Multiple sequence alignment - TraesCS5D01G219100

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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 TraesCS5D01G219100 chr5D 100.000 2831 0 0 1 2831 328436303 328433473 0.000000e+00 5228.0
1 TraesCS5D01G219100 chr5D 92.171 677 51 2 1388 2063 328405090 328404415 0.000000e+00 955.0
2 TraesCS5D01G219100 chr5D 100.000 66 0 0 3074 3139 328433230 328433165 4.250000e-24 122.0
3 TraesCS5D01G219100 chr5A 91.121 1543 63 32 916 2414 428152994 428154506 0.000000e+00 2023.0
4 TraesCS5D01G219100 chr5A 88.796 839 67 11 1410 2226 428247348 428248181 0.000000e+00 1003.0
5 TraesCS5D01G219100 chr5A 95.000 520 18 4 1 512 428151509 428152028 0.000000e+00 809.0
6 TraesCS5D01G219100 chr5A 91.557 379 28 3 2406 2781 428154556 428154933 1.290000e-143 520.0
7 TraesCS5D01G219100 chr5A 88.779 303 30 2 1383 1684 428244728 428245027 4.950000e-98 368.0
8 TraesCS5D01G219100 chr5A 93.220 236 13 3 517 750 428152444 428152678 8.340000e-91 344.0
9 TraesCS5D01G219100 chr5A 90.517 116 9 1 1681 1794 428247210 428247325 5.420000e-33 152.0
10 TraesCS5D01G219100 chr5A 85.714 119 5 4 735 853 428152700 428152806 7.110000e-22 115.0
11 TraesCS5D01G219100 chr5B 89.854 1301 74 25 1159 2422 381716091 381714812 0.000000e+00 1618.0
12 TraesCS5D01G219100 chr5B 83.990 381 35 11 36 402 381717155 381716787 3.000000e-90 342.0
13 TraesCS5D01G219100 chr5B 91.860 172 5 5 455 625 129721944 129721781 6.770000e-57 231.0
14 TraesCS5D01G219100 chr5B 90.588 170 8 5 455 623 608637862 608638024 5.270000e-53 219.0
15 TraesCS5D01G219100 chr5B 86.022 186 15 5 2416 2601 381714762 381714588 4.130000e-44 189.0
16 TraesCS5D01G219100 chr5B 85.143 175 14 6 893 1065 381716323 381716159 5.380000e-38 169.0
17 TraesCS5D01G219100 chr7B 90.857 175 7 5 451 623 490207985 490208152 3.150000e-55 226.0
18 TraesCS5D01G219100 chr2D 90.643 171 8 5 455 624 134301488 134301651 1.470000e-53 220.0
19 TraesCS5D01G219100 chr7D 89.831 177 7 6 451 623 465477778 465477947 1.900000e-52 217.0
20 TraesCS5D01G219100 chr7D 80.435 92 18 0 1898 1989 156455983 156456074 1.560000e-08 71.3
21 TraesCS5D01G219100 chr4B 89.326 178 10 7 451 626 406389291 406389461 6.820000e-52 215.0
22 TraesCS5D01G219100 chr2A 89.655 174 10 5 455 627 135473228 135473394 6.820000e-52 215.0
23 TraesCS5D01G219100 chr2A 81.106 217 41 0 1821 2037 148870578 148870794 1.160000e-39 174.0
24 TraesCS5D01G219100 chr3A 86.364 198 14 11 432 624 529671109 529671298 1.480000e-48 204.0
25 TraesCS5D01G219100 chr2B 81.106 217 41 0 1821 2037 210652590 210652374 1.160000e-39 174.0


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 TraesCS5D01G219100 chr5D 328433165 328436303 3138 True 2675.000000 5228 100.00000 1 3139 2 chr5D.!!$R2 3138
1 TraesCS5D01G219100 chr5D 328404415 328405090 675 True 955.000000 955 92.17100 1388 2063 1 chr5D.!!$R1 675
2 TraesCS5D01G219100 chr5A 428151509 428154933 3424 False 762.200000 2023 91.32240 1 2781 5 chr5A.!!$F1 2780
3 TraesCS5D01G219100 chr5A 428244728 428248181 3453 False 507.666667 1003 89.36400 1383 2226 3 chr5A.!!$F2 843
4 TraesCS5D01G219100 chr5B 381714588 381717155 2567 True 579.500000 1618 86.25225 36 2601 4 chr5B.!!$R2 2565

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
856 1404 0.038526 ACAGTTTCTACGACAGCGGG 60.039 55.0 0.0 0.0 43.17 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2506 5895 0.54851 GCTGGCTCAAGGGGAGTAAT 59.451 55.0 0.0 0.0 45.88 1.89 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
188 191 3.876309 ACACCTTGTCCCTTGTGTAAT 57.124 42.857 0.00 0.00 39.98 1.89
411 460 7.930217 CAGTTGACTGAGAAAGGTTTGAAATA 58.070 34.615 5.19 0.00 46.59 1.40
464 513 3.687125 TCAGCAGTATATACTCCCTCCG 58.313 50.000 12.62 2.17 33.46 4.63
478 527 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
479 528 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
512 561 5.760253 AGATTTCAATAAGGACTGCATACGG 59.240 40.000 0.00 0.00 0.00 4.02
513 562 4.746535 TTCAATAAGGACTGCATACGGA 57.253 40.909 0.00 0.00 0.00 4.69
514 563 4.955811 TCAATAAGGACTGCATACGGAT 57.044 40.909 0.00 0.00 0.00 4.18
515 564 4.883083 TCAATAAGGACTGCATACGGATC 58.117 43.478 0.00 0.00 0.00 3.36
517 566 2.604046 AAGGACTGCATACGGATCAC 57.396 50.000 0.00 0.00 0.00 3.06
574 1035 6.561614 TCACTCATTTTCTCCGTATGTAGTC 58.438 40.000 0.00 0.00 0.00 2.59
576 1037 5.421056 ACTCATTTTCTCCGTATGTAGTCCA 59.579 40.000 0.00 0.00 0.00 4.02
725 1204 4.144297 TGTCAAGTTTCTTCCATTCCTGG 58.856 43.478 0.00 0.00 44.64 4.45
726 1205 3.507622 GTCAAGTTTCTTCCATTCCTGGG 59.492 47.826 0.00 0.00 43.34 4.45
755 1303 3.567478 AGAGTTGGCTTCTTTCAGTGT 57.433 42.857 0.00 0.00 0.00 3.55
758 1306 3.620488 AGTTGGCTTCTTTCAGTGTCAA 58.380 40.909 0.00 0.00 0.00 3.18
759 1307 4.210331 AGTTGGCTTCTTTCAGTGTCAAT 58.790 39.130 0.00 0.00 0.00 2.57
792 1340 6.239945 CGTGAACAATGTTCAAACAAAAAGG 58.760 36.000 27.77 7.16 43.03 3.11
794 1342 5.123027 TGAACAATGTTCAAACAAAAAGGCC 59.877 36.000 24.63 0.00 43.03 5.19
797 1345 2.611518 TGTTCAAACAAAAAGGCCGTG 58.388 42.857 0.00 0.00 35.67 4.94
799 1347 2.857748 GTTCAAACAAAAAGGCCGTGAG 59.142 45.455 0.00 0.00 0.00 3.51
840 1388 0.605589 AGAAGAAGCCCACGAGACAG 59.394 55.000 0.00 0.00 0.00 3.51
853 1401 2.243407 CGAGACAGTTTCTACGACAGC 58.757 52.381 0.00 0.00 33.22 4.40
854 1402 2.243407 GAGACAGTTTCTACGACAGCG 58.757 52.381 0.00 0.00 37.99 5.18
855 1403 1.068472 AGACAGTTTCTACGACAGCGG 60.068 52.381 0.00 0.00 43.17 5.52
856 1404 0.038526 ACAGTTTCTACGACAGCGGG 60.039 55.000 0.00 0.00 43.17 6.13
857 1405 1.080025 AGTTTCTACGACAGCGGGC 60.080 57.895 0.00 0.00 43.17 6.13
859 1407 0.947180 GTTTCTACGACAGCGGGCAA 60.947 55.000 0.00 0.00 43.17 4.52
860 1408 0.249953 TTTCTACGACAGCGGGCAAA 60.250 50.000 0.00 0.00 43.17 3.68
861 1409 0.249953 TTCTACGACAGCGGGCAAAA 60.250 50.000 0.00 0.00 43.17 2.44
936 1609 4.021894 CCCTATCCTCATCTACTCCAAACG 60.022 50.000 0.00 0.00 0.00 3.60
986 1665 4.095400 GCTCCTCCCTCTCCCCCA 62.095 72.222 0.00 0.00 0.00 4.96
1020 1699 4.459089 GCGACTCCTCTGCCCACC 62.459 72.222 0.00 0.00 0.00 4.61
1128 1811 0.884704 AATGCTGAACCGTCGTTGCT 60.885 50.000 0.00 0.00 30.30 3.91
1176 1859 4.142359 TGAACTTCTGATCGAGCTTAGGAC 60.142 45.833 0.90 0.00 0.00 3.85
1402 2090 5.880054 AACTGAACCAATTTCATACTCCG 57.120 39.130 0.00 0.00 43.54 4.63
1403 2091 4.261801 ACTGAACCAATTTCATACTCCGG 58.738 43.478 0.00 0.00 43.54 5.14
1470 2167 1.904287 TTATTCCTGTGCTGCCGTTT 58.096 45.000 0.00 0.00 0.00 3.60
1533 2230 3.607661 GGATCGGAGCCGGAGTCC 61.608 72.222 5.05 9.79 40.25 3.85
1920 5212 1.745489 GATCAAGAACGGCCGCCTT 60.745 57.895 28.58 25.10 0.00 4.35
2053 5346 2.798834 ACGTACATGCAAATACACGC 57.201 45.000 10.38 0.00 32.90 5.34
2168 5479 1.074072 TGGCCAACGGTGTTGCTAT 59.926 52.632 0.61 0.00 0.00 2.97
2185 5496 2.867429 CTATGGCAGAAGGTTTTTGCG 58.133 47.619 0.00 0.00 38.69 4.85
2192 5503 2.099098 CAGAAGGTTTTTGCGGTGAACT 59.901 45.455 0.00 0.00 0.00 3.01
2201 5512 0.391228 TGCGGTGAACTTGAGCACTA 59.609 50.000 0.00 0.00 35.43 2.74
2202 5513 1.202592 TGCGGTGAACTTGAGCACTAA 60.203 47.619 0.00 0.00 35.43 2.24
2210 5521 3.492102 ACTTGAGCACTAAGGCTTTGA 57.508 42.857 15.50 0.00 45.99 2.69
2213 5524 1.003580 TGAGCACTAAGGCTTTGAGGG 59.996 52.381 15.50 5.29 45.99 4.30
2214 5525 0.322906 AGCACTAAGGCTTTGAGGGC 60.323 55.000 14.99 14.99 42.71 5.19
2215 5526 1.648467 GCACTAAGGCTTTGAGGGCG 61.648 60.000 15.50 0.00 36.85 6.13
2216 5527 0.321653 CACTAAGGCTTTGAGGGCGT 60.322 55.000 15.50 0.00 36.85 5.68
2222 5540 0.678048 GGCTTTGAGGGCGTCATCTT 60.678 55.000 11.09 0.00 34.17 2.40
2223 5541 0.449388 GCTTTGAGGGCGTCATCTTG 59.551 55.000 11.09 3.29 34.17 3.02
2275 5605 1.077429 GAGCCGGGGAAGATGCTTT 60.077 57.895 2.18 0.00 33.41 3.51
2276 5606 0.681243 GAGCCGGGGAAGATGCTTTT 60.681 55.000 2.18 0.00 33.41 2.27
2277 5607 0.623723 AGCCGGGGAAGATGCTTTTA 59.376 50.000 2.18 0.00 0.00 1.52
2278 5608 1.025041 GCCGGGGAAGATGCTTTTAG 58.975 55.000 2.18 0.00 0.00 1.85
2279 5609 1.682087 GCCGGGGAAGATGCTTTTAGT 60.682 52.381 2.18 0.00 0.00 2.24
2280 5610 2.017049 CCGGGGAAGATGCTTTTAGTG 58.983 52.381 0.00 0.00 0.00 2.74
2281 5611 2.355716 CCGGGGAAGATGCTTTTAGTGA 60.356 50.000 0.00 0.00 0.00 3.41
2335 5665 4.021456 AGGCCAAAACAAAATGCTACTACC 60.021 41.667 5.01 0.00 0.00 3.18
2347 5677 0.981183 CTACTACCACCACAGGCCAA 59.019 55.000 5.01 0.00 0.00 4.52
2366 5696 4.154195 GCCAAACAGTAACATCAGAATCGT 59.846 41.667 0.00 0.00 0.00 3.73
2370 5700 7.095397 CCAAACAGTAACATCAGAATCGTACAA 60.095 37.037 0.00 0.00 0.00 2.41
2454 5843 3.753842 ACGTGTGCAGTGTAAAACAAAG 58.246 40.909 0.00 0.00 0.00 2.77
2457 5846 3.093057 TGTGCAGTGTAAAACAAAGGGT 58.907 40.909 0.00 0.00 0.00 4.34
2479 5868 0.324614 AATGGTGTGGTCGATGCAGA 59.675 50.000 0.00 0.00 0.00 4.26
2485 5874 0.729116 GTGGTCGATGCAGACAATGG 59.271 55.000 8.22 0.00 42.62 3.16
2506 5895 1.063616 GCGCCGCTCGTCTATGATATA 59.936 52.381 0.00 0.00 41.07 0.86
2507 5896 2.287069 GCGCCGCTCGTCTATGATATAT 60.287 50.000 0.00 0.00 41.07 0.86
2508 5897 3.792459 GCGCCGCTCGTCTATGATATATT 60.792 47.826 0.00 0.00 41.07 1.28
2509 5898 4.554134 GCGCCGCTCGTCTATGATATATTA 60.554 45.833 0.00 0.00 41.07 0.98
2510 5899 4.904724 CGCCGCTCGTCTATGATATATTAC 59.095 45.833 0.00 0.00 0.00 1.89
2511 5900 5.277393 CGCCGCTCGTCTATGATATATTACT 60.277 44.000 0.00 0.00 0.00 2.24
2512 5901 6.137415 GCCGCTCGTCTATGATATATTACTC 58.863 44.000 0.00 0.00 0.00 2.59
2532 5923 1.605992 CCTTGAGCCAGCCATGAGA 59.394 57.895 0.00 0.00 0.00 3.27
2544 5935 5.278364 GCCAGCCATGAGATCATTTAGAAAG 60.278 44.000 0.00 0.00 33.61 2.62
2578 5969 2.176045 TCATGTCGTCCCTTGAGCTAA 58.824 47.619 0.00 0.00 0.00 3.09
2585 5976 2.674177 CGTCCCTTGAGCTAAACGATGT 60.674 50.000 0.00 0.00 32.17 3.06
2601 5992 2.742372 GTGTCAATGGTCGGCGCT 60.742 61.111 7.64 0.00 0.00 5.92
2626 6017 5.335897 GGTCTTTCAGCTCAAATATGTGCAA 60.336 40.000 0.00 0.00 46.03 4.08
2732 6123 3.004862 CCTGGAGATTTGCAATTTTGGC 58.995 45.455 0.00 0.00 0.00 4.52
2748 6139 5.379732 TTTTGGCGGTACAAGGAATTAAG 57.620 39.130 0.00 0.00 0.00 1.85
2781 6172 5.331876 ACAGTGTTAGAACATCTCTAGCC 57.668 43.478 0.00 0.00 41.59 3.93
2782 6173 4.142359 ACAGTGTTAGAACATCTCTAGCCG 60.142 45.833 0.00 0.00 41.59 5.52
2783 6174 4.096532 CAGTGTTAGAACATCTCTAGCCGA 59.903 45.833 0.00 0.00 41.59 5.54
2784 6175 4.705507 AGTGTTAGAACATCTCTAGCCGAA 59.294 41.667 0.00 0.00 41.59 4.30
2785 6176 4.799428 GTGTTAGAACATCTCTAGCCGAAC 59.201 45.833 0.00 0.00 41.59 3.95
2786 6177 4.142227 TGTTAGAACATCTCTAGCCGAACC 60.142 45.833 0.00 0.00 37.93 3.62
2787 6178 1.757699 AGAACATCTCTAGCCGAACCC 59.242 52.381 0.00 0.00 30.22 4.11
2788 6179 1.757699 GAACATCTCTAGCCGAACCCT 59.242 52.381 0.00 0.00 0.00 4.34
2789 6180 1.867363 ACATCTCTAGCCGAACCCTT 58.133 50.000 0.00 0.00 0.00 3.95
2790 6181 3.028094 ACATCTCTAGCCGAACCCTTA 57.972 47.619 0.00 0.00 0.00 2.69
2791 6182 2.959707 ACATCTCTAGCCGAACCCTTAG 59.040 50.000 0.00 0.00 0.00 2.18
2792 6183 3.223435 CATCTCTAGCCGAACCCTTAGA 58.777 50.000 0.00 0.00 0.00 2.10
2793 6184 3.377253 TCTCTAGCCGAACCCTTAGAA 57.623 47.619 0.00 0.00 0.00 2.10
2794 6185 3.705051 TCTCTAGCCGAACCCTTAGAAA 58.295 45.455 0.00 0.00 0.00 2.52
2795 6186 3.700038 TCTCTAGCCGAACCCTTAGAAAG 59.300 47.826 0.00 0.00 0.00 2.62
2796 6187 3.438183 TCTAGCCGAACCCTTAGAAAGT 58.562 45.455 0.00 0.00 0.00 2.66
2797 6188 3.836562 TCTAGCCGAACCCTTAGAAAGTT 59.163 43.478 0.00 0.00 0.00 2.66
2798 6189 3.503800 AGCCGAACCCTTAGAAAGTTT 57.496 42.857 0.00 0.00 0.00 2.66
2799 6190 4.628963 AGCCGAACCCTTAGAAAGTTTA 57.371 40.909 0.00 0.00 0.00 2.01
2800 6191 4.576879 AGCCGAACCCTTAGAAAGTTTAG 58.423 43.478 0.00 0.00 0.00 1.85
2801 6192 3.126514 GCCGAACCCTTAGAAAGTTTAGC 59.873 47.826 0.00 0.00 0.00 3.09
2802 6193 4.576879 CCGAACCCTTAGAAAGTTTAGCT 58.423 43.478 0.00 0.00 0.00 3.32
2803 6194 4.630505 CCGAACCCTTAGAAAGTTTAGCTC 59.369 45.833 0.00 0.00 0.00 4.09
2804 6195 5.235516 CGAACCCTTAGAAAGTTTAGCTCA 58.764 41.667 0.00 0.00 0.00 4.26
2805 6196 5.875359 CGAACCCTTAGAAAGTTTAGCTCAT 59.125 40.000 0.00 0.00 0.00 2.90
2806 6197 7.039882 CGAACCCTTAGAAAGTTTAGCTCATA 58.960 38.462 0.00 0.00 0.00 2.15
2807 6198 7.548075 CGAACCCTTAGAAAGTTTAGCTCATAA 59.452 37.037 0.00 0.00 0.00 1.90
2808 6199 9.397280 GAACCCTTAGAAAGTTTAGCTCATAAT 57.603 33.333 0.00 0.00 0.00 1.28
2809 6200 9.755122 AACCCTTAGAAAGTTTAGCTCATAATT 57.245 29.630 0.00 0.00 0.00 1.40
2810 6201 9.755122 ACCCTTAGAAAGTTTAGCTCATAATTT 57.245 29.630 0.00 0.00 0.00 1.82
2830 6221 1.799544 TTTTACGGAGAACCCTTCGC 58.200 50.000 0.00 0.00 45.19 4.70
3090 6481 2.562912 CCATGCCAGCGTCAACAC 59.437 61.111 0.00 0.00 0.00 3.32
3091 6482 2.562912 CATGCCAGCGTCAACACC 59.437 61.111 0.00 0.00 0.00 4.16
3092 6483 2.672996 ATGCCAGCGTCAACACCC 60.673 61.111 0.00 0.00 0.00 4.61
3094 6485 4.980805 GCCAGCGTCAACACCCGA 62.981 66.667 0.00 0.00 0.00 5.14
3095 6486 2.047274 CCAGCGTCAACACCCGAT 60.047 61.111 0.00 0.00 0.00 4.18
3096 6487 1.216977 CCAGCGTCAACACCCGATA 59.783 57.895 0.00 0.00 0.00 2.92
3097 6488 0.806102 CCAGCGTCAACACCCGATAG 60.806 60.000 0.00 0.00 0.00 2.08
3098 6489 1.153628 AGCGTCAACACCCGATAGC 60.154 57.895 0.00 0.00 0.00 2.97
3099 6490 1.447140 GCGTCAACACCCGATAGCA 60.447 57.895 0.00 0.00 0.00 3.49
3100 6491 1.421410 GCGTCAACACCCGATAGCAG 61.421 60.000 0.00 0.00 0.00 4.24
3101 6492 0.806102 CGTCAACACCCGATAGCAGG 60.806 60.000 0.00 0.00 0.00 4.85
3102 6493 1.090052 GTCAACACCCGATAGCAGGC 61.090 60.000 0.00 0.00 0.00 4.85
3103 6494 1.819632 CAACACCCGATAGCAGGCC 60.820 63.158 0.00 0.00 0.00 5.19
3104 6495 3.385749 AACACCCGATAGCAGGCCG 62.386 63.158 0.00 0.00 0.00 6.13
3109 6500 3.303135 CGATAGCAGGCCGCCCTA 61.303 66.667 14.64 8.86 44.04 3.53
3110 6501 2.344129 GATAGCAGGCCGCCCTAC 59.656 66.667 14.64 0.00 44.04 3.18
3111 6502 2.122813 ATAGCAGGCCGCCCTACT 60.123 61.111 14.64 3.63 44.04 2.57
3112 6503 1.759459 GATAGCAGGCCGCCCTACTT 61.759 60.000 14.64 0.06 44.04 2.24
3113 6504 1.759459 ATAGCAGGCCGCCCTACTTC 61.759 60.000 14.64 0.00 44.04 3.01
3117 6508 4.091939 GGCCGCCCTACTTCGGTT 62.092 66.667 0.00 0.00 46.79 4.44
3118 6509 2.510918 GCCGCCCTACTTCGGTTC 60.511 66.667 2.58 0.00 46.79 3.62
3119 6510 2.202703 CCGCCCTACTTCGGTTCG 60.203 66.667 0.00 0.00 40.72 3.95
3120 6511 2.884207 CGCCCTACTTCGGTTCGC 60.884 66.667 0.00 0.00 0.00 4.70
3121 6512 2.577593 GCCCTACTTCGGTTCGCT 59.422 61.111 0.00 0.00 0.00 4.93
3122 6513 1.079336 GCCCTACTTCGGTTCGCTT 60.079 57.895 0.00 0.00 0.00 4.68
3123 6514 1.082679 GCCCTACTTCGGTTCGCTTC 61.083 60.000 0.00 0.00 0.00 3.86
3124 6515 0.459759 CCCTACTTCGGTTCGCTTCC 60.460 60.000 0.00 0.00 0.00 3.46
3125 6516 0.459759 CCTACTTCGGTTCGCTTCCC 60.460 60.000 0.00 0.00 0.00 3.97
3126 6517 0.245539 CTACTTCGGTTCGCTTCCCA 59.754 55.000 0.00 0.00 0.00 4.37
3127 6518 0.037975 TACTTCGGTTCGCTTCCCAC 60.038 55.000 0.00 0.00 0.00 4.61
3128 6519 1.301401 CTTCGGTTCGCTTCCCACA 60.301 57.895 0.00 0.00 0.00 4.17
3129 6520 1.291877 CTTCGGTTCGCTTCCCACAG 61.292 60.000 0.00 0.00 0.00 3.66
3130 6521 3.423154 CGGTTCGCTTCCCACAGC 61.423 66.667 0.00 0.00 36.33 4.40
3131 6522 3.056328 GGTTCGCTTCCCACAGCC 61.056 66.667 0.00 0.00 36.31 4.85
3132 6523 3.423154 GTTCGCTTCCCACAGCCG 61.423 66.667 0.00 0.00 36.31 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 6.494491 AGGGATGAAATGTGAAAACAGATGAA 59.506 34.615 0.00 0.00 0.00 2.57
188 191 8.103305 AGACTAGCAGAATAAGATTTGTTCCAA 58.897 33.333 0.00 0.00 31.92 3.53
325 332 6.099125 TCACCCTCTATGAATCCGTAAATCAA 59.901 38.462 0.00 0.00 0.00 2.57
431 480 1.283347 ACTGCTGATCCCTGACATGT 58.717 50.000 0.00 0.00 0.00 3.21
494 543 4.449068 GTGATCCGTATGCAGTCCTTATTG 59.551 45.833 0.00 0.00 0.00 1.90
497 546 2.034179 CGTGATCCGTATGCAGTCCTTA 59.966 50.000 0.00 0.00 0.00 2.69
505 554 2.717580 TACATCCGTGATCCGTATGC 57.282 50.000 8.38 0.00 36.45 3.14
544 1004 7.923344 ACATACGGAGAAAATGAGTGAATCTAG 59.077 37.037 0.00 0.00 0.00 2.43
612 1073 9.747898 TTTTGTACCAAATGTAATACTCCATCT 57.252 29.630 0.00 0.00 0.00 2.90
614 1075 9.747898 TCTTTTGTACCAAATGTAATACTCCAT 57.252 29.630 0.00 0.00 0.00 3.41
615 1076 9.575868 TTCTTTTGTACCAAATGTAATACTCCA 57.424 29.630 0.00 0.00 0.00 3.86
660 1122 6.620877 TTTGGATGGACTAGTACTGACAAT 57.379 37.500 6.66 0.00 0.00 2.71
755 1303 1.071542 TGTTCACGGCCTTCTCATTGA 59.928 47.619 0.00 0.00 0.00 2.57
758 1306 2.086869 CATTGTTCACGGCCTTCTCAT 58.913 47.619 0.00 0.00 0.00 2.90
759 1307 1.202758 ACATTGTTCACGGCCTTCTCA 60.203 47.619 0.00 0.00 0.00 3.27
797 1345 1.031571 TGGATGCCCATTCGTTGCTC 61.032 55.000 0.00 0.00 37.58 4.26
799 1347 0.458370 GTTGGATGCCCATTCGTTGC 60.458 55.000 0.00 0.00 43.12 4.17
807 1355 3.873801 GCTTCTTCTAAGTTGGATGCCCA 60.874 47.826 0.00 0.00 41.64 5.36
840 1388 0.947180 TTGCCCGCTGTCGTAGAAAC 60.947 55.000 0.00 0.00 39.69 2.78
1030 1709 1.375908 GTTGGAGGCGACATGCTGA 60.376 57.895 0.00 0.00 45.43 4.26
1065 1744 4.870363 TCAAAGCAAATTTACCAGAGCAC 58.130 39.130 0.00 0.00 0.00 4.40
1128 1811 3.057548 CAAGCAGACGGGCATGCA 61.058 61.111 21.36 0.00 45.01 3.96
1195 1878 3.323758 ATTCTGCACCGGCGGCTTA 62.324 57.895 28.71 11.32 46.35 3.09
1402 2090 0.808755 ATTTTCCACGAACGATGCCC 59.191 50.000 0.14 0.00 0.00 5.36
1403 2091 2.536130 CGTATTTTCCACGAACGATGCC 60.536 50.000 0.14 0.00 41.91 4.40
1704 4587 3.285215 CCCATGAGCGCCATCTGC 61.285 66.667 2.29 0.00 31.94 4.26
1920 5212 4.393155 ACGAAGGCGAGCATGGCA 62.393 61.111 4.64 0.00 43.90 4.92
2045 5338 7.859325 AATCATAAGTAACCAAGCGTGTATT 57.141 32.000 0.00 0.00 0.00 1.89
2051 5344 5.235305 AGCAAATCATAAGTAACCAAGCG 57.765 39.130 0.00 0.00 0.00 4.68
2053 5346 7.752239 CACAGAAGCAAATCATAAGTAACCAAG 59.248 37.037 0.00 0.00 0.00 3.61
2168 5479 1.040339 ACCGCAAAAACCTTCTGCCA 61.040 50.000 0.00 0.00 32.27 4.92
2185 5496 1.807142 GCCTTAGTGCTCAAGTTCACC 59.193 52.381 0.00 0.00 33.90 4.02
2192 5503 2.553028 CCCTCAAAGCCTTAGTGCTCAA 60.553 50.000 0.00 0.00 41.80 3.02
2201 5512 0.678048 GATGACGCCCTCAAAGCCTT 60.678 55.000 0.00 0.00 30.60 4.35
2202 5513 1.078143 GATGACGCCCTCAAAGCCT 60.078 57.895 0.00 0.00 30.60 4.58
2213 5524 2.480555 CAACGGGCAAGATGACGC 59.519 61.111 0.00 0.00 0.00 5.19
2214 5525 0.953471 TTCCAACGGGCAAGATGACG 60.953 55.000 0.00 0.00 0.00 4.35
2215 5526 1.243902 TTTCCAACGGGCAAGATGAC 58.756 50.000 0.00 0.00 0.00 3.06
2216 5527 1.988293 TTTTCCAACGGGCAAGATGA 58.012 45.000 0.00 0.00 0.00 2.92
2222 5540 1.403814 TTCACATTTTCCAACGGGCA 58.596 45.000 0.00 0.00 0.00 5.36
2223 5541 2.741759 ATTCACATTTTCCAACGGGC 57.258 45.000 0.00 0.00 0.00 6.13
2227 5545 8.519526 TCCACTGTAATATTCACATTTTCCAAC 58.480 33.333 0.00 0.00 0.00 3.77
2258 5588 0.623723 TAAAAGCATCTTCCCCGGCT 59.376 50.000 0.00 0.00 38.45 5.52
2335 5665 1.336755 GTTACTGTTTGGCCTGTGGTG 59.663 52.381 3.32 0.00 0.00 4.17
2347 5677 7.116376 CAGTTGTACGATTCTGATGTTACTGTT 59.884 37.037 0.00 0.00 0.00 3.16
2366 5696 7.430211 CGCGTATCAAGAAGTATAACAGTTGTA 59.570 37.037 0.00 0.00 0.00 2.41
2370 5700 5.888105 ACGCGTATCAAGAAGTATAACAGT 58.112 37.500 11.67 0.00 0.00 3.55
2454 5843 0.899720 TCGACCACACCATTCTACCC 59.100 55.000 0.00 0.00 0.00 3.69
2457 5846 1.552792 TGCATCGACCACACCATTCTA 59.447 47.619 0.00 0.00 0.00 2.10
2485 5874 2.196382 TATCATAGACGAGCGGCGCC 62.196 60.000 30.40 19.07 46.04 6.53
2497 5886 7.345653 TGGCTCAAGGGGAGTAATATATCATAG 59.654 40.741 0.00 0.00 45.88 2.23
2506 5895 0.548510 GCTGGCTCAAGGGGAGTAAT 59.451 55.000 0.00 0.00 45.88 1.89
2507 5896 1.562672 GGCTGGCTCAAGGGGAGTAA 61.563 60.000 0.00 0.00 45.88 2.24
2508 5897 1.995626 GGCTGGCTCAAGGGGAGTA 60.996 63.158 0.00 0.00 45.88 2.59
2509 5898 3.334054 GGCTGGCTCAAGGGGAGT 61.334 66.667 0.00 0.00 45.88 3.85
2510 5899 2.687610 ATGGCTGGCTCAAGGGGAG 61.688 63.158 2.00 0.00 46.93 4.30
2511 5900 2.614969 ATGGCTGGCTCAAGGGGA 60.615 61.111 2.00 0.00 0.00 4.81
2512 5901 2.441532 CATGGCTGGCTCAAGGGG 60.442 66.667 2.00 0.00 0.00 4.79
2532 5923 6.879400 AGCTCGGTAAGACTTTCTAAATGAT 58.121 36.000 0.00 0.00 0.00 2.45
2544 5935 3.003482 ACGACATGATAGCTCGGTAAGAC 59.997 47.826 0.00 0.00 0.00 3.01
2578 5969 1.438651 CCGACCATTGACACATCGTT 58.561 50.000 0.00 0.00 0.00 3.85
2585 5976 2.741985 CAGCGCCGACCATTGACA 60.742 61.111 2.29 0.00 0.00 3.58
2601 5992 4.156556 GCACATATTTGAGCTGAAAGACCA 59.843 41.667 4.30 0.00 36.62 4.02
2617 6008 5.916883 GCTCTCGCATTTTATTTGCACATAT 59.083 36.000 0.00 0.00 40.14 1.78
2647 6038 1.238439 TGCTTCTTAACAGCACCAGC 58.762 50.000 1.13 0.00 42.49 4.85
2656 6047 6.401581 GCTGTCAGAACACTATGCTTCTTAAC 60.402 42.308 3.32 0.00 0.00 2.01
2695 6086 1.472904 CCAGGACTACATGAGCAGCTG 60.473 57.143 10.11 10.11 0.00 4.24
2732 6123 6.428771 TGGTTCTTTCTTAATTCCTTGTACCG 59.571 38.462 0.00 0.00 0.00 4.02
2748 6139 6.848451 TGTTCTAACACTGTTTGGTTCTTTC 58.152 36.000 0.00 0.00 33.17 2.62
2781 6172 5.235516 TGAGCTAAACTTTCTAAGGGTTCG 58.764 41.667 0.00 0.00 0.00 3.95
2782 6173 8.788325 TTATGAGCTAAACTTTCTAAGGGTTC 57.212 34.615 0.00 0.00 0.00 3.62
2783 6174 9.755122 AATTATGAGCTAAACTTTCTAAGGGTT 57.245 29.630 0.00 0.00 0.00 4.11
2784 6175 9.755122 AAATTATGAGCTAAACTTTCTAAGGGT 57.245 29.630 0.00 0.00 0.00 4.34
2810 6201 2.145536 GCGAAGGGTTCTCCGTAAAAA 58.854 47.619 0.00 0.00 41.52 1.94
2811 6202 1.799544 GCGAAGGGTTCTCCGTAAAA 58.200 50.000 0.00 0.00 41.52 1.52
2812 6203 3.520187 GCGAAGGGTTCTCCGTAAA 57.480 52.632 0.00 0.00 41.52 2.01
3073 6464 2.562912 GTGTTGACGCTGGCATGG 59.437 61.111 0.00 0.00 0.00 3.66
3074 6465 2.562912 GGTGTTGACGCTGGCATG 59.437 61.111 0.00 0.00 0.00 4.06
3075 6466 2.672996 GGGTGTTGACGCTGGCAT 60.673 61.111 0.00 0.00 32.30 4.40
3077 6468 2.845752 TATCGGGTGTTGACGCTGGC 62.846 60.000 0.00 0.00 32.85 4.85
3078 6469 0.806102 CTATCGGGTGTTGACGCTGG 60.806 60.000 0.00 0.00 32.85 4.85
3079 6470 1.421410 GCTATCGGGTGTTGACGCTG 61.421 60.000 0.00 0.00 32.85 5.18
3080 6471 1.153628 GCTATCGGGTGTTGACGCT 60.154 57.895 0.00 0.00 32.85 5.07
3081 6472 1.421410 CTGCTATCGGGTGTTGACGC 61.421 60.000 0.00 0.00 0.00 5.19
3082 6473 0.806102 CCTGCTATCGGGTGTTGACG 60.806 60.000 0.00 0.00 33.91 4.35
3083 6474 1.090052 GCCTGCTATCGGGTGTTGAC 61.090 60.000 0.00 0.00 40.99 3.18
3084 6475 1.220749 GCCTGCTATCGGGTGTTGA 59.779 57.895 0.00 0.00 40.99 3.18
3085 6476 1.819632 GGCCTGCTATCGGGTGTTG 60.820 63.158 0.00 0.00 40.99 3.33
3086 6477 2.590092 GGCCTGCTATCGGGTGTT 59.410 61.111 0.00 0.00 40.99 3.32
3087 6478 3.849951 CGGCCTGCTATCGGGTGT 61.850 66.667 0.00 0.00 40.99 4.16
3092 6483 3.303135 TAGGGCGGCCTGCTATCG 61.303 66.667 38.60 0.00 45.43 2.92
3093 6484 1.759459 AAGTAGGGCGGCCTGCTATC 61.759 60.000 41.13 24.12 45.43 2.08
3094 6485 1.759459 GAAGTAGGGCGGCCTGCTAT 61.759 60.000 41.13 30.98 45.43 2.97
3095 6486 2.365105 AAGTAGGGCGGCCTGCTA 60.365 61.111 41.13 21.44 45.43 3.49
3096 6487 3.787001 GAAGTAGGGCGGCCTGCT 61.787 66.667 37.39 37.39 45.43 4.24
3098 6489 4.530857 CCGAAGTAGGGCGGCCTG 62.531 72.222 38.60 21.98 41.17 4.85
3103 6494 2.830704 AAGCGAACCGAAGTAGGGCG 62.831 60.000 0.00 0.00 36.64 6.13
3104 6495 1.079336 AAGCGAACCGAAGTAGGGC 60.079 57.895 0.00 0.00 35.02 5.19
3105 6496 0.459759 GGAAGCGAACCGAAGTAGGG 60.460 60.000 0.00 0.00 35.02 3.53
3106 6497 0.459759 GGGAAGCGAACCGAAGTAGG 60.460 60.000 0.00 0.00 37.30 3.18
3107 6498 0.245539 TGGGAAGCGAACCGAAGTAG 59.754 55.000 0.00 0.00 0.00 2.57
3108 6499 0.037975 GTGGGAAGCGAACCGAAGTA 60.038 55.000 0.00 0.00 0.00 2.24
3109 6500 1.301479 GTGGGAAGCGAACCGAAGT 60.301 57.895 0.00 0.00 0.00 3.01
3110 6501 1.291877 CTGTGGGAAGCGAACCGAAG 61.292 60.000 0.00 0.00 0.00 3.79
3111 6502 1.301401 CTGTGGGAAGCGAACCGAA 60.301 57.895 0.00 0.00 0.00 4.30
3112 6503 2.342279 CTGTGGGAAGCGAACCGA 59.658 61.111 0.00 0.00 0.00 4.69
3113 6504 3.423154 GCTGTGGGAAGCGAACCG 61.423 66.667 0.00 0.00 32.56 4.44
3114 6505 3.056328 GGCTGTGGGAAGCGAACC 61.056 66.667 0.00 0.00 44.52 3.62
3115 6506 3.423154 CGGCTGTGGGAAGCGAAC 61.423 66.667 0.00 0.00 44.52 3.95


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

AutoCloner maintained by Alex Coulton.