Multiple sequence alignment - TraesCS1A01G427600

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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 TraesCS1A01G427600 chr1A 100.000 4029 0 0 1 4029 581874348 581870320 0.000000e+00 7441.0
1 TraesCS1A01G427600 chr1A 98.361 61 1 0 450 510 23453244 23453184 1.530000e-19 108.0
2 TraesCS1A01G427600 chr1A 95.082 61 2 1 450 510 561347966 561347907 1.190000e-15 95.3
3 TraesCS1A01G427600 chr1D 95.540 2646 98 8 584 3220 484558535 484555901 0.000000e+00 4215.0
4 TraesCS1A01G427600 chr1D 97.098 379 6 4 3654 4029 484555377 484555001 5.680000e-178 634.0
5 TraesCS1A01G427600 chr1D 90.640 406 30 2 3220 3622 484555863 484555463 2.130000e-147 532.0
6 TraesCS1A01G427600 chr1D 86.279 430 20 6 1 408 484559072 484558660 8.000000e-117 431.0
7 TraesCS1A01G427600 chr1D 88.750 80 7 1 3316 3393 204481553 204481632 3.310000e-16 97.1
8 TraesCS1A01G427600 chr1D 97.917 48 1 0 403 450 484558612 484558565 2.580000e-12 84.2
9 TraesCS1A01G427600 chr1B 92.980 1923 92 13 576 2486 674813836 674811945 0.000000e+00 2763.0
10 TraesCS1A01G427600 chr1B 88.687 716 46 10 2512 3220 674811966 674811279 0.000000e+00 841.0
11 TraesCS1A01G427600 chr1B 85.841 339 17 11 3706 4025 674810778 674810452 8.350000e-87 331.0
12 TraesCS1A01G427600 chr1B 86.084 309 15 8 1 284 674814400 674814095 1.410000e-79 307.0
13 TraesCS1A01G427600 chr1B 92.857 196 9 3 3433 3624 674811138 674810944 3.070000e-71 279.0
14 TraesCS1A01G427600 chr1B 93.519 108 4 1 285 392 674814066 674813962 1.500000e-34 158.0
15 TraesCS1A01G427600 chr1B 87.963 108 4 3 3219 3326 674811242 674811144 7.070000e-23 119.0
16 TraesCS1A01G427600 chr1B 97.500 40 0 1 663 701 674815041 674815002 2.600000e-07 67.6
17 TraesCS1A01G427600 chr7A 98.485 66 0 1 446 510 12226981 12226916 9.150000e-22 115.0
18 TraesCS1A01G427600 chr3D 94.366 71 4 0 3322 3392 121536237 121536167 4.260000e-20 110.0
19 TraesCS1A01G427600 chr2A 96.923 65 2 0 446 510 65475299 65475235 4.260000e-20 110.0
20 TraesCS1A01G427600 chr2A 98.361 61 1 0 450 510 634875411 634875471 1.530000e-19 108.0
21 TraesCS1A01G427600 chr2A 95.349 43 2 0 1 43 765599036 765598994 7.230000e-08 69.4
22 TraesCS1A01G427600 chr6A 98.361 61 1 0 450 510 50186511 50186451 1.530000e-19 108.0
23 TraesCS1A01G427600 chr6A 98.361 61 0 1 450 510 5281857 5281916 5.510000e-19 106.0
24 TraesCS1A01G427600 chr6A 96.774 62 1 1 449 510 64256802 64256862 7.120000e-18 102.0
25 TraesCS1A01G427600 chr6A 90.789 76 6 1 3319 3393 169203401 169203326 2.560000e-17 100.0
26 TraesCS1A01G427600 chr4B 93.056 72 5 0 3322 3393 519258918 519258989 5.510000e-19 106.0
27 TraesCS1A01G427600 chr6B 91.781 73 6 0 3321 3393 96970757 96970829 7.120000e-18 102.0
28 TraesCS1A01G427600 chr5D 91.549 71 6 0 3323 3393 562030920 562030990 9.220000e-17 99.0
29 TraesCS1A01G427600 chr3A 90.411 73 7 0 3321 3393 514270927 514270999 3.310000e-16 97.1
30 TraesCS1A01G427600 chr3A 97.436 39 1 0 1 39 111879986 111880024 2.600000e-07 67.6
31 TraesCS1A01G427600 chr2B 90.278 72 7 0 3322 3393 143488119 143488048 1.190000e-15 95.3
32 TraesCS1A01G427600 chr4A 94.643 56 2 1 451 505 731643829 731643774 7.170000e-13 86.1
33 TraesCS1A01G427600 chr5B 90.196 51 5 0 1 51 9071093 9071143 2.600000e-07 67.6
34 TraesCS1A01G427600 chr3B 93.023 43 3 0 1 43 78567882 78567840 3.360000e-06 63.9
35 TraesCS1A01G427600 chr3B 100.000 30 0 0 2 31 816065405 816065376 5.630000e-04 56.5


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 TraesCS1A01G427600 chr1A 581870320 581874348 4028 True 7441.00 7441 100.000000 1 4029 1 chr1A.!!$R3 4028
1 TraesCS1A01G427600 chr1D 484555001 484559072 4071 True 1179.24 4215 93.494800 1 4029 5 chr1D.!!$R1 4028
2 TraesCS1A01G427600 chr1B 674810452 674815041 4589 True 608.20 2763 90.678875 1 4025 8 chr1B.!!$R1 4024

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
622 1370 0.390866 ACTGCTCACTTCGGATGCTG 60.391 55.0 0.00 0.00 0.00 4.41 F
1435 2194 0.674895 GGCCACGCTCTTGACAAGAT 60.675 55.0 18.04 1.09 36.82 2.40 F
2232 2992 0.888736 TGTTGGCATCCACAAGACCG 60.889 55.0 0.00 0.00 30.78 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1447 2206 2.166050 TGTCATGCACAACTGTTTTGCT 59.834 40.909 26.24 13.2 37.16 3.91 R
2830 3595 0.317160 TCTCGAGCTCCTTTTTGCGA 59.683 50.000 7.81 0.0 0.00 5.10 R
3699 4627 0.256177 GCTAGCTTTTAGGCACCCCT 59.744 55.000 7.70 0.0 45.61 4.79 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
45 687 7.371936 ACTCTACTATTGTCGATATTTCAGCC 58.628 38.462 0.00 0.00 0.00 4.85
51 693 8.827677 ACTATTGTCGATATTTCAGCCTTTTAC 58.172 33.333 0.00 0.00 0.00 2.01
85 727 4.097551 TGTTCTGGGTGTTGATCATCAA 57.902 40.909 8.04 0.00 33.32 2.57
138 780 7.748691 TGAGTTACTAAAAACGCCCTTTATT 57.251 32.000 0.00 0.00 34.46 1.40
161 803 7.969690 TTGAAAAATCAAAGGGCATCCTATA 57.030 32.000 0.00 0.00 44.07 1.31
175 817 5.945784 GGCATCCTATACAAATGAAGGCATA 59.054 40.000 0.00 0.00 33.44 3.14
263 930 2.990740 TGGATTACAGGCCCAGTTTT 57.009 45.000 0.00 0.00 0.00 2.43
302 997 1.228228 GGCCCAAGATGCCTCATCA 59.772 57.895 9.19 0.00 45.70 3.07
360 1055 3.003173 CACTCCCCTCCGGCTCAA 61.003 66.667 0.00 0.00 0.00 3.02
399 1094 1.671901 GCGACTTCCTCTAGCCTGCT 61.672 60.000 0.00 0.00 0.00 4.24
450 1198 2.288666 CGCATTGTGCCAGGTATACTT 58.711 47.619 2.25 0.00 41.12 2.24
451 1199 2.682856 CGCATTGTGCCAGGTATACTTT 59.317 45.455 2.25 0.00 41.12 2.66
452 1200 3.128589 CGCATTGTGCCAGGTATACTTTT 59.871 43.478 2.25 0.00 41.12 2.27
453 1201 4.380444 CGCATTGTGCCAGGTATACTTTTT 60.380 41.667 2.25 0.00 41.12 1.94
472 1220 4.594123 TTTTTGATCGAAAGGGGTTTCC 57.406 40.909 8.14 0.00 0.00 3.13
494 1242 4.689071 CCCCCGCTCCATTTTATAAAAAC 58.311 43.478 14.35 2.45 0.00 2.43
495 1243 4.356289 CCCCGCTCCATTTTATAAAAACG 58.644 43.478 14.35 12.22 0.00 3.60
496 1244 4.096682 CCCCGCTCCATTTTATAAAAACGA 59.903 41.667 14.35 11.20 0.00 3.85
497 1245 5.393243 CCCCGCTCCATTTTATAAAAACGAA 60.393 40.000 14.35 1.20 0.00 3.85
498 1246 5.741982 CCCGCTCCATTTTATAAAAACGAAG 59.258 40.000 14.35 10.43 0.00 3.79
499 1247 5.229260 CCGCTCCATTTTATAAAAACGAAGC 59.771 40.000 14.35 16.95 0.00 3.86
500 1248 5.797934 CGCTCCATTTTATAAAAACGAAGCA 59.202 36.000 23.23 3.00 0.00 3.91
501 1249 6.306837 CGCTCCATTTTATAAAAACGAAGCAA 59.693 34.615 23.23 2.46 0.00 3.91
502 1250 7.148885 CGCTCCATTTTATAAAAACGAAGCAAA 60.149 33.333 23.23 1.92 0.00 3.68
503 1251 8.162245 GCTCCATTTTATAAAAACGAAGCAAAG 58.838 33.333 14.35 4.43 0.00 2.77
504 1252 8.013236 TCCATTTTATAAAAACGAAGCAAAGC 57.987 30.769 14.35 0.00 0.00 3.51
505 1253 6.947680 CCATTTTATAAAAACGAAGCAAAGCG 59.052 34.615 14.35 0.00 0.00 4.68
506 1254 7.148885 CCATTTTATAAAAACGAAGCAAAGCGA 60.149 33.333 14.35 0.00 0.00 4.93
507 1255 6.904954 TTTATAAAAACGAAGCAAAGCGAG 57.095 33.333 0.00 0.00 0.00 5.03
508 1256 2.844122 AAAAACGAAGCAAAGCGAGT 57.156 40.000 0.00 0.00 0.00 4.18
515 1263 0.685097 AAGCAAAGCGAGTCCCTACA 59.315 50.000 0.00 0.00 0.00 2.74
543 1291 5.014123 TCTCCTTGTTTCTCTCTCTCTCTCT 59.986 44.000 0.00 0.00 0.00 3.10
544 1292 5.253330 TCCTTGTTTCTCTCTCTCTCTCTC 58.747 45.833 0.00 0.00 0.00 3.20
545 1293 5.014123 TCCTTGTTTCTCTCTCTCTCTCTCT 59.986 44.000 0.00 0.00 0.00 3.10
546 1294 5.355350 CCTTGTTTCTCTCTCTCTCTCTCTC 59.645 48.000 0.00 0.00 0.00 3.20
547 1295 5.762179 TGTTTCTCTCTCTCTCTCTCTCT 57.238 43.478 0.00 0.00 0.00 3.10
548 1296 5.734720 TGTTTCTCTCTCTCTCTCTCTCTC 58.265 45.833 0.00 0.00 0.00 3.20
549 1297 5.485353 TGTTTCTCTCTCTCTCTCTCTCTCT 59.515 44.000 0.00 0.00 0.00 3.10
550 1298 5.860941 TTCTCTCTCTCTCTCTCTCTCTC 57.139 47.826 0.00 0.00 0.00 3.20
551 1299 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
552 1300 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
553 1301 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
554 1302 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
555 1303 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
556 1304 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
557 1305 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
558 1306 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
559 1307 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
560 1308 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
561 1309 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
562 1310 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
563 1311 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
564 1312 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
565 1313 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
566 1314 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
567 1315 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
568 1316 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
569 1317 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
570 1318 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
571 1319 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
572 1320 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
573 1321 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
574 1322 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
575 1323 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
576 1324 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
577 1325 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
578 1326 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
579 1327 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
580 1328 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
581 1329 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
582 1330 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
583 1331 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
584 1332 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
585 1333 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
586 1334 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
587 1335 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
588 1336 5.523588 TCTCTCTCTCTCTCTCTCTCTCTT 58.476 45.833 0.00 0.00 0.00 2.85
622 1370 0.390866 ACTGCTCACTTCGGATGCTG 60.391 55.000 0.00 0.00 0.00 4.41
649 1397 2.413634 CCGTTCCATTTACTTCGTTGCC 60.414 50.000 0.00 0.00 0.00 4.52
705 1457 4.097892 CCCACTGCCCTTGTAAATGAATAC 59.902 45.833 0.00 0.00 0.00 1.89
801 1553 0.878961 AACGAACCTGAACGCTCACC 60.879 55.000 0.00 0.00 0.00 4.02
855 1607 4.081031 CCTAGTTAGTTCCCCTTCTTCACC 60.081 50.000 0.00 0.00 0.00 4.02
872 1624 4.837896 TCACCGCATTTGTGATTTTGTA 57.162 36.364 0.00 0.00 37.80 2.41
1060 1816 1.439365 CGAACAGTCAAGCTTGCGC 60.439 57.895 21.99 15.91 0.00 6.09
1178 1934 1.526686 CACTGGCTTGCACAGGACA 60.527 57.895 7.62 0.00 40.23 4.02
1228 1987 3.429410 GGCCCATATTTGTTCTTCTGCAC 60.429 47.826 0.00 0.00 0.00 4.57
1288 2047 3.691118 AGACGATTGTCCACCATCAAATG 59.309 43.478 9.62 0.00 46.74 2.32
1293 2052 2.794103 TGTCCACCATCAAATGTGGAG 58.206 47.619 11.40 0.00 45.38 3.86
1435 2194 0.674895 GGCCACGCTCTTGACAAGAT 60.675 55.000 18.04 1.09 36.82 2.40
1525 2284 9.656323 AGTACAATCTGGAGGAGTAATACATTA 57.344 33.333 0.00 0.00 0.00 1.90
1663 2423 4.065088 TGCTCTTGTTATGGTCTGTGAAC 58.935 43.478 0.00 0.00 0.00 3.18
1679 2439 7.040823 GGTCTGTGAACTCTCTGAAAATTCAAT 60.041 37.037 0.00 0.00 36.64 2.57
1944 2704 5.966742 TGATCCTTCGTATATGGTCAGAG 57.033 43.478 0.00 0.00 0.00 3.35
2043 2803 4.529769 TCTGAGATGATGTCTGTGTTCCTT 59.470 41.667 0.00 0.00 37.29 3.36
2232 2992 0.888736 TGTTGGCATCCACAAGACCG 60.889 55.000 0.00 0.00 30.78 4.79
2250 3010 2.275318 CCGAAGCTTAAAGAGAGGCTG 58.725 52.381 0.00 0.00 35.08 4.85
2260 3020 1.859302 AGAGAGGCTGACCAAGGTAG 58.141 55.000 0.00 0.00 39.06 3.18
2304 3064 3.437395 TGCATTGCGTCCTAATACGTTTT 59.563 39.130 3.84 0.00 44.64 2.43
2305 3065 4.083217 TGCATTGCGTCCTAATACGTTTTT 60.083 37.500 3.84 0.00 44.64 1.94
2507 3267 7.640630 GTGATCGAGCCTATATAGACATTTACG 59.359 40.741 11.53 7.07 0.00 3.18
2508 3268 6.432607 TCGAGCCTATATAGACATTTACGG 57.567 41.667 11.53 0.00 0.00 4.02
2509 3269 6.175471 TCGAGCCTATATAGACATTTACGGA 58.825 40.000 11.53 0.00 0.00 4.69
2510 3270 6.315642 TCGAGCCTATATAGACATTTACGGAG 59.684 42.308 11.53 0.00 0.00 4.63
2512 3272 7.279536 CGAGCCTATATAGACATTTACGGAGTA 59.720 40.741 11.53 0.00 45.11 2.59
2513 3273 8.278729 AGCCTATATAGACATTTACGGAGTAC 57.721 38.462 11.53 0.00 45.76 2.73
2545 3305 9.638176 AATACATTTCTGATTGATCCTAAAGCT 57.362 29.630 0.00 0.00 0.00 3.74
2623 3383 7.337942 GGTGACATAATCTGAATTCCTTTGTCT 59.662 37.037 2.27 0.00 0.00 3.41
2694 3454 8.785329 TGTTTTATTAGAATGCCCCAAAAATC 57.215 30.769 0.00 0.00 0.00 2.17
2699 3459 7.588497 ATTAGAATGCCCCAAAAATCTAGAC 57.412 36.000 0.00 0.00 0.00 2.59
2700 3460 5.198602 AGAATGCCCCAAAAATCTAGACT 57.801 39.130 0.00 0.00 0.00 3.24
2738 3498 2.380064 ACTCCTTGCACCCATTGAAA 57.620 45.000 0.00 0.00 0.00 2.69
2790 3551 4.529769 TCATCTTCATCTTGTCCTGACACT 59.470 41.667 0.00 0.00 41.67 3.55
2799 3560 4.039245 TCTTGTCCTGACACTAACTCCAAG 59.961 45.833 0.00 0.00 41.67 3.61
2818 3583 6.715280 TCCAAGCTCTTACTTTTCATGATCT 58.285 36.000 0.00 0.00 0.00 2.75
2830 3595 1.831106 TCATGATCTAAGTGGCACGGT 59.169 47.619 12.71 7.05 0.00 4.83
2836 3601 1.225376 CTAAGTGGCACGGTCGCAAA 61.225 55.000 12.71 0.00 0.00 3.68
2861 3626 1.069568 AGCTCGAGATCGTGATAAGCG 60.070 52.381 18.75 0.00 38.63 4.68
2872 3637 0.739462 TGATAAGCGCACGGACAAGG 60.739 55.000 11.47 0.00 0.00 3.61
2956 3721 2.997897 GACCTGGTGACGGAGCCT 60.998 66.667 2.82 0.00 39.98 4.58
3071 3836 1.610522 GGCAGCAGGGTAGCATTTATG 59.389 52.381 0.00 0.00 36.85 1.90
3097 3862 7.415989 GCATTCATGGAGTTCTTACATTGATGT 60.416 37.037 1.84 1.84 44.48 3.06
3255 4061 3.442625 TCTTTGCCATGATTTCAGCTGAG 59.557 43.478 17.43 4.45 0.00 3.35
3268 4074 2.481568 TCAGCTGAGCAGACAAAAATCG 59.518 45.455 13.74 0.00 0.00 3.34
3349 4158 4.100498 TCCTTCCGTCCCATAATGTAAGAC 59.900 45.833 0.00 0.00 0.00 3.01
3350 4159 4.377897 CTTCCGTCCCATAATGTAAGACC 58.622 47.826 0.00 0.00 0.00 3.85
3353 4162 4.100498 TCCGTCCCATAATGTAAGACCTTC 59.900 45.833 0.00 0.00 0.00 3.46
3357 4166 7.270047 CGTCCCATAATGTAAGACCTTCTTTA 58.730 38.462 0.00 0.00 37.89 1.85
3362 4171 8.388103 CCATAATGTAAGACCTTCTTTAACACG 58.612 37.037 0.00 0.00 37.89 4.49
3364 4173 7.653767 AATGTAAGACCTTCTTTAACACGAG 57.346 36.000 0.00 0.00 37.89 4.18
3365 4174 6.152932 TGTAAGACCTTCTTTAACACGAGT 57.847 37.500 0.00 0.00 37.89 4.18
3366 4175 5.981315 TGTAAGACCTTCTTTAACACGAGTG 59.019 40.000 1.13 1.13 37.89 3.51
3417 4226 3.328382 TGAAACGGAGGGAGTACAATG 57.672 47.619 0.00 0.00 0.00 2.82
3531 4340 8.178313 TCGCCTACTCTTTGATGATTCTATTA 57.822 34.615 0.00 0.00 0.00 0.98
3800 4741 2.764314 CGCAGGCCGAAATCCCAAG 61.764 63.158 0.00 0.00 40.02 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 687 7.307219 CCAGAACAAACTAAGAGACGGTAAAAG 60.307 40.741 0.00 0.00 0.00 2.27
51 693 3.244112 ACCCAGAACAAACTAAGAGACGG 60.244 47.826 0.00 0.00 0.00 4.79
85 727 0.960364 ATCAGGCGGATGCAAAACGT 60.960 50.000 0.00 0.00 45.35 3.99
86 728 0.523968 CATCAGGCGGATGCAAAACG 60.524 55.000 14.51 0.00 46.35 3.60
87 729 3.334078 CATCAGGCGGATGCAAAAC 57.666 52.632 14.51 0.00 46.35 2.43
138 780 6.894654 TGTATAGGATGCCCTTTGATTTTTCA 59.105 34.615 0.00 0.00 40.78 2.69
161 803 8.084073 GTGTATATGCATTATGCCTTCATTTGT 58.916 33.333 15.06 0.00 44.23 2.83
175 817 5.876651 TGAGGAGTCTGTGTATATGCATT 57.123 39.130 3.54 0.00 0.00 3.56
263 930 2.192664 TGCGTCAATTCTGGGCTAAA 57.807 45.000 0.00 0.00 0.00 1.85
451 1199 4.594123 GGAAACCCCTTTCGATCAAAAA 57.406 40.909 0.00 0.00 37.27 1.94
472 1220 4.689071 GTTTTTATAAAATGGAGCGGGGG 58.311 43.478 11.33 0.00 0.00 5.40
473 1221 4.096682 TCGTTTTTATAAAATGGAGCGGGG 59.903 41.667 11.33 0.00 0.00 5.73
474 1222 5.238006 TCGTTTTTATAAAATGGAGCGGG 57.762 39.130 11.33 0.00 0.00 6.13
475 1223 5.229260 GCTTCGTTTTTATAAAATGGAGCGG 59.771 40.000 19.91 11.97 37.83 5.52
476 1224 5.797934 TGCTTCGTTTTTATAAAATGGAGCG 59.202 36.000 24.58 17.71 46.05 5.03
477 1225 7.575332 TTGCTTCGTTTTTATAAAATGGAGC 57.425 32.000 24.08 24.08 44.30 4.70
478 1226 8.162245 GCTTTGCTTCGTTTTTATAAAATGGAG 58.838 33.333 11.33 11.64 0.00 3.86
479 1227 7.148885 CGCTTTGCTTCGTTTTTATAAAATGGA 60.149 33.333 11.33 8.91 0.00 3.41
480 1228 6.947680 CGCTTTGCTTCGTTTTTATAAAATGG 59.052 34.615 11.33 6.89 0.00 3.16
481 1229 7.715821 TCGCTTTGCTTCGTTTTTATAAAATG 58.284 30.769 11.33 7.71 0.00 2.32
482 1230 7.593644 ACTCGCTTTGCTTCGTTTTTATAAAAT 59.406 29.630 11.33 0.00 0.00 1.82
483 1231 6.913673 ACTCGCTTTGCTTCGTTTTTATAAAA 59.086 30.769 6.54 6.54 0.00 1.52
484 1232 6.432107 ACTCGCTTTGCTTCGTTTTTATAAA 58.568 32.000 0.00 0.00 0.00 1.40
485 1233 5.992729 ACTCGCTTTGCTTCGTTTTTATAA 58.007 33.333 0.00 0.00 0.00 0.98
486 1234 5.390145 GGACTCGCTTTGCTTCGTTTTTATA 60.390 40.000 0.00 0.00 0.00 0.98
487 1235 4.464112 GACTCGCTTTGCTTCGTTTTTAT 58.536 39.130 0.00 0.00 0.00 1.40
488 1236 3.303526 GGACTCGCTTTGCTTCGTTTTTA 60.304 43.478 0.00 0.00 0.00 1.52
489 1237 2.540973 GGACTCGCTTTGCTTCGTTTTT 60.541 45.455 0.00 0.00 0.00 1.94
490 1238 1.002792 GGACTCGCTTTGCTTCGTTTT 60.003 47.619 0.00 0.00 0.00 2.43
491 1239 0.586802 GGACTCGCTTTGCTTCGTTT 59.413 50.000 0.00 0.00 0.00 3.60
492 1240 1.228657 GGGACTCGCTTTGCTTCGTT 61.229 55.000 0.00 0.00 0.00 3.85
493 1241 1.668151 GGGACTCGCTTTGCTTCGT 60.668 57.895 0.00 0.00 0.00 3.85
494 1242 0.108804 TAGGGACTCGCTTTGCTTCG 60.109 55.000 0.21 0.00 41.75 3.79
495 1243 1.337823 TGTAGGGACTCGCTTTGCTTC 60.338 52.381 0.21 0.00 41.75 3.86
496 1244 0.685097 TGTAGGGACTCGCTTTGCTT 59.315 50.000 0.21 0.00 41.75 3.91
497 1245 0.037232 GTGTAGGGACTCGCTTTGCT 60.037 55.000 0.21 0.00 41.75 3.91
498 1246 0.037232 AGTGTAGGGACTCGCTTTGC 60.037 55.000 0.21 0.00 41.75 3.68
499 1247 2.457366 AAGTGTAGGGACTCGCTTTG 57.543 50.000 0.21 0.00 41.75 2.77
500 1248 2.633481 AGAAAGTGTAGGGACTCGCTTT 59.367 45.455 0.21 3.88 43.39 3.51
501 1249 2.231721 GAGAAAGTGTAGGGACTCGCTT 59.768 50.000 0.21 0.00 41.75 4.68
502 1250 1.819903 GAGAAAGTGTAGGGACTCGCT 59.180 52.381 0.71 0.71 41.75 4.93
503 1251 1.135053 GGAGAAAGTGTAGGGACTCGC 60.135 57.143 0.00 0.00 41.75 5.03
504 1252 2.448453 AGGAGAAAGTGTAGGGACTCG 58.552 52.381 0.00 0.00 41.75 4.18
505 1253 3.579151 ACAAGGAGAAAGTGTAGGGACTC 59.421 47.826 0.00 0.00 41.75 3.36
506 1254 3.588569 ACAAGGAGAAAGTGTAGGGACT 58.411 45.455 0.00 0.00 46.37 3.85
507 1255 4.353383 AACAAGGAGAAAGTGTAGGGAC 57.647 45.455 0.00 0.00 0.00 4.46
508 1256 4.658901 AGAAACAAGGAGAAAGTGTAGGGA 59.341 41.667 0.00 0.00 0.00 4.20
515 1263 5.838521 AGAGAGAGAGAAACAAGGAGAAAGT 59.161 40.000 0.00 0.00 0.00 2.66
543 1291 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
544 1292 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
545 1293 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
546 1294 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
547 1295 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
548 1296 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
549 1297 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
550 1298 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
551 1299 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
552 1300 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
553 1301 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
554 1302 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
555 1303 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
556 1304 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
557 1305 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
558 1306 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
559 1307 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
560 1308 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
561 1309 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
562 1310 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
563 1311 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
564 1312 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
565 1313 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
566 1314 5.867903 AAGAGAGAGAGAGAGAGAGAGAG 57.132 47.826 0.00 0.00 0.00 3.20
567 1315 5.960811 AGAAAGAGAGAGAGAGAGAGAGAGA 59.039 44.000 0.00 0.00 0.00 3.10
568 1316 6.098124 AGAGAAAGAGAGAGAGAGAGAGAGAG 59.902 46.154 0.00 0.00 0.00 3.20
569 1317 5.960811 AGAGAAAGAGAGAGAGAGAGAGAGA 59.039 44.000 0.00 0.00 0.00 3.10
570 1318 6.098124 AGAGAGAAAGAGAGAGAGAGAGAGAG 59.902 46.154 0.00 0.00 0.00 3.20
571 1319 5.960811 AGAGAGAAAGAGAGAGAGAGAGAGA 59.039 44.000 0.00 0.00 0.00 3.10
572 1320 6.098124 AGAGAGAGAAAGAGAGAGAGAGAGAG 59.902 46.154 0.00 0.00 0.00 3.20
573 1321 5.960811 AGAGAGAGAAAGAGAGAGAGAGAGA 59.039 44.000 0.00 0.00 0.00 3.10
574 1322 6.232581 AGAGAGAGAAAGAGAGAGAGAGAG 57.767 45.833 0.00 0.00 0.00 3.20
575 1323 6.441924 AGAAGAGAGAGAAAGAGAGAGAGAGA 59.558 42.308 0.00 0.00 0.00 3.10
576 1324 6.648192 AGAAGAGAGAGAAAGAGAGAGAGAG 58.352 44.000 0.00 0.00 0.00 3.20
577 1325 6.627087 AGAAGAGAGAGAAAGAGAGAGAGA 57.373 41.667 0.00 0.00 0.00 3.10
578 1326 7.278868 GTGTAGAAGAGAGAGAAAGAGAGAGAG 59.721 44.444 0.00 0.00 0.00 3.20
579 1327 7.038302 AGTGTAGAAGAGAGAGAAAGAGAGAGA 60.038 40.741 0.00 0.00 0.00 3.10
580 1328 7.065085 CAGTGTAGAAGAGAGAGAAAGAGAGAG 59.935 44.444 0.00 0.00 0.00 3.20
581 1329 6.878923 CAGTGTAGAAGAGAGAGAAAGAGAGA 59.121 42.308 0.00 0.00 0.00 3.10
582 1330 6.403636 GCAGTGTAGAAGAGAGAGAAAGAGAG 60.404 46.154 0.00 0.00 0.00 3.20
583 1331 5.414454 GCAGTGTAGAAGAGAGAGAAAGAGA 59.586 44.000 0.00 0.00 0.00 3.10
584 1332 5.415701 AGCAGTGTAGAAGAGAGAGAAAGAG 59.584 44.000 0.00 0.00 0.00 2.85
585 1333 5.321102 AGCAGTGTAGAAGAGAGAGAAAGA 58.679 41.667 0.00 0.00 0.00 2.52
586 1334 5.182950 TGAGCAGTGTAGAAGAGAGAGAAAG 59.817 44.000 0.00 0.00 0.00 2.62
587 1335 5.048364 GTGAGCAGTGTAGAAGAGAGAGAAA 60.048 44.000 0.00 0.00 0.00 2.52
588 1336 4.457603 GTGAGCAGTGTAGAAGAGAGAGAA 59.542 45.833 0.00 0.00 0.00 2.87
622 1370 2.693267 AGTAAATGGAACGGAGCCTC 57.307 50.000 0.00 0.00 0.00 4.70
649 1397 6.873076 AGCTACTATAAGTACAGTACTAGGCG 59.127 42.308 13.87 6.15 38.26 5.52
705 1457 4.841422 AGGAAGATGAACTGATGTCAAGG 58.159 43.478 0.00 0.00 0.00 3.61
855 1607 9.674208 GTATTCATTTACAAAATCACAAATGCG 57.326 29.630 0.00 0.00 37.96 4.73
872 1624 5.589855 TGAGCCGATGTCAATGTATTCATTT 59.410 36.000 0.00 0.00 41.66 2.32
1072 1828 4.700365 CTGCTCCGACGACACGCA 62.700 66.667 0.00 0.00 0.00 5.24
1178 1934 1.601419 ATCCATGTCGTCGGACGGTT 61.601 55.000 28.07 11.99 46.49 4.44
1288 2047 4.303257 GGCACTGCCTAACTCCAC 57.697 61.111 13.28 0.00 46.69 4.02
1447 2206 2.166050 TGTCATGCACAACTGTTTTGCT 59.834 40.909 26.24 13.20 37.16 3.91
1525 2284 4.562347 CCTGTGCTCTACAACACAAGAGAT 60.562 45.833 3.60 0.00 45.55 2.75
1642 2402 4.319177 AGTTCACAGACCATAACAAGAGC 58.681 43.478 0.00 0.00 0.00 4.09
1663 2423 6.072064 AGCAACTGGATTGAATTTTCAGAGAG 60.072 38.462 9.79 0.00 41.23 3.20
1679 2439 2.443255 AGGAAAAAGGAGAGCAACTGGA 59.557 45.455 0.00 0.00 0.00 3.86
2043 2803 3.630312 CCCGTTCTTTCTCTTTGTTCCAA 59.370 43.478 0.00 0.00 0.00 3.53
2232 2992 3.266636 GGTCAGCCTCTCTTTAAGCTTC 58.733 50.000 0.00 0.00 31.93 3.86
2250 3010 3.344515 GGAAATGTCCACTACCTTGGTC 58.655 50.000 0.00 0.00 44.26 4.02
2333 3093 3.244561 ACCATCACTGTAAACAGAGGGTG 60.245 47.826 16.74 13.13 46.59 4.61
2512 3272 9.512588 GGATCAATCAGAAATGTATTAGGATGT 57.487 33.333 0.00 0.00 0.00 3.06
2513 3273 9.736414 AGGATCAATCAGAAATGTATTAGGATG 57.264 33.333 0.00 0.00 0.00 3.51
2545 3305 6.036626 GCAAGCAAAAAGTAACAAGCCTAAAA 59.963 34.615 0.00 0.00 0.00 1.52
2768 3528 4.829968 AGTGTCAGGACAAGATGAAGATG 58.170 43.478 3.28 0.00 43.77 2.90
2780 3541 2.300437 AGCTTGGAGTTAGTGTCAGGAC 59.700 50.000 0.00 0.00 0.00 3.85
2790 3551 7.450074 TCATGAAAAGTAAGAGCTTGGAGTTA 58.550 34.615 0.00 0.00 0.00 2.24
2799 3560 7.466590 GCCACTTAGATCATGAAAAGTAAGAGC 60.467 40.741 16.55 14.89 31.20 4.09
2818 3583 0.814410 TTTTGCGACCGTGCCACTTA 60.814 50.000 0.00 0.00 0.00 2.24
2830 3595 0.317160 TCTCGAGCTCCTTTTTGCGA 59.683 50.000 7.81 0.00 0.00 5.10
2836 3601 1.464734 TCACGATCTCGAGCTCCTTT 58.535 50.000 7.81 0.00 43.02 3.11
2875 3640 3.682292 CTTACGCAGCCCTCCACCC 62.682 68.421 0.00 0.00 0.00 4.61
2909 3674 2.492090 CCTCTCCACCGCTCTTCG 59.508 66.667 0.00 0.00 38.08 3.79
2942 3707 4.087892 CCCAGGCTCCGTCACCAG 62.088 72.222 0.00 0.00 0.00 4.00
3071 3836 6.441093 TCAATGTAAGAACTCCATGAATGC 57.559 37.500 0.00 0.00 0.00 3.56
3075 3840 7.167535 TCAACATCAATGTAAGAACTCCATGA 58.832 34.615 0.00 0.00 40.80 3.07
3097 3862 5.335897 GCCAACTAAAGCAAGACATCATCAA 60.336 40.000 0.00 0.00 0.00 2.57
3217 3985 4.869861 GGCAAAGAAAACACACAAGTTCAT 59.130 37.500 0.00 0.00 0.00 2.57
3255 4061 0.994263 GCATGGCGATTTTTGTCTGC 59.006 50.000 0.00 0.00 0.00 4.26
3329 4138 4.035112 AGGTCTTACATTATGGGACGGAA 58.965 43.478 0.00 0.00 0.00 4.30
3349 4158 5.175126 CACACTACACTCGTGTTAAAGAAGG 59.825 44.000 8.11 0.00 42.56 3.46
3350 4159 5.975344 TCACACTACACTCGTGTTAAAGAAG 59.025 40.000 8.11 1.33 42.56 2.85
3353 4162 6.578020 TTTCACACTACACTCGTGTTAAAG 57.422 37.500 8.11 2.73 42.56 1.85
3393 4202 4.360951 TGTACTCCCTCCGTTTCATTTT 57.639 40.909 0.00 0.00 0.00 1.82
3394 4203 4.360951 TTGTACTCCCTCCGTTTCATTT 57.639 40.909 0.00 0.00 0.00 2.32
3395 4204 4.261801 CATTGTACTCCCTCCGTTTCATT 58.738 43.478 0.00 0.00 0.00 2.57
3397 4206 2.635915 ACATTGTACTCCCTCCGTTTCA 59.364 45.455 0.00 0.00 0.00 2.69
3398 4207 3.329929 ACATTGTACTCCCTCCGTTTC 57.670 47.619 0.00 0.00 0.00 2.78
3399 4208 4.529377 TCTTACATTGTACTCCCTCCGTTT 59.471 41.667 0.00 0.00 0.00 3.60
3400 4209 4.091549 TCTTACATTGTACTCCCTCCGTT 58.908 43.478 0.00 0.00 0.00 4.44
3401 4210 3.705051 TCTTACATTGTACTCCCTCCGT 58.295 45.455 0.00 0.00 0.00 4.69
3402 4211 4.939052 ATCTTACATTGTACTCCCTCCG 57.061 45.455 0.00 0.00 0.00 4.63
3403 4212 6.487299 AGAATCTTACATTGTACTCCCTCC 57.513 41.667 0.00 0.00 0.00 4.30
3489 4298 2.064573 CGAAAAGCGCCTTCCAAAAT 57.935 45.000 2.29 0.00 0.00 1.82
3695 4623 1.359130 AGCTTTTAGGCACCCCTCAAT 59.641 47.619 0.00 0.00 41.75 2.57
3697 4625 1.559682 CTAGCTTTTAGGCACCCCTCA 59.440 52.381 0.00 0.00 41.75 3.86
3698 4626 1.747552 GCTAGCTTTTAGGCACCCCTC 60.748 57.143 7.70 0.00 41.75 4.30
3699 4627 0.256177 GCTAGCTTTTAGGCACCCCT 59.744 55.000 7.70 0.00 45.61 4.79
3813 4754 1.749638 GAGCGGAGGGAGAGACGAA 60.750 63.158 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.