Multiple sequence alignment - TraesCS5B01G120000

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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 TraesCS5B01G120000 chr5B 100.000 4127 0 0 1 4127 212637602 212633476 0.000000e+00 7622.0
1 TraesCS5B01G120000 chr5B 80.872 596 101 6 2057 2641 197193188 197192595 1.350000e-124 457.0
2 TraesCS5B01G120000 chr5B 91.060 302 25 1 824 1123 212649811 212649510 1.380000e-109 407.0
3 TraesCS5B01G120000 chr5B 74.858 883 201 12 21 887 473191009 473191886 8.370000e-102 381.0
4 TraesCS5B01G120000 chr5A 94.470 1718 64 13 1124 2830 225242177 225243874 0.000000e+00 2617.0
5 TraesCS5B01G120000 chr5A 91.986 836 32 11 3317 4127 225244704 225245529 0.000000e+00 1140.0
6 TraesCS5B01G120000 chr5A 81.711 596 96 6 2057 2641 230454341 230454934 6.200000e-133 484.0
7 TraesCS5B01G120000 chr5A 88.889 162 11 5 2820 2980 225244456 225244611 4.210000e-45 193.0
8 TraesCS5B01G120000 chr5A 80.769 130 22 2 1931 2060 230454118 230454244 9.440000e-17 99.0
9 TraesCS5B01G120000 chr5A 88.571 70 3 4 3071 3140 225244640 225244704 3.420000e-11 80.5
10 TraesCS5B01G120000 chr5D 97.626 1053 23 2 3076 4127 201807042 201805991 0.000000e+00 1805.0
11 TraesCS5B01G120000 chr5D 91.778 1277 72 11 1 1262 201853664 201852406 0.000000e+00 1746.0
12 TraesCS5B01G120000 chr5D 94.784 786 35 1 1250 2035 201851943 201851164 0.000000e+00 1219.0
13 TraesCS5B01G120000 chr5D 94.548 697 29 2 2061 2748 201851171 201850475 0.000000e+00 1068.0
14 TraesCS5B01G120000 chr5D 81.711 596 96 6 2057 2641 192538786 192539379 6.200000e-133 484.0
15 TraesCS5B01G120000 chr5D 91.333 300 18 2 824 1123 201899740 201899449 1.790000e-108 403.0
16 TraesCS5B01G120000 chr5D 93.061 245 13 2 2746 2990 201821560 201821320 5.070000e-94 355.0
17 TraesCS5B01G120000 chr5D 79.688 128 23 2 1931 2058 192538562 192538686 5.680000e-14 89.8
18 TraesCS5B01G120000 chr5D 89.474 57 6 0 2630 2686 357891668 357891612 5.720000e-09 73.1
19 TraesCS5B01G120000 chr3B 84.049 1141 154 18 1 1123 227415742 227416872 0.000000e+00 1074.0
20 TraesCS5B01G120000 chr3B 86.023 601 72 8 1 590 683340137 683340736 5.820000e-178 634.0
21 TraesCS5B01G120000 chr3B 86.023 601 72 8 1 590 683341430 683342029 5.820000e-178 634.0
22 TraesCS5B01G120000 chr3B 74.560 739 154 25 1931 2646 680477133 680476406 4.040000e-75 292.0
23 TraesCS5B01G120000 chr4B 80.878 638 111 6 2057 2684 106491961 106491325 3.710000e-135 492.0
24 TraesCS5B01G120000 chr4D 80.691 637 114 4 2057 2684 74159238 74158602 1.720000e-133 486.0
25 TraesCS5B01G120000 chr4A 80.251 638 115 6 2057 2684 513805335 513805971 1.740000e-128 470.0
26 TraesCS5B01G120000 chr7B 82.625 541 64 17 3416 3930 625899553 625899017 6.290000e-123 451.0
27 TraesCS5B01G120000 chr7B 82.413 489 51 18 3416 3882 625869838 625870313 1.080000e-105 394.0
28 TraesCS5B01G120000 chr2B 77.963 599 103 12 2057 2627 523234151 523234748 8.490000e-92 348.0
29 TraesCS5B01G120000 chr2B 74.038 832 197 14 2 818 88415706 88416533 5.150000e-84 322.0
30 TraesCS5B01G120000 chr2B 71.722 778 193 18 126 884 411487962 411488731 4.210000e-45 193.0
31 TraesCS5B01G120000 chr2D 78.007 582 102 10 2057 2613 445060739 445061319 3.950000e-90 342.0
32 TraesCS5B01G120000 chr6B 91.489 188 16 0 1 188 387093730 387093917 4.090000e-65 259.0
33 TraesCS5B01G120000 chr6B 88.095 210 21 3 824 1030 387089426 387089634 3.190000e-61 246.0
34 TraesCS5B01G120000 chr6B 90.526 95 9 0 288 382 387093916 387094010 4.330000e-25 126.0
35 TraesCS5B01G120000 chr7D 79.688 320 37 12 3418 3715 569155053 569155366 5.410000e-49 206.0


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 TraesCS5B01G120000 chr5B 212633476 212637602 4126 True 7622.000000 7622 100.000000 1 4127 1 chr5B.!!$R2 4126
1 TraesCS5B01G120000 chr5B 197192595 197193188 593 True 457.000000 457 80.872000 2057 2641 1 chr5B.!!$R1 584
2 TraesCS5B01G120000 chr5B 473191009 473191886 877 False 381.000000 381 74.858000 21 887 1 chr5B.!!$F1 866
3 TraesCS5B01G120000 chr5A 225242177 225245529 3352 False 1007.625000 2617 90.979000 1124 4127 4 chr5A.!!$F1 3003
4 TraesCS5B01G120000 chr5A 230454118 230454934 816 False 291.500000 484 81.240000 1931 2641 2 chr5A.!!$F2 710
5 TraesCS5B01G120000 chr5D 201805991 201807042 1051 True 1805.000000 1805 97.626000 3076 4127 1 chr5D.!!$R1 1051
6 TraesCS5B01G120000 chr5D 201850475 201853664 3189 True 1344.333333 1746 93.703333 1 2748 3 chr5D.!!$R5 2747
7 TraesCS5B01G120000 chr5D 192538562 192539379 817 False 286.900000 484 80.699500 1931 2641 2 chr5D.!!$F1 710
8 TraesCS5B01G120000 chr3B 227415742 227416872 1130 False 1074.000000 1074 84.049000 1 1123 1 chr3B.!!$F1 1122
9 TraesCS5B01G120000 chr3B 683340137 683342029 1892 False 634.000000 634 86.023000 1 590 2 chr3B.!!$F2 589
10 TraesCS5B01G120000 chr3B 680476406 680477133 727 True 292.000000 292 74.560000 1931 2646 1 chr3B.!!$R1 715
11 TraesCS5B01G120000 chr4B 106491325 106491961 636 True 492.000000 492 80.878000 2057 2684 1 chr4B.!!$R1 627
12 TraesCS5B01G120000 chr4D 74158602 74159238 636 True 486.000000 486 80.691000 2057 2684 1 chr4D.!!$R1 627
13 TraesCS5B01G120000 chr4A 513805335 513805971 636 False 470.000000 470 80.251000 2057 2684 1 chr4A.!!$F1 627
14 TraesCS5B01G120000 chr7B 625899017 625899553 536 True 451.000000 451 82.625000 3416 3930 1 chr7B.!!$R1 514
15 TraesCS5B01G120000 chr2B 523234151 523234748 597 False 348.000000 348 77.963000 2057 2627 1 chr2B.!!$F3 570
16 TraesCS5B01G120000 chr2B 88415706 88416533 827 False 322.000000 322 74.038000 2 818 1 chr2B.!!$F1 816
17 TraesCS5B01G120000 chr2D 445060739 445061319 580 False 342.000000 342 78.007000 2057 2613 1 chr2D.!!$F1 556

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
702 726 0.521291 GCAGCAACGCCATTCTGTAA 59.479 50.0 0.00 0.0 0.00 2.41 F
1136 1169 0.101399 CTCACATCCCCTCGTCTTCG 59.899 60.0 0.00 0.0 38.55 3.79 F
1168 1201 0.381089 CGAACTCGCGTCCTTCCTAT 59.619 55.0 5.77 0.0 0.00 2.57 F
2709 3348 0.451783 CCGCCATACCAAAACAGCTC 59.548 55.0 0.00 0.0 0.00 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2692 3331 0.451783 CCGAGCTGTTTTGGTATGGC 59.548 55.000 0.00 0.0 0.00 4.40 R
3045 4276 0.030235 GCCGTTGAACTGTGGTTTCC 59.970 55.000 0.00 0.0 35.58 3.13 R
3065 4296 0.613260 AGTAGTCTTTGGCGATGGCA 59.387 50.000 1.01 0.0 42.47 4.92 R
3692 4955 3.970410 CCCAGTTCCCCAGCAGCA 61.970 66.667 0.00 0.0 0.00 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
44 45 1.008449 ACTCTACAGCCTACCACCCAT 59.992 52.381 0.00 0.00 0.00 4.00
73 74 3.999229 GGTCAATCAGAGCGTGTAAAG 57.001 47.619 0.00 0.00 34.67 1.85
146 147 1.067635 GGAAGCGTTGATTGCCAATGT 60.068 47.619 0.00 0.00 42.38 2.71
161 162 4.142271 TGCCAATGTCGGAATTTTGGTATC 60.142 41.667 13.28 2.46 40.59 2.24
187 188 1.191535 CGTATCACACCTCCCTTGGA 58.808 55.000 0.00 0.00 0.00 3.53
234 235 4.410883 TGGTGTGGATCCTAATTTCGGTAT 59.589 41.667 14.23 0.00 0.00 2.73
240 241 6.879458 GTGGATCCTAATTTCGGTATTATGCT 59.121 38.462 14.23 0.00 0.00 3.79
306 307 3.745480 GCCGATCATGAGGATTTTCTGGA 60.745 47.826 0.09 0.00 36.00 3.86
314 315 7.348815 TCATGAGGATTTTCTGGATATGTTGT 58.651 34.615 0.00 0.00 0.00 3.32
328 329 9.161629 CTGGATATGTTGTGTGACAATTTACTA 57.838 33.333 0.00 0.00 40.59 1.82
406 417 5.642491 GGCGAGGAAGTTTTACTCAAGTTAT 59.358 40.000 2.28 0.00 0.00 1.89
526 537 3.964688 TGCTTATCGTTTGGATCTCCCTA 59.035 43.478 0.00 0.00 36.55 3.53
567 591 1.083401 GTTTCACGTGTCGCAGCTG 60.083 57.895 16.51 10.11 0.00 4.24
568 592 1.227118 TTTCACGTGTCGCAGCTGA 60.227 52.632 20.43 0.00 0.00 4.26
569 593 0.808060 TTTCACGTGTCGCAGCTGAA 60.808 50.000 20.43 0.54 0.00 3.02
570 594 0.808060 TTCACGTGTCGCAGCTGAAA 60.808 50.000 20.43 0.10 0.00 2.69
571 595 1.083401 CACGTGTCGCAGCTGAAAC 60.083 57.895 20.43 14.72 0.00 2.78
572 596 2.244651 ACGTGTCGCAGCTGAAACC 61.245 57.895 20.43 7.47 0.00 3.27
573 597 1.956170 CGTGTCGCAGCTGAAACCT 60.956 57.895 20.43 0.00 0.00 3.50
574 598 1.498865 CGTGTCGCAGCTGAAACCTT 61.499 55.000 20.43 0.00 0.00 3.50
575 599 0.663153 GTGTCGCAGCTGAAACCTTT 59.337 50.000 20.43 0.00 0.00 3.11
576 600 0.944386 TGTCGCAGCTGAAACCTTTC 59.056 50.000 20.43 0.00 37.69 2.62
577 601 0.944386 GTCGCAGCTGAAACCTTTCA 59.056 50.000 20.43 0.68 44.31 2.69
578 602 0.944386 TCGCAGCTGAAACCTTTCAC 59.056 50.000 20.43 0.00 41.88 3.18
579 603 0.947244 CGCAGCTGAAACCTTTCACT 59.053 50.000 20.43 0.00 41.88 3.41
592 616 3.136626 ACCTTTCACTGCCAACTACTCTT 59.863 43.478 0.00 0.00 0.00 2.85
684 708 1.377202 TCGCATGGTGAAGAAGGGC 60.377 57.895 0.00 0.00 0.00 5.19
686 710 1.651240 CGCATGGTGAAGAAGGGCAG 61.651 60.000 0.00 0.00 0.00 4.85
690 714 0.823356 TGGTGAAGAAGGGCAGCAAC 60.823 55.000 0.00 0.00 39.29 4.17
700 724 2.956987 GCAGCAACGCCATTCTGT 59.043 55.556 0.00 0.00 0.00 3.41
702 726 0.521291 GCAGCAACGCCATTCTGTAA 59.479 50.000 0.00 0.00 0.00 2.41
721 745 4.642437 TGTAAATCAAAGTTCAGTGGCACA 59.358 37.500 21.41 0.00 0.00 4.57
777 801 2.764251 ATGTGTTGCGCGCTCGTTTC 62.764 55.000 33.29 17.05 38.14 2.78
971 999 3.916172 GCGTGTGTGTGGGTATATATACG 59.084 47.826 15.15 5.16 34.11 3.06
980 1008 5.182570 TGTGGGTATATATACGTCTGCTGTC 59.817 44.000 15.15 0.41 34.11 3.51
996 1026 4.529897 TGCTGTCTAGGGAACGAGTTATA 58.470 43.478 0.00 0.00 34.30 0.98
1044 1076 0.250295 TCCCTGTTGCTCCGTTTCTG 60.250 55.000 0.00 0.00 0.00 3.02
1111 1144 0.984230 TTCCTGTGAGATCCACCACC 59.016 55.000 10.60 0.00 45.09 4.61
1136 1169 0.101399 CTCACATCCCCTCGTCTTCG 59.899 60.000 0.00 0.00 38.55 3.79
1167 1200 0.674581 TCGAACTCGCGTCCTTCCTA 60.675 55.000 5.77 0.00 39.60 2.94
1168 1201 0.381089 CGAACTCGCGTCCTTCCTAT 59.619 55.000 5.77 0.00 0.00 2.57
1247 1282 1.068541 TCGTGTGACTCGTCAATCCAG 60.069 52.381 6.94 0.00 41.85 3.86
1258 1769 0.541764 TCAATCCAGGCCACCAAACC 60.542 55.000 5.01 0.00 0.00 3.27
1660 2171 2.885644 CCAACCTCGTCGGCATCG 60.886 66.667 0.00 0.00 35.61 3.84
1727 2238 2.270986 GGGCCAACTGCTTCCACAG 61.271 63.158 4.39 0.00 43.59 3.66
1754 2265 4.643385 CGACAACGCGTGCCACAC 62.643 66.667 14.98 0.56 0.00 3.82
1867 2378 2.202932 CCTCCGCCATGTCCTTCG 60.203 66.667 0.00 0.00 0.00 3.79
2320 2932 1.521681 CCCATCTTCGCCTTCGTCC 60.522 63.158 0.00 0.00 36.96 4.79
2354 2966 2.429767 CCAGATGGCCAGAGAGCGA 61.430 63.158 13.05 0.00 0.00 4.93
2709 3348 0.451783 CCGCCATACCAAAACAGCTC 59.548 55.000 0.00 0.00 0.00 4.09
2726 3365 1.269166 CTCGGTGTCATCAAGTACGC 58.731 55.000 0.00 0.00 0.00 4.42
2768 3407 4.522722 AGAGTTGGTACTGAACTAGTGC 57.477 45.455 0.00 0.00 40.65 4.40
2769 3408 3.895656 AGAGTTGGTACTGAACTAGTGCA 59.104 43.478 2.81 2.81 43.04 4.57
2771 3410 4.822026 AGTTGGTACTGAACTAGTGCATC 58.178 43.478 3.33 0.00 43.04 3.91
2772 3411 3.503827 TGGTACTGAACTAGTGCATCG 57.496 47.619 3.33 0.00 43.04 3.84
2775 3414 2.949451 ACTGAACTAGTGCATCGAGG 57.051 50.000 3.33 0.00 38.49 4.63
2776 3415 1.478510 ACTGAACTAGTGCATCGAGGG 59.521 52.381 3.33 0.00 38.49 4.30
2777 3416 1.478510 CTGAACTAGTGCATCGAGGGT 59.521 52.381 3.33 0.00 0.00 4.34
2778 3417 2.688446 CTGAACTAGTGCATCGAGGGTA 59.312 50.000 3.33 0.00 0.00 3.69
2779 3418 2.426024 TGAACTAGTGCATCGAGGGTAC 59.574 50.000 0.00 0.00 0.00 3.34
2780 3419 2.139323 ACTAGTGCATCGAGGGTACA 57.861 50.000 0.00 0.00 0.00 2.90
2781 3420 2.025155 ACTAGTGCATCGAGGGTACAG 58.975 52.381 0.00 3.31 0.00 2.74
2782 3421 2.298610 CTAGTGCATCGAGGGTACAGA 58.701 52.381 0.00 0.00 0.00 3.41
2791 3430 2.098607 TCGAGGGTACAGAACTAATGCG 59.901 50.000 0.00 0.00 0.00 4.73
2817 3456 1.229428 CTTGTGACTTGTCATGGCGT 58.771 50.000 6.74 0.00 0.00 5.68
2843 4074 7.280428 TGTTTGTAATTGTACTGGAGACGAAAA 59.720 33.333 0.00 0.00 0.00 2.29
2844 4075 7.789273 TTGTAATTGTACTGGAGACGAAAAA 57.211 32.000 0.00 0.00 0.00 1.94
2846 4077 8.025243 TGTAATTGTACTGGAGACGAAAAATC 57.975 34.615 0.00 0.00 0.00 2.17
2847 4078 7.876068 TGTAATTGTACTGGAGACGAAAAATCT 59.124 33.333 0.00 0.00 0.00 2.40
2849 4080 4.566004 TGTACTGGAGACGAAAAATCTGG 58.434 43.478 0.00 0.00 0.00 3.86
2850 4081 3.771577 ACTGGAGACGAAAAATCTGGT 57.228 42.857 0.00 0.00 0.00 4.00
2852 4083 2.744202 CTGGAGACGAAAAATCTGGTGG 59.256 50.000 0.00 0.00 0.00 4.61
2853 4084 2.105821 TGGAGACGAAAAATCTGGTGGT 59.894 45.455 0.00 0.00 0.00 4.16
2862 4093 5.982516 CGAAAAATCTGGTGGTTTTCATTCA 59.017 36.000 8.36 0.00 39.93 2.57
2867 4098 6.862469 ATCTGGTGGTTTTCATTCATTGAT 57.138 33.333 0.00 0.00 33.34 2.57
2875 4106 7.603404 GTGGTTTTCATTCATTGATCATGGAAA 59.397 33.333 12.02 4.98 33.34 3.13
2876 4107 8.322828 TGGTTTTCATTCATTGATCATGGAAAT 58.677 29.630 12.02 1.76 29.94 2.17
2877 4108 9.169592 GGTTTTCATTCATTGATCATGGAAATT 57.830 29.630 12.02 0.00 29.94 1.82
2933 4164 7.552687 TCAGAAGATGAGCCGTTATACAAATTT 59.447 33.333 0.00 0.00 32.77 1.82
2944 4175 8.517862 GCCGTTATACAAATTTTATCAACGAAC 58.482 33.333 18.89 11.16 39.73 3.95
2956 4187 9.878599 ATTTTATCAACGAACAACTTAGAAGTG 57.121 29.630 0.00 0.00 39.66 3.16
2957 4188 8.651391 TTTATCAACGAACAACTTAGAAGTGA 57.349 30.769 0.00 0.00 39.66 3.41
2960 4191 7.548196 TCAACGAACAACTTAGAAGTGAAAT 57.452 32.000 0.00 0.00 39.66 2.17
2962 4193 8.545420 TCAACGAACAACTTAGAAGTGAAATAC 58.455 33.333 0.00 0.00 39.66 1.89
2964 4195 9.754382 AACGAACAACTTAGAAGTGAAATACTA 57.246 29.630 0.00 0.00 39.18 1.82
2980 4211 9.309516 GTGAAATACTATCAGTTCCGAAACATA 57.690 33.333 0.00 0.00 37.88 2.29
2981 4212 9.878667 TGAAATACTATCAGTTCCGAAACATAA 57.121 29.630 0.00 0.00 37.88 1.90
2986 4217 8.842358 ACTATCAGTTCCGAAACATAAAGAAA 57.158 30.769 0.00 0.00 37.88 2.52
2987 4218 9.280174 ACTATCAGTTCCGAAACATAAAGAAAA 57.720 29.630 0.00 0.00 37.88 2.29
2988 4219 9.543018 CTATCAGTTCCGAAACATAAAGAAAAC 57.457 33.333 0.00 0.00 37.88 2.43
2989 4220 7.562454 TCAGTTCCGAAACATAAAGAAAACT 57.438 32.000 0.00 0.00 37.88 2.66
2991 4222 6.856426 CAGTTCCGAAACATAAAGAAAACTCC 59.144 38.462 0.00 0.00 37.88 3.85
2992 4223 6.544564 AGTTCCGAAACATAAAGAAAACTCCA 59.455 34.615 0.00 0.00 37.88 3.86
2993 4224 6.308371 TCCGAAACATAAAGAAAACTCCAC 57.692 37.500 0.00 0.00 0.00 4.02
2995 4226 6.017440 TCCGAAACATAAAGAAAACTCCACAG 60.017 38.462 0.00 0.00 0.00 3.66
2996 4227 6.017440 CCGAAACATAAAGAAAACTCCACAGA 60.017 38.462 0.00 0.00 0.00 3.41
2997 4228 7.308589 CCGAAACATAAAGAAAACTCCACAGAT 60.309 37.037 0.00 0.00 0.00 2.90
2998 4229 8.076178 CGAAACATAAAGAAAACTCCACAGATT 58.924 33.333 0.00 0.00 0.00 2.40
3036 4267 6.592166 TCAAAAAGTACGTATAAACCAAGCG 58.408 36.000 0.00 0.00 0.00 4.68
3037 4268 6.202570 TCAAAAAGTACGTATAAACCAAGCGT 59.797 34.615 0.00 0.00 39.23 5.07
3038 4269 6.544038 AAAAGTACGTATAAACCAAGCGTT 57.456 33.333 0.00 0.00 37.05 4.84
3039 4270 6.544038 AAAGTACGTATAAACCAAGCGTTT 57.456 33.333 0.00 0.00 46.53 3.60
3040 4271 6.544038 AAGTACGTATAAACCAAGCGTTTT 57.456 33.333 0.00 0.00 42.15 2.43
3041 4272 6.544038 AGTACGTATAAACCAAGCGTTTTT 57.456 33.333 0.00 0.00 42.15 1.94
3042 4273 6.365050 AGTACGTATAAACCAAGCGTTTTTG 58.635 36.000 0.00 0.00 42.15 2.44
3047 4278 3.863606 CCAAGCGTTTTTGGGGGA 58.136 55.556 7.37 0.00 43.16 4.81
3048 4279 2.128729 CCAAGCGTTTTTGGGGGAA 58.871 52.632 7.37 0.00 43.16 3.97
3049 4280 0.466124 CCAAGCGTTTTTGGGGGAAA 59.534 50.000 7.37 0.00 43.16 3.13
3050 4281 1.577468 CAAGCGTTTTTGGGGGAAAC 58.423 50.000 0.00 0.00 34.48 2.78
3064 4295 0.030235 GGAAACCACAGTTCAACGGC 59.970 55.000 0.00 0.00 34.19 5.68
3065 4296 1.021968 GAAACCACAGTTCAACGGCT 58.978 50.000 0.00 0.00 34.19 5.52
3066 4297 0.738389 AAACCACAGTTCAACGGCTG 59.262 50.000 0.00 0.00 34.19 4.85
3067 4298 1.724582 AACCACAGTTCAACGGCTGC 61.725 55.000 0.00 0.00 36.26 5.25
3068 4299 2.639286 CACAGTTCAACGGCTGCC 59.361 61.111 9.11 9.11 36.26 4.85
3069 4300 2.186160 CACAGTTCAACGGCTGCCA 61.186 57.895 20.29 0.00 36.26 4.92
3084 4315 0.613260 TGCCATCGCCAAAGACTACT 59.387 50.000 0.00 0.00 0.00 2.57
3098 4329 7.407337 CCAAAGACTACTACACAAAGAACAAC 58.593 38.462 0.00 0.00 0.00 3.32
3160 4391 4.543689 TCCTACATACCTGGGACTAACAG 58.456 47.826 0.00 0.00 35.74 3.16
3202 4433 9.877178 ATCCTTACAACTAAAGAATGACTACTG 57.123 33.333 0.00 0.00 0.00 2.74
3294 4525 4.839121 ACACAGTTCTTCAGTTGGTTACA 58.161 39.130 0.00 0.00 0.00 2.41
3353 4584 3.351740 TGGTTGCTCAAGTTTCAGTTCA 58.648 40.909 0.00 0.00 0.00 3.18
3624 4887 5.976458 TGATTATTTTTGTCCAATGGCCTC 58.024 37.500 3.32 0.00 0.00 4.70
3692 4955 6.591834 CACTCTTCGTTCTGAATACCAAAGAT 59.408 38.462 0.00 0.00 35.63 2.40
3693 4956 6.591834 ACTCTTCGTTCTGAATACCAAAGATG 59.408 38.462 0.00 0.00 35.63 2.90
3694 4957 5.351465 TCTTCGTTCTGAATACCAAAGATGC 59.649 40.000 0.00 0.00 35.63 3.91
3987 5902 9.857656 AAAGAGATCATGGATTTTGAAGCTATA 57.142 29.630 0.00 0.00 0.00 1.31
4049 5964 5.246981 TGTTCAGATCCTTGAGTCCAATT 57.753 39.130 0.00 0.00 0.00 2.32
4109 6061 2.512692 TCTGGCACCAACATAGCAAT 57.487 45.000 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 2.362397 GCTCTGATTGACCGTCCATCTA 59.638 50.000 12.48 2.49 0.00 1.98
55 56 3.038788 TGCTTTACACGCTCTGATTGA 57.961 42.857 0.00 0.00 0.00 2.57
116 117 1.016130 CAACGCTTCCATCGAGCTGT 61.016 55.000 0.00 0.00 37.99 4.40
136 137 3.007831 ACCAAAATTCCGACATTGGCAAT 59.992 39.130 6.96 6.96 44.90 3.56
161 162 2.224066 GGGAGGTGTGATACGAGGAATG 60.224 54.545 0.00 0.00 0.00 2.67
234 235 7.308770 GCAGATCACCAGCATAAATTAGCATAA 60.309 37.037 0.00 0.00 0.00 1.90
240 241 5.052693 AGGCAGATCACCAGCATAAATTA 57.947 39.130 7.47 0.00 0.00 1.40
245 246 2.397597 TGTAGGCAGATCACCAGCATA 58.602 47.619 7.47 0.00 0.00 3.14
306 307 8.440059 CACGTAGTAAATTGTCACACAACATAT 58.560 33.333 0.00 0.00 39.26 1.78
314 315 4.623002 TGAGCACGTAGTAAATTGTCACA 58.377 39.130 0.00 0.00 41.61 3.58
328 329 0.599991 TGATTCGCTGTTGAGCACGT 60.600 50.000 0.00 0.00 46.62 4.49
406 417 5.132502 CAAGGATGATTGTGCATAGGGTTA 58.867 41.667 0.00 0.00 0.00 2.85
526 537 4.524714 CACGGGATGGATCAGACTAGTATT 59.475 45.833 0.00 0.00 0.00 1.89
567 591 3.883489 AGTAGTTGGCAGTGAAAGGTTTC 59.117 43.478 0.00 0.00 37.69 2.78
568 592 3.883489 GAGTAGTTGGCAGTGAAAGGTTT 59.117 43.478 0.00 0.00 0.00 3.27
569 593 3.136626 AGAGTAGTTGGCAGTGAAAGGTT 59.863 43.478 0.00 0.00 0.00 3.50
570 594 2.706190 AGAGTAGTTGGCAGTGAAAGGT 59.294 45.455 0.00 0.00 0.00 3.50
571 595 3.409026 AGAGTAGTTGGCAGTGAAAGG 57.591 47.619 0.00 0.00 0.00 3.11
572 596 4.380531 TGAAGAGTAGTTGGCAGTGAAAG 58.619 43.478 0.00 0.00 0.00 2.62
573 597 4.141711 ACTGAAGAGTAGTTGGCAGTGAAA 60.142 41.667 0.00 0.00 35.49 2.69
574 598 3.388024 ACTGAAGAGTAGTTGGCAGTGAA 59.612 43.478 0.00 0.00 35.49 3.18
575 599 2.965831 ACTGAAGAGTAGTTGGCAGTGA 59.034 45.455 0.00 0.00 35.49 3.41
576 600 3.062763 CACTGAAGAGTAGTTGGCAGTG 58.937 50.000 0.00 0.00 44.60 3.66
577 601 2.700897 ACACTGAAGAGTAGTTGGCAGT 59.299 45.455 0.00 0.00 37.09 4.40
578 602 3.393089 ACACTGAAGAGTAGTTGGCAG 57.607 47.619 0.00 0.00 0.00 4.85
579 603 3.838244 AACACTGAAGAGTAGTTGGCA 57.162 42.857 0.00 0.00 0.00 4.92
592 616 0.250467 GGCAGCTCCTGAAACACTGA 60.250 55.000 0.00 0.00 32.44 3.41
684 708 2.987413 TTTACAGAATGGCGTTGCTG 57.013 45.000 13.71 13.71 43.62 4.41
686 710 3.485947 TGATTTACAGAATGGCGTTGC 57.514 42.857 0.00 0.00 43.62 4.17
690 714 5.698832 TGAACTTTGATTTACAGAATGGCG 58.301 37.500 0.00 0.00 43.62 5.69
698 722 4.642437 TGTGCCACTGAACTTTGATTTACA 59.358 37.500 0.00 0.00 0.00 2.41
700 724 4.887071 ACTGTGCCACTGAACTTTGATTTA 59.113 37.500 8.84 0.00 0.00 1.40
702 726 3.067180 CACTGTGCCACTGAACTTTGATT 59.933 43.478 8.84 0.00 0.00 2.57
721 745 4.248859 GTTGCATGATCTACAGTGACACT 58.751 43.478 1.07 1.07 0.00 3.55
731 755 3.114606 TCTTCCCAGGTTGCATGATCTA 58.885 45.455 0.00 0.00 0.00 1.98
777 801 3.391098 CCCAAATTGCAGGGTGGG 58.609 61.111 14.24 14.24 44.69 4.61
780 804 0.040204 CTCCTCCCAAATTGCAGGGT 59.960 55.000 8.51 0.00 45.64 4.34
781 805 0.685458 CCTCCTCCCAAATTGCAGGG 60.685 60.000 2.23 2.23 46.90 4.45
889 915 4.329545 ACATTGGTGTCGCCCGCT 62.330 61.111 0.00 0.00 31.41 5.52
956 984 5.074804 ACAGCAGACGTATATATACCCACA 58.925 41.667 15.70 0.00 0.00 4.17
971 999 1.133407 CTCGTTCCCTAGACAGCAGAC 59.867 57.143 0.00 0.00 0.00 3.51
980 1008 8.630917 TCTTTCTTCATATAACTCGTTCCCTAG 58.369 37.037 0.00 0.00 0.00 3.02
996 1026 5.934781 AGGTTCAGACTTGTCTTTCTTCAT 58.065 37.500 0.00 0.00 0.00 2.57
1044 1076 3.134442 AGAGGATTGCAGAGAATGAGGAC 59.866 47.826 0.00 0.00 0.00 3.85
1136 1169 3.480505 CGCGAGTTCGAGAAATTGAAGAC 60.481 47.826 0.00 0.00 41.67 3.01
1240 1275 1.543944 GGGTTTGGTGGCCTGGATTG 61.544 60.000 3.32 0.00 0.00 2.67
1258 1769 3.197790 CACCATTGCGAGGCTCGG 61.198 66.667 35.03 21.50 40.84 4.63
1384 1895 3.777925 GACGATGTGCGCGCTTGT 61.778 61.111 33.29 21.73 46.04 3.16
1498 2009 1.941294 CGTGGAGCTGTAGTAGACGAT 59.059 52.381 0.00 0.00 0.00 3.73
1501 2012 3.626154 GCGTGGAGCTGTAGTAGAC 57.374 57.895 0.00 0.00 44.04 2.59
1614 2125 1.664965 GACGCCGCAGAACTTCACT 60.665 57.895 0.00 0.00 0.00 3.41
1727 2238 4.025401 CGTTGTCGTGCCCCTTGC 62.025 66.667 0.00 0.00 41.77 4.01
1754 2265 2.735772 ATGTAGGGCGTGCTGGAGG 61.736 63.158 0.00 0.00 0.00 4.30
1797 2308 3.697045 AGTTGGGTATCTGAGAGAAGACG 59.303 47.826 0.00 0.00 0.00 4.18
2692 3331 0.451783 CCGAGCTGTTTTGGTATGGC 59.548 55.000 0.00 0.00 0.00 4.40
2709 3348 1.640428 ATGCGTACTTGATGACACCG 58.360 50.000 0.00 0.00 0.00 4.94
2748 3387 4.252971 TGCACTAGTTCAGTACCAACTC 57.747 45.455 10.38 0.00 34.98 3.01
2749 3388 4.618460 CGATGCACTAGTTCAGTACCAACT 60.618 45.833 11.51 11.51 34.98 3.16
2750 3389 3.612860 CGATGCACTAGTTCAGTACCAAC 59.387 47.826 0.89 0.00 34.98 3.77
2751 3390 3.508402 TCGATGCACTAGTTCAGTACCAA 59.492 43.478 0.89 0.00 34.98 3.67
2753 3392 3.489398 CCTCGATGCACTAGTTCAGTACC 60.489 52.174 0.89 0.00 34.98 3.34
2754 3393 3.489398 CCCTCGATGCACTAGTTCAGTAC 60.489 52.174 0.89 0.00 34.98 2.73
2755 3394 2.688446 CCCTCGATGCACTAGTTCAGTA 59.312 50.000 0.89 0.00 34.98 2.74
2756 3395 1.478510 CCCTCGATGCACTAGTTCAGT 59.521 52.381 0.89 0.00 38.32 3.41
2757 3396 1.478510 ACCCTCGATGCACTAGTTCAG 59.521 52.381 0.89 0.00 0.00 3.02
2758 3397 1.557099 ACCCTCGATGCACTAGTTCA 58.443 50.000 0.00 0.00 0.00 3.18
2759 3398 2.426024 TGTACCCTCGATGCACTAGTTC 59.574 50.000 0.00 0.00 0.00 3.01
2760 3399 2.427453 CTGTACCCTCGATGCACTAGTT 59.573 50.000 0.00 0.00 0.00 2.24
2761 3400 2.025155 CTGTACCCTCGATGCACTAGT 58.975 52.381 0.00 0.00 0.00 2.57
2762 3401 2.298610 TCTGTACCCTCGATGCACTAG 58.701 52.381 0.00 0.00 0.00 2.57
2764 3403 1.204941 GTTCTGTACCCTCGATGCACT 59.795 52.381 0.00 0.00 0.00 4.40
2766 3405 1.557099 AGTTCTGTACCCTCGATGCA 58.443 50.000 0.00 0.00 0.00 3.96
2767 3406 3.795623 TTAGTTCTGTACCCTCGATGC 57.204 47.619 0.00 0.00 0.00 3.91
2768 3407 4.051922 GCATTAGTTCTGTACCCTCGATG 58.948 47.826 0.00 0.00 0.00 3.84
2769 3408 3.243434 CGCATTAGTTCTGTACCCTCGAT 60.243 47.826 0.00 0.00 0.00 3.59
2771 3410 2.159282 ACGCATTAGTTCTGTACCCTCG 60.159 50.000 0.00 0.00 0.00 4.63
2772 3411 3.521947 ACGCATTAGTTCTGTACCCTC 57.478 47.619 0.00 0.00 0.00 4.30
2775 3414 3.060363 CGTCAACGCATTAGTTCTGTACC 59.940 47.826 0.00 0.00 30.96 3.34
2776 3415 4.227177 CGTCAACGCATTAGTTCTGTAC 57.773 45.455 0.00 0.00 30.96 2.90
2791 3430 1.663643 TGACAAGTCACAAGCGTCAAC 59.336 47.619 0.00 0.00 33.86 3.18
2803 3442 1.333619 ACAAACACGCCATGACAAGTC 59.666 47.619 0.00 0.00 0.00 3.01
2805 3444 3.617540 TTACAAACACGCCATGACAAG 57.382 42.857 0.00 0.00 0.00 3.16
2817 3456 5.845103 TCGTCTCCAGTACAATTACAAACA 58.155 37.500 0.00 0.00 0.00 2.83
2843 4074 6.669125 TCAATGAATGAAAACCACCAGATT 57.331 33.333 0.00 0.00 34.30 2.40
2844 4075 6.438108 TGATCAATGAATGAAAACCACCAGAT 59.562 34.615 0.00 0.00 42.54 2.90
2846 4077 6.028146 TGATCAATGAATGAAAACCACCAG 57.972 37.500 0.00 0.00 42.54 4.00
2847 4078 6.399743 CATGATCAATGAATGAAAACCACCA 58.600 36.000 0.00 0.00 42.54 4.17
2849 4080 6.632909 TCCATGATCAATGAATGAAAACCAC 58.367 36.000 0.00 0.00 42.54 4.16
2850 4081 6.854091 TCCATGATCAATGAATGAAAACCA 57.146 33.333 0.00 0.00 42.54 3.67
2883 4114 8.631797 TGATGTTTCTCTTCAAAATTCATGTGA 58.368 29.630 0.00 0.00 0.00 3.58
2918 4149 8.517862 GTTCGTTGATAAAATTTGTATAACGGC 58.482 33.333 20.73 14.45 39.79 5.68
2933 4164 8.651391 TTCACTTCTAAGTTGTTCGTTGATAA 57.349 30.769 0.00 0.00 37.08 1.75
2950 4181 7.406031 TCGGAACTGATAGTATTTCACTTCT 57.594 36.000 0.00 0.00 38.80 2.85
2951 4182 8.381387 GTTTCGGAACTGATAGTATTTCACTTC 58.619 37.037 0.00 0.00 34.40 3.01
2952 4183 7.876068 TGTTTCGGAACTGATAGTATTTCACTT 59.124 33.333 8.32 0.00 36.38 3.16
2954 4185 7.591006 TGTTTCGGAACTGATAGTATTTCAC 57.409 36.000 8.32 0.00 36.70 3.18
2955 4186 9.878667 TTATGTTTCGGAACTGATAGTATTTCA 57.121 29.630 8.32 0.00 36.70 2.69
2960 4191 9.932207 TTTCTTTATGTTTCGGAACTGATAGTA 57.068 29.630 8.32 0.00 36.70 1.82
2962 4193 9.543018 GTTTTCTTTATGTTTCGGAACTGATAG 57.457 33.333 8.32 1.04 36.70 2.08
2964 4195 8.166422 AGTTTTCTTTATGTTTCGGAACTGAT 57.834 30.769 8.32 0.00 36.70 2.90
3010 4241 8.382130 CGCTTGGTTTATACGTACTTTTTGATA 58.618 33.333 0.00 0.00 0.00 2.15
3011 4242 7.095102 ACGCTTGGTTTATACGTACTTTTTGAT 60.095 33.333 0.00 0.00 34.79 2.57
3012 4243 6.202570 ACGCTTGGTTTATACGTACTTTTTGA 59.797 34.615 0.00 0.00 34.79 2.69
3013 4244 6.365050 ACGCTTGGTTTATACGTACTTTTTG 58.635 36.000 0.00 0.00 34.79 2.44
3014 4245 6.544038 ACGCTTGGTTTATACGTACTTTTT 57.456 33.333 0.00 0.00 34.79 1.94
3015 4246 6.544038 AACGCTTGGTTTATACGTACTTTT 57.456 33.333 0.00 0.00 34.41 2.27
3016 4247 6.544038 AAACGCTTGGTTTATACGTACTTT 57.456 33.333 0.00 0.00 46.76 2.66
3028 4259 0.688087 TCCCCCAAAAACGCTTGGTT 60.688 50.000 9.83 0.00 43.84 3.67
3029 4260 0.688087 TTCCCCCAAAAACGCTTGGT 60.688 50.000 9.83 0.00 43.84 3.67
3030 4261 0.466124 TTTCCCCCAAAAACGCTTGG 59.534 50.000 4.86 4.86 44.77 3.61
3031 4262 1.577468 GTTTCCCCCAAAAACGCTTG 58.423 50.000 0.00 0.00 0.00 4.01
3032 4263 0.466543 GGTTTCCCCCAAAAACGCTT 59.533 50.000 0.00 0.00 37.46 4.68
3033 4264 0.688087 TGGTTTCCCCCAAAAACGCT 60.688 50.000 0.00 0.00 37.46 5.07
3034 4265 0.531090 GTGGTTTCCCCCAAAAACGC 60.531 55.000 0.00 0.00 37.46 4.84
3035 4266 0.824759 TGTGGTTTCCCCCAAAAACG 59.175 50.000 0.00 0.00 37.46 3.60
3036 4267 1.834896 ACTGTGGTTTCCCCCAAAAAC 59.165 47.619 0.00 0.00 35.92 2.43
3037 4268 2.255770 ACTGTGGTTTCCCCCAAAAA 57.744 45.000 0.00 0.00 35.92 1.94
3038 4269 2.112190 GAACTGTGGTTTCCCCCAAAA 58.888 47.619 0.00 0.00 35.92 2.44
3039 4270 1.007238 TGAACTGTGGTTTCCCCCAAA 59.993 47.619 0.00 0.00 35.92 3.28
3040 4271 0.631753 TGAACTGTGGTTTCCCCCAA 59.368 50.000 0.00 0.00 35.92 4.12
3041 4272 0.631753 TTGAACTGTGGTTTCCCCCA 59.368 50.000 0.00 0.00 35.58 4.96
3042 4273 1.037493 GTTGAACTGTGGTTTCCCCC 58.963 55.000 0.00 0.00 35.58 5.40
3043 4274 0.666374 CGTTGAACTGTGGTTTCCCC 59.334 55.000 0.00 0.00 35.58 4.81
3044 4275 0.666374 CCGTTGAACTGTGGTTTCCC 59.334 55.000 0.00 0.00 35.58 3.97
3045 4276 0.030235 GCCGTTGAACTGTGGTTTCC 59.970 55.000 0.00 0.00 35.58 3.13
3046 4277 1.021968 AGCCGTTGAACTGTGGTTTC 58.978 50.000 0.00 0.00 35.58 2.78
3047 4278 0.738389 CAGCCGTTGAACTGTGGTTT 59.262 50.000 0.00 0.00 35.58 3.27
3048 4279 1.724582 GCAGCCGTTGAACTGTGGTT 61.725 55.000 0.00 0.00 38.52 3.67
3049 4280 2.186826 GCAGCCGTTGAACTGTGGT 61.187 57.895 0.00 0.00 36.26 4.16
3050 4281 2.639286 GCAGCCGTTGAACTGTGG 59.361 61.111 0.00 0.00 36.26 4.17
3051 4282 1.518056 ATGGCAGCCGTTGAACTGTG 61.518 55.000 7.03 0.00 36.26 3.66
3052 4283 1.228245 ATGGCAGCCGTTGAACTGT 60.228 52.632 7.03 0.00 36.26 3.55
3053 4284 1.503542 GATGGCAGCCGTTGAACTG 59.496 57.895 7.85 0.00 36.96 3.16
3054 4285 2.034879 CGATGGCAGCCGTTGAACT 61.035 57.895 15.40 0.00 0.00 3.01
3055 4286 2.480555 CGATGGCAGCCGTTGAAC 59.519 61.111 15.40 0.00 0.00 3.18
3056 4287 3.430862 GCGATGGCAGCCGTTGAA 61.431 61.111 23.72 0.00 39.62 2.69
3063 4294 0.744414 TAGTCTTTGGCGATGGCAGC 60.744 55.000 1.01 0.00 42.47 5.25
3064 4295 1.009829 GTAGTCTTTGGCGATGGCAG 58.990 55.000 1.01 0.00 42.47 4.85
3065 4296 0.613260 AGTAGTCTTTGGCGATGGCA 59.387 50.000 1.01 0.00 42.47 4.92
3066 4297 2.202566 GTAGTAGTCTTTGGCGATGGC 58.797 52.381 0.00 0.00 38.90 4.40
3067 4298 3.187700 GTGTAGTAGTCTTTGGCGATGG 58.812 50.000 0.00 0.00 0.00 3.51
3068 4299 3.845178 TGTGTAGTAGTCTTTGGCGATG 58.155 45.455 0.00 0.00 0.00 3.84
3069 4300 4.530710 TTGTGTAGTAGTCTTTGGCGAT 57.469 40.909 0.00 0.00 0.00 4.58
3084 4315 7.774134 TGTACAGTAGAGTTGTTCTTTGTGTA 58.226 34.615 0.00 0.00 37.36 2.90
3160 4391 3.550437 AGGATGTCTGTAAGGTGATGC 57.450 47.619 0.00 0.00 0.00 3.91
3202 4433 9.228949 AGATTGATATCATGGTTTAGATCTTGC 57.771 33.333 6.17 0.00 32.95 4.01
3294 4525 3.030291 TGCCCAAATGTGAAACTTCAGT 58.970 40.909 0.00 0.00 37.98 3.41
3353 4584 3.826157 TGAATTGGCTTTCGGAACTTGAT 59.174 39.130 0.00 0.00 0.00 2.57
3624 4887 4.407365 ACAAAGAGTGAATAACAAGGGGG 58.593 43.478 0.00 0.00 0.00 5.40
3692 4955 3.970410 CCCAGTTCCCCAGCAGCA 61.970 66.667 0.00 0.00 0.00 4.41
3693 4956 4.748144 CCCCAGTTCCCCAGCAGC 62.748 72.222 0.00 0.00 0.00 5.25
3694 4957 4.748144 GCCCCAGTTCCCCAGCAG 62.748 72.222 0.00 0.00 0.00 4.24
3987 5902 4.888326 TCAGGCATAAAAACCAAGCAAT 57.112 36.364 0.00 0.00 0.00 3.56
3998 5913 4.080526 GGAGGTAGGAAGTTCAGGCATAAA 60.081 45.833 5.01 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.