Multiple sequence alignment - TraesCS7D01G036100

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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 TraesCS7D01G036100 chr7D 100.000 8358 0 0 1 8358 18435397 18427040 0.000000e+00 15435.0
1 TraesCS7D01G036100 chr7D 94.022 368 22 0 1334 1701 18434010 18433643 7.330000e-155 558.0
2 TraesCS7D01G036100 chr7D 94.022 368 22 0 1388 1755 18434064 18433697 7.330000e-155 558.0
3 TraesCS7D01G036100 chr7D 90.764 314 29 0 1334 1647 18433956 18433643 3.610000e-113 420.0
4 TraesCS7D01G036100 chr7D 89.231 195 15 6 3518 3711 106106673 106106484 1.080000e-58 239.0
5 TraesCS7D01G036100 chr7A 94.063 5643 213 49 2728 8304 18881631 18876045 0.000000e+00 8453.0
6 TraesCS7D01G036100 chr7A 92.799 1708 94 10 1 1701 18884252 18882567 0.000000e+00 2446.0
7 TraesCS7D01G036100 chr7A 97.108 1314 38 0 1388 2701 18882934 18881621 0.000000e+00 2217.0
8 TraesCS7D01G036100 chrUn 94.916 3934 127 30 3961 7860 50839312 50835418 0.000000e+00 6089.0
9 TraesCS7D01G036100 chrUn 94.679 2725 113 16 1 2701 50843349 50840633 0.000000e+00 4200.0
10 TraesCS7D01G036100 chrUn 95.403 1240 40 7 2728 3962 50840643 50839416 0.000000e+00 1958.0
11 TraesCS7D01G036100 chrUn 91.617 501 35 4 7858 8356 50835346 50834851 0.000000e+00 686.0
12 TraesCS7D01G036100 chrUn 93.750 368 23 0 1388 1755 50842001 50841634 3.410000e-153 553.0
13 TraesCS7D01G036100 chrUn 93.478 368 24 0 1334 1701 50841947 50841580 1.590000e-151 547.0
14 TraesCS7D01G036100 chrUn 91.667 132 9 1 8027 8156 439559127 439559258 1.850000e-41 182.0
15 TraesCS7D01G036100 chr2D 86.830 1101 136 8 1596 2691 513457046 513458142 0.000000e+00 1221.0
16 TraesCS7D01G036100 chr2D 80.630 1461 199 60 5924 7354 513462853 513464259 0.000000e+00 1053.0
17 TraesCS7D01G036100 chr2D 83.692 883 127 15 4958 5832 513461898 513462771 0.000000e+00 817.0
18 TraesCS7D01G036100 chr2D 87.252 604 58 15 3108 3702 513458705 513459298 0.000000e+00 671.0
19 TraesCS7D01G036100 chr2D 79.464 560 78 14 939 1485 513456670 513457205 6.170000e-96 363.0
20 TraesCS7D01G036100 chr2D 84.958 359 32 13 4236 4579 513459893 513460244 2.230000e-90 344.0
21 TraesCS7D01G036100 chr2D 83.516 273 30 10 2732 2998 513458146 513458409 3.010000e-59 241.0
22 TraesCS7D01G036100 chr2D 89.474 190 16 4 3712 3900 513459345 513459531 3.900000e-58 237.0
23 TraesCS7D01G036100 chr2D 84.615 143 8 8 3485 3627 91144861 91144989 6.810000e-26 130.0
24 TraesCS7D01G036100 chr2A 85.886 1162 145 14 1542 2691 657519274 657520428 0.000000e+00 1219.0
25 TraesCS7D01G036100 chr2A 80.177 1468 208 62 5924 7354 657523921 657525342 0.000000e+00 1022.0
26 TraesCS7D01G036100 chr2A 84.437 861 119 14 4981 5832 657522989 657523843 0.000000e+00 833.0
27 TraesCS7D01G036100 chr2A 87.789 606 52 13 3108 3702 657520882 657521476 0.000000e+00 689.0
28 TraesCS7D01G036100 chr2A 84.314 357 37 9 4236 4579 657522068 657522418 1.740000e-86 331.0
29 TraesCS7D01G036100 chr2A 83.509 285 39 5 2732 3013 657520432 657520711 8.320000e-65 259.0
30 TraesCS7D01G036100 chr2A 89.474 190 16 4 3712 3900 657521523 657521709 3.900000e-58 237.0
31 TraesCS7D01G036100 chr2A 95.652 46 2 0 1704 1749 657519274 657519319 3.240000e-09 75.0
32 TraesCS7D01G036100 chr2B 86.751 1102 135 10 1596 2691 604994102 604995198 0.000000e+00 1216.0
33 TraesCS7D01G036100 chr2B 83.584 865 128 13 4975 5830 604999066 604999925 0.000000e+00 798.0
34 TraesCS7D01G036100 chr2B 82.340 906 126 24 5924 6809 605000005 605000896 0.000000e+00 756.0
35 TraesCS7D01G036100 chr2B 87.097 589 54 19 3125 3702 604997026 604997603 0.000000e+00 647.0
36 TraesCS7D01G036100 chr2B 84.637 358 35 11 4236 4579 604998155 604998506 1.040000e-88 339.0
37 TraesCS7D01G036100 chr2B 77.304 586 85 35 6800 7376 605001088 605001634 1.360000e-77 302.0
38 TraesCS7D01G036100 chr2B 81.703 317 45 9 2732 3045 604995202 604995508 1.390000e-62 252.0
39 TraesCS7D01G036100 chr2B 89.474 190 16 4 3712 3900 604997651 604997837 3.900000e-58 237.0
40 TraesCS7D01G036100 chr2B 91.473 129 9 1 8030 8156 542689173 542689045 8.620000e-40 176.0
41 TraesCS7D01G036100 chr2B 95.652 46 2 0 1704 1749 604994102 604994147 3.240000e-09 75.0
42 TraesCS7D01G036100 chr4A 80.135 594 94 13 6367 6953 704322612 704322036 1.000000e-113 422.0
43 TraesCS7D01G036100 chr4A 80.500 400 68 7 6561 6953 711215408 711215804 1.760000e-76 298.0
44 TraesCS7D01G036100 chr4B 85.965 228 22 5 7617 7843 195445273 195445491 1.400000e-57 235.0
45 TraesCS7D01G036100 chr6A 77.778 369 65 14 3339 3698 471871491 471871131 2.360000e-50 211.0
46 TraesCS7D01G036100 chr6A 87.742 155 19 0 5674 5828 471869304 471869150 1.850000e-41 182.0
47 TraesCS7D01G036100 chr6D 76.423 369 71 15 3339 3698 332546146 332545785 1.430000e-42 185.0
48 TraesCS7D01G036100 chr6D 82.759 87 15 0 6844 6930 147881591 147881677 2.500000e-10 78.7
49 TraesCS7D01G036100 chr5D 91.667 132 9 1 8027 8156 329164267 329164136 1.850000e-41 182.0
50 TraesCS7D01G036100 chr5D 91.667 132 9 1 8027 8156 560874561 560874430 1.850000e-41 182.0
51 TraesCS7D01G036100 chr5D 86.076 79 9 2 6680 6757 296868975 296868898 5.380000e-12 84.2
52 TraesCS7D01G036100 chr5D 86.076 79 9 2 6680 6757 501209645 501209568 5.380000e-12 84.2
53 TraesCS7D01G036100 chr1D 91.667 132 9 1 8027 8156 206075272 206075403 1.850000e-41 182.0
54 TraesCS7D01G036100 chr3B 90.909 132 10 1 8027 8156 201516772 201516641 8.620000e-40 176.0
55 TraesCS7D01G036100 chr1A 89.394 132 12 1 8027 8156 168448480 168448611 1.870000e-36 165.0
56 TraesCS7D01G036100 chr5B 85.542 83 10 2 6680 6761 622740260 622740179 1.490000e-12 86.1
57 TraesCS7D01G036100 chr6B 83.908 87 14 0 6844 6930 260547094 260547180 5.380000e-12 84.2


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 TraesCS7D01G036100 chr7D 18427040 18435397 8357 True 4242.750000 15435 94.702000 1 8358 4 chr7D.!!$R2 8357
1 TraesCS7D01G036100 chr7A 18876045 18884252 8207 True 4372.000000 8453 94.656667 1 8304 3 chr7A.!!$R1 8303
2 TraesCS7D01G036100 chrUn 50834851 50843349 8498 True 2338.833333 6089 93.973833 1 8356 6 chrUn.!!$R1 8355
3 TraesCS7D01G036100 chr2D 513456670 513464259 7589 False 618.375000 1221 84.477000 939 7354 8 chr2D.!!$F2 6415
4 TraesCS7D01G036100 chr2A 657519274 657525342 6068 False 583.125000 1219 86.404750 1542 7354 8 chr2A.!!$F1 5812
5 TraesCS7D01G036100 chr2B 604994102 605001634 7532 False 513.555556 1216 85.393556 1596 7376 9 chr2B.!!$F1 5780
6 TraesCS7D01G036100 chr4A 704322036 704322612 576 True 422.000000 422 80.135000 6367 6953 1 chr4A.!!$R1 586

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
386 407 0.995024 CTTCCTTCTCCCATGGTGGT 59.005 55.000 11.73 0.00 35.17 4.16 F
1575 1665 0.304705 CACCTGAATATCAACCGCGC 59.695 55.000 0.00 0.00 0.00 6.86 F
1683 1773 0.304705 CACCTGAATATCAACCGCGC 59.695 55.000 0.00 0.00 0.00 6.86 F
1687 1777 1.149361 TGAATATCAACCGCGCGACC 61.149 55.000 34.63 9.13 0.00 4.79 F
3092 4798 0.179062 CAGAGCATCCAGGTGTAGGC 60.179 60.000 0.00 0.00 33.66 3.93 F
3095 4801 0.618680 AGCATCCAGGTGTAGGCTGA 60.619 55.000 0.00 0.00 0.00 4.26 F
3564 5278 4.245660 CTGTTGATGATCGTGGTACTGTT 58.754 43.478 0.00 0.00 0.00 3.16 F
5050 8412 1.548719 TGGTCAATGGTGGTAGAGTCG 59.451 52.381 0.00 0.00 0.00 4.18 F
6356 9740 3.317711 TGTTTGAACTTGATGCCATTCGT 59.682 39.130 0.00 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1881 2025 0.884704 CCGGGGCTTGATATTGGACG 60.885 60.000 0.00 0.00 0.00 4.79 R
3025 4648 2.825836 GAGCATTCAGGCCACCCG 60.826 66.667 5.01 0.00 35.76 5.28 R
3064 4770 3.012518 CCTGGATGCTCTGTAAAACAGG 58.987 50.000 7.18 0.00 45.94 4.00 R
3095 4801 3.130516 CAGCAAGACCAATGAGCATTCAT 59.869 43.478 0.00 0.00 45.92 2.57 R
3915 5666 1.330306 GCAGCAACAATGTTACAGCG 58.670 50.000 0.00 0.00 0.00 5.18 R
4709 6876 6.379133 TGCAGAAATAATTTCCAGCTCAGATT 59.621 34.615 0.00 0.00 40.54 2.40 R
5473 8846 4.673968 AGGTCCCCTGGAGAAAATAAAAC 58.326 43.478 0.00 0.00 29.57 2.43 R
6616 10008 1.999024 AGCACAAAAACCTTGTTTGCG 59.001 42.857 0.00 0.00 39.16 4.85 R
7361 10997 0.107848 CACGGTAACCACCAGGATCC 60.108 60.000 2.48 2.48 46.14 3.36 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
217 231 1.802880 CGTCGAGGTTTAGGATGCTGG 60.803 57.143 0.00 0.00 0.00 4.85
247 261 1.153349 CTTGCGGAGGGAAGGTAGC 60.153 63.158 0.00 0.00 37.89 3.58
352 373 1.196808 GGGTTGTGTGCATCTGTTACG 59.803 52.381 0.00 0.00 0.00 3.18
365 386 3.718395 TTACGGGCGGGGAATGCA 61.718 61.111 0.00 0.00 0.00 3.96
386 407 0.995024 CTTCCTTCTCCCATGGTGGT 59.005 55.000 11.73 0.00 35.17 4.16
410 431 1.531602 GGCTTGTTGTGGAGGGCTT 60.532 57.895 0.00 0.00 0.00 4.35
500 521 2.981914 TTTGCTGCCCTCACCACCAG 62.982 60.000 0.00 0.00 0.00 4.00
572 597 4.648762 TCAAAGCATCTTTGAAGGTTTCCA 59.351 37.500 16.80 0.00 35.69 3.53
594 619 2.315925 ATGGTCTTGCAGTCATACGG 57.684 50.000 0.00 0.00 0.00 4.02
598 623 1.661112 GTCTTGCAGTCATACGGCTTC 59.339 52.381 3.95 0.00 40.02 3.86
614 639 1.882623 GCTTCCATTGGTATAGGCTGC 59.117 52.381 1.86 0.00 0.00 5.25
626 651 3.652057 ATAGGCTGCAGTGTGGTATTT 57.348 42.857 16.64 0.00 0.00 1.40
637 662 6.183360 TGCAGTGTGGTATTTGATTTCAAGTT 60.183 34.615 0.00 0.00 37.15 2.66
647 672 9.559958 GTATTTGATTTCAAGTTCCACTGTATG 57.440 33.333 0.00 0.00 37.15 2.39
675 700 3.508012 ACTATGCTGCCTACTCCTTATCG 59.492 47.826 0.00 0.00 0.00 2.92
700 725 4.955811 TGCTCGGGTGACATTATTCTAT 57.044 40.909 0.00 0.00 0.00 1.98
721 746 1.348036 AGAGTTTTCGGTCCTTGAGGG 59.652 52.381 0.00 0.00 35.41 4.30
752 777 1.533625 GCATGGTTTGCCTAGACACA 58.466 50.000 0.00 0.00 46.15 3.72
754 779 2.159338 GCATGGTTTGCCTAGACACATG 60.159 50.000 4.40 4.40 46.15 3.21
755 780 2.949177 TGGTTTGCCTAGACACATGT 57.051 45.000 0.00 0.00 35.27 3.21
818 845 4.891992 AGCTTGTGTTCTAGCTTTCCTA 57.108 40.909 0.00 0.00 46.91 2.94
872 899 5.277634 GGTTGTGTATGTTTGTTAGAAGCGT 60.278 40.000 0.00 0.00 0.00 5.07
893 920 2.039746 TGGAACGAATCTTGTCCCATGT 59.960 45.455 0.00 0.00 0.00 3.21
1575 1665 0.304705 CACCTGAATATCAACCGCGC 59.695 55.000 0.00 0.00 0.00 6.86
1599 1689 3.402681 CAGGGCCGTGGACATCCT 61.403 66.667 17.92 0.00 36.82 3.24
1631 1721 1.564622 CTGAATATCAACCGCGCGG 59.435 57.895 44.88 44.88 42.03 6.46
1679 1769 3.279434 GTGGTCCACCTGAATATCAACC 58.721 50.000 11.30 0.00 36.82 3.77
1680 1770 2.093181 TGGTCCACCTGAATATCAACCG 60.093 50.000 0.00 0.00 36.82 4.44
1683 1773 0.304705 CACCTGAATATCAACCGCGC 59.695 55.000 0.00 0.00 0.00 6.86
1687 1777 1.149361 TGAATATCAACCGCGCGACC 61.149 55.000 34.63 9.13 0.00 4.79
1688 1778 1.828331 GAATATCAACCGCGCGACCC 61.828 60.000 34.63 5.54 0.00 4.46
1842 1986 1.168714 GACACAATGTTCCTCCAGGC 58.831 55.000 0.00 0.00 34.44 4.85
1881 2025 2.674380 CTGCACCAAGCCCCAGAC 60.674 66.667 0.00 0.00 44.83 3.51
1936 2080 4.168291 CGGGAGCTGGCTCTTCCC 62.168 72.222 19.92 13.75 42.38 3.97
2230 2374 4.430137 TTTGCAGTTTCTGATCATCAGC 57.570 40.909 10.10 0.00 43.95 4.26
2701 2855 6.071560 GCCTACTGCCAGGTAAATTTTAGTTT 60.072 38.462 0.00 0.00 38.05 2.66
2702 2856 7.312899 CCTACTGCCAGGTAAATTTTAGTTTG 58.687 38.462 0.00 0.00 0.00 2.93
2703 2857 6.969993 ACTGCCAGGTAAATTTTAGTTTGA 57.030 33.333 0.00 0.00 0.00 2.69
2704 2858 6.981722 ACTGCCAGGTAAATTTTAGTTTGAG 58.018 36.000 0.00 0.00 0.00 3.02
2705 2859 6.549736 ACTGCCAGGTAAATTTTAGTTTGAGT 59.450 34.615 0.00 0.00 0.00 3.41
2706 2860 7.069455 ACTGCCAGGTAAATTTTAGTTTGAGTT 59.931 33.333 0.00 0.00 0.00 3.01
2707 2861 7.787028 TGCCAGGTAAATTTTAGTTTGAGTTT 58.213 30.769 0.00 0.00 0.00 2.66
2708 2862 8.261522 TGCCAGGTAAATTTTAGTTTGAGTTTT 58.738 29.630 0.00 0.00 0.00 2.43
2709 2863 9.104965 GCCAGGTAAATTTTAGTTTGAGTTTTT 57.895 29.630 0.00 0.00 0.00 1.94
2727 2881 4.855715 TTTTTCATGTGGCATCGGTTAA 57.144 36.364 0.00 0.00 0.00 2.01
2728 2882 4.855715 TTTTCATGTGGCATCGGTTAAA 57.144 36.364 0.00 0.00 0.00 1.52
2729 2883 4.855715 TTTCATGTGGCATCGGTTAAAA 57.144 36.364 0.00 0.00 0.00 1.52
2730 2884 5.398603 TTTCATGTGGCATCGGTTAAAAT 57.601 34.783 0.00 0.00 0.00 1.82
2731 2885 5.398603 TTCATGTGGCATCGGTTAAAATT 57.601 34.783 0.00 0.00 0.00 1.82
2732 2886 5.398603 TCATGTGGCATCGGTTAAAATTT 57.601 34.783 0.00 0.00 0.00 1.82
2733 2887 5.788450 TCATGTGGCATCGGTTAAAATTTT 58.212 33.333 8.75 8.75 0.00 1.82
2734 2888 6.925211 TCATGTGGCATCGGTTAAAATTTTA 58.075 32.000 6.54 6.54 0.00 1.52
2735 2889 7.032580 TCATGTGGCATCGGTTAAAATTTTAG 58.967 34.615 10.40 0.77 0.00 1.85
2736 2890 6.334102 TGTGGCATCGGTTAAAATTTTAGT 57.666 33.333 10.40 0.00 0.00 2.24
2737 2891 6.750148 TGTGGCATCGGTTAAAATTTTAGTT 58.250 32.000 10.40 0.00 0.00 2.24
2900 3054 2.159382 AGTTGGCGTGGATTTTACCAG 58.841 47.619 0.00 0.00 40.85 4.00
2915 3069 8.081025 GGATTTTACCAGAGTATAAGACCTACG 58.919 40.741 0.00 0.00 0.00 3.51
3025 4648 2.747446 AGTTGTGATAAATGTGGTCGGC 59.253 45.455 0.00 0.00 0.00 5.54
3064 4770 6.697892 GCTCAGTAATACATAGTGTCCAAGTC 59.302 42.308 0.00 0.00 36.49 3.01
3092 4798 0.179062 CAGAGCATCCAGGTGTAGGC 60.179 60.000 0.00 0.00 33.66 3.93
3095 4801 0.618680 AGCATCCAGGTGTAGGCTGA 60.619 55.000 0.00 0.00 0.00 4.26
3139 4845 6.851330 GCTGAAATAGTGATTTTATACGGTGC 59.149 38.462 0.00 0.00 35.33 5.01
3147 4853 6.535508 AGTGATTTTATACGGTGCTTCTTCTC 59.464 38.462 0.00 0.00 0.00 2.87
3564 5278 4.245660 CTGTTGATGATCGTGGTACTGTT 58.754 43.478 0.00 0.00 0.00 3.16
4709 6876 5.419155 TCACACAACTGGGAAACAATTAACA 59.581 36.000 0.00 0.00 0.00 2.41
5050 8412 1.548719 TGGTCAATGGTGGTAGAGTCG 59.451 52.381 0.00 0.00 0.00 4.18
5171 8533 4.814234 GGTATGGTTCGATCATGCAACTAA 59.186 41.667 15.25 0.00 0.00 2.24
5388 8761 5.110814 ACCTGCTAATTGTTATACTGCCA 57.889 39.130 0.00 0.00 0.00 4.92
6284 9668 6.868339 GCATGATTGCCTATTATTAACCAACC 59.132 38.462 0.00 0.00 43.38 3.77
6308 9692 3.814504 ATTTTCAGGGATGGTGTCAGT 57.185 42.857 0.00 0.00 0.00 3.41
6356 9740 3.317711 TGTTTGAACTTGATGCCATTCGT 59.682 39.130 0.00 0.00 0.00 3.85
6405 9794 6.512342 TTCTGTAGAGCTACTCTTAACCAC 57.488 41.667 1.88 0.00 41.50 4.16
6616 10008 2.230660 ACTGCCTGGTTAGTTTCTTGC 58.769 47.619 0.00 0.00 0.00 4.01
6764 10169 1.345415 CTGGCATTCAGGTTGGCTTTT 59.655 47.619 0.00 0.00 39.76 2.27
7113 10747 8.407457 TCGTACTAGATTCAATGCTGTTAAAG 57.593 34.615 0.00 0.00 0.00 1.85
7115 10749 8.321716 CGTACTAGATTCAATGCTGTTAAAGTC 58.678 37.037 0.00 0.00 0.00 3.01
7116 10750 9.151471 GTACTAGATTCAATGCTGTTAAAGTCA 57.849 33.333 0.00 0.00 0.00 3.41
7156 10792 1.871126 GCTTGCTTGCAGTTCCTCCC 61.871 60.000 0.00 0.00 0.00 4.30
7357 10993 2.534939 GCGCGTCATGTTTTACTGCTAG 60.535 50.000 8.43 0.00 0.00 3.42
7358 10994 2.921121 CGCGTCATGTTTTACTGCTAGA 59.079 45.455 0.00 0.00 0.00 2.43
7359 10995 3.551890 CGCGTCATGTTTTACTGCTAGAT 59.448 43.478 0.00 0.00 0.00 1.98
7360 10996 4.738252 CGCGTCATGTTTTACTGCTAGATA 59.262 41.667 0.00 0.00 0.00 1.98
7361 10997 5.108217 CGCGTCATGTTTTACTGCTAGATAG 60.108 44.000 0.00 0.00 0.00 2.08
7412 11049 2.409152 GCACCTGCGAGAGTAGTATC 57.591 55.000 0.00 0.00 42.74 2.24
7413 11050 1.676529 GCACCTGCGAGAGTAGTATCA 59.323 52.381 0.00 0.00 42.74 2.15
7414 11051 2.099263 GCACCTGCGAGAGTAGTATCAA 59.901 50.000 0.00 0.00 42.74 2.57
7415 11052 3.428999 GCACCTGCGAGAGTAGTATCAAA 60.429 47.826 0.00 0.00 42.74 2.69
7416 11053 4.737946 GCACCTGCGAGAGTAGTATCAAAT 60.738 45.833 0.00 0.00 42.74 2.32
7417 11054 5.507482 GCACCTGCGAGAGTAGTATCAAATA 60.507 44.000 0.00 0.00 42.74 1.40
7418 11055 6.682746 CACCTGCGAGAGTAGTATCAAATAT 58.317 40.000 0.00 0.00 42.74 1.28
7531 11168 2.045438 TTGCACCGGATTGGCGAT 60.045 55.556 9.46 0.00 43.94 4.58
7532 11169 1.656818 CTTGCACCGGATTGGCGATT 61.657 55.000 9.46 0.00 43.94 3.34
7573 11210 4.227300 AGCTATTTGACTGGATTGGGTGTA 59.773 41.667 0.00 0.00 0.00 2.90
7575 11212 5.417580 GCTATTTGACTGGATTGGGTGTAAA 59.582 40.000 0.00 0.00 0.00 2.01
7580 11217 9.707957 ATTTGACTGGATTGGGTGTAAATTATA 57.292 29.630 0.00 0.00 0.00 0.98
7621 11272 2.202388 CTTTCGCGGCTGTGCATG 60.202 61.111 6.13 0.00 34.15 4.06
7639 11308 5.473162 GTGCATGGCCATCTACATTTGTATA 59.527 40.000 17.61 0.00 0.00 1.47
7847 11516 4.706476 TCCAGAATTGAAGTTAGCATTGGG 59.294 41.667 0.00 0.00 0.00 4.12
7848 11517 4.706476 CCAGAATTGAAGTTAGCATTGGGA 59.294 41.667 0.00 0.00 0.00 4.37
7884 11627 3.758554 TGGTAGCAAAATCAGAAAGGAGC 59.241 43.478 0.00 0.00 0.00 4.70
7956 11699 2.921834 TTACCACCTCTGGAGTAGCT 57.078 50.000 0.00 0.00 40.55 3.32
7986 11729 2.093235 TGAAAAACCCCTGTTGGCTTTG 60.093 45.455 0.00 0.00 34.13 2.77
7991 11734 1.186917 CCCCTGTTGGCTTTGCATGA 61.187 55.000 0.00 0.00 0.00 3.07
8042 11787 7.650104 GCTAGGATCCTGCGTAATATAGAAATC 59.350 40.741 25.28 0.00 0.00 2.17
8065 11811 8.850007 ATCATCTTTGTGATCCTATGAATCAG 57.150 34.615 0.00 0.00 33.69 2.90
8128 11874 9.337396 TGATTTAGTCTTGAGCTAAACAAAAGA 57.663 29.630 0.00 0.00 40.04 2.52
8145 11891 7.145932 ACAAAAGATAAGGGTTCTTCGAATG 57.854 36.000 0.00 0.00 32.33 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 4.100981 GCTAGAGCAAGCGGACAG 57.899 61.111 0.00 0.00 41.59 3.51
33 34 0.797249 CCGAACGAACAGGACGCTAG 60.797 60.000 0.00 0.00 0.00 3.42
105 110 1.878953 ACAAACAAATCGGTCGCTCT 58.121 45.000 0.00 0.00 0.00 4.09
185 198 4.688419 TCGACGAACCACGCGGAC 62.688 66.667 12.47 0.00 46.94 4.79
186 199 4.394078 CTCGACGAACCACGCGGA 62.394 66.667 12.47 0.00 46.94 5.54
352 373 4.759205 AAGGTGCATTCCCCGCCC 62.759 66.667 0.00 0.00 33.33 6.13
365 386 0.995024 CACCATGGGAGAAGGAAGGT 59.005 55.000 18.09 0.00 0.00 3.50
386 407 0.535780 CTCCACAACAAGCCTGCAGA 60.536 55.000 17.39 0.00 0.00 4.26
410 431 2.181521 GGACACGGCCACGAACAAA 61.182 57.895 2.24 0.00 44.60 2.83
500 521 1.269621 ACGTGTTACTGCTCAGTCACC 60.270 52.381 5.72 0.50 42.54 4.02
553 578 3.837355 ACTGGAAACCTTCAAAGATGCT 58.163 40.909 0.00 0.00 0.00 3.79
565 590 2.749621 CTGCAAGACCATACTGGAAACC 59.250 50.000 0.00 0.00 41.78 3.27
572 597 3.181475 CCGTATGACTGCAAGACCATACT 60.181 47.826 17.55 0.00 44.03 2.12
592 617 1.072331 AGCCTATACCAATGGAAGCCG 59.928 52.381 6.16 0.00 0.00 5.52
594 619 1.882623 GCAGCCTATACCAATGGAAGC 59.117 52.381 6.16 0.82 0.00 3.86
598 623 2.224606 CACTGCAGCCTATACCAATGG 58.775 52.381 15.27 0.00 0.00 3.16
614 639 6.863126 GGAACTTGAAATCAAATACCACACTG 59.137 38.462 0.00 0.00 35.15 3.66
675 700 5.057149 AGAATAATGTCACCCGAGCATAAC 58.943 41.667 0.00 0.00 0.00 1.89
700 725 2.565834 CCCTCAAGGACCGAAAACTCTA 59.434 50.000 0.00 0.00 38.24 2.43
721 746 0.951558 AACCATGCACGACAACCTTC 59.048 50.000 0.00 0.00 0.00 3.46
752 777 4.345859 TTTAACCCTGACTCAACGACAT 57.654 40.909 0.00 0.00 0.00 3.06
754 779 3.367025 CGATTTAACCCTGACTCAACGAC 59.633 47.826 0.00 0.00 0.00 4.34
755 780 3.581755 CGATTTAACCCTGACTCAACGA 58.418 45.455 0.00 0.00 0.00 3.85
818 845 1.671845 GACGCTCTACTCGACCTGAAT 59.328 52.381 0.00 0.00 0.00 2.57
857 884 2.285756 CGTTCCACGCTTCTAACAAACA 59.714 45.455 0.00 0.00 33.65 2.83
872 899 2.039746 ACATGGGACAAGATTCGTTCCA 59.960 45.455 0.00 0.00 46.22 3.53
885 912 1.000274 GTCTGCAAACCAACATGGGAC 60.000 52.381 0.00 0.00 43.37 4.46
893 920 4.202202 CCCAATAACAAGTCTGCAAACCAA 60.202 41.667 0.00 0.00 0.00 3.67
1081 1108 2.434428 CTCTGCCAAGACAAGAATGCT 58.566 47.619 0.00 0.00 0.00 3.79
1687 1777 3.391665 GATGTCCACGGCCCTGAGG 62.392 68.421 2.94 0.00 0.00 3.86
1688 1778 2.187946 GATGTCCACGGCCCTGAG 59.812 66.667 2.94 0.00 0.00 3.35
1695 1839 2.268920 CCACCTGGATGTCCACGG 59.731 66.667 0.00 12.92 42.01 4.94
1842 1986 1.070134 TCGGGAACTGTTCTTGACTGG 59.930 52.381 19.05 3.01 35.30 4.00
1881 2025 0.884704 CCGGGGCTTGATATTGGACG 60.885 60.000 0.00 0.00 0.00 4.79
2230 2374 2.862541 TGGTCACCTGATGAAACAAGG 58.137 47.619 0.00 0.00 39.72 3.61
2706 2860 4.855715 TTAACCGATGCCACATGAAAAA 57.144 36.364 0.00 0.00 0.00 1.94
2707 2861 4.855715 TTTAACCGATGCCACATGAAAA 57.144 36.364 0.00 0.00 0.00 2.29
2708 2862 4.855715 TTTTAACCGATGCCACATGAAA 57.144 36.364 0.00 0.00 0.00 2.69
2709 2863 5.398603 AATTTTAACCGATGCCACATGAA 57.601 34.783 0.00 0.00 0.00 2.57
2710 2864 5.398603 AAATTTTAACCGATGCCACATGA 57.601 34.783 0.00 0.00 0.00 3.07
2711 2865 6.811170 ACTAAAATTTTAACCGATGCCACATG 59.189 34.615 11.62 0.00 0.00 3.21
2712 2866 6.930731 ACTAAAATTTTAACCGATGCCACAT 58.069 32.000 11.62 0.00 0.00 3.21
2713 2867 6.334102 ACTAAAATTTTAACCGATGCCACA 57.666 33.333 11.62 0.00 0.00 4.17
2714 2868 8.641155 GTTAACTAAAATTTTAACCGATGCCAC 58.359 33.333 11.62 0.00 33.74 5.01
2715 2869 7.813627 GGTTAACTAAAATTTTAACCGATGCCA 59.186 33.333 14.51 0.00 44.45 4.92
2716 2870 8.176814 GGTTAACTAAAATTTTAACCGATGCC 57.823 34.615 14.51 7.37 44.45 4.40
2900 3054 4.082679 CCCATCTGCGTAGGTCTTATACTC 60.083 50.000 0.00 0.00 0.00 2.59
3025 4648 2.825836 GAGCATTCAGGCCACCCG 60.826 66.667 5.01 0.00 35.76 5.28
3064 4770 3.012518 CCTGGATGCTCTGTAAAACAGG 58.987 50.000 7.18 0.00 45.94 4.00
3092 4798 4.733815 GCAAGACCAATGAGCATTCATCAG 60.734 45.833 0.00 0.00 43.20 2.90
3095 4801 3.130516 CAGCAAGACCAATGAGCATTCAT 59.869 43.478 0.00 0.00 45.92 2.57
3139 4845 5.830912 AGAAGACATATCTGCGAGAAGAAG 58.169 41.667 0.00 0.00 35.31 2.85
3147 4853 3.969899 TGCTGTAGAAGACATATCTGCG 58.030 45.455 0.00 0.00 35.31 5.18
3298 5005 6.817184 TGATAACTAGGCATAACCAGAAGTC 58.183 40.000 0.00 0.00 43.14 3.01
3498 5209 4.526262 CCAACAAGGAATCACCCACAAATA 59.474 41.667 0.00 0.00 41.22 1.40
3564 5278 4.286032 AGGAAGTATTGCACCACAGTCTTA 59.714 41.667 0.00 0.00 39.77 2.10
3915 5666 1.330306 GCAGCAACAATGTTACAGCG 58.670 50.000 0.00 0.00 0.00 5.18
4028 5907 7.990886 AGTAAACACATCAAACAGGAAGAACTA 59.009 33.333 0.00 0.00 0.00 2.24
4709 6876 6.379133 TGCAGAAATAATTTCCAGCTCAGATT 59.621 34.615 0.00 0.00 40.54 2.40
5171 8533 5.590530 AGCGACAGAGAAATATGAGAAGT 57.409 39.130 0.00 0.00 0.00 3.01
5473 8846 4.673968 AGGTCCCCTGGAGAAAATAAAAC 58.326 43.478 0.00 0.00 29.57 2.43
5478 8851 5.075900 TCTTTTAAGGTCCCCTGGAGAAAAT 59.924 40.000 0.00 0.00 32.13 1.82
6279 9663 2.500392 TCCCTGAAAATACCGGTTGG 57.500 50.000 15.04 4.08 42.84 3.77
6284 9668 2.943033 GACACCATCCCTGAAAATACCG 59.057 50.000 0.00 0.00 0.00 4.02
6308 9692 5.047021 CAGAACTTGATAGAACTGTCCCTCA 60.047 44.000 0.00 0.00 0.00 3.86
6437 9828 8.446273 CAACATAGTTAAGAAATGTCAGTCAGG 58.554 37.037 0.00 0.00 32.80 3.86
6438 9829 8.993121 ACAACATAGTTAAGAAATGTCAGTCAG 58.007 33.333 0.00 0.00 32.80 3.51
6616 10008 1.999024 AGCACAAAAACCTTGTTTGCG 59.001 42.857 0.00 0.00 39.16 4.85
6764 10169 6.985059 TCAAATGAACACATTGCAAATGAAGA 59.015 30.769 18.17 4.35 34.92 2.87
7127 10763 0.652071 GCAAGCAAGCAAACAACCAC 59.348 50.000 0.00 0.00 0.00 4.16
7357 10993 2.299297 CGGTAACCACCAGGATCCTATC 59.701 54.545 15.67 0.00 46.14 2.08
7358 10994 2.326428 CGGTAACCACCAGGATCCTAT 58.674 52.381 15.67 2.39 46.14 2.57
7359 10995 1.007479 ACGGTAACCACCAGGATCCTA 59.993 52.381 15.67 0.00 46.14 2.94
7360 10996 0.252558 ACGGTAACCACCAGGATCCT 60.253 55.000 9.02 9.02 46.14 3.24
7361 10997 0.107848 CACGGTAACCACCAGGATCC 60.108 60.000 2.48 2.48 46.14 3.36
7384 11021 1.067565 TCTCGCAGGTGCTTCAAGTAG 60.068 52.381 0.00 0.00 39.32 2.57
7410 11047 9.578576 ACAGCATCACCAATACTAATATTTGAT 57.421 29.630 3.83 0.00 32.18 2.57
7411 11048 8.978874 ACAGCATCACCAATACTAATATTTGA 57.021 30.769 3.83 0.00 0.00 2.69
7412 11049 9.669353 GAACAGCATCACCAATACTAATATTTG 57.331 33.333 0.00 0.00 0.00 2.32
7413 11050 9.407380 TGAACAGCATCACCAATACTAATATTT 57.593 29.630 0.00 0.00 0.00 1.40
7414 11051 8.978874 TGAACAGCATCACCAATACTAATATT 57.021 30.769 0.00 0.00 0.00 1.28
7415 11052 8.840321 GTTGAACAGCATCACCAATACTAATAT 58.160 33.333 0.00 0.00 0.00 1.28
7416 11053 7.826744 TGTTGAACAGCATCACCAATACTAATA 59.173 33.333 0.00 0.00 0.00 0.98
7417 11054 6.658816 TGTTGAACAGCATCACCAATACTAAT 59.341 34.615 0.00 0.00 0.00 1.73
7418 11055 6.000840 TGTTGAACAGCATCACCAATACTAA 58.999 36.000 0.00 0.00 0.00 2.24
7531 11168 3.196685 AGCTTAAAAGGTTTGTGCACCAA 59.803 39.130 15.69 6.86 39.62 3.67
7532 11169 2.763448 AGCTTAAAAGGTTTGTGCACCA 59.237 40.909 15.69 0.00 39.62 4.17
7573 11210 4.450976 TCTCGCAGCACCACATATAATTT 58.549 39.130 0.00 0.00 0.00 1.82
7575 11212 3.751479 TCTCGCAGCACCACATATAAT 57.249 42.857 0.00 0.00 0.00 1.28
7580 11217 2.037136 GCTTCTCGCAGCACCACAT 61.037 57.895 0.00 0.00 39.83 3.21
7619 11270 6.716628 CCAGTTATACAAATGTAGATGGCCAT 59.283 38.462 20.96 20.96 33.52 4.40
7621 11272 6.017109 CACCAGTTATACAAATGTAGATGGCC 60.017 42.308 0.00 0.00 33.52 5.36
7884 11627 3.498397 GTGGTGGTCAGTGTAAAGATGTG 59.502 47.826 0.00 0.00 0.00 3.21
7956 11699 7.501844 CCAACAGGGGTTTTTCACTTAAAATA 58.498 34.615 0.00 0.00 36.94 1.40
8042 11787 8.447924 AACTGATTCATAGGATCACAAAGATG 57.552 34.615 0.00 0.00 37.00 2.90
8145 11891 1.136500 CCTACTGGGTAAGCGGTTCTC 59.864 57.143 1.59 0.00 0.00 2.87
8168 11914 2.814805 ATTGAGGGCTGCACTTATGT 57.185 45.000 5.59 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.