Multiple sequence alignment - TraesCS2D01G305700

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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 TraesCS2D01G305700 chr2D 100.000 3386 0 0 1 3386 391391320 391394705 0.000000e+00 6253.0
1 TraesCS2D01G305700 chr2B 91.950 3267 194 33 1 3222 462948861 462952103 0.000000e+00 4512.0
2 TraesCS2D01G305700 chr2B 96.774 62 2 0 3325 3386 462952099 462952160 1.660000e-18 104.0
3 TraesCS2D01G305700 chr2A 94.969 1948 69 11 924 2865 528122027 528123951 0.000000e+00 3027.0
4 TraesCS2D01G305700 chr2A 88.877 971 59 23 1 932 528118559 528119519 0.000000e+00 1149.0
5 TraesCS2D01G305700 chr2A 85.450 433 45 12 2968 3386 528124244 528124672 5.190000e-118 435.0
6 TraesCS2D01G305700 chr4B 100.000 34 0 0 2939 2972 187728106 187728139 2.820000e-06 63.9
7 TraesCS2D01G305700 chr6D 100.000 33 0 0 2940 2972 289215039 289215071 1.010000e-05 62.1
8 TraesCS2D01G305700 chr1A 94.595 37 2 0 2936 2972 64711964 64712000 1.310000e-04 58.4


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 TraesCS2D01G305700 chr2D 391391320 391394705 3385 False 6253 6253 100.000000 1 3386 1 chr2D.!!$F1 3385
1 TraesCS2D01G305700 chr2B 462948861 462952160 3299 False 2308 4512 94.362000 1 3386 2 chr2B.!!$F1 3385
2 TraesCS2D01G305700 chr2A 528118559 528124672 6113 False 1537 3027 89.765333 1 3386 3 chr2A.!!$F1 3385

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
844 892 0.03716 AAGGTACGCCGTCCCAAAAT 59.963 50.0 0.54 0.0 40.5 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2483 5058 0.17576 GATCCTGTGAGCGTGGCTTA 59.824 55.0 0.0 0.0 39.88 3.09 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
42 43 4.037446 TGAAGTGTATTTGAAGCACCCAAC 59.963 41.667 0.00 0.00 33.96 3.77
48 49 5.830991 TGTATTTGAAGCACCCAACTAAACT 59.169 36.000 0.00 0.00 0.00 2.66
49 50 6.999272 TGTATTTGAAGCACCCAACTAAACTA 59.001 34.615 0.00 0.00 0.00 2.24
50 51 6.575162 ATTTGAAGCACCCAACTAAACTAG 57.425 37.500 0.00 0.00 0.00 2.57
118 119 7.377398 CCATCTGTTCACAAATATTGTTCCAA 58.623 34.615 0.00 0.00 43.23 3.53
119 120 7.329226 CCATCTGTTCACAAATATTGTTCCAAC 59.671 37.037 0.00 0.00 43.23 3.77
198 199 3.370672 CACGCACATACAATCTACTGCAA 59.629 43.478 0.00 0.00 0.00 4.08
233 240 7.330208 CGGTGCATGTTATAGTACCTTATAACC 59.670 40.741 16.51 7.28 42.11 2.85
234 241 8.373220 GGTGCATGTTATAGTACCTTATAACCT 58.627 37.037 16.51 8.67 42.11 3.50
292 302 5.074929 TGGATCCCCAAATGCTTCATAGTAT 59.925 40.000 9.90 0.00 40.09 2.12
295 305 5.132502 TCCCCAAATGCTTCATAGTATGTG 58.867 41.667 9.94 5.92 33.00 3.21
323 337 5.885352 TGATGGAAGAAATGGAGCGAAAATA 59.115 36.000 0.00 0.00 0.00 1.40
346 360 2.511637 AGAATTCCTCCATCCTTCCACC 59.488 50.000 0.65 0.00 0.00 4.61
352 366 2.505982 CATCCTTCCACCGGCGAT 59.494 61.111 9.30 0.00 0.00 4.58
353 367 1.889105 CATCCTTCCACCGGCGATG 60.889 63.158 9.30 0.00 0.00 3.84
395 437 7.874940 TGAAACATCACCAGAATACAGAAAAG 58.125 34.615 0.00 0.00 0.00 2.27
412 454 2.507547 GCGTTACCGTCATCGCCA 60.508 61.111 0.00 0.00 42.33 5.69
425 467 3.842923 CGCCAGCATCCTCCTCGT 61.843 66.667 0.00 0.00 0.00 4.18
431 473 3.917760 CATCCTCCTCGTCGCCCC 61.918 72.222 0.00 0.00 0.00 5.80
461 503 0.107703 GCCATCAACATCCTCGACCA 60.108 55.000 0.00 0.00 0.00 4.02
462 504 1.475751 GCCATCAACATCCTCGACCAT 60.476 52.381 0.00 0.00 0.00 3.55
480 522 5.575157 GACCATACCCTCTATCTCATCAGA 58.425 45.833 0.00 0.00 0.00 3.27
482 524 6.015918 ACCATACCCTCTATCTCATCAGAAG 58.984 44.000 0.00 0.00 30.24 2.85
485 527 3.640967 ACCCTCTATCTCATCAGAAGCAC 59.359 47.826 0.00 0.00 30.24 4.40
494 536 3.264947 TCATCAGAAGCACCATCTTTCG 58.735 45.455 0.00 0.00 0.00 3.46
495 537 2.839486 TCAGAAGCACCATCTTTCGT 57.161 45.000 0.00 0.00 0.00 3.85
496 538 2.688507 TCAGAAGCACCATCTTTCGTC 58.311 47.619 0.00 0.00 0.00 4.20
641 686 2.278330 GCCCAAGAACCAAGCAGGG 61.278 63.158 0.00 0.00 43.89 4.45
646 691 1.793820 AAGAACCAAGCAGGGGAGGG 61.794 60.000 0.04 0.00 43.89 4.30
653 698 0.253347 AAGCAGGGGAGGGAATCTCA 60.253 55.000 0.00 0.00 44.19 3.27
657 702 1.762460 GGGGAGGGAATCTCAGCGA 60.762 63.158 0.00 0.00 44.19 4.93
663 708 2.869192 GAGGGAATCTCAGCGATTTGAC 59.131 50.000 0.00 0.00 42.31 3.18
676 721 0.250513 ATTTGACGCCTCTCCAGGAC 59.749 55.000 0.00 0.00 43.65 3.85
824 872 6.759827 GCTTATCAGAGTTATCGGTTGGTTAA 59.240 38.462 0.00 0.00 0.00 2.01
844 892 0.037160 AAGGTACGCCGTCCCAAAAT 59.963 50.000 0.54 0.00 40.50 1.82
853 901 1.654023 CGTCCCAAAATCGCCTTCCC 61.654 60.000 0.00 0.00 0.00 3.97
915 964 2.158579 ACCCCGCTTCCTTAGAAAACAA 60.159 45.455 0.00 0.00 0.00 2.83
921 970 5.451381 CCGCTTCCTTAGAAAACAAAACCTT 60.451 40.000 0.00 0.00 0.00 3.50
959 3522 2.279582 AGACGAACGCAATCTAGTGG 57.720 50.000 0.00 0.00 0.00 4.00
961 3524 0.108329 ACGAACGCAATCTAGTGGGG 60.108 55.000 0.00 0.00 35.84 4.96
1320 3894 2.997315 TGCTCCCACCTCCTGTCG 60.997 66.667 0.00 0.00 0.00 4.35
1423 3997 0.173708 CGCCTCCTTCTACTCCACAC 59.826 60.000 0.00 0.00 0.00 3.82
1479 4053 0.321564 CCGTCTGCAAGTCCAATCCA 60.322 55.000 0.00 0.00 33.76 3.41
1914 4488 5.766150 TTACTGGAACTGTGGATTTTGTG 57.234 39.130 0.00 0.00 41.61 3.33
1929 4503 2.126502 GTGTTTGGGAATGCCGCG 60.127 61.111 0.00 0.00 33.83 6.46
2073 4647 2.070783 CAAAATTGCACAGTGGATGGC 58.929 47.619 1.84 0.00 0.00 4.40
2242 4816 2.827921 GGGGATTTTGCACTCAAGACAT 59.172 45.455 0.00 0.00 33.12 3.06
2378 4952 7.959658 TTATTCAAGGACATGAATGGATTGT 57.040 32.000 11.71 0.00 46.63 2.71
2451 5026 5.260027 GCTTCAACAGCTAAATGCAAAAG 57.740 39.130 0.00 0.00 46.27 2.27
2462 5037 5.105351 GCTAAATGCAAAAGTATCCAACCCT 60.105 40.000 0.00 0.00 42.31 4.34
2468 5043 4.747810 CAAAAGTATCCAACCCTTGATGC 58.252 43.478 0.00 0.00 0.00 3.91
2469 5044 4.322057 AAAGTATCCAACCCTTGATGCT 57.678 40.909 0.00 0.00 0.00 3.79
2470 5045 4.322057 AAGTATCCAACCCTTGATGCTT 57.678 40.909 0.00 0.00 0.00 3.91
2483 5058 4.321750 CCTTGATGCTTCTGAATTGCAAGT 60.322 41.667 4.94 0.59 40.24 3.16
2487 5062 4.164822 TGCTTCTGAATTGCAAGTAAGC 57.835 40.909 20.41 20.41 37.35 3.09
2495 5070 0.533978 TTGCAAGTAAGCCACGCTCA 60.534 50.000 0.00 0.00 38.25 4.26
2532 5107 9.477484 AGTCAAGTAACTAACTGTATTGACTTG 57.523 33.333 10.90 12.54 44.94 3.16
2533 5108 8.709646 GTCAAGTAACTAACTGTATTGACTTGG 58.290 37.037 16.01 5.18 41.69 3.61
2534 5109 8.426489 TCAAGTAACTAACTGTATTGACTTGGT 58.574 33.333 16.01 0.00 41.69 3.67
2535 5110 9.701098 CAAGTAACTAACTGTATTGACTTGGTA 57.299 33.333 11.57 0.00 39.09 3.25
2536 5111 9.924650 AAGTAACTAACTGTATTGACTTGGTAG 57.075 33.333 0.00 0.00 38.88 3.18
2734 5309 4.340097 TCGTGTGGTATTCAGGTCGATATT 59.660 41.667 0.00 0.00 0.00 1.28
2735 5310 4.444388 CGTGTGGTATTCAGGTCGATATTG 59.556 45.833 0.00 0.00 0.00 1.90
2736 5311 5.357257 GTGTGGTATTCAGGTCGATATTGT 58.643 41.667 0.00 0.00 0.00 2.71
2800 5375 2.601240 TGCATTCCAATCCAACCTGA 57.399 45.000 0.00 0.00 0.00 3.86
2801 5376 2.170166 TGCATTCCAATCCAACCTGAC 58.830 47.619 0.00 0.00 0.00 3.51
2874 5655 6.183360 TGTTTGGTTGTCAGTTTATGTCAGTC 60.183 38.462 0.00 0.00 0.00 3.51
2919 5701 4.604843 ATCAGACATACAAACATGCACG 57.395 40.909 0.00 0.00 0.00 5.34
2941 5723 3.559242 GCATCTCTCATGTTCCAAGCTAC 59.441 47.826 0.00 0.00 0.00 3.58
2943 5725 4.727507 TCTCTCATGTTCCAAGCTACTC 57.272 45.455 0.00 0.00 0.00 2.59
2944 5726 3.449018 TCTCTCATGTTCCAAGCTACTCC 59.551 47.826 0.00 0.00 0.00 3.85
2946 5728 2.503356 CTCATGTTCCAAGCTACTCCCT 59.497 50.000 0.00 0.00 0.00 4.20
2948 5730 2.327325 TGTTCCAAGCTACTCCCTCT 57.673 50.000 0.00 0.00 0.00 3.69
2950 5732 1.903183 GTTCCAAGCTACTCCCTCTGT 59.097 52.381 0.00 0.00 0.00 3.41
2951 5733 3.097614 GTTCCAAGCTACTCCCTCTGTA 58.902 50.000 0.00 0.00 0.00 2.74
2955 5737 3.515901 CCAAGCTACTCCCTCTGTAAACT 59.484 47.826 0.00 0.00 0.00 2.66
2956 5738 4.710375 CCAAGCTACTCCCTCTGTAAACTA 59.290 45.833 0.00 0.00 0.00 2.24
2957 5739 5.187186 CCAAGCTACTCCCTCTGTAAACTAA 59.813 44.000 0.00 0.00 0.00 2.24
2958 5740 6.127026 CCAAGCTACTCCCTCTGTAAACTAAT 60.127 42.308 0.00 0.00 0.00 1.73
2959 5741 6.718522 AGCTACTCCCTCTGTAAACTAATC 57.281 41.667 0.00 0.00 0.00 1.75
2960 5742 6.436890 AGCTACTCCCTCTGTAAACTAATCT 58.563 40.000 0.00 0.00 0.00 2.40
2962 5744 8.060075 AGCTACTCCCTCTGTAAACTAATCTAA 58.940 37.037 0.00 0.00 0.00 2.10
2963 5745 8.354426 GCTACTCCCTCTGTAAACTAATCTAAG 58.646 40.741 0.00 0.00 0.00 2.18
2964 5746 9.629878 CTACTCCCTCTGTAAACTAATCTAAGA 57.370 37.037 0.00 0.00 0.00 2.10
2965 5747 8.528044 ACTCCCTCTGTAAACTAATCTAAGAG 57.472 38.462 0.00 0.00 0.00 2.85
2966 5748 7.068962 ACTCCCTCTGTAAACTAATCTAAGAGC 59.931 40.741 0.00 0.00 0.00 4.09
3024 5812 3.873952 GTGACAAGGATAACTGATCTGCC 59.126 47.826 0.00 0.00 34.66 4.85
3045 5833 5.589855 TGCCATATACAATGTTCAGTTGAGG 59.410 40.000 0.00 0.00 0.00 3.86
3063 5852 1.092348 GGTATGAACAAGGCGGAACC 58.908 55.000 0.00 0.00 39.61 3.62
3134 5923 1.188863 GACCTGCCAAATGCTCCATT 58.811 50.000 0.00 0.00 42.00 3.16
3203 5998 0.835941 CTCCCTCCAGCAGCTTATGT 59.164 55.000 0.00 0.00 0.00 2.29
3217 6012 5.702865 CAGCTTATGTACACATTGCAAAGT 58.297 37.500 1.71 1.06 37.20 2.66
3218 6013 6.622679 GCAGCTTATGTACACATTGCAAAGTA 60.623 38.462 7.05 6.35 36.74 2.24
3219 6014 7.304735 CAGCTTATGTACACATTGCAAAGTAA 58.695 34.615 7.05 0.00 37.20 2.24
3220 6015 7.807433 CAGCTTATGTACACATTGCAAAGTAAA 59.193 33.333 7.05 4.87 37.20 2.01
3221 6016 8.356657 AGCTTATGTACACATTGCAAAGTAAAA 58.643 29.630 7.05 2.45 37.20 1.52
3222 6017 8.973378 GCTTATGTACACATTGCAAAGTAAAAA 58.027 29.630 7.05 0.00 37.76 1.94
3226 6021 8.572828 TGTACACATTGCAAAGTAAAAATGAG 57.427 30.769 7.05 0.00 34.75 2.90
3227 6022 6.529463 ACACATTGCAAAGTAAAAATGAGC 57.471 33.333 7.05 0.00 34.75 4.26
3228 6023 6.282930 ACACATTGCAAAGTAAAAATGAGCT 58.717 32.000 7.05 0.00 34.75 4.09
3229 6024 6.421801 ACACATTGCAAAGTAAAAATGAGCTC 59.578 34.615 7.05 6.82 34.75 4.09
3230 6025 5.928264 ACATTGCAAAGTAAAAATGAGCTCC 59.072 36.000 12.15 0.00 34.75 4.70
3231 6026 5.528043 TTGCAAAGTAAAAATGAGCTCCA 57.472 34.783 12.15 0.00 0.00 3.86
3232 6027 5.125100 TGCAAAGTAAAAATGAGCTCCAG 57.875 39.130 12.15 0.00 0.00 3.86
3233 6028 4.584325 TGCAAAGTAAAAATGAGCTCCAGT 59.416 37.500 12.15 0.00 0.00 4.00
3234 6029 4.919754 GCAAAGTAAAAATGAGCTCCAGTG 59.080 41.667 12.15 0.00 0.00 3.66
3235 6030 5.278463 GCAAAGTAAAAATGAGCTCCAGTGA 60.278 40.000 12.15 0.00 0.00 3.41
3236 6031 5.948992 AAGTAAAAATGAGCTCCAGTGAC 57.051 39.130 12.15 2.54 0.00 3.67
3237 6032 5.234466 AGTAAAAATGAGCTCCAGTGACT 57.766 39.130 12.15 4.93 0.00 3.41
3238 6033 4.999950 AGTAAAAATGAGCTCCAGTGACTG 59.000 41.667 12.15 5.42 0.00 3.51
3239 6034 3.777106 AAAATGAGCTCCAGTGACTGA 57.223 42.857 15.33 0.00 32.44 3.41
3240 6035 3.996921 AAATGAGCTCCAGTGACTGAT 57.003 42.857 15.33 0.00 32.44 2.90
3241 6036 5.426689 AAAATGAGCTCCAGTGACTGATA 57.573 39.130 15.33 0.54 32.44 2.15
3242 6037 5.627182 AAATGAGCTCCAGTGACTGATAT 57.373 39.130 15.33 0.00 32.44 1.63
3243 6038 4.603989 ATGAGCTCCAGTGACTGATATG 57.396 45.455 15.33 0.00 32.44 1.78
3244 6039 2.102084 TGAGCTCCAGTGACTGATATGC 59.898 50.000 15.33 11.81 32.44 3.14
3245 6040 2.102084 GAGCTCCAGTGACTGATATGCA 59.898 50.000 15.33 0.00 32.44 3.96
3246 6041 2.502947 AGCTCCAGTGACTGATATGCAA 59.497 45.455 15.33 0.00 32.44 4.08
3247 6042 2.871022 GCTCCAGTGACTGATATGCAAG 59.129 50.000 15.33 0.00 32.44 4.01
3248 6043 3.431346 GCTCCAGTGACTGATATGCAAGA 60.431 47.826 15.33 0.00 32.44 3.02
3249 6044 4.743045 GCTCCAGTGACTGATATGCAAGAT 60.743 45.833 15.33 0.00 32.44 2.40
3250 6045 4.700700 TCCAGTGACTGATATGCAAGATG 58.299 43.478 15.33 0.00 32.44 2.90
3251 6046 4.406649 TCCAGTGACTGATATGCAAGATGA 59.593 41.667 15.33 0.00 32.44 2.92
3252 6047 5.104817 TCCAGTGACTGATATGCAAGATGAA 60.105 40.000 15.33 0.00 32.44 2.57
3253 6048 5.587443 CCAGTGACTGATATGCAAGATGAAA 59.413 40.000 15.33 0.00 32.44 2.69
3254 6049 6.094464 CCAGTGACTGATATGCAAGATGAAAA 59.906 38.462 15.33 0.00 32.44 2.29
3255 6050 7.362315 CCAGTGACTGATATGCAAGATGAAAAA 60.362 37.037 15.33 0.00 32.44 1.94
3280 6075 8.697507 AAAAGAAAAGAATCACACCTCATACT 57.302 30.769 0.00 0.00 0.00 2.12
3281 6076 7.913674 AAGAAAAGAATCACACCTCATACTC 57.086 36.000 0.00 0.00 0.00 2.59
3282 6077 7.009179 AGAAAAGAATCACACCTCATACTCA 57.991 36.000 0.00 0.00 0.00 3.41
3283 6078 6.876257 AGAAAAGAATCACACCTCATACTCAC 59.124 38.462 0.00 0.00 0.00 3.51
3284 6079 6.365970 AAAGAATCACACCTCATACTCACT 57.634 37.500 0.00 0.00 0.00 3.41
3285 6080 5.590530 AGAATCACACCTCATACTCACTC 57.409 43.478 0.00 0.00 0.00 3.51
3286 6081 5.268387 AGAATCACACCTCATACTCACTCT 58.732 41.667 0.00 0.00 0.00 3.24
3287 6082 4.998671 ATCACACCTCATACTCACTCTG 57.001 45.455 0.00 0.00 0.00 3.35
3288 6083 3.092301 TCACACCTCATACTCACTCTGG 58.908 50.000 0.00 0.00 0.00 3.86
3289 6084 3.092301 CACACCTCATACTCACTCTGGA 58.908 50.000 0.00 0.00 0.00 3.86
3290 6085 3.093057 ACACCTCATACTCACTCTGGAC 58.907 50.000 0.00 0.00 0.00 4.02
3291 6086 2.098280 CACCTCATACTCACTCTGGACG 59.902 54.545 0.00 0.00 0.00 4.79
3292 6087 1.066303 CCTCATACTCACTCTGGACGC 59.934 57.143 0.00 0.00 0.00 5.19
3293 6088 0.733150 TCATACTCACTCTGGACGCG 59.267 55.000 3.53 3.53 0.00 6.01
3294 6089 0.452184 CATACTCACTCTGGACGCGT 59.548 55.000 13.85 13.85 0.00 6.01
3295 6090 1.135373 CATACTCACTCTGGACGCGTT 60.135 52.381 15.53 0.00 0.00 4.84
3296 6091 0.956633 TACTCACTCTGGACGCGTTT 59.043 50.000 15.53 0.00 0.00 3.60
3297 6092 0.597637 ACTCACTCTGGACGCGTTTG 60.598 55.000 15.53 6.99 0.00 2.93
3298 6093 0.597637 CTCACTCTGGACGCGTTTGT 60.598 55.000 15.53 5.45 0.00 2.83
3299 6094 0.874175 TCACTCTGGACGCGTTTGTG 60.874 55.000 15.53 17.23 0.00 3.33
3300 6095 2.244651 ACTCTGGACGCGTTTGTGC 61.245 57.895 15.53 0.00 0.00 4.57
3301 6096 1.956170 CTCTGGACGCGTTTGTGCT 60.956 57.895 15.53 0.00 0.00 4.40
3302 6097 1.498865 CTCTGGACGCGTTTGTGCTT 61.499 55.000 15.53 0.00 0.00 3.91
3303 6098 1.092921 TCTGGACGCGTTTGTGCTTT 61.093 50.000 15.53 0.00 0.00 3.51
3304 6099 0.248458 CTGGACGCGTTTGTGCTTTT 60.248 50.000 15.53 0.00 0.00 2.27
3305 6100 0.171455 TGGACGCGTTTGTGCTTTTT 59.829 45.000 15.53 0.00 0.00 1.94
3306 6101 0.570272 GGACGCGTTTGTGCTTTTTG 59.430 50.000 15.53 0.00 0.00 2.44
3307 6102 0.044246 GACGCGTTTGTGCTTTTTGC 60.044 50.000 15.53 0.00 43.25 3.68
3308 6103 1.084977 CGCGTTTGTGCTTTTTGCG 60.085 52.632 0.00 0.00 46.63 4.85
3309 6104 1.272423 GCGTTTGTGCTTTTTGCGG 59.728 52.632 0.00 0.00 46.63 5.69
3310 6105 1.142778 GCGTTTGTGCTTTTTGCGGA 61.143 50.000 0.00 0.00 46.63 5.54
3311 6106 0.845768 CGTTTGTGCTTTTTGCGGAG 59.154 50.000 0.00 0.00 46.63 4.63
3312 6107 1.532921 CGTTTGTGCTTTTTGCGGAGA 60.533 47.619 0.00 0.00 46.63 3.71
3313 6108 2.742774 GTTTGTGCTTTTTGCGGAGAT 58.257 42.857 0.00 0.00 46.63 2.75
3314 6109 3.123050 GTTTGTGCTTTTTGCGGAGATT 58.877 40.909 0.00 0.00 46.63 2.40
3315 6110 4.295051 GTTTGTGCTTTTTGCGGAGATTA 58.705 39.130 0.00 0.00 46.63 1.75
3316 6111 4.576216 TTGTGCTTTTTGCGGAGATTAA 57.424 36.364 0.00 0.00 46.63 1.40
3317 6112 4.159377 TGTGCTTTTTGCGGAGATTAAG 57.841 40.909 0.00 0.00 46.63 1.85
3318 6113 3.818210 TGTGCTTTTTGCGGAGATTAAGA 59.182 39.130 0.00 0.00 46.63 2.10
3319 6114 4.458989 TGTGCTTTTTGCGGAGATTAAGAT 59.541 37.500 0.00 0.00 46.63 2.40
3320 6115 4.795278 GTGCTTTTTGCGGAGATTAAGATG 59.205 41.667 0.00 0.00 46.63 2.90
3321 6116 4.142403 TGCTTTTTGCGGAGATTAAGATGG 60.142 41.667 0.00 0.00 46.63 3.51
3322 6117 4.354587 CTTTTTGCGGAGATTAAGATGGC 58.645 43.478 0.00 0.00 0.00 4.40
3323 6118 3.281727 TTTGCGGAGATTAAGATGGCT 57.718 42.857 0.00 0.00 0.00 4.75
3335 6242 9.860898 GAGATTAAGATGGCTTAAAATTGTTGT 57.139 29.630 0.00 0.00 46.44 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 0.101759 ATGGCATTCATCACTTGCGC 59.898 50.000 0.00 0.00 37.25 6.09
118 119 2.906389 TGTCACTCTAATTCAGGCCAGT 59.094 45.455 5.01 0.00 0.00 4.00
119 120 3.616956 TGTCACTCTAATTCAGGCCAG 57.383 47.619 5.01 0.00 0.00 4.85
198 199 5.880332 ACTATAACATGCACCGTCAGAAAAT 59.120 36.000 0.00 0.00 0.00 1.82
292 302 2.821378 CCATTTCTTCCATCACTGCACA 59.179 45.455 0.00 0.00 0.00 4.57
295 305 2.098770 GCTCCATTTCTTCCATCACTGC 59.901 50.000 0.00 0.00 0.00 4.40
323 337 3.054065 GTGGAAGGATGGAGGAATTCTGT 60.054 47.826 5.23 0.00 0.00 3.41
346 360 1.398390 CTTTCTTTTCCTCCATCGCCG 59.602 52.381 0.00 0.00 0.00 6.46
352 366 5.128499 TGTTTCATTGCTTTCTTTTCCTCCA 59.872 36.000 0.00 0.00 0.00 3.86
353 367 5.600696 TGTTTCATTGCTTTCTTTTCCTCC 58.399 37.500 0.00 0.00 0.00 4.30
412 454 3.532155 GGCGACGAGGAGGATGCT 61.532 66.667 0.00 0.00 42.52 3.79
431 473 2.066393 TTGATGGCGAGGAGGAGGG 61.066 63.158 0.00 0.00 0.00 4.30
461 503 5.480073 GTGCTTCTGATGAGATAGAGGGTAT 59.520 44.000 0.00 0.00 0.00 2.73
462 504 4.830046 GTGCTTCTGATGAGATAGAGGGTA 59.170 45.833 0.00 0.00 0.00 3.69
480 522 1.625818 AGGAGACGAAAGATGGTGCTT 59.374 47.619 0.00 0.00 0.00 3.91
482 524 1.205893 AGAGGAGACGAAAGATGGTGC 59.794 52.381 0.00 0.00 0.00 5.01
485 527 2.103373 TGGAGAGGAGACGAAAGATGG 58.897 52.381 0.00 0.00 0.00 3.51
494 536 1.739049 CGCCTGATGGAGAGGAGAC 59.261 63.158 0.00 0.00 34.95 3.36
495 537 1.456518 CCGCCTGATGGAGAGGAGA 60.457 63.158 0.00 0.00 34.95 3.71
496 538 3.136750 CCGCCTGATGGAGAGGAG 58.863 66.667 0.00 0.00 34.95 3.69
520 562 1.574263 AGAAGAGGAAGGGGTACAGC 58.426 55.000 0.00 0.00 0.00 4.40
657 702 0.250513 GTCCTGGAGAGGCGTCAAAT 59.749 55.000 9.41 0.00 39.57 2.32
688 733 1.633774 TCTCTGGGAGAGTGGTTCAC 58.366 55.000 0.00 0.00 42.83 3.18
708 756 4.183865 GCTGGGTTAAAAGATGGATTTGC 58.816 43.478 0.00 0.00 0.00 3.68
748 796 2.246789 CGCTCTCGTTCTCTCTGTTTC 58.753 52.381 0.00 0.00 0.00 2.78
760 808 4.427661 GTGCTCTGCCGCTCTCGT 62.428 66.667 0.00 0.00 0.00 4.18
781 829 2.030562 AACCACCACTTCGCTCCG 59.969 61.111 0.00 0.00 0.00 4.63
783 831 1.166531 AAGCAACCACCACTTCGCTC 61.167 55.000 0.00 0.00 0.00 5.03
824 872 0.179023 TTTTGGGACGGCGTACCTTT 60.179 50.000 38.50 3.51 37.45 3.11
844 892 1.820581 CGTATTCCTGGGAAGGCGA 59.179 57.895 17.15 0.00 37.37 5.54
853 901 0.921347 CGTTCGAAGGCGTATTCCTG 59.079 55.000 4.73 0.00 36.38 3.86
915 964 8.528044 TTTGTTTTCAGTATACTCCAAGGTTT 57.472 30.769 1.26 0.00 0.00 3.27
921 970 6.751157 TCGTCTTTGTTTTCAGTATACTCCA 58.249 36.000 1.26 0.00 0.00 3.86
959 3522 0.541764 AGAGAGAGATCCCGATGCCC 60.542 60.000 0.00 0.00 0.00 5.36
961 3524 1.812571 GAGAGAGAGAGATCCCGATGC 59.187 57.143 0.00 0.00 0.00 3.91
1479 4053 1.664965 GTTGGAGAAGTCGCACGCT 60.665 57.895 0.00 0.00 0.00 5.07
1737 4311 5.220989 CCCAGCAGTATTCTCAAATGTGATG 60.221 44.000 0.00 0.00 31.85 3.07
1914 4488 4.794439 GCCGCGGCATTCCCAAAC 62.794 66.667 43.55 11.09 41.49 2.93
1929 4503 2.017049 ACGCATTCCTCAAACATAGCC 58.983 47.619 0.00 0.00 0.00 3.93
2073 4647 4.104776 ACAACACAACGAAATCTTTGCTG 58.895 39.130 0.00 1.74 0.00 4.41
2242 4816 7.070198 TCGACTATCAAACTCCCCATAATACAA 59.930 37.037 0.00 0.00 0.00 2.41
2393 4967 6.542852 TCGCTAATCTGAACATTAACTTTGC 58.457 36.000 0.00 0.00 0.00 3.68
2394 4968 9.214953 GAATCGCTAATCTGAACATTAACTTTG 57.785 33.333 0.00 0.00 0.00 2.77
2395 4969 9.167311 AGAATCGCTAATCTGAACATTAACTTT 57.833 29.630 0.00 0.00 0.00 2.66
2397 4971 8.607459 CAAGAATCGCTAATCTGAACATTAACT 58.393 33.333 0.00 0.00 0.00 2.24
2398 4972 7.852945 CCAAGAATCGCTAATCTGAACATTAAC 59.147 37.037 0.00 0.00 0.00 2.01
2399 4973 7.552687 ACCAAGAATCGCTAATCTGAACATTAA 59.447 33.333 0.00 0.00 0.00 1.40
2447 5022 4.677182 AGCATCAAGGGTTGGATACTTTT 58.323 39.130 0.00 0.00 37.61 2.27
2448 5023 4.322057 AGCATCAAGGGTTGGATACTTT 57.678 40.909 0.00 0.00 37.61 2.66
2451 5026 3.629398 CAGAAGCATCAAGGGTTGGATAC 59.371 47.826 0.00 0.00 0.00 2.24
2462 5037 4.859304 ACTTGCAATTCAGAAGCATCAA 57.141 36.364 0.00 0.00 38.19 2.57
2468 5043 4.479619 GTGGCTTACTTGCAATTCAGAAG 58.520 43.478 0.00 0.00 34.04 2.85
2469 5044 3.058293 CGTGGCTTACTTGCAATTCAGAA 60.058 43.478 0.00 0.00 34.04 3.02
2470 5045 2.483877 CGTGGCTTACTTGCAATTCAGA 59.516 45.455 0.00 0.00 34.04 3.27
2483 5058 0.175760 GATCCTGTGAGCGTGGCTTA 59.824 55.000 0.00 0.00 39.88 3.09
2487 5062 1.153489 CCAGATCCTGTGAGCGTGG 60.153 63.158 0.00 0.00 30.37 4.94
2495 5070 4.421131 AGTTACTTGACTCCAGATCCTGT 58.579 43.478 0.00 0.00 0.00 4.00
2874 5655 6.331369 ACCAATCCAACAAATTAGTCAGTG 57.669 37.500 0.00 0.00 0.00 3.66
2919 5701 2.641305 AGCTTGGAACATGAGAGATGC 58.359 47.619 0.00 0.00 39.30 3.91
2941 5723 7.430441 GCTCTTAGATTAGTTTACAGAGGGAG 58.570 42.308 0.00 0.00 0.00 4.30
2943 5725 6.183360 ACGCTCTTAGATTAGTTTACAGAGGG 60.183 42.308 8.36 8.36 42.53 4.30
2944 5726 6.797454 ACGCTCTTAGATTAGTTTACAGAGG 58.203 40.000 0.00 0.00 0.00 3.69
2946 5728 9.565213 GTAAACGCTCTTAGATTAGTTTACAGA 57.435 33.333 24.78 7.46 46.09 3.41
2950 5732 8.866956 GCTTGTAAACGCTCTTAGATTAGTTTA 58.133 33.333 10.61 10.61 34.29 2.01
2951 5733 7.386848 TGCTTGTAAACGCTCTTAGATTAGTTT 59.613 33.333 12.00 12.00 36.11 2.66
2955 5737 7.661127 TTTGCTTGTAAACGCTCTTAGATTA 57.339 32.000 0.00 0.00 0.00 1.75
2956 5738 6.554334 TTTGCTTGTAAACGCTCTTAGATT 57.446 33.333 0.00 0.00 0.00 2.40
2957 5739 6.204882 ACTTTTGCTTGTAAACGCTCTTAGAT 59.795 34.615 0.00 0.00 0.00 1.98
2958 5740 5.526111 ACTTTTGCTTGTAAACGCTCTTAGA 59.474 36.000 0.00 0.00 0.00 2.10
2959 5741 5.621228 CACTTTTGCTTGTAAACGCTCTTAG 59.379 40.000 0.00 0.00 0.00 2.18
2960 5742 5.294799 TCACTTTTGCTTGTAAACGCTCTTA 59.705 36.000 0.00 0.00 0.00 2.10
2962 5744 3.625764 TCACTTTTGCTTGTAAACGCTCT 59.374 39.130 0.00 0.00 0.00 4.09
2963 5745 3.947626 TCACTTTTGCTTGTAAACGCTC 58.052 40.909 0.00 0.00 0.00 5.03
2964 5746 4.568152 ATCACTTTTGCTTGTAAACGCT 57.432 36.364 0.00 0.00 0.00 5.07
2965 5747 6.416750 ACTTTATCACTTTTGCTTGTAAACGC 59.583 34.615 0.00 0.00 0.00 4.84
2966 5748 7.642194 TCACTTTATCACTTTTGCTTGTAAACG 59.358 33.333 0.00 0.00 0.00 3.60
3024 5812 9.546428 TCATACCTCAACTGAACATTGTATATG 57.454 33.333 0.00 0.00 0.00 1.78
3134 5923 7.966812 ACCATACTGAGCTGTTTATGATGATA 58.033 34.615 0.00 0.00 0.00 2.15
3203 5998 7.432869 AGCTCATTTTTACTTTGCAATGTGTA 58.567 30.769 24.00 13.79 0.00 2.90
3217 6012 5.227569 TCAGTCACTGGAGCTCATTTTTA 57.772 39.130 17.19 0.00 31.51 1.52
3218 6013 4.090761 TCAGTCACTGGAGCTCATTTTT 57.909 40.909 17.19 0.00 31.51 1.94
3219 6014 3.777106 TCAGTCACTGGAGCTCATTTT 57.223 42.857 17.19 0.00 31.51 1.82
3220 6015 3.996921 ATCAGTCACTGGAGCTCATTT 57.003 42.857 17.19 0.00 31.51 2.32
3221 6016 4.743045 GCATATCAGTCACTGGAGCTCATT 60.743 45.833 17.19 0.00 31.51 2.57
3222 6017 3.244146 GCATATCAGTCACTGGAGCTCAT 60.244 47.826 17.19 0.00 31.51 2.90
3223 6018 2.102084 GCATATCAGTCACTGGAGCTCA 59.898 50.000 17.19 0.61 31.51 4.26
3224 6019 2.102084 TGCATATCAGTCACTGGAGCTC 59.898 50.000 4.71 4.71 31.51 4.09
3225 6020 2.113807 TGCATATCAGTCACTGGAGCT 58.886 47.619 4.57 0.00 31.51 4.09
3226 6021 2.609427 TGCATATCAGTCACTGGAGC 57.391 50.000 4.57 4.95 31.51 4.70
3227 6022 4.397481 TCTTGCATATCAGTCACTGGAG 57.603 45.455 4.57 0.00 31.51 3.86
3228 6023 4.406649 TCATCTTGCATATCAGTCACTGGA 59.593 41.667 4.57 0.00 31.51 3.86
3229 6024 4.700700 TCATCTTGCATATCAGTCACTGG 58.299 43.478 4.57 0.00 31.51 4.00
3230 6025 6.673154 TTTCATCTTGCATATCAGTCACTG 57.327 37.500 0.00 0.00 0.00 3.66
3231 6026 7.692460 TTTTTCATCTTGCATATCAGTCACT 57.308 32.000 0.00 0.00 0.00 3.41
3254 6049 9.136323 AGTATGAGGTGTGATTCTTTTCTTTTT 57.864 29.630 0.00 0.00 0.00 1.94
3255 6050 8.697507 AGTATGAGGTGTGATTCTTTTCTTTT 57.302 30.769 0.00 0.00 0.00 2.27
3256 6051 7.939039 TGAGTATGAGGTGTGATTCTTTTCTTT 59.061 33.333 0.00 0.00 0.00 2.52
3257 6052 7.389053 GTGAGTATGAGGTGTGATTCTTTTCTT 59.611 37.037 0.00 0.00 0.00 2.52
3258 6053 6.876257 GTGAGTATGAGGTGTGATTCTTTTCT 59.124 38.462 0.00 0.00 0.00 2.52
3259 6054 6.876257 AGTGAGTATGAGGTGTGATTCTTTTC 59.124 38.462 0.00 0.00 0.00 2.29
3260 6055 6.773638 AGTGAGTATGAGGTGTGATTCTTTT 58.226 36.000 0.00 0.00 0.00 2.27
3261 6056 6.212388 AGAGTGAGTATGAGGTGTGATTCTTT 59.788 38.462 0.00 0.00 0.00 2.52
3262 6057 5.719085 AGAGTGAGTATGAGGTGTGATTCTT 59.281 40.000 0.00 0.00 0.00 2.52
3263 6058 5.126869 CAGAGTGAGTATGAGGTGTGATTCT 59.873 44.000 0.00 0.00 0.00 2.40
3264 6059 5.347342 CAGAGTGAGTATGAGGTGTGATTC 58.653 45.833 0.00 0.00 0.00 2.52
3265 6060 4.161189 CCAGAGTGAGTATGAGGTGTGATT 59.839 45.833 0.00 0.00 0.00 2.57
3266 6061 3.703556 CCAGAGTGAGTATGAGGTGTGAT 59.296 47.826 0.00 0.00 0.00 3.06
3267 6062 3.092301 CCAGAGTGAGTATGAGGTGTGA 58.908 50.000 0.00 0.00 0.00 3.58
3268 6063 3.092301 TCCAGAGTGAGTATGAGGTGTG 58.908 50.000 0.00 0.00 0.00 3.82
3269 6064 3.093057 GTCCAGAGTGAGTATGAGGTGT 58.907 50.000 0.00 0.00 0.00 4.16
3270 6065 2.098280 CGTCCAGAGTGAGTATGAGGTG 59.902 54.545 0.00 0.00 0.00 4.00
3271 6066 2.370349 CGTCCAGAGTGAGTATGAGGT 58.630 52.381 0.00 0.00 0.00 3.85
3272 6067 1.066303 GCGTCCAGAGTGAGTATGAGG 59.934 57.143 0.00 0.00 0.00 3.86
3273 6068 1.268285 CGCGTCCAGAGTGAGTATGAG 60.268 57.143 0.00 0.00 0.00 2.90
3274 6069 0.733150 CGCGTCCAGAGTGAGTATGA 59.267 55.000 0.00 0.00 0.00 2.15
3275 6070 0.452184 ACGCGTCCAGAGTGAGTATG 59.548 55.000 5.58 0.00 0.00 2.39
3276 6071 1.174783 AACGCGTCCAGAGTGAGTAT 58.825 50.000 14.44 0.00 31.75 2.12
3277 6072 0.956633 AAACGCGTCCAGAGTGAGTA 59.043 50.000 14.44 0.00 31.75 2.59
3278 6073 0.597637 CAAACGCGTCCAGAGTGAGT 60.598 55.000 14.44 0.00 31.75 3.41
3279 6074 0.597637 ACAAACGCGTCCAGAGTGAG 60.598 55.000 14.44 0.00 31.75 3.51
3280 6075 0.874175 CACAAACGCGTCCAGAGTGA 60.874 55.000 14.44 0.00 31.75 3.41
3281 6076 1.564622 CACAAACGCGTCCAGAGTG 59.435 57.895 14.44 13.22 31.75 3.51
3282 6077 2.244651 GCACAAACGCGTCCAGAGT 61.245 57.895 14.44 4.03 0.00 3.24
3283 6078 1.498865 AAGCACAAACGCGTCCAGAG 61.499 55.000 14.44 5.38 36.85 3.35
3284 6079 1.092921 AAAGCACAAACGCGTCCAGA 61.093 50.000 14.44 0.00 36.85 3.86
3285 6080 0.248458 AAAAGCACAAACGCGTCCAG 60.248 50.000 14.44 8.23 36.85 3.86
3286 6081 0.171455 AAAAAGCACAAACGCGTCCA 59.829 45.000 14.44 0.00 36.85 4.02
3287 6082 0.570272 CAAAAAGCACAAACGCGTCC 59.430 50.000 14.44 0.00 36.85 4.79
3288 6083 0.044246 GCAAAAAGCACAAACGCGTC 60.044 50.000 14.44 0.00 44.79 5.19
3289 6084 1.738144 CGCAAAAAGCACAAACGCGT 61.738 50.000 5.58 5.58 46.13 6.01
3290 6085 1.084977 CGCAAAAAGCACAAACGCG 60.085 52.632 3.53 3.53 46.13 6.01
3291 6086 1.142778 TCCGCAAAAAGCACAAACGC 61.143 50.000 0.00 0.00 46.13 4.84
3292 6087 0.845768 CTCCGCAAAAAGCACAAACG 59.154 50.000 0.00 0.00 46.13 3.60
3293 6088 2.202295 TCTCCGCAAAAAGCACAAAC 57.798 45.000 0.00 0.00 46.13 2.93
3294 6089 3.451141 AATCTCCGCAAAAAGCACAAA 57.549 38.095 0.00 0.00 46.13 2.83
3295 6090 4.277174 TCTTAATCTCCGCAAAAAGCACAA 59.723 37.500 0.00 0.00 46.13 3.33
3296 6091 3.818210 TCTTAATCTCCGCAAAAAGCACA 59.182 39.130 0.00 0.00 46.13 4.57
3297 6092 4.419522 TCTTAATCTCCGCAAAAAGCAC 57.580 40.909 0.00 0.00 46.13 4.40
3298 6093 4.142403 CCATCTTAATCTCCGCAAAAAGCA 60.142 41.667 0.00 0.00 46.13 3.91
3299 6094 4.354587 CCATCTTAATCTCCGCAAAAAGC 58.645 43.478 0.00 0.00 40.87 3.51
3300 6095 4.096984 AGCCATCTTAATCTCCGCAAAAAG 59.903 41.667 0.00 0.00 0.00 2.27
3301 6096 4.016444 AGCCATCTTAATCTCCGCAAAAA 58.984 39.130 0.00 0.00 0.00 1.94
3302 6097 3.620488 AGCCATCTTAATCTCCGCAAAA 58.380 40.909 0.00 0.00 0.00 2.44
3303 6098 3.281727 AGCCATCTTAATCTCCGCAAA 57.718 42.857 0.00 0.00 0.00 3.68
3304 6099 3.281727 AAGCCATCTTAATCTCCGCAA 57.718 42.857 0.00 0.00 0.00 4.85
3305 6100 4.415881 TTAAGCCATCTTAATCTCCGCA 57.584 40.909 0.00 0.00 39.23 5.69
3306 6101 5.751243 TTTTAAGCCATCTTAATCTCCGC 57.249 39.130 0.00 0.00 42.47 5.54
3307 6102 7.707104 ACAATTTTAAGCCATCTTAATCTCCG 58.293 34.615 0.00 0.00 42.47 4.63
3308 6103 9.305925 CAACAATTTTAAGCCATCTTAATCTCC 57.694 33.333 0.00 0.00 42.47 3.71
3309 6104 9.860898 ACAACAATTTTAAGCCATCTTAATCTC 57.139 29.630 0.00 0.00 42.47 2.75
3312 6107 8.720562 GCAACAACAATTTTAAGCCATCTTAAT 58.279 29.630 0.00 0.00 42.47 1.40
3313 6108 7.930865 AGCAACAACAATTTTAAGCCATCTTAA 59.069 29.630 0.00 0.00 41.58 1.85
3314 6109 7.441017 AGCAACAACAATTTTAAGCCATCTTA 58.559 30.769 0.00 0.00 33.85 2.10
3315 6110 6.290605 AGCAACAACAATTTTAAGCCATCTT 58.709 32.000 0.00 0.00 36.35 2.40
3316 6111 5.857268 AGCAACAACAATTTTAAGCCATCT 58.143 33.333 0.00 0.00 0.00 2.90
3317 6112 6.424812 AGAAGCAACAACAATTTTAAGCCATC 59.575 34.615 0.00 0.00 0.00 3.51
3318 6113 6.290605 AGAAGCAACAACAATTTTAAGCCAT 58.709 32.000 0.00 0.00 0.00 4.40
3319 6114 5.669477 AGAAGCAACAACAATTTTAAGCCA 58.331 33.333 0.00 0.00 0.00 4.75
3320 6115 6.603237 AAGAAGCAACAACAATTTTAAGCC 57.397 33.333 0.00 0.00 0.00 4.35
3321 6116 9.584839 CATAAAGAAGCAACAACAATTTTAAGC 57.415 29.630 0.00 0.00 0.00 3.09
3335 6242 6.552859 TGTCGACAAATCATAAAGAAGCAA 57.447 33.333 17.62 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.