Multiple sequence alignment - TraesCS3B01G360600

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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 TraesCS3B01G360600 chr3B 100.000 5165 0 0 1 5165 572489269 572484105 0.000000e+00 9539.0
1 TraesCS3B01G360600 chr3B 92.857 56 3 1 5033 5088 388069714 388069768 4.290000e-11 80.5
2 TraesCS3B01G360600 chr3B 88.060 67 7 1 5022 5088 264328767 264328832 1.540000e-10 78.7
3 TraesCS3B01G360600 chr3D 96.132 4318 108 26 175 4451 437219138 437214839 0.000000e+00 6994.0
4 TraesCS3B01G360600 chr3D 89.666 329 29 4 4837 5165 437213651 437213328 1.030000e-111 414.0
5 TraesCS3B01G360600 chr3D 92.537 201 14 1 4489 4689 437214842 437214643 2.350000e-73 287.0
6 TraesCS3B01G360600 chr3A 94.967 4331 129 38 166 4451 575315161 575310875 0.000000e+00 6708.0
7 TraesCS3B01G360600 chr3A 90.937 331 25 4 4836 5165 575309777 575309451 1.710000e-119 440.0
8 TraesCS3B01G360600 chr3A 92.821 195 13 1 4489 4683 575310878 575310685 1.090000e-71 281.0
9 TraesCS3B01G360600 chr3A 88.199 161 15 4 5 163 492327904 492328062 6.830000e-44 189.0
10 TraesCS3B01G360600 chr1D 87.124 598 72 3 1072 1665 408432322 408432918 0.000000e+00 673.0
11 TraesCS3B01G360600 chr1B 86.622 598 75 3 1072 1665 549518385 549518981 0.000000e+00 656.0
12 TraesCS3B01G360600 chr1A 86.455 598 76 3 1072 1665 504313402 504313998 0.000000e+00 651.0
13 TraesCS3B01G360600 chr6A 90.184 163 13 3 4 164 266098613 266098774 5.240000e-50 209.0
14 TraesCS3B01G360600 chr5D 90.123 162 12 4 5 164 463084737 463084578 1.880000e-49 207.0
15 TraesCS3B01G360600 chr5D 89.441 161 14 3 6 164 550193628 550193469 3.150000e-47 200.0
16 TraesCS3B01G360600 chr5D 86.567 67 7 2 5022 5088 92632231 92632295 7.170000e-09 73.1
17 TraesCS3B01G360600 chr5B 89.441 161 17 0 3 163 623013676 623013516 2.440000e-48 204.0
18 TraesCS3B01G360600 chr5B 88.199 161 15 3 5 164 604918064 604918221 6.830000e-44 189.0
19 TraesCS3B01G360600 chr6D 89.441 161 14 3 6 164 202463790 202463631 3.150000e-47 200.0
20 TraesCS3B01G360600 chr6D 88.060 67 6 2 5022 5088 118973851 118973915 1.540000e-10 78.7
21 TraesCS3B01G360600 chr7D 89.375 160 14 3 7 164 164484864 164485022 1.130000e-46 198.0
22 TraesCS3B01G360600 chr5A 89.375 160 11 6 5 162 673927711 673927866 4.080000e-46 196.0
23 TraesCS3B01G360600 chr4D 88.060 67 6 2 5022 5088 362245760 362245824 1.540000e-10 78.7
24 TraesCS3B01G360600 chr4D 88.060 67 6 2 5022 5088 471108052 471108116 1.540000e-10 78.7
25 TraesCS3B01G360600 chr4D 88.060 67 4 3 5022 5088 357489361 357489299 5.550000e-10 76.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G360600 chr3B 572484105 572489269 5164 True 9539.000000 9539 100.000000 1 5165 1 chr3B.!!$R1 5164
1 TraesCS3B01G360600 chr3D 437213328 437219138 5810 True 2565.000000 6994 92.778333 175 5165 3 chr3D.!!$R1 4990
2 TraesCS3B01G360600 chr3A 575309451 575315161 5710 True 2476.333333 6708 92.908333 166 5165 3 chr3A.!!$R1 4999
3 TraesCS3B01G360600 chr1D 408432322 408432918 596 False 673.000000 673 87.124000 1072 1665 1 chr1D.!!$F1 593
4 TraesCS3B01G360600 chr1B 549518385 549518981 596 False 656.000000 656 86.622000 1072 1665 1 chr1B.!!$F1 593
5 TraesCS3B01G360600 chr1A 504313402 504313998 596 False 651.000000 651 86.455000 1072 1665 1 chr1A.!!$F1 593

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
551 579 0.173481 CGACACCATCATCAGTCCGT 59.827 55.000 0.0 0.0 0.00 4.69 F
1955 2012 0.453282 CCGATTGCGTTGCTGACAAG 60.453 55.000 0.0 0.0 36.16 3.16 F
2759 2819 0.687920 TTGGTGGTCCTAACATCGCA 59.312 50.000 0.0 0.0 34.23 5.10 F
3674 3741 3.193267 GTGTAATGCATCCAGAAGCCAAA 59.807 43.478 0.0 0.0 0.00 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2088 2145 0.740737 AATTTCCATAGCAGCGCACC 59.259 50.000 11.47 0.0 0.00 5.01 R
2943 3003 1.468520 CAAAAGCAGTGGGACATACGG 59.531 52.381 0.00 0.0 44.52 4.02 R
4068 4136 1.464608 CTTTCACGCGGATCACACATT 59.535 47.619 12.47 0.0 0.00 2.71 R
4999 5921 0.529555 GTGCCACGGTGTTTGCATTT 60.530 50.000 12.50 0.0 35.96 2.32 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
26 27 3.357079 CAGTGTGCTGGGTTCGGC 61.357 66.667 0.00 0.00 45.23 5.54
27 28 4.643387 AGTGTGCTGGGTTCGGCC 62.643 66.667 0.00 0.00 44.42 6.13
28 29 4.643387 GTGTGCTGGGTTCGGCCT 62.643 66.667 0.00 0.00 44.42 5.19
29 30 4.641645 TGTGCTGGGTTCGGCCTG 62.642 66.667 0.00 0.00 44.42 4.85
33 34 3.411517 CTGGGTTCGGCCTGGGAT 61.412 66.667 0.00 0.00 37.43 3.85
34 35 3.406595 CTGGGTTCGGCCTGGGATC 62.407 68.421 0.00 0.00 37.43 3.36
35 36 4.547367 GGGTTCGGCCTGGGATCG 62.547 72.222 0.00 0.00 37.43 3.69
48 49 3.065567 GATCGCCGGGCCCAAAAA 61.066 61.111 24.92 4.19 0.00 1.94
49 50 3.350909 GATCGCCGGGCCCAAAAAC 62.351 63.158 24.92 4.37 0.00 2.43
58 59 4.050934 CCCAAAAACGGGCCGAGC 62.051 66.667 35.78 0.00 40.07 5.03
70 71 4.796231 CCGAGCCCGTGGACTTCG 62.796 72.222 0.00 0.00 0.00 3.79
71 72 4.796231 CGAGCCCGTGGACTTCGG 62.796 72.222 0.00 0.00 46.49 4.30
76 77 4.052229 CCGTGGACTTCGGCGTCT 62.052 66.667 6.85 0.00 41.48 4.18
77 78 2.049433 CGTGGACTTCGGCGTCTT 60.049 61.111 6.85 0.00 34.38 3.01
78 79 2.372690 CGTGGACTTCGGCGTCTTG 61.373 63.158 6.85 0.00 34.38 3.02
79 80 2.027625 GTGGACTTCGGCGTCTTGG 61.028 63.158 6.85 0.00 34.38 3.61
80 81 2.434359 GGACTTCGGCGTCTTGGG 60.434 66.667 6.85 0.00 34.38 4.12
81 82 2.434359 GACTTCGGCGTCTTGGGG 60.434 66.667 6.85 0.00 0.00 4.96
82 83 4.699522 ACTTCGGCGTCTTGGGGC 62.700 66.667 6.85 0.00 0.00 5.80
97 98 4.796495 GGCGCGACTGGGGGATTT 62.796 66.667 12.10 0.00 0.00 2.17
98 99 3.508840 GCGCGACTGGGGGATTTG 61.509 66.667 12.10 0.00 0.00 2.32
99 100 2.046314 CGCGACTGGGGGATTTGT 60.046 61.111 0.00 0.00 0.00 2.83
100 101 2.106683 CGCGACTGGGGGATTTGTC 61.107 63.158 0.00 0.00 0.00 3.18
101 102 4.201951 CGACTGGGGGATTTGTCG 57.798 61.111 0.00 0.00 44.41 4.35
102 103 1.449601 CGACTGGGGGATTTGTCGG 60.450 63.158 6.49 0.00 45.54 4.79
103 104 1.749258 GACTGGGGGATTTGTCGGC 60.749 63.158 0.00 0.00 0.00 5.54
104 105 2.824041 CTGGGGGATTTGTCGGCG 60.824 66.667 0.00 0.00 0.00 6.46
106 107 4.796495 GGGGGATTTGTCGGCGCT 62.796 66.667 7.64 0.00 0.00 5.92
107 108 3.508840 GGGGATTTGTCGGCGCTG 61.509 66.667 10.86 10.86 0.00 5.18
108 109 2.435938 GGGATTTGTCGGCGCTGA 60.436 61.111 16.69 16.69 0.00 4.26
109 110 2.750888 GGGATTTGTCGGCGCTGAC 61.751 63.158 36.79 36.79 39.37 3.51
110 111 2.395690 GATTTGTCGGCGCTGACG 59.604 61.111 36.64 20.18 41.87 4.35
162 163 4.218578 CGCGGCTGGAGATGCTCT 62.219 66.667 0.00 0.00 0.00 4.09
163 164 2.849964 CGCGGCTGGAGATGCTCTA 61.850 63.158 0.00 0.00 0.00 2.43
164 165 1.670590 GCGGCTGGAGATGCTCTAT 59.329 57.895 0.00 0.00 0.00 1.98
170 171 3.443681 GGCTGGAGATGCTCTATACTCTC 59.556 52.174 0.00 0.00 34.66 3.20
173 174 4.068599 TGGAGATGCTCTATACTCTCACG 58.931 47.826 0.00 0.00 36.65 4.35
223 224 4.035558 TGTTGTGAACTTGACATGCTCTTC 59.964 41.667 0.00 0.00 0.00 2.87
239 240 9.956720 ACATGCTCTTCAAAAATATAATGCTAC 57.043 29.630 0.00 0.00 0.00 3.58
342 365 4.222145 TCAGCGGTCCAGTAGAAGTTTATT 59.778 41.667 0.00 0.00 0.00 1.40
527 555 1.378514 CGCCATGGCAAACTACCCT 60.379 57.895 34.93 0.00 42.06 4.34
543 571 2.408565 ACCCTAATCCGACACCATCAT 58.591 47.619 0.00 0.00 0.00 2.45
546 574 3.555795 CCCTAATCCGACACCATCATCAG 60.556 52.174 0.00 0.00 0.00 2.90
547 575 3.070159 CCTAATCCGACACCATCATCAGT 59.930 47.826 0.00 0.00 0.00 3.41
550 578 0.528466 CCGACACCATCATCAGTCCG 60.528 60.000 0.00 0.00 0.00 4.79
551 579 0.173481 CGACACCATCATCAGTCCGT 59.827 55.000 0.00 0.00 0.00 4.69
554 582 1.066858 ACACCATCATCAGTCCGTCAC 60.067 52.381 0.00 0.00 0.00 3.67
619 663 1.356527 CCGTCCTTTTCTTACCGCGG 61.357 60.000 26.86 26.86 0.00 6.46
623 667 1.376812 CTTTTCTTACCGCGGCCCT 60.377 57.895 28.58 8.89 0.00 5.19
1503 1550 2.359850 GTCATCAACGGCCTGCCA 60.360 61.111 9.17 0.00 35.37 4.92
1737 1784 4.456911 TGAAGAATTGATGTTGTCCTCTGC 59.543 41.667 0.00 0.00 0.00 4.26
1773 1820 3.035363 TGTTGTCCTCTGTACTTGGTGA 58.965 45.455 0.00 0.00 0.00 4.02
1792 1839 2.224018 TGAATTGCTGTTTGCCCTCAAC 60.224 45.455 0.00 0.00 42.00 3.18
1919 1973 6.436261 GCTGAAATGTCATCATGAGTTATGG 58.564 40.000 0.09 0.00 37.39 2.74
1955 2012 0.453282 CCGATTGCGTTGCTGACAAG 60.453 55.000 0.00 0.00 36.16 3.16
2072 2129 7.894376 AATGTTTAACTGAATTCATTGCCTG 57.106 32.000 8.96 0.00 0.00 4.85
2088 2145 1.678101 GCCTGGGCTTGCTAAATACTG 59.322 52.381 4.12 0.00 38.26 2.74
2105 2162 1.002746 TGGTGCGCTGCTATGGAAA 60.003 52.632 9.73 0.00 0.00 3.13
2137 2194 8.801913 GCTTGTGCATTGATATAGAAGTTTTTC 58.198 33.333 0.00 0.00 39.41 2.29
2140 2197 8.390354 TGTGCATTGATATAGAAGTTTTTCTCG 58.610 33.333 0.00 0.00 42.60 4.04
2436 2496 9.780186 GGGATATAACTAACTATTGAACTTGCT 57.220 33.333 0.00 0.00 0.00 3.91
2475 2535 9.319143 GTAGTATCTTCTGTTGCTTATGAATGT 57.681 33.333 0.00 0.00 0.00 2.71
2526 2586 4.858965 AGGCTCTTCCTGAATGAATTCT 57.141 40.909 7.05 0.00 45.54 2.40
2555 2615 6.472016 TCTATTTTCATGCTTCTACACACCA 58.528 36.000 0.00 0.00 0.00 4.17
2689 2749 7.766278 CCTATTTAACTCTGCATGTGACTTACT 59.234 37.037 0.00 0.00 0.00 2.24
2759 2819 0.687920 TTGGTGGTCCTAACATCGCA 59.312 50.000 0.00 0.00 34.23 5.10
2846 2906 5.070313 ACCTCTTGCTAAATTTTTGAGGCAA 59.930 36.000 17.00 14.30 42.20 4.52
2943 3003 5.007724 GCTATTGGTGCTGGTAAGTTATGTC 59.992 44.000 0.00 0.00 0.00 3.06
3032 3092 3.844640 ACTTTGGATTAGTTTGCCACCT 58.155 40.909 0.00 0.00 0.00 4.00
3073 3140 8.603304 ACAATGTCCTCAATAGGTAGTAACTTT 58.397 33.333 0.00 0.00 44.09 2.66
3172 3239 4.516698 GCTGTCAACATCCAGAAGAAAGAA 59.483 41.667 0.00 0.00 0.00 2.52
3205 3272 5.573337 AGAAAGGCTGAAATATCTGTTGC 57.427 39.130 0.00 0.00 0.00 4.17
3215 3282 7.465245 GCTGAAATATCTGTTGCACTTCTACTC 60.465 40.741 0.00 0.00 0.00 2.59
3542 3609 3.668191 CCATTTTGATTGTTGTCCGAACG 59.332 43.478 0.00 0.00 0.00 3.95
3674 3741 3.193267 GTGTAATGCATCCAGAAGCCAAA 59.807 43.478 0.00 0.00 0.00 3.28
3838 3905 7.410120 AGCTTCAAAAATACCTTCTAATGGG 57.590 36.000 0.00 0.00 0.00 4.00
3930 3997 5.643421 AAGATATGTTCATTCTCCTGGCT 57.357 39.130 0.00 0.00 0.00 4.75
3931 3998 4.970711 AGATATGTTCATTCTCCTGGCTG 58.029 43.478 0.00 0.00 0.00 4.85
3951 4019 4.503817 GCTGATTGCTACCCAGTATGATGA 60.504 45.833 0.00 0.00 37.11 2.92
4068 4136 6.368805 TCTTCAGGCTATAAGAGATGAGTCA 58.631 40.000 7.24 0.00 0.00 3.41
4107 4175 1.728490 GAATTGAGATGGCACGGGGC 61.728 60.000 3.20 3.20 43.74 5.80
4177 4245 5.810074 GTGAAAGCTTAGACAGATTCTCCTC 59.190 44.000 0.00 0.00 35.55 3.71
4195 4263 4.632153 TCCTCTCGTTTTCCTTCTTTCTG 58.368 43.478 0.00 0.00 0.00 3.02
4243 4311 0.321564 TGTGCTCTTGTCCATTCGGG 60.322 55.000 0.00 0.00 38.37 5.14
4275 4343 3.213506 TCTGCTGCTGTTGTTGTAACAT 58.786 40.909 0.00 0.00 38.95 2.71
4324 4392 7.227156 AGTTGACTATTTTGAGGAAGATGTGT 58.773 34.615 0.00 0.00 0.00 3.72
4325 4393 7.721399 AGTTGACTATTTTGAGGAAGATGTGTT 59.279 33.333 0.00 0.00 0.00 3.32
4446 4514 8.836268 AACAATACAATCACATTTCATGCTTT 57.164 26.923 0.00 0.00 0.00 3.51
4447 4515 8.246908 ACAATACAATCACATTTCATGCTTTG 57.753 30.769 0.00 0.00 0.00 2.77
4448 4516 8.089597 ACAATACAATCACATTTCATGCTTTGA 58.910 29.630 0.00 0.00 0.00 2.69
4449 4517 8.927721 CAATACAATCACATTTCATGCTTTGAA 58.072 29.630 0.00 0.00 42.62 2.69
4450 4518 9.661563 AATACAATCACATTTCATGCTTTGAAT 57.338 25.926 3.93 0.00 43.73 2.57
4452 4520 8.697846 ACAATCACATTTCATGCTTTGAATAG 57.302 30.769 3.93 3.27 43.73 1.73
4453 4521 8.525316 ACAATCACATTTCATGCTTTGAATAGA 58.475 29.630 3.93 1.96 43.73 1.98
4454 4522 9.020813 CAATCACATTTCATGCTTTGAATAGAG 57.979 33.333 3.93 0.73 43.73 2.43
4455 4523 7.092137 TCACATTTCATGCTTTGAATAGAGG 57.908 36.000 3.93 0.00 43.73 3.69
4456 4524 6.885918 TCACATTTCATGCTTTGAATAGAGGA 59.114 34.615 3.93 2.56 43.73 3.71
4457 4525 6.971184 CACATTTCATGCTTTGAATAGAGGAC 59.029 38.462 3.93 0.00 43.73 3.85
4458 4526 6.096001 ACATTTCATGCTTTGAATAGAGGACC 59.904 38.462 3.93 0.00 43.73 4.46
4459 4527 4.842531 TCATGCTTTGAATAGAGGACCA 57.157 40.909 0.00 0.00 0.00 4.02
4460 4528 4.517285 TCATGCTTTGAATAGAGGACCAC 58.483 43.478 0.00 0.00 0.00 4.16
4461 4529 4.225942 TCATGCTTTGAATAGAGGACCACT 59.774 41.667 0.00 0.00 0.00 4.00
4462 4530 4.640771 TGCTTTGAATAGAGGACCACTT 57.359 40.909 0.00 0.00 0.00 3.16
4463 4531 4.985538 TGCTTTGAATAGAGGACCACTTT 58.014 39.130 0.00 0.00 0.00 2.66
4464 4532 4.761739 TGCTTTGAATAGAGGACCACTTTG 59.238 41.667 0.00 0.00 0.00 2.77
4465 4533 4.762251 GCTTTGAATAGAGGACCACTTTGT 59.238 41.667 0.00 0.00 0.00 2.83
4466 4534 5.938125 GCTTTGAATAGAGGACCACTTTGTA 59.062 40.000 0.00 0.00 0.00 2.41
4467 4535 6.128254 GCTTTGAATAGAGGACCACTTTGTAC 60.128 42.308 0.00 0.00 0.00 2.90
4468 4536 6.428083 TTGAATAGAGGACCACTTTGTACA 57.572 37.500 0.00 0.00 0.00 2.90
4469 4537 6.037786 TGAATAGAGGACCACTTTGTACAG 57.962 41.667 0.00 0.00 0.00 2.74
4470 4538 5.778241 TGAATAGAGGACCACTTTGTACAGA 59.222 40.000 0.00 0.00 0.00 3.41
4471 4539 6.440647 TGAATAGAGGACCACTTTGTACAGAT 59.559 38.462 0.00 0.00 0.00 2.90
4472 4540 7.618117 TGAATAGAGGACCACTTTGTACAGATA 59.382 37.037 0.00 0.00 0.00 1.98
4473 4541 8.554490 AATAGAGGACCACTTTGTACAGATAT 57.446 34.615 0.00 0.00 0.00 1.63
4474 4542 6.875972 AGAGGACCACTTTGTACAGATATT 57.124 37.500 0.00 0.00 0.00 1.28
4475 4543 7.259088 AGAGGACCACTTTGTACAGATATTT 57.741 36.000 0.00 0.00 0.00 1.40
4476 4544 7.690256 AGAGGACCACTTTGTACAGATATTTT 58.310 34.615 0.00 0.00 0.00 1.82
4477 4545 8.822805 AGAGGACCACTTTGTACAGATATTTTA 58.177 33.333 0.00 0.00 0.00 1.52
4478 4546 8.788325 AGGACCACTTTGTACAGATATTTTAC 57.212 34.615 0.00 0.00 0.00 2.01
4479 4547 7.548075 AGGACCACTTTGTACAGATATTTTACG 59.452 37.037 0.00 0.00 0.00 3.18
4480 4548 7.068692 ACCACTTTGTACAGATATTTTACGC 57.931 36.000 0.00 0.00 0.00 4.42
4481 4549 6.877322 ACCACTTTGTACAGATATTTTACGCT 59.123 34.615 0.00 0.00 0.00 5.07
4482 4550 7.389607 ACCACTTTGTACAGATATTTTACGCTT 59.610 33.333 0.00 0.00 0.00 4.68
4483 4551 7.692291 CCACTTTGTACAGATATTTTACGCTTG 59.308 37.037 0.00 0.00 0.00 4.01
4484 4552 8.227791 CACTTTGTACAGATATTTTACGCTTGT 58.772 33.333 0.00 0.00 0.00 3.16
4485 4553 8.780249 ACTTTGTACAGATATTTTACGCTTGTT 58.220 29.630 0.00 0.00 0.00 2.83
4545 4613 1.552337 ACCTGCTCGAACAGATGTGAT 59.448 47.619 17.30 0.00 40.25 3.06
4548 4616 3.429410 CCTGCTCGAACAGATGTGATGTA 60.429 47.826 17.30 0.00 40.25 2.29
4587 4655 3.829886 TTTCGAGAACCAATGTGATGC 57.170 42.857 0.00 0.00 0.00 3.91
4622 4690 5.582665 CCAGTGATTAGTCTTCCTACAAAGC 59.417 44.000 0.00 0.00 0.00 3.51
4627 4695 6.156949 TGATTAGTCTTCCTACAAAGCTGGAT 59.843 38.462 0.00 0.00 0.00 3.41
4653 4721 4.903054 ACATGATGTCATCAGCCGAATAT 58.097 39.130 19.86 0.00 43.53 1.28
4690 5063 3.565482 AGAGAACGTGTGCAATGAAACAT 59.435 39.130 0.00 0.00 0.00 2.71
4702 5075 5.814188 TGCAATGAAACATAGCAGAGTAGAG 59.186 40.000 0.00 0.00 0.00 2.43
4723 5096 7.751768 AGAGTTTTTGTTAGCTAAGCAGAAT 57.248 32.000 6.38 0.00 0.00 2.40
4727 5100 8.722394 AGTTTTTGTTAGCTAAGCAGAATAGAC 58.278 33.333 6.38 5.75 0.00 2.59
4729 5102 5.578005 TGTTAGCTAAGCAGAATAGACGT 57.422 39.130 6.38 0.00 0.00 4.34
4753 5126 7.593875 TTTTGATGTCCAAAACAGACAAAAG 57.406 32.000 15.32 0.00 46.48 2.27
4760 5133 4.462483 TCCAAAACAGACAAAAGAACTGCT 59.538 37.500 0.00 0.00 35.38 4.24
4827 5201 4.728882 GCTGTTGCGAGATCATGGTTTAAG 60.729 45.833 0.00 0.00 0.00 1.85
4834 5208 5.221263 GCGAGATCATGGTTTAAGGACTAGA 60.221 44.000 0.00 0.00 0.00 2.43
4837 5211 5.604650 AGATCATGGTTTAAGGACTAGAGGG 59.395 44.000 0.00 0.00 0.00 4.30
4838 5212 4.037927 TCATGGTTTAAGGACTAGAGGGG 58.962 47.826 0.00 0.00 0.00 4.79
4840 5214 2.387861 TGGTTTAAGGACTAGAGGGGGA 59.612 50.000 0.00 0.00 0.00 4.81
4867 5789 3.904136 AGTCTTGTGAAAATCAAGCCG 57.096 42.857 0.00 0.00 41.13 5.52
4881 5803 3.648009 TCAAGCCGCACAATTTTTAAGG 58.352 40.909 0.00 0.00 0.00 2.69
4893 5815 7.468441 CACAATTTTTAAGGTTGGTGGTTTTC 58.532 34.615 0.00 0.00 0.00 2.29
4896 5818 8.341903 CAATTTTTAAGGTTGGTGGTTTTCATC 58.658 33.333 0.00 0.00 0.00 2.92
4897 5819 5.538849 TTTAAGGTTGGTGGTTTTCATCC 57.461 39.130 0.00 0.00 0.00 3.51
4909 5831 2.094100 TTTCATCCCCAGGCAACAAA 57.906 45.000 0.00 0.00 41.41 2.83
4910 5832 2.323999 TTCATCCCCAGGCAACAAAT 57.676 45.000 0.00 0.00 41.41 2.32
4936 5858 6.960468 ACTAAAAGAACTTAGCAAGCAAGAC 58.040 36.000 9.93 5.39 32.97 3.01
4941 5863 4.453819 AGAACTTAGCAAGCAAGACATCAC 59.546 41.667 9.93 0.00 0.00 3.06
4954 5876 4.128925 AGACATCACGAGTAATGCACAT 57.871 40.909 0.00 0.00 0.00 3.21
4966 5888 5.869350 AGTAATGCACATCGAAAAAGTAGC 58.131 37.500 0.00 0.00 0.00 3.58
4989 5911 3.611766 TCTTGCAAGTAAGTAGGAGGC 57.388 47.619 25.19 0.00 0.00 4.70
4999 5921 0.337428 AGTAGGAGGCCGGGTAAGAA 59.663 55.000 2.18 0.00 0.00 2.52
5010 5932 3.313690 CCGGGTAAGAAAATGCAAACAC 58.686 45.455 0.00 0.00 0.00 3.32
5011 5933 3.313690 CGGGTAAGAAAATGCAAACACC 58.686 45.455 0.00 0.00 0.00 4.16
5032 5955 3.236632 GTGGCACATGATTTTTCTCCC 57.763 47.619 13.86 0.00 44.52 4.30
5051 5974 1.134098 CCCATGGTTCGGATAGTTGCT 60.134 52.381 11.73 0.00 0.00 3.91
5061 5984 3.566742 TCGGATAGTTGCTGCTATCGTAA 59.433 43.478 16.31 6.74 44.97 3.18
5112 6035 7.365473 CCAAGAGGTTCTAGGATTCAAGAATCT 60.365 40.741 19.04 11.52 44.07 2.40
5113 6036 7.747809 AGAGGTTCTAGGATTCAAGAATCTT 57.252 36.000 19.04 15.29 42.01 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.357079 GCCGAACCCAGCACACTG 61.357 66.667 0.00 0.00 44.05 3.66
10 11 4.643387 GGCCGAACCCAGCACACT 62.643 66.667 0.00 0.00 0.00 3.55
11 12 4.643387 AGGCCGAACCCAGCACAC 62.643 66.667 0.00 0.00 40.58 3.82
12 13 4.641645 CAGGCCGAACCCAGCACA 62.642 66.667 0.00 0.00 40.58 4.57
16 17 3.406595 GATCCCAGGCCGAACCCAG 62.407 68.421 0.00 0.00 40.58 4.45
17 18 3.407967 GATCCCAGGCCGAACCCA 61.408 66.667 0.00 0.00 40.58 4.51
18 19 4.547367 CGATCCCAGGCCGAACCC 62.547 72.222 0.00 0.00 40.58 4.11
31 32 3.065567 TTTTTGGGCCCGGCGATC 61.066 61.111 19.37 0.00 0.00 3.69
32 33 3.378602 GTTTTTGGGCCCGGCGAT 61.379 61.111 19.37 0.00 0.00 4.58
42 43 4.050934 GGCTCGGCCCGTTTTTGG 62.051 66.667 1.63 0.00 44.06 3.28
53 54 4.796231 CGAAGTCCACGGGCTCGG 62.796 72.222 12.42 0.00 41.39 4.63
54 55 4.796231 CCGAAGTCCACGGGCTCG 62.796 72.222 3.27 3.27 45.65 5.03
60 61 2.049433 AAGACGCCGAAGTCCACG 60.049 61.111 0.00 0.00 41.83 4.94
61 62 2.027625 CCAAGACGCCGAAGTCCAC 61.028 63.158 0.00 0.00 41.83 4.02
62 63 2.342279 CCAAGACGCCGAAGTCCA 59.658 61.111 0.00 0.00 41.83 4.02
63 64 2.434359 CCCAAGACGCCGAAGTCC 60.434 66.667 0.00 0.00 41.83 3.85
64 65 2.434359 CCCCAAGACGCCGAAGTC 60.434 66.667 0.00 2.61 41.23 3.01
65 66 4.699522 GCCCCAAGACGCCGAAGT 62.700 66.667 0.00 0.00 0.00 3.01
80 81 4.796495 AAATCCCCCAGTCGCGCC 62.796 66.667 0.00 0.00 0.00 6.53
81 82 3.508840 CAAATCCCCCAGTCGCGC 61.509 66.667 0.00 0.00 0.00 6.86
82 83 2.046314 ACAAATCCCCCAGTCGCG 60.046 61.111 0.00 0.00 0.00 5.87
83 84 2.106683 CGACAAATCCCCCAGTCGC 61.107 63.158 0.00 0.00 45.68 5.19
84 85 4.201951 CGACAAATCCCCCAGTCG 57.798 61.111 0.00 0.00 46.12 4.18
85 86 1.749258 GCCGACAAATCCCCCAGTC 60.749 63.158 0.00 0.00 0.00 3.51
86 87 2.355115 GCCGACAAATCCCCCAGT 59.645 61.111 0.00 0.00 0.00 4.00
87 88 2.824041 CGCCGACAAATCCCCCAG 60.824 66.667 0.00 0.00 0.00 4.45
89 90 4.796495 AGCGCCGACAAATCCCCC 62.796 66.667 2.29 0.00 0.00 5.40
90 91 3.508840 CAGCGCCGACAAATCCCC 61.509 66.667 2.29 0.00 0.00 4.81
91 92 2.435938 TCAGCGCCGACAAATCCC 60.436 61.111 2.29 0.00 0.00 3.85
92 93 2.785258 GTCAGCGCCGACAAATCC 59.215 61.111 18.70 0.00 35.88 3.01
93 94 2.395690 CGTCAGCGCCGACAAATC 59.604 61.111 22.69 0.00 35.54 2.17
115 116 4.671590 CCCCCGGGGCGACTTTTT 62.672 66.667 36.20 0.00 35.35 1.94
155 156 5.209240 GTTCACGTGAGAGTATAGAGCATC 58.791 45.833 19.11 0.00 0.00 3.91
156 157 4.036971 GGTTCACGTGAGAGTATAGAGCAT 59.963 45.833 19.11 0.00 0.00 3.79
157 158 3.377485 GGTTCACGTGAGAGTATAGAGCA 59.623 47.826 19.11 0.00 0.00 4.26
158 159 3.243134 GGGTTCACGTGAGAGTATAGAGC 60.243 52.174 19.11 10.55 0.00 4.09
159 160 4.200874 AGGGTTCACGTGAGAGTATAGAG 58.799 47.826 19.11 0.00 0.00 2.43
160 161 4.232188 AGGGTTCACGTGAGAGTATAGA 57.768 45.455 19.11 0.00 0.00 1.98
161 162 4.985538 AAGGGTTCACGTGAGAGTATAG 57.014 45.455 19.11 0.00 0.00 1.31
162 163 4.768448 TCAAAGGGTTCACGTGAGAGTATA 59.232 41.667 19.11 0.00 0.00 1.47
163 164 3.576982 TCAAAGGGTTCACGTGAGAGTAT 59.423 43.478 19.11 3.94 0.00 2.12
164 165 2.960384 TCAAAGGGTTCACGTGAGAGTA 59.040 45.455 19.11 0.11 0.00 2.59
170 171 2.162608 TGTGTTTCAAAGGGTTCACGTG 59.837 45.455 9.94 9.94 0.00 4.49
173 174 4.090786 CGTTTTGTGTTTCAAAGGGTTCAC 59.909 41.667 0.00 0.00 45.14 3.18
204 205 4.818534 TTGAAGAGCATGTCAAGTTCAC 57.181 40.909 0.00 0.00 30.41 3.18
311 334 5.872963 TCTACTGGACCGCTGATATTACTA 58.127 41.667 0.00 0.00 0.00 1.82
313 336 5.009811 ACTTCTACTGGACCGCTGATATTAC 59.990 44.000 0.00 0.00 0.00 1.89
323 346 7.262772 TGTATGAATAAACTTCTACTGGACCG 58.737 38.462 0.00 0.00 0.00 4.79
359 387 8.713708 TTTTGATTGTATGTTCTTTTAGGGGA 57.286 30.769 0.00 0.00 0.00 4.81
364 392 9.619316 CGGTGATTTTGATTGTATGTTCTTTTA 57.381 29.630 0.00 0.00 0.00 1.52
369 397 5.286082 GCACGGTGATTTTGATTGTATGTTC 59.714 40.000 13.29 0.00 0.00 3.18
527 555 3.069586 GGACTGATGATGGTGTCGGATTA 59.930 47.826 0.00 0.00 0.00 1.75
543 571 2.603473 CAGGGGGTGACGGACTGA 60.603 66.667 0.00 0.00 0.00 3.41
598 642 1.642037 GCGGTAAGAAAAGGACGGGC 61.642 60.000 0.00 0.00 0.00 6.13
861 905 2.234300 AGACGAGAAAAGGACGCAAA 57.766 45.000 0.00 0.00 0.00 3.68
1044 1088 3.936772 ATTGGCGTGCCCGTTGGAT 62.937 57.895 8.69 0.00 35.87 3.41
1047 1091 4.418401 CCATTGGCGTGCCCGTTG 62.418 66.667 8.69 3.32 35.87 4.10
1737 1784 3.379372 GGACAACATCAATCCACCATCAG 59.621 47.826 0.00 0.00 32.35 2.90
1792 1839 4.058797 GGGAACCGACACCAACAG 57.941 61.111 0.00 0.00 40.86 3.16
1878 1932 4.503741 TCAGCCAAAGTTTGATAACTGC 57.496 40.909 17.33 10.25 43.74 4.40
1919 1973 6.093532 CAATCGGTTGCATCCAAAATTTAC 57.906 37.500 14.13 0.00 31.68 2.01
1985 2042 4.752661 TTTTACCAAGAACCATGTACGC 57.247 40.909 0.00 0.00 0.00 4.42
2072 2129 1.405463 GCACCAGTATTTAGCAAGCCC 59.595 52.381 0.00 0.00 0.00 5.19
2088 2145 0.740737 AATTTCCATAGCAGCGCACC 59.259 50.000 11.47 0.00 0.00 5.01
2123 2180 8.492673 TCATGCAACGAGAAAAACTTCTATAT 57.507 30.769 0.00 0.00 0.00 0.86
2137 2194 3.990469 AGTTAGACAACTCATGCAACGAG 59.010 43.478 13.45 13.45 41.25 4.18
2140 2197 3.499918 AGCAGTTAGACAACTCATGCAAC 59.500 43.478 0.00 0.00 43.30 4.17
2423 2483 7.912250 CCAATTACTTAGCAGCAAGTTCAATAG 59.088 37.037 13.32 3.82 39.45 1.73
2436 2496 8.978472 ACAGAAGATACTACCAATTACTTAGCA 58.022 33.333 0.00 0.00 0.00 3.49
2526 2586 9.719355 TGTGTAGAAGCATGAAAATAGAGTAAA 57.281 29.630 0.00 0.00 0.00 2.01
2689 2749 9.970395 CCTTAGCTGCAATAAAATCAATAATCA 57.030 29.630 1.02 0.00 0.00 2.57
2846 2906 9.799106 CTATTATCCCAGACAATAAAATGAGGT 57.201 33.333 0.00 0.00 0.00 3.85
2943 3003 1.468520 CAAAAGCAGTGGGACATACGG 59.531 52.381 0.00 0.00 44.52 4.02
3172 3239 2.158475 TCAGCCTTTCTTGTCCATTGGT 60.158 45.455 1.86 0.00 0.00 3.67
3542 3609 2.949644 AGGTTTGTGGTAGCAGTTGAAC 59.050 45.455 0.00 0.00 0.00 3.18
3674 3741 1.680735 TCAACTGGCGCAACAGATTTT 59.319 42.857 18.81 2.09 40.97 1.82
3812 3879 9.136323 CCCATTAGAAGGTATTTTTGAAGCTAT 57.864 33.333 0.00 0.00 0.00 2.97
3930 3997 5.554070 CATCATCATACTGGGTAGCAATCA 58.446 41.667 0.00 0.00 0.00 2.57
3931 3998 4.394300 GCATCATCATACTGGGTAGCAATC 59.606 45.833 0.00 0.00 0.00 2.67
4068 4136 1.464608 CTTTCACGCGGATCACACATT 59.535 47.619 12.47 0.00 0.00 2.71
4107 4175 2.233922 AGATGGTCGGTAAAGTGACTGG 59.766 50.000 0.00 0.00 35.45 4.00
4177 4245 6.345882 CGACTAACAGAAAGAAGGAAAACGAG 60.346 42.308 0.00 0.00 0.00 4.18
4195 4263 3.482786 TCGAAAACGTCTAGCGACTAAC 58.517 45.455 12.46 0.00 44.77 2.34
4243 4311 3.441290 CAGCAGAAGCAGCAGCCC 61.441 66.667 0.00 0.00 45.49 5.19
4324 4392 6.765989 ACATCAAGCTACTAACACACTCAAAA 59.234 34.615 0.00 0.00 0.00 2.44
4325 4393 6.202762 CACATCAAGCTACTAACACACTCAAA 59.797 38.462 0.00 0.00 0.00 2.69
4446 4514 5.778241 TCTGTACAAAGTGGTCCTCTATTCA 59.222 40.000 0.00 0.00 0.00 2.57
4447 4515 6.282199 TCTGTACAAAGTGGTCCTCTATTC 57.718 41.667 0.00 0.00 0.00 1.75
4448 4516 6.875972 ATCTGTACAAAGTGGTCCTCTATT 57.124 37.500 0.00 0.00 0.00 1.73
4449 4517 8.554490 AATATCTGTACAAAGTGGTCCTCTAT 57.446 34.615 0.00 0.00 0.00 1.98
4450 4518 7.973048 AATATCTGTACAAAGTGGTCCTCTA 57.027 36.000 0.00 0.00 0.00 2.43
4451 4519 6.875972 AATATCTGTACAAAGTGGTCCTCT 57.124 37.500 0.00 0.00 0.00 3.69
4452 4520 7.923414 AAAATATCTGTACAAAGTGGTCCTC 57.077 36.000 0.00 0.00 0.00 3.71
4453 4521 7.548075 CGTAAAATATCTGTACAAAGTGGTCCT 59.452 37.037 0.00 0.00 0.00 3.85
4454 4522 7.675637 GCGTAAAATATCTGTACAAAGTGGTCC 60.676 40.741 0.00 0.00 0.00 4.46
4455 4523 7.064253 AGCGTAAAATATCTGTACAAAGTGGTC 59.936 37.037 0.00 0.00 0.00 4.02
4456 4524 6.877322 AGCGTAAAATATCTGTACAAAGTGGT 59.123 34.615 0.00 0.00 0.00 4.16
4457 4525 7.303634 AGCGTAAAATATCTGTACAAAGTGG 57.696 36.000 0.00 0.00 0.00 4.00
4458 4526 8.227791 ACAAGCGTAAAATATCTGTACAAAGTG 58.772 33.333 0.00 0.00 0.00 3.16
4459 4527 8.319143 ACAAGCGTAAAATATCTGTACAAAGT 57.681 30.769 0.00 0.00 0.00 2.66
4463 4531 9.589111 TCATAACAAGCGTAAAATATCTGTACA 57.411 29.630 0.00 0.00 0.00 2.90
4466 4534 9.935682 CATTCATAACAAGCGTAAAATATCTGT 57.064 29.630 0.00 0.00 0.00 3.41
4472 4540 9.716507 GTGTATCATTCATAACAAGCGTAAAAT 57.283 29.630 0.00 0.00 0.00 1.82
4473 4541 8.178964 GGTGTATCATTCATAACAAGCGTAAAA 58.821 33.333 0.00 0.00 0.00 1.52
4474 4542 7.201661 GGGTGTATCATTCATAACAAGCGTAAA 60.202 37.037 0.00 0.00 0.00 2.01
4475 4543 6.259167 GGGTGTATCATTCATAACAAGCGTAA 59.741 38.462 0.00 0.00 0.00 3.18
4476 4544 5.756347 GGGTGTATCATTCATAACAAGCGTA 59.244 40.000 0.00 0.00 0.00 4.42
4477 4545 4.574828 GGGTGTATCATTCATAACAAGCGT 59.425 41.667 0.00 0.00 0.00 5.07
4478 4546 4.816385 AGGGTGTATCATTCATAACAAGCG 59.184 41.667 0.00 0.00 0.00 4.68
4479 4547 6.058183 AGAGGGTGTATCATTCATAACAAGC 58.942 40.000 0.00 0.00 0.00 4.01
4480 4548 9.784531 AATAGAGGGTGTATCATTCATAACAAG 57.215 33.333 0.00 0.00 0.00 3.16
4517 4585 4.832248 TCTGTTCGAGCAGGTAATCAAAT 58.168 39.130 26.28 0.00 37.12 2.32
4545 4613 7.593273 CGAAATGATAAAACCTGCAACTTTACA 59.407 33.333 0.00 0.00 0.00 2.41
4548 4616 6.744112 TCGAAATGATAAAACCTGCAACTTT 58.256 32.000 0.00 0.00 0.00 2.66
4587 4655 5.877012 AGACTAATCACTGGTTATTGCAGTG 59.123 40.000 0.00 0.00 45.40 3.66
4605 4673 5.104900 GGATCCAGCTTTGTAGGAAGACTAA 60.105 44.000 6.95 0.00 34.62 2.24
4646 4714 7.175119 TCTCTCTGTCCACTTACATATATTCGG 59.825 40.741 0.00 0.00 0.00 4.30
4653 4721 5.008331 ACGTTCTCTCTGTCCACTTACATA 58.992 41.667 0.00 0.00 0.00 2.29
4690 5063 6.994221 AGCTAACAAAAACTCTACTCTGCTA 58.006 36.000 0.00 0.00 0.00 3.49
4702 5075 7.688578 CGTCTATTCTGCTTAGCTAACAAAAAC 59.311 37.037 5.60 0.00 0.00 2.43
4753 5126 8.739972 TCCTTTTCCTTGATATAAAAGCAGTTC 58.260 33.333 0.00 0.00 38.37 3.01
4766 5139 7.067494 CGGTTGAATCTAATCCTTTTCCTTGAT 59.933 37.037 0.00 0.00 0.00 2.57
4767 5140 6.374333 CGGTTGAATCTAATCCTTTTCCTTGA 59.626 38.462 0.00 0.00 0.00 3.02
4827 5201 0.563672 ATCCACTCCCCCTCTAGTCC 59.436 60.000 0.00 0.00 0.00 3.85
4834 5208 1.366435 ACAAGACTATCCACTCCCCCT 59.634 52.381 0.00 0.00 0.00 4.79
4837 5211 4.553330 TTTCACAAGACTATCCACTCCC 57.447 45.455 0.00 0.00 0.00 4.30
4838 5212 6.173339 TGATTTTCACAAGACTATCCACTCC 58.827 40.000 0.00 0.00 0.00 3.85
4840 5214 6.150140 GCTTGATTTTCACAAGACTATCCACT 59.850 38.462 11.08 0.00 44.92 4.00
4867 5789 4.447290 ACCACCAACCTTAAAAATTGTGC 58.553 39.130 0.00 0.00 0.00 4.57
4881 5803 1.618343 CTGGGGATGAAAACCACCAAC 59.382 52.381 0.00 0.00 25.81 3.77
4893 5815 1.205417 GTCATTTGTTGCCTGGGGATG 59.795 52.381 0.00 0.00 0.00 3.51
4896 5818 2.214376 TAGTCATTTGTTGCCTGGGG 57.786 50.000 0.00 0.00 0.00 4.96
4897 5819 4.280677 TCTTTTAGTCATTTGTTGCCTGGG 59.719 41.667 0.00 0.00 0.00 4.45
4909 5831 7.445402 TCTTGCTTGCTAAGTTCTTTTAGTCAT 59.555 33.333 0.00 0.00 33.99 3.06
4910 5832 6.765989 TCTTGCTTGCTAAGTTCTTTTAGTCA 59.234 34.615 0.00 0.00 33.99 3.41
4936 5858 3.115554 TCGATGTGCATTACTCGTGATG 58.884 45.455 0.00 0.00 34.10 3.07
4941 5863 4.957971 ACTTTTTCGATGTGCATTACTCG 58.042 39.130 0.00 0.00 33.88 4.18
4966 5888 4.333926 GCCTCCTACTTACTTGCAAGATTG 59.666 45.833 32.50 21.02 0.00 2.67
4989 5911 3.313690 GTGTTTGCATTTTCTTACCCGG 58.686 45.455 0.00 0.00 0.00 5.73
4999 5921 0.529555 GTGCCACGGTGTTTGCATTT 60.530 50.000 12.50 0.00 35.96 2.32
5010 5932 2.415893 GGAGAAAAATCATGTGCCACGG 60.416 50.000 0.00 0.00 0.00 4.94
5011 5933 2.415893 GGGAGAAAAATCATGTGCCACG 60.416 50.000 0.00 0.00 0.00 4.94
5028 5951 1.424638 ACTATCCGAACCATGGGGAG 58.575 55.000 18.09 6.16 38.05 4.30
5030 5953 1.967319 CAACTATCCGAACCATGGGG 58.033 55.000 18.09 8.03 41.29 4.96
5031 5954 1.134098 AGCAACTATCCGAACCATGGG 60.134 52.381 18.09 0.00 0.00 4.00
5032 5955 1.942657 CAGCAACTATCCGAACCATGG 59.057 52.381 11.19 11.19 0.00 3.66
5051 5974 4.112716 TCAACGTGGATTTACGATAGCA 57.887 40.909 5.23 0.00 46.46 3.49
5061 5984 3.600388 GAAGTCTCCATCAACGTGGATT 58.400 45.455 1.58 0.00 46.67 3.01


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

AutoCloner maintained by Alex Coulton.