Multiple sequence alignment - TraesCS2A01G409100

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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 TraesCS2A01G409100 chr2A 100.000 3572 0 0 1 3572 666552955 666556526 0.000000e+00 6597.0
1 TraesCS2A01G409100 chr2B 94.035 2649 123 11 783 3411 614901000 614903633 0.000000e+00 3984.0
2 TraesCS2A01G409100 chr2B 88.834 2015 176 26 757 2744 227251953 227249961 0.000000e+00 2429.0
3 TraesCS2A01G409100 chr2B 89.286 504 43 6 1 504 614900511 614901003 3.920000e-174 621.0
4 TraesCS2A01G409100 chr2B 94.595 111 6 0 3462 3572 614903627 614903737 4.740000e-39 172.0
5 TraesCS2A01G409100 chr2B 100.000 39 0 0 2643 2681 614902975 614903013 4.950000e-09 73.1
6 TraesCS2A01G409100 chr2B 100.000 28 0 0 2727 2754 265428428 265428455 6.000000e-03 52.8
7 TraesCS2A01G409100 chr2D 89.083 1429 123 13 1350 2754 520651249 520649830 0.000000e+00 1744.0
8 TraesCS2A01G409100 chr2D 86.995 1484 94 37 709 2143 520652677 520651244 0.000000e+00 1580.0
9 TraesCS2A01G409100 chr2D 90.762 682 58 5 1 680 520653577 520652899 0.000000e+00 905.0
10 TraesCS2A01G409100 chr2D 90.608 181 15 1 2885 3065 520649759 520649581 4.610000e-59 239.0
11 TraesCS2A01G409100 chr2D 100.000 28 0 0 2727 2754 213702940 213702967 6.000000e-03 52.8
12 TraesCS2A01G409100 chr7B 88.000 50 6 0 734 783 534815582 534815631 3.850000e-05 60.2
13 TraesCS2A01G409100 chr6B 100.000 29 0 0 2726 2754 44462318 44462346 2.000000e-03 54.7
14 TraesCS2A01G409100 chr6A 100.000 29 0 0 2726 2754 479409173 479409201 2.000000e-03 54.7
15 TraesCS2A01G409100 chr3A 100.000 29 0 0 2726 2754 121330341 121330369 2.000000e-03 54.7
16 TraesCS2A01G409100 chr1B 94.286 35 2 0 2726 2760 645555419 645555385 2.000000e-03 54.7
17 TraesCS2A01G409100 chr5D 100.000 28 0 0 2727 2754 7503902 7503929 6.000000e-03 52.8


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 TraesCS2A01G409100 chr2A 666552955 666556526 3571 False 6597.000 6597 100.000 1 3572 1 chr2A.!!$F1 3571
1 TraesCS2A01G409100 chr2B 227249961 227251953 1992 True 2429.000 2429 88.834 757 2744 1 chr2B.!!$R1 1987
2 TraesCS2A01G409100 chr2B 614900511 614903737 3226 False 1212.525 3984 94.479 1 3572 4 chr2B.!!$F2 3571
3 TraesCS2A01G409100 chr2D 520649581 520653577 3996 True 1117.000 1744 89.362 1 3065 4 chr2D.!!$R1 3064

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
448 458 0.171007 ATCGAACCATGCCGCAAAAG 59.829 50.0 0.0 0.0 0.0 2.27 F
951 1170 0.179113 GCTCTCTTCGCCTCTCCTTG 60.179 60.0 0.0 0.0 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1472 2488 1.267121 CCTCCCTCCGTTTCTCTCAA 58.733 55.0 0.0 0.0 0.00 3.02 R
2912 3951 0.683973 ACACAGCCTGGAGAAGTGAG 59.316 55.0 0.0 0.0 34.47 3.51 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
44 45 1.330521 CACATTGGGATTAAGCGGTCG 59.669 52.381 0.00 0.00 0.00 4.79
57 58 1.000955 AGCGGTCGTGATCTTCAAAGT 59.999 47.619 0.00 0.00 0.00 2.66
70 71 9.950680 GTGATCTTCAAAGTTGTCAGATTTTTA 57.049 29.630 0.00 0.00 32.90 1.52
99 101 7.088589 TCAAAGCTAAAAGGCATCTTACATC 57.911 36.000 0.00 0.00 32.01 3.06
101 103 8.046708 TCAAAGCTAAAAGGCATCTTACATCTA 58.953 33.333 0.00 0.00 32.01 1.98
158 161 1.332375 ACAATTGGACACAAACCGACG 59.668 47.619 10.83 0.00 40.55 5.12
198 201 8.606040 TTACATTGTAAAACGTACTAGCCTTT 57.394 30.769 6.79 0.00 0.00 3.11
199 202 7.125536 ACATTGTAAAACGTACTAGCCTTTC 57.874 36.000 0.00 0.00 0.00 2.62
200 203 6.932960 ACATTGTAAAACGTACTAGCCTTTCT 59.067 34.615 0.00 0.00 0.00 2.52
201 204 7.117379 ACATTGTAAAACGTACTAGCCTTTCTC 59.883 37.037 0.00 0.00 0.00 2.87
202 205 6.336842 TGTAAAACGTACTAGCCTTTCTCT 57.663 37.500 0.00 0.00 0.00 3.10
203 206 6.752168 TGTAAAACGTACTAGCCTTTCTCTT 58.248 36.000 0.00 0.00 0.00 2.85
210 213 6.015265 ACGTACTAGCCTTTCTCTTCTTCTTT 60.015 38.462 0.00 0.00 0.00 2.52
219 228 9.267084 GCCTTTCTCTTCTTCTTTCGATTATAT 57.733 33.333 0.00 0.00 0.00 0.86
226 235 5.305585 TCTTCTTTCGATTATATGCCACCC 58.694 41.667 0.00 0.00 0.00 4.61
279 289 3.659850 AAAAAGGACGCCTGCAAAC 57.340 47.368 0.00 0.00 32.13 2.93
322 332 4.568152 ACAAACAACAATAGCCACTCAC 57.432 40.909 0.00 0.00 0.00 3.51
377 387 1.736645 ATCGGTTGAAGCGTCACCG 60.737 57.895 25.57 25.57 43.72 4.94
414 424 3.633418 TGCAATCCATCATCATTGGTCA 58.367 40.909 0.00 0.00 35.64 4.02
448 458 0.171007 ATCGAACCATGCCGCAAAAG 59.829 50.000 0.00 0.00 0.00 2.27
449 459 1.444212 CGAACCATGCCGCAAAAGG 60.444 57.895 0.00 2.57 0.00 3.11
458 469 2.509569 TGCCGCAAAAGGATACAGAAA 58.490 42.857 0.00 0.00 41.41 2.52
487 498 1.732259 GAAGTCATCGCGTCAATGGTT 59.268 47.619 5.77 0.42 0.00 3.67
501 512 5.291971 GTCAATGGTTTGTCAAATTGCTCT 58.708 37.500 0.40 0.00 34.32 4.09
507 518 2.099141 TGTCAAATTGCTCTCCTCGG 57.901 50.000 0.00 0.00 0.00 4.63
529 540 2.040813 AGGACACATCAACTGCCAAGAT 59.959 45.455 0.00 0.00 0.00 2.40
540 551 5.423290 TCAACTGCCAAGATATGAAGAGAGA 59.577 40.000 0.00 0.00 0.00 3.10
550 561 7.288810 AGATATGAAGAGAGACAACAGATCC 57.711 40.000 0.00 0.00 32.09 3.36
572 583 0.391597 GGACACAAACTCTCACGGGA 59.608 55.000 0.00 0.00 0.00 5.14
578 589 3.815401 CACAAACTCTCACGGGATCTTTT 59.185 43.478 0.00 0.00 0.00 2.27
584 595 2.758423 TCTCACGGGATCTTTTCGATGA 59.242 45.455 0.00 0.00 30.84 2.92
588 599 2.496070 ACGGGATCTTTTCGATGACAGA 59.504 45.455 0.00 0.00 30.84 3.41
594 605 6.367422 GGGATCTTTTCGATGACAGATCATAC 59.633 42.308 18.16 9.31 46.01 2.39
653 664 4.129737 ACCGCCACCATCTCGTCG 62.130 66.667 0.00 0.00 0.00 5.12
680 691 4.069232 CCACTCCTCTTGCCGCGA 62.069 66.667 8.23 0.00 0.00 5.87
681 692 2.507992 CACTCCTCTTGCCGCGAG 60.508 66.667 8.23 0.56 0.00 5.03
683 694 2.055042 ACTCCTCTTGCCGCGAGAT 61.055 57.895 8.23 0.00 0.00 2.75
684 695 1.591059 CTCCTCTTGCCGCGAGATG 60.591 63.158 8.23 8.54 0.00 2.90
685 696 2.587194 CCTCTTGCCGCGAGATGG 60.587 66.667 8.23 10.44 0.00 3.51
686 697 2.587194 CTCTTGCCGCGAGATGGG 60.587 66.667 8.23 0.00 0.00 4.00
693 704 2.419198 CGCGAGATGGGGAAGAGG 59.581 66.667 0.00 0.00 0.00 3.69
694 705 2.825264 GCGAGATGGGGAAGAGGG 59.175 66.667 0.00 0.00 0.00 4.30
695 706 1.762460 GCGAGATGGGGAAGAGGGA 60.762 63.158 0.00 0.00 0.00 4.20
696 707 1.753368 GCGAGATGGGGAAGAGGGAG 61.753 65.000 0.00 0.00 0.00 4.30
697 708 1.118356 CGAGATGGGGAAGAGGGAGG 61.118 65.000 0.00 0.00 0.00 4.30
698 709 0.766288 GAGATGGGGAAGAGGGAGGG 60.766 65.000 0.00 0.00 0.00 4.30
699 710 1.772156 GATGGGGAAGAGGGAGGGG 60.772 68.421 0.00 0.00 0.00 4.79
700 711 3.369161 ATGGGGAAGAGGGAGGGGG 62.369 68.421 0.00 0.00 0.00 5.40
729 933 1.671379 GGCGGTGTGAGGGAGAAAC 60.671 63.158 0.00 0.00 0.00 2.78
779 988 2.022240 GCGGCTAGGGTTGAGAGAGG 62.022 65.000 0.00 0.00 0.00 3.69
813 1022 3.198409 TGACATTGTGTGAGTTGCTCT 57.802 42.857 0.00 0.00 0.00 4.09
894 1113 3.775661 AGAGAGAAGCGAGCTAACTTC 57.224 47.619 16.78 16.78 42.13 3.01
939 1158 3.507233 TGCCAAAATTGAATCGCTCTCTT 59.493 39.130 0.00 0.00 0.00 2.85
951 1170 0.179113 GCTCTCTTCGCCTCTCCTTG 60.179 60.000 0.00 0.00 0.00 3.61
1084 1303 2.892425 CTGCATCTTCCGCCGTCC 60.892 66.667 0.00 0.00 0.00 4.79
1330 1549 3.764972 GGTTAATTCGTCCCCATTTTGGA 59.235 43.478 0.00 0.00 40.96 3.53
1364 1591 1.337447 TGCCGGTAGTGCTTGAAGTAC 60.337 52.381 5.22 5.22 0.00 2.73
1463 2479 6.094603 AGCATTTTGGATCTATGTTGACACTC 59.905 38.462 0.00 0.00 0.00 3.51
1472 2488 6.782082 TCTATGTTGACACTCTTGAGCTAT 57.218 37.500 0.00 0.00 0.00 2.97
1637 2654 2.739885 AAGCTTTGTTGTGTTGTGCA 57.260 40.000 0.00 0.00 0.00 4.57
1717 2734 1.067635 AGCCAAACAGCAAAATAGGCG 60.068 47.619 0.00 0.00 44.97 5.52
1733 2750 5.751243 ATAGGCGTAATTTTGTTAGGCAG 57.249 39.130 12.61 0.00 37.47 4.85
1749 2766 6.707608 TGTTAGGCAGACATGATCATCATAAC 59.292 38.462 16.13 16.13 34.28 1.89
2141 3178 9.206870 CCTTTGCAAATTCAACTAAATATGTGT 57.793 29.630 13.23 0.00 0.00 3.72
2418 3456 3.190535 ACGCCGAAGCTGAACAAAATATT 59.809 39.130 0.00 0.00 36.60 1.28
2420 3458 4.728608 CGCCGAAGCTGAACAAAATATTAC 59.271 41.667 0.00 0.00 36.60 1.89
2469 3507 2.551270 GAGGCAAATATCGCGGCG 59.449 61.111 17.70 17.70 0.00 6.46
2484 3522 1.452108 GGCGATGCCTAAGGTGCTT 60.452 57.895 0.00 0.00 46.69 3.91
2489 3527 2.559440 GATGCCTAAGGTGCTTGAGAG 58.441 52.381 0.00 0.00 0.00 3.20
2496 3534 5.435291 CCTAAGGTGCTTGAGAGAATGAAT 58.565 41.667 0.00 0.00 0.00 2.57
2511 3549 4.456911 AGAATGAATGAATGTGTTGCTCGT 59.543 37.500 0.00 0.00 0.00 4.18
2529 3567 1.202463 CGTATGGAGAAGGTGGAGCAG 60.202 57.143 0.00 0.00 0.00 4.24
2536 3574 3.416156 GAGAAGGTGGAGCAGTTGAATT 58.584 45.455 0.00 0.00 0.00 2.17
2541 3579 3.319122 AGGTGGAGCAGTTGAATTTGAAC 59.681 43.478 0.00 0.00 0.00 3.18
2564 3602 7.219484 ACATACATCCTGTTTTCCAAAGAAG 57.781 36.000 0.00 0.00 32.35 2.85
2565 3603 6.209391 ACATACATCCTGTTTTCCAAAGAAGG 59.791 38.462 0.00 0.00 32.35 3.46
2572 3610 2.882761 GTTTTCCAAAGAAGGCGGTAGT 59.117 45.455 0.00 0.00 32.35 2.73
2694 3733 4.989875 AGTAGTACTTAGGCGGGATCTA 57.010 45.455 0.00 0.00 0.00 1.98
2713 3752 7.254932 GGGATCTATTACTGACAAAGCATTGAC 60.255 40.741 8.96 2.68 38.94 3.18
2762 3801 5.527951 TGTCTCAAAATGTAACATGTTGGC 58.472 37.500 21.42 13.66 0.00 4.52
2837 3876 3.826729 GGCAGAGGGAGTAACATTTTGTT 59.173 43.478 0.00 0.00 43.88 2.83
2875 3914 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2877 3916 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2879 3918 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2881 3920 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2883 3922 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2885 3924 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2887 3926 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2891 3930 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2892 3931 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2893 3932 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2894 3933 1.136085 GTGTGTGTGTGTGTGTGTGTC 60.136 52.381 0.00 0.00 0.00 3.67
2895 3934 1.152510 GTGTGTGTGTGTGTGTGTCA 58.847 50.000 0.00 0.00 0.00 3.58
2896 3935 1.128507 GTGTGTGTGTGTGTGTGTCAG 59.871 52.381 0.00 0.00 0.00 3.51
2897 3936 1.270571 TGTGTGTGTGTGTGTGTCAGT 60.271 47.619 0.00 0.00 0.00 3.41
2898 3937 1.128507 GTGTGTGTGTGTGTGTCAGTG 59.871 52.381 0.00 0.00 0.00 3.66
2899 3938 1.270571 TGTGTGTGTGTGTGTCAGTGT 60.271 47.619 0.00 0.00 0.00 3.55
2900 3939 1.128507 GTGTGTGTGTGTGTCAGTGTG 59.871 52.381 0.00 0.00 0.00 3.82
2901 3940 1.270571 TGTGTGTGTGTGTCAGTGTGT 60.271 47.619 0.00 0.00 0.00 3.72
2912 3951 2.293122 TGTCAGTGTGTGGCTATTTTGC 59.707 45.455 0.00 0.00 0.00 3.68
2946 3985 3.072211 GCTGTGTACTCTTTGGTAACCC 58.928 50.000 0.00 0.00 0.00 4.11
2971 4010 7.910162 CCGTTTCTGAACATTATATGTGAAAGG 59.090 37.037 12.21 12.21 44.07 3.11
3016 4055 8.530311 TGTTTTGTCACCCGTAGTTCTAATATA 58.470 33.333 0.00 0.00 0.00 0.86
3025 4064 9.649167 ACCCGTAGTTCTAATATATTAATGTGC 57.351 33.333 6.63 0.00 0.00 4.57
3071 4110 4.014569 TGTGAAGCCTGTGTAATAGCAA 57.985 40.909 0.00 0.00 0.00 3.91
3109 4148 3.553511 CCTGCTAGCTGTTTTCTCATACG 59.446 47.826 17.23 0.00 0.00 3.06
3112 4151 4.805719 TGCTAGCTGTTTTCTCATACGATG 59.194 41.667 17.23 0.00 0.00 3.84
3141 4180 3.006940 TGGTCAGCATTCGGAACATTAC 58.993 45.455 0.00 0.00 29.19 1.89
3152 4200 5.134202 TCGGAACATTACGATGCTCATAT 57.866 39.130 0.00 0.00 38.89 1.78
3179 4227 8.589335 TTAAGCAGAAGTTATCGGATATCAAC 57.411 34.615 4.83 0.38 0.00 3.18
3180 4228 6.412362 AGCAGAAGTTATCGGATATCAACT 57.588 37.500 4.83 2.82 32.73 3.16
3291 4339 9.125026 ACTGTGATTATCAGTCTTTTCAGTTTT 57.875 29.630 0.00 0.00 41.52 2.43
3403 4451 4.069304 TCAAACTTAAACAGGATGGGTCG 58.931 43.478 0.00 0.00 43.62 4.79
3411 4459 0.034756 CAGGATGGGTCGTGTTGTGA 59.965 55.000 0.00 0.00 35.92 3.58
3412 4460 0.762418 AGGATGGGTCGTGTTGTGAA 59.238 50.000 0.00 0.00 0.00 3.18
3413 4461 1.351017 AGGATGGGTCGTGTTGTGAAT 59.649 47.619 0.00 0.00 0.00 2.57
3414 4462 1.468520 GGATGGGTCGTGTTGTGAATG 59.531 52.381 0.00 0.00 0.00 2.67
3415 4463 2.151202 GATGGGTCGTGTTGTGAATGT 58.849 47.619 0.00 0.00 0.00 2.71
3416 4464 1.588674 TGGGTCGTGTTGTGAATGTC 58.411 50.000 0.00 0.00 0.00 3.06
3417 4465 1.140052 TGGGTCGTGTTGTGAATGTCT 59.860 47.619 0.00 0.00 0.00 3.41
3418 4466 1.531149 GGGTCGTGTTGTGAATGTCTG 59.469 52.381 0.00 0.00 0.00 3.51
3419 4467 1.531149 GGTCGTGTTGTGAATGTCTGG 59.469 52.381 0.00 0.00 0.00 3.86
3420 4468 2.210116 GTCGTGTTGTGAATGTCTGGT 58.790 47.619 0.00 0.00 0.00 4.00
3421 4469 3.386486 GTCGTGTTGTGAATGTCTGGTA 58.614 45.455 0.00 0.00 0.00 3.25
3422 4470 3.994392 GTCGTGTTGTGAATGTCTGGTAT 59.006 43.478 0.00 0.00 0.00 2.73
3423 4471 4.451096 GTCGTGTTGTGAATGTCTGGTATT 59.549 41.667 0.00 0.00 0.00 1.89
3424 4472 5.049680 GTCGTGTTGTGAATGTCTGGTATTT 60.050 40.000 0.00 0.00 0.00 1.40
3425 4473 5.049749 TCGTGTTGTGAATGTCTGGTATTTG 60.050 40.000 0.00 0.00 0.00 2.32
3426 4474 4.917415 GTGTTGTGAATGTCTGGTATTTGC 59.083 41.667 0.00 0.00 0.00 3.68
3427 4475 4.826733 TGTTGTGAATGTCTGGTATTTGCT 59.173 37.500 0.00 0.00 0.00 3.91
3428 4476 5.156355 GTTGTGAATGTCTGGTATTTGCTG 58.844 41.667 0.00 0.00 0.00 4.41
3429 4477 4.650734 TGTGAATGTCTGGTATTTGCTGA 58.349 39.130 0.00 0.00 0.00 4.26
3430 4478 5.069318 TGTGAATGTCTGGTATTTGCTGAA 58.931 37.500 0.00 0.00 0.00 3.02
3431 4479 5.711506 TGTGAATGTCTGGTATTTGCTGAAT 59.288 36.000 0.00 0.00 0.00 2.57
3432 4480 6.032094 GTGAATGTCTGGTATTTGCTGAATG 58.968 40.000 0.00 0.00 0.00 2.67
3433 4481 4.644103 ATGTCTGGTATTTGCTGAATGC 57.356 40.909 0.00 0.00 43.25 3.56
3443 4491 3.181526 GCTGAATGCAGGGCTTACT 57.818 52.632 1.96 0.00 42.53 2.24
3444 4492 1.467920 GCTGAATGCAGGGCTTACTT 58.532 50.000 1.96 0.00 42.53 2.24
3445 4493 1.821136 GCTGAATGCAGGGCTTACTTT 59.179 47.619 1.96 0.00 42.53 2.66
3446 4494 2.159324 GCTGAATGCAGGGCTTACTTTC 60.159 50.000 1.96 0.00 42.53 2.62
3447 4495 3.350833 CTGAATGCAGGGCTTACTTTCT 58.649 45.455 0.00 0.00 38.51 2.52
3448 4496 3.084039 TGAATGCAGGGCTTACTTTCTG 58.916 45.455 0.00 0.00 0.00 3.02
3450 4498 2.184323 GCAGGGCTTACTTTCTGCC 58.816 57.895 0.00 0.00 44.70 4.85
3459 4507 6.709018 GGCTTACTTTCTGCCCAATAATAA 57.291 37.500 0.00 0.00 40.71 1.40
3460 4508 6.504398 GGCTTACTTTCTGCCCAATAATAAC 58.496 40.000 0.00 0.00 40.71 1.89
3461 4509 6.321435 GGCTTACTTTCTGCCCAATAATAACT 59.679 38.462 0.00 0.00 40.71 2.24
3462 4510 7.196331 GCTTACTTTCTGCCCAATAATAACTG 58.804 38.462 0.00 0.00 0.00 3.16
3463 4511 7.639113 TTACTTTCTGCCCAATAATAACTGG 57.361 36.000 0.00 0.00 0.00 4.00
3464 4512 5.580022 ACTTTCTGCCCAATAATAACTGGT 58.420 37.500 0.00 0.00 0.00 4.00
3465 4513 5.418840 ACTTTCTGCCCAATAATAACTGGTG 59.581 40.000 0.00 0.00 0.00 4.17
3466 4514 4.584638 TCTGCCCAATAATAACTGGTGT 57.415 40.909 0.00 0.00 0.00 4.16
3467 4515 4.269183 TCTGCCCAATAATAACTGGTGTG 58.731 43.478 0.00 0.00 0.00 3.82
3471 4519 4.141959 GCCCAATAATAACTGGTGTGCATT 60.142 41.667 0.00 0.00 0.00 3.56
3508 4556 7.271511 TGCACATGGTTAAGAAAGAAAATTGT 58.728 30.769 0.00 0.00 0.00 2.71
3567 4615 1.003118 AGTGGCCGTTTGCATAGAGAA 59.997 47.619 0.00 0.00 43.89 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 3.822735 CCGCTTAATCCCAATGTGATGAT 59.177 43.478 0.00 0.00 0.00 2.45
22 23 3.214328 GACCGCTTAATCCCAATGTGAT 58.786 45.455 0.00 0.00 0.00 3.06
25 26 1.065709 ACGACCGCTTAATCCCAATGT 60.066 47.619 0.00 0.00 0.00 2.71
36 37 2.069273 CTTTGAAGATCACGACCGCTT 58.931 47.619 0.00 0.00 0.00 4.68
44 45 8.862550 AAAAATCTGACAACTTTGAAGATCAC 57.137 30.769 0.00 0.00 35.58 3.06
70 71 9.208022 GTAAGATGCCTTTTAGCTTTGAAAAAT 57.792 29.630 0.00 0.00 33.94 1.82
148 151 9.465985 AATTTTATTTTGTATTCGTCGGTTTGT 57.534 25.926 0.00 0.00 0.00 2.83
210 213 2.676750 GCGATGGGTGGCATATAATCGA 60.677 50.000 21.15 0.00 39.30 3.59
219 228 3.965258 AACCTGCGATGGGTGGCA 61.965 61.111 0.00 0.00 37.13 4.92
279 289 3.867055 AAGCATGATATGACGAAAGCG 57.133 42.857 0.00 0.00 44.79 4.68
333 343 4.982999 TCTTCGGTGACTTCTAAATCTCG 58.017 43.478 0.00 0.00 0.00 4.04
439 449 3.569250 TTTTCTGTATCCTTTTGCGGC 57.431 42.857 0.00 0.00 0.00 6.53
487 498 2.038426 TCCGAGGAGAGCAATTTGACAA 59.962 45.455 0.00 0.00 0.00 3.18
501 512 0.895530 GTTGATGTGTCCTCCGAGGA 59.104 55.000 13.54 13.54 43.43 3.71
507 518 1.808945 CTTGGCAGTTGATGTGTCCTC 59.191 52.381 0.00 0.00 0.00 3.71
529 540 4.339530 CCGGATCTGTTGTCTCTCTTCATA 59.660 45.833 0.00 0.00 0.00 2.15
540 551 1.125093 TGTGTCCCCGGATCTGTTGT 61.125 55.000 0.73 0.00 0.00 3.32
550 561 0.944311 CGTGAGAGTTTGTGTCCCCG 60.944 60.000 0.00 0.00 0.00 5.73
572 583 8.366401 AGATGTATGATCTGTCATCGAAAAGAT 58.634 33.333 14.07 0.00 43.87 2.40
578 589 7.042797 TCAAAGATGTATGATCTGTCATCGA 57.957 36.000 14.07 0.00 43.87 3.59
584 595 6.841229 TCCTACCTCAAAGATGTATGATCTGT 59.159 38.462 0.00 0.00 0.00 3.41
592 603 8.388656 AGGTATTTTCCTACCTCAAAGATGTA 57.611 34.615 0.00 0.00 46.98 2.29
619 630 1.271934 CGGTGATGGCATGTTGGAAAA 59.728 47.619 3.81 0.00 0.00 2.29
620 631 0.887247 CGGTGATGGCATGTTGGAAA 59.113 50.000 3.81 0.00 0.00 3.13
637 648 3.138930 ATCGACGAGATGGTGGCGG 62.139 63.158 3.01 0.00 38.36 6.13
653 664 1.153549 GAGGAGTGGCGGTGACATC 60.154 63.158 0.00 0.00 0.00 3.06
680 691 1.319799 CCCTCCCTCTTCCCCATCT 59.680 63.158 0.00 0.00 0.00 2.90
681 692 1.772156 CCCCTCCCTCTTCCCCATC 60.772 68.421 0.00 0.00 0.00 3.51
683 694 4.038804 CCCCCTCCCTCTTCCCCA 62.039 72.222 0.00 0.00 0.00 4.96
779 988 1.463674 ATGTCATTTGAACGGAGCCC 58.536 50.000 0.00 0.00 0.00 5.19
813 1022 5.047448 TCTCGAATTCAAATGAAATTGGGCA 60.047 36.000 6.22 0.00 36.10 5.36
894 1113 2.438434 GAGGTGGGACCCGCATTG 60.438 66.667 25.42 0.00 39.75 2.82
939 1158 3.068691 CGGACCAAGGAGAGGCGA 61.069 66.667 0.00 0.00 0.00 5.54
951 1170 2.202676 CGAGCAGAGAAGCGGACC 60.203 66.667 0.00 0.00 40.15 4.46
980 1199 3.541713 GGAGCTAGGAGTGCGGGG 61.542 72.222 0.00 0.00 35.28 5.73
981 1200 3.541713 GGGAGCTAGGAGTGCGGG 61.542 72.222 0.00 0.00 35.28 6.13
982 1201 3.541713 GGGGAGCTAGGAGTGCGG 61.542 72.222 0.00 0.00 35.28 5.69
1084 1303 2.041405 GGAGGTGGAGGAGGAGGG 60.041 72.222 0.00 0.00 0.00 4.30
1221 1440 1.654743 GACGAGGCGCGATACTGTC 60.655 63.158 19.52 6.74 44.57 3.51
1261 1480 4.907034 AGCGCGCATACCGACGAG 62.907 66.667 35.10 0.00 40.02 4.18
1263 1482 3.972803 GAAGCGCGCATACCGACG 61.973 66.667 35.10 0.00 40.02 5.12
1264 1483 3.627218 GGAAGCGCGCATACCGAC 61.627 66.667 35.10 14.74 40.02 4.79
1287 1506 2.030371 GGAAACCCTAGTACCGGAGAG 58.970 57.143 9.46 0.00 0.00 3.20
1288 1507 1.683011 CGGAAACCCTAGTACCGGAGA 60.683 57.143 9.46 0.00 40.24 3.71
1330 1549 5.296780 CACTACCGGCAAATCATACAAATCT 59.703 40.000 0.00 0.00 0.00 2.40
1364 1591 2.099405 ACGGGGGCATTTTTCTATGTG 58.901 47.619 0.00 0.00 0.00 3.21
1463 2479 4.748892 TCCGTTTCTCTCAATAGCTCAAG 58.251 43.478 0.00 0.00 0.00 3.02
1472 2488 1.267121 CCTCCCTCCGTTTCTCTCAA 58.733 55.000 0.00 0.00 0.00 3.02
1637 2654 8.746530 TCCACGACTGATTATAAAGTTAGTTCT 58.253 33.333 0.00 0.00 0.00 3.01
1717 2734 7.761409 TGATCATGTCTGCCTAACAAAATTAC 58.239 34.615 0.00 0.00 0.00 1.89
1733 2750 4.151335 GCAGTCGGTTATGATGATCATGTC 59.849 45.833 17.74 9.98 37.70 3.06
1749 2766 2.162921 CTGTTTCACGCTGCAGTCGG 62.163 60.000 26.36 18.03 0.00 4.79
2141 3178 5.011431 ACTTCTGAGTTCTGATGATGTGACA 59.989 40.000 0.00 0.00 29.87 3.58
2418 3456 8.276252 ACTTGAACAACTTTAGCTTTTCAGTA 57.724 30.769 0.00 0.00 0.00 2.74
2420 3458 6.693113 GGACTTGAACAACTTTAGCTTTTCAG 59.307 38.462 0.00 0.00 0.00 3.02
2469 3507 2.169352 TCTCTCAAGCACCTTAGGCATC 59.831 50.000 0.00 0.00 0.00 3.91
2475 3513 6.053632 TCATTCATTCTCTCAAGCACCTTA 57.946 37.500 0.00 0.00 0.00 2.69
2481 3519 6.192234 ACACATTCATTCATTCTCTCAAGC 57.808 37.500 0.00 0.00 0.00 4.01
2484 3522 5.708697 AGCAACACATTCATTCATTCTCTCA 59.291 36.000 0.00 0.00 0.00 3.27
2489 3527 4.726416 ACGAGCAACACATTCATTCATTC 58.274 39.130 0.00 0.00 0.00 2.67
2496 3534 3.056179 TCTCCATACGAGCAACACATTCA 60.056 43.478 0.00 0.00 38.62 2.57
2511 3549 2.237143 CAACTGCTCCACCTTCTCCATA 59.763 50.000 0.00 0.00 0.00 2.74
2564 3602 2.124903 CACGATATCAACACTACCGCC 58.875 52.381 3.12 0.00 0.00 6.13
2565 3603 1.521423 GCACGATATCAACACTACCGC 59.479 52.381 3.12 0.00 0.00 5.68
2572 3610 5.940192 AAAACAGAAGCACGATATCAACA 57.060 34.783 3.12 0.00 0.00 3.33
2694 3733 8.575589 TGTAAATGTCAATGCTTTGTCAGTAAT 58.424 29.630 15.23 4.66 35.01 1.89
2762 3801 5.551760 ACTTGAATCAGGCTATTTCAACG 57.448 39.130 15.94 14.36 35.16 4.10
2798 3837 7.054124 CCCTCTGCCTAAAAATGTAAGACATA 58.946 38.462 0.00 0.00 37.97 2.29
2813 3852 4.288626 ACAAAATGTTACTCCCTCTGCCTA 59.711 41.667 0.00 0.00 0.00 3.93
2816 3855 4.518970 TGAACAAAATGTTACTCCCTCTGC 59.481 41.667 0.00 0.00 41.28 4.26
2837 3876 9.230122 ACACACACATTGATTAAATACATCTGA 57.770 29.630 0.00 0.00 0.00 3.27
2854 3893 1.468127 CACACACACACACACACACAT 59.532 47.619 0.00 0.00 0.00 3.21
2875 3914 1.152510 GACACACACACACACACACA 58.847 50.000 0.00 0.00 0.00 3.72
2877 3916 1.270571 ACTGACACACACACACACACA 60.271 47.619 0.00 0.00 0.00 3.72
2879 3918 1.270571 ACACTGACACACACACACACA 60.271 47.619 0.00 0.00 0.00 3.72
2881 3920 1.270571 ACACACTGACACACACACACA 60.271 47.619 0.00 0.00 0.00 3.72
2883 3922 1.437625 CACACACTGACACACACACA 58.562 50.000 0.00 0.00 0.00 3.72
2885 3924 1.024046 GCCACACACTGACACACACA 61.024 55.000 0.00 0.00 0.00 3.72
2887 3926 0.827368 TAGCCACACACTGACACACA 59.173 50.000 0.00 0.00 0.00 3.72
2891 3930 2.293122 GCAAAATAGCCACACACTGACA 59.707 45.455 0.00 0.00 0.00 3.58
2892 3931 2.554032 AGCAAAATAGCCACACACTGAC 59.446 45.455 0.00 0.00 34.23 3.51
2893 3932 2.813754 GAGCAAAATAGCCACACACTGA 59.186 45.455 0.00 0.00 34.23 3.41
2894 3933 2.553602 TGAGCAAAATAGCCACACACTG 59.446 45.455 0.00 0.00 34.23 3.66
2895 3934 2.554032 GTGAGCAAAATAGCCACACACT 59.446 45.455 0.00 0.00 39.95 3.55
2896 3935 2.554032 AGTGAGCAAAATAGCCACACAC 59.446 45.455 13.23 0.00 41.42 3.82
2897 3936 2.862541 AGTGAGCAAAATAGCCACACA 58.137 42.857 13.23 0.00 41.42 3.72
2898 3937 3.503748 AGAAGTGAGCAAAATAGCCACAC 59.496 43.478 0.00 0.00 40.25 3.82
2899 3938 3.753272 GAGAAGTGAGCAAAATAGCCACA 59.247 43.478 0.00 0.00 37.82 4.17
2900 3939 3.127721 GGAGAAGTGAGCAAAATAGCCAC 59.872 47.826 0.00 0.00 36.55 5.01
2901 3940 3.244875 TGGAGAAGTGAGCAAAATAGCCA 60.245 43.478 0.00 0.00 34.23 4.75
2912 3951 0.683973 ACACAGCCTGGAGAAGTGAG 59.316 55.000 0.00 0.00 34.47 3.51
2946 3985 7.429340 GCCTTTCACATATAATGTTCAGAAACG 59.571 37.037 0.00 0.00 42.70 3.60
2971 4010 0.676782 AGGAACATGTACCGCCTTGC 60.677 55.000 0.00 0.00 0.00 4.01
3016 4055 6.568462 GCAATGTTAGCCTATCGCACATTAAT 60.568 38.462 0.47 0.00 40.35 1.40
3071 4110 8.748412 CAGCTAGCAGGAGAATTAAGAGTATAT 58.252 37.037 18.83 0.00 0.00 0.86
3109 4148 4.494690 CGAATGCTGACCACATTGTACATC 60.495 45.833 0.00 0.00 37.85 3.06
3112 4151 2.095853 CCGAATGCTGACCACATTGTAC 59.904 50.000 0.00 0.00 37.85 2.90
3141 4180 7.824704 ACTTCTGCTTAATATATGAGCATCG 57.175 36.000 18.92 11.74 44.56 3.84
3247 4295 7.891498 TCACAGTGCTAGAAATACTACCATA 57.109 36.000 0.00 0.00 0.00 2.74
3249 4297 6.791867 ATCACAGTGCTAGAAATACTACCA 57.208 37.500 0.00 0.00 0.00 3.25
3291 4339 6.881065 AGCTCTGAAAAGTATTCATGTTGCTA 59.119 34.615 0.00 0.00 0.00 3.49
3293 4341 5.947443 AGCTCTGAAAAGTATTCATGTTGC 58.053 37.500 0.00 0.00 0.00 4.17
3377 4425 5.301805 ACCCATCCTGTTTAAGTTTGAACTG 59.698 40.000 0.00 1.57 39.66 3.16
3403 4451 4.917415 GCAAATACCAGACATTCACAACAC 59.083 41.667 0.00 0.00 0.00 3.32
3411 4459 5.002464 GCATTCAGCAAATACCAGACATT 57.998 39.130 0.00 0.00 44.79 2.71
3412 4460 4.644103 GCATTCAGCAAATACCAGACAT 57.356 40.909 0.00 0.00 44.79 3.06
3425 4473 1.467920 AAGTAAGCCCTGCATTCAGC 58.532 50.000 0.00 0.00 45.96 4.26
3426 4474 3.128242 CAGAAAGTAAGCCCTGCATTCAG 59.872 47.826 0.00 0.00 40.02 3.02
3427 4475 3.084039 CAGAAAGTAAGCCCTGCATTCA 58.916 45.455 0.00 0.00 0.00 2.57
3428 4476 3.772060 CAGAAAGTAAGCCCTGCATTC 57.228 47.619 0.00 0.00 0.00 2.67
3437 4485 7.196331 CAGTTATTATTGGGCAGAAAGTAAGC 58.804 38.462 0.00 0.00 0.00 3.09
3438 4486 7.339466 ACCAGTTATTATTGGGCAGAAAGTAAG 59.661 37.037 0.00 0.00 38.82 2.34
3439 4487 7.122055 CACCAGTTATTATTGGGCAGAAAGTAA 59.878 37.037 0.00 0.00 38.82 2.24
3440 4488 6.601613 CACCAGTTATTATTGGGCAGAAAGTA 59.398 38.462 0.00 0.00 38.82 2.24
3441 4489 5.418840 CACCAGTTATTATTGGGCAGAAAGT 59.581 40.000 0.00 0.00 38.82 2.66
3442 4490 5.418840 ACACCAGTTATTATTGGGCAGAAAG 59.581 40.000 0.00 0.00 38.82 2.62
3443 4491 5.184864 CACACCAGTTATTATTGGGCAGAAA 59.815 40.000 0.00 0.00 38.82 2.52
3444 4492 4.704540 CACACCAGTTATTATTGGGCAGAA 59.295 41.667 0.00 0.00 38.82 3.02
3445 4493 4.269183 CACACCAGTTATTATTGGGCAGA 58.731 43.478 0.00 0.00 38.82 4.26
3446 4494 3.181487 GCACACCAGTTATTATTGGGCAG 60.181 47.826 0.00 0.00 38.82 4.85
3447 4495 2.757868 GCACACCAGTTATTATTGGGCA 59.242 45.455 0.00 0.00 38.82 5.36
3448 4496 2.757868 TGCACACCAGTTATTATTGGGC 59.242 45.455 0.00 0.00 38.82 5.36
3449 4497 5.126869 TCAATGCACACCAGTTATTATTGGG 59.873 40.000 0.00 0.00 38.82 4.12
3450 4498 6.206395 TCAATGCACACCAGTTATTATTGG 57.794 37.500 0.00 0.00 40.38 3.16
3451 4499 9.970395 ATTATCAATGCACACCAGTTATTATTG 57.030 29.630 0.00 0.00 0.00 1.90
3453 4501 9.578576 AGATTATCAATGCACACCAGTTATTAT 57.421 29.630 0.00 0.00 0.00 1.28
3454 4502 8.978874 AGATTATCAATGCACACCAGTTATTA 57.021 30.769 0.00 0.00 0.00 0.98
3455 4503 7.557358 TGAGATTATCAATGCACACCAGTTATT 59.443 33.333 0.00 0.00 34.02 1.40
3456 4504 7.056006 TGAGATTATCAATGCACACCAGTTAT 58.944 34.615 0.00 0.00 34.02 1.89
3457 4505 6.413892 TGAGATTATCAATGCACACCAGTTA 58.586 36.000 0.00 0.00 34.02 2.24
3458 4506 5.255687 TGAGATTATCAATGCACACCAGTT 58.744 37.500 0.00 0.00 34.02 3.16
3459 4507 4.847198 TGAGATTATCAATGCACACCAGT 58.153 39.130 0.00 0.00 34.02 4.00
3460 4508 6.206498 CAATGAGATTATCAATGCACACCAG 58.794 40.000 0.00 0.00 42.53 4.00
3461 4509 6.139048 CAATGAGATTATCAATGCACACCA 57.861 37.500 0.00 0.00 42.53 4.17
3471 4519 7.774625 TCTTAACCATGTGCAATGAGATTATCA 59.225 33.333 9.56 0.00 43.70 2.15
3548 4596 1.398390 CTTCTCTATGCAAACGGCCAC 59.602 52.381 2.24 0.00 43.89 5.01


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

AutoCloner maintained by Alex Coulton.