Multiple sequence alignment - TraesCS3D01G095300

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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 TraesCS3D01G095300 chr3D 100.000 3299 0 0 1 3299 48404249 48407547 0.000000e+00 6093.0
1 TraesCS3D01G095300 chr3D 95.833 96 2 2 2635 2729 48419154 48419248 1.590000e-33 154.0
2 TraesCS3D01G095300 chr3A 92.012 1377 64 20 581 1928 60611028 60612387 0.000000e+00 1892.0
3 TraesCS3D01G095300 chr3A 94.344 389 17 4 1941 2328 60612452 60612836 2.830000e-165 592.0
4 TraesCS3D01G095300 chr3A 83.871 496 56 14 2762 3233 60614173 60614668 5.020000e-123 451.0
5 TraesCS3D01G095300 chr3A 84.034 476 51 16 2744 3195 60613618 60614092 5.060000e-118 435.0
6 TraesCS3D01G095300 chr3A 81.144 472 48 17 2762 3193 60624100 60624570 1.130000e-89 340.0
7 TraesCS3D01G095300 chr3A 91.367 139 9 2 2643 2781 60613445 60613580 1.560000e-43 187.0
8 TraesCS3D01G095300 chr3A 94.059 101 4 2 2631 2729 60627335 60627435 5.700000e-33 152.0
9 TraesCS3D01G095300 chr3B 94.315 1161 40 12 545 1697 76461969 76463111 0.000000e+00 1755.0
10 TraesCS3D01G095300 chr3B 84.101 434 42 12 2388 2804 76464067 76464490 8.580000e-106 394.0
11 TraesCS3D01G095300 chr3B 84.892 417 26 11 1695 2087 76463178 76463581 1.440000e-103 387.0
12 TraesCS3D01G095300 chr3B 98.010 201 4 0 2084 2284 76463664 76463864 1.880000e-92 350.0
13 TraesCS3D01G095300 chr3B 78.797 316 34 15 2387 2688 76469458 76469754 7.270000e-42 182.0
14 TraesCS3D01G095300 chr3B 86.598 97 13 0 2592 2688 76466168 76466264 1.250000e-19 108.0
15 TraesCS3D01G095300 chr5D 91.682 553 36 6 1 544 44411587 44412138 0.000000e+00 758.0
16 TraesCS3D01G095300 chr5D 89.680 562 40 6 1 544 532649170 532649731 0.000000e+00 701.0
17 TraesCS3D01G095300 chr5D 92.453 106 5 3 2647 2751 546684263 546684160 7.380000e-32 148.0
18 TraesCS3D01G095300 chr5D 90.265 113 8 3 2643 2753 490026024 490026135 9.540000e-31 145.0
19 TraesCS3D01G095300 chr6D 88.530 558 43 12 1 544 322579384 322579934 0.000000e+00 656.0
20 TraesCS3D01G095300 chr6D 88.372 129 10 5 2617 2741 89730257 89730130 2.050000e-32 150.0
21 TraesCS3D01G095300 chr4D 88.256 562 46 9 1 544 351676554 351675995 0.000000e+00 654.0
22 TraesCS3D01G095300 chr7D 89.080 522 45 6 33 544 554867342 554866823 3.590000e-179 638.0
23 TraesCS3D01G095300 chr2D 87.722 562 48 8 1 544 184847555 184848113 1.290000e-178 636.0
24 TraesCS3D01G095300 chr7A 87.862 552 45 8 3 544 547547347 547547886 2.160000e-176 628.0
25 TraesCS3D01G095300 chr1A 87.568 555 52 10 2 544 5870050 5870599 7.770000e-176 627.0
26 TraesCS3D01G095300 chr2B 86.879 564 49 16 1 543 160749864 160749305 2.810000e-170 608.0
27 TraesCS3D01G095300 chr6B 88.550 131 8 7 2617 2742 172262075 172261947 5.700000e-33 152.0
28 TraesCS3D01G095300 chr5B 92.381 105 5 3 2648 2751 689883669 689883567 2.650000e-31 147.0
29 TraesCS3D01G095300 chr5B 85.455 55 3 3 659 713 498291602 498291651 6.000000e-03 52.8
30 TraesCS3D01G095300 chrUn 91.892 37 3 0 684 720 228897536 228897500 6.000000e-03 52.8
31 TraesCS3D01G095300 chrUn 91.892 37 3 0 684 720 302118360 302118324 6.000000e-03 52.8
32 TraesCS3D01G095300 chr6A 85.455 55 3 3 659 713 12337981 12338030 6.000000e-03 52.8
33 TraesCS3D01G095300 chr4B 85.455 55 3 3 659 713 106832875 106832924 6.000000e-03 52.8


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 TraesCS3D01G095300 chr3D 48404249 48407547 3298 False 6093.000000 6093 100.0000 1 3299 1 chr3D.!!$F1 3298
1 TraesCS3D01G095300 chr3A 60611028 60614668 3640 False 711.400000 1892 89.1256 581 3233 5 chr3A.!!$F1 2652
2 TraesCS3D01G095300 chr3A 60624100 60627435 3335 False 246.000000 340 87.6015 2631 3193 2 chr3A.!!$F2 562
3 TraesCS3D01G095300 chr3B 76461969 76469754 7785 False 529.333333 1755 87.7855 545 2804 6 chr3B.!!$F1 2259
4 TraesCS3D01G095300 chr5D 44411587 44412138 551 False 758.000000 758 91.6820 1 544 1 chr5D.!!$F1 543
5 TraesCS3D01G095300 chr5D 532649170 532649731 561 False 701.000000 701 89.6800 1 544 1 chr5D.!!$F3 543
6 TraesCS3D01G095300 chr6D 322579384 322579934 550 False 656.000000 656 88.5300 1 544 1 chr6D.!!$F1 543
7 TraesCS3D01G095300 chr4D 351675995 351676554 559 True 654.000000 654 88.2560 1 544 1 chr4D.!!$R1 543
8 TraesCS3D01G095300 chr7D 554866823 554867342 519 True 638.000000 638 89.0800 33 544 1 chr7D.!!$R1 511
9 TraesCS3D01G095300 chr2D 184847555 184848113 558 False 636.000000 636 87.7220 1 544 1 chr2D.!!$F1 543
10 TraesCS3D01G095300 chr7A 547547347 547547886 539 False 628.000000 628 87.8620 3 544 1 chr7A.!!$F1 541
11 TraesCS3D01G095300 chr1A 5870050 5870599 549 False 627.000000 627 87.5680 2 544 1 chr1A.!!$F1 542
12 TraesCS3D01G095300 chr2B 160749305 160749864 559 True 608.000000 608 86.8790 1 543 1 chr2B.!!$R1 542

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
419 444 0.940519 GCATTTTTGTGCGCTGCTGA 60.941 50.0 9.73 0.0 35.10 4.26 F
1721 1861 0.179076 CAGAGGCCATGCATACGTGA 60.179 55.0 5.01 0.0 34.49 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2007 2224 0.033991 TCTTCCCCTCTCTCTGGACG 60.034 60.0 0.0 0.0 0.0 4.79 R
3235 6505 0.314302 CGTTTCCGTGAGACTGAGGT 59.686 55.0 0.0 0.0 0.0 3.85 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
244 256 5.798125 TTGCATTTGAACTTGGTTGGATA 57.202 34.783 0.00 0.00 0.00 2.59
264 276 6.438741 TGGATAAACTTGTGGGCATGATTTTA 59.561 34.615 0.00 0.00 0.00 1.52
419 444 0.940519 GCATTTTTGTGCGCTGCTGA 60.941 50.000 9.73 0.00 35.10 4.26
431 460 4.717629 TGCTGAAGCTACGCGCGT 62.718 61.111 39.05 39.05 45.59 6.01
516 547 2.350007 CGGCAAAGTAGTTTTTAGCGCA 60.350 45.455 11.47 0.00 0.00 6.09
550 582 1.081892 CTGTTGGAGATGCGTTGGAG 58.918 55.000 0.00 0.00 0.00 3.86
579 611 1.578583 AAGAAATATCGAACCGGCGG 58.421 50.000 27.06 27.06 0.00 6.13
596 628 3.643978 GATGATCGCGTGGCAGGC 61.644 66.667 21.49 21.49 0.00 4.85
647 680 6.676558 AGATTGACCCAAGATTACATCCAAT 58.323 36.000 0.00 0.00 0.00 3.16
722 755 2.363680 CCCATCTGAGTCGCATTCTAGT 59.636 50.000 0.00 0.00 0.00 2.57
794 834 1.682854 CACACTTGAACCAACCATGCT 59.317 47.619 0.00 0.00 0.00 3.79
795 835 2.101249 CACACTTGAACCAACCATGCTT 59.899 45.455 0.00 0.00 0.00 3.91
796 836 2.101249 ACACTTGAACCAACCATGCTTG 59.899 45.455 0.00 0.00 0.00 4.01
797 837 1.069049 ACTTGAACCAACCATGCTTGC 59.931 47.619 0.00 0.00 0.00 4.01
840 880 6.655003 CCTGGAATAACATCACAAAGTACACT 59.345 38.462 0.00 0.00 0.00 3.55
870 910 9.788889 AGTTAAGCAACAAAACCTAATACTACT 57.211 29.630 0.00 0.00 37.10 2.57
880 920 6.661304 AACCTAATACTACTATTGGACGGG 57.339 41.667 0.00 0.00 0.00 5.28
983 1030 1.665679 GAGCGAGAGAGAGACAGACAG 59.334 57.143 0.00 0.00 0.00 3.51
985 1032 1.396996 GCGAGAGAGAGACAGACAGAC 59.603 57.143 0.00 0.00 0.00 3.51
986 1033 2.694213 CGAGAGAGAGACAGACAGACA 58.306 52.381 0.00 0.00 0.00 3.41
987 1034 2.415168 CGAGAGAGAGACAGACAGACAC 59.585 54.545 0.00 0.00 0.00 3.67
988 1035 3.407698 GAGAGAGAGACAGACAGACACA 58.592 50.000 0.00 0.00 0.00 3.72
989 1036 4.009675 GAGAGAGAGACAGACAGACACAT 58.990 47.826 0.00 0.00 0.00 3.21
990 1037 5.172687 AGAGAGAGACAGACAGACACATA 57.827 43.478 0.00 0.00 0.00 2.29
991 1038 5.185454 AGAGAGAGACAGACAGACACATAG 58.815 45.833 0.00 0.00 0.00 2.23
995 1042 5.185454 AGAGACAGACAGACACATAGAGAG 58.815 45.833 0.00 0.00 0.00 3.20
1154 1201 4.460683 CCCCGACGCCGAATCCAA 62.461 66.667 0.00 0.00 38.22 3.53
1155 1202 2.890474 CCCGACGCCGAATCCAAG 60.890 66.667 0.00 0.00 38.22 3.61
1156 1203 3.564027 CCGACGCCGAATCCAAGC 61.564 66.667 0.00 0.00 38.22 4.01
1467 1538 3.795041 CTGCAGCAGGGAGGAGGG 61.795 72.222 15.35 0.00 0.00 4.30
1626 1697 3.728474 CTGATGGACATCTGCGCC 58.272 61.111 4.18 0.00 38.60 6.53
1687 1758 1.153369 CTCCTCCGGGTACGTACGA 60.153 63.158 24.41 10.16 38.78 3.43
1703 1843 1.066752 CGAACTCCCACGTCACACA 59.933 57.895 0.00 0.00 0.00 3.72
1721 1861 0.179076 CAGAGGCCATGCATACGTGA 60.179 55.000 5.01 0.00 34.49 4.35
1722 1862 0.761187 AGAGGCCATGCATACGTGAT 59.239 50.000 5.01 0.00 34.49 3.06
1723 1863 1.970640 AGAGGCCATGCATACGTGATA 59.029 47.619 5.01 0.00 34.49 2.15
1724 1864 2.069273 GAGGCCATGCATACGTGATAC 58.931 52.381 5.01 0.00 34.49 2.24
1736 1876 2.823196 CGTGATACGTACGTGGGTAA 57.177 50.000 30.25 10.89 36.74 2.85
1737 1877 2.440501 CGTGATACGTACGTGGGTAAC 58.559 52.381 30.25 18.26 36.74 2.50
1740 1880 6.429538 CGTGATACGTACGTGGGTAACACT 62.430 50.000 30.25 1.85 41.40 3.55
1755 1895 5.771165 GGGTAACACTTCAATTGGAAAGGTA 59.229 40.000 5.42 0.00 34.09 3.08
1817 1957 2.031120 GAAAATGATGGATCGCCCCAA 58.969 47.619 0.00 0.00 40.04 4.12
1837 1993 0.801872 CGATTTGGTGGCGAATCACA 59.198 50.000 0.00 0.00 39.27 3.58
1872 2028 1.896220 TCAGTTGGTGGAGAATGTGC 58.104 50.000 0.00 0.00 0.00 4.57
1905 2065 0.248336 CAAGCATGCATGTAGCCACG 60.248 55.000 26.79 6.32 44.83 4.94
1912 2074 4.557296 GCATGCATGTAGCCACGATAAAAT 60.557 41.667 26.79 0.00 44.83 1.82
1934 2098 9.503369 AAAATATCAAGTTAGAGTAGGGGTACT 57.497 33.333 0.00 0.00 0.00 2.73
1936 2100 9.810870 AATATCAAGTTAGAGTAGGGGTACTAG 57.189 37.037 0.00 0.00 30.77 2.57
1937 2101 6.649041 TCAAGTTAGAGTAGGGGTACTAGT 57.351 41.667 0.00 0.00 38.05 2.57
1938 2102 7.755666 TCAAGTTAGAGTAGGGGTACTAGTA 57.244 40.000 0.00 0.00 35.46 1.82
1939 2103 7.569240 TCAAGTTAGAGTAGGGGTACTAGTAC 58.431 42.308 22.53 22.53 35.46 2.73
1987 2203 7.170658 ACAATTAACCAAAGTACGTACGCTTTA 59.829 33.333 19.49 10.97 34.04 1.85
1988 2204 7.832503 ATTAACCAAAGTACGTACGCTTTAT 57.167 32.000 19.49 9.20 34.04 1.40
2073 2290 2.109126 GCACGGCTTCCAGATCACC 61.109 63.158 0.00 0.00 0.00 4.02
2256 2559 1.953686 CAGATCCTCCTCGACTTCCTC 59.046 57.143 0.00 0.00 0.00 3.71
2259 2562 0.256464 TCCTCCTCGACTTCCTCCTC 59.744 60.000 0.00 0.00 0.00 3.71
2284 2587 2.001803 CCTTCCTCCTCCAATGGCA 58.998 57.895 0.00 0.00 0.00 4.92
2285 2588 0.332632 CCTTCCTCCTCCAATGGCAA 59.667 55.000 0.00 0.00 0.00 4.52
2299 2602 2.874751 GCAACGCCGCCAAATAGT 59.125 55.556 0.00 0.00 0.00 2.12
2319 2622 3.908103 AGTAGTAGCTAGCTAGAGAGGCT 59.092 47.826 24.78 18.02 43.02 4.58
2328 2631 1.670949 CTAGAGAGGCTGCCGCTTGA 61.671 60.000 25.72 15.31 32.83 3.02
2331 2634 1.001641 AGAGGCTGCCGCTTGATTT 60.002 52.632 19.75 0.00 36.09 2.17
2332 2635 1.028868 AGAGGCTGCCGCTTGATTTC 61.029 55.000 19.75 5.64 36.09 2.17
2333 2636 1.303561 AGGCTGCCGCTTGATTTCA 60.304 52.632 13.96 0.00 36.09 2.69
2334 2637 0.682209 AGGCTGCCGCTTGATTTCAT 60.682 50.000 13.96 0.00 36.09 2.57
2335 2638 0.526954 GGCTGCCGCTTGATTTCATG 60.527 55.000 1.35 0.00 36.09 3.07
2337 2640 0.171679 CTGCCGCTTGATTTCATGCA 59.828 50.000 15.90 0.00 44.35 3.96
2338 2641 0.171679 TGCCGCTTGATTTCATGCAG 59.828 50.000 15.90 7.90 44.35 4.41
2340 2643 0.813184 CCGCTTGATTTCATGCAGGT 59.187 50.000 15.90 0.00 44.35 4.00
2341 2644 1.468565 CCGCTTGATTTCATGCAGGTG 60.469 52.381 15.90 0.00 44.35 4.00
2342 2645 1.200716 CGCTTGATTTCATGCAGGTGT 59.799 47.619 15.90 0.00 44.35 4.16
2345 2648 3.829948 CTTGATTTCATGCAGGTGTGTC 58.170 45.455 0.00 0.00 0.00 3.67
2347 2650 2.553602 TGATTTCATGCAGGTGTGTCAC 59.446 45.455 0.00 0.00 0.00 3.67
2350 2653 0.676736 TCATGCAGGTGTGTCACGTA 59.323 50.000 0.00 0.00 34.83 3.57
2353 2656 0.391228 TGCAGGTGTGTCACGTATGT 59.609 50.000 0.00 0.00 34.83 2.29
2355 2658 1.428448 CAGGTGTGTCACGTATGTGG 58.572 55.000 15.02 0.00 46.42 4.17
2357 2660 1.144969 GGTGTGTCACGTATGTGGTG 58.855 55.000 15.02 0.00 46.42 4.17
2361 2664 3.427528 GTGTGTCACGTATGTGGTGTAAG 59.572 47.826 15.02 0.00 46.42 2.34
2362 2665 3.068448 TGTGTCACGTATGTGGTGTAAGT 59.932 43.478 15.02 0.00 46.42 2.24
2363 2666 3.427528 GTGTCACGTATGTGGTGTAAGTG 59.572 47.826 15.02 0.00 46.42 3.16
2365 2668 1.730064 CACGTATGTGGTGTAAGTGGC 59.270 52.381 7.22 0.00 42.59 5.01
2366 2669 1.345089 ACGTATGTGGTGTAAGTGGCA 59.655 47.619 0.00 0.00 0.00 4.92
2370 2673 0.544223 TGTGGTGTAAGTGGCACTGT 59.456 50.000 22.83 13.59 37.07 3.55
2371 2674 0.944386 GTGGTGTAAGTGGCACTGTG 59.056 55.000 22.83 2.76 37.07 3.66
2372 2675 0.179032 TGGTGTAAGTGGCACTGTGG 60.179 55.000 22.83 0.00 37.07 4.17
2373 2676 1.515521 GGTGTAAGTGGCACTGTGGC 61.516 60.000 22.83 25.55 44.03 5.01
2450 2862 5.190677 TGAGAGGATCAGTACGTATTGACA 58.809 41.667 21.30 11.72 37.82 3.58
2460 2872 5.690409 CAGTACGTATTGACAGTTTGAGTGT 59.310 40.000 12.37 0.00 33.77 3.55
2482 2894 0.461870 TGCATATATCCGCCGGCATC 60.462 55.000 28.98 6.03 0.00 3.91
2550 2972 2.344441 AGCACGTGATTTCGAACATACG 59.656 45.455 22.23 19.44 37.54 3.06
2579 3002 3.515330 TGGCCGTAGTTAAGTAAGCTC 57.485 47.619 0.00 5.12 0.00 4.09
2584 3007 4.421948 CCGTAGTTAAGTAAGCTCAGGTG 58.578 47.826 0.00 0.00 0.00 4.00
2604 3226 4.201881 GGTGTGGTGTAAAAGATTATCCGC 60.202 45.833 0.00 0.00 33.25 5.54
2607 3229 5.813672 TGTGGTGTAAAAGATTATCCGCTAC 59.186 40.000 0.00 0.00 33.52 3.58
2613 3235 8.923683 GTGTAAAAGATTATCCGCTACTTATCC 58.076 37.037 0.00 0.00 0.00 2.59
2615 3237 9.141400 GTAAAAGATTATCCGCTACTTATCCAG 57.859 37.037 0.00 0.00 0.00 3.86
2617 3239 6.274157 AGATTATCCGCTACTTATCCAGTG 57.726 41.667 0.00 0.00 35.97 3.66
2628 3250 7.518689 CGCTACTTATCCAGTGAGTAGAGTTAC 60.519 44.444 16.88 2.70 45.27 2.50
2629 3251 6.680874 ACTTATCCAGTGAGTAGAGTTACG 57.319 41.667 0.00 0.00 32.83 3.18
2630 3252 6.179040 ACTTATCCAGTGAGTAGAGTTACGT 58.821 40.000 0.00 0.00 32.83 3.57
2631 3253 7.334090 ACTTATCCAGTGAGTAGAGTTACGTA 58.666 38.462 0.00 0.00 32.83 3.57
2632 3254 7.826252 ACTTATCCAGTGAGTAGAGTTACGTAA 59.174 37.037 3.29 3.29 32.83 3.18
2635 3257 6.233434 TCCAGTGAGTAGAGTTACGTAAGAA 58.767 40.000 8.60 0.00 43.62 2.52
2636 3258 6.712095 TCCAGTGAGTAGAGTTACGTAAGAAA 59.288 38.462 8.60 0.00 43.62 2.52
2637 3259 7.392673 TCCAGTGAGTAGAGTTACGTAAGAAAT 59.607 37.037 8.60 0.00 43.62 2.17
2638 3260 8.027771 CCAGTGAGTAGAGTTACGTAAGAAATT 58.972 37.037 8.60 0.00 43.62 1.82
2728 3352 1.530655 CGGTTGGGCCCTCTTGTTT 60.531 57.895 25.70 0.00 0.00 2.83
2729 3353 1.805428 CGGTTGGGCCCTCTTGTTTG 61.805 60.000 25.70 0.40 0.00 2.93
2732 3356 1.398958 TTGGGCCCTCTTGTTTGTGC 61.399 55.000 25.70 0.00 0.00 4.57
2806 3506 3.019799 ACTCATGTGGTCCTCTCGTAT 57.980 47.619 0.00 0.00 0.00 3.06
2807 3507 2.690497 ACTCATGTGGTCCTCTCGTATG 59.310 50.000 0.00 0.00 0.00 2.39
2808 3508 2.952310 CTCATGTGGTCCTCTCGTATGA 59.048 50.000 0.00 0.00 0.00 2.15
2809 3509 3.361786 TCATGTGGTCCTCTCGTATGAA 58.638 45.455 0.00 0.00 0.00 2.57
2810 3510 3.767131 TCATGTGGTCCTCTCGTATGAAA 59.233 43.478 0.00 0.00 0.00 2.69
2811 3511 4.221924 TCATGTGGTCCTCTCGTATGAAAA 59.778 41.667 0.00 0.00 0.00 2.29
2814 3514 4.174762 GTGGTCCTCTCGTATGAAAACTC 58.825 47.826 0.00 0.00 0.00 3.01
2815 3515 4.082136 GTGGTCCTCTCGTATGAAAACTCT 60.082 45.833 0.00 0.00 0.00 3.24
2828 3544 6.839124 ATGAAAACTCTGGCAAACATGATA 57.161 33.333 0.00 0.00 0.00 2.15
2912 3660 9.056005 CGAGAAGACATGGGATTTTTCATAATA 57.944 33.333 0.00 0.00 0.00 0.98
2923 4208 9.056005 GGGATTTTTCATAATATTTTCAAGGCC 57.944 33.333 0.00 0.00 0.00 5.19
2930 4215 0.806241 TATTTTCAAGGCCGCCGAAC 59.194 50.000 3.05 0.00 0.00 3.95
2934 4219 3.737172 CAAGGCCGCCGAACCAAG 61.737 66.667 3.05 0.00 0.00 3.61
2995 4292 8.085909 TGTGAGACTCGTATAACATTTTCTTCA 58.914 33.333 0.00 0.00 0.00 3.02
3016 4313 3.979497 CCCAACTCCCCACCCACC 61.979 72.222 0.00 0.00 0.00 4.61
3019 4316 3.182996 AACTCCCCACCCACCCAC 61.183 66.667 0.00 0.00 0.00 4.61
3025 4322 4.596585 CCACCCACCCACCCACAC 62.597 72.222 0.00 0.00 0.00 3.82
3026 4323 3.814906 CACCCACCCACCCACACA 61.815 66.667 0.00 0.00 0.00 3.72
3027 4324 3.024356 ACCCACCCACCCACACAA 61.024 61.111 0.00 0.00 0.00 3.33
3028 4325 2.280416 CCCACCCACCCACACAAA 59.720 61.111 0.00 0.00 0.00 2.83
3029 4326 1.832167 CCCACCCACCCACACAAAG 60.832 63.158 0.00 0.00 0.00 2.77
3030 4327 2.498056 CCACCCACCCACACAAAGC 61.498 63.158 0.00 0.00 0.00 3.51
3031 4328 1.756172 CACCCACCCACACAAAGCA 60.756 57.895 0.00 0.00 0.00 3.91
3032 4329 1.756561 ACCCACCCACACAAAGCAC 60.757 57.895 0.00 0.00 0.00 4.40
3033 4330 1.455587 CCCACCCACACAAAGCACT 60.456 57.895 0.00 0.00 0.00 4.40
3077 4821 1.603802 CATTCATGGACGATTTCCCGG 59.396 52.381 0.00 0.00 45.17 5.73
3083 6011 2.360726 ACGATTTCCCGGCCCAAC 60.361 61.111 0.00 0.00 0.00 3.77
3096 6024 2.352323 CGGCCCAACCAGTTTATTTCAC 60.352 50.000 0.00 0.00 39.03 3.18
3099 6027 3.572255 GCCCAACCAGTTTATTTCACAGA 59.428 43.478 0.00 0.00 0.00 3.41
3197 6360 5.703592 ACTAGTTGTTGAAACGATAATGGCA 59.296 36.000 0.00 0.00 0.00 4.92
3199 6362 3.485947 TGTTGAAACGATAATGGCAGC 57.514 42.857 0.00 0.00 0.00 5.25
3206 6369 0.317160 CGATAATGGCAGCGGGACTA 59.683 55.000 0.00 0.00 0.00 2.59
3208 6371 0.035458 ATAATGGCAGCGGGACTAGC 59.965 55.000 0.00 0.00 0.00 3.42
3235 6505 1.832883 AAACGATACAGCATTGGCCA 58.167 45.000 0.00 0.00 42.56 5.36
3241 6511 0.035152 TACAGCATTGGCCACCTCAG 60.035 55.000 3.88 0.00 42.56 3.35
3249 6519 2.262915 GCCACCTCAGTCTCACGG 59.737 66.667 0.00 0.00 0.00 4.94
3276 6548 1.002134 CAAAGTGGCCTCGTCCCAT 60.002 57.895 3.32 0.00 34.34 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
244 256 6.591001 AGTTTAAAATCATGCCCACAAGTTT 58.409 32.000 0.00 0.00 0.00 2.66
264 276 4.486125 AAAAGTTCATGCCCACAAGTTT 57.514 36.364 0.00 0.00 0.00 2.66
393 417 1.141645 CGCACAAAAATGCAGCATGT 58.858 45.000 9.18 0.00 46.47 3.21
431 460 1.154054 CAGCCGCGCTAAAATGCAA 60.154 52.632 5.56 0.00 36.40 4.08
465 496 0.038892 GTCTAGTTTGACGCGGTGGA 60.039 55.000 12.47 0.00 0.00 4.02
474 505 2.809446 CGCATCCATCGTCTAGTTTGA 58.191 47.619 0.00 0.00 0.00 2.69
491 522 0.382515 AAAAACTACTTTGCCGCGCA 59.617 45.000 8.75 0.00 36.47 6.09
550 582 5.181433 GGTTCGATATTTCTTTAGGGCATCC 59.819 44.000 0.00 0.00 0.00 3.51
579 611 3.643978 GCCTGCCACGCGATCATC 61.644 66.667 15.93 0.00 0.00 2.92
596 628 5.348164 ACAAAATTGACTGGTTTTTCCTCG 58.652 37.500 0.00 0.00 37.07 4.63
680 713 2.036992 GGATGCAGAGTATGGAGGAGTG 59.963 54.545 0.00 0.00 30.11 3.51
682 715 1.622811 GGGATGCAGAGTATGGAGGAG 59.377 57.143 0.00 0.00 30.11 3.69
722 755 2.975489 AGAGTTGGGAGAGAAAAGCTGA 59.025 45.455 0.00 0.00 0.00 4.26
794 834 1.279496 AGAGGTAGGTGAGCATGCAA 58.721 50.000 21.98 4.48 0.00 4.08
795 835 1.757118 GTAGAGGTAGGTGAGCATGCA 59.243 52.381 21.98 0.00 0.00 3.96
796 836 1.069358 GGTAGAGGTAGGTGAGCATGC 59.931 57.143 10.51 10.51 0.00 4.06
797 837 2.363680 CAGGTAGAGGTAGGTGAGCATG 59.636 54.545 0.00 0.00 0.00 4.06
869 909 2.009774 CTGCTTGTTCCCGTCCAATAG 58.990 52.381 0.00 0.00 0.00 1.73
870 910 1.626321 TCTGCTTGTTCCCGTCCAATA 59.374 47.619 0.00 0.00 0.00 1.90
871 911 0.400213 TCTGCTTGTTCCCGTCCAAT 59.600 50.000 0.00 0.00 0.00 3.16
880 920 2.555199 AGTCTGTGTGTCTGCTTGTTC 58.445 47.619 0.00 0.00 0.00 3.18
983 1030 3.494048 CCCCATTGCTCTCTCTATGTGTC 60.494 52.174 0.00 0.00 0.00 3.67
985 1032 2.437281 ACCCCATTGCTCTCTCTATGTG 59.563 50.000 0.00 0.00 0.00 3.21
986 1033 2.769209 ACCCCATTGCTCTCTCTATGT 58.231 47.619 0.00 0.00 0.00 2.29
987 1034 3.737850 GAACCCCATTGCTCTCTCTATG 58.262 50.000 0.00 0.00 0.00 2.23
988 1035 2.366916 CGAACCCCATTGCTCTCTCTAT 59.633 50.000 0.00 0.00 0.00 1.98
989 1036 1.757118 CGAACCCCATTGCTCTCTCTA 59.243 52.381 0.00 0.00 0.00 2.43
990 1037 0.539051 CGAACCCCATTGCTCTCTCT 59.461 55.000 0.00 0.00 0.00 3.10
991 1038 0.462759 CCGAACCCCATTGCTCTCTC 60.463 60.000 0.00 0.00 0.00 3.20
995 1042 3.508840 CGCCGAACCCCATTGCTC 61.509 66.667 0.00 0.00 0.00 4.26
1149 1196 4.809496 CCCCGCTGCTGCTTGGAT 62.809 66.667 18.51 0.00 36.97 3.41
1687 1758 0.389391 CTCTGTGTGACGTGGGAGTT 59.611 55.000 0.00 0.00 0.00 3.01
1703 1843 0.761187 ATCACGTATGCATGGCCTCT 59.239 50.000 10.16 0.00 0.00 3.69
1729 1869 5.508994 CCTTTCCAATTGAAGTGTTACCCAC 60.509 44.000 7.12 0.00 44.89 4.61
1730 1870 4.586841 CCTTTCCAATTGAAGTGTTACCCA 59.413 41.667 7.12 0.00 33.63 4.51
1731 1871 4.587262 ACCTTTCCAATTGAAGTGTTACCC 59.413 41.667 7.12 0.00 33.63 3.69
1735 1875 5.701224 TCCTACCTTTCCAATTGAAGTGTT 58.299 37.500 7.12 0.00 33.63 3.32
1736 1876 5.163088 ACTCCTACCTTTCCAATTGAAGTGT 60.163 40.000 7.12 6.63 33.63 3.55
1737 1877 5.316987 ACTCCTACCTTTCCAATTGAAGTG 58.683 41.667 7.12 1.20 33.63 3.16
1740 1880 6.043938 ACACTACTCCTACCTTTCCAATTGAA 59.956 38.462 7.12 0.00 0.00 2.69
1743 1883 5.803470 GCACACTACTCCTACCTTTCCAATT 60.803 44.000 0.00 0.00 0.00 2.32
1748 1888 3.955650 TGCACACTACTCCTACCTTTC 57.044 47.619 0.00 0.00 0.00 2.62
1755 1895 2.739932 GCGAATGATGCACACTACTCCT 60.740 50.000 0.00 0.00 0.00 3.69
1817 1957 0.802494 GTGATTCGCCACCAAATCGT 59.198 50.000 0.00 0.00 35.16 3.73
1837 1993 2.021068 CTGATCGGTCGGTGGCAGAT 62.021 60.000 0.00 0.00 0.00 2.90
1912 2074 8.342327 ACTAGTACCCCTACTCTAACTTGATA 57.658 38.462 0.00 0.00 34.79 2.15
1962 2178 5.520022 AGCGTACGTACTTTGGTTAATTG 57.480 39.130 22.55 4.54 0.00 2.32
2007 2224 0.033991 TCTTCCCCTCTCTCTGGACG 60.034 60.000 0.00 0.00 0.00 4.79
2256 2559 3.157949 GAGGAAGGCGGAGGGAGG 61.158 72.222 0.00 0.00 0.00 4.30
2259 2562 3.157949 GAGGAGGAAGGCGGAGGG 61.158 72.222 0.00 0.00 0.00 4.30
2284 2587 2.817901 CTACTACTATTTGGCGGCGTT 58.182 47.619 9.37 0.00 0.00 4.84
2285 2588 1.537562 GCTACTACTATTTGGCGGCGT 60.538 52.381 9.37 0.00 0.00 5.68
2293 2596 6.882678 GCCTCTCTAGCTAGCTACTACTATTT 59.117 42.308 20.67 0.00 0.00 1.40
2294 2597 6.214819 AGCCTCTCTAGCTAGCTACTACTATT 59.785 42.308 20.67 2.40 39.29 1.73
2295 2598 5.724854 AGCCTCTCTAGCTAGCTACTACTAT 59.275 44.000 20.67 1.92 39.29 2.12
2296 2599 5.046878 CAGCCTCTCTAGCTAGCTACTACTA 60.047 48.000 20.67 1.02 38.95 1.82
2297 2600 3.908103 AGCCTCTCTAGCTAGCTACTACT 59.092 47.826 20.67 9.26 39.29 2.57
2298 2601 4.000988 CAGCCTCTCTAGCTAGCTACTAC 58.999 52.174 20.67 7.25 38.95 2.73
2299 2602 3.558321 GCAGCCTCTCTAGCTAGCTACTA 60.558 52.174 20.67 10.66 38.95 1.82
2319 2622 0.171679 CTGCATGAAATCAAGCGGCA 59.828 50.000 6.53 4.85 42.84 5.69
2328 2631 1.536766 CGTGACACACCTGCATGAAAT 59.463 47.619 6.37 0.00 0.00 2.17
2331 2634 0.676736 TACGTGACACACCTGCATGA 59.323 50.000 6.37 0.00 0.00 3.07
2332 2635 1.394572 CATACGTGACACACCTGCATG 59.605 52.381 6.37 0.00 0.00 4.06
2333 2636 1.001974 ACATACGTGACACACCTGCAT 59.998 47.619 6.37 0.00 0.00 3.96
2334 2637 0.391228 ACATACGTGACACACCTGCA 59.609 50.000 6.37 0.00 0.00 4.41
2335 2638 0.790207 CACATACGTGACACACCTGC 59.210 55.000 6.37 0.00 46.80 4.85
2337 2640 1.045407 ACCACATACGTGACACACCT 58.955 50.000 6.37 0.00 46.80 4.00
2338 2641 1.144969 CACCACATACGTGACACACC 58.855 55.000 6.37 0.00 46.80 4.16
2340 2643 3.068448 ACTTACACCACATACGTGACACA 59.932 43.478 6.37 0.00 46.80 3.72
2341 2644 3.427528 CACTTACACCACATACGTGACAC 59.572 47.826 0.00 0.00 46.80 3.67
2342 2645 3.553302 CCACTTACACCACATACGTGACA 60.553 47.826 0.00 0.00 46.80 3.58
2345 2648 1.730064 GCCACTTACACCACATACGTG 59.270 52.381 0.00 0.00 43.21 4.49
2347 2650 1.730064 GTGCCACTTACACCACATACG 59.270 52.381 0.00 0.00 31.67 3.06
2350 2653 1.142870 ACAGTGCCACTTACACCACAT 59.857 47.619 0.00 0.00 38.87 3.21
2353 2656 0.179032 CCACAGTGCCACTTACACCA 60.179 55.000 0.00 0.00 38.87 4.17
2355 2658 0.817634 TGCCACAGTGCCACTTACAC 60.818 55.000 0.00 0.00 38.35 2.90
2357 2660 1.856265 GCTGCCACAGTGCCACTTAC 61.856 60.000 0.00 0.00 33.43 2.34
2361 2664 3.969802 GTGCTGCCACAGTGCCAC 61.970 66.667 0.00 0.00 41.67 5.01
2362 2665 4.193893 AGTGCTGCCACAGTGCCA 62.194 61.111 0.00 0.00 44.53 4.92
2363 2666 3.667282 CAGTGCTGCCACAGTGCC 61.667 66.667 0.00 0.00 44.53 5.01
2373 2676 2.789917 GATCAAGCGGCAGTGCTG 59.210 61.111 20.08 20.08 46.60 4.41
2382 2685 0.377554 AGTCTCGTACCGATCAAGCG 59.622 55.000 0.00 0.00 34.61 4.68
2384 2687 4.344448 GAAAGAGTCTCGTACCGATCAAG 58.656 47.826 0.00 0.00 34.61 3.02
2386 2689 2.350804 CGAAAGAGTCTCGTACCGATCA 59.649 50.000 0.00 0.00 34.61 2.92
2413 2823 9.525826 ACTGATCCTCTCATTTCAAAGTAAAAT 57.474 29.630 0.00 0.00 32.10 1.82
2450 2862 5.698089 CGGATATATGCATGACACTCAAACT 59.302 40.000 10.16 0.00 0.00 2.66
2460 2872 0.461870 GCCGGCGGATATATGCATGA 60.462 55.000 33.44 0.00 0.00 3.07
2464 2876 0.179073 AGATGCCGGCGGATATATGC 60.179 55.000 33.44 13.05 0.00 3.14
2579 3002 5.064707 CGGATAATCTTTTACACCACACCTG 59.935 44.000 0.00 0.00 0.00 4.00
2584 3007 6.047231 AGTAGCGGATAATCTTTTACACCAC 58.953 40.000 0.00 0.00 0.00 4.16
2604 3226 7.495279 ACGTAACTCTACTCACTGGATAAGTAG 59.505 40.741 0.00 3.01 42.43 2.57
2607 3229 6.680874 ACGTAACTCTACTCACTGGATAAG 57.319 41.667 0.00 0.00 0.00 1.73
2613 3235 8.967552 AATTTCTTACGTAACTCTACTCACTG 57.032 34.615 3.29 0.00 0.00 3.66
2628 3250 9.450807 GACCCATTTGATGATAAATTTCTTACG 57.549 33.333 0.00 0.00 0.00 3.18
2629 3251 9.750125 GGACCCATTTGATGATAAATTTCTTAC 57.250 33.333 0.00 0.00 0.00 2.34
2630 3252 9.486123 TGGACCCATTTGATGATAAATTTCTTA 57.514 29.630 0.00 0.00 0.00 2.10
2631 3253 8.378115 TGGACCCATTTGATGATAAATTTCTT 57.622 30.769 0.00 0.00 0.00 2.52
2632 3254 7.976414 TGGACCCATTTGATGATAAATTTCT 57.024 32.000 0.00 0.00 0.00 2.52
2635 3257 7.731688 AGCTATGGACCCATTTGATGATAAATT 59.268 33.333 6.88 0.00 37.82 1.82
2636 3258 7.243824 AGCTATGGACCCATTTGATGATAAAT 58.756 34.615 6.88 0.00 37.82 1.40
2637 3259 6.613699 AGCTATGGACCCATTTGATGATAAA 58.386 36.000 6.88 0.00 37.82 1.40
2638 3260 6.183361 TGAGCTATGGACCCATTTGATGATAA 60.183 38.462 6.88 0.00 37.82 1.75
2753 3449 7.730364 TTCTTTTCAAGAAGTGACATCTACC 57.270 36.000 0.00 0.00 42.31 3.18
2806 3506 6.265196 ACTTATCATGTTTGCCAGAGTTTTCA 59.735 34.615 0.00 0.00 0.00 2.69
2807 3507 6.681777 ACTTATCATGTTTGCCAGAGTTTTC 58.318 36.000 0.00 0.00 0.00 2.29
2808 3508 6.655078 ACTTATCATGTTTGCCAGAGTTTT 57.345 33.333 0.00 0.00 0.00 2.43
2809 3509 6.942576 AGTACTTATCATGTTTGCCAGAGTTT 59.057 34.615 0.00 0.00 0.00 2.66
2810 3510 6.476378 AGTACTTATCATGTTTGCCAGAGTT 58.524 36.000 0.00 0.00 0.00 3.01
2811 3511 6.054860 AGTACTTATCATGTTTGCCAGAGT 57.945 37.500 0.00 0.00 0.00 3.24
2814 3514 7.592938 TGAAAAGTACTTATCATGTTTGCCAG 58.407 34.615 8.92 0.00 0.00 4.85
2815 3515 7.517614 TGAAAAGTACTTATCATGTTTGCCA 57.482 32.000 8.92 0.00 0.00 4.92
2912 3660 1.584495 GTTCGGCGGCCTTGAAAAT 59.416 52.632 18.34 0.00 0.00 1.82
2923 4208 1.302671 TTTACCCCTTGGTTCGGCG 60.303 57.895 0.00 0.00 44.75 6.46
2930 4215 4.768448 ACCGATTTTAAGTTTACCCCTTGG 59.232 41.667 0.00 0.00 37.80 3.61
2967 4252 7.375834 AGAAAATGTTATACGAGTCTCACACA 58.624 34.615 0.00 0.00 0.00 3.72
3016 4313 0.751277 TGAGTGCTTTGTGTGGGTGG 60.751 55.000 0.00 0.00 0.00 4.61
3019 4316 1.608055 TCATGAGTGCTTTGTGTGGG 58.392 50.000 0.00 0.00 0.00 4.61
3020 4317 3.928727 ATTCATGAGTGCTTTGTGTGG 57.071 42.857 0.00 0.00 0.00 4.17
3021 4318 5.344128 GCTAAATTCATGAGTGCTTTGTGTG 59.656 40.000 0.00 0.00 0.00 3.82
3022 4319 5.009911 TGCTAAATTCATGAGTGCTTTGTGT 59.990 36.000 0.00 0.00 0.00 3.72
3023 4320 5.344128 GTGCTAAATTCATGAGTGCTTTGTG 59.656 40.000 0.00 0.00 0.00 3.33
3024 4321 5.009911 TGTGCTAAATTCATGAGTGCTTTGT 59.990 36.000 0.00 0.00 0.00 2.83
3025 4322 5.463286 TGTGCTAAATTCATGAGTGCTTTG 58.537 37.500 0.00 0.00 0.00 2.77
3026 4323 5.710513 TGTGCTAAATTCATGAGTGCTTT 57.289 34.783 0.00 0.00 0.00 3.51
3027 4324 5.909621 ATGTGCTAAATTCATGAGTGCTT 57.090 34.783 0.00 0.00 0.00 3.91
3028 4325 5.007039 CGTATGTGCTAAATTCATGAGTGCT 59.993 40.000 0.00 0.00 0.00 4.40
3029 4326 5.006649 TCGTATGTGCTAAATTCATGAGTGC 59.993 40.000 0.00 0.00 0.00 4.40
3030 4327 6.588348 TCGTATGTGCTAAATTCATGAGTG 57.412 37.500 0.00 0.00 0.00 3.51
3031 4328 7.792374 AATCGTATGTGCTAAATTCATGAGT 57.208 32.000 0.00 0.00 0.00 3.41
3032 4329 8.337532 TGAAATCGTATGTGCTAAATTCATGAG 58.662 33.333 0.00 0.00 0.00 2.90
3033 4330 8.207521 TGAAATCGTATGTGCTAAATTCATGA 57.792 30.769 0.00 0.00 0.00 3.07
3077 4821 3.572255 TCTGTGAAATAAACTGGTTGGGC 59.428 43.478 0.00 0.00 0.00 5.36
3083 6011 4.580580 GCCCCTATCTGTGAAATAAACTGG 59.419 45.833 0.00 0.00 0.00 4.00
3096 6024 1.956477 CCAATTTTCCGCCCCTATCTG 59.044 52.381 0.00 0.00 0.00 2.90
3099 6027 1.286553 TGACCAATTTTCCGCCCCTAT 59.713 47.619 0.00 0.00 0.00 2.57
3171 6334 7.388224 TGCCATTATCGTTTCAACAACTAGTTA 59.612 33.333 8.04 0.00 38.74 2.24
3208 6371 2.469826 TGCTGTATCGTTTAGCATCGG 58.530 47.619 0.00 0.00 42.05 4.18
3216 6379 1.472480 GTGGCCAATGCTGTATCGTTT 59.528 47.619 7.24 0.00 37.74 3.60
3217 6380 1.094785 GTGGCCAATGCTGTATCGTT 58.905 50.000 7.24 0.00 37.74 3.85
3225 6495 1.001641 GACTGAGGTGGCCAATGCT 60.002 57.895 7.24 0.00 37.74 3.79
3235 6505 0.314302 CGTTTCCGTGAGACTGAGGT 59.686 55.000 0.00 0.00 0.00 3.85
3241 6511 0.599204 TTGGCTCGTTTCCGTGAGAC 60.599 55.000 0.00 0.00 40.81 3.36


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

AutoCloner maintained by Alex Coulton.