Multiple sequence alignment - TraesCS5B01G531000

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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 TraesCS5B01G531000 chr5B 100.000 3488 0 0 1 3488 689332766 689329279 0.000000e+00 6442.0
1 TraesCS5B01G531000 chr5B 86.376 1424 169 12 969 2379 689315465 689316876 0.000000e+00 1531.0
2 TraesCS5B01G531000 chr5B 83.937 1214 149 27 1027 2235 480170801 480171973 0.000000e+00 1120.0
3 TraesCS5B01G531000 chr5B 86.170 1034 116 14 1208 2232 480165338 480166353 0.000000e+00 1092.0
4 TraesCS5B01G531000 chrUn 93.444 2700 104 28 2 2675 29845995 29848647 0.000000e+00 3938.0
5 TraesCS5B01G531000 chrUn 86.657 1454 165 17 984 2432 28787044 28785615 0.000000e+00 1583.0
6 TraesCS5B01G531000 chrUn 85.428 1448 189 10 969 2405 29852386 29850950 0.000000e+00 1485.0
7 TraesCS5B01G531000 chrUn 85.450 1457 172 19 997 2431 29527522 29526084 0.000000e+00 1480.0
8 TraesCS5B01G531000 chrUn 85.066 1212 145 11 997 2196 29652564 29651377 0.000000e+00 1203.0
9 TraesCS5B01G531000 chrUn 88.414 561 29 16 2951 3488 29849738 29850285 0.000000e+00 643.0
10 TraesCS5B01G531000 chrUn 84.144 555 62 9 1260 1802 29831314 29831854 6.680000e-142 514.0
11 TraesCS5B01G531000 chrUn 93.536 263 13 1 2695 2953 29849441 29849703 4.220000e-104 388.0
12 TraesCS5B01G531000 chr5A 85.432 1469 177 25 969 2416 684197265 684198717 0.000000e+00 1493.0
13 TraesCS5B01G531000 chr5A 83.825 1187 146 27 1027 2208 505597989 505599134 0.000000e+00 1086.0
14 TraesCS5B01G531000 chr5A 84.793 605 66 14 1220 1810 706295724 706296316 5.020000e-163 584.0
15 TraesCS5B01G531000 chr5A 100.000 28 0 0 2581 2608 522490428 522490401 6.000000e-03 52.8
16 TraesCS5B01G531000 chr4B 84.116 1448 188 25 997 2416 668100608 668102041 0.000000e+00 1362.0
17 TraesCS5B01G531000 chr4B 84.116 1448 188 25 997 2416 668108266 668109699 0.000000e+00 1362.0
18 TraesCS5B01G531000 chr4B 91.200 125 11 0 3358 3482 667693989 667694113 1.660000e-38 171.0
19 TraesCS5B01G531000 chr4A 84.496 129 18 1 2487 2615 113849235 113849109 3.650000e-25 126.0
20 TraesCS5B01G531000 chr4A 90.566 53 3 2 458 509 40868025 40868076 6.250000e-08 69.4
21 TraesCS5B01G531000 chr7A 80.233 86 16 1 401 485 677660262 677660177 2.910000e-06 63.9
22 TraesCS5B01G531000 chr3A 93.023 43 3 0 2664 2706 80501547 80501505 2.910000e-06 63.9
23 TraesCS5B01G531000 chr1B 93.333 45 0 3 2664 2705 415723235 415723191 2.910000e-06 63.9
24 TraesCS5B01G531000 chr1B 89.130 46 5 0 2660 2705 182642929 182642884 1.350000e-04 58.4
25 TraesCS5B01G531000 chr7B 95.000 40 1 1 2667 2705 549594819 549594780 1.050000e-05 62.1
26 TraesCS5B01G531000 chr6B 92.857 42 1 1 2664 2705 107177852 107177891 3.760000e-05 60.2
27 TraesCS5B01G531000 chr6B 86.792 53 4 2 2653 2705 7361037 7360988 4.860000e-04 56.5
28 TraesCS5B01G531000 chr6B 86.792 53 4 2 2653 2705 7402765 7402716 4.860000e-04 56.5
29 TraesCS5B01G531000 chr6B 82.090 67 11 1 419 485 84859997 84859932 4.860000e-04 56.5
30 TraesCS5B01G531000 chr2A 100.000 32 0 0 2674 2705 125456126 125456095 3.760000e-05 60.2
31 TraesCS5B01G531000 chr3B 86.538 52 5 2 2656 2705 369797971 369798022 4.860000e-04 56.5
32 TraesCS5B01G531000 chr1A 86.000 50 7 0 2581 2630 538682291 538682242 2.000000e-03 54.7
33 TraesCS5B01G531000 chr6D 100.000 28 0 0 458 485 36584218 36584191 6.000000e-03 52.8
34 TraesCS5B01G531000 chr3D 81.538 65 11 1 421 485 170929831 170929768 6.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G531000 chr5B 689329279 689332766 3487 True 6442.000000 6442 100.000 1 3488 1 chr5B.!!$R1 3487
1 TraesCS5B01G531000 chr5B 689315465 689316876 1411 False 1531.000000 1531 86.376 969 2379 1 chr5B.!!$F3 1410
2 TraesCS5B01G531000 chr5B 480170801 480171973 1172 False 1120.000000 1120 83.937 1027 2235 1 chr5B.!!$F2 1208
3 TraesCS5B01G531000 chr5B 480165338 480166353 1015 False 1092.000000 1092 86.170 1208 2232 1 chr5B.!!$F1 1024
4 TraesCS5B01G531000 chrUn 29845995 29850285 4290 False 1656.333333 3938 91.798 2 3488 3 chrUn.!!$F2 3486
5 TraesCS5B01G531000 chrUn 28785615 28787044 1429 True 1583.000000 1583 86.657 984 2432 1 chrUn.!!$R1 1448
6 TraesCS5B01G531000 chrUn 29850950 29852386 1436 True 1485.000000 1485 85.428 969 2405 1 chrUn.!!$R4 1436
7 TraesCS5B01G531000 chrUn 29526084 29527522 1438 True 1480.000000 1480 85.450 997 2431 1 chrUn.!!$R2 1434
8 TraesCS5B01G531000 chrUn 29651377 29652564 1187 True 1203.000000 1203 85.066 997 2196 1 chrUn.!!$R3 1199
9 TraesCS5B01G531000 chrUn 29831314 29831854 540 False 514.000000 514 84.144 1260 1802 1 chrUn.!!$F1 542
10 TraesCS5B01G531000 chr5A 684197265 684198717 1452 False 1493.000000 1493 85.432 969 2416 1 chr5A.!!$F2 1447
11 TraesCS5B01G531000 chr5A 505597989 505599134 1145 False 1086.000000 1086 83.825 1027 2208 1 chr5A.!!$F1 1181
12 TraesCS5B01G531000 chr5A 706295724 706296316 592 False 584.000000 584 84.793 1220 1810 1 chr5A.!!$F3 590
13 TraesCS5B01G531000 chr4B 668100608 668102041 1433 False 1362.000000 1362 84.116 997 2416 1 chr4B.!!$F2 1419
14 TraesCS5B01G531000 chr4B 668108266 668109699 1433 False 1362.000000 1362 84.116 997 2416 1 chr4B.!!$F3 1419

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
759 770 0.251634 AAGCAGAGCAGGACTAAGCC 59.748 55.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2587 2698 0.035458 CACTCCACAACTCCACTCCC 59.965 60.0 0.0 0.0 0.0 4.3 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
105 106 3.334881 AGATCAATGTCCCAGGAAAGGTT 59.665 43.478 0.00 0.00 0.00 3.50
203 206 3.521947 AATACAACTACTGACTCCGGC 57.478 47.619 0.00 0.00 0.00 6.13
246 249 1.873903 CGAGCACATATACCACCTGCC 60.874 57.143 0.00 0.00 0.00 4.85
254 257 0.398696 ATACCACCTGCCGTGAACAA 59.601 50.000 2.71 0.00 46.20 2.83
256 259 0.467290 ACCACCTGCCGTGAACAATT 60.467 50.000 2.71 0.00 46.20 2.32
265 268 6.866248 ACCTGCCGTGAACAATTAATTAAAAG 59.134 34.615 1.21 0.65 0.00 2.27
266 269 6.310224 CCTGCCGTGAACAATTAATTAAAAGG 59.690 38.462 1.21 1.98 0.00 3.11
269 272 8.091449 TGCCGTGAACAATTAATTAAAAGGAAT 58.909 29.630 1.21 0.00 0.00 3.01
315 318 5.493133 TGTTTAATGTTTCGAGTGCAAGT 57.507 34.783 0.00 0.00 0.00 3.16
326 329 4.627058 TCGAGTGCAAGTAAGTTTCATCA 58.373 39.130 0.00 0.00 0.00 3.07
353 356 1.261619 GTCATCGACGGAATTCATGGC 59.738 52.381 7.93 0.00 0.00 4.40
355 358 1.670295 CATCGACGGAATTCATGGCAA 59.330 47.619 7.93 0.00 0.00 4.52
356 359 1.814793 TCGACGGAATTCATGGCAAA 58.185 45.000 7.93 0.00 0.00 3.68
357 360 2.155279 TCGACGGAATTCATGGCAAAA 58.845 42.857 7.93 0.00 0.00 2.44
358 361 2.554462 TCGACGGAATTCATGGCAAAAA 59.446 40.909 7.93 0.00 0.00 1.94
405 408 8.831715 AAAATGCTTTTGAAAATCGGTTCTAT 57.168 26.923 0.00 0.00 0.00 1.98
408 411 5.475220 TGCTTTTGAAAATCGGTTCTATGGA 59.525 36.000 0.00 0.00 0.00 3.41
469 472 5.538053 TGGTATTCCTTCATGAAACTTTGCA 59.462 36.000 9.88 0.00 34.23 4.08
514 517 7.672983 TTGTTTGCCACAAAAGAAAACATAA 57.327 28.000 0.00 0.00 42.76 1.90
688 696 3.259064 GCCACGCAGATCAGTACTTAAA 58.741 45.455 0.00 0.00 0.00 1.52
692 703 6.622896 GCCACGCAGATCAGTACTTAAATTTT 60.623 38.462 0.00 0.00 0.00 1.82
745 756 6.804534 TTGTTTATTTTTGTGACGAAGCAG 57.195 33.333 0.00 0.00 0.00 4.24
758 769 1.650825 GAAGCAGAGCAGGACTAAGC 58.349 55.000 0.00 0.00 0.00 3.09
759 770 0.251634 AAGCAGAGCAGGACTAAGCC 59.748 55.000 0.00 0.00 0.00 4.35
760 771 1.153269 GCAGAGCAGGACTAAGCCC 60.153 63.158 0.00 0.00 0.00 5.19
800 811 7.806487 CGACTAAACTAACATCAGTTCACACTA 59.194 37.037 0.00 0.00 37.78 2.74
930 945 8.674607 CATCAATCGTGGCATATACTACTACTA 58.325 37.037 0.00 0.00 0.00 1.82
1161 1194 2.584608 GGGCAGTGGCTGTACGAT 59.415 61.111 17.16 0.00 40.87 3.73
1228 1267 0.250038 CGTGCCCAGCAGCATATACT 60.250 55.000 0.00 0.00 46.24 2.12
1445 1484 2.047655 GGCCATGTCGACGTCCAA 60.048 61.111 7.47 0.00 0.00 3.53
1446 1485 2.100631 GGCCATGTCGACGTCCAAG 61.101 63.158 7.47 0.00 0.00 3.61
1447 1486 2.100631 GCCATGTCGACGTCCAAGG 61.101 63.158 7.47 10.58 0.00 3.61
1460 1502 2.132996 CCAAGGCCAAGGCAACACA 61.133 57.895 13.87 0.00 44.11 3.72
1537 1609 2.272797 CGGAGGAGGACGAGGAGT 59.727 66.667 0.00 0.00 0.00 3.85
1710 1789 4.966787 GGCGGGGACAGTGGCAAA 62.967 66.667 0.00 0.00 0.00 3.68
1938 2039 1.034292 GGTACGCCTACTCGTTCCCT 61.034 60.000 1.35 0.00 41.91 4.20
1944 2045 2.105766 GCCTACTCGTTCCCTTTCCTA 58.894 52.381 0.00 0.00 0.00 2.94
1996 2097 4.203076 GCTATGTCGTCGGGCCGT 62.203 66.667 27.32 7.89 0.00 5.68
2016 2117 2.029964 TTCGAGCACGTGTTCCCC 59.970 61.111 24.21 4.43 40.69 4.81
2159 2260 2.202987 GGAGGAGATGCTGCGGTG 60.203 66.667 0.00 0.00 0.00 4.94
2187 2288 3.249189 AACCTCTGCGCCAGGGAA 61.249 61.111 22.82 0.00 32.95 3.97
2275 2379 2.531771 TCGGGGAGAAGTATTGTGACA 58.468 47.619 0.00 0.00 0.00 3.58
2385 2495 1.284982 ATGACAGCGAGAACGTGCAC 61.285 55.000 6.82 6.82 41.98 4.57
2444 2554 1.600413 GCTCAAGGTCAAGCAAAACCG 60.600 52.381 0.00 0.00 40.63 4.44
2445 2555 1.001378 CTCAAGGTCAAGCAAAACCGG 60.001 52.381 0.00 0.00 40.63 5.28
2446 2556 0.597377 CAAGGTCAAGCAAAACCGGC 60.597 55.000 0.00 0.00 40.63 6.13
2447 2557 1.744320 AAGGTCAAGCAAAACCGGCC 61.744 55.000 0.00 0.00 40.63 6.13
2454 2564 1.627864 AGCAAAACCGGCCAATAACT 58.372 45.000 0.00 0.00 0.00 2.24
2467 2577 3.382546 GCCAATAACTACTCCCGTAGACA 59.617 47.826 6.51 0.00 44.77 3.41
2516 2626 2.044946 AATTCCACCAGCTCCGCC 60.045 61.111 0.00 0.00 0.00 6.13
2534 2644 0.108138 CCAACTTCCGGGAGCTACAG 60.108 60.000 10.62 0.00 0.00 2.74
2572 2683 4.576873 TGCTCCACGATTTTCAACTGTAAA 59.423 37.500 0.00 0.00 0.00 2.01
2573 2684 5.066634 TGCTCCACGATTTTCAACTGTAAAA 59.933 36.000 0.00 0.00 0.00 1.52
2574 2685 5.398416 GCTCCACGATTTTCAACTGTAAAAC 59.602 40.000 0.00 0.00 0.00 2.43
2587 2698 0.992802 GTAAAACTCGAGCAGCTCCG 59.007 55.000 17.16 11.82 0.00 4.63
2603 2714 2.214216 CCGGGAGTGGAGTTGTGGA 61.214 63.158 0.00 0.00 0.00 4.02
2604 2715 1.293498 CGGGAGTGGAGTTGTGGAG 59.707 63.158 0.00 0.00 0.00 3.86
2605 2716 1.472662 CGGGAGTGGAGTTGTGGAGT 61.473 60.000 0.00 0.00 0.00 3.85
2606 2717 0.035458 GGGAGTGGAGTTGTGGAGTG 59.965 60.000 0.00 0.00 0.00 3.51
2607 2718 0.035458 GGAGTGGAGTTGTGGAGTGG 59.965 60.000 0.00 0.00 0.00 4.00
2608 2719 0.759346 GAGTGGAGTTGTGGAGTGGT 59.241 55.000 0.00 0.00 0.00 4.16
2609 2720 0.469917 AGTGGAGTTGTGGAGTGGTG 59.530 55.000 0.00 0.00 0.00 4.17
2610 2721 0.535102 GTGGAGTTGTGGAGTGGTGG 60.535 60.000 0.00 0.00 0.00 4.61
2615 2726 2.104281 GAGTTGTGGAGTGGTGGTACTT 59.896 50.000 0.00 0.00 0.00 2.24
2616 2727 2.508300 AGTTGTGGAGTGGTGGTACTTT 59.492 45.455 0.00 0.00 0.00 2.66
2619 2730 2.104111 TGTGGAGTGGTGGTACTTTGAG 59.896 50.000 0.00 0.00 0.00 3.02
2663 2774 8.145316 CAAAATTGATGTTGTGATTTTGGACT 57.855 30.769 10.83 0.00 41.91 3.85
2682 2793 7.510675 TGGACTTATCTTCCAATCTTTACCT 57.489 36.000 0.00 0.00 40.35 3.08
2714 3599 8.735692 AAAGCAAATTGGATTTTCAGAAAGAA 57.264 26.923 0.00 0.00 0.00 2.52
2768 3657 3.243359 TGAAACAGAAGGGATTTGGCT 57.757 42.857 0.00 0.00 0.00 4.75
2774 3663 5.198602 ACAGAAGGGATTTGGCTCTAAAT 57.801 39.130 0.00 0.00 33.19 1.40
2805 3694 5.065731 GCTGGGTCAAACAGATCTTATCTTG 59.934 44.000 0.00 0.00 37.58 3.02
2826 3715 1.980765 AGCCACATCTTCTGTTCTCCA 59.019 47.619 0.00 0.00 35.29 3.86
2851 3740 0.765510 GGGTGTCTGGTCCTCAGTTT 59.234 55.000 0.00 0.00 43.76 2.66
2864 3753 1.401905 CTCAGTTTAAATGCGGGAGGC 59.598 52.381 0.00 0.00 43.96 4.70
2912 3801 4.336433 TCCTTTTGCTCTTTGTCTCAACAG 59.664 41.667 0.00 0.00 36.57 3.16
2932 3821 6.336842 ACAGCTGATTTCTTGCAAACTATT 57.663 33.333 23.35 0.00 0.00 1.73
2934 3823 5.803967 CAGCTGATTTCTTGCAAACTATTCC 59.196 40.000 8.42 0.00 0.00 3.01
2953 3842 2.553602 TCCGAATAATGTCATGCATGCC 59.446 45.455 22.25 11.84 37.96 4.40
2954 3843 2.352030 CCGAATAATGTCATGCATGCCC 60.352 50.000 22.25 14.61 37.96 5.36
2955 3844 2.293955 CGAATAATGTCATGCATGCCCA 59.706 45.455 22.25 19.54 37.96 5.36
2956 3845 3.610821 CGAATAATGTCATGCATGCCCAG 60.611 47.826 22.25 4.93 37.96 4.45
2957 3846 2.732844 TAATGTCATGCATGCCCAGA 57.267 45.000 22.25 7.50 37.96 3.86
2958 3847 1.399714 AATGTCATGCATGCCCAGAG 58.600 50.000 22.25 0.23 37.96 3.35
2959 3848 0.257905 ATGTCATGCATGCCCAGAGT 59.742 50.000 22.25 3.71 36.26 3.24
2960 3849 0.038599 TGTCATGCATGCCCAGAGTT 59.961 50.000 22.25 0.00 0.00 3.01
2961 3850 1.180029 GTCATGCATGCCCAGAGTTT 58.820 50.000 22.25 0.00 0.00 2.66
2962 3851 1.133790 GTCATGCATGCCCAGAGTTTC 59.866 52.381 22.25 0.00 0.00 2.78
2965 3854 0.040058 TGCATGCCCAGAGTTTCCAT 59.960 50.000 16.68 0.00 0.00 3.41
3012 3938 7.400627 AGTCTGACTATAGAAAAAGTTAGCCCT 59.599 37.037 8.91 0.00 31.34 5.19
3017 3943 6.672657 ACTATAGAAAAAGTTAGCCCTCTGGA 59.327 38.462 6.78 0.00 0.00 3.86
3028 3954 2.172293 AGCCCTCTGGAATTCACTCATC 59.828 50.000 7.93 0.00 0.00 2.92
3046 3972 4.392047 TCATCTGAAGCAACTTGTGACAT 58.608 39.130 0.00 0.00 0.00 3.06
3125 4051 7.329226 CCCATTAAATGTGTGAGTTGACATTTC 59.671 37.037 12.13 0.00 45.40 2.17
3152 4078 6.313411 CAGAATCTTTCTCAAGTCCTAAGCTG 59.687 42.308 0.00 0.00 38.11 4.24
3161 4087 0.036875 GTCCTAAGCTGCCAAGTGGT 59.963 55.000 0.00 0.00 37.57 4.16
3202 4129 1.501582 GGACTGACCCTCTGCCTATT 58.498 55.000 0.00 0.00 0.00 1.73
3203 4130 1.414550 GGACTGACCCTCTGCCTATTC 59.585 57.143 0.00 0.00 0.00 1.75
3214 4141 5.529060 CCCTCTGCCTATTCAAACATAGAAC 59.471 44.000 0.00 0.00 0.00 3.01
3218 4145 5.492895 TGCCTATTCAAACATAGAACGGAA 58.507 37.500 0.00 0.00 0.00 4.30
3242 4169 9.113838 GAATTCTTTATGCCACTTATTGAGAGA 57.886 33.333 0.00 0.00 0.00 3.10
3244 4171 8.498054 TTCTTTATGCCACTTATTGAGAGAAG 57.502 34.615 0.00 0.00 0.00 2.85
3252 4179 5.335191 CCACTTATTGAGAGAAGCCACAAAC 60.335 44.000 0.00 0.00 0.00 2.93
3283 4210 8.048514 AGCGTATTCCCCAGTTTTTAACTTATA 58.951 33.333 0.00 0.00 40.46 0.98
3284 4211 8.676401 GCGTATTCCCCAGTTTTTAACTTATAA 58.324 33.333 0.00 0.00 40.46 0.98
3314 4242 2.825532 GGATGTTGGTGGTTAATGCAGT 59.174 45.455 0.00 0.00 0.00 4.40
3333 4278 2.620115 AGTCCTTTGTGATGTGTTGCTG 59.380 45.455 0.00 0.00 0.00 4.41
3392 4346 2.632996 TGAGGTACTGTTTGTGGAGAGG 59.367 50.000 0.00 0.00 41.55 3.69
3393 4347 2.633481 GAGGTACTGTTTGTGGAGAGGT 59.367 50.000 0.00 0.00 41.55 3.85
3394 4348 3.830755 GAGGTACTGTTTGTGGAGAGGTA 59.169 47.826 0.00 0.00 41.55 3.08
3395 4349 4.228824 AGGTACTGTTTGTGGAGAGGTAA 58.771 43.478 0.00 0.00 37.18 2.85
3396 4350 4.657039 AGGTACTGTTTGTGGAGAGGTAAA 59.343 41.667 0.00 0.00 37.18 2.01
3397 4351 4.995487 GGTACTGTTTGTGGAGAGGTAAAG 59.005 45.833 0.00 0.00 0.00 1.85
3398 4352 5.221581 GGTACTGTTTGTGGAGAGGTAAAGA 60.222 44.000 0.00 0.00 0.00 2.52
3399 4353 5.568620 ACTGTTTGTGGAGAGGTAAAGAT 57.431 39.130 0.00 0.00 0.00 2.40
3400 4354 5.941788 ACTGTTTGTGGAGAGGTAAAGATT 58.058 37.500 0.00 0.00 0.00 2.40
3401 4355 6.365520 ACTGTTTGTGGAGAGGTAAAGATTT 58.634 36.000 0.00 0.00 0.00 2.17
3402 4356 6.263168 ACTGTTTGTGGAGAGGTAAAGATTTG 59.737 38.462 0.00 0.00 0.00 2.32
3403 4357 5.534654 TGTTTGTGGAGAGGTAAAGATTTGG 59.465 40.000 0.00 0.00 0.00 3.28
3404 4358 5.576563 TTGTGGAGAGGTAAAGATTTGGA 57.423 39.130 0.00 0.00 0.00 3.53
3405 4359 5.576563 TGTGGAGAGGTAAAGATTTGGAA 57.423 39.130 0.00 0.00 0.00 3.53
3406 4360 5.947663 TGTGGAGAGGTAAAGATTTGGAAA 58.052 37.500 0.00 0.00 0.00 3.13
3407 4361 6.369629 TGTGGAGAGGTAAAGATTTGGAAAA 58.630 36.000 0.00 0.00 0.00 2.29
3408 4362 6.490040 TGTGGAGAGGTAAAGATTTGGAAAAG 59.510 38.462 0.00 0.00 0.00 2.27
3424 4378 3.641436 GGAAAAGATGAACCCACCACTTT 59.359 43.478 0.00 0.00 0.00 2.66
3439 4393 3.266772 ACCACTTTCTGCATGGGATCTTA 59.733 43.478 8.12 0.00 37.86 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
197 200 0.243907 TCTTTCTCTTGTCGCCGGAG 59.756 55.000 5.05 0.00 0.00 4.63
203 206 5.003872 CGTGATATGTGTCTTTCTCTTGTCG 59.996 44.000 0.00 0.00 0.00 4.35
265 268 9.741647 TTTTTGCCACAAATAAAATTCAATTCC 57.258 25.926 0.00 0.00 0.00 3.01
301 304 5.151632 TGAAACTTACTTGCACTCGAAAC 57.848 39.130 0.00 0.00 0.00 2.78
315 318 7.011389 GTCGATGACATTCCATGATGAAACTTA 59.989 37.037 0.00 0.00 32.09 2.24
326 329 2.979814 TTCCGTCGATGACATTCCAT 57.020 45.000 6.11 0.00 32.09 3.41
355 358 7.731054 TGGAGCACTGGTGTTTATTTATTTTT 58.269 30.769 2.64 0.00 0.00 1.94
356 359 7.296628 TGGAGCACTGGTGTTTATTTATTTT 57.703 32.000 2.64 0.00 0.00 1.82
357 360 6.909550 TGGAGCACTGGTGTTTATTTATTT 57.090 33.333 2.64 0.00 0.00 1.40
358 361 6.909550 TTGGAGCACTGGTGTTTATTTATT 57.090 33.333 2.64 0.00 0.00 1.40
359 362 6.909550 TTTGGAGCACTGGTGTTTATTTAT 57.090 33.333 2.64 0.00 0.00 1.40
360 363 6.716934 TTTTGGAGCACTGGTGTTTATTTA 57.283 33.333 2.64 0.00 0.00 1.40
361 364 5.606348 TTTTGGAGCACTGGTGTTTATTT 57.394 34.783 2.64 0.00 0.00 1.40
362 365 5.540911 CATTTTGGAGCACTGGTGTTTATT 58.459 37.500 2.64 0.00 0.00 1.40
363 366 4.561326 GCATTTTGGAGCACTGGTGTTTAT 60.561 41.667 2.64 0.00 0.00 1.40
364 367 3.243704 GCATTTTGGAGCACTGGTGTTTA 60.244 43.478 2.64 0.00 0.00 2.01
368 371 0.963962 AGCATTTTGGAGCACTGGTG 59.036 50.000 0.00 0.00 0.00 4.17
440 443 6.633856 AGTTTCATGAAGGAATACCATTTGC 58.366 36.000 8.41 0.00 38.94 3.68
469 472 7.614124 ACAACTTTGAATGTTTTGAATGCTT 57.386 28.000 0.00 0.00 0.00 3.91
539 542 5.125417 ACCCGGATGAACAATGAATTTACAG 59.875 40.000 0.73 0.00 0.00 2.74
541 544 5.576447 ACCCGGATGAACAATGAATTTAC 57.424 39.130 0.73 0.00 0.00 2.01
542 545 5.712446 TGAACCCGGATGAACAATGAATTTA 59.288 36.000 0.73 0.00 0.00 1.40
543 546 4.526262 TGAACCCGGATGAACAATGAATTT 59.474 37.500 0.73 0.00 0.00 1.82
745 756 0.036294 AAACGGGCTTAGTCCTGCTC 60.036 55.000 0.00 0.00 35.90 4.26
758 769 0.027063 GTCGTGTTGTGTCAAACGGG 59.973 55.000 12.81 0.00 36.70 5.28
759 770 1.003851 AGTCGTGTTGTGTCAAACGG 58.996 50.000 12.81 0.00 36.70 4.44
760 771 3.910862 TTAGTCGTGTTGTGTCAAACG 57.089 42.857 0.00 0.00 37.38 3.60
817 830 3.576078 AAAATGGCATCGATGGAGGTA 57.424 42.857 26.00 0.00 0.00 3.08
818 831 2.442236 AAAATGGCATCGATGGAGGT 57.558 45.000 26.00 0.00 0.00 3.85
867 880 6.876257 ACTGATGTTGGTTAGCTAAGAAGAAG 59.124 38.462 6.38 0.49 0.00 2.85
940 955 5.235401 GCTTAGCAAGGCTTGAGTAGATAAC 59.765 44.000 30.45 9.33 40.44 1.89
1161 1194 4.334118 TCGACGTCGGTCCTGGGA 62.334 66.667 35.05 12.79 40.17 4.37
1439 1478 2.597217 TTGCCTTGGCCTTGGACG 60.597 61.111 16.98 0.00 0.00 4.79
1443 1482 1.203052 CTATGTGTTGCCTTGGCCTTG 59.797 52.381 3.32 0.00 0.00 3.61
1445 1484 0.323725 CCTATGTGTTGCCTTGGCCT 60.324 55.000 3.32 0.00 0.00 5.19
1446 1485 0.611896 ACCTATGTGTTGCCTTGGCC 60.612 55.000 9.35 0.00 0.00 5.36
1447 1486 0.527565 CACCTATGTGTTGCCTTGGC 59.472 55.000 4.43 4.43 37.72 4.52
1460 1502 2.040606 ACCTCACCGCCCACCTAT 59.959 61.111 0.00 0.00 0.00 2.57
1505 1547 4.383880 CCTCCTCCGCATCATCATCATATT 60.384 45.833 0.00 0.00 0.00 1.28
1506 1548 3.134262 CCTCCTCCGCATCATCATCATAT 59.866 47.826 0.00 0.00 0.00 1.78
1507 1549 2.498885 CCTCCTCCGCATCATCATCATA 59.501 50.000 0.00 0.00 0.00 2.15
1537 1609 2.962786 CACCACGGCGTCGAACAA 60.963 61.111 20.03 0.00 40.11 2.83
1710 1789 2.787994 CAGAGGTCCAAAGCAATGTCT 58.212 47.619 0.00 0.00 0.00 3.41
1938 2039 2.975536 CCGCCCGTGTCTAGGAAA 59.024 61.111 0.00 0.00 0.00 3.13
1959 2060 2.446994 TTGTCCCCCACGGTGACT 60.447 61.111 10.28 0.00 33.08 3.41
1971 2072 1.138047 CGACGACATAGCCGTTGTCC 61.138 60.000 11.40 0.00 44.35 4.02
1996 2097 1.155424 GGGAACACGTGCTCGAACAA 61.155 55.000 17.22 0.00 40.62 2.83
2170 2271 3.249189 TTCCCTGGCGCAGAGGTT 61.249 61.111 20.07 0.00 32.44 3.50
2275 2379 3.893763 CTCCTCGAGCGGTGCGAT 61.894 66.667 6.99 0.00 37.13 4.58
2385 2495 2.056223 CCATTCCTGCAGGCCCTTG 61.056 63.158 28.91 19.78 34.44 3.61
2454 2564 2.040813 ACCTTCAGTGTCTACGGGAGTA 59.959 50.000 0.00 0.00 46.17 2.59
2482 2592 5.076873 TGGAATTCCAAACAGGGTCTAAAG 58.923 41.667 25.13 0.00 44.35 1.85
2516 2626 0.895530 TCTGTAGCTCCCGGAAGTTG 59.104 55.000 0.73 0.00 0.00 3.16
2534 2644 1.475930 GGAGCACCTATTTCCTGGCTC 60.476 57.143 0.00 0.00 45.18 4.70
2572 2683 3.764466 CCCGGAGCTGCTCGAGTT 61.764 66.667 22.25 0.00 0.00 3.01
2573 2684 4.742649 TCCCGGAGCTGCTCGAGT 62.743 66.667 22.25 0.00 0.00 4.18
2574 2685 3.898509 CTCCCGGAGCTGCTCGAG 61.899 72.222 22.25 18.42 0.00 4.04
2587 2698 0.035458 CACTCCACAACTCCACTCCC 59.965 60.000 0.00 0.00 0.00 4.30
2603 2714 1.072331 CCTGCTCAAAGTACCACCACT 59.928 52.381 0.00 0.00 0.00 4.00
2604 2715 1.523758 CCTGCTCAAAGTACCACCAC 58.476 55.000 0.00 0.00 0.00 4.16
2605 2716 0.400213 CCCTGCTCAAAGTACCACCA 59.600 55.000 0.00 0.00 0.00 4.17
2606 2717 0.960861 GCCCTGCTCAAAGTACCACC 60.961 60.000 0.00 0.00 0.00 4.61
2607 2718 0.960861 GGCCCTGCTCAAAGTACCAC 60.961 60.000 0.00 0.00 0.00 4.16
2608 2719 1.133809 AGGCCCTGCTCAAAGTACCA 61.134 55.000 0.00 0.00 0.00 3.25
2609 2720 0.038310 AAGGCCCTGCTCAAAGTACC 59.962 55.000 0.00 0.00 0.00 3.34
2610 2721 2.781681 TAAGGCCCTGCTCAAAGTAC 57.218 50.000 0.00 0.00 0.00 2.73
2615 2726 3.685550 GCTTCTATTAAGGCCCTGCTCAA 60.686 47.826 0.00 0.00 0.00 3.02
2616 2727 2.158755 GCTTCTATTAAGGCCCTGCTCA 60.159 50.000 0.00 0.00 0.00 4.26
2619 2730 1.133792 TGGCTTCTATTAAGGCCCTGC 60.134 52.381 0.00 0.00 43.50 4.85
2688 2799 9.829507 TTCTTTCTGAAAATCCAATTTGCTTTA 57.170 25.926 4.18 0.00 31.77 1.85
2689 2800 8.735692 TTCTTTCTGAAAATCCAATTTGCTTT 57.264 26.923 4.18 0.00 31.77 3.51
2690 2801 8.913487 ATTCTTTCTGAAAATCCAATTTGCTT 57.087 26.923 4.18 0.00 38.29 3.91
2691 2802 8.913487 AATTCTTTCTGAAAATCCAATTTGCT 57.087 26.923 4.18 0.00 38.29 3.91
2692 2803 9.389570 CAAATTCTTTCTGAAAATCCAATTTGC 57.610 29.630 21.18 0.00 38.29 3.68
2693 2804 9.389570 GCAAATTCTTTCTGAAAATCCAATTTG 57.610 29.630 24.36 24.36 37.92 2.32
2741 3630 7.607607 GCCAAATCCCTTCTGTTTCAAAATAAT 59.392 33.333 0.00 0.00 0.00 1.28
2768 3657 2.107378 TGACCCAGCAACACCATTTAGA 59.893 45.455 0.00 0.00 0.00 2.10
2774 3663 0.323816 TGTTTGACCCAGCAACACCA 60.324 50.000 0.00 0.00 0.00 4.17
2805 3694 2.027745 TGGAGAACAGAAGATGTGGCTC 60.028 50.000 0.00 0.00 43.00 4.70
2826 3715 0.253347 AGGACCAGACACCCCATCAT 60.253 55.000 0.00 0.00 0.00 2.45
2851 3740 0.825410 TTACTCGCCTCCCGCATTTA 59.175 50.000 0.00 0.00 37.30 1.40
2864 3753 3.697045 ACTGGATCCTCTTGTCTTACTCG 59.303 47.826 14.23 0.00 0.00 4.18
2912 3801 4.795278 CGGAATAGTTTGCAAGAAATCAGC 59.205 41.667 0.00 0.00 0.00 4.26
2932 3821 2.553602 GGCATGCATGACATTATTCGGA 59.446 45.455 30.64 0.00 36.64 4.55
2934 3823 2.293955 TGGGCATGCATGACATTATTCG 59.706 45.455 32.84 1.73 37.62 3.34
2953 3842 6.976925 GCATATTGAAGAAATGGAAACTCTGG 59.023 38.462 0.00 0.00 0.00 3.86
2954 3843 7.541162 TGCATATTGAAGAAATGGAAACTCTG 58.459 34.615 0.00 0.00 0.00 3.35
2955 3844 7.613022 TCTGCATATTGAAGAAATGGAAACTCT 59.387 33.333 0.00 0.00 26.47 3.24
2956 3845 7.765307 TCTGCATATTGAAGAAATGGAAACTC 58.235 34.615 0.00 0.00 26.47 3.01
2957 3846 7.707624 TCTGCATATTGAAGAAATGGAAACT 57.292 32.000 0.00 0.00 26.47 2.66
2958 3847 8.192774 TCATCTGCATATTGAAGAAATGGAAAC 58.807 33.333 0.00 0.00 35.26 2.78
2959 3848 8.296211 TCATCTGCATATTGAAGAAATGGAAA 57.704 30.769 0.00 0.00 35.26 3.13
2960 3849 7.885009 TCATCTGCATATTGAAGAAATGGAA 57.115 32.000 0.00 0.00 35.26 3.53
2961 3850 9.227777 CTATCATCTGCATATTGAAGAAATGGA 57.772 33.333 0.00 0.00 35.26 3.41
2962 3851 9.011095 ACTATCATCTGCATATTGAAGAAATGG 57.989 33.333 0.00 0.00 35.26 3.16
2965 3854 9.269453 CAGACTATCATCTGCATATTGAAGAAA 57.731 33.333 0.00 0.00 35.26 2.52
3010 3936 4.750021 TCAGATGAGTGAATTCCAGAGG 57.250 45.455 2.27 0.00 0.00 3.69
3012 3938 4.019950 TGCTTCAGATGAGTGAATTCCAGA 60.020 41.667 2.27 0.00 35.88 3.86
3017 3943 5.533903 ACAAGTTGCTTCAGATGAGTGAATT 59.466 36.000 1.81 0.00 35.88 2.17
3028 3954 9.630098 AAATTAATATGTCACAAGTTGCTTCAG 57.370 29.630 1.81 0.00 0.00 3.02
3124 4050 3.259374 AGGACTTGAGAAAGATTCTGCGA 59.741 43.478 0.00 0.00 40.87 5.10
3125 4051 3.594134 AGGACTTGAGAAAGATTCTGCG 58.406 45.455 0.00 0.00 40.87 5.18
3152 4078 3.069443 TGAATGGAAAAGAACCACTTGGC 59.931 43.478 0.00 0.00 40.36 4.52
3161 4087 7.454380 AGTCCCAAATATGTGAATGGAAAAGAA 59.546 33.333 0.00 0.00 34.82 2.52
3202 4129 8.181573 GCATAAAGAATTCCGTTCTATGTTTGA 58.818 33.333 0.65 0.00 46.39 2.69
3203 4130 7.432252 GGCATAAAGAATTCCGTTCTATGTTTG 59.568 37.037 0.65 0.00 46.39 2.93
3214 4141 7.012327 TCTCAATAAGTGGCATAAAGAATTCCG 59.988 37.037 0.65 0.00 0.00 4.30
3218 4145 9.118300 CTTCTCTCAATAAGTGGCATAAAGAAT 57.882 33.333 0.00 0.00 0.00 2.40
3283 4210 3.033184 CCACCAACATCCTGCCATTATT 58.967 45.455 0.00 0.00 0.00 1.40
3284 4211 2.024080 ACCACCAACATCCTGCCATTAT 60.024 45.455 0.00 0.00 0.00 1.28
3285 4212 1.357420 ACCACCAACATCCTGCCATTA 59.643 47.619 0.00 0.00 0.00 1.90
3286 4213 0.114954 ACCACCAACATCCTGCCATT 59.885 50.000 0.00 0.00 0.00 3.16
3314 4242 2.929641 TCAGCAACACATCACAAAGGA 58.070 42.857 0.00 0.00 0.00 3.36
3333 4278 9.669353 CATTACAAAATGTCCTATATGCAGTTC 57.331 33.333 0.00 0.00 38.15 3.01
3392 4346 7.598869 GTGGGTTCATCTTTTCCAAATCTTTAC 59.401 37.037 0.00 0.00 0.00 2.01
3393 4347 7.256154 GGTGGGTTCATCTTTTCCAAATCTTTA 60.256 37.037 0.00 0.00 0.00 1.85
3394 4348 6.464322 GGTGGGTTCATCTTTTCCAAATCTTT 60.464 38.462 0.00 0.00 0.00 2.52
3395 4349 5.012046 GGTGGGTTCATCTTTTCCAAATCTT 59.988 40.000 0.00 0.00 0.00 2.40
3396 4350 4.528206 GGTGGGTTCATCTTTTCCAAATCT 59.472 41.667 0.00 0.00 0.00 2.40
3397 4351 4.283212 TGGTGGGTTCATCTTTTCCAAATC 59.717 41.667 0.00 0.00 0.00 2.17
3398 4352 4.040339 GTGGTGGGTTCATCTTTTCCAAAT 59.960 41.667 0.00 0.00 0.00 2.32
3399 4353 3.386402 GTGGTGGGTTCATCTTTTCCAAA 59.614 43.478 0.00 0.00 0.00 3.28
3400 4354 2.962421 GTGGTGGGTTCATCTTTTCCAA 59.038 45.455 0.00 0.00 0.00 3.53
3401 4355 2.176798 AGTGGTGGGTTCATCTTTTCCA 59.823 45.455 0.00 0.00 0.00 3.53
3402 4356 2.876581 AGTGGTGGGTTCATCTTTTCC 58.123 47.619 0.00 0.00 0.00 3.13
3403 4357 4.584743 AGAAAGTGGTGGGTTCATCTTTTC 59.415 41.667 0.00 0.00 33.07 2.29
3404 4358 4.342092 CAGAAAGTGGTGGGTTCATCTTTT 59.658 41.667 0.00 0.00 0.00 2.27
3405 4359 3.891366 CAGAAAGTGGTGGGTTCATCTTT 59.109 43.478 0.00 0.00 0.00 2.52
3406 4360 3.490348 CAGAAAGTGGTGGGTTCATCTT 58.510 45.455 0.00 0.00 0.00 2.40
3407 4361 2.815589 GCAGAAAGTGGTGGGTTCATCT 60.816 50.000 0.00 0.00 0.00 2.90
3408 4362 1.541588 GCAGAAAGTGGTGGGTTCATC 59.458 52.381 0.00 0.00 0.00 2.92
3424 4378 6.155221 GTCCTACATATAAGATCCCATGCAGA 59.845 42.308 0.00 0.00 0.00 4.26
3439 4393 5.131142 CCCTTTGAGTCTTGGTCCTACATAT 59.869 44.000 0.00 0.00 0.00 1.78


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

AutoCloner maintained by Alex Coulton.