Multiple sequence alignment - TraesCS1B01G115100

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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 TraesCS1B01G115100 chr1B 100.000 3883 0 0 1 3883 135247756 135243874 0.000000e+00 7171.0
1 TraesCS1B01G115100 chr4A 91.124 3222 163 51 618 3808 140774093 140770964 0.000000e+00 4252.0
2 TraesCS1B01G115100 chr4D 96.047 2024 57 10 711 2726 329300216 329302224 0.000000e+00 3273.0
3 TraesCS1B01G115100 chr4D 95.664 369 16 0 1 369 329299341 329299709 9.290000e-166 593.0
4 TraesCS1B01G115100 chr4D 90.244 246 12 5 2726 2967 329302261 329302498 1.050000e-80 311.0
5 TraesCS1B01G115100 chr4D 89.427 227 18 3 457 680 329299705 329299928 8.210000e-72 281.0
6 TraesCS1B01G115100 chr4B 88.240 2296 170 51 1567 3836 409249387 409251608 0.000000e+00 2652.0
7 TraesCS1B01G115100 chr4B 93.717 955 44 7 618 1570 409236543 409237483 0.000000e+00 1417.0
8 TraesCS1B01G115100 chr4B 96.842 95 2 1 1 94 409236239 409236333 1.440000e-34 158.0
9 TraesCS1B01G115100 chr2B 78.098 347 58 15 3384 3727 785252171 785252502 1.830000e-48 204.0
10 TraesCS1B01G115100 chr2B 76.812 138 17 13 3283 3415 699831829 699831702 3.240000e-06 63.9
11 TraesCS1B01G115100 chr5A 77.946 331 63 10 2015 2340 327726587 327726912 8.510000e-47 198.0
12 TraesCS1B01G115100 chr2D 77.364 349 59 17 3384 3727 649515755 649516088 5.120000e-44 189.0
13 TraesCS1B01G115100 chr5D 77.410 332 63 11 2015 2340 229141907 229141582 1.840000e-43 187.0
14 TraesCS1B01G115100 chr5B 77.410 332 63 11 2015 2340 276824293 276824618 1.840000e-43 187.0
15 TraesCS1B01G115100 chr5B 100.000 28 0 0 524 551 467509176 467509203 7.000000e-03 52.8
16 TraesCS1B01G115100 chr7D 74.280 521 91 36 3234 3731 622617066 622616566 3.080000e-41 180.0
17 TraesCS1B01G115100 chr7D 76.536 358 53 27 3236 3580 17229772 17229433 2.400000e-37 167.0
18 TraesCS1B01G115100 chr6A 81.081 185 27 8 3373 3553 461977272 461977452 1.450000e-29 141.0
19 TraesCS1B01G115100 chr6A 75.692 325 55 19 3238 3544 542378269 542377951 1.450000e-29 141.0
20 TraesCS1B01G115100 chr6A 81.690 142 23 3 3585 3725 520314967 520315106 8.820000e-22 115.0
21 TraesCS1B01G115100 chr6A 84.043 94 15 0 1548 1641 100653175 100653082 1.490000e-14 91.6
22 TraesCS1B01G115100 chrUn 74.780 341 69 15 3384 3718 11260696 11261025 1.880000e-28 137.0
23 TraesCS1B01G115100 chrUn 74.780 341 69 15 3384 3718 364233194 364233523 1.880000e-28 137.0
24 TraesCS1B01G115100 chr6D 75.510 343 47 31 3236 3564 14972298 14972617 2.430000e-27 134.0
25 TraesCS1B01G115100 chr6D 89.286 56 6 0 496 551 446510698 446510753 1.940000e-08 71.3
26 TraesCS1B01G115100 chr1D 73.102 461 90 24 3269 3718 411596537 411596100 2.430000e-27 134.0
27 TraesCS1B01G115100 chr7A 74.269 342 66 16 3392 3727 149159744 149159419 1.460000e-24 124.0
28 TraesCS1B01G115100 chr7B 78.646 192 29 11 3379 3564 598900603 598900418 2.450000e-22 117.0
29 TraesCS1B01G115100 chr3D 84.375 96 15 0 1541 1636 613590366 613590271 1.150000e-15 95.3
30 TraesCS1B01G115100 chr2A 79.592 98 18 2 175 271 507388491 507388587 6.960000e-08 69.4


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 TraesCS1B01G115100 chr1B 135243874 135247756 3882 True 7171.0 7171 100.0000 1 3883 1 chr1B.!!$R1 3882
1 TraesCS1B01G115100 chr4A 140770964 140774093 3129 True 4252.0 4252 91.1240 618 3808 1 chr4A.!!$R1 3190
2 TraesCS1B01G115100 chr4D 329299341 329302498 3157 False 1114.5 3273 92.8455 1 2967 4 chr4D.!!$F1 2966
3 TraesCS1B01G115100 chr4B 409249387 409251608 2221 False 2652.0 2652 88.2400 1567 3836 1 chr4B.!!$F1 2269
4 TraesCS1B01G115100 chr4B 409236239 409237483 1244 False 787.5 1417 95.2795 1 1570 2 chr4B.!!$F2 1569

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
590 651 0.806868 CCAGTGCATTGCTGTCGATT 59.193 50.000 10.49 0.0 32.41 3.34 F
990 1352 1.000506 TCCGCTACTGACCAAACAGTC 59.999 52.381 4.63 0.0 46.36 3.51 F
1394 1766 1.595382 GCAAGCTGTGGACTCACGT 60.595 57.895 0.00 0.0 46.42 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2190 2562 0.174389 TGACGCTGAAGATGAGGAGC 59.826 55.0 0.00 0.00 0.00 4.70 R
2421 2793 0.248377 CGTAGAAGTTAGCCGTCCGG 60.248 60.0 0.24 0.24 38.57 5.14 R
3004 3430 0.317160 ACTGAATCGTTCTGTGCGGA 59.683 50.0 8.61 0.00 39.86 5.54 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
154 214 9.734620 CTCACTCTGTTCACAAATATTTTTGAA 57.265 29.630 20.61 20.61 44.11 2.69
249 309 8.939201 TTTCGGTTTGTACGTAATCCATATTA 57.061 30.769 0.00 0.00 0.00 0.98
252 312 9.376075 TCGGTTTGTACGTAATCCATATTAAAA 57.624 29.630 0.00 0.00 29.41 1.52
285 345 7.220030 AGCATCTTATATTTGTCAACGGAGAT 58.780 34.615 0.00 0.00 0.00 2.75
390 450 8.824159 ACTATCACAATTCAGATTAGGATTCG 57.176 34.615 0.00 0.00 0.00 3.34
391 451 8.642432 ACTATCACAATTCAGATTAGGATTCGA 58.358 33.333 0.00 0.00 0.00 3.71
392 452 9.481340 CTATCACAATTCAGATTAGGATTCGAA 57.519 33.333 0.00 0.00 0.00 3.71
393 453 8.737168 ATCACAATTCAGATTAGGATTCGAAA 57.263 30.769 0.00 0.00 0.00 3.46
394 454 8.560355 TCACAATTCAGATTAGGATTCGAAAA 57.440 30.769 0.00 0.00 0.00 2.29
395 455 9.008965 TCACAATTCAGATTAGGATTCGAAAAA 57.991 29.630 0.00 0.00 0.00 1.94
427 487 7.703328 TCCCTCTTTTTCATATTAATTGTCGC 58.297 34.615 0.00 0.00 0.00 5.19
428 488 7.338196 TCCCTCTTTTTCATATTAATTGTCGCA 59.662 33.333 0.00 0.00 0.00 5.10
429 489 7.973388 CCCTCTTTTTCATATTAATTGTCGCAA 59.027 33.333 0.00 0.00 0.00 4.85
430 490 9.352784 CCTCTTTTTCATATTAATTGTCGCAAA 57.647 29.630 0.00 0.00 0.00 3.68
435 495 9.482627 TTTTCATATTAATTGTCGCAAAAAGGT 57.517 25.926 0.00 0.00 0.00 3.50
436 496 9.482627 TTTCATATTAATTGTCGCAAAAAGGTT 57.517 25.926 0.00 0.00 0.00 3.50
437 497 8.459521 TCATATTAATTGTCGCAAAAAGGTTG 57.540 30.769 0.00 0.00 0.00 3.77
438 498 8.085296 TCATATTAATTGTCGCAAAAAGGTTGT 58.915 29.630 0.00 0.00 0.00 3.32
439 499 9.347934 CATATTAATTGTCGCAAAAAGGTTGTA 57.652 29.630 0.00 0.00 0.00 2.41
440 500 7.867445 ATTAATTGTCGCAAAAAGGTTGTAG 57.133 32.000 0.00 0.00 0.00 2.74
441 501 4.911514 ATTGTCGCAAAAAGGTTGTAGT 57.088 36.364 0.00 0.00 0.00 2.73
442 502 6.380095 AATTGTCGCAAAAAGGTTGTAGTA 57.620 33.333 0.00 0.00 0.00 1.82
443 503 4.799419 TGTCGCAAAAAGGTTGTAGTAC 57.201 40.909 0.00 0.00 0.00 2.73
444 504 4.444536 TGTCGCAAAAAGGTTGTAGTACT 58.555 39.130 0.00 0.00 0.00 2.73
445 505 4.271533 TGTCGCAAAAAGGTTGTAGTACTG 59.728 41.667 5.39 0.00 0.00 2.74
446 506 4.508861 GTCGCAAAAAGGTTGTAGTACTGA 59.491 41.667 5.39 0.00 0.00 3.41
447 507 5.006941 GTCGCAAAAAGGTTGTAGTACTGAA 59.993 40.000 5.39 0.00 0.00 3.02
448 508 5.235616 TCGCAAAAAGGTTGTAGTACTGAAG 59.764 40.000 5.39 0.00 0.00 3.02
449 509 5.007332 CGCAAAAAGGTTGTAGTACTGAAGT 59.993 40.000 5.39 0.00 0.00 3.01
450 510 6.457799 CGCAAAAAGGTTGTAGTACTGAAGTT 60.458 38.462 5.39 0.00 0.00 2.66
451 511 6.691388 GCAAAAAGGTTGTAGTACTGAAGTTG 59.309 38.462 5.39 0.00 0.00 3.16
452 512 7.627726 GCAAAAAGGTTGTAGTACTGAAGTTGT 60.628 37.037 5.39 0.00 0.00 3.32
453 513 6.920569 AAAGGTTGTAGTACTGAAGTTGTG 57.079 37.500 5.39 0.00 0.00 3.33
454 514 5.864418 AGGTTGTAGTACTGAAGTTGTGA 57.136 39.130 5.39 0.00 0.00 3.58
455 515 5.598769 AGGTTGTAGTACTGAAGTTGTGAC 58.401 41.667 5.39 0.00 0.00 3.67
456 516 5.128171 AGGTTGTAGTACTGAAGTTGTGACA 59.872 40.000 5.39 0.00 0.00 3.58
457 517 5.813672 GGTTGTAGTACTGAAGTTGTGACAA 59.186 40.000 5.39 1.73 0.00 3.18
458 518 6.482308 GGTTGTAGTACTGAAGTTGTGACAAT 59.518 38.462 5.39 0.00 0.00 2.71
475 535 9.473007 TTGTGACAATTAATATGGATTGAAGGA 57.527 29.630 14.77 0.00 36.87 3.36
477 537 9.342308 GTGACAATTAATATGGATTGAAGGAGA 57.658 33.333 14.77 0.00 36.87 3.71
480 540 9.872684 ACAATTAATATGGATTGAAGGAGATGT 57.127 29.630 14.77 0.00 36.87 3.06
487 547 6.519679 TGGATTGAAGGAGATGTGAAAATG 57.480 37.500 0.00 0.00 0.00 2.32
491 551 8.186821 GGATTGAAGGAGATGTGAAAATGTTAG 58.813 37.037 0.00 0.00 0.00 2.34
492 552 6.500684 TGAAGGAGATGTGAAAATGTTAGC 57.499 37.500 0.00 0.00 0.00 3.09
493 553 5.122239 TGAAGGAGATGTGAAAATGTTAGCG 59.878 40.000 0.00 0.00 0.00 4.26
502 562 4.092968 GTGAAAATGTTAGCGAGTGGTAGG 59.907 45.833 0.00 0.00 0.00 3.18
505 565 3.975168 ATGTTAGCGAGTGGTAGGTTT 57.025 42.857 0.00 0.00 0.00 3.27
521 581 4.937201 AGGTTTTTGAAACCCTAGCTTG 57.063 40.909 16.67 0.00 41.18 4.01
566 626 1.603802 ACTCGATGCTTGTTGGTGTTG 59.396 47.619 0.00 0.00 0.00 3.33
567 627 1.872952 CTCGATGCTTGTTGGTGTTGA 59.127 47.619 0.00 0.00 0.00 3.18
568 628 1.601903 TCGATGCTTGTTGGTGTTGAC 59.398 47.619 0.00 0.00 0.00 3.18
569 629 1.603802 CGATGCTTGTTGGTGTTGACT 59.396 47.619 0.00 0.00 0.00 3.41
590 651 0.806868 CCAGTGCATTGCTGTCGATT 59.193 50.000 10.49 0.00 32.41 3.34
659 750 2.770164 ACTTGACTGCATCCCTACAC 57.230 50.000 0.00 0.00 0.00 2.90
706 799 8.604640 TCTAAGTAGTGACAGTATATTCCTCG 57.395 38.462 0.00 0.00 0.00 4.63
740 1101 2.603075 TTTTTGTAGGCCAGCCATCT 57.397 45.000 12.03 0.00 38.92 2.90
840 1202 1.606189 TGCTGCAGCGTGTTGAAAATA 59.394 42.857 32.11 8.56 45.83 1.40
931 1293 1.667212 CATCGCAGCTGCAGATTTGTA 59.333 47.619 36.03 13.35 42.21 2.41
990 1352 1.000506 TCCGCTACTGACCAAACAGTC 59.999 52.381 4.63 0.00 46.36 3.51
1015 1384 4.106925 CTGGGCAGGGGCAGAGAC 62.107 72.222 0.00 0.00 43.71 3.36
1394 1766 1.595382 GCAAGCTGTGGACTCACGT 60.595 57.895 0.00 0.00 46.42 4.49
1752 2124 1.970114 GCTGCTGCACATCACCTGT 60.970 57.895 11.11 0.00 39.20 4.00
2136 2508 3.371097 GAACATGGAGCGCCTCGGA 62.371 63.158 8.34 0.00 34.31 4.55
2645 3017 2.367202 ACATCGCGATGGGGAGGTT 61.367 57.895 42.28 23.68 46.14 3.50
2707 3079 1.009675 CCGCCGCTGATACAAATGC 60.010 57.895 0.00 0.00 0.00 3.56
2715 3087 2.357009 GCTGATACAAATGCACAGGGAG 59.643 50.000 0.00 0.00 0.00 4.30
2716 3088 3.877559 CTGATACAAATGCACAGGGAGA 58.122 45.455 0.00 0.00 0.00 3.71
2718 3090 4.858850 TGATACAAATGCACAGGGAGAAT 58.141 39.130 0.00 0.00 0.00 2.40
2725 3097 2.436417 TGCACAGGGAGAATTAGTTGC 58.564 47.619 0.00 0.00 0.00 4.17
2726 3098 2.040278 TGCACAGGGAGAATTAGTTGCT 59.960 45.455 0.00 0.00 0.00 3.91
2727 3099 3.263170 TGCACAGGGAGAATTAGTTGCTA 59.737 43.478 0.00 0.00 0.00 3.49
2785 3195 1.466167 GTGTGCTGTTGCTCGATGATT 59.534 47.619 0.00 0.00 40.48 2.57
2963 3385 1.509923 GCTCAGGTGCCAGCAAATC 59.490 57.895 0.00 0.00 35.56 2.17
2973 3395 4.082026 GGTGCCAGCAAATCTTATCACTTT 60.082 41.667 0.00 0.00 0.00 2.66
2975 3397 4.766373 TGCCAGCAAATCTTATCACTTTCA 59.234 37.500 0.00 0.00 0.00 2.69
2976 3398 5.106038 TGCCAGCAAATCTTATCACTTTCAG 60.106 40.000 0.00 0.00 0.00 3.02
3004 3430 8.907222 ATTTTCACCATTGCATTTAGAAAGTT 57.093 26.923 0.00 0.00 0.00 2.66
3011 3437 2.881513 TGCATTTAGAAAGTTCCGCACA 59.118 40.909 0.00 0.00 0.00 4.57
3034 3460 3.207474 ACGATTCAGTGATTTGCAAGC 57.793 42.857 0.00 0.00 0.00 4.01
3048 3474 4.589216 TTGCAAGCCATATCCTATTTGC 57.411 40.909 0.00 0.43 40.81 3.68
3054 3480 3.009033 AGCCATATCCTATTTGCCGCTTA 59.991 43.478 0.00 0.00 0.00 3.09
3055 3481 3.375299 GCCATATCCTATTTGCCGCTTAG 59.625 47.826 0.00 0.00 0.00 2.18
3056 3482 3.375299 CCATATCCTATTTGCCGCTTAGC 59.625 47.826 0.00 0.00 0.00 3.09
3058 3484 2.710096 TCCTATTTGCCGCTTAGCTT 57.290 45.000 1.76 0.00 0.00 3.74
3059 3485 2.999331 TCCTATTTGCCGCTTAGCTTT 58.001 42.857 1.76 0.00 0.00 3.51
3060 3486 4.145365 TCCTATTTGCCGCTTAGCTTTA 57.855 40.909 1.76 0.00 0.00 1.85
3061 3487 4.714632 TCCTATTTGCCGCTTAGCTTTAT 58.285 39.130 1.76 0.00 0.00 1.40
3063 3489 5.592688 TCCTATTTGCCGCTTAGCTTTATTT 59.407 36.000 1.76 0.00 0.00 1.40
3065 3491 7.283580 TCCTATTTGCCGCTTAGCTTTATTTTA 59.716 33.333 1.76 0.00 0.00 1.52
3067 3493 9.463443 CTATTTGCCGCTTAGCTTTATTTTATT 57.537 29.630 1.76 0.00 0.00 1.40
3109 3541 4.395959 AAAACTAACGTGTGGAGAGTCA 57.604 40.909 0.00 0.00 0.00 3.41
3113 3545 2.981859 AACGTGTGGAGAGTCAAACT 57.018 45.000 0.00 0.00 0.00 2.66
3122 3554 5.202004 GTGGAGAGTCAAACTAGGGATCTA 58.798 45.833 0.00 0.00 0.00 1.98
3123 3555 5.068067 GTGGAGAGTCAAACTAGGGATCTAC 59.932 48.000 0.00 0.00 0.00 2.59
3124 3556 5.202004 GGAGAGTCAAACTAGGGATCTACA 58.798 45.833 0.00 0.00 0.00 2.74
3141 3573 1.740296 CAGTCCCCGGTAAACTGCG 60.740 63.158 13.22 0.00 34.55 5.18
3190 3622 8.169977 TGCTGTGATAACTTCTTCATTTTCTT 57.830 30.769 0.00 0.00 0.00 2.52
3191 3623 9.283768 TGCTGTGATAACTTCTTCATTTTCTTA 57.716 29.630 0.00 0.00 0.00 2.10
3559 4034 6.258160 ACTTTCTTTCAAGTTCATGAACGTG 58.742 36.000 34.79 34.79 46.97 4.49
3564 4039 6.526325 TCTTTCAAGTTCATGAACGTGTTTTG 59.474 34.615 36.75 29.55 46.15 2.44
3582 4057 5.357314 TGTTTTGAAAGTCCGTGGAATTGTA 59.643 36.000 1.90 0.00 32.53 2.41
3605 4096 9.829507 TGTATGAATTCACAATTGTTTTTCCTT 57.170 25.926 11.07 5.76 0.00 3.36
3609 4100 9.007901 TGAATTCACAATTGTTTTTCCTTTTGT 57.992 25.926 8.77 0.00 0.00 2.83
3610 4101 9.838975 GAATTCACAATTGTTTTTCCTTTTGTT 57.161 25.926 8.77 0.00 0.00 2.83
3611 4102 9.623350 AATTCACAATTGTTTTTCCTTTTGTTG 57.377 25.926 8.77 0.00 0.00 3.33
3612 4103 6.606768 TCACAATTGTTTTTCCTTTTGTTGC 58.393 32.000 8.77 0.00 0.00 4.17
3613 4104 5.507527 CACAATTGTTTTTCCTTTTGTTGCG 59.492 36.000 8.77 0.00 0.00 4.85
3614 4105 3.731274 TTGTTTTTCCTTTTGTTGCGC 57.269 38.095 0.00 0.00 0.00 6.09
3615 4106 2.966050 TGTTTTTCCTTTTGTTGCGCT 58.034 38.095 9.73 0.00 0.00 5.92
3616 4107 3.330267 TGTTTTTCCTTTTGTTGCGCTT 58.670 36.364 9.73 0.00 0.00 4.68
3617 4108 3.748568 TGTTTTTCCTTTTGTTGCGCTTT 59.251 34.783 9.73 0.00 0.00 3.51
3618 4109 4.214332 TGTTTTTCCTTTTGTTGCGCTTTT 59.786 33.333 9.73 0.00 0.00 2.27
3619 4110 5.150683 GTTTTTCCTTTTGTTGCGCTTTTT 58.849 33.333 9.73 0.00 0.00 1.94
3731 4222 1.581934 CCGAATGCGAGCTCCAATTA 58.418 50.000 8.47 0.00 40.82 1.40
3739 4230 3.134458 GCGAGCTCCAATTAGCAATACT 58.866 45.455 8.47 0.00 45.30 2.12
3798 4289 6.530120 AGTGATATATGTTTACGCCCAATCA 58.470 36.000 0.00 0.00 0.00 2.57
3809 4300 1.815421 CCCAATCAGTCGAAGGCCG 60.815 63.158 0.00 0.00 40.25 6.13
3810 4301 1.218047 CCAATCAGTCGAAGGCCGA 59.782 57.895 0.00 0.00 46.35 5.54
3836 4327 0.328258 ACTGGATGGCAGGTGTTACC 59.672 55.000 0.00 0.00 38.99 2.85
3837 4328 0.744414 CTGGATGGCAGGTGTTACCG 60.744 60.000 0.00 0.00 44.90 4.02
3838 4329 1.451387 GGATGGCAGGTGTTACCGG 60.451 63.158 0.00 0.00 44.90 5.28
3839 4330 1.600107 GATGGCAGGTGTTACCGGA 59.400 57.895 9.46 0.00 44.90 5.14
3840 4331 0.035820 GATGGCAGGTGTTACCGGAA 60.036 55.000 9.46 0.00 44.90 4.30
3841 4332 0.402504 ATGGCAGGTGTTACCGGAAA 59.597 50.000 9.46 0.00 44.90 3.13
3842 4333 0.402504 TGGCAGGTGTTACCGGAAAT 59.597 50.000 9.46 0.00 44.90 2.17
3843 4334 1.092348 GGCAGGTGTTACCGGAAATC 58.908 55.000 9.46 0.00 44.90 2.17
3844 4335 1.092348 GCAGGTGTTACCGGAAATCC 58.908 55.000 9.46 3.75 44.90 3.01
3856 4347 0.526211 GGAAATCCGTTGTTGCTCCC 59.474 55.000 0.00 0.00 0.00 4.30
3857 4348 0.526211 GAAATCCGTTGTTGCTCCCC 59.474 55.000 0.00 0.00 0.00 4.81
3858 4349 1.241315 AAATCCGTTGTTGCTCCCCG 61.241 55.000 0.00 0.00 0.00 5.73
3859 4350 3.622060 ATCCGTTGTTGCTCCCCGG 62.622 63.158 0.00 0.00 39.98 5.73
3860 4351 4.323477 CCGTTGTTGCTCCCCGGA 62.323 66.667 0.73 0.00 41.08 5.14
3861 4352 2.742372 CGTTGTTGCTCCCCGGAG 60.742 66.667 0.73 6.37 44.56 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 179 5.592054 TGTGAACAGAGTGAGTACTTTCTG 58.408 41.667 21.69 21.69 37.25 3.02
154 214 2.748388 AGTTAGAACATAGCCTCCGGT 58.252 47.619 0.00 0.00 0.00 5.28
155 215 3.821421 AAGTTAGAACATAGCCTCCGG 57.179 47.619 0.00 0.00 0.00 5.14
220 280 5.349270 TGGATTACGTACAAACCGAAATGAG 59.651 40.000 0.00 0.00 0.00 2.90
256 316 9.168451 TCCGTTGACAAATATAAGATGCTTTAA 57.832 29.630 0.00 0.00 0.00 1.52
261 321 6.844696 TCTCCGTTGACAAATATAAGATGC 57.155 37.500 0.00 0.00 0.00 3.91
273 333 6.839124 TTTAACCTACTATCTCCGTTGACA 57.161 37.500 0.00 0.00 0.00 3.58
285 345 7.092802 TGCATAAGGTGACCATTTAACCTACTA 60.093 37.037 3.63 0.00 43.62 1.82
367 427 9.830975 TTTCGAATCCTAATCTGAATTGTGATA 57.169 29.630 0.00 0.00 0.00 2.15
368 428 8.737168 TTTCGAATCCTAATCTGAATTGTGAT 57.263 30.769 0.00 0.00 0.00 3.06
369 429 8.560355 TTTTCGAATCCTAATCTGAATTGTGA 57.440 30.769 0.00 0.00 0.00 3.58
401 461 8.352942 GCGACAATTAATATGAAAAAGAGGGAT 58.647 33.333 0.00 0.00 0.00 3.85
402 462 7.338196 TGCGACAATTAATATGAAAAAGAGGGA 59.662 33.333 0.00 0.00 0.00 4.20
403 463 7.479980 TGCGACAATTAATATGAAAAAGAGGG 58.520 34.615 0.00 0.00 0.00 4.30
404 464 8.909708 TTGCGACAATTAATATGAAAAAGAGG 57.090 30.769 0.00 0.00 0.00 3.69
409 469 9.482627 ACCTTTTTGCGACAATTAATATGAAAA 57.517 25.926 0.00 0.00 0.00 2.29
410 470 9.482627 AACCTTTTTGCGACAATTAATATGAAA 57.517 25.926 0.00 0.00 0.00 2.69
411 471 8.920665 CAACCTTTTTGCGACAATTAATATGAA 58.079 29.630 0.00 0.00 0.00 2.57
412 472 8.085296 ACAACCTTTTTGCGACAATTAATATGA 58.915 29.630 0.00 0.00 0.00 2.15
413 473 8.238481 ACAACCTTTTTGCGACAATTAATATG 57.762 30.769 0.00 0.00 0.00 1.78
414 474 9.567848 CTACAACCTTTTTGCGACAATTAATAT 57.432 29.630 0.00 0.00 0.00 1.28
415 475 8.569641 ACTACAACCTTTTTGCGACAATTAATA 58.430 29.630 0.00 0.00 0.00 0.98
416 476 7.430441 ACTACAACCTTTTTGCGACAATTAAT 58.570 30.769 0.00 0.00 0.00 1.40
417 477 6.797454 ACTACAACCTTTTTGCGACAATTAA 58.203 32.000 0.00 0.00 0.00 1.40
418 478 6.380095 ACTACAACCTTTTTGCGACAATTA 57.620 33.333 0.00 0.00 0.00 1.40
419 479 5.257082 ACTACAACCTTTTTGCGACAATT 57.743 34.783 0.00 0.00 0.00 2.32
420 480 4.911514 ACTACAACCTTTTTGCGACAAT 57.088 36.364 0.00 0.00 0.00 2.71
421 481 4.877251 AGTACTACAACCTTTTTGCGACAA 59.123 37.500 0.00 0.00 0.00 3.18
422 482 4.271533 CAGTACTACAACCTTTTTGCGACA 59.728 41.667 0.00 0.00 0.00 4.35
423 483 4.508861 TCAGTACTACAACCTTTTTGCGAC 59.491 41.667 0.00 0.00 0.00 5.19
424 484 4.695396 TCAGTACTACAACCTTTTTGCGA 58.305 39.130 0.00 0.00 0.00 5.10
425 485 5.007332 ACTTCAGTACTACAACCTTTTTGCG 59.993 40.000 0.00 0.00 0.00 4.85
426 486 6.373186 ACTTCAGTACTACAACCTTTTTGC 57.627 37.500 0.00 0.00 0.00 3.68
427 487 7.696453 CACAACTTCAGTACTACAACCTTTTTG 59.304 37.037 0.00 0.00 0.00 2.44
428 488 7.608761 TCACAACTTCAGTACTACAACCTTTTT 59.391 33.333 0.00 0.00 0.00 1.94
429 489 7.065443 GTCACAACTTCAGTACTACAACCTTTT 59.935 37.037 0.00 0.00 0.00 2.27
430 490 6.537660 GTCACAACTTCAGTACTACAACCTTT 59.462 38.462 0.00 0.00 0.00 3.11
431 491 6.047231 GTCACAACTTCAGTACTACAACCTT 58.953 40.000 0.00 0.00 0.00 3.50
432 492 5.128171 TGTCACAACTTCAGTACTACAACCT 59.872 40.000 0.00 0.00 0.00 3.50
433 493 5.353938 TGTCACAACTTCAGTACTACAACC 58.646 41.667 0.00 0.00 0.00 3.77
434 494 6.897259 TTGTCACAACTTCAGTACTACAAC 57.103 37.500 0.00 0.00 0.00 3.32
435 495 9.602568 TTAATTGTCACAACTTCAGTACTACAA 57.397 29.630 0.00 0.00 0.00 2.41
436 496 9.772973 ATTAATTGTCACAACTTCAGTACTACA 57.227 29.630 0.00 0.00 0.00 2.74
440 500 9.988350 CCATATTAATTGTCACAACTTCAGTAC 57.012 33.333 0.00 0.00 0.00 2.73
441 501 9.952030 TCCATATTAATTGTCACAACTTCAGTA 57.048 29.630 0.00 0.00 0.00 2.74
442 502 8.862325 TCCATATTAATTGTCACAACTTCAGT 57.138 30.769 0.00 0.00 0.00 3.41
448 508 9.520204 CCTTCAATCCATATTAATTGTCACAAC 57.480 33.333 0.00 0.00 35.02 3.32
449 509 9.473007 TCCTTCAATCCATATTAATTGTCACAA 57.527 29.630 0.00 0.00 35.02 3.33
450 510 9.123902 CTCCTTCAATCCATATTAATTGTCACA 57.876 33.333 0.00 0.00 35.02 3.58
451 511 9.342308 TCTCCTTCAATCCATATTAATTGTCAC 57.658 33.333 0.00 0.00 35.02 3.67
454 514 9.872684 ACATCTCCTTCAATCCATATTAATTGT 57.127 29.630 0.00 0.00 35.02 2.71
458 518 9.919416 TTTCACATCTCCTTCAATCCATATTAA 57.081 29.630 0.00 0.00 0.00 1.40
469 529 5.122239 CGCTAACATTTTCACATCTCCTTCA 59.878 40.000 0.00 0.00 0.00 3.02
475 535 4.393062 CCACTCGCTAACATTTTCACATCT 59.607 41.667 0.00 0.00 0.00 2.90
477 537 4.072131 ACCACTCGCTAACATTTTCACAT 58.928 39.130 0.00 0.00 0.00 3.21
480 540 4.250464 CCTACCACTCGCTAACATTTTCA 58.750 43.478 0.00 0.00 0.00 2.69
487 547 4.060205 TCAAAAACCTACCACTCGCTAAC 58.940 43.478 0.00 0.00 0.00 2.34
491 551 3.549423 GGTTTCAAAAACCTACCACTCGC 60.549 47.826 13.14 0.00 37.34 5.03
492 552 3.004002 GGGTTTCAAAAACCTACCACTCG 59.996 47.826 18.32 0.00 42.60 4.18
493 553 4.579454 GGGTTTCAAAAACCTACCACTC 57.421 45.455 18.32 0.19 42.60 3.51
502 562 9.353999 CATAATACAAGCTAGGGTTTCAAAAAC 57.646 33.333 0.00 0.00 0.00 2.43
505 565 7.179269 ACCATAATACAAGCTAGGGTTTCAAA 58.821 34.615 0.00 0.00 27.88 2.69
545 605 2.805671 CAACACCAACAAGCATCGAGTA 59.194 45.455 0.00 0.00 0.00 2.59
548 608 1.601903 GTCAACACCAACAAGCATCGA 59.398 47.619 0.00 0.00 0.00 3.59
568 628 0.167470 CGACAGCAATGCACTGGAAG 59.833 55.000 8.35 0.00 39.55 3.46
569 629 0.250252 TCGACAGCAATGCACTGGAA 60.250 50.000 8.35 0.00 39.55 3.53
590 651 2.413765 GCTAGACACTTCGCTTGTACGA 60.414 50.000 0.00 0.00 41.04 3.43
659 750 9.610705 TTAGATACTAGTAGTACAGTGGAACAG 57.389 37.037 12.25 0.00 33.49 3.16
706 799 6.044682 CCTACAAAAATTCAATGATCCCTGC 58.955 40.000 0.00 0.00 0.00 4.85
740 1101 9.421806 CTTAATTGCAACTGACCAATGAAAATA 57.578 29.630 0.00 0.00 32.40 1.40
840 1202 8.062065 TGACAAAGTCTGGAAAGTGTAAAAAT 57.938 30.769 0.00 0.00 33.15 1.82
931 1293 2.162208 CAGAACAGCATGCCGTATGTTT 59.838 45.455 20.12 10.33 42.53 2.83
965 1327 2.167398 TTGGTCAGTAGCGGAGTGGC 62.167 60.000 0.00 0.00 31.75 5.01
967 1329 1.270094 TGTTTGGTCAGTAGCGGAGTG 60.270 52.381 0.00 0.00 0.00 3.51
990 1352 1.484444 GCCCCTGCCCAGATAGTAGG 61.484 65.000 0.00 0.00 36.91 3.18
1278 1650 4.144703 GAGTCCCGGCCGTCTTCC 62.145 72.222 26.12 6.35 0.00 3.46
1394 1766 4.648626 GCCTGCACCAGCTCACCA 62.649 66.667 0.00 0.00 42.74 4.17
1522 1894 2.664851 CGACCACTTCTTGCGCCA 60.665 61.111 4.18 0.00 0.00 5.69
1752 2124 0.545309 AGCAGAAGTACTGGGCCAGA 60.545 55.000 38.99 19.98 45.82 3.86
2136 2508 0.446222 GCACGTACATGTTGCCGAAT 59.554 50.000 2.30 0.00 0.00 3.34
2190 2562 0.174389 TGACGCTGAAGATGAGGAGC 59.826 55.000 0.00 0.00 0.00 4.70
2421 2793 0.248377 CGTAGAAGTTAGCCGTCCGG 60.248 60.000 0.24 0.24 38.57 5.14
2707 3079 5.091261 AGTAGCAACTAATTCTCCCTGTG 57.909 43.478 0.00 0.00 32.84 3.66
2715 3087 9.712305 ACATCCACATATAGTAGCAACTAATTC 57.288 33.333 0.00 0.00 41.49 2.17
2716 3088 9.494271 CACATCCACATATAGTAGCAACTAATT 57.506 33.333 0.00 0.00 41.49 1.40
2718 3090 8.018537 ACACATCCACATATAGTAGCAACTAA 57.981 34.615 0.00 0.00 41.49 2.24
2725 3097 6.582672 CGCTACAACACATCCACATATAGTAG 59.417 42.308 0.00 0.00 0.00 2.57
2726 3098 6.443792 CGCTACAACACATCCACATATAGTA 58.556 40.000 0.00 0.00 0.00 1.82
2727 3099 5.289595 CGCTACAACACATCCACATATAGT 58.710 41.667 0.00 0.00 0.00 2.12
2785 3195 2.032117 CCAAACGCGCATATAGCATGAA 60.032 45.455 5.73 0.00 46.13 2.57
2818 3228 5.753744 TGCGTTTATGGTGTTCTGTTTTAG 58.246 37.500 0.00 0.00 0.00 1.85
2973 3395 5.471556 AATGCAATGGTGAAAATCACTGA 57.528 34.783 10.06 0.00 46.19 3.41
2975 3397 7.230849 TCTAAATGCAATGGTGAAAATCACT 57.769 32.000 10.06 0.00 46.19 3.41
2976 3398 7.887996 TTCTAAATGCAATGGTGAAAATCAC 57.112 32.000 1.88 1.88 46.23 3.06
2980 3402 7.440856 GGAACTTTCTAAATGCAATGGTGAAAA 59.559 33.333 0.00 0.00 0.00 2.29
2981 3403 6.928492 GGAACTTTCTAAATGCAATGGTGAAA 59.072 34.615 0.00 0.00 0.00 2.69
2982 3404 6.454795 GGAACTTTCTAAATGCAATGGTGAA 58.545 36.000 0.00 0.00 0.00 3.18
2983 3405 5.335583 CGGAACTTTCTAAATGCAATGGTGA 60.336 40.000 0.00 0.00 0.00 4.02
2984 3406 4.858692 CGGAACTTTCTAAATGCAATGGTG 59.141 41.667 0.00 0.00 0.00 4.17
2988 3410 4.022416 TGTGCGGAACTTTCTAAATGCAAT 60.022 37.500 0.00 0.00 32.29 3.56
3004 3430 0.317160 ACTGAATCGTTCTGTGCGGA 59.683 50.000 8.61 0.00 39.86 5.54
3011 3437 4.614535 GCTTGCAAATCACTGAATCGTTCT 60.615 41.667 0.00 0.00 0.00 3.01
3017 3443 5.221382 GGATATGGCTTGCAAATCACTGAAT 60.221 40.000 0.00 0.00 0.00 2.57
3034 3460 3.375299 GCTAAGCGGCAAATAGGATATGG 59.625 47.826 1.45 0.00 0.00 2.74
3089 3515 4.395959 TTGACTCTCCACACGTTAGTTT 57.604 40.909 0.00 0.00 0.00 2.66
3090 3516 4.117685 GTTTGACTCTCCACACGTTAGTT 58.882 43.478 0.00 0.00 0.00 2.24
3091 3517 3.383825 AGTTTGACTCTCCACACGTTAGT 59.616 43.478 0.00 0.00 0.00 2.24
3094 3520 2.981859 AGTTTGACTCTCCACACGTT 57.018 45.000 0.00 0.00 0.00 3.99
3098 3530 3.254093 TCCCTAGTTTGACTCTCCACA 57.746 47.619 0.00 0.00 0.00 4.17
3122 3554 1.373812 GCAGTTTACCGGGGACTGT 59.626 57.895 25.21 1.16 42.07 3.55
3123 3555 1.740296 CGCAGTTTACCGGGGACTG 60.740 63.158 22.38 22.38 42.75 3.51
3124 3556 2.660802 CGCAGTTTACCGGGGACT 59.339 61.111 6.32 3.28 0.00 3.85
3141 3573 2.821378 GTGTTATGGTTGGGTGGTTACC 59.179 50.000 0.00 0.00 46.76 2.85
3245 3685 4.584327 ACTTCACCGATTTTGGAAAAGG 57.416 40.909 0.00 0.00 32.23 3.11
3335 3789 8.728088 TGATTTTAGAAAAAGTTCAGCGATTC 57.272 30.769 0.00 0.00 36.09 2.52
3340 3794 7.908193 TCGTTGATTTTAGAAAAAGTTCAGC 57.092 32.000 0.00 0.00 36.09 4.26
3508 3982 8.663911 TCATTGAATTTGAAAAAGTTCACCAAC 58.336 29.630 0.00 0.00 43.52 3.77
3540 4014 6.526325 TCAAAACACGTTCATGAACTTGAAAG 59.474 34.615 37.35 26.07 41.38 2.62
3559 4034 4.678622 ACAATTCCACGGACTTTCAAAAC 58.321 39.130 0.00 0.00 0.00 2.43
3564 4039 5.873179 TTCATACAATTCCACGGACTTTC 57.127 39.130 0.00 0.00 0.00 2.62
3596 4071 4.335082 AAAGCGCAACAAAAGGAAAAAC 57.665 36.364 11.47 0.00 0.00 2.43
3632 4123 4.321452 CCCATGTTCACCTTCACATTTGAG 60.321 45.833 0.00 0.00 30.90 3.02
3644 4135 3.070576 GGCTGGCCCATGTTCACC 61.071 66.667 0.00 0.00 0.00 4.02
3648 4139 2.604382 GGTTGGCTGGCCCATGTT 60.604 61.111 9.28 0.00 44.89 2.71
3727 4218 7.171678 GCTTTGATCGTCCTAGTATTGCTAATT 59.828 37.037 0.00 0.00 0.00 1.40
3731 4222 4.372656 GCTTTGATCGTCCTAGTATTGCT 58.627 43.478 0.00 0.00 0.00 3.91
3739 4230 2.939640 GCTTTGGGCTTTGATCGTCCTA 60.940 50.000 0.00 0.00 38.06 2.94
3809 4300 2.171448 ACCTGCCATCCAGTTATCTGTC 59.829 50.000 0.30 0.00 40.06 3.51
3810 4301 2.092753 CACCTGCCATCCAGTTATCTGT 60.093 50.000 0.30 0.00 40.06 3.41
3837 4328 0.526211 GGGAGCAACAACGGATTTCC 59.474 55.000 0.00 0.00 0.00 3.13
3838 4329 0.526211 GGGGAGCAACAACGGATTTC 59.474 55.000 0.00 0.00 0.00 2.17
3839 4330 1.241315 CGGGGAGCAACAACGGATTT 61.241 55.000 0.00 0.00 0.00 2.17
3840 4331 1.674322 CGGGGAGCAACAACGGATT 60.674 57.895 0.00 0.00 0.00 3.01
3841 4332 2.046314 CGGGGAGCAACAACGGAT 60.046 61.111 0.00 0.00 0.00 4.18
3843 4334 4.323477 TCCGGGGAGCAACAACGG 62.323 66.667 0.00 0.00 45.52 4.44
3844 4335 2.742372 CTCCGGGGAGCAACAACG 60.742 66.667 0.00 0.00 35.31 4.10


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

AutoCloner maintained by Alex Coulton.