Multiple sequence alignment - TraesCS6B01G082100

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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 TraesCS6B01G082100 chr6B 100.000 2540 0 0 1 2540 58811404 58813943 0.000000e+00 4691.0
1 TraesCS6B01G082100 chr6B 89.164 1615 89 34 1 1585 59099615 59101173 0.000000e+00 1934.0
2 TraesCS6B01G082100 chr6B 94.053 639 20 10 965 1585 59723166 59723804 0.000000e+00 953.0
3 TraesCS6B01G082100 chr6B 91.192 579 28 12 1 557 59722603 59723180 0.000000e+00 765.0
4 TraesCS6B01G082100 chr6B 100.000 36 0 0 1 36 59099588 59099623 1.630000e-07 67.6
5 TraesCS6B01G082100 chr6A 91.717 821 39 14 788 1585 33010611 33011425 0.000000e+00 1112.0
6 TraesCS6B01G082100 chr6A 93.207 633 21 10 974 1585 33535696 33535065 0.000000e+00 911.0
7 TraesCS6B01G082100 chr6A 90.769 195 16 2 579 771 33010431 33010625 2.510000e-65 259.0
8 TraesCS6B01G082100 chr6D 87.636 825 53 29 786 1585 29381477 29380677 0.000000e+00 913.0
9 TraesCS6B01G082100 chr6D 93.613 595 22 7 979 1559 29089687 29090279 0.000000e+00 874.0
10 TraesCS6B01G082100 chr6D 94.221 571 23 5 980 1542 24001558 24002126 0.000000e+00 863.0
11 TraesCS6B01G082100 chr6D 89.505 667 57 12 923 1585 16502837 16503494 0.000000e+00 832.0
12 TraesCS6B01G082100 chr6D 89.783 646 48 11 917 1556 16523255 16522622 0.000000e+00 811.0
13 TraesCS6B01G082100 chr6D 93.086 405 17 3 1701 2094 114835559 114835963 1.310000e-162 582.0
14 TraesCS6B01G082100 chr6D 82.697 393 57 8 147 530 29383165 29382775 3.130000e-89 339.0
15 TraesCS6B01G082100 chr6D 81.638 403 52 11 147 530 29382173 29381774 5.270000e-82 315.0
16 TraesCS6B01G082100 chr1A 98.458 454 7 0 2087 2540 461054777 461055230 0.000000e+00 800.0
17 TraesCS6B01G082100 chr1A 94.789 403 4 3 1701 2094 461054356 461054750 1.670000e-171 612.0
18 TraesCS6B01G082100 chr7B 97.802 455 10 0 2086 2540 1485513 1485967 0.000000e+00 785.0
19 TraesCS6B01G082100 chr7B 96.030 403 7 2 1701 2094 1485085 1485487 0.000000e+00 647.0
20 TraesCS6B01G082100 chr3A 97.802 455 10 0 2086 2540 123309491 123309037 0.000000e+00 785.0
21 TraesCS6B01G082100 chr3A 96.030 403 7 2 1701 2094 123309919 123309517 0.000000e+00 647.0
22 TraesCS6B01G082100 chr3A 91.803 61 3 2 1586 1645 679984426 679984367 1.620000e-12 84.2
23 TraesCS6B01G082100 chr5B 97.098 448 11 1 2095 2540 542695859 542695412 0.000000e+00 754.0
24 TraesCS6B01G082100 chr5B 95.285 403 6 3 1701 2094 542696292 542695894 5.970000e-176 627.0
25 TraesCS6B01G082100 chr5B 97.786 271 4 1 2270 2540 79789642 79789910 1.380000e-127 466.0
26 TraesCS6B01G082100 chr5B 93.146 321 11 3 1701 2010 79789303 79789623 6.400000e-126 460.0
27 TraesCS6B01G082100 chr5B 96.000 50 2 0 1586 1635 17463028 17462979 5.820000e-12 82.4
28 TraesCS6B01G082100 chr1B 95.425 459 12 4 2086 2540 667642188 667641735 0.000000e+00 723.0
29 TraesCS6B01G082100 chr1B 96.069 407 7 2 1697 2094 667642620 667642214 0.000000e+00 654.0
30 TraesCS6B01G082100 chr4D 94.335 406 12 3 1700 2094 58988575 58988980 1.670000e-171 612.0
31 TraesCS6B01G082100 chr4D 96.679 271 7 1 2270 2540 58989619 58989887 1.390000e-122 449.0
32 TraesCS6B01G082100 chr4D 93.923 181 11 0 2086 2266 58989158 58989338 8.950000e-70 274.0
33 TraesCS6B01G082100 chr4D 90.000 60 5 1 1586 1645 440408330 440408272 2.710000e-10 76.8
34 TraesCS6B01G082100 chr4A 93.781 402 17 4 1701 2094 708449265 708448864 4.680000e-167 597.0
35 TraesCS6B01G082100 chr4A 95.349 172 8 0 2095 2266 708448677 708448506 8.950000e-70 274.0
36 TraesCS6B01G082100 chrUn 91.927 384 20 3 1722 2094 289262459 289262076 6.220000e-146 527.0
37 TraesCS6B01G082100 chrUn 96.000 275 7 2 2270 2540 289260618 289260344 6.450000e-121 444.0
38 TraesCS6B01G082100 chrUn 97.778 45 1 0 1586 1630 281065553 281065509 7.530000e-11 78.7
39 TraesCS6B01G082100 chrUn 94.000 50 3 0 1586 1635 88101352 88101303 2.710000e-10 76.8
40 TraesCS6B01G082100 chr2A 97.417 271 5 1 2270 2540 684390790 684391058 6.400000e-126 460.0
41 TraesCS6B01G082100 chr2A 92.284 324 14 3 1698 2010 684390448 684390771 1.390000e-122 449.0
42 TraesCS6B01G082100 chr2A 91.765 170 14 0 2097 2266 507316996 507316827 1.170000e-58 237.0
43 TraesCS6B01G082100 chr5D 94.017 117 6 1 1586 1702 430984565 430984450 2.600000e-40 176.0
44 TraesCS6B01G082100 chr5D 94.000 50 3 0 1586 1635 2786100 2786149 2.710000e-10 76.8
45 TraesCS6B01G082100 chr3B 90.598 117 10 1 1586 1702 700233196 700233311 1.220000e-33 154.0
46 TraesCS6B01G082100 chr2D 81.308 107 16 4 3 107 79399174 79399278 1.620000e-12 84.2
47 TraesCS6B01G082100 chr3D 94.000 50 3 0 1586 1635 26152383 26152334 2.710000e-10 76.8


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 TraesCS6B01G082100 chr6B 58811404 58813943 2539 False 4691.000000 4691 100.000000 1 2540 1 chr6B.!!$F1 2539
1 TraesCS6B01G082100 chr6B 59099588 59101173 1585 False 1000.800000 1934 94.582000 1 1585 2 chr6B.!!$F2 1584
2 TraesCS6B01G082100 chr6B 59722603 59723804 1201 False 859.000000 953 92.622500 1 1585 2 chr6B.!!$F3 1584
3 TraesCS6B01G082100 chr6A 33535065 33535696 631 True 911.000000 911 93.207000 974 1585 1 chr6A.!!$R1 611
4 TraesCS6B01G082100 chr6A 33010431 33011425 994 False 685.500000 1112 91.243000 579 1585 2 chr6A.!!$F1 1006
5 TraesCS6B01G082100 chr6D 29089687 29090279 592 False 874.000000 874 93.613000 979 1559 1 chr6D.!!$F3 580
6 TraesCS6B01G082100 chr6D 24001558 24002126 568 False 863.000000 863 94.221000 980 1542 1 chr6D.!!$F2 562
7 TraesCS6B01G082100 chr6D 16502837 16503494 657 False 832.000000 832 89.505000 923 1585 1 chr6D.!!$F1 662
8 TraesCS6B01G082100 chr6D 16522622 16523255 633 True 811.000000 811 89.783000 917 1556 1 chr6D.!!$R1 639
9 TraesCS6B01G082100 chr6D 29380677 29383165 2488 True 522.333333 913 83.990333 147 1585 3 chr6D.!!$R2 1438
10 TraesCS6B01G082100 chr1A 461054356 461055230 874 False 706.000000 800 96.623500 1701 2540 2 chr1A.!!$F1 839
11 TraesCS6B01G082100 chr7B 1485085 1485967 882 False 716.000000 785 96.916000 1701 2540 2 chr7B.!!$F1 839
12 TraesCS6B01G082100 chr3A 123309037 123309919 882 True 716.000000 785 96.916000 1701 2540 2 chr3A.!!$R2 839
13 TraesCS6B01G082100 chr5B 542695412 542696292 880 True 690.500000 754 96.191500 1701 2540 2 chr5B.!!$R2 839
14 TraesCS6B01G082100 chr5B 79789303 79789910 607 False 463.000000 466 95.466000 1701 2540 2 chr5B.!!$F1 839
15 TraesCS6B01G082100 chr1B 667641735 667642620 885 True 688.500000 723 95.747000 1697 2540 2 chr1B.!!$R1 843
16 TraesCS6B01G082100 chr4D 58988575 58989887 1312 False 445.000000 612 94.979000 1700 2540 3 chr4D.!!$F1 840
17 TraesCS6B01G082100 chr4A 708448506 708449265 759 True 435.500000 597 94.565000 1701 2266 2 chr4A.!!$R1 565
18 TraesCS6B01G082100 chrUn 289260344 289262459 2115 True 485.500000 527 93.963500 1722 2540 2 chrUn.!!$R3 818
19 TraesCS6B01G082100 chr2A 684390448 684391058 610 False 454.500000 460 94.850500 1698 2540 2 chr2A.!!$F1 842

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
781 1749 0.597118 GCGCTGTGACCATGCAAAAA 60.597 50.0 0.0 0.0 0.0 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2267 3956 0.03601 AGCCACACCATTCTTCTCGG 60.036 55.0 0.0 0.0 0.0 4.63 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
66 94 2.860136 TGCGACGAAGAATCATCATCAC 59.140 45.455 0.00 0.00 0.00 3.06
263 1138 1.542915 CTTTTCTACCTCCACCGTCGA 59.457 52.381 0.00 0.00 0.00 4.20
324 1199 2.126596 CACCACAACAGCCTTGGCA 61.127 57.895 14.54 0.00 33.25 4.92
391 1267 2.111384 ACACTGACTATGCGGGATCTT 58.889 47.619 0.00 0.00 0.00 2.40
401 1277 2.577059 GGGATCTTGCGACGACCA 59.423 61.111 0.00 0.00 0.00 4.02
431 1308 1.602605 GCTTAGGCGGTGGTTTGGT 60.603 57.895 0.00 0.00 0.00 3.67
450 1327 1.555075 GTCTTCTATGGGCCACTGTCA 59.445 52.381 9.28 0.00 0.00 3.58
473 1350 2.072487 GCCCATGCCCTCCAGTAGA 61.072 63.158 0.00 0.00 0.00 2.59
572 1452 1.735369 CGGTTGCATATTTGTGGCACC 60.735 52.381 16.26 0.00 37.26 5.01
601 1563 2.166664 GTGCCCTGTTTTTGGTACACAA 59.833 45.455 0.00 0.00 39.29 3.33
613 1575 7.537596 TTTTGGTACACAATCAATTCCATCT 57.462 32.000 0.00 0.00 39.29 2.90
614 1576 8.642935 TTTTGGTACACAATCAATTCCATCTA 57.357 30.769 0.00 0.00 39.29 1.98
615 1577 7.624360 TTGGTACACAATCAATTCCATCTAC 57.376 36.000 0.00 0.00 39.29 2.59
662 1629 9.169592 CAAAATTAGAATTCAAGCCCATTTGAT 57.830 29.630 8.44 0.00 36.97 2.57
763 1731 1.226773 GCACGATGCAAATCCCTGC 60.227 57.895 0.00 0.00 44.26 4.85
764 1732 1.063006 CACGATGCAAATCCCTGCG 59.937 57.895 0.00 0.00 45.74 5.18
765 1733 2.025156 CGATGCAAATCCCTGCGC 59.975 61.111 0.00 0.00 45.74 6.09
766 1734 2.475466 CGATGCAAATCCCTGCGCT 61.475 57.895 9.73 0.00 45.74 5.92
767 1735 1.065273 GATGCAAATCCCTGCGCTG 59.935 57.895 9.73 8.47 45.74 5.18
768 1736 1.660560 GATGCAAATCCCTGCGCTGT 61.661 55.000 9.73 0.00 45.74 4.40
769 1737 1.940883 ATGCAAATCCCTGCGCTGTG 61.941 55.000 9.73 0.00 45.74 3.66
770 1738 2.334946 GCAAATCCCTGCGCTGTGA 61.335 57.895 9.73 5.20 31.50 3.58
771 1739 1.503542 CAAATCCCTGCGCTGTGAC 59.496 57.895 9.73 0.00 0.00 3.67
772 1740 1.675641 AAATCCCTGCGCTGTGACC 60.676 57.895 9.73 0.00 0.00 4.02
773 1741 2.410322 AAATCCCTGCGCTGTGACCA 62.410 55.000 9.73 0.00 0.00 4.02
774 1742 2.202236 AATCCCTGCGCTGTGACCAT 62.202 55.000 9.73 0.00 0.00 3.55
775 1743 2.881539 ATCCCTGCGCTGTGACCATG 62.882 60.000 9.73 0.00 0.00 3.66
776 1744 3.807538 CCTGCGCTGTGACCATGC 61.808 66.667 9.73 0.00 0.00 4.06
777 1745 3.051479 CTGCGCTGTGACCATGCA 61.051 61.111 9.73 0.00 32.79 3.96
778 1746 2.594013 TGCGCTGTGACCATGCAA 60.594 55.556 9.73 0.00 31.34 4.08
779 1747 2.132517 CTGCGCTGTGACCATGCAAA 62.133 55.000 9.73 0.00 33.22 3.68
780 1748 1.007502 GCGCTGTGACCATGCAAAA 60.008 52.632 0.00 0.00 0.00 2.44
781 1749 0.597118 GCGCTGTGACCATGCAAAAA 60.597 50.000 0.00 0.00 0.00 1.94
831 1800 1.758514 AGTGCTCCCACGGATCGAT 60.759 57.895 0.00 0.00 46.62 3.59
843 1812 4.534824 ATCGATCCCCGGTCCCGT 62.535 66.667 0.00 0.00 39.14 5.28
904 1874 0.626382 TCCCAACCCACAAACTCACA 59.374 50.000 0.00 0.00 0.00 3.58
905 1875 1.032014 CCCAACCCACAAACTCACAG 58.968 55.000 0.00 0.00 0.00 3.66
1186 2168 2.344500 CCGCCGAGGTAACCACAA 59.656 61.111 0.00 0.00 34.51 3.33
1545 2547 1.153823 CACCAAGGAGTAGCCGTCG 60.154 63.158 0.00 0.00 43.43 5.12
1585 2595 7.039011 AGTGTGTACTCTGTTCCATTTCTCATA 60.039 37.037 0.00 0.00 28.79 2.15
1586 2596 7.602644 GTGTGTACTCTGTTCCATTTCTCATAA 59.397 37.037 0.00 0.00 0.00 1.90
1587 2597 8.154203 TGTGTACTCTGTTCCATTTCTCATAAA 58.846 33.333 0.00 0.00 0.00 1.40
1588 2598 9.167311 GTGTACTCTGTTCCATTTCTCATAAAT 57.833 33.333 0.00 0.00 0.00 1.40
1591 2601 8.738645 ACTCTGTTCCATTTCTCATAAATACC 57.261 34.615 0.00 0.00 0.00 2.73
1592 2602 7.775561 ACTCTGTTCCATTTCTCATAAATACCC 59.224 37.037 0.00 0.00 0.00 3.69
1593 2603 7.638444 TCTGTTCCATTTCTCATAAATACCCA 58.362 34.615 0.00 0.00 0.00 4.51
1594 2604 8.112822 TCTGTTCCATTTCTCATAAATACCCAA 58.887 33.333 0.00 0.00 0.00 4.12
1595 2605 8.837099 TGTTCCATTTCTCATAAATACCCAAT 57.163 30.769 0.00 0.00 0.00 3.16
1596 2606 8.694540 TGTTCCATTTCTCATAAATACCCAATG 58.305 33.333 0.00 0.00 0.00 2.82
1597 2607 7.838079 TCCATTTCTCATAAATACCCAATGG 57.162 36.000 0.00 0.00 40.49 3.16
1599 2609 7.843760 TCCATTTCTCATAAATACCCAATGGTT 59.156 33.333 0.00 0.00 44.75 3.67
1600 2610 8.143835 CCATTTCTCATAAATACCCAATGGTTC 58.856 37.037 0.00 0.00 44.75 3.62
1601 2611 8.694540 CATTTCTCATAAATACCCAATGGTTCA 58.305 33.333 0.00 0.00 44.75 3.18
1602 2612 7.639113 TTCTCATAAATACCCAATGGTTCAC 57.361 36.000 0.00 0.00 44.75 3.18
1603 2613 5.820423 TCTCATAAATACCCAATGGTTCACG 59.180 40.000 0.00 0.00 44.75 4.35
1604 2614 4.884744 TCATAAATACCCAATGGTTCACGG 59.115 41.667 0.00 0.00 44.75 4.94
1605 2615 2.137810 AATACCCAATGGTTCACGGG 57.862 50.000 0.00 0.00 44.75 5.28
1606 2616 0.257616 ATACCCAATGGTTCACGGGG 59.742 55.000 0.00 0.00 44.75 5.73
1607 2617 0.841158 TACCCAATGGTTCACGGGGA 60.841 55.000 11.25 0.00 44.75 4.81
1608 2618 1.677633 CCCAATGGTTCACGGGGAC 60.678 63.158 0.00 0.00 41.49 4.46
1609 2619 1.074072 CCAATGGTTCACGGGGACA 59.926 57.895 0.00 0.00 0.00 4.02
1610 2620 0.323360 CCAATGGTTCACGGGGACAT 60.323 55.000 0.00 0.00 0.00 3.06
1611 2621 1.094785 CAATGGTTCACGGGGACATC 58.905 55.000 0.00 0.00 0.00 3.06
1612 2622 0.991920 AATGGTTCACGGGGACATCT 59.008 50.000 0.00 0.00 0.00 2.90
1613 2623 0.253044 ATGGTTCACGGGGACATCTG 59.747 55.000 0.00 0.00 0.00 2.90
1614 2624 1.125093 TGGTTCACGGGGACATCTGT 61.125 55.000 0.00 0.00 0.00 3.41
1615 2625 0.391263 GGTTCACGGGGACATCTGTC 60.391 60.000 0.00 1.59 44.04 3.51
1624 2634 3.688553 GACATCTGTCCCCGGAATC 57.311 57.895 0.73 0.00 39.07 2.52
1625 2635 1.123928 GACATCTGTCCCCGGAATCT 58.876 55.000 0.73 0.00 39.07 2.40
1626 2636 1.069358 GACATCTGTCCCCGGAATCTC 59.931 57.143 0.73 0.00 39.07 2.75
1627 2637 1.123077 CATCTGTCCCCGGAATCTCA 58.877 55.000 0.73 0.00 0.00 3.27
1628 2638 1.123928 ATCTGTCCCCGGAATCTCAC 58.876 55.000 0.73 0.00 0.00 3.51
1629 2639 0.976073 TCTGTCCCCGGAATCTCACC 60.976 60.000 0.73 0.00 0.00 4.02
1630 2640 1.229368 TGTCCCCGGAATCTCACCA 60.229 57.895 0.73 0.00 0.00 4.17
1631 2641 0.620410 TGTCCCCGGAATCTCACCAT 60.620 55.000 0.73 0.00 0.00 3.55
1632 2642 0.546598 GTCCCCGGAATCTCACCATT 59.453 55.000 0.73 0.00 0.00 3.16
1633 2643 0.837272 TCCCCGGAATCTCACCATTC 59.163 55.000 0.73 0.00 32.70 2.67
1634 2644 0.546122 CCCCGGAATCTCACCATTCA 59.454 55.000 0.73 0.00 34.84 2.57
1635 2645 1.668419 CCCGGAATCTCACCATTCAC 58.332 55.000 0.73 0.00 34.84 3.18
1636 2646 1.210478 CCCGGAATCTCACCATTCACT 59.790 52.381 0.73 0.00 34.84 3.41
1637 2647 2.555199 CCGGAATCTCACCATTCACTC 58.445 52.381 0.00 0.00 34.84 3.51
1638 2648 2.093500 CCGGAATCTCACCATTCACTCA 60.093 50.000 0.00 0.00 34.84 3.41
1639 2649 3.193263 CGGAATCTCACCATTCACTCAG 58.807 50.000 0.00 0.00 34.84 3.35
1640 2650 2.941720 GGAATCTCACCATTCACTCAGC 59.058 50.000 0.00 0.00 34.84 4.26
1641 2651 2.706339 ATCTCACCATTCACTCAGCC 57.294 50.000 0.00 0.00 0.00 4.85
1642 2652 0.615331 TCTCACCATTCACTCAGCCC 59.385 55.000 0.00 0.00 0.00 5.19
1643 2653 0.617413 CTCACCATTCACTCAGCCCT 59.383 55.000 0.00 0.00 0.00 5.19
1644 2654 0.325933 TCACCATTCACTCAGCCCTG 59.674 55.000 0.00 0.00 0.00 4.45
1645 2655 0.325933 CACCATTCACTCAGCCCTGA 59.674 55.000 0.00 0.00 38.06 3.86
1646 2656 1.064906 CACCATTCACTCAGCCCTGAT 60.065 52.381 0.00 0.00 39.13 2.90
1647 2657 1.211457 ACCATTCACTCAGCCCTGATC 59.789 52.381 0.00 0.00 39.13 2.92
1648 2658 1.489649 CCATTCACTCAGCCCTGATCT 59.510 52.381 0.00 0.00 39.13 2.75
1649 2659 2.485124 CCATTCACTCAGCCCTGATCTC 60.485 54.545 0.00 0.00 39.13 2.75
1650 2660 2.244486 TTCACTCAGCCCTGATCTCT 57.756 50.000 0.00 0.00 39.13 3.10
1651 2661 1.482954 TCACTCAGCCCTGATCTCTG 58.517 55.000 0.00 0.00 39.13 3.35
1652 2662 1.006400 TCACTCAGCCCTGATCTCTGA 59.994 52.381 0.00 1.32 39.13 3.27
1653 2663 1.136695 CACTCAGCCCTGATCTCTGAC 59.863 57.143 0.00 0.00 39.13 3.51
1654 2664 0.752054 CTCAGCCCTGATCTCTGACC 59.248 60.000 0.00 0.00 39.13 4.02
1655 2665 0.337773 TCAGCCCTGATCTCTGACCT 59.662 55.000 0.00 0.00 34.14 3.85
1656 2666 1.570979 TCAGCCCTGATCTCTGACCTA 59.429 52.381 0.00 0.00 34.14 3.08
1657 2667 1.686052 CAGCCCTGATCTCTGACCTAC 59.314 57.143 0.00 0.00 0.00 3.18
1658 2668 1.044611 GCCCTGATCTCTGACCTACC 58.955 60.000 0.00 0.00 0.00 3.18
1659 2669 1.412361 GCCCTGATCTCTGACCTACCT 60.412 57.143 0.00 0.00 0.00 3.08
1660 2670 2.158445 GCCCTGATCTCTGACCTACCTA 60.158 54.545 0.00 0.00 0.00 3.08
1661 2671 3.501385 GCCCTGATCTCTGACCTACCTAT 60.501 52.174 0.00 0.00 0.00 2.57
1662 2672 4.746466 CCCTGATCTCTGACCTACCTATT 58.254 47.826 0.00 0.00 0.00 1.73
1663 2673 5.752332 GCCCTGATCTCTGACCTACCTATTA 60.752 48.000 0.00 0.00 0.00 0.98
1664 2674 5.949354 CCCTGATCTCTGACCTACCTATTAG 59.051 48.000 0.00 0.00 0.00 1.73
1665 2675 6.468066 CCCTGATCTCTGACCTACCTATTAGT 60.468 46.154 0.00 0.00 0.00 2.24
1666 2676 7.257089 CCCTGATCTCTGACCTACCTATTAGTA 60.257 44.444 0.00 0.00 0.00 1.82
1667 2677 8.333235 CCTGATCTCTGACCTACCTATTAGTAT 58.667 40.741 0.00 0.00 0.00 2.12
1668 2678 9.747898 CTGATCTCTGACCTACCTATTAGTATT 57.252 37.037 0.00 0.00 0.00 1.89
1692 2702 6.884280 TTTTCTTTCTCTGGACCATTTCTC 57.116 37.500 0.00 0.00 0.00 2.87
1693 2703 5.832539 TTCTTTCTCTGGACCATTTCTCT 57.167 39.130 0.00 0.00 0.00 3.10
1694 2704 5.832539 TCTTTCTCTGGACCATTTCTCTT 57.167 39.130 0.00 0.00 0.00 2.85
1695 2705 5.799213 TCTTTCTCTGGACCATTTCTCTTC 58.201 41.667 0.00 0.00 0.00 2.87
1696 2706 3.876274 TCTCTGGACCATTTCTCTTCG 57.124 47.619 0.00 0.00 0.00 3.79
1697 2707 3.165875 TCTCTGGACCATTTCTCTTCGT 58.834 45.455 0.00 0.00 0.00 3.85
1698 2708 4.341487 TCTCTGGACCATTTCTCTTCGTA 58.659 43.478 0.00 0.00 0.00 3.43
1829 2839 3.372822 CCCTACGCACACAATTAATTCGT 59.627 43.478 14.02 14.02 0.00 3.85
1947 2968 2.604046 AGCACTCGTGTTCTTTCACT 57.396 45.000 0.00 0.00 36.33 3.41
2267 3956 2.512515 GCTCACGATCACCCAGGC 60.513 66.667 0.00 0.00 0.00 4.85
2408 4725 3.508744 AAAATTGAGCTAATGGCACCG 57.491 42.857 0.00 0.00 44.79 4.94
2448 4768 4.116747 TCTTTCATTTGTTGTTTGGCGT 57.883 36.364 0.00 0.00 0.00 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
263 1138 1.299976 GCCTCCCCTTTCATGTCGT 59.700 57.895 0.00 0.00 0.00 4.34
431 1308 1.951209 TGACAGTGGCCCATAGAAGA 58.049 50.000 0.00 0.00 0.00 2.87
473 1350 3.542676 TCTTCACGCCCACACGGT 61.543 61.111 0.00 0.00 37.37 4.83
614 1576 8.967664 TTTGTTGTTTGGTTGTAGATAGTAGT 57.032 30.769 0.00 0.00 0.00 2.73
662 1629 1.066471 AACTAAACCGGCCCCTGTAA 58.934 50.000 0.00 0.00 0.00 2.41
759 1727 3.807538 GCATGGTCACAGCGCAGG 61.808 66.667 11.47 3.29 0.00 4.85
760 1728 2.132517 TTTGCATGGTCACAGCGCAG 62.133 55.000 11.47 3.33 39.30 5.18
761 1729 1.732417 TTTTGCATGGTCACAGCGCA 61.732 50.000 11.47 0.00 37.23 6.09
762 1730 0.597118 TTTTTGCATGGTCACAGCGC 60.597 50.000 0.00 0.00 0.00 5.92
763 1731 3.566273 TTTTTGCATGGTCACAGCG 57.434 47.368 0.00 0.00 0.00 5.18
783 1751 1.549203 ATCACAGCGCAGGGATTTTT 58.451 45.000 12.32 0.00 0.00 1.94
784 1752 1.203052 CAATCACAGCGCAGGGATTTT 59.797 47.619 25.64 6.31 0.00 1.82
785 1753 0.813184 CAATCACAGCGCAGGGATTT 59.187 50.000 25.64 10.19 0.00 2.17
836 1805 2.266055 CAGGAGCTTCACGGGACC 59.734 66.667 0.00 0.00 0.00 4.46
837 1806 2.435059 GCAGGAGCTTCACGGGAC 60.435 66.667 0.00 0.00 37.91 4.46
904 1874 2.233605 CTGCTCTGCTCTGCTCTGCT 62.234 60.000 0.00 0.00 0.00 4.24
905 1875 1.812093 CTGCTCTGCTCTGCTCTGC 60.812 63.158 0.00 0.00 0.00 4.26
1203 2189 0.601311 AACAGAGCAGAACAGACGCC 60.601 55.000 0.00 0.00 0.00 5.68
1545 2547 0.533755 CACACTGGCTAGGCTATGGC 60.534 60.000 18.18 2.73 37.82 4.40
1590 2600 1.677633 GTCCCCGTGAACCATTGGG 60.678 63.158 7.78 0.00 41.56 4.12
1591 2601 0.323360 ATGTCCCCGTGAACCATTGG 60.323 55.000 0.00 0.00 0.00 3.16
1592 2602 1.094785 GATGTCCCCGTGAACCATTG 58.905 55.000 0.00 0.00 0.00 2.82
1593 2603 0.991920 AGATGTCCCCGTGAACCATT 59.008 50.000 0.00 0.00 0.00 3.16
1594 2604 0.253044 CAGATGTCCCCGTGAACCAT 59.747 55.000 0.00 0.00 0.00 3.55
1595 2605 1.125093 ACAGATGTCCCCGTGAACCA 61.125 55.000 0.00 0.00 0.00 3.67
1596 2606 0.391263 GACAGATGTCCCCGTGAACC 60.391 60.000 1.33 0.00 39.07 3.62
1597 2607 3.139029 GACAGATGTCCCCGTGAAC 57.861 57.895 1.33 0.00 39.07 3.18
1606 2616 1.069358 GAGATTCCGGGGACAGATGTC 59.931 57.143 0.00 4.33 44.04 3.06
1607 2617 1.123928 GAGATTCCGGGGACAGATGT 58.876 55.000 0.00 0.00 0.00 3.06
1608 2618 1.123077 TGAGATTCCGGGGACAGATG 58.877 55.000 0.00 0.00 0.00 2.90
1609 2619 1.123928 GTGAGATTCCGGGGACAGAT 58.876 55.000 0.00 0.00 0.00 2.90
1610 2620 0.976073 GGTGAGATTCCGGGGACAGA 60.976 60.000 0.00 0.00 0.00 3.41
1611 2621 1.264749 TGGTGAGATTCCGGGGACAG 61.265 60.000 0.00 0.00 0.00 3.51
1612 2622 0.620410 ATGGTGAGATTCCGGGGACA 60.620 55.000 0.00 0.00 0.00 4.02
1613 2623 0.546598 AATGGTGAGATTCCGGGGAC 59.453 55.000 0.00 0.00 0.00 4.46
1614 2624 0.837272 GAATGGTGAGATTCCGGGGA 59.163 55.000 0.00 0.00 0.00 4.81
1615 2625 0.546122 TGAATGGTGAGATTCCGGGG 59.454 55.000 0.00 0.00 32.20 5.73
1616 2626 1.210478 AGTGAATGGTGAGATTCCGGG 59.790 52.381 0.00 0.00 32.20 5.73
1617 2627 2.093500 TGAGTGAATGGTGAGATTCCGG 60.093 50.000 0.00 0.00 32.20 5.14
1618 2628 3.193263 CTGAGTGAATGGTGAGATTCCG 58.807 50.000 0.00 0.00 32.20 4.30
1619 2629 2.941720 GCTGAGTGAATGGTGAGATTCC 59.058 50.000 0.00 0.00 32.20 3.01
1620 2630 2.941720 GGCTGAGTGAATGGTGAGATTC 59.058 50.000 0.00 0.00 33.59 2.52
1621 2631 2.356535 GGGCTGAGTGAATGGTGAGATT 60.357 50.000 0.00 0.00 0.00 2.40
1622 2632 1.211457 GGGCTGAGTGAATGGTGAGAT 59.789 52.381 0.00 0.00 0.00 2.75
1623 2633 0.615331 GGGCTGAGTGAATGGTGAGA 59.385 55.000 0.00 0.00 0.00 3.27
1624 2634 0.617413 AGGGCTGAGTGAATGGTGAG 59.383 55.000 0.00 0.00 0.00 3.51
1625 2635 0.325933 CAGGGCTGAGTGAATGGTGA 59.674 55.000 0.00 0.00 0.00 4.02
1626 2636 0.325933 TCAGGGCTGAGTGAATGGTG 59.674 55.000 0.00 0.00 34.14 4.17
1627 2637 1.211457 GATCAGGGCTGAGTGAATGGT 59.789 52.381 0.00 0.00 43.61 3.55
1628 2638 1.489649 AGATCAGGGCTGAGTGAATGG 59.510 52.381 0.00 0.00 43.61 3.16
1629 2639 2.435069 AGAGATCAGGGCTGAGTGAATG 59.565 50.000 0.00 0.00 43.61 2.67
1630 2640 2.435069 CAGAGATCAGGGCTGAGTGAAT 59.565 50.000 0.00 0.00 43.61 2.57
1631 2641 1.829849 CAGAGATCAGGGCTGAGTGAA 59.170 52.381 0.00 0.00 43.61 3.18
1632 2642 1.006400 TCAGAGATCAGGGCTGAGTGA 59.994 52.381 0.00 0.00 43.61 3.41
1633 2643 1.136695 GTCAGAGATCAGGGCTGAGTG 59.863 57.143 7.55 0.00 43.61 3.51
1634 2644 1.484038 GTCAGAGATCAGGGCTGAGT 58.516 55.000 7.55 0.00 43.61 3.41
1635 2645 0.752054 GGTCAGAGATCAGGGCTGAG 59.248 60.000 7.55 0.00 43.61 3.35
1636 2646 0.337773 AGGTCAGAGATCAGGGCTGA 59.662 55.000 0.00 0.00 44.59 4.26
1637 2647 1.686052 GTAGGTCAGAGATCAGGGCTG 59.314 57.143 0.00 0.00 0.00 4.85
1638 2648 1.412361 GGTAGGTCAGAGATCAGGGCT 60.412 57.143 0.00 0.00 0.00 5.19
1639 2649 1.044611 GGTAGGTCAGAGATCAGGGC 58.955 60.000 0.00 0.00 0.00 5.19
1640 2650 2.765689 AGGTAGGTCAGAGATCAGGG 57.234 55.000 0.00 0.00 0.00 4.45
1641 2651 6.548321 ACTAATAGGTAGGTCAGAGATCAGG 58.452 44.000 0.00 0.00 33.68 3.86
1642 2652 9.747898 AATACTAATAGGTAGGTCAGAGATCAG 57.252 37.037 0.00 0.00 33.68 2.90
1668 2678 7.062957 AGAGAAATGGTCCAGAGAAAGAAAAA 58.937 34.615 0.00 0.00 0.00 1.94
1669 2679 6.605119 AGAGAAATGGTCCAGAGAAAGAAAA 58.395 36.000 0.00 0.00 0.00 2.29
1670 2680 6.192970 AGAGAAATGGTCCAGAGAAAGAAA 57.807 37.500 0.00 0.00 0.00 2.52
1671 2681 5.832539 AGAGAAATGGTCCAGAGAAAGAA 57.167 39.130 0.00 0.00 0.00 2.52
1672 2682 5.567623 CGAAGAGAAATGGTCCAGAGAAAGA 60.568 44.000 0.00 0.00 0.00 2.52
1673 2683 4.629200 CGAAGAGAAATGGTCCAGAGAAAG 59.371 45.833 0.00 0.00 0.00 2.62
1674 2684 4.040461 ACGAAGAGAAATGGTCCAGAGAAA 59.960 41.667 0.00 0.00 0.00 2.52
1675 2685 3.578716 ACGAAGAGAAATGGTCCAGAGAA 59.421 43.478 0.00 0.00 0.00 2.87
1676 2686 3.165875 ACGAAGAGAAATGGTCCAGAGA 58.834 45.455 0.00 0.00 0.00 3.10
1677 2687 3.601443 ACGAAGAGAAATGGTCCAGAG 57.399 47.619 0.00 0.00 0.00 3.35
1678 2688 5.677319 AATACGAAGAGAAATGGTCCAGA 57.323 39.130 0.00 0.00 0.00 3.86
1679 2689 6.574350 AGTAATACGAAGAGAAATGGTCCAG 58.426 40.000 0.00 0.00 0.00 3.86
1680 2690 6.406624 GGAGTAATACGAAGAGAAATGGTCCA 60.407 42.308 0.00 0.00 0.00 4.02
1681 2691 5.984323 GGAGTAATACGAAGAGAAATGGTCC 59.016 44.000 0.00 0.00 0.00 4.46
1682 2692 5.984323 GGGAGTAATACGAAGAGAAATGGTC 59.016 44.000 0.00 0.00 0.00 4.02
1683 2693 5.661759 AGGGAGTAATACGAAGAGAAATGGT 59.338 40.000 0.00 0.00 0.00 3.55
1684 2694 6.163135 AGGGAGTAATACGAAGAGAAATGG 57.837 41.667 0.00 0.00 0.00 3.16
1685 2695 6.041069 AGGAGGGAGTAATACGAAGAGAAATG 59.959 42.308 0.00 0.00 0.00 2.32
1686 2696 6.137559 AGGAGGGAGTAATACGAAGAGAAAT 58.862 40.000 0.00 0.00 0.00 2.17
1687 2697 5.516984 AGGAGGGAGTAATACGAAGAGAAA 58.483 41.667 0.00 0.00 0.00 2.52
1688 2698 5.126699 AGGAGGGAGTAATACGAAGAGAA 57.873 43.478 0.00 0.00 0.00 2.87
1689 2699 4.792513 AGGAGGGAGTAATACGAAGAGA 57.207 45.455 0.00 0.00 0.00 3.10
1690 2700 5.241285 GGTAAGGAGGGAGTAATACGAAGAG 59.759 48.000 0.00 0.00 0.00 2.85
1691 2701 5.136105 GGTAAGGAGGGAGTAATACGAAGA 58.864 45.833 0.00 0.00 0.00 2.87
1692 2702 4.891756 TGGTAAGGAGGGAGTAATACGAAG 59.108 45.833 0.00 0.00 0.00 3.79
1693 2703 4.870636 TGGTAAGGAGGGAGTAATACGAA 58.129 43.478 0.00 0.00 0.00 3.85
1694 2704 4.079558 ACTGGTAAGGAGGGAGTAATACGA 60.080 45.833 0.00 0.00 0.00 3.43
1695 2705 4.213513 ACTGGTAAGGAGGGAGTAATACG 58.786 47.826 0.00 0.00 0.00 3.06
1696 2706 6.556974 AAACTGGTAAGGAGGGAGTAATAC 57.443 41.667 0.00 0.00 0.00 1.89
1697 2707 9.956558 TTATAAACTGGTAAGGAGGGAGTAATA 57.043 33.333 0.00 0.00 0.00 0.98
1698 2708 8.865244 TTATAAACTGGTAAGGAGGGAGTAAT 57.135 34.615 0.00 0.00 0.00 1.89
1829 2839 0.666274 CGTACGAGAACAGCAGCCAA 60.666 55.000 10.44 0.00 0.00 4.52
1857 2867 0.391793 GAGAGGAAAGGAGTTGGCCG 60.392 60.000 0.00 0.00 0.00 6.13
1947 2968 4.622933 CGTATGTGGATGAAAAGAGGGTGA 60.623 45.833 0.00 0.00 0.00 4.02
2148 3837 2.934553 CACTTCATCATCAGCATCGTGT 59.065 45.455 0.00 0.00 0.00 4.49
2267 3956 0.036010 AGCCACACCATTCTTCTCGG 60.036 55.000 0.00 0.00 0.00 4.63
2408 4725 1.250840 AAGCACCGCCAAAATCCTCC 61.251 55.000 0.00 0.00 0.00 4.30
2448 4768 0.957362 TTCATGGTTTGCATGCACGA 59.043 45.000 22.58 9.59 0.00 4.35


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

AutoCloner maintained by Alex Coulton.