Multiple sequence alignment - TraesCS5D01G238600

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 TraesCS5D01G238600 chr5D 100.000 3520 0 0 1 3520 346680149 346683668 0.000000e+00 6501.0
1 TraesCS5D01G238600 chr5A 95.009 2124 60 10 843 2926 444902448 444900331 0.000000e+00 3293.0
2 TraesCS5D01G238600 chr5A 80.647 1762 250 54 957 2694 681458630 681456936 0.000000e+00 1280.0
3 TraesCS5D01G238600 chr5A 91.892 666 48 6 6 667 444904879 444904216 0.000000e+00 926.0
4 TraesCS5D01G238600 chr5A 92.701 137 4 2 664 794 444902585 444902449 3.590000e-45 193.0
5 TraesCS5D01G238600 chr7B 84.411 1655 219 25 957 2602 478474542 478476166 0.000000e+00 1591.0
6 TraesCS5D01G238600 chr7B 85.662 272 31 5 2931 3200 313776010 313775745 2.680000e-71 279.0
7 TraesCS5D01G238600 chr4D 88.665 794 78 8 957 1747 500495218 500494434 0.000000e+00 957.0
8 TraesCS5D01G238600 chr4D 83.652 575 73 10 2934 3506 98520613 98520058 4.030000e-144 521.0
9 TraesCS5D01G238600 chr4D 82.578 574 80 8 2935 3506 478230240 478229685 4.080000e-134 488.0
10 TraesCS5D01G238600 chr4D 79.091 550 97 13 1941 2483 500494442 500493904 2.580000e-96 363.0
11 TraesCS5D01G238600 chr3B 82.435 501 74 6 2934 3433 771777223 771776736 3.250000e-115 425.0
12 TraesCS5D01G238600 chr3B 83.154 279 40 5 2925 3200 771775518 771775792 7.550000e-62 248.0
13 TraesCS5D01G238600 chr6B 81.980 505 71 9 2934 3433 481264983 481265472 9.090000e-111 411.0
14 TraesCS5D01G238600 chr6B 82.877 146 22 2 47 189 159602525 159602380 1.030000e-25 128.0
15 TraesCS5D01G238600 chr7D 85.294 374 42 8 2919 3291 262998564 262998925 1.190000e-99 374.0
16 TraesCS5D01G238600 chr4B 82.210 371 54 8 2926 3292 188194628 188194990 3.410000e-80 309.0
17 TraesCS5D01G238600 chr6A 81.143 350 60 6 1174 1520 578926204 578926550 3.460000e-70 276.0
18 TraesCS5D01G238600 chr6A 82.313 147 21 5 47 189 100814613 100814468 4.770000e-24 122.0
19 TraesCS5D01G238600 chr3D 84.387 269 35 3 2934 3200 260971057 260971320 1.250000e-64 257.0
20 TraesCS5D01G238600 chr6D 78.517 391 72 9 1239 1620 432810773 432811160 2.710000e-61 246.0
21 TraesCS5D01G238600 chr6D 85.106 141 18 2 47 184 83553898 83553758 1.320000e-29 141.0
22 TraesCS5D01G238600 chr1B 79.808 312 51 8 66 365 549797165 549796854 2.130000e-52 217.0
23 TraesCS5D01G238600 chr7A 96.970 33 0 1 122 153 644106902 644106934 2.000000e-03 54.7


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 TraesCS5D01G238600 chr5D 346680149 346683668 3519 False 6501.000000 6501 100.000000 1 3520 1 chr5D.!!$F1 3519
1 TraesCS5D01G238600 chr5A 444900331 444904879 4548 True 1470.666667 3293 93.200667 6 2926 3 chr5A.!!$R2 2920
2 TraesCS5D01G238600 chr5A 681456936 681458630 1694 True 1280.000000 1280 80.647000 957 2694 1 chr5A.!!$R1 1737
3 TraesCS5D01G238600 chr7B 478474542 478476166 1624 False 1591.000000 1591 84.411000 957 2602 1 chr7B.!!$F1 1645
4 TraesCS5D01G238600 chr4D 500493904 500495218 1314 True 660.000000 957 83.878000 957 2483 2 chr4D.!!$R3 1526
5 TraesCS5D01G238600 chr4D 98520058 98520613 555 True 521.000000 521 83.652000 2934 3506 1 chr4D.!!$R1 572
6 TraesCS5D01G238600 chr4D 478229685 478230240 555 True 488.000000 488 82.578000 2935 3506 1 chr4D.!!$R2 571

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
811 2454 0.037697 TTTACTGATGCGCCGTGTCT 60.038 50.0 4.18 0.0 0.00 3.41 F
814 2457 0.037697 ACTGATGCGCCGTGTCTAAA 60.038 50.0 4.18 0.0 0.00 1.85 F
943 2592 0.038159 CGGAGGAGGCCTATTTAGCG 60.038 60.0 4.42 0.0 31.76 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1980 3658 1.021390 CGCCAAGACTGCTTACTGGG 61.021 60.000 0.0 0.0 31.81 4.45 R
2109 3787 1.375908 GCTCAGGGAATGCACGACA 60.376 57.895 0.0 0.0 0.00 4.35 R
2888 4628 0.892755 TACTTGGTGCTGGTCTACCG 59.107 55.000 0.0 0.0 39.87 4.02 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
38 39 2.100631 GGGAATGCTGACCACGTCG 61.101 63.158 0.00 0.00 34.95 5.12
141 143 0.984230 AATCTCCCGAAGACTTGGCA 59.016 50.000 0.00 0.00 36.65 4.92
157 159 1.369091 GGCACATACTCCAAGGCACG 61.369 60.000 0.00 0.00 0.00 5.34
162 164 0.739813 ATACTCCAAGGCACGAACGC 60.740 55.000 0.00 0.00 0.00 4.84
212 214 9.531158 GATAGACCTATGTGTAACCCTAAGTAT 57.469 37.037 0.00 0.00 34.36 2.12
213 215 7.836479 AGACCTATGTGTAACCCTAAGTATC 57.164 40.000 0.00 0.00 34.36 2.24
214 216 6.781507 AGACCTATGTGTAACCCTAAGTATCC 59.218 42.308 0.00 0.00 34.36 2.59
215 217 5.842874 ACCTATGTGTAACCCTAAGTATCCC 59.157 44.000 0.00 0.00 34.36 3.85
216 218 5.842328 CCTATGTGTAACCCTAAGTATCCCA 59.158 44.000 0.00 0.00 34.36 4.37
217 219 6.328148 CCTATGTGTAACCCTAAGTATCCCAA 59.672 42.308 0.00 0.00 34.36 4.12
219 221 5.996644 TGTGTAACCCTAAGTATCCCAATG 58.003 41.667 0.00 0.00 34.36 2.82
221 223 6.012333 TGTGTAACCCTAAGTATCCCAATGTT 60.012 38.462 0.00 0.00 34.36 2.71
237 239 8.299990 TCCCAATGTTTATATAAAACCAGTGG 57.700 34.615 24.52 24.52 37.26 4.00
240 242 7.491048 CCAATGTTTATATAAAACCAGTGGTGC 59.509 37.037 23.81 7.32 35.00 5.01
276 278 5.050499 GCCAACTCATTCATACTCAATCTCG 60.050 44.000 0.00 0.00 0.00 4.04
278 280 6.199908 CCAACTCATTCATACTCAATCTCGAC 59.800 42.308 0.00 0.00 0.00 4.20
283 285 6.207614 TCATTCATACTCAATCTCGACCTAGG 59.792 42.308 7.41 7.41 0.00 3.02
288 290 4.282496 ACTCAATCTCGACCTAGGTCAAT 58.718 43.478 35.32 23.80 44.77 2.57
296 298 6.570692 TCTCGACCTAGGTCAATTTGTATTC 58.429 40.000 35.32 10.28 44.77 1.75
299 301 5.006746 CGACCTAGGTCAATTTGTATTCTGC 59.993 44.000 35.32 9.06 44.77 4.26
305 307 2.752354 TCAATTTGTATTCTGCACCCCG 59.248 45.455 0.00 0.00 0.00 5.73
347 349 6.239204 ACAAAGCATTGTAAGGTTTTACCTCC 60.239 38.462 5.33 0.00 46.37 4.30
348 350 9.091343 ACAAAGCATTGTAAGGTTTTACCTCCC 62.091 40.741 5.33 0.00 46.37 4.30
379 381 2.632996 TGAACCTGAGTGGATTCGACTT 59.367 45.455 2.68 0.00 39.71 3.01
389 391 3.607209 GTGGATTCGACTTCGTTACTGTC 59.393 47.826 0.00 0.00 40.80 3.51
391 393 3.366679 GGATTCGACTTCGTTACTGTCCA 60.367 47.826 0.00 0.00 40.80 4.02
393 395 1.538512 TCGACTTCGTTACTGTCCAGG 59.461 52.381 0.00 0.00 40.80 4.45
412 414 0.645868 GTAGATGAAACGGCTCGTGC 59.354 55.000 0.00 0.00 39.99 5.34
432 434 4.785453 CCCCTGAGTTGCCCTCGC 62.785 72.222 0.00 0.00 43.64 5.03
518 521 5.538118 TGATACTGCACCATCCTTTATACG 58.462 41.667 0.00 0.00 0.00 3.06
544 547 0.323725 ATGATGCACGAAAGGCCCTT 60.324 50.000 0.00 0.00 0.00 3.95
558 561 1.883926 GGCCCTTCGCTGTAAAAGAAA 59.116 47.619 0.00 0.00 37.74 2.52
560 563 3.565516 GCCCTTCGCTGTAAAAGAAAAG 58.434 45.455 0.00 0.00 0.00 2.27
571 574 7.360946 CGCTGTAAAAGAAAAGCAAGTAGGTAT 60.361 37.037 0.00 0.00 35.33 2.73
608 611 2.953466 TACTGTGACGGTATCTTGCC 57.047 50.000 0.00 0.00 0.00 4.52
667 670 2.870411 GCATCCGGATTTGTACTGTACC 59.130 50.000 16.19 0.00 0.00 3.34
668 671 3.680475 GCATCCGGATTTGTACTGTACCA 60.680 47.826 16.19 1.42 0.00 3.25
727 2364 4.473520 AGGATTGGGAGCGGCGTG 62.474 66.667 9.37 0.00 0.00 5.34
794 2437 4.948004 GGTTCTTATTTCTCCACCCGATTT 59.052 41.667 0.00 0.00 0.00 2.17
795 2438 6.069847 AGGTTCTTATTTCTCCACCCGATTTA 60.070 38.462 0.00 0.00 0.00 1.40
796 2439 6.037940 GGTTCTTATTTCTCCACCCGATTTAC 59.962 42.308 0.00 0.00 0.00 2.01
797 2440 6.555463 TCTTATTTCTCCACCCGATTTACT 57.445 37.500 0.00 0.00 0.00 2.24
798 2441 6.346096 TCTTATTTCTCCACCCGATTTACTG 58.654 40.000 0.00 0.00 0.00 2.74
799 2442 4.837093 ATTTCTCCACCCGATTTACTGA 57.163 40.909 0.00 0.00 0.00 3.41
800 2443 4.837093 TTTCTCCACCCGATTTACTGAT 57.163 40.909 0.00 0.00 0.00 2.90
801 2444 3.819564 TCTCCACCCGATTTACTGATG 57.180 47.619 0.00 0.00 0.00 3.07
802 2445 2.158957 TCTCCACCCGATTTACTGATGC 60.159 50.000 0.00 0.00 0.00 3.91
803 2446 0.937304 CCACCCGATTTACTGATGCG 59.063 55.000 0.00 0.00 0.00 4.73
804 2447 0.304705 CACCCGATTTACTGATGCGC 59.695 55.000 0.00 0.00 0.00 6.09
805 2448 0.814010 ACCCGATTTACTGATGCGCC 60.814 55.000 4.18 0.00 0.00 6.53
806 2449 1.564622 CCGATTTACTGATGCGCCG 59.435 57.895 4.18 0.00 0.00 6.46
807 2450 1.151777 CCGATTTACTGATGCGCCGT 61.152 55.000 4.18 0.00 0.00 5.68
808 2451 0.043053 CGATTTACTGATGCGCCGTG 60.043 55.000 4.18 0.00 0.00 4.94
809 2452 1.006832 GATTTACTGATGCGCCGTGT 58.993 50.000 4.18 0.88 0.00 4.49
810 2453 1.004927 GATTTACTGATGCGCCGTGTC 60.005 52.381 4.18 0.00 0.00 3.67
811 2454 0.037697 TTTACTGATGCGCCGTGTCT 60.038 50.000 4.18 0.00 0.00 3.41
812 2455 0.812549 TTACTGATGCGCCGTGTCTA 59.187 50.000 4.18 0.00 0.00 2.59
813 2456 0.812549 TACTGATGCGCCGTGTCTAA 59.187 50.000 4.18 0.00 0.00 2.10
814 2457 0.037697 ACTGATGCGCCGTGTCTAAA 60.038 50.000 4.18 0.00 0.00 1.85
815 2458 1.290203 CTGATGCGCCGTGTCTAAAT 58.710 50.000 4.18 0.00 0.00 1.40
816 2459 2.159156 ACTGATGCGCCGTGTCTAAATA 60.159 45.455 4.18 0.00 0.00 1.40
817 2460 2.198406 TGATGCGCCGTGTCTAAATAC 58.802 47.619 4.18 0.00 0.00 1.89
818 2461 1.189446 GATGCGCCGTGTCTAAATACG 59.811 52.381 4.18 0.00 39.45 3.06
819 2462 0.109179 TGCGCCGTGTCTAAATACGT 60.109 50.000 4.18 0.00 38.22 3.57
820 2463 0.569349 GCGCCGTGTCTAAATACGTC 59.431 55.000 0.00 0.00 38.22 4.34
821 2464 0.835740 CGCCGTGTCTAAATACGTCG 59.164 55.000 0.00 0.00 38.22 5.12
822 2465 0.569349 GCCGTGTCTAAATACGTCGC 59.431 55.000 0.00 0.00 38.22 5.19
823 2466 1.796617 GCCGTGTCTAAATACGTCGCT 60.797 52.381 0.00 0.00 38.22 4.93
824 2467 1.844357 CCGTGTCTAAATACGTCGCTG 59.156 52.381 0.00 0.00 38.22 5.18
825 2468 1.844357 CGTGTCTAAATACGTCGCTGG 59.156 52.381 0.00 0.00 35.53 4.85
826 2469 2.476686 CGTGTCTAAATACGTCGCTGGA 60.477 50.000 0.00 0.00 35.53 3.86
827 2470 3.703420 GTGTCTAAATACGTCGCTGGAT 58.297 45.455 0.00 0.00 0.00 3.41
828 2471 3.486108 GTGTCTAAATACGTCGCTGGATG 59.514 47.826 0.00 0.00 35.23 3.51
829 2472 3.129813 TGTCTAAATACGTCGCTGGATGT 59.870 43.478 0.00 0.00 44.45 3.06
830 2473 4.110482 GTCTAAATACGTCGCTGGATGTT 58.890 43.478 0.00 0.00 42.35 2.71
831 2474 4.206609 GTCTAAATACGTCGCTGGATGTTC 59.793 45.833 0.00 0.00 42.35 3.18
832 2475 2.961526 AATACGTCGCTGGATGTTCT 57.038 45.000 0.00 0.00 42.35 3.01
833 2476 2.961526 ATACGTCGCTGGATGTTCTT 57.038 45.000 0.00 0.00 42.35 2.52
834 2477 2.736144 TACGTCGCTGGATGTTCTTT 57.264 45.000 0.00 0.00 42.35 2.52
835 2478 1.429463 ACGTCGCTGGATGTTCTTTC 58.571 50.000 0.00 0.00 39.36 2.62
836 2479 0.721718 CGTCGCTGGATGTTCTTTCC 59.278 55.000 0.00 0.00 0.00 3.13
837 2480 1.808411 GTCGCTGGATGTTCTTTCCA 58.192 50.000 0.00 0.00 40.96 3.53
841 2484 3.248043 TGGATGTTCTTTCCAGGCG 57.752 52.632 0.00 0.00 38.35 5.52
865 2508 0.563173 TCAGATCCCCCTTCGATCCT 59.437 55.000 0.00 0.00 37.45 3.24
913 2556 0.753479 TGATCTGAGGAGGCCGAGTC 60.753 60.000 0.00 0.00 0.00 3.36
943 2592 0.038159 CGGAGGAGGCCTATTTAGCG 60.038 60.000 4.42 0.00 31.76 4.26
956 2605 3.768185 TTAGCGCCGGTCGATGAGC 62.768 63.158 20.06 7.23 41.67 4.26
982 2634 2.226896 CGAGAGCAACGCATCCGAG 61.227 63.158 0.00 0.00 38.29 4.63
1531 3206 1.067821 CCGTCTACCAGAAGCTGATCC 59.932 57.143 0.00 0.00 32.44 3.36
1779 3454 3.053826 AGTCTACCCTCCAAAACCACTT 58.946 45.455 0.00 0.00 0.00 3.16
1841 3516 2.807837 GCAACCCATTTTTCTGCAGCTT 60.808 45.455 9.47 0.00 33.19 3.74
1980 3658 1.450312 CGGCCACTGGGAACTGATC 60.450 63.158 2.24 0.00 35.59 2.92
2004 3682 1.529152 TAAGCAGTCTTGGCGACCGA 61.529 55.000 0.00 0.00 43.91 4.69
2200 3878 2.552585 GAAGATTCGCCCGTCCGTCA 62.553 60.000 0.00 0.00 0.00 4.35
2332 4018 8.942338 TTCAGCGTGATAACTCTAATTAATGT 57.058 30.769 0.00 0.00 0.00 2.71
2502 4206 0.596577 GAAAGGGAAAAGGCGTGTCC 59.403 55.000 0.30 0.30 0.00 4.02
2520 4224 5.107065 CGTGTCCAACTGAAGAAGGAATAAC 60.107 44.000 0.00 0.00 0.00 1.89
2522 4226 7.159372 GTGTCCAACTGAAGAAGGAATAACTA 58.841 38.462 0.00 0.00 0.00 2.24
2787 4527 0.439985 CGCTGTTGAGTGTGAATCCG 59.560 55.000 0.00 0.00 0.00 4.18
2799 4539 4.340950 AGTGTGAATCCGGATTTGTTTGTT 59.659 37.500 29.74 6.77 0.00 2.83
2800 4540 5.533154 AGTGTGAATCCGGATTTGTTTGTTA 59.467 36.000 29.74 8.96 0.00 2.41
2835 4575 6.265876 GTCTTATCTTAGAGAAAGGTCGGGAT 59.734 42.308 7.11 0.00 35.75 3.85
2874 4614 5.507482 CCTTGATGAATCATGGCAGAATGTC 60.507 44.000 0.00 0.00 42.70 3.06
2888 4628 5.220931 GGCAGAATGTCACTGAATAACATCC 60.221 44.000 0.00 0.00 43.01 3.51
2889 4629 5.503031 GCAGAATGTCACTGAATAACATCCG 60.503 44.000 0.00 0.00 39.31 4.18
2926 4666 7.611467 ACCAAGTAATGCTCATTCTTGTCATTA 59.389 33.333 20.26 0.00 35.99 1.90
2927 4667 8.627403 CCAAGTAATGCTCATTCTTGTCATTAT 58.373 33.333 20.26 0.00 35.99 1.28
2930 4670 9.182214 AGTAATGCTCATTCTTGTCATTATTGT 57.818 29.630 0.00 0.00 34.84 2.71
2931 4671 9.793252 GTAATGCTCATTCTTGTCATTATTGTT 57.207 29.630 0.00 0.00 34.84 2.83
2968 4708 0.974383 AGGTGTCCTAACTTGTCCGG 59.026 55.000 0.00 0.00 28.47 5.14
2969 4709 0.683412 GGTGTCCTAACTTGTCCGGT 59.317 55.000 0.00 0.00 0.00 5.28
2986 4726 1.165270 GGTGCGGTAAGTTTGATGCT 58.835 50.000 0.00 0.00 0.00 3.79
3021 4761 5.652994 ATACACAAAAATGGTGCCGTAAT 57.347 34.783 0.00 0.00 39.87 1.89
3028 4768 3.848272 AATGGTGCCGTAATTTGTCTG 57.152 42.857 0.00 0.00 0.00 3.51
3030 4770 0.808755 GGTGCCGTAATTTGTCTGGG 59.191 55.000 0.00 0.00 0.00 4.45
3051 4791 2.223340 GCATTCAAATACGGTGCCTCTG 60.223 50.000 0.00 0.00 0.00 3.35
3065 4805 3.071837 TCTGGACGTATGCCGCCA 61.072 61.111 0.00 0.00 41.42 5.69
3066 4806 2.125310 CTGGACGTATGCCGCCAA 60.125 61.111 0.00 0.00 40.52 4.52
3076 4816 1.252904 ATGCCGCCAAATCAAGTGCT 61.253 50.000 0.00 0.00 0.00 4.40
3077 4817 0.607762 TGCCGCCAAATCAAGTGCTA 60.608 50.000 0.00 0.00 0.00 3.49
3079 4819 0.099436 CCGCCAAATCAAGTGCTAGC 59.901 55.000 8.10 8.10 0.00 3.42
3114 4854 2.672651 CGCTGGGCCACATGTCAA 60.673 61.111 0.00 0.00 0.00 3.18
3138 4878 2.210116 CTGTAGGCACGTTGTGAGTTT 58.790 47.619 0.24 0.00 35.23 2.66
3149 4889 3.243410 CGTTGTGAGTTTTGCGTGTAGTA 59.757 43.478 0.00 0.00 0.00 1.82
3155 4895 6.689241 TGTGAGTTTTGCGTGTAGTATTTTTG 59.311 34.615 0.00 0.00 0.00 2.44
3162 4902 8.906636 TTTGCGTGTAGTATTTTTGTTTACAA 57.093 26.923 0.00 0.00 0.00 2.41
3192 4932 6.481643 CCCCTGGACTTTAGTTAATTCTTGA 58.518 40.000 0.00 0.00 0.00 3.02
3250 4990 2.443887 TAGGTGAACGTGCTTGTACC 57.556 50.000 0.00 0.00 0.00 3.34
3286 5026 9.421806 TCTCACAAAAATATAAGCACAAATTGG 57.578 29.630 0.00 0.00 0.00 3.16
3287 5027 8.027440 TCACAAAAATATAAGCACAAATTGGC 57.973 30.769 0.00 0.00 0.00 4.52
3288 5028 7.658982 TCACAAAAATATAAGCACAAATTGGCA 59.341 29.630 8.65 0.00 0.00 4.92
3289 5029 8.452534 CACAAAAATATAAGCACAAATTGGCAT 58.547 29.630 8.65 0.70 0.00 4.40
3290 5030 8.452534 ACAAAAATATAAGCACAAATTGGCATG 58.547 29.630 8.65 0.00 0.00 4.06
3291 5031 7.556733 AAAATATAAGCACAAATTGGCATGG 57.443 32.000 8.65 0.00 0.00 3.66
3292 5032 5.874897 ATATAAGCACAAATTGGCATGGT 57.125 34.783 8.65 0.00 0.00 3.55
3314 5054 3.119009 TGGCATGGAGGGAATTCAAAT 57.881 42.857 7.93 0.00 0.00 2.32
3341 5082 2.582636 ACCTCCTGGTTGCCTATCAAAT 59.417 45.455 0.00 0.00 46.05 2.32
3342 5083 2.954318 CCTCCTGGTTGCCTATCAAATG 59.046 50.000 0.00 0.00 36.26 2.32
3352 5093 2.213499 CCTATCAAATGAGCGGACCAC 58.787 52.381 0.00 0.00 0.00 4.16
3365 5106 1.305930 GGACCACGAGGCCACATTTC 61.306 60.000 5.01 0.00 39.06 2.17
3371 5112 0.109781 CGAGGCCACATTTCGGTTTG 60.110 55.000 5.01 0.00 0.00 2.93
3374 5115 0.667184 GGCCACATTTCGGTTTGCAG 60.667 55.000 0.00 0.00 0.00 4.41
3411 5152 5.065914 AGCAACTTATATGCACGATTCCAT 58.934 37.500 0.00 0.00 46.22 3.41
3413 5154 5.049474 GCAACTTATATGCACGATTCCATGA 60.049 40.000 0.00 0.00 43.29 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.635009 TTATCCAGGACCCGAGGACT 59.365 55.000 0.00 0.00 33.57 3.85
2 3 3.533697 CTTATCCAGGACCCGAGGA 57.466 57.895 0.00 5.90 35.59 3.71
92 93 1.153289 CCTCAGGGCCTGACGAATG 60.153 63.158 32.01 20.92 35.39 2.67
141 143 1.671850 CGTTCGTGCCTTGGAGTATGT 60.672 52.381 0.00 0.00 0.00 2.29
157 159 7.023575 AGATAAATGTGTTGAAGATTGCGTTC 58.976 34.615 0.00 0.00 0.00 3.95
212 214 7.896496 ACCACTGGTTTTATATAAACATTGGGA 59.104 33.333 24.31 5.34 45.07 4.37
213 215 7.978975 CACCACTGGTTTTATATAAACATTGGG 59.021 37.037 24.31 14.93 45.07 4.12
214 216 7.491048 GCACCACTGGTTTTATATAAACATTGG 59.509 37.037 21.15 21.15 45.80 3.16
215 217 8.031864 TGCACCACTGGTTTTATATAAACATTG 58.968 33.333 7.43 7.92 31.02 2.82
216 218 8.128322 TGCACCACTGGTTTTATATAAACATT 57.872 30.769 7.43 0.00 31.02 2.71
217 219 7.613801 TCTGCACCACTGGTTTTATATAAACAT 59.386 33.333 7.43 0.00 31.02 2.71
219 221 7.248437 GTCTGCACCACTGGTTTTATATAAAC 58.752 38.462 7.43 3.87 31.02 2.01
221 223 5.883673 GGTCTGCACCACTGGTTTTATATAA 59.116 40.000 0.00 0.00 43.17 0.98
231 233 1.079819 CTACGGTCTGCACCACTGG 60.080 63.158 5.13 0.00 44.02 4.00
237 239 0.391130 TTGGCATCTACGGTCTGCAC 60.391 55.000 10.96 3.58 37.64 4.57
240 242 1.204704 TGAGTTGGCATCTACGGTCTG 59.795 52.381 0.00 0.00 0.00 3.51
276 278 5.880332 TGCAGAATACAAATTGACCTAGGTC 59.120 40.000 31.61 31.61 44.77 3.85
278 280 5.066505 GGTGCAGAATACAAATTGACCTAGG 59.933 44.000 7.41 7.41 0.00 3.02
283 285 3.427503 CGGGGTGCAGAATACAAATTGAC 60.428 47.826 0.00 0.00 0.00 3.18
288 290 1.612199 GGACGGGGTGCAGAATACAAA 60.612 52.381 0.00 0.00 0.00 2.83
296 298 2.034066 ATTGTGGACGGGGTGCAG 59.966 61.111 0.00 0.00 33.95 4.41
299 301 2.411628 TATTGATTGTGGACGGGGTG 57.588 50.000 0.00 0.00 0.00 4.61
305 307 8.931385 ATGCTTTGTTTATATTGATTGTGGAC 57.069 30.769 0.00 0.00 0.00 4.02
344 346 0.036294 GGTTCAGACCTTTCGGGGAG 60.036 60.000 0.00 0.00 42.99 4.30
356 358 2.231478 GTCGAATCCACTCAGGTTCAGA 59.769 50.000 0.00 0.00 39.02 3.27
359 361 3.254892 GAAGTCGAATCCACTCAGGTTC 58.745 50.000 0.00 0.00 39.02 3.62
379 381 3.959293 TCATCTACCTGGACAGTAACGA 58.041 45.455 0.00 0.00 0.00 3.85
389 391 1.802880 CGAGCCGTTTCATCTACCTGG 60.803 57.143 0.00 0.00 0.00 4.45
391 393 1.135083 CACGAGCCGTTTCATCTACCT 60.135 52.381 0.00 0.00 38.32 3.08
393 395 0.645868 GCACGAGCCGTTTCATCTAC 59.354 55.000 0.00 0.00 38.32 2.59
412 414 3.635268 GAGGGCAACTCAGGGGCTG 62.635 68.421 3.06 0.00 45.85 4.85
448 450 3.692406 GTCTCCCAGCCGTCCGTT 61.692 66.667 0.00 0.00 0.00 4.44
502 505 2.104281 ACTCCCGTATAAAGGATGGTGC 59.896 50.000 0.00 0.00 0.00 5.01
518 521 2.614057 CCTTTCGTGCATCATTACTCCC 59.386 50.000 0.00 0.00 0.00 4.30
544 547 4.893424 ACTTGCTTTTCTTTTACAGCGA 57.107 36.364 0.00 0.00 34.82 4.93
558 561 9.818270 TGTATGTATACCTATACCTACTTGCTT 57.182 33.333 14.17 0.00 39.21 3.91
560 563 9.458727 TCTGTATGTATACCTATACCTACTTGC 57.541 37.037 14.17 0.00 39.21 4.01
667 670 7.401860 TCTTTTCATTTCGCGATATCTTTCTG 58.598 34.615 10.88 0.00 0.00 3.02
668 671 7.539712 TCTTTTCATTTCGCGATATCTTTCT 57.460 32.000 10.88 0.00 0.00 2.52
727 2364 2.901042 CCGGAGTAGGGTGGAAGC 59.099 66.667 0.00 0.00 0.00 3.86
762 2405 1.132453 GAAATAAGAACCTGGCGTGGC 59.868 52.381 0.00 0.00 0.00 5.01
769 2412 3.055385 TCGGGTGGAGAAATAAGAACCTG 60.055 47.826 0.00 0.00 35.74 4.00
794 2437 0.812549 TTAGACACGGCGCATCAGTA 59.187 50.000 10.83 0.00 0.00 2.74
795 2438 0.037697 TTTAGACACGGCGCATCAGT 60.038 50.000 10.83 0.90 0.00 3.41
796 2439 1.290203 ATTTAGACACGGCGCATCAG 58.710 50.000 10.83 0.00 0.00 2.90
797 2440 2.198406 GTATTTAGACACGGCGCATCA 58.802 47.619 10.83 0.00 0.00 3.07
798 2441 1.189446 CGTATTTAGACACGGCGCATC 59.811 52.381 10.83 4.56 34.57 3.91
799 2442 1.205657 CGTATTTAGACACGGCGCAT 58.794 50.000 10.83 0.00 34.57 4.73
800 2443 0.109179 ACGTATTTAGACACGGCGCA 60.109 50.000 10.83 0.00 42.35 6.09
801 2444 0.569349 GACGTATTTAGACACGGCGC 59.431 55.000 6.90 0.00 42.35 6.53
803 2446 0.569349 GCGACGTATTTAGACACGGC 59.431 55.000 0.00 0.00 42.80 5.68
804 2447 1.844357 CAGCGACGTATTTAGACACGG 59.156 52.381 0.00 0.00 42.35 4.94
805 2448 1.844357 CCAGCGACGTATTTAGACACG 59.156 52.381 0.00 0.00 43.63 4.49
806 2449 3.141002 TCCAGCGACGTATTTAGACAC 57.859 47.619 0.00 0.00 0.00 3.67
807 2450 3.129813 ACATCCAGCGACGTATTTAGACA 59.870 43.478 0.00 0.00 0.00 3.41
808 2451 3.703420 ACATCCAGCGACGTATTTAGAC 58.297 45.455 0.00 0.00 0.00 2.59
809 2452 4.097437 AGAACATCCAGCGACGTATTTAGA 59.903 41.667 0.00 0.00 0.00 2.10
810 2453 4.360563 AGAACATCCAGCGACGTATTTAG 58.639 43.478 0.00 0.00 0.00 1.85
811 2454 4.380841 AGAACATCCAGCGACGTATTTA 57.619 40.909 0.00 0.00 0.00 1.40
812 2455 3.247006 AGAACATCCAGCGACGTATTT 57.753 42.857 0.00 0.00 0.00 1.40
813 2456 2.961526 AGAACATCCAGCGACGTATT 57.038 45.000 0.00 0.00 0.00 1.89
814 2457 2.961526 AAGAACATCCAGCGACGTAT 57.038 45.000 0.00 0.00 0.00 3.06
815 2458 2.602878 GAAAGAACATCCAGCGACGTA 58.397 47.619 0.00 0.00 0.00 3.57
816 2459 1.429463 GAAAGAACATCCAGCGACGT 58.571 50.000 0.00 0.00 0.00 4.34
817 2460 0.721718 GGAAAGAACATCCAGCGACG 59.278 55.000 0.00 0.00 36.92 5.12
818 2461 1.808411 TGGAAAGAACATCCAGCGAC 58.192 50.000 0.00 0.00 41.98 5.19
823 2466 0.960364 GCGCCTGGAAAGAACATCCA 60.960 55.000 0.00 0.00 44.58 3.41
824 2467 1.657751 GGCGCCTGGAAAGAACATCC 61.658 60.000 22.15 0.00 37.48 3.51
825 2468 1.803289 GGCGCCTGGAAAGAACATC 59.197 57.895 22.15 0.00 0.00 3.06
826 2469 2.040544 CGGCGCCTGGAAAGAACAT 61.041 57.895 26.68 0.00 0.00 2.71
827 2470 2.668212 CGGCGCCTGGAAAGAACA 60.668 61.111 26.68 0.00 0.00 3.18
828 2471 4.103103 GCGGCGCCTGGAAAGAAC 62.103 66.667 26.68 0.00 0.00 3.01
829 2472 4.329545 AGCGGCGCCTGGAAAGAA 62.330 61.111 30.40 0.00 0.00 2.52
830 2473 4.760047 GAGCGGCGCCTGGAAAGA 62.760 66.667 30.40 0.00 0.00 2.52
841 2484 3.468326 GAAGGGGGATCTGAGCGGC 62.468 68.421 0.00 0.00 0.00 6.53
865 2508 4.819630 CGATCCCAAATCGGAGGAATTAAA 59.180 41.667 0.00 0.00 37.84 1.52
913 2556 1.358402 CTCCTCCGATCAGTCTGCG 59.642 63.158 0.00 0.00 0.00 5.18
943 2592 4.933064 CCTCGCTCATCGACCGGC 62.933 72.222 0.00 0.00 43.16 6.13
1779 3454 4.954118 ACGACAGGGCCAGGACCA 62.954 66.667 16.27 0.00 29.21 4.02
1782 3457 4.329545 GCAACGACAGGGCCAGGA 62.330 66.667 6.18 0.00 0.00 3.86
1841 3516 2.495084 CATCGGACTCCACGAGATAGA 58.505 52.381 0.00 0.00 44.24 1.98
1980 3658 1.021390 CGCCAAGACTGCTTACTGGG 61.021 60.000 0.00 0.00 31.81 4.45
2004 3682 5.584136 CTGTCCATGGAGACAAACAATGCT 61.584 45.833 16.81 0.00 45.77 3.79
2109 3787 1.375908 GCTCAGGGAATGCACGACA 60.376 57.895 0.00 0.00 0.00 4.35
2200 3878 3.011517 AGCGATGGTGAAGGGCCT 61.012 61.111 0.00 0.00 0.00 5.19
2332 4018 7.556275 AGGAGGACGAAATGCAAATTATTAGAA 59.444 33.333 0.00 0.00 0.00 2.10
2502 4206 6.090898 CGGTGTAGTTATTCCTTCTTCAGTTG 59.909 42.308 0.00 0.00 0.00 3.16
2520 4224 5.892568 AGAGCAGTCTAAATTACGGTGTAG 58.107 41.667 0.00 0.00 0.00 2.74
2522 4226 4.803098 AGAGCAGTCTAAATTACGGTGT 57.197 40.909 0.00 0.00 0.00 4.16
2685 4398 3.392616 CAGATCCTAACTGGCATAACCCT 59.607 47.826 0.00 0.00 37.83 4.34
2779 4519 9.878599 CTATATAACAAACAAATCCGGATTCAC 57.121 33.333 29.32 0.00 0.00 3.18
2818 4558 4.648307 GGAGTAATCCCGACCTTTCTCTAA 59.352 45.833 0.00 0.00 0.00 2.10
2835 4575 2.897350 TCAAGGCACAGTAGGGAGTAA 58.103 47.619 0.00 0.00 0.00 2.24
2874 4614 4.142026 TGGTCTACCGGATGTTATTCAGTG 60.142 45.833 9.46 0.00 39.43 3.66
2888 4628 0.892755 TACTTGGTGCTGGTCTACCG 59.107 55.000 0.00 0.00 39.87 4.02
2889 4629 3.270877 CATTACTTGGTGCTGGTCTACC 58.729 50.000 0.00 0.00 37.48 3.18
2928 4668 9.344772 ACACCTGTAATGTATTTAACTCAAACA 57.655 29.630 0.00 0.00 0.00 2.83
2929 4669 9.821662 GACACCTGTAATGTATTTAACTCAAAC 57.178 33.333 0.00 0.00 0.00 2.93
2930 4670 9.005777 GGACACCTGTAATGTATTTAACTCAAA 57.994 33.333 0.00 0.00 0.00 2.69
2931 4671 8.380099 AGGACACCTGTAATGTATTTAACTCAA 58.620 33.333 0.00 0.00 29.57 3.02
2932 4672 7.913789 AGGACACCTGTAATGTATTTAACTCA 58.086 34.615 0.00 0.00 29.57 3.41
2945 4685 3.006110 CGGACAAGTTAGGACACCTGTAA 59.994 47.826 0.00 0.00 34.61 2.41
2968 4708 2.989422 AAGCATCAAACTTACCGCAC 57.011 45.000 0.00 0.00 0.00 5.34
2969 4709 4.517453 AGTTTAAGCATCAAACTTACCGCA 59.483 37.500 4.95 0.00 42.18 5.69
3021 4761 3.192422 CCGTATTTGAATGCCCAGACAAA 59.808 43.478 0.00 0.00 36.82 2.83
3028 4768 3.641031 GCACCGTATTTGAATGCCC 57.359 52.632 0.00 0.00 0.00 5.36
3030 4770 2.017049 AGAGGCACCGTATTTGAATGC 58.983 47.619 0.00 0.00 35.51 3.56
3065 4805 0.804989 GCCACGCTAGCACTTGATTT 59.195 50.000 16.45 0.00 0.00 2.17
3066 4806 0.321564 TGCCACGCTAGCACTTGATT 60.322 50.000 16.45 0.00 34.69 2.57
3076 4816 2.436469 CACTGGCATGCCACGCTA 60.436 61.111 35.59 14.70 41.89 4.26
3077 4817 4.648626 ACACTGGCATGCCACGCT 62.649 61.111 35.59 17.55 41.89 5.07
3079 4819 2.969806 GACACACTGGCATGCCACG 61.970 63.158 35.59 29.51 41.89 4.94
3114 4854 0.955428 CACAACGTGCCTACAGCCAT 60.955 55.000 0.00 0.00 42.71 4.40
3121 4861 1.332375 GCAAAACTCACAACGTGCCTA 59.668 47.619 0.00 0.00 32.98 3.93
3122 4862 0.100503 GCAAAACTCACAACGTGCCT 59.899 50.000 0.00 0.00 32.98 4.75
3126 4866 0.800012 ACACGCAAAACTCACAACGT 59.200 45.000 0.00 0.00 0.00 3.99
3138 4878 8.906636 TTTGTAAACAAAAATACTACACGCAA 57.093 26.923 5.82 0.00 42.26 4.85
3155 4895 3.323691 AGTCCAGGGGCATTTTTGTAAAC 59.676 43.478 0.00 0.00 0.00 2.01
3162 4902 3.542969 ACTAAAGTCCAGGGGCATTTT 57.457 42.857 0.00 0.00 0.00 1.82
3233 4973 1.589803 AAGGTACAAGCACGTTCACC 58.410 50.000 0.00 0.00 0.00 4.02
3235 4975 7.675962 ATTAATTAAGGTACAAGCACGTTCA 57.324 32.000 3.94 0.00 0.00 3.18
3241 4981 8.856153 TGTGAGAATTAATTAAGGTACAAGCA 57.144 30.769 0.00 0.00 0.00 3.91
3276 5016 1.536331 CCAAACCATGCCAATTTGTGC 59.464 47.619 0.00 0.00 32.53 4.57
3282 5022 0.253610 CCATGCCAAACCATGCCAAT 59.746 50.000 0.00 0.00 40.92 3.16
3283 5023 0.835115 TCCATGCCAAACCATGCCAA 60.835 50.000 0.00 0.00 40.92 4.52
3284 5024 1.229114 TCCATGCCAAACCATGCCA 60.229 52.632 0.00 0.00 40.92 4.92
3285 5025 1.518774 CTCCATGCCAAACCATGCC 59.481 57.895 0.00 0.00 40.92 4.40
3286 5026 1.518774 CCTCCATGCCAAACCATGC 59.481 57.895 0.00 0.00 40.92 4.06
3287 5027 0.324552 TCCCTCCATGCCAAACCATG 60.325 55.000 0.00 0.00 41.71 3.66
3288 5028 0.413037 TTCCCTCCATGCCAAACCAT 59.587 50.000 0.00 0.00 0.00 3.55
3289 5029 0.413037 ATTCCCTCCATGCCAAACCA 59.587 50.000 0.00 0.00 0.00 3.67
3290 5030 1.482182 GAATTCCCTCCATGCCAAACC 59.518 52.381 0.00 0.00 0.00 3.27
3291 5031 2.178580 TGAATTCCCTCCATGCCAAAC 58.821 47.619 2.27 0.00 0.00 2.93
3292 5032 2.619697 TGAATTCCCTCCATGCCAAA 57.380 45.000 2.27 0.00 0.00 3.28
3301 5041 2.683362 GGTCCGTGATTTGAATTCCCTC 59.317 50.000 2.27 0.00 0.00 4.30
3336 5076 0.389817 CTCGTGGTCCGCTCATTTGA 60.390 55.000 0.00 0.00 36.19 2.69
3352 5093 0.109781 CAAACCGAAATGTGGCCTCG 60.110 55.000 3.32 3.98 0.00 4.63
3385 5126 5.696724 GGAATCGTGCATATAAGTTGCTAGT 59.303 40.000 0.00 0.00 40.77 2.57
3411 5152 0.590682 AACATGTGCAACGCGATTCA 59.409 45.000 15.93 0.00 42.39 2.57
3413 5154 2.050691 GAAAACATGTGCAACGCGATT 58.949 42.857 15.93 0.00 42.39 3.34
3419 5160 6.885735 AAAACTGTAGAAAACATGTGCAAC 57.114 33.333 0.00 0.00 37.50 4.17


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

AutoCloner maintained by Alex Coulton.