Multiple sequence alignment - TraesCS1B01G209300

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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 TraesCS1B01G209300 chr1B 100.000 5149 0 0 1 5149 379632274 379627126 0.000000e+00 9509.0
1 TraesCS1B01G209300 chr1A 91.626 1863 87 21 13 1820 351609150 351607302 0.000000e+00 2512.0
2 TraesCS1B01G209300 chr1A 94.138 1160 52 3 2166 3320 351606679 351605531 0.000000e+00 1751.0
3 TraesCS1B01G209300 chr1A 95.823 790 25 3 3324 4111 351605450 351604667 0.000000e+00 1269.0
4 TraesCS1B01G209300 chr1A 96.254 347 10 3 1821 2165 351607200 351606855 2.690000e-157 566.0
5 TraesCS1B01G209300 chr1A 88.655 238 19 7 4111 4344 351604597 351604364 3.030000e-72 283.0
6 TraesCS1B01G209300 chr1A 98.837 86 1 0 2160 2245 351606765 351606680 2.480000e-33 154.0
7 TraesCS1B01G209300 chr1D 90.629 1494 90 19 968 2449 279524295 279522840 0.000000e+00 1938.0
8 TraesCS1B01G209300 chr1D 87.898 942 69 21 29 942 279525814 279524890 0.000000e+00 1066.0
9 TraesCS1B01G209300 chr1D 89.374 847 54 20 3226 4068 279522844 279522030 0.000000e+00 1033.0
10 TraesCS1B01G209300 chr1D 91.064 235 18 3 4110 4344 279521833 279521602 1.080000e-81 315.0
11 TraesCS1B01G209300 chr1D 85.408 233 30 4 4111 4342 287456553 287456324 6.660000e-59 239.0
12 TraesCS1B01G209300 chr2D 88.308 804 84 9 4341 5140 279048428 279049225 0.000000e+00 955.0
13 TraesCS1B01G209300 chr2D 78.988 514 68 22 75 560 304218538 304219039 1.080000e-81 315.0
14 TraesCS1B01G209300 chr2D 80.252 238 38 8 4110 4342 567011091 567010858 2.470000e-38 171.0
15 TraesCS1B01G209300 chr2D 100.000 30 0 0 618 647 174239258 174239287 7.200000e-04 56.5
16 TraesCS1B01G209300 chr5B 87.995 808 89 7 4336 5140 527288427 527289229 0.000000e+00 948.0
17 TraesCS1B01G209300 chr6A 86.940 804 99 5 4342 5142 451601686 451602486 0.000000e+00 898.0
18 TraesCS1B01G209300 chr6A 80.388 515 62 20 75 560 130409417 130409921 6.340000e-94 355.0
19 TraesCS1B01G209300 chr6A 75.781 128 21 6 618 738 549402639 549402515 7.200000e-04 56.5
20 TraesCS1B01G209300 chr3A 87.077 797 97 5 4350 5142 550471225 550470431 0.000000e+00 896.0
21 TraesCS1B01G209300 chrUn 87.028 794 98 3 4341 5131 332622646 332621855 0.000000e+00 891.0
22 TraesCS1B01G209300 chr4B 87.028 794 98 3 4341 5131 618630778 618629987 0.000000e+00 891.0
23 TraesCS1B01G209300 chr4B 87.028 794 98 3 4341 5131 618637551 618636760 0.000000e+00 891.0
24 TraesCS1B01G209300 chr4B 84.571 175 22 4 388 560 639969319 639969490 8.870000e-38 169.0
25 TraesCS1B01G209300 chr7D 86.104 806 98 9 4345 5140 558089898 558090699 0.000000e+00 856.0
26 TraesCS1B01G209300 chr5D 86.052 803 98 10 4345 5140 381813942 381813147 0.000000e+00 850.0
27 TraesCS1B01G209300 chr5D 83.830 235 33 4 4111 4344 349878419 349878189 8.680000e-53 219.0
28 TraesCS1B01G209300 chr5A 80.859 512 66 14 75 557 491567201 491567709 1.750000e-99 374.0
29 TraesCS1B01G209300 chr5A 77.252 444 66 13 139 553 31087493 31087930 1.440000e-55 228.0
30 TraesCS1B01G209300 chr5A 82.128 235 32 7 4112 4342 657209954 657210182 5.260000e-45 193.0
31 TraesCS1B01G209300 chr5A 80.252 238 37 9 4110 4342 650561558 650561790 2.470000e-38 171.0
32 TraesCS1B01G209300 chr5A 75.658 152 24 9 618 760 561682536 561682683 4.300000e-06 63.9
33 TraesCS1B01G209300 chr6D 91.195 159 13 1 402 560 106945817 106945974 1.120000e-51 215.0
34 TraesCS1B01G209300 chr4A 87.719 171 17 3 387 557 45869791 45869957 4.070000e-46 196.0
35 TraesCS1B01G209300 chr7A 80.252 238 38 9 4110 4342 632385879 632385646 2.470000e-38 171.0
36 TraesCS1B01G209300 chr7A 77.632 152 21 9 618 760 671218362 671218509 4.270000e-11 80.5
37 TraesCS1B01G209300 chr7A 75.497 151 25 8 618 760 177004022 177004168 4.300000e-06 63.9
38 TraesCS1B01G209300 chr6B 80.252 238 38 8 4110 4342 4852812 4853045 2.470000e-38 171.0


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 TraesCS1B01G209300 chr1B 379627126 379632274 5148 True 9509.000000 9509 100.000000 1 5149 1 chr1B.!!$R1 5148
1 TraesCS1B01G209300 chr1A 351604364 351609150 4786 True 1089.166667 2512 94.222167 13 4344 6 chr1A.!!$R1 4331
2 TraesCS1B01G209300 chr1D 279521602 279525814 4212 True 1088.000000 1938 89.741250 29 4344 4 chr1D.!!$R2 4315
3 TraesCS1B01G209300 chr2D 279048428 279049225 797 False 955.000000 955 88.308000 4341 5140 1 chr2D.!!$F2 799
4 TraesCS1B01G209300 chr2D 304218538 304219039 501 False 315.000000 315 78.988000 75 560 1 chr2D.!!$F3 485
5 TraesCS1B01G209300 chr5B 527288427 527289229 802 False 948.000000 948 87.995000 4336 5140 1 chr5B.!!$F1 804
6 TraesCS1B01G209300 chr6A 451601686 451602486 800 False 898.000000 898 86.940000 4342 5142 1 chr6A.!!$F2 800
7 TraesCS1B01G209300 chr6A 130409417 130409921 504 False 355.000000 355 80.388000 75 560 1 chr6A.!!$F1 485
8 TraesCS1B01G209300 chr3A 550470431 550471225 794 True 896.000000 896 87.077000 4350 5142 1 chr3A.!!$R1 792
9 TraesCS1B01G209300 chrUn 332621855 332622646 791 True 891.000000 891 87.028000 4341 5131 1 chrUn.!!$R1 790
10 TraesCS1B01G209300 chr4B 618629987 618630778 791 True 891.000000 891 87.028000 4341 5131 1 chr4B.!!$R1 790
11 TraesCS1B01G209300 chr4B 618636760 618637551 791 True 891.000000 891 87.028000 4341 5131 1 chr4B.!!$R2 790
12 TraesCS1B01G209300 chr7D 558089898 558090699 801 False 856.000000 856 86.104000 4345 5140 1 chr7D.!!$F1 795
13 TraesCS1B01G209300 chr5D 381813147 381813942 795 True 850.000000 850 86.052000 4345 5140 1 chr5D.!!$R2 795
14 TraesCS1B01G209300 chr5A 491567201 491567709 508 False 374.000000 374 80.859000 75 557 1 chr5A.!!$F2 482

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
815 908 0.319125 GATCGGGGCGAAGATCTGAC 60.319 60.000 0.00 0.00 39.99 3.51 F
965 1058 1.052124 TGGGTCGTGGAAACAGAGGT 61.052 55.000 0.00 0.00 44.46 3.85 F
1351 2035 1.500844 CTCTTGCAAGGCGCTCAAG 59.499 57.895 25.73 15.27 43.06 3.02 F
2500 3468 0.102481 GTGCGTGTAGATGTCCCGAT 59.898 55.000 0.00 0.00 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2085 2871 0.251832 AGAGGAGCTCAAGTCGGGAA 60.252 55.0 17.19 0.00 32.06 3.97 R
2090 2876 0.980423 ACCCAAGAGGAGCTCAAGTC 59.020 55.0 17.19 8.90 39.89 3.01 R
3158 4126 0.040425 CAAGTTTACTTTGCGCGGCT 60.040 50.0 8.83 0.00 33.11 5.52 R
4225 5432 0.179225 AAATTTGCACGCGCGTAGAG 60.179 50.0 37.24 24.57 42.97 2.43 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
39 42 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
41 44 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
45 48 2.101582 GAGAGAGAGAGAGAGAGAGCGT 59.898 54.545 0.00 0.00 0.00 5.07
49 52 1.078778 AGAGAGAGAGAGCGTGCGA 60.079 57.895 0.00 0.00 0.00 5.10
51 54 1.366111 GAGAGAGAGAGCGTGCGACT 61.366 60.000 0.00 0.00 0.00 4.18
57 60 0.388134 GAGAGCGTGCGACTTGGTTA 60.388 55.000 0.00 0.00 0.00 2.85
89 97 3.370104 TGGGCCTTCTTTTCTGTTTTCA 58.630 40.909 4.53 0.00 0.00 2.69
97 105 6.753744 CCTTCTTTTCTGTTTTCAGTTTCTGG 59.246 38.462 0.00 0.00 46.98 3.86
259 273 1.511850 GGCCCATTTGCAAAGTTGTC 58.488 50.000 18.19 5.79 0.00 3.18
268 282 7.307930 CCCATTTGCAAAGTTGTCTTTATTTCC 60.308 37.037 18.19 0.00 41.31 3.13
342 356 8.414003 TGCACAAATTACACTATTTACAAACCA 58.586 29.630 0.00 0.00 0.00 3.67
353 367 2.465860 TACAAACCATGGTCCACTCG 57.534 50.000 20.07 5.77 0.00 4.18
560 607 2.884639 AGGAGAAATTTGGGTTGTGACG 59.115 45.455 0.00 0.00 0.00 4.35
567 614 1.346479 TTGGGTTGTGACGGGAAGGA 61.346 55.000 0.00 0.00 0.00 3.36
661 728 3.998672 GGGTCGTGAGTGCGGGAA 61.999 66.667 0.00 0.00 0.00 3.97
666 733 1.079819 CGTGAGTGCGGGAAGATGT 60.080 57.895 0.00 0.00 0.00 3.06
669 736 1.476891 GTGAGTGCGGGAAGATGTAGA 59.523 52.381 0.00 0.00 0.00 2.59
676 743 3.512329 TGCGGGAAGATGTAGACAACTAA 59.488 43.478 0.00 0.00 0.00 2.24
700 767 1.597854 CGCAACTGGAGCCACTTCA 60.598 57.895 0.00 0.00 0.00 3.02
759 826 2.168313 GGTGGGGGCATCAAATTTACAG 59.832 50.000 0.00 0.00 0.00 2.74
784 876 7.759433 AGTTAGTTGCAATTGGAAATTTATCCG 59.241 33.333 17.64 0.00 42.76 4.18
815 908 0.319125 GATCGGGGCGAAGATCTGAC 60.319 60.000 0.00 0.00 39.99 3.51
820 913 1.590259 GGCGAAGATCTGACGGCTC 60.590 63.158 28.36 9.92 46.12 4.70
824 917 1.402852 CGAAGATCTGACGGCTCACAA 60.403 52.381 12.74 0.00 0.00 3.33
895 988 2.991190 GACGAGGCAACGTGAATCTAAA 59.009 45.455 13.68 0.00 46.52 1.85
896 989 2.993899 ACGAGGCAACGTGAATCTAAAG 59.006 45.455 8.74 0.00 44.84 1.85
897 990 2.222819 CGAGGCAACGTGAATCTAAAGC 60.223 50.000 0.00 0.00 46.39 3.51
898 991 3.003480 GAGGCAACGTGAATCTAAAGCT 58.997 45.455 0.00 0.00 46.39 3.74
926 1019 8.893560 TGGGATGAATAAATGAGGAGATGATTA 58.106 33.333 0.00 0.00 0.00 1.75
955 1048 3.726291 AAAAACAGATTTGGGTCGTGG 57.274 42.857 0.00 0.00 0.00 4.94
965 1058 1.052124 TGGGTCGTGGAAACAGAGGT 61.052 55.000 0.00 0.00 44.46 3.85
1351 2035 1.500844 CTCTTGCAAGGCGCTCAAG 59.499 57.895 25.73 15.27 43.06 3.02
1360 2044 4.436448 GCGCTCAAGTCGTGCTGC 62.436 66.667 0.00 0.00 35.16 5.25
1447 2131 6.202379 GTGAGGTTTAGCCCGATATAAGTTTC 59.798 42.308 0.00 0.00 38.26 2.78
1577 2261 2.432628 GAGGACAACACCGAGCCG 60.433 66.667 0.00 0.00 34.73 5.52
1612 2296 4.054359 AGGATCAGCTAGGATTCGGTAT 57.946 45.455 0.00 0.00 0.00 2.73
1647 2331 5.705609 TCATGCTTTTTCCTAAACTGGAC 57.294 39.130 0.00 0.00 35.58 4.02
1986 2772 3.128242 CGCAGCCTTCAGATTTCTTCATT 59.872 43.478 0.00 0.00 0.00 2.57
2090 2876 1.668419 CTTGAATAGCCTGGTTCCCG 58.332 55.000 0.00 0.00 0.00 5.14
2157 2944 3.251004 CGATAGCCAAGGCCTATTTTGTC 59.749 47.826 5.16 0.00 43.17 3.18
2158 2945 2.907458 AGCCAAGGCCTATTTTGTCT 57.093 45.000 5.16 0.00 43.17 3.41
2330 3293 3.365264 CGAATGCAAAAGCTTAGCAGACA 60.365 43.478 24.78 9.10 42.14 3.41
2374 3337 9.546909 CAGTAAGCATACAATTTGTTTCACTAG 57.453 33.333 7.45 0.00 34.29 2.57
2398 3361 0.526524 GAGGTGCTAGCTGCTACACG 60.527 60.000 23.34 11.26 43.37 4.49
2469 3437 5.295431 TGTGATGTAGCACAAAATAGCAC 57.705 39.130 0.00 0.00 45.08 4.40
2473 3441 2.410392 TGTAGCACAAAATAGCACGACG 59.590 45.455 0.00 0.00 0.00 5.12
2497 3465 2.024176 ATTGTGCGTGTAGATGTCCC 57.976 50.000 0.00 0.00 0.00 4.46
2500 3468 0.102481 GTGCGTGTAGATGTCCCGAT 59.898 55.000 0.00 0.00 0.00 4.18
2507 3475 4.499865 CGTGTAGATGTCCCGATCTTTCAT 60.500 45.833 0.00 0.00 34.42 2.57
2532 3500 2.596419 ACATGCAAAACAACAACGAACG 59.404 40.909 0.00 0.00 0.00 3.95
2551 3519 1.153369 ACGGCAGCAATAGTCGCAT 60.153 52.632 0.00 0.00 0.00 4.73
2554 3522 0.585357 GGCAGCAATAGTCGCATGAG 59.415 55.000 0.00 0.00 0.00 2.90
2575 3543 9.311916 CATGAGAAATAGACCTAGAAGAACAAG 57.688 37.037 0.00 0.00 0.00 3.16
2654 3622 1.088340 AGATCAGACGCATGCACAGC 61.088 55.000 19.57 3.18 0.00 4.40
2657 3625 2.031616 AGACGCATGCACAGCAGT 59.968 55.556 19.57 5.87 43.65 4.40
2702 3670 2.124570 CATCCTTGGTGCCTCCCG 60.125 66.667 0.00 0.00 34.77 5.14
2703 3671 2.610859 ATCCTTGGTGCCTCCCGT 60.611 61.111 0.00 0.00 34.77 5.28
2709 3677 2.358737 GGTGCCTCCCGTTGTGAG 60.359 66.667 0.00 0.00 0.00 3.51
2723 3691 3.813166 CGTTGTGAGGTGTTTTCTGGTAT 59.187 43.478 0.00 0.00 0.00 2.73
2778 3746 1.133167 TCTCCTGGGACAAGACTGACA 60.133 52.381 0.00 0.00 38.70 3.58
2783 3751 0.472471 GGGACAAGACTGACAACCCA 59.528 55.000 0.00 0.00 36.27 4.51
2807 3775 2.801077 TATCTCCGACTCACACCAGA 57.199 50.000 0.00 0.00 0.00 3.86
2808 3776 1.924731 ATCTCCGACTCACACCAGAA 58.075 50.000 0.00 0.00 0.00 3.02
2810 3778 0.962489 CTCCGACTCACACCAGAAGT 59.038 55.000 0.00 0.00 0.00 3.01
2850 3818 7.565323 TTTAACCGACTTAAAAGCAAAGGTA 57.435 32.000 0.00 0.00 32.37 3.08
2943 3911 9.905713 TTGATCACATAAGCCTAATTTAGACTT 57.094 29.630 9.53 9.53 33.03 3.01
2973 3941 3.865011 TTTGTTTGCTTGCACTCTTGA 57.135 38.095 0.00 0.00 0.00 3.02
2989 3957 3.603532 TCTTGAACTGCTCCATCATCAC 58.396 45.455 0.00 0.00 0.00 3.06
3002 3970 7.392953 TGCTCCATCATCACACATAAAAAGTAA 59.607 33.333 0.00 0.00 0.00 2.24
3045 4013 5.300792 GTGTCCTTCTTTGGTTCAATTGGTA 59.699 40.000 5.42 0.00 0.00 3.25
3129 4097 6.237542 CGGTATACTTGCATCAAAACAAATGC 60.238 38.462 2.25 0.51 46.68 3.56
3155 4123 6.425114 TCTTGCTTATCTTCTGTTCAACACTC 59.575 38.462 0.00 0.00 0.00 3.51
3156 4124 4.686091 TGCTTATCTTCTGTTCAACACTCG 59.314 41.667 0.00 0.00 0.00 4.18
3157 4125 4.092091 GCTTATCTTCTGTTCAACACTCGG 59.908 45.833 0.00 0.00 0.00 4.63
3158 4126 5.462530 TTATCTTCTGTTCAACACTCGGA 57.537 39.130 0.00 0.00 0.00 4.55
3159 4127 3.371102 TCTTCTGTTCAACACTCGGAG 57.629 47.619 2.83 2.83 0.00 4.63
3160 4128 1.795286 CTTCTGTTCAACACTCGGAGC 59.205 52.381 4.58 0.00 0.00 4.70
3161 4129 0.033504 TCTGTTCAACACTCGGAGCC 59.966 55.000 4.58 0.00 0.00 4.70
3162 4130 1.284982 CTGTTCAACACTCGGAGCCG 61.285 60.000 4.58 1.74 41.35 5.52
3163 4131 2.357034 TTCAACACTCGGAGCCGC 60.357 61.111 4.58 0.00 39.59 6.53
3210 4178 3.248602 CACCGGAAAGATAATAGCTGCAC 59.751 47.826 9.46 0.00 0.00 4.57
3219 4187 0.692476 AATAGCTGCACTGGTGGACA 59.308 50.000 1.02 0.00 0.00 4.02
3222 4190 1.601759 GCTGCACTGGTGGACACAT 60.602 57.895 4.69 0.00 0.00 3.21
3223 4191 1.174712 GCTGCACTGGTGGACACATT 61.175 55.000 4.69 0.00 0.00 2.71
3224 4192 1.881925 GCTGCACTGGTGGACACATTA 60.882 52.381 4.69 0.00 0.00 1.90
3346 4391 6.804677 TCTTTTACTCAATCTTTGCAAGCAA 58.195 32.000 2.89 2.89 0.00 3.91
3366 4411 9.895894 CAAGCAAAATGAAATATTGAGATTTCG 57.104 29.630 6.60 0.00 45.12 3.46
3526 4574 7.981789 CACTATGATGTTTACTCCTGAGCTTAA 59.018 37.037 0.00 0.00 0.00 1.85
3531 4579 5.925509 TGTTTACTCCTGAGCTTAAACTGT 58.074 37.500 14.40 2.50 34.06 3.55
3694 4742 8.475639 TGGTAAGTCAAGAAGAATGATACCTAC 58.524 37.037 0.00 0.00 35.15 3.18
3713 4761 5.940470 ACCTACTTGCTTGTTCTTCCATTAG 59.060 40.000 0.00 0.00 0.00 1.73
3740 4788 2.569404 TCCATGGGGTAATTTTTGTGCC 59.431 45.455 13.02 0.00 34.93 5.01
4021 5070 7.648908 TCTGCTTTGATTTTTCATGTGTACTTG 59.351 33.333 0.00 0.00 0.00 3.16
4156 5362 1.138859 CATGCTCCCGGATGAACAGTA 59.861 52.381 0.73 0.00 41.02 2.74
4225 5432 8.592105 TTTTGTCAAGGAACATTGATGATTTC 57.408 30.769 5.27 0.00 41.05 2.17
4231 5438 7.278646 TCAAGGAACATTGATGATTTCTCTACG 59.721 37.037 0.00 0.00 34.31 3.51
4246 5453 0.358549 CTACGCGCGTGCAAATTTTG 59.641 50.000 42.78 17.52 42.97 2.44
4319 5527 5.363939 CCCAAAATGCTTCCAAAAACACTA 58.636 37.500 0.00 0.00 0.00 2.74
4345 5553 9.801873 ATTTTTGGAGTATCGATTTTGTTATGG 57.198 29.630 1.71 0.00 34.37 2.74
4346 5554 6.371809 TTGGAGTATCGATTTTGTTATGGC 57.628 37.500 1.71 0.00 34.37 4.40
4347 5555 5.432645 TGGAGTATCGATTTTGTTATGGCA 58.567 37.500 1.71 0.00 34.37 4.92
4348 5556 5.527214 TGGAGTATCGATTTTGTTATGGCAG 59.473 40.000 1.71 0.00 34.37 4.85
4358 5566 3.088941 TTATGGCAGCCGCTACGCT 62.089 57.895 7.03 0.00 40.65 5.07
4378 5586 2.983907 TCCGCCGTTGGATGTATTAA 57.016 45.000 0.00 0.00 31.53 1.40
4469 5680 3.071167 GTGACCACCTTCTTACTTCCTGT 59.929 47.826 0.00 0.00 0.00 4.00
4498 5709 3.678072 CGCTCAGTTTCGGAAACAGATTA 59.322 43.478 29.32 10.08 43.79 1.75
4509 5720 1.276622 AACAGATTACCCTGTCCGCT 58.723 50.000 0.00 0.00 45.82 5.52
4619 5831 3.356639 CTCGCCGGAGTTGCTGCTA 62.357 63.158 5.05 0.00 35.48 3.49
4664 5876 0.460987 GCTGCTAGCTCCAATCACGT 60.461 55.000 17.23 0.00 38.45 4.49
4676 5888 1.526887 CAATCACGTATGATGGCGACC 59.473 52.381 0.00 0.00 45.26 4.79
4768 5980 2.158769 TGCAATGTCTGACCACTCACTT 60.159 45.455 5.17 0.00 0.00 3.16
4842 6054 3.801114 AGACCCTTGTTGCAGAAAAAC 57.199 42.857 0.00 0.00 0.00 2.43
4848 6062 3.370421 CCTTGTTGCAGAAAAACCCCTTT 60.370 43.478 0.00 0.00 0.00 3.11
4854 6068 4.027437 TGCAGAAAAACCCCTTTACAACT 58.973 39.130 0.00 0.00 0.00 3.16
4856 6070 4.739436 GCAGAAAAACCCCTTTACAACTGG 60.739 45.833 0.00 0.00 0.00 4.00
4864 6081 4.966168 ACCCCTTTACAACTGGAACATTTT 59.034 37.500 0.00 0.00 38.20 1.82
5008 6232 6.937465 AGAAATCTACTGAAACAAGACCCTTC 59.063 38.462 0.00 0.00 0.00 3.46
5011 6235 6.989155 TCTACTGAAACAAGACCCTTCTTA 57.011 37.500 0.00 0.00 40.34 2.10
5142 6368 3.574396 GCTGAAGGTAAGCTTTTCCCTTT 59.426 43.478 19.68 9.25 37.43 3.11
5143 6369 4.039245 GCTGAAGGTAAGCTTTTCCCTTTT 59.961 41.667 19.68 8.71 37.43 2.27
5144 6370 5.529581 TGAAGGTAAGCTTTTCCCTTTTG 57.470 39.130 19.68 0.00 37.43 2.44
5145 6371 4.959839 TGAAGGTAAGCTTTTCCCTTTTGT 59.040 37.500 19.68 4.44 37.43 2.83
5146 6372 5.423931 TGAAGGTAAGCTTTTCCCTTTTGTT 59.576 36.000 19.68 7.64 37.43 2.83
5147 6373 6.608002 TGAAGGTAAGCTTTTCCCTTTTGTTA 59.392 34.615 19.68 7.53 37.43 2.41
5148 6374 7.289084 TGAAGGTAAGCTTTTCCCTTTTGTTAT 59.711 33.333 19.68 3.05 37.43 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.881513 TCTCTCTCTCTCACACACACAC 59.118 50.000 0.00 0.00 0.00 3.82
4 5 3.407698 TCTCTCTCTCTCTCACACACAC 58.592 50.000 0.00 0.00 0.00 3.82
6 7 3.935203 CTCTCTCTCTCTCTCTCACACAC 59.065 52.174 0.00 0.00 0.00 3.82
7 8 3.837731 TCTCTCTCTCTCTCTCTCACACA 59.162 47.826 0.00 0.00 0.00 3.72
9 10 4.352893 TCTCTCTCTCTCTCTCTCTCACA 58.647 47.826 0.00 0.00 0.00 3.58
11 12 4.871822 TCTCTCTCTCTCTCTCTCTCTCA 58.128 47.826 0.00 0.00 0.00 3.27
39 42 0.388649 CTAACCAAGTCGCACGCTCT 60.389 55.000 0.00 0.00 0.00 4.09
41 44 2.027625 GCTAACCAAGTCGCACGCT 61.028 57.895 0.00 0.00 0.00 5.07
45 48 0.895530 AGCTAGCTAACCAAGTCGCA 59.104 50.000 17.69 0.00 0.00 5.10
49 52 2.290323 CCAACCAGCTAGCTAACCAAGT 60.290 50.000 18.86 5.46 0.00 3.16
51 54 1.004277 CCCAACCAGCTAGCTAACCAA 59.996 52.381 18.86 0.00 0.00 3.67
57 60 2.203549 GAAGGCCCAACCAGCTAGCT 62.204 60.000 12.68 12.68 43.14 3.32
89 97 3.281727 TGACAACAGAAGCCAGAAACT 57.718 42.857 0.00 0.00 0.00 2.66
97 105 8.389603 TCAAATTTGAAAAATGACAACAGAAGC 58.610 29.630 18.45 0.00 33.55 3.86
137 149 9.717892 GTAACTTAGAAACACTTTCTCTTTTGG 57.282 33.333 0.47 0.00 46.62 3.28
335 349 0.762418 TCGAGTGGACCATGGTTTGT 59.238 50.000 20.85 4.12 0.00 2.83
342 356 5.621193 CCCTATTTATTTCGAGTGGACCAT 58.379 41.667 0.00 0.00 0.00 3.55
560 607 1.911471 CTCTGCCTCCTTCCTTCCC 59.089 63.158 0.00 0.00 0.00 3.97
567 614 4.093291 CGCCAGCTCTGCCTCCTT 62.093 66.667 0.00 0.00 0.00 3.36
631 693 3.787001 GACCCCTCTTCCCAGCCG 61.787 72.222 0.00 0.00 0.00 5.52
661 728 4.096682 GCGGAGACTTAGTTGTCTACATCT 59.903 45.833 7.53 0.00 45.68 2.90
666 733 3.825014 AGTTGCGGAGACTTAGTTGTCTA 59.175 43.478 0.00 0.00 46.11 2.59
669 736 2.548067 CCAGTTGCGGAGACTTAGTTGT 60.548 50.000 0.00 0.00 0.00 3.32
695 762 7.598278 TCATTTGTTGGCGTATAAAATGAAGT 58.402 30.769 6.65 0.00 41.69 3.01
700 767 8.868916 GTCATTTCATTTGTTGGCGTATAAAAT 58.131 29.630 0.00 0.00 0.00 1.82
759 826 7.757624 TCGGATAAATTTCCAATTGCAACTAAC 59.242 33.333 0.00 0.00 35.34 2.34
784 876 2.897350 CCGATCGCCTTGGCCTTC 60.897 66.667 10.32 2.59 0.00 3.46
803 896 1.139734 TGAGCCGTCAGATCTTCGC 59.860 57.895 10.47 2.60 0.00 4.70
815 908 1.008538 GCTGGTTTGTTGTGAGCCG 60.009 57.895 0.00 0.00 0.00 5.52
820 913 0.817634 TCTCGGGCTGGTTTGTTGTG 60.818 55.000 0.00 0.00 0.00 3.33
824 917 1.597027 CGTTCTCGGGCTGGTTTGT 60.597 57.895 0.00 0.00 0.00 2.83
895 988 6.503217 TCTCCTCATTTATTCATCCCATAGCT 59.497 38.462 0.00 0.00 0.00 3.32
896 989 6.715280 TCTCCTCATTTATTCATCCCATAGC 58.285 40.000 0.00 0.00 0.00 2.97
897 990 8.546322 TCATCTCCTCATTTATTCATCCCATAG 58.454 37.037 0.00 0.00 0.00 2.23
898 991 8.453498 TCATCTCCTCATTTATTCATCCCATA 57.547 34.615 0.00 0.00 0.00 2.74
1313 1997 2.997897 GTCTGAGAGGTGGGCGGT 60.998 66.667 0.00 0.00 0.00 5.68
1634 2318 2.811431 CAATGCACGTCCAGTTTAGGAA 59.189 45.455 0.00 0.00 39.92 3.36
1647 2331 2.215907 TTCCAAACCAACAATGCACG 57.784 45.000 0.00 0.00 0.00 5.34
1986 2772 0.984230 GGATGGAGGGTGAACAGTGA 59.016 55.000 0.00 0.00 0.00 3.41
2021 2807 1.855360 GCGAGGATGAAGAACGATCAC 59.145 52.381 0.00 0.00 0.00 3.06
2023 2809 2.209838 TGCGAGGATGAAGAACGATC 57.790 50.000 0.00 0.00 0.00 3.69
2085 2871 0.251832 AGAGGAGCTCAAGTCGGGAA 60.252 55.000 17.19 0.00 32.06 3.97
2090 2876 0.980423 ACCCAAGAGGAGCTCAAGTC 59.020 55.000 17.19 8.90 39.89 3.01
2187 3070 7.706179 GCAGCAATCCTATGATCTATCTAGAAC 59.294 40.741 0.00 0.00 35.69 3.01
2330 3293 3.740115 ACTGGCGTTGATAAGAACTGTT 58.260 40.909 0.00 0.00 0.00 3.16
2374 3337 3.904586 GCAGCTAGCACCTCCTATC 57.095 57.895 18.83 0.00 44.79 2.08
2473 3441 4.494199 GGACATCTACACGCACAATTTAGC 60.494 45.833 0.00 0.00 0.00 3.09
2497 3465 4.880886 TTGCATGTACCATGAAAGATCG 57.119 40.909 8.34 0.00 0.00 3.69
2500 3468 5.781210 TGTTTTGCATGTACCATGAAAGA 57.219 34.783 8.34 0.00 0.00 2.52
2507 3475 3.128764 TCGTTGTTGTTTTGCATGTACCA 59.871 39.130 0.00 0.00 0.00 3.25
2532 3500 1.154205 ATGCGACTATTGCTGCCGTC 61.154 55.000 0.00 0.00 0.00 4.79
2551 3519 7.324178 GCTTGTTCTTCTAGGTCTATTTCTCA 58.676 38.462 0.00 0.00 0.00 3.27
2554 3522 6.645306 AGGCTTGTTCTTCTAGGTCTATTTC 58.355 40.000 0.00 0.00 0.00 2.17
2575 3543 5.408604 TCTTACTTTCGTTTGATCTGAAGGC 59.591 40.000 0.00 0.00 0.00 4.35
2702 3670 5.767816 AATACCAGAAAACACCTCACAAC 57.232 39.130 0.00 0.00 0.00 3.32
2703 3671 6.783708 AAAATACCAGAAAACACCTCACAA 57.216 33.333 0.00 0.00 0.00 3.33
2709 3677 9.406828 GAGTTGAATAAAATACCAGAAAACACC 57.593 33.333 0.00 0.00 0.00 4.16
2723 3691 8.744652 TGGAGTTTTGAGTTGAGTTGAATAAAA 58.255 29.630 0.00 0.00 0.00 1.52
2778 3746 4.941873 GTGAGTCGGAGATAAAAATGGGTT 59.058 41.667 0.00 0.00 40.67 4.11
2783 3751 5.046591 TCTGGTGTGAGTCGGAGATAAAAAT 60.047 40.000 0.00 0.00 40.67 1.82
2827 3795 6.293571 GCTACCTTTGCTTTTAAGTCGGTTAA 60.294 38.462 0.00 0.00 0.00 2.01
2844 3812 8.817876 AGAATAGAAGTTCTGTTAGCTACCTTT 58.182 33.333 15.90 0.00 37.08 3.11
2845 3813 8.368962 AGAATAGAAGTTCTGTTAGCTACCTT 57.631 34.615 15.90 0.00 37.08 3.50
2943 3911 5.465056 GTGCAAGCAAACAAATAGCCTTTTA 59.535 36.000 0.00 0.00 0.00 1.52
2949 3917 3.905784 AGAGTGCAAGCAAACAAATAGC 58.094 40.909 0.00 0.00 0.00 2.97
2973 3941 2.865119 TGTGTGATGATGGAGCAGTT 57.135 45.000 0.00 0.00 0.00 3.16
3002 3970 7.514721 AGGACACGGTGAATTAATATTGGTAT 58.485 34.615 16.29 0.00 0.00 2.73
3004 3972 5.751586 AGGACACGGTGAATTAATATTGGT 58.248 37.500 16.29 0.00 0.00 3.67
3020 3988 4.290155 CAATTGAACCAAAGAAGGACACG 58.710 43.478 0.00 0.00 0.00 4.49
3045 4013 4.080638 TGGCTCATTTTGGTTTGAGGTTTT 60.081 37.500 2.48 0.00 39.79 2.43
3129 4097 6.426328 AGTGTTGAACAGAAGATAAGCAAGAG 59.574 38.462 0.00 0.00 0.00 2.85
3155 4123 2.673114 TTTACTTTGCGCGGCTCCG 61.673 57.895 8.83 3.56 43.09 4.63
3156 4124 1.154282 GTTTACTTTGCGCGGCTCC 60.154 57.895 8.83 0.00 0.00 4.70
3157 4125 0.237498 AAGTTTACTTTGCGCGGCTC 59.763 50.000 8.83 0.00 30.82 4.70
3158 4126 0.040425 CAAGTTTACTTTGCGCGGCT 60.040 50.000 8.83 0.00 33.11 5.52
3159 4127 1.605481 GCAAGTTTACTTTGCGCGGC 61.605 55.000 8.83 0.00 33.11 6.53
3160 4128 0.317436 TGCAAGTTTACTTTGCGCGG 60.317 50.000 8.83 0.00 34.80 6.46
3161 4129 1.044725 CTGCAAGTTTACTTTGCGCG 58.955 50.000 0.00 0.00 34.80 6.86
3191 4159 3.496130 CCAGTGCAGCTATTATCTTTCCG 59.504 47.826 0.00 0.00 0.00 4.30
3210 4178 1.470098 GCAAGCTAATGTGTCCACCAG 59.530 52.381 0.00 0.00 0.00 4.00
3366 4411 0.605589 CAACCGGGAAGGGAACAGAC 60.606 60.000 6.32 0.00 46.96 3.51
3526 4574 8.715190 AAACATAACATTAACCCCTTACAGTT 57.285 30.769 0.00 0.00 0.00 3.16
3565 4613 4.284234 CAGACCTGAAATTGGGGAAACATT 59.716 41.667 0.00 0.00 0.00 2.71
3694 4742 4.335416 TCCCTAATGGAAGAACAAGCAAG 58.665 43.478 0.00 0.00 41.40 4.01
3713 4761 3.398318 AAATTACCCCATGGAGTTCCC 57.602 47.619 15.22 0.00 34.81 3.97
3724 4772 1.671556 CGCTGGCACAAAAATTACCCC 60.672 52.381 0.00 0.00 38.70 4.95
3740 4788 1.225855 TGAGTAAAGCCACAACGCTG 58.774 50.000 0.00 0.00 39.64 5.18
3924 4973 8.718158 ACTCTTTACTGGATGATCTGATGATA 57.282 34.615 0.00 0.00 32.19 2.15
3997 5046 7.434897 GTCAAGTACACATGAAAAATCAAAGCA 59.565 33.333 0.00 0.00 0.00 3.91
4021 5070 2.352503 TACTACCGTTTCGCAAGGTC 57.647 50.000 0.00 0.00 39.31 3.85
4089 5225 8.186821 CACTTTCTCCCATTCAATATCTTTGAC 58.813 37.037 0.00 0.00 0.00 3.18
4096 5232 7.781693 ACAATAGCACTTTCTCCCATTCAATAT 59.218 33.333 0.00 0.00 0.00 1.28
4210 5417 5.427082 CGCGTAGAGAAATCATCAATGTTC 58.573 41.667 0.00 0.00 0.00 3.18
4225 5432 0.179225 AAATTTGCACGCGCGTAGAG 60.179 50.000 37.24 24.57 42.97 2.43
4231 5438 1.201332 CACCAAAATTTGCACGCGC 59.799 52.632 5.73 0.00 39.24 6.86
4290 5497 0.903942 GGAAGCATTTTGGGGCATCA 59.096 50.000 0.00 0.00 29.86 3.07
4296 5503 4.198530 AGTGTTTTTGGAAGCATTTTGGG 58.801 39.130 0.00 0.00 0.00 4.12
4319 5527 9.801873 CCATAACAAAATCGATACTCCAAAAAT 57.198 29.630 0.00 0.00 0.00 1.82
4358 5566 2.983907 TAATACATCCAACGGCGGAA 57.016 45.000 13.24 0.00 38.95 4.30
4378 5586 0.813184 CTCCATGCGGCAGATGTTTT 59.187 50.000 9.25 0.00 0.00 2.43
4469 5680 1.504359 CCGAAACTGAGCGGTTGTTA 58.496 50.000 7.23 0.00 42.49 2.41
4498 5709 3.314331 CAGGACAGCGGACAGGGT 61.314 66.667 0.00 0.00 0.00 4.34
4509 5720 0.250234 GGCACAGCTATGTCAGGACA 59.750 55.000 4.37 4.37 46.44 4.02
4540 5752 2.143575 TTTTGCGATGGTGGGGGCTA 62.144 55.000 0.00 0.00 0.00 3.93
4619 5831 2.363147 GGGCTGAGACGGAGGAGT 60.363 66.667 0.00 0.00 0.00 3.85
4661 5873 1.143183 GGTGGTCGCCATCATACGT 59.857 57.895 4.51 0.00 34.21 3.57
4662 5874 0.597637 GAGGTGGTCGCCATCATACG 60.598 60.000 11.02 0.00 37.04 3.06
4664 5876 1.040646 GAGAGGTGGTCGCCATCATA 58.959 55.000 11.02 0.00 37.04 2.15
4676 5888 2.202797 CATCGGGCGTGAGAGGTG 60.203 66.667 0.00 0.00 0.00 4.00
4768 5980 0.896940 AGGAGCACCCGACGTTAGAA 60.897 55.000 0.00 0.00 40.87 2.10
4842 6054 5.545063 AAAATGTTCCAGTTGTAAAGGGG 57.455 39.130 0.00 0.00 0.00 4.79
4892 6112 4.218635 GGGGTCTTGTTTCAAAAGATCTCC 59.781 45.833 0.00 0.00 35.50 3.71
4895 6115 4.584743 ACTGGGGTCTTGTTTCAAAAGATC 59.415 41.667 0.00 0.00 36.14 2.75
4955 6179 6.049790 ACACAGGACTAGTTTCAGAAAGAAC 58.950 40.000 0.00 0.00 35.56 3.01
5040 6266 1.290009 GGTCATGTTGGCCACAAGC 59.710 57.895 3.88 0.00 42.98 4.01
5051 6277 0.904649 TCCTGATCAAGCGGTCATGT 59.095 50.000 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.