2592 2.732016 CGAGACAACCCACACGGA 59.268 61.111 0.00 0.00 34.64 4.69
2071 2595 1.004918 CTCCCGAGACAACCCACAC 60.005 63.158 0.00 0.00 0.00 3.82
2403 2936 9.617523 ACTTTCATCAAATTCAGGAACATTTTT 57.382 25.926 0.00 0.00 0.00 1.94
2445 2978 9.325198 GTTTTTCCAAGTGATTGTTTAGGATTT 57.675 29.630 0.00 0.00 0.00 2.17
2446 2979 8.704668 AGTTTTTCCAAGTGATTGTTTAGGATT 58.295 29.630 0.00 0.00 0.00 3.01
2541 3077 0.036010 GTGAAGAAGCTAGCCCTGCA 60.036 55.000 12.13 11.15 0.00 4.41
2542 3078 0.746204 GGTGAAGAAGCTAGCCCTGC 60.746 60.000 12.13 8.43 0.00 4.85
2547 3083 0.179234 GGAGGGGTGAAGAAGCTAGC 59.821 60.000 6.62 6.62 0.00 3.42
2550 3086 1.925972 GGGGAGGGGTGAAGAAGCT 60.926 63.158 0.00 0.00 0.00 3.74
2551 3087 2.677848 GGGGAGGGGTGAAGAAGC 59.322 66.667 0.00 0.00 0.00 3.86
2552 3088 3.416351 GGGGGAGGGGTGAAGAAG 58.584 66.667 0.00 0.00 0.00 2.85
2593 3341 1.243342 CGTGGGCAAAGCTCAATGGA 61.243 55.000 0.00 0.00 42.30 3.41
2605 3353 4.451150 GTCAGATCCGCGTGGGCA 62.451 66.667 16.49 0.00 39.92 5.36
2666 3414 1.053424 TTTGTCGCTACAGGAACCCT 58.947 50.000 0.00 0.00 36.83 4.34


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

AutoCloner maintained by Alex Coulton.