Multiple sequence alignment - TraesCS4A01G433900

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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 TraesCS4A01G433900 chr4A 100.000 5249 0 0 1 5249 704649094 704643846 0.000000e+00 9694.0
1 TraesCS4A01G433900 chr4A 95.647 1562 49 7 3696 5249 704629332 704627782 0.000000e+00 2490.0
2 TraesCS4A01G433900 chr4A 92.059 1020 58 8 3701 4712 704598249 704597245 0.000000e+00 1413.0
3 TraesCS4A01G433900 chr4A 91.839 1017 61 7 3704 4712 704578382 704577380 0.000000e+00 1399.0
4 TraesCS4A01G433900 chr4A 92.257 762 42 4 4031 4788 704576388 704575640 0.000000e+00 1064.0
5 TraesCS4A01G433900 chr4A 92.126 762 43 4 4031 4788 704596252 704595504 0.000000e+00 1059.0
6 TraesCS4A01G433900 chr4A 92.271 414 27 3 3704 4113 704581403 704580991 2.720000e-162 582.0
7 TraesCS4A01G433900 chr4A 80.491 815 104 30 2 782 704658052 704657259 1.640000e-159 573.0
8 TraesCS4A01G433900 chr4A 93.462 260 11 1 4996 5249 704575640 704575381 1.070000e-101 381.0
9 TraesCS4A01G433900 chr4A 93.462 260 11 1 4996 5249 704595504 704595245 1.070000e-101 381.0
10 TraesCS4A01G433900 chr4A 84.615 403 41 8 854 1238 704657131 704656732 1.070000e-101 381.0
11 TraesCS4A01G433900 chr4A 82.494 417 47 12 4156 4548 704620982 704620568 5.030000e-90 342.0
12 TraesCS4A01G433900 chr4A 85.401 137 20 0 1155 1291 710853715 710853579 5.480000e-30 143.0
13 TraesCS4A01G433900 chr4A 95.652 69 3 0 3596 3664 704578454 704578386 1.550000e-20 111.0
14 TraesCS4A01G433900 chr4A 94.203 69 4 0 3596 3664 704598319 704598251 7.190000e-19 106.0
15 TraesCS4A01G433900 chr7A 90.521 4009 285 55 840 4788 27282737 27278764 0.000000e+00 5210.0
16 TraesCS4A01G433900 chr7A 84.865 3079 322 65 1502 4517 27291300 27288303 0.000000e+00 2972.0
17 TraesCS4A01G433900 chr7A 87.437 398 40 7 963 1354 27291843 27291450 2.880000e-122 449.0
18 TraesCS4A01G433900 chr7A 94.510 255 13 1 4996 5249 27278738 27278484 4.930000e-105 392.0
19 TraesCS4A01G433900 chr7A 87.421 318 40 0 3348 3665 27244031 27243714 2.990000e-97 366.0
20 TraesCS4A01G433900 chr7A 78.466 339 44 17 1003 1340 27233959 27233649 1.490000e-45 195.0
21 TraesCS4A01G433900 chr7A 92.857 70 1 1 4786 4855 632041135 632041070 1.200000e-16 99.0
22 TraesCS4A01G433900 chr7D 86.001 2993 312 53 1563 4500 27096222 27093282 0.000000e+00 3107.0
23 TraesCS4A01G433900 chr7D 91.830 1934 116 20 2880 4788 26819628 26817712 0.000000e+00 2658.0
24 TraesCS4A01G433900 chr7D 91.645 1532 85 17 1452 2981 27049953 27048463 0.000000e+00 2080.0
25 TraesCS4A01G433900 chr7D 89.394 1452 109 13 1455 2888 26821144 26819720 0.000000e+00 1786.0
26 TraesCS4A01G433900 chr7D 92.979 1168 66 11 2788 3947 27048583 27047424 0.000000e+00 1688.0
27 TraesCS4A01G433900 chr7D 87.275 1391 123 27 12 1360 27051413 27050035 0.000000e+00 1539.0
28 TraesCS4A01G433900 chr7D 91.695 590 40 8 3965 4548 27047370 27046784 0.000000e+00 809.0
29 TraesCS4A01G433900 chr7D 82.389 812 104 25 4 781 26826698 26825892 0.000000e+00 671.0
30 TraesCS4A01G433900 chr7D 84.649 684 68 22 3896 4545 26833928 26833248 0.000000e+00 647.0
31 TraesCS4A01G433900 chr7D 90.787 445 30 8 921 1360 26821651 26821213 7.570000e-163 584.0
32 TraesCS4A01G433900 chr7D 82.542 590 69 18 3990 4548 27011606 27011020 6.110000e-134 488.0
33 TraesCS4A01G433900 chr7D 87.688 398 39 8 963 1353 27096865 27096471 6.200000e-124 455.0
34 TraesCS4A01G433900 chr7D 82.290 559 65 17 3990 4517 26977575 26977020 2.230000e-123 453.0
35 TraesCS4A01G433900 chr7D 85.755 351 47 2 3315 3665 26982394 26982047 8.300000e-98 368.0
36 TraesCS4A01G433900 chr7D 82.697 393 54 9 2019 2404 26983146 26982761 2.340000e-88 337.0
37 TraesCS4A01G433900 chr7D 93.836 146 7 2 4996 5141 26817712 26817569 8.850000e-53 219.0
38 TraesCS4A01G433900 chr7D 78.679 333 42 14 1009 1340 26792381 26792077 1.490000e-45 195.0
39 TraesCS4A01G433900 chr7D 80.913 241 34 10 3983 4219 268835845 268836077 4.180000e-41 180.0
40 TraesCS4A01G433900 chr7D 94.382 89 5 0 5161 5249 26812798 26812710 2.550000e-28 137.0
41 TraesCS4A01G433900 chr7D 97.143 70 2 0 3596 3665 26791690 26791621 9.230000e-23 119.0
42 TraesCS4A01G433900 chr7D 100.000 30 0 0 5215 5244 27046559 27046530 7.340000e-04 56.5
43 TraesCS4A01G433900 chrUn 84.740 616 72 13 1879 2483 296087788 296088392 9.730000e-167 597.0
44 TraesCS4A01G433900 chrUn 84.740 616 72 13 1879 2483 296092890 296093494 9.730000e-167 597.0
45 TraesCS4A01G433900 chrUn 84.740 616 72 13 1879 2483 352685284 352685888 9.730000e-167 597.0
46 TraesCS4A01G433900 chrUn 81.682 333 47 8 75 406 274859787 274859468 1.120000e-66 265.0
47 TraesCS4A01G433900 chrUn 81.682 333 47 8 75 406 296089848 296090167 1.120000e-66 265.0
48 TraesCS4A01G433900 chrUn 81.682 333 47 8 75 406 296094950 296095269 1.120000e-66 265.0
49 TraesCS4A01G433900 chr3D 85.167 209 17 6 4787 4995 568491558 568491364 8.910000e-48 202.0
50 TraesCS4A01G433900 chr3D 85.526 152 20 1 4570 4719 479626912 479627063 1.960000e-34 158.0
51 TraesCS4A01G433900 chr3D 93.182 44 3 0 5173 5216 423392167 423392210 1.220000e-06 65.8
52 TraesCS4A01G433900 chr3B 84.360 211 16 10 4786 4995 612304262 612304456 1.930000e-44 191.0
53 TraesCS4A01G433900 chr3B 82.648 219 13 9 4787 5004 605479423 605479229 2.510000e-38 171.0
54 TraesCS4A01G433900 chr3B 78.404 213 14 18 4784 4995 732054848 732054667 5.560000e-20 110.0
55 TraesCS4A01G433900 chr4D 86.928 153 18 1 4569 4719 75266757 75266909 2.510000e-38 171.0
56 TraesCS4A01G433900 chr1B 83.422 187 18 7 4819 5004 199680238 199680064 1.510000e-35 161.0
57 TraesCS4A01G433900 chr3A 83.951 162 24 2 4569 4730 522178324 522178483 2.530000e-33 154.0
58 TraesCS4A01G433900 chr3A 87.500 96 12 0 4884 4979 145265199 145265294 1.550000e-20 111.0
59 TraesCS4A01G433900 chr2D 92.079 101 6 2 4895 4995 598268752 598268654 1.970000e-29 141.0
60 TraesCS4A01G433900 chr2D 83.333 150 17 7 4841 4983 180530220 180530072 1.190000e-26 132.0
61 TraesCS4A01G433900 chr5A 92.135 89 7 0 4890 4978 380231653 380231565 5.520000e-25 126.0
62 TraesCS4A01G433900 chr7B 78.673 211 19 14 4787 4995 44770760 44770574 3.320000e-22 117.0
63 TraesCS4A01G433900 chr6B 90.909 77 2 2 4787 4863 542942018 542942089 1.200000e-16 99.0
64 TraesCS4A01G433900 chr6B 92.857 70 1 1 4786 4855 706024572 706024637 1.200000e-16 99.0
65 TraesCS4A01G433900 chr6B 92.857 70 1 1 4786 4855 706025364 706025429 1.200000e-16 99.0
66 TraesCS4A01G433900 chr6B 92.857 70 1 1 4786 4855 706230512 706230577 1.200000e-16 99.0
67 TraesCS4A01G433900 chr6B 91.304 46 2 2 5172 5216 655769016 655769060 1.580000e-05 62.1
68 TraesCS4A01G433900 chr6B 91.304 46 2 2 5172 5216 655850563 655850607 1.580000e-05 62.1
69 TraesCS4A01G433900 chr5B 92.857 70 1 2 4786 4855 704603934 704603869 1.200000e-16 99.0
70 TraesCS4A01G433900 chr2A 92.857 42 3 0 5176 5217 567733339 567733380 1.580000e-05 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G433900 chr4A 704643846 704649094 5248 True 9694.00 9694 100.00000 1 5249 1 chr4A.!!$R3 5248
1 TraesCS4A01G433900 chr4A 704627782 704629332 1550 True 2490.00 2490 95.64700 3696 5249 1 chr4A.!!$R2 1553
2 TraesCS4A01G433900 chr4A 704595245 704598319 3074 True 739.75 1413 92.96250 3596 5249 4 chr4A.!!$R6 1653
3 TraesCS4A01G433900 chr4A 704575381 704581403 6022 True 707.40 1399 93.09620 3596 5249 5 chr4A.!!$R5 1653
4 TraesCS4A01G433900 chr4A 704656732 704658052 1320 True 477.00 573 82.55300 2 1238 2 chr4A.!!$R7 1236
5 TraesCS4A01G433900 chr7A 27278484 27282737 4253 True 2801.00 5210 92.51550 840 5249 2 chr7A.!!$R4 4409
6 TraesCS4A01G433900 chr7A 27288303 27291843 3540 True 1710.50 2972 86.15100 963 4517 2 chr7A.!!$R5 3554
7 TraesCS4A01G433900 chr7D 27093282 27096865 3583 True 1781.00 3107 86.84450 963 4500 2 chr7D.!!$R10 3537
8 TraesCS4A01G433900 chr7D 26817569 26821651 4082 True 1311.75 2658 91.46175 921 5141 4 chr7D.!!$R7 4220
9 TraesCS4A01G433900 chr7D 27046530 27051413 4883 True 1234.50 2080 92.71880 12 5244 5 chr7D.!!$R9 5232
10 TraesCS4A01G433900 chr7D 26825892 26826698 806 True 671.00 671 82.38900 4 781 1 chr7D.!!$R2 777
11 TraesCS4A01G433900 chr7D 26833248 26833928 680 True 647.00 647 84.64900 3896 4545 1 chr7D.!!$R3 649
12 TraesCS4A01G433900 chr7D 27011020 27011606 586 True 488.00 488 82.54200 3990 4548 1 chr7D.!!$R5 558
13 TraesCS4A01G433900 chr7D 26977020 26977575 555 True 453.00 453 82.29000 3990 4517 1 chr7D.!!$R4 527
14 TraesCS4A01G433900 chr7D 26982047 26983146 1099 True 352.50 368 84.22600 2019 3665 2 chr7D.!!$R8 1646
15 TraesCS4A01G433900 chrUn 352685284 352685888 604 False 597.00 597 84.74000 1879 2483 1 chrUn.!!$F1 604
16 TraesCS4A01G433900 chrUn 296087788 296095269 7481 False 431.00 597 83.21100 75 2483 4 chrUn.!!$F2 2408

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
527 731 0.250234 TCCTGGATTGAGAGTTGCGG 59.750 55.000 0.00 0.00 0.00 5.69 F
1548 2353 0.384669 ATTAGCTCAGTACCGTCGCC 59.615 55.000 0.00 0.00 0.00 5.54 F
1566 2375 0.589729 CCGGCGAAGAAATGCGAATG 60.590 55.000 9.30 0.00 0.00 2.67 F
2825 6681 1.067974 TCTTATGCTGCAATGCCATGC 59.932 47.619 6.36 5.39 46.58 4.06 F
3185 7231 1.246737 CCTTGCTTGCCCTGTTCCTC 61.247 60.000 0.00 0.00 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2430 6273 0.109597 GGGCTCATGCTTGTTTGTCG 60.110 55.000 0.00 0.00 39.59 4.35 R
2446 6290 2.057137 TAATGGTGATTCTGCTGGGC 57.943 50.000 0.00 0.00 0.00 5.36 R
3555 7641 0.179097 GCCCGGTTTGAGCAAAAACA 60.179 50.000 14.05 0.00 41.00 2.83 R
4090 8229 1.553248 ACACTACTAGGCCATGCGAAA 59.447 47.619 5.01 0.00 0.00 3.46 R
4873 12438 0.448990 ACAGCAATGCACGCACTATG 59.551 50.000 8.35 4.43 0.00 2.23 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
38 46 5.246307 AGGTTTAAGAGGTATGAGTTGCAC 58.754 41.667 0.00 0.00 0.00 4.57
83 92 6.551601 AGCCTAACTAACTGTAGTGCTCATAT 59.448 38.462 0.00 0.00 39.79 1.78
95 104 7.658261 TGTAGTGCTCATATGTTATGTACCTC 58.342 38.462 1.90 0.55 0.00 3.85
130 139 9.034544 ACTTGCTACATGTTTTCATTTCTTTTC 57.965 29.630 2.30 0.00 38.64 2.29
253 292 4.572389 AGAATGCAGCTTTTATCTACCACG 59.428 41.667 0.00 0.00 0.00 4.94
328 532 7.839705 TGTAGATATTAGAGGAAACTGACCAGT 59.160 37.037 0.00 0.00 44.43 4.00
345 549 2.646930 CAGTTCATATGCTGCCTTCCA 58.353 47.619 0.00 0.00 0.00 3.53
461 665 5.657745 TGTCAAGGGTTCGTATCAATACCTA 59.342 40.000 0.00 0.00 0.00 3.08
492 696 6.885922 AGTTAATTAACAGGCTTCTCCGTAT 58.114 36.000 26.06 1.87 38.62 3.06
527 731 0.250234 TCCTGGATTGAGAGTTGCGG 59.750 55.000 0.00 0.00 0.00 5.69
542 746 2.042831 GCGGTCCAGCTTGCTCAAT 61.043 57.895 0.00 0.00 0.00 2.57
547 751 1.214589 CCAGCTTGCTCAATGTGGC 59.785 57.895 0.00 0.00 0.00 5.01
557 765 3.118775 TGCTCAATGTGGCGTAGTAAGAT 60.119 43.478 0.00 0.00 0.00 2.40
628 836 4.463186 AGACTTAGCCTTCTCGCTAGAAAA 59.537 41.667 1.98 0.00 42.15 2.29
667 885 1.611491 GTCGGGCAAAAGAATCAACCA 59.389 47.619 0.00 0.00 0.00 3.67
670 888 2.607771 CGGGCAAAAGAATCAACCAGTG 60.608 50.000 0.00 0.00 0.00 3.66
671 889 2.407090 GGCAAAAGAATCAACCAGTGC 58.593 47.619 0.00 0.00 0.00 4.40
682 925 1.064505 CAACCAGTGCAGTGTCAACAG 59.935 52.381 19.93 6.26 0.00 3.16
687 930 1.417517 AGTGCAGTGTCAACAGGATGA 59.582 47.619 0.00 0.00 39.69 2.92
837 1081 6.396829 AGGTTCACTTGGAGAAAGAAAATG 57.603 37.500 0.00 0.00 39.38 2.32
852 1547 8.989980 AGAAAGAAAATGTAGTACAGTACAAGC 58.010 33.333 13.37 3.32 36.51 4.01
854 1549 7.891183 AGAAAATGTAGTACAGTACAAGCAG 57.109 36.000 13.37 0.00 36.51 4.24
855 1550 6.874134 AGAAAATGTAGTACAGTACAAGCAGG 59.126 38.462 13.37 0.00 36.51 4.85
856 1551 3.587797 TGTAGTACAGTACAAGCAGGC 57.412 47.619 13.37 0.00 29.74 4.85
865 1560 0.970937 TACAAGCAGGCGAGCTACCT 60.971 55.000 7.88 1.80 45.89 3.08
874 1575 0.592754 GCGAGCTACCTACTGAAGCG 60.593 60.000 0.00 0.00 41.19 4.68
883 1584 1.634702 CTACTGAAGCGAGTGGAAGC 58.365 55.000 0.00 0.00 0.00 3.86
919 1624 1.892819 TTCTCCCCTTCGAGCAGCTG 61.893 60.000 10.11 10.11 0.00 4.24
926 1635 0.865218 CTTCGAGCAGCTGAGCTACG 60.865 60.000 20.43 13.60 46.75 3.51
1354 2108 5.098211 GGCTTGTAAGATGCAAATCTGTTC 58.902 41.667 0.00 0.00 0.00 3.18
1360 2127 6.821160 TGTAAGATGCAAATCTGTTCCGATTA 59.179 34.615 0.00 0.00 33.47 1.75
1363 2130 6.115446 AGATGCAAATCTGTTCCGATTAAGA 58.885 36.000 0.00 0.00 33.47 2.10
1395 2199 3.920231 ATCTGTCCAAATGAGCTGCTA 57.080 42.857 0.15 0.00 0.00 3.49
1428 2233 7.954906 GCAATTAGCAATGTGTAGTTACTTC 57.045 36.000 0.00 0.00 44.79 3.01
1438 2243 9.083080 CAATGTGTAGTTACTTCGATGTCAATA 57.917 33.333 7.29 0.00 0.00 1.90
1439 2244 9.647797 AATGTGTAGTTACTTCGATGTCAATAA 57.352 29.630 7.29 0.00 0.00 1.40
1440 2245 9.817809 ATGTGTAGTTACTTCGATGTCAATAAT 57.182 29.630 7.29 0.00 0.00 1.28
1441 2246 9.647797 TGTGTAGTTACTTCGATGTCAATAATT 57.352 29.630 7.29 0.00 0.00 1.40
1449 2254 8.783999 ACTTCGATGTCAATAATTAGTACTCG 57.216 34.615 0.00 0.00 0.00 4.18
1450 2255 8.404000 ACTTCGATGTCAATAATTAGTACTCGT 58.596 33.333 0.00 0.00 0.00 4.18
1465 2270 6.428385 AGTACTCGTAGTAATTAGCAACGT 57.572 37.500 11.66 0.00 31.62 3.99
1466 2271 6.253746 AGTACTCGTAGTAATTAGCAACGTG 58.746 40.000 11.66 11.62 31.62 4.49
1494 2299 8.730680 AGTTACTTTGGTGTCAATAATTAGCAG 58.269 33.333 0.00 0.00 32.28 4.24
1495 2300 8.512138 GTTACTTTGGTGTCAATAATTAGCAGT 58.488 33.333 0.00 0.00 32.28 4.40
1496 2301 6.913170 ACTTTGGTGTCAATAATTAGCAGTG 58.087 36.000 0.00 0.00 32.28 3.66
1498 2303 3.694072 TGGTGTCAATAATTAGCAGTGCC 59.306 43.478 12.58 0.00 0.00 5.01
1499 2304 3.947834 GGTGTCAATAATTAGCAGTGCCT 59.052 43.478 12.58 1.64 0.00 4.75
1500 2305 4.201950 GGTGTCAATAATTAGCAGTGCCTG 60.202 45.833 12.58 0.00 34.12 4.85
1501 2306 3.947196 TGTCAATAATTAGCAGTGCCTGG 59.053 43.478 12.58 0.00 31.21 4.45
1502 2307 3.947834 GTCAATAATTAGCAGTGCCTGGT 59.052 43.478 12.58 10.92 44.66 4.00
1503 2308 4.399303 GTCAATAATTAGCAGTGCCTGGTT 59.601 41.667 12.58 4.74 42.44 3.67
1504 2309 5.588648 GTCAATAATTAGCAGTGCCTGGTTA 59.411 40.000 12.58 6.88 42.44 2.85
1505 2310 6.094881 GTCAATAATTAGCAGTGCCTGGTTAA 59.905 38.462 12.58 3.73 42.44 2.01
1506 2311 6.833416 TCAATAATTAGCAGTGCCTGGTTAAT 59.167 34.615 12.58 6.12 42.44 1.40
1507 2312 7.341769 TCAATAATTAGCAGTGCCTGGTTAATT 59.658 33.333 12.58 16.15 42.44 1.40
1508 2313 7.660030 ATAATTAGCAGTGCCTGGTTAATTT 57.340 32.000 18.74 8.82 42.44 1.82
1510 2315 1.895131 AGCAGTGCCTGGTTAATTTGG 59.105 47.619 12.58 0.00 39.27 3.28
1511 2316 1.618343 GCAGTGCCTGGTTAATTTGGT 59.382 47.619 2.85 0.00 31.21 3.67
1514 2319 2.890945 AGTGCCTGGTTAATTTGGTGTC 59.109 45.455 0.00 0.00 0.00 3.67
1515 2320 2.625790 GTGCCTGGTTAATTTGGTGTCA 59.374 45.455 0.00 0.00 0.00 3.58
1516 2321 2.890311 TGCCTGGTTAATTTGGTGTCAG 59.110 45.455 0.00 0.00 0.00 3.51
1517 2322 2.890945 GCCTGGTTAATTTGGTGTCAGT 59.109 45.455 0.00 0.00 0.00 3.41
1518 2323 3.305335 GCCTGGTTAATTTGGTGTCAGTG 60.305 47.826 0.00 0.00 0.00 3.66
1520 2325 4.766891 CCTGGTTAATTTGGTGTCAGTGAT 59.233 41.667 0.00 0.00 0.00 3.06
1521 2326 5.106157 CCTGGTTAATTTGGTGTCAGTGATC 60.106 44.000 0.00 0.00 0.00 2.92
1539 2344 2.380084 TCCGCGAAAATTAGCTCAGT 57.620 45.000 8.23 0.00 0.00 3.41
1548 2353 0.384669 ATTAGCTCAGTACCGTCGCC 59.615 55.000 0.00 0.00 0.00 5.54
1549 2354 1.985447 TTAGCTCAGTACCGTCGCCG 61.985 60.000 0.00 0.00 0.00 6.46
1566 2375 0.589729 CCGGCGAAGAAATGCGAATG 60.590 55.000 9.30 0.00 0.00 2.67
1577 2386 4.098501 AGAAATGCGAATGGGAAATTCCTC 59.901 41.667 12.28 0.84 36.57 3.71
1644 2504 5.422214 AGTGGTCGGTTTCTCATTTCTAT 57.578 39.130 0.00 0.00 0.00 1.98
1903 5723 2.928116 CCGTCGACCAGAAAAACCTATC 59.072 50.000 10.58 0.00 0.00 2.08
1988 5809 6.263842 TGAGAAAAATGATGGTCCTGCATATC 59.736 38.462 0.00 0.00 0.00 1.63
2404 6246 9.899226 GCTACCATTTCCAATTTTACATATCTC 57.101 33.333 0.00 0.00 0.00 2.75
2446 6290 3.607422 TGTTCGACAAACAAGCATGAG 57.393 42.857 0.00 0.00 44.83 2.90
2486 6338 9.193133 CCATTAACTAATACTCACTATGTTCCG 57.807 37.037 0.00 0.00 0.00 4.30
2664 6519 8.028540 TGTACTGTTGTGAATGTTGATGTATC 57.971 34.615 0.00 0.00 0.00 2.24
2778 6633 3.766591 TGAACTTCTTGTTTCCTGGCAAA 59.233 39.130 0.00 0.00 39.30 3.68
2825 6681 1.067974 TCTTATGCTGCAATGCCATGC 59.932 47.619 6.36 5.39 46.58 4.06
2900 6858 3.358707 TCTCTGCTGCAATGTGTTTTG 57.641 42.857 3.02 0.00 0.00 2.44
3174 7220 7.601856 TCATTTATTTTACCAGACCTTGCTTG 58.398 34.615 0.00 0.00 0.00 4.01
3185 7231 1.246737 CCTTGCTTGCCCTGTTCCTC 61.247 60.000 0.00 0.00 0.00 3.71
3329 7414 8.356657 AGTATAGACTATGTTCAGAAGCACATC 58.643 37.037 5.17 0.00 33.62 3.06
3407 7493 8.684386 TGTTTGACTTAAGTATGATGGTTCAA 57.316 30.769 8.42 2.42 34.96 2.69
3656 7743 1.689273 GAGATCTGGGCATACGAGGTT 59.311 52.381 0.00 0.00 0.00 3.50
3669 7756 6.018669 GGCATACGAGGTTTAATTCTTCTCTG 60.019 42.308 0.00 0.00 0.00 3.35
3670 7757 6.757010 GCATACGAGGTTTAATTCTTCTCTGA 59.243 38.462 0.00 0.00 0.00 3.27
3675 7762 5.196695 AGGTTTAATTCTTCTCTGATGCCC 58.803 41.667 0.00 0.00 0.00 5.36
3730 7818 1.373748 CCCGTGTGGTACCAGTTCG 60.374 63.158 16.93 18.77 0.00 3.95
3741 7829 2.751166 ACCAGTTCGAGAACCTGATG 57.249 50.000 11.87 4.55 42.06 3.07
3855 7943 6.978343 ATTCGATATTGGAAACTTCACGAA 57.022 33.333 0.00 0.00 40.40 3.85
3857 7945 6.788684 TCGATATTGGAAACTTCACGAAAA 57.211 33.333 0.00 0.00 0.00 2.29
3893 7982 7.385267 AGAAGCTAAATACTCAGCCATCATAG 58.615 38.462 0.00 0.00 38.61 2.23
3947 8041 7.677276 GCAGTATCTTGTTGACACAATACATCC 60.677 40.741 13.35 3.25 42.21 3.51
3978 8112 8.138712 AGCGTCAAACATTGGAATTAACTTTTA 58.861 29.630 0.00 0.00 0.00 1.52
4090 8229 2.031120 TGCTGTTGCTAAACCTTTGCT 58.969 42.857 0.00 0.00 40.48 3.91
4566 10427 8.771286 AGGTAGTATTCCCTCCGTTTTTAAATA 58.229 33.333 0.00 0.00 0.00 1.40
4567 10428 9.565090 GGTAGTATTCCCTCCGTTTTTAAATAT 57.435 33.333 0.00 0.00 0.00 1.28
4569 10430 8.374327 AGTATTCCCTCCGTTTTTAAATATCG 57.626 34.615 0.00 0.00 0.00 2.92
4570 10431 7.989170 AGTATTCCCTCCGTTTTTAAATATCGT 59.011 33.333 0.00 0.00 0.00 3.73
4571 10432 7.634671 ATTCCCTCCGTTTTTAAATATCGTT 57.365 32.000 0.00 0.00 0.00 3.85
4572 10433 7.451501 TTCCCTCCGTTTTTAAATATCGTTT 57.548 32.000 0.00 0.00 0.00 3.60
4573 10434 7.451501 TCCCTCCGTTTTTAAATATCGTTTT 57.548 32.000 0.00 0.00 0.00 2.43
4574 10435 7.884257 TCCCTCCGTTTTTAAATATCGTTTTT 58.116 30.769 0.00 0.00 0.00 1.94
4575 10436 9.007901 TCCCTCCGTTTTTAAATATCGTTTTTA 57.992 29.630 0.00 0.00 0.00 1.52
4576 10437 9.623350 CCCTCCGTTTTTAAATATCGTTTTTAA 57.377 29.630 0.00 0.00 0.00 1.52
4667 10541 3.820689 TGACACATTTTGCTTCGTATGC 58.179 40.909 0.00 0.00 0.00 3.14
4679 10553 4.693095 TGCTTCGTATGCAGTTTGTATTGA 59.307 37.500 0.00 0.00 35.31 2.57
4766 12305 9.712305 TTTGGAGAGAGAAACTAGAAATACTTG 57.288 33.333 0.00 0.00 0.00 3.16
4828 12393 2.040544 GTGCATGCGCCCAACTAGT 61.041 57.895 20.70 0.00 37.32 2.57
4871 12436 7.653713 CCTTTTATTCATCTATGAGTAGTGCGT 59.346 37.037 0.00 0.00 38.19 5.24
4872 12437 7.930513 TTTATTCATCTATGAGTAGTGCGTG 57.069 36.000 0.00 0.00 38.19 5.34
4873 12438 3.355626 TCATCTATGAGTAGTGCGTGC 57.644 47.619 0.00 0.00 32.11 5.34
4874 12439 2.687935 TCATCTATGAGTAGTGCGTGCA 59.312 45.455 0.00 0.00 32.11 4.57
4875 12440 3.319122 TCATCTATGAGTAGTGCGTGCAT 59.681 43.478 0.00 0.00 32.11 3.96
4876 12441 4.518970 TCATCTATGAGTAGTGCGTGCATA 59.481 41.667 0.00 0.00 32.11 3.14
4877 12442 4.489679 TCTATGAGTAGTGCGTGCATAG 57.510 45.455 0.00 0.00 39.63 2.23
4878 12443 3.883489 TCTATGAGTAGTGCGTGCATAGT 59.117 43.478 0.00 0.00 39.41 2.12
4879 12444 2.278026 TGAGTAGTGCGTGCATAGTG 57.722 50.000 0.00 0.00 0.00 2.74
4880 12445 0.924090 GAGTAGTGCGTGCATAGTGC 59.076 55.000 0.00 0.00 45.29 4.40
4918 12483 1.415200 GAGCGAAGGGATAAGGTCCT 58.585 55.000 0.00 0.00 46.91 3.85
5098 12664 8.080417 GCAATACTCGAGTCCAACATTATACTA 58.920 37.037 23.89 0.00 0.00 1.82
5154 12971 6.682537 ACAAATAATTAGGGGGTGACATGAT 58.317 36.000 0.00 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 3.307762 GGAAGGTGCAACTCATACCTCTT 60.308 47.826 3.77 0.00 43.75 2.85
83 92 7.654568 CAAGTATGATACCGAGGTACATAACA 58.345 38.462 17.70 9.78 32.33 2.41
95 104 6.844696 AAACATGTAGCAAGTATGATACCG 57.155 37.500 0.00 0.00 45.63 4.02
130 139 3.305335 GCCTAACACACCAAGAAACATGG 60.305 47.826 0.00 0.00 43.84 3.66
176 185 5.048782 GTGGATCTTGCAAACATCAACTACA 60.049 40.000 16.27 5.56 0.00 2.74
253 292 8.722394 GTTTTACCCTAGCTTAATAGATGATGC 58.278 37.037 0.00 0.00 0.00 3.91
328 532 3.225104 GGAATGGAAGGCAGCATATGAA 58.775 45.455 6.97 0.00 0.00 2.57
335 539 0.743097 GTCATGGAATGGAAGGCAGC 59.257 55.000 0.00 0.00 46.73 5.25
338 542 2.425143 TGAGTCATGGAATGGAAGGC 57.575 50.000 0.00 0.00 46.73 4.35
345 549 6.946583 CCCATTGAAGATATGAGTCATGGAAT 59.053 38.462 16.15 0.98 0.00 3.01
461 665 9.914131 GAGAAGCCTGTTAATTAACTCAATTTT 57.086 29.630 24.81 13.58 37.93 1.82
527 731 0.524862 CCACATTGAGCAAGCTGGAC 59.475 55.000 0.00 0.00 0.00 4.02
542 746 3.257375 ACTTGTCATCTTACTACGCCACA 59.743 43.478 0.00 0.00 0.00 4.17
547 751 5.570344 ACATCGACTTGTCATCTTACTACG 58.430 41.667 0.00 0.00 0.00 3.51
557 765 5.008331 AGTCCTTAGTACATCGACTTGTCA 58.992 41.667 0.00 0.00 29.59 3.58
607 815 4.803098 TTTTCTAGCGAGAAGGCTAAGT 57.197 40.909 9.31 0.00 44.36 2.24
659 877 2.346766 TGACACTGCACTGGTTGATT 57.653 45.000 0.00 0.00 0.00 2.57
667 885 1.417517 TCATCCTGTTGACACTGCACT 59.582 47.619 0.00 0.00 0.00 4.40
670 888 0.801251 GCTCATCCTGTTGACACTGC 59.199 55.000 0.00 0.00 0.00 4.40
671 889 1.802960 GTGCTCATCCTGTTGACACTG 59.197 52.381 0.00 0.00 31.13 3.66
687 930 4.646492 GGGAAAGGATGAATACATTGTGCT 59.354 41.667 0.00 0.00 36.82 4.40
745 989 8.339714 TCAAAAACAAAATATCTCGACGAACTT 58.660 29.630 0.00 0.00 0.00 2.66
802 1046 9.362151 TCTCCAAGTGAACCTTTTATTTAACAT 57.638 29.630 0.00 0.00 0.00 2.71
819 1063 8.378172 TGTACTACATTTTCTTTCTCCAAGTG 57.622 34.615 0.00 0.00 33.66 3.16
837 1081 2.163010 TCGCCTGCTTGTACTGTACTAC 59.837 50.000 17.98 8.55 0.00 2.73
852 1547 1.066303 CTTCAGTAGGTAGCTCGCCTG 59.934 57.143 17.27 3.84 37.54 4.85
854 1549 0.249114 GCTTCAGTAGGTAGCTCGCC 60.249 60.000 0.00 0.00 32.26 5.54
855 1550 0.592754 CGCTTCAGTAGGTAGCTCGC 60.593 60.000 0.00 0.00 32.80 5.03
856 1551 1.003331 CTCGCTTCAGTAGGTAGCTCG 60.003 57.143 0.00 0.00 32.80 5.03
865 1560 1.202582 GAGCTTCCACTCGCTTCAGTA 59.797 52.381 0.00 0.00 36.45 2.74
874 1575 1.216710 CCTCCACGAGCTTCCACTC 59.783 63.158 0.00 0.00 0.00 3.51
883 1584 4.381411 GGAGAAAAATATCCCTCCACGAG 58.619 47.826 0.00 0.00 43.47 4.18
907 1608 0.865218 CGTAGCTCAGCTGCTCGAAG 60.865 60.000 10.31 1.35 42.97 3.79
1354 2108 3.328382 TCCACTGTGGTTCTTAATCGG 57.672 47.619 25.15 0.00 39.03 4.18
1405 2209 7.959733 TCGAAGTAACTACACATTGCTAATTG 58.040 34.615 0.00 0.00 0.00 2.32
1438 2243 9.443283 CGTTGCTAATTACTACGAGTACTAATT 57.557 33.333 0.00 0.00 38.29 1.40
1439 2244 8.616076 ACGTTGCTAATTACTACGAGTACTAAT 58.384 33.333 19.70 0.00 38.29 1.73
1440 2245 7.904977 CACGTTGCTAATTACTACGAGTACTAA 59.095 37.037 19.70 0.00 38.29 2.24
1441 2246 7.064609 ACACGTTGCTAATTACTACGAGTACTA 59.935 37.037 19.70 0.00 37.99 1.82
1443 2248 6.024049 ACACGTTGCTAATTACTACGAGTAC 58.976 40.000 19.70 0.00 37.99 2.73
1445 2250 5.051891 ACACGTTGCTAATTACTACGAGT 57.948 39.130 19.70 16.62 38.29 4.18
1448 2253 6.859715 AACTACACGTTGCTAATTACTACG 57.140 37.500 14.87 14.87 41.09 3.51
1449 2254 8.902040 AGTAACTACACGTTGCTAATTACTAC 57.098 34.615 0.00 0.00 45.12 2.73
1450 2255 9.912634 AAAGTAACTACACGTTGCTAATTACTA 57.087 29.630 6.97 0.00 46.04 1.82
1463 2268 5.917541 ATTGACACCAAAGTAACTACACG 57.082 39.130 0.00 0.00 35.67 4.49
1466 2271 9.983804 GCTAATTATTGACACCAAAGTAACTAC 57.016 33.333 0.00 0.00 35.67 2.73
1494 2299 2.625790 TGACACCAAATTAACCAGGCAC 59.374 45.455 0.00 0.00 0.00 5.01
1495 2300 2.890311 CTGACACCAAATTAACCAGGCA 59.110 45.455 0.00 0.00 0.00 4.75
1496 2301 2.890945 ACTGACACCAAATTAACCAGGC 59.109 45.455 0.00 0.00 0.00 4.85
1498 2303 5.106157 GGATCACTGACACCAAATTAACCAG 60.106 44.000 0.00 0.00 0.00 4.00
1499 2304 4.764823 GGATCACTGACACCAAATTAACCA 59.235 41.667 0.00 0.00 0.00 3.67
1500 2305 4.142687 CGGATCACTGACACCAAATTAACC 60.143 45.833 0.00 0.00 0.00 2.85
1501 2306 4.671766 GCGGATCACTGACACCAAATTAAC 60.672 45.833 0.00 0.00 0.00 2.01
1502 2307 3.438781 GCGGATCACTGACACCAAATTAA 59.561 43.478 0.00 0.00 0.00 1.40
1503 2308 3.006940 GCGGATCACTGACACCAAATTA 58.993 45.455 0.00 0.00 0.00 1.40
1504 2309 1.812571 GCGGATCACTGACACCAAATT 59.187 47.619 0.00 0.00 0.00 1.82
1505 2310 1.453155 GCGGATCACTGACACCAAAT 58.547 50.000 0.00 0.00 0.00 2.32
1506 2311 0.948623 CGCGGATCACTGACACCAAA 60.949 55.000 0.00 0.00 0.00 3.28
1507 2312 1.374125 CGCGGATCACTGACACCAA 60.374 57.895 0.00 0.00 0.00 3.67
1508 2313 1.811645 TTCGCGGATCACTGACACCA 61.812 55.000 6.13 0.00 0.00 4.17
1510 2315 1.144969 TTTTCGCGGATCACTGACAC 58.855 50.000 6.13 0.00 0.00 3.67
1511 2316 2.093306 ATTTTCGCGGATCACTGACA 57.907 45.000 6.13 0.00 0.00 3.58
1514 2319 2.609459 AGCTAATTTTCGCGGATCACTG 59.391 45.455 6.13 0.00 0.00 3.66
1515 2320 2.866762 GAGCTAATTTTCGCGGATCACT 59.133 45.455 6.13 0.00 0.00 3.41
1516 2321 2.607635 TGAGCTAATTTTCGCGGATCAC 59.392 45.455 6.13 0.00 0.00 3.06
1517 2322 2.866156 CTGAGCTAATTTTCGCGGATCA 59.134 45.455 6.13 1.14 0.00 2.92
1518 2323 2.866762 ACTGAGCTAATTTTCGCGGATC 59.133 45.455 6.13 0.00 0.00 3.36
1520 2325 2.380084 ACTGAGCTAATTTTCGCGGA 57.620 45.000 6.13 0.00 0.00 5.54
1521 2326 2.284417 GGTACTGAGCTAATTTTCGCGG 59.716 50.000 6.13 0.00 0.00 6.46
1548 2353 0.589729 CCATTCGCATTTCTTCGCCG 60.590 55.000 0.00 0.00 0.00 6.46
1549 2354 0.248621 CCCATTCGCATTTCTTCGCC 60.249 55.000 0.00 0.00 0.00 5.54
1903 5723 5.184340 ACCCTTCAAACTCGTATATCTCG 57.816 43.478 0.00 0.00 0.00 4.04
2037 5860 3.254166 GTGAAGCCAAGAATCAGAAGCAA 59.746 43.478 0.00 0.00 0.00 3.91
2430 6273 0.109597 GGGCTCATGCTTGTTTGTCG 60.110 55.000 0.00 0.00 39.59 4.35
2446 6290 2.057137 TAATGGTGATTCTGCTGGGC 57.943 50.000 0.00 0.00 0.00 5.36
2695 6550 8.834749 AAGTTCTATCTTTGTCCTAAGTCAAC 57.165 34.615 0.00 0.00 0.00 3.18
2735 6590 9.684702 AGTTCAGAAATATTAATACCCCCTCTA 57.315 33.333 0.00 0.00 0.00 2.43
2825 6681 7.478667 GTCTGCTTACTAATGAATGACAAAACG 59.521 37.037 0.00 0.00 0.00 3.60
2900 6858 5.175856 CGATGTCTGCTTACTAGTTAATGGC 59.824 44.000 0.00 0.00 0.00 4.40
2908 6935 2.427453 ACACCCGATGTCTGCTTACTAG 59.573 50.000 0.00 0.00 36.54 2.57
2986 7014 4.504858 AGGCAACATAGAAGAACTAACGG 58.495 43.478 0.00 0.00 41.41 4.44
3329 7414 5.817616 AGATCGCGTATAAATAAACGGTG 57.182 39.130 5.77 0.00 39.46 4.94
3358 7443 9.023962 ACAGTAACAAAATCATGAACATATGGT 57.976 29.630 7.80 0.00 0.00 3.55
3546 7632 4.589216 TTGAGCAAAAACATTCAGAGGG 57.411 40.909 0.00 0.00 0.00 4.30
3555 7641 0.179097 GCCCGGTTTGAGCAAAAACA 60.179 50.000 14.05 0.00 41.00 2.83
3656 7743 5.103982 TGGATGGGCATCAGAGAAGAATTAA 60.104 40.000 0.00 0.00 39.54 1.40
3675 7762 1.701292 TGACCCCAGATGCTATGGATG 59.299 52.381 4.25 0.00 40.51 3.51
3730 7818 2.983229 ACATGTGCTCATCAGGTTCTC 58.017 47.619 0.00 0.00 31.15 2.87
3741 7829 3.366679 CCCTGATGACAAAACATGTGCTC 60.367 47.826 0.00 0.00 44.12 4.26
3947 8041 4.481930 TTCCAATGTTTGACGCTACAAG 57.518 40.909 0.00 0.00 0.00 3.16
4090 8229 1.553248 ACACTACTAGGCCATGCGAAA 59.447 47.619 5.01 0.00 0.00 3.46
4294 8444 3.508840 CATTTGGGACTCGGCGGC 61.509 66.667 7.21 0.00 0.00 6.53
4647 10519 3.820689 TGCATACGAAGCAAAATGTGTC 58.179 40.909 0.00 0.00 39.39 3.67
4691 10565 7.564292 ACTCCCTTCGTTCCTAAATATAAGACT 59.436 37.037 0.00 0.00 0.00 3.24
4872 12437 0.864377 CAGCAATGCACGCACTATGC 60.864 55.000 8.35 14.85 43.68 3.14
4873 12438 0.448990 ACAGCAATGCACGCACTATG 59.551 50.000 8.35 4.43 0.00 2.23
4874 12439 1.935873 CTACAGCAATGCACGCACTAT 59.064 47.619 8.35 0.00 0.00 2.12
4875 12440 1.358877 CTACAGCAATGCACGCACTA 58.641 50.000 8.35 0.78 0.00 2.74
4876 12441 1.915614 GCTACAGCAATGCACGCACT 61.916 55.000 8.35 0.00 41.59 4.40
4877 12442 1.512734 GCTACAGCAATGCACGCAC 60.513 57.895 8.35 0.00 41.59 5.34
4878 12443 2.869646 GCTACAGCAATGCACGCA 59.130 55.556 8.35 0.00 41.59 5.24
4879 12444 2.276868 CGCTACAGCAATGCACGC 60.277 61.111 8.35 1.65 42.21 5.34
4880 12445 1.059369 GTCGCTACAGCAATGCACG 59.941 57.895 8.35 0.00 42.21 5.34
4881 12446 1.059369 CGTCGCTACAGCAATGCAC 59.941 57.895 8.35 0.00 42.21 4.57
4882 12447 1.078201 CTCGTCGCTACAGCAATGCA 61.078 55.000 8.35 0.00 42.21 3.96
4928 12493 1.482930 GGAGAGGAGAGGATGCTGGAT 60.483 57.143 0.00 0.00 0.00 3.41
4975 12540 3.389139 TAGGGATCTGCGGGCCTCA 62.389 63.158 0.84 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.