Multiple sequence alignment - TraesCS5A01G126900

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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 TraesCS5A01G126900 chr5A 100.000 6479 0 0 1 6479 281060496 281066974 0.000000e+00 11965.0
1 TraesCS5A01G126900 chr5B 93.722 5846 250 57 1 5781 229637319 229643112 0.000000e+00 8654.0
2 TraesCS5A01G126900 chr5B 91.021 568 48 3 5913 6479 229643694 229644259 0.000000e+00 763.0
3 TraesCS5A01G126900 chr5B 89.298 570 57 4 5913 6479 70694997 70694429 0.000000e+00 712.0
4 TraesCS5A01G126900 chr5D 95.392 4080 114 28 1723 5777 214715631 214719661 0.000000e+00 6425.0
5 TraesCS5A01G126900 chr5D 93.340 1066 46 9 607 1654 214714283 214715341 0.000000e+00 1552.0
6 TraesCS5A01G126900 chr5D 85.048 622 75 15 1 614 214713246 214713857 9.230000e-173 617.0
7 TraesCS5A01G126900 chr6D 90.702 570 49 4 5913 6479 468581921 468582489 0.000000e+00 756.0
8 TraesCS5A01G126900 chr2B 89.825 570 54 4 5913 6479 707961766 707962334 0.000000e+00 728.0
9 TraesCS5A01G126900 chr2B 78.107 338 56 13 1195 1523 582314051 582313723 1.420000e-46 198.0
10 TraesCS5A01G126900 chr7B 89.474 570 55 5 5913 6479 484274561 484273994 0.000000e+00 715.0
11 TraesCS5A01G126900 chr7D 89.085 568 58 4 5913 6477 3183030 3183596 0.000000e+00 702.0
12 TraesCS5A01G126900 chr7D 80.449 312 55 4 175 481 575078719 575078409 3.910000e-57 233.0
13 TraesCS5A01G126900 chr3A 88.947 570 59 4 5913 6479 550459402 550459970 0.000000e+00 701.0
14 TraesCS5A01G126900 chr3A 88.947 570 58 5 5913 6479 562894844 562894277 0.000000e+00 699.0
15 TraesCS5A01G126900 chr3A 81.029 311 53 5 176 481 9833431 9833122 6.490000e-60 243.0
16 TraesCS5A01G126900 chr3A 84.416 77 10 2 760 836 299529149 299529075 2.510000e-09 75.0
17 TraesCS5A01G126900 chr1B 88.772 570 60 4 5913 6479 46375758 46376326 0.000000e+00 695.0
18 TraesCS5A01G126900 chr1B 81.470 313 52 5 174 481 623240105 623240416 1.080000e-62 252.0
19 TraesCS5A01G126900 chr3D 83.974 312 44 5 175 481 63403628 63403318 1.770000e-75 294.0
20 TraesCS5A01G126900 chr3D 81.731 312 48 8 178 482 515967502 515967193 1.080000e-62 252.0
21 TraesCS5A01G126900 chr3D 83.696 184 22 5 5606 5781 579661724 579661541 4.020000e-37 167.0
22 TraesCS5A01G126900 chr1A 82.445 319 49 6 168 481 571740066 571740382 8.280000e-69 272.0
23 TraesCS5A01G126900 chr2D 80.892 314 54 6 173 481 179185697 179186009 6.490000e-60 243.0
24 TraesCS5A01G126900 chr2D 83.871 93 6 7 767 851 284573724 284573633 5.390000e-11 80.5
25 TraesCS5A01G126900 chr7A 85.401 137 20 0 5782 5918 425313996 425313860 6.770000e-30 143.0
26 TraesCS5A01G126900 chr7A 80.800 125 21 3 736 859 20051579 20051701 1.920000e-15 95.3
27 TraesCS5A01G126900 chr2A 77.869 244 44 9 4121 4359 639057055 639057293 6.770000e-30 143.0
28 TraesCS5A01G126900 chrUn 84.211 114 18 0 735 848 81694115 81694228 1.910000e-20 111.0
29 TraesCS5A01G126900 chr6A 82.353 119 19 2 735 851 532026730 532026612 1.150000e-17 102.0


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 TraesCS5A01G126900 chr5A 281060496 281066974 6478 False 11965.000000 11965 100.0000 1 6479 1 chr5A.!!$F1 6478
1 TraesCS5A01G126900 chr5B 229637319 229644259 6940 False 4708.500000 8654 92.3715 1 6479 2 chr5B.!!$F1 6478
2 TraesCS5A01G126900 chr5B 70694429 70694997 568 True 712.000000 712 89.2980 5913 6479 1 chr5B.!!$R1 566
3 TraesCS5A01G126900 chr5D 214713246 214719661 6415 False 2864.666667 6425 91.2600 1 5777 3 chr5D.!!$F1 5776
4 TraesCS5A01G126900 chr6D 468581921 468582489 568 False 756.000000 756 90.7020 5913 6479 1 chr6D.!!$F1 566
5 TraesCS5A01G126900 chr2B 707961766 707962334 568 False 728.000000 728 89.8250 5913 6479 1 chr2B.!!$F1 566
6 TraesCS5A01G126900 chr7B 484273994 484274561 567 True 715.000000 715 89.4740 5913 6479 1 chr7B.!!$R1 566
7 TraesCS5A01G126900 chr7D 3183030 3183596 566 False 702.000000 702 89.0850 5913 6477 1 chr7D.!!$F1 564
8 TraesCS5A01G126900 chr3A 550459402 550459970 568 False 701.000000 701 88.9470 5913 6479 1 chr3A.!!$F1 566
9 TraesCS5A01G126900 chr3A 562894277 562894844 567 True 699.000000 699 88.9470 5913 6479 1 chr3A.!!$R3 566
10 TraesCS5A01G126900 chr1B 46375758 46376326 568 False 695.000000 695 88.7720 5913 6479 1 chr1B.!!$F1 566

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
945 1402 0.739813 ATGCTACTCCGCGTCCAAAC 60.740 55.000 4.92 0.0 0.00 2.93 F
1810 2504 0.178964 TTGGCTTCCCCCTTGTCTTG 60.179 55.000 0.00 0.0 0.00 3.02 F
2786 3482 0.179029 AACTGAAACTGGACCCCACG 60.179 55.000 0.00 0.0 0.00 4.94 F
2844 3540 1.001378 AGCCGTTGCAAATGTCACTTC 60.001 47.619 0.00 0.0 41.13 3.01 F
4103 4824 1.005630 GGCTCGAGCTCAACTGTGT 60.006 57.895 34.46 0.0 41.70 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2786 3482 0.035458 ACACTAGCAACTCACAGGGC 59.965 55.000 0.00 0.0 0.00 5.19 R
3079 3786 2.151202 TCACAGGAAACGGAATCAAGC 58.849 47.619 0.00 0.0 0.00 4.01 R
4344 5065 0.040603 GATACGTACCGAGGAAGGCG 60.041 60.000 0.00 0.0 33.69 5.52 R
4542 5265 1.073199 AGCCCGGAAAGTCCACAAG 59.927 57.895 0.73 0.0 35.91 3.16 R
5934 7117 0.475048 TTTCTCCCCCTTTCCTCGGT 60.475 55.000 0.00 0.0 0.00 4.69 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
35 36 1.943968 GCTACCTTTGATGACGCACCA 60.944 52.381 0.00 0.00 0.00 4.17
50 52 2.969238 CCAGGTCATCGGCGATGC 60.969 66.667 37.71 31.00 39.63 3.91
133 136 0.970937 TTCTAGCAGTCCGTCCCCTG 60.971 60.000 0.00 0.00 0.00 4.45
184 187 1.561542 TGGAGAAGATTTCAGGGCTCC 59.438 52.381 0.00 0.00 41.69 4.70
258 261 7.248437 AGAAACTTTTTCTACGTTGGTTCTTG 58.752 34.615 0.00 0.00 0.00 3.02
276 279 6.779539 GGTTCTTGGATTCATAGGATTGGATT 59.220 38.462 0.00 0.00 0.00 3.01
277 280 7.040132 GGTTCTTGGATTCATAGGATTGGATTC 60.040 40.741 0.00 0.00 0.00 2.52
278 281 6.233434 TCTTGGATTCATAGGATTGGATTCG 58.767 40.000 0.00 0.00 0.00 3.34
338 341 7.397221 TCACAGAAATCTAACATCCACTTCAT 58.603 34.615 0.00 0.00 0.00 2.57
340 343 7.551974 CACAGAAATCTAACATCCACTTCATCT 59.448 37.037 0.00 0.00 0.00 2.90
395 401 5.186256 TCAAACACCCAATGCTAATCCTA 57.814 39.130 0.00 0.00 0.00 2.94
398 404 7.526041 TCAAACACCCAATGCTAATCCTATAT 58.474 34.615 0.00 0.00 0.00 0.86
426 432 1.000233 GGACATGCCACCCCAATCA 60.000 57.895 0.00 0.00 36.34 2.57
434 440 4.098914 TGCCACCCCAATCATATACTTC 57.901 45.455 0.00 0.00 0.00 3.01
436 442 3.074538 GCCACCCCAATCATATACTTCCT 59.925 47.826 0.00 0.00 0.00 3.36
441 447 7.365117 CCACCCCAATCATATACTTCCTCTATC 60.365 44.444 0.00 0.00 0.00 2.08
443 449 6.100424 CCCCAATCATATACTTCCTCTATCCC 59.900 46.154 0.00 0.00 0.00 3.85
447 453 9.480861 CAATCATATACTTCCTCTATCCCTACA 57.519 37.037 0.00 0.00 0.00 2.74
454 460 7.130681 ACTTCCTCTATCCCTACATTTTCAG 57.869 40.000 0.00 0.00 0.00 3.02
485 492 3.744940 ATCAAAGAGGCCCTCAATTGA 57.255 42.857 25.10 25.10 40.26 2.57
542 549 1.672881 GGATCTCTTGATTGTTGCCCG 59.327 52.381 0.00 0.00 32.19 6.13
563 570 6.183360 GCCCGTGTTTATTAAGATTGTTAGCT 60.183 38.462 0.00 0.00 0.00 3.32
586 593 5.204409 AGTTGTCCGTGTGTTATAGTCAA 57.796 39.130 0.00 0.00 0.00 3.18
660 1102 3.924114 TGACTGAAAAACACTCCCTCA 57.076 42.857 0.00 0.00 0.00 3.86
661 1103 4.229304 TGACTGAAAAACACTCCCTCAA 57.771 40.909 0.00 0.00 0.00 3.02
759 1201 7.959689 TTTTTGTGAATCAAATGTATGTGGG 57.040 32.000 0.00 0.00 44.15 4.61
764 1207 4.771577 TGAATCAAATGTATGTGGGCACTT 59.228 37.500 0.00 0.00 0.00 3.16
795 1238 6.019075 TGTGTTAGTTCACTCATTTCAGTTCG 60.019 38.462 0.00 0.00 38.90 3.95
855 1304 3.042059 TGTGAAGGGAGGGGTATCTAC 57.958 52.381 0.00 0.00 0.00 2.59
861 1310 5.197189 TGAAGGGAGGGGTATCTACTTTCTA 59.803 44.000 0.00 0.00 35.48 2.10
862 1311 5.077369 AGGGAGGGGTATCTACTTTCTAC 57.923 47.826 0.00 0.00 0.00 2.59
863 1312 4.140734 AGGGAGGGGTATCTACTTTCTACC 60.141 50.000 0.00 0.00 35.24 3.18
870 1319 6.608808 GGGGTATCTACTTTCTACCACAGTAA 59.391 42.308 0.00 0.00 38.55 2.24
945 1402 0.739813 ATGCTACTCCGCGTCCAAAC 60.740 55.000 4.92 0.00 0.00 2.93
1085 1553 1.004440 AGTTTCTGGAGCGGCACTC 60.004 57.895 1.45 0.00 45.45 3.51
1093 1561 3.781770 GAGCGGCACTCGGATCCTG 62.782 68.421 10.75 2.32 39.69 3.86
1603 2075 4.934602 CGCCATTAAACCAACCATCAATTT 59.065 37.500 0.00 0.00 0.00 1.82
1674 2146 3.797039 TCCCATGAGTATTTTGCTCTCG 58.203 45.455 0.00 0.00 34.30 4.04
1715 2187 2.432874 TGGAGTACGTCACATATTGGGG 59.567 50.000 0.00 0.00 0.00 4.96
1716 2188 2.224209 GGAGTACGTCACATATTGGGGG 60.224 54.545 0.00 0.00 0.00 5.40
1743 2436 7.440523 AAAATCGCATCCATCCTTAACTATC 57.559 36.000 0.00 0.00 0.00 2.08
1750 2443 3.260884 TCCATCCTTAACTATCCGATGGC 59.739 47.826 9.10 0.00 46.35 4.40
1757 2450 7.355101 TCCTTAACTATCCGATGGCTATCTAT 58.645 38.462 8.55 4.51 0.00 1.98
1758 2451 8.500238 TCCTTAACTATCCGATGGCTATCTATA 58.500 37.037 8.55 5.38 0.00 1.31
1759 2452 8.569641 CCTTAACTATCCGATGGCTATCTATAC 58.430 40.741 8.55 0.00 0.00 1.47
1795 2488 4.839668 TGTGTATACTTTGTGGTTTGGC 57.160 40.909 4.17 0.00 0.00 4.52
1802 2496 1.051556 TTTGTGGTTTGGCTTCCCCC 61.052 55.000 0.00 0.00 0.00 5.40
1810 2504 0.178964 TTGGCTTCCCCCTTGTCTTG 60.179 55.000 0.00 0.00 0.00 3.02
1811 2505 1.979155 GGCTTCCCCCTTGTCTTGC 60.979 63.158 0.00 0.00 0.00 4.01
1813 2507 1.374947 CTTCCCCCTTGTCTTGCGA 59.625 57.895 0.00 0.00 0.00 5.10
1880 2574 2.733671 TACGCGAGAGGTGTCGTCG 61.734 63.158 15.93 10.23 42.17 5.12
1908 2602 1.154413 GAACACGATGCCGCTGTTG 60.154 57.895 0.81 0.00 38.82 3.33
1972 2666 3.717400 TTCAGATAGATCACCTGCGAC 57.283 47.619 0.00 0.00 0.00 5.19
2018 2712 4.176271 ACCTAAATCCTTTGTACGTACGC 58.824 43.478 20.18 0.00 0.00 4.42
2038 2732 3.561103 CGTACGTACGTTCGTGCTA 57.439 52.632 33.95 9.72 44.13 3.49
2095 2789 7.867403 GGATTGAGATTTAGCAGAGTAGAAGAG 59.133 40.741 0.00 0.00 0.00 2.85
2130 2824 4.028993 ACGGGAGCAATTAAAGAAAGGA 57.971 40.909 0.00 0.00 0.00 3.36
2211 2905 6.077322 CCATATCCAGGAAATAATGTTGGGT 58.923 40.000 0.00 0.00 0.00 4.51
2295 2991 4.761739 CCTAGCTAACTCTCTCATCTCAGG 59.238 50.000 0.00 0.00 0.00 3.86
2308 3004 6.882656 TCTCATCTCAGGGTAAAAGATCTTG 58.117 40.000 9.17 0.00 0.00 3.02
2390 3086 0.320771 AATTCGCTGCGTTCCTGACT 60.321 50.000 22.48 0.00 0.00 3.41
2599 3295 4.788679 TGCATCTGCTACAGGTACTACTA 58.211 43.478 3.53 0.00 42.66 1.82
2600 3296 4.579340 TGCATCTGCTACAGGTACTACTAC 59.421 45.833 3.53 0.00 42.66 2.73
2603 3299 5.688814 TCTGCTACAGGTACTACTACTCA 57.311 43.478 0.00 0.00 36.02 3.41
2605 3301 6.289834 TCTGCTACAGGTACTACTACTCATC 58.710 44.000 0.00 0.00 36.02 2.92
2606 3302 5.374921 TGCTACAGGTACTACTACTCATCC 58.625 45.833 0.00 0.00 36.02 3.51
2607 3303 5.132312 TGCTACAGGTACTACTACTCATCCT 59.868 44.000 0.00 0.00 36.02 3.24
2608 3304 6.328410 TGCTACAGGTACTACTACTCATCCTA 59.672 42.308 0.00 0.00 36.02 2.94
2609 3305 6.650390 GCTACAGGTACTACTACTCATCCTAC 59.350 46.154 0.00 0.00 36.02 3.18
2610 3306 6.828307 ACAGGTACTACTACTCATCCTACT 57.172 41.667 0.00 0.00 36.02 2.57
2611 3307 7.927683 ACAGGTACTACTACTCATCCTACTA 57.072 40.000 0.00 0.00 36.02 1.82
2612 3308 7.734942 ACAGGTACTACTACTCATCCTACTAC 58.265 42.308 0.00 0.00 36.02 2.73
2745 3441 5.207768 GTGTTTTGCATGACTGTTGACTAG 58.792 41.667 0.00 0.00 0.00 2.57
2775 3471 1.593933 TGCACGACCGTTAACTGAAAC 59.406 47.619 3.84 0.00 0.00 2.78
2776 3472 1.862827 GCACGACCGTTAACTGAAACT 59.137 47.619 3.84 0.00 0.00 2.66
2786 3482 0.179029 AACTGAAACTGGACCCCACG 60.179 55.000 0.00 0.00 0.00 4.94
2844 3540 1.001378 AGCCGTTGCAAATGTCACTTC 60.001 47.619 0.00 0.00 41.13 3.01
2863 3559 9.899226 GTCACTTCACTTTTTGCTAGATTTTAT 57.101 29.630 0.00 0.00 0.00 1.40
3014 3721 4.422073 TCTGAACAAGCTTTTCTCCAGA 57.578 40.909 16.84 12.97 0.00 3.86
3079 3786 6.304624 TCTCTAGTACCCCTACATACATGTG 58.695 44.000 9.11 0.00 41.89 3.21
3111 3818 4.557301 CGTTTCCTGTGAAGTTCAAACAAC 59.443 41.667 7.25 5.98 0.00 3.32
3119 3826 4.331717 GTGAAGTTCAAACAACTCCGAGAA 59.668 41.667 7.25 0.00 0.00 2.87
3304 4011 3.650950 ATGGGCTTCTGGCGTGGT 61.651 61.111 0.00 0.00 42.94 4.16
3460 4167 4.821589 GAAGAGGTGGAGCGGCCG 62.822 72.222 24.05 24.05 40.66 6.13
3484 4191 2.189521 GACATCCCCATCGGCGTT 59.810 61.111 6.85 0.00 0.00 4.84
3808 4527 6.578023 AGCTGTATTAGAACAGGAGATTGAC 58.422 40.000 6.17 0.00 45.75 3.18
3862 4583 2.370849 TCCTTTCTACCTTTGCCTCGTT 59.629 45.455 0.00 0.00 0.00 3.85
3994 4715 5.584251 TGATCTATGTGCACGCAATTTCTTA 59.416 36.000 13.13 0.00 0.00 2.10
4085 4806 3.620374 CAGTATTTGACCTGCTACTGCTG 59.380 47.826 0.00 0.00 35.95 4.41
4102 4823 1.005748 TGGCTCGAGCTCAACTGTG 60.006 57.895 34.46 0.00 41.70 3.66
4103 4824 1.005630 GGCTCGAGCTCAACTGTGT 60.006 57.895 34.46 0.00 41.70 3.72
4104 4825 1.011451 GGCTCGAGCTCAACTGTGTC 61.011 60.000 34.46 11.99 41.70 3.67
4158 4879 1.990060 CTTCTCGGGGGCCTTCAGA 60.990 63.158 0.84 0.75 0.00 3.27
4378 5099 1.822613 TATCGCTCGCCGTCCTTCT 60.823 57.895 0.00 0.00 38.35 2.85
4542 5265 3.562635 CGACAACCTCGCCTTTCC 58.437 61.111 0.00 0.00 35.06 3.13
4655 5384 9.489084 GCAAAGGAAGTTTTAACCTGATTATTT 57.511 29.630 0.00 0.00 34.03 1.40
4682 5411 4.282068 CACGACAATGTCACTTTTCCTTG 58.718 43.478 14.24 0.00 32.09 3.61
4704 5433 7.712205 CCTTGGTTTTCTTCATTCATTTTGACT 59.288 33.333 0.00 0.00 0.00 3.41
5489 6220 0.253327 AAAACTGAGAGGATCGGGGC 59.747 55.000 0.00 0.00 42.67 5.80
5642 6375 9.945633 AAGGCTTCCCCACTTTATATTATAAAA 57.054 29.630 9.53 0.00 35.39 1.52
5703 6436 2.291465 CACACACACCCAAGACAAGATG 59.709 50.000 0.00 0.00 0.00 2.90
5722 6455 1.671054 CAAAGATGCCCGACACCGT 60.671 57.895 0.00 0.00 0.00 4.83
5732 6465 2.502093 GACACCGTCACACCACCA 59.498 61.111 0.00 0.00 32.09 4.17
5750 6483 3.562141 CACCACACCGACAAACAATAGAA 59.438 43.478 0.00 0.00 0.00 2.10
5753 6486 5.212194 CCACACCGACAAACAATAGAAAAG 58.788 41.667 0.00 0.00 0.00 2.27
5777 6510 1.671054 CGGACCACAACGAAGCCAT 60.671 57.895 0.00 0.00 0.00 4.40
5781 6514 2.267351 CCACAACGAAGCCATGCCA 61.267 57.895 0.00 0.00 0.00 4.92
5782 6515 1.210931 CACAACGAAGCCATGCCAG 59.789 57.895 0.00 0.00 0.00 4.85
5783 6516 2.180017 CAACGAAGCCATGCCAGC 59.820 61.111 0.00 0.00 0.00 4.85
5784 6517 2.282391 AACGAAGCCATGCCAGCA 60.282 55.556 0.00 0.00 0.00 4.41
5786 6519 1.870055 AACGAAGCCATGCCAGCAAG 61.870 55.000 0.00 0.00 0.00 4.01
5787 6520 2.042259 CGAAGCCATGCCAGCAAGA 61.042 57.895 0.00 0.00 0.00 3.02
5788 6521 1.381928 CGAAGCCATGCCAGCAAGAT 61.382 55.000 0.00 0.00 0.00 2.40
5803 6769 3.009916 AGCAAGATGACAAGAGTGGGAAT 59.990 43.478 0.00 0.00 0.00 3.01
5807 6773 0.770499 TGACAAGAGTGGGAATGCCA 59.230 50.000 0.00 0.00 35.15 4.92
5809 6775 0.478072 ACAAGAGTGGGAATGCCACA 59.522 50.000 25.44 0.00 40.28 4.17
5811 6777 1.270550 CAAGAGTGGGAATGCCACAAC 59.729 52.381 25.44 17.76 40.28 3.32
5812 6778 0.606401 AGAGTGGGAATGCCACAACG 60.606 55.000 25.44 0.00 40.28 4.10
5819 6785 1.228552 AATGCCACAACGGAGCCTT 60.229 52.632 0.00 0.00 36.56 4.35
5870 6836 2.429930 CGTGGGCCAGTCAAAGGA 59.570 61.111 6.40 0.00 0.00 3.36
5884 6850 1.071071 CAAAGGACCGGACAAGTGGTA 59.929 52.381 9.46 0.00 38.99 3.25
5890 6856 1.273438 ACCGGACAAGTGGTATACCCT 60.273 52.381 19.42 12.57 36.50 4.34
5960 7143 0.103337 AAAGGGGGAGAAAGGGGAGT 60.103 55.000 0.00 0.00 0.00 3.85
5966 7149 1.112950 GGAGAAAGGGGAGTAGACGG 58.887 60.000 0.00 0.00 0.00 4.79
5969 7152 3.032459 GAGAAAGGGGAGTAGACGGATT 58.968 50.000 0.00 0.00 0.00 3.01
5970 7153 3.451540 GAGAAAGGGGAGTAGACGGATTT 59.548 47.826 0.00 0.00 0.00 2.17
5975 7158 2.108970 GGGAGTAGACGGATTTGGACT 58.891 52.381 0.00 0.00 0.00 3.85
6097 7281 1.331756 GACGCATCCGAATCAGCAAAT 59.668 47.619 0.00 0.00 38.29 2.32
6268 7452 1.308069 AAATCAACTCGCAGCCGCAT 61.308 50.000 0.00 0.00 38.40 4.73
6282 7466 0.465097 CCGCATCCAAGGAAGCTCAT 60.465 55.000 13.66 0.00 36.79 2.90
6445 7632 2.579201 CAGATCCTTGTCGCCCGT 59.421 61.111 0.00 0.00 0.00 5.28
6450 7637 4.003788 CCTTGTCGCCCGTGACCT 62.004 66.667 5.97 0.00 38.11 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.550524 TGCGTCATCAAAGGTAGCTCT 59.449 47.619 0.00 0.00 0.00 4.09
35 36 2.369257 AATCGCATCGCCGATGACCT 62.369 55.000 29.82 10.24 46.29 3.85
41 42 1.882625 CTCCAAATCGCATCGCCGA 60.883 57.895 0.00 0.00 41.98 5.54
50 52 1.134946 GGTGGCATTTCCTCCAAATCG 59.865 52.381 0.00 0.00 45.69 3.34
110 113 0.889306 GGACGGACTGCTAGAAGTGT 59.111 55.000 8.55 0.00 0.00 3.55
112 115 0.971447 GGGGACGGACTGCTAGAAGT 60.971 60.000 1.84 1.84 0.00 3.01
133 136 4.327680 TCTTTCTTTCTCTAAAGCAGGCC 58.672 43.478 0.00 0.00 41.64 5.19
165 168 1.843206 AGGAGCCCTGAAATCTTCTCC 59.157 52.381 0.00 0.00 40.16 3.71
174 177 3.524095 TTGAATCAAAGGAGCCCTGAA 57.476 42.857 0.00 0.00 32.13 3.02
216 219 9.642343 AAAAGTTTCTAAGTATTTCAACCCTCT 57.358 29.630 0.00 0.00 0.00 3.69
235 238 6.151480 TCCAAGAACCAACGTAGAAAAAGTTT 59.849 34.615 0.00 0.00 0.00 2.66
238 241 5.744666 TCCAAGAACCAACGTAGAAAAAG 57.255 39.130 0.00 0.00 0.00 2.27
247 250 4.513442 TCCTATGAATCCAAGAACCAACG 58.487 43.478 0.00 0.00 0.00 4.10
249 252 5.893255 CCAATCCTATGAATCCAAGAACCAA 59.107 40.000 0.00 0.00 0.00 3.67
258 261 4.019321 TCCCGAATCCAATCCTATGAATCC 60.019 45.833 0.00 0.00 0.00 3.01
308 311 6.749118 GTGGATGTTAGATTTCTGTGAATTGC 59.251 38.462 0.00 0.00 0.00 3.56
309 312 8.048534 AGTGGATGTTAGATTTCTGTGAATTG 57.951 34.615 0.00 0.00 0.00 2.32
311 314 7.884877 TGAAGTGGATGTTAGATTTCTGTGAAT 59.115 33.333 0.00 0.00 0.00 2.57
364 370 6.128486 AGCATTGGGTGTTTGATGTCATATA 58.872 36.000 0.00 0.00 0.00 0.86
365 371 4.957954 AGCATTGGGTGTTTGATGTCATAT 59.042 37.500 0.00 0.00 0.00 1.78
366 372 4.343231 AGCATTGGGTGTTTGATGTCATA 58.657 39.130 0.00 0.00 0.00 2.15
367 373 3.167485 AGCATTGGGTGTTTGATGTCAT 58.833 40.909 0.00 0.00 0.00 3.06
410 416 3.398967 AGTATATGATTGGGGTGGCATGT 59.601 43.478 0.00 0.00 0.00 3.21
434 440 7.017056 AGGATTCTGAAAATGTAGGGATAGAGG 59.983 40.741 0.00 0.00 0.00 3.69
436 442 7.937700 AGGATTCTGAAAATGTAGGGATAGA 57.062 36.000 0.00 0.00 0.00 1.98
441 447 8.930846 ATTCATAGGATTCTGAAAATGTAGGG 57.069 34.615 0.00 0.00 35.20 3.53
454 460 4.764308 GGGCCTCTTTGATTCATAGGATTC 59.236 45.833 0.84 0.00 0.00 2.52
522 529 1.672881 CGGGCAACAATCAAGAGATCC 59.327 52.381 0.00 0.00 39.74 3.36
563 570 5.963176 TGACTATAACACACGGACAACTA 57.037 39.130 0.00 0.00 0.00 2.24
650 1092 5.880901 AGTATTTGTGAATTGAGGGAGTGT 58.119 37.500 0.00 0.00 0.00 3.55
660 1102 5.577164 CGAACGGAGAGAGTATTTGTGAATT 59.423 40.000 0.00 0.00 0.00 2.17
661 1103 5.103000 CGAACGGAGAGAGTATTTGTGAAT 58.897 41.667 0.00 0.00 0.00 2.57
748 1190 5.538433 ACACTAAAAAGTGCCCACATACATT 59.462 36.000 5.47 0.00 43.13 2.71
759 1201 6.782150 AGTGAACTAACACACTAAAAAGTGC 58.218 36.000 5.47 0.00 44.06 4.40
764 1207 9.168451 TGAAATGAGTGAACTAACACACTAAAA 57.832 29.630 0.00 0.00 45.54 1.52
821 1270 7.615757 CCCTCCCTTCACAAATATAAGAAGTTT 59.384 37.037 0.00 0.00 36.60 2.66
922 1372 1.084289 GGACGCGGAGTAGCATTTTT 58.916 50.000 12.47 0.00 36.85 1.94
1068 1536 2.383527 CGAGTGCCGCTCCAGAAAC 61.384 63.158 0.00 0.00 41.10 2.78
1085 1553 2.280389 CATGGCCGTCAGGATCCG 60.280 66.667 5.98 1.36 41.02 4.18
1093 1561 2.438434 CCCTTGTCCATGGCCGTC 60.438 66.667 6.96 0.00 0.00 4.79
1562 2034 2.479837 GCGTTATTCGGGTCATGATCA 58.520 47.619 8.54 0.00 40.26 2.92
1694 2166 2.432874 CCCCAATATGTGACGTACTCCA 59.567 50.000 0.00 0.00 0.00 3.86
1715 2187 2.310538 AGGATGGATGCGATTTTTCCC 58.689 47.619 0.00 0.00 0.00 3.97
1716 2188 5.067805 AGTTAAGGATGGATGCGATTTTTCC 59.932 40.000 0.00 0.00 0.00 3.13
1743 2436 7.255312 GGAAGATGTAGTATAGATAGCCATCGG 60.255 44.444 0.00 0.00 36.20 4.18
1757 2450 9.642343 AGTATACACATGAAGGAAGATGTAGTA 57.358 33.333 5.50 0.00 31.46 1.82
1758 2451 8.540507 AGTATACACATGAAGGAAGATGTAGT 57.459 34.615 5.50 0.00 31.46 2.73
1759 2452 9.823647 AAAGTATACACATGAAGGAAGATGTAG 57.176 33.333 5.50 0.00 31.46 2.74
1795 2488 1.374947 TCGCAAGACAAGGGGGAAG 59.625 57.895 0.00 0.00 45.01 3.46
1810 2504 1.523154 TTGGGCAACTGGACAATCGC 61.523 55.000 0.00 0.00 0.00 4.58
1811 2505 0.958091 TTTGGGCAACTGGACAATCG 59.042 50.000 0.00 0.00 0.00 3.34
1813 2507 2.485302 GCTTTTTGGGCAACTGGACAAT 60.485 45.455 0.00 0.00 0.00 2.71
1880 2574 2.452813 ATCGTGTTCATGCCGCGAC 61.453 57.895 18.68 0.00 46.17 5.19
1958 2652 1.313091 ACAGCGTCGCAGGTGATCTA 61.313 55.000 21.09 0.00 41.72 1.98
2028 2722 2.644227 TGCATACGTAGCACGAACG 58.356 52.632 14.18 7.40 46.05 3.95
2295 2991 4.378459 CGGCTGTGAACAAGATCTTTTACC 60.378 45.833 4.86 0.00 0.00 2.85
2339 3035 3.054878 CAAACAAACAATCAGCTCTGGC 58.945 45.455 0.00 0.00 39.06 4.85
2340 3036 3.054878 GCAAACAAACAATCAGCTCTGG 58.945 45.455 0.00 0.00 0.00 3.86
2341 3037 2.722629 CGCAAACAAACAATCAGCTCTG 59.277 45.455 0.00 0.00 0.00 3.35
2390 3086 1.224315 CATGATGAGGTTCGCCCCA 59.776 57.895 0.00 0.00 38.27 4.96
2599 3295 7.735326 AACAAATACTGGTAGTAGGATGAGT 57.265 36.000 0.00 0.00 33.66 3.41
2600 3296 9.099454 GAAAACAAATACTGGTAGTAGGATGAG 57.901 37.037 0.00 0.00 33.66 2.90
2603 3299 9.975218 AATGAAAACAAATACTGGTAGTAGGAT 57.025 29.630 0.00 0.00 33.66 3.24
2648 3344 8.260270 AGCAAAGCCAAAATGATTTCTTTATC 57.740 30.769 3.67 1.05 0.00 1.75
2745 3441 0.163788 CGGTCGTGCAAATCACACTC 59.836 55.000 0.00 0.00 45.92 3.51
2759 3455 2.473984 GTCCAGTTTCAGTTAACGGTCG 59.526 50.000 5.64 0.00 33.26 4.79
2767 3463 0.179029 CGTGGGGTCCAGTTTCAGTT 60.179 55.000 0.00 0.00 32.34 3.16
2786 3482 0.035458 ACACTAGCAACTCACAGGGC 59.965 55.000 0.00 0.00 0.00 5.19
2793 3489 4.815269 AGATTGACTGACACTAGCAACTC 58.185 43.478 0.00 0.00 0.00 3.01
2794 3490 4.881019 AGATTGACTGACACTAGCAACT 57.119 40.909 0.00 0.00 0.00 3.16
2829 3525 5.163874 GCAAAAAGTGAAGTGACATTTGCAA 60.164 36.000 13.56 0.00 43.38 4.08
2863 3559 5.790593 ACAACTAGAGCAAATCGAACCTTA 58.209 37.500 0.00 0.00 0.00 2.69
2908 3604 2.478894 GTCTTGCGGAACAAAATCTCGA 59.521 45.455 0.00 0.00 37.96 4.04
3014 3721 5.010415 CCCTTGTGAGATTCTTTCTTTGCTT 59.990 40.000 0.00 0.00 33.74 3.91
3079 3786 2.151202 TCACAGGAAACGGAATCAAGC 58.849 47.619 0.00 0.00 0.00 4.01
3139 3846 4.141711 TGTGCTCCTACCATGTTTCTATCC 60.142 45.833 0.00 0.00 0.00 2.59
3862 4583 1.501170 TGACCAACATCCCAAAAGGGA 59.499 47.619 5.60 5.60 42.75 4.20
3924 4645 3.929334 AAGCGTATTTGGGCCGGCA 62.929 57.895 30.85 7.96 0.00 5.69
3994 4715 9.706529 AAAGAAAAGAGAATAGGATAAAGGCAT 57.293 29.630 0.00 0.00 0.00 4.40
4085 4806 1.005630 ACACAGTTGAGCTCGAGCC 60.006 57.895 32.94 23.66 43.38 4.70
4102 4823 3.006940 TCTGAAAACACCACACACAGAC 58.993 45.455 0.00 0.00 0.00 3.51
4103 4824 3.342377 TCTGAAAACACCACACACAGA 57.658 42.857 0.00 0.00 0.00 3.41
4104 4825 3.303329 CGATCTGAAAACACCACACACAG 60.303 47.826 0.00 0.00 0.00 3.66
4344 5065 0.040603 GATACGTACCGAGGAAGGCG 60.041 60.000 0.00 0.00 33.69 5.52
4378 5099 5.946972 TGGTCAAAAGTGAAGGAAACAGTTA 59.053 36.000 0.00 0.00 34.87 2.24
4542 5265 1.073199 AGCCCGGAAAGTCCACAAG 59.927 57.895 0.73 0.00 35.91 3.16
4623 5352 6.366877 CAGGTTAAAACTTCCTTTGCATGATG 59.633 38.462 0.00 0.00 0.00 3.07
4655 5384 3.462483 AAGTGACATTGTCGTGGTACA 57.538 42.857 11.97 0.00 34.95 2.90
4732 5461 2.182030 GTCCTGCGAGGAGGAACG 59.818 66.667 14.92 0.00 46.90 3.95
5252 5981 1.167155 TCTCCTCGGCGTCATAGCTC 61.167 60.000 6.85 0.00 37.29 4.09
5489 6220 6.681777 CAAGTTCCAGGTAAAATCTCCTTTG 58.318 40.000 0.00 0.00 30.91 2.77
5655 6388 4.761235 TGTTCGGTATCTCGGATGTATC 57.239 45.455 0.00 0.00 0.00 2.24
5673 6406 1.504446 GGTGTGTGTGCGTGTTGTT 59.496 52.632 0.00 0.00 0.00 2.83
5714 6447 2.660552 GGTGGTGTGACGGTGTCG 60.661 66.667 0.00 0.00 43.02 4.35
5722 6455 1.900545 TTGTCGGTGTGGTGGTGTGA 61.901 55.000 0.00 0.00 0.00 3.58
5732 6465 5.587043 TCACTTTTCTATTGTTTGTCGGTGT 59.413 36.000 0.00 0.00 0.00 4.16
5750 6483 1.385528 GTTGTGGTCCGGTTCACTTT 58.614 50.000 22.92 0.00 35.15 2.66
5753 6486 0.810823 TTCGTTGTGGTCCGGTTCAC 60.811 55.000 18.32 18.32 34.71 3.18
5777 6510 1.072806 ACTCTTGTCATCTTGCTGGCA 59.927 47.619 0.00 0.00 0.00 4.92
5781 6514 1.980765 TCCCACTCTTGTCATCTTGCT 59.019 47.619 0.00 0.00 0.00 3.91
5782 6515 2.479566 TCCCACTCTTGTCATCTTGC 57.520 50.000 0.00 0.00 0.00 4.01
5783 6516 3.128242 GCATTCCCACTCTTGTCATCTTG 59.872 47.826 0.00 0.00 0.00 3.02
5784 6517 3.350833 GCATTCCCACTCTTGTCATCTT 58.649 45.455 0.00 0.00 0.00 2.40
5786 6519 2.019984 GGCATTCCCACTCTTGTCATC 58.980 52.381 0.00 0.00 0.00 2.92
5787 6520 1.355381 TGGCATTCCCACTCTTGTCAT 59.645 47.619 0.00 0.00 39.18 3.06
5788 6521 0.770499 TGGCATTCCCACTCTTGTCA 59.230 50.000 0.00 0.00 39.18 3.58
5803 6769 2.281484 GAAGGCTCCGTTGTGGCA 60.281 61.111 0.00 0.00 37.80 4.92
5807 6773 1.543429 CCTTTCTGAAGGCTCCGTTGT 60.543 52.381 0.00 0.00 45.59 3.32
5809 6775 3.633361 CCTTTCTGAAGGCTCCGTT 57.367 52.632 0.00 0.00 45.59 4.44
5819 6785 1.223487 GCCGCCATACCCTTTCTGA 59.777 57.895 0.00 0.00 0.00 3.27
5852 6818 3.365265 CCTTTGACTGGCCCACGC 61.365 66.667 0.00 0.00 0.00 5.34
5856 6822 2.359975 CGGTCCTTTGACTGGCCC 60.360 66.667 0.00 0.00 43.04 5.80
5870 6836 1.197812 GGGTATACCACTTGTCCGGT 58.802 55.000 23.33 0.00 39.85 5.28
5872 6838 1.138266 CCAGGGTATACCACTTGTCCG 59.862 57.143 23.33 6.10 43.89 4.79
5884 6850 2.584608 GTGTGAGCGCCAGGGTAT 59.415 61.111 2.29 0.00 0.00 2.73
5934 7117 0.475048 TTTCTCCCCCTTTCCTCGGT 60.475 55.000 0.00 0.00 0.00 4.69
5960 7143 1.271856 TGCCAGTCCAAATCCGTCTA 58.728 50.000 0.00 0.00 0.00 2.59
5966 7149 0.958822 ACGGTTTGCCAGTCCAAATC 59.041 50.000 0.00 0.00 37.09 2.17
5969 7152 2.485795 GCACGGTTTGCCAGTCCAA 61.486 57.895 0.00 0.00 46.63 3.53
5970 7153 2.904866 GCACGGTTTGCCAGTCCA 60.905 61.111 0.00 0.00 46.63 4.02
6016 7199 1.071314 TTGGTTGGAGGGATGGGTGT 61.071 55.000 0.00 0.00 0.00 4.16
6244 7428 0.179215 GCTGCGAGTTGATTTGGTCG 60.179 55.000 0.00 0.00 35.51 4.79
6268 7452 0.826715 CTCCGATGAGCTTCCTTGGA 59.173 55.000 0.00 0.00 0.00 3.53
6394 7580 2.282180 CCCTGGTTCGGGTTGGTG 60.282 66.667 0.00 0.00 39.51 4.17
6395 7581 4.280019 GCCCTGGTTCGGGTTGGT 62.280 66.667 0.00 0.00 46.47 3.67
6397 7583 2.672996 CTGCCCTGGTTCGGGTTG 60.673 66.667 0.00 0.00 46.47 3.77
6398 7584 3.966543 CCTGCCCTGGTTCGGGTT 61.967 66.667 0.00 0.00 46.47 4.11
6445 7632 2.510411 CAGTGGTGGTGCAGGTCA 59.490 61.111 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.