Multiple sequence alignment - TraesCS4A01G406500

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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 TraesCS4A01G406500 chr4A 100.000 3568 0 0 1 3568 679268957 679272524 0.000000e+00 6589
1 TraesCS4A01G406500 chr4B 92.284 1970 120 22 1548 3494 594868831 594870791 0.000000e+00 2767
2 TraesCS4A01G406500 chr4B 92.910 818 39 8 735 1549 594867969 594868770 0.000000e+00 1171
3 TraesCS4A01G406500 chr7D 90.336 1966 134 25 1549 3494 78497910 78499839 0.000000e+00 2527
4 TraesCS4A01G406500 chr7D 92.593 864 36 10 664 1502 78497044 78497904 0.000000e+00 1216
5 TraesCS4A01G406500 chr7D 85.851 629 71 13 3 622 78496426 78497045 0.000000e+00 652
6 TraesCS4A01G406500 chr4D 94.513 1622 78 7 1548 3164 472511837 472513452 0.000000e+00 2492
7 TraesCS4A01G406500 chr4D 96.165 339 10 3 933 1271 472511389 472511724 5.210000e-153 551
8 TraesCS4A01G406500 chr4D 82.482 548 59 20 3 519 472501467 472502008 2.530000e-121 446
9 TraesCS4A01G406500 chr4D 80.893 403 56 11 3162 3561 472517365 472517749 7.490000e-77 298
10 TraesCS4A01G406500 chr4D 94.565 92 5 0 520 611 472502162 472502253 3.710000e-30 143
11 TraesCS4A01G406500 chr2D 86.497 511 48 5 1048 1549 284553776 284553278 3.130000e-150 542
12 TraesCS4A01G406500 chr6B 79.143 537 34 28 2335 2822 712263928 712263421 2.080000e-77 300


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 TraesCS4A01G406500 chr4A 679268957 679272524 3567 False 6589.000000 6589 100.000000 1 3568 1 chr4A.!!$F1 3567
1 TraesCS4A01G406500 chr4B 594867969 594870791 2822 False 1969.000000 2767 92.597000 735 3494 2 chr4B.!!$F1 2759
2 TraesCS4A01G406500 chr7D 78496426 78499839 3413 False 1465.000000 2527 89.593333 3 3494 3 chr7D.!!$F1 3491
3 TraesCS4A01G406500 chr4D 472511389 472517749 6360 False 1113.666667 2492 90.523667 933 3561 3 chr4D.!!$F2 2628
4 TraesCS4A01G406500 chr4D 472501467 472502253 786 False 294.500000 446 88.523500 3 611 2 chr4D.!!$F1 608
5 TraesCS4A01G406500 chr6B 712263421 712263928 507 True 300.000000 300 79.143000 2335 2822 1 chr6B.!!$R1 487

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
146 147 0.537188 ATGTTGGAGCCACTCTACGG 59.463 55.0 0.0 0.0 0.0 4.02 F
1422 1630 0.107945 GTTCAGGTAGCTCAGCCCAG 60.108 60.0 0.0 0.0 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1970 2250 0.246635 GGGTGTAGAAAGCGAGCTCA 59.753 55.0 15.4 0.0 0.00 4.26 R
3352 7621 0.249868 TTCCAGAGAGTGCAACACCG 60.250 55.0 0.0 0.0 41.43 4.94 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
54 55 6.042666 AGAGCTAGATGAGGGTTTAGGAAATC 59.957 42.308 0.00 0.00 0.00 2.17
58 59 6.838401 AGATGAGGGTTTAGGAAATCAGAT 57.162 37.500 0.00 0.00 0.00 2.90
60 61 7.972301 AGATGAGGGTTTAGGAAATCAGATAG 58.028 38.462 0.00 0.00 0.00 2.08
64 65 5.369993 AGGGTTTAGGAAATCAGATAGGGTC 59.630 44.000 0.00 0.00 0.00 4.46
65 66 5.456330 GGGTTTAGGAAATCAGATAGGGTCC 60.456 48.000 0.00 0.00 0.00 4.46
66 67 5.298347 GTTTAGGAAATCAGATAGGGTCCG 58.702 45.833 0.00 0.00 0.00 4.79
67 68 3.330126 AGGAAATCAGATAGGGTCCGA 57.670 47.619 0.00 0.00 0.00 4.55
68 69 3.863086 AGGAAATCAGATAGGGTCCGAT 58.137 45.455 0.00 0.00 0.00 4.18
69 70 4.235372 AGGAAATCAGATAGGGTCCGATT 58.765 43.478 0.00 0.00 35.88 3.34
97 98 4.646572 ACCTCTGCCTTTATATTGCTAGC 58.353 43.478 8.10 8.10 0.00 3.42
98 99 4.103153 ACCTCTGCCTTTATATTGCTAGCA 59.897 41.667 14.93 14.93 0.00 3.49
121 122 9.836076 AGCATTTTTAAAGACGTTAGGATTTAC 57.164 29.630 0.00 0.00 0.00 2.01
130 131 8.937634 AAGACGTTAGGATTTACGAAATATGT 57.062 30.769 0.00 0.00 40.03 2.29
132 133 8.814235 AGACGTTAGGATTTACGAAATATGTTG 58.186 33.333 0.00 0.00 40.03 3.33
136 137 6.619801 AGGATTTACGAAATATGTTGGAGC 57.380 37.500 0.00 0.00 0.00 4.70
138 139 5.298276 GGATTTACGAAATATGTTGGAGCCA 59.702 40.000 0.00 0.00 0.00 4.75
144 145 4.508124 CGAAATATGTTGGAGCCACTCTAC 59.492 45.833 0.00 0.00 0.00 2.59
146 147 0.537188 ATGTTGGAGCCACTCTACGG 59.463 55.000 0.00 0.00 0.00 4.02
155 156 2.067013 GCCACTCTACGGTTTCTTGTC 58.933 52.381 0.00 0.00 0.00 3.18
156 157 2.685100 CCACTCTACGGTTTCTTGTCC 58.315 52.381 0.00 0.00 0.00 4.02
158 159 2.299297 CACTCTACGGTTTCTTGTCCCT 59.701 50.000 0.00 0.00 0.00 4.20
162 163 4.383173 TCTACGGTTTCTTGTCCCTTTTC 58.617 43.478 0.00 0.00 0.00 2.29
163 164 2.304092 ACGGTTTCTTGTCCCTTTTCC 58.696 47.619 0.00 0.00 0.00 3.13
164 166 1.611977 CGGTTTCTTGTCCCTTTTCCC 59.388 52.381 0.00 0.00 0.00 3.97
167 169 1.236708 TTCTTGTCCCTTTTCCCCCA 58.763 50.000 0.00 0.00 0.00 4.96
179 181 6.385467 TCCCTTTTCCCCCATTATTGTTTATG 59.615 38.462 0.00 0.00 0.00 1.90
180 182 6.157820 CCCTTTTCCCCCATTATTGTTTATGT 59.842 38.462 0.00 0.00 0.00 2.29
205 230 8.746751 GTTTCTTCTTCTTCTTGCAAATAACAC 58.253 33.333 0.00 0.00 0.00 3.32
221 248 9.810231 GCAAATAACACAATTTATTTTGTCTGG 57.190 29.630 0.00 0.00 38.87 3.86
226 253 8.761575 AACACAATTTATTTTGTCTGGCTATG 57.238 30.769 0.00 0.00 37.73 2.23
228 255 8.028938 ACACAATTTATTTTGTCTGGCTATGTC 58.971 33.333 0.00 0.00 37.73 3.06
231 258 8.461222 CAATTTATTTTGTCTGGCTATGTCTCA 58.539 33.333 0.00 0.00 0.00 3.27
342 369 8.791327 AAACCATGAAGTTTTTCAATGTCTTT 57.209 26.923 0.00 0.00 45.82 2.52
344 371 8.424274 ACCATGAAGTTTTTCAATGTCTTTTC 57.576 30.769 0.00 0.00 45.82 2.29
451 485 3.066621 GTGCTCCACATGAACACTTTCAA 59.933 43.478 0.00 0.00 45.01 2.69
453 487 4.341806 TGCTCCACATGAACACTTTCAATT 59.658 37.500 0.00 0.00 45.01 2.32
561 750 5.178623 TCTGATTGTTGTGATACACCGAAAC 59.821 40.000 0.00 0.00 32.73 2.78
567 756 2.801679 TGTGATACACCGAAACGTTTCC 59.198 45.455 29.95 17.07 32.73 3.13
629 818 7.521509 AGTACTATCGAATTACTTTGTGTGC 57.478 36.000 0.00 0.00 0.00 4.57
630 819 7.094631 AGTACTATCGAATTACTTTGTGTGCA 58.905 34.615 0.00 0.00 0.00 4.57
631 820 6.795098 ACTATCGAATTACTTTGTGTGCAA 57.205 33.333 0.00 0.00 0.00 4.08
632 821 7.377766 ACTATCGAATTACTTTGTGTGCAAT 57.622 32.000 0.00 0.00 34.18 3.56
633 822 7.464358 ACTATCGAATTACTTTGTGTGCAATC 58.536 34.615 0.00 0.00 34.18 2.67
634 823 5.940192 TCGAATTACTTTGTGTGCAATCT 57.060 34.783 0.00 0.00 34.18 2.40
635 824 5.927030 TCGAATTACTTTGTGTGCAATCTC 58.073 37.500 0.00 0.00 34.18 2.75
636 825 5.700832 TCGAATTACTTTGTGTGCAATCTCT 59.299 36.000 0.00 0.00 34.18 3.10
637 826 6.871492 TCGAATTACTTTGTGTGCAATCTCTA 59.129 34.615 0.00 0.00 34.18 2.43
638 827 6.955963 CGAATTACTTTGTGTGCAATCTCTAC 59.044 38.462 0.00 0.00 34.18 2.59
639 828 7.148573 CGAATTACTTTGTGTGCAATCTCTACT 60.149 37.037 0.00 0.00 34.18 2.57
640 829 7.986085 ATTACTTTGTGTGCAATCTCTACTT 57.014 32.000 0.00 0.00 34.18 2.24
641 830 5.679734 ACTTTGTGTGCAATCTCTACTTG 57.320 39.130 0.00 0.00 34.18 3.16
642 831 5.126067 ACTTTGTGTGCAATCTCTACTTGT 58.874 37.500 0.00 0.00 34.18 3.16
643 832 5.590259 ACTTTGTGTGCAATCTCTACTTGTT 59.410 36.000 0.00 0.00 34.18 2.83
644 833 5.673337 TTGTGTGCAATCTCTACTTGTTC 57.327 39.130 0.00 0.00 0.00 3.18
645 834 4.702831 TGTGTGCAATCTCTACTTGTTCA 58.297 39.130 0.00 0.00 0.00 3.18
646 835 5.308014 TGTGTGCAATCTCTACTTGTTCAT 58.692 37.500 0.00 0.00 0.00 2.57
647 836 5.764686 TGTGTGCAATCTCTACTTGTTCATT 59.235 36.000 0.00 0.00 0.00 2.57
648 837 6.262944 TGTGTGCAATCTCTACTTGTTCATTT 59.737 34.615 0.00 0.00 0.00 2.32
649 838 7.141363 GTGTGCAATCTCTACTTGTTCATTTT 58.859 34.615 0.00 0.00 0.00 1.82
650 839 7.649306 GTGTGCAATCTCTACTTGTTCATTTTT 59.351 33.333 0.00 0.00 0.00 1.94
689 878 7.321153 TCTACTTGTTCATCTGGTAGCTTTAC 58.679 38.462 0.00 0.00 32.49 2.01
696 885 5.312895 TCATCTGGTAGCTTTACTTTTGCA 58.687 37.500 0.00 0.00 0.00 4.08
700 889 5.048782 TCTGGTAGCTTTACTTTTGCACATG 60.049 40.000 0.00 0.00 0.00 3.21
718 907 6.593382 TGCACATGTAGCAAAAAGAAAGTTTT 59.407 30.769 17.06 0.00 39.39 2.43
720 909 7.401080 CACATGTAGCAAAAAGAAAGTTTTGG 58.599 34.615 0.00 0.00 44.90 3.28
1178 1374 1.804326 CTTACGCAAGCGCCTACGT 60.804 57.895 20.45 20.45 44.19 3.57
1334 1534 2.804527 GTTTCGTTCCTGGACAACTACC 59.195 50.000 0.00 0.00 0.00 3.18
1353 1561 1.482621 CGTCAATCGGTGATGCCTCG 61.483 60.000 0.00 0.00 38.90 4.63
1363 1571 1.741770 GATGCCTCGTTGCGGTTCT 60.742 57.895 0.00 0.00 0.00 3.01
1372 1580 2.734606 TCGTTGCGGTTCTGTCAATTAG 59.265 45.455 0.00 0.00 0.00 1.73
1385 1593 2.618241 GTCAATTAGCGAATGATGCCCA 59.382 45.455 0.00 0.00 0.00 5.36
1412 1620 2.239681 AGGAGGACAGGTTCAGGTAG 57.760 55.000 0.00 0.00 0.00 3.18
1422 1630 0.107945 GTTCAGGTAGCTCAGCCCAG 60.108 60.000 0.00 0.00 0.00 4.45
1427 1635 2.285668 TAGCTCAGCCCAGGCCTT 60.286 61.111 0.00 0.00 43.17 4.35
1468 1685 3.594603 TTTCTTCTCTTCCTAGCCGTG 57.405 47.619 0.00 0.00 0.00 4.94
1484 1701 4.939399 TGCAGCGATGTATGCACT 57.061 50.000 1.22 0.00 46.97 4.40
1491 1708 3.056962 CAGCGATGTATGCACTAGAGGAT 60.057 47.826 0.00 0.00 33.85 3.24
1504 1721 4.618912 CACTAGAGGATTCATTCGTATGCG 59.381 45.833 0.00 0.00 39.92 4.73
1505 1722 4.519350 ACTAGAGGATTCATTCGTATGCGA 59.481 41.667 0.30 0.30 46.36 5.10
1526 1743 2.299013 ACGATGCAGTGTTCCAGTAGAA 59.701 45.455 0.00 0.00 0.00 2.10
1570 1850 1.312371 GCCGCCTTATTTGTCAGCCA 61.312 55.000 0.00 0.00 0.00 4.75
1755 2035 0.179048 CGACCAAGCCATGCTGGATA 60.179 55.000 12.25 0.00 40.96 2.59
1760 2040 1.331756 CAAGCCATGCTGGATAACGAC 59.668 52.381 6.40 0.00 40.96 4.34
1766 2046 3.305403 CCATGCTGGATAACGACGATACT 60.305 47.826 0.00 0.00 40.96 2.12
1784 2064 5.277828 CGATACTGACGATGACTATGTGGAA 60.278 44.000 0.00 0.00 0.00 3.53
1850 2130 2.335316 AGAAGGCCGTGTACAACAAA 57.665 45.000 0.00 0.00 0.00 2.83
1919 2199 0.399454 ACTGGATGCACAAGCTCACT 59.601 50.000 0.00 0.00 42.74 3.41
1970 2250 2.494471 TGTGAACGATGATCTTACCCGT 59.506 45.455 0.00 0.00 34.74 5.28
2090 2370 1.137872 GCGGAGATGGTCAAGACTGAT 59.862 52.381 0.00 0.00 33.05 2.90
2246 2526 3.054508 CCAAGGAGAAGAAGGAGAGCATT 60.055 47.826 0.00 0.00 0.00 3.56
2411 2694 1.079127 TGGTCTTGCTAAGCGAGGC 60.079 57.895 0.00 0.00 43.32 4.70
2462 2749 3.694538 AAGTTTGGGCATGGCGGC 61.695 61.111 13.76 0.00 40.20 6.53
2692 2993 4.808042 CTTGAGGTATGGAATTTGGGGAT 58.192 43.478 0.00 0.00 0.00 3.85
2749 3074 6.326323 TGTGCTATTCTCCATAAGATGTGGTA 59.674 38.462 0.00 0.00 37.96 3.25
2754 3079 4.795469 TCTCCATAAGATGTGGTACCGTA 58.205 43.478 7.57 0.00 37.96 4.02
2901 3242 4.387862 CGTTCTGGAGCGTTTTATTGTACT 59.612 41.667 0.00 0.00 0.00 2.73
2908 3249 5.063060 GGAGCGTTTTATTGTACTAGTGTGG 59.937 44.000 5.39 0.00 0.00 4.17
2922 3264 6.115448 ACTAGTGTGGAAGCTAAAGTGAAT 57.885 37.500 0.00 0.00 0.00 2.57
2927 3269 3.127721 GTGGAAGCTAAAGTGAATGGAGC 59.872 47.826 0.00 0.00 0.00 4.70
2987 3329 7.227512 AGTCTTGGTTTCTCAAGTTATGTTCTG 59.772 37.037 4.79 0.00 43.25 3.02
3063 3407 3.679389 TCATCCTCCTTTTCTGCTGTTC 58.321 45.455 0.00 0.00 0.00 3.18
3112 3456 6.693545 CGTACTCCAATCAGACTAAACAGATC 59.306 42.308 0.00 0.00 0.00 2.75
3129 3474 2.426024 AGATCTGGTTGTGATGCATTGC 59.574 45.455 0.00 0.46 0.00 3.56
3143 3488 4.114058 TGCATTGCTCTTTCTTATTGCC 57.886 40.909 10.49 0.00 0.00 4.52
3227 7487 6.391227 AACAACTTTTGCATTAGCTACAGT 57.609 33.333 0.00 0.00 37.96 3.55
3228 7488 7.308348 GGAACAACTTTTGCATTAGCTACAGTA 60.308 37.037 0.00 0.00 35.90 2.74
3229 7489 6.899114 ACAACTTTTGCATTAGCTACAGTAC 58.101 36.000 0.00 0.00 35.90 2.73
3230 7490 6.072673 ACAACTTTTGCATTAGCTACAGTACC 60.073 38.462 0.00 0.00 35.90 3.34
3231 7491 5.556915 ACTTTTGCATTAGCTACAGTACCA 58.443 37.500 0.00 0.00 42.74 3.25
3232 7492 6.001460 ACTTTTGCATTAGCTACAGTACCAA 58.999 36.000 0.00 0.00 42.74 3.67
3233 7493 6.659242 ACTTTTGCATTAGCTACAGTACCAAT 59.341 34.615 0.00 0.00 42.74 3.16
3234 7494 7.827236 ACTTTTGCATTAGCTACAGTACCAATA 59.173 33.333 0.00 0.00 42.74 1.90
3264 7532 0.649475 GAGCTACACTGCTTGCGATG 59.351 55.000 0.00 0.00 44.17 3.84
3265 7533 0.247460 AGCTACACTGCTTGCGATGA 59.753 50.000 0.00 0.00 40.93 2.92
3286 7554 6.579666 TGAGAATGCATATGCCTAAATTCC 57.420 37.500 24.54 17.66 41.18 3.01
3298 7567 3.758554 GCCTAAATTCCTCAAGTTGCAGA 59.241 43.478 0.00 0.00 0.00 4.26
3312 7581 2.493278 GTTGCAGATTGGCTGGTTATGT 59.507 45.455 0.00 0.00 45.03 2.29
3315 7584 3.019564 GCAGATTGGCTGGTTATGTCTT 58.980 45.455 0.00 0.00 45.03 3.01
3316 7585 3.181493 GCAGATTGGCTGGTTATGTCTTG 60.181 47.826 0.00 0.00 45.03 3.02
3318 7587 4.460382 CAGATTGGCTGGTTATGTCTTGTT 59.540 41.667 0.00 0.00 41.07 2.83
3319 7588 4.460382 AGATTGGCTGGTTATGTCTTGTTG 59.540 41.667 0.00 0.00 0.00 3.33
3328 7597 5.982516 TGGTTATGTCTTGTTGATGTTTTGC 59.017 36.000 0.00 0.00 0.00 3.68
3330 7599 4.942761 ATGTCTTGTTGATGTTTTGCCT 57.057 36.364 0.00 0.00 0.00 4.75
3333 7602 5.108517 TGTCTTGTTGATGTTTTGCCTTTC 58.891 37.500 0.00 0.00 0.00 2.62
3339 7608 6.815089 TGTTGATGTTTTGCCTTTCTTATGT 58.185 32.000 0.00 0.00 0.00 2.29
3346 7615 5.726980 TTTGCCTTTCTTATGTGATTGCT 57.273 34.783 0.00 0.00 0.00 3.91
3348 7617 6.832520 TTGCCTTTCTTATGTGATTGCTTA 57.167 33.333 0.00 0.00 0.00 3.09
3352 7621 6.199719 GCCTTTCTTATGTGATTGCTTATTGC 59.800 38.462 0.00 0.00 43.25 3.56
3354 7623 5.422666 TCTTATGTGATTGCTTATTGCGG 57.577 39.130 0.00 0.00 46.63 5.69
3359 7628 2.916716 GTGATTGCTTATTGCGGTGTTG 59.083 45.455 0.00 0.00 46.63 3.33
3376 7647 4.083271 GGTGTTGCACTCTCTGGAAAATAC 60.083 45.833 0.00 0.00 30.97 1.89
3394 7665 8.827677 GGAAAATACTGGCACTATAACTTACAG 58.172 37.037 0.00 0.00 0.00 2.74
3401 7672 3.805207 CACTATAACTTACAGTGCCCCC 58.195 50.000 0.00 0.00 33.86 5.40
3403 7674 4.045022 ACTATAACTTACAGTGCCCCCAT 58.955 43.478 0.00 0.00 0.00 4.00
3404 7675 3.577805 ATAACTTACAGTGCCCCCATC 57.422 47.619 0.00 0.00 0.00 3.51
3405 7676 1.372501 AACTTACAGTGCCCCCATCT 58.627 50.000 0.00 0.00 0.00 2.90
3409 7680 3.332485 ACTTACAGTGCCCCCATCTTTTA 59.668 43.478 0.00 0.00 0.00 1.52
3411 7682 1.710809 ACAGTGCCCCCATCTTTTACT 59.289 47.619 0.00 0.00 0.00 2.24
3418 7689 7.123547 CAGTGCCCCCATCTTTTACTATTTTTA 59.876 37.037 0.00 0.00 0.00 1.52
3421 7692 7.123547 TGCCCCCATCTTTTACTATTTTTAGTG 59.876 37.037 0.00 0.00 0.00 2.74
3507 7783 3.352648 GGCCTGATAAAGCCTAACAACA 58.647 45.455 0.00 0.00 46.14 3.33
3508 7784 3.378427 GGCCTGATAAAGCCTAACAACAG 59.622 47.826 0.00 0.00 46.14 3.16
3512 7788 6.017852 GCCTGATAAAGCCTAACAACAGATAC 60.018 42.308 0.00 0.00 0.00 2.24
3532 7808 9.069078 CAGATACACTGTTTTATGCTGAAAATG 57.931 33.333 0.00 0.00 41.30 2.32
3533 7809 7.756722 AGATACACTGTTTTATGCTGAAAATGC 59.243 33.333 0.00 0.00 31.29 3.56
3537 7813 5.928264 ACTGTTTTATGCTGAAAATGCTTCC 59.072 36.000 0.64 0.00 31.29 3.46
3539 7815 6.286758 TGTTTTATGCTGAAAATGCTTCCAA 58.713 32.000 0.64 0.00 31.29 3.53
3543 7819 4.339872 TGCTGAAAATGCTTCCAAATGT 57.660 36.364 0.00 0.00 0.00 2.71
3545 7821 5.124645 TGCTGAAAATGCTTCCAAATGTTT 58.875 33.333 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 8.965819 CCTCATCTAGCTCTAATATTTCTAGCA 58.034 37.037 14.88 4.80 35.63 3.49
18 19 9.474313 ACCCTCATCTAGCTCTAATATTTCTAG 57.526 37.037 0.00 1.12 0.00 2.43
108 109 7.765360 TCCAACATATTTCGTAAATCCTAACGT 59.235 33.333 0.00 0.00 39.99 3.99
121 122 3.535561 AGAGTGGCTCCAACATATTTCG 58.464 45.455 0.00 0.00 0.00 3.46
130 131 1.001633 GAAACCGTAGAGTGGCTCCAA 59.998 52.381 0.00 0.00 0.00 3.53
132 133 0.896226 AGAAACCGTAGAGTGGCTCC 59.104 55.000 0.00 0.00 0.00 4.70
136 137 2.612221 GGGACAAGAAACCGTAGAGTGG 60.612 54.545 0.00 0.00 0.00 4.00
138 139 2.606378 AGGGACAAGAAACCGTAGAGT 58.394 47.619 0.00 0.00 0.00 3.24
144 145 1.611977 GGGAAAAGGGACAAGAAACCG 59.388 52.381 0.00 0.00 0.00 4.44
146 147 1.968493 GGGGGAAAAGGGACAAGAAAC 59.032 52.381 0.00 0.00 0.00 2.78
155 156 6.157820 ACATAAACAATAATGGGGGAAAAGGG 59.842 38.462 0.00 0.00 0.00 3.95
156 157 7.194112 ACATAAACAATAATGGGGGAAAAGG 57.806 36.000 0.00 0.00 0.00 3.11
158 159 8.885346 AGAAACATAAACAATAATGGGGGAAAA 58.115 29.630 0.00 0.00 0.00 2.29
162 163 8.078060 AGAAGAAACATAAACAATAATGGGGG 57.922 34.615 0.00 0.00 0.00 5.40
163 164 9.586435 GAAGAAGAAACATAAACAATAATGGGG 57.414 33.333 0.00 0.00 0.00 4.96
179 181 8.746751 GTGTTATTTGCAAGAAGAAGAAGAAAC 58.253 33.333 0.00 0.00 0.00 2.78
180 182 8.465999 TGTGTTATTTGCAAGAAGAAGAAGAAA 58.534 29.630 0.00 0.00 0.00 2.52
201 226 8.367156 ACATAGCCAGACAAAATAAATTGTGTT 58.633 29.630 0.19 0.00 43.31 3.32
205 230 8.461222 TGAGACATAGCCAGACAAAATAAATTG 58.539 33.333 0.00 0.00 36.37 2.32
312 339 7.278424 ACATTGAAAAACTTCATGGTTTCACAG 59.722 33.333 1.26 4.45 39.14 3.66
398 428 9.227777 ACTGTTCTGGTAGTTAAAAATATGTCC 57.772 33.333 0.00 0.00 0.00 4.02
409 440 4.984161 GCACGTAAACTGTTCTGGTAGTTA 59.016 41.667 0.00 0.00 36.19 2.24
418 449 2.206750 TGTGGAGCACGTAAACTGTTC 58.793 47.619 0.00 0.00 37.14 3.18
523 712 7.914871 CACAACAATCAGATTGACAGTTTACAA 59.085 33.333 26.94 0.00 42.83 2.41
526 715 7.800155 TCACAACAATCAGATTGACAGTTTA 57.200 32.000 26.94 10.83 42.83 2.01
527 716 6.698008 TCACAACAATCAGATTGACAGTTT 57.302 33.333 26.94 9.66 42.83 2.66
541 730 3.810941 ACGTTTCGGTGTATCACAACAAT 59.189 39.130 2.41 0.00 34.94 2.71
561 750 4.124238 TGAACCTAGTTGTTCTGGAAACG 58.876 43.478 11.60 0.00 43.96 3.60
567 756 5.757850 AGCTTTTGAACCTAGTTGTTCTG 57.242 39.130 11.60 3.51 43.96 3.02
613 802 5.931532 AGAGATTGCACACAAAGTAATTCG 58.068 37.500 0.00 0.00 39.77 3.34
622 811 5.122519 TGAACAAGTAGAGATTGCACACAA 58.877 37.500 0.00 0.00 40.87 3.33
624 813 5.869753 ATGAACAAGTAGAGATTGCACAC 57.130 39.130 0.00 0.00 0.00 3.82
625 814 6.882610 AAATGAACAAGTAGAGATTGCACA 57.117 33.333 0.00 0.00 0.00 4.57
650 839 6.545666 TGAACAAGTAGAGATTGCCTCAAAAA 59.454 34.615 0.00 0.00 44.40 1.94
651 840 6.061441 TGAACAAGTAGAGATTGCCTCAAAA 58.939 36.000 0.00 0.00 44.40 2.44
652 841 5.620206 TGAACAAGTAGAGATTGCCTCAAA 58.380 37.500 0.00 0.00 44.40 2.69
653 842 5.227569 TGAACAAGTAGAGATTGCCTCAA 57.772 39.130 0.00 0.00 44.40 3.02
654 843 4.890158 TGAACAAGTAGAGATTGCCTCA 57.110 40.909 0.00 0.00 44.40 3.86
655 844 5.523188 CAGATGAACAAGTAGAGATTGCCTC 59.477 44.000 0.00 0.00 42.28 4.70
656 845 5.426504 CAGATGAACAAGTAGAGATTGCCT 58.573 41.667 0.00 0.00 0.00 4.75
657 846 4.574013 CCAGATGAACAAGTAGAGATTGCC 59.426 45.833 0.00 0.00 0.00 4.52
658 847 5.181748 ACCAGATGAACAAGTAGAGATTGC 58.818 41.667 0.00 0.00 0.00 3.56
659 848 6.478344 GCTACCAGATGAACAAGTAGAGATTG 59.522 42.308 0.00 0.00 33.75 2.67
660 849 6.382570 AGCTACCAGATGAACAAGTAGAGATT 59.617 38.462 0.00 0.00 33.75 2.40
661 850 5.896678 AGCTACCAGATGAACAAGTAGAGAT 59.103 40.000 0.00 0.00 33.75 2.75
662 851 5.265191 AGCTACCAGATGAACAAGTAGAGA 58.735 41.667 0.00 0.00 33.75 3.10
663 852 5.590530 AGCTACCAGATGAACAAGTAGAG 57.409 43.478 0.00 0.00 33.75 2.43
664 853 6.360370 AAAGCTACCAGATGAACAAGTAGA 57.640 37.500 0.00 0.00 33.75 2.59
665 854 7.324178 AGTAAAGCTACCAGATGAACAAGTAG 58.676 38.462 0.00 0.00 34.78 2.57
666 855 7.241042 AGTAAAGCTACCAGATGAACAAGTA 57.759 36.000 0.00 0.00 0.00 2.24
667 856 6.115448 AGTAAAGCTACCAGATGAACAAGT 57.885 37.500 0.00 0.00 0.00 3.16
668 857 7.440523 AAAGTAAAGCTACCAGATGAACAAG 57.559 36.000 0.00 0.00 0.00 3.16
669 858 7.648142 CAAAAGTAAAGCTACCAGATGAACAA 58.352 34.615 0.00 0.00 0.00 2.83
670 859 6.293955 GCAAAAGTAAAGCTACCAGATGAACA 60.294 38.462 0.00 0.00 0.00 3.18
671 860 6.086871 GCAAAAGTAAAGCTACCAGATGAAC 58.913 40.000 0.00 0.00 0.00 3.18
696 885 7.102993 ACCAAAACTTTCTTTTTGCTACATGT 58.897 30.769 2.69 2.69 42.68 3.21
700 889 7.955324 GTCAAACCAAAACTTTCTTTTTGCTAC 59.045 33.333 3.31 0.00 42.68 3.58
720 909 5.299279 TCAGAAAACTTCAGGATGGTCAAAC 59.701 40.000 0.00 0.00 36.16 2.93
800 991 2.815647 CGGTGCTTTCTCGGGAGC 60.816 66.667 0.00 0.00 39.33 4.70
1334 1534 1.482621 CGAGGCATCACCGATTGACG 61.483 60.000 0.00 0.00 46.52 4.35
1343 1543 2.240612 GAACCGCAACGAGGCATCAC 62.241 60.000 0.00 0.00 0.00 3.06
1353 1561 2.724839 CGCTAATTGACAGAACCGCAAC 60.725 50.000 0.00 0.00 0.00 4.17
1363 1571 2.618241 GGGCATCATTCGCTAATTGACA 59.382 45.455 0.00 0.00 0.00 3.58
1372 1580 3.199551 TGCTTGGGCATCATTCGC 58.800 55.556 0.00 0.00 44.28 4.70
1385 1593 2.031495 ACCTGTCCTCCTACTTGCTT 57.969 50.000 0.00 0.00 0.00 3.91
1394 1602 0.537653 GCTACCTGAACCTGTCCTCC 59.462 60.000 0.00 0.00 0.00 4.30
1412 1620 2.191641 CTAAGGCCTGGGCTGAGC 59.808 66.667 24.69 0.00 38.81 4.26
1422 1630 4.143333 TCGGTCGCTGCTAAGGCC 62.143 66.667 0.00 0.00 37.74 5.19
1468 1685 2.057316 CTCTAGTGCATACATCGCTGC 58.943 52.381 0.00 0.00 38.87 5.25
1504 1721 2.094700 TCTACTGGAACACTGCATCGTC 60.095 50.000 0.00 0.00 0.00 4.20
1505 1722 1.893137 TCTACTGGAACACTGCATCGT 59.107 47.619 0.00 0.00 0.00 3.73
1517 1734 2.286536 GCGCAAAACGTTTTCTACTGGA 60.287 45.455 22.90 0.00 46.11 3.86
1526 1743 5.343860 GGTTGATTTATAGCGCAAAACGTTT 59.656 36.000 11.47 7.96 46.11 3.60
1640 1920 7.282224 TCCACAGAACCATATAAGAAAATTCCG 59.718 37.037 0.00 0.00 0.00 4.30
1755 2035 2.676839 AGTCATCGTCAGTATCGTCGTT 59.323 45.455 0.00 0.00 0.00 3.85
1760 2040 4.213482 TCCACATAGTCATCGTCAGTATCG 59.787 45.833 0.00 0.00 0.00 2.92
1766 2046 4.644685 TCTGATTCCACATAGTCATCGTCA 59.355 41.667 0.00 0.00 0.00 4.35
1784 2064 5.404395 TCCTCTGAATCATCATCCTCTGAT 58.596 41.667 0.00 0.00 45.78 2.90
1850 2130 1.271127 GCTTCTCAAGGAGCCCCTCT 61.271 60.000 0.00 0.00 43.48 3.69
1889 2169 1.911357 TGCATCCAGTCCACATTCTCT 59.089 47.619 0.00 0.00 0.00 3.10
1919 2199 2.290287 CCCCTGGTCATGGTCGACA 61.290 63.158 18.91 3.91 37.66 4.35
1970 2250 0.246635 GGGTGTAGAAAGCGAGCTCA 59.753 55.000 15.40 0.00 0.00 4.26
2018 2298 1.593196 TCCTGGACTGCAACTTTTCG 58.407 50.000 0.00 0.00 0.00 3.46
2090 2370 4.256110 CCTTGATCTTGTGCATGTGAGTA 58.744 43.478 0.00 0.00 0.00 2.59
2246 2526 1.613925 CTCCACTTCTTGACCGACTCA 59.386 52.381 0.00 0.00 0.00 3.41
2411 2694 5.534654 TGACCTATGGTTCTTTCCTTGTTTG 59.465 40.000 0.00 0.00 35.25 2.93
2462 2749 0.453390 GCTTCTTCATCCCTTTGCGG 59.547 55.000 0.00 0.00 0.00 5.69
2692 2993 2.042686 AGTCTTGTGTTTGAGCTGCA 57.957 45.000 1.02 0.00 0.00 4.41
2749 3074 3.945346 TCACAGGTTAAATGCATACGGT 58.055 40.909 0.00 0.00 0.00 4.83
2754 3079 3.118665 GGGCAATCACAGGTTAAATGCAT 60.119 43.478 0.00 0.00 34.14 3.96
2901 3242 5.012664 TCCATTCACTTTAGCTTCCACACTA 59.987 40.000 0.00 0.00 0.00 2.74
2908 3249 4.216257 TGTTGCTCCATTCACTTTAGCTTC 59.784 41.667 0.00 0.00 34.28 3.86
2922 3264 3.317711 CACAATTACCAAGTGTTGCTCCA 59.682 43.478 0.00 0.00 37.65 3.86
2927 3269 4.036734 AGCAGTCACAATTACCAAGTGTTG 59.963 41.667 0.00 0.00 37.65 3.33
2995 3339 4.577693 TGAGGTTTGATAGATGATGCAAGC 59.422 41.667 0.00 0.00 0.00 4.01
3009 3353 2.636647 TGTGATGCACTGAGGTTTGA 57.363 45.000 0.00 0.00 35.11 2.69
3096 3440 6.014242 TCACAACCAGATCTGTTTAGTCTGAT 60.014 38.462 21.11 0.00 41.38 2.90
3098 3442 5.541845 TCACAACCAGATCTGTTTAGTCTG 58.458 41.667 21.11 13.39 39.20 3.51
3112 3456 1.816835 AGAGCAATGCATCACAACCAG 59.183 47.619 8.35 0.00 0.00 4.00
3129 3474 4.990257 CCATGTGTGGCAATAAGAAAGAG 58.010 43.478 0.00 0.00 39.01 2.85
3143 3488 0.963856 ACTGCATCTGGCCATGTGTG 60.964 55.000 5.51 4.04 43.89 3.82
3250 7518 1.736126 CATTCTCATCGCAAGCAGTGT 59.264 47.619 0.00 0.00 37.18 3.55
3264 7532 6.432162 TGAGGAATTTAGGCATATGCATTCTC 59.568 38.462 28.07 21.76 44.36 2.87
3265 7533 6.309357 TGAGGAATTTAGGCATATGCATTCT 58.691 36.000 28.07 18.17 44.36 2.40
3286 7554 1.201647 CCAGCCAATCTGCAACTTGAG 59.798 52.381 8.99 2.22 41.50 3.02
3298 7567 4.406456 TCAACAAGACATAACCAGCCAAT 58.594 39.130 0.00 0.00 0.00 3.16
3312 7581 5.596836 AGAAAGGCAAAACATCAACAAGA 57.403 34.783 0.00 0.00 0.00 3.02
3315 7584 6.700960 CACATAAGAAAGGCAAAACATCAACA 59.299 34.615 0.00 0.00 0.00 3.33
3316 7585 6.922957 TCACATAAGAAAGGCAAAACATCAAC 59.077 34.615 0.00 0.00 0.00 3.18
3318 7587 6.647334 TCACATAAGAAAGGCAAAACATCA 57.353 33.333 0.00 0.00 0.00 3.07
3319 7588 7.412237 GCAATCACATAAGAAAGGCAAAACATC 60.412 37.037 0.00 0.00 0.00 3.06
3328 7597 6.415867 CGCAATAAGCAATCACATAAGAAAGG 59.584 38.462 0.00 0.00 46.13 3.11
3330 7599 6.127758 ACCGCAATAAGCAATCACATAAGAAA 60.128 34.615 0.00 0.00 46.13 2.52
3333 7602 4.971830 CACCGCAATAAGCAATCACATAAG 59.028 41.667 0.00 0.00 46.13 1.73
3339 7608 2.670789 GCAACACCGCAATAAGCAATCA 60.671 45.455 0.00 0.00 46.13 2.57
3346 7615 1.804151 GAGAGTGCAACACCGCAATAA 59.196 47.619 0.00 0.00 45.14 1.40
3348 7617 0.250467 AGAGAGTGCAACACCGCAAT 60.250 50.000 0.00 0.00 45.14 3.56
3352 7621 0.249868 TTCCAGAGAGTGCAACACCG 60.250 55.000 0.00 0.00 41.43 4.94
3354 7623 4.757149 AGTATTTTCCAGAGAGTGCAACAC 59.243 41.667 0.00 0.00 41.43 3.32
3359 7628 2.680339 GCCAGTATTTTCCAGAGAGTGC 59.320 50.000 0.00 0.00 0.00 4.40
3394 7665 5.932619 AAAATAGTAAAAGATGGGGGCAC 57.067 39.130 0.00 0.00 0.00 5.01
3409 7680 6.534079 GCCACGATAGACACACTAAAAATAGT 59.466 38.462 0.00 0.00 41.38 2.12
3411 7682 6.399743 TGCCACGATAGACACACTAAAAATA 58.600 36.000 0.00 0.00 41.38 1.40
3418 7689 3.002791 CAATTGCCACGATAGACACACT 58.997 45.455 0.00 0.00 41.38 3.55
3421 7692 2.029244 CGACAATTGCCACGATAGACAC 59.971 50.000 5.05 0.00 41.38 3.67
3507 7783 7.756722 GCATTTTCAGCATAAAACAGTGTATCT 59.243 33.333 0.00 0.00 31.50 1.98
3508 7784 7.756722 AGCATTTTCAGCATAAAACAGTGTATC 59.243 33.333 0.00 0.00 31.50 2.24
3512 7788 6.128742 GGAAGCATTTTCAGCATAAAACAGTG 60.129 38.462 0.00 0.00 31.50 3.66


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

AutoCloner maintained by Alex Coulton.