Multiple sequence alignment - TraesCS4B01G379100

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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 TraesCS4B01G379100 chr4B 100.000 3253 0 0 1 3253 660517550 660520802 0.000000e+00 6008.0
1 TraesCS4B01G379100 chr4B 92.435 1573 71 14 161 1698 660685813 660684254 0.000000e+00 2202.0
2 TraesCS4B01G379100 chr4B 93.192 852 39 8 1970 2821 660683718 660682886 0.000000e+00 1234.0
3 TraesCS4B01G379100 chr4B 84.783 782 87 23 1986 2746 660535829 660536599 0.000000e+00 756.0
4 TraesCS4B01G379100 chr4B 84.732 727 74 13 1011 1709 660677574 660676857 0.000000e+00 693.0
5 TraesCS4B01G379100 chr4B 93.000 300 17 3 1679 1975 660684243 660683945 4.980000e-118 435.0
6 TraesCS4B01G379100 chr4B 86.188 362 36 7 2387 2742 660676055 660675702 2.370000e-101 379.0
7 TraesCS4B01G379100 chr4B 84.401 359 36 11 1348 1701 660535423 660535766 5.200000e-88 335.0
8 TraesCS4B01G379100 chr4B 91.463 164 12 2 1 162 660686090 660685927 1.170000e-54 224.0
9 TraesCS4B01G379100 chr4B 92.188 64 5 0 2299 2362 660676108 660676045 1.240000e-14 91.6
10 TraesCS4B01G379100 chr4B 80.000 120 11 4 3136 3253 660525063 660525171 3.480000e-10 76.8
11 TraesCS4B01G379100 chr5A 90.547 2010 139 20 1 1974 700787700 700785706 0.000000e+00 2612.0
12 TraesCS4B01G379100 chr5A 86.723 1190 99 28 1978 3131 700695186 700694020 0.000000e+00 1267.0
13 TraesCS4B01G379100 chr5A 85.244 1003 88 20 999 1975 700696297 700695329 0.000000e+00 977.0
14 TraesCS4B01G379100 chr5A 87.931 464 30 6 1970 2433 700785512 700785075 1.030000e-144 523.0
15 TraesCS4B01G379100 chrUn 88.219 1757 162 21 1 1725 110702442 110700699 0.000000e+00 2056.0
16 TraesCS4B01G379100 chrUn 85.157 795 79 20 1001 1773 110688709 110687932 0.000000e+00 778.0
17 TraesCS4B01G379100 chrUn 83.805 778 72 28 2385 3131 110687411 110686657 0.000000e+00 689.0
18 TraesCS4B01G379100 chrUn 90.116 516 39 5 1998 2513 110700126 110699623 0.000000e+00 660.0
19 TraesCS4B01G379100 chrUn 89.362 423 36 5 1970 2386 110687902 110687483 1.030000e-144 523.0
20 TraesCS4B01G379100 chrUn 81.536 612 61 22 619 1201 110692716 110692128 1.060000e-124 457.0
21 TraesCS4B01G379100 chrUn 90.520 327 26 4 1989 2313 110690889 110690566 8.340000e-116 427.0
22 TraesCS4B01G379100 chrUn 85.609 271 34 4 1223 1491 110692133 110691866 2.470000e-71 279.0
23 TraesCS4B01G379100 chr1D 76.841 1589 237 70 224 1725 430470157 430468613 0.000000e+00 774.0
24 TraesCS4B01G379100 chr1D 87.812 320 34 4 1995 2312 430468148 430467832 1.430000e-98 370.0
25 TraesCS4B01G379100 chr1A 76.437 1583 249 70 224 1728 528067287 528065751 0.000000e+00 743.0
26 TraesCS4B01G379100 chr1A 88.328 317 36 1 1996 2312 528065305 528064990 2.370000e-101 379.0
27 TraesCS4B01G379100 chr1B 76.690 1450 216 67 362 1725 581415641 581414228 0.000000e+00 693.0
28 TraesCS4B01G379100 chr6D 95.146 103 5 0 3151 3253 16003701 16003803 2.600000e-36 163.0
29 TraesCS4B01G379100 chr6B 93.333 105 7 0 3149 3253 7079017 7078913 4.350000e-34 156.0
30 TraesCS4B01G379100 chr6B 93.333 105 7 0 3149 3253 7088927 7088823 4.350000e-34 156.0
31 TraesCS4B01G379100 chr6B 93.333 105 7 0 3149 3253 7294972 7294868 4.350000e-34 156.0


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 TraesCS4B01G379100 chr4B 660517550 660520802 3252 False 6008.000000 6008 100.000000 1 3253 1 chr4B.!!$F1 3252
1 TraesCS4B01G379100 chr4B 660682886 660686090 3204 True 1023.750000 2202 92.522500 1 2821 4 chr4B.!!$R2 2820
2 TraesCS4B01G379100 chr4B 660535423 660536599 1176 False 545.500000 756 84.592000 1348 2746 2 chr4B.!!$F3 1398
3 TraesCS4B01G379100 chr4B 660675702 660677574 1872 True 387.866667 693 87.702667 1011 2742 3 chr4B.!!$R1 1731
4 TraesCS4B01G379100 chr5A 700785075 700787700 2625 True 1567.500000 2612 89.239000 1 2433 2 chr5A.!!$R2 2432
5 TraesCS4B01G379100 chr5A 700694020 700696297 2277 True 1122.000000 1267 85.983500 999 3131 2 chr5A.!!$R1 2132
6 TraesCS4B01G379100 chrUn 110699623 110702442 2819 True 1358.000000 2056 89.167500 1 2513 2 chrUn.!!$R2 2512
7 TraesCS4B01G379100 chrUn 110686657 110692716 6059 True 525.500000 778 85.998167 619 3131 6 chrUn.!!$R1 2512
8 TraesCS4B01G379100 chr1D 430467832 430470157 2325 True 572.000000 774 82.326500 224 2312 2 chr1D.!!$R1 2088
9 TraesCS4B01G379100 chr1A 528064990 528067287 2297 True 561.000000 743 82.382500 224 2312 2 chr1A.!!$R1 2088
10 TraesCS4B01G379100 chr1B 581414228 581415641 1413 True 693.000000 693 76.690000 362 1725 1 chr1B.!!$R1 1363

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
305 426 0.545071 CCACTTGGCAATCCCCCTTT 60.545 55.0 0.0 0.0 0.0 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2293 6542 0.478072 ATTGTGAGGCAACACCAGGA 59.522 50.0 11.16 0.0 43.14 3.86 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
59 62 4.206477 AGAGCAATGCCCAAAAATTACC 57.794 40.909 0.00 0.00 0.00 2.85
60 63 3.055167 AGAGCAATGCCCAAAAATTACCC 60.055 43.478 0.00 0.00 0.00 3.69
65 68 3.113260 TGCCCAAAAATTACCCAAACG 57.887 42.857 0.00 0.00 0.00 3.60
67 70 2.062519 CCCAAAAATTACCCAAACGCG 58.937 47.619 3.53 3.53 0.00 6.01
82 85 2.512286 GCGTGATAGCCTGCTGCA 60.512 61.111 0.88 0.88 44.83 4.41
93 96 3.656559 AGCCTGCTGCATTGTTTAAAAG 58.343 40.909 1.31 0.00 44.83 2.27
212 330 8.698854 TCAAATTAGTCTTTGCTTAAATTTGCG 58.301 29.630 0.00 0.00 41.05 4.85
222 340 5.336744 TGCTTAAATTTGCGCATAACCTAC 58.663 37.500 12.75 0.00 0.00 3.18
271 391 0.638292 ATGGCCCTGTTCCATCCAAT 59.362 50.000 0.00 0.00 40.08 3.16
305 426 0.545071 CCACTTGGCAATCCCCCTTT 60.545 55.000 0.00 0.00 0.00 3.11
316 437 4.244862 CAATCCCCCTTTGAAACAATTCG 58.755 43.478 0.00 0.00 38.46 3.34
349 478 0.698238 TGTTAATGTGGCCAGGCTCT 59.302 50.000 5.11 0.00 0.00 4.09
352 481 0.698238 TAATGTGGCCAGGCTCTTGT 59.302 50.000 5.11 0.00 0.00 3.16
386 519 4.694760 AGTGGATGCAGTCATATGCTTA 57.305 40.909 0.00 0.00 46.63 3.09
394 527 5.551233 TGCAGTCATATGCTTACTATTCCC 58.449 41.667 0.00 0.00 46.63 3.97
586 744 6.095021 GGAAATACACAGTTAATGAGAACCCC 59.905 42.308 0.00 0.00 0.00 4.95
649 825 7.471721 TCAGAAATATGGCACTTATTGTTTCG 58.528 34.615 0.00 0.00 31.57 3.46
709 889 2.790433 GATTACCCACAGTTTGCAGGA 58.210 47.619 0.00 0.00 0.00 3.86
746 926 4.262164 CCCCAGCAATGCTAATAATTGGAC 60.262 45.833 7.70 0.00 36.40 4.02
762 942 6.811253 AATTGGACGACTTAAGCATAAACA 57.189 33.333 1.29 0.00 0.00 2.83
908 1092 8.738645 ATAAAGGTGAATAAGACAATCCTCAC 57.261 34.615 0.00 0.00 33.92 3.51
976 1172 4.407945 GGCCATAGAGAGGTAGGTTAACAA 59.592 45.833 8.10 0.00 0.00 2.83
1164 1386 0.532862 AGCCGCGAGTTGATATTGGG 60.533 55.000 8.23 0.00 0.00 4.12
1729 2041 6.463995 TGTTAAGTTCTTTGCCTCACATTT 57.536 33.333 0.00 0.00 0.00 2.32
1730 2042 6.272318 TGTTAAGTTCTTTGCCTCACATTTG 58.728 36.000 0.00 0.00 0.00 2.32
1776 2093 4.526970 CTCAAACCTGTTGCCTACCATAT 58.473 43.478 0.00 0.00 0.00 1.78
1781 2098 7.617723 TCAAACCTGTTGCCTACCATATAATTT 59.382 33.333 0.00 0.00 0.00 1.82
1832 2190 8.482943 AGGTAAAAGTTATTTCAAAGTTGGCTT 58.517 29.630 0.00 0.00 36.30 4.35
1975 2342 5.632034 ACAGGGATCCTAAAATAGTGGTC 57.368 43.478 12.58 0.00 29.64 4.02
1976 2343 4.101119 ACAGGGATCCTAAAATAGTGGTCG 59.899 45.833 12.58 0.00 29.64 4.79
2293 6542 9.815306 AGAGTACAGACCATTATATGACTGTAT 57.185 33.333 19.00 12.97 43.71 2.29
2295 6544 9.026121 AGTACAGACCATTATATGACTGTATCC 57.974 37.037 19.00 12.63 43.71 2.59
2305 6554 1.003118 TGACTGTATCCTGGTGTTGCC 59.997 52.381 0.00 0.00 37.90 4.52
2314 6563 1.812571 CCTGGTGTTGCCTCACAATAC 59.187 52.381 9.85 0.00 46.48 1.89
2408 6732 5.035784 TGTATCTTCATCTATGACGAGCG 57.964 43.478 5.53 0.00 38.27 5.03
2421 6745 4.783764 TGACGAGCGTGATGGAATATAT 57.216 40.909 0.00 0.00 0.00 0.86
2424 6748 4.883083 ACGAGCGTGATGGAATATATGTT 58.117 39.130 0.00 0.00 0.00 2.71
2494 6831 8.674263 ATCTGAACTCATTGCTAATTCTAAGG 57.326 34.615 0.00 0.00 0.00 2.69
2528 6866 8.969121 TGCATTTCAATAAGTTGTACTGAATG 57.031 30.769 0.00 0.00 36.69 2.67
2592 6935 6.398095 CCCAAACCCAAGATTTGTTTAGATC 58.602 40.000 0.00 0.00 35.65 2.75
2750 7101 7.326063 GTGCAAACCAAAAACTTAGCAGTATAG 59.674 37.037 0.00 0.00 30.68 1.31
2751 7102 7.013846 TGCAAACCAAAAACTTAGCAGTATAGT 59.986 33.333 0.00 0.00 30.68 2.12
2752 7103 8.508875 GCAAACCAAAAACTTAGCAGTATAGTA 58.491 33.333 0.00 0.00 30.68 1.82
2835 7217 3.571401 ACTCACAGGATTCCAAGCTTTTG 59.429 43.478 5.29 0.00 0.00 2.44
2836 7218 3.565307 TCACAGGATTCCAAGCTTTTGT 58.435 40.909 5.29 0.00 0.00 2.83
2837 7219 4.724399 TCACAGGATTCCAAGCTTTTGTA 58.276 39.130 5.29 0.00 0.00 2.41
2838 7220 4.518970 TCACAGGATTCCAAGCTTTTGTAC 59.481 41.667 5.29 0.00 0.00 2.90
2839 7221 4.520492 CACAGGATTCCAAGCTTTTGTACT 59.480 41.667 5.29 0.00 0.00 2.73
2840 7222 5.010012 CACAGGATTCCAAGCTTTTGTACTT 59.990 40.000 5.29 0.00 0.00 2.24
2841 7223 5.010012 ACAGGATTCCAAGCTTTTGTACTTG 59.990 40.000 5.29 0.00 42.35 3.16
2904 7298 2.038952 TCACTGGTTGGTTGATCTCTGG 59.961 50.000 0.00 0.00 0.00 3.86
2911 7305 2.626785 TGGTTGATCTCTGGTACCCAA 58.373 47.619 10.07 1.93 30.80 4.12
2916 7310 2.027192 TGATCTCTGGTACCCAAAGTGC 60.027 50.000 10.07 2.18 30.80 4.40
2922 7316 1.241315 GGTACCCAAAGTGCGCACAT 61.241 55.000 39.21 27.93 30.59 3.21
2925 7319 1.544724 ACCCAAAGTGCGCACATAAT 58.455 45.000 39.21 20.92 0.00 1.28
2929 7323 3.429272 CCCAAAGTGCGCACATAATTGAT 60.429 43.478 39.21 15.97 0.00 2.57
2932 7326 1.003545 AGTGCGCACATAATTGATCGC 60.004 47.619 39.21 10.53 42.65 4.58
2936 7330 2.539547 GCGCACATAATTGATCGCTTGT 60.540 45.455 0.30 0.00 40.81 3.16
3112 7515 4.312443 TCGCACTTACCAAAGTAGGAAAG 58.688 43.478 0.00 0.00 44.28 2.62
3131 7534 4.219999 GCGAGGAGGAGCAGAGGC 62.220 72.222 0.00 0.00 41.61 4.70
3132 7535 3.535962 CGAGGAGGAGCAGAGGCC 61.536 72.222 0.00 0.00 42.56 5.19
3133 7536 2.364842 GAGGAGGAGCAGAGGCCA 60.365 66.667 5.01 0.00 42.56 5.36
3134 7537 2.365370 AGGAGGAGCAGAGGCCAG 60.365 66.667 5.01 0.00 42.56 4.85
3135 7538 2.364842 GGAGGAGCAGAGGCCAGA 60.365 66.667 5.01 0.00 42.56 3.86
3136 7539 2.433994 GGAGGAGCAGAGGCCAGAG 61.434 68.421 5.01 0.00 42.56 3.35
3137 7540 2.365370 AGGAGCAGAGGCCAGAGG 60.365 66.667 5.01 0.00 42.56 3.69
3138 7541 3.478274 GGAGCAGAGGCCAGAGGG 61.478 72.222 5.01 0.00 42.56 4.30
3139 7542 3.478274 GAGCAGAGGCCAGAGGGG 61.478 72.222 5.01 0.00 42.56 4.79
3142 7545 3.406200 CAGAGGCCAGAGGGGGTG 61.406 72.222 5.01 0.00 37.04 4.61
3143 7546 4.748798 AGAGGCCAGAGGGGGTGG 62.749 72.222 5.01 0.00 38.21 4.61
3148 7551 4.748798 CCAGAGGGGGTGGGCTCT 62.749 72.222 0.00 0.00 0.00 4.09
3149 7552 3.406200 CAGAGGGGGTGGGCTCTG 61.406 72.222 0.00 0.00 37.56 3.35
3150 7553 3.947041 AGAGGGGGTGGGCTCTGT 61.947 66.667 0.00 0.00 0.00 3.41
3151 7554 2.936032 GAGGGGGTGGGCTCTGTT 60.936 66.667 0.00 0.00 0.00 3.16
3152 7555 1.615424 GAGGGGGTGGGCTCTGTTA 60.615 63.158 0.00 0.00 0.00 2.41
3153 7556 1.616628 AGGGGGTGGGCTCTGTTAG 60.617 63.158 0.00 0.00 0.00 2.34
3154 7557 1.615424 GGGGGTGGGCTCTGTTAGA 60.615 63.158 0.00 0.00 0.00 2.10
3155 7558 0.988678 GGGGGTGGGCTCTGTTAGAT 60.989 60.000 0.00 0.00 0.00 1.98
3156 7559 0.181350 GGGGTGGGCTCTGTTAGATG 59.819 60.000 0.00 0.00 0.00 2.90
3157 7560 1.204146 GGGTGGGCTCTGTTAGATGA 58.796 55.000 0.00 0.00 0.00 2.92
3158 7561 1.771255 GGGTGGGCTCTGTTAGATGAT 59.229 52.381 0.00 0.00 0.00 2.45
3159 7562 2.224402 GGGTGGGCTCTGTTAGATGATC 60.224 54.545 0.00 0.00 0.00 2.92
3160 7563 2.435805 GGTGGGCTCTGTTAGATGATCA 59.564 50.000 0.00 0.00 0.00 2.92
3161 7564 3.494048 GGTGGGCTCTGTTAGATGATCAG 60.494 52.174 0.09 0.00 0.00 2.90
3162 7565 2.103771 TGGGCTCTGTTAGATGATCAGC 59.896 50.000 1.78 1.78 0.00 4.26
3163 7566 2.368221 GGGCTCTGTTAGATGATCAGCT 59.632 50.000 18.88 18.88 0.00 4.24
3164 7567 3.391965 GGCTCTGTTAGATGATCAGCTG 58.608 50.000 23.45 7.63 0.00 4.24
3165 7568 2.801679 GCTCTGTTAGATGATCAGCTGC 59.198 50.000 23.45 12.89 0.00 5.25
3166 7569 3.740452 GCTCTGTTAGATGATCAGCTGCA 60.740 47.826 23.45 18.93 32.97 4.41
3167 7570 3.790091 TCTGTTAGATGATCAGCTGCAC 58.210 45.455 23.45 18.54 0.00 4.57
3168 7571 3.450096 TCTGTTAGATGATCAGCTGCACT 59.550 43.478 23.45 0.00 0.00 4.40
3169 7572 3.790091 TGTTAGATGATCAGCTGCACTC 58.210 45.455 23.45 9.18 0.00 3.51
3170 7573 2.789491 TAGATGATCAGCTGCACTCG 57.211 50.000 23.45 0.00 0.00 4.18
3171 7574 0.104487 AGATGATCAGCTGCACTCGG 59.896 55.000 13.77 0.00 0.00 4.63
3172 7575 0.179089 GATGATCAGCTGCACTCGGT 60.179 55.000 9.47 0.00 0.00 4.69
3173 7576 0.179089 ATGATCAGCTGCACTCGGTC 60.179 55.000 9.47 0.00 0.00 4.79
3174 7577 1.253593 TGATCAGCTGCACTCGGTCT 61.254 55.000 9.47 0.00 0.00 3.85
3175 7578 0.108424 GATCAGCTGCACTCGGTCTT 60.108 55.000 9.47 0.00 0.00 3.01
3176 7579 0.322975 ATCAGCTGCACTCGGTCTTT 59.677 50.000 9.47 0.00 0.00 2.52
3177 7580 0.106708 TCAGCTGCACTCGGTCTTTT 59.893 50.000 9.47 0.00 0.00 2.27
3178 7581 0.514691 CAGCTGCACTCGGTCTTTTC 59.485 55.000 0.00 0.00 0.00 2.29
3179 7582 0.603975 AGCTGCACTCGGTCTTTTCC 60.604 55.000 1.02 0.00 0.00 3.13
3180 7583 0.884704 GCTGCACTCGGTCTTTTCCA 60.885 55.000 0.00 0.00 0.00 3.53
3181 7584 1.151668 CTGCACTCGGTCTTTTCCAG 58.848 55.000 0.00 0.00 0.00 3.86
3182 7585 0.884704 TGCACTCGGTCTTTTCCAGC 60.885 55.000 0.00 0.00 0.00 4.85
3183 7586 0.884704 GCACTCGGTCTTTTCCAGCA 60.885 55.000 0.00 0.00 0.00 4.41
3184 7587 1.593196 CACTCGGTCTTTTCCAGCAA 58.407 50.000 0.00 0.00 0.00 3.91
3185 7588 1.532868 CACTCGGTCTTTTCCAGCAAG 59.467 52.381 0.00 0.00 0.00 4.01
3186 7589 1.141053 ACTCGGTCTTTTCCAGCAAGT 59.859 47.619 0.00 0.00 0.00 3.16
3187 7590 2.222027 CTCGGTCTTTTCCAGCAAGTT 58.778 47.619 0.00 0.00 0.00 2.66
3188 7591 2.218603 TCGGTCTTTTCCAGCAAGTTC 58.781 47.619 0.00 0.00 0.00 3.01
3189 7592 1.946768 CGGTCTTTTCCAGCAAGTTCA 59.053 47.619 0.00 0.00 0.00 3.18
3190 7593 2.031682 CGGTCTTTTCCAGCAAGTTCAG 60.032 50.000 0.00 0.00 0.00 3.02
3191 7594 3.214328 GGTCTTTTCCAGCAAGTTCAGA 58.786 45.455 0.00 0.00 0.00 3.27
3192 7595 3.632145 GGTCTTTTCCAGCAAGTTCAGAA 59.368 43.478 0.00 0.00 0.00 3.02
3193 7596 4.097892 GGTCTTTTCCAGCAAGTTCAGAAA 59.902 41.667 0.00 0.00 0.00 2.52
3194 7597 5.277047 GTCTTTTCCAGCAAGTTCAGAAAG 58.723 41.667 0.00 0.00 0.00 2.62
3195 7598 4.949856 TCTTTTCCAGCAAGTTCAGAAAGT 59.050 37.500 0.00 0.00 0.00 2.66
3196 7599 5.418840 TCTTTTCCAGCAAGTTCAGAAAGTT 59.581 36.000 0.00 0.00 0.00 2.66
3197 7600 4.900635 TTCCAGCAAGTTCAGAAAGTTC 57.099 40.909 0.00 0.00 0.00 3.01
3198 7601 3.884895 TCCAGCAAGTTCAGAAAGTTCA 58.115 40.909 0.00 0.00 0.00 3.18
3199 7602 3.879295 TCCAGCAAGTTCAGAAAGTTCAG 59.121 43.478 0.00 0.00 0.00 3.02
3200 7603 3.629398 CCAGCAAGTTCAGAAAGTTCAGT 59.371 43.478 0.00 0.00 0.00 3.41
3201 7604 4.096984 CCAGCAAGTTCAGAAAGTTCAGTT 59.903 41.667 0.00 0.00 0.00 3.16
3202 7605 5.296780 CCAGCAAGTTCAGAAAGTTCAGTTA 59.703 40.000 0.00 0.00 0.00 2.24
3203 7606 6.425504 CAGCAAGTTCAGAAAGTTCAGTTAG 58.574 40.000 0.00 0.00 0.00 2.34
3204 7607 6.037610 CAGCAAGTTCAGAAAGTTCAGTTAGT 59.962 38.462 0.00 0.00 0.00 2.24
3205 7608 6.599638 AGCAAGTTCAGAAAGTTCAGTTAGTT 59.400 34.615 0.00 0.00 0.00 2.24
3206 7609 7.121315 AGCAAGTTCAGAAAGTTCAGTTAGTTT 59.879 33.333 0.00 0.00 0.00 2.66
3207 7610 8.395633 GCAAGTTCAGAAAGTTCAGTTAGTTTA 58.604 33.333 0.00 0.00 0.00 2.01
3208 7611 9.922305 CAAGTTCAGAAAGTTCAGTTAGTTTAG 57.078 33.333 0.00 0.00 0.00 1.85
3209 7612 9.668497 AAGTTCAGAAAGTTCAGTTAGTTTAGT 57.332 29.630 0.00 0.00 0.00 2.24
3222 7625 9.688592 TCAGTTAGTTTAGTAAGTTCAGTTAGC 57.311 33.333 0.00 0.00 0.00 3.09
3223 7626 9.694137 CAGTTAGTTTAGTAAGTTCAGTTAGCT 57.306 33.333 0.00 0.00 0.00 3.32
3224 7627 9.694137 AGTTAGTTTAGTAAGTTCAGTTAGCTG 57.306 33.333 0.00 0.00 43.87 4.24
3241 7644 9.683069 CAGTTAGCTGAATAAAATTCAGTTTGT 57.317 29.630 23.54 12.86 45.66 2.83
3242 7645 9.899226 AGTTAGCTGAATAAAATTCAGTTTGTC 57.101 29.630 23.54 14.37 45.66 3.18
3243 7646 9.677567 GTTAGCTGAATAAAATTCAGTTTGTCA 57.322 29.630 23.54 6.93 45.66 3.58
3244 7647 9.897744 TTAGCTGAATAAAATTCAGTTTGTCAG 57.102 29.630 23.54 12.23 45.66 3.51
3245 7648 6.865205 AGCTGAATAAAATTCAGTTTGTCAGC 59.135 34.615 23.54 21.01 46.90 4.26
3246 7649 6.183359 GCTGAATAAAATTCAGTTTGTCAGCG 60.183 38.462 23.54 3.70 45.66 5.18
3247 7650 6.734137 TGAATAAAATTCAGTTTGTCAGCGT 58.266 32.000 0.00 0.00 0.00 5.07
3248 7651 6.636447 TGAATAAAATTCAGTTTGTCAGCGTG 59.364 34.615 0.00 0.00 0.00 5.34
3249 7652 4.370364 AAAATTCAGTTTGTCAGCGTGT 57.630 36.364 0.00 0.00 0.00 4.49
3250 7653 3.338818 AATTCAGTTTGTCAGCGTGTG 57.661 42.857 0.00 0.00 0.00 3.82
3251 7654 1.732941 TTCAGTTTGTCAGCGTGTGT 58.267 45.000 0.00 0.00 0.00 3.72
3252 7655 1.006086 TCAGTTTGTCAGCGTGTGTG 58.994 50.000 0.00 0.00 0.00 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 3.669536 CGTTTGGGTAATTTTTGGGCAT 58.330 40.909 0.00 0.00 0.00 4.40
59 62 1.715585 CAGGCTATCACGCGTTTGG 59.284 57.895 10.22 3.05 0.00 3.28
60 63 1.060937 GCAGGCTATCACGCGTTTG 59.939 57.895 10.22 0.00 0.00 2.93
65 68 1.442526 AATGCAGCAGGCTATCACGC 61.443 55.000 0.00 0.00 45.15 5.34
67 70 1.386533 ACAATGCAGCAGGCTATCAC 58.613 50.000 0.00 0.00 45.15 3.06
82 85 5.645497 TGTTGTTGGCTTGCTTTTAAACAAT 59.355 32.000 9.61 0.00 39.07 2.71
93 96 0.031178 CTCCTGTGTTGTTGGCTTGC 59.969 55.000 0.00 0.00 0.00 4.01
171 289 9.793259 AGACTAATTTGATCTGTTTCTTTACCA 57.207 29.630 0.00 0.00 0.00 3.25
175 293 9.468532 GCAAAGACTAATTTGATCTGTTTCTTT 57.531 29.630 3.49 0.00 41.71 2.52
190 308 6.155827 TGCGCAAATTTAAGCAAAGACTAAT 58.844 32.000 8.16 0.00 36.60 1.73
271 391 1.332195 AGTGGCAGCGATGCTCTATA 58.668 50.000 26.42 4.36 36.40 1.31
287 407 0.609662 CAAAGGGGGATTGCCAAGTG 59.390 55.000 0.00 0.00 35.15 3.16
297 417 1.616374 GCGAATTGTTTCAAAGGGGGA 59.384 47.619 0.00 0.00 0.00 4.81
302 423 9.956797 CATTTTATAAGGCGAATTGTTTCAAAG 57.043 29.630 0.00 0.00 0.00 2.77
305 426 9.299963 CATCATTTTATAAGGCGAATTGTTTCA 57.700 29.630 0.00 0.00 0.00 2.69
316 437 7.384932 GGCCACATTAACATCATTTTATAAGGC 59.615 37.037 0.00 0.00 0.00 4.35
349 478 2.039216 TCCACTTAATTGCCCTCGACAA 59.961 45.455 0.00 0.00 0.00 3.18
352 481 2.917933 CATCCACTTAATTGCCCTCGA 58.082 47.619 0.00 0.00 0.00 4.04
386 519 4.656112 CAGGAATGGACTAGTGGGAATAGT 59.344 45.833 0.00 0.00 36.19 2.12
394 527 3.209410 GGATTGCAGGAATGGACTAGTG 58.791 50.000 0.00 0.00 0.00 2.74
462 600 5.699458 AGTGTTAACAGATTTTACCCTGTCG 59.301 40.000 8.98 0.00 42.25 4.35
549 698 6.237901 ACTGTGTATTTCCAGTGATGCTAAA 58.762 36.000 0.00 0.00 40.30 1.85
553 703 6.494893 TTAACTGTGTATTTCCAGTGATGC 57.505 37.500 0.00 0.00 40.91 3.91
561 719 6.095021 GGGGTTCTCATTAACTGTGTATTTCC 59.905 42.308 0.00 0.00 0.00 3.13
613 784 6.318648 GTGCCATATTTCTGAACCTAATGACA 59.681 38.462 0.00 0.00 0.00 3.58
649 825 5.163561 TGTTCCTTTGGACACAATCTGTTTC 60.164 40.000 0.00 0.00 36.29 2.78
709 889 1.271926 GCTGGGGTGTACTGGAACAAT 60.272 52.381 0.00 0.00 38.70 2.71
746 926 9.517361 GATATTTCGATGTTTATGCTTAAGTCG 57.483 33.333 4.02 3.11 0.00 4.18
762 942 5.282055 TCTCAGGCTGTTGATATTTCGAT 57.718 39.130 15.27 0.00 0.00 3.59
817 997 4.174009 CACGTCGTCCTTGATATTTGTCT 58.826 43.478 0.00 0.00 0.00 3.41
908 1092 1.365699 ACTAGTTTTATGGTGCGCGG 58.634 50.000 8.83 0.00 0.00 6.46
976 1172 6.893020 ATACTGGACCCTTCTCTGTTATTT 57.107 37.500 0.00 0.00 0.00 1.40
1164 1386 2.941720 GAGAACTCTCATGTCATTGCCC 59.058 50.000 1.73 0.00 42.42 5.36
1667 1949 2.218603 CACAAGTTCAGCTAAACCCGT 58.781 47.619 0.00 0.00 0.00 5.28
1781 2098 8.721133 TGATTTAAGTGATAGCCCTATCTGTA 57.279 34.615 14.46 4.00 41.80 2.74
1882 2242 4.764679 ACACATGCATGTCATTTTACGT 57.235 36.364 29.23 17.94 39.39 3.57
1975 2342 3.817084 ACCATGGCATCAATTAGTCATCG 59.183 43.478 13.04 0.00 0.00 3.84
1976 2343 4.558095 GCACCATGGCATCAATTAGTCATC 60.558 45.833 13.04 0.00 0.00 2.92
2293 6542 0.478072 ATTGTGAGGCAACACCAGGA 59.522 50.000 11.16 0.00 43.14 3.86
2295 6544 2.485426 CTGTATTGTGAGGCAACACCAG 59.515 50.000 11.16 7.88 43.14 4.00
2305 6554 4.134379 ACAGAGCATCCTGTATTGTGAG 57.866 45.455 4.87 0.00 44.82 3.51
2314 6563 1.764723 TGGGTGATACAGAGCATCCTG 59.235 52.381 0.00 0.00 43.20 3.86
2396 6720 1.675552 TCCATCACGCTCGTCATAGA 58.324 50.000 0.00 0.00 0.00 1.98
2459 6786 7.141363 AGCAATGAGTTCAGATTAACAAACAC 58.859 34.615 0.00 0.00 0.00 3.32
2494 6831 4.397417 ACTTATTGAAATGCAGAGCAGGTC 59.603 41.667 0.00 0.00 43.65 3.85
2592 6935 3.694072 TCCGTTGATAATGCCTTCCTTTG 59.306 43.478 0.00 0.00 0.00 2.77
2750 7101 9.226345 GCTTCATTTTGCTGTTCTGTAATATAC 57.774 33.333 0.00 0.00 0.00 1.47
2751 7102 8.955388 TGCTTCATTTTGCTGTTCTGTAATATA 58.045 29.630 0.00 0.00 0.00 0.86
2752 7103 7.829725 TGCTTCATTTTGCTGTTCTGTAATAT 58.170 30.769 0.00 0.00 0.00 1.28
2835 7217 8.066000 GCATTTTATATAACGGACACCAAGTAC 58.934 37.037 0.00 0.00 0.00 2.73
2836 7218 7.769507 TGCATTTTATATAACGGACACCAAGTA 59.230 33.333 0.00 0.00 0.00 2.24
2837 7219 6.600032 TGCATTTTATATAACGGACACCAAGT 59.400 34.615 0.00 0.00 0.00 3.16
2838 7220 7.022055 TGCATTTTATATAACGGACACCAAG 57.978 36.000 0.00 0.00 0.00 3.61
2839 7221 7.121463 ACTTGCATTTTATATAACGGACACCAA 59.879 33.333 0.00 0.00 0.00 3.67
2840 7222 6.600032 ACTTGCATTTTATATAACGGACACCA 59.400 34.615 0.00 0.00 0.00 4.17
2841 7223 7.023197 ACTTGCATTTTATATAACGGACACC 57.977 36.000 0.00 0.00 0.00 4.16
2880 7274 3.007398 AGAGATCAACCAACCAGTGAGTC 59.993 47.826 0.00 0.00 0.00 3.36
2904 7298 1.444836 TATGTGCGCACTTTGGGTAC 58.555 50.000 37.59 11.93 43.95 3.34
2911 7305 2.539547 GCGATCAATTATGTGCGCACTT 60.540 45.455 37.59 33.00 43.90 3.16
2916 7310 3.001634 AGACAAGCGATCAATTATGTGCG 59.998 43.478 0.00 0.00 0.00 5.34
2922 7316 5.369685 TTTTGCAGACAAGCGATCAATTA 57.630 34.783 0.00 0.00 37.04 1.40
2925 7319 3.921119 ATTTTGCAGACAAGCGATCAA 57.079 38.095 0.00 0.00 37.04 2.57
2929 7323 2.877786 TCTGAATTTTGCAGACAAGCGA 59.122 40.909 0.00 0.00 37.46 4.93
2932 7326 7.327761 CCAAGTTATCTGAATTTTGCAGACAAG 59.672 37.037 0.00 0.00 44.39 3.16
2936 7330 7.523293 TTCCAAGTTATCTGAATTTTGCAGA 57.477 32.000 0.00 0.00 45.52 4.26
2977 7371 5.576128 AGAATTTCTTCGGTTATTCCCCAA 58.424 37.500 0.00 0.00 36.45 4.12
3045 7440 2.705658 TGAGGTGTGTTTGATCAGGAGT 59.294 45.455 0.00 0.00 0.00 3.85
3112 7515 4.567385 CTCTGCTCCTCCTCGCGC 62.567 72.222 0.00 0.00 0.00 6.86
3131 7534 4.748798 AGAGCCCACCCCCTCTGG 62.749 72.222 0.00 0.00 37.07 3.86
3132 7535 3.406200 CAGAGCCCACCCCCTCTG 61.406 72.222 3.58 3.58 46.20 3.35
3133 7536 2.119847 TAACAGAGCCCACCCCCTCT 62.120 60.000 0.00 0.00 38.91 3.69
3134 7537 1.615424 TAACAGAGCCCACCCCCTC 60.615 63.158 0.00 0.00 0.00 4.30
3135 7538 1.616628 CTAACAGAGCCCACCCCCT 60.617 63.158 0.00 0.00 0.00 4.79
3136 7539 0.988678 ATCTAACAGAGCCCACCCCC 60.989 60.000 0.00 0.00 0.00 5.40
3137 7540 0.181350 CATCTAACAGAGCCCACCCC 59.819 60.000 0.00 0.00 0.00 4.95
3138 7541 1.204146 TCATCTAACAGAGCCCACCC 58.796 55.000 0.00 0.00 0.00 4.61
3139 7542 2.435805 TGATCATCTAACAGAGCCCACC 59.564 50.000 0.00 0.00 0.00 4.61
3140 7543 3.726607 CTGATCATCTAACAGAGCCCAC 58.273 50.000 0.00 0.00 34.07 4.61
3141 7544 2.103771 GCTGATCATCTAACAGAGCCCA 59.896 50.000 0.00 0.00 34.07 5.36
3142 7545 2.368221 AGCTGATCATCTAACAGAGCCC 59.632 50.000 0.00 0.00 34.07 5.19
3143 7546 3.391965 CAGCTGATCATCTAACAGAGCC 58.608 50.000 8.42 0.00 34.07 4.70
3144 7547 2.801679 GCAGCTGATCATCTAACAGAGC 59.198 50.000 20.43 0.00 34.07 4.09
3145 7548 3.803231 GTGCAGCTGATCATCTAACAGAG 59.197 47.826 20.43 0.00 34.07 3.35
3146 7549 3.450096 AGTGCAGCTGATCATCTAACAGA 59.550 43.478 20.43 0.00 34.07 3.41
3147 7550 3.794717 AGTGCAGCTGATCATCTAACAG 58.205 45.455 20.43 0.00 35.14 3.16
3148 7551 3.736126 CGAGTGCAGCTGATCATCTAACA 60.736 47.826 20.43 0.00 0.00 2.41
3149 7552 2.793790 CGAGTGCAGCTGATCATCTAAC 59.206 50.000 20.43 1.56 0.00 2.34
3150 7553 2.223900 CCGAGTGCAGCTGATCATCTAA 60.224 50.000 20.43 0.00 0.00 2.10
3151 7554 1.339291 CCGAGTGCAGCTGATCATCTA 59.661 52.381 20.43 0.00 0.00 1.98
3152 7555 0.104487 CCGAGTGCAGCTGATCATCT 59.896 55.000 20.43 7.07 0.00 2.90
3153 7556 0.179089 ACCGAGTGCAGCTGATCATC 60.179 55.000 20.43 8.19 0.00 2.92
3154 7557 0.179089 GACCGAGTGCAGCTGATCAT 60.179 55.000 20.43 0.00 0.00 2.45
3155 7558 1.216444 GACCGAGTGCAGCTGATCA 59.784 57.895 20.43 3.45 0.00 2.92
3156 7559 0.108424 AAGACCGAGTGCAGCTGATC 60.108 55.000 20.43 10.84 0.00 2.92
3157 7560 0.322975 AAAGACCGAGTGCAGCTGAT 59.677 50.000 20.43 1.27 0.00 2.90
3158 7561 0.106708 AAAAGACCGAGTGCAGCTGA 59.893 50.000 20.43 0.00 0.00 4.26
3159 7562 0.514691 GAAAAGACCGAGTGCAGCTG 59.485 55.000 10.11 10.11 0.00 4.24
3160 7563 0.603975 GGAAAAGACCGAGTGCAGCT 60.604 55.000 0.00 0.00 0.00 4.24
3161 7564 0.884704 TGGAAAAGACCGAGTGCAGC 60.885 55.000 0.00 0.00 0.00 5.25
3162 7565 1.151668 CTGGAAAAGACCGAGTGCAG 58.848 55.000 0.00 0.00 0.00 4.41
3163 7566 0.884704 GCTGGAAAAGACCGAGTGCA 60.885 55.000 0.00 0.00 0.00 4.57
3164 7567 0.884704 TGCTGGAAAAGACCGAGTGC 60.885 55.000 0.00 0.00 0.00 4.40
3165 7568 1.532868 CTTGCTGGAAAAGACCGAGTG 59.467 52.381 0.00 0.00 0.00 3.51
3166 7569 1.141053 ACTTGCTGGAAAAGACCGAGT 59.859 47.619 0.00 0.00 0.00 4.18
3167 7570 1.884235 ACTTGCTGGAAAAGACCGAG 58.116 50.000 0.00 0.00 0.00 4.63
3168 7571 2.218603 GAACTTGCTGGAAAAGACCGA 58.781 47.619 0.00 0.00 0.00 4.69
3169 7572 1.946768 TGAACTTGCTGGAAAAGACCG 59.053 47.619 0.00 0.00 0.00 4.79
3170 7573 3.214328 TCTGAACTTGCTGGAAAAGACC 58.786 45.455 0.00 0.00 0.00 3.85
3171 7574 4.900635 TTCTGAACTTGCTGGAAAAGAC 57.099 40.909 0.00 0.00 0.00 3.01
3172 7575 4.949856 ACTTTCTGAACTTGCTGGAAAAGA 59.050 37.500 0.00 0.00 0.00 2.52
3173 7576 5.254339 ACTTTCTGAACTTGCTGGAAAAG 57.746 39.130 0.00 0.00 0.00 2.27
3174 7577 5.184864 TGAACTTTCTGAACTTGCTGGAAAA 59.815 36.000 0.00 0.00 0.00 2.29
3175 7578 4.704540 TGAACTTTCTGAACTTGCTGGAAA 59.295 37.500 0.00 0.00 0.00 3.13
3176 7579 4.269183 TGAACTTTCTGAACTTGCTGGAA 58.731 39.130 0.00 0.00 0.00 3.53
3177 7580 3.879295 CTGAACTTTCTGAACTTGCTGGA 59.121 43.478 0.00 0.00 0.00 3.86
3178 7581 3.629398 ACTGAACTTTCTGAACTTGCTGG 59.371 43.478 3.15 0.00 0.00 4.85
3179 7582 4.889832 ACTGAACTTTCTGAACTTGCTG 57.110 40.909 3.15 0.00 0.00 4.41
3180 7583 6.116126 ACTAACTGAACTTTCTGAACTTGCT 58.884 36.000 3.15 0.00 0.00 3.91
3181 7584 6.364945 ACTAACTGAACTTTCTGAACTTGC 57.635 37.500 3.15 0.00 0.00 4.01
3182 7585 9.922305 CTAAACTAACTGAACTTTCTGAACTTG 57.078 33.333 3.15 0.00 0.00 3.16
3183 7586 9.668497 ACTAAACTAACTGAACTTTCTGAACTT 57.332 29.630 3.15 0.00 0.00 2.66
3196 7599 9.688592 GCTAACTGAACTTACTAAACTAACTGA 57.311 33.333 0.00 0.00 0.00 3.41
3197 7600 9.694137 AGCTAACTGAACTTACTAAACTAACTG 57.306 33.333 0.00 0.00 0.00 3.16
3223 7626 6.636447 CACGCTGACAAACTGAATTTTATTCA 59.364 34.615 2.47 2.47 0.00 2.57
3224 7627 6.636850 ACACGCTGACAAACTGAATTTTATTC 59.363 34.615 0.00 0.00 0.00 1.75
3225 7628 6.417635 CACACGCTGACAAACTGAATTTTATT 59.582 34.615 0.00 0.00 0.00 1.40
3226 7629 5.914635 CACACGCTGACAAACTGAATTTTAT 59.085 36.000 0.00 0.00 0.00 1.40
3227 7630 5.163703 ACACACGCTGACAAACTGAATTTTA 60.164 36.000 0.00 0.00 0.00 1.52
3228 7631 4.104776 CACACGCTGACAAACTGAATTTT 58.895 39.130 0.00 0.00 0.00 1.82
3229 7632 3.128589 ACACACGCTGACAAACTGAATTT 59.871 39.130 0.00 0.00 0.00 1.82
3230 7633 2.682856 ACACACGCTGACAAACTGAATT 59.317 40.909 0.00 0.00 0.00 2.17
3231 7634 2.032054 CACACACGCTGACAAACTGAAT 59.968 45.455 0.00 0.00 0.00 2.57
3232 7635 1.396648 CACACACGCTGACAAACTGAA 59.603 47.619 0.00 0.00 0.00 3.02
3233 7636 1.006086 CACACACGCTGACAAACTGA 58.994 50.000 0.00 0.00 0.00 3.41
3234 7637 3.514510 CACACACGCTGACAAACTG 57.485 52.632 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.