Multiple sequence alignment - TraesCS2A01G190800

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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 TraesCS2A01G190800 chr2A 100.000 3195 0 0 954 4148 157534520 157537714 0.000000e+00 5901.0
1 TraesCS2A01G190800 chr2A 84.545 1087 92 38 2581 3658 81460145 81461164 0.000000e+00 1007.0
2 TraesCS2A01G190800 chr2A 100.000 542 0 0 1 542 157533567 157534108 0.000000e+00 1002.0
3 TraesCS2A01G190800 chr2A 86.462 879 68 26 2789 3658 43917515 43916679 0.000000e+00 917.0
4 TraesCS2A01G190800 chr2A 80.699 658 70 23 2580 3234 765404868 765405471 3.780000e-125 459.0
5 TraesCS2A01G190800 chr2A 86.391 169 22 1 2580 2748 43917867 43917700 2.550000e-42 183.0
6 TraesCS2A01G190800 chr2D 91.387 2798 152 35 954 3728 143894919 143892188 0.000000e+00 3749.0
7 TraesCS2A01G190800 chr2D 84.731 1061 93 35 2584 3635 623404541 623403541 0.000000e+00 998.0
8 TraesCS2A01G190800 chr2D 92.267 375 23 5 3775 4148 143892065 143891696 1.020000e-145 527.0
9 TraesCS2A01G190800 chr2D 86.334 461 20 16 1 455 143895575 143895152 2.920000e-126 462.0
10 TraesCS2A01G190800 chr2D 92.593 54 2 2 450 501 143895123 143895070 4.450000e-10 76.8
11 TraesCS2A01G190800 chr2B 89.379 2787 174 51 954 3727 202157098 202154421 0.000000e+00 3395.0
12 TraesCS2A01G190800 chr2B 93.062 418 25 3 3733 4148 202154325 202153910 3.550000e-170 608.0
13 TraesCS2A01G190800 chr2B 87.927 439 29 9 18 455 202166549 202166134 2.880000e-136 496.0
14 TraesCS2A01G190800 chr5D 84.260 1061 97 36 2584 3635 488187155 488186156 0.000000e+00 970.0
15 TraesCS2A01G190800 chr1B 86.514 875 74 23 2770 3635 20803326 20802487 0.000000e+00 922.0
16 TraesCS2A01G190800 chr1B 82.873 1086 109 38 2584 3658 20776980 20775961 0.000000e+00 904.0
17 TraesCS2A01G190800 chr1B 88.462 78 8 1 2584 2661 20803453 20803377 4.420000e-15 93.5
18 TraesCS2A01G190800 chr6D 86.286 875 70 25 2771 3635 79935881 79936715 0.000000e+00 905.0
19 TraesCS2A01G190800 chr7A 78.287 502 55 17 2580 3078 1877583 1877133 1.470000e-69 274.0
20 TraesCS2A01G190800 chr1A 77.689 502 58 21 2580 3078 251370391 251370841 1.480000e-64 257.0
21 TraesCS2A01G190800 chr1A 77.092 502 61 21 2580 3078 540637118 540637568 1.490000e-59 241.0


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 TraesCS2A01G190800 chr2A 157533567 157537714 4147 False 3451.50 5901 100.00000 1 4148 2 chr2A.!!$F3 4147
1 TraesCS2A01G190800 chr2A 81460145 81461164 1019 False 1007.00 1007 84.54500 2581 3658 1 chr2A.!!$F1 1077
2 TraesCS2A01G190800 chr2A 43916679 43917867 1188 True 550.00 917 86.42650 2580 3658 2 chr2A.!!$R1 1078
3 TraesCS2A01G190800 chr2A 765404868 765405471 603 False 459.00 459 80.69900 2580 3234 1 chr2A.!!$F2 654
4 TraesCS2A01G190800 chr2D 143891696 143895575 3879 True 1203.70 3749 90.64525 1 4148 4 chr2D.!!$R2 4147
5 TraesCS2A01G190800 chr2D 623403541 623404541 1000 True 998.00 998 84.73100 2584 3635 1 chr2D.!!$R1 1051
6 TraesCS2A01G190800 chr2B 202153910 202157098 3188 True 2001.50 3395 91.22050 954 4148 2 chr2B.!!$R2 3194
7 TraesCS2A01G190800 chr5D 488186156 488187155 999 True 970.00 970 84.26000 2584 3635 1 chr5D.!!$R1 1051
8 TraesCS2A01G190800 chr1B 20775961 20776980 1019 True 904.00 904 82.87300 2584 3658 1 chr1B.!!$R1 1074
9 TraesCS2A01G190800 chr1B 20802487 20803453 966 True 507.75 922 87.48800 2584 3635 2 chr1B.!!$R2 1051
10 TraesCS2A01G190800 chr6D 79935881 79936715 834 False 905.00 905 86.28600 2771 3635 1 chr6D.!!$F1 864

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
207 213 0.031994 CTTCCACGGCCACCAAAAAG 59.968 55.0 2.24 0.0 0.00 2.27 F
529 588 0.096976 CGCATTTTAGCAGGACACCG 59.903 55.0 0.00 0.0 0.00 4.94 F
530 589 0.451783 GCATTTTAGCAGGACACCGG 59.548 55.0 0.00 0.0 0.00 5.28 F
531 590 1.094785 CATTTTAGCAGGACACCGGG 58.905 55.0 6.32 0.0 0.00 5.73 F
2148 2210 0.790866 GCAATTGTGCGCTTCTCGTC 60.791 55.0 9.73 0.0 41.93 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1101 1163 1.507174 GGAGTCGGTGAGGTTCTCG 59.493 63.158 0.00 0.0 32.35 4.04 R
2106 2168 2.653115 CACTCGGAGCACAGCTGA 59.347 61.111 23.35 0.0 39.88 4.26 R
2133 2195 2.733218 CGGACGAGAAGCGCACAA 60.733 61.111 11.47 0.0 46.04 3.33 R
2160 2222 3.195698 GCAACGAGCGGTGGGATC 61.196 66.667 10.16 0.0 32.56 3.36 R
3374 3637 0.103208 CTAACCTTCCATCGCTCGCT 59.897 55.000 0.00 0.0 0.00 4.93 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
17 18 3.291383 CGGGAAAAAGCGGCACCA 61.291 61.111 1.45 0.00 0.00 4.17
68 74 4.504596 GCCATGGTGCCATCCGGA 62.505 66.667 14.67 6.61 33.90 5.14
69 75 2.203252 CCATGGTGCCATCCGGAG 60.203 66.667 11.34 0.00 33.90 4.63
70 76 2.903855 CATGGTGCCATCCGGAGC 60.904 66.667 11.34 9.84 33.90 4.70
117 123 3.010088 TGTCGCACGAGACAATACG 57.990 52.632 0.82 0.00 46.81 3.06
118 124 0.518195 TGTCGCACGAGACAATACGA 59.482 50.000 0.82 0.00 46.81 3.43
119 125 0.905839 GTCGCACGAGACAATACGAC 59.094 55.000 0.00 0.00 42.36 4.34
120 126 0.519792 TCGCACGAGACAATACGACG 60.520 55.000 0.00 0.00 35.46 5.12
121 127 0.519792 CGCACGAGACAATACGACGA 60.520 55.000 0.00 0.00 35.86 4.20
122 128 0.905839 GCACGAGACAATACGACGAC 59.094 55.000 0.00 0.00 0.00 4.34
163 169 0.872451 CGGGCGGGAACAAAACAAAC 60.872 55.000 0.00 0.00 0.00 2.93
164 170 0.175989 GGGCGGGAACAAAACAAACA 59.824 50.000 0.00 0.00 0.00 2.83
165 171 1.405661 GGGCGGGAACAAAACAAACAA 60.406 47.619 0.00 0.00 0.00 2.83
166 172 2.347731 GGCGGGAACAAAACAAACAAA 58.652 42.857 0.00 0.00 0.00 2.83
195 201 1.021390 AGCGATTCCTTGCTTCCACG 61.021 55.000 0.00 0.00 39.17 4.94
207 213 0.031994 CTTCCACGGCCACCAAAAAG 59.968 55.000 2.24 0.00 0.00 2.27
208 214 0.684805 TTCCACGGCCACCAAAAAGT 60.685 50.000 2.24 0.00 0.00 2.66
209 215 0.183014 TCCACGGCCACCAAAAAGTA 59.817 50.000 2.24 0.00 0.00 2.24
210 216 1.033574 CCACGGCCACCAAAAAGTAA 58.966 50.000 2.24 0.00 0.00 2.24
211 217 1.409427 CCACGGCCACCAAAAAGTAAA 59.591 47.619 2.24 0.00 0.00 2.01
250 256 4.115199 CCTGCCCACTGCCCCTAC 62.115 72.222 0.00 0.00 40.16 3.18
251 257 4.115199 CTGCCCACTGCCCCTACC 62.115 72.222 0.00 0.00 40.16 3.18
275 281 2.436824 GCTTTCCTCCCCGACTGC 60.437 66.667 0.00 0.00 0.00 4.40
281 287 3.710722 CTCCCCGACTGCTGCCTT 61.711 66.667 0.00 0.00 0.00 4.35
282 288 3.965539 CTCCCCGACTGCTGCCTTG 62.966 68.421 0.00 0.00 0.00 3.61
325 331 4.007644 CCCACTGACAGCTCCGCA 62.008 66.667 1.25 0.00 0.00 5.69
327 333 3.108289 CACTGACAGCTCCGCACG 61.108 66.667 1.25 0.00 0.00 5.34
504 545 2.056094 GGGCATCACCGTACGTATAC 57.944 55.000 15.21 0.00 40.62 1.47
520 561 5.156990 CGTATACGTCTACGCATTTTAGC 57.843 43.478 18.62 0.00 44.43 3.09
527 586 3.062234 GTCTACGCATTTTAGCAGGACAC 59.938 47.826 0.00 0.00 31.76 3.67
529 588 0.096976 CGCATTTTAGCAGGACACCG 59.903 55.000 0.00 0.00 0.00 4.94
530 589 0.451783 GCATTTTAGCAGGACACCGG 59.548 55.000 0.00 0.00 0.00 5.28
531 590 1.094785 CATTTTAGCAGGACACCGGG 58.905 55.000 6.32 0.00 0.00 5.73
1101 1163 3.539842 GAGGGGGACTCGGACATC 58.460 66.667 0.00 0.00 36.29 3.06
2097 2159 1.737008 GAAGGAGTTCGCCGTGGTC 60.737 63.158 0.00 0.00 0.00 4.02
2148 2210 0.790866 GCAATTGTGCGCTTCTCGTC 60.791 55.000 9.73 0.00 41.93 4.20
2228 2290 6.531439 CAAAGCACAAGGTATACGTTCTAAC 58.469 40.000 7.83 0.00 0.00 2.34
2238 2300 7.293073 AGGTATACGTTCTAACCCTCTCATTA 58.707 38.462 0.00 0.00 32.10 1.90
2265 2327 5.327616 TGTTATGCTGAAATTGGATGTGG 57.672 39.130 0.00 0.00 0.00 4.17
2271 2333 3.328505 CTGAAATTGGATGTGGTTTGCC 58.671 45.455 0.00 0.00 0.00 4.52
2272 2334 2.288702 TGAAATTGGATGTGGTTTGCCG 60.289 45.455 0.00 0.00 37.67 5.69
2282 2344 5.641636 GGATGTGGTTTGCCGAATTTTATTT 59.358 36.000 0.00 0.00 37.67 1.40
2286 2348 6.146347 TGTGGTTTGCCGAATTTTATTTTAGC 59.854 34.615 0.00 0.00 37.67 3.09
2287 2349 5.346281 TGGTTTGCCGAATTTTATTTTAGCG 59.654 36.000 0.00 0.00 37.67 4.26
2305 2367 9.950680 ATTTTAGCGATAACAATTGGTGATTAG 57.049 29.630 6.16 0.00 0.00 1.73
2306 2368 8.500753 TTTAGCGATAACAATTGGTGATTAGT 57.499 30.769 6.16 0.00 0.00 2.24
2308 2370 7.478520 AGCGATAACAATTGGTGATTAGTAC 57.521 36.000 6.16 0.00 0.00 2.73
2309 2371 6.200286 AGCGATAACAATTGGTGATTAGTACG 59.800 38.462 6.16 6.31 0.00 3.67
2310 2372 6.199531 GCGATAACAATTGGTGATTAGTACGA 59.800 38.462 6.16 0.00 0.00 3.43
2311 2373 7.567048 GCGATAACAATTGGTGATTAGTACGAG 60.567 40.741 6.16 0.00 0.00 4.18
2312 2374 7.434307 CGATAACAATTGGTGATTAGTACGAGT 59.566 37.037 6.16 0.00 0.00 4.18
2313 2375 9.740239 GATAACAATTGGTGATTAGTACGAGTA 57.260 33.333 6.16 0.00 0.00 2.59
2314 2376 7.823149 AACAATTGGTGATTAGTACGAGTAC 57.177 36.000 10.83 5.32 36.35 2.73
2316 2378 7.256286 ACAATTGGTGATTAGTACGAGTACTC 58.744 38.462 17.98 13.18 44.58 2.59
2317 2379 7.094075 ACAATTGGTGATTAGTACGAGTACTCA 60.094 37.037 22.37 9.17 44.58 3.41
2318 2380 7.584122 ATTGGTGATTAGTACGAGTACTCAT 57.416 36.000 22.37 10.40 44.58 2.90
2319 2381 7.400599 TTGGTGATTAGTACGAGTACTCATT 57.599 36.000 22.37 11.01 44.58 2.57
2320 2382 7.024340 TGGTGATTAGTACGAGTACTCATTC 57.976 40.000 22.37 5.55 44.58 2.67
2321 2383 6.600427 TGGTGATTAGTACGAGTACTCATTCA 59.400 38.462 22.37 15.46 44.58 2.57
2322 2384 7.284716 TGGTGATTAGTACGAGTACTCATTCAT 59.715 37.037 22.37 6.37 44.58 2.57
2323 2385 8.781196 GGTGATTAGTACGAGTACTCATTCATA 58.219 37.037 22.37 5.82 44.58 2.15
2369 2431 3.391506 AAGGTTTGAGCTTTTGATGCC 57.608 42.857 0.00 0.00 30.79 4.40
2403 2465 3.874543 ACTGAACAGTGTGCAACGAATTA 59.125 39.130 5.21 0.00 42.39 1.40
2449 2511 4.935205 TCCGATTGACAGTACTGGAAAATG 59.065 41.667 26.12 14.76 34.19 2.32
2489 2551 1.289109 AATGACAGCGTGCGTGTACC 61.289 55.000 0.00 0.00 0.00 3.34
2497 2559 1.931709 GCGTGCGTGTACCTGAGTTTA 60.932 52.381 0.00 0.00 0.00 2.01
2528 2590 7.797038 TTTCTACTACCTGGTCTTCAAAAAC 57.203 36.000 0.63 0.00 0.00 2.43
2530 2592 7.074653 TCTACTACCTGGTCTTCAAAAACAT 57.925 36.000 0.63 0.00 0.00 2.71
2541 2603 6.760770 GGTCTTCAAAAACATCCAAATCAACA 59.239 34.615 0.00 0.00 0.00 3.33
2545 2607 5.518128 TCAAAAACATCCAAATCAACACGTG 59.482 36.000 15.48 15.48 0.00 4.49
2550 2612 4.097135 ACATCCAAATCAACACGTGTTTCA 59.903 37.500 30.49 20.15 35.83 2.69
2554 2616 4.440758 CCAAATCAACACGTGTTTCATCAC 59.559 41.667 30.49 0.00 35.83 3.06
2565 2627 5.779806 GTGTTTCATCACGCTAGTTGTAT 57.220 39.130 0.00 0.00 0.00 2.29
2566 2628 5.550981 GTGTTTCATCACGCTAGTTGTATG 58.449 41.667 0.00 0.00 0.00 2.39
2567 2629 4.092821 TGTTTCATCACGCTAGTTGTATGC 59.907 41.667 0.00 0.00 0.00 3.14
2568 2630 3.518634 TCATCACGCTAGTTGTATGCA 57.481 42.857 0.00 0.00 0.00 3.96
2569 2631 4.058721 TCATCACGCTAGTTGTATGCAT 57.941 40.909 3.79 3.79 0.00 3.96
2570 2632 4.441792 TCATCACGCTAGTTGTATGCATT 58.558 39.130 3.54 0.00 0.00 3.56
2571 2633 4.270808 TCATCACGCTAGTTGTATGCATTG 59.729 41.667 3.54 0.00 0.00 2.82
2572 2634 2.351418 TCACGCTAGTTGTATGCATTGC 59.649 45.455 3.54 0.46 0.00 3.56
2573 2635 1.670811 ACGCTAGTTGTATGCATTGCC 59.329 47.619 3.54 0.00 0.00 4.52
2574 2636 1.942657 CGCTAGTTGTATGCATTGCCT 59.057 47.619 3.54 0.00 0.00 4.75
2575 2637 2.355756 CGCTAGTTGTATGCATTGCCTT 59.644 45.455 3.54 0.00 0.00 4.35
2576 2638 3.699067 GCTAGTTGTATGCATTGCCTTG 58.301 45.455 3.54 0.00 0.00 3.61
2582 2644 5.354234 AGTTGTATGCATTGCCTTGTACTAC 59.646 40.000 3.54 10.40 0.00 2.73
2625 2687 6.287525 TGACTTGTACATTCAGTTCACATGA 58.712 36.000 0.00 0.00 0.00 3.07
2633 2695 5.752472 ACATTCAGTTCACATGATCGAGATC 59.248 40.000 0.00 6.16 38.29 2.75
2634 2696 4.313277 TCAGTTCACATGATCGAGATCC 57.687 45.455 10.24 0.00 37.02 3.36
2642 2704 0.528466 TGATCGAGATCCGCACTTGC 60.528 55.000 10.24 0.00 37.02 4.01
2657 2719 4.739716 CGCACTTGCTTAATTTCACACTTT 59.260 37.500 0.00 0.00 39.32 2.66
2661 2723 7.393327 CACTTGCTTAATTTCACACTTTGTTG 58.607 34.615 0.00 0.00 0.00 3.33
2672 2748 4.161565 TCACACTTTGTTGAGTACAGTCCT 59.838 41.667 0.00 0.00 38.19 3.85
2674 2750 4.161565 ACACTTTGTTGAGTACAGTCCTGA 59.838 41.667 0.40 0.00 38.19 3.86
2683 2759 4.642437 TGAGTACAGTCCTGAATCTGCTAG 59.358 45.833 0.40 0.00 35.37 3.42
2708 2784 2.111384 TGGAAGTACAGGAGGATGAGC 58.889 52.381 0.00 0.00 0.00 4.26
2711 2794 1.068250 GTACAGGAGGATGAGCGCC 59.932 63.158 2.29 0.00 0.00 6.53
2725 2808 1.454111 GCGCCCTCTCTCCTACAGA 60.454 63.158 0.00 0.00 0.00 3.41
2737 2820 2.768527 CTCCTACAGATCAAAGAGGCCA 59.231 50.000 5.01 0.00 0.00 5.36
2741 2824 1.425066 ACAGATCAAAGAGGCCACCAA 59.575 47.619 5.01 0.00 0.00 3.67
2760 2843 6.540914 CCACCAAGTCAAAACTACAGTTCTTA 59.459 38.462 0.00 0.00 37.25 2.10
2761 2844 7.066525 CCACCAAGTCAAAACTACAGTTCTTAA 59.933 37.037 0.00 0.00 37.25 1.85
2762 2845 8.455682 CACCAAGTCAAAACTACAGTTCTTAAA 58.544 33.333 0.00 0.00 37.25 1.52
2763 2846 9.016438 ACCAAGTCAAAACTACAGTTCTTAAAA 57.984 29.630 0.00 0.00 37.25 1.52
2803 3055 1.270625 TGTCACTAGAAACCGGGCAAG 60.271 52.381 6.32 0.00 0.00 4.01
2811 3063 2.035449 AGAAACCGGGCAAGCTTAAAAC 59.965 45.455 6.32 0.00 0.00 2.43
2905 3160 4.739195 CCACTAGAGTCTGTCTACTTTGC 58.261 47.826 1.86 0.00 36.64 3.68
2910 3165 3.055530 AGAGTCTGTCTACTTTGCCATGG 60.056 47.826 7.63 7.63 31.71 3.66
2916 3171 4.199310 TGTCTACTTTGCCATGGCTAATC 58.801 43.478 35.53 20.28 42.51 1.75
2928 3183 3.413846 TGGCTAATCTGATCCTCATGC 57.586 47.619 0.00 0.00 0.00 4.06
2937 3192 1.417517 TGATCCTCATGCGTGCCTTAT 59.582 47.619 0.00 0.00 0.00 1.73
2941 3196 3.088532 TCCTCATGCGTGCCTTATTTTT 58.911 40.909 0.00 0.00 0.00 1.94
3030 3289 5.437060 TCCTGAATTCCAAGCCACTTATAC 58.563 41.667 2.27 0.00 0.00 1.47
3034 3293 5.708230 TGAATTCCAAGCCACTTATACGTTT 59.292 36.000 2.27 0.00 0.00 3.60
3035 3294 5.560966 ATTCCAAGCCACTTATACGTTTG 57.439 39.130 0.00 0.00 0.00 2.93
3052 3311 3.520569 GTTTGGTTGTGTGATTTGCAGT 58.479 40.909 0.00 0.00 0.00 4.40
3252 3512 4.388499 TTTCACCTCGCCGGCTCC 62.388 66.667 26.68 0.00 35.61 4.70
3264 3525 1.165270 CCGGCTCCGTTCTTGATTTT 58.835 50.000 7.59 0.00 37.81 1.82
3298 3559 1.211457 GAGCAGCCCTATATGGATGGG 59.789 57.143 13.31 2.30 42.12 4.00
3299 3560 1.203479 AGCAGCCCTATATGGATGGGA 60.203 52.381 13.31 0.00 42.12 4.37
3300 3561 1.065126 GCAGCCCTATATGGATGGGAC 60.065 57.143 13.31 0.00 42.12 4.46
3301 3562 1.208052 CAGCCCTATATGGATGGGACG 59.792 57.143 4.51 0.00 43.47 4.79
3302 3563 0.541863 GCCCTATATGGATGGGACGG 59.458 60.000 0.91 0.00 43.47 4.79
3336 3597 0.654160 GTGTAAATAACGGCCGGCTC 59.346 55.000 31.76 15.77 0.00 4.70
3348 3609 2.668632 CGGCTCTTGGCTGGGTTA 59.331 61.111 0.00 0.00 43.23 2.85
3374 3637 4.142049 TGAATACATATGTGGTCTGCGACA 60.142 41.667 18.81 3.38 37.71 4.35
3398 3661 2.103263 GAGCGATGGAAGGTTAGATGGT 59.897 50.000 0.00 0.00 0.00 3.55
3463 3727 1.022735 GAGGACATGGATTGCTGCTG 58.977 55.000 0.00 0.00 0.00 4.41
3464 3728 0.395311 AGGACATGGATTGCTGCTGG 60.395 55.000 0.00 0.00 0.00 4.85
3467 3731 0.251922 ACATGGATTGCTGCTGGGTT 60.252 50.000 0.00 0.00 0.00 4.11
3468 3732 1.005805 ACATGGATTGCTGCTGGGTTA 59.994 47.619 0.00 0.00 0.00 2.85
3483 3750 2.093394 TGGGTTATATGTGTGGTGTCGG 60.093 50.000 0.00 0.00 0.00 4.79
3536 3804 2.089201 GGTAATATGGTAATGCCGGCC 58.911 52.381 26.77 8.13 41.21 6.13
3635 3905 3.877508 CCCCAGTTCCGTTTTATGATCTC 59.122 47.826 0.00 0.00 0.00 2.75
3660 3930 0.708918 GCGTGACTAGTTTCGCAGAC 59.291 55.000 27.89 9.24 46.40 3.51
3661 3931 1.666311 GCGTGACTAGTTTCGCAGACT 60.666 52.381 27.89 0.00 46.40 3.24
3662 3932 1.979469 CGTGACTAGTTTCGCAGACTG 59.021 52.381 0.00 0.00 34.32 3.51
3663 3933 2.604855 CGTGACTAGTTTCGCAGACTGT 60.605 50.000 3.99 0.00 34.32 3.55
3664 3934 3.381949 GTGACTAGTTTCGCAGACTGTT 58.618 45.455 3.99 0.00 34.32 3.16
3669 3939 3.675467 AGTTTCGCAGACTGTTTGTTC 57.325 42.857 3.99 0.00 34.32 3.18
3674 3944 0.534203 GCAGACTGTTTGTTCCCCGA 60.534 55.000 3.99 0.00 0.00 5.14
3689 3959 0.253044 CCCGATTTCTCCTGCTCCAA 59.747 55.000 0.00 0.00 0.00 3.53
3706 3976 4.651778 CTCCAATTGGTCTGTTTCTACCA 58.348 43.478 23.76 0.00 43.99 3.25
3718 3988 5.938125 TCTGTTTCTACCATTTTGTAGCTCC 59.062 40.000 0.00 0.00 38.46 4.70
3728 3998 2.202810 GTAGCTCCGGCACTCAGC 60.203 66.667 3.94 3.94 41.70 4.26
3729 3999 2.363018 TAGCTCCGGCACTCAGCT 60.363 61.111 17.65 17.65 44.79 4.24
3730 4000 1.984570 TAGCTCCGGCACTCAGCTT 60.985 57.895 18.60 4.94 44.79 3.74
3746 4106 7.227512 GCACTCAGCTTATTTACCTGATGTAAT 59.772 37.037 0.00 0.00 38.57 1.89
3811 4171 2.528743 GCGGTGCGGTCATGATCAG 61.529 63.158 6.80 0.10 0.00 2.90
3813 4173 0.102300 CGGTGCGGTCATGATCAGTA 59.898 55.000 6.80 0.00 0.00 2.74
3825 4185 6.018425 GGTCATGATCAGTAAACACAGCTATG 60.018 42.308 0.00 0.00 0.00 2.23
3870 4230 5.525426 GGTATGCCATGGTTGCACTCAAC 62.525 52.174 14.67 2.73 42.38 3.18
3924 4286 0.770557 ACTAGTGGCCCCCTTTGTGA 60.771 55.000 0.00 0.00 0.00 3.58
3926 4288 0.770557 TAGTGGCCCCCTTTGTGACT 60.771 55.000 0.00 0.00 0.00 3.41
3940 4302 1.409064 TGTGACTGATCGACATAGGCC 59.591 52.381 0.00 0.00 0.00 5.19
3950 4312 2.029307 GACATAGGCCTGTCCCGACC 62.029 65.000 17.99 0.00 39.72 4.79
4031 4393 4.166011 GGTTCGTGCGATGCTGGC 62.166 66.667 0.00 0.00 0.00 4.85
4128 4490 2.103143 CTAGCTGGCCGAGTGACG 59.897 66.667 0.00 0.00 42.18 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.643387 AACCTGAGCCGTGGTGCC 62.643 66.667 0.00 0.00 36.57 5.01
17 18 2.030562 CCGTGAAACCTGAGCCGT 59.969 61.111 0.00 0.00 0.00 5.68
70 76 4.194720 CTTCGACCTCCGCCTCCG 62.195 72.222 0.00 0.00 38.37 4.63
103 109 0.905839 GTCGTCGTATTGTCTCGTGC 59.094 55.000 0.00 0.00 0.00 5.34
109 115 3.282740 CGGCGTCGTCGTATTGTC 58.717 61.111 11.83 0.00 39.49 3.18
163 169 2.724174 GGAATCGCTTGTTTTCCGTTTG 59.276 45.455 0.00 0.00 30.41 2.93
164 170 2.621526 AGGAATCGCTTGTTTTCCGTTT 59.378 40.909 0.00 0.00 43.01 3.60
165 171 2.227194 AGGAATCGCTTGTTTTCCGTT 58.773 42.857 0.00 0.00 43.01 4.44
166 172 1.892209 AGGAATCGCTTGTTTTCCGT 58.108 45.000 0.00 0.00 43.01 4.69
195 201 5.051816 GGTTTACTTTACTTTTTGGTGGCC 58.948 41.667 0.00 0.00 0.00 5.36
207 213 0.798159 CCACCGCCGGTTTACTTTAC 59.202 55.000 5.76 0.00 31.02 2.01
208 214 0.954938 GCCACCGCCGGTTTACTTTA 60.955 55.000 5.76 0.00 31.02 1.85
209 215 2.263021 GCCACCGCCGGTTTACTTT 61.263 57.895 5.76 0.00 31.02 2.66
210 216 2.670592 GCCACCGCCGGTTTACTT 60.671 61.111 5.76 0.00 31.02 2.24
244 250 3.358932 AAAGCGCCATGGGTAGGGG 62.359 63.158 15.13 0.00 41.62 4.79
248 254 1.223487 GAGGAAAGCGCCATGGGTA 59.777 57.895 15.13 0.00 0.00 3.69
249 255 2.044946 GAGGAAAGCGCCATGGGT 60.045 61.111 15.13 0.00 0.00 4.51
250 256 2.830370 GGAGGAAAGCGCCATGGG 60.830 66.667 15.13 4.77 0.00 4.00
251 257 2.830370 GGGAGGAAAGCGCCATGG 60.830 66.667 7.63 7.63 0.00 3.66
252 258 2.830370 GGGGAGGAAAGCGCCATG 60.830 66.667 2.29 0.00 38.18 3.66
253 259 4.489771 CGGGGAGGAAAGCGCCAT 62.490 66.667 2.29 0.00 38.18 4.40
294 300 3.625897 TGGGAGGAGTGTGCGGTG 61.626 66.667 0.00 0.00 0.00 4.94
295 301 3.626924 GTGGGAGGAGTGTGCGGT 61.627 66.667 0.00 0.00 0.00 5.68
377 383 1.369091 CCGCTGAAAATCTCACCCCG 61.369 60.000 0.00 0.00 0.00 5.73
378 384 1.657751 GCCGCTGAAAATCTCACCCC 61.658 60.000 0.00 0.00 0.00 4.95
379 385 1.803289 GCCGCTGAAAATCTCACCC 59.197 57.895 0.00 0.00 0.00 4.61
382 388 2.739704 CGCGCCGCTGAAAATCTCA 61.740 57.895 7.78 0.00 0.00 3.27
499 540 5.116680 CCTGCTAAAATGCGTAGACGTATAC 59.883 44.000 10.30 10.30 43.57 1.47
500 541 5.008911 TCCTGCTAAAATGCGTAGACGTATA 59.991 40.000 6.07 0.00 43.57 1.47
501 542 4.049186 CCTGCTAAAATGCGTAGACGTAT 58.951 43.478 3.73 1.56 46.16 3.06
503 544 2.094390 TCCTGCTAAAATGCGTAGACGT 60.094 45.455 3.73 0.00 42.22 4.34
504 545 2.281762 GTCCTGCTAAAATGCGTAGACG 59.718 50.000 0.00 0.00 43.27 4.18
505 546 3.062234 GTGTCCTGCTAAAATGCGTAGAC 59.938 47.826 0.00 0.00 35.36 2.59
509 550 1.165270 GGTGTCCTGCTAAAATGCGT 58.835 50.000 0.00 0.00 35.36 5.24
510 551 0.096976 CGGTGTCCTGCTAAAATGCG 59.903 55.000 0.00 0.00 35.36 4.73
512 553 1.094785 CCCGGTGTCCTGCTAAAATG 58.905 55.000 0.00 0.00 0.00 2.32
513 554 0.679960 GCCCGGTGTCCTGCTAAAAT 60.680 55.000 0.00 0.00 0.00 1.82
515 556 2.349755 GCCCGGTGTCCTGCTAAA 59.650 61.111 0.00 0.00 0.00 1.85
517 558 3.390521 CTGCCCGGTGTCCTGCTA 61.391 66.667 0.00 0.00 0.00 3.49
1101 1163 1.507174 GGAGTCGGTGAGGTTCTCG 59.493 63.158 0.00 0.00 32.35 4.04
1209 1271 4.193334 TCGAGCATCTCCGTGGCG 62.193 66.667 0.00 0.00 0.00 5.69
1410 1472 3.036084 ACGCACGCCAGAACGAAG 61.036 61.111 0.00 0.00 36.70 3.79
2097 2159 3.024782 GCACAGCTGAAGCAGAGCG 62.025 63.158 23.35 0.00 45.16 5.03
2106 2168 2.653115 CACTCGGAGCACAGCTGA 59.347 61.111 23.35 0.00 39.88 4.26
2133 2195 2.733218 CGGACGAGAAGCGCACAA 60.733 61.111 11.47 0.00 46.04 3.33
2134 2196 3.610791 CTCGGACGAGAAGCGCACA 62.611 63.158 16.15 0.00 44.53 4.57
2160 2222 3.195698 GCAACGAGCGGTGGGATC 61.196 66.667 10.16 0.00 32.56 3.36
2205 2267 5.640783 GGTTAGAACGTATACCTTGTGCTTT 59.359 40.000 0.00 0.00 0.00 3.51
2228 2290 6.543465 TCAGCATAACATTTGTAATGAGAGGG 59.457 38.462 6.42 0.00 0.00 4.30
2238 2300 7.332430 CACATCCAATTTCAGCATAACATTTGT 59.668 33.333 0.00 0.00 0.00 2.83
2265 2327 6.620253 TCGCTAAAATAAAATTCGGCAAAC 57.380 33.333 0.00 0.00 0.00 2.93
2282 2344 9.037737 GTACTAATCACCAATTGTTATCGCTAA 57.962 33.333 4.43 0.00 0.00 3.09
2286 2348 7.434307 ACTCGTACTAATCACCAATTGTTATCG 59.566 37.037 4.43 3.21 0.00 2.92
2287 2349 8.644318 ACTCGTACTAATCACCAATTGTTATC 57.356 34.615 4.43 0.00 0.00 1.75
2331 2393 8.962679 TCAAACCTTACACTGACAAGTTAAAAT 58.037 29.630 0.00 0.00 32.98 1.82
2332 2394 8.338072 TCAAACCTTACACTGACAAGTTAAAA 57.662 30.769 0.00 0.00 32.98 1.52
2347 2409 4.237724 GGCATCAAAAGCTCAAACCTTAC 58.762 43.478 0.00 0.00 0.00 2.34
2369 2431 5.334435 CACTGTTCAGTACAATGACAGTG 57.666 43.478 24.23 24.23 43.89 3.66
2403 2465 6.931840 GGACTTCAATCAAACTCTAACTGACT 59.068 38.462 0.00 0.00 0.00 3.41
2449 2511 5.841957 TTCTACCGGTCCAGAGTTAATAC 57.158 43.478 12.40 0.00 0.00 1.89
2509 2571 5.070685 GGATGTTTTTGAAGACCAGGTAGT 58.929 41.667 0.00 0.00 0.00 2.73
2528 2590 4.605968 TGAAACACGTGTTGATTTGGATG 58.394 39.130 32.89 0.00 38.44 3.51
2530 2592 4.336713 TGATGAAACACGTGTTGATTTGGA 59.663 37.500 32.89 12.29 38.44 3.53
2545 2607 4.092821 TGCATACAACTAGCGTGATGAAAC 59.907 41.667 1.18 0.00 0.00 2.78
2550 2612 3.002656 GCAATGCATACAACTAGCGTGAT 59.997 43.478 0.00 0.00 0.00 3.06
2554 2616 1.942657 AGGCAATGCATACAACTAGCG 59.057 47.619 7.79 0.00 0.00 4.26
2557 2619 5.496556 AGTACAAGGCAATGCATACAACTA 58.503 37.500 7.79 0.00 0.00 2.24
2558 2620 4.335416 AGTACAAGGCAATGCATACAACT 58.665 39.130 7.79 1.29 0.00 3.16
2559 2621 4.701956 AGTACAAGGCAATGCATACAAC 57.298 40.909 7.79 0.00 0.00 3.32
2560 2622 5.496556 AGTAGTACAAGGCAATGCATACAA 58.503 37.500 7.79 0.00 0.00 2.41
2561 2623 5.097742 AGTAGTACAAGGCAATGCATACA 57.902 39.130 7.79 0.00 0.00 2.29
2562 2624 6.201044 CAGTAGTAGTACAAGGCAATGCATAC 59.799 42.308 7.79 3.96 0.00 2.39
2563 2625 6.097696 TCAGTAGTAGTACAAGGCAATGCATA 59.902 38.462 7.79 0.00 0.00 3.14
2564 2626 5.104941 TCAGTAGTAGTACAAGGCAATGCAT 60.105 40.000 7.79 0.00 0.00 3.96
2565 2627 4.221924 TCAGTAGTAGTACAAGGCAATGCA 59.778 41.667 7.79 0.00 0.00 3.96
2566 2628 4.755411 TCAGTAGTAGTACAAGGCAATGC 58.245 43.478 10.33 0.00 0.00 3.56
2567 2629 6.573434 TGATCAGTAGTAGTACAAGGCAATG 58.427 40.000 10.33 0.00 0.00 2.82
2568 2630 6.791867 TGATCAGTAGTAGTACAAGGCAAT 57.208 37.500 10.33 0.00 0.00 3.56
2569 2631 6.351033 CCTTGATCAGTAGTAGTACAAGGCAA 60.351 42.308 17.18 7.83 43.56 4.52
2570 2632 5.127194 CCTTGATCAGTAGTAGTACAAGGCA 59.873 44.000 17.18 0.81 43.56 4.75
2571 2633 5.360144 TCCTTGATCAGTAGTAGTACAAGGC 59.640 44.000 20.92 2.85 46.79 4.35
2573 2635 6.603997 ACCTCCTTGATCAGTAGTAGTACAAG 59.396 42.308 10.33 0.00 34.85 3.16
2574 2636 6.377429 CACCTCCTTGATCAGTAGTAGTACAA 59.623 42.308 10.33 0.00 0.00 2.41
2575 2637 5.886474 CACCTCCTTGATCAGTAGTAGTACA 59.114 44.000 10.33 0.00 0.00 2.90
2576 2638 5.887035 ACACCTCCTTGATCAGTAGTAGTAC 59.113 44.000 0.00 0.00 0.00 2.73
2582 2644 4.221703 AGTCAACACCTCCTTGATCAGTAG 59.778 45.833 0.00 0.00 30.46 2.57
2594 2656 5.057149 ACTGAATGTACAAGTCAACACCTC 58.943 41.667 12.25 0.00 0.00 3.85
2625 2687 4.427394 GCAAGTGCGGATCTCGAT 57.573 55.556 7.64 0.00 42.43 3.59
2642 2704 9.438291 CTGTACTCAACAAAGTGTGAAATTAAG 57.562 33.333 0.00 0.00 37.74 1.85
2657 2719 4.561530 GCAGATTCAGGACTGTACTCAACA 60.562 45.833 0.00 0.00 36.62 3.33
2661 2723 4.884744 TCTAGCAGATTCAGGACTGTACTC 59.115 45.833 0.00 0.00 36.62 2.59
2672 2748 3.840666 ACTTCCAAGGTCTAGCAGATTCA 59.159 43.478 0.00 0.00 0.00 2.57
2674 2750 4.777896 TGTACTTCCAAGGTCTAGCAGATT 59.222 41.667 0.00 0.00 0.00 2.40
2683 2759 2.537143 TCCTCCTGTACTTCCAAGGTC 58.463 52.381 0.00 0.00 0.00 3.85
2708 2784 1.243902 GATCTGTAGGAGAGAGGGCG 58.756 60.000 0.00 0.00 32.80 6.13
2711 2794 4.584325 CCTCTTTGATCTGTAGGAGAGAGG 59.416 50.000 0.00 0.00 34.09 3.69
2725 2808 1.425066 TGACTTGGTGGCCTCTTTGAT 59.575 47.619 3.32 0.00 0.00 2.57
2737 2820 8.570068 TTTAAGAACTGTAGTTTTGACTTGGT 57.430 30.769 0.00 0.00 38.56 3.67
2760 2843 5.465056 CACCAAGCATTGTTTACGGAATTTT 59.535 36.000 0.00 0.00 46.99 1.82
2761 2844 4.987912 CACCAAGCATTGTTTACGGAATTT 59.012 37.500 0.00 0.00 46.99 1.82
2762 2845 4.038642 ACACCAAGCATTGTTTACGGAATT 59.961 37.500 0.00 0.00 46.99 2.17
2763 2846 3.572255 ACACCAAGCATTGTTTACGGAAT 59.428 39.130 0.00 0.00 46.99 3.01
2765 2848 2.550606 GACACCAAGCATTGTTTACGGA 59.449 45.455 0.00 0.00 46.99 4.69
2766 2849 2.292016 TGACACCAAGCATTGTTTACGG 59.708 45.455 0.00 0.00 46.99 4.02
2798 3050 1.666023 GCACGGAGTTTTAAGCTTGCC 60.666 52.381 9.86 0.03 41.61 4.52
2803 3055 2.304413 GTTTCGCACGGAGTTTTAAGC 58.696 47.619 0.00 0.00 41.61 3.09
2811 3063 1.497278 CACATGGTTTCGCACGGAG 59.503 57.895 0.00 0.00 0.00 4.63
2941 3196 3.818773 GGTGTGATCCCTCTTTTCGAAAA 59.181 43.478 21.35 21.35 0.00 2.29
2946 3201 1.679032 CGGGGTGTGATCCCTCTTTTC 60.679 57.143 1.72 0.00 46.27 2.29
3005 3263 3.463048 AGTGGCTTGGAATTCAGGAAT 57.537 42.857 7.93 0.00 0.00 3.01
3030 3289 2.534298 TGCAAATCACACAACCAAACG 58.466 42.857 0.00 0.00 0.00 3.60
3034 3293 2.358582 CAGACTGCAAATCACACAACCA 59.641 45.455 0.00 0.00 0.00 3.67
3035 3294 2.618241 TCAGACTGCAAATCACACAACC 59.382 45.455 0.00 0.00 0.00 3.77
3252 3512 1.193650 TCGACGCCAAAATCAAGAACG 59.806 47.619 0.00 0.00 0.00 3.95
3264 3525 2.258591 GCTCTGTTCTCGACGCCA 59.741 61.111 0.00 0.00 0.00 5.69
3298 3559 3.865929 ATGATCATCGCGCCCCGTC 62.866 63.158 1.18 0.00 38.35 4.79
3299 3560 3.928779 ATGATCATCGCGCCCCGT 61.929 61.111 1.18 0.00 38.35 5.28
3300 3561 3.417224 CATGATCATCGCGCCCCG 61.417 66.667 4.86 0.00 38.61 5.73
3301 3562 2.281070 ACATGATCATCGCGCCCC 60.281 61.111 4.86 0.00 0.00 5.80
3302 3563 0.599991 TACACATGATCATCGCGCCC 60.600 55.000 4.86 0.00 0.00 6.13
3336 3597 4.269183 TGTATTCACATAACCCAGCCAAG 58.731 43.478 0.00 0.00 0.00 3.61
3374 3637 0.103208 CTAACCTTCCATCGCTCGCT 59.897 55.000 0.00 0.00 0.00 4.93
3380 3643 3.206150 CCAACCATCTAACCTTCCATCG 58.794 50.000 0.00 0.00 0.00 3.84
3398 3661 5.511373 CCTCTCAACTGATGTTAGTGACCAA 60.511 44.000 0.00 0.00 34.60 3.67
3463 3727 2.557317 CCGACACCACACATATAACCC 58.443 52.381 0.00 0.00 0.00 4.11
3464 3728 2.093341 ACCCGACACCACACATATAACC 60.093 50.000 0.00 0.00 0.00 2.85
3467 3731 2.568062 ACAACCCGACACCACACATATA 59.432 45.455 0.00 0.00 0.00 0.86
3468 3732 1.349688 ACAACCCGACACCACACATAT 59.650 47.619 0.00 0.00 0.00 1.78
3483 3750 3.262420 CATCCTGTACACAGCTACAACC 58.738 50.000 3.75 0.00 42.47 3.77
3543 3811 1.343465 ACATTCCCCTATAACCTCGCG 59.657 52.381 0.00 0.00 0.00 5.87
3617 3886 7.201530 CGCTAAAAGAGATCATAAAACGGAACT 60.202 37.037 0.00 0.00 0.00 3.01
3635 3905 3.975093 GCGAAACTAGTCACGCTAAAAG 58.025 45.455 27.37 3.02 46.06 2.27
3658 3928 3.146847 AGAAATCGGGGAACAAACAGTC 58.853 45.455 0.00 0.00 0.00 3.51
3660 3930 2.488153 GGAGAAATCGGGGAACAAACAG 59.512 50.000 0.00 0.00 0.00 3.16
3661 3931 2.107552 AGGAGAAATCGGGGAACAAACA 59.892 45.455 0.00 0.00 0.00 2.83
3662 3932 2.488153 CAGGAGAAATCGGGGAACAAAC 59.512 50.000 0.00 0.00 0.00 2.93
3663 3933 2.790433 CAGGAGAAATCGGGGAACAAA 58.210 47.619 0.00 0.00 0.00 2.83
3664 3934 1.613255 GCAGGAGAAATCGGGGAACAA 60.613 52.381 0.00 0.00 0.00 2.83
3669 3939 1.147153 GGAGCAGGAGAAATCGGGG 59.853 63.158 0.00 0.00 0.00 5.73
3674 3944 3.011032 AGACCAATTGGAGCAGGAGAAAT 59.989 43.478 31.22 3.28 38.94 2.17
3706 3976 1.003118 TGAGTGCCGGAGCTACAAAAT 59.997 47.619 5.05 0.00 40.80 1.82
3718 3988 2.906354 AGGTAAATAAGCTGAGTGCCG 58.094 47.619 0.00 0.00 44.23 5.69
3746 4106 3.409201 GCAGCAGCTTCCATATGGA 57.591 52.632 20.98 20.98 43.73 3.41
3778 4138 1.519234 CCGCAGCTATCGCAGTGAA 60.519 57.895 0.00 0.00 35.44 3.18
3799 4159 3.062639 GCTGTGTTTACTGATCATGACCG 59.937 47.826 0.00 0.00 0.00 4.79
3811 4171 2.095372 GGTTCGCCATAGCTGTGTTTAC 59.905 50.000 9.80 2.34 36.60 2.01
3813 4173 1.165270 GGTTCGCCATAGCTGTGTTT 58.835 50.000 9.80 0.00 36.60 2.83
3825 4185 2.202783 GGCATGCATTGGTTCGCC 60.203 61.111 21.36 7.63 37.92 5.54
3870 4230 6.475727 CAGCCAGCTTAATCTTGAATGAATTG 59.524 38.462 0.00 0.00 0.00 2.32
3924 4286 1.683917 GACAGGCCTATGTCGATCAGT 59.316 52.381 3.98 0.00 40.18 3.41
3940 4302 1.004918 GAACCAGTGGTCGGGACAG 60.005 63.158 17.06 0.00 33.12 3.51
3950 4312 1.267806 GTGTTGCATCAGGAACCAGTG 59.732 52.381 0.00 0.00 44.50 3.66
4023 4385 0.861837 CGAAACCTATCGCCAGCATC 59.138 55.000 0.00 0.00 35.85 3.91
4031 4393 1.731700 TCGGAGCCGAAACCTATCG 59.268 57.895 9.50 0.00 46.01 2.92


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

AutoCloner maintained by Alex Coulton.