Multiple sequence alignment - TraesCS2D01G502900

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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 TraesCS2D01G502900 chr2D 100.000 3361 0 0 1 3361 596555125 596551765 0.000000e+00 6207.0
1 TraesCS2D01G502900 chr2D 100.000 2279 0 0 3685 5963 596551441 596549163 0.000000e+00 4209.0
2 TraesCS2D01G502900 chr2D 83.333 156 21 4 2455 2608 249195112 249194960 8.060000e-29 139.0
3 TraesCS2D01G502900 chr2D 94.286 35 2 0 5413 5447 349825919 349825953 3.000000e-03 54.7
4 TraesCS2D01G502900 chr2D 100.000 28 0 0 5416 5443 496636015 496635988 1.100000e-02 52.8
5 TraesCS2D01G502900 chr2B 95.802 2835 101 9 1 2818 725581295 725578462 0.000000e+00 4560.0
6 TraesCS2D01G502900 chr2B 97.260 1241 30 3 4216 5454 725576872 725575634 0.000000e+00 2100.0
7 TraesCS2D01G502900 chr2B 96.614 502 4 4 3723 4215 725577550 725577053 0.000000e+00 821.0
8 TraesCS2D01G502900 chr2B 93.983 482 22 4 2823 3298 725578404 725577924 0.000000e+00 723.0
9 TraesCS2D01G502900 chr2B 95.745 47 2 0 2769 2815 273740372 273740418 6.410000e-10 76.8
10 TraesCS2D01G502900 chr2A 92.633 2837 118 36 1 2774 730618434 730615626 0.000000e+00 3997.0
11 TraesCS2D01G502900 chr2A 93.325 794 38 7 3685 4471 730615152 730614367 0.000000e+00 1158.0
12 TraesCS2D01G502900 chr2A 90.728 852 42 17 4527 5359 730614200 730613367 0.000000e+00 1101.0
13 TraesCS2D01G502900 chr2A 89.184 490 24 12 2856 3344 730615575 730615114 8.610000e-163 584.0
14 TraesCS2D01G502900 chr2A 86.475 488 39 16 5436 5918 730613355 730612890 1.480000e-140 510.0
15 TraesCS2D01G502900 chr2A 95.652 46 2 0 2769 2814 352429320 352429275 2.300000e-09 75.0
16 TraesCS2D01G502900 chr6B 90.476 105 7 2 1516 1617 200511462 200511358 1.040000e-27 135.0
17 TraesCS2D01G502900 chr6B 80.982 163 28 3 2455 2615 655756544 655756705 6.270000e-25 126.0
18 TraesCS2D01G502900 chr6A 90.476 105 7 2 1516 1617 136542093 136542197 1.040000e-27 135.0
19 TraesCS2D01G502900 chr4A 82.781 151 22 4 2456 2605 37004799 37004946 1.350000e-26 132.0
20 TraesCS2D01G502900 chr3D 82.390 159 18 9 2455 2608 609468826 609468673 4.850000e-26 130.0
21 TraesCS2D01G502900 chr6D 91.398 93 7 1 1526 1617 111569452 111569360 6.270000e-25 126.0
22 TraesCS2D01G502900 chr1B 82.781 151 16 7 2456 2605 20741465 20741606 6.270000e-25 126.0
23 TraesCS2D01G502900 chr1A 81.410 156 23 5 2455 2608 518772208 518772057 8.120000e-24 122.0
24 TraesCS2D01G502900 chr1A 95.556 45 2 0 2771 2815 442476487 442476531 8.290000e-09 73.1
25 TraesCS2D01G502900 chr1A 100.000 28 0 0 5416 5443 577063240 577063267 1.100000e-02 52.8
26 TraesCS2D01G502900 chr7D 81.529 157 19 8 2454 2605 566574585 566574736 2.920000e-23 121.0
27 TraesCS2D01G502900 chr3B 97.778 45 1 0 2771 2815 637088493 637088537 1.780000e-10 78.7
28 TraesCS2D01G502900 chr7A 94.000 50 2 1 2770 2818 498590386 498590337 2.300000e-09 75.0
29 TraesCS2D01G502900 chr7A 100.000 28 0 0 1653 1680 170630644 170630671 1.100000e-02 52.8
30 TraesCS2D01G502900 chr5B 90.909 55 4 1 2765 2819 549974049 549974102 8.290000e-09 73.1
31 TraesCS2D01G502900 chr4B 95.556 45 2 0 2771 2815 525844460 525844416 8.290000e-09 73.1
32 TraesCS2D01G502900 chr4B 95.556 45 2 0 2771 2815 624766356 624766400 8.290000e-09 73.1
33 TraesCS2D01G502900 chr4B 100.000 28 0 0 5416 5443 663740627 663740600 1.100000e-02 52.8
34 TraesCS2D01G502900 chr1D 100.000 30 0 0 5416 5445 249558950 249558979 8.350000e-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 TraesCS2D01G502900 chr2D 596549163 596555125 5962 True 5208 6207 100.00000 1 5963 2 chr2D.!!$R3 5962
1 TraesCS2D01G502900 chr2B 725575634 725581295 5661 True 2051 4560 95.91475 1 5454 4 chr2B.!!$R1 5453
2 TraesCS2D01G502900 chr2A 730612890 730618434 5544 True 1470 3997 90.46900 1 5918 5 chr2A.!!$R2 5917

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
388 409 0.036671 GTTGCTGTAACCCTACCGCT 60.037 55.000 0.00 0.00 38.63 5.52 F
995 1029 0.515564 CGGATAAATTAAGCGGCCGG 59.484 55.000 29.38 8.95 34.08 6.13 F
2544 2613 0.393537 ACACTTGGCCTCTGCATAGC 60.394 55.000 3.32 0.00 40.13 2.97 F
3193 3338 1.152984 TACATGCATTGGCCTCCCG 60.153 57.895 3.32 0.00 40.13 5.14 F
4018 4175 1.111277 TTGCCTAGCTACTGCATCGA 58.889 50.000 12.62 0.00 42.74 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2027 2067 0.659957 GCAATTGCTCGAGGTGATCC 59.340 55.0 23.21 0.00 38.21 3.36 R
2668 2741 0.517316 CAAGCCAAGTCTTACGGTGC 59.483 55.0 0.00 0.00 0.00 5.01 R
3715 3863 0.397941 CACAGCCCACAGGAAAGAGA 59.602 55.0 0.00 0.00 33.47 3.10 R
4737 5209 0.612732 CATGGCCATGGTGTCCTTGT 60.613 55.0 34.31 0.00 35.24 3.16 R
5572 6052 0.252057 AAAAATAGGGCGCCCAACCT 60.252 50.0 45.13 28.32 40.89 3.50 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
199 211 3.967393 ATGCATGTACGCGCCACCA 62.967 57.895 5.73 5.05 33.35 4.17
388 409 0.036671 GTTGCTGTAACCCTACCGCT 60.037 55.000 0.00 0.00 38.63 5.52
393 414 3.149648 TAACCCTACCGCTCGCCC 61.150 66.667 0.00 0.00 0.00 6.13
394 415 3.961225 TAACCCTACCGCTCGCCCA 62.961 63.158 0.00 0.00 0.00 5.36
710 740 0.539986 GCGTCCATGGAACCCTAGAA 59.460 55.000 18.20 0.00 0.00 2.10
734 764 1.982938 GTACGCACCCTCCACTCCT 60.983 63.158 0.00 0.00 0.00 3.69
891 921 2.125753 GCCAGTGAGTGAGCGAGG 60.126 66.667 0.00 0.00 0.00 4.63
958 992 2.864378 CTAACCCCTTTCCGGCCGTC 62.864 65.000 26.12 0.00 0.00 4.79
995 1029 0.515564 CGGATAAATTAAGCGGCCGG 59.484 55.000 29.38 8.95 34.08 6.13
1410 1447 3.624777 CGAGTACTACTTCCCCACCTTA 58.375 50.000 0.00 0.00 0.00 2.69
1491 1528 0.685458 GCTACCGGACCTACTTCCCA 60.685 60.000 9.46 0.00 31.03 4.37
1684 1721 1.202582 AGTGCAGCAGGTTAGTAGTCG 59.797 52.381 0.00 0.00 0.00 4.18
1759 1796 1.467875 CGTGTCTGATCGACCGATTC 58.532 55.000 6.36 1.53 42.13 2.52
1794 1834 9.827198 AAAGAGAGATGGATAGATCTTGTAGAT 57.173 33.333 0.00 0.00 37.73 1.98
1964 2004 7.248437 CCTTCAAATTACCCATTTAGTTCGAC 58.752 38.462 0.00 0.00 32.90 4.20
2014 2054 6.384015 TCTTATTAGTTTGAGCTCCTGGATCA 59.616 38.462 12.15 0.00 38.70 2.92
2027 2067 4.976864 TCCTGGATCATGATACCAACATG 58.023 43.478 15.56 9.04 44.20 3.21
2101 2142 3.410631 TGGCCTCGAACTTGATGTTAA 57.589 42.857 3.32 0.00 39.30 2.01
2215 2257 1.475682 CGTTCCTACAGTACCTGTCCC 59.524 57.143 0.00 0.00 41.21 4.46
2259 2301 8.053072 CGAAACAAAACAAATATGAGCGAAAAA 58.947 29.630 0.00 0.00 0.00 1.94
2261 2303 9.862585 AAACAAAACAAATATGAGCGAAAAATC 57.137 25.926 0.00 0.00 0.00 2.17
2297 2339 6.042638 TCTTTCACTGTTCTCCCTCAATAG 57.957 41.667 0.00 0.00 0.00 1.73
2303 2345 4.100189 ACTGTTCTCCCTCAATAGATTCCG 59.900 45.833 0.00 0.00 0.00 4.30
2371 2415 2.254546 TACACCTCACCACAGCAAAG 57.745 50.000 0.00 0.00 0.00 2.77
2382 2426 1.667724 CACAGCAAAGCCCTCGATTAG 59.332 52.381 0.00 0.00 0.00 1.73
2389 2433 1.623163 AGCCCTCGATTAGTAGGAGC 58.377 55.000 0.00 0.00 34.58 4.70
2448 2492 1.253100 TGTCATACACTGCCAGACGA 58.747 50.000 0.00 0.00 32.08 4.20
2516 2561 9.423061 GTGAAGCATTAGGAAAATACAAAACAT 57.577 29.630 0.00 0.00 0.00 2.71
2544 2613 0.393537 ACACTTGGCCTCTGCATAGC 60.394 55.000 3.32 0.00 40.13 2.97
2611 2680 1.938625 GCAAAAAGCAAAGCCAGACA 58.061 45.000 0.00 0.00 44.79 3.41
2617 2686 6.536224 GCAAAAAGCAAAGCCAGACATTATAT 59.464 34.615 0.00 0.00 44.79 0.86
2653 2722 1.875514 GCTGCTTGACTGATCACACAA 59.124 47.619 0.00 0.48 33.38 3.33
2778 2851 9.832445 TCATCCTCTACAATTTTGTATTACCTC 57.168 33.333 3.76 0.00 42.26 3.85
2782 2855 7.224167 CCTCTACAATTTTGTATTACCTCCGTC 59.776 40.741 3.76 0.00 42.26 4.79
2785 2858 4.847990 ATTTTGTATTACCTCCGTCCCA 57.152 40.909 0.00 0.00 0.00 4.37
2805 2878 8.911662 CGTCCCAAATTACTTGTCTTAAATTTG 58.088 33.333 0.00 10.80 43.77 2.32
2925 3066 2.571202 TGACAGATTATGTGGTGCTCCA 59.429 45.455 2.64 2.64 44.17 3.86
2933 3074 2.118313 TGTGGTGCTCCATGATTCAG 57.882 50.000 11.31 0.00 46.20 3.02
2994 3136 3.386768 TCTACATATTTCGCTCTGCCC 57.613 47.619 0.00 0.00 0.00 5.36
2998 3140 2.159014 ACATATTTCGCTCTGCCCGTAA 60.159 45.455 0.00 0.00 0.00 3.18
3016 3161 5.416083 CCGTAATTGACAAGAGTCCATGTA 58.584 41.667 0.00 0.00 44.33 2.29
3083 3228 2.183679 GCTCCTTCTTTCTCTCCTCCA 58.816 52.381 0.00 0.00 0.00 3.86
3193 3338 1.152984 TACATGCATTGGCCTCCCG 60.153 57.895 3.32 0.00 40.13 5.14
3218 3363 3.373439 GTCAGAGAAGCATGGCTACTTTG 59.627 47.826 0.00 0.00 38.25 2.77
3344 3492 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3345 3493 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3346 3494 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3348 3496 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3349 3497 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3350 3498 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3352 3500 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3353 3501 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3354 3502 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3355 3503 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3356 3504 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3357 3505 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3358 3506 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3359 3507 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3360 3508 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3707 3855 6.232581 CTCTCTCTTTCTCTCTCTCTCTCT 57.767 45.833 0.00 0.00 0.00 3.10
3708 3856 6.227298 TCTCTCTTTCTCTCTCTCTCTCTC 57.773 45.833 0.00 0.00 0.00 3.20
3709 3857 5.960811 TCTCTCTTTCTCTCTCTCTCTCTCT 59.039 44.000 0.00 0.00 0.00 3.10
3710 3858 6.097554 TCTCTCTTTCTCTCTCTCTCTCTCTC 59.902 46.154 0.00 0.00 0.00 3.20
3711 3859 5.960811 TCTCTTTCTCTCTCTCTCTCTCTCT 59.039 44.000 0.00 0.00 0.00 3.10
3712 3860 6.097554 TCTCTTTCTCTCTCTCTCTCTCTCTC 59.902 46.154 0.00 0.00 0.00 3.20
3713 3861 5.960811 TCTTTCTCTCTCTCTCTCTCTCTCT 59.039 44.000 0.00 0.00 0.00 3.10
3714 3862 5.860941 TTCTCTCTCTCTCTCTCTCTCTC 57.139 47.826 0.00 0.00 0.00 3.20
3715 3863 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
3716 3864 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3717 3865 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3718 3866 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3719 3867 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3720 3868 5.523588 TCTCTCTCTCTCTCTCTCTCTCTT 58.476 45.833 0.00 0.00 0.00 2.85
3721 3869 5.960811 TCTCTCTCTCTCTCTCTCTCTCTTT 59.039 44.000 0.00 0.00 0.00 2.52
3748 3896 2.654863 GGCTGTGGCTGTGGTAATAAT 58.345 47.619 0.00 0.00 38.73 1.28
3764 3921 9.120538 GTGGTAATAATAATGTGTTGGACAGAT 57.879 33.333 0.00 0.00 38.23 2.90
4015 4172 3.072038 TCATCATTGCCTAGCTACTGCAT 59.928 43.478 12.62 3.06 42.74 3.96
4016 4173 3.117491 TCATTGCCTAGCTACTGCATC 57.883 47.619 12.62 0.00 42.74 3.91
4017 4174 1.797046 CATTGCCTAGCTACTGCATCG 59.203 52.381 12.62 5.15 42.74 3.84
4018 4175 1.111277 TTGCCTAGCTACTGCATCGA 58.889 50.000 12.62 0.00 42.74 3.59
4351 4688 1.957186 CAACCGCCGTCGAAGGAAA 60.957 57.895 22.33 0.00 38.10 3.13
4463 4804 7.841282 TCCGTCCATCTTTCTCTATCTAATT 57.159 36.000 0.00 0.00 0.00 1.40
4846 5318 0.735632 CCAAGCTGTCTCGAGCACTC 60.736 60.000 7.81 2.49 41.83 3.51
4908 5380 0.685458 GCTTGGGGTTCCATCAGCAT 60.685 55.000 4.71 0.00 43.18 3.79
5150 5628 1.289160 AGAGGTGCTTCAATGCCCTA 58.711 50.000 0.00 0.00 35.05 3.53
5254 5733 2.632377 ACGTCACAGCTGATTAATGGG 58.368 47.619 23.35 6.25 0.00 4.00
5361 5840 7.284034 ACCATATTGCACTCTAATCCAAAGAAG 59.716 37.037 0.00 0.00 0.00 2.85
5378 5857 9.184523 TCCAAAGAAGAAGAAAAATGTTGAGTA 57.815 29.630 0.00 0.00 0.00 2.59
5404 5883 3.446161 CCTCCGTCCAGTAATGTAAGACA 59.554 47.826 0.00 0.00 0.00 3.41
5502 5982 3.686916 AGTTCCTGAACCAGAACTAGC 57.313 47.619 6.41 0.00 42.06 3.42
5503 5983 2.972713 AGTTCCTGAACCAGAACTAGCA 59.027 45.455 6.41 0.00 42.06 3.49
5507 5987 4.985538 TCCTGAACCAGAACTAGCAAATT 58.014 39.130 0.00 0.00 32.44 1.82
5534 6014 5.869753 ATTTGTCTGACATAGAACACTGC 57.130 39.130 11.86 0.00 37.12 4.40
5535 6015 4.607293 TTGTCTGACATAGAACACTGCT 57.393 40.909 11.86 0.00 37.12 4.24
5536 6016 5.722021 TTGTCTGACATAGAACACTGCTA 57.278 39.130 11.86 0.00 37.12 3.49
5537 6017 5.921962 TGTCTGACATAGAACACTGCTAT 57.078 39.130 6.36 0.00 37.12 2.97
5538 6018 5.895928 TGTCTGACATAGAACACTGCTATC 58.104 41.667 6.36 0.00 37.12 2.08
5539 6019 5.418840 TGTCTGACATAGAACACTGCTATCA 59.581 40.000 6.36 0.00 37.12 2.15
5540 6020 6.071391 TGTCTGACATAGAACACTGCTATCAA 60.071 38.462 6.36 0.00 37.12 2.57
5541 6021 6.983307 GTCTGACATAGAACACTGCTATCAAT 59.017 38.462 2.24 0.00 37.12 2.57
5542 6022 8.138074 GTCTGACATAGAACACTGCTATCAATA 58.862 37.037 2.24 0.00 37.12 1.90
5543 6023 8.695456 TCTGACATAGAACACTGCTATCAATAA 58.305 33.333 0.00 0.00 30.84 1.40
5544 6024 9.317936 CTGACATAGAACACTGCTATCAATAAA 57.682 33.333 0.00 0.00 0.00 1.40
5545 6025 9.836864 TGACATAGAACACTGCTATCAATAAAT 57.163 29.630 0.00 0.00 0.00 1.40
5589 6069 1.379843 CAGGTTGGGCGCCCTATTT 60.380 57.895 43.34 25.73 36.94 1.40
5598 6078 1.136891 GGCGCCCTATTTTTGAATGCT 59.863 47.619 18.11 0.00 0.00 3.79
5617 6097 2.967887 GCTGAATGGAGGGGCAAAATAT 59.032 45.455 0.00 0.00 0.00 1.28
5636 6116 6.808008 AATATGCATAAAAGAGGACGATGG 57.192 37.500 11.13 0.00 0.00 3.51
5648 6128 1.546476 GGACGATGGTCTTGTGAGTCT 59.454 52.381 7.84 0.00 42.97 3.24
5676 6156 7.485913 GTGTTGCTATGATTTATTCTTGTGGTG 59.514 37.037 0.00 0.00 0.00 4.17
5677 6157 7.392953 TGTTGCTATGATTTATTCTTGTGGTGA 59.607 33.333 0.00 0.00 0.00 4.02
5729 6210 9.801714 CTATGTTTTCAAATCAAACAGAATTGC 57.198 29.630 4.69 0.00 45.07 3.56
5730 6211 7.014092 TGTTTTCAAATCAAACAGAATTGCC 57.986 32.000 0.00 0.00 38.84 4.52
5735 6216 7.099266 TCAAATCAAACAGAATTGCCGATAT 57.901 32.000 0.00 0.00 37.12 1.63
5741 6222 4.679373 ACAGAATTGCCGATATCACTCT 57.321 40.909 3.12 0.00 0.00 3.24
5742 6223 4.375272 ACAGAATTGCCGATATCACTCTG 58.625 43.478 3.12 7.20 0.00 3.35
5743 6224 4.141846 ACAGAATTGCCGATATCACTCTGT 60.142 41.667 3.12 7.75 0.00 3.41
5744 6225 4.447054 CAGAATTGCCGATATCACTCTGTC 59.553 45.833 3.12 0.00 0.00 3.51
5754 6235 5.345472 CGATATCACTCTGTCATCTTCATGC 59.655 44.000 3.12 0.00 0.00 4.06
5767 6248 9.176460 TGTCATCTTCATGCATTTCATAGTTTA 57.824 29.630 0.00 0.00 33.19 2.01
5813 6294 5.759763 GCAAATCAAACAGACCCTTTTGAAT 59.240 36.000 1.20 0.00 43.20 2.57
5825 6306 7.282901 CAGACCCTTTTGAATTGGAATTTTTGT 59.717 33.333 0.00 0.00 0.00 2.83
5831 6312 4.305769 TGAATTGGAATTTTTGTGAGGCG 58.694 39.130 0.00 0.00 0.00 5.52
5832 6313 4.038522 TGAATTGGAATTTTTGTGAGGCGA 59.961 37.500 0.00 0.00 0.00 5.54
5836 6317 0.665835 AATTTTTGTGAGGCGACGCA 59.334 45.000 23.09 0.00 38.03 5.24
5913 6397 5.649970 TTAAGTTAAAGTTGGGGGAGTGA 57.350 39.130 0.00 0.00 0.00 3.41
5918 6402 3.328535 AAAGTTGGGGGAGTGAAACAT 57.671 42.857 0.00 0.00 41.43 2.71
5919 6403 4.463050 AAAGTTGGGGGAGTGAAACATA 57.537 40.909 0.00 0.00 41.43 2.29
5920 6404 3.721087 AGTTGGGGGAGTGAAACATAG 57.279 47.619 0.00 0.00 41.43 2.23
5921 6405 2.092323 GTTGGGGGAGTGAAACATAGC 58.908 52.381 0.00 0.00 41.43 2.97
5922 6406 1.367346 TGGGGGAGTGAAACATAGCA 58.633 50.000 0.00 0.00 41.43 3.49
5923 6407 1.922447 TGGGGGAGTGAAACATAGCAT 59.078 47.619 0.00 0.00 41.43 3.79
5924 6408 2.092429 TGGGGGAGTGAAACATAGCATC 60.092 50.000 0.00 0.00 41.43 3.91
5925 6409 2.092429 GGGGGAGTGAAACATAGCATCA 60.092 50.000 0.00 0.00 41.43 3.07
5926 6410 3.435601 GGGGGAGTGAAACATAGCATCAT 60.436 47.826 0.00 0.00 41.43 2.45
5927 6411 4.210331 GGGGAGTGAAACATAGCATCATT 58.790 43.478 0.00 0.00 41.43 2.57
5928 6412 4.037208 GGGGAGTGAAACATAGCATCATTG 59.963 45.833 0.00 0.00 41.43 2.82
5929 6413 4.498682 GGGAGTGAAACATAGCATCATTGC 60.499 45.833 0.00 0.00 45.15 3.56
5944 6428 4.277239 TGCTCCACGCACATACAC 57.723 55.556 0.00 0.00 45.47 2.90
5945 6429 1.671166 TGCTCCACGCACATACACT 59.329 52.632 0.00 0.00 45.47 3.55
5946 6430 0.034756 TGCTCCACGCACATACACTT 59.965 50.000 0.00 0.00 45.47 3.16
5947 6431 0.443869 GCTCCACGCACATACACTTG 59.556 55.000 0.00 0.00 38.92 3.16
5948 6432 1.939381 GCTCCACGCACATACACTTGA 60.939 52.381 0.00 0.00 38.92 3.02
5949 6433 2.621338 CTCCACGCACATACACTTGAT 58.379 47.619 0.00 0.00 0.00 2.57
5950 6434 3.002791 CTCCACGCACATACACTTGATT 58.997 45.455 0.00 0.00 0.00 2.57
5951 6435 3.407698 TCCACGCACATACACTTGATTT 58.592 40.909 0.00 0.00 0.00 2.17
5952 6436 3.818210 TCCACGCACATACACTTGATTTT 59.182 39.130 0.00 0.00 0.00 1.82
5953 6437 4.277174 TCCACGCACATACACTTGATTTTT 59.723 37.500 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
155 166 4.901123 CGGCCGTGTGTGACACCA 62.901 66.667 19.50 0.00 45.93 4.17
199 211 1.276859 TGCATGTGAGCCAGAGGGAT 61.277 55.000 0.00 0.00 35.59 3.85
373 394 1.226888 GCGAGCGGTAGGGTTACAG 60.227 63.158 0.00 0.00 0.00 2.74
388 409 1.148273 GTATCCATTGGCTGGGCGA 59.852 57.895 0.00 0.00 45.98 5.54
393 414 0.886490 GCCTCCGTATCCATTGGCTG 60.886 60.000 0.00 0.00 37.58 4.85
394 415 1.451936 GCCTCCGTATCCATTGGCT 59.548 57.895 0.00 0.00 37.58 4.75
604 634 0.468029 CCAGGAGAGAGAGAGGGAGC 60.468 65.000 0.00 0.00 0.00 4.70
710 740 0.251653 TGGAGGGTGCGTACTTCTCT 60.252 55.000 19.62 7.81 32.11 3.10
734 764 1.429687 GATGGGAGGGAGCTCTAGGTA 59.570 57.143 14.64 0.00 0.00 3.08
958 992 1.603802 CCGCTAGAGAGAGCAGAGAAG 59.396 57.143 0.00 0.00 42.99 2.85
995 1029 0.548031 TGGCAGGTTCATCATCCTCC 59.452 55.000 0.00 0.00 30.91 4.30
1080 1114 0.179045 GGTGGTCCATGATCGGGAAG 60.179 60.000 7.45 0.00 35.88 3.46
1122 1156 3.625897 TGGTGGTCGTGCTCCCTG 61.626 66.667 0.00 0.00 0.00 4.45
1491 1528 3.391382 GTGTAGCCGCCTCTGGGT 61.391 66.667 0.00 0.00 43.46 4.51
1684 1721 8.251750 TGGCGAATTAATATAGTATCAAGTGC 57.748 34.615 0.00 0.00 0.00 4.40
1759 1796 8.275015 TCTATCCATCTCTCTTTAGAATAGCG 57.725 38.462 0.00 0.00 0.00 4.26
1794 1834 3.546724 TCATTTTCCAACTCAACACGGA 58.453 40.909 0.00 0.00 0.00 4.69
1904 1944 2.422479 CGAACGAGGTAACAGGATGAGA 59.578 50.000 0.00 0.00 39.69 3.27
1964 2004 7.969536 TCTCAAAACTTTCCTACTCATTCAG 57.030 36.000 0.00 0.00 0.00 3.02
2014 2054 4.503817 CGAGGTGATCCATGTTGGTATCAT 60.504 45.833 10.03 0.00 36.86 2.45
2027 2067 0.659957 GCAATTGCTCGAGGTGATCC 59.340 55.000 23.21 0.00 38.21 3.36
2101 2142 7.226523 GGTAACAGAAAATGTGGCAAAGAAATT 59.773 33.333 0.00 0.00 43.00 1.82
2215 2257 3.066369 TCGATCTAGCAGTTAAGCGTG 57.934 47.619 0.00 0.00 40.15 5.34
2259 2301 2.238646 TGAAAGAACAGGGTATGCGGAT 59.761 45.455 0.00 0.00 0.00 4.18
2261 2303 1.737793 GTGAAAGAACAGGGTATGCGG 59.262 52.381 0.00 0.00 0.00 5.69
2297 2339 3.863041 AGCTACTGTTTCCTTCGGAATC 58.137 45.455 0.00 0.00 41.71 2.52
2333 2375 6.701432 GTGTATTGTACAGTACACCAGTTC 57.299 41.667 34.50 18.92 44.03 3.01
2371 2415 1.271102 CAGCTCCTACTAATCGAGGGC 59.729 57.143 0.00 0.00 33.27 5.19
2382 2426 4.519540 TTGCAAAATTTCCAGCTCCTAC 57.480 40.909 0.00 0.00 0.00 3.18
2389 2433 8.747666 CAAAATTGTTCATTGCAAAATTTCCAG 58.252 29.630 15.54 8.21 31.13 3.86
2516 2561 4.832248 CAGAGGCCAAGTGTTACTCATTA 58.168 43.478 5.01 0.00 0.00 1.90
2544 2613 2.095567 GTGTTGGCTGTGTGCATCTTAG 60.096 50.000 0.00 0.00 45.15 2.18
2667 2736 0.949105 AAGCCAAGTCTTACGGTGCG 60.949 55.000 0.00 0.00 0.00 5.34
2668 2741 0.517316 CAAGCCAAGTCTTACGGTGC 59.483 55.000 0.00 0.00 0.00 5.01
2670 2743 1.414919 TGTCAAGCCAAGTCTTACGGT 59.585 47.619 0.00 0.00 0.00 4.83
2756 2829 7.046033 ACGGAGGTAATACAAAATTGTAGAGG 58.954 38.462 11.28 0.00 45.80 3.69
2778 2851 6.563222 TTTAAGACAAGTAATTTGGGACGG 57.437 37.500 0.00 0.00 41.25 4.79
2782 2855 9.981114 AGACAAATTTAAGACAAGTAATTTGGG 57.019 29.630 18.01 1.54 45.43 4.12
2805 2878 9.778993 TTGTACACTAACAAATAGTATCGAGAC 57.221 33.333 0.86 0.86 43.12 3.36
2925 3066 6.951778 TGATCATATTTGGATGGCTGAATCAT 59.048 34.615 0.00 0.00 0.00 2.45
2933 3074 7.663827 TGAATCTTTGATCATATTTGGATGGC 58.336 34.615 0.00 0.00 0.00 4.40
2994 3136 6.756542 TGATACATGGACTCTTGTCAATTACG 59.243 38.462 0.00 0.00 44.61 3.18
2998 3140 6.053632 TGTGATACATGGACTCTTGTCAAT 57.946 37.500 0.00 0.00 44.61 2.57
3016 3161 6.513180 CGTATAAGTGTTCCCTACATGTGAT 58.487 40.000 9.11 0.00 39.39 3.06
3193 3338 2.399916 AGCCATGCTTCTCTGACTTC 57.600 50.000 0.00 0.00 33.89 3.01
3218 3363 5.959618 ACAAACTTGCAATACTTAGGGAC 57.040 39.130 0.00 0.00 0.00 4.46
3284 3432 1.405105 AGAGAGAGAGATGCTTGCGAC 59.595 52.381 0.00 0.00 0.00 5.19
3684 3832 6.098124 AGAGAGAGAGAGAGAGAAAGAGAGAG 59.902 46.154 0.00 0.00 0.00 3.20
3685 3833 5.960811 AGAGAGAGAGAGAGAGAAAGAGAGA 59.039 44.000 0.00 0.00 0.00 3.10
3686 3834 6.098124 AGAGAGAGAGAGAGAGAGAAAGAGAG 59.902 46.154 0.00 0.00 0.00 3.20
3687 3835 5.960811 AGAGAGAGAGAGAGAGAGAAAGAGA 59.039 44.000 0.00 0.00 0.00 3.10
3688 3836 6.098124 AGAGAGAGAGAGAGAGAGAGAAAGAG 59.902 46.154 0.00 0.00 0.00 2.85
3689 3837 5.960811 AGAGAGAGAGAGAGAGAGAGAAAGA 59.039 44.000 0.00 0.00 0.00 2.52
3690 3838 6.098124 AGAGAGAGAGAGAGAGAGAGAGAAAG 59.902 46.154 0.00 0.00 0.00 2.62
3691 3839 5.960811 AGAGAGAGAGAGAGAGAGAGAGAAA 59.039 44.000 0.00 0.00 0.00 2.52
3692 3840 5.523588 AGAGAGAGAGAGAGAGAGAGAGAA 58.476 45.833 0.00 0.00 0.00 2.87
3693 3841 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3694 3842 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3695 3843 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3696 3844 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3697 3845 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
3698 3846 5.867903 AAGAGAGAGAGAGAGAGAGAGAG 57.132 47.826 0.00 0.00 0.00 3.20
3699 3847 5.129485 GGAAAGAGAGAGAGAGAGAGAGAGA 59.871 48.000 0.00 0.00 0.00 3.10
3700 3848 5.130145 AGGAAAGAGAGAGAGAGAGAGAGAG 59.870 48.000 0.00 0.00 0.00 3.20
3701 3849 5.032846 AGGAAAGAGAGAGAGAGAGAGAGA 58.967 45.833 0.00 0.00 0.00 3.10
3702 3850 5.121811 CAGGAAAGAGAGAGAGAGAGAGAG 58.878 50.000 0.00 0.00 0.00 3.20
3703 3851 4.536090 ACAGGAAAGAGAGAGAGAGAGAGA 59.464 45.833 0.00 0.00 0.00 3.10
3704 3852 4.637534 CACAGGAAAGAGAGAGAGAGAGAG 59.362 50.000 0.00 0.00 0.00 3.20
3705 3853 4.567537 CCACAGGAAAGAGAGAGAGAGAGA 60.568 50.000 0.00 0.00 0.00 3.10
3706 3854 3.696051 CCACAGGAAAGAGAGAGAGAGAG 59.304 52.174 0.00 0.00 0.00 3.20
3707 3855 3.563261 CCCACAGGAAAGAGAGAGAGAGA 60.563 52.174 0.00 0.00 33.47 3.10
3708 3856 2.760092 CCCACAGGAAAGAGAGAGAGAG 59.240 54.545 0.00 0.00 33.47 3.20
3709 3857 2.813907 CCCACAGGAAAGAGAGAGAGA 58.186 52.381 0.00 0.00 33.47 3.10
3710 3858 1.206849 GCCCACAGGAAAGAGAGAGAG 59.793 57.143 0.00 0.00 33.47 3.20
3711 3859 1.203237 AGCCCACAGGAAAGAGAGAGA 60.203 52.381 0.00 0.00 33.47 3.10
3712 3860 1.066286 CAGCCCACAGGAAAGAGAGAG 60.066 57.143 0.00 0.00 33.47 3.20
3713 3861 0.979665 CAGCCCACAGGAAAGAGAGA 59.020 55.000 0.00 0.00 33.47 3.10
3714 3862 0.689623 ACAGCCCACAGGAAAGAGAG 59.310 55.000 0.00 0.00 33.47 3.20
3715 3863 0.397941 CACAGCCCACAGGAAAGAGA 59.602 55.000 0.00 0.00 33.47 3.10
3716 3864 0.607489 CCACAGCCCACAGGAAAGAG 60.607 60.000 0.00 0.00 33.47 2.85
3717 3865 1.455849 CCACAGCCCACAGGAAAGA 59.544 57.895 0.00 0.00 33.47 2.52
3718 3866 2.270986 GCCACAGCCCACAGGAAAG 61.271 63.158 0.00 0.00 33.47 2.62
3719 3867 2.203480 GCCACAGCCCACAGGAAA 60.203 61.111 0.00 0.00 33.47 3.13
3720 3868 3.177884 AGCCACAGCCCACAGGAA 61.178 61.111 0.00 0.00 41.25 3.36
3721 3869 3.957586 CAGCCACAGCCCACAGGA 61.958 66.667 0.00 0.00 41.25 3.86
3748 3896 4.465632 ACGCTATCTGTCCAACACATTA 57.534 40.909 0.00 0.00 33.23 1.90
3764 3921 5.983720 GTCTGATAGAAATGCCTTTACGCTA 59.016 40.000 0.00 0.00 0.00 4.26
4256 4593 5.444122 CAGATGAAACCTGAACGAGAAAAC 58.556 41.667 0.00 0.00 33.65 2.43
4737 5209 0.612732 CATGGCCATGGTGTCCTTGT 60.613 55.000 34.31 0.00 35.24 3.16
4846 5318 3.128415 TGGCCGATATTTGATGTGTTGTG 59.872 43.478 0.00 0.00 0.00 3.33
4908 5380 1.134699 CCGAGCTGAAGGATGTTGCTA 60.135 52.381 0.00 0.00 33.83 3.49
5254 5733 3.802866 TGAAAAAGTTTGATGCCCCAAC 58.197 40.909 0.00 0.00 0.00 3.77
5312 5791 8.349245 TGGTCCATAAAAAGCATATATGTTTCG 58.651 33.333 14.30 3.52 30.66 3.46
5361 5840 6.149640 GGAGGGAGTACTCAACATTTTTCTTC 59.850 42.308 23.91 8.94 39.27 2.87
5378 5857 1.273098 ACATTACTGGACGGAGGGAGT 60.273 52.381 0.00 0.00 0.00 3.85
5415 5894 7.472741 TCTACTCCCTTCGTCCCATAATATAA 58.527 38.462 0.00 0.00 0.00 0.98
5425 5904 6.645790 TGTTAATATCTACTCCCTTCGTCC 57.354 41.667 0.00 0.00 0.00 4.79
5428 5907 9.011095 TGACTATGTTAATATCTACTCCCTTCG 57.989 37.037 0.00 0.00 0.00 3.79
5464 5943 4.215613 GGAACTTTTGCCTGATTTCGTACT 59.784 41.667 0.00 0.00 0.00 2.73
5467 5946 3.222603 AGGAACTTTTGCCTGATTTCGT 58.777 40.909 0.00 0.00 27.25 3.85
5468 5947 3.923017 AGGAACTTTTGCCTGATTTCG 57.077 42.857 0.00 0.00 27.25 3.46
5516 5996 5.895928 TGATAGCAGTGTTCTATGTCAGAC 58.104 41.667 0.00 0.00 31.12 3.51
5562 6042 1.540267 CGCCCAACCTGTTTTATCCA 58.460 50.000 0.00 0.00 0.00 3.41
5568 6048 2.150014 ATAGGGCGCCCAACCTGTTT 62.150 55.000 45.13 25.57 37.72 2.83
5572 6052 0.252057 AAAAATAGGGCGCCCAACCT 60.252 50.000 45.13 28.32 40.89 3.50
5589 6069 2.459644 CCCCTCCATTCAGCATTCAAA 58.540 47.619 0.00 0.00 0.00 2.69
5598 6078 2.699846 GCATATTTTGCCCCTCCATTCA 59.300 45.455 0.00 0.00 46.15 2.57
5617 6097 3.197766 AGACCATCGTCCTCTTTTATGCA 59.802 43.478 0.00 0.00 40.12 3.96
5623 6103 2.632996 TCACAAGACCATCGTCCTCTTT 59.367 45.455 0.00 0.00 40.12 2.52
5631 6111 2.733552 CACAAGACTCACAAGACCATCG 59.266 50.000 0.00 0.00 0.00 3.84
5636 6116 2.939103 AGCAACACAAGACTCACAAGAC 59.061 45.455 0.00 0.00 0.00 3.01
5648 6128 8.028354 CCACAAGAATAAATCATAGCAACACAA 58.972 33.333 0.00 0.00 0.00 3.33
5705 6186 7.518689 CGGCAATTCTGTTTGATTTGAAAACAT 60.519 33.333 2.51 0.00 44.25 2.71
5729 6210 5.444663 TGAAGATGACAGAGTGATATCGG 57.555 43.478 0.00 0.00 0.00 4.18
5730 6211 5.345472 GCATGAAGATGACAGAGTGATATCG 59.655 44.000 0.00 0.00 0.00 2.92
5735 6216 3.967332 TGCATGAAGATGACAGAGTGA 57.033 42.857 0.00 0.00 0.00 3.41
5741 6222 7.634671 AACTATGAAATGCATGAAGATGACA 57.365 32.000 0.00 0.00 37.87 3.58
5767 6248 5.420104 TGCACAATTTGGGGAAACAAAATTT 59.580 32.000 0.00 0.00 42.91 1.82
5768 6249 4.952335 TGCACAATTTGGGGAAACAAAATT 59.048 33.333 0.00 0.00 42.91 1.82
5774 6255 4.133078 TGATTTGCACAATTTGGGGAAAC 58.867 39.130 18.86 13.44 43.69 2.78
5784 6265 3.642848 AGGGTCTGTTTGATTTGCACAAT 59.357 39.130 0.00 0.00 0.00 2.71
5813 6294 2.287308 CGTCGCCTCACAAAAATTCCAA 60.287 45.455 0.00 0.00 0.00 3.53
5865 6349 8.472007 AAAATGGTAGTTTTGGACAGAACATA 57.528 30.769 8.20 0.00 30.55 2.29
5894 6378 4.212716 GTTTCACTCCCCCAACTTTAACT 58.787 43.478 0.00 0.00 0.00 2.24
5906 6390 5.179045 CAATGATGCTATGTTTCACTCCC 57.821 43.478 0.00 0.00 0.00 4.30
5929 6413 2.078849 TCAAGTGTATGTGCGTGGAG 57.921 50.000 0.00 0.00 0.00 3.86
5930 6414 2.760634 ATCAAGTGTATGTGCGTGGA 57.239 45.000 0.00 0.00 0.00 4.02
5931 6415 3.829886 AAATCAAGTGTATGTGCGTGG 57.170 42.857 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.