Multiple sequence alignment - TraesCS3A01G021500

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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 TraesCS3A01G021500 chr3A 100.000 6210 0 0 1 6210 12318164 12324373 0.000000e+00 11468.0
1 TraesCS3A01G021500 chr3A 86.667 615 47 17 5220 5816 12340203 12340800 0.000000e+00 649.0
2 TraesCS3A01G021500 chr3A 92.308 65 4 1 5141 5204 12339370 12339434 2.380000e-14 91.6
3 TraesCS3A01G021500 chr3A 100.000 40 0 0 5839 5878 12323964 12324003 2.400000e-09 75.0
4 TraesCS3A01G021500 chr3A 100.000 40 0 0 5801 5840 12324002 12324041 2.400000e-09 75.0
5 TraesCS3A01G021500 chr3D 93.616 5028 204 46 870 5818 8701689 8696700 0.000000e+00 7398.0
6 TraesCS3A01G021500 chr3D 87.518 697 52 21 5135 5818 8553893 8553219 0.000000e+00 773.0
7 TraesCS3A01G021500 chr3D 83.616 708 42 31 215 880 8702399 8701724 1.150000e-166 597.0
8 TraesCS3A01G021500 chr3D 79.937 638 73 28 4833 5459 8692169 8691576 9.630000e-113 418.0
9 TraesCS3A01G021500 chr3D 88.506 174 4 11 1 168 8702843 8702680 4.910000e-46 196.0
10 TraesCS3A01G021500 chr3B 92.946 4182 170 62 1730 5818 10630928 10626779 0.000000e+00 5973.0
11 TraesCS3A01G021500 chr3B 93.214 840 43 5 900 1731 10631865 10631032 0.000000e+00 1223.0
12 TraesCS3A01G021500 chr3B 84.896 576 62 13 869 1440 34652333 34651779 5.440000e-155 558.0
13 TraesCS3A01G021500 chr3B 82.553 619 58 22 240 822 10632499 10631895 3.340000e-137 499.0
14 TraesCS3A01G021500 chr3B 80.848 637 68 27 4826 5451 10623187 10622594 9.490000e-123 451.0
15 TraesCS3A01G021500 chr2D 91.959 485 32 5 870 1352 265706329 265706808 0.000000e+00 673.0
16 TraesCS3A01G021500 chr2D 91.111 360 32 0 5851 6210 553583971 553583612 7.240000e-134 488.0
17 TraesCS3A01G021500 chr6A 87.308 520 42 11 1442 1944 62948047 62948559 1.940000e-159 573.0
18 TraesCS3A01G021500 chr6A 93.296 358 24 0 5853 6210 578848753 578849110 4.260000e-146 529.0
19 TraesCS3A01G021500 chr6A 86.384 448 43 10 1002 1447 435954788 435954357 2.030000e-129 473.0
20 TraesCS3A01G021500 chr6A 93.213 221 15 0 5853 6073 601262314 601262534 6.000000e-85 326.0
21 TraesCS3A01G021500 chr6A 94.286 140 8 0 6071 6210 601262817 601262956 1.360000e-51 215.0
22 TraesCS3A01G021500 chr7A 94.413 358 20 0 5853 6210 502415904 502415547 9.100000e-153 551.0
23 TraesCS3A01G021500 chr4A 86.180 521 45 13 1442 1944 698545117 698545628 7.080000e-149 538.0
24 TraesCS3A01G021500 chr5A 92.201 359 27 1 5853 6210 471468866 471469224 2.000000e-139 507.0
25 TraesCS3A01G021500 chr5A 83.900 441 46 15 869 1306 13489814 13489396 1.250000e-106 398.0
26 TraesCS3A01G021500 chr5A 85.942 377 29 12 1523 1882 13449491 13449122 1.260000e-101 381.0
27 TraesCS3A01G021500 chr7B 85.095 369 45 2 5852 6210 114396581 114396213 9.830000e-98 368.0
28 TraesCS3A01G021500 chr5B 88.328 317 21 6 1644 1944 561017251 561017567 3.540000e-97 366.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G021500 chr3A 12318164 12324373 6209 False 3872.666667 11468 100.000000 1 6210 3 chr3A.!!$F1 6209
1 TraesCS3A01G021500 chr3A 12339370 12340800 1430 False 370.300000 649 89.487500 5141 5816 2 chr3A.!!$F2 675
2 TraesCS3A01G021500 chr3D 8696700 8702843 6143 True 2730.333333 7398 88.579333 1 5818 3 chr3D.!!$R3 5817
3 TraesCS3A01G021500 chr3D 8553219 8553893 674 True 773.000000 773 87.518000 5135 5818 1 chr3D.!!$R1 683
4 TraesCS3A01G021500 chr3D 8691576 8692169 593 True 418.000000 418 79.937000 4833 5459 1 chr3D.!!$R2 626
5 TraesCS3A01G021500 chr3B 10622594 10632499 9905 True 2036.500000 5973 87.390250 240 5818 4 chr3B.!!$R2 5578
6 TraesCS3A01G021500 chr3B 34651779 34652333 554 True 558.000000 558 84.896000 869 1440 1 chr3B.!!$R1 571
7 TraesCS3A01G021500 chr6A 62948047 62948559 512 False 573.000000 573 87.308000 1442 1944 1 chr6A.!!$F1 502
8 TraesCS3A01G021500 chr6A 601262314 601262956 642 False 270.500000 326 93.749500 5853 6210 2 chr6A.!!$F3 357
9 TraesCS3A01G021500 chr4A 698545117 698545628 511 False 538.000000 538 86.180000 1442 1944 1 chr4A.!!$F1 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
543 791 0.317103 CGAATCGTAGAGGCAGGTCG 60.317 60.0 0.00 0.0 43.63 4.79 F
616 867 1.797025 CGTCCCTCTCAAGTTCCAAC 58.203 55.0 0.00 0.0 0.00 3.77 F
1634 1980 1.909700 TTCATCTTGTCAACAGGGGC 58.090 50.0 0.00 0.0 0.00 5.80 F
1794 2246 2.437281 CACTGCTATGGATCAGAAGGGT 59.563 50.0 0.00 0.0 34.57 4.34 F
2846 3316 0.250727 AGTTTAGCGGCAGAGGCAAA 60.251 50.0 1.45 0.0 43.71 3.68 F
3632 4102 0.749649 TCGGCAGGCATGTTTTGTTT 59.250 45.0 0.00 0.0 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1617 1963 0.606401 ACGCCCCTGTTGACAAGATG 60.606 55.000 0.00 0.00 0.00 2.90 R
2327 2796 0.958822 AGCAATGTCACCGGGTTTTC 59.041 50.000 6.32 0.00 0.00 2.29 R
2518 2987 4.219115 TGGGGAGTTTTCTGTTGCATAAA 58.781 39.130 0.00 0.00 0.00 1.40 R
3192 3662 4.900684 AGCATCTCCAAGATCATGATCAG 58.099 43.478 31.99 23.97 40.22 2.90 R
4064 4534 2.266554 CGAGATGGAACTCTTGCACTC 58.733 52.381 0.00 0.00 32.41 3.51 R
5521 6839 0.607620 TGCCGACATCATGAGACACA 59.392 50.000 0.09 0.00 0.00 3.72 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.745492 GTCGTCTCGTCCGTCCCT 60.745 66.667 0.00 0.00 0.00 4.20
33 34 0.392706 CCCTGGGTCCAAAACAAAGC 59.607 55.000 3.97 0.00 0.00 3.51
38 39 1.760029 GGGTCCAAAACAAAGCCAGAA 59.240 47.619 0.00 0.00 0.00 3.02
73 80 0.453793 AGCATCTCCAGTCGTCGAAG 59.546 55.000 0.00 0.00 0.00 3.79
100 107 3.223589 GCCGCTCTCCTCTCCTCC 61.224 72.222 0.00 0.00 0.00 4.30
101 108 2.520741 CCGCTCTCCTCTCCTCCC 60.521 72.222 0.00 0.00 0.00 4.30
102 109 2.520741 CGCTCTCCTCTCCTCCCC 60.521 72.222 0.00 0.00 0.00 4.81
103 110 2.123033 GCTCTCCTCTCCTCCCCC 60.123 72.222 0.00 0.00 0.00 5.40
170 177 4.726304 CCCCCAACGCGCCCTAAA 62.726 66.667 5.73 0.00 0.00 1.85
171 178 2.439519 CCCCAACGCGCCCTAAAT 60.440 61.111 5.73 0.00 0.00 1.40
172 179 2.478033 CCCCAACGCGCCCTAAATC 61.478 63.158 5.73 0.00 0.00 2.17
173 180 2.478033 CCCAACGCGCCCTAAATCC 61.478 63.158 5.73 0.00 0.00 3.01
174 181 2.478033 CCAACGCGCCCTAAATCCC 61.478 63.158 5.73 0.00 0.00 3.85
175 182 2.124445 AACGCGCCCTAAATCCCC 60.124 61.111 5.73 0.00 0.00 4.81
176 183 3.709348 AACGCGCCCTAAATCCCCC 62.709 63.158 5.73 0.00 0.00 5.40
227 466 4.150454 CCTCCCGCCTCCCTCTCT 62.150 72.222 0.00 0.00 0.00 3.10
354 596 1.133976 AGGTATGTGATTGCTGGCCTC 60.134 52.381 3.32 0.00 0.00 4.70
356 598 0.918258 TATGTGATTGCTGGCCTCCA 59.082 50.000 3.32 0.00 0.00 3.86
410 652 5.475220 CGTCTAGATCTCTCTCTCTCTCTCT 59.525 48.000 0.00 0.00 32.66 3.10
413 655 6.945435 TCTAGATCTCTCTCTCTCTCTCTCTC 59.055 46.154 0.00 0.00 32.66 3.20
415 657 5.774690 AGATCTCTCTCTCTCTCTCTCTCTC 59.225 48.000 0.00 0.00 0.00 3.20
416 658 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
417 659 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
420 662 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
421 663 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
422 664 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
423 665 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
424 666 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
425 667 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
426 668 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
427 669 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
428 670 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
429 671 4.892345 TCTCTCTCTCTCTCTCTCTCTCTG 59.108 50.000 0.00 0.00 0.00 3.35
541 789 1.038130 AGCGAATCGTAGAGGCAGGT 61.038 55.000 4.07 0.00 43.63 4.00
543 791 0.317103 CGAATCGTAGAGGCAGGTCG 60.317 60.000 0.00 0.00 43.63 4.79
555 803 1.989966 GCAGGTCGTAGCGCTCTGTA 61.990 60.000 16.34 0.00 32.61 2.74
616 867 1.797025 CGTCCCTCTCAAGTTCCAAC 58.203 55.000 0.00 0.00 0.00 3.77
657 923 3.356290 CCTCCCCTGTTTTGGTATTGAG 58.644 50.000 0.00 0.00 0.00 3.02
805 1085 5.981174 TCTCGTTTCAAGTGTTTATTTCCG 58.019 37.500 0.00 0.00 0.00 4.30
806 1086 5.524646 TCTCGTTTCAAGTGTTTATTTCCGT 59.475 36.000 0.00 0.00 0.00 4.69
810 1090 6.032042 CGTTTCAAGTGTTTATTTCCGTATGC 59.968 38.462 0.00 0.00 0.00 3.14
846 1131 6.528321 TCATTTCTTGATGCCAGATACTAGG 58.472 40.000 0.00 0.00 0.00 3.02
877 1165 6.909357 GCACATTATTCAGTTGCTACTCATTC 59.091 38.462 0.00 0.00 30.26 2.67
1240 1582 7.271511 AGAGAGATTCTTACCACAATGATGTC 58.728 38.462 0.00 0.00 32.07 3.06
1245 1587 8.321353 AGATTCTTACCACAATGATGTCAGTAA 58.679 33.333 0.00 0.00 37.82 2.24
1289 1631 7.398904 ACCTACTATGGCATTTTACCATTGTTT 59.601 33.333 4.78 0.00 46.87 2.83
1290 1632 8.257306 CCTACTATGGCATTTTACCATTGTTTT 58.743 33.333 4.78 0.00 46.87 2.43
1332 1675 9.503427 AAAAGAGAGTTAAAGAATTGTGAAACG 57.497 29.630 0.00 0.00 42.39 3.60
1634 1980 1.909700 TTCATCTTGTCAACAGGGGC 58.090 50.000 0.00 0.00 0.00 5.80
1745 2197 9.932207 TTTTAACTCTTATTTCGTATGAGTGGA 57.068 29.630 0.00 0.00 43.30 4.02
1794 2246 2.437281 CACTGCTATGGATCAGAAGGGT 59.563 50.000 0.00 0.00 34.57 4.34
1855 2322 4.617808 TCGAGCTTGTGATCTGTAGTAC 57.382 45.455 0.00 0.00 0.00 2.73
1936 2405 8.908786 TCATTTCTGCTCCCTGTATAAATAAG 57.091 34.615 0.00 0.00 0.00 1.73
2219 2688 7.760794 CCTGTCAAAAGCATTGCTAATTAATGA 59.239 33.333 12.39 7.56 38.25 2.57
2287 2756 4.792189 CGTTTTACTAGTACTTCGGCTCAG 59.208 45.833 0.00 0.00 0.00 3.35
2510 2979 6.717084 GGGTATCCCTTTTCTAATCATTCTGG 59.283 42.308 0.00 0.00 41.34 3.86
2518 2987 9.566432 CCTTTTCTAATCATTCTGGTAGCTTAT 57.434 33.333 0.00 0.00 0.00 1.73
2595 3065 2.813754 GTCTCTGTGTAGCCAAAATGCA 59.186 45.455 0.00 0.00 0.00 3.96
2795 3265 6.981722 AGTTTTATTGGTGAAACAGGTCATC 58.018 36.000 0.00 0.00 39.98 2.92
2846 3316 0.250727 AGTTTAGCGGCAGAGGCAAA 60.251 50.000 1.45 0.00 43.71 3.68
2860 3330 5.159209 CAGAGGCAAAATTAAACAGCAGAG 58.841 41.667 0.00 0.00 0.00 3.35
2981 3451 7.118723 TGGTAAGACAGATGCTTTTCCATATT 58.881 34.615 0.00 0.00 0.00 1.28
3179 3649 5.930837 TCCTTGTTCAATTTTGGTCTGTT 57.069 34.783 0.00 0.00 0.00 3.16
3192 3662 6.861065 TTTGGTCTGTTGTATTTCTCTGAC 57.139 37.500 0.00 0.00 0.00 3.51
3373 3843 6.260271 GCTTTGAGTTAATGGAGGTATGTACC 59.740 42.308 0.81 0.81 46.82 3.34
3619 4089 1.202177 GCATTTGGTACATGTCGGCAG 60.202 52.381 0.00 0.00 39.30 4.85
3632 4102 0.749649 TCGGCAGGCATGTTTTGTTT 59.250 45.000 0.00 0.00 0.00 2.83
3636 4106 2.682352 GGCAGGCATGTTTTGTTTGTTT 59.318 40.909 0.00 0.00 0.00 2.83
3705 4175 4.316025 TTTACCTCTTCTTGAATGGGGG 57.684 45.455 7.21 0.00 0.00 5.40
4037 4507 8.829373 AAAATAATTCCTTAGCTTGTCTGGAT 57.171 30.769 0.00 0.00 0.00 3.41
4064 4534 8.856490 AGTTTATGTACAAGCTCAAACTTTTG 57.144 30.769 0.00 0.00 33.63 2.44
4088 4567 3.553511 GTGCAAGAGTTCCATCTCGTATG 59.446 47.826 0.00 0.00 39.21 2.39
4112 4594 5.971202 GGTTTATAATGAATCTGCAACCACG 59.029 40.000 0.00 0.00 33.89 4.94
4125 4607 2.440501 CAACCACGCGAAATAATCTGC 58.559 47.619 15.93 0.00 0.00 4.26
4178 4660 7.744087 TCTGTTAGTGTCAGTTTTATGCATT 57.256 32.000 3.54 0.00 34.86 3.56
4180 4662 8.935844 TCTGTTAGTGTCAGTTTTATGCATTAG 58.064 33.333 3.54 0.00 34.86 1.73
4184 4666 5.355350 AGTGTCAGTTTTATGCATTAGCTCC 59.645 40.000 3.54 0.00 42.74 4.70
4185 4667 5.123820 GTGTCAGTTTTATGCATTAGCTCCA 59.876 40.000 3.54 0.00 42.74 3.86
4218 4700 3.121738 ACTTCCAGTTTAAGGGACACG 57.878 47.619 0.00 0.00 31.59 4.49
4297 4782 9.263446 AGAACTGATATGTTAGTGGGTTACTAA 57.737 33.333 0.00 0.00 46.81 2.24
4414 4929 2.420022 GTGGTTTGCTGTGCTATACCTG 59.580 50.000 0.00 0.00 0.00 4.00
4454 4969 3.067106 AGTTGTATGTTCTTGAGCCGTG 58.933 45.455 0.00 0.00 0.00 4.94
4755 5270 4.370364 GTTGATTGCGATACCAACCATT 57.630 40.909 7.10 0.00 34.46 3.16
4822 5346 5.181748 CCACTAGCTTCAAACTTCATAGCT 58.818 41.667 0.00 0.00 43.93 3.32
5005 5529 2.223595 CCATGGTGAGTGCTACTAGTCG 60.224 54.545 2.57 0.00 0.00 4.18
5069 5599 1.069090 ATGTTGACCGTGTCGCTGT 59.931 52.632 0.59 0.00 34.95 4.40
5098 5628 0.533032 CAGGTCTCTTCCCGAAGTCC 59.467 60.000 4.45 6.27 39.38 3.85
5128 5658 3.493176 CGTGGCTGATCATATTCTGGACA 60.493 47.826 0.00 0.00 0.00 4.02
5131 5661 4.164796 TGGCTGATCATATTCTGGACAACT 59.835 41.667 0.00 0.00 0.00 3.16
5273 6563 4.963318 TCTCCTCCGATTCAATATTGCT 57.037 40.909 10.76 0.38 0.00 3.91
5365 6658 5.508224 GCGTTAGAAATTTCTTGTTGATCCG 59.492 40.000 25.02 15.25 38.70 4.18
5381 6674 1.451927 CCGCCAGCAGAATAAGCCA 60.452 57.895 0.00 0.00 0.00 4.75
5414 6717 5.103982 TCCATTCATGTACCCTGTCAATCAT 60.104 40.000 0.00 0.00 0.00 2.45
5416 6719 5.434182 TTCATGTACCCTGTCAATCATCA 57.566 39.130 0.00 0.00 0.00 3.07
5425 6728 4.155462 CCCTGTCAATCATCACTGAAACTG 59.845 45.833 0.00 0.00 34.37 3.16
5448 6752 1.937191 AATTCATTTGGCCCGACCTT 58.063 45.000 0.00 0.00 40.22 3.50
5466 6770 5.960105 CGACCTTCTTCGATTTAATGAAAGC 59.040 40.000 0.00 0.00 41.78 3.51
5514 6832 9.844257 CCCATAAGTTCTCTGATCTAAATTCTT 57.156 33.333 0.00 0.00 0.00 2.52
5521 6839 2.609459 CTGATCTAAATTCTTGCCGCGT 59.391 45.455 4.92 0.00 0.00 6.01
5529 6847 2.636778 TTCTTGCCGCGTGTGTCTCA 62.637 55.000 4.92 0.00 0.00 3.27
5544 6862 2.064762 GTCTCATGATGTCGGCATAGC 58.935 52.381 0.51 0.00 35.07 2.97
5691 7016 2.739292 TCAGTGTAGTTCAACAGTCGC 58.261 47.619 0.00 0.00 30.50 5.19
5782 7130 1.111277 GGCCGGCAAATTATTCAGGT 58.889 50.000 30.85 0.00 0.00 4.00
5818 7167 6.885922 ACTATGGGGTTGTAATCTTGTACTC 58.114 40.000 0.00 0.00 0.00 2.59
5820 7169 3.264964 TGGGGTTGTAATCTTGTACTCCC 59.735 47.826 0.00 0.00 37.73 4.30
5821 7170 3.522343 GGGGTTGTAATCTTGTACTCCCT 59.478 47.826 0.00 0.00 38.12 4.20
5822 7171 4.018688 GGGGTTGTAATCTTGTACTCCCTT 60.019 45.833 0.00 0.00 38.12 3.95
5824 7173 5.183969 GGTTGTAATCTTGTACTCCCTTCC 58.816 45.833 0.00 0.00 0.00 3.46
5826 7175 5.934402 TGTAATCTTGTACTCCCTTCCTC 57.066 43.478 0.00 0.00 0.00 3.71
5827 7176 4.715297 TGTAATCTTGTACTCCCTTCCTCC 59.285 45.833 0.00 0.00 0.00 4.30
5828 7177 1.848652 TCTTGTACTCCCTTCCTCCG 58.151 55.000 0.00 0.00 0.00 4.63
5829 7178 0.824759 CTTGTACTCCCTTCCTCCGG 59.175 60.000 0.00 0.00 0.00 5.14
5830 7179 0.616679 TTGTACTCCCTTCCTCCGGG 60.617 60.000 0.00 0.00 43.38 5.73
5831 7180 1.001376 GTACTCCCTTCCTCCGGGT 59.999 63.158 0.00 0.00 42.56 5.28
5832 7181 0.616964 GTACTCCCTTCCTCCGGGTT 60.617 60.000 0.00 0.00 42.56 4.11
5834 7183 0.117742 ACTCCCTTCCTCCGGGTTTA 59.882 55.000 0.00 0.00 42.56 2.01
5836 7185 1.844497 CTCCCTTCCTCCGGGTTTATT 59.156 52.381 0.00 0.00 42.56 1.40
5837 7186 3.043418 CTCCCTTCCTCCGGGTTTATTA 58.957 50.000 0.00 0.00 42.56 0.98
5838 7187 3.043418 TCCCTTCCTCCGGGTTTATTAG 58.957 50.000 0.00 0.00 42.56 1.73
5840 7189 2.105993 CCTTCCTCCGGGTTTATTAGGG 59.894 54.545 0.00 0.00 0.00 3.53
5842 7191 2.849537 TCCTCCGGGTTTATTAGGGTT 58.150 47.619 0.00 0.00 0.00 4.11
5844 7193 2.240414 CCTCCGGGTTTATTAGGGTTGT 59.760 50.000 0.00 0.00 0.00 3.32
5845 7194 3.455543 CCTCCGGGTTTATTAGGGTTGTA 59.544 47.826 0.00 0.00 0.00 2.41
5846 7195 4.080413 CCTCCGGGTTTATTAGGGTTGTAA 60.080 45.833 0.00 0.00 0.00 2.41
5847 7196 5.398239 CCTCCGGGTTTATTAGGGTTGTAAT 60.398 44.000 0.00 0.00 0.00 1.89
5848 7197 5.683681 TCCGGGTTTATTAGGGTTGTAATC 58.316 41.667 0.00 0.00 0.00 1.75
5849 7198 5.429435 TCCGGGTTTATTAGGGTTGTAATCT 59.571 40.000 0.00 0.00 0.00 2.40
5850 7199 6.069498 TCCGGGTTTATTAGGGTTGTAATCTT 60.069 38.462 0.00 0.00 0.00 2.40
5851 7200 6.038936 CCGGGTTTATTAGGGTTGTAATCTTG 59.961 42.308 0.00 0.00 0.00 3.02
5862 7211 5.183969 GGTTGTAATCTTGTACTCCCTTCC 58.816 45.833 0.00 0.00 0.00 3.46
5910 7592 2.328099 CGGCAAGACCAAGGCAGTC 61.328 63.158 0.00 0.00 39.03 3.51
5913 7595 0.036022 GCAAGACCAAGGCAGTCTCT 59.964 55.000 5.49 0.00 43.77 3.10
5952 7634 0.896940 AGGCGTTGTCCCTCGAGTAA 60.897 55.000 12.31 0.00 0.00 2.24
6004 7686 8.721478 CATTTACTGCAGATAATTTATACCGCT 58.279 33.333 23.35 0.00 0.00 5.52
6049 7731 0.674895 AGCATGCACGACTTTCCCTC 60.675 55.000 21.98 0.00 0.00 4.30
6117 10593 2.048444 AGCGAAATCTCCATGCATGT 57.952 45.000 24.58 5.40 0.00 3.21
6162 11242 1.232119 TGATAATGCTGCCTCATGCG 58.768 50.000 0.00 0.00 45.60 4.73
6200 11351 8.794553 TGCATGCATTCTTTCCAATTAATTTTT 58.205 25.926 18.46 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.059345 TTTTGGACCCAGGGACGGAC 62.059 60.000 14.54 0.00 0.00 4.79
9 10 1.770927 TTTTGGACCCAGGGACGGA 60.771 57.895 14.54 0.00 0.00 4.69
10 11 1.602605 GTTTTGGACCCAGGGACGG 60.603 63.158 14.54 0.00 0.00 4.79
15 16 0.392706 GGCTTTGTTTTGGACCCAGG 59.607 55.000 0.00 0.00 0.00 4.45
17 18 1.118838 CTGGCTTTGTTTTGGACCCA 58.881 50.000 0.00 0.00 0.00 4.51
33 34 1.685820 GAGGTGAAGGGGGTTCTGG 59.314 63.158 0.00 0.00 35.99 3.86
100 107 2.372172 GGTGATTAGTGGTATCAGGGGG 59.628 54.545 0.00 0.00 32.96 5.40
101 108 3.318313 AGGTGATTAGTGGTATCAGGGG 58.682 50.000 0.00 0.00 32.96 4.79
102 109 6.688073 AATAGGTGATTAGTGGTATCAGGG 57.312 41.667 0.00 0.00 32.96 4.45
108 115 9.886337 TGGAGTATAAATAGGTGATTAGTGGTA 57.114 33.333 0.00 0.00 0.00 3.25
132 139 3.549794 GGAGATTGATCCTGGTTCTTGG 58.450 50.000 6.35 0.00 36.35 3.61
210 217 4.150454 AGAGAGGGAGGCGGGAGG 62.150 72.222 0.00 0.00 0.00 4.30
211 218 2.520741 GAGAGAGGGAGGCGGGAG 60.521 72.222 0.00 0.00 0.00 4.30
212 219 3.024356 AGAGAGAGGGAGGCGGGA 61.024 66.667 0.00 0.00 0.00 5.14
213 220 2.520741 GAGAGAGAGGGAGGCGGG 60.521 72.222 0.00 0.00 0.00 6.13
214 221 2.904866 CGAGAGAGAGGGAGGCGG 60.905 72.222 0.00 0.00 0.00 6.13
215 222 3.591835 GCGAGAGAGAGGGAGGCG 61.592 72.222 0.00 0.00 0.00 5.52
216 223 3.591835 CGCGAGAGAGAGGGAGGC 61.592 72.222 0.00 0.00 0.00 4.70
217 224 3.591835 GCGCGAGAGAGAGGGAGG 61.592 72.222 12.10 0.00 0.00 4.30
218 225 3.947841 CGCGCGAGAGAGAGGGAG 61.948 72.222 28.94 0.00 0.00 4.30
327 569 1.541233 GCAATCACATACCTCGAGGGG 60.541 57.143 34.04 24.15 40.27 4.79
410 652 3.041211 CCCAGAGAGAGAGAGAGAGAGA 58.959 54.545 0.00 0.00 0.00 3.10
413 655 2.483714 CGTCCCAGAGAGAGAGAGAGAG 60.484 59.091 0.00 0.00 0.00 3.20
415 657 1.475034 CCGTCCCAGAGAGAGAGAGAG 60.475 61.905 0.00 0.00 0.00 3.20
416 658 0.544223 CCGTCCCAGAGAGAGAGAGA 59.456 60.000 0.00 0.00 0.00 3.10
417 659 0.544223 TCCGTCCCAGAGAGAGAGAG 59.456 60.000 0.00 0.00 0.00 3.20
420 662 1.078356 CGTCCGTCCCAGAGAGAGA 60.078 63.158 0.00 0.00 0.00 3.10
421 663 2.115911 CCGTCCGTCCCAGAGAGAG 61.116 68.421 0.00 0.00 0.00 3.20
422 664 2.045242 CCGTCCGTCCCAGAGAGA 60.045 66.667 0.00 0.00 0.00 3.10
423 665 3.827898 GCCGTCCGTCCCAGAGAG 61.828 72.222 0.00 0.00 0.00 3.20
424 666 3.957435 ATGCCGTCCGTCCCAGAGA 62.957 63.158 0.00 0.00 0.00 3.10
425 667 3.019003 AATGCCGTCCGTCCCAGAG 62.019 63.158 0.00 0.00 0.00 3.35
426 668 3.000819 AATGCCGTCCGTCCCAGA 61.001 61.111 0.00 0.00 0.00 3.86
427 669 2.819595 CAATGCCGTCCGTCCCAG 60.820 66.667 0.00 0.00 0.00 4.45
524 769 0.317103 CGACCTGCCTCTACGATTCG 60.317 60.000 4.14 4.14 0.00 3.34
530 778 1.355916 CGCTACGACCTGCCTCTAC 59.644 63.158 0.00 0.00 0.00 2.59
541 789 2.943690 AGAAAGATACAGAGCGCTACGA 59.056 45.455 11.50 0.00 0.00 3.43
543 791 5.344884 AGAAAGAAAGATACAGAGCGCTAC 58.655 41.667 11.50 4.00 0.00 3.58
555 803 9.755804 GGAAACAAATTCAGAAGAAAGAAAGAT 57.244 29.630 0.00 0.00 39.98 2.40
616 867 2.042435 AGGGGGAAGAGAGGAGCG 60.042 66.667 0.00 0.00 0.00 5.03
805 1085 1.575244 TGATTGAGCAGAGCGCATAC 58.425 50.000 11.47 0.00 46.13 2.39
806 1086 2.538512 ATGATTGAGCAGAGCGCATA 57.461 45.000 11.47 0.00 46.13 3.14
810 1090 3.373130 TCAAGAAATGATTGAGCAGAGCG 59.627 43.478 0.00 0.00 32.96 5.03
846 1131 3.504863 CAACTGAATAATGTGCCAGCAC 58.495 45.455 15.80 15.80 46.33 4.40
877 1165 1.927895 GTGATGCCACTCTTCCTACG 58.072 55.000 0.00 0.00 40.10 3.51
1009 1346 0.523072 GTAGGCTTGTGACGACCGTA 59.477 55.000 0.00 0.00 0.00 4.02
1116 1453 2.100631 CAACGAGATGGTCCGTGGC 61.101 63.158 0.00 0.00 39.14 5.01
1204 1545 9.543231 TGGTAAGAATCTCTCTAGGAAACTAAA 57.457 33.333 0.00 0.00 43.83 1.85
1240 1582 6.458751 GGTCAACCATCAGCAATGTATTACTG 60.459 42.308 0.00 0.00 33.07 2.74
1245 1587 4.240881 AGGTCAACCATCAGCAATGTAT 57.759 40.909 1.33 0.00 38.89 2.29
1310 1653 5.851703 GCCGTTTCACAATTCTTTAACTCTC 59.148 40.000 0.00 0.00 0.00 3.20
1332 1675 5.297776 ACAGATGCTCATTAAACATACAGCC 59.702 40.000 0.00 0.00 0.00 4.85
1399 1743 1.277557 TCAGCAGAGAAGCTTCCTTCC 59.722 52.381 22.81 9.84 46.97 3.46
1617 1963 0.606401 ACGCCCCTGTTGACAAGATG 60.606 55.000 0.00 0.00 0.00 2.90
1634 1980 1.129251 ACAGCAATCATCGCAAAGACG 59.871 47.619 0.00 0.00 0.00 4.18
1785 2237 7.327975 CACACATAAATACACTACCCTTCTGA 58.672 38.462 0.00 0.00 0.00 3.27
1828 2280 5.330455 ACAGATCACAAGCTCGAAGATAA 57.670 39.130 0.00 0.00 33.89 1.75
1936 2405 7.699812 GGAGAAGTCTGCAATAATCAATGTTTC 59.300 37.037 0.00 0.00 34.20 2.78
1955 2424 8.477419 TTCTGGAACAAAATTTATGGAGAAGT 57.523 30.769 0.00 0.00 38.70 3.01
2244 2713 1.669265 GCAATTCCCCGTGCTAAGTAC 59.331 52.381 0.00 0.00 37.78 2.73
2245 2714 1.741055 CGCAATTCCCCGTGCTAAGTA 60.741 52.381 0.00 0.00 38.66 2.24
2246 2715 1.024579 CGCAATTCCCCGTGCTAAGT 61.025 55.000 0.00 0.00 38.66 2.24
2254 2723 3.004862 ACTAGTAAAACGCAATTCCCCG 58.995 45.455 0.00 0.00 0.00 5.73
2287 2756 6.476706 GGCATATCTTTATTTTGTGTGAAGCC 59.523 38.462 0.00 0.00 0.00 4.35
2327 2796 0.958822 AGCAATGTCACCGGGTTTTC 59.041 50.000 6.32 0.00 0.00 2.29
2510 2979 9.278734 GAGTTTTCTGTTGCATAAATAAGCTAC 57.721 33.333 0.00 0.00 37.09 3.58
2518 2987 4.219115 TGGGGAGTTTTCTGTTGCATAAA 58.781 39.130 0.00 0.00 0.00 1.40
2795 3265 7.837505 TCTTAACATCGTTGCATCTTATTACG 58.162 34.615 0.00 0.00 0.00 3.18
2846 3316 9.726438 ACTAATTACAGTCTCTGCTGTTTAATT 57.274 29.630 4.01 7.77 46.45 1.40
2997 3467 7.709149 AAGGATTCCTTCAACAAGATAAAGG 57.291 36.000 12.37 0.00 40.17 3.11
3179 3649 8.247666 AGATCATGATCAGTCAGAGAAATACA 57.752 34.615 31.99 0.00 40.22 2.29
3192 3662 4.900684 AGCATCTCCAAGATCATGATCAG 58.099 43.478 31.99 23.97 40.22 2.90
3401 3871 8.739972 ACAACATTACATAAGGGATCTTGTTTC 58.260 33.333 0.00 0.00 34.59 2.78
3406 3876 7.402054 TCACACAACATTACATAAGGGATCTT 58.598 34.615 0.00 0.00 37.03 2.40
3619 4089 6.175712 TGAAGAAAACAAACAAAACATGCC 57.824 33.333 0.00 0.00 0.00 4.40
3834 4304 5.123186 TGGGCAACTCATTTTTCTATACACG 59.877 40.000 0.00 0.00 0.00 4.49
4025 4495 7.620880 TGTACATAAACTAATCCAGACAAGCT 58.379 34.615 0.00 0.00 0.00 3.74
4064 4534 2.266554 CGAGATGGAACTCTTGCACTC 58.733 52.381 0.00 0.00 32.41 3.51
4088 4567 5.971202 CGTGGTTGCAGATTCATTATAAACC 59.029 40.000 0.00 0.00 37.05 3.27
4112 4594 6.399986 GGAAAAACAGTTGCAGATTATTTCGC 60.400 38.462 0.00 0.00 0.00 4.70
4125 4607 5.762045 CATAGGTCAGTGGAAAAACAGTTG 58.238 41.667 0.00 0.00 0.00 3.16
4178 4660 6.267928 GGAAGTATCCATCTTAACTGGAGCTA 59.732 42.308 7.80 0.00 45.64 3.32
4180 4662 5.301555 GGAAGTATCCATCTTAACTGGAGC 58.698 45.833 7.80 4.35 45.64 4.70
4297 4782 8.414003 GGACATGAAGAAAGAGTTTTAAAAGGT 58.586 33.333 0.00 0.00 0.00 3.50
4482 4997 4.226427 TGAACTCATGAGCAAGGCTAAT 57.774 40.909 22.83 0.00 39.88 1.73
4755 5270 3.062909 GCAAATAGGTGTTGTATTCGCGA 59.937 43.478 3.71 3.71 0.00 5.87
4884 5408 7.278646 TCACAGAGTTCCTGAAATCATTTATCG 59.721 37.037 9.66 0.00 45.78 2.92
5005 5529 3.181487 TGCAAGCACCAAGAAAGAAACTC 60.181 43.478 0.00 0.00 0.00 3.01
5034 5564 1.271054 ACATGACAGAAGGAGGCACAC 60.271 52.381 0.00 0.00 0.00 3.82
5069 5599 3.325135 GGGAAGAGACCTGTTTCAGAAGA 59.675 47.826 0.00 0.00 32.44 2.87
5128 5658 1.598130 GAGAAGCGTGGCCACAGTT 60.598 57.895 34.16 25.56 0.00 3.16
5131 5661 1.672030 CATGAGAAGCGTGGCCACA 60.672 57.895 34.16 14.55 0.00 4.17
5365 6658 1.387295 GGGTGGCTTATTCTGCTGGC 61.387 60.000 0.00 0.00 0.00 4.85
5381 6674 3.053619 GGTACATGAATGGAAGGAAGGGT 60.054 47.826 0.00 0.00 0.00 4.34
5414 6717 6.979817 CCAAATGAATTTCACAGTTTCAGTGA 59.020 34.615 0.15 0.00 43.72 3.41
5416 6719 5.754890 GCCAAATGAATTTCACAGTTTCAGT 59.245 36.000 0.15 0.00 33.26 3.41
5425 6728 2.606108 GTCGGGCCAAATGAATTTCAC 58.394 47.619 4.39 0.00 0.00 3.18
5448 6752 9.859427 ATTTCATTGCTTTCATTAAATCGAAGA 57.141 25.926 0.00 0.00 45.75 2.87
5466 6770 8.292444 TGGGACAGAATAACCTTATTTCATTG 57.708 34.615 0.00 0.00 33.72 2.82
5514 6832 2.505635 ATCATGAGACACACGCGGCA 62.506 55.000 12.47 0.00 0.00 5.69
5521 6839 0.607620 TGCCGACATCATGAGACACA 59.392 50.000 0.09 0.00 0.00 3.72
5529 6847 1.069204 AGAACGCTATGCCGACATCAT 59.931 47.619 0.00 0.00 37.74 2.45
5544 6862 9.967346 TTCTTCAGATTATAATGGAGTAGAACG 57.033 33.333 1.78 0.00 0.00 3.95
5571 6889 3.309138 CCAAGAACAGCGAGATCATCTTG 59.691 47.826 0.00 0.00 41.97 3.02
5691 7016 1.991965 ACAGCACAAAAACAAAGCACG 59.008 42.857 0.00 0.00 0.00 5.34
5754 7101 0.667993 ATTTGCCGGCCATATCAACG 59.332 50.000 26.77 0.00 0.00 4.10
5782 7130 1.399714 CCCATAGTAGCGAGTGGACA 58.600 55.000 0.00 0.00 33.53 4.02
5824 7173 3.639672 ACAACCCTAATAAACCCGGAG 57.360 47.619 0.73 0.00 0.00 4.63
5826 7175 5.687780 AGATTACAACCCTAATAAACCCGG 58.312 41.667 0.00 0.00 0.00 5.73
5827 7176 6.600427 ACAAGATTACAACCCTAATAAACCCG 59.400 38.462 0.00 0.00 0.00 5.28
5828 7177 7.949690 ACAAGATTACAACCCTAATAAACCC 57.050 36.000 0.00 0.00 0.00 4.11
5829 7178 9.676861 AGTACAAGATTACAACCCTAATAAACC 57.323 33.333 0.00 0.00 0.00 3.27
5831 7180 9.895138 GGAGTACAAGATTACAACCCTAATAAA 57.105 33.333 0.00 0.00 0.00 1.40
5832 7181 8.488668 GGGAGTACAAGATTACAACCCTAATAA 58.511 37.037 0.00 0.00 37.61 1.40
5834 7183 6.677076 AGGGAGTACAAGATTACAACCCTAAT 59.323 38.462 13.02 0.00 43.33 1.73
5836 7185 5.596763 AGGGAGTACAAGATTACAACCCTA 58.403 41.667 13.02 0.00 43.33 3.53
5837 7186 4.436079 AGGGAGTACAAGATTACAACCCT 58.564 43.478 0.00 0.00 41.86 4.34
5838 7187 4.838904 AGGGAGTACAAGATTACAACCC 57.161 45.455 0.00 0.00 39.29 4.11
5840 7189 6.051179 AGGAAGGGAGTACAAGATTACAAC 57.949 41.667 0.00 0.00 0.00 3.32
5842 7191 4.715297 GGAGGAAGGGAGTACAAGATTACA 59.285 45.833 0.00 0.00 0.00 2.41
5844 7193 3.958798 CGGAGGAAGGGAGTACAAGATTA 59.041 47.826 0.00 0.00 0.00 1.75
5845 7194 2.766828 CGGAGGAAGGGAGTACAAGATT 59.233 50.000 0.00 0.00 0.00 2.40
5846 7195 2.389715 CGGAGGAAGGGAGTACAAGAT 58.610 52.381 0.00 0.00 0.00 2.40
5847 7196 1.848652 CGGAGGAAGGGAGTACAAGA 58.151 55.000 0.00 0.00 0.00 3.02
5862 7211 3.719816 GGGCCTAATAAACCCGGAG 57.280 57.895 0.73 0.00 32.92 4.63
5910 7592 5.737353 TCAATTAACATGCGCGAATAAGAG 58.263 37.500 12.10 0.00 0.00 2.85
5913 7595 4.788201 GCCTCAATTAACATGCGCGAATAA 60.788 41.667 12.10 0.00 0.00 1.40
5952 7634 4.388485 TGCCATACGAAGCATCATGTAAT 58.612 39.130 0.00 0.00 33.08 1.89
6004 7686 3.273434 GTGGAGAGCATGCAGAATTGTA 58.727 45.455 21.98 0.00 0.00 2.41
6049 7731 0.533531 TTCGCATGCATAGGCTCCAG 60.534 55.000 19.57 0.00 41.91 3.86
6090 10566 0.665298 GGAGATTTCGCTTGGCATCC 59.335 55.000 0.00 0.00 0.00 3.51
6117 10593 5.404366 GGTGATAATTAATTCGCTGACGCTA 59.596 40.000 3.39 0.00 39.84 4.26
6182 11333 8.970859 TGCCAAGAAAAATTAATTGGAAAGAA 57.029 26.923 0.39 0.00 44.04 2.52


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

AutoCloner maintained by Alex Coulton.