Multiple sequence alignment - TraesCS5B01G455400

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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 TraesCS5B01G455400 chr5B 100.000 3449 0 0 1 3449 629859257 629855809 0.000000e+00 6370.0
1 TraesCS5B01G455400 chr5B 96.312 2549 83 5 1 2546 623150410 623147870 0.000000e+00 4176.0
2 TraesCS5B01G455400 chr5B 95.842 2549 80 10 1 2546 626815102 626812577 0.000000e+00 4096.0
3 TraesCS5B01G455400 chr5B 85.240 1565 166 28 964 2492 629280203 629281738 0.000000e+00 1550.0
4 TraesCS5B01G455400 chr5B 85.240 1565 166 28 964 2492 629362497 629364032 0.000000e+00 1550.0
5 TraesCS5B01G455400 chr5B 91.397 1081 87 4 954 2031 633260188 633261265 0.000000e+00 1476.0
6 TraesCS5B01G455400 chr5B 91.812 916 63 4 1075 1984 630143801 630142892 0.000000e+00 1266.0
7 TraesCS5B01G455400 chr5B 94.444 792 32 2 1924 2715 628667813 628667034 0.000000e+00 1208.0
8 TraesCS5B01G455400 chr5B 94.192 792 34 2 1924 2715 625088207 625087428 0.000000e+00 1197.0
9 TraesCS5B01G455400 chr5B 90.459 849 69 5 963 1811 628668648 628667812 0.000000e+00 1109.0
10 TraesCS5B01G455400 chr5B 90.106 849 68 9 963 1811 625089038 625088206 0.000000e+00 1088.0
11 TraesCS5B01G455400 chr5B 78.267 1385 216 33 1117 2444 638678040 638679396 0.000000e+00 811.0
12 TraesCS5B01G455400 chr5B 93.042 503 28 3 2131 2633 633262670 633263165 0.000000e+00 728.0
13 TraesCS5B01G455400 chr5B 88.850 565 45 10 3 553 633258204 633258764 0.000000e+00 678.0
14 TraesCS5B01G455400 chr5B 91.355 428 21 7 3 423 625093661 625093243 3.860000e-159 571.0
15 TraesCS5B01G455400 chr5B 90.654 428 23 8 3 423 628673209 628672792 1.400000e-153 553.0
16 TraesCS5B01G455400 chr5B 80.705 596 103 7 1715 2307 631026868 631027454 1.460000e-123 453.0
17 TraesCS5B01G455400 chr5B 78.983 747 82 33 2718 3428 381058123 381058830 1.140000e-119 440.0
18 TraesCS5B01G455400 chr5B 80.682 528 68 16 1979 2494 630138720 630138215 2.510000e-101 379.0
19 TraesCS5B01G455400 chr5B 79.630 378 67 7 1117 1489 623139853 623139481 2.640000e-66 263.0
20 TraesCS5B01G455400 chr5B 79.630 378 67 7 1117 1489 626804290 626803918 2.640000e-66 263.0
21 TraesCS5B01G455400 chr5B 74.659 367 81 11 2086 2447 604717994 604717635 5.960000e-33 152.0
22 TraesCS5B01G455400 chr5B 94.565 92 4 1 2624 2715 623147870 623147780 1.290000e-29 141.0
23 TraesCS5B01G455400 chr5B 94.565 92 4 1 2624 2715 626812577 626812487 1.290000e-29 141.0
24 TraesCS5B01G455400 chr5D 90.917 1090 84 9 954 2031 501447024 501445938 0.000000e+00 1450.0
25 TraesCS5B01G455400 chr5D 93.439 503 26 3 2131 2633 501444519 501444024 0.000000e+00 739.0
26 TraesCS5B01G455400 chr5D 89.540 239 18 3 106 342 501447919 501447686 2.600000e-76 296.0
27 TraesCS5B01G455400 chr5D 96.825 126 4 0 2022 2147 501445718 501445843 9.700000e-51 211.0
28 TraesCS5B01G455400 chr5D 84.390 205 20 7 373 567 501447687 501447485 1.260000e-44 191.0
29 TraesCS5B01G455400 chr5D 73.569 367 85 12 2086 2447 498928263 498927904 2.790000e-26 130.0
30 TraesCS5B01G455400 chr5D 94.118 51 2 1 2398 2447 501709490 501709440 3.690000e-10 76.8
31 TraesCS5B01G455400 chr3A 80.888 743 78 30 2719 3428 691394485 691393774 8.480000e-146 527.0
32 TraesCS5B01G455400 chr3A 79.357 746 82 32 2719 3428 743689950 743690659 3.140000e-125 459.0
33 TraesCS5B01G455400 chr3A 79.032 744 80 40 2720 3428 525290540 525289838 1.140000e-119 440.0
34 TraesCS5B01G455400 chr5A 82.927 574 54 20 196 755 625758646 625759189 8.660000e-131 477.0
35 TraesCS5B01G455400 chr5A 91.843 331 27 0 957 1287 625759721 625760051 2.420000e-126 462.0
36 TraesCS5B01G455400 chr5A 91.133 203 15 2 1 201 625755748 625755949 4.390000e-69 272.0
37 TraesCS5B01G455400 chr7D 86.927 436 37 14 3025 3449 32340755 32340329 4.030000e-129 472.0
38 TraesCS5B01G455400 chr7D 97.674 43 0 1 2635 2677 378169049 378169008 4.770000e-09 73.1
39 TraesCS5B01G455400 chr7D 95.122 41 1 1 2636 2676 138285164 138285203 2.870000e-06 63.9
40 TraesCS5B01G455400 chr6A 79.463 745 86 33 2720 3428 236358804 236359517 1.870000e-127 466.0
41 TraesCS5B01G455400 chr7B 85.827 381 25 13 3096 3449 631236081 631235703 9.040000e-101 377.0
42 TraesCS5B01G455400 chr7B 79.065 449 53 16 2711 3138 631234343 631234771 1.580000e-68 270.0
43 TraesCS5B01G455400 chr7B 84.967 153 13 4 2854 2996 631236228 631236076 2.770000e-31 147.0
44 TraesCS5B01G455400 chr7B 91.667 48 4 0 2798 2845 631236302 631236255 2.220000e-07 67.6
45 TraesCS5B01G455400 chr7B 93.023 43 0 2 2635 2677 372827847 372827808 3.720000e-05 60.2
46 TraesCS5B01G455400 chr1A 92.776 263 11 3 3194 3449 585681342 585681603 1.170000e-99 374.0
47 TraesCS5B01G455400 chr1A 80.706 425 41 15 2720 3132 585682854 585682459 3.370000e-75 292.0
48 TraesCS5B01G455400 chr2D 81.236 437 41 25 2716 3143 571773287 571773691 7.190000e-82 315.0
49 TraesCS5B01G455400 chr2D 77.828 442 58 21 2718 3143 567802914 567803331 1.600000e-58 237.0
50 TraesCS5B01G455400 chr2D 89.256 121 7 3 3227 3347 571777383 571777497 2.770000e-31 147.0
51 TraesCS5B01G455400 chr6B 80.137 438 52 19 2720 3143 436502364 436502780 9.360000e-76 294.0
52 TraesCS5B01G455400 chr4B 95.238 105 4 1 3346 3449 405328227 405328331 7.660000e-37 165.0
53 TraesCS5B01G455400 chr4B 93.478 46 2 1 2632 2676 645330099 645330144 2.220000e-07 67.6
54 TraesCS5B01G455400 chrUn 95.652 46 1 1 2633 2677 10263767 10263812 4.770000e-09 73.1
55 TraesCS5B01G455400 chr7A 92.157 51 3 1 2627 2677 425783309 425783260 1.720000e-08 71.3
56 TraesCS5B01G455400 chr1B 95.000 40 0 2 2638 2677 650445196 650445233 1.030000e-05 62.1
57 TraesCS5B01G455400 chr2A 100.000 30 0 0 2837 2866 18183957 18183986 4.810000e-04 56.5


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 TraesCS5B01G455400 chr5B 629855809 629859257 3448 True 6370.000000 6370 100.000000 1 3449 1 chr5B.!!$R6 3448
1 TraesCS5B01G455400 chr5B 623147780 623150410 2630 True 2158.500000 4176 95.438500 1 2715 2 chr5B.!!$R9 2714
2 TraesCS5B01G455400 chr5B 626812487 626815102 2615 True 2118.500000 4096 95.203500 1 2715 2 chr5B.!!$R11 2714
3 TraesCS5B01G455400 chr5B 629280203 629281738 1535 False 1550.000000 1550 85.240000 964 2492 1 chr5B.!!$F2 1528
4 TraesCS5B01G455400 chr5B 629362497 629364032 1535 False 1550.000000 1550 85.240000 964 2492 1 chr5B.!!$F3 1528
5 TraesCS5B01G455400 chr5B 630142892 630143801 909 True 1266.000000 1266 91.812000 1075 1984 1 chr5B.!!$R8 909
6 TraesCS5B01G455400 chr5B 628667034 628668648 1614 True 1158.500000 1208 92.451500 963 2715 2 chr5B.!!$R12 1752
7 TraesCS5B01G455400 chr5B 625087428 625089038 1610 True 1142.500000 1197 92.149000 963 2715 2 chr5B.!!$R10 1752
8 TraesCS5B01G455400 chr5B 633258204 633263165 4961 False 960.666667 1476 91.096333 3 2633 3 chr5B.!!$F6 2630
9 TraesCS5B01G455400 chr5B 638678040 638679396 1356 False 811.000000 811 78.267000 1117 2444 1 chr5B.!!$F5 1327
10 TraesCS5B01G455400 chr5B 631026868 631027454 586 False 453.000000 453 80.705000 1715 2307 1 chr5B.!!$F4 592
11 TraesCS5B01G455400 chr5B 381058123 381058830 707 False 440.000000 440 78.983000 2718 3428 1 chr5B.!!$F1 710
12 TraesCS5B01G455400 chr5B 630138215 630138720 505 True 379.000000 379 80.682000 1979 2494 1 chr5B.!!$R7 515
13 TraesCS5B01G455400 chr5D 501444024 501447919 3895 True 669.000000 1450 89.571500 106 2633 4 chr5D.!!$R3 2527
14 TraesCS5B01G455400 chr3A 691393774 691394485 711 True 527.000000 527 80.888000 2719 3428 1 chr3A.!!$R2 709
15 TraesCS5B01G455400 chr3A 743689950 743690659 709 False 459.000000 459 79.357000 2719 3428 1 chr3A.!!$F1 709
16 TraesCS5B01G455400 chr3A 525289838 525290540 702 True 440.000000 440 79.032000 2720 3428 1 chr3A.!!$R1 708
17 TraesCS5B01G455400 chr5A 625755748 625760051 4303 False 403.666667 477 88.634333 1 1287 3 chr5A.!!$F1 1286
18 TraesCS5B01G455400 chr6A 236358804 236359517 713 False 466.000000 466 79.463000 2720 3428 1 chr6A.!!$F1 708
19 TraesCS5B01G455400 chr2D 571773287 571777497 4210 False 231.000000 315 85.246000 2716 3347 2 chr2D.!!$F2 631

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
583 3301 0.863144 GTACACCTCGCTTGCGAAAA 59.137 50.0 18.28 0.0 0.00 2.29 F
1386 5313 0.388649 CCGACAAAGACCTCGTCCTG 60.389 60.0 0.00 0.0 32.18 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2166 7453 0.033090 GGAACTCGGGAAGACGTTGT 59.967 55.0 0.0 0.0 34.94 3.32 R
3244 12175 0.035439 ATGGGTGGATGGAACGACAC 60.035 55.0 0.0 0.0 0.00 3.67 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
583 3301 0.863144 GTACACCTCGCTTGCGAAAA 59.137 50.000 18.28 0.00 0.00 2.29
997 4876 2.935676 GCTTTATTCCCGATCCCGATCC 60.936 54.545 0.00 0.00 38.22 3.36
1072 4969 3.946242 TCCGATTGGGAGATGGAGA 57.054 52.632 0.00 0.00 40.94 3.71
1080 4977 1.366082 TGGGAGATGGAGAAGGAGGAA 59.634 52.381 0.00 0.00 0.00 3.36
1386 5313 0.388649 CCGACAAAGACCTCGTCCTG 60.389 60.000 0.00 0.00 32.18 3.86
1494 5427 1.071385 GTGCAGCAGCTCCCTATGTAT 59.929 52.381 1.76 0.00 42.74 2.29
1803 5753 2.089980 GACTACTTCAGCGGTGTCCTA 58.910 52.381 15.22 1.56 0.00 2.94
2010 5972 2.124570 GACTGGCCATGGCGTCAT 60.125 61.111 29.32 17.62 43.06 3.06
2054 6019 4.512914 GCAGCATCAGGGTCCCCC 62.513 72.222 3.51 0.00 45.90 5.40
2166 7453 1.320344 ACGAAGCTCTGGGCATACGA 61.320 55.000 16.69 0.00 44.79 3.43
2169 7456 0.613260 AAGCTCTGGGCATACGACAA 59.387 50.000 0.74 0.00 44.79 3.18
2202 7489 2.158959 CCCAATCGTCAGCGTCGAC 61.159 63.158 5.18 5.18 40.07 4.20
2577 7869 5.426689 TGCATCAAGTTGTCCTAGAATCT 57.573 39.130 2.11 0.00 0.00 2.40
2800 8095 6.978343 AAAAATCGAAACTATGATCCGTCA 57.022 33.333 0.00 0.00 39.04 4.35
2803 8098 1.781429 CGAAACTATGATCCGTCAGCG 59.219 52.381 0.00 0.00 37.87 5.18
2808 8103 2.152016 CTATGATCCGTCAGCGTCCTA 58.848 52.381 0.00 0.00 37.87 2.94
2848 8143 4.484872 GCCTACCGTTGGCCTCCC 62.485 72.222 12.50 0.00 44.32 4.30
2849 8144 3.006728 CCTACCGTTGGCCTCCCA 61.007 66.667 3.32 0.00 40.06 4.37
2871 8184 3.298958 CCGAAGAGTGGCCAGCTA 58.701 61.111 5.11 0.00 0.00 3.32
2890 8203 3.757493 GCTAGGCCGAAGATAGTAGCTTA 59.243 47.826 11.92 0.00 32.00 3.09
2893 8206 2.231721 GGCCGAAGATAGTAGCTTAGGG 59.768 54.545 23.43 17.45 38.22 3.53
2894 8207 2.231721 GCCGAAGATAGTAGCTTAGGGG 59.768 54.545 23.43 15.43 38.22 4.79
2895 8208 2.231721 CCGAAGATAGTAGCTTAGGGGC 59.768 54.545 16.95 0.00 35.34 5.80
2896 8209 2.231721 CGAAGATAGTAGCTTAGGGGCC 59.768 54.545 0.00 0.00 0.00 5.80
2897 8210 1.926108 AGATAGTAGCTTAGGGGCCG 58.074 55.000 0.00 0.00 0.00 6.13
2898 8211 1.428139 AGATAGTAGCTTAGGGGCCGA 59.572 52.381 0.00 0.00 0.00 5.54
2900 8213 1.700955 TAGTAGCTTAGGGGCCGAAG 58.299 55.000 11.45 11.45 0.00 3.79
2901 8214 0.032416 AGTAGCTTAGGGGCCGAAGA 60.032 55.000 18.22 0.00 31.70 2.87
2902 8215 0.389757 GTAGCTTAGGGGCCGAAGAG 59.610 60.000 18.22 5.86 31.70 2.85
2903 8216 0.032416 TAGCTTAGGGGCCGAAGAGT 60.032 55.000 18.22 8.54 31.70 3.24
2904 8217 1.153349 GCTTAGGGGCCGAAGAGTG 60.153 63.158 18.22 0.00 31.70 3.51
2905 8218 1.522569 CTTAGGGGCCGAAGAGTGG 59.477 63.158 10.50 0.00 31.70 4.00
2906 8219 1.229400 TTAGGGGCCGAAGAGTGGT 60.229 57.895 0.00 0.00 0.00 4.16
2907 8220 1.262640 TTAGGGGCCGAAGAGTGGTC 61.263 60.000 0.00 0.00 0.00 4.02
2908 8221 2.164332 TAGGGGCCGAAGAGTGGTCT 62.164 60.000 0.00 0.00 32.81 3.85
2909 8222 2.593956 GGGGCCGAAGAGTGGTCTT 61.594 63.158 0.00 0.00 46.32 3.01
2915 8228 2.657237 AAGAGTGGTCTTCGGCCG 59.343 61.111 22.12 22.12 38.84 6.13
2916 8229 2.207924 AAGAGTGGTCTTCGGCCGT 61.208 57.895 27.15 1.71 38.84 5.68
2917 8230 2.432628 GAGTGGTCTTCGGCCGTG 60.433 66.667 27.15 19.13 0.00 4.94
2918 8231 3.222354 GAGTGGTCTTCGGCCGTGT 62.222 63.158 27.15 2.87 0.00 4.49
2919 8232 3.041940 GTGGTCTTCGGCCGTGTG 61.042 66.667 27.15 16.13 0.00 3.82
2920 8233 3.542676 TGGTCTTCGGCCGTGTGT 61.543 61.111 27.15 0.00 0.00 3.72
2921 8234 2.201708 TGGTCTTCGGCCGTGTGTA 61.202 57.895 27.15 1.01 0.00 2.90
2946 8259 0.321996 AAGAGTGGTCTTCGGCTTCC 59.678 55.000 0.00 0.00 38.84 3.46
2948 8261 0.321996 GAGTGGTCTTCGGCTTCCTT 59.678 55.000 0.00 0.00 0.00 3.36
2961 8274 1.657822 CTTCCTTAAGGCCGAAGAGC 58.342 55.000 17.32 0.00 35.99 4.09
2973 8287 4.514577 AAGAGCGCCGGACCATCG 62.515 66.667 5.05 0.00 0.00 3.84
2997 8311 4.099170 GTTGCCTCGCTGCAGCAG 62.099 66.667 36.03 28.77 43.21 4.24
2998 8312 4.631247 TTGCCTCGCTGCAGCAGT 62.631 61.111 36.03 0.00 43.21 4.40
3017 8331 3.481903 CAGCTGCACGTACGCTGG 61.482 66.667 16.72 6.49 45.47 4.85
3018 8332 3.991051 AGCTGCACGTACGCTGGT 61.991 61.111 16.72 6.84 36.83 4.00
3019 8333 3.041940 GCTGCACGTACGCTGGTT 61.042 61.111 16.72 0.00 0.00 3.67
3020 8334 2.853210 CTGCACGTACGCTGGTTG 59.147 61.111 16.72 6.83 0.00 3.77
3021 8335 2.663520 TGCACGTACGCTGGTTGG 60.664 61.111 16.72 0.00 0.00 3.77
3022 8336 4.084888 GCACGTACGCTGGTTGGC 62.085 66.667 16.72 4.23 0.00 4.52
3023 8337 2.357034 CACGTACGCTGGTTGGCT 60.357 61.111 16.72 0.00 0.00 4.75
3024 8338 1.959226 CACGTACGCTGGTTGGCTT 60.959 57.895 16.72 0.00 0.00 4.35
3025 8339 1.959226 ACGTACGCTGGTTGGCTTG 60.959 57.895 16.72 0.00 0.00 4.01
3026 8340 2.677003 CGTACGCTGGTTGGCTTGG 61.677 63.158 0.52 0.00 0.00 3.61
3027 8341 2.671619 TACGCTGGTTGGCTTGGC 60.672 61.111 0.00 0.00 0.00 4.52
3028 8342 3.190738 TACGCTGGTTGGCTTGGCT 62.191 57.895 0.00 0.00 0.00 4.75
3029 8343 4.047059 CGCTGGTTGGCTTGGCTG 62.047 66.667 0.00 0.00 0.00 4.85
3030 8344 3.688159 GCTGGTTGGCTTGGCTGG 61.688 66.667 0.00 0.00 0.00 4.85
3103 8425 0.035820 TCTCACATGCATGCAGCTGA 60.036 50.000 26.69 24.12 45.94 4.26
3114 8437 0.963225 TGCAGCTGAACGTACCTGTA 59.037 50.000 20.43 0.00 0.00 2.74
3176 8517 5.671493 GTTGGTGGTGCTACTGTATTATCT 58.329 41.667 0.00 0.00 0.00 1.98
3178 8519 6.650427 TGGTGGTGCTACTGTATTATCTAG 57.350 41.667 0.00 0.00 0.00 2.43
3179 8520 6.370453 TGGTGGTGCTACTGTATTATCTAGA 58.630 40.000 0.00 0.00 0.00 2.43
3180 8521 6.490381 TGGTGGTGCTACTGTATTATCTAGAG 59.510 42.308 0.00 0.00 0.00 2.43
3181 8522 6.490721 GGTGGTGCTACTGTATTATCTAGAGT 59.509 42.308 0.00 0.00 0.00 3.24
3182 8523 7.664731 GGTGGTGCTACTGTATTATCTAGAGTA 59.335 40.741 0.00 0.00 0.00 2.59
3183 8524 9.064706 GTGGTGCTACTGTATTATCTAGAGTAA 57.935 37.037 0.00 0.00 0.00 2.24
3244 12175 2.881074 ACAGACTCGATGGAATTGACG 58.119 47.619 0.00 0.00 32.08 4.35
3285 12216 2.490991 CATCGATCTCACATGGCATGT 58.509 47.619 26.78 26.78 46.22 3.21
3286 12217 2.696989 TCGATCTCACATGGCATGTT 57.303 45.000 29.57 16.07 42.70 2.71
3287 12218 2.989909 TCGATCTCACATGGCATGTTT 58.010 42.857 29.57 14.94 42.70 2.83
3288 12219 2.679336 TCGATCTCACATGGCATGTTTG 59.321 45.455 29.57 22.99 42.70 2.93
3348 12285 2.172679 TGGAGACGGTAGTGCATGTAA 58.827 47.619 0.00 0.00 0.00 2.41
3359 12296 6.740002 CGGTAGTGCATGTAATATCTACGTAC 59.260 42.308 0.19 0.00 31.65 3.67
3387 12324 1.816835 AGAGTGCTTTGCATGTGGATG 59.183 47.619 0.00 0.00 41.91 3.51
3424 12362 5.609533 ACTAGTACCGTGCAGGATTATTT 57.390 39.130 8.24 0.00 45.00 1.40
3428 12366 1.476488 ACCGTGCAGGATTATTTTGCC 59.524 47.619 8.24 0.00 45.00 4.52
3429 12367 1.476085 CCGTGCAGGATTATTTTGCCA 59.524 47.619 8.24 0.00 45.00 4.92
3430 12368 2.094286 CCGTGCAGGATTATTTTGCCAA 60.094 45.455 8.24 0.00 45.00 4.52
3431 12369 3.430651 CCGTGCAGGATTATTTTGCCAAT 60.431 43.478 8.24 0.00 45.00 3.16
3432 12370 3.798337 CGTGCAGGATTATTTTGCCAATC 59.202 43.478 0.00 0.00 37.03 2.67
3433 12371 4.677514 CGTGCAGGATTATTTTGCCAATCA 60.678 41.667 0.00 0.00 37.03 2.57
3434 12372 4.567959 GTGCAGGATTATTTTGCCAATCAC 59.432 41.667 0.00 0.00 37.03 3.06
3435 12373 3.798337 GCAGGATTATTTTGCCAATCACG 59.202 43.478 0.00 0.00 33.64 4.35
3436 12374 4.677779 GCAGGATTATTTTGCCAATCACGT 60.678 41.667 0.00 0.00 33.64 4.49
3437 12375 4.799949 CAGGATTATTTTGCCAATCACGTG 59.200 41.667 9.94 9.94 33.64 4.49
3438 12376 3.551485 GGATTATTTTGCCAATCACGTGC 59.449 43.478 11.67 0.00 33.64 5.34
3439 12377 3.650070 TTATTTTGCCAATCACGTGCA 57.350 38.095 11.67 1.19 0.00 4.57
3440 12378 2.522836 ATTTTGCCAATCACGTGCAA 57.477 40.000 11.67 8.53 42.77 4.08
3441 12379 1.850377 TTTTGCCAATCACGTGCAAG 58.150 45.000 11.67 0.00 44.85 4.01
3442 12380 0.743688 TTTGCCAATCACGTGCAAGT 59.256 45.000 11.67 0.00 44.85 3.16
3443 12381 0.030504 TTGCCAATCACGTGCAAGTG 59.969 50.000 24.56 24.56 39.86 3.16
3444 12382 1.730547 GCCAATCACGTGCAAGTGC 60.731 57.895 25.51 11.62 41.61 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1072 4969 1.007842 GGTCTCCTCCTCTTCCTCCTT 59.992 57.143 0.00 0.00 0.00 3.36
1080 4977 1.078285 GACGTCGGTCTCCTCCTCT 60.078 63.158 0.00 0.00 40.15 3.69
1494 5427 2.840203 ATTTCCCCCTCTCCTCGGCA 62.840 60.000 0.00 0.00 0.00 5.69
1803 5753 1.474879 GCGGAAGAGAAGTCAGCTAGT 59.525 52.381 0.00 0.00 33.95 2.57
1854 5810 4.270834 GGTATTCCTTTTCTCCAGGGAAC 58.729 47.826 0.00 0.00 40.10 3.62
2010 5972 1.187087 GGCTTCTTCTCTCGGGAAGA 58.813 55.000 5.16 5.16 46.57 2.87
2054 6019 8.090214 AGTTCAAAGTCCATATGGTGATTTTTG 58.910 33.333 21.28 20.68 36.34 2.44
2166 7453 0.033090 GGAACTCGGGAAGACGTTGT 59.967 55.000 0.00 0.00 34.94 3.32
2169 7456 1.117142 TTGGGAACTCGGGAAGACGT 61.117 55.000 0.00 0.00 34.94 4.34
2202 7489 1.466167 CAGCAAAGAACATCTGGGTCG 59.534 52.381 0.00 0.00 0.00 4.79
2300 7587 8.690884 AGGAATGTCGATTGATATATGGAGTAG 58.309 37.037 0.00 0.00 0.00 2.57
2639 7932 2.236395 GGATGTCCCCTCTTTTCGAAGA 59.764 50.000 0.00 0.00 0.00 2.87
2640 7933 2.633488 GGATGTCCCCTCTTTTCGAAG 58.367 52.381 0.00 0.00 0.00 3.79
2762 8056 9.269415 GTTTCGATTTTTATGTATTAGTGCGTT 57.731 29.630 0.00 0.00 0.00 4.84
2784 8078 2.789893 GACGCTGACGGATCATAGTTTC 59.210 50.000 0.00 0.00 46.04 2.78
2797 8091 4.126524 GGCCAATAGGACGCTGAC 57.873 61.111 0.00 0.00 36.89 3.51
2803 8098 0.106894 CCCTCTTCGGCCAATAGGAC 59.893 60.000 16.10 0.00 40.75 3.85
2845 8140 1.299648 CACTCTTCGGCCAATGGGA 59.700 57.895 2.24 0.00 35.59 4.37
2846 8141 1.750399 CCACTCTTCGGCCAATGGG 60.750 63.158 2.24 0.00 37.18 4.00
2847 8142 2.409870 GCCACTCTTCGGCCAATGG 61.410 63.158 2.24 0.00 44.22 3.16
2848 8143 3.190878 GCCACTCTTCGGCCAATG 58.809 61.111 2.24 0.00 44.22 2.82
2871 8184 3.158676 CCTAAGCTACTATCTTCGGCCT 58.841 50.000 0.00 0.00 0.00 5.19
2890 8203 3.003763 GACCACTCTTCGGCCCCT 61.004 66.667 0.00 0.00 0.00 4.79
2893 8206 4.600207 GAAGACCACTCTTCGGCC 57.400 61.111 0.00 0.00 42.40 6.13
2897 8210 1.446272 CGGCCGAAGACCACTCTTC 60.446 63.158 24.07 1.04 46.42 2.87
2898 8211 2.207924 ACGGCCGAAGACCACTCTT 61.208 57.895 35.90 0.00 39.64 2.85
2900 8213 2.432628 CACGGCCGAAGACCACTC 60.433 66.667 35.90 0.00 0.00 3.51
2901 8214 3.231736 ACACGGCCGAAGACCACT 61.232 61.111 35.90 2.60 0.00 4.00
2902 8215 2.424705 TACACACGGCCGAAGACCAC 62.425 60.000 35.90 0.00 0.00 4.16
2903 8216 2.149803 CTACACACGGCCGAAGACCA 62.150 60.000 35.90 11.02 0.00 4.02
2904 8217 1.445582 CTACACACGGCCGAAGACC 60.446 63.158 35.90 0.00 0.00 3.85
2905 8218 0.731855 GTCTACACACGGCCGAAGAC 60.732 60.000 35.90 27.28 0.00 3.01
2906 8219 1.582968 GTCTACACACGGCCGAAGA 59.417 57.895 35.90 21.36 0.00 2.87
2907 8220 1.445582 GGTCTACACACGGCCGAAG 60.446 63.158 35.90 25.60 0.00 3.79
2908 8221 2.652530 GGTCTACACACGGCCGAA 59.347 61.111 35.90 10.40 0.00 4.30
2909 8222 3.740397 CGGTCTACACACGGCCGA 61.740 66.667 35.90 7.96 44.57 5.54
2910 8223 3.271706 TTCGGTCTACACACGGCCG 62.272 63.158 26.86 26.86 43.32 6.13
2911 8224 1.445582 CTTCGGTCTACACACGGCC 60.446 63.158 0.00 0.00 0.00 6.13
2912 8225 0.456312 CTCTTCGGTCTACACACGGC 60.456 60.000 0.00 0.00 0.00 5.68
2913 8226 0.879765 ACTCTTCGGTCTACACACGG 59.120 55.000 0.00 0.00 0.00 4.94
2914 8227 1.401148 CCACTCTTCGGTCTACACACG 60.401 57.143 0.00 0.00 0.00 4.49
2915 8228 1.612463 ACCACTCTTCGGTCTACACAC 59.388 52.381 0.00 0.00 27.30 3.82
2916 8229 1.991121 ACCACTCTTCGGTCTACACA 58.009 50.000 0.00 0.00 27.30 3.72
2946 8259 3.400007 GCGCTCTTCGGCCTTAAG 58.600 61.111 0.00 4.64 38.94 1.85
2980 8294 4.099170 CTGCTGCAGCGAGGCAAC 62.099 66.667 32.11 5.47 44.40 4.17
3001 8315 3.515316 AACCAGCGTACGTGCAGCT 62.515 57.895 17.90 14.74 42.64 4.24
3002 8316 3.041940 AACCAGCGTACGTGCAGC 61.042 61.111 17.90 8.31 37.31 5.25
3003 8317 2.667318 CCAACCAGCGTACGTGCAG 61.667 63.158 17.90 6.18 37.31 4.41
3014 8328 3.688159 GCCAGCCAAGCCAACCAG 61.688 66.667 0.00 0.00 0.00 4.00
3015 8329 4.223125 AGCCAGCCAAGCCAACCA 62.223 61.111 0.00 0.00 0.00 3.67
3016 8330 3.688159 CAGCCAGCCAAGCCAACC 61.688 66.667 0.00 0.00 0.00 3.77
3017 8331 3.688159 CCAGCCAGCCAAGCCAAC 61.688 66.667 0.00 0.00 0.00 3.77
3021 8335 4.065281 CAAGCCAGCCAGCCAAGC 62.065 66.667 0.00 0.00 0.00 4.01
3022 8336 4.065281 GCAAGCCAGCCAGCCAAG 62.065 66.667 0.00 0.00 0.00 3.61
3023 8337 4.608774 AGCAAGCCAGCCAGCCAA 62.609 61.111 0.85 0.00 34.23 4.52
3056 8378 3.321111 TCCATATCCACGAGTAAAGGCTC 59.679 47.826 0.00 0.00 0.00 4.70
3103 8425 3.167485 TGGATGGAACTACAGGTACGTT 58.833 45.455 0.00 0.00 0.00 3.99
3114 8437 3.033909 TGTGAGATCGATGGATGGAACT 58.966 45.455 0.54 0.00 31.51 3.01
3176 8517 5.089970 ACATGCTGCAAGTGATTACTCTA 57.910 39.130 9.99 0.00 35.69 2.43
3178 8519 3.064545 GGACATGCTGCAAGTGATTACTC 59.935 47.826 15.87 0.00 35.69 2.59
3179 8520 3.012518 GGACATGCTGCAAGTGATTACT 58.987 45.455 15.87 0.00 39.32 2.24
3180 8521 2.098117 GGGACATGCTGCAAGTGATTAC 59.902 50.000 15.87 0.20 35.30 1.89
3181 8522 2.290832 TGGGACATGCTGCAAGTGATTA 60.291 45.455 15.87 0.00 35.30 1.75
3182 8523 1.180029 GGGACATGCTGCAAGTGATT 58.820 50.000 15.87 0.00 35.30 2.57
3183 8524 0.038599 TGGGACATGCTGCAAGTGAT 59.961 50.000 15.87 0.00 35.30 3.06
3185 8526 0.607217 TCTGGGACATGCTGCAAGTG 60.607 55.000 15.87 8.50 38.20 3.16
3186 8527 0.607489 GTCTGGGACATGCTGCAAGT 60.607 55.000 10.61 10.61 38.20 3.16
3187 8528 1.642037 CGTCTGGGACATGCTGCAAG 61.642 60.000 6.36 4.49 38.20 4.01
3188 8529 1.672030 CGTCTGGGACATGCTGCAA 60.672 57.895 6.36 0.00 38.20 4.08
3190 8531 3.503363 GCGTCTGGGACATGCTGC 61.503 66.667 0.00 0.00 38.20 5.25
3191 8532 1.812922 GAGCGTCTGGGACATGCTG 60.813 63.158 0.00 0.00 40.36 4.41
3192 8533 2.581354 GAGCGTCTGGGACATGCT 59.419 61.111 0.00 1.03 42.35 3.79
3244 12175 0.035439 ATGGGTGGATGGAACGACAC 60.035 55.000 0.00 0.00 0.00 3.67
3285 12216 2.033550 GGTGGACGTACAAACATGCAAA 59.966 45.455 0.00 0.00 0.00 3.68
3286 12217 1.604755 GGTGGACGTACAAACATGCAA 59.395 47.619 0.00 0.00 0.00 4.08
3287 12218 1.231221 GGTGGACGTACAAACATGCA 58.769 50.000 0.00 0.00 0.00 3.96
3288 12219 1.069500 GTGGTGGACGTACAAACATGC 60.069 52.381 0.00 0.00 0.00 4.06
3289 12220 1.193650 CGTGGTGGACGTACAAACATG 59.806 52.381 0.00 6.80 43.50 3.21
3290 12221 1.504359 CGTGGTGGACGTACAAACAT 58.496 50.000 0.00 0.00 43.50 2.71
3291 12222 2.974845 CGTGGTGGACGTACAAACA 58.025 52.632 0.00 1.33 43.50 2.83
3368 12305 1.542915 ACATCCACATGCAAAGCACTC 59.457 47.619 0.00 0.00 43.04 3.51
3387 12324 9.279904 CACGGTACTAGTATACGTAGATAGTAC 57.720 40.741 27.05 27.05 43.99 2.73
3409 12346 1.476085 TGGCAAAATAATCCTGCACGG 59.524 47.619 0.00 0.00 37.83 4.94
3424 12362 0.030504 CACTTGCACGTGATTGGCAA 59.969 50.000 22.23 14.80 44.50 4.52


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

AutoCloner maintained by Alex Coulton.