Multiple sequence alignment - TraesCS1D01G404900

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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 TraesCS1D01G404900 chr1D 100.000 6007 0 0 1 6007 469807228 469801222 0.000000e+00 11093.0
1 TraesCS1D01G404900 chr1B 89.967 3349 212 52 1 3293 651279939 651276659 0.000000e+00 4209.0
2 TraesCS1D01G404900 chr1B 87.268 1995 162 40 3919 5873 651275799 651273857 0.000000e+00 2193.0
3 TraesCS1D01G404900 chr1B 92.212 1207 86 5 4449 5648 649680172 649678967 0.000000e+00 1701.0
4 TraesCS1D01G404900 chr1B 90.635 630 39 9 3311 3922 651276672 651276045 0.000000e+00 819.0
5 TraesCS1D01G404900 chr1B 85.676 377 26 14 5639 6007 649676516 649676160 7.350000e-99 372.0
6 TraesCS1D01G404900 chr1B 73.476 328 49 29 1781 2087 651278520 651278210 8.290000e-14 89.8
7 TraesCS1D01G404900 chr1A 92.176 2799 122 40 1 2741 562913696 562910937 0.000000e+00 3866.0
8 TraesCS1D01G404900 chr1A 88.363 3231 213 59 2828 6007 562910936 562907818 0.000000e+00 3733.0
9 TraesCS1D01G404900 chr1A 74.206 252 49 10 1416 1667 562911867 562911632 2.310000e-14 91.6


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 TraesCS1D01G404900 chr1D 469801222 469807228 6006 True 11093.000000 11093 100.0000 1 6007 1 chr1D.!!$R1 6006
1 TraesCS1D01G404900 chr1B 651273857 651279939 6082 True 1827.700000 4209 85.3365 1 5873 4 chr1B.!!$R2 5872
2 TraesCS1D01G404900 chr1B 649676160 649680172 4012 True 1036.500000 1701 88.9440 4449 6007 2 chr1B.!!$R1 1558
3 TraesCS1D01G404900 chr1A 562907818 562913696 5878 True 2563.533333 3866 84.9150 1 6007 3 chr1A.!!$R1 6006

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
135 148 0.104855 CATCGGATTCCTCGAAGGCA 59.895 55.0 0.30 0.00 40.15 4.75 F
839 867 0.318441 CTCTGCGGAACTGTCCTGAA 59.682 55.0 0.00 0.00 42.44 3.02 F
1366 1425 0.250234 CCCATTTGGTGAGCTCTCGA 59.750 55.0 16.19 5.76 0.00 4.04 F
1473 1537 0.466189 ATGCCTAGGTCAATTGGGCG 60.466 55.0 11.31 0.00 45.06 6.13 F
2435 2513 0.177604 TGCTTTGGTGCTTGTTTGGG 59.822 50.0 0.00 0.00 0.00 4.12 F
2990 3077 0.235665 CGTGTTCAGCTTCGCACATT 59.764 50.0 10.61 0.00 32.62 2.71 F
3940 4312 0.819259 GCTGCTGTTGACCTGTTGGA 60.819 55.0 0.00 0.00 37.04 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1257 1316 1.293498 GAGCAGGAAGGCGAAGTCA 59.707 57.895 0.00 0.00 39.27 3.41 R
2415 2493 1.406614 CCCAAACAAGCACCAAAGCAA 60.407 47.619 0.00 0.00 36.85 3.91 R
2423 2501 1.975660 TCACCTACCCAAACAAGCAC 58.024 50.000 0.00 0.00 0.00 4.40 R
2466 2544 2.645802 ACCCAACGCTTGTGTAGAAAA 58.354 42.857 0.00 0.00 0.00 2.29 R
4224 4616 0.883833 GACTCCAATGTTGTGCCCAG 59.116 55.000 0.00 0.00 0.00 4.45 R
4446 4838 0.607489 ACAGCACCTGTGATTCCTGC 60.607 55.000 0.51 0.00 43.63 4.85 R
5680 8563 0.171903 AATCGGCTGAATTGCAGTGC 59.828 50.000 8.58 8.58 46.62 4.40 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
135 148 0.104855 CATCGGATTCCTCGAAGGCA 59.895 55.000 0.30 0.00 40.15 4.75
648 661 1.066114 CGAACTTGACGAGGACGAGC 61.066 60.000 0.00 0.00 42.66 5.03
651 664 1.512310 CTTGACGAGGACGAGCGAC 60.512 63.158 0.00 0.00 42.66 5.19
808 829 1.524008 CCACGGAAGGGTTTTGCCTC 61.524 60.000 0.00 0.00 37.43 4.70
809 830 0.537371 CACGGAAGGGTTTTGCCTCT 60.537 55.000 0.00 0.00 37.43 3.69
811 832 0.537371 CGGAAGGGTTTTGCCTCTGT 60.537 55.000 0.00 0.00 37.43 3.41
812 833 1.704641 GGAAGGGTTTTGCCTCTGTT 58.295 50.000 0.00 0.00 37.43 3.16
839 867 0.318441 CTCTGCGGAACTGTCCTGAA 59.682 55.000 0.00 0.00 42.44 3.02
840 868 0.756294 TCTGCGGAACTGTCCTGAAA 59.244 50.000 0.00 0.00 42.44 2.69
869 897 1.199327 GCTTAAAGGCCCTCGTGAAAC 59.801 52.381 0.00 0.00 0.00 2.78
878 906 4.080526 AGGCCCTCGTGAAACTGTATAATT 60.081 41.667 0.00 0.00 31.75 1.40
892 920 8.417273 AACTGTATAATTATAAATGTGGCCCC 57.583 34.615 6.75 0.00 0.00 5.80
965 1000 5.390387 AGTATTAGGGGTTGAACTGCAAAA 58.610 37.500 0.00 0.00 38.44 2.44
969 1004 3.037549 AGGGGTTGAACTGCAAAAATCA 58.962 40.909 0.00 0.00 38.44 2.57
1366 1425 0.250234 CCCATTTGGTGAGCTCTCGA 59.750 55.000 16.19 5.76 0.00 4.04
1368 1427 1.066573 CCATTTGGTGAGCTCTCGACT 60.067 52.381 16.19 0.00 0.00 4.18
1450 1514 2.284514 GCTTATTCAGTTCGTCGCTTCG 60.285 50.000 0.00 0.00 0.00 3.79
1470 1534 2.442236 ACCATGCCTAGGTCAATTGG 57.558 50.000 11.31 15.33 32.90 3.16
1471 1535 1.063717 ACCATGCCTAGGTCAATTGGG 60.064 52.381 20.60 15.97 32.90 4.12
1472 1536 1.035139 CATGCCTAGGTCAATTGGGC 58.965 55.000 11.31 13.85 42.73 5.36
1473 1537 0.466189 ATGCCTAGGTCAATTGGGCG 60.466 55.000 11.31 0.00 45.06 6.13
1519 1583 4.111375 ACGCCTAGATTTGTAGTGTGAG 57.889 45.455 0.00 0.00 0.00 3.51
1520 1584 3.762288 ACGCCTAGATTTGTAGTGTGAGA 59.238 43.478 0.00 0.00 0.00 3.27
1526 1590 6.591834 CCTAGATTTGTAGTGTGAGAACTTGG 59.408 42.308 0.00 0.00 0.00 3.61
1557 1621 9.255304 GTAAGGAATGCTTTGTTAATTTGTTCA 57.745 29.630 0.00 0.00 0.00 3.18
1636 1700 6.595772 CATCCTCTGCATTTCAGTAGTAAC 57.404 41.667 0.00 0.00 43.32 2.50
1712 1776 3.242712 GTGCAGTGTTGAAAATTCCAACG 59.757 43.478 14.83 6.17 44.92 4.10
1758 1835 8.846211 CCCTCTGTTTCATAGTTTTTCTGTAAA 58.154 33.333 0.00 0.00 0.00 2.01
1801 1878 4.993705 TTTACCTCCCTCTGTTCATTGT 57.006 40.909 0.00 0.00 0.00 2.71
1842 1920 3.252215 CGCTTCAACCATGTTTAGGTCAA 59.748 43.478 0.00 0.00 38.76 3.18
1843 1921 4.546570 GCTTCAACCATGTTTAGGTCAAC 58.453 43.478 0.00 0.00 38.76 3.18
1844 1922 4.278419 GCTTCAACCATGTTTAGGTCAACT 59.722 41.667 0.00 0.00 38.76 3.16
1864 1942 5.392767 ACTATTAGGTGATCCGTGCTATG 57.607 43.478 0.00 0.00 39.05 2.23
1937 2015 6.774354 TGTTCTGTTCCTAATCGTGTTAAC 57.226 37.500 0.00 0.00 0.00 2.01
2195 2273 7.750229 TTGTTTATGAGACTGCTTTGATTCT 57.250 32.000 0.00 0.00 0.00 2.40
2196 2274 8.846943 TTGTTTATGAGACTGCTTTGATTCTA 57.153 30.769 0.00 0.00 0.00 2.10
2197 2275 8.484641 TGTTTATGAGACTGCTTTGATTCTAG 57.515 34.615 0.00 0.00 0.00 2.43
2198 2276 8.097038 TGTTTATGAGACTGCTTTGATTCTAGT 58.903 33.333 0.00 0.00 0.00 2.57
2199 2277 8.599774 GTTTATGAGACTGCTTTGATTCTAGTC 58.400 37.037 0.00 0.00 38.37 2.59
2219 2297 9.422681 TCTAGTCTAGTGGTGCTAAGATTTTAT 57.577 33.333 6.77 0.00 0.00 1.40
2352 2430 6.599244 TGATTTAGCACCAGATTTTGAGGTAG 59.401 38.462 0.00 0.00 33.49 3.18
2353 2431 5.499004 TTAGCACCAGATTTTGAGGTAGT 57.501 39.130 0.00 0.00 33.49 2.73
2355 2433 4.833390 AGCACCAGATTTTGAGGTAGTAC 58.167 43.478 0.00 0.00 33.49 2.73
2356 2434 4.286032 AGCACCAGATTTTGAGGTAGTACA 59.714 41.667 2.06 0.00 33.49 2.90
2357 2435 5.045578 AGCACCAGATTTTGAGGTAGTACAT 60.046 40.000 2.06 0.00 33.49 2.29
2408 2486 8.581057 TGTGAAATGTATTGTTTTACGCAATT 57.419 26.923 0.00 0.00 37.65 2.32
2423 2501 7.804614 TTACGCAATTTATAACTTGCTTTGG 57.195 32.000 27.69 18.74 44.32 3.28
2435 2513 0.177604 TGCTTTGGTGCTTGTTTGGG 59.822 50.000 0.00 0.00 0.00 4.12
2461 2539 4.165372 GGTGATGTTTAGGTCCAATCCCTA 59.835 45.833 0.00 0.00 33.35 3.53
2464 2542 3.810623 TGTTTAGGTCCAATCCCTACCT 58.189 45.455 0.00 0.00 45.53 3.08
2465 2543 4.180723 TGTTTAGGTCCAATCCCTACCTT 58.819 43.478 0.00 0.00 40.82 3.50
2466 2544 4.604490 TGTTTAGGTCCAATCCCTACCTTT 59.396 41.667 0.00 0.00 40.82 3.11
2492 2570 1.769733 CACAAGCGTTGGGTTTGATG 58.230 50.000 0.00 0.00 38.98 3.07
2719 2798 5.010708 AGGTTTATTTGGATTGGTGGACT 57.989 39.130 0.00 0.00 0.00 3.85
2759 2846 5.257082 ACGAAACTATTGCACCTTTTTGT 57.743 34.783 0.00 0.00 0.00 2.83
2789 2876 0.687354 GTGGCTTCTTCACTCCAGGA 59.313 55.000 0.00 0.00 32.78 3.86
2790 2877 0.687354 TGGCTTCTTCACTCCAGGAC 59.313 55.000 0.00 0.00 0.00 3.85
2796 2883 2.182827 TCTTCACTCCAGGACCATCAG 58.817 52.381 0.00 0.00 0.00 2.90
2943 3030 6.451292 AAGAAGATCTACTACCCGAGGATA 57.549 41.667 0.00 0.00 0.00 2.59
2952 3039 5.793034 ACTACCCGAGGATATGGTACTAT 57.207 43.478 0.00 0.00 33.55 2.12
2987 3074 0.942410 TACCGTGTTCAGCTTCGCAC 60.942 55.000 0.00 0.00 0.00 5.34
2990 3077 0.235665 CGTGTTCAGCTTCGCACATT 59.764 50.000 10.61 0.00 32.62 2.71
3034 3121 7.962995 TGAATCATGGAAGAGTACTAAGAGT 57.037 36.000 0.00 0.00 0.00 3.24
3035 3122 8.001881 TGAATCATGGAAGAGTACTAAGAGTC 57.998 38.462 0.00 0.00 0.00 3.36
3036 3123 7.836685 TGAATCATGGAAGAGTACTAAGAGTCT 59.163 37.037 0.00 0.00 0.00 3.24
3037 3124 9.344772 GAATCATGGAAGAGTACTAAGAGTCTA 57.655 37.037 0.00 0.00 0.00 2.59
3038 3125 9.702253 AATCATGGAAGAGTACTAAGAGTCTAA 57.298 33.333 0.00 0.00 0.00 2.10
3039 3126 8.740123 TCATGGAAGAGTACTAAGAGTCTAAG 57.260 38.462 0.00 0.00 0.00 2.18
3040 3127 8.549731 TCATGGAAGAGTACTAAGAGTCTAAGA 58.450 37.037 0.00 0.00 0.00 2.10
3047 3134 7.501225 AGAGTACTAAGAGTCTAAGATTGCCTC 59.499 40.741 0.00 0.00 0.00 4.70
3051 3138 7.126733 ACTAAGAGTCTAAGATTGCCTCCTTA 58.873 38.462 0.00 0.00 0.00 2.69
3277 3381 9.793259 AATATTATGAGGTGTAAACGAATGGAT 57.207 29.630 0.00 0.00 0.00 3.41
3278 3382 9.793259 ATATTATGAGGTGTAAACGAATGGATT 57.207 29.630 0.00 0.00 0.00 3.01
3280 3384 9.793259 ATTATGAGGTGTAAACGAATGGATTAT 57.207 29.630 0.00 0.00 0.00 1.28
3281 3385 7.730364 ATGAGGTGTAAACGAATGGATTATC 57.270 36.000 0.00 0.00 0.00 1.75
3282 3386 6.884832 TGAGGTGTAAACGAATGGATTATCT 58.115 36.000 0.00 0.00 0.00 1.98
3283 3387 6.761242 TGAGGTGTAAACGAATGGATTATCTG 59.239 38.462 0.00 0.00 0.00 2.90
3284 3388 6.650120 AGGTGTAAACGAATGGATTATCTGT 58.350 36.000 0.00 0.00 0.00 3.41
3285 3389 7.110155 AGGTGTAAACGAATGGATTATCTGTT 58.890 34.615 0.00 0.00 0.00 3.16
3286 3390 8.262227 AGGTGTAAACGAATGGATTATCTGTTA 58.738 33.333 0.00 0.00 0.00 2.41
3287 3391 8.548721 GGTGTAAACGAATGGATTATCTGTTAG 58.451 37.037 0.00 0.00 0.00 2.34
3288 3392 9.309516 GTGTAAACGAATGGATTATCTGTTAGA 57.690 33.333 0.00 0.00 0.00 2.10
3400 3505 6.750501 TCTGTATACGAAGAAACCTTCAATCG 59.249 38.462 10.93 10.93 42.86 3.34
3419 3524 8.504812 TCAATCGAAATTCATATTTCCTGACA 57.495 30.769 0.00 0.00 44.40 3.58
3480 3585 7.924412 ACCTTATCAATTGCTGCAATCTAAATG 59.076 33.333 26.40 19.91 32.43 2.32
3485 3590 9.656040 ATCAATTGCTGCAATCTAAATGTTTAA 57.344 25.926 26.40 6.89 32.43 1.52
3500 3605 3.430931 TGTTTAAGTGCACTTTCGCAAC 58.569 40.909 35.20 27.88 45.14 4.17
3511 3616 3.990469 CACTTTCGCAACTCATGACTAGT 59.010 43.478 0.00 0.00 0.00 2.57
3543 3649 1.801309 CTAGCTAGCCCGTCTGCCTC 61.801 65.000 12.13 0.00 0.00 4.70
3565 3671 3.869246 CGTTATGCTACCATTTTCTCCGT 59.131 43.478 0.00 0.00 32.85 4.69
3603 3709 2.171003 GCAACAAGGATAGGGTGCTTT 58.829 47.619 0.00 0.00 36.20 3.51
3639 3745 1.467920 GCTATTCTGGCCACTGCTTT 58.532 50.000 0.00 0.00 37.74 3.51
3658 3764 2.430248 TCTGCTGCATTCACCATCAT 57.570 45.000 1.31 0.00 0.00 2.45
3686 3792 5.483685 TTTCCTGCACTACATACTCTGTT 57.516 39.130 0.00 0.00 39.39 3.16
3741 3847 8.988934 GCTTCCGTATTATTCTGATGATGTTAA 58.011 33.333 0.00 0.00 0.00 2.01
3869 3990 1.525306 CCGATTAAACCCTCCGCCC 60.525 63.158 0.00 0.00 0.00 6.13
3884 4005 4.010349 CTCCGCCCTTAATTTGTCTTCTT 58.990 43.478 0.00 0.00 0.00 2.52
3891 4012 6.624423 CCCTTAATTTGTCTTCTTCATGGTG 58.376 40.000 0.00 0.00 0.00 4.17
3940 4312 0.819259 GCTGCTGTTGACCTGTTGGA 60.819 55.000 0.00 0.00 37.04 3.53
3941 4313 1.233019 CTGCTGTTGACCTGTTGGAG 58.767 55.000 0.00 0.00 37.04 3.86
3961 4341 2.105477 AGTGTTGGTGTTCATCTGAGCT 59.895 45.455 0.00 0.00 0.00 4.09
4143 4535 5.922053 TGACTTGATATCCCTCTGTTCATG 58.078 41.667 0.00 0.00 0.00 3.07
4152 4544 5.246981 TCCCTCTGTTCATGTGATTTCTT 57.753 39.130 0.00 0.00 0.00 2.52
4224 4616 8.607459 ACGAAGATGATGAAATACTGATTCAAC 58.393 33.333 0.00 0.00 39.98 3.18
4316 4708 4.187694 GGAAAGATGCTGTTAGTCCTGAG 58.812 47.826 0.00 0.00 0.00 3.35
4337 4729 2.546778 CATGCCAGCAACATTCATTCC 58.453 47.619 0.00 0.00 0.00 3.01
4446 4838 2.724977 TTCAGACACTGAAGCCTACG 57.275 50.000 9.67 0.00 44.27 3.51
4461 4853 1.645034 CTACGCAGGAATCACAGGTG 58.355 55.000 0.00 0.00 0.00 4.00
4565 4957 2.900546 ACTCGATGGAACTCACCTTTCT 59.099 45.455 0.00 0.00 0.00 2.52
4658 5050 0.673985 AAGTCACGTCTAGCAGCACA 59.326 50.000 0.00 0.00 0.00 4.57
4694 5086 2.485814 GGCACTTTCTCCTGTTGATGAC 59.514 50.000 0.00 0.00 0.00 3.06
4728 5120 2.430465 TGCTTTCAGAGACATCCTTGC 58.570 47.619 0.00 0.00 0.00 4.01
4733 5125 1.277273 TCAGAGACATCCTTGCCTGTG 59.723 52.381 0.00 0.00 29.29 3.66
4772 5164 4.568359 GCTGCATCAAGTTTATCTTCTCGA 59.432 41.667 0.00 0.00 33.63 4.04
4820 5212 3.954200 TGACTTCAGATATGCCAAGCAA 58.046 40.909 0.00 0.00 43.62 3.91
4823 5215 6.121590 TGACTTCAGATATGCCAAGCAAATA 58.878 36.000 0.00 0.00 43.62 1.40
4889 5281 0.035630 CCCCTTTCTGCCTGAGTGAG 60.036 60.000 0.00 0.00 0.00 3.51
4890 5282 0.979665 CCCTTTCTGCCTGAGTGAGA 59.020 55.000 0.00 0.00 0.00 3.27
5026 5418 8.475639 ACTGTAGAAGTAGAAGAAACACTTTCA 58.524 33.333 0.00 0.00 38.64 2.69
5042 5434 1.522668 TTCAATGGTGAAGAGGTGCG 58.477 50.000 0.00 0.00 38.88 5.34
5045 5437 0.674895 AATGGTGAAGAGGTGCGAGC 60.675 55.000 0.00 0.00 0.00 5.03
5098 5492 7.715249 TCAGTTCATGAAACTAAGTAGCAAACT 59.285 33.333 10.35 0.00 46.69 2.66
5283 5687 3.557264 GGCTGACTGCTGTTAAACCTAGT 60.557 47.826 4.20 0.00 42.39 2.57
5291 5695 6.028146 TGCTGTTAAACCTAGTTGTCGATA 57.972 37.500 0.00 0.00 0.00 2.92
5306 5710 5.006153 TGTCGATATGTACCTTGGTGAAG 57.994 43.478 2.03 0.00 0.00 3.02
5514 5933 8.650143 ATTTGTTTGTACCTTTCATCCTACAT 57.350 30.769 0.00 0.00 0.00 2.29
5527 5946 6.611613 TCATCCTACATGTCATCCCTATTC 57.388 41.667 0.00 0.00 0.00 1.75
5551 5970 0.745845 CGAAGGGCTCAGGTGGATTG 60.746 60.000 0.00 0.00 0.00 2.67
5585 6005 0.163788 CAAAGCCTGTAACAGTCGCG 59.836 55.000 0.00 0.00 0.00 5.87
5598 6018 2.165845 ACAGTCGCGGCTTCTTACTATT 59.834 45.455 12.35 0.00 0.00 1.73
5626 6046 2.027561 CGATTCAGTAGTTGTTCCCCCA 60.028 50.000 0.00 0.00 0.00 4.96
5680 8563 0.250901 CACCACCTCAAGGACCAAGG 60.251 60.000 2.30 6.14 38.94 3.61
5681 8564 1.303643 CCACCTCAAGGACCAAGGC 60.304 63.158 2.30 0.00 38.94 4.35
5682 8565 1.455849 CACCTCAAGGACCAAGGCA 59.544 57.895 2.30 0.00 38.94 4.75
5683 8566 0.890996 CACCTCAAGGACCAAGGCAC 60.891 60.000 2.30 0.00 38.94 5.01
5684 8567 1.062488 ACCTCAAGGACCAAGGCACT 61.062 55.000 2.30 0.00 38.82 4.40
5685 8568 0.607489 CCTCAAGGACCAAGGCACTG 60.607 60.000 0.00 0.00 36.25 3.66
5686 8569 1.228245 TCAAGGACCAAGGCACTGC 60.228 57.895 0.00 0.00 40.86 4.40
5687 8570 1.529010 CAAGGACCAAGGCACTGCA 60.529 57.895 2.82 0.00 40.86 4.41
5696 8590 2.180017 GGCACTGCAATTCAGCCG 59.820 61.111 2.82 0.00 46.76 5.52
5701 8595 0.729116 ACTGCAATTCAGCCGATTCG 59.271 50.000 0.00 0.00 46.76 3.34
5703 8597 0.447406 TGCAATTCAGCCGATTCGTG 59.553 50.000 5.20 0.00 0.00 4.35
5712 8606 1.970917 GCCGATTCGTGGACTGCAAG 61.971 60.000 5.20 0.00 42.29 4.01
5721 8615 1.228245 GGACTGCAAGGTGCCAGAA 60.228 57.895 0.00 0.00 44.23 3.02
5810 8709 5.291858 GTCCAAACAAAGCCTTTTCTTCTTG 59.708 40.000 0.00 0.00 0.00 3.02
5874 8773 0.958091 CCGTGCAAAGGTTCCATTCA 59.042 50.000 0.00 0.00 0.00 2.57
5960 8864 1.112916 TCTGTCCAGGTTCGTGCTGA 61.113 55.000 0.00 0.00 0.00 4.26
5981 8885 5.331906 TGAGCTGAAGCCTATCATCTATCT 58.668 41.667 0.00 0.00 43.38 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
135 148 2.125961 GCACCTCGACCCGGAGTAT 61.126 63.158 0.73 0.00 31.98 2.12
648 661 1.134901 CTCGGTCTGGAACTCGTCG 59.865 63.158 0.00 0.00 0.00 5.12
651 664 1.213013 CACCTCGGTCTGGAACTCG 59.787 63.158 0.00 0.00 0.00 4.18
808 829 0.458197 CCGCAGAGCAGAGAGAACAG 60.458 60.000 0.00 0.00 0.00 3.16
809 830 0.895559 TCCGCAGAGCAGAGAGAACA 60.896 55.000 0.00 0.00 0.00 3.18
811 832 0.244994 GTTCCGCAGAGCAGAGAGAA 59.755 55.000 0.00 0.00 0.00 2.87
812 833 0.610509 AGTTCCGCAGAGCAGAGAGA 60.611 55.000 0.00 0.00 0.00 3.10
839 867 3.200165 AGGGCCTTTAAGCTTCTACGATT 59.800 43.478 0.00 0.00 0.00 3.34
840 868 2.772515 AGGGCCTTTAAGCTTCTACGAT 59.227 45.455 0.00 0.00 0.00 3.73
869 897 6.404293 GCGGGGCCACATTTATAATTATACAG 60.404 42.308 5.46 1.47 0.00 2.74
878 906 0.180642 TTCGCGGGGCCACATTTATA 59.819 50.000 5.46 0.00 0.00 0.98
885 913 1.381165 ATGTAAATTCGCGGGGCCAC 61.381 55.000 6.13 0.00 0.00 5.01
892 920 4.317839 CGAGGGTTTCTATGTAAATTCGCG 60.318 45.833 0.00 0.00 0.00 5.87
947 982 4.219115 TGATTTTTGCAGTTCAACCCCTA 58.781 39.130 0.00 0.00 33.73 3.53
965 1000 0.849417 GCAGAGGGGAGGGATTGATT 59.151 55.000 0.00 0.00 0.00 2.57
969 1004 1.385206 GGAGCAGAGGGGAGGGATT 60.385 63.158 0.00 0.00 0.00 3.01
1132 1185 2.042843 GGCGGAGGAAGAGGAGGA 60.043 66.667 0.00 0.00 0.00 3.71
1133 1186 3.157949 GGGCGGAGGAAGAGGAGG 61.158 72.222 0.00 0.00 0.00 4.30
1257 1316 1.293498 GAGCAGGAAGGCGAAGTCA 59.707 57.895 0.00 0.00 39.27 3.41
1458 1522 2.620251 TGATCGCCCAATTGACCTAG 57.380 50.000 7.12 0.00 0.00 3.02
1519 1583 6.819397 AGCATTCCTTACTTTACCAAGTTC 57.181 37.500 0.00 0.00 40.66 3.01
1520 1584 7.069455 ACAAAGCATTCCTTACTTTACCAAGTT 59.931 33.333 0.00 0.00 43.45 2.66
1557 1621 2.032030 GCGCTGCCGTTAACATGAATAT 60.032 45.455 0.00 0.00 36.67 1.28
1636 1700 4.489810 CAGTCCTAACAAGAGCACAGTAG 58.510 47.826 0.00 0.00 0.00 2.57
1712 1776 4.021016 AGGGTGAATAGAAGGCACGATATC 60.021 45.833 0.00 0.00 33.48 1.63
1725 1789 8.567285 AAAACTATGAAACAGAGGGTGAATAG 57.433 34.615 0.00 0.00 0.00 1.73
1728 1805 7.013274 CAGAAAAACTATGAAACAGAGGGTGAA 59.987 37.037 0.00 0.00 0.00 3.18
1801 1878 2.666508 GCGACGAACTGAATAAGCTTGA 59.333 45.455 9.86 0.00 0.00 3.02
1842 1920 4.322049 GCATAGCACGGATCACCTAATAGT 60.322 45.833 0.00 0.00 0.00 2.12
1843 1921 4.081972 AGCATAGCACGGATCACCTAATAG 60.082 45.833 0.00 0.00 0.00 1.73
1844 1922 3.832490 AGCATAGCACGGATCACCTAATA 59.168 43.478 0.00 0.00 0.00 0.98
1864 1942 8.186821 ACAGATTAAGTCATATTTGAAGCAAGC 58.813 33.333 0.00 0.00 32.48 4.01
1937 2015 3.686128 CACTCGATTCTAAGTCTCGGTG 58.314 50.000 0.00 0.00 33.38 4.94
2196 2274 9.740710 AAAATAAAATCTTAGCACCACTAGACT 57.259 29.630 0.00 0.00 30.79 3.24
2352 2430 8.678199 TGATATAGCACAGTAGCAGATATGTAC 58.322 37.037 0.00 0.00 36.85 2.90
2353 2431 8.807948 TGATATAGCACAGTAGCAGATATGTA 57.192 34.615 0.00 0.00 36.85 2.29
2355 2433 8.196103 ACATGATATAGCACAGTAGCAGATATG 58.804 37.037 0.00 0.00 36.85 1.78
2356 2434 8.303780 ACATGATATAGCACAGTAGCAGATAT 57.696 34.615 0.00 0.00 36.85 1.63
2357 2435 7.709149 ACATGATATAGCACAGTAGCAGATA 57.291 36.000 0.00 0.00 36.85 1.98
2408 2486 5.782893 ACAAGCACCAAAGCAAGTTATAA 57.217 34.783 0.00 0.00 36.85 0.98
2411 2489 4.180057 CAAACAAGCACCAAAGCAAGTTA 58.820 39.130 0.00 0.00 34.28 2.24
2415 2493 1.406614 CCCAAACAAGCACCAAAGCAA 60.407 47.619 0.00 0.00 36.85 3.91
2418 2496 2.035832 CCTACCCAAACAAGCACCAAAG 59.964 50.000 0.00 0.00 0.00 2.77
2423 2501 1.975660 TCACCTACCCAAACAAGCAC 58.024 50.000 0.00 0.00 0.00 4.40
2435 2513 5.123936 GGATTGGACCTAAACATCACCTAC 58.876 45.833 0.00 0.00 0.00 3.18
2465 2543 3.018149 ACCCAACGCTTGTGTAGAAAAA 58.982 40.909 0.00 0.00 0.00 1.94
2466 2544 2.645802 ACCCAACGCTTGTGTAGAAAA 58.354 42.857 0.00 0.00 0.00 2.29
2538 2616 6.408869 CCAGAATCCCATGCATTTTAAAACT 58.591 36.000 1.97 0.00 0.00 2.66
2542 2620 3.773667 TGCCAGAATCCCATGCATTTTAA 59.226 39.130 0.00 0.00 0.00 1.52
2543 2621 3.372897 TGCCAGAATCCCATGCATTTTA 58.627 40.909 0.00 0.00 0.00 1.52
2750 2837 5.427378 CCACCAAATTCTGAACAAAAAGGT 58.573 37.500 0.00 0.00 0.00 3.50
2759 2846 4.037923 GTGAAGAAGCCACCAAATTCTGAA 59.962 41.667 0.00 0.00 33.67 3.02
2790 2877 9.687210 CCATATGAATATGTGAAAAACTGATGG 57.313 33.333 3.65 0.00 38.73 3.51
2882 2969 4.780021 TGGGAGAGCTTAATCTTTGAGAGT 59.220 41.667 0.00 0.00 0.00 3.24
2952 3039 6.216801 ACACGGTAGCAATAGAACAGAATA 57.783 37.500 0.00 0.00 0.00 1.75
3037 3124 9.178758 CTGTTTTTACTATAAGGAGGCAATCTT 57.821 33.333 0.00 0.00 0.00 2.40
3038 3125 8.329502 ACTGTTTTTACTATAAGGAGGCAATCT 58.670 33.333 0.00 0.00 0.00 2.40
3039 3126 8.507524 ACTGTTTTTACTATAAGGAGGCAATC 57.492 34.615 0.00 0.00 0.00 2.67
3040 3127 9.392259 GTACTGTTTTTACTATAAGGAGGCAAT 57.608 33.333 0.00 0.00 0.00 3.56
3191 3287 6.668645 TGCACCTAATACCAAAATCTACCAT 58.331 36.000 0.00 0.00 0.00 3.55
3205 3301 5.800296 TCAGCAAACTTACTGCACCTAATA 58.200 37.500 0.00 0.00 42.48 0.98
3293 3397 9.581289 TCTAACAGATAATTTCCCAGTCAAAAA 57.419 29.630 0.00 0.00 0.00 1.94
3294 3398 9.753674 ATCTAACAGATAATTTCCCAGTCAAAA 57.246 29.630 0.00 0.00 32.12 2.44
3295 3399 9.753674 AATCTAACAGATAATTTCCCAGTCAAA 57.246 29.630 0.00 0.00 32.89 2.69
3296 3400 9.753674 AAATCTAACAGATAATTTCCCAGTCAA 57.246 29.630 0.00 0.00 32.89 3.18
3297 3401 9.753674 AAAATCTAACAGATAATTTCCCAGTCA 57.246 29.630 0.00 0.00 32.89 3.41
3299 3403 8.971073 CCAAAATCTAACAGATAATTTCCCAGT 58.029 33.333 0.00 0.00 32.89 4.00
3300 3404 9.189156 TCCAAAATCTAACAGATAATTTCCCAG 57.811 33.333 0.00 0.00 32.89 4.45
3301 3405 9.189156 CTCCAAAATCTAACAGATAATTTCCCA 57.811 33.333 0.00 0.00 32.89 4.37
3302 3406 9.408648 TCTCCAAAATCTAACAGATAATTTCCC 57.591 33.333 0.00 0.00 32.89 3.97
3305 3409 8.907885 GCCTCTCCAAAATCTAACAGATAATTT 58.092 33.333 0.00 0.00 32.89 1.82
3306 3410 7.503902 GGCCTCTCCAAAATCTAACAGATAATT 59.496 37.037 0.00 0.00 32.38 1.40
3309 3413 5.163195 GGGCCTCTCCAAAATCTAACAGATA 60.163 44.000 0.84 0.00 32.69 1.98
3422 3527 8.988546 ACCAAATGCATATGTTTATGGTAGTA 57.011 30.769 17.92 0.00 38.11 1.82
3480 3585 3.691498 AGTTGCGAAAGTGCACTTAAAC 58.309 40.909 31.31 27.38 46.25 2.01
3485 3590 1.265095 CATGAGTTGCGAAAGTGCACT 59.735 47.619 15.25 15.25 46.25 4.40
3500 3605 3.449018 AGGTGGCAACTACTAGTCATGAG 59.551 47.826 1.40 0.00 37.61 2.90
3511 3616 2.667470 CTAGCTAGGAGGTGGCAACTA 58.333 52.381 13.32 0.00 34.30 2.24
3543 3649 3.869246 ACGGAGAAAATGGTAGCATAACG 59.131 43.478 8.04 9.03 0.00 3.18
3565 3671 4.588106 TGTTGCAGAAAATTGGGAGATCAA 59.412 37.500 0.00 0.00 0.00 2.57
3603 3709 4.778213 ATAGCCAAAAGGTCAGATGCTA 57.222 40.909 0.00 0.00 34.69 3.49
3658 3764 2.284754 TGTAGTGCAGGAAATTGCCA 57.715 45.000 4.92 0.00 43.43 4.92
3741 3847 4.340950 ACAAACGTGTTCCTCCAATGAAAT 59.659 37.500 0.00 0.00 32.58 2.17
3869 3990 6.680810 TGCACCATGAAGAAGACAAATTAAG 58.319 36.000 0.00 0.00 0.00 1.85
3905 4026 9.618890 TCAACAGCAGCTTTATCTTTATCTATT 57.381 29.630 0.00 0.00 0.00 1.73
3914 4035 3.244700 ACAGGTCAACAGCAGCTTTATCT 60.245 43.478 0.00 0.00 0.00 1.98
3915 4036 3.077359 ACAGGTCAACAGCAGCTTTATC 58.923 45.455 0.00 0.00 0.00 1.75
3917 4038 2.618241 CAACAGGTCAACAGCAGCTTTA 59.382 45.455 0.00 0.00 0.00 1.85
3940 4312 2.105477 AGCTCAGATGAACACCAACACT 59.895 45.455 0.00 0.00 0.00 3.55
3941 4313 2.498167 AGCTCAGATGAACACCAACAC 58.502 47.619 0.00 0.00 0.00 3.32
4143 4535 6.991531 AGATGAATCAGCCTAGAAGAAATCAC 59.008 38.462 0.00 0.00 0.00 3.06
4152 4544 7.220030 GGAATAACAAGATGAATCAGCCTAGA 58.780 38.462 0.00 0.00 0.00 2.43
4224 4616 0.883833 GACTCCAATGTTGTGCCCAG 59.116 55.000 0.00 0.00 0.00 4.45
4316 4708 1.931172 GAATGAATGTTGCTGGCATGC 59.069 47.619 9.90 9.90 0.00 4.06
4337 4729 3.913548 TGTGTTTTCATTGGGTCATCG 57.086 42.857 0.00 0.00 0.00 3.84
4446 4838 0.607489 ACAGCACCTGTGATTCCTGC 60.607 55.000 0.51 0.00 43.63 4.85
4461 4853 1.079612 GGCCTGCATTTGGAACAGC 60.080 57.895 0.00 0.00 42.39 4.40
4565 4957 4.270834 ACGACTCATCTAAGTTGGAGCTA 58.729 43.478 0.00 0.00 35.32 3.32
4658 5050 3.428282 GCCGGCGATTTGGACGTT 61.428 61.111 12.58 0.00 36.47 3.99
4694 5086 3.461061 TGAAAGCAAGGCATCTAGATCG 58.539 45.455 1.03 0.13 0.00 3.69
4728 5120 4.691860 CAGAACCTTTATTCTGCACAGG 57.308 45.455 2.78 0.00 46.69 4.00
4740 5132 2.590821 ACTTGATGCAGCAGAACCTTT 58.409 42.857 4.20 0.00 0.00 3.11
4742 5134 2.283145 AACTTGATGCAGCAGAACCT 57.717 45.000 4.20 0.00 0.00 3.50
4889 5281 5.054477 TGTACAGGTGTAGCTTGTTTCTTC 58.946 41.667 0.00 0.00 38.43 2.87
4890 5282 5.031066 TGTACAGGTGTAGCTTGTTTCTT 57.969 39.130 0.00 0.00 38.43 2.52
4917 5309 3.002791 TGGCATTCGAGATGTTCTGTTC 58.997 45.455 8.64 0.00 0.00 3.18
5026 5418 0.674895 GCTCGCACCTCTTCACCATT 60.675 55.000 0.00 0.00 0.00 3.16
5059 5453 3.149436 TGAACTGAACAAAAGCACAGC 57.851 42.857 0.00 0.00 34.25 4.40
5155 5554 3.370104 TGGGTATCCATTTCCGCATTTT 58.630 40.909 0.00 0.00 38.32 1.82
5283 5687 5.046878 ACTTCACCAAGGTACATATCGACAA 60.047 40.000 0.00 0.00 33.37 3.18
5291 5695 5.305585 CAAGTACACTTCACCAAGGTACAT 58.694 41.667 0.00 0.00 38.01 2.29
5306 5710 5.989777 ACTACAAAGATGTGACCAAGTACAC 59.010 40.000 0.00 0.00 40.84 2.90
5514 5933 2.666317 TCGAGCTGAATAGGGATGACA 58.334 47.619 0.00 0.00 0.00 3.58
5527 5946 2.186384 CCTGAGCCCTTCGAGCTG 59.814 66.667 1.92 0.00 41.75 4.24
5551 5970 6.739112 ACAGGCTTTGAAGTTGAGTTATTTC 58.261 36.000 0.00 0.00 0.00 2.17
5585 6005 4.501071 TCGGACAACAATAGTAAGAAGCC 58.499 43.478 0.00 0.00 0.00 4.35
5598 6018 4.330944 ACAACTACTGAATCGGACAACA 57.669 40.909 0.00 0.00 0.00 3.33
5680 8563 0.171903 AATCGGCTGAATTGCAGTGC 59.828 50.000 8.58 8.58 46.62 4.40
5681 8564 1.530441 CGAATCGGCTGAATTGCAGTG 60.530 52.381 0.00 0.00 46.62 3.66
5682 8565 0.729116 CGAATCGGCTGAATTGCAGT 59.271 50.000 0.00 0.00 46.62 4.40
5684 8567 0.447406 CACGAATCGGCTGAATTGCA 59.553 50.000 7.80 0.00 34.04 4.08
5685 8568 0.248215 CCACGAATCGGCTGAATTGC 60.248 55.000 7.80 0.00 0.00 3.56
5686 8569 1.062587 GTCCACGAATCGGCTGAATTG 59.937 52.381 7.80 0.00 0.00 2.32
5687 8570 1.066143 AGTCCACGAATCGGCTGAATT 60.066 47.619 7.80 0.00 0.00 2.17
5696 8590 0.798776 CACCTTGCAGTCCACGAATC 59.201 55.000 0.00 0.00 0.00 2.52
5712 8606 3.423154 CCGCGAACTTCTGGCACC 61.423 66.667 8.23 0.00 0.00 5.01
5721 8615 2.126189 GTACCTTCGCCGCGAACT 60.126 61.111 23.79 13.98 41.05 3.01
5810 8709 4.142609 TCAAGCAGAAGATACCACCATC 57.857 45.455 0.00 0.00 0.00 3.51
5960 8864 6.269538 TCAAAGATAGATGATAGGCTTCAGCT 59.730 38.462 17.19 17.19 44.15 4.24
5981 8885 0.539438 GACATGGGCAGGGTGTCAAA 60.539 55.000 0.00 0.00 41.35 2.69


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

AutoCloner maintained by Alex Coulton.