Multiple sequence alignment - TraesCS4D01G175300

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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 TraesCS4D01G175300 chr4D 100.000 5357 0 0 1 5357 303834033 303839389 0.000000e+00 9893.0
1 TraesCS4D01G175300 chr4D 95.349 86 3 1 2781 2866 10971612 10971528 9.360000e-28 135.0
2 TraesCS4D01G175300 chr4D 94.382 89 3 2 2781 2868 449455697 449455610 9.360000e-28 135.0
3 TraesCS4D01G175300 chr4D 96.970 33 0 1 5055 5087 5569929 5569960 3.000000e-03 54.7
4 TraesCS4D01G175300 chr4B 92.353 2393 68 32 360 2705 378766259 378768583 0.000000e+00 3299.0
5 TraesCS4D01G175300 chr4B 98.462 1756 23 3 2781 4532 378768594 378770349 0.000000e+00 3090.0
6 TraesCS4D01G175300 chr4B 91.555 521 40 2 4837 5357 378771103 378771619 0.000000e+00 715.0
7 TraesCS4D01G175300 chr4B 90.123 243 14 2 4590 4823 378770591 378770832 1.870000e-79 307.0
8 TraesCS4D01G175300 chr4B 88.168 262 16 5 24 272 378762246 378762505 1.130000e-76 298.0
9 TraesCS4D01G175300 chr4B 91.667 120 9 1 5086 5204 182666224 182666343 1.190000e-36 165.0
10 TraesCS4D01G175300 chr4B 94.048 84 4 1 2781 2864 178078819 178078901 5.630000e-25 126.0
11 TraesCS4D01G175300 chr4B 96.721 61 2 0 4530 4590 378770370 378770430 9.490000e-18 102.0
12 TraesCS4D01G175300 chr4A 96.507 2004 43 4 2882 4859 175411101 175409099 0.000000e+00 3288.0
13 TraesCS4D01G175300 chr4A 96.959 1184 33 3 1599 2780 175412434 175411252 0.000000e+00 1984.0
14 TraesCS4D01G175300 chr4A 90.562 837 20 20 641 1468 175413365 175412579 0.000000e+00 1053.0
15 TraesCS4D01G175300 chr4A 92.427 647 25 8 951 1597 175413101 175412479 0.000000e+00 902.0
16 TraesCS4D01G175300 chr4A 90.713 603 34 5 4754 5355 175409098 175408517 0.000000e+00 784.0
17 TraesCS4D01G175300 chr4A 84.557 395 20 13 262 626 175414931 175414548 2.370000e-93 353.0
18 TraesCS4D01G175300 chr4A 93.023 129 5 1 1 125 175415249 175415121 9.160000e-43 185.0
19 TraesCS4D01G175300 chr4A 96.591 88 3 0 2693 2780 107430140 107430227 4.320000e-31 147.0
20 TraesCS4D01G175300 chr4A 86.486 111 8 3 159 264 175415130 175415022 1.220000e-21 115.0
21 TraesCS4D01G175300 chr6B 90.076 131 13 0 5213 5343 674366064 674366194 2.570000e-38 171.0
22 TraesCS4D01G175300 chr6B 90.076 131 13 0 5213 5343 674370601 674370731 2.570000e-38 171.0
23 TraesCS4D01G175300 chr6B 91.667 120 8 2 5086 5204 683376106 683376224 1.190000e-36 165.0
24 TraesCS4D01G175300 chr2B 90.076 131 13 0 5213 5343 28863621 28863751 2.570000e-38 171.0
25 TraesCS4D01G175300 chr2B 88.462 130 14 1 5086 5214 144406869 144406740 7.180000e-34 156.0
26 TraesCS4D01G175300 chr2B 90.099 101 7 3 2763 2863 798196664 798196761 1.570000e-25 128.0
27 TraesCS4D01G175300 chr2B 89.216 102 10 1 2680 2780 774106537 774106638 5.630000e-25 126.0
28 TraesCS4D01G175300 chr2B 73.121 346 69 20 1062 1395 528829570 528829903 9.490000e-18 102.0
29 TraesCS4D01G175300 chr1B 90.076 131 13 0 5213 5343 577202255 577202125 2.570000e-38 171.0
30 TraesCS4D01G175300 chr1B 94.624 93 3 2 2689 2780 39580156 39580065 5.590000e-30 143.0
31 TraesCS4D01G175300 chr1B 91.176 102 8 1 2680 2780 447815471 447815370 2.600000e-28 137.0
32 TraesCS4D01G175300 chrUn 89.313 131 14 0 5213 5343 311577889 311578019 1.190000e-36 165.0
33 TraesCS4D01G175300 chr5D 89.313 131 14 0 5213 5343 234852570 234852440 1.190000e-36 165.0
34 TraesCS4D01G175300 chr5D 89.313 131 14 0 5213 5343 234857017 234856887 1.190000e-36 165.0
35 TraesCS4D01G175300 chr5D 98.750 80 1 0 2701 2780 322375834 322375755 5.590000e-30 143.0
36 TraesCS4D01G175300 chr5D 95.294 85 3 1 2781 2865 56448542 56448459 3.370000e-27 134.0
37 TraesCS4D01G175300 chr5D 86.842 76 8 1 4752 4825 437569924 437569849 3.440000e-12 84.2
38 TraesCS4D01G175300 chr3D 89.313 131 13 1 5086 5215 87926129 87925999 4.290000e-36 163.0
39 TraesCS4D01G175300 chr3D 84.810 158 18 4 5063 5214 424015476 424015319 2.580000e-33 154.0
40 TraesCS4D01G175300 chr3D 84.868 152 22 1 5063 5214 458622147 458621997 9.290000e-33 152.0
41 TraesCS4D01G175300 chr3D 72.755 323 57 24 1076 1384 9450935 9450630 4.450000e-11 80.5
42 TraesCS4D01G175300 chr3D 85.714 70 8 1 4758 4825 568170409 568170340 7.440000e-09 73.1
43 TraesCS4D01G175300 chr7A 87.879 132 14 2 5086 5215 634927817 634927686 2.580000e-33 154.0
44 TraesCS4D01G175300 chr7A 86.111 72 8 1 4756 4825 727439386 727439315 5.750000e-10 76.8
45 TraesCS4D01G175300 chr7A 92.157 51 2 1 4753 4801 116644997 116644947 2.680000e-08 71.3
46 TraesCS4D01G175300 chr7A 84.000 75 9 2 4754 4825 20120309 20120383 9.630000e-08 69.4
47 TraesCS4D01G175300 chr3B 98.750 80 1 0 2701 2780 21406241 21406320 5.590000e-30 143.0
48 TraesCS4D01G175300 chr7B 97.561 82 2 0 2699 2780 93439154 93439073 2.010000e-29 141.0
49 TraesCS4D01G175300 chr7B 96.875 32 1 0 5056 5087 465549297 465549328 3.000000e-03 54.7
50 TraesCS4D01G175300 chr5B 94.318 88 5 0 2693 2780 105774103 105774016 9.360000e-28 135.0
51 TraesCS4D01G175300 chr5B 86.667 105 10 4 2678 2780 639145027 639144925 4.390000e-21 113.0
52 TraesCS4D01G175300 chr5B 97.727 44 0 1 4826 4868 531629718 531629675 2.070000e-09 75.0
53 TraesCS4D01G175300 chr5A 96.386 83 2 1 2781 2863 38014624 38014705 9.360000e-28 135.0
54 TraesCS4D01G175300 chr3A 95.294 85 3 1 2781 2865 747595955 747596038 3.370000e-27 134.0
55 TraesCS4D01G175300 chr3A 95.294 85 3 1 2781 2865 747598875 747598958 3.370000e-27 134.0
56 TraesCS4D01G175300 chr2A 73.389 357 69 22 1062 1405 593443431 593443774 5.670000e-20 110.0
57 TraesCS4D01G175300 chr2D 73.373 338 66 20 1062 1387 449556399 449556074 2.640000e-18 104.0
58 TraesCS4D01G175300 chr1A 79.114 158 22 3 5056 5203 531984921 531984765 1.230000e-16 99.0
59 TraesCS4D01G175300 chr7D 84.722 72 9 1 4756 4825 638465128 638465199 2.680000e-08 71.3
60 TraesCS4D01G175300 chr7D 90.244 41 3 1 5060 5099 265698736 265698696 1.000000e-02 52.8
61 TraesCS4D01G175300 chr1D 100.000 32 0 0 4837 4868 361815340 361815309 5.790000e-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 TraesCS4D01G175300 chr4D 303834033 303839389 5356 False 9893.000000 9893 100.00000 1 5357 1 chr4D.!!$F2 5356
1 TraesCS4D01G175300 chr4B 378762246 378771619 9373 False 1301.833333 3299 92.89700 24 5357 6 chr4B.!!$F3 5333
2 TraesCS4D01G175300 chr4A 175408517 175415249 6732 True 1083.000000 3288 91.40425 1 5355 8 chr4A.!!$R1 5354

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
766 5765 0.246635 CAGTACCACCGCTTAGCAGT 59.753 55.000 4.70 0.0 0.00 4.40 F
1469 6487 0.693049 ACCCAGCGGATGTTCTTTCT 59.307 50.000 0.00 0.0 0.00 2.52 F
2175 7268 0.953727 GTGGTGCTGCAATGTCAGAA 59.046 50.000 2.77 0.0 36.19 3.02 F
2184 7277 1.363744 CAATGTCAGAAGGTCCGAGC 58.636 55.000 0.00 0.0 0.00 5.03 F
3268 8464 2.765699 ACAATCCAAGCAAACCACTGTT 59.234 40.909 0.00 0.0 35.82 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2655 7749 0.458669 CAGCATGGGGAATGTCTTGC 59.541 55.000 0.00 0.0 38.65 4.01 R
2832 8025 2.490991 GGTCCCATAATGTAAGACGGC 58.509 52.381 0.00 0.0 0.00 5.68 R
3915 9112 1.366111 GAACCAGGCGCGCAGATTAA 61.366 55.000 34.42 0.0 0.00 1.40 R
4020 9219 2.927004 GTGATGAACACGCTTGGGA 58.073 52.632 0.00 0.0 39.78 4.37 R
4877 10630 0.178973 TCGAGTGGTCTTGTCCAGGA 60.179 55.000 0.00 0.0 38.23 3.86 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
94 99 1.395954 CACATCGTCATGTTGGAGCTG 59.604 52.381 0.00 0.00 40.66 4.24
128 133 1.614583 GGAGGTGGAGCTCCTTTTTCC 60.615 57.143 32.28 26.13 36.84 3.13
136 141 4.006989 GGAGCTCCTTTTTCCTCTTCTTC 58.993 47.826 26.25 0.00 0.00 2.87
159 171 3.114606 TGATTGATGAGGGTAAGGCTGA 58.885 45.455 0.00 0.00 0.00 4.26
279 390 9.590451 CAAAAGTGCATTTATTCATAACCTGAT 57.410 29.630 0.00 0.00 32.72 2.90
283 394 8.408601 AGTGCATTTATTCATAACCTGATCAAC 58.591 33.333 0.00 0.00 32.72 3.18
338 4026 8.071368 TCAATTACGGAAATGTTTTGTCAGTAC 58.929 33.333 0.00 0.00 0.00 2.73
341 4029 6.780706 ACGGAAATGTTTTGTCAGTACTAG 57.219 37.500 0.00 0.00 0.00 2.57
343 4031 7.436118 ACGGAAATGTTTTGTCAGTACTAGTA 58.564 34.615 0.00 0.00 0.00 1.82
410 4214 4.479993 AGCGCAGGTGGATGCCTC 62.480 66.667 11.47 0.00 43.49 4.70
478 4286 7.821566 TGCCCTGAAATTATCTATCCCTTTAA 58.178 34.615 0.00 0.00 0.00 1.52
504 4312 8.709386 TTATCTCAGAGAAGAACAATAGTTGC 57.291 34.615 3.63 0.00 38.30 4.17
505 4313 5.482908 TCTCAGAGAAGAACAATAGTTGCC 58.517 41.667 0.00 0.00 38.30 4.52
506 4314 5.012046 TCTCAGAGAAGAACAATAGTTGCCA 59.988 40.000 0.00 0.00 38.30 4.92
507 4315 5.240891 TCAGAGAAGAACAATAGTTGCCAG 58.759 41.667 0.00 0.00 38.30 4.85
511 4320 6.820656 AGAGAAGAACAATAGTTGCCAGTATG 59.179 38.462 0.00 0.00 38.30 2.39
622 5618 3.892522 AGACGAAACAATTAAAACCGCC 58.107 40.909 0.00 0.00 0.00 6.13
633 5629 1.652947 AAAACCGCCTCTCCTTCCTA 58.347 50.000 0.00 0.00 0.00 2.94
634 5630 1.652947 AAACCGCCTCTCCTTCCTAA 58.347 50.000 0.00 0.00 0.00 2.69
635 5631 1.196012 AACCGCCTCTCCTTCCTAAG 58.804 55.000 0.00 0.00 0.00 2.18
636 5632 1.331399 ACCGCCTCTCCTTCCTAAGC 61.331 60.000 0.00 0.00 0.00 3.09
637 5633 1.443828 CGCCTCTCCTTCCTAAGCC 59.556 63.158 0.00 0.00 0.00 4.35
638 5634 1.833606 GCCTCTCCTTCCTAAGCCC 59.166 63.158 0.00 0.00 0.00 5.19
639 5635 0.983378 GCCTCTCCTTCCTAAGCCCA 60.983 60.000 0.00 0.00 0.00 5.36
711 5710 1.148157 CTCGTAAGCACCCATCGCTG 61.148 60.000 0.00 0.00 40.35 5.18
752 5751 0.460311 AGCGATACCAGTGCCAGTAC 59.540 55.000 0.00 0.00 0.00 2.73
753 5752 0.529992 GCGATACCAGTGCCAGTACC 60.530 60.000 0.00 0.00 0.00 3.34
754 5753 0.821517 CGATACCAGTGCCAGTACCA 59.178 55.000 0.00 0.00 0.00 3.25
755 5754 1.470979 CGATACCAGTGCCAGTACCAC 60.471 57.143 0.00 0.00 0.00 4.16
756 5755 0.909623 ATACCAGTGCCAGTACCACC 59.090 55.000 0.00 0.00 33.75 4.61
757 5756 1.537814 TACCAGTGCCAGTACCACCG 61.538 60.000 0.00 0.00 33.75 4.94
758 5757 2.742372 CAGTGCCAGTACCACCGC 60.742 66.667 0.00 0.00 33.75 5.68
759 5758 2.923035 AGTGCCAGTACCACCGCT 60.923 61.111 0.00 0.00 33.75 5.52
760 5759 2.032071 GTGCCAGTACCACCGCTT 59.968 61.111 0.00 0.00 0.00 4.68
761 5760 1.189524 AGTGCCAGTACCACCGCTTA 61.190 55.000 0.00 0.00 33.75 3.09
762 5761 0.739813 GTGCCAGTACCACCGCTTAG 60.740 60.000 0.00 0.00 0.00 2.18
763 5762 1.814169 GCCAGTACCACCGCTTAGC 60.814 63.158 0.00 0.00 0.00 3.09
764 5763 1.594833 CCAGTACCACCGCTTAGCA 59.405 57.895 4.70 0.00 0.00 3.49
765 5764 0.460284 CCAGTACCACCGCTTAGCAG 60.460 60.000 4.70 0.00 0.00 4.24
766 5765 0.246635 CAGTACCACCGCTTAGCAGT 59.753 55.000 4.70 0.00 0.00 4.40
767 5766 1.475280 CAGTACCACCGCTTAGCAGTA 59.525 52.381 4.70 0.00 0.00 2.74
789 5796 2.500509 TTTGTTAAGCAAACGGCCAG 57.499 45.000 2.24 0.00 46.50 4.85
849 5862 1.213013 CTCCCACTTCACCTCGTCG 59.787 63.158 0.00 0.00 0.00 5.12
892 5905 1.463674 CTTCCGTTCCCATTCCAAGG 58.536 55.000 0.00 0.00 0.00 3.61
943 5956 4.671569 GCGGGAGGCGCTCATAGG 62.672 72.222 7.64 0.00 31.08 2.57
944 5957 4.671569 CGGGAGGCGCTCATAGGC 62.672 72.222 7.64 0.00 31.08 3.93
953 5966 2.594541 GCTCATAGGCGTTTCGAGG 58.405 57.895 0.00 0.00 0.00 4.63
1231 6244 1.294780 CGCAAGCTCTTCCTCTGGT 59.705 57.895 0.00 0.00 0.00 4.00
1434 6447 8.296713 CCTTCATTTTCGGTTTCAAAGATTAGA 58.703 33.333 0.00 0.00 0.00 2.10
1468 6486 1.087501 GACCCAGCGGATGTTCTTTC 58.912 55.000 0.00 0.00 0.00 2.62
1469 6487 0.693049 ACCCAGCGGATGTTCTTTCT 59.307 50.000 0.00 0.00 0.00 2.52
1470 6488 1.073923 ACCCAGCGGATGTTCTTTCTT 59.926 47.619 0.00 0.00 0.00 2.52
1471 6489 2.162681 CCCAGCGGATGTTCTTTCTTT 58.837 47.619 0.00 0.00 0.00 2.52
1472 6490 2.558359 CCCAGCGGATGTTCTTTCTTTT 59.442 45.455 0.00 0.00 0.00 2.27
1473 6491 3.568538 CCAGCGGATGTTCTTTCTTTTG 58.431 45.455 0.00 0.00 0.00 2.44
1474 6492 3.568538 CAGCGGATGTTCTTTCTTTTGG 58.431 45.455 0.00 0.00 0.00 3.28
1475 6493 3.004734 CAGCGGATGTTCTTTCTTTTGGT 59.995 43.478 0.00 0.00 0.00 3.67
1476 6494 4.215399 CAGCGGATGTTCTTTCTTTTGGTA 59.785 41.667 0.00 0.00 0.00 3.25
1477 6495 4.825085 AGCGGATGTTCTTTCTTTTGGTAA 59.175 37.500 0.00 0.00 0.00 2.85
1478 6496 5.476945 AGCGGATGTTCTTTCTTTTGGTAAT 59.523 36.000 0.00 0.00 0.00 1.89
1479 6497 6.015434 AGCGGATGTTCTTTCTTTTGGTAATT 60.015 34.615 0.00 0.00 0.00 1.40
1480 6498 6.089417 GCGGATGTTCTTTCTTTTGGTAATTG 59.911 38.462 0.00 0.00 0.00 2.32
1481 6499 7.145323 CGGATGTTCTTTCTTTTGGTAATTGT 58.855 34.615 0.00 0.00 0.00 2.71
1482 6500 7.651704 CGGATGTTCTTTCTTTTGGTAATTGTT 59.348 33.333 0.00 0.00 0.00 2.83
1483 6501 8.978539 GGATGTTCTTTCTTTTGGTAATTGTTC 58.021 33.333 0.00 0.00 0.00 3.18
1484 6502 8.887036 ATGTTCTTTCTTTTGGTAATTGTTCC 57.113 30.769 0.00 0.00 0.00 3.62
1485 6503 6.975772 TGTTCTTTCTTTTGGTAATTGTTCCG 59.024 34.615 0.00 0.00 0.00 4.30
1486 6504 6.079424 TCTTTCTTTTGGTAATTGTTCCGG 57.921 37.500 0.00 0.00 0.00 5.14
1487 6505 5.828859 TCTTTCTTTTGGTAATTGTTCCGGA 59.171 36.000 0.00 0.00 0.00 5.14
1488 6506 5.441709 TTCTTTTGGTAATTGTTCCGGAC 57.558 39.130 1.83 0.00 0.00 4.79
1489 6507 3.822167 TCTTTTGGTAATTGTTCCGGACC 59.178 43.478 1.83 0.00 0.00 4.46
1490 6508 1.810959 TTGGTAATTGTTCCGGACCG 58.189 50.000 1.83 6.99 32.55 4.79
1668 6754 8.738106 AGATCCATTCTGAAGATTTTGAAGAAC 58.262 33.333 0.00 0.00 31.79 3.01
1682 6768 5.429681 TTGAAGAACGATCCTCCCAATTA 57.570 39.130 0.00 0.00 0.00 1.40
1722 6811 9.985730 ATTTTATTGATCTGTTTGCTCTGAAAA 57.014 25.926 0.00 0.00 0.00 2.29
1723 6812 9.814899 TTTTATTGATCTGTTTGCTCTGAAAAA 57.185 25.926 0.00 0.00 0.00 1.94
2175 7268 0.953727 GTGGTGCTGCAATGTCAGAA 59.046 50.000 2.77 0.00 36.19 3.02
2184 7277 1.363744 CAATGTCAGAAGGTCCGAGC 58.636 55.000 0.00 0.00 0.00 5.03
2655 7749 5.446899 GCGTATCTTGGTTTCGTTTAATTCG 59.553 40.000 0.00 0.00 0.00 3.34
2709 7803 7.420800 CATTTTAGTTTGCATGATACTCCCTC 58.579 38.462 0.00 0.00 0.00 4.30
2724 7818 9.812347 TGATACTCCCTCCGTAAACTAATATAA 57.188 33.333 0.00 0.00 0.00 0.98
2731 7825 9.071276 CCCTCCGTAAACTAATATAAGAGTGTA 57.929 37.037 0.00 0.00 0.00 2.90
3268 8464 2.765699 ACAATCCAAGCAAACCACTGTT 59.234 40.909 0.00 0.00 35.82 3.16
3590 8786 8.708378 TGCTCTTATCTTCCAGATTTTAGATCA 58.292 33.333 0.00 0.00 36.20 2.92
4020 9219 0.107410 TCGGGCACGGAAAGCATTAT 60.107 50.000 9.32 0.00 41.39 1.28
4190 9389 1.014564 GGCTTCAAAGACGTCCGGAG 61.015 60.000 13.01 6.55 0.00 4.63
4574 9796 1.078848 AGCGAGAGGATGCACAACC 60.079 57.895 0.00 0.00 0.00 3.77
4719 10102 6.350194 CCACTACATATCCATAGCATACGTGT 60.350 42.308 0.00 0.00 0.00 4.49
4732 10124 0.244450 TACGTGTCCTAAGGCAACCG 59.756 55.000 0.00 0.00 37.17 4.44
4735 10127 1.019805 GTGTCCTAAGGCAACCGCTC 61.020 60.000 0.00 0.00 38.60 5.03
4797 10189 5.890985 CCACTTTACATGGGGTGATGATTTA 59.109 40.000 0.00 0.00 33.18 1.40
4859 10612 4.767409 AGAAGTAAACTGGGGCAAAAGATC 59.233 41.667 0.00 0.00 0.00 2.75
4877 10630 5.463051 AGATCCAATTTCTTCATCCCTGT 57.537 39.130 0.00 0.00 0.00 4.00
4981 10735 2.735478 CACGCGGGTGCTCGTTTA 60.735 61.111 20.24 0.00 37.35 2.01
4994 10748 0.108520 TCGTTTATGTCTCGGGTGCC 60.109 55.000 0.00 0.00 0.00 5.01
5040 10794 3.486108 GCGATGACCGATAGTTTGTACAG 59.514 47.826 0.00 0.00 41.76 2.74
5048 10802 5.243283 ACCGATAGTTTGTACAGTGTCTCTT 59.757 40.000 0.00 0.00 0.00 2.85
5155 10909 8.854614 AGAGTGTAGATTCACTTATTTTGCTT 57.145 30.769 0.98 0.00 46.81 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 63 4.329545 TGGCGCCTCACTGTTCCC 62.330 66.667 29.70 0.00 0.00 3.97
94 99 1.341209 CACCTCCACCTTTCCTTTTGC 59.659 52.381 0.00 0.00 0.00 3.68
128 133 5.743117 ACCCTCATCAATCAAGAAGAAGAG 58.257 41.667 0.00 0.00 0.00 2.85
136 141 3.881688 CAGCCTTACCCTCATCAATCAAG 59.118 47.826 0.00 0.00 0.00 3.02
181 193 0.246360 TCTGATTCATCACCGTGCGT 59.754 50.000 0.00 0.00 32.50 5.24
294 405 8.744011 CGTAATTGATTCAAGTAGTGCTAGTAC 58.256 37.037 6.80 2.24 0.00 2.73
295 406 7.919091 CCGTAATTGATTCAAGTAGTGCTAGTA 59.081 37.037 6.80 0.00 0.00 1.82
297 408 6.978659 TCCGTAATTGATTCAAGTAGTGCTAG 59.021 38.462 6.80 0.00 0.00 3.42
298 409 6.869695 TCCGTAATTGATTCAAGTAGTGCTA 58.130 36.000 6.80 0.00 0.00 3.49
299 410 5.730550 TCCGTAATTGATTCAAGTAGTGCT 58.269 37.500 6.80 0.00 0.00 4.40
341 4029 7.171508 TCGGAAATGCTGTTGAGATGATAATAC 59.828 37.037 0.00 0.00 0.00 1.89
343 4031 6.017605 GTCGGAAATGCTGTTGAGATGATAAT 60.018 38.462 0.00 0.00 0.00 1.28
348 4036 2.743664 TGTCGGAAATGCTGTTGAGATG 59.256 45.455 0.00 0.00 0.00 2.90
349 4037 2.744202 GTGTCGGAAATGCTGTTGAGAT 59.256 45.455 0.00 0.00 0.00 2.75
354 4042 2.254546 TGAGTGTCGGAAATGCTGTT 57.745 45.000 0.00 0.00 0.00 3.16
355 4043 2.146342 CTTGAGTGTCGGAAATGCTGT 58.854 47.619 0.00 0.00 0.00 4.40
356 4044 2.146342 ACTTGAGTGTCGGAAATGCTG 58.854 47.619 0.00 0.00 0.00 4.41
357 4045 2.550830 ACTTGAGTGTCGGAAATGCT 57.449 45.000 0.00 0.00 0.00 3.79
358 4046 3.003275 TGAAACTTGAGTGTCGGAAATGC 59.997 43.478 0.00 0.00 35.03 3.56
410 4214 0.678950 AACGGGTGCAGGAATTTTGG 59.321 50.000 0.00 0.00 0.00 3.28
478 4286 9.323985 GCAACTATTGTTCTTCTCTGAGATAAT 57.676 33.333 8.42 7.33 33.52 1.28
622 5618 2.682269 GCTTTGGGCTTAGGAAGGAGAG 60.682 54.545 0.00 0.00 38.06 3.20
633 5629 1.045911 TTCGTTTGGGCTTTGGGCTT 61.046 50.000 0.00 0.00 41.46 4.35
634 5630 1.456705 TTCGTTTGGGCTTTGGGCT 60.457 52.632 0.00 0.00 41.46 5.19
635 5631 1.300620 GTTCGTTTGGGCTTTGGGC 60.301 57.895 0.00 0.00 40.90 5.36
636 5632 1.007849 CGTTCGTTTGGGCTTTGGG 60.008 57.895 0.00 0.00 0.00 4.12
637 5633 0.317519 GTCGTTCGTTTGGGCTTTGG 60.318 55.000 0.00 0.00 0.00 3.28
638 5634 0.317519 GGTCGTTCGTTTGGGCTTTG 60.318 55.000 0.00 0.00 0.00 2.77
639 5635 0.748729 TGGTCGTTCGTTTGGGCTTT 60.749 50.000 0.00 0.00 0.00 3.51
711 5710 4.612412 TGTGTTGGGTCCGGCGAC 62.612 66.667 9.30 4.52 38.38 5.19
755 5754 5.600908 TTAACAAAAGTACTGCTAAGCGG 57.399 39.130 0.00 0.00 41.29 5.52
756 5755 5.080068 GCTTAACAAAAGTACTGCTAAGCG 58.920 41.667 10.95 0.00 38.18 4.68
757 5756 5.997385 TGCTTAACAAAAGTACTGCTAAGC 58.003 37.500 16.18 16.18 43.76 3.09
789 5796 0.391966 GTATTAGGGACCGGGTGCTC 59.608 60.000 18.54 8.68 0.00 4.26
849 5862 4.577246 TTTTTGGCGTGCGTGGGC 62.577 61.111 0.00 0.00 40.52 5.36
935 5948 0.179108 ACCTCGAAACGCCTATGAGC 60.179 55.000 0.00 0.00 0.00 4.26
936 5949 1.560923 CACCTCGAAACGCCTATGAG 58.439 55.000 0.00 0.00 0.00 2.90
937 5950 0.174845 CCACCTCGAAACGCCTATGA 59.825 55.000 0.00 0.00 0.00 2.15
938 5951 0.108329 ACCACCTCGAAACGCCTATG 60.108 55.000 0.00 0.00 0.00 2.23
939 5952 0.108329 CACCACCTCGAAACGCCTAT 60.108 55.000 0.00 0.00 0.00 2.57
940 5953 1.290955 CACCACCTCGAAACGCCTA 59.709 57.895 0.00 0.00 0.00 3.93
941 5954 2.030562 CACCACCTCGAAACGCCT 59.969 61.111 0.00 0.00 0.00 5.52
942 5955 2.438951 TACCACCACCTCGAAACGCC 62.439 60.000 0.00 0.00 0.00 5.68
943 5956 1.005867 TACCACCACCTCGAAACGC 60.006 57.895 0.00 0.00 0.00 4.84
944 5957 0.389426 CCTACCACCACCTCGAAACG 60.389 60.000 0.00 0.00 0.00 3.60
945 5958 0.036671 CCCTACCACCACCTCGAAAC 60.037 60.000 0.00 0.00 0.00 2.78
946 5959 1.196104 CCCCTACCACCACCTCGAAA 61.196 60.000 0.00 0.00 0.00 3.46
947 5960 1.611261 CCCCTACCACCACCTCGAA 60.611 63.158 0.00 0.00 0.00 3.71
948 5961 1.882189 ATCCCCTACCACCACCTCGA 61.882 60.000 0.00 0.00 0.00 4.04
949 5962 1.382695 ATCCCCTACCACCACCTCG 60.383 63.158 0.00 0.00 0.00 4.63
950 5963 0.031010 AGATCCCCTACCACCACCTC 60.031 60.000 0.00 0.00 0.00 3.85
951 5964 0.326618 CAGATCCCCTACCACCACCT 60.327 60.000 0.00 0.00 0.00 4.00
952 5965 0.620700 ACAGATCCCCTACCACCACC 60.621 60.000 0.00 0.00 0.00 4.61
953 5966 0.541863 CACAGATCCCCTACCACCAC 59.458 60.000 0.00 0.00 0.00 4.16
1323 6336 2.122547 AGGGTGAACTGGTCCGGT 60.123 61.111 0.00 0.00 0.00 5.28
1434 6447 3.614870 GCTGGGTCGAAAAGCATCAAAAT 60.615 43.478 9.65 0.00 36.91 1.82
1468 6486 3.365565 CGGTCCGGAACAATTACCAAAAG 60.366 47.826 21.79 0.00 0.00 2.27
1469 6487 2.553172 CGGTCCGGAACAATTACCAAAA 59.447 45.455 21.79 0.00 0.00 2.44
1470 6488 2.152830 CGGTCCGGAACAATTACCAAA 58.847 47.619 21.79 0.00 0.00 3.28
1471 6489 1.810959 CGGTCCGGAACAATTACCAA 58.189 50.000 21.79 0.00 0.00 3.67
1472 6490 3.536548 CGGTCCGGAACAATTACCA 57.463 52.632 21.79 0.00 0.00 3.25
1489 6507 4.092968 CCTTAAATCAGAACCGAAACTCCG 59.907 45.833 0.00 0.00 0.00 4.63
1490 6508 4.142665 GCCTTAAATCAGAACCGAAACTCC 60.143 45.833 0.00 0.00 0.00 3.85
1491 6509 4.435651 CGCCTTAAATCAGAACCGAAACTC 60.436 45.833 0.00 0.00 0.00 3.01
1492 6510 3.435671 CGCCTTAAATCAGAACCGAAACT 59.564 43.478 0.00 0.00 0.00 2.66
1493 6511 3.187842 ACGCCTTAAATCAGAACCGAAAC 59.812 43.478 0.00 0.00 0.00 2.78
1494 6512 3.187637 CACGCCTTAAATCAGAACCGAAA 59.812 43.478 0.00 0.00 0.00 3.46
1495 6513 2.739913 CACGCCTTAAATCAGAACCGAA 59.260 45.455 0.00 0.00 0.00 4.30
1496 6514 2.028839 TCACGCCTTAAATCAGAACCGA 60.029 45.455 0.00 0.00 0.00 4.69
1497 6515 2.343101 TCACGCCTTAAATCAGAACCG 58.657 47.619 0.00 0.00 0.00 4.44
1610 6695 0.879090 GGTTTAAGGGCAACTGTCCG 59.121 55.000 0.00 0.00 46.49 4.79
1722 6811 7.846644 TTGCAGAACAAACAGATGAATTTTT 57.153 28.000 0.00 0.00 34.56 1.94
1723 6812 7.846644 TTTGCAGAACAAACAGATGAATTTT 57.153 28.000 0.00 0.00 43.35 1.82
2040 7131 2.867429 CAACCAAGCGATCAATGGAAC 58.133 47.619 13.66 0.00 37.66 3.62
2184 7277 5.294356 CAACAATAATGATCATTGGGCTGG 58.706 41.667 27.59 14.36 37.64 4.85
2655 7749 0.458669 CAGCATGGGGAATGTCTTGC 59.541 55.000 0.00 0.00 38.65 4.01
2832 8025 2.490991 GGTCCCATAATGTAAGACGGC 58.509 52.381 0.00 0.00 0.00 5.68
3308 8504 4.448210 TGACACCTAAACTGAAACCTGTC 58.552 43.478 0.00 0.00 0.00 3.51
3438 8634 8.751335 CGTCAAACAATGCAAAATAAGTAAAGT 58.249 29.630 0.00 0.00 0.00 2.66
3590 8786 9.366216 GACTTCAAACCTTTTGTTCTGTTAAAT 57.634 29.630 0.00 0.00 35.67 1.40
3729 8925 3.806521 CAGCATTGACTACATACTGGAGC 59.193 47.826 0.00 0.00 29.04 4.70
3915 9112 1.366111 GAACCAGGCGCGCAGATTAA 61.366 55.000 34.42 0.00 0.00 1.40
4020 9219 2.927004 GTGATGAACACGCTTGGGA 58.073 52.632 0.00 0.00 39.78 4.37
4190 9389 1.529865 GTTCTGTGTAGTTGCGGTTCC 59.470 52.381 0.00 0.00 0.00 3.62
4574 9796 8.065473 AGTACAGATATAGATCAGAGGCAATG 57.935 38.462 0.00 0.00 34.17 2.82
4714 10097 1.005394 CGGTTGCCTTAGGACACGT 60.005 57.895 0.69 0.00 0.00 4.49
4719 10102 2.280552 ACGAGCGGTTGCCTTAGGA 61.281 57.895 0.69 0.00 44.31 2.94
4732 10124 1.448540 CAGGGATGTGGACACGAGC 60.449 63.158 0.00 0.00 0.00 5.03
4735 10127 1.446099 CGTCAGGGATGTGGACACG 60.446 63.158 0.00 0.00 0.00 4.49
4797 10189 7.556275 CACTAACCATTGACACAATAATAGGGT 59.444 37.037 0.00 0.00 0.00 4.34
4801 10193 8.871629 AACCACTAACCATTGACACAATAATA 57.128 30.769 0.00 0.00 0.00 0.98
4805 10197 6.945435 TGATAACCACTAACCATTGACACAAT 59.055 34.615 0.00 0.00 0.00 2.71
4859 10612 3.698040 CAGGACAGGGATGAAGAAATTGG 59.302 47.826 0.00 0.00 0.00 3.16
4877 10630 0.178973 TCGAGTGGTCTTGTCCAGGA 60.179 55.000 0.00 0.00 38.23 3.86
5048 10802 7.349598 ACGGAGGGAGTAGTAGTTATCTTAAA 58.650 38.462 0.00 0.00 0.00 1.52
5204 10958 5.358160 GGCAGCACTAACTCATATTCCTTTT 59.642 40.000 0.00 0.00 0.00 2.27
5205 10959 4.884164 GGCAGCACTAACTCATATTCCTTT 59.116 41.667 0.00 0.00 0.00 3.11
5207 10961 3.455910 TGGCAGCACTAACTCATATTCCT 59.544 43.478 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.