Multiple sequence alignment - TraesCS2D01G499800

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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 TraesCS2D01G499800 chr2D 100.000 3218 0 0 1 3218 594553928 594550711 0.000000e+00 5943
1 TraesCS2D01G499800 chr2D 94.690 113 6 0 2968 3080 499027106 499026994 3.300000e-40 176
2 TraesCS2D01G499800 chr2B 92.271 1462 76 14 985 2425 722096364 722094919 0.000000e+00 2039
3 TraesCS2D01G499800 chr2B 87.945 730 38 14 2521 3218 722094875 722094164 0.000000e+00 815
4 TraesCS2D01G499800 chr2B 88.818 313 19 6 2518 2830 102553492 102553788 1.410000e-98 370
5 TraesCS2D01G499800 chr2B 77.470 759 71 56 122 849 722097320 722096631 2.360000e-96 363
6 TraesCS2D01G499800 chr2A 89.360 1673 85 30 843 2485 729176443 729174834 0.000000e+00 2017
7 TraesCS2D01G499800 chr2A 91.489 611 29 10 2558 3151 729174816 729174212 0.000000e+00 819
8 TraesCS2D01G499800 chr2A 82.195 747 61 36 126 849 729177210 729176513 7.740000e-161 577
9 TraesCS2D01G499800 chr2A 95.575 113 5 0 2968 3080 622751738 622751850 7.090000e-42 182
10 TraesCS2D01G499800 chr2A 92.800 125 8 1 1 125 729177370 729177247 2.550000e-41 180
11 TraesCS2D01G499800 chr3B 90.096 313 16 5 2518 2830 604554675 604554378 3.010000e-105 392
12 TraesCS2D01G499800 chr3B 89.776 313 21 5 2518 2830 738229324 738229023 1.080000e-104 390
13 TraesCS2D01G499800 chrUn 89.776 313 17 5 2518 2830 249824328 249824031 1.400000e-103 387
14 TraesCS2D01G499800 chrUn 89.776 313 17 5 2518 2830 316039625 316039328 1.400000e-103 387
15 TraesCS2D01G499800 chr1B 89.776 313 17 5 2518 2830 45043151 45043448 1.400000e-103 387
16 TraesCS2D01G499800 chr1B 89.776 313 17 5 2518 2830 45050656 45050953 1.400000e-103 387
17 TraesCS2D01G499800 chr4B 89.137 313 19 5 2518 2830 610015379 610015676 3.030000e-100 375
18 TraesCS2D01G499800 chr6D 94.690 113 6 0 2968 3080 419598078 419597966 3.300000e-40 176
19 TraesCS2D01G499800 chr6D 97.000 100 3 0 2981 3080 427935965 427935866 5.520000e-38 169
20 TraesCS2D01G499800 chr7A 95.349 86 4 0 2995 3080 126704804 126704719 1.560000e-28 137
21 TraesCS2D01G499800 chr7B 89.720 107 7 2 2382 2484 673853183 673853077 2.010000e-27 134
22 TraesCS2D01G499800 chr1D 98.667 75 1 0 3006 3080 350880614 350880688 2.010000e-27 134


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 TraesCS2D01G499800 chr2D 594550711 594553928 3217 True 5943.000000 5943 100.000000 1 3218 1 chr2D.!!$R2 3217
1 TraesCS2D01G499800 chr2B 722094164 722097320 3156 True 1072.333333 2039 85.895333 122 3218 3 chr2B.!!$R1 3096
2 TraesCS2D01G499800 chr2A 729174212 729177370 3158 True 898.250000 2017 88.961000 1 3151 4 chr2A.!!$R1 3150

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
647 726 0.177836 GAGGCAGGAGAAGAGAAGGC 59.822 60.0 0.0 0.0 0.0 4.35 F
648 727 0.252650 AGGCAGGAGAAGAGAAGGCT 60.253 55.0 0.0 0.0 0.0 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2001 2239 0.105593 GAGGCTTCATGATCCGCTCA 59.894 55.0 0.0 0.0 38.53 4.26 R
2531 2794 1.119684 AGGTTTGTTTGACCAAGGCC 58.880 50.0 0.0 0.0 39.71 5.19 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
77 78 3.317149 GGAAAAACACCTCACCTAACACC 59.683 47.826 0.00 0.00 0.00 4.16
81 82 0.768622 CACCTCACCTAACACCCCAA 59.231 55.000 0.00 0.00 0.00 4.12
98 99 4.229582 ACCCCAAAGATTCTAGGTGCAATA 59.770 41.667 0.00 0.00 0.00 1.90
102 103 6.206243 CCCAAAGATTCTAGGTGCAATATCTG 59.794 42.308 0.00 0.00 0.00 2.90
118 119 5.752892 ATATCTGTCTACCACTGTACACG 57.247 43.478 0.00 0.00 0.00 4.49
124 161 4.945543 TGTCTACCACTGTACACGATATGT 59.054 41.667 0.00 0.00 46.06 2.29
133 170 6.582672 CACTGTACACGATATGTATGATGGAC 59.417 42.308 0.00 0.00 45.59 4.02
241 289 5.692115 TGCATACAGATACAGGGAGAAAA 57.308 39.130 0.00 0.00 0.00 2.29
242 290 5.428253 TGCATACAGATACAGGGAGAAAAC 58.572 41.667 0.00 0.00 0.00 2.43
243 291 5.045942 TGCATACAGATACAGGGAGAAAACA 60.046 40.000 0.00 0.00 0.00 2.83
244 292 5.294552 GCATACAGATACAGGGAGAAAACAC 59.705 44.000 0.00 0.00 0.00 3.32
292 340 5.220529 CGGTTAGGCCTTACGTATTTCTTTG 60.221 44.000 12.58 0.00 34.25 2.77
301 349 7.453838 CCTTACGTATTTCTTTGCTCAACTAC 58.546 38.462 0.00 0.00 0.00 2.73
309 357 6.691754 TTCTTTGCTCAACTACAATGTGAA 57.308 33.333 0.00 0.00 0.00 3.18
311 359 4.488126 TTGCTCAACTACAATGTGAAGC 57.512 40.909 0.00 0.00 0.00 3.86
317 365 7.011389 TGCTCAACTACAATGTGAAGCATATAC 59.989 37.037 0.00 0.00 36.67 1.47
318 366 7.225538 GCTCAACTACAATGTGAAGCATATACT 59.774 37.037 0.00 0.00 36.67 2.12
320 368 8.040727 TCAACTACAATGTGAAGCATATACTGT 58.959 33.333 0.00 0.00 36.67 3.55
321 369 9.313118 CAACTACAATGTGAAGCATATACTGTA 57.687 33.333 0.00 0.00 36.67 2.74
322 370 8.873215 ACTACAATGTGAAGCATATACTGTAC 57.127 34.615 0.00 0.00 36.67 2.90
323 371 8.696374 ACTACAATGTGAAGCATATACTGTACT 58.304 33.333 0.00 0.00 36.67 2.73
324 372 9.534565 CTACAATGTGAAGCATATACTGTACTT 57.465 33.333 0.00 0.00 36.67 2.24
355 403 5.870706 AGAAAAAGAAAGAGGAGGTAGGTG 58.129 41.667 0.00 0.00 0.00 4.00
356 404 3.704800 AAAGAAAGAGGAGGTAGGTGC 57.295 47.619 0.00 0.00 0.00 5.01
357 405 2.327325 AGAAAGAGGAGGTAGGTGCA 57.673 50.000 0.00 0.00 0.00 4.57
358 406 2.183679 AGAAAGAGGAGGTAGGTGCAG 58.816 52.381 0.00 0.00 0.00 4.41
401 452 2.159448 CGAACAAGGTGTTGAAAGTGCA 60.159 45.455 0.00 0.00 41.28 4.57
402 453 2.939460 ACAAGGTGTTGAAAGTGCAC 57.061 45.000 9.40 9.40 37.10 4.57
403 454 2.166829 ACAAGGTGTTGAAAGTGCACA 58.833 42.857 21.04 0.00 37.10 4.57
404 455 2.560542 ACAAGGTGTTGAAAGTGCACAA 59.439 40.909 21.04 0.77 37.10 3.33
405 456 3.181397 CAAGGTGTTGAAAGTGCACAAG 58.819 45.455 21.04 0.00 35.46 3.16
441 498 3.054503 CAGCTCAGCCGCTTTGCT 61.055 61.111 10.22 10.22 44.00 3.91
486 547 1.006571 TTCGACGGTGCCTCTGTTC 60.007 57.895 0.00 0.00 35.55 3.18
487 548 1.461091 TTCGACGGTGCCTCTGTTCT 61.461 55.000 0.00 0.00 35.55 3.01
488 549 1.734477 CGACGGTGCCTCTGTTCTG 60.734 63.158 0.00 0.00 35.55 3.02
491 552 0.249911 ACGGTGCCTCTGTTCTGTTC 60.250 55.000 0.00 0.00 30.45 3.18
499 560 2.141517 CTCTGTTCTGTTCTGTGGCTG 58.858 52.381 0.00 0.00 0.00 4.85
507 568 1.768275 TGTTCTGTGGCTGAAAGGAGA 59.232 47.619 0.00 0.00 0.00 3.71
508 569 2.373169 TGTTCTGTGGCTGAAAGGAGAT 59.627 45.455 0.00 0.00 0.00 2.75
509 570 3.181440 TGTTCTGTGGCTGAAAGGAGATT 60.181 43.478 0.00 0.00 0.00 2.40
511 572 4.104383 TCTGTGGCTGAAAGGAGATTTT 57.896 40.909 0.00 0.00 0.00 1.82
513 574 4.279169 TCTGTGGCTGAAAGGAGATTTTTG 59.721 41.667 0.00 0.00 0.00 2.44
514 575 3.243839 TGTGGCTGAAAGGAGATTTTTGC 60.244 43.478 0.00 0.00 0.00 3.68
515 576 2.964464 TGGCTGAAAGGAGATTTTTGCA 59.036 40.909 0.00 0.00 33.69 4.08
516 577 3.387374 TGGCTGAAAGGAGATTTTTGCAA 59.613 39.130 0.00 0.00 33.69 4.08
517 578 3.992427 GGCTGAAAGGAGATTTTTGCAAG 59.008 43.478 0.00 0.00 33.69 4.01
518 579 3.431233 GCTGAAAGGAGATTTTTGCAAGC 59.569 43.478 0.00 0.00 32.87 4.01
519 580 4.624015 CTGAAAGGAGATTTTTGCAAGCA 58.376 39.130 0.00 0.00 0.00 3.91
520 581 5.021033 TGAAAGGAGATTTTTGCAAGCAA 57.979 34.783 2.89 2.89 0.00 3.91
522 583 4.942761 AAGGAGATTTTTGCAAGCAAGA 57.057 36.364 7.60 0.41 37.24 3.02
523 584 5.479124 AAGGAGATTTTTGCAAGCAAGAT 57.521 34.783 7.60 6.52 37.24 2.40
524 585 4.817517 AGGAGATTTTTGCAAGCAAGATG 58.182 39.130 7.60 0.00 37.24 2.90
525 586 3.930848 GGAGATTTTTGCAAGCAAGATGG 59.069 43.478 7.60 0.00 37.24 3.51
526 587 3.930848 GAGATTTTTGCAAGCAAGATGGG 59.069 43.478 7.60 0.00 37.24 4.00
527 588 3.325716 AGATTTTTGCAAGCAAGATGGGT 59.674 39.130 7.60 0.00 37.24 4.51
555 616 1.137479 AGAAAGCAAGCAAGCAAGCAA 59.863 42.857 10.52 0.00 36.85 3.91
557 618 0.878961 AAGCAAGCAAGCAAGCAAGC 60.879 50.000 10.52 6.16 36.99 4.01
559 620 1.155424 GCAAGCAAGCAAGCAAGCAA 61.155 50.000 10.52 0.00 36.81 3.91
593 672 1.408127 CCTTGAACCAGACACACCACA 60.408 52.381 0.00 0.00 0.00 4.17
598 677 1.525995 CCAGACACACCACACCACC 60.526 63.158 0.00 0.00 0.00 4.61
599 678 1.223211 CAGACACACCACACCACCA 59.777 57.895 0.00 0.00 0.00 4.17
600 679 0.815213 CAGACACACCACACCACCAG 60.815 60.000 0.00 0.00 0.00 4.00
601 680 1.525995 GACACACCACACCACCAGG 60.526 63.158 0.00 0.00 42.21 4.45
602 681 2.906897 CACACCACACCACCAGGC 60.907 66.667 0.00 0.00 39.06 4.85
603 682 3.415983 ACACCACACCACCAGGCA 61.416 61.111 0.00 0.00 39.06 4.75
604 683 2.906897 CACCACACCACCAGGCAC 60.907 66.667 0.00 0.00 39.06 5.01
605 684 3.415983 ACCACACCACCAGGCACA 61.416 61.111 0.00 0.00 39.06 4.57
606 685 2.595463 CCACACCACCAGGCACAG 60.595 66.667 0.00 0.00 39.06 3.66
607 686 2.595463 CACACCACCAGGCACAGG 60.595 66.667 0.00 0.00 42.48 4.00
608 687 4.586235 ACACCACCAGGCACAGGC 62.586 66.667 0.00 0.00 39.28 4.85
609 688 4.584518 CACCACCAGGCACAGGCA 62.585 66.667 0.00 0.00 39.28 4.75
610 689 4.275508 ACCACCAGGCACAGGCAG 62.276 66.667 0.00 0.00 39.28 4.85
627 706 0.603707 CAGGCAGCAGGAACGAAAGA 60.604 55.000 0.00 0.00 0.00 2.52
647 726 0.177836 GAGGCAGGAGAAGAGAAGGC 59.822 60.000 0.00 0.00 0.00 4.35
648 727 0.252650 AGGCAGGAGAAGAGAAGGCT 60.253 55.000 0.00 0.00 0.00 4.58
649 728 0.177836 GGCAGGAGAAGAGAAGGCTC 59.822 60.000 0.00 0.00 41.62 4.70
683 764 1.123077 TAGCAGGCATCATCGGTTCT 58.877 50.000 0.00 0.00 0.00 3.01
684 765 0.463295 AGCAGGCATCATCGGTTCTG 60.463 55.000 0.00 0.00 0.00 3.02
685 766 0.745845 GCAGGCATCATCGGTTCTGT 60.746 55.000 0.00 0.00 0.00 3.41
686 767 1.742761 CAGGCATCATCGGTTCTGTT 58.257 50.000 0.00 0.00 0.00 3.16
687 768 1.399440 CAGGCATCATCGGTTCTGTTG 59.601 52.381 0.00 0.00 0.00 3.33
727 809 5.476945 CAGGTTAGTGCCTTATTTTCCTTGT 59.523 40.000 0.00 0.00 36.58 3.16
728 810 5.476945 AGGTTAGTGCCTTATTTTCCTTGTG 59.523 40.000 0.00 0.00 34.71 3.33
746 828 4.866508 TGTGTTTCTCGTGGAAGTATCT 57.133 40.909 0.00 0.00 35.16 1.98
811 901 5.502079 TGGTTTCTTCTTTCTTGGTGTGTA 58.498 37.500 0.00 0.00 0.00 2.90
831 921 6.433093 TGTGTACTGTATTTAGCTGAGACTGA 59.567 38.462 0.00 0.00 0.00 3.41
878 1051 3.173151 TGAGTGGCAATCAGTTCCTCTA 58.827 45.455 14.40 0.00 0.00 2.43
879 1052 3.055819 TGAGTGGCAATCAGTTCCTCTAC 60.056 47.826 14.40 0.00 0.00 2.59
905 1092 2.345641 ACGAATGAATTCTCAAGCGACG 59.654 45.455 7.05 0.00 36.35 5.12
920 1111 2.420022 AGCGACGGATTGATTTCCTTTG 59.580 45.455 0.00 0.00 33.30 2.77
939 1132 3.818787 CCGCATCAGGTTGGCAGC 61.819 66.667 0.00 0.00 0.00 5.25
940 1133 3.057548 CGCATCAGGTTGGCAGCA 61.058 61.111 3.14 0.00 0.00 4.41
941 1134 2.882876 GCATCAGGTTGGCAGCAG 59.117 61.111 3.14 0.00 0.00 4.24
951 1144 4.073200 GGCAGCAGGGCGCAAAAT 62.073 61.111 10.83 0.00 46.13 1.82
952 1145 2.047939 GCAGCAGGGCGCAAAATT 60.048 55.556 10.83 0.00 46.13 1.82
968 1161 5.009510 CGCAAAATTTTTGGGGATTTTTCCT 59.990 36.000 23.87 0.00 34.25 3.36
975 1168 2.402564 TGGGGATTTTTCCTTGTGCAA 58.597 42.857 0.00 0.00 0.00 4.08
980 1173 4.021192 GGGATTTTTCCTTGTGCAATCAGA 60.021 41.667 0.00 0.00 0.00 3.27
981 1174 5.511202 GGGATTTTTCCTTGTGCAATCAGAA 60.511 40.000 0.00 0.00 0.00 3.02
982 1175 5.406477 GGATTTTTCCTTGTGCAATCAGAAC 59.594 40.000 0.00 0.00 0.00 3.01
1035 1264 1.606601 CTCGTCCCACCACTCTCCA 60.607 63.158 0.00 0.00 0.00 3.86
1087 1316 4.697756 CGCCCAAGTTCCGGCTCA 62.698 66.667 0.00 0.00 43.38 4.26
1117 1346 1.686110 ACCTCATCACCGTCCTCCC 60.686 63.158 0.00 0.00 0.00 4.30
1386 1618 4.135153 CTGGACCTCGACCGCCTG 62.135 72.222 0.00 0.00 0.00 4.85
1512 1750 0.541998 TGGTCTCCGACATGGACTGT 60.542 55.000 0.00 0.00 43.74 3.55
1524 1762 2.433318 GACTGTCCGCTGCACCTC 60.433 66.667 0.00 0.00 0.00 3.85
1544 1782 2.336554 GTGCTCAGGTACGACGTTTA 57.663 50.000 5.50 0.00 0.00 2.01
1680 1918 2.647158 GGACTCGGCGGAGGTTCTT 61.647 63.158 23.45 3.76 44.93 2.52
1683 1921 1.258445 ACTCGGCGGAGGTTCTTGAT 61.258 55.000 23.45 0.00 44.93 2.57
1779 2017 1.880894 CAGGCTCTACGTCACCGAA 59.119 57.895 0.00 0.00 37.88 4.30
1803 2041 2.436824 GCGTGGCCCTTCTTCTCC 60.437 66.667 0.00 0.00 0.00 3.71
1827 2065 1.384989 CGAGAGGGCAGGTGTACGAT 61.385 60.000 0.00 0.00 0.00 3.73
1923 2161 1.964448 ACGCCTGTTCGTCATCTCA 59.036 52.632 0.00 0.00 38.44 3.27
2058 2296 0.179187 AGAGCAAGATCGTCGTCGTG 60.179 55.000 1.33 0.00 38.33 4.35
2103 2341 1.202222 GGCCATGTCAAGAAGCAATCG 60.202 52.381 0.00 0.00 0.00 3.34
2105 2343 1.202222 CCATGTCAAGAAGCAATCGGC 60.202 52.381 0.00 0.00 45.30 5.54
2229 2477 3.084786 ACATGCTTAAAACTCTGCCTCC 58.915 45.455 0.00 0.00 0.00 4.30
2235 2483 4.142513 GCTTAAAACTCTGCCTCCAGAATG 60.143 45.833 0.00 0.00 46.84 2.67
2245 2497 2.548875 CCTCCAGAATGAAAGCTCTCG 58.451 52.381 0.00 0.00 39.69 4.04
2257 2516 3.386768 AAGCTCTCGTAGTCTGCAAAA 57.613 42.857 0.00 0.00 0.00 2.44
2258 2517 3.386768 AGCTCTCGTAGTCTGCAAAAA 57.613 42.857 0.00 0.00 0.00 1.94
2285 2544 6.468956 GCCTTGTTTCATATTCGTGTATGTTG 59.531 38.462 8.78 0.00 34.44 3.33
2325 2584 7.129457 TCTTTCCTGCTGTCATCTTGTATAT 57.871 36.000 0.00 0.00 0.00 0.86
2326 2585 8.250143 TCTTTCCTGCTGTCATCTTGTATATA 57.750 34.615 0.00 0.00 0.00 0.86
2327 2586 8.874156 TCTTTCCTGCTGTCATCTTGTATATAT 58.126 33.333 0.00 0.00 0.00 0.86
2362 2625 7.838771 TGATGATGTATCAGTGAAGAAACAG 57.161 36.000 0.00 0.00 40.82 3.16
2383 2646 5.511234 AGTTCGAAACTGTACTGTACTGT 57.489 39.130 20.48 20.48 41.01 3.55
2426 2689 6.655930 TGTTTCTGGGTACTGAACTAAACTT 58.344 36.000 0.00 0.00 34.78 2.66
2454 2717 8.507249 ACTGTTGCATTTCACTTCTTATCTTAC 58.493 33.333 0.00 0.00 0.00 2.34
2467 2730 6.378710 TCTTATCTTACACTGATCCGACTG 57.621 41.667 0.00 0.00 0.00 3.51
2469 2732 1.476891 TCTTACACTGATCCGACTGGC 59.523 52.381 0.00 0.00 34.14 4.85
2481 2744 1.159285 CGACTGGCTGCTGAATTTCA 58.841 50.000 0.00 0.00 0.00 2.69
2485 2748 2.694628 ACTGGCTGCTGAATTTCAAACA 59.305 40.909 0.00 1.63 0.00 2.83
2486 2749 3.243636 ACTGGCTGCTGAATTTCAAACAG 60.244 43.478 18.28 18.28 35.14 3.16
2487 2750 2.957680 TGGCTGCTGAATTTCAAACAGA 59.042 40.909 23.43 8.77 34.39 3.41
2490 2753 3.924686 GCTGCTGAATTTCAAACAGATGG 59.075 43.478 23.43 7.19 34.39 3.51
2491 2754 4.321452 GCTGCTGAATTTCAAACAGATGGA 60.321 41.667 23.43 4.21 34.39 3.41
2492 2755 5.623824 GCTGCTGAATTTCAAACAGATGGAT 60.624 40.000 23.43 0.00 34.39 3.41
2493 2756 6.405065 GCTGCTGAATTTCAAACAGATGGATA 60.405 38.462 23.43 0.00 34.39 2.59
2494 2757 6.855836 TGCTGAATTTCAAACAGATGGATAC 58.144 36.000 0.01 0.00 34.07 2.24
2495 2758 6.660521 TGCTGAATTTCAAACAGATGGATACT 59.339 34.615 0.01 0.00 34.07 2.12
2496 2759 7.828717 TGCTGAATTTCAAACAGATGGATACTA 59.171 33.333 0.01 0.00 34.07 1.82
2497 2760 8.125448 GCTGAATTTCAAACAGATGGATACTAC 58.875 37.037 0.01 0.00 34.07 2.73
2498 2761 9.388506 CTGAATTTCAAACAGATGGATACTACT 57.611 33.333 0.01 0.00 34.07 2.57
2499 2762 9.739276 TGAATTTCAAACAGATGGATACTACTT 57.261 29.630 0.00 0.00 37.61 2.24
2531 2794 8.654230 ATGAGTGCTACTACATTTGTATTCTG 57.346 34.615 0.00 0.00 0.00 3.02
2549 2812 0.827368 TGGCCTTGGTCAAACAAACC 59.173 50.000 3.32 0.00 37.31 3.27
2551 2814 1.202521 GGCCTTGGTCAAACAAACCTG 60.203 52.381 0.00 0.00 37.69 4.00
2591 2859 3.763360 TGCCAGATGATTGGACGAAAAAT 59.237 39.130 0.00 0.00 40.87 1.82
2592 2860 4.946772 TGCCAGATGATTGGACGAAAAATA 59.053 37.500 0.00 0.00 40.87 1.40
2659 2944 2.017049 AGTCCACAACAGCACAAGAAC 58.983 47.619 0.00 0.00 0.00 3.01
2692 2977 0.607489 CCCTCTTGTCTTGTGGCCAG 60.607 60.000 5.11 0.00 0.00 4.85
2727 3015 5.519927 CCAACTGAAACCTGACATTGAAAAC 59.480 40.000 0.00 0.00 0.00 2.43
2804 3097 8.531146 TGATAAATCCTGAATTTTTCCCTTGTC 58.469 33.333 0.00 0.00 38.53 3.18
2809 3102 6.951971 TCCTGAATTTTTCCCTTGTCAAAAA 58.048 32.000 0.00 0.00 36.25 1.94
2810 3103 6.821160 TCCTGAATTTTTCCCTTGTCAAAAAC 59.179 34.615 0.00 0.00 35.00 2.43
2962 3259 4.052229 CGTTCCGCTCGAGGTGGT 62.052 66.667 15.58 0.00 45.32 4.16
2964 3261 3.691342 TTCCGCTCGAGGTGGTGG 61.691 66.667 15.58 5.01 45.32 4.61
3136 3433 4.458829 ATCGCCTCCACCTCCGGA 62.459 66.667 2.93 2.93 0.00 5.14
3155 3453 0.113580 ACCCGTGTAAGCCCCATTTT 59.886 50.000 0.00 0.00 0.00 1.82
3188 3500 3.192466 ACAAGTTTCGTACTCACACCAC 58.808 45.455 0.00 0.00 35.54 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 3.165875 TCCTTGAGTGTTAGGTGAGGAG 58.834 50.000 0.00 0.00 33.15 3.69
77 78 6.206243 CAGATATTGCACCTAGAATCTTTGGG 59.794 42.308 6.87 2.11 0.00 4.12
81 82 7.372260 AGACAGATATTGCACCTAGAATCTT 57.628 36.000 0.00 0.00 0.00 2.40
98 99 3.682696 TCGTGTACAGTGGTAGACAGAT 58.317 45.455 0.00 0.00 42.30 2.90
102 103 5.496133 ACATATCGTGTACAGTGGTAGAC 57.504 43.478 0.00 0.00 39.91 2.59
118 119 5.240891 CCACAGGTGTCCATCATACATATC 58.759 45.833 0.00 0.00 0.00 1.63
124 161 0.546122 GGCCACAGGTGTCCATCATA 59.454 55.000 0.00 0.00 0.00 2.15
157 194 0.962855 GAGGGGCTCCAGCTGAAAAC 60.963 60.000 17.39 2.41 41.70 2.43
292 340 4.691860 ATGCTTCACATTGTAGTTGAGC 57.308 40.909 0.00 0.00 34.40 4.26
324 372 9.862149 ACCTCCTCTTTCTTTTTCTTTGTAATA 57.138 29.630 0.00 0.00 0.00 0.98
325 373 8.768501 ACCTCCTCTTTCTTTTTCTTTGTAAT 57.231 30.769 0.00 0.00 0.00 1.89
327 375 7.937394 CCTACCTCCTCTTTCTTTTTCTTTGTA 59.063 37.037 0.00 0.00 0.00 2.41
329 377 6.773200 ACCTACCTCCTCTTTCTTTTTCTTTG 59.227 38.462 0.00 0.00 0.00 2.77
333 381 4.456222 GCACCTACCTCCTCTTTCTTTTTC 59.544 45.833 0.00 0.00 0.00 2.29
339 387 1.406205 GCTGCACCTACCTCCTCTTTC 60.406 57.143 0.00 0.00 0.00 2.62
340 388 0.615850 GCTGCACCTACCTCCTCTTT 59.384 55.000 0.00 0.00 0.00 2.52
347 395 0.911525 ACCATCTGCTGCACCTACCT 60.912 55.000 0.00 0.00 0.00 3.08
355 403 2.439156 GGTCCCACCATCTGCTGC 60.439 66.667 0.00 0.00 38.42 5.25
356 404 2.273449 GGGTCCCACCATCTGCTG 59.727 66.667 1.78 0.00 41.02 4.41
357 405 3.402681 CGGGTCCCACCATCTGCT 61.403 66.667 9.12 0.00 41.02 4.24
358 406 4.489771 CCGGGTCCCACCATCTGC 62.490 72.222 9.12 0.00 41.02 4.26
401 452 1.348036 CCTTTCCCCGTCTTCTCTTGT 59.652 52.381 0.00 0.00 0.00 3.16
402 453 1.348036 ACCTTTCCCCGTCTTCTCTTG 59.652 52.381 0.00 0.00 0.00 3.02
403 454 1.730851 ACCTTTCCCCGTCTTCTCTT 58.269 50.000 0.00 0.00 0.00 2.85
404 455 1.624312 GAACCTTTCCCCGTCTTCTCT 59.376 52.381 0.00 0.00 0.00 3.10
405 456 1.346722 TGAACCTTTCCCCGTCTTCTC 59.653 52.381 0.00 0.00 0.00 2.87
441 498 0.841289 AAAAACAGAGGGTCGGGTCA 59.159 50.000 0.00 0.00 0.00 4.02
442 499 1.235724 CAAAAACAGAGGGTCGGGTC 58.764 55.000 0.00 0.00 0.00 4.46
443 500 0.549469 ACAAAAACAGAGGGTCGGGT 59.451 50.000 0.00 0.00 0.00 5.28
444 501 1.687563 AACAAAAACAGAGGGTCGGG 58.312 50.000 0.00 0.00 0.00 5.14
445 502 2.223711 CCAAACAAAAACAGAGGGTCGG 60.224 50.000 0.00 0.00 0.00 4.79
486 547 2.149578 CTCCTTTCAGCCACAGAACAG 58.850 52.381 0.00 0.00 0.00 3.16
487 548 1.768275 TCTCCTTTCAGCCACAGAACA 59.232 47.619 0.00 0.00 0.00 3.18
488 549 2.550830 TCTCCTTTCAGCCACAGAAC 57.449 50.000 0.00 0.00 0.00 3.01
491 552 4.553323 CAAAAATCTCCTTTCAGCCACAG 58.447 43.478 0.00 0.00 0.00 3.66
499 560 5.291971 TCTTGCTTGCAAAAATCTCCTTTC 58.708 37.500 9.39 0.00 0.00 2.62
507 568 3.775261 ACCCATCTTGCTTGCAAAAAT 57.225 38.095 9.39 3.75 0.00 1.82
508 569 4.617995 CGATACCCATCTTGCTTGCAAAAA 60.618 41.667 9.39 0.00 0.00 1.94
509 570 3.119531 CGATACCCATCTTGCTTGCAAAA 60.120 43.478 9.39 0.00 0.00 2.44
511 572 2.016318 CGATACCCATCTTGCTTGCAA 58.984 47.619 7.83 7.83 0.00 4.08
513 574 0.947244 CCGATACCCATCTTGCTTGC 59.053 55.000 0.00 0.00 0.00 4.01
514 575 0.947244 GCCGATACCCATCTTGCTTG 59.053 55.000 0.00 0.00 0.00 4.01
515 576 0.839946 AGCCGATACCCATCTTGCTT 59.160 50.000 0.00 0.00 34.90 3.91
516 577 1.620819 CTAGCCGATACCCATCTTGCT 59.379 52.381 0.00 0.00 39.14 3.91
517 578 1.618837 TCTAGCCGATACCCATCTTGC 59.381 52.381 0.00 0.00 0.00 4.01
518 579 4.310769 CTTTCTAGCCGATACCCATCTTG 58.689 47.826 0.00 0.00 0.00 3.02
519 580 3.244249 GCTTTCTAGCCGATACCCATCTT 60.244 47.826 0.00 0.00 41.74 2.40
520 581 2.300437 GCTTTCTAGCCGATACCCATCT 59.700 50.000 0.00 0.00 41.74 2.90
522 583 2.841442 GCTTTCTAGCCGATACCCAT 57.159 50.000 0.00 0.00 41.74 4.00
549 610 0.385223 GACGTCTGCTTGCTTGCTTG 60.385 55.000 8.70 0.00 0.00 4.01
550 611 0.533755 AGACGTCTGCTTGCTTGCTT 60.534 50.000 19.30 0.00 0.00 3.91
551 612 0.948141 GAGACGTCTGCTTGCTTGCT 60.948 55.000 25.58 0.00 0.00 3.91
555 616 1.589113 GAGGAGACGTCTGCTTGCT 59.411 57.895 35.66 17.80 44.95 3.91
557 618 0.605589 AAGGAGGAGACGTCTGCTTG 59.394 55.000 35.66 0.00 44.95 4.01
593 672 4.275508 CTGCCTGTGCCTGGTGGT 62.276 66.667 0.00 0.00 36.33 4.16
602 681 3.855503 TTCCTGCTGCCTGCCTGTG 62.856 63.158 0.00 0.00 42.00 3.66
603 682 3.573229 TTCCTGCTGCCTGCCTGT 61.573 61.111 0.00 0.00 42.00 4.00
604 683 3.060615 GTTCCTGCTGCCTGCCTG 61.061 66.667 0.00 0.00 42.00 4.85
605 684 4.711949 CGTTCCTGCTGCCTGCCT 62.712 66.667 0.00 0.00 42.00 4.75
606 685 4.704833 TCGTTCCTGCTGCCTGCC 62.705 66.667 0.00 0.00 42.00 4.85
607 686 2.192608 CTTTCGTTCCTGCTGCCTGC 62.193 60.000 0.00 0.00 43.25 4.85
608 687 0.603707 TCTTTCGTTCCTGCTGCCTG 60.604 55.000 0.00 0.00 0.00 4.85
609 688 0.321122 CTCTTTCGTTCCTGCTGCCT 60.321 55.000 0.00 0.00 0.00 4.75
610 689 0.320771 TCTCTTTCGTTCCTGCTGCC 60.321 55.000 0.00 0.00 0.00 4.85
611 690 1.074752 CTCTCTTTCGTTCCTGCTGC 58.925 55.000 0.00 0.00 0.00 5.25
614 693 0.320771 TGCCTCTCTTTCGTTCCTGC 60.321 55.000 0.00 0.00 0.00 4.85
619 698 1.633774 TCTCCTGCCTCTCTTTCGTT 58.366 50.000 0.00 0.00 0.00 3.85
621 700 1.821753 TCTTCTCCTGCCTCTCTTTCG 59.178 52.381 0.00 0.00 0.00 3.46
627 706 1.864669 CCTTCTCTTCTCCTGCCTCT 58.135 55.000 0.00 0.00 0.00 3.69
647 726 2.306847 GCTACAAGGAGGAGAGGAGAG 58.693 57.143 0.00 0.00 0.00 3.20
648 727 1.641192 TGCTACAAGGAGGAGAGGAGA 59.359 52.381 0.00 0.00 0.00 3.71
649 728 2.031120 CTGCTACAAGGAGGAGAGGAG 58.969 57.143 0.00 0.00 37.07 3.69
650 729 2.151502 CTGCTACAAGGAGGAGAGGA 57.848 55.000 0.00 0.00 37.07 3.71
683 764 4.082625 CCTGAATTGCTTGCTGATACAACA 60.083 41.667 0.00 0.00 0.00 3.33
684 765 4.082571 ACCTGAATTGCTTGCTGATACAAC 60.083 41.667 0.00 0.00 0.00 3.32
685 766 4.081406 ACCTGAATTGCTTGCTGATACAA 58.919 39.130 0.00 0.00 0.00 2.41
686 767 3.689347 ACCTGAATTGCTTGCTGATACA 58.311 40.909 0.00 0.00 0.00 2.29
687 768 4.708726 AACCTGAATTGCTTGCTGATAC 57.291 40.909 0.00 0.00 0.00 2.24
727 809 4.022589 ACGAAGATACTTCCACGAGAAACA 60.023 41.667 0.00 0.00 32.88 2.83
728 810 4.323868 CACGAAGATACTTCCACGAGAAAC 59.676 45.833 0.00 0.00 32.88 2.78
746 828 4.384940 TGGAAGAACATGTGAATCACGAA 58.615 39.130 9.00 0.00 37.14 3.85
776 858 7.715686 AGAAAGAAGAAACCAGTACCTAAGTTG 59.284 37.037 0.00 0.00 0.00 3.16
784 866 5.589050 ACACCAAGAAAGAAGAAACCAGTAC 59.411 40.000 0.00 0.00 0.00 2.73
789 871 4.983671 ACACACCAAGAAAGAAGAAACC 57.016 40.909 0.00 0.00 0.00 3.27
811 901 5.623368 GCAGTCAGTCTCAGCTAAATACAGT 60.623 44.000 0.00 0.00 0.00 3.55
831 921 4.997395 AGAACAACTGATACAATTCGCAGT 59.003 37.500 0.00 0.00 42.91 4.40
878 1051 5.289675 CGCTTGAGAATTCATTCGTTCTAGT 59.710 40.000 8.44 0.00 41.56 2.57
879 1052 5.516696 TCGCTTGAGAATTCATTCGTTCTAG 59.483 40.000 8.44 3.11 41.56 2.43
905 1092 2.491693 TGCGGACAAAGGAAATCAATCC 59.508 45.455 0.00 0.00 39.96 3.01
920 1111 2.359850 TGCCAACCTGATGCGGAC 60.360 61.111 0.00 0.00 0.00 4.79
939 1132 0.873721 CCCAAAAATTTTGCGCCCTG 59.126 50.000 12.62 0.00 0.00 4.45
940 1133 0.250684 CCCCAAAAATTTTGCGCCCT 60.251 50.000 12.62 0.00 0.00 5.19
941 1134 0.250510 TCCCCAAAAATTTTGCGCCC 60.251 50.000 12.62 0.00 0.00 6.13
951 1144 4.203226 GCACAAGGAAAAATCCCCAAAAA 58.797 39.130 0.00 0.00 0.00 1.94
952 1145 3.200825 TGCACAAGGAAAAATCCCCAAAA 59.799 39.130 0.00 0.00 0.00 2.44
968 1161 4.873817 CAATCTTGGTTCTGATTGCACAA 58.126 39.130 0.00 0.00 41.67 3.33
975 1168 3.005554 CGTCTGCAATCTTGGTTCTGAT 58.994 45.455 0.00 0.00 0.00 2.90
980 1173 1.244019 GCCCGTCTGCAATCTTGGTT 61.244 55.000 0.00 0.00 0.00 3.67
981 1174 1.675641 GCCCGTCTGCAATCTTGGT 60.676 57.895 0.00 0.00 0.00 3.67
982 1175 1.033746 ATGCCCGTCTGCAATCTTGG 61.034 55.000 0.00 0.00 45.84 3.61
1057 1286 1.236616 TTGGGCGTCAGCTTCATGTG 61.237 55.000 0.00 0.00 44.37 3.21
1117 1346 1.372087 GGTTGAGATTGCTCCGGCTG 61.372 60.000 0.00 0.00 40.55 4.85
1356 1588 1.451936 GTCCAGCACCTTCCACTGT 59.548 57.895 0.00 0.00 0.00 3.55
1524 1762 0.662374 AAACGTCGTACCTGAGCACG 60.662 55.000 0.00 0.00 39.48 5.34
1544 1782 2.030562 CGGTCCAGCGGTTCTTGT 59.969 61.111 0.00 0.00 0.00 3.16
1923 2161 3.054287 TCACCTTCATCCTCTCGTACTCT 60.054 47.826 0.00 0.00 0.00 3.24
2001 2239 0.105593 GAGGCTTCATGATCCGCTCA 59.894 55.000 0.00 0.00 38.53 4.26
2067 2305 1.524621 GCCGATCACCACATGGAGG 60.525 63.158 4.53 0.62 38.94 4.30
2193 2437 5.557891 AAGCATGTAAAATCTGACTGCTC 57.442 39.130 0.00 0.00 37.49 4.26
2229 2477 4.797868 CAGACTACGAGAGCTTTCATTCTG 59.202 45.833 4.97 6.14 0.00 3.02
2235 2483 2.638556 TGCAGACTACGAGAGCTTTC 57.361 50.000 0.00 0.00 0.00 2.62
2257 2516 5.705609 ACACGAATATGAAACAAGGCTTT 57.294 34.783 0.00 0.00 0.00 3.51
2258 2517 6.374333 ACATACACGAATATGAAACAAGGCTT 59.626 34.615 14.74 0.00 36.27 4.35
2259 2518 5.880332 ACATACACGAATATGAAACAAGGCT 59.120 36.000 14.74 0.00 36.27 4.58
2263 2522 9.814507 GTAACAACATACACGAATATGAAACAA 57.185 29.630 14.74 0.00 36.27 2.83
2272 2531 9.309516 CCACTAATAGTAACAACATACACGAAT 57.690 33.333 0.00 0.00 0.00 3.34
2275 2534 7.972277 AGTCCACTAATAGTAACAACATACACG 59.028 37.037 0.00 0.00 0.00 4.49
2326 2585 9.516546 ACTGATACATCATCATTTGCAGATTAT 57.483 29.630 0.00 0.00 42.82 1.28
2327 2586 8.780249 CACTGATACATCATCATTTGCAGATTA 58.220 33.333 0.00 0.00 42.82 1.75
2328 2587 7.501225 TCACTGATACATCATCATTTGCAGATT 59.499 33.333 0.00 0.00 42.82 2.40
2362 2625 5.517770 ACAACAGTACAGTACAGTTTCGAAC 59.482 40.000 16.65 0.00 36.44 3.95
2426 2689 8.621532 AGATAAGAAGTGAAATGCAACAGTTA 57.378 30.769 10.44 0.04 31.11 2.24
2454 2717 1.812922 GCAGCCAGTCGGATCAGTG 60.813 63.158 0.00 0.00 0.00 3.66
2467 2730 3.648339 TCTGTTTGAAATTCAGCAGCC 57.352 42.857 18.26 0.74 33.94 4.85
2469 2732 5.381174 TCCATCTGTTTGAAATTCAGCAG 57.619 39.130 17.47 17.47 34.66 4.24
2505 2768 9.750125 CAGAATACAAATGTAGTAGCACTCATA 57.250 33.333 0.00 0.00 33.52 2.15
2506 2769 7.712639 CCAGAATACAAATGTAGTAGCACTCAT 59.287 37.037 0.00 0.00 33.52 2.90
2507 2770 7.041721 CCAGAATACAAATGTAGTAGCACTCA 58.958 38.462 0.00 0.00 33.52 3.41
2508 2771 6.018669 GCCAGAATACAAATGTAGTAGCACTC 60.019 42.308 0.00 0.00 33.52 3.51
2509 2772 5.817816 GCCAGAATACAAATGTAGTAGCACT 59.182 40.000 0.00 0.00 33.52 4.40
2510 2773 5.007724 GGCCAGAATACAAATGTAGTAGCAC 59.992 44.000 0.00 0.00 33.52 4.40
2511 2774 5.104527 AGGCCAGAATACAAATGTAGTAGCA 60.105 40.000 5.01 0.00 33.52 3.49
2512 2775 5.368989 AGGCCAGAATACAAATGTAGTAGC 58.631 41.667 5.01 1.59 33.52 3.58
2513 2776 6.260936 CCAAGGCCAGAATACAAATGTAGTAG 59.739 42.308 5.01 0.00 33.52 2.57
2514 2777 6.119536 CCAAGGCCAGAATACAAATGTAGTA 58.880 40.000 5.01 0.00 33.52 1.82
2515 2778 4.949856 CCAAGGCCAGAATACAAATGTAGT 59.050 41.667 5.01 0.00 33.52 2.73
2516 2779 4.949856 ACCAAGGCCAGAATACAAATGTAG 59.050 41.667 5.01 0.00 33.52 2.74
2519 2782 3.763360 TGACCAAGGCCAGAATACAAATG 59.237 43.478 5.01 0.00 0.00 2.32
2531 2794 1.119684 AGGTTTGTTTGACCAAGGCC 58.880 50.000 0.00 0.00 39.71 5.19
2549 2812 6.319446 TGGCACAAATGGAGACTGAATACAG 61.319 44.000 0.00 0.00 42.66 2.74
2551 2814 4.009675 TGGCACAAATGGAGACTGAATAC 58.990 43.478 0.00 0.00 31.92 1.89
2591 2859 6.317312 ACACGTAGGTAGATGGGGATTTATA 58.683 40.000 0.00 0.00 0.00 0.98
2592 2860 5.152934 ACACGTAGGTAGATGGGGATTTAT 58.847 41.667 0.00 0.00 0.00 1.40
2659 2944 0.545071 AGAGGGCATTTTGGGTTGGG 60.545 55.000 0.00 0.00 0.00 4.12
2692 2977 3.578688 GTTTCAGTTGGTGGATTGATGC 58.421 45.455 0.00 0.00 0.00 3.91
2727 3015 3.731652 TGAAATTGGTTCAGTTGCCTG 57.268 42.857 0.00 0.00 41.47 4.85
2774 3067 6.982724 GGGAAAAATTCAGGATTTATCAGCAG 59.017 38.462 0.00 0.00 36.96 4.24
2776 3069 7.117285 AGGGAAAAATTCAGGATTTATCAGC 57.883 36.000 0.00 0.00 36.96 4.26
2777 3070 8.534496 ACAAGGGAAAAATTCAGGATTTATCAG 58.466 33.333 0.00 0.00 36.96 2.90
2778 3071 8.434589 ACAAGGGAAAAATTCAGGATTTATCA 57.565 30.769 0.00 0.00 36.96 2.15
2779 3072 8.531146 TGACAAGGGAAAAATTCAGGATTTATC 58.469 33.333 0.00 0.00 36.96 1.75
2780 3073 8.434589 TGACAAGGGAAAAATTCAGGATTTAT 57.565 30.769 0.00 0.00 36.96 1.40
2781 3074 7.847711 TGACAAGGGAAAAATTCAGGATTTA 57.152 32.000 0.00 0.00 36.96 1.40
2804 3097 2.973224 CGATCTCCGCAACTTGTTTTTG 59.027 45.455 0.00 0.00 0.00 2.44
2809 3102 1.714794 CTTCGATCTCCGCAACTTGT 58.285 50.000 0.00 0.00 38.37 3.16
2810 3103 0.371645 GCTTCGATCTCCGCAACTTG 59.628 55.000 0.00 0.00 38.37 3.16
3116 3413 4.899239 GGAGGTGGAGGCGATGCG 62.899 72.222 0.00 0.00 0.00 4.73
3130 3427 2.183555 GCTTACACGGGTCCGGAG 59.816 66.667 3.06 8.28 44.69 4.63
3136 3433 0.113580 AAAATGGGGCTTACACGGGT 59.886 50.000 0.00 0.00 0.00 5.28
3155 3453 3.202906 CGAAACTTGTCAGGGAGTTGAA 58.797 45.455 0.00 0.00 36.31 2.69


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

AutoCloner maintained by Alex Coulton.