Multiple sequence alignment - TraesCS1D01G185300

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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 TraesCS1D01G185300 chr1D 100.000 3077 0 0 1 3077 256114710 256111634 0.000000e+00 5683.0
1 TraesCS1D01G185300 chr1D 93.511 262 15 2 2375 2635 423924497 423924757 3.720000e-104 388.0
2 TraesCS1D01G185300 chr1A 95.660 2143 72 12 243 2375 328842980 328840849 0.000000e+00 3422.0
3 TraesCS1D01G185300 chr1A 89.773 440 38 1 2638 3077 328840845 328840413 9.640000e-155 556.0
4 TraesCS1D01G185300 chr1A 77.273 418 73 15 2636 3036 321045548 321045960 3.090000e-55 226.0
5 TraesCS1D01G185300 chr1B 93.824 1700 78 14 507 2192 356947322 356949008 0.000000e+00 2532.0
6 TraesCS1D01G185300 chr1B 96.667 510 15 2 1 509 356946653 356947161 0.000000e+00 846.0
7 TraesCS1D01G185300 chr1B 82.040 451 62 12 2639 3077 110121769 110121326 1.740000e-97 366.0
8 TraesCS1D01G185300 chr1B 91.818 110 6 1 2270 2376 356949439 356949548 1.910000e-32 150.0
9 TraesCS1D01G185300 chr4D 81.591 1119 140 34 1000 2085 476321069 476319984 0.000000e+00 865.0
10 TraesCS1D01G185300 chr4D 81.062 433 63 12 2636 3056 49876793 49877218 8.230000e-86 327.0
11 TraesCS1D01G185300 chr4B 80.944 1102 144 38 990 2064 600874698 600873636 0.000000e+00 811.0
12 TraesCS1D01G185300 chr4B 93.436 259 16 1 2386 2643 418510971 418510713 1.730000e-102 383.0
13 TraesCS1D01G185300 chr4B 82.159 454 66 5 2635 3077 575652291 575652740 2.900000e-100 375.0
14 TraesCS1D01G185300 chr4B 94.595 37 2 0 1743 1779 146994551 146994587 1.190000e-04 58.4
15 TraesCS1D01G185300 chr4A 80.000 1130 150 32 990 2075 683536522 683535425 0.000000e+00 765.0
16 TraesCS1D01G185300 chr4A 92.193 269 19 2 2374 2641 632239261 632238994 2.240000e-101 379.0
17 TraesCS1D01G185300 chr4A 96.774 31 1 0 1743 1773 708923614 708923644 6.000000e-03 52.8
18 TraesCS1D01G185300 chr2A 83.778 450 54 12 2638 3077 564613439 564613879 2.860000e-110 409.0
19 TraesCS1D01G185300 chr6D 93.962 265 14 2 2373 2636 151317211 151317474 1.720000e-107 399.0
20 TraesCS1D01G185300 chr2B 92.937 269 17 2 2373 2640 157755982 157756249 1.030000e-104 390.0
21 TraesCS1D01G185300 chr2B 81.111 450 66 13 2638 3077 641652426 641651986 2.940000e-90 342.0
22 TraesCS1D01G185300 chr2B 86.458 96 13 0 2629 2724 17349950 17350045 4.200000e-19 106.0
23 TraesCS1D01G185300 chr6B 92.910 268 17 2 2375 2641 583188973 583189239 3.720000e-104 388.0
24 TraesCS1D01G185300 chr7B 92.565 269 17 3 2368 2635 713286454 713286188 1.730000e-102 383.0
25 TraesCS1D01G185300 chr3D 92.279 272 18 3 2372 2641 421266633 421266363 1.730000e-102 383.0
26 TraesCS1D01G185300 chr5A 91.941 273 19 3 2374 2645 614360415 614360145 2.240000e-101 379.0
27 TraesCS1D01G185300 chr5A 79.823 451 74 12 2638 3077 616918104 616917660 2.300000e-81 313.0
28 TraesCS1D01G185300 chr5A 80.000 95 12 4 2723 2810 564642375 564642469 2.560000e-06 63.9
29 TraesCS1D01G185300 chr6A 81.718 454 73 5 2632 3077 608085822 608085371 1.350000e-98 370.0
30 TraesCS1D01G185300 chr6A 79.773 440 73 10 2650 3077 452304734 452304299 3.850000e-79 305.0
31 TraesCS1D01G185300 chrUn 80.963 457 60 17 2638 3077 12317340 12317786 1.370000e-88 337.0
32 TraesCS1D01G185300 chr7D 79.521 459 70 18 2638 3077 403417284 403417737 3.850000e-79 305.0
33 TraesCS1D01G185300 chr7A 79.556 450 72 12 2639 3077 731133159 731133599 1.390000e-78 303.0
34 TraesCS1D01G185300 chr5D 94.286 70 4 0 2638 2707 260674532 260674601 1.170000e-19 108.0
35 TraesCS1D01G185300 chr5B 96.774 31 1 0 1743 1773 561715913 561715943 6.000000e-03 52.8


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 TraesCS1D01G185300 chr1D 256111634 256114710 3076 True 5683 5683 100.0000 1 3077 1 chr1D.!!$R1 3076
1 TraesCS1D01G185300 chr1A 328840413 328842980 2567 True 1989 3422 92.7165 243 3077 2 chr1A.!!$R1 2834
2 TraesCS1D01G185300 chr1B 356946653 356949548 2895 False 1176 2532 94.1030 1 2376 3 chr1B.!!$F1 2375
3 TraesCS1D01G185300 chr4D 476319984 476321069 1085 True 865 865 81.5910 1000 2085 1 chr4D.!!$R1 1085
4 TraesCS1D01G185300 chr4B 600873636 600874698 1062 True 811 811 80.9440 990 2064 1 chr4B.!!$R2 1074
5 TraesCS1D01G185300 chr4A 683535425 683536522 1097 True 765 765 80.0000 990 2075 1 chr4A.!!$R2 1085

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
553 726 1.457346 CTGTTCCTTCAGGCATGTCC 58.543 55.0 0.0 0.0 34.44 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2159 2399 1.217882 GGAATTCATAGACACCCGCG 58.782 55.0 7.93 0.0 0.0 6.46 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
35 36 3.651562 ACGAAAACGATAAATGAGGCG 57.348 42.857 0.00 0.00 0.00 5.52
123 124 2.170607 ACTGCTAAATGACATAGCCCGT 59.829 45.455 7.57 3.10 44.08 5.28
219 220 9.892130 AAAATCAAGTTCTCTAAGTATCGGAAT 57.108 29.630 0.00 0.00 0.00 3.01
307 309 9.528018 TGAAAAAGCTTAAAAATGAAGTACTGG 57.472 29.630 0.00 0.00 0.00 4.00
501 511 5.470777 CCAAATTTCCGGTGTGTCTTACTTA 59.529 40.000 0.00 0.00 0.00 2.24
531 704 3.141398 TGATCAAGAAACTGCCTGTGTC 58.859 45.455 0.00 0.00 33.08 3.67
553 726 1.457346 CTGTTCCTTCAGGCATGTCC 58.543 55.000 0.00 0.00 34.44 4.02
684 858 3.321682 CACCACCTCCATCACAAAATTGT 59.678 43.478 0.00 0.00 43.36 2.71
707 893 2.367894 TGCATTCCCAAGAAATGTTGCA 59.632 40.909 0.00 0.00 40.31 4.08
864 1052 5.732633 TCATTTACTTTTTACCGGGATCGA 58.267 37.500 6.32 0.00 39.00 3.59
1005 1193 2.975266 GCATTTGATTGCACCATGGAA 58.025 42.857 21.47 2.07 42.31 3.53
1089 1286 1.984817 CAACTTACCCGCCTACCCA 59.015 57.895 0.00 0.00 0.00 4.51
1270 1479 3.371063 TCACGCCCGTGGAGACTC 61.371 66.667 19.25 0.00 45.43 3.36
1296 1511 2.646175 GGTGTCGAGGCCAGCTGTA 61.646 63.158 13.81 0.00 0.00 2.74
1719 1952 4.971008 GCTTTAGGAAAGGAAGCTTTACG 58.029 43.478 0.00 0.00 41.83 3.18
1749 1982 1.956170 CGTCAAAGTCAGCTGCGGT 60.956 57.895 9.47 0.00 0.00 5.68
1753 1986 1.302033 AAAGTCAGCTGCGGTGGAG 60.302 57.895 9.47 0.00 0.00 3.86
1754 1987 2.738213 AAAGTCAGCTGCGGTGGAGG 62.738 60.000 9.47 0.00 0.00 4.30
2079 2319 2.813179 GCGCATCGATGGGTGACAC 61.813 63.158 34.25 19.09 42.11 3.67
2081 2321 1.018752 CGCATCGATGGGTGACACAA 61.019 55.000 28.84 0.00 36.16 3.33
2082 2322 0.729116 GCATCGATGGGTGACACAAG 59.271 55.000 26.00 0.00 0.00 3.16
2087 2327 1.877680 CGATGGGTGACACAAGCAAGA 60.878 52.381 8.08 0.00 0.00 3.02
2122 2362 2.224329 TGTGCAAACCCGTAGCTTTCTA 60.224 45.455 0.00 0.00 0.00 2.10
2147 2387 5.977635 TCGTGTGTCTATGAATTCCATCTT 58.022 37.500 2.27 0.00 36.71 2.40
2148 2388 6.042777 TCGTGTGTCTATGAATTCCATCTTC 58.957 40.000 2.27 0.00 36.71 2.87
2149 2389 6.045318 CGTGTGTCTATGAATTCCATCTTCT 58.955 40.000 2.27 0.00 36.71 2.85
2150 2390 6.536582 CGTGTGTCTATGAATTCCATCTTCTT 59.463 38.462 2.27 0.00 36.71 2.52
2185 2425 4.276926 GGGTGTCTATGAATTCCATCTTGC 59.723 45.833 2.27 0.00 36.71 4.01
2204 2444 4.371855 TGCTCGTTACTTCCTCATACTG 57.628 45.455 0.00 0.00 0.00 2.74
2219 2459 5.451381 CCTCATACTGTAGTTACGAATGCCA 60.451 44.000 0.00 0.00 0.00 4.92
2379 2991 7.458409 AAAATATCACCATGCATCATACTCC 57.542 36.000 0.00 0.00 0.00 3.85
2380 2992 6.384342 AATATCACCATGCATCATACTCCT 57.616 37.500 0.00 0.00 0.00 3.69
2381 2993 3.758755 TCACCATGCATCATACTCCTC 57.241 47.619 0.00 0.00 0.00 3.71
2382 2994 3.040477 TCACCATGCATCATACTCCTCA 58.960 45.455 0.00 0.00 0.00 3.86
2383 2995 3.070590 TCACCATGCATCATACTCCTCAG 59.929 47.826 0.00 0.00 0.00 3.35
2384 2996 2.224475 ACCATGCATCATACTCCTCAGC 60.224 50.000 0.00 0.00 0.00 4.26
2385 2997 2.038689 CCATGCATCATACTCCTCAGCT 59.961 50.000 0.00 0.00 0.00 4.24
2386 2998 3.496337 CCATGCATCATACTCCTCAGCTT 60.496 47.826 0.00 0.00 0.00 3.74
2387 2999 3.465742 TGCATCATACTCCTCAGCTTC 57.534 47.619 0.00 0.00 0.00 3.86
2388 3000 2.103771 TGCATCATACTCCTCAGCTTCC 59.896 50.000 0.00 0.00 0.00 3.46
2389 3001 2.103771 GCATCATACTCCTCAGCTTCCA 59.896 50.000 0.00 0.00 0.00 3.53
2390 3002 3.244491 GCATCATACTCCTCAGCTTCCAT 60.244 47.826 0.00 0.00 0.00 3.41
2391 3003 4.020751 GCATCATACTCCTCAGCTTCCATA 60.021 45.833 0.00 0.00 0.00 2.74
2392 3004 5.512060 GCATCATACTCCTCAGCTTCCATAA 60.512 44.000 0.00 0.00 0.00 1.90
2393 3005 6.709281 CATCATACTCCTCAGCTTCCATAAT 58.291 40.000 0.00 0.00 0.00 1.28
2394 3006 6.106648 TCATACTCCTCAGCTTCCATAATG 57.893 41.667 0.00 0.00 0.00 1.90
2395 3007 5.604231 TCATACTCCTCAGCTTCCATAATGT 59.396 40.000 0.00 0.00 0.00 2.71
2396 3008 6.782494 TCATACTCCTCAGCTTCCATAATGTA 59.218 38.462 0.00 0.00 0.00 2.29
2397 3009 5.543507 ACTCCTCAGCTTCCATAATGTAG 57.456 43.478 0.00 0.00 0.00 2.74
2398 3010 4.965532 ACTCCTCAGCTTCCATAATGTAGT 59.034 41.667 0.00 0.00 0.00 2.73
2399 3011 5.163364 ACTCCTCAGCTTCCATAATGTAGTG 60.163 44.000 0.00 0.00 0.00 2.74
2400 3012 3.812053 CCTCAGCTTCCATAATGTAGTGC 59.188 47.826 0.00 0.00 0.00 4.40
2401 3013 3.808728 TCAGCTTCCATAATGTAGTGCC 58.191 45.455 0.00 0.00 0.00 5.01
2402 3014 3.455910 TCAGCTTCCATAATGTAGTGCCT 59.544 43.478 0.00 0.00 0.00 4.75
2403 3015 4.653801 TCAGCTTCCATAATGTAGTGCCTA 59.346 41.667 0.00 0.00 0.00 3.93
2404 3016 5.307976 TCAGCTTCCATAATGTAGTGCCTAT 59.692 40.000 0.00 0.00 0.00 2.57
2405 3017 6.496911 TCAGCTTCCATAATGTAGTGCCTATA 59.503 38.462 0.00 0.00 0.00 1.31
2406 3018 6.815641 CAGCTTCCATAATGTAGTGCCTATAG 59.184 42.308 0.00 0.00 0.00 1.31
2407 3019 6.726299 AGCTTCCATAATGTAGTGCCTATAGA 59.274 38.462 0.00 0.00 0.00 1.98
2408 3020 7.401493 AGCTTCCATAATGTAGTGCCTATAGAT 59.599 37.037 0.00 0.00 0.00 1.98
2409 3021 8.043710 GCTTCCATAATGTAGTGCCTATAGATT 58.956 37.037 0.00 0.00 0.00 2.40
2410 3022 9.950496 CTTCCATAATGTAGTGCCTATAGATTT 57.050 33.333 0.00 0.00 0.00 2.17
2417 3029 9.826574 AATGTAGTGCCTATAGATTTTTACGAA 57.173 29.630 0.00 0.00 0.00 3.85
2418 3030 9.826574 ATGTAGTGCCTATAGATTTTTACGAAA 57.173 29.630 0.00 0.00 0.00 3.46
2419 3031 9.309516 TGTAGTGCCTATAGATTTTTACGAAAG 57.690 33.333 0.00 0.00 0.00 2.62
2438 3050 8.168681 ACGAAAGTCAAACATTACAAACTTTG 57.831 30.769 3.28 0.00 44.19 2.77
2439 3051 8.024285 ACGAAAGTCAAACATTACAAACTTTGA 58.976 29.630 8.55 0.00 44.19 2.69
2440 3052 9.019764 CGAAAGTCAAACATTACAAACTTTGAT 57.980 29.630 8.55 0.00 37.15 2.57
2442 3054 9.868277 AAAGTCAAACATTACAAACTTTGATCA 57.132 25.926 8.55 0.00 36.06 2.92
2478 3090 9.710818 AGAAAAGTAGGTACATCTAGAATACCA 57.289 33.333 26.72 15.98 40.81 3.25
2483 3095 8.368668 AGTAGGTACATCTAGAATACCAAATGC 58.631 37.037 26.72 15.90 40.81 3.56
2484 3096 7.136822 AGGTACATCTAGAATACCAAATGCA 57.863 36.000 26.72 0.00 40.81 3.96
2485 3097 6.992715 AGGTACATCTAGAATACCAAATGCAC 59.007 38.462 26.72 9.05 40.81 4.57
2486 3098 6.765989 GGTACATCTAGAATACCAAATGCACA 59.234 38.462 22.87 0.00 38.61 4.57
2487 3099 6.932356 ACATCTAGAATACCAAATGCACAG 57.068 37.500 0.00 0.00 0.00 3.66
2488 3100 6.418101 ACATCTAGAATACCAAATGCACAGT 58.582 36.000 0.00 0.00 0.00 3.55
2489 3101 7.564793 ACATCTAGAATACCAAATGCACAGTA 58.435 34.615 0.00 0.00 0.00 2.74
2490 3102 8.213679 ACATCTAGAATACCAAATGCACAGTAT 58.786 33.333 0.00 0.00 0.00 2.12
2491 3103 9.060347 CATCTAGAATACCAAATGCACAGTATT 57.940 33.333 0.00 10.56 37.94 1.89
2492 3104 8.437360 TCTAGAATACCAAATGCACAGTATTG 57.563 34.615 13.95 4.76 35.96 1.90
2493 3105 6.455360 AGAATACCAAATGCACAGTATTGG 57.545 37.500 13.95 13.35 46.14 3.16
2494 3106 6.186957 AGAATACCAAATGCACAGTATTGGA 58.813 36.000 18.38 7.41 44.01 3.53
2495 3107 6.835488 AGAATACCAAATGCACAGTATTGGAT 59.165 34.615 18.38 8.79 44.01 3.41
2496 3108 7.998383 AGAATACCAAATGCACAGTATTGGATA 59.002 33.333 18.38 10.46 44.01 2.59
2497 3109 5.835113 ACCAAATGCACAGTATTGGATAC 57.165 39.130 18.38 0.00 44.01 2.24
2571 3183 9.256228 AGATAGTTTTCTCTATACACTTGGTCA 57.744 33.333 0.00 0.00 31.71 4.02
2572 3184 9.871238 GATAGTTTTCTCTATACACTTGGTCAA 57.129 33.333 0.00 0.00 31.71 3.18
2574 3186 8.608844 AGTTTTCTCTATACACTTGGTCAAAG 57.391 34.615 0.00 0.00 42.07 2.77
2586 3198 5.816449 CTTGGTCAAAGTTGGCAAAATTT 57.184 34.783 0.00 3.54 34.05 1.82
2594 3206 6.435430 AAAGTTGGCAAAATTTGACTTTCC 57.565 33.333 13.24 2.96 40.19 3.13
2595 3207 4.450976 AGTTGGCAAAATTTGACTTTCCC 58.549 39.130 13.24 2.26 40.19 3.97
2596 3208 4.080638 AGTTGGCAAAATTTGACTTTCCCA 60.081 37.500 13.24 4.89 40.19 4.37
2597 3209 4.494091 TGGCAAAATTTGACTTTCCCAA 57.506 36.364 13.24 0.00 40.19 4.12
2598 3210 4.848357 TGGCAAAATTTGACTTTCCCAAA 58.152 34.783 13.24 0.00 40.19 3.28
2599 3211 5.256474 TGGCAAAATTTGACTTTCCCAAAA 58.744 33.333 13.24 0.00 40.19 2.44
2600 3212 5.711976 TGGCAAAATTTGACTTTCCCAAAAA 59.288 32.000 13.24 0.00 40.19 1.94
2601 3213 6.379417 TGGCAAAATTTGACTTTCCCAAAAAT 59.621 30.769 13.24 0.00 40.19 1.82
2602 3214 6.917477 GGCAAAATTTGACTTTCCCAAAAATC 59.083 34.615 10.26 0.00 37.11 2.17
2603 3215 7.201812 GGCAAAATTTGACTTTCCCAAAAATCT 60.202 33.333 10.26 0.00 37.11 2.40
2604 3216 8.835439 GCAAAATTTGACTTTCCCAAAAATCTA 58.165 29.630 10.26 0.00 37.11 1.98
2609 3221 7.404671 TTGACTTTCCCAAAAATCTATAGGC 57.595 36.000 0.00 0.00 0.00 3.93
2610 3222 6.489603 TGACTTTCCCAAAAATCTATAGGCA 58.510 36.000 0.00 0.00 0.00 4.75
2611 3223 6.377146 TGACTTTCCCAAAAATCTATAGGCAC 59.623 38.462 0.00 0.00 0.00 5.01
2612 3224 6.494059 ACTTTCCCAAAAATCTATAGGCACT 58.506 36.000 0.00 0.00 46.37 4.40
2674 3286 9.314321 GAAAACTTCCGATCTATTCATCAACTA 57.686 33.333 0.00 0.00 0.00 2.24
2701 3313 9.280174 TCAAGGTAGTATAAAGAACACCAAAAG 57.720 33.333 0.00 0.00 0.00 2.27
2716 3328 3.506067 ACCAAAAGTAAAATCCAGCTCCG 59.494 43.478 0.00 0.00 0.00 4.63
2725 3337 2.332063 ATCCAGCTCCGTAAACCATG 57.668 50.000 0.00 0.00 0.00 3.66
2726 3338 0.981183 TCCAGCTCCGTAAACCATGT 59.019 50.000 0.00 0.00 0.00 3.21
2727 3339 2.181125 TCCAGCTCCGTAAACCATGTA 58.819 47.619 0.00 0.00 0.00 2.29
2728 3340 2.167693 TCCAGCTCCGTAAACCATGTAG 59.832 50.000 0.00 0.00 0.00 2.74
2729 3341 1.933853 CAGCTCCGTAAACCATGTAGC 59.066 52.381 0.00 0.00 0.00 3.58
2730 3342 1.553248 AGCTCCGTAAACCATGTAGCA 59.447 47.619 0.00 0.00 0.00 3.49
2731 3343 2.027561 AGCTCCGTAAACCATGTAGCAA 60.028 45.455 0.00 0.00 0.00 3.91
2753 3365 0.319900 AGCGGTGACTACAAGCACTG 60.320 55.000 0.00 0.00 42.77 3.66
2787 3399 4.831307 CGCCGACGTCTTCCCTCG 62.831 72.222 14.70 0.00 33.53 4.63
2793 3405 1.580845 GACGTCTTCCCTCGTCGGAA 61.581 60.000 8.70 5.95 44.70 4.30
2824 3436 3.569701 ACCTTGTTGCAGTAGACAATTGG 59.430 43.478 10.83 4.41 35.44 3.16
2827 3439 5.437289 TTGTTGCAGTAGACAATTGGAAG 57.563 39.130 10.83 0.00 31.30 3.46
2831 3443 3.244078 TGCAGTAGACAATTGGAAGTCGT 60.244 43.478 10.83 0.00 39.67 4.34
2844 3456 1.812686 AAGTCGTCGTGCTAAGGCCA 61.813 55.000 5.01 0.00 37.74 5.36
2848 3460 1.213537 GTCGTGCTAAGGCCACGTA 59.786 57.895 5.01 0.00 40.74 3.57
2863 3475 1.736645 CGTAGGACCAACGCACCAG 60.737 63.158 0.00 0.00 33.04 4.00
2875 3487 1.299089 GCACCAGAACAACAACCGC 60.299 57.895 0.00 0.00 0.00 5.68
2877 3489 1.077357 ACCAGAACAACAACCGCCA 60.077 52.632 0.00 0.00 0.00 5.69
2883 3495 1.791103 AACAACAACCGCCACCGATG 61.791 55.000 0.00 0.00 36.29 3.84
2890 3502 1.218047 CCGCCACCGATGAAGAGAA 59.782 57.895 0.00 0.00 36.29 2.87
2901 3513 3.560503 GATGAAGAGAAGCGTAGATCGG 58.439 50.000 0.00 0.00 40.26 4.18
2932 3544 9.924650 ATCCAACCTATAGACATACGAAAATAC 57.075 33.333 0.00 0.00 0.00 1.89
2934 3546 9.706691 CCAACCTATAGACATACGAAAATACAT 57.293 33.333 0.00 0.00 0.00 2.29
2968 3580 0.608130 TCCACGTGGATCCACTGAAG 59.392 55.000 35.84 24.87 44.16 3.02
2975 3587 2.480419 GTGGATCCACTGAAGACAAACG 59.520 50.000 33.47 0.00 43.12 3.60
2976 3588 2.076863 GGATCCACTGAAGACAAACGG 58.923 52.381 6.95 0.00 0.00 4.44
2994 3606 1.434696 GCGACCGAATCCCGTAAGA 59.565 57.895 0.00 0.00 43.02 2.10
3018 3630 1.734163 CCGGATACAAACCTCCACAC 58.266 55.000 0.00 0.00 0.00 3.82
3035 3647 3.592814 CGCCCTCCGACGATGCTA 61.593 66.667 0.00 0.00 40.02 3.49
3036 3648 2.812499 GCCCTCCGACGATGCTAA 59.188 61.111 0.00 0.00 0.00 3.09
3042 3654 2.936498 CCTCCGACGATGCTAAAAACAT 59.064 45.455 0.00 0.00 0.00 2.71
3049 3661 2.223249 CGATGCTAAAAACATCACCGGG 60.223 50.000 6.32 0.00 43.36 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 7.222999 AGCTATGAAAAGTTATCGTGAAGCTAC 59.777 37.037 0.00 0.00 33.91 3.58
147 148 8.036273 AGTAGATATTTTACACGGGTTTGTTG 57.964 34.615 0.00 0.00 0.00 3.33
501 511 8.627403 CAGGCAGTTTCTTGATCATTACATTAT 58.373 33.333 0.00 0.00 0.00 1.28
553 726 0.931662 GCAGTGCAAAAGCAGACACG 60.932 55.000 11.09 0.00 38.08 4.49
684 858 4.222366 TGCAACATTTCTTGGGAATGCATA 59.778 37.500 0.00 0.00 38.21 3.14
707 893 6.620678 CAGAATGATTGGACCGTATGTTTTT 58.379 36.000 0.00 0.00 39.69 1.94
857 1045 3.480470 ACATGATTGGAACATCGATCCC 58.520 45.455 0.00 0.00 39.30 3.85
864 1052 3.366273 GCGACACAACATGATTGGAACAT 60.366 43.478 0.00 0.00 39.30 2.71
1005 1193 5.850557 TCAAATCACCATTTCTTGTGTGT 57.149 34.783 0.00 0.00 34.14 3.72
1073 1264 0.974525 GTCTGGGTAGGCGGGTAAGT 60.975 60.000 0.00 0.00 0.00 2.24
1270 1479 4.742201 CCTCGACACCGTGGCCAG 62.742 72.222 5.11 0.00 41.64 4.85
1401 1616 2.983229 CACTTCTTGCTGCTGTATCCT 58.017 47.619 0.00 0.00 0.00 3.24
1615 1848 2.358898 CGAGATTCAAATTTGGCGGGAT 59.641 45.455 17.90 5.25 0.00 3.85
1719 1952 1.301677 CTTTGACGGGAGCCTGAAGC 61.302 60.000 1.59 0.00 44.25 3.86
1937 2173 1.837051 TTCTGCCTCACGTCCACCT 60.837 57.895 0.00 0.00 0.00 4.00
1943 2179 4.003788 CCCGGTTCTGCCTCACGT 62.004 66.667 0.00 0.00 34.25 4.49
2079 2319 2.427360 GCATTGTGCGTCTTGCTTG 58.573 52.632 0.00 0.00 46.63 4.01
2122 2362 4.801330 TGGAATTCATAGACACACGAGT 57.199 40.909 7.93 0.00 0.00 4.18
2159 2399 1.217882 GGAATTCATAGACACCCGCG 58.782 55.000 7.93 0.00 0.00 6.46
2185 2425 6.680874 ACTACAGTATGAGGAAGTAACGAG 57.319 41.667 0.00 0.00 39.69 4.18
2204 2444 5.600908 TTCAGTTTGGCATTCGTAACTAC 57.399 39.130 1.48 0.00 30.19 2.73
2219 2459 4.082245 CCTATGCCCGTTTTCATTCAGTTT 60.082 41.667 0.00 0.00 0.00 2.66
2376 2988 5.295950 CACTACATTATGGAAGCTGAGGAG 58.704 45.833 0.00 0.00 0.00 3.69
2378 2990 3.812053 GCACTACATTATGGAAGCTGAGG 59.188 47.826 0.00 0.00 0.00 3.86
2379 2991 3.812053 GGCACTACATTATGGAAGCTGAG 59.188 47.826 0.00 0.00 0.00 3.35
2380 2992 3.455910 AGGCACTACATTATGGAAGCTGA 59.544 43.478 0.00 0.00 36.02 4.26
2381 2993 3.813443 AGGCACTACATTATGGAAGCTG 58.187 45.455 0.00 0.00 36.02 4.24
2396 3008 8.038944 TGACTTTCGTAAAAATCTATAGGCACT 58.961 33.333 0.00 0.00 46.37 4.40
2397 3009 8.193250 TGACTTTCGTAAAAATCTATAGGCAC 57.807 34.615 0.00 0.00 0.00 5.01
2398 3010 8.780846 TTGACTTTCGTAAAAATCTATAGGCA 57.219 30.769 0.00 0.00 0.00 4.75
2399 3011 9.486857 GTTTGACTTTCGTAAAAATCTATAGGC 57.513 33.333 0.00 0.00 0.00 3.93
2409 3021 9.843334 AGTTTGTAATGTTTGACTTTCGTAAAA 57.157 25.926 0.00 0.00 0.00 1.52
2410 3022 9.843334 AAGTTTGTAATGTTTGACTTTCGTAAA 57.157 25.926 0.00 0.00 0.00 2.01
2411 3023 9.843334 AAAGTTTGTAATGTTTGACTTTCGTAA 57.157 25.926 0.00 0.00 33.46 3.18
2412 3024 9.279904 CAAAGTTTGTAATGTTTGACTTTCGTA 57.720 29.630 7.48 0.00 35.75 3.43
2413 3025 8.024285 TCAAAGTTTGTAATGTTTGACTTTCGT 58.976 29.630 15.08 0.00 35.75 3.85
2414 3026 8.388319 TCAAAGTTTGTAATGTTTGACTTTCG 57.612 30.769 15.08 0.00 35.75 3.46
2416 3028 9.868277 TGATCAAAGTTTGTAATGTTTGACTTT 57.132 25.926 15.08 0.00 40.67 2.66
2452 3064 9.710818 TGGTATTCTAGATGTACCTACTTTTCT 57.289 33.333 24.31 0.00 38.89 2.52
2457 3069 8.368668 GCATTTGGTATTCTAGATGTACCTACT 58.631 37.037 24.31 14.71 38.89 2.57
2458 3070 8.148351 TGCATTTGGTATTCTAGATGTACCTAC 58.852 37.037 24.31 14.77 38.89 3.18
2459 3071 8.148351 GTGCATTTGGTATTCTAGATGTACCTA 58.852 37.037 24.31 18.45 38.89 3.08
2460 3072 6.992715 GTGCATTTGGTATTCTAGATGTACCT 59.007 38.462 24.31 10.63 38.89 3.08
2461 3073 6.765989 TGTGCATTTGGTATTCTAGATGTACC 59.234 38.462 20.29 20.29 38.65 3.34
2462 3074 7.495934 ACTGTGCATTTGGTATTCTAGATGTAC 59.504 37.037 0.00 0.27 32.91 2.90
2463 3075 7.564793 ACTGTGCATTTGGTATTCTAGATGTA 58.435 34.615 0.00 0.00 0.00 2.29
2464 3076 6.418101 ACTGTGCATTTGGTATTCTAGATGT 58.582 36.000 0.00 0.00 0.00 3.06
2465 3077 6.932356 ACTGTGCATTTGGTATTCTAGATG 57.068 37.500 0.00 0.00 0.00 2.90
2466 3078 9.060347 CAATACTGTGCATTTGGTATTCTAGAT 57.940 33.333 0.00 0.00 34.08 1.98
2467 3079 7.498900 CCAATACTGTGCATTTGGTATTCTAGA 59.501 37.037 11.06 0.00 34.08 2.43
2468 3080 7.498900 TCCAATACTGTGCATTTGGTATTCTAG 59.501 37.037 12.19 0.00 39.67 2.43
2469 3081 7.342581 TCCAATACTGTGCATTTGGTATTCTA 58.657 34.615 12.19 4.40 39.67 2.10
2470 3082 6.186957 TCCAATACTGTGCATTTGGTATTCT 58.813 36.000 12.19 0.00 39.67 2.40
2471 3083 6.449635 TCCAATACTGTGCATTTGGTATTC 57.550 37.500 12.19 0.00 39.67 1.75
2472 3084 7.559533 TGTATCCAATACTGTGCATTTGGTATT 59.440 33.333 12.19 10.72 39.67 1.89
2473 3085 7.059788 TGTATCCAATACTGTGCATTTGGTAT 58.940 34.615 12.19 6.61 39.67 2.73
2474 3086 6.418946 TGTATCCAATACTGTGCATTTGGTA 58.581 36.000 12.19 5.00 39.67 3.25
2475 3087 5.260424 TGTATCCAATACTGTGCATTTGGT 58.740 37.500 12.19 3.31 39.67 3.67
2476 3088 5.833406 TGTATCCAATACTGTGCATTTGG 57.167 39.130 0.00 0.00 39.98 3.28
2477 3089 7.030075 TGATGTATCCAATACTGTGCATTTG 57.970 36.000 0.00 0.00 36.70 2.32
2478 3090 7.503230 TCATGATGTATCCAATACTGTGCATTT 59.497 33.333 0.00 0.00 36.70 2.32
2479 3091 6.999871 TCATGATGTATCCAATACTGTGCATT 59.000 34.615 0.00 0.00 36.70 3.56
2480 3092 6.536447 TCATGATGTATCCAATACTGTGCAT 58.464 36.000 0.00 0.00 36.70 3.96
2481 3093 5.927819 TCATGATGTATCCAATACTGTGCA 58.072 37.500 0.00 0.00 36.70 4.57
2482 3094 5.994054 ACTCATGATGTATCCAATACTGTGC 59.006 40.000 0.00 0.00 36.70 4.57
2483 3095 9.716531 ATAACTCATGATGTATCCAATACTGTG 57.283 33.333 0.00 0.00 36.70 3.66
2545 3157 9.256228 TGACCAAGTGTATAGAGAAAACTATCT 57.744 33.333 0.00 0.00 35.19 1.98
2546 3158 9.871238 TTGACCAAGTGTATAGAGAAAACTATC 57.129 33.333 0.00 0.00 35.19 2.08
2548 3160 9.706691 CTTTGACCAAGTGTATAGAGAAAACTA 57.293 33.333 0.00 0.00 0.00 2.24
2549 3161 8.211629 ACTTTGACCAAGTGTATAGAGAAAACT 58.788 33.333 0.00 0.00 44.70 2.66
2550 3162 8.379457 ACTTTGACCAAGTGTATAGAGAAAAC 57.621 34.615 0.00 0.00 44.70 2.43
2551 3163 8.836413 CAACTTTGACCAAGTGTATAGAGAAAA 58.164 33.333 0.00 0.00 45.77 2.29
2552 3164 7.444183 CCAACTTTGACCAAGTGTATAGAGAAA 59.556 37.037 0.00 0.00 45.77 2.52
2553 3165 6.934645 CCAACTTTGACCAAGTGTATAGAGAA 59.065 38.462 0.00 0.00 45.77 2.87
2554 3166 6.464222 CCAACTTTGACCAAGTGTATAGAGA 58.536 40.000 0.00 0.00 45.77 3.10
2555 3167 5.122396 GCCAACTTTGACCAAGTGTATAGAG 59.878 44.000 0.00 0.00 45.77 2.43
2556 3168 5.001232 GCCAACTTTGACCAAGTGTATAGA 58.999 41.667 0.00 0.00 45.77 1.98
2557 3169 4.759693 TGCCAACTTTGACCAAGTGTATAG 59.240 41.667 0.00 0.00 45.77 1.31
2558 3170 4.720046 TGCCAACTTTGACCAAGTGTATA 58.280 39.130 0.00 0.00 45.77 1.47
2559 3171 3.561143 TGCCAACTTTGACCAAGTGTAT 58.439 40.909 0.00 0.00 45.77 2.29
2560 3172 3.006112 TGCCAACTTTGACCAAGTGTA 57.994 42.857 0.00 0.00 45.77 2.90
2561 3173 1.846007 TGCCAACTTTGACCAAGTGT 58.154 45.000 0.00 0.00 45.77 3.55
2562 3174 2.957491 TTGCCAACTTTGACCAAGTG 57.043 45.000 0.00 0.00 45.77 3.16
2563 3175 8.958648 GTCAAATTTTGCCAACTTTGACCAAGT 61.959 37.037 24.39 0.00 46.72 3.16
2564 3176 5.353678 TCAAATTTTGCCAACTTTGACCAAG 59.646 36.000 10.74 0.00 36.91 3.61
2565 3177 5.123027 GTCAAATTTTGCCAACTTTGACCAA 59.877 36.000 24.39 3.10 46.72 3.67
2566 3178 4.633565 GTCAAATTTTGCCAACTTTGACCA 59.366 37.500 24.39 3.37 46.72 4.02
2567 3179 5.155509 GTCAAATTTTGCCAACTTTGACC 57.844 39.130 24.39 13.40 46.72 4.02
2569 3181 6.093357 GGAAAGTCAAATTTTGCCAACTTTGA 59.907 34.615 22.18 10.74 38.54 2.69
2570 3182 6.257423 GGAAAGTCAAATTTTGCCAACTTTG 58.743 36.000 22.18 6.93 36.18 2.77
2571 3183 5.356751 GGGAAAGTCAAATTTTGCCAACTTT 59.643 36.000 19.36 19.36 43.21 2.66
2572 3184 4.881273 GGGAAAGTCAAATTTTGCCAACTT 59.119 37.500 4.19 6.58 43.21 2.66
2573 3185 4.450976 GGGAAAGTCAAATTTTGCCAACT 58.549 39.130 4.19 0.73 43.21 3.16
2574 3186 4.811555 GGGAAAGTCAAATTTTGCCAAC 57.188 40.909 4.19 0.00 43.21 3.77
2577 3189 5.826601 TTTTGGGAAAGTCAAATTTTGCC 57.173 34.783 4.19 1.86 43.78 4.52
2578 3190 7.706159 AGATTTTTGGGAAAGTCAAATTTTGC 58.294 30.769 4.19 0.57 34.85 3.68
2583 3195 8.478066 GCCTATAGATTTTTGGGAAAGTCAAAT 58.522 33.333 0.00 0.00 34.85 2.32
2584 3196 7.453126 TGCCTATAGATTTTTGGGAAAGTCAAA 59.547 33.333 0.00 0.00 34.85 2.69
2585 3197 6.951198 TGCCTATAGATTTTTGGGAAAGTCAA 59.049 34.615 0.00 0.00 34.85 3.18
2586 3198 6.377146 GTGCCTATAGATTTTTGGGAAAGTCA 59.623 38.462 0.00 0.00 34.85 3.41
2587 3199 6.603599 AGTGCCTATAGATTTTTGGGAAAGTC 59.396 38.462 0.00 0.00 33.17 3.01
2588 3200 6.494059 AGTGCCTATAGATTTTTGGGAAAGT 58.506 36.000 0.00 0.00 0.00 2.66
2589 3201 7.556275 TGTAGTGCCTATAGATTTTTGGGAAAG 59.444 37.037 0.00 0.00 0.00 2.62
2590 3202 7.406916 TGTAGTGCCTATAGATTTTTGGGAAA 58.593 34.615 0.00 0.00 0.00 3.13
2591 3203 6.964464 TGTAGTGCCTATAGATTTTTGGGAA 58.036 36.000 0.00 0.00 0.00 3.97
2592 3204 6.569127 TGTAGTGCCTATAGATTTTTGGGA 57.431 37.500 0.00 0.00 0.00 4.37
2593 3205 7.823745 AATGTAGTGCCTATAGATTTTTGGG 57.176 36.000 0.00 0.00 0.00 4.12
2599 3211 9.896645 CATTCCATAATGTAGTGCCTATAGATT 57.103 33.333 0.00 0.00 38.15 2.40
2600 3212 8.489489 CCATTCCATAATGTAGTGCCTATAGAT 58.511 37.037 0.00 0.00 40.84 1.98
2601 3213 7.678171 TCCATTCCATAATGTAGTGCCTATAGA 59.322 37.037 0.00 0.00 40.84 1.98
2602 3214 7.851228 TCCATTCCATAATGTAGTGCCTATAG 58.149 38.462 0.00 0.00 40.84 1.31
2603 3215 7.678171 TCTCCATTCCATAATGTAGTGCCTATA 59.322 37.037 0.00 0.00 40.84 1.31
2604 3216 6.501805 TCTCCATTCCATAATGTAGTGCCTAT 59.498 38.462 0.00 0.00 40.84 2.57
2605 3217 5.843969 TCTCCATTCCATAATGTAGTGCCTA 59.156 40.000 0.00 0.00 40.84 3.93
2606 3218 4.660303 TCTCCATTCCATAATGTAGTGCCT 59.340 41.667 0.00 0.00 40.84 4.75
2607 3219 4.973168 TCTCCATTCCATAATGTAGTGCC 58.027 43.478 0.00 0.00 40.84 5.01
2608 3220 5.858381 TCTCTCCATTCCATAATGTAGTGC 58.142 41.667 0.00 0.00 40.84 4.40
2609 3221 7.060383 ACTCTCTCCATTCCATAATGTAGTG 57.940 40.000 0.00 0.00 40.84 2.74
2610 3222 8.964533 ATACTCTCTCCATTCCATAATGTAGT 57.035 34.615 0.00 0.00 40.84 2.73
2674 3286 9.802039 TTTTGGTGTTCTTTATACTACCTTGAT 57.198 29.630 0.00 0.00 0.00 2.57
2686 3298 7.923878 GCTGGATTTTACTTTTGGTGTTCTTTA 59.076 33.333 0.00 0.00 0.00 1.85
2701 3313 4.004982 TGGTTTACGGAGCTGGATTTTAC 58.995 43.478 0.00 0.00 0.00 2.01
2716 3328 3.308866 CCGCTAGTTGCTACATGGTTTAC 59.691 47.826 0.13 0.00 40.11 2.01
2725 3337 2.163010 TGTAGTCACCGCTAGTTGCTAC 59.837 50.000 0.00 0.00 40.11 3.58
2726 3338 2.439409 TGTAGTCACCGCTAGTTGCTA 58.561 47.619 0.00 0.00 40.11 3.49
2727 3339 1.254026 TGTAGTCACCGCTAGTTGCT 58.746 50.000 0.00 0.00 40.11 3.91
2728 3340 1.993370 CTTGTAGTCACCGCTAGTTGC 59.007 52.381 0.00 0.00 38.57 4.17
2729 3341 1.993370 GCTTGTAGTCACCGCTAGTTG 59.007 52.381 0.00 0.00 0.00 3.16
2730 3342 1.616865 TGCTTGTAGTCACCGCTAGTT 59.383 47.619 0.00 0.00 0.00 2.24
2731 3343 1.067776 GTGCTTGTAGTCACCGCTAGT 60.068 52.381 0.00 0.00 0.00 2.57
2745 3357 2.091112 CGACTCGCTCCAGTGCTTG 61.091 63.158 0.00 0.00 0.00 4.01
2753 3365 2.507324 GCACCTTCGACTCGCTCC 60.507 66.667 0.00 0.00 0.00 4.70
2787 3399 0.822121 AAGGTTTGCCAGGTTCCGAC 60.822 55.000 0.00 0.00 37.19 4.79
2793 3405 1.822615 GCAACAAGGTTTGCCAGGT 59.177 52.632 0.00 0.00 45.22 4.00
2812 3424 3.255149 ACGACGACTTCCAATTGTCTACT 59.745 43.478 0.00 0.00 0.00 2.57
2824 3436 1.077089 GGCCTTAGCACGACGACTTC 61.077 60.000 0.00 0.00 42.56 3.01
2827 3439 2.092882 GTGGCCTTAGCACGACGAC 61.093 63.158 3.32 0.00 42.56 4.34
2831 3443 1.509463 CTACGTGGCCTTAGCACGA 59.491 57.895 18.34 2.78 42.37 4.35
2844 3456 2.341176 GGTGCGTTGGTCCTACGT 59.659 61.111 23.65 0.00 40.92 3.57
2848 3460 1.227853 GTTCTGGTGCGTTGGTCCT 60.228 57.895 0.00 0.00 0.00 3.85
2863 3475 1.512156 ATCGGTGGCGGTTGTTGTTC 61.512 55.000 0.00 0.00 0.00 3.18
2875 3487 0.108615 ACGCTTCTCTTCATCGGTGG 60.109 55.000 0.00 0.00 0.00 4.61
2877 3489 2.366533 TCTACGCTTCTCTTCATCGGT 58.633 47.619 0.00 0.00 0.00 4.69
2883 3495 3.694535 TTCCGATCTACGCTTCTCTTC 57.305 47.619 0.00 0.00 41.07 2.87
2901 3513 7.827701 TCGTATGTCTATAGGTTGGATCATTC 58.172 38.462 0.00 0.00 0.00 2.67
2932 3544 3.000623 CGTGGATCATGTCTTCGTTCATG 59.999 47.826 0.00 0.00 41.64 3.07
2934 3546 2.029380 ACGTGGATCATGTCTTCGTTCA 60.029 45.455 0.00 0.00 34.54 3.18
2939 3551 2.672961 TCCACGTGGATCATGTCTTC 57.327 50.000 33.23 0.00 39.78 2.87
2965 3577 2.851104 CGGTCGCCGTTTGTCTTC 59.149 61.111 9.69 0.00 42.73 2.87
2975 3587 1.590792 CTTACGGGATTCGGTCGCC 60.591 63.158 0.00 0.00 44.45 5.54
2976 3588 0.031721 ATCTTACGGGATTCGGTCGC 59.968 55.000 0.00 0.00 44.45 5.19
2991 3603 1.474498 GGTTTGTATCCGGCGGATCTT 60.474 52.381 41.83 24.48 42.11 2.40
2994 3606 0.106149 GAGGTTTGTATCCGGCGGAT 59.894 55.000 39.77 39.77 45.40 4.18
3018 3630 2.622903 TTTAGCATCGTCGGAGGGCG 62.623 60.000 0.00 0.00 33.15 6.13
3026 3638 3.485216 CCGGTGATGTTTTTAGCATCGTC 60.485 47.826 0.00 0.00 44.02 4.20
3035 3647 0.891904 CCCGTCCCGGTGATGTTTTT 60.892 55.000 0.00 0.00 46.80 1.94
3036 3648 1.302993 CCCGTCCCGGTGATGTTTT 60.303 57.895 0.00 0.00 46.80 2.43
3042 3654 3.650298 CTAGTCCCCGTCCCGGTGA 62.650 68.421 0.00 0.00 46.80 4.02


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

AutoCloner maintained by Alex Coulton.