Multiple sequence alignment - TraesCS7A01G562300

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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 TraesCS7A01G562300 chr7A 100.000 3119 0 0 1 3119 733084057 733087175 0.000000e+00 5760.0
1 TraesCS7A01G562300 chr7A 88.781 722 68 5 1787 2504 733246646 733247358 0.000000e+00 872.0
2 TraesCS7A01G562300 chr7A 90.200 449 42 2 1603 2050 733327798 733328245 4.480000e-163 584.0
3 TraesCS7A01G562300 chr7A 89.925 268 17 4 2852 3119 733247725 733247982 1.390000e-88 337.0
4 TraesCS7A01G562300 chr7A 93.264 193 7 2 2745 2937 733328694 733328880 2.370000e-71 279.0
5 TraesCS7A01G562300 chr7A 85.659 258 28 9 605 857 54875045 54875298 2.390000e-66 263.0
6 TraesCS7A01G562300 chr7A 88.688 221 17 5 1098 1310 733246336 733246556 2.390000e-66 263.0
7 TraesCS7A01G562300 chr7A 94.400 125 7 0 1186 1310 733327250 733327374 3.170000e-45 193.0
8 TraesCS7A01G562300 chr7A 85.350 157 18 3 1458 1613 733327466 733327618 1.160000e-34 158.0
9 TraesCS7A01G562300 chr7A 85.156 128 11 5 2994 3119 733328970 733329091 1.170000e-24 124.0
10 TraesCS7A01G562300 chr7A 83.824 136 7 1 2524 2659 733247415 733247535 7.070000e-22 115.0
11 TraesCS7A01G562300 chr7A 87.302 63 5 2 1048 1110 732931599 732931658 5.580000e-08 69.4
12 TraesCS7A01G562300 chr6A 92.202 872 43 11 7 856 26825519 26826387 0.000000e+00 1210.0
13 TraesCS7A01G562300 chr6A 87.639 898 67 18 1 857 590046981 590046087 0.000000e+00 1003.0
14 TraesCS7A01G562300 chr7B 86.976 906 80 16 1622 2511 750089444 750088561 0.000000e+00 985.0
15 TraesCS7A01G562300 chr7B 83.963 767 74 20 867 1613 750090310 750089573 0.000000e+00 689.0
16 TraesCS7A01G562300 chr7B 82.166 785 90 30 104 851 720467076 720466305 2.040000e-176 628.0
17 TraesCS7A01G562300 chr7B 85.597 243 24 4 2881 3119 750088194 750087959 8.640000e-61 244.0
18 TraesCS7A01G562300 chr7B 88.776 196 14 5 1 188 199292366 199292561 1.870000e-57 233.0
19 TraesCS7A01G562300 chr7B 75.676 259 41 10 886 1133 750093052 750092805 3.290000e-20 110.0
20 TraesCS7A01G562300 chr7B 90.476 63 3 1 2788 2850 750088257 750088198 2.580000e-11 80.5
21 TraesCS7A01G562300 chr5A 86.674 878 72 26 19 857 496994531 496993660 0.000000e+00 931.0
22 TraesCS7A01G562300 chr6D 85.538 892 78 24 3 857 422939893 422940770 0.000000e+00 885.0
23 TraesCS7A01G562300 chr6D 84.887 622 70 15 253 858 468246190 468245577 9.570000e-170 606.0
24 TraesCS7A01G562300 chr4B 83.995 881 98 26 7 859 526968000 526968865 0.000000e+00 806.0
25 TraesCS7A01G562300 chr4B 83.814 624 72 21 258 862 593402496 593401883 1.620000e-157 566.0
26 TraesCS7A01G562300 chr4B 89.286 196 13 5 1 188 57522067 57521872 4.020000e-59 239.0
27 TraesCS7A01G562300 chr4B 89.286 196 13 5 1 188 644395544 644395739 4.020000e-59 239.0
28 TraesCS7A01G562300 chr2B 83.485 878 91 26 1 854 51189559 51190406 0.000000e+00 769.0
29 TraesCS7A01G562300 chr2D 82.896 877 99 36 21 856 640037770 640036904 0.000000e+00 741.0
30 TraesCS7A01G562300 chr7D 88.686 548 44 8 1603 2142 633609540 633609003 0.000000e+00 652.0
31 TraesCS7A01G562300 chr7D 81.619 729 58 31 911 1613 633610396 633609718 4.580000e-148 534.0
32 TraesCS7A01G562300 chr7D 77.844 334 37 19 886 1200 633611416 633611101 4.140000e-39 172.0
33 TraesCS7A01G562300 chr7D 74.661 221 37 13 1616 1835 622370159 622369957 2.580000e-11 80.5
34 TraesCS7A01G562300 chr5B 81.223 458 62 13 1 438 683149766 683150219 6.400000e-92 348.0
35 TraesCS7A01G562300 chr5B 89.231 65 7 0 1254 1318 397294443 397294379 7.170000e-12 82.4
36 TraesCS7A01G562300 chr5D 84.328 268 31 7 1048 1311 12602795 12603055 5.160000e-63 252.0
37 TraesCS7A01G562300 chr2A 89.691 194 14 2 1 188 757296325 757296518 3.110000e-60 243.0
38 TraesCS7A01G562300 chr6B 88.776 196 14 5 1 188 49951748 49951553 1.870000e-57 233.0
39 TraesCS7A01G562300 chr6B 88.776 196 14 5 1 188 290228016 290228211 1.870000e-57 233.0


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 TraesCS7A01G562300 chr7A 733084057 733087175 3118 False 5760.000000 5760 100.000000 1 3119 1 chr7A.!!$F3 3118
1 TraesCS7A01G562300 chr7A 733246336 733247982 1646 False 396.750000 872 87.804500 1098 3119 4 chr7A.!!$F4 2021
2 TraesCS7A01G562300 chr7A 733327250 733329091 1841 False 267.600000 584 89.674000 1186 3119 5 chr7A.!!$F5 1933
3 TraesCS7A01G562300 chr6A 26825519 26826387 868 False 1210.000000 1210 92.202000 7 856 1 chr6A.!!$F1 849
4 TraesCS7A01G562300 chr6A 590046087 590046981 894 True 1003.000000 1003 87.639000 1 857 1 chr6A.!!$R1 856
5 TraesCS7A01G562300 chr7B 720466305 720467076 771 True 628.000000 628 82.166000 104 851 1 chr7B.!!$R1 747
6 TraesCS7A01G562300 chr7B 750087959 750093052 5093 True 421.700000 985 84.537600 867 3119 5 chr7B.!!$R2 2252
7 TraesCS7A01G562300 chr5A 496993660 496994531 871 True 931.000000 931 86.674000 19 857 1 chr5A.!!$R1 838
8 TraesCS7A01G562300 chr6D 422939893 422940770 877 False 885.000000 885 85.538000 3 857 1 chr6D.!!$F1 854
9 TraesCS7A01G562300 chr6D 468245577 468246190 613 True 606.000000 606 84.887000 253 858 1 chr6D.!!$R1 605
10 TraesCS7A01G562300 chr4B 526968000 526968865 865 False 806.000000 806 83.995000 7 859 1 chr4B.!!$F1 852
11 TraesCS7A01G562300 chr4B 593401883 593402496 613 True 566.000000 566 83.814000 258 862 1 chr4B.!!$R2 604
12 TraesCS7A01G562300 chr2B 51189559 51190406 847 False 769.000000 769 83.485000 1 854 1 chr2B.!!$F1 853
13 TraesCS7A01G562300 chr2D 640036904 640037770 866 True 741.000000 741 82.896000 21 856 1 chr2D.!!$R1 835
14 TraesCS7A01G562300 chr7D 633609003 633611416 2413 True 452.666667 652 82.716333 886 2142 3 chr7D.!!$R2 1256

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
881 984 0.108756 GACTGTAACCTGGCGTCTCC 60.109 60.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2738 6008 0.248866 GTTGTGCGTTGGGAACTTGG 60.249 55.0 0.0 0.0 0.0 3.61 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
83 86 6.801575 ACATACAAACAAATTTTGGAGACGT 58.198 32.000 13.42 0.00 33.92 4.34
179 186 9.801873 TTCAAAACAAAATTTGGAAACACAAAA 57.198 22.222 10.71 0.00 42.91 2.44
208 215 3.005684 TGCAGGCGAACATTTTCTGAAAT 59.994 39.130 3.31 0.00 35.90 2.17
215 222 6.095377 GCGAACATTTTCTGAAATTCCAGAT 58.905 36.000 3.31 0.00 42.18 2.90
216 223 6.587608 GCGAACATTTTCTGAAATTCCAGATT 59.412 34.615 3.31 0.00 42.18 2.40
217 224 7.116805 GCGAACATTTTCTGAAATTCCAGATTT 59.883 33.333 3.31 0.00 42.18 2.17
218 225 8.981647 CGAACATTTTCTGAAATTCCAGATTTT 58.018 29.630 3.31 0.00 42.18 1.82
463 513 6.295292 GCTGGAACACCTTTTGAAATTCCTAT 60.295 38.462 8.26 0.00 37.18 2.57
467 517 8.027189 GGAACACCTTTTGAAATTCCTATACAC 58.973 37.037 1.12 0.00 34.11 2.90
859 962 2.038033 CGGCGAATAGGATTTTCCCCTA 59.962 50.000 0.00 0.00 37.19 3.53
862 965 3.497262 GCGAATAGGATTTTCCCCTAACG 59.503 47.826 0.00 0.00 39.50 3.18
863 966 4.741536 GCGAATAGGATTTTCCCCTAACGA 60.742 45.833 16.68 0.00 39.50 3.85
864 967 4.748600 CGAATAGGATTTTCCCCTAACGAC 59.251 45.833 0.00 0.00 39.50 4.34
865 968 5.452917 CGAATAGGATTTTCCCCTAACGACT 60.453 44.000 0.00 0.00 39.50 4.18
866 969 3.629142 AGGATTTTCCCCTAACGACTG 57.371 47.619 0.00 0.00 37.19 3.51
867 970 2.910977 AGGATTTTCCCCTAACGACTGT 59.089 45.455 0.00 0.00 37.19 3.55
868 971 4.098894 AGGATTTTCCCCTAACGACTGTA 58.901 43.478 0.00 0.00 37.19 2.74
869 972 4.533311 AGGATTTTCCCCTAACGACTGTAA 59.467 41.667 0.00 0.00 37.19 2.41
870 973 4.633126 GGATTTTCCCCTAACGACTGTAAC 59.367 45.833 0.00 0.00 0.00 2.50
871 974 3.683365 TTTCCCCTAACGACTGTAACC 57.317 47.619 0.00 0.00 0.00 2.85
872 975 2.610438 TCCCCTAACGACTGTAACCT 57.390 50.000 0.00 0.00 0.00 3.50
873 976 2.173519 TCCCCTAACGACTGTAACCTG 58.826 52.381 0.00 0.00 0.00 4.00
874 977 1.206371 CCCCTAACGACTGTAACCTGG 59.794 57.143 0.00 0.00 0.00 4.45
875 978 1.405121 CCCTAACGACTGTAACCTGGC 60.405 57.143 0.00 0.00 0.00 4.85
876 979 1.625616 CTAACGACTGTAACCTGGCG 58.374 55.000 0.00 0.00 45.62 5.69
878 981 4.164252 CGACTGTAACCTGGCGTC 57.836 61.111 0.00 0.00 36.40 5.19
879 982 1.585006 CGACTGTAACCTGGCGTCT 59.415 57.895 0.00 0.00 36.40 4.18
880 983 0.456312 CGACTGTAACCTGGCGTCTC 60.456 60.000 0.00 0.00 36.40 3.36
881 984 0.108756 GACTGTAACCTGGCGTCTCC 60.109 60.000 0.00 0.00 0.00 3.71
882 985 0.830444 ACTGTAACCTGGCGTCTCCA 60.830 55.000 0.00 0.00 44.18 3.86
883 986 0.537188 CTGTAACCTGGCGTCTCCAT 59.463 55.000 0.00 0.00 45.50 3.41
884 987 0.249120 TGTAACCTGGCGTCTCCATG 59.751 55.000 0.00 0.00 45.50 3.66
891 994 2.892425 GCGTCTCCATGGGCTTCG 60.892 66.667 13.02 12.70 0.00 3.79
897 1000 1.115467 CTCCATGGGCTTCGTAGTCT 58.885 55.000 13.02 0.00 0.00 3.24
898 1001 1.067821 CTCCATGGGCTTCGTAGTCTC 59.932 57.143 13.02 0.00 0.00 3.36
903 1006 0.179169 GGGCTTCGTAGTCTCGTGAC 60.179 60.000 9.57 9.57 43.22 3.67
904 1007 0.179169 GGCTTCGTAGTCTCGTGACC 60.179 60.000 13.70 0.00 43.91 4.02
945 1048 3.561120 TAGCCCACCAAAGCCCACG 62.561 63.158 0.00 0.00 0.00 4.94
951 3839 1.826487 ACCAAAGCCCACGAACACC 60.826 57.895 0.00 0.00 0.00 4.16
959 3847 1.178534 CCCACGAACACCCAAGCAAT 61.179 55.000 0.00 0.00 0.00 3.56
960 3848 0.673437 CCACGAACACCCAAGCAATT 59.327 50.000 0.00 0.00 0.00 2.32
963 3851 2.034558 CACGAACACCCAAGCAATTCTT 59.965 45.455 0.00 0.00 34.78 2.52
978 3867 5.588568 CAATTCTTGCTCCATATCGTCTC 57.411 43.478 0.00 0.00 0.00 3.36
993 3882 1.491668 GTCTCCTTCCCCTCTTCCTC 58.508 60.000 0.00 0.00 0.00 3.71
994 3883 0.340208 TCTCCTTCCCCTCTTCCTCC 59.660 60.000 0.00 0.00 0.00 4.30
995 3884 0.692756 CTCCTTCCCCTCTTCCTCCC 60.693 65.000 0.00 0.00 0.00 4.30
1046 3935 1.589399 CCACCTCCTCCTCCTCCTCT 61.589 65.000 0.00 0.00 0.00 3.69
1092 3984 4.803426 GAGGAGTCGCGGTGGCTG 62.803 72.222 6.13 0.00 36.88 4.85
1150 4042 2.733517 CCCTTCTCGTCGCTCTTAATC 58.266 52.381 0.00 0.00 0.00 1.75
1162 4054 3.610585 CGCTCTTAATCTCTCGCCCTTAG 60.611 52.174 0.00 0.00 0.00 2.18
1220 4124 1.948145 CAGGATTTGCTCATCAGCCTC 59.052 52.381 0.00 0.00 46.26 4.70
1224 4128 2.574006 TTTGCTCATCAGCCTCAAGT 57.426 45.000 0.00 0.00 46.26 3.16
1323 4236 1.681793 TCGGTACTGCCTGCTTCTATC 59.318 52.381 0.00 0.00 34.25 2.08
1362 4285 4.101448 CTCCCCTCCCCGCAACAG 62.101 72.222 0.00 0.00 0.00 3.16
1369 4292 1.733402 CTCCCCGCAACAGCAACAAA 61.733 55.000 0.00 0.00 0.00 2.83
1374 4302 1.189884 CCGCAACAGCAACAAAAATCG 59.810 47.619 0.00 0.00 0.00 3.34
1409 4337 2.417933 GCTGATTGTGTGCTGGTAGAAG 59.582 50.000 0.00 0.00 0.00 2.85
1416 4344 1.026718 GTGCTGGTAGAAGGCGCAAT 61.027 55.000 10.83 0.00 36.61 3.56
1420 4348 2.352715 GCTGGTAGAAGGCGCAATTTTT 60.353 45.455 10.83 0.00 0.00 1.94
1424 4352 3.428534 GGTAGAAGGCGCAATTTTTGTTG 59.571 43.478 10.83 0.00 0.00 3.33
1426 4354 0.943673 AAGGCGCAATTTTTGTTGGC 59.056 45.000 10.83 0.00 35.22 4.52
1428 4356 0.235404 GGCGCAATTTTTGTTGGCTG 59.765 50.000 10.83 0.00 33.34 4.85
1448 4381 1.299541 GTTGCCATGTCGTCATAGGG 58.700 55.000 10.99 4.61 32.47 3.53
1499 4434 4.402155 ACTCTGAATTTTGTGTGCCAAAGA 59.598 37.500 0.00 0.00 43.63 2.52
1501 4436 4.644234 TCTGAATTTTGTGTGCCAAAGAGA 59.356 37.500 0.00 0.00 43.63 3.10
1507 4442 2.497138 TGTGTGCCAAAGAGACAGATG 58.503 47.619 0.00 0.00 0.00 2.90
1542 4477 5.663795 ATGAATTCAGTGCATACGACATC 57.336 39.130 14.54 0.00 0.00 3.06
1543 4478 4.758688 TGAATTCAGTGCATACGACATCT 58.241 39.130 3.38 0.00 0.00 2.90
1576 4511 8.315391 TGATTCAGAGTTGCAGTATATAATGC 57.685 34.615 24.51 24.51 46.42 3.56
1583 4518 7.655328 AGAGTTGCAGTATATAATGCTCTTCAC 59.345 37.037 29.18 19.01 46.39 3.18
1692 4824 5.811613 TGTTGTTTTGCTGGAAGATTTCAAG 59.188 36.000 0.00 0.00 34.07 3.02
1716 4848 2.418884 CCGGCTAAGAGAAGAAACCTCC 60.419 54.545 0.00 0.00 0.00 4.30
1730 4862 1.002134 CCTCCCTTGATGCAACCGT 60.002 57.895 0.00 0.00 0.00 4.83
1774 4906 2.170607 AGGGATCCTGTTACGGATGTTG 59.829 50.000 12.58 0.00 43.71 3.33
1783 4915 0.680618 TACGGATGTTGGTGTCGGTT 59.319 50.000 0.00 0.00 0.00 4.44
1887 5020 2.483013 GCAGACGCATGATGGGTAAGTA 60.483 50.000 15.36 0.00 43.89 2.24
1899 5032 9.784531 CATGATGGGTAAGTAATTTGAGTATCT 57.215 33.333 0.00 0.00 34.92 1.98
1992 5139 5.979517 GTGCTGAAACTTGCTCTATGTTTTT 59.020 36.000 0.00 0.00 36.94 1.94
1993 5140 6.142958 GTGCTGAAACTTGCTCTATGTTTTTC 59.857 38.462 0.00 0.00 36.94 2.29
1997 5144 7.476667 TGAAACTTGCTCTATGTTTTTCGAAA 58.523 30.769 6.47 6.47 36.94 3.46
2077 5224 1.893062 CGTCATGGAGAGGCTGTCA 59.107 57.895 14.14 0.24 0.00 3.58
2081 5228 3.350833 GTCATGGAGAGGCTGTCAAAAT 58.649 45.455 14.14 1.21 0.00 1.82
2108 5255 4.210832 AGAAAAGAAGAAAAACGAGCGG 57.789 40.909 0.00 0.00 0.00 5.52
2136 5283 1.419374 AGCGGCGATCATAAATCGAC 58.581 50.000 12.98 7.38 45.45 4.20
2153 5300 3.250744 TCGACTGCGACAATTTTCCTAG 58.749 45.455 0.00 0.00 42.51 3.02
2156 5303 4.246458 GACTGCGACAATTTTCCTAGAGT 58.754 43.478 0.00 0.00 0.00 3.24
2164 5311 6.291849 CGACAATTTTCCTAGAGTTAGCGATG 60.292 42.308 0.00 0.00 0.00 3.84
2203 5356 3.247173 GGATGTCGTTGAGCAAGATGATC 59.753 47.826 0.00 0.00 32.56 2.92
2214 5368 2.683152 GCAAGATGATCAGAGGCTTGGT 60.683 50.000 21.59 0.00 37.14 3.67
2263 5418 4.844655 ACCTGTTGTAGTCTACCTTTCCAT 59.155 41.667 7.56 0.00 0.00 3.41
2281 5436 2.675348 CCATCTTTTCTTCGTCTGGAGC 59.325 50.000 0.00 0.00 0.00 4.70
2319 5474 6.373216 AGAACTCGACTGGCAGATATATAGAC 59.627 42.308 23.66 4.80 0.00 2.59
2334 5489 0.179468 TAGACGCCCCTTATGTTGGC 59.821 55.000 0.00 0.00 41.85 4.52
2343 5498 3.835395 CCCCTTATGTTGGCCAAAGTTTA 59.165 43.478 22.47 6.79 0.00 2.01
2351 5507 7.872113 ATGTTGGCCAAAGTTTAATTTTTGA 57.128 28.000 22.47 0.00 36.61 2.69
2386 5542 3.008330 CCAAGCTCACTGATGAAAGGAG 58.992 50.000 0.00 0.00 33.30 3.69
2437 5593 3.010138 AGCCTCCTTATTTGCACCAAGTA 59.990 43.478 0.00 0.00 0.00 2.24
2448 5604 6.472686 TTTGCACCAAGTACACCTTAATTT 57.527 33.333 0.00 0.00 0.00 1.82
2467 5623 0.257328 TTTGGCTGTTCTGGGTGTCA 59.743 50.000 0.00 0.00 0.00 3.58
2480 5636 1.334869 GGGTGTCAGTTGCTCACTTTG 59.665 52.381 0.00 0.00 30.92 2.77
2488 5644 5.232838 GTCAGTTGCTCACTTTGATTTTTGG 59.767 40.000 0.00 0.00 30.92 3.28
2489 5645 4.508861 CAGTTGCTCACTTTGATTTTTGGG 59.491 41.667 0.00 0.00 30.92 4.12
2490 5646 4.405358 AGTTGCTCACTTTGATTTTTGGGA 59.595 37.500 0.00 0.00 27.32 4.37
2492 5648 6.267471 AGTTGCTCACTTTGATTTTTGGGATA 59.733 34.615 0.00 0.00 27.32 2.59
2511 5667 2.160721 AATTCCTGGGAGCTCGTAGA 57.839 50.000 15.21 4.23 0.00 2.59
2513 5669 1.403814 TTCCTGGGAGCTCGTAGATG 58.596 55.000 15.21 2.68 33.89 2.90
2514 5670 0.551396 TCCTGGGAGCTCGTAGATGA 59.449 55.000 15.21 4.65 33.89 2.92
2515 5671 1.063942 TCCTGGGAGCTCGTAGATGAA 60.064 52.381 15.21 0.00 33.89 2.57
2517 5673 2.028130 CTGGGAGCTCGTAGATGAACT 58.972 52.381 7.83 0.00 33.89 3.01
2521 5677 3.551863 GGGAGCTCGTAGATGAACTGATG 60.552 52.174 7.83 0.00 33.89 3.07
2659 5900 2.045561 TCCGTCTTCTTTGCACCAAA 57.954 45.000 0.00 0.00 0.00 3.28
2661 5902 2.955660 TCCGTCTTCTTTGCACCAAATT 59.044 40.909 0.00 0.00 32.70 1.82
2683 5953 9.595823 AAATTCATTGCTCATCTAATTTTCAGG 57.404 29.630 0.00 0.00 0.00 3.86
2708 5978 6.528321 CATTCATTCCTGGAACTCATAGCTA 58.472 40.000 12.11 0.00 0.00 3.32
2721 5991 5.248640 ACTCATAGCTAGCAACATGTTGTT 58.751 37.500 33.01 30.33 42.08 2.83
2738 6008 6.266168 TGTTGTTGTTTGATATGGATGTCC 57.734 37.500 0.00 0.00 0.00 4.02
2750 6032 1.203001 TGGATGTCCCAAGTTCCCAAC 60.203 52.381 0.00 0.00 43.29 3.77
2810 6092 7.387948 AGTTACCAAGTGCAGTTTACTGAATAG 59.612 37.037 13.83 0.00 46.59 1.73
2811 6093 5.621193 ACCAAGTGCAGTTTACTGAATAGT 58.379 37.500 13.83 0.55 46.59 2.12
2812 6094 6.765403 ACCAAGTGCAGTTTACTGAATAGTA 58.235 36.000 13.83 0.00 46.59 1.82
2873 6155 7.035840 ACTCATGGCATGATGAATTTTCTAC 57.964 36.000 28.91 0.00 38.85 2.59
2874 6156 6.832384 ACTCATGGCATGATGAATTTTCTACT 59.168 34.615 28.91 2.93 38.85 2.57
2875 6157 7.994911 ACTCATGGCATGATGAATTTTCTACTA 59.005 33.333 28.91 2.60 38.85 1.82
2959 6270 9.621629 AATTAATGAATCACCTACGTGGATTAA 57.378 29.630 0.00 1.59 40.65 1.40
2966 6277 2.829720 ACCTACGTGGATTAACTGCTGA 59.170 45.455 0.00 0.00 39.71 4.26
2967 6278 3.119101 ACCTACGTGGATTAACTGCTGAG 60.119 47.826 0.00 0.00 39.71 3.35
2990 6301 8.606602 TGAGTTAATGAATCATGAGTTCGATTG 58.393 33.333 0.09 0.00 32.05 2.67
3046 6362 5.184892 AGGATTGCACTTCCTATCTTGTT 57.815 39.130 14.41 0.00 41.89 2.83
3047 6363 5.189180 AGGATTGCACTTCCTATCTTGTTC 58.811 41.667 14.41 0.00 41.89 3.18
3048 6364 5.045286 AGGATTGCACTTCCTATCTTGTTCT 60.045 40.000 14.41 0.00 41.89 3.01
3049 6365 5.649831 GGATTGCACTTCCTATCTTGTTCTT 59.350 40.000 7.49 0.00 0.00 2.52
3050 6366 5.947228 TTGCACTTCCTATCTTGTTCTTG 57.053 39.130 0.00 0.00 0.00 3.02
3051 6367 4.973168 TGCACTTCCTATCTTGTTCTTGT 58.027 39.130 0.00 0.00 0.00 3.16
3070 6386 1.008875 TGCTTCAGCGCACGTCTAAG 61.009 55.000 11.47 4.66 45.83 2.18
3097 6413 7.010460 GCACAAGTTAAAAAGAGATTGCACTTT 59.990 33.333 0.00 0.00 36.65 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 65 6.438259 TCACGTCTCCAAAATTTGTTTGTA 57.562 33.333 4.92 0.00 0.00 2.41
69 72 9.541143 AAAAATATGTTCACGTCTCCAAAATTT 57.459 25.926 0.00 0.00 0.00 1.82
179 186 2.888834 ATGTTCGCCTGCAAAAGTTT 57.111 40.000 0.00 0.00 0.00 2.66
315 345 9.495572 AGTTTGAAAAATGTTCCTGTTACAAAA 57.504 25.926 0.00 0.00 0.00 2.44
316 346 9.145865 GAGTTTGAAAAATGTTCCTGTTACAAA 57.854 29.630 0.00 0.00 0.00 2.83
317 347 7.762159 GGAGTTTGAAAAATGTTCCTGTTACAA 59.238 33.333 0.00 0.00 0.00 2.41
318 348 7.262048 GGAGTTTGAAAAATGTTCCTGTTACA 58.738 34.615 0.00 0.00 0.00 2.41
319 349 6.700081 GGGAGTTTGAAAAATGTTCCTGTTAC 59.300 38.462 0.00 0.00 0.00 2.50
320 350 6.381420 TGGGAGTTTGAAAAATGTTCCTGTTA 59.619 34.615 0.00 0.00 0.00 2.41
325 355 5.877564 TGTTTGGGAGTTTGAAAAATGTTCC 59.122 36.000 0.00 0.00 0.00 3.62
380 429 9.823098 TTCATGTTTTCAAATTTTTGTTCACAG 57.177 25.926 3.18 1.36 39.18 3.66
613 670 9.462606 TTTAGTTTCTGTTTCTCTTCTTCCTTT 57.537 29.630 0.00 0.00 0.00 3.11
615 672 9.462606 TTTTTAGTTTCTGTTTCTCTTCTTCCT 57.537 29.630 0.00 0.00 0.00 3.36
859 962 0.319297 GACGCCAGGTTACAGTCGTT 60.319 55.000 0.00 0.00 0.00 3.85
862 965 0.108756 GGAGACGCCAGGTTACAGTC 60.109 60.000 0.00 0.00 36.34 3.51
863 966 0.830444 TGGAGACGCCAGGTTACAGT 60.830 55.000 0.00 0.00 43.33 3.55
864 967 1.972198 TGGAGACGCCAGGTTACAG 59.028 57.895 0.00 0.00 43.33 2.74
865 968 4.201523 TGGAGACGCCAGGTTACA 57.798 55.556 0.00 0.00 43.33 2.41
873 976 2.514824 GAAGCCCATGGAGACGCC 60.515 66.667 15.22 0.00 37.10 5.68
874 977 2.292794 TACGAAGCCCATGGAGACGC 62.293 60.000 15.22 8.10 0.00 5.19
875 978 0.249073 CTACGAAGCCCATGGAGACG 60.249 60.000 15.22 15.13 0.00 4.18
876 979 0.824759 ACTACGAAGCCCATGGAGAC 59.175 55.000 15.22 1.82 0.00 3.36
877 980 1.112113 GACTACGAAGCCCATGGAGA 58.888 55.000 15.22 0.00 0.00 3.71
878 981 1.067821 GAGACTACGAAGCCCATGGAG 59.932 57.143 15.22 4.39 0.00 3.86
879 982 1.112113 GAGACTACGAAGCCCATGGA 58.888 55.000 15.22 0.00 0.00 3.41
880 983 0.249073 CGAGACTACGAAGCCCATGG 60.249 60.000 4.14 4.14 35.09 3.66
881 984 0.456221 ACGAGACTACGAAGCCCATG 59.544 55.000 0.00 0.00 37.03 3.66
882 985 0.456221 CACGAGACTACGAAGCCCAT 59.544 55.000 0.00 0.00 37.03 4.00
883 986 0.607217 TCACGAGACTACGAAGCCCA 60.607 55.000 0.00 0.00 37.03 5.36
884 987 0.179169 GTCACGAGACTACGAAGCCC 60.179 60.000 5.68 0.00 41.64 5.19
897 1000 4.100284 CAACTTGATTGAGTCGGTCACGA 61.100 47.826 7.70 0.00 43.44 4.35
898 1001 2.065993 ACTTGATTGAGTCGGTCACG 57.934 50.000 0.00 0.00 42.74 4.35
903 1006 0.804989 GCCCAACTTGATTGAGTCGG 59.195 55.000 0.00 0.00 41.23 4.79
904 1007 0.804989 GGCCCAACTTGATTGAGTCG 59.195 55.000 0.00 0.00 41.23 4.18
959 3847 3.300388 AGGAGACGATATGGAGCAAGAA 58.700 45.455 0.00 0.00 0.00 2.52
960 3848 2.950781 AGGAGACGATATGGAGCAAGA 58.049 47.619 0.00 0.00 0.00 3.02
963 3851 1.964223 GGAAGGAGACGATATGGAGCA 59.036 52.381 0.00 0.00 0.00 4.26
969 3857 3.502356 GAAGAGGGGAAGGAGACGATAT 58.498 50.000 0.00 0.00 0.00 1.63
970 3858 2.424523 GGAAGAGGGGAAGGAGACGATA 60.425 54.545 0.00 0.00 0.00 2.92
978 3867 1.694525 GGGGAGGAAGAGGGGAAGG 60.695 68.421 0.00 0.00 0.00 3.46
1138 4030 1.600912 GGGCGAGAGATTAAGAGCGAC 60.601 57.143 0.00 0.00 0.00 5.19
1150 4042 1.331138 CTGTCGTACTAAGGGCGAGAG 59.669 57.143 0.00 0.00 39.07 3.20
1162 4054 3.120095 GGCACCATTAAAACCTGTCGTAC 60.120 47.826 0.00 0.00 0.00 3.67
1220 4124 1.283793 CTTCACGGCCAGCAACTTG 59.716 57.895 2.24 0.00 0.00 3.16
1277 4181 2.125512 AGGGTGCGCAGATCGAAC 60.126 61.111 12.22 0.00 46.06 3.95
1383 4311 1.271379 CCAGCACACAATCAGCACAAT 59.729 47.619 0.00 0.00 0.00 2.71
1391 4319 1.740025 GCCTTCTACCAGCACACAATC 59.260 52.381 0.00 0.00 0.00 2.67
1409 4337 0.235404 CAGCCAACAAAAATTGCGCC 59.765 50.000 4.18 0.00 0.00 6.53
1426 4354 1.935873 CTATGACGACATGGCAACCAG 59.064 52.381 10.69 0.00 36.75 4.00
1428 4356 1.299541 CCTATGACGACATGGCAACC 58.700 55.000 10.69 0.00 37.87 3.77
1448 4381 3.764885 ATAACAGAAACGGCTGAATGC 57.235 42.857 0.00 0.00 39.20 3.56
1576 4511 4.754372 TTAAGCTGCATTGTGTGAAGAG 57.246 40.909 1.02 0.00 35.21 2.85
1583 4518 6.715344 AACATTTGATTAAGCTGCATTGTG 57.285 33.333 1.02 0.00 0.00 3.33
1692 4824 1.732809 GTTTCTTCTCTTAGCCGGTGC 59.267 52.381 1.90 0.00 37.95 5.01
1716 4848 1.879380 TCAAGAACGGTTGCATCAAGG 59.121 47.619 0.00 0.00 0.00 3.61
1774 4906 1.291877 CTGCTGCTACAACCGACACC 61.292 60.000 0.00 0.00 0.00 4.16
1783 4915 0.894835 TCGGAATCACTGCTGCTACA 59.105 50.000 0.00 0.00 0.00 2.74
1887 5020 6.888632 AGCCAAACTGATCAGATACTCAAATT 59.111 34.615 29.27 6.66 0.00 1.82
1955 5091 4.516698 AGTTTCAGCACAAGATGTAACTGG 59.483 41.667 5.23 0.00 45.76 4.00
2015 5162 3.493350 CCATAACTGCATCGTAAGGAGCT 60.493 47.826 0.00 0.00 38.16 4.09
2017 5164 3.804325 CACCATAACTGCATCGTAAGGAG 59.196 47.826 0.00 0.00 38.47 3.69
2081 5228 6.526674 GCTCGTTTTTCTTCTTTTCTTGTTCA 59.473 34.615 0.00 0.00 0.00 3.18
2108 5255 1.244697 TGATCGCCGCTATCTCCTCC 61.245 60.000 6.46 0.00 0.00 4.30
2136 5283 5.220491 GCTAACTCTAGGAAAATTGTCGCAG 60.220 44.000 0.00 0.00 0.00 5.18
2143 5290 7.707035 CACTACATCGCTAACTCTAGGAAAATT 59.293 37.037 0.00 0.00 0.00 1.82
2153 5300 2.282820 GCTTGCACTACATCGCTAACTC 59.717 50.000 0.00 0.00 0.00 3.01
2156 5303 1.999735 GTGCTTGCACTACATCGCTAA 59.000 47.619 17.36 0.00 0.00 3.09
2164 5311 2.325082 CCGGTGGTGCTTGCACTAC 61.325 63.158 26.61 26.61 36.08 2.73
2214 5368 3.858129 GCAAAATTACAAGAGCAGCAGCA 60.858 43.478 3.17 0.00 45.49 4.41
2263 5418 3.131396 GTTGCTCCAGACGAAGAAAAGA 58.869 45.455 0.00 0.00 0.00 2.52
2281 5436 1.457303 CGAGTTCTTCGCCTCTTGTTG 59.543 52.381 0.00 0.00 43.22 3.33
2343 5498 9.439500 CTTGGTTACATCCATTCATCAAAAATT 57.561 29.630 0.00 0.00 37.33 1.82
2351 5507 4.641989 GTGAGCTTGGTTACATCCATTCAT 59.358 41.667 0.00 0.00 37.33 2.57
2386 5542 7.806487 CACATGATGCAGGATGACAATTATAAC 59.194 37.037 13.31 0.00 39.69 1.89
2437 5593 5.453198 CCAGAACAGCCAAAAATTAAGGTGT 60.453 40.000 0.00 0.00 0.00 4.16
2448 5604 0.257328 TGACACCCAGAACAGCCAAA 59.743 50.000 0.00 0.00 0.00 3.28
2467 5623 4.405358 TCCCAAAAATCAAAGTGAGCAACT 59.595 37.500 0.00 0.00 42.60 3.16
2488 5644 1.694696 ACGAGCTCCCAGGAATTATCC 59.305 52.381 8.47 0.00 46.98 2.59
2489 5645 3.827302 TCTACGAGCTCCCAGGAATTATC 59.173 47.826 8.47 0.00 0.00 1.75
2490 5646 3.845860 TCTACGAGCTCCCAGGAATTAT 58.154 45.455 8.47 0.00 0.00 1.28
2492 5648 2.160721 TCTACGAGCTCCCAGGAATT 57.839 50.000 8.47 0.00 0.00 2.17
2511 5667 6.906157 ACTTTGGACAAATCATCAGTTCAT 57.094 33.333 0.00 0.00 0.00 2.57
2513 5669 9.774742 GTTATACTTTGGACAAATCATCAGTTC 57.225 33.333 0.00 0.00 0.00 3.01
2514 5670 9.295825 TGTTATACTTTGGACAAATCATCAGTT 57.704 29.630 0.00 0.00 0.00 3.16
2515 5671 8.862325 TGTTATACTTTGGACAAATCATCAGT 57.138 30.769 0.00 0.00 0.00 3.41
2517 5673 8.862325 ACTGTTATACTTTGGACAAATCATCA 57.138 30.769 0.00 0.00 0.00 3.07
2574 5770 3.356290 AGCTTGGTTGTATAAAGGCCAG 58.644 45.455 5.01 0.00 0.00 4.85
2576 5772 3.621558 AGAGCTTGGTTGTATAAAGGCC 58.378 45.455 0.00 0.00 0.00 5.19
2577 5773 4.518249 AGAGAGCTTGGTTGTATAAAGGC 58.482 43.478 0.00 0.00 0.00 4.35
2578 5774 6.758886 CACTAGAGAGCTTGGTTGTATAAAGG 59.241 42.308 0.00 0.00 0.00 3.11
2579 5775 7.548097 TCACTAGAGAGCTTGGTTGTATAAAG 58.452 38.462 0.00 0.00 0.00 1.85
2580 5776 7.476540 TCACTAGAGAGCTTGGTTGTATAAA 57.523 36.000 0.00 0.00 0.00 1.40
2581 5777 7.476540 TTCACTAGAGAGCTTGGTTGTATAA 57.523 36.000 0.00 0.00 0.00 0.98
2586 5782 4.887748 TCTTTCACTAGAGAGCTTGGTTG 58.112 43.478 0.00 0.00 0.00 3.77
2659 5900 7.147794 TGCCTGAAAATTAGATGAGCAATGAAT 60.148 33.333 0.00 0.00 0.00 2.57
2661 5902 5.653330 TGCCTGAAAATTAGATGAGCAATGA 59.347 36.000 0.00 0.00 0.00 2.57
2683 5953 4.023365 GCTATGAGTTCCAGGAATGAATGC 60.023 45.833 4.80 3.02 0.00 3.56
2721 5991 5.191727 ACTTGGGACATCCATATCAAACA 57.808 39.130 0.00 0.00 46.52 2.83
2723 5993 5.200483 GGAACTTGGGACATCCATATCAAA 58.800 41.667 0.00 0.00 46.52 2.69
2726 5996 3.138283 TGGGAACTTGGGACATCCATATC 59.862 47.826 0.00 0.00 46.52 1.63
2728 5998 2.567862 TGGGAACTTGGGACATCCATA 58.432 47.619 0.00 0.00 46.52 2.74
2729 5999 1.381867 TGGGAACTTGGGACATCCAT 58.618 50.000 0.00 0.00 46.52 3.41
2730 6000 1.153539 TTGGGAACTTGGGACATCCA 58.846 50.000 0.00 0.00 45.43 3.41
2731 6001 1.545841 GTTGGGAACTTGGGACATCC 58.454 55.000 0.00 0.00 39.30 3.51
2735 6005 1.527380 TGCGTTGGGAACTTGGGAC 60.527 57.895 0.00 0.00 0.00 4.46
2738 6008 0.248866 GTTGTGCGTTGGGAACTTGG 60.249 55.000 0.00 0.00 0.00 3.61
2740 6010 0.738389 CTGTTGTGCGTTGGGAACTT 59.262 50.000 0.00 0.00 0.00 2.66
2741 6011 0.393808 ACTGTTGTGCGTTGGGAACT 60.394 50.000 0.00 0.00 0.00 3.01
2742 6012 0.454196 AACTGTTGTGCGTTGGGAAC 59.546 50.000 0.00 0.00 0.00 3.62
2743 6013 0.453793 CAACTGTTGTGCGTTGGGAA 59.546 50.000 12.30 0.00 37.45 3.97
2810 6092 7.367285 TGAAGGCACAACAATTAACTTCATAC 58.633 34.615 0.00 0.00 38.22 2.39
2811 6093 7.230510 ACTGAAGGCACAACAATTAACTTCATA 59.769 33.333 0.00 0.00 41.09 2.15
2812 6094 6.040842 ACTGAAGGCACAACAATTAACTTCAT 59.959 34.615 0.00 0.00 41.09 2.57
2873 6155 3.817647 GCTTGATTTGCCCTACCTGATAG 59.182 47.826 0.00 0.00 0.00 2.08
2874 6156 3.435026 GGCTTGATTTGCCCTACCTGATA 60.435 47.826 0.00 0.00 44.32 2.15
2875 6157 2.659428 GCTTGATTTGCCCTACCTGAT 58.341 47.619 0.00 0.00 0.00 2.90
2959 6270 6.413052 ACTCATGATTCATTAACTCAGCAGT 58.587 36.000 0.00 0.00 0.00 4.40
2966 6277 7.412853 GCAATCGAACTCATGATTCATTAACT 58.587 34.615 14.28 0.00 32.68 2.24
2967 6278 6.634436 GGCAATCGAACTCATGATTCATTAAC 59.366 38.462 14.28 9.74 32.68 2.01
2990 6301 1.622811 TGGTTTGGTTTGATGATGGGC 59.377 47.619 0.00 0.00 0.00 5.36
3051 6367 1.006688 TTAGACGTGCGCTGAAGCA 60.007 52.632 9.73 0.00 45.96 3.91
3070 6386 5.175673 GTGCAATCTCTTTTTAACTTGTGCC 59.824 40.000 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.