Multiple sequence alignment - TraesCS7D01G065700

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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 TraesCS7D01G065700 chr7D 100.000 2646 0 0 1 2646 36453078 36450433 0.000000e+00 4887.0
1 TraesCS7D01G065700 chr7D 91.765 255 16 3 1 251 83751983 83751730 1.510000e-92 350.0
2 TraesCS7D01G065700 chr7D 81.176 340 32 12 256 573 83749749 83749420 7.320000e-61 244.0
3 TraesCS7D01G065700 chr7D 94.245 139 6 2 256 393 264392285 264392148 7.420000e-51 211.0
4 TraesCS7D01G065700 chr7D 95.522 67 3 0 1692 1758 36451320 36451254 1.000000e-19 108.0
5 TraesCS7D01G065700 chr7D 95.522 67 3 0 1759 1825 36451387 36451321 1.000000e-19 108.0
6 TraesCS7D01G065700 chr4A 88.908 1190 88 15 573 1758 688591848 688590699 0.000000e+00 1426.0
7 TraesCS7D01G065700 chr4A 93.137 714 42 5 1939 2646 688799673 688798961 0.000000e+00 1040.0
8 TraesCS7D01G065700 chr4A 93.760 657 37 4 1994 2646 688586555 688585899 0.000000e+00 983.0
9 TraesCS7D01G065700 chr4A 90.112 536 47 4 1986 2516 688613292 688612758 0.000000e+00 691.0
10 TraesCS7D01G065700 chr4A 86.196 623 73 5 891 1504 688907055 688906437 0.000000e+00 662.0
11 TraesCS7D01G065700 chr4A 89.712 486 38 4 965 1441 688639511 688639029 6.260000e-171 610.0
12 TraesCS7D01G065700 chr4A 83.580 609 82 16 1827 2431 688906204 688905610 2.980000e-154 555.0
13 TraesCS7D01G065700 chr4A 83.929 560 76 8 1037 1590 688888978 688888427 8.390000e-145 523.0
14 TraesCS7D01G065700 chr4A 85.459 447 48 10 2204 2646 688865872 688865439 1.440000e-122 449.0
15 TraesCS7D01G065700 chr4A 98.319 238 4 0 1759 1996 688590765 688590528 4.070000e-113 418.0
16 TraesCS7D01G065700 chr4A 87.749 351 36 3 856 1201 688807209 688806861 1.140000e-108 403.0
17 TraesCS7D01G065700 chr4A 85.632 348 29 3 1020 1367 688700681 688700355 1.950000e-91 346.0
18 TraesCS7D01G065700 chr4A 85.632 348 29 3 1020 1367 688755690 688755364 1.950000e-91 346.0
19 TraesCS7D01G065700 chr4A 91.388 209 18 0 1020 1228 688850214 688850006 1.200000e-73 287.0
20 TraesCS7D01G065700 chr4A 92.814 167 12 0 1759 1925 688806831 688806665 2.630000e-60 243.0
21 TraesCS7D01G065700 chr7A 84.803 737 73 17 856 1588 36310410 36309709 0.000000e+00 704.0
22 TraesCS7D01G065700 chr7A 82.077 597 99 5 1759 2354 36309542 36308953 1.090000e-138 503.0
23 TraesCS7D01G065700 chr7A 89.683 252 24 2 1 251 29322729 29322479 1.180000e-83 320.0
24 TraesCS7D01G065700 chr7A 90.000 130 13 0 449 578 712050142 712050271 4.530000e-38 169.0
25 TraesCS7D01G065700 chr4D 90.476 252 23 1 1 251 461767244 461766993 5.460000e-87 331.0
26 TraesCS7D01G065700 chr4D 90.040 251 24 1 1 250 351687651 351687401 9.140000e-85 324.0
27 TraesCS7D01G065700 chr4D 82.849 344 32 8 256 576 461765052 461764713 1.550000e-72 283.0
28 TraesCS7D01G065700 chr1D 90.040 251 23 2 2 251 418099888 418099639 9.140000e-85 324.0
29 TraesCS7D01G065700 chr1D 89.922 129 13 0 449 577 410061147 410061275 1.630000e-37 167.0
30 TraesCS7D01G065700 chr1D 96.154 52 2 0 1282 1333 460982314 460982263 4.690000e-13 86.1
31 TraesCS7D01G065700 chr3D 89.412 255 23 2 1 251 380529935 380530189 4.250000e-83 318.0
32 TraesCS7D01G065700 chr3D 89.683 252 20 4 1 251 474508918 474509164 1.530000e-82 316.0
33 TraesCS7D01G065700 chr3D 89.796 245 19 4 10 251 47197011 47196770 2.560000e-80 309.0
34 TraesCS7D01G065700 chr3D 84.466 206 15 5 365 570 384252142 384251954 1.250000e-43 187.0
35 TraesCS7D01G065700 chr2B 89.683 252 23 2 3 251 160751833 160751582 4.250000e-83 318.0
36 TraesCS7D01G065700 chr2B 92.969 128 9 0 449 576 250273732 250273859 1.250000e-43 187.0
37 TraesCS7D01G065700 chrUn 82.229 332 44 12 253 575 34160740 34161065 3.360000e-69 272.0
38 TraesCS7D01G065700 chr2D 84.058 276 27 12 311 576 30429030 30428762 1.570000e-62 250.0
39 TraesCS7D01G065700 chr2D 78.363 342 40 19 265 577 73206358 73206694 9.670000e-45 191.0
40 TraesCS7D01G065700 chr2D 92.623 122 9 0 455 576 370634332 370634211 2.710000e-40 176.0
41 TraesCS7D01G065700 chr3B 79.827 347 42 18 256 576 572278047 572277703 7.370000e-56 228.0
42 TraesCS7D01G065700 chr1A 80.997 321 30 10 292 586 7198750 7199065 2.650000e-55 226.0
43 TraesCS7D01G065700 chr1B 79.261 352 39 14 253 573 648132023 648132371 5.740000e-52 215.0
44 TraesCS7D01G065700 chr1B 96.154 52 2 0 1282 1333 633260430 633260379 4.690000e-13 86.1
45 TraesCS7D01G065700 chr4B 86.567 201 14 9 256 446 566209454 566209257 2.670000e-50 209.0
46 TraesCS7D01G065700 chr7B 94.737 133 6 1 258 390 719640949 719641080 3.450000e-49 206.0
47 TraesCS7D01G065700 chr7B 93.985 133 7 1 258 390 717636200 717636069 1.610000e-47 200.0
48 TraesCS7D01G065700 chr7B 80.000 290 30 12 311 573 474485980 474485692 3.480000e-44 189.0
49 TraesCS7D01G065700 chr2A 92.029 138 10 1 253 390 766440334 766440470 2.690000e-45 193.0


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 TraesCS7D01G065700 chr7D 36450433 36453078 2645 True 1701.000000 4887 97.014667 1 2646 3 chr7D.!!$R2 2645
1 TraesCS7D01G065700 chr7D 83749420 83751983 2563 True 297.000000 350 86.470500 1 573 2 chr7D.!!$R3 572
2 TraesCS7D01G065700 chr4A 688798961 688799673 712 True 1040.000000 1040 93.137000 1939 2646 1 chr4A.!!$R5 707
3 TraesCS7D01G065700 chr4A 688585899 688591848 5949 True 942.333333 1426 93.662333 573 2646 3 chr4A.!!$R9 2073
4 TraesCS7D01G065700 chr4A 688612758 688613292 534 True 691.000000 691 90.112000 1986 2516 1 chr4A.!!$R1 530
5 TraesCS7D01G065700 chr4A 688905610 688907055 1445 True 608.500000 662 84.888000 891 2431 2 chr4A.!!$R11 1540
6 TraesCS7D01G065700 chr4A 688888427 688888978 551 True 523.000000 523 83.929000 1037 1590 1 chr4A.!!$R8 553
7 TraesCS7D01G065700 chr4A 688806665 688807209 544 True 323.000000 403 90.281500 856 1925 2 chr4A.!!$R10 1069
8 TraesCS7D01G065700 chr7A 36308953 36310410 1457 True 603.500000 704 83.440000 856 2354 2 chr7A.!!$R2 1498
9 TraesCS7D01G065700 chr4D 461764713 461767244 2531 True 307.000000 331 86.662500 1 576 2 chr4D.!!$R2 575

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
760 2808 0.321653 GAACGACCTGGCCATGTCTT 60.322 55.0 30.7 22.85 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1755 3918 0.108662 TGCATAGCAGGCGATATCCG 60.109 55.0 0.0 0.0 36.19 4.18 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
20 21 1.949133 GAATCACCATCGCGCGCTA 60.949 57.895 30.48 20.37 0.00 4.26
177 178 2.797278 CCCTTCCTACAGCCGCGAT 61.797 63.158 8.23 0.00 0.00 4.58
182 183 2.797278 CCTACAGCCGCGATCCCTT 61.797 63.158 8.23 0.00 0.00 3.95
254 2249 1.902938 GAGCTCCTCCAAGCACTTTT 58.097 50.000 0.87 0.00 45.00 2.27
276 2271 5.233957 TGTGTGAACTTTTGTGTCATGAG 57.766 39.130 0.00 0.00 0.00 2.90
354 2371 7.766283 TGTCATCAACTTGTTTGTGTGATTTA 58.234 30.769 0.00 0.00 35.17 1.40
358 2375 9.687717 CATCAACTTGTTTGTGTGATTTAAAAC 57.312 29.630 0.00 0.00 36.49 2.43
363 2380 9.528018 ACTTGTTTGTGTGATTTAAAACTATGG 57.472 29.630 0.00 0.00 34.39 2.74
405 2440 7.160049 TGTTTGAAATTCAACATATGGCATGT 58.840 30.769 10.98 0.00 35.89 3.21
418 2453 3.057548 CATGTGCCGGCTGCTCAA 61.058 61.111 29.70 1.94 45.69 3.02
428 2463 4.013702 CTGCTCAAGCCCTGCATT 57.986 55.556 0.00 0.00 41.18 3.56
429 2464 2.273908 CTGCTCAAGCCCTGCATTT 58.726 52.632 0.00 0.00 41.18 2.32
430 2465 0.606604 CTGCTCAAGCCCTGCATTTT 59.393 50.000 0.00 0.00 41.18 1.82
431 2466 1.001633 CTGCTCAAGCCCTGCATTTTT 59.998 47.619 0.00 0.00 41.18 1.94
432 2467 2.231964 CTGCTCAAGCCCTGCATTTTTA 59.768 45.455 0.00 0.00 41.18 1.52
509 2556 3.055719 CGCCGTGCCAAACCAGAT 61.056 61.111 0.00 0.00 0.00 2.90
513 2560 0.452987 CCGTGCCAAACCAGATGATG 59.547 55.000 0.00 0.00 0.00 3.07
537 2584 2.723658 CGCGCTGCAAACTGATTTTTAA 59.276 40.909 5.56 0.00 0.00 1.52
590 2637 2.279502 CTAAGTAGCAGACCCGCGCA 62.280 60.000 8.75 0.00 36.85 6.09
610 2657 2.655364 CATACAGCTCGTCGGCCG 60.655 66.667 22.12 22.12 38.13 6.13
633 2680 4.001248 GCCACTAAGCCATGCACA 57.999 55.556 0.00 0.00 0.00 4.57
645 2692 4.789977 TGCACACACGCATTACCT 57.210 50.000 0.00 0.00 36.86 3.08
646 2693 3.917072 TGCACACACGCATTACCTA 57.083 47.368 0.00 0.00 36.86 3.08
650 2697 2.418692 CACACACGCATTACCTAACCA 58.581 47.619 0.00 0.00 0.00 3.67
651 2698 2.158841 CACACACGCATTACCTAACCAC 59.841 50.000 0.00 0.00 0.00 4.16
652 2699 2.038033 ACACACGCATTACCTAACCACT 59.962 45.455 0.00 0.00 0.00 4.00
653 2700 3.258872 ACACACGCATTACCTAACCACTA 59.741 43.478 0.00 0.00 0.00 2.74
655 2702 4.092383 CACACGCATTACCTAACCACTAAC 59.908 45.833 0.00 0.00 0.00 2.34
656 2703 4.247258 CACGCATTACCTAACCACTAACA 58.753 43.478 0.00 0.00 0.00 2.41
658 2705 4.692155 ACGCATTACCTAACCACTAACAAC 59.308 41.667 0.00 0.00 0.00 3.32
659 2706 4.691685 CGCATTACCTAACCACTAACAACA 59.308 41.667 0.00 0.00 0.00 3.33
660 2707 5.353123 CGCATTACCTAACCACTAACAACAT 59.647 40.000 0.00 0.00 0.00 2.71
661 2708 6.551736 GCATTACCTAACCACTAACAACATG 58.448 40.000 0.00 0.00 0.00 3.21
662 2709 6.551736 CATTACCTAACCACTAACAACATGC 58.448 40.000 0.00 0.00 0.00 4.06
663 2710 4.093472 ACCTAACCACTAACAACATGCA 57.907 40.909 0.00 0.00 0.00 3.96
664 2711 3.818773 ACCTAACCACTAACAACATGCAC 59.181 43.478 0.00 0.00 0.00 4.57
665 2712 3.120338 CCTAACCACTAACAACATGCACG 60.120 47.826 0.00 0.00 0.00 5.34
699 2747 4.641645 CTCCACGGCTGCCCAACA 62.642 66.667 14.12 0.00 0.00 3.33
727 2775 0.460987 GACGCAGCTGCTCCACTTAT 60.461 55.000 34.22 10.69 39.32 1.73
746 2794 3.109547 GCCGCATGACACGAACGA 61.110 61.111 0.00 0.00 0.00 3.85
747 2795 2.769617 CCGCATGACACGAACGAC 59.230 61.111 0.00 0.00 0.00 4.34
748 2796 2.726691 CCGCATGACACGAACGACC 61.727 63.158 0.00 0.00 0.00 4.79
749 2797 1.733041 CGCATGACACGAACGACCT 60.733 57.895 0.00 0.00 0.00 3.85
750 2798 1.781555 GCATGACACGAACGACCTG 59.218 57.895 0.00 0.00 0.00 4.00
751 2799 1.626654 GCATGACACGAACGACCTGG 61.627 60.000 0.00 0.00 0.00 4.45
752 2800 1.374252 ATGACACGAACGACCTGGC 60.374 57.895 0.14 0.00 0.00 4.85
753 2801 2.737376 GACACGAACGACCTGGCC 60.737 66.667 0.00 0.00 0.00 5.36
754 2802 3.509137 GACACGAACGACCTGGCCA 62.509 63.158 4.71 4.71 0.00 5.36
755 2803 2.047274 CACGAACGACCTGGCCAT 60.047 61.111 5.51 0.00 0.00 4.40
756 2804 2.047274 ACGAACGACCTGGCCATG 60.047 61.111 5.51 6.06 0.00 3.66
757 2805 2.047274 CGAACGACCTGGCCATGT 60.047 61.111 14.10 14.10 0.00 3.21
758 2806 2.100631 CGAACGACCTGGCCATGTC 61.101 63.158 26.32 26.32 0.00 3.06
759 2807 1.296715 GAACGACCTGGCCATGTCT 59.703 57.895 30.70 18.25 0.00 3.41
760 2808 0.321653 GAACGACCTGGCCATGTCTT 60.322 55.000 30.70 22.85 0.00 3.01
761 2809 0.321653 AACGACCTGGCCATGTCTTC 60.322 55.000 30.70 12.59 0.00 2.87
762 2810 1.450312 CGACCTGGCCATGTCTTCC 60.450 63.158 30.70 12.27 0.00 3.46
763 2811 1.685224 GACCTGGCCATGTCTTCCA 59.315 57.895 28.13 0.00 0.00 3.53
764 2812 0.678048 GACCTGGCCATGTCTTCCAC 60.678 60.000 28.13 6.71 0.00 4.02
765 2813 1.379916 CCTGGCCATGTCTTCCACA 59.620 57.895 5.51 0.00 40.18 4.17
766 2814 0.962356 CCTGGCCATGTCTTCCACAC 60.962 60.000 5.51 0.00 38.04 3.82
767 2815 1.300971 CTGGCCATGTCTTCCACACG 61.301 60.000 5.51 0.00 38.04 4.49
768 2816 1.003839 GGCCATGTCTTCCACACGA 60.004 57.895 0.00 0.00 38.04 4.35
769 2817 0.605319 GGCCATGTCTTCCACACGAA 60.605 55.000 0.00 0.00 38.04 3.85
770 2818 0.517316 GCCATGTCTTCCACACGAAC 59.483 55.000 0.00 0.00 38.04 3.95
771 2819 1.156736 CCATGTCTTCCACACGAACC 58.843 55.000 0.00 0.00 38.04 3.62
777 2825 1.831389 CTTCCACACGAACCACGCAG 61.831 60.000 0.00 0.00 46.94 5.18
830 2878 0.744414 GAGCGCACTGGCCAAGATTA 60.744 55.000 11.47 0.00 36.38 1.75
843 2891 3.609853 CCAAGATTAGTGCTAACAGCCA 58.390 45.455 0.00 0.00 41.51 4.75
893 2941 3.394836 GGTTCTCCCTCGCAGCCT 61.395 66.667 0.00 0.00 0.00 4.58
915 2963 5.018539 TCGTCCACGAATATTCTGGATTT 57.981 39.130 26.02 2.79 46.30 2.17
916 2964 4.808895 TCGTCCACGAATATTCTGGATTTG 59.191 41.667 26.02 20.94 46.30 2.32
947 2995 1.818674 GAAACCGCCATGTCCAAATCT 59.181 47.619 0.00 0.00 0.00 2.40
952 3000 2.094675 CGCCATGTCCAAATCTTCCTT 58.905 47.619 0.00 0.00 0.00 3.36
956 3004 4.889409 GCCATGTCCAAATCTTCCTTGATA 59.111 41.667 0.00 0.00 0.00 2.15
962 3010 3.561725 CCAAATCTTCCTTGATACTCCGC 59.438 47.826 0.00 0.00 0.00 5.54
990 3038 2.367377 CCAGGCTCCCATCCTCCA 60.367 66.667 0.00 0.00 0.00 3.86
991 3039 1.773391 CCAGGCTCCCATCCTCCAT 60.773 63.158 0.00 0.00 0.00 3.41
1103 3156 4.327627 GGACAAGATGCTCGTCTTCTTTAC 59.672 45.833 1.59 4.61 37.16 2.01
1238 3303 1.703411 CAGCTTGGAAAGGGGAAACA 58.297 50.000 0.00 0.00 46.35 2.83
1245 3310 1.478654 GGAAAGGGGAAACAGCAGTCA 60.479 52.381 0.00 0.00 0.00 3.41
1262 3327 1.301244 CACAGTCGCAGCTTCCACT 60.301 57.895 0.00 0.00 0.00 4.00
1323 3388 0.320374 TCGACGGGATTGACTGCTTT 59.680 50.000 0.00 0.00 0.00 3.51
1390 3462 1.696097 GCTGATCCGGGGGTGTGTAT 61.696 60.000 0.00 0.00 0.00 2.29
1497 3573 1.276421 TGTTTCTAGCTGAGGCCAGAC 59.724 52.381 5.01 0.00 43.02 3.51
1551 3627 6.142320 GTGCGACCAAACTCTAATTTTCTTTG 59.858 38.462 0.00 0.00 0.00 2.77
1593 3669 0.944386 GAAGCAACGGACTCAAGCAA 59.056 50.000 0.00 0.00 0.00 3.91
1599 3702 2.372690 CGGACTCAAGCAACGGACG 61.373 63.158 0.00 0.00 0.00 4.79
1685 3846 4.895224 AAAGAACTTGACCGGTTTCTTC 57.105 40.909 24.98 16.13 0.00 2.87
1726 3889 6.115446 TCTGCAGATAAATTCCAATCTCGTT 58.885 36.000 13.74 0.00 29.93 3.85
1727 3890 6.037500 TCTGCAGATAAATTCCAATCTCGTTG 59.962 38.462 13.74 0.00 37.57 4.10
1728 3891 4.972440 GCAGATAAATTCCAATCTCGTTGC 59.028 41.667 0.00 0.00 36.46 4.17
1729 3892 5.449041 GCAGATAAATTCCAATCTCGTTGCA 60.449 40.000 0.00 0.00 36.46 4.08
1730 3893 6.732154 CAGATAAATTCCAATCTCGTTGCAT 58.268 36.000 0.00 0.00 36.46 3.96
1731 3894 7.520453 GCAGATAAATTCCAATCTCGTTGCATA 60.520 37.037 0.00 0.00 36.46 3.14
1732 3895 7.800380 CAGATAAATTCCAATCTCGTTGCATAC 59.200 37.037 0.00 0.00 36.46 2.39
1733 3896 7.716998 AGATAAATTCCAATCTCGTTGCATACT 59.283 33.333 0.00 0.00 36.46 2.12
1734 3897 8.902540 ATAAATTCCAATCTCGTTGCATACTA 57.097 30.769 0.00 0.00 36.46 1.82
1735 3898 6.604735 AATTCCAATCTCGTTGCATACTAC 57.395 37.500 0.00 0.00 36.46 2.73
1736 3899 3.702330 TCCAATCTCGTTGCATACTACG 58.298 45.455 2.24 2.24 44.76 3.51
1737 3900 3.129813 TCCAATCTCGTTGCATACTACGT 59.870 43.478 8.38 0.00 43.97 3.57
1738 3901 3.486108 CCAATCTCGTTGCATACTACGTC 59.514 47.826 8.38 0.00 43.97 4.34
1739 3902 4.102649 CAATCTCGTTGCATACTACGTCA 58.897 43.478 8.38 0.00 43.97 4.35
1740 3903 4.569761 ATCTCGTTGCATACTACGTCAT 57.430 40.909 8.38 0.18 43.97 3.06
1741 3904 5.684550 ATCTCGTTGCATACTACGTCATA 57.315 39.130 8.38 0.00 43.97 2.15
1742 3905 5.684550 TCTCGTTGCATACTACGTCATAT 57.315 39.130 8.38 0.00 43.97 1.78
1743 3906 6.068473 TCTCGTTGCATACTACGTCATATT 57.932 37.500 8.38 0.00 43.97 1.28
1744 3907 6.140786 TCTCGTTGCATACTACGTCATATTC 58.859 40.000 8.38 0.00 43.97 1.75
1745 3908 6.017357 TCTCGTTGCATACTACGTCATATTCT 60.017 38.462 8.38 0.00 43.97 2.40
1746 3909 6.500910 TCGTTGCATACTACGTCATATTCTT 58.499 36.000 8.38 0.00 43.97 2.52
1747 3910 7.641760 TCGTTGCATACTACGTCATATTCTTA 58.358 34.615 8.38 0.00 43.97 2.10
1748 3911 7.801783 TCGTTGCATACTACGTCATATTCTTAG 59.198 37.037 8.38 0.00 43.97 2.18
1749 3912 7.590322 CGTTGCATACTACGTCATATTCTTAGT 59.410 37.037 0.00 0.00 39.67 2.24
1750 3913 9.888878 GTTGCATACTACGTCATATTCTTAGTA 57.111 33.333 0.00 0.00 31.52 1.82
1756 3919 7.082602 ACTACGTCATATTCTTAGTAATGCCG 58.917 38.462 0.00 0.00 0.00 5.69
1757 3920 5.227908 ACGTCATATTCTTAGTAATGCCGG 58.772 41.667 0.00 0.00 0.00 6.13
1758 3921 5.010314 ACGTCATATTCTTAGTAATGCCGGA 59.990 40.000 5.05 0.00 0.00 5.14
1759 3922 6.100004 CGTCATATTCTTAGTAATGCCGGAT 58.900 40.000 5.05 0.00 0.00 4.18
1760 3923 7.094075 ACGTCATATTCTTAGTAATGCCGGATA 60.094 37.037 5.05 0.00 0.00 2.59
1761 3924 7.921214 CGTCATATTCTTAGTAATGCCGGATAT 59.079 37.037 5.05 0.00 0.00 1.63
1762 3925 9.250624 GTCATATTCTTAGTAATGCCGGATATC 57.749 37.037 5.05 0.00 0.00 1.63
1763 3926 8.135529 TCATATTCTTAGTAATGCCGGATATCG 58.864 37.037 5.05 0.00 38.88 2.92
1764 3927 4.106029 TCTTAGTAATGCCGGATATCGC 57.894 45.455 5.05 0.00 37.59 4.58
1765 3928 2.953466 TAGTAATGCCGGATATCGCC 57.047 50.000 5.05 0.00 37.59 5.54
1766 3929 1.267121 AGTAATGCCGGATATCGCCT 58.733 50.000 5.05 0.00 37.59 5.52
1767 3930 1.066858 AGTAATGCCGGATATCGCCTG 60.067 52.381 5.05 0.00 37.59 4.85
1768 3931 0.391130 TAATGCCGGATATCGCCTGC 60.391 55.000 5.05 0.00 38.48 4.85
1769 3932 2.116983 AATGCCGGATATCGCCTGCT 62.117 55.000 5.05 0.00 38.75 4.24
1770 3933 1.257750 ATGCCGGATATCGCCTGCTA 61.258 55.000 5.05 0.00 38.75 3.49
1771 3934 1.257750 TGCCGGATATCGCCTGCTAT 61.258 55.000 5.05 0.00 38.75 2.97
1772 3935 0.807667 GCCGGATATCGCCTGCTATG 60.808 60.000 5.05 0.00 35.55 2.23
1773 3936 0.807667 CCGGATATCGCCTGCTATGC 60.808 60.000 0.00 0.00 37.59 3.14
1774 3937 0.108662 CGGATATCGCCTGCTATGCA 60.109 55.000 0.00 0.00 36.92 3.96
1790 3953 7.444629 TGCTATGCAGATAAATTCCAATCTC 57.555 36.000 0.00 0.00 33.32 2.75
1791 3954 6.148315 TGCTATGCAGATAAATTCCAATCTCG 59.852 38.462 0.00 0.00 33.32 4.04
1792 3955 6.148480 GCTATGCAGATAAATTCCAATCTCGT 59.852 38.462 0.00 0.00 29.93 4.18
2010 8148 1.047801 GGCAGGTTGGTCAAATTGGT 58.952 50.000 0.00 0.00 0.00 3.67
2091 8229 7.730364 TCTTTTCGAATTGAGTAGCTTTTCT 57.270 32.000 0.00 0.00 0.00 2.52
2311 8454 8.709272 TGATGCATCTGATTCCCAAATATTTA 57.291 30.769 26.32 0.00 0.00 1.40
2363 8509 1.825474 TCTCTGGGTGCTGTTAGCTAC 59.175 52.381 0.00 0.00 42.97 3.58
2431 8577 8.642908 TCAAAGTGTATATGAACTTATGGACG 57.357 34.615 5.56 0.00 35.60 4.79
2446 8592 2.198406 TGGACGTTGCTATATGTTCGC 58.802 47.619 0.00 0.00 0.00 4.70
2551 8697 2.236644 TGTGGCATTTTCCCCATTGATG 59.763 45.455 0.00 0.00 32.95 3.07
2556 8702 3.448301 GCATTTTCCCCATTGATGAGTGA 59.552 43.478 0.00 0.00 0.00 3.41
2620 8768 3.387374 ACATTTGATTTGCACACTGGGAA 59.613 39.130 0.00 0.00 0.00 3.97
2625 8774 2.079170 TTTGCACACTGGGAATTGGA 57.921 45.000 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.319555 AATACATAGCGCGCGATGGT 60.320 50.000 42.59 32.59 34.15 3.55
20 21 2.770589 GCGGGCGCACCAAATACAT 61.771 57.895 10.83 0.00 40.22 2.29
118 119 0.508641 GCGTCCATCGGATCAATTCG 59.491 55.000 0.00 0.00 40.26 3.34
251 256 6.450545 TCATGACACAAAAGTTCACACAAAA 58.549 32.000 0.00 0.00 0.00 2.44
254 2249 4.438608 GCTCATGACACAAAAGTTCACACA 60.439 41.667 0.00 0.00 0.00 3.72
276 2271 4.273235 CCAAGTTCAAAATCCAAACCAAGC 59.727 41.667 0.00 0.00 0.00 4.01
354 2371 7.271511 TCAAAACAAAGACATGCCATAGTTTT 58.728 30.769 11.01 11.01 38.14 2.43
358 2375 6.392354 ACATCAAAACAAAGACATGCCATAG 58.608 36.000 0.00 0.00 0.00 2.23
363 2380 6.586868 TCAAACATCAAAACAAAGACATGC 57.413 33.333 0.00 0.00 0.00 4.06
417 2452 0.109319 CGCGTAAAAATGCAGGGCTT 60.109 50.000 0.00 0.00 0.00 4.35
418 2453 1.506262 CGCGTAAAAATGCAGGGCT 59.494 52.632 0.00 0.00 0.00 5.19
420 2455 0.798009 CAGCGCGTAAAAATGCAGGG 60.798 55.000 8.43 0.00 0.00 4.45
421 2456 1.405469 GCAGCGCGTAAAAATGCAGG 61.405 55.000 8.43 0.00 36.88 4.85
422 2457 0.728803 TGCAGCGCGTAAAAATGCAG 60.729 50.000 13.41 0.00 41.65 4.41
423 2458 1.284100 TGCAGCGCGTAAAAATGCA 59.716 47.368 13.41 13.41 44.10 3.96
424 2459 0.991344 AATGCAGCGCGTAAAAATGC 59.009 45.000 8.43 4.98 37.40 3.56
425 2460 3.703558 AAAATGCAGCGCGTAAAAATG 57.296 38.095 8.43 0.00 0.00 2.32
426 2461 3.664014 GCAAAAATGCAGCGCGTAAAAAT 60.664 39.130 8.43 0.00 34.41 1.82
427 2462 2.348032 GCAAAAATGCAGCGCGTAAAAA 60.348 40.909 8.43 0.00 34.41 1.94
428 2463 1.191204 GCAAAAATGCAGCGCGTAAAA 59.809 42.857 8.43 0.00 34.41 1.52
429 2464 0.781191 GCAAAAATGCAGCGCGTAAA 59.219 45.000 8.43 0.00 34.41 2.01
430 2465 1.333584 CGCAAAAATGCAGCGCGTAA 61.334 50.000 8.43 0.00 45.14 3.18
431 2466 1.795569 CGCAAAAATGCAGCGCGTA 60.796 52.632 8.43 0.00 45.14 4.42
432 2467 3.098958 CGCAAAAATGCAGCGCGT 61.099 55.556 8.43 0.00 45.14 6.01
497 2544 0.971959 GCCCATCATCTGGTTTGGCA 60.972 55.000 0.00 0.00 44.30 4.92
515 2562 1.277495 AAAATCAGTTTGCAGCGCGC 61.277 50.000 26.66 26.66 42.89 6.86
579 2626 2.125713 TATGTGTGCGCGGGTCTG 60.126 61.111 8.83 0.00 0.00 3.51
585 2632 2.697425 GAGCTGTATGTGTGCGCG 59.303 61.111 0.00 0.00 0.00 6.86
590 2637 1.153823 GCCGACGAGCTGTATGTGT 60.154 57.895 0.00 0.00 0.00 3.72
620 2667 1.135315 GCGTGTGTGCATGGCTTAG 59.865 57.895 0.00 0.00 34.15 2.18
633 2680 4.248058 GTTAGTGGTTAGGTAATGCGTGT 58.752 43.478 0.00 0.00 0.00 4.49
645 2692 2.224549 GCGTGCATGTTGTTAGTGGTTA 59.775 45.455 7.93 0.00 0.00 2.85
646 2693 1.001815 GCGTGCATGTTGTTAGTGGTT 60.002 47.619 7.93 0.00 0.00 3.67
650 2697 0.536233 TGGGCGTGCATGTTGTTAGT 60.536 50.000 7.93 0.00 0.00 2.24
651 2698 0.109781 GTGGGCGTGCATGTTGTTAG 60.110 55.000 7.93 0.00 0.00 2.34
652 2699 1.846849 CGTGGGCGTGCATGTTGTTA 61.847 55.000 7.93 0.00 0.00 2.41
653 2700 2.727544 GTGGGCGTGCATGTTGTT 59.272 55.556 7.93 0.00 0.00 2.83
727 2775 3.047280 GTTCGTGTCATGCGGCCA 61.047 61.111 2.24 0.00 0.00 5.36
746 2794 1.380302 GTGGAAGACATGGCCAGGT 59.620 57.895 25.58 25.58 31.18 4.00
747 2795 0.962356 GTGTGGAAGACATGGCCAGG 60.962 60.000 17.55 17.55 36.78 4.45
748 2796 1.300971 CGTGTGGAAGACATGGCCAG 61.301 60.000 13.05 6.08 37.86 4.85
749 2797 1.302431 CGTGTGGAAGACATGGCCA 60.302 57.895 8.56 8.56 37.86 5.36
750 2798 0.605319 TTCGTGTGGAAGACATGGCC 60.605 55.000 0.00 0.00 41.37 5.36
751 2799 0.517316 GTTCGTGTGGAAGACATGGC 59.483 55.000 0.00 0.00 41.37 4.40
752 2800 1.156736 GGTTCGTGTGGAAGACATGG 58.843 55.000 0.00 0.00 41.37 3.66
753 2801 1.531149 GTGGTTCGTGTGGAAGACATG 59.469 52.381 0.00 0.00 42.28 3.21
754 2802 1.872237 CGTGGTTCGTGTGGAAGACAT 60.872 52.381 0.00 0.00 36.78 3.06
755 2803 0.528901 CGTGGTTCGTGTGGAAGACA 60.529 55.000 0.00 0.00 34.69 3.41
756 2804 1.828331 GCGTGGTTCGTGTGGAAGAC 61.828 60.000 0.00 0.00 42.13 3.01
757 2805 1.593209 GCGTGGTTCGTGTGGAAGA 60.593 57.895 0.00 0.00 42.13 2.87
758 2806 1.831389 CTGCGTGGTTCGTGTGGAAG 61.831 60.000 0.00 0.00 42.13 3.46
759 2807 1.885388 CTGCGTGGTTCGTGTGGAA 60.885 57.895 0.00 0.00 42.13 3.53
760 2808 2.279851 CTGCGTGGTTCGTGTGGA 60.280 61.111 0.00 0.00 42.13 4.02
761 2809 4.012895 GCTGCGTGGTTCGTGTGG 62.013 66.667 0.00 0.00 42.13 4.17
762 2810 4.012895 GGCTGCGTGGTTCGTGTG 62.013 66.667 0.00 0.00 42.13 3.82
763 2811 4.539083 TGGCTGCGTGGTTCGTGT 62.539 61.111 0.00 0.00 42.13 4.49
764 2812 4.012895 GTGGCTGCGTGGTTCGTG 62.013 66.667 0.00 0.00 42.13 4.35
767 2815 4.980805 TCCGTGGCTGCGTGGTTC 62.981 66.667 0.00 0.00 0.00 3.62
819 2867 3.609853 CTGTTAGCACTAATCTTGGCCA 58.390 45.455 0.00 0.00 0.00 5.36
830 2878 2.358737 GCCGTGGCTGTTAGCACT 60.359 61.111 2.98 0.00 44.75 4.40
851 2899 1.867166 ATGAGCTCGTGATGCAGATG 58.133 50.000 7.89 0.00 0.00 2.90
893 2941 4.665833 AATCCAGAATATTCGTGGACGA 57.334 40.909 25.89 13.42 43.18 4.20
915 2963 2.324330 CGGTTTCATGCGCTGGACA 61.324 57.895 9.73 0.00 0.00 4.02
916 2964 2.480555 CGGTTTCATGCGCTGGAC 59.519 61.111 9.73 7.23 0.00 4.02
947 2995 1.766494 TACGGCGGAGTATCAAGGAA 58.234 50.000 13.24 0.00 36.25 3.36
952 3000 3.379372 GGCTTATATACGGCGGAGTATCA 59.621 47.826 13.24 0.00 38.23 2.15
956 3004 1.544691 CTGGCTTATATACGGCGGAGT 59.455 52.381 13.24 0.00 34.29 3.85
962 3010 1.207329 GGGAGCCTGGCTTATATACGG 59.793 57.143 24.26 0.00 39.88 4.02
990 3038 2.239907 GCTAAGGTTGGTGAAGGGAGAT 59.760 50.000 0.00 0.00 0.00 2.75
991 3039 1.628846 GCTAAGGTTGGTGAAGGGAGA 59.371 52.381 0.00 0.00 0.00 3.71
1215 3280 1.075482 CCCCTTTCCAAGCTGCTGA 59.925 57.895 1.35 0.00 0.00 4.26
1238 3303 2.356793 GCTGCGACTGTGACTGCT 60.357 61.111 0.00 0.00 0.00 4.24
1245 3310 1.301244 CAGTGGAAGCTGCGACTGT 60.301 57.895 24.84 0.00 39.05 3.55
1390 3462 6.561533 CGTCGAACGAAGAAAGAATCAAGAAA 60.562 38.462 4.35 0.00 46.05 2.52
1446 3519 2.107041 TTGAACGCACCGGTCCTCAT 62.107 55.000 2.59 0.00 43.57 2.90
1551 3627 7.991084 TCCATATGAATGTGATCTCAAATCC 57.009 36.000 3.65 0.00 0.00 3.01
1593 3669 1.300697 GTTCCTGAACTGCGTCCGT 60.301 57.895 2.80 0.00 38.25 4.69
1732 3895 6.527023 CCGGCATTACTAAGAATATGACGTAG 59.473 42.308 8.19 0.00 45.54 3.51
1733 3896 6.207221 TCCGGCATTACTAAGAATATGACGTA 59.793 38.462 0.00 0.00 45.54 3.57
1734 3897 5.010314 TCCGGCATTACTAAGAATATGACGT 59.990 40.000 0.00 0.00 45.54 4.34
1735 3898 5.466819 TCCGGCATTACTAAGAATATGACG 58.533 41.667 0.00 0.00 46.32 4.35
1736 3899 9.250624 GATATCCGGCATTACTAAGAATATGAC 57.749 37.037 0.00 0.00 0.00 3.06
1737 3900 8.135529 CGATATCCGGCATTACTAAGAATATGA 58.864 37.037 0.00 0.00 33.91 2.15
1738 3901 7.096023 GCGATATCCGGCATTACTAAGAATATG 60.096 40.741 0.00 0.00 39.04 1.78
1739 3902 6.924060 GCGATATCCGGCATTACTAAGAATAT 59.076 38.462 0.00 0.00 39.04 1.28
1740 3903 6.270815 GCGATATCCGGCATTACTAAGAATA 58.729 40.000 0.00 0.00 39.04 1.75
1741 3904 5.109903 GCGATATCCGGCATTACTAAGAAT 58.890 41.667 0.00 0.00 39.04 2.40
1742 3905 4.491676 GCGATATCCGGCATTACTAAGAA 58.508 43.478 0.00 0.00 39.04 2.52
1743 3906 4.106029 GCGATATCCGGCATTACTAAGA 57.894 45.455 0.00 0.00 39.04 2.10
1754 3917 0.807667 GCATAGCAGGCGATATCCGG 60.808 60.000 0.00 0.00 39.04 5.14
1755 3918 0.108662 TGCATAGCAGGCGATATCCG 60.109 55.000 0.00 0.00 36.19 4.18
1756 3919 3.840831 TGCATAGCAGGCGATATCC 57.159 52.632 0.00 0.00 33.32 2.59
1766 3929 6.148315 CGAGATTGGAATTTATCTGCATAGCA 59.852 38.462 0.00 0.00 36.92 3.49
1767 3930 6.148480 ACGAGATTGGAATTTATCTGCATAGC 59.852 38.462 0.00 0.00 31.46 2.97
1768 3931 7.664082 ACGAGATTGGAATTTATCTGCATAG 57.336 36.000 0.00 0.00 31.46 2.23
1769 3932 7.520453 GCAACGAGATTGGAATTTATCTGCATA 60.520 37.037 0.00 0.00 38.88 3.14
1770 3933 6.732154 CAACGAGATTGGAATTTATCTGCAT 58.268 36.000 0.00 0.00 34.34 3.96
1771 3934 5.449041 GCAACGAGATTGGAATTTATCTGCA 60.449 40.000 0.00 0.00 38.88 4.41
1772 3935 4.972440 GCAACGAGATTGGAATTTATCTGC 59.028 41.667 0.00 0.00 38.88 4.26
1773 3936 6.122850 TGCAACGAGATTGGAATTTATCTG 57.877 37.500 0.00 1.40 35.40 2.90
1774 3937 6.949352 ATGCAACGAGATTGGAATTTATCT 57.051 33.333 0.00 0.00 42.55 1.98
1775 3938 7.800380 CAGTATGCAACGAGATTGGAATTTATC 59.200 37.037 0.00 0.00 42.55 1.75
1776 3939 7.642669 CAGTATGCAACGAGATTGGAATTTAT 58.357 34.615 0.00 0.00 42.55 1.40
1777 3940 7.015226 CAGTATGCAACGAGATTGGAATTTA 57.985 36.000 0.00 0.00 42.55 1.40
1778 3941 5.883661 CAGTATGCAACGAGATTGGAATTT 58.116 37.500 0.00 0.00 42.55 1.82
1779 3942 5.490139 CAGTATGCAACGAGATTGGAATT 57.510 39.130 0.00 0.00 42.55 2.17
1954 4117 3.391506 TGGCATCATAGTTCTCCATCG 57.608 47.619 0.00 0.00 0.00 3.84
2010 8148 6.038161 CCGACATAGCAAATTCCATCTTAACA 59.962 38.462 0.00 0.00 0.00 2.41
2091 8229 3.674997 CTTCAGGAAACGAAATCAGGGA 58.325 45.455 0.00 0.00 0.00 4.20
2311 8454 2.444766 GAGATGATCCAAAGGGGTCCAT 59.555 50.000 0.00 0.00 44.30 3.41
2363 8509 8.022550 TGTTTGACATGTTAGAGTGCAAATATG 58.977 33.333 0.00 4.58 32.37 1.78
2424 8570 3.985279 GCGAACATATAGCAACGTCCATA 59.015 43.478 0.00 0.00 0.00 2.74
2425 8571 2.800544 GCGAACATATAGCAACGTCCAT 59.199 45.455 0.00 0.00 0.00 3.41
2431 8577 3.918258 TTCACGCGAACATATAGCAAC 57.082 42.857 15.93 0.00 0.00 4.17
2551 8697 3.003275 TGCAGAAAAACACCGATTCACTC 59.997 43.478 0.00 0.00 0.00 3.51
2556 8702 5.004922 TCTTTTGCAGAAAAACACCGATT 57.995 34.783 0.00 0.00 34.08 3.34
2620 8768 0.343372 TCCTGACCCTAGCCTCCAAT 59.657 55.000 0.00 0.00 0.00 3.16
2625 8774 1.076632 CGAGTCCTGACCCTAGCCT 60.077 63.158 0.00 0.00 0.00 4.58


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

AutoCloner maintained by Alex Coulton.