Multiple sequence alignment - TraesCS5A01G185400

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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 TraesCS5A01G185400 chr5A 100.000 2480 0 0 1 2480 385541908 385544387 0.000000e+00 4580
1 TraesCS5A01G185400 chr5B 91.759 1541 71 19 836 2368 333564220 333565712 0.000000e+00 2091
2 TraesCS5A01G185400 chr5B 95.000 140 7 0 679 818 333564096 333564235 1.150000e-53 220
3 TraesCS5A01G185400 chr5D 95.244 841 30 4 834 1666 292714169 292715007 0.000000e+00 1323
4 TraesCS5A01G185400 chr5D 94.337 618 23 6 1752 2368 292715121 292715727 0.000000e+00 937
5 TraesCS5A01G185400 chr5D 85.269 706 63 25 1 678 292713309 292714001 0.000000e+00 689
6 TraesCS5A01G185400 chr5D 98.571 140 2 0 679 818 292714047 292714186 5.300000e-62 248


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 TraesCS5A01G185400 chr5A 385541908 385544387 2479 False 4580.00 4580 100.00000 1 2480 1 chr5A.!!$F1 2479
1 TraesCS5A01G185400 chr5B 333564096 333565712 1616 False 1155.50 2091 93.37950 679 2368 2 chr5B.!!$F1 1689
2 TraesCS5A01G185400 chr5D 292713309 292715727 2418 False 799.25 1323 93.35525 1 2368 4 chr5D.!!$F1 2367

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
384 386 0.098728 GAGAGTGCGAGTGAGAGAGC 59.901 60.0 0.0 0.0 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2304 2451 0.682292 TGGTCACGATTGGCTGTACA 59.318 50.0 0.0 0.0 0.0 2.9 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 7.396055 CCTACATTCCAAATCTGAAACCCTAAA 59.604 37.037 0.00 0.00 0.00 1.85
31 32 8.096414 ACATTCCAAATCTGAAACCCTAAATTG 58.904 33.333 0.00 0.00 0.00 2.32
34 35 5.870978 CCAAATCTGAAACCCTAAATTGCAG 59.129 40.000 0.00 0.00 0.00 4.41
83 84 2.903135 GAGCTATAGAGGGGAATGCAGT 59.097 50.000 3.21 0.00 0.00 4.40
90 91 0.606401 AGGGGAATGCAGTTCACGTG 60.606 55.000 9.94 9.94 41.36 4.49
91 92 1.586154 GGGGAATGCAGTTCACGTGG 61.586 60.000 17.00 0.00 41.36 4.94
92 93 0.889186 GGGAATGCAGTTCACGTGGT 60.889 55.000 17.00 0.00 38.64 4.16
135 137 2.348998 GGCTCCTCCACCACACTG 59.651 66.667 0.00 0.00 34.01 3.66
148 150 2.046988 CACTGCAGGCGACATCCA 60.047 61.111 19.93 0.00 0.00 3.41
150 152 1.028330 CACTGCAGGCGACATCCATT 61.028 55.000 19.93 0.00 0.00 3.16
151 153 1.028330 ACTGCAGGCGACATCCATTG 61.028 55.000 19.93 0.00 0.00 2.82
152 154 0.745486 CTGCAGGCGACATCCATTGA 60.745 55.000 5.57 0.00 0.00 2.57
153 155 0.107066 TGCAGGCGACATCCATTGAT 60.107 50.000 0.00 0.00 0.00 2.57
175 177 2.117156 GGCAGTGGCAGCGATGAAT 61.117 57.895 12.58 0.00 43.71 2.57
176 178 1.063649 GCAGTGGCAGCGATGAATG 59.936 57.895 4.02 0.00 40.72 2.67
184 186 2.498167 GCAGCGATGAATGGAATAGGT 58.502 47.619 4.02 0.00 0.00 3.08
187 189 3.879295 CAGCGATGAATGGAATAGGTTGT 59.121 43.478 0.00 0.00 0.00 3.32
191 193 4.498009 CGATGAATGGAATAGGTTGTTGCC 60.498 45.833 0.00 0.00 0.00 4.52
252 254 3.492353 CCATCCGCCCCCATCTGT 61.492 66.667 0.00 0.00 0.00 3.41
261 263 0.256752 CCCCCATCTGTGCTTCATGA 59.743 55.000 0.00 0.00 0.00 3.07
267 269 3.560481 CCATCTGTGCTTCATGATCTGTC 59.440 47.826 0.00 0.00 0.00 3.51
275 277 0.988145 TCATGATCTGTCCCCACCCC 60.988 60.000 0.00 0.00 0.00 4.95
300 302 2.031516 GCCGATGGATCTGATGCCG 61.032 63.158 6.70 4.02 0.00 5.69
307 309 1.068083 GATCTGATGCCGCCTTCGA 59.932 57.895 0.00 0.00 38.10 3.71
308 310 0.320247 GATCTGATGCCGCCTTCGAT 60.320 55.000 0.00 0.00 38.10 3.59
340 342 2.586245 CCATGCCCTGCGAGAGAA 59.414 61.111 0.00 0.00 0.00 2.87
380 382 1.679305 GGGGAGAGTGCGAGTGAGA 60.679 63.158 0.00 0.00 0.00 3.27
384 386 0.098728 GAGAGTGCGAGTGAGAGAGC 59.901 60.000 0.00 0.00 0.00 4.09
385 387 0.607762 AGAGTGCGAGTGAGAGAGCA 60.608 55.000 0.00 0.00 37.26 4.26
392 394 2.202544 GTGAGAGAGCACGCTCGG 60.203 66.667 13.12 0.00 46.90 4.63
421 423 2.032528 CCCAGCCGCTTCTGACAA 59.967 61.111 0.00 0.00 36.19 3.18
422 424 1.600636 CCCAGCCGCTTCTGACAAA 60.601 57.895 0.00 0.00 36.19 2.83
424 426 1.208614 CAGCCGCTTCTGACAAAGC 59.791 57.895 10.51 10.51 46.54 3.51
433 445 2.595124 TCTGACAAAGCAGTCAACGA 57.405 45.000 7.83 1.43 46.90 3.85
436 448 0.928229 GACAAAGCAGTCAACGACGT 59.072 50.000 0.00 0.00 37.67 4.34
438 450 0.650512 CAAAGCAGTCAACGACGTGT 59.349 50.000 0.00 0.00 37.67 4.49
451 463 3.238241 CGTGTCGTCGCCGATGTC 61.238 66.667 6.17 1.10 46.30 3.06
499 511 3.936372 ACGTGCTTAGAAAGTAGCTCA 57.064 42.857 0.00 0.00 38.22 4.26
500 512 3.839293 ACGTGCTTAGAAAGTAGCTCAG 58.161 45.455 0.00 0.00 38.22 3.35
501 513 3.256136 ACGTGCTTAGAAAGTAGCTCAGT 59.744 43.478 0.00 0.00 38.22 3.41
502 514 3.610242 CGTGCTTAGAAAGTAGCTCAGTG 59.390 47.826 0.00 0.00 38.22 3.66
503 515 4.561105 GTGCTTAGAAAGTAGCTCAGTGT 58.439 43.478 0.00 0.00 38.22 3.55
537 549 4.218265 TGTCAAAAATTCGATGCAGTTCG 58.782 39.130 3.28 3.28 40.46 3.95
538 550 4.219033 GTCAAAAATTCGATGCAGTTCGT 58.781 39.130 9.37 0.00 40.03 3.85
547 574 4.989044 TCGATGCAGTTCGTAAAGTGATA 58.011 39.130 9.37 0.00 37.94 2.15
588 615 2.429971 ACAAATGTGGTGATTGTGTGCA 59.570 40.909 0.00 0.00 36.03 4.57
592 619 3.815856 TGTGGTGATTGTGTGCATTTT 57.184 38.095 0.00 0.00 0.00 1.82
593 620 3.455327 TGTGGTGATTGTGTGCATTTTG 58.545 40.909 0.00 0.00 0.00 2.44
594 621 2.221517 GTGGTGATTGTGTGCATTTTGC 59.778 45.455 0.00 0.00 45.29 3.68
599 626 4.618489 GTGATTGTGTGCATTTTGCTACTC 59.382 41.667 0.00 0.58 45.31 2.59
607 634 5.462729 TGTGCATTTTGCTACTCAATGTTTG 59.537 36.000 0.00 0.00 45.31 2.93
627 654 3.259064 TGTATGTAAACTCTCTTGGCGC 58.741 45.455 0.00 0.00 0.00 6.53
635 662 1.270147 ACTCTCTTGGCGCTAAAACGT 60.270 47.619 7.84 0.00 34.88 3.99
636 663 1.126846 CTCTCTTGGCGCTAAAACGTG 59.873 52.381 7.84 0.00 34.88 4.49
646 675 1.666189 GCTAAAACGTGCATCCTCTCC 59.334 52.381 0.00 0.00 0.00 3.71
801 875 2.263077 CACCAGCAGCTCGTTTAGTAG 58.737 52.381 0.00 0.00 0.00 2.57
802 876 1.893801 ACCAGCAGCTCGTTTAGTAGT 59.106 47.619 0.00 0.00 0.00 2.73
803 877 3.087031 ACCAGCAGCTCGTTTAGTAGTA 58.913 45.455 0.00 0.00 0.00 1.82
804 878 3.119566 ACCAGCAGCTCGTTTAGTAGTAC 60.120 47.826 0.00 0.00 0.00 2.73
805 879 3.128938 CCAGCAGCTCGTTTAGTAGTACT 59.871 47.826 8.14 8.14 0.00 2.73
806 880 4.334759 CCAGCAGCTCGTTTAGTAGTACTA 59.665 45.833 5.90 5.90 0.00 1.82
807 881 5.008811 CCAGCAGCTCGTTTAGTAGTACTAT 59.991 44.000 10.82 0.00 29.64 2.12
808 882 6.137415 CAGCAGCTCGTTTAGTAGTACTATC 58.863 44.000 10.82 6.85 29.64 2.08
809 883 5.821470 AGCAGCTCGTTTAGTAGTACTATCA 59.179 40.000 10.82 0.00 29.64 2.15
810 884 6.017770 AGCAGCTCGTTTAGTAGTACTATCAG 60.018 42.308 10.82 5.68 29.64 2.90
811 885 6.018098 GCAGCTCGTTTAGTAGTACTATCAGA 60.018 42.308 10.82 9.17 29.64 3.27
812 886 7.346695 CAGCTCGTTTAGTAGTACTATCAGAC 58.653 42.308 10.82 7.08 29.64 3.51
813 887 7.225145 CAGCTCGTTTAGTAGTACTATCAGACT 59.775 40.741 10.82 3.13 29.64 3.24
814 888 8.420222 AGCTCGTTTAGTAGTACTATCAGACTA 58.580 37.037 10.82 2.10 29.64 2.59
815 889 9.206870 GCTCGTTTAGTAGTACTATCAGACTAT 57.793 37.037 10.82 0.00 29.64 2.12
821 895 7.837202 AGTAGTACTATCAGACTATCATCGC 57.163 40.000 5.75 0.00 31.10 4.58
822 896 7.617225 AGTAGTACTATCAGACTATCATCGCT 58.383 38.462 5.75 0.00 31.10 4.93
823 897 6.978343 AGTACTATCAGACTATCATCGCTC 57.022 41.667 0.00 0.00 0.00 5.03
824 898 6.468543 AGTACTATCAGACTATCATCGCTCA 58.531 40.000 0.00 0.00 0.00 4.26
825 899 6.937465 AGTACTATCAGACTATCATCGCTCAA 59.063 38.462 0.00 0.00 0.00 3.02
826 900 6.641169 ACTATCAGACTATCATCGCTCAAA 57.359 37.500 0.00 0.00 0.00 2.69
827 901 7.043961 ACTATCAGACTATCATCGCTCAAAA 57.956 36.000 0.00 0.00 0.00 2.44
828 902 7.492524 ACTATCAGACTATCATCGCTCAAAAA 58.507 34.615 0.00 0.00 0.00 1.94
1024 1106 2.297597 CCTAGATCCTTCGTGATCACCC 59.702 54.545 20.03 0.00 42.95 4.61
1054 1136 2.202919 TGATCACCATGCTCGCCG 60.203 61.111 0.00 0.00 0.00 6.46
1179 1261 2.671963 GGAACGGGAACAGGTGGC 60.672 66.667 0.00 0.00 0.00 5.01
1485 1567 4.261781 CGGGCGCCGTAGAGTACC 62.262 72.222 22.54 1.28 42.73 3.34
1501 1583 7.114529 CGTAGAGTACCTTGTCTGTTTGTTAAG 59.885 40.741 0.00 0.00 0.00 1.85
1536 1618 4.461992 TTAGTTGCTACGAAGTGTTTGC 57.538 40.909 0.00 0.00 45.73 3.68
1666 1748 7.887996 AGCATATAGACTACAGAGTACGTAC 57.112 40.000 18.10 18.10 35.45 3.67
1667 1749 7.669427 AGCATATAGACTACAGAGTACGTACT 58.331 38.462 27.71 27.71 35.45 2.73
1682 1764 7.059202 AGTACGTACTCCCTTATATTTTGGG 57.941 40.000 22.45 0.00 42.20 4.12
1683 1765 6.840705 AGTACGTACTCCCTTATATTTTGGGA 59.159 38.462 22.45 8.98 46.78 4.37
1684 1766 5.922053 ACGTACTCCCTTATATTTTGGGAC 58.078 41.667 6.11 0.00 44.37 4.46
1685 1767 5.426185 ACGTACTCCCTTATATTTTGGGACA 59.574 40.000 6.11 0.00 44.37 4.02
1686 1768 5.989777 CGTACTCCCTTATATTTTGGGACAG 59.010 44.000 6.11 2.23 44.37 3.51
1687 1769 6.183360 CGTACTCCCTTATATTTTGGGACAGA 60.183 42.308 6.11 0.00 44.37 3.41
1688 1770 6.002653 ACTCCCTTATATTTTGGGACAGAC 57.997 41.667 6.11 0.00 44.37 3.51
1689 1771 5.031066 TCCCTTATATTTTGGGACAGACG 57.969 43.478 6.11 0.00 44.37 4.18
1690 1772 4.134563 CCCTTATATTTTGGGACAGACGG 58.865 47.826 0.00 0.00 43.47 4.79
1691 1773 4.141574 CCCTTATATTTTGGGACAGACGGA 60.142 45.833 0.00 0.00 43.47 4.69
1692 1774 5.057149 CCTTATATTTTGGGACAGACGGAG 58.943 45.833 0.00 0.00 42.39 4.63
1693 1775 8.320834 CCCTTATATTTTGGGACAGACGGAGT 62.321 46.154 0.00 0.00 44.45 3.85
1694 1776 9.046107 CCCTTATATTTTGGGACAGACGGAGTA 62.046 44.444 0.00 0.00 42.46 2.59
1709 1791 4.259356 ACGGAGTAATTTTGAAGGCTACC 58.741 43.478 0.00 0.00 41.94 3.18
1710 1792 3.308866 CGGAGTAATTTTGAAGGCTACCG 59.691 47.826 0.00 0.00 0.00 4.02
1718 1831 7.748691 AATTTTGAAGGCTACCGTTACTTTA 57.251 32.000 0.00 0.00 0.00 1.85
1780 1919 6.658831 TCAAAGTCTGTAATTTTCTGAAGCG 58.341 36.000 0.00 0.00 0.00 4.68
1782 1921 6.473397 AAGTCTGTAATTTTCTGAAGCGAG 57.527 37.500 0.00 0.00 0.00 5.03
1830 1969 2.900546 ACTGTACAGTTTCCCCTCTGAG 59.099 50.000 22.95 0.00 38.83 3.35
1917 2056 1.810151 GTTTCGTGCCAGCCTTTATCA 59.190 47.619 0.00 0.00 0.00 2.15
1937 2076 5.356882 TCAATCGATTGGTTTGTTGAGAC 57.643 39.130 32.03 0.00 38.30 3.36
2063 2202 4.040829 CCTTTTTGGGGCTCAATTTTCTCT 59.959 41.667 0.00 0.00 34.98 3.10
2086 2225 0.323451 AGGTTTTCGAGCCCAATCCC 60.323 55.000 0.00 0.00 0.00 3.85
2137 2277 3.944422 ACACGCCGATAATTGTTGATC 57.056 42.857 0.00 0.00 0.00 2.92
2163 2303 2.166459 TCGGCTGGTAAATCAGTGAGAG 59.834 50.000 0.00 0.00 37.12 3.20
2175 2315 9.178758 GTAAATCAGTGAGAGAAATTATTGGGT 57.821 33.333 0.00 0.00 0.00 4.51
2176 2316 8.655935 AAATCAGTGAGAGAAATTATTGGGTT 57.344 30.769 0.00 0.00 0.00 4.11
2177 2317 7.636150 ATCAGTGAGAGAAATTATTGGGTTG 57.364 36.000 0.00 0.00 0.00 3.77
2178 2318 6.778821 TCAGTGAGAGAAATTATTGGGTTGA 58.221 36.000 0.00 0.00 0.00 3.18
2201 2341 0.376152 ACGTACGTCATGGCGTAGAG 59.624 55.000 31.25 27.42 46.15 2.43
2253 2393 2.232696 TCTGGATGCTGCTTGTTACGTA 59.767 45.455 0.00 0.00 0.00 3.57
2254 2394 2.343101 TGGATGCTGCTTGTTACGTAC 58.657 47.619 0.00 0.00 0.00 3.67
2255 2395 1.323534 GGATGCTGCTTGTTACGTACG 59.676 52.381 15.01 15.01 0.00 3.67
2256 2396 1.990563 GATGCTGCTTGTTACGTACGT 59.009 47.619 25.98 25.98 0.00 3.57
2304 2451 3.321039 TCCTACCTGAAGGATCATGCAT 58.679 45.455 2.62 0.00 40.86 3.96
2338 2485 1.142060 TGACCACGGTTTTGGAGACAT 59.858 47.619 0.00 0.00 42.32 3.06
2368 2515 0.668535 GTTCGGCCTGCTTGTCTTTT 59.331 50.000 0.00 0.00 0.00 2.27
2369 2516 1.067060 GTTCGGCCTGCTTGTCTTTTT 59.933 47.619 0.00 0.00 0.00 1.94
2391 2538 6.622427 TTTTTAAACAAGGTCCTTTTGGGA 57.378 33.333 0.00 0.00 42.77 4.37
2402 2549 4.301072 TCCTTTTGGGACTCGATTCATT 57.699 40.909 5.06 0.00 39.58 2.57
2403 2550 5.429681 TCCTTTTGGGACTCGATTCATTA 57.570 39.130 5.06 0.00 39.58 1.90
2404 2551 5.811190 TCCTTTTGGGACTCGATTCATTAA 58.189 37.500 5.06 0.00 39.58 1.40
2405 2552 6.242396 TCCTTTTGGGACTCGATTCATTAAA 58.758 36.000 5.06 0.66 39.58 1.52
2406 2553 6.717540 TCCTTTTGGGACTCGATTCATTAAAA 59.282 34.615 5.06 7.66 39.58 1.52
2407 2554 7.231722 TCCTTTTGGGACTCGATTCATTAAAAA 59.768 33.333 5.06 5.02 39.58 1.94
2440 2587 8.992835 AAAAGAGAATGATCCTGTTAATTTGC 57.007 30.769 0.00 0.00 0.00 3.68
2441 2588 7.707624 AAGAGAATGATCCTGTTAATTTGCA 57.292 32.000 0.00 0.00 0.00 4.08
2442 2589 7.893124 AGAGAATGATCCTGTTAATTTGCAT 57.107 32.000 0.00 0.00 0.00 3.96
2443 2590 8.985315 AGAGAATGATCCTGTTAATTTGCATA 57.015 30.769 0.00 0.00 0.00 3.14
2444 2591 9.412460 AGAGAATGATCCTGTTAATTTGCATAA 57.588 29.630 0.00 0.00 0.00 1.90
2450 2597 9.381033 TGATCCTGTTAATTTGCATAAATTTGG 57.619 29.630 0.00 0.00 42.33 3.28
2451 2598 7.608308 TCCTGTTAATTTGCATAAATTTGGC 57.392 32.000 0.00 5.36 42.33 4.52
2452 2599 6.597280 TCCTGTTAATTTGCATAAATTTGGCC 59.403 34.615 12.37 0.00 42.33 5.36
2453 2600 6.373774 CCTGTTAATTTGCATAAATTTGGCCA 59.626 34.615 0.00 0.00 42.33 5.36
2454 2601 7.094463 CCTGTTAATTTGCATAAATTTGGCCAA 60.094 33.333 16.05 16.05 42.33 4.52
2455 2602 8.169977 TGTTAATTTGCATAAATTTGGCCAAA 57.830 26.923 32.12 32.12 42.33 3.28
2456 2603 8.632679 TGTTAATTTGCATAAATTTGGCCAAAA 58.367 25.926 33.43 18.78 42.33 2.44
2457 2604 9.468532 GTTAATTTGCATAAATTTGGCCAAAAA 57.531 25.926 33.43 21.74 42.33 1.94
2458 2605 7.943413 AATTTGCATAAATTTGGCCAAAAAC 57.057 28.000 33.43 18.67 42.33 2.43
2459 2606 6.705863 TTTGCATAAATTTGGCCAAAAACT 57.294 29.167 33.43 21.83 33.56 2.66
2460 2607 5.686159 TGCATAAATTTGGCCAAAAACTG 57.314 34.783 33.43 25.60 33.56 3.16
2461 2608 5.128919 TGCATAAATTTGGCCAAAAACTGT 58.871 33.333 33.43 15.92 33.56 3.55
2462 2609 5.591877 TGCATAAATTTGGCCAAAAACTGTT 59.408 32.000 33.43 20.13 33.56 3.16
2463 2610 6.767902 TGCATAAATTTGGCCAAAAACTGTTA 59.232 30.769 33.43 23.31 33.56 2.41
2464 2611 7.075121 GCATAAATTTGGCCAAAAACTGTTAC 58.925 34.615 33.43 15.58 33.56 2.50
2465 2612 7.254932 GCATAAATTTGGCCAAAAACTGTTACA 60.255 33.333 33.43 14.64 33.56 2.41
2466 2613 8.616076 CATAAATTTGGCCAAAAACTGTTACAA 58.384 29.630 33.43 12.73 33.56 2.41
2467 2614 6.429791 AATTTGGCCAAAAACTGTTACAAC 57.570 33.333 33.43 0.00 33.56 3.32
2468 2615 4.537135 TTGGCCAAAAACTGTTACAACA 57.463 36.364 17.98 0.00 37.37 3.33
2469 2616 3.851098 TGGCCAAAAACTGTTACAACAC 58.149 40.909 0.61 0.00 34.70 3.32
2470 2617 2.855370 GGCCAAAAACTGTTACAACACG 59.145 45.455 0.00 0.00 34.70 4.49
2471 2618 3.503891 GCCAAAAACTGTTACAACACGT 58.496 40.909 0.00 0.00 34.70 4.49
2472 2619 3.544682 GCCAAAAACTGTTACAACACGTC 59.455 43.478 0.00 0.00 34.70 4.34
2473 2620 4.099824 CCAAAAACTGTTACAACACGTCC 58.900 43.478 0.00 0.00 34.70 4.79
2474 2621 4.379603 CCAAAAACTGTTACAACACGTCCA 60.380 41.667 0.00 0.00 34.70 4.02
2475 2622 5.336744 CAAAAACTGTTACAACACGTCCAT 58.663 37.500 0.00 0.00 34.70 3.41
2476 2623 6.458478 CCAAAAACTGTTACAACACGTCCATA 60.458 38.462 0.00 0.00 34.70 2.74
2477 2624 5.917541 AAACTGTTACAACACGTCCATAG 57.082 39.130 0.00 0.00 34.70 2.23
2478 2625 4.859304 ACTGTTACAACACGTCCATAGA 57.141 40.909 0.00 0.00 34.70 1.98
2479 2626 5.204409 ACTGTTACAACACGTCCATAGAA 57.796 39.130 0.00 0.00 34.70 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 5.264395 AGGGTTTCAGATTTGGAATGTAGG 58.736 41.667 0.00 0.00 0.00 3.18
7 8 7.105588 GCAATTTAGGGTTTCAGATTTGGAAT 58.894 34.615 0.00 0.00 0.00 3.01
10 11 5.792741 TGCAATTTAGGGTTTCAGATTTGG 58.207 37.500 0.00 0.00 0.00 3.28
17 18 4.282957 TCATTGCTGCAATTTAGGGTTTCA 59.717 37.500 24.28 0.00 31.05 2.69
28 29 8.644216 TCTTTATATCCATTTCATTGCTGCAAT 58.356 29.630 21.48 21.48 34.04 3.56
31 32 7.879070 TCTCTTTATATCCATTTCATTGCTGC 58.121 34.615 0.00 0.00 0.00 5.25
34 35 7.094032 CCCCTCTCTTTATATCCATTTCATTGC 60.094 40.741 0.00 0.00 0.00 3.56
132 134 1.028330 CAATGGATGTCGCCTGCAGT 61.028 55.000 13.81 0.00 0.00 4.40
135 137 0.309922 CATCAATGGATGTCGCCTGC 59.690 55.000 1.46 0.00 44.79 4.85
148 150 1.304630 TGCCACTGCCAGCATCAAT 60.305 52.632 0.00 0.00 36.33 2.57
150 152 2.360726 CTGCCACTGCCAGCATCA 60.361 61.111 0.00 0.00 38.56 3.07
151 153 3.823330 GCTGCCACTGCCAGCATC 61.823 66.667 7.12 0.00 39.71 3.91
155 157 3.506096 CATCGCTGCCACTGCCAG 61.506 66.667 0.00 0.00 36.33 4.85
167 169 4.601019 CAACAACCTATTCCATTCATCGC 58.399 43.478 0.00 0.00 0.00 4.58
175 177 0.250945 TGCGGCAACAACCTATTCCA 60.251 50.000 0.00 0.00 0.00 3.53
176 178 0.451783 CTGCGGCAACAACCTATTCC 59.548 55.000 3.44 0.00 0.00 3.01
191 193 1.150567 CGAGGAGGAAGATTGCTGCG 61.151 60.000 0.25 0.00 41.64 5.18
216 218 4.572571 GGTGTTGCGGGGTGGACA 62.573 66.667 0.00 0.00 0.00 4.02
252 254 1.065199 GTGGGGACAGATCATGAAGCA 60.065 52.381 0.00 0.00 44.46 3.91
284 286 2.031516 GGCGGCATCAGATCCATCG 61.032 63.158 3.07 0.00 0.00 3.84
293 295 0.969149 ATCTATCGAAGGCGGCATCA 59.031 50.000 13.08 0.00 38.28 3.07
300 302 1.079750 GGCGGGATCTATCGAAGGC 60.080 63.158 0.00 0.00 0.00 4.35
307 309 3.681835 GGCGACGGCGGGATCTAT 61.682 66.667 15.06 0.00 41.24 1.98
330 332 1.753649 TCTCCCTCATTTCTCTCGCAG 59.246 52.381 0.00 0.00 0.00 5.18
334 336 3.255642 CCTCGATCTCCCTCATTTCTCTC 59.744 52.174 0.00 0.00 0.00 3.20
340 342 1.418334 CCACCTCGATCTCCCTCATT 58.582 55.000 0.00 0.00 0.00 2.57
380 382 2.172483 AATGAACCCGAGCGTGCTCT 62.172 55.000 18.79 0.69 40.69 4.09
384 386 3.486263 GGAATGAACCCGAGCGTG 58.514 61.111 0.00 0.00 0.00 5.34
421 423 1.206745 CGACACGTCGTTGACTGCTT 61.207 55.000 11.35 0.00 46.99 3.91
422 424 1.657487 CGACACGTCGTTGACTGCT 60.657 57.895 11.35 0.00 46.99 4.24
445 457 4.271816 CCTCTCGGGCCGACATCG 62.272 72.222 27.46 16.00 39.44 3.84
456 468 0.179134 GACGTGGTTGATCCCTCTCG 60.179 60.000 0.00 0.00 34.77 4.04
509 521 4.036144 TGCATCGAATTTTTGACAGTGACA 59.964 37.500 0.00 0.00 0.00 3.58
528 540 5.086104 ACCTATCACTTTACGAACTGCAT 57.914 39.130 0.00 0.00 0.00 3.96
592 619 8.615878 AGTTTACATACAAACATTGAGTAGCA 57.384 30.769 0.00 0.00 40.22 3.49
593 620 8.936864 AGAGTTTACATACAAACATTGAGTAGC 58.063 33.333 0.00 0.00 40.22 3.58
599 626 7.538678 GCCAAGAGAGTTTACATACAAACATTG 59.461 37.037 1.99 0.00 40.22 2.82
607 634 3.522553 AGCGCCAAGAGAGTTTACATAC 58.477 45.455 2.29 0.00 0.00 2.39
627 654 2.280628 GGGAGAGGATGCACGTTTTAG 58.719 52.381 0.00 0.00 0.00 1.85
635 662 4.147449 CGTGCGGGAGAGGATGCA 62.147 66.667 0.00 0.00 34.44 3.96
653 682 2.558795 CGAGATAGGTATGACCCCACAG 59.441 54.545 0.00 0.00 39.75 3.66
801 875 6.729391 TGAGCGATGATAGTCTGATAGTAC 57.271 41.667 0.00 0.00 0.00 2.73
802 876 7.745620 TTTGAGCGATGATAGTCTGATAGTA 57.254 36.000 0.00 0.00 0.00 1.82
803 877 6.641169 TTTGAGCGATGATAGTCTGATAGT 57.359 37.500 0.00 0.00 0.00 2.12
804 878 7.936950 TTTTTGAGCGATGATAGTCTGATAG 57.063 36.000 0.00 0.00 0.00 2.08
829 903 9.869667 ACACCTGATAGTCTGATACTACTTTAT 57.130 33.333 0.00 0.00 43.47 1.40
830 904 9.339850 GACACCTGATAGTCTGATACTACTTTA 57.660 37.037 0.00 0.00 43.47 1.85
831 905 7.285858 GGACACCTGATAGTCTGATACTACTTT 59.714 40.741 0.00 0.00 43.47 2.66
832 906 6.773685 GGACACCTGATAGTCTGATACTACTT 59.226 42.308 0.00 0.00 43.47 2.24
914 988 5.464722 AGAGCGCACTGAATATTTGATACTG 59.535 40.000 11.47 0.00 0.00 2.74
979 1055 0.314738 GTTGCGTACGTGTGTGTGTG 60.315 55.000 17.90 0.00 0.00 3.82
982 1058 0.531090 ATGGTTGCGTACGTGTGTGT 60.531 50.000 17.90 0.00 0.00 3.72
983 1059 0.110867 CATGGTTGCGTACGTGTGTG 60.111 55.000 17.90 5.26 0.00 3.82
1485 1567 5.036737 CACCTTGCTTAACAAACAGACAAG 58.963 41.667 0.00 0.00 37.96 3.16
1501 1583 3.004734 AGCAACTAATCAACACACCTTGC 59.995 43.478 0.00 0.00 34.32 4.01
1536 1618 6.991485 AAACAACATTGCAATTAACGAGAG 57.009 33.333 9.83 0.00 0.00 3.20
1668 1750 4.134563 CCGTCTGTCCCAAAATATAAGGG 58.865 47.826 0.00 0.00 44.22 3.95
1669 1751 5.031066 TCCGTCTGTCCCAAAATATAAGG 57.969 43.478 0.00 0.00 0.00 2.69
1670 1752 5.671493 ACTCCGTCTGTCCCAAAATATAAG 58.329 41.667 0.00 0.00 0.00 1.73
1671 1753 5.687166 ACTCCGTCTGTCCCAAAATATAA 57.313 39.130 0.00 0.00 0.00 0.98
1672 1754 6.795144 TTACTCCGTCTGTCCCAAAATATA 57.205 37.500 0.00 0.00 0.00 0.86
1673 1755 5.687166 TTACTCCGTCTGTCCCAAAATAT 57.313 39.130 0.00 0.00 0.00 1.28
1674 1756 5.687166 ATTACTCCGTCTGTCCCAAAATA 57.313 39.130 0.00 0.00 0.00 1.40
1675 1757 4.569719 ATTACTCCGTCTGTCCCAAAAT 57.430 40.909 0.00 0.00 0.00 1.82
1676 1758 4.360951 AATTACTCCGTCTGTCCCAAAA 57.639 40.909 0.00 0.00 0.00 2.44
1677 1759 4.360951 AAATTACTCCGTCTGTCCCAAA 57.639 40.909 0.00 0.00 0.00 3.28
1678 1760 4.069304 CAAAATTACTCCGTCTGTCCCAA 58.931 43.478 0.00 0.00 0.00 4.12
1679 1761 3.325425 TCAAAATTACTCCGTCTGTCCCA 59.675 43.478 0.00 0.00 0.00 4.37
1680 1762 3.934068 TCAAAATTACTCCGTCTGTCCC 58.066 45.455 0.00 0.00 0.00 4.46
1681 1763 4.392138 CCTTCAAAATTACTCCGTCTGTCC 59.608 45.833 0.00 0.00 0.00 4.02
1682 1764 4.142881 GCCTTCAAAATTACTCCGTCTGTC 60.143 45.833 0.00 0.00 0.00 3.51
1683 1765 3.751698 GCCTTCAAAATTACTCCGTCTGT 59.248 43.478 0.00 0.00 0.00 3.41
1684 1766 4.003648 AGCCTTCAAAATTACTCCGTCTG 58.996 43.478 0.00 0.00 0.00 3.51
1685 1767 4.287766 AGCCTTCAAAATTACTCCGTCT 57.712 40.909 0.00 0.00 0.00 4.18
1686 1768 4.331992 GGTAGCCTTCAAAATTACTCCGTC 59.668 45.833 0.00 0.00 0.00 4.79
1687 1769 4.259356 GGTAGCCTTCAAAATTACTCCGT 58.741 43.478 0.00 0.00 0.00 4.69
1688 1770 3.308866 CGGTAGCCTTCAAAATTACTCCG 59.691 47.826 0.00 0.00 0.00 4.63
1689 1771 4.259356 ACGGTAGCCTTCAAAATTACTCC 58.741 43.478 0.00 0.00 0.00 3.85
1690 1772 5.874895 AACGGTAGCCTTCAAAATTACTC 57.125 39.130 0.00 0.00 0.00 2.59
1691 1773 6.470278 AGTAACGGTAGCCTTCAAAATTACT 58.530 36.000 0.00 0.00 0.00 2.24
1692 1774 6.732531 AGTAACGGTAGCCTTCAAAATTAC 57.267 37.500 0.00 0.00 0.00 1.89
1693 1775 7.748691 AAAGTAACGGTAGCCTTCAAAATTA 57.251 32.000 0.00 0.00 0.00 1.40
1694 1776 6.644248 AAAGTAACGGTAGCCTTCAAAATT 57.356 33.333 0.00 0.00 0.00 1.82
1757 1896 6.658831 TCGCTTCAGAAAATTACAGACTTTG 58.341 36.000 0.00 0.00 0.00 2.77
1830 1969 1.671328 GAAAGCGCCTTTCTGTATCCC 59.329 52.381 18.85 0.00 44.33 3.85
1917 2056 3.813166 ACGTCTCAACAAACCAATCGATT 59.187 39.130 4.39 4.39 0.00 3.34
1937 2076 5.408299 TGAGTTGAATGTACAGATTTGGACG 59.592 40.000 0.33 0.00 41.35 4.79
2063 2202 3.606687 GATTGGGCTCGAAAACCTCTTA 58.393 45.455 0.00 0.00 0.00 2.10
2086 2225 2.351418 TCACTCGGCTTGAAATAATGCG 59.649 45.455 0.00 0.00 0.00 4.73
2137 2277 0.874175 TGATTTACCAGCCGATCGCG 60.874 55.000 10.32 0.00 44.76 5.87
2163 2303 6.685403 CGTACGTCAATCAACCCAATAATTTC 59.315 38.462 7.22 0.00 0.00 2.17
2201 2341 1.725164 GTCCGACGTTGTTCTCAATCC 59.275 52.381 1.30 0.00 35.92 3.01
2253 2393 0.946221 GCAGCTTGCACTACTGACGT 60.946 55.000 12.70 0.00 44.26 4.34
2254 2394 1.784062 GCAGCTTGCACTACTGACG 59.216 57.895 12.70 0.00 44.26 4.35
2255 2395 1.784062 CGCAGCTTGCACTACTGAC 59.216 57.895 12.70 4.73 45.36 3.51
2256 2396 4.266983 CGCAGCTTGCACTACTGA 57.733 55.556 12.70 0.00 45.36 3.41
2304 2451 0.682292 TGGTCACGATTGGCTGTACA 59.318 50.000 0.00 0.00 0.00 2.90
2338 2485 1.133598 CAGGCCGAACGTCACTATACA 59.866 52.381 0.00 0.00 0.00 2.29
2368 2515 6.622427 TCCCAAAAGGACCTTGTTTAAAAA 57.378 33.333 7.72 0.00 40.93 1.94
2381 2528 4.301072 AATGAATCGAGTCCCAAAAGGA 57.699 40.909 10.80 0.00 44.91 3.36
2382 2529 6.509418 TTTAATGAATCGAGTCCCAAAAGG 57.491 37.500 10.80 0.00 0.00 3.11
2415 2562 8.587608 TGCAAATTAACAGGATCATTCTCTTTT 58.412 29.630 0.00 0.00 0.00 2.27
2416 2563 8.125978 TGCAAATTAACAGGATCATTCTCTTT 57.874 30.769 0.00 0.00 0.00 2.52
2417 2564 7.707624 TGCAAATTAACAGGATCATTCTCTT 57.292 32.000 0.00 0.00 0.00 2.85
2418 2565 7.893124 ATGCAAATTAACAGGATCATTCTCT 57.107 32.000 0.00 0.00 0.00 3.10
2424 2571 9.381033 CCAAATTTATGCAAATTAACAGGATCA 57.619 29.630 0.00 0.00 42.29 2.92
2425 2572 8.337532 GCCAAATTTATGCAAATTAACAGGATC 58.662 33.333 0.00 0.00 42.29 3.36
2426 2573 7.282901 GGCCAAATTTATGCAAATTAACAGGAT 59.717 33.333 0.00 0.00 42.29 3.24
2427 2574 6.597280 GGCCAAATTTATGCAAATTAACAGGA 59.403 34.615 0.00 0.00 42.29 3.86
2428 2575 6.373774 TGGCCAAATTTATGCAAATTAACAGG 59.626 34.615 0.61 0.00 42.29 4.00
2429 2576 7.375106 TGGCCAAATTTATGCAAATTAACAG 57.625 32.000 0.61 0.00 42.29 3.16
2430 2577 7.750229 TTGGCCAAATTTATGCAAATTAACA 57.250 28.000 17.98 0.00 42.29 2.41
2431 2578 9.468532 TTTTTGGCCAAATTTATGCAAATTAAC 57.531 25.926 30.78 0.00 42.29 2.01
2432 2579 9.468532 GTTTTTGGCCAAATTTATGCAAATTAA 57.531 25.926 30.78 14.48 42.29 1.40
2433 2580 8.854117 AGTTTTTGGCCAAATTTATGCAAATTA 58.146 25.926 30.78 8.98 42.29 1.40
2434 2581 7.652507 CAGTTTTTGGCCAAATTTATGCAAATT 59.347 29.630 30.78 13.50 44.45 1.82
2435 2582 7.146648 CAGTTTTTGGCCAAATTTATGCAAAT 58.853 30.769 30.78 16.47 35.84 2.32
2436 2583 6.096001 ACAGTTTTTGGCCAAATTTATGCAAA 59.904 30.769 30.78 16.61 0.00 3.68
2437 2584 5.591877 ACAGTTTTTGGCCAAATTTATGCAA 59.408 32.000 30.78 17.33 0.00 4.08
2438 2585 5.128919 ACAGTTTTTGGCCAAATTTATGCA 58.871 33.333 30.78 12.04 0.00 3.96
2439 2586 5.687770 ACAGTTTTTGGCCAAATTTATGC 57.312 34.783 30.78 16.34 0.00 3.14
2440 2587 8.147642 TGTAACAGTTTTTGGCCAAATTTATG 57.852 30.769 30.78 25.41 0.00 1.90
2441 2588 8.616942 GTTGTAACAGTTTTTGGCCAAATTTAT 58.383 29.630 30.78 16.93 0.00 1.40
2442 2589 7.606456 TGTTGTAACAGTTTTTGGCCAAATTTA 59.394 29.630 30.78 14.37 34.30 1.40
2443 2590 6.431234 TGTTGTAACAGTTTTTGGCCAAATTT 59.569 30.769 30.78 19.34 34.30 1.82
2444 2591 5.940470 TGTTGTAACAGTTTTTGGCCAAATT 59.060 32.000 30.78 22.56 34.30 1.82
2445 2592 5.352846 GTGTTGTAACAGTTTTTGGCCAAAT 59.647 36.000 30.78 17.40 40.05 2.32
2446 2593 4.691216 GTGTTGTAACAGTTTTTGGCCAAA 59.309 37.500 27.13 27.13 40.05 3.28
2447 2594 4.246458 GTGTTGTAACAGTTTTTGGCCAA 58.754 39.130 16.05 16.05 40.05 4.52
2448 2595 3.673594 CGTGTTGTAACAGTTTTTGGCCA 60.674 43.478 0.00 0.00 40.05 5.36
2449 2596 2.855370 CGTGTTGTAACAGTTTTTGGCC 59.145 45.455 0.00 0.00 40.05 5.36
2450 2597 3.503891 ACGTGTTGTAACAGTTTTTGGC 58.496 40.909 0.00 0.00 40.05 4.52
2451 2598 4.099824 GGACGTGTTGTAACAGTTTTTGG 58.900 43.478 0.00 0.00 40.05 3.28
2452 2599 4.724303 TGGACGTGTTGTAACAGTTTTTG 58.276 39.130 0.00 0.00 40.05 2.44
2453 2600 5.570234 ATGGACGTGTTGTAACAGTTTTT 57.430 34.783 0.00 0.00 40.05 1.94
2454 2601 6.050432 TCTATGGACGTGTTGTAACAGTTTT 58.950 36.000 0.00 0.00 40.05 2.43
2455 2602 5.603596 TCTATGGACGTGTTGTAACAGTTT 58.396 37.500 0.00 0.00 40.05 2.66
2456 2603 5.204409 TCTATGGACGTGTTGTAACAGTT 57.796 39.130 0.00 0.00 40.05 3.16
2457 2604 4.859304 TCTATGGACGTGTTGTAACAGT 57.141 40.909 0.00 0.00 40.05 3.55


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

AutoCloner maintained by Alex Coulton.