Multiple sequence alignment - TraesCS1D01G275900

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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 TraesCS1D01G275900 chr1D 100.000 6505 0 0 1 6505 371757363 371750859 0.000000e+00 12013.0
1 TraesCS1D01G275900 chr1D 93.103 319 20 2 291 607 443299723 443300041 3.550000e-127 466.0
2 TraesCS1D01G275900 chr1D 86.559 186 22 3 3692 3875 371752321 371752505 1.110000e-47 202.0
3 TraesCS1D01G275900 chr1D 86.559 186 22 3 4859 5043 371753489 371753672 1.110000e-47 202.0
4 TraesCS1D01G275900 chr1B 93.199 5970 252 71 621 6505 496568251 496562351 0.000000e+00 8634.0
5 TraesCS1D01G275900 chr1B 84.946 186 24 4 4859 5043 496565007 496565189 1.110000e-42 185.0
6 TraesCS1D01G275900 chr1B 83.770 191 20 7 3692 3875 496563838 496564024 3.120000e-38 171.0
7 TraesCS1D01G275900 chr1A 95.372 1988 76 9 1575 3557 471493552 471491576 0.000000e+00 3147.0
8 TraesCS1D01G275900 chr1A 89.142 921 50 15 5130 6034 471490837 471489951 0.000000e+00 1101.0
9 TraesCS1D01G275900 chr1A 90.594 808 36 20 802 1580 471494383 471493587 0.000000e+00 1035.0
10 TraesCS1D01G275900 chr1A 87.257 463 37 18 6055 6505 471489896 471489444 5.820000e-140 508.0
11 TraesCS1D01G275900 chr1A 91.667 156 9 4 3556 3707 471491417 471491262 5.110000e-51 213.0
12 TraesCS1D01G275900 chr1A 86.364 176 21 3 3698 3873 374253230 374253058 8.610000e-44 189.0
13 TraesCS1D01G275900 chr1A 90.566 106 9 1 5036 5141 471491278 471491174 8.800000e-29 139.0
14 TraesCS1D01G275900 chr4A 87.728 823 87 11 1001 1820 592755925 592756736 0.000000e+00 948.0
15 TraesCS1D01G275900 chr4A 87.606 823 88 11 1001 1820 592477118 592477929 0.000000e+00 942.0
16 TraesCS1D01G275900 chr4A 87.485 823 89 11 1001 1820 593044005 593044816 0.000000e+00 937.0
17 TraesCS1D01G275900 chr4A 87.046 826 95 9 1001 1823 591566157 591565341 0.000000e+00 922.0
18 TraesCS1D01G275900 chr4A 88.161 473 47 7 1354 1823 702672401 702671935 7.370000e-154 555.0
19 TraesCS1D01G275900 chr4A 82.419 620 86 15 1 611 15490073 15490678 2.690000e-143 520.0
20 TraesCS1D01G275900 chr4A 91.351 370 31 1 3697 4066 609933409 609933777 7.530000e-139 505.0
21 TraesCS1D01G275900 chrUn 87.485 823 89 11 1001 1820 332730711 332731522 0.000000e+00 937.0
22 TraesCS1D01G275900 chrUn 80.556 108 19 2 5388 5495 123881573 123881468 1.500000e-11 82.4
23 TraesCS1D01G275900 chrUn 80.556 108 19 2 5388 5495 131896596 131896701 1.500000e-11 82.4
24 TraesCS1D01G275900 chr3D 88.905 703 63 12 1124 1823 575279282 575278592 0.000000e+00 852.0
25 TraesCS1D01G275900 chr3D 96.284 296 10 1 3 298 345072730 345072436 9.810000e-133 484.0
26 TraesCS1D01G275900 chr3D 95.302 298 13 1 1 298 37552874 37553170 7.630000e-129 472.0
27 TraesCS1D01G275900 chr3D 92.661 327 17 6 291 612 37458728 37459052 1.280000e-126 464.0
28 TraesCS1D01G275900 chr3D 92.331 326 20 4 291 612 37553216 37553540 5.940000e-125 459.0
29 TraesCS1D01G275900 chr3D 85.057 174 24 2 3699 3872 607884089 607884260 6.700000e-40 176.0
30 TraesCS1D01G275900 chr3D 81.818 176 27 5 4862 5036 607884260 607884089 6.800000e-30 143.0
31 TraesCS1D01G275900 chr5D 87.909 703 68 12 1124 1823 112835308 112834620 0.000000e+00 811.0
32 TraesCS1D01G275900 chr5D 96.309 298 10 1 1 298 107530328 107530032 7.580000e-134 488.0
33 TraesCS1D01G275900 chr5D 93.519 324 16 4 291 611 107529988 107529667 1.640000e-130 477.0
34 TraesCS1D01G275900 chr5D 83.978 181 24 5 3691 3870 263282865 263283041 1.120000e-37 169.0
35 TraesCS1D01G275900 chr7D 96.980 298 8 1 1 298 173113543 173113247 3.500000e-137 499.0
36 TraesCS1D01G275900 chr7D 92.638 326 19 5 291 613 173113203 173112880 1.280000e-126 464.0
37 TraesCS1D01G275900 chr3A 94.410 322 14 3 294 612 1971813 1971493 5.860000e-135 492.0
38 TraesCS1D01G275900 chr3A 95.302 298 13 1 1 298 1972157 1971861 7.630000e-129 472.0
39 TraesCS1D01G275900 chr3A 95.302 298 13 1 1 298 6344909 6344613 7.630000e-129 472.0
40 TraesCS1D01G275900 chr6B 95.973 298 11 1 1 298 1778120 1778416 3.530000e-132 483.0
41 TraesCS1D01G275900 chr6B 84.571 175 22 5 4863 5035 231369762 231369591 1.120000e-37 169.0
42 TraesCS1D01G275900 chr3B 93.417 319 18 3 291 607 273112 273429 2.750000e-128 470.0
43 TraesCS1D01G275900 chr3B 80.556 108 19 2 5388 5495 515214561 515214666 1.500000e-11 82.4
44 TraesCS1D01G275900 chr3B 80.734 109 17 4 5388 5495 515474813 515474918 1.500000e-11 82.4
45 TraesCS1D01G275900 chr3B 80.734 109 17 4 5388 5495 515999789 515999894 1.500000e-11 82.4
46 TraesCS1D01G275900 chr3B 80.734 109 17 4 5388 5495 516472794 516472899 1.500000e-11 82.4
47 TraesCS1D01G275900 chr3B 80.734 109 17 4 5388 5495 518914413 518914308 1.500000e-11 82.4
48 TraesCS1D01G275900 chr7A 94.966 298 14 1 1 298 641972100 641971804 3.550000e-127 466.0
49 TraesCS1D01G275900 chr6D 92.879 323 20 2 291 611 186840912 186841233 3.550000e-127 466.0
50 TraesCS1D01G275900 chr6A 90.459 283 26 1 3790 4072 614766547 614766266 7.970000e-99 372.0
51 TraesCS1D01G275900 chr6A 85.635 181 22 4 4862 5041 112758000 112757823 3.100000e-43 187.0
52 TraesCS1D01G275900 chr6A 85.556 180 23 3 3694 3872 112757823 112758000 1.110000e-42 185.0
53 TraesCS1D01G275900 chr6A 82.486 177 27 4 4858 5033 112759218 112759391 1.130000e-32 152.0
54 TraesCS1D01G275900 chr2D 84.946 186 25 3 3698 3882 398210788 398210605 1.110000e-42 185.0
55 TraesCS1D01G275900 chr2D 79.781 183 30 7 4858 5037 398210610 398210788 6.850000e-25 126.0
56 TraesCS1D01G275900 chr4B 82.584 178 24 7 4858 5033 662399152 662398980 4.060000e-32 150.0


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 TraesCS1D01G275900 chr1D 371750859 371757363 6504 True 12013.000000 12013 100.000000 1 6505 1 chr1D.!!$R1 6504
1 TraesCS1D01G275900 chr1D 371752321 371753672 1351 False 202.000000 202 86.559000 3692 5043 2 chr1D.!!$F2 1351
2 TraesCS1D01G275900 chr1B 496562351 496568251 5900 True 8634.000000 8634 93.199000 621 6505 1 chr1B.!!$R1 5884
3 TraesCS1D01G275900 chr1A 471489444 471494383 4939 True 1023.833333 3147 90.766333 802 6505 6 chr1A.!!$R2 5703
4 TraesCS1D01G275900 chr4A 592755925 592756736 811 False 948.000000 948 87.728000 1001 1820 1 chr4A.!!$F3 819
5 TraesCS1D01G275900 chr4A 592477118 592477929 811 False 942.000000 942 87.606000 1001 1820 1 chr4A.!!$F2 819
6 TraesCS1D01G275900 chr4A 593044005 593044816 811 False 937.000000 937 87.485000 1001 1820 1 chr4A.!!$F4 819
7 TraesCS1D01G275900 chr4A 591565341 591566157 816 True 922.000000 922 87.046000 1001 1823 1 chr4A.!!$R1 822
8 TraesCS1D01G275900 chr4A 15490073 15490678 605 False 520.000000 520 82.419000 1 611 1 chr4A.!!$F1 610
9 TraesCS1D01G275900 chrUn 332730711 332731522 811 False 937.000000 937 87.485000 1001 1820 1 chrUn.!!$F2 819
10 TraesCS1D01G275900 chr3D 575278592 575279282 690 True 852.000000 852 88.905000 1124 1823 1 chr3D.!!$R2 699
11 TraesCS1D01G275900 chr3D 37552874 37553540 666 False 465.500000 472 93.816500 1 612 2 chr3D.!!$F3 611
12 TraesCS1D01G275900 chr5D 112834620 112835308 688 True 811.000000 811 87.909000 1124 1823 1 chr5D.!!$R1 699
13 TraesCS1D01G275900 chr5D 107529667 107530328 661 True 482.500000 488 94.914000 1 611 2 chr5D.!!$R2 610
14 TraesCS1D01G275900 chr7D 173112880 173113543 663 True 481.500000 499 94.809000 1 613 2 chr7D.!!$R1 612
15 TraesCS1D01G275900 chr3A 1971493 1972157 664 True 482.000000 492 94.856000 1 612 2 chr3A.!!$R2 611

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
543 613 0.461548 CGAGTTATGCAGAGGCTGGA 59.538 55.0 0.00 0.00 41.91 3.86 F
1291 1373 0.468226 TTGCGACCAATAGGCTAGGG 59.532 55.0 12.16 12.16 39.06 3.53 F
2734 2888 0.173481 GCTCGACAGTGCACCTATGA 59.827 55.0 14.63 6.25 36.90 2.15 F
4027 4346 0.039911 ACCTCCAGCGTCTACTTCCT 59.960 55.0 0.00 0.00 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2243 2396 0.040514 TCGGTGCATGAAGTTTTGCG 60.041 50.0 0.00 0.0 41.80 4.85 R
2799 2953 0.942962 GCAATCTGGATGCTCCTTCG 59.057 55.0 4.21 0.0 40.64 3.79 R
4085 4404 0.259356 AGAGAAGGGAGGGGTAGTCG 59.741 60.0 0.00 0.0 0.00 4.18 R
5665 6932 0.179018 GTGGGCAAACCTCTGTCTGT 60.179 55.0 0.00 0.0 41.11 3.41 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
75 76 3.216292 GGCACCAAGGCGTGTGTT 61.216 61.111 0.00 0.00 36.08 3.32
180 181 5.049828 GCTTCAAATTTATACCCACCATGC 58.950 41.667 0.00 0.00 0.00 4.06
235 236 8.966868 TGAGGGGTATTGATAAACAAATTTCTC 58.033 33.333 0.00 0.00 42.03 2.87
299 353 7.612065 TGTAGCTTACCAGGAATGTATGTAT 57.388 36.000 0.00 0.00 0.00 2.29
518 588 0.605319 CGGTTGGCTTCTTGGCTGTA 60.605 55.000 0.00 0.00 42.34 2.74
543 613 0.461548 CGAGTTATGCAGAGGCTGGA 59.538 55.000 0.00 0.00 41.91 3.86
548 618 3.019564 GTTATGCAGAGGCTGGACATTT 58.980 45.455 0.00 0.00 41.91 2.32
571 641 7.624360 TTTTTAGATGCGATTGTATCACCTT 57.376 32.000 12.93 0.00 39.43 3.50
607 677 9.865321 ATTCAATGAAATGTCCTGTATCAAAAG 57.135 29.630 0.00 0.00 0.00 2.27
612 682 9.696917 ATGAAATGTCCTGTATCAAAAGAAAAC 57.303 29.630 0.00 0.00 0.00 2.43
613 683 8.690884 TGAAATGTCCTGTATCAAAAGAAAACA 58.309 29.630 0.00 0.00 0.00 2.83
614 684 9.528018 GAAATGTCCTGTATCAAAAGAAAACAA 57.472 29.630 0.00 0.00 0.00 2.83
615 685 9.533253 AAATGTCCTGTATCAAAAGAAAACAAG 57.467 29.630 0.00 0.00 0.00 3.16
616 686 6.503524 TGTCCTGTATCAAAAGAAAACAAGC 58.496 36.000 0.00 0.00 0.00 4.01
617 687 5.625311 GTCCTGTATCAAAAGAAAACAAGCG 59.375 40.000 0.00 0.00 0.00 4.68
618 688 4.382754 CCTGTATCAAAAGAAAACAAGCGC 59.617 41.667 0.00 0.00 0.00 5.92
619 689 3.971871 TGTATCAAAAGAAAACAAGCGCG 59.028 39.130 0.00 0.00 0.00 6.86
620 690 2.553079 TCAAAAGAAAACAAGCGCGT 57.447 40.000 8.43 0.00 0.00 6.01
621 691 2.181205 TCAAAAGAAAACAAGCGCGTG 58.819 42.857 21.97 21.97 0.00 5.34
622 692 0.920664 AAAAGAAAACAAGCGCGTGC 59.079 45.000 23.44 14.39 43.24 5.34
623 693 0.869880 AAAGAAAACAAGCGCGTGCC 60.870 50.000 23.44 9.98 44.31 5.01
624 694 1.724582 AAGAAAACAAGCGCGTGCCT 61.725 50.000 23.44 12.04 44.31 4.75
625 695 2.010817 GAAAACAAGCGCGTGCCTG 61.011 57.895 23.44 18.28 44.31 4.85
626 696 2.387125 GAAAACAAGCGCGTGCCTGA 62.387 55.000 25.35 0.00 44.31 3.86
627 697 1.999071 AAAACAAGCGCGTGCCTGAA 61.999 50.000 25.35 0.00 44.31 3.02
628 698 1.795170 AAACAAGCGCGTGCCTGAAT 61.795 50.000 25.35 11.12 44.31 2.57
649 725 2.557924 TGTGAATCACATTGAAGGTGGC 59.442 45.455 12.63 1.36 39.62 5.01
656 732 2.606587 ATTGAAGGTGGCCGAGGCT 61.607 57.895 14.33 0.00 41.60 4.58
674 750 3.325753 GCTCAGCCCAGGTCAGGT 61.326 66.667 0.00 0.00 0.00 4.00
690 766 3.378427 GTCAGGTGCCTATTTTAAGCTGG 59.622 47.826 0.00 0.00 38.40 4.85
819 895 1.876416 CGCACGAAAGAGGAAAAGGGA 60.876 52.381 0.00 0.00 0.00 4.20
821 897 2.226674 GCACGAAAGAGGAAAAGGGAAG 59.773 50.000 0.00 0.00 0.00 3.46
826 902 1.000486 GAGGAAAAGGGAAGGGGGC 60.000 63.158 0.00 0.00 0.00 5.80
827 903 1.782608 AGGAAAAGGGAAGGGGGCA 60.783 57.895 0.00 0.00 0.00 5.36
861 937 2.687935 GCAACAGAAAACCAGTCCAGAA 59.312 45.455 0.00 0.00 0.00 3.02
1090 1172 1.079057 GACAGGTTCGGCTCCTTCC 60.079 63.158 0.00 0.00 32.37 3.46
1242 1324 1.361993 CGGAGCTCGGGAATCTCTG 59.638 63.158 13.25 0.00 34.75 3.35
1245 1327 1.002274 AGCTCGGGAATCTCTGGGT 59.998 57.895 0.00 0.00 0.00 4.51
1291 1373 0.468226 TTGCGACCAATAGGCTAGGG 59.532 55.000 12.16 12.16 39.06 3.53
1479 1582 2.483876 TCTGACAGAAAGCGAAACAGG 58.516 47.619 1.64 0.00 0.00 4.00
1585 1729 8.700973 AGGATTTCTCTTCATAAGTACCTCTTC 58.299 37.037 0.00 0.00 37.56 2.87
1589 1733 6.732487 TCTCTTCATAAGTACCTCTTCCTCA 58.268 40.000 0.00 0.00 37.56 3.86
1617 1763 6.698008 TTGAATATGCTTGTTGTATCCTGG 57.302 37.500 0.00 0.00 0.00 4.45
1630 1776 7.101054 TGTTGTATCCTGGAATTACTGTGTAC 58.899 38.462 0.00 0.00 0.00 2.90
1649 1795 3.048337 ACCGCACCGATCTAAAGAAAA 57.952 42.857 0.00 0.00 0.00 2.29
1651 1797 4.761975 ACCGCACCGATCTAAAGAAAATA 58.238 39.130 0.00 0.00 0.00 1.40
1694 1845 6.989759 ACATTTTTCTTGTTATTGTCCCAACC 59.010 34.615 0.00 0.00 0.00 3.77
1717 1869 8.795842 ACCAACATGATATTTTAAGTACGGAA 57.204 30.769 0.00 0.00 0.00 4.30
1770 1922 2.237143 TGGTCTCTTCCAGTTAGCATGG 59.763 50.000 0.00 0.00 39.33 3.66
2147 2300 2.158971 TGCAGTTTGCTGACTGTACTCA 60.159 45.455 17.38 7.55 46.81 3.41
2243 2396 8.764524 AAGTTATACAAGATGACACTTCAGAC 57.235 34.615 0.00 0.00 34.35 3.51
2646 2800 1.687368 GGAGATGGGCTGGCATCTTTT 60.687 52.381 14.07 0.00 38.18 2.27
2734 2888 0.173481 GCTCGACAGTGCACCTATGA 59.827 55.000 14.63 6.25 36.90 2.15
2799 2953 8.674263 AACTCAGATATTCAGGAAATGATGTC 57.326 34.615 0.00 0.00 37.89 3.06
3003 3157 5.337894 CCATGAGAGCTTTACAAAGAGGAGA 60.338 44.000 5.89 0.00 38.28 3.71
3292 3446 1.479323 TCTACACGCTACAATCACCCC 59.521 52.381 0.00 0.00 0.00 4.95
3797 4116 2.293856 ACCCCCTGATCTGTCCAATACT 60.294 50.000 0.00 0.00 0.00 2.12
3888 4207 2.722201 CCAGTAGGGCCCTGTCGTC 61.722 68.421 35.81 17.98 0.00 4.20
3902 4221 1.533033 TCGTCAGGTGAAGAGGGCA 60.533 57.895 0.00 0.00 0.00 5.36
3907 4226 4.785453 GGTGAAGAGGGCAGCCGG 62.785 72.222 5.00 0.00 0.00 6.13
3935 4254 3.214250 CTCATCCTCGGCCGCCTAC 62.214 68.421 23.51 0.00 0.00 3.18
4027 4346 0.039911 ACCTCCAGCGTCTACTTCCT 59.960 55.000 0.00 0.00 0.00 3.36
4043 4362 2.352805 CTGGCCACCAGTTCTCCC 59.647 66.667 0.00 0.00 45.82 4.30
4052 4371 1.006102 CAGTTCTCCCGTCGTGCTT 60.006 57.895 0.00 0.00 0.00 3.91
4058 4377 0.458025 CTCCCGTCGTGCTTTCCTAC 60.458 60.000 0.00 0.00 0.00 3.18
4083 4402 2.888863 CTCTCCAGTCGGCACTCC 59.111 66.667 0.00 0.00 0.00 3.85
4085 4404 2.219325 CTCTCCAGTCGGCACTCCAC 62.219 65.000 0.00 0.00 0.00 4.02
4105 4424 1.751382 CGACTACCCCTCCCTTCTCTC 60.751 61.905 0.00 0.00 0.00 3.20
4108 4427 0.858598 TACCCCTCCCTTCTCTCCCA 60.859 60.000 0.00 0.00 0.00 4.37
4110 4429 2.069430 CCCTCCCTTCTCTCCCAGC 61.069 68.421 0.00 0.00 0.00 4.85
4148 4468 2.814023 CTCTAGACGAGGCCACCAT 58.186 57.895 5.01 0.00 36.06 3.55
4194 4514 1.079127 ACGCTGCCACCATAGACAC 60.079 57.895 0.00 0.00 0.00 3.67
4306 4626 2.048503 ACGCTTCACCGCTACCAC 60.049 61.111 0.00 0.00 0.00 4.16
4340 4660 2.124736 ACAACAGTGTGCGCCTGT 60.125 55.556 11.41 11.41 44.80 4.00
4457 5018 1.376037 GGAGTCAAACTGCCTCCGG 60.376 63.158 0.00 0.00 35.79 5.14
4474 5035 2.267324 GTGCTCCACAGCCTCCTC 59.733 66.667 0.00 0.00 46.26 3.71
4489 5050 1.961277 CCTCCAAAGTTCACGCGCT 60.961 57.895 5.73 0.00 0.00 5.92
4572 5133 1.043673 CCAGTCCGCTAGCCTAGGTT 61.044 60.000 11.31 7.07 0.00 3.50
4630 5191 1.871772 CTGGCTTGCTCGTTCCTTG 59.128 57.895 0.00 0.00 0.00 3.61
4686 5247 4.269523 ACTGGCGTGCACCACCAT 62.270 61.111 22.71 12.52 35.33 3.55
4692 5253 3.376078 GTGCACCACCATGCTGGG 61.376 66.667 11.77 3.20 46.28 4.45
4797 5358 1.685765 TGTGGCCGGCTGATAGAGT 60.686 57.895 28.56 0.00 0.00 3.24
4839 5400 7.598493 GCTTTTCTGTAAAATTAATGCCACAGA 59.402 33.333 16.47 16.47 40.30 3.41
4842 5403 7.615582 TCTGTAAAATTAATGCCACAGAGAG 57.384 36.000 16.47 0.94 37.93 3.20
4845 5406 9.113838 CTGTAAAATTAATGCCACAGAGAGTAT 57.886 33.333 14.14 0.00 36.37 2.12
4849 5410 3.550437 AATGCCACAGAGAGTATGTCC 57.450 47.619 0.00 0.00 0.00 4.02
4912 5805 1.342174 CAGCAAACCACCTGAGCAAAT 59.658 47.619 0.00 0.00 0.00 2.32
4919 5813 1.617804 CCACCTGAGCAAATCACCCAT 60.618 52.381 0.00 0.00 33.22 4.00
5118 6016 2.113986 GCACCCTGTGAAGGCTGT 59.886 61.111 0.00 0.00 35.23 4.40
5150 6396 1.227943 GTGGGCAAGCTCACAGACA 60.228 57.895 19.53 0.00 46.10 3.41
5160 6406 2.050077 CACAGACACGCGCTCTCA 60.050 61.111 5.73 0.00 0.00 3.27
5244 6491 6.500041 GTTCTTTTGTAGGCAACACACATTA 58.500 36.000 0.00 0.00 38.00 1.90
5324 6575 4.570772 ACGTATATTGTTGCCAGCTGTTAG 59.429 41.667 13.81 0.00 0.00 2.34
5380 6631 2.607631 TACATAACCTAACGGGCAGC 57.392 50.000 0.00 0.00 39.10 5.25
5388 6639 1.338769 CCTAACGGGCAGCAGTTAGTT 60.339 52.381 25.61 13.73 44.87 2.24
5418 6669 5.220931 CCTGCATCAAACCAAGCTAGTATTC 60.221 44.000 0.00 0.00 0.00 1.75
5440 6691 8.954834 ATTCTCCATAAGATGTATCTCTCTGT 57.045 34.615 0.00 0.00 35.76 3.41
5445 6696 7.026562 CCATAAGATGTATCTCTCTGTAAGCG 58.973 42.308 0.00 0.00 35.76 4.68
5448 6699 4.517453 AGATGTATCTCTCTGTAAGCGTCC 59.483 45.833 0.00 0.00 29.30 4.79
5544 6795 4.947388 TGTATCTAATTTTGGTCCCTGTGC 59.053 41.667 0.00 0.00 0.00 4.57
5558 6809 2.164219 CCCTGTGCATGTAACAATCACC 59.836 50.000 0.00 0.00 0.00 4.02
5567 6834 6.183360 TGCATGTAACAATCACCGTTATGTAC 60.183 38.462 0.00 0.00 31.85 2.90
5661 6928 1.748329 TAGGCTTCTGATCGCGGCAT 61.748 55.000 6.13 0.00 0.00 4.40
5664 6931 1.930100 CTTCTGATCGCGGCATGAC 59.070 57.895 6.13 0.00 0.00 3.06
5665 6932 0.807275 CTTCTGATCGCGGCATGACA 60.807 55.000 6.13 0.00 0.00 3.58
5682 6949 0.179018 ACACAGACAGAGGTTTGCCC 60.179 55.000 0.00 0.00 32.60 5.36
5726 6993 4.329545 GTTGGCTCCTCGGTGGCA 62.330 66.667 9.80 9.80 41.24 4.92
5733 7000 4.838152 CCTCGGTGGCATGACCCG 62.838 72.222 19.15 19.15 43.03 5.28
5745 7012 3.083997 GACCCGGCACCAGAGGAT 61.084 66.667 0.00 0.00 0.00 3.24
5779 7046 3.438360 CCGCTAATTGTCATTTTCTGGC 58.562 45.455 0.00 0.00 0.00 4.85
5939 7206 1.267732 CGAACGGAGCTGATTCATTGC 60.268 52.381 0.00 0.00 0.00 3.56
5940 7207 2.012673 GAACGGAGCTGATTCATTGCT 58.987 47.619 0.00 0.37 40.02 3.91
5945 7214 5.555017 ACGGAGCTGATTCATTGCTATATT 58.445 37.500 0.00 0.00 37.16 1.28
5987 7258 6.354130 TGCCTCTACCTGGTGATTAAATAAC 58.646 40.000 10.23 0.00 0.00 1.89
6050 7333 1.067821 TGTTTTGCGTGATTTGACCCC 59.932 47.619 0.00 0.00 0.00 4.95
6075 7380 2.580815 CCTGATGTGCGGCTCTGA 59.419 61.111 0.00 0.00 0.00 3.27
6076 7381 1.812922 CCTGATGTGCGGCTCTGAC 60.813 63.158 0.00 0.00 0.00 3.51
6077 7382 1.217511 CTGATGTGCGGCTCTGACT 59.782 57.895 0.00 0.00 0.00 3.41
6078 7383 1.079612 TGATGTGCGGCTCTGACTG 60.080 57.895 0.00 0.00 0.00 3.51
6106 7418 1.334869 CCGCTTTGAGTTTGTCTGCTT 59.665 47.619 0.00 0.00 0.00 3.91
6119 7431 0.606130 TCTGCTTGATGCGCCTTTGA 60.606 50.000 4.18 0.00 46.63 2.69
6145 7457 1.950758 TTTTTAGTGGAACCGGCGC 59.049 52.632 0.00 0.00 37.80 6.53
6284 7611 4.916249 CGTGAACTAAACTACTCCAGTGAC 59.084 45.833 0.00 0.00 37.63 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 2.948979 AGACTCGTCATGTTGGCAAAAA 59.051 40.909 0.00 0.00 0.00 1.94
140 141 3.263170 TGAAGCTACTTGAACTATGGCCA 59.737 43.478 8.56 8.56 0.00 5.36
180 181 1.390123 CCGAACATGTTACGAGCACTG 59.610 52.381 23.18 8.76 0.00 3.66
278 279 5.308825 GCATACATACATTCCTGGTAAGCT 58.691 41.667 0.00 0.00 0.00 3.74
299 353 1.153647 CAAGTACGGAGCCATCGCA 60.154 57.895 0.00 0.00 37.52 5.10
408 464 1.153369 CGGAGATCACACCGCCATT 60.153 57.895 11.69 0.00 42.39 3.16
427 483 5.432680 CCTATGATGTGGCAGATCCTATT 57.567 43.478 20.51 6.88 35.26 1.73
548 618 6.821160 TCAAGGTGATACAATCGCATCTAAAA 59.179 34.615 3.16 0.00 41.46 1.52
598 668 3.972502 ACGCGCTTGTTTTCTTTTGATAC 59.027 39.130 5.73 0.00 0.00 2.24
607 677 2.010817 CAGGCACGCGCTTGTTTTC 61.011 57.895 15.84 3.54 40.23 2.29
611 681 2.669569 ATTCAGGCACGCGCTTGT 60.670 55.556 15.84 0.00 45.11 3.16
612 682 2.202388 CATTCAGGCACGCGCTTG 60.202 61.111 9.92 9.92 46.18 4.01
613 683 2.669569 ACATTCAGGCACGCGCTT 60.670 55.556 5.73 0.00 38.60 4.68
614 684 3.425713 CACATTCAGGCACGCGCT 61.426 61.111 5.73 0.00 38.60 5.92
615 685 2.257286 ATTCACATTCAGGCACGCGC 62.257 55.000 5.73 0.00 37.44 6.86
616 686 0.247814 GATTCACATTCAGGCACGCG 60.248 55.000 3.53 3.53 0.00 6.01
617 687 0.804364 TGATTCACATTCAGGCACGC 59.196 50.000 0.00 0.00 0.00 5.34
618 688 1.805943 TGTGATTCACATTCAGGCACG 59.194 47.619 15.41 0.00 39.62 5.34
640 710 4.020617 CAGCCTCGGCCACCTTCA 62.021 66.667 2.24 0.00 43.17 3.02
656 732 3.324930 CCTGACCTGGGCTGAGCA 61.325 66.667 6.82 0.00 0.00 4.26
663 739 0.625849 AAATAGGCACCTGACCTGGG 59.374 55.000 0.00 0.00 38.26 4.45
664 740 2.514458 AAAATAGGCACCTGACCTGG 57.486 50.000 0.00 0.00 38.26 4.45
665 741 3.378427 GCTTAAAATAGGCACCTGACCTG 59.622 47.826 0.00 0.00 38.26 4.00
666 742 3.267031 AGCTTAAAATAGGCACCTGACCT 59.733 43.478 0.00 0.00 41.57 3.85
667 743 3.378427 CAGCTTAAAATAGGCACCTGACC 59.622 47.826 0.00 0.00 32.53 4.02
668 744 3.378427 CCAGCTTAAAATAGGCACCTGAC 59.622 47.826 0.00 0.00 32.53 3.51
669 745 3.265737 TCCAGCTTAAAATAGGCACCTGA 59.734 43.478 0.00 0.00 32.53 3.86
670 746 3.620488 TCCAGCTTAAAATAGGCACCTG 58.380 45.455 0.00 0.00 32.53 4.00
674 750 4.700213 GTCAGTTCCAGCTTAAAATAGGCA 59.300 41.667 0.00 0.00 32.53 4.75
690 766 4.415501 CTGCGTGCGCGTCAGTTC 62.416 66.667 25.62 10.01 45.51 3.01
819 895 3.665971 CCTCCTGCTTGCCCCCTT 61.666 66.667 0.00 0.00 0.00 3.95
821 897 3.661648 TTCCTCCTGCTTGCCCCC 61.662 66.667 0.00 0.00 0.00 5.40
826 902 1.165907 TGTTGCGTTCCTCCTGCTTG 61.166 55.000 0.00 0.00 0.00 4.01
827 903 0.886490 CTGTTGCGTTCCTCCTGCTT 60.886 55.000 0.00 0.00 0.00 3.91
861 937 0.251165 CCGGTTGGTGGATTTCTGGT 60.251 55.000 0.00 0.00 0.00 4.00
1090 1172 0.818296 ATCACGAAAGGAGACGGAGG 59.182 55.000 0.00 0.00 0.00 4.30
1186 1268 1.376812 AGAACCCGCACCGAATTCC 60.377 57.895 0.00 0.00 0.00 3.01
1242 1324 1.270550 CAGGCAGAAACAATCACACCC 59.729 52.381 0.00 0.00 0.00 4.61
1245 1327 2.655090 TCCAGGCAGAAACAATCACA 57.345 45.000 0.00 0.00 0.00 3.58
1291 1373 3.073678 GGGAATTCACCAAAAACATGGC 58.926 45.455 7.93 0.00 44.75 4.40
1460 1555 2.213499 ACCTGTTTCGCTTTCTGTCAG 58.787 47.619 0.00 0.00 0.00 3.51
1479 1582 5.445540 GCTAGTTCGTACCACATTAGCAAAC 60.446 44.000 5.79 0.00 33.92 2.93
1580 1684 9.894783 CAAGCATATTCAATTATTGAGGAAGAG 57.105 33.333 7.72 0.11 41.38 2.85
1596 1740 6.942532 TTCCAGGATACAACAAGCATATTC 57.057 37.500 0.00 0.00 41.41 1.75
1597 1741 7.902920 AATTCCAGGATACAACAAGCATATT 57.097 32.000 0.00 0.00 41.41 1.28
1630 1776 5.728351 TTATTTTCTTTAGATCGGTGCGG 57.272 39.130 0.00 0.00 0.00 5.69
1686 1837 7.836842 ACTTAAAATATCATGTTGGTTGGGAC 58.163 34.615 0.00 0.00 0.00 4.46
1755 1907 1.065199 TGCTCCCATGCTAACTGGAAG 60.065 52.381 0.00 0.00 42.29 3.46
1770 1922 0.817229 GTAGGATTGCCAGCTGCTCC 60.817 60.000 8.66 11.08 42.00 4.70
1890 2042 2.128771 AGCTTGGTGTGTTTCTGTGT 57.871 45.000 0.00 0.00 0.00 3.72
2147 2300 6.244654 CAACCCACCCAAAATTAAATCCAAT 58.755 36.000 0.00 0.00 0.00 3.16
2243 2396 0.040514 TCGGTGCATGAAGTTTTGCG 60.041 50.000 0.00 0.00 41.80 4.85
2646 2800 2.942804 TGATTGTTGCCACCAGAAAGA 58.057 42.857 0.00 0.00 0.00 2.52
2671 2825 6.332735 TGTATCAGTGGAGTAGTATGCATC 57.667 41.667 0.19 0.00 0.00 3.91
2799 2953 0.942962 GCAATCTGGATGCTCCTTCG 59.057 55.000 4.21 0.00 40.64 3.79
2813 2967 2.483877 TCTCCACGTGAACATTGCAATC 59.516 45.455 19.30 0.00 0.00 2.67
3003 3157 6.944862 AGCTATCAACAACTTCTCCATCTTTT 59.055 34.615 0.00 0.00 0.00 2.27
3113 3267 9.692749 GAAACGATGTCTGGATTGTAATATAGA 57.307 33.333 0.00 0.00 0.00 1.98
3134 3288 5.806286 TCAAAGAACTAACAAGCTGAAACG 58.194 37.500 0.00 0.00 0.00 3.60
3292 3446 5.591099 AGTGATGTTGCTACAAAAAGTTGG 58.409 37.500 4.79 0.00 39.22 3.77
3386 3540 5.049167 GTCGATTGATCTGAAGCTCTGAAT 58.951 41.667 0.00 0.00 0.00 2.57
3393 3547 4.629200 GGATATGGTCGATTGATCTGAAGC 59.371 45.833 0.00 0.00 0.00 3.86
3797 4116 7.663043 ACCAACCCAAGACTATTTTTAAACA 57.337 32.000 0.00 0.00 0.00 2.83
3888 4207 2.045536 GGCTGCCCTCTTCACCTG 60.046 66.667 7.66 0.00 0.00 4.00
3907 4226 1.067250 GAGGATGAGGACTGAGCGC 59.933 63.158 0.00 0.00 0.00 5.92
4027 4346 3.636231 CGGGAGAACTGGTGGCCA 61.636 66.667 0.00 0.00 0.00 5.36
4042 4361 3.763319 CGTAGGAAAGCACGACGG 58.237 61.111 0.00 0.00 40.56 4.79
4078 4397 1.321074 GGAGGGGTAGTCGTGGAGTG 61.321 65.000 0.00 0.00 0.00 3.51
4083 4402 0.324460 AGAAGGGAGGGGTAGTCGTG 60.324 60.000 0.00 0.00 0.00 4.35
4085 4404 0.259356 AGAGAAGGGAGGGGTAGTCG 59.741 60.000 0.00 0.00 0.00 4.18
4110 4429 3.917760 GAGCCTCGTCCCCATCGG 61.918 72.222 0.00 0.00 0.00 4.18
4194 4514 4.148825 CGGGGAGCTCCGGACTTG 62.149 72.222 26.36 8.25 45.78 3.16
4228 4548 2.336088 CGGTTGGTGCTTTGCAGG 59.664 61.111 0.00 0.00 40.08 4.85
4252 4572 1.451567 CCTGCAGAGGCTCACATGG 60.452 63.158 17.39 12.83 41.91 3.66
4324 4644 2.328989 CACAGGCGCACACTGTTG 59.671 61.111 14.11 7.44 46.38 3.33
4474 5035 1.132640 GCTAGCGCGTGAACTTTGG 59.867 57.895 8.43 0.00 0.00 3.28
4630 5191 1.606606 CGCTGCAATTTTCTTCCGAC 58.393 50.000 0.00 0.00 0.00 4.79
4686 5247 2.203480 GCAGTTTGGTCCCCAGCA 60.203 61.111 0.00 0.00 33.81 4.41
4797 5358 5.476945 CAGAAAAGCCCCTAAAAGCTAGAAA 59.523 40.000 0.00 0.00 38.74 2.52
4839 5400 2.891580 AGTGTTGACGTGGACATACTCT 59.108 45.455 0.00 0.00 0.00 3.24
4842 5403 2.066262 CCAGTGTTGACGTGGACATAC 58.934 52.381 0.00 0.00 32.60 2.39
4845 5406 0.179094 GACCAGTGTTGACGTGGACA 60.179 55.000 0.00 0.00 35.17 4.02
4849 5410 1.364721 TGTTGACCAGTGTTGACGTG 58.635 50.000 0.00 0.00 0.00 4.49
4912 5805 5.046159 ACCGTTCAGAAATAGTTATGGGTGA 60.046 40.000 0.00 0.00 0.00 4.02
4919 5813 6.698008 TCCGATACCGTTCAGAAATAGTTA 57.302 37.500 0.00 0.00 0.00 2.24
5050 5948 5.005779 GTGCTAATGTCTATTGGTCGAGTTG 59.994 44.000 0.00 0.00 0.00 3.16
5118 6016 1.228831 CCCACCCATGTTTGAGGCA 60.229 57.895 0.00 0.00 0.00 4.75
5124 6022 1.152269 AGCTTGCCCACCCATGTTT 60.152 52.632 0.00 0.00 0.00 2.83
5150 6396 2.483441 ACATAGAGTGAGAGCGCGT 58.517 52.632 8.43 0.00 0.00 6.01
5244 6491 2.998670 CGATCAACAGTCTGTGAGCAAT 59.001 45.455 6.18 0.00 0.00 3.56
5380 6631 6.801539 TTGATGCAGGTAAAGAACTAACTG 57.198 37.500 0.00 0.00 39.26 3.16
5388 6639 3.255642 GCTTGGTTTGATGCAGGTAAAGA 59.744 43.478 0.00 0.00 0.00 2.52
5418 6669 8.243426 GCTTACAGAGAGATACATCTTATGGAG 58.757 40.741 0.00 0.00 37.25 3.86
5439 6690 3.004839 TCATATCAGCTGAGGACGCTTAC 59.995 47.826 22.96 0.00 35.07 2.34
5440 6691 3.222603 TCATATCAGCTGAGGACGCTTA 58.777 45.455 22.96 7.97 35.07 3.09
5445 6696 4.626042 ACGAAATCATATCAGCTGAGGAC 58.374 43.478 22.96 7.10 0.00 3.85
5448 6699 4.625028 TGGACGAAATCATATCAGCTGAG 58.375 43.478 22.96 8.88 0.00 3.35
5567 6834 1.608966 CGCAGCGGCTGATACATACG 61.609 60.000 32.72 19.85 38.10 3.06
5661 6928 1.475034 GGCAAACCTCTGTCTGTGTCA 60.475 52.381 0.00 0.00 0.00 3.58
5664 6931 0.179020 TGGGCAAACCTCTGTCTGTG 60.179 55.000 0.00 0.00 41.11 3.66
5665 6932 0.179018 GTGGGCAAACCTCTGTCTGT 60.179 55.000 0.00 0.00 41.11 3.41
5682 6949 1.476074 ATCAACTGCGCAAAAACGTG 58.524 45.000 13.05 0.00 34.88 4.49
5726 6993 3.402681 CCTCTGGTGCCGGGTCAT 61.403 66.667 2.18 0.00 0.00 3.06
5745 7012 1.480789 TTAGCGGGAGTATCACAGCA 58.519 50.000 0.00 0.00 39.81 4.41
5939 7206 7.254590 GCAGGCAGTTTACAACTCAGAATATAG 60.255 40.741 0.00 0.00 40.46 1.31
5940 7207 6.538742 GCAGGCAGTTTACAACTCAGAATATA 59.461 38.462 0.00 0.00 40.46 0.86
5945 7214 2.494059 GCAGGCAGTTTACAACTCAGA 58.506 47.619 0.00 0.00 40.46 3.27
5987 7258 5.041287 CACCATGAGCAAAGCAGATTTATG 58.959 41.667 0.00 0.00 0.00 1.90
6050 7333 1.224075 CCGCACATCAGGCTTGATAG 58.776 55.000 11.43 8.37 42.12 2.08
6075 7380 1.738099 CAAAGCGGACTAGCGCAGT 60.738 57.895 11.47 11.48 43.00 4.40
6076 7381 1.416813 CTCAAAGCGGACTAGCGCAG 61.417 60.000 11.47 7.81 43.00 5.18
6077 7382 1.446099 CTCAAAGCGGACTAGCGCA 60.446 57.895 11.47 0.00 43.00 6.09
6078 7383 1.014564 AACTCAAAGCGGACTAGCGC 61.015 55.000 0.00 0.00 43.00 5.92
6106 7418 1.065199 AGGAGAATCAAAGGCGCATCA 60.065 47.619 10.83 0.00 36.25 3.07
6284 7611 3.984633 GCTTCTTATTTCGAGAGGGATCG 59.015 47.826 0.00 0.00 44.07 3.69


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

AutoCloner maintained by Alex Coulton.