Multiple sequence alignment - TraesCS2B01G518300

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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 TraesCS2B01G518300 chr2B 100.000 3326 0 0 1 3326 712888726 712892051 0.000000e+00 6143.0
1 TraesCS2B01G518300 chr2B 86.418 1340 170 8 993 2326 713791108 713792441 0.000000e+00 1456.0
2 TraesCS2B01G518300 chr2B 85.672 1361 173 15 974 2326 713940354 713939008 0.000000e+00 1413.0
3 TraesCS2B01G518300 chr2B 96.970 264 7 1 2350 2613 526267220 526266958 3.050000e-120 442.0
4 TraesCS2B01G518300 chr2B 94.326 282 13 3 2351 2631 35398221 35397942 2.370000e-116 429.0
5 TraesCS2B01G518300 chr2B 80.690 435 30 19 22 435 712844883 712845284 4.200000e-74 289.0
6 TraesCS2B01G518300 chr2A 91.977 1932 106 5 409 2340 723624799 723626681 0.000000e+00 2663.0
7 TraesCS2B01G518300 chr2A 86.041 1354 166 12 993 2326 723867205 723868555 0.000000e+00 1432.0
8 TraesCS2B01G518300 chr2A 85.873 1352 176 11 978 2326 724018476 724017137 0.000000e+00 1424.0
9 TraesCS2B01G518300 chr2A 82.019 634 57 19 2646 3269 723626957 723627543 1.390000e-133 486.0
10 TraesCS2B01G518300 chr2A 82.683 410 23 18 1 389 723624259 723624641 1.490000e-83 320.0
11 TraesCS2B01G518300 chr2A 84.416 308 18 11 1 283 723585437 723585739 3.270000e-70 276.0
12 TraesCS2B01G518300 chr2A 91.935 62 4 1 290 351 723613974 723614034 5.910000e-13 86.1
13 TraesCS2B01G518300 chr2A 90.323 62 6 0 290 351 723601301 723601362 7.650000e-12 82.4
14 TraesCS2B01G518300 chr2D 91.738 1743 83 16 633 2347 589281937 589283646 0.000000e+00 2364.0
15 TraesCS2B01G518300 chr2D 86.283 1356 172 11 978 2326 589522746 589524094 0.000000e+00 1461.0
16 TraesCS2B01G518300 chr2D 86.123 1362 173 11 971 2326 589684865 589683514 0.000000e+00 1454.0
17 TraesCS2B01G518300 chr2D 93.287 715 25 8 2615 3326 589283648 589284342 0.000000e+00 1033.0
18 TraesCS2B01G518300 chr2D 85.281 693 43 36 1 646 589280037 589280717 0.000000e+00 660.0
19 TraesCS2B01G518300 chr4B 96.324 272 9 1 2342 2613 423293471 423293741 2.350000e-121 446.0
20 TraesCS2B01G518300 chr4B 96.970 264 7 1 2350 2613 410992900 410993162 3.050000e-120 442.0
21 TraesCS2B01G518300 chr7B 96.283 269 9 1 2345 2613 372681189 372681456 1.100000e-119 440.0
22 TraesCS2B01G518300 chr5B 95.588 272 10 2 2347 2617 46143882 46144152 5.100000e-118 435.0
23 TraesCS2B01G518300 chr3B 95.604 273 9 3 2342 2613 19251357 19251087 5.100000e-118 435.0
24 TraesCS2B01G518300 chr3B 94.946 277 12 2 2345 2621 773841406 773841132 1.830000e-117 433.0
25 TraesCS2B01G518300 chr6B 94.946 277 11 3 2339 2614 417246211 417246485 6.590000e-117 431.0
26 TraesCS2B01G518300 chrUn 79.399 466 78 11 1862 2314 277979561 277980021 2.490000e-81 313.0
27 TraesCS2B01G518300 chrUn 79.023 348 61 7 1976 2314 441060428 441060772 9.280000e-56 228.0


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 TraesCS2B01G518300 chr2B 712888726 712892051 3325 False 6143.000000 6143 100.000000 1 3326 1 chr2B.!!$F2 3325
1 TraesCS2B01G518300 chr2B 713791108 713792441 1333 False 1456.000000 1456 86.418000 993 2326 1 chr2B.!!$F3 1333
2 TraesCS2B01G518300 chr2B 713939008 713940354 1346 True 1413.000000 1413 85.672000 974 2326 1 chr2B.!!$R3 1352
3 TraesCS2B01G518300 chr2A 723867205 723868555 1350 False 1432.000000 1432 86.041000 993 2326 1 chr2A.!!$F4 1333
4 TraesCS2B01G518300 chr2A 724017137 724018476 1339 True 1424.000000 1424 85.873000 978 2326 1 chr2A.!!$R1 1348
5 TraesCS2B01G518300 chr2A 723624259 723627543 3284 False 1156.333333 2663 85.559667 1 3269 3 chr2A.!!$F5 3268
6 TraesCS2B01G518300 chr2D 589522746 589524094 1348 False 1461.000000 1461 86.283000 978 2326 1 chr2D.!!$F1 1348
7 TraesCS2B01G518300 chr2D 589683514 589684865 1351 True 1454.000000 1454 86.123000 971 2326 1 chr2D.!!$R1 1355
8 TraesCS2B01G518300 chr2D 589280037 589284342 4305 False 1352.333333 2364 90.102000 1 3326 3 chr2D.!!$F2 3325

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
596 793 0.036105 TGCTAGCCAGTGTGATGTGG 60.036 55.0 13.29 0.0 36.85 4.17 F
599 796 0.324614 TAGCCAGTGTGATGTGGGTG 59.675 55.0 3.35 0.0 44.32 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1584 3042 0.601558 GGTGCTCGTACTCAACCTGA 59.398 55.0 0.0 0.0 0.0 3.86 R
2595 4082 0.702902 AGTACTCCCTCCGTTCCTCA 59.297 55.0 0.0 0.0 0.0 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
28 29 5.586243 TGCATGGCTTATCTGTAGACTTTTC 59.414 40.000 0.00 0.00 0.00 2.29
34 36 8.041323 TGGCTTATCTGTAGACTTTTCTTTAGG 58.959 37.037 0.00 0.00 32.75 2.69
118 127 7.441890 AGTATCTGACCACGATCTATACAAG 57.558 40.000 0.00 0.00 0.00 3.16
124 133 3.181465 ACCACGATCTATACAAGCTTGGG 60.181 47.826 29.18 18.15 0.00 4.12
127 136 5.116180 CACGATCTATACAAGCTTGGGAAA 58.884 41.667 29.18 12.69 0.00 3.13
133 142 8.593945 ATCTATACAAGCTTGGGAAAATTTGA 57.406 30.769 29.18 14.21 0.00 2.69
162 171 1.430632 GTCGCTCGATCGGGTAACA 59.569 57.895 17.85 0.00 39.74 2.41
182 191 1.137404 GCACATCGAATTTGCGGCT 59.863 52.632 0.00 0.00 0.00 5.52
281 309 1.670949 GGAGCTGAGCCACTCGATCA 61.671 60.000 0.00 0.00 33.55 2.92
282 310 0.388659 GAGCTGAGCCACTCGATCAT 59.611 55.000 0.00 0.00 32.35 2.45
326 354 3.463690 CGCACACCGACGTAACCG 61.464 66.667 0.00 0.00 40.02 4.44
351 381 1.263356 TTCGAGGAACCGACAGGAAT 58.737 50.000 0.00 0.00 41.02 3.01
361 391 3.175594 ACCGACAGGAATACCACCTTTA 58.824 45.455 0.00 0.00 41.02 1.85
363 393 3.197116 CCGACAGGAATACCACCTTTACT 59.803 47.826 0.00 0.00 41.02 2.24
368 398 7.551617 CGACAGGAATACCACCTTTACTTTTAT 59.448 37.037 0.00 0.00 38.94 1.40
371 401 9.901172 CAGGAATACCACCTTTACTTTTATACT 57.099 33.333 0.00 0.00 38.94 2.12
379 409 9.643693 CCACCTTTACTTTTATACTACGAAAGA 57.356 33.333 0.00 0.00 35.09 2.52
412 493 3.863424 CCAGAACAACGACGCAACTATAT 59.137 43.478 0.00 0.00 0.00 0.86
424 589 5.005740 ACGCAACTATATCCGTATGTAGGA 58.994 41.667 0.00 0.00 42.69 2.94
429 594 9.334947 GCAACTATATCCGTATGTAGGAGTATA 57.665 37.037 0.00 0.00 41.66 1.47
455 620 0.463833 CAGCCCAAACCTATCCGTCC 60.464 60.000 0.00 0.00 0.00 4.79
479 644 3.573491 GGCGGCTCGATTTTCCCG 61.573 66.667 0.00 0.00 43.38 5.14
537 707 0.107268 ACAGGTACCACCGTTGAACC 59.893 55.000 15.94 0.00 44.90 3.62
581 778 0.979709 AGTGCATGGAGGAGCTGCTA 60.980 55.000 8.12 0.00 36.84 3.49
582 779 0.532417 GTGCATGGAGGAGCTGCTAG 60.532 60.000 8.12 0.00 36.84 3.42
583 780 1.597578 GCATGGAGGAGCTGCTAGC 60.598 63.158 8.12 8.10 42.84 3.42
584 781 1.071128 CATGGAGGAGCTGCTAGCC 59.929 63.158 8.12 6.90 43.77 3.93
585 782 1.383664 ATGGAGGAGCTGCTAGCCA 60.384 57.895 16.50 16.50 43.77 4.75
586 783 1.409251 ATGGAGGAGCTGCTAGCCAG 61.409 60.000 18.53 10.78 43.77 4.85
587 784 2.063378 GGAGGAGCTGCTAGCCAGT 61.063 63.158 8.12 0.00 43.77 4.00
588 785 1.143620 GAGGAGCTGCTAGCCAGTG 59.856 63.158 8.12 0.96 43.77 3.66
589 786 1.611851 AGGAGCTGCTAGCCAGTGT 60.612 57.895 13.29 2.06 43.77 3.55
590 787 1.449246 GGAGCTGCTAGCCAGTGTG 60.449 63.158 13.29 0.00 43.77 3.82
591 788 1.593787 GAGCTGCTAGCCAGTGTGA 59.406 57.895 13.29 0.00 43.77 3.58
592 789 0.177604 GAGCTGCTAGCCAGTGTGAT 59.822 55.000 13.29 0.00 43.77 3.06
593 790 0.107800 AGCTGCTAGCCAGTGTGATG 60.108 55.000 13.29 0.00 43.77 3.07
594 791 0.392193 GCTGCTAGCCAGTGTGATGT 60.392 55.000 13.29 0.00 43.71 3.06
595 792 1.366679 CTGCTAGCCAGTGTGATGTG 58.633 55.000 13.29 0.00 36.79 3.21
596 793 0.036105 TGCTAGCCAGTGTGATGTGG 60.036 55.000 13.29 0.00 36.85 4.17
597 794 0.745845 GCTAGCCAGTGTGATGTGGG 60.746 60.000 2.29 0.00 34.06 4.61
598 795 0.615331 CTAGCCAGTGTGATGTGGGT 59.385 55.000 0.00 0.00 46.31 4.51
599 796 0.324614 TAGCCAGTGTGATGTGGGTG 59.675 55.000 3.35 0.00 44.32 4.61
600 797 1.973281 GCCAGTGTGATGTGGGTGG 60.973 63.158 0.00 0.00 34.06 4.61
601 798 1.455849 CCAGTGTGATGTGGGTGGT 59.544 57.895 0.00 0.00 0.00 4.16
602 799 0.606401 CCAGTGTGATGTGGGTGGTC 60.606 60.000 0.00 0.00 0.00 4.02
603 800 0.397941 CAGTGTGATGTGGGTGGTCT 59.602 55.000 0.00 0.00 0.00 3.85
604 801 0.397941 AGTGTGATGTGGGTGGTCTG 59.602 55.000 0.00 0.00 0.00 3.51
605 802 1.073025 TGTGATGTGGGTGGTCTGC 59.927 57.895 0.00 0.00 0.00 4.26
606 803 1.376466 GTGATGTGGGTGGTCTGCT 59.624 57.895 0.00 0.00 0.00 4.24
640 837 2.553602 TGCATTTGTTGGAGCAGTACAG 59.446 45.455 0.00 0.00 32.48 2.74
735 2161 4.034258 GTCGACGACTGACCGGCA 62.034 66.667 20.52 0.00 37.43 5.69
738 2164 4.736896 GACGACTGACCGGCACCC 62.737 72.222 0.00 0.00 37.55 4.61
740 2166 4.742201 CGACTGACCGGCACCCAG 62.742 72.222 0.00 6.79 0.00 4.45
741 2167 3.311110 GACTGACCGGCACCCAGA 61.311 66.667 17.12 0.00 0.00 3.86
742 2168 2.847234 ACTGACCGGCACCCAGAA 60.847 61.111 17.12 0.00 0.00 3.02
743 2169 2.046892 CTGACCGGCACCCAGAAG 60.047 66.667 0.00 0.00 0.00 2.85
744 2170 2.525629 TGACCGGCACCCAGAAGA 60.526 61.111 0.00 0.00 0.00 2.87
745 2171 1.903877 CTGACCGGCACCCAGAAGAT 61.904 60.000 0.00 0.00 0.00 2.40
746 2172 0.616395 TGACCGGCACCCAGAAGATA 60.616 55.000 0.00 0.00 0.00 1.98
747 2173 0.539986 GACCGGCACCCAGAAGATAA 59.460 55.000 0.00 0.00 0.00 1.75
748 2174 1.141053 GACCGGCACCCAGAAGATAAT 59.859 52.381 0.00 0.00 0.00 1.28
749 2175 1.564348 ACCGGCACCCAGAAGATAATT 59.436 47.619 0.00 0.00 0.00 1.40
750 2176 2.775384 ACCGGCACCCAGAAGATAATTA 59.225 45.455 0.00 0.00 0.00 1.40
751 2177 3.394606 ACCGGCACCCAGAAGATAATTAT 59.605 43.478 0.00 0.00 0.00 1.28
752 2178 4.141251 ACCGGCACCCAGAAGATAATTATT 60.141 41.667 0.00 0.00 0.00 1.40
753 2179 5.072600 ACCGGCACCCAGAAGATAATTATTA 59.927 40.000 0.00 0.00 0.00 0.98
869 2295 5.807520 TCTCTTCTCGTGCATTAACAATCTC 59.192 40.000 0.00 0.00 0.00 2.75
870 2296 5.724328 TCTTCTCGTGCATTAACAATCTCT 58.276 37.500 0.00 0.00 0.00 3.10
871 2297 5.578336 TCTTCTCGTGCATTAACAATCTCTG 59.422 40.000 0.00 0.00 0.00 3.35
872 2298 4.183865 TCTCGTGCATTAACAATCTCTGG 58.816 43.478 0.00 0.00 0.00 3.86
982 2440 7.115236 ACAAGGTTTTTGTTTTCTTTGTACGTC 59.885 33.333 0.00 0.00 0.00 4.34
1276 2734 2.485795 GCGATCCTGCTCTCCGACT 61.486 63.158 0.00 0.00 0.00 4.18
1303 2761 4.353437 GGTTCGTGGAGGCGACGT 62.353 66.667 0.00 0.00 40.85 4.34
1323 2781 4.664677 GACGTGGCGCTGGACAGT 62.665 66.667 7.64 4.85 0.00 3.55
1347 2805 4.776322 CCGATGAAGCCCACGCCA 62.776 66.667 0.00 0.00 34.57 5.69
1660 3118 3.754740 AACGACGACGAACGCCACA 62.755 57.895 15.32 0.00 46.94 4.17
1661 3119 2.803670 CGACGACGAACGCCACAT 60.804 61.111 0.00 0.00 46.94 3.21
1662 3120 2.774951 CGACGACGAACGCCACATC 61.775 63.158 0.00 0.00 46.94 3.06
1663 3121 1.731613 GACGACGAACGCCACATCA 60.732 57.895 0.00 0.00 46.94 3.07
1732 3208 2.171003 TCATCTCCAAGCTCAAGTCGA 58.829 47.619 0.00 0.00 0.00 4.20
1739 3215 2.048127 GCTCAAGTCGAGGGCGTT 60.048 61.111 0.00 0.00 42.55 4.84
1767 3243 4.673298 CACCGGCCGTACAGCACA 62.673 66.667 26.12 0.00 0.00 4.57
2124 3600 1.299976 GAGCCCCAACATCGAGGTT 59.700 57.895 10.11 10.11 0.00 3.50
2347 3831 6.515272 AGATTTGCATCGTTGGAGTTAATT 57.485 33.333 0.00 0.00 34.17 1.40
2364 3851 7.672122 AGTTAATTAATACTCCCTCGGTTCT 57.328 36.000 0.31 0.00 0.00 3.01
2366 3853 9.205513 AGTTAATTAATACTCCCTCGGTTCTTA 57.794 33.333 0.31 0.00 0.00 2.10
2367 3854 9.822185 GTTAATTAATACTCCCTCGGTTCTTAA 57.178 33.333 0.31 0.00 0.00 1.85
2376 3863 6.614496 ACTCCCTCGGTTCTTAAATATAAGGT 59.386 38.462 0.00 0.00 39.24 3.50
2377 3864 6.823497 TCCCTCGGTTCTTAAATATAAGGTG 58.177 40.000 0.00 0.00 39.24 4.00
2415 3902 8.687824 AAAAAGTCAACTGTTGTCTATGTTTG 57.312 30.769 18.10 0.00 0.00 2.93
2420 3907 5.883115 TCAACTGTTGTCTATGTTTGACCAA 59.117 36.000 19.12 0.00 33.83 3.67
2421 3908 5.751243 ACTGTTGTCTATGTTTGACCAAC 57.249 39.130 0.00 0.00 33.83 3.77
2426 3913 7.699566 TGTTGTCTATGTTTGACCAACTTTAC 58.300 34.615 0.00 0.00 36.21 2.01
2428 3915 7.490962 TGTCTATGTTTGACCAACTTTACAG 57.509 36.000 0.00 0.00 36.21 2.74
2429 3916 6.017440 TGTCTATGTTTGACCAACTTTACAGC 60.017 38.462 0.00 0.00 36.21 4.40
2434 3921 6.402222 TGTTTGACCAACTTTACAGCAAAAT 58.598 32.000 0.00 0.00 36.21 1.82
2435 3922 7.548097 TGTTTGACCAACTTTACAGCAAAATA 58.452 30.769 0.00 0.00 36.21 1.40
2557 4044 9.616156 TTGTCTATAAACTTGGTCAAACTTACA 57.384 29.630 0.00 0.00 0.00 2.41
2574 4061 6.451064 ACTTACAGAAGTTGGACTTTTTGG 57.549 37.500 0.00 0.00 43.70 3.28
2578 4065 6.353404 ACAGAAGTTGGACTTTTTGGAAAA 57.647 33.333 0.00 0.00 38.80 2.29
2579 4066 6.764379 ACAGAAGTTGGACTTTTTGGAAAAA 58.236 32.000 0.00 0.00 38.80 1.94
2581 4068 8.536175 ACAGAAGTTGGACTTTTTGGAAAAATA 58.464 29.630 0.00 0.00 38.80 1.40
2588 4075 9.549078 TTGGACTTTTTGGAAAAATAATACACC 57.451 29.630 0.00 0.00 37.27 4.16
2590 4077 9.772973 GGACTTTTTGGAAAAATAATACACCTT 57.227 29.630 0.00 0.00 37.27 3.50
2610 4101 4.021016 CCTTATATTGAGGAACGGAGGGAG 60.021 50.000 0.00 0.00 36.33 4.30
2611 4102 2.544844 TATTGAGGAACGGAGGGAGT 57.455 50.000 0.00 0.00 0.00 3.85
2612 4103 2.544844 ATTGAGGAACGGAGGGAGTA 57.455 50.000 0.00 0.00 0.00 2.59
2613 4104 1.553706 TTGAGGAACGGAGGGAGTAC 58.446 55.000 0.00 0.00 0.00 2.73
2661 4152 2.495155 AATGTATCTGCAGTGCCACA 57.505 45.000 14.67 13.24 0.00 4.17
2713 4204 1.992667 CATGCACTACGTGTGGTACTG 59.007 52.381 16.33 0.00 46.27 2.74
2840 4338 0.101759 GCAACATAGCAGTGGCCATG 59.898 55.000 9.72 9.86 43.61 3.66
2849 4347 1.673626 GCAGTGGCCATGAAAATGTGG 60.674 52.381 9.72 0.00 38.55 4.17
2866 4388 2.991250 GTGGCATACACCAGAGATTGT 58.009 47.619 0.00 0.00 44.49 2.71
2867 4389 2.679837 GTGGCATACACCAGAGATTGTG 59.320 50.000 0.00 0.00 44.49 3.33
2868 4390 2.305635 TGGCATACACCAGAGATTGTGT 59.694 45.455 0.00 0.00 46.72 3.72
2869 4391 3.244875 TGGCATACACCAGAGATTGTGTT 60.245 43.478 0.19 0.00 42.82 3.32
2870 4392 3.127548 GGCATACACCAGAGATTGTGTTG 59.872 47.826 0.19 1.74 42.82 3.33
2871 4393 3.127548 GCATACACCAGAGATTGTGTTGG 59.872 47.826 0.19 0.00 42.82 3.77
2872 4394 2.276732 ACACCAGAGATTGTGTTGGG 57.723 50.000 0.00 0.00 42.82 4.12
2873 4395 1.494721 ACACCAGAGATTGTGTTGGGT 59.505 47.619 0.00 0.00 42.82 4.51
2874 4396 1.881973 CACCAGAGATTGTGTTGGGTG 59.118 52.381 0.00 0.00 38.43 4.61
2875 4397 0.883833 CCAGAGATTGTGTTGGGTGC 59.116 55.000 0.00 0.00 0.00 5.01
2876 4398 1.546323 CCAGAGATTGTGTTGGGTGCT 60.546 52.381 0.00 0.00 0.00 4.40
2877 4399 2.233271 CAGAGATTGTGTTGGGTGCTT 58.767 47.619 0.00 0.00 0.00 3.91
2878 4400 2.624838 CAGAGATTGTGTTGGGTGCTTT 59.375 45.455 0.00 0.00 0.00 3.51
2879 4401 3.068590 CAGAGATTGTGTTGGGTGCTTTT 59.931 43.478 0.00 0.00 0.00 2.27
2880 4402 3.706086 AGAGATTGTGTTGGGTGCTTTTT 59.294 39.130 0.00 0.00 0.00 1.94
2881 4403 4.051237 GAGATTGTGTTGGGTGCTTTTTC 58.949 43.478 0.00 0.00 0.00 2.29
2882 4404 3.706086 AGATTGTGTTGGGTGCTTTTTCT 59.294 39.130 0.00 0.00 0.00 2.52
2883 4405 3.971245 TTGTGTTGGGTGCTTTTTCTT 57.029 38.095 0.00 0.00 0.00 2.52
2884 4406 3.971245 TGTGTTGGGTGCTTTTTCTTT 57.029 38.095 0.00 0.00 0.00 2.52
2885 4407 3.594134 TGTGTTGGGTGCTTTTTCTTTG 58.406 40.909 0.00 0.00 0.00 2.77
2886 4408 2.351418 GTGTTGGGTGCTTTTTCTTTGC 59.649 45.455 0.00 0.00 0.00 3.68
2887 4409 1.592543 GTTGGGTGCTTTTTCTTTGCG 59.407 47.619 0.00 0.00 0.00 4.85
2888 4410 1.107114 TGGGTGCTTTTTCTTTGCGA 58.893 45.000 0.00 0.00 0.00 5.10
2889 4411 1.066908 TGGGTGCTTTTTCTTTGCGAG 59.933 47.619 0.00 0.00 0.00 5.03
2890 4412 1.602920 GGGTGCTTTTTCTTTGCGAGG 60.603 52.381 0.00 0.00 0.00 4.63
2951 4474 3.242712 GCCAACACAAAATCTTGTTCGTG 59.757 43.478 0.00 0.00 43.45 4.35
2952 4475 4.420168 CCAACACAAAATCTTGTTCGTGT 58.580 39.130 0.00 0.00 43.45 4.49
2953 4476 4.265085 CCAACACAAAATCTTGTTCGTGTG 59.735 41.667 0.00 0.00 43.45 3.82
2954 4477 4.695217 ACACAAAATCTTGTTCGTGTGT 57.305 36.364 1.57 1.57 43.45 3.72
2957 4480 5.923684 ACACAAAATCTTGTTCGTGTGTTTT 59.076 32.000 1.57 0.00 45.33 2.43
2958 4481 6.088883 ACACAAAATCTTGTTCGTGTGTTTTC 59.911 34.615 1.57 0.00 45.33 2.29
2959 4482 5.285134 ACAAAATCTTGTTCGTGTGTTTTCG 59.715 36.000 0.00 0.00 43.45 3.46
2960 4483 4.609691 AATCTTGTTCGTGTGTTTTCGT 57.390 36.364 0.00 0.00 0.00 3.85
2961 4484 3.377434 TCTTGTTCGTGTGTTTTCGTG 57.623 42.857 0.00 0.00 0.00 4.35
2962 4485 1.837747 CTTGTTCGTGTGTTTTCGTGC 59.162 47.619 0.00 0.00 0.00 5.34
2963 4486 0.247340 TGTTCGTGTGTTTTCGTGCG 60.247 50.000 0.00 0.00 0.00 5.34
2964 4487 0.247379 GTTCGTGTGTTTTCGTGCGT 60.247 50.000 0.00 0.00 0.00 5.24
2965 4488 1.006183 GTTCGTGTGTTTTCGTGCGTA 60.006 47.619 0.00 0.00 0.00 4.42
2966 4489 1.489574 TCGTGTGTTTTCGTGCGTAT 58.510 45.000 0.00 0.00 0.00 3.06
2967 4490 1.859703 TCGTGTGTTTTCGTGCGTATT 59.140 42.857 0.00 0.00 0.00 1.89
2968 4491 2.097299 TCGTGTGTTTTCGTGCGTATTC 60.097 45.455 0.00 0.00 0.00 1.75
2969 4492 2.219355 GTGTGTTTTCGTGCGTATTCG 58.781 47.619 0.00 0.00 40.37 3.34
2970 4493 2.097299 GTGTGTTTTCGTGCGTATTCGA 60.097 45.455 0.00 0.00 39.71 3.71
2971 4494 2.154198 TGTGTTTTCGTGCGTATTCGAG 59.846 45.455 0.00 0.00 39.71 4.04
2972 4495 2.406024 GTGTTTTCGTGCGTATTCGAGA 59.594 45.455 0.00 0.00 39.71 4.04
2973 4496 2.659757 TGTTTTCGTGCGTATTCGAGAG 59.340 45.455 0.00 0.00 39.71 3.20
2974 4497 2.905959 TTTCGTGCGTATTCGAGAGA 57.094 45.000 0.00 0.00 39.71 3.10
3012 4535 7.202016 TGTGTTCAATAGCTCGAATTTTCTT 57.798 32.000 0.00 0.00 0.00 2.52
3037 4560 8.842358 TGGGATTAAGTTTGACTTGTTACTAG 57.158 34.615 3.70 0.00 39.11 2.57
3115 4638 7.333528 ACAAAATTAATATGGATGACACGCT 57.666 32.000 6.23 0.00 0.00 5.07
3247 4771 1.256812 CATGGGTTCCCAGGTGAAAC 58.743 55.000 16.04 0.00 39.73 2.78
3261 4785 1.068816 GTGAAACCCCAATCGTTTCCG 60.069 52.381 10.09 0.00 45.52 4.30
3298 4822 1.578206 GCTCTTGCGTTGTCCCCTTC 61.578 60.000 0.00 0.00 0.00 3.46
3301 4825 1.695242 TCTTGCGTTGTCCCCTTCTTA 59.305 47.619 0.00 0.00 0.00 2.10
3308 4832 1.640917 TGTCCCCTTCTTAGAAGCGT 58.359 50.000 15.95 0.00 0.00 5.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 58 8.858094 GCTTGGACTAAATGGTACTACTACTAT 58.142 37.037 0.00 0.00 0.00 2.12
55 59 8.057623 AGCTTGGACTAAATGGTACTACTACTA 58.942 37.037 0.00 0.00 0.00 1.82
56 60 6.896307 AGCTTGGACTAAATGGTACTACTACT 59.104 38.462 0.00 0.00 0.00 2.57
57 61 7.110043 AGCTTGGACTAAATGGTACTACTAC 57.890 40.000 0.00 0.00 0.00 2.73
124 133 3.812577 CCGGCTGGGTCAAATTTTC 57.187 52.632 2.57 0.00 0.00 2.29
162 171 0.526096 GCCGCAAATTCGATGTGCAT 60.526 50.000 13.75 0.00 38.19 3.96
333 363 1.747355 GTATTCCTGTCGGTTCCTCGA 59.253 52.381 0.00 0.00 36.76 4.04
389 470 0.179094 AGTTGCGTCGTTGTTCTGGA 60.179 50.000 0.00 0.00 0.00 3.86
412 493 5.426689 ACGGATATACTCCTACATACGGA 57.573 43.478 0.00 0.00 42.47 4.69
424 589 3.433173 GGTTTGGGCTGAACGGATATACT 60.433 47.826 0.00 0.00 0.00 2.12
429 594 0.988832 TAGGTTTGGGCTGAACGGAT 59.011 50.000 0.00 0.00 0.00 4.18
479 644 1.673665 CTGGGAGTTGGTGAGCAGC 60.674 63.158 0.00 0.00 0.00 5.25
537 707 2.639286 GTTGACAGTGCCGCTTGG 59.361 61.111 0.00 0.00 0.00 3.61
581 778 1.073722 CACCCACATCACACTGGCT 59.926 57.895 0.00 0.00 0.00 4.75
582 779 1.973281 CCACCCACATCACACTGGC 60.973 63.158 0.00 0.00 0.00 4.85
583 780 0.606401 GACCACCCACATCACACTGG 60.606 60.000 0.00 0.00 0.00 4.00
584 781 0.397941 AGACCACCCACATCACACTG 59.602 55.000 0.00 0.00 0.00 3.66
585 782 0.397941 CAGACCACCCACATCACACT 59.602 55.000 0.00 0.00 0.00 3.55
586 783 1.237285 GCAGACCACCCACATCACAC 61.237 60.000 0.00 0.00 0.00 3.82
587 784 1.073025 GCAGACCACCCACATCACA 59.927 57.895 0.00 0.00 0.00 3.58
588 785 0.674895 GAGCAGACCACCCACATCAC 60.675 60.000 0.00 0.00 0.00 3.06
589 786 1.679311 GAGCAGACCACCCACATCA 59.321 57.895 0.00 0.00 0.00 3.07
590 787 1.448540 CGAGCAGACCACCCACATC 60.449 63.158 0.00 0.00 0.00 3.06
591 788 1.913262 TCGAGCAGACCACCCACAT 60.913 57.895 0.00 0.00 0.00 3.21
592 789 2.523168 TCGAGCAGACCACCCACA 60.523 61.111 0.00 0.00 0.00 4.17
593 790 2.048127 GTCGAGCAGACCACCCAC 60.048 66.667 1.39 0.00 43.95 4.61
748 2174 9.052759 GGGCGAAAGTTATGATTTCTCTAATAA 57.947 33.333 0.00 0.00 35.05 1.40
749 2175 8.208224 TGGGCGAAAGTTATGATTTCTCTAATA 58.792 33.333 0.00 0.00 35.05 0.98
750 2176 7.054124 TGGGCGAAAGTTATGATTTCTCTAAT 58.946 34.615 0.00 0.00 35.05 1.73
751 2177 6.411376 TGGGCGAAAGTTATGATTTCTCTAA 58.589 36.000 0.00 0.00 35.05 2.10
752 2178 5.984725 TGGGCGAAAGTTATGATTTCTCTA 58.015 37.500 0.00 0.00 35.05 2.43
753 2179 4.843728 TGGGCGAAAGTTATGATTTCTCT 58.156 39.130 0.00 0.00 35.05 3.10
767 2193 8.647796 TCTCTAATAATTATCTTCTGGGCGAAA 58.352 33.333 0.00 0.00 0.00 3.46
771 2197 9.950496 TGATTCTCTAATAATTATCTTCTGGGC 57.050 33.333 0.00 0.00 0.00 5.36
892 2350 7.442364 GCTGTTAGCTAAAATCATCCAGTGATA 59.558 37.037 7.99 0.00 41.52 2.15
982 2440 2.186160 TGGCGACAAGTGCAAGGTG 61.186 57.895 0.00 0.00 37.44 4.00
1323 2781 1.451927 GGGCTTCATCGGCATGACA 60.452 57.895 0.00 0.00 38.86 3.58
1347 2805 3.154787 TGCAAGCTCAGCACCTCT 58.845 55.556 9.50 0.00 37.02 3.69
1476 2934 1.527433 GGAAGAAGTTGCTGGTGGCC 61.527 60.000 0.00 0.00 40.92 5.36
1555 3013 1.810755 GCGTGGTTTAAAGAAGGAGGG 59.189 52.381 0.00 0.00 0.00 4.30
1584 3042 0.601558 GGTGCTCGTACTCAACCTGA 59.398 55.000 0.00 0.00 0.00 3.86
1660 3118 4.129737 CACGTCGCCGTCCCTGAT 62.130 66.667 0.00 0.00 46.28 2.90
2124 3600 3.670637 GATCCGCAGCCAGCTGTCA 62.671 63.158 20.11 5.75 45.24 3.58
2390 3877 8.519526 TCAAACATAGACAACAGTTGACTTTTT 58.480 29.630 20.98 15.03 36.98 1.94
2391 3878 7.968405 GTCAAACATAGACAACAGTTGACTTTT 59.032 33.333 20.98 13.60 36.98 2.27
2392 3879 7.415206 GGTCAAACATAGACAACAGTTGACTTT 60.415 37.037 20.98 12.16 36.98 2.66
2400 3887 6.377327 AAGTTGGTCAAACATAGACAACAG 57.623 37.500 0.00 0.00 41.61 3.16
2402 3889 7.699566 TGTAAAGTTGGTCAAACATAGACAAC 58.300 34.615 0.00 0.00 41.61 3.32
2404 3891 6.017440 GCTGTAAAGTTGGTCAAACATAGACA 60.017 38.462 0.00 0.00 41.61 3.41
2405 3892 6.017440 TGCTGTAAAGTTGGTCAAACATAGAC 60.017 38.462 0.00 0.00 41.61 2.59
2406 3893 6.058833 TGCTGTAAAGTTGGTCAAACATAGA 58.941 36.000 0.00 0.00 41.61 1.98
2408 3895 6.701145 TTGCTGTAAAGTTGGTCAAACATA 57.299 33.333 0.00 0.00 41.61 2.29
2410 3897 5.392767 TTTGCTGTAAAGTTGGTCAAACA 57.607 34.783 0.00 0.00 41.61 2.83
2533 4020 9.485206 TCTGTAAGTTTGACCAAGTTTATAGAC 57.515 33.333 0.00 0.00 33.76 2.59
2536 4023 9.841295 ACTTCTGTAAGTTTGACCAAGTTTATA 57.159 29.630 0.00 0.00 43.60 0.98
2555 4042 5.993748 TTTCCAAAAAGTCCAACTTCTGT 57.006 34.783 0.00 0.00 37.47 3.41
2556 4043 7.848223 ATTTTTCCAAAAAGTCCAACTTCTG 57.152 32.000 3.74 0.00 40.78 3.02
2562 4049 9.549078 GGTGTATTATTTTTCCAAAAAGTCCAA 57.451 29.630 3.74 0.00 40.78 3.53
2564 4051 9.772973 AAGGTGTATTATTTTTCCAAAAAGTCC 57.227 29.630 3.74 0.00 40.78 3.85
2578 4065 9.720769 CCGTTCCTCAATATAAGGTGTATTATT 57.279 33.333 4.45 0.00 35.29 1.40
2579 4066 9.096823 TCCGTTCCTCAATATAAGGTGTATTAT 57.903 33.333 4.45 0.00 35.29 1.28
2581 4068 7.369551 TCCGTTCCTCAATATAAGGTGTATT 57.630 36.000 4.45 0.00 35.29 1.89
2585 4072 4.503296 CCCTCCGTTCCTCAATATAAGGTG 60.503 50.000 4.45 0.00 35.29 4.00
2587 4074 3.901844 TCCCTCCGTTCCTCAATATAAGG 59.098 47.826 0.00 0.00 35.05 2.69
2588 4075 4.589374 ACTCCCTCCGTTCCTCAATATAAG 59.411 45.833 0.00 0.00 0.00 1.73
2590 4077 4.194678 ACTCCCTCCGTTCCTCAATATA 57.805 45.455 0.00 0.00 0.00 0.86
2591 4078 3.047695 ACTCCCTCCGTTCCTCAATAT 57.952 47.619 0.00 0.00 0.00 1.28
2592 4079 2.544844 ACTCCCTCCGTTCCTCAATA 57.455 50.000 0.00 0.00 0.00 1.90
2594 4081 1.076677 AGTACTCCCTCCGTTCCTCAA 59.923 52.381 0.00 0.00 0.00 3.02
2595 4082 0.702902 AGTACTCCCTCCGTTCCTCA 59.297 55.000 0.00 0.00 0.00 3.86
2596 4083 1.477295 CAAGTACTCCCTCCGTTCCTC 59.523 57.143 0.00 0.00 0.00 3.71
2601 4092 1.893801 CAAGACAAGTACTCCCTCCGT 59.106 52.381 0.00 0.00 0.00 4.69
2610 4101 7.012044 ACAACCATACTTTGACAAGACAAGTAC 59.988 37.037 0.63 0.00 33.72 2.73
2611 4102 7.051623 ACAACCATACTTTGACAAGACAAGTA 58.948 34.615 1.05 1.05 33.72 2.24
2612 4103 5.885912 ACAACCATACTTTGACAAGACAAGT 59.114 36.000 0.00 0.00 33.72 3.16
2613 4104 6.377327 ACAACCATACTTTGACAAGACAAG 57.623 37.500 0.00 0.00 33.72 3.16
2661 4152 5.930405 CACGCATGCAACACATATGTATAT 58.070 37.500 19.57 0.00 38.45 0.86
2713 4204 5.945144 TCTAACCCATACTCCTTTACCAC 57.055 43.478 0.00 0.00 0.00 4.16
2840 4338 4.009675 TCTCTGGTGTATGCCACATTTTC 58.990 43.478 0.00 0.00 46.44 2.29
2849 4347 3.127548 CCAACACAATCTCTGGTGTATGC 59.872 47.826 0.00 0.00 46.82 3.14
2866 4388 2.626840 GCAAAGAAAAAGCACCCAACA 58.373 42.857 0.00 0.00 0.00 3.33
2867 4389 1.592543 CGCAAAGAAAAAGCACCCAAC 59.407 47.619 0.00 0.00 0.00 3.77
2868 4390 1.478510 TCGCAAAGAAAAAGCACCCAA 59.521 42.857 0.00 0.00 0.00 4.12
2869 4391 1.066908 CTCGCAAAGAAAAAGCACCCA 59.933 47.619 0.00 0.00 0.00 4.51
2870 4392 1.602920 CCTCGCAAAGAAAAAGCACCC 60.603 52.381 0.00 0.00 0.00 4.61
2871 4393 1.067060 ACCTCGCAAAGAAAAAGCACC 59.933 47.619 0.00 0.00 0.00 5.01
2872 4394 2.119457 CACCTCGCAAAGAAAAAGCAC 58.881 47.619 0.00 0.00 0.00 4.40
2873 4395 1.748493 ACACCTCGCAAAGAAAAAGCA 59.252 42.857 0.00 0.00 0.00 3.91
2874 4396 2.119457 CACACCTCGCAAAGAAAAAGC 58.881 47.619 0.00 0.00 0.00 3.51
2875 4397 3.420839 ACACACCTCGCAAAGAAAAAG 57.579 42.857 0.00 0.00 0.00 2.27
2876 4398 3.314080 CCTACACACCTCGCAAAGAAAAA 59.686 43.478 0.00 0.00 0.00 1.94
2877 4399 2.875933 CCTACACACCTCGCAAAGAAAA 59.124 45.455 0.00 0.00 0.00 2.29
2878 4400 2.489971 CCTACACACCTCGCAAAGAAA 58.510 47.619 0.00 0.00 0.00 2.52
2879 4401 1.270625 CCCTACACACCTCGCAAAGAA 60.271 52.381 0.00 0.00 0.00 2.52
2880 4402 0.320374 CCCTACACACCTCGCAAAGA 59.680 55.000 0.00 0.00 0.00 2.52
2881 4403 0.034896 ACCCTACACACCTCGCAAAG 59.965 55.000 0.00 0.00 0.00 2.77
2882 4404 0.250124 CACCCTACACACCTCGCAAA 60.250 55.000 0.00 0.00 0.00 3.68
2883 4405 1.369692 CACCCTACACACCTCGCAA 59.630 57.895 0.00 0.00 0.00 4.85
2884 4406 3.056458 CACCCTACACACCTCGCA 58.944 61.111 0.00 0.00 0.00 5.10
2885 4407 2.434359 GCACCCTACACACCTCGC 60.434 66.667 0.00 0.00 0.00 5.03
2886 4408 0.034896 AAAGCACCCTACACACCTCG 59.965 55.000 0.00 0.00 0.00 4.63
2887 4409 1.071699 TGAAAGCACCCTACACACCTC 59.928 52.381 0.00 0.00 0.00 3.85
2888 4410 1.072331 CTGAAAGCACCCTACACACCT 59.928 52.381 0.00 0.00 0.00 4.00
2889 4411 1.202770 ACTGAAAGCACCCTACACACC 60.203 52.381 0.00 0.00 37.60 4.16
2890 4412 2.256117 ACTGAAAGCACCCTACACAC 57.744 50.000 0.00 0.00 37.60 3.82
2951 4474 2.406024 TCTCGAATACGCACGAAAACAC 59.594 45.455 0.00 0.00 38.05 3.32
2952 4475 2.659757 CTCTCGAATACGCACGAAAACA 59.340 45.455 0.00 0.00 38.05 2.83
2953 4476 2.912967 TCTCTCGAATACGCACGAAAAC 59.087 45.455 0.00 0.00 38.05 2.43
2954 4477 3.206034 TCTCTCGAATACGCACGAAAA 57.794 42.857 0.00 0.00 38.05 2.29
2957 4480 2.905959 TTTCTCTCGAATACGCACGA 57.094 45.000 0.00 0.00 39.58 4.35
2958 4481 3.965209 TTTTTCTCTCGAATACGCACG 57.035 42.857 0.00 0.00 39.58 5.34
2976 4499 9.807649 GAGCTATTGAACACATGGATAATTTTT 57.192 29.630 0.00 0.00 0.00 1.94
2977 4500 8.131100 CGAGCTATTGAACACATGGATAATTTT 58.869 33.333 0.00 0.00 0.00 1.82
2978 4501 7.498900 TCGAGCTATTGAACACATGGATAATTT 59.501 33.333 0.00 0.00 0.00 1.82
2979 4502 6.992123 TCGAGCTATTGAACACATGGATAATT 59.008 34.615 0.00 0.00 0.00 1.40
2987 4510 7.383102 AGAAAATTCGAGCTATTGAACACAT 57.617 32.000 0.00 0.00 31.46 3.21
3012 4535 8.653191 TCTAGTAACAAGTCAAACTTAATCCCA 58.347 33.333 0.00 0.00 36.03 4.37
3037 4560 5.934625 ACAGACCTATTCAACTTCATGTGTC 59.065 40.000 0.00 0.00 0.00 3.67
3094 4617 8.621532 ACATAGCGTGTCATCCATATTAATTT 57.378 30.769 0.00 0.00 35.77 1.82
3115 4638 7.102993 TCTCATTTTGACCGAAGATTGACATA 58.897 34.615 0.00 0.00 0.00 2.29
3178 4701 8.236586 GCACAAACATCATAAACATGAGACTTA 58.763 33.333 0.00 0.00 33.59 2.24
3261 4785 1.209127 CGTTGTCGCCACCAAATCC 59.791 57.895 0.00 0.00 0.00 3.01
3298 4822 2.159379 GCCCCATTTTCACGCTTCTAAG 60.159 50.000 0.00 0.00 0.00 2.18
3301 4825 0.251341 AGCCCCATTTTCACGCTTCT 60.251 50.000 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.