Multiple sequence alignment - TraesCS7A01G039800

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 TraesCS7A01G039800 chr7A 100.000 5437 0 0 1 5437 18038260 18032824 0.000000e+00 10041
1 TraesCS7A01G039800 chr7A 89.057 3628 290 60 637 4189 17426160 17422565 0.000000e+00 4401
2 TraesCS7A01G039800 chr7A 91.507 1931 93 39 1 1913 17868674 17866797 0.000000e+00 2591
3 TraesCS7A01G039800 chr7A 82.765 2814 447 29 1404 4200 18200250 18203042 0.000000e+00 2475
4 TraesCS7A01G039800 chr7A 99.125 800 7 0 4638 5437 222946056 222946855 0.000000e+00 1439
5 TraesCS7A01G039800 chr7A 98.524 813 10 2 4625 5437 708345660 708346470 0.000000e+00 1434
6 TraesCS7A01G039800 chr7A 83.900 441 39 12 4222 4637 17422571 17422138 5.110000e-105 392
7 TraesCS7A01G039800 chr7A 78.033 478 64 27 4123 4571 18074769 18074304 4.180000e-66 263
8 TraesCS7A01G039800 chr7A 83.955 268 29 4 4255 4519 17711655 17711399 1.510000e-60 244
9 TraesCS7A01G039800 chr7A 90.909 121 11 0 1001 1121 17395045 17394925 4.360000e-36 163
10 TraesCS7A01G039800 chr7A 91.453 117 10 0 4403 4519 17417957 17417841 1.570000e-35 161
11 TraesCS7A01G039800 chr7A 88.321 137 13 2 4443 4579 18233583 18233716 1.570000e-35 161
12 TraesCS7A01G039800 chr4A 87.526 2437 285 12 1395 3826 714764728 714767150 0.000000e+00 2798
13 TraesCS7A01G039800 chr4A 87.571 2285 274 7 1395 3674 714520873 714523152 0.000000e+00 2638
14 TraesCS7A01G039800 chr4A 83.459 2787 451 9 1404 4185 714430951 714433732 0.000000e+00 2584
15 TraesCS7A01G039800 chr4A 81.968 2978 498 29 1404 4359 731694441 731697401 0.000000e+00 2488
16 TraesCS7A01G039800 chr4A 85.976 2018 271 12 1395 3406 714565372 714567383 0.000000e+00 2148
17 TraesCS7A01G039800 chr4A 80.178 2805 521 25 1395 4186 715006779 715009561 0.000000e+00 2067
18 TraesCS7A01G039800 chr4A 81.486 1831 256 44 2731 4538 715526398 715528168 0.000000e+00 1426
19 TraesCS7A01G039800 chr4A 83.212 822 109 19 3624 4443 715358805 715359599 0.000000e+00 726
20 TraesCS7A01G039800 chr4A 82.963 270 25 15 4267 4519 714388997 714389262 1.970000e-54 224
21 TraesCS7A01G039800 chr4A 90.984 122 11 0 1001 1122 714520203 714520324 1.210000e-36 165
22 TraesCS7A01G039800 chr4A 90.164 122 12 0 1001 1122 715297399 715297520 5.640000e-35 159
23 TraesCS7A01G039800 chr4A 87.903 124 9 4 4416 4538 714768569 714768687 2.040000e-29 141
24 TraesCS7A01G039800 chr4A 87.640 89 8 3 4298 4384 714768475 714768562 3.470000e-17 100
25 TraesCS7A01G039800 chr7D 82.108 2979 492 26 1404 4359 8192591 8189631 0.000000e+00 2510
26 TraesCS7A01G039800 chr7D 85.538 2275 317 12 1346 3614 18003750 18001482 0.000000e+00 2368
27 TraesCS7A01G039800 chr7D 87.283 173 16 6 998 1164 18004074 18003902 5.560000e-45 193
28 TraesCS7A01G039800 chr7D 93.137 102 4 2 4416 4517 18070685 18070587 4.390000e-31 147
29 TraesCS7A01G039800 chr2B 99.374 799 5 0 4639 5437 781783398 781782600 0.000000e+00 1448
30 TraesCS7A01G039800 chr2B 94.617 483 19 2 4637 5119 526838520 526838995 0.000000e+00 741
31 TraesCS7A01G039800 chr2B 82.222 405 57 10 4859 5262 473096911 473097301 8.730000e-88 335
32 TraesCS7A01G039800 chr2B 96.098 205 7 1 5234 5437 526839280 526839484 3.140000e-87 333
33 TraesCS7A01G039800 chr2B 86.344 227 30 1 4637 4862 799646830 799647056 4.210000e-61 246
34 TraesCS7A01G039800 chr6B 98.879 803 9 0 4635 5437 549705323 549706125 0.000000e+00 1434
35 TraesCS7A01G039800 chr6B 98.752 801 10 0 4637 5437 549714602 549715402 0.000000e+00 1424
36 TraesCS7A01G039800 chr6B 98.752 801 10 0 4637 5437 578688902 578689702 0.000000e+00 1424
37 TraesCS7A01G039800 chr6B 98.750 800 10 0 4638 5437 578679619 578680418 0.000000e+00 1423
38 TraesCS7A01G039800 chrUn 86.475 244 24 7 4298 4538 372106531 372106768 5.400000e-65 259
39 TraesCS7A01G039800 chrUn 87.640 89 8 3 4298 4384 455937182 455937269 3.470000e-17 100


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 TraesCS7A01G039800 chr7A 18032824 18038260 5436 True 10041.0 10041 100.000000 1 5437 1 chr7A.!!$R5 5436
1 TraesCS7A01G039800 chr7A 17866797 17868674 1877 True 2591.0 2591 91.507000 1 1913 1 chr7A.!!$R4 1912
2 TraesCS7A01G039800 chr7A 18200250 18203042 2792 False 2475.0 2475 82.765000 1404 4200 1 chr7A.!!$F1 2796
3 TraesCS7A01G039800 chr7A 17422138 17426160 4022 True 2396.5 4401 86.478500 637 4637 2 chr7A.!!$R7 4000
4 TraesCS7A01G039800 chr7A 222946056 222946855 799 False 1439.0 1439 99.125000 4638 5437 1 chr7A.!!$F3 799
5 TraesCS7A01G039800 chr7A 708345660 708346470 810 False 1434.0 1434 98.524000 4625 5437 1 chr7A.!!$F4 812
6 TraesCS7A01G039800 chr4A 714430951 714433732 2781 False 2584.0 2584 83.459000 1404 4185 1 chr4A.!!$F2 2781
7 TraesCS7A01G039800 chr4A 731694441 731697401 2960 False 2488.0 2488 81.968000 1404 4359 1 chr4A.!!$F8 2955
8 TraesCS7A01G039800 chr4A 714565372 714567383 2011 False 2148.0 2148 85.976000 1395 3406 1 chr4A.!!$F3 2011
9 TraesCS7A01G039800 chr4A 715006779 715009561 2782 False 2067.0 2067 80.178000 1395 4186 1 chr4A.!!$F4 2791
10 TraesCS7A01G039800 chr4A 715526398 715528168 1770 False 1426.0 1426 81.486000 2731 4538 1 chr4A.!!$F7 1807
11 TraesCS7A01G039800 chr4A 714520203 714523152 2949 False 1401.5 2638 89.277500 1001 3674 2 chr4A.!!$F9 2673
12 TraesCS7A01G039800 chr4A 714764728 714768687 3959 False 1013.0 2798 87.689667 1395 4538 3 chr4A.!!$F10 3143
13 TraesCS7A01G039800 chr4A 715358805 715359599 794 False 726.0 726 83.212000 3624 4443 1 chr4A.!!$F6 819
14 TraesCS7A01G039800 chr7D 8189631 8192591 2960 True 2510.0 2510 82.108000 1404 4359 1 chr7D.!!$R1 2955
15 TraesCS7A01G039800 chr7D 18001482 18004074 2592 True 1280.5 2368 86.410500 998 3614 2 chr7D.!!$R3 2616
16 TraesCS7A01G039800 chr2B 781782600 781783398 798 True 1448.0 1448 99.374000 4639 5437 1 chr2B.!!$R1 798
17 TraesCS7A01G039800 chr2B 526838520 526839484 964 False 537.0 741 95.357500 4637 5437 2 chr2B.!!$F3 800
18 TraesCS7A01G039800 chr6B 549705323 549706125 802 False 1434.0 1434 98.879000 4635 5437 1 chr6B.!!$F1 802
19 TraesCS7A01G039800 chr6B 549714602 549715402 800 False 1424.0 1424 98.752000 4637 5437 1 chr6B.!!$F2 800
20 TraesCS7A01G039800 chr6B 578688902 578689702 800 False 1424.0 1424 98.752000 4637 5437 1 chr6B.!!$F4 800
21 TraesCS7A01G039800 chr6B 578679619 578680418 799 False 1423.0 1423 98.750000 4638 5437 1 chr6B.!!$F3 799

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
756 772 0.462225 GCGAGGGCTACTTTCCTTCC 60.462 60.000 0.0 0.0 35.83 3.46 F
1452 1916 0.674581 CAAGCATTCCTCGTGGCTGA 60.675 55.000 0.0 0.0 36.58 4.26 F
3319 3787 1.970640 GGTGAACCCAAGGAATGCTTT 59.029 47.619 0.0 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2141 2605 1.475751 CCAGGCATCTATGGTCCACAC 60.476 57.143 0.00 0.00 0.00 3.82 R
3365 3833 0.463204 GCCTCAGCATGCTCACTAGA 59.537 55.000 19.68 10.96 39.53 2.43 R
4489 5923 0.170339 AAGCATCATCGTCGTCGTGA 59.830 50.000 1.33 5.96 38.33 4.35 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
167 169 6.971602 TGCATTTGACAAATTTTCATTGCAT 58.028 28.000 15.54 7.46 37.47 3.96
372 374 7.704789 AAAGCAAAAGCAAAAACTAGATGAG 57.295 32.000 0.00 0.00 0.00 2.90
392 394 9.874205 AGATGAGAAAAATGAAAAGACACAAAA 57.126 25.926 0.00 0.00 0.00 2.44
441 443 6.418946 ACTGAAGAGAACAAGAGAAAAAGGT 58.581 36.000 0.00 0.00 0.00 3.50
448 450 8.894731 AGAGAACAAGAGAAAAAGGTAGAAAAC 58.105 33.333 0.00 0.00 0.00 2.43
481 483 4.453819 CACATCCTTGAACCAGAAGAGAAC 59.546 45.833 0.00 0.00 0.00 3.01
490 492 8.519799 TTGAACCAGAAGAGAACAAAATAAGT 57.480 30.769 0.00 0.00 0.00 2.24
651 653 3.818210 TCTGCGATACTTTTTGCTTTGGA 59.182 39.130 0.00 0.00 0.00 3.53
682 684 2.106338 TGAGTGATGCTTTCCTTGGTGA 59.894 45.455 0.00 0.00 0.00 4.02
756 772 0.462225 GCGAGGGCTACTTTCCTTCC 60.462 60.000 0.00 0.00 35.83 3.46
757 773 1.196012 CGAGGGCTACTTTCCTTCCT 58.804 55.000 0.00 0.00 32.74 3.36
758 774 1.555533 CGAGGGCTACTTTCCTTCCTT 59.444 52.381 0.00 0.00 32.74 3.36
759 775 2.418884 CGAGGGCTACTTTCCTTCCTTC 60.419 54.545 0.00 0.00 32.74 3.46
760 776 1.916874 AGGGCTACTTTCCTTCCTTCC 59.083 52.381 0.00 0.00 0.00 3.46
761 777 1.916874 GGGCTACTTTCCTTCCTTCCT 59.083 52.381 0.00 0.00 0.00 3.36
762 778 2.309162 GGGCTACTTTCCTTCCTTCCTT 59.691 50.000 0.00 0.00 0.00 3.36
763 779 3.611970 GGCTACTTTCCTTCCTTCCTTC 58.388 50.000 0.00 0.00 0.00 3.46
787 803 5.363979 TTGCATCTTTAATTGCGTGTACA 57.636 34.783 0.00 0.00 41.80 2.90
802 818 3.805422 CGTGTACAAACAGGTAGAGCAAA 59.195 43.478 0.00 0.00 35.91 3.68
842 864 5.119743 GCCTCTTTTTGCTTTGCATCTTTAG 59.880 40.000 0.00 0.00 38.76 1.85
847 869 7.651704 TCTTTTTGCTTTGCATCTTTAGGTTAC 59.348 33.333 0.00 0.00 38.76 2.50
925 947 2.092914 ACAGCATCCTACCAAAGCTACC 60.093 50.000 0.00 0.00 33.59 3.18
1136 1163 6.796426 TCTGGTATGTACTTCTGAATTCTCG 58.204 40.000 7.05 0.00 0.00 4.04
1189 1569 9.409949 CGATTTTGTTTTTACTAGTCGATGATC 57.590 33.333 0.00 0.00 0.00 2.92
1192 1572 7.827819 TTGTTTTTACTAGTCGATGATCTGG 57.172 36.000 0.00 0.00 0.00 3.86
1195 1575 8.692710 TGTTTTTACTAGTCGATGATCTGGTAT 58.307 33.333 0.00 0.00 30.28 2.73
1198 1578 8.913487 TTTACTAGTCGATGATCTGGTATGTA 57.087 34.615 0.00 0.00 30.28 2.29
1200 1580 5.706369 ACTAGTCGATGATCTGGTATGTACC 59.294 44.000 2.18 2.18 46.62 3.34
1223 1618 2.562738 CTCACATATAGGCCGATGGACA 59.437 50.000 8.86 0.00 29.21 4.02
1285 1681 2.167075 TCTTTTAGCCCACGTACCTAGC 59.833 50.000 0.00 0.00 0.00 3.42
1287 1683 1.108776 TTAGCCCACGTACCTAGCTG 58.891 55.000 0.00 0.00 35.03 4.24
1357 1785 2.280628 GTTCCCTCCTATTTGTGAGCG 58.719 52.381 0.00 0.00 0.00 5.03
1378 1806 3.627577 CGGTAAAATGGCAGTAAGCTGAT 59.372 43.478 0.00 0.00 45.28 2.90
1452 1916 0.674581 CAAGCATTCCTCGTGGCTGA 60.675 55.000 0.00 0.00 36.58 4.26
1792 2256 2.623416 AGAGCTTGTGGGCTTTGTTAAC 59.377 45.455 0.00 0.00 43.20 2.01
2066 2530 4.704540 TGAAAGAACTTGAACAGAAGGCAA 59.295 37.500 0.00 0.00 0.00 4.52
2118 2582 5.540337 TCAGAGAAAAGCTAGAGGACAAGAA 59.460 40.000 0.00 0.00 0.00 2.52
2158 2622 2.158769 TGATGTGTGGACCATAGATGCC 60.159 50.000 5.54 0.00 0.00 4.40
2771 3236 6.946340 TCAAAAGTGAGCATAGAAGGACATA 58.054 36.000 0.00 0.00 0.00 2.29
2782 3247 7.659390 AGCATAGAAGGACATATTAAGAGTTGC 59.341 37.037 0.00 0.00 0.00 4.17
2840 3305 7.499232 TCTCGATATCCAGGGAAGAAAATTTTC 59.501 37.037 21.00 21.00 37.45 2.29
2978 3443 3.354948 CCATGTTTGGTGAGAGATCCA 57.645 47.619 0.00 0.00 38.30 3.41
3043 3508 2.035321 CCGAGCCTTGGATCTAGAGAAC 59.965 54.545 0.00 0.00 0.00 3.01
3058 3523 2.609459 AGAGAACGCACAGTTTGAAGTG 59.391 45.455 0.00 0.00 44.35 3.16
3094 3559 4.323417 TCAGCAACATAGGATTGTTTCGT 58.677 39.130 0.00 0.00 37.73 3.85
3183 3648 2.888212 AGGGAAATTACAAGGCTTGCA 58.112 42.857 26.45 12.05 0.00 4.08
3198 3663 5.954335 AGGCTTGCATACTTTGAACATAAC 58.046 37.500 0.00 0.00 0.00 1.89
3274 3739 3.662247 AGTCTCCGTTGTACCAGAAAG 57.338 47.619 0.00 0.00 0.00 2.62
3284 3749 6.264744 CCGTTGTACCAGAAAGAGATCCTATA 59.735 42.308 0.00 0.00 0.00 1.31
3294 3762 9.401058 CAGAAAGAGATCCTATAAATGGTTTGT 57.599 33.333 0.00 0.00 0.00 2.83
3304 3772 2.765689 AATGGTTTGTCCTGGGTGAA 57.234 45.000 0.00 0.00 37.07 3.18
3319 3787 1.970640 GGTGAACCCAAGGAATGCTTT 59.029 47.619 0.00 0.00 0.00 3.51
3345 3813 2.093553 ACACATTATGTTTGCCCATGCC 60.094 45.455 0.00 0.00 38.98 4.40
3362 3830 2.366533 TGCCGTTCACACCTTTGTTTA 58.633 42.857 0.00 0.00 31.66 2.01
3365 3833 4.142138 TGCCGTTCACACCTTTGTTTAATT 60.142 37.500 0.00 0.00 31.66 1.40
3416 3884 0.620030 ACACATGGCATGGTCTAGCA 59.380 50.000 29.49 0.00 33.60 3.49
3419 3887 2.034179 CACATGGCATGGTCTAGCAATG 59.966 50.000 29.49 12.66 45.55 2.82
3442 3910 2.625790 GTCAGAGTCAGAAGGTGTGAGT 59.374 50.000 0.00 0.00 0.00 3.41
3464 3932 2.385013 GCCAAAAGGAATCGGCAAAT 57.615 45.000 0.00 0.00 44.25 2.32
3596 4064 1.236616 GGCCACCAAGCAAAAATGCC 61.237 55.000 0.00 0.00 34.90 4.40
3605 4073 2.517959 AGCAAAAATGCCAGCTACTCA 58.482 42.857 0.00 0.00 35.19 3.41
3617 4085 2.612672 CAGCTACTCAGTGATGCCATTG 59.387 50.000 0.00 0.00 0.00 2.82
3644 4112 1.612442 ACTTGCCTCCGCTCCCTTA 60.612 57.895 0.00 0.00 35.36 2.69
3651 4131 0.613777 CTCCGCTCCCTTAAAGTGGT 59.386 55.000 5.38 0.00 43.50 4.16
3732 4244 2.084546 GTTGTATGGACACCTTGGAGC 58.915 52.381 0.00 0.00 34.48 4.70
3757 4269 1.616725 CCTGGCTGGTTTGGCAATCTA 60.617 52.381 0.00 0.00 41.92 1.98
3777 4289 5.713025 TCTAATGCATTTGGTCAAGCTTTC 58.287 37.500 18.75 0.00 0.00 2.62
3782 4294 4.022068 TGCATTTGGTCAAGCTTTCCTTAG 60.022 41.667 15.65 7.00 31.00 2.18
3848 5260 0.967380 GCCACTTCCCAACCTCATGG 60.967 60.000 0.00 0.00 40.35 3.66
3854 5266 0.329261 TCCCAACCTCATGGAGCTTG 59.671 55.000 0.00 0.00 43.54 4.01
3860 5272 2.551270 ACCTCATGGAGCTTGGTCTTA 58.449 47.619 0.00 0.00 37.04 2.10
3876 5288 4.037684 TGGTCTTAGAAGCGGCTCTTATAC 59.962 45.833 1.45 0.00 34.56 1.47
3885 5297 1.614413 CGGCTCTTATACTGGGGAGAC 59.386 57.143 0.00 0.00 0.00 3.36
3897 5309 1.616865 TGGGGAGACGTTAGTGTTCAG 59.383 52.381 0.00 0.00 0.00 3.02
3924 5336 5.349061 GGAGCATTCCCAAATCTCAAAAT 57.651 39.130 0.00 0.00 37.53 1.82
3977 5389 1.341531 AGTTGATATTCGAGGAGGGCG 59.658 52.381 0.00 0.00 0.00 6.13
4083 5495 7.391554 TCTCAAGGAGATTTGTCTTAATTGGTG 59.608 37.037 0.00 0.00 33.35 4.17
4086 5499 5.711976 AGGAGATTTGTCTTAATTGGTGTGG 59.288 40.000 0.00 0.00 0.00 4.17
4097 5510 2.978010 GGTGTGGTGAAGTGGCCG 60.978 66.667 0.00 0.00 0.00 6.13
4113 5526 2.760159 CCGGGCTTGGTATGTTGCG 61.760 63.158 0.00 0.00 0.00 4.85
4121 5534 2.087501 TGGTATGTTGCGACGTGAAT 57.912 45.000 9.21 0.00 0.00 2.57
4141 5554 2.597510 GAGGCACACCCCAACCAC 60.598 66.667 0.00 0.00 36.11 4.16
4212 5625 3.931907 TGTCCAAGGATCCACTATTGG 57.068 47.619 19.83 19.83 45.56 3.16
4239 5652 1.377202 TGGATGAAGCAACGGAGGC 60.377 57.895 0.00 0.00 0.00 4.70
4253 5666 0.250081 GGAGGCGGAGGAATCATCAC 60.250 60.000 0.00 0.00 0.00 3.06
4310 5726 2.658679 CTTGTCGCAGGTGGTGGTCA 62.659 60.000 0.00 0.00 0.00 4.02
4311 5727 2.357517 GTCGCAGGTGGTGGTCAG 60.358 66.667 0.00 0.00 0.00 3.51
4312 5728 2.523168 TCGCAGGTGGTGGTCAGA 60.523 61.111 0.00 0.00 0.00 3.27
4400 5834 5.965033 ACTGAACTGATGATGTCCCTTAT 57.035 39.130 0.00 0.00 0.00 1.73
4405 5839 7.174413 TGAACTGATGATGTCCCTTATTTTGA 58.826 34.615 0.00 0.00 0.00 2.69
4411 5845 7.396907 TGATGATGTCCCTTATTTTGATGTTGT 59.603 33.333 0.00 0.00 0.00 3.32
4412 5846 8.821686 ATGATGTCCCTTATTTTGATGTTGTA 57.178 30.769 0.00 0.00 0.00 2.41
4414 5848 6.509418 TGTCCCTTATTTTGATGTTGTAGC 57.491 37.500 0.00 0.00 0.00 3.58
4489 5923 3.012518 CGATTTCTGGTCCTGCAATTCT 58.987 45.455 0.00 0.00 0.00 2.40
4490 5924 3.064545 CGATTTCTGGTCCTGCAATTCTC 59.935 47.826 0.00 0.00 0.00 2.87
4501 5935 1.269166 GCAATTCTCACGACGACGAT 58.731 50.000 15.32 0.00 42.66 3.73
4504 5938 3.108881 CAATTCTCACGACGACGATGAT 58.891 45.455 15.32 0.00 42.66 2.45
4519 5953 3.949754 ACGATGATGCTTGATGATTGGTT 59.050 39.130 0.00 0.00 0.00 3.67
4520 5954 5.125356 ACGATGATGCTTGATGATTGGTTA 58.875 37.500 0.00 0.00 0.00 2.85
4528 5962 4.365723 CTTGATGATTGGTTAATGCTGCC 58.634 43.478 0.00 0.00 0.00 4.85
4535 5969 0.033109 GGTTAATGCTGCCCCCTTCT 60.033 55.000 0.00 0.00 0.00 2.85
4554 5988 5.047519 CCTTCTTTGTTCAGATCCATTGCTT 60.048 40.000 0.00 0.00 0.00 3.91
4571 6005 1.590147 TTCTTCTCGAAGACGCCCC 59.410 57.895 8.78 0.00 46.13 5.80
4578 6016 3.637273 GAAGACGCCCCCACAGGT 61.637 66.667 0.00 0.00 0.00 4.00
4579 6017 3.175710 AAGACGCCCCCACAGGTT 61.176 61.111 0.00 0.00 0.00 3.50
4585 6023 4.263572 CCCCCACAGGTTGACGCA 62.264 66.667 0.00 0.00 0.00 5.24
4587 6025 1.603455 CCCCACAGGTTGACGCATT 60.603 57.895 0.00 0.00 0.00 3.56
4598 6036 1.153628 GACGCATTCGCTGGTACCT 60.154 57.895 14.36 0.00 39.84 3.08
4600 6038 0.179119 ACGCATTCGCTGGTACCTAC 60.179 55.000 14.36 3.97 39.84 3.18
4627 6067 7.505585 AGGTGGAATTTCTGTCTGTTTATTTCA 59.494 33.333 0.00 0.00 0.00 2.69
4629 6069 9.132521 GTGGAATTTCTGTCTGTTTATTTCATG 57.867 33.333 0.00 0.00 0.00 3.07
4701 6141 3.776731 AAAGGGGCCCTAAAGCTAAAT 57.223 42.857 29.08 2.98 31.13 1.40
4850 6290 8.181573 CGGCACTTATATGTTTCAGTTATGTTT 58.818 33.333 0.00 0.00 0.00 2.83
5248 6921 9.942850 TGAAGTGTGAGAAAGAAATATGTATGA 57.057 29.630 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
131 133 9.719279 AATTTGTCAAATGCATTTAAAACACTG 57.281 25.926 23.69 10.41 0.00 3.66
410 412 9.449719 TTTCTCTTGTTCTCTTCAGTTTTTACT 57.550 29.630 0.00 0.00 0.00 2.24
432 434 4.103627 TCTCCGGGTTTTCTACCTTTTTCT 59.896 41.667 0.00 0.00 46.86 2.52
433 435 4.392047 TCTCCGGGTTTTCTACCTTTTTC 58.608 43.478 0.00 0.00 46.86 2.29
441 443 3.842007 TGTGTTTCTCCGGGTTTTCTA 57.158 42.857 0.00 0.00 0.00 2.10
448 450 1.003118 TCAAGGATGTGTTTCTCCGGG 59.997 52.381 0.00 0.00 36.62 5.73
481 483 3.888934 AGTGTGCGCTCAACTTATTTTG 58.111 40.909 14.56 0.00 0.00 2.44
490 492 4.032356 CACAGAGTGTGCGCTCAA 57.968 55.556 14.56 0.00 41.89 3.02
651 653 1.274728 AGCATCACTCAAGAAGCGTCT 59.725 47.619 0.00 0.00 37.32 4.18
682 684 4.017222 ACATGGCAATGGCATAGGGTATAT 60.017 41.667 21.89 0.00 47.00 0.86
756 772 6.034256 CGCAATTAAAGATGCAAAGAAGGAAG 59.966 38.462 10.60 0.00 42.68 3.46
757 773 5.863397 CGCAATTAAAGATGCAAAGAAGGAA 59.137 36.000 10.60 0.00 42.68 3.36
758 774 5.048083 ACGCAATTAAAGATGCAAAGAAGGA 60.048 36.000 10.60 0.00 42.68 3.36
759 775 5.061311 CACGCAATTAAAGATGCAAAGAAGG 59.939 40.000 10.60 0.00 42.68 3.46
760 776 5.630680 ACACGCAATTAAAGATGCAAAGAAG 59.369 36.000 10.60 0.00 42.68 2.85
761 777 5.527951 ACACGCAATTAAAGATGCAAAGAA 58.472 33.333 10.60 0.00 42.68 2.52
762 778 5.119931 ACACGCAATTAAAGATGCAAAGA 57.880 34.783 10.60 0.00 42.68 2.52
763 779 5.855925 TGTACACGCAATTAAAGATGCAAAG 59.144 36.000 10.60 3.81 42.68 2.77
787 803 4.102681 ACACCTAGTTTGCTCTACCTGTTT 59.897 41.667 0.00 0.00 0.00 2.83
802 818 0.614979 AGGCACGGATGACACCTAGT 60.615 55.000 0.00 0.00 35.60 2.57
842 864 2.745728 CCGACATGACACGGTAACC 58.254 57.895 17.35 0.00 43.53 2.85
905 927 2.092968 TGGTAGCTTTGGTAGGATGCTG 60.093 50.000 0.00 0.00 35.47 4.41
1189 1569 2.890808 ATGTGAGCGGTACATACCAG 57.109 50.000 8.76 2.86 46.80 4.00
1192 1572 4.421948 GCCTATATGTGAGCGGTACATAC 58.578 47.826 14.69 2.70 42.06 2.39
1195 1575 1.616865 GGCCTATATGTGAGCGGTACA 59.383 52.381 0.00 0.00 0.00 2.90
1198 1578 0.826256 TCGGCCTATATGTGAGCGGT 60.826 55.000 0.00 0.00 0.00 5.68
1200 1580 1.633561 CATCGGCCTATATGTGAGCG 58.366 55.000 0.00 0.00 0.00 5.03
1203 1583 2.562738 CTGTCCATCGGCCTATATGTGA 59.437 50.000 0.00 0.00 0.00 3.58
1204 1584 2.932622 GCTGTCCATCGGCCTATATGTG 60.933 54.545 0.00 0.00 42.19 3.21
1205 1585 1.276421 GCTGTCCATCGGCCTATATGT 59.724 52.381 0.00 0.00 42.19 2.29
1206 1586 2.015736 GCTGTCCATCGGCCTATATG 57.984 55.000 0.00 1.63 42.19 1.78
1349 1777 1.539388 CTGCCATTTTACCGCTCACAA 59.461 47.619 0.00 0.00 0.00 3.33
1357 1785 5.582689 AATCAGCTTACTGCCATTTTACC 57.417 39.130 0.00 0.00 44.10 2.85
1378 1806 7.696992 AGTCAACAAGGTTTCTTAGAACAAA 57.303 32.000 0.00 0.00 0.00 2.83
1452 1916 8.606602 GCATGTTTTTCTTCTTTGTTTTCTCAT 58.393 29.630 0.00 0.00 0.00 2.90
1792 2256 6.995091 CCATCTTAATCAACTCCTCTTTAGGG 59.005 42.308 0.00 0.00 43.84 3.53
2118 2582 9.466497 ACACATCATCAAGAACAATAAGGTATT 57.534 29.630 0.00 0.00 0.00 1.89
2141 2605 1.475751 CCAGGCATCTATGGTCCACAC 60.476 57.143 0.00 0.00 0.00 3.82
2158 2622 9.991906 AAAGCAATATATTTGATCCAATTCCAG 57.008 29.630 0.00 0.00 0.00 3.86
2332 2797 3.980646 TTCATGTCTTCCCGTGTTTTG 57.019 42.857 0.00 0.00 0.00 2.44
2771 3236 3.197766 TCATGGACTCGGCAACTCTTAAT 59.802 43.478 0.00 0.00 0.00 1.40
2840 3305 3.812053 GCATTATCTCCTGCCAAGTACAG 59.188 47.826 0.00 0.00 32.15 2.74
2930 3395 2.356135 ACGAACATGGCTACAATCCAC 58.644 47.619 0.00 0.00 36.26 4.02
2977 3442 5.163447 ACAAATTGAAGATGATGGCTCCATG 60.163 40.000 6.07 0.00 36.70 3.66
2978 3443 4.960469 ACAAATTGAAGATGATGGCTCCAT 59.040 37.500 0.00 0.14 39.69 3.41
3043 3508 1.396648 TGTGTCACTTCAAACTGTGCG 59.603 47.619 4.27 0.00 34.49 5.34
3058 3523 5.627499 TGTTGCTGATATCCTTTTGTGTC 57.373 39.130 0.00 0.00 0.00 3.67
3151 3616 7.017651 CCTTGTAATTTCCCTATGGATCTAGGT 59.982 40.741 7.15 0.00 41.40 3.08
3198 3663 7.470289 GGCAGTTCTGTAATATAACTGTCTG 57.530 40.000 14.01 3.44 46.97 3.51
3274 3739 6.712547 CCAGGACAAACCATTTATAGGATCTC 59.287 42.308 0.00 0.00 42.04 2.75
3284 3749 2.698274 GTTCACCCAGGACAAACCATTT 59.302 45.455 0.00 0.00 42.04 2.32
3304 3772 2.893489 GTTCAGAAAGCATTCCTTGGGT 59.107 45.455 0.00 0.00 36.12 4.51
3345 3813 7.586300 CACTAGAATTAAACAAAGGTGTGAACG 59.414 37.037 0.00 0.00 38.27 3.95
3362 3830 3.806380 CCTCAGCATGCTCACTAGAATT 58.194 45.455 19.68 0.00 34.76 2.17
3365 3833 0.463204 GCCTCAGCATGCTCACTAGA 59.537 55.000 19.68 10.96 39.53 2.43
3391 3859 0.914644 ACCATGCCATGTGTAGCTCT 59.085 50.000 3.63 0.00 0.00 4.09
3416 3884 2.304180 CACCTTCTGACTCTGACCCATT 59.696 50.000 0.00 0.00 0.00 3.16
3419 3887 1.001406 CACACCTTCTGACTCTGACCC 59.999 57.143 0.00 0.00 0.00 4.46
3442 3910 1.963679 GCCGATTCCTTTTGGCACA 59.036 52.632 0.00 0.00 44.43 4.57
3464 3932 7.394816 ACCTCTAGTATTTGCAGCTCTTTTAA 58.605 34.615 0.00 0.00 0.00 1.52
3596 4064 2.612672 CAATGGCATCACTGAGTAGCTG 59.387 50.000 0.00 0.00 0.00 4.24
3605 4073 2.026542 TGAGCTTCTCAATGGCATCACT 60.027 45.455 0.00 0.00 37.57 3.41
3617 4085 0.739112 CGGAGGCAAGTGAGCTTCTC 60.739 60.000 0.00 0.00 40.16 2.87
3644 4112 3.697166 ACTTGAGTGAACCAACCACTTT 58.303 40.909 0.00 0.00 44.14 2.66
3732 4244 2.268076 CCAAACCAGCCAGGAACCG 61.268 63.158 0.00 0.00 41.22 4.44
3757 4269 3.325716 AGGAAAGCTTGACCAAATGCATT 59.674 39.130 20.25 5.99 0.00 3.56
3777 4289 1.053424 TATTACGCTGCCCCCTAAGG 58.947 55.000 0.00 0.00 0.00 2.69
3782 4294 0.181824 TCCTTTATTACGCTGCCCCC 59.818 55.000 0.00 0.00 0.00 5.40
3848 5260 1.646189 CCGCTTCTAAGACCAAGCTC 58.354 55.000 2.45 0.00 42.51 4.09
3854 5266 3.737032 ATAAGAGCCGCTTCTAAGACC 57.263 47.619 0.00 0.00 38.05 3.85
3860 5272 1.689273 CCCAGTATAAGAGCCGCTTCT 59.311 52.381 0.00 0.00 38.05 2.85
3876 5288 1.616865 TGAACACTAACGTCTCCCCAG 59.383 52.381 0.00 0.00 0.00 4.45
3885 5297 2.325761 CTCCCGTTCTGAACACTAACG 58.674 52.381 19.56 5.90 44.13 3.18
3924 5336 5.647225 TGCTGCACATCACAAATATCAAGTA 59.353 36.000 0.00 0.00 0.00 2.24
4072 5484 4.141287 CCACTTCACCACACCAATTAAGA 58.859 43.478 0.00 0.00 0.00 2.10
4086 5499 3.365265 CAAGCCCGGCCACTTCAC 61.365 66.667 5.55 0.00 0.00 3.18
4097 5510 1.800681 GTCGCAACATACCAAGCCC 59.199 57.895 0.00 0.00 0.00 5.19
4113 5526 0.517316 GTGTGCCTCCAATTCACGTC 59.483 55.000 0.00 0.00 33.69 4.34
4121 5534 2.197324 GTTGGGGTGTGCCTCCAA 59.803 61.111 0.00 0.00 40.43 3.53
4162 5575 1.402259 AGGTCGTGATAGCTCTGTTCG 59.598 52.381 0.00 0.00 0.00 3.95
4212 5625 3.062639 CGTTGCTTCATCCACATGTACTC 59.937 47.826 0.00 0.00 0.00 2.59
4253 5666 1.370437 CATGCTCGGGATGGAGAGG 59.630 63.158 0.00 0.00 36.08 3.69
4293 5709 3.157949 TGACCACCACCTGCGACA 61.158 61.111 0.00 0.00 0.00 4.35
4294 5710 2.357517 CTGACCACCACCTGCGAC 60.358 66.667 0.00 0.00 0.00 5.19
4400 5834 2.030007 GGCTGCTGCTACAACATCAAAA 60.030 45.455 15.64 0.00 39.59 2.44
4405 5839 1.171308 CTTGGCTGCTGCTACAACAT 58.829 50.000 15.64 0.00 39.59 2.71
4411 5845 1.920325 AGGGTCTTGGCTGCTGCTA 60.920 57.895 15.64 6.53 39.59 3.49
4412 5846 3.255397 AGGGTCTTGGCTGCTGCT 61.255 61.111 15.64 0.00 39.59 4.24
4414 5848 1.673665 GTCAGGGTCTTGGCTGCTG 60.674 63.158 0.00 0.00 0.00 4.41
4489 5923 0.170339 AAGCATCATCGTCGTCGTGA 59.830 50.000 1.33 5.96 38.33 4.35
4490 5924 0.295763 CAAGCATCATCGTCGTCGTG 59.704 55.000 1.33 0.60 38.33 4.35
4501 5935 5.361571 AGCATTAACCAATCATCAAGCATCA 59.638 36.000 0.00 0.00 0.00 3.07
4504 5938 4.678574 GCAGCATTAACCAATCATCAAGCA 60.679 41.667 0.00 0.00 0.00 3.91
4519 5953 1.077005 ACAAAGAAGGGGGCAGCATTA 59.923 47.619 0.00 0.00 0.00 1.90
4520 5954 0.178924 ACAAAGAAGGGGGCAGCATT 60.179 50.000 0.00 0.00 0.00 3.56
4528 5962 3.439857 TGGATCTGAACAAAGAAGGGG 57.560 47.619 0.00 0.00 0.00 4.79
4535 5969 5.771666 AGAAGAAGCAATGGATCTGAACAAA 59.228 36.000 0.00 0.00 0.00 2.83
4554 5988 2.348888 GGGGGCGTCTTCGAGAAGA 61.349 63.158 11.14 11.14 44.47 2.87
4571 6005 1.497278 CGAATGCGTCAACCTGTGG 59.503 57.895 0.00 0.00 0.00 4.17
4598 6036 4.974645 ACAGACAGAAATTCCACCTGTA 57.025 40.909 9.06 0.00 40.80 2.74
4600 6038 6.824305 ATAAACAGACAGAAATTCCACCTG 57.176 37.500 0.00 0.00 0.00 4.00
4606 6044 7.814107 TGGCATGAAATAAACAGACAGAAATTC 59.186 33.333 0.00 0.00 0.00 2.17
4612 6052 6.639686 GCATATGGCATGAAATAAACAGACAG 59.360 38.462 10.98 0.00 43.97 3.51
5248 6921 7.854557 TCATTCGTTTCATGAAGATCATTCT 57.145 32.000 8.41 0.00 34.28 2.40


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

AutoCloner maintained by Alex Coulton.