Multiple sequence alignment - TraesCS6D01G147200

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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 TraesCS6D01G147200 chr6D 100.000 2441 0 0 1 2441 119291155 119293595 0.000000e+00 4508.0
1 TraesCS6D01G147200 chr6B 89.789 2272 128 40 5 2212 211208919 211211150 0.000000e+00 2815.0
2 TraesCS6D01G147200 chr6A 91.106 1709 69 27 583 2253 147469600 147471263 0.000000e+00 2237.0
3 TraesCS6D01G147200 chr6A 88.347 472 38 8 1 459 147469104 147469571 3.550000e-153 551.0
4 TraesCS6D01G147200 chr5B 88.301 359 38 4 218 575 480167618 480167973 6.240000e-116 427.0
5 TraesCS6D01G147200 chr5B 88.832 197 21 1 5 201 480167365 480167560 8.720000e-60 241.0
6 TraesCS6D01G147200 chr2D 86.908 359 44 3 218 575 650649486 650649842 1.360000e-107 399.0
7 TraesCS6D01G147200 chr2D 91.045 201 18 0 6 206 650649224 650649424 3.090000e-69 272.0
8 TraesCS6D01G147200 chr2D 89.908 109 9 2 2332 2440 546736953 546736847 3.270000e-29 139.0
9 TraesCS6D01G147200 chr3D 85.831 367 49 3 218 583 6979938 6979574 1.060000e-103 387.0
10 TraesCS6D01G147200 chr3D 90.826 109 8 2 2332 2440 323312261 323312367 7.030000e-31 145.0
11 TraesCS6D01G147200 chr3D 89.189 111 10 2 2332 2440 106739235 106739345 1.180000e-28 137.0
12 TraesCS6D01G147200 chr2A 85.237 359 46 5 218 572 771996966 771997321 1.780000e-96 363.0
13 TraesCS6D01G147200 chr2A 87.190 242 25 4 218 455 772060768 772061007 1.110000e-68 270.0
14 TraesCS6D01G147200 chr2A 88.614 202 19 3 5 206 772060507 772060704 2.420000e-60 243.0
15 TraesCS6D01G147200 chr2A 88.614 202 19 3 5 206 772140201 772140398 2.420000e-60 243.0
16 TraesCS6D01G147200 chr2A 88.119 202 20 3 5 206 772182908 772183105 1.130000e-58 237.0
17 TraesCS6D01G147200 chr3A 83.924 367 51 5 219 583 13400178 13400538 6.460000e-91 344.0
18 TraesCS6D01G147200 chr3A 90.826 109 8 2 2332 2440 739138769 739138663 7.030000e-31 145.0
19 TraesCS6D01G147200 chr4D 85.393 267 38 1 294 560 508821506 508821771 2.390000e-70 276.0
20 TraesCS6D01G147200 chr4D 86.364 198 27 0 4 201 494477260 494477457 1.470000e-52 217.0
21 TraesCS6D01G147200 chr4D 92.661 109 7 1 2332 2440 334160727 334160620 3.250000e-34 156.0
22 TraesCS6D01G147200 chr4D 86.364 110 10 5 2332 2440 3794428 3794323 5.520000e-22 115.0
23 TraesCS6D01G147200 chr4B 91.351 185 16 0 1 185 633937668 633937852 1.120000e-63 254.0
24 TraesCS6D01G147200 chr5A 89.447 199 20 1 3 201 706933616 706933813 1.450000e-62 250.0
25 TraesCS6D01G147200 chr7D 90.826 109 9 1 2332 2440 89076125 89076018 7.030000e-31 145.0
26 TraesCS6D01G147200 chr2B 88.991 109 10 2 2332 2440 391525925 391525819 1.520000e-27 134.0
27 TraesCS6D01G147200 chr1D 88.073 109 12 1 2332 2440 477484614 477484507 7.080000e-26 128.0
28 TraesCS6D01G147200 chr7B 80.769 130 15 9 1218 1339 642831299 642831172 2.580000e-15 93.5


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 TraesCS6D01G147200 chr6D 119291155 119293595 2440 False 4508.0 4508 100.0000 1 2441 1 chr6D.!!$F1 2440
1 TraesCS6D01G147200 chr6B 211208919 211211150 2231 False 2815.0 2815 89.7890 5 2212 1 chr6B.!!$F1 2207
2 TraesCS6D01G147200 chr6A 147469104 147471263 2159 False 1394.0 2237 89.7265 1 2253 2 chr6A.!!$F1 2252
3 TraesCS6D01G147200 chr5B 480167365 480167973 608 False 334.0 427 88.5665 5 575 2 chr5B.!!$F1 570
4 TraesCS6D01G147200 chr2D 650649224 650649842 618 False 335.5 399 88.9765 6 575 2 chr2D.!!$F1 569
5 TraesCS6D01G147200 chr2A 772060507 772061007 500 False 256.5 270 87.9020 5 455 2 chr2A.!!$F4 450

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
583 644 0.03392 TGCTGCAAGTCATCGACACT 59.966 50.0 0.0 0.0 34.6 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2271 2432 0.179108 GCCACTAGGTAGAAGCACCG 60.179 60.0 0.0 0.0 43.84 4.94 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
24 25 3.190953 GTCGGGTCCTAGATAAGAATCCG 59.809 52.174 0.00 0.00 34.29 4.18
45 46 0.178967 TTGCTGAATTGCCTCCACCA 60.179 50.000 0.00 0.00 0.00 4.17
108 110 6.883756 CCCCAAATTTGCCAACAAGTATATTT 59.116 34.615 12.92 0.00 37.04 1.40
124 126 9.696917 CAAGTATATTTCATTTCTAATTGCCCC 57.303 33.333 0.00 0.00 0.00 5.80
156 159 6.424812 CGCTGAATCAACATCTTGGATATGTA 59.575 38.462 0.00 0.00 36.56 2.29
189 192 5.537300 AGTCACTTCTGCTAGAAAGTCAA 57.463 39.130 0.00 0.00 33.19 3.18
201 205 4.021102 AGAAAGTCAACCCGTTCATCAT 57.979 40.909 0.00 0.00 0.00 2.45
269 328 4.587684 TGTTCTTTCTTCTAAGTCGGGAGT 59.412 41.667 0.00 0.00 0.00 3.85
279 339 0.680061 AGTCGGGAGTTTGGAGACAC 59.320 55.000 0.00 0.00 42.67 3.67
315 376 1.878088 TGTAGCTAGGACGCGAATAGG 59.122 52.381 15.93 0.40 34.40 2.57
319 380 0.664767 CTAGGACGCGAATAGGCAGC 60.665 60.000 15.93 0.00 0.00 5.25
437 498 5.596361 ACATGTACTCCATCCAAAACAACAA 59.404 36.000 0.00 0.00 0.00 2.83
472 533 2.692557 AGATATTCGCAGTGACTGAGCT 59.307 45.455 18.18 6.62 32.44 4.09
481 542 3.004106 GCAGTGACTGAGCTTGATTTGTT 59.996 43.478 18.18 0.00 32.44 2.83
484 545 4.514441 AGTGACTGAGCTTGATTTGTTCTG 59.486 41.667 0.00 0.00 0.00 3.02
489 550 5.766670 ACTGAGCTTGATTTGTTCTGATCAA 59.233 36.000 0.00 0.00 39.30 2.57
490 551 6.005583 TGAGCTTGATTTGTTCTGATCAAC 57.994 37.500 0.00 0.00 37.35 3.18
511 572 4.592942 ACTGCTCTTTGAATGGCATCTAA 58.407 39.130 0.00 0.00 34.12 2.10
579 640 2.831597 CAGTGCTGCAAGTCATCGA 58.168 52.632 2.77 0.00 35.30 3.59
583 644 0.033920 TGCTGCAAGTCATCGACACT 59.966 50.000 0.00 0.00 34.60 3.55
584 645 0.441533 GCTGCAAGTCATCGACACTG 59.558 55.000 0.00 0.00 34.60 3.66
585 646 1.788258 CTGCAAGTCATCGACACTGT 58.212 50.000 0.00 0.00 34.60 3.55
725 809 1.694169 ATCTTCCCTGCCCCGATGT 60.694 57.895 0.00 0.00 0.00 3.06
776 860 3.000727 GACACCAAAATACTCACGGAGG 58.999 50.000 5.98 0.00 33.35 4.30
791 875 4.385405 AGGCTGCACTGCTCCGTC 62.385 66.667 0.50 0.00 0.00 4.79
804 896 4.717629 CCGTCGCCTCAGTTCGCA 62.718 66.667 0.00 0.00 0.00 5.10
885 978 1.747355 CGGACACGTCTACCTACCAAT 59.253 52.381 0.00 0.00 34.81 3.16
895 988 2.773993 ACCTACCAATAACCCACACG 57.226 50.000 0.00 0.00 0.00 4.49
988 1104 1.450669 GAGCGAGAGGGAGAGACGT 60.451 63.158 0.00 0.00 0.00 4.34
1323 1442 4.190001 TCTACTACAGCTACACCTTCTCG 58.810 47.826 0.00 0.00 0.00 4.04
1449 1568 3.081409 AGCCATTAGCCGTCCCGT 61.081 61.111 0.00 0.00 45.47 5.28
1530 1650 3.917988 AGGCAGCAGCTTGTTTTAATTC 58.082 40.909 0.00 0.00 41.70 2.17
1535 1655 5.119125 GCAGCAGCTTGTTTTAATTCGATTT 59.881 36.000 0.00 0.00 37.91 2.17
1545 1665 9.620660 TTGTTTTAATTCGATTTAAGAAGAGCC 57.379 29.630 11.19 0.00 0.00 4.70
1636 1761 1.129437 GTGAGAAGAACGCCATTGCTC 59.871 52.381 0.00 0.00 34.43 4.26
1692 1822 2.133281 TCGGATTCTCAAGGACCGTA 57.867 50.000 0.00 0.00 43.36 4.02
2053 2191 1.141881 GCGAGACCGACCATGACAT 59.858 57.895 0.00 0.00 38.22 3.06
2166 2327 2.189257 CCGAATGCATCCCGGTCA 59.811 61.111 24.23 0.00 38.55 4.02
2167 2328 1.889105 CCGAATGCATCCCGGTCAG 60.889 63.158 24.23 6.66 38.55 3.51
2179 2340 0.753262 CCGGTCAGGGATTCTACAGG 59.247 60.000 0.00 0.00 35.97 4.00
2180 2341 1.688311 CCGGTCAGGGATTCTACAGGA 60.688 57.143 0.00 0.00 35.97 3.86
2181 2342 2.320781 CGGTCAGGGATTCTACAGGAT 58.679 52.381 0.00 0.00 0.00 3.24
2182 2343 2.700897 CGGTCAGGGATTCTACAGGATT 59.299 50.000 0.00 0.00 0.00 3.01
2183 2344 3.243907 CGGTCAGGGATTCTACAGGATTC 60.244 52.174 0.00 0.00 0.00 2.52
2184 2345 3.071747 GGTCAGGGATTCTACAGGATTCC 59.928 52.174 0.00 0.00 41.36 3.01
2185 2346 2.965831 TCAGGGATTCTACAGGATTCCG 59.034 50.000 0.00 0.00 42.39 4.30
2186 2347 2.037772 CAGGGATTCTACAGGATTCCGG 59.962 54.545 0.00 0.00 42.39 5.14
2187 2348 2.047830 GGGATTCTACAGGATTCCGGT 58.952 52.381 13.18 13.18 42.39 5.28
2188 2349 2.224305 GGGATTCTACAGGATTCCGGTG 60.224 54.545 17.51 4.69 42.39 4.94
2189 2350 2.484889 GATTCTACAGGATTCCGGTGC 58.515 52.381 17.51 0.00 33.35 5.01
2190 2351 1.568504 TTCTACAGGATTCCGGTGCT 58.431 50.000 17.51 0.00 33.35 4.40
2191 2352 0.824109 TCTACAGGATTCCGGTGCTG 59.176 55.000 17.51 11.40 42.52 4.41
2192 2353 0.811616 CTACAGGATTCCGGTGCTGC 60.812 60.000 17.51 0.00 40.76 5.25
2253 2414 1.265635 GTGTGTGTGTGTGTGTGTGTT 59.734 47.619 0.00 0.00 0.00 3.32
2254 2415 1.265365 TGTGTGTGTGTGTGTGTGTTG 59.735 47.619 0.00 0.00 0.00 3.33
2255 2416 1.533299 GTGTGTGTGTGTGTGTGTTGA 59.467 47.619 0.00 0.00 0.00 3.18
2256 2417 1.533299 TGTGTGTGTGTGTGTGTTGAC 59.467 47.619 0.00 0.00 0.00 3.18
2257 2418 1.533299 GTGTGTGTGTGTGTGTTGACA 59.467 47.619 0.00 0.00 0.00 3.58
2258 2419 1.803555 TGTGTGTGTGTGTGTTGACAG 59.196 47.619 0.00 0.00 30.74 3.51
2259 2420 2.073056 GTGTGTGTGTGTGTTGACAGA 58.927 47.619 0.00 0.00 30.74 3.41
2260 2421 2.073056 TGTGTGTGTGTGTTGACAGAC 58.927 47.619 4.61 4.61 44.75 3.51
2261 2422 1.060553 GTGTGTGTGTGTTGACAGACG 59.939 52.381 6.88 0.00 46.91 4.18
2262 2423 0.026285 GTGTGTGTGTTGACAGACGC 59.974 55.000 15.50 15.50 46.91 5.19
2263 2424 0.108377 TGTGTGTGTTGACAGACGCT 60.108 50.000 20.73 0.00 46.91 5.07
2264 2425 0.577269 GTGTGTGTTGACAGACGCTC 59.423 55.000 15.20 2.73 44.24 5.03
2265 2426 0.529773 TGTGTGTTGACAGACGCTCC 60.530 55.000 6.88 0.00 42.37 4.70
2266 2427 0.249489 GTGTGTTGACAGACGCTCCT 60.249 55.000 0.00 0.00 30.74 3.69
2267 2428 0.249447 TGTGTTGACAGACGCTCCTG 60.249 55.000 1.31 1.31 39.93 3.86
2268 2429 1.300931 TGTTGACAGACGCTCCTGC 60.301 57.895 2.61 0.00 37.68 4.85
2269 2430 2.029844 GTTGACAGACGCTCCTGCC 61.030 63.158 2.61 0.00 37.68 4.85
2270 2431 2.210013 TTGACAGACGCTCCTGCCT 61.210 57.895 2.61 0.00 37.68 4.75
2271 2432 2.159819 TTGACAGACGCTCCTGCCTC 62.160 60.000 2.61 0.00 37.68 4.70
2272 2433 3.691744 GACAGACGCTCCTGCCTCG 62.692 68.421 2.61 0.00 37.68 4.63
2273 2434 4.504916 CAGACGCTCCTGCCTCGG 62.505 72.222 0.00 0.00 35.36 4.63
2275 2436 4.803426 GACGCTCCTGCCTCGGTG 62.803 72.222 0.00 0.00 35.36 4.94
2278 2439 4.400961 GCTCCTGCCTCGGTGCTT 62.401 66.667 0.00 0.00 39.73 3.91
2279 2440 2.125350 CTCCTGCCTCGGTGCTTC 60.125 66.667 0.00 0.00 0.00 3.86
2280 2441 2.604686 TCCTGCCTCGGTGCTTCT 60.605 61.111 0.00 0.00 0.00 2.85
2281 2442 1.304962 TCCTGCCTCGGTGCTTCTA 60.305 57.895 0.00 0.00 0.00 2.10
2282 2443 1.153549 CCTGCCTCGGTGCTTCTAC 60.154 63.158 0.00 0.00 0.00 2.59
2283 2444 1.153549 CTGCCTCGGTGCTTCTACC 60.154 63.158 0.00 0.00 37.37 3.18
2284 2445 1.608717 CTGCCTCGGTGCTTCTACCT 61.609 60.000 0.00 0.00 38.62 3.08
2285 2446 0.323999 TGCCTCGGTGCTTCTACCTA 60.324 55.000 0.00 0.00 38.62 3.08
2286 2447 0.386113 GCCTCGGTGCTTCTACCTAG 59.614 60.000 0.00 0.00 38.62 3.02
2287 2448 1.765230 CCTCGGTGCTTCTACCTAGT 58.235 55.000 0.00 0.00 38.62 2.57
2288 2449 1.405821 CCTCGGTGCTTCTACCTAGTG 59.594 57.143 0.00 0.00 38.62 2.74
2289 2450 1.405821 CTCGGTGCTTCTACCTAGTGG 59.594 57.143 0.00 0.00 38.62 4.00
2290 2451 0.179108 CGGTGCTTCTACCTAGTGGC 60.179 60.000 0.00 0.00 38.62 5.01
2291 2452 1.196012 GGTGCTTCTACCTAGTGGCT 58.804 55.000 0.00 0.00 37.74 4.75
2292 2453 1.134670 GGTGCTTCTACCTAGTGGCTG 60.135 57.143 0.00 0.00 37.74 4.85
2293 2454 1.550976 GTGCTTCTACCTAGTGGCTGT 59.449 52.381 0.00 0.00 36.63 4.40
2294 2455 2.758979 GTGCTTCTACCTAGTGGCTGTA 59.241 50.000 0.00 0.00 36.63 2.74
2295 2456 2.758979 TGCTTCTACCTAGTGGCTGTAC 59.241 50.000 0.00 0.00 36.63 2.90
2296 2457 3.025262 GCTTCTACCTAGTGGCTGTACT 58.975 50.000 0.00 0.00 36.63 2.73
2297 2458 4.205587 GCTTCTACCTAGTGGCTGTACTA 58.794 47.826 0.00 0.00 36.63 1.82
2298 2459 4.036616 GCTTCTACCTAGTGGCTGTACTAC 59.963 50.000 0.00 0.00 36.63 2.73
2299 2460 4.849813 TCTACCTAGTGGCTGTACTACA 57.150 45.455 0.00 0.00 36.63 2.74
2300 2461 5.384145 TCTACCTAGTGGCTGTACTACAT 57.616 43.478 0.00 0.00 36.63 2.29
2301 2462 5.131067 TCTACCTAGTGGCTGTACTACATG 58.869 45.833 0.00 0.00 36.63 3.21
2302 2463 3.977312 ACCTAGTGGCTGTACTACATGA 58.023 45.455 0.00 0.00 36.63 3.07
2303 2464 4.350245 ACCTAGTGGCTGTACTACATGAA 58.650 43.478 0.00 0.00 36.63 2.57
2304 2465 4.962995 ACCTAGTGGCTGTACTACATGAAT 59.037 41.667 0.00 0.00 36.63 2.57
2305 2466 5.163405 ACCTAGTGGCTGTACTACATGAATG 60.163 44.000 0.00 0.00 36.63 2.67
2306 2467 3.535561 AGTGGCTGTACTACATGAATGC 58.464 45.455 0.00 0.00 30.71 3.56
2307 2468 3.055167 AGTGGCTGTACTACATGAATGCA 60.055 43.478 0.00 0.00 30.71 3.96
2308 2469 3.310774 GTGGCTGTACTACATGAATGCAG 59.689 47.826 0.00 4.61 0.00 4.41
2309 2470 3.197549 TGGCTGTACTACATGAATGCAGA 59.802 43.478 14.30 0.00 0.00 4.26
2310 2471 4.141642 TGGCTGTACTACATGAATGCAGAT 60.142 41.667 14.30 0.00 0.00 2.90
2311 2472 4.212847 GGCTGTACTACATGAATGCAGATG 59.787 45.833 14.30 0.00 0.00 2.90
2312 2473 5.052481 GCTGTACTACATGAATGCAGATGA 58.948 41.667 14.30 0.00 0.00 2.92
2313 2474 5.699915 GCTGTACTACATGAATGCAGATGAT 59.300 40.000 14.30 0.00 0.00 2.45
2314 2475 6.204301 GCTGTACTACATGAATGCAGATGATT 59.796 38.462 14.30 0.00 0.00 2.57
2315 2476 7.255035 GCTGTACTACATGAATGCAGATGATTT 60.255 37.037 14.30 0.00 0.00 2.17
2316 2477 7.922837 TGTACTACATGAATGCAGATGATTTG 58.077 34.615 0.00 0.00 0.00 2.32
2317 2478 7.553760 TGTACTACATGAATGCAGATGATTTGT 59.446 33.333 0.00 2.01 0.00 2.83
2318 2479 7.024340 ACTACATGAATGCAGATGATTTGTC 57.976 36.000 0.00 0.00 0.00 3.18
2319 2480 4.916870 ACATGAATGCAGATGATTTGTCG 58.083 39.130 0.00 0.00 0.00 4.35
2320 2481 4.201980 ACATGAATGCAGATGATTTGTCGG 60.202 41.667 0.00 0.00 0.00 4.79
2321 2482 3.608796 TGAATGCAGATGATTTGTCGGA 58.391 40.909 0.00 0.00 0.00 4.55
2322 2483 3.624410 TGAATGCAGATGATTTGTCGGAG 59.376 43.478 0.00 0.00 0.00 4.63
2323 2484 2.028420 TGCAGATGATTTGTCGGAGG 57.972 50.000 0.00 0.00 0.00 4.30
2324 2485 1.303309 GCAGATGATTTGTCGGAGGG 58.697 55.000 0.00 0.00 0.00 4.30
2325 2486 1.959042 CAGATGATTTGTCGGAGGGG 58.041 55.000 0.00 0.00 0.00 4.79
2326 2487 0.181350 AGATGATTTGTCGGAGGGGC 59.819 55.000 0.00 0.00 0.00 5.80
2327 2488 0.819666 GATGATTTGTCGGAGGGGCC 60.820 60.000 0.00 0.00 0.00 5.80
2336 2497 3.647771 GGAGGGGCCGTTTGGTCT 61.648 66.667 0.00 0.00 40.80 3.85
2337 2498 2.295602 GGAGGGGCCGTTTGGTCTA 61.296 63.158 0.00 0.00 40.80 2.59
2338 2499 1.632965 GGAGGGGCCGTTTGGTCTAT 61.633 60.000 0.00 0.00 40.80 1.98
2339 2500 0.463833 GAGGGGCCGTTTGGTCTATG 60.464 60.000 0.00 0.00 40.80 2.23
2340 2501 1.453197 GGGGCCGTTTGGTCTATGG 60.453 63.158 0.00 0.00 40.80 2.74
2341 2502 1.453197 GGGCCGTTTGGTCTATGGG 60.453 63.158 0.00 0.00 40.80 4.00
2342 2503 1.453197 GGCCGTTTGGTCTATGGGG 60.453 63.158 0.00 0.00 36.72 4.96
2343 2504 1.605453 GCCGTTTGGTCTATGGGGA 59.395 57.895 0.00 0.00 37.67 4.81
2344 2505 0.746923 GCCGTTTGGTCTATGGGGAC 60.747 60.000 0.00 0.00 37.67 4.46
2345 2506 3.397230 GCCGTTTGGTCTATGGGGACA 62.397 57.143 0.00 0.00 41.24 4.02
2346 2507 4.656483 GCCGTTTGGTCTATGGGGACAT 62.656 54.545 0.00 0.00 46.19 3.06
2359 2520 4.777877 TGGGGACATCTACACCCTATAT 57.222 45.455 0.00 0.00 43.72 0.86
2360 2521 5.889286 TGGGGACATCTACACCCTATATA 57.111 43.478 0.00 0.00 43.72 0.86
2361 2522 5.838955 TGGGGACATCTACACCCTATATAG 58.161 45.833 2.46 2.46 43.72 1.31
2362 2523 5.558339 TGGGGACATCTACACCCTATATAGA 59.442 44.000 11.53 0.00 43.72 1.98
2363 2524 6.047479 TGGGGACATCTACACCCTATATAGAA 59.953 42.308 11.53 0.00 43.72 2.10
2364 2525 6.958192 GGGGACATCTACACCCTATATAGAAA 59.042 42.308 11.53 0.00 42.86 2.52
2365 2526 7.456902 GGGGACATCTACACCCTATATAGAAAA 59.543 40.741 11.53 0.00 42.86 2.29
2366 2527 8.877195 GGGACATCTACACCCTATATAGAAAAA 58.123 37.037 11.53 0.00 40.39 1.94
2367 2528 9.930693 GGACATCTACACCCTATATAGAAAAAG 57.069 37.037 11.53 2.75 0.00 2.27
2440 2601 9.968743 GAAATAAACTTGACCTTCTATTGTACG 57.031 33.333 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.474077 GAGGCAATTCAGCAAACGGAT 59.526 47.619 0.00 0.00 35.83 4.18
24 25 1.337167 GGTGGAGGCAATTCAGCAAAC 60.337 52.381 0.00 0.00 35.83 2.93
45 46 5.413833 AGATTGAATCTGATTGCTCGTTTGT 59.586 36.000 6.93 0.00 38.44 2.83
108 110 2.092429 AGCTCGGGGCAATTAGAAATGA 60.092 45.455 1.17 0.00 44.79 2.57
156 159 3.879892 GCAGAAGTGACTTGGTTTCTTCT 59.120 43.478 0.90 0.00 43.36 2.85
189 192 2.027192 AGCTTGTGTATGATGAACGGGT 60.027 45.455 0.00 0.00 0.00 5.28
201 205 3.072330 TGGACTGATTTGGAGCTTGTGTA 59.928 43.478 0.00 0.00 0.00 2.90
236 292 9.442047 ACTTAGAAGAAAGAACATATGTGGAAG 57.558 33.333 9.63 4.12 0.00 3.46
269 328 2.567169 ACATCAGATCGGTGTCTCCAAA 59.433 45.455 0.00 0.00 35.57 3.28
279 339 6.587990 CCTAGCTACAAATTACATCAGATCGG 59.412 42.308 0.00 0.00 0.00 4.18
315 376 1.208614 CCTGAGAAAACAGCGCTGC 59.791 57.895 36.28 20.28 36.67 5.25
319 380 2.357637 TCAAAACCCTGAGAAAACAGCG 59.642 45.455 0.00 0.00 36.67 5.18
416 477 5.830457 TGATTGTTGTTTTGGATGGAGTACA 59.170 36.000 0.00 0.00 0.00 2.90
459 520 2.551459 ACAAATCAAGCTCAGTCACTGC 59.449 45.455 0.00 0.00 0.00 4.40
460 521 4.514441 AGAACAAATCAAGCTCAGTCACTG 59.486 41.667 0.00 0.00 0.00 3.66
472 533 5.766670 AGAGCAGTTGATCAGAACAAATCAA 59.233 36.000 0.00 0.00 39.06 2.57
481 542 4.698780 CCATTCAAAGAGCAGTTGATCAGA 59.301 41.667 0.00 0.00 35.03 3.27
484 545 3.192001 TGCCATTCAAAGAGCAGTTGATC 59.808 43.478 0.00 0.00 35.03 2.92
489 550 3.083122 AGATGCCATTCAAAGAGCAGT 57.917 42.857 0.00 0.00 38.89 4.40
490 551 5.571784 TTTAGATGCCATTCAAAGAGCAG 57.428 39.130 0.00 0.00 38.89 4.24
511 572 0.398318 GTGGTCTCAGCTGGGACTTT 59.602 55.000 38.44 0.00 33.46 2.66
579 640 6.109156 TCATACATACCTTGTTCACAGTGT 57.891 37.500 0.00 0.00 39.87 3.55
583 644 8.684386 TCTTTTTCATACATACCTTGTTCACA 57.316 30.769 0.00 0.00 39.87 3.58
584 645 9.959749 TTTCTTTTTCATACATACCTTGTTCAC 57.040 29.630 0.00 0.00 39.87 3.18
725 809 2.927856 ATGAGACCCGTGCACCCA 60.928 61.111 12.15 0.38 0.00 4.51
791 875 2.170985 CGTTTGCGAACTGAGGCG 59.829 61.111 14.84 0.00 41.33 5.52
804 896 1.371145 CCATTCGCGCAAACCGTTT 60.371 52.632 8.75 0.00 39.71 3.60
839 932 2.546789 CGTGATTTATAAAGGTCCGGCC 59.453 50.000 0.00 0.59 37.58 6.13
840 933 2.546789 CCGTGATTTATAAAGGTCCGGC 59.453 50.000 0.00 0.00 0.00 6.13
841 934 3.800531 ACCGTGATTTATAAAGGTCCGG 58.199 45.455 18.86 18.86 38.81 5.14
842 935 4.269363 GTGACCGTGATTTATAAAGGTCCG 59.731 45.833 22.24 13.50 45.37 4.79
996 1112 2.815308 CCGCCTTCTACCATCGCT 59.185 61.111 0.00 0.00 0.00 4.93
1530 1650 3.933332 ACGGAAAGGCTCTTCTTAAATCG 59.067 43.478 0.00 0.00 0.00 3.34
1535 1655 2.764572 CCCTACGGAAAGGCTCTTCTTA 59.235 50.000 0.00 0.00 35.09 2.10
1636 1761 2.158959 GGCACAACTCGATCGACCG 61.159 63.158 15.15 8.36 0.00 4.79
1996 2134 1.061502 AGGCATCTTCTCCTCCTCCAT 60.062 52.381 0.00 0.00 0.00 3.41
1997 2135 0.341258 AGGCATCTTCTCCTCCTCCA 59.659 55.000 0.00 0.00 0.00 3.86
2053 2191 0.248580 ATAATGCCGTTACGCGTCGA 60.249 50.000 18.63 2.19 39.32 4.20
2151 2289 4.147701 CCTGACCGGGATGCATTC 57.852 61.111 6.32 0.00 0.00 2.67
2165 2326 2.037772 CCGGAATCCTGTAGAATCCCTG 59.962 54.545 0.00 0.00 41.03 4.45
2166 2327 2.330216 CCGGAATCCTGTAGAATCCCT 58.670 52.381 0.00 0.00 41.03 4.20
2167 2328 2.047830 ACCGGAATCCTGTAGAATCCC 58.952 52.381 9.46 0.00 41.03 3.85
2169 2330 2.103263 AGCACCGGAATCCTGTAGAATC 59.897 50.000 9.46 0.00 0.00 2.52
2170 2331 2.119495 AGCACCGGAATCCTGTAGAAT 58.881 47.619 9.46 0.00 0.00 2.40
2171 2332 1.207089 CAGCACCGGAATCCTGTAGAA 59.793 52.381 9.46 0.00 0.00 2.10
2172 2333 0.824109 CAGCACCGGAATCCTGTAGA 59.176 55.000 9.46 0.00 0.00 2.59
2173 2334 0.811616 GCAGCACCGGAATCCTGTAG 60.812 60.000 9.46 0.00 0.00 2.74
2174 2335 1.220749 GCAGCACCGGAATCCTGTA 59.779 57.895 9.46 0.00 0.00 2.74
2175 2336 2.045926 GCAGCACCGGAATCCTGT 60.046 61.111 9.46 0.00 0.00 4.00
2176 2337 0.962356 AAAGCAGCACCGGAATCCTG 60.962 55.000 9.46 9.69 0.00 3.86
2177 2338 0.251341 AAAAGCAGCACCGGAATCCT 60.251 50.000 9.46 0.00 0.00 3.24
2178 2339 0.603065 AAAAAGCAGCACCGGAATCC 59.397 50.000 9.46 0.00 0.00 3.01
2179 2340 2.488153 AGTAAAAAGCAGCACCGGAATC 59.512 45.455 9.46 0.00 0.00 2.52
2180 2341 2.514803 AGTAAAAAGCAGCACCGGAAT 58.485 42.857 9.46 0.00 0.00 3.01
2181 2342 1.975660 AGTAAAAAGCAGCACCGGAA 58.024 45.000 9.46 0.00 0.00 4.30
2182 2343 1.975660 AAGTAAAAAGCAGCACCGGA 58.024 45.000 9.46 0.00 0.00 5.14
2183 2344 2.034053 TGAAAGTAAAAAGCAGCACCGG 59.966 45.455 0.00 0.00 0.00 5.28
2184 2345 3.042887 GTGAAAGTAAAAAGCAGCACCG 58.957 45.455 0.00 0.00 0.00 4.94
2185 2346 4.044426 CAGTGAAAGTAAAAAGCAGCACC 58.956 43.478 0.00 0.00 0.00 5.01
2186 2347 4.044426 CCAGTGAAAGTAAAAAGCAGCAC 58.956 43.478 0.00 0.00 0.00 4.40
2187 2348 3.068024 CCCAGTGAAAGTAAAAAGCAGCA 59.932 43.478 0.00 0.00 0.00 4.41
2188 2349 3.317993 TCCCAGTGAAAGTAAAAAGCAGC 59.682 43.478 0.00 0.00 0.00 5.25
2189 2350 5.712152 ATCCCAGTGAAAGTAAAAAGCAG 57.288 39.130 0.00 0.00 0.00 4.24
2190 2351 6.462347 GGAAATCCCAGTGAAAGTAAAAAGCA 60.462 38.462 0.00 0.00 34.14 3.91
2191 2352 5.926542 GGAAATCCCAGTGAAAGTAAAAAGC 59.073 40.000 0.00 0.00 34.14 3.51
2192 2353 6.016610 TCGGAAATCCCAGTGAAAGTAAAAAG 60.017 38.462 0.00 0.00 34.14 2.27
2253 2414 2.601666 AGGCAGGAGCGTCTGTCA 60.602 61.111 14.50 0.00 41.48 3.58
2261 2422 4.400961 AAGCACCGAGGCAGGAGC 62.401 66.667 12.07 12.07 46.17 4.70
2262 2423 1.323271 TAGAAGCACCGAGGCAGGAG 61.323 60.000 6.03 0.00 35.83 3.69
2263 2424 1.304962 TAGAAGCACCGAGGCAGGA 60.305 57.895 6.03 0.00 35.83 3.86
2264 2425 1.153549 GTAGAAGCACCGAGGCAGG 60.154 63.158 1.23 0.00 35.83 4.85
2265 2426 1.153549 GGTAGAAGCACCGAGGCAG 60.154 63.158 1.23 0.00 35.83 4.85
2266 2427 0.323999 TAGGTAGAAGCACCGAGGCA 60.324 55.000 1.23 0.00 43.84 4.75
2267 2428 0.386113 CTAGGTAGAAGCACCGAGGC 59.614 60.000 0.00 0.00 43.84 4.70
2268 2429 1.405821 CACTAGGTAGAAGCACCGAGG 59.594 57.143 7.23 0.00 43.46 4.63
2269 2430 1.405821 CCACTAGGTAGAAGCACCGAG 59.594 57.143 0.00 1.44 44.39 4.63
2270 2431 1.471119 CCACTAGGTAGAAGCACCGA 58.529 55.000 0.00 0.00 43.84 4.69
2271 2432 0.179108 GCCACTAGGTAGAAGCACCG 60.179 60.000 0.00 0.00 43.84 4.94
2272 2433 1.134670 CAGCCACTAGGTAGAAGCACC 60.135 57.143 0.00 0.00 39.02 5.01
2273 2434 1.550976 ACAGCCACTAGGTAGAAGCAC 59.449 52.381 0.00 0.00 37.19 4.40
2274 2435 1.938585 ACAGCCACTAGGTAGAAGCA 58.061 50.000 0.00 0.00 37.19 3.91
2275 2436 3.025262 AGTACAGCCACTAGGTAGAAGC 58.975 50.000 0.00 0.00 37.19 3.86
2276 2437 5.191426 TGTAGTACAGCCACTAGGTAGAAG 58.809 45.833 0.00 0.00 37.19 2.85
2277 2438 5.183530 TGTAGTACAGCCACTAGGTAGAA 57.816 43.478 0.00 0.00 37.19 2.10
2278 2439 4.849813 TGTAGTACAGCCACTAGGTAGA 57.150 45.455 0.00 0.00 37.19 2.59
2279 2440 5.131067 TCATGTAGTACAGCCACTAGGTAG 58.869 45.833 9.25 0.00 37.19 3.18
2280 2441 5.120054 TCATGTAGTACAGCCACTAGGTA 57.880 43.478 9.25 0.00 37.19 3.08
2281 2442 3.977312 TCATGTAGTACAGCCACTAGGT 58.023 45.455 9.25 0.00 37.19 3.08
2282 2443 5.292765 CATTCATGTAGTACAGCCACTAGG 58.707 45.833 9.25 0.00 31.73 3.02
2283 2444 4.747108 GCATTCATGTAGTACAGCCACTAG 59.253 45.833 9.25 0.00 31.73 2.57
2284 2445 4.161377 TGCATTCATGTAGTACAGCCACTA 59.839 41.667 9.25 0.00 0.00 2.74
2285 2446 3.055167 TGCATTCATGTAGTACAGCCACT 60.055 43.478 9.25 0.00 0.00 4.00
2286 2447 3.270027 TGCATTCATGTAGTACAGCCAC 58.730 45.455 9.25 0.00 0.00 5.01
2287 2448 3.197549 TCTGCATTCATGTAGTACAGCCA 59.802 43.478 9.25 0.00 40.72 4.75
2288 2449 3.797039 TCTGCATTCATGTAGTACAGCC 58.203 45.455 9.25 0.00 40.72 4.85
2289 2450 5.052481 TCATCTGCATTCATGTAGTACAGC 58.948 41.667 9.25 6.81 40.72 4.40
2290 2451 7.725818 AATCATCTGCATTCATGTAGTACAG 57.274 36.000 9.25 1.72 40.72 2.74
2291 2452 7.553760 ACAAATCATCTGCATTCATGTAGTACA 59.446 33.333 5.24 5.24 40.72 2.90
2292 2453 7.923888 ACAAATCATCTGCATTCATGTAGTAC 58.076 34.615 4.99 0.00 40.72 2.73
2293 2454 7.042523 CGACAAATCATCTGCATTCATGTAGTA 60.043 37.037 4.99 0.00 40.72 1.82
2294 2455 6.238293 CGACAAATCATCTGCATTCATGTAGT 60.238 38.462 4.99 0.00 40.72 2.73
2295 2456 6.134061 CGACAAATCATCTGCATTCATGTAG 58.866 40.000 0.00 0.00 41.16 2.74
2296 2457 5.007921 CCGACAAATCATCTGCATTCATGTA 59.992 40.000 0.00 0.00 0.00 2.29
2297 2458 4.201980 CCGACAAATCATCTGCATTCATGT 60.202 41.667 0.00 0.00 0.00 3.21
2298 2459 4.035909 TCCGACAAATCATCTGCATTCATG 59.964 41.667 0.00 0.00 0.00 3.07
2299 2460 4.201657 TCCGACAAATCATCTGCATTCAT 58.798 39.130 0.00 0.00 0.00 2.57
2300 2461 3.608796 TCCGACAAATCATCTGCATTCA 58.391 40.909 0.00 0.00 0.00 2.57
2301 2462 3.003068 CCTCCGACAAATCATCTGCATTC 59.997 47.826 0.00 0.00 0.00 2.67
2302 2463 2.947652 CCTCCGACAAATCATCTGCATT 59.052 45.455 0.00 0.00 0.00 3.56
2303 2464 2.569059 CCTCCGACAAATCATCTGCAT 58.431 47.619 0.00 0.00 0.00 3.96
2304 2465 1.407299 CCCTCCGACAAATCATCTGCA 60.407 52.381 0.00 0.00 0.00 4.41
2305 2466 1.303309 CCCTCCGACAAATCATCTGC 58.697 55.000 0.00 0.00 0.00 4.26
2306 2467 1.959042 CCCCTCCGACAAATCATCTG 58.041 55.000 0.00 0.00 0.00 2.90
2307 2468 0.181350 GCCCCTCCGACAAATCATCT 59.819 55.000 0.00 0.00 0.00 2.90
2308 2469 0.819666 GGCCCCTCCGACAAATCATC 60.820 60.000 0.00 0.00 0.00 2.92
2309 2470 1.227383 GGCCCCTCCGACAAATCAT 59.773 57.895 0.00 0.00 0.00 2.45
2310 2471 2.674754 GGCCCCTCCGACAAATCA 59.325 61.111 0.00 0.00 0.00 2.57
2319 2480 1.632965 ATAGACCAAACGGCCCCTCC 61.633 60.000 0.00 0.00 0.00 4.30
2320 2481 0.463833 CATAGACCAAACGGCCCCTC 60.464 60.000 0.00 0.00 0.00 4.30
2321 2482 1.607612 CATAGACCAAACGGCCCCT 59.392 57.895 0.00 0.00 0.00 4.79
2322 2483 1.453197 CCATAGACCAAACGGCCCC 60.453 63.158 0.00 0.00 0.00 5.80
2323 2484 1.453197 CCCATAGACCAAACGGCCC 60.453 63.158 0.00 0.00 0.00 5.80
2324 2485 1.453197 CCCCATAGACCAAACGGCC 60.453 63.158 0.00 0.00 0.00 6.13
2325 2486 0.746923 GTCCCCATAGACCAAACGGC 60.747 60.000 0.00 0.00 0.00 5.68
2326 2487 0.616371 TGTCCCCATAGACCAAACGG 59.384 55.000 0.00 0.00 35.83 4.44
2327 2488 2.170607 AGATGTCCCCATAGACCAAACG 59.829 50.000 0.00 0.00 35.83 3.60
2328 2489 3.933861 AGATGTCCCCATAGACCAAAC 57.066 47.619 0.00 0.00 35.83 2.93
2329 2490 4.163458 GTGTAGATGTCCCCATAGACCAAA 59.837 45.833 0.00 0.00 35.83 3.28
2330 2491 3.709653 GTGTAGATGTCCCCATAGACCAA 59.290 47.826 0.00 0.00 35.83 3.67
2331 2492 3.305720 GTGTAGATGTCCCCATAGACCA 58.694 50.000 0.00 0.00 35.83 4.02
2332 2493 2.633481 GGTGTAGATGTCCCCATAGACC 59.367 54.545 0.00 0.00 35.83 3.85
2333 2494 2.633481 GGGTGTAGATGTCCCCATAGAC 59.367 54.545 0.00 0.00 37.09 2.59
2334 2495 2.522705 AGGGTGTAGATGTCCCCATAGA 59.477 50.000 0.00 0.00 41.95 1.98
2335 2496 2.977808 AGGGTGTAGATGTCCCCATAG 58.022 52.381 0.00 0.00 41.95 2.23
2336 2497 4.777877 ATAGGGTGTAGATGTCCCCATA 57.222 45.455 0.00 0.00 41.95 2.74
2337 2498 3.655972 ATAGGGTGTAGATGTCCCCAT 57.344 47.619 0.00 0.00 41.95 4.00
2338 2499 4.777877 ATATAGGGTGTAGATGTCCCCA 57.222 45.455 0.00 0.00 41.95 4.96
2339 2500 6.088541 TCTATATAGGGTGTAGATGTCCCC 57.911 45.833 9.89 0.00 41.95 4.81
2340 2501 8.431910 TTTTCTATATAGGGTGTAGATGTCCC 57.568 38.462 9.89 0.00 41.36 4.46
2341 2502 9.930693 CTTTTTCTATATAGGGTGTAGATGTCC 57.069 37.037 9.89 0.00 31.59 4.02
2414 2575 9.968743 CGTACAATAGAAGGTCAAGTTTATTTC 57.031 33.333 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.