Multiple sequence alignment - TraesCS2B01G235300

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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 TraesCS2B01G235300 chr2B 100.000 3212 0 0 1 3212 235056647 235053436 0.000000e+00 5932.0
1 TraesCS2B01G235300 chr2B 96.671 1412 42 4 894 2302 235601168 235599759 0.000000e+00 2342.0
2 TraesCS2B01G235300 chr2B 86.768 922 65 18 1 890 195852458 195851562 0.000000e+00 974.0
3 TraesCS2B01G235300 chr2B 96.640 506 16 1 2461 2965 235599761 235599256 0.000000e+00 839.0
4 TraesCS2B01G235300 chr2B 88.636 264 12 3 2966 3212 235597295 235597033 4.030000e-79 305.0
5 TraesCS2B01G235300 chr2B 97.576 165 4 0 2301 2465 519180823 519180659 1.890000e-72 283.0
6 TraesCS2B01G235300 chr2A 95.742 1409 59 1 894 2302 193551939 193550532 0.000000e+00 2268.0
7 TraesCS2B01G235300 chr2A 86.117 922 93 9 1 891 584070516 584069599 0.000000e+00 961.0
8 TraesCS2B01G235300 chr2A 84.848 924 99 16 1 891 214741065 214741980 0.000000e+00 893.0
9 TraesCS2B01G235300 chr2A 96.825 504 16 0 2461 2964 193550534 193550031 0.000000e+00 843.0
10 TraesCS2B01G235300 chr2A 93.651 252 10 2 2966 3212 193549941 193549691 3.910000e-99 372.0
11 TraesCS2B01G235300 chr2D 95.783 1399 55 2 905 2300 178857419 178856022 0.000000e+00 2254.0
12 TraesCS2B01G235300 chr2D 95.243 883 38 2 1423 2302 178671186 178670305 0.000000e+00 1395.0
13 TraesCS2B01G235300 chr2D 94.769 822 39 2 894 1715 178518259 178517442 0.000000e+00 1277.0
14 TraesCS2B01G235300 chr2D 93.565 777 24 6 2461 3212 178508507 178507732 0.000000e+00 1134.0
15 TraesCS2B01G235300 chr2D 93.238 769 26 6 2465 3212 178856018 178855255 0.000000e+00 1109.0
16 TraesCS2B01G235300 chr2D 92.516 775 29 16 2461 3212 178670307 178669539 0.000000e+00 1083.0
17 TraesCS2B01G235300 chr2D 96.482 398 13 1 1024 1421 178691495 178691099 0.000000e+00 656.0
18 TraesCS2B01G235300 chr2D 96.496 371 13 0 1752 2122 178517450 178517080 5.890000e-172 614.0
19 TraesCS2B01G235300 chr2D 97.765 179 4 0 2124 2302 178508683 178508505 3.110000e-80 309.0
20 TraesCS2B01G235300 chr2D 96.970 165 5 0 2301 2465 391812508 391812344 8.780000e-71 278.0
21 TraesCS2B01G235300 chr5D 92.324 925 33 17 1 891 247343499 247344419 0.000000e+00 1280.0
22 TraesCS2B01G235300 chr5D 85.792 922 95 16 1 891 130173470 130174386 0.000000e+00 944.0
23 TraesCS2B01G235300 chr3B 89.336 919 59 14 1 891 38457188 38456281 0.000000e+00 1118.0
24 TraesCS2B01G235300 chr1A 86.768 922 87 9 1 891 285429750 285430667 0.000000e+00 994.0
25 TraesCS2B01G235300 chr1A 84.382 922 88 13 1 891 57751469 57750573 0.000000e+00 854.0
26 TraesCS2B01G235300 chr1A 84.125 926 88 27 1 891 494891843 494892744 0.000000e+00 841.0
27 TraesCS2B01G235300 chr5A 86.211 921 93 8 1 891 620405053 620404137 0.000000e+00 966.0
28 TraesCS2B01G235300 chr4A 86.255 924 85 18 1 891 532214526 532213612 0.000000e+00 965.0
29 TraesCS2B01G235300 chr4A 86.234 879 86 9 1 848 598145554 598144680 0.000000e+00 920.0
30 TraesCS2B01G235300 chr4A 82.777 929 93 24 1 891 609939501 609940400 0.000000e+00 767.0
31 TraesCS2B01G235300 chr3A 84.691 921 88 14 1 891 67576466 67577363 0.000000e+00 870.0
32 TraesCS2B01G235300 chr3A 83.605 921 87 25 1 891 715170328 715169442 0.000000e+00 806.0
33 TraesCS2B01G235300 chr7B 74.194 868 171 36 1029 1874 684930435 684931271 2.410000e-81 313.0
34 TraesCS2B01G235300 chr7B 76.325 604 115 16 1029 1627 698871397 698871977 6.740000e-77 298.0
35 TraesCS2B01G235300 chr7B 75.042 589 126 16 1046 1628 693258593 693258020 1.480000e-63 254.0
36 TraesCS2B01G235300 chr7B 82.143 112 10 8 1709 1812 733046607 733046716 1.590000e-13 87.9
37 TraesCS2B01G235300 chr7B 76.744 129 26 4 2163 2288 684970734 684970861 5.750000e-08 69.4
38 TraesCS2B01G235300 chr7B 76.744 129 26 4 2163 2288 694195359 694195486 5.750000e-08 69.4
39 TraesCS2B01G235300 chrUn 74.326 853 164 38 1045 1874 421073048 421072228 8.650000e-81 311.0
40 TraesCS2B01G235300 chr3D 95.000 180 7 2 2284 2463 486424964 486424787 6.780000e-72 281.0
41 TraesCS2B01G235300 chr3D 95.906 171 6 1 2296 2465 174415722 174415892 3.160000e-70 276.0
42 TraesCS2B01G235300 chr6B 95.906 171 7 0 2301 2471 20776958 20777128 8.780000e-71 278.0
43 TraesCS2B01G235300 chr6B 95.882 170 7 0 2297 2466 376866663 376866832 3.160000e-70 276.0
44 TraesCS2B01G235300 chr1D 96.970 165 5 0 2301 2465 311986612 311986776 8.780000e-71 278.0
45 TraesCS2B01G235300 chr7D 95.906 171 6 1 2301 2471 171308151 171307982 3.160000e-70 276.0
46 TraesCS2B01G235300 chr4D 93.989 183 7 3 2283 2463 470149917 470150097 1.140000e-69 274.0
47 TraesCS2B01G235300 chr7A 78.014 141 27 2 2163 2300 700073174 700073035 5.710000e-13 86.1
48 TraesCS2B01G235300 chr1B 71.901 363 78 17 1951 2300 676215553 676215202 2.050000e-12 84.2
49 TraesCS2B01G235300 chr1B 80.000 95 19 0 1533 1627 632218138 632218232 1.600000e-08 71.3


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 TraesCS2B01G235300 chr2B 235053436 235056647 3211 True 5932.0 5932 100.000000 1 3212 1 chr2B.!!$R2 3211
1 TraesCS2B01G235300 chr2B 235597033 235601168 4135 True 1162.0 2342 93.982333 894 3212 3 chr2B.!!$R4 2318
2 TraesCS2B01G235300 chr2B 195851562 195852458 896 True 974.0 974 86.768000 1 890 1 chr2B.!!$R1 889
3 TraesCS2B01G235300 chr2A 193549691 193551939 2248 True 1161.0 2268 95.406000 894 3212 3 chr2A.!!$R2 2318
4 TraesCS2B01G235300 chr2A 584069599 584070516 917 True 961.0 961 86.117000 1 891 1 chr2A.!!$R1 890
5 TraesCS2B01G235300 chr2A 214741065 214741980 915 False 893.0 893 84.848000 1 891 1 chr2A.!!$F1 890
6 TraesCS2B01G235300 chr2D 178855255 178857419 2164 True 1681.5 2254 94.510500 905 3212 2 chr2D.!!$R6 2307
7 TraesCS2B01G235300 chr2D 178669539 178671186 1647 True 1239.0 1395 93.879500 1423 3212 2 chr2D.!!$R5 1789
8 TraesCS2B01G235300 chr2D 178517080 178518259 1179 True 945.5 1277 95.632500 894 2122 2 chr2D.!!$R4 1228
9 TraesCS2B01G235300 chr2D 178507732 178508683 951 True 721.5 1134 95.665000 2124 3212 2 chr2D.!!$R3 1088
10 TraesCS2B01G235300 chr5D 247343499 247344419 920 False 1280.0 1280 92.324000 1 891 1 chr5D.!!$F2 890
11 TraesCS2B01G235300 chr5D 130173470 130174386 916 False 944.0 944 85.792000 1 891 1 chr5D.!!$F1 890
12 TraesCS2B01G235300 chr3B 38456281 38457188 907 True 1118.0 1118 89.336000 1 891 1 chr3B.!!$R1 890
13 TraesCS2B01G235300 chr1A 285429750 285430667 917 False 994.0 994 86.768000 1 891 1 chr1A.!!$F1 890
14 TraesCS2B01G235300 chr1A 57750573 57751469 896 True 854.0 854 84.382000 1 891 1 chr1A.!!$R1 890
15 TraesCS2B01G235300 chr1A 494891843 494892744 901 False 841.0 841 84.125000 1 891 1 chr1A.!!$F2 890
16 TraesCS2B01G235300 chr5A 620404137 620405053 916 True 966.0 966 86.211000 1 891 1 chr5A.!!$R1 890
17 TraesCS2B01G235300 chr4A 532213612 532214526 914 True 965.0 965 86.255000 1 891 1 chr4A.!!$R1 890
18 TraesCS2B01G235300 chr4A 598144680 598145554 874 True 920.0 920 86.234000 1 848 1 chr4A.!!$R2 847
19 TraesCS2B01G235300 chr4A 609939501 609940400 899 False 767.0 767 82.777000 1 891 1 chr4A.!!$F1 890
20 TraesCS2B01G235300 chr3A 67576466 67577363 897 False 870.0 870 84.691000 1 891 1 chr3A.!!$F1 890
21 TraesCS2B01G235300 chr3A 715169442 715170328 886 True 806.0 806 83.605000 1 891 1 chr3A.!!$R1 890
22 TraesCS2B01G235300 chr7B 684930435 684931271 836 False 313.0 313 74.194000 1029 1874 1 chr7B.!!$F1 845
23 TraesCS2B01G235300 chr7B 698871397 698871977 580 False 298.0 298 76.325000 1029 1627 1 chr7B.!!$F4 598
24 TraesCS2B01G235300 chr7B 693258020 693258593 573 True 254.0 254 75.042000 1046 1628 1 chr7B.!!$R1 582
25 TraesCS2B01G235300 chrUn 421072228 421073048 820 True 311.0 311 74.326000 1045 1874 1 chrUn.!!$R1 829

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
941 1022 2.591715 AACGCAGCTGCCGAGTTT 60.592 55.556 32.07 14.64 37.91 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2213 2353 0.036875 GCAACAGAGTGCTTACCCCT 59.963 55.0 0.0 0.0 41.51 4.79 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
53 54 5.750547 CAGTGCTCACTCATATTCGTGTAAT 59.249 40.000 0.00 0.00 40.20 1.89
86 89 9.927668 ATATCCGTGAACTTTTTGAAATTCATT 57.072 25.926 0.00 0.00 33.85 2.57
255 264 5.827326 TCCCCGTATTTTTCCCAAATTTT 57.173 34.783 0.00 0.00 0.00 1.82
433 471 8.459521 TGAAATCCACATATTTTTGCGTAAAG 57.540 30.769 0.00 0.00 0.00 1.85
532 577 6.570692 ACTCGAATATGAAAAGGTACATCGT 58.429 36.000 0.00 0.00 0.00 3.73
941 1022 2.591715 AACGCAGCTGCCGAGTTT 60.592 55.556 32.07 14.64 37.91 2.66
1161 1242 4.082523 CGCTTCCGCTCCCTCCAA 62.083 66.667 0.00 0.00 0.00 3.53
1611 1695 2.051879 TCGTCTTCTCTTCAAGCACG 57.948 50.000 0.00 0.00 32.68 5.34
1640 1724 3.575351 GAGCCGTTGCGTCTCAGGT 62.575 63.158 0.00 0.00 44.33 4.00
1776 1915 3.570975 AGAAATTGCTCATGCTTGACACA 59.429 39.130 0.00 0.00 40.48 3.72
1933 2072 7.345914 ACCTCTATTATACCATTAGGCAGATCC 59.654 40.741 0.00 0.00 39.06 3.36
2075 2214 2.285834 CCGCAAGTTCATCATCGTTAGC 60.286 50.000 0.00 0.00 0.00 3.09
2216 2356 4.330074 GTCGTCACAGACAATATGAAAGGG 59.670 45.833 0.00 0.00 40.65 3.95
2302 2448 8.208718 TGGTGCTTGATAGTTCATTATTGTAC 57.791 34.615 0.00 0.00 0.00 2.90
2303 2449 8.046708 TGGTGCTTGATAGTTCATTATTGTACT 58.953 33.333 0.00 2.99 37.29 2.73
2304 2450 8.552034 GGTGCTTGATAGTTCATTATTGTACTC 58.448 37.037 0.81 0.00 35.41 2.59
2305 2451 8.552034 GTGCTTGATAGTTCATTATTGTACTCC 58.448 37.037 0.81 0.00 35.41 3.85
2306 2452 7.715249 TGCTTGATAGTTCATTATTGTACTCCC 59.285 37.037 0.81 0.00 35.41 4.30
2307 2453 7.934120 GCTTGATAGTTCATTATTGTACTCCCT 59.066 37.037 0.81 0.00 35.41 4.20
2308 2454 9.482627 CTTGATAGTTCATTATTGTACTCCCTC 57.517 37.037 0.81 0.00 35.41 4.30
2309 2455 7.963532 TGATAGTTCATTATTGTACTCCCTCC 58.036 38.462 0.81 0.00 35.41 4.30
2310 2456 5.277857 AGTTCATTATTGTACTCCCTCCG 57.722 43.478 0.00 0.00 28.29 4.63
2311 2457 4.715297 AGTTCATTATTGTACTCCCTCCGT 59.285 41.667 0.00 0.00 28.29 4.69
2312 2458 5.189145 AGTTCATTATTGTACTCCCTCCGTT 59.811 40.000 0.00 0.00 28.29 4.44
2313 2459 5.272283 TCATTATTGTACTCCCTCCGTTC 57.728 43.478 0.00 0.00 0.00 3.95
2314 2460 4.100498 TCATTATTGTACTCCCTCCGTTCC 59.900 45.833 0.00 0.00 0.00 3.62
2315 2461 2.249309 ATTGTACTCCCTCCGTTCCT 57.751 50.000 0.00 0.00 0.00 3.36
2316 2462 2.905415 TTGTACTCCCTCCGTTCCTA 57.095 50.000 0.00 0.00 0.00 2.94
2317 2463 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
2318 2464 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
2319 2465 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
2320 2466 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
2321 2467 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
2322 2468 6.613699 TGTACTCCCTCCGTTCCTAAATATA 58.386 40.000 0.00 0.00 0.00 0.86
2323 2469 7.068702 TGTACTCCCTCCGTTCCTAAATATAA 58.931 38.462 0.00 0.00 0.00 0.98
2324 2470 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
2325 2471 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
2326 2472 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
2327 2473 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
2328 2474 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
2329 2475 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
2330 2476 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
2331 2477 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
2349 2495 9.646427 AGTCTTTGTAGAGATTTCACTATGAAC 57.354 33.333 0.00 0.00 35.89 3.18
2350 2496 8.874816 GTCTTTGTAGAGATTTCACTATGAACC 58.125 37.037 0.00 0.00 35.89 3.62
2351 2497 8.593679 TCTTTGTAGAGATTTCACTATGAACCA 58.406 33.333 0.00 0.00 35.89 3.67
2352 2498 8.547967 TTTGTAGAGATTTCACTATGAACCAC 57.452 34.615 0.00 0.00 35.89 4.16
2353 2499 7.239763 TGTAGAGATTTCACTATGAACCACA 57.760 36.000 0.00 0.00 35.89 4.17
2354 2500 7.851228 TGTAGAGATTTCACTATGAACCACAT 58.149 34.615 0.00 0.00 35.89 3.21
2355 2501 8.977412 TGTAGAGATTTCACTATGAACCACATA 58.023 33.333 0.00 0.00 35.89 2.29
2356 2502 9.250624 GTAGAGATTTCACTATGAACCACATAC 57.749 37.037 0.00 0.00 35.89 2.39
2357 2503 6.980978 AGAGATTTCACTATGAACCACATACG 59.019 38.462 0.00 0.00 35.89 3.06
2358 2504 6.049149 AGATTTCACTATGAACCACATACGG 58.951 40.000 0.00 0.00 35.89 4.02
2359 2505 5.408880 TTTCACTATGAACCACATACGGA 57.591 39.130 0.00 0.00 35.89 4.69
2360 2506 5.607939 TTCACTATGAACCACATACGGAT 57.392 39.130 0.00 0.00 40.07 4.18
2361 2507 4.944048 TCACTATGAACCACATACGGATG 58.056 43.478 5.94 5.94 40.07 3.51
2362 2508 5.105106 TTCACTATGAACCACATACGGATGT 60.105 40.000 7.68 7.68 37.89 3.06
2363 2509 5.595133 TCACTATGAACCACATACGGATGTA 59.405 40.000 14.23 0.00 44.82 2.29
2364 2510 6.266786 TCACTATGAACCACATACGGATGTAT 59.733 38.462 14.23 5.54 44.82 2.29
2365 2511 7.449086 TCACTATGAACCACATACGGATGTATA 59.551 37.037 14.23 6.48 44.82 1.47
2366 2512 8.251026 CACTATGAACCACATACGGATGTATAT 58.749 37.037 14.23 1.68 44.82 0.86
2367 2513 9.470399 ACTATGAACCACATACGGATGTATATA 57.530 33.333 14.23 7.10 44.82 0.86
2368 2514 9.952188 CTATGAACCACATACGGATGTATATAG 57.048 37.037 14.23 12.28 44.82 1.31
2369 2515 8.589701 ATGAACCACATACGGATGTATATAGA 57.410 34.615 14.23 0.00 44.82 1.98
2370 2516 8.589701 TGAACCACATACGGATGTATATAGAT 57.410 34.615 14.23 0.00 44.82 1.98
2371 2517 8.466798 TGAACCACATACGGATGTATATAGATG 58.533 37.037 14.23 0.00 44.82 2.90
2372 2518 6.806751 ACCACATACGGATGTATATAGATGC 58.193 40.000 14.23 0.00 44.82 3.91
2373 2519 6.379988 ACCACATACGGATGTATATAGATGCA 59.620 38.462 14.23 0.00 44.82 3.96
2374 2520 7.069950 ACCACATACGGATGTATATAGATGCAT 59.930 37.037 14.23 0.00 44.82 3.96
2375 2521 7.928167 CCACATACGGATGTATATAGATGCATT 59.072 37.037 14.23 1.23 44.82 3.56
2376 2522 9.317936 CACATACGGATGTATATAGATGCATTT 57.682 33.333 14.23 0.00 44.82 2.32
2377 2523 9.890629 ACATACGGATGTATATAGATGCATTTT 57.109 29.630 12.79 0.00 44.77 1.82
2381 2527 9.944376 ACGGATGTATATAGATGCATTTTAAGT 57.056 29.630 11.19 0.00 38.38 2.24
2404 2550 8.752766 AGTGTAAATTCATTCATTTTGCTCTG 57.247 30.769 0.00 0.00 0.00 3.35
2405 2551 8.362639 AGTGTAAATTCATTCATTTTGCTCTGT 58.637 29.630 0.00 0.00 0.00 3.41
2406 2552 9.624697 GTGTAAATTCATTCATTTTGCTCTGTA 57.375 29.630 0.00 0.00 0.00 2.74
2412 2558 8.565896 TTCATTCATTTTGCTCTGTATGTAGT 57.434 30.769 0.00 0.00 0.00 2.73
2413 2559 8.201554 TCATTCATTTTGCTCTGTATGTAGTC 57.798 34.615 0.00 0.00 0.00 2.59
2414 2560 6.985188 TTCATTTTGCTCTGTATGTAGTCC 57.015 37.500 0.00 0.00 0.00 3.85
2415 2561 6.048732 TCATTTTGCTCTGTATGTAGTCCA 57.951 37.500 0.00 0.00 0.00 4.02
2416 2562 6.653020 TCATTTTGCTCTGTATGTAGTCCAT 58.347 36.000 0.00 0.00 37.58 3.41
2417 2563 6.763135 TCATTTTGCTCTGTATGTAGTCCATC 59.237 38.462 0.00 0.00 34.86 3.51
2418 2564 5.939764 TTTGCTCTGTATGTAGTCCATCT 57.060 39.130 0.00 0.00 34.86 2.90
2419 2565 7.418337 TTTTGCTCTGTATGTAGTCCATCTA 57.582 36.000 0.00 0.00 34.86 1.98
2420 2566 6.641169 TTGCTCTGTATGTAGTCCATCTAG 57.359 41.667 0.00 0.00 34.86 2.43
2421 2567 5.696030 TGCTCTGTATGTAGTCCATCTAGT 58.304 41.667 0.00 0.00 34.86 2.57
2422 2568 5.532779 TGCTCTGTATGTAGTCCATCTAGTG 59.467 44.000 0.00 0.00 34.86 2.74
2439 2585 8.006298 CATCTAGTGGAATCTCTACAAAGACT 57.994 38.462 0.00 0.00 29.78 3.24
2440 2586 8.474025 CATCTAGTGGAATCTCTACAAAGACTT 58.526 37.037 0.00 0.00 29.78 3.01
2441 2587 9.702253 ATCTAGTGGAATCTCTACAAAGACTTA 57.298 33.333 0.00 0.00 29.78 2.24
2442 2588 9.702253 TCTAGTGGAATCTCTACAAAGACTTAT 57.298 33.333 0.00 0.00 29.47 1.73
2456 2602 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
2457 2603 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
2458 2604 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
2459 2605 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
2460 2606 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
2461 2607 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
2462 2608 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
2570 2717 5.739752 TTGCCATCTTGATTATTCAGACG 57.260 39.130 0.00 0.00 32.27 4.18
2629 2776 6.329986 TGAGTAATATCCATCCACCATTCAGT 59.670 38.462 0.00 0.00 0.00 3.41
2736 2884 9.968743 GAAGCAGTAATTGTGTAAATGTACTAC 57.031 33.333 0.00 0.00 0.00 2.73
2794 2944 4.000325 TGATGTAACTCGAACAACCATGG 59.000 43.478 11.19 11.19 0.00 3.66
2899 3049 4.704057 GCTTCATGTCTTCTTCCTTGGATT 59.296 41.667 0.00 0.00 0.00 3.01
3073 5183 5.277857 AGATATAAGGTCACCAAAGTCCG 57.722 43.478 0.00 0.00 0.00 4.79
3175 5302 7.764141 TGAATCTCATCAGAACCAATCAAAA 57.236 32.000 0.00 0.00 30.24 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 88 5.163602 ACTGCACGGATTTGAAAAGTGTAAA 60.164 36.000 11.21 0.00 35.46 2.01
86 89 4.336993 ACTGCACGGATTTGAAAAGTGTAA 59.663 37.500 11.21 3.05 35.46 2.41
433 471 3.366440 AGTACGCGGATATGGACTTTC 57.634 47.619 12.47 0.00 0.00 2.62
596 666 9.366513 GTACTTTTTCGAAGTTCATGTACTTTC 57.633 33.333 17.52 10.54 38.43 2.62
891 972 7.141100 AGGTCAAATGTCCAGTAATAAAACG 57.859 36.000 0.00 0.00 0.00 3.60
892 973 8.027189 GGAAGGTCAAATGTCCAGTAATAAAAC 58.973 37.037 0.00 0.00 0.00 2.43
941 1022 3.289704 TTTGGCGTCGCTGGATCGA 62.290 57.895 18.11 0.00 35.95 3.59
1527 1611 0.320374 ATGACGTTTCTTCCGCCTCA 59.680 50.000 0.00 0.00 0.00 3.86
1611 1695 3.682292 AACGGCTCGCCATTCTCCC 62.682 63.158 8.87 0.00 35.37 4.30
1640 1724 1.339631 CCACTAACAAATCGCCCCAGA 60.340 52.381 0.00 0.00 0.00 3.86
1683 1767 0.689623 AGAACACAGGGCTCTTGGAG 59.310 55.000 0.00 0.00 0.00 3.86
1933 2072 1.873591 CTGGTTGAAACTCGGACCTTG 59.126 52.381 0.00 0.00 33.33 3.61
2075 2214 4.692625 AGAAACATTCCAAGTCTGACATCG 59.307 41.667 10.88 0.00 0.00 3.84
2213 2353 0.036875 GCAACAGAGTGCTTACCCCT 59.963 55.000 0.00 0.00 41.51 4.79
2216 2356 1.740025 GGATGCAACAGAGTGCTTACC 59.260 52.381 0.00 0.00 45.17 2.85
2302 2448 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
2303 2449 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
2304 2450 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
2305 2451 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
2306 2452 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
2323 2469 9.646427 GTTCATAGTGAAATCTCTACAAAGACT 57.354 33.333 0.00 0.00 38.22 3.24
2324 2470 8.874816 GGTTCATAGTGAAATCTCTACAAAGAC 58.125 37.037 0.00 0.00 38.22 3.01
2325 2471 8.593679 TGGTTCATAGTGAAATCTCTACAAAGA 58.406 33.333 0.00 0.00 38.22 2.52
2326 2472 8.660373 GTGGTTCATAGTGAAATCTCTACAAAG 58.340 37.037 0.00 0.00 38.22 2.77
2327 2473 8.154203 TGTGGTTCATAGTGAAATCTCTACAAA 58.846 33.333 0.00 0.00 38.22 2.83
2328 2474 7.676004 TGTGGTTCATAGTGAAATCTCTACAA 58.324 34.615 0.00 0.00 38.22 2.41
2329 2475 7.239763 TGTGGTTCATAGTGAAATCTCTACA 57.760 36.000 0.00 0.00 38.22 2.74
2330 2476 9.250624 GTATGTGGTTCATAGTGAAATCTCTAC 57.749 37.037 0.00 0.00 38.22 2.59
2331 2477 8.135529 CGTATGTGGTTCATAGTGAAATCTCTA 58.864 37.037 0.00 0.00 38.22 2.43
2332 2478 6.980978 CGTATGTGGTTCATAGTGAAATCTCT 59.019 38.462 0.00 0.00 38.22 3.10
2333 2479 6.201044 CCGTATGTGGTTCATAGTGAAATCTC 59.799 42.308 0.00 0.00 38.22 2.75
2334 2480 6.049149 CCGTATGTGGTTCATAGTGAAATCT 58.951 40.000 0.00 0.00 38.22 2.40
2335 2481 6.046593 TCCGTATGTGGTTCATAGTGAAATC 58.953 40.000 0.00 0.00 38.22 2.17
2336 2482 5.984725 TCCGTATGTGGTTCATAGTGAAAT 58.015 37.500 0.00 0.00 38.22 2.17
2337 2483 5.408880 TCCGTATGTGGTTCATAGTGAAA 57.591 39.130 0.00 0.00 38.22 2.69
2338 2484 5.105106 ACATCCGTATGTGGTTCATAGTGAA 60.105 40.000 0.00 0.00 44.79 3.18
2339 2485 4.404394 ACATCCGTATGTGGTTCATAGTGA 59.596 41.667 0.00 0.00 44.79 3.41
2340 2486 4.693283 ACATCCGTATGTGGTTCATAGTG 58.307 43.478 0.00 0.00 44.79 2.74
2341 2487 6.665992 ATACATCCGTATGTGGTTCATAGT 57.334 37.500 3.56 0.00 45.99 2.12
2342 2488 9.952188 CTATATACATCCGTATGTGGTTCATAG 57.048 37.037 3.56 0.80 45.99 2.23
2343 2489 9.689501 TCTATATACATCCGTATGTGGTTCATA 57.310 33.333 3.56 0.00 45.99 2.15
2344 2490 8.589701 TCTATATACATCCGTATGTGGTTCAT 57.410 34.615 3.56 0.00 45.99 2.57
2345 2491 8.466798 CATCTATATACATCCGTATGTGGTTCA 58.533 37.037 3.56 0.00 45.99 3.18
2346 2492 7.435488 GCATCTATATACATCCGTATGTGGTTC 59.565 40.741 3.56 0.00 45.99 3.62
2347 2493 7.093509 TGCATCTATATACATCCGTATGTGGTT 60.094 37.037 3.56 0.00 45.99 3.67
2348 2494 6.379988 TGCATCTATATACATCCGTATGTGGT 59.620 38.462 3.56 0.00 45.99 4.16
2349 2495 6.805713 TGCATCTATATACATCCGTATGTGG 58.194 40.000 3.56 0.00 45.99 4.17
2350 2496 8.877808 AATGCATCTATATACATCCGTATGTG 57.122 34.615 3.56 0.00 45.99 3.21
2355 2501 9.944376 ACTTAAAATGCATCTATATACATCCGT 57.056 29.630 0.00 0.00 0.00 4.69
2378 2524 9.199982 CAGAGCAAAATGAATGAATTTACACTT 57.800 29.630 0.00 0.00 0.00 3.16
2379 2525 8.362639 ACAGAGCAAAATGAATGAATTTACACT 58.637 29.630 0.00 0.00 0.00 3.55
2380 2526 8.524870 ACAGAGCAAAATGAATGAATTTACAC 57.475 30.769 0.00 0.00 0.00 2.90
2386 2532 9.182214 ACTACATACAGAGCAAAATGAATGAAT 57.818 29.630 0.00 0.00 0.00 2.57
2387 2533 8.565896 ACTACATACAGAGCAAAATGAATGAA 57.434 30.769 0.00 0.00 0.00 2.57
2388 2534 7.280876 GGACTACATACAGAGCAAAATGAATGA 59.719 37.037 0.00 0.00 0.00 2.57
2389 2535 7.066163 TGGACTACATACAGAGCAAAATGAATG 59.934 37.037 0.00 0.00 0.00 2.67
2390 2536 7.112122 TGGACTACATACAGAGCAAAATGAAT 58.888 34.615 0.00 0.00 0.00 2.57
2391 2537 6.472016 TGGACTACATACAGAGCAAAATGAA 58.528 36.000 0.00 0.00 0.00 2.57
2392 2538 6.048732 TGGACTACATACAGAGCAAAATGA 57.951 37.500 0.00 0.00 0.00 2.57
2393 2539 6.765036 AGATGGACTACATACAGAGCAAAATG 59.235 38.462 0.00 0.00 40.72 2.32
2394 2540 6.893583 AGATGGACTACATACAGAGCAAAAT 58.106 36.000 0.00 0.00 40.72 1.82
2395 2541 6.299805 AGATGGACTACATACAGAGCAAAA 57.700 37.500 0.00 0.00 40.72 2.44
2396 2542 5.939764 AGATGGACTACATACAGAGCAAA 57.060 39.130 0.00 0.00 40.72 3.68
2397 2543 6.039829 CACTAGATGGACTACATACAGAGCAA 59.960 42.308 0.00 0.00 40.72 3.91
2398 2544 5.532779 CACTAGATGGACTACATACAGAGCA 59.467 44.000 0.00 0.00 40.72 4.26
2399 2545 6.007936 CACTAGATGGACTACATACAGAGC 57.992 45.833 0.00 0.00 40.72 4.09
2414 2560 8.006298 AGTCTTTGTAGAGATTCCACTAGATG 57.994 38.462 0.00 0.00 0.00 2.90
2415 2561 8.602472 AAGTCTTTGTAGAGATTCCACTAGAT 57.398 34.615 0.00 0.00 0.00 1.98
2416 2562 9.702253 ATAAGTCTTTGTAGAGATTCCACTAGA 57.298 33.333 0.00 0.00 0.00 2.43
2431 2577 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
2432 2578 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
2433 2579 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
2434 2580 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
2435 2581 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
2436 2582 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
2437 2583 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
2438 2584 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
2439 2585 7.300658 ACTACTCCCTCCGTTCCTAAATATAA 58.699 38.462 0.00 0.00 0.00 0.98
2440 2586 6.856757 ACTACTCCCTCCGTTCCTAAATATA 58.143 40.000 0.00 0.00 0.00 0.86
2441 2587 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
2442 2588 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
2443 2589 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
2444 2590 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
2445 2591 3.117738 CCTACTACTCCCTCCGTTCCTAA 60.118 52.174 0.00 0.00 0.00 2.69
2446 2592 2.441001 CCTACTACTCCCTCCGTTCCTA 59.559 54.545 0.00 0.00 0.00 2.94
2447 2593 1.214923 CCTACTACTCCCTCCGTTCCT 59.785 57.143 0.00 0.00 0.00 3.36
2448 2594 1.689984 CCTACTACTCCCTCCGTTCC 58.310 60.000 0.00 0.00 0.00 3.62
2449 2595 1.031235 GCCTACTACTCCCTCCGTTC 58.969 60.000 0.00 0.00 0.00 3.95
2450 2596 0.333993 TGCCTACTACTCCCTCCGTT 59.666 55.000 0.00 0.00 0.00 4.44
2451 2597 0.333993 TTGCCTACTACTCCCTCCGT 59.666 55.000 0.00 0.00 0.00 4.69
2452 2598 1.033574 CTTGCCTACTACTCCCTCCG 58.966 60.000 0.00 0.00 0.00 4.63
2453 2599 2.033372 GACTTGCCTACTACTCCCTCC 58.967 57.143 0.00 0.00 0.00 4.30
2454 2600 3.021177 AGACTTGCCTACTACTCCCTC 57.979 52.381 0.00 0.00 0.00 4.30
2455 2601 3.100671 CAAGACTTGCCTACTACTCCCT 58.899 50.000 1.43 0.00 0.00 4.20
2456 2602 2.832733 ACAAGACTTGCCTACTACTCCC 59.167 50.000 15.24 0.00 0.00 4.30
2457 2603 4.538746 AACAAGACTTGCCTACTACTCC 57.461 45.455 15.24 0.00 0.00 3.85
2458 2604 7.117956 CCTTTAAACAAGACTTGCCTACTACTC 59.882 40.741 15.24 0.00 0.00 2.59
2459 2605 6.935208 CCTTTAAACAAGACTTGCCTACTACT 59.065 38.462 15.24 0.00 0.00 2.57
2460 2606 6.148976 CCCTTTAAACAAGACTTGCCTACTAC 59.851 42.308 15.24 0.00 0.00 2.73
2461 2607 6.183361 ACCCTTTAAACAAGACTTGCCTACTA 60.183 38.462 15.24 0.00 0.00 1.82
2462 2608 5.070685 CCCTTTAAACAAGACTTGCCTACT 58.929 41.667 15.24 0.00 0.00 2.57
2570 2717 4.755629 GTGTGGAAGACCCTTTCTTTACTC 59.244 45.833 0.00 0.00 45.24 2.59
2629 2776 2.655090 TCTGCAATTCCACTTGGTCA 57.345 45.000 0.00 0.00 36.34 4.02
2683 2830 7.944554 CCAGATTAGGCAATCCCTTTATCTTTA 59.055 37.037 6.19 0.00 43.06 1.85
2736 2884 9.760077 ATACGTAAAAGGATATAAACCTGAGTG 57.240 33.333 0.00 0.00 37.85 3.51
2794 2944 5.877564 GGCTCTGCCCAGATATATTTCTTAC 59.122 44.000 0.00 0.00 44.06 2.34
2899 3049 6.267471 ACAATCTACCAAGGAAAAGCAATCAA 59.733 34.615 0.00 0.00 0.00 2.57
3084 5194 7.963981 TCATGAAAAATTACAGATGAGACGAC 58.036 34.615 0.00 0.00 0.00 4.34
3175 5302 0.110486 AGTTCTTGCCGGTTCACCAT 59.890 50.000 1.90 0.00 35.14 3.55
3184 5311 0.384725 CGAAGCACAAGTTCTTGCCG 60.385 55.000 11.79 5.57 39.75 5.69


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

AutoCloner maintained by Alex Coulton.