Multiple sequence alignment - TraesCS3A01G308100

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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 TraesCS3A01G308100 chr3A 100.000 4727 0 0 1 4727 546575365 546570639 0.000000e+00 8730.0
1 TraesCS3A01G308100 chr3B 92.001 4563 221 65 18 4486 142725375 142720863 0.000000e+00 6272.0
2 TraesCS3A01G308100 chr3B 94.242 330 18 1 4361 4690 142721018 142720690 1.960000e-138 503.0
3 TraesCS3A01G308100 chr3B 91.270 126 11 0 4391 4516 142721018 142720893 6.290000e-39 172.0
4 TraesCS3A01G308100 chr3B 98.305 59 1 0 3476 3534 142721804 142721746 2.330000e-18 104.0
5 TraesCS3A01G308100 chr3D 94.661 3933 160 21 578 4486 93479082 93482988 0.000000e+00 6054.0
6 TraesCS3A01G308100 chr3D 92.121 330 21 3 4362 4687 93482834 93483162 1.200000e-125 460.0
7 TraesCS3A01G308100 chr3D 91.860 172 6 4 318 482 93478726 93478896 2.840000e-57 233.0
8 TraesCS3A01G308100 chr3D 92.308 65 4 1 1136 1200 394925911 394925974 1.810000e-14 91.6
9 TraesCS3A01G308100 chr3D 91.045 67 5 1 1134 1200 154053315 154053250 6.520000e-14 89.8
10 TraesCS3A01G308100 chr4A 79.937 633 104 19 2633 3255 115788293 115788912 1.210000e-120 444.0
11 TraesCS3A01G308100 chr4D 76.313 857 170 25 2633 3474 349190346 349189508 1.220000e-115 427.0
12 TraesCS3A01G308100 chr4D 74.276 898 171 42 2620 3472 497666651 497667533 1.640000e-84 324.0
13 TraesCS3A01G308100 chr4B 76.146 851 180 17 2633 3473 431796115 431795278 4.370000e-115 425.0
14 TraesCS3A01G308100 chr4B 77.316 626 113 19 2649 3253 654125471 654126088 4.530000e-90 342.0
15 TraesCS3A01G308100 chr4B 74.738 859 170 31 2649 3473 654130706 654131551 1.630000e-89 340.0
16 TraesCS3A01G308100 chr5A 75.179 838 159 32 2649 3452 691813237 691814059 2.710000e-92 350.0
17 TraesCS3A01G308100 chr5A 90.000 70 7 0 3000 3069 8904690 8904621 1.810000e-14 91.6
18 TraesCS3A01G308100 chr5D 90.000 70 7 0 3000 3069 10775872 10775941 1.810000e-14 91.6
19 TraesCS3A01G308100 chr1A 91.045 67 5 1 1134 1200 314526929 314526994 6.520000e-14 89.8
20 TraesCS3A01G308100 chr5B 89.706 68 7 0 3002 3069 11306453 11306386 2.340000e-13 87.9
21 TraesCS3A01G308100 chr2B 89.552 67 6 1 1134 1200 760106216 760106151 3.030000e-12 84.2


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 TraesCS3A01G308100 chr3A 546570639 546575365 4726 True 8730.0 8730 100.000000 1 4727 1 chr3A.!!$R1 4726
1 TraesCS3A01G308100 chr3B 142720690 142725375 4685 True 3387.5 6272 93.121500 18 4690 2 chr3B.!!$R1 4672
2 TraesCS3A01G308100 chr3D 93478726 93483162 4436 False 2249.0 6054 92.880667 318 4687 3 chr3D.!!$F2 4369
3 TraesCS3A01G308100 chr4A 115788293 115788912 619 False 444.0 444 79.937000 2633 3255 1 chr4A.!!$F1 622
4 TraesCS3A01G308100 chr4D 349189508 349190346 838 True 427.0 427 76.313000 2633 3474 1 chr4D.!!$R1 841
5 TraesCS3A01G308100 chr4D 497666651 497667533 882 False 324.0 324 74.276000 2620 3472 1 chr4D.!!$F1 852
6 TraesCS3A01G308100 chr4B 431795278 431796115 837 True 425.0 425 76.146000 2633 3473 1 chr4B.!!$R1 840
7 TraesCS3A01G308100 chr4B 654125471 654126088 617 False 342.0 342 77.316000 2649 3253 1 chr4B.!!$F1 604
8 TraesCS3A01G308100 chr4B 654130706 654131551 845 False 340.0 340 74.738000 2649 3473 1 chr4B.!!$F2 824
9 TraesCS3A01G308100 chr5A 691813237 691814059 822 False 350.0 350 75.179000 2649 3452 1 chr5A.!!$F1 803

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
286 290 0.249447 GCAGGGCAGAAAAACCACAC 60.249 55.0 0.0 0.0 0.00 3.82 F
556 611 0.316204 GCTTCCAAGTGCAGCAACAT 59.684 50.0 0.0 0.0 33.45 2.71 F
2379 2533 0.391661 TTGCTCTCGCCATTGTCCTC 60.392 55.0 0.0 0.0 34.43 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1287 1441 0.531532 ATGATGAAGGCGCGGAGAAG 60.532 55.0 8.83 0.0 0.0 2.85 R
2390 2544 0.253207 TTCCTCCCCCTCCTTCTTCC 60.253 60.0 0.00 0.0 0.0 3.46 R
4084 4320 0.179029 CTTCCGGTGTTCACCCAGTT 60.179 55.0 15.20 0.0 0.0 3.16 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
37 38 7.119709 TCCCTCTTATTTCAACATGTATCGA 57.880 36.000 0.00 0.00 0.00 3.59
81 82 6.921486 TGTGTACTAGTAAACCCAATCAGA 57.079 37.500 18.67 0.48 0.00 3.27
87 88 9.498176 GTACTAGTAAACCCAATCAGAAAGAAA 57.502 33.333 3.61 0.00 0.00 2.52
103 104 8.632679 TCAGAAAGAAATGCACTCTTATTTGTT 58.367 29.630 12.13 0.00 33.02 2.83
104 105 8.697067 CAGAAAGAAATGCACTCTTATTTGTTG 58.303 33.333 12.13 3.80 32.32 3.33
108 109 8.353423 AGAAATGCACTCTTATTTGTTGGTAT 57.647 30.769 0.00 0.00 0.00 2.73
111 112 8.574251 AATGCACTCTTATTTGTTGGTATACA 57.426 30.769 5.01 0.00 0.00 2.29
112 113 8.752005 ATGCACTCTTATTTGTTGGTATACAT 57.248 30.769 5.01 0.00 0.00 2.29
114 115 9.674068 TGCACTCTTATTTGTTGGTATACATTA 57.326 29.630 5.01 0.00 0.00 1.90
136 137 2.240493 ACTTCACGAGACACTTTGGG 57.760 50.000 0.00 0.00 0.00 4.12
153 154 3.878160 TGGGACAAGGAAAAACACAAC 57.122 42.857 0.00 0.00 31.92 3.32
159 160 5.467063 GGACAAGGAAAAACACAACAAAACA 59.533 36.000 0.00 0.00 0.00 2.83
162 163 8.250538 ACAAGGAAAAACACAACAAAACATAG 57.749 30.769 0.00 0.00 0.00 2.23
163 164 7.875554 ACAAGGAAAAACACAACAAAACATAGT 59.124 29.630 0.00 0.00 0.00 2.12
164 165 9.360093 CAAGGAAAAACACAACAAAACATAGTA 57.640 29.630 0.00 0.00 0.00 1.82
233 237 3.990318 AGCACAAGTCTTAAAGCAACC 57.010 42.857 6.04 0.00 0.00 3.77
234 238 3.287222 AGCACAAGTCTTAAAGCAACCA 58.713 40.909 6.04 0.00 0.00 3.67
242 246 3.689649 GTCTTAAAGCAACCATGGTCGAT 59.310 43.478 20.07 1.35 35.91 3.59
244 248 5.353123 GTCTTAAAGCAACCATGGTCGATAA 59.647 40.000 20.07 12.08 35.91 1.75
273 277 3.566130 AAGATGTCTCTTGCAGGGC 57.434 52.632 0.00 0.00 40.28 5.19
277 281 0.694771 ATGTCTCTTGCAGGGCAGAA 59.305 50.000 0.00 0.00 40.61 3.02
284 288 0.463620 TTGCAGGGCAGAAAAACCAC 59.536 50.000 0.00 0.00 40.61 4.16
285 289 0.685785 TGCAGGGCAGAAAAACCACA 60.686 50.000 0.00 0.00 33.32 4.17
286 290 0.249447 GCAGGGCAGAAAAACCACAC 60.249 55.000 0.00 0.00 0.00 3.82
287 291 1.402787 CAGGGCAGAAAAACCACACT 58.597 50.000 0.00 0.00 0.00 3.55
288 292 1.338020 CAGGGCAGAAAAACCACACTC 59.662 52.381 0.00 0.00 0.00 3.51
289 293 0.673985 GGGCAGAAAAACCACACTCC 59.326 55.000 0.00 0.00 0.00 3.85
290 294 1.692411 GGCAGAAAAACCACACTCCT 58.308 50.000 0.00 0.00 0.00 3.69
291 295 2.488347 GGGCAGAAAAACCACACTCCTA 60.488 50.000 0.00 0.00 0.00 2.94
292 296 2.814336 GGCAGAAAAACCACACTCCTAG 59.186 50.000 0.00 0.00 0.00 3.02
293 297 3.477530 GCAGAAAAACCACACTCCTAGT 58.522 45.455 0.00 0.00 0.00 2.57
294 298 4.504340 GGCAGAAAAACCACACTCCTAGTA 60.504 45.833 0.00 0.00 0.00 1.82
295 299 4.691216 GCAGAAAAACCACACTCCTAGTAG 59.309 45.833 0.00 0.00 0.00 2.57
296 300 4.691216 CAGAAAAACCACACTCCTAGTAGC 59.309 45.833 0.00 0.00 0.00 3.58
297 301 4.347000 AGAAAAACCACACTCCTAGTAGCA 59.653 41.667 0.00 0.00 0.00 3.49
298 302 4.910458 AAAACCACACTCCTAGTAGCAT 57.090 40.909 0.00 0.00 0.00 3.79
299 303 4.910458 AAACCACACTCCTAGTAGCATT 57.090 40.909 0.00 0.00 0.00 3.56
300 304 4.910458 AACCACACTCCTAGTAGCATTT 57.090 40.909 0.00 0.00 0.00 2.32
301 305 4.910458 ACCACACTCCTAGTAGCATTTT 57.090 40.909 0.00 0.00 0.00 1.82
302 306 6.368779 AACCACACTCCTAGTAGCATTTTA 57.631 37.500 0.00 0.00 0.00 1.52
303 307 6.561519 ACCACACTCCTAGTAGCATTTTAT 57.438 37.500 0.00 0.00 0.00 1.40
304 308 6.958767 ACCACACTCCTAGTAGCATTTTATT 58.041 36.000 0.00 0.00 0.00 1.40
305 309 7.402862 ACCACACTCCTAGTAGCATTTTATTT 58.597 34.615 0.00 0.00 0.00 1.40
306 310 7.888546 ACCACACTCCTAGTAGCATTTTATTTT 59.111 33.333 0.00 0.00 0.00 1.82
307 311 8.739972 CCACACTCCTAGTAGCATTTTATTTTT 58.260 33.333 0.00 0.00 0.00 1.94
339 343 4.979197 CACTCCTAGTAGCATTGACGATTC 59.021 45.833 0.00 0.00 0.00 2.52
348 352 8.492673 AGTAGCATTGACGATTCAAAGATAAA 57.507 30.769 0.00 0.00 45.01 1.40
362 378 3.180891 AGATAAAACCAGCCTAGCGAC 57.819 47.619 0.00 0.00 0.00 5.19
368 384 1.739067 ACCAGCCTAGCGACAATTTC 58.261 50.000 0.00 0.00 0.00 2.17
471 488 1.440476 GGAATTCCCAGCATGCAGC 59.560 57.895 21.98 0.00 46.19 5.25
493 537 2.430921 CCTGTCGCCACTGTCGTC 60.431 66.667 0.00 0.00 0.00 4.20
506 550 4.082190 CCACTGTCGTCTTCTTCCTGAATA 60.082 45.833 0.00 0.00 33.71 1.75
555 610 0.752743 AGCTTCCAAGTGCAGCAACA 60.753 50.000 0.00 0.00 35.88 3.33
556 611 0.316204 GCTTCCAAGTGCAGCAACAT 59.684 50.000 0.00 0.00 33.45 2.71
557 612 1.269936 GCTTCCAAGTGCAGCAACATT 60.270 47.619 0.00 0.00 33.45 2.71
558 613 2.669364 CTTCCAAGTGCAGCAACATTC 58.331 47.619 0.00 0.00 0.00 2.67
703 825 2.751913 CCGTCTCTCTGACCGGTCG 61.752 68.421 28.70 22.28 42.49 4.79
722 849 1.674057 CCAGTGACCTCTGTGTCCC 59.326 63.158 0.00 0.00 34.25 4.46
731 858 0.615850 CTCTGTGTCCCCTTCTTCCC 59.384 60.000 0.00 0.00 0.00 3.97
806 947 1.099295 CAGCGCACATCATCCATGGT 61.099 55.000 11.47 0.00 36.72 3.55
861 1002 4.228567 GGAGCCTGGAGGTAGCGC 62.229 72.222 0.00 0.00 37.57 5.92
924 1072 3.587797 TCTGTGGTTCGATGTACTTCC 57.412 47.619 3.35 0.00 0.00 3.46
925 1073 2.094906 TCTGTGGTTCGATGTACTTCCG 60.095 50.000 3.35 0.22 0.00 4.30
926 1074 1.067425 TGTGGTTCGATGTACTTCCGG 60.067 52.381 0.00 0.00 0.00 5.14
938 1086 0.953960 ACTTCCGGCGGACATGTTTC 60.954 55.000 31.23 0.00 0.00 2.78
948 1096 2.783135 GGACATGTTTCCTTCTCTGCA 58.217 47.619 0.00 0.00 32.24 4.41
984 1132 3.659786 TCTTTTGATCGTGTGTAGGTGG 58.340 45.455 0.00 0.00 0.00 4.61
1287 1441 1.079336 GTACCAGAACGCCAGGGTC 60.079 63.158 0.00 0.00 34.88 4.46
1302 1456 2.261671 GTCTTCTCCGCGCCTTCA 59.738 61.111 0.00 0.00 0.00 3.02
1305 1459 1.153568 CTTCTCCGCGCCTTCATCA 60.154 57.895 0.00 0.00 0.00 3.07
1311 1465 1.278172 CCGCGCCTTCATCATACTCG 61.278 60.000 0.00 0.00 0.00 4.18
1597 1751 3.884581 TTCGTCAACGCCGTCGAGG 62.885 63.158 0.00 0.00 44.97 4.63
1607 1761 4.517703 CGTCGAGGTCGTCTCCGC 62.518 72.222 0.00 0.00 39.30 5.54
1785 1939 0.469917 TGCGATTCCTCTCCCATTCC 59.530 55.000 0.00 0.00 0.00 3.01
1909 2063 0.532573 GAGGGAGCTCGTGATCAACA 59.467 55.000 7.83 0.00 0.00 3.33
2211 2365 0.681733 ATAAGATCGTGATGCCCGCT 59.318 50.000 0.00 0.00 0.00 5.52
2331 2485 2.328099 CCTTCTTGGCTCCGTGTGC 61.328 63.158 0.00 0.00 0.00 4.57
2379 2533 0.391661 TTGCTCTCGCCATTGTCCTC 60.392 55.000 0.00 0.00 34.43 3.71
2390 2544 3.871485 CCATTGTCCTCAGGAAGAAGAG 58.129 50.000 0.00 0.00 31.38 2.85
2401 2555 3.197549 CAGGAAGAAGAGGAAGAAGGAGG 59.802 52.174 0.00 0.00 0.00 4.30
2402 2556 2.503765 GGAAGAAGAGGAAGAAGGAGGG 59.496 54.545 0.00 0.00 0.00 4.30
2408 2562 1.162951 AGGAAGAAGGAGGGGGAGGA 61.163 60.000 0.00 0.00 0.00 3.71
2409 2563 0.253207 GGAAGAAGGAGGGGGAGGAA 60.253 60.000 0.00 0.00 0.00 3.36
2410 2564 1.208706 GAAGAAGGAGGGGGAGGAAG 58.791 60.000 0.00 0.00 0.00 3.46
2411 2565 0.800239 AAGAAGGAGGGGGAGGAAGA 59.200 55.000 0.00 0.00 0.00 2.87
2418 2572 1.162951 AGGGGGAGGAAGAGGAGGAA 61.163 60.000 0.00 0.00 0.00 3.36
2419 2573 0.253207 GGGGGAGGAAGAGGAGGAAA 60.253 60.000 0.00 0.00 0.00 3.13
2423 2577 2.541466 GGAGGAAGAGGAGGAAAGTGA 58.459 52.381 0.00 0.00 0.00 3.41
2428 2582 5.594777 AGGAAGAGGAGGAAAGTGATAAGA 58.405 41.667 0.00 0.00 0.00 2.10
3327 3539 1.686052 GAGCTGGAGAAGATCGTGGAT 59.314 52.381 0.00 0.00 30.22 3.41
3532 3744 4.724602 TGACAGAGCTCACGCCGC 62.725 66.667 17.77 0.00 36.60 6.53
3562 3774 2.732282 CGTCAGAGAAGCGCAGTTGATA 60.732 50.000 11.47 0.00 0.00 2.15
3575 3787 3.733344 TTGATAGCGACGGCCTGGC 62.733 63.158 11.05 11.05 41.24 4.85
3672 3887 0.179156 TAGCCGACGACGATTTCACC 60.179 55.000 9.28 0.00 42.66 4.02
3675 3890 0.524816 CCGACGACGATTTCACCGAT 60.525 55.000 9.28 0.00 42.66 4.18
3822 4038 7.010160 AGATTGTTTCCCCTACATCTTTCAAA 58.990 34.615 0.00 0.00 0.00 2.69
3837 4053 8.784043 ACATCTTTCAAAGGACAAATACTACAC 58.216 33.333 0.00 0.00 0.00 2.90
3978 4210 9.128404 AGTATCAATACCGAAATAGAGTACACA 57.872 33.333 0.00 0.00 33.79 3.72
4022 4255 6.039616 GGCAAGTCTTTGTTCAACATGTTTA 58.960 36.000 8.77 0.00 36.65 2.01
4032 4265 6.943981 TGTTCAACATGTTTAGAGAGTTTCG 58.056 36.000 8.77 0.00 0.00 3.46
4035 4268 7.869016 TCAACATGTTTAGAGAGTTTCGTAG 57.131 36.000 8.77 0.00 0.00 3.51
4037 4270 5.779922 ACATGTTTAGAGAGTTTCGTAGCA 58.220 37.500 0.00 0.00 0.00 3.49
4079 4312 1.152419 TCGACCCTCACCAGGTGAA 60.152 57.895 23.11 4.46 42.26 3.18
4084 4320 0.764890 CCCTCACCAGGTGAACTTCA 59.235 55.000 23.11 0.00 42.26 3.02
4400 4636 1.447643 CCACGGGGGCTCTTCATAG 59.552 63.158 0.00 0.00 0.00 2.23
4401 4637 1.447643 CACGGGGGCTCTTCATAGG 59.552 63.158 0.00 0.00 0.00 2.57
4402 4638 1.766461 ACGGGGGCTCTTCATAGGG 60.766 63.158 0.00 0.00 0.00 3.53
4407 4643 4.040068 GCTCTTCATAGGGCTGCG 57.960 61.111 0.00 0.00 44.90 5.18
4408 4644 1.443407 GCTCTTCATAGGGCTGCGA 59.557 57.895 0.00 0.00 44.90 5.10
4409 4645 0.878086 GCTCTTCATAGGGCTGCGAC 60.878 60.000 0.00 0.00 44.90 5.19
4410 4646 0.749649 CTCTTCATAGGGCTGCGACT 59.250 55.000 0.00 0.00 0.00 4.18
4411 4647 0.461548 TCTTCATAGGGCTGCGACTG 59.538 55.000 5.84 0.00 0.00 3.51
4412 4648 0.176680 CTTCATAGGGCTGCGACTGT 59.823 55.000 5.84 0.00 0.00 3.55
4413 4649 0.175760 TTCATAGGGCTGCGACTGTC 59.824 55.000 0.00 0.00 0.00 3.51
4414 4650 1.589993 CATAGGGCTGCGACTGTCG 60.590 63.158 24.78 24.78 43.89 4.35
4444 4680 4.007644 CTGGGGCTGCGACTGTCA 62.008 66.667 8.73 0.00 0.00 3.58
4693 4932 7.817418 TTTTTACATTGGCATATACTCCCTC 57.183 36.000 0.00 0.00 0.00 4.30
4694 4933 5.499004 TTACATTGGCATATACTCCCTCC 57.501 43.478 0.00 0.00 0.00 4.30
4695 4934 2.303022 ACATTGGCATATACTCCCTCCG 59.697 50.000 0.00 0.00 0.00 4.63
4696 4935 0.685097 TTGGCATATACTCCCTCCGC 59.315 55.000 0.00 0.00 0.00 5.54
4697 4936 1.192146 TGGCATATACTCCCTCCGCC 61.192 60.000 0.00 0.00 38.56 6.13
4698 4937 1.597461 GCATATACTCCCTCCGCCC 59.403 63.158 0.00 0.00 0.00 6.13
4699 4938 1.900545 GCATATACTCCCTCCGCCCC 61.901 65.000 0.00 0.00 0.00 5.80
4700 4939 1.305046 ATATACTCCCTCCGCCCCG 60.305 63.158 0.00 0.00 0.00 5.73
4701 4940 1.797018 ATATACTCCCTCCGCCCCGA 61.797 60.000 0.00 0.00 0.00 5.14
4702 4941 2.010412 TATACTCCCTCCGCCCCGAA 62.010 60.000 0.00 0.00 0.00 4.30
4703 4942 2.884179 ATACTCCCTCCGCCCCGAAA 62.884 60.000 0.00 0.00 0.00 3.46
4704 4943 4.468689 CTCCCTCCGCCCCGAAAC 62.469 72.222 0.00 0.00 0.00 2.78
4706 4945 4.338710 CCCTCCGCCCCGAAACAA 62.339 66.667 0.00 0.00 0.00 2.83
4707 4946 2.746277 CCTCCGCCCCGAAACAAG 60.746 66.667 0.00 0.00 0.00 3.16
4708 4947 2.032071 CTCCGCCCCGAAACAAGT 59.968 61.111 0.00 0.00 0.00 3.16
4709 4948 2.281208 TCCGCCCCGAAACAAGTG 60.281 61.111 0.00 0.00 0.00 3.16
4710 4949 2.593436 CCGCCCCGAAACAAGTGT 60.593 61.111 0.00 0.00 0.00 3.55
4711 4950 2.613506 CCGCCCCGAAACAAGTGTC 61.614 63.158 0.00 0.00 0.00 3.67
4712 4951 1.597027 CGCCCCGAAACAAGTGTCT 60.597 57.895 0.00 0.00 0.00 3.41
4713 4952 1.566018 CGCCCCGAAACAAGTGTCTC 61.566 60.000 0.00 0.00 0.00 3.36
4714 4953 0.534203 GCCCCGAAACAAGTGTCTCA 60.534 55.000 0.00 0.00 0.00 3.27
4715 4954 1.961793 CCCCGAAACAAGTGTCTCAA 58.038 50.000 0.00 0.00 0.00 3.02
4716 4955 1.602377 CCCCGAAACAAGTGTCTCAAC 59.398 52.381 0.00 0.00 0.00 3.18
4717 4956 2.561569 CCCGAAACAAGTGTCTCAACT 58.438 47.619 0.00 0.00 0.00 3.16
4718 4957 2.943033 CCCGAAACAAGTGTCTCAACTT 59.057 45.455 0.00 0.00 41.08 2.66
4719 4958 3.377172 CCCGAAACAAGTGTCTCAACTTT 59.623 43.478 0.00 0.00 38.34 2.66
4720 4959 4.342772 CCGAAACAAGTGTCTCAACTTTG 58.657 43.478 0.00 0.00 38.34 2.77
4721 4960 4.142687 CCGAAACAAGTGTCTCAACTTTGT 60.143 41.667 0.00 0.00 38.34 2.83
4722 4961 5.064198 CCGAAACAAGTGTCTCAACTTTGTA 59.936 40.000 0.00 0.00 38.34 2.41
4723 4962 5.957796 CGAAACAAGTGTCTCAACTTTGTAC 59.042 40.000 0.00 0.00 38.34 2.90
4724 4963 6.183360 CGAAACAAGTGTCTCAACTTTGTACT 60.183 38.462 0.00 0.00 38.34 2.73
4725 4964 7.009815 CGAAACAAGTGTCTCAACTTTGTACTA 59.990 37.037 0.00 0.00 38.34 1.82
4726 4965 8.556213 AAACAAGTGTCTCAACTTTGTACTAA 57.444 30.769 0.00 0.00 38.34 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 8.673711 CGATACATGTTGAAATAAGAGGGAAAA 58.326 33.333 2.30 0.00 0.00 2.29
11 12 8.044309 TCGATACATGTTGAAATAAGAGGGAAA 58.956 33.333 2.30 0.00 0.00 3.13
12 13 7.561251 TCGATACATGTTGAAATAAGAGGGAA 58.439 34.615 2.30 0.00 0.00 3.97
13 14 7.119709 TCGATACATGTTGAAATAAGAGGGA 57.880 36.000 2.30 0.00 0.00 4.20
14 15 7.786178 TTCGATACATGTTGAAATAAGAGGG 57.214 36.000 2.30 0.00 0.00 4.30
15 16 9.655769 CATTTCGATACATGTTGAAATAAGAGG 57.344 33.333 22.33 12.66 39.20 3.69
21 22 9.859427 ATGAAACATTTCGATACATGTTGAAAT 57.141 25.926 19.44 19.44 41.74 2.17
34 35 7.918033 ACAACAATACACAATGAAACATTTCGA 59.082 29.630 0.18 0.00 40.01 3.71
37 38 8.715191 ACACAACAATACACAATGAAACATTT 57.285 26.923 0.00 0.00 0.00 2.32
55 56 6.828788 TGATTGGGTTTACTAGTACACAACA 58.171 36.000 14.27 11.99 40.19 3.33
72 73 4.461781 AGAGTGCATTTCTTTCTGATTGGG 59.538 41.667 0.00 0.00 0.00 4.12
81 82 7.500141 ACCAACAAATAAGAGTGCATTTCTTT 58.500 30.769 17.99 4.59 36.38 2.52
87 88 8.752005 ATGTATACCAACAAATAAGAGTGCAT 57.248 30.769 0.00 0.00 32.02 3.96
103 104 8.089597 TGTCTCGTGAAGTTTTAATGTATACCA 58.910 33.333 0.00 0.00 0.00 3.25
104 105 8.378421 GTGTCTCGTGAAGTTTTAATGTATACC 58.622 37.037 0.00 0.00 0.00 2.73
108 109 8.332464 CAAAGTGTCTCGTGAAGTTTTAATGTA 58.668 33.333 0.00 0.00 0.00 2.29
111 112 6.238648 CCCAAAGTGTCTCGTGAAGTTTTAAT 60.239 38.462 0.00 0.00 0.00 1.40
112 113 5.065474 CCCAAAGTGTCTCGTGAAGTTTTAA 59.935 40.000 0.00 0.00 0.00 1.52
114 115 3.377172 CCCAAAGTGTCTCGTGAAGTTTT 59.623 43.478 0.00 0.00 0.00 2.43
121 122 1.867233 CTTGTCCCAAAGTGTCTCGTG 59.133 52.381 0.00 0.00 0.00 4.35
136 137 6.532365 TGTTTTGTTGTGTTTTTCCTTGTC 57.468 33.333 0.00 0.00 0.00 3.18
200 204 9.555727 TTAAGACTTGTGCTACATTTCTTACTT 57.444 29.630 0.00 0.00 34.36 2.24
210 214 4.274950 GGTTGCTTTAAGACTTGTGCTACA 59.725 41.667 17.35 0.00 0.00 2.74
233 237 2.800544 GACCGTGGATTTATCGACCATG 59.199 50.000 4.60 4.60 39.54 3.66
234 238 2.432874 TGACCGTGGATTTATCGACCAT 59.567 45.455 0.00 0.00 36.09 3.55
242 246 4.466370 AGAGACATCTTGACCGTGGATTTA 59.534 41.667 0.00 0.00 28.57 1.40
244 248 2.834549 AGAGACATCTTGACCGTGGATT 59.165 45.455 0.00 0.00 28.57 3.01
273 277 4.691216 GCTACTAGGAGTGTGGTTTTTCTG 59.309 45.833 3.31 0.00 0.00 3.02
277 281 4.910458 ATGCTACTAGGAGTGTGGTTTT 57.090 40.909 3.31 0.00 0.00 2.43
305 309 7.004555 TGCTACTAGGAGTGATTCTCAAAAA 57.995 36.000 3.31 0.00 44.40 1.94
306 310 6.605471 TGCTACTAGGAGTGATTCTCAAAA 57.395 37.500 3.31 0.00 44.40 2.44
307 311 6.798427 ATGCTACTAGGAGTGATTCTCAAA 57.202 37.500 3.31 0.00 44.40 2.69
308 312 6.381133 TCAATGCTACTAGGAGTGATTCTCAA 59.619 38.462 3.31 0.00 44.40 3.02
309 313 5.893824 TCAATGCTACTAGGAGTGATTCTCA 59.106 40.000 3.31 0.00 44.40 3.27
310 314 6.212955 GTCAATGCTACTAGGAGTGATTCTC 58.787 44.000 10.42 0.00 42.21 2.87
311 315 5.221145 CGTCAATGCTACTAGGAGTGATTCT 60.221 44.000 10.42 0.00 42.21 2.40
312 316 4.979197 CGTCAATGCTACTAGGAGTGATTC 59.021 45.833 10.42 0.00 42.21 2.52
313 317 4.645136 TCGTCAATGCTACTAGGAGTGATT 59.355 41.667 10.42 0.00 42.21 2.57
314 318 4.207955 TCGTCAATGCTACTAGGAGTGAT 58.792 43.478 10.42 0.00 42.21 3.06
315 319 3.617284 TCGTCAATGCTACTAGGAGTGA 58.383 45.455 3.31 3.83 38.28 3.41
339 343 3.938963 TCGCTAGGCTGGTTTTATCTTTG 59.061 43.478 0.00 0.00 0.00 2.77
348 352 2.084546 GAAATTGTCGCTAGGCTGGTT 58.915 47.619 0.00 0.00 0.00 3.67
362 378 1.333177 TGTTTGGTCCCGGGAAATTG 58.667 50.000 28.84 0.00 0.00 2.32
368 384 1.302993 ACGATTGTTTGGTCCCGGG 60.303 57.895 16.85 16.85 0.00 5.73
478 495 1.007734 GAAGACGACAGTGGCGACA 60.008 57.895 28.44 0.00 38.70 4.35
479 496 0.318784 AAGAAGACGACAGTGGCGAC 60.319 55.000 28.44 20.46 0.00 5.19
487 531 6.280855 TGAATATTCAGGAAGAAGACGACA 57.719 37.500 14.23 0.00 40.15 4.35
506 550 4.347607 ACGTACTAACCCTACCACTGAAT 58.652 43.478 0.00 0.00 0.00 2.57
515 559 3.848272 CGTTGGAACGTACTAACCCTA 57.152 47.619 3.72 0.00 46.63 3.53
555 610 1.280457 GGACTGGACTGGACTGGAAT 58.720 55.000 0.00 0.00 0.00 3.01
556 611 0.836400 GGGACTGGACTGGACTGGAA 60.836 60.000 0.00 0.00 0.00 3.53
557 612 1.229209 GGGACTGGACTGGACTGGA 60.229 63.158 0.00 0.00 0.00 3.86
558 613 2.294078 GGGGACTGGACTGGACTGG 61.294 68.421 0.00 0.00 0.00 4.00
703 825 1.004440 GGACACAGAGGTCACTGGC 60.004 63.158 0.00 0.00 41.59 4.85
722 849 0.749454 CAGGGATTGCGGGAAGAAGG 60.749 60.000 0.00 0.00 0.00 3.46
806 947 2.601666 AGCAGCAGTCGAGGTCCA 60.602 61.111 0.00 0.00 0.00 4.02
810 951 0.108472 TGATTCAGCAGCAGTCGAGG 60.108 55.000 0.00 0.00 0.00 4.63
861 1002 4.430765 CGACAGGGGGACGAACGG 62.431 72.222 0.00 0.00 0.00 4.44
872 1013 0.321122 AGCCAAAGAAGAGCGACAGG 60.321 55.000 0.00 0.00 0.00 4.00
924 1072 0.673644 AGAAGGAAACATGTCCGCCG 60.674 55.000 0.00 0.00 43.03 6.46
925 1073 1.087501 GAGAAGGAAACATGTCCGCC 58.912 55.000 0.00 0.72 43.03 6.13
926 1074 1.734465 CAGAGAAGGAAACATGTCCGC 59.266 52.381 0.00 0.00 43.03 5.54
948 1096 3.441222 TCAAAAGATCATGCGCAGAACAT 59.559 39.130 18.32 4.41 0.00 2.71
961 1109 4.330074 CCACCTACACACGATCAAAAGATC 59.670 45.833 0.00 0.00 0.00 2.75
984 1132 1.026718 CCATGGCAAACTCCGAGGAC 61.027 60.000 0.00 0.00 0.00 3.85
1287 1441 0.531532 ATGATGAAGGCGCGGAGAAG 60.532 55.000 8.83 0.00 0.00 2.85
1299 1453 2.951457 TGGCGAACGAGTATGATGAA 57.049 45.000 0.00 0.00 0.00 2.57
1302 1456 2.288457 CCTGATGGCGAACGAGTATGAT 60.288 50.000 0.00 0.00 0.00 2.45
1305 1459 3.967886 CCTGATGGCGAACGAGTAT 57.032 52.632 0.00 0.00 0.00 2.12
1909 2063 2.185350 CCCGTCGAATGAGCTGCT 59.815 61.111 0.00 0.00 0.00 4.24
2314 2468 2.671177 CGCACACGGAGCCAAGAAG 61.671 63.158 0.00 0.00 34.97 2.85
2335 2489 3.479269 GGACACGAAAGCGAGCGG 61.479 66.667 0.00 0.00 41.64 5.52
2379 2533 3.197549 CCTCCTTCTTCCTCTTCTTCCTG 59.802 52.174 0.00 0.00 0.00 3.86
2390 2544 0.253207 TTCCTCCCCCTCCTTCTTCC 60.253 60.000 0.00 0.00 0.00 3.46
2392 2546 0.800239 TCTTCCTCCCCCTCCTTCTT 59.200 55.000 0.00 0.00 0.00 2.52
2401 2555 1.208706 CTTTCCTCCTCTTCCTCCCC 58.791 60.000 0.00 0.00 0.00 4.81
2402 2556 1.557371 CACTTTCCTCCTCTTCCTCCC 59.443 57.143 0.00 0.00 0.00 4.30
2408 2562 5.249393 TGCTTCTTATCACTTTCCTCCTCTT 59.751 40.000 0.00 0.00 0.00 2.85
2409 2563 4.780021 TGCTTCTTATCACTTTCCTCCTCT 59.220 41.667 0.00 0.00 0.00 3.69
2410 2564 5.091261 TGCTTCTTATCACTTTCCTCCTC 57.909 43.478 0.00 0.00 0.00 3.71
2411 2565 4.625083 GCTGCTTCTTATCACTTTCCTCCT 60.625 45.833 0.00 0.00 0.00 3.69
2418 2572 2.622436 GTCGGCTGCTTCTTATCACTT 58.378 47.619 0.00 0.00 0.00 3.16
2419 2573 1.469940 CGTCGGCTGCTTCTTATCACT 60.470 52.381 0.00 0.00 0.00 3.41
2423 2577 1.521681 GGCGTCGGCTGCTTCTTAT 60.522 57.895 12.17 0.00 39.81 1.73
2517 2671 1.721926 GCAGTAGTGAAGCTTGACGAC 59.278 52.381 18.84 18.84 0.00 4.34
2608 2774 2.128128 CGTCGCGTCTTGCAACAC 60.128 61.111 5.77 0.00 46.97 3.32
2802 2968 3.051479 TAGCCGACGAGCGACACA 61.051 61.111 0.00 0.00 44.57 3.72
2967 3139 3.931247 ACGGCCGTGTGCAGGTAA 61.931 61.111 33.75 0.00 43.89 2.85
3474 3686 2.283529 GGAGAAGTCCAGGCCGTCA 61.284 63.158 0.00 0.00 43.31 4.35
3532 3744 2.549611 CTTCTCTGACGGCGAGGTGG 62.550 65.000 16.62 0.30 0.00 4.61
3533 3745 1.153939 CTTCTCTGACGGCGAGGTG 60.154 63.158 16.62 4.14 0.00 4.00
3534 3746 2.995872 GCTTCTCTGACGGCGAGGT 61.996 63.158 16.62 0.00 0.00 3.85
3555 3767 1.141881 CAGGCCGTCGCTATCAACT 59.858 57.895 0.00 0.00 34.44 3.16
3575 3787 1.440893 CTGCTCACATCGGAGAGGG 59.559 63.158 0.00 0.00 45.68 4.30
3577 3789 1.227205 GGCTGCTCACATCGGAGAG 60.227 63.158 0.00 0.00 43.63 3.20
3585 3797 0.607217 CCATGTTGAGGCTGCTCACA 60.607 55.000 0.00 0.00 32.47 3.58
3624 3836 4.555709 TCCACGCTGCCGGTTTGT 62.556 61.111 1.90 0.00 39.22 2.83
3672 3887 0.683412 TCCCTCTCATGGATGCATCG 59.317 55.000 20.15 7.15 0.00 3.84
3675 3890 0.326904 AGGTCCCTCTCATGGATGCA 60.327 55.000 0.00 0.00 33.65 3.96
3811 4026 8.784043 GTGTAGTATTTGTCCTTTGAAAGATGT 58.216 33.333 6.49 0.00 0.00 3.06
3822 4038 5.163893 CGAAAATGCGTGTAGTATTTGTCCT 60.164 40.000 0.00 0.00 42.90 3.85
3837 4053 1.396648 TGCTACATGGTCGAAAATGCG 59.603 47.619 8.18 2.57 0.00 4.73
3978 4210 6.811253 TGCCTGTACGAGTTTGATTTTATT 57.189 33.333 0.00 0.00 0.00 1.40
4022 4255 3.952931 TCCTACTGCTACGAAACTCTCT 58.047 45.455 0.00 0.00 0.00 3.10
4032 4265 6.349300 TGGATCAAATTCTTCCTACTGCTAC 58.651 40.000 0.00 0.00 0.00 3.58
4035 4268 6.060788 AGATGGATCAAATTCTTCCTACTGC 58.939 40.000 0.00 0.00 0.00 4.40
4037 4270 7.471260 CGAGAGATGGATCAAATTCTTCCTACT 60.471 40.741 0.00 0.00 0.00 2.57
4079 4312 1.745827 CGGTGTTCACCCAGTTGAAGT 60.746 52.381 15.20 0.00 36.15 3.01
4084 4320 0.179029 CTTCCGGTGTTCACCCAGTT 60.179 55.000 15.20 0.00 0.00 3.16
4424 4660 4.463879 CAGTCGCAGCCCCAGGAG 62.464 72.222 0.00 0.00 0.00 3.69
4426 4662 4.767255 GACAGTCGCAGCCCCAGG 62.767 72.222 0.00 0.00 0.00 4.45
4427 4663 4.007644 TGACAGTCGCAGCCCCAG 62.008 66.667 0.00 0.00 0.00 4.45
4428 4664 4.314440 GTGACAGTCGCAGCCCCA 62.314 66.667 9.36 0.00 0.00 4.96
4614 4850 6.426937 ACATACTCGTGTTGTGCTTTAATTCT 59.573 34.615 0.00 0.00 0.00 2.40
4620 4856 4.893424 AAACATACTCGTGTTGTGCTTT 57.107 36.364 0.00 0.00 41.22 3.51
4623 4859 5.115021 GCTTTTAAACATACTCGTGTTGTGC 59.885 40.000 0.00 0.00 41.22 4.57
4677 4916 0.685097 GCGGAGGGAGTATATGCCAA 59.315 55.000 0.00 0.00 43.31 4.52
4687 4926 4.468689 GTTTCGGGGCGGAGGGAG 62.469 72.222 0.00 0.00 0.00 4.30
4690 4929 2.746277 CTTGTTTCGGGGCGGAGG 60.746 66.667 0.00 0.00 0.00 4.30
4691 4930 2.032071 ACTTGTTTCGGGGCGGAG 59.968 61.111 0.00 0.00 0.00 4.63
4692 4931 2.281208 CACTTGTTTCGGGGCGGA 60.281 61.111 0.00 0.00 0.00 5.54
4693 4932 2.593436 ACACTTGTTTCGGGGCGG 60.593 61.111 0.00 0.00 0.00 6.13
4694 4933 1.566018 GAGACACTTGTTTCGGGGCG 61.566 60.000 0.00 0.00 0.00 6.13
4695 4934 0.534203 TGAGACACTTGTTTCGGGGC 60.534 55.000 0.00 0.00 32.42 5.80
4696 4935 1.602377 GTTGAGACACTTGTTTCGGGG 59.398 52.381 0.00 0.00 32.42 5.73
4697 4936 2.561569 AGTTGAGACACTTGTTTCGGG 58.438 47.619 0.00 0.00 32.42 5.14
4698 4937 4.142687 ACAAAGTTGAGACACTTGTTTCGG 60.143 41.667 0.00 0.00 37.07 4.30
4699 4938 4.969816 ACAAAGTTGAGACACTTGTTTCG 58.030 39.130 0.00 0.00 37.07 3.46
4700 4939 7.073342 AGTACAAAGTTGAGACACTTGTTTC 57.927 36.000 0.00 0.00 37.07 2.78
4701 4940 8.556213 TTAGTACAAAGTTGAGACACTTGTTT 57.444 30.769 0.00 0.00 37.07 2.83


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

AutoCloner maintained by Alex Coulton.