Multiple sequence alignment - TraesCS7D01G158400

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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 TraesCS7D01G158400 chr7D 100.000 2594 0 0 1 2594 106479266 106476673 0.000000e+00 4791.0
1 TraesCS7D01G158400 chr7D 93.060 1023 48 12 806 1824 106363571 106364574 0.000000e+00 1474.0
2 TraesCS7D01G158400 chr7D 91.813 513 19 8 93 599 106360476 106360971 0.000000e+00 693.0
3 TraesCS7D01G158400 chr7D 91.579 380 26 4 1818 2191 106364988 106365367 1.060000e-143 520.0
4 TraesCS7D01G158400 chr7D 95.769 260 11 0 2173 2432 106367878 106368137 1.110000e-113 420.0
5 TraesCS7D01G158400 chr7D 93.774 257 14 1 2178 2432 106366116 106366372 4.050000e-103 385.0
6 TraesCS7D01G158400 chr7D 96.296 162 3 1 2434 2592 406339954 406339793 1.980000e-66 263.0
7 TraesCS7D01G158400 chr7D 95.758 165 4 1 2431 2592 550169662 550169826 1.980000e-66 263.0
8 TraesCS7D01G158400 chr7D 91.304 161 7 4 647 807 106363382 106363535 2.020000e-51 213.0
9 TraesCS7D01G158400 chr7D 90.756 119 6 3 20 133 106360354 106360472 1.240000e-33 154.0
10 TraesCS7D01G158400 chr2D 90.625 1536 87 15 806 2333 50669546 50671032 0.000000e+00 1986.0
11 TraesCS7D01G158400 chr2D 91.235 810 41 18 3 801 50668714 50669504 0.000000e+00 1075.0
12 TraesCS7D01G158400 chr2D 88.136 59 5 2 1828 1886 642702214 642702270 4.630000e-08 69.4
13 TraesCS7D01G158400 chr2B 92.679 1120 54 13 822 1936 78837071 78838167 0.000000e+00 1589.0
14 TraesCS7D01G158400 chr2B 91.508 789 36 16 3 779 78836301 78837070 0.000000e+00 1057.0
15 TraesCS7D01G158400 chr2B 90.640 203 16 1 2134 2333 78838275 78838477 1.530000e-67 267.0
16 TraesCS7D01G158400 chr2B 93.333 90 6 0 1990 2079 78838176 78838265 1.620000e-27 134.0
17 TraesCS7D01G158400 chr7B 93.803 468 23 3 109 571 64945098 64945564 0.000000e+00 699.0
18 TraesCS7D01G158400 chr7B 93.051 331 23 0 1887 2217 64945588 64945918 3.880000e-133 484.0
19 TraesCS7D01G158400 chr7B 96.875 32 1 0 776 807 337539785 337539816 1.000000e-03 54.7
20 TraesCS7D01G158400 chr6D 95.808 167 4 1 2431 2594 298319360 298319526 1.530000e-67 267.0
21 TraesCS7D01G158400 chr6D 93.478 46 2 1 1841 1886 453107805 453107849 1.670000e-07 67.6
22 TraesCS7D01G158400 chr5D 96.296 162 3 1 2434 2592 17030923 17030762 1.980000e-66 263.0
23 TraesCS7D01G158400 chr5D 96.296 162 3 1 2434 2592 513648651 513648490 1.980000e-66 263.0
24 TraesCS7D01G158400 chr3D 96.296 162 3 1 2434 2592 556775334 556775173 1.980000e-66 263.0
25 TraesCS7D01G158400 chr3D 95.758 165 4 1 2431 2592 573761426 573761590 1.980000e-66 263.0
26 TraesCS7D01G158400 chr1D 95.758 165 3 2 2434 2594 468270697 468270533 1.980000e-66 263.0
27 TraesCS7D01G158400 chr4D 95.732 164 4 1 2431 2591 36428465 36428628 7.120000e-66 261.0
28 TraesCS7D01G158400 chr4D 93.478 46 2 1 1841 1886 437861491 437861447 1.670000e-07 67.6
29 TraesCS7D01G158400 chr5A 88.136 59 5 2 1828 1886 73149363 73149307 4.630000e-08 69.4
30 TraesCS7D01G158400 chr3B 88.136 59 5 2 1828 1886 677274477 677274533 4.630000e-08 69.4
31 TraesCS7D01G158400 chr3B 88.136 59 4 3 1829 1886 69698178 69698234 1.670000e-07 67.6
32 TraesCS7D01G158400 chr1A 100.000 32 0 0 776 807 108963170 108963139 2.790000e-05 60.2
33 TraesCS7D01G158400 chr7A 96.875 32 1 0 776 807 652562856 652562825 1.000000e-03 54.7
34 TraesCS7D01G158400 chr7A 100.000 28 0 0 776 803 632520532 632520505 5.000000e-03 52.8
35 TraesCS7D01G158400 chr1B 100.000 28 0 0 780 807 507470344 507470317 5.000000e-03 52.8


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 TraesCS7D01G158400 chr7D 106476673 106479266 2593 True 4791.000000 4791 100.000000 1 2594 1 chr7D.!!$R1 2593
1 TraesCS7D01G158400 chr7D 106360354 106368137 7783 False 551.285714 1474 92.579286 20 2432 7 chr7D.!!$F2 2412
2 TraesCS7D01G158400 chr2D 50668714 50671032 2318 False 1530.500000 1986 90.930000 3 2333 2 chr2D.!!$F2 2330
3 TraesCS7D01G158400 chr2B 78836301 78838477 2176 False 761.750000 1589 92.040000 3 2333 4 chr2B.!!$F1 2330
4 TraesCS7D01G158400 chr7B 64945098 64945918 820 False 591.500000 699 93.427000 109 2217 2 chr7B.!!$F2 2108

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
880 3368 1.271656 GACAAAGGCAGCTGCTGAATT 59.728 47.619 35.82 22.32 41.7 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2569 8027 0.179081 GTAGGAGTTCACCCCGCATC 60.179 60.0 0.0 0.0 0.0 3.91 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
102 108 1.543614 CAACTCTCGAGCTGTCATCG 58.456 55.000 7.81 0.00 41.50 3.84
133 185 9.793259 CATTGGTCATATATAGGTTTACAAGGT 57.207 33.333 0.00 0.00 0.00 3.50
136 192 8.873144 TGGTCATATATAGGTTTACAAGGTACC 58.127 37.037 2.73 2.73 0.00 3.34
138 194 9.924650 GTCATATATAGGTTTACAAGGTACCTG 57.075 37.037 17.14 12.24 42.14 4.00
206 262 1.279271 ACAGCAGACACCATCCCTAAC 59.721 52.381 0.00 0.00 0.00 2.34
515 594 3.719268 TCCTTGCATTCCACATACAGT 57.281 42.857 0.00 0.00 0.00 3.55
536 615 2.976185 TCCACATACCACACAGGAGAAA 59.024 45.455 0.00 0.00 41.22 2.52
638 725 3.922171 ATCCCTAAAAGTGCTCCAGAG 57.078 47.619 0.00 0.00 0.00 3.35
696 3147 6.072175 TCCTCCAATTACTTTGAATTTCACGG 60.072 38.462 0.00 0.00 37.53 4.94
697 3148 5.465935 TCCAATTACTTTGAATTTCACGGC 58.534 37.500 0.00 0.00 37.53 5.68
698 3149 5.010112 TCCAATTACTTTGAATTTCACGGCA 59.990 36.000 0.00 0.00 37.53 5.69
699 3150 5.868801 CCAATTACTTTGAATTTCACGGCAT 59.131 36.000 0.00 0.00 37.53 4.40
747 3198 3.438781 CGCCACCAGAAGCATTTAACTTA 59.561 43.478 0.00 0.00 0.00 2.24
840 3328 2.032620 AGTACCTTCTAGGACATGCCG 58.967 52.381 0.00 0.00 43.43 5.69
880 3368 1.271656 GACAAAGGCAGCTGCTGAATT 59.728 47.619 35.82 22.32 41.70 2.17
1030 3522 2.688666 ATCTCAAGGCCCAGGCGA 60.689 61.111 0.00 0.00 43.06 5.54
1052 3544 3.736100 CGCGATGGGTTTGCTGCA 61.736 61.111 0.00 0.00 31.94 4.41
1064 3556 2.124024 GCTGCATGGCATCTCCCA 60.124 61.111 0.00 0.00 38.13 4.37
1101 3593 2.796304 GAGTTCATCGACTCAGCTCTG 58.204 52.381 0.00 0.00 44.30 3.35
1179 3671 2.743718 CAACGGCTCACCTCCAGT 59.256 61.111 0.00 0.00 0.00 4.00
1239 3731 3.699894 CTGTCGGTGGAGGCAGCT 61.700 66.667 0.00 0.00 37.02 4.24
1267 3759 1.078143 GTCTCCCGCTGGCTTGATT 60.078 57.895 0.00 0.00 0.00 2.57
1362 3854 1.033746 CCAATGCCGGTGAGATGCTT 61.034 55.000 1.90 0.00 0.00 3.91
1378 3870 1.592400 GCTTGAGGCAGCTGCAATGA 61.592 55.000 37.63 18.97 44.36 2.57
1447 3939 3.855255 TCAACCACATTCCTCTCAACA 57.145 42.857 0.00 0.00 0.00 3.33
1457 3949 0.108615 CCTCTCAACATTCGCGAGGT 60.109 55.000 9.59 9.47 37.17 3.85
1566 4058 4.479993 GCCAGAGCCCGTGATGCT 62.480 66.667 0.00 0.00 43.03 3.79
1601 4093 5.422331 TCCTTGACTTCCTGTAGTATCAAGG 59.578 44.000 20.03 20.03 44.08 3.61
1610 4102 4.526262 CCTGTAGTATCAAGGCTAGCATCT 59.474 45.833 18.24 4.86 0.00 2.90
1632 4128 8.562892 CATCTTTTTATGGCTTCCTGTAGTATG 58.437 37.037 0.00 0.00 0.00 2.39
1638 4134 4.353777 TGGCTTCCTGTAGTATGAAGACT 58.646 43.478 11.78 0.00 43.20 3.24
1639 4135 5.516044 TGGCTTCCTGTAGTATGAAGACTA 58.484 41.667 11.78 0.00 43.20 2.59
1640 4136 5.594725 TGGCTTCCTGTAGTATGAAGACTAG 59.405 44.000 11.78 0.00 43.20 2.57
1641 4137 5.508320 GGCTTCCTGTAGTATGAAGACTAGC 60.508 48.000 9.82 0.00 40.31 3.42
1642 4138 5.067936 GCTTCCTGTAGTATGAAGACTAGCA 59.932 44.000 9.82 0.00 38.16 3.49
1643 4139 6.239176 GCTTCCTGTAGTATGAAGACTAGCAT 60.239 42.308 9.82 0.00 38.16 3.79
1644 4140 6.885952 TCCTGTAGTATGAAGACTAGCATC 57.114 41.667 0.00 0.00 32.56 3.91
1645 4141 6.606069 TCCTGTAGTATGAAGACTAGCATCT 58.394 40.000 0.00 0.00 32.56 2.90
1646 4142 7.063593 TCCTGTAGTATGAAGACTAGCATCTT 58.936 38.462 0.00 0.00 41.74 2.40
1647 4143 7.561722 TCCTGTAGTATGAAGACTAGCATCTTT 59.438 37.037 0.00 0.00 39.08 2.52
1648 4144 8.200792 CCTGTAGTATGAAGACTAGCATCTTTT 58.799 37.037 0.00 0.00 39.08 2.27
1653 4149 8.709308 AGTATGAAGACTAGCATCTTTTATGGT 58.291 33.333 0.00 0.00 39.08 3.55
1654 4150 9.331282 GTATGAAGACTAGCATCTTTTATGGTT 57.669 33.333 0.00 0.00 39.08 3.67
1655 4151 7.849804 TGAAGACTAGCATCTTTTATGGTTC 57.150 36.000 0.00 0.00 39.08 3.62
1656 4152 6.535150 TGAAGACTAGCATCTTTTATGGTTCG 59.465 38.462 0.00 0.00 39.08 3.95
1657 4153 4.811557 AGACTAGCATCTTTTATGGTTCGC 59.188 41.667 0.00 0.00 0.00 4.70
1678 4174 3.001736 GCGCTGATGTTTATCCTTGACTC 59.998 47.826 0.00 0.00 32.09 3.36
1733 4233 1.350193 CGCTGCTGTTTATGACTCGT 58.650 50.000 0.00 0.00 0.00 4.18
1760 4260 8.464770 TCTTTTTGGATAAGAATTTGCATTCG 57.535 30.769 0.00 0.00 43.38 3.34
1824 4744 6.687604 GTTGGAAACTAAAGTGTATGGCATT 58.312 36.000 4.78 0.00 45.32 3.56
2103 5029 2.356069 CTCTGACGATCAGGATGTCGAA 59.644 50.000 12.89 0.00 44.39 3.71
2140 5066 6.377996 ACTTATGCCAAGTTTCATGAGCATAA 59.622 34.615 24.63 24.63 45.74 1.90
2147 5073 5.376854 AGTTTCATGAGCATAAACACACC 57.623 39.130 9.31 0.00 0.00 4.16
2179 5867 1.954382 TGGTCCATCGTATCCTCTTCG 59.046 52.381 0.00 0.00 0.00 3.79
2263 5954 0.809241 CAGCGCCAACCAAGCAAAAA 60.809 50.000 2.29 0.00 0.00 1.94
2342 6033 2.440627 TCATGCCCTGACATAGCATTCT 59.559 45.455 9.08 0.00 44.61 2.40
2398 7856 3.134127 GGCCACCAGAACGCATCC 61.134 66.667 0.00 0.00 0.00 3.51
2400 7858 2.819595 CCACCAGAACGCATCCGG 60.820 66.667 0.00 0.00 39.22 5.14
2403 7861 2.511600 CCAGAACGCATCCGGGAC 60.512 66.667 0.00 0.00 39.22 4.46
2432 7890 7.148000 CCATGTTCAGAGAGATGTGACTAACTA 60.148 40.741 0.00 0.00 0.00 2.24
2433 7891 7.946381 TGTTCAGAGAGATGTGACTAACTAT 57.054 36.000 0.00 0.00 0.00 2.12
2434 7892 7.766283 TGTTCAGAGAGATGTGACTAACTATG 58.234 38.462 0.00 0.00 0.00 2.23
2435 7893 7.611855 TGTTCAGAGAGATGTGACTAACTATGA 59.388 37.037 0.00 0.00 0.00 2.15
2436 7894 7.800155 TCAGAGAGATGTGACTAACTATGAG 57.200 40.000 0.00 0.00 0.00 2.90
2437 7895 6.262049 TCAGAGAGATGTGACTAACTATGAGC 59.738 42.308 0.00 0.00 0.00 4.26
2438 7896 5.238432 AGAGAGATGTGACTAACTATGAGCG 59.762 44.000 0.00 0.00 0.00 5.03
2439 7897 4.277174 AGAGATGTGACTAACTATGAGCGG 59.723 45.833 0.00 0.00 0.00 5.52
2440 7898 3.319405 AGATGTGACTAACTATGAGCGGG 59.681 47.826 0.00 0.00 0.00 6.13
2441 7899 1.754803 TGTGACTAACTATGAGCGGGG 59.245 52.381 0.00 0.00 0.00 5.73
2442 7900 0.750850 TGACTAACTATGAGCGGGGC 59.249 55.000 0.00 0.00 0.00 5.80
2443 7901 1.041437 GACTAACTATGAGCGGGGCT 58.959 55.000 0.00 0.00 43.88 5.19
2444 7902 2.236766 GACTAACTATGAGCGGGGCTA 58.763 52.381 0.00 0.00 39.88 3.93
2445 7903 1.962100 ACTAACTATGAGCGGGGCTAC 59.038 52.381 0.00 0.00 39.88 3.58
2446 7904 2.240279 CTAACTATGAGCGGGGCTACT 58.760 52.381 0.00 0.00 39.88 2.57
2447 7905 1.041437 AACTATGAGCGGGGCTACTC 58.959 55.000 0.00 0.00 39.88 2.59
2448 7906 0.186386 ACTATGAGCGGGGCTACTCT 59.814 55.000 0.00 0.00 39.88 3.24
2449 7907 0.600557 CTATGAGCGGGGCTACTCTG 59.399 60.000 0.00 0.00 39.88 3.35
2450 7908 0.185175 TATGAGCGGGGCTACTCTGA 59.815 55.000 0.00 0.00 39.88 3.27
2451 7909 1.395826 ATGAGCGGGGCTACTCTGAC 61.396 60.000 0.00 0.00 39.88 3.51
2452 7910 3.127352 GAGCGGGGCTACTCTGACG 62.127 68.421 0.00 0.00 39.88 4.35
2453 7911 3.138798 GCGGGGCTACTCTGACGA 61.139 66.667 0.00 0.00 0.00 4.20
2454 7912 2.707849 GCGGGGCTACTCTGACGAA 61.708 63.158 0.00 0.00 0.00 3.85
2455 7913 1.139095 CGGGGCTACTCTGACGAAC 59.861 63.158 0.00 0.00 0.00 3.95
2456 7914 1.592400 CGGGGCTACTCTGACGAACA 61.592 60.000 0.00 0.00 0.00 3.18
2457 7915 0.606604 GGGGCTACTCTGACGAACAA 59.393 55.000 0.00 0.00 0.00 2.83
2458 7916 1.207329 GGGGCTACTCTGACGAACAAT 59.793 52.381 0.00 0.00 0.00 2.71
2459 7917 2.429610 GGGGCTACTCTGACGAACAATA 59.570 50.000 0.00 0.00 0.00 1.90
2460 7918 3.069729 GGGGCTACTCTGACGAACAATAT 59.930 47.826 0.00 0.00 0.00 1.28
2461 7919 4.051922 GGGCTACTCTGACGAACAATATG 58.948 47.826 0.00 0.00 0.00 1.78
2462 7920 4.202121 GGGCTACTCTGACGAACAATATGA 60.202 45.833 0.00 0.00 0.00 2.15
2463 7921 5.348986 GGCTACTCTGACGAACAATATGAA 58.651 41.667 0.00 0.00 0.00 2.57
2464 7922 5.810587 GGCTACTCTGACGAACAATATGAAA 59.189 40.000 0.00 0.00 0.00 2.69
2465 7923 6.480320 GGCTACTCTGACGAACAATATGAAAT 59.520 38.462 0.00 0.00 0.00 2.17
2466 7924 7.340699 GCTACTCTGACGAACAATATGAAATG 58.659 38.462 0.00 0.00 0.00 2.32
2467 7925 6.111768 ACTCTGACGAACAATATGAAATGC 57.888 37.500 0.00 0.00 0.00 3.56
2468 7926 5.142635 TCTGACGAACAATATGAAATGCG 57.857 39.130 0.00 0.00 0.00 4.73
2469 7927 4.629634 TCTGACGAACAATATGAAATGCGT 59.370 37.500 0.00 0.00 0.00 5.24
2470 7928 5.808030 TCTGACGAACAATATGAAATGCGTA 59.192 36.000 0.00 0.00 0.00 4.42
2471 7929 6.311690 TCTGACGAACAATATGAAATGCGTAA 59.688 34.615 0.00 0.00 0.00 3.18
2472 7930 6.474364 TGACGAACAATATGAAATGCGTAAG 58.526 36.000 0.00 0.00 43.44 2.34
2521 7979 9.906660 TTATTACCATCATTTGTGTTGAGTTTC 57.093 29.630 0.00 0.00 0.00 2.78
2522 7980 5.850557 ACCATCATTTGTGTTGAGTTTCA 57.149 34.783 0.00 0.00 0.00 2.69
2523 7981 6.409524 ACCATCATTTGTGTTGAGTTTCAT 57.590 33.333 0.00 0.00 0.00 2.57
2524 7982 6.819284 ACCATCATTTGTGTTGAGTTTCATT 58.181 32.000 0.00 0.00 0.00 2.57
2525 7983 7.274447 ACCATCATTTGTGTTGAGTTTCATTT 58.726 30.769 0.00 0.00 0.00 2.32
2526 7984 8.420222 ACCATCATTTGTGTTGAGTTTCATTTA 58.580 29.630 0.00 0.00 0.00 1.40
2527 7985 9.426837 CCATCATTTGTGTTGAGTTTCATTTAT 57.573 29.630 0.00 0.00 0.00 1.40
2563 8021 7.938140 TGTATTGACCCCTTCTTCAAATTAG 57.062 36.000 0.00 0.00 35.42 1.73
2564 8022 7.695055 TGTATTGACCCCTTCTTCAAATTAGA 58.305 34.615 0.00 0.00 35.42 2.10
2565 8023 8.336235 TGTATTGACCCCTTCTTCAAATTAGAT 58.664 33.333 0.00 0.00 35.42 1.98
2566 8024 9.847224 GTATTGACCCCTTCTTCAAATTAGATA 57.153 33.333 0.00 0.00 35.42 1.98
2568 8026 9.942526 ATTGACCCCTTCTTCAAATTAGATATT 57.057 29.630 0.00 0.00 35.42 1.28
2569 8027 8.752005 TGACCCCTTCTTCAAATTAGATATTG 57.248 34.615 0.00 0.00 0.00 1.90
2570 8028 8.556589 TGACCCCTTCTTCAAATTAGATATTGA 58.443 33.333 0.00 0.00 33.93 2.57
2571 8029 9.579932 GACCCCTTCTTCAAATTAGATATTGAT 57.420 33.333 0.00 0.00 35.63 2.57
2572 8030 9.359653 ACCCCTTCTTCAAATTAGATATTGATG 57.640 33.333 0.00 0.00 35.63 3.07
2573 8031 8.302438 CCCCTTCTTCAAATTAGATATTGATGC 58.698 37.037 0.00 0.00 35.63 3.91
2574 8032 8.019669 CCCTTCTTCAAATTAGATATTGATGCG 58.980 37.037 0.00 0.00 35.63 4.73
2575 8033 8.019669 CCTTCTTCAAATTAGATATTGATGCGG 58.980 37.037 0.00 0.00 35.63 5.69
2576 8034 7.439157 TCTTCAAATTAGATATTGATGCGGG 57.561 36.000 0.00 0.00 35.63 6.13
2577 8035 6.430925 TCTTCAAATTAGATATTGATGCGGGG 59.569 38.462 0.00 0.00 35.63 5.73
2578 8036 5.630121 TCAAATTAGATATTGATGCGGGGT 58.370 37.500 0.00 0.00 30.94 4.95
2579 8037 5.473162 TCAAATTAGATATTGATGCGGGGTG 59.527 40.000 0.00 0.00 30.94 4.61
2580 8038 4.908601 ATTAGATATTGATGCGGGGTGA 57.091 40.909 0.00 0.00 0.00 4.02
2581 8039 4.698201 TTAGATATTGATGCGGGGTGAA 57.302 40.909 0.00 0.00 0.00 3.18
2582 8040 2.851195 AGATATTGATGCGGGGTGAAC 58.149 47.619 0.00 0.00 0.00 3.18
2583 8041 2.439507 AGATATTGATGCGGGGTGAACT 59.560 45.455 0.00 0.00 0.00 3.01
2584 8042 2.325583 TATTGATGCGGGGTGAACTC 57.674 50.000 0.00 0.00 0.00 3.01
2585 8043 0.394352 ATTGATGCGGGGTGAACTCC 60.394 55.000 0.00 0.00 0.00 3.85
2586 8044 1.488705 TTGATGCGGGGTGAACTCCT 61.489 55.000 0.00 0.00 0.00 3.69
2587 8045 0.616395 TGATGCGGGGTGAACTCCTA 60.616 55.000 0.00 0.00 0.00 2.94
2588 8046 0.179081 GATGCGGGGTGAACTCCTAC 60.179 60.000 0.00 0.00 0.00 3.18
2589 8047 1.623542 ATGCGGGGTGAACTCCTACC 61.624 60.000 0.00 0.00 36.21 3.18
2590 8048 2.288025 GCGGGGTGAACTCCTACCA 61.288 63.158 0.00 0.00 38.74 3.25
2591 8049 1.595357 CGGGGTGAACTCCTACCAC 59.405 63.158 0.00 0.00 38.74 4.16
2592 8050 0.903454 CGGGGTGAACTCCTACCACT 60.903 60.000 0.00 0.00 38.25 4.00
2593 8051 1.617804 CGGGGTGAACTCCTACCACTA 60.618 57.143 0.00 0.00 38.25 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.809636 TGTTCACAGTGGCAGTGACG 60.810 55.000 28.15 17.72 44.95 4.35
69 75 3.712187 GAGAGTTGCTTCGATCCTAAGG 58.288 50.000 5.00 0.00 0.00 2.69
133 185 0.888619 CTCGAGAGTTGTGCCAGGTA 59.111 55.000 6.58 0.00 0.00 3.08
134 186 1.668294 CTCGAGAGTTGTGCCAGGT 59.332 57.895 6.58 0.00 0.00 4.00
136 192 1.005748 TGCTCGAGAGTTGTGCCAG 60.006 57.895 18.75 0.00 0.00 4.85
138 194 2.029844 GGTGCTCGAGAGTTGTGCC 61.030 63.158 18.75 2.74 0.00 5.01
206 262 4.037208 CCTTGGTAATGGAAGCTAATGCAG 59.963 45.833 0.00 0.00 42.74 4.41
330 396 6.458615 GCCAAAAACACTGCTTCATGAAAATT 60.459 34.615 9.88 0.00 0.00 1.82
515 594 2.319025 TCTCCTGTGTGGTATGTGGA 57.681 50.000 0.00 0.00 37.07 4.02
536 615 0.254178 AATCGACCATGGCTCTTGCT 59.746 50.000 13.04 0.00 39.59 3.91
638 725 3.273434 TCCATGCTGTAAGATGTTCTGC 58.727 45.455 0.00 0.00 34.07 4.26
696 3147 2.728690 TCAGTTTGTTCCATGCATGC 57.271 45.000 21.69 11.82 0.00 4.06
697 3148 7.009815 GTCATTAATCAGTTTGTTCCATGCATG 59.990 37.037 20.19 20.19 0.00 4.06
698 3149 7.037438 GTCATTAATCAGTTTGTTCCATGCAT 58.963 34.615 0.00 0.00 0.00 3.96
699 3150 6.015603 TGTCATTAATCAGTTTGTTCCATGCA 60.016 34.615 0.00 0.00 0.00 3.96
747 3198 0.402504 TATGTTTCTTGTGGCCCCGT 59.597 50.000 0.00 0.00 0.00 5.28
1030 3522 2.671619 CAAACCCATCGCGGTGGT 60.672 61.111 34.89 21.05 37.57 4.16
1052 3544 1.072678 CTCGCATGGGAGATGCCAT 59.927 57.895 30.49 0.00 41.71 4.40
1101 3593 2.700773 GGTTTCCTGGATGGTGCGC 61.701 63.158 0.00 0.00 37.07 6.09
1179 3671 1.004560 CGCAAAGGCCAGAGAGTGA 60.005 57.895 5.01 0.00 36.38 3.41
1296 3788 2.022129 GACTCTCCACGTGTTGGCG 61.022 63.158 15.65 0.00 46.47 5.69
1317 3809 1.741732 GCAGCGACCAACTCATCTGAT 60.742 52.381 0.00 0.00 0.00 2.90
1362 3854 1.203758 CAATTCATTGCAGCTGCCTCA 59.796 47.619 34.64 19.61 41.18 3.86
1378 3870 5.116084 ACACCAGATGCATAGTACCAATT 57.884 39.130 0.00 0.00 0.00 2.32
1447 3939 2.332654 GCACCCAAACCTCGCGAAT 61.333 57.895 11.33 0.00 0.00 3.34
1457 3949 1.675310 CTCGCATCCTGCACCCAAA 60.675 57.895 0.00 0.00 45.36 3.28
1502 3994 2.933666 CGCGCGCATCATTCAGAT 59.066 55.556 32.61 0.00 37.48 2.90
1549 4041 4.479993 AGCATCACGGGCTCTGGC 62.480 66.667 0.00 0.00 36.81 4.85
1552 4044 3.790437 CCCAGCATCACGGGCTCT 61.790 66.667 0.00 0.00 40.23 4.09
1560 4052 4.413189 TCAAGGATAATCTTCCCAGCATCA 59.587 41.667 0.00 0.00 36.35 3.07
1563 4055 3.782523 AGTCAAGGATAATCTTCCCAGCA 59.217 43.478 0.00 0.00 36.35 4.41
1566 4058 5.373812 GGAAGTCAAGGATAATCTTCCCA 57.626 43.478 10.11 0.00 44.63 4.37
1590 4082 7.793927 AAAAAGATGCTAGCCTTGATACTAC 57.206 36.000 13.29 0.00 0.00 2.73
1601 4093 4.582240 AGGAAGCCATAAAAAGATGCTAGC 59.418 41.667 8.10 8.10 0.00 3.42
1610 4102 8.325787 TCTTCATACTACAGGAAGCCATAAAAA 58.674 33.333 0.00 0.00 43.30 1.94
1632 4128 6.510317 GCGAACCATAAAAGATGCTAGTCTTC 60.510 42.308 0.00 0.00 37.46 2.87
1638 4134 2.286833 GCGCGAACCATAAAAGATGCTA 59.713 45.455 12.10 0.00 0.00 3.49
1639 4135 1.064060 GCGCGAACCATAAAAGATGCT 59.936 47.619 12.10 0.00 0.00 3.79
1640 4136 1.064060 AGCGCGAACCATAAAAGATGC 59.936 47.619 12.10 0.00 0.00 3.91
1641 4137 2.351418 TCAGCGCGAACCATAAAAGATG 59.649 45.455 12.10 0.00 0.00 2.90
1642 4138 2.627945 TCAGCGCGAACCATAAAAGAT 58.372 42.857 12.10 0.00 0.00 2.40
1643 4139 2.087501 TCAGCGCGAACCATAAAAGA 57.912 45.000 12.10 0.00 0.00 2.52
1644 4140 2.095853 ACATCAGCGCGAACCATAAAAG 59.904 45.455 12.10 0.00 0.00 2.27
1645 4141 2.080693 ACATCAGCGCGAACCATAAAA 58.919 42.857 12.10 0.00 0.00 1.52
1646 4142 1.732941 ACATCAGCGCGAACCATAAA 58.267 45.000 12.10 0.00 0.00 1.40
1647 4143 1.732941 AACATCAGCGCGAACCATAA 58.267 45.000 12.10 0.00 0.00 1.90
1648 4144 1.732941 AAACATCAGCGCGAACCATA 58.267 45.000 12.10 0.00 0.00 2.74
1649 4145 1.732941 TAAACATCAGCGCGAACCAT 58.267 45.000 12.10 0.00 0.00 3.55
1650 4146 1.663643 GATAAACATCAGCGCGAACCA 59.336 47.619 12.10 0.00 0.00 3.67
1651 4147 1.003866 GGATAAACATCAGCGCGAACC 60.004 52.381 12.10 0.00 0.00 3.62
1652 4148 1.933853 AGGATAAACATCAGCGCGAAC 59.066 47.619 12.10 0.00 0.00 3.95
1653 4149 2.309528 AGGATAAACATCAGCGCGAA 57.690 45.000 12.10 0.00 0.00 4.70
1654 4150 1.933181 CAAGGATAAACATCAGCGCGA 59.067 47.619 12.10 2.54 0.00 5.87
1655 4151 1.933181 TCAAGGATAAACATCAGCGCG 59.067 47.619 0.00 0.00 0.00 6.86
1656 4152 2.939103 AGTCAAGGATAAACATCAGCGC 59.061 45.455 0.00 0.00 0.00 5.92
1657 4153 3.557595 GGAGTCAAGGATAAACATCAGCG 59.442 47.826 0.00 0.00 0.00 5.18
1678 4174 5.772672 AGATGCTACTCTTGATACTACAGGG 59.227 44.000 0.00 0.00 0.00 4.45
2103 5029 2.092267 TGGCATAAGTGTCTCATGGCAT 60.092 45.455 5.26 0.00 46.50 4.40
2140 5066 2.355716 CCACATCCTTATCCGGTGTGTT 60.356 50.000 15.46 0.00 35.84 3.32
2179 5867 4.156008 AGACCAAACTTCACTTGTTGTCAC 59.844 41.667 0.00 0.00 0.00 3.67
2224 5912 4.736168 GCTGCAATGTAGACTCTAGACCTG 60.736 50.000 1.65 0.00 0.00 4.00
2342 6033 2.030096 TGTACGGCGAGTTTCACATACA 60.030 45.455 16.62 5.42 0.00 2.29
2398 7856 0.742281 CTCTGAACATGGCTGTCCCG 60.742 60.000 0.00 0.00 33.36 5.14
2400 7858 1.552337 TCTCTCTGAACATGGCTGTCC 59.448 52.381 0.00 0.00 33.36 4.02
2403 7861 2.937149 CACATCTCTCTGAACATGGCTG 59.063 50.000 0.00 0.00 0.00 4.85
2432 7890 1.075970 TCAGAGTAGCCCCGCTCAT 60.076 57.895 0.00 0.00 40.44 2.90
2433 7891 2.052690 GTCAGAGTAGCCCCGCTCA 61.053 63.158 0.00 0.00 40.44 4.26
2434 7892 2.809010 GTCAGAGTAGCCCCGCTC 59.191 66.667 0.00 0.00 40.44 5.03
2435 7893 3.141488 CGTCAGAGTAGCCCCGCT 61.141 66.667 0.00 0.00 43.41 5.52
2436 7894 2.707849 TTCGTCAGAGTAGCCCCGC 61.708 63.158 0.00 0.00 0.00 6.13
2437 7895 1.139095 GTTCGTCAGAGTAGCCCCG 59.861 63.158 0.00 0.00 0.00 5.73
2438 7896 0.606604 TTGTTCGTCAGAGTAGCCCC 59.393 55.000 0.00 0.00 0.00 5.80
2439 7897 2.674796 ATTGTTCGTCAGAGTAGCCC 57.325 50.000 0.00 0.00 0.00 5.19
2440 7898 4.933330 TCATATTGTTCGTCAGAGTAGCC 58.067 43.478 0.00 0.00 0.00 3.93
2441 7899 6.887376 TTTCATATTGTTCGTCAGAGTAGC 57.113 37.500 0.00 0.00 0.00 3.58
2442 7900 7.340699 GCATTTCATATTGTTCGTCAGAGTAG 58.659 38.462 0.00 0.00 0.00 2.57
2443 7901 6.019881 CGCATTTCATATTGTTCGTCAGAGTA 60.020 38.462 0.00 0.00 0.00 2.59
2444 7902 5.220472 CGCATTTCATATTGTTCGTCAGAGT 60.220 40.000 0.00 0.00 0.00 3.24
2445 7903 5.193216 CGCATTTCATATTGTTCGTCAGAG 58.807 41.667 0.00 0.00 0.00 3.35
2446 7904 4.629634 ACGCATTTCATATTGTTCGTCAGA 59.370 37.500 0.00 0.00 0.00 3.27
2447 7905 4.897224 ACGCATTTCATATTGTTCGTCAG 58.103 39.130 0.00 0.00 0.00 3.51
2448 7906 4.937696 ACGCATTTCATATTGTTCGTCA 57.062 36.364 0.00 0.00 0.00 4.35
2449 7907 5.392585 GCTTACGCATTTCATATTGTTCGTC 59.607 40.000 0.00 0.00 35.78 4.20
2450 7908 5.163804 TGCTTACGCATTTCATATTGTTCGT 60.164 36.000 0.00 0.00 42.25 3.85
2451 7909 5.262422 TGCTTACGCATTTCATATTGTTCG 58.738 37.500 0.00 0.00 42.25 3.95
2465 7923 9.579768 AAAATTGTGAATATTATTGCTTACGCA 57.420 25.926 0.00 0.00 46.24 5.24
2495 7953 9.906660 GAAACTCAACACAAATGATGGTAATAA 57.093 29.630 0.00 0.00 0.00 1.40
2496 7954 9.072375 TGAAACTCAACACAAATGATGGTAATA 57.928 29.630 0.00 0.00 0.00 0.98
2497 7955 7.950512 TGAAACTCAACACAAATGATGGTAAT 58.049 30.769 0.00 0.00 0.00 1.89
2498 7956 7.340122 TGAAACTCAACACAAATGATGGTAA 57.660 32.000 0.00 0.00 0.00 2.85
2499 7957 6.951062 TGAAACTCAACACAAATGATGGTA 57.049 33.333 0.00 0.00 0.00 3.25
2500 7958 5.850557 TGAAACTCAACACAAATGATGGT 57.149 34.783 0.00 0.00 0.00 3.55
2501 7959 7.718272 AAATGAAACTCAACACAAATGATGG 57.282 32.000 0.00 0.00 0.00 3.51
2537 7995 9.627123 CTAATTTGAAGAAGGGGTCAATACATA 57.373 33.333 0.00 0.00 33.90 2.29
2538 7996 8.336235 TCTAATTTGAAGAAGGGGTCAATACAT 58.664 33.333 0.00 0.00 33.90 2.29
2539 7997 7.695055 TCTAATTTGAAGAAGGGGTCAATACA 58.305 34.615 0.00 0.00 33.90 2.29
2540 7998 8.753497 ATCTAATTTGAAGAAGGGGTCAATAC 57.247 34.615 0.00 0.00 33.90 1.89
2542 8000 9.942526 AATATCTAATTTGAAGAAGGGGTCAAT 57.057 29.630 0.00 0.00 33.90 2.57
2543 8001 9.189156 CAATATCTAATTTGAAGAAGGGGTCAA 57.811 33.333 0.00 0.00 31.99 3.18
2544 8002 8.556589 TCAATATCTAATTTGAAGAAGGGGTCA 58.443 33.333 0.00 0.00 0.00 4.02
2545 8003 8.980481 TCAATATCTAATTTGAAGAAGGGGTC 57.020 34.615 0.00 0.00 0.00 4.46
2546 8004 9.359653 CATCAATATCTAATTTGAAGAAGGGGT 57.640 33.333 0.00 0.00 35.63 4.95
2547 8005 8.302438 GCATCAATATCTAATTTGAAGAAGGGG 58.698 37.037 0.00 0.00 35.63 4.79
2548 8006 8.019669 CGCATCAATATCTAATTTGAAGAAGGG 58.980 37.037 0.00 0.00 35.63 3.95
2549 8007 8.019669 CCGCATCAATATCTAATTTGAAGAAGG 58.980 37.037 0.00 0.00 35.63 3.46
2550 8008 8.019669 CCCGCATCAATATCTAATTTGAAGAAG 58.980 37.037 0.00 0.00 35.63 2.85
2551 8009 7.040478 CCCCGCATCAATATCTAATTTGAAGAA 60.040 37.037 0.00 0.00 35.63 2.52
2552 8010 6.430925 CCCCGCATCAATATCTAATTTGAAGA 59.569 38.462 0.00 0.00 35.63 2.87
2553 8011 6.207417 ACCCCGCATCAATATCTAATTTGAAG 59.793 38.462 0.00 0.00 35.63 3.02
2554 8012 6.016360 CACCCCGCATCAATATCTAATTTGAA 60.016 38.462 0.00 0.00 35.63 2.69
2555 8013 5.473162 CACCCCGCATCAATATCTAATTTGA 59.527 40.000 0.00 0.00 36.38 2.69
2556 8014 5.473162 TCACCCCGCATCAATATCTAATTTG 59.527 40.000 0.00 0.00 0.00 2.32
2557 8015 5.630121 TCACCCCGCATCAATATCTAATTT 58.370 37.500 0.00 0.00 0.00 1.82
2558 8016 5.241403 TCACCCCGCATCAATATCTAATT 57.759 39.130 0.00 0.00 0.00 1.40
2559 8017 4.908601 TCACCCCGCATCAATATCTAAT 57.091 40.909 0.00 0.00 0.00 1.73
2560 8018 4.102524 AGTTCACCCCGCATCAATATCTAA 59.897 41.667 0.00 0.00 0.00 2.10
2561 8019 3.646162 AGTTCACCCCGCATCAATATCTA 59.354 43.478 0.00 0.00 0.00 1.98
2562 8020 2.439507 AGTTCACCCCGCATCAATATCT 59.560 45.455 0.00 0.00 0.00 1.98
2563 8021 2.808543 GAGTTCACCCCGCATCAATATC 59.191 50.000 0.00 0.00 0.00 1.63
2564 8022 2.487265 GGAGTTCACCCCGCATCAATAT 60.487 50.000 0.00 0.00 0.00 1.28
2565 8023 1.134220 GGAGTTCACCCCGCATCAATA 60.134 52.381 0.00 0.00 0.00 1.90
2566 8024 0.394352 GGAGTTCACCCCGCATCAAT 60.394 55.000 0.00 0.00 0.00 2.57
2567 8025 1.002624 GGAGTTCACCCCGCATCAA 60.003 57.895 0.00 0.00 0.00 2.57
2568 8026 0.616395 TAGGAGTTCACCCCGCATCA 60.616 55.000 0.00 0.00 0.00 3.07
2569 8027 0.179081 GTAGGAGTTCACCCCGCATC 60.179 60.000 0.00 0.00 0.00 3.91
2570 8028 1.623542 GGTAGGAGTTCACCCCGCAT 61.624 60.000 0.00 0.00 0.00 4.73
2571 8029 2.288025 GGTAGGAGTTCACCCCGCA 61.288 63.158 0.00 0.00 0.00 5.69
2572 8030 2.288025 TGGTAGGAGTTCACCCCGC 61.288 63.158 0.00 0.00 33.61 6.13
2573 8031 0.903454 AGTGGTAGGAGTTCACCCCG 60.903 60.000 0.00 0.00 33.61 5.73
2574 8032 2.242882 TAGTGGTAGGAGTTCACCCC 57.757 55.000 0.00 0.00 33.61 4.95


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

AutoCloner maintained by Alex Coulton.