Multiple sequence alignment - TraesCS6B01G458000

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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 TraesCS6B01G458000 chr6B 100.000 4731 0 0 1 4731 713328496 713333226 0.000000e+00 8737.0
1 TraesCS6B01G458000 chr6B 95.151 1918 63 17 2830 4731 713563575 713565478 0.000000e+00 3000.0
2 TraesCS6B01G458000 chr6B 98.055 1491 29 0 1 1491 713556212 713557702 0.000000e+00 2593.0
3 TraesCS6B01G458000 chr6B 93.230 1743 77 19 1004 2730 713881394 713883111 0.000000e+00 2527.0
4 TraesCS6B01G458000 chr6B 96.555 929 24 3 1487 2413 713562653 713563575 0.000000e+00 1531.0
5 TraesCS6B01G458000 chr6B 92.729 949 49 6 2852 3788 713883111 713884051 0.000000e+00 1352.0
6 TraesCS6B01G458000 chr6B 85.938 768 86 8 131 895 32828857 32828109 0.000000e+00 800.0
7 TraesCS6B01G458000 chr6B 86.025 644 78 5 2962 3605 508172995 508173626 0.000000e+00 680.0
8 TraesCS6B01G458000 chr6B 88.822 501 44 7 1015 1513 508168749 508169239 5.240000e-169 604.0
9 TraesCS6B01G458000 chr6B 96.617 266 3 2 4323 4588 713884050 713884309 2.020000e-118 436.0
10 TraesCS6B01G458000 chr6B 92.810 153 7 1 4583 4731 713884684 713884836 7.970000e-53 219.0
11 TraesCS6B01G458000 chr6D 90.571 806 46 18 1004 1784 467877067 467877867 0.000000e+00 1040.0
12 TraesCS6B01G458000 chr6D 92.659 722 36 5 2906 3611 467878620 467879340 0.000000e+00 1024.0
13 TraesCS6B01G458000 chr6D 86.508 630 73 5 2976 3605 316427875 316427258 0.000000e+00 682.0
14 TraesCS6B01G458000 chr6D 89.421 501 41 5 1015 1513 316429714 316429224 5.200000e-174 621.0
15 TraesCS6B01G458000 chr6D 94.139 273 11 5 3889 4158 470979358 470979088 1.230000e-110 411.0
16 TraesCS6B01G458000 chr7A 81.153 902 132 19 4 899 110769116 110768247 0.000000e+00 689.0
17 TraesCS6B01G458000 chr7A 73.859 723 154 29 189 897 239193234 239192533 6.080000e-64 255.0
18 TraesCS6B01G458000 chr7A 97.368 38 1 0 860 897 646595769 646595806 1.100000e-06 65.8
19 TraesCS6B01G458000 chr5B 86.885 610 72 6 297 901 67467009 67466403 0.000000e+00 676.0
20 TraesCS6B01G458000 chr5B 92.647 272 14 6 3889 4157 503083807 503084075 2.060000e-103 387.0
21 TraesCS6B01G458000 chr5B 100.000 30 0 0 860 889 571192056 571192027 6.610000e-04 56.5
22 TraesCS6B01G458000 chr6A 85.873 630 77 5 2976 3605 454386936 454386319 0.000000e+00 660.0
23 TraesCS6B01G458000 chr6A 89.022 501 43 7 1015 1513 454390615 454390125 1.130000e-170 610.0
24 TraesCS6B01G458000 chr6A 84.893 609 85 5 297 901 151507213 151507818 4.050000e-170 608.0
25 TraesCS6B01G458000 chr6A 93.066 274 13 5 3889 4158 11574156 11574427 3.430000e-106 396.0
26 TraesCS6B01G458000 chr1B 85.925 611 77 7 297 904 550351714 550352318 1.110000e-180 643.0
27 TraesCS6B01G458000 chr1B 92.701 274 15 5 3889 4159 403186241 403185970 1.600000e-104 390.0
28 TraesCS6B01G458000 chr1B 92.446 278 14 7 3886 4159 472632231 472632505 1.600000e-104 390.0
29 TraesCS6B01G458000 chr1B 94.118 136 7 1 2725 2860 626227009 626226875 6.210000e-49 206.0
30 TraesCS6B01G458000 chr1B 91.724 145 9 3 2713 2855 245943234 245943377 1.040000e-46 198.0
31 TraesCS6B01G458000 chr1B 93.023 86 6 0 2001 2086 50401047 50401132 4.970000e-25 126.0
32 TraesCS6B01G458000 chr3D 86.418 589 47 17 336 909 560351551 560350981 8.700000e-172 614.0
33 TraesCS6B01G458000 chr3D 91.724 145 9 3 2720 2864 67064919 67064778 1.040000e-46 198.0
34 TraesCS6B01G458000 chr3D 88.312 77 3 1 4646 4716 582121515 582121591 2.350000e-13 87.9
35 TraesCS6B01G458000 chr3D 91.071 56 5 0 4652 4707 599012670 599012615 5.080000e-10 76.8
36 TraesCS6B01G458000 chr3D 100.000 33 0 0 4646 4678 598945635 598945667 1.420000e-05 62.1
37 TraesCS6B01G458000 chr3A 84.158 606 65 10 297 895 729404066 729403485 4.140000e-155 558.0
38 TraesCS6B01G458000 chr3A 94.545 55 3 0 4646 4700 729118372 729118426 8.440000e-13 86.1
39 TraesCS6B01G458000 chr3A 94.000 50 2 1 4561 4609 724321716 724321667 1.830000e-09 75.0
40 TraesCS6B01G458000 chr2B 93.431 274 13 5 3889 4159 39931896 39931625 7.370000e-108 401.0
41 TraesCS6B01G458000 chr2B 87.986 283 28 2 2001 2278 523090111 523090392 3.530000e-86 329.0
42 TraesCS6B01G458000 chr1A 92.989 271 15 4 3889 4157 27394109 27393841 4.440000e-105 392.0
43 TraesCS6B01G458000 chr1A 90.604 149 11 3 2708 2855 92253699 92253845 1.340000e-45 195.0
44 TraesCS6B01G458000 chr1A 81.437 167 30 1 227 392 338637879 338638045 8.260000e-28 135.0
45 TraesCS6B01G458000 chr2A 92.647 272 15 5 3890 4158 608042859 608042590 2.060000e-103 387.0
46 TraesCS6B01G458000 chr2A 89.399 283 25 2 2004 2286 673194045 673193768 7.530000e-93 351.0
47 TraesCS6B01G458000 chr2A 91.480 223 18 1 2086 2307 378844313 378844091 5.950000e-79 305.0
48 TraesCS6B01G458000 chr2A 92.647 136 9 1 2720 2855 556742177 556742043 1.340000e-45 195.0
49 TraesCS6B01G458000 chr2A 93.182 44 3 0 853 896 691112858 691112901 1.100000e-06 65.8
50 TraesCS6B01G458000 chr1D 74.973 923 189 30 4 904 11209731 11210633 2.060000e-103 387.0
51 TraesCS6B01G458000 chr1D 84.015 269 32 8 2010 2270 283549538 283549803 1.020000e-61 248.0
52 TraesCS6B01G458000 chr1D 88.535 157 16 2 2719 2875 384835321 384835475 6.250000e-44 189.0
53 TraesCS6B01G458000 chrUn 93.659 205 13 0 2083 2287 155825 156029 1.650000e-79 307.0
54 TraesCS6B01G458000 chrUn 77.778 216 38 6 4164 4369 48373339 48373554 1.790000e-24 124.0
55 TraesCS6B01G458000 chrUn 77.778 216 38 6 4164 4369 338263782 338263567 1.790000e-24 124.0
56 TraesCS6B01G458000 chr3B 86.691 278 36 1 2001 2278 24019654 24019930 1.650000e-79 307.0
57 TraesCS6B01G458000 chr3B 93.571 140 7 2 2720 2858 175215929 175216067 1.730000e-49 207.0
58 TraesCS6B01G458000 chr3B 94.444 54 3 0 4646 4699 806192792 806192845 3.030000e-12 84.2
59 TraesCS6B01G458000 chr2D 86.054 294 31 3 2000 2286 33961700 33961990 1.650000e-79 307.0
60 TraesCS6B01G458000 chr2D 86.992 123 14 1 312 432 272236302 272236180 2.300000e-28 137.0
61 TraesCS6B01G458000 chr7B 91.705 217 17 1 2083 2299 750113120 750113335 2.770000e-77 300.0
62 TraesCS6B01G458000 chr5D 84.586 266 40 1 2004 2268 351952238 351951973 3.630000e-66 263.0
63 TraesCS6B01G458000 chr5D 76.154 260 45 13 297 548 481797629 481797379 2.310000e-23 121.0
64 TraesCS6B01G458000 chr4A 82.784 273 40 4 2004 2270 703303905 703304176 2.200000e-58 237.0
65 TraesCS6B01G458000 chr7D 73.408 628 130 33 293 900 63871938 63872548 2.890000e-47 200.0
66 TraesCS6B01G458000 chr7D 91.525 59 4 1 2416 2473 534029435 534029377 3.920000e-11 80.5
67 TraesCS6B01G458000 chr4B 91.724 145 9 3 2713 2855 245592625 245592768 1.040000e-46 198.0
68 TraesCS6B01G458000 chr4B 91.096 146 11 2 2718 2862 82019259 82019115 3.730000e-46 196.0
69 TraesCS6B01G458000 chr5A 76.498 217 39 8 4164 4369 541366140 541365925 1.800000e-19 108.0


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 TraesCS6B01G458000 chr6B 713328496 713333226 4730 False 8737.0 8737 100.0000 1 4731 1 chr6B.!!$F1 4730
1 TraesCS6B01G458000 chr6B 713556212 713557702 1490 False 2593.0 2593 98.0550 1 1491 1 chr6B.!!$F2 1490
2 TraesCS6B01G458000 chr6B 713562653 713565478 2825 False 2265.5 3000 95.8530 1487 4731 2 chr6B.!!$F4 3244
3 TraesCS6B01G458000 chr6B 713881394 713884836 3442 False 1133.5 2527 93.8465 1004 4731 4 chr6B.!!$F5 3727
4 TraesCS6B01G458000 chr6B 32828109 32828857 748 True 800.0 800 85.9380 131 895 1 chr6B.!!$R1 764
5 TraesCS6B01G458000 chr6B 508168749 508173626 4877 False 642.0 680 87.4235 1015 3605 2 chr6B.!!$F3 2590
6 TraesCS6B01G458000 chr6D 467877067 467879340 2273 False 1032.0 1040 91.6150 1004 3611 2 chr6D.!!$F1 2607
7 TraesCS6B01G458000 chr6D 316427258 316429714 2456 True 651.5 682 87.9645 1015 3605 2 chr6D.!!$R2 2590
8 TraesCS6B01G458000 chr7A 110768247 110769116 869 True 689.0 689 81.1530 4 899 1 chr7A.!!$R1 895
9 TraesCS6B01G458000 chr7A 239192533 239193234 701 True 255.0 255 73.8590 189 897 1 chr7A.!!$R2 708
10 TraesCS6B01G458000 chr5B 67466403 67467009 606 True 676.0 676 86.8850 297 901 1 chr5B.!!$R1 604
11 TraesCS6B01G458000 chr6A 454386319 454390615 4296 True 635.0 660 87.4475 1015 3605 2 chr6A.!!$R1 2590
12 TraesCS6B01G458000 chr6A 151507213 151507818 605 False 608.0 608 84.8930 297 901 1 chr6A.!!$F2 604
13 TraesCS6B01G458000 chr1B 550351714 550352318 604 False 643.0 643 85.9250 297 904 1 chr1B.!!$F4 607
14 TraesCS6B01G458000 chr3D 560350981 560351551 570 True 614.0 614 86.4180 336 909 1 chr3D.!!$R2 573
15 TraesCS6B01G458000 chr3A 729403485 729404066 581 True 558.0 558 84.1580 297 895 1 chr3A.!!$R2 598
16 TraesCS6B01G458000 chr1D 11209731 11210633 902 False 387.0 387 74.9730 4 904 1 chr1D.!!$F1 900

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
56 57 3.253838 ACCTTGGGTTGCCGGCTA 61.254 61.111 29.7 19.1 27.29 3.93 F
1899 1971 1.131638 GATCTGGTGGCCCATGTAGA 58.868 55.000 0.0 0.0 40.90 2.59 F
2199 5262 0.032515 TTCGGAGGTGCTCATAGGGA 60.033 55.000 0.0 0.0 31.08 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2046 2119 1.541588 GCATTTGAACCCTGGTGAGAC 59.458 52.381 0.00 0.0 0.00 3.36 R
3406 9271 0.622665 CACCCTTCTTCAGGCCATCT 59.377 55.000 5.01 0.0 42.29 2.90 R
3853 9730 2.357517 GTGCTCACCTCCACACCG 60.358 66.667 0.00 0.0 32.37 4.94 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
56 57 3.253838 ACCTTGGGTTGCCGGCTA 61.254 61.111 29.70 19.10 27.29 3.93
1278 1322 2.320587 CGAGGCGCTGTGCTTCTTT 61.321 57.895 20.63 0.08 46.85 2.52
1812 1880 5.542616 TTTGGCCAATTATTGCGAAAATG 57.457 34.783 21.26 0.00 33.23 2.32
1853 1925 2.443952 TGGATGCCGACGGATCCT 60.444 61.111 29.42 10.83 39.23 3.24
1854 1926 2.029666 GGATGCCGACGGATCCTG 59.970 66.667 25.70 6.11 36.04 3.86
1899 1971 1.131638 GATCTGGTGGCCCATGTAGA 58.868 55.000 0.00 0.00 40.90 2.59
2049 2122 1.755783 GACCGTGGTATCCCCGTCT 60.756 63.158 0.00 0.00 35.15 4.18
2117 2269 1.699730 TCAGTGGAAGGAGACGTTCA 58.300 50.000 0.00 0.00 0.00 3.18
2199 5262 0.032515 TTCGGAGGTGCTCATAGGGA 60.033 55.000 0.00 0.00 31.08 4.20
2203 5266 2.555448 CGGAGGTGCTCATAGGGATAGA 60.555 54.545 0.00 0.00 31.08 1.98
2204 5267 3.511477 GGAGGTGCTCATAGGGATAGAA 58.489 50.000 0.00 0.00 31.08 2.10
2435 6662 0.255890 GGGCCCACATGTCATACACT 59.744 55.000 19.95 0.00 0.00 3.55
2482 6709 2.339769 AGTTGCTCCCCTGTAAAGACT 58.660 47.619 0.00 0.00 0.00 3.24
2487 6714 2.821437 CTCCCCTGTAAAGACTCCTGA 58.179 52.381 0.00 0.00 0.00 3.86
2555 6782 1.067516 GGTCCAGCGTACGCCTATTTA 59.932 52.381 34.88 13.31 43.17 1.40
2658 6885 5.118990 ACGGATGGAATTGATTCAGTACAG 58.881 41.667 6.11 0.00 38.53 2.74
2740 7232 8.164058 AGTAATAACATAGTACTCCCTTCGTC 57.836 38.462 0.00 0.00 34.84 4.20
2741 7233 6.402456 AATAACATAGTACTCCCTTCGTCC 57.598 41.667 0.00 0.00 0.00 4.79
2742 7234 2.295885 ACATAGTACTCCCTTCGTCCG 58.704 52.381 0.00 0.00 0.00 4.79
2744 7236 2.787473 TAGTACTCCCTTCGTCCGAA 57.213 50.000 0.00 1.81 0.00 4.30
2746 7238 2.242043 AGTACTCCCTTCGTCCGAAAA 58.758 47.619 3.52 0.00 33.34 2.29
2751 7243 3.260128 ACTCCCTTCGTCCGAAAATACTT 59.740 43.478 3.52 0.00 33.34 2.24
2752 7244 3.592059 TCCCTTCGTCCGAAAATACTTG 58.408 45.455 3.52 0.00 33.34 3.16
2756 7248 4.630069 CCTTCGTCCGAAAATACTTGTCAT 59.370 41.667 3.52 0.00 33.34 3.06
2757 7249 5.220416 CCTTCGTCCGAAAATACTTGTCATC 60.220 44.000 3.52 0.00 33.34 2.92
2758 7250 4.811908 TCGTCCGAAAATACTTGTCATCA 58.188 39.130 0.00 0.00 0.00 3.07
2760 7252 5.697178 TCGTCCGAAAATACTTGTCATCAAA 59.303 36.000 0.00 0.00 32.87 2.69
2761 7253 6.203145 TCGTCCGAAAATACTTGTCATCAAAA 59.797 34.615 0.00 0.00 32.87 2.44
2763 7255 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
2765 7257 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
2766 7258 7.273381 CCGAAAATACTTGTCATCAAAATGGAC 59.727 37.037 0.00 0.00 33.42 4.02
2767 7259 7.007367 CGAAAATACTTGTCATCAAAATGGACG 59.993 37.037 0.00 0.00 33.42 4.79
2771 7263 6.142818 ACTTGTCATCAAAATGGACGAAAA 57.857 33.333 0.00 0.00 33.42 2.29
2772 7264 6.208644 ACTTGTCATCAAAATGGACGAAAAG 58.791 36.000 0.00 0.00 33.42 2.27
2773 7265 5.119931 TGTCATCAAAATGGACGAAAAGG 57.880 39.130 0.00 0.00 33.42 3.11
2774 7266 4.022416 TGTCATCAAAATGGACGAAAAGGG 60.022 41.667 0.00 0.00 33.42 3.95
2775 7267 4.217550 GTCATCAAAATGGACGAAAAGGGA 59.782 41.667 0.00 0.00 33.42 4.20
2776 7268 5.016173 TCATCAAAATGGACGAAAAGGGAT 58.984 37.500 0.00 0.00 33.42 3.85
2777 7269 4.782019 TCAAAATGGACGAAAAGGGATG 57.218 40.909 0.00 0.00 0.00 3.51
2780 7272 5.949354 TCAAAATGGACGAAAAGGGATGTAT 59.051 36.000 0.00 0.00 0.00 2.29
2781 7273 6.094881 TCAAAATGGACGAAAAGGGATGTATC 59.905 38.462 0.00 0.00 0.00 2.24
2783 7275 6.494666 AATGGACGAAAAGGGATGTATCTA 57.505 37.500 0.00 0.00 0.00 1.98
2785 7277 6.302535 TGGACGAAAAGGGATGTATCTAAA 57.697 37.500 0.00 0.00 0.00 1.85
2786 7278 6.346096 TGGACGAAAAGGGATGTATCTAAAG 58.654 40.000 0.00 0.00 0.00 1.85
2787 7279 5.236695 GGACGAAAAGGGATGTATCTAAAGC 59.763 44.000 0.00 0.00 0.00 3.51
2788 7280 5.990668 ACGAAAAGGGATGTATCTAAAGCT 58.009 37.500 0.00 0.00 0.00 3.74
2789 7281 7.120923 ACGAAAAGGGATGTATCTAAAGCTA 57.879 36.000 0.00 0.00 0.00 3.32
2790 7282 7.562135 ACGAAAAGGGATGTATCTAAAGCTAA 58.438 34.615 0.00 0.00 0.00 3.09
2791 7283 8.044908 ACGAAAAGGGATGTATCTAAAGCTAAA 58.955 33.333 0.00 0.00 0.00 1.85
2792 7284 8.889717 CGAAAAGGGATGTATCTAAAGCTAAAA 58.110 33.333 0.00 0.00 0.00 1.52
3127 8980 2.725008 CTCGTCCTCAGGCCGATC 59.275 66.667 0.00 0.00 0.00 3.69
3187 9040 2.110967 CAGGCGCATCAGGTCCTTG 61.111 63.158 10.83 0.00 0.00 3.61
3525 9390 2.159430 TGCATGTGTCGTACAGAATTGC 59.841 45.455 0.00 10.01 43.80 3.56
3680 9553 6.212888 AGTTTGGAAATCATCATGGTTAGC 57.787 37.500 0.00 0.00 0.00 3.09
3746 9623 4.462483 TGATTAAAGGATTTGAGTGGTGCC 59.538 41.667 0.00 0.00 39.63 5.01
3853 9730 7.801716 TTTCATATTATAGCCACTTGGTCAC 57.198 36.000 0.00 0.00 37.57 3.67
3901 9779 1.154197 GACTACGCCCTGTTTGGTTC 58.846 55.000 0.00 0.00 0.00 3.62
3908 9786 2.161609 CGCCCTGTTTGGTTCATAAGTC 59.838 50.000 0.00 0.00 0.00 3.01
3909 9787 2.492088 GCCCTGTTTGGTTCATAAGTCC 59.508 50.000 0.00 0.00 0.00 3.85
3915 9793 5.801380 TGTTTGGTTCATAAGTCCTAGGAC 58.199 41.667 31.29 31.29 44.86 3.85
3960 9838 4.041815 AGTCTCAAGTCCCTAAAAAGTCCC 59.958 45.833 0.00 0.00 0.00 4.46
4022 9901 9.091220 AGACCATATTACAACTATAAGTCCCTC 57.909 37.037 0.00 0.00 0.00 4.30
4024 9903 9.091220 ACCATATTACAACTATAAGTCCCTCTC 57.909 37.037 0.00 0.00 0.00 3.20
4025 9904 9.315363 CCATATTACAACTATAAGTCCCTCTCT 57.685 37.037 0.00 0.00 0.00 3.10
4060 9947 2.733956 TCATAAGTCCCAAATGCCCAC 58.266 47.619 0.00 0.00 0.00 4.61
4073 9961 6.282930 CCAAATGCCCACTTTAAATCCTATG 58.717 40.000 0.00 0.00 0.00 2.23
4109 9997 8.265055 TGTTTGGTTTAGATGAGACTTATAGGG 58.735 37.037 0.00 0.00 0.00 3.53
4111 9999 7.598759 TGGTTTAGATGAGACTTATAGGGAC 57.401 40.000 0.00 0.00 0.00 4.46
4153 10042 3.382083 AAGTCCCTGGAAACAAACACT 57.618 42.857 0.00 0.00 42.06 3.55
4156 10045 2.879026 GTCCCTGGAAACAAACACTCTC 59.121 50.000 0.00 0.00 42.06 3.20
4157 10046 2.777692 TCCCTGGAAACAAACACTCTCT 59.222 45.455 0.00 0.00 42.06 3.10
4158 10047 3.971305 TCCCTGGAAACAAACACTCTCTA 59.029 43.478 0.00 0.00 42.06 2.43
4200 10089 7.337942 ACTTTCTCTAACTTGATGGGCAAATAG 59.662 37.037 0.00 0.00 35.74 1.73
4247 10136 8.516234 TGCTAATGTTTGGTGAATACGTAATTT 58.484 29.630 0.00 0.00 0.00 1.82
4274 10163 6.655930 TGGTAATCTAATACTGTCAAACCCC 58.344 40.000 0.00 0.00 0.00 4.95
4311 10200 2.047655 CTTGCTTCGTGCCCGGTA 60.048 61.111 0.00 0.00 42.00 4.02
4318 10207 1.538075 CTTCGTGCCCGGTAACAAAAT 59.462 47.619 0.00 0.00 33.95 1.82
4367 10256 1.814527 GGTAATCCACGTCCTCGCT 59.185 57.895 0.00 0.00 41.18 4.93
4413 10302 1.786579 GCATTTTTCGCCGCCAATATC 59.213 47.619 0.00 0.00 0.00 1.63
4509 10398 7.657761 AGTTCATCACGAAAAGGATATATGGAC 59.342 37.037 0.00 0.00 34.69 4.02
4510 10399 6.464222 TCATCACGAAAAGGATATATGGACC 58.536 40.000 0.00 0.00 0.00 4.46
4511 10400 5.223449 TCACGAAAAGGATATATGGACCC 57.777 43.478 0.00 0.00 0.00 4.46
4512 10401 4.041198 TCACGAAAAGGATATATGGACCCC 59.959 45.833 0.00 0.00 0.00 4.95
4513 10402 4.041691 CACGAAAAGGATATATGGACCCCT 59.958 45.833 0.00 0.00 0.00 4.79
4605 10874 1.371467 TTCCCTTGCTCTTCATCCCA 58.629 50.000 0.00 0.00 0.00 4.37
4684 10953 1.953559 ACTATTGTATGCAGTGGCGG 58.046 50.000 0.00 0.00 45.35 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 0.108424 GTCTGAAGCACTGATCCGCT 60.108 55.000 0.00 0.00 41.20 5.52
1812 1880 2.622064 AATGCGACAGATAACCCTCC 57.378 50.000 0.00 0.00 0.00 4.30
1899 1971 9.337396 GGTTTCCTAGTGAAAATCCAAAAATTT 57.663 29.630 7.65 0.00 44.30 1.82
2046 2119 1.541588 GCATTTGAACCCTGGTGAGAC 59.458 52.381 0.00 0.00 0.00 3.36
2049 2122 1.619654 CAGCATTTGAACCCTGGTGA 58.380 50.000 0.00 0.00 40.00 4.02
2117 2269 2.097918 GCGTCTCGTCGTCGACAT 59.902 61.111 24.13 0.00 41.35 3.06
2199 5262 0.721154 CGCACACACGCACATTCTAT 59.279 50.000 0.00 0.00 0.00 1.98
2203 5266 1.010125 GAACGCACACACGCACATT 60.010 52.632 0.00 0.00 36.19 2.71
2204 5267 1.506309 ATGAACGCACACACGCACAT 61.506 50.000 0.00 0.00 36.19 3.21
2435 6662 3.244526 TGACTTACTGCATCTGCCTTTGA 60.245 43.478 0.00 0.00 41.18 2.69
2482 6709 1.138266 GGCCTAACTTACGCATCAGGA 59.862 52.381 0.00 0.00 0.00 3.86
2487 6714 2.026641 TCGTAGGCCTAACTTACGCAT 58.973 47.619 15.83 0.00 34.55 4.73
2658 6885 3.674997 ACATGTCCACTCAACCATGTAC 58.325 45.455 0.00 0.00 44.38 2.90
2727 7219 2.730550 TTTTCGGACGAAGGGAGTAC 57.269 50.000 7.25 0.00 35.38 2.73
2736 7228 4.811908 TGATGACAAGTATTTTCGGACGA 58.188 39.130 0.00 0.00 0.00 4.20
2740 7232 7.273381 GTCCATTTTGATGACAAGTATTTTCGG 59.727 37.037 0.00 0.00 37.32 4.30
2741 7233 7.007367 CGTCCATTTTGATGACAAGTATTTTCG 59.993 37.037 0.00 0.00 37.32 3.46
2742 7234 8.020819 TCGTCCATTTTGATGACAAGTATTTTC 58.979 33.333 0.00 0.00 37.32 2.29
2744 7236 7.447374 TCGTCCATTTTGATGACAAGTATTT 57.553 32.000 0.00 0.00 37.32 1.40
2746 7238 7.447374 TTTCGTCCATTTTGATGACAAGTAT 57.553 32.000 0.00 0.00 37.32 2.12
2751 7243 4.022416 CCCTTTTCGTCCATTTTGATGACA 60.022 41.667 0.00 0.00 30.19 3.58
2752 7244 4.217550 TCCCTTTTCGTCCATTTTGATGAC 59.782 41.667 0.00 0.00 30.19 3.06
2756 7248 4.148838 ACATCCCTTTTCGTCCATTTTGA 58.851 39.130 0.00 0.00 0.00 2.69
2757 7249 4.519540 ACATCCCTTTTCGTCCATTTTG 57.480 40.909 0.00 0.00 0.00 2.44
2758 7250 6.187682 AGATACATCCCTTTTCGTCCATTTT 58.812 36.000 0.00 0.00 0.00 1.82
2760 7252 5.373812 AGATACATCCCTTTTCGTCCATT 57.626 39.130 0.00 0.00 0.00 3.16
2761 7253 6.494666 TTAGATACATCCCTTTTCGTCCAT 57.505 37.500 0.00 0.00 0.00 3.41
2763 7255 5.236695 GCTTTAGATACATCCCTTTTCGTCC 59.763 44.000 0.00 0.00 0.00 4.79
2765 7257 5.990668 AGCTTTAGATACATCCCTTTTCGT 58.009 37.500 0.00 0.00 0.00 3.85
2766 7258 8.433421 TTTAGCTTTAGATACATCCCTTTTCG 57.567 34.615 0.00 0.00 0.00 3.46
2808 7300 9.918630 ACTTGTCATCAAAATGAATAAAAGGAG 57.081 29.630 0.00 0.00 43.42 3.69
2816 7308 7.975616 CCGGAAATACTTGTCATCAAAATGAAT 59.024 33.333 0.00 0.00 43.42 2.57
2817 7309 7.175816 TCCGGAAATACTTGTCATCAAAATGAA 59.824 33.333 0.00 0.00 43.42 2.57
2818 7310 6.657117 TCCGGAAATACTTGTCATCAAAATGA 59.343 34.615 0.00 0.00 39.63 2.57
2819 7311 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
2820 7312 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
2821 7313 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
2822 7314 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
2823 7315 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
2824 7316 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
2825 7317 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
2826 7318 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
2827 7319 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
2941 8250 4.142227 GGCATCAGAATTCATGCACTTCTT 60.142 41.667 24.24 0.00 46.19 2.52
2942 8251 3.380637 GGCATCAGAATTCATGCACTTCT 59.619 43.478 24.24 0.00 46.19 2.85
2943 8252 3.490419 GGGCATCAGAATTCATGCACTTC 60.490 47.826 24.24 12.04 44.69 3.01
2984 8837 2.184194 TATCCCCCGTCCTGGAACCA 62.184 60.000 0.00 0.00 42.00 3.67
3283 9148 2.758327 TGGTCGATACAGGCCGCT 60.758 61.111 0.00 0.00 39.14 5.52
3317 9182 3.148084 CGACACCCTGTCCACCTT 58.852 61.111 0.00 0.00 44.20 3.50
3406 9271 0.622665 CACCCTTCTTCAGGCCATCT 59.377 55.000 5.01 0.00 42.29 2.90
3680 9553 8.661352 ATCAATAAACAAAAACAGGGAAACAG 57.339 30.769 0.00 0.00 0.00 3.16
3746 9623 2.376915 TTTGTTTAGCAAGTCGCACG 57.623 45.000 0.00 0.00 46.13 5.34
3775 9652 2.366916 CTCTCCTGCCCATTTATCTCGT 59.633 50.000 0.00 0.00 0.00 4.18
3853 9730 2.357517 GTGCTCACCTCCACACCG 60.358 66.667 0.00 0.00 32.37 4.94
3937 9815 4.041815 GGGACTTTTTAGGGACTTGAGACT 59.958 45.833 0.00 0.00 41.75 3.24
3938 9816 4.041815 AGGGACTTTTTAGGGACTTGAGAC 59.958 45.833 0.00 0.00 34.75 3.36
3939 9817 4.240323 AGGGACTTTTTAGGGACTTGAGA 58.760 43.478 0.00 0.00 34.75 3.27
3940 9818 4.642466 AGGGACTTTTTAGGGACTTGAG 57.358 45.455 0.00 0.00 34.75 3.02
3941 9819 6.030082 AGATAGGGACTTTTTAGGGACTTGA 58.970 40.000 0.00 0.00 39.49 3.02
3960 9838 5.413309 AGTCTCAGGAACCAAACAGATAG 57.587 43.478 0.00 0.00 0.00 2.08
4119 10008 4.524053 CAGGGACTTATTGGTTTAGGGAC 58.476 47.826 0.00 0.00 34.60 4.46
4121 10010 3.526019 TCCAGGGACTTATTGGTTTAGGG 59.474 47.826 0.00 0.00 34.60 3.53
4153 10042 4.098960 AGTGGAACAAGTTTGTCGTAGAGA 59.901 41.667 0.00 0.00 44.16 3.10
4156 10045 5.293569 AGAAAGTGGAACAAGTTTGTCGTAG 59.706 40.000 0.00 0.00 44.16 3.51
4157 10046 5.180271 AGAAAGTGGAACAAGTTTGTCGTA 58.820 37.500 0.00 0.00 44.16 3.43
4158 10047 4.007659 AGAAAGTGGAACAAGTTTGTCGT 58.992 39.130 0.00 0.00 44.16 4.34
4200 10089 3.354089 CCATCATGGTACGGCATTTTC 57.646 47.619 0.00 0.00 31.35 2.29
4247 10136 7.990886 GGGTTTGACAGTATTAGATTACCATCA 59.009 37.037 0.00 0.00 0.00 3.07
4274 10163 5.671329 GCAAGTTTAACTGCTTAGGTCATCG 60.671 44.000 0.00 0.00 0.00 3.84
4311 10200 0.741915 ACGTTCGCCCACATTTTGTT 59.258 45.000 0.00 0.00 0.00 2.83
4413 10302 0.322187 ATGGAACGAAACGGGGAAGG 60.322 55.000 0.00 0.00 0.00 3.46
4512 10401 4.179599 GAGGGGAGGGGAGGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
4605 10874 1.642762 ACTTCATCCTCCCCTTGCAAT 59.357 47.619 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.