Multiple sequence alignment - TraesCS7D01G452000

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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 TraesCS7D01G452000 chr7D 100.000 3707 0 0 1 3707 571811764 571815470 0.000000e+00 6846
1 TraesCS7D01G452000 chr7B 92.416 2690 115 41 410 3045 628354690 628357344 0.000000e+00 3755
2 TraesCS7D01G452000 chr7B 88.860 386 23 5 1915 2290 644535033 644534658 1.210000e-124 457
3 TraesCS7D01G452000 chr7B 88.624 378 21 7 1915 2281 192092334 192091968 1.220000e-119 440
4 TraesCS7D01G452000 chr7B 93.833 227 14 0 1527 1753 434774604 434774830 3.550000e-90 342
5 TraesCS7D01G452000 chr7B 84.109 258 31 5 1189 1444 80847969 80847720 1.330000e-59 241
6 TraesCS7D01G452000 chr7B 79.211 380 32 23 1 374 628352803 628353141 1.730000e-53 220
7 TraesCS7D01G452000 chr7B 90.184 163 10 2 3057 3216 628357528 628357687 1.350000e-49 207
8 TraesCS7D01G452000 chr7B 93.827 81 5 0 1077 1157 80848041 80847961 5.030000e-24 122
9 TraesCS7D01G452000 chr7A 91.645 2693 117 46 410 3013 660939498 660942171 0.000000e+00 3627
10 TraesCS7D01G452000 chr7A 87.644 607 53 16 3057 3649 660942263 660942861 0.000000e+00 686
11 TraesCS7D01G452000 chr7A 84.797 296 22 8 1044 1338 577697495 577697222 3.650000e-70 276
12 TraesCS7D01G452000 chr7A 91.005 189 13 3 225 410 660939159 660939346 6.150000e-63 252
13 TraesCS7D01G452000 chr7A 82.377 244 6 10 1 235 660938790 660939005 1.060000e-40 178
14 TraesCS7D01G452000 chr1B 94.430 395 21 1 1527 1921 542691827 542692220 1.140000e-169 606
15 TraesCS7D01G452000 chr1B 88.114 387 24 7 1915 2290 542692652 542693027 1.220000e-119 440
16 TraesCS7D01G452000 chr1B 84.496 258 30 5 1189 1444 451085237 451084988 2.860000e-61 246
17 TraesCS7D01G452000 chr2B 92.658 395 29 0 1527 1921 791363054 791362660 1.490000e-158 569
18 TraesCS7D01G452000 chr2B 92.658 395 29 0 1527 1921 791376679 791376285 1.490000e-158 569
19 TraesCS7D01G452000 chr2B 95.000 220 11 0 1528 1747 526417672 526417891 2.740000e-91 346
20 TraesCS7D01G452000 chr2B 88.327 257 30 0 1384 1640 704873005 704873261 3.600000e-80 309
21 TraesCS7D01G452000 chr2B 81.030 369 45 8 1045 1389 704867592 704867959 1.700000e-68 270
22 TraesCS7D01G452000 chr2B 89.600 125 3 1 1915 2029 791375853 791375729 2.310000e-32 150
23 TraesCS7D01G452000 chr2B 88.800 125 4 1 1915 2029 791362229 791362105 1.070000e-30 145
24 TraesCS7D01G452000 chr5A 93.369 377 24 1 1527 1903 598252865 598252490 1.160000e-154 556
25 TraesCS7D01G452000 chr3B 92.042 377 24 3 1527 1903 744552460 744552090 3.280000e-145 525
26 TraesCS7D01G452000 chr3B 88.342 386 25 5 1915 2290 799005015 799004640 2.630000e-121 446
27 TraesCS7D01G452000 chr6A 89.119 386 22 5 1915 2290 479107890 479108265 2.610000e-126 462
28 TraesCS7D01G452000 chr6A 84.496 258 30 5 1189 1444 330379060 330379309 2.860000e-61 246
29 TraesCS7D01G452000 chr5B 89.119 386 22 5 1915 2290 680713106 680712731 2.610000e-126 462
30 TraesCS7D01G452000 chrUn 85.616 292 21 7 1044 1335 13751055 13751325 1.680000e-73 287
31 TraesCS7D01G452000 chr2A 85.616 292 21 7 1044 1335 177839321 177839591 1.680000e-73 287
32 TraesCS7D01G452000 chr2A 85.616 292 21 7 1044 1335 177946377 177946647 1.680000e-73 287
33 TraesCS7D01G452000 chr4B 84.109 258 31 5 1189 1444 624398688 624398937 1.330000e-59 241
34 TraesCS7D01G452000 chr4B 83.784 259 30 7 1189 1444 328908684 328908933 6.190000e-58 235
35 TraesCS7D01G452000 chr1A 82.759 290 29 7 1044 1333 343860794 343860526 4.780000e-59 239


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 TraesCS7D01G452000 chr7D 571811764 571815470 3706 False 6846.00 6846 100.000000 1 3707 1 chr7D.!!$F1 3706
1 TraesCS7D01G452000 chr7B 628352803 628357687 4884 False 1394.00 3755 87.270333 1 3216 3 chr7B.!!$F2 3215
2 TraesCS7D01G452000 chr7A 660938790 660942861 4071 False 1185.75 3627 88.167750 1 3649 4 chr7A.!!$F1 3648
3 TraesCS7D01G452000 chr1B 542691827 542693027 1200 False 523.00 606 91.272000 1527 2290 2 chr1B.!!$F1 763
4 TraesCS7D01G452000 chr2B 791375729 791376679 950 True 359.50 569 91.129000 1527 2029 2 chr2B.!!$R2 502
5 TraesCS7D01G452000 chr2B 791362105 791363054 949 True 357.00 569 90.729000 1527 2029 2 chr2B.!!$R1 502

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
623 2342 0.036164 CACACCAGGGACCATTCGAA 59.964 55.000 0.00 0.0 0.00 3.71 F
1034 2794 0.875040 ATCGCGCTGCTTGATCAGAG 60.875 55.000 5.56 0.0 36.19 3.35 F
2143 4386 1.541588 GTGCCAATTGTGTTCTCTCCC 59.458 52.381 4.43 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1443 3233 0.978907 GGTCCCCGAACACCTTCTTA 59.021 55.0 0.00 0.0 0.00 2.10 R
2574 4821 1.189524 GGCAACCAAAACCCCCTACC 61.190 60.0 0.00 0.0 0.00 3.18 R
3065 5523 0.036306 AGAGTTAGCAACGGGGTTGG 59.964 55.0 10.19 0.0 42.99 3.77 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
43 49 4.577246 GGGAGCACTCGCCGCTAG 62.577 72.222 3.45 0.00 40.63 3.42
51 57 3.138930 CTCGCCGCTAGCTTGCCTA 62.139 63.158 14.61 4.67 40.39 3.93
83 89 0.460109 CGAATGATGAGACGTGGCCA 60.460 55.000 0.00 0.00 0.00 5.36
84 90 1.293924 GAATGATGAGACGTGGCCAG 58.706 55.000 5.11 2.58 0.00 4.85
85 91 0.615331 AATGATGAGACGTGGCCAGT 59.385 50.000 5.11 6.62 0.00 4.00
86 92 0.107993 ATGATGAGACGTGGCCAGTG 60.108 55.000 5.11 4.02 0.00 3.66
87 93 1.448540 GATGAGACGTGGCCAGTGG 60.449 63.158 5.11 4.20 0.00 4.00
137 143 8.634335 TGATTTTCTTGGATTGATGTTCTACA 57.366 30.769 0.00 0.00 0.00 2.74
138 144 8.514594 TGATTTTCTTGGATTGATGTTCTACAC 58.485 33.333 0.00 0.00 0.00 2.90
139 145 7.815840 TTTTCTTGGATTGATGTTCTACACA 57.184 32.000 0.00 0.00 40.71 3.72
140 146 7.439157 TTTCTTGGATTGATGTTCTACACAG 57.561 36.000 0.00 0.00 39.40 3.66
144 150 3.307242 GGATTGATGTTCTACACAGACGC 59.693 47.826 0.00 0.00 39.40 5.19
145 151 1.977188 TGATGTTCTACACAGACGCG 58.023 50.000 3.53 3.53 39.40 6.01
147 153 0.885879 ATGTTCTACACAGACGCGGA 59.114 50.000 12.47 0.00 39.40 5.54
148 154 0.240145 TGTTCTACACAGACGCGGAG 59.760 55.000 12.47 1.42 0.00 4.63
149 155 0.520404 GTTCTACACAGACGCGGAGA 59.480 55.000 12.47 0.00 0.00 3.71
150 156 1.132643 GTTCTACACAGACGCGGAGAT 59.867 52.381 12.47 0.00 0.00 2.75
151 157 0.733150 TCTACACAGACGCGGAGATG 59.267 55.000 12.47 6.07 0.00 2.90
152 158 0.248661 CTACACAGACGCGGAGATGG 60.249 60.000 12.47 0.00 0.00 3.51
153 159 0.678684 TACACAGACGCGGAGATGGA 60.679 55.000 12.47 0.00 0.00 3.41
154 160 1.323271 ACACAGACGCGGAGATGGAT 61.323 55.000 12.47 0.00 0.00 3.41
163 176 2.787994 GCGGAGATGGATGATGGATTT 58.212 47.619 0.00 0.00 0.00 2.17
336 517 5.356470 TCATGGACAATCAAACGCATCATTA 59.644 36.000 0.00 0.00 0.00 1.90
337 518 5.833406 TGGACAATCAAACGCATCATTAT 57.167 34.783 0.00 0.00 0.00 1.28
342 523 8.531530 GGACAATCAAACGCATCATTATTTTAC 58.468 33.333 0.00 0.00 0.00 2.01
345 526 8.957028 CAATCAAACGCATCATTATTTTACGAT 58.043 29.630 0.00 0.00 0.00 3.73
347 528 8.981370 TCAAACGCATCATTATTTTACGATAC 57.019 30.769 0.00 0.00 0.00 2.24
348 529 7.790216 TCAAACGCATCATTATTTTACGATACG 59.210 33.333 0.00 0.00 32.27 3.06
352 536 7.756272 ACGCATCATTATTTTACGATACGGATA 59.244 33.333 0.00 0.00 30.66 2.59
353 537 8.259872 CGCATCATTATTTTACGATACGGATAG 58.740 37.037 0.00 0.00 0.00 2.08
386 570 2.669849 GCATGGGGCAAAATGGCA 59.330 55.556 6.25 0.00 45.76 4.92
529 2239 6.303839 ACATTCTTCACCTTTAAGCCTAACA 58.696 36.000 0.00 0.00 0.00 2.41
537 2248 4.278419 ACCTTTAAGCCTAACACAAAGCAG 59.722 41.667 0.00 0.00 0.00 4.24
563 2274 6.834168 AACAGAAGAAAAAGTCTCACCAAA 57.166 33.333 0.00 0.00 34.56 3.28
567 2278 6.094048 CAGAAGAAAAAGTCTCACCAAAGACA 59.906 38.462 6.79 0.00 46.65 3.41
580 2299 4.340894 CCAAAGACACATACATTGGTCG 57.659 45.455 0.00 0.00 36.60 4.79
623 2342 0.036164 CACACCAGGGACCATTCGAA 59.964 55.000 0.00 0.00 0.00 3.71
654 2373 4.822896 ACTAGTTGAGCTCCGGATTAGTAG 59.177 45.833 12.15 7.98 0.00 2.57
655 2374 3.633418 AGTTGAGCTCCGGATTAGTAGT 58.367 45.455 12.15 0.00 0.00 2.73
656 2375 4.789807 AGTTGAGCTCCGGATTAGTAGTA 58.210 43.478 12.15 0.00 0.00 1.82
657 2376 5.198965 AGTTGAGCTCCGGATTAGTAGTAA 58.801 41.667 12.15 0.00 0.00 2.24
658 2377 5.299782 AGTTGAGCTCCGGATTAGTAGTAAG 59.700 44.000 12.15 0.00 0.00 2.34
659 2378 3.568853 TGAGCTCCGGATTAGTAGTAAGC 59.431 47.826 12.15 0.00 0.00 3.09
668 2387 6.183360 CCGGATTAGTAGTAAGCTTTTTGGTG 60.183 42.308 3.20 0.00 0.00 4.17
725 2449 4.012895 CAACCTGTGGACGCACGC 62.013 66.667 0.00 0.00 0.00 5.34
966 2726 6.284459 GTGAAACCAATTATCTCCGATCTCT 58.716 40.000 0.00 0.00 0.00 3.10
1034 2794 0.875040 ATCGCGCTGCTTGATCAGAG 60.875 55.000 5.56 0.00 36.19 3.35
1423 3213 4.947147 GGCGTGGTGGGCTGTTCA 62.947 66.667 0.00 0.00 0.00 3.18
1424 3214 2.904866 GCGTGGTGGGCTGTTCAA 60.905 61.111 0.00 0.00 0.00 2.69
1426 3216 1.821759 CGTGGTGGGCTGTTCAACA 60.822 57.895 0.00 0.00 0.00 3.33
1445 3235 2.358984 GCCCGAGGCGGTGTTTAA 60.359 61.111 5.06 0.00 46.80 1.52
2084 4324 9.968870 TTTCACAATTTACACCTGGTTAATTAC 57.031 29.630 0.00 0.00 36.79 1.89
2143 4386 1.541588 GTGCCAATTGTGTTCTCTCCC 59.458 52.381 4.43 0.00 0.00 4.30
2320 4563 2.434884 ATGGACAGCAAGACGCCG 60.435 61.111 0.00 0.00 44.04 6.46
2464 4711 4.451652 GTCCGTCCGTCCGTCGAC 62.452 72.222 5.18 5.18 42.86 4.20
2714 4974 6.817765 AGATTTCTCTAGCTAGGATCGAAG 57.182 41.667 20.58 9.47 0.00 3.79
2747 5007 3.576356 GTGCGTGTGCTGTGCTGT 61.576 61.111 0.00 0.00 43.34 4.40
2770 5031 4.803613 TGCTGCAACTACGATGTAATACTG 59.196 41.667 0.00 0.00 0.00 2.74
2796 5057 3.364441 GTGCGGTGCCTGCAATGA 61.364 61.111 9.85 0.00 45.23 2.57
2855 5118 6.146837 AGCAGTGATAACTATCATGCGATTTC 59.853 38.462 18.18 2.30 43.82 2.17
2867 5130 1.737236 TGCGATTTCACAAAGGATCGG 59.263 47.619 6.71 0.00 41.08 4.18
2881 5144 1.594862 GGATCGGCTCAAACTTCATCG 59.405 52.381 0.00 0.00 0.00 3.84
2924 5188 1.115467 AAGGGTGTGGCTAGATCTCG 58.885 55.000 0.00 0.00 0.00 4.04
2926 5190 0.386113 GGGTGTGGCTAGATCTCGAC 59.614 60.000 0.00 0.00 0.00 4.20
2927 5191 1.394618 GGTGTGGCTAGATCTCGACT 58.605 55.000 0.00 0.00 0.00 4.18
2930 5194 2.032799 GTGTGGCTAGATCTCGACTGAG 59.967 54.545 0.00 0.00 43.99 3.35
2937 5205 6.096987 TGGCTAGATCTCGACTGAGTTTTAAT 59.903 38.462 0.00 0.00 43.09 1.40
2938 5206 7.284716 TGGCTAGATCTCGACTGAGTTTTAATA 59.715 37.037 0.00 0.00 43.09 0.98
2945 5213 8.967552 TCTCGACTGAGTTTTAATAAAGTCTC 57.032 34.615 10.68 10.68 41.99 3.36
2946 5214 7.749570 TCTCGACTGAGTTTTAATAAAGTCTCG 59.250 37.037 11.94 0.00 41.99 4.04
2954 5222 8.307921 AGTTTTAATAAAGTCTCGGTCAAGTC 57.692 34.615 0.00 0.00 0.00 3.01
2957 5225 9.932207 TTTTAATAAAGTCTCGGTCAAGTCATA 57.068 29.630 0.00 0.00 0.00 2.15
2960 5228 8.480643 AATAAAGTCTCGGTCAAGTCATAAAG 57.519 34.615 0.00 0.00 0.00 1.85
3013 5281 6.564709 AATAAAAACTTTGTACGGACCTCC 57.435 37.500 0.00 0.00 0.00 4.30
3015 5283 2.538512 AACTTTGTACGGACCTCCAC 57.461 50.000 0.00 0.00 35.14 4.02
3030 5308 5.279306 GGACCTCCACGTAAATATAGCATCA 60.279 44.000 0.00 0.00 35.64 3.07
3045 5323 4.623932 AGCATCAACTGAGACTTGGTTA 57.376 40.909 0.00 0.00 0.00 2.85
3046 5324 4.573900 AGCATCAACTGAGACTTGGTTAG 58.426 43.478 0.00 0.00 0.00 2.34
3051 5329 5.391256 TCAACTGAGACTTGGTTAGGTCTA 58.609 41.667 0.00 0.00 42.06 2.59
3053 5511 3.757493 ACTGAGACTTGGTTAGGTCTACG 59.243 47.826 0.00 0.00 42.06 3.51
3055 5513 4.597004 TGAGACTTGGTTAGGTCTACGAT 58.403 43.478 0.00 0.00 42.06 3.73
3059 5517 5.069501 ACTTGGTTAGGTCTACGATTGAC 57.930 43.478 0.00 0.00 0.00 3.18
3065 5523 7.037438 TGGTTAGGTCTACGATTGACATTTAC 58.963 38.462 0.00 0.00 36.26 2.01
3069 5527 5.873164 AGGTCTACGATTGACATTTACCAAC 59.127 40.000 0.00 0.00 36.26 3.77
3079 5537 2.224818 ACATTTACCAACCCCGTTGCTA 60.225 45.455 0.00 0.00 41.62 3.49
3080 5538 2.653234 TTTACCAACCCCGTTGCTAA 57.347 45.000 0.00 0.00 41.62 3.09
3081 5539 1.894881 TTACCAACCCCGTTGCTAAC 58.105 50.000 0.00 0.00 41.62 2.34
3082 5540 1.058284 TACCAACCCCGTTGCTAACT 58.942 50.000 0.00 0.00 41.62 2.24
3083 5541 0.250597 ACCAACCCCGTTGCTAACTC 60.251 55.000 0.00 0.00 41.62 3.01
3084 5542 0.036306 CCAACCCCGTTGCTAACTCT 59.964 55.000 0.00 0.00 41.62 3.24
3085 5543 1.156736 CAACCCCGTTGCTAACTCTG 58.843 55.000 0.00 0.00 36.73 3.35
3086 5544 0.036306 AACCCCGTTGCTAACTCTGG 59.964 55.000 0.00 0.00 0.00 3.86
3094 5552 1.644509 TGCTAACTCTGGAGGCTTGA 58.355 50.000 2.58 0.00 0.00 3.02
3186 5644 3.304293 GCAAACTTGTGAACAAACAGAGC 59.696 43.478 0.00 0.00 35.15 4.09
3196 5654 2.224606 ACAAACAGAGCACACATCCAG 58.775 47.619 0.00 0.00 0.00 3.86
3228 5686 4.430007 CTCTAGCATTTTGTACGGCTACA 58.570 43.478 0.00 0.00 37.79 2.74
3284 5742 4.127918 TCCAAGAGGGAGAAAGTACAGA 57.872 45.455 0.00 0.00 42.15 3.41
3285 5743 4.489737 TCCAAGAGGGAGAAAGTACAGAA 58.510 43.478 0.00 0.00 42.15 3.02
3286 5744 4.905456 TCCAAGAGGGAGAAAGTACAGAAA 59.095 41.667 0.00 0.00 42.15 2.52
3287 5745 5.368523 TCCAAGAGGGAGAAAGTACAGAAAA 59.631 40.000 0.00 0.00 42.15 2.29
3288 5746 6.062095 CCAAGAGGGAGAAAGTACAGAAAAA 58.938 40.000 0.00 0.00 40.01 1.94
3319 5777 5.870978 TCTTTTTGTATACTAGGTGGTTCGC 59.129 40.000 4.17 0.00 0.00 4.70
3438 5904 9.578576 TCATTATGCTTTTAGGCAAGATAATCT 57.421 29.630 0.00 0.00 45.68 2.40
3505 5972 9.114952 TGCAAATAAGTAATATCATCACCGAAA 57.885 29.630 0.00 0.00 0.00 3.46
3506 5973 9.944663 GCAAATAAGTAATATCATCACCGAAAA 57.055 29.630 0.00 0.00 0.00 2.29
3514 5981 3.557577 TCATCACCGAAAACAATGCAG 57.442 42.857 0.00 0.00 0.00 4.41
3541 6008 5.654603 TCGTAACTAGATGTGACACCAAT 57.345 39.130 2.45 0.00 30.22 3.16
3569 6037 6.528423 CAGAGTAGAGGTTTGTGTTATCTTCG 59.472 42.308 0.00 0.00 0.00 3.79
3585 6053 2.972625 CTTCGCATGAAGTCCTTACCA 58.027 47.619 0.00 0.00 45.38 3.25
3630 6098 3.500299 CCACCGACATGTTTGTGATGTTA 59.500 43.478 22.94 0.00 35.79 2.41
3645 6113 4.953667 TGATGTTATCACTGAGGAGCATC 58.046 43.478 11.02 11.02 33.59 3.91
3649 6117 4.223700 TGTTATCACTGAGGAGCATCACTT 59.776 41.667 0.00 0.00 36.25 3.16
3650 6118 3.540314 ATCACTGAGGAGCATCACTTC 57.460 47.619 0.00 0.00 36.25 3.01
3651 6119 2.533916 TCACTGAGGAGCATCACTTCT 58.466 47.619 0.00 0.00 36.69 2.85
3652 6120 3.701664 TCACTGAGGAGCATCACTTCTA 58.298 45.455 0.00 0.00 32.67 2.10
3653 6121 4.285020 TCACTGAGGAGCATCACTTCTAT 58.715 43.478 0.00 0.00 32.67 1.98
3654 6122 4.340666 TCACTGAGGAGCATCACTTCTATC 59.659 45.833 0.00 0.00 32.67 2.08
3655 6123 4.099113 CACTGAGGAGCATCACTTCTATCA 59.901 45.833 0.00 0.00 32.67 2.15
3656 6124 4.900652 ACTGAGGAGCATCACTTCTATCAT 59.099 41.667 0.00 0.00 32.67 2.45
3657 6125 5.366186 ACTGAGGAGCATCACTTCTATCATT 59.634 40.000 0.00 0.00 32.67 2.57
3658 6126 6.552725 ACTGAGGAGCATCACTTCTATCATTA 59.447 38.462 0.00 0.00 32.67 1.90
3659 6127 7.235193 ACTGAGGAGCATCACTTCTATCATTAT 59.765 37.037 0.00 0.00 32.67 1.28
3660 6128 8.655935 TGAGGAGCATCACTTCTATCATTATA 57.344 34.615 0.00 0.00 32.67 0.98
3661 6129 8.526978 TGAGGAGCATCACTTCTATCATTATAC 58.473 37.037 0.00 0.00 32.67 1.47
3662 6130 7.542890 AGGAGCATCACTTCTATCATTATACG 58.457 38.462 0.00 0.00 29.60 3.06
3663 6131 6.254589 GGAGCATCACTTCTATCATTATACGC 59.745 42.308 0.00 0.00 36.25 4.42
3664 6132 6.929625 AGCATCACTTCTATCATTATACGCT 58.070 36.000 0.00 0.00 0.00 5.07
3665 6133 7.382110 AGCATCACTTCTATCATTATACGCTT 58.618 34.615 0.00 0.00 0.00 4.68
3666 6134 7.543868 AGCATCACTTCTATCATTATACGCTTC 59.456 37.037 0.00 0.00 0.00 3.86
3667 6135 7.329471 GCATCACTTCTATCATTATACGCTTCA 59.671 37.037 0.00 0.00 0.00 3.02
3668 6136 9.196552 CATCACTTCTATCATTATACGCTTCAA 57.803 33.333 0.00 0.00 0.00 2.69
3669 6137 8.803201 TCACTTCTATCATTATACGCTTCAAG 57.197 34.615 0.00 0.00 0.00 3.02
3670 6138 7.382488 TCACTTCTATCATTATACGCTTCAAGC 59.618 37.037 0.00 0.00 38.02 4.01
3683 6151 4.274421 GCTTCAAGCGGGTATTTACTTC 57.726 45.455 0.00 0.00 0.00 3.01
3684 6152 3.939592 GCTTCAAGCGGGTATTTACTTCT 59.060 43.478 0.00 0.00 0.00 2.85
3685 6153 4.395231 GCTTCAAGCGGGTATTTACTTCTT 59.605 41.667 0.00 0.00 0.00 2.52
3686 6154 5.673818 GCTTCAAGCGGGTATTTACTTCTTG 60.674 44.000 0.00 0.00 33.08 3.02
3687 6155 5.155278 TCAAGCGGGTATTTACTTCTTGA 57.845 39.130 0.00 0.00 35.59 3.02
3688 6156 5.741011 TCAAGCGGGTATTTACTTCTTGAT 58.259 37.500 0.00 0.00 34.45 2.57
3689 6157 5.584649 TCAAGCGGGTATTTACTTCTTGATG 59.415 40.000 0.00 0.00 34.45 3.07
3690 6158 5.099042 AGCGGGTATTTACTTCTTGATGT 57.901 39.130 0.00 0.00 0.00 3.06
3691 6159 5.497474 AGCGGGTATTTACTTCTTGATGTT 58.503 37.500 0.00 0.00 0.00 2.71
3692 6160 6.646267 AGCGGGTATTTACTTCTTGATGTTA 58.354 36.000 0.00 0.00 0.00 2.41
3693 6161 7.280356 AGCGGGTATTTACTTCTTGATGTTAT 58.720 34.615 0.00 0.00 0.00 1.89
3694 6162 7.441458 AGCGGGTATTTACTTCTTGATGTTATC 59.559 37.037 0.00 0.00 0.00 1.75
3695 6163 7.307811 GCGGGTATTTACTTCTTGATGTTATCC 60.308 40.741 0.00 0.00 0.00 2.59
3696 6164 7.713507 CGGGTATTTACTTCTTGATGTTATCCA 59.286 37.037 0.00 0.00 0.00 3.41
3697 6165 9.574516 GGGTATTTACTTCTTGATGTTATCCAT 57.425 33.333 0.00 0.00 36.13 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 89 2.632377 CATGATTGGTTCGTAGCCACT 58.368 47.619 0.00 0.00 35.46 4.00
84 90 1.670811 CCATGATTGGTTCGTAGCCAC 59.329 52.381 0.00 0.00 38.30 5.01
85 91 1.408127 CCCATGATTGGTTCGTAGCCA 60.408 52.381 0.00 0.00 41.91 4.75
86 92 1.308998 CCCATGATTGGTTCGTAGCC 58.691 55.000 0.00 0.00 41.91 3.93
87 93 1.308998 CCCCATGATTGGTTCGTAGC 58.691 55.000 0.00 0.00 41.91 3.58
88 94 1.134098 AGCCCCATGATTGGTTCGTAG 60.134 52.381 0.00 0.00 41.91 3.51
89 95 0.916086 AGCCCCATGATTGGTTCGTA 59.084 50.000 0.00 0.00 41.91 3.43
90 96 0.680921 CAGCCCCATGATTGGTTCGT 60.681 55.000 0.00 0.00 41.91 3.85
136 142 0.873312 CATCCATCTCCGCGTCTGTG 60.873 60.000 4.92 0.00 0.00 3.66
137 143 1.037579 TCATCCATCTCCGCGTCTGT 61.038 55.000 4.92 0.00 0.00 3.41
138 144 0.316522 ATCATCCATCTCCGCGTCTG 59.683 55.000 4.92 0.00 0.00 3.51
139 145 0.316522 CATCATCCATCTCCGCGTCT 59.683 55.000 4.92 0.00 0.00 4.18
140 146 0.668706 CCATCATCCATCTCCGCGTC 60.669 60.000 4.92 0.00 0.00 5.19
144 150 3.079578 CCAAATCCATCATCCATCTCCG 58.920 50.000 0.00 0.00 0.00 4.63
145 151 4.377762 TCCAAATCCATCATCCATCTCC 57.622 45.455 0.00 0.00 0.00 3.71
147 153 6.141083 ACAAATCCAAATCCATCATCCATCT 58.859 36.000 0.00 0.00 0.00 2.90
148 154 6.415206 ACAAATCCAAATCCATCATCCATC 57.585 37.500 0.00 0.00 0.00 3.51
149 155 7.038587 CCATACAAATCCAAATCCATCATCCAT 60.039 37.037 0.00 0.00 0.00 3.41
150 156 6.268158 CCATACAAATCCAAATCCATCATCCA 59.732 38.462 0.00 0.00 0.00 3.41
151 157 6.494491 TCCATACAAATCCAAATCCATCATCC 59.506 38.462 0.00 0.00 0.00 3.51
152 158 7.373493 GTCCATACAAATCCAAATCCATCATC 58.627 38.462 0.00 0.00 0.00 2.92
153 159 6.016024 CGTCCATACAAATCCAAATCCATCAT 60.016 38.462 0.00 0.00 0.00 2.45
154 160 5.299028 CGTCCATACAAATCCAAATCCATCA 59.701 40.000 0.00 0.00 0.00 3.07
163 176 1.425267 CGCGCGTCCATACAAATCCA 61.425 55.000 24.19 0.00 0.00 3.41
336 517 8.063200 TCATCCATCTATCCGTATCGTAAAAT 57.937 34.615 0.00 0.00 0.00 1.82
337 518 7.457024 TCATCCATCTATCCGTATCGTAAAA 57.543 36.000 0.00 0.00 0.00 1.52
342 523 3.378427 TGCTCATCCATCTATCCGTATCG 59.622 47.826 0.00 0.00 0.00 2.92
345 526 3.507622 CACTGCTCATCCATCTATCCGTA 59.492 47.826 0.00 0.00 0.00 4.02
347 528 2.930023 GCACTGCTCATCCATCTATCCG 60.930 54.545 0.00 0.00 0.00 4.18
348 529 2.697654 GCACTGCTCATCCATCTATCC 58.302 52.381 0.00 0.00 0.00 2.59
352 536 1.523258 GCGCACTGCTCATCCATCT 60.523 57.895 0.30 0.00 41.73 2.90
353 537 1.164662 ATGCGCACTGCTCATCCATC 61.165 55.000 14.90 0.00 46.63 3.51
378 562 1.812571 GATCACCACTCGTGCCATTTT 59.187 47.619 0.00 0.00 42.69 1.82
379 563 1.271325 TGATCACCACTCGTGCCATTT 60.271 47.619 0.00 0.00 42.69 2.32
386 570 1.079819 CGCCTTGATCACCACTCGT 60.080 57.895 0.00 0.00 0.00 4.18
529 2239 7.154656 ACTTTTTCTTCTGTTTTCTGCTTTGT 58.845 30.769 0.00 0.00 0.00 2.83
537 2248 6.852664 TGGTGAGACTTTTTCTTCTGTTTTC 58.147 36.000 0.00 0.00 33.22 2.29
563 2274 2.233676 TCAGCGACCAATGTATGTGTCT 59.766 45.455 0.00 0.00 31.12 3.41
567 2278 6.054941 TGAATAATCAGCGACCAATGTATGT 58.945 36.000 0.00 0.00 0.00 2.29
597 2316 2.122413 TCCCTGGTGTGGTGAGCT 60.122 61.111 0.00 0.00 0.00 4.09
623 2342 5.187186 TCCGGAGCTCAACTAGTCTAAAAAT 59.813 40.000 17.19 0.00 0.00 1.82
654 2373 4.803613 CACTTTCACCACCAAAAAGCTTAC 59.196 41.667 0.00 0.00 34.15 2.34
655 2374 4.142049 CCACTTTCACCACCAAAAAGCTTA 60.142 41.667 0.00 0.00 34.15 3.09
656 2375 3.369366 CCACTTTCACCACCAAAAAGCTT 60.369 43.478 0.00 0.00 34.15 3.74
657 2376 2.168313 CCACTTTCACCACCAAAAAGCT 59.832 45.455 0.00 0.00 34.15 3.74
658 2377 2.549926 CCACTTTCACCACCAAAAAGC 58.450 47.619 0.00 0.00 34.15 3.51
659 2378 2.763448 TCCCACTTTCACCACCAAAAAG 59.237 45.455 0.00 0.00 36.35 2.27
668 2387 5.296035 CCTCGTATATTTTCCCACTTTCACC 59.704 44.000 0.00 0.00 0.00 4.02
947 2707 6.209788 GGTCTTAGAGATCGGAGATAATTGGT 59.790 42.308 0.00 0.00 45.12 3.67
962 2722 4.560919 GCTCTTGGTTTTCGGTCTTAGAGA 60.561 45.833 0.00 0.00 31.76 3.10
966 2726 3.478857 TGCTCTTGGTTTTCGGTCTTA 57.521 42.857 0.00 0.00 0.00 2.10
1416 3206 2.281484 TCGGGCCTGTTGAACAGC 60.281 61.111 19.45 14.14 44.63 4.40
1437 3227 2.551032 CCCGAACACCTTCTTAAACACC 59.449 50.000 0.00 0.00 0.00 4.16
1443 3233 0.978907 GGTCCCCGAACACCTTCTTA 59.021 55.000 0.00 0.00 0.00 2.10
1445 3235 1.152096 AGGTCCCCGAACACCTTCT 60.152 57.895 0.00 0.00 40.35 2.85
2084 4324 6.072008 TGACTCACATTTCACAATGGTAATGG 60.072 38.462 1.68 0.00 43.82 3.16
2085 4325 6.912082 TGACTCACATTTCACAATGGTAATG 58.088 36.000 0.31 0.00 43.82 1.90
2093 4336 5.553290 TTTCGTTGACTCACATTTCACAA 57.447 34.783 0.00 0.00 0.00 3.33
2143 4386 2.414785 GGTAATGCCGTTGCCCTGG 61.415 63.158 0.00 0.00 36.66 4.45
2197 4440 3.923645 AGGACCGACTCCACCCCA 61.924 66.667 2.34 0.00 42.46 4.96
2359 4602 4.477975 GTGGACGCCGACGAGGAG 62.478 72.222 0.00 5.04 45.00 3.69
2440 4683 4.748679 GACGGACGGACGGTGTCG 62.749 72.222 6.00 0.00 43.02 4.35
2441 4684 4.410743 GGACGGACGGACGGTGTC 62.411 72.222 6.00 1.07 38.39 3.67
2574 4821 1.189524 GGCAACCAAAACCCCCTACC 61.190 60.000 0.00 0.00 0.00 3.18
2649 4906 2.820037 CCTCTTTCTTCCGCGGCC 60.820 66.667 23.51 0.00 0.00 6.13
2654 4911 1.896465 ACCACTCTCCTCTTTCTTCCG 59.104 52.381 0.00 0.00 0.00 4.30
2714 4974 1.442857 CACTCGTCACTCTCACCGC 60.443 63.158 0.00 0.00 0.00 5.68
2747 5007 4.803613 CAGTATTACATCGTAGTTGCAGCA 59.196 41.667 2.55 0.00 0.00 4.41
2770 5031 4.445545 GCACCGCACAAGCTACGC 62.446 66.667 0.00 0.00 39.10 4.42
2796 5057 6.412214 AGCCACACCGATTTTAGTAGTATTT 58.588 36.000 0.00 0.00 0.00 1.40
2855 5118 2.154462 AGTTTGAGCCGATCCTTTGTG 58.846 47.619 0.00 0.00 0.00 3.33
2867 5130 3.125829 TGAAGATGCGATGAAGTTTGAGC 59.874 43.478 0.00 0.00 0.00 4.26
2881 5144 3.846360 AGCAAAGAAGCAATGAAGATGC 58.154 40.909 0.00 0.00 44.15 3.91
2924 5188 7.597743 TGACCGAGACTTTATTAAAACTCAGTC 59.402 37.037 19.31 19.31 34.98 3.51
2926 5190 7.884816 TGACCGAGACTTTATTAAAACTCAG 57.115 36.000 16.24 11.04 0.00 3.35
2927 5191 7.929785 ACTTGACCGAGACTTTATTAAAACTCA 59.070 33.333 16.24 3.36 0.00 3.41
2930 5194 8.080083 TGACTTGACCGAGACTTTATTAAAAC 57.920 34.615 0.00 0.00 0.00 2.43
2937 5205 5.867716 GCTTTATGACTTGACCGAGACTTTA 59.132 40.000 0.00 0.00 0.00 1.85
2938 5206 4.691216 GCTTTATGACTTGACCGAGACTTT 59.309 41.667 0.00 0.00 0.00 2.66
2987 5255 7.922278 GGAGGTCCGTACAAAGTTTTTATTTTT 59.078 33.333 0.00 0.00 0.00 1.94
2993 5261 3.628942 GTGGAGGTCCGTACAAAGTTTTT 59.371 43.478 0.00 0.00 39.43 1.94
3003 5271 4.216257 GCTATATTTACGTGGAGGTCCGTA 59.784 45.833 0.00 0.00 38.43 4.02
3009 5277 6.146184 CAGTTGATGCTATATTTACGTGGAGG 59.854 42.308 0.00 0.00 0.00 4.30
3013 5281 7.649705 AGTCTCAGTTGATGCTATATTTACGTG 59.350 37.037 0.00 0.00 0.00 4.49
3015 5283 8.483218 CAAGTCTCAGTTGATGCTATATTTACG 58.517 37.037 0.00 0.00 30.18 3.18
3030 5308 4.217983 CGTAGACCTAACCAAGTCTCAGTT 59.782 45.833 0.00 0.00 42.31 3.16
3045 5323 5.670792 TGGTAAATGTCAATCGTAGACCT 57.329 39.130 0.00 0.00 42.51 3.85
3046 5324 5.064325 GGTTGGTAAATGTCAATCGTAGACC 59.936 44.000 0.00 0.00 42.51 3.85
3051 5329 3.086282 GGGGTTGGTAAATGTCAATCGT 58.914 45.455 0.00 0.00 0.00 3.73
3053 5511 3.086282 ACGGGGTTGGTAAATGTCAATC 58.914 45.455 0.00 0.00 0.00 2.67
3055 5513 2.623889 CAACGGGGTTGGTAAATGTCAA 59.376 45.455 0.61 0.00 39.56 3.18
3059 5517 3.804601 GCAACGGGGTTGGTAAATG 57.195 52.632 10.19 0.00 42.99 2.32
3065 5523 0.036306 AGAGTTAGCAACGGGGTTGG 59.964 55.000 10.19 0.00 42.99 3.77
3069 5527 0.108138 CTCCAGAGTTAGCAACGGGG 60.108 60.000 0.00 0.00 36.23 5.73
3079 5537 0.767375 TTGCTCAAGCCTCCAGAGTT 59.233 50.000 0.00 0.00 41.18 3.01
3080 5538 0.767375 TTTGCTCAAGCCTCCAGAGT 59.233 50.000 0.00 0.00 41.18 3.24
3081 5539 1.538950 GTTTTGCTCAAGCCTCCAGAG 59.461 52.381 0.00 0.00 41.18 3.35
3082 5540 1.143684 AGTTTTGCTCAAGCCTCCAGA 59.856 47.619 0.00 0.00 41.18 3.86
3083 5541 1.613836 AGTTTTGCTCAAGCCTCCAG 58.386 50.000 0.00 0.00 41.18 3.86
3084 5542 1.682854 CAAGTTTTGCTCAAGCCTCCA 59.317 47.619 0.00 0.00 41.18 3.86
3085 5543 1.000171 CCAAGTTTTGCTCAAGCCTCC 60.000 52.381 0.00 0.00 41.18 4.30
3086 5544 1.683385 ACCAAGTTTTGCTCAAGCCTC 59.317 47.619 0.00 0.00 41.18 4.70
3094 5552 7.722285 TCCTAGTATGTAAAACCAAGTTTTGCT 59.278 33.333 17.74 9.11 44.30 3.91
3127 5585 1.331214 TTTGGAGCCTTGGAGCAAAG 58.669 50.000 0.00 0.00 34.23 2.77
3186 5644 2.092753 AGGTGCCTTATCTGGATGTGTG 60.093 50.000 0.00 0.00 0.00 3.82
3196 5654 4.884164 ACAAAATGCTAGAGGTGCCTTATC 59.116 41.667 0.00 0.00 0.00 1.75
3292 5750 8.943002 CGAACCACCTAGTATACAAAAAGAAAT 58.057 33.333 5.50 0.00 0.00 2.17
3294 5752 6.369615 GCGAACCACCTAGTATACAAAAAGAA 59.630 38.462 5.50 0.00 0.00 2.52
3295 5753 5.870978 GCGAACCACCTAGTATACAAAAAGA 59.129 40.000 5.50 0.00 0.00 2.52
3296 5754 5.220340 CGCGAACCACCTAGTATACAAAAAG 60.220 44.000 0.00 0.00 0.00 2.27
3297 5755 4.626604 CGCGAACCACCTAGTATACAAAAA 59.373 41.667 0.00 0.00 0.00 1.94
3299 5757 3.193267 ACGCGAACCACCTAGTATACAAA 59.807 43.478 15.93 0.00 0.00 2.83
3300 5758 2.754552 ACGCGAACCACCTAGTATACAA 59.245 45.455 15.93 0.00 0.00 2.41
3301 5759 2.097954 CACGCGAACCACCTAGTATACA 59.902 50.000 15.93 0.00 0.00 2.29
3302 5760 2.355756 TCACGCGAACCACCTAGTATAC 59.644 50.000 15.93 0.00 0.00 1.47
3303 5761 2.642427 TCACGCGAACCACCTAGTATA 58.358 47.619 15.93 0.00 0.00 1.47
3304 5762 1.466856 TCACGCGAACCACCTAGTAT 58.533 50.000 15.93 0.00 0.00 2.12
3317 5775 4.745125 AGTAGATTACATCCAAATCACGCG 59.255 41.667 3.53 3.53 36.09 6.01
3319 5777 7.095481 CCATGAGTAGATTACATCCAAATCACG 60.095 40.741 0.00 0.00 36.09 4.35
3357 5815 2.852449 GGATTTTCTCCCCCGATTCTC 58.148 52.381 0.00 0.00 38.19 2.87
3437 5903 9.771534 TTCAGGGTAATTTTGTTTCCAATAAAG 57.228 29.630 0.00 0.00 0.00 1.85
3438 5904 9.771534 CTTCAGGGTAATTTTGTTTCCAATAAA 57.228 29.630 0.00 0.00 0.00 1.40
3440 5906 7.015682 TGCTTCAGGGTAATTTTGTTTCCAATA 59.984 33.333 0.00 0.00 0.00 1.90
3441 5907 6.183361 TGCTTCAGGGTAATTTTGTTTCCAAT 60.183 34.615 0.00 0.00 0.00 3.16
3454 5921 2.489971 CTCGTGTTTGCTTCAGGGTAA 58.510 47.619 0.00 0.00 0.00 2.85
3505 5972 1.069500 GTTACGAACGGCTGCATTGTT 60.069 47.619 0.50 2.74 0.00 2.83
3506 5973 0.515564 GTTACGAACGGCTGCATTGT 59.484 50.000 0.50 0.00 0.00 2.71
3514 5981 2.850647 GTCACATCTAGTTACGAACGGC 59.149 50.000 0.00 0.00 36.23 5.68
3541 6008 6.493802 AGATAACACAAACCTCTACTCTGACA 59.506 38.462 0.00 0.00 0.00 3.58
3569 6037 5.128919 AGATTGATGGTAAGGACTTCATGC 58.871 41.667 0.00 0.00 0.00 4.06
3576 6044 7.158021 CCTCTATCAAGATTGATGGTAAGGAC 58.842 42.308 16.49 0.00 46.68 3.85
3585 6053 6.331042 TGGTGAATCCCTCTATCAAGATTGAT 59.669 38.462 12.40 12.40 42.10 2.57
3630 6098 3.106054 AGAAGTGATGCTCCTCAGTGAT 58.894 45.455 0.00 0.00 0.00 3.06
3645 6113 7.505646 GCTTGAAGCGTATAATGATAGAAGTG 58.494 38.462 0.00 0.00 0.00 3.16
3662 6130 3.939592 AGAAGTAAATACCCGCTTGAAGC 59.060 43.478 7.20 7.20 38.02 3.86
3663 6131 5.642063 TCAAGAAGTAAATACCCGCTTGAAG 59.358 40.000 13.39 0.00 36.30 3.02
3664 6132 5.553123 TCAAGAAGTAAATACCCGCTTGAA 58.447 37.500 13.39 3.81 36.30 2.69
3665 6133 5.155278 TCAAGAAGTAAATACCCGCTTGA 57.845 39.130 12.45 12.45 36.58 3.02
3666 6134 5.354234 ACATCAAGAAGTAAATACCCGCTTG 59.646 40.000 0.00 0.00 33.86 4.01
3667 6135 5.497474 ACATCAAGAAGTAAATACCCGCTT 58.503 37.500 0.00 0.00 0.00 4.68
3668 6136 5.099042 ACATCAAGAAGTAAATACCCGCT 57.901 39.130 0.00 0.00 0.00 5.52
3669 6137 5.813080 AACATCAAGAAGTAAATACCCGC 57.187 39.130 0.00 0.00 0.00 6.13
3670 6138 7.713507 TGGATAACATCAAGAAGTAAATACCCG 59.286 37.037 0.00 0.00 0.00 5.28
3671 6139 8.974060 TGGATAACATCAAGAAGTAAATACCC 57.026 34.615 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.