Multiple sequence alignment - TraesCS7A01G353800

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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 TraesCS7A01G353800 chr7A 100.000 3563 0 0 1 3563 517896582 517893020 0.000000e+00 6580
1 TraesCS7A01G353800 chr7A 89.902 1842 148 23 814 2641 518505836 518504019 0.000000e+00 2337
2 TraesCS7A01G353800 chr7A 89.880 1581 151 5 977 2548 675574099 675575679 0.000000e+00 2025
3 TraesCS7A01G353800 chr7D 93.740 2444 121 16 742 3158 477968513 477970951 0.000000e+00 3637
4 TraesCS7A01G353800 chr7D 92.019 1679 126 5 966 2638 477865486 477867162 0.000000e+00 2351
5 TraesCS7A01G353800 chr7D 90.668 1586 138 3 971 2547 585538056 585539640 0.000000e+00 2100
6 TraesCS7A01G353800 chr7D 87.179 195 15 4 3167 3361 478050950 478051134 2.790000e-51 213
7 TraesCS7A01G353800 chr7B 95.038 1733 84 2 929 2660 503106615 503108346 0.000000e+00 2723
8 TraesCS7A01G353800 chr7B 90.919 1806 130 19 814 2606 502908293 502910077 0.000000e+00 2396
9 TraesCS7A01G353800 chr7B 89.369 1665 158 10 976 2628 654252907 654251250 0.000000e+00 2076
10 TraesCS7A01G353800 chr7B 98.212 727 13 0 1 727 244212145 244211419 0.000000e+00 1271
11 TraesCS7A01G353800 chr7B 97.799 727 16 0 1 727 115691029 115691755 0.000000e+00 1254
12 TraesCS7A01G353800 chr7B 87.075 735 56 19 2654 3358 503114336 503115061 0.000000e+00 795
13 TraesCS7A01G353800 chr7B 95.935 123 5 0 742 864 503105847 503105969 2.170000e-47 200
14 TraesCS7A01G353800 chr2B 98.489 728 10 1 1 727 514326476 514325749 0.000000e+00 1282
15 TraesCS7A01G353800 chr2B 98.080 729 12 2 1 727 412288570 412289298 0.000000e+00 1267
16 TraesCS7A01G353800 chr4A 98.074 727 13 1 1 726 18026010 18025284 0.000000e+00 1264
17 TraesCS7A01G353800 chr6B 98.074 727 10 2 1 727 515573700 515574422 0.000000e+00 1262
18 TraesCS7A01G353800 chr4B 97.942 729 14 1 1 728 590061094 590061822 0.000000e+00 1262
19 TraesCS7A01G353800 chr3B 98.074 727 10 2 1 726 495106126 495105403 0.000000e+00 1262
20 TraesCS7A01G353800 chr1B 97.808 730 15 1 2 730 297303857 297303128 0.000000e+00 1258
21 TraesCS7A01G353800 chr3A 75.633 1383 291 41 1182 2541 33137250 33138609 0.000000e+00 645
22 TraesCS7A01G353800 chr5A 74.632 1360 283 47 1222 2544 475295025 475296359 8.700000e-151 544


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 TraesCS7A01G353800 chr7A 517893020 517896582 3562 True 6580.0 6580 100.0000 1 3563 1 chr7A.!!$R1 3562
1 TraesCS7A01G353800 chr7A 518504019 518505836 1817 True 2337.0 2337 89.9020 814 2641 1 chr7A.!!$R2 1827
2 TraesCS7A01G353800 chr7A 675574099 675575679 1580 False 2025.0 2025 89.8800 977 2548 1 chr7A.!!$F1 1571
3 TraesCS7A01G353800 chr7D 477968513 477970951 2438 False 3637.0 3637 93.7400 742 3158 1 chr7D.!!$F2 2416
4 TraesCS7A01G353800 chr7D 477865486 477867162 1676 False 2351.0 2351 92.0190 966 2638 1 chr7D.!!$F1 1672
5 TraesCS7A01G353800 chr7D 585538056 585539640 1584 False 2100.0 2100 90.6680 971 2547 1 chr7D.!!$F4 1576
6 TraesCS7A01G353800 chr7B 502908293 502910077 1784 False 2396.0 2396 90.9190 814 2606 1 chr7B.!!$F2 1792
7 TraesCS7A01G353800 chr7B 654251250 654252907 1657 True 2076.0 2076 89.3690 976 2628 1 chr7B.!!$R2 1652
8 TraesCS7A01G353800 chr7B 503105847 503108346 2499 False 1461.5 2723 95.4865 742 2660 2 chr7B.!!$F4 1918
9 TraesCS7A01G353800 chr7B 244211419 244212145 726 True 1271.0 1271 98.2120 1 727 1 chr7B.!!$R1 726
10 TraesCS7A01G353800 chr7B 115691029 115691755 726 False 1254.0 1254 97.7990 1 727 1 chr7B.!!$F1 726
11 TraesCS7A01G353800 chr7B 503114336 503115061 725 False 795.0 795 87.0750 2654 3358 1 chr7B.!!$F3 704
12 TraesCS7A01G353800 chr2B 514325749 514326476 727 True 1282.0 1282 98.4890 1 727 1 chr2B.!!$R1 726
13 TraesCS7A01G353800 chr2B 412288570 412289298 728 False 1267.0 1267 98.0800 1 727 1 chr2B.!!$F1 726
14 TraesCS7A01G353800 chr4A 18025284 18026010 726 True 1264.0 1264 98.0740 1 726 1 chr4A.!!$R1 725
15 TraesCS7A01G353800 chr6B 515573700 515574422 722 False 1262.0 1262 98.0740 1 727 1 chr6B.!!$F1 726
16 TraesCS7A01G353800 chr4B 590061094 590061822 728 False 1262.0 1262 97.9420 1 728 1 chr4B.!!$F1 727
17 TraesCS7A01G353800 chr3B 495105403 495106126 723 True 1262.0 1262 98.0740 1 726 1 chr3B.!!$R1 725
18 TraesCS7A01G353800 chr1B 297303128 297303857 729 True 1258.0 1258 97.8080 2 730 1 chr1B.!!$R1 728
19 TraesCS7A01G353800 chr3A 33137250 33138609 1359 False 645.0 645 75.6330 1182 2541 1 chr3A.!!$F1 1359
20 TraesCS7A01G353800 chr5A 475295025 475296359 1334 False 544.0 544 74.6320 1222 2544 1 chr5A.!!$F1 1322

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
730 733 1.292242 AGGAAGGAGGAGCCATCAGTA 59.708 52.381 0.0 0.0 36.07 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2583 3204 0.887387 AACGGCAACCACGCACTAAT 60.887 50.0 0.0 0.0 34.0 1.73 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
289 291 1.525077 GCACGACCCAAGACACCAA 60.525 57.895 0.00 0.00 0.00 3.67
730 733 1.292242 AGGAAGGAGGAGCCATCAGTA 59.708 52.381 0.00 0.00 36.07 2.74
731 734 2.090267 AGGAAGGAGGAGCCATCAGTAT 60.090 50.000 0.00 0.00 36.07 2.12
732 735 2.708325 GGAAGGAGGAGCCATCAGTATT 59.292 50.000 0.00 0.00 36.07 1.89
733 736 3.137360 GGAAGGAGGAGCCATCAGTATTT 59.863 47.826 0.00 0.00 36.07 1.40
734 737 4.385754 GGAAGGAGGAGCCATCAGTATTTT 60.386 45.833 0.00 0.00 36.07 1.82
735 738 4.162040 AGGAGGAGCCATCAGTATTTTG 57.838 45.455 0.00 0.00 40.02 2.44
736 739 3.782523 AGGAGGAGCCATCAGTATTTTGA 59.217 43.478 0.00 0.00 40.02 2.69
737 740 4.414846 AGGAGGAGCCATCAGTATTTTGAT 59.585 41.667 0.00 0.00 40.02 2.57
738 741 5.103771 AGGAGGAGCCATCAGTATTTTGATT 60.104 40.000 0.00 0.00 40.02 2.57
739 742 5.240403 GGAGGAGCCATCAGTATTTTGATTC 59.760 44.000 0.00 0.00 35.67 2.52
740 743 6.011122 AGGAGCCATCAGTATTTTGATTCT 57.989 37.500 0.00 0.00 35.67 2.40
820 823 3.591023 GAGACCTTGACTCAGCTAAACC 58.409 50.000 0.00 0.00 34.87 3.27
842 845 3.071874 TCCACATTTAGGTGAGCTTGG 57.928 47.619 0.00 0.00 41.32 3.61
930 940 3.586892 GCCTCCTATATAAGTTCACCGC 58.413 50.000 0.00 0.00 0.00 5.68
932 1515 3.833070 CCTCCTATATAAGTTCACCGCCT 59.167 47.826 0.00 0.00 0.00 5.52
950 1533 2.086869 CCTTGTCCTTGCGATGATGTT 58.913 47.619 0.00 0.00 0.00 2.71
991 1574 3.265791 CCACAGACATTCCAAGCTCTAC 58.734 50.000 0.00 0.00 0.00 2.59
1022 1605 1.590147 CGAACTGTAGGGCCTTCGT 59.410 57.895 13.45 6.60 32.65 3.85
1128 1726 1.967066 CTCATGAAGGAGATACCGGCT 59.033 52.381 0.00 0.00 44.74 5.52
1174 1772 1.304713 GACTACCCCACCGTCCTGA 60.305 63.158 0.00 0.00 0.00 3.86
1377 1975 2.426183 CGAGAAGTTCGCCGTCGTG 61.426 63.158 11.03 0.00 43.22 4.35
1602 2200 2.813908 GCCGCCGAGAACGTCATT 60.814 61.111 0.00 0.00 37.88 2.57
1677 2275 2.430367 GACCACTTCTGGGCCGTT 59.570 61.111 0.00 0.00 40.28 4.44
1918 2516 2.133641 GGCACCTGCAAAACCCTGT 61.134 57.895 0.00 0.00 44.36 4.00
2096 2711 4.479619 GAATACAAGTCGGACTACGTGTT 58.520 43.478 16.56 16.77 41.38 3.32
2097 2712 5.391950 GGAATACAAGTCGGACTACGTGTTA 60.392 44.000 16.56 6.30 41.38 2.41
2133 2751 0.036010 CCGTGTGGGAGCAGATCTTT 60.036 55.000 0.00 0.00 38.47 2.52
2340 2961 4.776349 TGTACAATTTCATGGAGCCGTAT 58.224 39.130 0.00 0.00 0.00 3.06
2349 2970 0.323302 TGGAGCCGTATGTGAGCAAA 59.677 50.000 0.00 0.00 0.00 3.68
2577 3198 0.247736 ACTGATCGAGGACCTTGCAC 59.752 55.000 3.51 1.43 0.00 4.57
2583 3204 1.671742 GAGGACCTTGCACGGAGAA 59.328 57.895 17.43 0.00 0.00 2.87
2610 3233 0.665835 GTGGTTGCCGTTTCACATGA 59.334 50.000 0.00 0.00 0.00 3.07
2622 3245 4.625742 CGTTTCACATGACCAACTAGTAGG 59.374 45.833 0.00 0.00 0.00 3.18
2628 3252 4.715297 ACATGACCAACTAGTAGGTAAGGG 59.285 45.833 0.00 0.00 38.50 3.95
2641 3265 2.428085 TAAGGGTCGCGCATAGGCA 61.428 57.895 8.75 0.00 41.24 4.75
2704 3331 6.603237 TGCTTCGTAGTGAATAAATGATGG 57.397 37.500 0.00 0.00 35.63 3.51
2731 3358 3.007506 TGTGCCCTCTTCGAGTTTATTCA 59.992 43.478 0.00 0.00 0.00 2.57
2823 3464 4.695455 GTGTCCGGATATTTCATGGGTATG 59.305 45.833 7.81 0.00 35.57 2.39
2824 3465 4.261801 GTCCGGATATTTCATGGGTATGG 58.738 47.826 7.81 0.00 34.97 2.74
2857 3498 0.594602 GTAAACCGAGCACCAAACCC 59.405 55.000 0.00 0.00 0.00 4.11
2870 3511 1.271163 CCAAACCCTAAAGAGCACGGA 60.271 52.381 0.00 0.00 0.00 4.69
2877 3518 3.119849 CCCTAAAGAGCACGGAACAAATG 60.120 47.826 0.00 0.00 0.00 2.32
2892 3533 6.514212 CGGAACAAATGTTTCACAGGTATTCA 60.514 38.462 5.48 0.00 38.56 2.57
2907 3548 6.874134 ACAGGTATTCAGTTCATACAAGTGTC 59.126 38.462 0.00 0.00 0.00 3.67
2926 3567 2.221299 AGCCGAGCACCAAACCCTA 61.221 57.895 0.00 0.00 0.00 3.53
2962 3603 1.978455 ATATTGACGCCGGCCCAGAA 61.978 55.000 23.46 9.16 0.00 3.02
2984 3625 4.406173 CGCGACCTCTCACTGCGT 62.406 66.667 0.00 0.00 43.50 5.24
2999 3640 3.118454 CGTCGGCATTGAAGCGGT 61.118 61.111 0.00 0.00 36.38 5.68
3000 3641 2.677003 CGTCGGCATTGAAGCGGTT 61.677 57.895 0.00 0.00 36.38 4.44
3003 3644 2.677003 CGGCATTGAAGCGGTTCGT 61.677 57.895 21.28 10.63 35.17 3.85
3060 3703 4.082523 CCGTGGCCGACCTCACAT 62.083 66.667 0.00 0.00 36.63 3.21
3061 3704 2.815211 CGTGGCCGACCTCACATG 60.815 66.667 0.00 0.00 36.63 3.21
3083 3731 0.809385 CCAATGAGCAAGCTCCACTG 59.191 55.000 18.54 12.36 42.09 3.66
3088 3739 2.378038 TGAGCAAGCTCCACTGTTTTT 58.622 42.857 18.54 0.00 42.09 1.94
3344 4001 5.494724 AGGATATATGCTTGTCGATGCAAT 58.505 37.500 13.12 10.65 42.74 3.56
3358 4015 3.999769 GATGCAATCGGAATGATGATCG 58.000 45.455 0.00 0.00 37.39 3.69
3359 4016 3.110447 TGCAATCGGAATGATGATCGA 57.890 42.857 0.00 0.00 37.39 3.59
3360 4017 3.667360 TGCAATCGGAATGATGATCGAT 58.333 40.909 0.00 0.00 43.06 3.59
3361 4018 3.434299 TGCAATCGGAATGATGATCGATG 59.566 43.478 0.54 0.00 41.36 3.84
3362 4019 3.181513 GCAATCGGAATGATGATCGATGG 60.182 47.826 0.54 0.00 41.36 3.51
3363 4020 4.248058 CAATCGGAATGATGATCGATGGA 58.752 43.478 0.54 0.00 41.36 3.41
3364 4021 3.582714 TCGGAATGATGATCGATGGAG 57.417 47.619 0.54 0.00 0.00 3.86
3365 4022 3.157087 TCGGAATGATGATCGATGGAGA 58.843 45.455 0.54 0.00 0.00 3.71
3366 4023 3.192212 TCGGAATGATGATCGATGGAGAG 59.808 47.826 0.54 0.00 0.00 3.20
3367 4024 3.675502 CGGAATGATGATCGATGGAGAGG 60.676 52.174 0.54 0.00 0.00 3.69
3368 4025 3.369261 GGAATGATGATCGATGGAGAGGG 60.369 52.174 0.54 0.00 0.00 4.30
3369 4026 2.388526 TGATGATCGATGGAGAGGGT 57.611 50.000 0.54 0.00 0.00 4.34
3370 4027 1.966354 TGATGATCGATGGAGAGGGTG 59.034 52.381 0.54 0.00 0.00 4.61
3371 4028 1.967066 GATGATCGATGGAGAGGGTGT 59.033 52.381 0.54 0.00 0.00 4.16
3372 4029 1.114627 TGATCGATGGAGAGGGTGTG 58.885 55.000 0.54 0.00 0.00 3.82
3373 4030 1.115467 GATCGATGGAGAGGGTGTGT 58.885 55.000 0.54 0.00 0.00 3.72
3374 4031 0.826715 ATCGATGGAGAGGGTGTGTG 59.173 55.000 0.00 0.00 0.00 3.82
3375 4032 0.541998 TCGATGGAGAGGGTGTGTGT 60.542 55.000 0.00 0.00 0.00 3.72
3376 4033 0.390340 CGATGGAGAGGGTGTGTGTG 60.390 60.000 0.00 0.00 0.00 3.82
3377 4034 0.687354 GATGGAGAGGGTGTGTGTGT 59.313 55.000 0.00 0.00 0.00 3.72
3378 4035 1.899814 GATGGAGAGGGTGTGTGTGTA 59.100 52.381 0.00 0.00 0.00 2.90
3379 4036 2.024176 TGGAGAGGGTGTGTGTGTAT 57.976 50.000 0.00 0.00 0.00 2.29
3380 4037 1.623311 TGGAGAGGGTGTGTGTGTATG 59.377 52.381 0.00 0.00 0.00 2.39
3381 4038 1.623811 GGAGAGGGTGTGTGTGTATGT 59.376 52.381 0.00 0.00 0.00 2.29
3382 4039 2.612972 GGAGAGGGTGTGTGTGTATGTG 60.613 54.545 0.00 0.00 0.00 3.21
3383 4040 2.037251 GAGAGGGTGTGTGTGTATGTGT 59.963 50.000 0.00 0.00 0.00 3.72
3384 4041 2.143122 GAGGGTGTGTGTGTATGTGTG 58.857 52.381 0.00 0.00 0.00 3.82
3385 4042 1.488812 AGGGTGTGTGTGTATGTGTGT 59.511 47.619 0.00 0.00 0.00 3.72
3386 4043 1.601903 GGGTGTGTGTGTATGTGTGTG 59.398 52.381 0.00 0.00 0.00 3.82
3387 4044 2.285083 GGTGTGTGTGTATGTGTGTGT 58.715 47.619 0.00 0.00 0.00 3.72
3388 4045 2.031560 GGTGTGTGTGTATGTGTGTGTG 59.968 50.000 0.00 0.00 0.00 3.82
3389 4046 1.668237 TGTGTGTGTATGTGTGTGTGC 59.332 47.619 0.00 0.00 0.00 4.57
3390 4047 0.933796 TGTGTGTATGTGTGTGTGCG 59.066 50.000 0.00 0.00 0.00 5.34
3391 4048 0.384230 GTGTGTATGTGTGTGTGCGC 60.384 55.000 0.00 0.00 0.00 6.09
3392 4049 1.154672 GTGTATGTGTGTGTGCGCG 60.155 57.895 0.00 0.00 0.00 6.86
3393 4050 2.202171 GTATGTGTGTGTGCGCGC 60.202 61.111 27.26 27.26 36.27 6.86
3394 4051 3.772560 TATGTGTGTGTGCGCGCG 61.773 61.111 28.44 28.44 38.36 6.86
3406 4063 4.016558 CGCGCGCGTGTTTGTTTG 62.017 61.111 42.49 13.34 34.35 2.93
3407 4064 2.947109 GCGCGCGTGTTTGTTTGT 60.947 55.556 32.35 0.00 0.00 2.83
3408 4065 2.902575 CGCGCGTGTTTGTTTGTG 59.097 55.556 24.19 0.00 0.00 3.33
3409 4066 1.865622 CGCGCGTGTTTGTTTGTGT 60.866 52.632 24.19 0.00 0.00 3.72
3410 4067 1.399504 CGCGCGTGTTTGTTTGTGTT 61.400 50.000 24.19 0.00 0.00 3.32
3411 4068 1.536149 GCGCGTGTTTGTTTGTGTTA 58.464 45.000 8.43 0.00 0.00 2.41
3412 4069 1.912110 GCGCGTGTTTGTTTGTGTTAA 59.088 42.857 8.43 0.00 0.00 2.01
3413 4070 2.532317 GCGCGTGTTTGTTTGTGTTAAT 59.468 40.909 8.43 0.00 0.00 1.40
3414 4071 3.598225 GCGCGTGTTTGTTTGTGTTAATG 60.598 43.478 8.43 0.00 0.00 1.90
3415 4072 3.544285 CGCGTGTTTGTTTGTGTTAATGT 59.456 39.130 0.00 0.00 0.00 2.71
3416 4073 4.729086 CGCGTGTTTGTTTGTGTTAATGTA 59.271 37.500 0.00 0.00 0.00 2.29
3417 4074 5.396947 CGCGTGTTTGTTTGTGTTAATGTAT 59.603 36.000 0.00 0.00 0.00 2.29
3418 4075 6.574093 CGCGTGTTTGTTTGTGTTAATGTATA 59.426 34.615 0.00 0.00 0.00 1.47
3419 4076 7.111732 CGCGTGTTTGTTTGTGTTAATGTATAA 59.888 33.333 0.00 0.00 0.00 0.98
3420 4077 8.907685 GCGTGTTTGTTTGTGTTAATGTATAAT 58.092 29.630 0.00 0.00 0.00 1.28
3473 4130 1.276415 AAAATTGTGTGTGTGTGCGC 58.724 45.000 0.00 0.00 0.00 6.09
3474 4131 0.865218 AAATTGTGTGTGTGTGCGCG 60.865 50.000 0.00 0.00 0.00 6.86
3475 4132 3.805385 ATTGTGTGTGTGTGCGCGC 62.805 57.895 27.26 27.26 36.27 6.86
3491 4148 3.860125 GCGTGTGTGCGTGTGTGT 61.860 61.111 0.00 0.00 0.00 3.72
3492 4149 2.021243 CGTGTGTGCGTGTGTGTG 59.979 61.111 0.00 0.00 0.00 3.82
3493 4150 2.277247 GTGTGTGCGTGTGTGTGC 60.277 61.111 0.00 0.00 0.00 4.57
3494 4151 3.858989 TGTGTGCGTGTGTGTGCG 61.859 61.111 0.00 0.00 0.00 5.34
3511 4168 3.607987 GCGCGCGTGTGTAGCTAG 61.608 66.667 32.35 0.00 0.00 3.42
3512 4169 2.099638 CGCGCGTGTGTAGCTAGA 59.900 61.111 24.19 0.00 0.00 2.43
3513 4170 1.298413 CGCGCGTGTGTAGCTAGAT 60.298 57.895 24.19 0.00 0.00 1.98
3514 4171 0.041576 CGCGCGTGTGTAGCTAGATA 60.042 55.000 24.19 0.00 0.00 1.98
3515 4172 1.676057 GCGCGTGTGTAGCTAGATAG 58.324 55.000 8.43 0.00 0.00 2.08
3516 4173 1.263484 GCGCGTGTGTAGCTAGATAGA 59.737 52.381 8.43 0.00 0.00 1.98
3517 4174 2.095668 GCGCGTGTGTAGCTAGATAGAT 60.096 50.000 8.43 0.00 0.00 1.98
3518 4175 3.609644 GCGCGTGTGTAGCTAGATAGATT 60.610 47.826 8.43 0.00 0.00 2.40
3519 4176 4.378149 GCGCGTGTGTAGCTAGATAGATTA 60.378 45.833 8.43 0.00 0.00 1.75
3520 4177 5.686834 CGCGTGTGTAGCTAGATAGATTAA 58.313 41.667 0.00 0.00 0.00 1.40
3521 4178 6.140786 CGCGTGTGTAGCTAGATAGATTAAA 58.859 40.000 0.00 0.00 0.00 1.52
3522 4179 6.802348 CGCGTGTGTAGCTAGATAGATTAAAT 59.198 38.462 0.00 0.00 0.00 1.40
3523 4180 7.326305 CGCGTGTGTAGCTAGATAGATTAAATT 59.674 37.037 0.00 0.00 0.00 1.82
3524 4181 8.979574 GCGTGTGTAGCTAGATAGATTAAATTT 58.020 33.333 0.00 0.00 0.00 1.82
3539 4196 7.596494 AGATTAAATTTGATATGGATGTGCCG 58.404 34.615 0.00 0.00 40.66 5.69
3540 4197 3.648339 AATTTGATATGGATGTGCCGC 57.352 42.857 0.00 0.00 40.66 6.53
3541 4198 0.943673 TTTGATATGGATGTGCCGCG 59.056 50.000 0.00 0.00 40.66 6.46
3542 4199 0.884259 TTGATATGGATGTGCCGCGG 60.884 55.000 24.05 24.05 40.66 6.46
3543 4200 1.005037 GATATGGATGTGCCGCGGA 60.005 57.895 33.48 8.89 40.66 5.54
3544 4201 1.004560 ATATGGATGTGCCGCGGAG 60.005 57.895 33.48 2.86 40.66 4.63
3545 4202 1.471829 ATATGGATGTGCCGCGGAGA 61.472 55.000 33.48 12.09 40.66 3.71
3546 4203 2.087462 TATGGATGTGCCGCGGAGAG 62.087 60.000 33.48 1.43 40.66 3.20
3547 4204 4.148825 GGATGTGCCGCGGAGAGT 62.149 66.667 33.48 11.79 0.00 3.24
3548 4205 2.125512 GATGTGCCGCGGAGAGTT 60.126 61.111 33.48 8.76 0.00 3.01
3549 4206 1.741770 GATGTGCCGCGGAGAGTTT 60.742 57.895 33.48 7.48 0.00 2.66
3550 4207 0.459585 GATGTGCCGCGGAGAGTTTA 60.460 55.000 33.48 7.26 0.00 2.01
3551 4208 0.178068 ATGTGCCGCGGAGAGTTTAT 59.822 50.000 33.48 9.46 0.00 1.40
3552 4209 0.818938 TGTGCCGCGGAGAGTTTATA 59.181 50.000 33.48 0.05 0.00 0.98
3553 4210 1.202371 TGTGCCGCGGAGAGTTTATAG 60.202 52.381 33.48 0.00 0.00 1.31
3554 4211 1.066605 GTGCCGCGGAGAGTTTATAGA 59.933 52.381 33.48 0.00 0.00 1.98
3555 4212 1.752498 TGCCGCGGAGAGTTTATAGAA 59.248 47.619 33.48 0.00 0.00 2.10
3556 4213 2.166870 TGCCGCGGAGAGTTTATAGAAA 59.833 45.455 33.48 0.00 0.00 2.52
3557 4214 3.181469 TGCCGCGGAGAGTTTATAGAAAT 60.181 43.478 33.48 0.00 0.00 2.17
3558 4215 4.038282 TGCCGCGGAGAGTTTATAGAAATA 59.962 41.667 33.48 0.00 0.00 1.40
3559 4216 5.169295 GCCGCGGAGAGTTTATAGAAATAT 58.831 41.667 33.48 0.00 0.00 1.28
3560 4217 5.638234 GCCGCGGAGAGTTTATAGAAATATT 59.362 40.000 33.48 0.00 0.00 1.28
3561 4218 6.401153 GCCGCGGAGAGTTTATAGAAATATTG 60.401 42.308 33.48 0.00 0.00 1.90
3562 4219 6.866770 CCGCGGAGAGTTTATAGAAATATTGA 59.133 38.462 24.07 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
495 498 1.219124 GCTGCTGTCGGATGAGGAA 59.781 57.895 0.00 0.00 0.00 3.36
730 733 3.245371 TGGAGGGAGCACAGAATCAAAAT 60.245 43.478 0.00 0.00 0.00 1.82
731 734 2.108075 TGGAGGGAGCACAGAATCAAAA 59.892 45.455 0.00 0.00 0.00 2.44
732 735 1.704628 TGGAGGGAGCACAGAATCAAA 59.295 47.619 0.00 0.00 0.00 2.69
733 736 1.361204 TGGAGGGAGCACAGAATCAA 58.639 50.000 0.00 0.00 0.00 2.57
734 737 1.361204 TTGGAGGGAGCACAGAATCA 58.639 50.000 0.00 0.00 0.00 2.57
735 738 2.725221 ATTGGAGGGAGCACAGAATC 57.275 50.000 0.00 0.00 0.00 2.52
736 739 3.094572 CAAATTGGAGGGAGCACAGAAT 58.905 45.455 0.00 0.00 0.00 2.40
737 740 2.517959 CAAATTGGAGGGAGCACAGAA 58.482 47.619 0.00 0.00 0.00 3.02
738 741 1.887956 GCAAATTGGAGGGAGCACAGA 60.888 52.381 0.00 0.00 0.00 3.41
739 742 0.529378 GCAAATTGGAGGGAGCACAG 59.471 55.000 0.00 0.00 0.00 3.66
740 743 1.243342 CGCAAATTGGAGGGAGCACA 61.243 55.000 0.00 0.00 0.00 4.57
820 823 3.441572 CCAAGCTCACCTAAATGTGGAAG 59.558 47.826 0.00 0.00 36.87 3.46
842 845 3.617531 CGGATCCATGGGTGAGCTATAAC 60.618 52.174 13.02 0.00 0.00 1.89
930 940 1.742761 ACATCATCGCAAGGACAAGG 58.257 50.000 0.00 0.00 38.47 3.61
932 1515 2.483877 GTGAACATCATCGCAAGGACAA 59.516 45.455 0.00 0.00 38.47 3.18
950 1533 2.073056 GTGTGTTGTGTGACTGTGTGA 58.927 47.619 0.00 0.00 0.00 3.58
1128 1726 0.397114 TCTTGGCATAGAGGAGGCGA 60.397 55.000 0.00 0.00 34.98 5.54
1174 1772 0.247736 GAGTTCCTGATGGTCTGCGT 59.752 55.000 0.00 0.00 34.23 5.24
1218 1816 0.390492 TGATGATGTAGAGCGGCTGG 59.610 55.000 7.50 0.00 0.00 4.85
1377 1975 1.026718 CCCGCATCTTGTTGAGGTCC 61.027 60.000 0.00 0.00 35.04 4.46
1602 2200 1.361271 GTCGACCACCTTGACGTCA 59.639 57.895 15.76 15.76 0.00 4.35
1866 2464 4.224274 AACGTCGCGGTGTTCCCA 62.224 61.111 6.13 0.00 0.00 4.37
2096 2711 2.612493 GGCTTGGGGAAGGGCTGTA 61.612 63.158 0.00 0.00 0.00 2.74
2097 2712 3.984732 GGCTTGGGGAAGGGCTGT 61.985 66.667 0.00 0.00 0.00 4.40
2304 2925 3.719268 TTGTACATGTCCTTGCTCCAT 57.281 42.857 0.00 0.00 0.00 3.41
2340 2961 1.398958 GCCTGGGGTTTTTGCTCACA 61.399 55.000 0.00 0.00 0.00 3.58
2577 3198 1.393539 CAACCACGCACTAATTCTCCG 59.606 52.381 0.00 0.00 0.00 4.63
2583 3204 0.887387 AACGGCAACCACGCACTAAT 60.887 50.000 0.00 0.00 34.00 1.73
2610 3233 3.359950 CGACCCTTACCTACTAGTTGGT 58.640 50.000 28.15 28.15 41.41 3.67
2622 3245 1.954651 GCCTATGCGCGACCCTTAC 60.955 63.158 12.10 0.00 0.00 2.34
2628 3252 3.622459 AAAAATGCCTATGCGCGAC 57.378 47.368 12.10 0.88 41.78 5.19
2647 3271 7.038587 TGAGCAGGGTACATAGAGAAGTAAAAA 60.039 37.037 0.00 0.00 0.00 1.94
2649 3273 5.955959 TGAGCAGGGTACATAGAGAAGTAAA 59.044 40.000 0.00 0.00 0.00 2.01
2704 3331 1.293498 TCGAAGAGGGCACAAGCTC 59.707 57.895 0.00 0.00 43.44 4.09
2755 3382 0.521735 GTGCGGTCCCAGAAAACATC 59.478 55.000 0.00 0.00 0.00 3.06
2857 3498 4.749245 ACATTTGTTCCGTGCTCTTTAG 57.251 40.909 0.00 0.00 0.00 1.85
2877 3518 7.667043 TGTATGAACTGAATACCTGTGAAAC 57.333 36.000 0.00 0.00 30.80 2.78
2892 3533 2.299013 TCGGCTGACACTTGTATGAACT 59.701 45.455 0.00 0.00 0.00 3.01
2907 3548 2.463589 TAGGGTTTGGTGCTCGGCTG 62.464 60.000 0.00 0.00 0.00 4.85
2926 3567 5.870978 GTCAATATTTGTGCCATGCTCTTTT 59.129 36.000 0.00 0.00 0.00 2.27
2962 3603 1.601197 AGTGAGAGGTCGCGTCTGT 60.601 57.895 5.77 3.57 38.32 3.41
2964 3605 2.983930 GCAGTGAGAGGTCGCGTCT 61.984 63.158 5.77 0.52 38.32 4.18
2984 3625 2.387445 CGAACCGCTTCAATGCCGA 61.387 57.895 0.00 0.00 0.00 5.54
3018 3659 1.064906 GGCGGGATCATGATCATGGAT 60.065 52.381 31.49 22.56 39.54 3.41
3057 3700 1.180029 GCTTGCTCATTGGGACATGT 58.820 50.000 0.00 0.00 39.30 3.21
3060 3703 0.322816 GGAGCTTGCTCATTGGGACA 60.323 55.000 21.97 0.00 0.00 4.02
3061 3704 0.322816 TGGAGCTTGCTCATTGGGAC 60.323 55.000 21.97 5.59 0.00 4.46
3122 3773 4.349048 AGCTAGCTATTTGGATCCACATGA 59.651 41.667 21.42 1.45 0.00 3.07
3208 3865 7.354751 TGGTCCAAACCCTAATAATTATTGC 57.645 36.000 18.98 0.00 45.83 3.56
3219 3876 4.601406 ATTAGCATTGGTCCAAACCCTA 57.399 40.909 8.75 6.75 45.83 3.53
3322 3979 5.804173 GATTGCATCGACAAGCATATATCC 58.196 41.667 9.46 0.00 40.94 2.59
3344 4001 3.157087 TCTCCATCGATCATCATTCCGA 58.843 45.455 0.00 0.00 35.43 4.55
3350 4007 1.966354 CACCCTCTCCATCGATCATCA 59.034 52.381 0.00 0.00 0.00 3.07
3351 4008 1.967066 ACACCCTCTCCATCGATCATC 59.033 52.381 0.00 0.00 0.00 2.92
3358 4015 0.687354 ACACACACACCCTCTCCATC 59.313 55.000 0.00 0.00 0.00 3.51
3359 4016 2.024176 TACACACACACCCTCTCCAT 57.976 50.000 0.00 0.00 0.00 3.41
3360 4017 1.623311 CATACACACACACCCTCTCCA 59.377 52.381 0.00 0.00 0.00 3.86
3361 4018 1.623811 ACATACACACACACCCTCTCC 59.376 52.381 0.00 0.00 0.00 3.71
3362 4019 2.037251 ACACATACACACACACCCTCTC 59.963 50.000 0.00 0.00 0.00 3.20
3363 4020 2.047061 ACACATACACACACACCCTCT 58.953 47.619 0.00 0.00 0.00 3.69
3364 4021 2.143122 CACACATACACACACACCCTC 58.857 52.381 0.00 0.00 0.00 4.30
3365 4022 1.488812 ACACACATACACACACACCCT 59.511 47.619 0.00 0.00 0.00 4.34
3366 4023 1.601903 CACACACATACACACACACCC 59.398 52.381 0.00 0.00 0.00 4.61
3367 4024 2.031560 CACACACACATACACACACACC 59.968 50.000 0.00 0.00 0.00 4.16
3368 4025 2.538737 GCACACACACATACACACACAC 60.539 50.000 0.00 0.00 0.00 3.82
3369 4026 1.668237 GCACACACACATACACACACA 59.332 47.619 0.00 0.00 0.00 3.72
3370 4027 1.332816 CGCACACACACATACACACAC 60.333 52.381 0.00 0.00 0.00 3.82
3371 4028 0.933796 CGCACACACACATACACACA 59.066 50.000 0.00 0.00 0.00 3.72
3372 4029 0.384230 GCGCACACACACATACACAC 60.384 55.000 0.30 0.00 0.00 3.82
3373 4030 1.826299 CGCGCACACACACATACACA 61.826 55.000 8.75 0.00 0.00 3.72
3374 4031 1.154672 CGCGCACACACACATACAC 60.155 57.895 8.75 0.00 0.00 2.90
3375 4032 2.949030 GCGCGCACACACACATACA 61.949 57.895 29.10 0.00 0.00 2.29
3376 4033 2.202171 GCGCGCACACACACATAC 60.202 61.111 29.10 0.00 0.00 2.39
3377 4034 3.772560 CGCGCGCACACACACATA 61.773 61.111 32.61 0.00 0.00 2.29
3390 4047 2.947109 ACAAACAAACACGCGCGC 60.947 55.556 32.58 23.91 0.00 6.86
3391 4048 1.399504 AACACAAACAAACACGCGCG 61.400 50.000 30.96 30.96 0.00 6.86
3392 4049 1.536149 TAACACAAACAAACACGCGC 58.464 45.000 5.73 0.00 0.00 6.86
3393 4050 3.544285 ACATTAACACAAACAAACACGCG 59.456 39.130 3.53 3.53 0.00 6.01
3394 4051 6.741448 ATACATTAACACAAACAAACACGC 57.259 33.333 0.00 0.00 0.00 5.34
3453 4110 1.658095 GCGCACACACACACAATTTTT 59.342 42.857 0.30 0.00 0.00 1.94
3454 4111 1.276415 GCGCACACACACACAATTTT 58.724 45.000 0.30 0.00 0.00 1.82
3455 4112 0.865218 CGCGCACACACACACAATTT 60.865 50.000 8.75 0.00 0.00 1.82
3456 4113 1.298264 CGCGCACACACACACAATT 60.298 52.632 8.75 0.00 0.00 2.32
3457 4114 2.327592 CGCGCACACACACACAAT 59.672 55.556 8.75 0.00 0.00 2.71
3458 4115 4.528740 GCGCGCACACACACACAA 62.529 61.111 29.10 0.00 0.00 3.33
3474 4131 3.860125 ACACACACGCACACACGC 61.860 61.111 0.00 0.00 36.19 5.34
3475 4132 2.021243 CACACACACGCACACACG 59.979 61.111 0.00 0.00 39.50 4.49
3476 4133 2.277247 GCACACACACGCACACAC 60.277 61.111 0.00 0.00 0.00 3.82
3477 4134 3.858989 CGCACACACACGCACACA 61.859 61.111 0.00 0.00 0.00 3.72
3494 4151 3.607987 CTAGCTACACACGCGCGC 61.608 66.667 32.58 23.91 0.00 6.86
3495 4152 0.041576 TATCTAGCTACACACGCGCG 60.042 55.000 30.96 30.96 0.00 6.86
3496 4153 1.263484 TCTATCTAGCTACACACGCGC 59.737 52.381 5.73 0.00 0.00 6.86
3497 4154 3.815337 ATCTATCTAGCTACACACGCG 57.185 47.619 3.53 3.53 0.00 6.01
3498 4155 8.522178 AATTTAATCTATCTAGCTACACACGC 57.478 34.615 0.00 0.00 0.00 5.34
3513 4170 8.729756 CGGCACATCCATATCAAATTTAATCTA 58.270 33.333 0.00 0.00 34.01 1.98
3514 4171 7.596494 CGGCACATCCATATCAAATTTAATCT 58.404 34.615 0.00 0.00 34.01 2.40
3515 4172 6.308766 GCGGCACATCCATATCAAATTTAATC 59.691 38.462 0.00 0.00 34.01 1.75
3516 4173 6.158598 GCGGCACATCCATATCAAATTTAAT 58.841 36.000 0.00 0.00 34.01 1.40
3517 4174 5.527951 GCGGCACATCCATATCAAATTTAA 58.472 37.500 0.00 0.00 34.01 1.52
3518 4175 4.320129 CGCGGCACATCCATATCAAATTTA 60.320 41.667 0.00 0.00 34.01 1.40
3519 4176 3.550639 CGCGGCACATCCATATCAAATTT 60.551 43.478 0.00 0.00 34.01 1.82
3520 4177 2.030893 CGCGGCACATCCATATCAAATT 60.031 45.455 0.00 0.00 34.01 1.82
3521 4178 1.536766 CGCGGCACATCCATATCAAAT 59.463 47.619 0.00 0.00 34.01 2.32
3522 4179 0.943673 CGCGGCACATCCATATCAAA 59.056 50.000 0.00 0.00 34.01 2.69
3523 4180 0.884259 CCGCGGCACATCCATATCAA 60.884 55.000 14.67 0.00 34.01 2.57
3524 4181 1.301637 CCGCGGCACATCCATATCA 60.302 57.895 14.67 0.00 34.01 2.15
3525 4182 1.005037 TCCGCGGCACATCCATATC 60.005 57.895 23.51 0.00 34.01 1.63
3526 4183 1.004560 CTCCGCGGCACATCCATAT 60.005 57.895 23.51 0.00 34.01 1.78
3527 4184 2.087462 CTCTCCGCGGCACATCCATA 62.087 60.000 23.51 0.00 34.01 2.74
3528 4185 3.451556 CTCTCCGCGGCACATCCAT 62.452 63.158 23.51 0.00 34.01 3.41
3529 4186 4.147449 CTCTCCGCGGCACATCCA 62.147 66.667 23.51 0.00 34.01 3.41
3530 4187 3.665675 AACTCTCCGCGGCACATCC 62.666 63.158 23.51 0.00 0.00 3.51
3531 4188 0.459585 TAAACTCTCCGCGGCACATC 60.460 55.000 23.51 0.00 0.00 3.06
3532 4189 0.178068 ATAAACTCTCCGCGGCACAT 59.822 50.000 23.51 6.75 0.00 3.21
3533 4190 0.818938 TATAAACTCTCCGCGGCACA 59.181 50.000 23.51 1.50 0.00 4.57
3534 4191 1.066605 TCTATAAACTCTCCGCGGCAC 59.933 52.381 23.51 0.00 0.00 5.01
3535 4192 1.395635 TCTATAAACTCTCCGCGGCA 58.604 50.000 23.51 8.58 0.00 5.69
3536 4193 2.503920 TTCTATAAACTCTCCGCGGC 57.496 50.000 23.51 0.00 0.00 6.53
3537 4194 6.866770 TCAATATTTCTATAAACTCTCCGCGG 59.133 38.462 22.12 22.12 0.00 6.46
3538 4195 7.869016 TCAATATTTCTATAAACTCTCCGCG 57.131 36.000 0.00 0.00 0.00 6.46


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

AutoCloner maintained by Alex Coulton.