Multiple sequence alignment - TraesCS6A01G166900

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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 TraesCS6A01G166900 chr6A 100.000 4585 0 0 1 4585 170014844 170010260 0.000000e+00 8468.0
1 TraesCS6A01G166900 chr6A 88.629 1240 79 21 2099 3288 169974639 169973412 0.000000e+00 1452.0
2 TraesCS6A01G166900 chr6A 84.381 525 37 23 3427 3909 169973415 169972894 1.490000e-129 473.0
3 TraesCS6A01G166900 chr6A 92.500 280 17 4 1627 1902 169989977 169989698 9.240000e-107 398.0
4 TraesCS6A01G166900 chr6A 92.344 209 13 2 1895 2102 169974762 169974556 1.250000e-75 294.0
5 TraesCS6A01G166900 chr6A 93.023 86 4 1 2017 2102 170012746 170012663 1.730000e-24 124.0
6 TraesCS6A01G166900 chr6A 93.023 86 4 1 2099 2182 170012828 170012743 1.730000e-24 124.0
7 TraesCS6A01G166900 chr6A 89.286 84 6 3 4269 4352 169971678 169971598 8.120000e-18 102.0
8 TraesCS6A01G166900 chr6A 91.549 71 4 2 3937 4007 169972157 169972089 3.780000e-16 97.1
9 TraesCS6A01G166900 chr6A 100.000 28 0 0 3957 3984 170010849 170010822 8.000000e-03 52.8
10 TraesCS6A01G166900 chr6A 100.000 28 0 0 3996 4023 170010888 170010861 8.000000e-03 52.8
11 TraesCS6A01G166900 chr6D 92.177 4065 194 44 1 3987 131690242 131686224 0.000000e+00 5631.0
12 TraesCS6A01G166900 chr6D 86.303 1942 134 49 2137 4003 131679708 131677824 0.000000e+00 1991.0
13 TraesCS6A01G166900 chr6D 88.465 1075 59 24 2099 3120 131683402 131682340 0.000000e+00 1238.0
14 TraesCS6A01G166900 chr6D 93.243 370 16 4 4024 4391 131686105 131685743 1.880000e-148 536.0
15 TraesCS6A01G166900 chr6D 95.604 273 11 1 1629 1900 131681848 131681576 1.960000e-118 436.0
16 TraesCS6A01G166900 chr6D 94.224 277 15 1 1627 1902 131685096 131684820 5.480000e-114 422.0
17 TraesCS6A01G166900 chr6D 90.476 315 15 4 4271 4585 131677477 131677178 7.150000e-108 401.0
18 TraesCS6A01G166900 chr6D 93.204 206 12 1 1897 2102 131683522 131683319 7.450000e-78 302.0
19 TraesCS6A01G166900 chr6D 93.431 137 7 2 1895 2030 131680005 131679870 7.780000e-48 202.0
20 TraesCS6A01G166900 chr6D 97.170 106 3 0 4480 4585 131685701 131685596 3.640000e-41 180.0
21 TraesCS6A01G166900 chr6D 95.349 86 2 1 2099 2182 131688222 131688137 8.000000e-28 135.0
22 TraesCS6A01G166900 chr6D 94.186 86 3 1 2017 2102 131688140 131688057 3.720000e-26 130.0
23 TraesCS6A01G166900 chr6D 88.235 68 8 0 1680 1747 131628525 131628458 1.060000e-11 82.4
24 TraesCS6A01G166900 chr6D 100.000 28 0 0 3996 4023 131677870 131677843 8.000000e-03 52.8
25 TraesCS6A01G166900 chr6B 87.309 1899 128 48 2099 3921 229202968 229201107 0.000000e+00 2067.0
26 TraesCS6A01G166900 chr6B 93.834 1346 68 10 763 2102 229207578 229206242 0.000000e+00 2012.0
27 TraesCS6A01G166900 chr6B 93.271 1278 49 9 2710 3987 229205744 229204504 0.000000e+00 1849.0
28 TraesCS6A01G166900 chr6B 87.162 740 85 8 1 734 229208252 229207517 0.000000e+00 832.0
29 TraesCS6A01G166900 chr6B 90.280 535 27 9 2099 2622 229206325 229205805 0.000000e+00 676.0
30 TraesCS6A01G166900 chr6B 94.427 323 15 3 4263 4585 229200032 229199713 1.150000e-135 494.0
31 TraesCS6A01G166900 chr6B 94.175 206 10 1 1897 2102 229203088 229202885 3.440000e-81 313.0
32 TraesCS6A01G166900 chr7D 76.750 800 160 21 2783 3578 510706513 510707290 1.520000e-114 424.0
33 TraesCS6A01G166900 chr7D 84.472 161 20 5 1631 1788 510705352 510705510 2.210000e-33 154.0
34 TraesCS6A01G166900 chr7B 85.093 161 21 3 1631 1789 539230381 539230540 1.320000e-35 161.0
35 TraesCS6A01G166900 chr7A 75.177 423 64 29 1631 2024 581430462 581430872 1.320000e-35 161.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G166900 chr6A 170010260 170014844 4584 True 8468.000000 8468 100.000000 1 4585 1 chr6A.!!$R2 4584
1 TraesCS6A01G166900 chr6A 169971598 169974762 3164 True 483.620000 1452 89.237800 1895 4352 5 chr6A.!!$R3 2457
2 TraesCS6A01G166900 chr6D 131677178 131690242 13064 True 896.676923 5631 93.371692 1 4585 13 chr6D.!!$R2 4584
3 TraesCS6A01G166900 chr6B 229199713 229208252 8539 True 1177.571429 2067 91.494000 1 4585 7 chr6B.!!$R1 4584
4 TraesCS6A01G166900 chr7D 510705352 510707290 1938 False 289.000000 424 80.611000 1631 3578 2 chr7D.!!$F1 1947

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
588 598 0.179234 TGACAAGCTCCCACGTTTCA 59.821 50.0 0.00 0.0 0.00 2.69 F
884 917 0.465824 TCCTCCGTCCGGATCTCTTC 60.466 60.0 7.81 0.0 44.24 2.87 F
1949 2025 0.037139 GCATGGGCTGTGCAAAATCA 60.037 50.0 9.23 0.0 42.08 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1706 1742 1.327764 GGCTTCGATTTGCTTCCTACG 59.672 52.381 5.74 0.0 0.00 3.51 R
2488 2588 4.202121 GCTCATTCTGCATCACCAAATCAT 60.202 41.667 0.00 0.0 0.00 2.45 R
3892 7672 0.107897 TGTTGGTCAGTGTTGCGACT 60.108 50.000 5.50 0.0 32.57 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
41 42 1.191944 CGTCATGATTCTCGTCACCG 58.808 55.000 0.00 0.00 0.00 4.94
117 124 0.616371 CATGTTCAACCCCCGTCCTA 59.384 55.000 0.00 0.00 0.00 2.94
122 129 3.330110 TGTTCAACCCCCGTCCTATTTTA 59.670 43.478 0.00 0.00 0.00 1.52
225 234 1.552337 GAGAGCAGAAGATGGTGTGGA 59.448 52.381 0.00 0.00 40.53 4.02
290 299 0.259647 TGAGCATGAAAGGGGATGGG 59.740 55.000 0.00 0.00 0.00 4.00
324 333 2.273179 CGAGGGGTGAGGTTGACGA 61.273 63.158 0.00 0.00 0.00 4.20
378 387 1.675641 GGGCCACGAGCTTGTGAAT 60.676 57.895 31.88 0.00 42.55 2.57
394 403 3.444034 TGTGAATGAACGACAACCCAAAA 59.556 39.130 0.00 0.00 0.00 2.44
441 450 2.938451 CGGAAGAAAGTAGCATGCATGA 59.062 45.455 30.64 7.50 0.00 3.07
461 470 9.049523 TGCATGAAGTAATACATGAGAGATTTC 57.950 33.333 0.00 0.00 44.28 2.17
503 512 3.536956 TCATAGAAATGTGTCGACCCC 57.463 47.619 14.12 4.12 34.50 4.95
512 521 2.531771 TGTGTCGACCCCTCTAATTCA 58.468 47.619 14.12 0.00 0.00 2.57
564 574 8.192774 CACTACCATTCTGCATGAAATTATGTT 58.807 33.333 0.00 0.00 38.29 2.71
588 598 0.179234 TGACAAGCTCCCACGTTTCA 59.821 50.000 0.00 0.00 0.00 2.69
594 604 1.899814 AGCTCCCACGTTTCATAGTGA 59.100 47.619 0.00 0.00 40.56 3.41
602 612 5.291128 CCCACGTTTCATAGTGAAGTATGAC 59.709 44.000 7.25 0.00 38.81 3.06
633 643 8.820933 GGCAGATTAGATTTCAAAAATTTAGGC 58.179 33.333 0.00 0.00 0.00 3.93
649 659 1.098712 AGGCACCGCGAAACAAAGAA 61.099 50.000 8.23 0.00 0.00 2.52
653 663 1.008329 ACCGCGAAACAAAGAAACGA 58.992 45.000 8.23 0.00 0.00 3.85
669 679 6.606234 AGAAACGAAGAGGAGAAGAAAAAC 57.394 37.500 0.00 0.00 0.00 2.43
675 685 7.772166 ACGAAGAGGAGAAGAAAAACAAAAAT 58.228 30.769 0.00 0.00 0.00 1.82
705 715 1.541379 TGTCTTCTCGAACCATCCGA 58.459 50.000 0.00 0.00 34.61 4.55
735 747 4.988598 ACCCAACACCGCGCTCAG 62.989 66.667 5.56 0.00 0.00 3.35
741 753 1.463056 CAACACCGCGCTCAGAATTTA 59.537 47.619 5.56 0.00 0.00 1.40
742 754 1.803334 ACACCGCGCTCAGAATTTAA 58.197 45.000 5.56 0.00 0.00 1.52
755 767 6.961554 GCTCAGAATTTAAGTACCACGAAATG 59.038 38.462 0.00 0.00 0.00 2.32
788 819 8.836959 AAAAACAACTAAAATGTCTTCTCGAC 57.163 30.769 0.00 0.00 43.14 4.20
843 875 0.603707 CGTAGCCTATCCGACCGGTA 60.604 60.000 7.34 0.00 36.47 4.02
884 917 0.465824 TCCTCCGTCCGGATCTCTTC 60.466 60.000 7.81 0.00 44.24 2.87
892 925 1.298713 CGGATCTCTTCAGCGACCG 60.299 63.158 0.00 0.00 0.00 4.79
922 955 4.835891 CCGGTAGCCTCCCTCCGT 62.836 72.222 0.00 0.00 41.17 4.69
1097 1130 0.466372 GGAGCCCTGCCCTAAATCAC 60.466 60.000 0.00 0.00 0.00 3.06
1099 1132 1.455773 GCCCTGCCCTAAATCACCC 60.456 63.158 0.00 0.00 0.00 4.61
1164 1197 2.467962 GCTTCCGGCTTAGTGTTCC 58.532 57.895 0.00 0.00 38.06 3.62
1207 1240 4.652822 CTCTGTTGCTAGGTTAGGGTTTT 58.347 43.478 0.00 0.00 0.00 2.43
1302 1335 0.533085 GGGGGTATTCAGAAGCTCGC 60.533 60.000 0.00 0.00 0.00 5.03
1433 1466 0.767375 TTGGAGCTGTCTGCCTCTTT 59.233 50.000 0.00 0.00 44.23 2.52
1542 1575 4.808364 GCTGGATACTAGTTCAAGCTGAAG 59.192 45.833 19.22 2.11 37.22 3.02
1570 1603 7.670009 TCCTACTAGTAATCTATGCTTCGAC 57.330 40.000 3.76 0.00 0.00 4.20
1706 1742 0.168128 CGGAGTCATTTCAAACCGGC 59.832 55.000 0.00 0.00 37.28 6.13
1949 2025 0.037139 GCATGGGCTGTGCAAAATCA 60.037 50.000 9.23 0.00 42.08 2.57
2028 2105 4.188462 CGAACAACCAGCCAGTAATATCA 58.812 43.478 0.00 0.00 0.00 2.15
2048 2125 9.445878 AATATCATATGATACAGCCTCTTGTTG 57.554 33.333 24.39 0.00 39.57 3.33
2322 2422 8.090214 AGCATCACAAGCAGTAATAAAATTTGT 58.910 29.630 0.00 0.00 0.00 2.83
2475 2575 4.997395 ACGCACATGAATAGTTTCTTGTCT 59.003 37.500 0.00 0.00 44.15 3.41
2476 2576 5.106948 ACGCACATGAATAGTTTCTTGTCTG 60.107 40.000 0.00 3.95 44.15 3.51
2486 2586 1.761449 TTCTTGTCTGCCAAACTGCA 58.239 45.000 0.00 0.00 39.37 4.41
2488 2588 3.138884 TCTTGTCTGCCAAACTGCATA 57.861 42.857 0.00 0.00 41.16 3.14
2519 2619 1.241165 TGCAGAATGAGCCAACACAG 58.759 50.000 0.00 0.00 39.69 3.66
2584 2684 8.489676 AGTTCCACTCTATATCAGAACATCAT 57.510 34.615 0.00 0.00 36.84 2.45
2599 2699 7.600375 TCAGAACATCATTCACTGTAGAACTTC 59.400 37.037 0.00 0.00 0.00 3.01
2634 2761 3.963129 TGGATTGTAAGTTTGCCCTAGG 58.037 45.455 0.06 0.06 0.00 3.02
2656 2783 7.093322 AGGATGTTTATTGTTCTTCAGATGC 57.907 36.000 0.00 0.00 0.00 3.91
2666 2793 4.937620 TGTTCTTCAGATGCTATCAACACC 59.062 41.667 0.00 0.00 0.00 4.16
2680 2807 7.661437 TGCTATCAACACCTGTAATCATATTCC 59.339 37.037 0.00 0.00 0.00 3.01
2713 2840 5.653507 TGGCTTATGAATTTTGATGTCTGC 58.346 37.500 0.00 0.00 0.00 4.26
2925 3053 0.850883 TCCCCAAGGAAGAATGCCCT 60.851 55.000 0.00 0.00 40.08 5.19
3260 3388 2.332063 ACACAAAGCAGATATCCCGG 57.668 50.000 0.00 0.00 0.00 5.73
3299 3427 1.591594 CATCCGGGACCACGAATCG 60.592 63.158 0.00 0.00 35.47 3.34
3305 3433 0.801067 GGGACCACGAATCGAACGAG 60.801 60.000 10.55 12.43 34.70 4.18
3398 3526 0.904865 TCTTCAGGATCAGTGGCGGT 60.905 55.000 0.00 0.00 0.00 5.68
3593 7373 2.008543 GCTGCCGTGTGAGATTGATCA 61.009 52.381 0.00 0.00 0.00 2.92
3597 7377 2.936993 GCCGTGTGAGATTGATCAACCT 60.937 50.000 11.07 6.04 0.00 3.50
3606 7386 3.074390 AGATTGATCAACCTCACCCAACA 59.926 43.478 11.07 0.00 0.00 3.33
3712 7492 8.805175 TGCCATCGATTTTATGGATTTCATATT 58.195 29.630 6.18 0.00 45.77 1.28
3742 7522 3.265791 CTCTTATCAGCCTGTTGTGGTC 58.734 50.000 0.00 0.00 0.00 4.02
3804 7584 6.096987 TCTGACTGACCTGAACTTGATATACC 59.903 42.308 0.00 0.00 0.00 2.73
3805 7585 5.719563 TGACTGACCTGAACTTGATATACCA 59.280 40.000 0.00 0.00 0.00 3.25
3806 7586 5.978814 ACTGACCTGAACTTGATATACCAC 58.021 41.667 0.00 0.00 0.00 4.16
3820 7600 1.340088 TACCACAACAAGTCGGCCTA 58.660 50.000 0.00 0.00 0.00 3.93
3849 7629 4.437682 TCATGTTGAAACCTGAACCTCT 57.562 40.909 0.00 0.00 31.94 3.69
3850 7630 4.136796 TCATGTTGAAACCTGAACCTCTG 58.863 43.478 0.00 0.00 31.94 3.35
3880 7660 3.866582 GAGGCCGGGGGAGACATG 61.867 72.222 2.18 0.00 0.00 3.21
3892 7672 3.559171 GGGGAGACATGTTAAGTTGCAGA 60.559 47.826 0.00 0.00 0.00 4.26
3912 7692 0.730265 GTCGCAACACTGACCAACAA 59.270 50.000 0.00 0.00 0.00 2.83
3915 7695 1.531677 CGCAACACTGACCAACAACAG 60.532 52.381 0.00 0.00 39.65 3.16
3920 7700 3.631250 ACACTGACCAACAACAGGATTT 58.369 40.909 0.00 0.00 38.30 2.17
3923 7703 2.558359 CTGACCAACAACAGGATTTCCC 59.442 50.000 0.00 0.00 36.42 3.97
3926 7706 2.176798 ACCAACAACAGGATTTCCCTCA 59.823 45.455 0.00 0.00 45.60 3.86
3927 7707 2.821969 CCAACAACAGGATTTCCCTCAG 59.178 50.000 0.00 0.00 45.60 3.35
3928 7708 3.498481 CCAACAACAGGATTTCCCTCAGA 60.498 47.826 0.00 0.00 45.60 3.27
3929 7709 3.425162 ACAACAGGATTTCCCTCAGAC 57.575 47.619 0.00 0.00 45.60 3.51
3930 7710 2.982488 ACAACAGGATTTCCCTCAGACT 59.018 45.455 0.00 0.00 45.60 3.24
3931 7711 3.008485 ACAACAGGATTTCCCTCAGACTC 59.992 47.826 0.00 0.00 45.60 3.36
3932 7712 3.197927 ACAGGATTTCCCTCAGACTCT 57.802 47.619 0.00 0.00 45.60 3.24
3933 7713 3.525862 ACAGGATTTCCCTCAGACTCTT 58.474 45.455 0.00 0.00 45.60 2.85
3934 7714 3.262915 ACAGGATTTCCCTCAGACTCTTG 59.737 47.826 0.00 0.00 45.60 3.02
3935 7715 2.843113 AGGATTTCCCTCAGACTCTTGG 59.157 50.000 0.00 0.00 43.31 3.61
3936 7716 2.573915 GGATTTCCCTCAGACTCTTGGT 59.426 50.000 0.00 0.00 0.00 3.67
3937 7717 3.369997 GGATTTCCCTCAGACTCTTGGTC 60.370 52.174 0.00 0.00 44.80 4.02
3938 7718 7.782273 AGGATTTCCCTCAGACTCTTGGTCT 62.782 48.000 0.00 0.00 46.29 3.85
3953 7733 0.992802 GGTCTGCGATCTCAACGTTC 59.007 55.000 0.00 0.00 0.00 3.95
3965 7745 2.016704 AACGTTCGTGCTCTGCTCG 61.017 57.895 0.00 7.55 45.04 5.03
3999 7820 1.627834 CTGGGGAGTTGAAGAAGCTCT 59.372 52.381 0.00 0.00 0.00 4.09
4003 7824 2.345876 GGAGTTGAAGAAGCTCTGCTC 58.654 52.381 0.00 0.00 38.25 4.26
4004 7825 1.991965 GAGTTGAAGAAGCTCTGCTCG 59.008 52.381 0.00 0.00 38.25 5.03
4005 7826 0.441921 GTTGAAGAAGCTCTGCTCGC 59.558 55.000 0.00 0.00 38.25 5.03
4006 7827 0.033920 TTGAAGAAGCTCTGCTCGCA 59.966 50.000 0.00 0.00 38.25 5.10
4008 7829 0.668706 GAAGAAGCTCTGCTCGCACA 60.669 55.000 0.00 0.00 38.25 4.57
4009 7830 0.036577 AAGAAGCTCTGCTCGCACAT 60.037 50.000 0.00 0.00 38.25 3.21
4010 7831 0.036577 AGAAGCTCTGCTCGCACATT 60.037 50.000 0.00 0.00 38.25 2.71
4011 7832 1.205655 AGAAGCTCTGCTCGCACATTA 59.794 47.619 0.00 0.00 38.25 1.90
4012 7833 2.002586 GAAGCTCTGCTCGCACATTAA 58.997 47.619 0.00 0.00 38.25 1.40
4013 7834 2.322355 AGCTCTGCTCGCACATTAAT 57.678 45.000 0.00 0.00 30.62 1.40
4014 7835 3.459232 AGCTCTGCTCGCACATTAATA 57.541 42.857 0.00 0.00 30.62 0.98
4015 7836 3.797039 AGCTCTGCTCGCACATTAATAA 58.203 40.909 0.00 0.00 30.62 1.40
4018 7839 2.872245 TCTGCTCGCACATTAATAAGCC 59.128 45.455 5.90 0.00 0.00 4.35
4020 7841 2.613595 TGCTCGCACATTAATAAGCCTG 59.386 45.455 5.90 1.67 0.00 4.85
4033 7895 2.683211 AAGCCTGGGAAAGTCACAAT 57.317 45.000 0.00 0.00 0.00 2.71
4053 7915 3.236003 GACGCCTCGTTCCTGGGTT 62.236 63.158 0.00 0.00 41.37 4.11
4060 7922 3.681593 CCTCGTTCCTGGGTTCATTTTA 58.318 45.455 0.00 0.00 0.00 1.52
4061 7923 4.076394 CCTCGTTCCTGGGTTCATTTTAA 58.924 43.478 0.00 0.00 0.00 1.52
4067 15935 8.269317 TCGTTCCTGGGTTCATTTTAATAGTAT 58.731 33.333 0.00 0.00 0.00 2.12
4093 17438 2.659610 CTAGCATAGGAGGGGCGC 59.340 66.667 0.00 0.00 34.22 6.53
4121 17466 2.526873 ACGTCCACTTGCCTCCCT 60.527 61.111 0.00 0.00 0.00 4.20
4123 17468 2.671682 GTCCACTTGCCTCCCTCC 59.328 66.667 0.00 0.00 0.00 4.30
4124 17469 3.003173 TCCACTTGCCTCCCTCCG 61.003 66.667 0.00 0.00 0.00 4.63
4196 17846 3.333189 CGCCTCGTGATGATGCCG 61.333 66.667 0.00 0.00 35.05 5.69
4201 17851 1.606480 CCTCGTGATGATGCCGCTATT 60.606 52.381 0.00 0.00 0.00 1.73
4202 17852 1.723542 CTCGTGATGATGCCGCTATTC 59.276 52.381 0.00 0.00 0.00 1.75
4203 17853 0.792640 CGTGATGATGCCGCTATTCC 59.207 55.000 0.00 0.00 0.00 3.01
4204 17854 1.606480 CGTGATGATGCCGCTATTCCT 60.606 52.381 0.00 0.00 0.00 3.36
4205 17855 2.072298 GTGATGATGCCGCTATTCCTC 58.928 52.381 0.00 0.00 0.00 3.71
4206 17856 1.002430 TGATGATGCCGCTATTCCTCC 59.998 52.381 0.00 0.00 0.00 4.30
4207 17857 0.326264 ATGATGCCGCTATTCCTCCC 59.674 55.000 0.00 0.00 0.00 4.30
4208 17858 0.764369 TGATGCCGCTATTCCTCCCT 60.764 55.000 0.00 0.00 0.00 4.20
4209 17859 0.036858 GATGCCGCTATTCCTCCCTC 60.037 60.000 0.00 0.00 0.00 4.30
4210 17860 1.484444 ATGCCGCTATTCCTCCCTCC 61.484 60.000 0.00 0.00 0.00 4.30
4211 17861 3.052081 CCGCTATTCCTCCCTCCG 58.948 66.667 0.00 0.00 0.00 4.63
4212 17862 1.833049 CCGCTATTCCTCCCTCCGT 60.833 63.158 0.00 0.00 0.00 4.69
4213 17863 1.660917 CGCTATTCCTCCCTCCGTC 59.339 63.158 0.00 0.00 0.00 4.79
4214 17864 1.660917 GCTATTCCTCCCTCCGTCG 59.339 63.158 0.00 0.00 0.00 5.12
4215 17865 1.660917 CTATTCCTCCCTCCGTCGC 59.339 63.158 0.00 0.00 0.00 5.19
4216 17866 1.807495 CTATTCCTCCCTCCGTCGCC 61.807 65.000 0.00 0.00 0.00 5.54
4217 17867 2.577020 TATTCCTCCCTCCGTCGCCA 62.577 60.000 0.00 0.00 0.00 5.69
4237 17888 2.872557 CCGAGGTACGCTCGTTCA 59.127 61.111 23.31 0.00 42.15 3.18
4239 17890 0.659427 CCGAGGTACGCTCGTTCATA 59.341 55.000 23.31 0.00 42.15 2.15
4241 17892 1.063027 CGAGGTACGCTCGTTCATACA 59.937 52.381 19.49 0.00 39.25 2.29
4242 17893 2.717530 GAGGTACGCTCGTTCATACAG 58.282 52.381 0.00 0.00 0.00 2.74
4243 17894 1.197910 GGTACGCTCGTTCATACAGC 58.802 55.000 0.00 0.00 0.00 4.40
4246 17897 0.797249 ACGCTCGTTCATACAGCGAC 60.797 55.000 18.59 0.00 45.84 5.19
4247 17898 1.788621 CGCTCGTTCATACAGCGACG 61.789 60.000 6.71 0.00 45.84 5.12
4249 17900 1.472276 CTCGTTCATACAGCGACGGC 61.472 60.000 0.00 0.00 36.27 5.68
4251 17902 2.202690 TTCATACAGCGACGGCCG 60.203 61.111 26.86 26.86 41.24 6.13
4252 17903 2.997075 TTCATACAGCGACGGCCGT 61.997 57.895 34.89 34.89 41.24 5.68
4253 17904 2.877360 TTCATACAGCGACGGCCGTC 62.877 60.000 41.75 41.75 41.24 4.79
4254 17905 3.138798 ATACAGCGACGGCCGTCT 61.139 61.111 44.83 32.79 42.54 4.18
4260 17911 2.126071 CGACGGCCGTCTGTCAAT 60.126 61.111 44.83 18.45 46.51 2.57
4266 17967 1.062587 CGGCCGTCTGTCAATTGATTC 59.937 52.381 19.50 0.00 0.00 2.52
4304 18005 2.069430 GCAAGGGAGGAGGAGGAGG 61.069 68.421 0.00 0.00 0.00 4.30
4307 18008 4.890306 GGGAGGAGGAGGAGGGGC 62.890 77.778 0.00 0.00 0.00 5.80
4314 18015 4.779733 GGAGGAGGGGCGGAGTGA 62.780 72.222 0.00 0.00 0.00 3.41
4322 18023 2.711922 GGGCGGAGTGACGTCATCT 61.712 63.158 23.12 19.47 40.90 2.90
4334 18035 2.124860 TCATCTCGAGGCGGACGA 60.125 61.111 13.56 0.00 38.11 4.20
4470 18183 1.246737 CCTTCCCAAACTCTGGCTGC 61.247 60.000 0.00 0.00 44.90 5.25
4471 18184 1.228552 TTCCCAAACTCTGGCTGCC 60.229 57.895 12.87 12.87 44.90 4.85
4472 18185 2.677875 CCCAAACTCTGGCTGCCC 60.678 66.667 17.53 0.00 44.90 5.36
4473 18186 3.058160 CCAAACTCTGGCTGCCCG 61.058 66.667 17.53 10.43 38.76 6.13
4474 18187 3.741476 CAAACTCTGGCTGCCCGC 61.741 66.667 17.53 0.00 38.13 6.13
4475 18188 3.958860 AAACTCTGGCTGCCCGCT 61.959 61.111 17.53 0.00 39.13 5.52
4476 18189 3.909086 AAACTCTGGCTGCCCGCTC 62.909 63.158 17.53 0.00 39.13 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.276138 AGAATCATGACGTGGTGAGCA 59.724 47.619 0.00 0.00 0.00 4.26
41 42 8.331022 CACAAGTGATACTATGTGAATGCTTAC 58.669 37.037 13.84 0.00 38.40 2.34
100 106 1.364269 AATAGGACGGGGGTTGAACA 58.636 50.000 0.00 0.00 0.00 3.18
117 124 9.911788 ATGAAGATGAGGAACACTACATAAAAT 57.088 29.630 0.00 0.00 0.00 1.82
122 129 5.587844 GCAATGAAGATGAGGAACACTACAT 59.412 40.000 0.00 0.00 0.00 2.29
142 149 2.066262 CACTACTCCGTTTCGTGCAAT 58.934 47.619 0.00 0.00 0.00 3.56
290 299 0.460987 CTCGGCTCATCCTTCACCAC 60.461 60.000 0.00 0.00 0.00 4.16
324 333 5.587844 GCCATGATATCACTCAGAACTTTGT 59.412 40.000 7.78 0.00 0.00 2.83
364 373 1.792367 TCGTTCATTCACAAGCTCGTG 59.208 47.619 0.00 0.00 38.29 4.35
394 403 4.974645 TGAAACCATTGACACTCTACCT 57.025 40.909 0.00 0.00 0.00 3.08
398 407 4.557296 CGCATTTGAAACCATTGACACTCT 60.557 41.667 0.00 0.00 0.00 3.24
476 485 7.305474 GGTCGACACATTTCTATGAACAAATT 58.695 34.615 18.91 0.00 35.65 1.82
550 560 9.693157 GCTTGTCAAAATAACATAATTTCATGC 57.307 29.630 0.00 0.00 0.00 4.06
564 574 3.134574 ACGTGGGAGCTTGTCAAAATA 57.865 42.857 0.00 0.00 0.00 1.40
588 598 3.774766 TGCCCACAGTCATACTTCACTAT 59.225 43.478 0.00 0.00 0.00 2.12
594 604 4.716784 TCTAATCTGCCCACAGTCATACTT 59.283 41.667 0.00 0.00 44.77 2.24
602 612 5.902613 TTTGAAATCTAATCTGCCCACAG 57.097 39.130 0.00 0.00 45.95 3.66
633 643 1.109296 CGTTTCTTTGTTTCGCGGTG 58.891 50.000 6.13 0.00 0.00 4.94
649 659 6.753107 TTTGTTTTTCTTCTCCTCTTCGTT 57.247 33.333 0.00 0.00 0.00 3.85
715 725 4.555709 AGCGCGGTGTTGGGTCAA 62.556 61.111 11.39 0.00 0.00 3.18
716 726 4.980805 GAGCGCGGTGTTGGGTCA 62.981 66.667 18.92 0.00 0.00 4.02
717 727 4.980805 TGAGCGCGGTGTTGGGTC 62.981 66.667 18.92 0.00 0.00 4.46
939 972 1.172812 GGGTTTGTGGCCTGTGAGTC 61.173 60.000 3.32 0.00 0.00 3.36
1127 1160 1.544691 GCTTCACCGGACTACAGAAGA 59.455 52.381 9.46 0.00 38.30 2.87
1131 1164 1.404315 GGAAGCTTCACCGGACTACAG 60.404 57.143 27.02 0.00 0.00 2.74
1133 1166 0.458025 CGGAAGCTTCACCGGACTAC 60.458 60.000 27.02 6.18 44.59 2.73
1156 1189 1.605453 GCATTCCCCGGGAACACTA 59.395 57.895 26.32 0.00 45.07 2.74
1311 1344 1.154413 GCGGCGAATTGGCATATCG 60.154 57.895 12.98 15.53 45.16 2.92
1433 1466 8.673711 AGTATTAATGCGCAGAATACAGAAAAA 58.326 29.630 35.48 15.07 38.13 1.94
1441 1474 4.819088 TGCCAAGTATTAATGCGCAGAATA 59.181 37.500 18.32 18.53 0.00 1.75
1542 1575 8.231837 CGAAGCATAGATTACTAGTAGGAACTC 58.768 40.741 2.23 0.00 37.15 3.01
1706 1742 1.327764 GGCTTCGATTTGCTTCCTACG 59.672 52.381 5.74 0.00 0.00 3.51
1949 2025 6.712095 TCTTGCACTTTCACATATTCAGAAGT 59.288 34.615 0.00 0.00 0.00 3.01
2028 2105 7.994911 TCAATTCAACAAGAGGCTGTATCATAT 59.005 33.333 0.00 0.00 0.00 1.78
2045 2122 9.956720 TTCAATCTTCTTTTCTCTCAATTCAAC 57.043 29.630 0.00 0.00 0.00 3.18
2292 2370 6.816134 TTATTACTGCTTGTGATGCTTCAA 57.184 33.333 3.51 0.00 32.48 2.69
2322 2422 5.632118 AGGCTCTCTTACGGATCATAAGTA 58.368 41.667 13.04 2.01 32.46 2.24
2405 2505 5.064452 CAGTTCCATAGTCAACATTCTCTGC 59.936 44.000 0.00 0.00 0.00 4.26
2454 2554 5.091431 GCAGACAAGAAACTATTCATGTGC 58.909 41.667 4.40 0.36 44.88 4.57
2486 2586 6.294564 GCTCATTCTGCATCACCAAATCATAT 60.295 38.462 0.00 0.00 0.00 1.78
2488 2588 4.202121 GCTCATTCTGCATCACCAAATCAT 60.202 41.667 0.00 0.00 0.00 2.45
2563 2663 8.366401 AGTGAATGATGTTCTGATATAGAGTGG 58.634 37.037 0.00 0.00 36.61 4.00
2584 2684 6.239064 GGACAGAAGAGAAGTTCTACAGTGAA 60.239 42.308 5.09 0.00 34.90 3.18
2634 2761 9.875675 GATAGCATCTGAAGAACAATAAACATC 57.124 33.333 0.00 0.00 0.00 3.06
2656 2783 9.212641 CAGGAATATGATTACAGGTGTTGATAG 57.787 37.037 0.00 0.00 0.00 2.08
2666 2793 7.255381 CCAAAAGGCTCAGGAATATGATTACAG 60.255 40.741 0.00 0.00 0.00 2.74
2680 2807 4.996788 ATTCATAAGCCAAAAGGCTCAG 57.003 40.909 9.77 3.27 45.26 3.35
2713 2840 4.970860 ACTGATATTGACTGGGAGGATG 57.029 45.455 0.00 0.00 0.00 3.51
2721 2848 8.453320 TCATTTAAGCACAACTGATATTGACTG 58.547 33.333 0.00 0.00 33.57 3.51
2777 2905 6.923508 CGGTACTGCACAATGAGAATAAGATA 59.076 38.462 0.00 0.00 0.00 1.98
2885 3013 1.837947 TGCAAATGCTTGGCCACCT 60.838 52.632 3.88 0.00 42.66 4.00
3233 3361 1.581934 TCTGCTTTGTGTTGACTCCG 58.418 50.000 0.00 0.00 0.00 4.63
3299 3427 3.643159 ATGTTTTTCAAGGCCTCGTTC 57.357 42.857 5.23 0.00 0.00 3.95
3305 3433 3.320626 GAGCTCAATGTTTTTCAAGGCC 58.679 45.455 9.40 0.00 0.00 5.19
3459 7239 2.011617 AAGTTGCTTCCCTGCCCACT 62.012 55.000 0.00 0.00 0.00 4.00
3586 7366 3.524095 TGTTGGGTGAGGTTGATCAAT 57.476 42.857 12.12 0.00 0.00 2.57
3593 7373 3.575805 ACAAATCATGTTGGGTGAGGTT 58.424 40.909 0.00 0.00 40.06 3.50
3597 7377 4.941263 GCTACTACAAATCATGTTGGGTGA 59.059 41.667 0.00 0.00 43.63 4.02
3712 7492 4.223700 ACAGGCTGATAAGAGTCATGACAA 59.776 41.667 27.02 10.24 0.00 3.18
3723 7503 3.340814 AGACCACAACAGGCTGATAAG 57.659 47.619 23.66 9.88 0.00 1.73
3742 7522 7.658179 TGAACATGTCAAGCTTTCTACTAAG 57.342 36.000 0.00 0.00 31.51 2.18
3804 7584 2.093306 TCATAGGCCGACTTGTTGTG 57.907 50.000 0.00 0.00 0.00 3.33
3805 7585 2.038557 AGTTCATAGGCCGACTTGTTGT 59.961 45.455 0.00 0.00 0.00 3.32
3806 7586 2.699954 AGTTCATAGGCCGACTTGTTG 58.300 47.619 0.00 0.00 0.00 3.33
3820 7600 6.713762 TCAGGTTTCAACATGAAAGTTCAT 57.286 33.333 4.60 0.54 45.83 2.57
3849 7629 2.741985 CCTCGGCAACATCACGCA 60.742 61.111 0.00 0.00 0.00 5.24
3850 7630 4.166011 GCCTCGGCAACATCACGC 62.166 66.667 2.41 0.00 41.49 5.34
3892 7672 0.107897 TGTTGGTCAGTGTTGCGACT 60.108 50.000 5.50 0.00 32.57 4.18
3915 7695 2.573915 ACCAAGAGTCTGAGGGAAATCC 59.426 50.000 14.52 0.00 0.00 3.01
3927 7707 1.474478 TGAGATCGCAGACCAAGAGTC 59.526 52.381 0.00 0.00 46.71 3.36
3928 7708 1.550327 TGAGATCGCAGACCAAGAGT 58.450 50.000 0.00 0.00 42.51 3.24
3929 7709 2.266554 GTTGAGATCGCAGACCAAGAG 58.733 52.381 0.00 0.00 42.51 2.85
3930 7710 1.402852 CGTTGAGATCGCAGACCAAGA 60.403 52.381 0.00 0.00 42.51 3.02
3931 7711 0.994995 CGTTGAGATCGCAGACCAAG 59.005 55.000 0.00 0.00 42.51 3.61
3932 7712 0.317160 ACGTTGAGATCGCAGACCAA 59.683 50.000 0.00 0.00 42.51 3.67
3933 7713 0.317160 AACGTTGAGATCGCAGACCA 59.683 50.000 0.00 0.00 42.51 4.02
3934 7714 0.992802 GAACGTTGAGATCGCAGACC 59.007 55.000 5.00 0.00 42.51 3.85
3935 7715 0.635731 CGAACGTTGAGATCGCAGAC 59.364 55.000 5.00 1.09 42.51 3.51
3936 7716 3.015799 CGAACGTTGAGATCGCAGA 57.984 52.632 5.00 0.00 45.75 4.26
3941 7721 1.651138 CAGAGCACGAACGTTGAGATC 59.349 52.381 5.00 3.29 0.00 2.75
3942 7722 1.702886 CAGAGCACGAACGTTGAGAT 58.297 50.000 5.00 0.00 0.00 2.75
3943 7723 0.939577 GCAGAGCACGAACGTTGAGA 60.940 55.000 5.00 0.00 0.00 3.27
3965 7745 2.887152 CTCCCCAGGCTTATTAATGTGC 59.113 50.000 0.00 2.24 0.00 4.57
3999 7820 2.613595 CAGGCTTATTAATGTGCGAGCA 59.386 45.455 0.00 0.00 32.01 4.26
4003 7824 2.571212 TCCCAGGCTTATTAATGTGCG 58.429 47.619 0.00 0.00 0.00 5.34
4004 7825 4.402474 ACTTTCCCAGGCTTATTAATGTGC 59.598 41.667 0.00 2.24 0.00 4.57
4005 7826 5.652014 TGACTTTCCCAGGCTTATTAATGTG 59.348 40.000 0.00 0.00 0.00 3.21
4006 7827 5.652452 GTGACTTTCCCAGGCTTATTAATGT 59.348 40.000 0.00 0.00 0.00 2.71
4008 7829 5.826643 TGTGACTTTCCCAGGCTTATTAAT 58.173 37.500 0.00 0.00 0.00 1.40
4009 7830 5.249780 TGTGACTTTCCCAGGCTTATTAA 57.750 39.130 0.00 0.00 0.00 1.40
4010 7831 4.919774 TGTGACTTTCCCAGGCTTATTA 57.080 40.909 0.00 0.00 0.00 0.98
4011 7832 3.806949 TGTGACTTTCCCAGGCTTATT 57.193 42.857 0.00 0.00 0.00 1.40
4012 7833 3.806949 TTGTGACTTTCCCAGGCTTAT 57.193 42.857 0.00 0.00 0.00 1.73
4013 7834 3.686016 GATTGTGACTTTCCCAGGCTTA 58.314 45.455 0.00 0.00 0.00 3.09
4014 7835 2.519013 GATTGTGACTTTCCCAGGCTT 58.481 47.619 0.00 0.00 0.00 4.35
4015 7836 1.611673 CGATTGTGACTTTCCCAGGCT 60.612 52.381 0.00 0.00 0.00 4.58
4018 7839 1.726791 CGTCGATTGTGACTTTCCCAG 59.273 52.381 0.00 0.00 36.71 4.45
4020 7841 0.442699 GCGTCGATTGTGACTTTCCC 59.557 55.000 0.00 0.00 36.71 3.97
4076 15944 2.659610 GCGCCCCTCCTATGCTAG 59.340 66.667 0.00 0.00 0.00 3.42
4077 15945 2.923035 GGCGCCCCTCCTATGCTA 60.923 66.667 18.11 0.00 0.00 3.49
4103 17448 2.358737 GGGAGGCAAGTGGACGTG 60.359 66.667 0.00 0.00 0.00 4.49
4131 17476 0.745468 GGGAACTCAGCCTAGTACGG 59.255 60.000 0.00 0.00 0.00 4.02
4132 17477 0.381089 CGGGAACTCAGCCTAGTACG 59.619 60.000 0.00 0.00 0.00 3.67
4133 17478 0.102663 GCGGGAACTCAGCCTAGTAC 59.897 60.000 0.00 0.00 0.00 2.73
4134 17479 1.041447 GGCGGGAACTCAGCCTAGTA 61.041 60.000 7.85 0.00 46.83 1.82
4135 17480 2.359967 GGCGGGAACTCAGCCTAGT 61.360 63.158 7.85 0.00 46.83 2.57
4136 17481 2.501610 GGCGGGAACTCAGCCTAG 59.498 66.667 7.85 0.00 46.83 3.02
4196 17846 1.660917 CGACGGAGGGAGGAATAGC 59.339 63.158 0.00 0.00 0.00 2.97
4215 17865 4.849329 GAGCGTACCTCGGCGTGG 62.849 72.222 24.98 24.98 40.26 4.94
4244 17895 0.669318 TCAATTGACAGACGGCCGTC 60.669 55.000 43.92 43.92 44.86 4.79
4246 17897 1.062587 GAATCAATTGACAGACGGCCG 59.937 52.381 26.86 26.86 0.00 6.13
4247 17898 2.083774 TGAATCAATTGACAGACGGCC 58.916 47.619 11.07 0.00 0.00 6.13
4249 17900 4.872124 TCAGATGAATCAATTGACAGACGG 59.128 41.667 11.07 5.36 0.00 4.79
4251 17902 5.220548 CGGTCAGATGAATCAATTGACAGAC 60.221 44.000 22.79 9.72 39.81 3.51
4252 17903 4.872124 CGGTCAGATGAATCAATTGACAGA 59.128 41.667 22.79 0.00 39.81 3.41
4253 17904 4.034858 CCGGTCAGATGAATCAATTGACAG 59.965 45.833 22.79 19.91 39.81 3.51
4254 17905 3.940852 CCGGTCAGATGAATCAATTGACA 59.059 43.478 22.79 5.71 39.81 3.58
4257 17908 2.033801 GGCCGGTCAGATGAATCAATTG 59.966 50.000 0.00 0.00 0.00 2.32
4258 17909 2.301346 GGCCGGTCAGATGAATCAATT 58.699 47.619 0.00 0.00 0.00 2.32
4259 17910 1.811558 CGGCCGGTCAGATGAATCAAT 60.812 52.381 20.10 0.00 0.00 2.57
4260 17911 0.461870 CGGCCGGTCAGATGAATCAA 60.462 55.000 20.10 0.00 0.00 2.57
4266 17967 2.355126 CGATCGGCCGGTCAGATG 60.355 66.667 35.82 17.47 29.62 2.90
4304 18005 2.202756 GATGACGTCACTCCGCCC 60.203 66.667 22.71 0.59 0.00 6.13
4307 18008 0.026933 CTCGAGATGACGTCACTCCG 59.973 60.000 27.42 24.75 34.70 4.63
4308 18009 0.378962 CCTCGAGATGACGTCACTCC 59.621 60.000 27.42 18.64 34.70 3.85
4309 18010 0.248296 GCCTCGAGATGACGTCACTC 60.248 60.000 22.71 24.56 34.70 3.51
4310 18011 1.803943 GCCTCGAGATGACGTCACT 59.196 57.895 22.71 19.23 34.70 3.41
4311 18012 1.583967 CGCCTCGAGATGACGTCAC 60.584 63.158 22.71 14.69 34.70 3.67
4314 18015 2.437895 TCCGCCTCGAGATGACGT 60.438 61.111 15.71 0.00 34.70 4.34
4322 18023 2.888464 ATCCTCTTCGTCCGCCTCGA 62.888 60.000 0.00 0.00 35.50 4.04
4334 18035 2.290464 CCTCGAGTACGTCATCCTCTT 58.710 52.381 12.31 0.00 40.69 2.85
4474 18187 4.767255 GGTGCACCTCCAGCCGAG 62.767 72.222 29.12 0.00 38.46 4.63
4477 18190 4.729918 CCAGGTGCACCTCCAGCC 62.730 72.222 35.79 7.37 46.65 4.85
4478 18191 3.618780 CTCCAGGTGCACCTCCAGC 62.619 68.421 35.79 8.03 46.65 4.85
4479 18192 2.667418 CTCCAGGTGCACCTCCAG 59.333 66.667 35.79 27.38 46.65 3.86
4480 18193 2.930019 CCTCCAGGTGCACCTCCA 60.930 66.667 35.79 22.67 46.65 3.86
4481 18194 4.416738 GCCTCCAGGTGCACCTCC 62.417 72.222 35.79 16.90 46.65 4.30


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

AutoCloner maintained by Alex Coulton.