Multiple sequence alignment - TraesCS4A01G059300

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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 TraesCS4A01G059300 chr4A 100.000 5527 0 0 1 5527 55399877 55394351 0.000000e+00 10207.0
1 TraesCS4A01G059300 chr4A 92.157 51 4 0 1 51 443028476 443028426 7.680000e-09 73.1
2 TraesCS4A01G059300 chr4A 82.432 74 5 8 5454 5523 608607692 608607623 2.150000e-04 58.4
3 TraesCS4A01G059300 chr4B 91.984 2807 171 32 2716 5501 489673448 489670675 0.000000e+00 3888.0
4 TraesCS4A01G059300 chr4B 92.651 1075 64 10 1621 2682 489674798 489673726 0.000000e+00 1533.0
5 TraesCS4A01G059300 chr4B 96.316 570 18 3 1075 1643 489675373 489674806 0.000000e+00 933.0
6 TraesCS4A01G059300 chr4B 88.889 558 50 3 30 587 490646067 490645522 0.000000e+00 676.0
7 TraesCS4A01G059300 chr4B 91.420 338 24 5 449 785 489679867 489679534 5.050000e-125 459.0
8 TraesCS4A01G059300 chr4B 95.789 190 7 1 860 1049 489675942 489675754 6.960000e-79 305.0
9 TraesCS4A01G059300 chr4B 97.196 107 3 0 2716 2822 489673635 489673529 1.220000e-41 182.0
10 TraesCS4A01G059300 chr4B 97.297 37 1 0 2754 2790 489673730 489673694 4.620000e-06 63.9
11 TraesCS4A01G059300 chr4B 97.143 35 1 0 5312 5346 276714280 276714246 5.980000e-05 60.2
12 TraesCS4A01G059300 chr4B 94.595 37 0 1 2764 2798 489673652 489673688 7.730000e-04 56.5
13 TraesCS4A01G059300 chr4D 93.685 1916 86 10 2094 3985 397693898 397691994 0.000000e+00 2835.0
14 TraesCS4A01G059300 chr4D 90.634 1452 89 18 4064 5501 397691996 397690578 0.000000e+00 1884.0
15 TraesCS4A01G059300 chr4D 93.392 1256 61 7 782 2020 397696130 397694880 0.000000e+00 1840.0
16 TraesCS4A01G059300 chr4D 95.553 787 34 1 1 787 397698072 397697287 0.000000e+00 1258.0
17 TraesCS4A01G059300 chr4D 93.382 544 36 0 49 592 398268961 398268418 0.000000e+00 806.0
18 TraesCS4A01G059300 chr4D 82.906 117 10 9 5362 5475 506288431 506288540 4.560000e-16 97.1
19 TraesCS4A01G059300 chr4D 97.368 38 0 1 5451 5487 264315411 264315448 4.620000e-06 63.9
20 TraesCS4A01G059300 chr3A 87.719 570 64 5 25 592 645600579 645601144 0.000000e+00 660.0
21 TraesCS4A01G059300 chr3A 89.796 49 5 0 1 49 704404073 704404025 4.620000e-06 63.9
22 TraesCS4A01G059300 chr7D 86.916 428 45 11 12 434 229240322 229239901 2.330000e-128 470.0
23 TraesCS4A01G059300 chr7D 83.774 265 32 9 1677 1938 13688438 13688694 1.990000e-59 241.0
24 TraesCS4A01G059300 chr7D 83.240 179 29 1 1761 1938 13692328 13692506 4.430000e-36 163.0
25 TraesCS4A01G059300 chr7D 88.776 98 11 0 1761 1858 13693580 13693677 2.700000e-23 121.0
26 TraesCS4A01G059300 chr2D 86.588 425 49 8 12 432 318219919 318219499 3.900000e-126 462.0
27 TraesCS4A01G059300 chr1D 85.301 449 57 9 8 452 356529064 356529507 6.530000e-124 455.0
28 TraesCS4A01G059300 chr7B 84.532 459 58 13 1 453 199939484 199939033 5.080000e-120 442.0
29 TraesCS4A01G059300 chr7B 100.000 33 0 0 5311 5343 741898879 741898911 1.660000e-05 62.1
30 TraesCS4A01G059300 chr5B 84.798 421 56 8 36 452 372079115 372078699 3.080000e-112 416.0
31 TraesCS4A01G059300 chr5B 88.608 79 8 1 5372 5449 644867358 644867280 1.640000e-15 95.3
32 TraesCS4A01G059300 chr5D 81.369 263 33 7 1677 1938 475900193 475900440 3.380000e-47 200.0
33 TraesCS4A01G059300 chr5D 92.000 75 5 1 5373 5446 2134739 2134813 2.720000e-18 104.0
34 TraesCS4A01G059300 chr5D 97.297 37 1 0 5312 5348 256747534 256747570 4.620000e-06 63.9
35 TraesCS4A01G059300 chr5D 90.909 44 1 3 5447 5489 134916486 134916527 7.730000e-04 56.5
36 TraesCS4A01G059300 chrUn 89.535 86 6 3 5366 5449 93239452 93239368 7.570000e-19 106.0
37 TraesCS4A01G059300 chr1A 88.889 81 8 1 5366 5446 554783325 554783404 1.270000e-16 99.0
38 TraesCS4A01G059300 chr1A 92.857 42 0 3 5450 5489 557490399 557490439 2.150000e-04 58.4
39 TraesCS4A01G059300 chr7A 86.905 84 10 1 5367 5450 515173072 515173154 5.900000e-15 93.5
40 TraesCS4A01G059300 chr7A 84.783 92 10 4 5366 5455 239188844 239188933 7.630000e-14 89.8
41 TraesCS4A01G059300 chr7A 91.111 45 2 2 5444 5486 15534938 15534982 5.980000e-05 60.2
42 TraesCS4A01G059300 chr3D 89.333 75 4 4 5366 5438 156891030 156891102 2.120000e-14 91.6
43 TraesCS4A01G059300 chr3D 97.222 36 1 0 5312 5347 126384918 126384953 1.660000e-05 62.1
44 TraesCS4A01G059300 chr2A 80.303 132 17 4 1 131 432371785 432371662 2.120000e-14 91.6
45 TraesCS4A01G059300 chr6A 97.297 37 1 0 5311 5347 363523507 363523471 4.620000e-06 63.9
46 TraesCS4A01G059300 chr6D 95.000 40 0 2 5451 5489 128910377 128910415 1.660000e-05 62.1
47 TraesCS4A01G059300 chr6D 93.023 43 1 2 5312 5354 296346066 296346026 1.660000e-05 62.1
48 TraesCS4A01G059300 chr3B 97.222 36 1 0 5311 5346 42678210 42678175 1.660000e-05 62.1
49 TraesCS4A01G059300 chr2B 92.857 42 0 3 5450 5489 87922792 87922752 2.150000e-04 58.4
50 TraesCS4A01G059300 chr6B 94.444 36 1 1 5313 5347 64689981 64690016 3.000000e-03 54.7


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 TraesCS4A01G059300 chr4A 55394351 55399877 5526 True 10207.000000 10207 100.000000 1 5527 1 chr4A.!!$R1 5526
1 TraesCS4A01G059300 chr4B 489670675 489679867 9192 True 1051.985714 3888 94.664714 449 5501 7 chr4B.!!$R3 5052
2 TraesCS4A01G059300 chr4B 490645522 490646067 545 True 676.000000 676 88.889000 30 587 1 chr4B.!!$R2 557
3 TraesCS4A01G059300 chr4D 397690578 397698072 7494 True 1954.250000 2835 93.316000 1 5501 4 chr4D.!!$R2 5500
4 TraesCS4A01G059300 chr4D 398268418 398268961 543 True 806.000000 806 93.382000 49 592 1 chr4D.!!$R1 543
5 TraesCS4A01G059300 chr3A 645600579 645601144 565 False 660.000000 660 87.719000 25 592 1 chr3A.!!$F1 567

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
500 503 1.203287 GCCTTCTTGTTTCCTCCATGC 59.797 52.381 0.00 0.00 0.00 4.06 F
970 5181 1.567357 AGGTCTGCTCCTCTTTCCTC 58.433 55.000 0.00 0.00 31.32 3.71 F
1541 6108 2.199652 TGGAGTTTGCTTTGCGGGG 61.200 57.895 0.00 0.00 0.00 5.73 F
2666 8194 1.425448 AGCAGTTAGGCCAAAGGAGTT 59.575 47.619 5.01 0.00 0.00 3.01 F
3600 9376 1.269448 GAAAAATGGAACCTCTGCGCA 59.731 47.619 10.98 10.98 0.00 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1330 5896 0.177836 GCTCCTCTGGCTTCTCCTTC 59.822 60.000 0.0 0.0 35.26 3.46 R
2085 7603 1.672881 GCATCTGCCTACACCATTGAC 59.327 52.381 0.0 0.0 34.31 3.18 R
2865 8639 2.276201 GTGCCCCACAAACACTTTTTC 58.724 47.619 0.0 0.0 34.08 2.29 R
3613 9389 0.038892 GTCGTACAGGAAGCGGACAA 60.039 55.000 0.0 0.0 0.00 3.18 R
5145 10933 0.028902 GACCAAACACACGCAGGTTC 59.971 55.000 0.0 0.0 31.57 3.62 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
185 186 6.928348 TTGTGGAGGTAAAGATCTACTTCA 57.072 37.500 9.29 2.80 37.93 3.02
332 335 6.672218 TCCCTAGGTTTACATGAGATTTCAGA 59.328 38.462 8.29 0.00 36.61 3.27
347 350 6.925211 AGATTTCAGATCGTACTCTCAACAA 58.075 36.000 0.00 0.00 0.00 2.83
348 351 7.551585 AGATTTCAGATCGTACTCTCAACAAT 58.448 34.615 0.00 0.00 0.00 2.71
500 503 1.203287 GCCTTCTTGTTTCCTCCATGC 59.797 52.381 0.00 0.00 0.00 4.06
595 599 3.050089 GGAACATCCCCAACAGCAA 57.950 52.632 0.00 0.00 0.00 3.91
638 642 3.624777 ACGATGGCTTCTTTGATTGGAT 58.375 40.909 0.00 0.00 0.00 3.41
655 659 6.974048 TGATTGGATGATTCTTAAAATGCACG 59.026 34.615 0.00 0.00 0.00 5.34
691 695 5.252969 TGAATTGCCATGTCTATTTGAGC 57.747 39.130 0.00 0.00 0.00 4.26
703 707 6.349300 TGTCTATTTGAGCCCTATGAGTTTC 58.651 40.000 0.00 0.00 0.00 2.78
731 735 4.202101 TGCACGGTTGAATCACAAAGAAAT 60.202 37.500 0.00 0.00 40.36 2.17
809 1976 2.517875 CTGCTACATGGGCTGGGC 60.518 66.667 12.78 1.86 0.00 5.36
931 5139 3.570638 GCGCACGCTGCTGATGAT 61.571 61.111 7.96 0.00 42.25 2.45
953 5161 1.897560 AAGGCAAGAAAGACGGAAGG 58.102 50.000 0.00 0.00 0.00 3.46
970 5181 1.567357 AGGTCTGCTCCTCTTTCCTC 58.433 55.000 0.00 0.00 31.32 3.71
1081 5647 2.890945 CAAAGACCCCCAATCTCGTTTT 59.109 45.455 0.00 0.00 0.00 2.43
1096 5662 5.617252 TCTCGTTTTTCTAACCTGGATTGT 58.383 37.500 0.00 0.00 0.00 2.71
1247 5813 2.485657 GGGGATGGTTAACTCTAGCAGC 60.486 54.545 5.42 0.00 0.00 5.25
1264 5830 2.288030 GCAGCTTGCTTGTGATTTGTCT 60.288 45.455 0.00 0.00 40.96 3.41
1330 5896 3.131933 ACATTGACGAGAAGGAGATCAGG 59.868 47.826 0.00 0.00 0.00 3.86
1541 6108 2.199652 TGGAGTTTGCTTTGCGGGG 61.200 57.895 0.00 0.00 0.00 5.73
1605 6172 3.243201 GCAAGCTGGCACATTATAGGTTC 60.243 47.826 8.66 0.00 38.20 3.62
1606 6173 3.931907 AGCTGGCACATTATAGGTTCA 57.068 42.857 0.00 0.00 38.20 3.18
1607 6174 3.813443 AGCTGGCACATTATAGGTTCAG 58.187 45.455 0.00 0.00 38.20 3.02
1608 6175 3.200825 AGCTGGCACATTATAGGTTCAGT 59.799 43.478 0.00 0.00 38.20 3.41
1611 6178 5.105756 GCTGGCACATTATAGGTTCAGTTTT 60.106 40.000 0.00 0.00 38.20 2.43
1612 6179 6.266168 TGGCACATTATAGGTTCAGTTTTG 57.734 37.500 0.00 0.00 0.00 2.44
1613 6180 5.772672 TGGCACATTATAGGTTCAGTTTTGT 59.227 36.000 0.00 0.00 0.00 2.83
1614 6181 6.072175 TGGCACATTATAGGTTCAGTTTTGTC 60.072 38.462 0.00 0.00 0.00 3.18
1637 6236 2.225255 TCTTTGTGTGTGTGTGTGTGTG 59.775 45.455 0.00 0.00 0.00 3.82
1746 6346 9.567776 TGTCAATTATCTCTAAGTTTGACCAAA 57.432 29.630 10.15 0.00 36.69 3.28
1879 6479 9.967346 TTTCTTCTATATATCTGGTCAAACTCG 57.033 33.333 0.00 0.00 0.00 4.18
1884 6484 9.090103 TCTATATATCTGGTCAAACTCGGAAAT 57.910 33.333 0.00 0.00 0.00 2.17
1889 6489 7.703058 ATCTGGTCAAACTCGGAAATAATTT 57.297 32.000 0.00 0.00 0.00 1.82
1933 6533 2.242196 CCATGTATTTGGGGACAGAGGT 59.758 50.000 0.00 0.00 44.54 3.85
2065 7583 8.470805 TGTAGTTCTGATTTTGCTTTGGTTTTA 58.529 29.630 0.00 0.00 0.00 1.52
2085 7603 8.122952 GGTTTTAAAGTGTGCTACTATGCTATG 58.877 37.037 0.00 0.00 39.18 2.23
2092 7610 5.178252 GTGTGCTACTATGCTATGTCAATGG 59.822 44.000 0.00 0.00 0.00 3.16
2172 7690 6.304624 TGTTGACTCTCAAGAGACTACCTTA 58.695 40.000 13.83 0.00 44.74 2.69
2196 7714 2.099141 TCACTGCTGACCAAGTATGC 57.901 50.000 0.00 0.00 0.00 3.14
2221 7739 6.636454 TCTTACAACATCCCCTCTAACAAT 57.364 37.500 0.00 0.00 0.00 2.71
2454 7974 2.895404 CCTGGAAATATGGCCCAATCTG 59.105 50.000 0.00 0.00 0.00 2.90
2456 7976 3.962718 CTGGAAATATGGCCCAATCTGTT 59.037 43.478 0.00 0.00 0.00 3.16
2666 8194 1.425448 AGCAGTTAGGCCAAAGGAGTT 59.575 47.619 5.01 0.00 0.00 3.01
2709 8238 3.515104 CCAAGAGGCACAAATTGGGTATT 59.485 43.478 0.00 0.00 38.82 1.89
2758 8531 2.500229 TCATGTTTCGGTCTTTGGGTC 58.500 47.619 0.00 0.00 0.00 4.46
2865 8639 8.469125 GTTACTTTTGTTAAAATTGCTGAGACG 58.531 33.333 0.00 0.00 0.00 4.18
2868 8642 7.757624 ACTTTTGTTAAAATTGCTGAGACGAAA 59.242 29.630 0.00 0.00 0.00 3.46
2869 8643 8.467402 TTTTGTTAAAATTGCTGAGACGAAAA 57.533 26.923 0.00 0.00 0.00 2.29
2879 8653 3.786048 GCTGAGACGAAAAAGTGTTTGTG 59.214 43.478 0.00 0.00 0.00 3.33
3146 8922 7.749126 CGTAAATTCATCCAAGGTTTGTCTTAC 59.251 37.037 0.00 0.00 0.00 2.34
3184 8960 4.278170 CGGGGCATGAGCTCAAATTATTTA 59.722 41.667 22.50 0.00 45.55 1.40
3291 9067 4.074627 TGTTACAAATGTGAAGACCGGA 57.925 40.909 9.46 0.00 0.00 5.14
3327 9103 9.579932 GAAGGATGGGATAAATCTGAAGTAATT 57.420 33.333 0.00 0.00 0.00 1.40
3376 9152 6.053005 TGAGAAATGAGTACCAAAGTCGTTT 58.947 36.000 0.78 0.78 45.44 3.60
3586 9362 1.541588 GAGCACGGCCTTCTGAAAAAT 59.458 47.619 0.00 0.00 0.00 1.82
3600 9376 1.269448 GAAAAATGGAACCTCTGCGCA 59.731 47.619 10.98 10.98 0.00 6.09
3613 9389 1.675483 TCTGCGCACATGACACTTTTT 59.325 42.857 5.66 0.00 0.00 1.94
3701 9477 0.107703 ATGTGCACCATCGTACAGGG 60.108 55.000 15.69 0.00 34.89 4.45
3718 9494 2.101582 CAGGGATCGGACGAAGAAGATT 59.898 50.000 0.00 0.00 0.00 2.40
3821 9597 8.593945 TTTCATAAAGCAGAAACCCATCTTAT 57.406 30.769 0.00 0.00 0.00 1.73
3891 9667 8.548025 TCATGGTTTAGTTCAGAATCCTTATGA 58.452 33.333 0.00 0.00 0.00 2.15
3907 9683 6.662755 TCCTTATGAGATTTTAGGTGCATGT 58.337 36.000 0.00 0.00 0.00 3.21
3979 9755 9.768662 GGCACAAAATATCAAATGAATCCTAAT 57.231 29.630 0.00 0.00 0.00 1.73
4030 9806 3.563808 TGTTTCCATCAGTTTGAGTTCCG 59.436 43.478 0.00 0.00 0.00 4.30
4031 9807 1.808411 TCCATCAGTTTGAGTTCCGC 58.192 50.000 0.00 0.00 0.00 5.54
4060 9836 1.068588 GTTTTGGCCTCACACTTTCCC 59.931 52.381 3.32 0.00 0.00 3.97
4152 9930 7.494298 AGTCCGAAAAACAAGCATTAATTTTGT 59.506 29.630 8.58 8.58 36.66 2.83
4243 10028 4.334481 AGTTACACCCACTGAAACTTTTCG 59.666 41.667 0.00 0.00 40.01 3.46
4374 10159 5.026121 TCCTGACATGTTCTCATTCTAGGT 58.974 41.667 0.00 0.00 31.15 3.08
4634 10421 3.010472 TCATCCTTTCTGGCAAATGGAGA 59.990 43.478 16.22 12.55 36.31 3.71
4635 10422 3.744940 TCCTTTCTGGCAAATGGAGAT 57.255 42.857 10.69 0.00 35.26 2.75
4636 10423 4.051661 TCCTTTCTGGCAAATGGAGATT 57.948 40.909 10.69 0.00 35.26 2.40
4637 10424 3.765511 TCCTTTCTGGCAAATGGAGATTG 59.234 43.478 10.69 0.00 35.26 2.67
4638 10425 3.118884 CCTTTCTGGCAAATGGAGATTGG 60.119 47.826 7.91 0.00 0.00 3.16
4639 10426 3.454719 TTCTGGCAAATGGAGATTGGA 57.545 42.857 0.00 0.00 0.00 3.53
4640 10427 3.008835 TCTGGCAAATGGAGATTGGAG 57.991 47.619 0.00 0.00 0.00 3.86
4646 10433 3.019564 CAAATGGAGATTGGAGTGGACC 58.980 50.000 0.00 0.00 0.00 4.46
4656 10443 1.273838 TGGAGTGGACCCTAATCAGCT 60.274 52.381 0.00 0.00 0.00 4.24
4658 10445 2.420687 GGAGTGGACCCTAATCAGCTTG 60.421 54.545 0.00 0.00 0.00 4.01
4683 10470 4.160814 TCAGCCTCGCTATACCAACTTTAA 59.839 41.667 0.00 0.00 36.40 1.52
4701 10488 9.807649 CAACTTTAATAGGCTGAATTTTAGCAT 57.192 29.630 14.29 10.11 42.88 3.79
4774 10562 2.930826 TTGGAGACCTTTCTGTGACC 57.069 50.000 0.00 0.00 29.47 4.02
4815 10603 6.040166 GGCTTCATTCTTCCATGTGATGTTAT 59.960 38.462 0.00 0.00 0.00 1.89
4840 10628 4.751060 GTCTGACGGACCAAACATATGTA 58.249 43.478 9.21 0.00 38.93 2.29
4873 10661 1.346062 ACCGCATGCTATCAGGAGAT 58.654 50.000 17.13 0.00 38.29 2.75
4904 10692 3.179048 GCGAATTGTTTTGGGCTATGAC 58.821 45.455 0.00 0.00 0.00 3.06
5011 10799 1.760192 ATCTTGGTTGATGGAGCAGC 58.240 50.000 0.00 0.00 0.00 5.25
5099 10887 0.107703 CAGCGGTCAATCCTGGCTTA 60.108 55.000 0.00 0.00 32.05 3.09
5111 10899 2.979678 TCCTGGCTTATGGGGTTCTATC 59.020 50.000 0.00 0.00 0.00 2.08
5145 10933 8.246871 TCTATGAATAGTCCATGCTAATCTTCG 58.753 37.037 0.00 0.00 0.00 3.79
5180 10968 3.208747 TGGTCTGGTCTTGTTCCTTTC 57.791 47.619 0.00 0.00 0.00 2.62
5221 11013 0.253044 TGCATCTGGTAGAGGTTGCC 59.747 55.000 0.00 0.00 32.94 4.52
5281 11073 2.128035 CAGGTTGTTGAGTCTGACGAC 58.872 52.381 1.52 3.91 40.54 4.34
5291 11083 4.986622 TGAGTCTGACGACATTACTGATG 58.013 43.478 1.52 0.00 42.73 3.07
5300 11111 5.050490 ACGACATTACTGATGATAAGTGGC 58.950 41.667 0.00 0.00 39.15 5.01
5307 11118 4.323417 ACTGATGATAAGTGGCACGAAAA 58.677 39.130 12.71 0.00 0.00 2.29
5309 11120 5.163723 ACTGATGATAAGTGGCACGAAAATG 60.164 40.000 12.71 1.45 0.00 2.32
5329 11140 8.947055 AAAATGCAAAGTTGAGACACTTATTT 57.053 26.923 0.00 0.00 35.87 1.40
5335 11146 7.649306 GCAAAGTTGAGACACTTATTTTGTGAT 59.351 33.333 0.00 0.00 35.87 3.06
5343 11154 5.640147 ACACTTATTTTGTGATGGAGGGAA 58.360 37.500 0.00 0.00 38.65 3.97
5372 11183 9.271921 TCTAGTATCGTAGTAATACCCTGGATA 57.728 37.037 0.00 0.00 31.26 2.59
5420 11232 6.025749 TGTACTACCTTGACAGTTGATGAG 57.974 41.667 0.00 0.00 0.00 2.90
5425 11237 5.140747 ACCTTGACAGTTGATGAGTAGAC 57.859 43.478 0.00 0.00 0.00 2.59
5426 11238 4.835615 ACCTTGACAGTTGATGAGTAGACT 59.164 41.667 0.00 0.00 0.00 3.24
5448 11260 5.371115 TGAAAGTTTTCCCGCAGAAATAG 57.629 39.130 2.41 0.00 43.93 1.73
5454 11266 7.549615 AGTTTTCCCGCAGAAATAGTAATAC 57.450 36.000 0.15 0.00 43.93 1.89
5484 11296 3.938963 TCCGATCCAAAATAAGTGTCTGC 59.061 43.478 0.00 0.00 0.00 4.26
5486 11298 4.336433 CCGATCCAAAATAAGTGTCTGCAT 59.664 41.667 0.00 0.00 0.00 3.96
5488 11300 6.324819 CGATCCAAAATAAGTGTCTGCATTT 58.675 36.000 0.00 0.00 0.00 2.32
5521 11333 8.554490 AGTGTATATTTTGATACAGAGGGAGT 57.446 34.615 0.00 0.00 41.76 3.85
5522 11334 9.656323 AGTGTATATTTTGATACAGAGGGAGTA 57.344 33.333 0.00 0.00 41.76 2.59
5523 11335 9.694137 GTGTATATTTTGATACAGAGGGAGTAC 57.306 37.037 0.00 0.00 41.76 2.73
5524 11336 9.656323 TGTATATTTTGATACAGAGGGAGTACT 57.344 33.333 0.00 0.00 37.38 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 4.947147 GACAGTTGGCGCCCACCA 62.947 66.667 25.83 3.07 38.16 4.17
130 131 0.898326 CCTGGGTAAACTTGTGCCCC 60.898 60.000 0.00 0.00 40.36 5.80
133 134 1.265905 CGAACCTGGGTAAACTTGTGC 59.734 52.381 0.00 0.00 0.00 4.57
177 178 7.718314 AGCAATATCAATCAAGCATGAAGTAGA 59.282 33.333 0.00 0.00 39.49 2.59
185 186 5.382616 TCTCCAGCAATATCAATCAAGCAT 58.617 37.500 0.00 0.00 0.00 3.79
332 335 5.860941 AGGATCATTGTTGAGAGTACGAT 57.139 39.130 0.00 0.00 34.73 3.73
592 596 9.937175 GTTTATAGAGAAATTCATGTAGGTTGC 57.063 33.333 0.00 0.00 0.00 4.17
655 659 9.369904 ACATGGCAATTCAATCTTGTATTTTAC 57.630 29.630 0.00 0.00 0.00 2.01
691 695 4.414852 CGTGCAAATTGAAACTCATAGGG 58.585 43.478 0.00 0.00 0.00 3.53
703 707 3.379240 TGTGATTCAACCGTGCAAATTG 58.621 40.909 0.00 0.00 0.00 2.32
731 735 9.713684 ATCCACCCAAATCTCTTGAAAATAATA 57.286 29.630 0.00 0.00 0.00 0.98
769 773 3.938963 CGGGCACTGTACTGTATTTCATT 59.061 43.478 4.96 0.00 0.00 2.57
830 1997 1.300233 GCGTCCAATAGGAGAGCGG 60.300 63.158 0.00 0.00 46.92 5.52
831 1998 0.596083 CTGCGTCCAATAGGAGAGCG 60.596 60.000 0.00 0.00 46.92 5.03
832 1999 0.878086 GCTGCGTCCAATAGGAGAGC 60.878 60.000 0.00 0.00 46.92 4.09
836 5032 1.437573 CTCGCTGCGTCCAATAGGA 59.562 57.895 22.48 0.00 43.21 2.94
931 5139 3.818773 CCTTCCGTCTTTCTTGCCTTTAA 59.181 43.478 0.00 0.00 0.00 1.52
953 5161 0.174617 CCGAGGAAAGAGGAGCAGAC 59.825 60.000 0.00 0.00 0.00 3.51
970 5181 0.397187 TCCCTCTCTCTCCGATACCG 59.603 60.000 0.00 0.00 0.00 4.02
1081 5647 3.820467 CACAAGCACAATCCAGGTTAGAA 59.180 43.478 0.00 0.00 0.00 2.10
1096 5662 0.805322 CCAAAGCAAACGCACAAGCA 60.805 50.000 0.00 0.00 42.27 3.91
1247 5813 6.501781 AGAAAGAAGACAAATCACAAGCAAG 58.498 36.000 0.00 0.00 0.00 4.01
1264 5830 8.630037 AGCGGAGAAAAATAAGAAAAGAAAGAA 58.370 29.630 0.00 0.00 0.00 2.52
1330 5896 0.177836 GCTCCTCTGGCTTCTCCTTC 59.822 60.000 0.00 0.00 35.26 3.46
1605 6172 5.343058 CACACACACAAAGAAGACAAAACTG 59.657 40.000 0.00 0.00 0.00 3.16
1606 6173 5.009610 ACACACACACAAAGAAGACAAAACT 59.990 36.000 0.00 0.00 0.00 2.66
1607 6174 5.116983 CACACACACACAAAGAAGACAAAAC 59.883 40.000 0.00 0.00 0.00 2.43
1608 6175 5.218885 CACACACACACAAAGAAGACAAAA 58.781 37.500 0.00 0.00 0.00 2.44
1611 6178 3.188254 CACACACACACACAAAGAAGACA 59.812 43.478 0.00 0.00 0.00 3.41
1612 6179 3.188460 ACACACACACACACAAAGAAGAC 59.812 43.478 0.00 0.00 0.00 3.01
1613 6180 3.188254 CACACACACACACACAAAGAAGA 59.812 43.478 0.00 0.00 0.00 2.87
1614 6181 3.058293 ACACACACACACACACAAAGAAG 60.058 43.478 0.00 0.00 0.00 2.85
1687 6286 7.707648 TGAATTATATGCCATCTATTTGGGGA 58.292 34.615 0.00 0.00 37.24 4.81
1720 6320 9.567776 TTTGGTCAAACTTAGAGATAATTGACA 57.432 29.630 15.67 2.93 45.11 3.58
1730 6330 9.577110 TGTATATACGTTTGGTCAAACTTAGAG 57.423 33.333 20.01 9.75 46.21 2.43
1867 6467 8.040716 AGTAAATTATTTCCGAGTTTGACCAG 57.959 34.615 0.00 0.00 0.00 4.00
1889 6489 8.815565 TGGCATATAAATCCAGTGAAAAAGTA 57.184 30.769 0.00 0.00 0.00 2.24
1933 6533 4.584638 TCCCTGTAAACGGGTAGTACTA 57.415 45.455 7.20 0.00 42.56 1.82
1949 6549 7.587037 TCCAAGAAAATAGCATTAATCCCTG 57.413 36.000 0.00 0.00 0.00 4.45
2043 6643 8.664798 ACTTTAAAACCAAAGCAAAATCAGAAC 58.335 29.630 0.00 0.00 38.79 3.01
2065 7583 5.977635 TGACATAGCATAGTAGCACACTTT 58.022 37.500 0.00 0.00 38.80 2.66
2085 7603 1.672881 GCATCTGCCTACACCATTGAC 59.327 52.381 0.00 0.00 34.31 3.18
2092 7610 4.136796 TCCAATATTGCATCTGCCTACAC 58.863 43.478 10.11 0.00 41.18 2.90
2196 7714 5.989477 TGTTAGAGGGGATGTTGTAAGATG 58.011 41.667 0.00 0.00 0.00 2.90
2221 7739 5.104982 AGCAAAAATCACTCCACAAAAAGGA 60.105 36.000 0.00 0.00 0.00 3.36
2258 7776 5.380900 TCCACATCACCACATGAAACTAAA 58.619 37.500 0.00 0.00 41.93 1.85
2433 7953 2.895404 CAGATTGGGCCATATTTCCAGG 59.105 50.000 7.26 0.00 31.59 4.45
2540 8068 2.746362 GAGCACCCTCTCAACATTCAAG 59.254 50.000 0.00 0.00 35.16 3.02
2666 8194 3.498481 GGCTTGGACCCAGATATTATGCA 60.498 47.826 0.00 0.00 0.00 3.96
2746 8519 2.543777 TCTTTCAGACCCAAAGACCG 57.456 50.000 0.00 0.00 35.40 4.79
2860 8634 3.488553 CCCCACAAACACTTTTTCGTCTC 60.489 47.826 0.00 0.00 0.00 3.36
2865 8639 2.276201 GTGCCCCACAAACACTTTTTC 58.724 47.619 0.00 0.00 34.08 2.29
2868 8642 2.983512 TGTGCCCCACAAACACTTT 58.016 47.368 0.00 0.00 41.69 2.66
2869 8643 4.774820 TGTGCCCCACAAACACTT 57.225 50.000 0.00 0.00 41.69 3.16
2879 8653 2.363306 TGGATGTCATAATGTGCCCC 57.637 50.000 0.00 0.00 0.00 5.80
2908 8682 8.012151 CATTCCACTATGAATGTTATCGAGAC 57.988 38.462 5.76 0.00 44.20 3.36
3164 8940 8.355169 TGATCTTAAATAATTTGAGCTCATGCC 58.645 33.333 19.04 0.00 40.80 4.40
3184 8960 7.687941 ACGGACAAGTCAAATAAATGATCTT 57.312 32.000 2.29 0.00 0.00 2.40
3194 8970 4.641094 TGTGGTTAAACGGACAAGTCAAAT 59.359 37.500 2.29 0.00 0.00 2.32
3197 8973 3.263489 TGTGGTTAAACGGACAAGTCA 57.737 42.857 2.29 0.00 0.00 3.41
3291 9067 3.508952 TCCCATCCTTCCCTTCTAGTT 57.491 47.619 0.00 0.00 0.00 2.24
3376 9152 9.671279 AAATCAATACTGATGTCTATGTGAACA 57.329 29.630 0.00 0.00 41.66 3.18
3430 9206 7.454260 AAGACCAAAATTCACTGATTAGGTC 57.546 36.000 0.00 0.00 40.74 3.85
3440 9216 8.822652 AATCTGAATCAAAGACCAAAATTCAC 57.177 30.769 0.00 0.00 33.89 3.18
3473 9249 5.819379 AGCATTACACCAGATCATGTTACTG 59.181 40.000 0.00 1.38 0.00 2.74
3586 9362 1.672030 CATGTGCGCAGAGGTTCCA 60.672 57.895 12.22 3.03 0.00 3.53
3613 9389 0.038892 GTCGTACAGGAAGCGGACAA 60.039 55.000 0.00 0.00 0.00 3.18
3620 9396 2.527100 GATCGGTTGTCGTACAGGAAG 58.473 52.381 0.00 0.00 40.32 3.46
3666 9442 2.095059 GCACATCAAACCATCCACACTC 60.095 50.000 0.00 0.00 0.00 3.51
3701 9477 4.149046 GCATACAATCTTCTTCGTCCGATC 59.851 45.833 0.00 0.00 0.00 3.69
3718 9494 4.037923 TCAGAGAACGCTGATATGCATACA 59.962 41.667 8.99 8.48 39.84 2.29
3935 9711 5.352284 TGTGCCAATGAAACGTTAAACATT 58.648 33.333 16.76 16.76 34.01 2.71
3979 9755 9.399797 GGATCATAACTGGATTATGCATATTCA 57.600 33.333 23.27 14.17 46.81 2.57
4030 9806 1.661509 GGCCAAAACTCTGCAACGC 60.662 57.895 0.00 0.00 0.00 4.84
4031 9807 0.040067 GAGGCCAAAACTCTGCAACG 60.040 55.000 5.01 0.00 32.28 4.10
4060 9836 3.480470 CCTGCACAGGGACAATTATAGG 58.520 50.000 8.93 0.00 44.87 2.57
4243 10028 5.412594 TCCTCAATCTGAAATACACACAAGC 59.587 40.000 0.00 0.00 0.00 4.01
4395 10180 6.918626 TGTTTGACTGTTTCATTTGTCTCAA 58.081 32.000 0.00 0.00 32.84 3.02
4538 10323 1.375908 CGCCAGCCAGCTTAGTTCA 60.376 57.895 0.00 0.00 0.00 3.18
4634 10421 2.173569 GCTGATTAGGGTCCACTCCAAT 59.826 50.000 0.00 0.00 0.00 3.16
4635 10422 1.559682 GCTGATTAGGGTCCACTCCAA 59.440 52.381 0.00 0.00 0.00 3.53
4636 10423 1.204146 GCTGATTAGGGTCCACTCCA 58.796 55.000 0.00 0.00 0.00 3.86
4637 10424 1.501582 AGCTGATTAGGGTCCACTCC 58.498 55.000 0.00 0.00 0.00 3.85
4638 10425 2.420687 CCAAGCTGATTAGGGTCCACTC 60.421 54.545 0.00 0.00 0.00 3.51
4639 10426 1.561542 CCAAGCTGATTAGGGTCCACT 59.438 52.381 0.00 0.00 0.00 4.00
4640 10427 1.282157 ACCAAGCTGATTAGGGTCCAC 59.718 52.381 0.00 0.00 0.00 4.02
4656 10443 0.750850 GGTATAGCGAGGCTGACCAA 59.249 55.000 14.88 0.00 42.09 3.67
4658 10445 0.750850 TTGGTATAGCGAGGCTGACC 59.249 55.000 13.56 13.56 42.52 4.02
4683 10470 6.830324 TCAGTGAATGCTAAAATTCAGCCTAT 59.170 34.615 8.96 0.00 44.96 2.57
4701 10488 3.754965 CCACCAAGAGGAATTCAGTGAA 58.245 45.455 8.27 8.27 38.69 3.18
4702 10489 2.553028 GCCACCAAGAGGAATTCAGTGA 60.553 50.000 7.93 0.00 38.69 3.41
4774 10562 1.153784 GCCCATTGATGCCGTGTTG 60.154 57.895 0.00 0.00 0.00 3.33
4780 10568 2.037144 AGAATGAAGCCCATTGATGCC 58.963 47.619 6.66 0.00 45.00 4.40
4840 10628 0.885879 TGCGGTAGAACAGATGACGT 59.114 50.000 0.00 0.00 0.00 4.34
4873 10661 1.169661 AACAATTCGCAACCCGCTGA 61.170 50.000 0.00 0.00 39.08 4.26
4904 10692 9.225436 GCCTATCCTCCTTTTCAGAATATAAAG 57.775 37.037 0.00 0.00 0.00 1.85
4963 10751 4.577677 TGCTTGGTGCGAAGGCCA 62.578 61.111 5.01 0.00 46.63 5.36
4966 10754 0.798776 CTAGTTGCTTGGTGCGAAGG 59.201 55.000 0.00 0.00 46.63 3.46
5011 10799 0.040958 GCAGTGAAAGAAGGTGTGCG 60.041 55.000 0.00 0.00 0.00 5.34
5083 10871 1.597742 CCATAAGCCAGGATTGACCG 58.402 55.000 0.00 0.00 44.74 4.79
5099 10887 3.979347 AGATCAAGCAGATAGAACCCCAT 59.021 43.478 0.00 0.00 37.00 4.00
5111 10899 6.092396 GCATGGACTATTCATAGATCAAGCAG 59.908 42.308 0.63 0.00 34.42 4.24
5145 10933 0.028902 GACCAAACACACGCAGGTTC 59.971 55.000 0.00 0.00 31.57 3.62
5180 10968 3.618594 ACACGCTGTAGCATGTTAAGATG 59.381 43.478 8.21 8.21 45.89 2.90
5246 11038 4.862371 ACAACCTGTCTTACTCCCAAAAA 58.138 39.130 0.00 0.00 0.00 1.94
5247 11039 4.513406 ACAACCTGTCTTACTCCCAAAA 57.487 40.909 0.00 0.00 0.00 2.44
5248 11040 4.080243 TCAACAACCTGTCTTACTCCCAAA 60.080 41.667 0.00 0.00 0.00 3.28
5249 11041 3.456644 TCAACAACCTGTCTTACTCCCAA 59.543 43.478 0.00 0.00 0.00 4.12
5250 11042 3.042682 TCAACAACCTGTCTTACTCCCA 58.957 45.455 0.00 0.00 0.00 4.37
5251 11043 3.071167 ACTCAACAACCTGTCTTACTCCC 59.929 47.826 0.00 0.00 0.00 4.30
5252 11044 4.039366 AGACTCAACAACCTGTCTTACTCC 59.961 45.833 0.00 0.00 36.50 3.85
5253 11045 4.985409 CAGACTCAACAACCTGTCTTACTC 59.015 45.833 0.00 0.00 37.64 2.59
5254 11046 4.649674 TCAGACTCAACAACCTGTCTTACT 59.350 41.667 0.00 0.00 37.64 2.24
5255 11047 4.745620 GTCAGACTCAACAACCTGTCTTAC 59.254 45.833 0.00 0.00 37.64 2.34
5256 11048 4.499188 CGTCAGACTCAACAACCTGTCTTA 60.499 45.833 0.00 0.00 37.64 2.10
5257 11049 3.738281 CGTCAGACTCAACAACCTGTCTT 60.738 47.826 0.00 0.00 37.64 3.01
5281 11073 5.049828 TCGTGCCACTTATCATCAGTAATG 58.950 41.667 0.00 0.00 36.65 1.90
5291 11083 3.485947 TGCATTTTCGTGCCACTTATC 57.514 42.857 0.00 0.00 44.43 1.75
5300 11111 4.204978 GTGTCTCAACTTTGCATTTTCGTG 59.795 41.667 0.00 0.00 0.00 4.35
5307 11118 7.436080 CACAAAATAAGTGTCTCAACTTTGCAT 59.564 33.333 0.00 0.00 40.77 3.96
5309 11120 6.972328 TCACAAAATAAGTGTCTCAACTTTGC 59.028 34.615 0.00 0.00 40.77 3.68
5329 11140 7.122799 CGATACTAGATATTCCCTCCATCACAA 59.877 40.741 0.00 0.00 0.00 3.33
5335 11146 7.268212 ACTACGATACTAGATATTCCCTCCA 57.732 40.000 0.00 0.00 0.00 3.86
5388 11200 6.127140 ACTGTCAAGGTAGTACAAAGAACACT 60.127 38.462 2.06 0.00 0.00 3.55
5420 11232 3.135994 TGCGGGAAAACTTTCAGTCTAC 58.864 45.455 4.67 0.00 38.92 2.59
5425 11237 3.708563 TTTCTGCGGGAAAACTTTCAG 57.291 42.857 4.67 0.00 40.51 3.02
5426 11238 4.825085 ACTATTTCTGCGGGAAAACTTTCA 59.175 37.500 8.38 0.00 45.56 2.69
5438 11250 7.216973 AGGGAGTAGTATTACTATTTCTGCG 57.783 40.000 6.82 0.00 40.21 5.18
5442 11254 7.992754 TCGGAGGGAGTAGTATTACTATTTC 57.007 40.000 6.82 7.91 40.21 2.17
5448 11260 4.660168 TGGATCGGAGGGAGTAGTATTAC 58.340 47.826 0.00 0.00 0.00 1.89
5454 11266 5.070580 ACTTATTTTGGATCGGAGGGAGTAG 59.929 44.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.