Multiple sequence alignment - TraesCS1D01G034000

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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 TraesCS1D01G034000 chr1D 100.000 3204 0 0 1 3204 14189221 14186018 0.000000e+00 5917.0
1 TraesCS1D01G034000 chr1D 90.452 1372 99 12 883 2227 13853320 13851954 0.000000e+00 1779.0
2 TraesCS1D01G034000 chr1D 90.000 400 35 2 1828 2227 13970053 13969659 2.200000e-141 512.0
3 TraesCS1D01G034000 chr1D 82.692 468 45 9 1828 2290 14001352 14000916 1.800000e-102 383.0
4 TraesCS1D01G034000 chr1D 92.199 141 11 0 883 1023 13970193 13970053 1.950000e-47 200.0
5 TraesCS1D01G034000 chr1D 92.199 141 11 0 883 1023 14001492 14001352 1.950000e-47 200.0
6 TraesCS1D01G034000 chr1D 80.423 189 19 14 99 274 236858660 236858843 9.330000e-26 128.0
7 TraesCS1D01G034000 chr1A 89.371 2211 169 29 883 3052 14858377 14856192 0.000000e+00 2721.0
8 TraesCS1D01G034000 chr1A 88.866 1437 120 22 883 2290 14800589 14799164 0.000000e+00 1731.0
9 TraesCS1D01G034000 chr1A 78.613 519 66 22 1 477 14985397 14984882 5.190000e-78 302.0
10 TraesCS1D01G034000 chr1A 83.562 292 44 4 203 491 14983278 14982988 1.460000e-68 270.0
11 TraesCS1D01G034000 chr1A 82.877 292 46 4 203 491 14984230 14983940 3.170000e-65 259.0
12 TraesCS1D01G034000 chr1A 85.263 190 25 3 342 530 14982983 14982796 3.260000e-45 193.0
13 TraesCS1D01G034000 chr1A 87.879 165 17 3 332 494 14983055 14982892 1.170000e-44 191.0
14 TraesCS1D01G034000 chr1A 89.189 148 14 2 333 479 14984006 14983860 1.960000e-42 183.0
15 TraesCS1D01G034000 chr1A 84.211 190 27 3 342 530 14983935 14983748 7.060000e-42 182.0
16 TraesCS1D01G034000 chr1A 81.347 193 28 5 306 491 14983117 14982926 1.990000e-32 150.0
17 TraesCS1D01G034000 chr1A 95.122 41 1 1 2576 2615 425717784 425717824 2.670000e-06 63.9
18 TraesCS1D01G034000 chr1B 90.526 1805 122 14 1 1786 20128402 20126628 0.000000e+00 2340.0
19 TraesCS1D01G034000 chr1B 89.971 1376 98 19 883 2227 20292887 20294253 0.000000e+00 1740.0
20 TraesCS1D01G034000 chr1B 89.942 1372 101 19 883 2227 20061176 20059815 0.000000e+00 1735.0
21 TraesCS1D01G034000 chr1B 88.834 1012 71 15 1789 2799 20102667 20101697 0.000000e+00 1205.0
22 TraesCS1D01G034000 chr1B 100.000 32 0 0 2259 2290 20059774 20059743 3.450000e-05 60.2
23 TraesCS1D01G034000 chr1B 100.000 32 0 0 2259 2290 20294294 20294325 3.450000e-05 60.2
24 TraesCS1D01G034000 chr3D 94.444 162 7 2 3043 3204 501081020 501081179 6.860000e-62 248.0
25 TraesCS1D01G034000 chr3D 95.484 155 6 1 3050 3204 347608161 347608008 2.470000e-61 246.0
26 TraesCS1D01G034000 chr5B 95.484 155 6 1 3050 3204 42251099 42250946 2.470000e-61 246.0
27 TraesCS1D01G034000 chr5B 94.839 155 7 1 3050 3204 482420088 482419935 1.150000e-59 241.0
28 TraesCS1D01G034000 chr3B 94.904 157 6 2 3048 3204 19747979 19747825 8.880000e-61 244.0
29 TraesCS1D01G034000 chr4B 94.839 155 7 1 3050 3204 25959904 25959751 1.150000e-59 241.0
30 TraesCS1D01G034000 chr4B 82.803 157 21 6 733 886 424279733 424279580 5.580000e-28 135.0
31 TraesCS1D01G034000 chr5D 94.194 155 8 1 3050 3204 3781948 3781795 5.340000e-58 235.0
32 TraesCS1D01G034000 chr5D 86.957 69 8 1 748 816 114913399 114913332 3.430000e-10 76.8
33 TraesCS1D01G034000 chr4D 93.590 156 9 1 3049 3204 505312052 505312206 6.910000e-57 231.0
34 TraesCS1D01G034000 chr4D 79.878 164 22 8 99 252 122208506 122208668 3.380000e-20 110.0
35 TraesCS1D01G034000 chr6B 93.548 155 9 1 3050 3204 720448119 720448272 2.490000e-56 230.0
36 TraesCS1D01G034000 chr7B 78.593 327 39 14 103 414 32552453 32552143 1.520000e-43 187.0
37 TraesCS1D01G034000 chr6A 86.047 172 19 4 718 888 550278657 550278490 2.540000e-41 180.0
38 TraesCS1D01G034000 chr6A 86.364 66 8 1 427 491 30795071 30795136 1.590000e-08 71.3
39 TraesCS1D01G034000 chr7D 82.199 191 20 10 95 274 39093964 39094151 5.540000e-33 152.0
40 TraesCS1D01G034000 chr7D 81.675 191 21 9 95 274 39020711 39020898 2.580000e-31 147.0
41 TraesCS1D01G034000 chr7D 86.792 106 13 1 100 205 586712969 586713073 2.020000e-22 117.0
42 TraesCS1D01G034000 chr2D 75.449 334 63 17 555 879 391869619 391869942 9.260000e-31 145.0
43 TraesCS1D01G034000 chr2D 81.548 168 16 10 96 251 563947007 563947171 1.210000e-24 124.0
44 TraesCS1D01G034000 chr2A 82.840 169 13 11 96 251 703980572 703980737 1.550000e-28 137.0
45 TraesCS1D01G034000 chr7A 97.143 35 1 0 785 819 127594007 127594041 3.450000e-05 60.2


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 TraesCS1D01G034000 chr1D 14186018 14189221 3203 True 5917.00 5917 100.000000 1 3204 1 chr1D.!!$R2 3203
1 TraesCS1D01G034000 chr1D 13851954 13853320 1366 True 1779.00 1779 90.452000 883 2227 1 chr1D.!!$R1 1344
2 TraesCS1D01G034000 chr1D 13969659 13970193 534 True 356.00 512 91.099500 883 2227 2 chr1D.!!$R3 1344
3 TraesCS1D01G034000 chr1D 14000916 14001492 576 True 291.50 383 87.445500 883 2290 2 chr1D.!!$R4 1407
4 TraesCS1D01G034000 chr1A 14856192 14858377 2185 True 2721.00 2721 89.371000 883 3052 1 chr1A.!!$R2 2169
5 TraesCS1D01G034000 chr1A 14799164 14800589 1425 True 1731.00 1731 88.866000 883 2290 1 chr1A.!!$R1 1407
6 TraesCS1D01G034000 chr1A 14982796 14985397 2601 True 216.25 302 84.117625 1 530 8 chr1A.!!$R3 529
7 TraesCS1D01G034000 chr1B 20126628 20128402 1774 True 2340.00 2340 90.526000 1 1786 1 chr1B.!!$R2 1785
8 TraesCS1D01G034000 chr1B 20101697 20102667 970 True 1205.00 1205 88.834000 1789 2799 1 chr1B.!!$R1 1010
9 TraesCS1D01G034000 chr1B 20292887 20294325 1438 False 900.10 1740 94.985500 883 2290 2 chr1B.!!$F1 1407
10 TraesCS1D01G034000 chr1B 20059743 20061176 1433 True 897.60 1735 94.971000 883 2290 2 chr1B.!!$R3 1407

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
482 1619 0.319555 CCAAGCTTGAGGACGAACGA 60.32 55.0 28.05 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2457 4183 0.243095 AGAGGACAACGAGTAACCGC 59.757 55.0 0.0 0.0 0.0 5.68 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
35 36 0.463654 GCCACCATCATCGGTAGCAA 60.464 55.000 0.00 0.00 42.52 3.91
82 83 4.371231 CCCCTCCCCCTTCCCAGT 62.371 72.222 0.00 0.00 0.00 4.00
94 95 0.550914 TTCCCAGTCCACTGTTTGCT 59.449 50.000 5.99 0.00 42.27 3.91
237 278 9.237187 TGTAATTTGATGTAAAACTATGCTCCA 57.763 29.630 0.00 0.00 0.00 3.86
239 280 8.986477 AATTTGATGTAAAACTATGCTCCAAC 57.014 30.769 0.00 0.00 0.00 3.77
240 281 7.517614 TTTGATGTAAAACTATGCTCCAACA 57.482 32.000 0.00 0.00 0.00 3.33
241 282 6.741992 TGATGTAAAACTATGCTCCAACAG 57.258 37.500 0.00 0.00 0.00 3.16
242 283 6.472016 TGATGTAAAACTATGCTCCAACAGA 58.528 36.000 0.00 0.00 0.00 3.41
243 284 7.112122 TGATGTAAAACTATGCTCCAACAGAT 58.888 34.615 0.00 0.00 0.00 2.90
244 285 6.741992 TGTAAAACTATGCTCCAACAGATG 57.258 37.500 0.00 0.00 0.00 2.90
245 286 6.472016 TGTAAAACTATGCTCCAACAGATGA 58.528 36.000 0.00 0.00 0.00 2.92
246 287 7.112122 TGTAAAACTATGCTCCAACAGATGAT 58.888 34.615 0.00 0.00 0.00 2.45
247 288 6.446781 AAAACTATGCTCCAACAGATGATG 57.553 37.500 0.00 0.00 0.00 3.07
248 289 4.767578 ACTATGCTCCAACAGATGATGT 57.232 40.909 0.00 0.00 46.97 3.06
249 290 5.876651 ACTATGCTCCAACAGATGATGTA 57.123 39.130 0.00 0.00 43.00 2.29
250 291 6.430962 ACTATGCTCCAACAGATGATGTAT 57.569 37.500 0.00 0.00 43.00 2.29
356 473 2.095252 GCCGAGCTTGGAGACGAAC 61.095 63.158 25.25 0.00 0.00 3.95
383 500 2.202676 GCGGACGAGCTTGGAGAG 60.203 66.667 5.79 0.00 0.00 3.20
390 507 2.999648 AGCTTGGAGAGGAGCGCA 61.000 61.111 11.47 0.00 43.53 6.09
482 1619 0.319555 CCAAGCTTGAGGACGAACGA 60.320 55.000 28.05 0.00 0.00 3.85
508 1645 3.423154 GGCGGAGTGGCGAAACAG 61.423 66.667 0.00 0.00 0.00 3.16
540 1677 0.603975 GGTGATTAGAGGCGATGGGC 60.604 60.000 0.00 0.00 42.51 5.36
550 1687 2.818841 CGATGGGCGGTGTGGATA 59.181 61.111 0.00 0.00 36.03 2.59
658 2269 4.752594 CGGGGAGGGGAGGGGAAA 62.753 72.222 0.00 0.00 0.00 3.13
685 2296 3.601685 GGTTGGGTTGGTGTGCGG 61.602 66.667 0.00 0.00 0.00 5.69
689 2300 4.947147 GGGTTGGTGTGCGGCTGA 62.947 66.667 0.00 0.00 0.00 4.26
709 2320 2.554893 GACCGTTTTGCATCTGGGTTTA 59.445 45.455 0.00 0.00 0.00 2.01
713 2324 4.156922 CCGTTTTGCATCTGGGTTTACATA 59.843 41.667 0.00 0.00 0.00 2.29
745 2356 7.066284 CGGTTGGAGATGAAAATTTGTATCTCT 59.934 37.037 27.14 13.17 43.09 3.10
787 2398 5.412594 TCACTTGAAGCAGGTGATGTAATTC 59.587 40.000 8.09 0.00 43.62 2.17
789 2400 6.006449 ACTTGAAGCAGGTGATGTAATTCTT 58.994 36.000 0.00 0.00 0.00 2.52
820 2431 8.041919 CATCTACATCATCTTATTGGAGATGCT 58.958 37.037 10.50 0.00 46.37 3.79
850 2461 4.204799 GCCCCCGAGATGTAAAAGTTAAT 58.795 43.478 0.00 0.00 0.00 1.40
853 2464 6.489022 GCCCCCGAGATGTAAAAGTTAATTAT 59.511 38.462 0.00 0.00 0.00 1.28
943 2555 2.612972 CGTAACCCTCACTGCAGATGTT 60.613 50.000 23.35 16.44 0.00 2.71
1114 2730 1.373570 CGTGAAGCTTGGAATCCCTC 58.626 55.000 2.10 0.00 0.00 4.30
1118 2734 1.680207 GAAGCTTGGAATCCCTCATGC 59.320 52.381 2.10 0.00 35.24 4.06
1300 2943 0.306533 CACGGTTTTCCACCTCAACG 59.693 55.000 0.00 0.00 44.69 4.10
1503 3164 1.029947 GCCGTGACCCCGAATTCAAT 61.030 55.000 6.22 0.00 0.00 2.57
1602 3263 1.942586 GCTGGGATAACGTCGTTGGTT 60.943 52.381 20.62 5.38 0.00 3.67
1726 3387 3.101209 CCGATGGCACGGTTGATG 58.899 61.111 16.88 0.00 46.70 3.07
1732 3393 1.107114 TGGCACGGTTGATGTTGTTT 58.893 45.000 0.00 0.00 0.00 2.83
1862 3542 7.309133 CCTTCCAGTTCATAATAAGTGTTGCAA 60.309 37.037 0.00 0.00 0.00 4.08
1980 3663 1.303317 GACAGGCCATTTCCCACGT 60.303 57.895 5.01 0.00 0.00 4.49
2026 3733 2.197792 TTGATACCGTCGTTGGATCG 57.802 50.000 2.72 0.00 0.00 3.69
2030 3737 4.444838 CCGTCGTTGGATCGCCCA 62.445 66.667 0.00 0.00 44.93 5.36
2034 3741 3.124921 CGTTGGATCGCCCACACC 61.125 66.667 0.00 0.00 46.62 4.16
2035 3742 2.351276 GTTGGATCGCCCACACCT 59.649 61.111 0.00 0.00 46.62 4.00
2054 3761 2.424956 CCTCAAATACTTGAAGGCCAGC 59.575 50.000 5.01 0.00 41.05 4.85
2056 3763 3.760684 CTCAAATACTTGAAGGCCAGCTT 59.239 43.478 5.01 0.00 41.05 3.74
2137 3844 2.730090 GCACAAGATGTTCATGGAAGCG 60.730 50.000 0.00 0.00 0.00 4.68
2216 3923 2.890808 TCCGTAGCTTGCTTATCCAG 57.109 50.000 0.00 0.00 0.00 3.86
2317 4042 5.544948 AGCCCTATTTCCGGTAATGTGTATA 59.455 40.000 15.89 0.00 0.00 1.47
2470 4196 1.214367 ACAACAGCGGTTACTCGTTG 58.786 50.000 11.75 11.75 44.76 4.10
2542 4268 5.559427 TCACATTTTGACCATATGGAACG 57.441 39.130 28.77 7.08 38.94 3.95
2563 4292 1.639635 ATCCTAGGTTGCAGGGCCTG 61.640 60.000 29.44 29.44 36.38 4.85
2569 4298 1.398958 GGTTGCAGGGCCTGTTTGAA 61.399 55.000 32.80 18.06 33.43 2.69
2607 4337 3.502211 ACGCAGGAATAGGAAAAACACAG 59.498 43.478 0.00 0.00 0.00 3.66
2617 4347 8.893563 AATAGGAAAAACACAGGATTGGAATA 57.106 30.769 0.00 0.00 0.00 1.75
2676 4406 9.691362 TGATTTAGCATAGGAAAAACAAAAGAC 57.309 29.630 0.00 0.00 0.00 3.01
2725 4456 9.685276 AATGATGGTATGAGATGTTTCAAGTAA 57.315 29.630 0.00 0.00 0.00 2.24
2764 4495 9.130312 GTATACTTGATATCATCGAAGGTTCAC 57.870 37.037 6.17 0.00 0.00 3.18
2768 4499 2.295253 ATCATCGAAGGTTCACGGAC 57.705 50.000 0.00 0.00 0.00 4.79
2776 4507 3.495377 CGAAGGTTCACGGACAACATTTA 59.505 43.478 0.00 0.00 28.28 1.40
2782 4513 7.269316 AGGTTCACGGACAACATTTAAATTTT 58.731 30.769 0.00 0.00 0.00 1.82
2844 4575 6.770785 ACACATCTTTAAGGTCTGCAACTAAA 59.229 34.615 0.00 0.00 0.00 1.85
2847 4578 6.613755 TCTTTAAGGTCTGCAACTAAACAC 57.386 37.500 0.00 0.00 0.00 3.32
2853 4584 2.221055 GTCTGCAACTAAACACGAGGTG 59.779 50.000 0.00 0.00 39.75 4.00
2861 4592 5.978934 ACTAAACACGAGGTGTAAAAGTG 57.021 39.130 1.32 0.00 46.79 3.16
2877 4608 2.566833 AGTGTGAGCTGTTATGCCAA 57.433 45.000 0.00 0.00 0.00 4.52
2882 4613 3.057386 TGTGAGCTGTTATGCCAACATTG 60.057 43.478 0.00 0.00 37.74 2.82
2891 4622 7.009540 GCTGTTATGCCAACATTGTTATTTCTC 59.990 37.037 0.86 0.00 37.74 2.87
2939 4670 8.713971 TCTCTTATTCAGAAATATAACCAGCCA 58.286 33.333 0.00 0.00 0.00 4.75
2941 4672 8.271458 TCTTATTCAGAAATATAACCAGCCACA 58.729 33.333 0.00 0.00 0.00 4.17
2945 4676 7.373617 TCAGAAATATAACCAGCCACAGATA 57.626 36.000 0.00 0.00 0.00 1.98
2948 4679 8.367911 CAGAAATATAACCAGCCACAGATACTA 58.632 37.037 0.00 0.00 0.00 1.82
2950 4681 4.957684 ATAACCAGCCACAGATACTACC 57.042 45.455 0.00 0.00 0.00 3.18
2986 4717 9.834628 TTAAAATACATTTCTCGTTGTCAATCC 57.165 29.630 0.00 0.00 32.27 3.01
3021 4752 7.968405 GTGAATTTACACTTATTCGCCTGAAAT 59.032 33.333 0.00 0.00 36.00 2.17
3054 4785 8.534333 TCAATATCAAGTAATTCTATGGACGC 57.466 34.615 0.00 0.00 0.00 5.19
3055 4786 7.328493 TCAATATCAAGTAATTCTATGGACGCG 59.672 37.037 3.53 3.53 0.00 6.01
3056 4787 3.713288 TCAAGTAATTCTATGGACGCGG 58.287 45.455 12.47 0.00 0.00 6.46
3057 4788 3.382227 TCAAGTAATTCTATGGACGCGGA 59.618 43.478 12.47 0.00 0.00 5.54
3058 4789 4.038763 TCAAGTAATTCTATGGACGCGGAT 59.961 41.667 12.47 1.42 0.00 4.18
3059 4790 4.602340 AGTAATTCTATGGACGCGGATT 57.398 40.909 12.47 0.00 0.00 3.01
3060 4791 4.957296 AGTAATTCTATGGACGCGGATTT 58.043 39.130 12.47 2.26 0.00 2.17
3061 4792 5.365619 AGTAATTCTATGGACGCGGATTTT 58.634 37.500 12.47 0.00 0.00 1.82
3062 4793 5.820947 AGTAATTCTATGGACGCGGATTTTT 59.179 36.000 12.47 0.00 0.00 1.94
3063 4794 4.552166 ATTCTATGGACGCGGATTTTTG 57.448 40.909 12.47 0.00 0.00 2.44
3064 4795 2.285083 TCTATGGACGCGGATTTTTGG 58.715 47.619 12.47 0.00 0.00 3.28
3065 4796 1.333619 CTATGGACGCGGATTTTTGGG 59.666 52.381 12.47 0.00 0.00 4.12
3066 4797 0.322997 ATGGACGCGGATTTTTGGGA 60.323 50.000 12.47 0.00 0.00 4.37
3067 4798 1.238625 TGGACGCGGATTTTTGGGAC 61.239 55.000 12.47 0.00 0.00 4.46
3068 4799 1.238625 GGACGCGGATTTTTGGGACA 61.239 55.000 12.47 0.00 0.00 4.02
3069 4800 0.808755 GACGCGGATTTTTGGGACAT 59.191 50.000 12.47 0.00 39.30 3.06
3070 4801 0.525761 ACGCGGATTTTTGGGACATG 59.474 50.000 12.47 0.00 39.30 3.21
3071 4802 0.179140 CGCGGATTTTTGGGACATGG 60.179 55.000 0.00 0.00 39.30 3.66
3072 4803 0.894835 GCGGATTTTTGGGACATGGT 59.105 50.000 0.00 0.00 39.30 3.55
3073 4804 1.275010 GCGGATTTTTGGGACATGGTT 59.725 47.619 0.00 0.00 39.30 3.67
3074 4805 2.673893 GCGGATTTTTGGGACATGGTTC 60.674 50.000 0.00 0.00 39.30 3.62
3075 4806 2.094234 CGGATTTTTGGGACATGGTTCC 60.094 50.000 0.00 0.00 39.30 3.62
3076 4807 2.903135 GGATTTTTGGGACATGGTTCCA 59.097 45.455 4.85 2.70 39.83 3.53
3077 4808 3.519107 GGATTTTTGGGACATGGTTCCAT 59.481 43.478 4.85 0.00 41.38 3.41
3078 4809 4.383010 GGATTTTTGGGACATGGTTCCATC 60.383 45.833 0.86 0.00 41.38 3.51
3079 4810 1.832883 TTTGGGACATGGTTCCATCG 58.167 50.000 0.86 1.39 41.38 3.84
3080 4811 0.679640 TTGGGACATGGTTCCATCGC 60.680 55.000 0.86 2.46 41.38 4.58
3081 4812 2.180204 GGGACATGGTTCCATCGCG 61.180 63.158 0.00 0.00 37.40 5.87
3082 4813 1.153449 GGACATGGTTCCATCGCGA 60.153 57.895 13.09 13.09 35.49 5.87
3083 4814 1.154205 GGACATGGTTCCATCGCGAG 61.154 60.000 16.66 6.78 35.49 5.03
3084 4815 1.153369 ACATGGTTCCATCGCGAGG 60.153 57.895 16.66 15.77 0.00 4.63
3085 4816 1.143838 CATGGTTCCATCGCGAGGA 59.856 57.895 24.13 21.21 0.00 3.71
3086 4817 0.877649 CATGGTTCCATCGCGAGGAG 60.878 60.000 24.13 12.53 36.33 3.69
3087 4818 2.586357 GGTTCCATCGCGAGGAGC 60.586 66.667 24.13 23.65 43.95 4.70
3103 4834 6.600246 CGAGGAGCATATCAAATCCATATG 57.400 41.667 0.00 0.00 37.30 1.78
3104 4835 6.111382 CGAGGAGCATATCAAATCCATATGT 58.889 40.000 1.24 0.00 36.81 2.29
3105 4836 6.596888 CGAGGAGCATATCAAATCCATATGTT 59.403 38.462 1.24 0.00 36.81 2.71
3106 4837 7.120285 CGAGGAGCATATCAAATCCATATGTTT 59.880 37.037 1.24 0.00 36.81 2.83
3107 4838 8.118976 AGGAGCATATCAAATCCATATGTTTG 57.881 34.615 10.94 10.94 36.81 2.93
3108 4839 7.727186 AGGAGCATATCAAATCCATATGTTTGT 59.273 33.333 14.87 8.07 36.81 2.83
3109 4840 7.811236 GGAGCATATCAAATCCATATGTTTGTG 59.189 37.037 14.87 9.54 36.81 3.33
3110 4841 8.241497 AGCATATCAAATCCATATGTTTGTGT 57.759 30.769 14.87 9.79 36.81 3.72
3111 4842 8.698210 AGCATATCAAATCCATATGTTTGTGTT 58.302 29.630 14.87 5.57 36.81 3.32
3112 4843 9.316730 GCATATCAAATCCATATGTTTGTGTTT 57.683 29.630 14.87 5.68 36.81 2.83
3116 4847 8.815141 TCAAATCCATATGTTTGTGTTTTGAG 57.185 30.769 14.87 0.00 36.83 3.02
3117 4848 8.637099 TCAAATCCATATGTTTGTGTTTTGAGA 58.363 29.630 14.87 0.00 36.83 3.27
3118 4849 9.426837 CAAATCCATATGTTTGTGTTTTGAGAT 57.573 29.630 9.55 0.00 32.19 2.75
3119 4850 9.643693 AAATCCATATGTTTGTGTTTTGAGATC 57.356 29.630 1.24 0.00 0.00 2.75
3120 4851 8.585471 ATCCATATGTTTGTGTTTTGAGATCT 57.415 30.769 0.00 0.00 0.00 2.75
3121 4852 7.819644 TCCATATGTTTGTGTTTTGAGATCTG 58.180 34.615 0.00 0.00 0.00 2.90
3122 4853 7.448161 TCCATATGTTTGTGTTTTGAGATCTGT 59.552 33.333 0.00 0.00 0.00 3.41
3123 4854 8.729756 CCATATGTTTGTGTTTTGAGATCTGTA 58.270 33.333 0.00 0.00 0.00 2.74
3156 4887 7.609760 AGCATTATTTTCAATACGTGACAGA 57.390 32.000 0.00 0.00 35.39 3.41
3157 4888 7.464358 AGCATTATTTTCAATACGTGACAGAC 58.536 34.615 0.00 0.00 35.39 3.51
3158 4889 7.119116 AGCATTATTTTCAATACGTGACAGACA 59.881 33.333 0.00 0.00 35.39 3.41
3159 4890 7.910162 GCATTATTTTCAATACGTGACAGACAT 59.090 33.333 0.00 0.00 35.39 3.06
3160 4891 9.213819 CATTATTTTCAATACGTGACAGACATG 57.786 33.333 0.00 0.00 40.93 3.21
3161 4892 5.605564 TTTTCAATACGTGACAGACATGG 57.394 39.130 0.00 0.00 39.59 3.66
3162 4893 3.245518 TCAATACGTGACAGACATGGG 57.754 47.619 0.00 0.00 39.59 4.00
3163 4894 1.665679 CAATACGTGACAGACATGGGC 59.334 52.381 0.00 0.00 39.59 5.36
3164 4895 1.195115 ATACGTGACAGACATGGGCT 58.805 50.000 0.00 0.00 39.59 5.19
3165 4896 1.842052 TACGTGACAGACATGGGCTA 58.158 50.000 0.00 0.00 39.59 3.93
3166 4897 1.195115 ACGTGACAGACATGGGCTAT 58.805 50.000 0.00 0.00 39.59 2.97
3167 4898 2.384828 ACGTGACAGACATGGGCTATA 58.615 47.619 0.00 0.00 39.59 1.31
3168 4899 2.100916 ACGTGACAGACATGGGCTATAC 59.899 50.000 0.00 0.00 39.59 1.47
3169 4900 2.100749 CGTGACAGACATGGGCTATACA 59.899 50.000 0.00 0.00 32.38 2.29
3170 4901 3.722147 GTGACAGACATGGGCTATACAG 58.278 50.000 0.00 0.00 0.00 2.74
3188 4919 8.424274 CTATACAGCAGTGAATACAAATGTGA 57.576 34.615 0.00 0.00 0.00 3.58
3189 4920 7.686438 ATACAGCAGTGAATACAAATGTGAA 57.314 32.000 0.00 0.00 0.00 3.18
3190 4921 6.579666 ACAGCAGTGAATACAAATGTGAAT 57.420 33.333 0.00 0.00 0.00 2.57
3191 4922 7.686438 ACAGCAGTGAATACAAATGTGAATA 57.314 32.000 0.00 0.00 0.00 1.75
3192 4923 7.530010 ACAGCAGTGAATACAAATGTGAATAC 58.470 34.615 0.00 0.00 0.00 1.89
3193 4924 7.391554 ACAGCAGTGAATACAAATGTGAATACT 59.608 33.333 0.00 0.00 0.00 2.12
3194 4925 8.882736 CAGCAGTGAATACAAATGTGAATACTA 58.117 33.333 0.00 0.00 0.00 1.82
3195 4926 9.448438 AGCAGTGAATACAAATGTGAATACTAA 57.552 29.630 0.00 0.00 0.00 2.24
3196 4927 9.708222 GCAGTGAATACAAATGTGAATACTAAG 57.292 33.333 0.00 0.00 0.00 2.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 4.800914 GCTCTAAGAGAAGCAAACAGTGGA 60.801 45.833 0.00 0.00 0.00 4.02
236 277 9.269453 ACATCATCTGTTATACATCATCTGTTG 57.731 33.333 0.00 0.00 35.27 3.33
249 290 9.314321 CCGAACTAGTTTTACATCATCTGTTAT 57.686 33.333 10.02 0.00 39.39 1.89
250 291 7.277098 GCCGAACTAGTTTTACATCATCTGTTA 59.723 37.037 10.02 0.00 39.39 2.41
286 341 2.329690 CTCGTCTCGATCTGCCGG 59.670 66.667 0.00 0.00 34.61 6.13
291 346 3.943034 CGCCGCTCGTCTCGATCT 61.943 66.667 0.00 0.00 34.61 2.75
315 370 2.095252 GCCGTTCGTCCTCAAGCTC 61.095 63.158 0.00 0.00 0.00 4.09
434 1571 2.202676 CCGCTCGTCCTCAAGCTC 60.203 66.667 0.00 0.00 36.35 4.09
456 1593 2.768492 CCTCAAGCTTGGCCATCGC 61.768 63.158 25.73 17.30 0.00 4.58
522 1659 0.946221 CGCCCATCGCCTCTAATCAC 60.946 60.000 0.00 0.00 0.00 3.06
540 1677 2.510691 GCCACCGTATCCACACCG 60.511 66.667 0.00 0.00 0.00 4.94
643 2249 1.147190 AAAGTTTCCCCTCCCCTCCC 61.147 60.000 0.00 0.00 0.00 4.30
650 2261 1.709115 ACCACCCTAAAGTTTCCCCTC 59.291 52.381 0.00 0.00 0.00 4.30
658 2269 1.133294 CCAACCCAACCACCCTAAAGT 60.133 52.381 0.00 0.00 0.00 2.66
685 2296 0.109597 CCAGATGCAAAACGGTCAGC 60.110 55.000 0.00 0.00 0.00 4.26
689 2300 1.408969 AAACCCAGATGCAAAACGGT 58.591 45.000 0.00 0.00 0.00 4.83
709 2320 1.046472 TCTCCAACCGCCGGATATGT 61.046 55.000 11.71 0.00 0.00 2.29
713 2324 1.622607 TTCATCTCCAACCGCCGGAT 61.623 55.000 11.71 0.00 0.00 4.18
753 2364 7.611467 TCACCTGCTTCAAGTGATGTAAAATAT 59.389 33.333 0.00 0.00 35.67 1.28
764 2375 5.413833 AGAATTACATCACCTGCTTCAAGTG 59.586 40.000 0.00 0.00 0.00 3.16
770 2381 8.177119 TGTAAAAAGAATTACATCACCTGCTT 57.823 30.769 0.00 0.00 40.03 3.91
829 2440 8.459911 AATAATTAACTTTTACATCTCGGGGG 57.540 34.615 0.00 0.00 0.00 5.40
969 2582 2.239654 TGTGGTCTGATCCATTTCCCTC 59.760 50.000 3.00 0.00 39.81 4.30
1230 2846 3.774959 CTCGGCCGTGAAGATCCCG 62.775 68.421 27.15 0.00 40.25 5.14
1289 2932 1.595929 GAAACCGCGTTGAGGTGGA 60.596 57.895 4.92 0.00 41.95 4.02
1300 2943 1.446272 CCAGGAGACGAGAAACCGC 60.446 63.158 0.00 0.00 0.00 5.68
1503 3164 2.909965 GCCCCGTTGAACAAGGCA 60.910 61.111 17.73 0.00 43.32 4.75
1602 3263 1.525077 GTTCCCACCAGCAACGTCA 60.525 57.895 0.00 0.00 0.00 4.35
1725 3386 3.569277 CCATCATGTCACCAGAAACAACA 59.431 43.478 0.00 0.00 0.00 3.33
1726 3387 3.820467 TCCATCATGTCACCAGAAACAAC 59.180 43.478 0.00 0.00 0.00 3.32
1732 3393 2.094026 CGAACTCCATCATGTCACCAGA 60.094 50.000 0.00 0.00 0.00 3.86
2026 3733 2.790433 TCAAGTATTTGAGGTGTGGGC 58.210 47.619 0.00 0.00 38.37 5.36
2030 3737 3.181434 TGGCCTTCAAGTATTTGAGGTGT 60.181 43.478 3.32 0.00 43.76 4.16
2034 3741 3.350833 AGCTGGCCTTCAAGTATTTGAG 58.649 45.455 3.32 0.00 43.76 3.02
2035 3742 3.439857 AGCTGGCCTTCAAGTATTTGA 57.560 42.857 3.32 0.00 41.44 2.69
2137 3844 6.263617 TGTGAATTTTGTAGTGACTAAACCCC 59.736 38.462 0.00 0.00 33.95 4.95
2228 3935 6.318648 TGATGTGGGAAATGTAAGCAAGTATC 59.681 38.462 0.00 0.00 0.00 2.24
2412 4138 7.992033 TCCCTGTCAAAAATCAATGTCATTTTT 59.008 29.630 0.00 1.12 41.86 1.94
2413 4139 7.507829 TCCCTGTCAAAAATCAATGTCATTTT 58.492 30.769 0.00 0.00 35.40 1.82
2414 4140 7.065120 TCCCTGTCAAAAATCAATGTCATTT 57.935 32.000 0.00 0.00 0.00 2.32
2415 4141 6.669125 TCCCTGTCAAAAATCAATGTCATT 57.331 33.333 0.00 0.00 0.00 2.57
2416 4142 6.862469 ATCCCTGTCAAAAATCAATGTCAT 57.138 33.333 0.00 0.00 0.00 3.06
2457 4183 0.243095 AGAGGACAACGAGTAACCGC 59.757 55.000 0.00 0.00 0.00 5.68
2538 4264 2.280628 CCTGCAACCTAGGATTCGTTC 58.719 52.381 17.98 0.00 37.52 3.95
2539 4265 1.065418 CCCTGCAACCTAGGATTCGTT 60.065 52.381 17.98 0.00 37.52 3.85
2542 4268 0.466372 GGCCCTGCAACCTAGGATTC 60.466 60.000 17.98 0.00 37.52 2.52
2563 4292 7.329717 TGCGTTTTACAATCCCATAATTCAAAC 59.670 33.333 0.00 0.00 0.00 2.93
2569 4298 5.197451 TCCTGCGTTTTACAATCCCATAAT 58.803 37.500 0.00 0.00 0.00 1.28
2607 4337 6.335471 TGAATGTGCATGATATTCCAATCC 57.665 37.500 0.00 0.00 32.51 3.01
2617 4347 7.709182 CACAAATAGGATTTGAATGTGCATGAT 59.291 33.333 16.69 0.00 33.83 2.45
2818 4549 5.865085 AGTTGCAGACCTTAAAGATGTGTA 58.135 37.500 0.00 0.00 0.00 2.90
2822 4553 7.078228 GTGTTTAGTTGCAGACCTTAAAGATG 58.922 38.462 0.00 0.00 0.00 2.90
2823 4554 6.073222 CGTGTTTAGTTGCAGACCTTAAAGAT 60.073 38.462 0.00 0.00 0.00 2.40
2824 4555 5.235616 CGTGTTTAGTTGCAGACCTTAAAGA 59.764 40.000 0.00 0.00 0.00 2.52
2832 4563 2.221055 CACCTCGTGTTTAGTTGCAGAC 59.779 50.000 0.00 0.00 0.00 3.51
2847 4578 2.476619 CAGCTCACACTTTTACACCTCG 59.523 50.000 0.00 0.00 0.00 4.63
2853 4584 4.215399 TGGCATAACAGCTCACACTTTTAC 59.785 41.667 0.00 0.00 34.17 2.01
2861 4592 3.057315 ACAATGTTGGCATAACAGCTCAC 60.057 43.478 10.83 0.00 34.39 3.51
2962 4693 7.881142 TGGATTGACAACGAGAAATGTATTTT 58.119 30.769 0.00 0.00 0.00 1.82
2968 4699 5.611796 TCTTGGATTGACAACGAGAAATG 57.388 39.130 0.00 0.00 0.00 2.32
2976 4707 9.696917 AAATTCACTTTATCTTGGATTGACAAC 57.303 29.630 0.00 0.00 0.00 3.32
3003 4734 5.242434 TGTGTATTTCAGGCGAATAAGTGT 58.758 37.500 0.00 0.00 0.00 3.55
3004 4735 5.794687 TGTGTATTTCAGGCGAATAAGTG 57.205 39.130 0.00 0.00 0.00 3.16
3039 4770 5.668558 AAAATCCGCGTCCATAGAATTAC 57.331 39.130 4.92 0.00 0.00 1.89
3045 4776 1.333619 CCCAAAAATCCGCGTCCATAG 59.666 52.381 4.92 0.00 0.00 2.23
3049 4780 1.238625 TGTCCCAAAAATCCGCGTCC 61.239 55.000 4.92 0.00 0.00 4.79
3052 4783 0.179140 CCATGTCCCAAAAATCCGCG 60.179 55.000 0.00 0.00 0.00 6.46
3053 4784 0.894835 ACCATGTCCCAAAAATCCGC 59.105 50.000 0.00 0.00 0.00 5.54
3054 4785 2.094234 GGAACCATGTCCCAAAAATCCG 60.094 50.000 0.00 0.00 0.00 4.18
3055 4786 2.903135 TGGAACCATGTCCCAAAAATCC 59.097 45.455 0.15 0.00 36.80 3.01
3056 4787 4.677779 CGATGGAACCATGTCCCAAAAATC 60.678 45.833 11.27 0.00 36.80 2.17
3057 4788 3.195396 CGATGGAACCATGTCCCAAAAAT 59.805 43.478 11.27 0.00 36.80 1.82
3058 4789 2.560542 CGATGGAACCATGTCCCAAAAA 59.439 45.455 11.27 0.00 36.80 1.94
3059 4790 2.166829 CGATGGAACCATGTCCCAAAA 58.833 47.619 11.27 0.00 36.80 2.44
3060 4791 1.832883 CGATGGAACCATGTCCCAAA 58.167 50.000 11.27 0.00 36.80 3.28
3061 4792 0.679640 GCGATGGAACCATGTCCCAA 60.680 55.000 11.27 0.00 36.80 4.12
3062 4793 1.077787 GCGATGGAACCATGTCCCA 60.078 57.895 11.27 0.71 36.80 4.37
3063 4794 2.180204 CGCGATGGAACCATGTCCC 61.180 63.158 11.27 0.00 36.80 4.46
3064 4795 1.153449 TCGCGATGGAACCATGTCC 60.153 57.895 3.71 0.00 36.70 4.02
3065 4796 1.154205 CCTCGCGATGGAACCATGTC 61.154 60.000 10.36 0.00 36.70 3.06
3066 4797 1.153369 CCTCGCGATGGAACCATGT 60.153 57.895 10.36 0.00 36.70 3.21
3067 4798 0.877649 CTCCTCGCGATGGAACCATG 60.878 60.000 22.04 10.80 36.70 3.66
3068 4799 1.443407 CTCCTCGCGATGGAACCAT 59.557 57.895 22.04 6.00 39.69 3.55
3069 4800 2.892640 CTCCTCGCGATGGAACCA 59.107 61.111 22.04 0.00 32.61 3.67
3070 4801 2.586357 GCTCCTCGCGATGGAACC 60.586 66.667 22.04 14.75 32.61 3.62
3071 4802 0.032130 TATGCTCCTCGCGATGGAAC 59.968 55.000 22.04 19.12 43.27 3.62
3072 4803 0.969149 ATATGCTCCTCGCGATGGAA 59.031 50.000 22.04 12.71 43.27 3.53
3073 4804 0.528017 GATATGCTCCTCGCGATGGA 59.472 55.000 21.00 21.00 43.27 3.41
3074 4805 0.244721 TGATATGCTCCTCGCGATGG 59.755 55.000 10.36 13.83 43.27 3.51
3075 4806 2.070262 TTGATATGCTCCTCGCGATG 57.930 50.000 10.36 7.29 43.27 3.84
3076 4807 2.820059 TTTGATATGCTCCTCGCGAT 57.180 45.000 10.36 0.00 43.27 4.58
3077 4808 2.610479 GGATTTGATATGCTCCTCGCGA 60.610 50.000 9.26 9.26 43.27 5.87
3078 4809 1.728971 GGATTTGATATGCTCCTCGCG 59.271 52.381 0.00 0.00 43.27 5.87
3079 4810 2.771089 TGGATTTGATATGCTCCTCGC 58.229 47.619 0.00 0.00 39.77 5.03
3080 4811 6.111382 ACATATGGATTTGATATGCTCCTCG 58.889 40.000 7.80 0.00 37.31 4.63
3081 4812 7.934855 AACATATGGATTTGATATGCTCCTC 57.065 36.000 7.80 0.00 37.31 3.71
3082 4813 7.727186 ACAAACATATGGATTTGATATGCTCCT 59.273 33.333 19.97 0.00 37.31 3.69
3083 4814 7.811236 CACAAACATATGGATTTGATATGCTCC 59.189 37.037 19.97 0.00 37.31 4.70
3084 4815 8.355169 ACACAAACATATGGATTTGATATGCTC 58.645 33.333 19.97 0.00 37.31 4.26
3085 4816 8.241497 ACACAAACATATGGATTTGATATGCT 57.759 30.769 19.97 0.67 37.31 3.79
3086 4817 8.876275 AACACAAACATATGGATTTGATATGC 57.124 30.769 19.97 0.00 37.31 3.14
3090 4821 9.426837 CTCAAAACACAAACATATGGATTTGAT 57.573 29.630 19.97 9.00 38.82 2.57
3091 4822 8.637099 TCTCAAAACACAAACATATGGATTTGA 58.363 29.630 19.97 15.28 38.82 2.69
3092 4823 8.815141 TCTCAAAACACAAACATATGGATTTG 57.185 30.769 14.19 14.19 40.83 2.32
3093 4824 9.643693 GATCTCAAAACACAAACATATGGATTT 57.356 29.630 7.80 0.00 0.00 2.17
3094 4825 9.028284 AGATCTCAAAACACAAACATATGGATT 57.972 29.630 7.80 0.00 0.00 3.01
3095 4826 8.464404 CAGATCTCAAAACACAAACATATGGAT 58.536 33.333 7.80 0.00 0.00 3.41
3096 4827 7.448161 ACAGATCTCAAAACACAAACATATGGA 59.552 33.333 7.80 0.00 0.00 3.41
3097 4828 7.596494 ACAGATCTCAAAACACAAACATATGG 58.404 34.615 7.80 0.00 0.00 2.74
3130 4861 9.325198 TCTGTCACGTATTGAAAATAATGCTAT 57.675 29.630 0.00 0.00 35.39 2.97
3131 4862 8.600625 GTCTGTCACGTATTGAAAATAATGCTA 58.399 33.333 0.00 0.00 35.39 3.49
3132 4863 7.119116 TGTCTGTCACGTATTGAAAATAATGCT 59.881 33.333 0.00 0.00 35.39 3.79
3133 4864 7.240674 TGTCTGTCACGTATTGAAAATAATGC 58.759 34.615 0.00 0.00 35.39 3.56
3134 4865 9.213819 CATGTCTGTCACGTATTGAAAATAATG 57.786 33.333 0.00 0.00 35.39 1.90
3135 4866 8.397906 CCATGTCTGTCACGTATTGAAAATAAT 58.602 33.333 0.00 0.00 35.39 1.28
3136 4867 7.148323 CCCATGTCTGTCACGTATTGAAAATAA 60.148 37.037 0.00 0.00 35.39 1.40
3137 4868 6.315144 CCCATGTCTGTCACGTATTGAAAATA 59.685 38.462 0.00 0.00 35.39 1.40
3138 4869 5.123820 CCCATGTCTGTCACGTATTGAAAAT 59.876 40.000 0.00 0.00 35.39 1.82
3139 4870 4.454161 CCCATGTCTGTCACGTATTGAAAA 59.546 41.667 0.00 0.00 35.39 2.29
3140 4871 4.000325 CCCATGTCTGTCACGTATTGAAA 59.000 43.478 0.00 0.00 35.39 2.69
3141 4872 3.595173 CCCATGTCTGTCACGTATTGAA 58.405 45.455 0.00 0.00 35.39 2.69
3142 4873 2.676750 GCCCATGTCTGTCACGTATTGA 60.677 50.000 0.00 0.00 0.00 2.57
3143 4874 1.665679 GCCCATGTCTGTCACGTATTG 59.334 52.381 0.00 0.00 0.00 1.90
3144 4875 1.555075 AGCCCATGTCTGTCACGTATT 59.445 47.619 0.00 0.00 0.00 1.89
3145 4876 1.195115 AGCCCATGTCTGTCACGTAT 58.805 50.000 0.00 0.00 0.00 3.06
3146 4877 1.842052 TAGCCCATGTCTGTCACGTA 58.158 50.000 0.00 0.00 0.00 3.57
3147 4878 1.195115 ATAGCCCATGTCTGTCACGT 58.805 50.000 0.00 0.00 0.00 4.49
3148 4879 2.100749 TGTATAGCCCATGTCTGTCACG 59.899 50.000 0.00 0.00 0.00 4.35
3149 4880 3.722147 CTGTATAGCCCATGTCTGTCAC 58.278 50.000 0.00 0.00 0.00 3.67
3150 4881 2.103094 GCTGTATAGCCCATGTCTGTCA 59.897 50.000 0.00 0.00 44.33 3.58
3151 4882 2.760374 GCTGTATAGCCCATGTCTGTC 58.240 52.381 0.00 0.00 44.33 3.51
3152 4883 2.918712 GCTGTATAGCCCATGTCTGT 57.081 50.000 0.00 0.00 44.33 3.41
3163 4894 8.424274 TCACATTTGTATTCACTGCTGTATAG 57.576 34.615 0.00 0.00 0.00 1.31
3164 4895 8.785329 TTCACATTTGTATTCACTGCTGTATA 57.215 30.769 0.00 0.00 0.00 1.47
3165 4896 7.686438 TTCACATTTGTATTCACTGCTGTAT 57.314 32.000 0.00 0.00 0.00 2.29
3166 4897 7.686438 ATTCACATTTGTATTCACTGCTGTA 57.314 32.000 0.00 0.00 0.00 2.74
3167 4898 6.579666 ATTCACATTTGTATTCACTGCTGT 57.420 33.333 0.00 0.00 0.00 4.40
3168 4899 7.755591 AGTATTCACATTTGTATTCACTGCTG 58.244 34.615 0.00 0.00 0.00 4.41
3169 4900 7.928307 AGTATTCACATTTGTATTCACTGCT 57.072 32.000 0.00 0.00 0.00 4.24
3170 4901 9.708222 CTTAGTATTCACATTTGTATTCACTGC 57.292 33.333 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.