Multiple sequence alignment - TraesCS5A01G297100

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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 TraesCS5A01G297100 chr5A 100.000 2734 0 0 1 2734 504954243 504956976 0.000000e+00 5049.0
1 TraesCS5A01G297100 chr5A 82.970 505 42 20 163 664 323656268 323655805 1.510000e-112 416.0
2 TraesCS5A01G297100 chr5A 91.139 79 7 0 2 80 54741016 54741094 1.040000e-19 108.0
3 TraesCS5A01G297100 chr5B 89.652 1266 93 20 814 2059 479714841 479716088 0.000000e+00 1578.0
4 TraesCS5A01G297100 chr5B 84.957 698 59 19 2041 2723 479716134 479716800 0.000000e+00 665.0
5 TraesCS5A01G297100 chr5D 91.116 923 61 10 1150 2061 399327901 399328813 0.000000e+00 1230.0
6 TraesCS5A01G297100 chr5D 90.029 682 56 7 2041 2719 399328860 399329532 0.000000e+00 872.0
7 TraesCS5A01G297100 chr5D 90.951 652 42 8 129 769 399326184 399326829 0.000000e+00 861.0
8 TraesCS5A01G297100 chr5D 88.403 457 38 8 753 1197 399327446 399327899 1.110000e-148 536.0
9 TraesCS5A01G297100 chr3D 79.976 1633 199 63 954 2524 51686995 51685429 0.000000e+00 1086.0
10 TraesCS5A01G297100 chr3D 84.891 503 34 13 165 664 207987412 207987875 1.150000e-128 470.0
11 TraesCS5A01G297100 chr3B 80.102 1573 202 56 954 2478 82630096 82628587 0.000000e+00 1068.0
12 TraesCS5A01G297100 chr3B 83.022 589 58 14 164 749 156987353 156987902 1.890000e-136 496.0
13 TraesCS5A01G297100 chr3B 93.243 74 5 0 8 81 10555779 10555852 2.880000e-20 110.0
14 TraesCS5A01G297100 chr3A 78.965 1526 215 51 958 2436 64285563 64284097 0.000000e+00 942.0
15 TraesCS5A01G297100 chr3A 92.593 81 6 0 1 81 566881453 566881373 1.720000e-22 117.0
16 TraesCS5A01G297100 chr3A 95.349 43 2 0 39 81 563837517 563837475 4.890000e-08 69.4
17 TraesCS5A01G297100 chr1A 87.664 608 54 12 147 750 266130856 266131446 0.000000e+00 688.0
18 TraesCS5A01G297100 chrUn 84.915 590 47 17 164 750 53183167 53183717 2.380000e-155 558.0
19 TraesCS5A01G297100 chrUn 84.915 590 47 17 164 750 327985427 327984877 2.380000e-155 558.0
20 TraesCS5A01G297100 chr2B 84.550 589 47 18 166 750 325041479 325042027 6.660000e-151 544.0
21 TraesCS5A01G297100 chr2B 95.062 81 4 0 1 81 163373481 163373561 7.950000e-26 128.0
22 TraesCS5A01G297100 chr4B 83.756 591 53 14 164 750 211051803 211051252 1.120000e-143 520.0
23 TraesCS5A01G297100 chr2D 84.127 504 38 13 164 664 244998237 244997773 1.490000e-122 449.0
24 TraesCS5A01G297100 chr7D 90.968 310 27 1 164 473 515282509 515282817 1.510000e-112 416.0
25 TraesCS5A01G297100 chr7B 95.062 81 4 0 1 81 701044456 701044376 7.950000e-26 128.0
26 TraesCS5A01G297100 chr2A 94.203 69 4 0 12 80 181839051 181838983 3.720000e-19 106.0


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 TraesCS5A01G297100 chr5A 504954243 504956976 2733 False 5049.00 5049 100.00000 1 2734 1 chr5A.!!$F2 2733
1 TraesCS5A01G297100 chr5B 479714841 479716800 1959 False 1121.50 1578 87.30450 814 2723 2 chr5B.!!$F1 1909
2 TraesCS5A01G297100 chr5D 399326184 399329532 3348 False 874.75 1230 90.12475 129 2719 4 chr5D.!!$F1 2590
3 TraesCS5A01G297100 chr3D 51685429 51686995 1566 True 1086.00 1086 79.97600 954 2524 1 chr3D.!!$R1 1570
4 TraesCS5A01G297100 chr3B 82628587 82630096 1509 True 1068.00 1068 80.10200 954 2478 1 chr3B.!!$R1 1524
5 TraesCS5A01G297100 chr3B 156987353 156987902 549 False 496.00 496 83.02200 164 749 1 chr3B.!!$F2 585
6 TraesCS5A01G297100 chr3A 64284097 64285563 1466 True 942.00 942 78.96500 958 2436 1 chr3A.!!$R1 1478
7 TraesCS5A01G297100 chr1A 266130856 266131446 590 False 688.00 688 87.66400 147 750 1 chr1A.!!$F1 603
8 TraesCS5A01G297100 chrUn 53183167 53183717 550 False 558.00 558 84.91500 164 750 1 chrUn.!!$F1 586
9 TraesCS5A01G297100 chrUn 327984877 327985427 550 True 558.00 558 84.91500 164 750 1 chrUn.!!$R1 586
10 TraesCS5A01G297100 chr2B 325041479 325042027 548 False 544.00 544 84.55000 166 750 1 chr2B.!!$F2 584
11 TraesCS5A01G297100 chr4B 211051252 211051803 551 True 520.00 520 83.75600 164 750 1 chr4B.!!$R1 586

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
991 1652 0.673985 TAATGGCAGACGAGCGCTAT 59.326 50.0 11.5 0.0 34.64 2.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2099 2924 0.527113 TGGACAGCAAATTCCGCATG 59.473 50.0 2.97 0.0 34.24 4.06 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
25 26 7.768807 ATTGTTATAACCCAAAGTTACAGCA 57.231 32.000 13.01 0.00 43.66 4.41
26 27 7.584122 TTGTTATAACCCAAAGTTACAGCAA 57.416 32.000 13.01 0.00 43.66 3.91
27 28 7.209471 TGTTATAACCCAAAGTTACAGCAAG 57.791 36.000 13.01 0.00 43.66 4.01
28 29 6.773685 TGTTATAACCCAAAGTTACAGCAAGT 59.226 34.615 13.01 0.00 43.66 3.16
29 30 5.705609 ATAACCCAAAGTTACAGCAAGTG 57.294 39.130 0.00 0.00 43.66 3.16
30 31 1.681264 ACCCAAAGTTACAGCAAGTGC 59.319 47.619 0.00 0.00 42.49 4.40
31 32 4.191739 AACCCAAAGTTACAGCAAGTGCT 61.192 43.478 0.00 0.00 45.00 4.40
32 33 5.654831 AACCCAAAGTTACAGCAAGTGCTT 61.655 41.667 2.25 0.00 42.78 3.91
33 34 7.402959 AACCCAAAGTTACAGCAAGTGCTTC 62.403 44.000 2.25 0.00 42.78 3.86
42 43 2.025589 GCAAGTGCTTCTACCCTACC 57.974 55.000 0.00 0.00 38.21 3.18
43 44 1.555533 GCAAGTGCTTCTACCCTACCT 59.444 52.381 0.00 0.00 38.21 3.08
44 45 2.418884 GCAAGTGCTTCTACCCTACCTC 60.419 54.545 0.00 0.00 38.21 3.85
45 46 3.100671 CAAGTGCTTCTACCCTACCTCT 58.899 50.000 0.00 0.00 0.00 3.69
46 47 3.476485 AGTGCTTCTACCCTACCTCTT 57.524 47.619 0.00 0.00 0.00 2.85
47 48 3.792515 AGTGCTTCTACCCTACCTCTTT 58.207 45.455 0.00 0.00 0.00 2.52
48 49 3.770388 AGTGCTTCTACCCTACCTCTTTC 59.230 47.826 0.00 0.00 0.00 2.62
49 50 3.514309 GTGCTTCTACCCTACCTCTTTCA 59.486 47.826 0.00 0.00 0.00 2.69
50 51 4.020485 GTGCTTCTACCCTACCTCTTTCAA 60.020 45.833 0.00 0.00 0.00 2.69
51 52 4.783227 TGCTTCTACCCTACCTCTTTCAAT 59.217 41.667 0.00 0.00 0.00 2.57
52 53 5.104900 TGCTTCTACCCTACCTCTTTCAATC 60.105 44.000 0.00 0.00 0.00 2.67
53 54 5.129650 GCTTCTACCCTACCTCTTTCAATCT 59.870 44.000 0.00 0.00 0.00 2.40
54 55 6.546428 TTCTACCCTACCTCTTTCAATCTG 57.454 41.667 0.00 0.00 0.00 2.90
55 56 5.590818 TCTACCCTACCTCTTTCAATCTGT 58.409 41.667 0.00 0.00 0.00 3.41
56 57 4.559862 ACCCTACCTCTTTCAATCTGTG 57.440 45.455 0.00 0.00 0.00 3.66
57 58 3.910627 ACCCTACCTCTTTCAATCTGTGT 59.089 43.478 0.00 0.00 0.00 3.72
58 59 4.351111 ACCCTACCTCTTTCAATCTGTGTT 59.649 41.667 0.00 0.00 0.00 3.32
59 60 5.163088 ACCCTACCTCTTTCAATCTGTGTTT 60.163 40.000 0.00 0.00 0.00 2.83
60 61 5.412904 CCCTACCTCTTTCAATCTGTGTTTC 59.587 44.000 0.00 0.00 0.00 2.78
61 62 6.234177 CCTACCTCTTTCAATCTGTGTTTCT 58.766 40.000 0.00 0.00 0.00 2.52
62 63 7.386851 CCTACCTCTTTCAATCTGTGTTTCTA 58.613 38.462 0.00 0.00 0.00 2.10
63 64 7.332182 CCTACCTCTTTCAATCTGTGTTTCTAC 59.668 40.741 0.00 0.00 0.00 2.59
64 65 6.591935 ACCTCTTTCAATCTGTGTTTCTACA 58.408 36.000 0.00 0.00 0.00 2.74
65 66 7.054124 ACCTCTTTCAATCTGTGTTTCTACAA 58.946 34.615 0.00 0.00 35.69 2.41
66 67 7.721399 ACCTCTTTCAATCTGTGTTTCTACAAT 59.279 33.333 0.00 0.00 35.69 2.71
67 68 9.219603 CCTCTTTCAATCTGTGTTTCTACAATA 57.780 33.333 0.00 0.00 35.69 1.90
69 70 9.554395 TCTTTCAATCTGTGTTTCTACAATACA 57.446 29.630 0.00 0.00 35.69 2.29
70 71 9.817365 CTTTCAATCTGTGTTTCTACAATACAG 57.183 33.333 5.39 5.39 35.69 2.74
71 72 9.554395 TTTCAATCTGTGTTTCTACAATACAGA 57.446 29.630 14.21 14.21 38.50 3.41
72 73 8.763049 TCAATCTGTGTTTCTACAATACAGAG 57.237 34.615 16.20 7.13 37.93 3.35
73 74 8.585018 TCAATCTGTGTTTCTACAATACAGAGA 58.415 33.333 16.20 8.86 43.48 3.10
74 75 9.208022 CAATCTGTGTTTCTACAATACAGAGAA 57.792 33.333 16.20 0.00 42.87 2.87
75 76 9.950496 AATCTGTGTTTCTACAATACAGAGAAT 57.050 29.630 16.20 6.09 42.87 2.40
78 79 9.307121 CTGTGTTTCTACAATACAGAGAATAGG 57.693 37.037 5.76 0.00 35.79 2.57
79 80 8.258007 TGTGTTTCTACAATACAGAGAATAGGG 58.742 37.037 0.00 0.00 35.69 3.53
80 81 7.711339 GTGTTTCTACAATACAGAGAATAGGGG 59.289 40.741 0.00 0.00 35.69 4.79
81 82 6.420913 TTCTACAATACAGAGAATAGGGGC 57.579 41.667 0.00 0.00 0.00 5.80
82 83 5.716979 TCTACAATACAGAGAATAGGGGCT 58.283 41.667 0.00 0.00 0.00 5.19
83 84 4.965200 ACAATACAGAGAATAGGGGCTC 57.035 45.455 0.00 0.00 0.00 4.70
84 85 4.298626 ACAATACAGAGAATAGGGGCTCA 58.701 43.478 0.00 0.00 33.62 4.26
85 86 4.721776 ACAATACAGAGAATAGGGGCTCAA 59.278 41.667 0.00 0.00 33.62 3.02
86 87 5.370880 ACAATACAGAGAATAGGGGCTCAAT 59.629 40.000 0.00 0.00 33.62 2.57
87 88 5.753721 ATACAGAGAATAGGGGCTCAATC 57.246 43.478 0.00 0.00 33.62 2.67
88 89 2.708325 ACAGAGAATAGGGGCTCAATCC 59.292 50.000 0.00 0.00 33.62 3.01
89 90 1.974236 AGAGAATAGGGGCTCAATCCG 59.026 52.381 0.00 0.00 33.62 4.18
90 91 1.002544 GAGAATAGGGGCTCAATCCGG 59.997 57.143 0.00 0.00 0.00 5.14
91 92 1.056660 GAATAGGGGCTCAATCCGGA 58.943 55.000 6.61 6.61 0.00 5.14
92 93 0.765510 AATAGGGGCTCAATCCGGAC 59.234 55.000 6.12 0.00 0.00 4.79
93 94 1.472662 ATAGGGGCTCAATCCGGACG 61.473 60.000 6.12 0.00 0.00 4.79
94 95 2.577020 TAGGGGCTCAATCCGGACGA 62.577 60.000 6.12 5.64 0.00 4.20
95 96 2.202892 GGGCTCAATCCGGACGAC 60.203 66.667 6.12 0.00 0.00 4.34
96 97 2.722201 GGGCTCAATCCGGACGACT 61.722 63.158 6.12 0.00 0.00 4.18
97 98 1.227002 GGCTCAATCCGGACGACTC 60.227 63.158 6.12 0.00 0.00 3.36
98 99 1.227002 GCTCAATCCGGACGACTCC 60.227 63.158 6.12 0.00 0.00 3.85
140 141 3.281341 CTCAGATAGCATCCGTCTCAC 57.719 52.381 0.00 0.00 0.00 3.51
175 176 2.511145 GCGAGCAGAGCCCAGAAG 60.511 66.667 0.00 0.00 0.00 2.85
351 363 3.441290 AACCTCGGCTCCTCGTCG 61.441 66.667 0.00 0.00 43.46 5.12
492 504 4.148838 TCTTGGTTAACTTGGGTTGGATG 58.851 43.478 5.42 0.00 36.92 3.51
547 559 3.563390 GCCTCTGATGGAATTAGTGCTTC 59.437 47.826 0.00 0.00 30.89 3.86
578 591 4.152284 TCTCGATCTGGTTGTAGCTAGA 57.848 45.455 0.00 0.00 0.00 2.43
581 594 2.294791 CGATCTGGTTGTAGCTAGAGGG 59.705 54.545 0.00 0.00 0.00 4.30
588 601 4.021916 GGTTGTAGCTAGAGGGAGTAACA 58.978 47.826 0.00 0.00 0.00 2.41
606 619 2.758009 ACATTGGTGCTCAATTGTTGC 58.242 42.857 15.56 15.56 43.04 4.17
644 657 3.712016 TCTAGTGGGCAGCACATAAAA 57.288 42.857 0.00 0.00 0.00 1.52
647 668 3.598019 AGTGGGCAGCACATAAAATTG 57.402 42.857 0.00 0.00 0.00 2.32
651 672 4.152223 GTGGGCAGCACATAAAATTGTTTC 59.848 41.667 0.00 0.00 0.00 2.78
652 673 4.040217 TGGGCAGCACATAAAATTGTTTCT 59.960 37.500 0.00 0.00 0.00 2.52
653 674 4.389687 GGGCAGCACATAAAATTGTTTCTG 59.610 41.667 0.00 0.00 33.82 3.02
654 675 4.990426 GGCAGCACATAAAATTGTTTCTGT 59.010 37.500 0.00 0.00 35.16 3.41
655 676 5.107375 GGCAGCACATAAAATTGTTTCTGTG 60.107 40.000 11.31 11.31 46.67 3.66
656 677 5.463061 GCAGCACATAAAATTGTTTCTGTGT 59.537 36.000 15.01 4.46 46.12 3.72
751 772 8.827177 ATCCAATGTAATTATGTACTGTACGG 57.173 34.615 12.87 0.00 32.46 4.02
755 1409 5.904941 TGTAATTATGTACTGTACGGGTGG 58.095 41.667 12.87 0.00 0.00 4.61
822 1476 9.787435 TTTCCTAGAAACTGTATTGTACATGTT 57.213 29.630 2.30 0.00 38.15 2.71
840 1494 4.746535 TGTTCCAGTAACACAAGTCAGA 57.253 40.909 0.00 0.00 43.22 3.27
846 1507 4.279671 CCAGTAACACAAGTCAGAGTCTCT 59.720 45.833 0.00 0.00 0.00 3.10
851 1512 3.701542 ACACAAGTCAGAGTCTCTGTTCA 59.298 43.478 25.68 7.60 44.58 3.18
946 1607 1.005394 CAGGACGTAAACTGGCCGT 60.005 57.895 0.00 0.00 37.56 5.68
947 1608 1.005394 AGGACGTAAACTGGCCGTG 60.005 57.895 0.00 0.00 34.51 4.94
973 1634 7.010552 GCTAGTTCTCATTCGCTCTTTTGATTA 59.989 37.037 0.00 0.00 0.00 1.75
991 1652 0.673985 TAATGGCAGACGAGCGCTAT 59.326 50.000 11.50 0.00 34.64 2.97
996 1661 2.135933 GGCAGACGAGCGCTATATTTT 58.864 47.619 11.50 0.00 34.64 1.82
1109 1775 4.638421 CAGTTTTACTTGGTTGGTGAGTGA 59.362 41.667 0.00 0.00 0.00 3.41
1116 1782 5.197451 ACTTGGTTGGTGAGTGACATTAAA 58.803 37.500 0.00 0.00 0.00 1.52
1117 1783 5.654650 ACTTGGTTGGTGAGTGACATTAAAA 59.345 36.000 0.00 0.00 0.00 1.52
1118 1784 6.153680 ACTTGGTTGGTGAGTGACATTAAAAA 59.846 34.615 0.00 0.00 0.00 1.94
1226 1945 0.758734 TAGTGGCGCTTGGATGCTAT 59.241 50.000 5.61 0.00 0.00 2.97
1282 2001 0.111253 CCAACCTGCCCTCAAGAAGT 59.889 55.000 0.00 0.00 0.00 3.01
1364 2102 8.084073 TCTGCAGTCTTATTTCCATTTTGAAAG 58.916 33.333 14.67 0.00 37.63 2.62
1368 2106 9.565213 CAGTCTTATTTCCATTTTGAAAGCTAG 57.435 33.333 0.00 0.00 37.63 3.42
1402 2140 6.494835 AGAACTTGCATCCTTTGTTATTTCCT 59.505 34.615 0.00 0.00 0.00 3.36
1494 2242 7.391148 TCAAGGTATTATGCAGAAAGGAAAC 57.609 36.000 0.00 0.00 0.00 2.78
1497 2245 7.396540 AGGTATTATGCAGAAAGGAAACAAG 57.603 36.000 0.00 0.00 0.00 3.16
1498 2246 6.378280 AGGTATTATGCAGAAAGGAAACAAGG 59.622 38.462 0.00 0.00 0.00 3.61
1499 2247 4.519540 TTATGCAGAAAGGAAACAAGGC 57.480 40.909 0.00 0.00 0.00 4.35
1595 2343 2.519013 AGAAAACCAAGCCACCTGATC 58.481 47.619 0.00 0.00 0.00 2.92
1606 2354 3.571401 AGCCACCTGATCTTGAAACTTTG 59.429 43.478 0.00 0.00 0.00 2.77
1679 2430 4.489810 CTCGACCAACTATGCAGGATATC 58.510 47.826 0.00 0.00 0.00 1.63
1694 2445 3.921486 AGGATATCATGGAGGCAAAGGAT 59.079 43.478 4.83 0.00 0.00 3.24
1786 2537 4.566488 CCAGTTTGAAGCTTCCTGGATACT 60.566 45.833 31.25 18.17 44.39 2.12
1863 2618 1.577468 TTGTGAGTGGCGTGTTACAG 58.423 50.000 0.00 0.00 0.00 2.74
1892 2647 5.833131 ACATTTTGTTAGTTCAGTGGATGGT 59.167 36.000 0.00 0.00 0.00 3.55
1899 2654 3.480470 AGTTCAGTGGATGGTTTGTCAG 58.520 45.455 0.00 0.00 0.00 3.51
1904 2659 4.474651 TCAGTGGATGGTTTGTCAGGATAT 59.525 41.667 0.00 0.00 0.00 1.63
1933 2688 4.780815 TGTCAGGAAAACAGTGTGAGAAT 58.219 39.130 0.00 0.00 0.00 2.40
1935 2690 5.991606 TGTCAGGAAAACAGTGTGAGAATAG 59.008 40.000 0.00 0.00 0.00 1.73
1936 2691 4.997395 TCAGGAAAACAGTGTGAGAATAGC 59.003 41.667 0.00 0.00 0.00 2.97
1937 2692 4.999950 CAGGAAAACAGTGTGAGAATAGCT 59.000 41.667 0.00 0.00 0.00 3.32
1938 2693 6.014584 TCAGGAAAACAGTGTGAGAATAGCTA 60.015 38.462 0.00 0.00 0.00 3.32
1939 2694 6.650807 CAGGAAAACAGTGTGAGAATAGCTAA 59.349 38.462 0.00 0.00 0.00 3.09
1940 2695 7.173218 CAGGAAAACAGTGTGAGAATAGCTAAA 59.827 37.037 0.00 0.00 0.00 1.85
1941 2696 7.885399 AGGAAAACAGTGTGAGAATAGCTAAAT 59.115 33.333 0.00 0.00 0.00 1.40
1942 2697 9.162764 GGAAAACAGTGTGAGAATAGCTAAATA 57.837 33.333 0.00 0.00 0.00 1.40
1974 2729 6.723298 ATGGTTTGTTAACAAGTCCATCAA 57.277 33.333 31.74 19.67 42.64 2.57
2099 2924 1.815003 CTTTGATGGTTCAGTCCCAGC 59.185 52.381 0.00 0.00 38.85 4.85
2100 2925 0.770499 TTGATGGTTCAGTCCCAGCA 59.230 50.000 0.00 0.00 46.01 4.41
2111 2938 0.179129 GTCCCAGCATGCGGAATTTG 60.179 55.000 24.22 11.82 37.23 2.32
2127 2954 4.943705 GGAATTTGCTGTCCAGTTCAGATA 59.056 41.667 0.00 0.00 35.20 1.98
2130 2957 3.827008 TGCTGTCCAGTTCAGATATCC 57.173 47.619 0.00 0.00 35.20 2.59
2154 2981 6.976925 CCTTCATTTGCTAAATCTGGAATGAC 59.023 38.462 0.00 0.00 34.38 3.06
2186 3036 9.958285 GAGTTTTTCAAATTTGACAAAGTTCTC 57.042 29.630 28.17 24.38 39.36 2.87
2210 3064 7.755591 TCAACTCATGATTAGCAAAAGATCAC 58.244 34.615 0.00 0.00 33.08 3.06
2211 3065 7.391275 TCAACTCATGATTAGCAAAAGATCACA 59.609 33.333 0.00 0.00 33.08 3.58
2249 3103 8.710749 ATACCATTATTGCTCCATGTTTACAT 57.289 30.769 0.00 0.00 36.96 2.29
2297 3151 0.179048 CCTGTGCAGTGAACCTGTGA 60.179 55.000 0.00 0.00 43.55 3.58
2298 3152 1.667236 CTGTGCAGTGAACCTGTGAA 58.333 50.000 0.00 0.00 43.55 3.18
2357 3220 2.280797 GTTGGCAGCAGACGGTCA 60.281 61.111 11.27 0.00 0.00 4.02
2422 3286 2.768527 GTCTGGTCCATCATCTTCTCCA 59.231 50.000 0.00 0.00 0.00 3.86
2444 3311 2.659016 CAGGAACTCGCTCTGCCA 59.341 61.111 0.00 0.00 34.60 4.92
2484 3351 3.782244 CTCGTCAGTTGCGCCTGC 61.782 66.667 4.18 1.69 43.20 4.85
2605 3478 9.197694 CAGGTAGTAGCTATCATGAATGTTTAC 57.802 37.037 0.00 0.00 0.00 2.01
2632 3505 0.323725 GGGGGCATCAGCTGAAGAAA 60.324 55.000 22.50 0.00 41.70 2.52
2678 3551 1.808531 GACCAATTGCAGTGCCAGCA 61.809 55.000 13.72 0.00 40.85 4.41
2719 3592 1.452651 CGACCTGCAGATGCCCAAT 60.453 57.895 17.39 0.00 41.18 3.16
2720 3593 1.033746 CGACCTGCAGATGCCCAATT 61.034 55.000 17.39 0.00 41.18 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.768807 TGCTGTAACTTTGGGTTATAACAAT 57.231 32.000 17.16 0.00 41.68 2.71
3 4 6.773685 ACTTGCTGTAACTTTGGGTTATAACA 59.226 34.615 17.16 0.00 41.68 2.41
4 5 7.081976 CACTTGCTGTAACTTTGGGTTATAAC 58.918 38.462 7.09 7.09 41.68 1.89
5 6 6.294286 GCACTTGCTGTAACTTTGGGTTATAA 60.294 38.462 0.00 0.00 39.04 0.98
6 7 5.182380 GCACTTGCTGTAACTTTGGGTTATA 59.818 40.000 0.00 0.00 39.04 0.98
7 8 4.022329 GCACTTGCTGTAACTTTGGGTTAT 60.022 41.667 0.00 0.00 39.04 1.89
8 9 3.316868 GCACTTGCTGTAACTTTGGGTTA 59.683 43.478 0.00 0.00 37.43 2.85
9 10 2.100749 GCACTTGCTGTAACTTTGGGTT 59.899 45.455 0.00 0.00 38.75 4.11
10 11 1.681264 GCACTTGCTGTAACTTTGGGT 59.319 47.619 0.00 0.00 38.21 4.51
11 12 2.422276 GCACTTGCTGTAACTTTGGG 57.578 50.000 0.00 0.00 38.21 4.12
23 24 1.555533 AGGTAGGGTAGAAGCACTTGC 59.444 52.381 0.00 0.00 42.49 4.01
24 25 3.100671 AGAGGTAGGGTAGAAGCACTTG 58.899 50.000 0.00 0.00 0.00 3.16
25 26 3.476485 AGAGGTAGGGTAGAAGCACTT 57.524 47.619 0.00 0.00 0.00 3.16
26 27 3.476485 AAGAGGTAGGGTAGAAGCACT 57.524 47.619 0.00 0.00 0.00 4.40
27 28 3.514309 TGAAAGAGGTAGGGTAGAAGCAC 59.486 47.826 0.00 0.00 0.00 4.40
28 29 3.786553 TGAAAGAGGTAGGGTAGAAGCA 58.213 45.455 0.00 0.00 0.00 3.91
29 30 4.820894 TTGAAAGAGGTAGGGTAGAAGC 57.179 45.455 0.00 0.00 0.00 3.86
30 31 6.155393 ACAGATTGAAAGAGGTAGGGTAGAAG 59.845 42.308 0.00 0.00 0.00 2.85
31 32 6.023603 ACAGATTGAAAGAGGTAGGGTAGAA 58.976 40.000 0.00 0.00 0.00 2.10
32 33 5.422331 CACAGATTGAAAGAGGTAGGGTAGA 59.578 44.000 0.00 0.00 0.00 2.59
33 34 5.187967 ACACAGATTGAAAGAGGTAGGGTAG 59.812 44.000 0.00 0.00 0.00 3.18
34 35 5.091552 ACACAGATTGAAAGAGGTAGGGTA 58.908 41.667 0.00 0.00 0.00 3.69
35 36 3.910627 ACACAGATTGAAAGAGGTAGGGT 59.089 43.478 0.00 0.00 0.00 4.34
36 37 4.559862 ACACAGATTGAAAGAGGTAGGG 57.440 45.455 0.00 0.00 0.00 3.53
37 38 6.234177 AGAAACACAGATTGAAAGAGGTAGG 58.766 40.000 0.00 0.00 0.00 3.18
38 39 7.872993 TGTAGAAACACAGATTGAAAGAGGTAG 59.127 37.037 0.00 0.00 0.00 3.18
39 40 7.732025 TGTAGAAACACAGATTGAAAGAGGTA 58.268 34.615 0.00 0.00 0.00 3.08
40 41 6.591935 TGTAGAAACACAGATTGAAAGAGGT 58.408 36.000 0.00 0.00 0.00 3.85
41 42 7.496529 TTGTAGAAACACAGATTGAAAGAGG 57.503 36.000 0.00 0.00 34.61 3.69
43 44 9.554395 TGTATTGTAGAAACACAGATTGAAAGA 57.446 29.630 0.00 0.00 34.61 2.52
44 45 9.817365 CTGTATTGTAGAAACACAGATTGAAAG 57.183 33.333 10.52 0.00 34.61 2.62
45 46 9.554395 TCTGTATTGTAGAAACACAGATTGAAA 57.446 29.630 13.31 0.00 33.61 2.69
46 47 9.208022 CTCTGTATTGTAGAAACACAGATTGAA 57.792 33.333 16.11 0.95 36.33 2.69
47 48 8.585018 TCTCTGTATTGTAGAAACACAGATTGA 58.415 33.333 16.11 10.78 36.33 2.57
48 49 8.763049 TCTCTGTATTGTAGAAACACAGATTG 57.237 34.615 16.11 9.26 36.33 2.67
49 50 9.950496 ATTCTCTGTATTGTAGAAACACAGATT 57.050 29.630 16.11 6.55 36.33 2.40
52 53 9.307121 CCTATTCTCTGTATTGTAGAAACACAG 57.693 37.037 10.01 10.01 34.61 3.66
53 54 8.258007 CCCTATTCTCTGTATTGTAGAAACACA 58.742 37.037 0.00 0.00 34.61 3.72
54 55 7.711339 CCCCTATTCTCTGTATTGTAGAAACAC 59.289 40.741 0.00 0.00 34.61 3.32
55 56 7.635089 GCCCCTATTCTCTGTATTGTAGAAACA 60.635 40.741 0.00 0.00 33.26 2.83
56 57 6.706716 GCCCCTATTCTCTGTATTGTAGAAAC 59.293 42.308 0.00 0.00 33.26 2.78
57 58 6.615726 AGCCCCTATTCTCTGTATTGTAGAAA 59.384 38.462 0.00 0.00 33.26 2.52
58 59 6.143915 AGCCCCTATTCTCTGTATTGTAGAA 58.856 40.000 0.00 0.00 34.00 2.10
59 60 5.716979 AGCCCCTATTCTCTGTATTGTAGA 58.283 41.667 0.00 0.00 0.00 2.59
60 61 5.540337 TGAGCCCCTATTCTCTGTATTGTAG 59.460 44.000 0.00 0.00 0.00 2.74
61 62 5.464069 TGAGCCCCTATTCTCTGTATTGTA 58.536 41.667 0.00 0.00 0.00 2.41
62 63 4.298626 TGAGCCCCTATTCTCTGTATTGT 58.701 43.478 0.00 0.00 0.00 2.71
63 64 4.963318 TGAGCCCCTATTCTCTGTATTG 57.037 45.455 0.00 0.00 0.00 1.90
64 65 5.013599 GGATTGAGCCCCTATTCTCTGTATT 59.986 44.000 0.00 0.00 0.00 1.89
65 66 4.534103 GGATTGAGCCCCTATTCTCTGTAT 59.466 45.833 0.00 0.00 0.00 2.29
66 67 3.904339 GGATTGAGCCCCTATTCTCTGTA 59.096 47.826 0.00 0.00 0.00 2.74
67 68 2.708325 GGATTGAGCCCCTATTCTCTGT 59.292 50.000 0.00 0.00 0.00 3.41
68 69 2.289320 CGGATTGAGCCCCTATTCTCTG 60.289 54.545 0.00 0.00 0.00 3.35
69 70 1.974236 CGGATTGAGCCCCTATTCTCT 59.026 52.381 0.00 0.00 0.00 3.10
70 71 1.002544 CCGGATTGAGCCCCTATTCTC 59.997 57.143 0.00 0.00 0.00 2.87
71 72 1.059913 CCGGATTGAGCCCCTATTCT 58.940 55.000 0.00 0.00 0.00 2.40
72 73 1.056660 TCCGGATTGAGCCCCTATTC 58.943 55.000 0.00 0.00 0.00 1.75
73 74 0.765510 GTCCGGATTGAGCCCCTATT 59.234 55.000 7.81 0.00 0.00 1.73
74 75 1.472662 CGTCCGGATTGAGCCCCTAT 61.473 60.000 7.81 0.00 0.00 2.57
75 76 2.131709 CGTCCGGATTGAGCCCCTA 61.132 63.158 7.81 0.00 0.00 3.53
76 77 3.470888 CGTCCGGATTGAGCCCCT 61.471 66.667 7.81 0.00 0.00 4.79
77 78 3.467226 TCGTCCGGATTGAGCCCC 61.467 66.667 7.81 0.00 0.00 5.80
78 79 2.202892 GTCGTCCGGATTGAGCCC 60.203 66.667 7.81 0.00 0.00 5.19
79 80 1.227002 GAGTCGTCCGGATTGAGCC 60.227 63.158 7.81 0.00 0.00 4.70
80 81 1.227002 GGAGTCGTCCGGATTGAGC 60.227 63.158 7.81 4.29 31.37 4.26
112 113 2.423446 GCTATCTGAGCCCACGGG 59.577 66.667 0.00 0.00 46.41 5.28
119 120 5.971927 CGTGAGACGGATGCTATCTGAGC 62.972 56.522 10.69 0.00 44.30 4.26
120 121 2.350293 CGTGAGACGGATGCTATCTGAG 60.350 54.545 10.69 0.96 38.08 3.35
121 122 1.604278 CGTGAGACGGATGCTATCTGA 59.396 52.381 10.69 0.00 38.08 3.27
122 123 1.928152 GCGTGAGACGGATGCTATCTG 60.928 57.143 0.00 4.12 42.82 2.90
123 124 0.312416 GCGTGAGACGGATGCTATCT 59.688 55.000 0.00 0.00 42.82 1.98
124 125 0.030773 TGCGTGAGACGGATGCTATC 59.969 55.000 0.00 0.00 42.82 2.08
125 126 0.031314 CTGCGTGAGACGGATGCTAT 59.969 55.000 0.00 0.00 42.05 2.97
126 127 1.433471 CTGCGTGAGACGGATGCTA 59.567 57.895 0.00 0.00 42.05 3.49
127 128 2.182791 CTGCGTGAGACGGATGCT 59.817 61.111 0.00 0.00 42.05 3.79
351 363 4.742201 TGGAAGACGGCGAGCTGC 62.742 66.667 16.62 9.07 45.38 5.25
370 382 0.248702 GAGATCTCGTCGACCTTGGC 60.249 60.000 10.58 0.00 0.00 4.52
492 504 1.337387 GCTAGTACACCAGACGGATCC 59.663 57.143 0.00 0.00 35.59 3.36
547 559 4.294416 ACCAGATCGAGAAATCGTACAG 57.706 45.455 0.00 0.00 0.00 2.74
578 591 1.985159 TGAGCACCAATGTTACTCCCT 59.015 47.619 0.00 0.00 0.00 4.20
581 594 5.376854 ACAATTGAGCACCAATGTTACTC 57.623 39.130 13.59 0.00 44.28 2.59
588 601 2.289195 CCAGCAACAATTGAGCACCAAT 60.289 45.455 22.72 5.76 46.86 3.16
651 672 9.764870 CATGTCTTGATTGTAAATCTAACACAG 57.235 33.333 1.99 0.00 0.00 3.66
652 673 9.283768 ACATGTCTTGATTGTAAATCTAACACA 57.716 29.630 0.00 1.57 0.00 3.72
670 691 9.624373 ATCTAGCAGAAATTCAATACATGTCTT 57.376 29.630 0.00 0.00 0.00 3.01
822 1476 4.215908 AGACTCTGACTTGTGTTACTGGA 58.784 43.478 0.00 0.00 0.00 3.86
838 1492 2.008242 ACTGGCTGAACAGAGACTCT 57.992 50.000 0.00 0.00 40.97 3.24
840 1494 2.175202 CCTACTGGCTGAACAGAGACT 58.825 52.381 5.97 0.00 40.97 3.24
873 1534 9.877178 GGTAAACTGTAGCAGCATCTATTATAT 57.123 33.333 0.00 0.00 34.37 0.86
874 1535 9.090103 AGGTAAACTGTAGCAGCATCTATTATA 57.910 33.333 0.00 0.00 34.37 0.98
880 1541 3.866651 CAGGTAAACTGTAGCAGCATCT 58.133 45.455 0.00 0.00 42.42 2.90
946 1607 3.876274 AAGAGCGAATGAGAACTAGCA 57.124 42.857 0.00 0.00 0.00 3.49
947 1608 4.627467 TCAAAAGAGCGAATGAGAACTAGC 59.373 41.667 0.00 0.00 0.00 3.42
973 1634 0.673985 TATAGCGCTCGTCTGCCATT 59.326 50.000 16.34 0.00 0.00 3.16
996 1661 9.788889 ATGATCTTGAATATGTGCTTCATCTAA 57.211 29.630 0.00 0.00 37.91 2.10
1116 1782 9.300681 TCTTCATGACATTAGGAGTGAAAATTT 57.699 29.630 0.00 0.00 0.00 1.82
1117 1783 8.734386 GTCTTCATGACATTAGGAGTGAAAATT 58.266 33.333 0.00 0.00 44.73 1.82
1118 1784 8.273780 GTCTTCATGACATTAGGAGTGAAAAT 57.726 34.615 0.00 0.00 44.73 1.82
1136 1802 9.412460 TCATAATTAAAAGGAGCATGTCTTCAT 57.588 29.630 0.00 0.00 34.21 2.57
1143 1809 8.545420 GCAAACATCATAATTAAAAGGAGCATG 58.455 33.333 0.00 0.00 0.00 4.06
1145 1811 7.839907 AGCAAACATCATAATTAAAAGGAGCA 58.160 30.769 0.00 0.00 0.00 4.26
1226 1945 4.653341 CCATATCCAACCATAAAAAGGCCA 59.347 41.667 5.01 0.00 0.00 5.36
1364 2102 5.821516 TGCAAGTTCTAGAGACTACTAGC 57.178 43.478 7.66 9.54 39.50 3.42
1368 2106 5.845391 AGGATGCAAGTTCTAGAGACTAC 57.155 43.478 0.00 0.00 0.00 2.73
1402 2140 2.685897 GCACAGGTGTGGAACTAAAACA 59.314 45.455 11.96 0.00 45.72 2.83
1412 2150 2.183478 TAGACAATGCACAGGTGTGG 57.817 50.000 11.96 0.00 45.72 4.17
1494 2242 4.997565 TGAAGTTTTCAGAGTTTGCCTTG 58.002 39.130 0.00 0.00 34.08 3.61
1497 2245 6.739112 ACTTATGAAGTTTTCAGAGTTTGCC 58.261 36.000 0.00 0.00 43.98 4.52
1606 2354 8.856490 AAAACATGTGATGTACAGAAAACTTC 57.144 30.769 0.00 0.00 44.07 3.01
1644 2395 5.491982 AGTTGGTCGAGCTCAAAGAATTAT 58.508 37.500 16.64 0.00 0.00 1.28
1679 2430 2.743553 AGGAAATCCTTTGCCTCCATG 58.256 47.619 0.00 0.00 46.09 3.66
1694 2445 7.505585 ACATCAACACCTCTTTTTGATAGGAAA 59.494 33.333 0.00 0.00 37.78 3.13
1836 2591 1.159713 CGCCACTCACAAAGACTGCA 61.160 55.000 0.00 0.00 0.00 4.41
1842 2597 1.937223 TGTAACACGCCACTCACAAAG 59.063 47.619 0.00 0.00 0.00 2.77
1863 2618 8.149973 TCCACTGAACTAACAAAATGTAGAAC 57.850 34.615 0.00 0.00 0.00 3.01
1892 2647 8.988060 TCCTGACATAACTAATATCCTGACAAA 58.012 33.333 0.00 0.00 0.00 2.83
1899 2654 9.614792 ACTGTTTTCCTGACATAACTAATATCC 57.385 33.333 0.00 0.00 0.00 2.59
1904 2659 7.276658 TCACACTGTTTTCCTGACATAACTAA 58.723 34.615 0.00 0.00 0.00 2.24
1942 2697 9.908152 GACTTGTTAACAAACCATTAATTAGCT 57.092 29.630 20.89 0.00 35.15 3.32
1943 2698 9.135843 GGACTTGTTAACAAACCATTAATTAGC 57.864 33.333 25.97 9.00 35.15 3.09
2078 2903 2.815589 GCTGGGACTGAACCATCAAAGT 60.816 50.000 0.00 0.00 37.38 2.66
2099 2924 0.527113 TGGACAGCAAATTCCGCATG 59.473 50.000 2.97 0.00 34.24 4.06
2100 2925 0.813184 CTGGACAGCAAATTCCGCAT 59.187 50.000 2.97 0.00 34.24 4.73
2111 2938 4.141846 TGAAGGATATCTGAACTGGACAGC 60.142 45.833 2.05 0.00 35.61 4.40
2127 2954 7.562454 TCATTCCAGATTTAGCAAATGAAGGAT 59.438 33.333 0.00 0.00 32.02 3.24
2130 2957 7.769220 AGTCATTCCAGATTTAGCAAATGAAG 58.231 34.615 0.00 0.00 35.56 3.02
2174 3001 7.095060 GCTAATCATGAGTTGAGAACTTTGTCA 60.095 37.037 8.77 0.00 43.03 3.58
2186 3036 7.532571 TGTGATCTTTTGCTAATCATGAGTTG 58.467 34.615 0.00 0.00 32.45 3.16
2210 3064 8.878769 GCAATAATGGTATTGGTAAAGGTTTTG 58.121 33.333 8.19 0.00 44.65 2.44
2422 3286 1.910772 AGAGCGAGTTCCTGGTGCT 60.911 57.895 0.00 0.00 38.89 4.40
2484 3351 1.373497 GAGGACACTGCACAGGTCG 60.373 63.158 2.21 0.00 32.80 4.79
2491 3358 4.687215 GCTGCCGAGGACACTGCA 62.687 66.667 0.00 0.00 0.00 4.41
2494 3361 3.386237 GAGGCTGCCGAGGACACT 61.386 66.667 13.96 0.00 0.00 3.55
2615 3488 1.888512 TGTTTTCTTCAGCTGATGCCC 59.111 47.619 19.04 8.59 40.80 5.36
2616 3489 2.555757 ACTGTTTTCTTCAGCTGATGCC 59.444 45.455 19.04 8.91 40.80 4.40
2617 3490 3.911661 ACTGTTTTCTTCAGCTGATGC 57.088 42.857 19.04 7.55 36.50 3.91
2620 3493 5.428253 ACAAGTACTGTTTTCTTCAGCTGA 58.572 37.500 13.74 13.74 32.99 4.26
2623 3496 7.171678 ACTCATACAAGTACTGTTTTCTTCAGC 59.828 37.037 0.00 0.00 39.64 4.26
2632 3505 9.190317 TCATCATCTACTCATACAAGTACTGTT 57.810 33.333 0.00 0.00 39.64 3.16
2678 3551 5.920273 CGATTGGATGTACTTTGTTGCTTTT 59.080 36.000 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.