Multiple sequence alignment - TraesCS5D01G026500

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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 TraesCS5D01G026500 chr5D 100.000 2772 0 0 1 2772 24321485 24324256 0.000000e+00 5120
1 TraesCS5D01G026500 chr5D 89.205 176 15 4 2600 2771 444354092 444353917 1.670000e-52 217
2 TraesCS5D01G026500 chr5B 87.367 1971 118 57 723 2597 17816245 17814310 0.000000e+00 2139
3 TraesCS5D01G026500 chr5B 85.191 1256 123 37 703 1908 18104181 18102939 0.000000e+00 1230
4 TraesCS5D01G026500 chr5B 84.004 1069 87 42 746 1778 18132143 18131123 0.000000e+00 950
5 TraesCS5D01G026500 chr5B 84.360 633 61 20 11 639 569347156 569346558 1.110000e-163 586
6 TraesCS5D01G026500 chr5B 87.026 501 40 7 2041 2541 18077985 18077510 2.430000e-150 542
7 TraesCS5D01G026500 chr5B 92.420 343 25 1 1421 1763 17819187 17818846 3.210000e-134 488
8 TraesCS5D01G026500 chr5B 79.567 646 92 28 11 640 38135414 38134793 2.550000e-115 425
9 TraesCS5D01G026500 chr5B 77.697 686 71 41 1 639 47566537 47567187 7.350000e-91 344
10 TraesCS5D01G026500 chr5B 78.998 419 76 10 232 639 13739696 13739279 2.720000e-70 276
11 TraesCS5D01G026500 chr5B 81.172 239 22 14 1169 1389 17819419 17819186 1.320000e-38 171
12 TraesCS5D01G026500 chr5A 85.749 1221 56 47 788 1910 17528204 17529404 0.000000e+00 1182
13 TraesCS5D01G026500 chr5A 84.509 581 46 19 1955 2531 17562536 17563076 4.060000e-148 534
14 TraesCS5D01G026500 chr7D 87.023 524 38 15 134 640 541381657 541381147 5.180000e-157 564
15 TraesCS5D01G026500 chr7D 90.286 175 15 2 2600 2772 575401987 575402161 7.720000e-56 228
16 TraesCS5D01G026500 chr7D 90.588 170 12 4 2600 2766 63379828 63379996 3.590000e-54 222
17 TraesCS5D01G026500 chr2D 81.720 651 85 25 11 639 35346934 35346296 1.900000e-141 512
18 TraesCS5D01G026500 chr2D 81.538 650 87 26 11 637 35390165 35389526 3.190000e-139 505
19 TraesCS5D01G026500 chr2D 80.521 652 89 17 7 639 555661045 555661677 1.500000e-127 466
20 TraesCS5D01G026500 chr2D 87.912 182 20 2 2593 2772 588718052 588717871 2.160000e-51 213
21 TraesCS5D01G026500 chr3D 85.455 495 43 15 159 632 143968241 143967755 3.210000e-134 488
22 TraesCS5D01G026500 chr7B 80.030 661 70 33 11 641 1696811 1697439 1.520000e-117 433
23 TraesCS5D01G026500 chr6A 78.571 644 109 20 11 641 50410895 50410268 5.560000e-107 398
24 TraesCS5D01G026500 chr2B 78.804 552 87 21 101 640 739549210 739549743 7.350000e-91 344
25 TraesCS5D01G026500 chr2B 89.831 177 14 4 2600 2772 764842151 764841975 9.990000e-55 224
26 TraesCS5D01G026500 chr2B 88.701 177 16 4 2600 2772 764501540 764501716 2.160000e-51 213
27 TraesCS5D01G026500 chr1B 79.828 466 73 9 188 642 22910174 22909719 1.240000e-83 320
28 TraesCS5D01G026500 chr1B 84.774 243 24 6 1 241 76330014 76330245 5.970000e-57 231
29 TraesCS5D01G026500 chr1B 89.714 175 15 3 2600 2772 65888971 65889144 1.290000e-53 220
30 TraesCS5D01G026500 chr3B 80.292 411 73 6 245 648 799750952 799751361 1.250000e-78 303
31 TraesCS5D01G026500 chr1D 86.909 275 19 5 365 639 473403223 473403480 2.700000e-75 292
32 TraesCS5D01G026500 chr4D 86.312 263 36 0 251 513 361880122 361879860 1.260000e-73 287
33 TraesCS5D01G026500 chr4B 85.455 275 29 7 7 279 25056578 25056313 2.720000e-70 276
34 TraesCS5D01G026500 chr4B 88.412 233 20 4 1 231 592069527 592069754 9.780000e-70 274
35 TraesCS5D01G026500 chr4B 87.554 233 22 4 1 231 592177996 592178223 2.120000e-66 263
36 TraesCS5D01G026500 chrUn 77.474 475 76 13 184 639 38944823 38945285 3.540000e-64 255
37 TraesCS5D01G026500 chr2A 91.975 162 12 1 2612 2772 593508501 593508662 2.780000e-55 226
38 TraesCS5D01G026500 chr1A 87.845 181 18 4 2595 2771 150896267 150896087 2.800000e-50 209


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 TraesCS5D01G026500 chr5D 24321485 24324256 2771 False 5120.000000 5120 100.000000 1 2772 1 chr5D.!!$F1 2771
1 TraesCS5D01G026500 chr5B 18102939 18104181 1242 True 1230.000000 1230 85.191000 703 1908 1 chr5B.!!$R3 1205
2 TraesCS5D01G026500 chr5B 18131123 18132143 1020 True 950.000000 950 84.004000 746 1778 1 chr5B.!!$R4 1032
3 TraesCS5D01G026500 chr5B 17814310 17819419 5109 True 932.666667 2139 86.986333 723 2597 3 chr5B.!!$R7 1874
4 TraesCS5D01G026500 chr5B 569346558 569347156 598 True 586.000000 586 84.360000 11 639 1 chr5B.!!$R6 628
5 TraesCS5D01G026500 chr5B 38134793 38135414 621 True 425.000000 425 79.567000 11 640 1 chr5B.!!$R5 629
6 TraesCS5D01G026500 chr5B 47566537 47567187 650 False 344.000000 344 77.697000 1 639 1 chr5B.!!$F1 638
7 TraesCS5D01G026500 chr5A 17528204 17529404 1200 False 1182.000000 1182 85.749000 788 1910 1 chr5A.!!$F1 1122
8 TraesCS5D01G026500 chr5A 17562536 17563076 540 False 534.000000 534 84.509000 1955 2531 1 chr5A.!!$F2 576
9 TraesCS5D01G026500 chr7D 541381147 541381657 510 True 564.000000 564 87.023000 134 640 1 chr7D.!!$R1 506
10 TraesCS5D01G026500 chr2D 35346296 35346934 638 True 512.000000 512 81.720000 11 639 1 chr2D.!!$R1 628
11 TraesCS5D01G026500 chr2D 35389526 35390165 639 True 505.000000 505 81.538000 11 637 1 chr2D.!!$R2 626
12 TraesCS5D01G026500 chr2D 555661045 555661677 632 False 466.000000 466 80.521000 7 639 1 chr2D.!!$F1 632
13 TraesCS5D01G026500 chr7B 1696811 1697439 628 False 433.000000 433 80.030000 11 641 1 chr7B.!!$F1 630
14 TraesCS5D01G026500 chr6A 50410268 50410895 627 True 398.000000 398 78.571000 11 641 1 chr6A.!!$R1 630
15 TraesCS5D01G026500 chr2B 739549210 739549743 533 False 344.000000 344 78.804000 101 640 1 chr2B.!!$F1 539

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
782 3235 0.038618 TCGTCATTCCAGGTGTCGTG 60.039 55.0 0.0 0.0 31.71 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2016 4670 0.108585 ATTGTGTGGAGTTGGCGAGT 59.891 50.0 0.0 0.0 0.0 4.18 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
239 312 2.666526 GCATAGCTACGGCCAGGC 60.667 66.667 1.26 1.26 39.73 4.85
294 400 0.249073 GCAGATATGCCGACGACAGT 60.249 55.000 0.00 0.00 0.00 3.55
321 437 3.111853 CATATATGCTGGTCGGTGTGT 57.888 47.619 0.00 0.00 0.00 3.72
556 716 2.032681 GCCGACAGCCTGAACCTT 59.967 61.111 0.00 0.00 34.35 3.50
641 804 0.252197 GCCCTGTTCCGGTAGTGAAT 59.748 55.000 0.00 0.00 0.00 2.57
642 805 1.339727 GCCCTGTTCCGGTAGTGAATT 60.340 52.381 0.00 0.00 0.00 2.17
644 807 2.268298 CCTGTTCCGGTAGTGAATTCG 58.732 52.381 0.00 0.00 0.00 3.34
646 809 1.004595 GTTCCGGTAGTGAATTCGCC 58.995 55.000 15.29 6.72 0.00 5.54
647 810 0.899720 TTCCGGTAGTGAATTCGCCT 59.100 50.000 15.29 8.81 0.00 5.52
648 811 0.899720 TCCGGTAGTGAATTCGCCTT 59.100 50.000 15.29 0.72 0.00 4.35
649 812 1.134907 TCCGGTAGTGAATTCGCCTTC 60.135 52.381 15.29 6.31 0.00 3.46
651 814 2.550978 CGGTAGTGAATTCGCCTTCAT 58.449 47.619 15.29 0.00 37.47 2.57
654 817 4.662145 GGTAGTGAATTCGCCTTCATTTG 58.338 43.478 15.29 0.00 37.47 2.32
656 819 2.094545 AGTGAATTCGCCTTCATTTGGC 60.095 45.455 15.29 0.00 46.42 4.52
668 831 5.481105 CCTTCATTTGGCATGTTTGTATGT 58.519 37.500 0.00 0.00 0.00 2.29
669 832 5.577945 CCTTCATTTGGCATGTTTGTATGTC 59.422 40.000 0.00 0.00 33.36 3.06
671 834 6.343716 TCATTTGGCATGTTTGTATGTCTT 57.656 33.333 0.00 0.00 33.88 3.01
672 835 7.459795 TCATTTGGCATGTTTGTATGTCTTA 57.540 32.000 0.00 0.00 33.88 2.10
675 838 9.153721 CATTTGGCATGTTTGTATGTCTTAATT 57.846 29.630 0.00 0.00 33.88 1.40
677 840 9.853555 TTTGGCATGTTTGTATGTCTTAATTAG 57.146 29.630 0.00 0.00 33.88 1.73
678 841 8.574251 TGGCATGTTTGTATGTCTTAATTAGT 57.426 30.769 0.00 0.00 33.88 2.24
680 843 9.503427 GGCATGTTTGTATGTCTTAATTAGTTC 57.497 33.333 0.00 0.00 30.17 3.01
691 854 9.899226 ATGTCTTAATTAGTTCTTTTCAGTTGC 57.101 29.630 0.00 0.00 0.00 4.17
692 855 8.898761 TGTCTTAATTAGTTCTTTTCAGTTGCA 58.101 29.630 0.00 0.00 0.00 4.08
693 856 9.170584 GTCTTAATTAGTTCTTTTCAGTTGCAC 57.829 33.333 0.00 0.00 0.00 4.57
694 857 8.067784 TCTTAATTAGTTCTTTTCAGTTGCACG 58.932 33.333 0.00 0.00 0.00 5.34
695 858 4.545823 TTAGTTCTTTTCAGTTGCACGG 57.454 40.909 0.00 0.00 0.00 4.94
696 859 2.365582 AGTTCTTTTCAGTTGCACGGT 58.634 42.857 0.00 0.00 0.00 4.83
697 860 2.097466 AGTTCTTTTCAGTTGCACGGTG 59.903 45.455 3.15 3.15 0.00 4.94
698 861 1.745232 TCTTTTCAGTTGCACGGTGT 58.255 45.000 10.24 0.00 0.00 4.16
699 862 2.907634 TCTTTTCAGTTGCACGGTGTA 58.092 42.857 10.24 1.67 0.00 2.90
730 3182 4.690719 CGCCGGCCCACACTACAA 62.691 66.667 23.46 0.00 0.00 2.41
733 3185 1.072505 CCGGCCCACACTACAAACT 59.927 57.895 0.00 0.00 0.00 2.66
782 3235 0.038618 TCGTCATTCCAGGTGTCGTG 60.039 55.000 0.00 0.00 31.71 4.35
882 3342 1.957765 GCTCTACCACCTTCCCGTCC 61.958 65.000 0.00 0.00 0.00 4.79
885 3345 3.929723 TACCACCTTCCCGTCCCCC 62.930 68.421 0.00 0.00 0.00 5.40
888 3348 3.612607 ACCTTCCCGTCCCCCTCT 61.613 66.667 0.00 0.00 0.00 3.69
889 3349 2.764547 CCTTCCCGTCCCCCTCTC 60.765 72.222 0.00 0.00 0.00 3.20
890 3350 2.038975 CTTCCCGTCCCCCTCTCA 59.961 66.667 0.00 0.00 0.00 3.27
910 3370 2.943033 CAGTCGTCACCATTTATTCCCC 59.057 50.000 0.00 0.00 0.00 4.81
929 3401 4.323477 CGACGCAAGGGGGTTGGA 62.323 66.667 0.00 0.00 40.72 3.53
972 3448 3.399181 CAGCAGCCTTCCCCGGTA 61.399 66.667 0.00 0.00 0.00 4.02
981 3489 0.459759 CTTCCCCGGTAAACTCTCGC 60.460 60.000 0.00 0.00 0.00 5.03
1214 3734 3.124921 CGGCGGCCAGGTAACAAG 61.125 66.667 20.71 0.00 41.41 3.16
1224 3744 2.390670 GTAACAAGCGCGCGTCTC 59.609 61.111 32.35 15.19 0.00 3.36
1273 3804 1.228094 TCCATGAACTTGCACGGCA 60.228 52.632 0.00 0.00 36.47 5.69
1276 3807 0.311790 CATGAACTTGCACGGCAACT 59.688 50.000 7.15 0.00 43.99 3.16
1278 3809 0.814457 TGAACTTGCACGGCAACTTT 59.186 45.000 7.15 4.44 43.99 2.66
1283 3814 3.142951 ACTTGCACGGCAACTTTATGTA 58.857 40.909 7.15 0.00 43.99 2.29
1295 3830 2.222931 ACTTTATGTACGTACGCGCGTA 60.223 45.455 36.55 36.55 45.06 4.42
1545 4100 1.899437 GAGACCAACATGAGGCCCGA 61.899 60.000 0.00 0.00 0.00 5.14
1663 4218 3.286751 GTGGCCACAGCTGCGAAA 61.287 61.111 31.23 0.00 39.73 3.46
1784 4384 2.368221 CAGGCTTAGGCTAGCAGAAGAT 59.632 50.000 24.51 13.21 43.02 2.40
1795 4395 1.737735 CAGAAGATCGTGCGTGGCA 60.738 57.895 0.00 0.00 35.60 4.92
1806 4406 1.444836 TGCGTGGCACTGTAAATACC 58.555 50.000 16.72 0.00 31.71 2.73
1923 4551 9.511144 TTCAGTAGTATTATGTACATCGTTGTG 57.489 33.333 12.68 1.81 36.53 3.33
1927 4555 7.853377 AGTATTATGTACATCGTTGTGATCG 57.147 36.000 12.68 0.00 36.53 3.69
1933 4561 1.141019 ATCGTTGTGATCGGACCGG 59.859 57.895 15.25 0.00 28.49 5.28
1937 4565 2.997075 TTGTGATCGGACCGGGTCG 61.997 63.158 20.35 15.30 32.65 4.79
1976 4630 0.530744 TGATAGTCGCAACGAAGGCT 59.469 50.000 0.00 0.00 37.72 4.58
2016 4670 1.538876 CCACCTCCCTCCCTCACAA 60.539 63.158 0.00 0.00 0.00 3.33
2017 4671 1.679898 CACCTCCCTCCCTCACAAC 59.320 63.158 0.00 0.00 0.00 3.32
2018 4672 0.838122 CACCTCCCTCCCTCACAACT 60.838 60.000 0.00 0.00 0.00 3.16
2019 4673 0.545548 ACCTCCCTCCCTCACAACTC 60.546 60.000 0.00 0.00 0.00 3.01
2020 4674 1.608717 CCTCCCTCCCTCACAACTCG 61.609 65.000 0.00 0.00 0.00 4.18
2021 4675 2.232298 CTCCCTCCCTCACAACTCGC 62.232 65.000 0.00 0.00 0.00 5.03
2022 4676 2.266055 CCTCCCTCACAACTCGCC 59.734 66.667 0.00 0.00 0.00 5.54
2023 4677 2.583441 CCTCCCTCACAACTCGCCA 61.583 63.158 0.00 0.00 0.00 5.69
2024 4678 1.371183 CTCCCTCACAACTCGCCAA 59.629 57.895 0.00 0.00 0.00 4.52
2052 4707 3.074412 ACAATCCAACTTCGAAATCGCT 58.926 40.909 0.00 0.00 39.60 4.93
2053 4708 3.120199 ACAATCCAACTTCGAAATCGCTG 60.120 43.478 0.00 0.00 39.60 5.18
2101 4760 0.106167 CCAGTGAGGAGGGTCCGATA 60.106 60.000 0.00 0.00 42.75 2.92
2102 4761 1.481428 CCAGTGAGGAGGGTCCGATAT 60.481 57.143 0.00 0.00 42.75 1.63
2103 4762 1.889829 CAGTGAGGAGGGTCCGATATC 59.110 57.143 0.00 0.00 42.75 1.63
2104 4763 0.882474 GTGAGGAGGGTCCGATATCG 59.118 60.000 18.31 18.31 42.75 2.92
2105 4764 0.769247 TGAGGAGGGTCCGATATCGA 59.231 55.000 26.32 9.71 42.75 3.59
2106 4765 1.354705 TGAGGAGGGTCCGATATCGAT 59.645 52.381 26.32 2.16 42.75 3.59
2107 4766 1.746220 GAGGAGGGTCCGATATCGATG 59.254 57.143 26.32 10.71 42.75 3.84
2108 4767 0.818296 GGAGGGTCCGATATCGATGG 59.182 60.000 26.32 9.97 43.02 3.51
2109 4768 1.616187 GGAGGGTCCGATATCGATGGA 60.616 57.143 26.32 12.23 43.02 3.41
2110 4769 1.746220 GAGGGTCCGATATCGATGGAG 59.254 57.143 26.32 9.22 43.02 3.86
2111 4770 0.173708 GGGTCCGATATCGATGGAGC 59.826 60.000 26.32 21.44 46.83 4.70
2223 4882 1.633915 AAGCTCATCCTGGCCCTGAG 61.634 60.000 14.22 14.22 39.50 3.35
2299 4958 3.053291 GGCGCCATGTGGAACGAA 61.053 61.111 24.80 0.00 42.39 3.85
2337 4996 0.877743 GAGCAGTTCTTCACCAAGGC 59.122 55.000 0.00 0.00 0.00 4.35
2533 5197 1.950973 GCCGAGAGTGAAGACCCCTC 61.951 65.000 0.00 0.00 0.00 4.30
2538 5202 1.006043 AGAGTGAAGACCCCTCGATGA 59.994 52.381 0.00 0.00 0.00 2.92
2542 5206 2.939103 GTGAAGACCCCTCGATGAAATG 59.061 50.000 0.00 0.00 0.00 2.32
2552 5216 3.081061 CTCGATGAAATGGTTTGGGTGA 58.919 45.455 0.00 0.00 0.00 4.02
2594 5259 5.230936 CGAGAATGCAAGTAGACATGTAGTG 59.769 44.000 0.00 0.00 0.00 2.74
2595 5260 6.042638 AGAATGCAAGTAGACATGTAGTGT 57.957 37.500 0.00 0.00 45.83 3.55
2596 5261 7.170393 AGAATGCAAGTAGACATGTAGTGTA 57.830 36.000 0.00 0.00 42.36 2.90
2597 5262 7.786030 AGAATGCAAGTAGACATGTAGTGTAT 58.214 34.615 0.00 0.00 42.36 2.29
2598 5263 7.923344 AGAATGCAAGTAGACATGTAGTGTATC 59.077 37.037 0.00 0.00 42.36 2.24
2599 5264 5.902681 TGCAAGTAGACATGTAGTGTATCC 58.097 41.667 0.00 0.00 42.36 2.59
2600 5265 5.163447 TGCAAGTAGACATGTAGTGTATCCC 60.163 44.000 0.00 0.00 42.36 3.85
2601 5266 5.739358 GCAAGTAGACATGTAGTGTATCCCC 60.739 48.000 0.00 0.00 42.36 4.81
2602 5267 5.405063 AGTAGACATGTAGTGTATCCCCT 57.595 43.478 0.00 0.00 42.36 4.79
2603 5268 5.386924 AGTAGACATGTAGTGTATCCCCTC 58.613 45.833 0.00 0.00 42.36 4.30
2604 5269 3.577919 AGACATGTAGTGTATCCCCTCC 58.422 50.000 0.00 0.00 42.36 4.30
2605 5270 2.296471 GACATGTAGTGTATCCCCTCCG 59.704 54.545 0.00 0.00 42.36 4.63
2606 5271 2.317040 CATGTAGTGTATCCCCTCCGT 58.683 52.381 0.00 0.00 0.00 4.69
2607 5272 2.537633 TGTAGTGTATCCCCTCCGTT 57.462 50.000 0.00 0.00 0.00 4.44
2608 5273 2.823959 TGTAGTGTATCCCCTCCGTTT 58.176 47.619 0.00 0.00 0.00 3.60
2609 5274 3.175594 TGTAGTGTATCCCCTCCGTTTT 58.824 45.455 0.00 0.00 0.00 2.43
2610 5275 4.352009 TGTAGTGTATCCCCTCCGTTTTA 58.648 43.478 0.00 0.00 0.00 1.52
2611 5276 4.776837 TGTAGTGTATCCCCTCCGTTTTAA 59.223 41.667 0.00 0.00 0.00 1.52
2612 5277 4.914177 AGTGTATCCCCTCCGTTTTAAA 57.086 40.909 0.00 0.00 0.00 1.52
2613 5278 5.245584 AGTGTATCCCCTCCGTTTTAAAA 57.754 39.130 0.00 0.00 0.00 1.52
2614 5279 5.250982 AGTGTATCCCCTCCGTTTTAAAAG 58.749 41.667 0.00 0.00 0.00 2.27
2615 5280 5.013391 AGTGTATCCCCTCCGTTTTAAAAGA 59.987 40.000 0.00 0.00 0.00 2.52
2616 5281 5.353400 GTGTATCCCCTCCGTTTTAAAAGAG 59.647 44.000 0.00 5.64 0.00 2.85
2617 5282 4.652679 ATCCCCTCCGTTTTAAAAGAGT 57.347 40.909 13.29 0.00 0.00 3.24
2618 5283 3.746940 TCCCCTCCGTTTTAAAAGAGTG 58.253 45.455 13.29 5.14 0.00 3.51
2619 5284 3.136992 TCCCCTCCGTTTTAAAAGAGTGT 59.863 43.478 13.29 0.00 0.00 3.55
2620 5285 4.347583 TCCCCTCCGTTTTAAAAGAGTGTA 59.652 41.667 13.29 0.35 0.00 2.90
2621 5286 4.453478 CCCCTCCGTTTTAAAAGAGTGTAC 59.547 45.833 13.29 0.00 0.00 2.90
2622 5287 5.303165 CCCTCCGTTTTAAAAGAGTGTACT 58.697 41.667 13.29 0.00 0.00 2.73
2623 5288 5.761726 CCCTCCGTTTTAAAAGAGTGTACTT 59.238 40.000 13.29 0.00 0.00 2.24
2624 5289 6.261603 CCCTCCGTTTTAAAAGAGTGTACTTT 59.738 38.462 13.29 0.00 41.09 2.66
2625 5290 7.201758 CCCTCCGTTTTAAAAGAGTGTACTTTT 60.202 37.037 13.29 0.00 46.94 2.27
2626 5291 8.829612 CCTCCGTTTTAAAAGAGTGTACTTTTA 58.170 33.333 13.29 0.00 44.70 1.52
2656 5321 9.793259 TTATTGGAAAGTCAAACTCTCTTATGT 57.207 29.630 0.00 0.00 0.00 2.29
2657 5322 8.697507 ATTGGAAAGTCAAACTCTCTTATGTT 57.302 30.769 0.00 0.00 0.00 2.71
2658 5323 9.793259 ATTGGAAAGTCAAACTCTCTTATGTTA 57.207 29.630 0.00 0.00 0.00 2.41
2659 5324 8.833231 TGGAAAGTCAAACTCTCTTATGTTAG 57.167 34.615 0.00 0.00 0.00 2.34
2660 5325 8.647796 TGGAAAGTCAAACTCTCTTATGTTAGA 58.352 33.333 0.00 0.00 0.00 2.10
2661 5326 9.660180 GGAAAGTCAAACTCTCTTATGTTAGAT 57.340 33.333 0.00 0.00 0.00 1.98
2714 5379 9.791801 TTATGCCATCAAATTAGTAGCATTAGA 57.208 29.630 0.00 0.00 39.89 2.10
2715 5380 8.874744 ATGCCATCAAATTAGTAGCATTAGAT 57.125 30.769 0.00 0.00 36.10 1.98
2716 5381 8.696043 TGCCATCAAATTAGTAGCATTAGATT 57.304 30.769 0.00 0.00 0.00 2.40
2717 5382 8.786898 TGCCATCAAATTAGTAGCATTAGATTC 58.213 33.333 0.00 0.00 0.00 2.52
2718 5383 8.786898 GCCATCAAATTAGTAGCATTAGATTCA 58.213 33.333 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 7.821595 TTGAGTACGTTAATAATGTGACCTG 57.178 36.000 8.04 0.00 0.00 4.00
319 435 1.751544 ACGTCATCGATCCGGGACA 60.752 57.895 15.95 0.00 40.62 4.02
321 437 2.486663 CCACGTCATCGATCCGGGA 61.487 63.158 15.80 0.00 40.62 5.14
376 501 1.944676 GCGTCCGAACTATGCCGAG 60.945 63.158 0.00 0.00 0.00 4.63
422 548 2.674754 CATACTTGTGGGCCCGGT 59.325 61.111 19.37 15.36 0.00 5.28
545 705 1.302033 CGACAGCAAGGTTCAGGCT 60.302 57.895 0.00 0.00 38.70 4.58
646 809 6.392354 AGACATACAAACATGCCAAATGAAG 58.608 36.000 0.00 0.00 0.00 3.02
647 810 6.343716 AGACATACAAACATGCCAAATGAA 57.656 33.333 0.00 0.00 0.00 2.57
648 811 5.981088 AGACATACAAACATGCCAAATGA 57.019 34.783 0.00 0.00 0.00 2.57
649 812 8.706492 ATTAAGACATACAAACATGCCAAATG 57.294 30.769 0.00 0.00 0.00 2.32
651 814 9.853555 CTAATTAAGACATACAAACATGCCAAA 57.146 29.630 0.00 0.00 0.00 3.28
654 817 9.503427 GAACTAATTAAGACATACAAACATGCC 57.497 33.333 0.00 0.00 0.00 4.40
665 828 9.899226 GCAACTGAAAAGAACTAATTAAGACAT 57.101 29.630 0.00 0.00 0.00 3.06
666 829 8.898761 TGCAACTGAAAAGAACTAATTAAGACA 58.101 29.630 0.00 0.00 0.00 3.41
667 830 9.170584 GTGCAACTGAAAAGAACTAATTAAGAC 57.829 33.333 0.00 0.00 0.00 3.01
668 831 8.067784 CGTGCAACTGAAAAGAACTAATTAAGA 58.932 33.333 0.00 0.00 31.75 2.10
669 832 7.323656 CCGTGCAACTGAAAAGAACTAATTAAG 59.676 37.037 0.00 0.00 31.75 1.85
671 834 6.261381 ACCGTGCAACTGAAAAGAACTAATTA 59.739 34.615 0.00 0.00 31.75 1.40
672 835 5.067283 ACCGTGCAACTGAAAAGAACTAATT 59.933 36.000 0.00 0.00 31.75 1.40
675 838 3.311322 CACCGTGCAACTGAAAAGAACTA 59.689 43.478 0.00 0.00 31.75 2.24
676 839 2.097466 CACCGTGCAACTGAAAAGAACT 59.903 45.455 0.00 0.00 31.75 3.01
677 840 2.159435 ACACCGTGCAACTGAAAAGAAC 60.159 45.455 0.00 0.00 31.75 3.01
678 841 2.088423 ACACCGTGCAACTGAAAAGAA 58.912 42.857 0.00 0.00 31.75 2.52
680 843 3.684103 TTACACCGTGCAACTGAAAAG 57.316 42.857 0.00 0.00 31.75 2.27
682 845 4.436242 TTTTTACACCGTGCAACTGAAA 57.564 36.364 0.00 0.00 31.75 2.69
716 879 1.234615 CCAGTTTGTAGTGTGGGCCG 61.235 60.000 0.00 0.00 0.00 6.13
723 886 1.574428 GCGGCACCAGTTTGTAGTG 59.426 57.895 0.00 0.00 34.58 2.74
725 888 0.668096 TACGCGGCACCAGTTTGTAG 60.668 55.000 12.47 0.00 0.00 2.74
730 3182 4.289245 ACGTACGCGGCACCAGTT 62.289 61.111 16.72 0.00 43.45 3.16
759 3211 2.417379 CGACACCTGGAATGACGATCTT 60.417 50.000 0.00 0.00 37.41 2.40
764 3216 1.626654 GCACGACACCTGGAATGACG 61.627 60.000 0.00 4.08 40.33 4.35
765 3217 0.320771 AGCACGACACCTGGAATGAC 60.321 55.000 0.00 0.00 0.00 3.06
766 3218 0.320683 CAGCACGACACCTGGAATGA 60.321 55.000 0.00 0.00 0.00 2.57
782 3235 2.549754 TGCAAAGTAGAAAGACAGCAGC 59.450 45.455 0.00 0.00 0.00 5.25
882 3342 0.972983 ATGGTGACGACTGAGAGGGG 60.973 60.000 0.00 0.00 0.00 4.79
885 3345 4.806247 GGAATAAATGGTGACGACTGAGAG 59.194 45.833 0.00 0.00 0.00 3.20
886 3346 4.382685 GGGAATAAATGGTGACGACTGAGA 60.383 45.833 0.00 0.00 0.00 3.27
888 3348 3.370103 GGGGAATAAATGGTGACGACTGA 60.370 47.826 0.00 0.00 0.00 3.41
889 3349 2.943033 GGGGAATAAATGGTGACGACTG 59.057 50.000 0.00 0.00 0.00 3.51
890 3350 2.419574 CGGGGAATAAATGGTGACGACT 60.420 50.000 0.00 0.00 0.00 4.18
920 3385 1.051556 TTGGCAAGTTTCCAACCCCC 61.052 55.000 2.54 0.00 38.57 5.40
924 3396 2.608016 GCTAGCTTGGCAAGTTTCCAAC 60.608 50.000 26.71 9.58 38.57 3.77
925 3397 1.613437 GCTAGCTTGGCAAGTTTCCAA 59.387 47.619 26.71 6.80 40.98 3.53
926 3398 1.202927 AGCTAGCTTGGCAAGTTTCCA 60.203 47.619 26.71 6.96 0.00 3.53
927 3399 1.539157 AGCTAGCTTGGCAAGTTTCC 58.461 50.000 26.71 15.31 0.00 3.13
928 3400 2.096657 GCTAGCTAGCTTGGCAAGTTTC 59.903 50.000 33.71 16.19 45.62 2.78
929 3401 2.087646 GCTAGCTAGCTTGGCAAGTTT 58.912 47.619 33.71 17.93 45.62 2.66
996 3504 2.265739 GGCTGGTCGCTCATGACA 59.734 61.111 0.00 0.00 40.72 3.58
998 3506 3.785859 GGGGCTGGTCGCTCATGA 61.786 66.667 0.00 0.00 42.52 3.07
1214 3734 0.854037 CGAGATATAGAGACGCGCGC 60.854 60.000 32.58 23.91 0.00 6.86
1224 3744 4.579270 CATGCATGCACACGAGATATAG 57.421 45.455 25.37 0.00 0.00 1.31
1273 3804 1.578915 CGCGCGTACGTACATAAAGTT 59.421 47.619 24.19 0.00 42.83 2.66
1276 3807 2.443820 TACGCGCGTACGTACATAAA 57.556 45.000 36.55 14.78 46.19 1.40
1295 3830 2.703798 GCGCCATCACCTGCATGTT 61.704 57.895 0.00 0.00 0.00 2.71
1738 4311 2.775856 GCGCGTCATCCTCCTCTCA 61.776 63.158 8.43 0.00 0.00 3.27
1795 4395 5.143376 ACGCAGTACAAGGTATTTACAGT 57.857 39.130 0.00 0.00 41.94 3.55
1796 4396 6.327934 ACTACGCAGTACAAGGTATTTACAG 58.672 40.000 0.00 0.00 45.11 2.74
1797 4397 6.271488 ACTACGCAGTACAAGGTATTTACA 57.729 37.500 0.00 0.00 45.11 2.41
1798 4398 6.254373 GGAACTACGCAGTACAAGGTATTTAC 59.746 42.308 0.00 0.00 45.11 2.01
1799 4399 6.071447 TGGAACTACGCAGTACAAGGTATTTA 60.071 38.462 0.00 0.00 45.11 1.40
1800 4400 5.173664 GGAACTACGCAGTACAAGGTATTT 58.826 41.667 0.00 0.00 45.11 1.40
1864 4479 3.564235 ACGCTGTAGATTACAACACGA 57.436 42.857 10.79 0.00 38.38 4.35
1910 4538 2.416296 GGTCCGATCACAACGATGTACA 60.416 50.000 0.00 0.00 37.82 2.90
1937 4565 3.827898 CGGAGTCGGTGCCTCTCC 61.828 72.222 14.70 14.70 42.83 3.71
1976 4630 4.157289 GGAGGAGACGGCGATGTATATAAA 59.843 45.833 16.62 0.00 0.00 1.40
2016 4670 0.108585 ATTGTGTGGAGTTGGCGAGT 59.891 50.000 0.00 0.00 0.00 4.18
2017 4671 0.798776 GATTGTGTGGAGTTGGCGAG 59.201 55.000 0.00 0.00 0.00 5.03
2018 4672 0.605319 GGATTGTGTGGAGTTGGCGA 60.605 55.000 0.00 0.00 0.00 5.54
2019 4673 0.888736 TGGATTGTGTGGAGTTGGCG 60.889 55.000 0.00 0.00 0.00 5.69
2020 4674 1.000274 GTTGGATTGTGTGGAGTTGGC 60.000 52.381 0.00 0.00 0.00 4.52
2021 4675 2.586425 AGTTGGATTGTGTGGAGTTGG 58.414 47.619 0.00 0.00 0.00 3.77
2022 4676 3.303990 CGAAGTTGGATTGTGTGGAGTTG 60.304 47.826 0.00 0.00 0.00 3.16
2023 4677 2.878406 CGAAGTTGGATTGTGTGGAGTT 59.122 45.455 0.00 0.00 0.00 3.01
2024 4678 2.104111 TCGAAGTTGGATTGTGTGGAGT 59.896 45.455 0.00 0.00 0.00 3.85
2084 4743 1.545875 CGATATCGGACCCTCCTCACT 60.546 57.143 17.51 0.00 33.30 3.41
2101 4760 1.153086 GGCAACCTGCTCCATCGAT 60.153 57.895 0.00 0.00 44.28 3.59
2102 4761 2.268920 GGCAACCTGCTCCATCGA 59.731 61.111 0.00 0.00 44.28 3.59
2103 4762 3.197790 CGGCAACCTGCTCCATCG 61.198 66.667 0.00 0.00 44.28 3.84
2104 4763 2.825836 CCGGCAACCTGCTCCATC 60.826 66.667 0.00 0.00 44.28 3.51
2185 4844 3.664223 GACGTCCGACTCCGACAGC 62.664 68.421 3.51 0.00 38.22 4.40
2283 4942 0.523335 GAATTCGTTCCACATGGCGC 60.523 55.000 0.00 0.00 34.44 6.53
2337 4996 1.982395 TGCTCCACCTCCACGTAGG 60.982 63.158 2.68 2.68 42.82 3.18
2389 5048 1.604378 CCACATCTCCCTGACCCAC 59.396 63.158 0.00 0.00 0.00 4.61
2423 5082 1.448013 GGTACAGCTCGAACCTGCC 60.448 63.158 11.48 3.95 33.65 4.85
2427 5086 2.508663 GGCGGTACAGCTCGAACC 60.509 66.667 17.57 0.00 37.29 3.62
2517 5176 1.407258 CATCGAGGGGTCTTCACTCTC 59.593 57.143 0.00 0.00 0.00 3.20
2533 5197 3.429272 CCATCACCCAAACCATTTCATCG 60.429 47.826 0.00 0.00 0.00 3.84
2538 5202 3.258722 ACTCCATCACCCAAACCATTT 57.741 42.857 0.00 0.00 0.00 2.32
2542 5206 1.203001 TGGAACTCCATCACCCAAACC 60.203 52.381 0.00 0.00 42.01 3.27
2594 5259 5.353400 CACTCTTTTAAAACGGAGGGGATAC 59.647 44.000 17.00 0.00 0.00 2.24
2595 5260 5.013391 ACACTCTTTTAAAACGGAGGGGATA 59.987 40.000 18.53 0.00 33.93 2.59
2596 5261 4.202535 ACACTCTTTTAAAACGGAGGGGAT 60.203 41.667 18.53 2.16 33.93 3.85
2597 5262 3.136992 ACACTCTTTTAAAACGGAGGGGA 59.863 43.478 18.53 4.64 33.93 4.81
2598 5263 3.483421 ACACTCTTTTAAAACGGAGGGG 58.517 45.455 18.53 13.16 33.93 4.79
2599 5264 5.303165 AGTACACTCTTTTAAAACGGAGGG 58.697 41.667 14.69 14.69 35.57 4.30
2600 5265 6.856135 AAGTACACTCTTTTAAAACGGAGG 57.144 37.500 17.00 10.72 0.00 4.30
2630 5295 9.793259 ACATAAGAGAGTTTGACTTTCCAATAA 57.207 29.630 0.00 0.00 30.31 1.40
2631 5296 9.793259 AACATAAGAGAGTTTGACTTTCCAATA 57.207 29.630 0.00 0.00 30.31 1.90
2632 5297 8.697507 AACATAAGAGAGTTTGACTTTCCAAT 57.302 30.769 0.00 0.00 30.31 3.16
2633 5298 9.273016 CTAACATAAGAGAGTTTGACTTTCCAA 57.727 33.333 0.00 0.00 30.31 3.53
2634 5299 8.647796 TCTAACATAAGAGAGTTTGACTTTCCA 58.352 33.333 0.00 0.00 30.31 3.53
2635 5300 9.660180 ATCTAACATAAGAGAGTTTGACTTTCC 57.340 33.333 0.00 0.00 33.63 3.13
2688 5353 9.791801 TCTAATGCTACTAATTTGATGGCATAA 57.208 29.630 0.00 0.00 37.85 1.90
2689 5354 9.964354 ATCTAATGCTACTAATTTGATGGCATA 57.036 29.630 0.00 0.00 37.85 3.14
2690 5355 8.874744 ATCTAATGCTACTAATTTGATGGCAT 57.125 30.769 0.00 0.00 40.04 4.40
2691 5356 8.696043 AATCTAATGCTACTAATTTGATGGCA 57.304 30.769 0.00 0.00 32.33 4.92
2692 5357 8.786898 TGAATCTAATGCTACTAATTTGATGGC 58.213 33.333 0.00 0.00 32.33 4.40


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

AutoCloner maintained by Alex Coulton.