Multiple sequence alignment - TraesCS6D01G276800

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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 TraesCS6D01G276800 chr6D 100.000 5579 0 0 1 5579 385660999 385666577 0.000000e+00 10303.0
1 TraesCS6D01G276800 chr6D 82.728 1818 270 34 2804 4604 46050894 46049104 0.000000e+00 1578.0
2 TraesCS6D01G276800 chr6D 92.308 104 6 2 5048 5150 379809054 379808952 4.500000e-31 147.0
3 TraesCS6D01G276800 chr6D 83.333 120 20 0 2150 2269 46052158 46052039 1.640000e-20 111.0
4 TraesCS6D01G276800 chr6A 95.117 4731 197 17 1 4700 530119438 530124165 0.000000e+00 7426.0
5 TraesCS6D01G276800 chr6A 82.649 1729 270 27 2881 4598 60224617 60222908 0.000000e+00 1504.0
6 TraesCS6D01G276800 chr6A 84.065 433 47 12 5150 5579 548663699 548664112 1.130000e-106 398.0
7 TraesCS6D01G276800 chr6A 88.660 291 32 1 4702 4991 548663242 548663532 2.470000e-93 353.0
8 TraesCS6D01G276800 chr6A 94.792 96 4 1 5042 5136 560694301 560694396 1.250000e-31 148.0
9 TraesCS6D01G276800 chr6A 90.265 113 6 5 5027 5136 374418828 374418718 5.830000e-30 143.0
10 TraesCS6D01G276800 chr6B 95.262 2364 101 8 2344 4700 576017140 576019499 0.000000e+00 3735.0
11 TraesCS6D01G276800 chr6B 94.150 1077 37 7 548 1601 576015169 576016242 0.000000e+00 1616.0
12 TraesCS6D01G276800 chr6B 82.379 1816 277 37 2804 4598 114509376 114507583 0.000000e+00 1541.0
13 TraesCS6D01G276800 chr6B 89.873 474 40 3 4 469 576014518 576014991 2.220000e-168 603.0
14 TraesCS6D01G276800 chr6B 93.983 349 16 2 1650 1993 576016237 576016585 1.780000e-144 523.0
15 TraesCS6D01G276800 chr6B 92.486 346 21 2 2002 2342 576016688 576017033 1.810000e-134 490.0
16 TraesCS6D01G276800 chr6B 93.069 101 5 2 5049 5148 291177556 291177655 4.500000e-31 147.0
17 TraesCS6D01G276800 chr6B 80.556 144 26 2 2131 2272 114510585 114510442 5.910000e-20 110.0
18 TraesCS6D01G276800 chr6B 100.000 28 0 0 1541 1568 117860775 117860748 1.000000e-02 52.8
19 TraesCS6D01G276800 chr7D 83.716 436 48 11 5151 5579 630607650 630607231 1.880000e-104 390.0
20 TraesCS6D01G276800 chr7D 87.197 289 26 6 4707 4984 630608094 630607806 9.020000e-83 318.0
21 TraesCS6D01G276800 chr7D 84.034 119 19 0 340 458 56291996 56291878 1.270000e-21 115.0
22 TraesCS6D01G276800 chr7D 83.761 117 19 0 342 458 249795043 249794927 1.640000e-20 111.0
23 TraesCS6D01G276800 chr7D 93.478 46 3 0 4993 5038 630607758 630607713 1.000000e-07 69.4
24 TraesCS6D01G276800 chr7A 82.460 439 51 11 5151 5579 726522408 726521986 1.480000e-95 361.0
25 TraesCS6D01G276800 chr7A 91.304 46 4 0 4993 5038 726522517 726522472 4.670000e-06 63.9
26 TraesCS6D01G276800 chr7B 84.334 383 33 8 5182 5559 66819964 66820324 3.200000e-92 350.0
27 TraesCS6D01G276800 chr7B 83.893 298 30 7 4701 4991 66819490 66819776 9.210000e-68 268.0
28 TraesCS6D01G276800 chr7B 86.765 204 23 4 4701 4903 24046202 24046002 2.020000e-54 224.0
29 TraesCS6D01G276800 chr7B 90.476 63 5 1 4993 5054 66819825 66819887 1.290000e-11 82.4
30 TraesCS6D01G276800 chr5D 84.488 303 31 10 4701 4994 95802467 95802172 9.150000e-73 285.0
31 TraesCS6D01G276800 chr3A 85.000 160 16 6 4740 4898 738060999 738060847 7.480000e-34 156.0
32 TraesCS6D01G276800 chr3A 93.069 101 4 3 5045 5143 51753240 51753339 1.620000e-30 145.0
33 TraesCS6D01G276800 chr4D 95.745 94 3 1 5044 5136 136689429 136689522 3.480000e-32 150.0
34 TraesCS6D01G276800 chr4D 84.545 110 16 1 353 462 338012827 338012719 2.130000e-19 108.0
35 TraesCS6D01G276800 chr4B 94.792 96 3 2 5040 5133 429694766 429694671 1.250000e-31 148.0
36 TraesCS6D01G276800 chr2D 93.069 101 5 2 5036 5134 174430732 174430832 4.500000e-31 147.0
37 TraesCS6D01G276800 chr2B 93.000 100 3 4 5036 5133 54766004 54765907 5.830000e-30 143.0
38 TraesCS6D01G276800 chrUn 82.540 63 11 0 373 435 103376386 103376324 7.810000e-04 56.5
39 TraesCS6D01G276800 chr1B 90.698 43 2 2 1533 1574 599314127 599314086 7.810000e-04 56.5
40 TraesCS6D01G276800 chr4A 100.000 28 0 0 1541 1568 740576854 740576881 1.000000e-02 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G276800 chr6D 385660999 385666577 5578 False 10303.000000 10303 100.000000 1 5579 1 chr6D.!!$F1 5578
1 TraesCS6D01G276800 chr6D 46049104 46052158 3054 True 844.500000 1578 83.030500 2150 4604 2 chr6D.!!$R2 2454
2 TraesCS6D01G276800 chr6A 530119438 530124165 4727 False 7426.000000 7426 95.117000 1 4700 1 chr6A.!!$F1 4699
3 TraesCS6D01G276800 chr6A 60222908 60224617 1709 True 1504.000000 1504 82.649000 2881 4598 1 chr6A.!!$R1 1717
4 TraesCS6D01G276800 chr6A 548663242 548664112 870 False 375.500000 398 86.362500 4702 5579 2 chr6A.!!$F3 877
5 TraesCS6D01G276800 chr6B 576014518 576019499 4981 False 1393.400000 3735 93.150800 4 4700 5 chr6B.!!$F2 4696
6 TraesCS6D01G276800 chr6B 114507583 114510585 3002 True 825.500000 1541 81.467500 2131 4598 2 chr6B.!!$R2 2467
7 TraesCS6D01G276800 chr7D 630607231 630608094 863 True 259.133333 390 88.130333 4707 5579 3 chr7D.!!$R3 872
8 TraesCS6D01G276800 chr7A 726521986 726522517 531 True 212.450000 361 86.882000 4993 5579 2 chr7A.!!$R1 586
9 TraesCS6D01G276800 chr7B 66819490 66820324 834 False 233.466667 350 86.234333 4701 5559 3 chr7B.!!$F1 858

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
502 517 0.244721 TGCATGACTGAGACCGACTG 59.755 55.0 0.0 0.0 0.00 3.51 F
925 1041 0.392595 CGTAGCTTCCTTCCCAACCC 60.393 60.0 0.0 0.0 0.00 4.11 F
1549 1686 0.171231 GAAAAACCATCGGCCTCTGC 59.829 55.0 0.0 0.0 0.00 4.26 F
2740 3758 2.297597 GTCAACAGTCTACAGCCTGACT 59.702 50.0 0.0 0.0 43.45 3.41 F
3462 4495 0.737715 GGAGCGAGCTATTATGGGCG 60.738 60.0 0.0 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1538 1675 1.065199 TCTTTTGATGCAGAGGCCGAT 60.065 47.619 0.00 0.00 40.13 4.18 R
2173 2416 1.147824 CTGCCATGGCTCTTCCGAT 59.852 57.895 35.53 0.00 42.51 4.18 R
3276 4309 0.752743 AGCCTTCACAGTTGCAGCAA 60.753 50.000 2.83 2.83 0.00 3.91 R
4361 5413 1.341531 CGACACTTTGAGACCCTGAGT 59.658 52.381 0.00 0.00 0.00 3.41 R
5143 6281 0.108377 ACTACGGCACATGCGAATCA 60.108 50.000 0.00 0.00 43.26 2.57 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
87 93 3.351794 TCATGGCCATGGTACGTTTTA 57.648 42.857 38.81 18.39 39.24 1.52
121 127 4.792513 TGGTGGTACTTTTTGGAAGGTA 57.207 40.909 0.00 0.00 0.00 3.08
124 130 3.187842 GTGGTACTTTTTGGAAGGTAGCG 59.812 47.826 0.00 0.00 44.22 4.26
133 139 2.362632 AAGGTAGCGTCGCCTCCT 60.363 61.111 20.38 20.38 34.68 3.69
192 198 4.084118 GGCTGCTATGCTCTTAATTTCTCG 60.084 45.833 0.00 0.00 0.00 4.04
197 203 5.509840 GCTATGCTCTTAATTTCTCGGGAGA 60.510 44.000 0.00 0.00 35.27 3.71
204 210 5.715279 TCTTAATTTCTCGGGAGACTCAAGA 59.285 40.000 4.53 2.04 37.14 3.02
334 340 2.403561 TCCATGTCCATCCGGTCATTA 58.596 47.619 0.00 0.00 38.78 1.90
338 344 3.924114 TGTCCATCCGGTCATTAATGT 57.076 42.857 14.97 0.00 0.00 2.71
344 350 5.104693 TCCATCCGGTCATTAATGTGTACTT 60.105 40.000 14.97 0.00 0.00 2.24
349 355 5.395324 CCGGTCATTAATGTGTACTTCCTCT 60.395 44.000 14.97 0.00 0.00 3.69
387 402 5.221422 TGTTCCAAGCTTGTTCCTTAAATGG 60.221 40.000 24.35 6.02 0.00 3.16
394 409 7.338800 AGCTTGTTCCTTAAATGGATGTATG 57.661 36.000 0.00 0.00 35.83 2.39
411 426 9.353431 TGGATGTATGTAGCATTAATTTGATGT 57.647 29.630 3.45 0.00 0.00 3.06
451 466 1.292992 ACAAACTTTGTCGGACGGAC 58.707 50.000 6.22 6.22 40.56 4.79
458 473 3.815396 GTCGGACGGACGGGGTAC 61.815 72.222 0.00 0.00 35.61 3.34
473 488 2.287608 GGGGTACGTACGTAATAGCCAC 60.288 54.545 29.06 23.22 38.06 5.01
474 489 2.357637 GGGTACGTACGTAATAGCCACA 59.642 50.000 28.34 3.51 36.64 4.17
479 494 5.694231 ACGTACGTAATAGCCACATATGA 57.306 39.130 21.41 0.00 0.00 2.15
502 517 0.244721 TGCATGACTGAGACCGACTG 59.755 55.000 0.00 0.00 0.00 3.51
564 678 4.149019 TGCCCTGCACCAACCCAA 62.149 61.111 0.00 0.00 31.71 4.12
646 760 6.008331 ACTGAAACTAACCCCAAGATTAACC 58.992 40.000 0.00 0.00 0.00 2.85
925 1041 0.392595 CGTAGCTTCCTTCCCAACCC 60.393 60.000 0.00 0.00 0.00 4.11
1156 1282 5.067283 TCACTTAACTTCTGGCTTTTGGAAC 59.933 40.000 0.00 0.00 0.00 3.62
1225 1351 8.940952 ACTATGTATCTTTGTTTCTTGCTTCTC 58.059 33.333 0.00 0.00 0.00 2.87
1233 1359 4.717877 TGTTTCTTGCTTCTCCTTGATCA 58.282 39.130 0.00 0.00 0.00 2.92
1247 1373 4.040829 TCCTTGATCAATCCGAGTGCATAT 59.959 41.667 8.96 0.00 0.00 1.78
1273 1399 6.445357 AACGATAAATTGGATTAGCCGTTT 57.555 33.333 0.00 0.00 40.66 3.60
1284 1410 4.331992 GGATTAGCCGTTTGTTCTCCTTAC 59.668 45.833 0.00 0.00 0.00 2.34
1302 1428 7.926555 TCTCCTTACATATTTCCTGAATCGTTC 59.073 37.037 0.00 0.00 0.00 3.95
1333 1459 3.981212 ACATAATCTTTGGGTCAAGGGG 58.019 45.455 0.00 0.00 0.00 4.79
1370 1496 9.717892 CATGAGTTCATATCTTGAGAATTGTTG 57.282 33.333 0.00 0.00 35.27 3.33
1391 1518 2.167693 GAGGTACACCAATCGACATGGA 59.832 50.000 22.33 1.21 40.56 3.41
1413 1550 5.388786 GGACCGTTAATTTCGTGTGTTCTAC 60.389 44.000 0.00 0.00 0.00 2.59
1538 1675 7.038941 TGGGACTTTGTTTTAGAAGAAAAACCA 60.039 33.333 9.10 7.03 44.89 3.67
1549 1686 0.171231 GAAAAACCATCGGCCTCTGC 59.829 55.000 0.00 0.00 0.00 4.26
1615 1752 5.105064 TGGTACAAGTGAGACTAATTAGGCC 60.105 44.000 15.01 7.23 31.92 5.19
1644 1783 7.875041 CCTTTAGGATGATATGTTCGATCTGTT 59.125 37.037 0.00 0.00 37.39 3.16
1649 1788 7.231519 AGGATGATATGTTCGATCTGTTAGACA 59.768 37.037 0.00 0.00 0.00 3.41
1657 1796 6.016527 TGTTCGATCTGTTAGACACAAGTACT 60.017 38.462 0.00 0.00 33.87 2.73
1662 1801 7.361031 CGATCTGTTAGACACAAGTACTACACT 60.361 40.741 0.00 0.00 40.05 3.55
1889 2033 3.818773 TGGACAAACTTAGCCTTGTAAGC 59.181 43.478 1.06 0.00 35.93 3.09
2128 2369 6.910433 CACATGTGTGTTTTAGGAGTGTTAAC 59.090 38.462 18.03 0.00 40.96 2.01
2173 2416 3.198417 TCTGGACTATCTTTGCAGCATCA 59.802 43.478 0.00 0.00 32.72 3.07
2338 2661 7.641411 CCACAATTCGAACTAGCTTCATTTATG 59.359 37.037 0.00 0.00 0.00 1.90
2490 3483 9.631257 AAATTCTCATTCCTTTTGTTTCCAAAT 57.369 25.926 0.00 0.00 40.14 2.32
2657 3653 2.757686 TCAGACGCTACTAGCATTCG 57.242 50.000 8.78 0.00 42.58 3.34
2681 3699 6.818644 CGGTTACATAGCTTATATTCTGCCAT 59.181 38.462 0.00 0.00 0.00 4.40
2740 3758 2.297597 GTCAACAGTCTACAGCCTGACT 59.702 50.000 0.00 0.00 43.45 3.41
2787 3805 7.338957 TGCAACATGTTCATATATTTCCTGACA 59.661 33.333 8.48 0.00 0.00 3.58
2788 3806 7.859377 GCAACATGTTCATATATTTCCTGACAG 59.141 37.037 8.48 0.00 0.00 3.51
3135 4168 6.260714 GCCACCAAGAACAAAATTGAAATCTT 59.739 34.615 0.00 4.45 33.20 2.40
3276 4309 3.181454 GGGTGGACGGATGATCAGTTTAT 60.181 47.826 0.09 0.00 0.00 1.40
3462 4495 0.737715 GGAGCGAGCTATTATGGGCG 60.738 60.000 0.00 0.00 0.00 6.13
3534 4567 3.345714 GCGAATGTAAGTTTGATGCTCG 58.654 45.455 0.00 0.00 0.00 5.03
3787 4828 5.752036 TTGACAAGAGATTGGAGTCTGAT 57.248 39.130 0.00 0.00 0.00 2.90
3826 4867 2.708325 AGACCTCCTGAAGCTTCAAACT 59.292 45.455 28.16 17.14 36.64 2.66
3999 5046 7.615455 ACGCAAAAACGTGTAAAATGGGACA 62.615 40.000 0.00 0.00 46.28 4.02
4147 5196 4.796830 CCTCATTCGCATCAATTTGTGAAG 59.203 41.667 10.83 5.11 46.06 3.02
4156 5205 6.446318 GCATCAATTTGTGAAGAACTAACCA 58.554 36.000 0.00 0.00 40.50 3.67
4677 5729 9.509855 GAGTAATAATAAGATAGCTCATGACGG 57.490 37.037 0.00 0.00 0.00 4.79
4700 5752 6.402118 CGGAACTCAATTATGGTTGTGTACAG 60.402 42.308 0.00 0.00 35.47 2.74
4761 5814 4.738998 CCCATGGCCCAAGTCGCA 62.739 66.667 6.09 0.00 0.00 5.10
4762 5815 3.443045 CCATGGCCCAAGTCGCAC 61.443 66.667 0.00 0.00 0.00 5.34
4763 5816 2.672651 CATGGCCCAAGTCGCACA 60.673 61.111 0.00 0.00 0.00 4.57
4764 5817 2.048023 CATGGCCCAAGTCGCACAT 61.048 57.895 0.00 0.00 0.00 3.21
4765 5818 0.747644 CATGGCCCAAGTCGCACATA 60.748 55.000 0.00 0.00 0.00 2.29
4766 5819 0.464373 ATGGCCCAAGTCGCACATAG 60.464 55.000 0.00 0.00 0.00 2.23
4767 5820 2.472909 GGCCCAAGTCGCACATAGC 61.473 63.158 0.00 0.00 40.87 2.97
4815 5882 2.108157 TGAGTTCGCCTGCGTTGT 59.892 55.556 11.68 0.00 40.74 3.32
4885 5952 1.641577 GCTGAAGTAAATCCGCTCGT 58.358 50.000 0.00 0.00 0.00 4.18
4899 5974 3.647649 CTCGTCGCCATGCACCTGA 62.648 63.158 0.00 0.00 0.00 3.86
4904 5979 2.359850 GCCATGCACCTGAACGGA 60.360 61.111 0.00 0.00 36.31 4.69
4949 6024 3.562176 CCAAGTCCCCTTGTGCTTATCTT 60.562 47.826 2.17 0.00 45.49 2.40
4984 6061 3.459145 CCTCTGAATCTCTGATGTGCAG 58.541 50.000 0.00 0.00 46.31 4.41
5003 6127 2.568956 CAGAGACAATCCCTTCCACTCA 59.431 50.000 0.00 0.00 0.00 3.41
5008 6132 5.397360 AGACAATCCCTTCCACTCATTTTT 58.603 37.500 0.00 0.00 0.00 1.94
5039 6171 1.944024 TGGTCACGTTTCAATGGTGTC 59.056 47.619 0.00 0.00 33.51 3.67
5049 6187 5.517411 CGTTTCAATGGTGTCGTAATAGCTA 59.483 40.000 0.00 0.00 0.00 3.32
5050 6188 6.507456 CGTTTCAATGGTGTCGTAATAGCTAC 60.507 42.308 0.00 0.00 0.00 3.58
5052 6190 5.828747 TCAATGGTGTCGTAATAGCTACTC 58.171 41.667 0.00 0.00 0.00 2.59
5053 6191 4.850347 ATGGTGTCGTAATAGCTACTCC 57.150 45.455 0.00 0.00 0.00 3.85
5054 6192 2.954318 TGGTGTCGTAATAGCTACTCCC 59.046 50.000 0.00 0.00 0.00 4.30
5056 6194 3.252944 GGTGTCGTAATAGCTACTCCCTC 59.747 52.174 0.00 0.00 0.00 4.30
5057 6195 3.252944 GTGTCGTAATAGCTACTCCCTCC 59.747 52.174 0.00 0.00 0.00 4.30
5059 6197 2.105477 TCGTAATAGCTACTCCCTCCGT 59.895 50.000 0.00 0.00 0.00 4.69
5060 6198 2.883386 CGTAATAGCTACTCCCTCCGTT 59.117 50.000 0.00 0.00 0.00 4.44
5061 6199 3.058363 CGTAATAGCTACTCCCTCCGTTC 60.058 52.174 0.00 0.00 0.00 3.95
5062 6200 1.998222 ATAGCTACTCCCTCCGTTCC 58.002 55.000 0.00 0.00 0.00 3.62
5063 6201 0.627451 TAGCTACTCCCTCCGTTCCA 59.373 55.000 0.00 0.00 0.00 3.53
5064 6202 0.252103 AGCTACTCCCTCCGTTCCAA 60.252 55.000 0.00 0.00 0.00 3.53
5065 6203 0.611714 GCTACTCCCTCCGTTCCAAA 59.388 55.000 0.00 0.00 0.00 3.28
5066 6204 1.209747 GCTACTCCCTCCGTTCCAAAT 59.790 52.381 0.00 0.00 0.00 2.32
5067 6205 2.433239 GCTACTCCCTCCGTTCCAAATA 59.567 50.000 0.00 0.00 0.00 1.40
5068 6206 3.492829 GCTACTCCCTCCGTTCCAAATAG 60.493 52.174 0.00 0.00 0.00 1.73
5069 6207 2.829023 ACTCCCTCCGTTCCAAATAGA 58.171 47.619 0.00 0.00 0.00 1.98
5070 6208 3.385115 ACTCCCTCCGTTCCAAATAGAT 58.615 45.455 0.00 0.00 0.00 1.98
5071 6209 3.134804 ACTCCCTCCGTTCCAAATAGATG 59.865 47.826 0.00 0.00 0.00 2.90
5072 6210 3.380393 TCCCTCCGTTCCAAATAGATGA 58.620 45.455 0.00 0.00 0.00 2.92
5073 6211 3.973973 TCCCTCCGTTCCAAATAGATGAT 59.026 43.478 0.00 0.00 0.00 2.45
5074 6212 4.040461 TCCCTCCGTTCCAAATAGATGATC 59.960 45.833 0.00 0.00 0.00 2.92
5075 6213 4.319177 CCTCCGTTCCAAATAGATGATCC 58.681 47.826 0.00 0.00 0.00 3.36
5076 6214 4.202357 CCTCCGTTCCAAATAGATGATCCA 60.202 45.833 0.00 0.00 0.00 3.41
5077 6215 5.366482 TCCGTTCCAAATAGATGATCCAA 57.634 39.130 0.00 0.00 0.00 3.53
5078 6216 5.123227 TCCGTTCCAAATAGATGATCCAAC 58.877 41.667 0.00 0.00 0.00 3.77
5079 6217 5.104527 TCCGTTCCAAATAGATGATCCAACT 60.105 40.000 0.00 0.00 0.00 3.16
5080 6218 5.590259 CCGTTCCAAATAGATGATCCAACTT 59.410 40.000 0.00 0.00 0.00 2.66
5081 6219 6.095440 CCGTTCCAAATAGATGATCCAACTTT 59.905 38.462 0.00 0.00 0.00 2.66
5082 6220 6.968904 CGTTCCAAATAGATGATCCAACTTTG 59.031 38.462 0.00 0.00 0.00 2.77
5083 6221 7.362056 CGTTCCAAATAGATGATCCAACTTTGT 60.362 37.037 0.00 0.00 0.00 2.83
5084 6222 8.956426 GTTCCAAATAGATGATCCAACTTTGTA 58.044 33.333 0.00 0.00 0.00 2.41
5085 6223 8.506168 TCCAAATAGATGATCCAACTTTGTAC 57.494 34.615 0.00 0.00 0.00 2.90
5086 6224 8.328758 TCCAAATAGATGATCCAACTTTGTACT 58.671 33.333 0.00 0.00 0.00 2.73
5087 6225 9.613428 CCAAATAGATGATCCAACTTTGTACTA 57.387 33.333 0.00 0.00 0.00 1.82
5119 6257 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
5120 6258 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
5121 6259 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
5122 6260 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
5123 6261 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
5124 6262 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
5125 6263 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
5126 6264 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
5127 6265 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
5128 6266 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
5129 6267 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
5130 6268 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
5131 6269 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
5157 6295 2.161012 CCTATGATGATTCGCATGTGCC 59.839 50.000 0.00 0.00 37.34 5.01
5164 6302 0.108377 ATTCGCATGTGCCGTAGTGA 60.108 50.000 0.00 0.00 37.91 3.41
5180 6353 6.745907 GCCGTAGTGAAAAATTTTAGTCCATC 59.254 38.462 3.34 0.00 0.00 3.51
5200 6373 2.548295 GCCCGTTCCGCTGTTTCAA 61.548 57.895 0.00 0.00 0.00 2.69
5253 6426 7.692460 TTGACTATTTCTTACTACACCGAGA 57.308 36.000 0.00 0.00 0.00 4.04
5255 6428 6.883217 TGACTATTTCTTACTACACCGAGAGT 59.117 38.462 0.00 0.00 0.00 3.24
5292 6465 8.950403 ATTGCAAGTTAACTTAGAATTTCGAC 57.050 30.769 20.15 3.81 34.28 4.20
5312 6488 3.577649 CGATGGACTCGGCTATTACAT 57.422 47.619 0.00 0.00 43.82 2.29
5362 6540 1.972588 AAAGGCCCACTCATACTCCT 58.027 50.000 0.00 0.00 0.00 3.69
5465 6647 9.462174 CAAACATCAAACTTAAATCAGTGCTAA 57.538 29.630 0.00 0.00 0.00 3.09
5508 6690 8.505625 ACTTTCTCTAGTAAACTCGTTCTACTG 58.494 37.037 11.44 5.78 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 93 1.222567 ACCACCAAAGGACACCTTCT 58.777 50.000 3.45 0.00 43.92 2.85
133 139 2.363276 ACGTACCCATCGAGCCCA 60.363 61.111 0.00 0.00 0.00 5.36
192 198 2.499289 TGAGCATTCTCTTGAGTCTCCC 59.501 50.000 0.00 0.00 40.03 4.30
197 203 1.895798 TCCGTGAGCATTCTCTTGAGT 59.104 47.619 0.00 0.00 40.03 3.41
281 287 2.611971 CCCGAATTCCGTCTTCAGTTCA 60.612 50.000 0.00 0.00 36.31 3.18
334 340 3.162666 TCGGTCAGAGGAAGTACACATT 58.837 45.455 0.00 0.00 0.00 2.71
338 344 4.675976 TTTTTCGGTCAGAGGAAGTACA 57.324 40.909 0.00 0.00 0.00 2.90
414 429 6.527423 AGTTTGTTCCTCAAATGAATGCATT 58.473 32.000 12.83 12.83 45.88 3.56
417 432 6.258507 ACAAAGTTTGTTCCTCAAATGAATGC 59.741 34.615 15.58 0.00 45.88 3.56
422 437 4.739716 CCGACAAAGTTTGTTCCTCAAATG 59.260 41.667 21.70 4.82 45.88 2.32
441 456 3.815396 GTACCCCGTCCGTCCGAC 61.815 72.222 0.00 0.00 38.21 4.79
451 466 1.069227 GGCTATTACGTACGTACCCCG 60.069 57.143 26.83 15.96 44.03 5.73
454 469 3.691049 TGTGGCTATTACGTACGTACC 57.309 47.619 26.83 23.05 0.00 3.34
458 473 5.916320 TGTTCATATGTGGCTATTACGTACG 59.084 40.000 15.01 15.01 0.00 3.67
473 488 5.049612 GGTCTCAGTCATGCATGTTCATATG 60.050 44.000 25.43 15.26 0.00 1.78
474 489 5.061853 GGTCTCAGTCATGCATGTTCATAT 58.938 41.667 25.43 4.66 0.00 1.78
479 494 1.276138 TCGGTCTCAGTCATGCATGTT 59.724 47.619 25.43 12.93 0.00 2.71
502 517 1.057636 TTGCGAGTCGTCAAATCGTC 58.942 50.000 15.08 0.00 38.66 4.20
939 1055 2.305009 AGCAGATTAATGAAGCTGGCC 58.695 47.619 10.11 0.00 46.95 5.36
941 1057 4.387598 AGCTAGCAGATTAATGAAGCTGG 58.612 43.478 18.83 11.88 46.95 4.85
947 1065 5.600069 TCAGGAAGAGCTAGCAGATTAATGA 59.400 40.000 18.83 9.63 0.00 2.57
1177 1303 3.846360 TGCTAGCTACGAGGAAAGAAAC 58.154 45.455 17.23 0.00 0.00 2.78
1225 1351 2.028420 TGCACTCGGATTGATCAAGG 57.972 50.000 14.54 6.00 0.00 3.61
1233 1359 9.817809 ATTTATCGTTATATATGCACTCGGATT 57.182 29.630 0.00 0.00 0.00 3.01
1247 1373 8.836268 AACGGCTAATCCAATTTATCGTTATA 57.164 30.769 0.00 0.00 33.36 0.98
1273 1399 7.710907 CGATTCAGGAAATATGTAAGGAGAACA 59.289 37.037 0.00 0.00 0.00 3.18
1284 1410 4.570772 ACACCGAACGATTCAGGAAATATG 59.429 41.667 0.00 0.00 0.00 1.78
1302 1428 7.281324 TGACCCAAAGATTATGTTATTACACCG 59.719 37.037 0.00 0.00 37.03 4.94
1370 1496 2.167693 TCCATGTCGATTGGTGTACCTC 59.832 50.000 14.79 0.00 35.64 3.85
1391 1518 5.049167 TGTAGAACACACGAAATTAACGGT 58.951 37.500 9.19 0.00 34.93 4.83
1538 1675 1.065199 TCTTTTGATGCAGAGGCCGAT 60.065 47.619 0.00 0.00 40.13 4.18
1549 1686 8.172484 CCAAATATTTGTGTGCATCTTTTGATG 58.828 33.333 23.24 2.02 45.51 3.07
1589 1726 7.048512 GCCTAATTAGTCTCACTTGTACCATT 58.951 38.462 11.50 0.00 0.00 3.16
1644 1783 6.131972 ACCCTAGTGTAGTACTTGTGTCTA 57.868 41.667 0.00 0.00 40.89 2.59
1649 1788 9.097946 AGAAATTTACCCTAGTGTAGTACTTGT 57.902 33.333 0.00 0.00 40.89 3.16
1662 1801 6.975949 TGGCTTGGATAAGAAATTTACCCTA 58.024 36.000 0.00 0.00 35.92 3.53
1745 1884 3.679980 CCACATGAAACGGTGTAGAAGAG 59.320 47.826 0.00 0.00 33.19 2.85
1889 2033 1.738099 CTCTTTGTGACGCTCCCCG 60.738 63.158 0.00 0.00 44.21 5.73
1939 2083 4.478206 TTAGAAGAGTTGAGGCATGAGG 57.522 45.455 0.00 0.00 0.00 3.86
2011 2249 6.060136 GGGCTTAGACGGGTTATAATTCTTT 58.940 40.000 0.00 0.00 0.00 2.52
2128 2369 9.760660 CAGAAATCCAAGTAATTTCGAAGTTAG 57.239 33.333 12.80 2.86 44.27 2.34
2173 2416 1.147824 CTGCCATGGCTCTTCCGAT 59.852 57.895 35.53 0.00 42.51 4.18
2450 3442 7.223387 GGAATGAGAATTTGTGCCAATTCATAC 59.777 37.037 12.93 6.82 37.75 2.39
2490 3483 6.878389 TCTTGCATGTGATGATGTAGTACAAA 59.122 34.615 7.16 0.00 0.00 2.83
2623 3618 5.431765 AGCGTCTGATGGAAAGACAATAAT 58.568 37.500 4.62 0.00 43.53 1.28
2657 3653 8.567285 AATGGCAGAATATAAGCTATGTAACC 57.433 34.615 0.00 0.00 29.59 2.85
2787 3805 6.418057 TTTGAAAATAGGATGGTGCAAACT 57.582 33.333 0.00 0.00 0.00 2.66
2788 3806 8.947055 ATATTTGAAAATAGGATGGTGCAAAC 57.053 30.769 0.00 0.00 34.62 2.93
3135 4168 4.141711 GGTTGGTTCTAGTATCCATGAGCA 60.142 45.833 0.00 0.00 0.00 4.26
3276 4309 0.752743 AGCCTTCACAGTTGCAGCAA 60.753 50.000 2.83 2.83 0.00 3.91
3462 4495 1.556911 TCACTGCCTCCTGAATCCTTC 59.443 52.381 0.00 0.00 0.00 3.46
3605 4640 4.819630 GGCATATGGTATGGACGAAGAAAA 59.180 41.667 4.56 0.00 0.00 2.29
3613 4648 2.162681 GCCAAGGCATATGGTATGGAC 58.837 52.381 6.14 0.00 40.23 4.02
3626 4661 3.885297 ACTTCACATATGTATGCCAAGGC 59.115 43.478 8.32 3.61 37.19 4.35
3787 4828 3.486383 GTCTTGAACATTCTTGACCCCA 58.514 45.455 6.41 0.00 0.00 4.96
3918 4965 7.228507 ACATGCCAACGAGCTAAAAATATATGA 59.771 33.333 0.00 0.00 0.00 2.15
3999 5046 7.765695 TCAGATTTGAAGATGTAGCCTTTTT 57.234 32.000 0.00 0.00 0.00 1.94
4200 5252 1.615392 GAGGCCAATTGCTTCACTTGT 59.385 47.619 5.01 0.00 45.00 3.16
4361 5413 1.341531 CGACACTTTGAGACCCTGAGT 59.658 52.381 0.00 0.00 0.00 3.41
4677 5729 6.128007 CCCTGTACACAACCATAATTGAGTTC 60.128 42.308 0.00 0.00 35.41 3.01
4759 5812 2.125673 ACGACGTGGGCTATGTGC 60.126 61.111 0.00 0.00 41.94 4.57
4760 5813 0.179111 ATGACGACGTGGGCTATGTG 60.179 55.000 4.58 0.00 0.00 3.21
4761 5814 0.179111 CATGACGACGTGGGCTATGT 60.179 55.000 4.58 0.00 0.00 2.29
4762 5815 0.179111 ACATGACGACGTGGGCTATG 60.179 55.000 4.58 9.31 37.35 2.23
4763 5816 1.395635 TACATGACGACGTGGGCTAT 58.604 50.000 4.58 0.00 37.35 2.97
4764 5817 1.395635 ATACATGACGACGTGGGCTA 58.604 50.000 4.58 0.00 37.35 3.93
4765 5818 0.535335 AATACATGACGACGTGGGCT 59.465 50.000 4.58 0.00 37.35 5.19
4766 5819 0.928229 GAATACATGACGACGTGGGC 59.072 55.000 4.58 0.00 37.35 5.36
4767 5820 1.136305 AGGAATACATGACGACGTGGG 59.864 52.381 4.58 0.00 37.35 4.61
4815 5882 0.826256 CCGGGGACATAGGATCGTCA 60.826 60.000 0.00 0.00 33.66 4.35
4868 5935 1.904144 CGACGAGCGGATTTACTTCA 58.096 50.000 0.00 0.00 36.03 3.02
4885 5952 2.741985 CGTTCAGGTGCATGGCGA 60.742 61.111 0.00 0.00 0.00 5.54
4899 5974 1.295423 CGATCACAAGGGGTCCGTT 59.705 57.895 0.00 0.00 0.00 4.44
4904 5979 1.002087 GAACTCACGATCACAAGGGGT 59.998 52.381 0.00 0.00 0.00 4.95
4949 6024 2.184322 GAGGCATCTCGCGGACAA 59.816 61.111 6.13 0.00 43.84 3.18
4984 6061 3.922171 ATGAGTGGAAGGGATTGTCTC 57.078 47.619 0.00 0.00 0.00 3.36
4991 6068 4.469469 AAGGAAAAATGAGTGGAAGGGA 57.531 40.909 0.00 0.00 0.00 4.20
5003 6127 5.105513 ACGTGACCAAACAGAAAGGAAAAAT 60.106 36.000 0.00 0.00 0.00 1.82
5008 6132 2.702592 ACGTGACCAAACAGAAAGGA 57.297 45.000 0.00 0.00 0.00 3.36
5039 6171 2.502295 ACGGAGGGAGTAGCTATTACG 58.498 52.381 0.00 0.00 37.35 3.18
5049 6187 2.829023 TCTATTTGGAACGGAGGGAGT 58.171 47.619 0.00 0.00 0.00 3.85
5050 6188 3.388024 TCATCTATTTGGAACGGAGGGAG 59.612 47.826 0.00 0.00 0.00 4.30
5052 6190 3.838244 TCATCTATTTGGAACGGAGGG 57.162 47.619 0.00 0.00 0.00 4.30
5053 6191 4.202357 TGGATCATCTATTTGGAACGGAGG 60.202 45.833 0.00 0.00 0.00 4.30
5054 6192 4.960938 TGGATCATCTATTTGGAACGGAG 58.039 43.478 0.00 0.00 0.00 4.63
5056 6194 5.126067 AGTTGGATCATCTATTTGGAACGG 58.874 41.667 0.00 0.00 0.00 4.44
5057 6195 6.683974 AAGTTGGATCATCTATTTGGAACG 57.316 37.500 0.00 0.00 0.00 3.95
5059 6197 8.956426 GTACAAAGTTGGATCATCTATTTGGAA 58.044 33.333 11.71 1.50 0.00 3.53
5060 6198 8.328758 AGTACAAAGTTGGATCATCTATTTGGA 58.671 33.333 0.00 3.70 0.00 3.53
5061 6199 8.511604 AGTACAAAGTTGGATCATCTATTTGG 57.488 34.615 0.00 0.00 0.00 3.28
5093 6231 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
5094 6232 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
5095 6233 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
5096 6234 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
5097 6235 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
5098 6236 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
5099 6237 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
5100 6238 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
5101 6239 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
5102 6240 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
5103 6241 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
5104 6242 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
5105 6243 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
5106 6244 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
5107 6245 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
5108 6246 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
5109 6247 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
5110 6248 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
5111 6249 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
5112 6250 3.118519 GCTACTCCCTCCGTTCCAAAATA 60.119 47.826 0.00 0.00 0.00 1.40
5113 6251 2.355818 GCTACTCCCTCCGTTCCAAAAT 60.356 50.000 0.00 0.00 0.00 1.82
5114 6252 1.002773 GCTACTCCCTCCGTTCCAAAA 59.997 52.381 0.00 0.00 0.00 2.44
5115 6253 0.611714 GCTACTCCCTCCGTTCCAAA 59.388 55.000 0.00 0.00 0.00 3.28
5116 6254 0.252103 AGCTACTCCCTCCGTTCCAA 60.252 55.000 0.00 0.00 0.00 3.53
5117 6255 0.683504 GAGCTACTCCCTCCGTTCCA 60.684 60.000 0.00 0.00 0.00 3.53
5118 6256 1.393487 GGAGCTACTCCCTCCGTTCC 61.393 65.000 1.98 0.00 44.36 3.62
5119 6257 2.117257 GGAGCTACTCCCTCCGTTC 58.883 63.158 1.98 0.00 44.36 3.95
5120 6258 4.358810 GGAGCTACTCCCTCCGTT 57.641 61.111 1.98 0.00 44.36 4.44
5128 6266 4.082517 TGCGAATCATCATAGGAGCTACTC 60.083 45.833 0.00 0.00 0.00 2.59
5129 6267 3.829026 TGCGAATCATCATAGGAGCTACT 59.171 43.478 2.64 2.64 0.00 2.57
5130 6268 4.179926 TGCGAATCATCATAGGAGCTAC 57.820 45.455 0.00 0.00 0.00 3.58
5131 6269 4.221482 ACATGCGAATCATCATAGGAGCTA 59.779 41.667 0.00 0.00 31.79 3.32
5143 6281 0.108377 ACTACGGCACATGCGAATCA 60.108 50.000 0.00 0.00 43.26 2.57
5157 6295 7.481798 GCAGATGGACTAAAATTTTTCACTACG 59.518 37.037 9.06 0.00 0.00 3.51
5164 6302 4.526650 ACGGGCAGATGGACTAAAATTTTT 59.473 37.500 9.06 0.00 0.00 1.94
5200 6373 0.250467 AGTGCGACACCAAGAGCAAT 60.250 50.000 6.39 0.00 41.56 3.56
5253 6426 5.841957 ACTTGCAATCAACAAAGAAGACT 57.158 34.783 0.00 0.00 0.00 3.24
5255 6428 7.771183 AGTTAACTTGCAATCAACAAAGAAGA 58.229 30.769 1.12 0.00 0.00 2.87
5312 6488 5.716228 ACAATGTTTGGATTGAAGCTATGGA 59.284 36.000 0.00 0.00 36.89 3.41
5346 6524 1.789523 TACAGGAGTATGAGTGGGCC 58.210 55.000 0.00 0.00 0.00 5.80
5407 6585 9.436957 GAACTATTATCCTCAGTTTGAAGTCAA 57.563 33.333 0.00 0.00 32.79 3.18
5437 6616 8.196771 AGCACTGATTTAAGTTTGATGTTTGAA 58.803 29.630 0.00 0.00 0.00 2.69
5438 6617 7.715657 AGCACTGATTTAAGTTTGATGTTTGA 58.284 30.769 0.00 0.00 0.00 2.69
5439 6618 7.935338 AGCACTGATTTAAGTTTGATGTTTG 57.065 32.000 0.00 0.00 0.00 2.93
5453 6635 9.905713 TGAATAGGTTAGAATTAGCACTGATTT 57.094 29.630 0.00 0.00 0.00 2.17
5481 6663 9.717942 AGTAGAACGAGTTTACTAGAGAAAGTA 57.282 33.333 0.00 0.00 0.00 2.24
5494 6676 4.021016 AGGATTCAGCAGTAGAACGAGTTT 60.021 41.667 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.