Multiple sequence alignment - TraesCS6D01G259800

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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 TraesCS6D01G259800 chr6D 100.000 2555 0 0 1801 4355 366536680 366539234 0.000000e+00 4719.0
1 TraesCS6D01G259800 chr6D 100.000 1408 0 0 1 1408 366534880 366536287 0.000000e+00 2601.0
2 TraesCS6D01G259800 chr6D 100.000 30 0 0 4299 4328 18862555 18862584 6.080000e-04 56.5
3 TraesCS6D01G259800 chr6B 92.227 1904 92 21 2404 4302 552242707 552244559 0.000000e+00 2645.0
4 TraesCS6D01G259800 chr6B 91.178 1451 69 23 1 1405 552240570 552242007 0.000000e+00 1916.0
5 TraesCS6D01G259800 chr6B 97.059 612 12 3 1801 2412 552242074 552242679 0.000000e+00 1026.0
6 TraesCS6D01G259800 chr6B 80.528 909 117 26 2559 3462 14635144 14634291 1.020000e-180 643.0
7 TraesCS6D01G259800 chr6B 96.970 33 1 0 4302 4334 6194487 6194455 6.080000e-04 56.5
8 TraesCS6D01G259800 chr6B 96.970 33 0 1 4300 4331 11959758 11959790 2.000000e-03 54.7
9 TraesCS6D01G259800 chr6A 90.734 1403 84 17 2466 3848 507091367 507092743 0.000000e+00 1829.0
10 TraesCS6D01G259800 chr6A 88.166 1445 89 32 1 1405 507088955 507090357 0.000000e+00 1646.0
11 TraesCS6D01G259800 chr6A 97.025 605 11 3 1801 2402 507090430 507091030 0.000000e+00 1011.0
12 TraesCS6D01G259800 chr6A 91.774 389 28 3 3911 4298 507092777 507093162 4.960000e-149 538.0
13 TraesCS6D01G259800 chr2A 79.693 911 122 28 2559 3462 733418299 733417445 2.240000e-167 599.0
14 TraesCS6D01G259800 chr5A 79.473 911 124 28 2559 3462 688482112 688482966 4.850000e-164 588.0
15 TraesCS6D01G259800 chr4B 79.605 912 114 35 2559 3462 483094245 483093398 4.850000e-164 588.0
16 TraesCS6D01G259800 chr4A 79.751 884 114 34 2559 3435 577728351 577729176 8.120000e-162 580.0
17 TraesCS6D01G259800 chr3A 77.682 699 107 20 2559 3253 538852133 538851480 8.840000e-102 381.0
18 TraesCS6D01G259800 chr3A 92.683 41 3 0 4299 4339 729117372 729117332 4.700000e-05 60.2
19 TraesCS6D01G259800 chr7A 97.368 38 1 0 4302 4339 180167016 180166979 1.010000e-06 65.8
20 TraesCS6D01G259800 chr7A 97.368 38 1 0 4302 4339 180373574 180373537 1.010000e-06 65.8
21 TraesCS6D01G259800 chr7A 89.583 48 3 2 4302 4349 179907498 179907453 4.700000e-05 60.2
22 TraesCS6D01G259800 chr2B 100.000 31 0 0 4301 4331 66951389 66951419 1.690000e-04 58.4
23 TraesCS6D01G259800 chr1B 100.000 30 0 0 4302 4331 367603279 367603308 6.080000e-04 56.5


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 TraesCS6D01G259800 chr6D 366534880 366539234 4354 False 3660.000000 4719 100.00000 1 4355 2 chr6D.!!$F2 4354
1 TraesCS6D01G259800 chr6B 552240570 552244559 3989 False 1862.333333 2645 93.48800 1 4302 3 chr6B.!!$F2 4301
2 TraesCS6D01G259800 chr6B 14634291 14635144 853 True 643.000000 643 80.52800 2559 3462 1 chr6B.!!$R2 903
3 TraesCS6D01G259800 chr6A 507088955 507093162 4207 False 1256.000000 1829 91.92475 1 4298 4 chr6A.!!$F1 4297
4 TraesCS6D01G259800 chr2A 733417445 733418299 854 True 599.000000 599 79.69300 2559 3462 1 chr2A.!!$R1 903
5 TraesCS6D01G259800 chr5A 688482112 688482966 854 False 588.000000 588 79.47300 2559 3462 1 chr5A.!!$F1 903
6 TraesCS6D01G259800 chr4B 483093398 483094245 847 True 588.000000 588 79.60500 2559 3462 1 chr4B.!!$R1 903
7 TraesCS6D01G259800 chr4A 577728351 577729176 825 False 580.000000 580 79.75100 2559 3435 1 chr4A.!!$F1 876
8 TraesCS6D01G259800 chr3A 538851480 538852133 653 True 381.000000 381 77.68200 2559 3253 1 chr3A.!!$R1 694

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
595 613 0.030638 TTCAGCGCACAAAAGGCTTC 59.969 50.000 11.47 0.0 34.13 3.86 F
1004 1052 0.116940 AACCCAACCAATCCCATGCT 59.883 50.000 0.00 0.0 0.00 3.79 F
1005 1053 0.615544 ACCCAACCAATCCCATGCTG 60.616 55.000 0.00 0.0 0.00 4.41 F
1032 1085 0.734942 CCACGGCGACAAACTCGTAT 60.735 55.000 16.62 0.0 44.92 3.06 F
2315 2386 1.000163 TGCTTGTCTGACTCCTCGTTC 60.000 52.381 9.51 0.0 0.00 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2446 2552 0.101219 GCCTGAAAGCTTAATGCCGG 59.899 55.000 0.00 0.00 44.23 6.13 R
2590 2938 3.055530 AGAGTTCCACCAGATTGCACTAG 60.056 47.826 0.00 0.00 0.00 2.57 R
2766 3116 4.141937 TGACTTAGCCTGCTGGTAATACTG 60.142 45.833 11.69 0.00 36.41 2.74 R
2963 3317 5.989477 AGTATATGCAGCTAAAAGTCCACA 58.011 37.500 0.00 0.00 0.00 4.17 R
4026 4400 0.036105 ATTGACATCTGTGCGCTCCA 60.036 50.000 9.73 4.36 0.00 3.86 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
74 75 0.251742 TGGAAAAGAGCCACCCCATG 60.252 55.000 0.00 0.00 0.00 3.66
77 78 0.779997 AAAAGAGCCACCCCATGTCT 59.220 50.000 0.00 0.00 0.00 3.41
86 87 2.357465 CCACCCCATGTCTGATGAATGT 60.357 50.000 0.00 0.00 0.00 2.71
102 103 4.676546 TGAATGTGTGAGCTAGATTCTCG 58.323 43.478 0.00 0.00 33.41 4.04
108 109 3.056536 TGTGAGCTAGATTCTCGCAAACT 60.057 43.478 12.19 0.00 44.94 2.66
109 110 3.549873 GTGAGCTAGATTCTCGCAAACTC 59.450 47.826 12.19 2.41 39.97 3.01
174 187 1.746991 CCGCTGGAAAGAGAAGCCC 60.747 63.158 0.00 0.00 33.24 5.19
175 188 2.103042 CGCTGGAAAGAGAAGCCCG 61.103 63.158 0.00 0.00 33.24 6.13
230 243 3.564511 GCTTGAAGCGAAAATGCTGTTA 58.435 40.909 0.00 0.00 46.60 2.41
244 257 4.558226 TGCTGTTATCAGAGTGGTGATT 57.442 40.909 4.94 0.00 43.76 2.57
245 258 4.507710 TGCTGTTATCAGAGTGGTGATTC 58.492 43.478 4.94 0.00 43.76 2.52
435 449 2.582636 AGGCAAGTGGGGAATAAGTGAT 59.417 45.455 0.00 0.00 0.00 3.06
504 522 8.682128 TCATTGTTTCTGTAAAACTTGTGTTC 57.318 30.769 2.73 0.00 34.96 3.18
533 551 3.188492 CTGACATCTCTGCTGCTACAAG 58.812 50.000 0.00 0.00 0.00 3.16
534 552 1.932511 GACATCTCTGCTGCTACAAGC 59.067 52.381 0.00 0.00 43.82 4.01
535 553 1.554160 ACATCTCTGCTGCTACAAGCT 59.446 47.619 0.00 0.00 42.97 3.74
536 554 2.762887 ACATCTCTGCTGCTACAAGCTA 59.237 45.455 0.00 0.00 42.97 3.32
537 555 3.196469 ACATCTCTGCTGCTACAAGCTAA 59.804 43.478 0.00 0.00 42.97 3.09
595 613 0.030638 TTCAGCGCACAAAAGGCTTC 59.969 50.000 11.47 0.00 34.13 3.86
613 631 7.453141 AGGCTTCTTACTCCCTATATTTTGT 57.547 36.000 0.00 0.00 0.00 2.83
678 697 1.618343 CTGCCTTTTTACCCCAGTTGG 59.382 52.381 0.00 0.00 0.00 3.77
695 714 5.484715 CAGTTGGGATGCAAGATTTTGATT 58.515 37.500 0.00 0.00 36.36 2.57
703 722 8.145767 GGGATGCAAGATTTTGATTGATCAATA 58.854 33.333 20.75 6.01 45.30 1.90
901 944 1.632589 GCCCCAGACCAAACAATCTT 58.367 50.000 0.00 0.00 0.00 2.40
904 947 2.562738 CCCCAGACCAAACAATCTTTCC 59.437 50.000 0.00 0.00 0.00 3.13
905 948 3.500343 CCCAGACCAAACAATCTTTCCT 58.500 45.455 0.00 0.00 0.00 3.36
928 971 3.552890 GCCCATAAAAATCCAGGCGATTC 60.553 47.826 0.00 0.00 40.47 2.52
946 989 3.931907 TTCCGTCCATGGAAATCTCAT 57.068 42.857 18.20 0.00 44.86 2.90
947 990 3.931907 TCCGTCCATGGAAATCTCATT 57.068 42.857 18.20 0.00 34.30 2.57
948 991 3.808728 TCCGTCCATGGAAATCTCATTC 58.191 45.455 18.20 0.00 34.30 2.67
950 993 2.880890 CGTCCATGGAAATCTCATTCCC 59.119 50.000 18.20 0.00 46.89 3.97
952 995 2.158623 TCCATGGAAATCTCATTCCCCG 60.159 50.000 13.46 0.00 46.89 5.73
953 996 2.423373 CCATGGAAATCTCATTCCCCGT 60.423 50.000 5.56 0.00 46.89 5.28
955 998 2.196595 TGGAAATCTCATTCCCCGTCT 58.803 47.619 3.78 0.00 46.89 4.18
956 999 2.576191 TGGAAATCTCATTCCCCGTCTT 59.424 45.455 3.78 0.00 46.89 3.01
957 1000 3.206964 GGAAATCTCATTCCCCGTCTTC 58.793 50.000 0.00 0.00 42.57 2.87
1002 1050 3.197549 CCTTAAACCCAACCAATCCCATG 59.802 47.826 0.00 0.00 0.00 3.66
1004 1052 0.116940 AACCCAACCAATCCCATGCT 59.883 50.000 0.00 0.00 0.00 3.79
1005 1053 0.615544 ACCCAACCAATCCCATGCTG 60.616 55.000 0.00 0.00 0.00 4.41
1006 1054 1.332144 CCCAACCAATCCCATGCTGG 61.332 60.000 0.00 0.00 37.25 4.85
1027 1080 3.276846 GTGCCACGGCGACAAACT 61.277 61.111 16.62 0.00 45.51 2.66
1032 1085 0.734942 CCACGGCGACAAACTCGTAT 60.735 55.000 16.62 0.00 44.92 3.06
1034 1087 1.065358 ACGGCGACAAACTCGTATTG 58.935 50.000 16.62 0.00 44.92 1.90
1036 1089 1.717194 GGCGACAAACTCGTATTGGA 58.283 50.000 0.00 0.00 44.92 3.53
1037 1090 1.392510 GGCGACAAACTCGTATTGGAC 59.607 52.381 0.00 0.00 44.92 4.02
1039 1092 2.092211 GCGACAAACTCGTATTGGACTG 59.908 50.000 0.00 0.00 44.92 3.51
1094 1159 1.398692 GCAATAATTGGGAGGCCGAA 58.601 50.000 0.00 0.00 0.00 4.30
1120 1185 1.906990 ATCGAATCGATACTCCCGGT 58.093 50.000 17.25 0.00 45.13 5.28
1389 1457 2.729479 CGCCATCCAGCTCCAGTCT 61.729 63.158 0.00 0.00 0.00 3.24
2005 2073 2.356667 CTGCCCTTCTTCCCCACC 59.643 66.667 0.00 0.00 0.00 4.61
2008 2076 2.933834 CCCTTCTTCCCCACCGGT 60.934 66.667 0.00 0.00 0.00 5.28
2185 2253 4.148825 CCCTGCTTCGAGACCGGG 62.149 72.222 6.32 0.00 36.24 5.73
2238 2306 3.410516 CGACGCCGACAATGTGCA 61.411 61.111 0.00 0.00 38.22 4.57
2284 2352 2.227388 CCAACTGTGCTGTGAATCCTTC 59.773 50.000 0.00 0.00 0.00 3.46
2287 2355 3.406764 ACTGTGCTGTGAATCCTTCTTC 58.593 45.455 0.00 0.00 0.00 2.87
2291 2359 3.817647 GTGCTGTGAATCCTTCTTCTTGT 59.182 43.478 0.00 0.00 0.00 3.16
2314 2385 1.000283 CTGCTTGTCTGACTCCTCGTT 60.000 52.381 9.51 0.00 0.00 3.85
2315 2386 1.000163 TGCTTGTCTGACTCCTCGTTC 60.000 52.381 9.51 0.00 0.00 3.95
2316 2387 1.970447 CTTGTCTGACTCCTCGTTCG 58.030 55.000 9.51 0.00 0.00 3.95
2317 2388 1.267261 CTTGTCTGACTCCTCGTTCGT 59.733 52.381 9.51 0.00 0.00 3.85
2402 2473 1.697432 CCAACTTCCCAGTGGTCAGTA 59.303 52.381 8.74 0.00 31.60 2.74
2406 2512 2.572104 ACTTCCCAGTGGTCAGTATTCC 59.428 50.000 8.74 0.00 0.00 3.01
2428 2534 5.763204 TCCTGTTCCTTTCTGTTTGTGATAC 59.237 40.000 0.00 0.00 0.00 2.24
2435 2541 5.180117 CCTTTCTGTTTGTGATACACAGAGG 59.820 44.000 4.82 0.00 45.39 3.69
2440 2546 5.003160 TGTTTGTGATACACAGAGGGATTG 58.997 41.667 4.82 0.00 45.39 2.67
2441 2547 5.221823 TGTTTGTGATACACAGAGGGATTGA 60.222 40.000 4.82 0.00 45.39 2.57
2442 2548 5.698741 TTGTGATACACAGAGGGATTGAT 57.301 39.130 4.82 0.00 45.39 2.57
2443 2549 5.698741 TGTGATACACAGAGGGATTGATT 57.301 39.130 0.25 0.00 39.62 2.57
2446 2552 5.992217 GTGATACACAGAGGGATTGATTACC 59.008 44.000 0.00 0.00 34.08 2.85
2457 2563 3.057526 GGATTGATTACCCGGCATTAAGC 60.058 47.826 0.00 0.00 44.65 3.09
2590 2938 5.890110 ACATGTCGTTATTGTCGATGATC 57.110 39.130 0.00 0.00 39.45 2.92
2704 3054 4.255833 AGTTGTCCGACCAAAATACGTA 57.744 40.909 0.00 0.00 0.00 3.57
2705 3055 4.824289 AGTTGTCCGACCAAAATACGTAT 58.176 39.130 1.14 1.14 0.00 3.06
2706 3056 5.240121 AGTTGTCCGACCAAAATACGTATT 58.760 37.500 15.07 15.07 0.00 1.89
2707 3057 5.349543 AGTTGTCCGACCAAAATACGTATTC 59.650 40.000 20.57 7.61 0.00 1.75
2708 3058 5.075858 TGTCCGACCAAAATACGTATTCT 57.924 39.130 20.57 4.63 0.00 2.40
2709 3059 5.104374 TGTCCGACCAAAATACGTATTCTC 58.896 41.667 20.57 11.70 0.00 2.87
2710 3060 5.105635 TGTCCGACCAAAATACGTATTCTCT 60.106 40.000 20.57 3.24 0.00 3.10
2711 3061 5.231568 GTCCGACCAAAATACGTATTCTCTG 59.768 44.000 20.57 16.57 0.00 3.35
2712 3062 5.105635 TCCGACCAAAATACGTATTCTCTGT 60.106 40.000 20.57 14.75 0.00 3.41
2713 3063 6.095300 TCCGACCAAAATACGTATTCTCTGTA 59.905 38.462 20.57 1.50 0.00 2.74
2714 3064 6.197842 CCGACCAAAATACGTATTCTCTGTAC 59.802 42.308 20.57 12.21 0.00 2.90
2715 3065 6.748658 CGACCAAAATACGTATTCTCTGTACA 59.251 38.462 20.57 0.00 0.00 2.90
2716 3066 7.274033 CGACCAAAATACGTATTCTCTGTACAA 59.726 37.037 20.57 0.00 0.00 2.41
2717 3067 9.095065 GACCAAAATACGTATTCTCTGTACAAT 57.905 33.333 20.57 0.00 0.00 2.71
2718 3068 8.879759 ACCAAAATACGTATTCTCTGTACAATG 58.120 33.333 20.57 7.77 0.00 2.82
2719 3069 8.335356 CCAAAATACGTATTCTCTGTACAATGG 58.665 37.037 20.57 11.69 0.00 3.16
2720 3070 8.879759 CAAAATACGTATTCTCTGTACAATGGT 58.120 33.333 20.57 0.00 0.00 3.55
2766 3116 5.873179 TTTTACCTGAATCCACATTCGAC 57.127 39.130 0.00 0.00 41.41 4.20
2848 3202 5.499004 AACCTGGTTATAGCAAGAGTCAA 57.501 39.130 11.07 0.00 0.00 3.18
2963 3317 7.334090 AGTGTCAATTAAGTATGATGCAGTCT 58.666 34.615 0.00 0.00 0.00 3.24
2993 3347 7.797819 ACTTTTAGCTGCATATACTATTTCGC 58.202 34.615 1.02 0.00 0.00 4.70
2994 3348 6.721571 TTTAGCTGCATATACTATTTCGCC 57.278 37.500 1.02 0.00 0.00 5.54
2995 3349 3.600388 AGCTGCATATACTATTTCGCCC 58.400 45.455 1.02 0.00 0.00 6.13
3363 3721 4.392940 CCCTTCAGATATGAACATGGACC 58.607 47.826 8.09 0.00 0.00 4.46
3386 3744 2.241941 TGAAATGGGCTGCTCCTGAATA 59.758 45.455 0.00 0.00 34.39 1.75
3442 3800 0.039437 TGTGGAGCGAGTTCGAGTTC 60.039 55.000 5.60 0.00 43.02 3.01
3556 3915 3.288092 TCGCTTCTAATGCTCTAGACCA 58.712 45.455 0.00 0.00 0.00 4.02
3595 3959 3.509967 TCCTGACATGACATGTACGAAGT 59.490 43.478 20.85 0.00 45.03 3.01
3602 3966 5.989168 ACATGACATGTACGAAGTCTGAAAA 59.011 36.000 19.53 0.00 43.93 2.29
3615 3988 3.065371 AGTCTGAAAAACCTGAGCGTTTG 59.935 43.478 0.91 0.00 36.12 2.93
3616 3989 2.119457 CTGAAAAACCTGAGCGTTTGC 58.881 47.619 0.91 0.00 36.12 3.68
3622 3995 1.317613 ACCTGAGCGTTTGCATTTGA 58.682 45.000 0.00 0.00 46.23 2.69
3631 4004 6.018098 TGAGCGTTTGCATTTGATTGAAATTT 60.018 30.769 0.00 0.00 46.23 1.82
3645 4018 7.367285 TGATTGAAATTTTAGGTCAGGTTTCG 58.633 34.615 0.00 0.00 0.00 3.46
3646 4019 5.699097 TGAAATTTTAGGTCAGGTTTCGG 57.301 39.130 0.00 0.00 0.00 4.30
3709 4083 6.070995 AGGATACATCAGTCGAAACCTGTTAA 60.071 38.462 1.91 0.00 41.41 2.01
3771 4145 3.946606 CCCTTCGGGTGTTACAGTTAAT 58.053 45.455 0.00 0.00 38.25 1.40
3820 4194 6.152661 TGTTTCCAAGGAATCGAAGCAAATAT 59.847 34.615 1.78 0.00 33.79 1.28
3822 4196 7.873719 TTCCAAGGAATCGAAGCAAATATTA 57.126 32.000 0.00 0.00 0.00 0.98
3859 4233 6.524101 TGAATTATTTAACCCTTGCCTGTC 57.476 37.500 0.00 0.00 0.00 3.51
3890 4264 0.607217 CCAGTCTTGCAGCATGGTGA 60.607 55.000 28.34 10.69 35.86 4.02
3891 4265 1.241165 CAGTCTTGCAGCATGGTGAA 58.759 50.000 28.34 16.19 35.86 3.18
3892 4266 1.610038 CAGTCTTGCAGCATGGTGAAA 59.390 47.619 28.34 22.70 35.86 2.69
3893 4267 2.230508 CAGTCTTGCAGCATGGTGAAAT 59.769 45.455 28.34 6.74 35.86 2.17
3909 4283 2.556189 TGAAATGTGGTGTGGCATGTAC 59.444 45.455 0.00 0.00 0.00 2.90
4014 4388 4.067896 AGTGGACACATTGAACTTAGCTG 58.932 43.478 5.14 0.00 0.00 4.24
4015 4389 3.189287 GTGGACACATTGAACTTAGCTGG 59.811 47.826 0.00 0.00 0.00 4.85
4016 4390 3.072330 TGGACACATTGAACTTAGCTGGA 59.928 43.478 0.00 0.00 0.00 3.86
4017 4391 3.686726 GGACACATTGAACTTAGCTGGAG 59.313 47.826 0.00 0.00 0.00 3.86
4018 4392 4.319177 GACACATTGAACTTAGCTGGAGT 58.681 43.478 0.00 0.00 0.00 3.85
4019 4393 4.067896 ACACATTGAACTTAGCTGGAGTG 58.932 43.478 0.00 0.00 0.00 3.51
4020 4394 3.077359 ACATTGAACTTAGCTGGAGTGC 58.923 45.455 0.00 0.00 0.00 4.40
4021 4395 2.928801 TTGAACTTAGCTGGAGTGCA 57.071 45.000 8.29 8.29 30.78 4.57
4022 4396 2.169832 TGAACTTAGCTGGAGTGCAC 57.830 50.000 9.40 9.40 34.99 4.57
4023 4397 1.270839 TGAACTTAGCTGGAGTGCACC 60.271 52.381 14.63 4.90 34.99 5.01
4024 4398 0.764890 AACTTAGCTGGAGTGCACCA 59.235 50.000 14.63 4.26 38.33 4.17
4025 4399 0.035458 ACTTAGCTGGAGTGCACCAC 59.965 55.000 14.63 7.38 35.91 4.16
4153 4541 5.098211 GTCAAACTGCATATTTCTGAAGGC 58.902 41.667 0.00 0.00 0.00 4.35
4279 4667 7.996644 TGAACTTAGTTATCCTGTCAAAAAGGT 59.003 33.333 0.00 0.00 36.14 3.50
4302 4690 6.071616 GGTGAAATTCAGGCAAATAGGTTGTA 60.072 38.462 0.00 0.00 39.63 2.41
4303 4691 6.806739 GTGAAATTCAGGCAAATAGGTTGTAC 59.193 38.462 0.00 0.00 39.63 2.90
4304 4692 6.719370 TGAAATTCAGGCAAATAGGTTGTACT 59.281 34.615 0.00 0.00 39.63 2.73
4305 4693 6.759497 AATTCAGGCAAATAGGTTGTACTC 57.241 37.500 0.00 0.00 39.63 2.59
4306 4694 4.216411 TCAGGCAAATAGGTTGTACTCC 57.784 45.455 0.00 0.00 39.63 3.85
4307 4695 3.054655 TCAGGCAAATAGGTTGTACTCCC 60.055 47.826 0.00 0.00 39.63 4.30
4308 4696 3.054361 CAGGCAAATAGGTTGTACTCCCT 60.054 47.826 8.63 8.63 39.63 4.20
4309 4697 3.200165 AGGCAAATAGGTTGTACTCCCTC 59.800 47.826 7.11 0.00 39.63 4.30
4310 4698 3.542648 GCAAATAGGTTGTACTCCCTCC 58.457 50.000 7.11 0.00 39.63 4.30
4311 4699 3.054655 GCAAATAGGTTGTACTCCCTCCA 60.055 47.826 7.11 0.00 39.63 3.86
4312 4700 4.385310 GCAAATAGGTTGTACTCCCTCCAT 60.385 45.833 7.11 0.00 39.63 3.41
4313 4701 5.368989 CAAATAGGTTGTACTCCCTCCATC 58.631 45.833 7.11 0.00 32.08 3.51
4314 4702 2.950990 AGGTTGTACTCCCTCCATCT 57.049 50.000 0.00 0.00 0.00 2.90
4315 4703 2.753247 AGGTTGTACTCCCTCCATCTC 58.247 52.381 0.00 0.00 0.00 2.75
4316 4704 2.044492 AGGTTGTACTCCCTCCATCTCA 59.956 50.000 0.00 0.00 0.00 3.27
4317 4705 3.041946 GGTTGTACTCCCTCCATCTCAT 58.958 50.000 0.00 0.00 0.00 2.90
4318 4706 4.078571 AGGTTGTACTCCCTCCATCTCATA 60.079 45.833 0.00 0.00 0.00 2.15
4319 4707 4.654262 GGTTGTACTCCCTCCATCTCATAA 59.346 45.833 0.00 0.00 0.00 1.90
4320 4708 5.308237 GGTTGTACTCCCTCCATCTCATAAT 59.692 44.000 0.00 0.00 0.00 1.28
4321 4709 6.497259 GGTTGTACTCCCTCCATCTCATAATA 59.503 42.308 0.00 0.00 0.00 0.98
4322 4710 7.181125 GGTTGTACTCCCTCCATCTCATAATAT 59.819 40.741 0.00 0.00 0.00 1.28
4323 4711 9.256228 GTTGTACTCCCTCCATCTCATAATATA 57.744 37.037 0.00 0.00 0.00 0.86
4324 4712 9.837681 TTGTACTCCCTCCATCTCATAATATAA 57.162 33.333 0.00 0.00 0.00 0.98
4325 4713 9.480861 TGTACTCCCTCCATCTCATAATATAAG 57.519 37.037 0.00 0.00 0.00 1.73
4326 4714 9.702253 GTACTCCCTCCATCTCATAATATAAGA 57.298 37.037 0.00 0.00 0.00 2.10
4327 4715 8.602472 ACTCCCTCCATCTCATAATATAAGAC 57.398 38.462 0.00 0.00 0.00 3.01
4328 4716 8.180165 ACTCCCTCCATCTCATAATATAAGACA 58.820 37.037 0.00 0.00 0.00 3.41
4329 4717 9.211410 CTCCCTCCATCTCATAATATAAGACAT 57.789 37.037 0.00 0.00 0.00 3.06
4330 4718 9.566331 TCCCTCCATCTCATAATATAAGACATT 57.434 33.333 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 5.003692 TCTAGCTCACACATTCATCAGAC 57.996 43.478 0.00 0.00 0.00 3.51
77 78 6.231258 AGAATCTAGCTCACACATTCATCA 57.769 37.500 0.00 0.00 0.00 3.07
86 87 3.056536 AGTTTGCGAGAATCTAGCTCACA 60.057 43.478 15.88 0.00 33.40 3.58
102 103 0.169009 GAGTGGATTGCCGAGTTTGC 59.831 55.000 0.00 0.00 36.79 3.68
108 109 1.475034 GCATAAGGAGTGGATTGCCGA 60.475 52.381 0.00 0.00 36.79 5.54
109 110 0.947244 GCATAAGGAGTGGATTGCCG 59.053 55.000 0.00 0.00 36.79 5.69
141 154 3.793144 CGGCGTTCCTCTGCTTGC 61.793 66.667 0.00 0.00 0.00 4.01
174 187 1.618861 GTGAGACTGAATCACCGACG 58.381 55.000 5.95 0.00 40.99 5.12
230 243 1.737029 CGTGCGAATCACCACTCTGAT 60.737 52.381 0.00 0.00 42.69 2.90
435 449 3.399305 TCTGCTACTGAGAGATATGGGGA 59.601 47.826 0.00 0.00 0.00 4.81
504 522 3.869832 CAGCAGAGATGTCAGTATGGTTG 59.130 47.826 0.00 0.00 36.16 3.77
533 551 6.442513 AAACACTGGATATGAAAGCTTAGC 57.557 37.500 0.00 0.00 0.00 3.09
534 552 8.514594 TGAAAAACACTGGATATGAAAGCTTAG 58.485 33.333 0.00 0.00 0.00 2.18
535 553 8.402798 TGAAAAACACTGGATATGAAAGCTTA 57.597 30.769 0.00 0.00 0.00 3.09
536 554 7.288810 TGAAAAACACTGGATATGAAAGCTT 57.711 32.000 0.00 0.00 0.00 3.74
537 555 6.899393 TGAAAAACACTGGATATGAAAGCT 57.101 33.333 0.00 0.00 0.00 3.74
595 613 6.509523 TGGGGACAAAATATAGGGAGTAAG 57.490 41.667 0.00 0.00 37.44 2.34
901 944 3.373830 CCTGGATTTTTATGGGCAGGAA 58.626 45.455 0.00 0.00 0.00 3.36
904 947 1.067516 CGCCTGGATTTTTATGGGCAG 59.932 52.381 0.00 0.00 39.53 4.85
905 948 1.110442 CGCCTGGATTTTTATGGGCA 58.890 50.000 0.00 0.00 39.53 5.36
928 971 2.880890 GGAATGAGATTTCCATGGACGG 59.119 50.000 15.91 0.00 43.92 4.79
943 986 1.280998 GGGAAAGAAGACGGGGAATGA 59.719 52.381 0.00 0.00 0.00 2.57
944 987 1.282157 AGGGAAAGAAGACGGGGAATG 59.718 52.381 0.00 0.00 0.00 2.67
946 989 0.690762 CAGGGAAAGAAGACGGGGAA 59.309 55.000 0.00 0.00 0.00 3.97
947 990 0.178915 TCAGGGAAAGAAGACGGGGA 60.179 55.000 0.00 0.00 0.00 4.81
948 991 0.912486 ATCAGGGAAAGAAGACGGGG 59.088 55.000 0.00 0.00 0.00 5.73
950 993 2.271800 CGAATCAGGGAAAGAAGACGG 58.728 52.381 0.00 0.00 0.00 4.79
952 995 2.933260 GAGCGAATCAGGGAAAGAAGAC 59.067 50.000 0.00 0.00 0.00 3.01
953 996 2.417379 CGAGCGAATCAGGGAAAGAAGA 60.417 50.000 0.00 0.00 0.00 2.87
955 998 2.007049 GCGAGCGAATCAGGGAAAGAA 61.007 52.381 0.00 0.00 0.00 2.52
956 999 0.460284 GCGAGCGAATCAGGGAAAGA 60.460 55.000 0.00 0.00 0.00 2.52
957 1000 1.432270 GGCGAGCGAATCAGGGAAAG 61.432 60.000 0.00 0.00 0.00 2.62
1027 1080 1.216977 CGGCACCAGTCCAATACGA 59.783 57.895 0.00 0.00 0.00 3.43
1120 1185 3.691342 CAAGCAGGTCGTCCGGGA 61.691 66.667 0.00 0.00 39.05 5.14
1234 1302 3.917760 CATCTCGTCCCGGGGAGC 61.918 72.222 23.50 10.66 29.39 4.70
1235 1303 3.227276 CCATCTCGTCCCGGGGAG 61.227 72.222 23.50 20.33 29.39 4.30
1236 1304 3.733507 CTCCATCTCGTCCCGGGGA 62.734 68.421 23.50 12.99 0.00 4.81
1238 1306 3.227276 CCTCCATCTCGTCCCGGG 61.227 72.222 16.85 16.85 0.00 5.73
1239 1307 2.442272 ACCTCCATCTCGTCCCGG 60.442 66.667 0.00 0.00 0.00 5.73
1240 1308 2.835705 CGACCTCCATCTCGTCCCG 61.836 68.421 0.00 0.00 0.00 5.14
1241 1309 3.121019 CGACCTCCATCTCGTCCC 58.879 66.667 0.00 0.00 0.00 4.46
1242 1310 2.122167 AGCGACCTCCATCTCGTCC 61.122 63.158 0.00 0.00 32.30 4.79
1243 1311 1.064946 CAGCGACCTCCATCTCGTC 59.935 63.158 0.00 0.00 32.30 4.20
1244 1312 3.069980 GCAGCGACCTCCATCTCGT 62.070 63.158 0.00 0.00 32.30 4.18
1888 1956 3.724914 GAAGGAGGCGAGGAAGGCG 62.725 68.421 0.00 0.00 41.99 5.52
2005 2073 4.471726 ACGCGCTCGAAGGTACCG 62.472 66.667 5.73 0.00 39.41 4.02
2238 2306 1.610379 GCAGGAAATGGCTGGGGTT 60.610 57.895 0.00 0.00 0.00 4.11
2284 2352 2.615447 TCAGACAAGCAGCAACAAGAAG 59.385 45.455 0.00 0.00 0.00 2.85
2287 2355 1.945394 AGTCAGACAAGCAGCAACAAG 59.055 47.619 2.66 0.00 0.00 3.16
2291 2359 0.761187 AGGAGTCAGACAAGCAGCAA 59.239 50.000 2.66 0.00 0.00 3.91
2314 2385 2.280119 GTGACCTGCAGCACACGA 60.280 61.111 19.88 0.00 35.19 4.35
2315 2386 3.349006 GGTGACCTGCAGCACACG 61.349 66.667 24.36 9.60 44.31 4.49
2402 2473 5.200483 TCACAAACAGAAAGGAACAGGAAT 58.800 37.500 0.00 0.00 0.00 3.01
2406 2512 6.038161 TGTGTATCACAAACAGAAAGGAACAG 59.962 38.462 0.00 0.00 41.69 3.16
2428 2534 2.485479 CCGGGTAATCAATCCCTCTGTG 60.485 54.545 0.00 0.00 41.40 3.66
2435 2541 3.057526 GCTTAATGCCGGGTAATCAATCC 60.058 47.826 2.18 0.00 35.15 3.01
2440 2546 3.630312 TGAAAGCTTAATGCCGGGTAATC 59.370 43.478 2.18 0.00 44.23 1.75
2441 2547 3.626930 TGAAAGCTTAATGCCGGGTAAT 58.373 40.909 2.18 0.00 44.23 1.89
2442 2548 3.013921 CTGAAAGCTTAATGCCGGGTAA 58.986 45.455 2.18 0.00 44.23 2.85
2443 2549 2.639065 CTGAAAGCTTAATGCCGGGTA 58.361 47.619 2.18 0.00 44.23 3.69
2446 2552 0.101219 GCCTGAAAGCTTAATGCCGG 59.899 55.000 0.00 0.00 44.23 6.13
2450 2556 5.138125 TCAAAAGGCCTGAAAGCTTAATG 57.862 39.130 5.69 0.00 0.00 1.90
2457 2563 3.765511 TCCATCATCAAAAGGCCTGAAAG 59.234 43.478 5.69 0.00 0.00 2.62
2583 2931 3.739810 CACCAGATTGCACTAGATCATCG 59.260 47.826 0.00 0.00 0.00 3.84
2590 2938 3.055530 AGAGTTCCACCAGATTGCACTAG 60.056 47.826 0.00 0.00 0.00 2.57
2704 3054 7.363793 GGCCATTTTTACCATTGTACAGAGAAT 60.364 37.037 0.00 0.00 0.00 2.40
2705 3055 6.071616 GGCCATTTTTACCATTGTACAGAGAA 60.072 38.462 0.00 0.00 0.00 2.87
2706 3056 5.417580 GGCCATTTTTACCATTGTACAGAGA 59.582 40.000 0.00 0.00 0.00 3.10
2707 3057 5.418840 AGGCCATTTTTACCATTGTACAGAG 59.581 40.000 5.01 0.00 0.00 3.35
2708 3058 5.184864 CAGGCCATTTTTACCATTGTACAGA 59.815 40.000 5.01 0.00 0.00 3.41
2709 3059 5.047377 ACAGGCCATTTTTACCATTGTACAG 60.047 40.000 5.01 0.00 0.00 2.74
2710 3060 4.835615 ACAGGCCATTTTTACCATTGTACA 59.164 37.500 5.01 0.00 0.00 2.90
2711 3061 5.400066 ACAGGCCATTTTTACCATTGTAC 57.600 39.130 5.01 0.00 0.00 2.90
2712 3062 6.010850 TGTACAGGCCATTTTTACCATTGTA 58.989 36.000 5.01 0.00 0.00 2.41
2713 3063 4.835615 TGTACAGGCCATTTTTACCATTGT 59.164 37.500 5.01 0.00 0.00 2.71
2714 3064 5.398603 TGTACAGGCCATTTTTACCATTG 57.601 39.130 5.01 0.00 0.00 2.82
2715 3065 6.405538 CATTGTACAGGCCATTTTTACCATT 58.594 36.000 5.01 0.00 0.00 3.16
2716 3066 5.626578 GCATTGTACAGGCCATTTTTACCAT 60.627 40.000 5.01 0.00 0.00 3.55
2717 3067 4.322349 GCATTGTACAGGCCATTTTTACCA 60.322 41.667 5.01 0.00 0.00 3.25
2718 3068 4.180817 GCATTGTACAGGCCATTTTTACC 58.819 43.478 5.01 0.00 0.00 2.85
2719 3069 4.815269 TGCATTGTACAGGCCATTTTTAC 58.185 39.130 5.01 0.00 0.00 2.01
2720 3070 5.474578 TTGCATTGTACAGGCCATTTTTA 57.525 34.783 5.01 0.00 0.00 1.52
2721 3071 4.348863 TTGCATTGTACAGGCCATTTTT 57.651 36.364 5.01 0.00 0.00 1.94
2722 3072 4.348863 TTTGCATTGTACAGGCCATTTT 57.651 36.364 5.01 0.00 0.00 1.82
2723 3073 4.556592 ATTTGCATTGTACAGGCCATTT 57.443 36.364 5.01 0.00 0.00 2.32
2728 3078 5.348451 CAGGTAAAATTTGCATTGTACAGGC 59.652 40.000 13.04 13.04 35.46 4.85
2766 3116 4.141937 TGACTTAGCCTGCTGGTAATACTG 60.142 45.833 11.69 0.00 36.41 2.74
2963 3317 5.989477 AGTATATGCAGCTAAAAGTCCACA 58.011 37.500 0.00 0.00 0.00 4.17
3222 3578 3.491598 AAACTGGTCACCTGGCCCG 62.492 63.158 5.59 0.00 39.61 6.13
3363 3721 1.377725 AGGAGCAGCCCATTTCACG 60.378 57.895 3.08 0.00 37.37 4.35
3442 3800 6.326375 AGCTTAAGACTCGACACAATTAGAG 58.674 40.000 6.67 0.00 36.83 2.43
3556 3915 9.003658 CATGTCAGGAAATTAAAACACTAGACT 57.996 33.333 0.00 0.00 0.00 3.24
3595 3959 2.223479 GCAAACGCTCAGGTTTTTCAGA 60.223 45.455 0.00 0.00 38.01 3.27
3602 3966 1.680735 TCAAATGCAAACGCTCAGGTT 59.319 42.857 0.00 0.00 0.00 3.50
3615 3988 7.603784 ACCTGACCTAAAATTTCAATCAAATGC 59.396 33.333 0.00 0.00 34.69 3.56
3616 3989 9.492973 AACCTGACCTAAAATTTCAATCAAATG 57.507 29.630 0.00 0.00 34.69 2.32
3622 3995 6.687604 CCGAAACCTGACCTAAAATTTCAAT 58.312 36.000 0.00 0.00 0.00 2.57
3631 4004 0.611714 GAGGCCGAAACCTGACCTAA 59.388 55.000 0.00 0.00 41.32 2.69
3645 4018 2.426842 AATTCAGTAAGCAGGAGGCC 57.573 50.000 0.00 0.00 46.50 5.19
3646 4019 3.758554 TGAAAATTCAGTAAGCAGGAGGC 59.241 43.478 0.00 0.00 36.24 4.70
3709 4083 8.588472 AGCAGAAAAAGGAAGCAAATAATAAGT 58.412 29.630 0.00 0.00 0.00 2.24
3832 4206 8.058847 ACAGGCAAGGGTTAAATAATTCATCTA 58.941 33.333 0.00 0.00 0.00 1.98
3859 4233 1.831652 AAGACTGGAGCTTGGACCGG 61.832 60.000 0.00 0.00 38.40 5.28
3890 4264 2.295909 GTGTACATGCCACACCACATTT 59.704 45.455 16.63 0.00 40.33 2.32
3891 4265 1.885887 GTGTACATGCCACACCACATT 59.114 47.619 16.63 0.00 40.33 2.71
3892 4266 1.073763 AGTGTACATGCCACACCACAT 59.926 47.619 21.45 6.30 46.01 3.21
3893 4267 0.472044 AGTGTACATGCCACACCACA 59.528 50.000 21.45 1.54 46.01 4.17
3909 4283 1.885388 TTGGTCGCACGTTCCAGTG 60.885 57.895 8.88 0.00 44.47 3.66
3993 4367 3.189287 CCAGCTAAGTTCAATGTGTCCAC 59.811 47.826 0.00 0.00 0.00 4.02
4014 4388 2.359230 GCTCCAGTGGTGCACTCC 60.359 66.667 27.29 7.50 43.43 3.85
4015 4389 2.740055 CGCTCCAGTGGTGCACTC 60.740 66.667 30.07 10.45 43.43 3.51
4016 4390 4.996434 GCGCTCCAGTGGTGCACT 62.996 66.667 30.07 0.00 46.51 4.40
4020 4394 2.793160 ATCTGTGCGCTCCAGTGGTG 62.793 60.000 21.53 8.11 0.00 4.17
4021 4395 2.587247 ATCTGTGCGCTCCAGTGGT 61.587 57.895 21.53 10.53 0.00 4.16
4022 4396 2.104859 CATCTGTGCGCTCCAGTGG 61.105 63.158 21.53 1.40 0.00 4.00
4023 4397 1.357258 GACATCTGTGCGCTCCAGTG 61.357 60.000 21.53 19.84 0.00 3.66
4024 4398 1.079543 GACATCTGTGCGCTCCAGT 60.080 57.895 21.53 9.42 0.00 4.00
4025 4399 0.671472 TTGACATCTGTGCGCTCCAG 60.671 55.000 17.99 17.99 0.00 3.86
4026 4400 0.036105 ATTGACATCTGTGCGCTCCA 60.036 50.000 9.73 4.36 0.00 3.86
4082 4470 0.249031 TGCACTGTCGACTGTCACAG 60.249 55.000 23.34 25.21 44.83 3.66
4084 4472 0.941463 CCTGCACTGTCGACTGTCAC 60.941 60.000 23.34 18.41 0.00 3.67
4092 4480 1.338674 TGTTATTCCCCTGCACTGTCG 60.339 52.381 0.00 0.00 0.00 4.35
4153 4541 6.018832 CCAGTTTTTCAGGCTACATTTTTGTG 60.019 38.462 0.00 0.00 0.00 3.33
4267 4655 4.746611 GCCTGAATTTCACCTTTTTGACAG 59.253 41.667 0.00 0.00 0.00 3.51
4279 4667 6.719370 AGTACAACCTATTTGCCTGAATTTCA 59.281 34.615 0.00 0.00 39.01 2.69
4302 4690 8.180165 TGTCTTATATTATGAGATGGAGGGAGT 58.820 37.037 1.91 0.00 0.00 3.85
4303 4691 8.601047 TGTCTTATATTATGAGATGGAGGGAG 57.399 38.462 1.91 0.00 0.00 4.30
4304 4692 9.566331 AATGTCTTATATTATGAGATGGAGGGA 57.434 33.333 1.91 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.