Multiple sequence alignment - TraesCS5D01G453000

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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 TraesCS5D01G453000 chr5D 100.000 4056 0 0 1 4056 500679998 500684053 0.000000e+00 7491.0
1 TraesCS5D01G453000 chr5D 80.114 699 98 23 1615 2297 500647038 500647711 2.190000e-132 483.0
2 TraesCS5D01G453000 chr5D 87.427 342 35 3 2344 2677 500647702 500648043 1.770000e-103 387.0
3 TraesCS5D01G453000 chr5D 81.263 475 63 16 886 1338 500646489 500646959 1.070000e-95 361.0
4 TraesCS5D01G453000 chr5D 84.401 359 53 2 2706 3061 500648156 500648514 2.320000e-92 350.0
5 TraesCS5D01G453000 chr5D 81.287 171 17 10 1350 1508 473469947 473469780 1.530000e-24 124.0
6 TraesCS5D01G453000 chr5B 90.696 2515 141 32 779 3220 622073137 622075631 0.000000e+00 3262.0
7 TraesCS5D01G453000 chr5B 95.200 625 16 9 157 777 622072415 622073029 0.000000e+00 976.0
8 TraesCS5D01G453000 chr5B 90.827 556 40 4 3502 4056 622323982 622324527 0.000000e+00 734.0
9 TraesCS5D01G453000 chr5B 80.974 657 94 14 1615 2252 622061454 622062098 3.640000e-135 492.0
10 TraesCS5D01G453000 chr5B 87.500 424 50 2 2248 2671 622063294 622063714 1.690000e-133 486.0
11 TraesCS5D01G453000 chr5B 84.807 362 47 7 2706 3061 622063835 622064194 1.390000e-94 357.0
12 TraesCS5D01G453000 chr5B 90.541 74 6 1 3453 3526 622075870 622075942 3.340000e-16 97.1
13 TraesCS5D01G453000 chr5A 91.902 1556 90 17 1707 3249 624966473 624964941 0.000000e+00 2143.0
14 TraesCS5D01G453000 chr5A 82.500 1240 162 31 1615 2815 627015414 627016637 0.000000e+00 1037.0
15 TraesCS5D01G453000 chr5A 89.835 787 41 15 567 1342 624967930 624967172 0.000000e+00 974.0
16 TraesCS5D01G453000 chr5A 92.593 621 29 8 3443 4056 624964810 624964200 0.000000e+00 876.0
17 TraesCS5D01G453000 chr5A 91.261 595 29 16 3476 4056 627025593 627026178 0.000000e+00 789.0
18 TraesCS5D01G453000 chr5A 80.122 493 58 25 884 1338 627014753 627015243 8.400000e-87 331.0
19 TraesCS5D01G453000 chr5A 84.836 244 30 6 1077 1315 680504704 680504463 5.240000e-59 239.0
20 TraesCS5D01G453000 chr5A 73.323 641 141 18 2002 2640 680532275 680531663 4.110000e-50 209.0
21 TraesCS5D01G453000 chr5A 82.960 223 38 0 2834 3056 627024655 627024877 6.870000e-48 202.0
22 TraesCS5D01G453000 chr5A 78.707 263 48 7 1077 1333 680764309 680764049 6.970000e-38 169.0
23 TraesCS5D01G453000 chr5A 82.822 163 13 11 1358 1508 451881968 451882127 9.150000e-27 132.0
24 TraesCS5D01G453000 chr5A 91.026 78 5 1 1541 1616 624967174 624967097 1.990000e-18 104.0
25 TraesCS5D01G453000 chr5A 75.758 198 43 3 1672 1865 680532597 680532401 1.200000e-15 95.3
26 TraesCS5D01G453000 chr4D 76.228 1384 229 61 1615 2968 499546980 499545667 3.420000e-180 641.0
27 TraesCS5D01G453000 chr4D 85.597 243 30 4 1077 1315 499504574 499504333 2.420000e-62 250.0
28 TraesCS5D01G453000 chr4D 84.783 138 21 0 2538 2675 499510318 499510181 5.470000e-29 139.0
29 TraesCS5D01G453000 chr4B 75.533 1455 246 62 1629 3057 642462802 642461432 7.450000e-172 614.0
30 TraesCS5D01G453000 chr4B 75.304 1069 201 35 1992 3044 642959323 642960344 1.720000e-123 453.0
31 TraesCS5D01G453000 chr4B 84.426 244 31 6 1077 1315 642458720 642458479 2.440000e-57 233.0
32 TraesCS5D01G453000 chr4B 78.599 257 47 8 1077 1326 642746619 642746874 3.240000e-36 163.0
33 TraesCS5D01G453000 chr7D 84.472 161 12 6 1350 1500 552186561 552186404 3.270000e-31 147.0
34 TraesCS5D01G453000 chr1D 83.041 171 14 11 1350 1508 100462071 100461904 1.520000e-29 141.0
35 TraesCS5D01G453000 chr7B 82.456 171 15 10 1350 1508 750566855 750567022 7.070000e-28 135.0
36 TraesCS5D01G453000 chr4A 81.871 171 17 11 1350 1508 491446566 491446734 9.150000e-27 132.0
37 TraesCS5D01G453000 chr4A 81.503 173 12 15 1350 1508 219185599 219185433 1.530000e-24 124.0
38 TraesCS5D01G453000 chr3A 81.657 169 18 10 1350 1508 717947572 717947737 1.180000e-25 128.0
39 TraesCS5D01G453000 chr6A 81.366 161 20 8 1350 1508 465441424 465441272 5.510000e-24 122.0


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 TraesCS5D01G453000 chr5D 500679998 500684053 4055 False 7491.000000 7491 100.000000 1 4056 1 chr5D.!!$F1 4055
1 TraesCS5D01G453000 chr5D 500646489 500648514 2025 False 395.250000 483 83.301250 886 3061 4 chr5D.!!$F2 2175
2 TraesCS5D01G453000 chr5B 622072415 622075942 3527 False 1445.033333 3262 92.145667 157 3526 3 chr5B.!!$F3 3369
3 TraesCS5D01G453000 chr5B 622323982 622324527 545 False 734.000000 734 90.827000 3502 4056 1 chr5B.!!$F1 554
4 TraesCS5D01G453000 chr5B 622061454 622064194 2740 False 445.000000 492 84.427000 1615 3061 3 chr5B.!!$F2 1446
5 TraesCS5D01G453000 chr5A 624964200 624967930 3730 True 1024.250000 2143 91.339000 567 4056 4 chr5A.!!$R3 3489
6 TraesCS5D01G453000 chr5A 627014753 627016637 1884 False 684.000000 1037 81.311000 884 2815 2 chr5A.!!$F2 1931
7 TraesCS5D01G453000 chr5A 627024655 627026178 1523 False 495.500000 789 87.110500 2834 4056 2 chr5A.!!$F3 1222
8 TraesCS5D01G453000 chr4D 499545667 499546980 1313 True 641.000000 641 76.228000 1615 2968 1 chr4D.!!$R3 1353
9 TraesCS5D01G453000 chr4B 642959323 642960344 1021 False 453.000000 453 75.304000 1992 3044 1 chr4B.!!$F2 1052
10 TraesCS5D01G453000 chr4B 642458479 642462802 4323 True 423.500000 614 79.979500 1077 3057 2 chr4B.!!$R1 1980

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
761 768 0.246635 TCAGGCGACTTGTTCCTAGC 59.753 55.000 0.00 0.00 40.21 3.42 F
1262 1426 1.461091 AACAGCGTCGACCTCCTCAA 61.461 55.000 10.58 0.00 0.00 3.02 F
1662 1973 1.064357 GTACTGCGACAGAGCTCCTAC 59.936 57.143 10.93 0.65 38.13 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1640 1951 0.179150 GGAGCTCTGTCGCAGTACTG 60.179 60.0 18.93 18.93 32.61 2.74 R
2798 5002 0.980423 AGGGACTGTTTCTCCAGCTC 59.020 55.0 0.00 0.00 37.18 4.09 R
3609 8063 0.109342 AGGGCCTCAACAGTCTTGTG 59.891 55.0 0.00 0.00 37.67 3.33 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
26 27 9.542462 CCAAATACGAGAAGGACTAATAAATGA 57.458 33.333 0.00 0.00 0.00 2.57
28 29 9.765795 AAATACGAGAAGGACTAATAAATGAGG 57.234 33.333 0.00 0.00 0.00 3.86
29 30 8.707796 ATACGAGAAGGACTAATAAATGAGGA 57.292 34.615 0.00 0.00 0.00 3.71
30 31 7.045126 ACGAGAAGGACTAATAAATGAGGAG 57.955 40.000 0.00 0.00 0.00 3.69
31 32 6.041069 ACGAGAAGGACTAATAAATGAGGAGG 59.959 42.308 0.00 0.00 0.00 4.30
32 33 6.517529 CGAGAAGGACTAATAAATGAGGAGGG 60.518 46.154 0.00 0.00 0.00 4.30
33 34 6.453476 AGAAGGACTAATAAATGAGGAGGGA 58.547 40.000 0.00 0.00 0.00 4.20
34 35 6.327887 AGAAGGACTAATAAATGAGGAGGGAC 59.672 42.308 0.00 0.00 0.00 4.46
36 37 6.935036 AGGACTAATAAATGAGGAGGGACTA 58.065 40.000 0.00 0.00 41.55 2.59
37 38 7.549141 AGGACTAATAAATGAGGAGGGACTAT 58.451 38.462 0.00 0.00 41.55 2.12
38 39 8.689054 AGGACTAATAAATGAGGAGGGACTATA 58.311 37.037 0.00 0.00 41.55 1.31
39 40 9.495382 GGACTAATAAATGAGGAGGGACTATAT 57.505 37.037 0.00 0.00 41.55 0.86
41 42 9.273137 ACTAATAAATGAGGAGGGACTATATGG 57.727 37.037 0.00 0.00 41.55 2.74
42 43 4.917906 AAATGAGGAGGGACTATATGGC 57.082 45.455 0.00 0.00 41.55 4.40
43 44 3.862600 ATGAGGAGGGACTATATGGCT 57.137 47.619 0.00 0.00 41.55 4.75
44 45 2.894731 TGAGGAGGGACTATATGGCTG 58.105 52.381 0.00 0.00 41.55 4.85
45 46 2.180086 TGAGGAGGGACTATATGGCTGT 59.820 50.000 0.00 0.00 41.55 4.40
46 47 3.401342 TGAGGAGGGACTATATGGCTGTA 59.599 47.826 0.00 0.00 41.55 2.74
47 48 4.045974 TGAGGAGGGACTATATGGCTGTAT 59.954 45.833 0.00 0.00 41.55 2.29
48 49 4.357325 AGGAGGGACTATATGGCTGTATG 58.643 47.826 0.00 0.00 41.55 2.39
49 50 4.045974 AGGAGGGACTATATGGCTGTATGA 59.954 45.833 0.00 0.00 41.55 2.15
50 51 4.777896 GGAGGGACTATATGGCTGTATGAA 59.222 45.833 0.00 0.00 41.55 2.57
51 52 5.248477 GGAGGGACTATATGGCTGTATGAAA 59.752 44.000 0.00 0.00 41.55 2.69
52 53 6.239887 GGAGGGACTATATGGCTGTATGAAAA 60.240 42.308 0.00 0.00 41.55 2.29
53 54 7.149202 AGGGACTATATGGCTGTATGAAAAA 57.851 36.000 0.00 0.00 36.02 1.94
54 55 6.998673 AGGGACTATATGGCTGTATGAAAAAC 59.001 38.462 0.00 0.00 36.02 2.43
55 56 6.206829 GGGACTATATGGCTGTATGAAAAACC 59.793 42.308 0.00 0.00 0.00 3.27
56 57 6.998673 GGACTATATGGCTGTATGAAAAACCT 59.001 38.462 0.00 0.00 0.00 3.50
57 58 8.154856 GGACTATATGGCTGTATGAAAAACCTA 58.845 37.037 0.00 0.00 0.00 3.08
58 59 9.726438 GACTATATGGCTGTATGAAAAACCTAT 57.274 33.333 0.00 0.00 0.00 2.57
59 60 9.726438 ACTATATGGCTGTATGAAAAACCTATC 57.274 33.333 0.00 0.00 0.00 2.08
60 61 9.725019 CTATATGGCTGTATGAAAAACCTATCA 57.275 33.333 0.00 0.00 0.00 2.15
61 62 6.949352 ATGGCTGTATGAAAAACCTATCAG 57.051 37.500 0.00 0.00 0.00 2.90
62 63 4.640201 TGGCTGTATGAAAAACCTATCAGC 59.360 41.667 0.00 0.00 43.88 4.26
63 64 4.884164 GGCTGTATGAAAAACCTATCAGCT 59.116 41.667 12.29 0.00 44.00 4.24
64 65 5.358160 GGCTGTATGAAAAACCTATCAGCTT 59.642 40.000 12.29 0.00 44.00 3.74
65 66 6.127619 GGCTGTATGAAAAACCTATCAGCTTT 60.128 38.462 12.29 0.00 44.00 3.51
66 67 7.067008 GGCTGTATGAAAAACCTATCAGCTTTA 59.933 37.037 12.29 0.00 44.00 1.85
67 68 8.125448 GCTGTATGAAAAACCTATCAGCTTTAG 58.875 37.037 0.00 0.00 42.16 1.85
68 69 9.167311 CTGTATGAAAAACCTATCAGCTTTAGT 57.833 33.333 0.00 0.00 0.00 2.24
69 70 8.946085 TGTATGAAAAACCTATCAGCTTTAGTG 58.054 33.333 0.00 0.00 0.00 2.74
70 71 6.817765 TGAAAAACCTATCAGCTTTAGTGG 57.182 37.500 0.00 0.00 0.00 4.00
71 72 6.539173 TGAAAAACCTATCAGCTTTAGTGGA 58.461 36.000 0.00 0.00 0.00 4.02
72 73 7.001674 TGAAAAACCTATCAGCTTTAGTGGAA 58.998 34.615 0.00 0.00 0.00 3.53
73 74 7.504238 TGAAAAACCTATCAGCTTTAGTGGAAA 59.496 33.333 0.00 0.00 0.00 3.13
74 75 7.833285 AAAACCTATCAGCTTTAGTGGAAAA 57.167 32.000 0.00 0.00 0.00 2.29
75 76 7.833285 AAACCTATCAGCTTTAGTGGAAAAA 57.167 32.000 0.00 0.00 0.00 1.94
150 151 9.981114 AAATCAATTTTCTAACGGTTGATTCTT 57.019 25.926 3.07 0.00 44.31 2.52
151 152 9.981114 AATCAATTTTCTAACGGTTGATTCTTT 57.019 25.926 3.07 0.00 42.59 2.52
152 153 8.795786 TCAATTTTCTAACGGTTGATTCTTTG 57.204 30.769 3.07 2.06 0.00 2.77
153 154 8.410141 TCAATTTTCTAACGGTTGATTCTTTGT 58.590 29.630 3.07 0.00 0.00 2.83
154 155 8.690840 CAATTTTCTAACGGTTGATTCTTTGTC 58.309 33.333 3.07 0.00 0.00 3.18
155 156 5.934935 TTCTAACGGTTGATTCTTTGTCC 57.065 39.130 3.07 0.00 0.00 4.02
349 352 8.680707 ATTGTTTTTATGCGTTTTTGCTTTTT 57.319 23.077 0.00 0.00 35.36 1.94
359 362 6.794636 TGCGTTTTTGCTTTTTCTTTTCTTTC 59.205 30.769 0.00 0.00 35.36 2.62
419 422 4.096833 TGGCATGTAGAATGAGTGAAATGC 59.903 41.667 0.00 0.00 38.70 3.56
442 445 8.192068 TGCATACACACACAAGTATTATACAC 57.808 34.615 5.11 0.00 0.00 2.90
443 446 8.038351 TGCATACACACACAAGTATTATACACT 58.962 33.333 5.11 0.00 0.00 3.55
444 447 9.524106 GCATACACACACAAGTATTATACACTA 57.476 33.333 5.11 0.00 0.00 2.74
447 450 7.031372 ACACACACAAGTATTATACACTACCG 58.969 38.462 5.11 0.00 0.00 4.02
563 566 5.447624 ACTAAGTTCCGGGTCAATTTTTG 57.552 39.130 0.00 0.00 0.00 2.44
573 576 4.173256 GGGTCAATTTTTGTTATGCCTCG 58.827 43.478 0.00 0.00 0.00 4.63
718 725 8.250332 ACATAATAAAATTGGTGCAAGTCGATT 58.750 29.630 0.00 0.00 0.00 3.34
719 726 9.086336 CATAATAAAATTGGTGCAAGTCGATTT 57.914 29.630 0.00 0.00 0.00 2.17
761 768 0.246635 TCAGGCGACTTGTTCCTAGC 59.753 55.000 0.00 0.00 40.21 3.42
773 780 1.810755 GTTCCTAGCCGGTCCAAAAAG 59.189 52.381 1.90 0.00 0.00 2.27
777 784 2.290450 CCTAGCCGGTCCAAAAAGGTAA 60.290 50.000 1.90 0.00 39.02 2.85
1262 1426 1.461091 AACAGCGTCGACCTCCTCAA 61.461 55.000 10.58 0.00 0.00 3.02
1360 1546 5.303747 AGTACTCTCTCAGATTTGTGTCG 57.696 43.478 0.00 0.00 0.00 4.35
1389 1575 5.244755 ACTTTGCAAAGTTTGACCACATTT 58.755 33.333 33.85 11.08 46.52 2.32
1390 1576 6.402222 ACTTTGCAAAGTTTGACCACATTTA 58.598 32.000 33.85 0.00 46.52 1.40
1524 1739 7.970384 TCGGACAAAACTTATATGCAAACTAG 58.030 34.615 0.00 0.00 0.00 2.57
1532 1747 9.740710 AAACTTATATGCAAACTAGAAAGGACT 57.259 29.630 0.00 0.00 0.00 3.85
1653 1964 1.446792 CCAGCCAGTACTGCGACAG 60.447 63.158 17.86 4.55 36.29 3.51
1662 1973 1.064357 GTACTGCGACAGAGCTCCTAC 59.936 57.143 10.93 0.65 38.13 3.18
1722 2539 4.251543 TGCATGTCTACGAAGAGTTCAA 57.748 40.909 0.00 0.00 30.45 2.69
1783 2600 6.826741 TGATCAGTGATGACATGACAATCAAT 59.173 34.615 11.20 2.00 0.00 2.57
1804 2621 1.475751 CCGGCATCTACCAGAAGCATT 60.476 52.381 5.83 0.00 40.42 3.56
1815 2632 2.464682 GAAGCATTCAGTCGCTGCT 58.535 52.632 0.00 0.00 46.62 4.24
1829 2646 2.430244 TGCTTCGAGCGTTCGGTC 60.430 61.111 21.60 13.27 46.26 4.79
1837 2654 2.227089 GAGCGTTCGGTCCTGATGGT 62.227 60.000 12.43 0.00 34.23 3.55
1841 2658 1.681793 CGTTCGGTCCTGATGGTATCT 59.318 52.381 0.00 0.00 34.23 1.98
1977 2814 4.537135 TGTCTAACATCTGGACTTGGTC 57.463 45.455 0.00 0.00 0.00 4.02
1986 2823 3.921677 TCTGGACTTGGTCACGATTTAC 58.078 45.455 0.00 0.00 33.68 2.01
1987 2824 3.576982 TCTGGACTTGGTCACGATTTACT 59.423 43.478 0.00 0.00 33.68 2.24
1988 2825 3.921677 TGGACTTGGTCACGATTTACTC 58.078 45.455 0.00 0.00 33.68 2.59
1989 2826 3.259902 GGACTTGGTCACGATTTACTCC 58.740 50.000 0.00 0.00 33.68 3.85
1990 2827 3.056035 GGACTTGGTCACGATTTACTCCT 60.056 47.826 0.00 0.00 33.68 3.69
2043 2880 6.187682 TCTTCAGATACCATACTCACTGACA 58.812 40.000 0.00 0.00 34.79 3.58
2190 3030 5.717119 TCAAGGTTTTCTACGACACCTATC 58.283 41.667 0.00 0.00 38.80 2.08
2298 4393 1.735920 CACACAGGAGCTCGCACTC 60.736 63.158 7.83 0.00 35.86 3.51
2428 4523 6.870965 AGCATTATGCCGTTTAACATTTTGAA 59.129 30.769 14.10 0.00 46.52 2.69
2798 5002 2.131972 TGACCGAAGTGTTCATTGACG 58.868 47.619 0.00 0.00 0.00 4.35
2819 5023 1.072965 AGCTGGAGAAACAGTCCCTTG 59.927 52.381 0.00 0.00 40.59 3.61
2994 5206 7.271511 AGCAGATATCTTAAAGACTTGTCCAG 58.728 38.462 1.33 0.00 0.00 3.86
3070 5328 5.821470 CAGGAAGTGATTGATAATGCAGTCT 59.179 40.000 0.00 0.00 0.00 3.24
3097 5355 4.814234 TGCTGTTGTTTAGTTCTGGTAGTG 59.186 41.667 0.00 0.00 0.00 2.74
3194 7022 3.938963 TGCTCAGAAACTTGAACTTTCGT 59.061 39.130 0.00 0.00 33.56 3.85
3261 7104 6.600822 AGCTGAAATTGTAGTATTGAGCATGT 59.399 34.615 0.00 0.00 31.18 3.21
3263 7106 8.397906 GCTGAAATTGTAGTATTGAGCATGTTA 58.602 33.333 0.00 0.00 0.00 2.41
3264 7107 9.708222 CTGAAATTGTAGTATTGAGCATGTTAC 57.292 33.333 0.00 0.00 0.00 2.50
3265 7108 9.225436 TGAAATTGTAGTATTGAGCATGTTACA 57.775 29.630 0.00 0.00 0.00 2.41
3267 7110 9.840427 AAATTGTAGTATTGAGCATGTTACAAC 57.160 29.630 0.00 0.00 32.36 3.32
3268 7111 8.792830 ATTGTAGTATTGAGCATGTTACAACT 57.207 30.769 0.00 0.00 32.36 3.16
3270 7113 8.028540 TGTAGTATTGAGCATGTTACAACTTG 57.971 34.615 0.00 4.15 37.19 3.16
3271 7114 6.500684 AGTATTGAGCATGTTACAACTTGG 57.499 37.500 9.28 0.00 35.36 3.61
3272 7115 6.237901 AGTATTGAGCATGTTACAACTTGGA 58.762 36.000 9.28 0.00 35.36 3.53
3273 7116 6.714810 AGTATTGAGCATGTTACAACTTGGAA 59.285 34.615 9.28 0.00 35.36 3.53
3275 7118 4.460263 TGAGCATGTTACAACTTGGAAGT 58.540 39.130 9.28 0.00 42.04 3.01
3278 7121 5.373222 AGCATGTTACAACTTGGAAGTACA 58.627 37.500 9.28 0.00 38.57 2.90
3331 7174 9.537848 GAGATTATTTTTAACCAACGTACACAG 57.462 33.333 0.00 0.00 0.00 3.66
3392 7450 7.867445 TCTTGTGAACACTGAAAAAGAAAAC 57.133 32.000 6.51 0.00 0.00 2.43
3422 7535 6.098838 AGAGAGTTGCCCTTTTCTGAATTTTT 59.901 34.615 0.00 0.00 0.00 1.94
3427 7540 6.676237 TGCCCTTTTCTGAATTTTTGTTTC 57.324 33.333 0.00 0.00 0.00 2.78
3428 7541 6.413892 TGCCCTTTTCTGAATTTTTGTTTCT 58.586 32.000 0.00 0.00 0.00 2.52
3429 7542 6.538381 TGCCCTTTTCTGAATTTTTGTTTCTC 59.462 34.615 0.00 0.00 0.00 2.87
3431 7544 6.200854 CCCTTTTCTGAATTTTTGTTTCTCGG 59.799 38.462 0.00 0.00 0.00 4.63
3432 7545 6.756542 CCTTTTCTGAATTTTTGTTTCTCGGT 59.243 34.615 0.00 0.00 0.00 4.69
3434 7547 5.432885 TCTGAATTTTTGTTTCTCGGTCC 57.567 39.130 0.00 0.00 0.00 4.46
3436 7549 5.534654 TCTGAATTTTTGTTTCTCGGTCCAT 59.465 36.000 0.00 0.00 0.00 3.41
3437 7550 5.768317 TGAATTTTTGTTTCTCGGTCCATC 58.232 37.500 0.00 0.00 0.00 3.51
3438 7551 4.783764 ATTTTTGTTTCTCGGTCCATCC 57.216 40.909 0.00 0.00 0.00 3.51
3441 7554 3.502123 TTGTTTCTCGGTCCATCCTTT 57.498 42.857 0.00 0.00 0.00 3.11
3463 7846 4.209452 TGTTCAATTCAACAGAGCGAAC 57.791 40.909 0.00 0.00 32.36 3.95
3473 7856 2.693069 ACAGAGCGAACAGATCCTTTG 58.307 47.619 0.00 0.00 35.47 2.77
3535 7926 3.254060 AGCGTCAACAACTGTAGCATAG 58.746 45.455 0.00 0.00 33.20 2.23
3537 7928 3.845178 CGTCAACAACTGTAGCATAGGA 58.155 45.455 0.00 0.00 0.00 2.94
3538 7929 3.859961 CGTCAACAACTGTAGCATAGGAG 59.140 47.826 0.00 0.00 0.00 3.69
3540 7931 5.392703 CGTCAACAACTGTAGCATAGGAGTA 60.393 44.000 0.00 0.00 0.00 2.59
3553 7944 4.392138 GCATAGGAGTACAACACTTCCAAC 59.608 45.833 0.00 0.00 37.72 3.77
3565 8014 4.451900 ACACTTCCAACTTACAGGACAAG 58.548 43.478 0.00 0.00 32.62 3.16
3609 8063 4.951094 CAGATCTAGTACACCCTATAGCCC 59.049 50.000 0.00 0.00 0.00 5.19
3624 8078 0.109342 AGCCCACAAGACTGTTGAGG 59.891 55.000 0.00 0.00 31.64 3.86
3649 8103 0.025001 CGTTTCACGATCGACCATGC 59.975 55.000 24.34 6.22 46.05 4.06
3840 8353 3.490759 GTCACCATGTCCTGCGCG 61.491 66.667 0.00 0.00 0.00 6.86
3841 8354 4.002506 TCACCATGTCCTGCGCGT 62.003 61.111 8.43 0.00 0.00 6.01
4042 8665 2.892425 GGGCGATGACCTTGCTCG 60.892 66.667 0.00 0.00 34.36 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.765795 CCTCATTTATTAGTCCTTCTCGTATTT 57.234 33.333 0.00 0.00 0.00 1.40
3 4 9.144298 TCCTCATTTATTAGTCCTTCTCGTATT 57.856 33.333 0.00 0.00 0.00 1.89
4 5 8.707796 TCCTCATTTATTAGTCCTTCTCGTAT 57.292 34.615 0.00 0.00 0.00 3.06
6 7 6.041069 CCTCCTCATTTATTAGTCCTTCTCGT 59.959 42.308 0.00 0.00 0.00 4.18
7 8 6.451393 CCTCCTCATTTATTAGTCCTTCTCG 58.549 44.000 0.00 0.00 0.00 4.04
8 9 6.555360 TCCCTCCTCATTTATTAGTCCTTCTC 59.445 42.308 0.00 0.00 0.00 2.87
9 10 6.327887 GTCCCTCCTCATTTATTAGTCCTTCT 59.672 42.308 0.00 0.00 0.00 2.85
10 11 6.327887 AGTCCCTCCTCATTTATTAGTCCTTC 59.672 42.308 0.00 0.00 0.00 3.46
11 12 6.213525 AGTCCCTCCTCATTTATTAGTCCTT 58.786 40.000 0.00 0.00 0.00 3.36
12 13 5.793967 AGTCCCTCCTCATTTATTAGTCCT 58.206 41.667 0.00 0.00 0.00 3.85
13 14 7.800300 ATAGTCCCTCCTCATTTATTAGTCC 57.200 40.000 0.00 0.00 0.00 3.85
15 16 9.273137 CCATATAGTCCCTCCTCATTTATTAGT 57.727 37.037 0.00 0.00 0.00 2.24
16 17 8.207545 GCCATATAGTCCCTCCTCATTTATTAG 58.792 40.741 0.00 0.00 0.00 1.73
17 18 7.906736 AGCCATATAGTCCCTCCTCATTTATTA 59.093 37.037 0.00 0.00 0.00 0.98
18 19 6.737608 AGCCATATAGTCCCTCCTCATTTATT 59.262 38.462 0.00 0.00 0.00 1.40
19 20 6.157645 CAGCCATATAGTCCCTCCTCATTTAT 59.842 42.308 0.00 0.00 0.00 1.40
20 21 5.485353 CAGCCATATAGTCCCTCCTCATTTA 59.515 44.000 0.00 0.00 0.00 1.40
21 22 4.288105 CAGCCATATAGTCCCTCCTCATTT 59.712 45.833 0.00 0.00 0.00 2.32
22 23 3.843027 CAGCCATATAGTCCCTCCTCATT 59.157 47.826 0.00 0.00 0.00 2.57
23 24 3.181402 ACAGCCATATAGTCCCTCCTCAT 60.181 47.826 0.00 0.00 0.00 2.90
24 25 2.180086 ACAGCCATATAGTCCCTCCTCA 59.820 50.000 0.00 0.00 0.00 3.86
25 26 2.896039 ACAGCCATATAGTCCCTCCTC 58.104 52.381 0.00 0.00 0.00 3.71
26 27 4.045974 TCATACAGCCATATAGTCCCTCCT 59.954 45.833 0.00 0.00 0.00 3.69
27 28 4.353777 TCATACAGCCATATAGTCCCTCC 58.646 47.826 0.00 0.00 0.00 4.30
28 29 6.360370 TTTCATACAGCCATATAGTCCCTC 57.640 41.667 0.00 0.00 0.00 4.30
29 30 6.763715 TTTTCATACAGCCATATAGTCCCT 57.236 37.500 0.00 0.00 0.00 4.20
30 31 6.206829 GGTTTTTCATACAGCCATATAGTCCC 59.793 42.308 0.00 0.00 0.00 4.46
31 32 6.998673 AGGTTTTTCATACAGCCATATAGTCC 59.001 38.462 0.00 0.00 0.00 3.85
32 33 9.726438 ATAGGTTTTTCATACAGCCATATAGTC 57.274 33.333 0.00 0.00 0.00 2.59
33 34 9.726438 GATAGGTTTTTCATACAGCCATATAGT 57.274 33.333 0.00 0.00 0.00 2.12
34 35 9.725019 TGATAGGTTTTTCATACAGCCATATAG 57.275 33.333 0.00 0.00 0.00 1.31
35 36 9.725019 CTGATAGGTTTTTCATACAGCCATATA 57.275 33.333 0.00 0.00 0.00 0.86
36 37 7.175641 GCTGATAGGTTTTTCATACAGCCATAT 59.824 37.037 0.00 0.00 42.04 1.78
37 38 6.486657 GCTGATAGGTTTTTCATACAGCCATA 59.513 38.462 0.00 0.00 42.04 2.74
38 39 5.300286 GCTGATAGGTTTTTCATACAGCCAT 59.700 40.000 0.00 0.00 42.04 4.40
39 40 4.640201 GCTGATAGGTTTTTCATACAGCCA 59.360 41.667 0.00 0.00 42.04 4.75
40 41 4.884164 AGCTGATAGGTTTTTCATACAGCC 59.116 41.667 0.00 0.00 46.75 4.85
41 42 6.442513 AAGCTGATAGGTTTTTCATACAGC 57.557 37.500 0.00 0.00 46.18 4.40
42 43 9.167311 ACTAAAGCTGATAGGTTTTTCATACAG 57.833 33.333 10.73 4.19 42.60 2.74
43 44 8.946085 CACTAAAGCTGATAGGTTTTTCATACA 58.054 33.333 10.73 0.00 42.60 2.29
44 45 8.398665 CCACTAAAGCTGATAGGTTTTTCATAC 58.601 37.037 10.73 0.00 42.60 2.39
45 46 8.325787 TCCACTAAAGCTGATAGGTTTTTCATA 58.674 33.333 10.73 0.00 42.60 2.15
46 47 7.175104 TCCACTAAAGCTGATAGGTTTTTCAT 58.825 34.615 10.73 0.00 42.60 2.57
47 48 6.539173 TCCACTAAAGCTGATAGGTTTTTCA 58.461 36.000 10.73 0.00 42.60 2.69
48 49 7.448748 TTCCACTAAAGCTGATAGGTTTTTC 57.551 36.000 10.73 0.00 42.60 2.29
49 50 7.833285 TTTCCACTAAAGCTGATAGGTTTTT 57.167 32.000 10.73 0.00 42.60 1.94
50 51 7.833285 TTTTCCACTAAAGCTGATAGGTTTT 57.167 32.000 10.73 0.00 42.60 2.43
51 52 7.833285 TTTTTCCACTAAAGCTGATAGGTTT 57.167 32.000 10.37 10.37 46.34 3.27
124 125 9.981114 AAGAATCAACCGTTAGAAAATTGATTT 57.019 25.926 10.80 1.42 45.42 2.17
126 127 9.410556 CAAAGAATCAACCGTTAGAAAATTGAT 57.589 29.630 0.00 0.00 40.77 2.57
127 128 8.410141 ACAAAGAATCAACCGTTAGAAAATTGA 58.590 29.630 0.00 0.00 34.03 2.57
128 129 8.574196 ACAAAGAATCAACCGTTAGAAAATTG 57.426 30.769 0.00 0.00 0.00 2.32
129 130 7.865889 GGACAAAGAATCAACCGTTAGAAAATT 59.134 33.333 0.00 0.00 0.00 1.82
130 131 7.013846 TGGACAAAGAATCAACCGTTAGAAAAT 59.986 33.333 0.00 0.00 0.00 1.82
131 132 6.319152 TGGACAAAGAATCAACCGTTAGAAAA 59.681 34.615 0.00 0.00 0.00 2.29
132 133 5.823570 TGGACAAAGAATCAACCGTTAGAAA 59.176 36.000 0.00 0.00 0.00 2.52
133 134 5.369833 TGGACAAAGAATCAACCGTTAGAA 58.630 37.500 0.00 0.00 0.00 2.10
134 135 4.963373 TGGACAAAGAATCAACCGTTAGA 58.037 39.130 0.00 0.00 0.00 2.10
135 136 5.682943 TTGGACAAAGAATCAACCGTTAG 57.317 39.130 0.00 0.00 0.00 2.34
136 137 6.642707 ATTTGGACAAAGAATCAACCGTTA 57.357 33.333 3.71 0.00 33.32 3.18
137 138 4.993029 TTTGGACAAAGAATCAACCGTT 57.007 36.364 0.00 0.00 0.00 4.44
138 139 5.068460 TGAATTTGGACAAAGAATCAACCGT 59.932 36.000 3.71 0.00 33.32 4.83
139 140 5.527951 TGAATTTGGACAAAGAATCAACCG 58.472 37.500 3.71 0.00 33.32 4.44
140 141 6.128472 GCATGAATTTGGACAAAGAATCAACC 60.128 38.462 0.00 0.00 33.32 3.77
141 142 6.647895 AGCATGAATTTGGACAAAGAATCAAC 59.352 34.615 0.00 8.92 33.32 3.18
142 143 6.761312 AGCATGAATTTGGACAAAGAATCAA 58.239 32.000 0.00 0.00 33.32 2.57
143 144 6.349243 AGCATGAATTTGGACAAAGAATCA 57.651 33.333 0.00 8.00 33.32 2.57
144 145 7.542025 ACTAGCATGAATTTGGACAAAGAATC 58.458 34.615 0.00 3.18 33.32 2.52
145 146 7.472334 ACTAGCATGAATTTGGACAAAGAAT 57.528 32.000 0.00 0.00 33.32 2.40
146 147 6.899393 ACTAGCATGAATTTGGACAAAGAA 57.101 33.333 0.00 0.00 33.32 2.52
147 148 6.899393 AACTAGCATGAATTTGGACAAAGA 57.101 33.333 0.00 0.00 33.32 2.52
148 149 7.951530 AAAACTAGCATGAATTTGGACAAAG 57.048 32.000 0.00 0.00 33.32 2.77
242 243 4.522789 GGCAAGTCAAAATTCACCCTAAGA 59.477 41.667 0.00 0.00 0.00 2.10
396 399 4.096833 GCATTTCACTCATTCTACATGCCA 59.903 41.667 0.00 0.00 31.49 4.92
529 532 5.359009 CCCGGAACTTAGTAGATACAAGACA 59.641 44.000 0.73 0.00 0.00 3.41
563 566 0.107654 AGCTTGGTCCGAGGCATAAC 60.108 55.000 8.30 0.00 0.00 1.89
573 576 1.093159 CAGATGCTTGAGCTTGGTCC 58.907 55.000 4.44 0.00 42.66 4.46
761 768 4.594123 ACAAATTACCTTTTTGGACCGG 57.406 40.909 0.00 0.00 38.18 5.28
773 780 9.285770 GTCTCCGAAATTTCATTACAAATTACC 57.714 33.333 17.99 0.00 35.35 2.85
777 784 7.333423 TCTCGTCTCCGAAATTTCATTACAAAT 59.667 33.333 17.99 0.00 43.69 2.32
980 1098 2.890474 GTACGCACGCATGGGGAG 60.890 66.667 14.94 7.37 42.98 4.30
1491 1686 7.903431 GCATATAAGTTTTGTCCGAACTTACAG 59.097 37.037 10.56 6.24 46.44 2.74
1492 1687 7.388224 TGCATATAAGTTTTGTCCGAACTTACA 59.612 33.333 10.56 1.79 46.44 2.41
1493 1688 7.745015 TGCATATAAGTTTTGTCCGAACTTAC 58.255 34.615 10.56 1.63 46.44 2.34
1495 1690 6.811253 TGCATATAAGTTTTGTCCGAACTT 57.189 33.333 7.32 7.32 46.09 2.66
1497 1692 7.081976 AGTTTGCATATAAGTTTTGTCCGAAC 58.918 34.615 0.00 0.00 0.00 3.95
1498 1693 7.209471 AGTTTGCATATAAGTTTTGTCCGAA 57.791 32.000 0.00 0.00 0.00 4.30
1500 1695 7.970384 TCTAGTTTGCATATAAGTTTTGTCCG 58.030 34.615 0.00 0.00 0.00 4.79
1506 1721 9.740710 AGTCCTTTCTAGTTTGCATATAAGTTT 57.259 29.630 0.00 0.00 0.00 2.66
1524 1739 9.921637 CATTTATATACTCTCTCCAGTCCTTTC 57.078 37.037 0.00 0.00 0.00 2.62
1547 1762 9.482627 GATGAAAACTCGGACTTATAGATCATT 57.517 33.333 0.00 0.00 0.00 2.57
1636 1947 0.457509 CTCTGTCGCAGTACTGGCTG 60.458 60.000 23.95 12.08 39.37 4.85
1640 1951 0.179150 GGAGCTCTGTCGCAGTACTG 60.179 60.000 18.93 18.93 32.61 2.74
1783 2600 0.975556 TGCTTCTGGTAGATGCCGGA 60.976 55.000 5.05 0.00 42.66 5.14
1804 2621 2.126307 GCTCGAAGCAGCGACTGA 60.126 61.111 10.46 0.00 41.89 3.41
1837 2654 3.432749 GCTCCTCAAAGTCATGGCAGATA 60.433 47.826 0.00 0.00 0.00 1.98
1841 2658 0.694771 AGCTCCTCAAAGTCATGGCA 59.305 50.000 0.00 0.00 0.00 4.92
1977 2814 7.372451 TGAATAAAACCAGGAGTAAATCGTG 57.628 36.000 0.00 0.00 42.31 4.35
1986 2823 6.624423 CCTTCAACATGAATAAAACCAGGAG 58.376 40.000 0.00 0.00 35.59 3.69
1987 2824 5.047377 GCCTTCAACATGAATAAAACCAGGA 60.047 40.000 0.00 0.00 35.59 3.86
1988 2825 5.170748 GCCTTCAACATGAATAAAACCAGG 58.829 41.667 0.00 0.00 35.59 4.45
1989 2826 5.047092 AGGCCTTCAACATGAATAAAACCAG 60.047 40.000 0.00 0.00 35.59 4.00
1990 2827 4.837860 AGGCCTTCAACATGAATAAAACCA 59.162 37.500 0.00 0.00 35.59 3.67
2043 2880 8.358148 GGCATCAGATTCATTTGATAGAAATGT 58.642 33.333 0.00 0.00 38.44 2.71
2162 3002 5.754890 GGTGTCGTAGAAAACCTTGAACTTA 59.245 40.000 0.00 0.00 40.98 2.24
2190 3030 2.416547 CAGCATACACGACCTCCTTTTG 59.583 50.000 0.00 0.00 0.00 2.44
2360 4455 1.228245 GAGGCCACCTGTGAAGCAA 60.228 57.895 5.01 0.00 31.76 3.91
2428 4523 1.347707 ACCGACCAGACATGATGTTGT 59.652 47.619 0.00 0.00 0.00 3.32
2758 4954 4.092091 GTCAGTGCATTCTTCGAAGTAAGG 59.908 45.833 23.85 17.96 0.00 2.69
2798 5002 0.980423 AGGGACTGTTTCTCCAGCTC 59.020 55.000 0.00 0.00 37.18 4.09
2819 5023 5.528690 TGGCAAATATCTGCATCTTCTGTAC 59.471 40.000 2.94 0.00 44.52 2.90
2994 5206 2.348666 ACGAGATTGTAATCAGCAACGC 59.651 45.455 7.30 0.00 37.89 4.84
3064 5276 2.566952 AACAACAGCAAACAGACTGC 57.433 45.000 1.25 0.00 37.42 4.40
3070 5328 4.461081 ACCAGAACTAAACAACAGCAAACA 59.539 37.500 0.00 0.00 0.00 2.83
3124 5382 2.433318 GAGCACGAGACCCACTGC 60.433 66.667 0.00 0.00 0.00 4.40
3134 5394 1.476891 GACCATTACAGGAGAGCACGA 59.523 52.381 0.00 0.00 0.00 4.35
3261 7104 9.709495 ATATAAACGTGTACTTCCAAGTTGTAA 57.291 29.630 1.45 0.00 40.37 2.41
3263 7106 8.611654 AATATAAACGTGTACTTCCAAGTTGT 57.388 30.769 1.45 0.00 40.37 3.32
3264 7107 9.887406 AAAATATAAACGTGTACTTCCAAGTTG 57.113 29.630 0.00 0.00 40.37 3.16
3311 7154 6.680874 TCACTGTGTACGTTGGTTAAAAAT 57.319 33.333 7.79 0.00 0.00 1.82
3317 7160 3.530265 TCTTCACTGTGTACGTTGGTT 57.470 42.857 7.79 0.00 0.00 3.67
3392 7450 3.007831 AGAAAAGGGCAACTCTCTCTCTG 59.992 47.826 0.00 0.00 0.00 3.35
3422 7535 3.146066 CAAAAGGATGGACCGAGAAACA 58.854 45.455 0.00 0.00 44.74 2.83
3427 7540 2.778299 TGAACAAAAGGATGGACCGAG 58.222 47.619 0.00 0.00 44.74 4.63
3428 7541 2.940994 TGAACAAAAGGATGGACCGA 57.059 45.000 0.00 0.00 44.74 4.69
3429 7542 4.022416 TGAATTGAACAAAAGGATGGACCG 60.022 41.667 0.00 0.00 44.74 4.79
3431 7544 6.279882 TGTTGAATTGAACAAAAGGATGGAC 58.720 36.000 8.09 0.00 32.84 4.02
3432 7545 6.323482 TCTGTTGAATTGAACAAAAGGATGGA 59.677 34.615 11.66 0.66 35.44 3.41
3434 7547 6.145048 GCTCTGTTGAATTGAACAAAAGGATG 59.855 38.462 11.66 0.00 35.44 3.51
3436 7549 5.591099 GCTCTGTTGAATTGAACAAAAGGA 58.409 37.500 11.66 4.89 35.44 3.36
3437 7550 4.442073 CGCTCTGTTGAATTGAACAAAAGG 59.558 41.667 11.66 0.68 35.44 3.11
3438 7551 5.273170 TCGCTCTGTTGAATTGAACAAAAG 58.727 37.500 11.66 12.19 35.44 2.27
3441 7554 4.095632 TGTTCGCTCTGTTGAATTGAACAA 59.904 37.500 11.66 2.94 40.63 2.83
3535 7926 5.362263 TGTAAGTTGGAAGTGTTGTACTCC 58.638 41.667 0.00 0.00 39.18 3.85
3537 7928 5.129815 TCCTGTAAGTTGGAAGTGTTGTACT 59.870 40.000 0.00 0.00 42.89 2.73
3538 7929 5.235831 GTCCTGTAAGTTGGAAGTGTTGTAC 59.764 44.000 0.00 0.00 33.72 2.90
3540 7931 4.196971 GTCCTGTAAGTTGGAAGTGTTGT 58.803 43.478 0.00 0.00 33.72 3.32
3553 7944 1.071605 GCTGCGACTTGTCCTGTAAG 58.928 55.000 0.00 0.00 0.00 2.34
3592 8046 3.977489 TGTGGGCTATAGGGTGTACTA 57.023 47.619 1.04 0.00 0.00 1.82
3593 8047 2.860817 TGTGGGCTATAGGGTGTACT 57.139 50.000 1.04 0.00 0.00 2.73
3594 8048 3.036091 TCTTGTGGGCTATAGGGTGTAC 58.964 50.000 1.04 0.00 0.00 2.90
3609 8063 0.109342 AGGGCCTCAACAGTCTTGTG 59.891 55.000 0.00 0.00 37.67 3.33
3761 8274 3.535629 CTCCACTGGCTGCGTTCCA 62.536 63.158 0.00 0.00 0.00 3.53
4028 8651 2.125552 TGGCGAGCAAGGTCATCG 60.126 61.111 0.00 0.00 39.40 3.84
4034 8657 4.988598 ACACGGTGGCGAGCAAGG 62.989 66.667 13.48 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.