Multiple sequence alignment - TraesCS7A01G401200

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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 TraesCS7A01G401200 chr7A 100.000 4785 0 0 898 5682 580670400 580665616 0.000000e+00 8837
1 TraesCS7A01G401200 chr7A 100.000 730 0 0 1 730 580671297 580670568 0.000000e+00 1349
2 TraesCS7A01G401200 chr7B 92.780 3892 170 44 1403 5241 538226366 538222533 0.000000e+00 5528
3 TraesCS7A01G401200 chr7B 93.830 470 19 5 898 1365 538226899 538226438 0.000000e+00 699
4 TraesCS7A01G401200 chr7B 89.062 576 38 7 143 718 2223676 2224226 0.000000e+00 691
5 TraesCS7A01G401200 chr7B 88.586 587 43 6 144 730 412898908 412898346 0.000000e+00 691
6 TraesCS7A01G401200 chr7D 95.354 3444 115 17 2258 5682 509927170 509923753 0.000000e+00 5432
7 TraesCS7A01G401200 chr7D 87.120 691 43 21 898 1566 509929776 509929110 0.000000e+00 741
8 TraesCS7A01G401200 chr7D 86.580 693 57 15 1583 2263 509929119 509928451 0.000000e+00 732
9 TraesCS7A01G401200 chr7D 86.017 236 25 3 2591 2823 185911124 185910894 4.400000e-61 246
10 TraesCS7A01G401200 chr4B 99.178 730 5 1 1 730 491042253 491042981 0.000000e+00 1314
11 TraesCS7A01G401200 chr4B 84.226 672 65 13 1 666 448796065 448796701 2.910000e-172 616
12 TraesCS7A01G401200 chr4B 92.754 138 10 0 2969 3106 182666354 182666217 3.470000e-47 200
13 TraesCS7A01G401200 chr4B 86.000 150 21 0 1119 1268 507362798 507362947 1.640000e-35 161
14 TraesCS7A01G401200 chr3B 99.041 730 7 0 1 730 688394961 688395690 0.000000e+00 1310
15 TraesCS7A01G401200 chr3B 92.857 140 10 0 2969 3108 552226569 552226430 2.680000e-48 204
16 TraesCS7A01G401200 chr5B 89.410 576 37 6 143 718 542939340 542939891 0.000000e+00 704
17 TraesCS7A01G401200 chr5B 84.014 294 35 7 2444 2731 433291463 433291750 7.250000e-69 272
18 TraesCS7A01G401200 chr3A 88.946 588 41 8 143 730 457933136 457932573 0.000000e+00 704
19 TraesCS7A01G401200 chr3A 88.571 560 40 8 143 702 708638949 708638414 0.000000e+00 658
20 TraesCS7A01G401200 chr3A 84.539 304 34 8 2435 2731 514468952 514469249 7.200000e-74 289
21 TraesCS7A01G401200 chr3A 89.474 152 13 3 2960 3110 53566341 53566490 7.520000e-44 189
22 TraesCS7A01G401200 chr6B 89.217 575 38 6 144 718 35029978 35030528 0.000000e+00 697
23 TraesCS7A01G401200 chrUn 88.605 588 43 6 143 730 286006747 286006184 0.000000e+00 693
24 TraesCS7A01G401200 chr6A 88.605 588 43 8 143 730 83603522 83602959 0.000000e+00 693
25 TraesCS7A01G401200 chr6A 88.750 560 39 8 143 702 83604667 83604132 0.000000e+00 664
26 TraesCS7A01G401200 chr6A 88.689 557 39 8 143 699 360474567 360475099 0.000000e+00 658
27 TraesCS7A01G401200 chr6A 88.561 542 38 8 143 684 454428558 454428041 2.230000e-178 636
28 TraesCS7A01G401200 chr6A 87.153 576 34 12 143 718 360475712 360476247 8.090000e-173 617
29 TraesCS7A01G401200 chr4A 89.062 576 38 7 143 718 309239850 309240400 0.000000e+00 691
30 TraesCS7A01G401200 chr4A 91.429 140 12 0 2966 3105 37306862 37307001 5.810000e-45 193
31 TraesCS7A01G401200 chr2B 86.224 588 41 7 143 730 132502871 132503418 8.150000e-168 601
32 TraesCS7A01G401200 chr1B 86.577 298 28 7 2440 2731 608861021 608860730 9.190000e-83 318
33 TraesCS7A01G401200 chr2A 85.235 298 32 7 2440 2731 755718916 755718625 4.300000e-76 296
34 TraesCS7A01G401200 chr1D 85.714 231 26 2 2450 2677 413723467 413723693 2.650000e-58 237
35 TraesCS7A01G401200 chr1D 91.971 137 11 0 2969 3105 103408717 103408853 5.810000e-45 193
36 TraesCS7A01G401200 chr1A 83.404 235 32 2 2450 2681 510536824 510537054 1.600000e-50 211
37 TraesCS7A01G401200 chr3D 93.284 134 9 0 2970 3103 87926000 87926133 1.250000e-46 198
38 TraesCS7A01G401200 chr3D 91.489 141 12 0 2968 3108 588123711 588123571 1.620000e-45 195
39 TraesCS7A01G401200 chr6D 89.333 150 12 4 2957 3104 287890191 287890338 9.720000e-43 185


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 TraesCS7A01G401200 chr7A 580665616 580671297 5681 True 5093.000000 8837 100.000000 1 5682 2 chr7A.!!$R1 5681
1 TraesCS7A01G401200 chr7B 538222533 538226899 4366 True 3113.500000 5528 93.305000 898 5241 2 chr7B.!!$R2 4343
2 TraesCS7A01G401200 chr7B 2223676 2224226 550 False 691.000000 691 89.062000 143 718 1 chr7B.!!$F1 575
3 TraesCS7A01G401200 chr7B 412898346 412898908 562 True 691.000000 691 88.586000 144 730 1 chr7B.!!$R1 586
4 TraesCS7A01G401200 chr7D 509923753 509929776 6023 True 2301.666667 5432 89.684667 898 5682 3 chr7D.!!$R2 4784
5 TraesCS7A01G401200 chr4B 491042253 491042981 728 False 1314.000000 1314 99.178000 1 730 1 chr4B.!!$F2 729
6 TraesCS7A01G401200 chr4B 448796065 448796701 636 False 616.000000 616 84.226000 1 666 1 chr4B.!!$F1 665
7 TraesCS7A01G401200 chr3B 688394961 688395690 729 False 1310.000000 1310 99.041000 1 730 1 chr3B.!!$F1 729
8 TraesCS7A01G401200 chr5B 542939340 542939891 551 False 704.000000 704 89.410000 143 718 1 chr5B.!!$F2 575
9 TraesCS7A01G401200 chr3A 457932573 457933136 563 True 704.000000 704 88.946000 143 730 1 chr3A.!!$R1 587
10 TraesCS7A01G401200 chr3A 708638414 708638949 535 True 658.000000 658 88.571000 143 702 1 chr3A.!!$R2 559
11 TraesCS7A01G401200 chr6B 35029978 35030528 550 False 697.000000 697 89.217000 144 718 1 chr6B.!!$F1 574
12 TraesCS7A01G401200 chrUn 286006184 286006747 563 True 693.000000 693 88.605000 143 730 1 chrUn.!!$R1 587
13 TraesCS7A01G401200 chr6A 83602959 83604667 1708 True 678.500000 693 88.677500 143 730 2 chr6A.!!$R2 587
14 TraesCS7A01G401200 chr6A 360474567 360476247 1680 False 637.500000 658 87.921000 143 718 2 chr6A.!!$F1 575
15 TraesCS7A01G401200 chr6A 454428041 454428558 517 True 636.000000 636 88.561000 143 684 1 chr6A.!!$R1 541
16 TraesCS7A01G401200 chr4A 309239850 309240400 550 False 691.000000 691 89.062000 143 718 1 chr4A.!!$F2 575
17 TraesCS7A01G401200 chr2B 132502871 132503418 547 False 601.000000 601 86.224000 143 730 1 chr2B.!!$F1 587

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
973 2134 0.535102 CACACAGGAACACCACTCCC 60.535 60.0 0.00 0.0 32.95 4.30 F
1561 2777 0.522180 AGCCACTCGACTTACTCACG 59.478 55.0 0.00 0.0 0.00 4.35 F
2216 3488 0.537371 AAAGGTTCTTGGCGGACAGG 60.537 55.0 0.00 0.0 0.00 4.00 F
2288 4846 0.803768 GCGATCAGTGCGACAGATGT 60.804 55.0 0.00 0.0 0.00 3.06 F
2914 5476 1.028905 TTGCCAACTTGGAGTTTCCG 58.971 50.0 12.37 0.0 40.96 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2411 4969 0.323360 TATGCCCTCACAAACCTGGC 60.323 55.0 0.0 0.00 42.49 4.85 R
2575 5133 0.874390 GTGATGCAGCGAGGTTTCAA 59.126 50.0 0.0 0.00 0.00 2.69 R
3751 6337 0.250467 GCTCCTGCAGGAACAGTTGA 60.250 55.0 34.3 11.53 44.91 3.18 R
3752 6338 0.250640 AGCTCCTGCAGGAACAGTTG 60.251 55.0 34.3 22.67 44.91 3.16 R
4870 7464 0.622665 AGGCATCTCCAACTCCCAAG 59.377 55.0 0.0 0.00 37.29 3.61 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
408 423 4.838904 AACCCCTCTCTATAACAACCAC 57.161 45.455 0.00 0.00 0.00 4.16
961 2122 2.159627 GGAAGAAATACACGCACACAGG 59.840 50.000 0.00 0.00 0.00 4.00
973 2134 0.535102 CACACAGGAACACCACTCCC 60.535 60.000 0.00 0.00 32.95 4.30
974 2135 0.986019 ACACAGGAACACCACTCCCA 60.986 55.000 0.00 0.00 32.95 4.37
975 2136 0.535102 CACAGGAACACCACTCCCAC 60.535 60.000 0.00 0.00 32.95 4.61
976 2137 1.073199 CAGGAACACCACTCCCACC 59.927 63.158 0.00 0.00 32.95 4.61
977 2138 2.032071 GGAACACCACTCCCACCG 59.968 66.667 0.00 0.00 0.00 4.94
979 2140 4.619227 AACACCACTCCCACCGCG 62.619 66.667 0.00 0.00 0.00 6.46
993 2154 2.104331 CGCGTTCTATCGGCTGGT 59.896 61.111 0.00 0.00 0.00 4.00
995 2156 1.153628 GCGTTCTATCGGCTGGTGT 60.154 57.895 0.00 0.00 0.00 4.16
1004 2165 3.127533 GGCTGGTGTGGCGATGTC 61.128 66.667 0.00 0.00 0.00 3.06
1294 2455 4.142182 CCCGCACCACTTGATTTTTGATAT 60.142 41.667 0.00 0.00 0.00 1.63
1323 2484 5.389642 ACGCATTATTACATGACGAACTG 57.610 39.130 0.00 0.00 31.94 3.16
1325 2486 4.318760 CGCATTATTACATGACGAACTGGG 60.319 45.833 0.00 0.00 0.00 4.45
1384 2546 1.454847 TGCGTTGGGGCAAAGACTT 60.455 52.632 0.00 0.00 40.59 3.01
1402 2564 1.075536 CTTGGGAGGGTTTGGCTAACT 59.924 52.381 11.41 0.00 36.93 2.24
1420 2582 1.085893 CTGTTGCTGTGTGTGTGTGA 58.914 50.000 0.00 0.00 0.00 3.58
1422 2584 1.338579 TGTTGCTGTGTGTGTGTGAGA 60.339 47.619 0.00 0.00 0.00 3.27
1423 2585 1.942657 GTTGCTGTGTGTGTGTGAGAT 59.057 47.619 0.00 0.00 0.00 2.75
1424 2586 1.585297 TGCTGTGTGTGTGTGAGATG 58.415 50.000 0.00 0.00 0.00 2.90
1440 2656 1.837439 AGATGTCCCCTTGATTGCGTA 59.163 47.619 0.00 0.00 0.00 4.42
1473 2689 1.202770 ACGACTCAAAGTCAAAGGGGG 60.203 52.381 7.78 0.00 45.30 5.40
1495 2711 3.067040 GGGAGAGTACGAGGAGAATTCAC 59.933 52.174 8.44 0.52 0.00 3.18
1516 2732 7.430992 TCACAACTGATTTCAATCTTCAGAG 57.569 36.000 6.19 1.69 39.36 3.35
1519 2735 7.802251 CACAACTGATTTCAATCTTCAGAGTTC 59.198 37.037 6.19 0.00 39.36 3.01
1520 2736 7.718753 ACAACTGATTTCAATCTTCAGAGTTCT 59.281 33.333 6.19 0.00 39.36 3.01
1521 2737 7.670009 ACTGATTTCAATCTTCAGAGTTCTG 57.330 36.000 6.19 2.69 39.36 3.02
1522 2738 6.654161 ACTGATTTCAATCTTCAGAGTTCTGG 59.346 38.462 9.13 0.00 39.36 3.86
1523 2739 5.413833 TGATTTCAATCTTCAGAGTTCTGGC 59.586 40.000 9.13 0.00 39.01 4.85
1524 2740 4.630644 TTCAATCTTCAGAGTTCTGGCT 57.369 40.909 9.13 0.00 43.91 4.75
1525 2741 4.630644 TCAATCTTCAGAGTTCTGGCTT 57.369 40.909 9.13 0.00 43.91 4.35
1526 2742 4.321718 TCAATCTTCAGAGTTCTGGCTTG 58.678 43.478 9.13 7.93 43.91 4.01
1539 2755 0.746063 TGGCTTGGTTTGCTTCAGTG 59.254 50.000 0.00 0.00 0.00 3.66
1556 2772 1.699343 GTGACAGCCACTCGACTTAC 58.301 55.000 0.00 0.00 42.44 2.34
1557 2773 1.269998 GTGACAGCCACTCGACTTACT 59.730 52.381 0.00 0.00 42.44 2.24
1559 2775 1.540267 GACAGCCACTCGACTTACTCA 59.460 52.381 0.00 0.00 0.00 3.41
1560 2776 1.269998 ACAGCCACTCGACTTACTCAC 59.730 52.381 0.00 0.00 0.00 3.51
1561 2777 0.522180 AGCCACTCGACTTACTCACG 59.478 55.000 0.00 0.00 0.00 4.35
1576 2799 0.675208 TCACGCCACACACACAACTT 60.675 50.000 0.00 0.00 0.00 2.66
1577 2800 1.010580 CACGCCACACACACAACTTA 58.989 50.000 0.00 0.00 0.00 2.24
1578 2801 1.003972 CACGCCACACACACAACTTAG 60.004 52.381 0.00 0.00 0.00 2.18
1579 2802 1.295792 CGCCACACACACAACTTAGT 58.704 50.000 0.00 0.00 0.00 2.24
1580 2803 1.668751 CGCCACACACACAACTTAGTT 59.331 47.619 0.00 0.00 0.00 2.24
1632 2856 2.757099 CCTTGCTGGATGGCACCC 60.757 66.667 0.00 0.00 42.27 4.61
1638 2862 1.626356 GCTGGATGGCACCCTCACTA 61.626 60.000 0.00 0.00 0.00 2.74
1644 2868 2.684001 TGGCACCCTCACTATTTACG 57.316 50.000 0.00 0.00 0.00 3.18
1650 2874 3.128242 CACCCTCACTATTTACGTCTCGT 59.872 47.826 0.00 0.00 44.35 4.18
1654 2878 4.036498 CCTCACTATTTACGTCTCGTCCAT 59.964 45.833 0.00 0.00 41.54 3.41
1655 2879 4.916870 TCACTATTTACGTCTCGTCCATG 58.083 43.478 0.00 0.00 41.54 3.66
1656 2880 4.397103 TCACTATTTACGTCTCGTCCATGT 59.603 41.667 0.00 0.00 41.54 3.21
1657 2881 4.733887 CACTATTTACGTCTCGTCCATGTC 59.266 45.833 0.00 0.00 41.54 3.06
1658 2882 2.642139 TTTACGTCTCGTCCATGTCC 57.358 50.000 0.00 0.00 41.54 4.02
1659 2883 1.536940 TTACGTCTCGTCCATGTCCA 58.463 50.000 0.00 0.00 41.54 4.02
1670 2894 2.435805 GTCCATGTCCATAGCCTGAGAA 59.564 50.000 0.00 0.00 0.00 2.87
1750 2974 6.912051 GCAAATTGAGGTTGAAATTTTGGTTC 59.088 34.615 0.00 0.00 34.55 3.62
1759 2983 7.812669 AGGTTGAAATTTTGGTTCATTCGTATC 59.187 33.333 0.00 0.00 35.03 2.24
1760 2984 7.596995 GGTTGAAATTTTGGTTCATTCGTATCA 59.403 33.333 0.00 0.00 35.03 2.15
1802 3026 2.480037 CGTGCTGCACTATCAAGTTTGA 59.520 45.455 28.04 0.00 35.37 2.69
1809 3033 6.241207 TGCACTATCAAGTTTGAAAGTAGC 57.759 37.500 0.00 1.73 41.13 3.58
1871 3101 2.604046 TGCTTCGGAGAATAAGGAGC 57.396 50.000 0.00 0.00 45.90 4.70
1909 3145 5.419788 TGTTGCATAGCTTCTGAAAATCCAT 59.580 36.000 0.00 0.00 0.00 3.41
1913 3149 3.744940 AGCTTCTGAAAATCCATCCCA 57.255 42.857 0.00 0.00 0.00 4.37
1914 3150 4.261411 AGCTTCTGAAAATCCATCCCAT 57.739 40.909 0.00 0.00 0.00 4.00
1916 3152 4.404715 AGCTTCTGAAAATCCATCCCATTG 59.595 41.667 0.00 0.00 0.00 2.82
1933 3169 3.211865 CATTGCTGACTGATGCAGGTAT 58.788 45.455 0.00 0.00 40.46 2.73
1939 3175 1.797046 GACTGATGCAGGTATCATGCG 59.203 52.381 0.52 0.00 46.87 4.73
2032 3268 4.863689 CAGACAGAGATATGCCAATCGATC 59.136 45.833 0.00 0.00 0.00 3.69
2090 3326 1.481772 ACACAATGCAGCAGGTTTGTT 59.518 42.857 9.70 1.21 30.23 2.83
2117 3353 1.269448 TGTTCAAGCCGCAATTTCCTC 59.731 47.619 0.00 0.00 0.00 3.71
2127 3369 1.402852 GCAATTTCCTCGCCCTGTTTC 60.403 52.381 0.00 0.00 0.00 2.78
2144 3386 5.390885 CCTGTTTCATGTTATCACAGGTTCG 60.391 44.000 16.63 0.00 46.50 3.95
2167 3439 1.902508 TCAAGGGCCTTACTCTGTCTG 59.097 52.381 20.44 3.86 0.00 3.51
2216 3488 0.537371 AAAGGTTCTTGGCGGACAGG 60.537 55.000 0.00 0.00 0.00 4.00
2288 4846 0.803768 GCGATCAGTGCGACAGATGT 60.804 55.000 0.00 0.00 0.00 3.06
2346 4904 2.124778 GCAAGGCAGGAGGAGCTC 60.125 66.667 4.71 4.71 0.00 4.09
2411 4969 5.331902 CATGTGCTTAACTTTTACCATCCG 58.668 41.667 0.00 0.00 0.00 4.18
2575 5133 1.360393 TGCCTGGTTGAAGGAAGGGT 61.360 55.000 0.00 0.00 40.02 4.34
2579 5137 2.424234 CCTGGTTGAAGGAAGGGTTGAA 60.424 50.000 0.00 0.00 40.02 2.69
2580 5138 3.295973 CTGGTTGAAGGAAGGGTTGAAA 58.704 45.455 0.00 0.00 0.00 2.69
2671 5229 1.434622 CCATCCATCTGAGCACGCAC 61.435 60.000 0.00 0.00 0.00 5.34
2682 5240 2.553602 TGAGCACGCACAGATTCATTTT 59.446 40.909 0.00 0.00 0.00 1.82
2716 5277 6.723298 TCTCCCATGTTTGTGTTAATGTTT 57.277 33.333 0.00 0.00 0.00 2.83
2719 5280 6.276847 TCCCATGTTTGTGTTAATGTTTGTC 58.723 36.000 0.00 0.00 0.00 3.18
2720 5281 5.465056 CCCATGTTTGTGTTAATGTTTGTCC 59.535 40.000 0.00 0.00 0.00 4.02
2766 5327 2.434185 GTCTGGTTCGATGCGCCA 60.434 61.111 4.18 0.00 0.00 5.69
2790 5351 1.531149 GGATACATTTCCATCACGGCG 59.469 52.381 4.80 4.80 35.72 6.46
2914 5476 1.028905 TTGCCAACTTGGAGTTTCCG 58.971 50.000 12.37 0.00 40.96 4.30
3027 5589 9.367444 GGAGATTTTAATATGGACTACATACGG 57.633 37.037 0.00 0.00 44.41 4.02
3276 5860 7.212976 TGGACTCTGATGAAGAATATTAGTGC 58.787 38.462 0.00 0.00 33.37 4.40
3309 5893 7.767250 ATCTCAACTATGAATCAGGTATCGA 57.233 36.000 0.00 0.00 34.49 3.59
3350 5936 8.424133 GGCCATTATTTATTCTTGGACATCTTT 58.576 33.333 0.00 0.00 35.45 2.52
3351 5937 9.822185 GCCATTATTTATTCTTGGACATCTTTT 57.178 29.630 0.00 0.00 0.00 2.27
3605 6191 2.162681 CAGTTTTCACATGGGGAGGTC 58.837 52.381 0.00 0.00 0.00 3.85
3820 6406 6.974932 CACCTAATGCTGATATACATCCAC 57.025 41.667 0.00 0.00 0.00 4.02
3844 6430 4.517832 TGAGTCAGTCGTTAGCAGAAACTA 59.482 41.667 0.00 0.00 0.00 2.24
3916 6502 3.914426 AACCTGAACTGTGTGAACTCT 57.086 42.857 0.00 0.00 0.00 3.24
4569 7163 4.032960 TCATCCCTTGTATGTTTGCTGT 57.967 40.909 0.00 0.00 0.00 4.40
4590 7184 2.154462 CTTCATTTCCTTGACGCCTGT 58.846 47.619 0.00 0.00 0.00 4.00
4623 7217 2.422479 CACAGAAAGATGATGCAGTGGG 59.578 50.000 0.00 0.00 0.00 4.61
4678 7272 2.664698 CGAAAGAAACGCAAGGGCTAAC 60.665 50.000 0.00 0.00 46.39 2.34
4680 7274 1.523758 AGAAACGCAAGGGCTAACTG 58.476 50.000 0.00 0.00 46.39 3.16
4682 7276 1.197036 GAAACGCAAGGGCTAACTGAC 59.803 52.381 0.00 0.00 46.39 3.51
4745 7339 8.752766 AATATTTCTTGCAAAGTTGATCACAG 57.247 30.769 0.00 0.00 46.34 3.66
4870 7464 7.596749 ACATAAACTGAACTACATGCTGTAC 57.403 36.000 0.00 0.00 0.00 2.90
5044 7641 3.062763 CGTCATCAAGCTCACAGAACTT 58.937 45.455 0.00 0.00 0.00 2.66
5111 7708 4.423625 AGGTGATAAGCCTGGTATTGAC 57.576 45.455 0.00 0.00 34.56 3.18
5133 7730 5.291971 ACTTGCAGATTTTTGATGTTCCAC 58.708 37.500 0.00 0.00 0.00 4.02
5317 7914 2.803492 CGTATGACCCAAGCTAAGCTCC 60.803 54.545 0.00 0.00 38.25 4.70
5335 7932 1.549620 TCCGCAATTGCATTGTTCCAT 59.450 42.857 28.77 0.00 42.20 3.41
5343 7940 6.568844 GCAATTGCATTGTTCCATGATTTGTT 60.569 34.615 25.36 0.00 42.20 2.83
5344 7941 7.364200 CAATTGCATTGTTCCATGATTTGTTT 58.636 30.769 0.00 0.00 35.57 2.83
5345 7942 5.926214 TGCATTGTTCCATGATTTGTTTG 57.074 34.783 0.00 0.00 0.00 2.93
5346 7943 4.213694 TGCATTGTTCCATGATTTGTTTGC 59.786 37.500 0.00 0.00 0.00 3.68
5347 7944 4.213694 GCATTGTTCCATGATTTGTTTGCA 59.786 37.500 0.00 0.00 0.00 4.08
5348 7945 5.106475 GCATTGTTCCATGATTTGTTTGCAT 60.106 36.000 0.00 0.00 0.00 3.96
5349 7946 6.568844 GCATTGTTCCATGATTTGTTTGCATT 60.569 34.615 0.00 0.00 0.00 3.56
5350 7947 7.361031 GCATTGTTCCATGATTTGTTTGCATTA 60.361 33.333 0.00 0.00 0.00 1.90
5351 7948 7.655236 TTGTTCCATGATTTGTTTGCATTAG 57.345 32.000 0.00 0.00 0.00 1.73
5352 7949 6.164876 TGTTCCATGATTTGTTTGCATTAGG 58.835 36.000 0.00 0.00 0.00 2.69
5402 8006 7.437862 GCATGAACTTTTGTCTTTAAACATCCA 59.562 33.333 0.00 0.00 0.00 3.41
5447 8051 4.277921 TGCATGAAACAGTATTGCAACAGA 59.722 37.500 0.00 0.00 40.11 3.41
5452 8056 8.767085 CATGAAACAGTATTGCAACAGAATTTT 58.233 29.630 0.00 0.00 0.00 1.82
5496 8100 1.073923 ACACCTCAAATCCACCCACTC 59.926 52.381 0.00 0.00 0.00 3.51
5507 8111 2.756760 TCCACCCACTCGAGTACAATAC 59.243 50.000 19.57 0.00 0.00 1.89
5520 8124 0.991920 ACAATACTGTGGTGGGGGAG 59.008 55.000 0.00 0.00 33.30 4.30
5540 8144 1.002624 TGGTCGATTGGGCTGTTCC 60.003 57.895 0.00 0.00 0.00 3.62
5548 8152 2.359975 GGGCTGTTCCACCTTCCG 60.360 66.667 0.00 0.00 36.21 4.30
5619 8223 2.613691 TGGCGTACTTAGCAAGTTAGC 58.386 47.619 6.82 11.16 42.81 3.09
5670 8274 2.157668 TGAGAAATTCGAAGCAGCGTTC 59.842 45.455 3.35 0.81 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
557 573 7.758076 ACTTTCCTAACTTTTTCAAAGTTTCCG 59.242 33.333 17.41 8.54 40.58 4.30
961 2122 2.668550 GCGGTGGGAGTGGTGTTC 60.669 66.667 0.00 0.00 0.00 3.18
976 2137 2.104331 ACCAGCCGATAGAACGCG 59.896 61.111 3.53 3.53 39.76 6.01
977 2138 1.153628 ACACCAGCCGATAGAACGC 60.154 57.895 0.00 0.00 39.76 4.84
979 2140 1.090052 GCCACACCAGCCGATAGAAC 61.090 60.000 0.00 0.00 39.76 3.01
980 2141 1.220749 GCCACACCAGCCGATAGAA 59.779 57.895 0.00 0.00 39.76 2.10
990 2151 2.048597 GACGACATCGCCACACCA 60.049 61.111 0.14 0.00 44.43 4.17
1015 2176 4.778143 CACCTTCGCCTTCCCCGG 62.778 72.222 0.00 0.00 0.00 5.73
1245 2406 0.534412 ACTTGTCGCAGATCTCCAGG 59.466 55.000 0.00 0.00 40.67 4.45
1317 2478 1.688772 TAGCCTACTAGCCCAGTTCG 58.311 55.000 0.00 0.00 38.80 3.95
1323 2484 3.008485 AGCATCATTTAGCCTACTAGCCC 59.992 47.826 0.00 0.00 0.00 5.19
1325 2486 4.636249 ACAGCATCATTTAGCCTACTAGC 58.364 43.478 0.00 0.00 0.00 3.42
1378 2540 0.178961 GCCAAACCCTCCCAAGTCTT 60.179 55.000 0.00 0.00 0.00 3.01
1380 2542 0.696501 TAGCCAAACCCTCCCAAGTC 59.303 55.000 0.00 0.00 0.00 3.01
1384 2546 0.404040 CAGTTAGCCAAACCCTCCCA 59.596 55.000 0.00 0.00 39.03 4.37
1402 2564 1.085893 CTCACACACACACAGCAACA 58.914 50.000 0.00 0.00 0.00 3.33
1420 2582 0.620556 ACGCAATCAAGGGGACATCT 59.379 50.000 0.00 0.00 0.00 2.90
1422 2584 2.643551 CTTACGCAATCAAGGGGACAT 58.356 47.619 0.00 0.00 0.00 3.06
1423 2585 1.339631 CCTTACGCAATCAAGGGGACA 60.340 52.381 0.00 0.00 38.12 4.02
1424 2586 1.065709 TCCTTACGCAATCAAGGGGAC 60.066 52.381 0.79 0.00 41.47 4.46
1440 2656 4.939052 TTGAGTCGTCTTCTTCTTCCTT 57.061 40.909 0.00 0.00 0.00 3.36
1473 2689 3.067040 GTGAATTCTCCTCGTACTCTCCC 59.933 52.174 7.05 0.00 0.00 4.30
1474 2690 3.695060 TGTGAATTCTCCTCGTACTCTCC 59.305 47.826 7.05 0.00 0.00 3.71
1475 2691 4.966965 TGTGAATTCTCCTCGTACTCTC 57.033 45.455 7.05 0.00 0.00 3.20
1482 2698 5.409520 TGAAATCAGTTGTGAATTCTCCTCG 59.590 40.000 7.05 0.00 41.47 4.63
1495 2711 8.016229 CAGAACTCTGAAGATTGAAATCAGTTG 58.984 37.037 0.03 0.00 46.59 3.16
1516 2732 1.408702 TGAAGCAAACCAAGCCAGAAC 59.591 47.619 0.00 0.00 0.00 3.01
1519 2735 1.035139 ACTGAAGCAAACCAAGCCAG 58.965 50.000 0.00 0.00 0.00 4.85
1520 2736 0.746063 CACTGAAGCAAACCAAGCCA 59.254 50.000 0.00 0.00 0.00 4.75
1521 2737 1.032014 TCACTGAAGCAAACCAAGCC 58.968 50.000 0.00 0.00 0.00 4.35
1522 2738 1.405105 TGTCACTGAAGCAAACCAAGC 59.595 47.619 0.00 0.00 0.00 4.01
1523 2739 2.542411 GCTGTCACTGAAGCAAACCAAG 60.542 50.000 7.80 0.00 39.31 3.61
1524 2740 1.405105 GCTGTCACTGAAGCAAACCAA 59.595 47.619 7.80 0.00 39.31 3.67
1525 2741 1.024271 GCTGTCACTGAAGCAAACCA 58.976 50.000 7.80 0.00 39.31 3.67
1526 2742 0.312102 GGCTGTCACTGAAGCAAACC 59.688 55.000 12.41 0.00 41.36 3.27
1539 2755 1.540267 TGAGTAAGTCGAGTGGCTGTC 59.460 52.381 0.00 0.00 0.00 3.51
1548 2764 0.039798 GTGTGGCGTGAGTAAGTCGA 60.040 55.000 0.00 0.00 0.00 4.20
1555 2771 1.078778 TTGTGTGTGTGGCGTGAGT 60.079 52.632 0.00 0.00 0.00 3.41
1556 2772 1.089481 AGTTGTGTGTGTGGCGTGAG 61.089 55.000 0.00 0.00 0.00 3.51
1557 2773 0.675208 AAGTTGTGTGTGTGGCGTGA 60.675 50.000 0.00 0.00 0.00 4.35
1559 2775 1.295792 CTAAGTTGTGTGTGTGGCGT 58.704 50.000 0.00 0.00 0.00 5.68
1560 2776 1.295792 ACTAAGTTGTGTGTGTGGCG 58.704 50.000 0.00 0.00 0.00 5.69
1561 2777 3.875134 AGTAACTAAGTTGTGTGTGTGGC 59.125 43.478 0.00 0.00 0.00 5.01
1576 2799 1.259609 CCGGGTGGTGTGAGTAACTA 58.740 55.000 0.00 0.00 0.00 2.24
1577 2800 2.055299 CCGGGTGGTGTGAGTAACT 58.945 57.895 0.00 0.00 0.00 2.24
1578 2801 1.670083 GCCGGGTGGTGTGAGTAAC 60.670 63.158 2.18 0.00 37.67 2.50
1579 2802 2.745037 GCCGGGTGGTGTGAGTAA 59.255 61.111 2.18 0.00 37.67 2.24
1580 2803 3.687102 CGCCGGGTGGTGTGAGTA 61.687 66.667 2.18 0.00 41.05 2.59
1602 2825 1.221840 GCAAGGGAGAAGATCGGCA 59.778 57.895 0.00 0.00 0.00 5.69
1632 2856 4.611310 TGGACGAGACGTAAATAGTGAG 57.389 45.455 0.00 0.00 41.37 3.51
1638 2862 2.494471 TGGACATGGACGAGACGTAAAT 59.506 45.455 0.00 0.00 41.37 1.40
1644 2868 1.269831 GGCTATGGACATGGACGAGAC 60.270 57.143 0.00 0.00 0.00 3.36
1650 2874 2.477104 TCTCAGGCTATGGACATGGA 57.523 50.000 0.00 0.00 0.00 3.41
1654 2878 2.497675 GTCACTTCTCAGGCTATGGACA 59.502 50.000 0.00 0.00 0.00 4.02
1655 2879 2.497675 TGTCACTTCTCAGGCTATGGAC 59.502 50.000 0.00 0.00 0.00 4.02
1656 2880 2.762887 CTGTCACTTCTCAGGCTATGGA 59.237 50.000 0.00 0.00 0.00 3.41
1657 2881 2.499289 ACTGTCACTTCTCAGGCTATGG 59.501 50.000 0.00 0.00 36.17 2.74
1658 2882 3.056250 ACACTGTCACTTCTCAGGCTATG 60.056 47.826 0.00 0.00 36.17 2.23
1659 2883 3.056250 CACACTGTCACTTCTCAGGCTAT 60.056 47.826 0.00 0.00 36.17 2.97
1670 2894 6.437477 TCTCCACTAAATATCACACTGTCACT 59.563 38.462 0.00 0.00 0.00 3.41
1750 2974 0.319900 CCGCCCCTCTGATACGAATG 60.320 60.000 0.00 0.00 0.00 2.67
1759 2983 1.121407 TCATCCATACCGCCCCTCTG 61.121 60.000 0.00 0.00 0.00 3.35
1760 2984 0.178891 ATCATCCATACCGCCCCTCT 60.179 55.000 0.00 0.00 0.00 3.69
1802 3026 5.473066 AATCCAAATTGCAGTGCTACTTT 57.527 34.783 17.60 10.08 0.00 2.66
1846 3070 4.096382 TCCTTATTCTCCGAAGCAATTTGC 59.904 41.667 13.55 13.55 45.46 3.68
1858 3088 2.858941 GTCGTTTCGCTCCTTATTCTCC 59.141 50.000 0.00 0.00 0.00 3.71
1867 3097 0.716108 CACAGATGTCGTTTCGCTCC 59.284 55.000 0.00 0.00 0.00 4.70
1871 3101 1.260297 TGCAACACAGATGTCGTTTCG 59.740 47.619 0.00 0.00 38.45 3.46
1909 3145 0.328926 TGCATCAGTCAGCAATGGGA 59.671 50.000 0.00 0.00 37.90 4.37
1913 3149 3.118149 TGATACCTGCATCAGTCAGCAAT 60.118 43.478 0.00 0.00 40.73 3.56
1914 3150 2.236893 TGATACCTGCATCAGTCAGCAA 59.763 45.455 0.00 0.00 40.73 3.91
1916 3152 2.609427 TGATACCTGCATCAGTCAGC 57.391 50.000 0.00 0.00 31.34 4.26
1933 3169 1.278985 ACTTCCTTGTGGATCGCATGA 59.721 47.619 0.00 0.00 42.81 3.07
1939 3175 3.056749 ACTCGTACACTTCCTTGTGGATC 60.057 47.826 0.00 0.00 42.81 3.36
2032 3268 1.679139 TGTCCAGCAGTTTGTGGAAG 58.321 50.000 0.00 0.00 44.58 3.46
2117 3353 2.746904 TGTGATAACATGAAACAGGGCG 59.253 45.455 0.00 0.00 0.00 6.13
2127 3369 3.684305 TGAAGCGAACCTGTGATAACATG 59.316 43.478 0.00 0.00 0.00 3.21
2144 3386 1.003696 ACAGAGTAAGGCCCTTGAAGC 59.996 52.381 6.16 0.00 0.00 3.86
2187 3459 4.276058 CCAAGAACCTTTGGCATGATTT 57.724 40.909 0.00 0.00 41.02 2.17
2216 3488 2.740714 GCATGAGCCCACGACGAAC 61.741 63.158 0.00 0.00 33.58 3.95
2288 4846 0.405198 TTGAATTCAGCAGCCTCCCA 59.595 50.000 8.41 0.00 0.00 4.37
2346 4904 3.922171 AGAGCCAAATAGAACTGGAGG 57.078 47.619 0.00 0.00 34.35 4.30
2411 4969 0.323360 TATGCCCTCACAAACCTGGC 60.323 55.000 0.00 0.00 42.49 4.85
2575 5133 0.874390 GTGATGCAGCGAGGTTTCAA 59.126 50.000 0.00 0.00 0.00 2.69
2579 5137 1.376424 CTGGTGATGCAGCGAGGTT 60.376 57.895 0.00 0.00 34.27 3.50
2580 5138 2.267006 CTGGTGATGCAGCGAGGT 59.733 61.111 0.00 0.00 34.27 3.85
2671 5229 9.578439 GGAGATAAACTTTCCAAAATGAATCTG 57.422 33.333 0.00 0.00 0.00 2.90
2682 5240 6.015519 CACAAACATGGGAGATAAACTTTCCA 60.016 38.462 0.00 0.00 36.93 3.53
2716 5277 3.245193 TGAACCCATTCATCACATGGACA 60.245 43.478 0.00 0.00 43.70 4.02
2719 5280 2.691526 CCTGAACCCATTCATCACATGG 59.308 50.000 0.00 0.00 43.92 3.66
2720 5281 3.129813 CACCTGAACCCATTCATCACATG 59.870 47.826 0.00 0.00 43.92 3.21
2766 5327 4.065088 CCGTGATGGAAATGTATCCGATT 58.935 43.478 0.00 0.00 42.76 3.34
2775 5336 1.226379 GCACGCCGTGATGGAAATG 60.226 57.895 23.33 0.00 42.00 2.32
2802 5363 1.217916 TCCACCACTTTTCCCACTCA 58.782 50.000 0.00 0.00 0.00 3.41
3027 5589 8.976986 AAAGTGTAGATTCATTCATTTTGCTC 57.023 30.769 0.00 0.00 0.00 4.26
3080 5653 8.907885 GCCCTTTTAGAGATTTCAATATGAACT 58.092 33.333 0.00 0.00 35.89 3.01
3081 5654 8.907885 AGCCCTTTTAGAGATTTCAATATGAAC 58.092 33.333 0.00 0.00 35.89 3.18
3085 5658 9.525826 CCATAGCCCTTTTAGAGATTTCAATAT 57.474 33.333 0.00 0.00 0.00 1.28
3276 5860 9.127006 CTGATTCATAGTTGAGATATTCAGTCG 57.873 37.037 0.00 0.00 37.07 4.18
3357 5943 4.002982 TGTGCATGATAACAGAGTGAACC 58.997 43.478 0.00 0.00 0.00 3.62
3605 6191 5.469373 TCGTTGTTATGCTTTATCTGCAG 57.531 39.130 7.63 7.63 44.04 4.41
3724 6310 3.848272 AAAATATCAGCACCACCAACG 57.152 42.857 0.00 0.00 0.00 4.10
3751 6337 0.250467 GCTCCTGCAGGAACAGTTGA 60.250 55.000 34.30 11.53 44.91 3.18
3752 6338 0.250640 AGCTCCTGCAGGAACAGTTG 60.251 55.000 34.30 22.67 44.91 3.16
3754 6340 1.374190 CAGCTCCTGCAGGAACAGT 59.626 57.895 34.30 17.08 44.91 3.55
3755 6341 4.298009 CAGCTCCTGCAGGAACAG 57.702 61.111 34.30 23.79 44.91 3.16
3820 6406 3.560902 TTCTGCTAACGACTGACTCAG 57.439 47.619 4.36 4.36 37.52 3.35
4569 7163 2.224523 ACAGGCGTCAAGGAAATGAAGA 60.225 45.455 0.00 0.00 31.49 2.87
4590 7184 5.184287 TCATCTTTCTGTGTATGGTGTACGA 59.816 40.000 0.00 0.00 0.00 3.43
4623 7217 3.255642 TGCAAATGTTTCCCTGAAGCTAC 59.744 43.478 0.00 0.00 0.00 3.58
4678 7272 1.528586 CAACTTCACTGGCTTCGTCAG 59.471 52.381 0.00 0.00 41.54 3.51
4680 7274 1.583054 ACAACTTCACTGGCTTCGTC 58.417 50.000 0.00 0.00 0.00 4.20
4682 7276 1.597937 GCAACAACTTCACTGGCTTCG 60.598 52.381 0.00 0.00 0.00 3.79
4690 7284 3.211045 TCCAGTTAGGCAACAACTTCAC 58.789 45.455 0.00 0.00 36.31 3.18
4870 7464 0.622665 AGGCATCTCCAACTCCCAAG 59.377 55.000 0.00 0.00 37.29 3.61
5044 7641 1.310904 GACCCAAGCACGTTTACCAA 58.689 50.000 0.00 0.00 0.00 3.67
5097 7694 2.040278 TCTGCAAGTCAATACCAGGCTT 59.960 45.455 0.00 0.00 33.76 4.35
5111 7708 5.291178 TGTGGAACATCAAAAATCTGCAAG 58.709 37.500 0.00 0.00 45.67 4.01
5297 7894 2.803492 CGGAGCTTAGCTTGGGTCATAC 60.803 54.545 8.58 0.00 39.88 2.39
5335 7932 5.076182 TCCTCACCTAATGCAAACAAATCA 58.924 37.500 0.00 0.00 0.00 2.57
5343 7940 6.959639 GGAATAAATCCTCACCTAATGCAA 57.040 37.500 0.00 0.00 45.56 4.08
5463 8067 7.054124 GGATTTGAGGTGTCCAATCATTACTA 58.946 38.462 2.69 0.00 36.82 1.82
5475 8079 1.073923 AGTGGGTGGATTTGAGGTGTC 59.926 52.381 0.00 0.00 0.00 3.67
5496 8100 2.418197 CCCCACCACAGTATTGTACTCG 60.418 54.545 0.00 0.00 36.76 4.18
5507 8111 3.650950 CCACCTCCCCCACCACAG 61.651 72.222 0.00 0.00 0.00 3.66
5520 8124 1.303317 AACAGCCCAATCGACCACC 60.303 57.895 0.00 0.00 0.00 4.61
5540 8144 4.202223 ACTGTATATGTTAGGCGGAAGGTG 60.202 45.833 0.00 0.00 0.00 4.00
5548 8152 9.712305 ATCAGAACAATACTGTATATGTTAGGC 57.288 33.333 19.06 12.14 36.22 3.93
5603 8207 5.634896 TGTACTCGCTAACTTGCTAAGTAC 58.365 41.667 15.54 15.54 41.91 2.73
5610 8214 9.790389 ATATCTAATATGTACTCGCTAACTTGC 57.210 33.333 0.00 0.00 0.00 4.01
5617 8221 9.790389 GCAAGTAATATCTAATATGTACTCGCT 57.210 33.333 0.00 0.00 0.00 4.93


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

AutoCloner maintained by Alex Coulton.