Multiple sequence alignment - TraesCS6D01G088400

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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 TraesCS6D01G088400 chr6D 100.000 5350 0 0 1 5350 53663994 53669343 0.000000e+00 9880.0
1 TraesCS6D01G088400 chr6A 94.059 4427 190 40 952 5349 61434996 61430614 0.000000e+00 6650.0
2 TraesCS6D01G088400 chr6A 90.969 908 59 11 1 901 61435883 61434992 0.000000e+00 1201.0
3 TraesCS6D01G088400 chr6B 93.786 3267 117 33 2122 5349 117853111 117849892 0.000000e+00 4830.0
4 TraesCS6D01G088400 chr6B 95.993 1223 45 3 912 2130 117855438 117854216 0.000000e+00 1984.0
5 TraesCS6D01G088400 chr6B 80.583 515 61 24 1 496 117856992 117856498 1.420000e-95 361.0
6 TraesCS6D01G088400 chr6B 84.000 75 7 5 235 304 671217975 671217901 3.460000e-07 67.6
7 TraesCS6D01G088400 chrUn 95.775 71 3 0 138 208 354743611 354743541 1.220000e-21 115.0
8 TraesCS6D01G088400 chrUn 95.775 71 3 0 138 208 363863334 363863264 1.220000e-21 115.0
9 TraesCS6D01G088400 chrUn 95.775 71 3 0 138 208 430358584 430358654 1.220000e-21 115.0
10 TraesCS6D01G088400 chr4D 95.775 71 3 0 138 208 354587441 354587511 1.220000e-21 115.0
11 TraesCS6D01G088400 chr4D 100.000 31 0 0 331 361 353919724 353919754 2.080000e-04 58.4
12 TraesCS6D01G088400 chr4B 95.775 71 3 0 138 208 151526136 151526206 1.220000e-21 115.0
13 TraesCS6D01G088400 chr4B 95.775 71 3 0 138 208 151526648 151526718 1.220000e-21 115.0
14 TraesCS6D01G088400 chr4B 95.775 71 3 0 138 208 151527050 151527120 1.220000e-21 115.0
15 TraesCS6D01G088400 chr7A 84.615 91 7 6 235 320 207896393 207896481 3.430000e-12 84.2
16 TraesCS6D01G088400 chr7A 81.250 96 13 4 257 349 83289369 83289276 7.430000e-09 73.1
17 TraesCS6D01G088400 chr7A 82.278 79 13 1 541 618 688947925 688947847 3.460000e-07 67.6
18 TraesCS6D01G088400 chr7B 85.000 80 11 1 541 619 366800920 366800999 4.440000e-11 80.5
19 TraesCS6D01G088400 chr7D 84.337 83 10 2 504 583 22744005 22744087 1.600000e-10 78.7
20 TraesCS6D01G088400 chr7D 80.851 94 13 5 541 631 306661194 306661103 9.610000e-08 69.4
21 TraesCS6D01G088400 chr7D 88.889 45 4 1 296 339 634406209 634406253 3.000000e-03 54.7
22 TraesCS6D01G088400 chr5D 81.707 82 11 3 334 411 545509834 545509915 1.240000e-06 65.8
23 TraesCS6D01G088400 chr3A 91.667 48 1 3 235 280 1600920 1600966 4.470000e-06 63.9
24 TraesCS6D01G088400 chr3A 100.000 31 0 0 236 266 1596098 1596128 2.080000e-04 58.4
25 TraesCS6D01G088400 chr5B 84.058 69 4 6 297 360 544183612 544183678 5.790000e-05 60.2
26 TraesCS6D01G088400 chr5B 100.000 28 0 0 297 324 348052381 348052354 1.000000e-02 52.8
27 TraesCS6D01G088400 chr5B 100.000 28 0 0 297 324 586180230 586180257 1.000000e-02 52.8
28 TraesCS6D01G088400 chr3D 88.636 44 3 2 283 324 13324734 13324777 1.000000e-02 52.8
29 TraesCS6D01G088400 chr3D 100.000 28 0 0 297 324 209699232 209699205 1.000000e-02 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 TraesCS6D01G088400 chr6D 53663994 53669343 5349 False 9880.000000 9880 100.000000 1 5350 1 chr6D.!!$F1 5349
1 TraesCS6D01G088400 chr6A 61430614 61435883 5269 True 3925.500000 6650 92.514000 1 5349 2 chr6A.!!$R1 5348
2 TraesCS6D01G088400 chr6B 117849892 117856992 7100 True 2391.666667 4830 90.120667 1 5349 3 chr6B.!!$R2 5348

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
920 1567 0.172803 ACCACGATACTTCCTGCGTC 59.827 55.000 0.00 0.0 34.37 5.19 F
921 1568 0.456221 CCACGATACTTCCTGCGTCT 59.544 55.000 0.00 0.0 34.37 4.18 F
922 1569 1.534175 CCACGATACTTCCTGCGTCTC 60.534 57.143 0.00 0.0 34.37 3.36 F
2375 4168 1.523758 AGTGGTAAGGAAGCGCTTTG 58.476 50.000 25.84 0.0 43.79 2.77 F
3490 5286 1.005394 ACGGGTACGGCTGTTCAAG 60.005 57.895 1.99 0.0 46.48 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2351 4144 0.323629 CGCTTCCTTACCACTTCCCA 59.676 55.000 0.0 0.0 0.0 4.37 R
2375 4168 2.103263 CCAGGGCATAAGACTACTCCAC 59.897 54.545 0.0 0.0 0.0 4.02 R
2466 4259 7.148222 TGCTCTTAGTGTTAGTGATCTGTAGAC 60.148 40.741 0.0 0.0 0.0 2.59 R
3624 5435 1.202806 AGCAACAGCTCTAACTGCCAA 60.203 47.619 0.0 0.0 41.6 4.52 R
5092 6918 0.108615 CAAGCACCCTCCTACGACAG 60.109 60.000 0.0 0.0 0.0 3.51 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
195 197 8.999431 TGAATATTCGGGAGCAGTAATTTAATC 58.001 33.333 10.80 0.00 0.00 1.75
371 385 8.243426 ACATTGTACATTTTTATGCACACCTAG 58.757 33.333 0.00 0.00 28.38 3.02
375 391 8.634444 TGTACATTTTTATGCACACCTAGTTTT 58.366 29.630 0.00 0.00 0.00 2.43
377 393 8.364129 ACATTTTTATGCACACCTAGTTTTTG 57.636 30.769 0.00 0.00 0.00 2.44
382 398 7.569639 TTATGCACACCTAGTTTTTGTACAA 57.430 32.000 3.59 3.59 0.00 2.41
383 399 5.493133 TGCACACCTAGTTTTTGTACAAG 57.507 39.130 8.56 0.00 0.00 3.16
526 559 0.680061 AAAGACGGAGACAGGGACAC 59.320 55.000 0.00 0.00 0.00 3.67
528 561 3.628280 GACGGAGACAGGGACACGC 62.628 68.421 0.00 0.00 0.00 5.34
578 611 2.673043 GCTTCAATGCCAACACCATGAG 60.673 50.000 0.00 0.00 0.00 2.90
637 670 1.128692 GATTTTCTGGAGCGACGTTGG 59.871 52.381 4.64 0.00 0.00 3.77
651 684 3.462483 ACGTTGGTCGGCATGAATATA 57.538 42.857 0.00 0.00 44.69 0.86
679 713 0.391661 GCTTTGTGCGGGAGAGATCA 60.392 55.000 0.00 0.00 0.00 2.92
680 714 1.745141 GCTTTGTGCGGGAGAGATCAT 60.745 52.381 0.00 0.00 0.00 2.45
693 727 2.237143 AGAGATCATTGGCACGGAAGAA 59.763 45.455 0.00 0.00 0.00 2.52
707 741 3.317149 ACGGAAGAAGTTTTAAAGTGGGC 59.683 43.478 0.00 0.00 0.00 5.36
755 1021 0.968393 GCCCGCAAACCCCTGATTTA 60.968 55.000 0.00 0.00 0.00 1.40
764 1030 1.207329 ACCCCTGATTTACGTCTGCTC 59.793 52.381 0.00 0.00 0.00 4.26
776 1042 1.153568 TCTGCTCGCGGGAATTCAG 60.154 57.895 12.03 7.74 0.00 3.02
777 1043 2.125147 TGCTCGCGGGAATTCAGG 60.125 61.111 12.03 0.00 0.00 3.86
783 1049 2.038269 GCGGGAATTCAGGCAACGA 61.038 57.895 7.93 0.00 46.39 3.85
784 1050 1.982073 GCGGGAATTCAGGCAACGAG 61.982 60.000 7.93 0.00 46.39 4.18
785 1051 1.369091 CGGGAATTCAGGCAACGAGG 61.369 60.000 7.93 0.00 46.39 4.63
786 1052 1.657751 GGGAATTCAGGCAACGAGGC 61.658 60.000 7.93 0.00 46.39 4.70
846 1492 1.496060 TTGACGGGAGGATATGTGCT 58.504 50.000 0.00 0.00 0.00 4.40
849 1495 2.628178 TGACGGGAGGATATGTGCTTAG 59.372 50.000 0.00 0.00 0.00 2.18
853 1499 3.809832 CGGGAGGATATGTGCTTAGTTTG 59.190 47.826 0.00 0.00 0.00 2.93
875 1521 6.691754 TGCATGTGTATGGACGAAATAAAT 57.308 33.333 0.00 0.00 34.79 1.40
905 1552 8.601845 AAATGCCTAATTTGAACTAAAACCAC 57.398 30.769 0.00 0.00 37.09 4.16
909 1556 7.390996 TGCCTAATTTGAACTAAAACCACGATA 59.609 33.333 0.00 0.00 0.00 2.92
910 1557 7.695201 GCCTAATTTGAACTAAAACCACGATAC 59.305 37.037 0.00 0.00 0.00 2.24
914 1561 6.790285 TTGAACTAAAACCACGATACTTCC 57.210 37.500 0.00 0.00 0.00 3.46
917 1564 4.251268 ACTAAAACCACGATACTTCCTGC 58.749 43.478 0.00 0.00 0.00 4.85
918 1565 1.722011 AAACCACGATACTTCCTGCG 58.278 50.000 0.00 0.00 0.00 5.18
919 1566 0.606604 AACCACGATACTTCCTGCGT 59.393 50.000 0.00 0.00 37.48 5.24
920 1567 0.172803 ACCACGATACTTCCTGCGTC 59.827 55.000 0.00 0.00 34.37 5.19
921 1568 0.456221 CCACGATACTTCCTGCGTCT 59.544 55.000 0.00 0.00 34.37 4.18
922 1569 1.534175 CCACGATACTTCCTGCGTCTC 60.534 57.143 0.00 0.00 34.37 3.36
945 1621 3.347216 TCTTGGCTTGGAATGTTCTAGC 58.653 45.455 10.06 10.06 35.55 3.42
946 1622 1.737838 TGGCTTGGAATGTTCTAGCG 58.262 50.000 11.41 0.00 36.43 4.26
992 1668 3.706373 GCAGCTTCCCTCCGTCCA 61.706 66.667 0.00 0.00 0.00 4.02
998 1674 1.613255 GCTTCCCTCCGTCCATTCAAA 60.613 52.381 0.00 0.00 0.00 2.69
1019 1695 3.823330 GGACGGGCACGATCGACT 61.823 66.667 24.34 0.00 44.60 4.18
1505 2181 3.634910 GGTGAGCTTTTGGTTAACTTCCA 59.365 43.478 5.42 0.00 0.00 3.53
1616 2292 5.313280 TGACCATAGCCCCGTATATTTTT 57.687 39.130 0.00 0.00 0.00 1.94
1731 2407 9.190858 CAATTTTGAGATATTTTCGTTGGTTCA 57.809 29.630 0.00 0.00 0.00 3.18
1752 2428 6.593268 TCATTTTCATGGCAGATTTGAAGA 57.407 33.333 0.00 0.00 31.54 2.87
1753 2429 6.627243 TCATTTTCATGGCAGATTTGAAGAG 58.373 36.000 0.00 0.00 31.54 2.85
1788 2464 5.392380 GGAGATGTCCATTTGTACTGCAAAG 60.392 44.000 3.49 0.00 43.31 2.77
1895 2573 6.861572 TGTTTACTCTTCAGTTACATGTCTCG 59.138 38.462 0.00 0.00 33.62 4.04
2045 2724 6.035650 CGATCTTAATCAAACCGCACTCTTAA 59.964 38.462 0.00 0.00 31.76 1.85
2066 2745 9.793259 TCTTAACAGAAACTGGAAAGATGTTAT 57.207 29.630 11.26 0.00 34.13 1.89
2282 4075 3.119424 TCATCGCATCGTAGTGGTTTACA 60.119 43.478 0.00 0.00 0.00 2.41
2351 4144 4.401022 TGAATTTGTCTGAGGAGCAACAT 58.599 39.130 0.00 0.00 0.00 2.71
2375 4168 1.523758 AGTGGTAAGGAAGCGCTTTG 58.476 50.000 25.84 0.00 43.79 2.77
2392 4185 3.623510 GCTTTGTGGAGTAGTCTTATGCC 59.376 47.826 0.00 0.00 0.00 4.40
2426 4219 9.613428 CACTTGGAAGATATACTATTGGTTCAA 57.387 33.333 0.00 0.00 0.00 2.69
2465 4258 8.821894 AGAATCTAAGTTCTAAAAATAGCTGCG 58.178 33.333 0.00 0.00 36.71 5.18
2466 4259 6.903883 TCTAAGTTCTAAAAATAGCTGCGG 57.096 37.500 0.00 0.00 0.00 5.69
2612 4405 2.610374 GACGTGAAAACTAGGTGCACAA 59.390 45.455 20.43 4.96 0.00 3.33
3234 5030 5.012561 ACATAGAGCAAACTTCTCAAGAGGT 59.987 40.000 0.00 0.00 35.79 3.85
3240 5036 5.595952 AGCAAACTTCTCAAGAGGTTGATTT 59.404 36.000 8.12 0.00 42.44 2.17
3358 5154 9.207868 AGTATCTCTCTTGGAAGTAGCTTTATT 57.792 33.333 0.00 0.00 0.00 1.40
3400 5196 5.888724 TGTGAAAGATGTTAACTGGGTTGAA 59.111 36.000 7.22 0.00 0.00 2.69
3466 5262 3.181523 CGCAATATTCAGATGCTCCATCG 60.182 47.826 0.04 0.00 44.67 3.84
3490 5286 1.005394 ACGGGTACGGCTGTTCAAG 60.005 57.895 1.99 0.00 46.48 3.02
3543 5339 3.560025 GGTCCTCATGATGTGTTCAGGTT 60.560 47.826 0.00 0.00 37.89 3.50
3544 5340 4.323485 GGTCCTCATGATGTGTTCAGGTTA 60.323 45.833 0.00 0.00 37.89 2.85
3545 5341 4.872691 GTCCTCATGATGTGTTCAGGTTAG 59.127 45.833 0.00 0.00 37.89 2.34
3579 5390 7.648039 TTCTCTCTAGTTTTGAGATACTCCC 57.352 40.000 0.00 0.00 39.49 4.30
3666 5477 5.569630 GCTCCTTGTAACTCTCTGAATGGAA 60.570 44.000 0.00 0.00 0.00 3.53
3694 5505 5.009631 TGCATTAGCTTGGTGTTCATAAGT 58.990 37.500 0.00 0.00 42.74 2.24
4024 5835 8.418662 TGGTATATGCTAAACTTACACCTAGTG 58.581 37.037 0.00 0.00 39.75 2.74
4051 5862 8.877864 TTTTGTTGATGGGAAGTATACTGATT 57.122 30.769 6.06 0.00 0.00 2.57
4133 5944 7.112122 ACAGATGATTGTATTTCCTGCAAGTA 58.888 34.615 0.00 0.00 32.69 2.24
4172 5983 4.277174 CACAATGGCAGTAACCTGTGTTTA 59.723 41.667 0.00 0.00 41.02 2.01
4174 5985 5.183140 ACAATGGCAGTAACCTGTGTTTATC 59.817 40.000 0.00 0.00 41.02 1.75
4244 6055 4.319046 GCTGAACAGTTATACATGATGGCG 60.319 45.833 0.00 0.00 0.00 5.69
4245 6056 3.559655 TGAACAGTTATACATGATGGCGC 59.440 43.478 0.00 0.00 0.00 6.53
4364 6175 6.759356 TGGAGCGTTGATTCGATTTTAAGATA 59.241 34.615 0.00 0.00 0.00 1.98
4453 6264 8.629821 AGACCCTAATCATATATACCAAGCAT 57.370 34.615 0.00 0.00 0.00 3.79
4461 6272 8.798859 ATCATATATACCAAGCATTGTTCCTC 57.201 34.615 0.00 0.00 46.99 3.71
4485 6296 6.541641 TCCCTATCTCAGTTTAGTAGTCGTTC 59.458 42.308 0.00 0.00 0.00 3.95
4501 6312 1.269102 CGTTCGGCGATCTGGTTATCT 60.269 52.381 11.76 0.00 44.77 1.98
4507 6318 3.440522 CGGCGATCTGGTTATCTCATCTA 59.559 47.826 0.00 0.00 0.00 1.98
4528 6339 7.129457 TCTATACACTGCAAGATTTCTGGAT 57.871 36.000 0.00 0.00 37.43 3.41
4538 6349 2.174424 AGATTTCTGGATTCCCTCCTGC 59.826 50.000 0.00 0.00 45.21 4.85
4546 6357 0.326264 ATTCCCTCCTGCTGACACAC 59.674 55.000 0.00 0.00 0.00 3.82
4547 6358 1.768684 TTCCCTCCTGCTGACACACC 61.769 60.000 0.00 0.00 0.00 4.16
4560 6374 4.152644 ACACCGAGTGACAGACGA 57.847 55.556 10.46 0.00 36.96 4.20
4561 6375 1.950007 ACACCGAGTGACAGACGAG 59.050 57.895 10.46 0.00 36.96 4.18
4576 6390 3.862267 CAGACGAGGTTCTTATTCAGCTG 59.138 47.826 7.63 7.63 0.00 4.24
4585 6399 2.493278 TCTTATTCAGCTGGCTTTTGGC 59.507 45.455 15.13 0.00 46.23 4.52
4586 6400 2.220653 TATTCAGCTGGCTTTTGGCT 57.779 45.000 15.13 0.00 46.20 4.75
4594 6408 1.494721 CTGGCTTTTGGCTATAGGGGA 59.505 52.381 1.04 0.00 46.20 4.81
4613 6427 2.123342 GATTCAGCCTTCTCGTCATCG 58.877 52.381 0.00 0.00 38.55 3.84
4620 6434 2.550606 GCCTTCTCGTCATCGACTCTAT 59.449 50.000 0.00 0.00 41.35 1.98
4621 6435 3.747010 GCCTTCTCGTCATCGACTCTATA 59.253 47.826 0.00 0.00 41.35 1.31
4623 6437 5.615984 GCCTTCTCGTCATCGACTCTATAAG 60.616 48.000 0.00 0.00 41.35 1.73
4624 6438 4.994220 TCTCGTCATCGACTCTATAAGC 57.006 45.455 0.00 0.00 41.35 3.09
4637 6451 5.368989 ACTCTATAAGCAGTATTTGGCACC 58.631 41.667 0.00 0.00 0.00 5.01
4649 6463 1.604604 TTGGCACCTTGTTGTAGCTC 58.395 50.000 0.00 0.00 0.00 4.09
4652 6466 2.028112 TGGCACCTTGTTGTAGCTCTAG 60.028 50.000 0.00 0.00 0.00 2.43
4655 6469 3.193691 GCACCTTGTTGTAGCTCTAGAGA 59.806 47.826 24.24 0.00 0.00 3.10
4663 6477 7.939784 TGTTGTAGCTCTAGAGAGTTAATGA 57.060 36.000 24.24 0.00 43.85 2.57
4671 6485 6.041523 GCTCTAGAGAGTTAATGATCAACCCT 59.958 42.308 24.24 0.00 43.85 4.34
4699 6513 4.274459 CCTGCTTGTATTCTGTATTCTGGC 59.726 45.833 0.00 0.00 0.00 4.85
4701 6515 4.635765 TGCTTGTATTCTGTATTCTGGCAC 59.364 41.667 0.00 0.00 0.00 5.01
4707 6521 1.001974 TCTGTATTCTGGCACGTTGCT 59.998 47.619 9.31 0.00 44.28 3.91
4708 6522 1.129251 CTGTATTCTGGCACGTTGCTG 59.871 52.381 9.31 4.38 44.28 4.41
4709 6523 1.270571 TGTATTCTGGCACGTTGCTGA 60.271 47.619 9.31 6.19 44.28 4.26
4710 6524 1.394917 GTATTCTGGCACGTTGCTGAG 59.605 52.381 9.31 6.59 44.28 3.35
4719 6533 3.058224 GGCACGTTGCTGAGTAGATTTTT 60.058 43.478 9.31 0.00 44.28 1.94
4720 6534 4.153475 GGCACGTTGCTGAGTAGATTTTTA 59.847 41.667 9.31 0.00 44.28 1.52
4723 6537 6.183360 GCACGTTGCTGAGTAGATTTTTATCT 60.183 38.462 0.00 0.00 40.96 1.98
4781 6595 8.973378 CATTATATTTCTTCGACTCTTCTGGTC 58.027 37.037 0.00 0.00 0.00 4.02
4783 6597 3.924918 TTCTTCGACTCTTCTGGTCAG 57.075 47.619 0.00 0.00 33.73 3.51
4799 6614 6.644347 TCTGGTCAGAGATATTTCTTCAACC 58.356 40.000 10.28 10.28 32.82 3.77
4836 6654 6.017400 ACAAATGAAGCATCCTTGTAACAG 57.983 37.500 5.09 0.00 32.07 3.16
4868 6686 7.141758 TCCTAGGAAACTGCAGATTAATCAT 57.858 36.000 23.35 10.52 43.88 2.45
4869 6687 8.262601 TCCTAGGAAACTGCAGATTAATCATA 57.737 34.615 23.35 11.06 43.88 2.15
4870 6688 8.370940 TCCTAGGAAACTGCAGATTAATCATAG 58.629 37.037 23.35 18.44 43.88 2.23
4871 6689 7.605691 CCTAGGAAACTGCAGATTAATCATAGG 59.394 40.741 23.35 22.45 43.88 2.57
4877 6703 5.071519 ACTGCAGATTAATCATAGGCTCTGT 59.928 40.000 23.35 11.49 34.13 3.41
4886 6712 4.397481 TCATAGGCTCTGTTGATGTCTG 57.603 45.455 0.00 0.00 0.00 3.51
4889 6715 3.331478 AGGCTCTGTTGATGTCTGAAG 57.669 47.619 0.00 0.00 0.00 3.02
4905 6731 4.947388 GTCTGAAGCCCAAATACAACCATA 59.053 41.667 0.00 0.00 0.00 2.74
4935 6761 5.710513 TTGACATTAAGAATGCTGCTTGT 57.289 34.783 0.00 0.00 42.69 3.16
4980 6806 6.314896 GCCTGGTTACATTCATCAGATATAGC 59.685 42.308 0.00 0.00 0.00 2.97
4981 6807 6.820656 CCTGGTTACATTCATCAGATATAGCC 59.179 42.308 0.00 0.00 0.00 3.93
4982 6808 7.310921 CCTGGTTACATTCATCAGATATAGCCT 60.311 40.741 0.00 0.00 0.00 4.58
4983 6809 7.389232 TGGTTACATTCATCAGATATAGCCTG 58.611 38.462 0.00 0.00 0.00 4.85
4984 6810 7.235399 TGGTTACATTCATCAGATATAGCCTGA 59.765 37.037 9.27 9.27 43.84 3.86
4985 6811 7.763528 GGTTACATTCATCAGATATAGCCTGAG 59.236 40.741 11.67 6.15 43.07 3.35
4986 6812 8.526978 GTTACATTCATCAGATATAGCCTGAGA 58.473 37.037 11.67 7.73 43.07 3.27
4987 6813 7.736881 ACATTCATCAGATATAGCCTGAGAT 57.263 36.000 11.67 5.30 43.07 2.75
4988 6814 8.835550 ACATTCATCAGATATAGCCTGAGATA 57.164 34.615 11.67 2.78 43.07 1.98
5029 6855 6.991531 AGCACACAAATATGAATGGTTTTGTT 59.008 30.769 0.00 0.00 39.55 2.83
5030 6856 8.147058 AGCACACAAATATGAATGGTTTTGTTA 58.853 29.630 0.00 0.00 39.55 2.41
5091 6917 3.751518 ACAAGAGTACAACCATTGTCCC 58.248 45.455 0.00 0.00 44.12 4.46
5092 6918 3.081804 CAAGAGTACAACCATTGTCCCC 58.918 50.000 0.00 0.00 44.12 4.81
5093 6919 2.632537 AGAGTACAACCATTGTCCCCT 58.367 47.619 0.00 0.00 44.12 4.79
5094 6920 2.305927 AGAGTACAACCATTGTCCCCTG 59.694 50.000 0.00 0.00 44.12 4.45
5095 6921 2.039879 GAGTACAACCATTGTCCCCTGT 59.960 50.000 0.00 0.00 44.12 4.00
5096 6922 2.039879 AGTACAACCATTGTCCCCTGTC 59.960 50.000 0.00 0.00 44.12 3.51
5097 6923 0.250727 ACAACCATTGTCCCCTGTCG 60.251 55.000 0.00 0.00 40.56 4.35
5098 6924 0.250727 CAACCATTGTCCCCTGTCGT 60.251 55.000 0.00 0.00 0.00 4.34
5099 6925 1.002659 CAACCATTGTCCCCTGTCGTA 59.997 52.381 0.00 0.00 0.00 3.43
5100 6926 0.902531 ACCATTGTCCCCTGTCGTAG 59.097 55.000 0.00 0.00 0.00 3.51
5101 6927 0.178068 CCATTGTCCCCTGTCGTAGG 59.822 60.000 2.09 2.09 46.88 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
195 197 7.749539 AAGTTGTTAACCAAAAATCTGAACG 57.250 32.000 2.48 0.00 34.07 3.95
207 210 7.867305 TCATGTACTTGAAAGTTGTTAACCA 57.133 32.000 8.89 0.00 40.37 3.67
425 441 9.579768 TTCAACCATTGAAAAATATCCATAACG 57.420 29.630 1.54 0.00 45.94 3.18
500 527 5.297527 GTCCCTGTCTCCGTCTTTTTAAAAA 59.702 40.000 12.62 12.62 0.00 1.94
501 528 4.818005 GTCCCTGTCTCCGTCTTTTTAAAA 59.182 41.667 0.00 0.00 0.00 1.52
502 529 4.141665 TGTCCCTGTCTCCGTCTTTTTAAA 60.142 41.667 0.00 0.00 0.00 1.52
528 561 1.448540 CTAAGAGCACTGCCCACGG 60.449 63.158 0.00 0.00 0.00 4.94
578 611 0.039437 TTCAGAGCGAACGTGACCTC 60.039 55.000 0.00 0.00 0.00 3.85
637 670 5.615544 GCAGTTGTCATATATTCATGCCGAC 60.616 44.000 0.00 0.00 0.00 4.79
673 706 2.315925 TCTTCCGTGCCAATGATCTC 57.684 50.000 0.00 0.00 0.00 2.75
679 713 5.068591 ACTTTAAAACTTCTTCCGTGCCAAT 59.931 36.000 0.00 0.00 0.00 3.16
680 714 4.399934 ACTTTAAAACTTCTTCCGTGCCAA 59.600 37.500 0.00 0.00 0.00 4.52
693 727 2.167662 CATCGGGCCCACTTTAAAACT 58.832 47.619 24.92 0.00 0.00 2.66
755 1021 3.296709 AATTCCCGCGAGCAGACGT 62.297 57.895 8.23 0.00 35.59 4.34
764 1030 2.485122 GTTGCCTGAATTCCCGCG 59.515 61.111 0.00 0.00 0.00 6.46
776 1042 2.292794 TACGGATCAGCCTCGTTGCC 62.293 60.000 0.00 0.00 38.19 4.52
777 1043 0.872021 CTACGGATCAGCCTCGTTGC 60.872 60.000 0.00 0.00 38.19 4.17
783 1049 1.827969 GCATATCCTACGGATCAGCCT 59.172 52.381 0.00 0.00 42.11 4.58
784 1050 1.469940 CGCATATCCTACGGATCAGCC 60.470 57.143 0.00 0.00 42.11 4.85
785 1051 1.914634 CGCATATCCTACGGATCAGC 58.085 55.000 0.00 4.37 42.11 4.26
786 1052 1.474478 AGCGCATATCCTACGGATCAG 59.526 52.381 11.47 0.00 42.11 2.90
787 1053 1.545841 AGCGCATATCCTACGGATCA 58.454 50.000 11.47 0.00 42.11 2.92
788 1054 2.656560 AAGCGCATATCCTACGGATC 57.343 50.000 11.47 0.00 42.11 3.36
789 1055 3.090037 ACTAAGCGCATATCCTACGGAT 58.910 45.455 11.47 0.55 45.40 4.18
790 1056 2.511659 ACTAAGCGCATATCCTACGGA 58.488 47.619 11.47 0.00 35.55 4.69
791 1057 3.299340 AACTAAGCGCATATCCTACGG 57.701 47.619 11.47 0.00 0.00 4.02
836 1102 5.163622 ACACATGCAAACTAAGCACATATCC 60.164 40.000 0.00 0.00 45.95 2.59
846 1492 4.570930 TCGTCCATACACATGCAAACTAA 58.429 39.130 0.00 0.00 0.00 2.24
849 1495 3.822594 TTCGTCCATACACATGCAAAC 57.177 42.857 0.00 0.00 0.00 2.93
853 1499 6.972328 ACAATTTATTTCGTCCATACACATGC 59.028 34.615 0.00 0.00 0.00 4.06
905 1552 1.002251 GAGGAGACGCAGGAAGTATCG 60.002 57.143 0.00 0.00 31.22 2.92
909 1556 0.605589 CAAGAGGAGACGCAGGAAGT 59.394 55.000 0.00 0.00 0.00 3.01
910 1557 0.108424 CCAAGAGGAGACGCAGGAAG 60.108 60.000 0.00 0.00 36.89 3.46
913 1560 2.125350 GCCAAGAGGAGACGCAGG 60.125 66.667 0.00 0.00 36.89 4.85
914 1561 1.018226 CAAGCCAAGAGGAGACGCAG 61.018 60.000 0.00 0.00 36.89 5.18
917 1564 0.321671 TTCCAAGCCAAGAGGAGACG 59.678 55.000 0.00 0.00 36.89 4.18
918 1565 2.290577 ACATTCCAAGCCAAGAGGAGAC 60.291 50.000 0.00 0.00 36.89 3.36
919 1566 1.988107 ACATTCCAAGCCAAGAGGAGA 59.012 47.619 0.00 0.00 36.89 3.71
920 1567 2.503895 ACATTCCAAGCCAAGAGGAG 57.496 50.000 0.00 0.00 36.89 3.69
921 1568 2.376518 AGAACATTCCAAGCCAAGAGGA 59.623 45.455 0.00 0.00 36.89 3.71
922 1569 2.800250 AGAACATTCCAAGCCAAGAGG 58.200 47.619 0.00 0.00 38.23 3.69
945 1621 0.179081 GTCTAGTGCTTTAGGCCCCG 60.179 60.000 0.00 0.00 40.92 5.73
946 1622 0.180642 GGTCTAGTGCTTTAGGCCCC 59.819 60.000 0.00 0.00 39.11 5.80
992 1668 1.463674 GTGCCCGTCCATCTTTGAAT 58.536 50.000 0.00 0.00 0.00 2.57
998 1674 2.815308 GATCGTGCCCGTCCATCT 59.185 61.111 0.00 0.00 35.01 2.90
1019 1695 0.931468 TTCTAGGTCAGATCCCCCGA 59.069 55.000 0.00 0.00 31.77 5.14
1027 1703 2.992847 TGGTGAGGTTCTAGGTCAGA 57.007 50.000 0.00 0.00 0.00 3.27
1146 1822 2.736995 CACGTGTACCGCCACTGG 60.737 66.667 7.58 0.00 41.42 4.00
1505 2181 3.309296 TCGCTTAATCTCAGAGGGGAAT 58.691 45.455 0.00 0.00 0.00 3.01
1731 2407 6.436532 AGACTCTTCAAATCTGCCATGAAAAT 59.563 34.615 0.00 0.00 33.08 1.82
1752 2428 5.136068 TGGACATCTCCAGAAGATAGACT 57.864 43.478 0.00 0.00 43.13 3.24
1788 2464 1.471287 TGTCAATCTTGCTGAGCATGC 59.529 47.619 8.44 10.51 38.76 4.06
1895 2573 6.983910 TGAATTTTTCAACGTGTAAACAAGC 58.016 32.000 0.00 0.00 36.59 4.01
2045 2724 9.965902 AGATAATAACATCTTTCCAGTTTCTGT 57.034 29.630 0.00 0.00 30.93 3.41
2066 2745 8.100791 ACTTGTATTGCACTTTCCACTAGATAA 58.899 33.333 0.00 0.00 0.00 1.75
2185 3977 6.630444 ATGGAGATGATATGAAAGTGCAAC 57.370 37.500 0.00 0.00 0.00 4.17
2282 4075 8.695456 AGAACATTTACATTCCAACAGAACTTT 58.305 29.630 0.00 0.00 37.29 2.66
2351 4144 0.323629 CGCTTCCTTACCACTTCCCA 59.676 55.000 0.00 0.00 0.00 4.37
2375 4168 2.103263 CCAGGGCATAAGACTACTCCAC 59.897 54.545 0.00 0.00 0.00 4.02
2465 4258 7.627298 TCTTAGTGTTAGTGATCTGTAGACC 57.373 40.000 0.00 0.00 0.00 3.85
2466 4259 7.148222 TGCTCTTAGTGTTAGTGATCTGTAGAC 60.148 40.741 0.00 0.00 0.00 2.59
3214 5010 4.133078 CAACCTCTTGAGAAGTTTGCTCT 58.867 43.478 0.00 0.00 33.57 4.09
3274 5070 2.912956 AGCTTTTCCACTATCTCCACCA 59.087 45.455 0.00 0.00 0.00 4.17
3275 5071 3.274288 CAGCTTTTCCACTATCTCCACC 58.726 50.000 0.00 0.00 0.00 4.61
3358 5154 6.591750 TTCACAAGGTTTGGTTCTTTAACA 57.408 33.333 0.00 0.00 37.34 2.41
3400 5196 5.078411 ACGAGCAATGAGAACATAGAAGT 57.922 39.130 0.00 0.00 35.50 3.01
3466 5262 3.152400 AGCCGTACCCGTCCATCC 61.152 66.667 0.00 0.00 0.00 3.51
3490 5286 8.949612 CAGGAAGGTCTGAGGATGTGTAACAC 62.950 50.000 0.00 0.00 43.27 3.32
3544 5340 8.972127 TCAAAACTAGAGAGAAGCACATATACT 58.028 33.333 0.00 0.00 0.00 2.12
3545 5341 9.243637 CTCAAAACTAGAGAGAAGCACATATAC 57.756 37.037 0.00 0.00 35.09 1.47
3624 5435 1.202806 AGCAACAGCTCTAACTGCCAA 60.203 47.619 0.00 0.00 41.60 4.52
3666 5477 4.523943 TGAACACCAAGCTAATGCAGAATT 59.476 37.500 0.00 0.00 42.74 2.17
3983 5794 7.897864 AGCATATACCATACCTTAAGTCTGTC 58.102 38.462 0.97 0.00 0.00 3.51
4013 5824 6.039941 CCCATCAACAAAAACACTAGGTGTAA 59.960 38.462 3.69 0.00 46.79 2.41
4024 5835 8.106247 TCAGTATACTTCCCATCAACAAAAAC 57.894 34.615 1.56 0.00 0.00 2.43
4172 5983 4.349342 ACTGTCCTGAAAACAGAAGGAGAT 59.651 41.667 10.04 0.00 45.64 2.75
4174 5985 4.078639 ACTGTCCTGAAAACAGAAGGAG 57.921 45.455 10.04 0.00 45.64 3.69
4244 6055 4.570772 TCAGTAAGTTCATTTATCTGCCGC 59.429 41.667 0.00 0.00 0.00 6.53
4245 6056 6.662414 TTCAGTAAGTTCATTTATCTGCCG 57.338 37.500 0.00 0.00 0.00 5.69
4364 6175 5.995897 GGGGCATCACGAATAAAGTATTAGT 59.004 40.000 0.00 0.00 34.91 2.24
4376 6187 2.361104 GGCTTGGGGCATCACGAA 60.361 61.111 0.00 0.00 44.01 3.85
4453 6264 6.023603 ACTAAACTGAGATAGGGAGGAACAA 58.976 40.000 0.00 0.00 0.00 2.83
4461 6272 6.511444 CGAACGACTACTAAACTGAGATAGGG 60.511 46.154 0.00 0.00 0.00 3.53
4485 6296 2.230025 AGATGAGATAACCAGATCGCCG 59.770 50.000 0.00 0.00 0.00 6.46
4491 6302 6.777580 TGCAGTGTATAGATGAGATAACCAGA 59.222 38.462 0.00 0.00 0.00 3.86
4501 6312 6.988580 CCAGAAATCTTGCAGTGTATAGATGA 59.011 38.462 0.00 0.00 0.00 2.92
4507 6318 5.591877 GGAATCCAGAAATCTTGCAGTGTAT 59.408 40.000 0.00 0.00 0.00 2.29
4528 6339 1.754745 GTGTGTCAGCAGGAGGGAA 59.245 57.895 0.00 0.00 0.00 3.97
4546 6357 0.109689 GAACCTCGTCTGTCACTCGG 60.110 60.000 0.00 0.00 0.00 4.63
4547 6358 0.875728 AGAACCTCGTCTGTCACTCG 59.124 55.000 0.00 0.00 0.00 4.18
4560 6374 3.728385 AAGCCAGCTGAATAAGAACCT 57.272 42.857 17.39 0.00 0.00 3.50
4561 6375 4.488879 CAAAAGCCAGCTGAATAAGAACC 58.511 43.478 17.39 0.00 0.00 3.62
4576 6390 2.980246 ATCCCCTATAGCCAAAAGCC 57.020 50.000 0.00 0.00 45.47 4.35
4585 6399 3.194542 CGAGAAGGCTGAATCCCCTATAG 59.805 52.174 0.00 0.00 0.00 1.31
4586 6400 3.165875 CGAGAAGGCTGAATCCCCTATA 58.834 50.000 0.00 0.00 0.00 1.31
4594 6408 1.751351 TCGATGACGAGAAGGCTGAAT 59.249 47.619 0.00 0.00 43.81 2.57
4613 6427 5.467063 GGTGCCAAATACTGCTTATAGAGTC 59.533 44.000 0.00 0.00 0.00 3.36
4620 6434 3.761897 ACAAGGTGCCAAATACTGCTTA 58.238 40.909 0.00 0.00 0.00 3.09
4621 6435 2.597455 ACAAGGTGCCAAATACTGCTT 58.403 42.857 0.00 0.00 0.00 3.91
4623 6437 2.035832 ACAACAAGGTGCCAAATACTGC 59.964 45.455 0.00 0.00 0.00 4.40
4624 6438 4.615912 GCTACAACAAGGTGCCAAATACTG 60.616 45.833 0.00 0.00 0.00 2.74
4637 6451 8.462811 TCATTAACTCTCTAGAGCTACAACAAG 58.537 37.037 15.35 7.04 45.79 3.16
4655 6469 6.653989 CAGGTTAGAGGGTTGATCATTAACT 58.346 40.000 0.00 0.00 0.00 2.24
4663 6477 2.644798 ACAAGCAGGTTAGAGGGTTGAT 59.355 45.455 9.44 0.00 41.23 2.57
4671 6485 7.981789 CAGAATACAGAATACAAGCAGGTTAGA 59.018 37.037 0.00 0.00 0.00 2.10
4699 6513 7.295952 AGATAAAAATCTACTCAGCAACGTG 57.704 36.000 0.00 0.00 0.00 4.49
4701 6515 8.443160 TCAAAGATAAAAATCTACTCAGCAACG 58.557 33.333 0.00 0.00 0.00 4.10
4719 6533 9.187996 TCACTCCATAAATGCATTTCAAAGATA 57.812 29.630 27.28 9.37 0.00 1.98
4720 6534 8.070034 TCACTCCATAAATGCATTTCAAAGAT 57.930 30.769 27.28 12.70 0.00 2.40
4723 6537 7.977293 CAGATCACTCCATAAATGCATTTCAAA 59.023 33.333 27.28 11.61 0.00 2.69
4781 6595 9.213799 GCTATAAGGGTTGAAGAAATATCTCTG 57.786 37.037 0.00 0.00 33.77 3.35
4783 6597 8.379331 AGGCTATAAGGGTTGAAGAAATATCTC 58.621 37.037 0.00 0.00 33.77 2.75
4799 6614 7.771183 TGCTTCATTTGTAAAAGGCTATAAGG 58.229 34.615 0.00 0.00 0.00 2.69
4836 6654 4.579869 TGCAGTTTCCTAGGAGTCATTTC 58.420 43.478 12.26 0.59 0.00 2.17
4868 6686 3.368843 GCTTCAGACATCAACAGAGCCTA 60.369 47.826 0.00 0.00 0.00 3.93
4869 6687 2.614987 GCTTCAGACATCAACAGAGCCT 60.615 50.000 0.00 0.00 0.00 4.58
4870 6688 1.736681 GCTTCAGACATCAACAGAGCC 59.263 52.381 0.00 0.00 0.00 4.70
4871 6689 1.736681 GGCTTCAGACATCAACAGAGC 59.263 52.381 0.00 0.00 0.00 4.09
4877 6703 4.661222 TGTATTTGGGCTTCAGACATCAA 58.339 39.130 0.00 0.00 0.00 2.57
4915 6741 6.846350 AGTTACAAGCAGCATTCTTAATGTC 58.154 36.000 0.00 0.00 41.01 3.06
4917 6743 6.034256 GCAAGTTACAAGCAGCATTCTTAATG 59.966 38.462 0.00 0.00 41.85 1.90
4922 6748 2.886523 TGCAAGTTACAAGCAGCATTCT 59.113 40.909 0.00 0.00 33.75 2.40
4928 6754 5.174398 CACAAATCTTGCAAGTTACAAGCAG 59.826 40.000 25.19 9.72 43.40 4.24
4931 6757 5.459762 CACCACAAATCTTGCAAGTTACAAG 59.540 40.000 25.19 9.26 44.76 3.16
4935 6761 3.243704 GGCACCACAAATCTTGCAAGTTA 60.244 43.478 25.19 8.37 36.66 2.24
4980 6806 3.243704 GCTAGTTGCTCCAGTATCTCAGG 60.244 52.174 0.00 0.00 38.95 3.86
4981 6807 3.549827 CGCTAGTTGCTCCAGTATCTCAG 60.550 52.174 0.00 0.00 40.11 3.35
4982 6808 2.359214 CGCTAGTTGCTCCAGTATCTCA 59.641 50.000 0.00 0.00 40.11 3.27
4983 6809 2.619177 TCGCTAGTTGCTCCAGTATCTC 59.381 50.000 0.00 0.00 40.11 2.75
4984 6810 2.621055 CTCGCTAGTTGCTCCAGTATCT 59.379 50.000 0.00 0.00 40.11 1.98
4985 6811 2.860582 GCTCGCTAGTTGCTCCAGTATC 60.861 54.545 0.00 0.00 40.11 2.24
4986 6812 1.067821 GCTCGCTAGTTGCTCCAGTAT 59.932 52.381 0.00 0.00 40.11 2.12
4987 6813 0.456221 GCTCGCTAGTTGCTCCAGTA 59.544 55.000 0.00 0.00 40.11 2.74
4988 6814 1.216710 GCTCGCTAGTTGCTCCAGT 59.783 57.895 0.00 0.00 40.11 4.00
5029 6855 7.552687 CCAGCACTGTTTCCTTTATTGACTATA 59.447 37.037 0.00 0.00 0.00 1.31
5030 6856 6.375455 CCAGCACTGTTTCCTTTATTGACTAT 59.625 38.462 0.00 0.00 0.00 2.12
5044 6870 1.109323 GCAAGACCCCAGCACTGTTT 61.109 55.000 0.00 0.00 0.00 2.83
5076 6902 2.433436 GACAGGGGACAATGGTTGTAC 58.567 52.381 0.00 0.00 45.52 2.90
5077 6903 1.002659 CGACAGGGGACAATGGTTGTA 59.997 52.381 0.00 0.00 45.52 2.41
5079 6905 0.250727 ACGACAGGGGACAATGGTTG 60.251 55.000 0.00 0.00 0.00 3.77
5080 6906 1.278127 CTACGACAGGGGACAATGGTT 59.722 52.381 0.00 0.00 0.00 3.67
5081 6907 0.902531 CTACGACAGGGGACAATGGT 59.097 55.000 0.00 0.00 0.00 3.55
5082 6908 0.178068 CCTACGACAGGGGACAATGG 59.822 60.000 0.00 0.00 41.26 3.16
5083 6909 1.191535 TCCTACGACAGGGGACAATG 58.808 55.000 7.78 0.00 45.58 2.82
5084 6910 3.703804 TCCTACGACAGGGGACAAT 57.296 52.632 7.78 0.00 45.58 2.71
5092 6918 0.108615 CAAGCACCCTCCTACGACAG 60.109 60.000 0.00 0.00 0.00 3.51
5093 6919 1.541310 CCAAGCACCCTCCTACGACA 61.541 60.000 0.00 0.00 0.00 4.35
5094 6920 1.218316 CCAAGCACCCTCCTACGAC 59.782 63.158 0.00 0.00 0.00 4.34
5095 6921 2.656069 GCCAAGCACCCTCCTACGA 61.656 63.158 0.00 0.00 0.00 3.43
5096 6922 2.125106 GCCAAGCACCCTCCTACG 60.125 66.667 0.00 0.00 0.00 3.51
5097 6923 0.678048 CAAGCCAAGCACCCTCCTAC 60.678 60.000 0.00 0.00 0.00 3.18
5098 6924 1.685224 CAAGCCAAGCACCCTCCTA 59.315 57.895 0.00 0.00 0.00 2.94
5099 6925 2.437897 CAAGCCAAGCACCCTCCT 59.562 61.111 0.00 0.00 0.00 3.69
5100 6926 3.376918 GCAAGCCAAGCACCCTCC 61.377 66.667 0.00 0.00 0.00 4.30
5101 6927 3.376918 GGCAAGCCAAGCACCCTC 61.377 66.667 6.14 0.00 35.81 4.30
5226 7090 4.771577 ACCAAATCATACACAGCCAAATGA 59.228 37.500 0.00 0.00 33.20 2.57
5233 7097 7.475771 TTTTTCAAACCAAATCATACACAGC 57.524 32.000 0.00 0.00 0.00 4.40
5320 7184 5.868454 TGACATACCATGTGATCAATAGGG 58.132 41.667 9.62 9.62 45.03 3.53


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

AutoCloner maintained by Alex Coulton.