Multiple sequence alignment - TraesCS3A01G073100

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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 TraesCS3A01G073100 chr3A 100.000 2580 0 0 1 2580 45172344 45169765 0.000000e+00 4765.0
1 TraesCS3A01G073100 chr3A 93.293 328 22 0 2060 2387 45162330 45162003 4.310000e-133 484.0
2 TraesCS3A01G073100 chr3A 87.814 279 17 5 1676 1940 45192513 45192238 7.740000e-81 311.0
3 TraesCS3A01G073100 chr3A 92.562 121 7 1 1939 2059 45187983 45187865 3.810000e-39 172.0
4 TraesCS3A01G073100 chr3A 81.481 162 19 8 27 178 171130759 171130599 3.890000e-24 122.0
5 TraesCS3A01G073100 chr3A 100.000 62 0 0 2817 2878 45169528 45169467 6.520000e-22 115.0
6 TraesCS3A01G073100 chr3A 79.195 149 25 6 36 180 9891292 9891146 6.560000e-17 99.0
7 TraesCS3A01G073100 chr3A 83.036 112 13 4 74 181 63031879 63031988 2.360000e-16 97.1
8 TraesCS3A01G073100 chr3B 90.034 2087 125 30 2 2029 55372767 55370705 0.000000e+00 2625.0
9 TraesCS3A01G073100 chr3B 87.255 1224 99 21 872 2059 55394337 55393135 0.000000e+00 1343.0
10 TraesCS3A01G073100 chr3B 92.857 42 1 2 182 222 741884837 741884797 3.100000e-05 60.2
11 TraesCS3A01G073100 chr3D 91.590 1082 63 9 782 1838 32743799 32742721 0.000000e+00 1469.0
12 TraesCS3A01G073100 chr3D 90.071 141 11 2 1898 2035 32742726 32742586 2.280000e-41 180.0
13 TraesCS3A01G073100 chr4D 95.427 328 15 0 2060 2387 388100122 388100449 9.140000e-145 523.0
14 TraesCS3A01G073100 chr4D 98.305 59 1 0 2396 2454 339481070 339481012 1.410000e-18 104.0
15 TraesCS3A01G073100 chr4D 87.671 73 3 3 2500 2572 169086004 169085938 2.380000e-11 80.5
16 TraesCS3A01G073100 chr4D 87.671 73 3 3 2500 2572 287738239 287738173 2.380000e-11 80.5
17 TraesCS3A01G073100 chr4D 85.714 77 8 2 2496 2572 325648447 325648520 8.550000e-11 78.7
18 TraesCS3A01G073100 chr5D 92.378 328 25 0 2060 2387 411701044 411701371 4.340000e-128 468.0
19 TraesCS3A01G073100 chr5D 85.301 415 46 12 265 672 338382324 338381918 5.740000e-112 414.0
20 TraesCS3A01G073100 chr5D 82.237 152 21 4 32 181 426502109 426502256 3.010000e-25 126.0
21 TraesCS3A01G073100 chr5D 87.671 73 3 3 2500 2572 295258554 295258620 2.380000e-11 80.5
22 TraesCS3A01G073100 chr5A 85.442 419 49 12 265 675 342046541 342046127 2.650000e-115 425.0
23 TraesCS3A01G073100 chr5A 88.415 328 38 0 2060 2387 618250050 618250377 2.080000e-106 396.0
24 TraesCS3A01G073100 chr5A 82.670 427 62 10 262 682 340476208 340475788 4.530000e-98 368.0
25 TraesCS3A01G073100 chr5A 87.368 95 10 1 2485 2579 618249122 618249214 1.090000e-19 108.0
26 TraesCS3A01G073100 chr5A 97.436 39 1 0 184 222 118752274 118752312 1.850000e-07 67.6
27 TraesCS3A01G073100 chr5B 89.908 327 33 0 2060 2386 507363523 507363849 3.430000e-114 422.0
28 TraesCS3A01G073100 chr5B 89.024 328 36 0 2060 2387 418003628 418003301 9.600000e-110 407.0
29 TraesCS3A01G073100 chr5B 84.521 407 50 12 262 663 488858902 488859300 9.670000e-105 390.0
30 TraesCS3A01G073100 chr5B 89.583 96 8 1 2485 2580 418004506 418004413 1.400000e-23 121.0
31 TraesCS3A01G073100 chr5B 87.500 96 10 1 2485 2580 507362372 507362465 3.030000e-20 110.0
32 TraesCS3A01G073100 chr6B 89.634 328 34 0 2060 2387 550208314 550207987 4.440000e-113 418.0
33 TraesCS3A01G073100 chr6B 95.918 49 2 0 1087 1135 8997156 8997204 2.380000e-11 80.5
34 TraesCS3A01G073100 chr2B 85.784 408 43 14 264 666 750033766 750033369 4.440000e-113 418.0
35 TraesCS3A01G073100 chr2B 80.380 158 16 7 35 181 24813524 24813677 3.920000e-19 106.0
36 TraesCS3A01G073100 chr2A 88.344 326 38 0 2062 2387 216630070 216630395 2.690000e-105 392.0
37 TraesCS3A01G073100 chr2A 83.254 418 58 11 262 674 109325458 109325868 9.740000e-100 374.0
38 TraesCS3A01G073100 chr2A 82.423 421 60 13 262 675 136338004 136338417 3.530000e-94 355.0
39 TraesCS3A01G073100 chr1B 82.734 417 57 8 262 675 328153585 328153181 9.810000e-95 357.0
40 TraesCS3A01G073100 chr2D 81.928 166 15 4 30 181 570997844 570997680 3.010000e-25 126.0
41 TraesCS3A01G073100 chr2D 75.598 209 20 10 42 222 41481348 41481553 1.110000e-09 75.0
42 TraesCS3A01G073100 chr6A 87.619 105 9 2 2478 2580 597472968 597473070 5.040000e-23 119.0
43 TraesCS3A01G073100 chr6A 91.525 59 3 2 1087 1144 3855964 3855907 2.380000e-11 80.5
44 TraesCS3A01G073100 chr7D 81.333 150 23 4 32 179 86290976 86290830 1.810000e-22 117.0
45 TraesCS3A01G073100 chr6D 83.621 116 16 3 65 177 380733671 380733556 3.920000e-19 106.0
46 TraesCS3A01G073100 chr6D 93.878 49 3 0 1087 1135 4779144 4779096 1.110000e-09 75.0
47 TraesCS3A01G073100 chr1D 75.243 206 33 12 32 223 412466082 412465881 6.610000e-12 82.4
48 TraesCS3A01G073100 chr1D 87.671 73 3 3 2500 2572 129326445 129326379 2.380000e-11 80.5
49 TraesCS3A01G073100 chr7A 80.392 102 13 5 80 178 514560172 514560269 1.430000e-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 TraesCS3A01G073100 chr3A 45169467 45172344 2877 True 2440.0 4765 100.0000 1 2878 2 chr3A.!!$R6 2877
1 TraesCS3A01G073100 chr3B 55370705 55372767 2062 True 2625.0 2625 90.0340 2 2029 1 chr3B.!!$R1 2027
2 TraesCS3A01G073100 chr3B 55393135 55394337 1202 True 1343.0 1343 87.2550 872 2059 1 chr3B.!!$R2 1187
3 TraesCS3A01G073100 chr3D 32742586 32743799 1213 True 824.5 1469 90.8305 782 2035 2 chr3D.!!$R1 1253
4 TraesCS3A01G073100 chr5A 618249122 618250377 1255 False 252.0 396 87.8915 2060 2579 2 chr5A.!!$F2 519
5 TraesCS3A01G073100 chr5B 507362372 507363849 1477 False 266.0 422 88.7040 2060 2580 2 chr5B.!!$F2 520
6 TraesCS3A01G073100 chr5B 418003301 418004506 1205 True 264.0 407 89.3035 2060 2580 2 chr5B.!!$R1 520

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
148 164 0.618458 AATTCAGAGGTAGCGCCCAA 59.382 50.0 2.29 0.0 38.26 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2059 2132 0.460284 GCGATGGACCGAGAACATGT 60.46 55.0 0.0 0.0 0.0 3.21 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
70 71 3.058432 GCTAAGGAAGACCGGTGAAAAAC 60.058 47.826 14.63 0.00 41.83 2.43
109 124 6.969828 TCATTTAAAAAGCCAAAAACACGT 57.030 29.167 0.00 0.00 0.00 4.49
148 164 0.618458 AATTCAGAGGTAGCGCCCAA 59.382 50.000 2.29 0.00 38.26 4.12
222 238 2.710760 CTCGCTAACTAGTTGCTCTCG 58.289 52.381 18.56 12.82 0.00 4.04
241 257 3.405831 TCGTCCTTGAGTAGTTCGAGAA 58.594 45.455 0.00 0.00 39.36 2.87
310 327 5.705397 ATCATGAGATCAGACCCAAAAGA 57.295 39.130 0.09 0.00 0.00 2.52
379 396 9.101655 CAACATTCATGTGAGATATGTCTACAA 57.898 33.333 1.10 0.00 41.61 2.41
456 473 8.755941 AGTCAAATTCGAATGTGAATAGTATCG 58.244 33.333 28.36 1.09 37.59 2.92
545 562 7.224297 TGTAAGTTGAATTAGAAGCTTGGACT 58.776 34.615 2.10 0.00 0.00 3.85
558 575 2.159114 GCTTGGACTTTTTGAGGTTGCA 60.159 45.455 0.00 0.00 0.00 4.08
675 692 2.472695 TCTCACACAAATCTTCCCCG 57.527 50.000 0.00 0.00 0.00 5.73
677 694 2.370519 TCTCACACAAATCTTCCCCGAA 59.629 45.455 0.00 0.00 0.00 4.30
998 1020 5.259632 ACGTAACCTAGTCACTAGTCCAAT 58.740 41.667 11.06 0.00 32.62 3.16
1059 1087 1.524621 CTCATCCGCACCCACCATC 60.525 63.158 0.00 0.00 0.00 3.51
1417 1454 2.375345 CCCCAATACCCGGCTGTCT 61.375 63.158 0.00 0.00 0.00 3.41
1551 1591 0.181587 TCACACCCATGTCCAACGTT 59.818 50.000 0.00 0.00 36.72 3.99
1596 1636 1.896465 CTCAACGGAGAAGAGAAGGGT 59.104 52.381 0.00 0.00 44.26 4.34
1632 1672 3.766591 AGAAGTCTGTCAAGATCGGTCAT 59.233 43.478 0.00 0.00 34.13 3.06
1642 1682 1.759445 AGATCGGTCATCAAGAGGTGG 59.241 52.381 0.00 0.00 33.29 4.61
1648 1688 2.771943 GGTCATCAAGAGGTGGGTGATA 59.228 50.000 0.00 0.00 30.85 2.15
1649 1689 3.181461 GGTCATCAAGAGGTGGGTGATAG 60.181 52.174 0.00 0.00 30.85 2.08
1727 1774 5.329191 TGCAGGGATTGGATATTCTCAAT 57.671 39.130 0.00 0.00 36.43 2.57
1728 1775 5.708544 TGCAGGGATTGGATATTCTCAATT 58.291 37.500 0.00 0.00 34.18 2.32
1736 1783 7.176340 GGATTGGATATTCTCAATTCTTCCCTG 59.824 40.741 0.00 0.00 34.18 4.45
1829 1882 1.375551 GTACATCCGGTGGCGAAATT 58.624 50.000 0.00 0.00 0.00 1.82
1902 1960 2.864343 GGTAGGACGTCATGTATGTTGC 59.136 50.000 18.91 0.00 0.00 4.17
1903 1961 2.024176 AGGACGTCATGTATGTTGCC 57.976 50.000 18.91 0.00 0.00 4.52
1904 1962 1.277842 AGGACGTCATGTATGTTGCCA 59.722 47.619 18.91 0.00 0.00 4.92
2055 2128 9.871238 GTTAAAGGTACTCTAATTCACATCTGA 57.129 33.333 0.00 0.00 38.49 3.27
2059 2132 5.128827 GGTACTCTAATTCACATCTGACCCA 59.871 44.000 0.00 0.00 0.00 4.51
2060 2133 5.091261 ACTCTAATTCACATCTGACCCAC 57.909 43.478 0.00 0.00 0.00 4.61
2061 2134 4.532126 ACTCTAATTCACATCTGACCCACA 59.468 41.667 0.00 0.00 0.00 4.17
2062 2135 5.190528 ACTCTAATTCACATCTGACCCACAT 59.809 40.000 0.00 0.00 0.00 3.21
2063 2136 5.430886 TCTAATTCACATCTGACCCACATG 58.569 41.667 0.00 0.00 0.00 3.21
2072 2145 0.320374 TGACCCACATGTTCTCGGTC 59.680 55.000 18.09 18.09 42.78 4.79
2175 2248 2.434359 CACGGTTCCGCCTTCTCC 60.434 66.667 11.32 0.00 34.25 3.71
2186 2259 2.511145 CTTCTCCTGCGCCTCTGC 60.511 66.667 4.18 0.00 0.00 4.26
2255 2328 1.146041 CGAAATCTCCGGCATCCCA 59.854 57.895 0.00 0.00 0.00 4.37
2297 2370 2.184579 GCCGTGACTCTACTGGCC 59.815 66.667 0.00 0.00 39.83 5.36
2332 2405 3.222855 CGAGCTCGCCCCAGAGAT 61.223 66.667 25.07 0.00 40.57 2.75
2333 2406 2.420890 GAGCTCGCCCCAGAGATG 59.579 66.667 0.00 0.00 40.57 2.90
2345 2418 3.040763 GAGATGCGCGATGGCTCC 61.041 66.667 12.10 0.00 36.88 4.70
2354 2427 1.592669 CGATGGCTCCGACATGTCC 60.593 63.158 20.03 6.92 27.61 4.02
2363 2436 1.078759 CCGACATGTCCGTCTTCAGC 61.079 60.000 20.03 0.00 33.54 4.26
2366 2439 0.388649 ACATGTCCGTCTTCAGCGTC 60.389 55.000 0.00 0.00 0.00 5.19
2372 2445 2.569134 GTCTTCAGCGTCTCGGCT 59.431 61.111 0.00 0.00 46.13 5.52
2387 2460 2.539081 GGCTTGGACTCCCAACCCT 61.539 63.158 0.00 0.00 46.94 4.34
2388 2461 1.205460 GGCTTGGACTCCCAACCCTA 61.205 60.000 0.00 0.00 46.94 3.53
2389 2462 0.696501 GCTTGGACTCCCAACCCTAA 59.303 55.000 0.00 0.00 46.94 2.69
2390 2463 1.285078 GCTTGGACTCCCAACCCTAAT 59.715 52.381 0.00 0.00 46.94 1.73
2391 2464 2.291605 GCTTGGACTCCCAACCCTAATT 60.292 50.000 0.00 0.00 46.94 1.40
2392 2465 3.621558 CTTGGACTCCCAACCCTAATTC 58.378 50.000 0.00 0.00 46.94 2.17
2393 2466 2.638325 TGGACTCCCAACCCTAATTCA 58.362 47.619 0.00 0.00 40.09 2.57
2394 2467 2.307686 TGGACTCCCAACCCTAATTCAC 59.692 50.000 0.00 0.00 40.09 3.18
2395 2468 2.307686 GGACTCCCAACCCTAATTCACA 59.692 50.000 0.00 0.00 0.00 3.58
2396 2469 3.053619 GGACTCCCAACCCTAATTCACAT 60.054 47.826 0.00 0.00 0.00 3.21
2397 2470 3.947834 GACTCCCAACCCTAATTCACATG 59.052 47.826 0.00 0.00 0.00 3.21
2398 2471 3.333680 ACTCCCAACCCTAATTCACATGT 59.666 43.478 0.00 0.00 0.00 3.21
2399 2472 3.696045 TCCCAACCCTAATTCACATGTG 58.304 45.455 20.18 20.18 0.00 3.21
2400 2473 3.332187 TCCCAACCCTAATTCACATGTGA 59.668 43.478 24.56 24.56 37.91 3.58
2401 2474 4.017591 TCCCAACCCTAATTCACATGTGAT 60.018 41.667 28.32 17.32 39.64 3.06
2402 2475 4.098349 CCCAACCCTAATTCACATGTGATG 59.902 45.833 28.32 19.52 39.64 3.07
2403 2476 4.098349 CCAACCCTAATTCACATGTGATGG 59.902 45.833 28.32 23.88 39.64 3.51
2404 2477 4.860802 ACCCTAATTCACATGTGATGGA 57.139 40.909 28.32 14.94 39.64 3.41
2405 2478 5.393068 ACCCTAATTCACATGTGATGGAT 57.607 39.130 28.32 16.57 39.64 3.41
2406 2479 5.769835 ACCCTAATTCACATGTGATGGATT 58.230 37.500 28.32 24.46 39.64 3.01
2407 2480 5.595542 ACCCTAATTCACATGTGATGGATTG 59.404 40.000 28.32 17.54 39.64 2.67
2408 2481 5.829391 CCCTAATTCACATGTGATGGATTGA 59.171 40.000 28.32 12.69 39.64 2.57
2409 2482 6.492429 CCCTAATTCACATGTGATGGATTGAT 59.508 38.462 28.32 14.42 39.64 2.57
2410 2483 7.368059 CCTAATTCACATGTGATGGATTGATG 58.632 38.462 28.32 17.07 39.64 3.07
2411 2484 5.784578 ATTCACATGTGATGGATTGATGG 57.215 39.130 28.32 0.00 39.64 3.51
2412 2485 3.558033 TCACATGTGATGGATTGATGGG 58.442 45.455 24.56 0.00 34.14 4.00
2413 2486 3.202595 TCACATGTGATGGATTGATGGGA 59.797 43.478 24.56 0.00 34.14 4.37
2414 2487 4.141111 TCACATGTGATGGATTGATGGGAT 60.141 41.667 24.56 0.00 34.14 3.85
2415 2488 4.022329 CACATGTGATGGATTGATGGGATG 60.022 45.833 21.64 0.00 33.60 3.51
2416 2489 2.589720 TGTGATGGATTGATGGGATGC 58.410 47.619 0.00 0.00 0.00 3.91
2417 2490 2.176148 TGTGATGGATTGATGGGATGCT 59.824 45.455 0.00 0.00 0.00 3.79
2418 2491 2.557056 GTGATGGATTGATGGGATGCTG 59.443 50.000 0.00 0.00 0.00 4.41
2419 2492 2.168496 GATGGATTGATGGGATGCTGG 58.832 52.381 0.00 0.00 0.00 4.85
2420 2493 1.224436 TGGATTGATGGGATGCTGGA 58.776 50.000 0.00 0.00 0.00 3.86
2421 2494 1.144298 TGGATTGATGGGATGCTGGAG 59.856 52.381 0.00 0.00 0.00 3.86
2422 2495 1.144503 GGATTGATGGGATGCTGGAGT 59.855 52.381 0.00 0.00 0.00 3.85
2423 2496 2.423947 GGATTGATGGGATGCTGGAGTT 60.424 50.000 0.00 0.00 0.00 3.01
2424 2497 2.133281 TTGATGGGATGCTGGAGTTG 57.867 50.000 0.00 0.00 0.00 3.16
2425 2498 0.256752 TGATGGGATGCTGGAGTTGG 59.743 55.000 0.00 0.00 0.00 3.77
2426 2499 0.548031 GATGGGATGCTGGAGTTGGA 59.452 55.000 0.00 0.00 0.00 3.53
2427 2500 1.002069 ATGGGATGCTGGAGTTGGAA 58.998 50.000 0.00 0.00 0.00 3.53
2428 2501 0.776810 TGGGATGCTGGAGTTGGAAA 59.223 50.000 0.00 0.00 0.00 3.13
2438 2511 2.635338 GTTGGAAACGTGGCCGAC 59.365 61.111 10.56 10.56 36.92 4.79
2439 2512 2.181521 GTTGGAAACGTGGCCGACA 61.182 57.895 17.95 0.00 36.92 4.35
2440 2513 2.181521 TTGGAAACGTGGCCGACAC 61.182 57.895 0.00 0.00 46.78 3.67
2448 2521 4.589046 TGGCCGACACATGGTTTT 57.411 50.000 0.00 0.00 0.00 2.43
2449 2522 2.037053 TGGCCGACACATGGTTTTG 58.963 52.632 0.00 0.00 0.00 2.44
2450 2523 0.753479 TGGCCGACACATGGTTTTGT 60.753 50.000 0.00 0.00 0.00 2.83
2461 2534 6.985188 CACATGGTTTTGTGCTAGTACTAT 57.015 37.500 12.42 0.00 40.45 2.12
2463 2536 7.906160 CACATGGTTTTGTGCTAGTACTATAC 58.094 38.462 12.42 9.49 40.45 1.47
2464 2537 7.764443 CACATGGTTTTGTGCTAGTACTATACT 59.236 37.037 12.42 0.00 40.45 2.12
2465 2538 7.980099 ACATGGTTTTGTGCTAGTACTATACTC 59.020 37.037 12.42 1.18 40.14 2.59
2466 2539 7.470935 TGGTTTTGTGCTAGTACTATACTCA 57.529 36.000 12.42 3.72 40.14 3.41
2467 2540 7.898918 TGGTTTTGTGCTAGTACTATACTCAA 58.101 34.615 12.42 9.21 40.14 3.02
2468 2541 8.033038 TGGTTTTGTGCTAGTACTATACTCAAG 58.967 37.037 12.42 0.00 40.14 3.02
2469 2542 8.248945 GGTTTTGTGCTAGTACTATACTCAAGA 58.751 37.037 12.42 5.33 40.14 3.02
2470 2543 9.804758 GTTTTGTGCTAGTACTATACTCAAGAT 57.195 33.333 12.42 0.00 40.14 2.40
2472 2545 8.982091 TTGTGCTAGTACTATACTCAAGATCT 57.018 34.615 12.42 0.00 40.14 2.75
2480 2553 9.978336 AGTACTATACTCAAGATCTATTACCCC 57.022 37.037 0.00 0.00 32.47 4.95
2481 2554 7.941431 ACTATACTCAAGATCTATTACCCCG 57.059 40.000 0.00 0.00 0.00 5.73
2482 2555 5.662674 ATACTCAAGATCTATTACCCCGC 57.337 43.478 0.00 0.00 0.00 6.13
2483 2556 3.577919 ACTCAAGATCTATTACCCCGCT 58.422 45.455 0.00 0.00 0.00 5.52
2484 2557 3.574826 ACTCAAGATCTATTACCCCGCTC 59.425 47.826 0.00 0.00 0.00 5.03
2485 2558 2.897969 TCAAGATCTATTACCCCGCTCC 59.102 50.000 0.00 0.00 0.00 4.70
2486 2559 1.546961 AGATCTATTACCCCGCTCCG 58.453 55.000 0.00 0.00 0.00 4.63
2487 2560 0.108756 GATCTATTACCCCGCTCCGC 60.109 60.000 0.00 0.00 0.00 5.54
2488 2561 1.542187 ATCTATTACCCCGCTCCGCC 61.542 60.000 0.00 0.00 0.00 6.13
2489 2562 3.236003 CTATTACCCCGCTCCGCCC 62.236 68.421 0.00 0.00 0.00 6.13
2496 2569 4.530857 CCGCTCCGCCCCTTACTG 62.531 72.222 0.00 0.00 0.00 2.74
2498 2571 4.096003 GCTCCGCCCCTTACTGCA 62.096 66.667 0.00 0.00 0.00 4.41
2499 2572 2.125106 CTCCGCCCCTTACTGCAC 60.125 66.667 0.00 0.00 0.00 4.57
2500 2573 3.682292 CTCCGCCCCTTACTGCACC 62.682 68.421 0.00 0.00 0.00 5.01
2503 2576 4.029809 GCCCCTTACTGCACCGGT 62.030 66.667 0.00 0.00 0.00 5.28
2504 2577 2.046314 CCCCTTACTGCACCGGTG 60.046 66.667 30.66 30.66 0.00 4.94
2505 2578 2.046314 CCCTTACTGCACCGGTGG 60.046 66.667 34.58 21.73 0.00 4.61
2506 2579 2.746277 CCTTACTGCACCGGTGGC 60.746 66.667 34.58 25.77 0.00 5.01
2507 2580 2.746277 CTTACTGCACCGGTGGCC 60.746 66.667 34.58 20.04 0.00 5.36
2508 2581 3.545124 CTTACTGCACCGGTGGCCA 62.545 63.158 34.58 23.42 0.00 5.36
2509 2582 3.835790 TTACTGCACCGGTGGCCAC 62.836 63.158 34.58 28.57 0.00 5.01
2833 2906 3.295800 GGATCTGGTCCGACCGTT 58.704 61.111 13.02 3.35 42.58 4.44
2834 2907 1.153628 GGATCTGGTCCGACCGTTG 60.154 63.158 13.02 5.97 42.58 4.10
2835 2908 1.810030 GATCTGGTCCGACCGTTGC 60.810 63.158 13.02 0.00 42.58 4.17
2836 2909 3.642778 ATCTGGTCCGACCGTTGCG 62.643 63.158 13.02 0.00 42.58 4.85
2837 2910 4.351938 CTGGTCCGACCGTTGCGA 62.352 66.667 13.02 0.00 42.58 5.10
2838 2911 4.651008 TGGTCCGACCGTTGCGAC 62.651 66.667 13.02 0.00 42.58 5.19
2847 2920 4.403137 CGTTGCGACGTACCGGGA 62.403 66.667 18.62 0.00 44.08 5.14
2848 2921 2.182537 GTTGCGACGTACCGGGAT 59.817 61.111 6.32 0.00 0.00 3.85
2849 2922 2.162754 GTTGCGACGTACCGGGATG 61.163 63.158 6.32 4.93 0.00 3.51
2850 2923 3.993376 TTGCGACGTACCGGGATGC 62.993 63.158 5.55 0.49 0.00 3.91
2851 2924 4.203076 GCGACGTACCGGGATGCT 62.203 66.667 5.55 0.00 0.00 3.79
2852 2925 2.025727 CGACGTACCGGGATGCTC 59.974 66.667 5.55 2.06 0.00 4.26
2853 2926 2.478890 CGACGTACCGGGATGCTCT 61.479 63.158 5.55 0.00 0.00 4.09
2854 2927 1.065928 GACGTACCGGGATGCTCTG 59.934 63.158 5.55 0.00 0.00 3.35
2855 2928 2.279517 CGTACCGGGATGCTCTGC 60.280 66.667 6.32 0.00 0.00 4.26
2856 2929 2.786495 CGTACCGGGATGCTCTGCT 61.786 63.158 6.32 0.00 0.00 4.24
2857 2930 1.068250 GTACCGGGATGCTCTGCTC 59.932 63.158 6.32 0.00 0.00 4.26
2858 2931 2.490148 TACCGGGATGCTCTGCTCG 61.490 63.158 6.32 0.00 0.00 5.03
2861 2934 3.859414 GGGATGCTCTGCTCGCCT 61.859 66.667 0.00 0.00 0.00 5.52
2862 2935 2.280052 GGATGCTCTGCTCGCCTC 60.280 66.667 0.00 0.00 0.00 4.70
2863 2936 2.280052 GATGCTCTGCTCGCCTCC 60.280 66.667 0.00 0.00 0.00 4.30
2864 2937 3.805891 GATGCTCTGCTCGCCTCCC 62.806 68.421 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 6.673316 GCACGTGTTTTTGGCTTTTTAAATGA 60.673 34.615 18.38 0.00 0.00 2.57
87 88 5.450704 GCACGTGTTTTTGGCTTTTTAAATG 59.549 36.000 18.38 0.00 0.00 2.32
97 112 0.992802 TTTTCGCACGTGTTTTTGGC 59.007 45.000 18.38 0.00 0.00 4.52
134 150 2.269241 GCTTTGGGCGCTACCTCT 59.731 61.111 7.64 0.00 39.10 3.69
254 270 4.780021 AGTGAGATCTCATACAACCCAACT 59.220 41.667 27.51 13.10 42.18 3.16
258 274 5.606348 AAGAGTGAGATCTCATACAACCC 57.394 43.478 27.51 13.17 42.18 4.11
456 473 7.065443 GTGTCAAAGTACTATTCACCCATAACC 59.935 40.741 0.00 0.00 0.00 2.85
675 692 5.952347 TTAACCTCCCTCTCCAACTATTC 57.048 43.478 0.00 0.00 0.00 1.75
677 694 8.019652 AGATAATTAACCTCCCTCTCCAACTAT 58.980 37.037 0.00 0.00 0.00 2.12
998 1020 2.180769 CGACGGCGGAAGACATGA 59.819 61.111 13.24 0.00 41.50 3.07
1036 1064 3.785859 GGGTGCGGATGAGGCAGA 61.786 66.667 0.00 0.00 41.83 4.26
1044 1072 1.077501 CTTGATGGTGGGTGCGGAT 60.078 57.895 0.00 0.00 0.00 4.18
1045 1073 2.350895 CTTGATGGTGGGTGCGGA 59.649 61.111 0.00 0.00 0.00 5.54
1059 1087 2.699809 GCGTCGATGAGCAGCTTG 59.300 61.111 9.31 0.00 0.00 4.01
1200 1228 3.573491 GCGTAGATGTTGGCCGCC 61.573 66.667 1.04 1.04 38.52 6.13
1218 1246 0.815615 GATTCATCCCTTCGGCGCTT 60.816 55.000 7.64 0.00 0.00 4.68
1551 1591 1.742880 GAGCAGCGCCATGACAGAA 60.743 57.895 2.29 0.00 0.00 3.02
1596 1636 2.510382 AGACTTCTCCCCGAGTATGAGA 59.490 50.000 0.00 0.00 33.50 3.27
1607 1647 2.159170 CCGATCTTGACAGACTTCTCCC 60.159 54.545 0.00 0.00 0.00 4.30
1632 1672 0.824109 CGCTATCACCCACCTCTTGA 59.176 55.000 0.00 0.00 0.00 3.02
1642 1682 3.313526 ACAAATTGAGCATCGCTATCACC 59.686 43.478 0.00 0.00 39.88 4.02
1648 1688 4.370917 ACAAAAACAAATTGAGCATCGCT 58.629 34.783 0.00 0.00 43.88 4.93
1649 1689 4.713854 ACAAAAACAAATTGAGCATCGC 57.286 36.364 0.00 0.00 38.61 4.58
1682 1727 3.873952 AGCAAATTAGTTGAGAGCGGATC 59.126 43.478 0.00 0.00 39.87 3.36
1688 1735 4.380233 CCCTGCAAGCAAATTAGTTGAGAG 60.380 45.833 0.00 0.00 39.87 3.20
1689 1736 3.507233 CCCTGCAAGCAAATTAGTTGAGA 59.493 43.478 0.00 0.00 39.87 3.27
1727 1774 1.376466 GCTGGACTGCAGGGAAGAA 59.624 57.895 19.93 0.00 0.00 2.52
1728 1775 1.842920 TGCTGGACTGCAGGGAAGA 60.843 57.895 19.93 0.00 38.12 2.87
1736 1783 3.941657 GAGGACGGTGCTGGACTGC 62.942 68.421 6.97 1.40 33.72 4.40
1829 1882 9.567776 TTATCATTTTTCTCCTGAACAACACTA 57.432 29.630 0.00 0.00 31.02 2.74
1902 1960 2.227388 GCATGTGGAAAGAGACTTGTGG 59.773 50.000 0.00 0.00 0.00 4.17
1903 1961 2.880268 TGCATGTGGAAAGAGACTTGTG 59.120 45.455 0.00 0.00 0.00 3.33
1904 1962 3.213206 TGCATGTGGAAAGAGACTTGT 57.787 42.857 0.00 0.00 0.00 3.16
2043 2116 4.038271 ACATGTGGGTCAGATGTGAATT 57.962 40.909 9.40 0.00 44.66 2.17
2055 2128 1.125093 TGGACCGAGAACATGTGGGT 61.125 55.000 0.00 4.90 0.00 4.51
2059 2132 0.460284 GCGATGGACCGAGAACATGT 60.460 55.000 0.00 0.00 0.00 3.21
2060 2133 1.154205 GGCGATGGACCGAGAACATG 61.154 60.000 0.00 0.00 0.00 3.21
2061 2134 1.144057 GGCGATGGACCGAGAACAT 59.856 57.895 0.00 0.00 0.00 2.71
2062 2135 2.279810 TGGCGATGGACCGAGAACA 61.280 57.895 0.00 0.00 0.00 3.18
2063 2136 1.810030 GTGGCGATGGACCGAGAAC 60.810 63.158 0.00 0.00 0.00 3.01
2157 2230 2.654877 GAGAAGGCGGAACCGTGA 59.345 61.111 14.63 0.00 46.52 4.35
2159 2232 2.603776 AGGAGAAGGCGGAACCGT 60.604 61.111 14.63 0.00 46.52 4.83
2222 2295 5.363939 GAGATTTCGAGATCCACCTTGAAT 58.636 41.667 12.04 0.00 36.68 2.57
2297 2370 1.860078 GTCGACTTTGCAGAACGGG 59.140 57.895 8.70 0.00 0.00 5.28
2327 2400 2.028778 GAGCCATCGCGCATCTCT 59.971 61.111 8.75 0.00 41.18 3.10
2345 2418 1.406219 CGCTGAAGACGGACATGTCG 61.406 60.000 19.33 16.15 43.70 4.35
2354 2427 2.804368 AAGCCGAGACGCTGAAGACG 62.804 60.000 0.00 0.00 39.64 4.18
2363 2436 2.182030 GGAGTCCAAGCCGAGACG 59.818 66.667 3.60 0.00 38.08 4.18
2387 2460 6.265876 CCCATCAATCCATCACATGTGAATTA 59.734 38.462 31.00 18.95 43.58 1.40
2388 2461 5.069914 CCCATCAATCCATCACATGTGAATT 59.930 40.000 31.00 22.33 43.58 2.17
2389 2462 4.587262 CCCATCAATCCATCACATGTGAAT 59.413 41.667 31.00 17.95 43.58 2.57
2390 2463 3.955551 CCCATCAATCCATCACATGTGAA 59.044 43.478 31.00 16.42 43.58 3.18
2391 2464 3.202595 TCCCATCAATCCATCACATGTGA 59.797 43.478 29.67 29.67 44.59 3.58
2392 2465 3.558033 TCCCATCAATCCATCACATGTG 58.442 45.455 20.18 20.18 0.00 3.21
2393 2466 3.957508 TCCCATCAATCCATCACATGT 57.042 42.857 0.00 0.00 0.00 3.21
2394 2467 3.056821 GCATCCCATCAATCCATCACATG 60.057 47.826 0.00 0.00 0.00 3.21
2395 2468 3.162666 GCATCCCATCAATCCATCACAT 58.837 45.455 0.00 0.00 0.00 3.21
2396 2469 2.176148 AGCATCCCATCAATCCATCACA 59.824 45.455 0.00 0.00 0.00 3.58
2397 2470 2.557056 CAGCATCCCATCAATCCATCAC 59.443 50.000 0.00 0.00 0.00 3.06
2398 2471 2.490168 CCAGCATCCCATCAATCCATCA 60.490 50.000 0.00 0.00 0.00 3.07
2399 2472 2.168496 CCAGCATCCCATCAATCCATC 58.832 52.381 0.00 0.00 0.00 3.51
2400 2473 1.784593 TCCAGCATCCCATCAATCCAT 59.215 47.619 0.00 0.00 0.00 3.41
2401 2474 1.144298 CTCCAGCATCCCATCAATCCA 59.856 52.381 0.00 0.00 0.00 3.41
2402 2475 1.144503 ACTCCAGCATCCCATCAATCC 59.855 52.381 0.00 0.00 0.00 3.01
2403 2476 2.621998 CAACTCCAGCATCCCATCAATC 59.378 50.000 0.00 0.00 0.00 2.67
2404 2477 2.662866 CAACTCCAGCATCCCATCAAT 58.337 47.619 0.00 0.00 0.00 2.57
2405 2478 1.341285 CCAACTCCAGCATCCCATCAA 60.341 52.381 0.00 0.00 0.00 2.57
2406 2479 0.256752 CCAACTCCAGCATCCCATCA 59.743 55.000 0.00 0.00 0.00 3.07
2407 2480 0.548031 TCCAACTCCAGCATCCCATC 59.452 55.000 0.00 0.00 0.00 3.51
2408 2481 1.002069 TTCCAACTCCAGCATCCCAT 58.998 50.000 0.00 0.00 0.00 4.00
2409 2482 0.776810 TTTCCAACTCCAGCATCCCA 59.223 50.000 0.00 0.00 0.00 4.37
2410 2483 1.177401 GTTTCCAACTCCAGCATCCC 58.823 55.000 0.00 0.00 0.00 3.85
2411 2484 0.804989 CGTTTCCAACTCCAGCATCC 59.195 55.000 0.00 0.00 0.00 3.51
2412 2485 1.197721 CACGTTTCCAACTCCAGCATC 59.802 52.381 0.00 0.00 0.00 3.91
2413 2486 1.238439 CACGTTTCCAACTCCAGCAT 58.762 50.000 0.00 0.00 0.00 3.79
2414 2487 0.817634 CCACGTTTCCAACTCCAGCA 60.818 55.000 0.00 0.00 0.00 4.41
2415 2488 1.949257 CCACGTTTCCAACTCCAGC 59.051 57.895 0.00 0.00 0.00 4.85
2416 2489 1.515521 GGCCACGTTTCCAACTCCAG 61.516 60.000 0.00 0.00 0.00 3.86
2417 2490 1.527380 GGCCACGTTTCCAACTCCA 60.527 57.895 0.00 0.00 0.00 3.86
2418 2491 2.613506 CGGCCACGTTTCCAACTCC 61.614 63.158 2.24 0.00 34.81 3.85
2419 2492 1.595929 TCGGCCACGTTTCCAACTC 60.596 57.895 2.24 0.00 41.85 3.01
2420 2493 1.890510 GTCGGCCACGTTTCCAACT 60.891 57.895 2.24 0.00 41.85 3.16
2421 2494 2.181521 TGTCGGCCACGTTTCCAAC 61.182 57.895 2.24 0.00 41.85 3.77
2422 2495 2.181521 GTGTCGGCCACGTTTCCAA 61.182 57.895 2.24 0.00 41.85 3.53
2423 2496 2.589442 GTGTCGGCCACGTTTCCA 60.589 61.111 2.24 0.00 41.85 3.53
2430 2503 0.318614 CAAAACCATGTGTCGGCCAC 60.319 55.000 2.24 0.25 44.78 5.01
2431 2504 0.753479 ACAAAACCATGTGTCGGCCA 60.753 50.000 2.24 0.00 30.82 5.36
2432 2505 0.318614 CACAAAACCATGTGTCGGCC 60.319 55.000 0.00 0.00 44.46 6.13
2433 2506 3.177883 CACAAAACCATGTGTCGGC 57.822 52.632 0.00 0.00 44.46 5.54
2438 2511 7.764443 AGTATAGTACTAGCACAAAACCATGTG 59.236 37.037 8.85 3.16 44.19 3.21
2439 2512 7.848128 AGTATAGTACTAGCACAAAACCATGT 58.152 34.615 8.85 0.00 37.23 3.21
2440 2513 7.979537 TGAGTATAGTACTAGCACAAAACCATG 59.020 37.037 8.85 0.00 39.59 3.66
2441 2514 8.074613 TGAGTATAGTACTAGCACAAAACCAT 57.925 34.615 8.85 0.00 39.59 3.55
2442 2515 7.470935 TGAGTATAGTACTAGCACAAAACCA 57.529 36.000 8.85 2.12 39.59 3.67
2443 2516 8.248945 TCTTGAGTATAGTACTAGCACAAAACC 58.751 37.037 8.85 0.00 39.59 3.27
2444 2517 9.804758 ATCTTGAGTATAGTACTAGCACAAAAC 57.195 33.333 8.85 3.86 39.59 2.43
2446 2519 9.409918 AGATCTTGAGTATAGTACTAGCACAAA 57.590 33.333 8.85 6.95 39.59 2.83
2447 2520 8.982091 AGATCTTGAGTATAGTACTAGCACAA 57.018 34.615 8.85 12.46 39.59 3.33
2454 2527 9.978336 GGGGTAATAGATCTTGAGTATAGTACT 57.022 37.037 0.00 0.00 42.86 2.73
2455 2528 8.891720 CGGGGTAATAGATCTTGAGTATAGTAC 58.108 40.741 0.00 0.00 0.00 2.73
2456 2529 7.555554 GCGGGGTAATAGATCTTGAGTATAGTA 59.444 40.741 0.00 0.00 0.00 1.82
2457 2530 6.377712 GCGGGGTAATAGATCTTGAGTATAGT 59.622 42.308 0.00 0.00 0.00 2.12
2458 2531 6.603997 AGCGGGGTAATAGATCTTGAGTATAG 59.396 42.308 0.00 0.00 0.00 1.31
2459 2532 6.491383 AGCGGGGTAATAGATCTTGAGTATA 58.509 40.000 0.00 0.00 0.00 1.47
2460 2533 5.334421 AGCGGGGTAATAGATCTTGAGTAT 58.666 41.667 0.00 0.00 0.00 2.12
2461 2534 4.737578 AGCGGGGTAATAGATCTTGAGTA 58.262 43.478 0.00 0.00 0.00 2.59
2462 2535 3.574826 GAGCGGGGTAATAGATCTTGAGT 59.425 47.826 0.00 0.00 0.00 3.41
2463 2536 3.056465 GGAGCGGGGTAATAGATCTTGAG 60.056 52.174 0.00 0.00 0.00 3.02
2464 2537 2.897969 GGAGCGGGGTAATAGATCTTGA 59.102 50.000 0.00 0.00 0.00 3.02
2465 2538 2.352814 CGGAGCGGGGTAATAGATCTTG 60.353 54.545 0.00 0.00 0.00 3.02
2466 2539 1.893801 CGGAGCGGGGTAATAGATCTT 59.106 52.381 0.00 0.00 0.00 2.40
2467 2540 1.546961 CGGAGCGGGGTAATAGATCT 58.453 55.000 0.00 0.00 0.00 2.75
2482 2555 2.125106 GTGCAGTAAGGGGCGGAG 60.125 66.667 0.00 0.00 0.00 4.63
2483 2556 3.712907 GGTGCAGTAAGGGGCGGA 61.713 66.667 0.00 0.00 0.00 5.54
2486 2559 4.029809 ACCGGTGCAGTAAGGGGC 62.030 66.667 6.12 0.00 0.00 5.80
2487 2560 2.046314 CACCGGTGCAGTAAGGGG 60.046 66.667 24.02 0.00 0.00 4.79
2488 2561 2.046314 CCACCGGTGCAGTAAGGG 60.046 66.667 29.75 9.18 0.00 3.95
2489 2562 2.746277 GCCACCGGTGCAGTAAGG 60.746 66.667 29.75 14.88 0.00 2.69
2490 2563 2.746277 GGCCACCGGTGCAGTAAG 60.746 66.667 29.75 15.26 0.00 2.34
2491 2564 3.561241 TGGCCACCGGTGCAGTAA 61.561 61.111 29.75 9.24 0.00 2.24
2492 2565 4.323477 GTGGCCACCGGTGCAGTA 62.323 66.667 29.75 11.77 0.00 2.74
2816 2889 1.153628 CAACGGTCGGACCAGATCC 60.154 63.158 25.80 0.00 45.20 3.36
2817 2890 1.810030 GCAACGGTCGGACCAGATC 60.810 63.158 25.80 9.01 38.47 2.75
2818 2891 2.264794 GCAACGGTCGGACCAGAT 59.735 61.111 25.80 11.18 38.47 2.90
2819 2892 4.351938 CGCAACGGTCGGACCAGA 62.352 66.667 25.80 0.00 38.47 3.86
2820 2893 4.351938 TCGCAACGGTCGGACCAG 62.352 66.667 25.80 19.62 38.47 4.00
2821 2894 4.651008 GTCGCAACGGTCGGACCA 62.651 66.667 25.80 3.21 38.47 4.02
2839 2912 1.068250 GAGCAGAGCATCCCGGTAC 59.932 63.158 0.00 0.00 33.66 3.34
2840 2913 2.490148 CGAGCAGAGCATCCCGGTA 61.490 63.158 0.00 0.00 33.66 4.02
2841 2914 3.842923 CGAGCAGAGCATCCCGGT 61.843 66.667 0.00 0.00 33.66 5.28
2844 2917 3.805891 GAGGCGAGCAGAGCATCCC 62.806 68.421 0.00 0.00 39.22 3.85
2845 2918 2.280052 GAGGCGAGCAGAGCATCC 60.280 66.667 0.00 0.00 39.22 3.51
2846 2919 2.280052 GGAGGCGAGCAGAGCATC 60.280 66.667 4.54 4.54 43.71 3.91
2847 2920 3.859414 GGGAGGCGAGCAGAGCAT 61.859 66.667 0.00 0.00 36.08 3.79


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

AutoCloner maintained by Alex Coulton.