Multiple sequence alignment - TraesCS6B01G248500

Loading Multiple Alignment...

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 TraesCS6B01G248500 chr6B 100.000 5298 0 0 1 5298 445887075 445881778 0.000000e+00 9784.0
1 TraesCS6B01G248500 chr6D 93.530 2504 98 18 2842 5296 285021961 285019473 0.000000e+00 3668.0
2 TraesCS6B01G248500 chr6D 95.348 1827 67 12 902 2719 285023776 285021959 0.000000e+00 2887.0
3 TraesCS6B01G248500 chr6D 91.176 374 16 9 323 682 285024532 285024162 4.770000e-135 492.0
4 TraesCS6B01G248500 chr6D 95.385 65 3 0 4963 5027 285019872 285019808 2.610000e-18 104.0
5 TraesCS6B01G248500 chr6A 93.449 1786 77 19 298 2061 405452309 405450542 0.000000e+00 2614.0
6 TraesCS6B01G248500 chr6A 91.348 1699 90 24 3620 5296 405448825 405447162 0.000000e+00 2270.0
7 TraesCS6B01G248500 chr6A 92.607 771 33 13 2853 3621 405449828 405449080 0.000000e+00 1086.0
8 TraesCS6B01G248500 chr6A 93.387 620 33 3 2108 2719 405450538 405449919 0.000000e+00 911.0
9 TraesCS6B01G248500 chr6A 87.908 306 28 5 2 299 127525829 127525525 8.440000e-93 351.0
10 TraesCS6B01G248500 chr6A 87.541 305 29 5 2 298 541001549 541001246 1.410000e-90 344.0
11 TraesCS6B01G248500 chr6A 88.479 217 23 2 4039 4254 405448436 405448221 1.460000e-65 261.0
12 TraesCS6B01G248500 chr6A 97.778 135 3 0 2717 2851 349575056 349574922 3.190000e-57 233.0
13 TraesCS6B01G248500 chr6A 96.454 141 5 0 2710 2850 617047912 617047772 3.190000e-57 233.0
14 TraesCS6B01G248500 chr5B 95.724 304 11 2 1 302 108053979 108054282 6.170000e-134 488.0
15 TraesCS6B01G248500 chr5B 95.395 304 12 2 1 302 107948519 107948822 2.870000e-132 483.0
16 TraesCS6B01G248500 chr5B 96.047 253 9 1 1 252 107948076 107948328 1.370000e-110 411.0
17 TraesCS6B01G248500 chr5B 88.462 52 2 4 367 416 16777476 16777525 5.730000e-05 60.2
18 TraesCS6B01G248500 chr5B 88.462 52 2 4 367 416 16787228 16787277 5.730000e-05 60.2
19 TraesCS6B01G248500 chr4B 93.960 298 10 4 1 290 650794175 650793878 1.350000e-120 444.0
20 TraesCS6B01G248500 chr4B 88.449 303 27 4 4 298 20686278 20686580 5.040000e-95 359.0
21 TraesCS6B01G248500 chr4B 97.037 135 4 0 2710 2844 210282750 210282884 1.480000e-55 228.0
22 TraesCS6B01G248500 chr3A 87.622 307 29 5 2 300 343312616 343312311 1.090000e-91 348.0
23 TraesCS6B01G248500 chr3A 95.105 143 6 1 2702 2844 158174815 158174956 1.920000e-54 224.0
24 TraesCS6B01G248500 chr4A 86.971 307 30 7 2 298 580666026 580665720 2.360000e-88 337.0
25 TraesCS6B01G248500 chr3B 100.000 128 0 0 2717 2844 200483882 200484009 2.470000e-58 237.0
26 TraesCS6B01G248500 chr3D 97.761 134 3 0 2711 2844 464998729 464998596 1.150000e-56 231.0
27 TraesCS6B01G248500 chr1A 98.473 131 2 0 2716 2846 213289390 213289520 1.150000e-56 231.0
28 TraesCS6B01G248500 chr1A 96.377 138 5 0 2707 2844 14080502 14080639 1.480000e-55 228.0
29 TraesCS6B01G248500 chr1A 83.523 176 15 5 5131 5296 23615465 23615294 9.190000e-33 152.0
30 TraesCS6B01G248500 chr2A 96.377 138 4 1 2707 2844 356575361 356575497 5.340000e-55 226.0
31 TraesCS6B01G248500 chr7B 87.838 148 8 9 5159 5296 663110032 663109885 1.180000e-36 165.0
32 TraesCS6B01G248500 chr7B 88.000 75 9 0 295 369 72980077 72980003 7.310000e-14 89.8


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 TraesCS6B01G248500 chr6B 445881778 445887075 5297 True 9784.00 9784 100.00000 1 5298 1 chr6B.!!$R1 5297
1 TraesCS6B01G248500 chr6D 285019473 285024532 5059 True 1787.75 3668 93.85975 323 5296 4 chr6D.!!$R1 4973
2 TraesCS6B01G248500 chr6A 405447162 405452309 5147 True 1428.40 2614 91.85400 298 5296 5 chr6A.!!$R5 4998
3 TraesCS6B01G248500 chr5B 107948076 107948822 746 False 447.00 483 95.72100 1 302 2 chr5B.!!$F4 301

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
862 1333 0.179189 CCTTTGCGCTTCATTCCGTC 60.179 55.0 9.73 0.0 0.00 4.79 F
1148 1787 2.429610 AGCAGTACGGTACATACCCTTG 59.570 50.0 19.62 8.7 43.51 3.61 F
2733 3387 0.033796 ATGTACTCCCTCCGTTCCGA 60.034 55.0 0.00 0.0 0.00 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1806 2450 0.673644 GGTACAACTGAGCCATGCGT 60.674 55.0 0.0 0.0 0.0 5.24 R
2829 3483 0.831307 ATTGCTACTCCCTCCGTTCC 59.169 55.0 0.0 0.0 0.0 3.62 R
4338 5405 0.472471 TCAAGGAAACAAGCGGAGGT 59.528 50.0 0.0 0.0 44.6 3.85 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
135 579 4.828939 GGAATCAATGTGAGATTATGCCCA 59.171 41.667 0.00 0.00 35.93 5.36
226 670 5.278169 GCGGCATGTTCTTCATAATGAATCT 60.278 40.000 0.00 0.00 35.59 2.40
258 702 4.305769 GGACATTATGCTTGCACAAAACA 58.694 39.130 0.00 0.00 0.00 2.83
261 705 4.622313 ACATTATGCTTGCACAAAACATCG 59.378 37.500 0.00 0.00 0.00 3.84
304 749 8.236084 CACGGGTATATGTGCTAGTATTAAAC 57.764 38.462 0.00 0.00 0.00 2.01
321 766 5.523438 TTAAACTCATGTTCCAACCAACC 57.477 39.130 0.00 0.00 34.96 3.77
335 780 3.039252 ACCAACCCATTCAAAAGTCCA 57.961 42.857 0.00 0.00 0.00 4.02
353 798 4.590647 AGTCCAAACTGATGAAGAGAGACA 59.409 41.667 0.00 0.00 33.32 3.41
426 871 7.619512 TGGGGTGGTGTTTTCTAAAATAAAT 57.380 32.000 0.00 0.00 0.00 1.40
428 873 7.101054 GGGGTGGTGTTTTCTAAAATAAATCC 58.899 38.462 0.00 0.00 0.00 3.01
579 1049 1.477553 CAATCCACATCCCAACCCAG 58.522 55.000 0.00 0.00 0.00 4.45
607 1077 1.067060 GAATTCCGTAAATGCCCCTGC 59.933 52.381 0.00 0.00 38.26 4.85
608 1078 0.755327 ATTCCGTAAATGCCCCTGCC 60.755 55.000 0.00 0.00 36.33 4.85
609 1079 2.833121 CCGTAAATGCCCCTGCCC 60.833 66.667 0.00 0.00 36.33 5.36
628 1098 2.032071 CCGAGGCGTCAACCCTTT 59.968 61.111 7.26 0.00 31.41 3.11
652 1122 2.109304 CCTAAAAACACCTTCCCTCCCA 59.891 50.000 0.00 0.00 0.00 4.37
801 1272 2.436115 GCAAGTACGCCCCCAGAC 60.436 66.667 0.00 0.00 0.00 3.51
802 1273 2.267961 CAAGTACGCCCCCAGACC 59.732 66.667 0.00 0.00 0.00 3.85
803 1274 3.007323 AAGTACGCCCCCAGACCC 61.007 66.667 0.00 0.00 0.00 4.46
862 1333 0.179189 CCTTTGCGCTTCATTCCGTC 60.179 55.000 9.73 0.00 0.00 4.79
900 1371 2.605837 TTTTGGGGCGTTTTTCCTTC 57.394 45.000 0.00 0.00 0.00 3.46
1148 1787 2.429610 AGCAGTACGGTACATACCCTTG 59.570 50.000 19.62 8.70 43.51 3.61
1213 1852 5.104941 TGCCTGTAGACATGCTAAGTTGTAT 60.105 40.000 10.62 0.00 38.16 2.29
1219 1858 9.278978 TGTAGACATGCTAAGTTGTATTTTCAA 57.721 29.630 0.00 0.00 0.00 2.69
1238 1877 6.647334 TTCAAATTTCATGTTCAGCTGGTA 57.353 33.333 15.13 0.00 0.00 3.25
1397 2036 7.538575 TGTTTGAGGAATAGAAGCTTTTATGC 58.461 34.615 10.07 8.22 0.00 3.14
1535 2178 6.408107 TTTTTATTTAAGTTCAACGGGGCT 57.592 33.333 0.00 0.00 0.00 5.19
1643 2287 8.974060 TGAAACAGTGAAGGTTAGAAAAGTAT 57.026 30.769 0.00 0.00 0.00 2.12
1762 2406 2.949177 TTATGTTGGACTGCCAGTGT 57.051 45.000 0.00 0.00 46.91 3.55
1800 2444 9.268268 CTTAGAAGTACCAACAGTTAATGTGAA 57.732 33.333 0.00 0.00 43.00 3.18
1806 2450 9.398538 AGTACCAACAGTTAATGTGAAAACTAA 57.601 29.630 0.00 0.00 43.00 2.24
1921 2565 7.283354 GTCTCATCTTTTCCCCTAAGTTATTGG 59.717 40.741 0.00 0.00 0.00 3.16
1948 2592 8.946085 TGTATTTCTGAATGTATCAAACTGGTC 58.054 33.333 0.00 0.00 37.67 4.02
1962 2606 5.995282 TCAAACTGGTCGATCTTGTATTTGT 59.005 36.000 0.00 0.00 0.00 2.83
1992 2636 7.306225 GCAAAGAGTTATGTTGTTTCTGCTTTC 60.306 37.037 0.00 0.00 0.00 2.62
2134 2778 3.753797 TCCTATATGTTTTTGTGCGTGCA 59.246 39.130 0.00 0.00 0.00 4.57
2146 2790 0.322366 TGCGTGCAGAAATGGGATCA 60.322 50.000 0.00 0.00 0.00 2.92
2150 2794 3.066621 GCGTGCAGAAATGGGATCAATTA 59.933 43.478 0.00 0.00 0.00 1.40
2166 2810 8.023706 GGGATCAATTAGTTTTGACTTGACTTC 58.976 37.037 0.00 0.00 38.37 3.01
2395 3045 4.842531 TGCTCATTGATCCTTAACCTCA 57.157 40.909 0.00 0.00 0.00 3.86
2412 3062 6.380079 AACCTCATCCTGATAAGTTCACTT 57.620 37.500 0.00 0.00 39.85 3.16
2514 3168 3.307762 GGTCTAGTGAATTCAGGCCTGTT 60.308 47.826 31.58 20.09 0.00 3.16
2527 3181 1.272147 GGCCTGTTCTTGTGGGATTCT 60.272 52.381 0.00 0.00 0.00 2.40
2553 3207 6.544038 TTGAATGGTCTGATGTATAATGCG 57.456 37.500 0.00 0.00 0.00 4.73
2573 3227 2.603173 CGTTCTGTTGCCTTTTCAGAGC 60.603 50.000 0.00 0.00 39.00 4.09
2599 3253 5.003096 ACTCCTGTCCATCAAAGGAAAAT 57.997 39.130 0.00 0.00 39.59 1.82
2672 3326 5.220970 CCTGTACTTGAAAACCGTGAATTGT 60.221 40.000 0.00 0.00 0.00 2.71
2706 3360 9.656323 ACCAGGAACTAATAACTGATCAGTATA 57.344 33.333 28.10 20.56 37.61 1.47
2726 3380 9.344772 CAGTATATATAGTCATGTACTCCCTCC 57.655 40.741 0.00 0.00 39.80 4.30
2727 3381 8.212312 AGTATATATAGTCATGTACTCCCTCCG 58.788 40.741 0.00 0.00 39.80 4.63
2728 3382 3.596940 ATAGTCATGTACTCCCTCCGT 57.403 47.619 0.00 0.00 39.80 4.69
2729 3383 2.233305 AGTCATGTACTCCCTCCGTT 57.767 50.000 0.00 0.00 30.33 4.44
2730 3384 2.100989 AGTCATGTACTCCCTCCGTTC 58.899 52.381 0.00 0.00 30.33 3.95
2731 3385 1.136500 GTCATGTACTCCCTCCGTTCC 59.864 57.143 0.00 0.00 0.00 3.62
2732 3386 0.102481 CATGTACTCCCTCCGTTCCG 59.898 60.000 0.00 0.00 0.00 4.30
2733 3387 0.033796 ATGTACTCCCTCCGTTCCGA 60.034 55.000 0.00 0.00 0.00 4.55
2734 3388 0.251297 TGTACTCCCTCCGTTCCGAA 60.251 55.000 0.00 0.00 0.00 4.30
2735 3389 1.109609 GTACTCCCTCCGTTCCGAAT 58.890 55.000 0.00 0.00 0.00 3.34
2736 3390 1.479730 GTACTCCCTCCGTTCCGAATT 59.520 52.381 0.00 0.00 0.00 2.17
2737 3391 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
2738 3392 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
2739 3393 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
2740 3394 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
2741 3395 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2742 3396 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2743 3397 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2744 3398 3.368116 CCTCCGTTCCGAATTACTTGTCT 60.368 47.826 0.00 0.00 0.00 3.41
2745 3399 4.243270 CTCCGTTCCGAATTACTTGTCTT 58.757 43.478 0.00 0.00 0.00 3.01
2746 3400 5.389859 TCCGTTCCGAATTACTTGTCTTA 57.610 39.130 0.00 0.00 0.00 2.10
2747 3401 5.404946 TCCGTTCCGAATTACTTGTCTTAG 58.595 41.667 0.00 0.00 0.00 2.18
2748 3402 5.183713 TCCGTTCCGAATTACTTGTCTTAGA 59.816 40.000 0.00 0.00 0.00 2.10
2749 3403 6.040878 CCGTTCCGAATTACTTGTCTTAGAT 58.959 40.000 0.00 0.00 0.00 1.98
2750 3404 6.534079 CCGTTCCGAATTACTTGTCTTAGATT 59.466 38.462 0.00 0.00 0.00 2.40
2751 3405 7.064253 CCGTTCCGAATTACTTGTCTTAGATTT 59.936 37.037 0.00 0.00 0.00 2.17
2752 3406 7.898309 CGTTCCGAATTACTTGTCTTAGATTTG 59.102 37.037 0.00 0.00 0.00 2.32
2753 3407 8.718734 GTTCCGAATTACTTGTCTTAGATTTGT 58.281 33.333 0.00 0.00 0.00 2.83
2754 3408 8.475331 TCCGAATTACTTGTCTTAGATTTGTC 57.525 34.615 0.00 0.00 0.00 3.18
2755 3409 8.311836 TCCGAATTACTTGTCTTAGATTTGTCT 58.688 33.333 0.00 0.00 0.00 3.41
2756 3410 9.582431 CCGAATTACTTGTCTTAGATTTGTCTA 57.418 33.333 0.00 0.00 0.00 2.59
2786 3440 8.700051 ACAGATGTATCTAGCACTAAAATGAGT 58.300 33.333 0.00 0.00 34.85 3.41
2787 3441 9.190858 CAGATGTATCTAGCACTAAAATGAGTC 57.809 37.037 0.00 0.00 34.85 3.36
2788 3442 9.142014 AGATGTATCTAGCACTAAAATGAGTCT 57.858 33.333 0.00 0.00 34.85 3.24
2791 3445 9.628500 TGTATCTAGCACTAAAATGAGTCTAGA 57.372 33.333 11.59 11.59 38.76 2.43
2795 3449 9.628500 TCTAGCACTAAAATGAGTCTAGATACA 57.372 33.333 0.00 0.00 34.65 2.29
2798 3452 9.142014 AGCACTAAAATGAGTCTAGATACATCT 57.858 33.333 12.66 0.00 40.86 2.90
2799 3453 9.190858 GCACTAAAATGAGTCTAGATACATCTG 57.809 37.037 12.66 7.80 37.76 2.90
2818 3472 8.311395 ACATCTGTATCTAGACAAATCCAAGA 57.689 34.615 0.00 0.00 0.00 3.02
2819 3473 8.200792 ACATCTGTATCTAGACAAATCCAAGAC 58.799 37.037 0.00 0.00 0.00 3.01
2820 3474 7.718334 TCTGTATCTAGACAAATCCAAGACA 57.282 36.000 0.00 0.00 0.00 3.41
2821 3475 8.134202 TCTGTATCTAGACAAATCCAAGACAA 57.866 34.615 0.00 0.00 0.00 3.18
2822 3476 8.253810 TCTGTATCTAGACAAATCCAAGACAAG 58.746 37.037 0.00 0.00 0.00 3.16
2823 3477 7.907389 TGTATCTAGACAAATCCAAGACAAGT 58.093 34.615 0.00 0.00 0.00 3.16
2824 3478 9.031537 TGTATCTAGACAAATCCAAGACAAGTA 57.968 33.333 0.00 0.00 0.00 2.24
2825 3479 9.871238 GTATCTAGACAAATCCAAGACAAGTAA 57.129 33.333 0.00 0.00 0.00 2.24
2827 3481 9.965902 ATCTAGACAAATCCAAGACAAGTAATT 57.034 29.630 0.00 0.00 0.00 1.40
2828 3482 9.436957 TCTAGACAAATCCAAGACAAGTAATTC 57.563 33.333 0.00 0.00 0.00 2.17
2829 3483 7.133891 AGACAAATCCAAGACAAGTAATTCG 57.866 36.000 0.00 0.00 0.00 3.34
2830 3484 6.149474 AGACAAATCCAAGACAAGTAATTCGG 59.851 38.462 0.00 0.00 0.00 4.30
2831 3485 6.001460 ACAAATCCAAGACAAGTAATTCGGA 58.999 36.000 0.00 0.00 0.00 4.55
2832 3486 6.488683 ACAAATCCAAGACAAGTAATTCGGAA 59.511 34.615 0.00 0.00 0.00 4.30
2833 3487 6.496338 AATCCAAGACAAGTAATTCGGAAC 57.504 37.500 0.00 0.00 0.00 3.62
2849 3585 1.209747 GGAACGGAGGGAGTAGCAATT 59.790 52.381 0.00 0.00 0.00 2.32
2851 3587 2.403252 ACGGAGGGAGTAGCAATTTG 57.597 50.000 0.00 0.00 0.00 2.32
2910 3646 5.936372 CACATATTGGCTATAGCATGACTGT 59.064 40.000 25.53 18.23 44.36 3.55
2927 3663 6.252599 TGACTGTGGATGGCTAAGATAATT 57.747 37.500 0.00 0.00 0.00 1.40
2929 3665 7.445121 TGACTGTGGATGGCTAAGATAATTAG 58.555 38.462 0.00 0.00 0.00 1.73
2933 3669 6.500400 TGTGGATGGCTAAGATAATTAGGCTA 59.500 38.462 18.32 0.00 44.78 3.93
3019 3755 8.243961 TCAAAATAAAGAAACTTGGATGACCA 57.756 30.769 0.00 0.00 45.34 4.02
3096 3860 9.654663 AAAACTGCTAAGATTTACGAGTTCTAT 57.345 29.630 0.00 0.00 0.00 1.98
3137 3901 8.786898 TCTCTTAGATTTGAACAAGTTCCAATG 58.213 33.333 14.60 3.78 35.78 2.82
3146 3910 7.144722 TGAACAAGTTCCAATGTCATCATAC 57.855 36.000 10.19 0.00 38.77 2.39
3284 4048 8.285394 GTGATTATGACAATCGTGCTGATTATT 58.715 33.333 4.74 0.00 45.59 1.40
3285 4049 9.487790 TGATTATGACAATCGTGCTGATTATTA 57.512 29.630 4.74 0.00 45.59 0.98
3298 4062 7.331934 CGTGCTGATTATTATGTGCTAATAGGT 59.668 37.037 0.00 0.00 34.53 3.08
3409 4173 3.807209 GCTATGAGTGTGGTGAAAGTGGT 60.807 47.826 0.00 0.00 0.00 4.16
3648 4668 8.180920 GCTTGAAGAACAAAGGAAGAATATCTC 58.819 37.037 0.00 0.00 38.08 2.75
3649 4669 8.567285 TTGAAGAACAAAGGAAGAATATCTCC 57.433 34.615 0.00 0.00 35.39 3.71
3713 4734 8.723942 AATATTTCTCAGTACATGTGAAGTCC 57.276 34.615 9.11 0.00 41.18 3.85
3729 4750 4.458989 TGAAGTCCATTCTTCAATTTCCGG 59.541 41.667 0.00 0.00 46.88 5.14
3766 4787 5.990668 ACCCAAGTCCTATGTCATTTACTC 58.009 41.667 0.00 0.00 0.00 2.59
3773 4794 6.043411 GTCCTATGTCATTTACTCCTGTGTC 58.957 44.000 0.00 0.00 0.00 3.67
3790 4819 5.105635 CCTGTGTCGGTAAAGTGGTCTAATA 60.106 44.000 0.00 0.00 0.00 0.98
3803 4832 6.120220 AGTGGTCTAATATTTCCCTTTTCGG 58.880 40.000 0.00 0.00 0.00 4.30
3909 4940 2.284754 TACTGACAATTGCCTTGCCA 57.715 45.000 5.05 0.00 38.50 4.92
3912 4943 2.493278 ACTGACAATTGCCTTGCCATAC 59.507 45.455 5.05 0.00 38.50 2.39
4252 5319 1.668294 CTATAGCAGGTCCCCAGCG 59.332 63.158 0.00 0.00 41.05 5.18
4625 5692 4.202000 TGTCACCGTCTTGTTACGTTTCTA 60.202 41.667 0.00 0.00 41.27 2.10
4644 5711 7.010367 CGTTTCTATTCTCTAGAGACGTGTAGT 59.990 40.741 22.25 5.40 43.05 2.73
4664 5731 7.534578 GTGTAGTCACTATTACGCATAGTCATC 59.465 40.741 5.13 1.03 44.32 2.92
4918 5990 1.827394 CCGTCCAATACCGGTCCAT 59.173 57.895 12.40 0.00 39.38 3.41
4928 6000 5.592688 CCAATACCGGTCCATAATTTTGTCT 59.407 40.000 12.40 0.00 0.00 3.41
4938 6010 8.160106 GGTCCATAATTTTGTCTGGATAGATCT 58.840 37.037 0.00 0.00 39.81 2.75
4952 6024 7.558807 TCTGGATAGATCTGCATGTTTGAAATT 59.441 33.333 5.18 0.00 0.00 1.82
4970 6043 2.147436 TTCCACAAATCTTTTGCCGC 57.853 45.000 0.06 0.00 0.00 6.53
4972 6045 0.318120 CCACAAATCTTTTGCCGCCT 59.682 50.000 0.06 0.00 0.00 5.52
5052 6126 2.132686 AGTAAACACAGGGGAGGTTGT 58.867 47.619 0.00 0.00 0.00 3.32
5074 6148 2.359531 AGACGTTCGGATCTCCTTCATC 59.640 50.000 0.00 0.00 0.00 2.92
5088 6162 4.019858 TCCTTCATCTCGAACTCTGACAT 58.980 43.478 0.00 0.00 0.00 3.06
5121 6195 4.080863 ACTCAAAATACCTCATCCGAAGCT 60.081 41.667 0.00 0.00 0.00 3.74
5141 6215 4.254709 TGCGGTGTTGCAGAGGCT 62.255 61.111 0.00 0.00 40.62 4.58
5151 6225 2.119655 GCAGAGGCTGGGCTTCATG 61.120 63.158 0.00 0.00 37.11 3.07
5153 6227 1.617536 AGAGGCTGGGCTTCATGGA 60.618 57.895 0.00 0.00 37.11 3.41
5250 6330 8.885722 TGTTCGTCAAGTATGTAAAAAGTTTCT 58.114 29.630 0.00 0.00 0.00 2.52
5275 6355 6.969366 TCAGGTAATTCGATTATTTGCATGG 58.031 36.000 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
135 579 2.543777 TAGCCGTGTTCTTCTTTGCT 57.456 45.000 0.00 0.00 0.00 3.91
226 670 5.476599 GCAAGCATAATGTCCCATAATACCA 59.523 40.000 0.00 0.00 0.00 3.25
249 693 2.661195 CGGGAAAATCGATGTTTTGTGC 59.339 45.455 1.50 0.00 31.80 4.57
258 702 2.629639 GTTGCAACGGGAAAATCGAT 57.370 45.000 14.90 0.00 0.00 3.59
304 749 1.993956 TGGGTTGGTTGGAACATGAG 58.006 50.000 0.00 0.00 39.30 2.90
310 755 3.777522 ACTTTTGAATGGGTTGGTTGGAA 59.222 39.130 0.00 0.00 0.00 3.53
321 766 6.088016 TCATCAGTTTGGACTTTTGAATGG 57.912 37.500 0.00 0.00 32.54 3.16
335 780 5.798125 TGTCTGTCTCTCTTCATCAGTTT 57.202 39.130 0.00 0.00 0.00 2.66
538 996 2.197643 GAAGAGGACGACGGACGCTT 62.198 60.000 9.11 9.11 46.94 4.68
579 1049 5.260900 GGCATTTACGGAATTCTCGTTTAC 58.739 41.667 21.47 10.80 41.38 2.01
628 1098 1.422402 AGGGAAGGTGTTTTTAGGCGA 59.578 47.619 0.00 0.00 0.00 5.54
652 1122 0.624795 GAAGAGGGGGATGGAGGGTT 60.625 60.000 0.00 0.00 0.00 4.11
737 1208 4.547367 GGGGACTGGCGAATCGGG 62.547 72.222 4.35 0.00 0.00 5.14
802 1273 3.937447 GAAGATACCGGGGGCGGG 61.937 72.222 6.32 0.00 0.00 6.13
803 1274 4.295119 CGAAGATACCGGGGGCGG 62.295 72.222 6.32 0.00 0.00 6.13
804 1275 4.295119 CCGAAGATACCGGGGGCG 62.295 72.222 6.32 0.01 43.05 6.13
862 1333 2.195123 AAAATGCTCGCGTTTCGGGG 62.195 55.000 5.77 0.00 39.59 5.73
900 1371 2.446435 CTAACCTCCACCCACAAATGG 58.554 52.381 0.00 0.00 46.81 3.16
1148 1787 4.226761 CACCAAACTCGTGAAAATAAGCC 58.773 43.478 0.00 0.00 32.77 4.35
1213 1852 6.347696 ACCAGCTGAACATGAAATTTGAAAA 58.652 32.000 17.39 0.00 0.00 2.29
1219 1858 6.127897 GCTAGTTACCAGCTGAACATGAAATT 60.128 38.462 17.39 0.00 36.07 1.82
1238 1877 4.522722 ACTTTTAGCAGACGAGCTAGTT 57.477 40.909 0.00 0.00 46.77 2.24
1535 2178 5.363868 AGCTATAGAAGACCTGTACATGCAA 59.636 40.000 3.21 0.00 0.00 4.08
1643 2287 8.535335 GCCTCTACATCTCTTATATCCATTTCA 58.465 37.037 0.00 0.00 0.00 2.69
1720 2364 5.840243 TTATGCTGCATGTGCTTTAGAAT 57.160 34.783 24.59 0.00 42.66 2.40
1762 2406 7.011499 TGGTACTTCTAAGTGAAAAGGCATA 57.989 36.000 5.62 0.00 40.07 3.14
1800 2444 2.185004 ACTGAGCCATGCGTTAGTTT 57.815 45.000 0.00 0.00 0.00 2.66
1806 2450 0.673644 GGTACAACTGAGCCATGCGT 60.674 55.000 0.00 0.00 0.00 5.24
1886 2530 6.621514 AGGGGAAAAGATGAGACATATAACCT 59.378 38.462 0.00 0.00 0.00 3.50
1921 2565 8.730680 ACCAGTTTGATACATTCAGAAATACAC 58.269 33.333 0.00 0.00 35.27 2.90
1942 2586 4.690748 CACACAAATACAAGATCGACCAGT 59.309 41.667 0.00 0.00 0.00 4.00
1948 2592 4.418013 TTGCCACACAAATACAAGATCG 57.582 40.909 0.00 0.00 34.56 3.69
1962 2606 5.359576 AGAAACAACATAACTCTTTGCCACA 59.640 36.000 0.00 0.00 0.00 4.17
1992 2636 2.089980 AGCAAGCCAGCAACTAATGAG 58.910 47.619 0.55 0.00 36.85 2.90
2044 2688 2.811431 CAGCGGAACATCTTTGTTACCA 59.189 45.455 0.00 0.00 46.01 3.25
2053 2697 3.987404 GCAACCAGCGGAACATCT 58.013 55.556 1.50 0.00 0.00 2.90
2134 2778 8.655935 AGTCAAAACTAATTGATCCCATTTCT 57.344 30.769 0.00 0.00 41.09 2.52
2146 2790 9.503427 CGAAAAGAAGTCAAGTCAAAACTAATT 57.497 29.630 0.00 0.00 33.48 1.40
2150 2794 6.496338 ACGAAAAGAAGTCAAGTCAAAACT 57.504 33.333 0.00 0.00 37.32 2.66
2166 2810 1.533756 CCCACACACTGCAACGAAAAG 60.534 52.381 0.00 0.00 0.00 2.27
2514 3168 6.493166 ACCATTCAATAAGAATCCCACAAGA 58.507 36.000 0.00 0.00 45.06 3.02
2527 3181 8.720562 CGCATTATACATCAGACCATTCAATAA 58.279 33.333 0.00 0.00 0.00 1.40
2553 3207 2.620585 AGCTCTGAAAAGGCAACAGAAC 59.379 45.455 0.00 0.00 39.60 3.01
2573 3227 5.165961 TCCTTTGATGGACAGGAGTTAAG 57.834 43.478 0.00 0.00 0.00 1.85
2611 3265 5.278266 GCAGGTTTCTGTGCAAATACAGTTA 60.278 40.000 5.89 0.00 46.32 2.24
2634 3288 7.979444 TCAAGTACAGGGCTAATATATTTGC 57.021 36.000 19.66 19.66 37.71 3.68
2672 3326 5.487488 AGTTATTAGTTCCTGGTCATGGTCA 59.513 40.000 0.00 0.00 0.00 4.02
2706 3360 5.258216 ACGGAGGGAGTACATGACTATAT 57.742 43.478 0.00 0.00 39.06 0.86
2711 3365 1.136500 GGAACGGAGGGAGTACATGAC 59.864 57.143 0.00 0.00 0.00 3.06
2727 3381 8.718734 ACAAATCTAAGACAAGTAATTCGGAAC 58.281 33.333 0.00 0.00 0.00 3.62
2728 3382 8.842358 ACAAATCTAAGACAAGTAATTCGGAA 57.158 30.769 0.00 0.00 0.00 4.30
2729 3383 8.311836 AGACAAATCTAAGACAAGTAATTCGGA 58.688 33.333 0.00 0.00 31.46 4.55
2730 3384 8.480643 AGACAAATCTAAGACAAGTAATTCGG 57.519 34.615 0.00 0.00 31.46 4.30
2760 3414 8.700051 ACTCATTTTAGTGCTAGATACATCTGT 58.300 33.333 1.88 0.00 37.76 3.41
2761 3415 9.190858 GACTCATTTTAGTGCTAGATACATCTG 57.809 37.037 1.88 0.00 37.76 2.90
2762 3416 9.142014 AGACTCATTTTAGTGCTAGATACATCT 57.858 33.333 0.00 0.00 40.86 2.90
2765 3419 9.628500 TCTAGACTCATTTTAGTGCTAGATACA 57.372 33.333 0.00 0.00 34.69 2.29
2769 3423 9.628500 TGTATCTAGACTCATTTTAGTGCTAGA 57.372 33.333 0.00 0.00 38.76 2.43
2772 3426 9.142014 AGATGTATCTAGACTCATTTTAGTGCT 57.858 33.333 11.25 2.44 34.85 4.40
2773 3427 9.190858 CAGATGTATCTAGACTCATTTTAGTGC 57.809 37.037 11.25 0.69 34.85 4.40
2792 3446 9.421399 TCTTGGATTTGTCTAGATACAGATGTA 57.579 33.333 0.00 0.00 34.67 2.29
2793 3447 8.200792 GTCTTGGATTTGTCTAGATACAGATGT 58.799 37.037 0.00 0.00 0.00 3.06
2794 3448 8.200120 TGTCTTGGATTTGTCTAGATACAGATG 58.800 37.037 0.00 0.00 0.00 2.90
2795 3449 8.311395 TGTCTTGGATTTGTCTAGATACAGAT 57.689 34.615 0.00 0.00 0.00 2.90
2796 3450 7.718334 TGTCTTGGATTTGTCTAGATACAGA 57.282 36.000 0.00 0.00 0.00 3.41
2797 3451 8.037758 ACTTGTCTTGGATTTGTCTAGATACAG 58.962 37.037 0.00 0.00 0.00 2.74
2798 3452 7.907389 ACTTGTCTTGGATTTGTCTAGATACA 58.093 34.615 0.00 0.00 0.00 2.29
2799 3453 9.871238 TTACTTGTCTTGGATTTGTCTAGATAC 57.129 33.333 0.00 0.00 0.00 2.24
2801 3455 9.965902 AATTACTTGTCTTGGATTTGTCTAGAT 57.034 29.630 0.00 0.00 0.00 1.98
2802 3456 9.436957 GAATTACTTGTCTTGGATTTGTCTAGA 57.563 33.333 0.00 0.00 0.00 2.43
2803 3457 8.383619 CGAATTACTTGTCTTGGATTTGTCTAG 58.616 37.037 0.00 0.00 0.00 2.43
2804 3458 7.333423 CCGAATTACTTGTCTTGGATTTGTCTA 59.667 37.037 0.00 0.00 0.00 2.59
2805 3459 6.149474 CCGAATTACTTGTCTTGGATTTGTCT 59.851 38.462 0.00 0.00 0.00 3.41
2806 3460 6.148811 TCCGAATTACTTGTCTTGGATTTGTC 59.851 38.462 0.00 0.00 0.00 3.18
2807 3461 6.001460 TCCGAATTACTTGTCTTGGATTTGT 58.999 36.000 0.00 0.00 0.00 2.83
2808 3462 6.494893 TCCGAATTACTTGTCTTGGATTTG 57.505 37.500 0.00 0.00 0.00 2.32
2809 3463 6.348213 CGTTCCGAATTACTTGTCTTGGATTT 60.348 38.462 0.00 0.00 0.00 2.17
2810 3464 5.121768 CGTTCCGAATTACTTGTCTTGGATT 59.878 40.000 0.00 0.00 0.00 3.01
2811 3465 4.630069 CGTTCCGAATTACTTGTCTTGGAT 59.370 41.667 0.00 0.00 0.00 3.41
2812 3466 3.991773 CGTTCCGAATTACTTGTCTTGGA 59.008 43.478 0.00 0.00 0.00 3.53
2813 3467 3.124636 CCGTTCCGAATTACTTGTCTTGG 59.875 47.826 0.00 0.00 0.00 3.61
2814 3468 3.991773 TCCGTTCCGAATTACTTGTCTTG 59.008 43.478 0.00 0.00 0.00 3.02
2815 3469 4.243270 CTCCGTTCCGAATTACTTGTCTT 58.757 43.478 0.00 0.00 0.00 3.01
2816 3470 3.368116 CCTCCGTTCCGAATTACTTGTCT 60.368 47.826 0.00 0.00 0.00 3.41
2817 3471 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2818 3472 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2819 3473 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2820 3474 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
2821 3475 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
2822 3476 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
2823 3477 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
2824 3478 1.755380 CTACTCCCTCCGTTCCGAATT 59.245 52.381 0.00 0.00 0.00 2.17
2825 3479 1.400737 CTACTCCCTCCGTTCCGAAT 58.599 55.000 0.00 0.00 0.00 3.34
2826 3480 1.318158 GCTACTCCCTCCGTTCCGAA 61.318 60.000 0.00 0.00 0.00 4.30
2827 3481 1.751927 GCTACTCCCTCCGTTCCGA 60.752 63.158 0.00 0.00 0.00 4.55
2828 3482 1.601419 TTGCTACTCCCTCCGTTCCG 61.601 60.000 0.00 0.00 0.00 4.30
2829 3483 0.831307 ATTGCTACTCCCTCCGTTCC 59.169 55.000 0.00 0.00 0.00 3.62
2830 3484 2.678336 CAAATTGCTACTCCCTCCGTTC 59.322 50.000 0.00 0.00 0.00 3.95
2831 3485 2.039879 ACAAATTGCTACTCCCTCCGTT 59.960 45.455 0.00 0.00 0.00 4.44
2832 3486 1.628846 ACAAATTGCTACTCCCTCCGT 59.371 47.619 0.00 0.00 0.00 4.69
2833 3487 2.403252 ACAAATTGCTACTCCCTCCG 57.597 50.000 0.00 0.00 0.00 4.63
2834 3488 9.740710 ATATTAATACAAATTGCTACTCCCTCC 57.259 33.333 0.00 0.00 0.00 4.30
2851 3587 8.531982 TGCTGACTGGATAGGACATATTAATAC 58.468 37.037 0.00 0.00 0.00 1.89
2910 3646 6.500400 TGTAGCCTAATTATCTTAGCCATCCA 59.500 38.462 0.00 0.00 0.00 3.41
2927 3663 6.363065 AGCAGTTATAGTGTAGTGTAGCCTA 58.637 40.000 0.00 0.00 0.00 3.93
2929 3665 5.517322 AGCAGTTATAGTGTAGTGTAGCC 57.483 43.478 0.00 0.00 0.00 3.93
2933 3669 8.446599 AAACAAAAGCAGTTATAGTGTAGTGT 57.553 30.769 0.00 0.00 0.00 3.55
3125 3889 5.487433 TCGTATGATGACATTGGAACTTGT 58.513 37.500 0.00 0.00 37.87 3.16
3146 3910 2.014335 TGCTGATCAAGTGGTCATCG 57.986 50.000 0.00 0.00 0.00 3.84
3183 3947 3.689161 CAGAAGTCCAATCGCCAATAACA 59.311 43.478 0.00 0.00 0.00 2.41
3284 4048 7.450074 CACCCATTCTTACCTATTAGCACATA 58.550 38.462 0.00 0.00 0.00 2.29
3285 4049 6.299141 CACCCATTCTTACCTATTAGCACAT 58.701 40.000 0.00 0.00 0.00 3.21
3298 4062 3.055094 GCTCAACTCTCCACCCATTCTTA 60.055 47.826 0.00 0.00 0.00 2.10
3409 4173 1.792367 CGACATTCTCGTGCAAAGTGA 59.208 47.619 0.00 0.00 37.64 3.41
3496 4260 2.635899 CTACGGCTACGGCTACGG 59.364 66.667 0.00 0.00 46.48 4.02
3497 4261 2.051525 GCTACGGCTACGGCTACG 60.052 66.667 0.00 0.00 46.48 3.51
3498 4262 2.334295 GGCTACGGCTACGGCTAC 59.666 66.667 0.00 0.00 46.48 3.58
3499 4263 2.908940 GGGCTACGGCTACGGCTA 60.909 66.667 0.00 0.00 46.48 3.93
3501 4265 4.151582 TTGGGCTACGGCTACGGC 62.152 66.667 0.00 0.00 46.48 5.68
3648 4668 8.103948 AGAACTTTCACAAACAATATCTCAGG 57.896 34.615 0.00 0.00 0.00 3.86
3713 4734 7.145932 AGTAAGAACCGGAAATTGAAGAATG 57.854 36.000 9.46 0.00 0.00 2.67
3727 4748 5.303165 ACTTGGGTAAGAAAGTAAGAACCG 58.697 41.667 0.00 0.00 34.90 4.44
3729 4750 6.531923 AGGACTTGGGTAAGAAAGTAAGAAC 58.468 40.000 0.00 0.00 36.77 3.01
3766 4787 1.343465 AGACCACTTTACCGACACAGG 59.657 52.381 0.00 0.00 37.30 4.00
3773 4794 6.589135 AGGGAAATATTAGACCACTTTACCG 58.411 40.000 5.96 0.00 35.38 4.02
3790 4819 3.243737 GCAGACAAACCGAAAAGGGAAAT 60.244 43.478 0.00 0.00 46.96 2.17
3954 4985 7.420800 CCTGAATCAGGTAAAGATAAATGCAC 58.579 38.462 20.76 0.00 45.82 4.57
4338 5405 0.472471 TCAAGGAAACAAGCGGAGGT 59.528 50.000 0.00 0.00 44.60 3.85
4664 5731 7.052873 AGTCATCAGGATCATGAAAGGTTTAG 58.947 38.462 14.88 0.00 31.98 1.85
4734 5806 3.360533 CATTGCTTTTAGCTGCAGATCG 58.639 45.455 20.43 1.81 42.97 3.69
4908 5980 4.225492 TCCAGACAAAATTATGGACCGGTA 59.775 41.667 7.34 0.00 36.92 4.02
4918 5990 7.994911 ACATGCAGATCTATCCAGACAAAATTA 59.005 33.333 0.00 0.00 32.25 1.40
4928 6000 7.201848 GGAATTTCAAACATGCAGATCTATCCA 60.202 37.037 0.00 0.00 0.00 3.41
4938 6010 6.289834 AGATTTGTGGAATTTCAAACATGCA 58.710 32.000 0.00 0.00 36.58 3.96
4952 6024 0.316841 GGCGGCAAAAGATTTGTGGA 59.683 50.000 3.07 0.00 0.00 4.02
4970 6043 2.194201 AATTGTGGACCGGTGTTAGG 57.806 50.000 14.63 0.00 0.00 2.69
4972 6045 3.288964 ACAAAATTGTGGACCGGTGTTA 58.711 40.909 14.63 0.00 40.49 2.41
5012 6085 3.702045 ACTTCCGTTTTGTGGGATTTCAA 59.298 39.130 0.00 0.00 31.11 2.69
5052 6126 2.995283 TGAAGGAGATCCGAACGTCTA 58.005 47.619 0.00 0.00 42.08 2.59
5074 6148 1.998315 CCAAGCATGTCAGAGTTCGAG 59.002 52.381 0.00 0.00 0.00 4.04
5088 6162 3.153919 GGTATTTTGAGTGGACCAAGCA 58.846 45.455 0.00 0.00 0.00 3.91
5121 6195 1.005037 CCTCTGCAACACCGCACTA 60.005 57.895 0.00 0.00 36.86 2.74
5151 6225 2.323968 TTTTTGGCAAAACAGGCTCC 57.676 45.000 24.04 0.00 34.73 4.70
5250 6330 7.068103 ACCATGCAAATAATCGAATTACCTGAA 59.932 33.333 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.