Multiple sequence alignment - TraesCS2D01G360400

Loading Multiple Alignment...

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 TraesCS2D01G360400 chr2D 100.000 5370 0 0 1 5370 462246161 462240792 0.000000e+00 9917.0
1 TraesCS2D01G360400 chr2D 83.288 742 101 13 4533 5266 131641673 131642399 0.000000e+00 662.0
2 TraesCS2D01G360400 chr2D 87.978 183 20 2 4056 4238 462210914 462210734 1.170000e-51 215.0
3 TraesCS2D01G360400 chr2D 82.990 194 18 5 548 738 462784263 462784082 1.550000e-35 161.0
4 TraesCS2D01G360400 chr2D 94.118 85 5 0 400 484 462784454 462784370 4.360000e-26 130.0
5 TraesCS2D01G360400 chr2D 86.842 76 8 2 401 475 462785008 462784934 3.450000e-12 84.2
6 TraesCS2D01G360400 chr2A 92.311 4604 213 57 724 5290 607517974 607513475 0.000000e+00 6410.0
7 TraesCS2D01G360400 chr2A 97.056 1019 22 2 4278 5290 610178447 610177431 0.000000e+00 1709.0
8 TraesCS2D01G360400 chr2A 92.236 747 46 8 1 738 607518751 607518008 0.000000e+00 1048.0
9 TraesCS2D01G360400 chr2A 94.949 495 23 1 1 493 610210974 610210480 0.000000e+00 774.0
10 TraesCS2D01G360400 chr2A 90.304 526 27 3 903 1416 610210005 610209492 0.000000e+00 667.0
11 TraesCS2D01G360400 chr2A 83.770 382 46 9 18 392 607598424 607598052 1.110000e-91 348.0
12 TraesCS2D01G360400 chr2A 89.349 169 16 2 4070 4238 610124646 610124480 1.520000e-50 211.0
13 TraesCS2D01G360400 chr2A 90.323 124 12 0 2315 2438 607516335 607516212 4.300000e-36 163.0
14 TraesCS2D01G360400 chr2A 93.976 83 5 0 406 488 607597904 607597822 5.650000e-25 126.0
15 TraesCS2D01G360400 chr2A 88.710 62 7 0 3952 4013 81088620 81088559 5.770000e-10 76.8
16 TraesCS2D01G360400 chr2A 92.000 50 1 3 4236 4282 708044969 708044920 3.470000e-07 67.6
17 TraesCS2D01G360400 chr2B 91.867 3123 178 40 1 3099 545158963 545155893 0.000000e+00 4290.0
18 TraesCS2D01G360400 chr2B 92.079 1414 61 22 3088 4499 545155732 545154368 0.000000e+00 1943.0
19 TraesCS2D01G360400 chr2B 96.526 950 21 3 4353 5290 545154140 545153191 0.000000e+00 1561.0
20 TraesCS2D01G360400 chr2B 81.928 332 42 7 68 392 545227349 545227029 1.150000e-66 265.0
21 TraesCS2D01G360400 chr2B 90.798 163 15 0 2378 2540 545156717 545156555 9.060000e-53 219.0
22 TraesCS2D01G360400 chr2B 87.047 193 22 3 548 738 545226680 545226489 1.170000e-51 215.0
23 TraesCS2D01G360400 chr2B 94.118 85 5 0 400 484 545226871 545226787 4.360000e-26 130.0
24 TraesCS2D01G360400 chr2B 92.045 88 7 0 5283 5370 21211481 21211568 2.030000e-24 124.0
25 TraesCS2D01G360400 chr2B 98.182 55 1 0 4184 4238 544997088 544997034 4.430000e-16 97.1
26 TraesCS2D01G360400 chr1A 86.406 743 88 7 4525 5259 246127767 246128504 0.000000e+00 800.0
27 TraesCS2D01G360400 chr1B 85.752 765 96 7 4531 5287 275359910 275359151 0.000000e+00 797.0
28 TraesCS2D01G360400 chr1B 85.733 764 97 6 4531 5287 275554854 275554096 0.000000e+00 797.0
29 TraesCS2D01G360400 chr1B 85.621 765 97 7 4531 5287 275673476 275672717 0.000000e+00 791.0
30 TraesCS2D01G360400 chr1B 85.490 765 98 7 4531 5287 275459900 275459141 0.000000e+00 785.0
31 TraesCS2D01G360400 chr7D 96.429 84 3 0 5287 5370 246397228 246397145 7.250000e-29 139.0
32 TraesCS2D01G360400 chr7D 94.048 84 5 0 5287 5370 346239629 346239546 1.570000e-25 128.0
33 TraesCS2D01G360400 chr7D 81.553 103 11 6 4240 4336 611229702 611229602 1.600000e-10 78.7
34 TraesCS2D01G360400 chr1D 96.429 84 3 0 5287 5370 232558458 232558541 7.250000e-29 139.0
35 TraesCS2D01G360400 chr4D 95.294 85 4 0 5286 5370 23978645 23978729 9.380000e-28 135.0
36 TraesCS2D01G360400 chr4D 92.157 51 1 3 4233 4280 62734571 62734621 9.650000e-08 69.4
37 TraesCS2D01G360400 chr4D 89.286 56 2 4 4229 4280 35618786 35618731 3.470000e-07 67.6
38 TraesCS2D01G360400 chr4B 93.023 86 6 0 5285 5370 54567191 54567106 5.650000e-25 126.0
39 TraesCS2D01G360400 chr4A 93.023 86 6 0 5285 5370 17382882 17382967 5.650000e-25 126.0
40 TraesCS2D01G360400 chr4A 89.091 55 3 3 4226 4277 339483243 339483297 1.250000e-06 65.8
41 TraesCS2D01G360400 chr4A 89.091 55 3 3 4226 4277 423964413 423964467 1.250000e-06 65.8
42 TraesCS2D01G360400 chr4A 89.091 55 3 3 4226 4277 629596651 629596597 1.250000e-06 65.8
43 TraesCS2D01G360400 chr3D 93.976 83 5 0 5288 5370 420822368 420822286 5.650000e-25 126.0
44 TraesCS2D01G360400 chr6B 88.660 97 10 1 5275 5370 431701450 431701354 3.400000e-22 117.0
45 TraesCS2D01G360400 chr6B 89.831 59 2 3 4232 4286 550272423 550272481 7.460000e-09 73.1


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 TraesCS2D01G360400 chr2D 462240792 462246161 5369 True 9917.000000 9917 100.000000 1 5370 1 chr2D.!!$R2 5369
1 TraesCS2D01G360400 chr2D 131641673 131642399 726 False 662.000000 662 83.288000 4533 5266 1 chr2D.!!$F1 733
2 TraesCS2D01G360400 chr2A 607513475 607518751 5276 True 2540.333333 6410 91.623333 1 5290 3 chr2A.!!$R5 5289
3 TraesCS2D01G360400 chr2A 610177431 610178447 1016 True 1709.000000 1709 97.056000 4278 5290 1 chr2A.!!$R3 1012
4 TraesCS2D01G360400 chr2A 610209492 610210974 1482 True 720.500000 774 92.626500 1 1416 2 chr2A.!!$R7 1415
5 TraesCS2D01G360400 chr2A 607597822 607598424 602 True 237.000000 348 88.873000 18 488 2 chr2A.!!$R6 470
6 TraesCS2D01G360400 chr2B 545153191 545158963 5772 True 2003.250000 4290 92.817500 1 5290 4 chr2B.!!$R2 5289
7 TraesCS2D01G360400 chr2B 545226489 545227349 860 True 203.333333 265 87.697667 68 738 3 chr2B.!!$R3 670
8 TraesCS2D01G360400 chr1A 246127767 246128504 737 False 800.000000 800 86.406000 4525 5259 1 chr1A.!!$F1 734
9 TraesCS2D01G360400 chr1B 275359151 275359910 759 True 797.000000 797 85.752000 4531 5287 1 chr1B.!!$R1 756
10 TraesCS2D01G360400 chr1B 275554096 275554854 758 True 797.000000 797 85.733000 4531 5287 1 chr1B.!!$R3 756
11 TraesCS2D01G360400 chr1B 275672717 275673476 759 True 791.000000 791 85.621000 4531 5287 1 chr1B.!!$R4 756
12 TraesCS2D01G360400 chr1B 275459141 275459900 759 True 785.000000 785 85.490000 4531 5287 1 chr1B.!!$R2 756

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
658 1044 0.172803 AGCCCACGATACAACGAGAC 59.827 55.0 0.00 0.0 37.03 3.36 F
1049 1597 0.400815 ATCTGGTGGGCCGGGTAATA 60.401 55.0 2.18 0.0 41.53 0.98 F
1960 2526 0.532862 AACCCATTATCAGCGCTCCG 60.533 55.0 7.13 0.0 0.00 4.63 F
2947 3523 0.252421 TGGGAGTCTCTGGTCTGCAT 60.252 55.0 0.00 0.0 0.00 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1800 2363 0.113776 TCCGGCGTTATAGAGGGGAT 59.886 55.0 6.01 0.00 0.00 3.85 R
1963 2529 0.179150 CTTCGGAGTCTGAAGGCTCG 60.179 60.0 27.65 8.36 39.30 5.03 R
3487 4246 1.091771 CCTCAAGGCTATGGTGCACG 61.092 60.0 11.45 0.00 34.04 5.34 R
4908 6056 0.036765 TATGGCGGGCGGATTATGTC 60.037 55.0 0.00 0.00 0.00 3.06 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
94 95 6.036953 TGTTGCCATGAAAAATCAAACTGAAC 59.963 34.615 0.00 0.00 0.00 3.18
99 100 6.538021 CCATGAAAAATCAAACTGAACACCAA 59.462 34.615 0.00 0.00 0.00 3.67
108 114 5.527214 TCAAACTGAACACCAACTCATAGTG 59.473 40.000 0.00 0.00 37.53 2.74
124 132 7.675062 ACTCATAGTGAAACAAGAGAAGACAT 58.325 34.615 0.00 0.00 41.43 3.06
179 187 2.538437 TGAAACACAGCACACAAATGC 58.462 42.857 0.00 0.00 46.50 3.56
221 229 5.046950 ACAACTCAGTCCCTTAGATGTTCTC 60.047 44.000 0.00 0.00 0.00 2.87
392 402 2.493278 CAACTCTGCCCCATTGGTTTAG 59.507 50.000 1.20 0.00 36.04 1.85
398 558 5.690865 TCTGCCCCATTGGTTTAGTATAAG 58.309 41.667 1.20 0.00 36.04 1.73
500 660 0.604578 ACGTACGTGCACAACCCTAT 59.395 50.000 22.14 0.00 0.00 2.57
501 661 1.818060 ACGTACGTGCACAACCCTATA 59.182 47.619 22.14 0.00 0.00 1.31
564 782 4.264253 TCCCACATGCTAGAACAAATCAG 58.736 43.478 0.00 0.00 0.00 2.90
571 789 5.862924 TGCTAGAACAAATCAGTAACAGC 57.137 39.130 0.00 0.00 0.00 4.40
574 792 5.639506 GCTAGAACAAATCAGTAACAGCAGA 59.360 40.000 0.00 0.00 0.00 4.26
658 1044 0.172803 AGCCCACGATACAACGAGAC 59.827 55.000 0.00 0.00 37.03 3.36
754 1188 6.578163 AGCGGTAGATCTAATCTAAGTTCC 57.422 41.667 3.40 0.00 43.04 3.62
755 1189 6.069331 AGCGGTAGATCTAATCTAAGTTCCA 58.931 40.000 3.40 0.00 43.04 3.53
780 1214 2.376842 GGATGGAGGGAAGGGGGA 59.623 66.667 0.00 0.00 0.00 4.81
938 1486 2.114670 AGTTGGAATGGCGATGCGG 61.115 57.895 0.00 0.00 0.00 5.69
1046 1594 2.766651 GATCTGGTGGGCCGGGTA 60.767 66.667 2.18 0.00 41.53 3.69
1049 1597 0.400815 ATCTGGTGGGCCGGGTAATA 60.401 55.000 2.18 0.00 41.53 0.98
1623 2183 4.410400 AAAGCCGCTTCCTCCCCG 62.410 66.667 5.98 0.00 0.00 5.73
1640 2200 2.585153 GCCCTCCCGTTTCTCCTC 59.415 66.667 0.00 0.00 0.00 3.71
1745 2305 3.445518 GATGATGACTGGGCGCCGA 62.446 63.158 22.54 17.25 0.00 5.54
1800 2363 2.092429 AGGATATTGGAAAAGCGCAGGA 60.092 45.455 11.47 0.00 0.00 3.86
1939 2502 3.508840 GCAGCGAATTCCACCGGG 61.509 66.667 6.32 0.00 0.00 5.73
1960 2526 0.532862 AACCCATTATCAGCGCTCCG 60.533 55.000 7.13 0.00 0.00 4.63
1963 2529 0.946221 CCATTATCAGCGCTCCGGAC 60.946 60.000 7.13 0.00 0.00 4.79
2064 2630 0.736325 GCCAGCGTCGACAATGTACT 60.736 55.000 17.16 0.00 0.00 2.73
2070 2636 0.989890 GTCGACAATGTACTGCCGAC 59.010 55.000 11.55 7.90 39.32 4.79
2102 2668 0.460987 AGCAGCGCTTCCATCTACAC 60.461 55.000 7.50 0.00 33.89 2.90
2110 2676 4.910585 CCATCTACACCGCCGGGC 62.911 72.222 8.57 9.54 36.48 6.13
2153 2719 1.023513 GCGCAAGAGAGCTTCCATGT 61.024 55.000 0.30 0.00 37.60 3.21
2278 2850 4.643387 GCCAACACCAGCTCCGGT 62.643 66.667 0.00 0.00 41.07 5.28
2280 2852 1.373435 CCAACACCAGCTCCGGTAA 59.627 57.895 0.00 0.00 37.07 2.85
2281 2853 0.953960 CCAACACCAGCTCCGGTAAC 60.954 60.000 0.00 0.00 37.07 2.50
2282 2854 0.953960 CAACACCAGCTCCGGTAACC 60.954 60.000 0.00 0.00 37.07 2.85
2283 2855 1.412453 AACACCAGCTCCGGTAACCA 61.412 55.000 0.00 0.00 37.07 3.67
2284 2856 1.375523 CACCAGCTCCGGTAACCAC 60.376 63.158 0.00 0.00 37.07 4.16
2285 2857 1.839747 ACCAGCTCCGGTAACCACA 60.840 57.895 0.00 0.00 37.57 4.17
2286 2858 1.079127 CCAGCTCCGGTAACCACAG 60.079 63.158 0.00 0.00 0.00 3.66
2287 2859 1.741770 CAGCTCCGGTAACCACAGC 60.742 63.158 0.00 0.07 0.00 4.40
2288 2860 2.813908 GCTCCGGTAACCACAGCG 60.814 66.667 0.00 0.00 39.07 5.18
2289 2861 2.967397 CTCCGGTAACCACAGCGA 59.033 61.111 0.00 0.00 41.79 4.93
2290 2862 1.445582 CTCCGGTAACCACAGCGAC 60.446 63.158 0.00 0.00 41.79 5.19
2291 2863 2.807895 CCGGTAACCACAGCGACG 60.808 66.667 0.00 0.00 41.79 5.12
2292 2864 2.049802 CGGTAACCACAGCGACGT 60.050 61.111 0.00 0.00 41.79 4.34
2293 2865 2.084681 CGGTAACCACAGCGACGTC 61.085 63.158 5.18 5.18 41.79 4.34
2294 2866 1.007038 GGTAACCACAGCGACGTCA 60.007 57.895 17.16 0.00 0.00 4.35
2295 2867 0.389426 GGTAACCACAGCGACGTCAT 60.389 55.000 17.16 0.00 0.00 3.06
2296 2868 0.989890 GTAACCACAGCGACGTCATC 59.010 55.000 17.16 6.53 0.00 2.92
2304 2876 2.277949 CGACGTCATCGGCATCGT 60.278 61.111 17.16 0.00 46.73 3.73
2309 2881 3.911698 TCATCGGCATCGTCGGGG 61.912 66.667 0.00 0.00 37.69 5.73
2716 3288 3.971702 AACTGGAGGTGGCAGCCC 61.972 66.667 13.95 14.43 0.00 5.19
2718 3290 4.421515 CTGGAGGTGGCAGCCCAG 62.422 72.222 27.74 27.74 43.18 4.45
2770 3345 9.192642 CATCCTCTGACTAGATTCTGATCATAT 57.807 37.037 0.00 0.00 34.60 1.78
2783 3358 7.482654 TTCTGATCATATCAATTGTTCCGAC 57.517 36.000 5.13 0.00 39.11 4.79
2795 3370 7.835822 TCAATTGTTCCGACCAATTTCATTAT 58.164 30.769 5.13 0.00 39.77 1.28
2798 3373 6.371809 TGTTCCGACCAATTTCATTATAGC 57.628 37.500 0.00 0.00 0.00 2.97
2805 3380 6.363577 ACCAATTTCATTATAGCACACTCG 57.636 37.500 0.00 0.00 0.00 4.18
2827 3402 4.267928 CGGTGATCGAAACTTGAGTTATCC 59.732 45.833 0.00 0.00 42.43 2.59
2947 3523 0.252421 TGGGAGTCTCTGGTCTGCAT 60.252 55.000 0.00 0.00 0.00 3.96
2969 3545 1.077501 CCGCCATGGTGTCAGGAAT 60.078 57.895 23.44 0.00 0.00 3.01
3071 3654 1.012841 GCTGCCTCACTGAATACTGC 58.987 55.000 0.00 0.00 0.00 4.40
3134 3889 7.309770 AGAGAAACTTGGTAGAATCTTGTCT 57.690 36.000 0.00 0.00 0.00 3.41
3135 3890 8.423906 AGAGAAACTTGGTAGAATCTTGTCTA 57.576 34.615 0.00 0.00 0.00 2.59
3399 4158 1.229658 CCCCCAGAACTCCTCAGGT 60.230 63.158 0.00 0.00 0.00 4.00
3400 4159 0.842467 CCCCCAGAACTCCTCAGGTT 60.842 60.000 0.00 0.00 0.00 3.50
3401 4160 1.554822 CCCCCAGAACTCCTCAGGTTA 60.555 57.143 0.00 0.00 0.00 2.85
3472 4231 5.468746 TGTTTGTGACAGGCTGAACTATTAC 59.531 40.000 23.66 11.61 33.40 1.89
3487 4246 2.327200 ATTACCAAGAAGGCTACCGC 57.673 50.000 0.00 0.00 43.14 5.68
3625 4387 6.934645 TCTCCCTAACACACTTCAAGTAATTG 59.065 38.462 0.00 0.00 0.00 2.32
3626 4388 6.597562 TCCCTAACACACTTCAAGTAATTGT 58.402 36.000 2.43 0.00 31.59 2.71
3627 4389 7.057894 TCCCTAACACACTTCAAGTAATTGTT 58.942 34.615 13.28 13.28 32.79 2.83
3653 4415 1.901464 GACCGCCACCACAACCATT 60.901 57.895 0.00 0.00 0.00 3.16
3654 4416 0.606944 GACCGCCACCACAACCATTA 60.607 55.000 0.00 0.00 0.00 1.90
3655 4417 0.039035 ACCGCCACCACAACCATTAT 59.961 50.000 0.00 0.00 0.00 1.28
3656 4418 0.455410 CCGCCACCACAACCATTATG 59.545 55.000 0.00 0.00 0.00 1.90
3762 4528 1.068194 GGAGACCGAGCCGATATTCAG 60.068 57.143 0.00 0.00 0.00 3.02
3787 4553 0.393537 CGTACCTCACCGAGTACCCT 60.394 60.000 0.00 0.00 0.00 4.34
3799 4565 2.593026 GAGTACCCTGAGAGGATGAGG 58.407 57.143 0.00 0.00 37.67 3.86
3857 4623 5.453762 CCTGTGATATACCTCAACATCAGCA 60.454 44.000 0.00 0.00 0.00 4.41
4006 4772 1.736681 GACACTTGGAATGAGCTGCTC 59.263 52.381 22.38 22.38 0.00 4.26
4082 4848 7.206687 TGGTTACATGAATTTTGTTTGTCCTC 58.793 34.615 0.00 0.00 0.00 3.71
4088 4854 7.653311 ACATGAATTTTGTTTGTCCTCTTTAGC 59.347 33.333 0.00 0.00 0.00 3.09
4089 4855 7.346751 TGAATTTTGTTTGTCCTCTTTAGCT 57.653 32.000 0.00 0.00 0.00 3.32
4090 4856 7.781056 TGAATTTTGTTTGTCCTCTTTAGCTT 58.219 30.769 0.00 0.00 0.00 3.74
4091 4857 7.706179 TGAATTTTGTTTGTCCTCTTTAGCTTG 59.294 33.333 0.00 0.00 0.00 4.01
4092 4858 4.568152 TTGTTTGTCCTCTTTAGCTTGC 57.432 40.909 0.00 0.00 0.00 4.01
4093 4859 3.820557 TGTTTGTCCTCTTTAGCTTGCT 58.179 40.909 0.00 0.00 0.00 3.91
4095 4861 5.560724 TGTTTGTCCTCTTTAGCTTGCTAT 58.439 37.500 2.99 0.00 0.00 2.97
4096 4862 6.707290 TGTTTGTCCTCTTTAGCTTGCTATA 58.293 36.000 2.99 0.00 0.00 1.31
4108 4874 7.719871 TTAGCTTGCTATAAGGGGTAGATAG 57.280 40.000 2.99 0.00 0.00 2.08
4116 4882 7.341256 TGCTATAAGGGGTAGATAGGATTTACG 59.659 40.741 0.00 0.00 0.00 3.18
4118 4884 4.482400 AGGGGTAGATAGGATTTACGGT 57.518 45.455 0.00 0.00 0.00 4.83
4123 4889 6.071672 GGGGTAGATAGGATTTACGGTTAGTC 60.072 46.154 0.00 0.00 0.00 2.59
4140 4906 2.233271 AGTCCACGAAGTTCGGTTCTA 58.767 47.619 27.62 7.04 45.59 2.10
4170 4936 4.923415 AGGTGGATAAACTTCCAGGAAAG 58.077 43.478 2.72 0.39 46.31 2.62
4243 5009 3.673809 CGGCGGCATTTTAGATACTACTC 59.326 47.826 10.53 0.00 0.00 2.59
4908 6056 4.087892 CCTGTGGTGGCGAGGAGG 62.088 72.222 0.00 0.00 0.00 4.30
5204 6352 1.600413 GGGTCAGTCAAGCGCAAAAAG 60.600 52.381 11.47 0.00 0.00 2.27
5290 6446 8.824756 AAAGGGGGAAATTAAGAGAAATACTC 57.175 34.615 0.00 0.00 45.22 2.59
5291 6447 6.912426 AGGGGGAAATTAAGAGAAATACTCC 58.088 40.000 0.00 0.00 45.96 3.85
5292 6448 6.069331 GGGGGAAATTAAGAGAAATACTCCC 58.931 44.000 0.00 0.00 45.96 4.30
5293 6449 6.126156 GGGGGAAATTAAGAGAAATACTCCCT 60.126 42.308 12.76 0.00 45.96 4.20
5294 6450 6.999272 GGGGAAATTAAGAGAAATACTCCCTC 59.001 42.308 12.76 0.00 45.96 4.30
5295 6451 6.999272 GGGAAATTAAGAGAAATACTCCCTCC 59.001 42.308 0.00 0.00 45.96 4.30
5296 6452 6.706716 GGAAATTAAGAGAAATACTCCCTCCG 59.293 42.308 0.00 0.00 45.96 4.63
5297 6453 6.809976 AATTAAGAGAAATACTCCCTCCGT 57.190 37.500 0.00 0.00 45.96 4.69
5298 6454 5.848833 TTAAGAGAAATACTCCCTCCGTC 57.151 43.478 0.00 0.00 45.96 4.79
5299 6455 2.668625 AGAGAAATACTCCCTCCGTCC 58.331 52.381 0.00 0.00 45.96 4.79
5300 6456 1.687660 GAGAAATACTCCCTCCGTCCC 59.312 57.143 0.00 0.00 39.53 4.46
5301 6457 1.007963 AGAAATACTCCCTCCGTCCCA 59.992 52.381 0.00 0.00 0.00 4.37
5302 6458 1.835531 GAAATACTCCCTCCGTCCCAA 59.164 52.381 0.00 0.00 0.00 4.12
5303 6459 1.961133 AATACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
5304 6460 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
5305 6461 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
5306 6462 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
5307 6463 2.488836 ACTCCCTCCGTCCCAAAATAT 58.511 47.619 0.00 0.00 0.00 1.28
5308 6464 3.660959 ACTCCCTCCGTCCCAAAATATA 58.339 45.455 0.00 0.00 0.00 0.86
5309 6465 4.042174 ACTCCCTCCGTCCCAAAATATAA 58.958 43.478 0.00 0.00 0.00 0.98
5310 6466 4.102681 ACTCCCTCCGTCCCAAAATATAAG 59.897 45.833 0.00 0.00 0.00 1.73
5311 6467 4.300345 TCCCTCCGTCCCAAAATATAAGA 58.700 43.478 0.00 0.00 0.00 2.10
5312 6468 4.347000 TCCCTCCGTCCCAAAATATAAGAG 59.653 45.833 0.00 0.00 0.00 2.85
5313 6469 4.065789 CCTCCGTCCCAAAATATAAGAGC 58.934 47.826 0.00 0.00 0.00 4.09
5314 6470 3.724374 TCCGTCCCAAAATATAAGAGCG 58.276 45.455 0.00 0.00 0.00 5.03
5315 6471 3.133362 TCCGTCCCAAAATATAAGAGCGT 59.867 43.478 0.00 0.00 0.00 5.07
5316 6472 3.875134 CCGTCCCAAAATATAAGAGCGTT 59.125 43.478 0.00 0.00 0.00 4.84
5317 6473 4.334481 CCGTCCCAAAATATAAGAGCGTTT 59.666 41.667 0.00 0.00 0.00 3.60
5318 6474 5.163693 CCGTCCCAAAATATAAGAGCGTTTT 60.164 40.000 0.00 0.00 0.00 2.43
5319 6475 6.319399 CGTCCCAAAATATAAGAGCGTTTTT 58.681 36.000 0.00 0.00 0.00 1.94
5320 6476 7.414319 CCGTCCCAAAATATAAGAGCGTTTTTA 60.414 37.037 0.00 0.00 0.00 1.52
5321 6477 7.964011 CGTCCCAAAATATAAGAGCGTTTTTAA 59.036 33.333 0.00 0.00 0.00 1.52
5322 6478 9.069078 GTCCCAAAATATAAGAGCGTTTTTAAC 57.931 33.333 0.00 0.00 0.00 2.01
5323 6479 8.794553 TCCCAAAATATAAGAGCGTTTTTAACA 58.205 29.630 0.00 0.00 0.00 2.41
5324 6480 8.856247 CCCAAAATATAAGAGCGTTTTTAACAC 58.144 33.333 0.00 0.00 0.00 3.32
5325 6481 9.620660 CCAAAATATAAGAGCGTTTTTAACACT 57.379 29.630 0.00 0.00 0.00 3.55
5330 6486 7.958053 ATAAGAGCGTTTTTAACACTACACT 57.042 32.000 0.00 0.00 0.00 3.55
5332 6488 7.404139 AAGAGCGTTTTTAACACTACACTAG 57.596 36.000 0.00 0.00 0.00 2.57
5333 6489 6.510536 AGAGCGTTTTTAACACTACACTAGT 58.489 36.000 0.00 0.00 40.28 2.57
5363 6519 9.921637 AAAAATGCTTTTATATTTTGAGACGGA 57.078 25.926 0.00 0.00 36.80 4.69
5364 6520 9.573133 AAAATGCTTTTATATTTTGAGACGGAG 57.427 29.630 0.00 0.00 35.73 4.63
5365 6521 6.677781 TGCTTTTATATTTTGAGACGGAGG 57.322 37.500 0.00 0.00 0.00 4.30
5366 6522 5.588648 TGCTTTTATATTTTGAGACGGAGGG 59.411 40.000 0.00 0.00 0.00 4.30
5367 6523 5.820947 GCTTTTATATTTTGAGACGGAGGGA 59.179 40.000 0.00 0.00 0.00 4.20
5368 6524 6.017852 GCTTTTATATTTTGAGACGGAGGGAG 60.018 42.308 0.00 0.00 0.00 4.30
5369 6525 6.555463 TTTATATTTTGAGACGGAGGGAGT 57.445 37.500 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 95 5.991606 TCTCTTGTTTCACTATGAGTTGGTG 59.008 40.000 0.00 0.00 0.00 4.17
99 100 7.055667 TGTCTTCTCTTGTTTCACTATGAGT 57.944 36.000 0.00 0.00 0.00 3.41
108 114 9.813080 GTATGTGTTTATGTCTTCTCTTGTTTC 57.187 33.333 0.00 0.00 0.00 2.78
124 132 5.470777 GCCCAACAGTTACTGTATGTGTTTA 59.529 40.000 18.93 0.00 44.62 2.01
221 229 2.222886 CGGAAATGATCGCACAGTTCAG 60.223 50.000 17.83 12.72 43.56 3.02
342 351 3.485463 TGTGAATTCTGTTTCCGGAGT 57.515 42.857 3.34 0.00 0.00 3.85
545 718 7.132694 TGTTACTGATTTGTTCTAGCATGTG 57.867 36.000 0.00 0.00 0.00 3.21
564 782 6.334202 AGCTCTTACATACTTCTGCTGTTAC 58.666 40.000 0.00 0.00 0.00 2.50
571 789 4.033817 GCAGCAAGCTCTTACATACTTCTG 59.966 45.833 0.00 0.00 41.15 3.02
574 792 2.932614 CGCAGCAAGCTCTTACATACTT 59.067 45.455 0.00 0.00 42.61 2.24
603 987 3.298317 CTCTTCGTAGCGTTACCTATGC 58.702 50.000 3.68 0.00 39.16 3.14
658 1044 0.804989 GTTCCCTTGAAGCCACATCG 59.195 55.000 0.00 0.00 0.00 3.84
754 1188 1.461075 CCCTCCATCCCTCTCCCTG 60.461 68.421 0.00 0.00 0.00 4.45
755 1189 1.238896 TTCCCTCCATCCCTCTCCCT 61.239 60.000 0.00 0.00 0.00 4.20
780 1214 2.076863 GCCAACAAGTAATGCTCGACT 58.923 47.619 0.00 0.00 0.00 4.18
847 1288 2.179517 CGGCGGCGGCATTTTTAA 59.820 55.556 32.59 0.00 42.47 1.52
938 1486 1.429148 GATCCACCCGAATGTCGCAC 61.429 60.000 0.00 0.00 38.82 5.34
1012 1560 3.539842 CCCTCGCTTCCTAGGGTC 58.460 66.667 9.46 0.00 46.45 4.46
1081 1629 3.817210 TTGGGCCCAAATCCACGCA 62.817 57.895 35.47 9.15 32.44 5.24
1107 1655 6.872547 AGAGTTTATGGAGAAAAGTCCGTTAC 59.127 38.462 0.00 0.00 39.81 2.50
1207 1755 2.465097 GATCGCCGATCACTCCCTCG 62.465 65.000 21.52 0.00 38.77 4.63
1234 1782 3.818787 CAGCCGGCCATTGTGCTC 61.819 66.667 26.15 0.00 30.08 4.26
1427 1987 1.594293 CCTTGGTGCTCACGAACGT 60.594 57.895 0.00 0.00 0.00 3.99
1431 1991 4.680237 CGGCCTTGGTGCTCACGA 62.680 66.667 0.00 0.00 0.00 4.35
1606 2166 4.410400 CGGGGAGGAAGCGGCTTT 62.410 66.667 17.51 0.94 0.00 3.51
1623 2183 1.627297 ATGAGGAGAAACGGGAGGGC 61.627 60.000 0.00 0.00 0.00 5.19
1640 2200 1.006832 GTGCCGGTGCTACTTACATG 58.993 55.000 1.90 0.00 38.71 3.21
1786 2349 1.378514 GGGATCCTGCGCTTTTCCA 60.379 57.895 12.58 0.00 0.00 3.53
1789 2352 1.077429 GAGGGGATCCTGCGCTTTT 60.077 57.895 12.58 0.00 45.05 2.27
1800 2363 0.113776 TCCGGCGTTATAGAGGGGAT 59.886 55.000 6.01 0.00 0.00 3.85
1921 2484 3.864686 CCGGTGGAATTCGCTGCG 61.865 66.667 17.25 17.25 0.00 5.18
1939 2502 1.604278 GGAGCGCTGATAATGGGTTTC 59.396 52.381 18.48 0.00 0.00 2.78
1948 2511 2.515290 TCGTCCGGAGCGCTGATA 60.515 61.111 18.48 0.00 0.00 2.15
1960 2526 1.513622 GGAGTCTGAAGGCTCGTCC 59.486 63.158 5.88 0.00 32.83 4.79
1963 2529 0.179150 CTTCGGAGTCTGAAGGCTCG 60.179 60.000 27.65 8.36 39.30 5.03
1969 2535 2.261671 GCGCCTTCGGAGTCTGAA 59.738 61.111 13.75 13.75 35.95 3.02
1972 2538 4.070552 GTGGCGCCTTCGGAGTCT 62.071 66.667 29.70 0.00 35.95 3.24
2092 2658 3.151710 CCCGGCGGTGTAGATGGA 61.152 66.667 26.32 0.00 0.00 3.41
2110 2676 0.390472 GTCTGTCCTCCTTTCGCTGG 60.390 60.000 0.00 0.00 0.00 4.85
2146 2712 0.955428 GCTTGTGCCTCGACATGGAA 60.955 55.000 0.00 0.00 0.00 3.53
2263 2835 0.953960 GGTTACCGGAGCTGGTGTTG 60.954 60.000 9.46 0.00 43.68 3.33
2273 2845 2.652530 GTCGCTGTGGTTACCGGA 59.347 61.111 9.46 0.00 0.00 5.14
2274 2846 2.807895 CGTCGCTGTGGTTACCGG 60.808 66.667 0.00 0.00 0.00 5.28
2275 2847 2.049802 ACGTCGCTGTGGTTACCG 60.050 61.111 0.00 0.00 0.00 4.02
2277 2849 0.989890 GATGACGTCGCTGTGGTTAC 59.010 55.000 11.62 0.00 0.00 2.50
2278 2850 0.455464 CGATGACGTCGCTGTGGTTA 60.455 55.000 11.62 0.00 44.33 2.85
2280 2852 2.126463 CGATGACGTCGCTGTGGT 60.126 61.111 11.62 0.00 44.33 4.16
2288 2860 3.601981 GACGATGCCGATGACGTC 58.398 61.111 9.11 9.11 45.51 4.34
2289 2861 2.277949 CGACGATGCCGATGACGT 60.278 61.111 0.00 0.00 41.57 4.34
2290 2862 3.024609 CCGACGATGCCGATGACG 61.025 66.667 0.00 0.00 39.50 4.35
2291 2863 2.658593 CCCGACGATGCCGATGAC 60.659 66.667 0.00 0.00 39.50 3.06
2292 2864 3.911698 CCCCGACGATGCCGATGA 61.912 66.667 0.00 0.00 39.50 2.92
2716 3288 2.180017 GGAATGTTGCAGCCGCTG 59.820 61.111 16.47 16.47 39.64 5.18
2718 3290 3.346631 CTGGGAATGTTGCAGCCGC 62.347 63.158 0.00 0.00 39.24 6.53
2770 3345 5.720371 ATGAAATTGGTCGGAACAATTGA 57.280 34.783 29.03 20.49 32.48 2.57
2774 3349 6.375736 TGCTATAATGAAATTGGTCGGAACAA 59.624 34.615 11.42 11.42 36.99 2.83
2783 3358 5.296780 ACCGAGTGTGCTATAATGAAATTGG 59.703 40.000 0.00 0.00 36.99 3.16
2795 3370 2.862738 TCGATCACCGAGTGTGCTA 58.137 52.632 0.00 0.00 45.03 3.49
2805 3380 5.420409 AGGATAACTCAAGTTTCGATCACC 58.580 41.667 0.00 0.00 39.31 4.02
2819 3394 4.246458 ACGCAAACAAGAGAGGATAACTC 58.754 43.478 0.00 0.00 46.98 3.01
2827 3402 1.493311 GCCGACGCAAACAAGAGAG 59.507 57.895 0.00 0.00 34.03 3.20
2947 3523 1.296392 CTGACACCATGGCGGAGAA 59.704 57.895 13.04 0.00 31.94 2.87
2969 3545 5.334414 GGACTTCTCGTACACGTTCTTCTTA 60.334 44.000 1.19 0.00 40.80 2.10
3134 3889 2.637382 TCAAGTGCCAGTGAGTTGGATA 59.363 45.455 0.00 0.00 40.87 2.59
3135 3890 1.421268 TCAAGTGCCAGTGAGTTGGAT 59.579 47.619 0.00 0.00 40.87 3.41
3399 4158 3.117926 TGGCCAGCAGATCAGCTTAATAA 60.118 43.478 10.30 0.00 43.70 1.40
3400 4159 2.439135 TGGCCAGCAGATCAGCTTAATA 59.561 45.455 10.30 0.00 43.70 0.98
3401 4160 1.213678 TGGCCAGCAGATCAGCTTAAT 59.786 47.619 10.30 0.00 43.70 1.40
3417 4176 3.620488 TCAGGATGTAAACAGATTGGCC 58.380 45.455 0.00 0.00 37.40 5.36
3472 4231 2.100631 CACGCGGTAGCCTTCTTGG 61.101 63.158 12.47 0.00 41.18 3.61
3487 4246 1.091771 CCTCAAGGCTATGGTGCACG 61.092 60.000 11.45 0.00 34.04 5.34
3625 4387 2.934553 GTGGTGGCGGTCTCTTAATAAC 59.065 50.000 0.00 0.00 0.00 1.89
3626 4388 2.568062 TGTGGTGGCGGTCTCTTAATAA 59.432 45.455 0.00 0.00 0.00 1.40
3627 4389 2.181125 TGTGGTGGCGGTCTCTTAATA 58.819 47.619 0.00 0.00 0.00 0.98
3653 4415 6.872628 AAGATTAGTCGTACCGATGACATA 57.127 37.500 2.17 0.00 43.11 2.29
3654 4416 5.769484 AAGATTAGTCGTACCGATGACAT 57.231 39.130 0.00 0.00 43.11 3.06
3655 4417 5.819379 AGTAAGATTAGTCGTACCGATGACA 59.181 40.000 7.53 0.00 43.11 3.58
3656 4418 6.202570 AGAGTAAGATTAGTCGTACCGATGAC 59.797 42.308 7.53 0.00 39.29 3.06
3667 4433 8.181573 GGATCGATCATGAGAGTAAGATTAGTC 58.818 40.741 25.93 0.01 34.12 2.59
3669 4435 7.148323 ACGGATCGATCATGAGAGTAAGATTAG 60.148 40.741 25.93 1.76 0.00 1.73
3731 4497 2.187946 GGTCTCCCTGTGGCATCG 59.812 66.667 0.00 0.00 0.00 3.84
3762 4528 2.181021 CGGTGAGGTACGTCTGGC 59.819 66.667 16.00 6.90 0.00 4.85
3787 4553 3.724209 TCTCCAGTATCCTCATCCTCTCA 59.276 47.826 0.00 0.00 0.00 3.27
3799 4565 3.386078 TGCTCATGACCTTCTCCAGTATC 59.614 47.826 0.00 0.00 0.00 2.24
3939 4705 3.241530 AGTCCTGCTTGGTCGCCA 61.242 61.111 0.00 0.00 37.07 5.69
3991 4757 2.569059 GCATAGAGCAGCTCATTCCAA 58.431 47.619 24.64 2.91 44.79 3.53
4006 4772 1.300775 CTGGAGCAGCGAGGCATAG 60.301 63.158 1.57 0.00 35.83 2.23
4082 4848 6.420913 TCTACCCCTTATAGCAAGCTAAAG 57.579 41.667 5.81 10.33 31.73 1.85
4087 4853 5.024118 TCCTATCTACCCCTTATAGCAAGC 58.976 45.833 0.00 0.00 0.00 4.01
4088 4854 7.741554 AATCCTATCTACCCCTTATAGCAAG 57.258 40.000 0.00 0.00 0.00 4.01
4089 4855 9.043548 GTAAATCCTATCTACCCCTTATAGCAA 57.956 37.037 0.00 0.00 0.00 3.91
4090 4856 7.341256 CGTAAATCCTATCTACCCCTTATAGCA 59.659 40.741 0.00 0.00 0.00 3.49
4091 4857 7.201893 CCGTAAATCCTATCTACCCCTTATAGC 60.202 44.444 0.00 0.00 0.00 2.97
4092 4858 7.838193 ACCGTAAATCCTATCTACCCCTTATAG 59.162 40.741 0.00 0.00 0.00 1.31
4093 4859 7.712537 ACCGTAAATCCTATCTACCCCTTATA 58.287 38.462 0.00 0.00 0.00 0.98
4095 4861 5.969086 ACCGTAAATCCTATCTACCCCTTA 58.031 41.667 0.00 0.00 0.00 2.69
4096 4862 4.824276 ACCGTAAATCCTATCTACCCCTT 58.176 43.478 0.00 0.00 0.00 3.95
4108 4874 3.508744 TCGTGGACTAACCGTAAATCC 57.491 47.619 0.00 0.00 42.61 3.01
4116 4882 1.000171 ACCGAACTTCGTGGACTAACC 60.000 52.381 10.22 0.00 38.40 2.85
4118 4884 2.624838 AGAACCGAACTTCGTGGACTAA 59.375 45.455 10.22 0.00 38.40 2.24
4123 4889 3.226346 TCATAGAACCGAACTTCGTGG 57.774 47.619 10.22 0.00 38.40 4.94
4140 4906 7.420680 CCTGGAAGTTTATCCACCTCTAATCAT 60.421 40.741 0.00 0.00 44.52 2.45
4170 4936 4.035675 GGGTCTAACTAACTGAATGCATGC 59.964 45.833 11.82 11.82 0.00 4.06
4269 5035 9.030452 ACTGAAGTAGTGATCTAAAAGTGATCT 57.970 33.333 0.00 0.00 40.51 2.75
4388 5154 4.188462 TGTCCAACTATTTGCGAATCGAT 58.812 39.130 6.91 0.00 0.00 3.59
4527 5675 1.577328 CGTGGATGTTGTGGACTGCC 61.577 60.000 0.00 0.00 0.00 4.85
4908 6056 0.036765 TATGGCGGGCGGATTATGTC 60.037 55.000 0.00 0.00 0.00 3.06
5187 6335 0.667993 CCCTTTTTGCGCTTGACTGA 59.332 50.000 9.73 0.00 0.00 3.41
5204 6352 7.741027 ATAATGATGATTATGATGCGATCCC 57.259 36.000 0.00 0.00 34.09 3.85
5290 6446 4.642429 CTCTTATATTTTGGGACGGAGGG 58.358 47.826 0.00 0.00 0.00 4.30
5291 6447 4.065789 GCTCTTATATTTTGGGACGGAGG 58.934 47.826 0.00 0.00 0.00 4.30
5292 6448 3.741344 CGCTCTTATATTTTGGGACGGAG 59.259 47.826 0.00 0.00 0.00 4.63
5293 6449 3.133362 ACGCTCTTATATTTTGGGACGGA 59.867 43.478 0.00 0.00 0.00 4.69
5294 6450 3.463944 ACGCTCTTATATTTTGGGACGG 58.536 45.455 0.00 0.00 0.00 4.79
5295 6451 5.479716 AAACGCTCTTATATTTTGGGACG 57.520 39.130 0.00 0.00 0.00 4.79
5296 6452 9.069078 GTTAAAAACGCTCTTATATTTTGGGAC 57.931 33.333 0.00 0.00 0.00 4.46
5297 6453 8.794553 TGTTAAAAACGCTCTTATATTTTGGGA 58.205 29.630 0.00 0.00 0.00 4.37
5298 6454 8.856247 GTGTTAAAAACGCTCTTATATTTTGGG 58.144 33.333 0.00 0.00 38.81 4.12
5339 6495 8.190784 CCTCCGTCTCAAAATATAAAAGCATTT 58.809 33.333 0.00 0.00 42.41 2.32
5340 6496 7.201821 CCCTCCGTCTCAAAATATAAAAGCATT 60.202 37.037 0.00 0.00 0.00 3.56
5341 6497 6.263168 CCCTCCGTCTCAAAATATAAAAGCAT 59.737 38.462 0.00 0.00 0.00 3.79
5342 6498 5.588648 CCCTCCGTCTCAAAATATAAAAGCA 59.411 40.000 0.00 0.00 0.00 3.91
5343 6499 5.820947 TCCCTCCGTCTCAAAATATAAAAGC 59.179 40.000 0.00 0.00 0.00 3.51
5344 6500 7.048512 ACTCCCTCCGTCTCAAAATATAAAAG 58.951 38.462 0.00 0.00 0.00 2.27
5345 6501 6.954232 ACTCCCTCCGTCTCAAAATATAAAA 58.046 36.000 0.00 0.00 0.00 1.52
5346 6502 6.555463 ACTCCCTCCGTCTCAAAATATAAA 57.445 37.500 0.00 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.