Multiple sequence alignment - TraesCS7B01G073200

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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 TraesCS7B01G073200 chr7B 100.000 5523 0 0 1 5523 81684064 81689586 0.000000e+00 10200
1 TraesCS7B01G073200 chr7A 93.343 2839 106 26 2744 5523 125258549 125261363 0.000000e+00 4119
2 TraesCS7B01G073200 chr7A 90.991 2320 126 39 480 2755 125256254 125258534 0.000000e+00 3049
3 TraesCS7B01G073200 chr7A 92.037 427 30 2 1 427 125255738 125256160 1.020000e-166 597
4 TraesCS7B01G073200 chr7A 89.085 284 18 9 3666 3942 696324827 696324550 1.910000e-89 340
5 TraesCS7B01G073200 chr7A 98.438 64 1 0 3009 3072 696325032 696324969 4.520000e-21 113
6 TraesCS7B01G073200 chr7A 90.909 77 7 0 4999 5075 68881171 68881095 2.720000e-18 104
7 TraesCS7B01G073200 chr7D 93.966 2088 60 19 870 2923 120314239 120316294 0.000000e+00 3097
8 TraesCS7B01G073200 chr7D 95.009 1643 65 9 3386 5023 120316776 120318406 0.000000e+00 2564
9 TraesCS7B01G073200 chr7D 85.229 853 78 24 1 815 120312862 120313704 0.000000e+00 833
10 TraesCS7B01G073200 chr7D 92.355 484 24 7 5044 5523 120318488 120318962 0.000000e+00 676
11 TraesCS7B01G073200 chr7D 90.497 463 16 10 2920 3354 120316322 120316784 2.220000e-163 586
12 TraesCS7B01G073200 chr7D 94.118 68 4 0 4999 5066 179191219 179191286 2.720000e-18 104
13 TraesCS7B01G073200 chr1A 91.221 262 14 6 3679 3937 582876878 582876623 1.140000e-91 348
14 TraesCS7B01G073200 chr1A 93.000 100 6 1 3417 3516 582876999 582876901 1.600000e-30 145
15 TraesCS7B01G073200 chr1A 98.438 64 1 0 3009 3072 582877099 582877036 4.520000e-21 113
16 TraesCS7B01G073200 chr4A 89.324 281 20 7 3666 3942 225615088 225614814 1.470000e-90 344
17 TraesCS7B01G073200 chr4A 91.416 233 14 3 3711 3942 700325320 700325093 1.150000e-81 315
18 TraesCS7B01G073200 chr4A 97.030 101 3 0 2974 3074 700325474 700325374 2.650000e-38 171
19 TraesCS7B01G073200 chr4A 93.000 100 6 1 3417 3516 225615192 225615094 1.600000e-30 145
20 TraesCS7B01G073200 chr3B 94.521 73 4 0 4999 5071 796309913 796309841 4.520000e-21 113
21 TraesCS7B01G073200 chr3B 95.588 68 3 0 4999 5066 520447968 520448035 5.850000e-20 110
22 TraesCS7B01G073200 chr2D 94.203 69 3 1 4998 5066 267707166 267707099 2.720000e-18 104
23 TraesCS7B01G073200 chr6A 88.889 81 8 1 4999 5078 501479360 501479280 1.270000e-16 99
24 TraesCS7B01G073200 chr1B 89.024 82 5 3 4997 5075 421421366 421421286 1.270000e-16 99


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 TraesCS7B01G073200 chr7B 81684064 81689586 5522 False 10200.000000 10200 100.000000 1 5523 1 chr7B.!!$F1 5522
1 TraesCS7B01G073200 chr7A 125255738 125261363 5625 False 2588.333333 4119 92.123667 1 5523 3 chr7A.!!$F1 5522
2 TraesCS7B01G073200 chr7D 120312862 120318962 6100 False 1551.200000 3097 91.411200 1 5523 5 chr7D.!!$F2 5522

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
392 396 0.321653 ATTTCTGTGGGTGCTCGGAC 60.322 55.0 0.00 0.0 0.00 4.79 F
1511 2060 0.453282 CACGAACAATCTGGCTTGCG 60.453 55.0 0.00 0.0 0.00 4.85 F
2372 2956 0.392336 GGACTGATCTAGCTGCCTGG 59.608 60.0 0.00 0.0 0.00 4.45 F
2937 3585 0.028505 GCATATGTGGTGCTGCTTCG 59.971 55.0 4.29 0.0 39.45 3.79 F
3726 4450 0.248661 CTGGATAGACAGACACGGCG 60.249 60.0 4.80 4.8 40.97 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2143 2723 0.036952 GCTGCTCACACTGAAGCCTA 60.037 55.000 0.00 0.00 26.97 3.93 R
2588 3179 0.392336 GCAGATCTAGGCCTCCAGTG 59.608 60.000 9.68 2.72 0.00 3.66 R
3709 4433 0.029567 CTCGCCGTGTCTGTCTATCC 59.970 60.000 0.00 0.00 0.00 2.59 R
4441 5166 0.250338 GGTCGGTGCTCCTCACTTTT 60.250 55.000 2.85 0.00 44.98 2.27 R
4896 5622 1.407979 CCATGCCAAAAGCCTCTGATC 59.592 52.381 0.00 0.00 42.71 2.92 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
47 48 2.157834 TGCGATACACGAACCAAAGT 57.842 45.000 0.00 0.00 45.77 2.66
235 236 0.737219 GCAGCTGGAGTGGCAATAAG 59.263 55.000 17.12 0.00 0.00 1.73
259 260 2.677836 ACGTTTGACATCAATGATCGGG 59.322 45.455 0.00 0.00 35.55 5.14
268 269 4.019950 ACATCAATGATCGGGCTATCATGA 60.020 41.667 13.95 0.00 44.08 3.07
274 275 1.269958 TCGGGCTATCATGATCCCTG 58.730 55.000 23.48 21.98 36.61 4.45
296 297 7.117397 CCTGCTATTGATCATCAAAGGGATAT 58.883 38.462 3.63 0.00 40.12 1.63
314 315 1.135094 ATGATGAGAGTTCCGCCCAT 58.865 50.000 0.00 0.00 0.00 4.00
316 317 1.412710 TGATGAGAGTTCCGCCCATAC 59.587 52.381 0.00 0.00 0.00 2.39
317 318 1.689273 GATGAGAGTTCCGCCCATACT 59.311 52.381 0.00 0.00 0.00 2.12
318 319 0.824109 TGAGAGTTCCGCCCATACTG 59.176 55.000 0.00 0.00 0.00 2.74
377 381 6.160664 TCGGTAAGACGATTTCAACATTTC 57.839 37.500 0.00 0.00 38.06 2.17
385 389 4.229096 CGATTTCAACATTTCTGTGGGTG 58.771 43.478 0.00 0.00 35.22 4.61
387 391 2.363306 TCAACATTTCTGTGGGTGCT 57.637 45.000 0.00 0.00 35.22 4.40
389 393 1.069022 CAACATTTCTGTGGGTGCTCG 60.069 52.381 0.00 0.00 35.22 5.03
392 396 0.321653 ATTTCTGTGGGTGCTCGGAC 60.322 55.000 0.00 0.00 0.00 4.79
403 407 0.958382 TGCTCGGACAATTTTCCCGG 60.958 55.000 5.04 0.00 43.16 5.73
409 413 0.526211 GACAATTTTCCCGGGTCAGC 59.474 55.000 22.86 0.00 0.00 4.26
450 480 7.716799 ACAGAGAAATAACAGAGTCTCATCT 57.283 36.000 1.94 0.00 39.20 2.90
455 485 9.730420 GAGAAATAACAGAGTCTCATCTAACTC 57.270 37.037 1.94 0.00 41.81 3.01
461 491 6.486056 ACAGAGTCTCATCTAACTCCTACAA 58.514 40.000 1.94 0.00 42.34 2.41
465 495 9.875708 AGAGTCTCATCTAACTCCTACAATATT 57.124 33.333 1.94 0.00 42.34 1.28
468 498 8.983724 GTCTCATCTAACTCCTACAATATTTGC 58.016 37.037 0.00 0.00 0.00 3.68
488 533 6.917217 TTGCTTAACCAAACAAAAATCCTG 57.083 33.333 0.00 0.00 0.00 3.86
489 534 5.363939 TGCTTAACCAAACAAAAATCCTGG 58.636 37.500 0.00 0.00 0.00 4.45
496 541 3.592898 AACAAAAATCCTGGCGAATCC 57.407 42.857 0.00 0.00 0.00 3.01
498 543 1.824230 CAAAAATCCTGGCGAATCCCA 59.176 47.619 0.00 0.00 0.00 4.37
508 553 2.820787 TGGCGAATCCCAACGTAAAATT 59.179 40.909 0.00 0.00 30.32 1.82
509 554 4.008330 TGGCGAATCCCAACGTAAAATTA 58.992 39.130 0.00 0.00 30.32 1.40
510 555 4.641094 TGGCGAATCCCAACGTAAAATTAT 59.359 37.500 0.00 0.00 30.32 1.28
512 557 6.487331 TGGCGAATCCCAACGTAAAATTATAT 59.513 34.615 0.00 0.00 30.32 0.86
514 559 6.799925 GCGAATCCCAACGTAAAATTATATGG 59.200 38.462 0.00 0.00 0.00 2.74
515 560 7.520937 GCGAATCCCAACGTAAAATTATATGGT 60.521 37.037 0.00 0.00 0.00 3.55
520 565 8.266473 TCCCAACGTAAAATTATATGGTGTAGT 58.734 33.333 0.00 0.00 29.23 2.73
537 582 9.642343 ATGGTGTAGTAGTTAGATGAGACATAA 57.358 33.333 0.00 0.00 0.00 1.90
565 610 8.815565 ATTTCACTTCTAGATGAGAGTAGACA 57.184 34.615 12.31 0.00 34.93 3.41
566 611 7.618502 TTCACTTCTAGATGAGAGTAGACAC 57.381 40.000 12.31 0.00 34.93 3.67
567 612 6.712276 TCACTTCTAGATGAGAGTAGACACA 58.288 40.000 12.31 0.00 34.93 3.72
568 613 7.342581 TCACTTCTAGATGAGAGTAGACACAT 58.657 38.462 12.31 0.00 34.93 3.21
571 616 6.508030 TCTAGATGAGAGTAGACACATCCT 57.492 41.667 0.00 0.00 39.61 3.24
573 618 7.350382 TCTAGATGAGAGTAGACACATCCTTT 58.650 38.462 0.00 0.00 39.61 3.11
574 619 6.865834 AGATGAGAGTAGACACATCCTTTT 57.134 37.500 0.00 0.00 39.61 2.27
575 620 7.251321 AGATGAGAGTAGACACATCCTTTTT 57.749 36.000 0.00 0.00 39.61 1.94
576 621 8.367660 AGATGAGAGTAGACACATCCTTTTTA 57.632 34.615 0.00 0.00 39.61 1.52
694 741 5.163385 ACATGAATAATGGAGCCAATTGTGG 60.163 40.000 0.00 0.00 43.54 4.17
741 792 7.056635 CACACATTAAATCACCTCCTTATCCT 58.943 38.462 0.00 0.00 0.00 3.24
754 805 7.615757 CACCTCCTTATCCTAAAATTTCACCTT 59.384 37.037 0.00 0.00 0.00 3.50
816 871 3.732048 TCCTCCAATTACCCACCTTTC 57.268 47.619 0.00 0.00 0.00 2.62
864 919 3.013417 TCCCTCTCTTCCTTCCTTCATCT 59.987 47.826 0.00 0.00 0.00 2.90
865 920 3.779738 CCCTCTCTTCCTTCCTTCATCTT 59.220 47.826 0.00 0.00 0.00 2.40
866 921 4.383989 CCCTCTCTTCCTTCCTTCATCTTG 60.384 50.000 0.00 0.00 0.00 3.02
884 1419 9.905713 TTCATCTTGTGCTATAAATAACCTCTT 57.094 29.630 0.00 0.00 0.00 2.85
920 1455 1.821759 CACACCCACACCGCTCAAA 60.822 57.895 0.00 0.00 0.00 2.69
952 1487 1.238439 CAAAGCACACCCATCTCGTT 58.762 50.000 0.00 0.00 0.00 3.85
954 1489 1.237285 AAGCACACCCATCTCGTTGC 61.237 55.000 0.00 0.00 0.00 4.17
955 1490 1.965930 GCACACCCATCTCGTTGCA 60.966 57.895 0.00 0.00 0.00 4.08
956 1491 1.514678 GCACACCCATCTCGTTGCAA 61.515 55.000 0.00 0.00 0.00 4.08
960 1496 2.030007 ACACCCATCTCGTTGCAAATTG 60.030 45.455 0.00 0.00 0.00 2.32
1287 1830 1.604378 CCTCAACCTCCGCTCCATT 59.396 57.895 0.00 0.00 0.00 3.16
1299 1842 1.134580 CGCTCCATTGTGTGAGGATCT 60.135 52.381 0.00 0.00 34.92 2.75
1300 1843 2.559440 GCTCCATTGTGTGAGGATCTC 58.441 52.381 0.00 0.00 34.92 2.75
1304 1847 0.833287 ATTGTGTGAGGATCTCCCCG 59.167 55.000 0.00 0.00 36.42 5.73
1305 1848 1.899437 TTGTGTGAGGATCTCCCCGC 61.899 60.000 0.00 0.00 36.42 6.13
1307 1850 2.444895 GTGAGGATCTCCCCGCCT 60.445 66.667 0.00 0.00 36.42 5.52
1322 1866 4.567385 CCTCTCTCTGCTCCGCGC 62.567 72.222 0.00 0.00 39.77 6.86
1350 1894 1.358725 TTATTGCGCTGCTCGTGTCC 61.359 55.000 9.73 0.00 41.07 4.02
1511 2060 0.453282 CACGAACAATCTGGCTTGCG 60.453 55.000 0.00 0.00 0.00 4.85
1578 2144 1.936547 GGAAGGTAGAATCGCAGCTTG 59.063 52.381 6.99 0.00 32.89 4.01
1596 2162 7.543520 CGCAGCTTGTAGATAGATAATCATGAA 59.456 37.037 0.00 0.00 37.03 2.57
1607 2173 9.877178 GATAGATAATCATGAATACTTTCCGGT 57.123 33.333 0.00 0.00 34.46 5.28
1676 2242 6.414408 GCTATTACGCGTCCTAGATTAGTA 57.586 41.667 18.63 0.00 0.00 1.82
1677 2243 6.247176 GCTATTACGCGTCCTAGATTAGTAC 58.753 44.000 18.63 0.00 0.00 2.73
1742 2310 8.199449 CACTGGCTGGATTTTATTTGTTATCAT 58.801 33.333 0.00 0.00 0.00 2.45
1775 2343 6.402222 CCTAATAGGCGCATCTATCTCTTTT 58.598 40.000 10.83 0.00 0.00 2.27
1786 2354 6.041523 GCATCTATCTCTTTTCTCCTACCACT 59.958 42.308 0.00 0.00 0.00 4.00
1865 2433 1.953559 TGATTAATCGACCCAGCTGC 58.046 50.000 8.66 0.00 0.00 5.25
1893 2466 7.924940 TGCTGATTTTAAACAACAATTTTCCC 58.075 30.769 0.00 0.00 0.00 3.97
1939 2512 3.821033 GGTTTGCTCCTGTGATAACAAGT 59.179 43.478 0.00 0.00 0.00 3.16
1993 2566 6.721208 GCATCTCCATTATCCCCTTTCATTTA 59.279 38.462 0.00 0.00 0.00 1.40
1994 2567 7.398332 GCATCTCCATTATCCCCTTTCATTTAT 59.602 37.037 0.00 0.00 0.00 1.40
1998 2571 9.987272 CTCCATTATCCCCTTTCATTTATTTTC 57.013 33.333 0.00 0.00 0.00 2.29
1999 2572 9.728100 TCCATTATCCCCTTTCATTTATTTTCT 57.272 29.630 0.00 0.00 0.00 2.52
2042 2621 7.899178 TCTTGTTTGAGTGATATTTTCGCTA 57.101 32.000 0.00 0.00 45.22 4.26
2122 2701 7.945033 TTTGCAAGAAGGACACAATTTATTC 57.055 32.000 0.00 0.00 0.00 1.75
2143 2723 9.675464 TTATTCGGTACAGGAATTTTCTTGTAT 57.325 29.630 15.53 6.00 46.70 2.29
2185 2765 5.394738 CTCATGGGACCTGTAACTCCTATA 58.605 45.833 0.00 0.00 0.00 1.31
2189 2769 3.640498 GGGACCTGTAACTCCTATACACC 59.360 52.174 0.00 0.00 0.00 4.16
2202 2782 5.162637 TCCTATACACCCCATATGCTCTTT 58.837 41.667 0.00 0.00 0.00 2.52
2203 2783 6.327781 TCCTATACACCCCATATGCTCTTTA 58.672 40.000 0.00 0.00 0.00 1.85
2204 2784 6.440647 TCCTATACACCCCATATGCTCTTTAG 59.559 42.308 0.00 0.00 0.00 1.85
2205 2785 3.864789 ACACCCCATATGCTCTTTAGG 57.135 47.619 0.00 0.00 0.00 2.69
2207 2787 3.136626 ACACCCCATATGCTCTTTAGGTC 59.863 47.826 0.00 0.00 0.00 3.85
2208 2788 2.368875 ACCCCATATGCTCTTTAGGTCG 59.631 50.000 0.00 0.00 0.00 4.79
2209 2789 2.368875 CCCCATATGCTCTTTAGGTCGT 59.631 50.000 0.00 0.00 0.00 4.34
2210 2790 3.181454 CCCCATATGCTCTTTAGGTCGTT 60.181 47.826 0.00 0.00 0.00 3.85
2211 2791 4.451900 CCCATATGCTCTTTAGGTCGTTT 58.548 43.478 0.00 0.00 0.00 3.60
2213 2793 6.053005 CCCATATGCTCTTTAGGTCGTTTTA 58.947 40.000 0.00 0.00 0.00 1.52
2372 2956 0.392336 GGACTGATCTAGCTGCCTGG 59.608 60.000 0.00 0.00 0.00 4.45
2585 3176 5.429762 TGTTCTTGATGAGAGGGGATAACAT 59.570 40.000 0.00 0.00 35.37 2.71
2586 3177 6.615316 TGTTCTTGATGAGAGGGGATAACATA 59.385 38.462 0.00 0.00 35.37 2.29
2587 3178 7.127186 TGTTCTTGATGAGAGGGGATAACATAA 59.873 37.037 0.00 0.00 35.37 1.90
2588 3179 7.067496 TCTTGATGAGAGGGGATAACATAAC 57.933 40.000 0.00 0.00 0.00 1.89
2589 3180 6.615316 TCTTGATGAGAGGGGATAACATAACA 59.385 38.462 0.00 0.00 0.00 2.41
2690 3281 4.080299 AGGACAGTACATTGGATTCTTCCC 60.080 45.833 0.00 0.00 41.83 3.97
2937 3585 0.028505 GCATATGTGGTGCTGCTTCG 59.971 55.000 4.29 0.00 39.45 3.79
2972 3620 4.237724 GCTGGTTTTCCTGAATAGCAAAC 58.762 43.478 4.31 0.00 40.71 2.93
3060 3708 5.469479 AGTTGCAGTAAATTGTTGGTATGC 58.531 37.500 0.00 0.00 0.00 3.14
3176 3874 7.255486 CCTTTTACTTTTGGAGGTTTAGGTGAG 60.255 40.741 0.00 0.00 0.00 3.51
3212 3910 2.224992 TGTGGGCAAAGCTTCCAGATTA 60.225 45.455 5.63 0.00 0.00 1.75
3317 4037 6.090223 CGTTTTAATTATTTGGGAACTGGTGC 59.910 38.462 0.00 0.00 0.00 5.01
3403 4124 4.651778 TGAATGACAAGAAACTACCCCAG 58.348 43.478 0.00 0.00 0.00 4.45
3420 4142 9.682465 ACTACCCCAGTTATTTCTTTTCTTATC 57.318 33.333 0.00 0.00 31.59 1.75
3459 4183 7.457024 TCATCCATGACCTAATGCATAATTG 57.543 36.000 0.00 0.00 0.00 2.32
3556 4280 8.311109 TGTGTGTCATAGTTTCTTAGATTAGCA 58.689 33.333 0.00 0.00 0.00 3.49
3568 4292 9.453572 TTTCTTAGATTAGCATTGTCATTGTCT 57.546 29.630 0.00 0.00 0.00 3.41
3571 4295 8.791327 TTAGATTAGCATTGTCATTGTCTGAA 57.209 30.769 0.00 0.00 35.07 3.02
3575 4299 8.697846 ATTAGCATTGTCATTGTCTGAATTTG 57.302 30.769 0.00 0.00 35.07 2.32
3656 4380 8.281212 ACCTTGAAAAATAGTACATGATGGAC 57.719 34.615 0.00 0.00 0.00 4.02
3722 4446 4.158579 TCATGTCACTGGATAGACAGACAC 59.841 45.833 0.00 0.00 46.70 3.67
3726 4450 0.248661 CTGGATAGACAGACACGGCG 60.249 60.000 4.80 4.80 40.97 6.46
3883 4607 6.691255 TTACTGGACCTTGGTACATTTAGT 57.309 37.500 5.03 2.83 39.30 2.24
4142 4867 0.469917 TTGATCCTTCCCATCTCGGC 59.530 55.000 0.00 0.00 0.00 5.54
4173 4898 6.018098 CCATCACAGCATTTCATCTCTCTTAC 60.018 42.308 0.00 0.00 0.00 2.34
4174 4899 6.041423 TCACAGCATTTCATCTCTCTTACA 57.959 37.500 0.00 0.00 0.00 2.41
4175 4900 6.104665 TCACAGCATTTCATCTCTCTTACAG 58.895 40.000 0.00 0.00 0.00 2.74
4176 4901 5.873712 CACAGCATTTCATCTCTCTTACAGT 59.126 40.000 0.00 0.00 0.00 3.55
4177 4902 6.035866 CACAGCATTTCATCTCTCTTACAGTC 59.964 42.308 0.00 0.00 0.00 3.51
4178 4903 6.070881 ACAGCATTTCATCTCTCTTACAGTCT 60.071 38.462 0.00 0.00 0.00 3.24
4179 4904 6.817641 CAGCATTTCATCTCTCTTACAGTCTT 59.182 38.462 0.00 0.00 0.00 3.01
4180 4905 6.817641 AGCATTTCATCTCTCTTACAGTCTTG 59.182 38.462 0.00 0.00 0.00 3.02
4218 4943 9.573166 TTCTTTCTTCCAGATGTAAGAAATCAA 57.427 29.630 12.06 7.16 45.64 2.57
4221 4946 7.020827 TCTTCCAGATGTAAGAAATCAACCT 57.979 36.000 0.00 0.00 0.00 3.50
4257 4982 2.746362 CAAGAGAGGCAAGGTAAGCTTG 59.254 50.000 9.86 0.00 35.13 4.01
4267 4992 5.509670 GGCAAGGTAAGCTTGATCAGTTTTT 60.510 40.000 9.86 0.00 33.98 1.94
4300 5025 2.568956 TGCAGCTGGTATCTTCAAGTCT 59.431 45.455 17.12 0.00 0.00 3.24
4332 5057 4.267349 ACTTACTCACCGTGCAATACTT 57.733 40.909 0.00 0.00 0.00 2.24
4621 5347 4.130118 GGACCGAATCAGCAGTGAATAAT 58.870 43.478 0.00 0.00 35.88 1.28
4670 5396 2.017782 GATAGTGACGAGACCTCTGCA 58.982 52.381 0.00 0.00 0.00 4.41
4789 5515 5.752892 AGAGGTTTTCTTTTTCTTCGGTC 57.247 39.130 0.00 0.00 29.61 4.79
4940 5672 1.442526 CGACTGATTGGGCTGGCATC 61.443 60.000 2.88 0.00 0.00 3.91
4942 5674 1.153107 CTGATTGGGCTGGCATCGA 60.153 57.895 2.88 0.00 0.00 3.59
4963 5695 5.805486 TCGACACACATAGAACTTAATGAGC 59.195 40.000 0.00 0.00 0.00 4.26
4969 5701 8.618677 CACACATAGAACTTAATGAGCAATGAT 58.381 33.333 0.00 0.00 0.00 2.45
4989 5721 3.401033 TCGTATGAATGGCGGATGATT 57.599 42.857 0.00 0.00 0.00 2.57
5034 5766 9.874215 GTCCCATAATATAAGAGCGTTTTTAAC 57.126 33.333 0.00 0.00 0.00 2.01
5059 5852 9.085645 ACACTACAATCTTATATTATGGGACGA 57.914 33.333 0.00 0.00 0.00 4.20
5066 5859 3.983044 ATATTATGGGACGAAGGGAGC 57.017 47.619 0.00 0.00 0.00 4.70
5115 5908 0.318955 GGGTGCTGTTCATGTGCAAC 60.319 55.000 10.56 10.56 43.00 4.17
5142 5935 4.974399 ACGAGGAAATTTTCAACCTCTCT 58.026 39.130 17.15 4.41 44.47 3.10
5212 6005 4.780815 TGTGAGACAAAATGTGGACTCTT 58.219 39.130 0.00 0.00 36.43 2.85
5254 6047 8.779303 CATAACTAATGTTGTACCACTGTTTCA 58.221 33.333 0.00 0.00 37.59 2.69
5255 6048 6.613755 ACTAATGTTGTACCACTGTTTCAC 57.386 37.500 0.00 0.00 0.00 3.18
5256 6049 6.116806 ACTAATGTTGTACCACTGTTTCACA 58.883 36.000 0.00 0.00 0.00 3.58
5265 6058 5.461032 ACCACTGTTTCACAAAGTTTCAA 57.539 34.783 0.00 0.00 0.00 2.69
5371 6164 9.210426 CGTATAAAGAAGTAACATGATTTGTGC 57.790 33.333 0.00 0.00 38.99 4.57
5489 6286 6.557633 GGTAGGGACTGAGGAAAATCCTATTA 59.442 42.308 0.00 0.00 44.29 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 7.739911 GTGTATCGCAATTTTTGTTCCATTTTC 59.260 33.333 0.00 0.00 0.00 2.29
15 16 4.856487 CGTGTATCGCAATTTTTGTTCCAT 59.144 37.500 0.00 0.00 0.00 3.41
99 100 7.286316 TGAGTCATGCTAGAGATGTGATTAGAA 59.714 37.037 0.00 0.00 0.00 2.10
107 108 3.029570 TGCTGAGTCATGCTAGAGATGT 58.970 45.455 13.40 0.00 0.00 3.06
235 236 5.333339 CCCGATCATTGATGTCAAACGTATC 60.333 44.000 3.32 0.00 39.55 2.24
259 260 5.095145 TCAATAGCAGGGATCATGATAGC 57.905 43.478 8.54 10.55 0.00 2.97
268 269 5.322754 CCTTTGATGATCAATAGCAGGGAT 58.677 41.667 8.90 0.00 36.11 3.85
274 275 8.749026 ATCATATCCCTTTGATGATCAATAGC 57.251 34.615 8.90 0.00 35.84 2.97
296 297 1.412710 GTATGGGCGGAACTCTCATCA 59.587 52.381 0.00 0.00 0.00 3.07
314 315 5.508200 AAATTTGTTTGTCCTTCGCAGTA 57.492 34.783 0.00 0.00 0.00 2.74
316 317 5.173131 GTGTAAATTTGTTTGTCCTTCGCAG 59.827 40.000 0.00 0.00 0.00 5.18
317 318 5.038033 GTGTAAATTTGTTTGTCCTTCGCA 58.962 37.500 0.00 0.00 0.00 5.10
318 319 5.278604 AGTGTAAATTTGTTTGTCCTTCGC 58.721 37.500 0.00 0.00 0.00 4.70
350 354 1.822990 TGAAATCGTCTTACCGAGGCT 59.177 47.619 0.00 0.00 40.68 4.58
377 381 0.606401 AATTGTCCGAGCACCCACAG 60.606 55.000 0.00 0.00 0.00 3.66
385 389 1.654023 CCCGGGAAAATTGTCCGAGC 61.654 60.000 18.48 0.00 45.96 5.03
387 391 0.321830 GACCCGGGAAAATTGTCCGA 60.322 55.000 32.02 0.00 45.96 4.55
389 393 1.173913 CTGACCCGGGAAAATTGTCC 58.826 55.000 32.02 6.05 36.90 4.02
392 396 1.185315 ATGCTGACCCGGGAAAATTG 58.815 50.000 32.02 11.69 0.00 2.32
427 431 9.515020 GTTAGATGAGACTCTGTTATTTCTCTG 57.485 37.037 3.68 0.00 36.29 3.35
428 432 9.474313 AGTTAGATGAGACTCTGTTATTTCTCT 57.526 33.333 3.68 0.00 36.29 3.10
450 480 9.742144 TTGGTTAAGCAAATATTGTAGGAGTTA 57.258 29.630 17.34 0.00 0.00 2.24
455 485 9.482627 TTTGTTTGGTTAAGCAAATATTGTAGG 57.517 29.630 29.46 0.00 40.54 3.18
461 491 9.791801 AGGATTTTTGTTTGGTTAAGCAAATAT 57.208 25.926 29.46 18.99 43.42 1.28
465 495 5.819901 CCAGGATTTTTGTTTGGTTAAGCAA 59.180 36.000 15.83 15.83 35.58 3.91
468 498 4.447389 CGCCAGGATTTTTGTTTGGTTAAG 59.553 41.667 0.00 0.00 0.00 1.85
486 531 1.444836 TTTACGTTGGGATTCGCCAG 58.555 50.000 0.00 0.00 38.95 4.85
488 533 3.497297 AATTTTACGTTGGGATTCGCC 57.503 42.857 0.00 0.00 0.00 5.54
489 534 6.799925 CCATATAATTTTACGTTGGGATTCGC 59.200 38.462 0.00 0.00 0.00 4.70
509 554 9.815306 ATGTCTCATCTAACTACTACACCATAT 57.185 33.333 0.00 0.00 0.00 1.78
512 557 9.642343 ATTATGTCTCATCTAACTACTACACCA 57.358 33.333 0.00 0.00 0.00 4.17
545 590 6.770785 GGATGTGTCTACTCTCATCTAGAAGT 59.229 42.308 0.00 0.00 37.99 3.01
546 591 6.998074 AGGATGTGTCTACTCTCATCTAGAAG 59.002 42.308 0.00 0.00 37.99 2.85
547 592 6.905736 AGGATGTGTCTACTCTCATCTAGAA 58.094 40.000 0.00 0.00 37.99 2.10
582 627 5.556915 TGGTTCAACAGACTATACCAAAGG 58.443 41.667 0.00 0.00 33.05 3.11
583 628 6.899114 GTTGGTTCAACAGACTATACCAAAG 58.101 40.000 0.00 0.00 44.51 2.77
668 713 4.595762 ATTGGCTCCATTATTCATGTGC 57.404 40.909 0.00 0.00 32.59 4.57
694 741 7.911205 GTGTGTTATGACATCTAGAGTGTCTAC 59.089 40.741 23.74 19.93 44.80 2.59
741 792 9.087871 TGATTGATGAGGAAAGGTGAAATTTTA 57.912 29.630 0.00 0.00 0.00 1.52
754 805 5.997843 AGTGTGATGATGATTGATGAGGAA 58.002 37.500 0.00 0.00 0.00 3.36
864 919 7.773690 GGAAGGAAGAGGTTATTTATAGCACAA 59.226 37.037 0.00 0.00 0.00 3.33
865 920 7.092623 TGGAAGGAAGAGGTTATTTATAGCACA 60.093 37.037 0.00 0.00 0.00 4.57
866 921 7.280356 TGGAAGGAAGAGGTTATTTATAGCAC 58.720 38.462 0.00 0.00 0.00 4.40
884 1419 1.559682 GTGATGGCCTAACTGGAAGGA 59.440 52.381 3.32 0.00 39.30 3.36
920 1455 1.100463 TGCTTTGTGTGCGTGATGGT 61.100 50.000 0.00 0.00 0.00 3.55
952 1487 0.313672 GGCAGAACCGTCAATTTGCA 59.686 50.000 0.00 0.00 33.42 4.08
954 1489 1.247567 AGGGCAGAACCGTCAATTTG 58.752 50.000 0.00 0.00 40.62 2.32
955 1490 1.613437 CAAGGGCAGAACCGTCAATTT 59.387 47.619 0.00 0.00 40.62 1.82
956 1491 1.247567 CAAGGGCAGAACCGTCAATT 58.752 50.000 0.00 0.00 40.62 2.32
960 1496 3.056328 GGCAAGGGCAGAACCGTC 61.056 66.667 0.00 0.00 43.71 4.79
985 1528 2.094675 CTTCATGATGGCTTCCGGTTT 58.905 47.619 0.00 0.00 0.00 3.27
986 1529 1.755179 CTTCATGATGGCTTCCGGTT 58.245 50.000 0.00 0.00 0.00 4.44
1287 1830 2.359169 GCGGGGAGATCCTCACACA 61.359 63.158 0.00 0.00 35.24 3.72
1299 1842 4.067512 AGCAGAGAGAGGCGGGGA 62.068 66.667 0.00 0.00 34.54 4.81
1300 1843 3.535962 GAGCAGAGAGAGGCGGGG 61.536 72.222 0.00 0.00 34.54 5.73
1350 1894 2.506544 CGTCAGAACCACGTGACAG 58.493 57.895 19.30 2.42 42.79 3.51
1492 2040 0.453282 CGCAAGCCAGATTGTTCGTG 60.453 55.000 0.00 0.00 32.56 4.35
1596 2162 7.368833 CAATTCTCGTATCTACCGGAAAGTAT 58.631 38.462 9.46 3.92 0.00 2.12
1607 2173 4.400529 TGGCAAGCAATTCTCGTATCTA 57.599 40.909 0.00 0.00 0.00 1.98
1676 2242 3.915575 CCACCTAGGCGAGTACGT 58.084 61.111 9.30 0.00 41.98 3.57
1717 2285 7.716799 TGATAACAAATAAAATCCAGCCAGT 57.283 32.000 0.00 0.00 0.00 4.00
1772 2340 2.838202 CCAGGCTAGTGGTAGGAGAAAA 59.162 50.000 0.00 0.00 32.32 2.29
1775 2343 0.261991 CCCAGGCTAGTGGTAGGAGA 59.738 60.000 0.00 0.00 35.60 3.71
1786 2354 3.825908 ACTTGAAAAATCCCCAGGCTA 57.174 42.857 0.00 0.00 0.00 3.93
1865 2433 5.827568 ATTGTTGTTTAAAATCAGCAGCG 57.172 34.783 0.00 0.00 0.00 5.18
1893 2466 8.891671 CCAATTAGAAACCATTGGGAATATTG 57.108 34.615 7.78 8.57 44.05 1.90
1939 2512 3.431415 ACTATGCACACTCACTACCAGA 58.569 45.455 0.00 0.00 0.00 3.86
2014 2593 8.751335 GCGAAAATATCACTCAAACAAGAAAAA 58.249 29.630 0.00 0.00 0.00 1.94
2039 2618 5.119694 AGCTACCTACTTTGCAGAAATAGC 58.880 41.667 0.00 0.00 34.15 2.97
2042 2621 5.165961 TGAGCTACCTACTTTGCAGAAAT 57.834 39.130 0.00 0.00 0.00 2.17
2097 2676 7.168972 CGAATAAATTGTGTCCTTCTTGCAAAA 59.831 33.333 0.00 0.00 0.00 2.44
2122 2701 6.018180 GCCTATACAAGAAAATTCCTGTACCG 60.018 42.308 6.74 2.59 37.05 4.02
2143 2723 0.036952 GCTGCTCACACTGAAGCCTA 60.037 55.000 0.00 0.00 26.97 3.93
2185 2765 3.123273 ACCTAAAGAGCATATGGGGTGT 58.877 45.455 4.56 0.00 0.00 4.16
2189 2769 3.753294 ACGACCTAAAGAGCATATGGG 57.247 47.619 4.56 0.00 0.00 4.00
2202 2782 8.550710 TTAAAGCTGCTTAATAAAACGACCTA 57.449 30.769 16.31 0.00 0.00 3.08
2203 2783 5.959618 AAAGCTGCTTAATAAAACGACCT 57.040 34.783 16.31 0.00 0.00 3.85
2204 2784 7.220108 CCATTAAAGCTGCTTAATAAAACGACC 59.780 37.037 16.31 0.00 31.67 4.79
2205 2785 7.753580 ACCATTAAAGCTGCTTAATAAAACGAC 59.246 33.333 16.31 0.00 31.67 4.34
2207 2787 7.220108 GGACCATTAAAGCTGCTTAATAAAACG 59.780 37.037 16.31 6.11 31.67 3.60
2208 2788 7.491372 GGGACCATTAAAGCTGCTTAATAAAAC 59.509 37.037 16.31 5.97 31.67 2.43
2209 2789 7.179338 TGGGACCATTAAAGCTGCTTAATAAAA 59.821 33.333 16.31 6.00 31.67 1.52
2210 2790 6.665680 TGGGACCATTAAAGCTGCTTAATAAA 59.334 34.615 16.31 8.37 31.67 1.40
2211 2791 6.191315 TGGGACCATTAAAGCTGCTTAATAA 58.809 36.000 16.31 11.76 31.67 1.40
2213 2793 4.609301 TGGGACCATTAAAGCTGCTTAAT 58.391 39.130 16.31 12.15 32.80 1.40
2255 2838 8.618702 TGCATCAACCAACAATTTTAATTCAT 57.381 26.923 0.00 0.00 0.00 2.57
2372 2956 6.730960 TTATACATTTCGTCCAACTTGACC 57.269 37.500 0.00 0.00 31.35 4.02
2585 3176 3.300388 CAGATCTAGGCCTCCAGTGTTA 58.700 50.000 9.68 0.00 0.00 2.41
2586 3177 2.114616 CAGATCTAGGCCTCCAGTGTT 58.885 52.381 9.68 0.00 0.00 3.32
2587 3178 1.786937 CAGATCTAGGCCTCCAGTGT 58.213 55.000 9.68 0.00 0.00 3.55
2588 3179 0.392336 GCAGATCTAGGCCTCCAGTG 59.608 60.000 9.68 2.72 0.00 3.66
2589 3180 0.762461 GGCAGATCTAGGCCTCCAGT 60.762 60.000 9.68 0.00 46.74 4.00
2690 3281 0.996462 CAGCAATCATTTTGCCAGCG 59.004 50.000 6.69 0.00 45.98 5.18
2853 3470 5.477291 TGAAAACAGGGAACAGTACAACAAA 59.523 36.000 0.00 0.00 0.00 2.83
2937 3585 0.675633 AACCAGCAAGAACACATGGC 59.324 50.000 0.00 0.00 34.24 4.40
2972 3620 8.514136 AAAATTACATGTAAAACACCATGACG 57.486 30.769 21.57 0.00 40.70 4.35
3176 3874 6.449635 TTGCCCACAACTATATCACAATTC 57.550 37.500 0.00 0.00 0.00 2.17
3212 3910 4.724279 ACTGTAGTCACCCCTTGAAAAT 57.276 40.909 0.00 0.00 35.39 1.82
3317 4037 5.490139 AATATGATTTGTCTTGACCGCTG 57.510 39.130 0.00 0.00 0.00 5.18
3354 4074 8.380743 AGCATCAATCAAAAGCAACAAAATAA 57.619 26.923 0.00 0.00 0.00 1.40
3361 4082 7.490079 TCATTCATAGCATCAATCAAAAGCAAC 59.510 33.333 0.00 0.00 0.00 4.17
3372 4093 7.692460 AGTTTCTTGTCATTCATAGCATCAA 57.308 32.000 0.00 0.00 0.00 2.57
3415 4137 5.667539 TGACCTGGAAGTTCAGAGATAAG 57.332 43.478 0.00 0.00 36.93 1.73
3418 4140 3.454082 GGATGACCTGGAAGTTCAGAGAT 59.546 47.826 0.00 0.00 36.93 2.75
3420 4142 2.568956 TGGATGACCTGGAAGTTCAGAG 59.431 50.000 0.00 0.00 36.93 3.35
3459 4183 8.477709 CGGTTCGTATAAATGACAAATCTACTC 58.522 37.037 0.00 0.00 0.00 2.59
3556 4280 7.280428 TGCAAAACAAATTCAGACAATGACAAT 59.720 29.630 0.00 0.00 37.77 2.71
3593 4317 4.487714 TTTGGATGTCCCTGCTAACTAG 57.512 45.455 0.00 0.00 35.38 2.57
3656 4380 3.197116 AGGGTTCAGTATAAGGTCAACCG 59.803 47.826 0.00 0.00 42.08 4.44
3709 4433 0.029567 CTCGCCGTGTCTGTCTATCC 59.970 60.000 0.00 0.00 0.00 2.59
3722 4446 1.170290 AGAAAAACCCCAACTCGCCG 61.170 55.000 0.00 0.00 0.00 6.46
3726 4450 7.712204 TTATATTGGAGAAAAACCCCAACTC 57.288 36.000 0.00 0.00 42.08 3.01
3790 4514 1.908483 GCTGGTTAGCTAGTGCCCT 59.092 57.895 0.00 0.00 46.57 5.19
3905 4630 9.489084 GTGGTGCATAGAGTTACATATAAATCA 57.511 33.333 0.00 0.00 37.76 2.57
4091 4816 7.607615 TGAAGTACCTAGGACAACTTTAAGT 57.392 36.000 17.98 0.00 32.51 2.24
4142 4867 1.747355 GAAATGCTGTGATGGAGGTGG 59.253 52.381 0.00 0.00 0.00 4.61
4173 4898 3.561725 AGAAAACGAAAGGAGCAAGACTG 59.438 43.478 0.00 0.00 0.00 3.51
4174 4899 3.809905 AGAAAACGAAAGGAGCAAGACT 58.190 40.909 0.00 0.00 0.00 3.24
4175 4900 4.553756 AAGAAAACGAAAGGAGCAAGAC 57.446 40.909 0.00 0.00 0.00 3.01
4176 4901 4.881850 AGAAAGAAAACGAAAGGAGCAAGA 59.118 37.500 0.00 0.00 0.00 3.02
4177 4902 5.175090 AGAAAGAAAACGAAAGGAGCAAG 57.825 39.130 0.00 0.00 0.00 4.01
4178 4903 5.449999 GGAAGAAAGAAAACGAAAGGAGCAA 60.450 40.000 0.00 0.00 0.00 3.91
4179 4904 4.036380 GGAAGAAAGAAAACGAAAGGAGCA 59.964 41.667 0.00 0.00 0.00 4.26
4180 4905 4.036380 TGGAAGAAAGAAAACGAAAGGAGC 59.964 41.667 0.00 0.00 0.00 4.70
4218 4943 4.144297 TCTTGCAGTGAATAAGCAAAGGT 58.856 39.130 0.00 0.00 46.30 3.50
4221 4946 4.456911 CCTCTCTTGCAGTGAATAAGCAAA 59.543 41.667 0.00 0.00 46.30 3.68
4257 4982 8.002433 TGCAAAGCGTAAAATAAAAACTGATC 57.998 30.769 0.00 0.00 0.00 2.92
4267 4992 2.817258 ACCAGCTGCAAAGCGTAAAATA 59.183 40.909 8.66 0.00 40.27 1.40
4300 5025 7.094248 TGCACGGTGAGTAAGTAGAAAGTTATA 60.094 37.037 13.29 0.00 0.00 0.98
4332 5057 1.804151 GGTGCTGCAGATACAAACGAA 59.196 47.619 20.43 0.00 0.00 3.85
4435 5160 0.466007 TGCTCCTCACTTTTGCAGCA 60.466 50.000 0.00 0.00 34.54 4.41
4441 5166 0.250338 GGTCGGTGCTCCTCACTTTT 60.250 55.000 2.85 0.00 44.98 2.27
4559 5285 5.600069 ACAGCATGGAGATGTACTAGAATCA 59.400 40.000 0.00 0.00 46.79 2.57
4600 5326 5.741388 AATTATTCACTGCTGATTCGGTC 57.259 39.130 0.00 0.00 0.00 4.79
4621 5347 5.184287 GGATTCATTCTACGGGTTCCAAAAA 59.816 40.000 0.00 0.00 0.00 1.94
4877 5603 8.459911 TCTGATCAATTTAGATGCATTCATGT 57.540 30.769 0.00 0.00 31.96 3.21
4896 5622 1.407979 CCATGCCAAAAGCCTCTGATC 59.592 52.381 0.00 0.00 42.71 2.92
4940 5672 5.576774 TGCTCATTAAGTTCTATGTGTGTCG 59.423 40.000 0.00 0.00 0.00 4.35
4942 5674 7.607607 TCATTGCTCATTAAGTTCTATGTGTGT 59.392 33.333 0.00 0.00 0.00 3.72
4963 5695 3.066380 TCCGCCATTCATACGATCATTG 58.934 45.455 0.00 0.00 0.00 2.82
4969 5701 3.006859 AGAATCATCCGCCATTCATACGA 59.993 43.478 0.00 0.00 32.28 3.43
4989 5721 3.285484 GACGGAGGGAGTACATGTTAGA 58.715 50.000 2.30 0.00 0.00 2.10
5034 5766 9.923143 TTCGTCCCATAATATAAGATTGTAGTG 57.077 33.333 0.00 0.00 0.00 2.74
5041 5773 6.127026 GCTCCCTTCGTCCCATAATATAAGAT 60.127 42.308 0.00 0.00 0.00 2.40
5059 5852 3.840666 TCTCAAATGTCTACTGCTCCCTT 59.159 43.478 0.00 0.00 0.00 3.95
5066 5859 5.300752 AGTTGTGGTCTCAAATGTCTACTG 58.699 41.667 0.00 0.00 0.00 2.74
5115 5908 4.634443 AGGTTGAAAATTTCCTCGTATCGG 59.366 41.667 3.00 0.00 0.00 4.18
5142 5935 7.501225 TGTGTAGACGAATTACATGATCTCCTA 59.499 37.037 0.00 0.00 33.92 2.94
5253 6046 9.903682 ATTTCTATCTCACATTGAAACTTTGTG 57.096 29.630 0.00 0.00 41.60 3.33


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

AutoCloner maintained by Alex Coulton.