Multiple sequence alignment - TraesCS7B01G314100

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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 TraesCS7B01G314100 chr7B 100.000 4428 0 0 1 4428 561079730 561075303 0.000000e+00 8178.0
1 TraesCS7B01G314100 chr7A 87.814 1551 90 42 539 2023 604822336 604820819 0.000000e+00 1725.0
2 TraesCS7B01G314100 chr7A 93.548 1085 48 11 2568 3644 604820191 604819121 0.000000e+00 1596.0
3 TraesCS7B01G314100 chr7A 93.939 561 20 6 2022 2570 604820782 604820224 0.000000e+00 835.0
4 TraesCS7B01G314100 chr7A 93.309 538 22 2 3905 4428 604818612 604818075 0.000000e+00 782.0
5 TraesCS7B01G314100 chr7A 87.845 543 29 17 1 538 724320318 724320828 1.760000e-168 603.0
6 TraesCS7B01G314100 chr7A 83.146 267 20 9 3636 3879 604819095 604818831 2.070000e-53 220.0
7 TraesCS7B01G314100 chr7D 90.653 1241 78 19 790 2024 524865951 524864743 0.000000e+00 1615.0
8 TraesCS7B01G314100 chr7D 92.448 1099 56 13 2568 3644 524864116 524863023 0.000000e+00 1544.0
9 TraesCS7B01G314100 chr7D 91.577 558 33 3 2026 2570 524864705 524864149 0.000000e+00 758.0
10 TraesCS7B01G314100 chr7D 83.990 381 48 10 159 537 15116557 15116188 1.960000e-93 353.0
11 TraesCS7B01G314100 chr2D 88.390 913 73 12 1124 2024 52490320 52491211 0.000000e+00 1068.0
12 TraesCS7B01G314100 chr2D 86.848 441 22 9 1 437 101689589 101689997 1.120000e-125 460.0
13 TraesCS7B01G314100 chr1B 88.326 908 67 16 1133 2024 623628683 623627799 0.000000e+00 1053.0
14 TraesCS7B01G314100 chr3B 87.419 922 64 22 1133 2024 699799420 699798521 0.000000e+00 1013.0
15 TraesCS7B01G314100 chr3B 90.253 554 38 11 1 549 32795246 32794704 0.000000e+00 710.0
16 TraesCS7B01G314100 chr3B 83.750 240 23 8 2027 2252 699798481 699798244 3.470000e-51 213.0
17 TraesCS7B01G314100 chr5B 86.413 920 69 25 1133 2024 321527374 321526483 0.000000e+00 955.0
18 TraesCS7B01G314100 chr5B 88.312 693 56 15 1339 2024 222726205 222726879 0.000000e+00 808.0
19 TraesCS7B01G314100 chr5B 85.833 240 21 7 2026 2252 222726918 222727157 4.420000e-60 243.0
20 TraesCS7B01G314100 chr5B 84.167 240 22 9 2027 2252 321526443 321526206 7.460000e-53 219.0
21 TraesCS7B01G314100 chr5B 83.125 160 22 2 1177 1336 222724620 222724774 1.660000e-29 141.0
22 TraesCS7B01G314100 chr2A 89.098 532 39 10 4 531 730034853 730035369 1.040000e-180 643.0
23 TraesCS7B01G314100 chr2A 88.393 448 34 9 4 448 103095663 103096095 1.410000e-144 523.0
24 TraesCS7B01G314100 chr3A 88.376 542 26 11 1 537 47090690 47091199 6.290000e-173 617.0
25 TraesCS7B01G314100 chr3A 87.840 551 30 13 1 546 194187723 194187205 2.930000e-171 612.0
26 TraesCS7B01G314100 chr3A 86.933 551 35 11 1 546 194214694 194214176 6.380000e-163 584.0
27 TraesCS7B01G314100 chr5A 87.523 545 29 13 2 541 527342782 527343292 1.060000e-165 593.0
28 TraesCS7B01G314100 chr2B 86.827 539 33 15 4 537 707021845 707021340 6.430000e-158 568.0
29 TraesCS7B01G314100 chr6D 83.712 528 45 20 4 516 414500641 414500140 1.120000e-125 460.0
30 TraesCS7B01G314100 chr1A 85.407 418 25 15 1 414 440146496 440146881 6.900000e-108 401.0
31 TraesCS7B01G314100 chr4A 93.981 216 13 0 1809 2024 201125340 201125555 1.190000e-85 327.0
32 TraesCS7B01G314100 chr4A 93.981 216 13 0 1809 2024 204661519 204661734 1.190000e-85 327.0
33 TraesCS7B01G314100 chr4A 85.246 244 22 9 2022 2252 201125591 201125833 5.720000e-59 239.0
34 TraesCS7B01G314100 chr4A 85.246 244 22 3 2022 2252 204405453 204405211 5.720000e-59 239.0
35 TraesCS7B01G314100 chr4A 85.246 244 22 3 2022 2252 204661773 204662015 5.720000e-59 239.0
36 TraesCS7B01G314100 chr4A 84.836 244 23 9 2022 2252 223341980 223342222 2.660000e-57 233.0
37 TraesCS7B01G314100 chr4A 84.937 239 22 9 2022 2247 203910666 203910903 3.440000e-56 230.0
38 TraesCS7B01G314100 chrUn 84.836 244 23 8 2022 2252 196191132 196190890 2.660000e-57 233.0
39 TraesCS7B01G314100 chr3D 88.136 59 5 2 3905 3962 294603970 294604027 7.950000e-08 69.4


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 TraesCS7B01G314100 chr7B 561075303 561079730 4427 True 8178.000000 8178 100.000000 1 4428 1 chr7B.!!$R1 4427
1 TraesCS7B01G314100 chr7A 604818075 604822336 4261 True 1031.600000 1725 90.351200 539 4428 5 chr7A.!!$R1 3889
2 TraesCS7B01G314100 chr7A 724320318 724320828 510 False 603.000000 603 87.845000 1 538 1 chr7A.!!$F1 537
3 TraesCS7B01G314100 chr7D 524863023 524865951 2928 True 1305.666667 1615 91.559333 790 3644 3 chr7D.!!$R2 2854
4 TraesCS7B01G314100 chr2D 52490320 52491211 891 False 1068.000000 1068 88.390000 1124 2024 1 chr2D.!!$F1 900
5 TraesCS7B01G314100 chr1B 623627799 623628683 884 True 1053.000000 1053 88.326000 1133 2024 1 chr1B.!!$R1 891
6 TraesCS7B01G314100 chr3B 32794704 32795246 542 True 710.000000 710 90.253000 1 549 1 chr3B.!!$R1 548
7 TraesCS7B01G314100 chr3B 699798244 699799420 1176 True 613.000000 1013 85.584500 1133 2252 2 chr3B.!!$R2 1119
8 TraesCS7B01G314100 chr5B 321526206 321527374 1168 True 587.000000 955 85.290000 1133 2252 2 chr5B.!!$R1 1119
9 TraesCS7B01G314100 chr5B 222724620 222727157 2537 False 397.333333 808 85.756667 1177 2252 3 chr5B.!!$F1 1075
10 TraesCS7B01G314100 chr2A 730034853 730035369 516 False 643.000000 643 89.098000 4 531 1 chr2A.!!$F2 527
11 TraesCS7B01G314100 chr3A 47090690 47091199 509 False 617.000000 617 88.376000 1 537 1 chr3A.!!$F1 536
12 TraesCS7B01G314100 chr3A 194187205 194187723 518 True 612.000000 612 87.840000 1 546 1 chr3A.!!$R1 545
13 TraesCS7B01G314100 chr3A 194214176 194214694 518 True 584.000000 584 86.933000 1 546 1 chr3A.!!$R2 545
14 TraesCS7B01G314100 chr5A 527342782 527343292 510 False 593.000000 593 87.523000 2 541 1 chr5A.!!$F1 539
15 TraesCS7B01G314100 chr2B 707021340 707021845 505 True 568.000000 568 86.827000 4 537 1 chr2B.!!$R1 533
16 TraesCS7B01G314100 chr6D 414500140 414500641 501 True 460.000000 460 83.712000 4 516 1 chr6D.!!$R1 512

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
755 797 0.108019 AGGTTCAGGGTCGTTTGGAC 59.892 55.000 0.00 0.00 45.31 4.02 F
1065 1128 0.319555 TTCGTTCTCACCCAGCTTCG 60.320 55.000 0.00 0.00 0.00 3.79 F
1441 2941 0.612453 TCCATGCTTGCATGCCTTCA 60.612 50.000 25.12 10.20 0.00 3.02 F
1524 3058 1.065102 GCTATCGTCTGACGGCAAGTA 59.935 52.381 27.69 9.74 42.81 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2024 3584 1.001181 ACGCTGCAAATTGCTTCCAAT 59.999 42.857 19.34 0.00 45.31 3.16 R
2860 4513 0.655915 TGCGACAAAAATGACGTGCG 60.656 50.000 0.00 0.00 0.00 5.34 R
3259 4920 0.918983 TGCTTGGAAGGGGGTATGAG 59.081 55.000 0.00 0.00 0.00 2.90 R
3480 5141 1.153597 TGTGCTGAACGTCACTGCAG 61.154 55.000 20.68 13.48 41.31 4.41 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
58 59 9.899661 AGCACATACACCTCTAATTTAAACATA 57.100 29.630 0.00 0.00 0.00 2.29
99 100 8.964476 TCTTATTTCCATCTACCATGAAAGAC 57.036 34.615 0.00 0.00 0.00 3.01
132 134 3.404899 AGAAGAGGATCCGTCGACTATC 58.595 50.000 14.70 15.28 33.66 2.08
208 214 3.570125 TCAGCTCAGGGACATTATACTCG 59.430 47.826 0.00 0.00 0.00 4.18
233 240 0.678950 ACCAAGGTCCCAAAAATGCG 59.321 50.000 0.00 0.00 0.00 4.73
356 386 2.428171 TGGCAGGATCTTAAGCAATTGC 59.572 45.455 23.05 23.05 42.49 3.56
376 406 3.189702 TGCTTGTCATGTCATGTCATGTG 59.810 43.478 25.46 17.13 43.70 3.21
609 648 0.814010 AGTGTGCACAACGAACCCTC 60.814 55.000 23.59 5.59 0.00 4.30
619 658 4.329545 GAACCCTCGCAGCACCCA 62.330 66.667 0.00 0.00 0.00 4.51
620 659 3.842925 GAACCCTCGCAGCACCCAA 62.843 63.158 0.00 0.00 0.00 4.12
663 702 5.536161 TGCTTCTTCTTTGCACTTTCCTAAT 59.464 36.000 0.00 0.00 0.00 1.73
671 710 8.691661 TCTTTGCACTTTCCTAATTAGAGTTT 57.308 30.769 14.28 0.00 0.00 2.66
683 722 9.462606 TCCTAATTAGAGTTTCTCAATTTTCCC 57.537 33.333 14.28 0.00 32.06 3.97
755 797 0.108019 AGGTTCAGGGTCGTTTGGAC 59.892 55.000 0.00 0.00 45.31 4.02
903 966 3.839432 CGGTCGCTCCTCCTTCCC 61.839 72.222 0.00 0.00 0.00 3.97
1046 1109 3.657038 TACGCGGCCTCCCTCTCTT 62.657 63.158 12.47 0.00 0.00 2.85
1047 1110 3.775654 CGCGGCCTCCCTCTCTTT 61.776 66.667 0.00 0.00 0.00 2.52
1049 1112 2.496817 CGGCCTCCCTCTCTTTCG 59.503 66.667 0.00 0.00 0.00 3.46
1056 1119 2.094442 CCTCCCTCTCTTTCGTTCTCAC 60.094 54.545 0.00 0.00 0.00 3.51
1065 1128 0.319555 TTCGTTCTCACCCAGCTTCG 60.320 55.000 0.00 0.00 0.00 3.79
1175 1243 1.616628 GAAGGCCAAGGAGGAGGGA 60.617 63.158 5.01 0.00 41.22 4.20
1262 1332 1.079127 CTCAACCCAATCGGCTCGT 60.079 57.895 0.00 0.00 33.26 4.18
1417 2916 4.025396 CAGGTATTAGCATGCTCAGTTTCG 60.025 45.833 26.57 5.78 0.00 3.46
1435 2935 1.069090 GCCCATCCATGCTTGCATG 59.931 57.895 23.99 23.99 0.00 4.06
1440 2940 0.750850 ATCCATGCTTGCATGCCTTC 59.249 50.000 25.12 4.18 0.00 3.46
1441 2941 0.612453 TCCATGCTTGCATGCCTTCA 60.612 50.000 25.12 10.20 0.00 3.02
1446 2946 1.203758 TGCTTGCATGCCTTCATTCAG 59.796 47.619 20.65 0.00 28.17 3.02
1524 3058 1.065102 GCTATCGTCTGACGGCAAGTA 59.935 52.381 27.69 9.74 42.81 2.24
1731 3267 2.037772 GCGGAAGTGGTGAGATGGATAT 59.962 50.000 0.00 0.00 0.00 1.63
1732 3268 3.495100 GCGGAAGTGGTGAGATGGATATT 60.495 47.826 0.00 0.00 0.00 1.28
1733 3269 4.060900 CGGAAGTGGTGAGATGGATATTG 58.939 47.826 0.00 0.00 0.00 1.90
1736 3272 5.222007 GGAAGTGGTGAGATGGATATTGGAT 60.222 44.000 0.00 0.00 0.00 3.41
1737 3273 6.013379 GGAAGTGGTGAGATGGATATTGGATA 60.013 42.308 0.00 0.00 0.00 2.59
1738 3274 6.617782 AGTGGTGAGATGGATATTGGATAG 57.382 41.667 0.00 0.00 0.00 2.08
1739 3275 6.326161 AGTGGTGAGATGGATATTGGATAGA 58.674 40.000 0.00 0.00 0.00 1.98
1740 3276 6.212388 AGTGGTGAGATGGATATTGGATAGAC 59.788 42.308 0.00 0.00 0.00 2.59
1744 3280 7.310921 GGTGAGATGGATATTGGATAGACACAT 60.311 40.741 0.00 0.00 0.00 3.21
2135 3733 8.649973 TTAAAATGTTTACTTTCGGTGCAATT 57.350 26.923 0.00 0.00 0.00 2.32
2136 3734 9.745880 TTAAAATGTTTACTTTCGGTGCAATTA 57.254 25.926 0.00 0.00 0.00 1.40
2151 3751 9.915629 TCGGTGCAATTACTTATTTGTATTTTT 57.084 25.926 0.00 0.00 0.00 1.94
2179 3779 8.415950 TTGTACATTGGACCATTTTTACTCAT 57.584 30.769 0.00 0.00 0.00 2.90
2180 3780 8.415950 TGTACATTGGACCATTTTTACTCATT 57.584 30.769 0.00 0.00 0.00 2.57
2182 3782 6.620678 ACATTGGACCATTTTTACTCATTCG 58.379 36.000 0.00 0.00 0.00 3.34
2190 3802 5.343058 CCATTTTTACTCATTCGTTGCTGTG 59.657 40.000 0.00 0.00 0.00 3.66
2527 4139 3.784701 TCGAGGAAGTTAGTCATCAGC 57.215 47.619 0.00 0.00 0.00 4.26
2543 4155 6.040166 AGTCATCAGCTTTCATGTGTCTTTTT 59.960 34.615 0.00 0.00 0.00 1.94
2624 4272 8.801715 ATTGCTACAATTTTACACTCTGTTTG 57.198 30.769 0.00 0.00 0.00 2.93
2654 4302 7.944729 AGTGGCATTTAACTTACTGATTCAT 57.055 32.000 0.00 0.00 0.00 2.57
2670 4318 6.110543 TGATTCATTCTAGATGTTTGCACG 57.889 37.500 0.00 0.00 0.00 5.34
2689 4337 3.562141 CACGAGGTGTTTATGTGGAAACA 59.438 43.478 0.00 0.00 44.89 2.83
2798 4446 3.767673 ACTCAAGTATCGGTAAGCCTTCA 59.232 43.478 0.00 0.00 0.00 3.02
2799 4447 4.113354 CTCAAGTATCGGTAAGCCTTCAC 58.887 47.826 0.00 0.00 0.00 3.18
2816 4465 5.248640 CCTTCACTGCTTAAAGGAGAATGA 58.751 41.667 0.00 0.00 41.78 2.57
2821 4470 5.702670 CACTGCTTAAAGGAGAATGAGTCAA 59.297 40.000 0.00 0.00 35.49 3.18
2853 4506 6.378280 CCTTTTGTATGTCTGCCTATTTTCCT 59.622 38.462 0.00 0.00 0.00 3.36
2860 4513 9.372369 GTATGTCTGCCTATTTTCCTATATGAC 57.628 37.037 0.00 0.00 0.00 3.06
2861 4514 6.455647 TGTCTGCCTATTTTCCTATATGACG 58.544 40.000 0.00 0.00 0.00 4.35
2934 4590 8.301720 GCATTGATAATATTTCCTGCTTGATGA 58.698 33.333 0.00 0.00 0.00 2.92
3080 4741 1.072015 CTCCTTCTGGGGCTGATGATC 59.928 57.143 0.00 0.00 35.33 2.92
3144 4805 7.170828 GCTGAACGTATGATACATGATACCAAA 59.829 37.037 0.00 0.00 0.00 3.28
3229 4890 1.244019 ACATCCCGTTTCTGGCTTGC 61.244 55.000 0.00 0.00 0.00 4.01
3232 4893 2.978010 CCGTTTCTGGCTTGCGGT 60.978 61.111 0.00 0.00 37.87 5.68
3259 4920 2.285154 CGGTTACGATTCAGACCGC 58.715 57.895 8.83 0.00 46.93 5.68
3271 4932 1.003051 AGACCGCTCATACCCCCTT 59.997 57.895 0.00 0.00 0.00 3.95
3274 4935 2.070039 CCGCTCATACCCCCTTCCA 61.070 63.158 0.00 0.00 0.00 3.53
3346 5007 1.247419 CCCCGCCATACAAAACTGCA 61.247 55.000 0.00 0.00 0.00 4.41
3399 5060 2.806434 TGGCACAGATACCAGCAAATT 58.194 42.857 0.00 0.00 0.00 1.82
3406 5067 6.261826 GCACAGATACCAGCAAATTATCTCTT 59.738 38.462 0.00 0.00 31.46 2.85
3413 5074 3.633986 CAGCAAATTATCTCTTGACCCCC 59.366 47.826 0.00 0.00 0.00 5.40
3418 5079 4.946160 ATTATCTCTTGACCCCCAAACA 57.054 40.909 0.00 0.00 33.76 2.83
3430 5091 4.683643 ACCCCCAAACAACATTATAGCTT 58.316 39.130 0.00 0.00 0.00 3.74
3434 5095 5.343249 CCCAAACAACATTATAGCTTCAGC 58.657 41.667 0.00 0.00 42.49 4.26
3486 5147 3.827008 ACATATGAATCGTCCTGCAGT 57.173 42.857 13.81 0.00 0.00 4.40
3571 5232 4.913335 ATCTTGAAGGCAATAGCATGTG 57.087 40.909 0.00 0.00 44.61 3.21
3648 5349 7.217200 TGTAATGAACTATAAGCCTGGATCAC 58.783 38.462 0.00 0.00 0.00 3.06
3664 5365 4.941263 TGGATCACCATTGTAGTACTTTGC 59.059 41.667 0.00 0.00 41.77 3.68
3673 5374 3.735591 TGTAGTACTTTGCCTTGTGGTC 58.264 45.455 0.00 0.00 35.27 4.02
3696 5397 8.695456 GGTCATTTCTGGTATTTTCCATATTGT 58.305 33.333 0.00 0.00 36.84 2.71
3701 5402 7.801716 TCTGGTATTTTCCATATTGTACTGC 57.198 36.000 0.00 0.00 36.84 4.40
3709 5410 4.116961 TCCATATTGTACTGCGTGTAAGC 58.883 43.478 0.00 0.00 32.25 3.09
3710 5411 3.060540 CCATATTGTACTGCGTGTAAGCG 60.061 47.826 0.00 0.00 40.67 4.68
3754 5476 8.164153 CGGTGCTTTATGAGAAATTCAAAAATG 58.836 33.333 0.00 0.00 39.77 2.32
3802 5524 8.049117 TGATTATTAAGCAATGTGAAGGAGAGT 58.951 33.333 0.00 0.00 0.00 3.24
3805 5527 1.701847 AGCAATGTGAAGGAGAGTGGT 59.298 47.619 0.00 0.00 0.00 4.16
3806 5528 2.906389 AGCAATGTGAAGGAGAGTGGTA 59.094 45.455 0.00 0.00 0.00 3.25
3813 5535 4.104102 TGTGAAGGAGAGTGGTAATTTGGT 59.896 41.667 0.00 0.00 0.00 3.67
3819 5541 2.042979 AGAGTGGTAATTTGGTGCCCAT 59.957 45.455 0.00 0.00 31.53 4.00
3831 5553 2.313342 TGGTGCCCATGGGTATAAAAGT 59.687 45.455 31.58 0.00 37.65 2.66
3842 5565 9.031537 CCATGGGTATAAAAGTAACCTTTCTTT 57.968 33.333 2.85 0.00 40.01 2.52
3859 5582 3.843422 TCTTTTTCCTCAAGCCCAATCA 58.157 40.909 0.00 0.00 0.00 2.57
3879 5603 5.779241 TCATTCCATTTGAACTACCCTCT 57.221 39.130 0.00 0.00 35.31 3.69
3881 5605 6.889198 TCATTCCATTTGAACTACCCTCTAG 58.111 40.000 0.00 0.00 35.31 2.43
3883 5607 5.677319 TCCATTTGAACTACCCTCTAGTG 57.323 43.478 0.00 0.00 0.00 2.74
3888 5800 4.122337 TGAACTACCCTCTAGTGGACAA 57.878 45.455 12.54 0.00 0.00 3.18
3928 5846 7.704899 GCTACTGTTGTTTTTCAATACTTTGGT 59.295 33.333 0.00 0.00 38.38 3.67
4075 5993 2.283966 ACGAGCTGCCCAGGTAGT 60.284 61.111 7.30 7.30 39.57 2.73
4099 6017 0.671781 CCAGCAGACCTTGGAGAACG 60.672 60.000 0.00 0.00 0.00 3.95
4127 6045 2.553086 CTGCACACAAAATTGTTGCCT 58.447 42.857 20.34 0.00 40.81 4.75
4144 6062 1.545428 GCCTTTCAGTGATGGGTGTCA 60.545 52.381 12.74 0.00 0.00 3.58
4181 6099 0.828677 AGGAATAGCCACGGTGGTAC 59.171 55.000 26.86 12.41 40.46 3.34
4242 6173 1.067693 TCATGCGAGCAAACTGTACG 58.932 50.000 0.57 0.00 0.00 3.67
4247 6178 1.059264 GCGAGCAAACTGTACGATGTC 59.941 52.381 0.00 0.00 0.00 3.06
4338 6269 3.825328 CCAGGGGGAATTGTCAGATAAG 58.175 50.000 0.00 0.00 35.59 1.73
4347 6278 6.016777 GGGAATTGTCAGATAAGCATTAGTGG 60.017 42.308 0.00 0.00 31.76 4.00
4360 6291 4.396166 AGCATTAGTGGTACTTCATGTTGC 59.604 41.667 0.00 0.00 33.52 4.17
4361 6292 4.727734 GCATTAGTGGTACTTCATGTTGCG 60.728 45.833 0.00 0.00 0.00 4.85
4362 6293 2.543777 AGTGGTACTTCATGTTGCGT 57.456 45.000 0.00 0.00 0.00 5.24
4373 6304 7.393551 ACTTCATGTTGCGTTGAAAAATAAG 57.606 32.000 0.00 0.00 31.85 1.73
4401 6332 2.867647 GCCTTTGTTCATCAGGCAAACC 60.868 50.000 14.74 0.00 44.42 3.27
4412 6343 2.557924 TCAGGCAAACCACATGTGATTC 59.442 45.455 27.46 5.20 39.06 2.52
4415 6346 2.486203 GGCAAACCACATGTGATTCGTA 59.514 45.455 27.46 0.00 35.26 3.43
4416 6347 3.057876 GGCAAACCACATGTGATTCGTAA 60.058 43.478 27.46 0.00 35.26 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 9.396022 GTCTTTCATGGTAGATGGAAATAAGAA 57.604 33.333 0.00 0.00 0.00 2.52
74 75 8.548025 TGTCTTTCATGGTAGATGGAAATAAGA 58.452 33.333 0.00 0.00 0.00 2.10
75 76 8.616076 GTGTCTTTCATGGTAGATGGAAATAAG 58.384 37.037 0.00 0.00 0.00 1.73
99 100 6.039941 ACGGATCCTCTTCTTGTATCTTAGTG 59.960 42.308 10.75 0.00 0.00 2.74
132 134 3.064207 TGAACCGAAGATTTGGAAGTCG 58.936 45.455 5.83 0.00 35.58 4.18
208 214 3.808218 TTGGGACCTTGGTGCAGGC 62.808 63.158 13.10 0.00 37.47 4.85
233 240 7.337942 ACCAGTATCTTCATCATCTTTTTCACC 59.662 37.037 0.00 0.00 0.00 4.02
278 308 0.177836 TACTGTCATCATGGTGGCCG 59.822 55.000 8.37 3.96 0.00 6.13
284 314 2.540515 GGTCGTGTACTGTCATCATGG 58.459 52.381 0.00 0.00 0.00 3.66
289 319 0.609957 TCCCGGTCGTGTACTGTCAT 60.610 55.000 0.00 0.00 31.96 3.06
362 392 4.127566 TCGACATCACATGACATGACAT 57.872 40.909 22.19 4.76 0.00 3.06
363 393 3.591196 TCGACATCACATGACATGACA 57.409 42.857 22.19 7.88 0.00 3.58
364 394 3.867493 ACATCGACATCACATGACATGAC 59.133 43.478 22.19 0.00 0.00 3.06
365 395 4.127566 ACATCGACATCACATGACATGA 57.872 40.909 22.19 1.41 0.00 3.07
366 396 4.805192 TGTACATCGACATCACATGACATG 59.195 41.667 14.02 14.02 0.00 3.21
376 406 2.459934 TGCATCGTGTACATCGACATC 58.540 47.619 18.33 12.42 40.07 3.06
568 607 6.478673 CACTGGTTTAATGGAAAAGTGGTTTC 59.521 38.462 0.00 0.00 44.31 2.78
572 611 5.288804 CACACTGGTTTAATGGAAAAGTGG 58.711 41.667 0.00 0.00 39.02 4.00
591 630 1.647084 GAGGGTTCGTTGTGCACAC 59.353 57.895 21.56 13.79 0.00 3.82
609 648 4.389576 GCGTCTTTGGGTGCTGCG 62.390 66.667 0.00 0.00 0.00 5.18
610 649 4.043200 GGCGTCTTTGGGTGCTGC 62.043 66.667 0.00 0.00 0.00 5.25
616 655 3.741476 GCTGCTGGCGTCTTTGGG 61.741 66.667 0.00 0.00 0.00 4.12
617 656 1.026182 TATGCTGCTGGCGTCTTTGG 61.026 55.000 0.00 0.00 45.43 3.28
618 657 1.019673 ATATGCTGCTGGCGTCTTTG 58.980 50.000 0.00 0.00 45.43 2.77
619 658 1.019673 CATATGCTGCTGGCGTCTTT 58.980 50.000 0.00 0.00 45.43 2.52
620 659 0.107508 ACATATGCTGCTGGCGTCTT 60.108 50.000 1.58 0.00 45.43 3.01
658 697 9.467796 AGGGAAAATTGAGAAACTCTAATTAGG 57.532 33.333 12.54 6.10 0.00 2.69
712 751 9.887406 CCTAGCAAAGTTTTATTTTTCGTTCTA 57.113 29.630 0.00 0.00 0.00 2.10
715 754 8.936070 AACCTAGCAAAGTTTTATTTTTCGTT 57.064 26.923 0.00 0.00 0.00 3.85
716 755 8.192110 TGAACCTAGCAAAGTTTTATTTTTCGT 58.808 29.630 0.00 0.00 0.00 3.85
717 756 8.568732 TGAACCTAGCAAAGTTTTATTTTTCG 57.431 30.769 0.00 0.00 0.00 3.46
718 757 8.978539 CCTGAACCTAGCAAAGTTTTATTTTTC 58.021 33.333 0.00 0.00 0.00 2.29
719 758 7.931407 CCCTGAACCTAGCAAAGTTTTATTTTT 59.069 33.333 0.00 0.00 0.00 1.94
720 759 7.070696 ACCCTGAACCTAGCAAAGTTTTATTTT 59.929 33.333 0.00 0.00 0.00 1.82
721 760 6.553476 ACCCTGAACCTAGCAAAGTTTTATTT 59.447 34.615 0.00 0.00 0.00 1.40
722 761 6.075315 ACCCTGAACCTAGCAAAGTTTTATT 58.925 36.000 0.00 0.00 0.00 1.40
724 763 5.056553 ACCCTGAACCTAGCAAAGTTTTA 57.943 39.130 0.00 0.00 0.00 1.52
737 779 2.625375 GTCCAAACGACCCTGAACC 58.375 57.895 0.00 0.00 35.23 3.62
755 797 0.462759 GCCCGTTCTCTTGAGATGGG 60.463 60.000 23.34 23.34 37.10 4.00
847 910 1.153745 GCGGGTAGTCTGTCTGCTG 60.154 63.158 0.00 0.00 0.00 4.41
899 962 3.467226 GGAGATGACGGCGGGGAA 61.467 66.667 13.24 0.00 0.00 3.97
903 966 1.951130 CGATTGGAGATGACGGCGG 60.951 63.158 13.24 0.00 0.00 6.13
1046 1109 0.319555 CGAAGCTGGGTGAGAACGAA 60.320 55.000 0.00 0.00 0.00 3.85
1047 1110 1.289066 CGAAGCTGGGTGAGAACGA 59.711 57.895 0.00 0.00 0.00 3.85
1402 2900 2.042831 GGGCGAAACTGAGCATGCT 61.043 57.895 22.92 22.92 34.54 3.79
1417 2916 3.546009 ATGCAAGCATGGATGGGC 58.454 55.556 6.76 0.00 36.11 5.36
1435 2935 4.637534 TGAGATAAGCAACTGAATGAAGGC 59.362 41.667 0.00 0.00 0.00 4.35
1440 2940 5.203370 GCGATTGAGATAAGCAACTGAATG 58.797 41.667 0.00 0.00 0.00 2.67
1441 2941 4.877823 TGCGATTGAGATAAGCAACTGAAT 59.122 37.500 0.00 0.00 34.66 2.57
1524 3058 1.162698 TCGCACTGACGCTACTACTT 58.837 50.000 0.00 0.00 0.00 2.24
1582 3118 6.538742 GGTATAAGCAGAGCACAGAAACAATA 59.461 38.462 0.00 0.00 0.00 1.90
2024 3584 1.001181 ACGCTGCAAATTGCTTCCAAT 59.999 42.857 19.34 0.00 45.31 3.16
2042 3640 6.918892 TTTGGACAATGTATCTTATGGACG 57.081 37.500 0.00 0.00 0.00 4.79
2157 3757 7.392113 ACGAATGAGTAAAAATGGTCCAATGTA 59.608 33.333 0.00 0.00 0.00 2.29
2179 3779 4.623002 TCTACAACATACACAGCAACGAA 58.377 39.130 0.00 0.00 0.00 3.85
2180 3780 4.245845 TCTACAACATACACAGCAACGA 57.754 40.909 0.00 0.00 0.00 3.85
2182 3782 5.924475 AGTTCTACAACATACACAGCAAC 57.076 39.130 0.00 0.00 34.60 4.17
2190 3802 8.866956 GTTACACCATGTAGTTCTACAACATAC 58.133 37.037 15.16 5.81 33.92 2.39
2252 3864 4.874970 ACTAAGCCAATGAAAACTGCAAG 58.125 39.130 0.00 0.00 42.29 4.01
2505 4117 4.047822 GCTGATGACTAACTTCCTCGATG 58.952 47.826 0.00 0.00 0.00 3.84
2550 4162 9.944376 ACTTAAGAGACTATTTGTAATCAAGCA 57.056 29.630 10.09 0.00 34.88 3.91
2570 4182 6.504398 TGACAACTCTACTGTGACACTTAAG 58.496 40.000 7.20 0.00 0.00 1.85
2572 4184 6.264518 TCATGACAACTCTACTGTGACACTTA 59.735 38.462 7.20 0.00 0.00 2.24
2573 4185 5.069119 TCATGACAACTCTACTGTGACACTT 59.931 40.000 7.20 0.00 0.00 3.16
2574 4186 4.584743 TCATGACAACTCTACTGTGACACT 59.415 41.667 7.20 0.00 0.00 3.55
2577 4189 7.254252 GCAATATCATGACAACTCTACTGTGAC 60.254 40.741 0.00 0.00 0.00 3.67
2578 4190 6.758416 GCAATATCATGACAACTCTACTGTGA 59.242 38.462 0.00 0.00 0.00 3.58
2582 4230 8.011844 TGTAGCAATATCATGACAACTCTACT 57.988 34.615 18.71 6.32 0.00 2.57
2617 4265 3.788227 ATGCCACTTCTACCAAACAGA 57.212 42.857 0.00 0.00 0.00 3.41
2624 4272 6.877322 TCAGTAAGTTAAATGCCACTTCTACC 59.123 38.462 0.00 0.00 34.92 3.18
2654 4302 3.244078 ACACCTCGTGCAAACATCTAGAA 60.244 43.478 0.00 0.00 36.98 2.10
2670 4318 7.822822 ACTATACTGTTTCCACATAAACACCTC 59.177 37.037 0.00 0.00 42.78 3.85
2798 4446 5.489792 TGACTCATTCTCCTTTAAGCAGT 57.510 39.130 0.00 0.00 0.00 4.40
2799 4447 5.702670 TGTTGACTCATTCTCCTTTAAGCAG 59.297 40.000 0.00 0.00 0.00 4.24
2816 4465 7.173218 CAGACATACAAAAGGTACATGTTGACT 59.827 37.037 16.99 1.10 30.63 3.41
2821 4470 4.700213 GGCAGACATACAAAAGGTACATGT 59.300 41.667 2.69 2.69 32.63 3.21
2860 4513 0.655915 TGCGACAAAAATGACGTGCG 60.656 50.000 0.00 0.00 0.00 5.34
2861 4514 1.685302 ATGCGACAAAAATGACGTGC 58.315 45.000 0.00 0.00 0.00 5.34
2912 4568 9.281371 CTTCTCATCAAGCAGGAAATATTATCA 57.719 33.333 0.00 0.00 0.00 2.15
3080 4741 7.701539 AGAGCATATCATTCTCAGTACCTAG 57.298 40.000 0.00 0.00 0.00 3.02
3144 4805 8.153479 TGCACGTGAAAAATAGCATAGATAAT 57.847 30.769 22.23 0.00 0.00 1.28
3147 4808 5.817296 TCTGCACGTGAAAAATAGCATAGAT 59.183 36.000 22.23 0.00 0.00 1.98
3259 4920 0.918983 TGCTTGGAAGGGGGTATGAG 59.081 55.000 0.00 0.00 0.00 2.90
3271 4932 2.032528 CCGCCTTCTGTGCTTGGA 59.967 61.111 0.00 0.00 0.00 3.53
3274 4935 2.980233 GTGCCGCCTTCTGTGCTT 60.980 61.111 0.00 0.00 0.00 3.91
3334 4995 6.660521 TCTTCATCTCCAATGCAGTTTTGTAT 59.339 34.615 0.00 0.00 0.00 2.29
3346 5007 2.503356 AGACGCCTTCTTCATCTCCAAT 59.497 45.455 0.00 0.00 0.00 3.16
3383 5044 7.497249 GTCAAGAGATAATTTGCTGGTATCTGT 59.503 37.037 0.00 0.00 35.26 3.41
3399 5060 3.396276 TGTTGTTTGGGGGTCAAGAGATA 59.604 43.478 0.00 0.00 36.62 1.98
3406 5067 4.020543 GCTATAATGTTGTTTGGGGGTCA 58.979 43.478 0.00 0.00 0.00 4.02
3434 5095 3.681897 GCGATTGGGTAGATGAGCATAAG 59.318 47.826 0.00 0.00 0.00 1.73
3451 5112 4.206375 TCATATGTTTCCATGTGGCGATT 58.794 39.130 1.90 0.00 39.78 3.34
3470 5131 2.015736 GTCACTGCAGGACGATTCAT 57.984 50.000 19.93 0.00 0.00 2.57
3478 5139 1.300931 GCTGAACGTCACTGCAGGA 60.301 57.895 19.93 9.75 33.57 3.86
3480 5141 1.153597 TGTGCTGAACGTCACTGCAG 61.154 55.000 20.68 13.48 41.31 4.41
3571 5232 4.262506 CCCTCGGTTTATACCATCTCTTCC 60.263 50.000 3.13 0.00 45.31 3.46
3593 5262 3.781760 CCCATGGCATGCATACCC 58.218 61.111 22.02 10.69 0.00 3.69
3617 5286 7.770897 CCAGGCTTATAGTTCATTACAGAGTTT 59.229 37.037 0.00 0.00 0.00 2.66
3648 5349 4.082787 CCACAAGGCAAAGTACTACAATGG 60.083 45.833 0.00 0.00 0.00 3.16
3664 5365 5.982890 AAATACCAGAAATGACCACAAGG 57.017 39.130 0.00 0.00 42.21 3.61
3701 5402 1.126113 ACGATTCTTTGCGCTTACACG 59.874 47.619 9.73 8.56 0.00 4.49
3709 5410 1.052287 GTTTGCCACGATTCTTTGCG 58.948 50.000 0.00 0.00 0.00 4.85
3754 5476 7.658179 TCAACTGTGTATGATTCAAGACTTC 57.342 36.000 0.00 0.00 0.00 3.01
3768 5490 9.225436 TCACATTGCTTAATAATCAACTGTGTA 57.775 29.630 19.12 11.24 34.61 2.90
3771 5493 8.246180 CCTTCACATTGCTTAATAATCAACTGT 58.754 33.333 0.00 0.00 0.00 3.55
3813 5535 4.230964 AGGTTACTTTTATACCCATGGGCA 59.769 41.667 31.73 20.13 39.32 5.36
3831 5553 4.587262 GGGCTTGAGGAAAAAGAAAGGTTA 59.413 41.667 0.00 0.00 0.00 2.85
3842 5565 3.099141 GGAATGATTGGGCTTGAGGAAA 58.901 45.455 0.00 0.00 0.00 3.13
3849 5572 4.533311 AGTTCAAATGGAATGATTGGGCTT 59.467 37.500 0.00 0.00 37.93 4.35
3859 5582 6.353082 CCACTAGAGGGTAGTTCAAATGGAAT 60.353 42.308 0.00 0.00 37.93 3.01
3879 5603 5.414454 GCTTGTTTGTATCCATTGTCCACTA 59.586 40.000 0.00 0.00 0.00 2.74
3881 5605 4.218417 AGCTTGTTTGTATCCATTGTCCAC 59.782 41.667 0.00 0.00 0.00 4.02
3883 5607 5.648092 AGTAGCTTGTTTGTATCCATTGTCC 59.352 40.000 0.00 0.00 0.00 4.02
3888 5800 6.003950 ACAACAGTAGCTTGTTTGTATCCAT 58.996 36.000 0.90 0.00 39.17 3.41
3898 5810 7.996385 AGTATTGAAAAACAACAGTAGCTTGT 58.004 30.769 0.00 0.00 41.52 3.16
3901 5813 7.920682 CCAAAGTATTGAAAAACAACAGTAGCT 59.079 33.333 0.00 0.00 41.52 3.32
3928 5846 8.125448 GTGTTTGGCAGCAAATTATTGTAAAAA 58.875 29.630 0.00 0.00 38.85 1.94
4044 5962 1.880675 AGCTCGTGGAGTACATATCCG 59.119 52.381 0.00 0.00 39.91 4.18
4075 5993 3.181329 TCTCCAAGGTCTGCTGGATAAA 58.819 45.455 0.00 0.00 40.92 1.40
4099 6017 3.715628 ATTTTGTGTGCAGGTCAGAAC 57.284 42.857 0.00 0.00 0.00 3.01
4144 6062 7.121315 GCTATTCCTGACCTGAAAAATAACTGT 59.879 37.037 0.00 0.00 0.00 3.55
4181 6099 1.517257 CGACTAACTCCGGCTGCTG 60.517 63.158 0.00 0.26 0.00 4.41
4338 6269 4.662145 GCAACATGAAGTACCACTAATGC 58.338 43.478 0.00 0.00 30.01 3.56
4347 6278 6.747659 ATTTTTCAACGCAACATGAAGTAC 57.252 33.333 0.00 0.00 36.93 2.73
4360 6291 2.663119 GCTGCCTGCTTATTTTTCAACG 59.337 45.455 0.00 0.00 38.95 4.10
4361 6292 2.995939 GGCTGCCTGCTTATTTTTCAAC 59.004 45.455 12.43 0.00 42.39 3.18
4362 6293 2.899256 AGGCTGCCTGCTTATTTTTCAA 59.101 40.909 22.71 0.00 42.39 2.69
4373 6304 0.108945 GATGAACAAAGGCTGCCTGC 60.109 55.000 24.16 10.08 41.94 4.85
4387 6318 2.296752 CACATGTGGTTTGCCTGATGAA 59.703 45.455 18.51 0.00 35.27 2.57
4389 6320 1.887854 TCACATGTGGTTTGCCTGATG 59.112 47.619 25.16 0.00 35.27 3.07
4401 6332 8.419435 CAGAAACAATTTTACGAATCACATGTG 58.581 33.333 20.18 20.18 0.00 3.21


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

AutoCloner maintained by Alex Coulton.