Multiple sequence alignment - TraesCS4A01G089100

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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 TraesCS4A01G089100 chr4A 100.000 4315 0 0 1 4315 95174051 95178365 0.000000e+00 7969
1 TraesCS4A01G089100 chr4A 94.624 93 4 1 2203 2295 511040567 511040476 4.500000e-30 143
2 TraesCS4A01G089100 chr4A 93.478 92 5 1 2205 2295 608078157 608078248 7.530000e-28 135
3 TraesCS4A01G089100 chr4A 100.000 62 0 0 3894 3955 95177883 95177944 9.810000e-22 115
4 TraesCS4A01G089100 chr4A 100.000 62 0 0 3833 3894 95177944 95178005 9.810000e-22 115
5 TraesCS4A01G089100 chr4D 94.346 2211 100 11 9 2204 369335175 369332975 0.000000e+00 3367
6 TraesCS4A01G089100 chr4D 90.898 1637 83 24 2303 3894 369332942 369331327 0.000000e+00 2137
7 TraesCS4A01G089100 chr4D 81.988 322 36 14 3894 4203 369331390 369331079 1.990000e-63 254
8 TraesCS4A01G089100 chr4D 94.382 89 4 1 2203 2291 252173785 252173698 7.530000e-28 135
9 TraesCS4A01G089100 chr4B 96.136 1501 49 5 710 2204 454707641 454706144 0.000000e+00 2442
10 TraesCS4A01G089100 chr4B 91.454 1451 55 22 2291 3698 454706118 454704694 0.000000e+00 1929
11 TraesCS4A01G089100 chr4B 81.465 437 54 18 3894 4315 454704294 454703870 2.490000e-87 333
12 TraesCS4A01G089100 chr4B 95.935 123 5 0 593 715 454739205 454739083 2.630000e-47 200
13 TraesCS4A01G089100 chr5D 80.233 602 87 15 2 573 539797175 539796576 1.430000e-114 424
14 TraesCS4A01G089100 chr5D 76.923 377 76 8 218 588 416264294 416263923 2.030000e-48 204
15 TraesCS4A01G089100 chr5D 76.012 346 64 14 245 582 468352615 468352281 1.240000e-35 161
16 TraesCS4A01G089100 chr6D 79.216 587 102 12 1 574 28661520 28660941 1.450000e-104 390
17 TraesCS4A01G089100 chr6D 78.291 585 115 7 2 574 127480858 127481442 2.450000e-97 366
18 TraesCS4A01G089100 chr6D 75.059 425 68 22 1 399 367532428 367532840 3.450000e-36 163
19 TraesCS4A01G089100 chr2B 79.745 548 90 12 1 527 197144263 197143716 1.130000e-100 377
20 TraesCS4A01G089100 chr2B 79.325 474 71 14 1 462 578045720 578045262 1.510000e-79 307
21 TraesCS4A01G089100 chr1D 80.342 468 82 3 1 459 6739960 6740426 3.190000e-91 346
22 TraesCS4A01G089100 chr6A 77.377 610 113 10 2 588 377482681 377483288 5.340000e-89 339
23 TraesCS4A01G089100 chr3B 77.547 530 84 20 1 501 81339391 81339914 1.960000e-73 287
24 TraesCS4A01G089100 chr3B 95.506 89 1 3 2203 2288 11070080 11069992 5.820000e-29 139
25 TraesCS4A01G089100 chr2D 75.820 579 119 14 1 568 113651555 113650987 1.530000e-69 274
26 TraesCS4A01G089100 chr2D 93.407 91 5 1 2203 2293 556926432 556926521 2.710000e-27 134
27 TraesCS4A01G089100 chr5B 76.029 559 72 32 1 527 332439531 332439003 2.590000e-57 233
28 TraesCS4A01G089100 chr5B 82.381 210 29 4 1 202 139408744 139408535 4.430000e-40 176
29 TraesCS4A01G089100 chr7D 76.134 419 55 13 9 406 448759453 448759059 1.230000e-40 178
30 TraesCS4A01G089100 chr7D 96.386 83 3 0 2203 2285 63928438 63928520 2.090000e-28 137
31 TraesCS4A01G089100 chr1A 72.948 536 104 22 2 500 297261520 297260989 9.670000e-32 148
32 TraesCS4A01G089100 chr1B 93.617 94 5 1 2203 2295 665690214 665690121 5.820000e-29 139
33 TraesCS4A01G089100 chr1B 93.478 92 5 1 2205 2295 433452979 433452888 7.530000e-28 135
34 TraesCS4A01G089100 chr2A 92.473 93 6 1 2203 2295 617636115 617636024 9.740000e-27 132


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 TraesCS4A01G089100 chr4A 95174051 95178365 4314 False 2733.000000 7969 100.000000 1 4315 3 chr4A.!!$F2 4314
1 TraesCS4A01G089100 chr4D 369331079 369335175 4096 True 1919.333333 3367 89.077333 9 4203 3 chr4D.!!$R2 4194
2 TraesCS4A01G089100 chr4B 454703870 454707641 3771 True 1568.000000 2442 89.685000 710 4315 3 chr4B.!!$R2 3605
3 TraesCS4A01G089100 chr5D 539796576 539797175 599 True 424.000000 424 80.233000 2 573 1 chr5D.!!$R3 571
4 TraesCS4A01G089100 chr6D 28660941 28661520 579 True 390.000000 390 79.216000 1 574 1 chr6D.!!$R1 573
5 TraesCS4A01G089100 chr6D 127480858 127481442 584 False 366.000000 366 78.291000 2 574 1 chr6D.!!$F1 572
6 TraesCS4A01G089100 chr2B 197143716 197144263 547 True 377.000000 377 79.745000 1 527 1 chr2B.!!$R1 526
7 TraesCS4A01G089100 chr6A 377482681 377483288 607 False 339.000000 339 77.377000 2 588 1 chr6A.!!$F1 586
8 TraesCS4A01G089100 chr3B 81339391 81339914 523 False 287.000000 287 77.547000 1 501 1 chr3B.!!$F1 500
9 TraesCS4A01G089100 chr2D 113650987 113651555 568 True 274.000000 274 75.820000 1 568 1 chr2D.!!$R1 567
10 TraesCS4A01G089100 chr5B 332439003 332439531 528 True 233.000000 233 76.029000 1 527 1 chr5B.!!$R2 526

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
503 599 0.024619 GTTCGTTTAGATCGGCGTGC 59.975 55.0 6.85 0.0 0.0 5.34 F
1840 1942 0.320697 GAACCTCGGCCACTTAGTGT 59.679 55.0 11.68 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1898 2000 0.250727 TTGAACTGTGGGCAGCTACC 60.251 55.000 0.0 0.0 46.30 3.18 R
3391 3525 1.792273 GCTAGACTCTTCACAGCGTCG 60.792 57.143 0.0 0.0 39.41 5.12 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
46 47 1.570347 CCGTCGAACAATTTGCGGGA 61.570 55.000 0.00 0.00 36.05 5.14
67 68 1.404391 GTCATCGAAGAAGTAGGCCGA 59.596 52.381 0.00 0.00 43.58 5.54
132 172 3.973516 TCTGACGAGCGTGGCGTT 61.974 61.111 0.00 0.00 42.77 4.84
148 189 0.167470 CGTTGTCGTCGAAGGAGCTA 59.833 55.000 0.00 0.00 0.00 3.32
159 235 4.273257 GGAGCTAGCCGAGGACGC 62.273 72.222 12.13 0.00 38.29 5.19
311 405 1.961277 CGACAATGGGATAGGGCGC 60.961 63.158 0.00 0.00 0.00 6.53
346 440 2.432510 GTCGATGGGAGGAAGAGAATGT 59.567 50.000 0.00 0.00 0.00 2.71
363 457 0.682292 TGTCCTATGTGCAACCGACA 59.318 50.000 0.00 0.00 34.36 4.35
486 582 2.652941 ATGAAAAATGGATGCGCGTT 57.347 40.000 8.43 0.00 0.00 4.84
503 599 0.024619 GTTCGTTTAGATCGGCGTGC 59.975 55.000 6.85 0.00 0.00 5.34
527 625 6.403200 GCTGAGTCAACTTTGTGTCTGTTTTA 60.403 38.462 0.00 0.00 0.00 1.52
556 654 1.565156 GACACACGCTGGCGAAATGA 61.565 55.000 21.77 0.00 42.83 2.57
616 714 2.746362 AGTCGTCCGATAGAAACTCGTT 59.254 45.455 0.00 0.00 39.76 3.85
722 821 5.505173 TCTTAACCGATAAGGAACCTACG 57.495 43.478 7.73 1.57 45.00 3.51
739 838 1.367471 CGAAGCCACTGACAGGTGA 59.633 57.895 7.51 0.00 39.34 4.02
892 991 1.196012 GAATCCCCTCCTCACTTCGT 58.804 55.000 0.00 0.00 0.00 3.85
973 1072 4.803908 GAAGAGGGCGGCAAGGGG 62.804 72.222 12.47 0.00 0.00 4.79
1209 1310 1.406069 CGCAGGCTGGTCTGTCTATTT 60.406 52.381 17.64 0.00 37.12 1.40
1287 1388 6.484643 ACAATATCATCTTGTGGATTCCTTCG 59.515 38.462 3.95 0.00 35.57 3.79
1313 1414 5.095490 GCCACATACTGTATGTTTGCTTTC 58.905 41.667 28.08 13.69 46.69 2.62
1521 1623 9.931210 GTTGCATTCCTTTACATTACATACTAC 57.069 33.333 0.00 0.00 0.00 2.73
1535 1637 5.099042 ACATACTACCACCAATTCCAGAC 57.901 43.478 0.00 0.00 0.00 3.51
1546 1648 3.638160 CCAATTCCAGACCCCACATAATG 59.362 47.826 0.00 0.00 0.00 1.90
1572 1674 7.201767 GGATGAGTTCTTTCCATGTTGATTAGG 60.202 40.741 0.00 0.00 0.00 2.69
1588 1690 3.814005 TTAGGTCCAAATAGCCGAGTC 57.186 47.619 0.00 0.00 0.00 3.36
1652 1754 6.287525 TCTTTATTTGTTGCCAAAAAGAGGG 58.712 36.000 0.00 0.00 43.43 4.30
1840 1942 0.320697 GAACCTCGGCCACTTAGTGT 59.679 55.000 11.68 0.00 0.00 3.55
1898 2000 9.370126 CGTTAGAAATTAGTTTGAGTGAAACAG 57.630 33.333 7.96 0.00 45.69 3.16
1945 2051 7.709182 GGACCAAAGTAAACAATTGCTAGTTTT 59.291 33.333 5.05 0.78 38.71 2.43
1946 2052 8.642908 ACCAAAGTAAACAATTGCTAGTTTTC 57.357 30.769 5.05 0.00 38.71 2.29
2015 2121 4.202441 GCTAGGATGGTGATTCATTGTGT 58.798 43.478 0.00 0.00 0.00 3.72
2051 2157 7.426929 ACAGCGGCATTTCTAGATTATTTAG 57.573 36.000 1.45 0.00 0.00 1.85
2056 2162 7.255139 GCGGCATTTCTAGATTATTTAGGTGTT 60.255 37.037 0.00 0.00 0.00 3.32
2067 2173 9.643693 AGATTATTTAGGTGTTGCTCAAATTTG 57.356 29.630 12.15 12.15 0.00 2.32
2095 2201 4.697352 CCTAAGGGACACTGTTTCATGAAG 59.303 45.833 8.41 0.00 33.58 3.02
2104 2210 7.206981 ACACTGTTTCATGAAGTAATTCTGG 57.793 36.000 8.41 0.00 0.00 3.86
2186 2292 6.051717 GCATGTAAGACCTAAGTGATGACAT 58.948 40.000 0.00 0.00 0.00 3.06
2194 2300 6.765036 AGACCTAAGTGATGACATGCTAATTG 59.235 38.462 0.00 0.00 0.00 2.32
2204 2310 4.022416 TGACATGCTAATTGTGTTTGGTCC 60.022 41.667 0.00 0.00 0.00 4.46
2205 2311 3.258123 ACATGCTAATTGTGTTTGGTCCC 59.742 43.478 0.00 0.00 0.00 4.46
2206 2312 3.237268 TGCTAATTGTGTTTGGTCCCT 57.763 42.857 0.00 0.00 0.00 4.20
2207 2313 3.153919 TGCTAATTGTGTTTGGTCCCTC 58.846 45.455 0.00 0.00 0.00 4.30
2208 2314 2.492088 GCTAATTGTGTTTGGTCCCTCC 59.508 50.000 0.00 0.00 0.00 4.30
2213 2319 1.489649 TGTGTTTGGTCCCTCCGTAAA 59.510 47.619 0.00 0.00 39.52 2.01
2214 2320 2.148768 GTGTTTGGTCCCTCCGTAAAG 58.851 52.381 0.00 0.00 39.52 1.85
2216 2322 2.438763 TGTTTGGTCCCTCCGTAAAGAA 59.561 45.455 0.00 0.00 39.52 2.52
2217 2323 3.117963 TGTTTGGTCCCTCCGTAAAGAAA 60.118 43.478 0.00 0.00 39.52 2.52
2219 2325 5.221884 TGTTTGGTCCCTCCGTAAAGAAATA 60.222 40.000 0.00 0.00 39.52 1.40
2220 2326 5.703730 TTGGTCCCTCCGTAAAGAAATAT 57.296 39.130 0.00 0.00 39.52 1.28
2221 2327 6.811634 TTGGTCCCTCCGTAAAGAAATATA 57.188 37.500 0.00 0.00 39.52 0.86
2222 2328 6.811634 TGGTCCCTCCGTAAAGAAATATAA 57.188 37.500 0.00 0.00 39.52 0.98
2223 2329 6.823497 TGGTCCCTCCGTAAAGAAATATAAG 58.177 40.000 0.00 0.00 39.52 1.73
2224 2330 6.612456 TGGTCCCTCCGTAAAGAAATATAAGA 59.388 38.462 0.00 0.00 39.52 2.10
2225 2331 7.153315 GGTCCCTCCGTAAAGAAATATAAGAG 58.847 42.308 0.00 0.00 0.00 2.85
2226 2332 6.645827 GTCCCTCCGTAAAGAAATATAAGAGC 59.354 42.308 0.00 0.00 0.00 4.09
2227 2333 5.634020 CCCTCCGTAAAGAAATATAAGAGCG 59.366 44.000 0.00 0.00 0.00 5.03
2228 2334 6.214399 CCTCCGTAAAGAAATATAAGAGCGT 58.786 40.000 0.00 0.00 0.00 5.07
2229 2335 6.700520 CCTCCGTAAAGAAATATAAGAGCGTT 59.299 38.462 0.00 0.00 0.00 4.84
2230 2336 7.224167 CCTCCGTAAAGAAATATAAGAGCGTTT 59.776 37.037 0.00 0.00 0.00 3.60
2231 2337 9.241317 CTCCGTAAAGAAATATAAGAGCGTTTA 57.759 33.333 0.00 0.00 0.00 2.01
2232 2338 9.241317 TCCGTAAAGAAATATAAGAGCGTTTAG 57.759 33.333 0.00 0.00 0.00 1.85
2233 2339 9.241317 CCGTAAAGAAATATAAGAGCGTTTAGA 57.759 33.333 0.00 0.00 0.00 2.10
2247 2353 9.570488 AAGAGCGTTTAGATTACTAAAGTAGTG 57.430 33.333 0.00 0.00 45.42 2.74
2248 2354 8.954350 AGAGCGTTTAGATTACTAAAGTAGTGA 58.046 33.333 0.00 0.00 45.42 3.41
2249 2355 9.733219 GAGCGTTTAGATTACTAAAGTAGTGAT 57.267 33.333 0.00 0.00 45.42 3.06
2250 2356 9.733219 AGCGTTTAGATTACTAAAGTAGTGATC 57.267 33.333 10.62 10.62 46.38 2.92
2258 2364 9.733219 GATTACTAAAGTAGTGATCTAAACGCT 57.267 33.333 11.11 0.00 44.10 5.07
2259 2365 9.733219 ATTACTAAAGTAGTGATCTAAACGCTC 57.267 33.333 0.00 0.00 39.81 5.03
2260 2366 7.393841 ACTAAAGTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
2261 2367 7.828712 ACTAAAGTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
2262 2368 8.954350 ACTAAAGTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
2263 2369 9.953697 CTAAAGTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
2277 2383 7.787725 AACGCTCTTATATTTCTTTACAGGG 57.212 36.000 0.00 0.00 0.00 4.45
2278 2384 6.289064 ACGCTCTTATATTTCTTTACAGGGG 58.711 40.000 0.00 0.00 0.00 4.79
2279 2385 5.701290 CGCTCTTATATTTCTTTACAGGGGG 59.299 44.000 0.00 0.00 0.00 5.40
2280 2386 6.463897 CGCTCTTATATTTCTTTACAGGGGGA 60.464 42.308 0.00 0.00 0.00 4.81
2281 2387 7.287810 GCTCTTATATTTCTTTACAGGGGGAA 58.712 38.462 0.00 0.00 0.00 3.97
2282 2388 7.945109 GCTCTTATATTTCTTTACAGGGGGAAT 59.055 37.037 0.00 0.00 0.00 3.01
2369 2475 6.597562 AGACTGGTTCATTTGGTGTAACTTA 58.402 36.000 0.00 0.00 36.74 2.24
2397 2503 3.618690 AAGTGGAGCATACTCACTTCC 57.381 47.619 0.00 0.00 45.42 3.46
2398 2504 1.478510 AGTGGAGCATACTCACTTCCG 59.521 52.381 0.00 0.00 45.42 4.30
2412 2518 1.271926 ACTTCCGGGTGATTTCTTGGG 60.272 52.381 0.00 0.00 0.00 4.12
2415 2521 1.986631 TCCGGGTGATTTCTTGGGTTA 59.013 47.619 0.00 0.00 0.00 2.85
2417 2523 3.781407 TCCGGGTGATTTCTTGGGTTATA 59.219 43.478 0.00 0.00 0.00 0.98
2418 2524 4.414182 TCCGGGTGATTTCTTGGGTTATAT 59.586 41.667 0.00 0.00 0.00 0.86
2419 2525 5.103855 TCCGGGTGATTTCTTGGGTTATATT 60.104 40.000 0.00 0.00 0.00 1.28
2420 2526 5.009610 CCGGGTGATTTCTTGGGTTATATTG 59.990 44.000 0.00 0.00 0.00 1.90
2422 2528 5.362430 GGGTGATTTCTTGGGTTATATTGCA 59.638 40.000 0.00 0.00 0.00 4.08
2423 2529 6.273071 GGTGATTTCTTGGGTTATATTGCAC 58.727 40.000 0.00 0.00 0.00 4.57
2433 2540 6.163476 TGGGTTATATTGCACTTATAGAGCG 58.837 40.000 0.00 0.00 34.43 5.03
2460 2575 4.708726 ATTGGTGCTAGCAGTTTCATTC 57.291 40.909 20.03 3.12 0.00 2.67
2475 2590 1.550524 TCATTCGTCAGTTCCTGGAGG 59.449 52.381 0.00 0.00 31.51 4.30
2514 2635 5.009854 ACAAGTTTGAGGTGACATTTTGG 57.990 39.130 0.00 0.00 0.00 3.28
2520 2641 1.541588 GAGGTGACATTTTGGAGGCAC 59.458 52.381 0.00 0.00 0.00 5.01
2552 2673 4.853924 TTGATCACTCCTTGGCTTTTTC 57.146 40.909 0.00 0.00 0.00 2.29
2566 2687 4.737353 GCTTTTTCCTGAAGCCAAAATG 57.263 40.909 0.00 0.00 42.79 2.32
2600 2721 7.264221 AGCATTCACAGTGTTGTATTTGAAAA 58.736 30.769 0.00 0.00 35.25 2.29
2633 2754 5.519566 TCACTTTTTAGCATGCACAAAGTTG 59.480 36.000 26.72 22.47 35.89 3.16
2635 2756 2.049077 TTAGCATGCACAAAGTTGCG 57.951 45.000 21.98 0.00 46.20 4.85
2636 2757 1.233919 TAGCATGCACAAAGTTGCGA 58.766 45.000 21.98 0.00 46.20 5.10
2656 2777 4.437390 GCGAAATTCACCCTTGAGTACATG 60.437 45.833 0.00 0.00 31.71 3.21
2665 2786 5.357878 CACCCTTGAGTACATGTAATTGCAT 59.642 40.000 7.25 2.84 0.00 3.96
2696 2817 6.389091 TGAATTTGTTCGGATTCATTTCTGG 58.611 36.000 0.00 0.00 37.35 3.86
2750 2871 9.582431 CTTCTTTTGATCTTAAGTCCGTATGTA 57.418 33.333 1.63 0.00 0.00 2.29
2752 2873 9.529325 TCTTTTGATCTTAAGTCCGTATGTATG 57.471 33.333 1.63 0.00 0.00 2.39
2753 2874 9.314321 CTTTTGATCTTAAGTCCGTATGTATGT 57.686 33.333 1.63 0.00 0.00 2.29
2785 2906 6.128254 GCTTTCATTTAAGTAGGACTGTGACC 60.128 42.308 0.00 0.00 0.00 4.02
2855 2989 4.820775 TCTGGAGACTAAGCATAATCCCT 58.179 43.478 0.00 0.00 0.00 4.20
3013 3147 9.144085 GAGTTAAAACACAATATAATTCTCGCG 57.856 33.333 0.00 0.00 0.00 5.87
3209 3343 6.485313 ACGATCAGAGTAAGTCCTATCTTCTG 59.515 42.308 0.00 0.00 0.00 3.02
3258 3392 6.376299 TCAGAATGGTGGATTTGAGATTTCTG 59.624 38.462 0.00 0.00 39.08 3.02
3319 3453 1.890979 CCTGCTGCGGATGACATCC 60.891 63.158 22.66 22.66 46.22 3.51
3391 3525 3.226346 TCAGCAGAGCAAAATCATTGC 57.774 42.857 5.06 5.06 45.22 3.56
3397 3531 3.020102 GCAAAATCATTGCGACGCT 57.980 47.368 22.08 0.00 35.58 5.07
3417 3551 3.433709 CTGTGAAGAGTCTAGCATGTCG 58.566 50.000 0.00 0.00 0.00 4.35
3477 3616 5.062528 TGTATTCATCATCGCTTTGCCATA 58.937 37.500 0.00 0.00 0.00 2.74
3555 3699 8.673711 TGTGCAATGTGAATTTACTATACCTTC 58.326 33.333 1.75 0.00 0.00 3.46
3576 3720 8.211629 ACCTTCTGTCTACTTTGTAATTCTGTT 58.788 33.333 0.00 0.00 0.00 3.16
3586 3730 7.875971 ACTTTGTAATTCTGTTGAGATTGGAC 58.124 34.615 0.00 0.00 0.00 4.02
3590 3734 7.223584 TGTAATTCTGTTGAGATTGGACTTGA 58.776 34.615 0.00 0.00 0.00 3.02
3604 3748 4.130857 TGGACTTGACGAATTGTTTGCTA 58.869 39.130 0.00 0.00 0.00 3.49
3606 3750 5.240623 TGGACTTGACGAATTGTTTGCTATT 59.759 36.000 0.00 0.00 0.00 1.73
3610 3754 6.636850 ACTTGACGAATTGTTTGCTATTTGTC 59.363 34.615 12.11 12.11 44.30 3.18
3620 3764 3.656651 TGCTATTTGTCGAATTCAGCG 57.343 42.857 6.22 0.00 33.77 5.18
3653 3797 5.776173 TGGAACAACGTGAAATTTACCAT 57.224 34.783 0.00 0.00 31.92 3.55
3733 4170 5.611374 TGAAACTGTTCTAGGAGGAAAGTG 58.389 41.667 0.00 0.00 34.60 3.16
3755 4192 8.370493 AGTGTTCATGATTCTTATATCGGTTG 57.630 34.615 0.00 0.00 0.00 3.77
3756 4193 7.442364 AGTGTTCATGATTCTTATATCGGTTGG 59.558 37.037 0.00 0.00 0.00 3.77
3759 4196 6.464222 TCATGATTCTTATATCGGTTGGGTC 58.536 40.000 0.00 0.00 0.00 4.46
3772 4209 1.733402 TTGGGTCAGCAAGCAAACCG 61.733 55.000 8.98 0.00 32.34 4.44
3785 4222 0.608640 CAAACCGCTGTCCTACTCCT 59.391 55.000 0.00 0.00 0.00 3.69
3787 4224 2.226962 AACCGCTGTCCTACTCCTTA 57.773 50.000 0.00 0.00 0.00 2.69
3796 4233 6.239064 CGCTGTCCTACTCCTTATCATTTACT 60.239 42.308 0.00 0.00 0.00 2.24
3797 4234 7.501844 GCTGTCCTACTCCTTATCATTTACTT 58.498 38.462 0.00 0.00 0.00 2.24
3798 4235 8.639761 GCTGTCCTACTCCTTATCATTTACTTA 58.360 37.037 0.00 0.00 0.00 2.24
3800 4237 9.483489 TGTCCTACTCCTTATCATTTACTTACA 57.517 33.333 0.00 0.00 0.00 2.41
3824 4261 4.329392 ACCAGAAGTTTAACCCCATAACG 58.671 43.478 0.00 0.00 0.00 3.18
3853 4290 1.006102 ACTTCGACCAAGGAGCACG 60.006 57.895 0.00 0.00 36.26 5.34
3855 4292 0.242825 CTTCGACCAAGGAGCACGTA 59.757 55.000 0.00 0.00 0.00 3.57
3872 4309 6.986424 GCACGTAGCAAAGAAACTAAAATT 57.014 33.333 5.30 0.00 44.79 1.82
3873 4310 7.389603 GCACGTAGCAAAGAAACTAAAATTT 57.610 32.000 5.30 0.00 44.79 1.82
3874 4311 8.496872 GCACGTAGCAAAGAAACTAAAATTTA 57.503 30.769 5.30 0.00 44.79 1.40
3875 4312 8.414923 GCACGTAGCAAAGAAACTAAAATTTAC 58.585 33.333 5.30 0.00 44.79 2.01
3876 4313 9.659830 CACGTAGCAAAGAAACTAAAATTTACT 57.340 29.630 0.00 0.00 0.00 2.24
3903 4340 8.882415 TGTAAATTAATATCCTGGACTTCGAC 57.118 34.615 0.00 0.00 0.00 4.20
3904 4341 7.929785 TGTAAATTAATATCCTGGACTTCGACC 59.070 37.037 0.00 0.00 0.00 4.79
3905 4342 6.494666 AATTAATATCCTGGACTTCGACCA 57.505 37.500 0.00 0.00 35.96 4.02
3906 4343 5.943349 TTAATATCCTGGACTTCGACCAA 57.057 39.130 0.00 0.00 36.95 3.67
3907 4344 4.408182 AATATCCTGGACTTCGACCAAG 57.592 45.455 0.00 0.00 36.95 3.61
3908 4345 0.905357 ATCCTGGACTTCGACCAAGG 59.095 55.000 0.00 0.00 36.26 3.61
3909 4346 0.178944 TCCTGGACTTCGACCAAGGA 60.179 55.000 0.00 1.65 36.26 3.36
3910 4347 0.247736 CCTGGACTTCGACCAAGGAG 59.752 60.000 0.00 0.00 36.26 3.69
3911 4348 0.390472 CTGGACTTCGACCAAGGAGC 60.390 60.000 0.00 0.00 36.26 4.70
3912 4349 1.118965 TGGACTTCGACCAAGGAGCA 61.119 55.000 0.00 0.00 36.26 4.26
3913 4350 0.670854 GGACTTCGACCAAGGAGCAC 60.671 60.000 0.00 0.00 36.26 4.40
3914 4351 1.006102 ACTTCGACCAAGGAGCACG 60.006 57.895 0.00 0.00 36.26 5.34
3915 4352 1.006102 CTTCGACCAAGGAGCACGT 60.006 57.895 0.00 0.00 0.00 4.49
3916 4353 0.242825 CTTCGACCAAGGAGCACGTA 59.757 55.000 0.00 0.00 0.00 3.57
3917 4354 0.242825 TTCGACCAAGGAGCACGTAG 59.757 55.000 0.00 0.00 0.00 3.51
3918 4355 1.805945 CGACCAAGGAGCACGTAGC 60.806 63.158 0.00 0.00 46.19 3.58
3935 4372 8.496872 GCACGTAGCAAAGAAACTAAAATTTA 57.503 30.769 5.30 0.00 44.79 1.40
3937 4374 9.659830 CACGTAGCAAAGAAACTAAAATTTACT 57.340 29.630 0.00 0.00 0.00 2.24
3976 4413 6.324512 TCCTTATGTTAATCGTACCTAAGGCA 59.675 38.462 10.41 1.44 40.63 4.75
3980 4417 7.875327 ATGTTAATCGTACCTAAGGCAATTT 57.125 32.000 0.00 0.00 0.00 1.82
3981 4418 7.079182 TGTTAATCGTACCTAAGGCAATTTG 57.921 36.000 0.00 0.00 0.00 2.32
3982 4419 6.879993 TGTTAATCGTACCTAAGGCAATTTGA 59.120 34.615 0.00 0.00 0.00 2.69
3985 4422 5.616488 TCGTACCTAAGGCAATTTGAAAC 57.384 39.130 0.00 0.00 0.00 2.78
3986 4423 5.064558 TCGTACCTAAGGCAATTTGAAACA 58.935 37.500 0.00 0.00 0.00 2.83
3987 4424 5.531659 TCGTACCTAAGGCAATTTGAAACAA 59.468 36.000 0.00 0.00 0.00 2.83
4003 4440 4.564769 TGAAACAAAATCGCCTTTGTCAAC 59.435 37.500 13.03 9.21 46.32 3.18
4055 4498 6.775629 ACCTTTGTAAACAGTGATGGTATGTT 59.224 34.615 0.00 0.00 38.76 2.71
4061 4504 7.934665 TGTAAACAGTGATGGTATGTTGTACTT 59.065 33.333 0.00 0.00 37.24 2.24
4062 4505 6.801539 AACAGTGATGGTATGTTGTACTTG 57.198 37.500 0.00 0.00 35.89 3.16
4077 4521 5.375417 TGTACTTGCTGAAATGGTTCATG 57.625 39.130 0.00 0.00 42.85 3.07
4107 4551 6.564854 GCTCATGCTCAAACATTTTATGTC 57.435 37.500 0.00 0.00 38.24 3.06
4108 4552 6.327934 GCTCATGCTCAAACATTTTATGTCT 58.672 36.000 0.00 0.00 38.24 3.41
4109 4553 7.475015 GCTCATGCTCAAACATTTTATGTCTA 58.525 34.615 0.00 0.00 38.24 2.59
4110 4554 8.133627 GCTCATGCTCAAACATTTTATGTCTAT 58.866 33.333 0.00 0.00 38.24 1.98
4204 4665 9.856162 ACCAAACCTAAACAAACTCTAAATAGA 57.144 29.630 0.00 0.00 0.00 1.98
4208 4669 9.841295 AACCTAAACAAACTCTAAATAGACACA 57.159 29.630 0.00 0.00 0.00 3.72
4209 4670 9.841295 ACCTAAACAAACTCTAAATAGACACAA 57.159 29.630 0.00 0.00 0.00 3.33
4215 4678 5.836024 ACTCTAAATAGACACAACCCCAA 57.164 39.130 0.00 0.00 0.00 4.12
4262 4725 1.140312 TGAGACCAACAAGAAGGCCT 58.860 50.000 0.00 0.00 0.00 5.19
4268 4732 4.584743 AGACCAACAAGAAGGCCTAAAAAG 59.415 41.667 5.16 0.00 0.00 2.27
4269 4733 3.069586 ACCAACAAGAAGGCCTAAAAAGC 59.930 43.478 5.16 0.00 0.00 3.51
4280 4744 4.265904 GCCTAAAAAGCCTTTTGCCTTA 57.734 40.909 2.64 0.00 42.71 2.69
4301 4765 7.722285 GCCTTACATAGTATTTCCATTAACCCA 59.278 37.037 0.00 0.00 0.00 4.51
4302 4766 9.635404 CCTTACATAGTATTTCCATTAACCCAA 57.365 33.333 0.00 0.00 0.00 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.961793 TTGCTCGCAAGGTACAAACT 58.038 45.000 0.00 0.00 38.47 2.66
7 8 2.381589 GTTTGCTCGCAAGGTACAAAC 58.618 47.619 4.39 0.00 42.64 2.93
46 47 1.405821 CGGCCTACTTCTTCGATGACT 59.594 52.381 0.00 0.00 0.00 3.41
132 172 1.654954 GGCTAGCTCCTTCGACGACA 61.655 60.000 15.72 0.00 0.00 4.35
292 386 1.445942 CGCCCTATCCCATTGTCGT 59.554 57.895 0.00 0.00 0.00 4.34
297 391 2.743718 CGAGCGCCCTATCCCATT 59.256 61.111 2.29 0.00 0.00 3.16
311 405 2.842394 ATCGACAGCAAGCACCCGAG 62.842 60.000 0.00 0.00 0.00 4.63
346 440 0.249120 CCTGTCGGTTGCACATAGGA 59.751 55.000 0.00 0.00 0.00 2.94
371 465 1.396594 CCACCTACTCCTCCCCCTT 59.603 63.158 0.00 0.00 0.00 3.95
468 564 1.727535 CGAACGCGCATCCATTTTTCA 60.728 47.619 5.73 0.00 0.00 2.69
474 570 0.650512 CTAAACGAACGCGCATCCAT 59.349 50.000 5.73 0.00 42.48 3.41
486 582 0.800683 CAGCACGCCGATCTAAACGA 60.801 55.000 0.00 0.00 0.00 3.85
503 599 5.551760 AAACAGACACAAAGTTGACTCAG 57.448 39.130 0.00 0.00 0.00 3.35
527 625 3.871594 GCCAGCGTGTGTCTATTTAGATT 59.128 43.478 0.00 0.00 34.39 2.40
535 633 0.037697 ATTTCGCCAGCGTGTGTCTA 60.038 50.000 12.32 0.00 40.74 2.59
556 654 2.521105 AAAACTCTAACGTGCCGACT 57.479 45.000 0.00 0.00 0.00 4.18
593 691 3.181512 ACGAGTTTCTATCGGACGACTTC 60.182 47.826 0.00 0.00 44.36 3.01
594 692 2.746362 ACGAGTTTCTATCGGACGACTT 59.254 45.455 0.00 0.00 44.36 3.01
595 693 2.354259 ACGAGTTTCTATCGGACGACT 58.646 47.619 0.00 0.00 44.36 4.18
596 694 2.821307 ACGAGTTTCTATCGGACGAC 57.179 50.000 0.00 0.00 44.36 4.34
597 695 2.096496 GGAACGAGTTTCTATCGGACGA 59.904 50.000 0.00 0.00 44.36 4.20
598 696 2.448219 GGAACGAGTTTCTATCGGACG 58.552 52.381 0.00 0.00 44.36 4.79
722 821 0.603975 GGTCACCTGTCAGTGGCTTC 60.604 60.000 0.00 0.00 42.14 3.86
739 838 2.284405 CTAGGGGTCGTGTGGGGT 60.284 66.667 0.00 0.00 0.00 4.95
892 991 1.223337 GAAATAGGAGAGGGGGAGGGA 59.777 57.143 0.00 0.00 0.00 4.20
973 1072 3.858868 TTGCGCTATCCGGATCGCC 62.859 63.158 34.31 25.70 46.14 5.54
1209 1310 7.915397 GCTGTTGATGTTTTTCTAGAAAACTGA 59.085 33.333 26.47 15.18 39.70 3.41
1313 1414 4.151867 GCTAGGTTTTTCCTTACACGTCTG 59.848 45.833 0.00 0.00 45.67 3.51
1521 1623 0.611896 GTGGGGTCTGGAATTGGTGG 60.612 60.000 0.00 0.00 0.00 4.61
1546 1648 6.521151 AATCAACATGGAAAGAACTCATCC 57.479 37.500 0.00 0.00 0.00 3.51
1572 1674 1.480954 TGAGGACTCGGCTATTTGGAC 59.519 52.381 0.00 0.00 0.00 4.02
1840 1942 2.972021 TCTTCAGTGACCCACAGAATGA 59.028 45.455 5.60 3.96 38.71 2.57
1898 2000 0.250727 TTGAACTGTGGGCAGCTACC 60.251 55.000 0.00 0.00 46.30 3.18
1945 2051 3.527533 ACTCACAAACAGTACGCAAAGA 58.472 40.909 0.00 0.00 0.00 2.52
1946 2052 3.944422 ACTCACAAACAGTACGCAAAG 57.056 42.857 0.00 0.00 0.00 2.77
2015 2121 4.145365 ATGCCGCTGTTAGTGGTATTAA 57.855 40.909 9.87 0.00 46.78 1.40
2051 2157 4.051237 GGAAGACAAATTTGAGCAACACC 58.949 43.478 24.64 13.02 0.00 4.16
2056 2162 4.766891 CCCTTAGGAAGACAAATTTGAGCA 59.233 41.667 24.64 0.01 33.47 4.26
2067 2173 4.202326 TGAAACAGTGTCCCTTAGGAAGAC 60.202 45.833 0.00 0.00 46.38 3.01
2095 2201 7.483307 TGAAGCTCATAATTTGCCAGAATTAC 58.517 34.615 0.00 0.00 35.10 1.89
2104 2210 4.082026 ACAGGGTTGAAGCTCATAATTTGC 60.082 41.667 0.00 0.00 0.00 3.68
2142 2248 3.691118 TGCCTAACAGATGCTTTGATCAC 59.309 43.478 0.00 0.00 0.00 3.06
2186 2292 3.153919 GAGGGACCAAACACAATTAGCA 58.846 45.455 0.00 0.00 0.00 3.49
2194 2300 2.148768 CTTTACGGAGGGACCAAACAC 58.851 52.381 0.00 0.00 38.90 3.32
2204 2310 6.214399 ACGCTCTTATATTTCTTTACGGAGG 58.786 40.000 0.00 0.00 0.00 4.30
2205 2311 7.695869 AACGCTCTTATATTTCTTTACGGAG 57.304 36.000 0.00 0.00 0.00 4.63
2206 2312 9.241317 CTAAACGCTCTTATATTTCTTTACGGA 57.759 33.333 0.00 0.00 0.00 4.69
2207 2313 9.241317 TCTAAACGCTCTTATATTTCTTTACGG 57.759 33.333 0.00 0.00 0.00 4.02
2221 2327 9.570488 CACTACTTTAGTAATCTAAACGCTCTT 57.430 33.333 0.00 0.00 40.05 2.85
2222 2328 8.954350 TCACTACTTTAGTAATCTAAACGCTCT 58.046 33.333 0.00 0.00 40.05 4.09
2223 2329 9.733219 ATCACTACTTTAGTAATCTAAACGCTC 57.267 33.333 0.00 0.00 40.05 5.03
2224 2330 9.733219 GATCACTACTTTAGTAATCTAAACGCT 57.267 33.333 0.00 0.00 40.05 5.07
2225 2331 9.733219 AGATCACTACTTTAGTAATCTAAACGC 57.267 33.333 0.00 0.00 40.05 4.84
2231 2337 9.733219 GCGTTTAGATCACTACTTTAGTAATCT 57.267 33.333 4.72 4.72 37.23 2.40
2232 2338 9.733219 AGCGTTTAGATCACTACTTTAGTAATC 57.267 33.333 0.00 0.00 37.23 1.75
2233 2339 9.733219 GAGCGTTTAGATCACTACTTTAGTAAT 57.267 33.333 0.00 0.00 37.23 1.89
2234 2340 8.954350 AGAGCGTTTAGATCACTACTTTAGTAA 58.046 33.333 0.00 0.00 37.82 2.24
2235 2341 8.503458 AGAGCGTTTAGATCACTACTTTAGTA 57.497 34.615 0.00 0.00 37.82 1.82
2236 2342 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
2237 2343 9.953697 ATAAGAGCGTTTAGATCACTACTTTAG 57.046 33.333 0.00 0.00 37.82 1.85
2251 2357 9.321562 CCCTGTAAAGAAATATAAGAGCGTTTA 57.678 33.333 0.00 0.00 0.00 2.01
2252 2358 7.282450 CCCCTGTAAAGAAATATAAGAGCGTTT 59.718 37.037 0.00 0.00 0.00 3.60
2253 2359 6.766467 CCCCTGTAAAGAAATATAAGAGCGTT 59.234 38.462 0.00 0.00 0.00 4.84
2254 2360 6.289064 CCCCTGTAAAGAAATATAAGAGCGT 58.711 40.000 0.00 0.00 0.00 5.07
2255 2361 5.701290 CCCCCTGTAAAGAAATATAAGAGCG 59.299 44.000 0.00 0.00 0.00 5.03
2256 2362 6.838382 TCCCCCTGTAAAGAAATATAAGAGC 58.162 40.000 0.00 0.00 0.00 4.09
2264 2370 9.951866 AACATTATATTCCCCCTGTAAAGAAAT 57.048 29.630 0.00 0.00 0.00 2.17
2271 2377 9.802039 GTCAATTAACATTATATTCCCCCTGTA 57.198 33.333 0.00 0.00 0.00 2.74
2272 2378 8.511126 AGTCAATTAACATTATATTCCCCCTGT 58.489 33.333 0.00 0.00 0.00 4.00
2273 2379 8.940397 AGTCAATTAACATTATATTCCCCCTG 57.060 34.615 0.00 0.00 0.00 4.45
2274 2380 9.367160 CAAGTCAATTAACATTATATTCCCCCT 57.633 33.333 0.00 0.00 0.00 4.79
2275 2381 8.585018 CCAAGTCAATTAACATTATATTCCCCC 58.415 37.037 0.00 0.00 0.00 5.40
2276 2382 8.088365 GCCAAGTCAATTAACATTATATTCCCC 58.912 37.037 0.00 0.00 0.00 4.81
2277 2383 8.860088 AGCCAAGTCAATTAACATTATATTCCC 58.140 33.333 0.00 0.00 0.00 3.97
2369 2475 7.398024 AGTGAGTATGCTCCACTTAAAATCTT 58.602 34.615 8.45 0.00 40.95 2.40
2397 2503 5.507315 GCAATATAACCCAAGAAATCACCCG 60.507 44.000 0.00 0.00 0.00 5.28
2398 2504 5.362430 TGCAATATAACCCAAGAAATCACCC 59.638 40.000 0.00 0.00 0.00 4.61
2412 2518 9.569167 TCATACGCTCTATAAGTGCAATATAAC 57.431 33.333 0.00 0.00 39.21 1.89
2415 2521 9.658799 AATTCATACGCTCTATAAGTGCAATAT 57.341 29.630 0.00 0.00 39.21 1.28
2417 2523 7.095060 CCAATTCATACGCTCTATAAGTGCAAT 60.095 37.037 0.00 0.00 39.21 3.56
2418 2524 6.202762 CCAATTCATACGCTCTATAAGTGCAA 59.797 38.462 0.00 0.00 39.21 4.08
2419 2525 5.696270 CCAATTCATACGCTCTATAAGTGCA 59.304 40.000 2.38 0.00 39.21 4.57
2420 2526 5.696724 ACCAATTCATACGCTCTATAAGTGC 59.303 40.000 0.00 0.00 39.21 4.40
2422 2528 5.696724 GCACCAATTCATACGCTCTATAAGT 59.303 40.000 0.00 0.00 0.00 2.24
2423 2529 5.928839 AGCACCAATTCATACGCTCTATAAG 59.071 40.000 0.00 0.00 0.00 1.73
2433 2540 5.123820 TGAAACTGCTAGCACCAATTCATAC 59.876 40.000 14.93 0.00 0.00 2.39
2520 2641 0.606401 AGTGATCAAACGTGGCCAGG 60.606 55.000 23.61 23.61 0.00 4.45
2552 2673 4.559153 CCAAACTACATTTTGGCTTCAGG 58.441 43.478 1.81 0.00 46.92 3.86
2566 2687 3.815401 ACACTGTGAATGCTCCAAACTAC 59.185 43.478 15.86 0.00 0.00 2.73
2600 2721 7.277098 GTGCATGCTAAAAAGTGATCAATCAAT 59.723 33.333 20.33 0.00 38.75 2.57
2612 2733 4.606673 CGCAACTTTGTGCATGCTAAAAAG 60.607 41.667 25.44 25.44 45.19 2.27
2633 2754 3.071479 TGTACTCAAGGGTGAATTTCGC 58.929 45.455 1.20 1.20 31.88 4.70
2635 2756 7.681939 TTACATGTACTCAAGGGTGAATTTC 57.318 36.000 4.68 0.00 31.88 2.17
2636 2757 8.522830 CAATTACATGTACTCAAGGGTGAATTT 58.477 33.333 4.68 0.00 31.88 1.82
2656 2777 9.157259 GAACAAATTCAACAACAATGCAATTAC 57.843 29.630 0.00 0.00 32.20 1.89
2665 2786 6.333416 TGAATCCGAACAAATTCAACAACAA 58.667 32.000 0.00 0.00 38.57 2.83
2719 2840 5.408604 GGACTTAAGATCAAAAGAAGTCGCA 59.591 40.000 10.09 0.00 44.48 5.10
2720 2841 5.444745 CGGACTTAAGATCAAAAGAAGTCGC 60.445 44.000 10.09 8.03 44.48 5.19
2739 2860 3.568853 GCCTACTCACATACATACGGACT 59.431 47.826 0.00 0.00 0.00 3.85
2750 2871 7.770897 CCTACTTAAATGAAAGCCTACTCACAT 59.229 37.037 0.00 0.00 0.00 3.21
2751 2872 7.038587 TCCTACTTAAATGAAAGCCTACTCACA 60.039 37.037 0.00 0.00 0.00 3.58
2752 2873 7.278203 GTCCTACTTAAATGAAAGCCTACTCAC 59.722 40.741 0.00 0.00 0.00 3.51
2753 2874 7.180408 AGTCCTACTTAAATGAAAGCCTACTCA 59.820 37.037 0.00 0.00 0.00 3.41
2785 2906 6.097356 CCTGGAAACACAAATGAGATTGATG 58.903 40.000 0.00 0.00 35.60 3.07
2855 2989 7.224297 AGTTCACAATAGCCTTAAAGAAGTCA 58.776 34.615 0.00 0.00 0.00 3.41
3013 3147 8.912787 TGTTTTCTCGATCTACAAGATAAGAC 57.087 34.615 0.00 0.00 34.53 3.01
3209 3343 8.663911 TGAACAAACAACAAAATCTGGAATTTC 58.336 29.630 0.00 0.00 0.00 2.17
3258 3392 6.765915 ACCTGAAATTAGAGAATTTGGCTC 57.234 37.500 0.56 0.00 43.76 4.70
3336 3470 7.556844 ACGGTAGTTCTTCTGTCATTAATCAT 58.443 34.615 0.00 0.00 0.00 2.45
3337 3471 6.931838 ACGGTAGTTCTTCTGTCATTAATCA 58.068 36.000 0.00 0.00 0.00 2.57
3338 3472 9.530633 AATACGGTAGTTCTTCTGTCATTAATC 57.469 33.333 0.00 0.00 0.00 1.75
3339 3473 9.886132 AAATACGGTAGTTCTTCTGTCATTAAT 57.114 29.630 0.00 0.00 0.00 1.40
3340 3474 9.362539 GAAATACGGTAGTTCTTCTGTCATTAA 57.637 33.333 18.19 0.00 30.69 1.40
3352 3486 6.837992 TGCTGAAATTGAAATACGGTAGTTC 58.162 36.000 18.53 18.53 33.69 3.01
3357 3491 4.142600 GCTCTGCTGAAATTGAAATACGGT 60.143 41.667 0.00 0.00 0.00 4.83
3391 3525 1.792273 GCTAGACTCTTCACAGCGTCG 60.792 57.143 0.00 0.00 39.41 5.12
3397 3531 3.081804 TCGACATGCTAGACTCTTCACA 58.918 45.455 0.00 0.00 0.00 3.58
3451 3590 4.277258 GCAAAGCGATGATGAATACAGTG 58.723 43.478 0.00 0.00 0.00 3.66
3477 3616 2.915604 ACTCCATCCAGGACAATTCAGT 59.084 45.455 0.00 0.00 43.07 3.41
3555 3699 8.818141 TCTCAACAGAATTACAAAGTAGACAG 57.182 34.615 0.00 0.00 0.00 3.51
3573 3717 3.744238 TCGTCAAGTCCAATCTCAACA 57.256 42.857 0.00 0.00 0.00 3.33
3576 3720 4.641396 ACAATTCGTCAAGTCCAATCTCA 58.359 39.130 0.00 0.00 0.00 3.27
3586 3730 6.183359 CGACAAATAGCAAACAATTCGTCAAG 60.183 38.462 0.00 0.00 0.00 3.02
3590 3734 5.351233 TCGACAAATAGCAAACAATTCGT 57.649 34.783 0.00 0.00 0.00 3.85
3604 3748 2.972625 TCCTCGCTGAATTCGACAAAT 58.027 42.857 0.04 0.00 32.08 2.32
3606 3750 2.448926 TTCCTCGCTGAATTCGACAA 57.551 45.000 0.04 0.00 32.08 3.18
3610 3754 4.260375 CCAACTATTTCCTCGCTGAATTCG 60.260 45.833 0.04 0.00 0.00 3.34
3620 3764 4.753107 TCACGTTGTTCCAACTATTTCCTC 59.247 41.667 5.65 0.00 0.00 3.71
3652 3796 8.554490 AGTTTACAGGACTATCAGATAACCAT 57.446 34.615 12.94 6.04 0.00 3.55
3653 3797 7.069578 GGAGTTTACAGGACTATCAGATAACCA 59.930 40.741 12.94 0.00 0.00 3.67
3716 4153 5.306937 TCATGAACACTTTCCTCCTAGAACA 59.693 40.000 0.00 0.00 0.00 3.18
3733 4170 6.710744 ACCCAACCGATATAAGAATCATGAAC 59.289 38.462 0.00 0.00 0.00 3.18
3755 4192 2.644992 CGGTTTGCTTGCTGACCC 59.355 61.111 10.60 0.00 0.00 4.46
3756 4193 2.050077 GCGGTTTGCTTGCTGACC 60.050 61.111 7.54 7.54 41.73 4.02
3772 4209 7.056844 AGTAAATGATAAGGAGTAGGACAGC 57.943 40.000 0.00 0.00 0.00 4.40
3796 4233 6.451292 TGGGGTTAAACTTCTGGTATGTAA 57.549 37.500 0.00 0.00 0.00 2.41
3797 4234 6.645884 ATGGGGTTAAACTTCTGGTATGTA 57.354 37.500 0.00 0.00 0.00 2.29
3798 4235 5.530176 ATGGGGTTAAACTTCTGGTATGT 57.470 39.130 0.00 0.00 0.00 2.29
3800 4237 6.070078 TCGTTATGGGGTTAAACTTCTGGTAT 60.070 38.462 0.00 0.00 0.00 2.73
3801 4238 5.248020 TCGTTATGGGGTTAAACTTCTGGTA 59.752 40.000 0.00 0.00 0.00 3.25
3802 4239 4.041938 TCGTTATGGGGTTAAACTTCTGGT 59.958 41.667 0.00 0.00 0.00 4.00
3803 4240 4.581868 TCGTTATGGGGTTAAACTTCTGG 58.418 43.478 0.00 0.00 0.00 3.86
3804 4241 7.551617 ACTTATCGTTATGGGGTTAAACTTCTG 59.448 37.037 0.00 0.00 0.00 3.02
3805 4242 7.627311 ACTTATCGTTATGGGGTTAAACTTCT 58.373 34.615 0.00 0.00 0.00 2.85
3806 4243 7.854557 ACTTATCGTTATGGGGTTAAACTTC 57.145 36.000 0.00 0.00 0.00 3.01
3877 4314 9.490379 GTCGAAGTCCAGGATATTAATTTACAT 57.510 33.333 0.00 0.00 0.00 2.29
3878 4315 7.929785 GGTCGAAGTCCAGGATATTAATTTACA 59.070 37.037 0.00 0.00 35.31 2.41
3879 4316 7.929785 TGGTCGAAGTCCAGGATATTAATTTAC 59.070 37.037 0.00 0.00 41.55 2.01
3880 4317 8.025270 TGGTCGAAGTCCAGGATATTAATTTA 57.975 34.615 0.00 0.00 41.55 1.40
3881 4318 6.895782 TGGTCGAAGTCCAGGATATTAATTT 58.104 36.000 0.00 0.00 41.55 1.82
3882 4319 6.494666 TGGTCGAAGTCCAGGATATTAATT 57.505 37.500 0.00 0.00 41.55 1.40
3893 4330 1.118965 TGCTCCTTGGTCGAAGTCCA 61.119 55.000 0.00 0.00 45.39 4.02
3894 4331 0.670854 GTGCTCCTTGGTCGAAGTCC 60.671 60.000 0.00 0.00 35.92 3.85
3895 4332 1.009389 CGTGCTCCTTGGTCGAAGTC 61.009 60.000 0.00 0.00 0.00 3.01
3896 4333 1.006102 CGTGCTCCTTGGTCGAAGT 60.006 57.895 0.00 0.00 0.00 3.01
3897 4334 0.242825 TACGTGCTCCTTGGTCGAAG 59.757 55.000 0.00 0.00 0.00 3.79
3898 4335 0.242825 CTACGTGCTCCTTGGTCGAA 59.757 55.000 0.00 0.00 0.00 3.71
3899 4336 1.880894 CTACGTGCTCCTTGGTCGA 59.119 57.895 0.00 0.00 0.00 4.20
3900 4337 1.805945 GCTACGTGCTCCTTGGTCG 60.806 63.158 0.00 0.00 38.95 4.79
3901 4338 0.320421 TTGCTACGTGCTCCTTGGTC 60.320 55.000 0.00 0.00 43.37 4.02
3902 4339 0.107831 TTTGCTACGTGCTCCTTGGT 59.892 50.000 0.00 0.00 43.37 3.67
3903 4340 0.798776 CTTTGCTACGTGCTCCTTGG 59.201 55.000 0.00 0.00 43.37 3.61
3904 4341 1.795768 TCTTTGCTACGTGCTCCTTG 58.204 50.000 0.00 0.00 43.37 3.61
3905 4342 2.543777 TTCTTTGCTACGTGCTCCTT 57.456 45.000 0.00 0.00 43.37 3.36
3906 4343 2.143925 GTTTCTTTGCTACGTGCTCCT 58.856 47.619 0.00 0.00 43.37 3.69
3907 4344 2.143925 AGTTTCTTTGCTACGTGCTCC 58.856 47.619 0.00 0.00 43.37 4.70
3908 4345 4.985044 TTAGTTTCTTTGCTACGTGCTC 57.015 40.909 0.00 0.00 43.37 4.26
3909 4346 5.744666 TTTTAGTTTCTTTGCTACGTGCT 57.255 34.783 0.00 0.00 43.37 4.40
3910 4347 6.986424 AATTTTAGTTTCTTTGCTACGTGC 57.014 33.333 0.00 0.00 43.25 5.34
3911 4348 9.659830 AGTAAATTTTAGTTTCTTTGCTACGTG 57.340 29.630 0.00 0.00 0.00 4.49
3956 4393 7.554835 TCAAATTGCCTTAGGTACGATTAACAT 59.445 33.333 0.00 0.00 0.00 2.71
3962 4399 5.708230 TGTTTCAAATTGCCTTAGGTACGAT 59.292 36.000 0.00 0.00 0.00 3.73
3966 4403 7.596995 CGATTTTGTTTCAAATTGCCTTAGGTA 59.403 33.333 0.00 0.00 0.00 3.08
3968 4405 6.618379 GCGATTTTGTTTCAAATTGCCTTAGG 60.618 38.462 7.01 0.00 38.98 2.69
3970 4407 6.221858 GCGATTTTGTTTCAAATTGCCTTA 57.778 33.333 7.01 0.00 38.98 2.69
3976 4413 6.676237 ACAAAGGCGATTTTGTTTCAAATT 57.324 29.167 10.70 0.00 46.18 1.82
3985 4422 4.566360 AGTTTGTTGACAAAGGCGATTTTG 59.434 37.500 9.40 9.62 45.36 2.44
3986 4423 4.754322 AGTTTGTTGACAAAGGCGATTTT 58.246 34.783 9.40 0.00 45.36 1.82
3987 4424 4.385358 AGTTTGTTGACAAAGGCGATTT 57.615 36.364 9.40 0.00 45.36 2.17
4055 4498 4.826733 ACATGAACCATTTCAGCAAGTACA 59.173 37.500 0.00 0.00 45.07 2.90
4061 4504 4.241590 GTTCACATGAACCATTTCAGCA 57.758 40.909 12.83 0.00 45.07 4.41
4114 4558 2.817258 CACAATAGACCCCGCTCAAAAA 59.183 45.455 0.00 0.00 0.00 1.94
4115 4559 2.224670 ACACAATAGACCCCGCTCAAAA 60.225 45.455 0.00 0.00 0.00 2.44
4116 4560 1.349688 ACACAATAGACCCCGCTCAAA 59.650 47.619 0.00 0.00 0.00 2.69
4117 4561 0.981183 ACACAATAGACCCCGCTCAA 59.019 50.000 0.00 0.00 0.00 3.02
4118 4562 0.981183 AACACAATAGACCCCGCTCA 59.019 50.000 0.00 0.00 0.00 4.26
4119 4563 1.066430 TCAACACAATAGACCCCGCTC 60.066 52.381 0.00 0.00 0.00 5.03
4120 4564 0.981183 TCAACACAATAGACCCCGCT 59.019 50.000 0.00 0.00 0.00 5.52
4121 4565 1.670811 CATCAACACAATAGACCCCGC 59.329 52.381 0.00 0.00 0.00 6.13
4122 4566 3.198068 CTCATCAACACAATAGACCCCG 58.802 50.000 0.00 0.00 0.00 5.73
4123 4567 2.945668 GCTCATCAACACAATAGACCCC 59.054 50.000 0.00 0.00 0.00 4.95
4124 4568 3.609853 TGCTCATCAACACAATAGACCC 58.390 45.455 0.00 0.00 0.00 4.46
4125 4569 4.877823 TGATGCTCATCAACACAATAGACC 59.122 41.667 9.88 0.00 44.14 3.85
4153 4597 0.235404 CCAAAACAATGCTTTGCGCC 59.765 50.000 4.18 0.00 36.22 6.53
4154 4598 0.936600 ACCAAAACAATGCTTTGCGC 59.063 45.000 11.96 0.00 36.22 6.09
4155 4599 1.333081 GCACCAAAACAATGCTTTGCG 60.333 47.619 11.96 1.03 36.22 4.85
4215 4678 6.594937 GGCACACATTGATCCATGTTATTTTT 59.405 34.615 9.62 0.00 0.00 1.94
4224 4687 2.097036 CACTGGCACACATTGATCCAT 58.903 47.619 0.00 0.00 31.88 3.41
4225 4688 1.073603 TCACTGGCACACATTGATCCA 59.926 47.619 0.00 0.00 34.28 3.41
4228 4691 2.430465 GTCTCACTGGCACACATTGAT 58.570 47.619 0.00 0.00 38.00 2.57
4262 4725 7.533289 ACTATGTAAGGCAAAAGGCTTTTTA 57.467 32.000 22.02 9.78 38.94 1.52
4268 4732 6.096282 TGGAAATACTATGTAAGGCAAAAGGC 59.904 38.462 0.00 0.00 43.74 4.35
4269 4733 7.639113 TGGAAATACTATGTAAGGCAAAAGG 57.361 36.000 0.00 0.00 0.00 3.11


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

AutoCloner maintained by Alex Coulton.