Multiple sequence alignment - TraesCS7A01G144300

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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 TraesCS7A01G144300 chr7A 100.000 5273 0 0 1 5273 95125366 95120094 0.000000e+00 9738.0
1 TraesCS7A01G144300 chr7A 89.356 3354 325 22 906 4250 726503444 726500114 0.000000e+00 4187.0
2 TraesCS7A01G144300 chr7B 95.696 5204 205 16 41 5233 29636066 29630871 0.000000e+00 8351.0
3 TraesCS7A01G144300 chr7B 89.568 3355 317 23 906 4250 651194037 651197368 0.000000e+00 4226.0
4 TraesCS7A01G144300 chr7B 91.243 2067 168 8 2858 4918 149676178 149678237 0.000000e+00 2802.0
5 TraesCS7A01G144300 chr7B 88.781 517 40 9 390 901 149674602 149675105 7.500000e-173 617.0
6 TraesCS7A01G144300 chr7B 86.239 327 38 3 4914 5235 149678362 149678686 1.090000e-91 348.0
7 TraesCS7A01G144300 chr7B 83.430 344 46 6 408 741 651193406 651193748 5.130000e-80 309.0
8 TraesCS7A01G144300 chr7B 86.076 79 11 0 408 486 127775134 127775212 9.410000e-13 86.1
9 TraesCS7A01G144300 chr7B 97.826 46 1 0 41 86 29630488 29630533 4.380000e-11 80.5
10 TraesCS7A01G144300 chr1B 95.694 5202 204 17 41 5233 107526933 107521743 0.000000e+00 8347.0
11 TraesCS7A01G144300 chr1B 97.872 47 1 0 40 86 107521360 107521406 1.220000e-11 82.4
12 TraesCS7A01G144300 chr1B 93.617 47 2 1 40 85 198554234 198554280 9.480000e-08 69.4
13 TraesCS7A01G144300 chr1D 96.399 4888 163 8 41 4918 348115893 348120777 0.000000e+00 8039.0
14 TraesCS7A01G144300 chr1D 92.778 360 25 1 4915 5273 348120857 348121216 2.180000e-143 520.0
15 TraesCS7A01G144300 chr1D 82.948 346 47 10 408 742 67973189 67973533 8.580000e-78 302.0
16 TraesCS7A01G144300 chr6B 94.170 4134 193 17 48 4165 399049411 399045310 0.000000e+00 6255.0
17 TraesCS7A01G144300 chr6B 90.198 2877 231 25 2276 5140 487797142 487799979 0.000000e+00 3703.0
18 TraesCS7A01G144300 chr6B 92.695 1451 95 9 3827 5273 399045579 399044136 0.000000e+00 2082.0
19 TraesCS7A01G144300 chr2D 89.845 4185 308 46 1132 5273 645277157 645281267 0.000000e+00 5265.0
20 TraesCS7A01G144300 chr2D 89.512 2479 227 17 1437 3903 506528282 506525825 0.000000e+00 3107.0
21 TraesCS7A01G144300 chr2D 87.615 977 98 16 408 1374 506530112 506529149 0.000000e+00 1112.0
22 TraesCS7A01G144300 chr2D 100.000 40 0 0 1 40 232185530 232185491 2.040000e-09 75.0
23 TraesCS7A01G144300 chr2D 100.000 40 0 0 1 40 524264539 524264578 2.040000e-09 75.0
24 TraesCS7A01G144300 chr1A 90.869 3614 268 32 1053 4642 267172953 267176528 0.000000e+00 4789.0
25 TraesCS7A01G144300 chr1A 86.364 506 48 13 4778 5273 267176600 267177094 2.800000e-147 532.0
26 TraesCS7A01G144300 chr3B 90.628 1131 95 8 3548 4676 650050119 650051240 0.000000e+00 1491.0
27 TraesCS7A01G144300 chr7D 84.743 1324 150 22 3966 5273 260722943 260724230 0.000000e+00 1279.0
28 TraesCS7A01G144300 chr7D 91.755 473 20 11 724 1195 260720448 260720902 1.600000e-179 640.0
29 TraesCS7A01G144300 chr7D 87.833 526 38 2 228 727 260697836 260698361 1.260000e-165 593.0
30 TraesCS7A01G144300 chr5A 89.976 419 42 0 906 1324 570379810 570380228 4.640000e-150 542.0
31 TraesCS7A01G144300 chr5A 84.348 345 43 9 408 742 570379175 570379518 1.420000e-85 327.0
32 TraesCS7A01G144300 chr5A 100.000 40 0 0 1 40 433433981 433434020 2.040000e-09 75.0
33 TraesCS7A01G144300 chr5D 86.786 280 26 8 5002 5273 538584805 538585081 8.580000e-78 302.0
34 TraesCS7A01G144300 chr6A 100.000 40 0 0 1 40 62866638 62866677 2.040000e-09 75.0
35 TraesCS7A01G144300 chr4B 100.000 40 0 0 1 40 210975177 210975216 2.040000e-09 75.0
36 TraesCS7A01G144300 chr2B 100.000 40 0 0 1 40 109351409 109351370 2.040000e-09 75.0
37 TraesCS7A01G144300 chr2B 100.000 40 0 0 1 40 736921903 736921942 2.040000e-09 75.0
38 TraesCS7A01G144300 chr2B 100.000 39 0 0 3 41 38679701 38679663 7.320000e-09 73.1
39 TraesCS7A01G144300 chr5B 100.000 39 0 0 3 41 528731713 528731751 7.320000e-09 73.1


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 TraesCS7A01G144300 chr7A 95120094 95125366 5272 True 9738.000000 9738 100.000000 1 5273 1 chr7A.!!$R1 5272
1 TraesCS7A01G144300 chr7A 726500114 726503444 3330 True 4187.000000 4187 89.356000 906 4250 1 chr7A.!!$R2 3344
2 TraesCS7A01G144300 chr7B 29630871 29636066 5195 True 8351.000000 8351 95.696000 41 5233 1 chr7B.!!$R1 5192
3 TraesCS7A01G144300 chr7B 651193406 651197368 3962 False 2267.500000 4226 86.499000 408 4250 2 chr7B.!!$F4 3842
4 TraesCS7A01G144300 chr7B 149674602 149678686 4084 False 1255.666667 2802 88.754333 390 5235 3 chr7B.!!$F3 4845
5 TraesCS7A01G144300 chr1B 107521743 107526933 5190 True 8347.000000 8347 95.694000 41 5233 1 chr1B.!!$R1 5192
6 TraesCS7A01G144300 chr1D 348115893 348121216 5323 False 4279.500000 8039 94.588500 41 5273 2 chr1D.!!$F2 5232
7 TraesCS7A01G144300 chr6B 399044136 399049411 5275 True 4168.500000 6255 93.432500 48 5273 2 chr6B.!!$R1 5225
8 TraesCS7A01G144300 chr6B 487797142 487799979 2837 False 3703.000000 3703 90.198000 2276 5140 1 chr6B.!!$F1 2864
9 TraesCS7A01G144300 chr2D 645277157 645281267 4110 False 5265.000000 5265 89.845000 1132 5273 1 chr2D.!!$F2 4141
10 TraesCS7A01G144300 chr2D 506525825 506530112 4287 True 2109.500000 3107 88.563500 408 3903 2 chr2D.!!$R2 3495
11 TraesCS7A01G144300 chr1A 267172953 267177094 4141 False 2660.500000 4789 88.616500 1053 5273 2 chr1A.!!$F1 4220
12 TraesCS7A01G144300 chr3B 650050119 650051240 1121 False 1491.000000 1491 90.628000 3548 4676 1 chr3B.!!$F1 1128
13 TraesCS7A01G144300 chr7D 260720448 260724230 3782 False 959.500000 1279 88.249000 724 5273 2 chr7D.!!$F2 4549
14 TraesCS7A01G144300 chr7D 260697836 260698361 525 False 593.000000 593 87.833000 228 727 1 chr7D.!!$F1 499
15 TraesCS7A01G144300 chr5A 570379175 570380228 1053 False 434.500000 542 87.162000 408 1324 2 chr5A.!!$F2 916

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
511 552 0.239347 GCTATGGTGCATCAATCGGC 59.761 55.000 2.42 2.25 0.00 5.54 F
566 610 0.625849 TCTTCTTCCCCATGGCTTCC 59.374 55.000 6.09 0.00 0.00 3.46 F
1230 1506 1.066587 GCATCCGAAGAGGGAGTCG 59.933 63.158 0.00 0.00 40.02 4.18 F
1922 3011 2.905415 AGGAAACTTGATGATGGGCA 57.095 45.000 0.00 0.00 37.44 5.36 F
2533 3625 0.861837 GTGTGACTTCAAGGCGTCAG 59.138 55.000 0.00 0.00 40.48 3.51 F
3787 4921 0.392998 CGCCAAGTCATGCTTACCCT 60.393 55.000 2.68 0.00 35.27 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1577 2662 0.161870 GACTTTGCGACTTCAGCGTC 59.838 55.000 0.00 0.0 37.44 5.19 R
2076 3165 1.407618 GCCATTGCTGCATCTTCATCA 59.592 47.619 1.84 0.0 33.53 3.07 R
2299 3388 2.197283 TGCAGCCACATATTGTCACA 57.803 45.000 0.00 0.0 0.00 3.58 R
3016 4110 3.316029 TGCACATTTAGCAGCCATATCAC 59.684 43.478 0.00 0.0 37.02 3.06 R
4145 7065 1.754226 TGGCTTTTGTTGTTGGGAGAC 59.246 47.619 0.00 0.0 0.00 3.36 R
5175 8284 0.766674 AGTGAAGGTGGTGGTGGCTA 60.767 55.000 0.00 0.0 0.00 3.93 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
19 20 1.795768 ACGTGTCATGTCCATGTGTC 58.204 50.000 10.74 1.44 39.72 3.67
20 21 1.069978 ACGTGTCATGTCCATGTGTCA 59.930 47.619 10.74 3.65 39.72 3.58
21 22 2.142319 CGTGTCATGTCCATGTGTCAA 58.858 47.619 7.13 0.00 39.72 3.18
22 23 2.743664 CGTGTCATGTCCATGTGTCAAT 59.256 45.455 7.13 0.00 39.72 2.57
23 24 3.189080 CGTGTCATGTCCATGTGTCAATT 59.811 43.478 7.13 0.00 39.72 2.32
24 25 4.320421 CGTGTCATGTCCATGTGTCAATTT 60.320 41.667 7.13 0.00 39.72 1.82
25 26 5.531634 GTGTCATGTCCATGTGTCAATTTT 58.468 37.500 7.13 0.00 39.72 1.82
26 27 5.984926 GTGTCATGTCCATGTGTCAATTTTT 59.015 36.000 7.13 0.00 39.72 1.94
27 28 5.984323 TGTCATGTCCATGTGTCAATTTTTG 59.016 36.000 7.13 0.00 39.72 2.44
28 29 4.989797 TCATGTCCATGTGTCAATTTTTGC 59.010 37.500 7.13 0.00 39.72 3.68
29 30 3.726607 TGTCCATGTGTCAATTTTTGCC 58.273 40.909 0.00 0.00 0.00 4.52
30 31 3.066380 GTCCATGTGTCAATTTTTGCCC 58.934 45.455 0.00 0.00 0.00 5.36
31 32 2.971330 TCCATGTGTCAATTTTTGCCCT 59.029 40.909 0.00 0.00 0.00 5.19
32 33 4.021544 GTCCATGTGTCAATTTTTGCCCTA 60.022 41.667 0.00 0.00 0.00 3.53
33 34 4.220382 TCCATGTGTCAATTTTTGCCCTAG 59.780 41.667 0.00 0.00 0.00 3.02
34 35 4.497300 CATGTGTCAATTTTTGCCCTAGG 58.503 43.478 0.06 0.06 0.00 3.02
35 36 3.571590 TGTGTCAATTTTTGCCCTAGGT 58.428 40.909 8.29 0.00 0.00 3.08
36 37 3.964031 TGTGTCAATTTTTGCCCTAGGTT 59.036 39.130 8.29 0.00 0.00 3.50
37 38 4.202202 TGTGTCAATTTTTGCCCTAGGTTG 60.202 41.667 8.29 3.87 0.00 3.77
38 39 3.964031 TGTCAATTTTTGCCCTAGGTTGT 59.036 39.130 8.29 0.00 0.00 3.32
39 40 4.202202 TGTCAATTTTTGCCCTAGGTTGTG 60.202 41.667 8.29 0.00 0.00 3.33
78 79 3.785859 GTCGCCTGCTCCCATCCA 61.786 66.667 0.00 0.00 0.00 3.41
93 95 1.630126 ATCCATGCTCCCAGCGAGTT 61.630 55.000 0.00 0.00 46.26 3.01
100 102 1.671328 GCTCCCAGCGAGTTATTTTCC 59.329 52.381 0.00 0.00 41.10 3.13
101 103 2.939640 GCTCCCAGCGAGTTATTTTCCA 60.940 50.000 0.00 0.00 41.10 3.53
102 104 3.545703 CTCCCAGCGAGTTATTTTCCAT 58.454 45.455 0.00 0.00 33.51 3.41
112 114 1.948104 TATTTTCCATCGACGGCTGG 58.052 50.000 10.14 10.14 0.00 4.85
142 144 2.115266 CACCCACGCCCCTTTTCT 59.885 61.111 0.00 0.00 0.00 2.52
163 165 6.476243 TCTAGCGAAAGAAAACACATTACC 57.524 37.500 0.00 0.00 0.00 2.85
171 173 7.486551 CGAAAGAAAACACATTACCAAAACTCA 59.513 33.333 0.00 0.00 0.00 3.41
239 243 0.391927 ACCCACGTCTCTCTCTCTCG 60.392 60.000 0.00 0.00 0.00 4.04
262 274 4.586001 GGTTATCTGTCCGTAATACCTGGA 59.414 45.833 0.00 0.00 0.00 3.86
269 281 5.263599 TGTCCGTAATACCTGGAAAGACTA 58.736 41.667 0.00 0.00 32.60 2.59
271 283 5.359292 GTCCGTAATACCTGGAAAGACTACT 59.641 44.000 0.00 0.00 32.60 2.57
275 287 5.346181 AATACCTGGAAAGACTACTGCTC 57.654 43.478 0.00 0.00 0.00 4.26
329 341 3.608316 ATTTTTGCCGCCAACATACAT 57.392 38.095 0.00 0.00 0.00 2.29
342 354 6.322491 GCCAACATACATAACAAAGAGGTTC 58.678 40.000 0.00 0.00 32.29 3.62
378 390 7.182930 ACCTCTTAGACCTTTGTTAATCCAGAT 59.817 37.037 0.00 0.00 0.00 2.90
466 501 7.167302 CAGAAGCACGTCAAACAAATTCAATAA 59.833 33.333 0.00 0.00 0.00 1.40
467 502 7.867403 AGAAGCACGTCAAACAAATTCAATAAT 59.133 29.630 0.00 0.00 0.00 1.28
496 537 4.222124 AGACGGAAATTCACAAGGCTAT 57.778 40.909 0.00 0.00 0.00 2.97
511 552 0.239347 GCTATGGTGCATCAATCGGC 59.761 55.000 2.42 2.25 0.00 5.54
517 558 0.810648 GTGCATCAATCGGCCAGAAA 59.189 50.000 2.24 0.00 0.00 2.52
551 595 2.373224 CTGAAGGAAAGGGGCATCTTC 58.627 52.381 0.00 0.00 35.65 2.87
566 610 0.625849 TCTTCTTCCCCATGGCTTCC 59.374 55.000 6.09 0.00 0.00 3.46
660 705 7.852971 TCTCTTTTCGTTGTTCTTTTCCTTA 57.147 32.000 0.00 0.00 0.00 2.69
784 832 8.554528 GTCGATCATGATCATAAAACATCTGTT 58.445 33.333 30.13 0.00 37.49 3.16
1010 1276 8.676454 TTTTTAATCCGTGTTTCATAAATCCG 57.324 30.769 0.00 0.00 0.00 4.18
1121 1397 8.715191 AGAAAATGTTGCAACAAATTTCACTA 57.285 26.923 40.00 21.41 43.61 2.74
1129 1405 6.625362 TGCAACAAATTTCACTAACAACAGA 58.375 32.000 0.00 0.00 0.00 3.41
1230 1506 1.066587 GCATCCGAAGAGGGAGTCG 59.933 63.158 0.00 0.00 40.02 4.18
1459 2542 7.290014 TGTCAAGCCCATATGAAGATAAGTCTA 59.710 37.037 3.65 0.00 33.30 2.59
1571 2656 3.825328 AGGAAAGTCACAGAAGCACAAT 58.175 40.909 0.00 0.00 0.00 2.71
1577 2662 3.750130 AGTCACAGAAGCACAATTAGCAG 59.250 43.478 5.04 0.00 0.00 4.24
1616 2701 6.418057 AGTCTGTGGGCATTTCAAATAAAA 57.582 33.333 0.00 0.00 0.00 1.52
1734 2819 5.009410 CACTTCAAGCAAAGAAAGGAGACAT 59.991 40.000 1.11 0.00 0.00 3.06
1911 3000 6.151144 GCTTTGACACCACATATAGGAAACTT 59.849 38.462 0.00 0.00 43.67 2.66
1922 3011 2.905415 AGGAAACTTGATGATGGGCA 57.095 45.000 0.00 0.00 37.44 5.36
1955 3044 5.574891 TTGATTGTTGGGGTGAATAATCG 57.425 39.130 0.00 0.00 36.65 3.34
2000 3089 6.818644 GGTGCTACACTTCTCTATGATGAAAA 59.181 38.462 0.00 0.00 34.40 2.29
2076 3165 6.380079 AAACATCCAAGGACTATTCTGACT 57.620 37.500 0.00 0.00 0.00 3.41
2299 3388 3.671740 TGCTAGACAGGTATGGACTCT 57.328 47.619 0.00 0.00 0.00 3.24
2428 3519 9.846248 GTGAAAGCATGAATAATGAACTAAAGT 57.154 29.630 0.00 0.00 38.72 2.66
2533 3625 0.861837 GTGTGACTTCAAGGCGTCAG 59.138 55.000 0.00 0.00 40.48 3.51
2557 3649 1.003580 CTACTCCCAAGCTGAAGGCAA 59.996 52.381 0.00 0.00 44.79 4.52
2601 3693 3.231818 AGCCGCAACTACATATACTCCT 58.768 45.455 0.00 0.00 0.00 3.69
2652 3744 2.093658 GCTTCGGACCCTGAACTATGAA 60.094 50.000 0.00 0.00 0.00 2.57
2718 3811 6.142139 CACAGTAAAATTTCATGAACGCAGA 58.858 36.000 7.89 0.00 0.00 4.26
2748 3841 8.200792 AGCATGTTGTTAGTTTTTATCCAAACA 58.799 29.630 0.00 0.00 38.86 2.83
2810 3903 2.842496 TGGAATCCTCTGCTCTCATTGT 59.158 45.455 0.00 0.00 0.00 2.71
2824 3917 8.044060 TGCTCTCATTGTTTAAAGATACTTGG 57.956 34.615 0.00 0.00 0.00 3.61
2916 4010 6.146184 GCTAGAGATAACAAGCAATCGCAATA 59.854 38.462 0.00 0.00 42.27 1.90
3016 4110 1.325640 CGCAGAGTCCGATGAAACATG 59.674 52.381 0.00 0.00 0.00 3.21
3073 4167 3.015327 GAGATGTGGAGCAAAGCTTGAT 58.985 45.455 0.00 0.00 39.88 2.57
3120 4215 2.093235 CCAGATTTGGGTGACTCCTCTC 60.093 54.545 0.00 0.00 41.05 3.20
3301 4408 2.130272 AGACTGTACGAGGATCAGCA 57.870 50.000 0.00 0.00 33.17 4.41
3385 4492 2.552315 ACAACTACAACCTGAAATGCCG 59.448 45.455 0.00 0.00 0.00 5.69
3395 4502 3.823873 ACCTGAAATGCCGTTCACAAATA 59.176 39.130 0.00 0.00 33.92 1.40
3545 4652 2.906389 TGTACCAAGATCAGCAAGACCT 59.094 45.455 0.00 0.00 0.00 3.85
3630 4740 2.095567 CGACCTGAAATGCCTTTGACAG 60.096 50.000 0.00 0.00 0.00 3.51
3723 4857 9.082313 ACTATTTCTCATTTTCAATCACCTGTT 57.918 29.630 0.00 0.00 0.00 3.16
3760 4894 6.921857 GCTATTTATCTGCGTAGGTTCAACTA 59.078 38.462 0.00 0.00 0.00 2.24
3787 4921 0.392998 CGCCAAGTCATGCTTACCCT 60.393 55.000 2.68 0.00 35.27 4.34
3802 4936 8.629158 CATGCTTACCCTTATTTAGCACATTAA 58.371 33.333 0.00 0.00 43.78 1.40
3823 4957 5.841957 AAAACTCAAGTCTGCAACAATCT 57.158 34.783 0.00 0.00 0.00 2.40
3994 6913 2.203252 CCCACGATGATGCCAGGG 60.203 66.667 0.00 0.00 0.00 4.45
4007 6926 2.645838 GCCAGGGCAGAATCTATCAA 57.354 50.000 5.20 0.00 41.49 2.57
4034 6953 2.826128 CAACAGCAGACTCCTACCAGTA 59.174 50.000 0.00 0.00 0.00 2.74
4076 6995 1.688735 TGCCCGGACAGAATCTATCAG 59.311 52.381 0.73 0.00 0.00 2.90
4099 7018 4.365514 TCTCCAGCAACAAAATCCTACA 57.634 40.909 0.00 0.00 0.00 2.74
4101 7020 4.074970 CTCCAGCAACAAAATCCTACAGT 58.925 43.478 0.00 0.00 0.00 3.55
4145 7065 5.500234 TGATCCCAAGACAAAATCTACCAG 58.500 41.667 0.00 0.00 36.27 4.00
4457 7417 2.646175 GGAGCGCCACTGTCACCTA 61.646 63.158 2.29 0.00 0.00 3.08
4584 7544 8.894768 ATCACCATCAGTAGCTAATTAACTTC 57.105 34.615 0.00 0.00 0.00 3.01
4608 7568 8.294954 TCCAGTTTATTTTCAACCAGTAAACA 57.705 30.769 8.46 0.00 37.58 2.83
4737 7700 5.705609 AAAATTGAGCACCTTCATTACGT 57.294 34.783 0.00 0.00 0.00 3.57
4926 8026 8.082852 GTGTGCTTAATTGATACTAGCTAGCTA 58.917 37.037 22.85 22.85 33.15 3.32
4937 8037 7.885922 TGATACTAGCTAGCTATAGACTTGCTT 59.114 37.037 24.36 16.74 42.34 3.91
4967 8069 4.519906 ACTGAAGGGAAAAGAAACCAGA 57.480 40.909 0.00 0.00 0.00 3.86
4968 8070 4.464947 ACTGAAGGGAAAAGAAACCAGAG 58.535 43.478 0.00 0.00 0.00 3.35
4969 8071 4.079730 ACTGAAGGGAAAAGAAACCAGAGT 60.080 41.667 0.00 0.00 0.00 3.24
4976 8078 6.500751 AGGGAAAAGAAACCAGAGTAGACATA 59.499 38.462 0.00 0.00 0.00 2.29
4990 8092 7.380870 CAGAGTAGACATATGTATTCTGCACAC 59.619 40.741 13.52 2.31 0.00 3.82
4993 8095 8.040727 AGTAGACATATGTATTCTGCACACAAA 58.959 33.333 8.71 0.00 0.00 2.83
4995 8097 8.109705 AGACATATGTATTCTGCACACAAAAA 57.890 30.769 8.71 0.00 0.00 1.94
5046 8148 1.977854 AGTTGCTGTACTGACCATGGA 59.022 47.619 21.47 0.00 0.00 3.41
5052 8155 1.278985 TGTACTGACCATGGAGCAAGG 59.721 52.381 21.47 7.78 0.00 3.61
5056 8160 0.547471 TGACCATGGAGCAAGGAGGA 60.547 55.000 21.47 0.00 0.00 3.71
5058 8162 0.549950 ACCATGGAGCAAGGAGGATG 59.450 55.000 21.47 0.00 0.00 3.51
5060 8164 0.841961 CATGGAGCAAGGAGGATGGA 59.158 55.000 0.00 0.00 0.00 3.41
5061 8165 1.213678 CATGGAGCAAGGAGGATGGAA 59.786 52.381 0.00 0.00 0.00 3.53
5107 8212 2.283529 ACGAAGACCCGCTGGATGT 61.284 57.895 0.00 0.00 34.81 3.06
5175 8284 1.073025 TCTTCAGTGGCGGCACAAT 59.927 52.632 38.86 20.64 0.00 2.71
5190 8302 0.777446 ACAATAGCCACCACCACCTT 59.223 50.000 0.00 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.794512 TGACACATGGACATGACACG 58.205 50.000 18.38 6.73 41.20 4.49
2 3 4.771590 AATTGACACATGGACATGACAC 57.228 40.909 18.38 9.11 41.20 3.67
4 5 5.107375 GCAAAAATTGACACATGGACATGAC 60.107 40.000 18.38 9.70 41.20 3.06
6 7 4.152759 GGCAAAAATTGACACATGGACATG 59.847 41.667 10.57 10.57 44.15 3.21
7 8 4.317488 GGCAAAAATTGACACATGGACAT 58.683 39.130 0.00 0.00 38.99 3.06
8 9 3.494048 GGGCAAAAATTGACACATGGACA 60.494 43.478 0.00 0.00 41.76 4.02
9 10 3.066380 GGGCAAAAATTGACACATGGAC 58.934 45.455 0.00 0.00 41.76 4.02
10 11 2.971330 AGGGCAAAAATTGACACATGGA 59.029 40.909 0.00 0.00 41.76 3.41
11 12 3.405823 AGGGCAAAAATTGACACATGG 57.594 42.857 0.00 0.00 41.76 3.66
12 13 4.021192 ACCTAGGGCAAAAATTGACACATG 60.021 41.667 14.81 0.00 41.76 3.21
13 14 4.159557 ACCTAGGGCAAAAATTGACACAT 58.840 39.130 14.81 0.00 41.76 3.21
14 15 3.571590 ACCTAGGGCAAAAATTGACACA 58.428 40.909 14.81 0.00 41.76 3.72
15 16 4.202212 ACAACCTAGGGCAAAAATTGACAC 60.202 41.667 14.81 0.00 41.76 3.67
16 17 3.964031 ACAACCTAGGGCAAAAATTGACA 59.036 39.130 14.81 0.00 41.76 3.58
17 18 4.306600 CACAACCTAGGGCAAAAATTGAC 58.693 43.478 14.81 0.00 38.21 3.18
18 19 3.323403 CCACAACCTAGGGCAAAAATTGA 59.677 43.478 14.81 0.00 0.00 2.57
19 20 3.556843 CCCACAACCTAGGGCAAAAATTG 60.557 47.826 14.81 9.01 38.44 2.32
20 21 2.637382 CCCACAACCTAGGGCAAAAATT 59.363 45.455 14.81 0.00 38.44 1.82
21 22 2.158234 TCCCACAACCTAGGGCAAAAAT 60.158 45.455 14.81 0.00 45.07 1.82
22 23 1.218196 TCCCACAACCTAGGGCAAAAA 59.782 47.619 14.81 0.00 45.07 1.94
23 24 0.854218 TCCCACAACCTAGGGCAAAA 59.146 50.000 14.81 0.00 45.07 2.44
24 25 0.111639 GTCCCACAACCTAGGGCAAA 59.888 55.000 14.81 0.00 45.07 3.68
25 26 1.765074 GTCCCACAACCTAGGGCAA 59.235 57.895 14.81 0.00 45.07 4.52
26 27 2.589157 CGTCCCACAACCTAGGGCA 61.589 63.158 14.81 0.00 45.07 5.36
27 28 2.267961 CGTCCCACAACCTAGGGC 59.732 66.667 14.81 0.00 45.07 5.19
28 29 2.666098 CCCGTCCCACAACCTAGGG 61.666 68.421 14.81 0.00 46.90 3.53
29 30 2.666098 CCCCGTCCCACAACCTAGG 61.666 68.421 7.41 7.41 0.00 3.02
30 31 2.987125 CCCCGTCCCACAACCTAG 59.013 66.667 0.00 0.00 0.00 3.02
31 32 3.324108 GCCCCGTCCCACAACCTA 61.324 66.667 0.00 0.00 0.00 3.08
33 34 4.280019 AAGCCCCGTCCCACAACC 62.280 66.667 0.00 0.00 0.00 3.77
34 35 2.983592 CAAGCCCCGTCCCACAAC 60.984 66.667 0.00 0.00 0.00 3.32
35 36 4.966787 GCAAGCCCCGTCCCACAA 62.967 66.667 0.00 0.00 0.00 3.33
93 95 1.474320 CCCAGCCGTCGATGGAAAATA 60.474 52.381 28.06 0.00 39.02 1.40
112 114 0.464554 GTGGGTGGAGATAAGCTGCC 60.465 60.000 0.00 0.00 33.36 4.85
142 144 6.621316 TTGGTAATGTGTTTTCTTTCGCTA 57.379 33.333 0.00 0.00 0.00 4.26
184 186 7.051623 TGTGCCAAGTATTACGGAAAGATAAT 58.948 34.615 0.00 0.00 0.00 1.28
239 243 4.586001 TCCAGGTATTACGGACAGATAACC 59.414 45.833 0.00 0.00 0.00 2.85
262 274 5.105146 CCAGATTAGTGGAGCAGTAGTCTTT 60.105 44.000 0.00 0.00 40.44 2.52
275 287 5.116084 TCATTTTCCCTCCAGATTAGTGG 57.884 43.478 0.00 0.00 39.19 4.00
329 341 0.952010 GCGCCCGAACCTCTTTGTTA 60.952 55.000 0.00 0.00 0.00 2.41
342 354 2.046700 TAAGAGGTTTGGCGCCCG 60.047 61.111 26.77 0.00 0.00 6.13
378 390 2.706555 TGCGTGTTTGTGTGTTTTCA 57.293 40.000 0.00 0.00 0.00 2.69
466 501 4.469945 TGTGAATTTCCGTCTTCCTCCTAT 59.530 41.667 0.00 0.00 0.00 2.57
467 502 3.835978 TGTGAATTTCCGTCTTCCTCCTA 59.164 43.478 0.00 0.00 0.00 2.94
478 513 3.016736 ACCATAGCCTTGTGAATTTCCG 58.983 45.455 0.00 0.00 0.00 4.30
496 537 1.750018 CTGGCCGATTGATGCACCA 60.750 57.895 0.00 0.00 0.00 4.17
511 552 1.340114 GCCCCTAGGTCTTGTTTCTGG 60.340 57.143 8.29 0.00 34.57 3.86
517 558 1.280457 CTTCAGCCCCTAGGTCTTGT 58.720 55.000 8.29 0.00 34.57 3.16
551 595 0.332632 TTGAGGAAGCCATGGGGAAG 59.667 55.000 15.13 0.00 35.59 3.46
784 832 6.423905 GCTGTATCATCCTATACGAAGCAAAA 59.576 38.462 0.00 0.00 34.17 2.44
842 890 5.163248 TGTGAAGTTTCTTCATGTACCAGGA 60.163 40.000 13.93 0.00 0.00 3.86
927 1192 3.386726 TGTAGACTAATATGCACGGGCTT 59.613 43.478 12.74 7.40 41.91 4.35
1010 1276 3.127895 TGCTTACCATGCGTAATTTGACC 59.872 43.478 7.09 0.00 36.35 4.02
1116 1392 8.783093 CAATCTTTGGTAATCTGTTGTTAGTGA 58.217 33.333 0.00 0.00 0.00 3.41
1121 1397 7.581213 TGTCAATCTTTGGTAATCTGTTGTT 57.419 32.000 0.00 0.00 0.00 2.83
1160 1436 4.936685 AAAATGAGTAGGCCTCCTCTTT 57.063 40.909 24.28 20.81 39.65 2.52
1230 1506 9.595823 TTACAGTAGTATTCTTCACTTTATGGC 57.404 33.333 0.00 0.00 0.00 4.40
1265 1541 1.280710 ACGGGAGCACATAAATGTCCA 59.719 47.619 0.00 0.00 39.39 4.02
1577 2662 0.161870 GACTTTGCGACTTCAGCGTC 59.838 55.000 0.00 0.00 37.44 5.19
1616 2701 8.034313 TCTTTGGCCATAAGATCTATAGTTGT 57.966 34.615 19.97 0.00 0.00 3.32
1748 2836 9.103861 CTTCTTTTACCTTCTTCTCCATGTATC 57.896 37.037 0.00 0.00 0.00 2.24
1922 3011 3.327464 CCCAACAATCAAACCAAAGGGAT 59.673 43.478 0.00 0.00 35.81 3.85
1955 3044 3.392882 CCAAAGACCATGGTTTTCTTGC 58.607 45.455 20.85 3.87 33.08 4.01
2000 3089 2.435437 AGCCAACCAAAACTTTCAGCAT 59.565 40.909 0.00 0.00 0.00 3.79
2076 3165 1.407618 GCCATTGCTGCATCTTCATCA 59.592 47.619 1.84 0.00 33.53 3.07
2182 3271 9.232473 GAACTTCTTATATTCTTCAACAACCCT 57.768 33.333 0.00 0.00 0.00 4.34
2299 3388 2.197283 TGCAGCCACATATTGTCACA 57.803 45.000 0.00 0.00 0.00 3.58
2533 3625 3.339141 CCTTCAGCTTGGGAGTAGTTTC 58.661 50.000 0.00 0.00 0.00 2.78
2557 3649 5.174037 TGCCTTAACACATAGCTACCTTT 57.826 39.130 0.00 0.00 0.00 3.11
2601 3693 6.405065 GCTCCTGAAACATCTTGAATATTGCA 60.405 38.462 0.00 0.00 0.00 4.08
2718 3811 4.568152 AAAAACTAACAACATGCTCGCT 57.432 36.364 0.00 0.00 0.00 4.93
2748 3841 4.571984 GCAACTGCAATTGACCTTTTCTTT 59.428 37.500 12.91 0.00 41.59 2.52
2916 4010 7.400599 TTCTTGCTTTTAGATCTTCATGCAT 57.599 32.000 0.00 0.00 0.00 3.96
3016 4110 3.316029 TGCACATTTAGCAGCCATATCAC 59.684 43.478 0.00 0.00 37.02 3.06
3073 4167 6.884472 TTGGGTCTGGATCAACTCTAATTA 57.116 37.500 0.00 0.00 0.00 1.40
3329 4436 8.856490 TCTATCTTCTTTTTCTTTGTTGTTGC 57.144 30.769 0.00 0.00 0.00 4.17
3630 4740 3.383505 GGTAAATACCCAGGCATTTGGTC 59.616 47.826 5.31 0.00 40.53 4.02
3723 4857 6.423905 CGCAGATAAATAGCAAAGCTTAGGTA 59.576 38.462 0.00 0.00 40.44 3.08
3802 4936 7.365741 CAATAGATTGTTGCAGACTTGAGTTT 58.634 34.615 0.00 0.00 33.22 2.66
3994 6913 6.911511 GCTGTTGAAAGATTGATAGATTCTGC 59.088 38.462 0.00 0.00 0.00 4.26
4007 6926 4.323104 GGTAGGAGTCTGCTGTTGAAAGAT 60.323 45.833 3.76 0.00 0.00 2.40
4034 6953 5.482175 GCATCATCATAGGGGTAGAAGTACT 59.518 44.000 0.00 0.00 0.00 2.73
4076 6995 4.518970 TGTAGGATTTTGTTGCTGGAGAAC 59.481 41.667 0.00 0.00 0.00 3.01
4145 7065 1.754226 TGGCTTTTGTTGTTGGGAGAC 59.246 47.619 0.00 0.00 0.00 3.36
4193 7113 9.507280 CTAATAGAATTGCACAAAAGTACATGG 57.493 33.333 0.00 0.00 0.00 3.66
4222 7142 6.946009 TCAATCCATGGTCGTATACTCATAGA 59.054 38.462 12.58 2.17 0.00 1.98
4285 7205 9.715123 TTATATTTATCACAGTCACAAATTGCG 57.285 29.630 0.00 0.00 0.00 4.85
4457 7417 1.918262 TGGTTTGGCTCATCCTCATCT 59.082 47.619 0.00 0.00 35.26 2.90
4584 7544 8.813282 GTTGTTTACTGGTTGAAAATAAACTGG 58.187 33.333 0.00 0.00 36.90 4.00
4737 7700 8.635765 AATTCCTTTCTATCACTGTTTTGCTA 57.364 30.769 0.00 0.00 0.00 3.49
4913 7884 7.122055 CCAAGCAAGTCTATAGCTAGCTAGTAT 59.878 40.741 27.42 15.92 37.70 2.12
4926 8026 4.940046 CAGTTCACATCCAAGCAAGTCTAT 59.060 41.667 0.00 0.00 0.00 1.98
4928 8028 3.144506 CAGTTCACATCCAAGCAAGTCT 58.855 45.455 0.00 0.00 0.00 3.24
4937 8037 3.874383 TTTCCCTTCAGTTCACATCCA 57.126 42.857 0.00 0.00 0.00 3.41
4967 8069 7.112452 TGTGTGCAGAATACATATGTCTACT 57.888 36.000 12.68 7.16 0.00 2.57
4968 8070 7.770801 TTGTGTGCAGAATACATATGTCTAC 57.229 36.000 12.68 4.91 29.02 2.59
4969 8071 8.785329 TTTTGTGTGCAGAATACATATGTCTA 57.215 30.769 12.68 0.00 29.02 2.59
4993 8095 3.268072 CCCTTCCATCCTCCTCTCTTTTT 59.732 47.826 0.00 0.00 0.00 1.94
4995 8097 2.046447 TCCCTTCCATCCTCCTCTCTTT 59.954 50.000 0.00 0.00 0.00 2.52
4996 8098 1.653918 TCCCTTCCATCCTCCTCTCTT 59.346 52.381 0.00 0.00 0.00 2.85
5046 8148 1.210204 TGCCTTCCATCCTCCTTGCT 61.210 55.000 0.00 0.00 0.00 3.91
5052 8155 2.203126 CGGCTGCCTTCCATCCTC 60.203 66.667 17.92 0.00 0.00 3.71
5056 8160 2.831742 CATGCGGCTGCCTTCCAT 60.832 61.111 16.57 13.03 41.78 3.41
5175 8284 0.766674 AGTGAAGGTGGTGGTGGCTA 60.767 55.000 0.00 0.00 0.00 3.93
5190 8302 1.826921 GCTCGGGTCGGGATAGTGA 60.827 63.158 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.