Multiple sequence alignment - TraesCS3D01G462500

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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 TraesCS3D01G462500 chr3D 100.000 2873 0 0 1 2873 567066135 567063263 0.000000e+00 5306.0
1 TraesCS3D01G462500 chr3D 85.561 1399 163 26 1382 2760 568818559 568817180 0.000000e+00 1428.0
2 TraesCS3D01G462500 chr3D 91.985 786 37 18 1 783 569790955 569791717 0.000000e+00 1079.0
3 TraesCS3D01G462500 chr3D 89.681 407 26 12 980 1374 568819251 568818849 3.300000e-139 505.0
4 TraesCS3D01G462500 chr3D 79.406 539 78 21 2226 2749 566910149 566909629 1.640000e-92 350.0
5 TraesCS3D01G462500 chr3D 79.198 524 77 17 2309 2821 567048972 567048470 4.590000e-88 335.0
6 TraesCS3D01G462500 chr3D 76.560 593 120 13 1382 1964 568018059 568018642 1.000000e-79 307.0
7 TraesCS3D01G462500 chr3D 80.189 318 33 14 479 788 566912303 566912008 8.070000e-51 211.0
8 TraesCS3D01G462500 chr3D 88.166 169 20 0 1054 1222 568017505 568017673 4.850000e-48 202.0
9 TraesCS3D01G462500 chr3D 79.470 302 42 16 997 1279 565641894 565642194 2.260000e-46 196.0
10 TraesCS3D01G462500 chr3D 87.500 152 14 5 1124 1270 566911693 566911542 1.370000e-38 171.0
11 TraesCS3D01G462500 chr3D 94.505 91 5 0 894 984 569793408 569793498 1.070000e-29 141.0
12 TraesCS3D01G462500 chr3D 96.875 32 1 0 2241 2272 566613024 566613055 1.000000e-03 54.7
13 TraesCS3D01G462500 chr3A 89.831 590 55 2 1382 1971 700739930 700740514 0.000000e+00 752.0
14 TraesCS3D01G462500 chr3A 88.871 611 20 12 799 1374 700739058 700739655 0.000000e+00 708.0
15 TraesCS3D01G462500 chr3A 80.464 604 86 16 2226 2804 700741344 700741940 1.580000e-117 433.0
16 TraesCS3D01G462500 chr3A 84.814 349 32 5 1040 1367 700444801 700444453 5.930000e-87 331.0
17 TraesCS3D01G462500 chr3A 80.602 299 43 7 1003 1286 702407900 702407602 1.730000e-52 217.0
18 TraesCS3D01G462500 chr3A 88.125 160 10 1 1217 1367 700444168 700444009 6.320000e-42 182.0
19 TraesCS3D01G462500 chr3A 76.524 328 54 11 2379 2696 700740527 700740841 1.070000e-34 158.0
20 TraesCS3D01G462500 chr3A 90.000 80 6 2 710 788 700738881 700738959 5.060000e-18 102.0
21 TraesCS3D01G462500 chr3B 80.732 410 57 11 982 1374 756105965 756105561 1.670000e-77 300.0
22 TraesCS3D01G462500 chrUn 80.337 356 52 11 1030 1374 286487348 286487696 1.320000e-63 254.0
23 TraesCS3D01G462500 chrUn 80.337 356 52 11 1030 1374 293133093 293133441 1.320000e-63 254.0
24 TraesCS3D01G462500 chrUn 80.913 241 28 9 1064 1286 41059793 41059553 1.060000e-39 174.0
25 TraesCS3D01G462500 chr6D 84.878 205 19 6 1006 1198 380452947 380452743 2.260000e-46 196.0


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 TraesCS3D01G462500 chr3D 567063263 567066135 2872 True 5306.0 5306 100.0000 1 2873 1 chr3D.!!$R2 2872
1 TraesCS3D01G462500 chr3D 568817180 568819251 2071 True 966.5 1428 87.6210 980 2760 2 chr3D.!!$R4 1780
2 TraesCS3D01G462500 chr3D 569790955 569793498 2543 False 610.0 1079 93.2450 1 984 2 chr3D.!!$F4 983
3 TraesCS3D01G462500 chr3D 567048470 567048972 502 True 335.0 335 79.1980 2309 2821 1 chr3D.!!$R1 512
4 TraesCS3D01G462500 chr3D 568017505 568018642 1137 False 254.5 307 82.3630 1054 1964 2 chr3D.!!$F3 910
5 TraesCS3D01G462500 chr3D 566909629 566912303 2674 True 244.0 350 82.3650 479 2749 3 chr3D.!!$R3 2270
6 TraesCS3D01G462500 chr3A 700738881 700741940 3059 False 430.6 752 85.1380 710 2804 5 chr3A.!!$F1 2094
7 TraesCS3D01G462500 chr3A 700444009 700444801 792 True 256.5 331 86.4695 1040 1367 2 chr3A.!!$R2 327

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
253 255 0.179001 CCCCACCCCGGATCATAAAC 60.179 60.0 0.73 0.0 36.56 2.01 F
633 647 0.330941 TGGCTATGCACAATGACCCA 59.669 50.0 0.00 0.0 0.00 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1374 3528 0.036164 AATGCAGGCTACCGTTGTGA 59.964 50.0 0.00 0.0 0.00 3.58 R
2296 5353 0.034059 AACTGGTGCTCCGAGTTCTG 59.966 55.0 13.46 0.0 33.29 3.02 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
221 223 4.989279 ATTTTCTATTGGCGCATCTTGT 57.011 36.364 10.83 0.00 0.00 3.16
253 255 0.179001 CCCCACCCCGGATCATAAAC 60.179 60.000 0.73 0.00 36.56 2.01
339 342 5.322754 TCCGATCACCTAACCCTTAGATAG 58.677 45.833 0.00 0.00 35.20 2.08
451 454 5.502153 TTTCTACAGCGCTTTTGGTAAAA 57.498 34.783 7.50 7.80 0.00 1.52
585 589 2.367377 CATGGGGAGGGAGAGGCA 60.367 66.667 0.00 0.00 0.00 4.75
602 606 4.431131 AGGGATGTTGCCGCCCAG 62.431 66.667 0.00 0.00 44.55 4.45
605 615 4.120331 GATGTTGCCGCCCAGTGC 62.120 66.667 0.00 0.00 0.00 4.40
626 640 1.175654 CATGTGGTGGCTATGCACAA 58.824 50.000 0.00 0.00 0.00 3.33
631 645 0.740737 GGTGGCTATGCACAATGACC 59.259 55.000 0.00 0.00 0.00 4.02
632 646 0.740737 GTGGCTATGCACAATGACCC 59.259 55.000 0.00 0.00 0.00 4.46
633 647 0.330941 TGGCTATGCACAATGACCCA 59.669 50.000 0.00 0.00 0.00 4.51
634 648 0.740737 GGCTATGCACAATGACCCAC 59.259 55.000 0.00 0.00 0.00 4.61
635 649 0.378257 GCTATGCACAATGACCCACG 59.622 55.000 0.00 0.00 0.00 4.94
636 650 1.737838 CTATGCACAATGACCCACGT 58.262 50.000 0.00 0.00 0.00 4.49
637 651 1.665679 CTATGCACAATGACCCACGTC 59.334 52.381 0.00 0.00 39.66 4.34
675 689 1.019673 CATGAACTCCGCTTCCATGG 58.980 55.000 4.97 4.97 0.00 3.66
676 690 0.911769 ATGAACTCCGCTTCCATGGA 59.088 50.000 11.44 11.44 0.00 3.41
677 691 0.911769 TGAACTCCGCTTCCATGGAT 59.088 50.000 17.06 0.00 32.83 3.41
678 692 1.281867 TGAACTCCGCTTCCATGGATT 59.718 47.619 17.06 4.53 32.83 3.01
679 693 1.672881 GAACTCCGCTTCCATGGATTG 59.327 52.381 17.06 12.84 32.83 2.67
680 694 0.620556 ACTCCGCTTCCATGGATTGT 59.379 50.000 17.06 5.70 32.83 2.71
732 746 3.686227 TCCAAAAGGGACCATGCATAT 57.314 42.857 0.00 0.00 42.15 1.78
733 747 3.298619 TCCAAAAGGGACCATGCATATG 58.701 45.455 0.00 0.00 42.15 1.78
736 750 4.262292 CCAAAAGGGACCATGCATATGATG 60.262 45.833 6.97 7.44 40.01 3.07
749 764 3.701040 GCATATGATGTTTGGAGTTGGGT 59.299 43.478 6.97 0.00 0.00 4.51
892 2556 3.775661 TTCATCTCAACGAGATACGCA 57.224 42.857 6.19 0.00 46.25 5.24
1011 2693 3.644719 AGCAGGATGAGCTCCCAG 58.355 61.111 12.15 4.10 46.27 4.45
1167 2861 3.239253 ACCTCCACCCGCGACTTT 61.239 61.111 8.23 0.00 0.00 2.66
1374 3528 1.764054 CGATGGGCTCCTCCTCCTT 60.764 63.158 0.00 0.00 34.39 3.36
1375 3529 1.753368 CGATGGGCTCCTCCTCCTTC 61.753 65.000 0.00 0.00 34.39 3.46
1376 3530 0.692419 GATGGGCTCCTCCTCCTTCA 60.692 60.000 0.00 0.00 34.39 3.02
1378 3823 1.613630 GGGCTCCTCCTCCTTCACA 60.614 63.158 0.00 0.00 34.39 3.58
1380 3825 0.035915 GGCTCCTCCTCCTTCACAAC 60.036 60.000 0.00 0.00 0.00 3.32
1405 3850 2.081462 GCCTGCATTGGTACGTAAACT 58.919 47.619 0.00 0.00 0.00 2.66
1432 3877 6.827586 ACATAACGGTATTTGACACCATTT 57.172 33.333 0.00 0.00 35.67 2.32
1441 3886 1.795768 TGACACCATTTCTGAGTCGC 58.204 50.000 0.00 0.00 32.93 5.19
1454 3899 2.434185 GTCGCTCCGGTTGATGCA 60.434 61.111 0.00 0.00 0.00 3.96
1459 3904 0.527565 GCTCCGGTTGATGCAATGTT 59.472 50.000 0.00 0.00 0.00 2.71
1570 4015 1.668419 GGCGATGCAGGACTACAAAT 58.332 50.000 0.00 0.00 0.00 2.32
1818 4263 6.318648 TCAAACAAAGTCTAGTTTCACATGCT 59.681 34.615 0.00 0.00 35.90 3.79
1826 4271 6.073548 AGTCTAGTTTCACATGCTTTCTTTCG 60.074 38.462 0.00 0.00 0.00 3.46
1848 4293 4.677250 CGGACACTAGAGGGTTATGTTGTC 60.677 50.000 0.00 0.00 0.00 3.18
1853 4298 5.995282 CACTAGAGGGTTATGTTGTCAACAA 59.005 40.000 21.71 9.08 45.86 2.83
1883 4328 6.769341 CCTTTCATCAGATGATAATGTGGTGA 59.231 38.462 14.11 0.00 39.39 4.02
1884 4329 7.041303 CCTTTCATCAGATGATAATGTGGTGAG 60.041 40.741 14.11 0.00 36.50 3.51
1885 4330 5.303165 TCATCAGATGATAATGTGGTGAGC 58.697 41.667 9.21 0.00 31.14 4.26
1908 4358 4.514441 CACACATATCCTTTCATCTGAGGC 59.486 45.833 0.00 0.00 32.93 4.70
1987 4438 8.644374 TGCAGTATTTAATTTAGGGTCAGTTT 57.356 30.769 0.00 0.00 0.00 2.66
2004 4455 4.821260 TCAGTTTGTTTCAGCTGCAGATTA 59.179 37.500 20.43 0.00 0.00 1.75
2045 4804 1.504912 ACTGGATGCACTATGAGCCT 58.495 50.000 0.00 0.00 0.00 4.58
2067 4826 3.815401 TGCTAGCTTCTTTGTTGAGGTTC 59.185 43.478 17.23 0.00 0.00 3.62
2085 4844 7.885297 TGAGGTTCAAAAACTTATGATCAAGG 58.115 34.615 0.00 0.00 35.61 3.61
2095 4854 4.713814 ACTTATGATCAAGGAGCTCTGACA 59.286 41.667 14.64 11.13 0.00 3.58
2109 4868 3.865446 CTCTGACACTTACATGGATGCA 58.135 45.455 0.00 0.00 0.00 3.96
2138 4897 3.642141 TCTTTGAATATCCTTTGGGGCC 58.358 45.455 0.00 0.00 34.39 5.80
2139 4898 3.012274 TCTTTGAATATCCTTTGGGGCCA 59.988 43.478 4.39 0.00 34.39 5.36
2144 4903 2.452600 TATCCTTTGGGGCCAATGTC 57.547 50.000 4.39 0.00 35.70 3.06
2146 4905 1.606313 CCTTTGGGGCCAATGTCGT 60.606 57.895 4.39 0.00 35.70 4.34
2148 4907 1.540267 CTTTGGGGCCAATGTCGTTA 58.460 50.000 4.39 0.00 35.70 3.18
2150 4909 0.402504 TTGGGGCCAATGTCGTTACT 59.597 50.000 4.39 0.00 0.00 2.24
2151 4910 0.322098 TGGGGCCAATGTCGTTACTG 60.322 55.000 4.39 0.00 0.00 2.74
2156 4915 2.747446 GGCCAATGTCGTTACTGTGATT 59.253 45.455 0.00 0.00 0.00 2.57
2201 5025 5.941555 TTTGGGTAAGTGGTTGAAATGTT 57.058 34.783 0.00 0.00 0.00 2.71
2204 5029 4.055360 GGGTAAGTGGTTGAAATGTTTGC 58.945 43.478 0.00 0.00 0.00 3.68
2205 5030 4.202212 GGGTAAGTGGTTGAAATGTTTGCT 60.202 41.667 0.00 0.00 0.00 3.91
2208 5033 6.981559 GGTAAGTGGTTGAAATGTTTGCTAAA 59.018 34.615 0.00 0.00 0.00 1.85
2209 5034 7.492994 GGTAAGTGGTTGAAATGTTTGCTAAAA 59.507 33.333 0.00 0.00 0.00 1.52
2210 5035 9.040939 GTAAGTGGTTGAAATGTTTGCTAAAAT 57.959 29.630 0.00 0.00 0.00 1.82
2211 5036 8.504812 AAGTGGTTGAAATGTTTGCTAAAATT 57.495 26.923 0.00 0.00 0.00 1.82
2212 5037 9.606631 AAGTGGTTGAAATGTTTGCTAAAATTA 57.393 25.926 0.00 0.00 0.00 1.40
2216 5041 8.495148 GGTTGAAATGTTTGCTAAAATTACAGG 58.505 33.333 0.00 0.00 0.00 4.00
2237 5290 3.332034 GCGGTTTCCTGTTTCTAAGCTA 58.668 45.455 0.00 0.00 0.00 3.32
2239 5292 4.214758 GCGGTTTCCTGTTTCTAAGCTAAA 59.785 41.667 0.00 0.00 0.00 1.85
2242 5295 6.204108 CGGTTTCCTGTTTCTAAGCTAAAGAA 59.796 38.462 7.22 7.22 0.00 2.52
2249 5302 8.239998 CCTGTTTCTAAGCTAAAGAAGAAATGG 58.760 37.037 10.39 10.96 39.43 3.16
2257 5310 4.403752 GCTAAAGAAGAAATGGGGCAGATT 59.596 41.667 0.00 0.00 0.00 2.40
2274 5329 5.189180 GCAGATTATCCTCCTTGTTGAAGT 58.811 41.667 0.00 0.00 0.00 3.01
2277 5332 7.336931 GCAGATTATCCTCCTTGTTGAAGTAAA 59.663 37.037 0.00 0.00 0.00 2.01
2293 5348 7.048629 TGAAGTAAATTGCACCTGATTTTGA 57.951 32.000 0.00 0.00 0.00 2.69
2296 5353 6.223120 AGTAAATTGCACCTGATTTTGAACC 58.777 36.000 0.00 0.00 0.00 3.62
2300 5357 3.295093 TGCACCTGATTTTGAACCAGAA 58.705 40.909 0.00 0.00 0.00 3.02
2304 5361 3.815401 ACCTGATTTTGAACCAGAACTCG 59.185 43.478 0.00 0.00 0.00 4.18
2311 5368 0.670854 GAACCAGAACTCGGAGCACC 60.671 60.000 4.58 0.00 0.00 5.01
2394 5460 4.998672 CCTTTGTGTTGCATCATTTGGAAT 59.001 37.500 0.00 0.00 38.01 3.01
2396 5462 5.926214 TTGTGTTGCATCATTTGGAATTG 57.074 34.783 0.00 0.00 38.01 2.32
2418 5485 9.590451 AATTGTATTTATCATTCACCTTTGCTG 57.410 29.630 0.00 0.00 0.00 4.41
2429 5496 3.640967 TCACCTTTGCTGCTAACCATTTT 59.359 39.130 0.00 0.00 0.00 1.82
2467 5536 8.562892 ACTTCTTGTGATGTTCAATCTTAACAG 58.437 33.333 0.00 0.00 40.00 3.16
2468 5537 8.675705 TTCTTGTGATGTTCAATCTTAACAGA 57.324 30.769 0.00 0.00 40.00 3.41
2469 5538 8.675705 TCTTGTGATGTTCAATCTTAACAGAA 57.324 30.769 0.00 0.00 40.00 3.02
2475 5544 6.942532 TGTTCAATCTTAACAGAAGCTTGT 57.057 33.333 2.10 0.00 33.13 3.16
2481 5550 8.632679 TCAATCTTAACAGAAGCTTGTGAAATT 58.367 29.630 28.57 15.38 30.76 1.82
2482 5551 9.897744 CAATCTTAACAGAAGCTTGTGAAATTA 57.102 29.630 28.57 14.42 30.76 1.40
2489 5564 7.308435 ACAGAAGCTTGTGAAATTATACTTGC 58.692 34.615 28.57 0.00 0.00 4.01
2518 5594 8.689061 TGATAAGCAGAAGCAATGTTTATCATT 58.311 29.630 20.64 0.00 46.65 2.57
2530 5606 4.835678 TGTTTATCATTGCTCAGCTCAGA 58.164 39.130 0.00 0.00 0.00 3.27
2543 5619 2.093075 CAGCTCAGATCCCAGATTGTGT 60.093 50.000 0.00 0.00 0.00 3.72
2544 5620 2.575279 AGCTCAGATCCCAGATTGTGTT 59.425 45.455 0.00 0.00 0.00 3.32
2583 5666 2.369532 ACTGCCAGCCATGTTCATTTTT 59.630 40.909 0.00 0.00 0.00 1.94
2667 5750 4.104383 ACATCACCAGGAATTGTGTCTT 57.896 40.909 0.00 0.00 34.14 3.01
2670 5753 5.473504 ACATCACCAGGAATTGTGTCTTAAC 59.526 40.000 0.00 0.00 34.14 2.01
2685 5768 5.409826 GTGTCTTAACCAGATTGTCTCAAGG 59.590 44.000 0.00 0.00 32.60 3.61
2714 5797 7.094205 ACTCCAATCATTTGTTTCTGGATGTAC 60.094 37.037 0.00 0.00 32.70 2.90
2720 5803 8.492673 TCATTTGTTTCTGGATGTACTATGTC 57.507 34.615 0.00 0.00 0.00 3.06
2721 5804 7.552687 TCATTTGTTTCTGGATGTACTATGTCC 59.447 37.037 0.00 0.00 0.00 4.02
2729 5812 4.141505 TGGATGTACTATGTCCCATTGGTG 60.142 45.833 1.20 0.00 0.00 4.17
2772 5855 3.521126 ACTTGGAGGCTACTCACATTCAT 59.479 43.478 0.00 0.00 45.81 2.57
2793 5876 6.457355 TCATTTTTCTGTAGCATGCACATTT 58.543 32.000 21.98 0.16 0.00 2.32
2794 5877 6.587226 TCATTTTTCTGTAGCATGCACATTTC 59.413 34.615 21.98 3.84 0.00 2.17
2800 5883 3.628942 TGTAGCATGCACATTTCCATCTC 59.371 43.478 21.98 0.00 0.00 2.75
2804 5887 3.205338 CATGCACATTTCCATCTCCGTA 58.795 45.455 0.00 0.00 0.00 4.02
2806 5889 3.466836 TGCACATTTCCATCTCCGTATC 58.533 45.455 0.00 0.00 0.00 2.24
2810 5893 5.545588 CACATTTCCATCTCCGTATCTGAT 58.454 41.667 0.00 0.00 0.00 2.90
2839 5922 5.933187 TTTTGTGCGTGACATGTTATAGT 57.067 34.783 0.00 0.00 33.40 2.12
2840 5923 5.933187 TTTGTGCGTGACATGTTATAGTT 57.067 34.783 0.00 0.00 33.40 2.24
2841 5924 5.933187 TTGTGCGTGACATGTTATAGTTT 57.067 34.783 0.00 0.00 33.40 2.66
2842 5925 7.422878 TTTGTGCGTGACATGTTATAGTTTA 57.577 32.000 0.00 0.00 33.40 2.01
2843 5926 7.422878 TTGTGCGTGACATGTTATAGTTTAA 57.577 32.000 0.00 0.00 33.40 1.52
2844 5927 7.422878 TGTGCGTGACATGTTATAGTTTAAA 57.577 32.000 0.00 0.00 0.00 1.52
2845 5928 7.292292 TGTGCGTGACATGTTATAGTTTAAAC 58.708 34.615 10.47 10.47 0.00 2.01
2846 5929 7.171848 TGTGCGTGACATGTTATAGTTTAAACT 59.828 33.333 23.58 23.58 42.91 2.66
2847 5930 7.477422 GTGCGTGACATGTTATAGTTTAAACTG 59.523 37.037 27.40 13.97 40.07 3.16
2848 5931 7.171848 TGCGTGACATGTTATAGTTTAAACTGT 59.828 33.333 27.40 23.46 40.07 3.55
2849 5932 7.686938 GCGTGACATGTTATAGTTTAAACTGTC 59.313 37.037 27.40 22.98 40.07 3.51
2850 5933 8.166706 CGTGACATGTTATAGTTTAAACTGTCC 58.833 37.037 27.40 16.31 40.07 4.02
2851 5934 8.995220 GTGACATGTTATAGTTTAAACTGTCCA 58.005 33.333 27.40 20.43 40.07 4.02
2852 5935 9.733556 TGACATGTTATAGTTTAAACTGTCCAT 57.266 29.630 27.40 21.46 40.07 3.41
2853 5936 9.988350 GACATGTTATAGTTTAAACTGTCCATG 57.012 33.333 30.56 30.56 40.84 3.66
2854 5937 8.956426 ACATGTTATAGTTTAAACTGTCCATGG 58.044 33.333 32.51 23.89 40.20 3.66
2855 5938 9.173021 CATGTTATAGTTTAAACTGTCCATGGA 57.827 33.333 28.01 11.44 40.07 3.41
2856 5939 9.747898 ATGTTATAGTTTAAACTGTCCATGGAA 57.252 29.630 27.40 10.54 40.07 3.53
2857 5940 9.226606 TGTTATAGTTTAAACTGTCCATGGAAG 57.773 33.333 27.40 17.68 40.07 3.46
2858 5941 9.444600 GTTATAGTTTAAACTGTCCATGGAAGA 57.555 33.333 27.40 5.18 40.07 2.87
2869 5952 9.614792 AACTGTCCATGGAAGATATAAGTTTAC 57.385 33.333 18.20 0.00 0.00 2.01
2870 5953 7.926555 ACTGTCCATGGAAGATATAAGTTTACG 59.073 37.037 18.20 0.00 0.00 3.18
2871 5954 8.014070 TGTCCATGGAAGATATAAGTTTACGA 57.986 34.615 18.20 0.00 0.00 3.43
2872 5955 8.479689 TGTCCATGGAAGATATAAGTTTACGAA 58.520 33.333 18.20 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
179 181 9.730420 GAAAATAGCAACCGTAAATGATATTGT 57.270 29.630 0.00 0.00 37.95 2.71
235 237 0.843984 AGTTTATGATCCGGGGTGGG 59.156 55.000 0.00 0.00 38.76 4.61
236 238 1.967319 CAGTTTATGATCCGGGGTGG 58.033 55.000 0.00 0.00 40.09 4.61
301 303 4.385748 GTGATCGGAGCATTTTGTTTTTCC 59.614 41.667 0.00 0.00 0.00 3.13
319 322 5.540719 ACTGCTATCTAAGGGTTAGGTGATC 59.459 44.000 0.00 0.00 34.00 2.92
339 342 2.358737 CCACCAAGGGTCGACTGC 60.359 66.667 16.46 0.00 31.02 4.40
363 366 3.560636 AATTAATGAGGCACGGCTAGT 57.439 42.857 0.00 0.00 0.00 2.57
378 381 5.633655 TGCGTCCCTTCCCTATAAATTAA 57.366 39.130 0.00 0.00 0.00 1.40
585 589 4.431131 CTGGGCGGCAACATCCCT 62.431 66.667 12.47 0.00 46.34 4.20
631 645 4.602259 ACGTGCCCAGTGACGTGG 62.602 66.667 7.60 0.00 46.60 4.94
732 746 5.600484 ACAATAAACCCAACTCCAAACATCA 59.400 36.000 0.00 0.00 0.00 3.07
733 747 6.096673 ACAATAAACCCAACTCCAAACATC 57.903 37.500 0.00 0.00 0.00 3.06
736 750 6.567132 CGTCTACAATAAACCCAACTCCAAAC 60.567 42.308 0.00 0.00 0.00 2.93
749 764 6.394809 TGCAGAGATTCACGTCTACAATAAA 58.605 36.000 0.00 0.00 0.00 1.40
803 935 6.431234 ACTCAAAAACCTCTATGCTCGAAAAT 59.569 34.615 0.00 0.00 0.00 1.82
892 2556 1.202769 ATGCATTTGGGCTGGGCTTT 61.203 50.000 0.00 0.00 34.04 3.51
939 2607 2.682494 GGCGGTGGAGTGGTAGGA 60.682 66.667 0.00 0.00 0.00 2.94
1210 2905 2.125832 GGCGCAGTTGTAGCCGTA 60.126 61.111 10.83 0.00 41.53 4.02
1285 3439 2.580867 CGCGCTGTACTGGAGCTC 60.581 66.667 4.71 4.71 34.03 4.09
1374 3528 0.036164 AATGCAGGCTACCGTTGTGA 59.964 50.000 0.00 0.00 0.00 3.58
1375 3529 0.168788 CAATGCAGGCTACCGTTGTG 59.831 55.000 9.80 0.00 0.00 3.33
1376 3530 0.960364 CCAATGCAGGCTACCGTTGT 60.960 55.000 14.44 0.00 0.00 3.32
1378 3823 0.616371 TACCAATGCAGGCTACCGTT 59.384 50.000 0.00 0.00 0.00 4.44
1380 3825 1.151777 CGTACCAATGCAGGCTACCG 61.152 60.000 0.00 0.00 0.00 4.02
1405 3850 5.187381 TGGTGTCAAATACCGTTATGTAGGA 59.813 40.000 0.00 0.00 41.18 2.94
1432 3877 0.965866 ATCAACCGGAGCGACTCAGA 60.966 55.000 9.46 0.00 31.08 3.27
1441 3886 1.202065 CGAACATTGCATCAACCGGAG 60.202 52.381 9.46 0.00 0.00 4.63
1454 3899 5.323900 CGCAGTCAATAACAATCGAACATT 58.676 37.500 0.00 0.00 0.00 2.71
1459 3904 1.663643 GGCGCAGTCAATAACAATCGA 59.336 47.619 10.83 0.00 0.00 3.59
1570 4015 1.762957 CTTTAAGGCCCAGATCTCGGA 59.237 52.381 11.01 0.00 0.00 4.55
1818 4263 3.236896 ACCCTCTAGTGTCCGAAAGAAA 58.763 45.455 0.00 0.00 0.00 2.52
1826 4271 4.222145 TGACAACATAACCCTCTAGTGTCC 59.778 45.833 0.00 0.00 0.00 4.02
1848 4293 2.807967 TCTGATGAAAGGCGAGTTGTTG 59.192 45.455 0.00 0.00 0.00 3.33
1853 4298 3.834489 ATCATCTGATGAAAGGCGAGT 57.166 42.857 22.91 2.59 43.50 4.18
1883 4328 5.363562 TCAGATGAAAGGATATGTGTGCT 57.636 39.130 0.00 0.00 0.00 4.40
1884 4329 4.514441 CCTCAGATGAAAGGATATGTGTGC 59.486 45.833 0.00 0.00 34.35 4.57
1885 4330 4.514441 GCCTCAGATGAAAGGATATGTGTG 59.486 45.833 0.00 0.00 34.35 3.82
1908 4358 0.381801 GCACCACCACACTCAACAAG 59.618 55.000 0.00 0.00 0.00 3.16
2004 4455 0.323725 AGCAAAATCCACCTCCGCAT 60.324 50.000 0.00 0.00 0.00 4.73
2045 4804 3.492102 ACCTCAACAAAGAAGCTAGCA 57.508 42.857 18.83 0.00 0.00 3.49
2067 4826 7.120285 TCAGAGCTCCTTGATCATAAGTTTTTG 59.880 37.037 10.93 0.00 32.67 2.44
2085 4844 3.876274 TCCATGTAAGTGTCAGAGCTC 57.124 47.619 5.27 5.27 0.00 4.09
2095 4854 7.886629 AGAAACATAATGCATCCATGTAAGT 57.113 32.000 21.01 12.83 32.70 2.24
2138 4897 5.590104 TCACAATCACAGTAACGACATTG 57.410 39.130 0.00 0.00 0.00 2.82
2139 4898 5.390885 GCATCACAATCACAGTAACGACATT 60.391 40.000 0.00 0.00 0.00 2.71
2144 4903 2.741517 TGGCATCACAATCACAGTAACG 59.258 45.455 0.00 0.00 0.00 3.18
2146 4905 5.781210 TTTTGGCATCACAATCACAGTAA 57.219 34.783 0.00 0.00 0.00 2.24
2148 4907 4.877378 ATTTTGGCATCACAATCACAGT 57.123 36.364 0.00 0.00 0.00 3.55
2150 4909 6.094193 TGTAATTTTGGCATCACAATCACA 57.906 33.333 0.00 0.00 0.00 3.58
2151 4910 6.646240 ACTTGTAATTTTGGCATCACAATCAC 59.354 34.615 0.00 0.00 0.00 3.06
2156 4915 5.781210 TGACTTGTAATTTTGGCATCACA 57.219 34.783 0.00 0.00 0.00 3.58
2201 5025 4.321378 GGAAACCGCCTGTAATTTTAGCAA 60.321 41.667 0.00 0.00 0.00 3.91
2216 5041 2.152016 AGCTTAGAAACAGGAAACCGC 58.848 47.619 0.00 0.00 0.00 5.68
2237 5290 5.600069 GGATAATCTGCCCCATTTCTTCTTT 59.400 40.000 0.00 0.00 0.00 2.52
2239 5292 4.418190 AGGATAATCTGCCCCATTTCTTCT 59.582 41.667 0.00 0.00 0.00 2.85
2242 5295 3.075134 GGAGGATAATCTGCCCCATTTCT 59.925 47.826 0.00 0.00 0.00 2.52
2249 5302 3.117888 TCAACAAGGAGGATAATCTGCCC 60.118 47.826 0.00 0.00 0.00 5.36
2257 5310 6.945435 TGCAATTTACTTCAACAAGGAGGATA 59.055 34.615 0.00 0.00 33.37 2.59
2274 5329 6.041409 TCTGGTTCAAAATCAGGTGCAATTTA 59.959 34.615 0.00 0.00 0.00 1.40
2277 5332 3.896888 TCTGGTTCAAAATCAGGTGCAAT 59.103 39.130 0.00 0.00 0.00 3.56
2293 5348 1.371558 GGTGCTCCGAGTTCTGGTT 59.628 57.895 0.00 0.00 0.00 3.67
2296 5353 0.034059 AACTGGTGCTCCGAGTTCTG 59.966 55.000 13.46 0.00 33.29 3.02
2300 5357 1.692519 AGTTTAACTGGTGCTCCGAGT 59.307 47.619 0.00 2.55 36.30 4.18
2304 5361 4.134563 TCTTTCAGTTTAACTGGTGCTCC 58.865 43.478 22.82 0.00 45.94 4.70
2361 5418 4.331108 TGCAACACAAAGGCAGATGTATA 58.669 39.130 0.00 0.00 32.95 1.47
2365 5422 2.029739 TGATGCAACACAAAGGCAGATG 60.030 45.455 0.00 0.00 41.40 2.90
2372 5434 6.017770 ACAATTCCAAATGATGCAACACAAAG 60.018 34.615 0.00 0.00 0.00 2.77
2394 5460 7.035004 GCAGCAAAGGTGAATGATAAATACAA 58.965 34.615 0.00 0.00 32.22 2.41
2396 5462 6.799512 AGCAGCAAAGGTGAATGATAAATAC 58.200 36.000 0.00 0.00 32.22 1.89
2408 5474 3.665745 AAATGGTTAGCAGCAAAGGTG 57.334 42.857 0.00 0.00 33.01 4.00
2414 5481 5.714333 TGATTCCTTAAAATGGTTAGCAGCA 59.286 36.000 0.00 0.00 34.07 4.41
2418 5485 7.602753 AGTGTTGATTCCTTAAAATGGTTAGC 58.397 34.615 0.00 0.00 0.00 3.09
2429 5496 6.998074 ACATCACAAGAAGTGTTGATTCCTTA 59.002 34.615 11.86 0.00 46.25 2.69
2467 5536 7.272084 CAGTGCAAGTATAATTTCACAAGCTTC 59.728 37.037 16.00 0.56 0.00 3.86
2468 5537 7.040478 TCAGTGCAAGTATAATTTCACAAGCTT 60.040 33.333 16.00 0.00 0.00 3.74
2469 5538 6.430925 TCAGTGCAAGTATAATTTCACAAGCT 59.569 34.615 16.00 0.00 0.00 3.74
2475 5544 8.504812 TGCTTATCAGTGCAAGTATAATTTCA 57.495 30.769 0.00 0.00 36.15 2.69
2481 5550 5.755375 GCTTCTGCTTATCAGTGCAAGTATA 59.245 40.000 0.00 0.00 43.32 1.47
2482 5551 4.574013 GCTTCTGCTTATCAGTGCAAGTAT 59.426 41.667 0.00 0.00 43.32 2.12
2483 5552 3.935203 GCTTCTGCTTATCAGTGCAAGTA 59.065 43.478 0.00 1.96 43.32 2.24
2489 5564 4.959596 ACATTGCTTCTGCTTATCAGTG 57.040 40.909 0.00 0.00 43.32 3.66
2508 5584 4.835678 TCTGAGCTGAGCAATGATAAACA 58.164 39.130 7.39 0.00 0.00 2.83
2518 5594 0.325016 TCTGGGATCTGAGCTGAGCA 60.325 55.000 7.39 0.00 0.00 4.26
2520 5596 2.435069 ACAATCTGGGATCTGAGCTGAG 59.565 50.000 0.00 0.00 0.00 3.35
2530 5606 1.686236 AGGGGAACACAATCTGGGAT 58.314 50.000 0.00 0.00 0.00 3.85
2543 5619 4.020485 GCAGTTACAGAGTCTAAAGGGGAA 60.020 45.833 0.00 0.00 0.00 3.97
2544 5620 3.514309 GCAGTTACAGAGTCTAAAGGGGA 59.486 47.826 0.00 0.00 0.00 4.81
2583 5666 2.037902 TGGTCTTGTGCCGTTCATAGAA 59.962 45.455 0.00 0.00 0.00 2.10
2587 5670 1.003580 AGATGGTCTTGTGCCGTTCAT 59.996 47.619 0.00 0.00 0.00 2.57
2591 5674 2.932663 CAAGATGGTCTTGTGCCGT 58.067 52.632 10.72 0.00 46.50 5.68
2613 5696 1.098050 ATCTGCTTTCGACCAATGGC 58.902 50.000 0.00 0.00 0.00 4.40
2644 5727 3.822735 AGACACAATTCCTGGTGATGTTG 59.177 43.478 0.00 0.00 38.38 3.33
2645 5728 4.104383 AGACACAATTCCTGGTGATGTT 57.896 40.909 0.00 0.00 38.38 2.71
2667 5750 4.593206 AGTGACCTTGAGACAATCTGGTTA 59.407 41.667 0.00 0.00 36.21 2.85
2670 5753 3.594134 GAGTGACCTTGAGACAATCTGG 58.406 50.000 0.00 0.00 0.00 3.86
2685 5768 5.241506 TCCAGAAACAAATGATTGGAGTGAC 59.758 40.000 0.00 0.00 41.01 3.67
2720 5803 0.458669 GCTGAGCAATCACCAATGGG 59.541 55.000 3.55 0.00 41.29 4.00
2721 5804 1.471119 AGCTGAGCAATCACCAATGG 58.529 50.000 7.39 0.00 0.00 3.16
2729 5812 2.216898 GATGTGGGTAGCTGAGCAATC 58.783 52.381 7.39 0.00 0.00 2.67
2772 5855 5.221402 TGGAAATGTGCATGCTACAGAAAAA 60.221 36.000 20.33 6.48 0.00 1.94
2819 5902 5.933187 AAACTATAACATGTCACGCACAA 57.067 34.783 0.00 0.00 38.97 3.33
2821 5904 7.477422 CAGTTTAAACTATAACATGTCACGCAC 59.523 37.037 20.15 0.00 37.08 5.34
2823 5906 7.515643 ACAGTTTAAACTATAACATGTCACGC 58.484 34.615 20.15 0.00 37.08 5.34
2824 5907 8.166706 GGACAGTTTAAACTATAACATGTCACG 58.833 37.037 24.25 11.88 37.08 4.35
2825 5908 8.995220 TGGACAGTTTAAACTATAACATGTCAC 58.005 33.333 24.25 17.67 37.08 3.67
2826 5909 9.733556 ATGGACAGTTTAAACTATAACATGTCA 57.266 29.630 24.25 15.97 37.08 3.58
2827 5910 9.988350 CATGGACAGTTTAAACTATAACATGTC 57.012 33.333 26.38 23.10 37.08 3.06
2828 5911 8.956426 CCATGGACAGTTTAAACTATAACATGT 58.044 33.333 28.89 20.68 37.08 3.21
2829 5912 9.173021 TCCATGGACAGTTTAAACTATAACATG 57.827 33.333 27.02 27.02 37.08 3.21
2830 5913 9.747898 TTCCATGGACAGTTTAAACTATAACAT 57.252 29.630 20.15 17.28 37.08 2.71
2831 5914 9.226606 CTTCCATGGACAGTTTAAACTATAACA 57.773 33.333 20.15 15.99 37.08 2.41
2832 5915 9.444600 TCTTCCATGGACAGTTTAAACTATAAC 57.555 33.333 20.15 11.42 37.08 1.89
2843 5926 9.614792 GTAAACTTATATCTTCCATGGACAGTT 57.385 33.333 15.91 12.25 0.00 3.16
2844 5927 7.926555 CGTAAACTTATATCTTCCATGGACAGT 59.073 37.037 15.91 5.54 0.00 3.55
2845 5928 8.141909 TCGTAAACTTATATCTTCCATGGACAG 58.858 37.037 15.91 14.94 0.00 3.51
2846 5929 8.014070 TCGTAAACTTATATCTTCCATGGACA 57.986 34.615 15.91 4.19 0.00 4.02
2847 5930 8.882415 TTCGTAAACTTATATCTTCCATGGAC 57.118 34.615 15.91 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.