Multiple sequence alignment - TraesCS7A01G490800

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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 TraesCS7A01G490800 chr7A 100.000 2754 0 0 1 2754 680189982 680187229 0.000000e+00 5086.0
1 TraesCS7A01G490800 chr7B 87.821 1946 101 62 448 2285 661431261 661429344 0.000000e+00 2156.0
2 TraesCS7A01G490800 chr7B 86.422 464 40 8 1 450 661431745 661431291 1.150000e-133 486.0
3 TraesCS7A01G490800 chr7B 87.018 285 32 3 2314 2596 661429221 661428940 1.590000e-82 316.0
4 TraesCS7A01G490800 chr7B 92.638 163 11 1 2593 2754 661428994 661428832 1.650000e-57 233.0
5 TraesCS7A01G490800 chr7B 75.152 330 60 17 1329 1649 3721854 3722170 4.780000e-28 135.0
6 TraesCS7A01G490800 chr7B 100.000 29 0 0 2341 2369 632307217 632307189 1.000000e-03 54.7
7 TraesCS7A01G490800 chr7D 92.887 956 48 8 1023 1962 588160120 588159169 0.000000e+00 1371.0
8 TraesCS7A01G490800 chr7D 85.406 603 20 21 448 1023 588160727 588160166 5.150000e-157 564.0
9 TraesCS7A01G490800 chr7D 83.258 442 31 16 39 450 588161185 588160757 1.560000e-97 366.0
10 TraesCS7A01G490800 chr7D 85.813 289 21 10 2005 2285 588154023 588153747 3.470000e-74 289.0
11 TraesCS7A01G490800 chr7D 87.006 177 18 3 2422 2596 588153471 588153298 7.780000e-46 195.0
12 TraesCS7A01G490800 chr7D 85.625 160 16 5 2314 2473 588153624 588153472 7.890000e-36 161.0
13 TraesCS7A01G490800 chr7D 100.000 30 0 0 2341 2370 8183655 8183626 3.830000e-04 56.5
14 TraesCS7A01G490800 chr7D 100.000 30 0 0 2341 2370 83648765 83648736 3.830000e-04 56.5
15 TraesCS7A01G490800 chr5B 80.743 296 46 6 1332 1623 521032338 521032050 1.280000e-53 220.0
16 TraesCS7A01G490800 chr5A 80.000 300 49 6 1328 1623 546576352 546576060 7.730000e-51 211.0
17 TraesCS7A01G490800 chr5A 86.905 84 9 2 2668 2750 616168442 616168524 2.920000e-15 93.5
18 TraesCS7A01G490800 chr2D 100.000 30 0 0 2341 2370 566770126 566770155 3.830000e-04 56.5
19 TraesCS7A01G490800 chr1D 100.000 30 0 0 2341 2370 479708661 479708690 3.830000e-04 56.5


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 TraesCS7A01G490800 chr7A 680187229 680189982 2753 True 5086.00 5086 100.000000 1 2754 1 chr7A.!!$R1 2753
1 TraesCS7A01G490800 chr7B 661428832 661431745 2913 True 797.75 2156 88.474750 1 2754 4 chr7B.!!$R2 2753
2 TraesCS7A01G490800 chr7D 588159169 588161185 2016 True 767.00 1371 87.183667 39 1962 3 chr7D.!!$R4 1923
3 TraesCS7A01G490800 chr7D 588153298 588154023 725 True 215.00 289 86.148000 2005 2596 3 chr7D.!!$R3 591

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
671 802 0.040067 CTCATGATGCCGTCGATCGA 60.04 55.0 15.15 15.15 42.86 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2542 2957 0.107456 AGCTTCATCAATCCGCGGAT 59.893 50.0 34.6 34.6 36.23 4.18 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
37 38 2.892425 CCTCCATCTCCGTTGCGC 60.892 66.667 0.00 0.00 0.00 6.09
70 71 7.703621 CACATGTTAGACATTTTGGAATGATCC 59.296 37.037 0.00 0.00 44.37 3.36
72 73 7.703621 CATGTTAGACATTTTGGAATGATCCAC 59.296 37.037 6.17 0.00 45.69 4.02
81 82 1.017387 GAATGATCCACAAGGCGTCC 58.983 55.000 0.00 0.00 33.74 4.79
127 129 3.112075 CGCGCGAGTGAATGTGGT 61.112 61.111 28.94 0.00 46.66 4.16
144 146 3.503363 TGTGGTCAGCAGCAAAAGAATAG 59.497 43.478 0.00 0.00 0.00 1.73
148 150 5.477984 TGGTCAGCAGCAAAAGAATAGAAAT 59.522 36.000 0.00 0.00 0.00 2.17
149 151 6.658816 TGGTCAGCAGCAAAAGAATAGAAATA 59.341 34.615 0.00 0.00 0.00 1.40
150 152 7.176515 TGGTCAGCAGCAAAAGAATAGAAATAA 59.823 33.333 0.00 0.00 0.00 1.40
155 157 8.876790 AGCAGCAAAAGAATAGAAATAAAATGC 58.123 29.630 0.00 0.00 0.00 3.56
186 190 3.830744 TGGCTTATAATACTGCGTGGT 57.169 42.857 0.00 0.00 0.00 4.16
193 197 4.672587 ATAATACTGCGTGGTGTGAGAT 57.327 40.909 0.00 0.00 0.00 2.75
203 207 1.002868 GTGTGAGATGGCCTGCACT 60.003 57.895 3.32 0.00 32.69 4.40
204 208 1.002990 TGTGAGATGGCCTGCACTG 60.003 57.895 3.32 0.00 32.69 3.66
213 217 3.036577 CCTGCACTGCCAACACAG 58.963 61.111 0.00 0.00 43.59 3.66
227 231 3.117794 CAACACAGCACATTTTCACCTG 58.882 45.455 0.00 0.00 0.00 4.00
235 239 0.245539 CATTTTCACCTGCCTGGCTG 59.754 55.000 21.03 19.25 40.22 4.85
238 258 3.557903 TTCACCTGCCTGGCTGCTC 62.558 63.158 21.03 0.00 40.22 4.26
247 267 4.377708 TGGCTGCTCGCGACATGT 62.378 61.111 3.71 0.00 40.44 3.21
315 347 1.006832 CCGGGAATTCAACGCACTAG 58.993 55.000 14.17 0.00 0.00 2.57
377 409 1.643832 CTAAAGAATCAGCGGCGGC 59.356 57.895 9.78 8.43 40.37 6.53
378 410 1.078778 TAAAGAATCAGCGGCGGCA 60.079 52.632 19.21 0.00 43.41 5.69
379 411 1.089481 TAAAGAATCAGCGGCGGCAG 61.089 55.000 19.21 10.85 43.41 4.85
380 412 4.845580 AGAATCAGCGGCGGCAGG 62.846 66.667 19.21 10.12 43.41 4.85
421 453 4.332637 CCACGAACGACCGACCGT 62.333 66.667 8.04 2.49 45.64 4.83
658 789 2.124612 CATGGCCACCGCTCATGA 60.125 61.111 8.16 0.00 42.00 3.07
659 790 1.527611 CATGGCCACCGCTCATGAT 60.528 57.895 8.16 0.00 42.00 2.45
661 792 3.589881 GGCCACCGCTCATGATGC 61.590 66.667 0.00 1.25 34.44 3.91
662 793 3.589881 GCCACCGCTCATGATGCC 61.590 66.667 0.00 0.00 0.00 4.40
663 794 3.274586 CCACCGCTCATGATGCCG 61.275 66.667 0.00 0.00 0.00 5.69
664 795 2.512286 CACCGCTCATGATGCCGT 60.512 61.111 0.00 0.82 0.00 5.68
665 796 2.202932 ACCGCTCATGATGCCGTC 60.203 61.111 0.00 0.00 0.00 4.79
666 797 3.333189 CCGCTCATGATGCCGTCG 61.333 66.667 0.00 0.00 0.00 5.12
667 798 2.278792 CGCTCATGATGCCGTCGA 60.279 61.111 0.00 0.00 0.00 4.20
668 799 1.662760 CGCTCATGATGCCGTCGAT 60.663 57.895 0.00 0.00 0.00 3.59
669 800 1.612469 CGCTCATGATGCCGTCGATC 61.612 60.000 0.00 0.00 0.00 3.69
670 801 1.612469 GCTCATGATGCCGTCGATCG 61.612 60.000 9.36 9.36 39.52 3.69
671 802 0.040067 CTCATGATGCCGTCGATCGA 60.040 55.000 15.15 15.15 42.86 3.59
672 803 0.598065 TCATGATGCCGTCGATCGAT 59.402 50.000 22.50 4.16 42.86 3.59
678 821 4.266070 CCGTCGATCGATGGGCGT 62.266 66.667 37.98 0.00 45.14 5.68
807 965 1.986698 AACTGCACGTGTACGATACC 58.013 50.000 18.38 0.00 43.02 2.73
896 1055 0.043652 CGTCTTTAAATACGCGCCCG 60.044 55.000 5.73 0.00 41.14 6.13
943 1102 2.177531 CCGTCGTTCGTCGTCCAT 59.822 61.111 10.21 0.00 40.80 3.41
944 1103 1.866496 CCGTCGTTCGTCGTCCATC 60.866 63.158 10.21 0.00 40.80 3.51
945 1104 2.206487 CGTCGTTCGTCGTCCATCG 61.206 63.158 4.05 0.00 40.80 3.84
1029 1237 0.378257 GAGAGCGAGAGAGTGCTGAG 59.622 60.000 0.00 0.00 42.60 3.35
1045 1253 4.479993 AGGCTGGCGGAGATGTGC 62.480 66.667 0.00 0.00 0.00 4.57
1249 1457 1.506718 GATGACCACGTCGAGCTCA 59.493 57.895 15.40 0.00 34.95 4.26
1270 1478 3.681835 GTGTCCACGGCCGACTCT 61.682 66.667 35.90 6.02 0.00 3.24
1279 1487 4.400109 GCCGACTCTGCGACGACA 62.400 66.667 0.00 0.00 32.56 4.35
1596 1813 3.626924 GGTGCTCGTGGAGGTGGT 61.627 66.667 0.00 0.00 0.00 4.16
1597 1814 2.048127 GTGCTCGTGGAGGTGGTC 60.048 66.667 0.00 0.00 0.00 4.02
1773 1996 9.427127 CGTTCGTTAATTTAGTAGTAGTACTCC 57.573 37.037 13.60 0.00 40.23 3.85
1837 2060 8.950208 ATCTTGTTGTTAGTTAGAAGGATAGC 57.050 34.615 0.00 0.00 0.00 2.97
1896 2123 1.734707 GCAGCAAAGTGGATCACATGC 60.735 52.381 15.89 15.89 44.15 4.06
1907 2134 2.611292 GGATCACATGCTGTTCAGTAGC 59.389 50.000 0.00 0.00 41.49 3.58
1944 2177 2.998316 AGCTGGACTGATTAGGCTTC 57.002 50.000 0.00 0.00 30.42 3.86
1947 2180 2.559440 CTGGACTGATTAGGCTTCTGC 58.441 52.381 0.00 0.00 38.76 4.26
1953 2186 4.133078 ACTGATTAGGCTTCTGCATTAGC 58.867 43.478 10.80 10.80 41.91 3.09
1954 2187 3.133691 TGATTAGGCTTCTGCATTAGCG 58.866 45.455 12.42 0.00 46.23 4.26
1966 2199 2.257894 GCATTAGCGATGGATCTCTCG 58.742 52.381 11.51 11.51 36.21 4.04
1970 2203 1.393603 AGCGATGGATCTCTCGACAA 58.606 50.000 17.69 0.00 37.05 3.18
1998 2231 9.772973 ATGTAGAATGGTTTATATACTCGCAAA 57.227 29.630 0.00 0.00 0.00 3.68
2064 2326 3.512680 GCGGGGATATCGTTCATTCTAG 58.487 50.000 0.00 0.00 0.00 2.43
2065 2327 3.056749 GCGGGGATATCGTTCATTCTAGT 60.057 47.826 0.00 0.00 0.00 2.57
2066 2328 4.157289 GCGGGGATATCGTTCATTCTAGTA 59.843 45.833 0.00 0.00 0.00 1.82
2077 2339 5.174035 CGTTCATTCTAGTATTTGCGAGGAG 59.826 44.000 0.00 0.00 0.00 3.69
2090 2352 1.726853 CGAGGAGACAAACCATGGTC 58.273 55.000 20.07 5.39 0.00 4.02
2095 2357 2.009774 GAGACAAACCATGGTCCATCG 58.990 52.381 20.07 7.59 34.58 3.84
2130 2392 4.988716 ACCGTCGTGGGAGGCAGA 62.989 66.667 1.57 0.00 44.64 4.26
2131 2393 4.135153 CCGTCGTGGGAGGCAGAG 62.135 72.222 0.00 0.00 0.00 3.35
2132 2394 4.135153 CGTCGTGGGAGGCAGAGG 62.135 72.222 0.00 0.00 0.00 3.69
2133 2395 4.459089 GTCGTGGGAGGCAGAGGC 62.459 72.222 0.00 0.00 40.13 4.70
2135 2397 4.463879 CGTGGGAGGCAGAGGCAG 62.464 72.222 0.00 0.00 43.71 4.85
2136 2398 3.005539 GTGGGAGGCAGAGGCAGA 61.006 66.667 0.00 0.00 43.71 4.26
2137 2399 2.686470 TGGGAGGCAGAGGCAGAG 60.686 66.667 0.00 0.00 43.71 3.35
2140 2402 4.527583 GAGGCAGAGGCAGAGGCG 62.528 72.222 0.00 0.00 43.71 5.52
2296 2615 7.177832 TCTCTATGATTTTTGGAACTACGGA 57.822 36.000 0.00 0.00 0.00 4.69
2398 2761 0.372334 GTTATACACAACGGCGGCTG 59.628 55.000 13.24 7.39 0.00 4.85
2404 2767 4.077184 CAACGGCGGCTGAGGGTA 62.077 66.667 17.15 0.00 0.00 3.69
2408 2771 2.737830 GGCGGCTGAGGGTATCTC 59.262 66.667 0.00 0.00 42.74 2.75
2416 2779 2.809665 GCTGAGGGTATCTCCATTGCTG 60.810 54.545 0.00 0.00 41.76 4.41
2422 2785 3.372025 GGGTATCTCCATTGCTGACCTTT 60.372 47.826 0.00 0.00 38.11 3.11
2440 2803 6.594937 TGACCTTTAAATTGTACACCGTATCC 59.405 38.462 0.00 0.00 0.00 2.59
2443 2806 6.092533 CCTTTAAATTGTACACCGTATCCGTT 59.907 38.462 0.00 0.00 0.00 4.44
2444 2807 7.361116 CCTTTAAATTGTACACCGTATCCGTTT 60.361 37.037 0.00 0.00 0.00 3.60
2451 2814 1.203994 CACCGTATCCGTTTGAGGACT 59.796 52.381 0.00 0.00 44.07 3.85
2460 2875 2.480419 CCGTTTGAGGACTGATGAACAC 59.520 50.000 0.00 0.00 0.00 3.32
2463 2878 3.855255 TTGAGGACTGATGAACACCAA 57.145 42.857 0.00 0.00 0.00 3.67
2482 2897 7.600065 ACACCAATATACGGACAGTGATATAC 58.400 38.462 0.00 0.00 0.00 1.47
2483 2898 7.450634 ACACCAATATACGGACAGTGATATACT 59.549 37.037 0.00 0.00 41.36 2.12
2484 2899 8.953313 CACCAATATACGGACAGTGATATACTA 58.047 37.037 0.00 0.00 37.60 1.82
2485 2900 9.175312 ACCAATATACGGACAGTGATATACTAG 57.825 37.037 0.00 0.00 37.60 2.57
2486 2901 9.392259 CCAATATACGGACAGTGATATACTAGA 57.608 37.037 0.00 0.00 37.60 2.43
2497 2912 2.376695 TATACTAGAAGCCAGGCGGT 57.623 50.000 5.55 0.00 33.28 5.68
2533 2948 6.068010 TCATTGGTGACCTTCAAATTGTACT 58.932 36.000 2.11 0.00 0.00 2.73
2534 2949 6.549364 TCATTGGTGACCTTCAAATTGTACTT 59.451 34.615 2.11 0.00 0.00 2.24
2542 2957 6.469410 ACCTTCAAATTGTACTTCGTATCCA 58.531 36.000 0.00 0.00 0.00 3.41
2552 2967 0.677288 TTCGTATCCATCCGCGGATT 59.323 50.000 37.36 25.39 43.58 3.01
2561 2976 0.107456 ATCCGCGGATTGATGAAGCT 59.893 50.000 34.60 10.05 0.00 3.74
2562 2977 0.750249 TCCGCGGATTGATGAAGCTA 59.250 50.000 27.28 0.00 0.00 3.32
2563 2978 1.143305 CCGCGGATTGATGAAGCTAG 58.857 55.000 24.07 0.00 0.00 3.42
2564 2979 1.539065 CCGCGGATTGATGAAGCTAGT 60.539 52.381 24.07 0.00 0.00 2.57
2565 2980 1.789464 CGCGGATTGATGAAGCTAGTC 59.211 52.381 0.00 0.00 0.00 2.59
2566 2981 2.544694 CGCGGATTGATGAAGCTAGTCT 60.545 50.000 0.00 0.00 0.00 3.24
2567 2982 3.304726 CGCGGATTGATGAAGCTAGTCTA 60.305 47.826 0.00 0.00 0.00 2.59
2568 2983 3.984633 GCGGATTGATGAAGCTAGTCTAC 59.015 47.826 0.00 0.00 0.00 2.59
2569 2984 4.222886 CGGATTGATGAAGCTAGTCTACG 58.777 47.826 0.00 0.00 0.00 3.51
2570 2985 4.551388 GGATTGATGAAGCTAGTCTACGG 58.449 47.826 0.00 0.00 0.00 4.02
2571 2986 4.551388 GATTGATGAAGCTAGTCTACGGG 58.449 47.826 0.00 0.00 0.00 5.28
2572 2987 1.681793 TGATGAAGCTAGTCTACGGGC 59.318 52.381 0.00 0.00 0.00 6.13
2573 2988 1.681793 GATGAAGCTAGTCTACGGGCA 59.318 52.381 0.00 0.00 0.00 5.36
2574 2989 0.815734 TGAAGCTAGTCTACGGGCAC 59.184 55.000 0.00 0.00 0.00 5.01
2575 2990 1.104630 GAAGCTAGTCTACGGGCACT 58.895 55.000 0.00 0.00 0.00 4.40
2576 2991 0.818296 AAGCTAGTCTACGGGCACTG 59.182 55.000 0.00 0.00 42.99 3.66
2577 2992 0.034380 AGCTAGTCTACGGGCACTGA 60.034 55.000 0.00 0.00 38.67 3.41
2578 2993 1.033574 GCTAGTCTACGGGCACTGAT 58.966 55.000 0.00 0.00 38.67 2.90
2579 2994 2.158652 AGCTAGTCTACGGGCACTGATA 60.159 50.000 0.00 0.00 38.67 2.15
2580 2995 2.820787 GCTAGTCTACGGGCACTGATAT 59.179 50.000 0.00 0.00 38.67 1.63
2581 2996 4.008330 GCTAGTCTACGGGCACTGATATA 58.992 47.826 0.00 0.00 38.67 0.86
2582 2997 4.095185 GCTAGTCTACGGGCACTGATATAG 59.905 50.000 0.00 0.00 38.67 1.31
2583 2998 3.422796 AGTCTACGGGCACTGATATAGG 58.577 50.000 0.00 0.00 38.67 2.57
2584 2999 3.074094 AGTCTACGGGCACTGATATAGGA 59.926 47.826 0.00 0.00 38.67 2.94
2585 3000 3.440872 GTCTACGGGCACTGATATAGGAG 59.559 52.174 0.00 0.00 38.67 3.69
2586 3001 0.969894 ACGGGCACTGATATAGGAGC 59.030 55.000 0.00 0.00 38.67 4.70
2587 3002 0.247736 CGGGCACTGATATAGGAGCC 59.752 60.000 0.00 0.00 45.58 4.70
2589 3004 2.464157 GGCACTGATATAGGAGCCAC 57.536 55.000 9.73 0.00 45.60 5.01
2590 3005 1.002544 GGCACTGATATAGGAGCCACC 59.997 57.143 9.73 0.00 45.60 4.61
2591 3006 1.694150 GCACTGATATAGGAGCCACCA 59.306 52.381 0.47 0.00 42.04 4.17
2592 3007 2.304180 GCACTGATATAGGAGCCACCAT 59.696 50.000 0.47 0.00 42.04 3.55
2593 3008 3.618507 GCACTGATATAGGAGCCACCATC 60.619 52.174 0.47 0.00 42.04 3.51
2594 3009 3.055530 CACTGATATAGGAGCCACCATCC 60.056 52.174 0.47 0.00 42.04 3.51
2595 3010 3.176411 CTGATATAGGAGCCACCATCCA 58.824 50.000 0.47 0.00 42.04 3.41
2596 3011 2.906389 TGATATAGGAGCCACCATCCAC 59.094 50.000 0.47 0.00 42.04 4.02
2597 3012 1.338107 TATAGGAGCCACCATCCACG 58.662 55.000 0.47 0.00 42.04 4.94
2598 3013 1.410850 ATAGGAGCCACCATCCACGG 61.411 60.000 0.47 0.00 42.04 4.94
2599 3014 2.523740 TAGGAGCCACCATCCACGGA 62.524 60.000 0.47 0.00 42.04 4.69
2600 3015 2.746375 GGAGCCACCATCCACGGAT 61.746 63.158 0.00 0.00 36.79 4.18
2601 3016 1.227674 GAGCCACCATCCACGGATC 60.228 63.158 0.00 0.00 31.62 3.36
2602 3017 1.971505 GAGCCACCATCCACGGATCA 61.972 60.000 0.00 0.00 35.28 2.92
2603 3018 1.077787 GCCACCATCCACGGATCAA 60.078 57.895 0.00 0.00 31.62 2.57
2604 3019 0.466189 GCCACCATCCACGGATCAAT 60.466 55.000 0.00 0.00 31.62 2.57
2605 3020 1.311859 CCACCATCCACGGATCAATG 58.688 55.000 0.00 0.00 31.62 2.82
2606 3021 1.134128 CCACCATCCACGGATCAATGA 60.134 52.381 0.00 0.00 31.62 2.57
2607 3022 2.642427 CACCATCCACGGATCAATGAA 58.358 47.619 0.00 0.00 31.62 2.57
2608 3023 2.615447 CACCATCCACGGATCAATGAAG 59.385 50.000 0.00 0.00 31.62 3.02
2609 3024 1.605710 CCATCCACGGATCAATGAAGC 59.394 52.381 0.00 0.00 31.62 3.86
2610 3025 1.605710 CATCCACGGATCAATGAAGCC 59.394 52.381 0.00 0.00 31.62 4.35
2611 3026 0.617935 TCCACGGATCAATGAAGCCA 59.382 50.000 6.38 0.00 0.00 4.75
2618 3033 3.557595 CGGATCAATGAAGCCAAGTCTAC 59.442 47.826 6.38 0.00 0.00 2.59
2633 3048 4.368565 AGTCTACGGGCAGTGATATAGA 57.631 45.455 0.00 0.00 0.00 1.98
2666 3082 1.169577 ACGTGGCCGCATCAATTTAA 58.830 45.000 18.18 0.00 37.70 1.52
2736 3152 5.429957 AGAATTCAGCAAAGTTCAGACAC 57.570 39.130 8.44 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 0.389296 TGTCTAACATGTGGACCGCG 60.389 55.000 21.67 0.00 0.00 6.46
70 71 1.308069 CCTGGAATGGACGCCTTGTG 61.308 60.000 0.00 0.00 0.00 3.33
72 73 2.409870 GCCTGGAATGGACGCCTTG 61.410 63.158 0.00 0.00 0.00 3.61
81 82 4.820744 CACCCCCGGCCTGGAATG 62.821 72.222 16.02 8.48 42.00 2.67
153 155 5.595257 TTATAAGCCATGCTGATTTTGCA 57.405 34.783 0.00 0.00 44.95 4.08
155 157 7.327761 GCAGTATTATAAGCCATGCTGATTTTG 59.672 37.037 6.19 0.00 39.62 2.44
169 171 5.588240 TCTCACACCACGCAGTATTATAAG 58.412 41.667 0.00 0.00 41.61 1.73
186 190 1.002990 CAGTGCAGGCCATCTCACA 60.003 57.895 5.01 0.00 32.25 3.58
203 207 1.479730 TGAAAATGTGCTGTGTTGGCA 59.520 42.857 0.00 0.00 37.36 4.92
204 208 1.860326 GTGAAAATGTGCTGTGTTGGC 59.140 47.619 0.00 0.00 0.00 4.52
213 217 0.037975 CCAGGCAGGTGAAAATGTGC 60.038 55.000 0.00 0.00 35.07 4.57
241 261 3.239941 CCGTATCGTTCTTTCGACATGTC 59.760 47.826 16.21 16.21 42.56 3.06
247 267 2.797087 GCCATCCGTATCGTTCTTTCGA 60.797 50.000 0.00 0.00 43.86 3.71
315 347 2.824041 CCATGGGGTGCTACGTGC 60.824 66.667 2.85 0.00 43.25 5.34
390 422 2.010817 CGTGGCTTTGCTTTGTCGC 61.011 57.895 0.00 0.00 0.00 5.19
532 641 2.733593 GACGTGAGCCGCGAGTTT 60.734 61.111 8.23 0.00 39.94 2.66
602 733 4.935495 ACACCTGGTGGCGCACTG 62.935 66.667 29.05 3.46 37.94 3.66
658 789 2.340078 CCCATCGATCGACGGCAT 59.660 61.111 24.30 3.24 42.82 4.40
659 790 4.585526 GCCCATCGATCGACGGCA 62.586 66.667 35.83 13.41 40.59 5.69
661 792 4.266070 ACGCCCATCGATCGACGG 62.266 66.667 22.89 22.89 42.82 4.79
662 793 3.024609 CACGCCCATCGATCGACG 61.025 66.667 22.06 20.92 41.67 5.12
663 794 1.658717 CTCACGCCCATCGATCGAC 60.659 63.158 22.06 6.67 41.67 4.20
664 795 2.721859 CTCACGCCCATCGATCGA 59.278 61.111 21.86 21.86 41.67 3.59
665 796 2.355126 CCTCACGCCCATCGATCG 60.355 66.667 9.36 9.36 41.67 3.69
666 797 2.663188 GCCTCACGCCCATCGATC 60.663 66.667 0.00 0.00 41.67 3.69
860 1018 2.409651 GACGACCGAGCTAGCCAG 59.590 66.667 12.13 5.51 0.00 4.85
862 1020 3.452024 GACGACGACCGAGCTAGCC 62.452 68.421 12.13 1.79 41.76 3.93
870 1028 2.036250 GCGTATTTAAAGACGACGACCG 60.036 50.000 32.75 10.34 45.62 4.79
872 1030 2.590632 GCGCGTATTTAAAGACGACGAC 60.591 50.000 33.99 26.06 45.62 4.34
896 1055 2.435059 GTGTGCTTCTCCTCGCCC 60.435 66.667 0.00 0.00 0.00 6.13
933 1092 1.690283 GACGAGACGATGGACGACGA 61.690 60.000 0.00 0.00 45.77 4.20
941 1100 1.644372 CGGGAGAGACGAGACGATG 59.356 63.158 0.00 0.00 0.00 3.84
943 1102 2.125229 CCGGGAGAGACGAGACGA 60.125 66.667 0.00 0.00 0.00 4.20
944 1103 3.878519 GCCGGGAGAGACGAGACG 61.879 72.222 2.18 0.00 0.00 4.18
945 1104 2.438795 AGCCGGGAGAGACGAGAC 60.439 66.667 2.18 0.00 0.00 3.36
965 1124 1.652930 CGCGCGCTCTTCTAGACTC 60.653 63.158 30.48 0.00 0.00 3.36
1015 1187 1.139308 CAGCCTCAGCACTCTCTCG 59.861 63.158 0.00 0.00 43.56 4.04
1270 1478 2.050714 GGAGTCGTTGTCGTCGCA 60.051 61.111 0.00 0.00 38.33 5.10
1273 1481 2.804090 GCCGGAGTCGTTGTCGTC 60.804 66.667 5.05 0.00 38.33 4.20
1691 1911 1.247567 GGGTCATGTGTTGTTGGAGG 58.752 55.000 0.00 0.00 0.00 4.30
1747 1967 9.427127 GGAGTACTACTACTAAATTAACGAACG 57.573 37.037 0.00 0.00 32.96 3.95
1770 1993 8.028354 TCGACTCTCTAGAAATATACTACGGAG 58.972 40.741 0.00 0.00 0.00 4.63
1771 1994 7.890515 TCGACTCTCTAGAAATATACTACGGA 58.109 38.462 0.00 0.00 0.00 4.69
1772 1995 7.814107 ACTCGACTCTCTAGAAATATACTACGG 59.186 40.741 0.00 0.00 0.00 4.02
1773 1996 8.746922 ACTCGACTCTCTAGAAATATACTACG 57.253 38.462 0.00 0.00 0.00 3.51
1794 2017 8.895845 CAACAAGATTTGATCAACTTTTACTCG 58.104 33.333 7.89 0.00 0.00 4.18
1837 2060 5.815222 TCCATTTGGATTACATCGTACAGTG 59.185 40.000 0.00 0.00 39.78 3.66
1869 2096 2.263540 CACTTTGCTGCCATGGCC 59.736 61.111 33.44 19.61 41.09 5.36
1896 2123 8.981724 TTACTAACAAGTATGCTACTGAACAG 57.018 34.615 0.00 0.00 39.39 3.16
1907 2134 9.601217 AGTCCAGCTAAATTACTAACAAGTATG 57.399 33.333 0.00 0.00 0.00 2.39
1914 2142 9.262358 CCTAATCAGTCCAGCTAAATTACTAAC 57.738 37.037 0.00 0.00 0.00 2.34
1944 2177 3.252400 GAGAGATCCATCGCTAATGCAG 58.748 50.000 0.00 0.00 37.07 4.41
1947 2180 3.057946 TGTCGAGAGATCCATCGCTAATG 60.058 47.826 11.31 0.00 45.19 1.90
1953 2186 5.053140 ACATATTGTCGAGAGATCCATCG 57.947 43.478 10.17 10.17 45.19 3.84
1954 2187 7.384439 TCTACATATTGTCGAGAGATCCATC 57.616 40.000 0.00 0.00 45.19 3.51
1994 2227 7.010460 GCATAAACCATCCTACATTCTTTTTGC 59.990 37.037 0.00 0.00 0.00 3.68
1998 2231 7.560991 TCATGCATAAACCATCCTACATTCTTT 59.439 33.333 0.00 0.00 0.00 2.52
2001 2234 6.882610 TCATGCATAAACCATCCTACATTC 57.117 37.500 0.00 0.00 0.00 2.67
2009 2271 8.190122 TGACAATAGTTTCATGCATAAACCATC 58.810 33.333 19.39 13.59 37.51 3.51
2064 2326 3.071479 TGGTTTGTCTCCTCGCAAATAC 58.929 45.455 0.00 0.00 37.02 1.89
2065 2327 3.410631 TGGTTTGTCTCCTCGCAAATA 57.589 42.857 0.00 0.00 37.02 1.40
2066 2328 2.270352 TGGTTTGTCTCCTCGCAAAT 57.730 45.000 0.00 0.00 37.02 2.32
2077 2339 1.737793 GACGATGGACCATGGTTTGTC 59.262 52.381 20.85 18.08 33.22 3.18
2090 2352 3.325870 TGCAACTTGTTCTAGACGATGG 58.674 45.455 0.00 0.00 0.00 3.51
2095 2357 3.311596 ACGGTTTGCAACTTGTTCTAGAC 59.688 43.478 0.00 0.00 0.00 2.59
2116 2378 4.459089 GCCTCTGCCTCCCACGAC 62.459 72.222 0.00 0.00 0.00 4.34
2118 2380 4.463879 CTGCCTCTGCCTCCCACG 62.464 72.222 0.00 0.00 36.33 4.94
2133 2395 3.982316 TTGATGCTGCCCGCCTCTG 62.982 63.158 0.00 0.00 38.05 3.35
2134 2396 3.052909 ATTGATGCTGCCCGCCTCT 62.053 57.895 0.00 0.00 38.05 3.69
2135 2397 2.517875 ATTGATGCTGCCCGCCTC 60.518 61.111 0.00 0.00 38.05 4.70
2136 2398 2.831742 CATTGATGCTGCCCGCCT 60.832 61.111 0.00 0.00 38.05 5.52
2137 2399 3.908081 CCATTGATGCTGCCCGCC 61.908 66.667 0.00 0.00 38.05 6.13
2140 2402 2.046938 CATCCCATTGATGCTGCCC 58.953 57.895 0.00 0.00 44.16 5.36
2184 2446 5.375417 TGTATTGTGGATGCTGTTTTCTG 57.625 39.130 0.00 0.00 0.00 3.02
2279 2548 4.759516 TGCTTCCGTAGTTCCAAAAATC 57.240 40.909 0.00 0.00 0.00 2.17
2296 2615 6.827586 AATTTGCCATGATTGAATTTGCTT 57.172 29.167 0.00 0.00 0.00 3.91
2339 2702 6.097839 TGCGGGAGAAATACTTGTATTACTCT 59.902 38.462 6.46 6.86 0.00 3.24
2372 2735 3.598299 GCCGTTGTGTATAACTGGGTTA 58.402 45.455 0.00 0.00 32.36 2.85
2388 2751 3.081409 ATACCCTCAGCCGCCGTT 61.081 61.111 0.00 0.00 0.00 4.44
2398 2761 2.224402 GGTCAGCAATGGAGATACCCTC 60.224 54.545 0.00 0.00 41.22 4.30
2404 2767 6.438425 ACAATTTAAAGGTCAGCAATGGAGAT 59.562 34.615 0.00 0.00 0.00 2.75
2408 2771 6.586082 GTGTACAATTTAAAGGTCAGCAATGG 59.414 38.462 0.00 0.00 0.00 3.16
2416 2779 7.008440 GGATACGGTGTACAATTTAAAGGTC 57.992 40.000 0.00 0.00 0.00 3.85
2440 2803 2.480419 GGTGTTCATCAGTCCTCAAACG 59.520 50.000 0.00 0.00 0.00 3.60
2443 2806 3.855255 TTGGTGTTCATCAGTCCTCAA 57.145 42.857 0.00 0.00 0.00 3.02
2444 2807 5.698741 ATATTGGTGTTCATCAGTCCTCA 57.301 39.130 0.00 0.00 0.00 3.86
2451 2814 5.105106 ACTGTCCGTATATTGGTGTTCATCA 60.105 40.000 0.00 0.00 0.00 3.07
2460 2875 9.392259 TCTAGTATATCACTGTCCGTATATTGG 57.608 37.037 0.00 0.00 38.24 3.16
2463 2878 9.111613 GCTTCTAGTATATCACTGTCCGTATAT 57.888 37.037 0.00 0.00 38.24 0.86
2482 2897 1.473434 CCTAAACCGCCTGGCTTCTAG 60.473 57.143 17.92 11.20 39.70 2.43
2483 2898 0.539986 CCTAAACCGCCTGGCTTCTA 59.460 55.000 17.92 2.09 39.70 2.10
2484 2899 1.299976 CCTAAACCGCCTGGCTTCT 59.700 57.895 17.92 0.90 39.70 2.85
2485 2900 1.749258 CCCTAAACCGCCTGGCTTC 60.749 63.158 17.92 0.00 39.70 3.86
2486 2901 1.202769 TACCCTAAACCGCCTGGCTT 61.203 55.000 17.92 7.01 39.70 4.35
2497 2912 5.491078 AGGTCACCAATGAAGATACCCTAAA 59.509 40.000 0.00 0.00 36.31 1.85
2533 2948 2.347630 ATCCGCGGATGGATACGAA 58.652 52.632 38.62 9.34 46.95 3.85
2534 2949 4.090723 ATCCGCGGATGGATACGA 57.909 55.556 38.62 10.21 46.95 3.43
2542 2957 0.107456 AGCTTCATCAATCCGCGGAT 59.893 50.000 34.60 34.60 36.23 4.18
2552 2967 1.681793 GCCCGTAGACTAGCTTCATCA 59.318 52.381 0.00 0.00 0.00 3.07
2561 2976 4.287845 TCCTATATCAGTGCCCGTAGACTA 59.712 45.833 0.00 0.00 0.00 2.59
2562 2977 3.074094 TCCTATATCAGTGCCCGTAGACT 59.926 47.826 0.00 0.00 0.00 3.24
2563 2978 3.418995 TCCTATATCAGTGCCCGTAGAC 58.581 50.000 0.00 0.00 0.00 2.59
2564 2979 3.687125 CTCCTATATCAGTGCCCGTAGA 58.313 50.000 0.00 0.00 0.00 2.59
2565 2980 2.164624 GCTCCTATATCAGTGCCCGTAG 59.835 54.545 0.00 0.00 0.00 3.51
2566 2981 2.168496 GCTCCTATATCAGTGCCCGTA 58.832 52.381 0.00 0.00 0.00 4.02
2567 2982 0.969894 GCTCCTATATCAGTGCCCGT 59.030 55.000 0.00 0.00 0.00 5.28
2568 2983 0.247736 GGCTCCTATATCAGTGCCCG 59.752 60.000 6.70 0.00 36.52 6.13
2569 2984 1.002544 GTGGCTCCTATATCAGTGCCC 59.997 57.143 12.83 4.26 39.74 5.36
2570 2985 1.002544 GGTGGCTCCTATATCAGTGCC 59.997 57.143 9.84 9.84 40.44 5.01
2571 2986 1.694150 TGGTGGCTCCTATATCAGTGC 59.306 52.381 7.19 0.00 37.07 4.40
2572 2987 3.055530 GGATGGTGGCTCCTATATCAGTG 60.056 52.174 7.19 0.00 37.07 3.66
2573 2988 3.177228 GGATGGTGGCTCCTATATCAGT 58.823 50.000 7.19 0.00 37.07 3.41
2574 2989 3.055530 GTGGATGGTGGCTCCTATATCAG 60.056 52.174 7.19 0.00 37.07 2.90
2575 2990 2.906389 GTGGATGGTGGCTCCTATATCA 59.094 50.000 7.19 0.00 37.07 2.15
2576 2991 2.093973 CGTGGATGGTGGCTCCTATATC 60.094 54.545 7.19 1.83 37.07 1.63
2577 2992 1.902508 CGTGGATGGTGGCTCCTATAT 59.097 52.381 7.19 0.00 37.07 0.86
2578 2993 1.338107 CGTGGATGGTGGCTCCTATA 58.662 55.000 7.19 0.00 37.07 1.31
2579 2994 1.410850 CCGTGGATGGTGGCTCCTAT 61.411 60.000 7.19 0.00 37.07 2.57
2580 2995 2.063979 CCGTGGATGGTGGCTCCTA 61.064 63.158 7.19 0.00 37.07 2.94
2581 2996 3.402681 CCGTGGATGGTGGCTCCT 61.403 66.667 7.19 0.00 37.07 3.69
2582 2997 2.666596 GATCCGTGGATGGTGGCTCC 62.667 65.000 6.03 0.00 34.60 4.70
2583 2998 1.227674 GATCCGTGGATGGTGGCTC 60.228 63.158 6.03 0.00 34.60 4.70
2584 2999 1.561769 TTGATCCGTGGATGGTGGCT 61.562 55.000 6.03 0.00 34.60 4.75
2585 3000 0.466189 ATTGATCCGTGGATGGTGGC 60.466 55.000 6.03 0.00 34.60 5.01
2586 3001 1.134128 TCATTGATCCGTGGATGGTGG 60.134 52.381 6.03 0.00 34.60 4.61
2587 3002 2.330440 TCATTGATCCGTGGATGGTG 57.670 50.000 6.03 2.67 34.60 4.17
2588 3003 2.923121 CTTCATTGATCCGTGGATGGT 58.077 47.619 6.03 0.00 34.60 3.55
2589 3004 1.605710 GCTTCATTGATCCGTGGATGG 59.394 52.381 6.03 0.00 34.60 3.51
2590 3005 1.605710 GGCTTCATTGATCCGTGGATG 59.394 52.381 6.03 0.00 34.60 3.51
2591 3006 1.212688 TGGCTTCATTGATCCGTGGAT 59.787 47.619 0.00 0.00 37.59 3.41
2592 3007 0.617935 TGGCTTCATTGATCCGTGGA 59.382 50.000 0.00 0.00 0.00 4.02
2593 3008 1.402968 CTTGGCTTCATTGATCCGTGG 59.597 52.381 0.00 0.00 0.00 4.94
2594 3009 2.086869 ACTTGGCTTCATTGATCCGTG 58.913 47.619 0.00 0.00 0.00 4.94
2595 3010 2.026822 AGACTTGGCTTCATTGATCCGT 60.027 45.455 0.00 0.00 0.00 4.69
2596 3011 2.636830 AGACTTGGCTTCATTGATCCG 58.363 47.619 0.00 0.00 0.00 4.18
2597 3012 3.557595 CGTAGACTTGGCTTCATTGATCC 59.442 47.826 0.00 0.00 0.00 3.36
2598 3013 3.557595 CCGTAGACTTGGCTTCATTGATC 59.442 47.826 0.00 0.00 0.00 2.92
2599 3014 3.535561 CCGTAGACTTGGCTTCATTGAT 58.464 45.455 0.00 0.00 0.00 2.57
2600 3015 2.354704 CCCGTAGACTTGGCTTCATTGA 60.355 50.000 0.00 0.00 0.00 2.57
2601 3016 2.009774 CCCGTAGACTTGGCTTCATTG 58.990 52.381 0.00 0.00 0.00 2.82
2602 3017 1.679032 GCCCGTAGACTTGGCTTCATT 60.679 52.381 0.00 0.00 42.01 2.57
2603 3018 0.107654 GCCCGTAGACTTGGCTTCAT 60.108 55.000 0.00 0.00 42.01 2.57
2604 3019 1.295423 GCCCGTAGACTTGGCTTCA 59.705 57.895 0.00 0.00 42.01 3.02
2605 3020 0.741221 CTGCCCGTAGACTTGGCTTC 60.741 60.000 10.56 0.00 45.56 3.86
2606 3021 1.296715 CTGCCCGTAGACTTGGCTT 59.703 57.895 10.56 0.00 45.56 4.35
2607 3022 1.913762 ACTGCCCGTAGACTTGGCT 60.914 57.895 10.56 0.00 45.56 4.75
2608 3023 1.741770 CACTGCCCGTAGACTTGGC 60.742 63.158 0.00 0.00 45.56 4.52
2609 3024 0.537188 ATCACTGCCCGTAGACTTGG 59.463 55.000 0.00 0.00 0.00 3.61
2610 3025 3.735237 ATATCACTGCCCGTAGACTTG 57.265 47.619 0.00 0.00 0.00 3.16
2611 3026 4.726583 TCTATATCACTGCCCGTAGACTT 58.273 43.478 0.00 0.00 0.00 3.01
2618 3033 1.344438 TGGCTTCTATATCACTGCCCG 59.656 52.381 0.00 0.00 39.60 6.13
2633 3048 1.973281 CACGTTGGATGGCTGGCTT 60.973 57.895 2.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.