Multiple sequence alignment - TraesCS2D01G033300

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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 TraesCS2D01G033300 chr2D 100.000 4435 0 0 1 4435 12889080 12893514 0.000000e+00 8191.0
1 TraesCS2D01G033300 chr2D 88.571 245 17 4 2682 2924 12891295 12891530 2.020000e-73 287.0
2 TraesCS2D01G033300 chr2D 88.571 245 17 4 2216 2451 12891761 12892003 2.020000e-73 287.0
3 TraesCS2D01G033300 chr2A 95.536 1501 48 8 1503 2989 15008502 15009997 0.000000e+00 2383.0
4 TraesCS2D01G033300 chr2A 88.121 926 62 21 600 1510 15006954 15007846 0.000000e+00 1057.0
5 TraesCS2D01G033300 chr2A 88.525 244 18 3 2682 2924 15009215 15009449 2.020000e-73 287.0
6 TraesCS2D01G033300 chr2A 86.585 246 22 4 2216 2451 15009679 15009923 1.220000e-65 261.0
7 TraesCS2D01G033300 chr2A 85.294 136 15 5 2802 2934 15023938 15024071 7.740000e-28 135.0
8 TraesCS2D01G033300 chr2A 93.617 47 3 0 3581 3627 55565713 55565759 2.210000e-08 71.3
9 TraesCS2D01G033300 chr2A 94.872 39 2 0 3588 3626 1372343 1372305 1.330000e-05 62.1
10 TraesCS2D01G033300 chr2B 91.600 1131 61 11 2167 3287 23591933 23593039 0.000000e+00 1531.0
11 TraesCS2D01G033300 chr2B 92.926 933 41 16 592 1510 23589332 23590253 0.000000e+00 1334.0
12 TraesCS2D01G033300 chr2B 93.264 579 29 8 2727 3300 23628107 23628680 0.000000e+00 845.0
13 TraesCS2D01G033300 chr2B 94.231 468 25 2 3294 3761 23635060 23635525 0.000000e+00 713.0
14 TraesCS2D01G033300 chr2B 86.777 605 54 9 3840 4435 23636013 23636600 0.000000e+00 651.0
15 TraesCS2D01G033300 chr2B 86.978 599 31 14 1 584 23588528 23589094 8.100000e-177 630.0
16 TraesCS2D01G033300 chr2B 90.452 398 33 5 1510 1903 23590816 23591212 1.830000e-143 520.0
17 TraesCS2D01G033300 chr2B 90.000 240 23 1 2685 2924 23591985 23592223 4.310000e-80 309.0
18 TraesCS2D01G033300 chr2B 88.672 256 18 3 1105 1356 416252796 416252548 7.210000e-78 302.0
19 TraesCS2D01G033300 chr2B 89.175 194 20 1 2547 2739 23624968 23625161 1.590000e-59 241.0
20 TraesCS2D01G033300 chr2B 86.082 194 13 6 2268 2451 23628113 23628302 3.500000e-46 196.0
21 TraesCS2D01G033300 chr2B 82.186 247 17 9 1951 2170 23591658 23591904 2.110000e-43 187.0
22 TraesCS2D01G033300 chr2B 85.185 135 16 4 2802 2934 23624835 23624967 7.740000e-28 135.0
23 TraesCS2D01G033300 chr2B 97.619 42 1 0 3756 3797 23635810 23635851 6.150000e-09 73.1
24 TraesCS2D01G033300 chr1A 84.018 219 23 3 1253 1471 343964010 343964216 2.710000e-47 200.0
25 TraesCS2D01G033300 chr5B 93.617 47 3 0 3581 3627 22817720 22817674 2.210000e-08 71.3
26 TraesCS2D01G033300 chr5B 95.000 40 2 0 3588 3627 22510869 22510830 3.700000e-06 63.9
27 TraesCS2D01G033300 chr5B 95.000 40 2 0 3588 3627 355601191 355601152 3.700000e-06 63.9
28 TraesCS2D01G033300 chr3A 95.000 40 2 0 3588 3627 113800425 113800464 3.700000e-06 63.9
29 TraesCS2D01G033300 chr3B 94.872 39 2 0 3588 3626 149467834 149467872 1.330000e-05 62.1
30 TraesCS2D01G033300 chr4D 94.737 38 2 0 3589 3626 37934252 37934289 4.790000e-05 60.2


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 TraesCS2D01G033300 chr2D 12889080 12893514 4434 False 2921.666667 8191 92.380667 1 4435 3 chr2D.!!$F1 4434
1 TraesCS2D01G033300 chr2A 15006954 15009997 3043 False 997.000000 2383 89.691750 600 2989 4 chr2A.!!$F3 2389
2 TraesCS2D01G033300 chr2B 23588528 23593039 4511 False 751.833333 1531 89.023667 1 3287 6 chr2B.!!$F1 3286
3 TraesCS2D01G033300 chr2B 23635060 23636600 1540 False 479.033333 713 92.875667 3294 4435 3 chr2B.!!$F3 1141
4 TraesCS2D01G033300 chr2B 23624835 23628680 3845 False 354.250000 845 88.426500 2268 3300 4 chr2B.!!$F2 1032

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
249 261 0.248289 GGAGCCATGTTGCAAAGCAT 59.752 50.000 0.00 0.0 38.76 3.79 F
264 276 1.037030 AGCATATGGGTTGTTGCGGG 61.037 55.000 4.56 0.0 40.00 6.13 F
860 1116 1.203440 AGGGGTGAGTGGTGGTAGATT 60.203 52.381 0.00 0.0 0.00 2.40 F
1222 1485 0.033366 TGTGTGTGTGACATCGAGGG 59.967 55.000 0.69 0.0 36.78 4.30 F
1936 3036 1.134965 ACTGAGGTTGACGAGCTATGC 60.135 52.381 0.00 0.0 35.91 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1205 1468 0.317160 GACCCTCGATGTCACACACA 59.683 55.000 9.63 0.0 40.18 3.72 R
1206 1469 0.389948 GGACCCTCGATGTCACACAC 60.390 60.000 14.83 0.0 34.36 3.82 R
2073 3463 3.498397 AGTTAAACGAGTGACCTGCATTG 59.502 43.478 0.00 0.0 0.00 2.82 R
2886 7283 3.806521 AGTACATTCATCGAGAGCAATGC 59.193 43.478 0.00 0.0 30.63 3.56 R
3896 8722 0.235665 CGCGACTCATGCAACTTTGT 59.764 50.000 0.00 0.0 0.00 2.83 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
101 105 2.262915 CTTCTTCCCGCTGCGACT 59.737 61.111 25.45 0.00 0.00 4.18
117 121 1.071502 CGACTATATGCGTTGCGGTTG 60.072 52.381 0.00 0.00 0.00 3.77
126 130 4.892965 TTGCGGTTGCTGCAGGGT 62.893 61.111 17.12 0.00 46.84 4.34
136 140 1.880819 GCTGCAGGGTTGGATGGTTG 61.881 60.000 17.12 0.00 0.00 3.77
152 156 1.153524 TTGTGGTTGCTGCAGGGAT 59.846 52.632 17.12 0.00 0.00 3.85
212 223 0.597377 GGCAACAAGGAGGTTTTGCG 60.597 55.000 0.00 0.00 44.34 4.85
223 234 1.652563 GTTTTGCGCTCGAAAGGGT 59.347 52.632 9.73 0.00 37.74 4.34
241 253 2.267351 TTGCACGGGAGCCATGTTG 61.267 57.895 0.00 0.00 0.00 3.33
248 260 1.667151 GGAGCCATGTTGCAAAGCA 59.333 52.632 0.00 0.00 36.47 3.91
249 261 0.248289 GGAGCCATGTTGCAAAGCAT 59.752 50.000 0.00 0.00 38.76 3.79
250 262 1.477700 GGAGCCATGTTGCAAAGCATA 59.522 47.619 0.00 0.00 38.76 3.14
251 263 2.101917 GGAGCCATGTTGCAAAGCATAT 59.898 45.455 0.00 0.00 38.76 1.78
252 264 3.120792 GAGCCATGTTGCAAAGCATATG 58.879 45.455 0.00 0.00 38.76 1.78
253 265 2.159014 AGCCATGTTGCAAAGCATATGG 60.159 45.455 21.59 21.59 46.64 2.74
254 266 2.828877 CCATGTTGCAAAGCATATGGG 58.171 47.619 19.65 0.00 43.50 4.00
255 267 2.168936 CCATGTTGCAAAGCATATGGGT 59.831 45.455 19.65 0.00 43.50 4.51
256 268 3.369681 CCATGTTGCAAAGCATATGGGTT 60.370 43.478 19.65 0.00 43.50 4.11
257 269 3.316071 TGTTGCAAAGCATATGGGTTG 57.684 42.857 0.00 0.00 38.76 3.77
258 270 2.632028 TGTTGCAAAGCATATGGGTTGT 59.368 40.909 0.00 0.00 38.76 3.32
259 271 3.070734 TGTTGCAAAGCATATGGGTTGTT 59.929 39.130 0.00 0.00 38.76 2.83
260 272 3.316071 TGCAAAGCATATGGGTTGTTG 57.684 42.857 4.56 0.00 37.28 3.33
264 276 1.037030 AGCATATGGGTTGTTGCGGG 61.037 55.000 4.56 0.00 40.00 6.13
294 306 1.541310 AAACTCGGATCTGACGCCCA 61.541 55.000 0.00 0.00 0.00 5.36
295 307 1.949847 AACTCGGATCTGACGCCCAG 61.950 60.000 0.00 0.00 44.27 4.45
308 320 3.972227 CCCAGAAGGCAGTCAACG 58.028 61.111 0.00 0.00 0.00 4.10
309 321 2.328099 CCCAGAAGGCAGTCAACGC 61.328 63.158 0.00 0.00 0.00 4.84
310 322 1.597854 CCAGAAGGCAGTCAACGCA 60.598 57.895 0.00 0.00 0.00 5.24
311 323 1.571460 CAGAAGGCAGTCAACGCAC 59.429 57.895 0.00 0.00 0.00 5.34
312 324 1.956170 AGAAGGCAGTCAACGCACG 60.956 57.895 0.00 0.00 0.00 5.34
313 325 2.203015 AAGGCAGTCAACGCACGT 60.203 55.556 0.00 0.00 0.00 4.49
314 326 1.772063 GAAGGCAGTCAACGCACGTT 61.772 55.000 1.93 1.93 39.13 3.99
322 334 2.665185 AACGCACGTTGGGAGCTC 60.665 61.111 7.76 4.71 36.91 4.09
470 482 1.355971 GAATCAACGGCTCAACGCTA 58.644 50.000 0.00 0.00 39.13 4.26
477 489 1.745115 GGCTCAACGCTATGGCACA 60.745 57.895 0.74 0.00 40.75 4.57
479 491 1.298157 GCTCAACGCTATGGCACACA 61.298 55.000 0.74 0.00 36.95 3.72
533 548 3.818210 ACAACACTCCAATTGACGCATTA 59.182 39.130 7.12 0.00 0.00 1.90
709 956 2.706339 ACCATCTCAAGCATCACCTC 57.294 50.000 0.00 0.00 0.00 3.85
802 1054 6.588373 TGTGAAAAGTTTGCAGGAAAAACTAC 59.412 34.615 0.00 0.00 44.93 2.73
860 1116 1.203440 AGGGGTGAGTGGTGGTAGATT 60.203 52.381 0.00 0.00 0.00 2.40
1132 1392 4.689549 TCTTCCTCCCCCGCACGA 62.690 66.667 0.00 0.00 0.00 4.35
1205 1468 4.269523 ATGGGCGTGGCTGTGTGT 62.270 61.111 0.00 0.00 0.00 3.72
1222 1485 0.033366 TGTGTGTGTGACATCGAGGG 59.967 55.000 0.69 0.00 36.78 4.30
1431 1698 2.186243 AGCTGGATGTGTCAGTCTCAT 58.814 47.619 0.00 0.00 34.89 2.90
1510 1779 1.394917 CTGAGTACAATGTTGAGCGGC 59.605 52.381 0.00 0.00 0.00 6.53
1511 1780 1.270571 TGAGTACAATGTTGAGCGGCA 60.271 47.619 1.45 0.00 0.00 5.69
1524 2491 2.158841 TGAGCGGCATAGTTTTTCGAAC 59.841 45.455 1.45 0.00 0.00 3.95
1651 2620 5.279456 GGCACCTTACATTTTGGATTTGAGT 60.279 40.000 0.00 0.00 0.00 3.41
1653 2622 6.738453 GCACCTTACATTTTGGATTTGAGTGT 60.738 38.462 0.00 0.00 0.00 3.55
1673 2642 4.623595 GTGTGTAGTTTTTGGTTGTTGTGG 59.376 41.667 0.00 0.00 0.00 4.17
1762 2731 3.006112 TCTGCAACCCTTTGTGTGTTA 57.994 42.857 0.00 0.00 34.90 2.41
1763 2732 3.357203 TCTGCAACCCTTTGTGTGTTAA 58.643 40.909 0.00 0.00 34.90 2.01
1935 3035 2.949451 ACTGAGGTTGACGAGCTATG 57.051 50.000 0.00 0.00 35.91 2.23
1936 3036 1.134965 ACTGAGGTTGACGAGCTATGC 60.135 52.381 0.00 0.00 35.91 3.14
2073 3463 2.369394 CCCCCAAATGTAGTTCTCAGC 58.631 52.381 0.00 0.00 0.00 4.26
2118 3508 5.895636 TTTGACAGCTGTTTCTCTTTTGA 57.104 34.783 22.65 0.00 0.00 2.69
2445 3881 9.483916 TCTCGATGAATGTACTCTTAACAAAAA 57.516 29.630 0.00 0.00 0.00 1.94
2612 4050 5.409214 GCTTGGTAGACTAGACTCCTATACG 59.591 48.000 0.00 0.00 0.00 3.06
2637 4075 6.535150 GGCGAGGAAATATCGAATTGATCATA 59.465 38.462 0.00 0.00 42.76 2.15
2683 4121 3.814625 TGAGATGTTTGTAGTTGGCACA 58.185 40.909 0.00 0.00 0.00 4.57
2708 4146 7.992754 AAGTGAGTTGAAATGCTTATTCTCT 57.007 32.000 0.00 0.00 0.00 3.10
2858 7254 5.458041 AGTGCATTTGTTTGCTGATAGTT 57.542 34.783 0.00 0.00 43.18 2.24
2867 7263 8.677148 TTTGTTTGCTGATAGTTCTTAGAACT 57.323 30.769 27.54 27.54 0.00 3.01
2886 7283 5.888161 AGAACTTGTATCCCAGCTATTTTGG 59.112 40.000 0.00 0.00 35.41 3.28
2955 7364 1.699634 CCTTGTCTCTGGGACCTTGAA 59.300 52.381 5.00 0.00 43.89 2.69
3040 7449 7.707624 TGAGCTTGAAATCATCCTGTATTTT 57.292 32.000 0.00 0.00 0.00 1.82
3074 7483 8.710835 TTGAAATCACGCTGTATAATTAGTCA 57.289 30.769 0.00 0.00 0.00 3.41
3075 7484 8.352752 TGAAATCACGCTGTATAATTAGTCAG 57.647 34.615 12.50 12.50 0.00 3.51
3080 7489 7.094631 TCACGCTGTATAATTAGTCAGTTGTT 58.905 34.615 16.00 2.53 0.00 2.83
3187 7596 1.748950 TTGTGACAAAGAGCTGCACA 58.251 45.000 1.02 0.00 37.66 4.57
3290 7701 6.402011 GGTGCATCCAAATCCGTTTAATTTTG 60.402 38.462 0.00 0.00 35.97 2.44
3322 7733 0.037139 TGACGGTACATCCAAACCCG 60.037 55.000 0.00 0.00 44.06 5.28
3370 7781 4.527509 TGTTTTGGAGCAAGTTTGTTGA 57.472 36.364 0.00 0.00 0.00 3.18
3397 7808 4.458989 TGAAAGTTTATGCCACATGGACTC 59.541 41.667 0.87 0.00 37.39 3.36
3404 7815 1.490693 GCCACATGGACTCGTATGCG 61.491 60.000 0.87 0.00 37.39 4.73
3417 7828 1.846541 GTATGCGACTCTTCCTCTGC 58.153 55.000 0.00 0.00 0.00 4.26
3425 7836 3.492309 CGACTCTTCCTCTGCTATGCATT 60.492 47.826 3.54 0.00 38.13 3.56
3426 7837 4.450053 GACTCTTCCTCTGCTATGCATTT 58.550 43.478 3.54 0.00 38.13 2.32
3435 7846 6.886459 TCCTCTGCTATGCATTTAGTTTTTCT 59.114 34.615 3.54 0.00 38.13 2.52
3483 7894 1.911293 CTGGTTCACGTGGATTGGCG 61.911 60.000 17.00 0.00 0.00 5.69
3547 7958 4.813027 TGTGAAATCGTAGGTTAGTCCAC 58.187 43.478 0.00 0.00 39.02 4.02
3585 7996 8.312564 GTTTAGAATGTACTCCCTCTGTACTTT 58.687 37.037 0.00 0.00 40.44 2.66
3587 7998 5.187967 AGAATGTACTCCCTCTGTACTTTGG 59.812 44.000 8.98 0.00 40.44 3.28
3588 7999 3.853207 TGTACTCCCTCTGTACTTTGGT 58.147 45.455 0.00 0.00 40.44 3.67
3589 8000 3.576982 TGTACTCCCTCTGTACTTTGGTG 59.423 47.826 0.00 0.00 40.44 4.17
3590 8001 2.972348 ACTCCCTCTGTACTTTGGTGA 58.028 47.619 0.00 0.00 0.00 4.02
3591 8002 2.633481 ACTCCCTCTGTACTTTGGTGAC 59.367 50.000 0.00 0.00 0.00 3.67
3592 8003 1.975680 TCCCTCTGTACTTTGGTGACC 59.024 52.381 0.00 0.00 0.00 4.02
3628 8039 4.718940 TTAGTTTACAGGGGTAGTACGC 57.281 45.455 8.80 8.80 0.00 4.42
3674 8085 5.665916 AATATTCTTTTGAACTGGCCTGG 57.334 39.130 14.82 4.64 41.77 4.45
3676 8087 2.746279 TCTTTTGAACTGGCCTGGAA 57.254 45.000 14.82 0.96 0.00 3.53
3696 8107 4.994852 GGAAGGGTTTAAACAGATTTTGCC 59.005 41.667 19.57 8.92 0.00 4.52
3744 8155 4.518970 TCTTGTTGTAAGAATTGAGGGCAC 59.481 41.667 0.00 0.00 0.00 5.01
3793 8494 3.936902 TGTTGCACGTTCTGAAAGTAC 57.063 42.857 8.61 4.37 33.76 2.73
3811 8637 7.170320 TGAAAGTACGTAGAACAATCCTTCAAC 59.830 37.037 0.00 0.00 0.00 3.18
3814 8640 5.862924 ACGTAGAACAATCCTTCAACATG 57.137 39.130 0.00 0.00 0.00 3.21
3816 8642 5.179368 ACGTAGAACAATCCTTCAACATGTG 59.821 40.000 0.00 0.00 0.00 3.21
3817 8643 5.390885 CGTAGAACAATCCTTCAACATGTGG 60.391 44.000 0.00 0.00 0.00 4.17
3818 8644 3.828451 AGAACAATCCTTCAACATGTGGG 59.172 43.478 0.00 0.00 0.00 4.61
3819 8645 3.524095 ACAATCCTTCAACATGTGGGA 57.476 42.857 0.00 5.86 0.00 4.37
3820 8646 4.051661 ACAATCCTTCAACATGTGGGAT 57.948 40.909 0.00 8.00 38.29 3.85
3821 8647 4.419282 ACAATCCTTCAACATGTGGGATT 58.581 39.130 20.35 20.35 44.53 3.01
3822 8648 5.579047 ACAATCCTTCAACATGTGGGATTA 58.421 37.500 23.12 1.69 42.63 1.75
3823 8649 5.418840 ACAATCCTTCAACATGTGGGATTAC 59.581 40.000 23.12 0.00 42.63 1.89
3824 8650 4.649267 TCCTTCAACATGTGGGATTACA 57.351 40.909 0.00 0.00 34.63 2.41
3826 8652 6.320434 TCCTTCAACATGTGGGATTACATA 57.680 37.500 0.00 0.00 39.17 2.29
3827 8653 6.910191 TCCTTCAACATGTGGGATTACATAT 58.090 36.000 0.00 0.00 39.17 1.78
3829 8655 7.936847 TCCTTCAACATGTGGGATTACATATAC 59.063 37.037 0.00 0.00 39.17 1.47
3830 8656 7.939039 CCTTCAACATGTGGGATTACATATACT 59.061 37.037 0.00 0.00 39.17 2.12
3831 8657 9.342308 CTTCAACATGTGGGATTACATATACTT 57.658 33.333 0.00 0.00 39.17 2.24
3833 8659 8.490311 TCAACATGTGGGATTACATATACTTGA 58.510 33.333 0.00 0.00 39.17 3.02
3834 8660 9.288576 CAACATGTGGGATTACATATACTTGAT 57.711 33.333 0.00 0.00 39.17 2.57
3835 8661 8.853077 ACATGTGGGATTACATATACTTGATG 57.147 34.615 0.00 0.00 39.17 3.07
3836 8662 7.391554 ACATGTGGGATTACATATACTTGATGC 59.608 37.037 0.00 0.00 39.17 3.91
3837 8663 6.836242 TGTGGGATTACATATACTTGATGCA 58.164 36.000 0.00 0.00 0.00 3.96
3838 8664 7.286313 TGTGGGATTACATATACTTGATGCAA 58.714 34.615 0.00 0.00 0.00 4.08
3848 8674 9.881649 ACATATACTTGATGCAATATGTAGAGG 57.118 33.333 14.80 9.63 41.44 3.69
3912 8738 5.530519 TTCGATACAAAGTTGCATGAGTC 57.469 39.130 0.00 0.00 0.00 3.36
3932 8758 6.125327 AGTCGCGACTCCAATGATATATAG 57.875 41.667 34.98 0.00 36.92 1.31
3933 8759 5.648526 AGTCGCGACTCCAATGATATATAGT 59.351 40.000 34.98 7.93 36.92 2.12
3934 8760 6.822170 AGTCGCGACTCCAATGATATATAGTA 59.178 38.462 34.98 0.00 36.92 1.82
3935 8761 7.011576 AGTCGCGACTCCAATGATATATAGTAG 59.988 40.741 34.98 0.00 36.92 2.57
3936 8762 6.822170 TCGCGACTCCAATGATATATAGTAGT 59.178 38.462 3.71 0.00 0.00 2.73
3937 8763 7.983484 TCGCGACTCCAATGATATATAGTAGTA 59.017 37.037 3.71 0.00 0.00 1.82
3938 8764 8.775527 CGCGACTCCAATGATATATAGTAGTAT 58.224 37.037 0.00 0.00 0.00 2.12
3985 8811 4.074970 GGGCGATTCCAATGATATCTTGT 58.925 43.478 3.98 0.00 36.21 3.16
3988 8814 4.023792 GCGATTCCAATGATATCTTGTGCA 60.024 41.667 3.98 0.00 0.00 4.57
4001 8827 8.349983 TGATATCTTGTGCAAAATCATCATCAG 58.650 33.333 3.98 0.00 0.00 2.90
4004 8830 6.153756 TCTTGTGCAAAATCATCATCAGTTG 58.846 36.000 0.00 0.00 0.00 3.16
4015 8842 7.713734 ATCATCATCAGTTGTCCATTTCTTT 57.286 32.000 0.00 0.00 0.00 2.52
4016 8843 7.528996 TCATCATCAGTTGTCCATTTCTTTT 57.471 32.000 0.00 0.00 0.00 2.27
4017 8844 7.372714 TCATCATCAGTTGTCCATTTCTTTTG 58.627 34.615 0.00 0.00 0.00 2.44
4021 8848 5.108517 TCAGTTGTCCATTTCTTTTGTTGC 58.891 37.500 0.00 0.00 0.00 4.17
4024 8851 2.768527 TGTCCATTTCTTTTGTTGCCCA 59.231 40.909 0.00 0.00 0.00 5.36
4028 8855 3.070015 CCATTTCTTTTGTTGCCCAGAGT 59.930 43.478 0.00 0.00 0.00 3.24
4031 8858 5.923733 TTTCTTTTGTTGCCCAGAGTTAA 57.076 34.783 0.00 0.00 0.00 2.01
4038 8865 2.691011 GTTGCCCAGAGTTAAACCACAA 59.309 45.455 0.00 0.00 0.00 3.33
4058 8885 4.143389 ACAAACTTTACTCGAATTCTCGCG 60.143 41.667 0.00 0.00 45.04 5.87
4063 8890 2.849966 CTCGAATTCTCGCGGCGTG 61.850 63.158 22.90 20.04 45.04 5.34
4135 8962 4.008933 AGCACCTCGGCAGACACC 62.009 66.667 0.00 0.00 35.83 4.16
4144 8971 3.637273 GCAGACACCGTCCCCCTT 61.637 66.667 0.00 0.00 32.18 3.95
4149 8976 2.359975 CACCGTCCCCCTTTCTGC 60.360 66.667 0.00 0.00 0.00 4.26
4150 8977 3.647771 ACCGTCCCCCTTTCTGCC 61.648 66.667 0.00 0.00 0.00 4.85
4155 8982 2.045926 CCCCCTTTCTGCCGTCTG 60.046 66.667 0.00 0.00 0.00 3.51
4176 9003 3.803231 TGCAAAGCAGCAACAACATAAAG 59.197 39.130 0.00 0.00 42.46 1.85
4180 9007 6.146021 GCAAAGCAGCAACAACATAAAGTAAT 59.854 34.615 0.00 0.00 0.00 1.89
4184 9011 6.430925 AGCAGCAACAACATAAAGTAATCAGA 59.569 34.615 0.00 0.00 0.00 3.27
4209 9036 8.039603 ACGTAATTTCAGTGAATTATCTTGCA 57.960 30.769 6.36 0.00 34.87 4.08
4239 9068 8.826710 GCATGTGTAAGCAAGTATAGTATGAAA 58.173 33.333 0.00 0.00 0.00 2.69
4254 9083 8.762481 ATAGTATGAAAAATTGGTTAGGACCC 57.238 34.615 0.00 0.00 45.92 4.46
4263 9092 1.363080 GTTAGGACCCGCCGATCTC 59.637 63.158 0.00 0.00 43.43 2.75
4267 9096 2.562876 GGACCCGCCGATCTCTACC 61.563 68.421 0.00 0.00 0.00 3.18
4278 9107 4.629204 GCCGATCTCTACCTATACCTGGAT 60.629 50.000 0.00 0.00 0.00 3.41
4279 9108 5.511363 CCGATCTCTACCTATACCTGGATT 58.489 45.833 0.00 0.00 0.00 3.01
4282 9111 7.446013 CCGATCTCTACCTATACCTGGATTATC 59.554 44.444 0.00 0.00 0.00 1.75
4283 9112 7.446013 CGATCTCTACCTATACCTGGATTATCC 59.554 44.444 3.91 3.91 36.96 2.59
4284 9113 6.982899 TCTCTACCTATACCTGGATTATCCC 58.017 44.000 8.98 0.00 35.03 3.85
4296 9125 4.721060 TGGATTATCCCCAGTGTTGGAGG 61.721 52.174 8.98 0.00 44.69 4.30
4317 9146 1.135315 CCGGACGTACAACGACGAT 59.865 57.895 17.53 0.00 46.05 3.73
4337 9166 4.473520 CCATCGGCGCTGGAACCT 62.474 66.667 24.50 0.00 35.70 3.50
4361 9190 0.671781 CAGCGGAGTTTGGAGGAGTG 60.672 60.000 0.00 0.00 0.00 3.51
4364 9193 1.481056 CGGAGTTTGGAGGAGTGGGT 61.481 60.000 0.00 0.00 0.00 4.51
4368 9197 0.476771 GTTTGGAGGAGTGGGTGGAA 59.523 55.000 0.00 0.00 0.00 3.53
4384 9219 0.169894 GGAAGTTTAGCAGCAGCAGC 59.830 55.000 3.17 0.46 45.49 5.25
4404 9239 2.674220 GGGCTTGGAGGAGTGGGAG 61.674 68.421 0.00 0.00 0.00 4.30
4405 9240 2.674220 GGCTTGGAGGAGTGGGAGG 61.674 68.421 0.00 0.00 0.00 4.30
4406 9241 1.613630 GCTTGGAGGAGTGGGAGGA 60.614 63.158 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.498056 CCCAGCACGCAACCCTTTT 61.498 57.895 0.00 0.00 0.00 2.27
84 88 0.103208 ATAGTCGCAGCGGGAAGAAG 59.897 55.000 16.42 0.00 0.00 2.85
101 105 0.655208 CAGCAACCGCAACGCATATA 59.345 50.000 0.00 0.00 42.27 0.86
117 121 1.607467 AACCATCCAACCCTGCAGC 60.607 57.895 8.66 0.00 0.00 5.25
122 126 0.560688 AACCACAACCATCCAACCCT 59.439 50.000 0.00 0.00 0.00 4.34
126 130 1.039068 CAGCAACCACAACCATCCAA 58.961 50.000 0.00 0.00 0.00 3.53
136 140 2.345760 CCATCCCTGCAGCAACCAC 61.346 63.158 8.66 0.00 0.00 4.16
212 223 2.556287 CGTGCAACCCTTTCGAGC 59.444 61.111 0.00 0.00 0.00 5.03
223 234 2.115052 AACATGGCTCCCGTGCAA 59.885 55.556 0.00 0.00 43.81 4.08
241 253 2.001872 GCAACAACCCATATGCTTTGC 58.998 47.619 12.23 10.20 35.93 3.68
248 260 0.395173 GGACCCGCAACAACCCATAT 60.395 55.000 0.00 0.00 0.00 1.78
249 261 1.001887 GGACCCGCAACAACCCATA 60.002 57.895 0.00 0.00 0.00 2.74
250 262 2.282887 GGACCCGCAACAACCCAT 60.283 61.111 0.00 0.00 0.00 4.00
251 263 3.494254 AGGACCCGCAACAACCCA 61.494 61.111 0.00 0.00 0.00 4.51
252 264 2.983592 CAGGACCCGCAACAACCC 60.984 66.667 0.00 0.00 0.00 4.11
253 265 3.670377 GCAGGACCCGCAACAACC 61.670 66.667 0.00 0.00 0.00 3.77
254 266 4.025401 CGCAGGACCCGCAACAAC 62.025 66.667 0.00 0.00 0.00 3.32
255 267 3.545124 ATCGCAGGACCCGCAACAA 62.545 57.895 0.00 0.00 0.00 2.83
256 268 3.950794 GATCGCAGGACCCGCAACA 62.951 63.158 0.00 0.00 0.00 3.33
257 269 3.195698 GATCGCAGGACCCGCAAC 61.196 66.667 0.00 0.00 0.00 4.17
258 270 2.739849 TTTGATCGCAGGACCCGCAA 62.740 55.000 0.00 0.00 0.00 4.85
259 271 3.247056 TTTGATCGCAGGACCCGCA 62.247 57.895 0.00 0.00 0.00 5.69
260 272 2.435938 TTTGATCGCAGGACCCGC 60.436 61.111 0.00 0.00 0.00 6.13
264 276 0.108804 TCCGAGTTTGATCGCAGGAC 60.109 55.000 0.00 0.00 41.37 3.85
294 306 1.956170 CGTGCGTTGACTGCCTTCT 60.956 57.895 0.00 0.00 0.00 2.85
295 307 1.772063 AACGTGCGTTGACTGCCTTC 61.772 55.000 9.27 0.00 36.91 3.46
296 308 1.817941 AACGTGCGTTGACTGCCTT 60.818 52.632 9.27 0.00 36.91 4.35
297 309 2.203015 AACGTGCGTTGACTGCCT 60.203 55.556 9.27 0.00 36.91 4.75
305 317 2.665185 GAGCTCCCAACGTGCGTT 60.665 61.111 0.87 3.97 39.13 4.84
312 324 4.475135 GAGGGCCGAGCTCCCAAC 62.475 72.222 8.47 0.00 46.36 3.77
477 489 0.394938 TCCACGTAGGCACAACATGT 59.605 50.000 0.00 0.00 37.29 3.21
479 491 3.620427 TTATCCACGTAGGCACAACAT 57.380 42.857 0.00 0.00 37.29 2.71
519 534 3.440173 AGGACTTGTAATGCGTCAATTGG 59.560 43.478 5.42 0.00 0.00 3.16
522 537 3.937814 TGAGGACTTGTAATGCGTCAAT 58.062 40.909 0.00 0.00 0.00 2.57
533 548 8.932610 ACTATCATTCTCATATTGAGGACTTGT 58.067 33.333 4.78 0.00 44.39 3.16
558 573 1.239347 GCTTGTGTCCCTTCCTCAAC 58.761 55.000 0.00 0.00 0.00 3.18
860 1116 1.800586 GCTTGAGCACGATTTGTCAGA 59.199 47.619 0.00 0.00 41.59 3.27
1155 1415 5.773176 TCATCTACTGACTACTGGACAACAA 59.227 40.000 0.00 0.00 0.00 2.83
1158 1421 5.416013 CACTCATCTACTGACTACTGGACAA 59.584 44.000 0.00 0.00 0.00 3.18
1205 1468 0.317160 GACCCTCGATGTCACACACA 59.683 55.000 9.63 0.00 40.18 3.72
1206 1469 0.389948 GGACCCTCGATGTCACACAC 60.390 60.000 14.83 0.00 34.36 3.82
1207 1470 1.541310 GGGACCCTCGATGTCACACA 61.541 60.000 2.09 0.00 36.15 3.72
1289 1552 1.078848 GATGCAGGACTTGAGGCGT 60.079 57.895 0.00 0.00 0.00 5.68
1510 1779 6.073765 ACACTACTGCAGTTCGAAAAACTATG 60.074 38.462 27.06 10.23 34.26 2.23
1511 1780 5.989777 ACACTACTGCAGTTCGAAAAACTAT 59.010 36.000 27.06 0.00 34.26 2.12
1524 2491 3.519579 CAAGGATCTGACACTACTGCAG 58.480 50.000 13.48 13.48 0.00 4.41
1651 2620 4.281182 ACCACAACAACCAAAAACTACACA 59.719 37.500 0.00 0.00 0.00 3.72
1653 2622 6.183360 GGATACCACAACAACCAAAAACTACA 60.183 38.462 0.00 0.00 0.00 2.74
1673 2642 5.796424 TTCTTAGGTAACCATCCGGATAC 57.204 43.478 18.63 11.74 39.30 2.24
1706 2675 7.093902 TGGTGTTGTCTCTAGGTAAAGTGATAG 60.094 40.741 0.00 0.00 0.00 2.08
1935 3035 6.885735 AAATTCTTAATGTAAACATGCCGC 57.114 33.333 0.00 0.00 36.56 6.53
1936 3036 7.172757 GCAAAATTCTTAATGTAAACATGCCG 58.827 34.615 0.00 0.00 36.56 5.69
2073 3463 3.498397 AGTTAAACGAGTGACCTGCATTG 59.502 43.478 0.00 0.00 0.00 2.82
2118 3508 7.148289 GCAGCATCTTATATGCATTACTGACAT 60.148 37.037 3.54 0.00 46.77 3.06
2612 4050 4.690748 TGATCAATTCGATATTTCCTCGCC 59.309 41.667 0.00 0.00 36.11 5.54
2683 4121 8.295288 CAGAGAATAAGCATTTCAACTCACTTT 58.705 33.333 0.00 0.00 0.00 2.66
2858 7254 7.676683 AATAGCTGGGATACAAGTTCTAAGA 57.323 36.000 0.00 0.00 39.74 2.10
2867 7263 3.974719 TGCCAAAATAGCTGGGATACAA 58.025 40.909 0.00 0.00 34.25 2.41
2886 7283 3.806521 AGTACATTCATCGAGAGCAATGC 59.193 43.478 0.00 0.00 30.63 3.56
2955 7364 4.881273 GGTTTTTCCAGGCTCAACAAAAAT 59.119 37.500 0.00 0.00 35.97 1.82
3080 7489 9.719355 AATAACACAGTACATCATGTTAAGTCA 57.281 29.630 0.00 0.00 40.05 3.41
3089 7498 5.175127 TGACGCAATAACACAGTACATCAT 58.825 37.500 0.00 0.00 0.00 2.45
3187 7596 6.953520 TCCCTAATGTTCATTGGTTTCTTCAT 59.046 34.615 8.11 0.00 0.00 2.57
3263 7674 1.933115 AACGGATTTGGATGCACCGC 61.933 55.000 13.54 0.00 46.18 5.68
3290 7701 4.286910 TGTACCGTCAGTTTACACGTTAC 58.713 43.478 0.00 0.00 35.24 2.50
3370 7781 4.403432 CCATGTGGCATAAACTTTCAGGAT 59.597 41.667 0.00 0.00 0.00 3.24
3397 7808 1.862008 GCAGAGGAAGAGTCGCATACG 60.862 57.143 0.00 0.00 42.01 3.06
3404 7815 3.749665 ATGCATAGCAGAGGAAGAGTC 57.250 47.619 0.00 0.00 43.65 3.36
3417 7828 8.462016 AGGCTACAAGAAAAACTAAATGCATAG 58.538 33.333 0.00 0.00 0.00 2.23
3425 7836 9.797556 GAAAGAAAAGGCTACAAGAAAAACTAA 57.202 29.630 0.00 0.00 0.00 2.24
3426 7837 8.126700 CGAAAGAAAAGGCTACAAGAAAAACTA 58.873 33.333 0.00 0.00 0.00 2.24
3547 7958 4.813027 ACATTCTAAACAAAGCAGGCATG 58.187 39.130 0.00 0.00 0.00 4.06
3585 7996 8.752187 ACTAATATAAGACGTTTTAGGTCACCA 58.248 33.333 0.00 0.00 35.60 4.17
3628 8039 2.069273 GTGTCACTCCCTCAAATGACG 58.931 52.381 0.00 0.00 43.58 4.35
3667 8078 1.218196 TGTTTAAACCCTTCCAGGCCA 59.782 47.619 15.59 0.00 32.73 5.36
3674 8085 4.684242 CGGCAAAATCTGTTTAAACCCTTC 59.316 41.667 15.59 0.00 0.00 3.46
3676 8087 3.639561 ACGGCAAAATCTGTTTAAACCCT 59.360 39.130 15.59 0.00 0.00 4.34
3679 8090 8.597227 AGTTAAAACGGCAAAATCTGTTTAAAC 58.403 29.630 11.54 11.54 42.78 2.01
3696 8107 9.678247 GAATTGGTTAAACAAACAGTTAAAACG 57.322 29.630 10.54 0.00 40.26 3.60
3736 8147 2.254152 AATCTAGTCTGGTGCCCTCA 57.746 50.000 0.00 0.00 0.00 3.86
3744 8155 6.851609 CAGTATAGCTGCTAATCTAGTCTGG 58.148 44.000 14.13 0.00 38.52 3.86
3793 8494 5.390885 CCACATGTTGAAGGATTGTTCTACG 60.391 44.000 0.00 0.00 35.65 3.51
3811 8637 7.391275 TGCATCAAGTATATGTAATCCCACATG 59.609 37.037 0.00 0.00 39.46 3.21
3814 8640 7.744087 TTGCATCAAGTATATGTAATCCCAC 57.256 36.000 0.00 0.00 0.00 4.61
3822 8648 9.881649 CCTCTACATATTGCATCAAGTATATGT 57.118 33.333 18.56 18.56 43.16 2.29
3823 8649 9.322773 CCCTCTACATATTGCATCAAGTATATG 57.677 37.037 10.80 10.80 37.13 1.78
3824 8650 8.489489 CCCCTCTACATATTGCATCAAGTATAT 58.511 37.037 0.00 0.00 0.00 0.86
3826 8652 6.715280 CCCCTCTACATATTGCATCAAGTAT 58.285 40.000 0.00 0.00 0.00 2.12
3827 8653 5.513094 GCCCCTCTACATATTGCATCAAGTA 60.513 44.000 0.00 0.00 0.00 2.24
3829 8655 3.755378 GCCCCTCTACATATTGCATCAAG 59.245 47.826 0.00 0.00 0.00 3.02
3830 8656 3.754965 GCCCCTCTACATATTGCATCAA 58.245 45.455 0.00 0.00 0.00 2.57
3831 8657 2.289631 CGCCCCTCTACATATTGCATCA 60.290 50.000 0.00 0.00 0.00 3.07
3833 8659 1.699634 ACGCCCCTCTACATATTGCAT 59.300 47.619 0.00 0.00 0.00 3.96
3834 8660 1.128200 ACGCCCCTCTACATATTGCA 58.872 50.000 0.00 0.00 0.00 4.08
3835 8661 1.512926 CACGCCCCTCTACATATTGC 58.487 55.000 0.00 0.00 0.00 3.56
3836 8662 1.878102 GCCACGCCCCTCTACATATTG 60.878 57.143 0.00 0.00 0.00 1.90
3837 8663 0.396811 GCCACGCCCCTCTACATATT 59.603 55.000 0.00 0.00 0.00 1.28
3838 8664 0.471971 AGCCACGCCCCTCTACATAT 60.472 55.000 0.00 0.00 0.00 1.78
3895 8721 1.459209 CGCGACTCATGCAACTTTGTA 59.541 47.619 0.00 0.00 0.00 2.41
3896 8722 0.235665 CGCGACTCATGCAACTTTGT 59.764 50.000 0.00 0.00 0.00 2.83
3897 8723 0.512518 TCGCGACTCATGCAACTTTG 59.487 50.000 3.71 0.00 0.00 2.77
3898 8724 0.512952 GTCGCGACTCATGCAACTTT 59.487 50.000 31.12 0.00 0.00 2.66
3899 8725 0.319900 AGTCGCGACTCATGCAACTT 60.320 50.000 34.98 10.31 36.92 2.66
3912 8738 7.017498 ACTACTATATATCATTGGAGTCGCG 57.983 40.000 0.00 0.00 0.00 5.87
3985 8811 4.523558 TGGACAACTGATGATGATTTTGCA 59.476 37.500 0.00 0.00 0.00 4.08
3988 8814 8.130671 AGAAATGGACAACTGATGATGATTTT 57.869 30.769 0.00 0.00 0.00 1.82
4001 8827 3.559655 GGGCAACAAAAGAAATGGACAAC 59.440 43.478 0.00 0.00 39.74 3.32
4004 8830 3.069443 TCTGGGCAACAAAAGAAATGGAC 59.931 43.478 0.00 0.00 39.74 4.02
4015 8842 2.691011 GTGGTTTAACTCTGGGCAACAA 59.309 45.455 0.00 0.00 39.74 2.83
4016 8843 2.303175 GTGGTTTAACTCTGGGCAACA 58.697 47.619 0.00 0.00 39.74 3.33
4017 8844 2.303175 TGTGGTTTAACTCTGGGCAAC 58.697 47.619 0.00 0.00 0.00 4.17
4021 8848 5.592104 AAAGTTTGTGGTTTAACTCTGGG 57.408 39.130 0.00 0.00 33.66 4.45
4024 8851 7.043565 TCGAGTAAAGTTTGTGGTTTAACTCT 58.956 34.615 0.00 0.00 33.66 3.24
4028 8855 8.895737 AGAATTCGAGTAAAGTTTGTGGTTTAA 58.104 29.630 0.00 0.00 0.00 1.52
4031 8858 6.937436 AGAATTCGAGTAAAGTTTGTGGTT 57.063 33.333 0.00 0.00 0.00 3.67
4063 8890 2.847327 TGCTCCTCCATGCTAATAGC 57.153 50.000 5.12 5.12 42.82 2.97
4132 8959 2.359975 GCAGAAAGGGGGACGGTG 60.360 66.667 0.00 0.00 0.00 4.94
4135 8962 3.952628 GACGGCAGAAAGGGGGACG 62.953 68.421 0.00 0.00 39.42 4.79
4155 8982 3.803778 ACTTTATGTTGTTGCTGCTTTGC 59.196 39.130 0.00 0.00 0.00 3.68
4180 9007 9.653287 AAGATAATTCACTGAAATTACGTCTGA 57.347 29.630 0.00 0.00 34.75 3.27
4184 9011 8.039603 TGCAAGATAATTCACTGAAATTACGT 57.960 30.769 0.00 0.00 34.75 3.57
4248 9077 1.528776 GTAGAGATCGGCGGGTCCT 60.529 63.158 7.21 7.99 0.00 3.85
4254 9083 2.678836 CAGGTATAGGTAGAGATCGGCG 59.321 54.545 0.00 0.00 0.00 6.46
4263 9092 5.850278 TGGGGATAATCCAGGTATAGGTAG 58.150 45.833 0.00 0.00 38.64 3.18
4297 9126 3.167945 GTCGTTGTACGTCCGGCG 61.168 66.667 15.25 15.25 43.14 6.46
4337 9166 0.603707 CTCCAAACTCCGCTGCTGAA 60.604 55.000 0.00 0.00 0.00 3.02
4361 9190 1.168714 CTGCTGCTAAACTTCCACCC 58.831 55.000 0.00 0.00 0.00 4.61
4364 9193 1.527034 CTGCTGCTGCTAAACTTCCA 58.473 50.000 17.00 0.00 40.48 3.53
4368 9197 0.959372 CCTGCTGCTGCTGCTAAACT 60.959 55.000 27.67 0.00 40.48 2.66
4384 9219 2.673523 CCACTCCTCCAAGCCCTG 59.326 66.667 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.