Multiple sequence alignment - TraesCS3B01G606900

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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 TraesCS3B01G606900 chr3B 100.000 3082 0 0 1 3082 825848367 825851448 0.000000e+00 5692.0
1 TraesCS3B01G606900 chr3B 86.729 535 68 3 1600 2133 28607217 28606685 2.910000e-165 592.0
2 TraesCS3B01G606900 chr3B 83.546 626 81 16 875 1485 28608032 28607414 1.770000e-157 566.0
3 TraesCS3B01G606900 chr3B 86.936 421 39 11 2118 2526 28606663 28606247 3.080000e-125 459.0
4 TraesCS3B01G606900 chr3B 91.071 224 19 1 1 224 747750789 747750567 5.500000e-78 302.0
5 TraesCS3B01G606900 chr3B 100.000 62 0 0 3328 3389 825851694 825851755 7.680000e-22 115.0
6 TraesCS3B01G606900 chr3A 97.760 1250 19 3 881 2126 749877537 749876293 0.000000e+00 2145.0
7 TraesCS3B01G606900 chr3A 98.653 965 11 1 2118 3082 749876265 749875303 0.000000e+00 1709.0
8 TraesCS3B01G606900 chr3A 84.543 634 66 19 875 1485 748339358 748339982 1.740000e-167 599.0
9 TraesCS3B01G606900 chr3A 86.330 534 68 3 1600 2130 748340179 748340710 8.150000e-161 577.0
10 TraesCS3B01G606900 chr3A 86.667 420 40 12 2118 2525 748340735 748341150 5.160000e-123 451.0
11 TraesCS3B01G606900 chr3A 90.714 280 26 0 291 570 712286235 712285956 1.150000e-99 374.0
12 TraesCS3B01G606900 chr3A 90.106 283 28 0 288 570 686788521 686788803 5.340000e-98 368.0
13 TraesCS3B01G606900 chr3A 100.000 62 0 0 3328 3389 749875100 749875039 7.680000e-22 115.0
14 TraesCS3B01G606900 chrUn 93.149 978 52 6 2118 3082 37114060 37113085 0.000000e+00 1421.0
15 TraesCS3B01G606900 chrUn 93.149 978 52 6 2118 3082 247033216 247034191 0.000000e+00 1421.0
16 TraesCS3B01G606900 chrUn 93.149 978 52 6 2118 3082 300942789 300941814 0.000000e+00 1421.0
17 TraesCS3B01G606900 chrUn 91.877 751 35 3 875 1600 247031262 247032011 0.000000e+00 1026.0
18 TraesCS3B01G606900 chrUn 95.033 604 30 0 997 1600 37115868 37115265 0.000000e+00 950.0
19 TraesCS3B01G606900 chrUn 95.033 604 30 0 997 1600 300944597 300943994 0.000000e+00 950.0
20 TraesCS3B01G606900 chrUn 93.446 534 34 1 1600 2133 37114614 37114082 0.000000e+00 791.0
21 TraesCS3B01G606900 chrUn 93.597 531 33 1 1600 2130 247032662 247033191 0.000000e+00 791.0
22 TraesCS3B01G606900 chrUn 93.446 534 34 1 1600 2133 300943343 300942811 0.000000e+00 791.0
23 TraesCS3B01G606900 chrUn 82.920 363 46 13 304 656 31355920 31355564 2.540000e-81 313.0
24 TraesCS3B01G606900 chr3D 89.701 602 60 1 997 1598 615455490 615456089 0.000000e+00 767.0
25 TraesCS3B01G606900 chr3D 88.593 526 54 5 1600 2120 615456763 615457287 4.770000e-178 634.0
26 TraesCS3B01G606900 chr3D 95.294 340 16 0 231 570 67012056 67012395 1.070000e-149 540.0
27 TraesCS3B01G606900 chr3D 88.729 417 36 6 2118 2525 615457321 615457735 1.820000e-137 499.0
28 TraesCS3B01G606900 chr3D 83.200 125 9 5 767 879 67012909 67013033 1.660000e-18 104.0
29 TraesCS3B01G606900 chr7A 87.838 444 35 9 331 769 124220453 124220024 1.400000e-138 503.0
30 TraesCS3B01G606900 chr7A 91.111 225 18 2 1 224 519102760 519102537 1.530000e-78 303.0
31 TraesCS3B01G606900 chr7A 94.737 57 3 0 823 879 674264613 674264669 4.660000e-14 89.8
32 TraesCS3B01G606900 chr5B 91.643 359 25 3 416 769 50510045 50509687 3.040000e-135 492.0
33 TraesCS3B01G606900 chr5B 82.063 223 39 1 1598 1819 672627599 672627377 4.460000e-44 189.0
34 TraesCS3B01G606900 chr2A 91.071 336 30 0 231 566 90065875 90066210 3.990000e-124 455.0
35 TraesCS3B01G606900 chr2A 96.491 57 2 0 823 879 90066788 90066844 1.000000e-15 95.3
36 TraesCS3B01G606900 chr2A 96.491 57 2 0 823 879 753742159 753742103 1.000000e-15 95.3
37 TraesCS3B01G606900 chr6A 90.991 333 30 0 234 566 599803440 599803108 1.850000e-122 449.0
38 TraesCS3B01G606900 chr6A 89.222 334 35 1 216 549 172349438 172349770 1.880000e-112 416.0
39 TraesCS3B01G606900 chr6A 91.556 225 18 1 1 224 172348272 172348496 3.280000e-80 309.0
40 TraesCS3B01G606900 chr6A 98.246 57 1 0 823 879 599802530 599802474 2.150000e-17 100.0
41 TraesCS3B01G606900 chr7D 90.419 334 32 0 216 549 539828693 539829026 1.120000e-119 440.0
42 TraesCS3B01G606900 chr7D 93.820 178 9 2 593 769 403106472 403106296 2.000000e-67 267.0
43 TraesCS3B01G606900 chr7D 90.000 80 5 3 692 769 539829041 539829119 2.150000e-17 100.0
44 TraesCS3B01G606900 chr7D 83.654 104 10 3 786 882 403105896 403105793 1.300000e-14 91.6
45 TraesCS3B01G606900 chr1D 87.500 304 38 0 216 519 491752041 491751738 5.380000e-93 351.0
46 TraesCS3B01G606900 chr1D 80.580 345 61 3 965 1303 28165355 28165699 9.330000e-66 261.0
47 TraesCS3B01G606900 chr7B 91.071 224 19 1 1 224 673675623 673675401 5.500000e-78 302.0
48 TraesCS3B01G606900 chr6B 91.071 224 19 1 1 224 397530025 397529803 5.500000e-78 302.0
49 TraesCS3B01G606900 chr5D 91.071 224 19 1 1 224 106986675 106986897 5.500000e-78 302.0
50 TraesCS3B01G606900 chr5D 81.773 203 37 0 1617 1819 532651315 532651113 1.620000e-38 171.0
51 TraesCS3B01G606900 chr5D 87.097 62 7 1 2945 3005 560238667 560238606 6.070000e-08 69.4
52 TraesCS3B01G606900 chr4A 91.071 224 19 1 1 224 446616899 446617121 5.500000e-78 302.0
53 TraesCS3B01G606900 chr4A 81.951 205 37 0 1615 1819 639199053 639199257 1.250000e-39 174.0
54 TraesCS3B01G606900 chr4A 80.952 189 30 3 1023 1211 639196023 639196205 9.800000e-31 145.0
55 TraesCS3B01G606900 chr1B 90.991 222 19 1 3 224 651496220 651496000 7.110000e-77 298.0
56 TraesCS3B01G606900 chr1A 90.667 225 17 4 1 224 592570721 592570500 2.560000e-76 296.0
57 TraesCS3B01G606900 chr5A 76.286 447 82 17 2639 3081 589040541 589040967 2.050000e-52 217.0
58 TraesCS3B01G606900 chr6D 98.113 53 0 1 827 879 9162439 9162490 1.300000e-14 91.6
59 TraesCS3B01G606900 chr2D 92.982 57 4 0 828 884 343099610 343099554 2.170000e-12 84.2
60 TraesCS3B01G606900 chr4B 91.379 58 5 0 821 878 630088724 630088781 2.800000e-11 80.5


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 TraesCS3B01G606900 chr3B 825848367 825851755 3388 False 2903.500000 5692 100.000000 1 3389 2 chr3B.!!$F1 3388
1 TraesCS3B01G606900 chr3B 28606247 28608032 1785 True 539.000000 592 85.737000 875 2526 3 chr3B.!!$R2 1651
2 TraesCS3B01G606900 chr3A 749875039 749877537 2498 True 1323.000000 2145 98.804333 881 3389 3 chr3A.!!$R2 2508
3 TraesCS3B01G606900 chr3A 748339358 748341150 1792 False 542.333333 599 85.846667 875 2525 3 chr3A.!!$F2 1650
4 TraesCS3B01G606900 chrUn 247031262 247034191 2929 False 1079.333333 1421 92.874333 875 3082 3 chrUn.!!$F1 2207
5 TraesCS3B01G606900 chrUn 37113085 37115868 2783 True 1054.000000 1421 93.876000 997 3082 3 chrUn.!!$R2 2085
6 TraesCS3B01G606900 chrUn 300941814 300944597 2783 True 1054.000000 1421 93.876000 997 3082 3 chrUn.!!$R3 2085
7 TraesCS3B01G606900 chr3D 615455490 615457735 2245 False 633.333333 767 89.007667 997 2525 3 chr3D.!!$F2 1528
8 TraesCS3B01G606900 chr3D 67012056 67013033 977 False 322.000000 540 89.247000 231 879 2 chr3D.!!$F1 648
9 TraesCS3B01G606900 chr2A 90065875 90066844 969 False 275.150000 455 93.781000 231 879 2 chr2A.!!$F1 648
10 TraesCS3B01G606900 chr6A 172348272 172349770 1498 False 362.500000 416 90.389000 1 549 2 chr6A.!!$F1 548
11 TraesCS3B01G606900 chr6A 599802474 599803440 966 True 274.500000 449 94.618500 234 879 2 chr6A.!!$R1 645

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
803 1756 0.164647 GTGCGCCGATTGATAGATGC 59.835 55.0 4.18 0.0 0.00 3.91 F
804 1757 0.249826 TGCGCCGATTGATAGATGCA 60.250 50.0 4.18 0.0 0.00 3.96 F
1819 3642 0.107831 ACTACAAGTGCCGCTTCCAA 59.892 50.0 0.00 0.0 34.69 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1819 3642 0.179009 ATGTGTGCTGGTGTCTTGCT 60.179 50.000 0.0 0.0 0.0 3.91 R
2133 4004 1.599542 AGCTCGCAGTTCTTGTCAAAC 59.400 47.619 0.0 0.0 0.0 2.93 R
2632 4518 5.785243 ACTAGAGCTTAGTGTGGAAGAAAC 58.215 41.667 0.0 0.0 0.0 2.78 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
31 32 2.457366 AGGTGTGGCGAAGTCTTAAG 57.543 50.000 0.00 0.00 0.00 1.85
32 33 1.968493 AGGTGTGGCGAAGTCTTAAGA 59.032 47.619 0.00 0.00 0.00 2.10
36 37 4.215613 GGTGTGGCGAAGTCTTAAGAAAAT 59.784 41.667 6.78 0.00 0.00 1.82
67 68 7.703298 TTTCATGCAAATCAAAAGAGTCAAG 57.297 32.000 0.00 0.00 0.00 3.02
87 89 6.195798 GTCAAGACACATTACAAACGAAAACC 59.804 38.462 0.00 0.00 0.00 3.27
88 90 5.821516 AGACACATTACAAACGAAAACCA 57.178 34.783 0.00 0.00 0.00 3.67
101 103 8.599774 ACAAACGAAAACCAAATACAATGAAAG 58.400 29.630 0.00 0.00 0.00 2.62
152 154 9.599322 CAACCTAAAACATATCGATAATGAAGC 57.401 33.333 9.61 0.00 0.00 3.86
162 164 5.173774 TCGATAATGAAGCTTTCAATGGC 57.826 39.130 0.00 0.00 43.95 4.40
175 177 2.457598 TCAATGGCGTCTAGAAGACCT 58.542 47.619 9.19 0.00 42.12 3.85
205 207 2.579873 CAATGCCCTACCCTCATTCTG 58.420 52.381 0.00 0.00 0.00 3.02
240 1192 5.717078 AATTTTGATGAGTGACATGTGCT 57.283 34.783 1.15 0.21 39.56 4.40
324 1276 9.045223 AGCACTTCAAAATACTTTTTCAAATCC 57.955 29.630 0.00 0.00 32.72 3.01
325 1277 8.825745 GCACTTCAAAATACTTTTTCAAATCCA 58.174 29.630 0.00 0.00 32.72 3.41
393 1345 4.271776 GCTTCAAGCTGCTGTTCAAAATTT 59.728 37.500 1.35 0.00 38.45 1.82
453 1405 5.473039 CCCTTTTCTTTGGATTTGCTAGTG 58.527 41.667 0.00 0.00 0.00 2.74
566 1518 6.037830 AGCAAAAACTTGTTCGTACAGTACAT 59.962 34.615 11.37 0.00 35.28 2.29
569 1521 8.545420 CAAAAACTTGTTCGTACAGTACATAGT 58.455 33.333 11.37 3.59 35.28 2.12
570 1522 9.748708 AAAAACTTGTTCGTACAGTACATAGTA 57.251 29.630 11.37 0.00 35.28 1.82
571 1523 9.748708 AAAACTTGTTCGTACAGTACATAGTAA 57.251 29.630 11.37 0.00 35.28 2.24
572 1524 9.748708 AAACTTGTTCGTACAGTACATAGTAAA 57.251 29.630 11.37 0.00 35.28 2.01
573 1525 8.733857 ACTTGTTCGTACAGTACATAGTAAAC 57.266 34.615 11.37 5.63 35.28 2.01
574 1526 8.571336 ACTTGTTCGTACAGTACATAGTAAACT 58.429 33.333 11.37 0.00 35.28 2.66
577 1529 8.177663 TGTTCGTACAGTACATAGTAAACTAGC 58.822 37.037 11.37 0.00 0.00 3.42
578 1530 7.848223 TCGTACAGTACATAGTAAACTAGCA 57.152 36.000 11.37 0.00 0.00 3.49
579 1531 8.442632 TCGTACAGTACATAGTAAACTAGCAT 57.557 34.615 11.37 0.00 0.00 3.79
580 1532 8.340443 TCGTACAGTACATAGTAAACTAGCATG 58.660 37.037 11.37 0.00 0.00 4.06
581 1533 8.340443 CGTACAGTACATAGTAAACTAGCATGA 58.660 37.037 11.37 0.00 0.00 3.07
614 1566 7.849322 ATAAACAAACTTTCCACCCTATTGT 57.151 32.000 0.00 0.00 0.00 2.71
615 1567 8.943594 ATAAACAAACTTTCCACCCTATTGTA 57.056 30.769 0.00 0.00 0.00 2.41
616 1568 6.644248 AACAAACTTTCCACCCTATTGTAC 57.356 37.500 0.00 0.00 0.00 2.90
617 1569 5.697067 ACAAACTTTCCACCCTATTGTACA 58.303 37.500 0.00 0.00 0.00 2.90
618 1570 6.130569 ACAAACTTTCCACCCTATTGTACAA 58.869 36.000 11.41 11.41 0.00 2.41
619 1571 6.264518 ACAAACTTTCCACCCTATTGTACAAG 59.735 38.462 14.65 0.71 0.00 3.16
620 1572 4.918588 ACTTTCCACCCTATTGTACAAGG 58.081 43.478 14.65 12.13 0.00 3.61
621 1573 4.352893 ACTTTCCACCCTATTGTACAAGGT 59.647 41.667 14.65 12.78 0.00 3.50
622 1574 4.563140 TTCCACCCTATTGTACAAGGTC 57.437 45.455 14.65 0.00 0.00 3.85
623 1575 3.522759 TCCACCCTATTGTACAAGGTCA 58.477 45.455 14.65 2.61 0.00 4.02
624 1576 3.262405 TCCACCCTATTGTACAAGGTCAC 59.738 47.826 14.65 0.00 0.00 3.67
625 1577 3.263425 CCACCCTATTGTACAAGGTCACT 59.737 47.826 14.65 0.00 0.00 3.41
626 1578 4.468510 CCACCCTATTGTACAAGGTCACTA 59.531 45.833 14.65 0.00 0.00 2.74
627 1579 5.416947 CACCCTATTGTACAAGGTCACTAC 58.583 45.833 14.65 0.00 0.00 2.73
628 1580 5.046878 CACCCTATTGTACAAGGTCACTACA 60.047 44.000 14.65 0.00 0.00 2.74
629 1581 5.724854 ACCCTATTGTACAAGGTCACTACAT 59.275 40.000 14.65 0.00 0.00 2.29
630 1582 6.899075 ACCCTATTGTACAAGGTCACTACATA 59.101 38.462 14.65 0.00 0.00 2.29
631 1583 7.400915 ACCCTATTGTACAAGGTCACTACATAA 59.599 37.037 14.65 0.00 0.00 1.90
632 1584 8.262227 CCCTATTGTACAAGGTCACTACATAAA 58.738 37.037 14.65 0.00 0.00 1.40
633 1585 9.832445 CCTATTGTACAAGGTCACTACATAAAT 57.168 33.333 14.65 0.00 0.00 1.40
636 1588 9.959721 ATTGTACAAGGTCACTACATAAATCTT 57.040 29.630 14.65 0.00 0.00 2.40
637 1589 8.997621 TGTACAAGGTCACTACATAAATCTTC 57.002 34.615 0.00 0.00 0.00 2.87
638 1590 8.590204 TGTACAAGGTCACTACATAAATCTTCA 58.410 33.333 0.00 0.00 0.00 3.02
639 1591 9.601217 GTACAAGGTCACTACATAAATCTTCAT 57.399 33.333 0.00 0.00 0.00 2.57
640 1592 8.723942 ACAAGGTCACTACATAAATCTTCATC 57.276 34.615 0.00 0.00 0.00 2.92
641 1593 8.543774 ACAAGGTCACTACATAAATCTTCATCT 58.456 33.333 0.00 0.00 0.00 2.90
642 1594 8.824781 CAAGGTCACTACATAAATCTTCATCTG 58.175 37.037 0.00 0.00 0.00 2.90
664 1616 8.370493 TCTGTTATATTCAGAATTACTGCAGC 57.630 34.615 15.27 0.00 45.38 5.25
686 1638 3.437213 TGGTTCGGAACTTCAGATCCTA 58.563 45.455 19.40 4.78 35.13 2.94
710 1662 6.606768 AGAGAATTGACAGAAGAAAAATCGC 58.393 36.000 0.00 0.00 0.00 4.58
735 1688 2.597455 ACCTAACAAAGTGGCTGCAAT 58.403 42.857 0.50 0.00 0.00 3.56
741 1694 2.558359 ACAAAGTGGCTGCAATTAGTCC 59.442 45.455 0.50 0.00 0.00 3.85
774 1727 2.773993 TGGGGAATTACCAGTCGAAC 57.226 50.000 9.50 0.00 41.20 3.95
776 1729 1.205417 GGGGAATTACCAGTCGAACGA 59.795 52.381 9.50 0.00 41.20 3.85
777 1730 2.537401 GGGAATTACCAGTCGAACGAG 58.463 52.381 0.21 0.00 41.20 4.18
778 1731 2.094338 GGGAATTACCAGTCGAACGAGT 60.094 50.000 0.21 0.00 41.20 4.18
779 1732 3.177487 GGAATTACCAGTCGAACGAGTC 58.823 50.000 1.42 0.00 38.79 3.36
780 1733 2.935481 ATTACCAGTCGAACGAGTCC 57.065 50.000 1.42 0.00 0.00 3.85
781 1734 1.608055 TTACCAGTCGAACGAGTCCA 58.392 50.000 1.42 0.00 0.00 4.02
782 1735 1.162698 TACCAGTCGAACGAGTCCAG 58.837 55.000 1.42 0.00 0.00 3.86
783 1736 0.536687 ACCAGTCGAACGAGTCCAGA 60.537 55.000 1.42 0.00 0.00 3.86
784 1737 0.169230 CCAGTCGAACGAGTCCAGAG 59.831 60.000 1.42 0.00 0.00 3.35
785 1738 0.875728 CAGTCGAACGAGTCCAGAGT 59.124 55.000 1.42 0.00 0.00 3.24
786 1739 0.875728 AGTCGAACGAGTCCAGAGTG 59.124 55.000 0.00 0.00 0.00 3.51
787 1740 0.729816 GTCGAACGAGTCCAGAGTGC 60.730 60.000 0.00 0.00 0.00 4.40
788 1741 1.797933 CGAACGAGTCCAGAGTGCG 60.798 63.158 0.00 0.00 0.00 5.34
789 1742 2.049063 AACGAGTCCAGAGTGCGC 60.049 61.111 0.00 0.00 0.00 6.09
790 1743 3.575351 AACGAGTCCAGAGTGCGCC 62.575 63.158 4.18 0.00 0.00 6.53
792 1745 3.749064 GAGTCCAGAGTGCGCCGA 61.749 66.667 4.18 0.00 0.00 5.54
793 1746 3.069980 GAGTCCAGAGTGCGCCGAT 62.070 63.158 4.18 0.00 0.00 4.18
794 1747 2.125512 GTCCAGAGTGCGCCGATT 60.126 61.111 4.18 0.00 0.00 3.34
795 1748 2.125552 TCCAGAGTGCGCCGATTG 60.126 61.111 4.18 0.00 0.00 2.67
796 1749 2.125552 CCAGAGTGCGCCGATTGA 60.126 61.111 4.18 0.00 0.00 2.57
797 1750 1.522355 CCAGAGTGCGCCGATTGAT 60.522 57.895 4.18 0.00 0.00 2.57
798 1751 0.249447 CCAGAGTGCGCCGATTGATA 60.249 55.000 4.18 0.00 0.00 2.15
799 1752 1.135046 CAGAGTGCGCCGATTGATAG 58.865 55.000 4.18 0.00 0.00 2.08
800 1753 1.032794 AGAGTGCGCCGATTGATAGA 58.967 50.000 4.18 0.00 0.00 1.98
801 1754 1.615883 AGAGTGCGCCGATTGATAGAT 59.384 47.619 4.18 0.00 0.00 1.98
802 1755 1.723542 GAGTGCGCCGATTGATAGATG 59.276 52.381 4.18 0.00 0.00 2.90
803 1756 0.164647 GTGCGCCGATTGATAGATGC 59.835 55.000 4.18 0.00 0.00 3.91
804 1757 0.249826 TGCGCCGATTGATAGATGCA 60.250 50.000 4.18 0.00 0.00 3.96
805 1758 1.081892 GCGCCGATTGATAGATGCAT 58.918 50.000 0.00 0.00 0.00 3.96
806 1759 2.270923 GCGCCGATTGATAGATGCATA 58.729 47.619 0.00 0.00 0.00 3.14
807 1760 2.029728 GCGCCGATTGATAGATGCATAC 59.970 50.000 0.00 0.00 0.00 2.39
808 1761 2.279921 CGCCGATTGATAGATGCATACG 59.720 50.000 0.00 0.00 0.00 3.06
809 1762 3.254060 GCCGATTGATAGATGCATACGT 58.746 45.455 0.00 0.00 0.00 3.57
810 1763 4.421058 GCCGATTGATAGATGCATACGTA 58.579 43.478 0.00 0.00 0.00 3.57
811 1764 5.043903 GCCGATTGATAGATGCATACGTAT 58.956 41.667 1.14 1.14 0.00 3.06
812 1765 6.206498 GCCGATTGATAGATGCATACGTATA 58.794 40.000 7.96 0.00 0.00 1.47
813 1766 6.695713 GCCGATTGATAGATGCATACGTATAA 59.304 38.462 7.96 0.00 0.00 0.98
814 1767 7.222031 GCCGATTGATAGATGCATACGTATAAA 59.778 37.037 7.96 0.00 0.00 1.40
815 1768 9.083080 CCGATTGATAGATGCATACGTATAAAA 57.917 33.333 7.96 0.00 0.00 1.52
838 1791 5.852282 AAAATCCCCGAAATCAAGGTATG 57.148 39.130 0.00 0.00 0.00 2.39
839 1792 3.508845 ATCCCCGAAATCAAGGTATGG 57.491 47.619 0.00 0.00 0.00 2.74
840 1793 1.133915 TCCCCGAAATCAAGGTATGGC 60.134 52.381 0.00 0.00 0.00 4.40
841 1794 0.944386 CCCGAAATCAAGGTATGGCG 59.056 55.000 0.00 0.00 0.00 5.69
842 1795 0.944386 CCGAAATCAAGGTATGGCGG 59.056 55.000 0.00 0.00 0.00 6.13
843 1796 0.307760 CGAAATCAAGGTATGGCGGC 59.692 55.000 0.00 0.00 0.00 6.53
844 1797 1.680338 GAAATCAAGGTATGGCGGCT 58.320 50.000 11.43 0.00 0.00 5.52
845 1798 1.334869 GAAATCAAGGTATGGCGGCTG 59.665 52.381 11.43 0.00 0.00 4.85
846 1799 1.103398 AATCAAGGTATGGCGGCTGC 61.103 55.000 9.72 9.72 41.71 5.25
858 1811 4.902645 GGCTGCCATACCCTGCCC 62.903 72.222 15.17 0.00 40.27 5.36
859 1812 4.127744 GCTGCCATACCCTGCCCA 62.128 66.667 0.00 0.00 0.00 5.36
860 1813 2.124151 CTGCCATACCCTGCCCAC 60.124 66.667 0.00 0.00 0.00 4.61
861 1814 3.721370 CTGCCATACCCTGCCCACC 62.721 68.421 0.00 0.00 0.00 4.61
862 1815 4.522975 GCCATACCCTGCCCACCC 62.523 72.222 0.00 0.00 0.00 4.61
863 1816 4.189580 CCATACCCTGCCCACCCG 62.190 72.222 0.00 0.00 0.00 5.28
864 1817 3.087253 CATACCCTGCCCACCCGA 61.087 66.667 0.00 0.00 0.00 5.14
865 1818 2.768344 ATACCCTGCCCACCCGAG 60.768 66.667 0.00 0.00 0.00 4.63
1021 2011 2.845659 TGGAGGGTGTGGTGATTAGAT 58.154 47.619 0.00 0.00 0.00 1.98
1263 2398 4.012374 CAGCCTTTCACATAGTTGGTGAT 58.988 43.478 0.00 0.00 44.11 3.06
1631 3454 3.383185 TGAAATGAAGGTGTTTGTGGTCC 59.617 43.478 0.00 0.00 0.00 4.46
1685 3508 3.069318 GCCTCTTCCGTCCGGAGT 61.069 66.667 3.06 0.00 46.06 3.85
1819 3642 0.107831 ACTACAAGTGCCGCTTCCAA 59.892 50.000 0.00 0.00 34.69 3.53
1845 3668 3.138304 GACACCAGCACACATTTGTCTA 58.862 45.455 0.00 0.00 31.66 2.59
2081 3916 0.981183 TACCCAACATCACCGCTTCT 59.019 50.000 0.00 0.00 0.00 2.85
2133 4004 8.186178 ACTATTTTGTCAACTACTATCGCAAG 57.814 34.615 0.00 0.00 0.00 4.01
2156 4027 0.601311 GACAAGAACTGCGAGCTGGT 60.601 55.000 0.00 0.00 0.00 4.00
2632 4518 5.237996 CCAGTGTCATGCCTTATTACAGATG 59.762 44.000 0.00 0.00 0.00 2.90
2661 4547 4.013728 CCACACTAAGCTCTAGTCTGACT 58.986 47.826 15.57 15.57 0.00 3.41
3070 4964 1.640917 GTGTCTCCACCCTTCCACTA 58.359 55.000 0.00 0.00 35.44 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.922740 AGACTTCGCCACACCTTAAA 57.077 45.000 0.00 0.00 0.00 1.52
46 47 6.143438 GTGTCTTGACTCTTTTGATTTGCATG 59.857 38.462 2.35 0.00 0.00 4.06
55 56 7.164171 CGTTTGTAATGTGTCTTGACTCTTTTG 59.836 37.037 2.35 0.00 0.00 2.44
56 57 7.065324 TCGTTTGTAATGTGTCTTGACTCTTTT 59.935 33.333 2.35 1.16 0.00 2.27
67 68 6.872670 TTTGGTTTTCGTTTGTAATGTGTC 57.127 33.333 0.00 0.00 0.00 3.67
87 89 9.897744 AACATGTCTACACTTTCATTGTATTTG 57.102 29.630 0.00 0.00 0.00 2.32
101 103 8.564574 TGTTTTCCTATTGAAACATGTCTACAC 58.435 33.333 0.00 0.00 42.56 2.90
107 109 7.360113 AGGTTGTTTTCCTATTGAAACATGT 57.640 32.000 0.00 0.00 42.56 3.21
140 142 4.260743 CGCCATTGAAAGCTTCATTATCGA 60.261 41.667 0.00 0.00 39.84 3.59
147 149 1.896220 AGACGCCATTGAAAGCTTCA 58.104 45.000 0.00 0.00 38.04 3.02
152 154 3.619038 GGTCTTCTAGACGCCATTGAAAG 59.381 47.826 0.00 0.00 45.96 2.62
162 164 3.243569 CCATTGCCTAGGTCTTCTAGACG 60.244 52.174 11.31 0.00 45.96 4.18
224 226 4.959596 ATTTCAGCACATGTCACTCATC 57.040 40.909 0.00 0.00 34.09 2.92
240 1192 5.049060 CACCCGTGAAAGTGTCAATATTTCA 60.049 40.000 5.46 5.46 39.84 2.69
353 1305 6.843069 TTGAAGCCTTAAATTCAAGCAAAC 57.157 33.333 6.22 0.00 39.76 2.93
453 1405 6.532826 AGAAGATGGATAGAAAGAGGAATGC 58.467 40.000 0.00 0.00 0.00 3.56
536 1488 7.271868 ACTGTACGAACAAGTTTTTGCTTTTAC 59.728 33.333 0.00 0.00 37.85 2.01
542 1494 5.561993 TGTACTGTACGAACAAGTTTTTGC 58.438 37.500 12.87 0.00 37.85 3.68
588 1540 9.541884 ACAATAGGGTGGAAAGTTTGTTTATAT 57.458 29.630 0.00 0.00 0.00 0.86
589 1541 8.943594 ACAATAGGGTGGAAAGTTTGTTTATA 57.056 30.769 0.00 0.00 0.00 0.98
590 1542 7.849322 ACAATAGGGTGGAAAGTTTGTTTAT 57.151 32.000 0.00 0.00 0.00 1.40
591 1543 7.778853 TGTACAATAGGGTGGAAAGTTTGTTTA 59.221 33.333 0.00 0.00 0.00 2.01
592 1544 6.608002 TGTACAATAGGGTGGAAAGTTTGTTT 59.392 34.615 0.00 0.00 0.00 2.83
593 1545 6.130569 TGTACAATAGGGTGGAAAGTTTGTT 58.869 36.000 0.00 0.00 0.00 2.83
594 1546 5.697067 TGTACAATAGGGTGGAAAGTTTGT 58.303 37.500 0.00 0.00 0.00 2.83
595 1547 6.294508 CCTTGTACAATAGGGTGGAAAGTTTG 60.295 42.308 9.13 0.00 0.00 2.93
596 1548 5.773176 CCTTGTACAATAGGGTGGAAAGTTT 59.227 40.000 9.13 0.00 0.00 2.66
597 1549 5.163023 ACCTTGTACAATAGGGTGGAAAGTT 60.163 40.000 15.22 0.00 35.79 2.66
598 1550 4.352893 ACCTTGTACAATAGGGTGGAAAGT 59.647 41.667 15.22 0.00 35.79 2.66
599 1551 4.918588 ACCTTGTACAATAGGGTGGAAAG 58.081 43.478 15.22 0.00 35.79 2.62
600 1552 4.351407 TGACCTTGTACAATAGGGTGGAAA 59.649 41.667 19.57 4.35 35.79 3.13
601 1553 3.911260 TGACCTTGTACAATAGGGTGGAA 59.089 43.478 19.57 5.68 35.79 3.53
602 1554 3.262405 GTGACCTTGTACAATAGGGTGGA 59.738 47.826 19.57 6.32 35.79 4.02
603 1555 3.263425 AGTGACCTTGTACAATAGGGTGG 59.737 47.826 19.57 13.63 35.79 4.61
604 1556 4.553330 AGTGACCTTGTACAATAGGGTG 57.447 45.455 19.57 3.42 35.79 4.61
605 1557 5.088730 TGTAGTGACCTTGTACAATAGGGT 58.911 41.667 15.76 15.76 35.79 4.34
606 1558 5.670792 TGTAGTGACCTTGTACAATAGGG 57.329 43.478 16.32 13.24 35.79 3.53
607 1559 9.832445 ATTTATGTAGTGACCTTGTACAATAGG 57.168 33.333 9.13 10.43 37.56 2.57
610 1562 9.959721 AAGATTTATGTAGTGACCTTGTACAAT 57.040 29.630 9.13 0.00 30.70 2.71
611 1563 9.431887 GAAGATTTATGTAGTGACCTTGTACAA 57.568 33.333 8.28 8.28 30.70 2.41
612 1564 8.590204 TGAAGATTTATGTAGTGACCTTGTACA 58.410 33.333 0.00 0.00 0.00 2.90
613 1565 8.997621 TGAAGATTTATGTAGTGACCTTGTAC 57.002 34.615 0.00 0.00 0.00 2.90
614 1566 9.817809 GATGAAGATTTATGTAGTGACCTTGTA 57.182 33.333 0.00 0.00 0.00 2.41
615 1567 8.543774 AGATGAAGATTTATGTAGTGACCTTGT 58.456 33.333 0.00 0.00 0.00 3.16
616 1568 8.824781 CAGATGAAGATTTATGTAGTGACCTTG 58.175 37.037 0.00 0.00 0.00 3.61
617 1569 8.543774 ACAGATGAAGATTTATGTAGTGACCTT 58.456 33.333 0.00 0.00 0.00 3.50
618 1570 8.083828 ACAGATGAAGATTTATGTAGTGACCT 57.916 34.615 0.00 0.00 0.00 3.85
619 1571 8.723942 AACAGATGAAGATTTATGTAGTGACC 57.276 34.615 0.00 0.00 0.00 4.02
638 1590 8.997323 GCTGCAGTAATTCTGAATATAACAGAT 58.003 33.333 16.64 3.53 46.27 2.90
639 1591 8.206867 AGCTGCAGTAATTCTGAATATAACAGA 58.793 33.333 16.64 8.00 46.27 3.41
640 1592 8.281194 CAGCTGCAGTAATTCTGAATATAACAG 58.719 37.037 16.64 9.03 46.27 3.16
641 1593 7.227314 CCAGCTGCAGTAATTCTGAATATAACA 59.773 37.037 16.64 0.00 46.27 2.41
642 1594 7.227512 ACCAGCTGCAGTAATTCTGAATATAAC 59.772 37.037 16.64 3.27 46.27 1.89
664 1616 2.234908 AGGATCTGAAGTTCCGAACCAG 59.765 50.000 20.62 9.00 38.59 4.00
686 1638 6.348868 GGCGATTTTTCTTCTGTCAATTCTCT 60.349 38.462 0.00 0.00 0.00 3.10
710 1662 3.119495 GCAGCCACTTTGTTAGGTATTGG 60.119 47.826 0.00 0.00 0.00 3.16
768 1721 0.729816 GCACTCTGGACTCGTTCGAC 60.730 60.000 0.00 0.00 0.00 4.20
769 1722 1.579932 GCACTCTGGACTCGTTCGA 59.420 57.895 0.00 0.00 0.00 3.71
770 1723 1.797933 CGCACTCTGGACTCGTTCG 60.798 63.158 0.00 0.00 0.00 3.95
771 1724 2.089349 GCGCACTCTGGACTCGTTC 61.089 63.158 0.30 0.00 0.00 3.95
773 1726 4.057428 GGCGCACTCTGGACTCGT 62.057 66.667 10.83 0.00 0.00 4.18
776 1729 2.650116 AATCGGCGCACTCTGGACT 61.650 57.895 10.83 0.00 0.00 3.85
777 1730 2.125512 AATCGGCGCACTCTGGAC 60.126 61.111 10.83 0.00 0.00 4.02
778 1731 1.960040 ATCAATCGGCGCACTCTGGA 61.960 55.000 10.83 0.00 0.00 3.86
779 1732 0.249447 TATCAATCGGCGCACTCTGG 60.249 55.000 10.83 0.00 0.00 3.86
780 1733 1.135046 CTATCAATCGGCGCACTCTG 58.865 55.000 10.83 0.45 0.00 3.35
781 1734 1.032794 TCTATCAATCGGCGCACTCT 58.967 50.000 10.83 0.00 0.00 3.24
782 1735 1.723542 CATCTATCAATCGGCGCACTC 59.276 52.381 10.83 0.00 0.00 3.51
783 1736 1.788258 CATCTATCAATCGGCGCACT 58.212 50.000 10.83 0.00 0.00 4.40
784 1737 0.164647 GCATCTATCAATCGGCGCAC 59.835 55.000 10.83 0.00 0.00 5.34
785 1738 0.249826 TGCATCTATCAATCGGCGCA 60.250 50.000 10.83 0.00 0.00 6.09
786 1739 1.081892 ATGCATCTATCAATCGGCGC 58.918 50.000 0.00 0.00 0.00 6.53
787 1740 2.279921 CGTATGCATCTATCAATCGGCG 59.720 50.000 0.19 0.00 0.00 6.46
788 1741 3.254060 ACGTATGCATCTATCAATCGGC 58.746 45.455 0.19 0.00 0.00 5.54
789 1742 8.628882 TTTATACGTATGCATCTATCAATCGG 57.371 34.615 18.37 0.00 0.00 4.18
815 1768 5.128663 CCATACCTTGATTTCGGGGATTTTT 59.871 40.000 0.00 0.00 0.00 1.94
816 1769 4.649218 CCATACCTTGATTTCGGGGATTTT 59.351 41.667 0.00 0.00 0.00 1.82
817 1770 4.215109 CCATACCTTGATTTCGGGGATTT 58.785 43.478 0.00 0.00 0.00 2.17
818 1771 3.832527 CCATACCTTGATTTCGGGGATT 58.167 45.455 0.00 0.00 0.00 3.01
819 1772 2.489073 GCCATACCTTGATTTCGGGGAT 60.489 50.000 0.00 0.00 0.00 3.85
820 1773 1.133915 GCCATACCTTGATTTCGGGGA 60.134 52.381 0.00 0.00 0.00 4.81
821 1774 1.318576 GCCATACCTTGATTTCGGGG 58.681 55.000 0.00 0.00 0.00 5.73
822 1775 0.944386 CGCCATACCTTGATTTCGGG 59.056 55.000 0.00 0.00 0.00 5.14
823 1776 0.944386 CCGCCATACCTTGATTTCGG 59.056 55.000 0.00 0.00 0.00 4.30
824 1777 0.307760 GCCGCCATACCTTGATTTCG 59.692 55.000 0.00 0.00 0.00 3.46
825 1778 1.334869 CAGCCGCCATACCTTGATTTC 59.665 52.381 0.00 0.00 0.00 2.17
826 1779 1.392589 CAGCCGCCATACCTTGATTT 58.607 50.000 0.00 0.00 0.00 2.17
827 1780 1.103398 GCAGCCGCCATACCTTGATT 61.103 55.000 0.00 0.00 0.00 2.57
828 1781 1.526917 GCAGCCGCCATACCTTGAT 60.527 57.895 0.00 0.00 0.00 2.57
829 1782 2.124736 GCAGCCGCCATACCTTGA 60.125 61.111 0.00 0.00 0.00 3.02
846 1799 4.189580 CGGGTGGGCAGGGTATGG 62.190 72.222 0.00 0.00 0.00 2.74
847 1800 3.087253 TCGGGTGGGCAGGGTATG 61.087 66.667 0.00 0.00 0.00 2.39
848 1801 2.768344 CTCGGGTGGGCAGGGTAT 60.768 66.667 0.00 0.00 0.00 2.73
863 1816 4.459089 GTCACTGGCGGAGGGCTC 62.459 72.222 0.00 0.00 42.94 4.70
866 1819 4.394712 GTGGTCACTGGCGGAGGG 62.395 72.222 0.00 0.00 0.00 4.30
867 1820 4.742201 CGTGGTCACTGGCGGAGG 62.742 72.222 0.00 0.00 0.00 4.30
868 1821 4.742201 CCGTGGTCACTGGCGGAG 62.742 72.222 0.00 0.00 46.33 4.63
1021 2011 0.178955 TTCACCTCCACAGTCCGGTA 60.179 55.000 0.00 0.00 0.00 4.02
1263 2398 1.372997 GTCGAGGAGCGCAACAAGA 60.373 57.895 11.47 0.00 40.61 3.02
1819 3642 0.179009 ATGTGTGCTGGTGTCTTGCT 60.179 50.000 0.00 0.00 0.00 3.91
1845 3668 2.703007 ACAGAGACCAGCTGAAAGTTCT 59.297 45.455 17.39 8.30 36.86 3.01
2081 3916 4.020617 CCTCGGTGAGCCAAGGCA 62.021 66.667 14.40 0.00 44.88 4.75
2133 4004 1.599542 AGCTCGCAGTTCTTGTCAAAC 59.400 47.619 0.00 0.00 0.00 2.93
2156 4027 4.720902 CATCTGCCCACGGTGCCA 62.721 66.667 1.68 1.20 0.00 4.92
2632 4518 5.785243 ACTAGAGCTTAGTGTGGAAGAAAC 58.215 41.667 0.00 0.00 0.00 2.78
2661 4547 9.219603 CCAATTCTTTGTGAACTAGTTGATAGA 57.780 33.333 14.14 6.63 37.52 1.98


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

AutoCloner maintained by Alex Coulton.