Multiple sequence alignment - TraesCS4A01G267600

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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 TraesCS4A01G267600 chr4A 100.000 5533 0 0 1 5533 579864556 579859024 0.000000e+00 10218.0
1 TraesCS4A01G267600 chr4A 89.409 812 62 17 1225 2024 221701022 221701821 0.000000e+00 1002.0
2 TraesCS4A01G267600 chr4D 94.396 2391 93 17 2702 5073 22023828 22026196 0.000000e+00 3635.0
3 TraesCS4A01G267600 chr4D 84.793 1210 120 41 1426 2603 22022478 22023655 0.000000e+00 1157.0
4 TraesCS4A01G267600 chr4D 90.061 815 44 7 1 803 22019166 22019955 0.000000e+00 1022.0
5 TraesCS4A01G267600 chr4D 93.651 630 37 3 803 1429 22021815 22022444 0.000000e+00 939.0
6 TraesCS4A01G267600 chr4D 88.578 429 45 3 5105 5533 22026195 22026619 8.220000e-143 518.0
7 TraesCS4A01G267600 chr4D 93.913 115 6 1 2616 2729 22023712 22023826 7.370000e-39 172.0
8 TraesCS4A01G267600 chr4B 91.942 2631 147 29 2928 5527 34029551 34032147 0.000000e+00 3624.0
9 TraesCS4A01G267600 chr4B 88.615 1458 83 24 1 1429 34026384 34027787 0.000000e+00 1696.0
10 TraesCS4A01G267600 chr4B 86.355 1026 95 17 1598 2603 34028033 34029033 0.000000e+00 1077.0
11 TraesCS4A01G267600 chr4B 97.419 310 7 1 2622 2931 34029121 34029429 1.370000e-145 527.0
12 TraesCS4A01G267600 chr4B 80.841 214 24 9 1421 1617 34027810 34028023 9.600000e-33 152.0
13 TraesCS4A01G267600 chr1B 89.163 812 62 17 1226 2024 190284596 190285394 0.000000e+00 989.0
14 TraesCS4A01G267600 chr6D 80.359 779 78 27 1425 2161 66627232 66626487 6.350000e-144 521.0
15 TraesCS4A01G267600 chr6D 80.231 779 78 28 1425 2161 66262236 66261492 2.960000e-142 516.0
16 TraesCS4A01G267600 chr6D 88.000 50 5 1 2862 2911 113475308 113475260 2.150000e-04 58.4
17 TraesCS4A01G267600 chr1D 83.768 499 58 11 1664 2161 470455727 470456203 8.450000e-123 451.0
18 TraesCS4A01G267600 chr1D 88.158 76 3 2 2837 2909 313296278 313296350 9.880000e-13 86.1
19 TraesCS4A01G267600 chr1D 76.316 152 22 10 5234 5382 212015847 212015987 9.950000e-08 69.4
20 TraesCS4A01G267600 chr7A 83.333 498 61 12 1664 2161 63313910 63313435 1.830000e-119 440.0
21 TraesCS4A01G267600 chr5B 82.530 498 63 12 1664 2161 649866741 649867214 3.080000e-112 416.0
22 TraesCS4A01G267600 chr5B 87.500 264 31 2 1899 2161 425669241 425669503 2.500000e-78 303.0
23 TraesCS4A01G267600 chr5B 82.036 167 17 4 1420 1585 649866466 649866620 4.500000e-26 130.0
24 TraesCS4A01G267600 chr5B 78.400 125 27 0 2797 2921 436818000 436817876 1.280000e-11 82.4
25 TraesCS4A01G267600 chr5B 90.164 61 6 0 2849 2909 78194887 78194947 4.590000e-11 80.5
26 TraesCS4A01G267600 chr2A 83.607 183 21 8 2760 2938 720387072 720386895 4.430000e-36 163.0
27 TraesCS4A01G267600 chr6B 82.270 141 22 3 2763 2903 566547155 566547018 9.740000e-23 119.0
28 TraesCS4A01G267600 chr5A 91.803 61 5 0 2849 2909 69318092 69318032 9.880000e-13 86.1
29 TraesCS4A01G267600 chr5D 95.000 40 1 1 2600 2639 459576206 459576168 1.660000e-05 62.1


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 TraesCS4A01G267600 chr4A 579859024 579864556 5532 True 10218.0 10218 100.000000 1 5533 1 chr4A.!!$R1 5532
1 TraesCS4A01G267600 chr4A 221701022 221701821 799 False 1002.0 1002 89.409000 1225 2024 1 chr4A.!!$F1 799
2 TraesCS4A01G267600 chr4D 22019166 22026619 7453 False 1240.5 3635 90.898667 1 5533 6 chr4D.!!$F1 5532
3 TraesCS4A01G267600 chr4B 34026384 34032147 5763 False 1415.2 3624 89.034400 1 5527 5 chr4B.!!$F1 5526
4 TraesCS4A01G267600 chr1B 190284596 190285394 798 False 989.0 989 89.163000 1226 2024 1 chr1B.!!$F1 798
5 TraesCS4A01G267600 chr6D 66626487 66627232 745 True 521.0 521 80.359000 1425 2161 1 chr6D.!!$R2 736
6 TraesCS4A01G267600 chr6D 66261492 66262236 744 True 516.0 516 80.231000 1425 2161 1 chr6D.!!$R1 736
7 TraesCS4A01G267600 chr5B 649866466 649867214 748 False 273.0 416 82.283000 1420 2161 2 chr5B.!!$F3 741

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
684 690 0.368907 CACTACCCGCGTGATTTTCG 59.631 55.0 4.92 0.0 34.35 3.46 F
1186 3090 1.197430 AGTGACCCAAGAGCCAGGAG 61.197 60.0 0.00 0.0 0.00 3.69 F
2295 4331 0.589729 GTGAAAGCTGTGTGTGTGCG 60.590 55.0 0.00 0.0 0.00 5.34 F
3544 5825 0.961019 AATGTTTGCGCTGTGATGGT 59.039 45.0 9.73 0.0 0.00 3.55 F
3800 6082 0.393537 CAGGAGAATGGGAGTGTGCC 60.394 60.0 0.00 0.0 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2274 4310 1.135431 GCACACACACAGCTTTCACAA 60.135 47.619 0.00 0.00 0.00 3.33 R
2786 4936 1.028905 CTTCAGCAAAAACCCGGTCA 58.971 50.000 0.00 0.00 0.00 4.02 R
3722 6004 0.037697 AGCACCGTGTATTCTTCGCA 60.038 50.000 0.00 0.00 0.00 5.10 R
4466 6760 0.501854 AGATATCGTCGTCGTCGTCG 59.498 55.000 14.18 14.18 46.06 5.12 R
4644 6938 0.674895 ATGTTCTCACGGAAGCTGCC 60.675 55.000 0.00 0.00 34.23 4.85 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
129 130 1.324736 GGATCATTCTGACAACGACGC 59.675 52.381 0.00 0.00 0.00 5.19
194 195 1.683943 AGGGATGATTGATGGTTGCG 58.316 50.000 0.00 0.00 0.00 4.85
258 260 4.234530 AGACTCTGTTGCTGAAAAATGC 57.765 40.909 0.00 0.00 0.00 3.56
259 261 3.005155 AGACTCTGTTGCTGAAAAATGCC 59.995 43.478 0.00 0.00 0.00 4.40
267 269 1.468520 GCTGAAAAATGCCGAGCTACA 59.531 47.619 0.00 0.00 0.00 2.74
268 270 2.476854 GCTGAAAAATGCCGAGCTACAG 60.477 50.000 0.00 0.00 0.00 2.74
497 503 5.346551 TGTCGTCGTAAAAATGGTATGAGTG 59.653 40.000 0.00 0.00 0.00 3.51
498 504 4.865925 TCGTCGTAAAAATGGTATGAGTGG 59.134 41.667 0.00 0.00 0.00 4.00
500 506 3.942748 TCGTAAAAATGGTATGAGTGGCC 59.057 43.478 0.00 0.00 0.00 5.36
501 507 3.692101 CGTAAAAATGGTATGAGTGGCCA 59.308 43.478 0.00 0.00 36.64 5.36
502 508 4.156922 CGTAAAAATGGTATGAGTGGCCAA 59.843 41.667 7.24 0.00 35.74 4.52
503 509 5.336055 CGTAAAAATGGTATGAGTGGCCAAA 60.336 40.000 7.24 0.00 35.74 3.28
504 510 4.806640 AAAATGGTATGAGTGGCCAAAG 57.193 40.909 7.24 0.00 35.74 2.77
505 511 3.737559 AATGGTATGAGTGGCCAAAGA 57.262 42.857 7.24 0.00 35.74 2.52
506 512 3.737559 ATGGTATGAGTGGCCAAAGAA 57.262 42.857 7.24 0.00 35.74 2.52
507 513 3.737559 TGGTATGAGTGGCCAAAGAAT 57.262 42.857 7.24 1.34 0.00 2.40
508 514 3.620488 TGGTATGAGTGGCCAAAGAATC 58.380 45.455 7.24 1.20 0.00 2.52
509 515 3.266772 TGGTATGAGTGGCCAAAGAATCT 59.733 43.478 7.24 0.00 0.00 2.40
510 516 4.473196 TGGTATGAGTGGCCAAAGAATCTA 59.527 41.667 7.24 0.00 0.00 1.98
511 517 5.132648 TGGTATGAGTGGCCAAAGAATCTAT 59.867 40.000 7.24 0.00 0.00 1.98
512 518 5.471456 GGTATGAGTGGCCAAAGAATCTATG 59.529 44.000 7.24 0.00 0.00 2.23
513 519 3.282021 TGAGTGGCCAAAGAATCTATGC 58.718 45.455 7.24 0.00 0.00 3.14
570 576 3.804873 GGCCAAAGATGTCGAAGATAGTC 59.195 47.826 0.00 0.00 40.67 2.59
571 577 4.433615 GCCAAAGATGTCGAAGATAGTCA 58.566 43.478 0.00 0.00 40.67 3.41
572 578 4.870426 GCCAAAGATGTCGAAGATAGTCAA 59.130 41.667 0.00 0.00 40.67 3.18
573 579 5.351465 GCCAAAGATGTCGAAGATAGTCAAA 59.649 40.000 0.00 0.00 40.67 2.69
574 580 6.128282 GCCAAAGATGTCGAAGATAGTCAAAA 60.128 38.462 0.00 0.00 40.67 2.44
575 581 7.459486 CCAAAGATGTCGAAGATAGTCAAAAG 58.541 38.462 0.00 0.00 40.67 2.27
576 582 7.331934 CCAAAGATGTCGAAGATAGTCAAAAGA 59.668 37.037 0.00 0.00 40.67 2.52
577 583 8.712363 CAAAGATGTCGAAGATAGTCAAAAGAA 58.288 33.333 0.00 0.00 40.67 2.52
578 584 8.472683 AAGATGTCGAAGATAGTCAAAAGAAG 57.527 34.615 0.00 0.00 40.67 2.85
579 585 7.831753 AGATGTCGAAGATAGTCAAAAGAAGA 58.168 34.615 0.00 0.00 40.67 2.87
580 586 8.307483 AGATGTCGAAGATAGTCAAAAGAAGAA 58.693 33.333 0.00 0.00 40.67 2.52
581 587 8.833231 ATGTCGAAGATAGTCAAAAGAAGAAA 57.167 30.769 0.00 0.00 40.67 2.52
582 588 8.833231 TGTCGAAGATAGTCAAAAGAAGAAAT 57.167 30.769 0.00 0.00 40.67 2.17
613 619 5.520376 AATTTCATGCCTGGTACTATTGC 57.480 39.130 0.00 0.00 0.00 3.56
616 622 1.949525 CATGCCTGGTACTATTGCACC 59.050 52.381 5.85 0.00 34.33 5.01
634 640 5.192927 TGCACCCAACATAATTCTTCTAGG 58.807 41.667 0.00 0.00 0.00 3.02
675 681 3.128632 TATGCCGACACTACCCGCG 62.129 63.158 0.00 0.00 0.00 6.46
684 690 0.368907 CACTACCCGCGTGATTTTCG 59.631 55.000 4.92 0.00 34.35 3.46
743 762 6.811665 CGAGTGTCTGGATCAGTAAAATGTTA 59.188 38.462 0.00 0.00 32.61 2.41
764 783 8.800370 TGTTATCTTATACACATCCTTTTGCA 57.200 30.769 0.00 0.00 0.00 4.08
780 799 5.522460 CCTTTTGCAATAAGATCTTGCCATG 59.478 40.000 18.47 11.65 46.61 3.66
831 2710 6.527423 ACAAGTTGAAATCAGAAATGCCAAT 58.473 32.000 10.54 0.00 0.00 3.16
911 2791 2.924880 GCTGGGCCAAAAACGATGTAAC 60.925 50.000 8.04 0.00 0.00 2.50
920 2800 5.008217 CCAAAAACGATGTAACAGTCCAAGA 59.992 40.000 0.00 0.00 0.00 3.02
987 2889 2.494530 GCCGGGCAAACAGAAACCA 61.495 57.895 15.62 0.00 0.00 3.67
995 2899 2.099756 GCAAACAGAAACCAGTCTTGCT 59.900 45.455 0.00 0.00 29.86 3.91
998 2902 4.423625 AACAGAAACCAGTCTTGCTAGT 57.576 40.909 0.00 0.00 0.00 2.57
1170 3074 2.703798 CCGGGAGCAATGGCAAGTG 61.704 63.158 0.00 0.00 44.61 3.16
1186 3090 1.197430 AGTGACCCAAGAGCCAGGAG 61.197 60.000 0.00 0.00 0.00 3.69
1517 3465 2.187493 TTTGCGTTGCCCTGCGTTA 61.187 52.632 0.00 0.00 0.00 3.18
1681 3711 7.502226 CCTAATAGTGGGATAATCAGTGCAAAA 59.498 37.037 0.00 0.00 0.00 2.44
2095 4126 4.118410 GTGCTCATGTAGGACTTGATGAG 58.882 47.826 0.00 0.00 42.92 2.90
2125 4156 7.001674 AGGTAAGTACATGAAAATGTGTCCAA 58.998 34.615 0.00 0.00 36.08 3.53
2138 4169 6.581171 AATGTGTCCAAAGGAATTTCTCTC 57.419 37.500 0.00 0.00 31.38 3.20
2140 4171 5.694995 TGTGTCCAAAGGAATTTCTCTCTT 58.305 37.500 0.00 0.00 31.38 2.85
2149 4183 9.684448 CAAAGGAATTTCTCTCTTTTTACCTTC 57.316 33.333 0.00 0.00 33.73 3.46
2150 4184 8.410673 AAGGAATTTCTCTCTTTTTACCTTCC 57.589 34.615 0.00 0.00 29.71 3.46
2151 4185 7.760607 AGGAATTTCTCTCTTTTTACCTTCCT 58.239 34.615 0.00 0.00 35.20 3.36
2222 4256 9.460019 TTTTGGAGAAAATTTGAACCAGAAAAT 57.540 25.926 9.57 0.00 0.00 1.82
2244 4279 5.673337 TGTTTTCTGAACCAAGAGAATCG 57.327 39.130 0.00 0.00 42.67 3.34
2249 4284 5.152623 TCTGAACCAAGAGAATCGAACAT 57.847 39.130 0.00 0.00 42.67 2.71
2255 4290 6.824305 ACCAAGAGAATCGAACATTCAAAT 57.176 33.333 0.00 0.00 42.67 2.32
2271 4307 8.419076 ACATTCAAATTGTTAAACACAGGAAC 57.581 30.769 0.00 0.00 36.48 3.62
2272 4308 8.257306 ACATTCAAATTGTTAAACACAGGAACT 58.743 29.630 0.00 0.00 43.88 3.01
2274 4310 9.665719 ATTCAAATTGTTAAACACAGGAACTTT 57.334 25.926 0.00 0.00 34.60 2.66
2295 4331 0.589729 GTGAAAGCTGTGTGTGTGCG 60.590 55.000 0.00 0.00 0.00 5.34
2296 4332 1.655350 GAAAGCTGTGTGTGTGCGC 60.655 57.895 0.00 0.00 0.00 6.09
2297 4333 2.988942 GAAAGCTGTGTGTGTGCGCC 62.989 60.000 4.18 0.00 0.00 6.53
2560 4596 9.830975 ATTCAACCTAAAAGCTAAAACATGTTT 57.169 25.926 18.13 18.13 0.00 2.83
2579 4615 5.049167 TGTTTTGCTGCAAACTAGGAAATG 58.951 37.500 25.99 0.00 35.79 2.32
2581 4617 4.503741 TTGCTGCAAACTAGGAAATGTC 57.496 40.909 13.51 0.00 0.00 3.06
2591 4627 7.414540 GCAAACTAGGAAATGTCAGGAGTTATG 60.415 40.741 0.00 0.00 0.00 1.90
2674 4795 6.625532 AGGATATTTGGCTTTCAACCAATT 57.374 33.333 0.00 0.00 46.25 2.32
2680 4801 5.549742 TTGGCTTTCAACCAATTCATTCT 57.450 34.783 0.00 0.00 42.23 2.40
2786 4936 6.752168 ACAATGCAAAGTGCTTAGAGAAATT 58.248 32.000 0.00 0.00 45.31 1.82
2791 4941 5.385617 CAAAGTGCTTAGAGAAATTGACCG 58.614 41.667 0.00 0.00 0.00 4.79
2832 4982 3.316308 GGTGCTTATTTGTAGATGGCAGG 59.684 47.826 0.00 0.00 0.00 4.85
2971 5246 1.281867 CCTGTGGTTAGCCCTCAATCA 59.718 52.381 0.00 0.00 36.32 2.57
2972 5247 2.092212 CCTGTGGTTAGCCCTCAATCAT 60.092 50.000 0.00 0.00 36.32 2.45
2973 5248 3.136443 CCTGTGGTTAGCCCTCAATCATA 59.864 47.826 0.00 0.00 36.32 2.15
2974 5249 4.202503 CCTGTGGTTAGCCCTCAATCATAT 60.203 45.833 0.00 0.00 36.32 1.78
2976 5251 5.132502 TGTGGTTAGCCCTCAATCATATTG 58.867 41.667 0.00 0.00 33.84 1.90
2978 5253 6.126623 TGTGGTTAGCCCTCAATCATATTGTA 60.127 38.462 0.00 0.00 33.84 2.41
3291 5571 8.974060 TTAAGAAACTACTGAATGAGGTTGTT 57.026 30.769 0.00 0.00 34.17 2.83
3345 5625 5.416083 ACTGATAAAGCTGCACAACGTATA 58.584 37.500 1.02 0.00 0.00 1.47
3346 5626 5.291128 ACTGATAAAGCTGCACAACGTATAC 59.709 40.000 1.02 0.00 0.00 1.47
3502 5783 6.037172 ACGTGTATATTTCCAGATGCAACTTC 59.963 38.462 0.00 0.00 0.00 3.01
3538 5819 5.314923 AGAATATCAAATGTTTGCGCTGT 57.685 34.783 9.73 0.00 38.05 4.40
3544 5825 0.961019 AATGTTTGCGCTGTGATGGT 59.039 45.000 9.73 0.00 0.00 3.55
3568 5849 8.610896 GGTGAATTTCAAGAGAGATATCACTTG 58.389 37.037 18.07 18.07 40.37 3.16
3637 5919 2.037901 TGCAAAAGGTGAGATGCCAAA 58.962 42.857 0.00 0.00 38.00 3.28
3643 5925 3.515602 AGGTGAGATGCCAAAAAGTCT 57.484 42.857 0.00 0.00 0.00 3.24
3673 5955 3.502051 TTAAGATGGACTGGGGGTACT 57.498 47.619 0.00 0.00 0.00 2.73
3713 5995 4.518970 TCCTACATTTTCAGGTGCAACTTC 59.481 41.667 0.00 0.00 36.74 3.01
3722 6004 5.596836 TCAGGTGCAACTTCTTGAATTTT 57.403 34.783 0.00 0.00 36.74 1.82
3725 6007 3.060339 GGTGCAACTTCTTGAATTTTGCG 60.060 43.478 17.39 0.00 44.47 4.85
3731 6013 6.074142 GCAACTTCTTGAATTTTGCGAAGAAT 60.074 34.615 11.48 0.00 34.71 2.40
3737 6019 4.717991 TGAATTTTGCGAAGAATACACGG 58.282 39.130 0.00 0.00 0.00 4.94
3798 6080 1.065854 GTCCAGGAGAATGGGAGTGTG 60.066 57.143 0.00 0.00 41.01 3.82
3800 6082 0.393537 CAGGAGAATGGGAGTGTGCC 60.394 60.000 0.00 0.00 0.00 5.01
3816 6098 2.299013 TGTGCCTCGTGAGTGACTATTT 59.701 45.455 0.00 0.00 0.00 1.40
3817 6099 2.924290 GTGCCTCGTGAGTGACTATTTC 59.076 50.000 0.00 0.00 0.00 2.17
3825 6107 5.125578 TCGTGAGTGACTATTTCTACTGCAT 59.874 40.000 0.00 0.00 0.00 3.96
3826 6108 6.317893 TCGTGAGTGACTATTTCTACTGCATA 59.682 38.462 0.00 0.00 0.00 3.14
3827 6109 6.634837 CGTGAGTGACTATTTCTACTGCATAG 59.365 42.308 0.00 0.00 0.00 2.23
3828 6110 7.484975 GTGAGTGACTATTTCTACTGCATAGT 58.515 38.462 0.00 0.00 40.99 2.12
3829 6111 7.433719 GTGAGTGACTATTTCTACTGCATAGTG 59.566 40.741 0.00 0.00 37.78 2.74
3830 6112 6.276847 AGTGACTATTTCTACTGCATAGTGC 58.723 40.000 0.00 0.00 45.29 4.40
3831 6113 6.097554 AGTGACTATTTCTACTGCATAGTGCT 59.902 38.462 3.41 0.00 45.31 4.40
3832 6114 6.758886 GTGACTATTTCTACTGCATAGTGCTT 59.241 38.462 3.41 0.00 45.31 3.91
3865 6147 9.490663 GTATATTTGCACTGTTTTGATGTCTAC 57.509 33.333 0.00 0.00 0.00 2.59
3870 6152 4.376413 GCACTGTTTTGATGTCTACTGTCG 60.376 45.833 0.00 0.00 0.00 4.35
3894 6176 3.874383 TGAGACAGAACATGGGGAAAA 57.126 42.857 0.00 0.00 0.00 2.29
3907 6189 1.957877 GGGGAAAATGGTGTCAACGAA 59.042 47.619 0.00 0.00 0.00 3.85
3925 6207 0.953960 AAGTGGCTAACCTTTCCGCG 60.954 55.000 0.00 0.00 36.63 6.46
3937 6219 3.067040 ACCTTTCCGCGTTGTTATTTTGT 59.933 39.130 4.92 0.00 0.00 2.83
3982 6264 9.011095 AGAATCAGCATAATCATATTGTTGAGG 57.989 33.333 0.00 0.00 0.00 3.86
4004 6286 3.877508 GGATTGATGGCAGGTGTAACTAC 59.122 47.826 0.00 0.00 36.74 2.73
4022 6304 5.216614 ACTACCTGAACTTCAAGAGGAAC 57.783 43.478 0.00 0.00 0.00 3.62
4025 6307 1.457303 CTGAACTTCAAGAGGAACGCG 59.543 52.381 3.53 3.53 0.00 6.01
4234 6516 2.441164 GAGCTCGGAGGAGGCAGA 60.441 66.667 7.20 0.00 40.80 4.26
4235 6517 2.757917 AGCTCGGAGGAGGCAGAC 60.758 66.667 7.20 0.00 40.80 3.51
4455 6749 1.883678 TCCCAGAAGCATGGAGATGA 58.116 50.000 4.33 0.00 43.57 2.92
4461 6755 2.299582 AGAAGCATGGAGATGATCGAGG 59.700 50.000 0.00 0.00 0.00 4.63
4462 6756 2.006805 AGCATGGAGATGATCGAGGA 57.993 50.000 0.00 0.00 0.00 3.71
4566 6860 3.610677 GTGTAAATGCCGGTAATTTGTGC 59.389 43.478 20.88 13.73 0.00 4.57
4618 6912 5.182001 CCAGAGGTACAAAATTCAGTGAAGG 59.818 44.000 11.91 3.72 0.00 3.46
4626 6920 6.585416 ACAAAATTCAGTGAAGGCATCTTTT 58.415 32.000 11.91 8.89 32.52 2.27
4644 6938 6.295039 TCTTTTACTGCTGTTCTTTTACCG 57.705 37.500 0.09 0.00 0.00 4.02
4648 6942 1.197721 CTGCTGTTCTTTTACCGGCAG 59.802 52.381 0.00 5.41 37.45 4.85
4707 7007 9.578576 AATTTATGGCAGACTACAATGACATAT 57.421 29.630 1.81 0.00 44.73 1.78
4800 7100 1.852309 TACCAGTGGTCCCGTAGGATA 59.148 52.381 20.72 0.00 46.41 2.59
4871 7172 4.800471 GGATTTTCGCAGGAATTGATGAAC 59.200 41.667 0.00 0.00 30.88 3.18
4926 7227 4.438148 CACCAACCCTTTGAAAACGAAAT 58.562 39.130 0.00 0.00 34.24 2.17
5001 7318 4.065789 CCTACATATTTTTCTCGAGCCCC 58.934 47.826 7.81 0.00 0.00 5.80
5029 7346 9.255304 GTTTGTTTAATGCTTGGTTCAAGATTA 57.745 29.630 11.35 9.08 43.42 1.75
5070 7387 0.468226 TGAGTGACTTTTGCGGAGGT 59.532 50.000 0.00 0.00 0.00 3.85
5122 7439 9.387123 GTTGTTTATAAGCAACAAGAGAGAAAG 57.613 33.333 29.45 0.00 45.66 2.62
5173 7490 5.609088 CCAAAAACTGATAAGACGAGTTCG 58.391 41.667 0.00 0.00 46.33 3.95
5178 7495 2.422479 CTGATAAGACGAGTTCGACCCA 59.578 50.000 8.72 0.00 43.02 4.51
5200 7517 5.174395 CAGCTAGCTAATTAGGGCATGTAG 58.826 45.833 18.86 0.00 0.00 2.74
5205 7522 4.901849 AGCTAATTAGGGCATGTAGAGTGA 59.098 41.667 14.28 0.00 0.00 3.41
5217 7534 8.097038 GGGCATGTAGAGTGATTGATAAGATAA 58.903 37.037 0.00 0.00 0.00 1.75
5238 7555 9.338968 AGATAATCTAATCTTAACCCTGCCATA 57.661 33.333 0.00 0.00 32.09 2.74
5254 7571 6.610830 CCCTGCCATATAATCTAGAGATGACT 59.389 42.308 0.00 0.00 34.49 3.41
5294 7611 6.127225 TGGGTTGTCTCTTCATCTTATCTCTG 60.127 42.308 0.00 0.00 0.00 3.35
5327 7644 5.841957 ATTCCTAGAAATGTGAATGTGGC 57.158 39.130 0.00 0.00 0.00 5.01
5328 7645 4.299586 TCCTAGAAATGTGAATGTGGCA 57.700 40.909 0.00 0.00 0.00 4.92
5338 7655 3.248266 GTGAATGTGGCAAGAGATTTGC 58.752 45.455 3.39 3.39 44.22 3.68
5470 7787 7.950242 GCATCATTGTGCATACCCTTAGGTAC 61.950 46.154 0.00 0.00 44.30 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 130 1.374758 GGAACTCCAGGCAGTCGTG 60.375 63.158 0.00 0.00 35.64 4.35
194 195 3.975035 GTCAACGAAACAAAAGATCCAGC 59.025 43.478 0.00 0.00 0.00 4.85
258 260 2.417515 GGAGAAGGTTTCTGTAGCTCGG 60.418 54.545 0.00 0.00 40.87 4.63
259 261 2.417515 GGGAGAAGGTTTCTGTAGCTCG 60.418 54.545 0.00 0.00 40.87 5.03
267 269 3.009584 GGAACATCTGGGAGAAGGTTTCT 59.990 47.826 0.00 0.00 44.21 2.52
268 270 3.348119 GGAACATCTGGGAGAAGGTTTC 58.652 50.000 0.00 0.00 29.66 2.78
441 447 2.910688 TTCTTGACCGAAGAAGCACT 57.089 45.000 0.00 0.00 44.32 4.40
470 476 6.767080 TCATACCATTTTTACGACGACATTG 58.233 36.000 0.00 0.00 0.00 2.82
613 619 6.001449 TCCCTAGAAGAATTATGTTGGGTG 57.999 41.667 0.00 0.00 31.10 4.61
616 622 6.763610 GTGTCTCCCTAGAAGAATTATGTTGG 59.236 42.308 0.00 0.00 32.16 3.77
684 690 7.923878 TCCCTGTTAGTGTTTTTATTTTCTTGC 59.076 33.333 0.00 0.00 0.00 4.01
693 699 7.041916 CGTGTGTTATCCCTGTTAGTGTTTTTA 60.042 37.037 0.00 0.00 0.00 1.52
704 711 2.743636 CACTCGTGTGTTATCCCTGT 57.256 50.000 9.42 0.00 39.24 4.00
764 783 6.322969 TCATTTCAGCATGGCAAGATCTTATT 59.677 34.615 7.86 0.00 36.16 1.40
780 799 3.428589 GGCTCCATGAACTTCATTTCAGC 60.429 47.826 13.55 13.55 38.87 4.26
869 2748 6.080406 CAGCTAGTGCAGTTTTAGTTTTAGC 58.920 40.000 0.00 0.00 42.74 3.09
889 2769 0.827507 ACATCGTTTTTGGCCCAGCT 60.828 50.000 0.00 0.00 0.00 4.24
980 2882 4.573900 CATCACTAGCAAGACTGGTTTCT 58.426 43.478 0.00 0.00 38.17 2.52
987 2889 1.404717 CGGTGCATCACTAGCAAGACT 60.405 52.381 0.00 0.00 44.64 3.24
995 2899 4.830765 GGCGGCGGTGCATCACTA 62.831 66.667 9.78 0.00 36.28 2.74
1170 3074 2.993853 CCTCCTGGCTCTTGGGTC 59.006 66.667 0.00 0.00 0.00 4.46
1277 3181 2.582978 GGTCGAGGTGGCCCTTAC 59.417 66.667 0.00 0.00 42.86 2.34
1278 3182 2.686106 GGGTCGAGGTGGCCCTTA 60.686 66.667 0.00 0.00 42.86 2.69
1371 3275 1.818363 CCTGACGATCTCCGGACGA 60.818 63.158 18.64 12.26 43.93 4.20
1374 3278 0.748367 CTCACCTGACGATCTCCGGA 60.748 60.000 2.93 2.93 43.93 5.14
1523 3471 2.610694 CCACCTTGTCTGCACTGCG 61.611 63.158 0.00 0.00 0.00 5.18
1559 3516 2.849942 GCAAAAGGCAACATTTTCCCT 58.150 42.857 0.00 0.00 43.97 4.20
1681 3711 9.383519 CTCAACTTCATACAACAACCATAGTAT 57.616 33.333 0.00 0.00 0.00 2.12
1802 3833 8.790718 GTCCTGAAATTGCATATATTGACTGAT 58.209 33.333 0.00 0.00 0.00 2.90
2095 4126 6.316390 CACATTTTCATGTACTTACCTCTCCC 59.684 42.308 0.00 0.00 42.14 4.30
2125 4156 8.228206 AGGAAGGTAAAAAGAGAGAAATTCCTT 58.772 33.333 0.00 0.00 39.74 3.36
2166 4200 7.665690 TGTACAAATGGGTACGTTCTAAACTA 58.334 34.615 0.00 0.00 45.16 2.24
2198 4232 8.046107 ACATTTTCTGGTTCAAATTTTCTCCAA 58.954 29.630 0.00 0.00 0.00 3.53
2222 4256 5.364778 TCGATTCTCTTGGTTCAGAAAACA 58.635 37.500 0.00 0.00 32.40 2.83
2230 4265 5.862924 TGAATGTTCGATTCTCTTGGTTC 57.137 39.130 0.00 0.00 0.00 3.62
2241 4276 8.864069 TGTGTTTAACAATTTGAATGTTCGAT 57.136 26.923 0.00 0.00 41.11 3.59
2244 4279 8.641499 TCCTGTGTTTAACAATTTGAATGTTC 57.359 30.769 0.00 0.00 41.11 3.18
2249 4284 9.495572 AAAAGTTCCTGTGTTTAACAATTTGAA 57.504 25.926 0.00 0.00 38.67 2.69
2255 4290 6.982852 TCACAAAAGTTCCTGTGTTTAACAA 58.017 32.000 14.46 0.00 42.86 2.83
2271 4307 3.609373 CACACACACAGCTTTCACAAAAG 59.391 43.478 0.00 0.00 43.99 2.27
2272 4308 3.573598 CACACACACAGCTTTCACAAAA 58.426 40.909 0.00 0.00 0.00 2.44
2274 4310 1.135431 GCACACACACAGCTTTCACAA 60.135 47.619 0.00 0.00 0.00 3.33
2295 4331 4.345547 AGCCTAAGAGGTAAGATAGTTGGC 59.654 45.833 0.00 0.00 37.80 4.52
2296 4332 5.598830 TGAGCCTAAGAGGTAAGATAGTTGG 59.401 44.000 0.00 0.00 37.80 3.77
2297 4333 6.716934 TGAGCCTAAGAGGTAAGATAGTTG 57.283 41.667 0.00 0.00 37.80 3.16
2402 4438 7.973388 TGTATTTGTAGTTAAGATTTGCATGGC 59.027 33.333 0.00 0.00 0.00 4.40
2560 4596 3.888323 TGACATTTCCTAGTTTGCAGCAA 59.112 39.130 2.83 2.83 0.00 3.91
2591 4627 7.907214 ACGCTCTTATATTATGGAAATGTCC 57.093 36.000 0.00 0.00 45.21 4.02
2660 4781 4.886579 ACAGAATGAATTGGTTGAAAGCC 58.113 39.130 0.00 0.00 39.69 4.35
2674 4795 6.818644 GTCTTTTGCAGAGGTATACAGAATGA 59.181 38.462 5.01 0.00 33.24 2.57
2680 4801 6.237901 ACATTGTCTTTTGCAGAGGTATACA 58.762 36.000 5.01 0.00 29.34 2.29
2786 4936 1.028905 CTTCAGCAAAAACCCGGTCA 58.971 50.000 0.00 0.00 0.00 4.02
2832 4982 2.165641 GCAGGGGTGCCTAATTAAACAC 59.834 50.000 8.39 8.39 0.00 3.32
2973 5248 9.042008 CATGTAGGCGAAAATACTAACTACAAT 57.958 33.333 0.00 0.00 41.50 2.71
2974 5249 8.036575 ACATGTAGGCGAAAATACTAACTACAA 58.963 33.333 0.00 0.00 41.50 2.41
2976 5251 7.703621 TCACATGTAGGCGAAAATACTAACTAC 59.296 37.037 0.00 0.00 0.00 2.73
2978 5253 6.534079 GTCACATGTAGGCGAAAATACTAACT 59.466 38.462 0.00 0.00 0.00 2.24
3291 5571 1.984570 CCCCTTGGAGTCGAGCTCA 60.985 63.158 15.40 0.00 45.88 4.26
3300 5580 2.356667 GAACCAGGCCCCTTGGAG 59.643 66.667 16.13 0.00 0.00 3.86
3417 5697 4.018870 TGTGGGCAAGTGATATGAGGTAAA 60.019 41.667 0.00 0.00 0.00 2.01
3418 5698 3.521531 TGTGGGCAAGTGATATGAGGTAA 59.478 43.478 0.00 0.00 0.00 2.85
3419 5699 3.111484 TGTGGGCAAGTGATATGAGGTA 58.889 45.455 0.00 0.00 0.00 3.08
3425 5705 4.174704 ACATCATGTGGGCAAGTGATAT 57.825 40.909 0.00 0.00 30.63 1.63
3434 5714 7.945134 AGAAAAATAGATTACATCATGTGGGC 58.055 34.615 0.00 0.00 0.00 5.36
3435 5715 9.956720 GAAGAAAAATAGATTACATCATGTGGG 57.043 33.333 0.00 0.00 0.00 4.61
3538 5819 8.488668 TGATATCTCTCTTGAAATTCACCATCA 58.511 33.333 3.98 0.00 0.00 3.07
3568 5849 3.204306 TGATCTTGGTCCTCATGCATC 57.796 47.619 0.00 0.00 0.00 3.91
3610 5891 4.491676 CATCTCACCTTTTGCAAATCCAG 58.508 43.478 13.65 7.55 0.00 3.86
3616 5897 1.702182 TGGCATCTCACCTTTTGCAA 58.298 45.000 0.00 0.00 36.82 4.08
3643 5925 8.665906 CCCCCAGTCCATCTTAAATATAAACTA 58.334 37.037 0.00 0.00 0.00 2.24
3654 5936 2.590611 AGAGTACCCCCAGTCCATCTTA 59.409 50.000 0.00 0.00 0.00 2.10
3655 5937 1.366435 AGAGTACCCCCAGTCCATCTT 59.634 52.381 0.00 0.00 0.00 2.40
3656 5938 1.019650 AGAGTACCCCCAGTCCATCT 58.980 55.000 0.00 0.00 0.00 2.90
3657 5939 1.062810 AGAGAGTACCCCCAGTCCATC 60.063 57.143 0.00 0.00 0.00 3.51
3658 5940 1.019650 AGAGAGTACCCCCAGTCCAT 58.980 55.000 0.00 0.00 0.00 3.41
3659 5941 0.335361 GAGAGAGTACCCCCAGTCCA 59.665 60.000 0.00 0.00 0.00 4.02
3673 5955 1.213182 AGGATCAGTACAGGCGAGAGA 59.787 52.381 0.00 0.00 0.00 3.10
3713 5995 5.283717 CCGTGTATTCTTCGCAAAATTCAAG 59.716 40.000 0.00 0.00 0.00 3.02
3722 6004 0.037697 AGCACCGTGTATTCTTCGCA 60.038 50.000 0.00 0.00 0.00 5.10
3725 6007 1.804151 TGCAAGCACCGTGTATTCTTC 59.196 47.619 0.00 0.00 0.00 2.87
3731 6013 0.878523 GACACTGCAAGCACCGTGTA 60.879 55.000 16.75 0.00 36.11 2.90
3737 6019 0.946528 TGTCATGACACTGCAAGCAC 59.053 50.000 24.56 0.00 37.60 4.40
3798 6080 3.512033 AGAAATAGTCACTCACGAGGC 57.488 47.619 0.00 0.00 0.00 4.70
3800 6082 5.031578 GCAGTAGAAATAGTCACTCACGAG 58.968 45.833 0.00 0.00 0.00 4.18
3825 6107 7.925993 GTGCAAATATACAATGGTAAGCACTA 58.074 34.615 0.00 0.00 43.62 2.74
3826 6108 6.795399 GTGCAAATATACAATGGTAAGCACT 58.205 36.000 0.00 0.00 43.62 4.40
3827 6109 6.692681 CAGTGCAAATATACAATGGTAAGCAC 59.307 38.462 13.05 13.05 46.34 4.40
3828 6110 6.376864 ACAGTGCAAATATACAATGGTAAGCA 59.623 34.615 0.00 0.00 36.25 3.91
3829 6111 6.795399 ACAGTGCAAATATACAATGGTAAGC 58.205 36.000 0.00 0.00 36.25 3.09
3830 6112 9.638239 AAAACAGTGCAAATATACAATGGTAAG 57.362 29.630 0.00 0.00 36.25 2.34
3831 6113 9.416794 CAAAACAGTGCAAATATACAATGGTAA 57.583 29.630 0.00 0.00 36.25 2.85
3832 6114 8.797438 TCAAAACAGTGCAAATATACAATGGTA 58.203 29.630 0.00 0.00 36.25 3.25
3870 6152 4.963318 TCCCCATGTTCTGTCTCATATC 57.037 45.455 0.00 0.00 0.00 1.63
3886 6168 1.133761 TCGTTGACACCATTTTCCCCA 60.134 47.619 0.00 0.00 0.00 4.96
3894 6176 0.108585 AGCCACTTCGTTGACACCAT 59.891 50.000 0.00 0.00 0.00 3.55
3907 6189 1.375523 CGCGGAAAGGTTAGCCACT 60.376 57.895 0.00 0.00 37.19 4.00
3937 6219 9.562408 CTGATTCTATGGTAGTAGAGTACAGAA 57.438 37.037 0.00 0.00 33.76 3.02
3970 6252 4.585581 TGCCATCAATCCCTCAACAATATG 59.414 41.667 0.00 0.00 0.00 1.78
3976 6258 1.341383 ACCTGCCATCAATCCCTCAAC 60.341 52.381 0.00 0.00 0.00 3.18
3982 6264 3.004752 AGTTACACCTGCCATCAATCC 57.995 47.619 0.00 0.00 0.00 3.01
4004 6286 1.801178 GCGTTCCTCTTGAAGTTCAGG 59.199 52.381 8.64 8.64 32.37 3.86
4025 6307 3.068024 TCCAACCACATTTCAAGCAGAAC 59.932 43.478 0.00 0.00 35.56 3.01
4234 6516 1.467342 TCTCATTGTCGTCATCGTCGT 59.533 47.619 0.00 0.00 38.33 4.34
4235 6517 2.174060 TCTCATTGTCGTCATCGTCG 57.826 50.000 0.00 0.00 38.33 5.12
4325 6619 1.699634 TCCAGAGGTTCTTGGGAAGTG 59.300 52.381 0.00 0.00 31.46 3.16
4382 6676 3.011517 TCTCCTGGAAGCCCCTGC 61.012 66.667 0.00 0.00 35.38 4.85
4461 6755 2.566765 GTCGTCGTCGTCGTCGTC 60.567 66.667 18.44 11.28 45.27 4.20
4462 6756 4.400776 CGTCGTCGTCGTCGTCGT 62.401 66.667 18.87 0.00 45.27 4.34
4466 6760 0.501854 AGATATCGTCGTCGTCGTCG 59.498 55.000 14.18 14.18 46.06 5.12
4592 6886 5.551233 TCACTGAATTTTGTACCTCTGGAG 58.449 41.667 0.00 0.00 0.00 3.86
4618 6912 6.582672 GGTAAAAGAACAGCAGTAAAAGATGC 59.417 38.462 0.00 0.00 42.87 3.91
4626 6920 2.224329 TGCCGGTAAAAGAACAGCAGTA 60.224 45.455 1.90 0.00 0.00 2.74
4644 6938 0.674895 ATGTTCTCACGGAAGCTGCC 60.675 55.000 0.00 0.00 34.23 4.85
4648 6942 2.380084 TACCATGTTCTCACGGAAGC 57.620 50.000 0.00 0.00 34.23 3.86
4707 7007 2.916269 TGGATGACCTAACATGGACCAA 59.084 45.455 0.00 0.00 37.04 3.67
4871 7172 2.741985 TGGACATGCTCGTTGCCG 60.742 61.111 0.00 0.00 42.00 5.69
4884 7185 4.598257 CGGTCATGACTGGTGGAC 57.402 61.111 24.60 6.38 34.12 4.02
4926 7227 7.919091 GTGTGTATGTCGTATCTTCTCCAATTA 59.081 37.037 0.00 0.00 0.00 1.40
5001 7318 6.756074 TCTTGAACCAAGCATTAAACAAACAG 59.244 34.615 2.04 0.00 40.84 3.16
5029 7346 3.265489 TCATCTACCCCTTTTTCACCCT 58.735 45.455 0.00 0.00 0.00 4.34
5089 7406 9.073475 TCTTGTTGCTTATAAACAACCAATAGT 57.927 29.630 22.67 0.00 44.38 2.12
5103 7420 7.992754 AATGTCTTTCTCTCTTGTTGCTTAT 57.007 32.000 0.00 0.00 0.00 1.73
5136 7453 3.389002 AGTTTTTGGCTGGCTTTTCTCAT 59.611 39.130 2.00 0.00 0.00 2.90
5145 7462 3.670627 CGTCTTATCAGTTTTTGGCTGGC 60.671 47.826 0.00 0.00 34.89 4.85
5173 7490 2.289756 GCCCTAATTAGCTAGCTGGGTC 60.290 54.545 28.68 20.33 35.79 4.46
5178 7495 5.087323 TCTACATGCCCTAATTAGCTAGCT 58.913 41.667 23.12 23.12 0.00 3.32
5228 7545 6.382570 GTCATCTCTAGATTATATGGCAGGGT 59.617 42.308 0.00 0.00 31.21 4.34
5229 7546 6.610830 AGTCATCTCTAGATTATATGGCAGGG 59.389 42.308 0.00 0.00 31.21 4.45
5312 7629 4.771590 TCTCTTGCCACATTCACATTTC 57.228 40.909 0.00 0.00 0.00 2.17
5327 7644 6.499172 TGATCTCGTAGTAGCAAATCTCTTG 58.501 40.000 0.00 0.00 0.00 3.02
5328 7645 6.701145 TGATCTCGTAGTAGCAAATCTCTT 57.299 37.500 0.00 0.00 0.00 2.85
5375 7692 7.397476 AGAGAAACCAGAAAGAAAGAAAAAGGT 59.603 33.333 0.00 0.00 0.00 3.50
5378 7695 9.996554 AAAAGAGAAACCAGAAAGAAAGAAAAA 57.003 25.926 0.00 0.00 0.00 1.94
5379 7696 9.639601 GAAAAGAGAAACCAGAAAGAAAGAAAA 57.360 29.630 0.00 0.00 0.00 2.29
5383 7700 7.067494 TGGAGAAAAGAGAAACCAGAAAGAAAG 59.933 37.037 0.00 0.00 0.00 2.62
5387 7704 5.009110 GGTGGAGAAAAGAGAAACCAGAAAG 59.991 44.000 0.00 0.00 0.00 2.62
5470 7787 1.342082 GCCGGCGTGTATATGCTACG 61.342 60.000 12.58 9.97 38.87 3.51


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

AutoCloner maintained by Alex Coulton.