Multiple sequence alignment - TraesCS5A01G166000

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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 TraesCS5A01G166000 chr5A 100.000 5763 0 0 1 5763 354960166 354965928 0.000000e+00 10643.0
1 TraesCS5A01G166000 chr5D 94.962 4367 151 30 1 4324 267613527 267617867 0.000000e+00 6782.0
2 TraesCS5A01G166000 chr5D 92.818 724 28 10 4366 5077 267617946 267618657 0.000000e+00 1027.0
3 TraesCS5A01G166000 chr5D 83.845 619 66 13 5157 5742 380491260 380491877 5.040000e-155 558.0
4 TraesCS5A01G166000 chr5B 94.152 4429 149 45 713 5082 302060468 302064845 0.000000e+00 6643.0
5 TraesCS5A01G166000 chr7D 86.676 698 62 16 5094 5763 590075294 590074600 0.000000e+00 745.0
6 TraesCS5A01G166000 chr7D 78.777 278 33 18 3883 4153 628227649 628227391 4.620000e-36 163.0
7 TraesCS5A01G166000 chr7D 78.623 276 35 16 3883 4151 628228372 628228114 1.660000e-35 161.0
8 TraesCS5A01G166000 chr1A 84.000 575 67 7 5213 5763 60950145 60950718 3.950000e-146 529.0
9 TraesCS5A01G166000 chr1A 77.305 282 27 19 3886 4152 557424058 557424317 1.300000e-26 132.0
10 TraesCS5A01G166000 chr4B 83.399 506 57 14 5095 5575 134775349 134775852 1.470000e-120 444.0
11 TraesCS5A01G166000 chr4B 82.784 273 24 6 3883 4152 362143976 362144228 7.520000e-54 222.0
12 TraesCS5A01G166000 chr4B 89.157 83 6 1 5684 5763 134811358 134811440 3.670000e-17 100.0
13 TraesCS5A01G166000 chr1B 87.879 231 17 11 5094 5322 658734765 658734544 1.590000e-65 261.0
14 TraesCS5A01G166000 chr1B 82.645 242 21 9 3883 4120 174110170 174109946 1.640000e-45 195.0
15 TraesCS5A01G166000 chr1B 94.737 38 2 0 5413 5450 653973605 653973568 6.240000e-05 60.2
16 TraesCS5A01G166000 chrUn 87.446 231 18 11 5094 5322 349649233 349649454 7.410000e-64 255.0
17 TraesCS5A01G166000 chrUn 90.604 149 11 3 5176 5322 451317745 451317598 1.640000e-45 195.0
18 TraesCS5A01G166000 chrUn 97.143 35 1 0 5413 5447 353868572 353868606 6.240000e-05 60.2
19 TraesCS5A01G166000 chrUn 97.143 35 1 0 5413 5447 467532872 467532906 6.240000e-05 60.2
20 TraesCS5A01G166000 chr4D 82.784 273 24 13 3883 4152 294346215 294346467 7.520000e-54 222.0
21 TraesCS5A01G166000 chr3D 81.206 282 31 8 3883 4158 178651811 178652076 2.100000e-49 207.0
22 TraesCS5A01G166000 chr3B 80.851 282 32 8 3883 4158 257098941 257099206 9.790000e-48 202.0
23 TraesCS5A01G166000 chr3B 86.905 84 7 4 5157 5237 377314222 377314140 2.210000e-14 91.6
24 TraesCS5A01G166000 chr7B 78.700 277 35 18 3883 4153 730778666 730778924 4.620000e-36 163.0
25 TraesCS5A01G166000 chr7B 78.700 277 35 18 3883 4153 730805446 730805704 4.620000e-36 163.0
26 TraesCS5A01G166000 chr7A 100.000 32 0 0 5416 5447 5235273 5235242 6.240000e-05 60.2
27 TraesCS5A01G166000 chr7A 100.000 32 0 0 5416 5447 5252471 5252440 6.240000e-05 60.2


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 TraesCS5A01G166000 chr5A 354960166 354965928 5762 False 10643.0 10643 100.000 1 5763 1 chr5A.!!$F1 5762
1 TraesCS5A01G166000 chr5D 267613527 267618657 5130 False 3904.5 6782 93.890 1 5077 2 chr5D.!!$F2 5076
2 TraesCS5A01G166000 chr5D 380491260 380491877 617 False 558.0 558 83.845 5157 5742 1 chr5D.!!$F1 585
3 TraesCS5A01G166000 chr5B 302060468 302064845 4377 False 6643.0 6643 94.152 713 5082 1 chr5B.!!$F1 4369
4 TraesCS5A01G166000 chr7D 590074600 590075294 694 True 745.0 745 86.676 5094 5763 1 chr7D.!!$R1 669
5 TraesCS5A01G166000 chr1A 60950145 60950718 573 False 529.0 529 84.000 5213 5763 1 chr1A.!!$F1 550
6 TraesCS5A01G166000 chr4B 134775349 134775852 503 False 444.0 444 83.399 5095 5575 1 chr4B.!!$F1 480

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
511 514 0.874175 TCTCCGCGTATTTGGCATCG 60.874 55.000 4.92 0.00 0.00 3.84 F
1537 1577 0.037326 TCCCACATTGTGAGCTCGTC 60.037 55.000 18.33 5.51 35.23 4.20 F
1591 1631 0.719465 CGACCAAACTATGCGGTGAC 59.281 55.000 0.00 0.00 31.63 3.67 F
2058 2108 1.816835 CATCATGCTCTGGCTGTTGTT 59.183 47.619 0.00 0.00 39.59 2.83 F
2789 2846 2.290641 TGGAACAATTAGGCATGACCGT 60.291 45.455 0.00 0.00 38.91 4.83 F
3029 3094 4.504858 GACTGTACCATCACTAAGGTTGG 58.495 47.826 0.00 0.00 39.31 3.77 F
3578 3646 4.632153 TGAGTGCTGGACTTCTTACTTTC 58.368 43.478 2.58 0.00 33.83 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1572 1612 0.719465 GTCACCGCATAGTTTGGTCG 59.281 55.000 0.00 0.00 32.48 4.79 R
2725 2782 1.621814 TGCACCCCTACTGTAGTTGTC 59.378 52.381 13.42 5.67 0.00 3.18 R
2735 2792 2.640184 GAACTACCATTGCACCCCTAC 58.360 52.381 0.00 0.00 0.00 3.18 R
3660 3728 0.813184 CATCAATATCGGCATGGGGC 59.187 55.000 0.00 0.00 43.74 5.80 R
4294 4376 0.393077 AACAGGTCTACGCTGTTGCT 59.607 50.000 12.97 0.00 36.62 3.91 R
4353 4453 1.487976 GATTCTGCAGGGATGGTCAGA 59.512 52.381 15.13 0.00 34.16 3.27 R
5501 5667 0.189574 TTGTGCCCAAATTCCTCCCA 59.810 50.000 0.00 0.00 0.00 4.37 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 5.126869 TGAAAATGGCAGTTCAAGAAACTCA 59.873 36.000 12.53 2.74 45.28 3.41
63 64 1.202486 TGACGAGGAAGACAACACACC 60.202 52.381 0.00 0.00 0.00 4.16
65 66 1.485066 ACGAGGAAGACAACACACCTT 59.515 47.619 0.00 0.00 0.00 3.50
69 70 4.755123 CGAGGAAGACAACACACCTTATTT 59.245 41.667 0.00 0.00 0.00 1.40
93 94 1.396996 CACCGCCTACATGCTTAACAC 59.603 52.381 0.00 0.00 0.00 3.32
182 183 4.275689 TGCAAAGCCACTAAATCGATATGG 59.724 41.667 0.00 5.96 0.00 2.74
186 187 3.313012 CCACTAAATCGATATGGCCGA 57.687 47.619 0.00 0.00 40.53 5.54
193 194 8.135529 CACTAAATCGATATGGCCGAATAGATA 58.864 37.037 11.47 0.00 39.62 1.98
196 197 6.716934 ATCGATATGGCCGAATAGATACTT 57.283 37.500 9.95 0.00 39.62 2.24
250 251 6.698008 ATCACACACACATTTCTTTCTCAA 57.302 33.333 0.00 0.00 0.00 3.02
284 285 4.586001 AGCATAAATAATGGTCTTGCCCAG 59.414 41.667 0.00 0.00 42.70 4.45
329 331 7.873719 TCTTTACTTGTGAAACTTCAATGGA 57.126 32.000 0.00 0.00 39.21 3.41
378 380 9.201989 ACTCTAGTCATTAATCTGGTTGTATCA 57.798 33.333 0.00 0.00 0.00 2.15
403 406 6.714278 TCAACCCTTACCCTAATTTCTACAC 58.286 40.000 0.00 0.00 0.00 2.90
408 411 7.017850 ACCCTTACCCTAATTTCTACACTGAAA 59.982 37.037 0.00 0.00 39.79 2.69
424 427 1.270094 TGAAACCATATAGCCTCCGCG 60.270 52.381 0.00 0.00 41.18 6.46
435 438 2.567049 CTCCGCGGAAGAGACGTT 59.433 61.111 30.53 0.00 32.86 3.99
450 453 6.777213 AGAGACGTTGTAACCTCTAATCAT 57.223 37.500 0.67 0.00 34.54 2.45
507 510 0.876342 CTCCTCTCCGCGTATTTGGC 60.876 60.000 4.92 0.00 0.00 4.52
511 514 0.874175 TCTCCGCGTATTTGGCATCG 60.874 55.000 4.92 0.00 0.00 3.84
530 533 1.380380 CTGGATCTGCCCAAACCCC 60.380 63.158 0.00 0.00 35.47 4.95
531 534 2.153898 CTGGATCTGCCCAAACCCCA 62.154 60.000 0.00 0.00 35.47 4.96
532 535 1.682344 GGATCTGCCCAAACCCCAC 60.682 63.158 0.00 0.00 0.00 4.61
542 545 4.785376 TGCCCAAACCCCACATTTATTATT 59.215 37.500 0.00 0.00 0.00 1.40
543 546 5.251700 TGCCCAAACCCCACATTTATTATTT 59.748 36.000 0.00 0.00 0.00 1.40
548 551 6.709018 AACCCCACATTTATTATTTCCTCG 57.291 37.500 0.00 0.00 0.00 4.63
599 602 3.088552 CGACGATTAAACAATCAACCGC 58.911 45.455 0.00 0.00 0.00 5.68
602 605 5.054390 ACGATTAAACAATCAACCGCAAT 57.946 34.783 0.00 0.00 0.00 3.56
603 606 5.092781 ACGATTAAACAATCAACCGCAATC 58.907 37.500 0.00 0.00 0.00 2.67
619 622 4.438797 CCGCAATCTATGAAATTTTCAGCG 59.561 41.667 23.35 23.35 43.98 5.18
658 661 8.195436 AGCAAATCTGAAATGATAATCTGTTGG 58.805 33.333 0.00 0.00 0.00 3.77
671 674 2.766313 TCTGTTGGATCTTCGGTGTTG 58.234 47.619 0.00 0.00 0.00 3.33
673 676 2.878406 CTGTTGGATCTTCGGTGTTGTT 59.122 45.455 0.00 0.00 0.00 2.83
685 688 2.024414 GGTGTTGTTTGTCTCTTGGCT 58.976 47.619 0.00 0.00 0.00 4.75
693 696 4.141620 TGTTTGTCTCTTGGCTCTTCTTCT 60.142 41.667 0.00 0.00 0.00 2.85
699 702 4.082679 TCTCTTGGCTCTTCTTCTACGTTC 60.083 45.833 0.00 0.00 0.00 3.95
701 704 1.201647 TGGCTCTTCTTCTACGTTCGG 59.798 52.381 0.00 0.00 0.00 4.30
1376 1413 4.573900 TGCCTCTCTTTCTTCATTGACTC 58.426 43.478 0.00 0.00 0.00 3.36
1433 1473 2.030805 GCACGGCAACTTTCTCATTTCT 60.031 45.455 0.00 0.00 0.00 2.52
1529 1569 1.894466 TGGATTGCTTCCCACATTGTG 59.106 47.619 9.92 9.92 44.77 3.33
1531 1571 2.165030 GGATTGCTTCCCACATTGTGAG 59.835 50.000 18.33 5.05 38.75 3.51
1537 1577 0.037326 TCCCACATTGTGAGCTCGTC 60.037 55.000 18.33 5.51 35.23 4.20
1568 1608 6.043012 ACATTTTGTCCTCATCCAAAATTCCA 59.957 34.615 7.42 0.00 44.60 3.53
1572 1612 6.284891 TGTCCTCATCCAAAATTCCAAATC 57.715 37.500 0.00 0.00 0.00 2.17
1581 1621 5.069781 TCCAAAATTCCAAATCGACCAAACT 59.930 36.000 0.00 0.00 0.00 2.66
1591 1631 0.719465 CGACCAAACTATGCGGTGAC 59.281 55.000 0.00 0.00 31.63 3.67
1626 1666 4.019858 TGATCTTGATTCGGAGAGACAGT 58.980 43.478 0.00 0.00 38.43 3.55
1643 1683 2.623889 ACAGTCATATCCGTGTCCTAGC 59.376 50.000 0.00 0.00 0.00 3.42
1652 1692 4.184079 TCCGTGTCCTAGCTTAAGTTTC 57.816 45.455 4.02 0.00 0.00 2.78
1685 1725 7.153985 ACAATCATTTTCAATTGTTGATCCGT 58.846 30.769 5.13 8.30 42.00 4.69
1757 1805 8.253113 CCATATTGGAAAGTGCATTTTAAGACT 58.747 33.333 7.22 0.00 40.96 3.24
1813 1861 8.650490 CCATTAAATTTGGCTTAGGTCCAATAT 58.350 33.333 0.00 0.00 42.57 1.28
1911 1961 8.819643 ACTGCTTTCTAAGATTTACGATATCC 57.180 34.615 0.00 0.00 0.00 2.59
1928 1978 7.839438 CGATATCCGTAGAAAACAGACTTAG 57.161 40.000 0.00 0.00 0.00 2.18
1929 1979 7.416022 CGATATCCGTAGAAAACAGACTTAGT 58.584 38.462 0.00 0.00 0.00 2.24
1930 1980 8.554528 CGATATCCGTAGAAAACAGACTTAGTA 58.445 37.037 0.00 0.00 0.00 1.82
1994 2044 7.838771 TTCAGTGACATGATTACTTGATGAG 57.161 36.000 0.00 0.00 0.00 2.90
2051 2101 2.273538 AAGGATCATCATGCTCTGGC 57.726 50.000 0.00 0.00 39.26 4.85
2058 2108 1.816835 CATCATGCTCTGGCTGTTGTT 59.183 47.619 0.00 0.00 39.59 2.83
2082 2132 4.942852 TGTGTTTGGCTTTCCAGTTATTG 58.057 39.130 0.00 0.00 44.53 1.90
2095 2145 5.347342 TCCAGTTATTGTTTGTTGCACTTG 58.653 37.500 0.00 0.00 0.00 3.16
2102 2152 6.799926 ATTGTTTGTTGCACTTGTTTCTTT 57.200 29.167 0.00 0.00 0.00 2.52
2332 2383 7.044181 CCGCATCCAAATCATGATAGTAGTAT 58.956 38.462 9.04 0.00 0.00 2.12
2471 2525 7.339212 AGCAGCTTTAATTGGTATCACAATACA 59.661 33.333 0.00 0.00 40.01 2.29
2472 2526 7.973388 GCAGCTTTAATTGGTATCACAATACAA 59.027 33.333 0.00 0.00 40.01 2.41
2789 2846 2.290641 TGGAACAATTAGGCATGACCGT 60.291 45.455 0.00 0.00 38.91 4.83
2794 2851 4.776349 ACAATTAGGCATGACCGTAATGA 58.224 39.130 0.00 0.00 46.52 2.57
2854 2916 8.429641 TCTGTCACTTTAGAGTTTAGACCAAAT 58.570 33.333 0.00 0.00 32.54 2.32
3029 3094 4.504858 GACTGTACCATCACTAAGGTTGG 58.495 47.826 0.00 0.00 39.31 3.77
3384 3452 8.768397 ACACTTATAGATGGTAACTGAAATGGA 58.232 33.333 0.00 0.00 37.61 3.41
3578 3646 4.632153 TGAGTGCTGGACTTCTTACTTTC 58.368 43.478 2.58 0.00 33.83 2.62
3797 3865 6.648725 CCGTTTGATGTTAATTGTTTTGGGAT 59.351 34.615 0.00 0.00 0.00 3.85
3813 3881 5.540400 TTGGGATTGATAGTTAGTACCCG 57.460 43.478 0.00 0.00 38.96 5.28
3990 4066 5.665459 AGATGCACTAAGATCTACAACACC 58.335 41.667 0.00 0.00 0.00 4.16
3991 4067 4.882842 TGCACTAAGATCTACAACACCA 57.117 40.909 0.00 0.00 0.00 4.17
3992 4068 5.222079 TGCACTAAGATCTACAACACCAA 57.778 39.130 0.00 0.00 0.00 3.67
3993 4069 5.616270 TGCACTAAGATCTACAACACCAAA 58.384 37.500 0.00 0.00 0.00 3.28
3994 4070 6.058833 TGCACTAAGATCTACAACACCAAAA 58.941 36.000 0.00 0.00 0.00 2.44
3995 4071 6.714810 TGCACTAAGATCTACAACACCAAAAT 59.285 34.615 0.00 0.00 0.00 1.82
3996 4072 7.880713 TGCACTAAGATCTACAACACCAAAATA 59.119 33.333 0.00 0.00 0.00 1.40
3997 4073 8.175716 GCACTAAGATCTACAACACCAAAATAC 58.824 37.037 0.00 0.00 0.00 1.89
4066 4146 9.871238 TGAGACTAATTTGGTGTTCTACTAATC 57.129 33.333 0.00 0.00 29.30 1.75
4324 4406 4.849883 CGTAGACCTGTTCTATGCTAGTG 58.150 47.826 0.00 0.00 39.13 2.74
4347 4447 9.740710 AGTGAAAAGGCTTGTAGTTATAAATCT 57.259 29.630 0.00 0.00 0.00 2.40
4348 4448 9.774742 GTGAAAAGGCTTGTAGTTATAAATCTG 57.225 33.333 0.00 0.00 0.00 2.90
4349 4449 9.733556 TGAAAAGGCTTGTAGTTATAAATCTGA 57.266 29.630 0.00 0.00 0.00 3.27
4386 4505 5.388654 CCTGCAGAATCCATTATTTAGGGT 58.611 41.667 17.39 0.00 0.00 4.34
4388 4507 6.324770 CCTGCAGAATCCATTATTTAGGGTTT 59.675 38.462 17.39 0.00 0.00 3.27
4435 4563 3.809832 ACAAATAGCTCATCATGGCGTAC 59.190 43.478 0.00 0.00 0.00 3.67
4436 4564 4.060900 CAAATAGCTCATCATGGCGTACT 58.939 43.478 0.00 0.00 0.00 2.73
4437 4565 2.800881 TAGCTCATCATGGCGTACTG 57.199 50.000 0.00 0.00 0.00 2.74
4438 4566 0.531532 AGCTCATCATGGCGTACTGC 60.532 55.000 0.00 1.72 45.38 4.40
4651 4779 0.384669 CGGGTTCGTCCTATCCTGAC 59.615 60.000 0.00 0.00 36.25 3.51
4955 5085 8.414003 GTTCCTGATGTCTGTAGATGTATGTAA 58.586 37.037 0.00 0.00 0.00 2.41
5034 5165 6.183360 GGTTTCTCCTGATTCCGTAAATCTTG 60.183 42.308 8.65 3.34 43.61 3.02
5042 5173 5.705441 TGATTCCGTAAATCTTGTTTGAGCT 59.295 36.000 8.65 0.00 43.61 4.09
5043 5174 6.876789 TGATTCCGTAAATCTTGTTTGAGCTA 59.123 34.615 8.65 0.00 43.61 3.32
5044 5175 7.552687 TGATTCCGTAAATCTTGTTTGAGCTAT 59.447 33.333 8.65 0.00 43.61 2.97
5082 5213 6.791867 TCTGTTGAGCAACCTACATATACT 57.208 37.500 10.54 0.00 40.46 2.12
5083 5214 7.891498 TCTGTTGAGCAACCTACATATACTA 57.109 36.000 10.54 0.00 40.46 1.82
5084 5215 8.478775 TCTGTTGAGCAACCTACATATACTAT 57.521 34.615 10.54 0.00 40.46 2.12
5085 5216 8.924303 TCTGTTGAGCAACCTACATATACTATT 58.076 33.333 10.54 0.00 40.46 1.73
5155 5286 2.132762 GCCCTTACAATGACCGATACG 58.867 52.381 0.00 0.00 0.00 3.06
5160 5291 4.266976 CCTTACAATGACCGATACGAACAC 59.733 45.833 0.00 0.00 0.00 3.32
5163 5294 2.288961 ATGACCGATACGAACACCAC 57.711 50.000 0.00 0.00 0.00 4.16
5164 5295 0.960286 TGACCGATACGAACACCACA 59.040 50.000 0.00 0.00 0.00 4.17
5167 5298 1.068895 ACCGATACGAACACCACAACA 59.931 47.619 0.00 0.00 0.00 3.33
5168 5299 1.458064 CCGATACGAACACCACAACAC 59.542 52.381 0.00 0.00 0.00 3.32
5181 5312 2.985809 CCACAACACACAACAACAACAG 59.014 45.455 0.00 0.00 0.00 3.16
5182 5313 3.304996 CCACAACACACAACAACAACAGA 60.305 43.478 0.00 0.00 0.00 3.41
5185 5316 5.233050 CACAACACACAACAACAACAGAAAA 59.767 36.000 0.00 0.00 0.00 2.29
5186 5317 5.233263 ACAACACACAACAACAACAGAAAAC 59.767 36.000 0.00 0.00 0.00 2.43
5190 5321 6.019156 ACACACAACAACAACAGAAAACAAAG 60.019 34.615 0.00 0.00 0.00 2.77
5191 5322 6.199908 CACACAACAACAACAGAAAACAAAGA 59.800 34.615 0.00 0.00 0.00 2.52
5192 5323 6.200097 ACACAACAACAACAGAAAACAAAGAC 59.800 34.615 0.00 0.00 0.00 3.01
5193 5324 5.401079 ACAACAACAACAGAAAACAAAGACG 59.599 36.000 0.00 0.00 0.00 4.18
5194 5325 4.481463 ACAACAACAGAAAACAAAGACGG 58.519 39.130 0.00 0.00 0.00 4.79
5195 5326 3.145212 ACAACAGAAAACAAAGACGGC 57.855 42.857 0.00 0.00 0.00 5.68
5238 5374 3.119637 ACGAACAACAAAACCCACAAGAG 60.120 43.478 0.00 0.00 0.00 2.85
5330 5487 0.763035 ACCGAAGCAAGGTACTGGTT 59.237 50.000 0.00 0.00 40.86 3.67
5356 5513 2.025981 TGAAGCAATGCCACTACCATCT 60.026 45.455 0.00 0.00 0.00 2.90
5414 5571 2.860971 AAAGGAGCCCACCTGCCT 60.861 61.111 0.00 0.00 40.49 4.75
5441 5607 4.587189 GCTCGAAGGGCGCCGTAT 62.587 66.667 23.92 12.65 40.61 3.06
5501 5667 1.070786 ACAAACGCCGAGACCACAT 59.929 52.632 0.00 0.00 0.00 3.21
5522 5688 0.243636 GGAGGAATTTGGGCACAACG 59.756 55.000 0.00 0.00 36.06 4.10
5565 5731 2.711922 GGTCACCATCGTCGAGGCT 61.712 63.158 0.33 0.00 0.00 4.58
5566 5732 1.381928 GGTCACCATCGTCGAGGCTA 61.382 60.000 0.33 0.00 0.00 3.93
5583 5749 1.398071 GCTACAAAACCGTCGAAGTGC 60.398 52.381 0.00 0.00 0.00 4.40
5587 5753 1.329292 CAAAACCGTCGAAGTGCAGAA 59.671 47.619 0.00 0.00 0.00 3.02
5628 5794 2.825836 CCTCGGCCACCAGCAATC 60.826 66.667 2.24 0.00 46.50 2.67
5632 5798 1.452651 CGGCCACCAGCAATCAGAT 60.453 57.895 2.24 0.00 46.50 2.90
5659 5825 2.235650 CTCATGAGACAGAGCCTCCAAA 59.764 50.000 18.34 0.00 0.00 3.28
5669 5835 0.539669 AGCCTCCAAAAAGGGAACGG 60.540 55.000 0.00 0.00 36.27 4.44
5680 5846 1.302511 GGGAACGGCATGACAGTGT 60.303 57.895 0.00 0.00 0.00 3.55
5682 5848 0.602638 GGAACGGCATGACAGTGTCA 60.603 55.000 27.35 27.35 46.90 3.58
5756 5925 0.759346 GAGGACAACCCACAGTGACT 59.241 55.000 0.62 0.00 37.41 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 5.643777 CCTCGTCAAGGTATTCATCAACTTT 59.356 40.000 0.00 0.00 40.67 2.66
57 58 2.292292 GCGGTGTTGAAATAAGGTGTGT 59.708 45.455 0.00 0.00 0.00 3.72
63 64 4.730613 GCATGTAGGCGGTGTTGAAATAAG 60.731 45.833 0.00 0.00 0.00 1.73
65 66 2.680841 GCATGTAGGCGGTGTTGAAATA 59.319 45.455 0.00 0.00 0.00 1.40
69 70 0.036164 AAGCATGTAGGCGGTGTTGA 59.964 50.000 0.00 0.00 39.27 3.18
93 94 1.596954 CCTTTCAACACCGACGCTTTG 60.597 52.381 0.00 0.00 0.00 2.77
98 99 4.939509 ATTATTCCTTTCAACACCGACG 57.060 40.909 0.00 0.00 0.00 5.12
99 100 7.548196 TCATATTATTCCTTTCAACACCGAC 57.452 36.000 0.00 0.00 0.00 4.79
182 183 5.106908 GCCAAGAATGAAGTATCTATTCGGC 60.107 44.000 0.00 0.00 36.27 5.54
186 187 8.757982 AATGTGCCAAGAATGAAGTATCTATT 57.242 30.769 0.00 0.00 0.00 1.73
193 194 5.534207 TTTGAATGTGCCAAGAATGAAGT 57.466 34.783 0.00 0.00 0.00 3.01
196 197 5.179742 GCAAATTTGAATGTGCCAAGAATGA 59.820 36.000 22.31 0.00 42.56 2.57
308 310 7.556275 ACTCTTCCATTGAAGTTTCACAAGTAA 59.444 33.333 6.45 0.00 46.66 2.24
329 331 2.158623 TCCAAGTGCAATGACCACTCTT 60.159 45.455 2.43 0.00 42.37 2.85
333 335 3.347216 AGTATCCAAGTGCAATGACCAC 58.653 45.455 2.43 0.00 0.00 4.16
378 380 7.184022 AGTGTAGAAATTAGGGTAAGGGTTGAT 59.816 37.037 0.00 0.00 0.00 2.57
379 381 6.502863 AGTGTAGAAATTAGGGTAAGGGTTGA 59.497 38.462 0.00 0.00 0.00 3.18
380 382 6.598064 CAGTGTAGAAATTAGGGTAAGGGTTG 59.402 42.308 0.00 0.00 0.00 3.77
403 406 2.417719 GCGGAGGCTATATGGTTTCAG 58.582 52.381 0.00 0.00 35.83 3.02
408 411 0.830444 TTCCGCGGAGGCTATATGGT 60.830 55.000 29.20 0.00 40.77 3.55
476 479 0.532573 GAGAGGAGCCGATGACAACA 59.467 55.000 0.00 0.00 0.00 3.33
507 510 0.749091 TTTGGGCAGATCCAGCGATG 60.749 55.000 0.00 0.00 38.17 3.84
511 514 2.054453 GGGTTTGGGCAGATCCAGC 61.054 63.158 0.00 0.00 38.17 4.85
530 533 6.564125 GCCGAGTCGAGGAAATAATAAATGTG 60.564 42.308 15.64 0.00 0.00 3.21
531 534 5.465724 GCCGAGTCGAGGAAATAATAAATGT 59.534 40.000 15.64 0.00 0.00 2.71
532 535 5.388475 CGCCGAGTCGAGGAAATAATAAATG 60.388 44.000 15.64 0.00 0.00 2.32
548 551 0.528466 TGATTCATGCTCGCCGAGTC 60.528 55.000 16.50 8.68 31.39 3.36
599 602 7.911727 TCATGTCGCTGAAAATTTCATAGATTG 59.088 33.333 9.02 12.07 39.30 2.67
602 605 6.983474 TCATGTCGCTGAAAATTTCATAGA 57.017 33.333 9.02 8.70 39.30 1.98
603 606 7.752239 AGTTTCATGTCGCTGAAAATTTCATAG 59.248 33.333 9.02 6.56 44.38 2.23
658 661 4.058817 AGAGACAAACAACACCGAAGATC 58.941 43.478 0.00 0.00 0.00 2.75
671 674 4.384940 AGAAGAAGAGCCAAGAGACAAAC 58.615 43.478 0.00 0.00 0.00 2.93
673 676 4.321304 CGTAGAAGAAGAGCCAAGAGACAA 60.321 45.833 0.00 0.00 0.00 3.18
685 688 3.152341 AGGTTCCGAACGTAGAAGAAGA 58.848 45.455 4.66 0.00 0.00 2.87
701 704 5.241728 ACAGAGCTGTAAATTTGGAAGGTTC 59.758 40.000 0.41 0.00 42.90 3.62
771 774 2.188837 GCCGCTGCCACTATTTTAAC 57.811 50.000 0.00 0.00 0.00 2.01
1122 1145 1.380650 GAGGAAGACGGAGGAGCCT 60.381 63.158 0.00 0.00 0.00 4.58
1206 1229 1.298014 CTTCTTCTTGGCGAGCCCT 59.702 57.895 12.05 0.00 34.56 5.19
1376 1413 1.097547 GGGCACATCTGGATTGACCG 61.098 60.000 0.00 0.00 42.61 4.79
1529 1569 5.232414 GGACAAAATGTGTATAGACGAGCTC 59.768 44.000 2.73 2.73 41.96 4.09
1531 1571 5.109903 AGGACAAAATGTGTATAGACGAGC 58.890 41.667 0.00 0.00 41.96 5.03
1537 1577 7.864108 TTGGATGAGGACAAAATGTGTATAG 57.136 36.000 0.00 0.00 41.96 1.31
1568 1608 2.418628 CACCGCATAGTTTGGTCGATTT 59.581 45.455 0.00 0.00 32.48 2.17
1572 1612 0.719465 GTCACCGCATAGTTTGGTCG 59.281 55.000 0.00 0.00 32.48 4.79
1581 1621 2.661718 TGGTAGATCTGTCACCGCATA 58.338 47.619 5.18 0.00 34.94 3.14
1626 1666 5.138276 ACTTAAGCTAGGACACGGATATGA 58.862 41.667 1.29 0.00 0.00 2.15
1643 1683 9.965824 AAATGATTGTAACCACAGAAACTTAAG 57.034 29.630 0.00 0.00 35.67 1.85
1652 1692 8.592105 ACAATTGAAAATGATTGTAACCACAG 57.408 30.769 13.59 0.00 42.82 3.66
1781 1829 5.422012 CCTAAGCCAAATTTAATGGAGTGGT 59.578 40.000 0.00 0.00 40.56 4.16
1813 1861 2.373169 AGGATGCTCAAGAGGTTGACAA 59.627 45.455 0.00 0.00 37.79 3.18
1930 1980 8.968969 CGTCTTAGGCCCTTTAGTAGAATATAT 58.031 37.037 0.00 0.00 0.00 0.86
2051 2101 4.142924 GGAAAGCCAAACACAAAACAACAG 60.143 41.667 0.00 0.00 0.00 3.16
2058 2108 3.971245 AACTGGAAAGCCAAACACAAA 57.029 38.095 0.00 0.00 45.41 2.83
2082 2132 8.439286 TGATAAAAAGAAACAAGTGCAACAAAC 58.561 29.630 0.00 0.00 41.43 2.93
2116 2166 5.063204 TCAGCTGAAAAGAAAATCGAGGAA 58.937 37.500 15.67 0.00 0.00 3.36
2332 2383 7.930325 CACTGAGCTGGAAGATGAAAGATATAA 59.070 37.037 0.00 0.00 34.07 0.98
2471 2525 9.338622 GGTACCAGCACAGATAGTTAAATTATT 57.661 33.333 7.15 0.00 0.00 1.40
2472 2526 8.491134 TGGTACCAGCACAGATAGTTAAATTAT 58.509 33.333 11.60 0.00 0.00 1.28
2481 2535 5.791336 TCTATTGGTACCAGCACAGATAG 57.209 43.478 15.65 16.86 0.00 2.08
2725 2782 1.621814 TGCACCCCTACTGTAGTTGTC 59.378 52.381 13.42 5.67 0.00 3.18
2735 2792 2.640184 GAACTACCATTGCACCCCTAC 58.360 52.381 0.00 0.00 0.00 3.18
2831 2893 8.379457 ACATTTGGTCTAAACTCTAAAGTGAC 57.621 34.615 0.00 0.00 35.36 3.67
3029 3094 5.530519 TCGATTTTGCTAACATCACAGAC 57.469 39.130 0.00 0.00 0.00 3.51
3078 3143 6.390165 AGCAGAAGGGGGTAAAAGAGTATAAT 59.610 38.462 0.00 0.00 0.00 1.28
3455 3523 6.589523 CAGAAATGTGAACAAAAGTTCAACCA 59.410 34.615 12.10 8.05 43.84 3.67
3578 3646 7.099266 TCCTACATTAAATCAATTGCCAGTG 57.901 36.000 0.00 0.00 0.00 3.66
3660 3728 0.813184 CATCAATATCGGCATGGGGC 59.187 55.000 0.00 0.00 43.74 5.80
3797 3865 3.368248 AGGCACGGGTACTAACTATCAA 58.632 45.455 0.00 0.00 0.00 2.57
3813 3881 6.956299 TTTGATACGAGTAGTTTTAGGCAC 57.044 37.500 0.00 0.00 0.00 5.01
4114 4194 9.632807 CAAAATAATTGAAGTTCCGGATTTGTA 57.367 29.630 4.15 0.00 0.00 2.41
4120 4200 6.568844 CGTTCCAAAATAATTGAAGTTCCGGA 60.569 38.462 0.00 0.00 0.00 5.14
4294 4376 0.393077 AACAGGTCTACGCTGTTGCT 59.607 50.000 12.97 0.00 36.62 3.91
4301 4383 2.873133 AGCATAGAACAGGTCTACGC 57.127 50.000 5.35 5.35 46.27 4.42
4346 4446 2.036992 GCAGGGATGGTCAGATACTCAG 59.963 54.545 0.00 0.00 0.00 3.35
4347 4447 2.042464 GCAGGGATGGTCAGATACTCA 58.958 52.381 0.00 0.00 0.00 3.41
4348 4448 2.036992 CTGCAGGGATGGTCAGATACTC 59.963 54.545 5.57 0.00 0.00 2.59
4349 4449 2.045524 CTGCAGGGATGGTCAGATACT 58.954 52.381 5.57 0.00 0.00 2.12
4350 4450 2.042464 TCTGCAGGGATGGTCAGATAC 58.958 52.381 15.13 0.00 31.35 2.24
4352 4452 1.588239 TTCTGCAGGGATGGTCAGAT 58.412 50.000 15.13 0.00 35.74 2.90
4353 4453 1.487976 GATTCTGCAGGGATGGTCAGA 59.512 52.381 15.13 0.00 34.16 3.27
4651 4779 1.798813 GTTACAAACTGGCGGAGAGTG 59.201 52.381 0.00 0.00 0.00 3.51
4756 4884 6.006449 AGCAGTTCCATTTACTCATCAAGTT 58.994 36.000 0.00 0.00 39.55 2.66
4763 4891 5.129634 TGTTGAAGCAGTTCCATTTACTCA 58.870 37.500 0.00 0.00 0.00 3.41
5034 5165 5.352569 ACATGCACAAGTCTATAGCTCAAAC 59.647 40.000 0.00 0.00 0.00 2.93
5042 5173 6.463360 TCAACAGAACATGCACAAGTCTATA 58.537 36.000 0.00 0.00 0.00 1.31
5043 5174 5.308014 TCAACAGAACATGCACAAGTCTAT 58.692 37.500 0.00 0.00 0.00 1.98
5044 5175 4.702831 TCAACAGAACATGCACAAGTCTA 58.297 39.130 0.00 0.00 0.00 2.59
5095 5226 3.586100 GCGATGGCCTCCTTTTAAAAA 57.414 42.857 3.32 0.00 0.00 1.94
5155 5286 2.983803 GTTGTTGTGTGTTGTGGTGTTC 59.016 45.455 0.00 0.00 0.00 3.18
5160 5291 2.985809 CTGTTGTTGTTGTGTGTTGTGG 59.014 45.455 0.00 0.00 0.00 4.17
5163 5294 5.233050 TGTTTTCTGTTGTTGTTGTGTGTTG 59.767 36.000 0.00 0.00 0.00 3.33
5164 5295 5.352284 TGTTTTCTGTTGTTGTTGTGTGTT 58.648 33.333 0.00 0.00 0.00 3.32
5167 5298 6.200097 GTCTTTGTTTTCTGTTGTTGTTGTGT 59.800 34.615 0.00 0.00 0.00 3.72
5168 5299 6.580476 GTCTTTGTTTTCTGTTGTTGTTGTG 58.420 36.000 0.00 0.00 0.00 3.33
5181 5312 5.103290 TGTATCTTGCCGTCTTTGTTTTC 57.897 39.130 0.00 0.00 0.00 2.29
5182 5313 5.705609 ATGTATCTTGCCGTCTTTGTTTT 57.294 34.783 0.00 0.00 0.00 2.43
5185 5316 4.081087 ACCTATGTATCTTGCCGTCTTTGT 60.081 41.667 0.00 0.00 0.00 2.83
5186 5317 4.271049 CACCTATGTATCTTGCCGTCTTTG 59.729 45.833 0.00 0.00 0.00 2.77
5190 5321 3.454371 ACACCTATGTATCTTGCCGTC 57.546 47.619 0.00 0.00 37.26 4.79
5191 5322 3.196901 TCAACACCTATGTATCTTGCCGT 59.803 43.478 0.00 0.00 38.45 5.68
5192 5323 3.792401 TCAACACCTATGTATCTTGCCG 58.208 45.455 0.00 0.00 38.45 5.69
5193 5324 4.130118 CCTCAACACCTATGTATCTTGCC 58.870 47.826 0.00 0.00 38.45 4.52
5194 5325 4.811557 GTCCTCAACACCTATGTATCTTGC 59.188 45.833 0.00 0.00 38.45 4.01
5195 5326 5.043903 CGTCCTCAACACCTATGTATCTTG 58.956 45.833 0.00 0.00 38.45 3.02
5238 5374 2.423538 CCCACCTTATGCTTGCTTGTAC 59.576 50.000 0.00 0.00 0.00 2.90
5277 5413 1.001633 GTTGAGGGCCTCGTTGACTTA 59.998 52.381 27.58 5.41 32.35 2.24
5302 5438 0.239347 CTTGCTTCGGTTGGCTTGAG 59.761 55.000 0.00 0.00 0.00 3.02
5330 5487 1.913778 AGTGGCATTGCTTCATGTCA 58.086 45.000 8.82 0.00 0.00 3.58
5371 5528 2.609427 TGCAGCTGGATGACACTATC 57.391 50.000 17.12 0.00 0.00 2.08
5501 5667 0.189574 TTGTGCCCAAATTCCTCCCA 59.810 50.000 0.00 0.00 0.00 4.37
5522 5688 1.337728 GGGGTGTTAGTTTGCATTGCC 60.338 52.381 6.12 0.00 0.00 4.52
5565 5731 1.862201 CTGCACTTCGACGGTTTTGTA 59.138 47.619 0.00 0.00 0.00 2.41
5566 5732 0.655733 CTGCACTTCGACGGTTTTGT 59.344 50.000 0.00 0.00 0.00 2.83
5583 5749 1.813513 ATGGACGGCAGTTTCTTCTG 58.186 50.000 0.00 0.00 38.35 3.02
5587 5753 1.349688 TGGTAATGGACGGCAGTTTCT 59.650 47.619 0.00 0.00 0.00 2.52
5628 5794 4.756502 TCTGTCTCATGAGCAAAGATCTG 58.243 43.478 18.36 6.04 0.00 2.90
5659 5825 0.110486 ACTGTCATGCCGTTCCCTTT 59.890 50.000 0.00 0.00 0.00 3.11
5680 5846 3.066190 CGGACTAGGCGGTGGTGA 61.066 66.667 0.00 0.00 0.00 4.02
5682 5848 3.066814 GTCGGACTAGGCGGTGGT 61.067 66.667 2.68 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.