Multiple sequence alignment - TraesCS5B01G165000

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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 TraesCS5B01G165000 chr5B 100.000 2848 0 0 1 2848 305049890 305047043 0.000000e+00 5260.0
1 TraesCS5B01G165000 chr5B 85.161 155 23 0 1246 1400 526991932 526991778 3.260000e-35 159.0
2 TraesCS5B01G165000 chr5B 85.161 155 23 0 1246 1400 527015312 527015158 3.260000e-35 159.0
3 TraesCS5B01G165000 chr5B 100.000 77 0 0 3078 3154 305046813 305046737 3.280000e-30 143.0
4 TraesCS5B01G165000 chr5D 96.037 1615 51 7 1183 2796 269295762 269294160 0.000000e+00 2615.0
5 TraesCS5B01G165000 chr5D 87.360 625 31 18 560 1162 269296436 269295838 0.000000e+00 673.0
6 TraesCS5B01G165000 chr5D 83.878 490 65 12 88 568 269297301 269296817 3.710000e-124 455.0
7 TraesCS5B01G165000 chr5D 91.441 222 18 1 1 222 269297427 269297207 1.420000e-78 303.0
8 TraesCS5B01G165000 chr5D 91.525 59 4 1 261 318 521491041 521491099 2.610000e-11 80.5
9 TraesCS5B01G165000 chr5D 89.091 55 6 0 264 318 535725833 535725887 5.640000e-08 69.4
10 TraesCS5B01G165000 chr5A 94.340 1219 42 9 1183 2393 357807163 357805964 0.000000e+00 1844.0
11 TraesCS5B01G165000 chr5A 94.086 372 10 4 791 1162 357807599 357807240 3.550000e-154 555.0
12 TraesCS5B01G165000 chr5A 85.922 412 45 8 1 406 357811138 357810734 8.080000e-116 427.0
13 TraesCS5B01G165000 chr2B 85.374 294 39 4 1 290 106315785 106315492 5.110000e-78 302.0
14 TraesCS5B01G165000 chr2D 81.437 334 50 10 1 326 70033504 70033833 2.410000e-66 263.0
15 TraesCS5B01G165000 chr1A 81.470 313 49 6 15 319 589855052 589854741 6.760000e-62 248.0
16 TraesCS5B01G165000 chr4B 89.706 68 5 2 259 325 147700790 147700856 5.600000e-13 86.1
17 TraesCS5B01G165000 chr4D 83.333 90 9 6 238 325 503812498 503812413 9.380000e-11 78.7


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 TraesCS5B01G165000 chr5B 305046737 305049890 3153 True 2701.5 5260 100.000000 1 3154 2 chr5B.!!$R3 3153
1 TraesCS5B01G165000 chr5D 269294160 269297427 3267 True 1011.5 2615 89.679000 1 2796 4 chr5D.!!$R1 2795
2 TraesCS5B01G165000 chr5A 357805964 357811138 5174 True 942.0 1844 91.449333 1 2393 3 chr5A.!!$R1 2392

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
311 360 0.768221 TTGCCCCTCTTGAGGTGTCT 60.768 55.0 14.77 0.0 0.00 3.41 F
987 4226 0.879765 CCAGCTTCAGGTTCAGCTTG 59.120 55.0 0.00 0.0 44.28 4.01 F
1056 4295 0.967887 TCCTCGCCTCTCCAACTCAG 60.968 60.0 0.00 0.0 0.00 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1301 4598 1.072332 CATGGTGTTGTCCACGGGA 59.928 57.895 0.0 0.0 45.52 5.14 R
1990 5287 1.078848 GACCCAGCGTCATCAAGCT 60.079 57.895 0.0 0.0 45.74 3.74 R
2820 6126 1.227853 AGACCTCCGTTGTGTTGCC 60.228 57.895 0.0 0.0 0.00 4.52 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
132 133 6.726379 TGTCCCTTTATCAATCATGTGGTTA 58.274 36.000 0.00 0.00 0.00 2.85
152 153 2.365582 AGAGTTTTTGCACGGTTGTCT 58.634 42.857 0.00 0.00 0.00 3.41
164 165 4.391830 GCACGGTTGTCTCTTTATCAATCA 59.608 41.667 0.00 0.00 0.00 2.57
168 169 6.655003 ACGGTTGTCTCTTTATCAATCATGTT 59.345 34.615 0.00 0.00 0.00 2.71
174 176 6.535150 GTCTCTTTATCAATCATGTTGTCGGA 59.465 38.462 0.00 0.00 0.00 4.55
240 286 1.061566 GTTTATCGAGTTTTCGCCCGG 59.938 52.381 0.00 0.00 46.28 5.73
288 337 7.383102 TCTCTTCTTAATGAAATGCAGGAAC 57.617 36.000 0.00 0.00 33.79 3.62
311 360 0.768221 TTGCCCCTCTTGAGGTGTCT 60.768 55.000 14.77 0.00 0.00 3.41
314 363 1.352083 CCCCTCTTGAGGTGTCTTGA 58.648 55.000 14.77 0.00 0.00 3.02
357 406 2.007608 CTTAGGCCTTGTTCGCTTACC 58.992 52.381 12.58 0.00 0.00 2.85
359 408 1.302993 GGCCTTGTTCGCTTACCCA 60.303 57.895 0.00 0.00 0.00 4.51
454 2581 4.750833 TCCCCCTAAATTCCTTGTCAAA 57.249 40.909 0.00 0.00 0.00 2.69
486 2614 3.610911 CCTATGAGTGTTTGGTCCCTTC 58.389 50.000 0.00 0.00 0.00 3.46
522 2679 3.446161 GCCTACAAACAACCCTATTTCCC 59.554 47.826 0.00 0.00 0.00 3.97
527 2684 4.966168 ACAAACAACCCTATTTCCCTGTTT 59.034 37.500 0.00 0.00 37.45 2.83
550 2707 4.893608 TGATCGAATGGAGAACACTTCAA 58.106 39.130 0.00 0.00 0.00 2.69
561 2718 3.380004 AGAACACTTCAATGCCGACAAAA 59.620 39.130 0.00 0.00 0.00 2.44
562 2719 4.037923 AGAACACTTCAATGCCGACAAAAT 59.962 37.500 0.00 0.00 0.00 1.82
570 3116 5.837437 TCAATGCCGACAAAATAACAAAGT 58.163 33.333 0.00 0.00 0.00 2.66
586 3132 2.552315 CAAAGTCACGGGTGCACTAAAT 59.448 45.455 17.98 0.00 0.00 1.40
607 3153 4.422073 TTACCAGGATTGATGCAGGTAG 57.578 45.455 6.82 0.00 40.31 3.18
608 3154 2.200081 ACCAGGATTGATGCAGGTAGT 58.800 47.619 0.00 0.00 36.30 2.73
609 3155 3.384168 ACCAGGATTGATGCAGGTAGTA 58.616 45.455 0.00 0.00 36.30 1.82
610 3156 3.134804 ACCAGGATTGATGCAGGTAGTAC 59.865 47.826 0.00 0.00 36.30 2.73
611 3157 3.495100 CCAGGATTGATGCAGGTAGTACC 60.495 52.174 11.73 11.73 38.99 3.34
644 3211 5.641709 GAGTTAAATAAAGTTGCAGAGCCC 58.358 41.667 0.00 0.00 0.00 5.19
645 3212 4.462834 AGTTAAATAAAGTTGCAGAGCCCC 59.537 41.667 0.00 0.00 0.00 5.80
646 3213 1.852633 AATAAAGTTGCAGAGCCCCC 58.147 50.000 0.00 0.00 0.00 5.40
728 3296 6.295719 CAAGGGTCCTTGTAATAGTACAGT 57.704 41.667 18.84 0.00 45.91 3.55
729 3297 7.414222 CAAGGGTCCTTGTAATAGTACAGTA 57.586 40.000 18.84 0.00 45.91 2.74
730 3298 7.844009 CAAGGGTCCTTGTAATAGTACAGTAA 58.156 38.462 18.84 0.00 45.91 2.24
731 3299 8.483758 CAAGGGTCCTTGTAATAGTACAGTAAT 58.516 37.037 18.84 0.00 45.91 1.89
913 4139 3.857052 TCGACCAGCTTATAACAAGTGG 58.143 45.455 0.00 0.00 0.00 4.00
987 4226 0.879765 CCAGCTTCAGGTTCAGCTTG 59.120 55.000 0.00 0.00 44.28 4.01
1056 4295 0.967887 TCCTCGCCTCTCCAACTCAG 60.968 60.000 0.00 0.00 0.00 3.35
1062 4303 1.349357 GCCTCTCCAACTCAGTTTCCT 59.651 52.381 0.00 0.00 0.00 3.36
1102 4343 2.709397 TCGTTTTCCTCTCCCCTCTTTT 59.291 45.455 0.00 0.00 0.00 2.27
1120 4361 6.536224 CCTCTTTTGACATGTTTTGCTTCTTT 59.464 34.615 0.00 0.00 0.00 2.52
1147 4388 2.860194 GCTGTGTCGATGCGATCTATGT 60.860 50.000 0.00 0.00 38.42 2.29
1181 4422 4.937201 AACCCTTTGTTCAACTCCATTC 57.063 40.909 0.00 0.00 28.45 2.67
1196 4493 2.609002 TCCATTCGCTTGATTGATCACG 59.391 45.455 0.00 0.00 36.36 4.35
1250 4547 4.101448 AGCTCCCACGCCATCACC 62.101 66.667 0.00 0.00 0.00 4.02
1283 4580 3.145551 GCCTACTCCTTCGGCGGA 61.146 66.667 7.21 0.00 33.64 5.54
1292 4589 1.446272 CTTCGGCGGAGAGTTCACC 60.446 63.158 10.37 0.00 0.00 4.02
1301 4598 4.699522 GAGTTCACCCCGCGCCTT 62.700 66.667 0.00 0.00 0.00 4.35
1511 4808 2.122729 AGCACCTGGACCCTGCTA 59.877 61.111 7.67 0.00 39.52 3.49
1742 5039 2.434774 GGGAAGGTGTGGGTGGTC 59.565 66.667 0.00 0.00 0.00 4.02
2003 5300 2.042831 GGCCAAGCTTGATGACGCT 61.043 57.895 28.05 0.00 38.30 5.07
2021 5318 2.529389 GGGTCTGGTCACCACCCT 60.529 66.667 14.40 0.00 42.99 4.34
2172 5469 2.997315 TCAGCACGCCAGCTAGGT 60.997 61.111 0.00 0.00 44.54 3.08
2234 5532 3.120121 CGAACTTGCTGCTTTGTTAATGC 59.880 43.478 0.00 0.00 0.00 3.56
2244 5542 4.037803 TGCTTTGTTAATGCTGTGTGTCAT 59.962 37.500 0.00 0.00 33.15 3.06
2245 5543 5.240403 TGCTTTGTTAATGCTGTGTGTCATA 59.760 36.000 0.00 0.00 33.15 2.15
2246 5544 5.796935 GCTTTGTTAATGCTGTGTGTCATAG 59.203 40.000 0.00 0.00 0.00 2.23
2247 5545 6.568462 GCTTTGTTAATGCTGTGTGTCATAGT 60.568 38.462 0.00 0.00 0.00 2.12
2248 5546 7.360861 GCTTTGTTAATGCTGTGTGTCATAGTA 60.361 37.037 0.00 0.00 0.00 1.82
2249 5547 6.961359 TGTTAATGCTGTGTGTCATAGTAC 57.039 37.500 0.00 0.00 0.00 2.73
2437 5743 0.890542 TTTGCGCCTCTGTCTGCATT 60.891 50.000 4.18 0.00 37.17 3.56
2460 5766 1.371635 GTTCGTGGTTGGCATGCAC 60.372 57.895 21.36 9.99 0.00 4.57
2494 5800 0.388907 GGCAGCAATCGCACAAACAT 60.389 50.000 0.00 0.00 42.27 2.71
2496 5802 0.711670 CAGCAATCGCACAAACATGC 59.288 50.000 0.00 0.00 42.27 4.06
2514 5820 1.340114 TGCCCACTTAACACACACACA 60.340 47.619 0.00 0.00 0.00 3.72
2515 5821 1.064952 GCCCACTTAACACACACACAC 59.935 52.381 0.00 0.00 0.00 3.82
2516 5822 2.639065 CCCACTTAACACACACACACT 58.361 47.619 0.00 0.00 0.00 3.55
2551 5857 2.452114 CCCCACTCACCCCTCTCT 59.548 66.667 0.00 0.00 0.00 3.10
2595 5901 1.661112 GCAGTGGTTCTTCATAGTCGC 59.339 52.381 0.00 0.00 0.00 5.19
2662 5968 3.501548 GCGCGACGTCCTCTCTCT 61.502 66.667 12.10 0.00 0.00 3.10
2664 5970 1.812093 CGCGACGTCCTCTCTCTCT 60.812 63.158 10.58 0.00 0.00 3.10
2665 5971 1.758319 CGCGACGTCCTCTCTCTCTC 61.758 65.000 10.58 0.00 0.00 3.20
2666 5972 0.461339 GCGACGTCCTCTCTCTCTCT 60.461 60.000 10.58 0.00 0.00 3.10
2668 5974 1.805120 CGACGTCCTCTCTCTCTCTCC 60.805 61.905 10.58 0.00 0.00 3.71
2669 5975 0.544697 ACGTCCTCTCTCTCTCTCCC 59.455 60.000 0.00 0.00 0.00 4.30
2670 5976 0.544223 CGTCCTCTCTCTCTCTCCCA 59.456 60.000 0.00 0.00 0.00 4.37
2796 6102 3.446516 ACGTGTATCAGGGTTTAGAGACC 59.553 47.826 0.00 0.00 39.04 3.85
2797 6103 3.488721 CGTGTATCAGGGTTTAGAGACCG 60.489 52.174 0.00 0.00 40.75 4.79
2798 6104 3.028850 TGTATCAGGGTTTAGAGACCGG 58.971 50.000 0.00 0.00 40.75 5.28
2799 6105 1.497161 ATCAGGGTTTAGAGACCGGG 58.503 55.000 6.32 0.00 40.75 5.73
2800 6106 0.616679 TCAGGGTTTAGAGACCGGGG 60.617 60.000 6.32 0.00 40.75 5.73
2801 6107 1.306739 AGGGTTTAGAGACCGGGGG 60.307 63.158 6.32 0.00 40.75 5.40
2816 6122 4.548513 GGGGTGTTGGTGGGGCAA 62.549 66.667 0.00 0.00 0.00 4.52
2817 6123 3.230990 GGGTGTTGGTGGGGCAAC 61.231 66.667 0.00 0.00 0.00 4.17
2818 6124 3.601685 GGTGTTGGTGGGGCAACG 61.602 66.667 0.00 0.00 34.30 4.10
2829 6135 4.560856 GGCAACGCGGCAACACAA 62.561 61.111 12.47 0.00 40.76 3.33
2830 6136 3.319316 GCAACGCGGCAACACAAC 61.319 61.111 12.47 0.00 0.00 3.32
2831 6137 3.016203 CAACGCGGCAACACAACG 61.016 61.111 12.47 0.00 0.00 4.10
2832 6138 4.244802 AACGCGGCAACACAACGG 62.245 61.111 12.47 0.00 0.00 4.44
2834 6140 4.368808 CGCGGCAACACAACGGAG 62.369 66.667 0.00 0.00 0.00 4.63
2835 6141 4.025401 GCGGCAACACAACGGAGG 62.025 66.667 0.00 0.00 0.00 4.30
2836 6142 2.590575 CGGCAACACAACGGAGGT 60.591 61.111 0.00 0.00 0.00 3.85
2837 6143 2.604174 CGGCAACACAACGGAGGTC 61.604 63.158 0.00 0.00 0.00 3.85
2838 6144 1.227853 GGCAACACAACGGAGGTCT 60.228 57.895 0.00 0.00 0.00 3.85
2839 6145 1.228657 GGCAACACAACGGAGGTCTC 61.229 60.000 0.00 0.00 0.00 3.36
2840 6146 1.557443 GCAACACAACGGAGGTCTCG 61.557 60.000 0.00 0.00 0.00 4.04
2841 6147 1.300697 AACACAACGGAGGTCTCGC 60.301 57.895 0.00 0.00 0.00 5.03
2842 6148 2.805353 CACAACGGAGGTCTCGCG 60.805 66.667 0.00 0.00 0.00 5.87
2843 6149 4.052229 ACAACGGAGGTCTCGCGG 62.052 66.667 6.13 0.00 0.00 6.46
2844 6150 4.052229 CAACGGAGGTCTCGCGGT 62.052 66.667 6.13 0.00 0.00 5.68
2845 6151 3.300765 AACGGAGGTCTCGCGGTT 61.301 61.111 6.13 0.00 33.09 4.44
2846 6152 3.569049 AACGGAGGTCTCGCGGTTG 62.569 63.158 6.13 0.00 35.62 3.77
3096 6402 2.662596 CTCCCAGGCGTTGCAGTA 59.337 61.111 0.00 0.00 0.00 2.74
3097 6403 1.741770 CTCCCAGGCGTTGCAGTAC 60.742 63.158 0.00 0.00 0.00 2.73
3098 6404 2.746277 CCCAGGCGTTGCAGTACC 60.746 66.667 0.00 0.00 0.00 3.34
3099 6405 2.031919 CCAGGCGTTGCAGTACCA 59.968 61.111 4.09 0.00 0.00 3.25
3100 6406 1.599518 CCAGGCGTTGCAGTACCAA 60.600 57.895 4.09 0.00 0.00 3.67
3101 6407 0.960364 CCAGGCGTTGCAGTACCAAT 60.960 55.000 4.09 0.00 0.00 3.16
3102 6408 0.447801 CAGGCGTTGCAGTACCAATC 59.552 55.000 4.09 0.00 0.00 2.67
3103 6409 0.036164 AGGCGTTGCAGTACCAATCA 59.964 50.000 4.09 0.00 0.00 2.57
3104 6410 1.094785 GGCGTTGCAGTACCAATCAT 58.905 50.000 0.00 0.00 0.00 2.45
3105 6411 1.202177 GGCGTTGCAGTACCAATCATG 60.202 52.381 0.00 0.00 0.00 3.07
3106 6412 1.468520 GCGTTGCAGTACCAATCATGT 59.531 47.619 0.00 0.00 0.00 3.21
3107 6413 2.728846 GCGTTGCAGTACCAATCATGTG 60.729 50.000 0.00 0.00 0.00 3.21
3108 6414 2.728846 CGTTGCAGTACCAATCATGTGC 60.729 50.000 0.00 0.00 0.00 4.57
3109 6415 2.489329 GTTGCAGTACCAATCATGTGCT 59.511 45.455 0.00 0.00 0.00 4.40
3110 6416 2.358957 TGCAGTACCAATCATGTGCTC 58.641 47.619 0.00 0.00 0.00 4.26
3111 6417 1.328680 GCAGTACCAATCATGTGCTCG 59.671 52.381 0.00 0.00 0.00 5.03
3112 6418 2.621338 CAGTACCAATCATGTGCTCGT 58.379 47.619 0.00 0.00 0.00 4.18
3113 6419 2.604914 CAGTACCAATCATGTGCTCGTC 59.395 50.000 0.00 0.00 0.00 4.20
3114 6420 2.233676 AGTACCAATCATGTGCTCGTCA 59.766 45.455 0.00 0.00 0.00 4.35
3115 6421 2.408271 ACCAATCATGTGCTCGTCAT 57.592 45.000 0.00 0.00 0.00 3.06
3116 6422 2.011947 ACCAATCATGTGCTCGTCATG 58.988 47.619 0.00 0.00 42.53 3.07
3117 6423 1.332686 CCAATCATGTGCTCGTCATGG 59.667 52.381 6.15 0.00 41.79 3.66
3118 6424 2.011947 CAATCATGTGCTCGTCATGGT 58.988 47.619 6.15 0.00 41.79 3.55
3119 6425 1.660167 ATCATGTGCTCGTCATGGTG 58.340 50.000 6.15 0.00 41.79 4.17
3120 6426 0.391528 TCATGTGCTCGTCATGGTGG 60.392 55.000 6.15 0.00 41.79 4.61
3121 6427 1.078214 ATGTGCTCGTCATGGTGGG 60.078 57.895 0.00 0.00 0.00 4.61
3122 6428 1.552799 ATGTGCTCGTCATGGTGGGA 61.553 55.000 0.00 0.00 0.00 4.37
3123 6429 1.003839 GTGCTCGTCATGGTGGGAA 60.004 57.895 0.00 0.00 0.00 3.97
3124 6430 1.021390 GTGCTCGTCATGGTGGGAAG 61.021 60.000 0.00 0.00 0.00 3.46
3125 6431 1.450312 GCTCGTCATGGTGGGAAGG 60.450 63.158 0.00 0.00 0.00 3.46
3126 6432 1.221840 CTCGTCATGGTGGGAAGGG 59.778 63.158 0.00 0.00 0.00 3.95
3127 6433 1.537889 TCGTCATGGTGGGAAGGGT 60.538 57.895 0.00 0.00 0.00 4.34
3128 6434 1.131303 TCGTCATGGTGGGAAGGGTT 61.131 55.000 0.00 0.00 0.00 4.11
3129 6435 0.676782 CGTCATGGTGGGAAGGGTTC 60.677 60.000 0.00 0.00 0.00 3.62
3130 6436 0.698818 GTCATGGTGGGAAGGGTTCT 59.301 55.000 0.00 0.00 0.00 3.01
3131 6437 1.913419 GTCATGGTGGGAAGGGTTCTA 59.087 52.381 0.00 0.00 0.00 2.10
3132 6438 2.307686 GTCATGGTGGGAAGGGTTCTAA 59.692 50.000 0.00 0.00 0.00 2.10
3133 6439 2.576191 TCATGGTGGGAAGGGTTCTAAG 59.424 50.000 0.00 0.00 0.00 2.18
3134 6440 2.127651 TGGTGGGAAGGGTTCTAAGT 57.872 50.000 0.00 0.00 0.00 2.24
3135 6441 1.702957 TGGTGGGAAGGGTTCTAAGTG 59.297 52.381 0.00 0.00 0.00 3.16
3136 6442 1.613520 GGTGGGAAGGGTTCTAAGTGC 60.614 57.143 0.00 0.00 0.00 4.40
3137 6443 1.351350 GTGGGAAGGGTTCTAAGTGCT 59.649 52.381 0.00 0.00 0.00 4.40
3138 6444 1.628846 TGGGAAGGGTTCTAAGTGCTC 59.371 52.381 0.00 0.00 0.00 4.26
3139 6445 1.405661 GGGAAGGGTTCTAAGTGCTCG 60.406 57.143 0.00 0.00 0.00 5.03
3140 6446 1.275573 GGAAGGGTTCTAAGTGCTCGT 59.724 52.381 0.00 0.00 0.00 4.18
3141 6447 2.608268 GAAGGGTTCTAAGTGCTCGTC 58.392 52.381 0.00 0.00 0.00 4.20
3142 6448 1.629043 AGGGTTCTAAGTGCTCGTCA 58.371 50.000 0.00 0.00 0.00 4.35
3143 6449 1.546476 AGGGTTCTAAGTGCTCGTCAG 59.454 52.381 0.00 0.00 0.00 3.51
3144 6450 1.544691 GGGTTCTAAGTGCTCGTCAGA 59.455 52.381 0.00 0.00 0.00 3.27
3145 6451 2.029290 GGGTTCTAAGTGCTCGTCAGAA 60.029 50.000 0.00 0.00 0.00 3.02
3146 6452 3.368531 GGGTTCTAAGTGCTCGTCAGAAT 60.369 47.826 4.04 0.00 0.00 2.40
3147 6453 3.860536 GGTTCTAAGTGCTCGTCAGAATC 59.139 47.826 4.04 0.92 0.00 2.52
3148 6454 4.486090 GTTCTAAGTGCTCGTCAGAATCA 58.514 43.478 4.04 0.00 0.00 2.57
3149 6455 4.362932 TCTAAGTGCTCGTCAGAATCAG 57.637 45.455 0.00 0.00 0.00 2.90
3150 6456 3.759086 TCTAAGTGCTCGTCAGAATCAGT 59.241 43.478 0.00 0.00 0.00 3.41
3151 6457 2.360553 AGTGCTCGTCAGAATCAGTG 57.639 50.000 0.00 0.00 0.00 3.66
3152 6458 1.615883 AGTGCTCGTCAGAATCAGTGT 59.384 47.619 0.00 0.00 0.00 3.55
3153 6459 2.820197 AGTGCTCGTCAGAATCAGTGTA 59.180 45.455 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
132 133 2.354821 GAGACAACCGTGCAAAAACTCT 59.645 45.455 0.00 0.00 0.00 3.24
152 153 7.864108 AATCCGACAACATGATTGATAAAGA 57.136 32.000 0.00 0.00 0.00 2.52
184 186 5.404366 CCACACGATTGATAAGGTATAACCG 59.596 44.000 0.00 0.00 44.90 4.44
191 193 3.773119 ACCTACCACACGATTGATAAGGT 59.227 43.478 0.00 0.00 0.00 3.50
288 337 2.679716 CTCAAGAGGGGCAAGGGG 59.320 66.667 0.00 0.00 0.00 4.79
468 2595 2.185004 CGAAGGGACCAAACACTCAT 57.815 50.000 0.00 0.00 0.00 2.90
469 2596 3.698250 CGAAGGGACCAAACACTCA 57.302 52.632 0.00 0.00 0.00 3.41
486 2614 1.739466 TGTAGGCTCTTGTACGTACCG 59.261 52.381 22.43 13.56 0.00 4.02
506 2636 5.663556 TCAAAACAGGGAAATAGGGTTGTTT 59.336 36.000 0.00 0.00 39.59 2.83
522 2679 5.180117 AGTGTTCTCCATTCGATCAAAACAG 59.820 40.000 0.00 0.00 0.00 3.16
527 2684 4.893608 TGAAGTGTTCTCCATTCGATCAA 58.106 39.130 0.00 0.00 0.00 2.57
550 2707 5.219633 GTGACTTTGTTATTTTGTCGGCAT 58.780 37.500 0.00 0.00 0.00 4.40
561 2718 1.877443 GTGCACCCGTGACTTTGTTAT 59.123 47.619 5.22 0.00 0.00 1.89
562 2719 1.134340 AGTGCACCCGTGACTTTGTTA 60.134 47.619 14.63 0.00 0.00 2.41
570 3116 2.038689 TGGTAATTTAGTGCACCCGTGA 59.961 45.455 14.63 0.00 0.00 4.35
586 3132 3.780294 ACTACCTGCATCAATCCTGGTAA 59.220 43.478 0.00 0.00 35.84 2.85
607 3153 9.420551 CTTTATTTAACTCGGATCCATAGGTAC 57.579 37.037 13.41 0.00 0.00 3.34
608 3154 9.151177 ACTTTATTTAACTCGGATCCATAGGTA 57.849 33.333 13.41 8.64 0.00 3.08
609 3155 8.030913 ACTTTATTTAACTCGGATCCATAGGT 57.969 34.615 13.41 9.71 0.00 3.08
610 3156 8.774586 CAACTTTATTTAACTCGGATCCATAGG 58.225 37.037 13.41 0.65 0.00 2.57
611 3157 8.283291 GCAACTTTATTTAACTCGGATCCATAG 58.717 37.037 13.41 10.97 0.00 2.23
612 3158 7.771361 TGCAACTTTATTTAACTCGGATCCATA 59.229 33.333 13.41 0.00 0.00 2.74
613 3159 6.601613 TGCAACTTTATTTAACTCGGATCCAT 59.398 34.615 13.41 0.00 0.00 3.41
614 3160 5.941058 TGCAACTTTATTTAACTCGGATCCA 59.059 36.000 13.41 0.00 0.00 3.41
615 3161 6.315393 TCTGCAACTTTATTTAACTCGGATCC 59.685 38.462 0.00 0.00 0.00 3.36
616 3162 7.303634 TCTGCAACTTTATTTAACTCGGATC 57.696 36.000 0.00 0.00 0.00 3.36
617 3163 6.183360 GCTCTGCAACTTTATTTAACTCGGAT 60.183 38.462 0.00 0.00 0.00 4.18
618 3164 5.121768 GCTCTGCAACTTTATTTAACTCGGA 59.878 40.000 0.00 0.00 0.00 4.55
658 3225 0.031178 CTGCGGCTCTGCAACTTTTT 59.969 50.000 4.82 0.00 45.74 1.94
659 3226 1.103398 ACTGCGGCTCTGCAACTTTT 61.103 50.000 4.82 0.00 45.74 2.27
660 3227 1.526917 ACTGCGGCTCTGCAACTTT 60.527 52.632 4.82 0.00 45.74 2.66
661 3228 2.111878 ACTGCGGCTCTGCAACTT 59.888 55.556 4.82 0.00 45.74 2.66
662 3229 2.460662 ATCACTGCGGCTCTGCAACT 62.461 55.000 4.82 0.00 45.74 3.16
663 3230 0.740868 TATCACTGCGGCTCTGCAAC 60.741 55.000 4.82 0.00 45.74 4.17
664 3231 0.178767 ATATCACTGCGGCTCTGCAA 59.821 50.000 4.82 0.00 45.74 4.08
665 3232 0.249615 GATATCACTGCGGCTCTGCA 60.250 55.000 0.00 3.13 43.95 4.41
666 3233 0.249615 TGATATCACTGCGGCTCTGC 60.250 55.000 0.00 0.00 0.00 4.26
667 3234 2.335752 GATGATATCACTGCGGCTCTG 58.664 52.381 7.78 0.00 0.00 3.35
668 3235 1.274728 GGATGATATCACTGCGGCTCT 59.725 52.381 7.78 0.00 0.00 4.09
669 3236 1.001293 TGGATGATATCACTGCGGCTC 59.999 52.381 7.78 0.00 0.00 4.70
670 3237 1.051008 TGGATGATATCACTGCGGCT 58.949 50.000 7.78 0.00 0.00 5.52
671 3238 1.882912 TTGGATGATATCACTGCGGC 58.117 50.000 7.78 0.00 0.00 6.53
672 3239 4.758674 AGAATTTGGATGATATCACTGCGG 59.241 41.667 7.78 0.00 0.00 5.69
673 3240 5.686834 CAGAATTTGGATGATATCACTGCG 58.313 41.667 7.78 0.00 0.00 5.18
717 3285 9.003658 GCCGTACTAGGAATTACTGTACTATTA 57.996 37.037 19.48 0.00 33.47 0.98
718 3286 7.308229 CGCCGTACTAGGAATTACTGTACTATT 60.308 40.741 19.48 0.00 33.47 1.73
719 3287 6.148480 CGCCGTACTAGGAATTACTGTACTAT 59.852 42.308 19.48 0.00 33.47 2.12
721 3289 4.274459 CGCCGTACTAGGAATTACTGTACT 59.726 45.833 19.48 0.00 33.47 2.73
722 3290 4.531332 CGCCGTACTAGGAATTACTGTAC 58.469 47.826 15.19 15.19 0.00 2.90
723 3291 3.565482 CCGCCGTACTAGGAATTACTGTA 59.435 47.826 0.00 0.00 0.00 2.74
725 3293 2.861360 GCCGCCGTACTAGGAATTACTG 60.861 54.545 0.00 0.00 0.00 2.74
727 3295 1.339291 AGCCGCCGTACTAGGAATTAC 59.661 52.381 0.00 0.00 0.00 1.89
728 3296 1.610522 GAGCCGCCGTACTAGGAATTA 59.389 52.381 0.00 0.00 0.00 1.40
729 3297 0.388294 GAGCCGCCGTACTAGGAATT 59.612 55.000 0.00 0.00 0.00 2.17
730 3298 0.754217 TGAGCCGCCGTACTAGGAAT 60.754 55.000 0.00 0.00 0.00 3.01
731 3299 0.754217 ATGAGCCGCCGTACTAGGAA 60.754 55.000 0.00 0.00 0.00 3.36
776 3839 2.333926 TCTCAATAACGCCACTGTTCG 58.666 47.619 0.00 0.00 33.32 3.95
913 4139 1.114627 GGGAAAGTGATGATTGGGGC 58.885 55.000 0.00 0.00 0.00 5.80
1056 4295 6.004574 AGATGGAGTAGGAAACAAAGGAAAC 58.995 40.000 0.00 0.00 0.00 2.78
1062 4303 5.223449 ACGAAGATGGAGTAGGAAACAAA 57.777 39.130 0.00 0.00 0.00 2.83
1102 4343 5.581126 AGTGAAAGAAGCAAAACATGTCA 57.419 34.783 0.00 0.00 0.00 3.58
1131 4372 6.877556 ATGAATTACATAGATCGCATCGAC 57.122 37.500 0.00 0.00 36.66 4.20
1162 4403 2.351738 GCGAATGGAGTTGAACAAAGGG 60.352 50.000 0.00 0.00 0.00 3.95
1163 4404 2.554032 AGCGAATGGAGTTGAACAAAGG 59.446 45.455 0.00 0.00 0.00 3.11
1164 4405 3.904136 AGCGAATGGAGTTGAACAAAG 57.096 42.857 0.00 0.00 0.00 2.77
1165 4406 3.629855 TCAAGCGAATGGAGTTGAACAAA 59.370 39.130 0.00 0.00 0.00 2.83
1169 4410 4.071423 TCAATCAAGCGAATGGAGTTGAA 58.929 39.130 0.00 0.00 32.85 2.69
1171 4412 4.095334 TGATCAATCAAGCGAATGGAGTTG 59.905 41.667 0.00 0.00 33.08 3.16
1172 4413 4.095483 GTGATCAATCAAGCGAATGGAGTT 59.905 41.667 0.00 0.00 38.75 3.01
1173 4414 3.624861 GTGATCAATCAAGCGAATGGAGT 59.375 43.478 0.00 0.00 38.75 3.85
1174 4415 3.302935 CGTGATCAATCAAGCGAATGGAG 60.303 47.826 0.00 0.00 38.75 3.86
1175 4416 2.609002 CGTGATCAATCAAGCGAATGGA 59.391 45.455 0.00 0.00 38.75 3.41
1176 4417 2.978013 CGTGATCAATCAAGCGAATGG 58.022 47.619 0.00 0.00 38.75 3.16
1196 4493 2.438075 CCCTTCTGCTCCAGCTGC 60.438 66.667 8.66 0.00 42.66 5.25
1301 4598 1.072332 CATGGTGTTGTCCACGGGA 59.928 57.895 0.00 0.00 45.52 5.14
1775 5072 2.632544 CGGGTCGTAGGAGTGCACA 61.633 63.158 21.04 0.00 0.00 4.57
1990 5287 1.078848 GACCCAGCGTCATCAAGCT 60.079 57.895 0.00 0.00 45.74 3.74
1994 5291 1.888436 GACCAGACCCAGCGTCATCA 61.888 60.000 0.00 0.00 44.66 3.07
2003 5300 2.852075 GGGTGGTGACCAGACCCA 60.852 66.667 21.88 0.00 45.25 4.51
2030 5327 2.556287 GAGAAAGCGCACCAACCG 59.444 61.111 11.47 0.00 0.00 4.44
2072 5369 2.813179 GCCGTAGACAAGCATGCCG 61.813 63.158 15.66 8.79 0.00 5.69
2234 5532 8.664211 TCATCTACTAGTACTATGACACACAG 57.336 38.462 14.89 0.00 0.00 3.66
2389 5695 4.577875 AGAGCTGACGTTAGTACAGTAGT 58.422 43.478 9.29 0.00 34.60 2.73
2437 5743 2.589442 GCCAACCACGAACGGTCA 60.589 61.111 0.00 0.00 38.76 4.02
2460 5766 2.582498 GCCCCACGTCGAGATTCG 60.582 66.667 0.00 0.00 42.10 3.34
2494 5800 1.340114 TGTGTGTGTGTTAAGTGGGCA 60.340 47.619 0.00 0.00 0.00 5.36
2496 5802 2.612212 GAGTGTGTGTGTGTTAAGTGGG 59.388 50.000 0.00 0.00 0.00 4.61
2546 5852 4.803426 GCGGGCGGACACAGAGAG 62.803 72.222 0.00 0.00 0.00 3.20
2570 5876 1.229428 ATGAAGAACCACTGCGTGTG 58.771 50.000 7.68 5.50 45.80 3.82
2573 5879 2.671351 CGACTATGAAGAACCACTGCGT 60.671 50.000 0.00 0.00 0.00 5.24
2704 6010 1.883021 CAACCGCTGAAATCCCCAC 59.117 57.895 0.00 0.00 0.00 4.61
2727 6033 1.676635 GAAACGGCCACCCTAACCC 60.677 63.158 2.24 0.00 0.00 4.11
2780 6086 1.497161 CCCGGTCTCTAAACCCTGAT 58.503 55.000 0.00 0.00 35.79 2.90
2799 6105 4.548513 TTGCCCCACCAACACCCC 62.549 66.667 0.00 0.00 0.00 4.95
2800 6106 3.230990 GTTGCCCCACCAACACCC 61.231 66.667 0.57 0.00 43.45 4.61
2801 6107 3.601685 CGTTGCCCCACCAACACC 61.602 66.667 5.96 0.00 44.01 4.16
2802 6108 4.279043 GCGTTGCCCCACCAACAC 62.279 66.667 5.96 0.00 44.01 3.32
2812 6118 4.560856 TTGTGTTGCCGCGTTGCC 62.561 61.111 4.92 0.00 0.00 4.52
2813 6119 3.319316 GTTGTGTTGCCGCGTTGC 61.319 61.111 4.92 2.15 0.00 4.17
2814 6120 3.016203 CGTTGTGTTGCCGCGTTG 61.016 61.111 4.92 0.00 0.00 4.10
2815 6121 4.244802 CCGTTGTGTTGCCGCGTT 62.245 61.111 4.92 0.00 0.00 4.84
2817 6123 4.368808 CTCCGTTGTGTTGCCGCG 62.369 66.667 0.00 0.00 0.00 6.46
2818 6124 4.025401 CCTCCGTTGTGTTGCCGC 62.025 66.667 0.00 0.00 0.00 6.53
2819 6125 2.590575 ACCTCCGTTGTGTTGCCG 60.591 61.111 0.00 0.00 0.00 5.69
2820 6126 1.227853 AGACCTCCGTTGTGTTGCC 60.228 57.895 0.00 0.00 0.00 4.52
2821 6127 1.557443 CGAGACCTCCGTTGTGTTGC 61.557 60.000 0.00 0.00 0.00 4.17
2822 6128 1.557443 GCGAGACCTCCGTTGTGTTG 61.557 60.000 0.00 0.00 0.00 3.33
2823 6129 1.300697 GCGAGACCTCCGTTGTGTT 60.301 57.895 0.00 0.00 0.00 3.32
2824 6130 2.338984 GCGAGACCTCCGTTGTGT 59.661 61.111 0.00 0.00 0.00 3.72
2825 6131 2.805353 CGCGAGACCTCCGTTGTG 60.805 66.667 0.00 0.00 0.00 3.33
2826 6132 4.052229 CCGCGAGACCTCCGTTGT 62.052 66.667 8.23 0.00 0.00 3.32
2827 6133 3.569049 AACCGCGAGACCTCCGTTG 62.569 63.158 8.23 0.00 0.00 4.10
2828 6134 3.300765 AACCGCGAGACCTCCGTT 61.301 61.111 8.23 0.00 0.00 4.44
2829 6135 4.052229 CAACCGCGAGACCTCCGT 62.052 66.667 8.23 0.00 0.00 4.69
3078 6384 3.605749 TACTGCAACGCCTGGGAGC 62.606 63.158 0.00 0.00 0.00 4.70
3079 6385 1.741770 GTACTGCAACGCCTGGGAG 60.742 63.158 0.00 0.00 0.00 4.30
3080 6386 2.345991 GTACTGCAACGCCTGGGA 59.654 61.111 0.00 0.00 0.00 4.37
3081 6387 2.746277 GGTACTGCAACGCCTGGG 60.746 66.667 0.00 0.00 0.00 4.45
3082 6388 0.960364 ATTGGTACTGCAACGCCTGG 60.960 55.000 0.00 0.00 0.00 4.45
3083 6389 0.447801 GATTGGTACTGCAACGCCTG 59.552 55.000 0.00 0.00 0.00 4.85
3084 6390 0.036164 TGATTGGTACTGCAACGCCT 59.964 50.000 0.00 0.00 0.00 5.52
3085 6391 1.094785 ATGATTGGTACTGCAACGCC 58.905 50.000 0.00 0.00 0.00 5.68
3086 6392 1.468520 ACATGATTGGTACTGCAACGC 59.531 47.619 0.00 0.00 0.00 4.84
3087 6393 2.728846 GCACATGATTGGTACTGCAACG 60.729 50.000 0.00 0.00 0.00 4.10
3088 6394 2.489329 AGCACATGATTGGTACTGCAAC 59.511 45.455 0.00 0.00 0.00 4.17
3089 6395 2.749076 GAGCACATGATTGGTACTGCAA 59.251 45.455 0.00 0.00 0.00 4.08
3090 6396 2.358957 GAGCACATGATTGGTACTGCA 58.641 47.619 0.00 0.00 0.00 4.41
3091 6397 1.328680 CGAGCACATGATTGGTACTGC 59.671 52.381 0.00 0.00 0.00 4.40
3092 6398 2.604914 GACGAGCACATGATTGGTACTG 59.395 50.000 0.00 0.00 0.00 2.74
3093 6399 2.233676 TGACGAGCACATGATTGGTACT 59.766 45.455 0.00 0.00 0.00 2.73
3094 6400 2.616960 TGACGAGCACATGATTGGTAC 58.383 47.619 0.00 0.00 0.00 3.34
3095 6401 3.197265 CATGACGAGCACATGATTGGTA 58.803 45.455 0.00 0.00 45.22 3.25
3096 6402 2.011947 CATGACGAGCACATGATTGGT 58.988 47.619 0.00 0.00 45.22 3.67
3097 6403 1.332686 CCATGACGAGCACATGATTGG 59.667 52.381 0.00 2.53 45.22 3.16
3098 6404 2.011947 ACCATGACGAGCACATGATTG 58.988 47.619 0.00 0.00 45.22 2.67
3099 6405 2.011947 CACCATGACGAGCACATGATT 58.988 47.619 0.00 0.00 45.22 2.57
3100 6406 1.660167 CACCATGACGAGCACATGAT 58.340 50.000 0.00 0.00 45.22 2.45
3101 6407 0.391528 CCACCATGACGAGCACATGA 60.392 55.000 0.00 0.00 45.22 3.07
3102 6408 1.371337 CCCACCATGACGAGCACATG 61.371 60.000 0.00 0.00 42.99 3.21
3103 6409 1.078214 CCCACCATGACGAGCACAT 60.078 57.895 0.00 0.00 0.00 3.21
3104 6410 1.763546 TTCCCACCATGACGAGCACA 61.764 55.000 0.00 0.00 0.00 4.57
3105 6411 1.003839 TTCCCACCATGACGAGCAC 60.004 57.895 0.00 0.00 0.00 4.40
3106 6412 1.296392 CTTCCCACCATGACGAGCA 59.704 57.895 0.00 0.00 0.00 4.26
3107 6413 1.450312 CCTTCCCACCATGACGAGC 60.450 63.158 0.00 0.00 0.00 5.03
3108 6414 1.221840 CCCTTCCCACCATGACGAG 59.778 63.158 0.00 0.00 0.00 4.18
3109 6415 1.131303 AACCCTTCCCACCATGACGA 61.131 55.000 0.00 0.00 0.00 4.20
3110 6416 0.676782 GAACCCTTCCCACCATGACG 60.677 60.000 0.00 0.00 0.00 4.35
3111 6417 0.698818 AGAACCCTTCCCACCATGAC 59.301 55.000 0.00 0.00 0.00 3.06
3112 6418 2.352561 TAGAACCCTTCCCACCATGA 57.647 50.000 0.00 0.00 0.00 3.07
3113 6419 2.308866 ACTTAGAACCCTTCCCACCATG 59.691 50.000 0.00 0.00 0.00 3.66
3114 6420 2.308866 CACTTAGAACCCTTCCCACCAT 59.691 50.000 0.00 0.00 0.00 3.55
3115 6421 1.702957 CACTTAGAACCCTTCCCACCA 59.297 52.381 0.00 0.00 0.00 4.17
3116 6422 1.613520 GCACTTAGAACCCTTCCCACC 60.614 57.143 0.00 0.00 0.00 4.61
3117 6423 1.351350 AGCACTTAGAACCCTTCCCAC 59.649 52.381 0.00 0.00 0.00 4.61
3118 6424 1.628846 GAGCACTTAGAACCCTTCCCA 59.371 52.381 0.00 0.00 0.00 4.37
3119 6425 1.405661 CGAGCACTTAGAACCCTTCCC 60.406 57.143 0.00 0.00 0.00 3.97
3120 6426 1.275573 ACGAGCACTTAGAACCCTTCC 59.724 52.381 0.00 0.00 0.00 3.46
3121 6427 2.029290 TGACGAGCACTTAGAACCCTTC 60.029 50.000 0.00 0.00 0.00 3.46
3122 6428 1.968493 TGACGAGCACTTAGAACCCTT 59.032 47.619 0.00 0.00 0.00 3.95
3123 6429 1.546476 CTGACGAGCACTTAGAACCCT 59.454 52.381 0.00 0.00 0.00 4.34
3124 6430 1.544691 TCTGACGAGCACTTAGAACCC 59.455 52.381 0.00 0.00 0.00 4.11
3125 6431 3.299340 TTCTGACGAGCACTTAGAACC 57.701 47.619 0.00 0.00 0.00 3.62
3126 6432 4.486090 TGATTCTGACGAGCACTTAGAAC 58.514 43.478 0.00 0.00 31.00 3.01
3127 6433 4.218635 ACTGATTCTGACGAGCACTTAGAA 59.781 41.667 0.00 0.00 32.57 2.10
3128 6434 3.759086 ACTGATTCTGACGAGCACTTAGA 59.241 43.478 0.00 0.00 0.00 2.10
3129 6435 3.856521 CACTGATTCTGACGAGCACTTAG 59.143 47.826 0.00 0.00 0.00 2.18
3130 6436 3.255888 ACACTGATTCTGACGAGCACTTA 59.744 43.478 0.00 0.00 0.00 2.24
3131 6437 2.036475 ACACTGATTCTGACGAGCACTT 59.964 45.455 0.00 0.00 0.00 3.16
3132 6438 1.615883 ACACTGATTCTGACGAGCACT 59.384 47.619 0.00 0.00 0.00 4.40
3133 6439 2.071688 ACACTGATTCTGACGAGCAC 57.928 50.000 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.