Multiple sequence alignment - TraesCS6A01G409100

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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 TraesCS6A01G409100 chr6A 100.000 6545 0 0 1 6545 613333031 613326487 0.000000e+00 12087.0
1 TraesCS6A01G409100 chr6A 89.375 160 13 1 6390 6545 613310373 613310214 1.440000e-46 198.0
2 TraesCS6A01G409100 chr6A 89.375 160 13 1 6390 6545 613319463 613319304 1.440000e-46 198.0
3 TraesCS6A01G409100 chr6D 95.631 4097 126 17 2354 6432 467034625 467030564 0.000000e+00 6525.0
4 TraesCS6A01G409100 chr6D 96.962 1251 35 1 1111 2361 467035917 467034670 0.000000e+00 2097.0
5 TraesCS6A01G409100 chr6D 92.284 324 18 2 7 324 467037037 467036715 2.780000e-123 453.0
6 TraesCS6A01G409100 chr6B 94.788 4221 147 21 2358 6545 712238796 712234616 0.000000e+00 6508.0
7 TraesCS6A01G409100 chr6B 90.315 2065 88 49 348 2361 712240848 712238845 0.000000e+00 2603.0
8 TraesCS6A01G409100 chr6B 88.554 332 23 12 12 334 712241446 712241121 7.960000e-104 388.0
9 TraesCS6A01G409100 chr6B 86.893 206 12 4 96 286 699123253 699123048 3.970000e-52 217.0
10 TraesCS6A01G409100 chr7A 84.592 662 55 24 425 1066 579218732 579219366 1.210000e-171 614.0
11 TraesCS6A01G409100 chr7A 89.671 213 12 7 855 1066 541268698 541268495 5.030000e-66 263.0
12 TraesCS6A01G409100 chr7A 77.508 329 40 14 6191 6491 4895587 4895909 4.060000e-37 167.0
13 TraesCS6A01G409100 chr7A 90.196 51 5 0 1058 1108 14183656 14183706 4.240000e-07 67.6
14 TraesCS6A01G409100 chr2D 89.765 469 39 6 4391 4854 595721252 595720788 5.650000e-165 592.0
15 TraesCS6A01G409100 chr7B 87.846 469 47 8 4391 4854 397830010 397830473 5.770000e-150 542.0
16 TraesCS6A01G409100 chr7B 85.437 206 15 5 96 286 616528945 616528740 4.000000e-47 200.0
17 TraesCS6A01G409100 chr1D 77.639 559 81 26 6008 6544 462089739 462089203 3.840000e-77 300.0
18 TraesCS6A01G409100 chr3B 85.467 289 25 5 15 286 807586038 807586326 1.070000e-72 285.0
19 TraesCS6A01G409100 chr3B 90.196 51 5 0 1058 1108 517863201 517863251 4.240000e-07 67.6
20 TraesCS6A01G409100 chr2B 85.121 289 26 5 15 286 780742993 780742705 5.000000e-71 279.0
21 TraesCS6A01G409100 chr2B 85.859 198 20 4 96 286 73103335 73103139 3.090000e-48 204.0
22 TraesCS6A01G409100 chr2B 94.340 53 1 1 4285 4335 423659906 423659854 5.440000e-11 80.5
23 TraesCS6A01G409100 chr2B 92.308 52 2 2 4284 4333 513282974 513283025 9.100000e-09 73.1
24 TraesCS6A01G409100 chr3D 93.714 175 8 1 4680 4854 91313682 91313853 6.510000e-65 259.0
25 TraesCS6A01G409100 chr3D 92.157 51 4 0 1058 1108 1591343 1591393 9.100000e-09 73.1
26 TraesCS6A01G409100 chr4A 84.127 252 23 5 51 286 111068039 111068289 1.840000e-55 228.0
27 TraesCS6A01G409100 chr4A 84.884 86 11 2 4287 4372 514413369 514413286 1.170000e-12 86.1
28 TraesCS6A01G409100 chr4A 87.931 58 7 0 4278 4335 696210134 696210191 1.180000e-07 69.4
29 TraesCS6A01G409100 chr4A 90.196 51 5 0 1058 1108 491513513 491513463 4.240000e-07 67.6
30 TraesCS6A01G409100 chrUn 89.375 160 13 1 6390 6545 328090415 328090256 1.440000e-46 198.0
31 TraesCS6A01G409100 chrUn 90.196 51 5 0 1058 1108 88054107 88054057 4.240000e-07 67.6
32 TraesCS6A01G409100 chr7D 74.742 582 78 35 5964 6491 4992784 4993350 5.180000e-46 196.0
33 TraesCS6A01G409100 chr1B 93.182 88 6 0 199 286 85713605 85713692 5.330000e-26 130.0
34 TraesCS6A01G409100 chr5B 94.118 51 2 1 4292 4342 45388523 45388572 7.040000e-10 76.8
35 TraesCS6A01G409100 chr5A 92.308 52 2 2 1058 1108 514409494 514409444 9.100000e-09 73.1
36 TraesCS6A01G409100 chr5A 90.196 51 5 0 1058 1108 555334862 555334812 4.240000e-07 67.6
37 TraesCS6A01G409100 chr2A 88.889 63 2 3 4278 4339 423207456 423207514 9.100000e-09 73.1
38 TraesCS6A01G409100 chr2A 93.878 49 1 2 4287 4333 552493006 552492958 9.100000e-09 73.1
39 TraesCS6A01G409100 chr5D 90.196 51 5 0 1058 1108 528409878 528409828 4.240000e-07 67.6


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 TraesCS6A01G409100 chr6A 613326487 613333031 6544 True 12087.000000 12087 100.000 1 6545 1 chr6A.!!$R3 6544
1 TraesCS6A01G409100 chr6D 467030564 467037037 6473 True 3025.000000 6525 94.959 7 6432 3 chr6D.!!$R1 6425
2 TraesCS6A01G409100 chr6B 712234616 712241446 6830 True 3166.333333 6508 91.219 12 6545 3 chr6B.!!$R2 6533
3 TraesCS6A01G409100 chr7A 579218732 579219366 634 False 614.000000 614 84.592 425 1066 1 chr7A.!!$F3 641
4 TraesCS6A01G409100 chr1D 462089203 462089739 536 True 300.000000 300 77.639 6008 6544 1 chr1D.!!$R1 536

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
382 655 1.026718 ATCAGGAAAAAGAGGCCGCG 61.027 55.0 0.00 0.0 0.00 6.46 F
1109 1750 0.179163 GCTCAACCAAATACAGCCGC 60.179 55.0 0.00 0.0 0.00 6.53 F
1902 2577 0.526211 TGTACTCTGTAGCAGCCACG 59.474 55.0 0.00 0.0 0.00 4.94 F
2964 3691 0.400213 AACCTTGCAACGATCAGGGA 59.600 50.0 5.71 0.0 35.04 4.20 F
4096 4835 0.809385 GCAGTTGATGTGCTGATGCT 59.191 50.0 0.00 0.0 40.48 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2361 3088 1.455383 AAGGCGGCAACTTTGGTGAG 61.455 55.000 13.08 0.00 0.00 3.51 R
2394 3121 1.620819 AGACCAGTGCCTGACTAACAG 59.379 52.381 4.00 0.00 45.36 3.16 R
3689 4422 0.251354 ACTCATGCTACAGGCTGTGG 59.749 55.000 29.65 27.18 42.39 4.17 R
4557 5307 2.191641 GATGTGGGCAGAGGAGGC 59.808 66.667 0.00 0.00 0.00 4.70 R
5759 6509 0.034670 GGCAAGCAGATCCCAAGAGT 60.035 55.000 0.00 0.00 0.00 3.24 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
308 322 4.680237 CCAACTGCCGACGCTCCA 62.680 66.667 0.00 0.00 35.36 3.86
309 323 3.114616 CAACTGCCGACGCTCCAG 61.115 66.667 6.79 6.79 35.36 3.86
378 651 7.661968 AGTAAAAAGAATCAGGAAAAAGAGGC 58.338 34.615 0.00 0.00 0.00 4.70
379 652 5.474578 AAAAGAATCAGGAAAAAGAGGCC 57.525 39.130 0.00 0.00 0.00 5.19
381 654 1.133216 GAATCAGGAAAAAGAGGCCGC 59.867 52.381 0.00 0.00 0.00 6.53
382 655 1.026718 ATCAGGAAAAAGAGGCCGCG 61.027 55.000 0.00 0.00 0.00 6.46
383 656 2.359975 AGGAAAAAGAGGCCGCGG 60.360 61.111 24.05 24.05 0.00 6.46
384 657 3.440415 GGAAAAAGAGGCCGCGGG 61.440 66.667 29.38 8.95 0.00 6.13
616 954 1.848835 TTCCTCCCCATTCCCTCCCT 61.849 60.000 0.00 0.00 0.00 4.20
617 955 1.772156 CCTCCCCATTCCCTCCCTC 60.772 68.421 0.00 0.00 0.00 4.30
618 956 1.772156 CTCCCCATTCCCTCCCTCC 60.772 68.421 0.00 0.00 0.00 4.30
620 958 2.378522 CCCATTCCCTCCCTCCCT 59.621 66.667 0.00 0.00 0.00 4.20
621 959 1.772156 CCCATTCCCTCCCTCCCTC 60.772 68.421 0.00 0.00 0.00 4.30
624 962 1.954994 ATTCCCTCCCTCCCTCCCT 60.955 63.158 0.00 0.00 0.00 4.20
625 963 1.979389 ATTCCCTCCCTCCCTCCCTC 61.979 65.000 0.00 0.00 0.00 4.30
626 964 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
627 965 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
654 1254 1.152984 CTTGTGCCACTGTCACCCA 60.153 57.895 0.00 0.00 33.71 4.51
797 1422 4.118093 TGATGTATTGGTCAGTACGTGG 57.882 45.455 0.00 0.00 0.00 4.94
862 1494 3.428452 GCTTGCTTGTATGCATGACATGT 60.428 43.478 16.62 0.00 42.96 3.21
863 1495 4.201940 GCTTGCTTGTATGCATGACATGTA 60.202 41.667 16.62 12.88 42.96 2.29
864 1496 4.880886 TGCTTGTATGCATGACATGTAC 57.119 40.909 16.62 12.10 40.06 2.90
865 1497 4.260170 TGCTTGTATGCATGACATGTACA 58.740 39.130 16.62 14.31 40.06 2.90
866 1498 4.333372 TGCTTGTATGCATGACATGTACAG 59.667 41.667 16.62 11.87 40.06 2.74
1033 1671 4.654091 TTACCGGGCAATGTAGTAGTAC 57.346 45.455 6.32 0.37 0.00 2.73
1034 1672 1.406539 ACCGGGCAATGTAGTAGTACG 59.593 52.381 6.32 0.00 30.95 3.67
1039 1680 2.724690 GGCAATGTAGTAGTACGCATCG 59.275 50.000 11.83 4.80 30.95 3.84
1069 1710 8.795786 TTTACAGTCAATTAGCATTTTCACAC 57.204 30.769 0.00 0.00 0.00 3.82
1071 1712 6.804677 ACAGTCAATTAGCATTTTCACACAA 58.195 32.000 0.00 0.00 0.00 3.33
1072 1713 6.919662 ACAGTCAATTAGCATTTTCACACAAG 59.080 34.615 0.00 0.00 0.00 3.16
1086 1727 6.455360 TTCACACAAGCTTTTTCAGAATCT 57.545 33.333 0.00 0.00 0.00 2.40
1101 1742 3.192844 CAGAATCTGCAGCTCAACCAAAT 59.807 43.478 9.47 0.00 0.00 2.32
1108 1749 1.131126 CAGCTCAACCAAATACAGCCG 59.869 52.381 0.00 0.00 0.00 5.52
1109 1750 0.179163 GCTCAACCAAATACAGCCGC 60.179 55.000 0.00 0.00 0.00 6.53
1117 1792 4.530857 ATACAGCCGCCGCCAGAC 62.531 66.667 0.00 0.00 34.57 3.51
1731 2406 3.967715 GCGTCCTTCGGCTTCTTT 58.032 55.556 0.00 0.00 40.26 2.52
1900 2575 1.275291 GGTTGTACTCTGTAGCAGCCA 59.725 52.381 0.00 0.00 33.35 4.75
1902 2577 0.526211 TGTACTCTGTAGCAGCCACG 59.474 55.000 0.00 0.00 0.00 4.94
1973 2648 2.818169 TTATGCCGGCTGCTAGGGG 61.818 63.158 29.70 6.14 42.00 4.79
2214 2889 4.828925 GGTGCTGAGAGGAGGCGC 62.829 72.222 0.00 0.00 35.98 6.53
2263 2938 9.411189 TGTTTACCAATAAAAGGTTACACTCTT 57.589 29.630 0.00 0.00 40.54 2.85
2339 3014 2.882137 TGTGGCCTGCTAACTTTGTAAC 59.118 45.455 3.32 0.00 0.00 2.50
2361 3088 3.533606 AGTAGTGTCTGCATGGATGAC 57.466 47.619 8.98 8.98 0.00 3.06
2367 3094 1.065926 GTCTGCATGGATGACTCACCA 60.066 52.381 8.74 0.00 40.57 4.17
2376 3103 1.197721 GATGACTCACCAAAGTTGCCG 59.802 52.381 0.00 0.00 0.00 5.69
2394 3121 3.190535 TGCCGCCTTATGAAGTTTCTTTC 59.809 43.478 0.00 0.00 0.00 2.62
2691 3418 1.471676 GCATCTCCCCACTTACTGTCG 60.472 57.143 0.00 0.00 0.00 4.35
2759 3486 2.158696 AGCAGCTCTTCCAGTTTGTCTT 60.159 45.455 0.00 0.00 0.00 3.01
2845 3572 4.396790 TCACAACCTTTTGGCGGTAATATC 59.603 41.667 0.00 0.00 45.59 1.63
2859 3586 4.448210 GGTAATATCATGGGACGTGTTGT 58.552 43.478 0.00 0.00 0.00 3.32
2964 3691 0.400213 AACCTTGCAACGATCAGGGA 59.600 50.000 5.71 0.00 35.04 4.20
2979 3706 0.915364 AGGGAATTGCTCCTCACTCC 59.085 55.000 0.00 0.00 44.68 3.85
2983 3710 2.626840 GAATTGCTCCTCACTCCTCAC 58.373 52.381 0.00 0.00 0.00 3.51
3099 3829 2.940994 TGGGATGTTGTTCCTTTCGA 57.059 45.000 0.00 0.00 35.97 3.71
3132 3862 7.875554 TGTCCTTCAACCAATTTATTAAAAGCC 59.124 33.333 0.00 0.00 0.00 4.35
3224 3954 5.437060 GAGTGTCTCCAATATTTGCCCTTA 58.563 41.667 0.00 0.00 0.00 2.69
3271 4001 0.835971 TCCAGGTTACAGCTGAGGCA 60.836 55.000 23.35 0.00 45.98 4.75
3325 4055 4.505039 GGTGTTCAGTCTCTTATTGGTGGT 60.505 45.833 0.00 0.00 0.00 4.16
3328 4058 5.176592 GTTCAGTCTCTTATTGGTGGTACC 58.823 45.833 4.43 4.43 39.22 3.34
3346 4076 4.574013 GGTACCAGATTCAAGCTTGATCAG 59.426 45.833 28.89 21.45 37.00 2.90
3352 4082 3.942130 TTCAAGCTTGATCAGAGACGA 57.058 42.857 28.89 8.74 37.00 4.20
3489 4222 1.374947 GCAACACCTGGTAGGCTGA 59.625 57.895 0.00 0.00 39.63 4.26
3684 4417 5.122396 CCAAAAGAGGTAATGTAGTCAGCAC 59.878 44.000 0.00 0.00 0.00 4.40
3685 4418 5.483685 AAAGAGGTAATGTAGTCAGCACA 57.516 39.130 0.00 0.00 0.00 4.57
3686 4419 4.727507 AGAGGTAATGTAGTCAGCACAG 57.272 45.455 0.00 0.00 0.00 3.66
3687 4420 3.118956 AGAGGTAATGTAGTCAGCACAGC 60.119 47.826 0.00 0.00 0.00 4.40
3688 4421 1.927174 GGTAATGTAGTCAGCACAGCG 59.073 52.381 0.00 0.00 0.00 5.18
3689 4422 1.324736 GTAATGTAGTCAGCACAGCGC 59.675 52.381 0.00 0.00 42.91 5.92
3690 4423 1.021390 AATGTAGTCAGCACAGCGCC 61.021 55.000 2.29 0.00 44.04 6.53
3691 4424 2.048222 GTAGTCAGCACAGCGCCA 60.048 61.111 2.29 0.00 44.04 5.69
3692 4425 2.048222 TAGTCAGCACAGCGCCAC 60.048 61.111 2.29 0.00 44.04 5.01
3733 4466 8.233190 GTGCCTTTCTTGTATCATATAATCTGC 58.767 37.037 0.00 0.00 0.00 4.26
4031 4764 4.919754 GGTTGACATTCTCACTTTGCATTC 59.080 41.667 0.00 0.00 0.00 2.67
4046 4779 2.311542 TGCATTCCCCTTACCAGATGTT 59.688 45.455 0.00 0.00 0.00 2.71
4047 4780 3.245586 TGCATTCCCCTTACCAGATGTTT 60.246 43.478 0.00 0.00 0.00 2.83
4096 4835 0.809385 GCAGTTGATGTGCTGATGCT 59.191 50.000 0.00 0.00 40.48 3.79
4102 4841 4.129380 GTTGATGTGCTGATGCTATGGTA 58.871 43.478 0.00 0.00 40.48 3.25
4225 4964 9.720667 ATGTCGACATTCACATAAACATTTATG 57.279 29.630 25.18 18.56 43.03 1.90
4280 5019 6.091305 CAGCACTTCTGAACGAATTTGATCTA 59.909 38.462 0.00 0.00 45.72 1.98
4400 5149 6.591935 TCTGTAATAGCCTTTCTGTTATGGG 58.408 40.000 0.00 0.00 32.24 4.00
4404 5154 8.330247 TGTAATAGCCTTTCTGTTATGGGTTTA 58.670 33.333 0.00 0.00 32.24 2.01
4494 5244 2.436417 GTGGTACCACATGAACTGCAT 58.564 47.619 35.21 0.00 45.53 3.96
4934 5684 3.696051 TGAGCAAGAACATTTATCTGCCC 59.304 43.478 0.00 0.00 0.00 5.36
5258 6008 7.480229 CGTACTTGTTCATATTTTGCATTTCGA 59.520 33.333 0.00 0.00 0.00 3.71
5259 6009 9.289303 GTACTTGTTCATATTTTGCATTTCGAT 57.711 29.630 0.00 0.00 0.00 3.59
5280 6030 7.312899 TCGATGTTATATGCATACATTCTCGT 58.687 34.615 8.99 0.00 37.74 4.18
5309 6059 9.803315 GATTATTTTCCTGAATTTTCTGGTACC 57.197 33.333 4.43 4.43 44.08 3.34
5436 6186 1.974875 CATGCTTGCTGACCTGGCA 60.975 57.895 0.00 0.00 37.97 4.92
5481 6231 1.217244 GGAAAAGCCTCCGACGCTA 59.783 57.895 0.00 0.00 34.84 4.26
5583 6333 3.531538 TGTCTCCCATTCTGTAATTCGC 58.468 45.455 0.00 0.00 0.00 4.70
5647 6397 3.554934 TGTCTTGTTGACTGGCTCAAAT 58.445 40.909 0.00 0.00 45.54 2.32
5664 6414 5.201713 TCAAATGAAGAACGACTCTCACT 57.798 39.130 0.00 0.00 31.02 3.41
5689 6439 3.520290 TCTTACGGCCTTACACTCATG 57.480 47.619 0.00 0.00 0.00 3.07
5693 6443 1.555075 ACGGCCTTACACTCATGTGAT 59.445 47.619 0.00 0.00 46.55 3.06
5704 6454 2.490903 ACTCATGTGATTGAGCTTTGGC 59.509 45.455 0.94 0.00 45.75 4.52
5706 6456 1.546923 CATGTGATTGAGCTTTGGCCA 59.453 47.619 0.00 0.00 39.73 5.36
5719 6469 3.411446 CTTTGGCCAACTGTGACAGATA 58.589 45.455 20.35 0.00 35.18 1.98
5721 6471 2.989909 TGGCCAACTGTGACAGATATG 58.010 47.619 20.97 14.04 35.18 1.78
5723 6473 2.679837 GGCCAACTGTGACAGATATGTG 59.320 50.000 20.97 8.50 35.18 3.21
5733 6483 4.332819 GTGACAGATATGTGTTACCCTTGC 59.667 45.833 14.83 0.00 32.22 4.01
5743 6493 3.447229 GTGTTACCCTTGCCATTATTGCT 59.553 43.478 0.00 0.00 0.00 3.91
5744 6494 4.642885 GTGTTACCCTTGCCATTATTGCTA 59.357 41.667 0.00 0.00 0.00 3.49
5759 6509 4.712051 ATTGCTATATTGTCCAGCCTCA 57.288 40.909 0.00 0.00 34.31 3.86
5760 6510 3.475566 TGCTATATTGTCCAGCCTCAC 57.524 47.619 0.00 0.00 34.31 3.51
5761 6511 3.041211 TGCTATATTGTCCAGCCTCACT 58.959 45.455 0.00 0.00 34.31 3.41
5764 6517 4.202305 GCTATATTGTCCAGCCTCACTCTT 60.202 45.833 0.00 0.00 0.00 2.85
5770 6523 0.179936 CCAGCCTCACTCTTGGGATC 59.820 60.000 0.00 0.00 0.00 3.36
5772 6525 1.134461 CAGCCTCACTCTTGGGATCTG 60.134 57.143 0.00 0.00 0.00 2.90
5778 6531 0.034670 ACTCTTGGGATCTGCTTGCC 60.035 55.000 0.00 0.00 0.00 4.52
5788 6541 3.299977 TGCTTGCCTGCAGCCAAG 61.300 61.111 28.40 28.40 42.71 3.61
5789 6542 3.300765 GCTTGCCTGCAGCCAAGT 61.301 61.111 31.28 0.00 42.71 3.16
5790 6543 2.649034 CTTGCCTGCAGCCAAGTG 59.351 61.111 25.39 5.83 42.71 3.16
5791 6544 3.569049 CTTGCCTGCAGCCAAGTGC 62.569 63.158 25.39 15.07 44.27 4.40
5794 6547 3.060615 CCTGCAGCCAAGTGCCTC 61.061 66.667 8.66 0.00 43.28 4.70
5795 6548 2.033757 CTGCAGCCAAGTGCCTCT 59.966 61.111 0.00 0.00 43.28 3.69
5836 6591 8.090831 GGTAATATCATGCTTGTCTCTCATGTA 58.909 37.037 0.00 0.00 38.82 2.29
5845 6600 5.395103 GCTTGTCTCTCATGTAAGATGGACT 60.395 44.000 0.00 0.00 0.00 3.85
5948 6703 4.816385 TGAGAGCTTAAGGTCAGTTTGTTG 59.184 41.667 30.59 0.00 44.42 3.33
6025 6791 2.561478 TCCTGAAGCAGTTGGGTTAC 57.439 50.000 0.00 0.00 37.33 2.50
6026 6792 2.054799 TCCTGAAGCAGTTGGGTTACT 58.945 47.619 0.00 0.00 37.33 2.24
6027 6793 3.244582 TCCTGAAGCAGTTGGGTTACTA 58.755 45.455 0.00 0.00 37.33 1.82
6028 6794 3.649023 TCCTGAAGCAGTTGGGTTACTAA 59.351 43.478 0.00 0.00 37.33 2.24
6029 6795 4.288626 TCCTGAAGCAGTTGGGTTACTAAT 59.711 41.667 0.00 0.00 37.33 1.73
6030 6796 4.396166 CCTGAAGCAGTTGGGTTACTAATG 59.604 45.833 0.00 0.00 37.33 1.90
6031 6797 3.756434 TGAAGCAGTTGGGTTACTAATGC 59.244 43.478 0.00 0.00 37.33 3.56
6032 6798 2.356135 AGCAGTTGGGTTACTAATGCG 58.644 47.619 0.00 0.00 0.00 4.73
6033 6799 2.027561 AGCAGTTGGGTTACTAATGCGA 60.028 45.455 0.00 0.00 0.00 5.10
6034 6800 2.943033 GCAGTTGGGTTACTAATGCGAT 59.057 45.455 0.00 0.00 0.00 4.58
6035 6801 3.377172 GCAGTTGGGTTACTAATGCGATT 59.623 43.478 0.00 0.00 0.00 3.34
6155 6925 0.895530 TTCTTACAGACAGGAGGCCG 59.104 55.000 0.00 0.00 0.00 6.13
6157 6927 0.970937 CTTACAGACAGGAGGCCGGA 60.971 60.000 5.05 0.00 0.00 5.14
6178 6948 5.864474 CGGAGGATTGTAGTACATATTCTGC 59.136 44.000 3.28 8.92 0.00 4.26
6181 6951 7.715249 GGAGGATTGTAGTACATATTCTGCAAA 59.285 37.037 3.28 0.00 39.03 3.68
6298 7102 1.623811 TCTCACCAGTTAACCTCCTGC 59.376 52.381 0.88 0.00 0.00 4.85
6312 7116 1.606668 CTCCTGCTATCTCCTGACGTC 59.393 57.143 9.11 9.11 0.00 4.34
6363 7168 8.567285 TTCTTTCTCTAATCCTGAATTGAACC 57.433 34.615 0.00 0.00 0.00 3.62
6432 7237 1.204941 GGCCTGTAGAAAGCTCGAGAA 59.795 52.381 18.75 0.00 0.00 2.87
6439 7244 2.495084 AGAAAGCTCGAGAAAACACCC 58.505 47.619 18.75 0.00 0.00 4.61
6451 7256 1.977056 AAACACCCCGAGGAAAGTTC 58.023 50.000 0.00 0.00 36.73 3.01
6480 7285 7.265647 AGAGCTTTCAAGGTTTTCTAAAGAC 57.734 36.000 0.00 0.00 36.78 3.01
6497 7302 2.056906 GACGGGGATCCTCCATTGGG 62.057 65.000 12.58 0.00 38.64 4.12
6499 7304 1.645402 CGGGGATCCTCCATTGGGTT 61.645 60.000 12.58 0.00 38.64 4.11
6500 7305 0.636647 GGGGATCCTCCATTGGGTTT 59.363 55.000 12.58 0.00 38.64 3.27
6501 7306 1.689258 GGGGATCCTCCATTGGGTTTG 60.689 57.143 12.58 0.00 38.64 2.93
6530 7339 0.960861 GAGCCCAAGGTCCGAAAAGG 60.961 60.000 0.00 0.00 42.97 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.246635 TCCTGGTTAGCGCTCTTGTC 59.753 55.000 16.34 0.68 0.00 3.18
1 2 0.037232 GTCCTGGTTAGCGCTCTTGT 60.037 55.000 16.34 0.00 0.00 3.16
2 3 1.078759 CGTCCTGGTTAGCGCTCTTG 61.079 60.000 16.34 0.47 0.00 3.02
3 4 1.215647 CGTCCTGGTTAGCGCTCTT 59.784 57.895 16.34 0.00 0.00 2.85
4 5 2.711922 CCGTCCTGGTTAGCGCTCT 61.712 63.158 16.34 0.00 0.00 4.09
5 6 2.202756 CCGTCCTGGTTAGCGCTC 60.203 66.667 16.34 0.00 0.00 5.03
36 37 4.386100 AGGCCCCTCCCCATTCCA 62.386 66.667 0.00 0.00 34.51 3.53
271 279 1.821272 GCAGATCGGAGATGGAGAGGA 60.821 57.143 0.00 0.00 45.12 3.71
304 318 3.971453 TTCGCTTCGCTCGCTGGAG 62.971 63.158 0.00 0.00 43.46 3.86
305 319 3.971453 CTTCGCTTCGCTCGCTGGA 62.971 63.158 0.00 0.00 0.00 3.86
306 320 3.549150 CTTCGCTTCGCTCGCTGG 61.549 66.667 0.00 0.00 0.00 4.85
307 321 4.202196 GCTTCGCTTCGCTCGCTG 62.202 66.667 0.00 0.00 0.00 5.18
308 322 4.724602 TGCTTCGCTTCGCTCGCT 62.725 61.111 0.00 0.00 0.00 4.93
309 323 2.764251 TTTTGCTTCGCTTCGCTCGC 62.764 55.000 0.00 0.00 0.00 5.03
310 324 0.384230 TTTTTGCTTCGCTTCGCTCG 60.384 50.000 0.00 0.00 0.00 5.03
311 325 1.969103 ATTTTTGCTTCGCTTCGCTC 58.031 45.000 0.00 0.00 0.00 5.03
312 326 3.552604 TTATTTTTGCTTCGCTTCGCT 57.447 38.095 0.00 0.00 0.00 4.93
352 366 8.144478 GCCTCTTTTTCCTGATTCTTTTTACTT 58.856 33.333 0.00 0.00 0.00 2.24
353 367 7.255977 GGCCTCTTTTTCCTGATTCTTTTTACT 60.256 37.037 0.00 0.00 0.00 2.24
410 683 1.431440 CTGAAGAGGGACGAGCGAG 59.569 63.158 0.00 0.00 0.00 5.03
411 684 2.701780 GCTGAAGAGGGACGAGCGA 61.702 63.158 0.00 0.00 0.00 4.93
422 695 1.886585 GGACTCGCTGAGCTGAAGA 59.113 57.895 1.78 0.00 32.04 2.87
573 900 1.544703 GAGAGGGAGGTAGGAGGGG 59.455 68.421 0.00 0.00 0.00 4.79
616 954 3.036959 GAGGGAGGGAGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
617 955 4.179599 GGAGGGAGGGAGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
618 956 4.179599 GGGAGGGAGGGAGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
620 958 4.761304 AGGGGAGGGAGGGAGGGA 62.761 72.222 0.00 0.00 0.00 4.20
621 959 3.711782 AAGGGGAGGGAGGGAGGG 61.712 72.222 0.00 0.00 0.00 4.30
624 962 2.124996 CACAAGGGGAGGGAGGGA 59.875 66.667 0.00 0.00 0.00 4.20
625 963 3.732849 GCACAAGGGGAGGGAGGG 61.733 72.222 0.00 0.00 0.00 4.30
626 964 3.732849 GGCACAAGGGGAGGGAGG 61.733 72.222 0.00 0.00 0.00 4.30
627 965 2.935481 TGGCACAAGGGGAGGGAG 60.935 66.667 0.00 0.00 31.92 4.30
720 1342 2.615227 AATAAGGGAGGCCTGCAGCG 62.615 60.000 26.95 2.70 45.17 5.18
797 1422 6.363357 GGTTCATACAAAGAATTTCACACAGC 59.637 38.462 0.00 0.00 35.03 4.40
892 1524 9.477484 GATGGACCATACAAAATAGTACTACTG 57.523 37.037 7.05 5.90 0.00 2.74
1039 1680 5.567138 ATGCTAATTGACTGTAAAGCACC 57.433 39.130 0.00 0.00 42.23 5.01
1069 1710 3.673809 GCTGCAGATTCTGAAAAAGCTTG 59.326 43.478 20.43 0.00 32.44 4.01
1071 1712 3.155501 AGCTGCAGATTCTGAAAAAGCT 58.844 40.909 20.43 18.85 33.83 3.74
1072 1713 3.057736 TGAGCTGCAGATTCTGAAAAAGC 60.058 43.478 20.43 17.19 32.44 3.51
1086 1727 1.541147 GCTGTATTTGGTTGAGCTGCA 59.459 47.619 1.02 0.00 0.00 4.41
1108 1749 4.704833 TGGCTCTTGTCTGGCGGC 62.705 66.667 0.00 0.00 0.00 6.53
1109 1750 2.435586 CTGGCTCTTGTCTGGCGG 60.436 66.667 0.00 0.00 0.00 6.13
1117 1792 1.530771 CCCCCATCTCTGGCTCTTG 59.469 63.158 0.00 0.00 41.64 3.02
1700 2375 2.604686 ACGCCTCCTTCCTCTGCA 60.605 61.111 0.00 0.00 0.00 4.41
1731 2406 2.025155 GAGTAGCATCTCTTCGGACCA 58.975 52.381 0.00 0.00 0.00 4.02
1973 2648 2.293399 ACGAATTTTGCCAACCTCAGAC 59.707 45.455 0.00 0.00 0.00 3.51
2010 2685 2.464865 GGTTCATCATCTTCCGACTCG 58.535 52.381 0.00 0.00 0.00 4.18
2214 2889 2.761208 AGATTCACCCCTTGACTCGTAG 59.239 50.000 0.00 0.00 38.62 3.51
2263 2938 3.610040 ACAACATCAGAGATAACGGCA 57.390 42.857 0.00 0.00 0.00 5.69
2339 3014 3.620374 GTCATCCATGCAGACACTACTTG 59.380 47.826 0.00 0.00 32.68 3.16
2361 3088 1.455383 AAGGCGGCAACTTTGGTGAG 61.455 55.000 13.08 0.00 0.00 3.51
2367 3094 2.514803 ACTTCATAAGGCGGCAACTTT 58.485 42.857 13.08 0.00 0.00 2.66
2376 3103 8.100508 ACTAACAGAAAGAAACTTCATAAGGC 57.899 34.615 0.00 0.00 0.00 4.35
2394 3121 1.620819 AGACCAGTGCCTGACTAACAG 59.379 52.381 4.00 0.00 45.36 3.16
2569 3296 6.724893 TCATAACTTGTCGATAAGATGGGA 57.275 37.500 26.27 14.07 0.00 4.37
2845 3572 1.946768 AGTCAAACAACACGTCCCATG 59.053 47.619 0.00 0.00 0.00 3.66
2859 3586 9.332502 TGCTAAATACAAACTACTGAAGTCAAA 57.667 29.630 0.00 0.00 37.50 2.69
2964 3691 2.027377 CAGTGAGGAGTGAGGAGCAATT 60.027 50.000 0.00 0.00 0.00 2.32
2979 3706 6.166279 TCTTTACCTGCATTTAGACAGTGAG 58.834 40.000 0.00 0.00 31.76 3.51
2983 3710 6.992063 ACATCTTTACCTGCATTTAGACAG 57.008 37.500 0.00 0.00 0.00 3.51
3132 3862 5.747197 GCAGGAAGCTGTTTATCAATTCATG 59.253 40.000 0.00 0.00 41.15 3.07
3325 4055 5.423290 TCTCTGATCAAGCTTGAATCTGGTA 59.577 40.000 31.55 18.48 41.13 3.25
3328 4058 4.268167 CGTCTCTGATCAAGCTTGAATCTG 59.732 45.833 31.55 26.64 41.13 2.90
3346 4076 5.698832 CATGGATCAGACTCTAATCGTCTC 58.301 45.833 0.00 0.00 39.59 3.36
3352 4082 3.327172 CCTGGCATGGATCAGACTCTAAT 59.673 47.826 0.00 0.00 33.11 1.73
3361 4091 2.945440 GCTACAAACCTGGCATGGATCA 60.945 50.000 9.53 0.00 0.00 2.92
3397 4127 8.930760 CAGTTAGGAGTTTAGACTTGATCTTTG 58.069 37.037 0.00 0.00 39.04 2.77
3489 4222 9.636789 TGAAGATCTGTTTTCAATATGATCCAT 57.363 29.630 0.00 0.00 32.01 3.41
3518 4251 0.911769 ATCCCATCAAGCGGACAGAA 59.088 50.000 0.00 0.00 0.00 3.02
3575 4308 3.131223 TGTCTTTGCGAAAACCCAAATCA 59.869 39.130 0.00 0.00 31.29 2.57
3684 4417 2.816958 CTACAGGCTGTGGCGCTG 60.817 66.667 29.65 8.92 40.25 5.18
3685 4418 4.767255 GCTACAGGCTGTGGCGCT 62.767 66.667 34.83 9.20 44.56 5.92
3689 4422 0.251354 ACTCATGCTACAGGCTGTGG 59.749 55.000 29.65 27.18 42.39 4.17
3690 4423 1.366679 CACTCATGCTACAGGCTGTG 58.633 55.000 29.65 19.34 42.39 3.66
3691 4424 3.849002 CACTCATGCTACAGGCTGT 57.151 52.632 25.34 25.34 42.39 4.40
3733 4466 5.414765 GGGTGTCCATAAAGAAGGTAAACTG 59.585 44.000 0.00 0.00 0.00 3.16
4031 4764 3.696051 CACATCAAACATCTGGTAAGGGG 59.304 47.826 0.00 0.00 0.00 4.79
4225 4964 3.822594 TCATACAACGTGACATTTGGC 57.177 42.857 0.00 0.00 0.00 4.52
4280 5019 9.121658 GATCGGAGGGAGAAATATTTTACTTTT 57.878 33.333 1.43 0.00 0.00 2.27
4295 5034 6.054860 ACAATTAATATGGATCGGAGGGAG 57.945 41.667 0.00 0.00 0.00 4.30
4404 5154 8.061304 AGGGATCAATATTCTACCACACAAAAT 58.939 33.333 0.00 0.00 0.00 1.82
4494 5244 5.192927 AGAAGGCGATGAACCATATGAAAA 58.807 37.500 3.65 0.00 0.00 2.29
4557 5307 2.191641 GATGTGGGCAGAGGAGGC 59.808 66.667 0.00 0.00 0.00 4.70
4934 5684 2.740981 CTCCTGCAGTTGCTTTAGTCTG 59.259 50.000 13.81 0.00 42.66 3.51
5258 6008 8.306761 TCAGACGAGAATGTATGCATATAACAT 58.693 33.333 10.16 8.71 34.39 2.71
5259 6009 7.657336 TCAGACGAGAATGTATGCATATAACA 58.343 34.615 10.16 6.46 34.39 2.41
5280 6030 9.312904 ACCAGAAAATTCAGGAAAATAATCAGA 57.687 29.630 11.09 0.00 37.31 3.27
5309 6059 2.204237 TGATCGAATCATCAACCTGCG 58.796 47.619 0.00 0.00 33.59 5.18
5436 6186 2.119801 TAGAGACGCCGAACCTACTT 57.880 50.000 0.00 0.00 0.00 2.24
5481 6231 4.403734 TCTTCAAGGCGGTTTTCCTAAAT 58.596 39.130 0.00 0.00 37.95 1.40
5563 6313 2.872858 GGCGAATTACAGAATGGGAGAC 59.127 50.000 0.00 0.00 43.62 3.36
5598 6348 6.161855 TCAGTTTCAGACTTGATGTACTGT 57.838 37.500 0.00 0.00 38.02 3.55
5601 6351 6.093404 TCGATCAGTTTCAGACTTGATGTAC 58.907 40.000 0.00 0.00 36.10 2.90
5689 6439 1.615392 AGTTGGCCAAAGCTCAATCAC 59.385 47.619 22.47 3.95 39.73 3.06
5693 6443 0.746063 CACAGTTGGCCAAAGCTCAA 59.254 50.000 22.47 0.00 39.73 3.02
5704 6454 5.351465 GGTAACACATATCTGTCACAGTTGG 59.649 44.000 4.28 0.00 31.62 3.77
5706 6456 5.248477 AGGGTAACACATATCTGTCACAGTT 59.752 40.000 4.28 0.00 39.74 3.16
5719 6469 4.141959 GCAATAATGGCAAGGGTAACACAT 60.142 41.667 0.00 0.00 39.74 3.21
5721 6471 3.447229 AGCAATAATGGCAAGGGTAACAC 59.553 43.478 0.00 0.00 39.74 3.32
5723 6473 7.703058 ATATAGCAATAATGGCAAGGGTAAC 57.297 36.000 0.00 0.00 0.00 2.50
5733 6483 5.948162 AGGCTGGACAATATAGCAATAATGG 59.052 40.000 0.00 0.00 39.15 3.16
5743 6493 4.101585 CCAAGAGTGAGGCTGGACAATATA 59.898 45.833 0.00 0.00 0.00 0.86
5744 6494 3.118112 CCAAGAGTGAGGCTGGACAATAT 60.118 47.826 0.00 0.00 0.00 1.28
5759 6509 0.034670 GGCAAGCAGATCCCAAGAGT 60.035 55.000 0.00 0.00 0.00 3.24
5760 6510 0.255318 AGGCAAGCAGATCCCAAGAG 59.745 55.000 0.00 0.00 0.00 2.85
5761 6511 0.034767 CAGGCAAGCAGATCCCAAGA 60.035 55.000 0.00 0.00 0.00 3.02
5764 6517 2.044650 GCAGGCAAGCAGATCCCA 60.045 61.111 0.00 0.00 0.00 4.37
5793 6546 7.567250 TGATATTACCTATGTGAACCCTCAAGA 59.433 37.037 0.00 0.00 31.88 3.02
5794 6547 7.735917 TGATATTACCTATGTGAACCCTCAAG 58.264 38.462 0.00 0.00 31.88 3.02
5795 6548 7.684317 TGATATTACCTATGTGAACCCTCAA 57.316 36.000 0.00 0.00 31.88 3.02
5797 6550 6.595716 GCATGATATTACCTATGTGAACCCTC 59.404 42.308 0.00 0.00 0.00 4.30
5804 6559 8.093307 AGAGACAAGCATGATATTACCTATGTG 58.907 37.037 0.00 0.00 0.00 3.21
5836 6591 7.628234 AGACATTGATTTACAGAGTCCATCTT 58.372 34.615 0.00 0.00 35.47 2.40
5845 6600 7.038729 ACTCCTGAAGAGACATTGATTTACAGA 60.039 37.037 0.00 0.00 46.50 3.41
5948 6703 9.013229 AGATGATAGTCTCATAGTTCATCTGAC 57.987 37.037 11.31 0.00 44.81 3.51
6025 6791 4.085055 ACGTTCGCATTAGAATCGCATTAG 60.085 41.667 0.00 0.00 32.28 1.73
6026 6792 3.799963 ACGTTCGCATTAGAATCGCATTA 59.200 39.130 0.00 0.00 32.28 1.90
6027 6793 2.607635 ACGTTCGCATTAGAATCGCATT 59.392 40.909 0.00 0.00 32.28 3.56
6028 6794 2.201732 ACGTTCGCATTAGAATCGCAT 58.798 42.857 0.00 0.00 32.28 4.73
6029 6795 1.586578 GACGTTCGCATTAGAATCGCA 59.413 47.619 0.00 0.00 32.28 5.10
6030 6796 1.586578 TGACGTTCGCATTAGAATCGC 59.413 47.619 0.00 0.00 32.28 4.58
6031 6797 3.899835 TTGACGTTCGCATTAGAATCG 57.100 42.857 0.00 0.00 33.89 3.34
6032 6798 4.578601 CCTTTGACGTTCGCATTAGAATC 58.421 43.478 0.00 0.00 32.25 2.52
6033 6799 3.181510 GCCTTTGACGTTCGCATTAGAAT 60.182 43.478 0.00 0.00 32.25 2.40
6034 6800 2.158841 GCCTTTGACGTTCGCATTAGAA 59.841 45.455 0.00 0.00 0.00 2.10
6035 6801 1.730064 GCCTTTGACGTTCGCATTAGA 59.270 47.619 0.00 0.00 0.00 2.10
6155 6925 6.759272 TGCAGAATATGTACTACAATCCTCC 58.241 40.000 0.00 0.00 0.00 4.30
6157 6927 8.046708 TGTTTGCAGAATATGTACTACAATCCT 58.953 33.333 0.00 0.00 0.00 3.24
6165 6935 5.449041 CGCCATTGTTTGCAGAATATGTACT 60.449 40.000 0.00 0.00 0.00 2.73
6166 6936 4.734854 CGCCATTGTTTGCAGAATATGTAC 59.265 41.667 0.00 0.00 0.00 2.90
6167 6937 4.397730 ACGCCATTGTTTGCAGAATATGTA 59.602 37.500 0.00 0.00 0.00 2.29
6168 6938 3.193267 ACGCCATTGTTTGCAGAATATGT 59.807 39.130 0.00 0.00 0.00 2.29
6169 6939 3.772932 ACGCCATTGTTTGCAGAATATG 58.227 40.909 0.00 0.00 0.00 1.78
6170 6940 5.125417 ACTTACGCCATTGTTTGCAGAATAT 59.875 36.000 0.00 0.00 0.00 1.28
6171 6941 4.457603 ACTTACGCCATTGTTTGCAGAATA 59.542 37.500 0.00 0.00 0.00 1.75
6172 6942 3.255642 ACTTACGCCATTGTTTGCAGAAT 59.744 39.130 0.00 0.00 0.00 2.40
6173 6943 2.621055 ACTTACGCCATTGTTTGCAGAA 59.379 40.909 0.00 0.00 0.00 3.02
6174 6944 2.031245 CACTTACGCCATTGTTTGCAGA 60.031 45.455 0.00 0.00 0.00 4.26
6175 6945 2.318578 CACTTACGCCATTGTTTGCAG 58.681 47.619 0.00 0.00 0.00 4.41
6178 6948 3.634568 TTCCACTTACGCCATTGTTTG 57.365 42.857 0.00 0.00 0.00 2.93
6181 6951 3.134574 TCTTTCCACTTACGCCATTGT 57.865 42.857 0.00 0.00 0.00 2.71
6272 7076 4.508662 GAGGTTAACTGGTGAGATTGGAG 58.491 47.826 5.42 0.00 0.00 3.86
6298 7102 6.567687 ATGTGATAAGACGTCAGGAGATAG 57.432 41.667 19.50 0.00 0.00 2.08
6312 7116 4.925054 CCAACCACTTTGCAATGTGATAAG 59.075 41.667 34.69 23.98 36.49 1.73
6363 7168 6.510746 TTAGTGCATCGATCTGTTTATTCG 57.489 37.500 0.00 0.00 0.00 3.34
6395 7200 0.035176 GCCTTTGGTACGTACACCCA 59.965 55.000 26.02 13.26 37.84 4.51
6398 7203 1.270465 ACAGGCCTTTGGTACGTACAC 60.270 52.381 26.02 15.90 0.00 2.90
6401 7206 2.806434 TCTACAGGCCTTTGGTACGTA 58.194 47.619 0.00 0.00 0.00 3.57
6432 7237 1.213430 TGAACTTTCCTCGGGGTGTTT 59.787 47.619 0.00 0.00 0.00 2.83
6439 7244 2.933056 GCTCTTCCTGAACTTTCCTCGG 60.933 54.545 0.00 0.00 0.00 4.63
6451 7256 4.582240 AGAAAACCTTGAAAGCTCTTCCTG 59.418 41.667 0.00 0.00 0.00 3.86
6497 7302 1.248486 GGGCTCACCTTCTTCCAAAC 58.752 55.000 0.00 0.00 35.85 2.93
6499 7304 0.850100 TTGGGCTCACCTTCTTCCAA 59.150 50.000 0.00 0.00 41.11 3.53
6500 7305 0.401738 CTTGGGCTCACCTTCTTCCA 59.598 55.000 0.00 0.00 41.11 3.53
6501 7306 0.322906 CCTTGGGCTCACCTTCTTCC 60.323 60.000 0.00 0.00 41.11 3.46


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

AutoCloner maintained by Alex Coulton.