Multiple sequence alignment - TraesCS7A01G450100

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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 TraesCS7A01G450100 chr7A 100.000 4439 0 0 1 4439 643863293 643858855 0.000000e+00 8198.0
1 TraesCS7A01G450100 chr7A 86.128 1485 149 37 2212 3676 643421719 643423166 0.000000e+00 1548.0
2 TraesCS7A01G450100 chr7A 81.608 821 104 31 964 1756 643420385 643421186 1.740000e-178 636.0
3 TraesCS7A01G450100 chr7A 91.256 446 39 0 2306 2751 643416096 643416541 3.800000e-170 608.0
4 TraesCS7A01G450100 chr7A 87.669 519 62 2 2947 3464 643416541 643417058 1.770000e-168 603.0
5 TraesCS7A01G450100 chr7A 89.121 239 26 0 1517 1755 643415153 643415391 9.330000e-77 298.0
6 TraesCS7A01G450100 chr7A 86.275 153 12 3 3679 3823 643423261 643423412 1.650000e-34 158.0
7 TraesCS7A01G450100 chr7D 91.613 1407 67 26 1385 2758 558972379 558970991 0.000000e+00 1897.0
8 TraesCS7A01G450100 chr7D 92.251 1226 51 18 2810 4020 558970985 558969789 0.000000e+00 1698.0
9 TraesCS7A01G450100 chr7D 87.310 725 69 13 2889 3609 557843126 557843831 0.000000e+00 808.0
10 TraesCS7A01G450100 chr7D 91.328 542 35 5 1 541 558973762 558973232 0.000000e+00 730.0
11 TraesCS7A01G450100 chr7D 89.455 550 54 3 2221 2770 557842592 557843137 0.000000e+00 691.0
12 TraesCS7A01G450100 chr7D 85.942 626 78 8 2851 3470 557838191 557838812 0.000000e+00 660.0
13 TraesCS7A01G450100 chr7D 91.480 446 38 0 2306 2751 557837682 557838127 8.160000e-172 614.0
14 TraesCS7A01G450100 chr7D 92.857 406 18 8 945 1347 558972782 558972385 2.980000e-161 579.0
15 TraesCS7A01G450100 chr7D 81.358 692 104 17 1509 2190 557836721 557837397 1.400000e-149 540.0
16 TraesCS7A01G450100 chr7D 89.589 365 17 5 557 905 558973248 558972889 1.130000e-120 444.0
17 TraesCS7A01G450100 chr7D 87.955 357 42 1 964 1319 557841194 557841550 1.910000e-113 420.0
18 TraesCS7A01G450100 chr7D 85.714 350 35 9 1422 1761 557841786 557842130 5.460000e-94 355.0
19 TraesCS7A01G450100 chr7D 87.241 290 15 9 4083 4351 558969574 558969286 1.200000e-80 311.0
20 TraesCS7A01G450100 chr7B 92.521 1297 64 17 2247 3526 606645575 606644295 0.000000e+00 1827.0
21 TraesCS7A01G450100 chr7B 91.255 709 50 8 1 706 606795967 606795268 0.000000e+00 955.0
22 TraesCS7A01G450100 chr7B 92.250 671 36 8 1520 2190 606646402 606645748 0.000000e+00 937.0
23 TraesCS7A01G450100 chr7B 88.156 667 68 6 2944 3609 605956837 605957493 0.000000e+00 784.0
24 TraesCS7A01G450100 chr7B 88.486 634 41 9 323 937 606647497 606646877 0.000000e+00 737.0
25 TraesCS7A01G450100 chr7B 89.253 549 53 5 2212 2760 605956206 605956748 0.000000e+00 682.0
26 TraesCS7A01G450100 chr7B 94.533 439 15 3 945 1383 606646830 606646401 0.000000e+00 669.0
27 TraesCS7A01G450100 chr7B 92.152 446 35 0 2306 2751 605908591 605909036 8.100000e-177 630.0
28 TraesCS7A01G450100 chr7B 86.348 586 71 5 2947 3531 605909036 605909613 8.100000e-177 630.0
29 TraesCS7A01G450100 chr7B 89.665 358 34 3 964 1319 605954808 605955164 1.880000e-123 453.0
30 TraesCS7A01G450100 chr7B 95.018 281 13 1 1 281 606648100 606647821 1.470000e-119 440.0
31 TraesCS7A01G450100 chr7B 84.746 413 49 11 1352 1761 605955278 605955679 6.920000e-108 401.0
32 TraesCS7A01G450100 chr7B 84.548 343 45 3 988 1322 605906785 605907127 2.560000e-87 333.0
33 TraesCS7A01G450100 chr7B 88.077 260 30 1 1496 1755 605907627 605907885 1.550000e-79 307.0
34 TraesCS7A01G450100 chr7B 81.768 362 39 14 3612 3946 606644088 606643727 1.220000e-70 278.0
35 TraesCS7A01G450100 chr7B 90.395 177 14 1 945 1121 606779264 606779091 3.450000e-56 230.0
36 TraesCS7A01G450100 chr7B 86.463 229 8 4 726 937 606779533 606779311 3.450000e-56 230.0
37 TraesCS7A01G450100 chr1B 78.814 118 13 6 434 541 246771131 246771016 7.970000e-08 69.4
38 TraesCS7A01G450100 chr1D 91.304 46 4 0 434 479 165201176 165201221 3.710000e-06 63.9
39 TraesCS7A01G450100 chr1A 91.304 46 4 0 434 479 216420323 216420278 3.710000e-06 63.9
40 TraesCS7A01G450100 chr3A 100.000 29 0 0 4367 4395 10822977 10822949 2.000000e-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 TraesCS7A01G450100 chr7A 643858855 643863293 4438 True 8198.000000 8198 100.000000 1 4439 1 chr7A.!!$R1 4438
1 TraesCS7A01G450100 chr7A 643415153 643423412 8259 False 641.833333 1548 87.009500 964 3823 6 chr7A.!!$F1 2859
2 TraesCS7A01G450100 chr7D 558969286 558973762 4476 True 943.166667 1897 90.813167 1 4351 6 chr7D.!!$R1 4350
3 TraesCS7A01G450100 chr7D 557836721 557843831 7110 False 584.000000 808 87.030571 964 3609 7 chr7D.!!$F1 2645
4 TraesCS7A01G450100 chr7B 606795268 606795967 699 True 955.000000 955 91.255000 1 706 1 chr7B.!!$R1 705
5 TraesCS7A01G450100 chr7B 606643727 606648100 4373 True 814.666667 1827 90.762667 1 3946 6 chr7B.!!$R2 3945
6 TraesCS7A01G450100 chr7B 605954808 605957493 2685 False 580.000000 784 87.955000 964 3609 4 chr7B.!!$F2 2645
7 TraesCS7A01G450100 chr7B 605906785 605909613 2828 False 475.000000 630 87.781250 988 3531 4 chr7B.!!$F1 2543

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
272 274 1.871039 TGTTTTCCCTCTTTTCGAGCG 59.129 47.619 0.0 0.0 38.49 5.03 F
1251 5877 1.676678 CCCACGACATCATCCCTCGT 61.677 60.000 0.0 0.0 41.23 4.18 F
2106 7318 1.064758 AGTTCTTCCCTTGCACACACA 60.065 47.619 0.0 0.0 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1621 6678 0.890996 CGGCTGCTCCTTTGTTTCCT 60.891 55.000 0.00 0.00 0.00 3.36 R
2659 8104 1.815408 GCAACACTTCCTCTCTTGCCA 60.815 52.381 0.00 0.00 32.71 4.92 R
4000 9717 0.532862 AAACTCACCGACCTGCAGTG 60.533 55.000 13.81 4.73 0.00 3.66 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
57 58 2.016604 GCACCTCGTATCATTTGGCCA 61.017 52.381 0.00 0.00 0.00 5.36
272 274 1.871039 TGTTTTCCCTCTTTTCGAGCG 59.129 47.619 0.00 0.00 38.49 5.03
293 295 4.127171 CGGGATATTCGTTGTTTCTGGAT 58.873 43.478 0.00 0.00 0.00 3.41
329 613 3.815809 TGTGTTCTTTAGGTGGTGGAAG 58.184 45.455 0.00 0.00 0.00 3.46
336 620 7.125053 TGTTCTTTAGGTGGTGGAAGAAAAATT 59.875 33.333 0.00 0.00 39.15 1.82
367 651 4.267214 CGAGCAAGAACACATGAGATGTAG 59.733 45.833 0.00 0.00 42.70 2.74
431 716 9.950680 TTTGTTTTCTGCAGAAAGAAGTATTAG 57.049 29.630 33.76 0.00 43.90 1.73
461 746 9.872757 TGTTCTGAATTATAAGACGTTTTGAAC 57.127 29.630 0.83 4.83 0.00 3.18
475 760 9.878599 AGACGTTTTGAACATTTTAGTATGAAG 57.121 29.630 0.00 0.00 0.00 3.02
576 862 7.496529 TGGACAATTCAGAGAAAAGTTACTG 57.503 36.000 0.00 0.00 0.00 2.74
898 1228 2.095059 CCAATTGAGCCAAAACCTCGAG 60.095 50.000 7.12 5.13 31.98 4.04
940 1272 2.027625 CAACCGGCGGTCTGTTCTC 61.028 63.158 34.23 0.00 33.12 2.87
941 1273 3.569049 AACCGGCGGTCTGTTCTCG 62.569 63.158 34.23 0.71 33.12 4.04
943 1275 2.202492 CGGCGGTCTGTTCTCGAG 60.202 66.667 5.93 5.93 0.00 4.04
1251 5877 1.676678 CCCACGACATCATCCCTCGT 61.677 60.000 0.00 0.00 41.23 4.18
1343 6120 7.871853 TCTTTTGAACTTTTTCTATTCTCCCG 58.128 34.615 0.00 0.00 32.36 5.14
1348 6125 4.824289 ACTTTTTCTATTCTCCCGCGTTA 58.176 39.130 4.92 0.00 0.00 3.18
1349 6126 5.240121 ACTTTTTCTATTCTCCCGCGTTAA 58.760 37.500 4.92 0.00 0.00 2.01
1383 6361 4.475028 CTCTGAGCTTCTGATACATAGCG 58.525 47.826 0.00 0.00 38.62 4.26
1399 6377 1.792006 AGCGTGTTCGGTAAAGAAGG 58.208 50.000 0.00 0.00 46.01 3.46
1461 6463 4.152580 GCTAGACAGGAGCAGTTAACAAAC 59.847 45.833 8.61 0.00 39.84 2.93
1602 6659 6.039270 CGGATCTAGTGAGAGAAATTCTGTCT 59.961 42.308 18.88 3.32 37.64 3.41
1621 6678 6.436218 TCTGTCTAACAAGCTTGGACACTATA 59.564 38.462 29.18 13.10 34.02 1.31
1693 6750 3.565764 ATCATGAAGGCGAGAAATGGA 57.434 42.857 0.00 0.00 0.00 3.41
1728 6785 3.967467 ATCCTCAATCCTGCCTTTCAT 57.033 42.857 0.00 0.00 0.00 2.57
1756 6814 2.433436 AGATAAAGGTGCCGGTTCAAC 58.567 47.619 1.90 0.00 0.00 3.18
1799 6867 5.417266 TCTCATTTTAAATCGCAACATGGGA 59.583 36.000 0.00 0.00 43.55 4.37
1814 7017 3.162666 CATGGGAATTGCATAGGCTGAT 58.837 45.455 0.00 0.00 41.91 2.90
1815 7018 4.202599 ACATGGGAATTGCATAGGCTGATA 60.203 41.667 0.00 0.00 41.91 2.15
1816 7019 4.025040 TGGGAATTGCATAGGCTGATAG 57.975 45.455 0.00 0.00 41.91 2.08
1817 7020 2.751806 GGGAATTGCATAGGCTGATAGC 59.248 50.000 0.00 0.00 41.91 2.97
1843 7055 4.853924 AATGTTTCGTTTGCAGAGGATT 57.146 36.364 0.01 0.00 0.00 3.01
1918 7130 1.646912 TGTCCGGTGAAGGGTTATCA 58.353 50.000 0.00 0.00 0.00 2.15
2063 7275 4.144297 ACTAATGCAGGCTTTTCAGACAA 58.856 39.130 0.00 0.00 0.00 3.18
2065 7277 3.587797 ATGCAGGCTTTTCAGACAATG 57.412 42.857 0.00 0.00 0.00 2.82
2103 7315 2.552743 GGTAAGTTCTTCCCTTGCACAC 59.447 50.000 0.00 0.00 0.00 3.82
2104 7316 2.435372 AAGTTCTTCCCTTGCACACA 57.565 45.000 0.00 0.00 0.00 3.72
2105 7317 1.680338 AGTTCTTCCCTTGCACACAC 58.320 50.000 0.00 0.00 0.00 3.82
2106 7318 1.064758 AGTTCTTCCCTTGCACACACA 60.065 47.619 0.00 0.00 0.00 3.72
2107 7319 1.748493 GTTCTTCCCTTGCACACACAA 59.252 47.619 0.00 0.00 0.00 3.33
2108 7320 2.136298 TCTTCCCTTGCACACACAAA 57.864 45.000 0.00 0.00 0.00 2.83
2109 7321 2.451490 TCTTCCCTTGCACACACAAAA 58.549 42.857 0.00 0.00 0.00 2.44
2110 7322 2.828520 TCTTCCCTTGCACACACAAAAA 59.171 40.909 0.00 0.00 0.00 1.94
2184 7455 7.663905 TGTAACGCAAGCCCATATAATTTCTAT 59.336 33.333 0.00 0.00 45.62 1.98
2190 7461 9.933723 GCAAGCCCATATAATTTCTATCAAATT 57.066 29.630 0.00 0.00 34.55 1.82
2220 7592 9.705290 TTTGATTAAATAGTTGGCTTCCTTTTC 57.295 29.630 0.00 0.00 0.00 2.29
2342 7787 7.615582 TTTCTTTCCTATGATGACATGTCAC 57.384 36.000 30.09 22.20 43.11 3.67
2402 7847 5.064558 AGGATGAGAGCAATTGATCATGAC 58.935 41.667 24.50 15.26 32.68 3.06
2659 8104 3.710722 CCCGGAGTGGCAAGAGCT 61.711 66.667 0.73 0.00 41.70 4.09
2783 8228 7.707893 GCACATACTGCAGGATAAAATGAAATT 59.292 33.333 19.93 0.00 46.29 1.82
2849 8299 9.838339 AACAATAAAACCTACTCCTATCAGATG 57.162 33.333 0.00 0.00 0.00 2.90
2965 8430 8.408043 AAACAGGATGATGTGATGTTTTAAGA 57.592 30.769 0.00 0.00 40.22 2.10
2969 8434 9.941664 CAGGATGATGTGATGTTTTAAGAATAC 57.058 33.333 0.00 0.00 39.69 1.89
2999 8464 6.035112 GTCGGAGTAATGTTCTTGATCTTGTC 59.965 42.308 0.00 0.00 0.00 3.18
3000 8465 5.292101 CGGAGTAATGTTCTTGATCTTGTCC 59.708 44.000 0.00 0.00 0.00 4.02
3043 8508 5.918608 TGATTCTGTATGAGGTTCTTAGGC 58.081 41.667 0.00 0.00 0.00 3.93
3498 8964 4.124594 GCGTTTGCGTAGAGTTTAAAGT 57.875 40.909 0.00 0.00 40.81 2.66
3609 9185 6.913873 AGTTTTAGTTGAACTGCTCGTTTA 57.086 33.333 8.33 0.00 36.08 2.01
3623 9211 4.201753 TGCTCGTTTACTAGTACTACTGCG 60.202 45.833 0.91 1.99 0.00 5.18
3625 9213 5.456192 TCGTTTACTAGTACTACTGCGAC 57.544 43.478 0.91 0.00 0.00 5.19
3635 9223 5.002516 AGTACTACTGCGACTCTGTAACTT 58.997 41.667 0.00 0.00 0.00 2.66
3671 9259 3.079578 TCCTTTCATCAAGCTGCAGAAG 58.920 45.455 20.43 9.20 0.00 2.85
3756 9461 2.025418 GGTAACCGTGCACGACAGG 61.025 63.158 39.10 24.43 43.02 4.00
3769 9474 2.800544 CACGACAGGTACTTGGTTTCTG 59.199 50.000 10.04 0.91 34.60 3.02
3794 9506 2.159240 CCGAAACAGGATCATCGACTCA 60.159 50.000 0.00 0.00 37.48 3.41
3929 9643 0.329261 CCCCTGATCTTGCCTCAACA 59.671 55.000 0.00 0.00 0.00 3.33
3972 9686 7.703328 AGTGTCAATTCGCTCTAAAAGAAAAA 58.297 30.769 0.00 0.00 0.00 1.94
4000 9717 4.825085 TGAATTGTCAGTGTAAAAGGACCC 59.175 41.667 0.00 0.00 0.00 4.46
4022 9918 2.002586 CTGCAGGTCGGTGAGTTTATG 58.997 52.381 5.57 0.00 0.00 1.90
4080 9976 9.908152 AGAAAACAAAACTAATTAATTCTCCCG 57.092 29.630 3.39 0.00 0.00 5.14
4081 9977 8.528917 AAAACAAAACTAATTAATTCTCCCGC 57.471 30.769 3.39 0.00 0.00 6.13
4082 9978 6.827586 ACAAAACTAATTAATTCTCCCGCA 57.172 33.333 3.39 0.00 0.00 5.69
4083 9979 7.222000 ACAAAACTAATTAATTCTCCCGCAA 57.778 32.000 3.39 0.00 0.00 4.85
4084 9980 7.662897 ACAAAACTAATTAATTCTCCCGCAAA 58.337 30.769 3.39 0.00 0.00 3.68
4085 9981 8.145122 ACAAAACTAATTAATTCTCCCGCAAAA 58.855 29.630 3.39 0.00 0.00 2.44
4086 9982 8.983724 CAAAACTAATTAATTCTCCCGCAAAAA 58.016 29.630 3.39 0.00 0.00 1.94
4163 10059 5.512788 CGTTGGCAAAATATACTTGCTCTTG 59.487 40.000 17.42 6.64 46.74 3.02
4214 10110 2.185350 CCTTGTCGATCGCTGCCT 59.815 61.111 11.09 0.00 0.00 4.75
4249 10145 0.817013 CCTCTCTGGTCTCTGCTCAC 59.183 60.000 0.00 0.00 0.00 3.51
4259 10155 0.590195 CTCTGCTCACTGGTTGTTGC 59.410 55.000 0.00 0.00 0.00 4.17
4261 10157 1.799258 CTGCTCACTGGTTGTTGCCC 61.799 60.000 0.00 0.00 0.00 5.36
4269 10184 2.203480 GTTGTTGCCCTGCCTCCA 60.203 61.111 0.00 0.00 0.00 3.86
4276 10191 2.123982 CCCTGCCTCCATCCAAGC 60.124 66.667 0.00 0.00 0.00 4.01
4277 10192 2.687610 CCCTGCCTCCATCCAAGCT 61.688 63.158 0.00 0.00 0.00 3.74
4281 10196 2.587194 CCTCCATCCAAGCTCGCG 60.587 66.667 0.00 0.00 0.00 5.87
4335 10250 2.191400 CTGATCCTGAGGGTTTGAGGA 58.809 52.381 0.00 0.00 40.22 3.71
4351 10266 2.630098 TGAGGAGAAATCCTATCTGCCG 59.370 50.000 0.00 0.00 40.86 5.69
4352 10267 2.630580 GAGGAGAAATCCTATCTGCCGT 59.369 50.000 0.00 0.00 40.86 5.68
4353 10268 3.041946 AGGAGAAATCCTATCTGCCGTT 58.958 45.455 0.00 0.00 38.58 4.44
4354 10269 3.456277 AGGAGAAATCCTATCTGCCGTTT 59.544 43.478 0.00 0.00 38.58 3.60
4355 10270 4.654262 AGGAGAAATCCTATCTGCCGTTTA 59.346 41.667 0.00 0.00 38.58 2.01
4356 10271 5.308237 AGGAGAAATCCTATCTGCCGTTTAT 59.692 40.000 0.00 0.00 38.58 1.40
4357 10272 5.639931 GGAGAAATCCTATCTGCCGTTTATC 59.360 44.000 0.00 0.00 29.86 1.75
4358 10273 6.426646 AGAAATCCTATCTGCCGTTTATCT 57.573 37.500 0.00 0.00 0.00 1.98
4359 10274 7.309867 GGAGAAATCCTATCTGCCGTTTATCTA 60.310 40.741 0.00 0.00 29.86 1.98
4360 10275 7.963532 AGAAATCCTATCTGCCGTTTATCTAA 58.036 34.615 0.00 0.00 0.00 2.10
4361 10276 8.429641 AGAAATCCTATCTGCCGTTTATCTAAA 58.570 33.333 0.00 0.00 0.00 1.85
4362 10277 8.974060 AAATCCTATCTGCCGTTTATCTAAAA 57.026 30.769 0.00 0.00 0.00 1.52
4363 10278 8.974060 AATCCTATCTGCCGTTTATCTAAAAA 57.026 30.769 0.00 0.00 0.00 1.94
4364 10279 7.781548 TCCTATCTGCCGTTTATCTAAAAAC 57.218 36.000 0.00 0.00 36.26 2.43
4365 10280 7.332557 TCCTATCTGCCGTTTATCTAAAAACA 58.667 34.615 0.00 0.00 38.93 2.83
4366 10281 7.990886 TCCTATCTGCCGTTTATCTAAAAACAT 59.009 33.333 0.00 0.00 38.93 2.71
4367 10282 8.283291 CCTATCTGCCGTTTATCTAAAAACATC 58.717 37.037 0.00 0.00 38.93 3.06
4368 10283 6.431198 TCTGCCGTTTATCTAAAAACATCC 57.569 37.500 0.00 0.00 38.93 3.51
4369 10284 6.177610 TCTGCCGTTTATCTAAAAACATCCT 58.822 36.000 0.00 0.00 38.93 3.24
4370 10285 7.332557 TCTGCCGTTTATCTAAAAACATCCTA 58.667 34.615 0.00 0.00 38.93 2.94
4371 10286 7.990886 TCTGCCGTTTATCTAAAAACATCCTAT 59.009 33.333 0.00 0.00 38.93 2.57
4372 10287 8.149973 TGCCGTTTATCTAAAAACATCCTATC 57.850 34.615 0.00 0.00 38.93 2.08
4373 10288 7.990886 TGCCGTTTATCTAAAAACATCCTATCT 59.009 33.333 0.00 0.00 38.93 1.98
4374 10289 8.283291 GCCGTTTATCTAAAAACATCCTATCTG 58.717 37.037 0.00 0.00 38.93 2.90
4375 10290 8.283291 CCGTTTATCTAAAAACATCCTATCTGC 58.717 37.037 0.00 0.00 38.93 4.26
4376 10291 8.283291 CGTTTATCTAAAAACATCCTATCTGCC 58.717 37.037 0.00 0.00 38.93 4.85
4377 10292 7.962964 TTATCTAAAAACATCCTATCTGCCG 57.037 36.000 0.00 0.00 0.00 5.69
4378 10293 4.127171 TCTAAAAACATCCTATCTGCCGC 58.873 43.478 0.00 0.00 0.00 6.53
4379 10294 2.418368 AAAACATCCTATCTGCCGCA 57.582 45.000 0.00 0.00 0.00 5.69
4380 10295 2.645838 AAACATCCTATCTGCCGCAT 57.354 45.000 0.00 0.00 0.00 4.73
4381 10296 2.645838 AACATCCTATCTGCCGCATT 57.354 45.000 0.00 0.00 0.00 3.56
4382 10297 3.769739 AACATCCTATCTGCCGCATTA 57.230 42.857 0.00 0.00 0.00 1.90
4383 10298 3.988976 ACATCCTATCTGCCGCATTAT 57.011 42.857 0.00 0.00 0.00 1.28
4384 10299 3.603532 ACATCCTATCTGCCGCATTATG 58.396 45.455 0.00 0.00 0.00 1.90
4385 10300 2.099141 TCCTATCTGCCGCATTATGC 57.901 50.000 7.19 7.19 40.69 3.14
4395 10310 2.397751 GCATTATGCGGCAGACTGT 58.602 52.632 14.95 0.00 31.71 3.55
4396 10311 1.581934 GCATTATGCGGCAGACTGTA 58.418 50.000 14.95 0.00 31.71 2.74
4397 10312 1.528586 GCATTATGCGGCAGACTGTAG 59.471 52.381 14.95 0.00 31.71 2.74
4398 10313 2.826428 CATTATGCGGCAGACTGTAGT 58.174 47.619 9.25 0.00 0.00 2.73
4399 10314 3.198068 CATTATGCGGCAGACTGTAGTT 58.802 45.455 9.25 0.00 0.00 2.24
4400 10315 3.328382 TTATGCGGCAGACTGTAGTTT 57.672 42.857 9.25 0.00 0.00 2.66
4401 10316 2.185004 ATGCGGCAGACTGTAGTTTT 57.815 45.000 9.25 0.00 0.00 2.43
4402 10317 1.961793 TGCGGCAGACTGTAGTTTTT 58.038 45.000 0.00 0.00 0.00 1.94
4424 10339 2.420628 TTTTTGAGACAATGCGGCAG 57.579 45.000 9.25 0.00 0.00 4.85
4425 10340 1.603456 TTTTGAGACAATGCGGCAGA 58.397 45.000 9.25 0.00 0.00 4.26
4426 10341 0.874390 TTTGAGACAATGCGGCAGAC 59.126 50.000 9.25 0.00 0.00 3.51
4427 10342 0.035317 TTGAGACAATGCGGCAGACT 59.965 50.000 9.25 1.08 0.00 3.24
4428 10343 0.671472 TGAGACAATGCGGCAGACTG 60.671 55.000 9.25 8.30 0.00 3.51
4429 10344 0.671781 GAGACAATGCGGCAGACTGT 60.672 55.000 9.25 11.56 0.00 3.55
4430 10345 0.608130 AGACAATGCGGCAGACTGTA 59.392 50.000 9.25 0.00 0.00 2.74
4431 10346 1.002366 GACAATGCGGCAGACTGTAG 58.998 55.000 9.25 0.00 0.00 2.74
4432 10347 0.321671 ACAATGCGGCAGACTGTAGT 59.678 50.000 9.25 0.00 0.00 2.73
4433 10348 1.270839 ACAATGCGGCAGACTGTAGTT 60.271 47.619 9.25 0.00 0.00 2.24
4434 10349 1.129251 CAATGCGGCAGACTGTAGTTG 59.871 52.381 9.25 1.41 0.00 3.16
4435 10350 0.608130 ATGCGGCAGACTGTAGTTGA 59.392 50.000 9.25 0.00 0.00 3.18
4436 10351 0.608130 TGCGGCAGACTGTAGTTGAT 59.392 50.000 0.00 0.00 0.00 2.57
4437 10352 1.822371 TGCGGCAGACTGTAGTTGATA 59.178 47.619 0.00 0.00 0.00 2.15
4438 10353 2.194271 GCGGCAGACTGTAGTTGATAC 58.806 52.381 3.99 0.00 34.72 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
193 194 9.585099 TGTATAAATTTCATCCAACTTCATTGC 57.415 29.630 0.00 0.00 36.93 3.56
272 274 5.123227 TCATCCAGAAACAACGAATATCCC 58.877 41.667 0.00 0.00 0.00 3.85
367 651 9.334693 CAAAGCATACTTTTCATCAGTACTTTC 57.665 33.333 0.00 0.00 43.74 2.62
431 716 7.829378 AACGTCTTATAATTCAGAACAGACC 57.171 36.000 0.00 0.00 0.00 3.85
475 760 7.807433 TGCATTTGTTCACTCATTTGTATGTAC 59.193 33.333 0.00 0.00 33.34 2.90
547 833 5.360714 ACTTTTCTCTGAATTGTCCAGCAAA 59.639 36.000 0.00 0.00 40.91 3.68
548 834 4.889409 ACTTTTCTCTGAATTGTCCAGCAA 59.111 37.500 0.00 0.00 41.89 3.91
550 836 5.444663 AACTTTTCTCTGAATTGTCCAGC 57.555 39.130 0.00 0.00 0.00 4.85
551 837 7.442364 TCAGTAACTTTTCTCTGAATTGTCCAG 59.558 37.037 0.00 0.00 34.61 3.86
555 841 8.956426 TGTTTCAGTAACTTTTCTCTGAATTGT 58.044 29.630 7.17 0.00 43.32 2.71
576 862 9.884465 CCTTCATTCCGAATTATAAGATGTTTC 57.116 33.333 8.32 0.00 31.69 2.78
937 1269 2.478709 GGAGTCGTACGTAGTCTCGAGA 60.479 54.545 12.08 12.08 44.26 4.04
940 1272 1.587490 CAGGAGTCGTACGTAGTCTCG 59.413 57.143 16.05 0.00 43.93 4.04
941 1273 2.602660 GTCAGGAGTCGTACGTAGTCTC 59.397 54.545 16.05 16.67 43.93 3.36
943 1275 1.663135 GGTCAGGAGTCGTACGTAGTC 59.337 57.143 16.05 13.36 43.93 2.59
1343 6120 3.248602 CAGAGCACATCCCTAATTAACGC 59.751 47.826 0.00 0.00 0.00 4.84
1348 6125 2.776536 AGCTCAGAGCACATCCCTAATT 59.223 45.455 24.64 0.00 45.56 1.40
1349 6126 2.406559 AGCTCAGAGCACATCCCTAAT 58.593 47.619 24.64 0.00 45.56 1.73
1383 6361 2.349155 CGTTGCCTTCTTTACCGAACAC 60.349 50.000 0.00 0.00 0.00 3.32
1453 6455 7.825681 AGTGCATGCATGTTATAGTTTGTTAA 58.174 30.769 25.64 0.00 0.00 2.01
1461 6463 6.976349 ACAATCAAAGTGCATGCATGTTATAG 59.024 34.615 25.64 13.00 0.00 1.31
1602 6659 6.614694 TTCCTATAGTGTCCAAGCTTGTTA 57.385 37.500 24.35 10.01 0.00 2.41
1621 6678 0.890996 CGGCTGCTCCTTTGTTTCCT 60.891 55.000 0.00 0.00 0.00 3.36
1693 6750 2.224523 TGAGGATTCTTCGGTGCTTTGT 60.225 45.455 0.00 0.00 0.00 2.83
1728 6785 3.432186 CCGGCACCTTTATCTTCTCATGA 60.432 47.826 0.00 0.00 0.00 3.07
1771 6829 8.494347 CCATGTTGCGATTTAAAATGAGAAAAA 58.506 29.630 0.00 0.00 0.00 1.94
1799 6867 5.495926 ACTAGCTATCAGCCTATGCAATT 57.504 39.130 0.00 0.00 43.77 2.32
1814 7017 6.160684 TCTGCAAACGAAACATTACTAGCTA 58.839 36.000 0.00 0.00 0.00 3.32
1815 7018 4.994852 TCTGCAAACGAAACATTACTAGCT 59.005 37.500 0.00 0.00 0.00 3.32
1816 7019 5.277601 TCTGCAAACGAAACATTACTAGC 57.722 39.130 0.00 0.00 0.00 3.42
1817 7020 5.637810 TCCTCTGCAAACGAAACATTACTAG 59.362 40.000 0.00 0.00 0.00 2.57
1918 7130 5.480642 ACTCAGAACATGTGTCAATCTCT 57.519 39.130 0.00 0.00 29.71 3.10
2063 7275 4.814224 ACCAATAGCCTGGGATAAACAT 57.186 40.909 0.00 0.00 41.16 2.71
2065 7277 5.691896 ACTTACCAATAGCCTGGGATAAAC 58.308 41.667 0.00 0.00 41.16 2.01
2159 7375 6.313744 AGAAATTATATGGGCTTGCGTTAC 57.686 37.500 0.00 0.00 0.00 2.50
2190 7461 9.474313 AGGAAGCCAACTATTTAATCAAATACA 57.526 29.630 0.00 0.00 35.88 2.29
2195 7466 9.088987 AGAAAAGGAAGCCAACTATTTAATCAA 57.911 29.630 0.00 0.00 0.00 2.57
2197 7468 9.929180 AAAGAAAAGGAAGCCAACTATTTAATC 57.071 29.630 0.00 0.00 0.00 1.75
2200 7471 8.919145 TCAAAAGAAAAGGAAGCCAACTATTTA 58.081 29.630 0.00 0.00 0.00 1.40
2303 7748 9.692325 ATAGGAAAGAAAATCTTGATTGCTAGT 57.308 29.630 0.00 0.00 36.71 2.57
2304 7749 9.947669 CATAGGAAAGAAAATCTTGATTGCTAG 57.052 33.333 0.00 0.00 36.71 3.42
2342 7787 4.582701 TGGTAAGAACCTGCAAATGTTG 57.417 40.909 1.09 0.00 46.91 3.33
2659 8104 1.815408 GCAACACTTCCTCTCTTGCCA 60.815 52.381 0.00 0.00 32.71 4.92
2783 8228 9.444668 TCAATTTGATGATTGGGGGATTATTTA 57.555 29.630 0.00 0.00 37.56 1.40
2790 8235 4.058417 TGTCAATTTGATGATTGGGGGA 57.942 40.909 1.78 0.00 37.56 4.81
2806 8251 7.575414 TTATTGTTGGCTACTCTTTTGTCAA 57.425 32.000 0.01 0.00 0.00 3.18
2887 8337 7.066887 TGAGTATTTGTTTTCACTCACATGTGT 59.933 33.333 24.63 4.31 41.76 3.72
2888 8338 7.416817 TGAGTATTTGTTTTCACTCACATGTG 58.583 34.615 20.18 20.18 41.76 3.21
2965 8430 5.187186 AGAACATTACTCCGACCACTGTATT 59.813 40.000 0.00 0.00 0.00 1.89
2969 8434 3.594603 AGAACATTACTCCGACCACTG 57.405 47.619 0.00 0.00 0.00 3.66
3609 9185 4.205065 ACAGAGTCGCAGTAGTACTAGT 57.795 45.455 1.87 3.18 0.00 2.57
3623 9211 6.173339 TCCATTGGATGAAAGTTACAGAGTC 58.827 40.000 0.00 0.00 0.00 3.36
3625 9213 6.656693 AGTTCCATTGGATGAAAGTTACAGAG 59.343 38.462 6.15 0.00 0.00 3.35
3635 9223 4.996793 TGAAAGGAGTTCCATTGGATGAA 58.003 39.130 6.15 0.00 38.89 2.57
3671 9259 8.430801 AGAGTTATCACTGTCATCTTTTATGC 57.569 34.615 0.00 0.00 31.22 3.14
3756 9461 2.762745 TCGGCTTCAGAAACCAAGTAC 58.237 47.619 3.46 0.00 0.00 2.73
3769 9474 1.594862 CGATGATCCTGTTTCGGCTTC 59.405 52.381 0.00 0.00 0.00 3.86
3972 9686 7.973944 GTCCTTTTACACTGACAATTCAACTTT 59.026 33.333 0.00 0.00 0.00 2.66
4000 9717 0.532862 AAACTCACCGACCTGCAGTG 60.533 55.000 13.81 4.73 0.00 3.66
4060 9956 8.527567 TTTTGCGGGAGAATTAATTAGTTTTG 57.472 30.769 0.00 0.00 0.00 2.44
4179 10075 0.313987 GGCCGCTGGTTAAATATGCC 59.686 55.000 0.00 0.00 0.00 4.40
4249 10145 2.203538 AGGCAGGGCAACAACCAG 60.204 61.111 0.00 0.00 39.74 4.00
4259 10155 2.123982 GCTTGGATGGAGGCAGGG 60.124 66.667 0.00 0.00 0.00 4.45
4261 10157 1.523258 CGAGCTTGGATGGAGGCAG 60.523 63.158 0.00 0.00 0.00 4.85
4269 10184 0.179134 GTCTACACGCGAGCTTGGAT 60.179 55.000 15.93 0.00 0.00 3.41
4277 10192 4.806481 GCGCTCGTCTACACGCGA 62.806 66.667 15.93 0.00 46.28 5.87
4281 10196 1.935327 AAGAGGGCGCTCGTCTACAC 61.935 60.000 23.41 0.00 39.43 2.90
4306 10221 1.063341 CCTCAGGATCAGGACTCAGGA 60.063 57.143 0.00 0.00 31.91 3.86
4307 10222 1.412079 CCTCAGGATCAGGACTCAGG 58.588 60.000 0.00 0.00 31.91 3.86
4308 10223 1.342874 ACCCTCAGGATCAGGACTCAG 60.343 57.143 0.00 0.00 36.73 3.35
4321 10236 3.615155 GGATTTCTCCTCAAACCCTCAG 58.385 50.000 0.00 0.00 38.65 3.35
4322 10237 3.721087 GGATTTCTCCTCAAACCCTCA 57.279 47.619 0.00 0.00 38.65 3.86
4335 10250 6.426646 AGATAAACGGCAGATAGGATTTCT 57.573 37.500 0.00 0.00 0.00 2.52
4351 10266 8.283291 CGGCAGATAGGATGTTTTTAGATAAAC 58.717 37.037 0.00 0.00 38.26 2.01
4352 10267 7.041372 GCGGCAGATAGGATGTTTTTAGATAAA 60.041 37.037 0.00 0.00 0.00 1.40
4353 10268 6.426937 GCGGCAGATAGGATGTTTTTAGATAA 59.573 38.462 0.00 0.00 0.00 1.75
4354 10269 5.932303 GCGGCAGATAGGATGTTTTTAGATA 59.068 40.000 0.00 0.00 0.00 1.98
4355 10270 4.757149 GCGGCAGATAGGATGTTTTTAGAT 59.243 41.667 0.00 0.00 0.00 1.98
4356 10271 4.127171 GCGGCAGATAGGATGTTTTTAGA 58.873 43.478 0.00 0.00 0.00 2.10
4357 10272 3.876914 TGCGGCAGATAGGATGTTTTTAG 59.123 43.478 0.00 0.00 0.00 1.85
4358 10273 3.879998 TGCGGCAGATAGGATGTTTTTA 58.120 40.909 0.00 0.00 0.00 1.52
4359 10274 2.722094 TGCGGCAGATAGGATGTTTTT 58.278 42.857 0.00 0.00 0.00 1.94
4360 10275 2.418368 TGCGGCAGATAGGATGTTTT 57.582 45.000 0.00 0.00 0.00 2.43
4361 10276 2.645838 ATGCGGCAGATAGGATGTTT 57.354 45.000 9.25 0.00 0.00 2.83
4362 10277 2.645838 AATGCGGCAGATAGGATGTT 57.354 45.000 9.25 0.00 0.00 2.71
4363 10278 3.603532 CATAATGCGGCAGATAGGATGT 58.396 45.455 9.25 0.00 0.00 3.06
4364 10279 2.353889 GCATAATGCGGCAGATAGGATG 59.646 50.000 9.25 6.51 31.71 3.51
4365 10280 2.636830 GCATAATGCGGCAGATAGGAT 58.363 47.619 9.25 0.00 31.71 3.24
4366 10281 2.099141 GCATAATGCGGCAGATAGGA 57.901 50.000 9.25 0.00 31.71 2.94
4377 10292 1.528586 CTACAGTCTGCCGCATAATGC 59.471 52.381 6.15 0.00 40.69 3.56
4378 10293 2.826428 ACTACAGTCTGCCGCATAATG 58.174 47.619 4.82 4.82 0.00 1.90
4379 10294 3.543680 AACTACAGTCTGCCGCATAAT 57.456 42.857 0.00 0.00 0.00 1.28
4380 10295 3.328382 AAACTACAGTCTGCCGCATAA 57.672 42.857 0.00 0.00 0.00 1.90
4381 10296 3.328382 AAAACTACAGTCTGCCGCATA 57.672 42.857 0.00 0.00 0.00 3.14
4382 10297 2.185004 AAAACTACAGTCTGCCGCAT 57.815 45.000 0.00 0.00 0.00 4.73
4383 10298 1.961793 AAAAACTACAGTCTGCCGCA 58.038 45.000 0.00 0.00 0.00 5.69
4405 10320 1.952990 TCTGCCGCATTGTCTCAAAAA 59.047 42.857 0.00 0.00 0.00 1.94
4406 10321 1.266718 GTCTGCCGCATTGTCTCAAAA 59.733 47.619 0.00 0.00 0.00 2.44
4407 10322 0.874390 GTCTGCCGCATTGTCTCAAA 59.126 50.000 0.00 0.00 0.00 2.69
4408 10323 0.035317 AGTCTGCCGCATTGTCTCAA 59.965 50.000 0.00 0.00 0.00 3.02
4409 10324 0.671472 CAGTCTGCCGCATTGTCTCA 60.671 55.000 0.00 0.00 0.00 3.27
4410 10325 0.671781 ACAGTCTGCCGCATTGTCTC 60.672 55.000 0.00 0.00 0.00 3.36
4411 10326 0.608130 TACAGTCTGCCGCATTGTCT 59.392 50.000 0.00 0.00 0.00 3.41
4412 10327 1.002366 CTACAGTCTGCCGCATTGTC 58.998 55.000 0.00 0.00 0.00 3.18
4413 10328 0.321671 ACTACAGTCTGCCGCATTGT 59.678 50.000 0.00 2.15 0.00 2.71
4414 10329 1.129251 CAACTACAGTCTGCCGCATTG 59.871 52.381 0.00 0.00 0.00 2.82
4415 10330 1.001974 TCAACTACAGTCTGCCGCATT 59.998 47.619 0.00 0.00 0.00 3.56
4416 10331 0.608130 TCAACTACAGTCTGCCGCAT 59.392 50.000 0.00 0.00 0.00 4.73
4417 10332 0.608130 ATCAACTACAGTCTGCCGCA 59.392 50.000 0.00 0.00 0.00 5.69
4418 10333 2.194271 GTATCAACTACAGTCTGCCGC 58.806 52.381 0.00 0.00 0.00 6.53


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

AutoCloner maintained by Alex Coulton.