Multiple sequence alignment - TraesCS7D01G122600

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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 TraesCS7D01G122600 chr7D 100.000 4200 0 0 1 4200 76734957 76730758 0.000000e+00 7757.0
1 TraesCS7D01G122600 chr7D 96.484 256 9 0 2871 3126 76621655 76621400 1.400000e-114 424.0
2 TraesCS7D01G122600 chr7D 91.597 238 5 1 3122 3359 76614883 76614661 8.770000e-82 315.0
3 TraesCS7D01G122600 chr7D 83.453 278 32 9 3348 3618 76613424 76613154 3.240000e-61 246.0
4 TraesCS7D01G122600 chr7A 90.962 3640 207 62 618 4200 80854759 80851185 0.000000e+00 4787.0
5 TraesCS7D01G122600 chr7A 92.618 867 45 9 3045 3899 80839357 80838498 0.000000e+00 1229.0
6 TraesCS7D01G122600 chr7A 92.180 844 42 11 3045 3874 80704057 80703224 0.000000e+00 1171.0
7 TraesCS7D01G122600 chr7A 92.062 844 43 11 3045 3874 80806987 80806154 0.000000e+00 1166.0
8 TraesCS7D01G122600 chr7A 89.823 226 16 5 3890 4112 80804127 80803906 2.470000e-72 283.0
9 TraesCS7D01G122600 chr7A 89.381 226 17 5 3890 4112 80701196 80700975 1.150000e-70 278.0
10 TraesCS7D01G122600 chr7A 89.381 226 17 5 3890 4112 80726996 80726775 1.150000e-70 278.0
11 TraesCS7D01G122600 chr7A 88.938 226 18 5 3890 4112 80749221 80749000 5.350000e-69 272.0
12 TraesCS7D01G122600 chr7A 100.000 33 0 0 581 613 13643783 13643751 1.260000e-05 62.1
13 TraesCS7D01G122600 chr7B 91.781 3419 173 53 618 3967 23443231 23439852 0.000000e+00 4658.0
14 TraesCS7D01G122600 chr7B 89.630 540 44 5 2885 3412 23396970 23396431 0.000000e+00 676.0
15 TraesCS7D01G122600 chr7B 91.803 122 9 1 4013 4134 23439857 23439737 7.220000e-38 169.0
16 TraesCS7D01G122600 chr1A 83.513 1577 223 22 1691 3240 308814417 308812851 0.000000e+00 1437.0
17 TraesCS7D01G122600 chr1A 83.499 1509 232 12 1688 3181 37480010 37481516 0.000000e+00 1391.0
18 TraesCS7D01G122600 chr1A 81.000 200 23 9 1051 1246 308816021 308815833 1.220000e-30 145.0
19 TraesCS7D01G122600 chr1A 80.500 200 25 10 1042 1235 37478585 37478776 1.570000e-29 141.0
20 TraesCS7D01G122600 chr1D 83.730 1512 221 18 1688 3181 38551133 38552637 0.000000e+00 1406.0
21 TraesCS7D01G122600 chr1D 85.210 1217 168 7 2028 3240 236806078 236807286 0.000000e+00 1240.0
22 TraesCS7D01G122600 chr1D 79.556 225 30 9 1025 1246 236803291 236803502 3.380000e-31 147.0
23 TraesCS7D01G122600 chr1D 78.879 232 33 12 1025 1252 38549747 38549966 4.380000e-30 143.0
24 TraesCS7D01G122600 chr1B 83.279 1525 234 9 1677 3181 58323210 58324733 0.000000e+00 1384.0
25 TraesCS7D01G122600 chr1B 86.590 1126 151 0 2056 3181 342116466 342117591 0.000000e+00 1243.0
26 TraesCS7D01G122600 chr1B 93.190 558 28 4 56 613 623364416 623364963 0.000000e+00 811.0
27 TraesCS7D01G122600 chr1B 85.034 294 40 4 1688 1977 342116064 342116357 3.180000e-76 296.0
28 TraesCS7D01G122600 chr1B 78.448 232 34 12 1025 1252 58321788 58322007 2.040000e-28 137.0
29 TraesCS7D01G122600 chr1B 94.737 38 2 0 577 614 19159089 19159126 4.530000e-05 60.2
30 TraesCS7D01G122600 chr1B 94.737 38 2 0 577 614 19159218 19159255 4.530000e-05 60.2
31 TraesCS7D01G122600 chr5B 97.297 37 0 1 583 618 328222845 328222881 1.260000e-05 62.1
32 TraesCS7D01G122600 chr2A 100.000 33 0 0 581 613 723514901 723514869 1.260000e-05 62.1
33 TraesCS7D01G122600 chrUn 97.143 35 0 1 584 617 5311815 5311781 1.630000e-04 58.4
34 TraesCS7D01G122600 chr5A 94.595 37 2 0 577 613 451247045 451247081 1.630000e-04 58.4
35 TraesCS7D01G122600 chr5A 92.105 38 3 0 580 617 428945786 428945823 2.000000e-03 54.7


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 TraesCS7D01G122600 chr7D 76730758 76734957 4199 True 7757.0 7757 100.0000 1 4200 1 chr7D.!!$R2 4199
1 TraesCS7D01G122600 chr7D 76613154 76614883 1729 True 280.5 315 87.5250 3122 3618 2 chr7D.!!$R3 496
2 TraesCS7D01G122600 chr7A 80851185 80854759 3574 True 4787.0 4787 90.9620 618 4200 1 chr7A.!!$R5 3582
3 TraesCS7D01G122600 chr7A 80838498 80839357 859 True 1229.0 1229 92.6180 3045 3899 1 chr7A.!!$R4 854
4 TraesCS7D01G122600 chr7A 80700975 80704057 3082 True 724.5 1171 90.7805 3045 4112 2 chr7A.!!$R6 1067
5 TraesCS7D01G122600 chr7A 80803906 80806987 3081 True 724.5 1166 90.9425 3045 4112 2 chr7A.!!$R7 1067
6 TraesCS7D01G122600 chr7B 23439737 23443231 3494 True 2413.5 4658 91.7920 618 4134 2 chr7B.!!$R2 3516
7 TraesCS7D01G122600 chr7B 23396431 23396970 539 True 676.0 676 89.6300 2885 3412 1 chr7B.!!$R1 527
8 TraesCS7D01G122600 chr1A 308812851 308816021 3170 True 791.0 1437 82.2565 1051 3240 2 chr1A.!!$R1 2189
9 TraesCS7D01G122600 chr1A 37478585 37481516 2931 False 766.0 1391 81.9995 1042 3181 2 chr1A.!!$F1 2139
10 TraesCS7D01G122600 chr1D 38549747 38552637 2890 False 774.5 1406 81.3045 1025 3181 2 chr1D.!!$F1 2156
11 TraesCS7D01G122600 chr1D 236803291 236807286 3995 False 693.5 1240 82.3830 1025 3240 2 chr1D.!!$F2 2215
12 TraesCS7D01G122600 chr1B 623364416 623364963 547 False 811.0 811 93.1900 56 613 1 chr1B.!!$F1 557
13 TraesCS7D01G122600 chr1B 342116064 342117591 1527 False 769.5 1243 85.8120 1688 3181 2 chr1B.!!$F4 1493
14 TraesCS7D01G122600 chr1B 58321788 58324733 2945 False 760.5 1384 80.8635 1025 3181 2 chr1B.!!$F3 2156

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
32 33 0.108041 GTTTTCCTGTATCGGGCCGA 60.108 55.0 33.1 33.1 41.13 5.54 F
1248 1268 0.322008 GTGAGTTCCTTGCCTCCCTG 60.322 60.0 0.0 0.0 0.00 4.45 F
2631 4916 0.523072 CCATTGTTCACCAAGGAGCG 59.477 55.0 0.0 0.0 36.99 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1250 1270 0.340208 GGGAGGAAGAGAGGGGAAGA 59.660 60.0 0.00 0.0 0.00 2.87 R
2800 5085 0.615827 GGGCCTCCATTGCTTTCCTT 60.616 55.0 0.84 0.0 0.00 3.36 R
4176 9797 1.471119 CATCAGGTGCCTGCAAGATT 58.529 50.0 13.12 0.0 43.31 2.40 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
17 18 2.203042 TTGACCCGGACGCGTTTT 60.203 55.556 15.53 0.00 0.00 2.43
18 19 2.246042 TTGACCCGGACGCGTTTTC 61.246 57.895 15.53 5.61 0.00 2.29
20 21 3.871248 GACCCGGACGCGTTTTCCT 62.871 63.158 15.53 0.00 0.00 3.36
22 23 2.663852 CCGGACGCGTTTTCCTGT 60.664 61.111 15.53 0.00 0.00 4.00
25 26 0.643820 CGGACGCGTTTTCCTGTATC 59.356 55.000 15.53 0.00 0.00 2.24
26 27 0.643820 GGACGCGTTTTCCTGTATCG 59.356 55.000 15.53 0.00 0.00 2.92
28 29 0.738412 ACGCGTTTTCCTGTATCGGG 60.738 55.000 5.58 0.00 39.58 5.14
30 31 1.712018 GCGTTTTCCTGTATCGGGCC 61.712 60.000 0.00 0.00 0.00 5.80
31 32 1.426041 CGTTTTCCTGTATCGGGCCG 61.426 60.000 22.51 22.51 0.00 6.13
32 33 0.108041 GTTTTCCTGTATCGGGCCGA 60.108 55.000 33.10 33.10 41.13 5.54
34 35 1.707106 TTTCCTGTATCGGGCCGATA 58.293 50.000 37.59 37.59 45.13 2.92
40 41 3.591979 TATCGGGCCGATAAAACCG 57.408 52.632 38.68 6.92 45.13 4.44
41 42 0.600782 TATCGGGCCGATAAAACCGC 60.601 55.000 38.68 0.00 45.13 5.68
42 43 3.932313 CGGGCCGATAAAACCGCG 61.932 66.667 24.41 0.00 39.85 6.46
43 44 4.246206 GGGCCGATAAAACCGCGC 62.246 66.667 0.00 0.00 0.00 6.86
44 45 4.584862 GGCCGATAAAACCGCGCG 62.585 66.667 25.67 25.67 0.00 6.86
45 46 4.584862 GCCGATAAAACCGCGCGG 62.585 66.667 44.88 44.88 44.47 6.46
46 47 4.584862 CCGATAAAACCGCGCGGC 62.585 66.667 46.22 28.28 39.32 6.53
47 48 4.584862 CGATAAAACCGCGCGGCC 62.585 66.667 46.22 26.10 39.32 6.13
48 49 4.246206 GATAAAACCGCGCGGCCC 62.246 66.667 46.22 24.86 39.32 5.80
51 52 2.944409 ATAAAACCGCGCGGCCCATA 62.944 55.000 46.22 32.11 39.32 2.74
52 53 2.944409 TAAAACCGCGCGGCCCATAT 62.944 55.000 46.22 27.97 39.32 1.78
68 69 7.378181 CGGCCCATATGCTTCTAATTAATTTT 58.622 34.615 5.91 0.00 0.00 1.82
69 70 7.542130 CGGCCCATATGCTTCTAATTAATTTTC 59.458 37.037 5.91 0.00 0.00 2.29
121 122 7.027161 ACCAATTCGTAATAGCACAAATCAAC 58.973 34.615 0.00 0.00 0.00 3.18
149 150 8.999431 TGAAGAAGTTTTATGAGCGAATAACTT 58.001 29.630 0.00 0.00 38.22 2.66
215 216 1.558756 AGAAGCTGCTGCCAGTTATCT 59.441 47.619 12.44 0.00 41.26 1.98
218 219 2.012237 CTGCTGCCAGTTATCTGCG 58.988 57.895 0.00 0.00 40.09 5.18
238 239 1.808945 GGTGTCACTTTGATCAGCCTG 59.191 52.381 2.35 0.00 0.00 4.85
278 279 3.041940 GGTTCTGGTGTCGTGCCG 61.042 66.667 0.00 0.00 0.00 5.69
306 307 2.787601 CGCCACTCCGCTATAGTTAA 57.212 50.000 0.84 0.00 0.00 2.01
307 308 3.299340 CGCCACTCCGCTATAGTTAAT 57.701 47.619 0.84 0.00 0.00 1.40
308 309 2.987149 CGCCACTCCGCTATAGTTAATG 59.013 50.000 0.84 0.00 0.00 1.90
309 310 3.305131 CGCCACTCCGCTATAGTTAATGA 60.305 47.826 0.84 0.00 0.00 2.57
310 311 4.618460 CGCCACTCCGCTATAGTTAATGAT 60.618 45.833 0.84 0.00 0.00 2.45
311 312 5.392703 CGCCACTCCGCTATAGTTAATGATA 60.393 44.000 0.84 0.00 0.00 2.15
319 320 8.480501 TCCGCTATAGTTAATGATAATAACCCC 58.519 37.037 0.84 0.00 34.50 4.95
339 340 0.693049 AACCTCTGCAACTACCCCAG 59.307 55.000 0.00 0.00 0.00 4.45
340 341 0.473886 ACCTCTGCAACTACCCCAGT 60.474 55.000 0.00 0.00 40.05 4.00
365 366 3.955650 ACGTAAGCAATACTCCACTGT 57.044 42.857 0.00 0.00 45.62 3.55
401 402 0.678048 ACGAGAAAGGCATCAAGGGC 60.678 55.000 0.00 0.00 0.00 5.19
406 407 1.475682 GAAAGGCATCAAGGGCTGAAG 59.524 52.381 0.00 0.00 43.71 3.02
417 418 3.064900 AGGGCTGAAGTCTTCATCAAC 57.935 47.619 15.60 8.59 39.30 3.18
430 431 5.940470 GTCTTCATCAACAAATACACCTCCT 59.060 40.000 0.00 0.00 0.00 3.69
432 433 4.588899 TCATCAACAAATACACCTCCTGG 58.411 43.478 0.00 0.00 39.83 4.45
437 438 0.919710 AAATACACCTCCTGGCTCCC 59.080 55.000 0.00 0.00 36.63 4.30
440 441 3.721706 CACCTCCTGGCTCCCCAC 61.722 72.222 0.00 0.00 35.79 4.61
476 477 4.582869 TCACCATCATCCTTGTTCTTCAG 58.417 43.478 0.00 0.00 0.00 3.02
522 523 8.892723 CCAATTGATACAAGTGCATCTACTTAA 58.107 33.333 7.12 0.00 38.78 1.85
613 614 2.466846 GCGCGCCTTTATGTTCTAGTA 58.533 47.619 23.24 0.00 0.00 1.82
614 615 2.471743 GCGCGCCTTTATGTTCTAGTAG 59.528 50.000 23.24 0.00 0.00 2.57
615 616 3.703420 CGCGCCTTTATGTTCTAGTAGT 58.297 45.455 0.00 0.00 0.00 2.73
616 617 4.790766 GCGCGCCTTTATGTTCTAGTAGTA 60.791 45.833 23.24 0.00 0.00 1.82
647 648 1.324005 AAGTAGAGCACGAGGGCCTC 61.324 60.000 24.06 24.06 0.00 4.70
667 669 5.448632 GCCTCGTGGAATAATAAAACAGTGG 60.449 44.000 7.92 0.00 34.57 4.00
670 672 4.668289 GTGGAATAATAAAACAGTGGCGG 58.332 43.478 0.00 0.00 0.00 6.13
703 710 2.102553 GCTGACCGTAGACCGAGC 59.897 66.667 0.00 0.00 39.56 5.03
704 711 2.799371 CTGACCGTAGACCGAGCC 59.201 66.667 0.00 0.00 39.56 4.70
705 712 2.753043 TGACCGTAGACCGAGCCC 60.753 66.667 0.00 0.00 39.56 5.19
706 713 3.885521 GACCGTAGACCGAGCCCG 61.886 72.222 0.00 0.00 39.56 6.13
707 714 4.415150 ACCGTAGACCGAGCCCGA 62.415 66.667 0.00 0.00 39.56 5.14
708 715 3.136123 CCGTAGACCGAGCCCGAA 61.136 66.667 0.00 0.00 39.56 4.30
709 716 2.101770 CGTAGACCGAGCCCGAAC 59.898 66.667 0.00 0.00 39.56 3.95
785 792 4.922026 GTCACCACCAACCGCCGT 62.922 66.667 0.00 0.00 0.00 5.68
874 885 1.449601 CAATTCCACGTCCCCTCCG 60.450 63.158 0.00 0.00 0.00 4.63
938 949 4.447054 CACATCTCTCTCATTTATCCACGC 59.553 45.833 0.00 0.00 0.00 5.34
998 1009 3.207669 CTGCTGCATTCCTCGCCC 61.208 66.667 1.31 0.00 0.00 6.13
1240 1259 2.027625 GCCGACCGTGAGTTCCTTG 61.028 63.158 0.00 0.00 0.00 3.61
1244 1264 0.670854 GACCGTGAGTTCCTTGCCTC 60.671 60.000 0.00 0.00 0.00 4.70
1245 1265 1.376037 CCGTGAGTTCCTTGCCTCC 60.376 63.158 0.00 0.00 0.00 4.30
1246 1266 1.376037 CGTGAGTTCCTTGCCTCCC 60.376 63.158 0.00 0.00 0.00 4.30
1247 1267 1.831652 CGTGAGTTCCTTGCCTCCCT 61.832 60.000 0.00 0.00 0.00 4.20
1248 1268 0.322008 GTGAGTTCCTTGCCTCCCTG 60.322 60.000 0.00 0.00 0.00 4.45
1249 1269 1.377856 GAGTTCCTTGCCTCCCTGC 60.378 63.158 0.00 0.00 0.00 4.85
1250 1270 1.846712 GAGTTCCTTGCCTCCCTGCT 61.847 60.000 0.00 0.00 0.00 4.24
1251 1271 1.377856 GTTCCTTGCCTCCCTGCTC 60.378 63.158 0.00 0.00 0.00 4.26
1252 1272 1.539869 TTCCTTGCCTCCCTGCTCT 60.540 57.895 0.00 0.00 0.00 4.09
1253 1273 1.136329 TTCCTTGCCTCCCTGCTCTT 61.136 55.000 0.00 0.00 0.00 2.85
1254 1274 1.077858 CCTTGCCTCCCTGCTCTTC 60.078 63.158 0.00 0.00 0.00 2.87
1255 1275 1.077858 CTTGCCTCCCTGCTCTTCC 60.078 63.158 0.00 0.00 0.00 3.46
1256 1276 2.549169 CTTGCCTCCCTGCTCTTCCC 62.549 65.000 0.00 0.00 0.00 3.97
1369 1420 2.129555 ATCTTTGCGGTGGGTGCTCT 62.130 55.000 0.00 0.00 0.00 4.09
1583 3808 6.197842 GCTTCATTTCTGTATTACAAGCATGC 59.802 38.462 10.51 10.51 0.00 4.06
1584 3809 6.756299 TCATTTCTGTATTACAAGCATGCA 57.244 33.333 21.98 0.00 0.00 3.96
1789 4032 1.079819 ACCGGTTGAGATGCGTGAG 60.080 57.895 0.00 0.00 0.00 3.51
1876 4119 2.006169 GAAGAGGCTGCTGTTCTTAGC 58.994 52.381 12.18 0.00 43.95 3.09
1980 4225 7.086685 AGGTAAGGGTTCTTTTATCAACTGA 57.913 36.000 0.00 0.00 34.59 3.41
2024 4296 2.757868 TGTTCAAGAACACAGTTTGGGG 59.242 45.455 11.34 0.00 45.42 4.96
2040 4313 0.822164 GGGGTAGAAGCTCTAACGCA 59.178 55.000 15.54 0.00 45.58 5.24
2050 4335 2.231478 AGCTCTAACGCAGCACTTCTTA 59.769 45.455 0.00 0.00 39.56 2.10
2116 4401 0.867746 TCTTCATGTTGCGTGACAGC 59.132 50.000 0.00 0.00 32.19 4.40
2122 4407 2.664518 TTGCGTGACAGCGATGCA 60.665 55.556 0.00 0.00 40.67 3.96
2302 4587 4.406173 CGTGTCCGCAGCGAGACT 62.406 66.667 26.45 0.00 34.02 3.24
2473 4758 3.686016 AGGATGCACGAAGGTTGTTATT 58.314 40.909 0.00 0.00 0.00 1.40
2631 4916 0.523072 CCATTGTTCACCAAGGAGCG 59.477 55.000 0.00 0.00 36.99 5.03
2686 4971 0.589708 GCGGTGTTAGGCTTTTCGTT 59.410 50.000 0.00 0.00 0.00 3.85
2740 5025 1.307355 TGTCTGATGTTGGCCATGCG 61.307 55.000 6.09 0.00 32.56 4.73
2798 5083 2.626780 GCCAACAAGGAAGACCGGC 61.627 63.158 0.00 0.00 41.22 6.13
2800 5085 0.323629 CCAACAAGGAAGACCGGCTA 59.676 55.000 0.00 0.00 41.22 3.93
2908 5193 6.436738 ACCATCAAGAAGCTGAGATCATAT 57.563 37.500 0.00 0.00 0.00 1.78
3412 6979 7.014905 ACAGCTTTTGTGCATTATCATGGATAT 59.985 33.333 0.00 0.00 38.99 1.63
3470 7037 7.272978 CGGAGGAGGAAATGTAGAAATAGAAA 58.727 38.462 0.00 0.00 0.00 2.52
3592 7178 7.038373 ACAAAGCATTTACAATCCACCCTAATT 60.038 33.333 0.00 0.00 35.03 1.40
3593 7179 6.715347 AGCATTTACAATCCACCCTAATTC 57.285 37.500 0.00 0.00 0.00 2.17
3594 7180 6.435164 AGCATTTACAATCCACCCTAATTCT 58.565 36.000 0.00 0.00 0.00 2.40
3595 7181 6.547510 AGCATTTACAATCCACCCTAATTCTC 59.452 38.462 0.00 0.00 0.00 2.87
3803 7392 5.262588 ACAAATCAAGTGAAGGACAAACC 57.737 39.130 0.00 0.00 39.35 3.27
3811 7400 3.165071 GTGAAGGACAAACCCCATCAAT 58.835 45.455 0.00 0.00 40.05 2.57
3913 9532 9.241919 TGTACACACTGAAATTATTCATGGATT 57.758 29.630 0.00 0.00 44.29 3.01
3916 9535 6.477688 CACACTGAAATTATTCATGGATTGCC 59.522 38.462 0.00 0.00 44.29 4.52
3972 9591 9.387123 GTCTTGTTGTTAAATCTCTTTGTCATC 57.613 33.333 0.00 0.00 0.00 2.92
3983 9602 5.789521 TCTCTTTGTCATCGTCCAACATTA 58.210 37.500 0.00 0.00 0.00 1.90
3989 9608 6.189677 TGTCATCGTCCAACATTATTTTCC 57.810 37.500 0.00 0.00 0.00 3.13
3998 9617 6.313658 GTCCAACATTATTTTCCCTGCATTTC 59.686 38.462 0.00 0.00 0.00 2.17
4069 9688 3.290948 TGTTGTAGACTGGGTTGCTTT 57.709 42.857 0.00 0.00 0.00 3.51
4072 9691 3.788227 TGTAGACTGGGTTGCTTTCAT 57.212 42.857 0.00 0.00 0.00 2.57
4096 9717 3.063510 TCTTGAGGATTCAACTGCCAG 57.936 47.619 0.00 0.00 38.37 4.85
4125 9746 7.549488 AGGTTTGAACAACTCATAGTATGTAGC 59.451 37.037 9.94 0.00 32.78 3.58
4129 9750 7.555965 TGAACAACTCATAGTATGTAGCATGT 58.444 34.615 9.94 10.96 0.00 3.21
4145 9766 9.672673 ATGTAGCATGTTTAGTCTTTAATCTGT 57.327 29.630 0.00 0.00 0.00 3.41
4149 9770 7.277981 AGCATGTTTAGTCTTTAATCTGTACCG 59.722 37.037 0.00 0.00 0.00 4.02
4158 9779 9.978044 AGTCTTTAATCTGTACCGTATATTTCC 57.022 33.333 0.00 0.00 0.00 3.13
4159 9780 9.978044 GTCTTTAATCTGTACCGTATATTTCCT 57.022 33.333 0.00 0.00 0.00 3.36
4162 9783 8.597662 TTAATCTGTACCGTATATTTCCTTGC 57.402 34.615 0.00 0.00 0.00 4.01
4163 9784 5.601583 TCTGTACCGTATATTTCCTTGCA 57.398 39.130 0.00 0.00 0.00 4.08
4175 9796 2.363306 TCCTTGCATGTCTGTGGTTT 57.637 45.000 0.00 0.00 0.00 3.27
4176 9797 3.500448 TCCTTGCATGTCTGTGGTTTA 57.500 42.857 0.00 0.00 0.00 2.01
4179 9800 4.458989 TCCTTGCATGTCTGTGGTTTAATC 59.541 41.667 0.00 0.00 0.00 1.75
4189 9810 2.295909 TGTGGTTTAATCTTGCAGGCAC 59.704 45.455 0.00 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.417224 GGAAAACGCGTCCGGGTC 61.417 66.667 14.44 5.62 40.45 4.46
3 4 3.932483 AGGAAAACGCGTCCGGGT 61.932 61.111 14.44 3.37 43.21 5.28
6 7 0.643820 GATACAGGAAAACGCGTCCG 59.356 55.000 14.44 8.85 40.36 4.79
7 8 0.643820 CGATACAGGAAAACGCGTCC 59.356 55.000 14.44 10.30 35.17 4.79
9 10 0.738412 CCCGATACAGGAAAACGCGT 60.738 55.000 5.58 5.58 0.00 6.01
11 12 1.712018 GGCCCGATACAGGAAAACGC 61.712 60.000 0.00 0.00 0.00 4.84
12 13 1.426041 CGGCCCGATACAGGAAAACG 61.426 60.000 0.00 0.00 0.00 3.60
13 14 0.108041 TCGGCCCGATACAGGAAAAC 60.108 55.000 0.00 0.00 0.00 2.43
14 15 0.834612 ATCGGCCCGATACAGGAAAA 59.165 50.000 18.86 0.00 45.13 2.29
15 16 1.707106 TATCGGCCCGATACAGGAAA 58.293 50.000 21.53 0.00 45.13 3.13
16 17 1.707106 TTATCGGCCCGATACAGGAA 58.293 50.000 24.81 9.72 46.35 3.36
17 18 1.707106 TTTATCGGCCCGATACAGGA 58.293 50.000 24.81 8.24 46.35 3.86
18 19 2.140717 GTTTTATCGGCCCGATACAGG 58.859 52.381 24.81 0.00 46.35 4.00
20 21 1.538634 CGGTTTTATCGGCCCGATACA 60.539 52.381 24.81 16.42 46.35 2.29
22 23 0.600782 GCGGTTTTATCGGCCCGATA 60.601 55.000 21.53 21.53 45.13 2.92
25 26 3.932313 CGCGGTTTTATCGGCCCG 61.932 66.667 0.00 0.00 43.22 6.13
26 27 4.246206 GCGCGGTTTTATCGGCCC 62.246 66.667 8.83 0.00 0.00 5.80
28 29 4.584862 CCGCGCGGTTTTATCGGC 62.585 66.667 39.71 0.00 33.36 5.54
30 31 4.584862 GGCCGCGCGGTTTTATCG 62.585 66.667 45.02 21.47 37.65 2.92
31 32 4.246206 GGGCCGCGCGGTTTTATC 62.246 66.667 45.02 29.10 37.65 1.75
32 33 2.944409 TATGGGCCGCGCGGTTTTAT 62.944 55.000 45.02 33.34 37.65 1.40
33 34 2.944409 ATATGGGCCGCGCGGTTTTA 62.944 55.000 45.02 30.89 37.65 1.52
35 36 4.868116 ATATGGGCCGCGCGGTTT 62.868 61.111 45.02 29.58 37.65 3.27
40 41 4.030452 GAAGCATATGGGCCGCGC 62.030 66.667 0.00 0.00 0.00 6.86
41 42 0.602638 TTAGAAGCATATGGGCCGCG 60.603 55.000 4.56 0.00 0.00 6.46
42 43 1.826385 ATTAGAAGCATATGGGCCGC 58.174 50.000 4.56 0.00 0.00 6.53
43 44 6.515272 AATTAATTAGAAGCATATGGGCCG 57.485 37.500 4.56 0.00 0.00 6.13
44 45 8.367156 TGAAAATTAATTAGAAGCATATGGGCC 58.633 33.333 4.56 0.00 0.00 5.80
45 46 9.762933 TTGAAAATTAATTAGAAGCATATGGGC 57.237 29.630 4.56 0.00 0.00 5.36
68 69 8.964476 AGAAAGAGTCAACAGAAGTATTTTGA 57.036 30.769 0.00 0.00 0.00 2.69
80 81 6.540914 ACGAATTGGTAAAGAAAGAGTCAACA 59.459 34.615 0.00 0.00 0.00 3.33
92 93 9.221775 GATTTGTGCTATTACGAATTGGTAAAG 57.778 33.333 15.72 14.23 35.36 1.85
121 122 4.903638 TCGCTCATAAAACTTCTTCACG 57.096 40.909 0.00 0.00 0.00 4.35
215 216 1.511850 CTGATCAAAGTGACACCGCA 58.488 50.000 0.84 0.00 0.00 5.69
218 219 1.808945 CAGGCTGATCAAAGTGACACC 59.191 52.381 9.42 0.00 0.00 4.16
247 248 1.200020 CAGAACCCGATGCTTTCCAAC 59.800 52.381 0.00 0.00 0.00 3.77
260 261 2.668550 GGCACGACACCAGAACCC 60.669 66.667 0.00 0.00 0.00 4.11
292 293 9.530633 GGGTTATTATCATTAACTATAGCGGAG 57.469 37.037 0.00 0.00 31.62 4.63
304 305 6.126332 TGCAGAGGTTGGGGTTATTATCATTA 60.126 38.462 0.00 0.00 0.00 1.90
305 306 5.140454 GCAGAGGTTGGGGTTATTATCATT 58.860 41.667 0.00 0.00 0.00 2.57
306 307 4.167892 TGCAGAGGTTGGGGTTATTATCAT 59.832 41.667 0.00 0.00 0.00 2.45
307 308 3.525609 TGCAGAGGTTGGGGTTATTATCA 59.474 43.478 0.00 0.00 0.00 2.15
308 309 4.164843 TGCAGAGGTTGGGGTTATTATC 57.835 45.455 0.00 0.00 0.00 1.75
309 310 4.017499 AGTTGCAGAGGTTGGGGTTATTAT 60.017 41.667 0.00 0.00 0.00 1.28
310 311 3.332485 AGTTGCAGAGGTTGGGGTTATTA 59.668 43.478 0.00 0.00 0.00 0.98
311 312 2.110011 AGTTGCAGAGGTTGGGGTTATT 59.890 45.455 0.00 0.00 0.00 1.40
319 320 0.400213 TGGGGTAGTTGCAGAGGTTG 59.600 55.000 0.00 0.00 0.00 3.77
339 340 3.991773 TGGAGTATTGCTTACGTTGTCAC 59.008 43.478 0.00 0.00 35.84 3.67
340 341 3.991773 GTGGAGTATTGCTTACGTTGTCA 59.008 43.478 0.00 0.00 35.84 3.58
365 366 0.250295 CGTCTTTGCAGTCCCCTGAA 60.250 55.000 0.00 0.00 41.50 3.02
401 402 7.173907 AGGTGTATTTGTTGATGAAGACTTCAG 59.826 37.037 21.78 0.00 43.98 3.02
406 407 5.940470 AGGAGGTGTATTTGTTGATGAAGAC 59.060 40.000 0.00 0.00 0.00 3.01
417 418 1.408822 GGGAGCCAGGAGGTGTATTTG 60.409 57.143 0.00 0.00 37.19 2.32
430 431 3.138283 CCTCTTAATTATGTGGGGAGCCA 59.862 47.826 10.26 0.00 0.00 4.75
432 433 4.439253 ACCTCTTAATTATGTGGGGAGC 57.561 45.455 18.46 0.00 0.00 4.70
437 438 6.828273 TGATGGTGAACCTCTTAATTATGTGG 59.172 38.462 14.64 14.64 36.82 4.17
440 441 7.941238 AGGATGATGGTGAACCTCTTAATTATG 59.059 37.037 0.37 0.00 36.82 1.90
476 477 4.843728 TGGAAGATCCAACCACTATGTTC 58.156 43.478 0.00 0.00 45.00 3.18
490 491 6.441093 TGCACTTGTATCAATTGGAAGATC 57.559 37.500 5.42 0.00 0.00 2.75
575 576 3.869272 GTTGCCGCGCCTGATCAG 61.869 66.667 16.24 16.24 0.00 2.90
613 614 7.755822 CGTGCTCTACTTCTTGTCTAAAATACT 59.244 37.037 0.00 0.00 0.00 2.12
614 615 7.754027 TCGTGCTCTACTTCTTGTCTAAAATAC 59.246 37.037 0.00 0.00 0.00 1.89
615 616 7.823665 TCGTGCTCTACTTCTTGTCTAAAATA 58.176 34.615 0.00 0.00 0.00 1.40
616 617 6.688578 TCGTGCTCTACTTCTTGTCTAAAAT 58.311 36.000 0.00 0.00 0.00 1.82
624 625 1.737363 GCCCTCGTGCTCTACTTCTTG 60.737 57.143 0.00 0.00 0.00 3.02
630 631 2.809010 GAGGCCCTCGTGCTCTAC 59.191 66.667 0.00 0.00 0.00 2.59
647 648 4.339429 CGCCACTGTTTTATTATTCCACG 58.661 43.478 0.00 0.00 0.00 4.94
667 669 0.459759 CTCTCCCCGTTTTCTACCGC 60.460 60.000 0.00 0.00 0.00 5.68
670 672 1.549170 TCAGCTCTCCCCGTTTTCTAC 59.451 52.381 0.00 0.00 0.00 2.59
874 885 3.791586 GGCTGTGGAGAGGAGGGC 61.792 72.222 0.00 0.00 0.00 5.19
998 1009 2.202919 TGGTGCTCGCCATCATCG 60.203 61.111 0.00 0.00 32.81 3.84
1240 1259 3.803162 GGGGAAGAGCAGGGAGGC 61.803 72.222 0.00 0.00 0.00 4.70
1244 1264 0.620121 AAGAGAGGGGAAGAGCAGGG 60.620 60.000 0.00 0.00 0.00 4.45
1245 1265 0.829990 GAAGAGAGGGGAAGAGCAGG 59.170 60.000 0.00 0.00 0.00 4.85
1246 1266 0.829990 GGAAGAGAGGGGAAGAGCAG 59.170 60.000 0.00 0.00 0.00 4.24
1247 1267 0.415429 AGGAAGAGAGGGGAAGAGCA 59.585 55.000 0.00 0.00 0.00 4.26
1248 1268 1.119684 GAGGAAGAGAGGGGAAGAGC 58.880 60.000 0.00 0.00 0.00 4.09
1249 1269 1.691163 GGGAGGAAGAGAGGGGAAGAG 60.691 61.905 0.00 0.00 0.00 2.85
1250 1270 0.340208 GGGAGGAAGAGAGGGGAAGA 59.660 60.000 0.00 0.00 0.00 2.87
1251 1271 0.692756 GGGGAGGAAGAGAGGGGAAG 60.693 65.000 0.00 0.00 0.00 3.46
1252 1272 1.396594 GGGGAGGAAGAGAGGGGAA 59.603 63.158 0.00 0.00 0.00 3.97
1253 1273 3.010226 CGGGGAGGAAGAGAGGGGA 62.010 68.421 0.00 0.00 0.00 4.81
1254 1274 2.444895 CGGGGAGGAAGAGAGGGG 60.445 72.222 0.00 0.00 0.00 4.79
1255 1275 3.157949 GCGGGGAGGAAGAGAGGG 61.158 72.222 0.00 0.00 0.00 4.30
1256 1276 3.157949 GGCGGGGAGGAAGAGAGG 61.158 72.222 0.00 0.00 0.00 3.69
1379 1430 4.400529 AAAATTGTTGACCAACTCCCAC 57.599 40.909 13.26 0.00 41.67 4.61
1478 2605 2.884639 GGAAACAAGCTTTCCTGTGCTA 59.115 45.455 8.21 0.00 43.45 3.49
1543 3083 1.199789 TGAAGCATGTTCCGAATGTGC 59.800 47.619 10.92 10.92 36.11 4.57
1550 3768 3.837213 ACAGAAATGAAGCATGTTCCG 57.163 42.857 0.00 0.00 0.00 4.30
1753 3996 1.338105 GGTGCTGTGTGTATGCTGAGA 60.338 52.381 0.00 0.00 0.00 3.27
1789 4032 4.778415 TCTGCGACCGCGAGCTTC 62.778 66.667 8.23 0.00 45.51 3.86
1825 4068 2.350522 AGATTGGTTAGCTCTGCAACG 58.649 47.619 0.00 0.00 0.00 4.10
1876 4119 0.958091 TTTCCATTCGGTTGCAGGTG 59.042 50.000 0.00 0.00 0.00 4.00
1980 4225 6.594937 ACAACAACAAAAGACAAGCAAATGAT 59.405 30.769 0.00 0.00 0.00 2.45
2024 4296 1.921230 GTGCTGCGTTAGAGCTTCTAC 59.079 52.381 0.00 0.00 37.35 2.59
2040 4313 6.201615 GCTTTTCTGCAAAAATAAGAAGTGCT 59.798 34.615 7.08 0.00 36.18 4.40
2050 4335 3.588955 GATCCCGCTTTTCTGCAAAAAT 58.411 40.909 7.08 0.00 30.90 1.82
2122 4407 1.577328 CCTCAAACAGATGGCGCGTT 61.577 55.000 8.43 0.00 0.00 4.84
2294 4579 4.797604 GCCACATGATATGTTAGTCTCGCT 60.798 45.833 0.00 0.00 42.70 4.93
2302 4587 2.871633 CACAGCGCCACATGATATGTTA 59.128 45.455 2.29 0.00 42.70 2.41
2460 4745 3.805823 CGGTTCACAATAACAACCTTCG 58.194 45.455 0.00 0.00 37.95 3.79
2740 5025 3.181520 GGTCATCAACATTGTACACTCGC 60.182 47.826 0.00 0.00 0.00 5.03
2798 5083 2.027385 GGCCTCCATTGCTTTCCTTAG 58.973 52.381 0.00 0.00 0.00 2.18
2800 5085 0.615827 GGGCCTCCATTGCTTTCCTT 60.616 55.000 0.84 0.00 0.00 3.36
2908 5193 0.764369 AAGCCCTGATCCTATCGGCA 60.764 55.000 8.06 0.00 37.99 5.69
3442 7009 1.757118 TCTACATTTCCTCCTCCGCTG 59.243 52.381 0.00 0.00 0.00 5.18
3476 7045 9.851686 TCATTAGATGAATATTGCCACTAAAGT 57.148 29.630 0.00 0.00 36.11 2.66
3694 7280 6.071334 GGGAAAAACACAAAAATCCCCAAAAA 60.071 34.615 0.00 0.00 40.54 1.94
3972 9591 3.192422 TGCAGGGAAAATAATGTTGGACG 59.808 43.478 0.00 0.00 0.00 4.79
4069 9688 5.356190 GCAGTTGAATCCTCAAGATCAATGA 59.644 40.000 0.00 0.00 42.27 2.57
4072 9691 4.012374 GGCAGTTGAATCCTCAAGATCAA 58.988 43.478 0.00 0.00 42.27 2.57
4096 9717 3.746492 ACTATGAGTTGTTCAAACCTCGC 59.254 43.478 0.00 0.00 39.77 5.03
4125 9746 8.475331 ACGGTACAGATTAAAGACTAAACATG 57.525 34.615 0.00 0.00 0.00 3.21
4145 9766 5.989168 CAGACATGCAAGGAAATATACGGTA 59.011 40.000 0.00 0.00 0.00 4.02
4147 9768 4.816385 ACAGACATGCAAGGAAATATACGG 59.184 41.667 0.00 0.00 0.00 4.02
4149 9770 5.590259 ACCACAGACATGCAAGGAAATATAC 59.410 40.000 0.00 0.00 0.00 1.47
4153 9774 2.880443 ACCACAGACATGCAAGGAAAT 58.120 42.857 0.00 0.00 0.00 2.17
4155 9776 2.363306 AACCACAGACATGCAAGGAA 57.637 45.000 0.00 0.00 0.00 3.36
4156 9777 2.363306 AAACCACAGACATGCAAGGA 57.637 45.000 0.00 0.00 0.00 3.36
4157 9778 4.460382 AGATTAAACCACAGACATGCAAGG 59.540 41.667 0.00 0.00 0.00 3.61
4158 9779 5.633830 AGATTAAACCACAGACATGCAAG 57.366 39.130 0.00 0.00 0.00 4.01
4159 9780 5.771469 CAAGATTAAACCACAGACATGCAA 58.229 37.500 0.00 0.00 0.00 4.08
4160 9781 4.321156 GCAAGATTAAACCACAGACATGCA 60.321 41.667 0.00 0.00 0.00 3.96
4161 9782 4.168760 GCAAGATTAAACCACAGACATGC 58.831 43.478 0.00 0.00 0.00 4.06
4162 9783 5.375417 TGCAAGATTAAACCACAGACATG 57.625 39.130 0.00 0.00 0.00 3.21
4163 9784 4.460382 CCTGCAAGATTAAACCACAGACAT 59.540 41.667 0.00 0.00 34.07 3.06
4175 9796 2.646930 CATCAGGTGCCTGCAAGATTA 58.353 47.619 13.12 0.00 43.31 1.75
4176 9797 1.471119 CATCAGGTGCCTGCAAGATT 58.529 50.000 13.12 0.00 43.31 2.40


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

AutoCloner maintained by Alex Coulton.