Multiple sequence alignment - TraesCS2A01G503300

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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 TraesCS2A01G503300 chr2A 100.000 4101 0 0 1 4101 732598178 732602278 0.000000e+00 7574.0
1 TraesCS2A01G503300 chr2A 94.604 1390 56 3 1198 2568 732853335 732851946 0.000000e+00 2134.0
2 TraesCS2A01G503300 chr2A 83.333 720 95 13 3201 3905 736552757 736553466 3.460000e-180 641.0
3 TraesCS2A01G503300 chr2A 77.637 1024 183 25 1524 2533 722072238 722071247 7.640000e-162 580.0
4 TraesCS2A01G503300 chr2A 74.052 659 120 26 12 624 261641940 261642593 5.340000e-54 222.0
5 TraesCS2A01G503300 chr2B 94.747 3179 121 15 1 3140 727083694 727086865 0.000000e+00 4903.0
6 TraesCS2A01G503300 chr2B 94.484 1396 57 4 1198 2573 727206452 727205057 0.000000e+00 2134.0
7 TraesCS2A01G503300 chr2B 94.812 906 42 5 3140 4042 727086909 727087812 0.000000e+00 1408.0
8 TraesCS2A01G503300 chr2B 76.774 1339 232 37 1212 2533 709784618 709783342 0.000000e+00 676.0
9 TraesCS2A01G503300 chr2B 88.060 67 8 0 1637 1703 101073273 101073339 3.400000e-11 80.5
10 TraesCS2A01G503300 chr2B 83.951 81 12 1 717 797 767519707 767519628 4.400000e-10 76.8
11 TraesCS2A01G503300 chr1B 80.890 1371 213 35 1197 2538 656422867 656421517 0.000000e+00 1035.0
12 TraesCS2A01G503300 chr1B 79.147 211 39 4 422 628 484135825 484135616 1.540000e-29 141.0
13 TraesCS2A01G503300 chr1B 84.615 91 11 3 709 797 666556639 666556550 2.030000e-13 87.9
14 TraesCS2A01G503300 chr7A 80.535 822 127 12 3203 3999 122066557 122067370 5.870000e-168 601.0
15 TraesCS2A01G503300 chr7A 83.178 107 7 9 2645 2742 231238396 231238500 2.030000e-13 87.9
16 TraesCS2A01G503300 chr2D 77.134 621 110 15 1923 2538 587242009 587241416 8.500000e-87 331.0
17 TraesCS2A01G503300 chr2D 78.171 339 52 12 418 752 54146088 54145768 3.230000e-46 196.0
18 TraesCS2A01G503300 chr2D 78.814 236 39 10 3746 3973 567976618 567976850 9.180000e-32 148.0
19 TraesCS2A01G503300 chr2D 75.984 254 54 4 3215 3461 18877896 18877643 1.550000e-24 124.0
20 TraesCS2A01G503300 chr2D 88.060 67 8 0 1637 1703 64732719 64732785 3.400000e-11 80.5
21 TraesCS2A01G503300 chr3D 75.031 813 149 29 3201 3999 153508642 153509414 1.100000e-85 327.0
22 TraesCS2A01G503300 chr3D 83.182 220 28 8 416 632 277217597 277217810 4.180000e-45 193.0
23 TraesCS2A01G503300 chr3D 88.506 87 9 1 713 799 532240358 532240273 2.020000e-18 104.0
24 TraesCS2A01G503300 chr7B 88.346 266 30 1 3734 3999 702534858 702534594 6.620000e-83 318.0
25 TraesCS2A01G503300 chr7B 88.889 63 5 2 736 797 619127153 619127214 4.400000e-10 76.8
26 TraesCS2A01G503300 chr3B 75.033 749 130 23 3266 3999 225175866 225176572 1.110000e-75 294.0
27 TraesCS2A01G503300 chr1A 74.731 744 142 23 3211 3939 12035373 12036085 1.440000e-74 291.0
28 TraesCS2A01G503300 chr6D 78.663 389 58 13 416 799 265306460 265306828 6.850000e-58 235.0
29 TraesCS2A01G503300 chr4B 79.439 321 56 7 307 624 449526960 449526647 6.900000e-53 219.0
30 TraesCS2A01G503300 chr4B 84.158 101 15 1 2642 2741 155761939 155762039 3.370000e-16 97.1
31 TraesCS2A01G503300 chr4B 94.872 39 1 1 755 793 645330657 645330620 4.430000e-05 60.2
32 TraesCS2A01G503300 chr4A 85.253 217 26 5 416 627 631622395 631622180 6.900000e-53 219.0
33 TraesCS2A01G503300 chr4A 84.211 95 13 2 2653 2745 674524557 674524463 1.570000e-14 91.6
34 TraesCS2A01G503300 chr4D 84.018 219 31 3 416 632 499261251 499261035 1.490000e-49 207.0
35 TraesCS2A01G503300 chr5D 83.945 218 29 3 416 631 519201362 519201149 1.930000e-48 204.0
36 TraesCS2A01G503300 chr3A 86.029 136 15 4 3824 3955 149082140 149082275 4.270000e-30 143.0
37 TraesCS2A01G503300 chr5B 88.119 101 9 3 2642 2740 360464289 360464190 2.590000e-22 117.0
38 TraesCS2A01G503300 chr6A 84.848 99 14 1 2645 2742 93885304 93885206 9.380000e-17 99.0
39 TraesCS2A01G503300 chr6A 89.474 57 6 0 4045 4101 585414435 585414491 5.690000e-09 73.1
40 TraesCS2A01G503300 chrUn 89.474 76 4 3 723 797 86361164 86361236 4.360000e-15 93.5
41 TraesCS2A01G503300 chrUn 100.000 28 0 0 2282 2309 31695654 31695681 7.000000e-03 52.8
42 TraesCS2A01G503300 chr6B 84.946 93 12 2 2653 2743 605587268 605587360 4.360000e-15 93.5
43 TraesCS2A01G503300 chr6B 85.556 90 12 1 2653 2741 645547979 645548068 4.360000e-15 93.5
44 TraesCS2A01G503300 chr6B 86.207 87 10 2 2640 2725 658478970 658479055 4.360000e-15 93.5
45 TraesCS2A01G503300 chr1D 82.955 88 13 2 711 797 291205561 291205647 1.220000e-10 78.7


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 TraesCS2A01G503300 chr2A 732598178 732602278 4100 False 7574.0 7574 100.0000 1 4101 1 chr2A.!!$F2 4100
1 TraesCS2A01G503300 chr2A 732851946 732853335 1389 True 2134.0 2134 94.6040 1198 2568 1 chr2A.!!$R2 1370
2 TraesCS2A01G503300 chr2A 736552757 736553466 709 False 641.0 641 83.3330 3201 3905 1 chr2A.!!$F3 704
3 TraesCS2A01G503300 chr2A 722071247 722072238 991 True 580.0 580 77.6370 1524 2533 1 chr2A.!!$R1 1009
4 TraesCS2A01G503300 chr2A 261641940 261642593 653 False 222.0 222 74.0520 12 624 1 chr2A.!!$F1 612
5 TraesCS2A01G503300 chr2B 727083694 727087812 4118 False 3155.5 4903 94.7795 1 4042 2 chr2B.!!$F2 4041
6 TraesCS2A01G503300 chr2B 727205057 727206452 1395 True 2134.0 2134 94.4840 1198 2573 1 chr2B.!!$R2 1375
7 TraesCS2A01G503300 chr2B 709783342 709784618 1276 True 676.0 676 76.7740 1212 2533 1 chr2B.!!$R1 1321
8 TraesCS2A01G503300 chr1B 656421517 656422867 1350 True 1035.0 1035 80.8900 1197 2538 1 chr1B.!!$R2 1341
9 TraesCS2A01G503300 chr7A 122066557 122067370 813 False 601.0 601 80.5350 3203 3999 1 chr7A.!!$F1 796
10 TraesCS2A01G503300 chr2D 587241416 587242009 593 True 331.0 331 77.1340 1923 2538 1 chr2D.!!$R3 615
11 TraesCS2A01G503300 chr3D 153508642 153509414 772 False 327.0 327 75.0310 3201 3999 1 chr3D.!!$F1 798
12 TraesCS2A01G503300 chr3B 225175866 225176572 706 False 294.0 294 75.0330 3266 3999 1 chr3B.!!$F1 733
13 TraesCS2A01G503300 chr1A 12035373 12036085 712 False 291.0 291 74.7310 3211 3939 1 chr1A.!!$F1 728

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
415 440 0.107017 ACATGTGGCAGGTGGATAGC 60.107 55.0 0.00 0.00 0.00 2.97 F
574 619 0.247736 GACCGCATCTCCACTTGACT 59.752 55.0 0.00 0.00 0.00 3.41 F
2107 2203 0.178981 AGGCCACAATCTGCAGTGTT 60.179 50.0 14.67 7.44 33.99 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1425 1481 1.053424 TCCCGCTTGTACAAGGAAGT 58.947 50.0 31.42 0.0 38.8 3.01 R
2227 2325 1.560860 GCAGCACGACTTCACCAGAC 61.561 60.0 0.00 0.0 0.0 3.51 R
3194 3340 0.178068 GGCGACTGATCTTTAGGGCA 59.822 55.0 0.00 0.0 0.0 5.36 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
49 50 4.195334 GGACCGGCCATGGAGCAT 62.195 66.667 18.40 0.00 36.34 3.79
65 72 1.420641 GCATGCGCACTATGACGTCA 61.421 55.000 22.48 22.48 38.36 4.35
67 74 1.594397 CATGCGCACTATGACGTCATT 59.406 47.619 34.06 16.37 37.76 2.57
124 131 3.033764 GCGTTCCGACAGTCGCAA 61.034 61.111 18.02 6.28 46.40 4.85
149 156 2.668457 GAGCAGAGGTACAACATGTTCG 59.332 50.000 8.48 7.26 0.00 3.95
163 170 1.803519 GTTCGTCCTCGAGCAGCAG 60.804 63.158 6.99 0.00 46.81 4.24
346 371 1.979693 GCTGGTGGTCGAGGACTCT 60.980 63.158 0.00 0.00 32.47 3.24
350 375 1.202964 TGGTGGTCGAGGACTCTAACA 60.203 52.381 0.00 0.00 32.47 2.41
351 376 2.100989 GGTGGTCGAGGACTCTAACAT 58.899 52.381 0.00 0.00 32.47 2.71
364 389 1.003959 TAACATCGCCAGCTGCACA 60.004 52.632 8.66 0.00 41.33 4.57
390 415 1.005294 GCGTCGCCGTCTAACTTTCA 61.005 55.000 5.75 0.00 36.15 2.69
415 440 0.107017 ACATGTGGCAGGTGGATAGC 60.107 55.000 0.00 0.00 0.00 2.97
465 509 1.027357 GACGGATAGGTTGCGGACTA 58.973 55.000 0.00 0.00 44.44 2.59
487 532 4.229639 ACTCTGAGATGAATAGGGCATGA 58.770 43.478 12.44 0.00 0.00 3.07
574 619 0.247736 GACCGCATCTCCACTTGACT 59.752 55.000 0.00 0.00 0.00 3.41
594 640 1.227853 GTCTTGAACCCGCCACTGT 60.228 57.895 0.00 0.00 0.00 3.55
637 683 1.794222 GTGGTTGCCTATGTGACGC 59.206 57.895 0.00 0.00 0.00 5.19
650 696 0.458889 GTGACGCGGTTGCCTATGTA 60.459 55.000 12.47 0.00 38.08 2.29
765 812 8.700722 TTTCATTTGGTTCATATGAAAATCCG 57.299 30.769 19.55 7.53 43.31 4.18
775 822 5.410132 TCATATGAAAATCCGTCGTGTTTGT 59.590 36.000 1.98 0.00 0.00 2.83
788 835 5.077424 GTCGTGTTTGTATGAATTTCGTCC 58.923 41.667 0.00 0.00 0.00 4.79
794 841 6.128499 TGTTTGTATGAATTTCGTCCGGTTAG 60.128 38.462 0.00 0.00 0.00 2.34
810 857 3.365820 CGGTTAGTTGAGCGAACGTTTAT 59.634 43.478 0.46 0.00 42.69 1.40
843 890 1.590932 CGAATCAGCCTTGGAGATGG 58.409 55.000 0.00 0.00 0.00 3.51
860 907 7.529555 TGGAGATGGCCAAAATAGAGATAAAT 58.470 34.615 10.96 0.00 34.31 1.40
861 908 8.668653 TGGAGATGGCCAAAATAGAGATAAATA 58.331 33.333 10.96 0.00 34.31 1.40
862 909 9.520515 GGAGATGGCCAAAATAGAGATAAATAA 57.479 33.333 10.96 0.00 0.00 1.40
892 939 8.943002 AGAAAAACGGTCGAGATTGTATTATTT 58.057 29.630 0.00 0.00 0.00 1.40
957 1004 0.819582 GATGTCCTTAACCGGGTCGA 59.180 55.000 6.32 0.00 0.00 4.20
1016 1063 5.604758 ATGATCATATACCACCCTGATCG 57.395 43.478 6.36 0.00 44.41 3.69
1056 1103 5.186198 CCTAAGTTCCAATCTGGTCGAAAT 58.814 41.667 0.00 0.00 39.03 2.17
1069 1116 4.124238 TGGTCGAAATAAAATAGCCGGAG 58.876 43.478 5.05 0.00 0.00 4.63
1087 1134 1.407979 GAGGAAGAATCGCCGGAAGTA 59.592 52.381 5.05 0.00 0.00 2.24
1180 1227 0.391597 GCCGAACCCATATCTTCCGA 59.608 55.000 0.00 0.00 0.00 4.55
1279 1326 4.671250 CGCTGAGGAAGAGAATTTTGCTTC 60.671 45.833 0.00 0.00 37.80 3.86
1280 1327 4.217118 GCTGAGGAAGAGAATTTTGCTTCA 59.783 41.667 14.04 0.00 39.72 3.02
1406 1462 2.747989 GTTTTCAATTCCTCCCGTCCTC 59.252 50.000 0.00 0.00 0.00 3.71
1425 1481 6.106673 GTCCTCTTACCTTTGATTGATCGAA 58.893 40.000 0.00 0.00 0.00 3.71
1443 1499 1.804748 GAACTTCCTTGTACAAGCGGG 59.195 52.381 27.05 19.63 37.11 6.13
1459 1515 4.034285 AGCGGGAAGGGAATATATTTGG 57.966 45.455 0.00 0.00 0.00 3.28
1531 1614 0.384309 CGCAATTGAGCTCCATGCAT 59.616 50.000 25.53 0.00 45.94 3.96
1609 1692 4.774124 TGCAGATCCTCTCCATTAAACTG 58.226 43.478 0.00 0.00 0.00 3.16
1613 1696 6.409704 CAGATCCTCTCCATTAAACTGACAA 58.590 40.000 0.00 0.00 0.00 3.18
1686 1769 1.471287 TCGGGACAGTGTCGATAACAG 59.529 52.381 16.89 3.99 38.97 3.16
1930 2026 2.814336 AGACCCTGTTCGCTTTGAAATC 59.186 45.455 0.00 0.00 38.60 2.17
2107 2203 0.178981 AGGCCACAATCTGCAGTGTT 60.179 50.000 14.67 7.44 33.99 3.32
2227 2325 2.297701 ACTTATGTTGCTAATGCCCCG 58.702 47.619 0.00 0.00 38.71 5.73
2284 2382 1.843368 CAATGCCCAGTGGTTCAGAT 58.157 50.000 8.74 0.00 0.00 2.90
2350 2451 0.040958 GCAGCCTGAAAGTTGTCGTG 60.041 55.000 0.00 0.00 0.00 4.35
2548 2649 1.128200 ACCTCCAAGCACTACACACA 58.872 50.000 0.00 0.00 0.00 3.72
2599 2700 0.661020 CGGACAAGACCAACCAACAC 59.339 55.000 0.00 0.00 0.00 3.32
2610 2711 3.420839 CAACCAACACTGTTGGAAGTC 57.579 47.619 37.12 0.00 42.06 3.01
2615 2716 0.532862 ACACTGTTGGAAGTCTGCCG 60.533 55.000 0.00 0.00 0.00 5.69
2634 2735 1.264288 CGAGGGCATTTTATCGGAAGC 59.736 52.381 0.00 0.00 0.00 3.86
2650 2751 4.772624 TCGGAAGCTTGGCTATATACTCAT 59.227 41.667 2.10 0.00 38.25 2.90
2651 2752 5.105716 TCGGAAGCTTGGCTATATACTCATC 60.106 44.000 2.10 0.00 38.25 2.92
2657 2758 4.317530 TGGCTATATACTCATCCCGTCT 57.682 45.455 0.00 0.00 0.00 4.18
2735 2837 6.590234 AGGCACTTATTTTAAGACAAAGGG 57.410 37.500 1.47 0.00 27.25 3.95
2769 2871 7.915508 TCATGTTGTGTGATTCGATTATAACC 58.084 34.615 0.00 0.00 0.00 2.85
2849 2951 2.873472 TGTTGTGCGACGGACTTTTAAT 59.127 40.909 20.39 0.00 0.00 1.40
2917 3019 7.041372 TGTCACTCAACTTTTTATTCTGGTAGC 60.041 37.037 0.00 0.00 0.00 3.58
3000 3102 3.616379 CAGAAAGATTCGAGACTTGCCTC 59.384 47.826 6.88 2.72 34.02 4.70
3016 3118 4.524316 TGCCTCTTTCAATTGGACATTG 57.476 40.909 5.42 0.00 0.00 2.82
3042 3144 1.906574 TCATACGCCTCCTGGAAAAGT 59.093 47.619 0.00 0.41 34.57 2.66
3050 3152 0.545787 TCCTGGAAAAGTAGGCGGGA 60.546 55.000 0.00 0.00 34.00 5.14
3054 3156 1.353022 TGGAAAAGTAGGCGGGAACAT 59.647 47.619 0.00 0.00 0.00 2.71
3058 3160 4.448210 GAAAAGTAGGCGGGAACATATCA 58.552 43.478 0.00 0.00 0.00 2.15
3059 3161 4.497291 AAAGTAGGCGGGAACATATCAA 57.503 40.909 0.00 0.00 0.00 2.57
3087 3189 8.857216 ACATAGTTCGTAATACAAAAGTTCTCG 58.143 33.333 0.00 0.00 0.00 4.04
3183 3329 4.753107 GGAGACAACGAACAAAGATTGGTA 59.247 41.667 0.00 0.00 34.12 3.25
3242 3388 6.037500 CGAGCTGTCCAATCTGATGAATTAAA 59.962 38.462 0.00 0.00 0.00 1.52
3545 3712 1.002624 ACCATGTCGGCCGAAACAT 60.003 52.632 32.93 27.01 39.03 2.71
3605 3772 1.072505 AACTTCCCGCAATGGACGT 59.927 52.632 0.00 0.00 42.00 4.34
3613 3780 0.248336 CGCAATGGACGTAGACGCTA 60.248 55.000 1.14 0.00 44.43 4.26
3773 3963 1.668294 CGAGGAGGTGTGAGCTTGT 59.332 57.895 0.00 0.00 0.00 3.16
3814 4005 2.071540 CATGTGACGACTGCACTCAAT 58.928 47.619 0.00 0.00 37.18 2.57
3977 4171 2.147958 ACACACGCATTGTTATCCGTT 58.852 42.857 0.00 0.00 35.67 4.44
3985 4179 2.983907 TTGTTATCCGTTGGGCGATA 57.016 45.000 0.00 0.00 44.77 2.92
3999 4193 2.290134 GGGCGATACTAATCCTTTCCCC 60.290 54.545 0.00 0.00 0.00 4.81
4018 4213 1.021968 CCCAAAATACTACCAGCCGC 58.978 55.000 0.00 0.00 0.00 6.53
4050 4245 8.445361 AAAGGTAAAAGGAAGATAGTACTCCA 57.555 34.615 0.00 0.00 0.00 3.86
4051 4246 8.625467 AAGGTAAAAGGAAGATAGTACTCCAT 57.375 34.615 0.00 0.00 0.00 3.41
4052 4247 8.252624 AGGTAAAAGGAAGATAGTACTCCATC 57.747 38.462 0.00 0.00 0.00 3.51
4053 4248 7.290481 AGGTAAAAGGAAGATAGTACTCCATCC 59.710 40.741 0.00 5.03 0.00 3.51
4054 4249 6.502074 AAAAGGAAGATAGTACTCCATCCC 57.498 41.667 0.00 0.00 0.00 3.85
4055 4250 5.426325 AAGGAAGATAGTACTCCATCCCT 57.574 43.478 0.00 0.00 0.00 4.20
4056 4251 5.426325 AGGAAGATAGTACTCCATCCCTT 57.574 43.478 0.00 0.00 0.00 3.95
4057 4252 5.399113 AGGAAGATAGTACTCCATCCCTTC 58.601 45.833 0.00 4.74 0.00 3.46
4058 4253 4.528987 GGAAGATAGTACTCCATCCCTTCC 59.471 50.000 0.00 9.80 40.79 3.46
4059 4254 4.134933 AGATAGTACTCCATCCCTTCCC 57.865 50.000 0.00 0.00 0.00 3.97
4060 4255 2.376695 TAGTACTCCATCCCTTCCCG 57.623 55.000 0.00 0.00 0.00 5.14
4061 4256 0.338814 AGTACTCCATCCCTTCCCGT 59.661 55.000 0.00 0.00 0.00 5.28
4062 4257 0.751452 GTACTCCATCCCTTCCCGTC 59.249 60.000 0.00 0.00 0.00 4.79
4063 4258 0.635009 TACTCCATCCCTTCCCGTCT 59.365 55.000 0.00 0.00 0.00 4.18
4064 4259 0.635009 ACTCCATCCCTTCCCGTCTA 59.365 55.000 0.00 0.00 0.00 2.59
4065 4260 1.220750 ACTCCATCCCTTCCCGTCTAT 59.779 52.381 0.00 0.00 0.00 1.98
4066 4261 2.449730 ACTCCATCCCTTCCCGTCTATA 59.550 50.000 0.00 0.00 0.00 1.31
4067 4262 3.093057 CTCCATCCCTTCCCGTCTATAG 58.907 54.545 0.00 0.00 0.00 1.31
4068 4263 2.180276 CCATCCCTTCCCGTCTATAGG 58.820 57.143 0.00 0.00 0.00 2.57
4069 4264 2.492940 CCATCCCTTCCCGTCTATAGGT 60.493 54.545 0.00 0.00 0.00 3.08
4070 4265 3.240302 CATCCCTTCCCGTCTATAGGTT 58.760 50.000 0.00 0.00 0.00 3.50
4071 4266 3.409804 TCCCTTCCCGTCTATAGGTTT 57.590 47.619 0.00 0.00 0.00 3.27
4072 4267 3.727948 TCCCTTCCCGTCTATAGGTTTT 58.272 45.455 0.00 0.00 0.00 2.43
4073 4268 4.882559 TCCCTTCCCGTCTATAGGTTTTA 58.117 43.478 0.00 0.00 0.00 1.52
4074 4269 5.470501 TCCCTTCCCGTCTATAGGTTTTAT 58.529 41.667 0.00 0.00 0.00 1.40
4075 4270 5.541484 TCCCTTCCCGTCTATAGGTTTTATC 59.459 44.000 0.00 0.00 0.00 1.75
4076 4271 5.543020 CCCTTCCCGTCTATAGGTTTTATCT 59.457 44.000 0.00 0.00 0.00 1.98
4077 4272 6.042897 CCCTTCCCGTCTATAGGTTTTATCTT 59.957 42.308 0.00 0.00 0.00 2.40
4078 4273 7.234166 CCCTTCCCGTCTATAGGTTTTATCTTA 59.766 40.741 0.00 0.00 0.00 2.10
4079 4274 8.645110 CCTTCCCGTCTATAGGTTTTATCTTAA 58.355 37.037 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 2.570442 TAATGACGTCATAGTGCGCA 57.430 45.000 30.16 5.66 35.10 6.09
65 72 0.991355 TGTTCCCCCTCCGCCATAAT 60.991 55.000 0.00 0.00 0.00 1.28
67 74 2.041430 TGTTCCCCCTCCGCCATA 59.959 61.111 0.00 0.00 0.00 2.74
124 131 2.310779 TGTTGTACCTCTGCTCCTCT 57.689 50.000 0.00 0.00 0.00 3.69
173 180 2.289631 GCTTGCTTTACATTTGGCCCTT 60.290 45.455 0.00 0.00 0.00 3.95
250 272 2.658593 GCACGCGCGACCTCATAT 60.659 61.111 39.36 8.45 0.00 1.78
274 296 3.635734 CTCTGCGTTTCAAGCGGCG 62.636 63.158 0.51 0.51 40.59 6.46
281 303 4.617520 TGCCGGCTCTGCGTTTCA 62.618 61.111 29.70 0.00 0.00 2.69
382 407 2.513753 CACATGTGCCCCTGAAAGTTA 58.486 47.619 13.94 0.00 0.00 2.24
390 415 4.371417 CCTGCCACATGTGCCCCT 62.371 66.667 20.81 0.00 0.00 4.79
465 509 4.229639 TCATGCCCTATTCATCTCAGAGT 58.770 43.478 0.00 0.00 0.00 3.24
487 532 0.395311 CACAATGCCCTGCCATCTCT 60.395 55.000 0.00 0.00 0.00 3.10
594 640 3.434596 CCTTCATCTGCCATCTCCATGAA 60.435 47.826 0.00 0.00 33.48 2.57
637 683 5.236478 CCTTTGTATTCTACATAGGCAACCG 59.764 44.000 9.77 0.00 46.05 4.44
650 696 2.378547 TGGCCCACTTCCTTTGTATTCT 59.621 45.455 0.00 0.00 0.00 2.40
765 812 5.077424 GGACGAAATTCATACAAACACGAC 58.923 41.667 0.00 0.00 0.00 4.34
775 822 5.722263 TCAACTAACCGGACGAAATTCATA 58.278 37.500 9.46 0.00 0.00 2.15
788 835 1.134226 AACGTTCGCTCAACTAACCG 58.866 50.000 0.00 0.00 32.09 4.44
794 841 3.482112 GCTCTCATAAACGTTCGCTCAAC 60.482 47.826 0.00 0.00 0.00 3.18
860 907 8.314143 ACAATCTCGACCGTTTTTCTTATTTA 57.686 30.769 0.00 0.00 0.00 1.40
861 908 7.198306 ACAATCTCGACCGTTTTTCTTATTT 57.802 32.000 0.00 0.00 0.00 1.40
862 909 6.796705 ACAATCTCGACCGTTTTTCTTATT 57.203 33.333 0.00 0.00 0.00 1.40
863 910 8.488651 AATACAATCTCGACCGTTTTTCTTAT 57.511 30.769 0.00 0.00 0.00 1.73
864 911 7.894376 AATACAATCTCGACCGTTTTTCTTA 57.106 32.000 0.00 0.00 0.00 2.10
873 920 6.838198 TGGAAAATAATACAATCTCGACCG 57.162 37.500 0.00 0.00 0.00 4.79
892 939 0.108709 GTACCGTACGTGCCATGGAA 60.109 55.000 18.40 0.00 0.00 3.53
957 1004 1.923148 AGCCTTATAACCAGCCCTGTT 59.077 47.619 0.00 0.00 0.00 3.16
1016 1063 0.245813 AGGGTTTCTACCGAAGACGC 59.754 55.000 0.00 0.00 46.04 5.19
1056 1103 4.628074 CGATTCTTCCTCCGGCTATTTTA 58.372 43.478 0.00 0.00 0.00 1.52
1069 1116 1.407979 TCTACTTCCGGCGATTCTTCC 59.592 52.381 9.30 0.00 0.00 3.46
1087 1134 1.433053 CTCGTCCTCGATGCTCGTCT 61.433 60.000 5.66 0.00 45.21 4.18
1113 1160 4.856664 TCGATAGTTATCTGCTTCCGTTC 58.143 43.478 0.00 0.00 37.40 3.95
1180 1227 3.804036 TCGTCAACAACTTCCAATCTGT 58.196 40.909 0.00 0.00 0.00 3.41
1279 1326 2.787473 TTCCCAGGCACTTCTGTATG 57.213 50.000 0.00 0.00 34.60 2.39
1280 1327 3.118531 AGATTCCCAGGCACTTCTGTAT 58.881 45.455 0.00 0.00 34.60 2.29
1406 1462 6.595716 AGGAAGTTCGATCAATCAAAGGTAAG 59.404 38.462 0.00 0.00 0.00 2.34
1425 1481 1.053424 TCCCGCTTGTACAAGGAAGT 58.947 50.000 31.42 0.00 38.80 3.01
1443 1499 8.734386 CATGAACTAGCCAAATATATTCCCTTC 58.266 37.037 0.00 0.00 0.00 3.46
1459 1515 8.289618 TGTGTTAGAAATCAAACATGAACTAGC 58.710 33.333 0.00 0.00 0.00 3.42
1531 1614 4.396790 GGTTTAGGTGTCAAGTGTGTGAAA 59.603 41.667 0.00 0.00 0.00 2.69
1609 1692 7.546778 TTTGAAGCCACCTTTAATTTTTGTC 57.453 32.000 0.00 0.00 0.00 3.18
1613 1696 6.969366 GCAATTTGAAGCCACCTTTAATTTT 58.031 32.000 0.00 0.00 30.13 1.82
1686 1769 1.782181 GCGAAGAGAAGGTTGCGAC 59.218 57.895 0.00 0.00 0.00 5.19
1930 2026 2.875933 TCCACGTTCAACTTTTAGCTGG 59.124 45.455 0.00 0.00 0.00 4.85
2107 2203 2.093075 TGTCCCCTGTTTAACAACACGA 60.093 45.455 0.00 0.00 38.03 4.35
2227 2325 1.560860 GCAGCACGACTTCACCAGAC 61.561 60.000 0.00 0.00 0.00 3.51
2284 2382 1.751351 CTCGACAGATCAAGGTAGCCA 59.249 52.381 0.00 0.00 0.00 4.75
2350 2451 2.909080 CCGAATGACGAGCAAGTCTGC 61.909 57.143 11.86 0.00 45.77 4.26
2367 2468 3.387699 TCCTTCTGCAATGATATCACCGA 59.612 43.478 7.78 0.00 0.00 4.69
2599 2700 0.671781 CCTCGGCAGACTTCCAACAG 60.672 60.000 0.00 0.00 0.00 3.16
2615 2716 2.576615 AGCTTCCGATAAAATGCCCTC 58.423 47.619 0.00 0.00 0.00 4.30
2623 2724 7.039293 TGAGTATATAGCCAAGCTTCCGATAAA 60.039 37.037 0.00 0.00 40.44 1.40
2634 2735 4.707448 AGACGGGATGAGTATATAGCCAAG 59.293 45.833 0.00 0.00 0.00 3.61
2650 2751 5.800296 TGAGACATTTATTTTGAGACGGGA 58.200 37.500 0.00 0.00 0.00 5.14
2651 2752 6.149474 AGTTGAGACATTTATTTTGAGACGGG 59.851 38.462 0.00 0.00 0.00 5.28
2688 2789 9.715121 CCTTGACCTTAGTACAATTTTACACTA 57.285 33.333 4.66 0.00 0.00 2.74
2689 2790 7.174426 GCCTTGACCTTAGTACAATTTTACACT 59.826 37.037 4.66 0.00 0.00 3.55
2690 2791 7.040961 TGCCTTGACCTTAGTACAATTTTACAC 60.041 37.037 4.66 0.00 0.00 2.90
2697 2799 4.910458 AGTGCCTTGACCTTAGTACAAT 57.090 40.909 0.00 0.00 0.00 2.71
2702 2804 8.161425 TCTTAAAATAAGTGCCTTGACCTTAGT 58.839 33.333 0.00 0.00 0.00 2.24
2725 2827 7.259088 ACATGAGTTATACTCCCTTTGTCTT 57.741 36.000 0.00 0.00 44.44 3.01
2735 2837 7.488150 TCGAATCACACAACATGAGTTATACTC 59.512 37.037 0.00 0.00 45.26 2.59
2745 2847 7.919690 AGGTTATAATCGAATCACACAACATG 58.080 34.615 0.00 0.00 0.00 3.21
2788 2890 6.627508 CGGATAACATAGGAGTTATACAGGGC 60.628 46.154 9.10 0.00 42.77 5.19
2849 2951 4.262121 CCATGCACAAAATCAGACTCCAAA 60.262 41.667 0.00 0.00 0.00 3.28
2942 3044 2.818130 TTCCCGTGTGGTTACAGTAC 57.182 50.000 0.00 0.00 37.52 2.73
3022 3124 1.906574 ACTTTTCCAGGAGGCGTATGA 59.093 47.619 0.00 0.00 33.74 2.15
3042 3144 4.223556 TGTTTTGATATGTTCCCGCCTA 57.776 40.909 0.00 0.00 0.00 3.93
3194 3340 0.178068 GGCGACTGATCTTTAGGGCA 59.822 55.000 0.00 0.00 0.00 5.36
3242 3388 9.221933 CAGTAGTAGTAGATAATCCTCAATCGT 57.778 37.037 0.00 0.00 0.00 3.73
3331 3477 8.299570 CAAAAATAATCTGCAACTTGACCTAGT 58.700 33.333 0.00 0.00 0.00 2.57
3473 3640 5.559035 CGAGTTTCTGCAACAAGGTCTTTAG 60.559 44.000 0.00 0.00 37.93 1.85
3545 3712 2.300967 CCAAGGGAGCACCAGCCTA 61.301 63.158 1.58 0.00 43.89 3.93
3605 3772 1.381928 CGGGGAAGCACTAGCGTCTA 61.382 60.000 3.65 0.00 46.58 2.59
3613 3780 3.411517 CCATCCCGGGGAAGCACT 61.412 66.667 23.50 0.00 34.34 4.40
3773 3963 3.901087 CTCCTCCTGAGCTCTCTGA 57.099 57.895 16.19 7.68 33.47 3.27
3814 4005 2.342659 GGGATCTGGATCTGGATTCCA 58.657 52.381 15.95 5.05 37.51 3.53
3854 4045 4.158394 AGTTGTTGTTGCAATCTTCACACT 59.842 37.500 0.59 0.00 0.00 3.55
3977 4171 2.370849 GGGAAAGGATTAGTATCGCCCA 59.629 50.000 0.00 0.00 32.90 5.36
3999 4193 1.021968 GCGGCTGGTAGTATTTTGGG 58.978 55.000 0.00 0.00 0.00 4.12
4006 4200 5.776716 ACCTTTTATATAGCGGCTGGTAGTA 59.223 40.000 13.86 3.40 0.00 1.82
4042 4237 0.338814 ACGGGAAGGGATGGAGTACT 59.661 55.000 0.00 0.00 0.00 2.73
4043 4238 0.751452 GACGGGAAGGGATGGAGTAC 59.249 60.000 0.00 0.00 0.00 2.73
4044 4239 0.635009 AGACGGGAAGGGATGGAGTA 59.365 55.000 0.00 0.00 0.00 2.59
4045 4240 0.635009 TAGACGGGAAGGGATGGAGT 59.365 55.000 0.00 0.00 0.00 3.85
4046 4241 2.016905 ATAGACGGGAAGGGATGGAG 57.983 55.000 0.00 0.00 0.00 3.86
4047 4242 2.225293 CCTATAGACGGGAAGGGATGGA 60.225 54.545 0.00 0.00 0.00 3.41
4048 4243 2.180276 CCTATAGACGGGAAGGGATGG 58.820 57.143 0.00 0.00 0.00 3.51
4049 4244 2.890814 ACCTATAGACGGGAAGGGATG 58.109 52.381 0.00 0.00 33.16 3.51
4050 4245 3.632420 AACCTATAGACGGGAAGGGAT 57.368 47.619 0.00 0.00 33.16 3.85
4051 4246 3.409804 AAACCTATAGACGGGAAGGGA 57.590 47.619 0.00 0.00 33.16 4.20
4052 4247 5.543020 AGATAAAACCTATAGACGGGAAGGG 59.457 44.000 0.00 0.00 33.16 3.95
4053 4248 6.667558 AGATAAAACCTATAGACGGGAAGG 57.332 41.667 0.00 0.00 35.14 3.46


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

AutoCloner maintained by Alex Coulton.