Multiple sequence alignment - TraesCS7A01G018900

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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 TraesCS7A01G018900 chr7A 100.000 2528 0 0 1 2528 7876804 7879331 0.000000e+00 4669.0
1 TraesCS7A01G018900 chr7A 85.452 818 69 23 111 896 8079207 8078408 0.000000e+00 806.0
2 TraesCS7A01G018900 chr7A 85.452 818 69 23 111 896 8199473 8198674 0.000000e+00 806.0
3 TraesCS7A01G018900 chr7A 86.628 516 48 14 1547 2055 7911211 7911712 3.680000e-153 551.0
4 TraesCS7A01G018900 chr7A 76.471 1139 159 62 584 1637 7912428 7913542 3.730000e-143 518.0
5 TraesCS7A01G018900 chr7A 81.250 576 67 26 736 1286 7775969 7776528 6.460000e-116 427.0
6 TraesCS7A01G018900 chr7A 88.657 335 27 6 951 1276 8078411 8078079 5.070000e-107 398.0
7 TraesCS7A01G018900 chr7A 88.657 335 27 6 951 1276 8198677 8198345 5.070000e-107 398.0
8 TraesCS7A01G018900 chr7A 84.593 344 45 3 1716 2052 8077565 8077223 4.030000e-88 335.0
9 TraesCS7A01G018900 chr7A 84.593 344 45 3 1716 2052 8197840 8197498 4.030000e-88 335.0
10 TraesCS7A01G018900 chr7A 89.524 210 12 5 1173 1376 7841272 7841477 8.970000e-65 257.0
11 TraesCS7A01G018900 chr7A 85.549 173 8 8 395 555 7835653 7835820 5.590000e-37 165.0
12 TraesCS7A01G018900 chr7A 95.556 90 4 0 2049 2138 7981866 7981777 7.290000e-31 145.0
13 TraesCS7A01G018900 chr7A 95.556 90 4 0 2049 2138 8083171 8083082 7.290000e-31 145.0
14 TraesCS7A01G018900 chr7A 95.556 90 4 0 2049 2138 8119865 8119776 7.290000e-31 145.0
15 TraesCS7A01G018900 chr7A 95.556 90 4 0 2049 2138 8203437 8203348 7.290000e-31 145.0
16 TraesCS7A01G018900 chr7A 78.161 261 32 17 1209 1448 7941549 7941293 2.620000e-30 143.0
17 TraesCS7A01G018900 chr7A 93.333 90 6 0 2049 2138 7943056 7942967 1.580000e-27 134.0
18 TraesCS7A01G018900 chr7A 77.866 253 27 11 111 352 7835423 7835657 2.040000e-26 130.0
19 TraesCS7A01G018900 chr7A 85.714 112 14 2 1 110 699824529 699824418 1.590000e-22 117.0
20 TraesCS7A01G018900 chr7A 78.698 169 30 6 2317 2482 409264698 409264863 9.560000e-20 108.0
21 TraesCS7A01G018900 chr7A 76.163 172 23 12 2321 2491 696814978 696814824 9.700000e-10 75.0
22 TraesCS7A01G018900 chr7D 91.889 1985 109 19 111 2052 7069364 7071339 0.000000e+00 2726.0
23 TraesCS7A01G018900 chr7D 84.421 1303 100 53 374 1614 6962436 6963697 0.000000e+00 1186.0
24 TraesCS7A01G018900 chr7D 78.440 872 119 39 584 1403 6966289 6967143 2.900000e-139 505.0
25 TraesCS7A01G018900 chr7D 79.114 790 98 40 907 1637 7072322 7073103 1.360000e-132 483.0
26 TraesCS7A01G018900 chr7D 85.507 345 40 5 1716 2052 7191660 7191318 4.000000e-93 351.0
27 TraesCS7A01G018900 chr7D 94.444 90 5 0 2049 2138 7071391 7071480 3.390000e-29 139.0
28 TraesCS7A01G018900 chr7D 94.444 90 5 0 2049 2138 7213290 7213201 3.390000e-29 139.0
29 TraesCS7A01G018900 chr7D 78.035 173 33 5 2313 2482 12906251 12906421 1.240000e-18 104.0
30 TraesCS7A01G018900 chr7D 97.059 34 1 0 349 382 6926737 6926770 9.770000e-05 58.4
31 TraesCS7A01G018900 chr4A 87.022 1518 117 45 584 2052 733246756 733245270 0.000000e+00 1639.0
32 TraesCS7A01G018900 chr4A 89.286 644 43 11 111 732 732966338 732966977 0.000000e+00 784.0
33 TraesCS7A01G018900 chr4A 86.709 632 60 13 1524 2138 733123249 733122625 0.000000e+00 680.0
34 TraesCS7A01G018900 chr4A 86.572 633 62 14 1524 2138 733063438 733062811 0.000000e+00 676.0
35 TraesCS7A01G018900 chr4A 86.149 657 45 19 976 1590 732966989 732967641 0.000000e+00 667.0
36 TraesCS7A01G018900 chr4A 92.982 342 21 3 2155 2493 733245040 733244699 1.750000e-136 496.0
37 TraesCS7A01G018900 chr4A 92.669 341 23 2 2155 2493 733122536 733122196 8.130000e-135 490.0
38 TraesCS7A01G018900 chr4A 92.375 341 23 3 2155 2493 733062722 733062383 1.360000e-132 483.0
39 TraesCS7A01G018900 chr4A 83.012 518 71 9 1545 2052 732970497 732971007 1.070000e-123 453.0
40 TraesCS7A01G018900 chr4A 76.196 920 136 44 478 1343 732976664 732977554 2.340000e-110 409.0
41 TraesCS7A01G018900 chr4A 77.937 698 84 46 845 1495 732904423 732905097 3.070000e-99 372.0
42 TraesCS7A01G018900 chr4A 81.699 459 60 16 479 925 733140312 733139866 6.650000e-96 361.0
43 TraesCS7A01G018900 chr4A 81.562 461 57 19 479 925 733006323 733005877 3.090000e-94 355.0
44 TraesCS7A01G018900 chr4A 92.704 233 12 3 252 479 732999457 732999689 5.210000e-87 331.0
45 TraesCS7A01G018900 chr4A 83.924 367 23 11 1190 1529 733132342 733131985 4.060000e-83 318.0
46 TraesCS7A01G018900 chr4A 83.106 367 26 14 1190 1529 733072325 733071968 4.090000e-78 302.0
47 TraesCS7A01G018900 chr4A 83.039 283 25 10 117 392 733253276 733253010 4.200000e-58 235.0
48 TraesCS7A01G018900 chr4A 90.076 131 13 0 330 460 733006503 733006373 1.200000e-38 171.0
49 TraesCS7A01G018900 chr4A 88.550 131 15 0 330 460 733140493 733140363 2.600000e-35 159.0
50 TraesCS7A01G018900 chr4A 94.444 90 5 0 2049 2138 732973071 732973160 3.390000e-29 139.0
51 TraesCS7A01G018900 chr4A 93.333 90 6 0 2049 2138 733001031 733001120 1.580000e-27 134.0
52 TraesCS7A01G018900 chr4A 90.196 102 6 3 572 669 732969945 732970046 2.040000e-26 130.0
53 TraesCS7A01G018900 chr4A 82.143 112 18 2 1 110 503479225 503479114 7.450000e-16 95.3
54 TraesCS7A01G018900 chr4A 100.000 36 0 0 2493 2528 733062251 733062216 1.620000e-07 67.6
55 TraesCS7A01G018900 chr4A 100.000 36 0 0 2493 2528 733122064 733122029 1.620000e-07 67.6
56 TraesCS7A01G018900 chr4A 100.000 36 0 0 2493 2528 733244567 733244532 1.620000e-07 67.6
57 TraesCS7A01G018900 chrUn 85.936 903 73 24 1282 2138 51229833 51230727 0.000000e+00 915.0
58 TraesCS7A01G018900 chrUn 85.936 903 73 24 1282 2138 289098974 289098080 0.000000e+00 915.0
59 TraesCS7A01G018900 chrUn 93.003 343 20 4 2155 2493 51230816 51231158 4.860000e-137 497.0
60 TraesCS7A01G018900 chrUn 93.003 343 20 4 2155 2493 289097991 289097649 4.860000e-137 497.0
61 TraesCS7A01G018900 chrUn 74.975 987 142 61 587 1501 51220862 51219909 8.600000e-95 357.0
62 TraesCS7A01G018900 chrUn 100.000 36 0 0 2493 2528 51231290 51231325 1.620000e-07 67.6
63 TraesCS7A01G018900 chrUn 100.000 36 0 0 2493 2528 289097517 289097482 1.620000e-07 67.6
64 TraesCS7A01G018900 chr7B 89.655 116 10 1 1 114 143251945 143251830 2.030000e-31 147.0
65 TraesCS7A01G018900 chr7B 82.075 106 15 2 8 110 745039912 745039808 1.250000e-13 87.9
66 TraesCS7A01G018900 chr6B 82.883 111 17 2 5 113 713362825 713362935 5.760000e-17 99.0
67 TraesCS7A01G018900 chr1D 86.154 65 7 1 45 107 323869946 323869882 4.510000e-08 69.4


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 TraesCS7A01G018900 chr7A 7876804 7879331 2527 False 4669.000000 4669 100.000000 1 2528 1 chr7A.!!$F3 2527
1 TraesCS7A01G018900 chr7A 7911211 7913542 2331 False 534.500000 551 81.549500 584 2055 2 chr7A.!!$F6 1471
2 TraesCS7A01G018900 chr7A 7775969 7776528 559 False 427.000000 427 81.250000 736 1286 1 chr7A.!!$F1 550
3 TraesCS7A01G018900 chr7A 8077223 8083171 5948 True 421.000000 806 88.564500 111 2138 4 chr7A.!!$R6 2027
4 TraesCS7A01G018900 chr7A 8197498 8203437 5939 True 421.000000 806 88.564500 111 2138 4 chr7A.!!$R7 2027
5 TraesCS7A01G018900 chr7D 7069364 7073103 3739 False 1116.000000 2726 88.482333 111 2138 3 chr7D.!!$F4 2027
6 TraesCS7A01G018900 chr7D 6962436 6967143 4707 False 845.500000 1186 81.430500 374 1614 2 chr7D.!!$F3 1240
7 TraesCS7A01G018900 chr4A 733244532 733246756 2224 True 734.200000 1639 93.334667 584 2528 3 chr4A.!!$R9 1944
8 TraesCS7A01G018900 chr4A 732966338 732977554 11216 False 430.333333 784 86.547167 111 2138 6 chr4A.!!$F2 2027
9 TraesCS7A01G018900 chr4A 733122029 733123249 1220 True 412.533333 680 93.126000 1524 2528 3 chr4A.!!$R7 1004
10 TraesCS7A01G018900 chr4A 733062216 733063438 1222 True 408.866667 676 92.982333 1524 2528 3 chr4A.!!$R6 1004
11 TraesCS7A01G018900 chr4A 732904423 732905097 674 False 372.000000 372 77.937000 845 1495 1 chr4A.!!$F1 650
12 TraesCS7A01G018900 chr4A 733005877 733006503 626 True 263.000000 355 85.819000 330 925 2 chr4A.!!$R5 595
13 TraesCS7A01G018900 chr4A 733139866 733140493 627 True 260.000000 361 85.124500 330 925 2 chr4A.!!$R8 595
14 TraesCS7A01G018900 chr4A 732999457 733001120 1663 False 232.500000 331 93.018500 252 2138 2 chr4A.!!$F3 1886
15 TraesCS7A01G018900 chrUn 51229833 51231325 1492 False 493.200000 915 92.979667 1282 2528 3 chrUn.!!$F1 1246
16 TraesCS7A01G018900 chrUn 289097482 289098974 1492 True 493.200000 915 92.979667 1282 2528 3 chrUn.!!$R2 1246
17 TraesCS7A01G018900 chrUn 51219909 51220862 953 True 357.000000 357 74.975000 587 1501 1 chrUn.!!$R1 914

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
501 4484 0.034896 AACGCCAACCACTAGACTGG 59.965 55.0 0.0 0.0 37.33 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2064 10532 0.039035 ACTTTCGCATAGGCCCCAAA 59.961 50.0 0.0 0.0 36.38 3.28 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
22 23 5.488645 GACTAAACTTGTCCGGTTTCAAA 57.511 39.130 0.00 0.00 37.88 2.69
23 24 5.882553 GACTAAACTTGTCCGGTTTCAAAA 58.117 37.500 0.00 0.00 37.88 2.44
24 25 5.886992 ACTAAACTTGTCCGGTTTCAAAAG 58.113 37.500 0.00 0.00 37.88 2.27
26 27 4.794278 AACTTGTCCGGTTTCAAAAGTT 57.206 36.364 0.00 2.00 34.05 2.66
27 28 5.900865 AACTTGTCCGGTTTCAAAAGTTA 57.099 34.783 7.27 0.00 36.40 2.24
28 29 5.900865 ACTTGTCCGGTTTCAAAAGTTAA 57.099 34.783 0.00 0.00 0.00 2.01
29 30 5.886992 ACTTGTCCGGTTTCAAAAGTTAAG 58.113 37.500 0.00 0.00 0.00 1.85
30 31 5.648960 ACTTGTCCGGTTTCAAAAGTTAAGA 59.351 36.000 0.00 0.00 0.00 2.10
31 32 5.744666 TGTCCGGTTTCAAAAGTTAAGAG 57.255 39.130 0.00 0.00 0.00 2.85
32 33 5.187687 TGTCCGGTTTCAAAAGTTAAGAGT 58.812 37.500 0.00 0.00 0.00 3.24
33 34 5.065474 TGTCCGGTTTCAAAAGTTAAGAGTG 59.935 40.000 0.00 0.00 0.00 3.51
34 35 4.035909 TCCGGTTTCAAAAGTTAAGAGTGC 59.964 41.667 0.00 0.00 0.00 4.40
35 36 4.201970 CCGGTTTCAAAAGTTAAGAGTGCA 60.202 41.667 0.00 0.00 0.00 4.57
36 37 5.336744 CGGTTTCAAAAGTTAAGAGTGCAA 58.663 37.500 0.00 0.00 0.00 4.08
38 39 5.232202 GGTTTCAAAAGTTAAGAGTGCAAGC 59.768 40.000 0.00 0.00 0.00 4.01
39 40 5.835113 TTCAAAAGTTAAGAGTGCAAGCT 57.165 34.783 0.00 0.00 0.00 3.74
40 41 5.173774 TCAAAAGTTAAGAGTGCAAGCTG 57.826 39.130 0.00 0.00 0.00 4.24
41 42 4.640201 TCAAAAGTTAAGAGTGCAAGCTGT 59.360 37.500 0.00 0.00 0.00 4.40
42 43 4.820284 AAAGTTAAGAGTGCAAGCTGTC 57.180 40.909 0.00 0.00 0.00 3.51
43 44 3.760580 AGTTAAGAGTGCAAGCTGTCT 57.239 42.857 0.00 0.00 0.00 3.41
44 45 3.397482 AGTTAAGAGTGCAAGCTGTCTG 58.603 45.455 0.00 0.00 0.00 3.51
45 46 2.462456 TAAGAGTGCAAGCTGTCTGG 57.538 50.000 0.00 0.00 0.00 3.86
46 47 0.471617 AAGAGTGCAAGCTGTCTGGT 59.528 50.000 0.00 0.00 0.00 4.00
47 48 0.471617 AGAGTGCAAGCTGTCTGGTT 59.528 50.000 0.00 0.00 36.75 3.67
49 50 1.678101 GAGTGCAAGCTGTCTGGTTTT 59.322 47.619 0.00 0.00 33.63 2.43
50 51 1.406539 AGTGCAAGCTGTCTGGTTTTG 59.593 47.619 0.00 0.00 33.63 2.44
52 53 2.098614 TGCAAGCTGTCTGGTTTTGAA 58.901 42.857 0.00 0.00 33.63 2.69
53 54 2.099592 TGCAAGCTGTCTGGTTTTGAAG 59.900 45.455 0.00 0.00 33.63 3.02
54 55 2.099756 GCAAGCTGTCTGGTTTTGAAGT 59.900 45.455 0.00 0.00 33.63 3.01
56 57 4.202010 GCAAGCTGTCTGGTTTTGAAGTTA 60.202 41.667 0.00 0.00 33.63 2.24
57 58 5.678616 GCAAGCTGTCTGGTTTTGAAGTTAA 60.679 40.000 0.00 0.00 33.63 2.01
60 61 4.261614 GCTGTCTGGTTTTGAAGTTAAGGG 60.262 45.833 0.00 0.00 0.00 3.95
62 63 4.885325 TGTCTGGTTTTGAAGTTAAGGGAC 59.115 41.667 0.00 0.00 0.00 4.46
64 65 4.131596 CTGGTTTTGAAGTTAAGGGACGA 58.868 43.478 0.00 0.00 0.00 4.20
66 67 4.948621 TGGTTTTGAAGTTAAGGGACGAAA 59.051 37.500 0.00 0.00 0.00 3.46
67 68 5.595133 TGGTTTTGAAGTTAAGGGACGAAAT 59.405 36.000 0.00 0.00 0.00 2.17
68 69 6.147581 GGTTTTGAAGTTAAGGGACGAAATC 58.852 40.000 0.00 0.00 0.00 2.17
69 70 6.016527 GGTTTTGAAGTTAAGGGACGAAATCT 60.017 38.462 0.00 0.00 0.00 2.40
70 71 7.173735 GGTTTTGAAGTTAAGGGACGAAATCTA 59.826 37.037 0.00 0.00 0.00 1.98
71 72 7.900782 TTTGAAGTTAAGGGACGAAATCTAG 57.099 36.000 0.00 0.00 0.00 2.43
72 73 6.845758 TGAAGTTAAGGGACGAAATCTAGA 57.154 37.500 0.00 0.00 0.00 2.43
73 74 6.628185 TGAAGTTAAGGGACGAAATCTAGAC 58.372 40.000 0.00 0.00 0.00 2.59
74 75 6.436532 TGAAGTTAAGGGACGAAATCTAGACT 59.563 38.462 0.00 0.00 0.00 3.24
75 76 6.453926 AGTTAAGGGACGAAATCTAGACTC 57.546 41.667 0.00 0.00 0.00 3.36
76 77 5.066246 AGTTAAGGGACGAAATCTAGACTCG 59.934 44.000 19.50 19.50 38.53 4.18
77 78 2.299521 AGGGACGAAATCTAGACTCGG 58.700 52.381 23.05 10.55 36.90 4.63
78 79 2.092538 AGGGACGAAATCTAGACTCGGA 60.093 50.000 23.05 0.00 36.90 4.55
79 80 2.686915 GGGACGAAATCTAGACTCGGAA 59.313 50.000 23.05 0.00 36.90 4.30
80 81 3.129988 GGGACGAAATCTAGACTCGGAAA 59.870 47.826 23.05 0.00 36.90 3.13
81 82 4.381292 GGGACGAAATCTAGACTCGGAAAA 60.381 45.833 23.05 0.00 36.90 2.29
82 83 4.799428 GGACGAAATCTAGACTCGGAAAAG 59.201 45.833 23.05 3.05 36.90 2.27
83 84 5.388408 ACGAAATCTAGACTCGGAAAAGT 57.612 39.130 23.05 5.35 36.90 2.66
84 85 5.780984 ACGAAATCTAGACTCGGAAAAGTT 58.219 37.500 23.05 4.80 36.90 2.66
85 86 5.634020 ACGAAATCTAGACTCGGAAAAGTTG 59.366 40.000 23.05 1.41 36.90 3.16
88 89 4.785511 TCTAGACTCGGAAAAGTTGAGG 57.214 45.455 0.00 0.00 34.03 3.86
90 91 2.326428 AGACTCGGAAAAGTTGAGGGA 58.674 47.619 0.00 0.00 34.03 4.20
91 92 2.907042 AGACTCGGAAAAGTTGAGGGAT 59.093 45.455 0.00 0.00 34.03 3.85
93 94 2.637872 ACTCGGAAAAGTTGAGGGATGA 59.362 45.455 0.00 0.00 34.03 2.92
94 95 3.072476 ACTCGGAAAAGTTGAGGGATGAA 59.928 43.478 0.00 0.00 34.03 2.57
96 97 4.465886 TCGGAAAAGTTGAGGGATGAAAA 58.534 39.130 0.00 0.00 0.00 2.29
97 98 4.518970 TCGGAAAAGTTGAGGGATGAAAAG 59.481 41.667 0.00 0.00 0.00 2.27
98 99 4.278419 CGGAAAAGTTGAGGGATGAAAAGT 59.722 41.667 0.00 0.00 0.00 2.66
99 100 5.472137 CGGAAAAGTTGAGGGATGAAAAGTA 59.528 40.000 0.00 0.00 0.00 2.24
101 102 7.335924 CGGAAAAGTTGAGGGATGAAAAGTATA 59.664 37.037 0.00 0.00 0.00 1.47
103 104 9.232473 GAAAAGTTGAGGGATGAAAAGTATACT 57.768 33.333 0.00 0.00 0.00 2.12
104 105 9.588096 AAAAGTTGAGGGATGAAAAGTATACTT 57.412 29.630 12.50 12.50 37.91 2.24
315 4221 7.789202 AGACAGCCATGTATCAGTCTATTAT 57.211 36.000 0.00 0.00 40.68 1.28
328 4234 8.873215 ATCAGTCTATTATCACAAGGTTAACG 57.127 34.615 0.00 0.00 0.00 3.18
484 4467 5.086104 ACATACAGGTGTCCATAGTCAAC 57.914 43.478 0.00 0.00 0.00 3.18
501 4484 0.034896 AACGCCAACCACTAGACTGG 59.965 55.000 0.00 0.00 37.33 4.00
505 4488 1.270907 CCAACCACTAGACTGGAGCT 58.729 55.000 6.39 0.00 35.04 4.09
520 4503 1.222300 GAGCTGCTGCATCATCAGAG 58.778 55.000 18.42 0.00 42.74 3.35
526 4509 1.138464 GCTGCATCATCAGAGAGGACA 59.862 52.381 0.00 0.00 36.19 4.02
527 4510 2.419713 GCTGCATCATCAGAGAGGACAA 60.420 50.000 0.00 0.00 36.19 3.18
528 4511 3.744846 GCTGCATCATCAGAGAGGACAAT 60.745 47.826 0.00 0.00 36.19 2.71
555 4538 9.439500 AATTAGTGCAAATGATTAGCAACAAAT 57.561 25.926 0.00 0.00 40.35 2.32
599 4582 3.450457 TGCCCCCAATTAACAAGCATAAG 59.550 43.478 0.00 0.00 0.00 1.73
605 4588 5.521010 CCCAATTAACAAGCATAAGCACATG 59.479 40.000 0.00 0.00 45.49 3.21
803 4832 2.756760 GGCCAAATCATGACTGTGACAT 59.243 45.455 0.00 0.00 0.00 3.06
1061 5149 2.141011 CTCCTTCACCACCATGGGCA 62.141 60.000 18.09 0.00 43.37 5.36
1068 5156 0.482446 ACCACCATGGGCAAGAAAGA 59.518 50.000 18.09 0.00 43.37 2.52
1108 5196 4.480115 TCAGAGTCTACAAGGGTGAAAGA 58.520 43.478 0.00 0.00 0.00 2.52
1226 5342 3.390967 TCCTGTTCTGGATCACAAGTGAA 59.609 43.478 7.02 0.00 43.58 3.18
1404 5688 6.009589 TCTTGCATCCTTTTGTCCTCATTTA 58.990 36.000 0.00 0.00 0.00 1.40
1405 5689 5.643379 TGCATCCTTTTGTCCTCATTTAC 57.357 39.130 0.00 0.00 0.00 2.01
1406 5690 5.324409 TGCATCCTTTTGTCCTCATTTACT 58.676 37.500 0.00 0.00 0.00 2.24
1407 5691 6.480763 TGCATCCTTTTGTCCTCATTTACTA 58.519 36.000 0.00 0.00 0.00 1.82
1409 5693 6.183360 GCATCCTTTTGTCCTCATTTACTACC 60.183 42.308 0.00 0.00 0.00 3.18
1410 5694 6.442541 TCCTTTTGTCCTCATTTACTACCA 57.557 37.500 0.00 0.00 0.00 3.25
1413 5702 7.393234 TCCTTTTGTCCTCATTTACTACCAATG 59.607 37.037 0.00 0.00 33.55 2.82
1438 5727 3.004862 GGTTGTTTATCACCCGATTCGT 58.995 45.455 5.20 0.00 32.73 3.85
1444 5733 1.486211 ATCACCCGATTCGTTCTCCT 58.514 50.000 5.20 0.00 0.00 3.69
1445 5734 0.815734 TCACCCGATTCGTTCTCCTC 59.184 55.000 5.20 0.00 0.00 3.71
1446 5735 0.525668 CACCCGATTCGTTCTCCTCG 60.526 60.000 5.20 0.00 0.00 4.63
1447 5736 0.964358 ACCCGATTCGTTCTCCTCGT 60.964 55.000 5.20 0.00 0.00 4.18
1448 5737 0.172803 CCCGATTCGTTCTCCTCGTT 59.827 55.000 5.20 0.00 0.00 3.85
1449 5738 1.546834 CCGATTCGTTCTCCTCGTTC 58.453 55.000 5.20 0.00 0.00 3.95
1450 5739 1.135489 CCGATTCGTTCTCCTCGTTCA 60.135 52.381 5.20 0.00 0.00 3.18
1592 5899 0.796312 GGTGTACTTGACATGCACCG 59.204 55.000 1.21 0.00 41.99 4.94
1663 10053 3.126073 CTCTTTGCTTGTTTGGGCTTTC 58.874 45.455 0.00 0.00 0.00 2.62
1850 10256 1.608590 CACGTTCATGAGCCCAAAACT 59.391 47.619 3.76 0.00 0.00 2.66
1856 10262 4.846779 TCATGAGCCCAAAACTACAAAC 57.153 40.909 0.00 0.00 0.00 2.93
1946 10358 3.608662 ACCTCGCCAACCGACGAA 61.609 61.111 0.00 0.00 41.89 3.85
1958 10370 0.871722 CCGACGAAGCATTTGACCAA 59.128 50.000 0.00 0.00 32.44 3.67
1988 10400 2.619074 GCTACCTCCACCTGCTTCATTT 60.619 50.000 0.00 0.00 0.00 2.32
1991 10403 1.542492 CTCCACCTGCTTCATTTGCT 58.458 50.000 0.00 0.00 0.00 3.91
2005 10417 0.815213 TTTGCTGAGCTCAGTTGCGT 60.815 50.000 37.25 0.00 45.45 5.24
2044 10457 2.424812 GGGGCATTAAGGTGATGTGGAT 60.425 50.000 0.00 0.00 0.00 3.41
2064 10532 1.758280 TGTTGTTGAGTAGTGGACCGT 59.242 47.619 0.00 0.00 0.00 4.83
2083 10551 0.039035 TTTGGGGCCTATGCGAAAGT 59.961 50.000 0.84 0.00 38.85 2.66
2184 10923 4.782019 TTTCTTTTGCCTCGCACATATT 57.218 36.364 0.00 0.00 38.71 1.28
2197 10937 4.637977 TCGCACATATTAGGTTGATTTGCA 59.362 37.500 0.00 0.00 0.00 4.08
2234 12780 0.674895 CAAGGCAGTGGTAGTGAGGC 60.675 60.000 0.00 0.00 0.00 4.70
2235 12781 1.842381 AAGGCAGTGGTAGTGAGGCC 61.842 60.000 0.00 0.00 41.65 5.19
2245 12791 1.823610 GTAGTGAGGCCGAGTTAGGTT 59.176 52.381 0.00 0.00 0.00 3.50
2278 12827 6.370994 TGGTTCTTCTGTTACACGTTTTTGTA 59.629 34.615 0.00 0.00 0.00 2.41
2282 12831 8.700722 TCTTCTGTTACACGTTTTTGTACTTA 57.299 30.769 0.00 0.00 31.53 2.24
2315 13091 2.542595 CCGATAATACGGCAACAACTCC 59.457 50.000 0.00 0.00 46.20 3.85
2316 13092 3.191669 CGATAATACGGCAACAACTCCA 58.808 45.455 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 5.886992 ACTTTTGAAACCGGACAAGTTTAG 58.113 37.500 9.46 9.65 37.55 1.85
3 4 5.900865 ACTTTTGAAACCGGACAAGTTTA 57.099 34.783 9.46 0.00 37.55 2.01
6 7 5.648960 TCTTAACTTTTGAAACCGGACAAGT 59.351 36.000 9.46 3.66 0.00 3.16
7 8 6.126568 TCTTAACTTTTGAAACCGGACAAG 57.873 37.500 9.46 2.99 0.00 3.16
8 9 5.648960 ACTCTTAACTTTTGAAACCGGACAA 59.351 36.000 9.46 8.98 0.00 3.18
11 12 4.035909 GCACTCTTAACTTTTGAAACCGGA 59.964 41.667 9.46 0.00 0.00 5.14
12 13 4.201970 TGCACTCTTAACTTTTGAAACCGG 60.202 41.667 0.00 0.00 0.00 5.28
14 15 5.232202 GCTTGCACTCTTAACTTTTGAAACC 59.768 40.000 0.00 0.00 0.00 3.27
16 17 6.035843 CAGCTTGCACTCTTAACTTTTGAAA 58.964 36.000 0.00 0.00 0.00 2.69
19 20 4.925068 ACAGCTTGCACTCTTAACTTTTG 58.075 39.130 0.00 0.00 0.00 2.44
20 21 4.884164 AGACAGCTTGCACTCTTAACTTTT 59.116 37.500 0.00 0.00 0.00 2.27
21 22 4.274459 CAGACAGCTTGCACTCTTAACTTT 59.726 41.667 0.00 0.00 0.00 2.66
22 23 3.812053 CAGACAGCTTGCACTCTTAACTT 59.188 43.478 0.00 0.00 0.00 2.66
23 24 3.397482 CAGACAGCTTGCACTCTTAACT 58.603 45.455 0.00 0.00 0.00 2.24
24 25 2.481952 CCAGACAGCTTGCACTCTTAAC 59.518 50.000 0.00 0.00 0.00 2.01
26 27 1.694150 ACCAGACAGCTTGCACTCTTA 59.306 47.619 0.00 0.00 0.00 2.10
27 28 0.471617 ACCAGACAGCTTGCACTCTT 59.528 50.000 0.00 0.00 0.00 2.85
28 29 0.471617 AACCAGACAGCTTGCACTCT 59.528 50.000 0.00 0.00 0.00 3.24
29 30 1.312815 AAACCAGACAGCTTGCACTC 58.687 50.000 0.00 0.00 0.00 3.51
30 31 1.406539 CAAAACCAGACAGCTTGCACT 59.593 47.619 0.00 0.00 0.00 4.40
31 32 1.405105 TCAAAACCAGACAGCTTGCAC 59.595 47.619 0.00 0.00 0.00 4.57
32 33 1.761449 TCAAAACCAGACAGCTTGCA 58.239 45.000 0.00 0.00 0.00 4.08
33 34 2.099756 ACTTCAAAACCAGACAGCTTGC 59.900 45.455 0.00 0.00 0.00 4.01
34 35 4.376340 AACTTCAAAACCAGACAGCTTG 57.624 40.909 0.00 0.00 0.00 4.01
35 36 5.067805 CCTTAACTTCAAAACCAGACAGCTT 59.932 40.000 0.00 0.00 0.00 3.74
36 37 4.580580 CCTTAACTTCAAAACCAGACAGCT 59.419 41.667 0.00 0.00 0.00 4.24
38 39 5.008712 GTCCCTTAACTTCAAAACCAGACAG 59.991 44.000 0.00 0.00 0.00 3.51
39 40 4.885325 GTCCCTTAACTTCAAAACCAGACA 59.115 41.667 0.00 0.00 0.00 3.41
40 41 4.024302 CGTCCCTTAACTTCAAAACCAGAC 60.024 45.833 0.00 0.00 0.00 3.51
41 42 4.131596 CGTCCCTTAACTTCAAAACCAGA 58.868 43.478 0.00 0.00 0.00 3.86
42 43 4.131596 TCGTCCCTTAACTTCAAAACCAG 58.868 43.478 0.00 0.00 0.00 4.00
43 44 4.153673 TCGTCCCTTAACTTCAAAACCA 57.846 40.909 0.00 0.00 0.00 3.67
44 45 5.503662 TTTCGTCCCTTAACTTCAAAACC 57.496 39.130 0.00 0.00 0.00 3.27
45 46 6.967135 AGATTTCGTCCCTTAACTTCAAAAC 58.033 36.000 0.00 0.00 0.00 2.43
46 47 8.152246 TCTAGATTTCGTCCCTTAACTTCAAAA 58.848 33.333 0.00 0.00 0.00 2.44
47 48 7.601508 GTCTAGATTTCGTCCCTTAACTTCAAA 59.398 37.037 0.00 0.00 0.00 2.69
49 50 6.436532 AGTCTAGATTTCGTCCCTTAACTTCA 59.563 38.462 0.00 0.00 0.00 3.02
50 51 6.865411 AGTCTAGATTTCGTCCCTTAACTTC 58.135 40.000 0.00 0.00 0.00 3.01
52 53 5.066246 CGAGTCTAGATTTCGTCCCTTAACT 59.934 44.000 16.89 0.00 0.00 2.24
53 54 5.272397 CGAGTCTAGATTTCGTCCCTTAAC 58.728 45.833 16.89 0.00 0.00 2.01
54 55 4.337555 CCGAGTCTAGATTTCGTCCCTTAA 59.662 45.833 20.97 0.00 32.73 1.85
56 57 2.688958 CCGAGTCTAGATTTCGTCCCTT 59.311 50.000 20.97 0.00 32.73 3.95
57 58 2.092538 TCCGAGTCTAGATTTCGTCCCT 60.093 50.000 20.97 2.67 32.73 4.20
60 61 5.400703 ACTTTTCCGAGTCTAGATTTCGTC 58.599 41.667 20.97 4.64 32.73 4.20
62 63 5.862323 TCAACTTTTCCGAGTCTAGATTTCG 59.138 40.000 17.75 17.75 0.00 3.46
64 65 6.166982 CCTCAACTTTTCCGAGTCTAGATTT 58.833 40.000 0.00 0.00 0.00 2.17
66 67 4.160626 CCCTCAACTTTTCCGAGTCTAGAT 59.839 45.833 0.00 0.00 0.00 1.98
67 68 3.510360 CCCTCAACTTTTCCGAGTCTAGA 59.490 47.826 0.00 0.00 0.00 2.43
68 69 3.510360 TCCCTCAACTTTTCCGAGTCTAG 59.490 47.826 0.00 0.00 0.00 2.43
69 70 3.503365 TCCCTCAACTTTTCCGAGTCTA 58.497 45.455 0.00 0.00 0.00 2.59
70 71 2.326428 TCCCTCAACTTTTCCGAGTCT 58.674 47.619 0.00 0.00 0.00 3.24
71 72 2.833631 TCCCTCAACTTTTCCGAGTC 57.166 50.000 0.00 0.00 0.00 3.36
72 73 2.637872 TCATCCCTCAACTTTTCCGAGT 59.362 45.455 0.00 0.00 0.00 4.18
73 74 3.334583 TCATCCCTCAACTTTTCCGAG 57.665 47.619 0.00 0.00 0.00 4.63
74 75 3.780804 TTCATCCCTCAACTTTTCCGA 57.219 42.857 0.00 0.00 0.00 4.55
75 76 4.278419 ACTTTTCATCCCTCAACTTTTCCG 59.722 41.667 0.00 0.00 0.00 4.30
76 77 5.791336 ACTTTTCATCCCTCAACTTTTCC 57.209 39.130 0.00 0.00 0.00 3.13
77 78 9.232473 AGTATACTTTTCATCCCTCAACTTTTC 57.768 33.333 0.00 0.00 0.00 2.29
78 79 9.588096 AAGTATACTTTTCATCCCTCAACTTTT 57.412 29.630 12.50 0.00 30.82 2.27
79 80 9.588096 AAAGTATACTTTTCATCCCTCAACTTT 57.412 29.630 22.49 0.00 43.07 2.66
96 97 9.877178 CAGGACAGAATAAGACAAAAGTATACT 57.123 33.333 0.00 0.00 0.00 2.12
97 98 9.871238 TCAGGACAGAATAAGACAAAAGTATAC 57.129 33.333 0.00 0.00 0.00 1.47
99 100 9.793259 TTTCAGGACAGAATAAGACAAAAGTAT 57.207 29.630 0.00 0.00 0.00 2.12
101 102 7.013369 GGTTTCAGGACAGAATAAGACAAAAGT 59.987 37.037 0.00 0.00 0.00 2.66
103 104 7.013274 CAGGTTTCAGGACAGAATAAGACAAAA 59.987 37.037 0.00 0.00 0.00 2.44
104 105 6.486657 CAGGTTTCAGGACAGAATAAGACAAA 59.513 38.462 0.00 0.00 0.00 2.83
105 106 5.997746 CAGGTTTCAGGACAGAATAAGACAA 59.002 40.000 0.00 0.00 0.00 3.18
106 107 5.071788 ACAGGTTTCAGGACAGAATAAGACA 59.928 40.000 0.00 0.00 0.00 3.41
107 108 5.552178 ACAGGTTTCAGGACAGAATAAGAC 58.448 41.667 0.00 0.00 0.00 3.01
117 4010 4.580580 ACTTTTGATGACAGGTTTCAGGAC 59.419 41.667 0.00 0.00 0.00 3.85
315 4221 4.281435 TGGACATACTCGTTAACCTTGTGA 59.719 41.667 0.00 0.00 0.00 3.58
328 4234 3.618690 AGAGCTTGGTTGGACATACTC 57.381 47.619 0.00 0.00 0.00 2.59
436 4344 4.670896 AGACATTTTGGTCAACCCTTTG 57.329 40.909 0.00 0.00 40.29 2.77
484 4467 0.108615 CTCCAGTCTAGTGGTTGGCG 60.109 60.000 3.80 0.00 38.88 5.69
501 4484 1.202545 TCTCTGATGATGCAGCAGCTC 60.203 52.381 21.91 10.22 45.97 4.09
505 4488 1.138464 GTCCTCTCTGATGATGCAGCA 59.862 52.381 7.31 7.31 35.86 4.41
528 4511 9.920133 TTTGTTGCTAATCATTTGCACTAATTA 57.080 25.926 5.96 0.00 36.37 1.40
555 4538 5.188434 CAATCAGAAGGTTCCTCATAGCAA 58.812 41.667 0.00 0.00 0.00 3.91
605 4588 9.757227 ATTAGTAATCTGTCTATGAAGAAGCAC 57.243 33.333 0.00 0.00 32.16 4.40
638 4621 1.131638 GCCTGTGATGTCCCCAGATA 58.868 55.000 0.00 0.00 0.00 1.98
803 4832 4.100963 TGAGAAGCTTCTGTTGGTCTGTTA 59.899 41.667 33.07 0.00 37.73 2.41
1061 5149 1.961277 CGCCGGCACAGTCTTTCTT 60.961 57.895 28.98 0.00 0.00 2.52
1068 5156 2.635229 GATGAGATCGCCGGCACAGT 62.635 60.000 28.98 7.79 0.00 3.55
1404 5688 2.675658 AACAACCTGGCATTGGTAGT 57.324 45.000 5.86 0.00 36.69 2.73
1405 5689 4.704540 TGATAAACAACCTGGCATTGGTAG 59.295 41.667 5.86 0.00 36.69 3.18
1406 5690 4.461081 GTGATAAACAACCTGGCATTGGTA 59.539 41.667 5.86 0.00 36.69 3.25
1407 5691 3.258123 GTGATAAACAACCTGGCATTGGT 59.742 43.478 5.86 0.00 39.91 3.67
1409 5693 3.848726 GGTGATAAACAACCTGGCATTG 58.151 45.455 0.00 0.00 0.00 2.82
1438 5727 0.173481 CAGGCGATGAACGAGGAGAA 59.827 55.000 0.00 0.00 45.77 2.87
1447 5736 1.879380 CCAACAAGTTCAGGCGATGAA 59.121 47.619 0.00 0.00 45.79 2.57
1448 5737 1.202758 ACCAACAAGTTCAGGCGATGA 60.203 47.619 0.00 0.00 35.62 2.92
1449 5738 1.069022 CACCAACAAGTTCAGGCGATG 60.069 52.381 0.00 0.00 0.00 3.84
1450 5739 1.238439 CACCAACAAGTTCAGGCGAT 58.762 50.000 0.00 0.00 0.00 4.58
1592 5899 4.199310 TGTAAAGCTGCCTCCACATATTC 58.801 43.478 0.00 0.00 0.00 1.75
1641 10019 1.043022 AGCCCAAACAAGCAAAGAGG 58.957 50.000 0.00 0.00 0.00 3.69
1663 10053 1.830477 CTCTTCTCCAACCCTCTCCAG 59.170 57.143 0.00 0.00 0.00 3.86
1798 10191 0.704076 AGGTTTAGGCAGCCCATTCA 59.296 50.000 8.22 0.00 0.00 2.57
1850 10256 2.265182 GGCAGCTTGGGCGTTTGTA 61.265 57.895 0.00 0.00 44.37 2.41
1856 10262 4.729856 GCTTTGGCAGCTTGGGCG 62.730 66.667 0.00 0.00 46.27 6.13
1943 10355 6.251376 GCTATTTAAGTTGGTCAAATGCTTCG 59.749 38.462 0.00 0.00 0.00 3.79
1946 10358 6.840780 AGCTATTTAAGTTGGTCAAATGCT 57.159 33.333 0.00 0.00 0.00 3.79
1958 10370 4.141688 GCAGGTGGAGGTAGCTATTTAAGT 60.142 45.833 0.00 0.00 0.00 2.24
1991 10403 4.661461 CTCACGCAACTGAGCTCA 57.339 55.556 17.19 17.19 31.57 4.26
2005 10417 1.080093 CGCTCGGGTTACAAGCTCA 60.080 57.895 0.00 0.00 33.83 4.26
2022 10434 1.024271 CACATCACCTTAATGCCCCG 58.976 55.000 0.00 0.00 0.00 5.73
2044 10457 1.758280 ACGGTCCACTACTCAACAACA 59.242 47.619 0.00 0.00 0.00 3.33
2064 10532 0.039035 ACTTTCGCATAGGCCCCAAA 59.961 50.000 0.00 0.00 36.38 3.28
2184 10923 8.177119 ACAAAAAGAGTATGCAAATCAACCTA 57.823 30.769 0.00 0.00 0.00 3.08
2197 10937 8.322091 ACTGCCTTGATAGTACAAAAAGAGTAT 58.678 33.333 0.00 0.00 0.00 2.12
2234 12780 3.244318 ACCACTAACCAAACCTAACTCGG 60.244 47.826 0.00 0.00 0.00 4.63
2235 12781 3.999046 ACCACTAACCAAACCTAACTCG 58.001 45.455 0.00 0.00 0.00 4.18
2245 12791 5.818857 GTGTAACAGAAGAACCACTAACCAA 59.181 40.000 0.00 0.00 36.32 3.67
2315 13091 9.981114 ACCTTAAAACTTCACTATTTTGGAATG 57.019 29.630 0.00 0.00 30.80 2.67
2442 13220 8.599624 ACATCAAATTAGTCCCATGAGATTTT 57.400 30.769 0.00 0.00 0.00 1.82
2483 13261 9.186837 ACAGATTCAGAATTATCAGAGCAAAAT 57.813 29.630 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.