Multiple sequence alignment - TraesCS5A01G394900

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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 TraesCS5A01G394900 chr5A 100.000 3443 0 0 1 3443 590539043 590542485 0.000000e+00 6359.0
1 TraesCS5A01G394900 chr5D 90.428 3155 161 61 2 3046 469500768 469503891 0.000000e+00 4023.0
2 TraesCS5A01G394900 chr5B 91.129 2852 148 42 1 2792 577226232 577229038 0.000000e+00 3768.0
3 TraesCS5A01G394900 chr5B 82.006 628 45 31 2792 3375 577229076 577229679 4.020000e-129 472.0
4 TraesCS5A01G394900 chr5B 81.592 201 30 4 471 670 78209897 78210091 3.560000e-35 159.0
5 TraesCS5A01G394900 chr5B 81.592 201 30 4 471 670 406551257 406551451 3.560000e-35 159.0
6 TraesCS5A01G394900 chr4A 90.186 1508 139 7 942 2447 576932020 576930520 0.000000e+00 1956.0
7 TraesCS5A01G394900 chr4A 83.162 1455 227 17 997 2441 547046170 547044724 0.000000e+00 1314.0
8 TraesCS5A01G394900 chr4A 80.399 1454 279 5 993 2443 486126022 486124572 0.000000e+00 1101.0
9 TraesCS5A01G394900 chr4A 87.121 132 15 2 471 601 740036316 740036446 7.700000e-32 148.0
10 TraesCS5A01G394900 chr4D 89.987 1508 142 7 942 2447 26479953 26481453 0.000000e+00 1940.0
11 TraesCS5A01G394900 chr4D 83.333 1458 222 19 994 2441 50070786 50072232 0.000000e+00 1327.0
12 TraesCS5A01G394900 chr4B 89.987 1508 142 7 942 2447 39014799 39016299 0.000000e+00 1940.0
13 TraesCS5A01G394900 chr4B 83.322 1457 224 17 997 2444 73609979 73608533 0.000000e+00 1327.0
14 TraesCS5A01G394900 chr7A 81.538 195 29 4 477 670 497657906 497657718 1.650000e-33 154.0
15 TraesCS5A01G394900 chr3A 81.095 201 31 4 471 670 82906775 82906969 1.650000e-33 154.0
16 TraesCS5A01G394900 chr3B 80.100 201 33 6 471 670 815340931 815341125 3.580000e-30 143.0
17 TraesCS5A01G394900 chr3B 84.962 133 16 4 471 601 47611509 47611639 7.750000e-27 132.0
18 TraesCS5A01G394900 chr7B 83.333 90 9 4 942 1030 595212942 595212858 1.020000e-10 78.7
19 TraesCS5A01G394900 chr2A 83.333 90 9 4 942 1030 732300873 732300789 1.020000e-10 78.7
20 TraesCS5A01G394900 chr2A 83.333 90 9 4 942 1030 777178500 777178584 1.020000e-10 78.7
21 TraesCS5A01G394900 chr1A 83.333 90 9 4 942 1030 10727565 10727481 1.020000e-10 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 TraesCS5A01G394900 chr5A 590539043 590542485 3442 False 6359 6359 100.0000 1 3443 1 chr5A.!!$F1 3442
1 TraesCS5A01G394900 chr5D 469500768 469503891 3123 False 4023 4023 90.4280 2 3046 1 chr5D.!!$F1 3044
2 TraesCS5A01G394900 chr5B 577226232 577229679 3447 False 2120 3768 86.5675 1 3375 2 chr5B.!!$F3 3374
3 TraesCS5A01G394900 chr4A 576930520 576932020 1500 True 1956 1956 90.1860 942 2447 1 chr4A.!!$R3 1505
4 TraesCS5A01G394900 chr4A 547044724 547046170 1446 True 1314 1314 83.1620 997 2441 1 chr4A.!!$R2 1444
5 TraesCS5A01G394900 chr4A 486124572 486126022 1450 True 1101 1101 80.3990 993 2443 1 chr4A.!!$R1 1450
6 TraesCS5A01G394900 chr4D 26479953 26481453 1500 False 1940 1940 89.9870 942 2447 1 chr4D.!!$F1 1505
7 TraesCS5A01G394900 chr4D 50070786 50072232 1446 False 1327 1327 83.3330 994 2441 1 chr4D.!!$F2 1447
8 TraesCS5A01G394900 chr4B 39014799 39016299 1500 False 1940 1940 89.9870 942 2447 1 chr4B.!!$F1 1505
9 TraesCS5A01G394900 chr4B 73608533 73609979 1446 True 1327 1327 83.3220 997 2444 1 chr4B.!!$R1 1447

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
636 662 0.102120 TTTTCGTTTGGCCTGCTGTG 59.898 50.0 3.32 0.0 0.0 3.66 F
642 668 0.682532 TTTGGCCTGCTGTGTGTTGA 60.683 50.0 3.32 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2373 2455 1.112113 TGGAGTAGACGATGAAGCCC 58.888 55.000 0.00 0.0 0.0 5.19 R
2597 2714 2.954316 ACAGACGCAAACATGTATCGA 58.046 42.857 17.38 0.0 0.0 3.59 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
64 65 0.670546 GGTGGTGTGTCATGGACTCG 60.671 60.000 0.00 0.00 33.15 4.18
71 72 2.288213 TGTGTCATGGACTCGTCTGAAC 60.288 50.000 0.00 0.00 33.15 3.18
84 85 5.073311 TCGTCTGAACCCTTTTCTATCAG 57.927 43.478 0.00 0.00 39.04 2.90
142 143 0.886490 ACTTTGCCTTGCGAGACCAG 60.886 55.000 1.22 0.00 0.00 4.00
143 144 2.192608 CTTTGCCTTGCGAGACCAGC 62.193 60.000 1.22 0.00 0.00 4.85
144 145 4.704833 TGCCTTGCGAGACCAGCC 62.705 66.667 1.22 0.00 0.00 4.85
148 149 3.535629 CTTGCGAGACCAGCCCACA 62.536 63.158 0.00 0.00 0.00 4.17
193 194 3.516615 CTTCTGAATTCTGACCGGTCTC 58.483 50.000 33.39 22.53 0.00 3.36
212 213 3.816523 TCTCCACACGGTTAATTTTCCAC 59.183 43.478 0.00 0.00 0.00 4.02
217 224 2.224549 CACGGTTAATTTTCCACAGCGA 59.775 45.455 0.00 0.00 32.81 4.93
219 226 2.727916 CGGTTAATTTTCCACAGCGAGC 60.728 50.000 0.00 0.00 0.00 5.03
221 228 3.305064 GGTTAATTTTCCACAGCGAGCAA 60.305 43.478 0.00 0.00 0.00 3.91
245 255 0.107165 GTAGATCCAACCTGGTGGCC 60.107 60.000 0.00 0.00 39.03 5.36
341 354 1.376037 CACCAAGAAGTCGCCTCCC 60.376 63.158 0.00 0.00 0.00 4.30
347 360 1.003233 GAAGTCGCCTCCCTTGCTT 60.003 57.895 0.00 0.00 0.00 3.91
348 361 0.606673 GAAGTCGCCTCCCTTGCTTT 60.607 55.000 0.00 0.00 0.00 3.51
349 362 0.606673 AAGTCGCCTCCCTTGCTTTC 60.607 55.000 0.00 0.00 0.00 2.62
350 363 2.041115 GTCGCCTCCCTTGCTTTCC 61.041 63.158 0.00 0.00 0.00 3.13
389 402 1.616159 CCCTCCTCTCGAGATCTTCC 58.384 60.000 17.03 0.00 41.63 3.46
413 426 1.830477 AGTTCCTGAGATCTGGTGAGC 59.170 52.381 0.00 0.00 36.48 4.26
431 451 0.103937 GCGTCTTCCTCCCTGATCTG 59.896 60.000 0.00 0.00 0.00 2.90
432 452 0.749649 CGTCTTCCTCCCTGATCTGG 59.250 60.000 11.58 11.58 0.00 3.86
435 455 3.375699 GTCTTCCTCCCTGATCTGGTTA 58.624 50.000 16.63 4.62 0.00 2.85
443 463 2.369394 CCTGATCTGGTTAGGTTTGGC 58.631 52.381 10.40 0.00 0.00 4.52
480 502 0.107945 ATCTTTGCGAGGAGAGTGGC 60.108 55.000 0.00 0.00 0.00 5.01
512 534 1.131315 GGATGCTGTTCTTTTCTCGGC 59.869 52.381 0.00 0.00 0.00 5.54
533 555 1.735386 TCTCTGAAGATGCTTGCTGC 58.265 50.000 0.00 0.00 43.25 5.25
549 571 2.203126 GCCTTCAGATCTGGCCGG 60.203 66.667 22.42 19.01 40.71 6.13
550 572 3.036429 GCCTTCAGATCTGGCCGGT 62.036 63.158 22.42 0.00 40.71 5.28
558 583 2.764637 GATCTGGCCGGTGGTTGGTT 62.765 60.000 12.43 0.00 0.00 3.67
636 662 0.102120 TTTTCGTTTGGCCTGCTGTG 59.898 50.000 3.32 0.00 0.00 3.66
639 665 2.480610 CGTTTGGCCTGCTGTGTGT 61.481 57.895 3.32 0.00 0.00 3.72
642 668 0.682532 TTTGGCCTGCTGTGTGTTGA 60.683 50.000 3.32 0.00 0.00 3.18
643 669 0.682532 TTGGCCTGCTGTGTGTTGAA 60.683 50.000 3.32 0.00 0.00 2.69
698 724 2.615869 GTTCAGTCTGTCATGCTCCTC 58.384 52.381 0.00 0.00 0.00 3.71
722 748 1.080995 GCAGTCTGCAGAAGTAGGCG 61.081 60.000 20.19 3.08 44.26 5.52
852 895 6.791887 TTTAACTCTGAGAGCATTTCTGTG 57.208 37.500 12.44 0.00 35.87 3.66
866 938 6.203723 AGCATTTCTGTGACTTACTGTCTTTC 59.796 38.462 0.00 0.00 45.54 2.62
868 940 7.254932 GCATTTCTGTGACTTACTGTCTTTCTT 60.255 37.037 0.00 0.00 45.54 2.52
882 954 7.781056 ACTGTCTTTCTTAGATCTGAATCTCC 58.219 38.462 5.18 0.00 41.46 3.71
891 963 5.369409 AGATCTGAATCTCCATTGCTTCA 57.631 39.130 0.00 0.00 37.75 3.02
896 968 5.771666 TCTGAATCTCCATTGCTTCAGTTTT 59.228 36.000 10.05 0.00 43.17 2.43
897 969 6.266103 TCTGAATCTCCATTGCTTCAGTTTTT 59.734 34.615 10.05 0.00 43.17 1.94
898 970 6.449698 TGAATCTCCATTGCTTCAGTTTTTC 58.550 36.000 0.00 0.00 0.00 2.29
922 998 6.803642 CATCTCTGAGATGTGTGATAACTGA 58.196 40.000 30.57 0.00 45.33 3.41
924 1000 8.574737 CATCTCTGAGATGTGTGATAACTGATA 58.425 37.037 30.57 0.00 45.33 2.15
925 1001 8.525290 TCTCTGAGATGTGTGATAACTGATAA 57.475 34.615 2.58 0.00 0.00 1.75
928 1004 6.820335 TGAGATGTGTGATAACTGATAAGGG 58.180 40.000 0.00 0.00 0.00 3.95
929 1005 5.615289 AGATGTGTGATAACTGATAAGGGC 58.385 41.667 0.00 0.00 0.00 5.19
930 1006 5.367937 AGATGTGTGATAACTGATAAGGGCT 59.632 40.000 0.00 0.00 0.00 5.19
931 1007 4.769688 TGTGTGATAACTGATAAGGGCTG 58.230 43.478 0.00 0.00 0.00 4.85
932 1008 4.225042 TGTGTGATAACTGATAAGGGCTGT 59.775 41.667 0.00 0.00 0.00 4.40
933 1009 4.811557 GTGTGATAACTGATAAGGGCTGTC 59.188 45.833 0.00 0.00 0.00 3.51
1518 1597 3.972227 CTGTTCAAGCCCGACAGG 58.028 61.111 0.00 0.00 37.67 4.00
2228 2310 4.849329 GGACGCGTACGAGGCCTG 62.849 72.222 33.51 5.11 43.93 4.85
2373 2455 0.388659 CCGAGAAGCTCAGGGAGATG 59.611 60.000 0.00 0.00 0.00 2.90
2456 2545 1.077089 GCCTAAGTTCACCTCGTCGC 61.077 60.000 0.00 0.00 0.00 5.19
2459 2548 1.880819 TAAGTTCACCTCGTCGCCCC 61.881 60.000 0.00 0.00 0.00 5.80
2537 2654 2.165845 GCATTTTGCAGGAGAAGCATCT 59.834 45.455 0.00 0.00 44.26 2.90
2549 2666 6.258287 CAGGAGAAGCATCTACATTTTCTCTG 59.742 42.308 3.60 0.00 42.00 3.35
2560 2677 4.331968 ACATTTTCTCTGTCGGCCATAAA 58.668 39.130 2.24 0.00 0.00 1.40
2562 2679 5.418840 ACATTTTCTCTGTCGGCCATAAAAT 59.581 36.000 2.24 0.00 0.00 1.82
2568 2685 5.065988 TCTCTGTCGGCCATAAAATTTTAGC 59.934 40.000 15.45 13.45 0.00 3.09
2586 2703 8.976986 ATTTTAGCAAATCTTCATGTCTTGTC 57.023 30.769 0.00 0.00 0.00 3.18
2594 2711 5.657470 TCTTCATGTCTTGTCAAGTTTCG 57.343 39.130 12.30 1.32 0.00 3.46
2595 2712 5.356426 TCTTCATGTCTTGTCAAGTTTCGA 58.644 37.500 12.30 3.51 0.00 3.71
2596 2713 5.991606 TCTTCATGTCTTGTCAAGTTTCGAT 59.008 36.000 12.30 0.00 0.00 3.59
2597 2714 6.483307 TCTTCATGTCTTGTCAAGTTTCGATT 59.517 34.615 12.30 0.00 0.00 3.34
2754 2896 1.285578 TTTTTCGCCAAGTTTGCAGC 58.714 45.000 0.00 0.00 0.00 5.25
2763 2905 1.233285 AAGTTTGCAGCTGCTCCTCG 61.233 55.000 36.61 0.00 42.66 4.63
2815 2998 2.147958 CTTGTTGGCCAGTAGCGTAAA 58.852 47.619 5.11 0.00 45.17 2.01
2816 2999 2.257691 TGTTGGCCAGTAGCGTAAAA 57.742 45.000 5.11 0.00 45.17 1.52
2817 3000 2.785562 TGTTGGCCAGTAGCGTAAAAT 58.214 42.857 5.11 0.00 45.17 1.82
2818 3001 2.745281 TGTTGGCCAGTAGCGTAAAATC 59.255 45.455 5.11 0.00 45.17 2.17
2819 3002 1.647346 TGGCCAGTAGCGTAAAATCG 58.353 50.000 0.00 0.00 45.17 3.34
2820 3003 1.205179 TGGCCAGTAGCGTAAAATCGA 59.795 47.619 0.00 0.00 45.17 3.59
2821 3004 1.591619 GGCCAGTAGCGTAAAATCGAC 59.408 52.381 0.00 0.00 45.17 4.20
2823 3006 3.489738 GGCCAGTAGCGTAAAATCGACTA 60.490 47.826 0.00 0.00 45.17 2.59
2841 3026 5.060506 CGACTAGTAGTCACATGATCCTCT 58.939 45.833 26.06 0.00 45.30 3.69
2884 3070 2.851195 TGGAGTTTCAGTTTCCTCTGC 58.149 47.619 0.00 0.00 35.63 4.26
2905 3091 1.609208 GCGGAATATGTTGCAGGGAT 58.391 50.000 0.00 0.00 0.00 3.85
2916 3102 1.189752 TGCAGGGATCAGACAGAGAC 58.810 55.000 0.00 0.00 0.00 3.36
2917 3103 1.189752 GCAGGGATCAGACAGAGACA 58.810 55.000 0.00 0.00 0.00 3.41
2918 3104 1.136695 GCAGGGATCAGACAGAGACAG 59.863 57.143 0.00 0.00 0.00 3.51
2919 3105 2.732763 CAGGGATCAGACAGAGACAGA 58.267 52.381 0.00 0.00 0.00 3.41
2920 3106 2.689471 CAGGGATCAGACAGAGACAGAG 59.311 54.545 0.00 0.00 0.00 3.35
2921 3107 2.580322 AGGGATCAGACAGAGACAGAGA 59.420 50.000 0.00 0.00 0.00 3.10
2923 3109 2.951642 GGATCAGACAGAGACAGAGAGG 59.048 54.545 0.00 0.00 0.00 3.69
2924 3110 1.832883 TCAGACAGAGACAGAGAGGC 58.167 55.000 0.00 0.00 0.00 4.70
2925 3111 0.817013 CAGACAGAGACAGAGAGGCC 59.183 60.000 0.00 0.00 0.00 5.19
2926 3112 0.704076 AGACAGAGACAGAGAGGCCT 59.296 55.000 3.86 3.86 0.00 5.19
2927 3113 1.919654 AGACAGAGACAGAGAGGCCTA 59.080 52.381 4.42 0.00 0.00 3.93
2929 3115 1.341581 ACAGAGACAGAGAGGCCTACC 60.342 57.143 4.42 0.00 0.00 3.18
3024 3227 1.666580 GCATCTCTACCGGCCTACC 59.333 63.158 0.00 0.00 0.00 3.18
3034 3237 4.065281 GGCCTACCGCACACGTCT 62.065 66.667 0.00 0.00 40.31 4.18
3036 3239 2.092882 GCCTACCGCACACGTCTTC 61.093 63.158 0.00 0.00 37.70 2.87
3054 3257 1.661463 TCCAGTTCCAGCTTCCATCT 58.339 50.000 0.00 0.00 0.00 2.90
3056 3259 2.376518 TCCAGTTCCAGCTTCCATCTTT 59.623 45.455 0.00 0.00 0.00 2.52
3058 3261 2.751806 CAGTTCCAGCTTCCATCTTTCC 59.248 50.000 0.00 0.00 0.00 3.13
3059 3262 2.376518 AGTTCCAGCTTCCATCTTTCCA 59.623 45.455 0.00 0.00 0.00 3.53
3060 3263 2.489722 GTTCCAGCTTCCATCTTTCCAC 59.510 50.000 0.00 0.00 0.00 4.02
3062 3265 1.089920 CAGCTTCCATCTTTCCACGG 58.910 55.000 0.00 0.00 0.00 4.94
3063 3266 0.693049 AGCTTCCATCTTTCCACGGT 59.307 50.000 0.00 0.00 0.00 4.83
3148 3373 4.758251 TGGAGTGCGCGTGGATGG 62.758 66.667 8.43 0.00 0.00 3.51
3175 3400 2.508891 GGCGATCGCGTCAGACAAG 61.509 63.158 31.76 0.00 42.82 3.16
3191 3416 5.582269 TCAGACAAGTTTGATGATCGAATCC 59.418 40.000 0.00 0.00 0.00 3.01
3194 3419 2.905075 AGTTTGATGATCGAATCCGCA 58.095 42.857 0.00 0.00 35.37 5.69
3304 3540 3.220658 TGTGCCAGTCGACGACCA 61.221 61.111 23.76 12.40 32.18 4.02
3305 3541 2.430921 GTGCCAGTCGACGACCAG 60.431 66.667 23.76 16.24 32.18 4.00
3335 3577 2.363795 TCGCCTAGGTGGGTGGAG 60.364 66.667 22.11 0.00 37.46 3.86
3363 3605 2.358247 CCCACTTTCCCACCGACG 60.358 66.667 0.00 0.00 0.00 5.12
3398 3640 3.542712 CGTAGTAGTACGTGGTTGTGT 57.457 47.619 19.78 0.00 45.84 3.72
3399 3641 3.228749 CGTAGTAGTACGTGGTTGTGTG 58.771 50.000 19.78 0.00 45.84 3.82
3400 3642 2.144482 AGTAGTACGTGGTTGTGTGC 57.856 50.000 0.00 0.00 0.00 4.57
3401 3643 0.780002 GTAGTACGTGGTTGTGTGCG 59.220 55.000 0.00 0.00 0.00 5.34
3402 3644 0.940519 TAGTACGTGGTTGTGTGCGC 60.941 55.000 0.00 0.00 0.00 6.09
3403 3645 3.331630 TACGTGGTTGTGTGCGCG 61.332 61.111 0.00 0.00 0.00 6.86
3418 3660 4.135493 GCGCGCGACACCTTTCTC 62.135 66.667 37.18 7.60 0.00 2.87
3419 3661 3.479269 CGCGCGACACCTTTCTCC 61.479 66.667 28.94 0.00 0.00 3.71
3420 3662 2.357034 GCGCGACACCTTTCTCCA 60.357 61.111 12.10 0.00 0.00 3.86
3421 3663 2.383527 GCGCGACACCTTTCTCCAG 61.384 63.158 12.10 0.00 0.00 3.86
3422 3664 2.383527 CGCGACACCTTTCTCCAGC 61.384 63.158 0.00 0.00 0.00 4.85
3423 3665 1.004440 GCGACACCTTTCTCCAGCT 60.004 57.895 0.00 0.00 0.00 4.24
3424 3666 1.016653 GCGACACCTTTCTCCAGCTC 61.017 60.000 0.00 0.00 0.00 4.09
3425 3667 0.390472 CGACACCTTTCTCCAGCTCC 60.390 60.000 0.00 0.00 0.00 4.70
3426 3668 0.687354 GACACCTTTCTCCAGCTCCA 59.313 55.000 0.00 0.00 0.00 3.86
3427 3669 0.689623 ACACCTTTCTCCAGCTCCAG 59.310 55.000 0.00 0.00 0.00 3.86
3428 3670 0.689623 CACCTTTCTCCAGCTCCAGT 59.310 55.000 0.00 0.00 0.00 4.00
3429 3671 1.072965 CACCTTTCTCCAGCTCCAGTT 59.927 52.381 0.00 0.00 0.00 3.16
3430 3672 1.349357 ACCTTTCTCCAGCTCCAGTTC 59.651 52.381 0.00 0.00 0.00 3.01
3431 3673 1.349026 CCTTTCTCCAGCTCCAGTTCA 59.651 52.381 0.00 0.00 0.00 3.18
3432 3674 2.421619 CTTTCTCCAGCTCCAGTTCAC 58.578 52.381 0.00 0.00 0.00 3.18
3433 3675 1.423584 TTCTCCAGCTCCAGTTCACA 58.576 50.000 0.00 0.00 0.00 3.58
3434 3676 0.681733 TCTCCAGCTCCAGTTCACAC 59.318 55.000 0.00 0.00 0.00 3.82
3435 3677 0.394192 CTCCAGCTCCAGTTCACACA 59.606 55.000 0.00 0.00 0.00 3.72
3436 3678 0.106708 TCCAGCTCCAGTTCACACAC 59.893 55.000 0.00 0.00 0.00 3.82
3437 3679 1.224069 CCAGCTCCAGTTCACACACG 61.224 60.000 0.00 0.00 0.00 4.49
3438 3680 0.530650 CAGCTCCAGTTCACACACGT 60.531 55.000 0.00 0.00 0.00 4.49
3439 3681 1.037493 AGCTCCAGTTCACACACGTA 58.963 50.000 0.00 0.00 0.00 3.57
3440 3682 1.411246 AGCTCCAGTTCACACACGTAA 59.589 47.619 0.00 0.00 0.00 3.18
3441 3683 2.159014 AGCTCCAGTTCACACACGTAAA 60.159 45.455 0.00 0.00 0.00 2.01
3442 3684 2.033151 GCTCCAGTTCACACACGTAAAC 60.033 50.000 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 3.619038 CGCTGATAGAAAAGGGTTCAGAC 59.381 47.826 2.60 0.00 36.72 3.51
71 72 2.359900 ACTTGCGCTGATAGAAAAGGG 58.640 47.619 9.73 0.00 0.00 3.95
84 85 3.558099 GAGCCCACCAAACTTGCGC 62.558 63.158 0.00 0.00 0.00 6.09
135 136 1.598130 GTGTGTGTGGGCTGGTCTC 60.598 63.158 0.00 0.00 0.00 3.36
142 143 0.107831 TTGAGTAGGTGTGTGTGGGC 59.892 55.000 0.00 0.00 0.00 5.36
143 144 2.859165 ATTGAGTAGGTGTGTGTGGG 57.141 50.000 0.00 0.00 0.00 4.61
144 145 6.128007 GGAATAAATTGAGTAGGTGTGTGTGG 60.128 42.308 0.00 0.00 0.00 4.17
145 146 6.402118 CGGAATAAATTGAGTAGGTGTGTGTG 60.402 42.308 0.00 0.00 0.00 3.82
148 149 5.183228 CCGGAATAAATTGAGTAGGTGTGT 58.817 41.667 0.00 0.00 0.00 3.72
193 194 3.855524 GCTGTGGAAAATTAACCGTGTGG 60.856 47.826 0.00 0.00 42.84 4.17
212 213 0.179000 ATCTACCCCTTTGCTCGCTG 59.821 55.000 0.00 0.00 0.00 5.18
217 224 1.285078 GGTTGGATCTACCCCTTTGCT 59.715 52.381 6.35 0.00 38.00 3.91
219 226 2.357154 CCAGGTTGGATCTACCCCTTTG 60.357 54.545 12.19 5.99 40.96 2.77
221 228 1.203570 ACCAGGTTGGATCTACCCCTT 60.204 52.381 12.19 0.00 40.96 3.95
245 255 1.259609 TATATACCCCGTTGCCCGAG 58.740 55.000 0.00 0.00 39.56 4.63
309 322 2.568956 TCTTGGTGTATGCAGAGAAGCT 59.431 45.455 0.00 0.00 34.99 3.74
310 323 2.977914 TCTTGGTGTATGCAGAGAAGC 58.022 47.619 0.00 0.00 0.00 3.86
322 335 1.371558 GGAGGCGACTTCTTGGTGT 59.628 57.895 0.00 0.00 44.43 4.16
341 354 1.172175 GCTGGAGGAAGGAAAGCAAG 58.828 55.000 0.00 0.00 34.01 4.01
347 360 1.376466 GCACTGCTGGAGGAAGGAA 59.624 57.895 0.14 0.00 0.00 3.36
348 361 2.947532 CGCACTGCTGGAGGAAGGA 61.948 63.158 0.14 0.00 0.00 3.36
349 362 2.435586 CGCACTGCTGGAGGAAGG 60.436 66.667 0.14 0.00 0.00 3.46
350 363 3.123620 GCGCACTGCTGGAGGAAG 61.124 66.667 0.30 0.00 41.73 3.46
389 402 0.749649 CCAGATCTCAGGAACTCGGG 59.250 60.000 0.00 0.00 34.60 5.14
413 426 0.749649 CCAGATCAGGGAGGAAGACG 59.250 60.000 0.00 0.00 0.00 4.18
443 463 0.540365 ATCAGGCACCAAACCACAGG 60.540 55.000 0.00 0.00 0.00 4.00
448 470 1.337167 GCAAAGATCAGGCACCAAACC 60.337 52.381 0.00 0.00 0.00 3.27
512 534 2.096174 GCAGCAAGCATCTTCAGAGAAG 59.904 50.000 0.39 0.39 44.79 2.85
533 555 1.153289 CACCGGCCAGATCTGAAGG 60.153 63.158 24.62 22.76 0.00 3.46
549 571 5.010012 AGACAATGAATCTCAAACCAACCAC 59.990 40.000 0.00 0.00 0.00 4.16
550 572 5.139727 AGACAATGAATCTCAAACCAACCA 58.860 37.500 0.00 0.00 0.00 3.67
636 662 2.639286 CACCGGCAGCTTCAACAC 59.361 61.111 0.00 0.00 0.00 3.32
639 665 1.377202 GATCCACCGGCAGCTTCAA 60.377 57.895 0.00 0.00 0.00 2.69
642 668 4.473520 CCGATCCACCGGCAGCTT 62.474 66.667 0.00 0.00 43.25 3.74
736 762 5.128205 TCACAGCATGATCTAATTTGAGGG 58.872 41.667 0.00 0.00 39.69 4.30
820 863 7.233389 TGCTCTCAGAGTTAAAACTACAGAT 57.767 36.000 2.93 0.00 39.88 2.90
828 871 6.992123 TCACAGAAATGCTCTCAGAGTTAAAA 59.008 34.615 2.93 0.00 29.07 1.52
831 874 5.244851 AGTCACAGAAATGCTCTCAGAGTTA 59.755 40.000 2.93 0.00 29.07 2.24
839 882 5.220710 ACAGTAAGTCACAGAAATGCTCT 57.779 39.130 0.00 0.00 33.23 4.09
840 883 5.523013 GACAGTAAGTCACAGAAATGCTC 57.477 43.478 0.00 0.00 46.77 4.26
866 938 6.990939 TGAAGCAATGGAGATTCAGATCTAAG 59.009 38.462 0.00 0.00 42.66 2.18
868 940 6.490241 TGAAGCAATGGAGATTCAGATCTA 57.510 37.500 0.00 0.00 42.66 1.98
882 954 6.675026 TCAGAGATGAAAAACTGAAGCAATG 58.325 36.000 0.00 0.00 36.63 2.82
913 989 3.958147 TCGACAGCCCTTATCAGTTATCA 59.042 43.478 0.00 0.00 0.00 2.15
914 990 4.585955 TCGACAGCCCTTATCAGTTATC 57.414 45.455 0.00 0.00 0.00 1.75
915 991 4.800914 GCATCGACAGCCCTTATCAGTTAT 60.801 45.833 0.35 0.00 0.00 1.89
919 995 1.069823 AGCATCGACAGCCCTTATCAG 59.930 52.381 7.97 0.00 0.00 2.90
920 996 1.069204 GAGCATCGACAGCCCTTATCA 59.931 52.381 7.97 0.00 0.00 2.15
922 998 1.069823 CAGAGCATCGACAGCCCTTAT 59.930 52.381 7.97 0.00 42.67 1.73
924 1000 1.220206 CAGAGCATCGACAGCCCTT 59.780 57.895 7.97 0.00 42.67 3.95
925 1001 1.548357 AACAGAGCATCGACAGCCCT 61.548 55.000 7.97 0.00 42.67 5.19
928 1004 2.224079 TGAAAAACAGAGCATCGACAGC 59.776 45.455 3.61 3.61 42.67 4.40
1491 1570 1.646189 GCTTGAACAGGTCCTCGATC 58.354 55.000 0.00 0.00 0.00 3.69
1604 1683 1.468520 GGTTGGTGGTGATGATGTTCG 59.531 52.381 0.00 0.00 0.00 3.95
2373 2455 1.112113 TGGAGTAGACGATGAAGCCC 58.888 55.000 0.00 0.00 0.00 5.19
2537 2654 3.627395 ATGGCCGACAGAGAAAATGTA 57.373 42.857 0.00 0.00 0.00 2.29
2549 2666 6.756542 AGATTTGCTAAAATTTTATGGCCGAC 59.243 34.615 10.97 5.00 36.10 4.79
2560 2677 9.415544 GACAAGACATGAAGATTTGCTAAAATT 57.584 29.630 0.00 0.00 36.10 1.82
2562 2679 7.939782 TGACAAGACATGAAGATTTGCTAAAA 58.060 30.769 0.00 0.00 0.00 1.52
2568 2685 7.112565 CGAAACTTGACAAGACATGAAGATTTG 59.887 37.037 21.95 0.00 0.00 2.32
2586 2703 6.022251 GCAAACATGTATCGAATCGAAACTTG 60.022 38.462 10.12 8.29 39.99 3.16
2594 2711 4.032900 ACAGACGCAAACATGTATCGAATC 59.967 41.667 17.38 8.33 0.00 2.52
2595 2712 3.932710 ACAGACGCAAACATGTATCGAAT 59.067 39.130 17.38 6.01 0.00 3.34
2596 2713 3.322369 ACAGACGCAAACATGTATCGAA 58.678 40.909 17.38 0.00 0.00 3.71
2597 2714 2.954316 ACAGACGCAAACATGTATCGA 58.046 42.857 17.38 0.00 0.00 3.59
2742 2874 1.177256 AGGAGCAGCTGCAAACTTGG 61.177 55.000 38.24 0.00 45.16 3.61
2754 2896 1.373497 ACGAGCAAACGAGGAGCAG 60.373 57.895 5.12 0.00 37.03 4.24
2763 2905 1.908065 AGCAAAACACACGAGCAAAC 58.092 45.000 0.00 0.00 0.00 2.93
2815 2998 6.205853 GAGGATCATGTGACTACTAGTCGATT 59.794 42.308 0.00 0.00 41.07 3.34
2816 2999 5.703592 GAGGATCATGTGACTACTAGTCGAT 59.296 44.000 0.00 7.60 41.07 3.59
2817 3000 5.057819 GAGGATCATGTGACTACTAGTCGA 58.942 45.833 0.00 3.55 41.07 4.20
2818 3001 5.060506 AGAGGATCATGTGACTACTAGTCG 58.939 45.833 0.00 0.00 42.93 4.18
2819 3002 6.204688 CAGAGAGGATCATGTGACTACTAGTC 59.795 46.154 9.04 9.04 41.26 2.59
2820 3003 6.061441 CAGAGAGGATCATGTGACTACTAGT 58.939 44.000 0.00 0.00 37.82 2.57
2821 3004 6.295249 TCAGAGAGGATCATGTGACTACTAG 58.705 44.000 0.00 0.00 37.82 2.57
2823 3006 5.122707 TCAGAGAGGATCATGTGACTACT 57.877 43.478 0.00 0.00 37.82 2.57
2841 3026 1.352083 CTGGGTCCTTCTGGTTCAGA 58.648 55.000 0.00 0.00 38.87 3.27
2884 3070 1.648720 CCTGCAACATATTCCGCGG 59.351 57.895 22.12 22.12 0.00 6.46
2905 3091 1.615651 GGCCTCTCTGTCTCTGTCTGA 60.616 57.143 0.00 0.00 0.00 3.27
2916 3102 2.049627 GCCATGGGTAGGCCTCTCTG 62.050 65.000 9.68 0.64 46.50 3.35
2917 3103 1.768077 GCCATGGGTAGGCCTCTCT 60.768 63.158 9.68 0.00 46.50 3.10
2918 3104 2.832498 GCCATGGGTAGGCCTCTC 59.168 66.667 9.68 3.44 46.50 3.20
2924 3110 0.462047 GTTGTCTCGCCATGGGTAGG 60.462 60.000 15.13 0.00 0.00 3.18
2925 3111 0.462047 GGTTGTCTCGCCATGGGTAG 60.462 60.000 15.13 4.06 0.00 3.18
2926 3112 1.600107 GGTTGTCTCGCCATGGGTA 59.400 57.895 15.13 0.00 0.00 3.69
2927 3113 2.351276 GGTTGTCTCGCCATGGGT 59.649 61.111 15.13 0.00 0.00 4.51
2929 3115 2.819595 CCGGTTGTCTCGCCATGG 60.820 66.667 7.63 7.63 0.00 3.66
3024 3227 1.557443 GGAACTGGAAGACGTGTGCG 61.557 60.000 0.00 0.00 40.29 5.34
3025 3228 0.531974 TGGAACTGGAAGACGTGTGC 60.532 55.000 0.00 0.00 37.43 4.57
3034 3237 1.988107 AGATGGAAGCTGGAACTGGAA 59.012 47.619 0.00 0.00 0.00 3.53
3036 3239 2.503895 AAGATGGAAGCTGGAACTGG 57.496 50.000 0.00 0.00 24.31 4.00
3058 3261 1.299541 GAATAGCATCCCACACCGTG 58.700 55.000 0.00 0.00 0.00 4.94
3059 3262 0.180406 GGAATAGCATCCCACACCGT 59.820 55.000 0.00 0.00 33.05 4.83
3060 3263 3.006672 GGAATAGCATCCCACACCG 57.993 57.895 0.00 0.00 33.05 4.94
3090 3313 1.082104 CGACGACTTTGCCTTTGCC 60.082 57.895 0.00 0.00 36.33 4.52
3093 3316 1.068474 CGATCGACGACTTTGCCTTT 58.932 50.000 10.26 0.00 45.77 3.11
3159 3384 1.060713 AAACTTGTCTGACGCGATCG 58.939 50.000 15.93 11.69 42.43 3.69
3167 3392 5.582269 GGATTCGATCATCAAACTTGTCTGA 59.418 40.000 0.00 0.00 0.00 3.27
3175 3400 2.600792 GCTGCGGATTCGATCATCAAAC 60.601 50.000 0.00 0.00 39.00 2.93
3219 3444 1.078848 ATCGACCTTGACCTGCAGC 60.079 57.895 8.66 0.00 0.00 5.25
3283 3508 1.372872 TCGTCGACTGGCACACATG 60.373 57.895 14.70 0.00 0.00 3.21
3284 3509 1.372997 GTCGTCGACTGGCACACAT 60.373 57.895 18.09 0.00 0.00 3.21
3321 3563 3.470888 CCGCTCCACCCACCTAGG 61.471 72.222 7.41 7.41 37.03 3.02
3322 3564 4.162690 GCCGCTCCACCCACCTAG 62.163 72.222 0.00 0.00 0.00 3.02
3349 3591 4.324991 GGGCGTCGGTGGGAAAGT 62.325 66.667 0.00 0.00 0.00 2.66
3379 3621 2.982470 GCACACAACCACGTACTACTAC 59.018 50.000 0.00 0.00 0.00 2.73
3380 3622 2.350676 CGCACACAACCACGTACTACTA 60.351 50.000 0.00 0.00 0.00 1.82
3381 3623 1.601162 CGCACACAACCACGTACTACT 60.601 52.381 0.00 0.00 0.00 2.57
3382 3624 0.780002 CGCACACAACCACGTACTAC 59.220 55.000 0.00 0.00 0.00 2.73
3383 3625 0.940519 GCGCACACAACCACGTACTA 60.941 55.000 0.30 0.00 0.00 1.82
3384 3626 2.241880 GCGCACACAACCACGTACT 61.242 57.895 0.30 0.00 0.00 2.73
3385 3627 2.247267 GCGCACACAACCACGTAC 59.753 61.111 0.30 0.00 0.00 3.67
3386 3628 3.331630 CGCGCACACAACCACGTA 61.332 61.111 8.75 0.00 0.00 3.57
3401 3643 4.135493 GAGAAAGGTGTCGCGCGC 62.135 66.667 27.95 23.91 0.00 6.86
3402 3644 3.479269 GGAGAAAGGTGTCGCGCG 61.479 66.667 26.76 26.76 0.00 6.86
3403 3645 2.357034 TGGAGAAAGGTGTCGCGC 60.357 61.111 0.00 0.00 0.00 6.86
3404 3646 2.383527 GCTGGAGAAAGGTGTCGCG 61.384 63.158 0.00 0.00 0.00 5.87
3405 3647 1.004440 AGCTGGAGAAAGGTGTCGC 60.004 57.895 0.00 0.00 0.00 5.19
3406 3648 0.390472 GGAGCTGGAGAAAGGTGTCG 60.390 60.000 0.00 0.00 0.00 4.35
3407 3649 0.687354 TGGAGCTGGAGAAAGGTGTC 59.313 55.000 0.00 0.00 0.00 3.67
3408 3650 0.689623 CTGGAGCTGGAGAAAGGTGT 59.310 55.000 0.00 0.00 0.00 4.16
3409 3651 0.689623 ACTGGAGCTGGAGAAAGGTG 59.310 55.000 0.00 0.00 0.00 4.00
3410 3652 1.349357 GAACTGGAGCTGGAGAAAGGT 59.651 52.381 0.00 0.00 0.00 3.50
3411 3653 1.349026 TGAACTGGAGCTGGAGAAAGG 59.651 52.381 0.00 0.00 0.00 3.11
3412 3654 2.224378 TGTGAACTGGAGCTGGAGAAAG 60.224 50.000 0.00 0.00 0.00 2.62
3413 3655 1.768275 TGTGAACTGGAGCTGGAGAAA 59.232 47.619 0.00 0.00 0.00 2.52
3414 3656 1.070758 GTGTGAACTGGAGCTGGAGAA 59.929 52.381 0.00 0.00 0.00 2.87
3415 3657 0.681733 GTGTGAACTGGAGCTGGAGA 59.318 55.000 0.00 0.00 0.00 3.71
3416 3658 0.394192 TGTGTGAACTGGAGCTGGAG 59.606 55.000 0.00 0.00 0.00 3.86
3417 3659 0.106708 GTGTGTGAACTGGAGCTGGA 59.893 55.000 0.00 0.00 0.00 3.86
3418 3660 1.224069 CGTGTGTGAACTGGAGCTGG 61.224 60.000 0.00 0.00 0.00 4.85
3419 3661 0.530650 ACGTGTGTGAACTGGAGCTG 60.531 55.000 0.00 0.00 0.00 4.24
3420 3662 1.037493 TACGTGTGTGAACTGGAGCT 58.963 50.000 0.00 0.00 0.00 4.09
3421 3663 1.860676 TTACGTGTGTGAACTGGAGC 58.139 50.000 0.00 0.00 0.00 4.70
3422 3664 3.854286 GTTTACGTGTGTGAACTGGAG 57.146 47.619 0.00 0.00 40.40 3.86


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

AutoCloner maintained by Alex Coulton.