Multiple sequence alignment - TraesCS6B01G275100

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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 TraesCS6B01G275100 chr6B 100.000 2315 0 0 1 2315 497217751 497215437 0.000000e+00 4276.0
1 TraesCS6B01G275100 chr6B 100.000 386 0 0 2535 2920 497215217 497214832 0.000000e+00 713.0
2 TraesCS6B01G275100 chr6A 93.186 1805 79 22 356 2131 464537269 464539058 0.000000e+00 2612.0
3 TraesCS6B01G275100 chr6A 95.652 368 14 2 1 368 464535913 464536278 9.010000e-165 590.0
4 TraesCS6B01G275100 chr6A 95.918 196 6 1 2725 2920 464539908 464540101 1.690000e-82 316.0
5 TraesCS6B01G275100 chr6A 93.370 181 12 0 2132 2312 464539544 464539724 4.800000e-68 268.0
6 TraesCS6B01G275100 chr6A 83.969 262 36 6 2561 2819 201376515 201376773 2.250000e-61 246.0
7 TraesCS6B01G275100 chr6D 92.276 1683 89 19 464 2117 325755131 325756801 0.000000e+00 2350.0
8 TraesCS6B01G275100 chr2D 81.789 928 132 29 1001 1918 526345277 526346177 0.000000e+00 743.0
9 TraesCS6B01G275100 chr2D 86.458 96 11 1 2823 2916 41199109 41199014 1.430000e-18 104.0
10 TraesCS6B01G275100 chr2B 83.287 724 100 13 1213 1918 622657248 622657968 0.000000e+00 647.0
11 TraesCS6B01G275100 chr2A 89.840 374 35 2 1545 1918 671282784 671283154 7.320000e-131 477.0
12 TraesCS6B01G275100 chr2A 84.015 269 38 4 2561 2826 725413543 725413277 1.340000e-63 254.0
13 TraesCS6B01G275100 chr4B 85.448 268 33 5 2561 2824 178379280 178379545 1.030000e-69 274.0
14 TraesCS6B01G275100 chr4B 86.538 104 8 2 2821 2918 105954427 105954324 3.080000e-20 110.0
15 TraesCS6B01G275100 chr4D 85.824 261 27 8 2563 2819 456281604 456281350 4.800000e-68 268.0
16 TraesCS6B01G275100 chr4D 84.762 105 10 2 2821 2919 72796581 72796477 1.850000e-17 100.0
17 TraesCS6B01G275100 chr3D 85.603 257 34 3 2564 2819 239600576 239600322 1.730000e-67 267.0
18 TraesCS6B01G275100 chr3D 81.771 192 35 0 1596 1787 612272837 612272646 8.370000e-36 161.0
19 TraesCS6B01G275100 chr3A 84.644 267 36 4 2561 2824 340277169 340276905 8.030000e-66 261.0
20 TraesCS6B01G275100 chr3A 81.092 238 43 2 1596 1832 746917835 746917599 3.840000e-44 189.0
21 TraesCS6B01G275100 chr7B 83.521 267 37 6 2561 2824 722335390 722335128 2.910000e-60 243.0
22 TraesCS6B01G275100 chr7B 83.521 267 37 6 2561 2824 722592626 722592364 2.910000e-60 243.0
23 TraesCS6B01G275100 chr7B 88.506 87 8 2 2821 2905 608332239 608332325 1.430000e-18 104.0
24 TraesCS6B01G275100 chr3B 84.158 202 32 0 1596 1797 826725618 826725819 2.300000e-46 196.0
25 TraesCS6B01G275100 chr3B 85.849 106 9 2 2821 2920 403376830 403376935 1.110000e-19 108.0
26 TraesCS6B01G275100 chr3B 85.714 105 10 2 2821 2920 109090577 109090473 3.980000e-19 106.0
27 TraesCS6B01G275100 chr7A 88.679 106 5 2 2820 2918 290293491 290293596 3.950000e-24 122.0
28 TraesCS6B01G275100 chr5D 86.598 97 11 2 2826 2920 172266499 172266595 3.980000e-19 106.0
29 TraesCS6B01G275100 chr1D 91.045 67 6 0 2132 2198 318644936 318645002 1.110000e-14 91.6


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 TraesCS6B01G275100 chr6B 497214832 497217751 2919 True 2494.5 4276 100.0000 1 2920 2 chr6B.!!$R1 2919
1 TraesCS6B01G275100 chr6A 464535913 464540101 4188 False 946.5 2612 94.5315 1 2920 4 chr6A.!!$F2 2919
2 TraesCS6B01G275100 chr6D 325755131 325756801 1670 False 2350.0 2350 92.2760 464 2117 1 chr6D.!!$F1 1653
3 TraesCS6B01G275100 chr2D 526345277 526346177 900 False 743.0 743 81.7890 1001 1918 1 chr2D.!!$F1 917
4 TraesCS6B01G275100 chr2B 622657248 622657968 720 False 647.0 647 83.2870 1213 1918 1 chr2B.!!$F1 705

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
408 1412 0.318275 GCAAACGGCCGAAACATTGA 60.318 50.0 35.9 0.0 36.11 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2292 3850 0.423544 AGGGAGAGGGGGAGAATTGT 59.576 55.0 0.0 0.0 0.0 2.71 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
48 49 2.450609 AGATGCAAAAGCTTTGCCAG 57.549 45.000 22.41 11.87 44.32 4.85
54 55 1.410153 CAAAAGCTTTGCCAGTCTGGT 59.590 47.619 20.24 0.00 40.46 4.00
149 150 2.200092 GGTTGGTGCCCAGGGAAA 59.800 61.111 10.89 0.00 33.81 3.13
180 181 9.675464 TGTCCAGTAGAGAAAACTAAAGAAAAA 57.325 29.630 0.00 0.00 0.00 1.94
208 209 4.559862 TCCAAAACACCACCAACAAAAT 57.440 36.364 0.00 0.00 0.00 1.82
290 291 2.099921 CCTGTCATGGAGAACCGTAGAG 59.900 54.545 0.00 0.00 39.42 2.43
330 331 0.819582 ATGCACTACCAAATGGCTGC 59.180 50.000 0.00 5.03 39.32 5.25
371 1375 7.219484 ACCAGGATGAGTTTTGTATTTGAAG 57.781 36.000 0.00 0.00 39.69 3.02
408 1412 0.318275 GCAAACGGCCGAAACATTGA 60.318 50.000 35.90 0.00 36.11 2.57
409 1413 1.404477 CAAACGGCCGAAACATTGAC 58.596 50.000 35.90 0.00 0.00 3.18
410 1414 1.025812 AAACGGCCGAAACATTGACA 58.974 45.000 35.90 0.00 0.00 3.58
416 1420 3.365465 CGGCCGAAACATTGACAACATAA 60.365 43.478 24.07 0.00 0.00 1.90
445 1449 2.487775 TCACTGTACCAGCCCCATAAT 58.512 47.619 0.00 0.00 34.37 1.28
451 1455 5.044402 ACTGTACCAGCCCCATAATACTTTT 60.044 40.000 0.00 0.00 34.37 2.27
499 1503 4.035558 TGATCAATCAAGCGGATAAAGTGC 59.964 41.667 0.00 0.00 34.28 4.40
515 1519 5.959652 AAAGTGCCATTTAAAACGAACAC 57.040 34.783 0.00 0.00 0.00 3.32
587 1592 5.915196 GCTGAATAACTTGACTTGGTTTCAC 59.085 40.000 0.00 0.00 0.00 3.18
658 1663 4.743955 GCGATCTAATTGCTCCCCTTAACT 60.744 45.833 0.00 0.00 36.71 2.24
718 1726 7.768240 TGTCTAGAAGTTCATAATAGCAACGA 58.232 34.615 5.50 0.00 0.00 3.85
736 1744 5.669848 GCAACGAAACATTTGAACAAAGCAA 60.670 36.000 6.18 0.00 33.32 3.91
737 1745 6.302615 CAACGAAACATTTGAACAAAGCAAA 58.697 32.000 6.18 0.00 39.31 3.68
760 1768 2.349755 GTTGGGCGGCCTAACAGA 59.650 61.111 34.61 6.88 43.16 3.41
850 1858 2.568956 ACTCTAGTCTGCAATTGGAGCA 59.431 45.455 21.14 8.33 40.19 4.26
892 1900 3.614588 GATTTCGCGTGTATAAAAGGGC 58.385 45.455 5.77 0.00 0.00 5.19
902 1910 5.455040 CGTGTATAAAAGGGCCCTAATGGTA 60.455 44.000 28.96 13.29 36.04 3.25
925 1933 1.634702 GGACTTCGCTCATCAGTGTC 58.365 55.000 0.00 0.00 0.00 3.67
929 1937 2.036475 ACTTCGCTCATCAGTGTCAAGT 59.964 45.455 0.00 0.00 0.00 3.16
933 1941 3.443681 TCGCTCATCAGTGTCAAGTCATA 59.556 43.478 0.00 0.00 0.00 2.15
943 1951 4.042187 AGTGTCAAGTCATAAGCCCTCTTT 59.958 41.667 0.00 0.00 33.85 2.52
953 1961 3.857157 AAGCCCTCTTTTGAGTGTGTA 57.143 42.857 0.00 0.00 44.82 2.90
963 1971 6.869695 TCTTTTGAGTGTGTAGTACAGACAA 58.130 36.000 26.93 15.11 43.94 3.18
985 1993 6.723977 ACAATAATTTTCCAGGGTAGCAAGAA 59.276 34.615 0.00 0.00 0.00 2.52
998 2006 3.978718 AGCAAGAAAGAGTGAAAGCAC 57.021 42.857 0.00 0.00 45.49 4.40
1026 2034 2.185350 CTCGCATTCGGGAGCTGT 59.815 61.111 0.00 0.00 44.24 4.40
1051 2059 4.680237 CCTTCAGCGCCACGTCCA 62.680 66.667 2.29 0.00 0.00 4.02
1092 2100 0.909610 TCATCGCCACCCTCCTCTTT 60.910 55.000 0.00 0.00 0.00 2.52
1150 2158 1.964223 AGTCACCGTGTCTCTGTGAAT 59.036 47.619 0.00 0.00 40.76 2.57
1153 2161 1.000843 CACCGTGTCTCTGTGAATCCA 59.999 52.381 0.00 0.00 34.01 3.41
1154 2162 1.273606 ACCGTGTCTCTGTGAATCCAG 59.726 52.381 0.00 0.00 0.00 3.86
1157 2165 2.072298 GTGTCTCTGTGAATCCAGTGC 58.928 52.381 0.00 0.00 34.02 4.40
1161 2195 0.037326 TCTGTGAATCCAGTGCCGAC 60.037 55.000 0.00 0.00 34.02 4.79
1168 2202 1.040893 ATCCAGTGCCGACCGTATGA 61.041 55.000 0.00 0.00 0.00 2.15
1197 2234 6.597832 AGAGTTCAGTACTTCAGTGCTAAT 57.402 37.500 0.00 0.00 38.95 1.73
1200 2237 5.409826 AGTTCAGTACTTCAGTGCTAATTGC 59.590 40.000 0.00 0.00 38.95 3.56
1208 2247 3.587923 TCAGTGCTAATTGCCAATTTGC 58.412 40.909 23.67 23.67 45.60 3.68
1240 2279 0.464373 AAATCACCGATGATGGCGCT 60.464 50.000 7.64 0.00 45.26 5.92
1249 2288 3.838271 GATGGCGCTCTCGACCCA 61.838 66.667 7.64 0.00 44.89 4.51
1520 2588 6.238648 GGAATATAGCCGTGCAATTTACTGTT 60.239 38.462 0.00 0.00 0.00 3.16
1953 3022 2.981909 AACGCTCGACCCGTCTCA 60.982 61.111 6.81 0.00 38.06 3.27
1964 3033 1.303309 CCCGTCTCAGATTTGCATCC 58.697 55.000 0.00 0.00 0.00 3.51
1995 3064 2.227865 TCTTCGTCGTGTGATGTGATGA 59.772 45.455 0.00 0.00 32.69 2.92
1998 3067 2.163412 TCGTCGTGTGATGTGATGATCA 59.837 45.455 0.00 0.00 32.69 2.92
2023 3092 3.378742 GGTTGTGTACAAATGGTGTGTCA 59.621 43.478 0.00 0.00 41.89 3.58
2024 3093 4.347813 GTTGTGTACAAATGGTGTGTCAC 58.652 43.478 0.00 0.00 41.89 3.67
2025 3094 2.609916 TGTGTACAAATGGTGTGTCACG 59.390 45.455 0.00 0.00 43.27 4.35
2026 3095 2.032377 GTGTACAAATGGTGTGTCACGG 60.032 50.000 0.00 0.00 41.89 4.94
2027 3096 2.158943 TGTACAAATGGTGTGTCACGGA 60.159 45.455 0.00 0.00 41.89 4.69
2028 3097 1.305201 ACAAATGGTGTGTCACGGAC 58.695 50.000 0.00 0.00 39.72 4.79
2029 3098 0.591170 CAAATGGTGTGTCACGGACC 59.409 55.000 5.68 5.68 34.83 4.46
2030 3099 0.472471 AAATGGTGTGTCACGGACCT 59.528 50.000 12.39 0.00 34.83 3.85
2031 3100 0.034896 AATGGTGTGTCACGGACCTC 59.965 55.000 12.39 0.00 34.83 3.85
2072 3141 4.577988 TTCCCTTTCCATTCAATCCGTA 57.422 40.909 0.00 0.00 0.00 4.02
2094 3163 7.121272 CGTATAAAATATTTTCGTTCGGCAGT 58.879 34.615 16.56 0.00 0.00 4.40
2096 3165 5.365403 AAAATATTTTCGTTCGGCAGTCA 57.635 34.783 7.64 0.00 0.00 3.41
2098 3167 2.900122 ATTTTCGTTCGGCAGTCATG 57.100 45.000 0.00 0.00 0.00 3.07
2137 3695 9.865321 AAGAAACATGAATATGAACTGATTTGG 57.135 29.630 0.00 0.00 37.73 3.28
2141 3699 7.121382 ACATGAATATGAACTGATTTGGACCT 58.879 34.615 0.00 0.00 37.73 3.85
2148 3706 1.780309 ACTGATTTGGACCTTGGTGGA 59.220 47.619 0.00 0.00 39.71 4.02
2154 3712 0.105194 TGGACCTTGGTGGACTGAGA 60.105 55.000 0.00 0.00 39.71 3.27
2158 3716 3.118592 GGACCTTGGTGGACTGAGAATAG 60.119 52.174 0.00 0.00 39.71 1.73
2178 3736 1.679032 GCACTGTCCACCTAACCATCC 60.679 57.143 0.00 0.00 0.00 3.51
2186 3744 0.326927 ACCTAACCATCCCAACCACG 59.673 55.000 0.00 0.00 0.00 4.94
2268 3826 3.189080 TCCACGCATTGTTCATCTTCTTG 59.811 43.478 0.00 0.00 0.00 3.02
2284 3842 3.120468 TCTTGATCACCTCTCCCATGA 57.880 47.619 0.00 0.00 0.00 3.07
2292 3850 2.501316 CACCTCTCCCATGACACATACA 59.499 50.000 0.00 0.00 0.00 2.29
2312 3870 1.203622 ACAATTCTCCCCCTCTCCCTT 60.204 52.381 0.00 0.00 0.00 3.95
2559 4117 0.248215 GCATGCGATGTTGTGGCTAC 60.248 55.000 0.00 0.00 32.08 3.58
2577 4135 4.519350 GGCTACTGGAAATATGCCCTAAAC 59.481 45.833 0.00 0.00 34.81 2.01
2578 4136 5.130350 GCTACTGGAAATATGCCCTAAACA 58.870 41.667 0.00 0.00 0.00 2.83
2579 4137 5.008712 GCTACTGGAAATATGCCCTAAACAC 59.991 44.000 0.00 0.00 0.00 3.32
2581 4139 5.329399 ACTGGAAATATGCCCTAAACACAA 58.671 37.500 0.00 0.00 0.00 3.33
2584 4142 7.617723 ACTGGAAATATGCCCTAAACACAATAA 59.382 33.333 0.00 0.00 0.00 1.40
2585 4143 8.546083 TGGAAATATGCCCTAAACACAATAAT 57.454 30.769 0.00 0.00 0.00 1.28
2586 4144 9.647918 TGGAAATATGCCCTAAACACAATAATA 57.352 29.630 0.00 0.00 0.00 0.98
2657 4215 8.347004 TGTTCTATAATTGCATTGGTTCTTGA 57.653 30.769 0.00 0.00 0.00 3.02
2658 4216 8.801299 TGTTCTATAATTGCATTGGTTCTTGAA 58.199 29.630 0.00 0.00 0.00 2.69
2659 4217 9.807649 GTTCTATAATTGCATTGGTTCTTGAAT 57.192 29.630 0.00 0.00 0.00 2.57
2664 4222 9.976511 ATAATTGCATTGGTTCTTGAATATGAG 57.023 29.630 0.00 0.00 0.00 2.90
2665 4223 7.649533 ATTGCATTGGTTCTTGAATATGAGA 57.350 32.000 0.00 0.00 0.00 3.27
2666 4224 7.649533 TTGCATTGGTTCTTGAATATGAGAT 57.350 32.000 0.00 0.00 0.00 2.75
2667 4225 7.649533 TGCATTGGTTCTTGAATATGAGATT 57.350 32.000 0.00 0.00 0.00 2.40
2668 4226 7.709947 TGCATTGGTTCTTGAATATGAGATTC 58.290 34.615 0.00 0.00 0.00 2.52
2669 4227 7.339976 TGCATTGGTTCTTGAATATGAGATTCA 59.660 33.333 0.00 0.00 36.37 2.57
2670 4228 8.192774 GCATTGGTTCTTGAATATGAGATTCAA 58.807 33.333 13.78 13.78 43.34 2.69
2673 4231 9.519191 TTGGTTCTTGAATATGAGATTCAAAGA 57.481 29.630 15.10 11.74 44.40 2.52
2674 4232 9.519191 TGGTTCTTGAATATGAGATTCAAAGAA 57.481 29.630 15.10 15.74 44.40 2.52
2686 4244 6.643770 TGAGATTCAAAGAAAAGCTCAATTGC 59.356 34.615 0.00 0.00 43.84 3.56
2687 4245 6.518493 AGATTCAAAGAAAAGCTCAATTGCA 58.482 32.000 0.00 0.00 34.99 4.08
2688 4246 7.159372 AGATTCAAAGAAAAGCTCAATTGCAT 58.841 30.769 0.00 0.00 34.99 3.96
2689 4247 6.533819 TTCAAAGAAAAGCTCAATTGCATG 57.466 33.333 0.00 0.00 34.99 4.06
2690 4248 5.603596 TCAAAGAAAAGCTCAATTGCATGT 58.396 33.333 0.00 0.00 34.99 3.21
2691 4249 5.464057 TCAAAGAAAAGCTCAATTGCATGTG 59.536 36.000 0.00 0.00 34.99 3.21
2692 4250 4.595762 AGAAAAGCTCAATTGCATGTGT 57.404 36.364 0.00 0.00 34.99 3.72
2693 4251 4.304110 AGAAAAGCTCAATTGCATGTGTG 58.696 39.130 0.00 0.00 34.99 3.82
2694 4252 2.736144 AAGCTCAATTGCATGTGTGG 57.264 45.000 0.00 0.00 34.99 4.17
2695 4253 1.913778 AGCTCAATTGCATGTGTGGA 58.086 45.000 0.00 0.00 34.99 4.02
2696 4254 2.241160 AGCTCAATTGCATGTGTGGAA 58.759 42.857 0.00 0.00 40.09 3.53
2697 4255 2.629137 AGCTCAATTGCATGTGTGGAAA 59.371 40.909 0.00 0.00 39.21 3.13
2698 4256 3.069872 AGCTCAATTGCATGTGTGGAAAA 59.930 39.130 0.00 0.00 39.21 2.29
2699 4257 3.808726 GCTCAATTGCATGTGTGGAAAAA 59.191 39.130 0.00 0.00 39.21 1.94
2700 4258 4.453136 GCTCAATTGCATGTGTGGAAAAAT 59.547 37.500 0.00 0.00 39.21 1.82
2701 4259 5.638657 GCTCAATTGCATGTGTGGAAAAATA 59.361 36.000 0.00 0.00 39.21 1.40
2702 4260 6.147492 GCTCAATTGCATGTGTGGAAAAATAA 59.853 34.615 0.00 0.00 39.21 1.40
2703 4261 7.307870 GCTCAATTGCATGTGTGGAAAAATAAA 60.308 33.333 0.00 0.00 39.21 1.40
2704 4262 7.859598 TCAATTGCATGTGTGGAAAAATAAAC 58.140 30.769 0.00 0.00 39.21 2.01
2705 4263 7.496920 TCAATTGCATGTGTGGAAAAATAAACA 59.503 29.630 0.00 0.00 39.21 2.83
2706 4264 7.982761 ATTGCATGTGTGGAAAAATAAACAT 57.017 28.000 0.00 0.00 39.21 2.71
2707 4265 7.418840 TTGCATGTGTGGAAAAATAAACATC 57.581 32.000 0.00 0.00 32.35 3.06
2708 4266 6.519382 TGCATGTGTGGAAAAATAAACATCA 58.481 32.000 0.00 0.00 0.00 3.07
2709 4267 6.988580 TGCATGTGTGGAAAAATAAACATCAA 59.011 30.769 0.00 0.00 0.00 2.57
2710 4268 7.496920 TGCATGTGTGGAAAAATAAACATCAAA 59.503 29.630 0.00 0.00 0.00 2.69
2711 4269 8.505625 GCATGTGTGGAAAAATAAACATCAAAT 58.494 29.630 0.00 0.00 0.00 2.32
2712 4270 9.814507 CATGTGTGGAAAAATAAACATCAAATG 57.185 29.630 0.00 0.00 0.00 2.32
2713 4271 8.375608 TGTGTGGAAAAATAAACATCAAATGG 57.624 30.769 0.00 0.00 33.60 3.16
2714 4272 8.206867 TGTGTGGAAAAATAAACATCAAATGGA 58.793 29.630 0.00 0.00 33.60 3.41
2715 4273 9.218440 GTGTGGAAAAATAAACATCAAATGGAT 57.782 29.630 0.00 0.00 36.39 3.41
2716 4274 9.434420 TGTGGAAAAATAAACATCAAATGGATC 57.566 29.630 0.00 0.00 32.57 3.36
2717 4275 8.882736 GTGGAAAAATAAACATCAAATGGATCC 58.117 33.333 4.20 4.20 32.57 3.36
2718 4276 8.046107 TGGAAAAATAAACATCAAATGGATCCC 58.954 33.333 9.90 0.00 32.57 3.85
2719 4277 8.267183 GGAAAAATAAACATCAAATGGATCCCT 58.733 33.333 9.90 0.00 32.57 4.20
2722 4280 9.492730 AAAATAAACATCAAATGGATCCCTAGT 57.507 29.630 9.90 0.00 32.57 2.57
2723 4281 8.697507 AATAAACATCAAATGGATCCCTAGTC 57.302 34.615 9.90 0.00 32.57 2.59
2724 4282 5.715439 AACATCAAATGGATCCCTAGTCA 57.285 39.130 9.90 0.00 32.57 3.41
2725 4283 5.919348 ACATCAAATGGATCCCTAGTCAT 57.081 39.130 9.90 0.00 32.57 3.06
2726 4284 5.628130 ACATCAAATGGATCCCTAGTCATG 58.372 41.667 9.90 7.16 32.57 3.07
2727 4285 4.090761 TCAAATGGATCCCTAGTCATGC 57.909 45.455 9.90 0.00 0.00 4.06
2728 4286 3.718434 TCAAATGGATCCCTAGTCATGCT 59.282 43.478 9.90 0.00 0.00 3.79
2729 4287 4.070716 CAAATGGATCCCTAGTCATGCTC 58.929 47.826 9.90 0.00 0.00 4.26
2730 4288 1.722034 TGGATCCCTAGTCATGCTCC 58.278 55.000 9.90 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 8.144478 TCATTCTATTATGCTCTGTTACCAGAC 58.856 37.037 0.00 0.00 42.80 3.51
69 70 7.672351 TTCGTGTGTGTTTTGTAAATCATTC 57.328 32.000 0.00 0.00 0.00 2.67
149 150 3.910627 AGTTTTCTCTACTGGACATGGGT 59.089 43.478 0.00 0.00 0.00 4.51
180 181 4.559862 TGGTGGTGTTTTGGAACATTTT 57.440 36.364 0.00 0.00 46.63 1.82
181 182 4.257731 GTTGGTGGTGTTTTGGAACATTT 58.742 39.130 0.00 0.00 46.63 2.32
308 309 2.032054 CAGCCATTTGGTAGTGCATACG 59.968 50.000 0.00 0.00 34.99 3.06
354 355 8.783093 CCATGTAGACTTCAAATACAAAACTCA 58.217 33.333 0.00 0.00 33.44 3.41
371 1375 5.393962 GTTTGCAATGAAGTCCATGTAGAC 58.606 41.667 0.00 0.00 35.24 2.59
408 1412 5.445964 ACAGTGAACTTTCCCTTATGTTGT 58.554 37.500 0.00 0.00 0.00 3.32
409 1413 6.072673 GGTACAGTGAACTTTCCCTTATGTTG 60.073 42.308 0.00 0.00 0.00 3.33
410 1414 6.002082 GGTACAGTGAACTTTCCCTTATGTT 58.998 40.000 0.00 0.00 0.00 2.71
445 1449 6.935741 TTGCTAAAGAGTTGCTCAAAAGTA 57.064 33.333 0.00 0.00 32.06 2.24
451 1455 8.668353 CAATAACTATTGCTAAAGAGTTGCTCA 58.332 33.333 8.35 0.00 45.17 4.26
499 1503 6.978024 TGAAATCGTGTTCGTTTTAAATGG 57.022 33.333 0.00 0.00 38.51 3.16
587 1592 1.939934 TGCCTCTGTTTGTGTTTCTCG 59.060 47.619 0.00 0.00 0.00 4.04
694 1702 8.630278 TTCGTTGCTATTATGAACTTCTAGAC 57.370 34.615 0.00 0.00 0.00 2.59
695 1703 9.084164 GTTTCGTTGCTATTATGAACTTCTAGA 57.916 33.333 0.00 0.00 0.00 2.43
718 1726 5.630061 GCACTTTGCTTTGTTCAAATGTTT 58.370 33.333 0.00 0.00 40.96 2.83
755 1763 4.702131 GCTTGGTCTATGATTGGTTCTGTT 59.298 41.667 0.00 0.00 0.00 3.16
756 1764 4.018960 AGCTTGGTCTATGATTGGTTCTGT 60.019 41.667 0.00 0.00 0.00 3.41
757 1765 4.521146 AGCTTGGTCTATGATTGGTTCTG 58.479 43.478 0.00 0.00 0.00 3.02
760 1768 6.064717 GGATTAGCTTGGTCTATGATTGGTT 58.935 40.000 0.00 0.00 0.00 3.67
850 1858 2.369394 GTGCTAACAGCTTAATGGCCT 58.631 47.619 3.32 0.00 42.97 5.19
902 1910 1.625818 ACTGATGAGCGAAGTCCCTTT 59.374 47.619 0.00 0.00 0.00 3.11
925 1933 5.006386 ACTCAAAAGAGGGCTTATGACTTG 58.994 41.667 0.00 0.00 32.98 3.16
929 1937 4.202461 ACACACTCAAAAGAGGGCTTATGA 60.202 41.667 0.00 0.00 32.98 2.15
933 1941 2.736670 ACACACTCAAAAGAGGGCTT 57.263 45.000 0.00 0.00 35.37 4.35
943 1951 9.772973 AAATTATTGTCTGTACTACACACTCAA 57.227 29.630 0.00 0.00 32.71 3.02
953 1961 6.790319 ACCCTGGAAAATTATTGTCTGTACT 58.210 36.000 0.00 0.00 0.00 2.73
963 1971 7.182060 TCTTTCTTGCTACCCTGGAAAATTAT 58.818 34.615 0.00 0.00 0.00 1.28
985 1993 3.554934 TCACCATTGTGCTTTCACTCTT 58.445 40.909 0.00 0.00 43.49 2.85
998 2006 1.530441 CGAATGCGAGCTTCACCATTG 60.530 52.381 0.00 0.00 40.82 2.82
1026 2034 2.343758 GCGCTGAAGGAGTCACCA 59.656 61.111 0.00 0.00 42.04 4.17
1051 2059 2.108976 CGCCACATACGCCCTGAT 59.891 61.111 0.00 0.00 0.00 2.90
1150 2158 1.040893 ATCATACGGTCGGCACTGGA 61.041 55.000 0.00 0.00 32.44 3.86
1161 2195 6.423302 AGTACTGAACTCTACGTATCATACGG 59.577 42.308 21.05 5.95 45.55 4.02
1168 2202 6.403418 GCACTGAAGTACTGAACTCTACGTAT 60.403 42.308 0.00 0.00 37.50 3.06
1175 2209 6.401581 GCAATTAGCACTGAAGTACTGAACTC 60.402 42.308 0.00 0.00 44.79 3.01
1208 2247 1.133025 GGTGATTTTCCCTGCACGATG 59.867 52.381 0.00 0.00 32.24 3.84
1209 2248 1.463674 GGTGATTTTCCCTGCACGAT 58.536 50.000 0.00 0.00 32.24 3.73
1223 2262 1.301244 GAGCGCCATCATCGGTGAT 60.301 57.895 5.02 5.02 45.87 3.06
1520 2588 1.045407 ACAGTTCACCGGTAAGCTGA 58.955 50.000 26.72 8.15 0.00 4.26
1703 2772 2.357638 TTGGCGCCGACGATGAAA 60.358 55.556 23.90 4.45 43.93 2.69
1853 2922 3.293714 TCGCCGTACACGAACCCA 61.294 61.111 2.76 0.00 43.02 4.51
1964 3033 0.861837 ACGACGAAGAGCAAAGCAAG 59.138 50.000 0.00 0.00 0.00 4.01
1995 3064 5.362430 ACACCATTTGTACACAACCTTTGAT 59.638 36.000 0.00 0.00 36.32 2.57
1998 3067 4.464597 ACACACCATTTGTACACAACCTTT 59.535 37.500 0.00 0.00 35.67 3.11
2029 3098 2.432628 GAAGGCCGTGACCGTGAG 60.433 66.667 0.00 0.00 33.69 3.51
2030 3099 4.351938 CGAAGGCCGTGACCGTGA 62.352 66.667 0.00 0.00 33.69 4.35
2072 3141 7.079182 TGACTGCCGAACGAAAATATTTTAT 57.921 32.000 13.34 2.69 0.00 1.40
2094 3163 6.467677 TGTTTCTTTTTGTTCCAAACCATGA 58.532 32.000 0.00 0.00 0.00 3.07
2096 3165 7.108847 TCATGTTTCTTTTTGTTCCAAACCAT 58.891 30.769 0.00 0.00 0.00 3.55
2098 3167 6.976636 TCATGTTTCTTTTTGTTCCAAACC 57.023 33.333 0.00 0.00 0.00 3.27
2137 3695 3.680196 GCTATTCTCAGTCCACCAAGGTC 60.680 52.174 0.00 0.00 39.02 3.85
2141 3699 2.906389 AGTGCTATTCTCAGTCCACCAA 59.094 45.455 0.00 0.00 0.00 3.67
2148 3706 2.234908 GGTGGACAGTGCTATTCTCAGT 59.765 50.000 0.00 0.00 0.00 3.41
2154 3712 2.910319 TGGTTAGGTGGACAGTGCTATT 59.090 45.455 0.00 0.00 0.00 1.73
2158 3716 1.679032 GGATGGTTAGGTGGACAGTGC 60.679 57.143 0.00 0.00 0.00 4.40
2186 3744 1.883021 CCATTCTGCGAACCAACCC 59.117 57.895 0.00 0.00 0.00 4.11
2245 3803 3.005554 AGAAGATGAACAATGCGTGGAG 58.994 45.455 0.00 0.00 0.00 3.86
2250 3808 5.026462 GTGATCAAGAAGATGAACAATGCG 58.974 41.667 0.00 0.00 37.00 4.73
2268 3826 1.833630 TGTGTCATGGGAGAGGTGATC 59.166 52.381 0.00 0.00 0.00 2.92
2284 3842 2.919602 AGGGGGAGAATTGTGTATGTGT 59.080 45.455 0.00 0.00 0.00 3.72
2292 3850 0.423544 AGGGAGAGGGGGAGAATTGT 59.576 55.000 0.00 0.00 0.00 2.71
2559 4117 5.913137 TTGTGTTTAGGGCATATTTCCAG 57.087 39.130 0.00 0.00 0.00 3.86
2631 4189 8.970020 TCAAGAACCAATGCAATTATAGAACAT 58.030 29.630 0.00 0.00 32.46 2.71
2632 4190 8.347004 TCAAGAACCAATGCAATTATAGAACA 57.653 30.769 0.00 0.00 32.46 3.18
2633 4191 9.807649 ATTCAAGAACCAATGCAATTATAGAAC 57.192 29.630 0.00 0.00 32.46 3.01
2638 4196 9.976511 CTCATATTCAAGAACCAATGCAATTAT 57.023 29.630 0.00 0.00 32.46 1.28
2639 4197 9.187996 TCTCATATTCAAGAACCAATGCAATTA 57.812 29.630 0.00 0.00 32.46 1.40
2640 4198 8.070034 TCTCATATTCAAGAACCAATGCAATT 57.930 30.769 0.00 0.00 36.63 2.32
2641 4199 7.649533 TCTCATATTCAAGAACCAATGCAAT 57.350 32.000 0.00 0.00 0.00 3.56
2642 4200 7.649533 ATCTCATATTCAAGAACCAATGCAA 57.350 32.000 0.00 0.00 0.00 4.08
2643 4201 7.339976 TGAATCTCATATTCAAGAACCAATGCA 59.660 33.333 0.00 0.00 35.35 3.96
2644 4202 7.709947 TGAATCTCATATTCAAGAACCAATGC 58.290 34.615 0.00 0.00 35.35 3.56
2647 4205 9.519191 TCTTTGAATCTCATATTCAAGAACCAA 57.481 29.630 11.67 0.00 45.29 3.67
2648 4206 9.519191 TTCTTTGAATCTCATATTCAAGAACCA 57.481 29.630 11.67 0.00 45.29 3.67
2655 4213 9.234827 TGAGCTTTTCTTTGAATCTCATATTCA 57.765 29.630 0.00 0.00 36.37 2.57
2659 4217 9.850628 CAATTGAGCTTTTCTTTGAATCTCATA 57.149 29.630 0.00 0.00 0.00 2.15
2660 4218 7.331193 GCAATTGAGCTTTTCTTTGAATCTCAT 59.669 33.333 10.34 0.00 0.00 2.90
2661 4219 6.643770 GCAATTGAGCTTTTCTTTGAATCTCA 59.356 34.615 10.34 0.00 0.00 3.27
2662 4220 6.643770 TGCAATTGAGCTTTTCTTTGAATCTC 59.356 34.615 10.34 0.00 34.99 2.75
2663 4221 6.518493 TGCAATTGAGCTTTTCTTTGAATCT 58.482 32.000 10.34 0.00 34.99 2.40
2664 4222 6.774354 TGCAATTGAGCTTTTCTTTGAATC 57.226 33.333 10.34 0.00 34.99 2.52
2665 4223 6.708949 ACATGCAATTGAGCTTTTCTTTGAAT 59.291 30.769 10.34 0.00 34.99 2.57
2666 4224 6.018588 CACATGCAATTGAGCTTTTCTTTGAA 60.019 34.615 10.34 0.00 34.99 2.69
2667 4225 5.464057 CACATGCAATTGAGCTTTTCTTTGA 59.536 36.000 10.34 0.00 34.99 2.69
2668 4226 5.235616 ACACATGCAATTGAGCTTTTCTTTG 59.764 36.000 10.34 0.00 34.99 2.77
2669 4227 5.235616 CACACATGCAATTGAGCTTTTCTTT 59.764 36.000 10.34 0.00 34.99 2.52
2670 4228 4.748102 CACACATGCAATTGAGCTTTTCTT 59.252 37.500 10.34 0.00 34.99 2.52
2671 4229 4.304110 CACACATGCAATTGAGCTTTTCT 58.696 39.130 10.34 0.00 34.99 2.52
2672 4230 3.430895 CCACACATGCAATTGAGCTTTTC 59.569 43.478 10.34 0.00 34.99 2.29
2673 4231 3.069872 TCCACACATGCAATTGAGCTTTT 59.930 39.130 10.34 0.00 34.99 2.27
2674 4232 2.629137 TCCACACATGCAATTGAGCTTT 59.371 40.909 10.34 0.00 34.99 3.51
2675 4233 2.241160 TCCACACATGCAATTGAGCTT 58.759 42.857 10.34 0.00 34.99 3.74
2676 4234 1.913778 TCCACACATGCAATTGAGCT 58.086 45.000 10.34 0.00 34.99 4.09
2677 4235 2.728690 TTCCACACATGCAATTGAGC 57.271 45.000 10.34 0.00 0.00 4.26
2678 4236 7.655236 TTATTTTTCCACACATGCAATTGAG 57.345 32.000 10.34 0.27 0.00 3.02
2679 4237 7.496920 TGTTTATTTTTCCACACATGCAATTGA 59.503 29.630 10.34 0.00 0.00 2.57
2680 4238 7.637229 TGTTTATTTTTCCACACATGCAATTG 58.363 30.769 0.00 0.00 0.00 2.32
2681 4239 7.798596 TGTTTATTTTTCCACACATGCAATT 57.201 28.000 0.00 0.00 0.00 2.32
2682 4240 7.660617 TGATGTTTATTTTTCCACACATGCAAT 59.339 29.630 0.00 0.00 0.00 3.56
2683 4241 6.988580 TGATGTTTATTTTTCCACACATGCAA 59.011 30.769 0.00 0.00 0.00 4.08
2684 4242 6.519382 TGATGTTTATTTTTCCACACATGCA 58.481 32.000 0.00 0.00 0.00 3.96
2685 4243 7.418840 TTGATGTTTATTTTTCCACACATGC 57.581 32.000 0.00 0.00 0.00 4.06
2686 4244 9.814507 CATTTGATGTTTATTTTTCCACACATG 57.185 29.630 0.00 0.00 0.00 3.21
2687 4245 9.001542 CCATTTGATGTTTATTTTTCCACACAT 57.998 29.630 0.00 0.00 0.00 3.21
2688 4246 8.206867 TCCATTTGATGTTTATTTTTCCACACA 58.793 29.630 0.00 0.00 0.00 3.72
2689 4247 8.600449 TCCATTTGATGTTTATTTTTCCACAC 57.400 30.769 0.00 0.00 0.00 3.82
2690 4248 9.434420 GATCCATTTGATGTTTATTTTTCCACA 57.566 29.630 0.00 0.00 32.41 4.17
2691 4249 8.882736 GGATCCATTTGATGTTTATTTTTCCAC 58.117 33.333 6.95 0.00 32.41 4.02
2692 4250 8.046107 GGGATCCATTTGATGTTTATTTTTCCA 58.954 33.333 15.23 0.00 32.41 3.53
2693 4251 8.267183 AGGGATCCATTTGATGTTTATTTTTCC 58.733 33.333 15.23 0.00 32.41 3.13
2696 4254 9.492730 ACTAGGGATCCATTTGATGTTTATTTT 57.507 29.630 15.23 0.00 32.41 1.82
2697 4255 9.136323 GACTAGGGATCCATTTGATGTTTATTT 57.864 33.333 15.23 0.00 32.41 1.40
2698 4256 8.281531 TGACTAGGGATCCATTTGATGTTTATT 58.718 33.333 15.23 0.00 32.41 1.40
2699 4257 7.815383 TGACTAGGGATCCATTTGATGTTTAT 58.185 34.615 15.23 0.00 32.41 1.40
2700 4258 7.206789 TGACTAGGGATCCATTTGATGTTTA 57.793 36.000 15.23 0.00 32.41 2.01
2701 4259 6.078456 TGACTAGGGATCCATTTGATGTTT 57.922 37.500 15.23 0.00 32.41 2.83
2702 4260 5.715439 TGACTAGGGATCCATTTGATGTT 57.285 39.130 15.23 0.00 32.41 2.71
2703 4261 5.628130 CATGACTAGGGATCCATTTGATGT 58.372 41.667 15.23 1.89 32.41 3.06
2704 4262 4.458295 GCATGACTAGGGATCCATTTGATG 59.542 45.833 15.23 8.29 32.41 3.07
2705 4263 4.353191 AGCATGACTAGGGATCCATTTGAT 59.647 41.667 15.23 0.00 36.01 2.57
2706 4264 3.718434 AGCATGACTAGGGATCCATTTGA 59.282 43.478 15.23 0.00 0.00 2.69
2707 4265 4.070716 GAGCATGACTAGGGATCCATTTG 58.929 47.826 15.23 5.82 0.00 2.32
2708 4266 3.073650 GGAGCATGACTAGGGATCCATTT 59.926 47.826 15.23 0.65 0.00 2.32
2709 4267 2.641815 GGAGCATGACTAGGGATCCATT 59.358 50.000 15.23 3.45 0.00 3.16
2710 4268 2.158035 AGGAGCATGACTAGGGATCCAT 60.158 50.000 15.23 9.63 0.00 3.41
2711 4269 1.221523 AGGAGCATGACTAGGGATCCA 59.778 52.381 15.23 0.00 0.00 3.41
2712 4270 2.022718 AGGAGCATGACTAGGGATCC 57.977 55.000 1.92 1.92 0.00 3.36
2719 4277 3.396276 AGCTAGTCCTAGGAGCATGACTA 59.604 47.826 20.29 13.06 38.85 2.59
2720 4278 2.176798 AGCTAGTCCTAGGAGCATGACT 59.823 50.000 20.29 12.66 40.87 3.41
2721 4279 2.556622 GAGCTAGTCCTAGGAGCATGAC 59.443 54.545 20.29 6.15 38.73 3.06
2722 4280 2.175715 TGAGCTAGTCCTAGGAGCATGA 59.824 50.000 20.29 4.27 38.73 3.07
2723 4281 2.591923 TGAGCTAGTCCTAGGAGCATG 58.408 52.381 20.29 9.64 38.73 4.06
2724 4282 3.164268 CATGAGCTAGTCCTAGGAGCAT 58.836 50.000 20.29 9.66 38.73 3.79
2725 4283 2.091610 ACATGAGCTAGTCCTAGGAGCA 60.092 50.000 20.29 7.94 38.73 4.26
2726 4284 2.593026 ACATGAGCTAGTCCTAGGAGC 58.407 52.381 13.15 12.76 36.42 4.70
2727 4285 6.007076 TCAATACATGAGCTAGTCCTAGGAG 58.993 44.000 13.15 1.28 33.04 3.69
2728 4286 5.953571 TCAATACATGAGCTAGTCCTAGGA 58.046 41.667 7.62 7.62 33.04 2.94
2729 4287 6.435591 TCATCAATACATGAGCTAGTCCTAGG 59.564 42.308 0.82 0.82 42.53 3.02
2730 4288 7.459795 TCATCAATACATGAGCTAGTCCTAG 57.540 40.000 0.00 0.00 42.53 3.02
2801 4359 7.282224 TCCCAACAATGTACTAATTAGTGATGC 59.718 37.037 25.27 13.91 37.10 3.91
2847 4405 4.597004 AGTGTTCCTAGTTGATCGTAGGA 58.403 43.478 12.22 12.22 42.62 2.94
2852 4410 6.796426 TCTTCATAGTGTTCCTAGTTGATCG 58.204 40.000 0.00 0.00 0.00 3.69
2856 4414 6.108687 TGCATCTTCATAGTGTTCCTAGTTG 58.891 40.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.