Multiple sequence alignment - TraesCS2A01G321500

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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 TraesCS2A01G321500 chr2A 100.000 8055 0 0 1 8055 551241997 551250051 0.000000e+00 14875.0
1 TraesCS2A01G321500 chr2A 97.059 34 0 1 6814 6847 551248667 551248699 1.000000e-03 56.5
2 TraesCS2A01G321500 chr2A 97.059 34 0 1 6671 6703 551248810 551248843 1.000000e-03 56.5
3 TraesCS2A01G321500 chr2B 96.396 5633 180 12 800 6416 514040008 514034383 0.000000e+00 9256.0
4 TraesCS2A01G321500 chr2B 91.972 1557 68 25 6508 8055 514034385 514032877 0.000000e+00 2130.0
5 TraesCS2A01G321500 chr2B 83.709 798 107 14 1 779 32142689 32141896 0.000000e+00 732.0
6 TraesCS2A01G321500 chr2B 79.752 242 24 7 5489 5707 514035558 514035319 1.400000e-32 152.0
7 TraesCS2A01G321500 chr2B 97.059 34 0 1 6814 6847 514034226 514034194 1.000000e-03 56.5
8 TraesCS2A01G321500 chr2D 97.956 3914 80 0 1758 5671 437684621 437680708 0.000000e+00 6785.0
9 TraesCS2A01G321500 chr2D 95.238 1512 59 9 5701 7204 437680708 437679202 0.000000e+00 2381.0
10 TraesCS2A01G321500 chr2D 95.042 1069 42 6 812 1875 437685685 437684623 0.000000e+00 1670.0
11 TraesCS2A01G321500 chr2D 91.941 546 29 5 7515 8055 437678735 437678200 0.000000e+00 750.0
12 TraesCS2A01G321500 chr2D 87.050 139 14 2 5489 5625 437681136 437681000 3.890000e-33 154.0
13 TraesCS2A01G321500 chr2D 97.059 34 0 1 6671 6703 437679593 437679560 1.000000e-03 56.5
14 TraesCS2A01G321500 chr2D 97.059 34 0 1 6814 6847 437679738 437679706 1.000000e-03 56.5
15 TraesCS2A01G321500 chr1D 88.776 784 82 6 1 781 337209081 337209861 0.000000e+00 955.0
16 TraesCS2A01G321500 chr3D 87.964 781 88 6 1 778 326712189 326711412 0.000000e+00 917.0
17 TraesCS2A01G321500 chr5A 84.860 786 106 13 1 781 395248127 395247350 0.000000e+00 780.0
18 TraesCS2A01G321500 chr4A 84.237 793 111 13 1 784 589481053 589480266 0.000000e+00 760.0
19 TraesCS2A01G321500 chr4A 77.325 785 152 19 1 778 603124468 603125233 2.670000e-119 440.0
20 TraesCS2A01G321500 chr7B 84.137 788 109 16 1 781 635888309 635887531 0.000000e+00 749.0
21 TraesCS2A01G321500 chr7B 80.427 797 125 20 1 788 14163577 14162803 5.420000e-161 579.0
22 TraesCS2A01G321500 chr4B 80.424 802 137 18 1 787 665456646 665455850 1.940000e-165 593.0
23 TraesCS2A01G321500 chr3B 76.972 786 154 23 1 778 787400283 787399517 2.690000e-114 424.0


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 TraesCS2A01G321500 chr2A 551241997 551250051 8054 False 4996.000000 14875 98.039333 1 8055 3 chr2A.!!$F1 8054
1 TraesCS2A01G321500 chr2B 514032877 514040008 7131 True 3814.166667 9256 95.142333 800 8055 3 chr2B.!!$R3 7255
2 TraesCS2A01G321500 chr2B 32141896 32142689 793 True 732.000000 732 83.709000 1 779 1 chr2B.!!$R1 778
3 TraesCS2A01G321500 chr2D 437678200 437685685 7485 True 1693.285714 6785 94.477857 812 8055 7 chr2D.!!$R1 7243
4 TraesCS2A01G321500 chr1D 337209081 337209861 780 False 955.000000 955 88.776000 1 781 1 chr1D.!!$F1 780
5 TraesCS2A01G321500 chr3D 326711412 326712189 777 True 917.000000 917 87.964000 1 778 1 chr3D.!!$R1 777
6 TraesCS2A01G321500 chr5A 395247350 395248127 777 True 780.000000 780 84.860000 1 781 1 chr5A.!!$R1 780
7 TraesCS2A01G321500 chr4A 589480266 589481053 787 True 760.000000 760 84.237000 1 784 1 chr4A.!!$R1 783
8 TraesCS2A01G321500 chr4A 603124468 603125233 765 False 440.000000 440 77.325000 1 778 1 chr4A.!!$F1 777
9 TraesCS2A01G321500 chr7B 635887531 635888309 778 True 749.000000 749 84.137000 1 781 1 chr7B.!!$R2 780
10 TraesCS2A01G321500 chr7B 14162803 14163577 774 True 579.000000 579 80.427000 1 788 1 chr7B.!!$R1 787
11 TraesCS2A01G321500 chr4B 665455850 665456646 796 True 593.000000 593 80.424000 1 787 1 chr4B.!!$R1 786
12 TraesCS2A01G321500 chr3B 787399517 787400283 766 True 424.000000 424 76.972000 1 778 1 chr3B.!!$R1 777

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
716 754 1.148498 GGAATCGGGTGGGGATGAC 59.852 63.158 0.00 0.00 0.00 3.06 F
1195 1253 0.109723 CCCTTTCAAACCCAGACCGA 59.890 55.000 0.00 0.00 0.00 4.69 F
2638 2816 0.824109 TGTCATCCTCGTCACATCCC 59.176 55.000 0.00 0.00 0.00 3.85 F
3303 3487 0.886563 AGCAGAGACAAAGCAATGGC 59.113 50.000 0.00 0.00 41.61 4.40 F
3309 3493 1.202976 AGACAAAGCAATGGCCAGACT 60.203 47.619 13.05 5.21 42.56 3.24 F
4989 5173 1.525784 CGCAGCGATTCGTTCTGAAAG 60.526 52.381 9.98 0.00 40.71 2.62 F
6784 6974 0.031721 GTAGCCGTCTTGTATCCCCG 59.968 60.000 0.00 0.00 0.00 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1747 1806 0.471211 AGTCCAGGACAACGAAGGGA 60.471 55.000 22.31 0.00 34.60 4.20 R
2821 2999 0.817634 TTGTCCCCACTTGCTTGTCG 60.818 55.000 0.00 0.00 0.00 4.35 R
3982 4166 4.513692 TCACCAGTTGGATTTTCTGTTACG 59.486 41.667 4.92 0.00 38.94 3.18 R
4969 5153 0.438445 TTTCAGAACGAATCGCTGCG 59.562 50.000 17.25 17.25 32.32 5.18 R
5146 5330 2.358957 TCTGGCAGATCATTTGGTTCG 58.641 47.619 14.43 0.00 0.00 3.95 R
6947 7138 0.178975 CTACTGGAGCCTCGGAGGAT 60.179 60.000 27.95 22.46 37.67 3.24 R
7765 8254 0.533085 GGATCCCAAGCGCTAAGGTC 60.533 60.000 22.76 18.14 0.00 3.85 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
228 230 4.317839 GGTTTCGTGAATCCGTCATATTCG 60.318 45.833 0.00 0.00 38.90 3.34
240 242 7.500720 TCCGTCATATTCGTCTATTAGAACA 57.499 36.000 0.00 0.00 0.00 3.18
294 296 2.971598 CGCCATGTTCCAGTCCCCT 61.972 63.158 0.00 0.00 0.00 4.79
387 389 3.193479 ACGCCGATCTCATATCAGCATAA 59.807 43.478 0.00 0.00 0.00 1.90
481 491 4.541714 TCCTCCTTGAATTCTTCTTCCCAT 59.458 41.667 7.05 0.00 0.00 4.00
660 670 2.282816 CCCACCGCACAATCCCAA 60.283 61.111 0.00 0.00 0.00 4.12
716 754 1.148498 GGAATCGGGTGGGGATGAC 59.852 63.158 0.00 0.00 0.00 3.06
793 841 1.439543 CCTAGGGAGGGGAGGATTTG 58.560 60.000 0.00 0.00 39.48 2.32
794 842 1.345526 CCTAGGGAGGGGAGGATTTGT 60.346 57.143 0.00 0.00 39.48 2.83
795 843 2.493091 CTAGGGAGGGGAGGATTTGTT 58.507 52.381 0.00 0.00 0.00 2.83
796 844 1.773541 AGGGAGGGGAGGATTTGTTT 58.226 50.000 0.00 0.00 0.00 2.83
797 845 2.942905 AGGGAGGGGAGGATTTGTTTA 58.057 47.619 0.00 0.00 0.00 2.01
798 846 3.274383 AGGGAGGGGAGGATTTGTTTAA 58.726 45.455 0.00 0.00 0.00 1.52
1190 1248 0.777446 TCTCCCCCTTTCAAACCCAG 59.223 55.000 0.00 0.00 0.00 4.45
1195 1253 0.109723 CCCTTTCAAACCCAGACCGA 59.890 55.000 0.00 0.00 0.00 4.69
1223 1281 5.003804 ACCTTATCTGATTCGCTTGTTTGT 58.996 37.500 0.00 0.00 0.00 2.83
1384 1443 2.034812 GGTAGTAAGCTCCTCATGGTCG 59.965 54.545 0.00 0.00 34.23 4.79
1389 1448 1.418334 AGCTCCTCATGGTCGCTTAT 58.582 50.000 0.00 0.00 37.71 1.73
1424 1483 3.057019 TGACATGTACTTTGTCTCGTGC 58.943 45.455 21.94 4.74 43.12 5.34
1432 1491 0.948623 TTTGTCTCGTGCATGGACGG 60.949 55.000 34.54 25.49 39.88 4.79
1481 1540 6.341316 TGTTAGGTGATCAGATGCTTTAGTC 58.659 40.000 0.00 0.00 0.00 2.59
1486 1545 3.776969 TGATCAGATGCTTTAGTCTGGGT 59.223 43.478 0.00 0.00 41.64 4.51
1498 1557 6.347160 GCTTTAGTCTGGGTACGTTTTACTTG 60.347 42.308 0.00 0.00 0.00 3.16
1667 1726 6.580041 GCAATAGATGGCTATCAAAATTGACG 59.420 38.462 24.17 9.07 40.49 4.35
1747 1806 4.225942 TGATAGTCAGGGCAACTCATTTCT 59.774 41.667 0.00 0.00 0.00 2.52
1751 1810 1.005215 CAGGGCAACTCATTTCTCCCT 59.995 52.381 0.00 0.00 44.44 4.20
1756 1815 2.814336 GCAACTCATTTCTCCCTTCGTT 59.186 45.455 0.00 0.00 0.00 3.85
1854 2031 4.290155 AGCGCAAGTTTCTAAATGTGTTG 58.710 39.130 11.47 0.00 41.68 3.33
1859 2036 7.523219 CGCAAGTTTCTAAATGTGTTGGTATA 58.477 34.615 0.00 0.00 0.00 1.47
1864 2041 8.262227 AGTTTCTAAATGTGTTGGTATATCCGA 58.738 33.333 0.00 0.00 39.52 4.55
2182 2359 4.692625 AGTCAAGTTAGCATTGCTACTGTG 59.307 41.667 17.79 14.51 41.12 3.66
2311 2489 5.882557 GTCAAATCTCCTGTGTATGGTCAAT 59.117 40.000 0.00 0.00 0.00 2.57
2451 2629 5.585820 TTATGCTGTCCGTAGTTGTATCA 57.414 39.130 0.00 0.00 0.00 2.15
2462 2640 5.043903 CGTAGTTGTATCATCTGTTGAGGG 58.956 45.833 0.00 0.00 37.89 4.30
2638 2816 0.824109 TGTCATCCTCGTCACATCCC 59.176 55.000 0.00 0.00 0.00 3.85
2736 2914 8.166706 CAGTAGATTTTCAAATCAAAGCAATGC 58.833 33.333 13.50 0.00 45.59 3.56
2761 2939 2.907042 CCTGGTTGGAGAGGAGTTACTT 59.093 50.000 0.00 0.00 38.35 2.24
2792 2970 4.072131 GGAAAACCTTCTGCATAGTGTCA 58.928 43.478 0.00 0.00 0.00 3.58
2821 2999 2.622942 TGATCTTGGTGTTGTTTCTGGC 59.377 45.455 0.00 0.00 0.00 4.85
2899 3077 0.898320 CCTCTCAGGAAAAGGAGCGA 59.102 55.000 0.00 0.00 37.67 4.93
2946 3124 2.264109 AACACGTCAGCTGTAGATCG 57.736 50.000 14.67 13.54 0.00 3.69
3113 3291 4.160814 TCCAGCCTGAAAATCCAATCATTG 59.839 41.667 0.00 0.00 0.00 2.82
3303 3487 0.886563 AGCAGAGACAAAGCAATGGC 59.113 50.000 0.00 0.00 41.61 4.40
3309 3493 1.202976 AGACAAAGCAATGGCCAGACT 60.203 47.619 13.05 5.21 42.56 3.24
3312 3496 3.434309 ACAAAGCAATGGCCAGACTATT 58.566 40.909 13.05 0.00 42.56 1.73
3351 3535 6.375174 CCATCATCACAACTCAATAGTGGAAA 59.625 38.462 0.00 0.00 35.62 3.13
4027 4211 3.408634 TGGGAAGCGTAAAAAGAAGAGG 58.591 45.455 0.00 0.00 0.00 3.69
4380 4564 6.486253 TGATGTTTTGACTGAGAATACAGC 57.514 37.500 0.00 0.00 41.06 4.40
4438 4622 5.389307 GCGTCAGAGAAAGAAGACTTCATTG 60.389 44.000 17.34 1.24 35.05 2.82
4447 4631 6.645790 AAGAAGACTTCATTGAAGCATGTT 57.354 33.333 23.22 11.58 42.79 2.71
4723 4907 7.339212 CAGGAAAAATATGTAACTGATGGTGGA 59.661 37.037 0.00 0.00 0.00 4.02
4969 5153 3.989817 GTGCTGTTGAACCAAATGATTCC 59.010 43.478 0.00 0.00 0.00 3.01
4989 5173 1.525784 CGCAGCGATTCGTTCTGAAAG 60.526 52.381 9.98 0.00 40.71 2.62
5002 5186 6.565234 TCGTTCTGAAAGTGGCAAAATTAAA 58.435 32.000 3.36 0.00 33.76 1.52
5146 5330 4.504461 CAGTCTCAACGTGCTGGTATTATC 59.496 45.833 0.00 0.00 0.00 1.75
5254 5438 4.202040 CCATCTGTTTCAGCAGAAAACACA 60.202 41.667 5.79 0.53 46.93 3.72
5284 5468 3.016736 AGATGGTAATGTGGAAAAGGCG 58.983 45.455 0.00 0.00 0.00 5.52
5302 5486 3.071747 AGGCGAAGGAGAAAAAGAAGAGT 59.928 43.478 0.00 0.00 0.00 3.24
5344 5528 0.109913 AACCCGAGTCTGAAAACCCC 59.890 55.000 0.00 0.00 0.00 4.95
5423 5607 3.452627 GCAGAAGGGAGGAATAGAACAGA 59.547 47.826 0.00 0.00 0.00 3.41
5485 5669 0.391130 GTATGCCGCAACAGGAGACA 60.391 55.000 0.00 0.00 0.00 3.41
5597 5781 3.868077 CGAGTCTCAAAATCCTGATGGTC 59.132 47.826 0.00 0.00 34.23 4.02
5654 5838 3.723681 AGGAAGAATGGATCAGGGCAATA 59.276 43.478 0.00 0.00 0.00 1.90
5667 5851 5.248640 TCAGGGCAATACAAAAGAGAAGAG 58.751 41.667 0.00 0.00 0.00 2.85
5675 5859 8.401709 GCAATACAAAAGAGAAGAGGGATAAAG 58.598 37.037 0.00 0.00 0.00 1.85
5801 5985 2.494870 ACTGATTTGCCCATTGAGAAGC 59.505 45.455 0.00 0.00 0.00 3.86
5866 6050 5.412594 TCAGACAAAGCATCATGGTAAGAAC 59.587 40.000 0.00 0.00 0.00 3.01
6255 6439 2.497273 GGCCAACTTTATGCTGGATTGT 59.503 45.455 0.00 0.00 33.88 2.71
6324 6511 4.365514 TCTTTTATGTGTTCCTCTGCCA 57.634 40.909 0.00 0.00 0.00 4.92
6464 6651 3.945285 GACATCCATAATCCACGGTTTGT 59.055 43.478 0.00 0.00 0.00 2.83
6478 6665 3.127376 ACGGTTTGTCCTGTGTTTGTTAC 59.873 43.478 0.00 0.00 0.00 2.50
6486 6673 4.634443 GTCCTGTGTTTGTTACTCAGTGTT 59.366 41.667 0.00 0.00 43.55 3.32
6489 6676 4.006989 TGTGTTTGTTACTCAGTGTTGCT 58.993 39.130 0.00 0.00 0.00 3.91
6497 6684 1.302366 CTCAGTGTTGCTTGCTCACA 58.698 50.000 17.47 8.45 34.94 3.58
6529 6716 5.981174 TCTGACTTTGCATCTGATGATACA 58.019 37.500 21.30 7.05 0.00 2.29
6536 6723 3.708121 TGCATCTGATGATACACTGGTCT 59.292 43.478 21.30 0.00 0.00 3.85
6537 6724 4.056740 GCATCTGATGATACACTGGTCTG 58.943 47.826 21.30 0.00 0.00 3.51
6539 6726 2.432146 TCTGATGATACACTGGTCTGCC 59.568 50.000 0.00 0.00 0.00 4.85
6547 6734 1.757306 ACTGGTCTGCCTGTGGAAG 59.243 57.895 0.00 0.00 43.92 3.46
6575 6762 2.867624 ACTGATGTGCATTCAACAGGT 58.132 42.857 15.83 3.90 40.74 4.00
6654 6841 7.633361 TCGTTGTAAGTTCTTGAATCTGTAC 57.367 36.000 0.00 0.00 0.00 2.90
6751 6941 5.362556 GCAGGGTGCACATTAATATACTG 57.637 43.478 20.43 12.01 44.26 2.74
6784 6974 0.031721 GTAGCCGTCTTGTATCCCCG 59.968 60.000 0.00 0.00 0.00 5.73
7082 7273 1.737793 GACGGACCTGGTGCTTAAATG 59.262 52.381 16.57 2.08 0.00 2.32
7108 7299 1.880027 GAGTTTCACGCAATTCCCAGT 59.120 47.619 0.00 0.00 0.00 4.00
7153 7344 0.321919 GGCTGCTGAACATGTCTGGA 60.322 55.000 0.00 0.00 0.00 3.86
7157 7348 3.497640 GCTGCTGAACATGTCTGGATATC 59.502 47.826 0.00 0.00 0.00 1.63
7158 7349 4.700700 CTGCTGAACATGTCTGGATATCA 58.299 43.478 0.00 0.00 0.00 2.15
7159 7350 5.300411 TGCTGAACATGTCTGGATATCAT 57.700 39.130 0.00 0.00 0.00 2.45
7160 7351 5.061179 TGCTGAACATGTCTGGATATCATG 58.939 41.667 0.00 2.58 42.86 3.07
7209 7404 2.388310 TTGAGTTTGTGGTCGTGACA 57.612 45.000 2.00 0.00 0.00 3.58
7230 7425 6.039270 TGACAGTCCTCAAAATTCGTCAATTT 59.961 34.615 0.00 0.00 42.95 1.82
7247 7442 3.535280 ATTTTGTCCTTTTTGCCGTGT 57.465 38.095 0.00 0.00 0.00 4.49
7315 7788 4.351131 GTGGAACAAATTAGCCGGTAAG 57.649 45.455 1.90 0.00 44.16 2.34
7328 7801 1.664151 CCGGTAAGAAATTCGCAGTCC 59.336 52.381 0.00 0.00 0.00 3.85
7355 7836 6.427853 GCTTTGTTTAATGCCAATTTCTCCTT 59.572 34.615 0.00 0.00 32.47 3.36
7356 7837 7.602265 GCTTTGTTTAATGCCAATTTCTCCTTA 59.398 33.333 0.00 0.00 32.47 2.69
7387 7868 8.621532 TTAGAGACAAGTTCAAATGCTAACAT 57.378 30.769 0.00 0.00 38.49 2.71
7413 7894 8.925161 TTTTCTTTTGAGTAGTTTGGATTGTG 57.075 30.769 0.00 0.00 0.00 3.33
7416 7897 8.149973 TCTTTTGAGTAGTTTGGATTGTGTAC 57.850 34.615 0.00 0.00 0.00 2.90
7420 7901 5.163290 TGAGTAGTTTGGATTGTGTACCACA 60.163 40.000 0.00 0.00 43.02 4.17
7421 7902 5.876357 AGTAGTTTGGATTGTGTACCACAT 58.124 37.500 0.00 0.00 44.16 3.21
7456 7937 8.537016 TGGTAGTTCAAATGCTAACATAGTAGT 58.463 33.333 0.00 0.00 34.62 2.73
7561 8045 5.648572 AGCTACACCTAAGAACGTTCATAC 58.351 41.667 28.78 8.67 0.00 2.39
7686 8175 2.767505 CGAGCCTTCCTTGTTACTTGT 58.232 47.619 0.00 0.00 0.00 3.16
7716 8205 5.509716 GATCTTCATCCATGATGTTTGCA 57.490 39.130 0.00 0.00 40.55 4.08
7727 8216 3.499338 TGATGTTTGCAGTCTTCCCAAT 58.501 40.909 0.00 0.00 0.00 3.16
7746 8235 4.261909 CCAATGGATTTCTGGCTAAGCATC 60.262 45.833 0.00 0.00 0.00 3.91
7755 8244 1.656441 GCTAAGCATCCGGGCAATG 59.344 57.895 0.00 0.00 35.83 2.82
7772 8261 1.739338 ATGCCGCCTCTCGACCTTAG 61.739 60.000 0.00 0.00 41.67 2.18
7851 8340 5.798125 AGAGAGACTTCACAAGAACATCA 57.202 39.130 0.00 0.00 0.00 3.07
7890 8379 9.478768 GATGTAGGATATCTCGATATCGACTTA 57.521 37.037 23.48 16.94 46.61 2.24
7911 8401 6.150140 ACTTAGTGATTCCTTGCAATCTTGAC 59.850 38.462 0.00 0.00 34.35 3.18
7914 8404 3.436704 TGATTCCTTGCAATCTTGACGAC 59.563 43.478 0.00 0.00 34.35 4.34
7918 8408 2.290367 CCTTGCAATCTTGACGACACAA 59.710 45.455 0.00 0.00 0.00 3.33
7921 8411 2.286950 TGCAATCTTGACGACACAAAGC 60.287 45.455 0.00 0.00 0.00 3.51
7961 8451 7.783090 AGCAAATATCAGTGATAGTGTTGAG 57.217 36.000 24.47 12.13 0.00 3.02
7964 8454 7.628235 CAAATATCAGTGATAGTGTTGAGCAG 58.372 38.462 17.52 0.00 0.00 4.24
8019 8509 4.402583 CAAATGCGTCGATTTCTGCTTTA 58.597 39.130 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 7.815068 GTCAGAGTTGAGCTTATTGTCTCTAAA 59.185 37.037 0.00 0.00 32.98 1.85
228 230 6.051179 AGGAACCAAGGTGTTCTAATAGAC 57.949 41.667 0.00 0.00 43.31 2.59
240 242 1.497286 TGGCTGTTTAGGAACCAAGGT 59.503 47.619 0.00 0.00 34.80 3.50
294 296 1.820519 ACGGTACAGTTCGGATGCTTA 59.179 47.619 0.00 0.00 0.00 3.09
387 389 1.546548 GGTTCAGCCCTTCTGCTCTTT 60.547 52.381 0.00 0.00 40.32 2.52
481 491 2.180276 GAGGAGGAGGAGCAGTTTGTA 58.820 52.381 0.00 0.00 0.00 2.41
660 670 2.286732 ATCCCTGGGAAGCCTGCT 60.287 61.111 21.42 0.00 34.34 4.24
685 707 2.041265 ATTCCCGCACCTCTCCCT 59.959 61.111 0.00 0.00 0.00 4.20
689 711 3.470888 CCCGATTCCCGCACCTCT 61.471 66.667 0.00 0.00 36.84 3.69
700 728 2.742116 CGGTCATCCCCACCCGATT 61.742 63.158 0.00 0.00 43.01 3.34
716 754 4.090588 TCCTACCTTTGCCGCCGG 62.091 66.667 0.00 0.00 0.00 6.13
814 862 8.201464 AGGCGGAAAATTTCTTTTCTTTAAGAA 58.799 29.630 2.94 2.94 46.24 2.52
815 863 7.722363 AGGCGGAAAATTTCTTTTCTTTAAGA 58.278 30.769 5.65 0.00 46.24 2.10
816 864 7.867909 AGAGGCGGAAAATTTCTTTTCTTTAAG 59.132 33.333 5.65 0.00 46.24 1.85
817 865 7.722363 AGAGGCGGAAAATTTCTTTTCTTTAA 58.278 30.769 5.65 0.00 46.24 1.52
818 866 7.284919 AGAGGCGGAAAATTTCTTTTCTTTA 57.715 32.000 5.65 0.00 46.24 1.85
820 868 5.791336 AGAGGCGGAAAATTTCTTTTCTT 57.209 34.783 5.65 0.00 46.24 2.52
821 869 5.791336 AAGAGGCGGAAAATTTCTTTTCT 57.209 34.783 5.65 2.13 46.24 2.52
822 870 8.534333 AATAAAGAGGCGGAAAATTTCTTTTC 57.466 30.769 5.65 0.00 46.27 2.29
823 871 8.902540 AAATAAAGAGGCGGAAAATTTCTTTT 57.097 26.923 5.65 0.00 38.58 2.27
831 879 3.920446 GCCAAAATAAAGAGGCGGAAAA 58.080 40.909 0.00 0.00 37.41 2.29
1102 1155 2.342648 GACGTTCAGGGCGAGGTT 59.657 61.111 0.00 0.00 0.00 3.50
1168 1221 0.039764 GGTTTGAAAGGGGGAGAGGG 59.960 60.000 0.00 0.00 0.00 4.30
1171 1224 0.777446 CTGGGTTTGAAAGGGGGAGA 59.223 55.000 0.00 0.00 0.00 3.71
1180 1238 1.712056 TCTCTCGGTCTGGGTTTGAA 58.288 50.000 0.00 0.00 0.00 2.69
1190 1248 5.523438 AATCAGATAAGGTTCTCTCGGTC 57.477 43.478 0.00 0.00 0.00 4.79
1195 1253 5.105146 ACAAGCGAATCAGATAAGGTTCTCT 60.105 40.000 0.00 0.00 0.00 3.10
1384 1443 9.716507 ACATGTCAAAATACACGAAATATAAGC 57.283 29.630 0.00 0.00 30.75 3.09
1412 1471 0.439985 CGTCCATGCACGAGACAAAG 59.560 55.000 2.06 0.00 42.69 2.77
1424 1483 0.459585 CCTACACCGAACCGTCCATG 60.460 60.000 0.00 0.00 0.00 3.66
1432 1491 2.546789 CACTGGAAAACCTACACCGAAC 59.453 50.000 0.00 0.00 0.00 3.95
1481 1540 4.379082 GCCAATCAAGTAAAACGTACCCAG 60.379 45.833 0.00 0.00 0.00 4.45
1486 1545 4.150980 CAGACGCCAATCAAGTAAAACGTA 59.849 41.667 0.00 0.00 31.89 3.57
1498 1557 0.935898 CAGCTGATCAGACGCCAATC 59.064 55.000 27.04 5.77 0.00 2.67
1747 1806 0.471211 AGTCCAGGACAACGAAGGGA 60.471 55.000 22.31 0.00 34.60 4.20
1751 1810 2.549992 CCATTCAGTCCAGGACAACGAA 60.550 50.000 22.31 19.22 34.60 3.85
1756 1815 0.994247 ATGCCATTCAGTCCAGGACA 59.006 50.000 22.31 0.96 34.60 4.02
1833 2010 3.425193 CCAACACATTTAGAAACTTGCGC 59.575 43.478 0.00 0.00 0.00 6.09
1834 2011 4.606961 ACCAACACATTTAGAAACTTGCG 58.393 39.130 0.00 0.00 0.00 4.85
1854 2031 2.095364 CGTAGCACCTGTCGGATATACC 60.095 54.545 0.00 0.00 0.00 2.73
2182 2359 8.859517 TTAACCAACAATAAGCAAACTACAAC 57.140 30.769 0.00 0.00 0.00 3.32
2311 2489 3.245087 ACTGAGTGAGAAGGAGCTGTAGA 60.245 47.826 0.00 0.00 0.00 2.59
2451 2629 3.184628 TCAACCTCATCCCTCAACAGAT 58.815 45.455 0.00 0.00 0.00 2.90
2529 2707 8.040716 ACCTACAAAAGCACATGAACTATTAC 57.959 34.615 0.00 0.00 0.00 1.89
2638 2816 5.095490 GCATCCTTCTTTGTTTCCGTATTG 58.905 41.667 0.00 0.00 0.00 1.90
2736 2914 4.101448 CCTCTCCAACCAGGGCCG 62.101 72.222 0.00 0.00 38.24 6.13
2821 2999 0.817634 TTGTCCCCACTTGCTTGTCG 60.818 55.000 0.00 0.00 0.00 4.35
2899 3077 4.936685 ATCAGTCCTTCTAGCCCTTTTT 57.063 40.909 0.00 0.00 0.00 1.94
3003 3181 7.639113 AGAGAATTAGTGTTTGTTTCCAACA 57.361 32.000 0.00 0.00 40.21 3.33
3113 3291 8.887036 TTTTTCCTTTTCTTATTCTTTCCAGC 57.113 30.769 0.00 0.00 0.00 4.85
3303 3487 5.008415 GGAAGATGCATGTCAAATAGTCTGG 59.992 44.000 2.46 0.00 0.00 3.86
3309 3493 6.773685 TGATGATGGAAGATGCATGTCAAATA 59.226 34.615 2.46 0.00 0.00 1.40
3312 3496 4.337274 GTGATGATGGAAGATGCATGTCAA 59.663 41.667 2.46 0.00 0.00 3.18
3982 4166 4.513692 TCACCAGTTGGATTTTCTGTTACG 59.486 41.667 4.92 0.00 38.94 3.18
4438 4622 6.284475 CTGCTATCAGTAGAAACATGCTTC 57.716 41.667 0.33 0.33 35.61 3.86
4791 4975 5.220548 GCATTAGGCTTATCATGCGTGATAG 60.221 44.000 24.00 19.21 45.44 2.08
4969 5153 0.438445 TTTCAGAACGAATCGCTGCG 59.562 50.000 17.25 17.25 32.32 5.18
4989 5173 5.994668 TGGTCCAAGAATTTAATTTTGCCAC 59.005 36.000 0.00 0.30 0.00 5.01
5002 5186 3.245948 TGGGGCTAAAATGGTCCAAGAAT 60.246 43.478 0.00 0.00 0.00 2.40
5146 5330 2.358957 TCTGGCAGATCATTTGGTTCG 58.641 47.619 14.43 0.00 0.00 3.95
5254 5438 6.126863 TCCACATTACCATCTTCTCTGTTT 57.873 37.500 0.00 0.00 0.00 2.83
5302 5486 6.723298 TTGACCAAATCCTGCTTTCTTTTA 57.277 33.333 0.00 0.00 0.00 1.52
5411 5595 4.970662 TTGCATTGCTCTGTTCTATTCC 57.029 40.909 10.49 0.00 0.00 3.01
5423 5607 3.633525 TCACTGTTCTCTTTTGCATTGCT 59.366 39.130 10.49 0.00 0.00 3.91
5485 5669 7.716998 TCTTCTCTGTTAATGTTTTCTGCTTCT 59.283 33.333 0.00 0.00 0.00 2.85
5597 5781 7.862873 TGCAGAAGTATCAGTATCTTGATTACG 59.137 37.037 0.00 0.00 38.65 3.18
5679 5863 7.227314 CCTGTTGCAGCATACTATTATTCTGAA 59.773 37.037 2.87 0.00 32.35 3.02
5750 5934 1.821936 CACCAACCTTGCTTTGGCA 59.178 52.632 0.92 0.00 46.58 4.92
5866 6050 4.935205 TCAATAGACCCGTCATGTTTTCTG 59.065 41.667 0.00 0.00 0.00 3.02
6450 6637 2.105134 ACACAGGACAAACCGTGGATTA 59.895 45.455 0.00 0.00 42.69 1.75
6478 6665 1.302366 TGTGAGCAAGCAACACTGAG 58.698 50.000 17.78 0.00 35.83 3.35
6486 6673 3.193267 AGAAAACAGTTTGTGAGCAAGCA 59.807 39.130 0.00 0.00 38.13 3.91
6489 6676 4.458989 AGTCAGAAAACAGTTTGTGAGCAA 59.541 37.500 10.39 0.00 44.92 3.91
6497 6684 6.038356 CAGATGCAAAGTCAGAAAACAGTTT 58.962 36.000 0.00 0.00 0.00 2.66
6529 6716 1.056700 ACTTCCACAGGCAGACCAGT 61.057 55.000 0.00 0.00 39.06 4.00
6537 6724 1.545651 AGTTAGCCAACTTCCACAGGC 60.546 52.381 0.00 0.00 42.51 4.85
6539 6726 3.126001 TCAGTTAGCCAACTTCCACAG 57.874 47.619 0.00 0.00 42.51 3.66
6547 6734 3.191162 TGAATGCACATCAGTTAGCCAAC 59.809 43.478 0.00 0.00 34.67 3.77
6746 6936 5.221461 GGCTACAACATAGCTACCACAGTAT 60.221 44.000 0.00 0.00 40.25 2.12
6751 6941 2.159142 ACGGCTACAACATAGCTACCAC 60.159 50.000 0.00 0.00 40.25 4.16
6791 6981 2.135139 CGTTACCGTGCATGCATCTAT 58.865 47.619 25.64 12.41 0.00 1.98
6811 7001 5.948992 AGTCAAGCAGTTCTATCCAAAAC 57.051 39.130 0.00 0.00 0.00 2.43
6947 7138 0.178975 CTACTGGAGCCTCGGAGGAT 60.179 60.000 27.95 22.46 37.67 3.24
7119 7310 1.608542 GCAGCCAAATCCACAAATGCA 60.609 47.619 0.00 0.00 32.79 3.96
7134 7325 0.321919 TCCAGACATGTTCAGCAGCC 60.322 55.000 0.00 0.00 0.00 4.85
7178 7373 4.318332 CACAAACTCAATACAGCTGGAGA 58.682 43.478 19.93 2.84 0.00 3.71
7230 7425 1.757682 AGACACGGCAAAAAGGACAA 58.242 45.000 0.00 0.00 0.00 3.18
7231 7426 2.623878 TAGACACGGCAAAAAGGACA 57.376 45.000 0.00 0.00 0.00 4.02
7241 7436 1.467342 GGACACCAAAATAGACACGGC 59.533 52.381 0.00 0.00 0.00 5.68
7247 7442 4.037446 GCAACAACAGGACACCAAAATAGA 59.963 41.667 0.00 0.00 0.00 1.98
7315 7788 2.030805 ACAAAGCTGGACTGCGAATTTC 60.031 45.455 0.00 0.00 38.13 2.17
7328 7801 6.128472 GGAGAAATTGGCATTAAACAAAGCTG 60.128 38.462 0.00 0.00 0.00 4.24
7356 7837 9.624373 AGCATTTGAACTTGTCTCTAATATCAT 57.376 29.630 0.00 0.00 0.00 2.45
7363 7844 8.621532 AATGTTAGCATTTGAACTTGTCTCTA 57.378 30.769 0.00 0.00 42.19 2.43
7387 7868 9.364989 CACAATCCAAACTACTCAAAAGAAAAA 57.635 29.630 0.00 0.00 0.00 1.94
7388 7869 8.527810 ACACAATCCAAACTACTCAAAAGAAAA 58.472 29.630 0.00 0.00 0.00 2.29
7389 7870 8.062065 ACACAATCCAAACTACTCAAAAGAAA 57.938 30.769 0.00 0.00 0.00 2.52
7392 7873 7.012894 TGGTACACAATCCAAACTACTCAAAAG 59.987 37.037 0.00 0.00 0.00 2.27
7396 7877 5.554437 TGGTACACAATCCAAACTACTCA 57.446 39.130 0.00 0.00 0.00 3.41
7420 7901 5.064707 GCATTTGAACTACCACGTGACATAT 59.935 40.000 19.30 0.00 0.00 1.78
7421 7902 4.390603 GCATTTGAACTACCACGTGACATA 59.609 41.667 19.30 5.56 0.00 2.29
7456 7937 8.797350 TTTATGAGAAATCTTGCAAGATCTCA 57.203 30.769 39.25 39.25 46.70 3.27
7727 8216 2.746142 CGGATGCTTAGCCAGAAATCCA 60.746 50.000 17.02 0.00 37.22 3.41
7755 8244 2.413765 CTAAGGTCGAGAGGCGGC 59.586 66.667 0.00 0.00 45.73 6.53
7765 8254 0.533085 GGATCCCAAGCGCTAAGGTC 60.533 60.000 22.76 18.14 0.00 3.85
7772 8261 3.122850 CCAATGGATCCCAAGCGC 58.877 61.111 9.90 0.00 36.95 5.92
7851 8340 2.073816 CCTACATCCAAGCGTCGTTTT 58.926 47.619 0.00 0.00 0.00 2.43
7890 8379 3.438087 CGTCAAGATTGCAAGGAATCACT 59.562 43.478 15.19 1.13 35.16 3.41
7911 8401 1.572085 CCTGCTCCTGCTTTGTGTCG 61.572 60.000 0.00 0.00 40.48 4.35
7914 8404 2.960170 GCCTGCTCCTGCTTTGTG 59.040 61.111 0.00 0.00 40.48 3.33
7918 8408 2.124507 TAAACCGCCTGCTCCTGCTT 62.125 55.000 0.00 0.00 40.48 3.91
7921 8411 2.109126 GCTAAACCGCCTGCTCCTG 61.109 63.158 0.00 0.00 0.00 3.86
7961 8451 3.181489 CCCTGCTCATTCTTTCATTCTGC 60.181 47.826 0.00 0.00 0.00 4.26
7964 8454 2.223433 CGCCCTGCTCATTCTTTCATTC 60.223 50.000 0.00 0.00 0.00 2.67
8019 8509 2.569059 CCATCACTGAATGAGCGGAAT 58.431 47.619 0.00 0.00 41.91 3.01


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

AutoCloner maintained by Alex Coulton.