Multiple sequence alignment - TraesCS7A01G531700

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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 TraesCS7A01G531700 chr7A 100.000 3413 0 0 1 3413 709991653 709988241 0.000000e+00 6303.0
1 TraesCS7A01G531700 chr7A 82.214 551 68 17 978 1509 709697988 709698527 6.720000e-122 448.0
2 TraesCS7A01G531700 chr7A 81.733 427 52 13 1009 1416 709677848 709678267 1.960000e-87 333.0
3 TraesCS7A01G531700 chr7A 79.915 473 67 19 956 1411 709710627 709711088 4.250000e-84 322.0
4 TraesCS7A01G531700 chr7A 92.105 114 9 0 1405 1518 709711241 709711354 9.800000e-36 161.0
5 TraesCS7A01G531700 chr7A 88.462 52 5 1 3350 3401 714216965 714216915 1.020000e-05 62.1
6 TraesCS7A01G531700 chr7B 91.674 1117 55 13 1 1103 711484028 711482936 0.000000e+00 1513.0
7 TraesCS7A01G531700 chr7B 88.978 1116 87 19 1564 2669 711481644 711480555 0.000000e+00 1347.0
8 TraesCS7A01G531700 chr7B 93.483 445 20 6 1107 1547 711482395 711481956 0.000000e+00 652.0
9 TraesCS7A01G531700 chr7B 80.680 647 102 20 1848 2478 711050444 711051083 6.620000e-132 481.0
10 TraesCS7A01G531700 chr7D 91.001 1089 59 18 486 1547 617115103 617114027 0.000000e+00 1432.0
11 TraesCS7A01G531700 chr7D 92.390 841 58 3 1830 2669 617113761 617112926 0.000000e+00 1194.0
12 TraesCS7A01G531700 chr7D 95.374 454 20 1 1 454 617115555 617115103 0.000000e+00 721.0
13 TraesCS7A01G531700 chr7D 84.605 708 82 18 2725 3413 617104694 617103995 0.000000e+00 678.0
14 TraesCS7A01G531700 chr7D 83.514 552 60 18 978 1509 616943299 616943839 1.420000e-133 486.0
15 TraesCS7A01G531700 chr7D 89.340 197 16 4 1328 1523 616954329 616954521 3.400000e-60 243.0
16 TraesCS7A01G531700 chr7D 83.857 223 22 8 1544 1762 617113972 617113760 2.080000e-47 200.0
17 TraesCS7A01G531700 chr5B 74.514 463 68 33 2682 3123 666819021 666818588 4.560000e-34 156.0
18 TraesCS7A01G531700 chr5B 74.026 462 71 32 2682 3123 666853573 666853141 3.550000e-30 143.0
19 TraesCS7A01G531700 chr3B 81.879 149 19 6 2960 3102 806042875 806043021 5.980000e-23 119.0
20 TraesCS7A01G531700 chr3B 81.373 102 16 3 3024 3124 822572225 822572324 2.820000e-11 80.5
21 TraesCS7A01G531700 chr3B 87.931 58 4 3 3353 3409 705562016 705562071 7.910000e-07 65.8
22 TraesCS7A01G531700 chr3B 89.583 48 2 3 2705 2752 323358743 323358787 1.320000e-04 58.4
23 TraesCS7A01G531700 chrUn 73.288 292 56 20 3134 3413 92855129 92854848 1.690000e-13 87.9
24 TraesCS7A01G531700 chr3A 97.368 38 1 0 3349 3386 653926105 653926142 7.910000e-07 65.8
25 TraesCS7A01G531700 chr3A 97.059 34 1 0 3353 3386 103968758 103968725 1.320000e-04 58.4
26 TraesCS7A01G531700 chr3A 81.081 74 13 1 2679 2752 728933559 728933631 1.320000e-04 58.4
27 TraesCS7A01G531700 chr5A 89.583 48 5 0 3353 3400 465279524 465279571 1.020000e-05 62.1
28 TraesCS7A01G531700 chr6A 82.432 74 8 4 2725 2796 332196302 332196372 3.680000e-05 60.2
29 TraesCS7A01G531700 chr2B 90.909 44 4 0 3359 3402 14612213 14612256 3.680000e-05 60.2
30 TraesCS7A01G531700 chr2B 89.130 46 3 2 2705 2750 31364619 31364662 4.760000e-04 56.5
31 TraesCS7A01G531700 chr2D 81.013 79 9 5 2725 2800 59633389 59633464 1.320000e-04 58.4
32 TraesCS7A01G531700 chr2D 83.871 62 5 5 2724 2785 20659812 20659868 2.000000e-03 54.7
33 TraesCS7A01G531700 chr2A 90.698 43 4 0 3354 3396 192135340 192135298 1.320000e-04 58.4
34 TraesCS7A01G531700 chr6B 85.965 57 2 5 2724 2779 538302744 538302693 4.760000e-04 56.5
35 TraesCS7A01G531700 chr6B 100.000 29 0 0 3353 3381 511371948 511371976 2.000000e-03 54.7
36 TraesCS7A01G531700 chr1D 100.000 29 0 0 2724 2752 204048556 204048584 2.000000e-03 54.7


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 TraesCS7A01G531700 chr7A 709988241 709991653 3412 True 6303.000000 6303 100.000000 1 3413 1 chr7A.!!$R1 3412
1 TraesCS7A01G531700 chr7A 709697988 709698527 539 False 448.000000 448 82.214000 978 1509 1 chr7A.!!$F2 531
2 TraesCS7A01G531700 chr7A 709710627 709711354 727 False 241.500000 322 86.010000 956 1518 2 chr7A.!!$F3 562
3 TraesCS7A01G531700 chr7B 711480555 711484028 3473 True 1170.666667 1513 91.378333 1 2669 3 chr7B.!!$R1 2668
4 TraesCS7A01G531700 chr7B 711050444 711051083 639 False 481.000000 481 80.680000 1848 2478 1 chr7B.!!$F1 630
5 TraesCS7A01G531700 chr7D 617112926 617115555 2629 True 886.750000 1432 90.655500 1 2669 4 chr7D.!!$R2 2668
6 TraesCS7A01G531700 chr7D 617103995 617104694 699 True 678.000000 678 84.605000 2725 3413 1 chr7D.!!$R1 688
7 TraesCS7A01G531700 chr7D 616943299 616943839 540 False 486.000000 486 83.514000 978 1509 1 chr7D.!!$F1 531

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
958 985 0.032267 CTTTATCGTCGCTCCCCTCC 59.968 60.0 0.0 0.0 0.0 4.30 F
959 986 0.685131 TTTATCGTCGCTCCCCTCCA 60.685 55.0 0.0 0.0 0.0 3.86 F
2131 3190 0.836400 GGACTGGGACTGGGAACTCA 60.836 60.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2151 3210 0.173935 CGGTCATGGCTACCAACGTA 59.826 55.0 0.00 0.00 36.95 3.57 R
2370 3435 0.820871 GACTCTCCATTGCTCTCGGT 59.179 55.0 0.00 0.00 0.00 4.69 R
3277 4358 0.823460 ATGCCCGCGGATTCAAAATT 59.177 45.0 30.73 3.36 0.00 1.82 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 8.142994 CACTATTCACCGAGCTAAAAATACAT 57.857 34.615 0.00 0.00 0.00 2.29
48 50 9.474920 ACATTGTTTACCAAAAATGTCACTATG 57.525 29.630 0.00 0.00 36.44 2.23
240 242 6.500684 TTTAAGCCAAAAATGTTTTGTGCA 57.499 29.167 19.60 0.00 32.13 4.57
256 258 2.229792 GTGCAGATTCCACTCCAACAA 58.770 47.619 0.00 0.00 0.00 2.83
269 271 8.391075 TCCACTCCAACAACTTTTCTTATAAG 57.609 34.615 6.11 6.11 0.00 1.73
293 295 1.939934 TGAGAACAAAGTTGCGTCTGG 59.060 47.619 3.30 0.00 0.00 3.86
301 303 4.142271 ACAAAGTTGCGTCTGGAAAATTGA 60.142 37.500 0.00 0.00 31.79 2.57
305 307 3.624326 TGCGTCTGGAAAATTGACAAG 57.376 42.857 0.00 0.00 0.00 3.16
440 442 5.629435 GGAAAGTGCAAGTTTAACAGCATAC 59.371 40.000 15.80 6.74 40.14 2.39
501 503 7.684670 TCAATTTGCGATAAACTACATGTCTC 58.315 34.615 0.00 0.00 0.00 3.36
549 551 6.238484 GGTGACTATGATCCAACAAATACAGC 60.238 42.308 0.00 0.00 0.00 4.40
679 693 4.583871 TGCATCTCTCTTCTTTCCCTTTC 58.416 43.478 0.00 0.00 0.00 2.62
796 820 1.202879 TGTTCTACCCAAGTTGGCCTG 60.203 52.381 17.07 5.74 35.79 4.85
823 847 3.462982 TGTCGTCATTATGTGGCCATAC 58.537 45.455 9.72 0.00 33.29 2.39
859 883 0.179089 ATGTGCTCACTCTCGCATCC 60.179 55.000 1.47 0.00 38.56 3.51
897 921 1.298157 ATCGTCGCAACACCATGTGG 61.298 55.000 0.00 0.00 37.94 4.17
954 981 2.580966 AAGTCTTTATCGTCGCTCCC 57.419 50.000 0.00 0.00 0.00 4.30
955 982 0.745468 AGTCTTTATCGTCGCTCCCC 59.255 55.000 0.00 0.00 0.00 4.81
956 983 0.745468 GTCTTTATCGTCGCTCCCCT 59.255 55.000 0.00 0.00 0.00 4.79
957 984 1.030457 TCTTTATCGTCGCTCCCCTC 58.970 55.000 0.00 0.00 0.00 4.30
958 985 0.032267 CTTTATCGTCGCTCCCCTCC 59.968 60.000 0.00 0.00 0.00 4.30
959 986 0.685131 TTTATCGTCGCTCCCCTCCA 60.685 55.000 0.00 0.00 0.00 3.86
1053 1084 4.767255 GACTGCCTGGCCCTCGTG 62.767 72.222 17.53 2.04 0.00 4.35
1152 1720 1.925972 GGTCTGGGGGAGCTTCCTT 60.926 63.158 11.94 0.00 39.18 3.36
1272 1849 2.811317 CTCCTCGACGGCTGCAAC 60.811 66.667 0.50 0.00 0.00 4.17
1310 1889 7.095229 TGCTGTTGCAGACTTAATTGTTAGTAG 60.095 37.037 0.00 0.00 45.31 2.57
1311 1890 7.095187 GCTGTTGCAGACTTAATTGTTAGTAGT 60.095 37.037 0.00 0.00 39.41 2.73
1313 1892 9.199982 TGTTGCAGACTTAATTGTTAGTAGTAC 57.800 33.333 0.00 0.00 0.00 2.73
1314 1893 8.654215 GTTGCAGACTTAATTGTTAGTAGTACC 58.346 37.037 0.00 0.00 0.00 3.34
1542 2296 7.850982 CGATAATTTCCGGTTGAATTTCTGTAG 59.149 37.037 14.87 0.00 31.67 2.74
1543 2297 8.801882 ATAATTTCCGGTTGAATTTCTGTAGA 57.198 30.769 14.87 0.00 31.67 2.59
1547 2301 8.624367 TTTCCGGTTGAATTTCTGTAGATTTA 57.376 30.769 0.00 0.00 31.67 1.40
1548 2302 7.843490 TCCGGTTGAATTTCTGTAGATTTAG 57.157 36.000 0.00 0.00 0.00 1.85
1549 2303 6.821665 TCCGGTTGAATTTCTGTAGATTTAGG 59.178 38.462 0.00 0.00 0.00 2.69
1550 2304 6.458342 CCGGTTGAATTTCTGTAGATTTAGGC 60.458 42.308 0.00 0.00 0.00 3.93
1561 2610 5.730550 TGTAGATTTAGGCAAGTACTGTGG 58.269 41.667 0.00 0.00 0.00 4.17
1571 2620 3.689649 GCAAGTACTGTGGAATTAGGTGG 59.310 47.826 0.00 0.00 0.00 4.61
1593 2645 7.764901 GGTGGTCGAGATCTAGAAAACTTTAAT 59.235 37.037 7.15 0.00 0.00 1.40
1674 2728 2.571653 AGATTGAGTTGGACATTCCGGA 59.428 45.455 0.00 0.00 40.17 5.14
1675 2729 2.178912 TTGAGTTGGACATTCCGGAC 57.821 50.000 1.83 0.00 40.17 4.79
1676 2730 1.348064 TGAGTTGGACATTCCGGACT 58.652 50.000 1.83 0.00 40.17 3.85
1677 2731 1.697432 TGAGTTGGACATTCCGGACTT 59.303 47.619 1.83 0.00 40.17 3.01
1678 2732 2.289444 TGAGTTGGACATTCCGGACTTC 60.289 50.000 1.83 0.00 40.17 3.01
1679 2733 1.076332 GTTGGACATTCCGGACTTCG 58.924 55.000 1.83 0.00 40.17 3.79
1710 2764 2.092753 TGAGAATCCTGTCTGCCCAATC 60.093 50.000 0.00 0.00 0.00 2.67
1716 2770 3.653164 TCCTGTCTGCCCAATCTATACA 58.347 45.455 0.00 0.00 0.00 2.29
1717 2771 3.388024 TCCTGTCTGCCCAATCTATACAC 59.612 47.826 0.00 0.00 0.00 2.90
1720 2774 5.070446 CCTGTCTGCCCAATCTATACACTTA 59.930 44.000 0.00 0.00 0.00 2.24
1760 2814 8.519492 TTTAGTATTTGTTTGATCTGCTTTGC 57.481 30.769 0.00 0.00 0.00 3.68
1763 2818 3.374220 TTGTTTGATCTGCTTTGCCTG 57.626 42.857 0.00 0.00 0.00 4.85
1782 2837 4.741342 CCTGCTTTTGAGGCTAATTTCTG 58.259 43.478 0.00 0.00 0.00 3.02
1794 2850 6.064060 AGGCTAATTTCTGCAGCACATTATA 58.936 36.000 9.47 0.00 37.02 0.98
1797 2853 7.869429 GGCTAATTTCTGCAGCACATTATAAAT 59.131 33.333 9.47 4.39 37.02 1.40
1803 2859 6.429624 TCTGCAGCACATTATAAATTAAGCG 58.570 36.000 9.47 0.00 0.00 4.68
1842 2898 6.037391 CAGTTCAACAACCCGTAAACTAAGAA 59.963 38.462 0.00 0.00 32.22 2.52
1983 3039 3.603532 CGCCTATCTCGTATACAGGGTA 58.396 50.000 3.32 0.00 0.00 3.69
2131 3190 0.836400 GGACTGGGACTGGGAACTCA 60.836 60.000 0.00 0.00 0.00 3.41
2142 3201 3.136763 CTGGGAACTCAATGGATCATCG 58.863 50.000 0.00 0.00 0.00 3.84
2151 3210 1.309950 ATGGATCATCGTCGTCGTCT 58.690 50.000 1.33 0.00 38.33 4.18
2152 3211 1.944032 TGGATCATCGTCGTCGTCTA 58.056 50.000 1.33 0.00 38.33 2.59
2192 3257 3.339141 AGAAGAATCAAAGTCGGAAGCC 58.661 45.455 0.00 0.00 0.00 4.35
2299 3364 3.587061 TGTGGAGGGAAAAGAGAGCAATA 59.413 43.478 0.00 0.00 0.00 1.90
2370 3435 3.656264 TCATAGAGGGGATCGAGGTAAGA 59.344 47.826 0.00 0.00 0.00 2.10
2389 3455 0.820871 ACCGAGAGCAATGGAGAGTC 59.179 55.000 0.00 0.00 0.00 3.36
2448 3518 5.171337 CAGTCGTATTGTGAAGTTTGTTTGC 59.829 40.000 0.00 0.00 0.00 3.68
2617 3687 4.709397 TCTTTGGCTTTTGAGGTTTGAAGA 59.291 37.500 0.00 0.00 0.00 2.87
2669 3739 3.441500 AGGAAACACATTTCTCCCCTC 57.558 47.619 0.23 0.00 43.33 4.30
2670 3740 2.989571 AGGAAACACATTTCTCCCCTCT 59.010 45.455 0.23 0.00 43.33 3.69
2671 3741 4.175962 AGGAAACACATTTCTCCCCTCTA 58.824 43.478 0.23 0.00 43.33 2.43
2672 3742 4.226168 AGGAAACACATTTCTCCCCTCTAG 59.774 45.833 0.23 0.00 43.33 2.43
2673 3743 4.019231 GGAAACACATTTCTCCCCTCTAGT 60.019 45.833 0.23 0.00 43.33 2.57
2674 3744 4.559862 AACACATTTCTCCCCTCTAGTG 57.440 45.455 0.00 0.00 0.00 2.74
2675 3745 3.791320 ACACATTTCTCCCCTCTAGTGA 58.209 45.455 0.00 0.00 0.00 3.41
2676 3746 4.168101 ACACATTTCTCCCCTCTAGTGAA 58.832 43.478 0.00 0.00 0.00 3.18
2677 3747 4.020128 ACACATTTCTCCCCTCTAGTGAAC 60.020 45.833 0.00 0.00 0.00 3.18
2678 3748 4.223923 CACATTTCTCCCCTCTAGTGAACT 59.776 45.833 0.00 0.00 0.00 3.01
2679 3749 4.846940 ACATTTCTCCCCTCTAGTGAACTT 59.153 41.667 0.00 0.00 0.00 2.66
2680 3750 5.310857 ACATTTCTCCCCTCTAGTGAACTTT 59.689 40.000 0.00 0.00 0.00 2.66
2681 3751 5.906772 TTTCTCCCCTCTAGTGAACTTTT 57.093 39.130 0.00 0.00 0.00 2.27
2682 3752 5.906772 TTCTCCCCTCTAGTGAACTTTTT 57.093 39.130 0.00 0.00 0.00 1.94
2683 3753 5.485209 TCTCCCCTCTAGTGAACTTTTTC 57.515 43.478 0.00 0.00 0.00 2.29
2684 3754 4.286291 TCTCCCCTCTAGTGAACTTTTTCC 59.714 45.833 0.00 0.00 0.00 3.13
2685 3755 3.977999 TCCCCTCTAGTGAACTTTTTCCA 59.022 43.478 0.00 0.00 0.00 3.53
2686 3756 4.414182 TCCCCTCTAGTGAACTTTTTCCAA 59.586 41.667 0.00 0.00 0.00 3.53
2687 3757 5.103855 TCCCCTCTAGTGAACTTTTTCCAAA 60.104 40.000 0.00 0.00 0.00 3.28
2688 3758 5.775195 CCCCTCTAGTGAACTTTTTCCAAAT 59.225 40.000 0.00 0.00 0.00 2.32
2689 3759 6.071896 CCCCTCTAGTGAACTTTTTCCAAATC 60.072 42.308 0.00 0.00 0.00 2.17
2690 3760 6.071896 CCCTCTAGTGAACTTTTTCCAAATCC 60.072 42.308 0.00 0.00 0.00 3.01
2691 3761 6.490040 CCTCTAGTGAACTTTTTCCAAATCCA 59.510 38.462 0.00 0.00 0.00 3.41
2692 3762 7.272037 TCTAGTGAACTTTTTCCAAATCCAC 57.728 36.000 0.00 0.00 0.00 4.02
2693 3763 5.930837 AGTGAACTTTTTCCAAATCCACA 57.069 34.783 0.00 0.00 0.00 4.17
2694 3764 6.293004 AGTGAACTTTTTCCAAATCCACAA 57.707 33.333 0.00 0.00 0.00 3.33
2695 3765 6.706295 AGTGAACTTTTTCCAAATCCACAAA 58.294 32.000 0.00 0.00 0.00 2.83
2696 3766 6.593770 AGTGAACTTTTTCCAAATCCACAAAC 59.406 34.615 0.00 0.00 0.00 2.93
2697 3767 6.593770 GTGAACTTTTTCCAAATCCACAAACT 59.406 34.615 0.00 0.00 0.00 2.66
2698 3768 7.119116 GTGAACTTTTTCCAAATCCACAAACTT 59.881 33.333 0.00 0.00 0.00 2.66
2699 3769 7.663493 TGAACTTTTTCCAAATCCACAAACTTT 59.337 29.630 0.00 0.00 0.00 2.66
2700 3770 7.994425 ACTTTTTCCAAATCCACAAACTTTT 57.006 28.000 0.00 0.00 0.00 2.27
2701 3771 8.402798 ACTTTTTCCAAATCCACAAACTTTTT 57.597 26.923 0.00 0.00 0.00 1.94
2763 3833 9.912634 AATCCATGAACTTTTACAGTTTACATG 57.087 29.630 0.00 0.00 46.53 3.21
2803 3873 8.620116 AAACCCATGAACATTTTTAAATCCAG 57.380 30.769 0.00 0.00 0.00 3.86
2955 4028 6.037062 CGTTTCTTTCTTTCCCAAAAATGCTT 59.963 34.615 0.00 0.00 0.00 3.91
2957 4030 5.988287 TCTTTCTTTCCCAAAAATGCTTGT 58.012 33.333 0.00 0.00 0.00 3.16
2965 4038 5.431765 TCCCAAAAATGCTTGTGCTTTTAA 58.568 33.333 0.00 0.00 42.97 1.52
2967 4040 6.545298 TCCCAAAAATGCTTGTGCTTTTAAAT 59.455 30.769 0.00 0.00 42.97 1.40
2970 4043 9.727627 CCAAAAATGCTTGTGCTTTTAAATTTA 57.272 25.926 0.00 0.00 42.97 1.40
2989 4062 8.462589 AAATTTATCAACAAAATGGTTGCCTT 57.537 26.923 0.00 0.00 45.98 4.35
2990 4063 8.462589 AATTTATCAACAAAATGGTTGCCTTT 57.537 26.923 0.00 0.00 45.98 3.11
2993 4066 8.964476 TTATCAACAAAATGGTTGCCTTTTAA 57.036 26.923 0.00 0.00 45.98 1.52
3088 4165 9.598517 TTTAAAAGTTGCTCAGAATGACAAAAT 57.401 25.926 0.00 0.00 42.56 1.82
3091 4168 6.882610 AGTTGCTCAGAATGACAAAATACA 57.117 33.333 0.00 0.00 42.56 2.29
3096 4173 7.660112 TGCTCAGAATGACAAAATACAAACAT 58.340 30.769 0.00 0.00 42.56 2.71
3128 4205 3.066203 AGAGCGAACAAAATTTTGACCGT 59.934 39.130 32.20 22.10 40.55 4.83
3216 4297 5.529060 TGAAACCAATTTTTGAATTTCCCCG 59.471 36.000 11.25 0.00 36.00 5.73
3217 4298 4.965200 ACCAATTTTTGAATTTCCCCGA 57.035 36.364 0.00 0.00 0.00 5.14
3262 4343 9.508642 AAAAAGGTTTGAAAACAGGAACATTTA 57.491 25.926 8.11 0.00 40.63 1.40
3263 4344 9.508642 AAAAGGTTTGAAAACAGGAACATTTAA 57.491 25.926 8.11 0.00 40.63 1.52
3272 4353 7.619512 AAACAGGAACATTTAATAAACCCCA 57.380 32.000 0.00 0.00 0.00 4.96
3289 4370 7.680442 AAACCCCAAATAAATTTTGAATCCG 57.320 32.000 0.00 0.00 0.00 4.18
3293 4374 4.269844 CCAAATAAATTTTGAATCCGCGGG 59.730 41.667 27.83 6.80 0.00 6.13
3313 4394 4.672409 GGGCATTATTTGAAACTTCTCGG 58.328 43.478 0.00 0.00 0.00 4.63
3317 4398 6.149633 GCATTATTTGAAACTTCTCGGTTGT 58.850 36.000 0.00 0.00 0.00 3.32
3320 4401 8.690840 CATTATTTGAAACTTCTCGGTTGTTTC 58.309 33.333 9.90 9.90 45.51 2.78
3322 4403 5.479716 TTGAAACTTCTCGGTTGTTTCTC 57.520 39.130 15.58 0.00 45.51 2.87
3328 4409 6.451064 ACTTCTCGGTTGTTTCTCAATTTT 57.549 33.333 0.00 0.00 38.38 1.82
3329 4410 6.265577 ACTTCTCGGTTGTTTCTCAATTTTG 58.734 36.000 0.00 0.00 38.38 2.44
3332 4413 5.534654 TCTCGGTTGTTTCTCAATTTTGGAT 59.465 36.000 0.00 0.00 38.38 3.41
3371 4456 9.190858 CGGAAAGATTTTATGAATTTGTGAACA 57.809 29.630 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 7.483691 GGTAAACAATGTATTTTTAGCTCGGTG 59.516 37.037 0.00 0.00 32.79 4.94
39 40 5.808366 ACTCTTCACCTTTCATAGTGACA 57.192 39.130 0.00 0.00 42.49 3.58
48 50 6.645306 AGCCTTCTTATACTCTTCACCTTTC 58.355 40.000 0.00 0.00 0.00 2.62
240 242 5.449553 AGAAAAGTTGTTGGAGTGGAATCT 58.550 37.500 0.00 0.00 0.00 2.40
269 271 3.433615 AGACGCAACTTTGTTCTCATAGC 59.566 43.478 0.00 0.00 0.00 2.97
301 303 1.404717 CCGCTGAGTATGACTGCTTGT 60.405 52.381 0.00 0.00 0.00 3.16
305 307 2.010145 TTTCCGCTGAGTATGACTGC 57.990 50.000 0.00 0.00 0.00 4.40
389 391 5.350504 TGAATGGAAGAACAAGCCAAAAA 57.649 34.783 0.00 0.00 34.95 1.94
418 420 6.142818 TGTATGCTGTTAAACTTGCACTTT 57.857 33.333 0.00 0.00 38.29 2.66
440 442 6.009115 TCACATACTACCTACGTGCATATG 57.991 41.667 0.00 0.00 0.00 1.78
477 479 6.907212 GGAGACATGTAGTTTATCGCAAATTG 59.093 38.462 0.00 0.00 0.00 2.32
558 560 9.169592 CTTTATAATTCGAGTACCTTGGGAAAA 57.830 33.333 0.00 0.00 0.00 2.29
559 561 8.542080 TCTTTATAATTCGAGTACCTTGGGAAA 58.458 33.333 0.00 0.00 0.00 3.13
679 693 5.600898 TGGGGTAGAAAGAAAAAGAAAAGGG 59.399 40.000 0.00 0.00 0.00 3.95
796 820 3.248602 GCCACATAATGACGACATTCCTC 59.751 47.826 16.17 0.00 44.34 3.71
823 847 1.152902 ATGGTGATCATGCCGTGGG 60.153 57.895 0.00 0.00 34.22 4.61
859 883 3.725895 CGATGACAACATTTCTTGCTCCG 60.726 47.826 0.00 0.00 36.82 4.63
897 921 2.056577 GTACTACGTTGCTGGTCACAC 58.943 52.381 0.00 0.00 0.00 3.82
954 981 1.395826 GGTCGATCCTGGAGTGGAGG 61.396 65.000 1.52 0.00 39.78 4.30
955 982 0.684479 TGGTCGATCCTGGAGTGGAG 60.684 60.000 1.52 0.00 39.78 3.86
956 983 0.252057 TTGGTCGATCCTGGAGTGGA 60.252 55.000 1.52 0.00 40.82 4.02
957 984 0.613260 TTTGGTCGATCCTGGAGTGG 59.387 55.000 1.52 0.00 37.07 4.00
958 985 2.009042 GCTTTGGTCGATCCTGGAGTG 61.009 57.143 1.52 0.00 37.07 3.51
959 986 0.250513 GCTTTGGTCGATCCTGGAGT 59.749 55.000 1.52 0.00 37.07 3.85
1267 1844 2.557924 CAGCAAAGATTACCAGGTTGCA 59.442 45.455 13.12 0.00 45.47 4.08
1272 1849 2.557924 TGCAACAGCAAAGATTACCAGG 59.442 45.455 0.00 0.00 34.85 4.45
1542 2296 6.759497 AATTCCACAGTACTTGCCTAAATC 57.241 37.500 0.00 0.00 0.00 2.17
1543 2297 6.828785 CCTAATTCCACAGTACTTGCCTAAAT 59.171 38.462 0.00 0.00 0.00 1.40
1547 2301 3.587506 ACCTAATTCCACAGTACTTGCCT 59.412 43.478 0.00 0.00 0.00 4.75
1548 2302 3.689649 CACCTAATTCCACAGTACTTGCC 59.310 47.826 0.00 0.00 0.00 4.52
1549 2303 3.689649 CCACCTAATTCCACAGTACTTGC 59.310 47.826 0.00 0.00 0.00 4.01
1550 2304 4.906618 ACCACCTAATTCCACAGTACTTG 58.093 43.478 0.00 0.00 0.00 3.16
1561 2610 6.636562 TTCTAGATCTCGACCACCTAATTC 57.363 41.667 0.00 0.00 0.00 2.17
1571 2620 9.355215 TGTGATTAAAGTTTTCTAGATCTCGAC 57.645 33.333 0.00 0.00 0.00 4.20
1593 2645 7.390440 CCTGTTTAACTAGGAAACATCATGTGA 59.610 37.037 19.60 2.11 43.78 3.58
1674 2728 4.202367 GGATTCTCATAATCCACCCGAAGT 60.202 45.833 11.08 0.00 44.33 3.01
1675 2729 4.040952 AGGATTCTCATAATCCACCCGAAG 59.959 45.833 16.83 0.00 46.70 3.79
1676 2730 3.973973 AGGATTCTCATAATCCACCCGAA 59.026 43.478 16.83 0.00 46.70 4.30
1677 2731 3.324846 CAGGATTCTCATAATCCACCCGA 59.675 47.826 16.83 0.00 46.70 5.14
1678 2732 3.071602 ACAGGATTCTCATAATCCACCCG 59.928 47.826 16.83 6.71 46.70 5.28
1679 2733 4.349342 AGACAGGATTCTCATAATCCACCC 59.651 45.833 16.83 6.80 46.70 4.61
1741 2795 4.312443 CAGGCAAAGCAGATCAAACAAAT 58.688 39.130 0.00 0.00 0.00 2.32
1760 2814 4.741342 CAGAAATTAGCCTCAAAAGCAGG 58.259 43.478 0.00 0.00 0.00 4.85
1763 2818 4.171754 CTGCAGAAATTAGCCTCAAAAGC 58.828 43.478 8.42 0.00 0.00 3.51
1780 2835 6.201517 ACGCTTAATTTATAATGTGCTGCAG 58.798 36.000 10.11 10.11 0.00 4.41
1782 2837 6.303259 GCTACGCTTAATTTATAATGTGCTGC 59.697 38.462 0.00 0.00 0.00 5.25
1794 2850 6.961576 TGTGTTTTAGTGCTACGCTTAATTT 58.038 32.000 0.00 0.00 0.00 1.82
1797 2853 5.051816 ACTGTGTTTTAGTGCTACGCTTAA 58.948 37.500 0.00 0.00 0.00 1.85
1803 2859 6.114221 TGTTGAACTGTGTTTTAGTGCTAC 57.886 37.500 0.00 0.00 32.30 3.58
1822 2878 7.300320 GGTAATTCTTAGTTTACGGGTTGTTG 58.700 38.462 0.00 0.00 30.66 3.33
1842 2898 9.588096 AATCTACAAGACAAAAGAAAGGGTAAT 57.412 29.630 0.00 0.00 0.00 1.89
1983 3039 1.412079 TTGGAGCTTGCAACCAATGT 58.588 45.000 14.26 0.00 38.52 2.71
2022 3078 1.135139 GAGGACGCTGTAGCATTCTCA 59.865 52.381 3.51 0.00 42.21 3.27
2023 3079 1.407258 AGAGGACGCTGTAGCATTCTC 59.593 52.381 0.07 0.07 42.21 2.87
2025 3081 1.134965 ACAGAGGACGCTGTAGCATTC 60.135 52.381 6.92 0.00 46.67 2.67
2026 3082 0.898320 ACAGAGGACGCTGTAGCATT 59.102 50.000 6.92 0.00 46.67 3.56
2028 3084 4.097218 ACAGAGGACGCTGTAGCA 57.903 55.556 6.92 0.00 46.67 3.49
2131 3190 1.676529 AGACGACGACGATGATCCATT 59.323 47.619 15.32 0.00 42.66 3.16
2151 3210 0.173935 CGGTCATGGCTACCAACGTA 59.826 55.000 0.00 0.00 36.95 3.57
2152 3211 1.079405 CGGTCATGGCTACCAACGT 60.079 57.895 0.00 0.00 36.95 3.99
2192 3257 1.721487 CCATCAGGTTTAAGCCGCG 59.279 57.895 0.00 0.00 0.00 6.46
2211 3276 1.954146 GTCGCTCCTCACGCAAACA 60.954 57.895 0.00 0.00 0.00 2.83
2214 3279 4.717629 CCGTCGCTCCTCACGCAA 62.718 66.667 0.00 0.00 34.58 4.85
2299 3364 2.372172 ACCCTCTGAACTCAACGGAAAT 59.628 45.455 0.00 0.00 0.00 2.17
2370 3435 0.820871 GACTCTCCATTGCTCTCGGT 59.179 55.000 0.00 0.00 0.00 4.69
2658 3728 6.455690 AAAAGTTCACTAGAGGGGAGAAAT 57.544 37.500 0.00 0.00 0.00 2.17
2662 3732 4.041691 TGGAAAAAGTTCACTAGAGGGGAG 59.958 45.833 0.00 0.00 35.25 4.30
2669 3739 7.038154 TGTGGATTTGGAAAAAGTTCACTAG 57.962 36.000 0.00 0.00 35.25 2.57
2670 3740 7.411486 TTGTGGATTTGGAAAAAGTTCACTA 57.589 32.000 0.00 0.00 35.25 2.74
2671 3741 5.930837 TGTGGATTTGGAAAAAGTTCACT 57.069 34.783 0.00 0.00 35.25 3.41
2672 3742 6.593770 AGTTTGTGGATTTGGAAAAAGTTCAC 59.406 34.615 0.00 0.00 35.25 3.18
2673 3743 6.706295 AGTTTGTGGATTTGGAAAAAGTTCA 58.294 32.000 0.00 0.00 35.25 3.18
2674 3744 7.609760 AAGTTTGTGGATTTGGAAAAAGTTC 57.390 32.000 0.00 0.00 0.00 3.01
2675 3745 7.994425 AAAGTTTGTGGATTTGGAAAAAGTT 57.006 28.000 0.00 0.00 0.00 2.66
2676 3746 7.994425 AAAAGTTTGTGGATTTGGAAAAAGT 57.006 28.000 0.00 0.00 0.00 2.66
2706 3776 7.787725 AAGTTCACTAGAGTGTTCGATTTTT 57.212 32.000 9.43 0.00 45.76 1.94
2707 3777 7.787725 AAAGTTCACTAGAGTGTTCGATTTT 57.212 32.000 9.43 2.57 45.76 1.82
2708 3778 7.787725 AAAAGTTCACTAGAGTGTTCGATTT 57.212 32.000 9.43 8.02 45.76 2.17
2709 3779 7.787725 AAAAAGTTCACTAGAGTGTTCGATT 57.212 32.000 9.43 0.00 45.76 3.34
2775 3845 9.061435 GGATTTAAAAATGTTCATGGGTTTTGA 57.939 29.630 0.00 0.00 0.00 2.69
2776 3846 8.844244 TGGATTTAAAAATGTTCATGGGTTTTG 58.156 29.630 0.00 0.00 0.00 2.44
2855 3925 4.281657 AGAAAAAGAGGCAGGTTTTCTGT 58.718 39.130 16.38 0.74 45.35 3.41
2926 3999 7.964604 TTTTTGGGAAAGAAAGAAACGAAAA 57.035 28.000 0.00 0.00 0.00 2.29
2927 4000 7.413548 GCATTTTTGGGAAAGAAAGAAACGAAA 60.414 33.333 0.00 0.00 0.00 3.46
2928 4001 6.036626 GCATTTTTGGGAAAGAAAGAAACGAA 59.963 34.615 0.00 0.00 0.00 3.85
2929 4002 5.522097 GCATTTTTGGGAAAGAAAGAAACGA 59.478 36.000 0.00 0.00 0.00 3.85
2944 4017 8.631676 AAATTTAAAAGCACAAGCATTTTTGG 57.368 26.923 0.00 0.00 38.39 3.28
2965 4038 8.462589 AAAGGCAACCATTTTGTTGATAAATT 57.537 26.923 8.01 0.00 46.77 1.82
2967 4040 7.872113 AAAAGGCAACCATTTTGTTGATAAA 57.128 28.000 8.01 0.00 46.77 1.40
2970 4043 7.872113 TTTAAAAGGCAACCATTTTGTTGAT 57.128 28.000 8.01 0.00 46.77 2.57
2971 4044 7.687941 TTTTAAAAGGCAACCATTTTGTTGA 57.312 28.000 8.01 0.00 46.77 3.18
2972 4045 8.923609 AATTTTAAAAGGCAACCATTTTGTTG 57.076 26.923 6.79 0.00 46.59 3.33
2973 4046 9.935241 AAAATTTTAAAAGGCAACCATTTTGTT 57.065 22.222 0.37 0.00 31.41 2.83
2975 4048 9.363763 ACAAAATTTTAAAAGGCAACCATTTTG 57.636 25.926 20.14 20.14 42.28 2.44
3042 4119 2.504367 AGACACGAACATTTCCTTGGG 58.496 47.619 0.00 0.00 0.00 4.12
3044 4121 7.700656 ACTTTTAAAGACACGAACATTTCCTTG 59.299 33.333 12.02 0.00 0.00 3.61
3048 4125 7.220108 AGCAACTTTTAAAGACACGAACATTTC 59.780 33.333 12.02 0.00 0.00 2.17
3111 4188 6.641176 AAGTTCACGGTCAAAATTTTGTTC 57.359 33.333 25.98 19.92 39.18 3.18
3139 4217 9.862371 TGAAATTCCAATTTATTAGCGCTTTTA 57.138 25.926 18.68 4.87 38.64 1.52
3200 4279 7.873719 AAAAAGTTCGGGGAAATTCAAAAAT 57.126 28.000 0.00 0.00 28.39 1.82
3231 4312 6.994221 TCCTGTTTTCAAACCTTTTTACACA 58.006 32.000 0.00 0.00 38.11 3.72
3245 4326 8.151596 GGGGTTTATTAAATGTTCCTGTTTTCA 58.848 33.333 0.00 0.00 0.00 2.69
3246 4327 8.151596 TGGGGTTTATTAAATGTTCCTGTTTTC 58.848 33.333 0.00 0.00 0.00 2.29
3263 4344 9.389755 CGGATTCAAAATTTATTTGGGGTTTAT 57.610 29.630 0.00 0.00 0.00 1.40
3268 4349 4.269844 CGCGGATTCAAAATTTATTTGGGG 59.730 41.667 0.00 0.00 0.00 4.96
3272 4353 3.868661 GCCCGCGGATTCAAAATTTATTT 59.131 39.130 30.73 0.00 0.00 1.40
3277 4358 0.823460 ATGCCCGCGGATTCAAAATT 59.177 45.000 30.73 3.36 0.00 1.82
3281 4362 1.686355 AATAATGCCCGCGGATTCAA 58.314 45.000 30.73 9.55 0.00 2.69
3287 4368 1.134175 AGTTTCAAATAATGCCCGCGG 59.866 47.619 21.04 21.04 0.00 6.46
3289 4370 4.105486 GAGAAGTTTCAAATAATGCCCGC 58.895 43.478 0.00 0.00 0.00 6.13
3293 4374 6.149633 ACAACCGAGAAGTTTCAAATAATGC 58.850 36.000 0.00 0.00 0.00 3.56
3345 4430 9.190858 TGTTCACAAATTCATAAAATCTTTCCG 57.809 29.630 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.