Multiple sequence alignment - TraesCS4D01G143900

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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 TraesCS4D01G143900 chr4D 100.000 4462 0 0 3556 8017 132130848 132135309 0.000000e+00 8240.0
1 TraesCS4D01G143900 chr4D 100.000 3194 0 0 1 3194 132127293 132130486 0.000000e+00 5899.0
2 TraesCS4D01G143900 chr4D 83.871 124 16 2 4928 5047 420942201 420942324 1.830000e-21 115.0
3 TraesCS4D01G143900 chr4B 94.498 3344 124 29 3990 7301 166002570 165999255 0.000000e+00 5101.0
4 TraesCS4D01G143900 chr4B 96.609 1740 46 8 1 1729 166005413 166003676 0.000000e+00 2874.0
5 TraesCS4D01G143900 chr4B 88.275 742 63 9 7293 8017 165998837 165998103 0.000000e+00 867.0
6 TraesCS4D01G143900 chr4B 91.107 506 12 11 2242 2721 166003071 166002573 0.000000e+00 654.0
7 TraesCS4D01G143900 chr4B 86.245 538 33 26 1714 2243 166003657 166003153 5.470000e-151 545.0
8 TraesCS4D01G143900 chr4B 80.263 456 58 11 3559 3990 629748374 629747927 1.680000e-81 315.0
9 TraesCS4D01G143900 chr4B 90.588 85 7 1 4963 5047 518097529 518097612 2.370000e-20 111.0
10 TraesCS4D01G143900 chr4A 95.065 3161 120 8 4870 8015 430868560 430865421 0.000000e+00 4940.0
11 TraesCS4D01G143900 chr4A 88.145 911 44 23 1737 2613 430870524 430869644 0.000000e+00 1026.0
12 TraesCS4D01G143900 chr4A 90.456 461 29 13 2719 3175 700729475 700729924 1.930000e-165 593.0
13 TraesCS4D01G143900 chr4A 88.958 480 37 12 2719 3194 726732928 726733395 5.390000e-161 579.0
14 TraesCS4D01G143900 chr4A 93.443 244 15 1 1459 1702 430871209 430870967 2.130000e-95 361.0
15 TraesCS4D01G143900 chr4A 86.760 287 23 3 4050 4326 430868932 430868651 1.010000e-78 305.0
16 TraesCS4D01G143900 chr4A 82.629 213 14 6 3763 3954 726734232 726734442 4.980000e-37 167.0
17 TraesCS4D01G143900 chr4A 83.740 123 16 2 4928 5046 43233712 43233590 6.580000e-21 113.0
18 TraesCS4D01G143900 chr4A 92.857 42 3 0 2632 2673 430869639 430869598 2.420000e-05 62.1
19 TraesCS4D01G143900 chr7B 91.213 478 29 8 2719 3194 611933884 611934350 8.770000e-179 638.0
20 TraesCS4D01G143900 chr7B 86.057 459 37 9 3557 3992 664352487 664352941 1.220000e-127 468.0
21 TraesCS4D01G143900 chr7B 85.965 456 36 10 3560 3992 664324550 664325000 5.670000e-126 462.0
22 TraesCS4D01G143900 chr7B 89.773 264 18 3 2931 3194 664351828 664352082 6.000000e-86 329.0
23 TraesCS4D01G143900 chr7B 89.015 264 20 3 2931 3194 664323655 664323909 1.300000e-82 318.0
24 TraesCS4D01G143900 chr7B 82.873 181 25 3 4332 4506 290835757 290835577 3.000000e-34 158.0
25 TraesCS4D01G143900 chr7B 83.051 177 24 4 4337 4507 93316811 93316987 1.080000e-33 156.0
26 TraesCS4D01G143900 chr7B 82.822 163 22 3 4354 4510 290732145 290731983 3.020000e-29 141.0
27 TraesCS4D01G143900 chr3A 89.404 453 33 12 2746 3194 746057366 746057807 2.530000e-154 556.0
28 TraesCS4D01G143900 chr3A 77.469 324 45 20 4569 4880 362208859 362208552 1.380000e-37 169.0
29 TraesCS4D01G143900 chr3A 81.461 178 26 3 4336 4507 13412177 13412353 1.080000e-28 139.0
30 TraesCS4D01G143900 chr2A 89.838 433 30 12 2719 3148 691842339 691842760 1.970000e-150 544.0
31 TraesCS4D01G143900 chr2A 78.135 311 55 8 4911 5219 745014874 745015173 1.370000e-42 185.0
32 TraesCS4D01G143900 chr5D 93.931 346 21 0 2719 3064 472748699 472749044 2.560000e-144 523.0
33 TraesCS4D01G143900 chr5D 83.636 220 21 9 4569 4778 73744798 73745012 8.210000e-45 193.0
34 TraesCS4D01G143900 chr3B 87.061 456 35 7 3559 3990 20464045 20464500 2.010000e-135 494.0
35 TraesCS4D01G143900 chr3B 86.341 410 35 8 3599 3987 703127320 703127729 2.070000e-115 427.0
36 TraesCS4D01G143900 chr3B 92.701 137 4 1 3056 3192 703126882 703127012 8.210000e-45 193.0
37 TraesCS4D01G143900 chr6B 90.026 391 23 13 2719 3106 657261943 657261566 7.230000e-135 492.0
38 TraesCS4D01G143900 chr6B 93.380 287 17 1 3559 3843 712336388 712336674 2.670000e-114 424.0
39 TraesCS4D01G143900 chr1B 90.173 346 28 5 2719 3064 595606560 595606899 5.710000e-121 446.0
40 TraesCS4D01G143900 chr1B 86.893 206 18 4 2989 3194 595606890 595607086 1.050000e-53 222.0
41 TraesCS4D01G143900 chr1B 82.432 222 25 9 4568 4780 32758929 32759145 1.780000e-41 182.0
42 TraesCS4D01G143900 chr2B 83.333 468 46 12 3559 3996 105854164 105853699 3.480000e-108 403.0
43 TraesCS4D01G143900 chr2B 78.322 286 45 11 4907 5188 748723199 748723471 1.380000e-37 169.0
44 TraesCS4D01G143900 chr6D 82.780 482 43 32 2719 3194 9197401 9196954 2.100000e-105 394.0
45 TraesCS4D01G143900 chr7A 83.814 451 31 16 3557 3984 35249980 35249549 2.710000e-104 390.0
46 TraesCS4D01G143900 chr7A 82.937 463 33 16 3557 3992 35285950 35285507 7.600000e-100 375.0
47 TraesCS4D01G143900 chr7A 82.119 453 64 9 3 443 70193045 70193492 9.830000e-99 372.0
48 TraesCS4D01G143900 chrUn 81.400 457 40 16 3557 3992 201300404 201299972 1.670000e-86 331.0
49 TraesCS4D01G143900 chrUn 94.815 135 5 1 3559 3691 10654543 10654677 8.150000e-50 209.0
50 TraesCS4D01G143900 chrUn 81.818 154 20 7 4332 4478 1714626 1714778 1.090000e-23 122.0
51 TraesCS4D01G143900 chr2D 83.690 374 30 4 3645 3992 584851906 584852274 2.790000e-84 324.0
52 TraesCS4D01G143900 chr2D 78.947 285 42 12 4909 5188 613344471 613344742 2.300000e-40 178.0
53 TraesCS4D01G143900 chr7D 76.056 497 82 26 1 472 263449217 263449701 2.910000e-54 224.0
54 TraesCS4D01G143900 chr7D 80.543 221 30 7 4569 4780 40581396 40581612 3.000000e-34 158.0
55 TraesCS4D01G143900 chr5B 85.625 160 17 4 4354 4507 93470171 93470012 6.440000e-36 163.0
56 TraesCS4D01G143900 chr5B 82.390 159 21 5 4354 4506 662049264 662049107 1.820000e-26 132.0
57 TraesCS4D01G143900 chr3D 82.703 185 26 4 4332 4510 250383086 250382902 8.330000e-35 159.0


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 TraesCS4D01G143900 chr4D 132127293 132135309 8016 False 7069.50 8240 100.0000 1 8017 2 chr4D.!!$F2 8016
1 TraesCS4D01G143900 chr4B 165998103 166005413 7310 True 2008.20 5101 91.3468 1 8017 5 chr4B.!!$R2 8016
2 TraesCS4D01G143900 chr4A 430865421 430871209 5788 True 1338.82 4940 91.2540 1459 8015 5 chr4A.!!$R2 6556
3 TraesCS4D01G143900 chr4A 726732928 726734442 1514 False 373.00 579 85.7935 2719 3954 2 chr4A.!!$F2 1235
4 TraesCS4D01G143900 chr7B 664351828 664352941 1113 False 398.50 468 87.9150 2931 3992 2 chr7B.!!$F4 1061
5 TraesCS4D01G143900 chr7B 664323655 664325000 1345 False 390.00 462 87.4900 2931 3992 2 chr7B.!!$F3 1061
6 TraesCS4D01G143900 chr3B 703126882 703127729 847 False 310.00 427 89.5210 3056 3987 2 chr3B.!!$F2 931
7 TraesCS4D01G143900 chr1B 595606560 595607086 526 False 334.00 446 88.5330 2719 3194 2 chr1B.!!$F2 475

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
666 669 0.460311 CTCGGTGTATGTGAGGGACC 59.540 60.000 0.00 0.00 0.00 4.46 F
1615 1622 1.471684 GGCACCAATCTCAAAGCAGAG 59.528 52.381 0.00 0.00 36.97 3.35 F
2579 3130 1.229082 TGGGAAGTACTCCGCCAGT 60.229 57.895 0.00 0.00 46.51 4.00 F
3845 5632 0.325671 AATCTTCTCCCTCCGCCTGA 60.326 55.000 0.00 0.00 0.00 3.86 F
4276 6418 0.378257 GATTGCGCGGTTGTCATCAT 59.622 50.000 8.83 0.00 0.00 2.45 F
4767 6910 0.037326 TGTGCAGTGCCTAGCTGTAC 60.037 55.000 13.72 9.19 45.48 2.90 F
6165 8331 0.110056 ACATTGCTTTCGCGCAGAAG 60.110 50.000 8.75 11.83 41.55 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2579 3130 0.391130 GATAGGCGGCAACAGTGTCA 60.391 55.000 13.08 0.0 0.00 3.58 R
3079 3953 4.124351 TTCTCGGCGGCGTCGAAT 62.124 61.111 36.19 0.0 39.77 3.34 R
4257 6399 0.378257 ATGATGACAACCGCGCAATC 59.622 50.000 8.75 0.0 0.00 2.67 R
4747 6890 0.247460 TACAGCTAGGCACTGCACAG 59.753 55.000 2.82 0.0 41.52 3.66 R
5580 7746 0.598942 CGATGACGGTGTTGGTGACA 60.599 55.000 0.00 0.0 35.32 3.58 R
6625 8791 0.320771 CGTTGTGTTGAGGGAGGAGG 60.321 60.000 0.00 0.0 0.00 4.30 R
7097 9263 0.320374 CCACCTTTGCGGAGACAGTA 59.680 55.000 0.00 0.0 36.31 2.74 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
43 44 4.148825 CGGAAGTGCCCCTCCTCG 62.149 72.222 0.00 0.00 0.00 4.63
52 53 2.581354 CCCTCCTCGAAGCACCTG 59.419 66.667 0.00 0.00 0.00 4.00
93 94 2.893398 CGAAACCTCCCTCCTCGG 59.107 66.667 0.00 0.00 0.00 4.63
98 99 4.465446 CCTCCCTCCTCGGCCTCA 62.465 72.222 0.00 0.00 0.00 3.86
254 256 4.247380 CCCATCGCCTCTGAGCCC 62.247 72.222 0.00 0.00 0.00 5.19
325 327 2.722201 GGCGGAAGGTGGAGTCGAT 61.722 63.158 0.00 0.00 0.00 3.59
375 377 2.571757 CGACTAACGGGAGCAGCA 59.428 61.111 0.00 0.00 38.46 4.41
579 581 6.019075 TCGTTAAATCTCAAGATGTTATGCCG 60.019 38.462 0.00 0.00 34.49 5.69
595 597 4.874534 CGGCTAAGTCCGTCGAAA 57.125 55.556 0.00 0.00 44.18 3.46
596 598 3.111536 CGGCTAAGTCCGTCGAAAA 57.888 52.632 0.00 0.00 44.18 2.29
605 607 3.857052 AGTCCGTCGAAAATGCTCATAA 58.143 40.909 0.00 0.00 0.00 1.90
606 608 3.865745 AGTCCGTCGAAAATGCTCATAAG 59.134 43.478 0.00 0.00 0.00 1.73
612 614 4.511826 GTCGAAAATGCTCATAAGGGTAGG 59.488 45.833 0.00 0.00 0.00 3.18
629 631 0.961019 AGGATTGTTTGTGCGTGCAT 59.039 45.000 0.00 0.00 0.00 3.96
662 665 2.100749 TGTATGCTCGGTGTATGTGAGG 59.899 50.000 0.00 0.00 0.00 3.86
666 669 0.460311 CTCGGTGTATGTGAGGGACC 59.540 60.000 0.00 0.00 0.00 4.46
679 682 1.825474 GAGGGACCTCGATGTTCAAGA 59.175 52.381 2.05 0.00 33.06 3.02
723 729 6.463995 TCGGATAGCCAAATAAGCATTTTT 57.536 33.333 0.00 0.00 31.82 1.94
972 979 3.500289 CCCCTCTCCATTTCCACAAAAGA 60.500 47.826 0.00 0.00 0.00 2.52
1615 1622 1.471684 GGCACCAATCTCAAAGCAGAG 59.528 52.381 0.00 0.00 36.97 3.35
1675 1682 3.735237 TGATTACCTTGCCGAGAGATC 57.265 47.619 0.00 0.00 0.00 2.75
1752 2172 4.663334 ACCCCCAAACAACTCTCTTATTC 58.337 43.478 0.00 0.00 0.00 1.75
1802 2222 7.116075 TCAGTAAACTTAGTGTGTTGTAGGT 57.884 36.000 4.62 0.00 35.92 3.08
1807 2227 5.609533 ACTTAGTGTGTTGTAGGTTCAGT 57.390 39.130 0.00 0.00 0.00 3.41
2011 2442 6.988580 CCTACTACAACATGTGTGATGATGAT 59.011 38.462 0.00 0.00 41.89 2.45
2065 2498 2.790433 CAAGTGGCTGCCTTTAACCTA 58.210 47.619 21.03 0.00 0.00 3.08
2267 2787 7.604657 TTAAGTAAACACCCCAAATGTGATT 57.395 32.000 0.00 0.00 37.18 2.57
2268 2788 5.467035 AGTAAACACCCCAAATGTGATTG 57.533 39.130 0.00 0.00 37.18 2.67
2309 2832 7.871463 GTGTAGTGTCCAGATTTTTGTAGTACT 59.129 37.037 0.00 0.00 0.00 2.73
2310 2833 7.870954 TGTAGTGTCCAGATTTTTGTAGTACTG 59.129 37.037 5.39 0.00 0.00 2.74
2444 2984 1.544246 AGCGTGTAATTTGGGAAAGCC 59.456 47.619 0.00 0.00 0.00 4.35
2579 3130 1.229082 TGGGAAGTACTCCGCCAGT 60.229 57.895 0.00 0.00 46.51 4.00
2621 3172 7.263100 TCTGCTTTTCGCACAATGAATATAT 57.737 32.000 0.00 0.00 45.47 0.86
2622 3173 8.376889 TCTGCTTTTCGCACAATGAATATATA 57.623 30.769 0.00 0.00 45.47 0.86
2623 3174 9.002600 TCTGCTTTTCGCACAATGAATATATAT 57.997 29.630 0.00 0.00 45.47 0.86
2667 3218 9.665264 AATCGTTTTTAAGACAATGAAGACTTC 57.335 29.630 8.34 8.34 0.00 3.01
3648 4797 2.125512 GGCACGCTGTGAGTAGGG 60.126 66.667 11.94 0.00 35.23 3.53
3821 5608 0.537143 TGACAGTGGGCCATTGACAC 60.537 55.000 32.64 21.97 35.43 3.67
3835 5622 3.896648 TTGACACGCAAAATCTTCTCC 57.103 42.857 0.00 0.00 32.46 3.71
3843 5630 1.065126 CAAAATCTTCTCCCTCCGCCT 60.065 52.381 0.00 0.00 0.00 5.52
3844 5631 0.543749 AAATCTTCTCCCTCCGCCTG 59.456 55.000 0.00 0.00 0.00 4.85
3845 5632 0.325671 AATCTTCTCCCTCCGCCTGA 60.326 55.000 0.00 0.00 0.00 3.86
3885 5693 2.037641 GGCTCTGTTTTTGGCCAAATCT 59.962 45.455 30.78 0.00 43.59 2.40
3886 5694 3.258123 GGCTCTGTTTTTGGCCAAATCTA 59.742 43.478 30.78 14.37 43.59 1.98
3889 5697 3.057596 TCTGTTTTTGGCCAAATCTAGCG 60.058 43.478 30.78 16.68 0.00 4.26
3929 5738 1.931172 CGTGAGTGGTGAGTTTTTCGT 59.069 47.619 0.00 0.00 0.00 3.85
3956 5765 1.227999 CGCTGAAAAAGTGCCTCCGA 61.228 55.000 0.00 0.00 0.00 4.55
3957 5766 0.951558 GCTGAAAAAGTGCCTCCGAA 59.048 50.000 0.00 0.00 0.00 4.30
3980 5789 3.539593 TTCTCGGGGAGCCCAGTGA 62.540 63.158 8.02 7.11 45.83 3.41
3987 5796 1.606531 GGAGCCCAGTGAAGATGCT 59.393 57.895 0.00 0.00 34.40 3.79
3999 5808 5.350914 CAGTGAAGATGCTCTTAAACTCTGG 59.649 44.000 9.10 0.00 36.73 3.86
4024 5833 8.283291 GGGATTCGAGATTAAACAATGATGTAC 58.717 37.037 0.00 0.00 39.40 2.90
4074 6206 3.181471 ACTTGTGTCTTCTGGTCTGTGAG 60.181 47.826 0.00 0.00 0.00 3.51
4219 6361 1.487976 CCAGCCAGATTCCTCTTGCTA 59.512 52.381 1.41 0.00 45.93 3.49
4257 6399 6.632909 TCTTTCACATTTGATAATGGCTTGG 58.367 36.000 0.00 0.00 44.42 3.61
4273 6415 1.240641 TTGGATTGCGCGGTTGTCAT 61.241 50.000 8.83 0.00 0.00 3.06
4274 6416 1.062525 GGATTGCGCGGTTGTCATC 59.937 57.895 8.83 0.00 0.00 2.92
4276 6418 0.378257 GATTGCGCGGTTGTCATCAT 59.622 50.000 8.83 0.00 0.00 2.45
4277 6419 0.810648 ATTGCGCGGTTGTCATCATT 59.189 45.000 8.83 0.00 0.00 2.57
4278 6420 0.595588 TTGCGCGGTTGTCATCATTT 59.404 45.000 8.83 0.00 0.00 2.32
4279 6421 0.595588 TGCGCGGTTGTCATCATTTT 59.404 45.000 8.83 0.00 0.00 1.82
4280 6422 1.000827 TGCGCGGTTGTCATCATTTTT 60.001 42.857 8.83 0.00 0.00 1.94
4282 6424 2.920227 GCGCGGTTGTCATCATTTTTGA 60.920 45.455 8.83 0.00 0.00 2.69
4286 6428 5.107530 CGCGGTTGTCATCATTTTTGATTTT 60.108 36.000 0.00 0.00 0.00 1.82
4517 6659 8.813643 TTTAACACAAATTACCAATAAACCGG 57.186 30.769 0.00 0.00 0.00 5.28
4519 6661 6.262193 ACACAAATTACCAATAAACCGGAG 57.738 37.500 9.46 0.00 0.00 4.63
4520 6662 5.099575 CACAAATTACCAATAAACCGGAGC 58.900 41.667 9.46 0.00 0.00 4.70
4534 6676 2.985406 CGGAGCGGAGGTAGTAATAC 57.015 55.000 0.00 0.00 39.88 1.89
4535 6677 2.502295 CGGAGCGGAGGTAGTAATACT 58.498 52.381 0.00 0.00 39.88 2.12
4558 6700 4.518970 TCAGTACCATTCTTTCTTTGCCAC 59.481 41.667 0.00 0.00 0.00 5.01
4561 6703 4.961438 ACCATTCTTTCTTTGCCACAAT 57.039 36.364 0.00 0.00 0.00 2.71
4591 6733 3.791973 AAAGACACAAATTTGACCGCA 57.208 38.095 24.64 0.00 0.00 5.69
4655 6798 3.136443 TCATCCAGCTAACCCCTAATGTG 59.864 47.826 0.00 0.00 0.00 3.21
4669 6812 1.442526 AATGTGCAGCGCCTGATAGC 61.443 55.000 2.29 0.00 32.44 2.97
4673 6816 2.541120 GCAGCGCCTGATAGCAAGG 61.541 63.158 2.29 0.00 32.44 3.61
4685 6828 4.598257 GCAAGGCGCTTCACTCTA 57.402 55.556 7.64 0.00 37.77 2.43
4690 6833 3.376540 CAAGGCGCTTCACTCTATCTAC 58.623 50.000 7.64 0.00 0.00 2.59
4693 6836 2.359531 GGCGCTTCACTCTATCTACTGT 59.640 50.000 7.64 0.00 0.00 3.55
4705 6848 2.125832 TACTGTGCCGCGCCTAAC 60.126 61.111 0.00 0.00 0.00 2.34
4709 6852 3.488090 GTGCCGCGCCTAACACTC 61.488 66.667 0.00 0.00 0.00 3.51
4720 6863 0.391661 CTAACACTCAGGCGCCACAT 60.392 55.000 31.54 4.59 0.00 3.21
4723 6866 4.025858 ACTCAGGCGCCACATGCT 62.026 61.111 31.54 2.66 38.05 3.79
4739 6882 2.743195 GCTCGACAGCTAGGTGTTG 58.257 57.895 29.03 29.03 43.09 3.33
4747 6890 2.069273 CAGCTAGGTGTTGCACTACAC 58.931 52.381 13.89 12.37 45.99 2.90
4765 6908 1.004080 CTGTGCAGTGCCTAGCTGT 60.004 57.895 13.72 0.00 36.42 4.40
4767 6910 0.037326 TGTGCAGTGCCTAGCTGTAC 60.037 55.000 13.72 9.19 45.48 2.90
4814 6980 8.831715 AAAAAGATCAAGGCGTGAAATATTTT 57.168 26.923 7.31 5.50 40.50 1.82
4815 6981 8.831715 AAAAGATCAAGGCGTGAAATATTTTT 57.168 26.923 7.31 7.36 40.50 1.94
4849 7015 9.636965 GTTTGATTTGTGAAATACTTTTGCTTC 57.363 29.630 0.00 0.00 0.00 3.86
4854 7020 4.819630 TGTGAAATACTTTTGCTTCGAGGT 59.180 37.500 0.00 0.00 0.00 3.85
4859 7025 6.575162 AATACTTTTGCTTCGAGGTCAAAT 57.425 33.333 14.39 6.78 30.89 2.32
4898 7064 7.958567 CCACAATTTTCGTGTTAACATACGTAT 59.041 33.333 12.26 1.14 40.87 3.06
5571 7737 2.431942 GTGACCGACGCCGACATT 60.432 61.111 0.00 0.00 38.22 2.71
5746 7912 1.289066 CTCCTCAAGAACGACGGCA 59.711 57.895 0.00 0.00 0.00 5.69
6153 8319 4.778143 GGGCCCGTCGACATTGCT 62.778 66.667 17.16 0.00 0.00 3.91
6165 8331 0.110056 ACATTGCTTTCGCGCAGAAG 60.110 50.000 8.75 11.83 41.55 2.85
6287 8453 6.978338 TGTACACTTCGACAGTCTCTATTTT 58.022 36.000 0.00 0.00 30.92 1.82
6458 8624 1.226379 GACAAACATGGCGATGCGG 60.226 57.895 8.81 1.19 32.14 5.69
7097 9263 1.188863 GGATTTTCATGGTGCCAGCT 58.811 50.000 0.00 0.00 0.00 4.24
7124 9290 1.078848 CGCAAAGGTGGAGAGAGGG 60.079 63.158 0.00 0.00 0.00 4.30
7175 9344 1.459209 TCTACGCACTGCAAACGATTG 59.541 47.619 9.37 0.29 39.65 2.67
7291 9460 1.093972 CATAACCATGCGCTTCACCA 58.906 50.000 9.73 0.00 0.00 4.17
7383 9978 3.096852 TCTAAAGCTCATCTCCAACGGA 58.903 45.455 0.00 0.00 0.00 4.69
7422 10017 0.108585 ACATGCCAACCGAGTTGTCT 59.891 50.000 13.41 0.00 41.41 3.41
7456 10052 2.637872 CCATCCATCACGGTACCCTATT 59.362 50.000 6.25 0.00 35.57 1.73
7528 10124 2.125106 GGAGATTTGCGGGCGTCT 60.125 61.111 0.00 0.00 0.00 4.18
7657 10253 1.248785 TGGTCACTAGAGCCGTCACC 61.249 60.000 0.00 0.00 41.53 4.02
7698 10294 2.258591 GCCGCGTCTCAGTCTTCA 59.741 61.111 4.92 0.00 0.00 3.02
7702 10298 1.132453 CCGCGTCTCAGTCTTCACATA 59.868 52.381 4.92 0.00 0.00 2.29
7759 10369 4.907875 TGAAGAAGAAAGAGAGGGAAGGAA 59.092 41.667 0.00 0.00 0.00 3.36
7769 10379 4.171841 AGAGAGGGAAGGAAGAGGACATAT 59.828 45.833 0.00 0.00 0.00 1.78
7774 10384 1.794714 AGGAAGAGGACATATGGCGT 58.205 50.000 2.71 2.71 0.00 5.68
7816 10426 1.658717 CGGCAGCTTACGGAGATCG 60.659 63.158 0.00 0.00 45.88 3.69
7898 10508 2.928396 CACGAACCCTCCCCTGGT 60.928 66.667 0.00 0.00 37.85 4.00
7911 10521 1.392589 CCCTGGTGGATGTATGCAAC 58.607 55.000 0.00 0.00 36.26 4.17
7987 10597 2.364579 ACGCCGAATGGTAGGGGA 60.365 61.111 5.56 0.00 42.30 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 1.269257 GGTTTGTGCTTCAGGTGCTTC 60.269 52.381 0.00 0.00 0.00 3.86
52 53 1.200948 GAGATGGCAGGTTTGTGCTTC 59.799 52.381 0.00 0.00 43.45 3.86
254 256 2.558821 CTATCCTCGAGCTCGGCG 59.441 66.667 33.98 24.18 40.29 6.46
325 327 2.117423 TGACGAGTCCCTGCTCCA 59.883 61.111 0.34 0.00 32.11 3.86
367 369 2.045536 CCTCCAACCTGCTGCTCC 60.046 66.667 0.00 0.00 0.00 4.70
375 377 0.684805 CTCCGCTAGTCCTCCAACCT 60.685 60.000 0.00 0.00 0.00 3.50
556 558 6.430451 CCGGCATAACATCTTGAGATTTAAC 58.570 40.000 0.00 0.00 31.21 2.01
579 581 1.062148 GCATTTTCGACGGACTTAGCC 59.938 52.381 0.00 0.00 0.00 3.93
591 593 4.703897 TCCTACCCTTATGAGCATTTTCG 58.296 43.478 0.00 0.00 0.00 3.46
595 597 5.653255 ACAATCCTACCCTTATGAGCATT 57.347 39.130 0.00 0.00 0.00 3.56
596 598 5.653255 AACAATCCTACCCTTATGAGCAT 57.347 39.130 0.00 0.00 0.00 3.79
605 607 1.073284 ACGCACAAACAATCCTACCCT 59.927 47.619 0.00 0.00 0.00 4.34
606 608 1.199097 CACGCACAAACAATCCTACCC 59.801 52.381 0.00 0.00 0.00 3.69
612 614 2.392821 TGAATGCACGCACAAACAATC 58.607 42.857 0.00 0.00 0.00 2.67
723 729 0.781278 AAACCATTTCGGGAGGGGAA 59.219 50.000 0.00 0.00 40.22 3.97
724 730 0.781278 AAAACCATTTCGGGAGGGGA 59.219 50.000 0.00 0.00 40.22 4.81
826 833 8.495361 AAAATAATTTAACCGGTTATTTGGCC 57.505 30.769 27.03 0.00 37.80 5.36
972 979 1.404035 GTGGTTGGTTTTCTTGCGAGT 59.596 47.619 0.00 0.00 0.00 4.18
1615 1622 2.102553 GACTCTGCGCGGTAGGAC 59.897 66.667 17.37 7.55 0.00 3.85
1675 1682 3.188254 TGTGCGTCCATTCTGTGTTATTG 59.812 43.478 0.00 0.00 0.00 1.90
1828 2248 3.932710 TGGCTGAATCTACGACACAATTC 59.067 43.478 0.00 0.00 0.00 2.17
2011 2442 2.247358 GGATTGTTTGCCTTTCCTGGA 58.753 47.619 0.00 0.00 0.00 3.86
2065 2498 9.700831 AGATTTGTCTTAAAGTGCCCTTATAAT 57.299 29.630 0.00 0.00 0.00 1.28
2267 2787 6.948589 ACACTACACTCTACTAGATCTGTCA 58.051 40.000 5.18 0.00 0.00 3.58
2268 2788 6.480981 GGACACTACACTCTACTAGATCTGTC 59.519 46.154 5.18 0.00 0.00 3.51
2309 2832 4.716784 ACCAACTCATTCCTATCTGCTACA 59.283 41.667 0.00 0.00 0.00 2.74
2310 2833 5.053145 CACCAACTCATTCCTATCTGCTAC 58.947 45.833 0.00 0.00 0.00 3.58
2579 3130 0.391130 GATAGGCGGCAACAGTGTCA 60.391 55.000 13.08 0.00 0.00 3.58
2621 3172 6.544931 ACGATTGAAGGCAGTAGTAGTACATA 59.455 38.462 10.33 0.00 0.00 2.29
2622 3173 5.360144 ACGATTGAAGGCAGTAGTAGTACAT 59.640 40.000 10.33 0.00 0.00 2.29
2623 3174 4.703575 ACGATTGAAGGCAGTAGTAGTACA 59.296 41.667 10.33 0.00 0.00 2.90
2998 3847 4.609018 AGTCAAGGCTGCGCACGT 62.609 61.111 5.66 2.28 0.00 4.49
3065 3939 4.814294 GAATGCGACGACGGGGCT 62.814 66.667 9.67 0.00 40.15 5.19
3079 3953 4.124351 TTCTCGGCGGCGTCGAAT 62.124 61.111 36.19 0.00 39.77 3.34
3634 4783 3.760035 CCGCCCTACTCACAGCGT 61.760 66.667 2.40 0.00 46.85 5.07
3722 4871 4.351054 CTCGCCCCCTTGCTGGTT 62.351 66.667 0.00 0.00 0.00 3.67
3730 4879 2.768344 CCCACATACTCGCCCCCT 60.768 66.667 0.00 0.00 0.00 4.79
3821 5608 1.009829 CGGAGGGAGAAGATTTTGCG 58.990 55.000 0.00 0.00 0.00 4.85
3835 5622 4.292178 GGCGATCTCAGGCGGAGG 62.292 72.222 14.68 0.09 44.19 4.30
3843 5630 2.125326 CGGTACCAGGGCGATCTCA 61.125 63.158 13.54 0.00 0.00 3.27
3844 5631 2.728817 CGGTACCAGGGCGATCTC 59.271 66.667 13.54 0.00 0.00 2.75
3845 5632 3.537874 GCGGTACCAGGGCGATCT 61.538 66.667 13.54 0.00 0.00 2.75
3904 5713 0.759436 AACTCACCACTCACGTCCCT 60.759 55.000 0.00 0.00 0.00 4.20
3908 5717 1.931172 CGAAAAACTCACCACTCACGT 59.069 47.619 0.00 0.00 0.00 4.49
3954 5763 3.075005 TCCCCGAGAAGCCCTTCG 61.075 66.667 2.63 0.00 43.97 3.79
3956 5765 3.403558 GCTCCCCGAGAAGCCCTT 61.404 66.667 0.00 0.00 0.00 3.95
3987 5796 6.546428 AATCTCGAATCCCAGAGTTTAAGA 57.454 37.500 0.00 0.00 36.03 2.10
3999 5808 9.046296 AGTACATCATTGTTTAATCTCGAATCC 57.954 33.333 0.00 0.00 37.28 3.01
4024 5833 7.115520 CAGTACGCAATAACTCCTTCATCATAG 59.884 40.741 0.00 0.00 0.00 2.23
4027 5836 5.109210 CAGTACGCAATAACTCCTTCATCA 58.891 41.667 0.00 0.00 0.00 3.07
4028 5837 4.508124 CCAGTACGCAATAACTCCTTCATC 59.492 45.833 0.00 0.00 0.00 2.92
4074 6206 0.884704 ATGCACGTGGTTCAGTGGAC 60.885 55.000 18.88 0.00 41.26 4.02
4219 6361 9.971922 CAAATGTGAAAGAAAAATACTTCTCCT 57.028 29.630 0.00 0.00 34.49 3.69
4248 6390 2.491152 CGCGCAATCCAAGCCATT 59.509 55.556 8.75 0.00 0.00 3.16
4257 6399 0.378257 ATGATGACAACCGCGCAATC 59.622 50.000 8.75 0.00 0.00 2.67
4326 6468 5.063060 GCACGAAATATAATGGGGACGTATC 59.937 44.000 0.00 0.00 0.00 2.24
4495 6637 6.651975 TCCGGTTTATTGGTAATTTGTGTT 57.348 33.333 0.00 0.00 0.00 3.32
4502 6644 2.567985 CCGCTCCGGTTTATTGGTAAT 58.432 47.619 0.00 0.00 42.73 1.89
4517 6659 4.136051 ACTGAGTATTACTACCTCCGCTC 58.864 47.826 0.00 0.00 0.00 5.03
4519 6661 4.215185 GGTACTGAGTATTACTACCTCCGC 59.785 50.000 0.00 0.00 0.00 5.54
4520 6662 5.371526 TGGTACTGAGTATTACTACCTCCG 58.628 45.833 12.53 0.00 27.36 4.63
4522 6664 8.694581 AGAATGGTACTGAGTATTACTACCTC 57.305 38.462 12.53 5.41 27.36 3.85
4523 6665 9.490083 AAAGAATGGTACTGAGTATTACTACCT 57.510 33.333 12.53 0.00 27.36 3.08
4529 6671 9.162764 GCAAAGAAAGAATGGTACTGAGTATTA 57.837 33.333 0.00 0.00 0.00 0.98
4530 6672 7.121315 GGCAAAGAAAGAATGGTACTGAGTATT 59.879 37.037 0.00 0.00 0.00 1.89
4531 6673 6.599638 GGCAAAGAAAGAATGGTACTGAGTAT 59.400 38.462 0.00 0.00 0.00 2.12
4532 6674 5.938125 GGCAAAGAAAGAATGGTACTGAGTA 59.062 40.000 0.00 0.00 0.00 2.59
4533 6675 4.762251 GGCAAAGAAAGAATGGTACTGAGT 59.238 41.667 0.00 0.00 0.00 3.41
4534 6676 4.761739 TGGCAAAGAAAGAATGGTACTGAG 59.238 41.667 0.00 0.00 0.00 3.35
4535 6677 4.518970 GTGGCAAAGAAAGAATGGTACTGA 59.481 41.667 0.00 0.00 0.00 3.41
4558 6700 5.947503 TTGTGTCTTTTGCTCGAAAATTG 57.052 34.783 0.00 0.00 32.98 2.32
4561 6703 6.587990 TCAAATTTGTGTCTTTTGCTCGAAAA 59.412 30.769 17.47 0.00 31.88 2.29
4623 6765 6.831868 GGGGTTAGCTGGATGAAATACTTTTA 59.168 38.462 0.00 0.00 0.00 1.52
4624 6766 5.656859 GGGGTTAGCTGGATGAAATACTTTT 59.343 40.000 0.00 0.00 0.00 2.27
4625 6767 5.044105 AGGGGTTAGCTGGATGAAATACTTT 60.044 40.000 0.00 0.00 0.00 2.66
4626 6768 4.478686 AGGGGTTAGCTGGATGAAATACTT 59.521 41.667 0.00 0.00 0.00 2.24
4627 6769 4.047883 AGGGGTTAGCTGGATGAAATACT 58.952 43.478 0.00 0.00 0.00 2.12
4628 6770 4.439253 AGGGGTTAGCTGGATGAAATAC 57.561 45.455 0.00 0.00 0.00 1.89
4638 6781 2.292267 CTGCACATTAGGGGTTAGCTG 58.708 52.381 0.00 0.00 0.00 4.24
4643 6786 2.046285 GCGCTGCACATTAGGGGTT 61.046 57.895 0.00 0.00 0.00 4.11
4655 6798 2.541120 CCTTGCTATCAGGCGCTGC 61.541 63.158 7.64 3.29 34.52 5.25
4669 6812 2.593346 AGATAGAGTGAAGCGCCTTG 57.407 50.000 2.29 0.00 0.00 3.61
4673 6816 3.367607 CACAGTAGATAGAGTGAAGCGC 58.632 50.000 0.00 0.00 33.99 5.92
4675 6818 3.712187 GGCACAGTAGATAGAGTGAAGC 58.288 50.000 0.00 0.00 33.99 3.86
4678 6821 1.676529 GCGGCACAGTAGATAGAGTGA 59.323 52.381 0.00 0.00 33.99 3.41
4682 6825 1.359117 GCGCGGCACAGTAGATAGA 59.641 57.895 8.83 0.00 0.00 1.98
4683 6826 1.661821 GGCGCGGCACAGTAGATAG 60.662 63.158 29.32 0.00 0.00 2.08
4684 6827 0.820482 TAGGCGCGGCACAGTAGATA 60.820 55.000 34.94 12.70 0.00 1.98
4685 6828 1.672854 TTAGGCGCGGCACAGTAGAT 61.673 55.000 34.94 13.82 0.00 1.98
4690 6833 3.788766 GTGTTAGGCGCGGCACAG 61.789 66.667 34.94 0.00 32.62 3.66
4693 6836 3.932580 CTGAGTGTTAGGCGCGGCA 62.933 63.158 34.94 17.74 0.00 5.69
4705 6848 3.807538 GCATGTGGCGCCTGAGTG 61.808 66.667 29.70 20.64 0.00 3.51
4723 6866 0.319555 GTGCAACACCTAGCTGTCGA 60.320 55.000 0.00 0.00 36.32 4.20
4726 6869 1.691976 TGTAGTGCAACACCTAGCTGT 59.308 47.619 0.00 0.00 41.43 4.40
4747 6890 0.247460 TACAGCTAGGCACTGCACAG 59.753 55.000 2.82 0.00 41.52 3.66
4754 6897 1.227002 GCTCCGTACAGCTAGGCAC 60.227 63.158 0.00 0.00 36.38 5.01
4755 6898 3.207354 GCTCCGTACAGCTAGGCA 58.793 61.111 0.00 0.00 36.38 4.75
4765 6908 4.082523 GCCCTGTGCAGCTCCGTA 62.083 66.667 0.00 0.00 40.77 4.02
4793 6959 9.921637 TTTTAAAAATATTTCACGCCTTGATCT 57.078 25.926 0.10 0.00 32.84 2.75
4828 6994 6.863126 CCTCGAAGCAAAAGTATTTCACAAAT 59.137 34.615 0.00 0.00 37.28 2.32
4849 7015 6.589523 TGGCAAAATTGATAAATTTGACCTCG 59.410 34.615 15.87 0.00 40.56 4.63
4859 7025 8.066595 CACGAAAATTGTGGCAAAATTGATAAA 58.933 29.630 16.10 0.00 33.69 1.40
5289 7455 2.743538 GAGCACATGACGCTGGCA 60.744 61.111 17.14 0.00 40.63 4.92
5520 7686 4.367023 GCGCCCTCGGTGTACACA 62.367 66.667 26.51 7.09 35.34 3.72
5542 7708 4.373116 GGTCACCTTCCGCTGCGA 62.373 66.667 25.45 6.86 0.00 5.10
5557 7723 2.431942 GTCAATGTCGGCGTCGGT 60.432 61.111 10.62 0.00 36.95 4.69
5571 7737 4.228567 TTGGTGACAGCGGCGTCA 62.229 61.111 18.75 18.75 44.54 4.35
5580 7746 0.598942 CGATGACGGTGTTGGTGACA 60.599 55.000 0.00 0.00 35.32 3.58
5724 7890 1.009389 CGTCGTTCTTGAGGAGCACC 61.009 60.000 0.00 0.00 0.00 5.01
5992 8158 2.181021 GAGGCCAACGACGACGAT 59.819 61.111 15.32 0.00 42.66 3.73
6153 8319 2.736995 CGGTCCTTCTGCGCGAAA 60.737 61.111 12.10 0.00 0.00 3.46
6165 8331 2.107141 CCAGCGATCTTCCGGTCC 59.893 66.667 0.00 0.00 38.28 4.46
6287 8453 4.929819 TCGATCCCGACTTGAATCATTA 57.070 40.909 0.00 0.00 40.30 1.90
6624 8790 0.606673 GTTGTGTTGAGGGAGGAGGC 60.607 60.000 0.00 0.00 0.00 4.70
6625 8791 0.320771 CGTTGTGTTGAGGGAGGAGG 60.321 60.000 0.00 0.00 0.00 4.30
6626 8792 0.679505 TCGTTGTGTTGAGGGAGGAG 59.320 55.000 0.00 0.00 0.00 3.69
6665 8831 2.432456 GAGACACGCACATCGGCA 60.432 61.111 0.00 0.00 43.86 5.69
6696 8862 3.801997 CGGGATGCTCAGGCCCTT 61.802 66.667 0.00 0.00 39.79 3.95
7071 9237 3.534554 GCACCATGAAAATCCAATTCCC 58.465 45.455 0.00 0.00 0.00 3.97
7097 9263 0.320374 CCACCTTTGCGGAGACAGTA 59.680 55.000 0.00 0.00 36.31 2.74
7124 9290 8.718102 TTTAGTAATCAGGTGCAGTTCTAATC 57.282 34.615 0.00 0.00 0.00 1.75
7175 9344 6.072112 TCTTTGTATTGCTTCCAGTTTCAC 57.928 37.500 0.00 0.00 0.00 3.18
7291 9460 2.743718 CACTCGGGCCTTGACAGT 59.256 61.111 0.84 0.00 0.00 3.55
7383 9978 1.677942 TTACGGCCGTTTTGAGGTTT 58.322 45.000 38.94 9.80 0.00 3.27
7422 10017 4.785767 GATGGCTCGCATCATCCA 57.214 55.556 0.00 0.00 35.11 3.41
7456 10052 3.627395 AGCGAATAACTTCATGGACCA 57.373 42.857 0.00 0.00 0.00 4.02
7467 10063 4.593597 TGATTTCGGACAAGCGAATAAC 57.406 40.909 0.00 0.00 0.00 1.89
7470 10066 3.747099 CTTGATTTCGGACAAGCGAAT 57.253 42.857 0.00 0.00 37.32 3.34
7608 10204 2.504367 GCTGTGGACCGGCATTAATAT 58.496 47.619 0.00 0.00 45.37 1.28
7698 10294 5.188434 CCTCTCACCACATTGAACATATGT 58.812 41.667 1.41 1.41 36.70 2.29
7702 10298 2.291153 CCCCTCTCACCACATTGAACAT 60.291 50.000 0.00 0.00 0.00 2.71
7759 10369 1.410850 CCCCACGCCATATGTCCTCT 61.411 60.000 1.24 0.00 0.00 3.69
7769 10379 4.974438 ACCTCCTTCCCCACGCCA 62.974 66.667 0.00 0.00 0.00 5.69
7810 10420 4.335584 CGCGCTCCTCCCGATCTC 62.336 72.222 5.56 0.00 0.00 2.75
7886 10496 1.833055 TACATCCACCAGGGGAGGGT 61.833 60.000 5.47 3.59 42.88 4.34
7898 10508 3.792401 CCTAAGACGTTGCATACATCCA 58.208 45.455 0.00 0.00 0.00 3.41
7973 10583 1.447643 CAGCTCCCCTACCATTCGG 59.552 63.158 0.00 0.00 38.77 4.30
7976 10586 0.916358 ACTGCAGCTCCCCTACCATT 60.916 55.000 15.27 0.00 0.00 3.16
7987 10597 4.290622 CCCCCACCAACTGCAGCT 62.291 66.667 15.27 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.