Multiple sequence alignment - TraesCS3B01G214000
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 | TraesCS3B01G214000 | chr3B | 100.000 | 4095 | 0 | 0 | 1 | 4095 | 253897591 | 253893497 | 0.000000e+00 | 7563 |
1 | TraesCS3B01G214000 | chr3D | 96.580 | 3421 | 76 | 18 | 1 | 3398 | 174927310 | 174923908 | 0.000000e+00 | 5631 |
2 | TraesCS3B01G214000 | chr3A | 95.940 | 3424 | 89 | 21 | 1 | 3398 | 214291315 | 214287916 | 0.000000e+00 | 5507 |
3 | TraesCS3B01G214000 | chr4D | 92.100 | 481 | 37 | 1 | 3616 | 4095 | 394957037 | 394956557 | 0.000000e+00 | 676 |
4 | TraesCS3B01G214000 | chr4D | 94.977 | 219 | 10 | 1 | 3399 | 3616 | 394957222 | 394957004 | 3.920000e-90 | 342 |
5 | TraesCS3B01G214000 | chr6B | 88.358 | 481 | 54 | 2 | 3616 | 4095 | 646235507 | 646235028 | 9.870000e-161 | 577 |
6 | TraesCS3B01G214000 | chr6B | 88.991 | 218 | 23 | 1 | 3400 | 3616 | 225199665 | 225199448 | 6.750000e-68 | 268 |
7 | TraesCS3B01G214000 | chr1A | 88.494 | 478 | 54 | 1 | 3616 | 4092 | 257408751 | 257408274 | 9.870000e-161 | 577 |
8 | TraesCS3B01G214000 | chr1A | 91.705 | 217 | 17 | 1 | 3401 | 3616 | 257408934 | 257408718 | 2.390000e-77 | 300 |
9 | TraesCS3B01G214000 | chr1A | 88.938 | 226 | 22 | 3 | 3393 | 3616 | 19848258 | 19848482 | 4.030000e-70 | 276 |
10 | TraesCS3B01G214000 | chr1A | 88.053 | 226 | 24 | 3 | 3393 | 3616 | 19817537 | 19817761 | 8.730000e-67 | 265 |
11 | TraesCS3B01G214000 | chr7D | 88.715 | 319 | 35 | 1 | 3778 | 4095 | 179023770 | 179023452 | 4.960000e-104 | 388 |
12 | TraesCS3B01G214000 | chr7D | 92.202 | 218 | 17 | 0 | 3399 | 3616 | 179119349 | 179119132 | 3.980000e-80 | 309 |
13 | TraesCS3B01G214000 | chr7D | 94.410 | 161 | 9 | 0 | 3616 | 3776 | 179119165 | 179119005 | 8.790000e-62 | 248 |
14 | TraesCS3B01G214000 | chr4B | 94.495 | 218 | 11 | 1 | 3400 | 3616 | 180562633 | 180562416 | 6.560000e-88 | 335 |
15 | TraesCS3B01G214000 | chr6D | 90.909 | 220 | 19 | 1 | 3398 | 3616 | 443748179 | 443748398 | 1.110000e-75 | 294 |
16 | TraesCS3B01G214000 | chr2D | 90.000 | 220 | 21 | 1 | 3398 | 3616 | 68622979 | 68622760 | 2.410000e-72 | 283 |
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 | TraesCS3B01G214000 | chr3B | 253893497 | 253897591 | 4094 | True | 7563.0 | 7563 | 100.0000 | 1 | 4095 | 1 | chr3B.!!$R1 | 4094 |
1 | TraesCS3B01G214000 | chr3D | 174923908 | 174927310 | 3402 | True | 5631.0 | 5631 | 96.5800 | 1 | 3398 | 1 | chr3D.!!$R1 | 3397 |
2 | TraesCS3B01G214000 | chr3A | 214287916 | 214291315 | 3399 | True | 5507.0 | 5507 | 95.9400 | 1 | 3398 | 1 | chr3A.!!$R1 | 3397 |
3 | TraesCS3B01G214000 | chr4D | 394956557 | 394957222 | 665 | True | 509.0 | 676 | 93.5385 | 3399 | 4095 | 2 | chr4D.!!$R1 | 696 |
4 | TraesCS3B01G214000 | chr1A | 257408274 | 257408934 | 660 | True | 438.5 | 577 | 90.0995 | 3401 | 4092 | 2 | chr1A.!!$R1 | 691 |
AutoCloner calculated primer pairsThese primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible. |
---|
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
612 | 625 | 1.860676 | TTTCTCGTGACACCCGAAAG | 58.139 | 50.000 | 11.01 | 0.0 | 33.34 | 2.62 | F |
1015 | 1030 | 2.290577 | ACAGAGATGGCTGGAAAAGGAC | 60.291 | 50.000 | 0.00 | 0.0 | 40.20 | 3.85 | F |
2161 | 2183 | 2.009042 | GCCTTTCTGGATGTCGTCTGG | 61.009 | 57.143 | 0.00 | 0.0 | 38.35 | 3.86 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1786 | 1808 | 0.177604 | GCTCCAGTGAGATGTCAGGG | 59.822 | 60.0 | 0.00 | 0.0 | 41.42 | 4.45 | R |
2297 | 2319 | 0.249398 | AATGGACGTAGGACCAGCAC | 59.751 | 55.0 | 11.98 | 0.0 | 40.68 | 4.40 | R |
3756 | 3789 | 0.319297 | GCACTTCAAAGGCAAGCTGG | 60.319 | 55.0 | 0.00 | 0.0 | 0.00 | 4.85 | R |
All possible primersListed 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. |
---|
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
234 | 235 | 3.665745 | TTGGATTTCTGCTTGCTTTCC | 57.334 | 42.857 | 0.00 | 0.00 | 0.00 | 3.13 |
422 | 435 | 3.576118 | CTCACGTCATCCCTGATAGGATT | 59.424 | 47.826 | 0.00 | 0.00 | 44.61 | 3.01 |
453 | 466 | 2.502538 | TGTTATAAGAGTTCCGTGGGGG | 59.497 | 50.000 | 0.00 | 0.00 | 37.02 | 5.40 |
475 | 488 | 4.633126 | GGTGTAACGGTAAGAAAGAATCCC | 59.367 | 45.833 | 0.00 | 0.00 | 38.12 | 3.85 |
490 | 503 | 2.194201 | ATCCCTTGTTACCGTTGTGG | 57.806 | 50.000 | 0.00 | 0.00 | 46.41 | 4.17 |
544 | 557 | 7.792032 | TCCATAATTCCGTTTCTATCTTGAGT | 58.208 | 34.615 | 0.00 | 0.00 | 0.00 | 3.41 |
578 | 591 | 3.383185 | ACACCGAATTGGAAAGCTTGAAA | 59.617 | 39.130 | 0.00 | 0.00 | 42.00 | 2.69 |
612 | 625 | 1.860676 | TTTCTCGTGACACCCGAAAG | 58.139 | 50.000 | 11.01 | 0.00 | 33.34 | 2.62 |
622 | 635 | 2.465860 | CACCCGAAAGTATGGTGTGA | 57.534 | 50.000 | 0.00 | 0.00 | 43.62 | 3.58 |
705 | 719 | 2.539688 | GCTTGTTTTTGCCAACTGCTAC | 59.460 | 45.455 | 0.00 | 0.00 | 42.00 | 3.58 |
719 | 733 | 6.504398 | CCAACTGCTACTGTTCTCGATTATA | 58.496 | 40.000 | 0.00 | 0.00 | 0.00 | 0.98 |
758 | 772 | 4.459330 | TCGGAATTATGACATGCCATCAA | 58.541 | 39.130 | 0.00 | 0.00 | 0.00 | 2.57 |
767 | 781 | 4.338012 | TGACATGCCATCAATTCAAGAGT | 58.662 | 39.130 | 0.00 | 0.00 | 0.00 | 3.24 |
795 | 810 | 7.951591 | ACTGGTAAACATGCATTTACTCTTTT | 58.048 | 30.769 | 17.94 | 4.57 | 42.34 | 2.27 |
876 | 891 | 5.767816 | ATCAAACACACCAGAAGTTTACC | 57.232 | 39.130 | 0.00 | 0.00 | 34.03 | 2.85 |
920 | 935 | 3.599412 | GGTCTCTGCACCGTGTTAA | 57.401 | 52.632 | 0.00 | 0.00 | 0.00 | 2.01 |
943 | 958 | 3.364621 | GCGGCACTGTTGAATGTTTTATG | 59.635 | 43.478 | 0.00 | 0.00 | 0.00 | 1.90 |
984 | 999 | 6.040391 | TGTGCTTTTATTTTACCAGAACTGCT | 59.960 | 34.615 | 0.00 | 0.00 | 0.00 | 4.24 |
1015 | 1030 | 2.290577 | ACAGAGATGGCTGGAAAAGGAC | 60.291 | 50.000 | 0.00 | 0.00 | 40.20 | 3.85 |
1253 | 1268 | 5.163530 | TGCTATTTGGTTGCATGATAGGTTG | 60.164 | 40.000 | 0.00 | 0.00 | 33.63 | 3.77 |
1278 | 1293 | 9.179909 | TGAAAAGTAAATCTTCAAACTGTACCA | 57.820 | 29.630 | 0.00 | 0.00 | 35.02 | 3.25 |
1395 | 1417 | 4.373156 | AGGAAGTAGGAACAAGTGCATT | 57.627 | 40.909 | 0.00 | 0.00 | 0.00 | 3.56 |
1447 | 1469 | 6.120507 | ACTTATGAGAGAAACTTCTTGCCT | 57.879 | 37.500 | 0.00 | 0.00 | 37.73 | 4.75 |
1448 | 1470 | 6.538263 | ACTTATGAGAGAAACTTCTTGCCTT | 58.462 | 36.000 | 0.00 | 0.00 | 37.73 | 4.35 |
1449 | 1471 | 7.001073 | ACTTATGAGAGAAACTTCTTGCCTTT | 58.999 | 34.615 | 0.00 | 0.00 | 37.73 | 3.11 |
1450 | 1472 | 8.157476 | ACTTATGAGAGAAACTTCTTGCCTTTA | 58.843 | 33.333 | 0.00 | 0.00 | 37.73 | 1.85 |
1601 | 1623 | 4.672587 | ATCTGGTCGAATGCTTAGCTAA | 57.327 | 40.909 | 5.60 | 5.94 | 0.00 | 3.09 |
1772 | 1794 | 4.054780 | ACTGTCTTGTTCAGCGTTCTAA | 57.945 | 40.909 | 0.00 | 0.00 | 36.50 | 2.10 |
1786 | 1808 | 6.091713 | TCAGCGTTCTAAGTGCTAAAATTACC | 59.908 | 38.462 | 0.00 | 0.00 | 37.15 | 2.85 |
1788 | 1810 | 5.448225 | GCGTTCTAAGTGCTAAAATTACCCC | 60.448 | 44.000 | 0.00 | 0.00 | 0.00 | 4.95 |
1791 | 1813 | 6.630203 | TCTAAGTGCTAAAATTACCCCTGA | 57.370 | 37.500 | 0.00 | 0.00 | 0.00 | 3.86 |
1846 | 1868 | 6.692486 | TGAGACAAACTGAGATCCTTAAGAC | 58.308 | 40.000 | 3.36 | 0.00 | 0.00 | 3.01 |
1886 | 1908 | 8.292448 | GTGATAATGTGCCAATTTATCGAGAAT | 58.708 | 33.333 | 0.00 | 0.00 | 35.87 | 2.40 |
1914 | 1936 | 3.246403 | GCTTTCTGCTGCCTTCTCT | 57.754 | 52.632 | 0.00 | 0.00 | 38.95 | 3.10 |
2161 | 2183 | 2.009042 | GCCTTTCTGGATGTCGTCTGG | 61.009 | 57.143 | 0.00 | 0.00 | 38.35 | 3.86 |
2297 | 2319 | 5.048782 | TGTTTAAGACACATTAAGCCTGCAG | 60.049 | 40.000 | 6.78 | 6.78 | 32.00 | 4.41 |
2345 | 2372 | 7.659390 | CCACCTCTTAATTCTGCTTCCTAATAG | 59.341 | 40.741 | 0.00 | 0.00 | 0.00 | 1.73 |
2604 | 2631 | 0.879400 | CTCTCGCTGGATCATGCACC | 60.879 | 60.000 | 9.33 | 0.00 | 0.00 | 5.01 |
2607 | 2634 | 1.746239 | CGCTGGATCATGCACCACA | 60.746 | 57.895 | 6.60 | 0.00 | 32.44 | 4.17 |
2730 | 2757 | 0.949105 | ACCGCCAAGCACTAAGAACG | 60.949 | 55.000 | 0.00 | 0.00 | 0.00 | 3.95 |
2770 | 2797 | 2.032030 | CGTAGTTTGAACTTGTGCCAGG | 60.032 | 50.000 | 1.20 | 0.00 | 40.37 | 4.45 |
2775 | 2802 | 0.819259 | TGAACTTGTGCCAGGCTGTC | 60.819 | 55.000 | 14.15 | 0.00 | 0.00 | 3.51 |
2837 | 2864 | 6.038161 | TGACATGTTATTAATCCTTTGGCTCG | 59.962 | 38.462 | 0.00 | 0.00 | 0.00 | 5.03 |
2866 | 2893 | 4.435425 | GCAATTGCCTTATCTTGCATTCA | 58.565 | 39.130 | 20.06 | 0.00 | 42.66 | 2.57 |
2870 | 2897 | 5.664294 | TTGCCTTATCTTGCATTCATGTT | 57.336 | 34.783 | 0.00 | 0.00 | 37.33 | 2.71 |
2882 | 2909 | 6.528014 | TGCATTCATGTTGTGATTTGTTTC | 57.472 | 33.333 | 0.00 | 0.00 | 36.54 | 2.78 |
3033 | 3060 | 0.171455 | ATCCGCGAGAGAACAGACAC | 59.829 | 55.000 | 8.23 | 0.00 | 0.00 | 3.67 |
3088 | 3115 | 0.729116 | CGGTGCAGACAATGGATGAC | 59.271 | 55.000 | 0.00 | 0.00 | 0.00 | 3.06 |
3132 | 3164 | 5.677091 | GCAAACATATCCTGACTCGCAAATT | 60.677 | 40.000 | 0.00 | 0.00 | 0.00 | 1.82 |
3210 | 3242 | 3.245797 | CCACAACTACGATGTCAGACTG | 58.754 | 50.000 | 1.31 | 0.00 | 0.00 | 3.51 |
3235 | 3267 | 4.910458 | ACAGCTGGTGTAAAGATAACCT | 57.090 | 40.909 | 19.93 | 0.00 | 37.75 | 3.50 |
3286 | 3318 | 1.388547 | ACCTGTTGTTGCACGATTGT | 58.611 | 45.000 | 0.00 | 0.00 | 0.00 | 2.71 |
3392 | 3424 | 0.034896 | GTGCCTATACACCCGGATGG | 59.965 | 60.000 | 0.73 | 0.00 | 41.37 | 3.51 |
3446 | 3478 | 7.717875 | AGCATACCGTATTTTTATAGAAGGCAA | 59.282 | 33.333 | 0.00 | 0.00 | 0.00 | 4.52 |
3450 | 3482 | 7.255569 | ACCGTATTTTTATAGAAGGCAAAAGC | 58.744 | 34.615 | 0.00 | 0.00 | 0.00 | 3.51 |
3468 | 3500 | 3.828875 | AGCTTATGTACAAGAGCCCTC | 57.171 | 47.619 | 22.77 | 4.08 | 35.79 | 4.30 |
3486 | 3518 | 2.061773 | CTCACGAGATGCGAACAAGTT | 58.938 | 47.619 | 0.00 | 0.00 | 44.57 | 2.66 |
3571 | 3604 | 1.192146 | AAGCACCAACTCCGCCTAGA | 61.192 | 55.000 | 0.00 | 0.00 | 0.00 | 2.43 |
3602 | 3635 | 7.618907 | CCTTCCTCCAATCATCTATCTCATCTA | 59.381 | 40.741 | 0.00 | 0.00 | 0.00 | 1.98 |
3603 | 3636 | 8.592529 | TTCCTCCAATCATCTATCTCATCTAG | 57.407 | 38.462 | 0.00 | 0.00 | 0.00 | 2.43 |
3604 | 3637 | 7.124721 | TCCTCCAATCATCTATCTCATCTAGG | 58.875 | 42.308 | 0.00 | 0.00 | 0.00 | 3.02 |
3605 | 3638 | 7.036279 | TCCTCCAATCATCTATCTCATCTAGGA | 60.036 | 40.741 | 0.00 | 0.00 | 0.00 | 2.94 |
3606 | 3639 | 7.785985 | CCTCCAATCATCTATCTCATCTAGGAT | 59.214 | 40.741 | 0.00 | 0.00 | 0.00 | 3.24 |
3607 | 3640 | 8.765488 | TCCAATCATCTATCTCATCTAGGATC | 57.235 | 38.462 | 0.00 | 0.00 | 0.00 | 3.36 |
3608 | 3641 | 8.567851 | TCCAATCATCTATCTCATCTAGGATCT | 58.432 | 37.037 | 0.00 | 0.00 | 0.00 | 2.75 |
3609 | 3642 | 8.853126 | CCAATCATCTATCTCATCTAGGATCTC | 58.147 | 40.741 | 0.00 | 0.00 | 0.00 | 2.75 |
3610 | 3643 | 9.636789 | CAATCATCTATCTCATCTAGGATCTCT | 57.363 | 37.037 | 0.00 | 0.00 | 0.00 | 3.10 |
3611 | 3644 | 9.636789 | AATCATCTATCTCATCTAGGATCTCTG | 57.363 | 37.037 | 0.00 | 0.00 | 0.00 | 3.35 |
3612 | 3645 | 8.161640 | TCATCTATCTCATCTAGGATCTCTGT | 57.838 | 38.462 | 0.00 | 0.00 | 0.00 | 3.41 |
3613 | 3646 | 8.267183 | TCATCTATCTCATCTAGGATCTCTGTC | 58.733 | 40.741 | 0.00 | 0.00 | 0.00 | 3.51 |
3614 | 3647 | 7.813087 | TCTATCTCATCTAGGATCTCTGTCT | 57.187 | 40.000 | 0.00 | 0.00 | 0.00 | 3.41 |
3615 | 3648 | 8.218423 | TCTATCTCATCTAGGATCTCTGTCTT | 57.782 | 38.462 | 0.00 | 0.00 | 0.00 | 3.01 |
3616 | 3649 | 8.321353 | TCTATCTCATCTAGGATCTCTGTCTTC | 58.679 | 40.741 | 0.00 | 0.00 | 0.00 | 2.87 |
3617 | 3650 | 5.630121 | TCTCATCTAGGATCTCTGTCTTCC | 58.370 | 45.833 | 0.00 | 0.00 | 0.00 | 3.46 |
3618 | 3651 | 5.133491 | TCTCATCTAGGATCTCTGTCTTCCA | 59.867 | 44.000 | 0.00 | 0.00 | 31.65 | 3.53 |
3619 | 3652 | 5.770919 | TCATCTAGGATCTCTGTCTTCCAA | 58.229 | 41.667 | 0.00 | 0.00 | 31.65 | 3.53 |
3620 | 3653 | 6.380414 | TCATCTAGGATCTCTGTCTTCCAAT | 58.620 | 40.000 | 0.00 | 0.00 | 31.65 | 3.16 |
3621 | 3654 | 6.493115 | TCATCTAGGATCTCTGTCTTCCAATC | 59.507 | 42.308 | 0.00 | 0.00 | 31.65 | 2.67 |
3622 | 3655 | 5.770919 | TCTAGGATCTCTGTCTTCCAATCA | 58.229 | 41.667 | 0.00 | 0.00 | 31.65 | 2.57 |
3623 | 3656 | 6.380414 | TCTAGGATCTCTGTCTTCCAATCAT | 58.620 | 40.000 | 0.00 | 0.00 | 31.65 | 2.45 |
3624 | 3657 | 5.549742 | AGGATCTCTGTCTTCCAATCATC | 57.450 | 43.478 | 0.00 | 0.00 | 31.65 | 2.92 |
3625 | 3658 | 5.218179 | AGGATCTCTGTCTTCCAATCATCT | 58.782 | 41.667 | 0.00 | 0.00 | 31.65 | 2.90 |
3626 | 3659 | 6.380414 | AGGATCTCTGTCTTCCAATCATCTA | 58.620 | 40.000 | 0.00 | 0.00 | 31.65 | 1.98 |
3627 | 3660 | 7.018150 | AGGATCTCTGTCTTCCAATCATCTAT | 58.982 | 38.462 | 0.00 | 0.00 | 31.65 | 1.98 |
3628 | 3661 | 7.178983 | AGGATCTCTGTCTTCCAATCATCTATC | 59.821 | 40.741 | 0.00 | 0.00 | 31.65 | 2.08 |
3629 | 3662 | 7.178983 | GGATCTCTGTCTTCCAATCATCTATCT | 59.821 | 40.741 | 0.00 | 0.00 | 0.00 | 1.98 |
3630 | 3663 | 7.523293 | TCTCTGTCTTCCAATCATCTATCTC | 57.477 | 40.000 | 0.00 | 0.00 | 0.00 | 2.75 |
3631 | 3664 | 7.065504 | TCTCTGTCTTCCAATCATCTATCTCA | 58.934 | 38.462 | 0.00 | 0.00 | 0.00 | 3.27 |
3632 | 3665 | 7.729431 | TCTCTGTCTTCCAATCATCTATCTCAT | 59.271 | 37.037 | 0.00 | 0.00 | 0.00 | 2.90 |
3633 | 3666 | 7.894708 | TCTGTCTTCCAATCATCTATCTCATC | 58.105 | 38.462 | 0.00 | 0.00 | 0.00 | 2.92 |
3634 | 3667 | 7.729431 | TCTGTCTTCCAATCATCTATCTCATCT | 59.271 | 37.037 | 0.00 | 0.00 | 0.00 | 2.90 |
3667 | 3700 | 2.472695 | TAAGTTGTGCAGCCGATCTT | 57.527 | 45.000 | 0.00 | 0.00 | 0.00 | 2.40 |
3673 | 3706 | 1.303561 | TGCAGCCGATCTTTGCCTT | 60.304 | 52.632 | 9.52 | 0.00 | 37.03 | 4.35 |
3676 | 3709 | 1.167851 | CAGCCGATCTTTGCCTTGAA | 58.832 | 50.000 | 0.00 | 0.00 | 0.00 | 2.69 |
3733 | 3766 | 2.601905 | AGGGCCCATGCAATTAGAATC | 58.398 | 47.619 | 27.56 | 0.00 | 40.13 | 2.52 |
3738 | 3771 | 3.254166 | GCCCATGCAATTAGAATCGTGAT | 59.746 | 43.478 | 0.00 | 0.00 | 37.47 | 3.06 |
3756 | 3789 | 2.695666 | TGATGGAGTCGAATCCTCTTCC | 59.304 | 50.000 | 30.04 | 15.47 | 40.29 | 3.46 |
3796 | 3829 | 0.339859 | TCCTCTGGTCTAGCCACCAT | 59.660 | 55.000 | 3.88 | 0.00 | 45.76 | 3.55 |
3805 | 3838 | 2.819608 | GTCTAGCCACCATTGCAAGAAA | 59.180 | 45.455 | 4.94 | 0.00 | 0.00 | 2.52 |
3836 | 3870 | 4.582869 | TGTGGATGAGATTTGAGGTTGAG | 58.417 | 43.478 | 0.00 | 0.00 | 0.00 | 3.02 |
3844 | 3878 | 5.013495 | TGAGATTTGAGGTTGAGTCTCCATT | 59.987 | 40.000 | 0.00 | 0.00 | 33.04 | 3.16 |
3873 | 3907 | 1.188219 | ATGAGTGCCACACCTCTCGT | 61.188 | 55.000 | 0.00 | 0.00 | 34.49 | 4.18 |
3887 | 3921 | 3.196901 | ACCTCTCGTGCATAACCACAATA | 59.803 | 43.478 | 0.00 | 0.00 | 35.47 | 1.90 |
3888 | 3922 | 3.555956 | CCTCTCGTGCATAACCACAATAC | 59.444 | 47.826 | 0.00 | 0.00 | 35.47 | 1.89 |
3910 | 3944 | 0.394352 | AAGGATGTGGTCGGGATTGC | 60.394 | 55.000 | 0.00 | 0.00 | 0.00 | 3.56 |
3930 | 3964 | 0.108186 | CCTCATCTTGCAGGCACGTA | 60.108 | 55.000 | 0.00 | 0.00 | 0.00 | 3.57 |
3960 | 3994 | 1.003580 | GAAGGTGCATCTTGGAGACCA | 59.996 | 52.381 | 19.03 | 0.00 | 0.00 | 4.02 |
4032 | 4066 | 5.929992 | CCACATGAAGATTTTGCATTTGAGT | 59.070 | 36.000 | 0.00 | 0.00 | 0.00 | 3.41 |
4080 | 4114 | 1.207791 | CAGTGGGGGATCTAGCTTGT | 58.792 | 55.000 | 0.00 | 0.00 | 0.00 | 3.16 |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
5 | 6 | 0.387565 | GAGCTTAGCTCGGGGAAGAG | 59.612 | 60.000 | 18.89 | 0.00 | 45.85 | 2.85 |
120 | 121 | 0.767998 | GGCAGATAAGAGGGAAGGGG | 59.232 | 60.000 | 0.00 | 0.00 | 0.00 | 4.79 |
234 | 235 | 6.854892 | GCGGATTACAGATTTCAATTGATCAG | 59.145 | 38.462 | 9.40 | 4.53 | 0.00 | 2.90 |
279 | 280 | 2.654079 | CCAGTCCAGGAGCGCTCTT | 61.654 | 63.158 | 34.46 | 26.82 | 0.00 | 2.85 |
389 | 402 | 9.035890 | TCAGGGATGACGTGAGATATATAAAAT | 57.964 | 33.333 | 0.00 | 0.00 | 38.93 | 1.82 |
390 | 403 | 8.417273 | TCAGGGATGACGTGAGATATATAAAA | 57.583 | 34.615 | 0.00 | 0.00 | 38.93 | 1.52 |
405 | 418 | 7.918076 | TGGTAAATAATCCTATCAGGGATGAC | 58.082 | 38.462 | 0.00 | 0.00 | 44.50 | 3.06 |
446 | 459 | 0.390209 | CTTACCGTTACACCCCCACG | 60.390 | 60.000 | 0.00 | 0.00 | 0.00 | 4.94 |
453 | 466 | 5.485620 | AGGGATTCTTTCTTACCGTTACAC | 58.514 | 41.667 | 0.00 | 0.00 | 0.00 | 2.90 |
490 | 503 | 5.803020 | AAGCTATCCACAAATCGAGAAAC | 57.197 | 39.130 | 0.00 | 0.00 | 0.00 | 2.78 |
496 | 509 | 7.819415 | TGGATCTAATAAGCTATCCACAAATCG | 59.181 | 37.037 | 9.18 | 0.00 | 42.25 | 3.34 |
544 | 557 | 0.684535 | TTCGGTGTCAGGCTCATGAA | 59.315 | 50.000 | 0.00 | 0.00 | 0.00 | 2.57 |
578 | 591 | 8.082242 | TGTCACGAGAAATACATCGATATGAAT | 58.918 | 33.333 | 0.00 | 0.00 | 41.40 | 2.57 |
598 | 611 | 1.337447 | ACCATACTTTCGGGTGTCACG | 60.337 | 52.381 | 0.00 | 0.00 | 32.60 | 4.35 |
612 | 625 | 3.350219 | ACCACCATCTTCACACCATAC | 57.650 | 47.619 | 0.00 | 0.00 | 0.00 | 2.39 |
622 | 635 | 1.950484 | GCATCACGGAACCACCATCTT | 60.950 | 52.381 | 0.00 | 0.00 | 38.90 | 2.40 |
758 | 772 | 7.230510 | TGCATGTTTACCAGTTAACTCTTGAAT | 59.769 | 33.333 | 4.77 | 0.00 | 0.00 | 2.57 |
767 | 781 | 8.630054 | AGAGTAAATGCATGTTTACCAGTTAA | 57.370 | 30.769 | 15.92 | 0.00 | 42.68 | 2.01 |
876 | 891 | 5.295292 | AGCTTTAGTGATGACATTTCGGATG | 59.705 | 40.000 | 0.00 | 0.00 | 0.00 | 3.51 |
914 | 929 | 0.941542 | TCAACAGTGCCGCTTAACAC | 59.058 | 50.000 | 0.00 | 0.00 | 37.05 | 3.32 |
915 | 930 | 1.669604 | TTCAACAGTGCCGCTTAACA | 58.330 | 45.000 | 0.00 | 0.00 | 0.00 | 2.41 |
920 | 935 | 1.032014 | AAACATTCAACAGTGCCGCT | 58.968 | 45.000 | 0.00 | 0.00 | 0.00 | 5.52 |
943 | 958 | 4.820284 | AGCACAGCTTCACTAAGAAAAC | 57.180 | 40.909 | 0.00 | 0.00 | 33.89 | 2.43 |
984 | 999 | 4.278170 | CCAGCCATCTCTGTAACACAAAAA | 59.722 | 41.667 | 0.00 | 0.00 | 32.32 | 1.94 |
1015 | 1030 | 2.947118 | TACTGCGGCGGAACATAGCG | 62.947 | 60.000 | 17.15 | 0.00 | 0.00 | 4.26 |
1434 | 1456 | 8.593492 | ATTCACAAATAAAGGCAAGAAGTTTC | 57.407 | 30.769 | 0.00 | 0.00 | 0.00 | 2.78 |
1447 | 1469 | 9.743057 | CACCAACTACTGAAATTCACAAATAAA | 57.257 | 29.630 | 0.00 | 0.00 | 0.00 | 1.40 |
1448 | 1470 | 8.356657 | CCACCAACTACTGAAATTCACAAATAA | 58.643 | 33.333 | 0.00 | 0.00 | 0.00 | 1.40 |
1449 | 1471 | 7.504238 | ACCACCAACTACTGAAATTCACAAATA | 59.496 | 33.333 | 0.00 | 0.00 | 0.00 | 1.40 |
1450 | 1472 | 6.323739 | ACCACCAACTACTGAAATTCACAAAT | 59.676 | 34.615 | 0.00 | 0.00 | 0.00 | 2.32 |
1732 | 1754 | 9.944376 | AAGACAGTTGATTTTGCTACTCTTATA | 57.056 | 29.630 | 0.00 | 0.00 | 0.00 | 0.98 |
1772 | 1794 | 4.650972 | TGTCAGGGGTAATTTTAGCACT | 57.349 | 40.909 | 0.00 | 0.00 | 45.07 | 4.40 |
1786 | 1808 | 0.177604 | GCTCCAGTGAGATGTCAGGG | 59.822 | 60.000 | 0.00 | 0.00 | 41.42 | 4.45 |
1788 | 1810 | 0.900421 | TGGCTCCAGTGAGATGTCAG | 59.100 | 55.000 | 0.00 | 0.00 | 41.42 | 3.51 |
1791 | 1813 | 1.701847 | AGTTTGGCTCCAGTGAGATGT | 59.298 | 47.619 | 0.00 | 0.00 | 41.42 | 3.06 |
1900 | 1922 | 4.039730 | GTCCATATAAGAGAAGGCAGCAGA | 59.960 | 45.833 | 0.00 | 0.00 | 0.00 | 4.26 |
1914 | 1936 | 6.068461 | TGGCAGTAACCAAAGTCCATATAA | 57.932 | 37.500 | 0.00 | 0.00 | 36.55 | 0.98 |
2073 | 2095 | 6.366877 | GTGCTACTGAAACAGGTTACGAATAA | 59.633 | 38.462 | 0.00 | 0.00 | 35.51 | 1.40 |
2161 | 2183 | 6.164176 | ACTAAGCACCTTGTTACTGTGATAC | 58.836 | 40.000 | 0.00 | 0.00 | 31.66 | 2.24 |
2297 | 2319 | 0.249398 | AATGGACGTAGGACCAGCAC | 59.751 | 55.000 | 11.98 | 0.00 | 40.68 | 4.40 |
2345 | 2372 | 9.124807 | GCTACAATAGTCCACACAAAATTAAAC | 57.875 | 33.333 | 0.00 | 0.00 | 0.00 | 2.01 |
2438 | 2465 | 5.869649 | AAGGGTATTTTTATGCATGTCCC | 57.130 | 39.130 | 10.16 | 9.92 | 0.00 | 4.46 |
2770 | 2797 | 5.593010 | AGAACAATAGAGGATAACGACAGC | 58.407 | 41.667 | 0.00 | 0.00 | 0.00 | 4.40 |
2799 | 2826 | 1.378250 | ATGTCAGCAGGCAAGGAGC | 60.378 | 57.895 | 0.00 | 0.00 | 44.65 | 4.70 |
2837 | 2864 | 5.207768 | CAAGATAAGGCAATTGCGTATGAC | 58.792 | 41.667 | 24.59 | 15.81 | 43.26 | 3.06 |
2866 | 2893 | 4.942761 | AGCCTGAAACAAATCACAACAT | 57.057 | 36.364 | 0.00 | 0.00 | 0.00 | 2.71 |
2870 | 2897 | 7.148086 | GGAACATATAGCCTGAAACAAATCACA | 60.148 | 37.037 | 0.00 | 0.00 | 0.00 | 3.58 |
2882 | 2909 | 4.103153 | TCAAGGGAAGGAACATATAGCCTG | 59.897 | 45.833 | 0.00 | 0.00 | 31.06 | 4.85 |
2956 | 2983 | 5.107104 | GCAGAATAAGTGTGTCGTCAAATCA | 60.107 | 40.000 | 0.00 | 0.00 | 0.00 | 2.57 |
3033 | 3060 | 1.078567 | GGAGCTGAAGAGGTGCCAG | 60.079 | 63.158 | 0.00 | 0.00 | 32.19 | 4.85 |
3088 | 3115 | 4.183865 | TGCGTCATCTACTCAATCAAAGG | 58.816 | 43.478 | 0.00 | 0.00 | 0.00 | 3.11 |
3132 | 3164 | 0.534652 | GCATGCCAAGCCAACCAAAA | 60.535 | 50.000 | 6.36 | 0.00 | 0.00 | 2.44 |
3167 | 3199 | 0.519175 | GCAGTGCGCGATAACACAAG | 60.519 | 55.000 | 12.10 | 6.50 | 39.30 | 3.16 |
3194 | 3226 | 5.007823 | GCTGTATACAGTCTGACATCGTAGT | 59.992 | 44.000 | 28.95 | 1.64 | 45.45 | 2.73 |
3210 | 3242 | 7.498443 | AGGTTATCTTTACACCAGCTGTATAC | 58.502 | 38.462 | 13.81 | 0.00 | 35.18 | 1.47 |
3235 | 3267 | 2.413796 | CGCGCTGTCCATTAGTTTACAA | 59.586 | 45.455 | 5.56 | 0.00 | 0.00 | 2.41 |
3338 | 3370 | 2.637382 | TCCATGTGCAGGAGAACACTTA | 59.363 | 45.455 | 0.00 | 0.00 | 35.69 | 2.24 |
3339 | 3371 | 1.421268 | TCCATGTGCAGGAGAACACTT | 59.579 | 47.619 | 0.00 | 0.00 | 35.69 | 3.16 |
3340 | 3372 | 1.059098 | TCCATGTGCAGGAGAACACT | 58.941 | 50.000 | 0.00 | 0.00 | 35.69 | 3.55 |
3341 | 3373 | 3.631453 | TCCATGTGCAGGAGAACAC | 57.369 | 52.632 | 0.00 | 0.00 | 35.69 | 3.32 |
3446 | 3478 | 4.019321 | TGAGGGCTCTTGTACATAAGCTTT | 60.019 | 41.667 | 22.20 | 14.18 | 35.12 | 3.51 |
3450 | 3482 | 3.130516 | TCGTGAGGGCTCTTGTACATAAG | 59.869 | 47.826 | 0.00 | 0.00 | 0.00 | 1.73 |
3468 | 3500 | 1.526887 | ACAACTTGTTCGCATCTCGTG | 59.473 | 47.619 | 0.00 | 0.00 | 39.67 | 4.35 |
3571 | 3604 | 1.639635 | ATGATTGGAGGAAGGCCGCT | 61.640 | 55.000 | 0.00 | 0.00 | 39.96 | 5.52 |
3602 | 3635 | 5.218179 | AGATGATTGGAAGACAGAGATCCT | 58.782 | 41.667 | 0.00 | 0.00 | 34.24 | 3.24 |
3603 | 3636 | 5.549742 | AGATGATTGGAAGACAGAGATCC | 57.450 | 43.478 | 0.00 | 0.00 | 0.00 | 3.36 |
3604 | 3637 | 8.125978 | AGATAGATGATTGGAAGACAGAGATC | 57.874 | 38.462 | 0.00 | 0.00 | 0.00 | 2.75 |
3605 | 3638 | 7.729431 | TGAGATAGATGATTGGAAGACAGAGAT | 59.271 | 37.037 | 0.00 | 0.00 | 0.00 | 2.75 |
3606 | 3639 | 7.065504 | TGAGATAGATGATTGGAAGACAGAGA | 58.934 | 38.462 | 0.00 | 0.00 | 0.00 | 3.10 |
3607 | 3640 | 7.287512 | TGAGATAGATGATTGGAAGACAGAG | 57.712 | 40.000 | 0.00 | 0.00 | 0.00 | 3.35 |
3608 | 3641 | 7.729431 | AGATGAGATAGATGATTGGAAGACAGA | 59.271 | 37.037 | 0.00 | 0.00 | 0.00 | 3.41 |
3609 | 3642 | 7.898918 | AGATGAGATAGATGATTGGAAGACAG | 58.101 | 38.462 | 0.00 | 0.00 | 0.00 | 3.51 |
3610 | 3643 | 7.852550 | AGATGAGATAGATGATTGGAAGACA | 57.147 | 36.000 | 0.00 | 0.00 | 0.00 | 3.41 |
3611 | 3644 | 8.469200 | CCTAGATGAGATAGATGATTGGAAGAC | 58.531 | 40.741 | 0.00 | 0.00 | 0.00 | 3.01 |
3612 | 3645 | 8.397172 | TCCTAGATGAGATAGATGATTGGAAGA | 58.603 | 37.037 | 0.00 | 0.00 | 0.00 | 2.87 |
3613 | 3646 | 8.592529 | TCCTAGATGAGATAGATGATTGGAAG | 57.407 | 38.462 | 0.00 | 0.00 | 0.00 | 3.46 |
3614 | 3647 | 9.199645 | GATCCTAGATGAGATAGATGATTGGAA | 57.800 | 37.037 | 0.00 | 0.00 | 0.00 | 3.53 |
3615 | 3648 | 8.567851 | AGATCCTAGATGAGATAGATGATTGGA | 58.432 | 37.037 | 0.00 | 0.00 | 0.00 | 3.53 |
3616 | 3649 | 8.771521 | AGATCCTAGATGAGATAGATGATTGG | 57.228 | 38.462 | 0.00 | 0.00 | 0.00 | 3.16 |
3617 | 3650 | 9.636789 | AGAGATCCTAGATGAGATAGATGATTG | 57.363 | 37.037 | 0.00 | 0.00 | 0.00 | 2.67 |
3618 | 3651 | 9.636789 | CAGAGATCCTAGATGAGATAGATGATT | 57.363 | 37.037 | 0.00 | 0.00 | 0.00 | 2.57 |
3619 | 3652 | 8.784880 | ACAGAGATCCTAGATGAGATAGATGAT | 58.215 | 37.037 | 0.00 | 0.00 | 0.00 | 2.45 |
3620 | 3653 | 8.161640 | ACAGAGATCCTAGATGAGATAGATGA | 57.838 | 38.462 | 0.00 | 0.00 | 0.00 | 2.92 |
3621 | 3654 | 8.270030 | AGACAGAGATCCTAGATGAGATAGATG | 58.730 | 40.741 | 0.00 | 0.00 | 0.00 | 2.90 |
3622 | 3655 | 8.397951 | AGACAGAGATCCTAGATGAGATAGAT | 57.602 | 38.462 | 0.00 | 0.00 | 0.00 | 1.98 |
3623 | 3656 | 7.813087 | AGACAGAGATCCTAGATGAGATAGA | 57.187 | 40.000 | 0.00 | 0.00 | 0.00 | 1.98 |
3624 | 3657 | 9.958180 | TTAAGACAGAGATCCTAGATGAGATAG | 57.042 | 37.037 | 0.00 | 0.00 | 0.00 | 2.08 |
3625 | 3658 | 9.958180 | CTTAAGACAGAGATCCTAGATGAGATA | 57.042 | 37.037 | 0.00 | 0.00 | 0.00 | 1.98 |
3626 | 3659 | 8.448008 | ACTTAAGACAGAGATCCTAGATGAGAT | 58.552 | 37.037 | 10.09 | 0.00 | 0.00 | 2.75 |
3627 | 3660 | 7.811282 | ACTTAAGACAGAGATCCTAGATGAGA | 58.189 | 38.462 | 10.09 | 0.00 | 0.00 | 3.27 |
3628 | 3661 | 8.352201 | CAACTTAAGACAGAGATCCTAGATGAG | 58.648 | 40.741 | 10.09 | 0.00 | 0.00 | 2.90 |
3629 | 3662 | 7.836685 | ACAACTTAAGACAGAGATCCTAGATGA | 59.163 | 37.037 | 10.09 | 0.00 | 0.00 | 2.92 |
3630 | 3663 | 7.920151 | CACAACTTAAGACAGAGATCCTAGATG | 59.080 | 40.741 | 10.09 | 0.00 | 0.00 | 2.90 |
3631 | 3664 | 7.417342 | GCACAACTTAAGACAGAGATCCTAGAT | 60.417 | 40.741 | 10.09 | 0.00 | 0.00 | 1.98 |
3632 | 3665 | 6.127591 | GCACAACTTAAGACAGAGATCCTAGA | 60.128 | 42.308 | 10.09 | 0.00 | 0.00 | 2.43 |
3633 | 3666 | 6.039616 | GCACAACTTAAGACAGAGATCCTAG | 58.960 | 44.000 | 10.09 | 0.00 | 0.00 | 3.02 |
3634 | 3667 | 5.480422 | TGCACAACTTAAGACAGAGATCCTA | 59.520 | 40.000 | 10.09 | 0.00 | 0.00 | 2.94 |
3667 | 3700 | 4.629200 | GTGTTCAACAATGTTTCAAGGCAA | 59.371 | 37.500 | 0.00 | 0.00 | 0.00 | 4.52 |
3673 | 3706 | 4.657055 | CACGAGTGTTCAACAATGTTTCA | 58.343 | 39.130 | 0.00 | 0.00 | 0.00 | 2.69 |
3676 | 3709 | 2.421775 | TGCACGAGTGTTCAACAATGTT | 59.578 | 40.909 | 0.00 | 0.00 | 0.00 | 2.71 |
3733 | 3766 | 1.678627 | AGAGGATTCGACTCCATCACG | 59.321 | 52.381 | 22.40 | 0.00 | 37.81 | 4.35 |
3738 | 3771 | 1.273041 | TGGGAAGAGGATTCGACTCCA | 60.273 | 52.381 | 22.40 | 0.98 | 37.81 | 3.86 |
3756 | 3789 | 0.319297 | GCACTTCAAAGGCAAGCTGG | 60.319 | 55.000 | 0.00 | 0.00 | 0.00 | 4.85 |
3796 | 3829 | 5.129634 | TCCACAGATGTTACTTTCTTGCAA | 58.870 | 37.500 | 0.00 | 0.00 | 0.00 | 4.08 |
3822 | 3855 | 5.511386 | AATGGAGACTCAACCTCAAATCT | 57.489 | 39.130 | 4.53 | 0.00 | 32.48 | 2.40 |
3836 | 3870 | 4.217118 | ACTCATGCTTCAACAAATGGAGAC | 59.783 | 41.667 | 0.00 | 0.00 | 36.68 | 3.36 |
3873 | 3907 | 2.421775 | CCTTGCGTATTGTGGTTATGCA | 59.578 | 45.455 | 0.00 | 0.00 | 39.24 | 3.96 |
3879 | 3913 | 2.083774 | CACATCCTTGCGTATTGTGGT | 58.916 | 47.619 | 0.00 | 0.00 | 35.25 | 4.16 |
3887 | 3921 | 2.047274 | CCGACCACATCCTTGCGT | 60.047 | 61.111 | 0.00 | 0.00 | 0.00 | 5.24 |
3888 | 3922 | 2.593468 | ATCCCGACCACATCCTTGCG | 62.593 | 60.000 | 0.00 | 0.00 | 0.00 | 4.85 |
3910 | 3944 | 2.110967 | CGTGCCTGCAAGATGAGGG | 61.111 | 63.158 | 0.00 | 0.00 | 34.07 | 4.30 |
3915 | 3949 | 1.138859 | TGCTATACGTGCCTGCAAGAT | 59.861 | 47.619 | 11.95 | 4.20 | 34.07 | 2.40 |
3930 | 3964 | 1.987807 | ATGCACCTTCGGCCTGCTAT | 61.988 | 55.000 | 14.32 | 4.71 | 0.00 | 2.97 |
4062 | 4096 | 1.501582 | GACAAGCTAGATCCCCCACT | 58.498 | 55.000 | 0.00 | 0.00 | 0.00 | 4.00 |
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.