Multiple sequence alignment - TraesCS4B01G215600

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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 TraesCS4B01G215600 chr4B 100.000 4398 0 0 1 4398 455028760 455024363 0.000000e+00 8122.0
1 TraesCS4B01G215600 chr4B 84.300 293 34 12 284 569 413819403 413819116 4.330000e-70 276.0
2 TraesCS4B01G215600 chr4D 91.147 2869 180 39 939 3772 369901475 369898646 0.000000e+00 3823.0
3 TraesCS4B01G215600 chr4D 89.557 316 14 4 569 883 369901972 369901675 2.480000e-102 383.0
4 TraesCS4B01G215600 chr4A 90.153 2153 126 37 568 2686 94753230 94755330 0.000000e+00 2723.0
5 TraesCS4B01G215600 chr4A 94.858 1089 45 8 2693 3772 94756190 94757276 0.000000e+00 1690.0
6 TraesCS4B01G215600 chr6B 96.181 576 10 8 1 572 54100098 54099531 0.000000e+00 931.0
7 TraesCS4B01G215600 chr6B 83.774 265 34 7 308 565 142780533 142780271 4.390000e-60 243.0
8 TraesCS4B01G215600 chr7A 92.691 643 28 12 3772 4398 170896292 170895653 0.000000e+00 909.0
9 TraesCS4B01G215600 chr7A 88.872 647 30 12 3772 4398 63372120 63372744 0.000000e+00 758.0
10 TraesCS4B01G215600 chr3A 91.850 638 29 13 3781 4396 6725343 6724707 0.000000e+00 869.0
11 TraesCS4B01G215600 chr3A 91.719 640 30 13 3781 4398 6714355 6713717 0.000000e+00 867.0
12 TraesCS4B01G215600 chr3A 87.793 639 64 10 3773 4398 712343437 712342800 0.000000e+00 736.0
13 TraesCS4B01G215600 chr3A 87.421 636 68 7 3773 4398 32855751 32855118 0.000000e+00 721.0
14 TraesCS4B01G215600 chr3A 86.142 635 78 6 3772 4398 32725571 32724939 0.000000e+00 676.0
15 TraesCS4B01G215600 chr3A 86.028 637 76 8 3772 4398 32666445 32665812 0.000000e+00 671.0
16 TraesCS4B01G215600 chr3A 85.893 638 78 7 3772 4398 32736827 32736191 0.000000e+00 669.0
17 TraesCS4B01G215600 chr3A 93.662 142 8 1 3781 3922 6784825 6784685 1.240000e-50 211.0
18 TraesCS4B01G215600 chr7B 90.796 565 35 12 1 555 541952868 541953425 0.000000e+00 739.0
19 TraesCS4B01G215600 chr7B 90.141 355 26 6 217 563 543001028 543001381 1.860000e-123 453.0
20 TraesCS4B01G215600 chr7B 89.028 319 27 5 252 563 542900836 542901153 5.330000e-104 388.0
21 TraesCS4B01G215600 chrUn 87.441 637 63 10 3772 4398 275589309 275589938 0.000000e+00 717.0
22 TraesCS4B01G215600 chr2A 97.361 341 8 1 229 569 199579578 199579239 2.950000e-161 579.0
23 TraesCS4B01G215600 chr2A 93.642 173 2 5 1 165 199580031 199579860 2.630000e-62 250.0
24 TraesCS4B01G215600 chr5D 88.828 367 23 14 1 352 450519148 450519511 6.760000e-118 435.0
25 TraesCS4B01G215600 chr5D 89.143 175 8 11 2 168 496012893 496012722 1.600000e-49 207.0
26 TraesCS4B01G215600 chr7D 88.462 364 26 15 1 352 160560158 160560517 4.070000e-115 425.0
27 TraesCS4B01G215600 chr3B 83.158 285 39 8 286 565 681754742 681755022 7.300000e-63 252.0
28 TraesCS4B01G215600 chr3B 83.505 97 16 0 1192 1288 31992537 31992633 1.680000e-14 91.6
29 TraesCS4B01G215600 chr5A 82.456 285 41 6 289 566 454687457 454687175 1.580000e-59 241.0
30 TraesCS4B01G215600 chr1D 87.861 173 12 7 1 169 455901425 455901592 1.250000e-45 195.0


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 TraesCS4B01G215600 chr4B 455024363 455028760 4397 True 8122.0 8122 100.0000 1 4398 1 chr4B.!!$R2 4397
1 TraesCS4B01G215600 chr4D 369898646 369901972 3326 True 2103.0 3823 90.3520 569 3772 2 chr4D.!!$R1 3203
2 TraesCS4B01G215600 chr4A 94753230 94757276 4046 False 2206.5 2723 92.5055 568 3772 2 chr4A.!!$F1 3204
3 TraesCS4B01G215600 chr6B 54099531 54100098 567 True 931.0 931 96.1810 1 572 1 chr6B.!!$R1 571
4 TraesCS4B01G215600 chr7A 170895653 170896292 639 True 909.0 909 92.6910 3772 4398 1 chr7A.!!$R1 626
5 TraesCS4B01G215600 chr7A 63372120 63372744 624 False 758.0 758 88.8720 3772 4398 1 chr7A.!!$F1 626
6 TraesCS4B01G215600 chr3A 6724707 6725343 636 True 869.0 869 91.8500 3781 4396 1 chr3A.!!$R2 615
7 TraesCS4B01G215600 chr3A 6713717 6714355 638 True 867.0 867 91.7190 3781 4398 1 chr3A.!!$R1 617
8 TraesCS4B01G215600 chr3A 712342800 712343437 637 True 736.0 736 87.7930 3773 4398 1 chr3A.!!$R8 625
9 TraesCS4B01G215600 chr3A 32855118 32855751 633 True 721.0 721 87.4210 3773 4398 1 chr3A.!!$R7 625
10 TraesCS4B01G215600 chr3A 32724939 32725571 632 True 676.0 676 86.1420 3772 4398 1 chr3A.!!$R5 626
11 TraesCS4B01G215600 chr3A 32665812 32666445 633 True 671.0 671 86.0280 3772 4398 1 chr3A.!!$R4 626
12 TraesCS4B01G215600 chr3A 32736191 32736827 636 True 669.0 669 85.8930 3772 4398 1 chr3A.!!$R6 626
13 TraesCS4B01G215600 chr7B 541952868 541953425 557 False 739.0 739 90.7960 1 555 1 chr7B.!!$F1 554
14 TraesCS4B01G215600 chrUn 275589309 275589938 629 False 717.0 717 87.4410 3772 4398 1 chrUn.!!$F1 626
15 TraesCS4B01G215600 chr2A 199579239 199580031 792 True 414.5 579 95.5015 1 569 2 chr2A.!!$R1 568

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
446 680 0.032217 ATCCCGGCCATCCAAACAAT 60.032 50.0 2.24 0.0 0.00 2.71 F
1551 1948 0.108138 GCTACTCGGACATTGCTGGT 60.108 55.0 0.00 0.0 0.00 4.00 F
2307 2709 0.107263 TTGTCACAGGCTCACAGCAA 60.107 50.0 0.00 0.0 44.75 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2288 2690 0.107263 TTGCTGTGAGCCTGTGACAA 60.107 50.000 0.00 0.0 41.51 3.18 R
2879 4162 1.137872 GTTGTCTGCGGGATGAGAGAT 59.862 52.381 0.00 0.0 0.00 2.75 R
3860 5154 0.249031 GGTGCACCAAACAAGCTGTC 60.249 55.000 31.23 0.0 35.64 3.51 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
91 101 8.748380 AAAAGAAACAGAAACAGAAAACAGAG 57.252 30.769 0.00 0.00 0.00 3.35
92 102 7.687941 AAGAAACAGAAACAGAAAACAGAGA 57.312 32.000 0.00 0.00 0.00 3.10
93 103 7.872113 AGAAACAGAAACAGAAAACAGAGAT 57.128 32.000 0.00 0.00 0.00 2.75
126 137 4.329545 GCGGACAAGTCTGGGCCA 62.330 66.667 5.85 5.85 36.50 5.36
263 492 2.226437 GCATCGATCAAACAACACCAGT 59.774 45.455 0.00 0.00 0.00 4.00
368 597 5.947503 TGCGAATTTTTGTTTCTTGACAG 57.052 34.783 0.00 0.00 0.00 3.51
446 680 0.032217 ATCCCGGCCATCCAAACAAT 60.032 50.000 2.24 0.00 0.00 2.71
860 1094 1.377856 GAGAGCAAGGGTCAAGGGC 60.378 63.158 0.00 0.00 31.89 5.19
864 1098 3.966543 CAAGGGTCAAGGGCGGGT 61.967 66.667 0.00 0.00 0.00 5.28
865 1099 3.647771 AAGGGTCAAGGGCGGGTC 61.648 66.667 0.00 0.00 0.00 4.46
866 1100 4.658786 AGGGTCAAGGGCGGGTCT 62.659 66.667 0.00 0.00 0.00 3.85
867 1101 4.097361 GGGTCAAGGGCGGGTCTC 62.097 72.222 0.00 0.00 0.00 3.36
868 1102 4.452733 GGTCAAGGGCGGGTCTCG 62.453 72.222 0.00 0.00 42.76 4.04
869 1103 4.452733 GTCAAGGGCGGGTCTCGG 62.453 72.222 0.00 0.00 39.69 4.63
1098 1492 1.992277 GGAGCAGCTGGGGAAGAGA 60.992 63.158 17.12 0.00 0.00 3.10
1302 1696 2.221981 GCAGGTCTCTCAAACAGAAACG 59.778 50.000 0.00 0.00 0.00 3.60
1310 1704 0.537371 CAAACAGAAACGGGCTCCCT 60.537 55.000 3.11 0.00 0.00 4.20
1345 1741 2.365105 CTTCCCGCTCCCCTGGTA 60.365 66.667 0.00 0.00 0.00 3.25
1524 1921 6.238293 GCAAGTTTGGTTTCTACGAGTACTTT 60.238 38.462 0.00 0.00 0.00 2.66
1551 1948 0.108138 GCTACTCGGACATTGCTGGT 60.108 55.000 0.00 0.00 0.00 4.00
1934 2334 2.388310 TGCATGCCAATGGTTGAATG 57.612 45.000 16.68 1.88 34.09 2.67
1959 2359 6.259387 GGTACATGGCCAAACAATAGTAGTAC 59.741 42.308 10.96 9.63 0.00 2.73
1972 2372 6.877322 ACAATAGTAGTACCGCTGAACATTTT 59.123 34.615 0.00 0.00 0.00 1.82
1973 2373 6.903883 ATAGTAGTACCGCTGAACATTTTG 57.096 37.500 0.00 0.00 0.00 2.44
2023 2423 7.979444 TTCCGAGACAAACAATTTTAGAGAT 57.021 32.000 0.00 0.00 0.00 2.75
2024 2424 7.596749 TCCGAGACAAACAATTTTAGAGATC 57.403 36.000 0.00 0.00 0.00 2.75
2025 2425 7.158697 TCCGAGACAAACAATTTTAGAGATCA 58.841 34.615 0.00 0.00 0.00 2.92
2026 2426 7.824289 TCCGAGACAAACAATTTTAGAGATCAT 59.176 33.333 0.00 0.00 0.00 2.45
2027 2427 9.098355 CCGAGACAAACAATTTTAGAGATCATA 57.902 33.333 0.00 0.00 0.00 2.15
2028 2428 9.907576 CGAGACAAACAATTTTAGAGATCATAC 57.092 33.333 0.00 0.00 0.00 2.39
2094 2495 1.009060 TGGGACATAGAGTTGGGGCTA 59.991 52.381 0.00 0.00 0.00 3.93
2107 2508 2.204463 TGGGGCTAACATGATTCCAGA 58.796 47.619 0.00 0.00 0.00 3.86
2115 2516 2.381911 ACATGATTCCAGAATGCCCAC 58.618 47.619 0.00 0.00 31.97 4.61
2116 2517 1.684983 CATGATTCCAGAATGCCCACC 59.315 52.381 0.00 0.00 31.97 4.61
2142 2543 6.054860 ACTGAGTTAGCCATTTATCACTGT 57.945 37.500 0.00 0.00 0.00 3.55
2151 2552 4.627035 GCCATTTATCACTGTTGCTTTTCC 59.373 41.667 0.00 0.00 0.00 3.13
2159 2560 4.997395 TCACTGTTGCTTTTCCATAGACTC 59.003 41.667 0.00 0.00 0.00 3.36
2174 2576 5.406780 CCATAGACTCACAAGTTTGACACTC 59.593 44.000 0.00 0.00 35.28 3.51
2188 2590 9.574516 AAGTTTGACACTCCTTAATTTCTGTAT 57.425 29.630 0.00 0.00 32.94 2.29
2212 2614 1.168714 GACCTAGTTTGCAGCCCTTG 58.831 55.000 0.00 0.00 0.00 3.61
2239 2641 6.945435 TCAACCATGAAAAGCCTAGTTGATTA 59.055 34.615 0.00 0.00 37.72 1.75
2251 2653 9.700831 AAGCCTAGTTGATTATATTTGTTTCCT 57.299 29.630 0.00 0.00 0.00 3.36
2297 2699 6.266330 TCCAGATCATCTATAGTTGTCACAGG 59.734 42.308 10.00 8.98 0.00 4.00
2298 2700 5.925397 CAGATCATCTATAGTTGTCACAGGC 59.075 44.000 10.00 0.00 0.00 4.85
2299 2701 5.837979 AGATCATCTATAGTTGTCACAGGCT 59.162 40.000 10.00 0.00 0.00 4.58
2300 2702 5.521906 TCATCTATAGTTGTCACAGGCTC 57.478 43.478 10.00 0.00 0.00 4.70
2301 2703 4.956075 TCATCTATAGTTGTCACAGGCTCA 59.044 41.667 10.00 0.00 0.00 4.26
2302 2704 4.720649 TCTATAGTTGTCACAGGCTCAC 57.279 45.455 0.00 0.00 0.00 3.51
2304 2706 2.820059 TAGTTGTCACAGGCTCACAG 57.180 50.000 0.00 0.00 0.00 3.66
2305 2707 0.533755 AGTTGTCACAGGCTCACAGC 60.534 55.000 0.00 0.00 41.46 4.40
2306 2708 0.815213 GTTGTCACAGGCTCACAGCA 60.815 55.000 0.00 0.00 44.75 4.41
2307 2709 0.107263 TTGTCACAGGCTCACAGCAA 60.107 50.000 0.00 0.00 44.75 3.91
2308 2710 0.107263 TGTCACAGGCTCACAGCAAA 60.107 50.000 0.00 0.00 44.75 3.68
2310 2712 1.405105 GTCACAGGCTCACAGCAAAAA 59.595 47.619 0.00 0.00 44.75 1.94
2331 2743 3.451402 AGATGACCTTTTAACCCCCAC 57.549 47.619 0.00 0.00 0.00 4.61
2346 2758 3.072038 ACCCCCACACTCTAGTTTACAAC 59.928 47.826 0.00 0.00 0.00 3.32
2354 2766 6.089551 CACACTCTAGTTTACAACTGATTCCG 59.910 42.308 0.00 0.00 42.84 4.30
2382 2794 1.216178 GATGCCACGCTTTTGCCAT 59.784 52.632 0.00 0.00 43.93 4.40
2383 2795 1.079681 ATGCCACGCTTTTGCCATG 60.080 52.632 0.00 0.00 43.93 3.66
2387 2799 1.696988 CCACGCTTTTGCCATGTTAC 58.303 50.000 0.00 0.00 43.93 2.50
2413 2825 9.352784 CTAAACAAATCAGTAGAGAGAGAACAG 57.647 37.037 0.00 0.00 0.00 3.16
2431 2844 8.484575 AGAGAACAGATGAGAAATATGACATGT 58.515 33.333 0.00 0.00 0.00 3.21
2439 2859 9.716531 GATGAGAAATATGACATGTGGAATAGA 57.283 33.333 1.15 0.00 0.00 1.98
2443 2863 7.877097 AGAAATATGACATGTGGAATAGAGAGC 59.123 37.037 1.15 0.00 0.00 4.09
2444 2864 6.931790 ATATGACATGTGGAATAGAGAGCT 57.068 37.500 1.15 0.00 0.00 4.09
2447 2867 4.099113 TGACATGTGGAATAGAGAGCTCAG 59.901 45.833 17.77 0.00 0.00 3.35
2449 2869 4.141981 ACATGTGGAATAGAGAGCTCAGTG 60.142 45.833 17.77 0.00 0.00 3.66
2450 2870 2.167281 TGTGGAATAGAGAGCTCAGTGC 59.833 50.000 17.77 0.02 43.29 4.40
2466 2888 2.100989 AGTGCGGTTTTAACCCAAACA 58.899 42.857 6.09 0.00 46.53 2.83
2471 2893 4.341520 TGCGGTTTTAACCCAAACAATACT 59.658 37.500 6.09 0.00 46.53 2.12
2476 2898 7.308951 CGGTTTTAACCCAAACAATACTCATCT 60.309 37.037 6.09 0.00 46.53 2.90
2480 2902 3.245229 ACCCAAACAATACTCATCTGGCA 60.245 43.478 0.00 0.00 0.00 4.92
2505 2927 5.771153 TGTGAGCTGATTTGTTTGATGAA 57.229 34.783 0.00 0.00 0.00 2.57
2527 2949 8.378172 TGAAATGGCAGTTATATAGTAGCAAC 57.622 34.615 0.00 0.00 0.00 4.17
2531 2953 5.068067 TGGCAGTTATATAGTAGCAACGTGA 59.932 40.000 0.00 0.00 0.00 4.35
2534 2956 6.074994 GCAGTTATATAGTAGCAACGTGACAC 60.075 42.308 0.00 0.00 0.00 3.67
2540 2966 1.194547 GTAGCAACGTGACACATGGTG 59.805 52.381 18.27 8.32 40.65 4.17
2558 2984 6.550854 ACATGGTGTCCAGAAAAATATATGGG 59.449 38.462 0.00 0.00 36.75 4.00
2583 3009 8.072567 GGAAGCATGATACTAGTTAGCAAATTG 58.927 37.037 0.00 0.00 27.47 2.32
2612 3041 8.753497 AGGAAGGAAGATAATTGGTTGAATAC 57.247 34.615 0.00 0.00 0.00 1.89
2619 3048 5.885912 AGATAATTGGTTGAATACGGTGCTT 59.114 36.000 0.00 0.00 0.00 3.91
2634 3063 4.051922 CGGTGCTTATGGATGAAGTACTC 58.948 47.826 0.00 0.00 38.92 2.59
2651 3080 5.784177 AGTACTCGATTGTTCAACATGACT 58.216 37.500 0.00 0.00 0.00 3.41
2667 3096 8.681806 TCAACATGACTATGAAACAGTTTTTGA 58.318 29.630 0.00 0.00 37.73 2.69
2668 3097 9.467258 CAACATGACTATGAAACAGTTTTTGAT 57.533 29.630 0.00 0.00 37.73 2.57
2680 3109 9.294030 GAAACAGTTTTTGATGCCATCTTATAG 57.706 33.333 6.21 0.00 0.00 1.31
2690 3119 7.233632 TGATGCCATCTTATAGCCTTTATGTT 58.766 34.615 6.21 0.00 0.00 2.71
2699 3981 7.497909 TCTTATAGCCTTTATGTTAAGGTGTGC 59.502 37.037 0.00 0.00 45.34 4.57
2700 3982 4.034285 AGCCTTTATGTTAAGGTGTGCT 57.966 40.909 0.00 0.00 45.34 4.40
2709 3991 1.951209 TAAGGTGTGCTCCCTGATCA 58.049 50.000 0.00 0.00 30.99 2.92
2710 3992 1.293062 AAGGTGTGCTCCCTGATCAT 58.707 50.000 0.00 0.00 30.99 2.45
2714 3996 2.424956 GGTGTGCTCCCTGATCATTTTC 59.575 50.000 0.00 0.00 0.00 2.29
2723 4005 6.325993 TCCCTGATCATTTTCTCCATTACA 57.674 37.500 0.00 0.00 0.00 2.41
2752 4035 7.310664 CAGACACTATGATGAAATTTGCTTGT 58.689 34.615 0.00 0.00 0.00 3.16
2833 4116 2.234908 CAGTAAACCACTCCAGCTAGCT 59.765 50.000 12.68 12.68 34.26 3.32
2869 4152 2.504175 GGGGTACATTGCTGGAGTCTTA 59.496 50.000 0.00 0.00 0.00 2.10
2879 4162 2.159043 GCTGGAGTCTTATGTGCTGCTA 60.159 50.000 0.00 0.00 0.00 3.49
3027 4310 1.077930 CACCCATCTGGCTGTCAGG 60.078 63.158 9.73 0.00 43.53 3.86
3033 4316 1.961180 ATCTGGCTGTCAGGCGGTAC 61.961 60.000 28.85 0.09 46.24 3.34
3192 4478 0.670162 GAGCGCAATGGGCAACATAT 59.330 50.000 23.85 1.91 44.06 1.78
3240 4527 6.201806 GGCTGTAAGTATCTCTTGCTGTTATG 59.798 42.308 0.00 0.00 38.90 1.90
3275 4562 6.377712 TCTGACATCATCAACAATTTATGCCA 59.622 34.615 0.00 0.00 36.69 4.92
3311 4598 5.627499 TCTCATGGTTGCTTGTGATTAAC 57.373 39.130 0.00 0.00 0.00 2.01
3419 4706 0.606673 GCACCAGGGAAGGTCTTGTC 60.607 60.000 0.00 0.00 40.77 3.18
3617 4906 4.699637 ACGTTGGAGAACATACAAGAACA 58.300 39.130 0.00 0.00 31.78 3.18
3680 4970 7.360691 GCGTAATCATCTGAATACATCTTGCAT 60.361 37.037 6.31 0.00 31.60 3.96
3860 5154 6.931838 TGAAGTAACAGGTATCAGTACAAGG 58.068 40.000 0.00 0.00 32.25 3.61
3936 5261 2.181196 AGAGGAATAGAGGGGAGAAGGG 59.819 54.545 0.00 0.00 0.00 3.95
4065 5392 6.648310 GTCTGCTGCATATAGACATGTGTATT 59.352 38.462 19.49 6.39 40.33 1.89
4066 5393 6.647895 TCTGCTGCATATAGACATGTGTATTG 59.352 38.462 19.49 16.75 0.00 1.90
4110 5437 4.081972 TGAAGACTCTGTCATTCCTAGCAC 60.082 45.833 0.46 0.00 34.60 4.40
4163 5490 4.497300 CCACATTCCATTTGTGCCTAAAG 58.503 43.478 0.00 0.00 42.47 1.85
4165 5492 3.055891 ACATTCCATTTGTGCCTAAAGCC 60.056 43.478 0.00 0.00 42.71 4.35
4166 5493 2.300956 TCCATTTGTGCCTAAAGCCA 57.699 45.000 0.00 0.00 42.71 4.75
4238 5565 0.036010 CCAGAACGTCCAGCTCCATT 60.036 55.000 0.00 0.00 0.00 3.16
4262 5589 4.404654 CAAAGAACGCTGGCGGGC 62.405 66.667 18.99 10.08 44.69 6.13
4301 5628 2.995939 GTGATCGATTGACTCAACAGCA 59.004 45.455 0.00 0.00 0.00 4.41
4326 5653 3.772932 CAAGTGTCACAATGTGCAAACT 58.227 40.909 8.78 8.80 32.98 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 101 1.580815 GCTGCTGCCTCTCTGTTATC 58.419 55.000 3.85 0.00 0.00 1.75
92 102 0.179089 CGCTGCTGCCTCTCTGTTAT 60.179 55.000 10.24 0.00 35.36 1.89
93 103 1.216444 CGCTGCTGCCTCTCTGTTA 59.784 57.895 10.24 0.00 35.36 2.41
263 492 0.673333 CATAAGCTCACGGTGTGGCA 60.673 55.000 22.44 9.89 34.10 4.92
390 623 0.249489 GACTCACACCTGCTCAACGT 60.249 55.000 0.00 0.00 0.00 3.99
565 799 3.673484 GTGCCACCTGCGTGCAAT 61.673 61.111 0.00 0.00 45.60 3.56
809 1043 4.719369 GCCGAGACGCGAAGTGGT 62.719 66.667 15.93 0.00 45.78 4.16
837 1071 3.706373 GACCCTTGCTCTCCCGCA 61.706 66.667 0.00 0.00 38.31 5.69
982 1370 2.805313 ATCTGGGGACGTGAGCTGGA 62.805 60.000 0.00 0.00 0.00 3.86
1098 1492 3.606662 CGGACGGCGATCTCCCAT 61.607 66.667 16.62 0.00 0.00 4.00
1291 1685 0.537371 AGGGAGCCCGTTTCTGTTTG 60.537 55.000 0.00 0.00 41.95 2.93
1294 1688 1.073199 CAAGGGAGCCCGTTTCTGT 59.927 57.895 0.00 0.00 41.95 3.41
1302 1696 4.811364 GGAGCAGCAAGGGAGCCC 62.811 72.222 0.00 0.00 34.23 5.19
1310 1704 1.601759 GCTTGGACAGGAGCAGCAA 60.602 57.895 0.00 0.00 38.73 3.91
1340 1734 3.021695 TCCCGTCAGACATTAGTACCAG 58.978 50.000 0.41 0.00 0.00 4.00
1343 1739 4.270325 GCAATTCCCGTCAGACATTAGTAC 59.730 45.833 0.41 0.00 0.00 2.73
1344 1740 4.161565 AGCAATTCCCGTCAGACATTAGTA 59.838 41.667 0.41 0.00 0.00 1.82
1345 1741 3.055094 AGCAATTCCCGTCAGACATTAGT 60.055 43.478 0.41 0.00 0.00 2.24
1524 1921 4.744570 CAATGTCCGAGTAGCACTTCTTA 58.255 43.478 0.00 0.00 0.00 2.10
1551 1948 0.904865 ACCTGTCAGCATTCTCGGGA 60.905 55.000 0.00 0.00 0.00 5.14
1580 1977 0.665670 CGATGCAGCGAGGTAGATGG 60.666 60.000 21.79 0.00 0.00 3.51
1793 2193 1.396815 GCGTTAACGAGTGTTCTGCAC 60.397 52.381 31.03 5.19 43.09 4.57
1806 2206 6.021596 CCTGAAATGAACACATAGCGTTAAC 58.978 40.000 0.00 0.00 0.00 2.01
1934 2334 5.190677 ACTACTATTGTTTGGCCATGTACC 58.809 41.667 6.09 0.00 0.00 3.34
1959 2359 3.689161 TCTGGTATCAAAATGTTCAGCGG 59.311 43.478 0.00 0.00 0.00 5.52
1972 2372 6.222038 AGCTAAACGAAGATTCTGGTATCA 57.778 37.500 0.00 0.00 0.00 2.15
1973 2373 5.399892 CGAGCTAAACGAAGATTCTGGTATC 59.600 44.000 0.00 0.00 0.00 2.24
2027 2427 9.036980 ACTCTAAAGAACTCCATACACAATAGT 57.963 33.333 0.00 0.00 0.00 2.12
2028 2428 9.307121 CACTCTAAAGAACTCCATACACAATAG 57.693 37.037 0.00 0.00 0.00 1.73
2029 2429 8.812972 ACACTCTAAAGAACTCCATACACAATA 58.187 33.333 0.00 0.00 0.00 1.90
2030 2430 7.680730 ACACTCTAAAGAACTCCATACACAAT 58.319 34.615 0.00 0.00 0.00 2.71
2031 2431 7.062749 ACACTCTAAAGAACTCCATACACAA 57.937 36.000 0.00 0.00 0.00 3.33
2032 2432 6.665992 ACACTCTAAAGAACTCCATACACA 57.334 37.500 0.00 0.00 0.00 3.72
2033 2433 9.485206 TTTAACACTCTAAAGAACTCCATACAC 57.515 33.333 0.00 0.00 0.00 2.90
2034 2434 9.706691 CTTTAACACTCTAAAGAACTCCATACA 57.293 33.333 0.00 0.00 40.05 2.29
2035 2435 9.152595 CCTTTAACACTCTAAAGAACTCCATAC 57.847 37.037 4.97 0.00 40.05 2.39
2036 2436 7.822822 GCCTTTAACACTCTAAAGAACTCCATA 59.177 37.037 4.97 0.00 40.05 2.74
2037 2437 6.655425 GCCTTTAACACTCTAAAGAACTCCAT 59.345 38.462 4.97 0.00 40.05 3.41
2038 2438 5.995897 GCCTTTAACACTCTAAAGAACTCCA 59.004 40.000 4.97 0.00 40.05 3.86
2039 2439 6.231951 AGCCTTTAACACTCTAAAGAACTCC 58.768 40.000 4.97 0.00 40.05 3.85
2040 2440 8.305317 TCTAGCCTTTAACACTCTAAAGAACTC 58.695 37.037 4.97 0.00 40.05 3.01
2041 2441 8.191534 TCTAGCCTTTAACACTCTAAAGAACT 57.808 34.615 4.97 4.93 40.05 3.01
2042 2442 8.828688 TTCTAGCCTTTAACACTCTAAAGAAC 57.171 34.615 4.97 0.00 40.05 3.01
2094 2495 2.762327 GTGGGCATTCTGGAATCATGTT 59.238 45.455 0.00 0.00 0.00 2.71
2107 2508 2.086610 AACTCAGTTTGGTGGGCATT 57.913 45.000 0.00 0.00 0.00 3.56
2115 2516 6.375455 AGTGATAAATGGCTAACTCAGTTTGG 59.625 38.462 0.00 0.00 0.00 3.28
2116 2517 7.094634 ACAGTGATAAATGGCTAACTCAGTTTG 60.095 37.037 0.00 0.00 0.00 2.93
2142 2543 5.376625 ACTTGTGAGTCTATGGAAAAGCAA 58.623 37.500 0.00 0.00 0.00 3.91
2151 2552 5.406780 GGAGTGTCAAACTTGTGAGTCTATG 59.593 44.000 0.00 0.00 40.07 2.23
2159 2560 7.645340 CAGAAATTAAGGAGTGTCAAACTTGTG 59.355 37.037 0.00 0.00 40.07 3.33
2188 2590 3.073946 AGGGCTGCAAACTAGGTCTAAAA 59.926 43.478 0.50 0.00 0.00 1.52
2212 2614 3.084786 ACTAGGCTTTTCATGGTTGAGC 58.915 45.455 0.00 0.00 32.27 4.26
2266 2668 7.687388 ACAACTATAGATGATCTGGATTGCAT 58.313 34.615 16.18 0.00 0.00 3.96
2282 2684 4.428209 CTGTGAGCCTGTGACAACTATAG 58.572 47.826 0.00 0.00 0.00 1.31
2288 2690 0.107263 TTGCTGTGAGCCTGTGACAA 60.107 50.000 0.00 0.00 41.51 3.18
2310 2712 3.141272 TGTGGGGGTTAAAAGGTCATCTT 59.859 43.478 0.00 0.00 37.28 2.40
2311 2713 2.719705 TGTGGGGGTTAAAAGGTCATCT 59.280 45.455 0.00 0.00 0.00 2.90
2312 2714 2.823747 GTGTGGGGGTTAAAAGGTCATC 59.176 50.000 0.00 0.00 0.00 2.92
2313 2715 2.449345 AGTGTGGGGGTTAAAAGGTCAT 59.551 45.455 0.00 0.00 0.00 3.06
2315 2717 2.107726 AGAGTGTGGGGGTTAAAAGGTC 59.892 50.000 0.00 0.00 0.00 3.85
2316 2718 2.141067 AGAGTGTGGGGGTTAAAAGGT 58.859 47.619 0.00 0.00 0.00 3.50
2346 2758 0.174845 TCCACGTTAGCCGGAATCAG 59.825 55.000 5.05 0.00 42.24 2.90
2354 2766 3.497879 GTGGCATCCACGTTAGCC 58.502 61.111 9.65 9.65 44.95 3.93
2371 2783 4.541779 TGTTTAGTAACATGGCAAAAGCG 58.458 39.130 0.00 0.00 39.29 4.68
2387 2799 9.352784 CTGTTCTCTCTCTACTGATTTGTTTAG 57.647 37.037 0.00 0.00 0.00 1.85
2399 2811 9.897744 CATATTTCTCATCTGTTCTCTCTCTAC 57.102 37.037 0.00 0.00 0.00 2.59
2413 2825 9.716531 TCTATTCCACATGTCATATTTCTCATC 57.283 33.333 0.00 0.00 0.00 2.92
2431 2844 1.406898 CGCACTGAGCTCTCTATTCCA 59.593 52.381 16.19 0.00 42.61 3.53
2439 2859 2.143925 GTTAAAACCGCACTGAGCTCT 58.856 47.619 16.19 0.00 42.61 4.09
2466 2888 4.337555 GCTCACAATTGCCAGATGAGTATT 59.662 41.667 18.78 0.00 39.21 1.89
2471 2893 2.089201 CAGCTCACAATTGCCAGATGA 58.911 47.619 14.44 6.17 0.00 2.92
2476 2898 2.629137 ACAAATCAGCTCACAATTGCCA 59.371 40.909 5.05 0.00 0.00 4.92
2480 2902 6.751157 TCATCAAACAAATCAGCTCACAATT 58.249 32.000 0.00 0.00 0.00 2.32
2505 2927 6.423905 CACGTTGCTACTATATAACTGCCATT 59.576 38.462 0.00 0.00 0.00 3.16
2534 2956 6.777091 TCCCATATATTTTTCTGGACACCATG 59.223 38.462 0.00 0.00 30.82 3.66
2540 2966 6.959639 TGCTTCCCATATATTTTTCTGGAC 57.040 37.500 0.00 0.00 0.00 4.02
2558 2984 7.589221 GCAATTTGCTAACTAGTATCATGCTTC 59.411 37.037 14.11 0.00 40.96 3.86
2575 3001 3.642848 TCTTCCTTCCTTTGCAATTTGCT 59.357 39.130 21.19 0.00 45.31 3.91
2583 3009 5.921962 ACCAATTATCTTCCTTCCTTTGC 57.078 39.130 0.00 0.00 0.00 3.68
2588 3015 7.255139 CCGTATTCAACCAATTATCTTCCTTCC 60.255 40.741 0.00 0.00 0.00 3.46
2612 3041 4.051922 GAGTACTTCATCCATAAGCACCG 58.948 47.826 0.00 0.00 0.00 4.94
2619 3048 7.107639 TGAACAATCGAGTACTTCATCCATA 57.892 36.000 0.00 0.00 0.00 2.74
2634 3063 7.297391 TGTTTCATAGTCATGTTGAACAATCG 58.703 34.615 0.62 0.00 32.77 3.34
2651 3080 7.230849 AGATGGCATCAAAAACTGTTTCATA 57.769 32.000 27.93 0.00 0.00 2.15
2667 3096 9.236006 CTTAACATAAAGGCTATAAGATGGCAT 57.764 33.333 0.00 0.00 38.67 4.40
2668 3097 7.665559 CCTTAACATAAAGGCTATAAGATGGCA 59.334 37.037 0.00 0.00 39.69 4.92
2690 3119 1.951209 TGATCAGGGAGCACACCTTA 58.049 50.000 0.00 0.00 35.78 2.69
2699 3981 6.359804 TGTAATGGAGAAAATGATCAGGGAG 58.640 40.000 0.09 0.00 0.00 4.30
2700 3982 6.325993 TGTAATGGAGAAAATGATCAGGGA 57.674 37.500 0.09 0.00 0.00 4.20
2714 3996 6.051074 TCATAGTGTCTGCAATGTAATGGAG 58.949 40.000 0.00 0.00 39.84 3.86
2723 4005 6.755141 GCAAATTTCATCATAGTGTCTGCAAT 59.245 34.615 0.00 0.00 0.00 3.56
2752 4035 5.710513 CCATCTCAACAATGGTCTCAAAA 57.289 39.130 0.00 0.00 39.11 2.44
2833 4116 4.597032 CCCCCTGCAAAACTCACA 57.403 55.556 0.00 0.00 0.00 3.58
2869 4152 2.302445 GGGATGAGAGATAGCAGCACAT 59.698 50.000 0.00 0.00 0.00 3.21
2879 4162 1.137872 GTTGTCTGCGGGATGAGAGAT 59.862 52.381 0.00 0.00 0.00 2.75
3027 4310 3.968649 TGATACCACGATTTAGTACCGC 58.031 45.455 0.00 0.00 0.00 5.68
3072 4358 4.276926 GCCTGGAAGCTCAATTAATCGATT 59.723 41.667 16.15 16.15 0.00 3.34
3076 4362 7.445402 TGTTATAGCCTGGAAGCTCAATTAATC 59.555 37.037 0.00 0.00 43.67 1.75
3192 4478 5.206299 CCAACAAATACTTTAAACGCGTCA 58.794 37.500 14.44 0.00 0.00 4.35
3240 4527 4.377897 TGATGATGTCAGAGATGCATGTC 58.622 43.478 15.79 15.79 31.80 3.06
3275 4562 7.342799 AGCAACCATGAGATAATTTGGTATTGT 59.657 33.333 0.00 0.00 41.53 2.71
3311 4598 1.293498 CGGTGGTTGGTCTGGAGAG 59.707 63.158 0.00 0.00 0.00 3.20
3419 4706 3.700038 ACTCCGGTTACAGATAACTCAGG 59.300 47.826 0.00 0.65 40.59 3.86
3617 4906 7.495055 ACAAATCAATCTCTGAAGCTTGTTTT 58.505 30.769 2.10 0.00 37.67 2.43
3806 5100 6.095440 GCTCTGGCCTGTTTTGAAATATAAGA 59.905 38.462 3.32 0.00 0.00 2.10
3860 5154 0.249031 GGTGCACCAAACAAGCTGTC 60.249 55.000 31.23 0.00 35.64 3.51
3922 5225 3.273886 TGATGTAACCCTTCTCCCCTCTA 59.726 47.826 0.00 0.00 0.00 2.43
4065 5392 4.974645 ACTCCAAAATCTGGTCTGTACA 57.025 40.909 0.00 0.00 46.51 2.90
4066 5393 5.305585 TCAACTCCAAAATCTGGTCTGTAC 58.694 41.667 0.00 0.00 46.51 2.90
4110 5437 1.732941 TGTGCTATTACCTTGTGGCG 58.267 50.000 0.00 0.00 36.63 5.69
4163 5490 0.675633 AAGCACAACACCAGATTGGC 59.324 50.000 0.00 0.00 42.67 4.52
4165 5492 1.338973 AGCAAGCACAACACCAGATTG 59.661 47.619 0.00 0.00 0.00 2.67
4166 5493 1.610522 GAGCAAGCACAACACCAGATT 59.389 47.619 0.00 0.00 0.00 2.40
4238 5565 1.739049 CAGCGTTCTTTGGGGCAAA 59.261 52.632 0.00 0.00 0.00 3.68
4301 5628 1.321474 CACATTGTGACACTTGCCCT 58.679 50.000 11.45 0.00 35.23 5.19


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

AutoCloner maintained by Alex Coulton.