Multiple sequence alignment - TraesCS7B01G017900

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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 TraesCS7B01G017900 chr7B 100.000 3193 0 0 1 3193 15073299 15070107 0.000000e+00 5897.0
1 TraesCS7B01G017900 chr7B 89.077 1831 108 42 505 2277 15301407 15299611 0.000000e+00 2189.0
2 TraesCS7B01G017900 chr7B 89.612 953 89 5 1266 2217 15269787 15268844 0.000000e+00 1203.0
3 TraesCS7B01G017900 chr7B 88.260 937 78 17 946 1855 15020796 15019865 0.000000e+00 1092.0
4 TraesCS7B01G017900 chr7B 95.644 505 20 2 1 503 15078454 15077950 0.000000e+00 809.0
5 TraesCS7B01G017900 chr7B 92.955 511 34 2 1 510 740988370 740988879 0.000000e+00 743.0
6 TraesCS7B01G017900 chr7B 94.602 389 18 1 1889 2277 15019868 15019483 1.640000e-167 599.0
7 TraesCS7B01G017900 chr7B 84.274 585 46 15 608 1180 15289357 15288807 2.180000e-146 529.0
8 TraesCS7B01G017900 chr7B 93.291 313 19 2 2643 2954 15298433 15298122 8.070000e-126 460.0
9 TraesCS7B01G017900 chr7B 91.401 314 24 3 2643 2954 15018246 15017934 8.190000e-116 427.0
10 TraesCS7B01G017900 chr7B 92.157 255 8 3 2950 3193 15017871 15017618 1.820000e-92 350.0
11 TraesCS7B01G017900 chr7B 77.033 418 66 20 1835 2249 14778336 14778726 2.500000e-51 213.0
12 TraesCS7B01G017900 chr7B 83.575 207 13 5 2322 2523 286566423 286566613 1.180000e-39 174.0
13 TraesCS7B01G017900 chr7B 83.854 192 13 5 2322 2511 15299613 15299438 1.970000e-37 167.0
14 TraesCS7B01G017900 chr7B 95.238 84 4 0 2560 2643 286566615 286566698 2.000000e-27 134.0
15 TraesCS7B01G017900 chr7B 85.938 64 7 2 850 912 437673037 437672975 2.060000e-07 67.6
16 TraesCS7B01G017900 chr6D 93.988 499 29 1 1 498 6421678 6422176 0.000000e+00 754.0
17 TraesCS7B01G017900 chr6D 100.000 51 0 0 2272 2322 197193414 197193364 9.430000e-16 95.3
18 TraesCS7B01G017900 chr6D 87.500 64 8 0 849 912 363455179 363455116 1.230000e-09 75.0
19 TraesCS7B01G017900 chr3B 93.574 498 32 0 1 498 172095754 172096251 0.000000e+00 743.0
20 TraesCS7B01G017900 chr2B 93.587 499 30 2 1 498 91620875 91621372 0.000000e+00 743.0
21 TraesCS7B01G017900 chr2B 93.574 498 31 1 1 498 91626034 91626530 0.000000e+00 741.0
22 TraesCS7B01G017900 chr2B 81.646 158 23 6 759 913 198760063 198759909 3.340000e-25 126.0
23 TraesCS7B01G017900 chr6B 93.083 506 31 4 1 503 30305841 30306345 0.000000e+00 737.0
24 TraesCS7B01G017900 chr6B 78.014 141 26 5 771 907 46531652 46531513 2.040000e-12 84.2
25 TraesCS7B01G017900 chr6B 100.000 34 0 0 2422 2455 172268928 172268961 2.660000e-06 63.9
26 TraesCS7B01G017900 chr5A 93.069 505 33 2 1 503 41911237 41911741 0.000000e+00 737.0
27 TraesCS7B01G017900 chr5A 100.000 34 0 0 2422 2455 616789670 616789637 2.660000e-06 63.9
28 TraesCS7B01G017900 chr5A 100.000 33 0 0 2423 2455 582940825 582940793 9.560000e-06 62.1
29 TraesCS7B01G017900 chr1A 93.069 505 33 2 1 503 561685118 561684614 0.000000e+00 737.0
30 TraesCS7B01G017900 chr1A 76.821 151 26 5 761 905 442606677 442606824 3.420000e-10 76.8
31 TraesCS7B01G017900 chr1A 100.000 39 0 0 768 806 34409785 34409747 4.420000e-09 73.1
32 TraesCS7B01G017900 chr7D 83.073 768 64 27 893 1621 73115287 73116027 3.470000e-179 638.0
33 TraesCS7B01G017900 chr7D 89.189 370 24 9 504 857 73114930 73115299 6.280000e-122 448.0
34 TraesCS7B01G017900 chr7D 80.858 606 75 19 1266 1871 72218629 72218065 3.780000e-119 438.0
35 TraesCS7B01G017900 chr7D 83.281 317 37 12 2643 2954 72216424 72216119 8.720000e-71 278.0
36 TraesCS7B01G017900 chr7D 86.667 255 18 6 2950 3193 72216056 72215807 5.250000e-68 268.0
37 TraesCS7B01G017900 chr7D 78.462 325 50 12 2643 2951 73117070 73117390 9.040000e-46 195.0
38 TraesCS7B01G017900 chr7D 87.850 107 7 6 2643 2745 71812640 71812536 1.560000e-23 121.0
39 TraesCS7B01G017900 chr7D 92.593 81 4 2 2643 2722 71864448 71864527 7.240000e-22 115.0
40 TraesCS7B01G017900 chr7D 100.000 51 0 0 2272 2322 393594157 393594107 9.430000e-16 95.3
41 TraesCS7B01G017900 chr7A 92.580 283 21 0 1995 2277 77197167 77196885 1.070000e-109 407.0
42 TraesCS7B01G017900 chr7A 89.590 317 24 7 2643 2954 77194969 77194657 8.300000e-106 394.0
43 TraesCS7B01G017900 chr7A 89.667 300 12 7 2349 2645 77196874 77196591 6.510000e-97 364.0
44 TraesCS7B01G017900 chr7A 86.000 250 21 10 2952 3193 77194590 77194347 4.090000e-64 255.0
45 TraesCS7B01G017900 chr7A 82.787 122 15 5 2643 2763 76954080 76954196 1.570000e-18 104.0
46 TraesCS7B01G017900 chr7A 89.796 49 5 0 1393 1441 77197268 77197220 2.660000e-06 63.9
47 TraesCS7B01G017900 chr2A 81.149 435 61 13 1765 2187 619761846 619761421 2.370000e-86 329.0
48 TraesCS7B01G017900 chr5D 78.797 349 43 20 2322 2645 47779403 47779745 4.180000e-49 206.0
49 TraesCS7B01G017900 chr4D 93.421 76 4 1 2643 2717 415583662 415583737 9.360000e-21 111.0
50 TraesCS7B01G017900 chr4D 100.000 51 0 0 2272 2322 36583494 36583544 9.430000e-16 95.3
51 TraesCS7B01G017900 chr4D 98.039 51 1 0 2272 2322 344864656 344864706 4.390000e-14 89.8
52 TraesCS7B01G017900 chr4D 98.039 51 1 0 2272 2322 485141411 485141361 4.390000e-14 89.8
53 TraesCS7B01G017900 chr4D 98.039 51 1 0 2272 2322 488339584 488339534 4.390000e-14 89.8
54 TraesCS7B01G017900 chr1D 100.000 50 0 0 2272 2321 383294672 383294721 3.390000e-15 93.5
55 TraesCS7B01G017900 chr1D 98.077 52 1 0 2272 2323 49359019 49358968 1.220000e-14 91.6
56 TraesCS7B01G017900 chr1D 76.821 151 26 5 761 905 342873068 342873215 3.420000e-10 76.8
57 TraesCS7B01G017900 chr1D 100.000 39 0 0 768 806 35654227 35654189 4.420000e-09 73.1
58 TraesCS7B01G017900 chr1D 100.000 30 0 0 2464 2493 442117417 442117446 4.450000e-04 56.5
59 TraesCS7B01G017900 chrUn 98.039 51 1 0 2272 2322 91673757 91673807 4.390000e-14 89.8
60 TraesCS7B01G017900 chrUn 78.873 142 23 7 771 907 95444644 95444505 4.390000e-14 89.8
61 TraesCS7B01G017900 chr6A 78.014 141 26 5 771 907 26815953 26815814 2.040000e-12 84.2
62 TraesCS7B01G017900 chr6A 87.500 64 8 0 849 912 504394544 504394481 1.230000e-09 75.0
63 TraesCS7B01G017900 chr1B 100.000 39 0 0 768 806 54136164 54136126 4.420000e-09 73.1
64 TraesCS7B01G017900 chr4A 100.000 34 0 0 2422 2455 95388048 95388081 2.660000e-06 63.9
65 TraesCS7B01G017900 chr4A 100.000 31 0 0 2425 2455 90328337 90328307 1.240000e-04 58.4
66 TraesCS7B01G017900 chr3D 100.000 30 0 0 2464 2493 189780232 189780203 4.450000e-04 56.5
67 TraesCS7B01G017900 chr3D 100.000 28 0 0 2428 2455 189780252 189780225 6.000000e-03 52.8


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 TraesCS7B01G017900 chr7B 15070107 15073299 3192 True 5897.000000 5897 100.000000 1 3193 1 chr7B.!!$R1 3192
1 TraesCS7B01G017900 chr7B 15268844 15269787 943 True 1203.000000 1203 89.612000 1266 2217 1 chr7B.!!$R3 951
2 TraesCS7B01G017900 chr7B 15298122 15301407 3285 True 938.666667 2189 88.740667 505 2954 3 chr7B.!!$R7 2449
3 TraesCS7B01G017900 chr7B 15077950 15078454 504 True 809.000000 809 95.644000 1 503 1 chr7B.!!$R2 502
4 TraesCS7B01G017900 chr7B 740988370 740988879 509 False 743.000000 743 92.955000 1 510 1 chr7B.!!$F2 509
5 TraesCS7B01G017900 chr7B 15017618 15020796 3178 True 617.000000 1092 91.605000 946 3193 4 chr7B.!!$R6 2247
6 TraesCS7B01G017900 chr7B 15288807 15289357 550 True 529.000000 529 84.274000 608 1180 1 chr7B.!!$R4 572
7 TraesCS7B01G017900 chr6B 30305841 30306345 504 False 737.000000 737 93.083000 1 503 1 chr6B.!!$F1 502
8 TraesCS7B01G017900 chr5A 41911237 41911741 504 False 737.000000 737 93.069000 1 503 1 chr5A.!!$F1 502
9 TraesCS7B01G017900 chr1A 561684614 561685118 504 True 737.000000 737 93.069000 1 503 1 chr1A.!!$R2 502
10 TraesCS7B01G017900 chr7D 73114930 73117390 2460 False 427.000000 638 83.574667 504 2951 3 chr7D.!!$F2 2447
11 TraesCS7B01G017900 chr7D 72215807 72218629 2822 True 328.000000 438 83.602000 1266 3193 3 chr7D.!!$R3 1927
12 TraesCS7B01G017900 chr7A 77194347 77197268 2921 True 296.780000 407 89.526600 1393 3193 5 chr7A.!!$R1 1800

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
498 500 0.039256 CATTGTTGTTGTCCAGCCCG 60.039 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2450 2608 0.242017 GTGCATTCAGAACTGGGTGC 59.758 55.0 18.01 18.01 39.77 5.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 3.691118 CCGATTGAGCTGAAATTTGGAGA 59.309 43.478 0.00 0.00 0.00 3.71
142 143 2.225293 ACTGGAGGGTACAGAAGCTGTA 60.225 50.000 3.32 3.32 43.46 2.74
171 172 5.072741 TCTACTTTGCTGAAATCTTGCCTT 58.927 37.500 0.00 0.00 0.00 4.35
338 339 3.211045 TCAAGTTGAGGAGGTTTTTCCG 58.789 45.455 0.08 0.00 42.29 4.30
348 349 3.189910 GGAGGTTTTTCCGCGTTAAATCT 59.810 43.478 4.92 7.81 41.99 2.40
408 409 5.047660 TGCTTACTTGTTGGTTGAAGTTGTT 60.048 36.000 0.00 0.00 34.28 2.83
409 410 5.867174 GCTTACTTGTTGGTTGAAGTTGTTT 59.133 36.000 0.00 0.00 34.28 2.83
426 427 8.600449 AAGTTGTTTTCAAAGTTCATCACAAA 57.400 26.923 0.00 0.00 41.76 2.83
432 433 9.086336 GTTTTCAAAGTTCATCACAAATGAAGA 57.914 29.630 0.88 0.00 38.69 2.87
498 500 0.039256 CATTGTTGTTGTCCAGCCCG 60.039 55.000 0.00 0.00 0.00 6.13
510 512 3.258372 TGTCCAGCCCGACAATATATCTC 59.742 47.826 1.10 0.00 39.78 2.75
523 525 7.222031 CGACAATATATCTCCAGTTTCGAAACA 59.778 37.037 35.29 19.48 41.30 2.83
630 644 2.421314 CCACGACACAGCCACTGA 59.579 61.111 0.78 0.00 35.18 3.41
632 646 1.068083 CACGACACAGCCACTGAGT 59.932 57.895 0.78 0.00 37.94 3.41
912 948 4.319622 CCTCGTCATCGACTTCATAGGTAC 60.320 50.000 0.00 0.00 41.35 3.34
913 949 4.449131 TCGTCATCGACTTCATAGGTACT 58.551 43.478 0.00 0.00 41.35 2.73
914 950 4.510711 TCGTCATCGACTTCATAGGTACTC 59.489 45.833 0.00 0.00 41.35 2.59
915 951 4.319622 CGTCATCGACTTCATAGGTACTCC 60.320 50.000 0.00 0.00 38.68 3.85
916 952 6.484041 CGTCATCGACTTCATAGGTACTCCT 61.484 48.000 0.00 0.00 42.52 3.69
917 953 7.234361 CGTCATCGACTTCATAGGTACTCCTA 61.234 46.154 0.00 0.00 43.64 2.94
929 965 3.483808 GTACTCCTAGGTACCTACGCT 57.516 52.381 18.10 5.57 36.88 5.07
931 980 1.202627 ACTCCTAGGTACCTACGCTCG 60.203 57.143 18.10 7.78 0.00 5.03
936 985 3.885521 GTACCTACGCTCGCCGCT 61.886 66.667 0.00 0.00 41.76 5.52
942 991 2.515947 CTACGCTCGCCGCTCTATCC 62.516 65.000 0.00 0.00 41.76 2.59
950 999 1.300233 CCGCTCTATCCAGCCGTTC 60.300 63.158 0.00 0.00 35.84 3.95
958 1007 2.684001 ATCCAGCCGTTCGTTTGATA 57.316 45.000 0.00 0.00 0.00 2.15
980 1029 5.599999 AGTATAATTCTGACGGCTTGACT 57.400 39.130 0.00 0.00 0.00 3.41
1121 1174 2.559840 GTCGCTCTTCGTCACCGA 59.440 61.111 0.00 0.00 42.41 4.69
1209 1262 3.053896 GGCGGCACCAGTGGTAAC 61.054 66.667 16.22 10.31 38.86 2.50
1210 1263 2.032071 GCGGCACCAGTGGTAACT 59.968 61.111 16.22 0.00 36.98 2.24
1215 1271 2.879646 CGGCACCAGTGGTAACTAAAAA 59.120 45.455 16.22 0.00 33.79 1.94
1217 1273 3.005050 GGCACCAGTGGTAACTAAAAACC 59.995 47.826 16.22 1.94 33.79 3.27
1255 1320 8.868522 AACATGGTCTGAATTCTCTGAATTTA 57.131 30.769 7.05 2.94 31.99 1.40
1257 1322 8.954350 ACATGGTCTGAATTCTCTGAATTTAAG 58.046 33.333 7.05 8.06 31.99 1.85
1259 1324 9.917887 ATGGTCTGAATTCTCTGAATTTAAGAT 57.082 29.630 7.05 5.12 31.99 2.40
1260 1325 9.170734 TGGTCTGAATTCTCTGAATTTAAGATG 57.829 33.333 7.05 1.75 31.99 2.90
1261 1326 8.127954 GGTCTGAATTCTCTGAATTTAAGATGC 58.872 37.037 7.05 8.85 31.99 3.91
1423 1501 2.223829 CGGTTATCAGCCAGATCTCGTT 60.224 50.000 0.00 0.00 38.19 3.85
1544 1630 2.421424 CTGCTCAACTATTTGCAGGACC 59.579 50.000 5.98 0.00 46.24 4.46
1579 1668 2.610232 GGCTCGCAAATTCATGGTGTTT 60.610 45.455 0.00 0.00 0.00 2.83
1637 1726 1.156645 GGAGCTTCCACATAGCAGCG 61.157 60.000 0.00 0.00 41.11 5.18
1681 1770 3.181511 GCATGACAAGTTACAATAGCGCA 60.182 43.478 11.47 0.00 0.00 6.09
1721 1810 2.417978 CTGAACAACAGCTTGGCCA 58.582 52.632 0.00 0.00 39.86 5.36
1744 1833 2.413837 GTTAGGAAGACGCTGCAGAAA 58.586 47.619 20.43 0.00 0.00 2.52
1860 1993 3.717707 CCATCCGACGAGTACATGAATT 58.282 45.455 0.00 0.00 0.00 2.17
1920 2059 6.053005 TCAAGTACTACTGAAACTGGTTTGG 58.947 40.000 0.00 0.00 32.11 3.28
1921 2060 5.625568 AGTACTACTGAAACTGGTTTGGT 57.374 39.130 3.30 5.37 32.11 3.67
1928 2067 2.955660 TGAAACTGGTTTGGTGGTGATC 59.044 45.455 3.30 0.00 32.11 2.92
1942 2081 2.295885 GGTGATCATTTCAGGGCTCAG 58.704 52.381 0.00 0.00 34.17 3.35
2003 2142 6.721318 AGCTTACAATTTTGACCCAGATCTA 58.279 36.000 0.00 0.00 0.00 1.98
2275 2422 3.861341 GCTGTCAGATAACAGGGCA 57.139 52.632 3.32 0.00 45.52 5.36
2276 2423 2.113860 GCTGTCAGATAACAGGGCAA 57.886 50.000 3.32 0.00 45.52 4.52
2277 2424 2.436417 GCTGTCAGATAACAGGGCAAA 58.564 47.619 3.32 0.00 45.52 3.68
2278 2425 3.019564 GCTGTCAGATAACAGGGCAAAT 58.980 45.455 3.32 0.00 45.52 2.32
2279 2426 3.181493 GCTGTCAGATAACAGGGCAAATG 60.181 47.826 3.32 0.00 45.52 2.32
2280 2427 4.264253 CTGTCAGATAACAGGGCAAATGA 58.736 43.478 0.00 0.00 42.42 2.57
2281 2428 4.858850 TGTCAGATAACAGGGCAAATGAT 58.141 39.130 0.00 0.00 0.00 2.45
2282 2429 4.883585 TGTCAGATAACAGGGCAAATGATC 59.116 41.667 0.00 0.00 0.00 2.92
2283 2430 4.883585 GTCAGATAACAGGGCAAATGATCA 59.116 41.667 0.00 0.00 0.00 2.92
2284 2431 5.357878 GTCAGATAACAGGGCAAATGATCAA 59.642 40.000 0.00 0.00 0.00 2.57
2285 2432 5.951148 TCAGATAACAGGGCAAATGATCAAA 59.049 36.000 0.00 0.00 0.00 2.69
2286 2433 6.608405 TCAGATAACAGGGCAAATGATCAAAT 59.392 34.615 0.00 0.00 0.00 2.32
2287 2434 6.700081 CAGATAACAGGGCAAATGATCAAATG 59.300 38.462 0.00 2.90 0.00 2.32
2288 2435 3.899052 ACAGGGCAAATGATCAAATGG 57.101 42.857 0.00 0.00 0.00 3.16
2289 2436 3.443052 ACAGGGCAAATGATCAAATGGA 58.557 40.909 0.00 0.00 0.00 3.41
2290 2437 3.449737 ACAGGGCAAATGATCAAATGGAG 59.550 43.478 0.00 0.00 0.00 3.86
2291 2438 3.702548 CAGGGCAAATGATCAAATGGAGA 59.297 43.478 0.00 0.00 0.00 3.71
2292 2439 4.160814 CAGGGCAAATGATCAAATGGAGAA 59.839 41.667 0.00 0.00 0.00 2.87
2293 2440 4.404715 AGGGCAAATGATCAAATGGAGAAG 59.595 41.667 0.00 0.00 0.00 2.85
2294 2441 4.161001 GGGCAAATGATCAAATGGAGAAGT 59.839 41.667 0.00 0.00 0.00 3.01
2295 2442 5.360714 GGGCAAATGATCAAATGGAGAAGTA 59.639 40.000 0.00 0.00 0.00 2.24
2296 2443 6.127366 GGGCAAATGATCAAATGGAGAAGTAA 60.127 38.462 0.00 0.00 0.00 2.24
2297 2444 7.322664 GGCAAATGATCAAATGGAGAAGTAAA 58.677 34.615 0.00 0.00 0.00 2.01
2298 2445 7.490402 GGCAAATGATCAAATGGAGAAGTAAAG 59.510 37.037 0.00 0.00 0.00 1.85
2299 2446 8.031277 GCAAATGATCAAATGGAGAAGTAAAGT 58.969 33.333 0.00 0.00 0.00 2.66
2300 2447 9.350357 CAAATGATCAAATGGAGAAGTAAAGTG 57.650 33.333 0.00 0.00 0.00 3.16
2301 2448 7.636150 ATGATCAAATGGAGAAGTAAAGTGG 57.364 36.000 0.00 0.00 0.00 4.00
2302 2449 5.945784 TGATCAAATGGAGAAGTAAAGTGGG 59.054 40.000 0.00 0.00 0.00 4.61
2303 2450 4.662278 TCAAATGGAGAAGTAAAGTGGGG 58.338 43.478 0.00 0.00 0.00 4.96
2304 2451 2.808906 ATGGAGAAGTAAAGTGGGGC 57.191 50.000 0.00 0.00 0.00 5.80
2305 2452 1.440618 TGGAGAAGTAAAGTGGGGCA 58.559 50.000 0.00 0.00 0.00 5.36
2306 2453 1.777878 TGGAGAAGTAAAGTGGGGCAA 59.222 47.619 0.00 0.00 0.00 4.52
2307 2454 2.175931 TGGAGAAGTAAAGTGGGGCAAA 59.824 45.455 0.00 0.00 0.00 3.68
2308 2455 3.227614 GGAGAAGTAAAGTGGGGCAAAA 58.772 45.455 0.00 0.00 0.00 2.44
2309 2456 3.255888 GGAGAAGTAAAGTGGGGCAAAAG 59.744 47.826 0.00 0.00 0.00 2.27
2310 2457 4.142038 GAGAAGTAAAGTGGGGCAAAAGA 58.858 43.478 0.00 0.00 0.00 2.52
2311 2458 4.740902 AGAAGTAAAGTGGGGCAAAAGAT 58.259 39.130 0.00 0.00 0.00 2.40
2312 2459 4.767409 AGAAGTAAAGTGGGGCAAAAGATC 59.233 41.667 0.00 0.00 0.00 2.75
2313 2460 3.431415 AGTAAAGTGGGGCAAAAGATCC 58.569 45.455 0.00 0.00 0.00 3.36
2314 2461 2.397044 AAAGTGGGGCAAAAGATCCA 57.603 45.000 0.00 0.00 0.00 3.41
2315 2462 2.397044 AAGTGGGGCAAAAGATCCAA 57.603 45.000 0.00 0.00 0.00 3.53
2316 2463 2.629017 AGTGGGGCAAAAGATCCAAT 57.371 45.000 0.00 0.00 0.00 3.16
2317 2464 2.906568 AGTGGGGCAAAAGATCCAATT 58.093 42.857 0.00 0.00 0.00 2.32
2318 2465 3.250617 AGTGGGGCAAAAGATCCAATTT 58.749 40.909 0.00 0.00 0.00 1.82
2319 2466 3.261643 AGTGGGGCAAAAGATCCAATTTC 59.738 43.478 0.00 0.00 0.00 2.17
2320 2467 3.261643 GTGGGGCAAAAGATCCAATTTCT 59.738 43.478 0.00 0.00 0.00 2.52
2347 2494 2.810439 AGTCAGAGACAGTGTTGCTC 57.190 50.000 0.00 0.00 34.60 4.26
2399 2551 5.468072 ACAGCTGTGTAGAATGACAGAAAAG 59.532 40.000 20.97 0.00 41.90 2.27
2408 2560 8.367911 TGTAGAATGACAGAAAAGAAGAGCTTA 58.632 33.333 0.00 0.00 35.24 3.09
2447 2605 9.197306 TCCTGTTATAGACTTGTTTCTGCTATA 57.803 33.333 0.00 0.00 0.00 1.31
2452 2610 9.830975 TTATAGACTTGTTTCTGCTATAATGCA 57.169 29.630 0.00 0.00 41.05 3.96
2453 2611 6.428385 AGACTTGTTTCTGCTATAATGCAC 57.572 37.500 0.00 0.00 38.12 4.57
2454 2612 5.355350 AGACTTGTTTCTGCTATAATGCACC 59.645 40.000 0.00 0.00 38.12 5.01
2455 2613 4.399303 ACTTGTTTCTGCTATAATGCACCC 59.601 41.667 0.00 0.00 38.12 4.61
2456 2614 3.961849 TGTTTCTGCTATAATGCACCCA 58.038 40.909 0.00 0.00 38.12 4.51
2458 2616 3.931907 TTCTGCTATAATGCACCCAGT 57.068 42.857 0.00 0.00 38.12 4.00
2459 2617 3.931907 TCTGCTATAATGCACCCAGTT 57.068 42.857 0.00 0.00 38.12 3.16
2462 2620 3.544684 TGCTATAATGCACCCAGTTCTG 58.455 45.455 0.00 0.00 38.12 3.02
2555 2737 5.220154 GCAAATTTCTGATGCACAAGAATCG 60.220 40.000 12.38 4.79 39.81 3.34
2803 4682 0.837940 GCTTAAGTAGGGGTGGGGAG 59.162 60.000 4.02 0.00 0.00 4.30
2804 4683 1.508256 CTTAAGTAGGGGTGGGGAGG 58.492 60.000 0.00 0.00 0.00 4.30
2805 4684 1.009183 CTTAAGTAGGGGTGGGGAGGA 59.991 57.143 0.00 0.00 0.00 3.71
2808 4688 0.426022 AGTAGGGGTGGGGAGGATTT 59.574 55.000 0.00 0.00 0.00 2.17
2822 4702 3.186390 GATTTGAGGATGGCGCGCC 62.186 63.158 42.35 42.35 0.00 6.53
2837 4717 3.127533 GCCGCTGGAGCATTTCGT 61.128 61.111 0.00 0.00 42.21 3.85
2839 4719 2.753966 CCGCTGGAGCATTTCGTGG 61.754 63.158 0.00 0.00 42.21 4.94
3016 4968 7.339212 TGACCCTTTACAACATGATTCATTAGG 59.661 37.037 0.00 0.00 0.00 2.69
3189 5155 2.202676 CGTCGCTTCTCCCTGAGC 60.203 66.667 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 2.828520 ACACACGAGTTCATGAGATCCT 59.171 45.455 0.00 0.00 0.00 3.24
142 143 8.239998 GCAAGATTTCAGCAAAGTAGAGTTTAT 58.760 33.333 0.00 0.00 0.00 1.40
171 172 3.062763 CAACAGCAACAACAACCACAAA 58.937 40.909 0.00 0.00 0.00 2.83
208 209 8.410673 TCTAGAGAGATTTACAACACACTCTT 57.589 34.615 0.00 0.00 35.34 2.85
338 339 4.670621 CACAAGTGACACAAGATTTAACGC 59.329 41.667 8.59 0.00 0.00 4.84
348 349 2.491298 ACAACATGCACAAGTGACACAA 59.509 40.909 8.59 0.00 0.00 3.33
408 409 9.304731 CTTCTTCATTTGTGATGAACTTTGAAA 57.695 29.630 0.00 0.00 34.66 2.69
409 410 7.436080 GCTTCTTCATTTGTGATGAACTTTGAA 59.564 33.333 0.00 0.89 34.66 2.69
426 427 3.070018 GCACACTACACAGCTTCTTCAT 58.930 45.455 0.00 0.00 0.00 2.57
432 433 5.300969 CAAATATGCACACTACACAGCTT 57.699 39.130 0.00 0.00 0.00 3.74
460 462 0.447801 GCGCTGGACAAATTCATCGT 59.552 50.000 0.00 0.00 0.00 3.73
463 465 2.231964 ACAATGCGCTGGACAAATTCAT 59.768 40.909 9.73 0.00 0.00 2.57
498 500 8.328864 GTGTTTCGAAACTGGAGATATATTGTC 58.671 37.037 33.94 8.96 39.59 3.18
503 505 7.165460 TCTGTGTTTCGAAACTGGAGATATA 57.835 36.000 33.94 13.80 39.59 0.86
510 512 4.811555 TCAATCTGTGTTTCGAAACTGG 57.188 40.909 33.94 24.33 39.59 4.00
523 525 4.395231 TCGTACTGATCGAGTTCAATCTGT 59.605 41.667 0.00 0.00 37.66 3.41
549 551 0.960364 GGGCTCGAGATTTGGTTGCA 60.960 55.000 18.75 0.00 0.00 4.08
630 644 2.256764 CGAGCGAGCTCACACACT 59.743 61.111 22.81 2.15 42.86 3.55
632 646 3.977244 TGCGAGCGAGCTCACACA 61.977 61.111 22.81 14.99 42.86 3.72
756 792 3.109592 TTGAACACGGCCGGGAACT 62.110 57.895 38.56 18.58 0.00 3.01
912 948 1.510776 CGAGCGTAGGTACCTAGGAG 58.489 60.000 35.08 23.63 39.88 3.69
913 949 0.533755 GCGAGCGTAGGTACCTAGGA 60.534 60.000 35.08 11.98 39.88 2.94
914 950 1.513836 GGCGAGCGTAGGTACCTAGG 61.514 65.000 29.42 29.42 39.88 3.02
915 951 1.839598 CGGCGAGCGTAGGTACCTAG 61.840 65.000 22.37 16.10 39.88 3.02
916 952 1.889105 CGGCGAGCGTAGGTACCTA 60.889 63.158 18.10 18.10 39.88 3.08
917 953 3.207669 CGGCGAGCGTAGGTACCT 61.208 66.667 20.57 20.57 39.88 3.08
929 965 3.606662 GGCTGGATAGAGCGGCGA 61.607 66.667 12.98 0.00 40.13 5.54
931 980 3.447025 AACGGCTGGATAGAGCGGC 62.447 63.158 0.00 0.00 41.69 6.53
936 985 1.546923 TCAAACGAACGGCTGGATAGA 59.453 47.619 0.00 0.00 0.00 1.98
942 991 6.764877 ATTATACTATCAAACGAACGGCTG 57.235 37.500 0.00 0.00 0.00 4.85
950 999 6.641314 AGCCGTCAGAATTATACTATCAAACG 59.359 38.462 0.00 0.00 0.00 3.60
958 1007 5.361285 AGAGTCAAGCCGTCAGAATTATACT 59.639 40.000 0.00 0.00 0.00 2.12
980 1029 1.620739 GGCCTGAGCTGATCACCAGA 61.621 60.000 13.63 0.00 45.78 3.86
1018 1067 3.798511 GGACTGCAGGTAGGGGCC 61.799 72.222 19.93 0.00 0.00 5.80
1121 1174 0.985490 GAGGGAGAAGGGGCTGATGT 60.985 60.000 0.00 0.00 0.00 3.06
1261 1326 3.364565 GCCTGCAAATCAAGCAAACAATG 60.365 43.478 0.00 0.00 42.17 2.82
1264 1342 1.540797 GGCCTGCAAATCAAGCAAACA 60.541 47.619 0.00 0.00 42.17 2.83
1268 1346 1.969085 CTGGCCTGCAAATCAAGCA 59.031 52.632 3.32 0.00 40.19 3.91
1275 1353 2.601367 GGGAAGCTGGCCTGCAAA 60.601 61.111 32.96 0.00 34.99 3.68
1374 1452 1.190323 CGTTTGCTTGACACTCTCGAC 59.810 52.381 0.00 0.00 0.00 4.20
1423 1501 5.968676 ACTCCAAATTACCTGTATAGCCA 57.031 39.130 0.00 0.00 0.00 4.75
1472 1558 8.902806 AGATTCGCCAGTTATTTTGATCATTTA 58.097 29.630 0.00 0.00 0.00 1.40
1544 1630 1.227380 GAGCCCCGATGCTGTACAG 60.227 63.158 18.93 18.93 42.95 2.74
1579 1668 2.279851 CCGATCGGCGCCATGTTA 60.280 61.111 28.98 6.03 39.11 2.41
1637 1726 4.505808 CAGCCATACTCATCCAGATCATC 58.494 47.826 0.00 0.00 0.00 2.92
1702 1791 0.395586 TGGCCAAGCTGTTGTTCAGT 60.396 50.000 0.61 0.00 45.23 3.41
1721 1810 0.685097 TGCAGCGTCTTCCTAACCTT 59.315 50.000 0.00 0.00 0.00 3.50
1744 1833 0.315951 CGACGTACATGATCGACGCT 60.316 55.000 19.00 7.26 40.19 5.07
1860 1993 5.104151 TCAGATATGGCTATGAACCAAACCA 60.104 40.000 0.00 0.00 41.49 3.67
1920 2059 2.019984 GAGCCCTGAAATGATCACCAC 58.980 52.381 0.00 0.00 33.47 4.16
1921 2060 1.634973 TGAGCCCTGAAATGATCACCA 59.365 47.619 0.00 0.00 33.47 4.17
1928 2067 2.579873 CCATACCTGAGCCCTGAAATG 58.420 52.381 0.00 0.00 0.00 2.32
2003 2142 0.692476 TCTTGCTGGTGCCACAGTAT 59.308 50.000 0.00 0.00 40.59 2.12
2274 2421 9.350357 CACTTTACTTCTCCATTTGATCATTTG 57.650 33.333 0.00 0.00 0.00 2.32
2275 2422 8.526147 CCACTTTACTTCTCCATTTGATCATTT 58.474 33.333 0.00 0.00 0.00 2.32
2276 2423 7.123247 CCCACTTTACTTCTCCATTTGATCATT 59.877 37.037 0.00 0.00 0.00 2.57
2277 2424 6.604795 CCCACTTTACTTCTCCATTTGATCAT 59.395 38.462 0.00 0.00 0.00 2.45
2278 2425 5.945784 CCCACTTTACTTCTCCATTTGATCA 59.054 40.000 0.00 0.00 0.00 2.92
2279 2426 5.358160 CCCCACTTTACTTCTCCATTTGATC 59.642 44.000 0.00 0.00 0.00 2.92
2280 2427 5.264395 CCCCACTTTACTTCTCCATTTGAT 58.736 41.667 0.00 0.00 0.00 2.57
2281 2428 4.662278 CCCCACTTTACTTCTCCATTTGA 58.338 43.478 0.00 0.00 0.00 2.69
2282 2429 3.193479 GCCCCACTTTACTTCTCCATTTG 59.807 47.826 0.00 0.00 0.00 2.32
2283 2430 3.181423 TGCCCCACTTTACTTCTCCATTT 60.181 43.478 0.00 0.00 0.00 2.32
2284 2431 2.378547 TGCCCCACTTTACTTCTCCATT 59.621 45.455 0.00 0.00 0.00 3.16
2285 2432 1.992557 TGCCCCACTTTACTTCTCCAT 59.007 47.619 0.00 0.00 0.00 3.41
2286 2433 1.440618 TGCCCCACTTTACTTCTCCA 58.559 50.000 0.00 0.00 0.00 3.86
2287 2434 2.579410 TTGCCCCACTTTACTTCTCC 57.421 50.000 0.00 0.00 0.00 3.71
2288 2435 4.142038 TCTTTTGCCCCACTTTACTTCTC 58.858 43.478 0.00 0.00 0.00 2.87
2289 2436 4.178956 TCTTTTGCCCCACTTTACTTCT 57.821 40.909 0.00 0.00 0.00 2.85
2290 2437 4.082190 GGATCTTTTGCCCCACTTTACTTC 60.082 45.833 0.00 0.00 0.00 3.01
2291 2438 3.832490 GGATCTTTTGCCCCACTTTACTT 59.168 43.478 0.00 0.00 0.00 2.24
2292 2439 3.181423 TGGATCTTTTGCCCCACTTTACT 60.181 43.478 0.00 0.00 0.00 2.24
2293 2440 3.161866 TGGATCTTTTGCCCCACTTTAC 58.838 45.455 0.00 0.00 0.00 2.01
2294 2441 3.534357 TGGATCTTTTGCCCCACTTTA 57.466 42.857 0.00 0.00 0.00 1.85
2295 2442 2.397044 TGGATCTTTTGCCCCACTTT 57.603 45.000 0.00 0.00 0.00 2.66
2296 2443 2.397044 TTGGATCTTTTGCCCCACTT 57.603 45.000 0.00 0.00 0.00 3.16
2297 2444 2.629017 ATTGGATCTTTTGCCCCACT 57.371 45.000 0.00 0.00 0.00 4.00
2298 2445 3.261643 AGAAATTGGATCTTTTGCCCCAC 59.738 43.478 0.00 0.00 0.00 4.61
2299 2446 3.515104 GAGAAATTGGATCTTTTGCCCCA 59.485 43.478 0.00 0.00 0.00 4.96
2300 2447 3.515104 TGAGAAATTGGATCTTTTGCCCC 59.485 43.478 0.00 0.00 0.00 5.80
2301 2448 4.806640 TGAGAAATTGGATCTTTTGCCC 57.193 40.909 0.00 0.00 0.00 5.36
2302 2449 5.787380 ACTTGAGAAATTGGATCTTTTGCC 58.213 37.500 0.00 0.00 0.00 4.52
2303 2450 7.719778 AAACTTGAGAAATTGGATCTTTTGC 57.280 32.000 0.00 0.00 0.00 3.68
2304 2451 9.971922 ACTAAACTTGAGAAATTGGATCTTTTG 57.028 29.630 0.00 0.00 0.00 2.44
2306 2453 9.354673 TGACTAAACTTGAGAAATTGGATCTTT 57.645 29.630 0.00 0.00 0.00 2.52
2307 2454 8.924511 TGACTAAACTTGAGAAATTGGATCTT 57.075 30.769 0.00 0.00 0.00 2.40
2308 2455 8.378565 TCTGACTAAACTTGAGAAATTGGATCT 58.621 33.333 0.00 0.00 0.00 2.75
2309 2456 8.553459 TCTGACTAAACTTGAGAAATTGGATC 57.447 34.615 0.00 0.00 0.00 3.36
2310 2457 8.378565 TCTCTGACTAAACTTGAGAAATTGGAT 58.621 33.333 0.00 0.00 31.80 3.41
2311 2458 7.657761 GTCTCTGACTAAACTTGAGAAATTGGA 59.342 37.037 0.00 0.00 35.85 3.53
2312 2459 7.442364 TGTCTCTGACTAAACTTGAGAAATTGG 59.558 37.037 0.00 0.00 35.85 3.16
2313 2460 8.370493 TGTCTCTGACTAAACTTGAGAAATTG 57.630 34.615 0.00 0.00 35.85 2.32
2314 2461 8.207545 ACTGTCTCTGACTAAACTTGAGAAATT 58.792 33.333 0.00 0.00 35.85 1.82
2315 2462 7.655328 CACTGTCTCTGACTAAACTTGAGAAAT 59.345 37.037 0.00 0.00 35.85 2.17
2316 2463 6.980978 CACTGTCTCTGACTAAACTTGAGAAA 59.019 38.462 0.00 0.00 35.85 2.52
2317 2464 6.096987 ACACTGTCTCTGACTAAACTTGAGAA 59.903 38.462 0.00 0.00 35.85 2.87
2318 2465 5.594725 ACACTGTCTCTGACTAAACTTGAGA 59.405 40.000 0.00 0.00 33.15 3.27
2319 2466 5.837437 ACACTGTCTCTGACTAAACTTGAG 58.163 41.667 0.00 0.00 33.15 3.02
2320 2467 5.854010 ACACTGTCTCTGACTAAACTTGA 57.146 39.130 0.00 0.00 33.15 3.02
2347 2494 6.205464 ACTGACAGAATGAGTAATTTGGTGTG 59.795 38.462 10.08 0.00 39.69 3.82
2399 2551 7.489757 CAGGACACACTTACTATTAAGCTCTTC 59.510 40.741 0.00 0.00 38.71 2.87
2408 2560 9.476928 AGTCTATAACAGGACACACTTACTATT 57.523 33.333 0.00 0.00 35.18 1.73
2447 2605 1.547372 GCATTCAGAACTGGGTGCATT 59.453 47.619 19.10 0.00 39.43 3.56
2450 2608 0.242017 GTGCATTCAGAACTGGGTGC 59.758 55.000 18.01 18.01 39.77 5.01
2451 2609 0.883833 GGTGCATTCAGAACTGGGTG 59.116 55.000 0.00 3.21 0.00 4.61
2452 2610 0.478072 TGGTGCATTCAGAACTGGGT 59.522 50.000 0.00 0.00 0.00 4.51
2453 2611 0.883833 GTGGTGCATTCAGAACTGGG 59.116 55.000 0.00 0.00 0.00 4.45
2454 2612 1.901591 AGTGGTGCATTCAGAACTGG 58.098 50.000 0.00 0.00 0.00 4.00
2455 2613 3.402110 TGTAGTGGTGCATTCAGAACTG 58.598 45.455 0.00 0.00 0.00 3.16
2456 2614 3.769739 TGTAGTGGTGCATTCAGAACT 57.230 42.857 0.00 0.00 0.00 3.01
2458 2616 4.019792 ACATGTAGTGGTGCATTCAGAA 57.980 40.909 0.00 0.00 0.00 3.02
2459 2617 3.701205 ACATGTAGTGGTGCATTCAGA 57.299 42.857 0.00 0.00 0.00 3.27
2462 2620 5.520288 CAGTACTACATGTAGTGGTGCATTC 59.480 44.000 37.47 20.53 44.67 2.67
2617 2814 8.437360 TTGATGTTATGTCTGGTGAATGATAC 57.563 34.615 0.00 0.00 0.00 2.24
2630 2827 3.944015 AGGAAGCAGCTTGATGTTATGTC 59.056 43.478 13.91 0.00 0.00 3.06
2754 4633 2.171003 CTCCCCCAAATCCTCACAAAC 58.829 52.381 0.00 0.00 0.00 2.93
2803 4682 3.025619 CGCGCCATCCTCAAATCC 58.974 61.111 0.00 0.00 0.00 3.01
2804 4683 2.329339 GCGCGCCATCCTCAAATC 59.671 61.111 23.24 0.00 0.00 2.17
2805 4684 3.211963 GGCGCGCCATCCTCAAAT 61.212 61.111 43.55 0.00 35.81 2.32
2822 4702 2.753966 CCCACGAAATGCTCCAGCG 61.754 63.158 0.00 0.00 45.83 5.18
3055 5010 6.367969 AGCGTGTTCTAATTATTTTCGTCAGT 59.632 34.615 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.