Multiple sequence alignment - TraesCS4D01G159100

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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 TraesCS4D01G159100 chr4D 100.000 2815 0 0 1 2815 225308306 225305492 0.000000e+00 5199
1 TraesCS4D01G159100 chr4D 91.696 2565 160 19 107 2628 196910136 196912690 0.000000e+00 3507
2 TraesCS4D01G159100 chr4D 90.297 2659 177 27 107 2712 236674464 236671834 0.000000e+00 3406
3 TraesCS4D01G159100 chr4D 91.489 2397 159 16 107 2473 261233877 261231496 0.000000e+00 3254
4 TraesCS4D01G159100 chr4D 91.357 2395 162 15 107 2473 222625497 222623120 0.000000e+00 3234
5 TraesCS4D01G159100 chr4D 89.972 359 35 1 2458 2815 239785104 239784746 1.980000e-126 462
6 TraesCS4D01G159100 chr4D 92.784 194 14 0 2622 2815 196954663 196954856 5.940000e-72 281
7 TraesCS4D01G159100 chr4D 95.283 106 5 0 1 106 225333826 225333721 4.820000e-38 169
8 TraesCS4D01G159100 chr4D 94.231 104 6 0 1 104 483122426 483122323 2.900000e-35 159
9 TraesCS4D01G159100 chr4D 93.396 106 7 0 1 106 454807101 454807206 1.040000e-34 158
10 TraesCS4D01G159100 chr5B 89.971 2752 221 21 107 2815 189831307 189834046 0.000000e+00 3502
11 TraesCS4D01G159100 chr5B 89.340 2608 224 23 107 2666 399762651 399765252 0.000000e+00 3227
12 TraesCS4D01G159100 chr1D 90.408 2648 180 23 107 2712 336732016 336729401 0.000000e+00 3415
13 TraesCS4D01G159100 chr1D 90.034 2659 180 31 107 2712 463795446 463792820 0.000000e+00 3363
14 TraesCS4D01G159100 chr3B 89.539 2734 204 21 143 2815 715971919 715974631 0.000000e+00 3389
15 TraesCS4D01G159100 chr4B 89.864 2654 188 25 107 2706 505005385 505002759 0.000000e+00 3336
16 TraesCS4D01G159100 chr4A 91.785 2386 169 9 108 2473 24486814 24489192 0.000000e+00 3295
17 TraesCS4D01G159100 chr4A 95.283 106 5 0 1 106 264827136 264827031 4.820000e-38 169
18 TraesCS4D01G159100 chr3D 91.562 2394 154 15 107 2473 416550080 416552452 0.000000e+00 3258
19 TraesCS4D01G159100 chr7D 91.357 2395 146 13 107 2473 501762345 501764706 0.000000e+00 3219
20 TraesCS4D01G159100 chr7D 90.487 1745 112 14 764 2469 152009361 152007632 0.000000e+00 2254
21 TraesCS4D01G159100 chr2D 91.480 2371 151 10 139 2467 648993488 648995849 0.000000e+00 3212
22 TraesCS4D01G159100 chr2D 89.167 360 28 7 2457 2815 648995892 648996241 3.330000e-119 438
23 TraesCS4D01G159100 chr2D 94.340 106 6 0 1 106 180551580 180551685 2.240000e-36 163
24 TraesCS4D01G159100 chr1B 90.340 2412 182 15 107 2473 681897283 681899688 0.000000e+00 3116
25 TraesCS4D01G159100 chr1B 89.260 2393 188 20 139 2469 516779694 516782079 0.000000e+00 2931
26 TraesCS4D01G159100 chr6B 90.758 2348 157 21 107 2425 674458026 674460342 0.000000e+00 3079
27 TraesCS4D01G159100 chr6B 89.227 1411 142 7 1404 2814 443372098 443373498 0.000000e+00 1755
28 TraesCS4D01G159100 chr1A 92.361 576 44 0 2240 2815 168324159 168324734 0.000000e+00 821
29 TraesCS4D01G159100 chr5A 92.286 350 25 2 2467 2815 545036518 545036866 1.950000e-136 496
30 TraesCS4D01G159100 chrUn 97.196 107 3 0 1 107 147514492 147514386 6.190000e-42 182
31 TraesCS4D01G159100 chr7A 89.051 137 15 0 2679 2815 387062252 387062388 1.340000e-38 171
32 TraesCS4D01G159100 chr6D 94.340 106 6 0 1 106 258017095 258016990 2.240000e-36 163
33 TraesCS4D01G159100 chr3A 94.340 106 6 0 1 106 491349406 491349511 2.240000e-36 163
34 TraesCS4D01G159100 chr7B 90.598 117 8 2 1 114 452747320 452747436 4.860000e-33 152


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 TraesCS4D01G159100 chr4D 225305492 225308306 2814 True 5199 5199 100.0000 1 2815 1 chr4D.!!$R2 2814
1 TraesCS4D01G159100 chr4D 196910136 196912690 2554 False 3507 3507 91.6960 107 2628 1 chr4D.!!$F1 2521
2 TraesCS4D01G159100 chr4D 236671834 236674464 2630 True 3406 3406 90.2970 107 2712 1 chr4D.!!$R4 2605
3 TraesCS4D01G159100 chr4D 261231496 261233877 2381 True 3254 3254 91.4890 107 2473 1 chr4D.!!$R6 2366
4 TraesCS4D01G159100 chr4D 222623120 222625497 2377 True 3234 3234 91.3570 107 2473 1 chr4D.!!$R1 2366
5 TraesCS4D01G159100 chr5B 189831307 189834046 2739 False 3502 3502 89.9710 107 2815 1 chr5B.!!$F1 2708
6 TraesCS4D01G159100 chr5B 399762651 399765252 2601 False 3227 3227 89.3400 107 2666 1 chr5B.!!$F2 2559
7 TraesCS4D01G159100 chr1D 336729401 336732016 2615 True 3415 3415 90.4080 107 2712 1 chr1D.!!$R1 2605
8 TraesCS4D01G159100 chr1D 463792820 463795446 2626 True 3363 3363 90.0340 107 2712 1 chr1D.!!$R2 2605
9 TraesCS4D01G159100 chr3B 715971919 715974631 2712 False 3389 3389 89.5390 143 2815 1 chr3B.!!$F1 2672
10 TraesCS4D01G159100 chr4B 505002759 505005385 2626 True 3336 3336 89.8640 107 2706 1 chr4B.!!$R1 2599
11 TraesCS4D01G159100 chr4A 24486814 24489192 2378 False 3295 3295 91.7850 108 2473 1 chr4A.!!$F1 2365
12 TraesCS4D01G159100 chr3D 416550080 416552452 2372 False 3258 3258 91.5620 107 2473 1 chr3D.!!$F1 2366
13 TraesCS4D01G159100 chr7D 501762345 501764706 2361 False 3219 3219 91.3570 107 2473 1 chr7D.!!$F1 2366
14 TraesCS4D01G159100 chr7D 152007632 152009361 1729 True 2254 2254 90.4870 764 2469 1 chr7D.!!$R1 1705
15 TraesCS4D01G159100 chr2D 648993488 648996241 2753 False 1825 3212 90.3235 139 2815 2 chr2D.!!$F2 2676
16 TraesCS4D01G159100 chr1B 681897283 681899688 2405 False 3116 3116 90.3400 107 2473 1 chr1B.!!$F2 2366
17 TraesCS4D01G159100 chr1B 516779694 516782079 2385 False 2931 2931 89.2600 139 2469 1 chr1B.!!$F1 2330
18 TraesCS4D01G159100 chr6B 674458026 674460342 2316 False 3079 3079 90.7580 107 2425 1 chr6B.!!$F2 2318
19 TraesCS4D01G159100 chr6B 443372098 443373498 1400 False 1755 1755 89.2270 1404 2814 1 chr6B.!!$F1 1410
20 TraesCS4D01G159100 chr1A 168324159 168324734 575 False 821 821 92.3610 2240 2815 1 chr1A.!!$F1 575

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
97 98 0.035458 CCCTTGTCTCAAGGTTCGCT 59.965 55.0 21.87 0.0 35.65 4.93 F
1209 1280 0.179156 GCATGGATGAAAGTGGCACG 60.179 55.0 12.71 0.0 0.00 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1553 1651 0.103937 CTCTGGACGCTTCATCCCTC 59.896 60.0 0.0 0.0 35.12 4.30 R
2307 2418 0.248843 CAGACAGCTCCTCACCCTTC 59.751 60.0 0.0 0.0 0.00 3.46 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
18 19 2.745728 ACATCTTCGTAAACCCGCG 58.254 52.632 0.00 0.00 0.00 6.46
19 20 0.244450 ACATCTTCGTAAACCCGCGA 59.756 50.000 8.23 0.00 35.17 5.87
20 21 0.643820 CATCTTCGTAAACCCGCGAC 59.356 55.000 8.23 0.00 36.82 5.19
21 22 0.529378 ATCTTCGTAAACCCGCGACT 59.471 50.000 8.23 0.00 36.82 4.18
22 23 0.314935 TCTTCGTAAACCCGCGACTT 59.685 50.000 8.23 0.00 36.82 3.01
23 24 0.437295 CTTCGTAAACCCGCGACTTG 59.563 55.000 8.23 0.00 36.82 3.16
24 25 0.249405 TTCGTAAACCCGCGACTTGT 60.249 50.000 8.23 0.00 36.82 3.16
25 26 0.249405 TCGTAAACCCGCGACTTGTT 60.249 50.000 8.23 2.20 31.76 2.83
26 27 0.162294 CGTAAACCCGCGACTTGTTC 59.838 55.000 8.23 0.00 0.00 3.18
27 28 1.505425 GTAAACCCGCGACTTGTTCT 58.495 50.000 8.23 0.17 0.00 3.01
28 29 1.869132 GTAAACCCGCGACTTGTTCTT 59.131 47.619 8.23 0.00 0.00 2.52
29 30 0.661020 AAACCCGCGACTTGTTCTTG 59.339 50.000 8.23 0.00 0.00 3.02
30 31 1.782028 AACCCGCGACTTGTTCTTGC 61.782 55.000 8.23 0.00 0.00 4.01
31 32 1.961277 CCCGCGACTTGTTCTTGCT 60.961 57.895 8.23 0.00 0.00 3.91
32 33 1.205064 CCGCGACTTGTTCTTGCTG 59.795 57.895 8.23 0.00 0.00 4.41
33 34 1.439365 CGCGACTTGTTCTTGCTGC 60.439 57.895 0.00 0.00 0.00 5.25
34 35 1.439365 GCGACTTGTTCTTGCTGCG 60.439 57.895 0.00 0.00 0.00 5.18
35 36 1.831389 GCGACTTGTTCTTGCTGCGA 61.831 55.000 0.00 0.00 0.00 5.10
36 37 0.792640 CGACTTGTTCTTGCTGCGAT 59.207 50.000 0.00 0.00 0.00 4.58
37 38 1.463034 CGACTTGTTCTTGCTGCGATG 60.463 52.381 0.00 0.00 0.00 3.84
38 39 0.877071 ACTTGTTCTTGCTGCGATGG 59.123 50.000 0.00 0.00 0.00 3.51
39 40 1.159285 CTTGTTCTTGCTGCGATGGA 58.841 50.000 0.00 0.00 0.00 3.41
40 41 1.129998 CTTGTTCTTGCTGCGATGGAG 59.870 52.381 0.00 0.00 0.00 3.86
41 42 0.321346 TGTTCTTGCTGCGATGGAGA 59.679 50.000 0.00 0.00 0.00 3.71
42 43 1.065926 TGTTCTTGCTGCGATGGAGAT 60.066 47.619 0.00 0.00 0.00 2.75
43 44 2.012673 GTTCTTGCTGCGATGGAGATT 58.987 47.619 0.00 0.00 0.00 2.40
44 45 2.408271 TCTTGCTGCGATGGAGATTT 57.592 45.000 0.00 0.00 0.00 2.17
45 46 2.011947 TCTTGCTGCGATGGAGATTTG 58.988 47.619 0.00 0.00 0.00 2.32
46 47 1.741706 CTTGCTGCGATGGAGATTTGT 59.258 47.619 0.00 0.00 0.00 2.83
47 48 1.089112 TGCTGCGATGGAGATTTGTG 58.911 50.000 0.00 0.00 0.00 3.33
48 49 0.248377 GCTGCGATGGAGATTTGTGC 60.248 55.000 0.00 0.00 0.00 4.57
49 50 0.379669 CTGCGATGGAGATTTGTGCC 59.620 55.000 0.00 0.00 0.00 5.01
50 51 1.353103 GCGATGGAGATTTGTGCCG 59.647 57.895 0.00 0.00 0.00 5.69
51 52 1.369091 GCGATGGAGATTTGTGCCGT 61.369 55.000 0.00 0.00 0.00 5.68
52 53 0.374758 CGATGGAGATTTGTGCCGTG 59.625 55.000 0.00 0.00 0.00 4.94
53 54 1.737838 GATGGAGATTTGTGCCGTGA 58.262 50.000 0.00 0.00 0.00 4.35
54 55 2.083774 GATGGAGATTTGTGCCGTGAA 58.916 47.619 0.00 0.00 0.00 3.18
55 56 1.974265 TGGAGATTTGTGCCGTGAAA 58.026 45.000 0.00 0.00 0.00 2.69
56 57 1.879380 TGGAGATTTGTGCCGTGAAAG 59.121 47.619 0.00 0.00 0.00 2.62
57 58 2.151202 GGAGATTTGTGCCGTGAAAGA 58.849 47.619 0.00 0.00 0.00 2.52
58 59 2.749621 GGAGATTTGTGCCGTGAAAGAT 59.250 45.455 0.00 0.00 0.00 2.40
59 60 3.181506 GGAGATTTGTGCCGTGAAAGATC 60.182 47.826 0.00 0.00 0.00 2.75
60 61 2.416547 AGATTTGTGCCGTGAAAGATCG 59.583 45.455 0.00 0.00 0.00 3.69
62 63 0.953471 TTGTGCCGTGAAAGATCGGG 60.953 55.000 5.78 0.00 45.85 5.14
63 64 2.435938 TGCCGTGAAAGATCGGGC 60.436 61.111 5.78 0.00 45.85 6.13
64 65 3.202706 GCCGTGAAAGATCGGGCC 61.203 66.667 0.00 0.00 45.85 5.80
65 66 2.267642 CCGTGAAAGATCGGGCCA 59.732 61.111 4.39 0.00 42.61 5.36
66 67 1.376683 CCGTGAAAGATCGGGCCAA 60.377 57.895 4.39 0.00 42.61 4.52
67 68 1.644786 CCGTGAAAGATCGGGCCAAC 61.645 60.000 4.39 0.00 42.61 3.77
68 69 0.953471 CGTGAAAGATCGGGCCAACA 60.953 55.000 4.39 0.00 0.00 3.33
69 70 1.243902 GTGAAAGATCGGGCCAACAA 58.756 50.000 4.39 0.00 0.00 2.83
70 71 1.818674 GTGAAAGATCGGGCCAACAAT 59.181 47.619 4.39 0.00 0.00 2.71
71 72 1.818060 TGAAAGATCGGGCCAACAATG 59.182 47.619 4.39 0.00 0.00 2.82
86 87 2.698855 CAATGGATCGACCCTTGTCT 57.301 50.000 0.00 0.00 38.74 3.41
87 88 2.555199 CAATGGATCGACCCTTGTCTC 58.445 52.381 0.00 0.00 38.74 3.36
88 89 1.866015 ATGGATCGACCCTTGTCTCA 58.134 50.000 0.00 0.00 39.47 3.27
89 90 1.639722 TGGATCGACCCTTGTCTCAA 58.360 50.000 0.00 0.00 39.47 3.02
90 91 1.550524 TGGATCGACCCTTGTCTCAAG 59.449 52.381 0.00 2.90 39.47 3.02
91 92 1.134670 GGATCGACCCTTGTCTCAAGG 60.135 57.143 18.32 18.32 39.47 3.61
92 93 1.550976 GATCGACCCTTGTCTCAAGGT 59.449 52.381 21.87 12.96 39.47 3.50
93 94 1.420430 TCGACCCTTGTCTCAAGGTT 58.580 50.000 21.87 11.96 39.47 3.50
94 95 1.343465 TCGACCCTTGTCTCAAGGTTC 59.657 52.381 21.87 17.76 39.47 3.62
95 96 1.797025 GACCCTTGTCTCAAGGTTCG 58.203 55.000 21.87 12.44 38.53 3.95
96 97 0.250338 ACCCTTGTCTCAAGGTTCGC 60.250 55.000 21.87 0.00 35.65 4.70
97 98 0.035458 CCCTTGTCTCAAGGTTCGCT 59.965 55.000 21.87 0.00 35.65 4.93
98 99 1.543429 CCCTTGTCTCAAGGTTCGCTT 60.543 52.381 21.87 0.00 35.65 4.68
99 100 1.801178 CCTTGTCTCAAGGTTCGCTTC 59.199 52.381 17.35 0.00 32.78 3.86
100 101 2.483876 CTTGTCTCAAGGTTCGCTTCA 58.516 47.619 2.01 0.00 0.00 3.02
101 102 1.865865 TGTCTCAAGGTTCGCTTCAC 58.134 50.000 0.00 0.00 0.00 3.18
102 103 1.138069 TGTCTCAAGGTTCGCTTCACA 59.862 47.619 0.00 0.00 0.00 3.58
103 104 2.224281 TGTCTCAAGGTTCGCTTCACAT 60.224 45.455 0.00 0.00 0.00 3.21
104 105 2.413453 GTCTCAAGGTTCGCTTCACATC 59.587 50.000 0.00 0.00 0.00 3.06
105 106 2.037121 TCTCAAGGTTCGCTTCACATCA 59.963 45.455 0.00 0.00 0.00 3.07
156 158 5.671742 TTAATGTATGTGCATGATGGTCG 57.328 39.130 0.00 0.00 0.00 4.79
203 205 6.377327 AGTGCATCATTTTACTTTATCCCG 57.623 37.500 0.00 0.00 0.00 5.14
260 280 3.894759 CACCACCTCAAGATCATCCATT 58.105 45.455 0.00 0.00 0.00 3.16
288 308 3.855255 TGACAAGGTCAAACATGAGGA 57.145 42.857 0.00 0.00 39.78 3.71
385 405 4.802039 GTGAAATGTATTGCTGCAATCTGG 59.198 41.667 29.29 0.00 35.54 3.86
432 452 3.007614 GTGCTGTTAGTCTTCCTTACCCA 59.992 47.826 0.00 0.00 0.00 4.51
561 584 2.159490 GCCTCTCACTGAGTACGAGAAC 60.159 54.545 10.70 1.07 41.11 3.01
567 590 7.550601 CTCTCACTGAGTACGAGAACGTTAGA 61.551 46.154 0.00 0.00 42.68 2.10
617 640 1.480954 GTTCTAGTCCCTTGGCATCGA 59.519 52.381 0.00 0.00 0.00 3.59
678 701 5.046950 ACAAGAAGGTAGAACTGATGAGGTC 60.047 44.000 0.00 0.00 35.97 3.85
703 726 7.622081 TCCAAGAAGGTAGTGGAGTTATCAATA 59.378 37.037 0.00 0.00 36.51 1.90
727 750 4.942944 TGACCCAGAGTACAATCCTAAGA 58.057 43.478 0.00 0.00 0.00 2.10
785 808 5.853936 TGTTGTAGTGCAGAAGACTGTTAT 58.146 37.500 0.00 0.00 45.04 1.89
863 886 4.952262 TGTGCTCACATATTTCTCTTGC 57.048 40.909 0.00 0.00 36.21 4.01
916 942 2.106684 GGGGCACTAAAGGAATCTAGGG 59.893 54.545 0.00 0.00 0.00 3.53
942 998 2.303311 GAGGCCTGGTGTTAAGAAGACT 59.697 50.000 12.00 0.00 0.00 3.24
984 1055 3.376234 GCTCAGAAACATCTGCTGCAATA 59.624 43.478 3.02 0.00 37.11 1.90
1023 1094 0.889186 CCCCACTTCCAGGACAAACG 60.889 60.000 0.00 0.00 0.00 3.60
1092 1163 1.153765 GAAAGCAAAGATGGCGGCC 60.154 57.895 13.32 13.32 36.08 6.13
1107 1178 2.815211 GCCGCGACAGAGCATCAA 60.815 61.111 8.23 0.00 37.82 2.57
1131 1202 1.079612 TCTGCTGTGCATGGACTCG 60.080 57.895 18.75 10.44 38.13 4.18
1175 1246 0.886490 GAGTTGCCGCCCATGGATAG 60.886 60.000 15.22 3.54 0.00 2.08
1209 1280 0.179156 GCATGGATGAAAGTGGCACG 60.179 55.000 12.71 0.00 0.00 5.34
1267 1362 1.228367 AGCCCTGTTGCACCTTCTG 60.228 57.895 0.00 0.00 0.00 3.02
1270 1365 1.817740 GCCCTGTTGCACCTTCTGTTA 60.818 52.381 0.00 0.00 0.00 2.41
1409 1506 8.016654 ATGCTTACCTGTTTAGCAGAACCATTA 61.017 37.037 0.00 0.00 46.86 1.90
1438 1535 9.346725 GCATTTGTCGATTTCTCTTCTAATTTT 57.653 29.630 0.00 0.00 0.00 1.82
1460 1558 9.902196 ATTTTTGATTTCAATTTCATTTCCAGC 57.098 25.926 0.00 0.00 35.55 4.85
1553 1651 1.077787 TGCCTATCCAAGTTGCCGG 60.078 57.895 0.00 0.00 0.00 6.13
1688 1791 9.959721 AAAAATGCTAGTCTATTGGAGAACTAA 57.040 29.630 0.00 0.00 35.37 2.24
1716 1819 5.529800 GGGAAAGTTGTTGTAAGCTACTTGA 59.470 40.000 0.00 0.00 33.59 3.02
1729 1832 9.865321 TGTAAGCTACTTGATTCGTAGTTAATT 57.135 29.630 0.00 0.00 37.31 1.40
1765 1868 4.408596 TCTGGTACACCTATGCATGATCAA 59.591 41.667 10.16 0.00 36.82 2.57
1766 1869 5.072193 TCTGGTACACCTATGCATGATCAAT 59.928 40.000 10.16 0.00 36.82 2.57
1767 1870 6.269769 TCTGGTACACCTATGCATGATCAATA 59.730 38.462 10.16 0.00 36.82 1.90
1768 1871 6.836242 TGGTACACCTATGCATGATCAATAA 58.164 36.000 10.16 0.00 36.82 1.40
1769 1872 7.286313 TGGTACACCTATGCATGATCAATAAA 58.714 34.615 10.16 0.00 36.82 1.40
1813 1916 4.402829 TGCTGTCTTGGTAGGCAAATTTA 58.597 39.130 0.00 0.00 35.13 1.40
1846 1949 3.192422 CAGACTCGAAGACCATCAAGACT 59.808 47.826 0.00 0.00 0.00 3.24
1888 1992 9.545105 TTGCAGAAAAATTCAAAGAACATACAT 57.455 25.926 0.00 0.00 0.00 2.29
1938 2043 2.356382 CCGTAGCCACAAACAAAGTCAA 59.644 45.455 0.00 0.00 0.00 3.18
1956 2061 2.369860 TCAACATCAAGTCTCTGGTGCT 59.630 45.455 0.00 0.00 29.94 4.40
2033 2138 4.523083 ACACAAGGTTTGTCTCTGCTTTA 58.477 39.130 0.00 0.00 43.23 1.85
2307 2418 4.756084 AACATTTCAGAAAGAAGAGCGG 57.244 40.909 1.28 0.00 37.57 5.52
2362 2473 2.127232 GCCACCCACAACAGCAAGT 61.127 57.895 0.00 0.00 0.00 3.16
2429 2540 0.963962 ATGCTTTGTCCAGCCAGTTG 59.036 50.000 0.00 0.00 39.25 3.16
2469 2580 3.446161 CCTCAGCCATGTTTGATTCACAT 59.554 43.478 0.00 0.00 35.10 3.21
2538 2731 7.713073 GCTAGAGCCTAAGATAGTTCAACAAAT 59.287 37.037 0.00 0.00 34.31 2.32
2635 2828 1.378514 GGCTCATTCGGGAAGCCAA 60.379 57.895 7.71 0.00 44.42 4.52
2656 2849 6.770785 GCCAACTTATATAGAACCACCATTCA 59.229 38.462 0.00 0.00 0.00 2.57
2736 2929 8.814235 GTGTGTACACTTGCTATAACGAATATT 58.186 33.333 25.60 0.00 43.25 1.28
2798 2991 6.096987 TGTCAGGTTACTAGTCATCATCTTCC 59.903 42.308 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.244450 TCGCGGGTTTACGAAGATGT 59.756 50.000 6.13 0.00 34.93 3.06
1 2 0.643820 GTCGCGGGTTTACGAAGATG 59.356 55.000 6.13 0.00 40.47 2.90
2 3 0.529378 AGTCGCGGGTTTACGAAGAT 59.471 50.000 6.13 0.00 40.47 2.40
3 4 0.314935 AAGTCGCGGGTTTACGAAGA 59.685 50.000 6.13 0.00 40.47 2.87
4 5 0.437295 CAAGTCGCGGGTTTACGAAG 59.563 55.000 6.13 0.00 40.47 3.79
5 6 0.249405 ACAAGTCGCGGGTTTACGAA 60.249 50.000 6.13 0.00 40.47 3.85
6 7 0.249405 AACAAGTCGCGGGTTTACGA 60.249 50.000 6.13 0.00 35.47 3.43
7 8 0.162294 GAACAAGTCGCGGGTTTACG 59.838 55.000 6.13 0.00 0.00 3.18
8 9 1.505425 AGAACAAGTCGCGGGTTTAC 58.495 50.000 6.13 0.00 0.00 2.01
9 10 1.868498 CAAGAACAAGTCGCGGGTTTA 59.132 47.619 6.13 0.00 0.00 2.01
10 11 0.661020 CAAGAACAAGTCGCGGGTTT 59.339 50.000 6.13 0.00 0.00 3.27
11 12 1.782028 GCAAGAACAAGTCGCGGGTT 61.782 55.000 6.13 6.16 0.00 4.11
12 13 2.251642 GCAAGAACAAGTCGCGGGT 61.252 57.895 6.13 0.00 0.00 5.28
13 14 1.961277 AGCAAGAACAAGTCGCGGG 60.961 57.895 6.13 0.00 0.00 6.13
14 15 1.205064 CAGCAAGAACAAGTCGCGG 59.795 57.895 6.13 0.00 0.00 6.46
15 16 1.439365 GCAGCAAGAACAAGTCGCG 60.439 57.895 0.00 0.00 0.00 5.87
16 17 1.439365 CGCAGCAAGAACAAGTCGC 60.439 57.895 0.00 0.00 0.00 5.19
17 18 0.792640 ATCGCAGCAAGAACAAGTCG 59.207 50.000 0.00 0.00 0.00 4.18
18 19 1.135859 CCATCGCAGCAAGAACAAGTC 60.136 52.381 0.00 0.00 0.00 3.01
19 20 0.877071 CCATCGCAGCAAGAACAAGT 59.123 50.000 0.00 0.00 0.00 3.16
20 21 1.129998 CTCCATCGCAGCAAGAACAAG 59.870 52.381 0.00 0.00 0.00 3.16
21 22 1.159285 CTCCATCGCAGCAAGAACAA 58.841 50.000 0.00 0.00 0.00 2.83
22 23 0.321346 TCTCCATCGCAGCAAGAACA 59.679 50.000 0.00 0.00 0.00 3.18
23 24 1.661341 ATCTCCATCGCAGCAAGAAC 58.339 50.000 0.00 0.00 0.00 3.01
24 25 2.408271 AATCTCCATCGCAGCAAGAA 57.592 45.000 0.00 0.00 0.00 2.52
25 26 2.011947 CAAATCTCCATCGCAGCAAGA 58.988 47.619 0.00 0.00 0.00 3.02
26 27 1.741706 ACAAATCTCCATCGCAGCAAG 59.258 47.619 0.00 0.00 0.00 4.01
27 28 1.469703 CACAAATCTCCATCGCAGCAA 59.530 47.619 0.00 0.00 0.00 3.91
28 29 1.089112 CACAAATCTCCATCGCAGCA 58.911 50.000 0.00 0.00 0.00 4.41
29 30 0.248377 GCACAAATCTCCATCGCAGC 60.248 55.000 0.00 0.00 0.00 5.25
30 31 0.379669 GGCACAAATCTCCATCGCAG 59.620 55.000 0.00 0.00 0.00 5.18
31 32 1.368345 CGGCACAAATCTCCATCGCA 61.368 55.000 0.00 0.00 0.00 5.10
32 33 1.353103 CGGCACAAATCTCCATCGC 59.647 57.895 0.00 0.00 0.00 4.58
33 34 0.374758 CACGGCACAAATCTCCATCG 59.625 55.000 0.00 0.00 0.00 3.84
34 35 1.737838 TCACGGCACAAATCTCCATC 58.262 50.000 0.00 0.00 0.00 3.51
35 36 2.198827 TTCACGGCACAAATCTCCAT 57.801 45.000 0.00 0.00 0.00 3.41
36 37 1.879380 CTTTCACGGCACAAATCTCCA 59.121 47.619 0.00 0.00 0.00 3.86
37 38 2.151202 TCTTTCACGGCACAAATCTCC 58.849 47.619 0.00 0.00 0.00 3.71
38 39 3.484229 CGATCTTTCACGGCACAAATCTC 60.484 47.826 0.00 0.00 0.00 2.75
39 40 2.416547 CGATCTTTCACGGCACAAATCT 59.583 45.455 0.00 0.00 0.00 2.40
40 41 2.476185 CCGATCTTTCACGGCACAAATC 60.476 50.000 0.00 0.00 42.55 2.17
41 42 1.468520 CCGATCTTTCACGGCACAAAT 59.531 47.619 0.00 0.00 42.55 2.32
42 43 0.871722 CCGATCTTTCACGGCACAAA 59.128 50.000 0.00 0.00 42.55 2.83
43 44 0.953471 CCCGATCTTTCACGGCACAA 60.953 55.000 0.00 0.00 46.59 3.33
44 45 1.375396 CCCGATCTTTCACGGCACA 60.375 57.895 0.00 0.00 46.59 4.57
45 46 2.750888 GCCCGATCTTTCACGGCAC 61.751 63.158 0.00 0.00 46.59 5.01
46 47 2.435938 GCCCGATCTTTCACGGCA 60.436 61.111 0.00 0.00 46.59 5.69
47 48 3.202706 GGCCCGATCTTTCACGGC 61.203 66.667 0.00 0.00 46.59 5.68
49 50 0.953471 TGTTGGCCCGATCTTTCACG 60.953 55.000 0.00 0.00 0.00 4.35
50 51 1.243902 TTGTTGGCCCGATCTTTCAC 58.756 50.000 0.00 0.00 0.00 3.18
51 52 1.818060 CATTGTTGGCCCGATCTTTCA 59.182 47.619 0.00 0.00 0.00 2.69
52 53 1.134946 CCATTGTTGGCCCGATCTTTC 59.865 52.381 0.00 0.00 35.85 2.62
53 54 1.185315 CCATTGTTGGCCCGATCTTT 58.815 50.000 0.00 0.00 35.85 2.52
54 55 0.331278 TCCATTGTTGGCCCGATCTT 59.669 50.000 0.00 0.00 43.29 2.40
55 56 0.552848 ATCCATTGTTGGCCCGATCT 59.447 50.000 0.00 0.00 43.29 2.75
56 57 0.954452 GATCCATTGTTGGCCCGATC 59.046 55.000 0.00 0.00 43.29 3.69
57 58 0.819259 CGATCCATTGTTGGCCCGAT 60.819 55.000 0.00 0.00 43.29 4.18
58 59 1.451207 CGATCCATTGTTGGCCCGA 60.451 57.895 0.00 0.00 43.29 5.14
59 60 1.451207 TCGATCCATTGTTGGCCCG 60.451 57.895 0.00 0.00 43.29 6.13
60 61 1.384222 GGTCGATCCATTGTTGGCCC 61.384 60.000 0.00 0.00 43.29 5.80
61 62 1.384222 GGGTCGATCCATTGTTGGCC 61.384 60.000 10.69 0.00 43.29 5.36
62 63 0.394352 AGGGTCGATCCATTGTTGGC 60.394 55.000 19.03 0.00 43.29 4.52
63 64 2.128771 AAGGGTCGATCCATTGTTGG 57.871 50.000 19.03 0.00 45.15 3.77
77 78 0.250338 GCGAACCTTGAGACAAGGGT 60.250 55.000 26.94 23.47 40.78 4.34
78 79 0.035458 AGCGAACCTTGAGACAAGGG 59.965 55.000 26.94 14.86 41.71 3.95
79 80 1.801178 GAAGCGAACCTTGAGACAAGG 59.199 52.381 23.49 23.49 43.05 3.61
80 81 2.221981 GTGAAGCGAACCTTGAGACAAG 59.778 50.000 4.73 4.73 32.78 3.16
81 82 2.210116 GTGAAGCGAACCTTGAGACAA 58.790 47.619 0.00 0.00 32.78 3.18
82 83 1.138069 TGTGAAGCGAACCTTGAGACA 59.862 47.619 0.00 0.00 32.78 3.41
83 84 1.865865 TGTGAAGCGAACCTTGAGAC 58.134 50.000 0.00 0.00 32.78 3.36
84 85 2.037121 TGATGTGAAGCGAACCTTGAGA 59.963 45.455 0.00 0.00 32.78 3.27
85 86 2.416747 TGATGTGAAGCGAACCTTGAG 58.583 47.619 0.00 0.00 32.78 3.02
86 87 2.542020 TGATGTGAAGCGAACCTTGA 57.458 45.000 0.00 0.00 32.78 3.02
87 88 3.189080 TCAATGATGTGAAGCGAACCTTG 59.811 43.478 0.00 0.00 32.78 3.61
88 89 3.411446 TCAATGATGTGAAGCGAACCTT 58.589 40.909 0.00 0.00 36.19 3.50
89 90 3.057969 TCAATGATGTGAAGCGAACCT 57.942 42.857 0.00 0.00 0.00 3.50
90 91 3.242870 GGATCAATGATGTGAAGCGAACC 60.243 47.826 0.00 0.00 0.00 3.62
91 92 3.374988 TGGATCAATGATGTGAAGCGAAC 59.625 43.478 0.00 0.00 0.00 3.95
92 93 3.608796 TGGATCAATGATGTGAAGCGAA 58.391 40.909 0.00 0.00 0.00 4.70
93 94 3.264998 TGGATCAATGATGTGAAGCGA 57.735 42.857 0.00 0.00 0.00 4.93
94 95 3.562557 TGATGGATCAATGATGTGAAGCG 59.437 43.478 0.00 0.00 33.08 4.68
95 96 5.067413 ACTTGATGGATCAATGATGTGAAGC 59.933 40.000 0.00 0.00 44.92 3.86
96 97 6.694877 ACTTGATGGATCAATGATGTGAAG 57.305 37.500 0.00 0.00 44.92 3.02
97 98 7.470935 AAACTTGATGGATCAATGATGTGAA 57.529 32.000 0.00 0.00 44.92 3.18
98 99 7.395206 AGAAAACTTGATGGATCAATGATGTGA 59.605 33.333 0.00 0.00 44.92 3.58
99 100 7.544622 AGAAAACTTGATGGATCAATGATGTG 58.455 34.615 0.00 0.00 44.92 3.21
100 101 7.713734 AGAAAACTTGATGGATCAATGATGT 57.286 32.000 0.00 0.00 44.92 3.06
101 102 8.248253 TGAAGAAAACTTGATGGATCAATGATG 58.752 33.333 0.00 0.00 44.92 3.07
102 103 8.248945 GTGAAGAAAACTTGATGGATCAATGAT 58.751 33.333 0.00 0.00 44.92 2.45
103 104 7.231115 TGTGAAGAAAACTTGATGGATCAATGA 59.769 33.333 2.56 0.00 44.92 2.57
104 105 7.372714 TGTGAAGAAAACTTGATGGATCAATG 58.627 34.615 2.56 1.16 44.92 2.82
105 106 7.528996 TGTGAAGAAAACTTGATGGATCAAT 57.471 32.000 2.56 0.00 44.92 2.57
260 280 3.117701 TGTTTGACCTTGTCATCCTTCCA 60.118 43.478 0.00 0.00 42.40 3.53
466 486 2.989909 TGGACAGACAGCCAATATGTG 58.010 47.619 0.00 0.00 0.00 3.21
468 488 2.292569 GCATGGACAGACAGCCAATATG 59.707 50.000 0.00 0.00 37.78 1.78
561 584 7.821652 TCCTCATCATATTTCTAGCTCTAACG 58.178 38.462 0.00 0.00 0.00 3.18
567 590 7.601886 CGATTGTTCCTCATCATATTTCTAGCT 59.398 37.037 0.00 0.00 0.00 3.32
617 640 5.308014 TCCTAATCATTGACGCTATTGCAT 58.692 37.500 0.00 0.00 39.64 3.96
678 701 5.677319 TGATAACTCCACTACCTTCTTGG 57.323 43.478 0.00 0.00 42.93 3.61
703 726 5.964477 TCTTAGGATTGTACTCTGGGTCATT 59.036 40.000 0.00 0.00 0.00 2.57
727 750 6.388100 TCCTCTCCATCAATAACTTCATCCTT 59.612 38.462 0.00 0.00 0.00 3.36
785 808 1.024271 GCAAGACAGAGTTTGCACCA 58.976 50.000 4.48 0.00 46.72 4.17
884 910 3.547054 TTAGTGCCCCGTATAAACAGG 57.453 47.619 0.00 0.00 0.00 4.00
896 922 2.487445 GCCCTAGATTCCTTTAGTGCCC 60.487 54.545 0.00 0.00 0.00 5.36
916 942 0.321298 TTAACACCAGGCCTCTTCGC 60.321 55.000 0.00 0.00 0.00 4.70
942 998 5.028549 AGCTCTTCTTCTTCTTGTTGACA 57.971 39.130 0.00 0.00 0.00 3.58
984 1055 0.916358 CCATCACCCTTCCTGGAGGT 60.916 60.000 5.02 3.41 38.35 3.85
1023 1094 2.472029 TCAGGTTCCAGGATCCTCTTC 58.528 52.381 12.69 2.77 30.19 2.87
1092 1163 1.060266 CTTTCTTGATGCTCTGTCGCG 59.940 52.381 0.00 0.00 0.00 5.87
1101 1172 2.667724 GCACAGCAGACTTTCTTGATGC 60.668 50.000 0.00 0.00 37.15 3.91
1107 1178 1.072806 TCCATGCACAGCAGACTTTCT 59.927 47.619 0.00 0.00 43.65 2.52
1131 1202 0.890683 CCATTTGCACCAAGGTCTCC 59.109 55.000 0.00 0.00 0.00 3.71
1175 1246 1.363744 CATGCGGAGAGTGGTTTCTC 58.636 55.000 0.00 0.00 42.31 2.87
1209 1280 1.691434 CCTCCTTCATCTAGGCAGACC 59.309 57.143 0.00 0.00 35.15 3.85
1267 1362 6.595326 TCACTGATGACATCATTCCTGTTAAC 59.405 38.462 18.28 0.00 38.85 2.01
1270 1365 5.169992 TCACTGATGACATCATTCCTGTT 57.830 39.130 18.28 0.00 38.85 3.16
1409 1506 4.999950 AGAAGAGAAATCGACAAATGCAGT 59.000 37.500 0.00 0.00 0.00 4.40
1438 1535 6.148150 GCAGCTGGAAATGAAATTGAAATCAA 59.852 34.615 17.12 0.00 36.10 2.57
1442 1539 4.958509 TGCAGCTGGAAATGAAATTGAAA 58.041 34.783 17.12 0.00 36.10 2.69
1456 1554 1.741706 CTTGGTAGTCATTGCAGCTGG 59.258 52.381 17.12 0.00 0.00 4.85
1460 1558 5.105554 AGTCTAGTCTTGGTAGTCATTGCAG 60.106 44.000 0.00 0.00 0.00 4.41
1553 1651 0.103937 CTCTGGACGCTTCATCCCTC 59.896 60.000 0.00 0.00 35.12 4.30
1688 1791 5.869649 AGCTTACAACAACTTTCCCAATT 57.130 34.783 0.00 0.00 0.00 2.32
1729 1832 9.769677 ATAGGTGTACCAGAATATAGATAGCAA 57.230 33.333 3.56 0.00 38.89 3.91
1740 1843 5.072193 TGATCATGCATAGGTGTACCAGAAT 59.928 40.000 0.00 0.00 38.89 2.40
1767 1870 9.869757 GCAAACAAGGTAGGAACAATATTATTT 57.130 29.630 0.00 0.00 0.00 1.40
1768 1871 9.255029 AGCAAACAAGGTAGGAACAATATTATT 57.745 29.630 0.00 0.00 0.00 1.40
1769 1872 8.686334 CAGCAAACAAGGTAGGAACAATATTAT 58.314 33.333 0.00 0.00 0.00 1.28
1813 1916 4.075682 TCTTCGAGTCTGTGTTCATCTCT 58.924 43.478 0.00 0.00 0.00 3.10
1888 1992 9.948964 TCAAAATACTTCTTCTTGATCTGATGA 57.051 29.630 0.00 0.00 0.00 2.92
1938 2043 3.435275 TCTAGCACCAGAGACTTGATGT 58.565 45.455 0.00 0.00 0.00 3.06
1956 2061 2.118313 TTCACCGTCCGTCAGATCTA 57.882 50.000 0.00 0.00 0.00 1.98
2033 2138 4.240096 GTGCAGAACATAAAGCAGCAAAT 58.760 39.130 0.00 0.00 37.72 2.32
2106 2212 3.726291 TCATCTTGTTCGACACACAGA 57.274 42.857 0.00 0.77 33.98 3.41
2211 2319 2.500504 AGGATCAAACGGTAAGGTCTCC 59.499 50.000 0.00 0.00 0.00 3.71
2307 2418 0.248843 CAGACAGCTCCTCACCCTTC 59.751 60.000 0.00 0.00 0.00 3.46
2362 2473 1.375013 GCTCCGAAAACCCGTGCTA 60.375 57.895 0.00 0.00 0.00 3.49
2429 2540 6.431278 GCTGAGGTTTCTAGACAAAAGTTTC 58.569 40.000 0.00 0.00 0.00 2.78
2469 2580 5.227569 ACATAGTGTGTGTTCTTGATGGA 57.772 39.130 0.00 0.00 40.28 3.41
2623 2816 6.285990 GTTCTATATAAGTTGGCTTCCCGAA 58.714 40.000 0.00 0.00 36.22 4.30
2635 2828 6.998673 GCCTTGAATGGTGGTTCTATATAAGT 59.001 38.462 0.00 0.00 0.00 2.24
2656 2849 7.362920 AACAATATGTTCGCTTCATTAAGCCTT 60.363 33.333 6.05 0.00 43.60 4.35
2673 2866 7.396907 TGGAGACATGAAATTGGAACAATATGT 59.603 33.333 0.00 8.00 38.98 2.29
2689 2882 5.423290 ACACTTATGTGATCTGGAGACATGA 59.577 40.000 15.13 0.00 46.55 3.07


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

AutoCloner maintained by Alex Coulton.