Multiple sequence alignment - TraesCS2A01G236900

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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 TraesCS2A01G236900 chr2A 100.000 5998 0 0 1 5998 306144909 306150906 0.000000e+00 11077.0
1 TraesCS2A01G236900 chr2A 93.548 155 9 1 788 941 177895710 177895864 4.680000e-56 230.0
2 TraesCS2A01G236900 chr2A 87.850 107 12 1 5562 5667 367582275 367582169 2.270000e-24 124.0
3 TraesCS2A01G236900 chr2A 100.000 35 0 0 4719 4753 306149564 306149598 1.400000e-06 65.8
4 TraesCS2A01G236900 chr2A 100.000 35 0 0 4656 4690 306149627 306149661 1.400000e-06 65.8
5 TraesCS2A01G236900 chr2B 97.628 3246 62 6 972 4210 272670534 272673771 0.000000e+00 5553.0
6 TraesCS2A01G236900 chr2B 91.278 1158 33 17 4393 5508 272673771 272674902 0.000000e+00 1517.0
7 TraesCS2A01G236900 chr2B 88.550 655 64 8 1 651 547852805 547853452 0.000000e+00 784.0
8 TraesCS2A01G236900 chr2B 95.156 289 10 4 5658 5943 272674903 272675190 2.550000e-123 453.0
9 TraesCS2A01G236900 chr2B 99.454 183 1 0 4210 4392 234534903 234534721 3.460000e-87 333.0
10 TraesCS2A01G236900 chr2B 99.454 183 1 0 4210 4392 449213081 449212899 3.460000e-87 333.0
11 TraesCS2A01G236900 chr2B 99.454 183 1 0 4210 4392 474915237 474915055 3.460000e-87 333.0
12 TraesCS2A01G236900 chr2B 93.548 155 10 0 788 942 710995283 710995437 1.300000e-56 231.0
13 TraesCS2A01G236900 chr2B 91.875 160 11 2 788 945 357161044 357161203 7.820000e-54 222.0
14 TraesCS2A01G236900 chr2D 98.282 3143 41 4 955 4085 215828487 215831628 0.000000e+00 5493.0
15 TraesCS2A01G236900 chr2D 96.481 1165 17 12 4390 5544 215831968 215833118 0.000000e+00 1903.0
16 TraesCS2A01G236900 chr2D 96.247 453 16 1 5547 5998 215833181 215833633 0.000000e+00 741.0
17 TraesCS2A01G236900 chr2D 98.421 190 3 0 4208 4397 215831625 215831814 9.630000e-88 335.0
18 TraesCS2A01G236900 chr2D 90.000 100 10 0 5562 5661 71386473 71386572 4.880000e-26 130.0
19 TraesCS2A01G236900 chr2D 88.462 104 11 1 5565 5667 291856769 291856666 2.270000e-24 124.0
20 TraesCS2A01G236900 chr2D 100.000 35 0 0 4719 4753 215832234 215832268 1.400000e-06 65.8
21 TraesCS2A01G236900 chr1A 94.656 786 38 3 1 786 27207852 27208633 0.000000e+00 1216.0
22 TraesCS2A01G236900 chr1A 99.454 183 1 0 4210 4392 278527445 278527627 3.460000e-87 333.0
23 TraesCS2A01G236900 chr5A 94.311 791 39 4 1 791 488034324 488033540 0.000000e+00 1206.0
24 TraesCS2A01G236900 chr5A 83.684 190 28 3 596 784 13418926 13419113 6.180000e-40 176.0
25 TraesCS2A01G236900 chr1B 87.900 562 49 11 1 550 453520362 453520916 1.410000e-180 643.0
26 TraesCS2A01G236900 chr3B 86.689 586 66 10 1 576 703903540 703904123 1.820000e-179 640.0
27 TraesCS2A01G236900 chr3B 99.454 183 1 0 4210 4392 101917974 101917792 3.460000e-87 333.0
28 TraesCS2A01G236900 chr3B 92.903 155 10 1 788 941 728289174 728289328 2.180000e-54 224.0
29 TraesCS2A01G236900 chr3B 83.684 190 28 3 596 784 769887219 769887406 6.180000e-40 176.0
30 TraesCS2A01G236900 chr3B 83.598 189 30 1 597 784 805490489 805490677 6.180000e-40 176.0
31 TraesCS2A01G236900 chr3B 90.909 99 9 0 5564 5662 801294361 801294263 3.770000e-27 134.0
32 TraesCS2A01G236900 chr7B 87.344 561 48 10 1 550 606586334 606586882 6.600000e-174 621.0
33 TraesCS2A01G236900 chr7B 93.038 158 10 1 788 944 723887655 723887812 4.680000e-56 230.0
34 TraesCS2A01G236900 chr4B 86.477 562 62 9 1 550 31818974 31819533 6.650000e-169 604.0
35 TraesCS2A01G236900 chr4B 83.598 189 30 1 602 789 617432821 617432633 6.180000e-40 176.0
36 TraesCS2A01G236900 chr6B 85.885 418 48 9 1 411 532156811 532157224 9.230000e-118 435.0
37 TraesCS2A01G236900 chr6B 88.889 54 6 0 222 275 532157172 532157225 3.880000e-07 67.6
38 TraesCS2A01G236900 chr6B 91.111 45 4 0 360 404 532161018 532161062 1.810000e-05 62.1
39 TraesCS2A01G236900 chr6B 100.000 28 0 0 5505 5532 561548122 561548095 1.100000e-02 52.8
40 TraesCS2A01G236900 chrUn 99.454 183 1 0 4210 4392 352978466 352978284 3.460000e-87 333.0
41 TraesCS2A01G236900 chrUn 93.548 155 9 1 788 941 13810286 13810440 4.680000e-56 230.0
42 TraesCS2A01G236900 chrUn 93.548 155 9 1 788 941 362507869 362508023 4.680000e-56 230.0
43 TraesCS2A01G236900 chr6D 99.454 183 1 0 4210 4392 168264464 168264282 3.460000e-87 333.0
44 TraesCS2A01G236900 chr6D 89.899 99 10 0 5562 5660 418957085 418956987 1.750000e-25 128.0
45 TraesCS2A01G236900 chr6D 89.796 49 4 1 5497 5544 144464721 144464769 1.810000e-05 62.1
46 TraesCS2A01G236900 chr5D 99.454 183 1 0 4210 4392 503225013 503224831 3.460000e-87 333.0
47 TraesCS2A01G236900 chr5D 88.571 105 12 0 5562 5666 40725591 40725695 1.750000e-25 128.0
48 TraesCS2A01G236900 chr5D 89.899 99 10 0 5562 5660 361884402 361884304 1.750000e-25 128.0
49 TraesCS2A01G236900 chr5B 87.023 262 24 8 298 550 45024565 45024305 2.740000e-73 287.0
50 TraesCS2A01G236900 chr5B 92.500 40 3 0 5505 5544 447270418 447270457 2.330000e-04 58.4
51 TraesCS2A01G236900 chr3A 93.038 158 10 1 788 944 645801341 645801498 4.680000e-56 230.0
52 TraesCS2A01G236900 chr3A 83.838 198 28 4 602 797 259837909 259837714 1.030000e-42 185.0
53 TraesCS2A01G236900 chr3A 82.741 197 30 4 602 796 451657784 451657590 7.990000e-39 172.0
54 TraesCS2A01G236900 chr7A 92.857 154 11 0 788 941 518143794 518143947 2.180000e-54 224.0
55 TraesCS2A01G236900 chr7A 100.000 31 0 0 5506 5536 726516599 726516569 2.330000e-04 58.4
56 TraesCS2A01G236900 chr7A 100.000 28 0 0 5505 5532 272187422 272187449 1.100000e-02 52.8
57 TraesCS2A01G236900 chr4A 82.902 193 33 0 597 789 176876462 176876270 2.220000e-39 174.0
58 TraesCS2A01G236900 chr4A 96.875 32 1 0 5501 5532 678183156 678183125 3.000000e-03 54.7
59 TraesCS2A01G236900 chr6A 89.109 101 11 0 5562 5662 34028610 34028510 6.310000e-25 126.0
60 TraesCS2A01G236900 chr3D 95.122 41 2 0 5504 5544 541634439 541634399 1.400000e-06 65.8
61 TraesCS2A01G236900 chr7D 94.595 37 2 0 214 250 322261940 322261904 2.330000e-04 58.4
62 TraesCS2A01G236900 chr1D 100.000 28 0 0 5506 5533 261380035 261380062 1.100000e-02 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 TraesCS2A01G236900 chr2A 306144909 306150906 5997 False 3736.200000 11077 100.000000 1 5998 3 chr2A.!!$F2 5997
1 TraesCS2A01G236900 chr2B 272670534 272675190 4656 False 2507.666667 5553 94.687333 972 5943 3 chr2B.!!$F4 4971
2 TraesCS2A01G236900 chr2B 547852805 547853452 647 False 784.000000 784 88.550000 1 651 1 chr2B.!!$F2 650
3 TraesCS2A01G236900 chr2D 215828487 215833633 5146 False 1707.560000 5493 97.886200 955 5998 5 chr2D.!!$F2 5043
4 TraesCS2A01G236900 chr1A 27207852 27208633 781 False 1216.000000 1216 94.656000 1 786 1 chr1A.!!$F1 785
5 TraesCS2A01G236900 chr5A 488033540 488034324 784 True 1206.000000 1206 94.311000 1 791 1 chr5A.!!$R1 790
6 TraesCS2A01G236900 chr1B 453520362 453520916 554 False 643.000000 643 87.900000 1 550 1 chr1B.!!$F1 549
7 TraesCS2A01G236900 chr3B 703903540 703904123 583 False 640.000000 640 86.689000 1 576 1 chr3B.!!$F1 575
8 TraesCS2A01G236900 chr7B 606586334 606586882 548 False 621.000000 621 87.344000 1 550 1 chr7B.!!$F1 549
9 TraesCS2A01G236900 chr4B 31818974 31819533 559 False 604.000000 604 86.477000 1 550 1 chr4B.!!$F1 549

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
935 948 0.110419 GCAACGCACGAGCATTTGTA 60.110 50.0 14.66 0.0 42.27 2.41 F
2455 2480 0.512952 CCACAAGCAGTTACTCGTGC 59.487 55.0 0.00 0.0 40.17 5.34 F
2673 2698 0.746659 GGCACTTGAAGCAGGTGTTT 59.253 50.0 10.65 0.0 42.26 2.83 F
3146 3171 1.136329 ATGTCCTTCCCCTGCAGTGT 61.136 55.0 13.81 0.0 0.00 3.55 F
4299 4324 0.661552 ACATGGATCCGTACGTCTCG 59.338 55.0 15.21 0.0 0.00 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2519 2544 1.817357 CCTATCACGCATGGCATCAT 58.183 50.000 0.00 0.0 0.00 2.45 R
3777 3802 1.066002 CATAGTTTTGATGCCTGCCCG 59.934 52.381 0.00 0.0 0.00 6.13 R
4144 4169 2.159114 GCAAAAGGGTTGCACTGAGAAA 60.159 45.455 6.19 0.0 44.34 2.52 R
4642 4831 2.514824 GCTCACCCCAATCTCGGC 60.515 66.667 0.00 0.0 0.00 5.54 R
5573 5862 0.031178 CCAACAAGACCAACTGCAGC 59.969 55.000 15.27 0.0 0.00 5.25 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
58 59 2.048503 GACGTTCCACCACTCGGG 60.049 66.667 0.00 0.00 44.81 5.14
61 62 1.070105 CGTTCCACCACTCGGGAAA 59.930 57.895 0.00 0.00 44.30 3.13
193 194 3.058160 GCACCCAGCGTTGCATCT 61.058 61.111 0.00 0.00 0.00 2.90
241 242 2.665000 CGCTGCTTGAGGGAGGAA 59.335 61.111 0.00 0.00 36.74 3.36
287 288 4.008933 GAGCCCGCTGTGTCCTGT 62.009 66.667 0.00 0.00 0.00 4.00
316 317 1.380515 CTGCCCGAGGAAGGAGAGA 60.381 63.158 0.00 0.00 0.00 3.10
325 326 1.380650 GAAGGAGAGAGACCCCGCT 60.381 63.158 0.00 0.00 0.00 5.52
589 602 2.285220 CGCGTAGGGATTTTGATGAGTG 59.715 50.000 0.00 0.00 46.37 3.51
719 732 5.128827 TCAAGAGGCTATAATTTCTCCGTGT 59.871 40.000 0.00 0.00 0.00 4.49
742 755 6.183360 TGTTGTTGTGTGTAGATTAGTCTGGA 60.183 38.462 0.00 0.00 35.87 3.86
881 894 8.890124 TTGGATATAAAAATGATGCACAATGG 57.110 30.769 0.00 0.00 0.00 3.16
882 895 6.930164 TGGATATAAAAATGATGCACAATGGC 59.070 34.615 0.00 0.00 0.00 4.40
900 913 4.019792 TGGCACATGAAGTAGATTGTGT 57.980 40.909 0.00 0.00 41.14 3.72
901 914 4.002982 TGGCACATGAAGTAGATTGTGTC 58.997 43.478 0.00 0.00 43.25 3.67
902 915 4.002982 GGCACATGAAGTAGATTGTGTCA 58.997 43.478 0.00 0.00 42.66 3.58
903 916 4.637534 GGCACATGAAGTAGATTGTGTCAT 59.362 41.667 0.00 0.00 42.66 3.06
904 917 5.124457 GGCACATGAAGTAGATTGTGTCATT 59.876 40.000 0.00 0.00 42.66 2.57
905 918 6.349611 GGCACATGAAGTAGATTGTGTCATTT 60.350 38.462 0.00 0.00 42.66 2.32
906 919 7.086376 GCACATGAAGTAGATTGTGTCATTTT 58.914 34.615 0.00 0.00 41.14 1.82
907 920 7.596248 GCACATGAAGTAGATTGTGTCATTTTT 59.404 33.333 0.00 0.00 41.14 1.94
931 944 3.737172 GGGCAACGCACGAGCATT 61.737 61.111 5.50 0.00 42.27 3.56
932 945 2.255252 GGCAACGCACGAGCATTT 59.745 55.556 5.50 0.00 42.27 2.32
933 946 2.082366 GGCAACGCACGAGCATTTG 61.082 57.895 5.50 8.55 42.27 2.32
934 947 1.370414 GCAACGCACGAGCATTTGT 60.370 52.632 14.66 0.00 42.27 2.83
935 948 0.110419 GCAACGCACGAGCATTTGTA 60.110 50.000 14.66 0.00 42.27 2.41
936 949 1.465689 GCAACGCACGAGCATTTGTAT 60.466 47.619 14.66 0.00 42.27 2.29
937 950 2.850321 CAACGCACGAGCATTTGTATT 58.150 42.857 5.50 0.00 42.27 1.89
938 951 3.726486 GCAACGCACGAGCATTTGTATTA 60.726 43.478 14.66 0.00 42.27 0.98
939 952 3.925688 ACGCACGAGCATTTGTATTAG 57.074 42.857 5.50 0.00 42.27 1.73
940 953 3.259064 ACGCACGAGCATTTGTATTAGT 58.741 40.909 5.50 0.00 42.27 2.24
941 954 4.426416 ACGCACGAGCATTTGTATTAGTA 58.574 39.130 5.50 0.00 42.27 1.82
942 955 5.047847 ACGCACGAGCATTTGTATTAGTAT 58.952 37.500 5.50 0.00 42.27 2.12
943 956 6.210796 ACGCACGAGCATTTGTATTAGTATA 58.789 36.000 5.50 0.00 42.27 1.47
944 957 6.698329 ACGCACGAGCATTTGTATTAGTATAA 59.302 34.615 5.50 0.00 42.27 0.98
945 958 7.001922 CGCACGAGCATTTGTATTAGTATAAC 58.998 38.462 5.50 0.00 42.27 1.89
946 959 7.001922 GCACGAGCATTTGTATTAGTATAACG 58.998 38.462 0.00 0.00 41.58 3.18
947 960 7.001922 CACGAGCATTTGTATTAGTATAACGC 58.998 38.462 0.00 0.00 0.00 4.84
948 961 6.129273 ACGAGCATTTGTATTAGTATAACGCG 60.129 38.462 3.53 3.53 0.00 6.01
949 962 6.462073 AGCATTTGTATTAGTATAACGCGG 57.538 37.500 12.47 0.00 0.00 6.46
950 963 5.077424 GCATTTGTATTAGTATAACGCGGC 58.923 41.667 12.47 0.00 0.00 6.53
951 964 5.107220 GCATTTGTATTAGTATAACGCGGCT 60.107 40.000 12.47 0.00 0.00 5.52
952 965 5.893512 TTTGTATTAGTATAACGCGGCTG 57.106 39.130 12.47 0.00 0.00 4.85
953 966 4.572985 TGTATTAGTATAACGCGGCTGT 57.427 40.909 12.47 0.00 0.00 4.40
956 969 2.212869 TAGTATAACGCGGCTGTTGG 57.787 50.000 12.47 0.00 33.32 3.77
962 975 2.434884 CGCGGCTGTTGGAGATGT 60.435 61.111 0.00 0.00 0.00 3.06
964 977 1.503542 GCGGCTGTTGGAGATGTTG 59.496 57.895 0.00 0.00 0.00 3.33
978 991 6.413892 TGGAGATGTTGTAAGCACATTCATA 58.586 36.000 0.00 0.00 33.06 2.15
980 993 6.238484 GGAGATGTTGTAAGCACATTCATACC 60.238 42.308 0.00 0.00 33.06 2.73
981 994 6.179756 AGATGTTGTAAGCACATTCATACCA 58.820 36.000 0.00 0.00 33.06 3.25
1087 1104 1.205893 CAACCTCTTCTTCCTCCTCCG 59.794 57.143 0.00 0.00 0.00 4.63
1095 1114 3.608759 TTCCTCCTCCGGCTGCTCT 62.609 63.158 0.00 0.00 0.00 4.09
1725 1750 4.424566 CACACCATTGCCGCTGCC 62.425 66.667 0.00 0.00 36.33 4.85
2151 2176 2.447379 ATGAGGGCTCGAGGGCAT 60.447 61.111 15.58 4.88 42.84 4.40
2300 2325 2.555732 ATGGCACCTGATGGGAATTT 57.444 45.000 0.00 0.00 38.76 1.82
2455 2480 0.512952 CCACAAGCAGTTACTCGTGC 59.487 55.000 0.00 0.00 40.17 5.34
2519 2544 2.570415 TGGGTATTTCAGGCGTTTGA 57.430 45.000 0.00 0.00 0.00 2.69
2673 2698 0.746659 GGCACTTGAAGCAGGTGTTT 59.253 50.000 10.65 0.00 42.26 2.83
2958 2983 2.800544 TCTGCTGTTCTTCAAGCGTTAC 59.199 45.455 0.00 0.00 0.00 2.50
3146 3171 1.136329 ATGTCCTTCCCCTGCAGTGT 61.136 55.000 13.81 0.00 0.00 3.55
3559 3584 6.317140 GCATCTGGATGAAATTCTACAGACAA 59.683 38.462 13.96 0.00 41.20 3.18
3777 3802 2.048603 GGACTGGTGGATGCTTGGC 61.049 63.158 0.00 0.00 0.00 4.52
4134 4159 2.952310 GGGCAACAAGTATCTCCAATCC 59.048 50.000 0.00 0.00 39.74 3.01
4144 4169 7.570607 ACAAGTATCTCCAATCCCTTATCTCTT 59.429 37.037 0.00 0.00 0.00 2.85
4163 4188 4.023291 TCTTTTCTCAGTGCAACCCTTTT 58.977 39.130 0.00 0.00 37.80 2.27
4171 4196 2.050442 CAACCCTTTTGCGCGTCC 60.050 61.111 8.43 0.00 0.00 4.79
4202 4227 2.612212 CCGTGGGCTGATGTGTAATTAC 59.388 50.000 8.75 8.75 0.00 1.89
4209 4234 4.700213 GGCTGATGTGTAATTACCAGTTGT 59.300 41.667 13.01 0.00 0.00 3.32
4294 4319 2.356695 TGTAGACACATGGATCCGTACG 59.643 50.000 8.69 8.69 0.00 3.67
4299 4324 0.661552 ACATGGATCCGTACGTCTCG 59.338 55.000 15.21 0.00 0.00 4.04
4560 4749 4.819769 AGAAGCTTTTCTTTGTTGTTGCA 58.180 34.783 0.00 0.00 34.56 4.08
4724 4913 9.798994 AATTTTGAGTCATTTTCATATGAGCTC 57.201 29.630 6.82 6.82 35.32 4.09
4726 4915 8.515695 TTTGAGTCATTTTCATATGAGCTCAT 57.484 30.769 30.85 30.85 39.51 2.90
4727 4916 7.725818 TGAGTCATTTTCATATGAGCTCATC 57.274 36.000 31.92 14.52 37.54 2.92
4729 4918 8.645110 TGAGTCATTTTCATATGAGCTCATCTA 58.355 33.333 31.92 16.89 37.54 1.98
4730 4919 9.486497 GAGTCATTTTCATATGAGCTCATCTAA 57.514 33.333 31.92 20.41 35.32 2.10
4734 4923 9.343103 CATTTTCATATGAGCTCATCTAATTGC 57.657 33.333 31.92 0.00 37.76 3.56
4735 4924 8.687292 TTTTCATATGAGCTCATCTAATTGCT 57.313 30.769 31.92 9.21 37.76 3.91
4738 4927 9.783081 TTCATATGAGCTCATCTAATTGCTTTA 57.217 29.630 31.92 11.00 37.76 1.85
4739 4928 9.212641 TCATATGAGCTCATCTAATTGCTTTAC 57.787 33.333 31.92 0.00 37.76 2.01
4740 4929 6.874288 ATGAGCTCATCTAATTGCTTTACC 57.126 37.500 23.75 0.00 35.76 2.85
4741 4930 4.811024 TGAGCTCATCTAATTGCTTTACCG 59.189 41.667 13.74 0.00 35.76 4.02
4742 4931 4.770795 AGCTCATCTAATTGCTTTACCGT 58.229 39.130 0.00 0.00 30.96 4.83
4743 4932 5.186198 AGCTCATCTAATTGCTTTACCGTT 58.814 37.500 0.00 0.00 30.96 4.44
4744 4933 5.065218 AGCTCATCTAATTGCTTTACCGTTG 59.935 40.000 0.00 0.00 30.96 4.10
4745 4934 5.064707 GCTCATCTAATTGCTTTACCGTTGA 59.935 40.000 0.00 0.00 0.00 3.18
4746 4935 6.417191 TCATCTAATTGCTTTACCGTTGAC 57.583 37.500 0.00 0.00 0.00 3.18
4747 4936 5.353123 TCATCTAATTGCTTTACCGTTGACC 59.647 40.000 0.00 0.00 0.00 4.02
4748 4937 4.901868 TCTAATTGCTTTACCGTTGACCT 58.098 39.130 0.00 0.00 0.00 3.85
4749 4938 6.040209 TCTAATTGCTTTACCGTTGACCTA 57.960 37.500 0.00 0.00 0.00 3.08
4752 4941 6.584185 AATTGCTTTACCGTTGACCTAATT 57.416 33.333 0.00 0.00 0.00 1.40
5022 5246 3.493873 GGTTCAGTCGGTTCCTTGTAGTT 60.494 47.826 0.00 0.00 0.00 2.24
5536 5765 0.250510 TTCACAATGTAGTGCGCCCA 60.251 50.000 4.18 0.00 39.35 5.36
5552 5841 1.369692 CCACGCTTCCTGTACCACA 59.630 57.895 0.00 0.00 0.00 4.17
5571 5860 5.473504 ACCACAGAATTCGTATTTTTGCTCT 59.526 36.000 0.00 0.00 0.00 4.09
5573 5862 5.729883 CACAGAATTCGTATTTTTGCTCTCG 59.270 40.000 0.00 0.00 0.00 4.04
5587 5876 0.320247 CTCTCGCTGCAGTTGGTCTT 60.320 55.000 16.64 0.00 0.00 3.01
5646 5935 1.732405 CGTGAGCGCTCTACATTGTGA 60.732 52.381 35.27 11.55 0.00 3.58
5655 5944 4.517285 GCTCTACATTGTGAAATGGAGGA 58.483 43.478 10.11 2.05 40.68 3.71
5665 5954 7.880160 TTGTGAAATGGAGGAAGTATTATGG 57.120 36.000 0.00 0.00 0.00 2.74
5699 5988 1.608055 CATTTCTGGTCACCACTGCA 58.392 50.000 0.00 0.00 0.00 4.41
5709 5998 0.610174 CACCACTGCAGGAAGCTCTA 59.390 55.000 19.93 0.00 45.94 2.43
5945 6235 5.982356 TGGACTGTGATCTCAAATTCTAGG 58.018 41.667 0.00 0.00 0.00 3.02
5952 6242 9.126151 CTGTGATCTCAAATTCTAGGTAGTAGA 57.874 37.037 0.00 0.00 35.84 2.59
5954 6244 8.573035 GTGATCTCAAATTCTAGGTAGTAGAGG 58.427 40.741 0.00 0.00 39.05 3.69
5965 6255 2.866762 GGTAGTAGAGGAAATTGCTGCG 59.133 50.000 0.00 0.00 0.00 5.18
5987 6277 6.871492 TGCGTTCAGTAATCTTGAAGACAATA 59.129 34.615 0.00 0.00 35.37 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 0.895559 CCAAGGACCAGGGCAGTTTC 60.896 60.000 0.00 0.00 0.00 2.78
61 62 3.971702 GCCAAGGACCAGGGCAGT 61.972 66.667 18.66 0.00 46.92 4.40
148 149 2.883828 CGGCTCTTGTGGGACAGGT 61.884 63.158 0.00 0.00 41.80 4.00
435 445 3.292460 CCTCCTCTCTTATCCTCGTTGT 58.708 50.000 0.00 0.00 0.00 3.32
437 447 2.514582 TCCCTCCTCTCTTATCCTCGTT 59.485 50.000 0.00 0.00 0.00 3.85
438 448 2.107552 CTCCCTCCTCTCTTATCCTCGT 59.892 54.545 0.00 0.00 0.00 4.18
480 490 1.224120 TCTAGGGAGGATCAAGCCCAT 59.776 52.381 16.32 2.81 44.55 4.00
481 491 0.642156 TCTAGGGAGGATCAAGCCCA 59.358 55.000 16.32 4.84 44.55 5.36
520 531 0.460311 CTGTCGTTCCTATCGCCCTT 59.540 55.000 0.00 0.00 0.00 3.95
589 602 3.127352 CTCTGCCGTCCCGAGTAGC 62.127 68.421 0.00 0.00 0.00 3.58
705 718 5.298276 ACACACAACAACACGGAGAAATTAT 59.702 36.000 0.00 0.00 0.00 1.28
719 732 6.413783 TCCAGACTAATCTACACACAACAA 57.586 37.500 0.00 0.00 32.25 2.83
742 755 6.238374 GCAAACATATTCACCGCTAACTACAT 60.238 38.462 0.00 0.00 0.00 2.29
855 868 9.496873 CCATTGTGCATCATTTTTATATCCAAT 57.503 29.630 0.00 0.00 0.00 3.16
856 869 7.441760 GCCATTGTGCATCATTTTTATATCCAA 59.558 33.333 0.00 0.00 0.00 3.53
857 870 6.930164 GCCATTGTGCATCATTTTTATATCCA 59.070 34.615 0.00 0.00 0.00 3.41
858 871 6.930164 TGCCATTGTGCATCATTTTTATATCC 59.070 34.615 0.00 0.00 36.04 2.59
859 872 7.438757 TGTGCCATTGTGCATCATTTTTATATC 59.561 33.333 0.00 0.00 44.30 1.63
860 873 7.273712 TGTGCCATTGTGCATCATTTTTATAT 58.726 30.769 0.00 0.00 44.30 0.86
861 874 6.637657 TGTGCCATTGTGCATCATTTTTATA 58.362 32.000 0.00 0.00 44.30 0.98
862 875 5.489249 TGTGCCATTGTGCATCATTTTTAT 58.511 33.333 0.00 0.00 44.30 1.40
863 876 4.891260 TGTGCCATTGTGCATCATTTTTA 58.109 34.783 0.00 0.00 44.30 1.52
864 877 3.741249 TGTGCCATTGTGCATCATTTTT 58.259 36.364 0.00 0.00 44.30 1.94
865 878 3.404224 TGTGCCATTGTGCATCATTTT 57.596 38.095 0.00 0.00 44.30 1.82
866 879 3.055747 TCATGTGCCATTGTGCATCATTT 60.056 39.130 0.00 0.00 44.30 2.32
867 880 2.498078 TCATGTGCCATTGTGCATCATT 59.502 40.909 0.00 0.00 44.30 2.57
868 881 2.104170 TCATGTGCCATTGTGCATCAT 58.896 42.857 0.00 6.35 44.30 2.45
869 882 1.546961 TCATGTGCCATTGTGCATCA 58.453 45.000 0.00 4.76 44.30 3.07
870 883 2.094390 ACTTCATGTGCCATTGTGCATC 60.094 45.455 0.00 0.00 44.30 3.91
871 884 1.897133 ACTTCATGTGCCATTGTGCAT 59.103 42.857 0.00 0.00 44.30 3.96
872 885 1.330234 ACTTCATGTGCCATTGTGCA 58.670 45.000 0.00 0.00 39.37 4.57
873 886 2.749076 TCTACTTCATGTGCCATTGTGC 59.251 45.455 0.00 0.00 0.00 4.57
874 887 5.106038 ACAATCTACTTCATGTGCCATTGTG 60.106 40.000 0.00 0.00 34.79 3.33
875 888 5.012239 ACAATCTACTTCATGTGCCATTGT 58.988 37.500 0.00 0.00 33.00 2.71
876 889 5.106038 ACACAATCTACTTCATGTGCCATTG 60.106 40.000 4.78 0.00 45.36 2.82
877 890 5.012239 ACACAATCTACTTCATGTGCCATT 58.988 37.500 4.78 0.00 45.36 3.16
878 891 4.592942 ACACAATCTACTTCATGTGCCAT 58.407 39.130 4.78 0.00 45.36 4.40
879 892 4.002982 GACACAATCTACTTCATGTGCCA 58.997 43.478 4.78 0.00 45.36 4.92
880 893 4.002982 TGACACAATCTACTTCATGTGCC 58.997 43.478 4.78 0.00 45.36 5.01
881 894 5.808042 ATGACACAATCTACTTCATGTGC 57.192 39.130 4.78 0.00 45.36 4.57
914 927 3.267597 AAATGCTCGTGCGTTGCCC 62.268 57.895 16.88 0.00 46.57 5.36
915 928 2.082366 CAAATGCTCGTGCGTTGCC 61.082 57.895 16.88 0.00 46.57 4.52
916 929 0.110419 TACAAATGCTCGTGCGTTGC 60.110 50.000 16.88 5.71 46.57 4.17
917 930 2.525750 ATACAAATGCTCGTGCGTTG 57.474 45.000 16.88 17.84 46.57 4.10
919 932 3.259064 ACTAATACAAATGCTCGTGCGT 58.741 40.909 4.84 0.99 43.34 5.24
920 933 3.925688 ACTAATACAAATGCTCGTGCG 57.074 42.857 4.84 0.00 43.34 5.34
921 934 7.001922 CGTTATACTAATACAAATGCTCGTGC 58.998 38.462 1.71 1.71 40.20 5.34
922 935 7.001922 GCGTTATACTAATACAAATGCTCGTG 58.998 38.462 0.00 0.00 0.00 4.35
923 936 6.129273 CGCGTTATACTAATACAAATGCTCGT 60.129 38.462 0.00 0.00 31.45 4.18
924 937 6.224293 CGCGTTATACTAATACAAATGCTCG 58.776 40.000 0.00 0.00 31.45 5.03
925 938 6.522761 CCGCGTTATACTAATACAAATGCTC 58.477 40.000 4.92 0.00 31.45 4.26
926 939 5.107220 GCCGCGTTATACTAATACAAATGCT 60.107 40.000 4.92 0.00 31.45 3.79
927 940 5.077424 GCCGCGTTATACTAATACAAATGC 58.923 41.667 4.92 0.00 0.00 3.56
928 941 6.073980 ACAGCCGCGTTATACTAATACAAATG 60.074 38.462 4.92 0.00 0.00 2.32
929 942 5.987347 ACAGCCGCGTTATACTAATACAAAT 59.013 36.000 4.92 0.00 0.00 2.32
930 943 5.350633 ACAGCCGCGTTATACTAATACAAA 58.649 37.500 4.92 0.00 0.00 2.83
931 944 4.935702 ACAGCCGCGTTATACTAATACAA 58.064 39.130 4.92 0.00 0.00 2.41
932 945 4.572985 ACAGCCGCGTTATACTAATACA 57.427 40.909 4.92 0.00 0.00 2.29
933 946 4.149396 CCAACAGCCGCGTTATACTAATAC 59.851 45.833 4.92 0.00 0.00 1.89
934 947 4.037803 TCCAACAGCCGCGTTATACTAATA 59.962 41.667 4.92 0.00 0.00 0.98
935 948 3.128349 CCAACAGCCGCGTTATACTAAT 58.872 45.455 4.92 0.00 0.00 1.73
936 949 2.166050 TCCAACAGCCGCGTTATACTAA 59.834 45.455 4.92 0.00 0.00 2.24
937 950 1.750206 TCCAACAGCCGCGTTATACTA 59.250 47.619 4.92 0.00 0.00 1.82
938 951 0.533491 TCCAACAGCCGCGTTATACT 59.467 50.000 4.92 0.00 0.00 2.12
939 952 0.928229 CTCCAACAGCCGCGTTATAC 59.072 55.000 4.92 0.00 0.00 1.47
940 953 0.818938 TCTCCAACAGCCGCGTTATA 59.181 50.000 4.92 0.00 0.00 0.98
941 954 0.178068 ATCTCCAACAGCCGCGTTAT 59.822 50.000 4.92 0.00 0.00 1.89
942 955 0.739462 CATCTCCAACAGCCGCGTTA 60.739 55.000 4.92 0.00 0.00 3.18
943 956 2.034879 CATCTCCAACAGCCGCGTT 61.035 57.895 4.92 0.00 0.00 4.84
944 957 2.434884 CATCTCCAACAGCCGCGT 60.435 61.111 4.92 0.00 0.00 6.01
945 958 2.034879 AACATCTCCAACAGCCGCG 61.035 57.895 0.00 0.00 0.00 6.46
946 959 1.237285 ACAACATCTCCAACAGCCGC 61.237 55.000 0.00 0.00 0.00 6.53
947 960 2.093306 TACAACATCTCCAACAGCCG 57.907 50.000 0.00 0.00 0.00 5.52
948 961 2.162408 GCTTACAACATCTCCAACAGCC 59.838 50.000 0.00 0.00 0.00 4.85
949 962 2.813754 TGCTTACAACATCTCCAACAGC 59.186 45.455 0.00 0.00 0.00 4.40
950 963 3.814842 TGTGCTTACAACATCTCCAACAG 59.185 43.478 0.00 0.00 0.00 3.16
951 964 3.814625 TGTGCTTACAACATCTCCAACA 58.185 40.909 0.00 0.00 0.00 3.33
952 965 5.048782 TGAATGTGCTTACAACATCTCCAAC 60.049 40.000 0.00 0.00 0.00 3.77
953 966 5.069318 TGAATGTGCTTACAACATCTCCAA 58.931 37.500 0.00 0.00 0.00 3.53
956 969 6.316140 TGGTATGAATGTGCTTACAACATCTC 59.684 38.462 0.00 0.00 0.00 2.75
962 975 6.072175 GGTCTTTGGTATGAATGTGCTTACAA 60.072 38.462 0.00 0.00 0.00 2.41
964 977 5.414454 TGGTCTTTGGTATGAATGTGCTTAC 59.586 40.000 0.00 0.00 0.00 2.34
978 991 0.107410 TGTGAGCGTTGGTCTTTGGT 60.107 50.000 0.00 0.00 0.00 3.67
980 993 0.042188 CGTGTGAGCGTTGGTCTTTG 60.042 55.000 0.00 0.00 0.00 2.77
981 994 0.179094 TCGTGTGAGCGTTGGTCTTT 60.179 50.000 0.00 0.00 0.00 2.52
1087 1104 1.931007 AATGAAGGGGGAGAGCAGCC 61.931 60.000 0.00 0.00 0.00 4.85
1095 1114 1.357761 GTTTGGAGGAATGAAGGGGGA 59.642 52.381 0.00 0.00 0.00 4.81
2300 2325 4.943705 CAGCCCAGAAGAAATTTACAGCTA 59.056 41.667 0.00 0.00 0.00 3.32
2519 2544 1.817357 CCTATCACGCATGGCATCAT 58.183 50.000 0.00 0.00 0.00 2.45
2673 2698 3.119316 TGCCAAAACTTTTCGAGCTTTCA 60.119 39.130 0.00 0.00 0.00 2.69
2921 2946 5.682659 ACAGCAGAATATCTTCTTGCTCAT 58.317 37.500 11.92 4.85 40.61 2.90
3146 3171 0.758734 CTCTGACACTGTCCCAACCA 59.241 55.000 6.72 0.00 0.00 3.67
3198 3223 2.994578 TGCATCAAATTTCACAATGGCG 59.005 40.909 0.00 0.00 0.00 5.69
3559 3584 3.782523 TGGTTTCCATTCTCAGGATAGCT 59.217 43.478 0.00 0.00 36.16 3.32
3777 3802 1.066002 CATAGTTTTGATGCCTGCCCG 59.934 52.381 0.00 0.00 0.00 6.13
3809 3834 2.890311 ACACAGAGGACAAGAGACTGAG 59.110 50.000 0.00 0.00 33.53 3.35
3811 3836 3.181471 ACAACACAGAGGACAAGAGACTG 60.181 47.826 0.00 0.00 35.14 3.51
4134 4159 5.123027 GGTTGCACTGAGAAAAGAGATAAGG 59.877 44.000 0.00 0.00 0.00 2.69
4144 4169 2.159114 GCAAAAGGGTTGCACTGAGAAA 60.159 45.455 6.19 0.00 44.34 2.52
4183 4208 3.616219 TGGTAATTACACATCAGCCCAC 58.384 45.455 17.16 0.00 0.00 4.61
4187 4212 5.880054 ACAACTGGTAATTACACATCAGC 57.120 39.130 17.16 0.00 0.00 4.26
4202 4227 2.636830 CCTCTGCCATTCTACAACTGG 58.363 52.381 0.00 0.00 0.00 4.00
4209 4234 4.744867 GCTCTATTTGCCTCTGCCATTCTA 60.745 45.833 0.00 0.00 36.33 2.10
4294 4319 5.975410 ATTGATTCTTTTCCGATCGAGAC 57.025 39.130 18.66 1.19 0.00 3.36
4299 4324 7.928706 TCTCCTTCTATTGATTCTTTTCCGATC 59.071 37.037 0.00 0.00 0.00 3.69
4376 4401 6.378710 AGACAGCATTGATCATGATTTCTG 57.621 37.500 10.14 13.78 37.02 3.02
4560 4749 4.826274 ATAGAATATGTGGCGGCTATGT 57.174 40.909 11.43 0.14 0.00 2.29
4642 4831 2.514824 GCTCACCCCAATCTCGGC 60.515 66.667 0.00 0.00 0.00 5.54
4719 4908 4.811557 ACGGTAAAGCAATTAGATGAGCTC 59.188 41.667 6.82 6.82 36.07 4.09
4724 4913 5.354234 AGGTCAACGGTAAAGCAATTAGATG 59.646 40.000 0.00 0.00 0.00 2.90
4726 4915 4.901868 AGGTCAACGGTAAAGCAATTAGA 58.098 39.130 0.00 0.00 0.00 2.10
4727 4916 6.730960 TTAGGTCAACGGTAAAGCAATTAG 57.269 37.500 0.00 0.00 0.00 1.73
4729 4918 6.584185 AATTAGGTCAACGGTAAAGCAATT 57.416 33.333 0.00 0.00 0.00 2.32
4730 4919 6.882678 AGTAATTAGGTCAACGGTAAAGCAAT 59.117 34.615 0.00 0.00 0.00 3.56
4733 4922 5.064325 CCAGTAATTAGGTCAACGGTAAAGC 59.936 44.000 0.00 0.00 0.00 3.51
4734 4923 6.168389 ACCAGTAATTAGGTCAACGGTAAAG 58.832 40.000 0.00 0.00 30.79 1.85
4735 4924 6.112927 ACCAGTAATTAGGTCAACGGTAAA 57.887 37.500 0.00 0.00 30.79 2.01
4738 4927 4.285260 AGAACCAGTAATTAGGTCAACGGT 59.715 41.667 0.00 0.00 37.07 4.83
4739 4928 4.630069 CAGAACCAGTAATTAGGTCAACGG 59.370 45.833 0.00 0.00 37.07 4.44
4740 4929 5.347907 GTCAGAACCAGTAATTAGGTCAACG 59.652 44.000 0.00 0.00 37.07 4.10
4741 4930 6.465084 AGTCAGAACCAGTAATTAGGTCAAC 58.535 40.000 0.00 0.00 37.07 3.18
4742 4931 6.681729 AGTCAGAACCAGTAATTAGGTCAA 57.318 37.500 0.00 0.00 37.07 3.18
4743 4932 6.681729 AAGTCAGAACCAGTAATTAGGTCA 57.318 37.500 0.00 0.00 37.07 4.02
4744 4933 8.312564 ACTTAAGTCAGAACCAGTAATTAGGTC 58.687 37.037 1.12 0.00 37.07 3.85
4745 4934 8.203681 ACTTAAGTCAGAACCAGTAATTAGGT 57.796 34.615 1.12 0.00 40.61 3.08
4746 4935 9.503399 AAACTTAAGTCAGAACCAGTAATTAGG 57.497 33.333 8.95 0.00 0.00 2.69
4854 5044 7.001674 TGACAGGAAGGTACAAATTAACACAT 58.998 34.615 0.00 0.00 0.00 3.21
5022 5246 8.902806 CCATACTTCAACATAGATTTGGCTAAA 58.097 33.333 0.00 0.00 0.00 1.85
5412 5641 7.558081 ACAGAACTTAGATACAGCATACAGAGA 59.442 37.037 0.00 0.00 0.00 3.10
5413 5642 7.711846 ACAGAACTTAGATACAGCATACAGAG 58.288 38.462 0.00 0.00 0.00 3.35
5414 5643 7.646548 ACAGAACTTAGATACAGCATACAGA 57.353 36.000 0.00 0.00 0.00 3.41
5467 5696 4.166725 AGCAGGGGACATAAATGATTCTGA 59.833 41.667 0.00 0.00 0.00 3.27
5518 5747 0.953471 GTGGGCGCACTACATTGTGA 60.953 55.000 25.28 0.00 40.12 3.58
5536 5765 1.045407 TTCTGTGGTACAGGAAGCGT 58.955 50.000 8.91 0.00 45.94 5.07
5544 5773 6.205853 AGCAAAAATACGAATTCTGTGGTACA 59.794 34.615 3.52 0.00 0.00 2.90
5571 5860 0.463654 AACAAGACCAACTGCAGCGA 60.464 50.000 15.27 0.00 0.00 4.93
5573 5862 0.031178 CCAACAAGACCAACTGCAGC 59.969 55.000 15.27 0.00 0.00 5.25
5646 5935 7.410174 TGACAACCATAATACTTCCTCCATTT 58.590 34.615 0.00 0.00 0.00 2.32
5655 5944 7.048512 GGCTAGTTCTGACAACCATAATACTT 58.951 38.462 0.00 0.00 0.00 2.24
5699 5988 4.464069 CTGTTTAGCAGTAGAGCTTCCT 57.536 45.455 0.00 0.00 43.70 3.36
5945 6235 3.522553 ACGCAGCAATTTCCTCTACTAC 58.477 45.455 0.00 0.00 0.00 2.73
5952 6242 1.609208 ACTGAACGCAGCAATTTCCT 58.391 45.000 0.00 0.00 46.26 3.36
5954 6244 4.974591 AGATTACTGAACGCAGCAATTTC 58.025 39.130 0.00 0.00 46.26 2.17


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

AutoCloner maintained by Alex Coulton.