Multiple sequence alignment - TraesCS4A01G241200

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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 TraesCS4A01G241200 chr4A 100.000 6109 0 0 1 6109 550500738 550506846 0.000000e+00 11282.0
1 TraesCS4A01G241200 chr4A 100.000 2597 0 0 6409 9005 550507146 550509742 0.000000e+00 4796.0
2 TraesCS4A01G241200 chr4A 94.497 1599 63 14 7412 9005 550291662 550293240 0.000000e+00 2442.0
3 TraesCS4A01G241200 chr4B 95.424 5463 173 33 101 5518 69312036 69306606 0.000000e+00 8632.0
4 TraesCS4A01G241200 chr4B 93.237 2410 87 34 6409 8782 69306140 69303771 0.000000e+00 3478.0
5 TraesCS4A01G241200 chr4B 86.756 1042 102 17 1884 2920 115400100 115401110 0.000000e+00 1127.0
6 TraesCS4A01G241200 chr4B 93.074 231 11 4 8780 9005 69303660 69303430 5.210000e-87 333.0
7 TraesCS4A01G241200 chr4D 97.137 4680 107 14 796 5459 47492594 47487926 0.000000e+00 7875.0
8 TraesCS4A01G241200 chr4D 94.660 2135 78 15 6413 8533 47486835 47484723 0.000000e+00 3278.0
9 TraesCS4A01G241200 chr4D 90.470 808 52 13 1 788 47493687 47492885 0.000000e+00 1042.0
10 TraesCS4A01G241200 chr4D 95.588 476 14 2 5596 6070 47487810 47487341 0.000000e+00 756.0
11 TraesCS4A01G241200 chr4D 90.244 369 22 8 8642 9005 47484318 47483959 3.810000e-128 470.0
12 TraesCS4A01G241200 chr4D 96.154 52 2 0 5551 5602 47487908 47487857 1.610000e-12 86.1
13 TraesCS4A01G241200 chr5D 86.600 903 90 18 1958 2853 432447408 432448286 0.000000e+00 968.0
14 TraesCS4A01G241200 chr5D 86.364 132 12 5 8405 8533 277831244 277831116 1.220000e-28 139.0
15 TraesCS4A01G241200 chr1A 90.393 458 40 4 1950 2403 137737815 137738272 4.650000e-167 599.0
16 TraesCS4A01G241200 chr1A 85.282 496 57 8 2436 2920 137738273 137738763 1.750000e-136 497.0
17 TraesCS4A01G241200 chrUn 88.565 481 49 5 5596 6070 37795452 37794972 6.060000e-161 579.0
18 TraesCS4A01G241200 chrUn 88.770 187 20 1 1051 1236 136403740 136403926 2.530000e-55 228.0
19 TraesCS4A01G241200 chrUn 82.520 246 38 5 762 1005 136395341 136395583 2.550000e-50 211.0
20 TraesCS4A01G241200 chr6D 86.313 453 46 8 5559 6000 100336152 100336599 6.320000e-131 479.0
21 TraesCS4A01G241200 chr3A 82.796 558 70 16 3167 3712 712625687 712626230 8.180000e-130 475.0
22 TraesCS4A01G241200 chr3A 88.953 344 35 3 5712 6054 24531360 24531701 1.080000e-113 422.0
23 TraesCS4A01G241200 chr3A 87.179 117 4 5 5596 5709 24531212 24531320 1.230000e-23 122.0
24 TraesCS4A01G241200 chr3A 80.645 155 25 4 8375 8526 104424139 104423987 2.050000e-21 115.0
25 TraesCS4A01G241200 chr7A 82.585 557 71 15 3167 3711 134554109 134554651 1.370000e-127 468.0
26 TraesCS4A01G241200 chr7B 89.667 300 30 1 5596 5895 504213283 504212985 1.830000e-101 381.0
27 TraesCS4A01G241200 chr7D 87.926 323 34 2 5748 6070 13701027 13701344 8.540000e-100 375.0
28 TraesCS4A01G241200 chr7D 89.655 174 14 3 5580 5752 13699602 13699772 1.520000e-52 219.0
29 TraesCS4A01G241200 chr2B 88.667 300 34 0 5596 5895 87914518 87914817 5.140000e-97 366.0
30 TraesCS4A01G241200 chr2B 77.725 211 22 16 5624 5832 159350110 159349923 1.240000e-18 106.0
31 TraesCS4A01G241200 chr2A 78.788 231 26 8 5610 5840 105624811 105624604 5.670000e-27 134.0
32 TraesCS4A01G241200 chr3D 81.481 162 25 4 8375 8533 87938330 87938171 2.640000e-25 128.0
33 TraesCS4A01G241200 chr3B 81.098 164 23 8 8375 8533 137330132 137329972 3.410000e-24 124.0
34 TraesCS4A01G241200 chr1D 81.132 159 21 8 8372 8526 302097017 302097170 1.590000e-22 119.0
35 TraesCS4A01G241200 chr5A 85.714 105 12 2 8432 8533 367145894 367145790 3.440000e-19 108.0


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 TraesCS4A01G241200 chr4A 550500738 550509742 9004 False 8039.000000 11282 100.000000 1 9005 2 chr4A.!!$F2 9004
1 TraesCS4A01G241200 chr4A 550291662 550293240 1578 False 2442.000000 2442 94.497000 7412 9005 1 chr4A.!!$F1 1593
2 TraesCS4A01G241200 chr4B 69303430 69312036 8606 True 4147.666667 8632 93.911667 101 9005 3 chr4B.!!$R1 8904
3 TraesCS4A01G241200 chr4B 115400100 115401110 1010 False 1127.000000 1127 86.756000 1884 2920 1 chr4B.!!$F1 1036
4 TraesCS4A01G241200 chr4D 47483959 47493687 9728 True 2251.183333 7875 94.042167 1 9005 6 chr4D.!!$R1 9004
5 TraesCS4A01G241200 chr5D 432447408 432448286 878 False 968.000000 968 86.600000 1958 2853 1 chr5D.!!$F1 895
6 TraesCS4A01G241200 chr1A 137737815 137738763 948 False 548.000000 599 87.837500 1950 2920 2 chr1A.!!$F1 970
7 TraesCS4A01G241200 chr3A 712625687 712626230 543 False 475.000000 475 82.796000 3167 3712 1 chr3A.!!$F1 545
8 TraesCS4A01G241200 chr7A 134554109 134554651 542 False 468.000000 468 82.585000 3167 3711 1 chr7A.!!$F1 544
9 TraesCS4A01G241200 chr7D 13699602 13701344 1742 False 297.000000 375 88.790500 5580 6070 2 chr7D.!!$F1 490

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
310 325 0.038618 TGCTGCGTGTAGTGTACAGG 60.039 55.000 0.00 3.03 44.83 4.00 F
333 348 0.459759 GATCGTTGGAGTTCCCCGAC 60.460 60.000 10.86 0.00 39.86 4.79 F
836 1145 0.875059 GGGAGAAGAAAGGTTGTGCG 59.125 55.000 0.00 0.00 0.00 5.34 F
1364 1680 1.993956 TGAACATGTGGGTTCCCTTG 58.006 50.000 0.00 6.91 45.12 3.61 F
1817 2133 2.309613 ACAGAGAAATGGTTTGCTGCA 58.690 42.857 0.00 0.00 0.00 4.41 F
1947 2264 2.871633 GTTTTGCCCAAAATGACCAGTG 59.128 45.455 9.16 0.00 41.64 3.66 F
2453 2778 3.635836 GTCTATACCTGCCCTCGTACTTT 59.364 47.826 0.00 0.00 0.00 2.66 F
4052 4411 3.181510 CGTGGGTTTGCTAATTCTACTGC 60.182 47.826 0.00 0.00 0.00 4.40 F
5518 5878 0.321564 TGGCCTCACAGAAATCCACG 60.322 55.000 3.32 0.00 0.00 4.94 F
5897 7571 0.321298 ACATAACTGCTTCGGCCGTT 60.321 50.000 27.15 13.56 46.88 4.44 F
7160 9003 0.463295 CATGTGAATCCCGCTCTGCT 60.463 55.000 0.00 0.00 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1873 2190 2.107366 TCCATCGCACATGAGGACTAA 58.893 47.619 0.00 0.00 0.00 2.24 R
2004 2321 5.184479 CCACCAAAGTGTAGTAGTACTGCTA 59.816 44.000 15.82 15.82 42.88 3.49 R
2668 2996 0.790207 CACCATTCAGTCCAACGACG 59.210 55.000 0.00 0.00 44.28 5.12 R
3139 3488 2.158475 TGCAACCCTGGTCTTTCAATCT 60.158 45.455 0.00 0.00 0.00 2.40 R
3171 3520 2.867109 ACAGCCCCTATATCATGCAC 57.133 50.000 0.00 0.00 0.00 4.57 R
3194 3543 3.673956 CTATGGCCCGCACGAACCA 62.674 63.158 0.00 6.48 36.43 3.67 R
4214 4573 6.351626 GGAGCTGAATCTGATTTTGGGATTTT 60.352 38.462 4.11 0.00 30.98 1.82 R
5533 5893 0.892755 AAGGTTGCATGCATGGAGTG 59.107 50.000 27.34 4.17 0.00 3.51 R
6614 8454 1.342674 ACCTGCATACCCCTTCGACTA 60.343 52.381 0.00 0.00 0.00 2.59 R
7530 9373 0.898789 ACCACCCGACCTGTCTGTAG 60.899 60.000 0.00 0.00 0.00 2.74 R
8008 9851 0.179100 CTTCGATGCAGTCCGGTCAT 60.179 55.000 0.00 0.89 0.00 3.06 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
88 90 3.716195 CACTCGCCCATCCACCCA 61.716 66.667 0.00 0.00 0.00 4.51
96 98 1.930656 CCATCCACCCACCTCCCTT 60.931 63.158 0.00 0.00 0.00 3.95
147 150 3.318017 CCTGTAAGTCTTCAACTGGTCG 58.682 50.000 0.00 0.00 38.58 4.79
149 152 2.696707 TGTAAGTCTTCAACTGGTCGGT 59.303 45.455 0.00 0.00 38.58 4.69
150 153 2.240493 AAGTCTTCAACTGGTCGGTG 57.760 50.000 0.00 0.00 38.58 4.94
295 298 6.631636 CGATTCTGATAAATTGTGATGTGCTG 59.368 38.462 0.00 0.00 0.00 4.41
296 299 5.239359 TCTGATAAATTGTGATGTGCTGC 57.761 39.130 0.00 0.00 0.00 5.25
297 300 4.018649 TGATAAATTGTGATGTGCTGCG 57.981 40.909 0.00 0.00 0.00 5.18
298 301 3.439825 TGATAAATTGTGATGTGCTGCGT 59.560 39.130 0.00 0.00 0.00 5.24
300 303 0.953727 AATTGTGATGTGCTGCGTGT 59.046 45.000 0.00 0.00 0.00 4.49
301 304 1.807139 ATTGTGATGTGCTGCGTGTA 58.193 45.000 0.00 0.00 0.00 2.90
310 325 0.038618 TGCTGCGTGTAGTGTACAGG 60.039 55.000 0.00 3.03 44.83 4.00
322 337 0.528924 TGTACAGGGTCGATCGTTGG 59.471 55.000 15.94 4.41 0.00 3.77
323 338 0.813184 GTACAGGGTCGATCGTTGGA 59.187 55.000 15.94 3.89 0.00 3.53
324 339 1.100510 TACAGGGTCGATCGTTGGAG 58.899 55.000 15.94 6.55 0.00 3.86
325 340 0.898789 ACAGGGTCGATCGTTGGAGT 60.899 55.000 15.94 7.18 0.00 3.85
333 348 0.459759 GATCGTTGGAGTTCCCCGAC 60.460 60.000 10.86 0.00 39.86 4.79
362 377 8.418597 TCTTTCTAATACCGTCTGCCTATATT 57.581 34.615 0.00 0.00 0.00 1.28
439 454 3.683365 TTCTGGTCCGGGTTTAGTTAC 57.317 47.619 0.00 0.00 0.00 2.50
499 514 1.214305 TATTTGACCTGCCTGGCCCT 61.214 55.000 17.53 0.00 40.22 5.19
511 526 2.162681 CCTGGCCCTGACTTTTTAGTG 58.837 52.381 0.00 0.00 0.00 2.74
515 530 2.229062 GGCCCTGACTTTTTAGTGAAGC 59.771 50.000 0.00 0.00 0.00 3.86
540 555 4.060038 ACGAGTCTGTGATGTTCTTTGT 57.940 40.909 0.00 0.00 0.00 2.83
594 619 4.156739 CAGGATGTTCTTTTTAGGAGGCAC 59.843 45.833 0.00 0.00 0.00 5.01
628 653 3.818773 ACATGATTCGACCCTTTTTCGTT 59.181 39.130 0.00 0.00 37.73 3.85
648 673 7.427989 TCGTTCCCCTTGTAATAAATCTAGT 57.572 36.000 0.00 0.00 0.00 2.57
836 1145 0.875059 GGGAGAAGAAAGGTTGTGCG 59.125 55.000 0.00 0.00 0.00 5.34
856 1166 9.944663 TTGTGCGAAATATCTAATTATTTGACC 57.055 29.630 0.00 0.00 33.11 4.02
921 1237 9.520204 CTTTAATAATTAATGTGGCCAACTCTG 57.480 33.333 7.24 0.00 0.00 3.35
934 1250 5.649395 TGGCCAACTCTGATTTCTTAATCTG 59.351 40.000 0.61 0.00 40.68 2.90
938 1254 7.459486 CCAACTCTGATTTCTTAATCTGTTCG 58.541 38.462 0.00 0.00 40.68 3.95
958 1274 5.862678 TCGTGGTATTTAGACATGATCCA 57.137 39.130 0.00 0.00 0.00 3.41
1005 1321 6.868622 TCTTTTTCTCTAGCTGTAGATGGAC 58.131 40.000 0.00 0.00 34.63 4.02
1014 1330 4.701765 AGCTGTAGATGGACATCACAATC 58.298 43.478 14.16 10.06 40.22 2.67
1207 1523 6.038356 CCATGATTGTTCTGCATAAGGAAAC 58.962 40.000 0.00 0.00 0.00 2.78
1364 1680 1.993956 TGAACATGTGGGTTCCCTTG 58.006 50.000 0.00 6.91 45.12 3.61
1501 1817 4.727507 TTCTTGCAACTAAAACAAGGCA 57.272 36.364 0.00 0.00 40.90 4.75
1509 1825 5.276820 GCAACTAAAACAAGGCAATGTTGAC 60.277 40.000 9.08 0.00 42.49 3.18
1619 1935 7.082602 GGATTGACAGCATGCTATTGATTTAG 58.917 38.462 22.19 7.14 42.53 1.85
1816 2132 3.375782 AACAGAGAAATGGTTTGCTGC 57.624 42.857 0.00 0.00 0.00 5.25
1817 2133 2.309613 ACAGAGAAATGGTTTGCTGCA 58.690 42.857 0.00 0.00 0.00 4.41
1947 2264 2.871633 GTTTTGCCCAAAATGACCAGTG 59.128 45.455 9.16 0.00 41.64 3.66
2004 2321 6.720288 AGCATTATATGTAGTCGGACTAACCT 59.280 38.462 18.86 9.41 31.62 3.50
2453 2778 3.635836 GTCTATACCTGCCCTCGTACTTT 59.364 47.826 0.00 0.00 0.00 2.66
2668 2996 5.848406 CAGAAGTCTGTCCCAAGTATATCC 58.152 45.833 0.00 0.00 39.09 2.59
3082 3431 6.995686 TGTTAACCAGTCAATCTCTAAGCAAA 59.004 34.615 2.48 0.00 0.00 3.68
3139 3488 4.148838 CCTGTGTCAAATCTTGGGGTAAA 58.851 43.478 0.00 0.00 0.00 2.01
3171 3520 4.016444 ACCAGGGTTGCAATTATACACAG 58.984 43.478 0.59 0.00 0.00 3.66
3194 3543 3.909995 TGCATGATATAGGGGCTGTAGTT 59.090 43.478 0.00 0.00 0.00 2.24
3356 3707 5.552870 AGTGCCTCTTCTTGTCTCTTTTA 57.447 39.130 0.00 0.00 0.00 1.52
3495 3847 9.135189 AGTATTATTAATGTTCATGTGCATGGT 57.865 29.630 11.68 0.00 39.24 3.55
3809 4168 7.528712 AGTTGTTACTGTATGATCCATGTTGGA 60.529 37.037 0.00 0.00 41.48 3.53
3858 4217 8.577296 AGTGCTATAGATTTGCTAAATACGAGA 58.423 33.333 3.21 0.00 31.66 4.04
3966 4325 3.679917 CGACAACTATGCCTGGTGAAGAT 60.680 47.826 0.00 0.00 0.00 2.40
4052 4411 3.181510 CGTGGGTTTGCTAATTCTACTGC 60.182 47.826 0.00 0.00 0.00 4.40
4214 4573 4.654262 ACCAGGAACTTCTCAAGACAAGTA 59.346 41.667 0.00 0.00 34.60 2.24
4515 4874 3.058639 GTGACCACAGATTCTGCAAAGAC 60.059 47.826 13.64 2.33 34.37 3.01
4558 4917 1.964223 CGTATGCCTGATGGACCTAGT 59.036 52.381 0.00 0.00 34.57 2.57
4626 4985 5.656416 AGACTTTTGTGGATGAAAACCAAGA 59.344 36.000 0.00 0.00 42.00 3.02
4987 5347 4.252878 CAGTGGGGGAAATTATTTGTTGC 58.747 43.478 0.00 0.00 0.00 4.17
5106 5466 7.041235 GCAGAGAGAAGCTAGCATTAAATTCAT 60.041 37.037 18.83 3.80 0.00 2.57
5115 5475 6.860023 GCTAGCATTAAATTCATAAGGCACAG 59.140 38.462 10.63 6.57 43.13 3.66
5337 5697 1.938585 TCCGATCTGTGAAGGAAGGT 58.061 50.000 0.00 0.00 0.00 3.50
5518 5878 0.321564 TGGCCTCACAGAAATCCACG 60.322 55.000 3.32 0.00 0.00 4.94
5519 5879 0.321653 GGCCTCACAGAAATCCACGT 60.322 55.000 0.00 0.00 0.00 4.49
5520 5880 0.798776 GCCTCACAGAAATCCACGTG 59.201 55.000 9.08 9.08 0.00 4.49
5521 5881 1.608025 GCCTCACAGAAATCCACGTGA 60.608 52.381 19.30 3.36 36.92 4.35
5522 5882 2.936993 GCCTCACAGAAATCCACGTGAT 60.937 50.000 19.30 5.87 37.72 3.06
5523 5883 3.678806 GCCTCACAGAAATCCACGTGATA 60.679 47.826 19.30 4.90 37.72 2.15
5524 5884 4.697514 CCTCACAGAAATCCACGTGATAT 58.302 43.478 19.30 7.37 37.72 1.63
5525 5885 4.747108 CCTCACAGAAATCCACGTGATATC 59.253 45.833 19.30 9.63 37.72 1.63
5526 5886 5.452496 CCTCACAGAAATCCACGTGATATCT 60.452 44.000 19.30 11.80 37.72 1.98
5527 5887 5.351458 TCACAGAAATCCACGTGATATCTG 58.649 41.667 25.35 25.35 33.61 2.90
5528 5888 4.509230 CACAGAAATCCACGTGATATCTGG 59.491 45.833 27.93 19.33 31.83 3.86
5529 5889 4.162320 ACAGAAATCCACGTGATATCTGGT 59.838 41.667 27.93 18.14 31.83 4.00
5530 5890 5.362717 ACAGAAATCCACGTGATATCTGGTA 59.637 40.000 27.93 5.34 31.83 3.25
5531 5891 6.042093 ACAGAAATCCACGTGATATCTGGTAT 59.958 38.462 27.93 15.09 31.83 2.73
5532 5892 6.587990 CAGAAATCCACGTGATATCTGGTATC 59.412 42.308 19.30 0.85 39.76 2.24
5533 5893 5.407407 AATCCACGTGATATCTGGTATCC 57.593 43.478 19.30 0.00 38.76 2.59
5534 5894 3.839778 TCCACGTGATATCTGGTATCCA 58.160 45.455 19.30 0.00 38.76 3.41
5535 5895 3.572682 TCCACGTGATATCTGGTATCCAC 59.427 47.826 19.30 3.69 38.76 4.02
5536 5896 3.574396 CCACGTGATATCTGGTATCCACT 59.426 47.826 19.30 0.00 38.76 4.00
5537 5897 4.321304 CCACGTGATATCTGGTATCCACTC 60.321 50.000 19.30 0.00 38.76 3.51
5538 5898 3.827302 ACGTGATATCTGGTATCCACTCC 59.173 47.826 5.52 0.00 38.76 3.85
5539 5899 3.826729 CGTGATATCTGGTATCCACTCCA 59.173 47.826 5.52 0.00 38.76 3.86
5540 5900 4.464244 CGTGATATCTGGTATCCACTCCAT 59.536 45.833 5.52 0.00 38.76 3.41
5541 5901 5.623141 CGTGATATCTGGTATCCACTCCATG 60.623 48.000 5.52 0.00 38.76 3.66
5542 5902 4.223700 TGATATCTGGTATCCACTCCATGC 59.776 45.833 5.52 0.00 38.76 4.06
5543 5903 1.878211 TCTGGTATCCACTCCATGCA 58.122 50.000 0.00 0.00 33.01 3.96
5544 5904 2.411583 TCTGGTATCCACTCCATGCAT 58.588 47.619 0.00 0.00 33.01 3.96
5545 5905 2.105306 TCTGGTATCCACTCCATGCATG 59.895 50.000 20.19 20.19 33.01 4.06
5546 5906 1.242076 GGTATCCACTCCATGCATGC 58.758 55.000 21.69 11.82 0.00 4.06
5547 5907 1.477377 GGTATCCACTCCATGCATGCA 60.477 52.381 25.04 25.04 0.00 3.96
5548 5908 2.300433 GTATCCACTCCATGCATGCAA 58.700 47.619 26.68 7.52 0.00 4.08
5549 5909 1.108776 ATCCACTCCATGCATGCAAC 58.891 50.000 26.68 0.00 0.00 4.17
5581 5941 1.064758 TCTTACAATCAGCGGGGCAAT 60.065 47.619 0.00 0.00 0.00 3.56
5855 7529 1.009829 GGATTTTCGTGAGCATCGCT 58.990 50.000 0.00 0.00 45.19 4.93
5856 7530 1.267732 GGATTTTCGTGAGCATCGCTG 60.268 52.381 0.00 0.00 45.19 5.18
5897 7571 0.321298 ACATAACTGCTTCGGCCGTT 60.321 50.000 27.15 13.56 46.88 4.44
5959 7633 3.256136 CAGCCCTTCTCCTATAACTACCG 59.744 52.174 0.00 0.00 0.00 4.02
6073 7779 2.238898 GACCAACTAGTAATGGGCCTGT 59.761 50.000 16.32 0.00 38.93 4.00
6449 8289 6.014669 CGACCTACCTACCTACTACTCAGTAT 60.015 46.154 0.00 0.00 36.66 2.12
6721 8561 7.422399 TGAGCCTTGTTTTACAGAAATTACAC 58.578 34.615 0.00 0.00 0.00 2.90
6854 8695 1.529438 CGCGAGTGTCTTTTTGGCTTA 59.471 47.619 0.00 0.00 0.00 3.09
6867 8708 9.699703 GTCTTTTTGGCTTAAAATATACACCAA 57.300 29.630 0.00 0.00 38.03 3.67
7066 8909 3.517296 TTTGGTCCATAAGCTGGTCAA 57.483 42.857 0.00 0.00 46.08 3.18
7067 8910 2.489938 TGGTCCATAAGCTGGTCAAC 57.510 50.000 0.00 0.00 46.08 3.18
7083 8926 3.123621 GGTCAACGTATGCTTGAACTCTG 59.876 47.826 0.00 0.00 33.28 3.35
7153 8996 1.683943 AATCCTGCATGTGAATCCCG 58.316 50.000 0.00 0.00 0.00 5.14
7158 9001 0.745486 TGCATGTGAATCCCGCTCTG 60.745 55.000 0.00 0.00 0.00 3.35
7159 9002 2.020131 CATGTGAATCCCGCTCTGC 58.980 57.895 0.00 0.00 0.00 4.26
7160 9003 0.463295 CATGTGAATCCCGCTCTGCT 60.463 55.000 0.00 0.00 0.00 4.24
7482 9325 5.120208 CGAATCGTCAATCTGTTAAAGTGGT 59.880 40.000 0.00 0.00 0.00 4.16
7530 9373 3.112205 ATCTGGATCGCACTGGGGC 62.112 63.158 0.00 0.00 0.00 5.80
7749 9592 6.871492 TCGTGATTGCAGAGTAGTATTTTTGA 59.129 34.615 0.00 0.00 0.00 2.69
7803 9646 0.895530 TTACTTCTCTGGCAGGACCG 59.104 55.000 15.73 7.18 43.94 4.79
7805 9648 0.832135 ACTTCTCTGGCAGGACCGAA 60.832 55.000 15.73 11.11 43.94 4.30
8008 9851 5.340027 GGAGGTGATGAAAAGAAATAGGGGA 60.340 44.000 0.00 0.00 0.00 4.81
8030 9897 0.892755 ACCGGACTGCATCGAAGTTA 59.107 50.000 9.46 0.00 0.00 2.24
8032 9899 1.134367 CCGGACTGCATCGAAGTTAGA 59.866 52.381 0.00 0.00 0.00 2.10
8046 9913 7.165460 TCGAAGTTAGATGATACTTGAACCA 57.835 36.000 0.00 0.00 34.88 3.67
8184 10059 0.676782 GGCACGTGCAACCCTAGAAT 60.677 55.000 38.60 0.00 44.36 2.40
8264 10139 2.453521 TGTAGTATCTCGTGCTTGGGT 58.546 47.619 0.00 0.00 0.00 4.51
8356 10231 1.133606 AGGCCTCCTTCGGTTCAAAAA 60.134 47.619 0.00 0.00 0.00 1.94
8466 10346 6.715264 TCACTTGGACCTCTTTTAATTTCCTC 59.285 38.462 0.00 0.00 0.00 3.71
8606 10513 4.382254 GCATTCCAATCCAATTTCTGCTGA 60.382 41.667 0.00 0.00 0.00 4.26
8609 10516 5.587388 TCCAATCCAATTTCTGCTGATTC 57.413 39.130 0.00 0.00 0.00 2.52
8610 10517 5.266788 TCCAATCCAATTTCTGCTGATTCT 58.733 37.500 0.00 0.00 0.00 2.40
8611 10518 5.718130 TCCAATCCAATTTCTGCTGATTCTT 59.282 36.000 0.00 0.00 0.00 2.52
8612 10519 5.810587 CCAATCCAATTTCTGCTGATTCTTG 59.189 40.000 0.00 0.00 0.00 3.02
8613 10520 6.395629 CAATCCAATTTCTGCTGATTCTTGT 58.604 36.000 0.00 0.00 0.00 3.16
8669 10845 6.966534 TCTTCTGAATCAAAAGAGGCTTTT 57.033 33.333 0.00 0.00 0.00 2.27
8689 10865 9.076596 GGCTTTTAGCTCTTGTTACAATTTATG 57.923 33.333 0.00 0.00 41.99 1.90
8749 10925 8.265764 ACTAATTCTACCCTAAAAGGCTAACTG 58.734 37.037 0.00 0.00 32.73 3.16
8992 11283 1.734655 TTGGCTTTCTCCACCTCTCT 58.265 50.000 0.00 0.00 35.50 3.10
8996 11287 2.093711 GGCTTTCTCCACCTCTCTTCTC 60.094 54.545 0.00 0.00 0.00 2.87
8997 11288 2.831526 GCTTTCTCCACCTCTCTTCTCT 59.168 50.000 0.00 0.00 0.00 3.10
8998 11289 3.368323 GCTTTCTCCACCTCTCTTCTCTG 60.368 52.174 0.00 0.00 0.00 3.35
8999 11290 2.523325 TCTCCACCTCTCTTCTCTGG 57.477 55.000 0.00 0.00 0.00 3.86
9000 11291 1.996291 TCTCCACCTCTCTTCTCTGGA 59.004 52.381 0.00 0.00 0.00 3.86
9001 11292 2.380249 TCTCCACCTCTCTTCTCTGGAA 59.620 50.000 0.00 0.00 30.54 3.53
9002 11293 3.169099 CTCCACCTCTCTTCTCTGGAAA 58.831 50.000 0.00 0.00 30.54 3.13
9003 11294 2.900546 TCCACCTCTCTTCTCTGGAAAC 59.099 50.000 0.00 0.00 0.00 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 1.619669 GGAAGGGAGGTGGGTGGAT 60.620 63.158 0.00 0.00 0.00 3.41
88 90 1.693103 GAATCCGGGGAAGGGAGGT 60.693 63.158 0.00 0.00 36.91 3.85
96 98 2.762459 CGGTCCTGAATCCGGGGA 60.762 66.667 0.00 0.00 42.61 4.81
163 166 1.927174 CTACTGGTCAAGAATTCGGCG 59.073 52.381 0.00 0.00 0.00 6.46
166 169 5.389516 CCGAAAACTACTGGTCAAGAATTCG 60.390 44.000 0.00 0.00 35.81 3.34
295 298 0.455633 CGACCCTGTACACTACACGC 60.456 60.000 0.00 0.00 34.46 5.34
296 299 1.159285 TCGACCCTGTACACTACACG 58.841 55.000 0.00 0.00 34.46 4.49
297 300 2.223203 CGATCGACCCTGTACACTACAC 60.223 54.545 10.26 0.00 34.46 2.90
298 301 2.011947 CGATCGACCCTGTACACTACA 58.988 52.381 10.26 0.00 37.13 2.74
300 303 2.408271 ACGATCGACCCTGTACACTA 57.592 50.000 24.34 0.00 0.00 2.74
301 304 1.201647 CAACGATCGACCCTGTACACT 59.798 52.381 24.34 0.00 0.00 3.55
310 325 0.459759 GGGAACTCCAACGATCGACC 60.460 60.000 24.34 10.63 37.91 4.79
322 337 0.535797 AAAGATCGGTCGGGGAACTC 59.464 55.000 0.00 0.00 0.00 3.01
323 338 0.535797 GAAAGATCGGTCGGGGAACT 59.464 55.000 0.00 0.00 0.00 3.01
324 339 0.535797 AGAAAGATCGGTCGGGGAAC 59.464 55.000 0.00 0.00 0.00 3.62
325 340 2.148446 TAGAAAGATCGGTCGGGGAA 57.852 50.000 0.00 0.00 0.00 3.97
333 348 3.982058 GCAGACGGTATTAGAAAGATCGG 59.018 47.826 0.00 0.00 0.00 4.18
362 377 0.250989 CAACCGGGGCTTACCAAGAA 60.251 55.000 6.32 0.00 42.91 2.52
407 422 3.181461 CCGGACCAGAAAGATAGCTCAAT 60.181 47.826 0.00 0.00 0.00 2.57
439 454 1.440708 CAAAGCACAGAGAGAGCCAG 58.559 55.000 0.00 0.00 33.99 4.85
499 514 6.759827 ACTCGTTAAGCTTCACTAAAAAGTCA 59.240 34.615 0.00 0.00 0.00 3.41
511 526 4.238514 ACATCACAGACTCGTTAAGCTTC 58.761 43.478 0.00 0.00 0.00 3.86
515 530 6.201044 ACAAAGAACATCACAGACTCGTTAAG 59.799 38.462 0.00 0.00 0.00 1.85
568 588 5.335976 GCCTCCTAAAAAGAACATCCTGTTG 60.336 44.000 0.00 0.00 41.28 3.33
571 591 4.156739 GTGCCTCCTAAAAAGAACATCCTG 59.843 45.833 0.00 0.00 0.00 3.86
575 595 4.762251 GTCTGTGCCTCCTAAAAAGAACAT 59.238 41.667 0.00 0.00 0.00 2.71
578 598 3.751518 GGTCTGTGCCTCCTAAAAAGAA 58.248 45.455 0.00 0.00 0.00 2.52
579 599 2.289444 CGGTCTGTGCCTCCTAAAAAGA 60.289 50.000 0.00 0.00 0.00 2.52
580 600 2.076863 CGGTCTGTGCCTCCTAAAAAG 58.923 52.381 0.00 0.00 0.00 2.27
581 601 1.418637 ACGGTCTGTGCCTCCTAAAAA 59.581 47.619 0.00 0.00 0.00 1.94
594 619 2.009774 GAATCATGTTCCCACGGTCTG 58.990 52.381 0.00 0.00 0.00 3.51
648 673 4.974368 AACCAAACACGAGTCAAAATCA 57.026 36.364 0.00 0.00 0.00 2.57
894 1204 9.474313 AGAGTTGGCCACATTAATTATTAAAGA 57.526 29.630 3.88 0.00 0.00 2.52
934 1250 6.046593 TGGATCATGTCTAAATACCACGAAC 58.953 40.000 0.00 0.00 0.00 3.95
938 1254 6.349300 ACACTGGATCATGTCTAAATACCAC 58.651 40.000 0.00 0.00 0.00 4.16
958 1274 5.946942 AAGAGTATGATGACATGGACACT 57.053 39.130 0.00 0.00 37.87 3.55
1005 1321 5.300969 ACGTCAAGGAATTGATTGTGATG 57.699 39.130 0.00 0.00 33.02 3.07
1014 1330 5.432885 AACCTTTGTACGTCAAGGAATTG 57.567 39.130 21.91 5.63 37.35 2.32
1207 1523 8.735315 CAGACAGGATTGTACTGGATAGTATAG 58.265 40.741 0.00 0.00 41.22 1.31
1364 1680 4.283722 TCTTCTGTACAAGGGAGGAAGTTC 59.716 45.833 15.77 0.00 33.94 3.01
1436 1752 2.192175 CCACCTGCGAATACCCCC 59.808 66.667 0.00 0.00 0.00 5.40
1501 1817 2.704725 AATTGAAGCGCGTCAACATT 57.295 40.000 35.10 25.05 40.22 2.71
1509 1825 2.525750 TAGCTGAAAATTGAAGCGCG 57.474 45.000 0.00 0.00 41.88 6.86
1863 2180 6.923508 CGCACATGAGGACTAATCTTTACATA 59.076 38.462 0.00 0.00 0.00 2.29
1864 2181 5.755375 CGCACATGAGGACTAATCTTTACAT 59.245 40.000 0.00 0.00 0.00 2.29
1865 2182 5.105513 TCGCACATGAGGACTAATCTTTACA 60.106 40.000 0.00 0.00 0.00 2.41
1873 2190 2.107366 TCCATCGCACATGAGGACTAA 58.893 47.619 0.00 0.00 0.00 2.24
2004 2321 5.184479 CCACCAAAGTGTAGTAGTACTGCTA 59.816 44.000 15.82 15.82 42.88 3.49
2085 2409 8.082672 TCAATTAGAAGATCAGATGAGACCAA 57.917 34.615 0.00 0.00 0.00 3.67
2668 2996 0.790207 CACCATTCAGTCCAACGACG 59.210 55.000 0.00 0.00 44.28 5.12
2969 3305 3.281727 TGAACTCTGCCACTCAAAGTT 57.718 42.857 0.00 0.00 33.09 2.66
3139 3488 2.158475 TGCAACCCTGGTCTTTCAATCT 60.158 45.455 0.00 0.00 0.00 2.40
3171 3520 2.867109 ACAGCCCCTATATCATGCAC 57.133 50.000 0.00 0.00 0.00 4.57
3194 3543 3.673956 CTATGGCCCGCACGAACCA 62.674 63.158 0.00 6.48 36.43 3.67
3356 3707 7.537306 CGAACTCGACAATTAATTGACCAAAAT 59.463 33.333 30.18 9.67 43.02 1.82
3801 4160 8.393366 CACTAGTGTGAAGAATAATCCAACATG 58.607 37.037 15.06 0.00 46.55 3.21
3858 4217 7.510675 TGTCTCCTAAAAAGATCCCAAGTAT 57.489 36.000 0.00 0.00 0.00 2.12
3966 4325 8.868522 AATGATTTTCTGAAGTAGATGAACCA 57.131 30.769 0.00 0.00 34.80 3.67
4214 4573 6.351626 GGAGCTGAATCTGATTTTGGGATTTT 60.352 38.462 4.11 0.00 30.98 1.82
4515 4874 3.136009 TGGCCAGCTGAATATCATCTG 57.864 47.619 17.39 4.62 39.57 2.90
4558 4917 7.498900 TCTTCTTTTGTCAGTTTAATCTGCAGA 59.501 33.333 20.79 20.79 35.63 4.26
4950 5309 1.482593 CCACTGGTAGTAGGAAGCAGG 59.517 57.143 7.16 0.00 44.74 4.85
4987 5347 5.886715 TTCAAAGAAAATGCAATGACACG 57.113 34.783 0.00 0.00 0.00 4.49
5106 5466 9.733556 TTTCTTCTTATTATGAACTGTGCCTTA 57.266 29.630 0.00 0.00 0.00 2.69
5125 5485 5.531634 TGCGAGCATTTCAATTTTTCTTCT 58.468 33.333 0.00 0.00 0.00 2.85
5209 5569 9.884636 TCTATTACCGCATATATTTTACATGCT 57.115 29.630 5.99 0.00 42.28 3.79
5259 5619 3.495806 GCAGAGGGGAAGAATACCTGATG 60.496 52.174 0.00 0.00 34.02 3.07
5389 5749 1.067635 GCAAAATCGTCCAAGCCACAT 60.068 47.619 0.00 0.00 0.00 3.21
5518 5878 5.728471 CATGGAGTGGATACCAGATATCAC 58.272 45.833 5.32 0.00 41.51 3.06
5519 5879 4.223700 GCATGGAGTGGATACCAGATATCA 59.776 45.833 5.32 0.00 41.51 2.15
5520 5880 4.223700 TGCATGGAGTGGATACCAGATATC 59.776 45.833 0.00 0.00 39.62 1.63
5521 5881 4.170449 TGCATGGAGTGGATACCAGATAT 58.830 43.478 0.00 0.00 39.62 1.63
5522 5882 3.586429 TGCATGGAGTGGATACCAGATA 58.414 45.455 0.00 0.00 39.62 1.98
5523 5883 2.411583 TGCATGGAGTGGATACCAGAT 58.588 47.619 0.00 0.00 39.62 2.90
5524 5884 1.878211 TGCATGGAGTGGATACCAGA 58.122 50.000 0.00 0.00 39.62 3.86
5525 5885 2.501261 CATGCATGGAGTGGATACCAG 58.499 52.381 19.40 0.00 36.66 4.00
5526 5886 1.477377 GCATGCATGGAGTGGATACCA 60.477 52.381 27.34 0.00 36.66 3.25
5527 5887 1.242076 GCATGCATGGAGTGGATACC 58.758 55.000 27.34 3.43 36.66 2.73
5528 5888 1.971481 TGCATGCATGGAGTGGATAC 58.029 50.000 27.34 8.37 36.66 2.24
5529 5889 2.300433 GTTGCATGCATGGAGTGGATA 58.700 47.619 27.34 6.36 36.66 2.59
5530 5890 1.108776 GTTGCATGCATGGAGTGGAT 58.891 50.000 27.34 0.00 39.77 3.41
5531 5891 0.966875 GGTTGCATGCATGGAGTGGA 60.967 55.000 27.34 7.54 0.00 4.02
5532 5892 0.968901 AGGTTGCATGCATGGAGTGG 60.969 55.000 27.34 1.69 0.00 4.00
5533 5893 0.892755 AAGGTTGCATGCATGGAGTG 59.107 50.000 27.34 4.17 0.00 3.51
5534 5894 1.636148 AAAGGTTGCATGCATGGAGT 58.364 45.000 27.34 10.98 0.00 3.85
5535 5895 2.028839 TCAAAAGGTTGCATGCATGGAG 60.029 45.455 27.34 11.48 34.50 3.86
5536 5896 1.969208 TCAAAAGGTTGCATGCATGGA 59.031 42.857 27.34 22.97 34.50 3.41
5537 5897 2.459060 TCAAAAGGTTGCATGCATGG 57.541 45.000 27.34 3.39 34.50 3.66
5538 5898 7.375834 AGATATATCAAAAGGTTGCATGCATG 58.624 34.615 23.37 22.70 34.50 4.06
5539 5899 7.534723 AGATATATCAAAAGGTTGCATGCAT 57.465 32.000 23.37 3.27 34.50 3.96
5540 5900 6.964807 AGATATATCAAAAGGTTGCATGCA 57.035 33.333 18.46 18.46 34.50 3.96
5541 5901 8.352201 TGTAAGATATATCAAAAGGTTGCATGC 58.648 33.333 11.82 11.82 34.50 4.06
5548 5908 8.993121 CGCTGATTGTAAGATATATCAAAAGGT 58.007 33.333 15.08 0.00 0.00 3.50
5549 5909 8.446273 CCGCTGATTGTAAGATATATCAAAAGG 58.554 37.037 15.08 0.08 0.00 3.11
5959 7633 1.807573 GCTGCGTGCCTGTCTCTAC 60.808 63.158 0.00 0.00 35.15 2.59
6426 8263 6.848631 TCATACTGAGTAGTAGGTAGGTAGGT 59.151 42.308 0.00 0.00 42.36 3.08
6427 8264 7.160726 GTCATACTGAGTAGTAGGTAGGTAGG 58.839 46.154 0.00 0.00 42.36 3.18
6432 8272 7.467539 GCTTGTGTCATACTGAGTAGTAGGTAG 60.468 44.444 0.00 0.00 42.36 3.18
6449 8289 2.961741 AGAGAGAAGTCTGCTTGTGTCA 59.038 45.455 4.91 0.00 39.64 3.58
6614 8454 1.342674 ACCTGCATACCCCTTCGACTA 60.343 52.381 0.00 0.00 0.00 2.59
6867 8708 2.501316 AGCAAAACTTCAAGCCAACCTT 59.499 40.909 0.00 0.00 0.00 3.50
7014 8857 8.030106 GCCTTACTTCATAGTCCATACTATCAC 58.970 40.741 0.00 0.00 44.05 3.06
7066 8909 3.944055 AGACAGAGTTCAAGCATACGT 57.056 42.857 0.00 0.00 0.00 3.57
7067 8910 3.181526 GCAAGACAGAGTTCAAGCATACG 60.182 47.826 0.00 0.00 0.00 3.06
7137 8980 1.442526 GAGCGGGATTCACATGCAGG 61.443 60.000 0.00 0.00 0.00 4.85
7153 8996 5.334957 GGAAGTTAAAGTTAACCAGCAGAGC 60.335 44.000 9.75 0.00 43.03 4.09
7158 9001 4.217767 CCCAGGAAGTTAAAGTTAACCAGC 59.782 45.833 9.75 1.51 43.03 4.85
7159 9002 4.217767 GCCCAGGAAGTTAAAGTTAACCAG 59.782 45.833 9.75 0.00 43.03 4.00
7160 9003 4.146564 GCCCAGGAAGTTAAAGTTAACCA 58.853 43.478 9.75 0.00 43.03 3.67
7381 9224 9.264719 GTTTCCAGATCTGAACAAAAATTTGAT 57.735 29.630 24.62 0.53 40.55 2.57
7482 9325 1.742831 GCAATGACGATTGGTGCCTTA 59.257 47.619 0.00 0.00 39.62 2.69
7530 9373 0.898789 ACCACCCGACCTGTCTGTAG 60.899 60.000 0.00 0.00 0.00 2.74
7803 9646 3.990959 AGAGGTTGGGATTCAGAGTTC 57.009 47.619 0.00 0.00 0.00 3.01
7805 9648 2.234908 CGAAGAGGTTGGGATTCAGAGT 59.765 50.000 0.00 0.00 0.00 3.24
8008 9851 0.179100 CTTCGATGCAGTCCGGTCAT 60.179 55.000 0.00 0.89 0.00 3.06
8052 9919 5.361285 CGTTCCCAACATATTTATTTCCCCA 59.639 40.000 0.00 0.00 0.00 4.96
8114 9989 8.696374 TGTAATTTAACACCTCAATTTGTTCCA 58.304 29.630 0.00 0.00 37.19 3.53
8123 9998 6.952773 AAGCACTGTAATTTAACACCTCAA 57.047 33.333 0.00 0.00 0.00 3.02
8156 10031 2.422127 GGTTGCACGTGCCATATTACTT 59.578 45.455 35.72 0.00 41.18 2.24
8184 10059 3.955524 TCCTGGGGTGAACAAAGTAAA 57.044 42.857 0.00 0.00 0.00 2.01
8356 10231 4.098914 TCCTGTGTTTGCTCCACTATTT 57.901 40.909 0.00 0.00 33.92 1.40
8429 10305 9.533831 AAGAGGTCCAAGTGAATTGTAAAATAT 57.466 29.630 0.00 0.00 37.17 1.28
8430 10306 8.934023 AAGAGGTCCAAGTGAATTGTAAAATA 57.066 30.769 0.00 0.00 37.17 1.40
8466 10346 4.124970 TCTCAATCTCATTCTTCATGCGG 58.875 43.478 0.00 0.00 32.13 5.69
8621 10528 3.452755 AAAAACGCAGGAAAGGAAAGG 57.547 42.857 0.00 0.00 0.00 3.11
8689 10865 6.759827 TGTTTTACAGACTACAGGAGAAACAC 59.240 38.462 0.00 0.00 31.77 3.32


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

AutoCloner maintained by Alex Coulton.