Multiple sequence alignment - TraesCS3D01G501500

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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 TraesCS3D01G501500 chr3D 100.000 3511 0 0 1 3511 590332704 590329194 0.000000e+00 6484.0
1 TraesCS3D01G501500 chr3D 81.671 1424 216 34 1142 2530 590356977 590355564 0.000000e+00 1142.0
2 TraesCS3D01G501500 chr3D 81.004 279 21 11 2769 3017 615094492 615094768 3.580000e-45 193.0
3 TraesCS3D01G501500 chr3D 96.552 58 2 0 2714 2771 607320701 607320758 2.880000e-16 97.1
4 TraesCS3D01G501500 chr3B 93.262 1692 106 5 1097 2782 789324141 789322452 0.000000e+00 2486.0
5 TraesCS3D01G501500 chr3B 82.217 1389 210 23 1177 2542 789622711 789621337 0.000000e+00 1162.0
6 TraesCS3D01G501500 chr3B 79.315 1431 251 33 1104 2510 789333637 789335046 0.000000e+00 961.0
7 TraesCS3D01G501500 chr3B 88.710 620 35 8 2893 3511 789322362 789321777 0.000000e+00 725.0
8 TraesCS3D01G501500 chr3B 93.891 442 23 4 4 442 789327314 789326874 0.000000e+00 664.0
9 TraesCS3D01G501500 chr3B 84.749 518 18 21 455 936 789324770 789324278 2.470000e-126 462.0
10 TraesCS3D01G501500 chr3B 92.800 125 8 1 298 421 789630408 789630532 2.780000e-41 180.0
11 TraesCS3D01G501500 chr3B 91.406 128 8 3 2774 2899 789322513 789322387 4.660000e-39 172.0
12 TraesCS3D01G501500 chr3A 79.786 2147 307 70 458 2524 720417847 720415748 0.000000e+00 1443.0
13 TraesCS3D01G501500 chr3A 91.565 818 68 1 1827 2644 720252618 720251802 0.000000e+00 1127.0
14 TraesCS3D01G501500 chr3A 80.602 1428 244 26 1104 2510 720435639 720437054 0.000000e+00 1072.0
15 TraesCS3D01G501500 chr3A 78.726 1570 269 45 994 2524 720449581 720451124 0.000000e+00 989.0
16 TraesCS3D01G501500 chr3A 89.305 748 63 6 1083 1830 720367954 720367224 0.000000e+00 922.0
17 TraesCS3D01G501500 chr3A 78.758 1304 170 48 500 1739 720394801 720393541 0.000000e+00 774.0
18 TraesCS3D01G501500 chr3A 80.976 820 136 8 1734 2543 720393371 720392562 1.780000e-177 632.0
19 TraesCS3D01G501500 chr3A 82.365 499 66 13 3022 3511 720251702 720251217 7.010000e-112 414.0
20 TraesCS3D01G501500 chr3A 84.595 383 27 11 683 1047 720368325 720367957 5.580000e-93 351.0
21 TraesCS3D01G501500 chr3A 88.811 143 11 2 340 482 720449073 720449210 1.680000e-38 171.0
22 TraesCS3D01G501500 chr3A 86.726 113 13 1 343 453 720398593 720398481 1.320000e-24 124.0
23 TraesCS3D01G501500 chr3A 100.000 30 0 0 2624 2653 720251762 720251733 4.900000e-04 56.5
24 TraesCS3D01G501500 chrUn 79.301 1430 253 32 1104 2510 237856745 237858154 0.000000e+00 961.0
25 TraesCS3D01G501500 chrUn 79.301 1430 253 32 1104 2510 297376530 297375121 0.000000e+00 961.0
26 TraesCS3D01G501500 chrUn 79.315 1431 251 33 1104 2510 305637786 305636377 0.000000e+00 961.0
27 TraesCS3D01G501500 chr6D 86.590 261 21 10 2769 3017 32241714 32241972 3.450000e-70 276.0
28 TraesCS3D01G501500 chr6D 86.408 103 12 2 3 103 122992090 122992192 1.030000e-20 111.0
29 TraesCS3D01G501500 chr2D 85.185 270 18 10 2769 3018 471637979 471638246 1.250000e-64 257.0
30 TraesCS3D01G501500 chr2D 90.000 130 10 3 2889 3017 645315013 645315140 7.800000e-37 165.0
31 TraesCS3D01G501500 chr5D 83.395 271 22 14 2769 3018 481419803 481419535 2.730000e-56 230.0
32 TraesCS3D01G501500 chr5D 96.000 125 4 1 2893 3017 513026847 513026724 5.940000e-48 202.0
33 TraesCS3D01G501500 chr4A 82.374 278 15 14 2772 3017 602736313 602736038 9.870000e-51 211.0
34 TraesCS3D01G501500 chr4A 84.112 107 14 3 8 112 625404872 625404767 2.230000e-17 100.0
35 TraesCS3D01G501500 chr7D 86.802 197 15 6 284 476 526194063 526193874 3.550000e-50 209.0
36 TraesCS3D01G501500 chr7D 87.778 90 10 1 17 106 131468451 131468363 1.720000e-18 104.0
37 TraesCS3D01G501500 chr7D 94.737 38 2 0 284 321 629498431 629498394 3.780000e-05 60.2
38 TraesCS3D01G501500 chr7B 81.685 273 19 16 2774 3017 51765007 51765277 7.690000e-47 198.0
39 TraesCS3D01G501500 chr7B 92.366 131 8 2 2772 2901 600589929 600589800 5.980000e-43 185.0
40 TraesCS3D01G501500 chr7B 90.152 132 8 5 2889 3017 600589782 600589653 2.170000e-37 167.0
41 TraesCS3D01G501500 chr7B 89.552 134 9 5 2887 3017 335833471 335833602 7.800000e-37 165.0
42 TraesCS3D01G501500 chr7B 94.737 57 3 0 2715 2771 51764999 51765055 4.830000e-14 89.8
43 TraesCS3D01G501500 chr2B 84.500 200 20 6 281 476 129214863 129215055 1.660000e-43 187.0
44 TraesCS3D01G501500 chr2B 86.957 92 10 2 12 102 394722946 394723036 6.200000e-18 102.0
45 TraesCS3D01G501500 chr2A 91.667 132 9 2 2769 2899 771187744 771187874 7.740000e-42 182.0
46 TraesCS3D01G501500 chr2A 93.162 117 6 2 2774 2889 74779777 74779662 1.680000e-38 171.0
47 TraesCS3D01G501500 chr2A 76.699 309 40 19 2715 3017 74779785 74779503 3.650000e-30 143.0
48 TraesCS3D01G501500 chr2A 86.170 94 11 2 11 102 705588282 705588375 2.230000e-17 100.0
49 TraesCS3D01G501500 chr1A 92.248 129 8 2 2772 2899 453522528 453522401 7.740000e-42 182.0
50 TraesCS3D01G501500 chr1A 84.314 102 15 1 13 113 417400614 417400715 8.020000e-17 99.0
51 TraesCS3D01G501500 chr1A 83.810 105 15 2 11 113 425264020 425264124 8.020000e-17 99.0
52 TraesCS3D01G501500 chr5A 91.045 134 7 5 2887 3017 512621962 512622093 3.600000e-40 176.0
53 TraesCS3D01G501500 chr5A 91.304 69 4 1 2714 2780 519855765 519855697 3.730000e-15 93.5
54 TraesCS3D01G501500 chr4B 90.769 130 9 3 2889 3017 662612682 662612555 1.680000e-38 171.0
55 TraesCS3D01G501500 chr1D 94.366 71 2 1 2714 2782 463548545 463548615 1.330000e-19 108.0
56 TraesCS3D01G501500 chr6A 83.784 111 17 1 17 127 548408145 548408036 1.720000e-18 104.0
57 TraesCS3D01G501500 chr6A 91.549 71 4 1 2714 2782 564085729 564085799 2.880000e-16 97.1
58 TraesCS3D01G501500 chr4D 90.411 73 4 2 2712 2782 499845374 499845445 3.730000e-15 93.5


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 TraesCS3D01G501500 chr3D 590329194 590332704 3510 True 6484.0 6484 100.000000 1 3511 1 chr3D.!!$R1 3510
1 TraesCS3D01G501500 chr3D 590355564 590356977 1413 True 1142.0 1142 81.671000 1142 2530 1 chr3D.!!$R2 1388
2 TraesCS3D01G501500 chr3B 789621337 789622711 1374 True 1162.0 1162 82.217000 1177 2542 1 chr3B.!!$R1 1365
3 TraesCS3D01G501500 chr3B 789333637 789335046 1409 False 961.0 961 79.315000 1104 2510 1 chr3B.!!$F1 1406
4 TraesCS3D01G501500 chr3B 789321777 789327314 5537 True 901.8 2486 90.403600 4 3511 5 chr3B.!!$R2 3507
5 TraesCS3D01G501500 chr3A 720415748 720417847 2099 True 1443.0 1443 79.786000 458 2524 1 chr3A.!!$R1 2066
6 TraesCS3D01G501500 chr3A 720435639 720437054 1415 False 1072.0 1072 80.602000 1104 2510 1 chr3A.!!$F1 1406
7 TraesCS3D01G501500 chr3A 720367224 720368325 1101 True 636.5 922 86.950000 683 1830 2 chr3A.!!$R3 1147
8 TraesCS3D01G501500 chr3A 720449073 720451124 2051 False 580.0 989 83.768500 340 2524 2 chr3A.!!$F2 2184
9 TraesCS3D01G501500 chr3A 720251217 720252618 1401 True 532.5 1127 91.310000 1827 3511 3 chr3A.!!$R2 1684
10 TraesCS3D01G501500 chr3A 720392562 720398593 6031 True 510.0 774 82.153333 343 2543 3 chr3A.!!$R4 2200
11 TraesCS3D01G501500 chrUn 237856745 237858154 1409 False 961.0 961 79.301000 1104 2510 1 chrUn.!!$F1 1406
12 TraesCS3D01G501500 chrUn 297375121 297376530 1409 True 961.0 961 79.301000 1104 2510 1 chrUn.!!$R1 1406
13 TraesCS3D01G501500 chrUn 305636377 305637786 1409 True 961.0 961 79.315000 1104 2510 1 chrUn.!!$R2 1406

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
946 6728 0.246635 GTCCAGGAGCGCAAGAACTA 59.753 55.0 11.47 0.0 43.02 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2796 8934 0.671251 TCGGTGATTTTGGTTGGTGC 59.329 50.0 0.0 0.0 0.0 5.01 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
43 44 5.661458 ACCTTCAATCCACTATAAGTGTCG 58.339 41.667 6.33 0.00 44.50 4.35
51 52 7.596749 ATCCACTATAAGTGTCGAAGTTTTG 57.403 36.000 6.33 0.00 44.50 2.44
53 54 7.211573 TCCACTATAAGTGTCGAAGTTTTGAA 58.788 34.615 6.33 0.00 44.50 2.69
54 55 7.170320 TCCACTATAAGTGTCGAAGTTTTGAAC 59.830 37.037 6.33 0.00 44.50 3.18
62 63 4.505191 TGTCGAAGTTTTGAACTAAGACCG 59.495 41.667 17.74 8.44 42.40 4.79
66 67 5.557703 CGAAGTTTTGAACTAAGACCGGTTC 60.558 44.000 9.42 0.60 41.91 3.62
287 289 7.657336 ACACTTTTCACGGACAAAAATATGAT 58.343 30.769 0.00 0.00 0.00 2.45
301 303 5.464030 AAATATGATGCCCTCTCATTTGC 57.536 39.130 0.00 0.00 35.12 3.68
338 341 6.173044 GCAAGTTAAGTTAAAAACACAACGC 58.827 36.000 0.00 0.00 34.48 4.84
453 456 3.327757 GGTAGCAAGATGGACCATGGATA 59.672 47.826 21.47 4.11 31.89 2.59
490 2585 0.390492 GCAGGAAAAGCAGCCAAGTT 59.610 50.000 0.00 0.00 0.00 2.66
603 6323 2.698274 ACGCCAAACCATTCTTCCTTTT 59.302 40.909 0.00 0.00 0.00 2.27
722 6470 4.036852 TGACTCGAGCTGATATGTCGATTT 59.963 41.667 13.61 0.00 41.59 2.17
749 6500 8.667987 TTTTCGCAAAGTGTGTCAATTATATC 57.332 30.769 0.00 0.00 0.00 1.63
750 6501 6.976636 TCGCAAAGTGTGTCAATTATATCA 57.023 33.333 0.00 0.00 0.00 2.15
751 6502 7.003939 TCGCAAAGTGTGTCAATTATATCAG 57.996 36.000 0.00 0.00 0.00 2.90
752 6503 5.678483 CGCAAAGTGTGTCAATTATATCAGC 59.322 40.000 0.00 0.00 0.00 4.26
839 6601 7.042335 CCTCAACGAAATGTAAAGTAGGAGAT 58.958 38.462 0.00 0.00 0.00 2.75
867 6639 4.504864 GGTTACATATACAGATGCCAGCCA 60.505 45.833 0.00 0.00 0.00 4.75
923 6699 1.722034 TGAGAGGGCAACAGAACTCT 58.278 50.000 0.00 0.00 42.60 3.24
924 6700 2.378445 GAGAGGGCAACAGAACTCTC 57.622 55.000 4.97 4.97 46.15 3.20
925 6701 1.722034 AGAGGGCAACAGAACTCTCA 58.278 50.000 0.00 0.00 35.51 3.27
926 6702 2.050144 AGAGGGCAACAGAACTCTCAA 58.950 47.619 0.00 0.00 35.51 3.02
927 6703 2.038295 AGAGGGCAACAGAACTCTCAAG 59.962 50.000 0.00 0.00 35.51 3.02
928 6704 1.771255 AGGGCAACAGAACTCTCAAGT 59.229 47.619 0.00 0.00 35.82 3.16
929 6705 2.147150 GGGCAACAGAACTCTCAAGTC 58.853 52.381 0.00 0.00 33.45 3.01
941 6720 1.004560 TCAAGTCCAGGAGCGCAAG 60.005 57.895 11.47 0.00 43.44 4.01
946 6728 0.246635 GTCCAGGAGCGCAAGAACTA 59.753 55.000 11.47 0.00 43.02 2.24
961 6743 3.558033 AGAACTACTACTCTGCTAGGCC 58.442 50.000 0.00 0.00 0.00 5.19
963 6745 1.489649 ACTACTACTCTGCTAGGCCGA 59.510 52.381 0.00 0.00 0.00 5.54
973 6755 2.427453 CTGCTAGGCCGAAGAGAGTAAA 59.573 50.000 11.92 0.00 0.00 2.01
1047 6844 4.700213 ACTTATCCTCCCGTTTGTTCAATG 59.300 41.667 0.00 0.00 0.00 2.82
1048 6845 2.649531 TCCTCCCGTTTGTTCAATGT 57.350 45.000 0.00 0.00 0.00 2.71
1052 6849 4.048504 CCTCCCGTTTGTTCAATGTTTTC 58.951 43.478 0.00 0.00 0.00 2.29
1054 6851 5.269505 TCCCGTTTGTTCAATGTTTTCAT 57.730 34.783 0.00 0.00 43.05 2.57
1055 6852 5.046529 TCCCGTTTGTTCAATGTTTTCATG 58.953 37.500 0.00 0.00 40.79 3.07
1056 6853 4.808364 CCCGTTTGTTCAATGTTTTCATGT 59.192 37.500 0.00 0.00 40.79 3.21
1058 6855 6.074569 CCCGTTTGTTCAATGTTTTCATGTAC 60.075 38.462 0.00 0.00 40.79 2.90
1078 6887 1.852895 CGTGCTAACTAATCACGCTCC 59.147 52.381 1.09 0.00 45.22 4.70
1128 6983 1.450531 CCAATCCAGCGATTCTGCCC 61.451 60.000 0.00 0.00 41.50 5.36
1160 7015 0.688749 TAGAGATGGCTCAGCTGGCA 60.689 55.000 23.05 14.67 43.81 4.92
1196 7051 0.526662 AACTAGACGCCCTCAACTCG 59.473 55.000 0.00 0.00 0.00 4.18
1392 7250 1.905922 GCTGACGAGTCTTGGCAAGC 61.906 60.000 22.31 16.48 0.00 4.01
1423 7281 1.900351 CAAGAGCCATGAGACCCGA 59.100 57.895 0.00 0.00 0.00 5.14
1463 7327 0.610174 TCAACGAGCTCAGATGCCTT 59.390 50.000 15.40 0.00 0.00 4.35
1472 7336 3.054582 AGCTCAGATGCCTTGAAGAATCA 60.055 43.478 9.48 0.00 0.00 2.57
1709 7592 4.607239 ACCAGATACCTTTCTTCGTCCTA 58.393 43.478 0.00 0.00 0.00 2.94
1761 7819 6.540914 GGATGGTAAGGATCGTGTGATTAAAA 59.459 38.462 0.00 0.00 34.09 1.52
1880 7938 7.075851 TCTTCTCCATCTTCTTCATATGCAT 57.924 36.000 3.79 3.79 0.00 3.96
2006 8079 1.076777 CAAGGGTCGGGCCATGAAT 60.077 57.895 4.39 0.00 39.65 2.57
2023 8099 1.099879 AATGAGAAGGGCATGCGCTC 61.100 55.000 34.14 25.72 39.82 5.03
2048 8124 2.097629 CCTCGACGTGAAGCTGAATAGA 59.902 50.000 0.00 0.00 0.00 1.98
2051 8127 2.097629 CGACGTGAAGCTGAATAGAGGA 59.902 50.000 0.00 0.00 0.00 3.71
2055 8131 2.169352 GTGAAGCTGAATAGAGGAGGCA 59.831 50.000 0.00 0.00 0.00 4.75
2470 8546 2.103042 CAGCTGTCGTTGGGCTAGC 61.103 63.158 6.04 6.04 34.71 3.42
2526 8605 6.544928 TGAGTTAGAAGCATGGATGAAGTA 57.455 37.500 0.00 0.00 0.00 2.24
2667 8805 4.286297 TCTTGTTGGGATTGTCTACTGG 57.714 45.455 0.00 0.00 0.00 4.00
2676 8814 3.370953 GGATTGTCTACTGGCCAGTCAAT 60.371 47.826 41.00 37.03 42.54 2.57
2707 8845 6.209986 TCTCACTTTGGGTTAGTCGAATTCTA 59.790 38.462 3.52 0.00 0.00 2.10
2721 8859 7.762382 AGTCGAATTCTAATCCAATGGTTTTC 58.238 34.615 3.52 0.00 0.00 2.29
2734 8872 9.844257 ATCCAATGGTTTTCAATTTCAGTTTTA 57.156 25.926 0.00 0.00 0.00 1.52
2750 8888 8.419076 TTCAGTTTTAGAAAAATTTCAGCACC 57.581 30.769 8.47 0.00 39.61 5.01
2751 8889 7.551585 TCAGTTTTAGAAAAATTTCAGCACCA 58.448 30.769 8.47 0.00 39.61 4.17
2752 8890 8.037758 TCAGTTTTAGAAAAATTTCAGCACCAA 58.962 29.630 8.47 0.00 39.61 3.67
2753 8891 8.116136 CAGTTTTAGAAAAATTTCAGCACCAAC 58.884 33.333 8.47 3.20 39.61 3.77
2754 8892 7.279981 AGTTTTAGAAAAATTTCAGCACCAACC 59.720 33.333 8.47 0.00 39.61 3.77
2755 8893 4.751767 AGAAAAATTTCAGCACCAACCA 57.248 36.364 8.47 0.00 39.61 3.67
2756 8894 5.096443 AGAAAAATTTCAGCACCAACCAA 57.904 34.783 8.47 0.00 39.61 3.67
2757 8895 5.495640 AGAAAAATTTCAGCACCAACCAAA 58.504 33.333 8.47 0.00 39.61 3.28
2758 8896 5.942826 AGAAAAATTTCAGCACCAACCAAAA 59.057 32.000 8.47 0.00 39.61 2.44
2759 8897 6.602803 AGAAAAATTTCAGCACCAACCAAAAT 59.397 30.769 8.47 0.00 39.61 1.82
2760 8898 6.375945 AAAATTTCAGCACCAACCAAAATC 57.624 33.333 0.00 0.00 0.00 2.17
2761 8899 4.686191 ATTTCAGCACCAACCAAAATCA 57.314 36.364 0.00 0.00 0.00 2.57
2762 8900 3.451141 TTCAGCACCAACCAAAATCAC 57.549 42.857 0.00 0.00 0.00 3.06
2763 8901 1.686052 TCAGCACCAACCAAAATCACC 59.314 47.619 0.00 0.00 0.00 4.02
2764 8902 0.673437 AGCACCAACCAAAATCACCG 59.327 50.000 0.00 0.00 0.00 4.94
2765 8903 0.671251 GCACCAACCAAAATCACCGA 59.329 50.000 0.00 0.00 0.00 4.69
2766 8904 1.067821 GCACCAACCAAAATCACCGAA 59.932 47.619 0.00 0.00 0.00 4.30
2767 8905 2.482142 GCACCAACCAAAATCACCGAAA 60.482 45.455 0.00 0.00 0.00 3.46
2768 8906 3.801983 GCACCAACCAAAATCACCGAAAT 60.802 43.478 0.00 0.00 0.00 2.17
2769 8907 4.376146 CACCAACCAAAATCACCGAAATT 58.624 39.130 0.00 0.00 0.00 1.82
2770 8908 4.447389 CACCAACCAAAATCACCGAAATTC 59.553 41.667 0.00 0.00 0.00 2.17
2771 8909 4.343814 ACCAACCAAAATCACCGAAATTCT 59.656 37.500 0.00 0.00 0.00 2.40
2772 8910 4.923281 CCAACCAAAATCACCGAAATTCTC 59.077 41.667 0.00 0.00 0.00 2.87
2773 8911 5.508825 CCAACCAAAATCACCGAAATTCTCA 60.509 40.000 0.00 0.00 0.00 3.27
2774 8912 5.782893 ACCAAAATCACCGAAATTCTCAA 57.217 34.783 0.00 0.00 0.00 3.02
2775 8913 6.345096 ACCAAAATCACCGAAATTCTCAAT 57.655 33.333 0.00 0.00 0.00 2.57
2776 8914 6.758254 ACCAAAATCACCGAAATTCTCAATT 58.242 32.000 0.00 0.00 0.00 2.32
2777 8915 7.216494 ACCAAAATCACCGAAATTCTCAATTT 58.784 30.769 0.00 0.00 43.43 1.82
2797 8935 9.683069 TCAATTTCAGTCTTAGAAAAATTCAGC 57.317 29.630 7.71 0.00 38.36 4.26
2805 8943 5.596361 TCTTAGAAAAATTCAGCACCAACCA 59.404 36.000 0.00 0.00 0.00 3.67
2810 8948 6.260714 AGAAAAATTCAGCACCAACCAAAATC 59.739 34.615 0.00 0.00 0.00 2.17
2851 8989 7.846644 TTTCAGTGATTTCAGTTTGCATTTT 57.153 28.000 0.00 0.00 0.00 1.82
2852 8990 7.467557 TTCAGTGATTTCAGTTTGCATTTTC 57.532 32.000 0.00 0.00 0.00 2.29
2878 9016 6.624861 GCCAAATGACCGAAATATTCACTTGA 60.625 38.462 0.00 0.00 29.95 3.02
2909 9079 9.601971 CAATTAAAAATTTGAATTCCTGTGCAG 57.398 29.630 2.27 0.00 0.00 4.41
3003 9173 6.253746 GTGAATTTCCATCGAAATCTCACTG 58.746 40.000 20.43 0.00 45.92 3.66
3067 9239 3.701040 ACCAGAAACAACTTCAGTGCAAT 59.299 39.130 0.00 0.00 36.40 3.56
3074 9246 5.368256 ACAACTTCAGTGCAATCAGAATC 57.632 39.130 0.00 0.00 0.00 2.52
3079 9251 4.718940 TCAGTGCAATCAGAATCGACTA 57.281 40.909 0.00 0.00 0.00 2.59
3083 9255 4.081420 AGTGCAATCAGAATCGACTAACCT 60.081 41.667 0.00 0.00 0.00 3.50
3087 9259 6.876789 TGCAATCAGAATCGACTAACCTAAAA 59.123 34.615 0.00 0.00 0.00 1.52
3088 9260 7.064609 TGCAATCAGAATCGACTAACCTAAAAG 59.935 37.037 0.00 0.00 0.00 2.27
3173 9345 1.044611 GCCCAACTAAAACAGGCCAA 58.955 50.000 5.01 0.00 37.66 4.52
3227 9401 5.617528 TTAGTGTTCTCTAACAACCACCA 57.382 39.130 0.00 0.00 46.84 4.17
3274 9461 0.496382 TCTTCTTCCTCCCTTCCCCA 59.504 55.000 0.00 0.00 0.00 4.96
3315 9503 4.216257 CCATGGACGAAGAAGAAAACACAT 59.784 41.667 5.56 0.00 0.00 3.21
3316 9504 5.411361 CCATGGACGAAGAAGAAAACACATA 59.589 40.000 5.56 0.00 0.00 2.29
3317 9505 6.072728 CCATGGACGAAGAAGAAAACACATAA 60.073 38.462 5.56 0.00 0.00 1.90
3318 9506 6.295039 TGGACGAAGAAGAAAACACATAAC 57.705 37.500 0.00 0.00 0.00 1.89
3319 9507 5.237779 TGGACGAAGAAGAAAACACATAACC 59.762 40.000 0.00 0.00 0.00 2.85
3320 9508 5.237779 GGACGAAGAAGAAAACACATAACCA 59.762 40.000 0.00 0.00 0.00 3.67
3326 9514 6.273071 AGAAGAAAACACATAACCAAAGCAC 58.727 36.000 0.00 0.00 0.00 4.40
3360 9548 8.900983 TGGGACAAAAATTAAATGAAAGAAGG 57.099 30.769 0.00 0.00 31.92 3.46
3445 9638 7.282585 CCCATCAAAATTCCTACTCATCACTA 58.717 38.462 0.00 0.00 0.00 2.74
3446 9639 7.941238 CCCATCAAAATTCCTACTCATCACTAT 59.059 37.037 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 9.970395 TCTTAGTTCAAAACTTCGACACTTATA 57.030 29.630 0.00 0.00 42.81 0.98
43 44 5.295045 TGAACCGGTCTTAGTTCAAAACTTC 59.705 40.000 8.04 0.00 46.93 3.01
51 52 4.554134 GCAGTTTTGAACCGGTCTTAGTTC 60.554 45.833 8.04 0.00 42.20 3.01
53 54 2.876550 GCAGTTTTGAACCGGTCTTAGT 59.123 45.455 8.04 0.00 0.00 2.24
54 55 2.096417 CGCAGTTTTGAACCGGTCTTAG 60.096 50.000 8.04 0.00 0.00 2.18
62 63 2.844122 AAGTGTCGCAGTTTTGAACC 57.156 45.000 0.00 0.00 0.00 3.62
66 67 5.277825 TCCAAAATAAGTGTCGCAGTTTTG 58.722 37.500 5.46 11.07 36.70 2.44
71 72 3.928211 CGATCCAAAATAAGTGTCGCAG 58.072 45.455 0.00 0.00 0.00 5.18
287 289 4.623814 CTCGCAAATGAGAGGGCA 57.376 55.556 6.30 0.00 38.15 5.36
301 303 3.058160 CTTGCAAGGTGGCCCTCG 61.058 66.667 19.14 0.00 41.56 4.63
338 341 2.098607 AGTCGACCGTGTGTATGTATGG 59.901 50.000 13.01 0.00 0.00 2.74
453 456 3.233355 CTTGGCAACGAGGCTAAGT 57.767 52.632 16.47 0.00 44.45 2.24
490 2585 5.701750 CGAGAAAGGAGTACTATAGCTAGCA 59.298 44.000 18.83 3.19 0.00 3.49
553 6273 1.234821 GTGCACGTTTGATTCCCTGA 58.765 50.000 0.00 0.00 0.00 3.86
603 6323 1.332375 GCAACGTTGAGTGGCTACAAA 59.668 47.619 31.62 0.00 46.29 2.83
722 6470 4.630894 ATTGACACACTTTGCGAAAAGA 57.369 36.364 22.95 0.00 34.06 2.52
751 6502 2.431454 ACTTAGGAAGCTGCTCAAAGC 58.569 47.619 1.00 0.00 43.88 3.51
752 6503 6.112058 AGATTACTTAGGAAGCTGCTCAAAG 58.888 40.000 1.00 7.11 0.00 2.77
839 6601 5.368230 TGGCATCTGTATATGTAACCCTTCA 59.632 40.000 0.00 0.00 0.00 3.02
867 6639 3.857157 TTGTTTCAGAGTTGGTAGCCT 57.143 42.857 0.00 0.00 0.00 4.58
923 6699 1.004560 CTTGCGCTCCTGGACTTGA 60.005 57.895 9.73 0.00 0.00 3.02
924 6700 0.603707 TTCTTGCGCTCCTGGACTTG 60.604 55.000 9.73 0.00 0.00 3.16
925 6701 0.603975 GTTCTTGCGCTCCTGGACTT 60.604 55.000 9.73 0.00 0.00 3.01
926 6702 1.004440 GTTCTTGCGCTCCTGGACT 60.004 57.895 9.73 0.00 0.00 3.85
927 6703 0.246635 TAGTTCTTGCGCTCCTGGAC 59.753 55.000 9.73 0.69 0.00 4.02
928 6704 0.246635 GTAGTTCTTGCGCTCCTGGA 59.753 55.000 9.73 0.00 0.00 3.86
929 6705 0.247736 AGTAGTTCTTGCGCTCCTGG 59.752 55.000 9.73 0.00 0.00 4.45
941 6720 2.291190 CGGCCTAGCAGAGTAGTAGTTC 59.709 54.545 0.00 0.00 0.00 3.01
946 6728 1.064611 TCTTCGGCCTAGCAGAGTAGT 60.065 52.381 0.00 0.00 33.94 2.73
1047 6844 7.686938 GTGATTAGTTAGCACGTACATGAAAAC 59.313 37.037 0.00 0.00 0.00 2.43
1048 6845 7.735500 GTGATTAGTTAGCACGTACATGAAAA 58.264 34.615 0.00 0.00 0.00 2.29
1077 6886 1.300620 TCGACCAGTCAGCAAACGG 60.301 57.895 0.00 0.00 0.00 4.44
1078 6887 0.597637 AGTCGACCAGTCAGCAAACG 60.598 55.000 13.01 0.00 0.00 3.60
1128 6983 6.071896 TGAGCCATCTCTATAACGTAGGAATG 60.072 42.308 0.00 0.00 40.03 2.67
1160 7015 3.515602 AGTTTCCCAGTGAGCTCATTT 57.484 42.857 21.47 8.86 0.00 2.32
1658 7541 1.642952 GGTAGAAGACGTCGCGGACT 61.643 60.000 10.46 8.74 0.00 3.85
1709 7592 2.426738 CGTCAGCTCTCCAATCTTCTCT 59.573 50.000 0.00 0.00 0.00 3.10
1761 7819 2.363680 CGAGGGCATACTCTGTGATCTT 59.636 50.000 0.00 0.00 35.33 2.40
1880 7938 1.228552 GGGTGGAGCAGGCTTCAAA 60.229 57.895 3.33 0.00 32.63 2.69
2006 8079 2.124983 GAGCGCATGCCCTTCTCA 60.125 61.111 13.15 0.00 44.31 3.27
2023 8099 0.803768 CAGCTTCACGTCGAGGATGG 60.804 60.000 12.85 1.19 33.73 3.51
2470 8546 1.159713 TGCCTGCACGACTTCACAAG 61.160 55.000 0.00 0.00 0.00 3.16
2526 8605 3.623060 AGCGCGTGATGTTCATATTTCTT 59.377 39.130 8.43 0.00 0.00 2.52
2667 8805 5.382618 AAGTGAGAATTCAATTGACTGGC 57.617 39.130 7.89 0.00 39.89 4.85
2676 8814 5.468746 CGACTAACCCAAAGTGAGAATTCAA 59.531 40.000 8.44 0.00 34.49 2.69
2707 8845 8.750515 AAACTGAAATTGAAAACCATTGGATT 57.249 26.923 10.37 0.00 0.00 3.01
2734 8872 4.751767 TGGTTGGTGCTGAAATTTTTCT 57.248 36.364 4.80 0.00 38.02 2.52
2740 8878 4.379652 GTGATTTTGGTTGGTGCTGAAAT 58.620 39.130 0.00 0.00 0.00 2.17
2748 8886 4.343814 AGAATTTCGGTGATTTTGGTTGGT 59.656 37.500 0.00 0.00 0.00 3.67
2749 8887 4.881920 AGAATTTCGGTGATTTTGGTTGG 58.118 39.130 0.00 0.00 0.00 3.77
2750 8888 5.527951 TGAGAATTTCGGTGATTTTGGTTG 58.472 37.500 0.00 0.00 0.00 3.77
2751 8889 5.782893 TGAGAATTTCGGTGATTTTGGTT 57.217 34.783 0.00 0.00 0.00 3.67
2752 8890 5.782893 TTGAGAATTTCGGTGATTTTGGT 57.217 34.783 0.00 0.00 0.00 3.67
2753 8891 7.656707 AAATTGAGAATTTCGGTGATTTTGG 57.343 32.000 0.00 0.00 36.38 3.28
2771 8909 9.683069 GCTGAATTTTTCTAAGACTGAAATTGA 57.317 29.630 0.00 0.00 34.04 2.57
2772 8910 9.467258 TGCTGAATTTTTCTAAGACTGAAATTG 57.533 29.630 0.00 0.00 34.04 2.32
2773 8911 9.468532 GTGCTGAATTTTTCTAAGACTGAAATT 57.531 29.630 0.00 0.00 34.04 1.82
2774 8912 8.084684 GGTGCTGAATTTTTCTAAGACTGAAAT 58.915 33.333 0.00 0.00 34.04 2.17
2775 8913 7.068103 TGGTGCTGAATTTTTCTAAGACTGAAA 59.932 33.333 0.00 0.00 0.00 2.69
2776 8914 6.545666 TGGTGCTGAATTTTTCTAAGACTGAA 59.454 34.615 0.00 0.00 0.00 3.02
2777 8915 6.061441 TGGTGCTGAATTTTTCTAAGACTGA 58.939 36.000 0.00 0.00 0.00 3.41
2778 8916 6.317789 TGGTGCTGAATTTTTCTAAGACTG 57.682 37.500 0.00 0.00 0.00 3.51
2779 8917 6.239036 GGTTGGTGCTGAATTTTTCTAAGACT 60.239 38.462 0.00 0.00 0.00 3.24
2780 8918 5.920840 GGTTGGTGCTGAATTTTTCTAAGAC 59.079 40.000 0.00 0.00 0.00 3.01
2781 8919 5.596361 TGGTTGGTGCTGAATTTTTCTAAGA 59.404 36.000 0.00 0.00 0.00 2.10
2782 8920 5.841810 TGGTTGGTGCTGAATTTTTCTAAG 58.158 37.500 0.00 0.00 0.00 2.18
2783 8921 5.860941 TGGTTGGTGCTGAATTTTTCTAA 57.139 34.783 0.00 0.00 0.00 2.10
2784 8922 5.860941 TTGGTTGGTGCTGAATTTTTCTA 57.139 34.783 0.00 0.00 0.00 2.10
2785 8923 4.751767 TTGGTTGGTGCTGAATTTTTCT 57.248 36.364 0.00 0.00 0.00 2.52
2786 8924 5.809719 TTTTGGTTGGTGCTGAATTTTTC 57.190 34.783 0.00 0.00 0.00 2.29
2787 8925 5.884792 TGATTTTGGTTGGTGCTGAATTTTT 59.115 32.000 0.00 0.00 0.00 1.94
2788 8926 5.296531 GTGATTTTGGTTGGTGCTGAATTTT 59.703 36.000 0.00 0.00 0.00 1.82
2789 8927 4.815846 GTGATTTTGGTTGGTGCTGAATTT 59.184 37.500 0.00 0.00 0.00 1.82
2790 8928 4.379652 GTGATTTTGGTTGGTGCTGAATT 58.620 39.130 0.00 0.00 0.00 2.17
2791 8929 3.244181 GGTGATTTTGGTTGGTGCTGAAT 60.244 43.478 0.00 0.00 0.00 2.57
2792 8930 2.102252 GGTGATTTTGGTTGGTGCTGAA 59.898 45.455 0.00 0.00 0.00 3.02
2793 8931 1.686052 GGTGATTTTGGTTGGTGCTGA 59.314 47.619 0.00 0.00 0.00 4.26
2794 8932 1.602668 CGGTGATTTTGGTTGGTGCTG 60.603 52.381 0.00 0.00 0.00 4.41
2795 8933 0.673437 CGGTGATTTTGGTTGGTGCT 59.327 50.000 0.00 0.00 0.00 4.40
2796 8934 0.671251 TCGGTGATTTTGGTTGGTGC 59.329 50.000 0.00 0.00 0.00 5.01
2797 8935 3.444703 TTTCGGTGATTTTGGTTGGTG 57.555 42.857 0.00 0.00 0.00 4.17
2851 8989 3.942115 TGAATATTTCGGTCATTTGGCGA 59.058 39.130 0.00 0.00 0.00 5.54
2852 8990 4.035017 GTGAATATTTCGGTCATTTGGCG 58.965 43.478 0.00 0.00 0.00 5.69
2909 9079 7.010460 GGCCAAATATTTCAGCAATTTCAGTAC 59.990 37.037 17.31 0.00 0.00 2.73
3003 9173 3.383185 TGGATGTGGTGGTTTTCACTTTC 59.617 43.478 0.00 0.00 45.38 2.62
3017 9187 2.742053 CAGAAACTTACGGTGGATGTGG 59.258 50.000 0.00 0.00 0.00 4.17
3067 9239 6.127423 CCTCCTTTTAGGTTAGTCGATTCTGA 60.127 42.308 0.00 0.00 36.53 3.27
3074 9246 3.512724 TGACCCTCCTTTTAGGTTAGTCG 59.487 47.826 0.00 0.00 36.53 4.18
3079 9251 2.302157 CGAGTGACCCTCCTTTTAGGTT 59.698 50.000 0.00 0.00 36.82 3.50
3083 9255 2.426024 CGATCGAGTGACCCTCCTTTTA 59.574 50.000 10.26 0.00 36.82 1.52
3087 9259 1.454111 CCGATCGAGTGACCCTCCT 60.454 63.158 18.66 0.00 36.82 3.69
3088 9260 3.121019 CCGATCGAGTGACCCTCC 58.879 66.667 18.66 0.00 36.82 4.30
3104 9276 3.368571 GAACTGCTGTGCTGGGCC 61.369 66.667 0.00 0.00 0.00 5.80
3139 9311 1.118838 TGGGCTTGGTTTTTGTGGAG 58.881 50.000 0.00 0.00 0.00 3.86
3173 9345 3.151554 GGTTAATGGGTTTTCTCGGTGT 58.848 45.455 0.00 0.00 0.00 4.16
3227 9401 1.270907 CTTGACCTAGGGCTCTGTGT 58.729 55.000 17.75 0.00 0.00 3.72
3299 9487 6.142320 GCTTTGGTTATGTGTTTTCTTCTTCG 59.858 38.462 0.00 0.00 0.00 3.79
3300 9488 6.978080 TGCTTTGGTTATGTGTTTTCTTCTTC 59.022 34.615 0.00 0.00 0.00 2.87
3315 9503 3.317711 CCATGTCTGTTGTGCTTTGGTTA 59.682 43.478 0.00 0.00 0.00 2.85
3316 9504 2.101249 CCATGTCTGTTGTGCTTTGGTT 59.899 45.455 0.00 0.00 0.00 3.67
3317 9505 1.682854 CCATGTCTGTTGTGCTTTGGT 59.317 47.619 0.00 0.00 0.00 3.67
3318 9506 1.000060 CCCATGTCTGTTGTGCTTTGG 60.000 52.381 0.00 0.00 0.00 3.28
3319 9507 1.955778 TCCCATGTCTGTTGTGCTTTG 59.044 47.619 0.00 0.00 0.00 2.77
3320 9508 1.956477 GTCCCATGTCTGTTGTGCTTT 59.044 47.619 0.00 0.00 0.00 3.51
3326 9514 8.497554 CATTTAATTTTTGTCCCATGTCTGTTG 58.502 33.333 0.00 0.00 0.00 3.33
3351 9539 3.636764 GGTTCTTTCTTGCCCTTCTTTCA 59.363 43.478 0.00 0.00 0.00 2.69
3360 9548 1.866853 CGCCCAGGTTCTTTCTTGCC 61.867 60.000 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.