Multiple sequence alignment - TraesCS6A01G086800

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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 TraesCS6A01G086800 chr6A 100.000 5028 0 0 1 5028 55546346 55551373 0.000000e+00 9286.0
1 TraesCS6A01G086800 chrUn 95.445 3403 99 22 725 4099 21203136 21199762 0.000000e+00 5374.0
2 TraesCS6A01G086800 chrUn 91.944 571 29 2 4135 4700 21199757 21199199 0.000000e+00 784.0
3 TraesCS6A01G086800 chrUn 92.542 295 15 4 4735 5028 21199213 21198925 2.800000e-112 416.0
4 TraesCS6A01G086800 chrUn 90.654 214 14 3 531 738 21204062 21203849 3.830000e-71 279.0
5 TraesCS6A01G086800 chr6B 94.067 2781 103 19 1968 4707 98854532 98857291 0.000000e+00 4165.0
6 TraesCS6A01G086800 chr6B 95.854 1978 52 7 3 1969 98852336 98854294 0.000000e+00 3171.0
7 TraesCS6A01G086800 chr6B 82.071 647 80 22 2314 2938 699802433 699803065 2.070000e-143 520.0
8 TraesCS6A01G086800 chr6B 81.944 648 81 22 2313 2938 699842045 699842678 2.680000e-142 516.0
9 TraesCS6A01G086800 chr6B 81.607 647 83 26 2314 2938 699932219 699932851 2.090000e-138 503.0
10 TraesCS6A01G086800 chr6B 81.453 647 84 25 2314 2938 699881950 699882582 9.720000e-137 497.0
11 TraesCS6A01G086800 chr6B 90.977 266 19 3 4762 5027 98857289 98857549 2.230000e-93 353.0
12 TraesCS6A01G086800 chr6B 86.752 234 24 1 2707 2940 214031613 214031387 2.320000e-63 254.0
13 TraesCS6A01G086800 chr6B 92.913 127 8 1 2375 2500 214036702 214036576 3.090000e-42 183.0
14 TraesCS6A01G086800 chr4B 83.854 576 36 29 8 528 22847750 22848323 3.500000e-136 496.0
15 TraesCS6A01G086800 chr2B 97.251 291 8 0 1 291 113282435 113282725 1.260000e-135 494.0
16 TraesCS6A01G086800 chr2B 93.478 184 10 2 345 528 113283102 113283283 6.410000e-69 272.0
17 TraesCS6A01G086800 chr2B 86.420 162 20 2 542 701 532082973 532082812 5.170000e-40 176.0
18 TraesCS6A01G086800 chr3A 83.803 568 39 29 13 528 79447149 79446583 1.630000e-134 490.0
19 TraesCS6A01G086800 chr3A 87.798 377 19 10 8 359 264030922 264030548 2.800000e-112 416.0
20 TraesCS6A01G086800 chr3A 91.192 193 10 4 345 532 264030533 264030343 6.460000e-64 255.0
21 TraesCS6A01G086800 chr3A 85.714 238 31 3 2698 2933 12476176 12475940 1.080000e-61 248.0
22 TraesCS6A01G086800 chr1B 89.250 400 28 7 2314 2711 532673527 532673141 2.100000e-133 486.0
23 TraesCS6A01G086800 chr1B 88.503 374 20 13 8 359 252972444 252972816 1.000000e-116 431.0
24 TraesCS6A01G086800 chr3B 82.301 565 42 31 15 528 114103754 114104311 2.150000e-118 436.0
25 TraesCS6A01G086800 chr3B 87.105 380 21 9 8 359 299138547 299138926 6.060000e-109 405.0
26 TraesCS6A01G086800 chr3B 91.579 190 12 2 345 531 299138941 299139129 4.990000e-65 259.0
27 TraesCS6A01G086800 chr3D 88.594 377 18 8 8 359 225858604 225858228 7.730000e-118 435.0
28 TraesCS6A01G086800 chr3D 87.534 369 17 12 15 359 67720559 67720196 2.820000e-107 399.0
29 TraesCS6A01G086800 chr3D 89.674 184 16 2 345 528 67720181 67720001 1.090000e-56 231.0
30 TraesCS6A01G086800 chr2D 83.080 526 28 20 8 474 78382883 78383406 6.020000e-114 422.0
31 TraesCS6A01G086800 chr2D 93.011 186 10 3 345 528 263506782 263506966 8.300000e-68 268.0
32 TraesCS6A01G086800 chr2D 87.654 162 18 2 542 701 451961798 451961637 2.390000e-43 187.0
33 TraesCS6A01G086800 chr7B 82.447 376 49 13 2575 2940 677241766 677242134 3.780000e-81 313.0
34 TraesCS6A01G086800 chr7B 96.040 101 2 2 4920 5019 79316402 79316501 4.030000e-36 163.0
35 TraesCS6A01G086800 chr7B 85.897 156 19 3 2311 2465 677241369 677241522 4.030000e-36 163.0
36 TraesCS6A01G086800 chr7B 94.393 107 3 3 4921 5025 79312991 79312886 1.450000e-35 161.0
37 TraesCS6A01G086800 chr4D 93.085 188 8 5 345 529 10977998 10977813 2.310000e-68 270.0
38 TraesCS6A01G086800 chr4D 96.721 61 1 1 282 342 10978086 10978027 3.200000e-17 100.0
39 TraesCS6A01G086800 chr2A 88.820 161 17 1 542 701 597511357 597511517 3.970000e-46 196.0
40 TraesCS6A01G086800 chr7D 97.030 101 1 2 4920 5019 118162230 118162329 8.660000e-38 169.0
41 TraesCS6A01G086800 chr7D 95.918 98 3 1 4928 5025 25345958 25345862 1.870000e-34 158.0
42 TraesCS6A01G086800 chr7D 95.876 97 3 1 4929 5025 25338960 25338865 6.740000e-34 156.0
43 TraesCS6A01G086800 chr7A 95.960 99 2 2 4921 5019 122682333 122682237 5.210000e-35 159.0
44 TraesCS6A01G086800 chr5A 90.756 119 7 3 4907 5025 688958389 688958275 6.740000e-34 156.0
45 TraesCS6A01G086800 chr5D 82.873 181 8 2 202 359 274768382 274768562 1.890000e-29 141.0
46 TraesCS6A01G086800 chr5D 81.935 155 22 6 543 693 534614744 534614592 5.280000e-25 126.0
47 TraesCS6A01G086800 chr6D 86.275 51 5 2 4395 4443 23354396 23354446 3.000000e-03 54.7
48 TraesCS6A01G086800 chr6D 86.275 51 5 2 4395 4443 23368937 23368987 3.000000e-03 54.7


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 TraesCS6A01G086800 chr6A 55546346 55551373 5027 False 9286.00 9286 100.000000 1 5028 1 chr6A.!!$F1 5027
1 TraesCS6A01G086800 chrUn 21198925 21204062 5137 True 1713.25 5374 92.646250 531 5028 4 chrUn.!!$R1 4497
2 TraesCS6A01G086800 chr6B 98852336 98857549 5213 False 2563.00 4165 93.632667 3 5027 3 chr6B.!!$F5 5024
3 TraesCS6A01G086800 chr6B 699802433 699803065 632 False 520.00 520 82.071000 2314 2938 1 chr6B.!!$F1 624
4 TraesCS6A01G086800 chr6B 699842045 699842678 633 False 516.00 516 81.944000 2313 2938 1 chr6B.!!$F2 625
5 TraesCS6A01G086800 chr6B 699932219 699932851 632 False 503.00 503 81.607000 2314 2938 1 chr6B.!!$F4 624
6 TraesCS6A01G086800 chr6B 699881950 699882582 632 False 497.00 497 81.453000 2314 2938 1 chr6B.!!$F3 624
7 TraesCS6A01G086800 chr4B 22847750 22848323 573 False 496.00 496 83.854000 8 528 1 chr4B.!!$F1 520
8 TraesCS6A01G086800 chr2B 113282435 113283283 848 False 383.00 494 95.364500 1 528 2 chr2B.!!$F1 527
9 TraesCS6A01G086800 chr3A 79446583 79447149 566 True 490.00 490 83.803000 13 528 1 chr3A.!!$R2 515
10 TraesCS6A01G086800 chr3A 264030343 264030922 579 True 335.50 416 89.495000 8 532 2 chr3A.!!$R3 524
11 TraesCS6A01G086800 chr3B 114103754 114104311 557 False 436.00 436 82.301000 15 528 1 chr3B.!!$F1 513
12 TraesCS6A01G086800 chr3B 299138547 299139129 582 False 332.00 405 89.342000 8 531 2 chr3B.!!$F2 523
13 TraesCS6A01G086800 chr3D 67720001 67720559 558 True 315.00 399 88.604000 15 528 2 chr3D.!!$R2 513
14 TraesCS6A01G086800 chr2D 78382883 78383406 523 False 422.00 422 83.080000 8 474 1 chr2D.!!$F1 466
15 TraesCS6A01G086800 chr7B 677241369 677242134 765 False 238.00 313 84.172000 2311 2940 2 chr7B.!!$F2 629

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
169 171 0.679505 AGAAGATATAAGCGGCGGCA 59.320 50.0 19.21 0.0 43.41 5.69 F
1215 2292 0.179200 GTACAAACTCAATGCGCCCG 60.179 55.0 4.18 0.0 0.00 6.13 F
2435 3769 0.037419 GCCATTGCAACCGTCCAAAT 60.037 50.0 0.00 0.0 37.47 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1262 2339 2.302733 TGATTACACTCTGCTGCAGGAA 59.697 45.455 27.79 14.85 31.51 3.36 R
2768 4280 0.385473 CGATGGCGAGCAAAACGTTT 60.385 50.000 7.96 7.96 40.82 3.60 R
4095 5638 0.032130 GAGCCACGATTGCCGATCTA 59.968 55.000 0.00 0.00 41.76 1.98 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
169 171 0.679505 AGAAGATATAAGCGGCGGCA 59.320 50.000 19.21 0.00 43.41 5.69
216 226 4.447342 CAGGCGGCTGGGGGAAAT 62.447 66.667 30.03 0.00 0.00 2.17
509 852 1.829222 GTATCCCTGTCTTTCCGTCCA 59.171 52.381 0.00 0.00 0.00 4.02
560 905 2.159179 AGGCCATGTTTGGATTACCC 57.841 50.000 5.01 0.00 46.92 3.69
728 1805 5.163426 TGGTTCTCACTTTACGTTAACTCCA 60.163 40.000 3.71 0.00 0.00 3.86
788 1865 5.798934 CCTCTTGATTTTCTGCTTGAATTCG 59.201 40.000 0.04 0.00 34.24 3.34
791 1868 7.424803 TCTTGATTTTCTGCTTGAATTCGAAA 58.575 30.769 0.00 1.50 34.24 3.46
801 1878 4.591202 CTTGAATTCGAAATGATGACCCG 58.409 43.478 0.00 0.00 0.00 5.28
973 2050 5.908831 TGGGGGTGTTGATATTATCTAGTGT 59.091 40.000 5.33 0.00 0.00 3.55
1212 2289 2.032030 AGTGTGTACAAACTCAATGCGC 60.032 45.455 13.22 0.00 31.33 6.09
1215 2292 0.179200 GTACAAACTCAATGCGCCCG 60.179 55.000 4.18 0.00 0.00 6.13
1262 2339 7.334421 ACTGATGCGTGTCTTAAATCTTTGTAT 59.666 33.333 0.00 0.00 0.00 2.29
1372 2449 5.596836 TGAAATTGACTTGGATATTGGGC 57.403 39.130 0.00 0.00 0.00 5.36
1865 2943 5.634859 GCCACACTAAATCAAATGTCTTTGG 59.365 40.000 0.00 0.00 41.74 3.28
1933 3018 6.096141 TCAAAGTAACTTCCACATGCTGAAAA 59.904 34.615 0.00 0.00 0.00 2.29
1963 3049 2.716424 TCAACACTTGGGGGAAGAATCT 59.284 45.455 0.00 0.00 35.42 2.40
2061 3386 2.203153 GCACGGGGAACACACAGT 60.203 61.111 0.00 0.00 0.00 3.55
2072 3397 4.503296 GGGAACACACAGTGAGAGTAACAT 60.503 45.833 7.81 0.00 36.96 2.71
2073 3398 5.057149 GGAACACACAGTGAGAGTAACATT 58.943 41.667 7.81 0.00 36.96 2.71
2190 3516 8.896744 CACATGTTGAAGATACAATAGGAATGT 58.103 33.333 0.00 0.00 34.81 2.71
2435 3769 0.037419 GCCATTGCAACCGTCCAAAT 60.037 50.000 0.00 0.00 37.47 2.32
2500 3945 4.863131 CGTCTTGTAACCACTGTAATCCTC 59.137 45.833 0.00 0.00 0.00 3.71
2505 3950 5.310451 TGTAACCACTGTAATCCTCCAAAC 58.690 41.667 0.00 0.00 0.00 2.93
2891 4406 2.831526 ACTACCAAAATTCATGGGCCAC 59.168 45.455 9.28 0.00 42.48 5.01
2979 4495 1.213182 TGTTCTTGGTACCCTTGCACA 59.787 47.619 10.07 3.49 0.00 4.57
2989 4505 5.072741 GGTACCCTTGCACATATCATGATT 58.927 41.667 14.65 0.00 0.00 2.57
3250 4771 4.455190 GGAAATATCAGATGCTTGGCTCTC 59.545 45.833 0.00 0.00 0.00 3.20
3379 4900 2.039480 CAGGCCATACAGCTGTCCATAT 59.961 50.000 25.56 8.52 0.00 1.78
3397 4918 0.035630 ATGCAGGTTCAGAGTGCCTC 60.036 55.000 0.00 0.00 36.31 4.70
3487 5008 1.003812 TGCACCTTTAACCACCGCTAT 59.996 47.619 0.00 0.00 0.00 2.97
3520 5041 1.868498 CCTTACGAAGTGGAAAACGCA 59.132 47.619 0.00 0.00 45.73 5.24
3578 5099 3.188460 GCATGTTAAACACGGACAGACAT 59.812 43.478 0.00 0.00 0.00 3.06
3579 5100 4.711721 CATGTTAAACACGGACAGACATG 58.288 43.478 0.00 0.00 37.59 3.21
3587 5108 0.807667 CGGACAGACATGCAGTAGGC 60.808 60.000 0.00 0.00 45.13 3.93
3608 5138 2.993539 GCCTATCTCTTGGCGTTCC 58.006 57.895 0.00 0.00 39.71 3.62
3632 5162 5.635280 CGAATGCGATTATAGTCCTGTCATT 59.365 40.000 0.00 0.00 40.82 2.57
3674 5204 0.033504 TCTTCGGCTGTGTTCAGTCC 59.966 55.000 0.00 0.00 42.66 3.85
3721 5251 5.854431 TTTTGCAGGTTTTCAAGTGTTTC 57.146 34.783 0.00 0.00 0.00 2.78
3724 5254 2.798145 GCAGGTTTTCAAGTGTTTCGGG 60.798 50.000 0.00 0.00 0.00 5.14
3970 5500 0.178891 TGGCCCTCTTCTTCTCCAGT 60.179 55.000 0.00 0.00 0.00 4.00
4003 5533 2.736236 CTCAAGCTGCGCGTGACT 60.736 61.111 8.43 0.00 41.52 3.41
4072 5615 1.076192 GCCTACCTCTCCTCCGGAA 60.076 63.158 5.23 0.00 0.00 4.30
4094 5637 4.099170 CCGCTGCAGCAAGAGCAC 62.099 66.667 36.03 6.57 45.49 4.40
4095 5638 3.048475 CGCTGCAGCAAGAGCACT 61.048 61.111 36.03 0.00 45.49 4.40
4109 5653 0.747255 AGCACTAGATCGGCAATCGT 59.253 50.000 0.00 0.00 39.55 3.73
4188 5736 0.581053 CATTGTTTTGTTGCCGTGCC 59.419 50.000 0.00 0.00 0.00 5.01
4208 5756 1.133407 CGGGAGACTGTCTGCTACTTC 59.867 57.143 25.26 10.14 35.01 3.01
4346 5897 2.662596 CTGTTCCTGGTAGGCGCA 59.337 61.111 10.83 0.00 34.61 6.09
4362 5913 1.306296 GCAGCCCTGGTTCCCATAA 59.694 57.895 0.00 0.00 30.82 1.90
4408 5964 4.298763 GGCGACGTTCCTATCGAC 57.701 61.111 0.00 0.00 40.86 4.20
4411 5967 0.098376 GCGACGTTCCTATCGACAGT 59.902 55.000 0.00 0.00 40.86 3.55
4412 5968 1.811428 CGACGTTCCTATCGACAGTG 58.189 55.000 0.00 0.00 40.86 3.66
4480 6036 4.322953 GCCAATCCATCCTTTTGAATGTGT 60.323 41.667 0.00 0.00 0.00 3.72
4487 6043 8.187913 TCCATCCTTTTGAATGTGTTCATAAA 57.812 30.769 0.00 0.00 43.49 1.40
4490 6046 9.350357 CATCCTTTTGAATGTGTTCATAAAGAG 57.650 33.333 17.41 12.03 43.49 2.85
4530 6086 7.451877 GTCTACTGATCTATTCATAGGGGTGAA 59.548 40.741 0.00 0.00 41.88 3.18
4580 6138 8.371571 AGATATAGACTCACAATGCCATATGA 57.628 34.615 3.65 0.00 0.00 2.15
4599 6157 2.872245 TGAGAGGCACTTTCGACTTTTG 59.128 45.455 0.00 0.00 43.12 2.44
4654 6212 1.067495 GGAGGTCTTGTCGTCTCAAGG 60.067 57.143 13.96 1.94 43.25 3.61
4706 6272 2.206576 ATCTGGGTGGAAGCTGTTTC 57.793 50.000 0.00 0.00 34.93 2.78
4707 6273 0.250295 TCTGGGTGGAAGCTGTTTCG 60.250 55.000 0.00 0.00 36.62 3.46
4708 6274 1.228124 TGGGTGGAAGCTGTTTCGG 60.228 57.895 0.00 0.00 36.62 4.30
4709 6275 1.072505 GGGTGGAAGCTGTTTCGGA 59.927 57.895 0.00 0.00 36.62 4.55
4710 6276 1.235281 GGGTGGAAGCTGTTTCGGAC 61.235 60.000 0.00 0.00 36.62 4.79
4711 6277 1.235281 GGTGGAAGCTGTTTCGGACC 61.235 60.000 7.85 7.85 36.62 4.46
4712 6278 1.072505 TGGAAGCTGTTTCGGACCC 59.927 57.895 0.00 0.00 36.62 4.46
4713 6279 1.674651 GGAAGCTGTTTCGGACCCC 60.675 63.158 0.00 0.00 36.62 4.95
4724 6290 3.756727 GGACCCCGACCGTGTCTC 61.757 72.222 8.48 0.00 0.00 3.36
4725 6291 2.675772 GACCCCGACCGTGTCTCT 60.676 66.667 3.15 0.00 0.00 3.10
4726 6292 1.377725 GACCCCGACCGTGTCTCTA 60.378 63.158 3.15 0.00 0.00 2.43
4727 6293 0.750911 GACCCCGACCGTGTCTCTAT 60.751 60.000 3.15 0.00 0.00 1.98
4728 6294 0.750911 ACCCCGACCGTGTCTCTATC 60.751 60.000 3.15 0.00 0.00 2.08
4729 6295 0.465824 CCCCGACCGTGTCTCTATCT 60.466 60.000 3.15 0.00 0.00 1.98
4730 6296 0.945813 CCCGACCGTGTCTCTATCTC 59.054 60.000 3.15 0.00 0.00 2.75
4731 6297 1.475392 CCCGACCGTGTCTCTATCTCT 60.475 57.143 3.15 0.00 0.00 3.10
4732 6298 1.868498 CCGACCGTGTCTCTATCTCTC 59.132 57.143 3.15 0.00 0.00 3.20
4733 6299 2.552031 CGACCGTGTCTCTATCTCTCA 58.448 52.381 3.15 0.00 0.00 3.27
4734 6300 2.542178 CGACCGTGTCTCTATCTCTCAG 59.458 54.545 3.15 0.00 0.00 3.35
4735 6301 3.738590 CGACCGTGTCTCTATCTCTCAGA 60.739 52.174 3.15 0.00 0.00 3.27
4736 6302 4.193090 GACCGTGTCTCTATCTCTCAGAA 58.807 47.826 0.00 0.00 0.00 3.02
4737 6303 4.787551 ACCGTGTCTCTATCTCTCAGAAT 58.212 43.478 0.00 0.00 0.00 2.40
4738 6304 4.819630 ACCGTGTCTCTATCTCTCAGAATC 59.180 45.833 0.00 0.00 0.00 2.52
4739 6305 4.084066 CCGTGTCTCTATCTCTCAGAATCG 60.084 50.000 0.00 0.00 0.00 3.34
4740 6306 4.747605 CGTGTCTCTATCTCTCAGAATCGA 59.252 45.833 0.00 0.00 0.00 3.59
4741 6307 5.107491 CGTGTCTCTATCTCTCAGAATCGAG 60.107 48.000 0.00 0.00 0.00 4.04
4742 6308 5.179368 GTGTCTCTATCTCTCAGAATCGAGG 59.821 48.000 0.00 0.00 33.59 4.63
4743 6309 5.163248 TGTCTCTATCTCTCAGAATCGAGGT 60.163 44.000 0.00 0.00 33.59 3.85
4744 6310 5.179368 GTCTCTATCTCTCAGAATCGAGGTG 59.821 48.000 0.00 0.00 33.59 4.00
4745 6311 4.393834 TCTATCTCTCAGAATCGAGGTGG 58.606 47.826 0.00 0.00 33.59 4.61
4746 6312 2.808906 TCTCTCAGAATCGAGGTGGA 57.191 50.000 0.00 0.00 33.59 4.02
4747 6313 3.087370 TCTCTCAGAATCGAGGTGGAA 57.913 47.619 0.00 0.00 33.59 3.53
4748 6314 3.020274 TCTCTCAGAATCGAGGTGGAAG 58.980 50.000 0.00 0.00 33.59 3.46
4749 6315 1.478510 TCTCAGAATCGAGGTGGAAGC 59.521 52.381 0.00 0.00 33.59 3.86
4750 6316 0.537188 TCAGAATCGAGGTGGAAGCC 59.463 55.000 0.00 0.00 32.25 4.35
4751 6317 0.250234 CAGAATCGAGGTGGAAGCCA 59.750 55.000 0.00 0.00 32.25 4.75
4752 6318 1.134280 CAGAATCGAGGTGGAAGCCAT 60.134 52.381 0.00 0.00 35.28 4.40
4753 6319 1.561542 AGAATCGAGGTGGAAGCCATT 59.438 47.619 0.00 0.00 35.28 3.16
4754 6320 2.025887 AGAATCGAGGTGGAAGCCATTT 60.026 45.455 0.00 0.00 35.28 2.32
4755 6321 1.755179 ATCGAGGTGGAAGCCATTTG 58.245 50.000 0.00 0.00 35.28 2.32
4756 6322 0.322456 TCGAGGTGGAAGCCATTTGG 60.322 55.000 0.00 0.00 35.28 3.28
4786 6352 8.506168 TTCTGTGTTGAAAAGAGAAACTATGT 57.494 30.769 0.00 0.00 0.00 2.29
4824 6390 0.584876 GGAAACCAACGAACACGAGG 59.415 55.000 0.00 0.00 34.25 4.63
4913 6479 0.981183 TAAGAAGGCCTCCGAAGCAA 59.019 50.000 5.23 0.00 0.00 3.91
4916 6482 1.303643 AAGGCCTCCGAAGCAAAGG 60.304 57.895 5.23 0.00 0.00 3.11
4918 6484 2.041115 GGCCTCCGAAGCAAAGGAC 61.041 63.158 0.00 0.00 32.33 3.85
5013 6579 2.287069 CGAATCTCTCAGGCGTCGTATT 60.287 50.000 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
169 171 4.630111 CAGAGAGCAGAAGAAAAGACTGT 58.370 43.478 0.00 0.00 34.60 3.55
210 220 2.010497 GCCGTTCTCTTCTCATTTCCC 58.990 52.381 0.00 0.00 0.00 3.97
216 226 2.026169 TCCTCTAGCCGTTCTCTTCTCA 60.026 50.000 0.00 0.00 0.00 3.27
457 798 5.644636 GGGACACAGGATACGACATTTTTAA 59.355 40.000 0.00 0.00 46.39 1.52
458 799 5.180271 GGGACACAGGATACGACATTTTTA 58.820 41.667 0.00 0.00 46.39 1.52
728 1805 2.203773 GGCCCCACCCACACATTT 60.204 61.111 0.00 0.00 0.00 2.32
788 1865 0.734889 CCTGCACGGGTCATCATTTC 59.265 55.000 0.00 0.00 0.00 2.17
791 1868 0.038166 AAACCTGCACGGGTCATCAT 59.962 50.000 0.61 0.00 38.87 2.45
801 1878 3.328050 AGAGGGGCTATATAAACCTGCAC 59.672 47.826 4.71 0.00 0.00 4.57
858 1935 7.083875 ACATGTGTAAAATAATTGTAGCGCT 57.916 32.000 17.26 17.26 0.00 5.92
1212 2289 2.897969 ACATACCTGAAGTATAGGCGGG 59.102 50.000 0.00 0.00 39.79 6.13
1215 2292 6.264744 TCAGTACACATACCTGAAGTATAGGC 59.735 42.308 0.00 0.00 39.79 3.93
1262 2339 2.302733 TGATTACACTCTGCTGCAGGAA 59.697 45.455 27.79 14.85 31.51 3.36
1372 2449 5.215160 GCACAACTTTCTACACAAATCCAG 58.785 41.667 0.00 0.00 0.00 3.86
1470 2547 4.609947 TGTTGTCACAAATGCAACATCTC 58.390 39.130 0.00 0.00 42.58 2.75
1716 2793 6.785337 TCAGAATAGAACGATCAAGGGTAA 57.215 37.500 0.00 0.00 0.00 2.85
1865 2943 3.696898 TGCAATACGGTGAACACAAAAC 58.303 40.909 7.25 0.00 0.00 2.43
1900 2985 7.496529 TGTGGAAGTTACTTTGAAGATCAAG 57.503 36.000 0.00 0.00 37.70 3.02
1933 3018 5.212745 TCCCCCAAGTGTTGAGTTATTTTT 58.787 37.500 0.00 0.00 0.00 1.94
2190 3516 5.129634 TCAAACCAAGCAACTGTTCTCATA 58.870 37.500 0.00 0.00 0.00 2.15
2365 3699 4.762289 TTTTGGTAATGCCCACACTTTT 57.238 36.364 0.00 0.00 33.14 2.27
2500 3945 6.397272 ACCAAGTATGTGCATAAATGTTTGG 58.603 36.000 15.18 15.18 0.00 3.28
2505 3950 7.566760 TTCCTACCAAGTATGTGCATAAATG 57.433 36.000 0.00 0.00 0.00 2.32
2704 4211 5.538813 GTGGGTCCCTTGACTTTTTCTTATT 59.461 40.000 10.00 0.00 41.47 1.40
2768 4280 0.385473 CGATGGCGAGCAAAACGTTT 60.385 50.000 7.96 7.96 40.82 3.60
2979 4495 8.692710 AGTTGCAGAAATGAACAATCATGATAT 58.307 29.630 9.04 0.00 45.60 1.63
3128 4644 4.577693 GCACTGCAGGAAGAATATGAATCA 59.422 41.667 19.93 0.00 0.00 2.57
3250 4771 1.878522 CGATTCGGCCACCTTCTCG 60.879 63.158 2.24 0.00 0.00 4.04
3379 4900 3.567308 AGGCACTCTGAACCTGCA 58.433 55.556 0.00 0.00 32.20 4.41
3487 5008 2.040939 TCGTAAGGGTTGGACTTCACA 58.959 47.619 0.00 0.00 38.47 3.58
3520 5041 4.292186 ACTTACAGTGAGCATCCATGTT 57.708 40.909 0.00 0.00 34.97 2.71
3608 5138 4.546570 TGACAGGACTATAATCGCATTCG 58.453 43.478 0.00 0.00 0.00 3.34
3632 5162 3.056393 TCGATCGGAAGGCTACAAAGAAA 60.056 43.478 16.41 0.00 0.00 2.52
3674 5204 4.297510 GCAGAGAGCATATCACTACAGTG 58.702 47.826 2.84 2.84 44.56 3.66
3709 5239 0.383949 GCTGCCCGAAACACTTGAAA 59.616 50.000 0.00 0.00 0.00 2.69
4003 5533 3.008517 TCCTTCCAGATGCGGCCA 61.009 61.111 2.24 0.00 0.00 5.36
4089 5632 1.269309 ACGATTGCCGATCTAGTGCTC 60.269 52.381 0.00 0.00 41.76 4.26
4090 5633 0.747255 ACGATTGCCGATCTAGTGCT 59.253 50.000 0.00 0.00 41.76 4.40
4091 5634 0.855349 CACGATTGCCGATCTAGTGC 59.145 55.000 0.00 0.00 41.76 4.40
4092 5635 1.491670 CCACGATTGCCGATCTAGTG 58.508 55.000 0.00 0.00 41.76 2.74
4093 5636 0.249489 GCCACGATTGCCGATCTAGT 60.249 55.000 0.00 0.00 41.76 2.57
4094 5637 0.032678 AGCCACGATTGCCGATCTAG 59.967 55.000 0.00 0.00 41.76 2.43
4095 5638 0.032130 GAGCCACGATTGCCGATCTA 59.968 55.000 0.00 0.00 41.76 1.98
4147 5695 2.080286 ATCACGGAGAGAACAAACGG 57.920 50.000 0.00 0.00 0.00 4.44
4188 5736 1.133407 GAAGTAGCAGACAGTCTCCCG 59.867 57.143 0.00 0.00 0.00 5.14
4208 5756 2.455674 TGTACACCAAGTAGCAGCAG 57.544 50.000 0.00 0.00 32.19 4.24
4266 5814 5.912396 TGCAAGAAATTTCACAACATACGTC 59.088 36.000 19.99 0.00 0.00 4.34
4267 5815 5.826586 TGCAAGAAATTTCACAACATACGT 58.173 33.333 19.99 0.00 0.00 3.57
4362 5913 4.220602 CCGAAATCAATCACCCTCCTTTTT 59.779 41.667 0.00 0.00 0.00 1.94
4375 5926 1.094785 CGCCTCCAACCGAAATCAAT 58.905 50.000 0.00 0.00 0.00 2.57
4408 5964 2.828520 AGTCACCATAGACACCTCACTG 59.171 50.000 0.00 0.00 40.98 3.66
4411 5967 3.646162 ACAAAGTCACCATAGACACCTCA 59.354 43.478 0.00 0.00 40.98 3.86
4412 5968 4.273148 ACAAAGTCACCATAGACACCTC 57.727 45.455 0.00 0.00 40.98 3.85
4460 6016 6.669125 TGAACACATTCAAAAGGATGGATT 57.331 33.333 0.00 0.00 41.99 3.01
4480 6036 4.019411 TCATGCACACCCTCTCTTTATGAA 60.019 41.667 0.00 0.00 0.00 2.57
4487 6043 0.901124 GACTCATGCACACCCTCTCT 59.099 55.000 0.00 0.00 0.00 3.10
4490 6046 1.827969 AGTAGACTCATGCACACCCTC 59.172 52.381 0.00 0.00 0.00 4.30
4530 6086 2.035961 ACTCGAAGCACAGTACACACAT 59.964 45.455 0.00 0.00 0.00 3.21
4580 6138 2.872858 GACAAAAGTCGAAAGTGCCTCT 59.127 45.455 0.00 0.00 0.00 3.69
4599 6157 1.826921 CATGCCATGGCCTCCAGAC 60.827 63.158 33.44 4.41 36.75 3.51
4707 6273 2.826777 TAGAGACACGGTCGGGGTCC 62.827 65.000 9.05 1.92 37.67 4.46
4708 6274 0.750911 ATAGAGACACGGTCGGGGTC 60.751 60.000 4.66 4.66 37.67 4.46
4709 6275 0.750911 GATAGAGACACGGTCGGGGT 60.751 60.000 0.00 0.00 37.67 4.95
4710 6276 0.465824 AGATAGAGACACGGTCGGGG 60.466 60.000 0.00 0.00 37.67 5.73
4711 6277 0.945813 GAGATAGAGACACGGTCGGG 59.054 60.000 0.00 0.00 37.67 5.14
4712 6278 1.868498 GAGAGATAGAGACACGGTCGG 59.132 57.143 0.00 0.00 37.67 4.79
4713 6279 2.542178 CTGAGAGATAGAGACACGGTCG 59.458 54.545 0.00 0.00 37.67 4.79
4714 6280 3.799366 TCTGAGAGATAGAGACACGGTC 58.201 50.000 0.00 0.00 0.00 4.79
4715 6281 3.916359 TCTGAGAGATAGAGACACGGT 57.084 47.619 0.00 0.00 0.00 4.83
4716 6282 4.084066 CGATTCTGAGAGATAGAGACACGG 60.084 50.000 0.00 0.00 0.00 4.94
4717 6283 4.747605 TCGATTCTGAGAGATAGAGACACG 59.252 45.833 0.00 0.00 0.00 4.49
4718 6284 5.179368 CCTCGATTCTGAGAGATAGAGACAC 59.821 48.000 12.54 0.00 38.28 3.67
4719 6285 5.163248 ACCTCGATTCTGAGAGATAGAGACA 60.163 44.000 12.54 0.00 38.28 3.41
4720 6286 5.179368 CACCTCGATTCTGAGAGATAGAGAC 59.821 48.000 12.54 0.00 38.28 3.36
4721 6287 5.304778 CACCTCGATTCTGAGAGATAGAGA 58.695 45.833 12.54 0.00 38.28 3.10
4722 6288 4.455533 CCACCTCGATTCTGAGAGATAGAG 59.544 50.000 6.97 7.34 38.28 2.43
4723 6289 4.103311 TCCACCTCGATTCTGAGAGATAGA 59.897 45.833 6.97 0.00 38.28 1.98
4724 6290 4.393834 TCCACCTCGATTCTGAGAGATAG 58.606 47.826 6.97 0.00 38.28 2.08
4725 6291 4.439253 TCCACCTCGATTCTGAGAGATA 57.561 45.455 6.97 0.00 38.28 1.98
4726 6292 3.304911 TCCACCTCGATTCTGAGAGAT 57.695 47.619 6.97 0.00 38.28 2.75
4727 6293 2.808906 TCCACCTCGATTCTGAGAGA 57.191 50.000 6.97 0.00 38.28 3.10
4728 6294 2.481104 GCTTCCACCTCGATTCTGAGAG 60.481 54.545 6.97 0.00 38.28 3.20
4729 6295 1.478510 GCTTCCACCTCGATTCTGAGA 59.521 52.381 6.97 0.00 38.28 3.27
4730 6296 1.472376 GGCTTCCACCTCGATTCTGAG 60.472 57.143 0.00 0.38 35.70 3.35
4731 6297 0.537188 GGCTTCCACCTCGATTCTGA 59.463 55.000 0.00 0.00 0.00 3.27
4732 6298 0.250234 TGGCTTCCACCTCGATTCTG 59.750 55.000 0.00 0.00 0.00 3.02
4733 6299 1.207791 ATGGCTTCCACCTCGATTCT 58.792 50.000 0.00 0.00 35.80 2.40
4734 6300 2.044123 AATGGCTTCCACCTCGATTC 57.956 50.000 0.00 0.00 35.80 2.52
4735 6301 2.094675 CAAATGGCTTCCACCTCGATT 58.905 47.619 0.00 0.00 35.80 3.34
4736 6302 1.683011 CCAAATGGCTTCCACCTCGAT 60.683 52.381 0.00 0.00 35.80 3.59
4737 6303 0.322456 CCAAATGGCTTCCACCTCGA 60.322 55.000 0.00 0.00 35.80 4.04
4738 6304 2.183409 CCAAATGGCTTCCACCTCG 58.817 57.895 0.00 0.00 35.80 4.63
4749 6315 3.318839 TCAACACAGAAGAAGCCAAATGG 59.681 43.478 0.00 0.00 38.53 3.16
4750 6316 4.572985 TCAACACAGAAGAAGCCAAATG 57.427 40.909 0.00 0.00 0.00 2.32
4751 6317 5.596836 TTTCAACACAGAAGAAGCCAAAT 57.403 34.783 0.00 0.00 0.00 2.32
4752 6318 5.184864 TCTTTTCAACACAGAAGAAGCCAAA 59.815 36.000 0.00 0.00 0.00 3.28
4753 6319 4.704540 TCTTTTCAACACAGAAGAAGCCAA 59.295 37.500 0.00 0.00 0.00 4.52
4754 6320 4.269183 TCTTTTCAACACAGAAGAAGCCA 58.731 39.130 0.00 0.00 0.00 4.75
4755 6321 4.576463 TCTCTTTTCAACACAGAAGAAGCC 59.424 41.667 0.00 0.00 0.00 4.35
4756 6322 5.741388 TCTCTTTTCAACACAGAAGAAGC 57.259 39.130 0.00 0.00 0.00 3.86
4757 6323 7.756558 AGTTTCTCTTTTCAACACAGAAGAAG 58.243 34.615 0.00 0.00 0.00 2.85
4758 6324 7.687941 AGTTTCTCTTTTCAACACAGAAGAA 57.312 32.000 0.00 0.00 0.00 2.52
4759 6325 8.830580 CATAGTTTCTCTTTTCAACACAGAAGA 58.169 33.333 0.00 0.00 0.00 2.87
4760 6326 8.616076 ACATAGTTTCTCTTTTCAACACAGAAG 58.384 33.333 0.00 0.00 0.00 2.85
4761 6327 8.397906 CACATAGTTTCTCTTTTCAACACAGAA 58.602 33.333 0.00 0.00 0.00 3.02
4762 6328 7.467267 GCACATAGTTTCTCTTTTCAACACAGA 60.467 37.037 0.00 0.00 0.00 3.41
4786 6352 2.107378 TCCCTTACCACATTGTTCTGCA 59.893 45.455 0.00 0.00 0.00 4.41
4824 6390 4.757149 CGGATGGTAATCTCCATTTCTTCC 59.243 45.833 0.00 0.00 46.72 3.46
4845 6411 2.202932 CTGGCAAGGTCGGATCGG 60.203 66.667 0.00 0.00 0.00 4.18
4846 6412 0.673644 AAACTGGCAAGGTCGGATCG 60.674 55.000 0.00 0.00 0.00 3.69
4847 6413 0.804989 CAAACTGGCAAGGTCGGATC 59.195 55.000 0.00 0.00 0.00 3.36
4848 6414 0.400213 TCAAACTGGCAAGGTCGGAT 59.600 50.000 0.00 0.00 0.00 4.18
4849 6415 0.250295 CTCAAACTGGCAAGGTCGGA 60.250 55.000 0.00 0.00 0.00 4.55
4850 6416 0.250295 TCTCAAACTGGCAAGGTCGG 60.250 55.000 0.00 0.00 0.00 4.79
4913 6479 0.878961 GCGTCGGTTGTTGAGTCCTT 60.879 55.000 0.00 0.00 0.00 3.36
4916 6482 0.935196 AAAGCGTCGGTTGTTGAGTC 59.065 50.000 10.91 0.00 0.00 3.36
4918 6484 0.041312 CCAAAGCGTCGGTTGTTGAG 60.041 55.000 10.91 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.