Multiple sequence alignment - TraesCS3B01G213500

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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 TraesCS3B01G213500 chr3B 100.000 5449 0 0 1 5449 252928727 252934175 0.000000e+00 10063.0
1 TraesCS3B01G213500 chr3B 99.016 610 4 2 1 610 444684586 444683979 0.000000e+00 1092.0
2 TraesCS3B01G213500 chr3B 88.154 363 28 10 250 599 118577905 118577545 8.440000e-113 418.0
3 TraesCS3B01G213500 chr3B 90.991 111 10 0 1630 1740 754856156 754856266 3.400000e-32 150.0
4 TraesCS3B01G213500 chr3B 92.381 105 6 2 760 864 252929436 252929538 1.220000e-31 148.0
5 TraesCS3B01G213500 chr3B 92.381 105 6 2 710 812 252929486 252929590 1.220000e-31 148.0
6 TraesCS3B01G213500 chr3A 96.044 2932 84 14 710 3628 213128985 213131897 0.000000e+00 4743.0
7 TraesCS3B01G213500 chr3A 96.949 1049 24 4 3626 4673 213131978 213133019 0.000000e+00 1753.0
8 TraesCS3B01G213500 chr3A 92.537 402 26 2 5049 5449 213133016 213133414 1.700000e-159 573.0
9 TraesCS3B01G213500 chr3A 86.590 261 28 4 608 864 213128780 213129037 1.160000e-71 281.0
10 TraesCS3B01G213500 chr3A 93.333 105 5 2 710 812 213129035 213129139 2.630000e-33 154.0
11 TraesCS3B01G213500 chr3A 97.619 42 1 0 712 753 213129087 213129128 7.570000e-09 73.1
12 TraesCS3B01G213500 chr3D 97.127 2750 62 7 1999 4745 174415888 174418623 0.000000e+00 4625.0
13 TraesCS3B01G213500 chr3D 92.632 1303 55 15 712 2001 174414455 174415729 0.000000e+00 1836.0
14 TraesCS3B01G213500 chr3D 92.958 284 8 2 4792 5075 174425644 174425915 2.360000e-108 403.0
15 TraesCS3B01G213500 chr3D 90.283 247 18 5 608 853 174414305 174414546 8.810000e-83 318.0
16 TraesCS3B01G213500 chr3D 97.273 110 3 0 5329 5438 174426052 174426161 2.590000e-43 187.0
17 TraesCS3B01G213500 chr3D 90.099 101 8 2 764 864 174414407 174414505 4.430000e-26 130.0
18 TraesCS3B01G213500 chr3D 83.465 127 7 7 5122 5234 174425918 174426044 7.460000e-19 106.0
19 TraesCS3B01G213500 chr3D 92.424 66 4 1 710 774 174414503 174414568 5.810000e-15 93.5
20 TraesCS3B01G213500 chr3D 100.000 29 0 0 5107 5135 64650794 64650766 3.000000e-03 54.7
21 TraesCS3B01G213500 chr7A 90.049 613 31 10 1 612 119296553 119295970 0.000000e+00 767.0
22 TraesCS3B01G213500 chr7A 89.803 608 32 10 1 607 119299498 119298920 0.000000e+00 752.0
23 TraesCS3B01G213500 chr7B 87.092 612 48 10 1 607 678539728 678539143 0.000000e+00 664.0
24 TraesCS3B01G213500 chr1D 80.946 782 129 17 3707 4478 324618510 324619281 7.810000e-168 601.0
25 TraesCS3B01G213500 chr1D 88.587 368 31 7 250 607 251792687 251792321 2.330000e-118 436.0
26 TraesCS3B01G213500 chr1D 94.022 184 11 0 1214 1397 324617136 324617319 4.160000e-71 279.0
27 TraesCS3B01G213500 chr1D 87.413 143 15 1 995 1134 324616902 324617044 1.570000e-35 161.0
28 TraesCS3B01G213500 chr1A 81.137 774 116 20 3713 4478 420395481 420394730 1.310000e-165 593.0
29 TraesCS3B01G213500 chr1A 93.478 184 12 0 1214 1397 420396875 420396692 1.930000e-69 274.0
30 TraesCS3B01G213500 chr1A 86.861 137 15 1 1001 1134 420397117 420396981 3.400000e-32 150.0
31 TraesCS3B01G213500 chr1A 90.179 112 9 2 1631 1741 115437175 115437285 1.580000e-30 145.0
32 TraesCS3B01G213500 chr7D 84.091 616 66 12 2 604 319919230 319919826 2.850000e-157 566.0
33 TraesCS3B01G213500 chr2A 88.070 285 28 4 332 611 757560486 757560769 3.150000e-87 333.0
34 TraesCS3B01G213500 chr2A 88.364 275 24 4 328 594 757559205 757559479 1.890000e-84 324.0
35 TraesCS3B01G213500 chr5B 88.722 266 26 3 343 607 694204401 694204139 6.810000e-84 322.0
36 TraesCS3B01G213500 chr6A 93.578 109 7 0 1630 1738 603185284 603185176 4.370000e-36 163.0
37 TraesCS3B01G213500 chr4D 92.727 110 8 0 1629 1738 83277520 83277629 5.650000e-35 159.0
38 TraesCS3B01G213500 chrUn 90.991 111 10 0 1630 1740 40878331 40878221 3.400000e-32 150.0
39 TraesCS3B01G213500 chrUn 90.991 111 10 0 1630 1740 310312377 310312487 3.400000e-32 150.0
40 TraesCS3B01G213500 chrUn 90.991 111 10 0 1630 1740 315278002 315277892 3.400000e-32 150.0


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 TraesCS3B01G213500 chr3B 252928727 252934175 5448 False 10063.00 10063 100.000000 1 5449 1 chr3B.!!$F1 5448
1 TraesCS3B01G213500 chr3B 444683979 444684586 607 True 1092.00 1092 99.016000 1 610 1 chr3B.!!$R2 609
2 TraesCS3B01G213500 chr3A 213128780 213133414 4634 False 1262.85 4743 93.845333 608 5449 6 chr3A.!!$F1 4841
3 TraesCS3B01G213500 chr3D 174414305 174418623 4318 False 1400.50 4625 92.513000 608 4745 5 chr3D.!!$F1 4137
4 TraesCS3B01G213500 chr3D 174425644 174426161 517 False 232.00 403 91.232000 4792 5438 3 chr3D.!!$F2 646
5 TraesCS3B01G213500 chr7A 119295970 119299498 3528 True 759.50 767 89.926000 1 612 2 chr7A.!!$R1 611
6 TraesCS3B01G213500 chr7B 678539143 678539728 585 True 664.00 664 87.092000 1 607 1 chr7B.!!$R1 606
7 TraesCS3B01G213500 chr1D 324616902 324619281 2379 False 347.00 601 87.460333 995 4478 3 chr1D.!!$F1 3483
8 TraesCS3B01G213500 chr1A 420394730 420397117 2387 True 339.00 593 87.158667 1001 4478 3 chr1A.!!$R1 3477
9 TraesCS3B01G213500 chr7D 319919230 319919826 596 False 566.00 566 84.091000 2 604 1 chr7D.!!$F1 602
10 TraesCS3B01G213500 chr2A 757559205 757560769 1564 False 328.50 333 88.217000 328 611 2 chr2A.!!$F1 283

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
808 5163 0.468029 CCAGCCCACTTCAAACCAGT 60.468 55.000 0.0 0.00 0.00 4.00 F
1011 5423 0.107945 GAGAAGCCATGGAGCGACTT 60.108 55.000 18.4 8.75 38.01 3.01 F
1442 5898 1.134220 TGTTGCTCCTGTCGTTTTCCT 60.134 47.619 0.0 0.00 0.00 3.36 F
2123 6846 1.755179 CCCTTTCATGGCTACCACTG 58.245 55.000 0.0 0.00 35.80 3.66 F
3100 7824 1.349688 ACCCGTTCTAGGAATGCAACA 59.650 47.619 0.0 0.00 0.00 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2575 7299 0.978146 CAGCTGTAGGGCTACCACCT 60.978 60.000 5.25 0.0 41.00 4.00 R
2576 7300 1.522569 CAGCTGTAGGGCTACCACC 59.477 63.158 5.25 0.0 41.00 4.61 R
2578 7302 2.367202 GCCAGCTGTAGGGCTACCA 61.367 63.158 13.81 0.0 46.74 3.25 R
3758 9092 0.178906 TGACACTCTGGATGGGGTCA 60.179 55.000 0.00 0.0 33.31 4.02 R
4771 10146 0.179468 GGGTTAGGAGCGGCACATTA 59.821 55.000 1.45 0.0 0.00 1.90 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
560 4811 2.480845 AGTTGTGTACGTTTCCTGAGC 58.519 47.619 0.00 0.00 0.00 4.26
722 4977 1.673993 CACTACGGCCCATGCAACA 60.674 57.895 0.00 0.00 40.13 3.33
757 5012 1.398958 GGCAGCCCACTTCAAACCAA 61.399 55.000 0.00 0.00 0.00 3.67
808 5163 0.468029 CCAGCCCACTTCAAACCAGT 60.468 55.000 0.00 0.00 0.00 4.00
814 5169 0.535102 CACTTCAAACCAGTCGGCCT 60.535 55.000 0.00 0.00 34.57 5.19
816 5171 1.270678 ACTTCAAACCAGTCGGCCTAC 60.271 52.381 0.00 0.00 34.57 3.18
899 5301 3.748568 GTGCTCGAAGAAAGAAATCCAGT 59.251 43.478 0.00 0.00 34.09 4.00
990 5402 1.399215 CCGAACCAAATCGAACAACCG 60.399 52.381 0.00 0.00 45.48 4.44
1008 5420 1.819229 GAGAGAAGCCATGGAGCGA 59.181 57.895 18.40 0.00 38.01 4.93
1011 5423 0.107945 GAGAAGCCATGGAGCGACTT 60.108 55.000 18.40 8.75 38.01 3.01
1172 5587 2.562876 GGTCCCGATCTACGCCCTC 61.563 68.421 0.00 0.00 41.07 4.30
1177 5592 2.618219 CGATCTACGCCCTCCTCCG 61.618 68.421 0.00 0.00 34.51 4.63
1200 5615 2.496470 CTCCACGAAGCTAGGGTTAACT 59.504 50.000 5.42 0.00 0.00 2.24
1442 5898 1.134220 TGTTGCTCCTGTCGTTTTCCT 60.134 47.619 0.00 0.00 0.00 3.36
1472 5928 4.278678 CGTCAGATTTGATGCCCTTAAC 57.721 45.455 0.00 0.00 35.39 2.01
1607 6063 8.492673 TTGCTACTAGTTCCAGATGTTAATTG 57.507 34.615 0.00 0.00 0.00 2.32
1635 6091 4.274147 AGATAGGCCATATGGAGTACTCG 58.726 47.826 26.47 2.97 37.39 4.18
1755 6211 8.038492 AGGGAGTACTATATACGACGATTTTC 57.962 38.462 0.00 0.00 0.00 2.29
2028 6751 5.948162 ACTTGGAGCACAGTTCATTATCATT 59.052 36.000 0.00 0.00 0.00 2.57
2123 6846 1.755179 CCCTTTCATGGCTACCACTG 58.245 55.000 0.00 0.00 35.80 3.66
2129 6852 2.261729 TCATGGCTACCACTGTACCAA 58.738 47.619 0.00 0.00 35.80 3.67
2359 7082 8.223769 GGTTATGTATCATGAATCGTTGATGAC 58.776 37.037 0.00 4.72 34.52 3.06
2595 7319 1.522569 GTGGTAGCCCTACAGCTGG 59.477 63.158 19.93 0.08 44.67 4.85
2812 7536 9.943465 CATCATATCATATTGTTAAAGACGTCG 57.057 33.333 10.46 0.00 0.00 5.12
2889 7613 8.169977 TGCCAACAGAATAATTTCATATCCTC 57.830 34.615 0.00 0.00 34.08 3.71
3100 7824 1.349688 ACCCGTTCTAGGAATGCAACA 59.650 47.619 0.00 0.00 0.00 3.33
3102 7826 1.737793 CCGTTCTAGGAATGCAACACC 59.262 52.381 0.00 0.00 0.00 4.16
3245 7969 3.068732 GGAGCCTGGATTTTAAAGATGGC 59.931 47.826 0.00 9.99 39.40 4.40
3467 8191 1.894466 CATTGCCACCTTGGATGTTCA 59.106 47.619 0.00 0.00 40.96 3.18
3758 9092 3.253955 GCAGTTGCCGTCGTGATT 58.746 55.556 0.00 0.00 34.31 2.57
4045 9382 7.393327 CAATAAATTACCGCAAAAATGAGCTG 58.607 34.615 0.00 0.00 0.00 4.24
4217 9590 7.284489 TGTTAATATAATGCAGGGTGAAAGTCC 59.716 37.037 0.00 0.00 0.00 3.85
4224 9597 0.038744 AGGGTGAAAGTCCATGCAGG 59.961 55.000 0.00 0.00 39.47 4.85
4241 9614 2.825532 GCAGGTTCTTAGATTTTGGCCA 59.174 45.455 0.00 0.00 0.00 5.36
4316 9689 2.235898 GCAAGAGGAGGATGAGTTGTCT 59.764 50.000 0.00 0.00 0.00 3.41
4358 9731 2.045926 GTGGGACGGCAAGATGCT 60.046 61.111 2.00 0.00 44.28 3.79
4400 9773 3.849911 TGTCTCAAATCTGATGTCGTCC 58.150 45.455 0.00 0.00 0.00 4.79
4730 10105 3.188159 TGACTTGTGGTGGAGTAACAC 57.812 47.619 0.00 0.00 40.60 3.32
4745 10120 0.607489 AACACAGTGAGATGGCAGCC 60.607 55.000 7.81 3.66 0.00 4.85
4746 10121 2.104859 CACAGTGAGATGGCAGCCG 61.105 63.158 7.03 0.00 0.00 5.52
4747 10122 3.200593 CAGTGAGATGGCAGCCGC 61.201 66.667 7.03 0.80 37.44 6.53
4748 10123 3.397439 AGTGAGATGGCAGCCGCT 61.397 61.111 7.03 6.65 38.60 5.52
4749 10124 2.437359 GTGAGATGGCAGCCGCTT 60.437 61.111 7.03 0.00 38.60 4.68
4750 10125 2.124983 TGAGATGGCAGCCGCTTC 60.125 61.111 7.03 3.76 38.60 3.86
4751 10126 2.188994 GAGATGGCAGCCGCTTCT 59.811 61.111 7.03 9.02 38.60 2.85
4752 10127 1.886777 GAGATGGCAGCCGCTTCTC 60.887 63.158 18.18 18.18 38.92 2.87
4753 10128 2.188994 GATGGCAGCCGCTTCTCT 59.811 61.111 7.03 0.00 38.60 3.10
4754 10129 1.886777 GATGGCAGCCGCTTCTCTC 60.887 63.158 7.03 0.00 38.60 3.20
4755 10130 3.729965 ATGGCAGCCGCTTCTCTCG 62.730 63.158 7.03 0.00 38.60 4.04
4756 10131 4.443266 GGCAGCCGCTTCTCTCGT 62.443 66.667 0.00 0.00 38.60 4.18
4757 10132 3.184683 GCAGCCGCTTCTCTCGTG 61.185 66.667 0.00 0.00 34.30 4.35
4758 10133 2.259818 CAGCCGCTTCTCTCGTGT 59.740 61.111 0.00 0.00 0.00 4.49
4759 10134 1.373497 CAGCCGCTTCTCTCGTGTT 60.373 57.895 0.00 0.00 0.00 3.32
4760 10135 1.080434 AGCCGCTTCTCTCGTGTTC 60.080 57.895 0.00 0.00 0.00 3.18
4761 10136 2.095252 GCCGCTTCTCTCGTGTTCC 61.095 63.158 0.00 0.00 0.00 3.62
4762 10137 1.801913 CCGCTTCTCTCGTGTTCCG 60.802 63.158 0.00 0.00 38.13 4.30
4763 10138 1.801913 CGCTTCTCTCGTGTTCCGG 60.802 63.158 0.00 0.00 37.11 5.14
4764 10139 2.095252 GCTTCTCTCGTGTTCCGGC 61.095 63.158 0.00 0.00 37.11 6.13
4765 10140 1.801913 CTTCTCTCGTGTTCCGGCG 60.802 63.158 0.00 0.00 37.11 6.46
4766 10141 2.473664 CTTCTCTCGTGTTCCGGCGT 62.474 60.000 6.01 0.00 37.11 5.68
4767 10142 1.236616 TTCTCTCGTGTTCCGGCGTA 61.237 55.000 6.01 0.00 37.11 4.42
4768 10143 1.210931 CTCTCGTGTTCCGGCGTAA 59.789 57.895 6.01 0.00 37.11 3.18
4769 10144 0.179145 CTCTCGTGTTCCGGCGTAAT 60.179 55.000 6.01 0.00 37.11 1.89
4770 10145 1.064505 CTCTCGTGTTCCGGCGTAATA 59.935 52.381 6.01 0.00 37.11 0.98
4771 10146 1.677576 TCTCGTGTTCCGGCGTAATAT 59.322 47.619 6.01 0.00 37.11 1.28
4772 10147 2.877786 TCTCGTGTTCCGGCGTAATATA 59.122 45.455 6.01 0.00 37.11 0.86
4773 10148 3.314913 TCTCGTGTTCCGGCGTAATATAA 59.685 43.478 6.01 0.00 37.11 0.98
4774 10149 4.022935 TCTCGTGTTCCGGCGTAATATAAT 60.023 41.667 6.01 0.00 37.11 1.28
4775 10150 3.982701 TCGTGTTCCGGCGTAATATAATG 59.017 43.478 6.01 0.00 37.11 1.90
4776 10151 3.737266 CGTGTTCCGGCGTAATATAATGT 59.263 43.478 6.01 0.00 0.00 2.71
4777 10152 4.375606 CGTGTTCCGGCGTAATATAATGTG 60.376 45.833 6.01 0.00 0.00 3.21
4778 10153 3.495377 TGTTCCGGCGTAATATAATGTGC 59.505 43.478 6.01 0.00 0.00 4.57
4779 10154 2.690786 TCCGGCGTAATATAATGTGCC 58.309 47.619 6.01 0.00 39.10 5.01
4781 10156 2.520686 GGCGTAATATAATGTGCCGC 57.479 50.000 0.00 0.00 38.97 6.53
4782 10157 2.073816 GGCGTAATATAATGTGCCGCT 58.926 47.619 0.00 0.00 39.57 5.52
4783 10158 2.093783 GGCGTAATATAATGTGCCGCTC 59.906 50.000 0.00 0.00 39.57 5.03
4784 10159 2.093783 GCGTAATATAATGTGCCGCTCC 59.906 50.000 0.00 0.00 36.94 4.70
4785 10160 3.585862 CGTAATATAATGTGCCGCTCCT 58.414 45.455 0.00 0.00 0.00 3.69
4786 10161 4.740268 CGTAATATAATGTGCCGCTCCTA 58.260 43.478 0.00 0.00 0.00 2.94
4787 10162 5.165676 CGTAATATAATGTGCCGCTCCTAA 58.834 41.667 0.00 0.00 0.00 2.69
4788 10163 5.061808 CGTAATATAATGTGCCGCTCCTAAC 59.938 44.000 0.00 0.00 0.00 2.34
4789 10164 2.256117 ATAATGTGCCGCTCCTAACC 57.744 50.000 0.00 0.00 0.00 2.85
4790 10165 0.179468 TAATGTGCCGCTCCTAACCC 59.821 55.000 0.00 0.00 0.00 4.11
4958 10333 8.432110 AAAATTTTGGTGTATCAAACTTGGTC 57.568 30.769 1.75 0.00 36.49 4.02
4977 10352 4.462834 TGGTCGACAATTCTACTCTCATGT 59.537 41.667 18.91 0.00 0.00 3.21
4988 10363 6.405278 TCTACTCTCATGTGAAGTTTGTGA 57.595 37.500 0.00 0.00 0.00 3.58
4989 10364 6.816136 TCTACTCTCATGTGAAGTTTGTGAA 58.184 36.000 0.00 0.00 0.00 3.18
4990 10365 5.998454 ACTCTCATGTGAAGTTTGTGAAG 57.002 39.130 0.00 0.00 0.00 3.02
4991 10366 5.431765 ACTCTCATGTGAAGTTTGTGAAGT 58.568 37.500 0.00 0.00 0.00 3.01
4992 10367 6.582636 ACTCTCATGTGAAGTTTGTGAAGTA 58.417 36.000 0.00 0.00 0.00 2.24
4993 10368 7.220030 ACTCTCATGTGAAGTTTGTGAAGTAT 58.780 34.615 0.00 0.00 0.00 2.12
4994 10369 8.367911 ACTCTCATGTGAAGTTTGTGAAGTATA 58.632 33.333 0.00 0.00 0.00 1.47
4995 10370 8.763049 TCTCATGTGAAGTTTGTGAAGTATAG 57.237 34.615 0.00 0.00 0.00 1.31
4996 10371 8.585018 TCTCATGTGAAGTTTGTGAAGTATAGA 58.415 33.333 0.00 0.00 0.00 1.98
4997 10372 8.534333 TCATGTGAAGTTTGTGAAGTATAGAC 57.466 34.615 0.00 0.00 0.00 2.59
4998 10373 8.147704 TCATGTGAAGTTTGTGAAGTATAGACA 58.852 33.333 0.00 0.00 0.00 3.41
5075 10450 7.648142 TCAGTGTTTTCTTAATGTAGCTTTGG 58.352 34.615 0.00 0.00 0.00 3.28
5084 10459 8.911918 TCTTAATGTAGCTTTGGTTTTGTCTA 57.088 30.769 0.00 0.00 0.00 2.59
5085 10460 9.344772 TCTTAATGTAGCTTTGGTTTTGTCTAA 57.655 29.630 0.00 0.00 0.00 2.10
5094 10469 7.070696 AGCTTTGGTTTTGTCTAATTTACCCTT 59.929 33.333 0.00 0.00 0.00 3.95
5095 10470 8.361889 GCTTTGGTTTTGTCTAATTTACCCTTA 58.638 33.333 0.00 0.00 0.00 2.69
5103 10478 4.451435 GTCTAATTTACCCTTAGCGGATGC 59.549 45.833 0.00 0.00 43.24 3.91
5154 10529 6.633500 TTAACAGAATAGCAGTGCTTTGTT 57.367 33.333 25.23 25.72 40.44 2.83
5155 10530 7.737972 TTAACAGAATAGCAGTGCTTTGTTA 57.262 32.000 25.23 24.83 40.44 2.41
5274 10663 1.002430 TCTGAGCCAAAACAGCGATCT 59.998 47.619 0.00 0.00 34.57 2.75
5279 10668 1.464189 GCCAAAACAGCGATCTCGTTC 60.464 52.381 1.14 0.00 42.22 3.95
5281 10670 2.480419 CCAAAACAGCGATCTCGTTCTT 59.520 45.455 1.14 0.00 42.22 2.52
5282 10671 3.473367 CAAAACAGCGATCTCGTTCTTG 58.527 45.455 1.14 0.00 42.22 3.02
5283 10672 2.440539 AACAGCGATCTCGTTCTTGT 57.559 45.000 1.14 0.00 42.22 3.16
5286 10675 2.488545 ACAGCGATCTCGTTCTTGTACT 59.511 45.455 1.14 0.00 42.22 2.73
5287 10676 3.688185 ACAGCGATCTCGTTCTTGTACTA 59.312 43.478 1.14 0.00 42.22 1.82
5288 10677 4.201832 ACAGCGATCTCGTTCTTGTACTAG 60.202 45.833 1.14 0.00 42.22 2.57
5299 10688 7.236474 TCGTTCTTGTACTAGTATTGTACACG 58.764 38.462 5.75 10.60 46.47 4.49
5404 10793 7.411486 ACTCGAGATATCTTCCTTCTTGAAA 57.589 36.000 21.68 0.00 31.22 2.69
5444 10833 4.082523 TCCAGGCGCGCTAGCTTT 62.083 61.111 32.29 6.99 42.32 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
504 4755 8.213679 CCATCAGATCATCCCTCTTAAGTAAAA 58.786 37.037 1.63 0.00 0.00 1.52
640 4894 6.422400 GGTCTCTTAATATCTTCTGCTTTCCG 59.578 42.308 0.00 0.00 0.00 4.30
649 4903 9.187455 GATTTCGTCAGGTCTCTTAATATCTTC 57.813 37.037 0.00 0.00 0.00 2.87
650 4904 8.919145 AGATTTCGTCAGGTCTCTTAATATCTT 58.081 33.333 0.00 0.00 0.00 2.40
718 4973 0.861837 GTGGCGAACTCTGTCTGTTG 59.138 55.000 0.00 0.00 0.00 3.33
722 4977 2.651361 CCGTGGCGAACTCTGTCT 59.349 61.111 0.00 0.00 0.00 3.41
757 5012 3.965258 TCTGTTGCATGGGCCGGT 61.965 61.111 1.90 0.00 40.13 5.28
808 5163 2.260434 GTCTGTTGCGTAGGCCGA 59.740 61.111 4.72 0.00 39.56 5.54
814 5169 1.929038 GCGAACTCTGTCTGTTGCGTA 60.929 52.381 0.00 0.00 0.00 4.42
816 5171 1.488957 GCGAACTCTGTCTGTTGCG 59.511 57.895 0.00 0.00 0.00 4.85
899 5301 2.352814 GCTTCTTCTTCTACTGCGACCA 60.353 50.000 0.00 0.00 0.00 4.02
969 5373 1.874872 GGTTGTTCGATTTGGTTCGGA 59.125 47.619 0.00 0.00 39.56 4.55
990 5402 0.529555 GTCGCTCCATGGCTTCTCTC 60.530 60.000 6.96 0.00 0.00 3.20
1008 5420 1.153549 GCCGAAGATCCGCTGAAGT 60.154 57.895 0.00 0.00 0.00 3.01
1011 5423 4.873129 GCGCCGAAGATCCGCTGA 62.873 66.667 0.00 0.00 43.95 4.26
1063 5478 3.592070 CTCGGAGGAGTCGAGCAA 58.408 61.111 0.00 0.00 45.67 3.91
1177 5592 0.896226 AACCCTAGCTTCGTGGAGAC 59.104 55.000 0.00 0.00 0.00 3.36
1200 5615 1.557832 CCTCCCTGTAATTTCCGACCA 59.442 52.381 0.00 0.00 0.00 4.02
1416 5872 1.067283 ACGACAGGAGCAACAGATCTG 60.067 52.381 21.37 21.37 0.00 2.90
1442 5898 1.001520 TCAAATCTGACGCGGGAGAAA 59.998 47.619 12.47 0.00 0.00 2.52
1472 5928 7.063426 TCAGCTTTATCAACGAGTATGAACAAG 59.937 37.037 0.00 0.00 0.00 3.16
1607 6063 2.912956 TCCATATGGCCTATCTTCCACC 59.087 50.000 17.58 0.00 34.81 4.61
1635 6091 3.242518 GCCTTACAAAAATGAACGGAGC 58.757 45.455 0.00 0.00 0.00 4.70
1755 6211 8.684655 GCAACAATATACATCAAACAATGATCG 58.315 33.333 0.00 0.00 45.91 3.69
2028 6751 8.744652 TGAAACCTTGAAATTTTCAACTAGACA 58.255 29.630 18.29 13.31 44.21 3.41
2079 6802 3.388024 GTGAGGAGTATAGTCCAATGGCA 59.612 47.826 25.40 13.39 39.34 4.92
2123 6846 7.241042 TGCAATATATCCCTAGAGTTGGTAC 57.759 40.000 0.00 0.00 0.00 3.34
2129 6852 9.944079 ACTATGTATGCAATATATCCCTAGAGT 57.056 33.333 0.00 0.00 32.57 3.24
2359 7082 5.278218 CCCATCATATCGTCTATGGAGATCG 60.278 48.000 0.00 0.00 41.20 3.69
2575 7299 0.978146 CAGCTGTAGGGCTACCACCT 60.978 60.000 5.25 0.00 41.00 4.00
2576 7300 1.522569 CAGCTGTAGGGCTACCACC 59.477 63.158 5.25 0.00 41.00 4.61
2577 7301 1.522569 CCAGCTGTAGGGCTACCAC 59.477 63.158 13.81 0.00 41.00 4.16
2578 7302 2.367202 GCCAGCTGTAGGGCTACCA 61.367 63.158 13.81 0.00 46.74 3.25
2579 7303 2.506472 GCCAGCTGTAGGGCTACC 59.494 66.667 13.81 0.00 46.74 3.18
2595 7319 8.840867 CGAAGAAATATTAAGTTTCACACAAGC 58.159 33.333 14.79 0.00 37.89 4.01
2794 7518 9.454585 TCTATTACCGACGTCTTTAACAATATG 57.545 33.333 14.70 0.00 0.00 1.78
2797 7521 8.937634 AATCTATTACCGACGTCTTTAACAAT 57.062 30.769 14.70 6.90 0.00 2.71
2798 7522 8.246180 AGAATCTATTACCGACGTCTTTAACAA 58.754 33.333 14.70 0.00 0.00 2.83
2812 7536 7.158021 AGCTATGTTGCTCAGAATCTATTACC 58.842 38.462 0.00 0.00 39.34 2.85
3332 8056 2.954318 TCCTTAGTACTCCATACACGGC 59.046 50.000 0.00 0.00 36.09 5.68
3758 9092 0.178906 TGACACTCTGGATGGGGTCA 60.179 55.000 0.00 0.00 33.31 4.02
3884 9218 8.443953 AGAATCAGCATTTTACCTGAATAGAC 57.556 34.615 0.00 0.00 41.04 2.59
4045 9382 0.829333 TGAGCAGCATCTTCTCCTCC 59.171 55.000 0.00 0.00 0.00 4.30
4063 9400 6.256321 CAGTCCATTTCTTTTTGTGAAGGTTG 59.744 38.462 0.00 0.00 0.00 3.77
4217 9590 4.427312 GCCAAAATCTAAGAACCTGCATG 58.573 43.478 0.00 0.00 0.00 4.06
4224 9597 7.728847 AAAAACATGGCCAAAATCTAAGAAC 57.271 32.000 10.96 0.00 0.00 3.01
4358 9731 6.323482 AGACATGCTCTTCTAGATGCTTCTTA 59.677 38.462 7.51 0.00 33.17 2.10
4400 9773 5.163437 GGTACCTAGGGTCTGAACTATGTTG 60.163 48.000 14.81 0.00 37.09 3.33
4730 10105 3.200593 GCGGCTGCCATCTCACTG 61.201 66.667 20.29 0.12 33.98 3.66
4754 10129 3.737266 ACATTATATTACGCCGGAACACG 59.263 43.478 5.05 0.27 43.80 4.49
4755 10130 4.609783 GCACATTATATTACGCCGGAACAC 60.610 45.833 5.05 0.00 0.00 3.32
4756 10131 3.495377 GCACATTATATTACGCCGGAACA 59.505 43.478 5.05 0.00 0.00 3.18
4757 10132 3.120442 GGCACATTATATTACGCCGGAAC 60.120 47.826 5.05 0.00 0.00 3.62
4758 10133 3.068560 GGCACATTATATTACGCCGGAA 58.931 45.455 5.05 0.00 0.00 4.30
4759 10134 2.690786 GGCACATTATATTACGCCGGA 58.309 47.619 5.05 0.00 0.00 5.14
4762 10137 2.073816 AGCGGCACATTATATTACGCC 58.926 47.619 1.45 0.00 45.86 5.68
4763 10138 2.093783 GGAGCGGCACATTATATTACGC 59.906 50.000 1.45 0.00 45.15 4.42
4764 10139 3.585862 AGGAGCGGCACATTATATTACG 58.414 45.455 1.45 0.00 0.00 3.18
4765 10140 5.350640 GGTTAGGAGCGGCACATTATATTAC 59.649 44.000 1.45 0.00 0.00 1.89
4766 10141 5.484715 GGTTAGGAGCGGCACATTATATTA 58.515 41.667 1.45 0.00 0.00 0.98
4767 10142 4.324267 GGTTAGGAGCGGCACATTATATT 58.676 43.478 1.45 0.00 0.00 1.28
4768 10143 3.307480 GGGTTAGGAGCGGCACATTATAT 60.307 47.826 1.45 0.00 0.00 0.86
4769 10144 2.038033 GGGTTAGGAGCGGCACATTATA 59.962 50.000 1.45 0.00 0.00 0.98
4770 10145 1.202770 GGGTTAGGAGCGGCACATTAT 60.203 52.381 1.45 0.00 0.00 1.28
4771 10146 0.179468 GGGTTAGGAGCGGCACATTA 59.821 55.000 1.45 0.00 0.00 1.90
4772 10147 1.077716 GGGTTAGGAGCGGCACATT 60.078 57.895 1.45 0.00 0.00 2.71
4773 10148 1.972660 GAGGGTTAGGAGCGGCACAT 61.973 60.000 1.45 0.00 0.00 3.21
4774 10149 2.606519 AGGGTTAGGAGCGGCACA 60.607 61.111 1.45 0.00 0.00 4.57
4775 10150 1.900545 AAGAGGGTTAGGAGCGGCAC 61.901 60.000 1.45 0.00 0.00 5.01
4776 10151 1.198759 AAAGAGGGTTAGGAGCGGCA 61.199 55.000 1.45 0.00 0.00 5.69
4777 10152 0.828677 TAAAGAGGGTTAGGAGCGGC 59.171 55.000 0.00 0.00 0.00 6.53
4778 10153 1.138464 GGTAAAGAGGGTTAGGAGCGG 59.862 57.143 0.00 0.00 0.00 5.52
4779 10154 1.138464 GGGTAAAGAGGGTTAGGAGCG 59.862 57.143 0.00 0.00 0.00 5.03
4780 10155 2.435069 GAGGGTAAAGAGGGTTAGGAGC 59.565 54.545 0.00 0.00 0.00 4.70
4781 10156 3.996957 AGAGGGTAAAGAGGGTTAGGAG 58.003 50.000 0.00 0.00 0.00 3.69
4782 10157 5.763239 ATAGAGGGTAAAGAGGGTTAGGA 57.237 43.478 0.00 0.00 0.00 2.94
4783 10158 5.666265 ACAATAGAGGGTAAAGAGGGTTAGG 59.334 44.000 0.00 0.00 0.00 2.69
4784 10159 6.809976 ACAATAGAGGGTAAAGAGGGTTAG 57.190 41.667 0.00 0.00 0.00 2.34
4785 10160 7.847848 ACATACAATAGAGGGTAAAGAGGGTTA 59.152 37.037 0.00 0.00 0.00 2.85
4786 10161 6.677076 ACATACAATAGAGGGTAAAGAGGGTT 59.323 38.462 0.00 0.00 0.00 4.11
4787 10162 6.210522 ACATACAATAGAGGGTAAAGAGGGT 58.789 40.000 0.00 0.00 0.00 4.34
4788 10163 6.749036 ACATACAATAGAGGGTAAAGAGGG 57.251 41.667 0.00 0.00 0.00 4.30
4789 10164 9.765795 CTAAACATACAATAGAGGGTAAAGAGG 57.234 37.037 0.00 0.00 0.00 3.69
4853 10228 4.935352 TGAAACCATGTTAAAGCAGCTT 57.065 36.364 0.21 0.21 0.00 3.74
4958 10333 6.096036 ACTTCACATGAGAGTAGAATTGTCG 58.904 40.000 0.00 0.00 0.00 4.35
4977 10352 8.367911 ACAGATGTCTATACTTCACAAACTTCA 58.632 33.333 0.00 0.00 33.32 3.02
4994 10369 9.739276 TCTTCATTAAAAATACCACAGATGTCT 57.261 29.630 0.00 0.00 0.00 3.41
5075 10450 6.372381 TCCGCTAAGGGTAAATTAGACAAAAC 59.628 38.462 0.00 0.00 41.52 2.43
5084 10459 3.290948 TGCATCCGCTAAGGGTAAATT 57.709 42.857 0.00 0.00 41.52 1.82
5085 10460 3.508845 ATGCATCCGCTAAGGGTAAAT 57.491 42.857 0.00 0.00 41.52 1.40
5094 10469 5.826601 TTGTTTTGAATATGCATCCGCTA 57.173 34.783 0.19 0.00 39.64 4.26
5095 10470 4.717233 TTGTTTTGAATATGCATCCGCT 57.283 36.364 0.19 0.00 39.64 5.52
5281 10670 7.254898 GCATACCTCGTGTACAATACTAGTACA 60.255 40.741 4.31 0.00 46.81 2.90
5282 10671 7.074502 GCATACCTCGTGTACAATACTAGTAC 58.925 42.308 4.31 0.00 41.63 2.73
5283 10672 6.205464 GGCATACCTCGTGTACAATACTAGTA 59.795 42.308 4.77 4.77 30.62 1.82
5286 10675 5.135383 AGGCATACCTCGTGTACAATACTA 58.865 41.667 0.00 0.00 46.34 1.82
5287 10676 3.958798 AGGCATACCTCGTGTACAATACT 59.041 43.478 0.00 0.00 46.34 2.12
5288 10677 4.317671 AGGCATACCTCGTGTACAATAC 57.682 45.455 0.00 0.00 46.34 1.89


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

AutoCloner maintained by Alex Coulton.