Multiple sequence alignment - TraesCS2A01G306900

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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 TraesCS2A01G306900 chr2A 100.000 3518 0 0 1 3518 527902484 527898967 0.000000e+00 6497.0
1 TraesCS2A01G306900 chr2A 80.093 216 40 3 1 215 532431337 532431550 1.310000e-34 158.0
2 TraesCS2A01G306900 chr2B 93.903 1837 60 16 471 2278 462884837 462883024 0.000000e+00 2724.0
3 TraesCS2A01G306900 chr2B 87.991 891 42 31 2286 3136 462882981 462882116 0.000000e+00 992.0
4 TraesCS2A01G306900 chr2B 90.793 391 32 2 3131 3518 462882084 462881695 1.450000e-143 520.0
5 TraesCS2A01G306900 chr2B 80.435 322 53 8 4 322 462885149 462884835 1.630000e-58 237.0
6 TraesCS2A01G306900 chr2D 92.246 1741 90 19 550 2278 391262434 391260727 0.000000e+00 2425.0
7 TraesCS2A01G306900 chr2D 88.679 1219 48 41 2249 3429 391260710 391259544 0.000000e+00 1404.0
8 TraesCS2A01G306900 chr3D 79.861 288 53 4 1 284 488120911 488121197 4.600000e-49 206.0
9 TraesCS2A01G306900 chr4A 79.365 252 47 4 19 266 544169116 544168866 4.670000e-39 172.0
10 TraesCS2A01G306900 chr4A 80.189 212 40 1 25 234 737050696 737050485 1.310000e-34 158.0
11 TraesCS2A01G306900 chr1A 78.182 275 50 8 8 277 100041216 100041485 2.170000e-37 167.0
12 TraesCS2A01G306900 chr1A 94.737 95 3 2 611 704 531051539 531051446 2.830000e-31 147.0
13 TraesCS2A01G306900 chr1A 76.493 268 58 5 2 267 248619635 248619899 1.320000e-29 141.0
14 TraesCS2A01G306900 chr5B 79.911 224 43 1 1 222 166322218 166322441 2.810000e-36 163.0
15 TraesCS2A01G306900 chr5B 94.792 96 2 3 618 712 450665363 450665270 2.830000e-31 147.0
16 TraesCS2A01G306900 chr1D 78.788 231 43 4 1 231 459524229 459524453 2.190000e-32 150.0
17 TraesCS2A01G306900 chr1D 96.591 88 2 1 618 704 432400483 432400396 1.020000e-30 145.0
18 TraesCS2A01G306900 chr7A 93.939 99 2 4 623 721 227030993 227030899 2.830000e-31 147.0
19 TraesCS2A01G306900 chr1B 96.552 87 3 0 618 704 583974541 583974455 1.020000e-30 145.0
20 TraesCS2A01G306900 chr6A 95.556 90 2 2 618 707 441496862 441496775 3.660000e-30 143.0
21 TraesCS2A01G306900 chr6A 85.714 77 8 1 992 1068 484068104 484068031 1.050000e-10 78.7
22 TraesCS2A01G306900 chr3B 92.079 101 6 2 606 704 723266371 723266471 1.320000e-29 141.0


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 TraesCS2A01G306900 chr2A 527898967 527902484 3517 True 6497.00 6497 100.0000 1 3518 1 chr2A.!!$R1 3517
1 TraesCS2A01G306900 chr2B 462881695 462885149 3454 True 1118.25 2724 88.2805 4 3518 4 chr2B.!!$R1 3514
2 TraesCS2A01G306900 chr2D 391259544 391262434 2890 True 1914.50 2425 90.4625 550 3429 2 chr2D.!!$R1 2879

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
183 184 0.110688 CACTGAACGCACATTGTCGG 60.111 55.0 11.45 0.0 0.00 4.79 F
270 273 0.178981 CCTATCCCCCAACCATGCAG 60.179 60.0 0.00 0.0 0.00 4.41 F
427 430 0.319383 CTGCCTCTCGGAATCGGATG 60.319 60.0 0.00 0.0 36.95 3.51 F
809 847 0.458025 CTCCTACGTCGCAGTTTCCC 60.458 60.0 0.00 0.0 0.00 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2133 2173 2.202440 CAGACGTACGACCGCCAG 60.202 66.667 24.41 0.0 0.00 4.85 R
2274 2318 0.830648 TGCTTGGACGAGGGATTAGG 59.169 55.000 0.00 0.0 0.00 2.69 R
2280 2324 0.250727 TTTTCCTGCTTGGACGAGGG 60.251 55.000 0.00 0.0 46.14 4.30 R
2756 2878 0.040499 ACACACCTCCTCCTCTCTCC 59.960 60.000 0.00 0.0 0.00 3.71 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
17 18 4.615901 CAGTATGGACGCAGGCAA 57.384 55.556 0.00 0.00 0.00 4.52
19 20 0.940126 CAGTATGGACGCAGGCAATC 59.060 55.000 0.00 0.00 0.00 2.67
31 32 2.285834 GCAGGCAATCATATATACGCGC 60.286 50.000 5.73 0.00 0.00 6.86
44 45 1.029681 TACGCGCATACACTCATCCT 58.970 50.000 5.73 0.00 0.00 3.24
47 48 2.035961 ACGCGCATACACTCATCCTTAT 59.964 45.455 5.73 0.00 0.00 1.73
51 52 4.084328 GCGCATACACTCATCCTTATGAAC 60.084 45.833 0.30 0.00 41.57 3.18
52 53 5.049828 CGCATACACTCATCCTTATGAACA 58.950 41.667 0.00 0.00 41.57 3.18
53 54 5.050769 CGCATACACTCATCCTTATGAACAC 60.051 44.000 0.00 0.00 41.57 3.32
54 55 5.817296 GCATACACTCATCCTTATGAACACA 59.183 40.000 0.00 0.00 41.57 3.72
55 56 6.238211 GCATACACTCATCCTTATGAACACAC 60.238 42.308 0.00 0.00 41.57 3.82
56 57 5.227569 ACACTCATCCTTATGAACACACA 57.772 39.130 0.00 0.00 41.57 3.72
57 58 4.997395 ACACTCATCCTTATGAACACACAC 59.003 41.667 0.00 0.00 41.57 3.82
58 59 4.091945 CACTCATCCTTATGAACACACACG 59.908 45.833 0.00 0.00 41.57 4.49
59 60 3.000041 TCATCCTTATGAACACACACGC 59.000 45.455 0.00 0.00 39.20 5.34
70 71 1.533273 ACACACGCAGACCCTACCT 60.533 57.895 0.00 0.00 0.00 3.08
71 72 1.119574 ACACACGCAGACCCTACCTT 61.120 55.000 0.00 0.00 0.00 3.50
74 75 1.274447 ACACGCAGACCCTACCTTTAC 59.726 52.381 0.00 0.00 0.00 2.01
75 76 0.529378 ACGCAGACCCTACCTTTACG 59.471 55.000 0.00 0.00 0.00 3.18
81 82 0.900421 ACCCTACCTTTACGAGCACC 59.100 55.000 0.00 0.00 0.00 5.01
84 85 2.100989 CCTACCTTTACGAGCACCTCT 58.899 52.381 0.00 0.00 0.00 3.69
87 88 1.968493 ACCTTTACGAGCACCTCTGAA 59.032 47.619 0.00 0.00 0.00 3.02
89 90 3.181458 ACCTTTACGAGCACCTCTGAAAA 60.181 43.478 0.00 0.00 0.00 2.29
95 96 2.872245 CGAGCACCTCTGAAAAACTGAA 59.128 45.455 0.00 0.00 0.00 3.02
99 100 2.290641 CACCTCTGAAAAACTGAACCGG 59.709 50.000 0.00 0.00 0.00 5.28
105 106 4.394920 TCTGAAAAACTGAACCGGCATATC 59.605 41.667 0.00 0.00 0.00 1.63
111 112 4.955811 ACTGAACCGGCATATCATCTTA 57.044 40.909 0.00 0.00 0.00 2.10
112 113 4.887748 ACTGAACCGGCATATCATCTTAG 58.112 43.478 0.00 0.00 0.00 2.18
115 116 4.532126 TGAACCGGCATATCATCTTAGGAT 59.468 41.667 0.00 0.00 0.00 3.24
127 128 7.856145 ATCATCTTAGGATTGACAAAGTCAC 57.144 36.000 0.00 0.00 42.60 3.67
132 133 3.214328 AGGATTGACAAAGTCACCACAC 58.786 45.455 0.00 0.00 42.60 3.82
134 135 3.243068 GGATTGACAAAGTCACCACACAC 60.243 47.826 0.00 0.00 42.60 3.82
143 144 1.733041 CACCACACACGCCTCGTAG 60.733 63.158 0.00 0.00 38.32 3.51
149 150 1.962822 ACACGCCTCGTAGTCGACA 60.963 57.895 19.50 0.48 41.35 4.35
155 156 1.162698 CCTCGTAGTCGACAGGAACA 58.837 55.000 19.50 0.00 41.35 3.18
159 160 3.079578 TCGTAGTCGACAGGAACATCTT 58.920 45.455 19.50 0.00 41.35 2.40
163 164 3.426615 AGTCGACAGGAACATCTTCTCT 58.573 45.455 19.50 0.00 0.00 3.10
175 176 2.423926 TCTTCTCTCACTGAACGCAC 57.576 50.000 0.00 0.00 0.00 5.34
183 184 0.110688 CACTGAACGCACATTGTCGG 60.111 55.000 11.45 0.00 0.00 4.79
184 185 1.154413 CTGAACGCACATTGTCGGC 60.154 57.895 11.45 2.29 0.00 5.54
188 189 0.313672 AACGCACATTGTCGGCAATT 59.686 45.000 13.64 1.99 42.91 2.32
189 190 1.160989 ACGCACATTGTCGGCAATTA 58.839 45.000 13.64 0.00 42.91 1.40
228 229 2.472695 ATACAAGCGCCAGAACTTGA 57.527 45.000 2.29 0.00 44.89 3.02
232 233 1.172812 AAGCGCCAGAACTTGAACCC 61.173 55.000 2.29 0.00 0.00 4.11
239 241 1.815003 CAGAACTTGAACCCTGATGGC 59.185 52.381 0.00 0.00 37.83 4.40
241 243 2.108952 AGAACTTGAACCCTGATGGCTT 59.891 45.455 0.00 0.00 37.83 4.35
243 245 1.425066 ACTTGAACCCTGATGGCTTGA 59.575 47.619 0.00 0.00 37.83 3.02
251 253 2.486191 CCCTGATGGCTTGAGATACCAC 60.486 54.545 0.00 0.00 35.99 4.16
255 257 4.234550 TGATGGCTTGAGATACCACCTAT 58.765 43.478 0.00 0.00 35.99 2.57
267 270 0.185901 CCACCTATCCCCCAACCATG 59.814 60.000 0.00 0.00 0.00 3.66
270 273 0.178981 CCTATCCCCCAACCATGCAG 60.179 60.000 0.00 0.00 0.00 4.41
277 280 1.033746 CCCAACCATGCAGCTACAGG 61.034 60.000 0.00 0.00 0.00 4.00
280 283 2.617788 CCAACCATGCAGCTACAGGTTA 60.618 50.000 15.97 0.00 40.39 2.85
284 287 3.244911 ACCATGCAGCTACAGGTTAGTTT 60.245 43.478 0.00 0.00 0.00 2.66
286 289 2.151202 TGCAGCTACAGGTTAGTTTGC 58.849 47.619 0.00 0.00 0.00 3.68
318 321 0.893270 TTCTGAAATGGCGGGGTGTG 60.893 55.000 0.00 0.00 0.00 3.82
319 322 1.303236 CTGAAATGGCGGGGTGTGA 60.303 57.895 0.00 0.00 0.00 3.58
320 323 1.303236 TGAAATGGCGGGGTGTGAG 60.303 57.895 0.00 0.00 0.00 3.51
321 324 1.303317 GAAATGGCGGGGTGTGAGT 60.303 57.895 0.00 0.00 0.00 3.41
322 325 1.586154 GAAATGGCGGGGTGTGAGTG 61.586 60.000 0.00 0.00 0.00 3.51
323 326 4.722700 ATGGCGGGGTGTGAGTGC 62.723 66.667 0.00 0.00 0.00 4.40
327 330 3.345808 CGGGGTGTGAGTGCGTTG 61.346 66.667 0.00 0.00 0.00 4.10
328 331 3.660111 GGGGTGTGAGTGCGTTGC 61.660 66.667 0.00 0.00 0.00 4.17
329 332 4.012895 GGGTGTGAGTGCGTTGCG 62.013 66.667 0.00 0.00 0.00 4.85
330 333 3.269347 GGTGTGAGTGCGTTGCGT 61.269 61.111 0.00 0.00 0.00 5.24
331 334 2.053116 GTGTGAGTGCGTTGCGTG 60.053 61.111 0.00 0.00 0.00 5.34
332 335 3.935872 TGTGAGTGCGTTGCGTGC 61.936 61.111 0.00 0.00 0.00 5.34
333 336 3.640000 GTGAGTGCGTTGCGTGCT 61.640 61.111 0.00 0.00 0.00 4.40
334 337 2.894879 TGAGTGCGTTGCGTGCTT 60.895 55.556 0.00 0.00 0.00 3.91
335 338 2.425773 GAGTGCGTTGCGTGCTTG 60.426 61.111 0.00 0.00 0.00 4.01
336 339 3.168237 GAGTGCGTTGCGTGCTTGT 62.168 57.895 0.00 0.00 0.00 3.16
337 340 3.018428 GTGCGTTGCGTGCTTGTG 61.018 61.111 0.00 0.00 0.00 3.33
338 341 3.504273 TGCGTTGCGTGCTTGTGT 61.504 55.556 0.00 0.00 0.00 3.72
339 342 3.018428 GCGTTGCGTGCTTGTGTG 61.018 61.111 0.00 0.00 0.00 3.82
340 343 3.018428 CGTTGCGTGCTTGTGTGC 61.018 61.111 0.00 0.00 0.00 4.57
341 344 2.101965 GTTGCGTGCTTGTGTGCA 59.898 55.556 0.00 0.00 41.05 4.57
342 345 1.299316 GTTGCGTGCTTGTGTGCAT 60.299 52.632 0.00 0.00 45.23 3.96
343 346 1.008652 TTGCGTGCTTGTGTGCATC 60.009 52.632 0.00 0.00 45.23 3.91
344 347 1.446516 TTGCGTGCTTGTGTGCATCT 61.447 50.000 0.00 0.00 45.23 2.90
345 348 1.283793 GCGTGCTTGTGTGCATCTT 59.716 52.632 0.00 0.00 45.23 2.40
346 349 0.727122 GCGTGCTTGTGTGCATCTTC 60.727 55.000 0.00 0.00 45.23 2.87
347 350 0.451628 CGTGCTTGTGTGCATCTTCG 60.452 55.000 0.00 0.00 45.23 3.79
348 351 0.867746 GTGCTTGTGTGCATCTTCGA 59.132 50.000 0.00 0.00 45.23 3.71
349 352 1.466167 GTGCTTGTGTGCATCTTCGAT 59.534 47.619 0.00 0.00 45.23 3.59
350 353 2.095567 GTGCTTGTGTGCATCTTCGATT 60.096 45.455 0.00 0.00 45.23 3.34
351 354 2.553602 TGCTTGTGTGCATCTTCGATTT 59.446 40.909 0.00 0.00 38.12 2.17
352 355 2.912967 GCTTGTGTGCATCTTCGATTTG 59.087 45.455 0.00 0.00 0.00 2.32
353 356 3.495193 CTTGTGTGCATCTTCGATTTGG 58.505 45.455 0.00 0.00 0.00 3.28
354 357 2.777094 TGTGTGCATCTTCGATTTGGA 58.223 42.857 0.00 0.00 0.00 3.53
355 358 3.346315 TGTGTGCATCTTCGATTTGGAT 58.654 40.909 0.00 0.00 0.00 3.41
356 359 4.512484 TGTGTGCATCTTCGATTTGGATA 58.488 39.130 0.00 0.00 0.00 2.59
357 360 4.940654 TGTGTGCATCTTCGATTTGGATAA 59.059 37.500 0.00 0.00 0.00 1.75
358 361 5.414144 TGTGTGCATCTTCGATTTGGATAAA 59.586 36.000 0.00 0.00 0.00 1.40
359 362 6.095300 TGTGTGCATCTTCGATTTGGATAAAT 59.905 34.615 0.00 0.00 39.16 1.40
360 363 7.281999 TGTGTGCATCTTCGATTTGGATAAATA 59.718 33.333 0.00 0.00 36.66 1.40
361 364 7.800380 GTGTGCATCTTCGATTTGGATAAATAG 59.200 37.037 0.00 0.00 36.66 1.73
362 365 7.498900 TGTGCATCTTCGATTTGGATAAATAGT 59.501 33.333 0.00 0.00 36.66 2.12
363 366 7.800380 GTGCATCTTCGATTTGGATAAATAGTG 59.200 37.037 0.00 0.00 36.66 2.74
364 367 7.714813 TGCATCTTCGATTTGGATAAATAGTGA 59.285 33.333 0.00 0.00 36.66 3.41
365 368 8.725148 GCATCTTCGATTTGGATAAATAGTGAT 58.275 33.333 0.00 0.00 36.66 3.06
383 386 6.079424 AGTGATTATCCTTCTCGAAGTAGC 57.921 41.667 5.99 0.00 36.72 3.58
384 387 5.594725 AGTGATTATCCTTCTCGAAGTAGCA 59.405 40.000 5.99 0.00 36.72 3.49
385 388 6.266558 AGTGATTATCCTTCTCGAAGTAGCAT 59.733 38.462 5.99 0.00 36.72 3.79
386 389 6.364706 GTGATTATCCTTCTCGAAGTAGCATG 59.635 42.308 5.99 0.00 36.72 4.06
387 390 5.854010 TTATCCTTCTCGAAGTAGCATGT 57.146 39.130 5.99 0.00 36.72 3.21
388 391 4.744795 ATCCTTCTCGAAGTAGCATGTT 57.255 40.909 5.99 0.00 36.72 2.71
389 392 4.537135 TCCTTCTCGAAGTAGCATGTTT 57.463 40.909 5.99 0.00 36.72 2.83
390 393 4.245660 TCCTTCTCGAAGTAGCATGTTTG 58.754 43.478 5.99 0.00 36.72 2.93
391 394 3.997021 CCTTCTCGAAGTAGCATGTTTGT 59.003 43.478 5.99 0.00 36.72 2.83
392 395 4.143030 CCTTCTCGAAGTAGCATGTTTGTG 60.143 45.833 5.99 0.00 36.72 3.33
393 396 2.736721 TCTCGAAGTAGCATGTTTGTGC 59.263 45.455 0.00 0.00 45.38 4.57
394 397 7.032646 CTTCTCGAAGTAGCATGTTTGTGCA 62.033 44.000 1.47 0.00 39.24 4.57
395 398 8.931501 CTTCTCGAAGTAGCATGTTTGTGCAC 62.932 46.154 10.75 10.75 39.24 4.57
400 403 3.843632 GCATGTTTGTGCACGAGAA 57.156 47.368 13.13 4.16 44.43 2.87
401 404 2.336554 GCATGTTTGTGCACGAGAAT 57.663 45.000 13.13 5.10 44.43 2.40
402 405 1.980844 GCATGTTTGTGCACGAGAATG 59.019 47.619 19.59 19.59 44.43 2.67
403 406 2.605338 GCATGTTTGTGCACGAGAATGT 60.605 45.455 22.47 7.08 44.43 2.71
404 407 3.364864 GCATGTTTGTGCACGAGAATGTA 60.365 43.478 22.47 2.26 44.43 2.29
405 408 4.397382 CATGTTTGTGCACGAGAATGTAG 58.603 43.478 13.13 0.00 0.00 2.74
406 409 3.462982 TGTTTGTGCACGAGAATGTAGT 58.537 40.909 13.13 0.00 0.00 2.73
407 410 3.874543 TGTTTGTGCACGAGAATGTAGTT 59.125 39.130 13.13 0.00 0.00 2.24
408 411 4.025229 TGTTTGTGCACGAGAATGTAGTTC 60.025 41.667 13.13 0.00 37.08 3.01
417 420 3.791973 AGAATGTAGTTCTGCCTCTCG 57.208 47.619 0.00 0.00 45.38 4.04
418 421 2.428890 AGAATGTAGTTCTGCCTCTCGG 59.571 50.000 0.00 0.00 45.38 4.63
419 422 2.145397 ATGTAGTTCTGCCTCTCGGA 57.855 50.000 0.00 0.00 0.00 4.55
420 423 1.919240 TGTAGTTCTGCCTCTCGGAA 58.081 50.000 0.00 0.00 37.72 4.30
421 424 2.457598 TGTAGTTCTGCCTCTCGGAAT 58.542 47.619 0.00 0.00 41.72 3.01
422 425 2.427453 TGTAGTTCTGCCTCTCGGAATC 59.573 50.000 0.00 0.00 41.72 2.52
423 426 0.457851 AGTTCTGCCTCTCGGAATCG 59.542 55.000 0.00 0.00 41.72 3.34
424 427 0.528684 GTTCTGCCTCTCGGAATCGG 60.529 60.000 0.00 0.00 41.72 4.18
425 428 0.683179 TTCTGCCTCTCGGAATCGGA 60.683 55.000 0.00 0.00 35.24 4.55
426 429 0.468214 TCTGCCTCTCGGAATCGGAT 60.468 55.000 0.00 0.00 36.95 4.18
427 430 0.319383 CTGCCTCTCGGAATCGGATG 60.319 60.000 0.00 0.00 36.95 3.51
428 431 0.755327 TGCCTCTCGGAATCGGATGA 60.755 55.000 0.00 0.00 36.95 2.92
429 432 0.605589 GCCTCTCGGAATCGGATGAT 59.394 55.000 0.00 0.00 36.95 2.45
430 433 1.671261 GCCTCTCGGAATCGGATGATG 60.671 57.143 0.00 0.00 34.24 3.07
431 434 1.889170 CCTCTCGGAATCGGATGATGA 59.111 52.381 0.00 0.00 34.24 2.92
432 435 2.352225 CCTCTCGGAATCGGATGATGAC 60.352 54.545 0.00 0.00 34.24 3.06
433 436 2.556189 CTCTCGGAATCGGATGATGACT 59.444 50.000 0.00 0.00 34.24 3.41
434 437 2.959030 TCTCGGAATCGGATGATGACTT 59.041 45.455 0.00 0.00 34.24 3.01
435 438 3.384789 TCTCGGAATCGGATGATGACTTT 59.615 43.478 0.00 0.00 34.24 2.66
436 439 3.457234 TCGGAATCGGATGATGACTTTG 58.543 45.455 0.00 0.00 34.24 2.77
437 440 3.118775 TCGGAATCGGATGATGACTTTGT 60.119 43.478 0.00 0.00 34.24 2.83
438 441 3.623060 CGGAATCGGATGATGACTTTGTT 59.377 43.478 0.00 0.00 34.24 2.83
439 442 4.260375 CGGAATCGGATGATGACTTTGTTC 60.260 45.833 0.00 0.00 34.24 3.18
440 443 4.035675 GGAATCGGATGATGACTTTGTTCC 59.964 45.833 0.00 0.00 34.24 3.62
441 444 3.694043 TCGGATGATGACTTTGTTCCA 57.306 42.857 0.00 0.00 0.00 3.53
442 445 4.014569 TCGGATGATGACTTTGTTCCAA 57.985 40.909 0.00 0.00 0.00 3.53
443 446 4.588899 TCGGATGATGACTTTGTTCCAAT 58.411 39.130 0.00 0.00 0.00 3.16
444 447 5.739959 TCGGATGATGACTTTGTTCCAATA 58.260 37.500 0.00 0.00 0.00 1.90
445 448 6.356556 TCGGATGATGACTTTGTTCCAATAT 58.643 36.000 0.00 0.00 0.00 1.28
446 449 7.505258 TCGGATGATGACTTTGTTCCAATATA 58.495 34.615 0.00 0.00 0.00 0.86
447 450 7.990314 TCGGATGATGACTTTGTTCCAATATAA 59.010 33.333 0.00 0.00 0.00 0.98
448 451 8.620416 CGGATGATGACTTTGTTCCAATATAAA 58.380 33.333 0.00 0.00 0.00 1.40
526 533 6.793505 AAAACTCGGGAGATAGAGTACATT 57.206 37.500 2.08 0.00 45.91 2.71
529 536 6.150396 ACTCGGGAGATAGAGTACATTTTG 57.850 41.667 2.08 0.00 44.93 2.44
530 537 5.657302 ACTCGGGAGATAGAGTACATTTTGT 59.343 40.000 2.08 0.00 44.93 2.83
532 539 4.508124 CGGGAGATAGAGTACATTTTGTGC 59.492 45.833 0.00 0.00 32.95 4.57
535 542 6.037610 GGGAGATAGAGTACATTTTGTGCTTG 59.962 42.308 0.00 0.00 43.31 4.01
536 543 6.037610 GGAGATAGAGTACATTTTGTGCTTGG 59.962 42.308 0.00 0.00 43.31 3.61
537 544 6.476378 AGATAGAGTACATTTTGTGCTTGGT 58.524 36.000 0.00 0.00 43.31 3.67
543 563 6.402222 AGTACATTTTGTGCTTGGTTTTTCA 58.598 32.000 0.00 0.00 40.41 2.69
576 596 5.345202 GCTCAGAAATCAACAGCAAAATCTG 59.655 40.000 0.00 0.00 39.86 2.90
591 611 8.437742 CAGCAAAATCTGGAAACAATATTGAAC 58.562 33.333 22.16 11.49 42.06 3.18
600 620 7.585867 TGGAAACAATATTGAACGATTTCGAA 58.414 30.769 22.16 9.49 39.41 3.71
601 621 8.076781 TGGAAACAATATTGAACGATTTCGAAA 58.923 29.630 22.16 13.91 39.41 3.46
602 622 9.072294 GGAAACAATATTGAACGATTTCGAAAT 57.928 29.630 22.93 22.93 43.02 2.17
605 625 8.310677 ACAATATTGAACGATTTCGAAATTCG 57.689 30.769 23.49 25.34 43.02 3.34
622 642 9.594038 TCGAAATTCGAAGACTAAATCAAAAAG 57.406 29.630 16.25 0.00 46.90 2.27
705 736 1.041437 AACTGAGCTATCCCCGCTAC 58.959 55.000 0.00 0.00 37.96 3.58
706 737 1.173444 ACTGAGCTATCCCCGCTACG 61.173 60.000 0.00 0.00 37.96 3.51
713 744 0.601558 TATCCCCGCTACGATGCTTC 59.398 55.000 0.00 0.00 0.00 3.86
714 745 1.399744 ATCCCCGCTACGATGCTTCA 61.400 55.000 0.08 0.00 0.00 3.02
717 748 1.270094 CCCCGCTACGATGCTTCATAA 60.270 52.381 0.08 0.00 0.00 1.90
724 755 6.292649 CCGCTACGATGCTTCATAATTTGTAA 60.293 38.462 0.08 0.00 0.00 2.41
727 758 9.107367 GCTACGATGCTTCATAATTTGTAATTC 57.893 33.333 0.08 0.00 0.00 2.17
729 760 7.995289 ACGATGCTTCATAATTTGTAATTCCA 58.005 30.769 0.08 0.00 0.00 3.53
730 761 8.131100 ACGATGCTTCATAATTTGTAATTCCAG 58.869 33.333 0.08 0.00 0.00 3.86
780 816 6.405278 ACTTAGTTTGACAATTTTCCCAGG 57.595 37.500 0.00 0.00 0.00 4.45
797 833 2.936498 CCAGGTTAATGCAACTCCTACG 59.064 50.000 0.00 0.00 37.30 3.51
809 847 0.458025 CTCCTACGTCGCAGTTTCCC 60.458 60.000 0.00 0.00 0.00 3.97
863 901 5.505654 GCCACAATACATCCGGACAATTTAG 60.506 44.000 6.12 0.00 0.00 1.85
879 917 5.934625 ACAATTTAGTCTCTCAATTGACGCT 59.065 36.000 17.52 3.18 37.29 5.07
882 920 3.667497 AGTCTCTCAATTGACGCTTGA 57.333 42.857 3.38 0.00 38.16 3.02
884 922 3.993081 AGTCTCTCAATTGACGCTTGAAG 59.007 43.478 3.38 0.00 38.16 3.02
983 1023 8.764524 AACTTACAGCTTACAAGAACATCTAG 57.235 34.615 5.87 0.00 0.00 2.43
1003 1043 6.770542 TCTAGATCCTCGCTAACTCTAATGA 58.229 40.000 0.00 0.00 0.00 2.57
1004 1044 5.957842 AGATCCTCGCTAACTCTAATGAG 57.042 43.478 0.00 0.00 45.43 2.90
1661 1701 2.432628 GACGAAGGACGCCAGGTG 60.433 66.667 0.00 0.00 46.94 4.00
1662 1702 3.222354 GACGAAGGACGCCAGGTGT 62.222 63.158 4.94 4.94 46.94 4.16
1812 1852 3.303135 TGGAAGACGAGCGGCAGT 61.303 61.111 1.45 1.08 0.00 4.40
2136 2176 3.190849 CACCGCTCGATGCACTGG 61.191 66.667 0.00 3.64 43.06 4.00
2278 2322 6.369629 TCCAACAAGAAATGGAAGAACCTAA 58.630 36.000 0.00 0.00 42.61 2.69
2279 2323 7.010160 TCCAACAAGAAATGGAAGAACCTAAT 58.990 34.615 0.00 0.00 42.61 1.73
2280 2324 7.176690 TCCAACAAGAAATGGAAGAACCTAATC 59.823 37.037 0.00 0.00 42.61 1.75
2282 2326 5.952347 ACAAGAAATGGAAGAACCTAATCCC 59.048 40.000 0.00 0.00 39.86 3.85
2283 2327 6.190587 CAAGAAATGGAAGAACCTAATCCCT 58.809 40.000 0.00 0.00 39.86 4.20
2323 2414 4.137543 GAGAATCACAAACCACTCCACTT 58.862 43.478 0.00 0.00 33.17 3.16
2344 2435 6.036083 CACTTATACCAACCAAGAACTCATCG 59.964 42.308 0.00 0.00 0.00 3.84
2355 2446 2.637872 AGAACTCATCGAGAAAACCCCA 59.362 45.455 0.00 0.00 33.32 4.96
2366 2457 2.037121 AGAAAACCCCAAAAAGATGGCG 59.963 45.455 0.00 0.00 39.26 5.69
2451 2542 0.798776 GGAATGCGGTCACACAGAAG 59.201 55.000 0.00 0.00 0.00 2.85
2455 2546 1.292223 GCGGTCACACAGAAGGCTA 59.708 57.895 0.00 0.00 0.00 3.93
2460 2551 4.250464 CGGTCACACAGAAGGCTATTTTA 58.750 43.478 0.00 0.00 0.00 1.52
2462 2553 5.390567 CGGTCACACAGAAGGCTATTTTAAC 60.391 44.000 0.00 0.00 0.00 2.01
2463 2554 5.705905 GGTCACACAGAAGGCTATTTTAACT 59.294 40.000 0.00 0.00 0.00 2.24
2464 2555 6.348540 GGTCACACAGAAGGCTATTTTAACTG 60.349 42.308 0.00 0.00 0.00 3.16
2465 2556 5.705441 TCACACAGAAGGCTATTTTAACTGG 59.295 40.000 0.00 0.00 0.00 4.00
2467 2558 4.702131 CACAGAAGGCTATTTTAACTGGCT 59.298 41.667 0.00 0.00 36.89 4.75
2468 2559 4.702131 ACAGAAGGCTATTTTAACTGGCTG 59.298 41.667 0.00 0.00 35.50 4.85
2469 2560 3.696548 AGAAGGCTATTTTAACTGGCTGC 59.303 43.478 0.00 0.00 35.50 5.25
2470 2561 3.372440 AGGCTATTTTAACTGGCTGCT 57.628 42.857 0.00 0.00 34.03 4.24
2487 2593 1.681666 CTGGCACTCACTCCCATGT 59.318 57.895 0.00 0.00 0.00 3.21
2518 2624 3.876914 TCAAGAATCCATGGCGATGTAAC 59.123 43.478 6.96 0.00 0.00 2.50
2709 2831 2.679837 CTCTCTCTGTCTGTCTCTCTGC 59.320 54.545 0.00 0.00 0.00 4.26
2713 2835 1.202989 TCTGTCTGTCTCTCTGCCTGT 60.203 52.381 0.00 0.00 0.00 4.00
2714 2836 1.202114 CTGTCTGTCTCTCTGCCTGTC 59.798 57.143 0.00 0.00 0.00 3.51
2715 2837 1.202989 TGTCTGTCTCTCTGCCTGTCT 60.203 52.381 0.00 0.00 0.00 3.41
2716 2838 1.892474 GTCTGTCTCTCTGCCTGTCTT 59.108 52.381 0.00 0.00 0.00 3.01
2718 2840 0.972134 TGTCTCTCTGCCTGTCTTGG 59.028 55.000 0.00 0.00 0.00 3.61
2719 2841 1.261480 GTCTCTCTGCCTGTCTTGGA 58.739 55.000 0.00 0.00 0.00 3.53
2720 2842 1.204467 GTCTCTCTGCCTGTCTTGGAG 59.796 57.143 0.00 0.00 0.00 3.86
2728 2850 1.618345 GCCTGTCTTGGAGGAGAGAGA 60.618 57.143 1.12 0.00 38.87 3.10
2729 2851 2.378038 CCTGTCTTGGAGGAGAGAGAG 58.622 57.143 1.12 0.00 38.87 3.20
2749 2871 1.076632 GGAGAGGAGGAGCGAGGAA 60.077 63.158 0.00 0.00 0.00 3.36
2753 2875 1.720694 GAGGAGGAGCGAGGAAGACG 61.721 65.000 0.00 0.00 0.00 4.18
2754 2876 1.749638 GGAGGAGCGAGGAAGACGA 60.750 63.158 0.00 0.00 0.00 4.20
2755 2877 1.720694 GGAGGAGCGAGGAAGACGAG 61.721 65.000 0.00 0.00 0.00 4.18
2756 2878 1.720694 GAGGAGCGAGGAAGACGAGG 61.721 65.000 0.00 0.00 0.00 4.63
2949 3074 2.124151 GGACTGGCCGGAATGCAT 60.124 61.111 21.41 0.00 0.00 3.96
2967 3092 0.537143 ATTGTGCAGCTTGGAACGGA 60.537 50.000 0.00 0.00 0.00 4.69
2968 3093 0.749818 TTGTGCAGCTTGGAACGGAA 60.750 50.000 0.00 0.00 0.00 4.30
2969 3094 1.282875 GTGCAGCTTGGAACGGAAC 59.717 57.895 0.00 0.00 0.00 3.62
3008 3133 1.624336 TGAGAGGCTGCAGCATTTTT 58.376 45.000 37.63 21.40 44.36 1.94
3060 3198 4.448395 GCAATTTGACTGCTGTTTTGCATA 59.552 37.500 19.66 3.93 42.48 3.14
3061 3199 5.613142 GCAATTTGACTGCTGTTTTGCATAC 60.613 40.000 19.66 0.00 42.48 2.39
3062 3200 4.916983 TTTGACTGCTGTTTTGCATACT 57.083 36.364 0.00 0.00 42.48 2.12
3239 3419 2.685388 TGTGGACTATTCTGAGCTCTCG 59.315 50.000 16.19 6.27 0.00 4.04
3244 3424 3.211045 ACTATTCTGAGCTCTCGACTCC 58.789 50.000 16.19 0.00 32.98 3.85
3253 3433 2.014574 GCTCTCGACTCCTCAGCAGTA 61.015 57.143 0.00 0.00 0.00 2.74
3267 3447 3.394606 TCAGCAGTAAACCTTTTCCTCCT 59.605 43.478 0.00 0.00 0.00 3.69
3275 3455 3.739401 ACCTTTTCCTCCTTACATGGG 57.261 47.619 0.00 0.00 0.00 4.00
3278 3458 3.267031 CCTTTTCCTCCTTACATGGGTCT 59.733 47.826 0.00 0.00 0.00 3.85
3279 3459 4.263949 CCTTTTCCTCCTTACATGGGTCTT 60.264 45.833 0.00 0.00 0.00 3.01
3298 3478 5.509501 GGTCTTGATTGTTCCATTTGCAGAA 60.510 40.000 0.00 0.00 0.00 3.02
3299 3479 5.632347 GTCTTGATTGTTCCATTTGCAGAAG 59.368 40.000 0.00 0.00 0.00 2.85
3347 3532 8.621532 ACTGTTATTAGTGTATGCCATAATGG 57.378 34.615 0.00 0.00 41.55 3.16
3453 3639 8.383318 AGTACTCCATTGTATCATTGTATTGC 57.617 34.615 0.00 0.00 0.00 3.56
3458 3644 5.049198 CCATTGTATCATTGTATTGCTCGCT 60.049 40.000 0.00 0.00 0.00 4.93
3464 3650 5.973651 TCATTGTATTGCTCGCTAAGAAG 57.026 39.130 0.00 0.00 0.00 2.85
3465 3651 5.419542 TCATTGTATTGCTCGCTAAGAAGT 58.580 37.500 0.00 0.00 0.00 3.01
3478 3664 4.201724 CGCTAAGAAGTGTATGCTTTGGTC 60.202 45.833 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.940126 GATTGCCTGCGTCCATACTG 59.060 55.000 0.00 0.00 0.00 2.74
2 3 1.597742 ATGATTGCCTGCGTCCATAC 58.402 50.000 0.00 0.00 0.00 2.39
3 4 3.701205 ATATGATTGCCTGCGTCCATA 57.299 42.857 0.00 0.00 0.00 2.74
4 5 2.574006 ATATGATTGCCTGCGTCCAT 57.426 45.000 0.00 0.00 0.00 3.41
5 6 3.701205 ATATATGATTGCCTGCGTCCA 57.299 42.857 0.00 0.00 0.00 4.02
6 7 3.551890 CGTATATATGATTGCCTGCGTCC 59.448 47.826 0.00 0.00 0.00 4.79
7 8 3.000322 GCGTATATATGATTGCCTGCGTC 60.000 47.826 6.12 0.00 0.00 5.19
8 9 2.930040 GCGTATATATGATTGCCTGCGT 59.070 45.455 6.12 0.00 0.00 5.24
9 10 2.034591 CGCGTATATATGATTGCCTGCG 60.035 50.000 6.12 0.00 35.74 5.18
16 17 6.560711 TGAGTGTATGCGCGTATATATGATT 58.439 36.000 19.79 5.30 0.00 2.57
17 18 6.131544 TGAGTGTATGCGCGTATATATGAT 57.868 37.500 19.79 7.88 0.00 2.45
19 20 5.399596 GGATGAGTGTATGCGCGTATATATG 59.600 44.000 19.79 0.00 0.00 1.78
31 32 6.818142 TGTGTGTTCATAAGGATGAGTGTATG 59.182 38.462 0.00 0.00 43.03 2.39
44 45 2.139917 GGTCTGCGTGTGTGTTCATAA 58.860 47.619 0.00 0.00 0.00 1.90
47 48 1.522806 GGGTCTGCGTGTGTGTTCA 60.523 57.895 0.00 0.00 0.00 3.18
51 52 1.374252 GGTAGGGTCTGCGTGTGTG 60.374 63.158 0.00 0.00 0.00 3.82
52 53 1.119574 AAGGTAGGGTCTGCGTGTGT 61.120 55.000 0.00 0.00 0.00 3.72
53 54 0.034896 AAAGGTAGGGTCTGCGTGTG 59.965 55.000 0.00 0.00 0.00 3.82
54 55 1.274447 GTAAAGGTAGGGTCTGCGTGT 59.726 52.381 0.00 0.00 0.00 4.49
55 56 1.734707 CGTAAAGGTAGGGTCTGCGTG 60.735 57.143 0.00 0.00 0.00 5.34
56 57 0.529378 CGTAAAGGTAGGGTCTGCGT 59.471 55.000 0.00 0.00 0.00 5.24
57 58 0.813184 TCGTAAAGGTAGGGTCTGCG 59.187 55.000 0.00 0.00 0.00 5.18
58 59 1.471153 GCTCGTAAAGGTAGGGTCTGC 60.471 57.143 0.00 0.00 0.00 4.26
59 60 1.822990 TGCTCGTAAAGGTAGGGTCTG 59.177 52.381 0.00 0.00 0.00 3.51
70 71 4.272504 CAGTTTTTCAGAGGTGCTCGTAAA 59.727 41.667 0.00 0.00 35.36 2.01
71 72 3.807622 CAGTTTTTCAGAGGTGCTCGTAA 59.192 43.478 0.00 0.00 35.36 3.18
74 75 2.483876 TCAGTTTTTCAGAGGTGCTCG 58.516 47.619 0.00 0.00 35.36 5.03
75 76 3.003793 GGTTCAGTTTTTCAGAGGTGCTC 59.996 47.826 0.00 0.00 0.00 4.26
81 82 1.946768 TGCCGGTTCAGTTTTTCAGAG 59.053 47.619 1.90 0.00 0.00 3.35
84 85 4.075682 TGATATGCCGGTTCAGTTTTTCA 58.924 39.130 1.90 0.00 0.00 2.69
87 88 4.526970 AGATGATATGCCGGTTCAGTTTT 58.473 39.130 1.90 0.00 0.00 2.43
89 90 3.845781 AGATGATATGCCGGTTCAGTT 57.154 42.857 1.90 0.00 0.00 3.16
95 96 4.532126 TCAATCCTAAGATGATATGCCGGT 59.468 41.667 1.90 0.00 31.29 5.28
99 100 8.388484 ACTTTGTCAATCCTAAGATGATATGC 57.612 34.615 0.00 0.00 31.29 3.14
105 106 5.939883 TGGTGACTTTGTCAATCCTAAGATG 59.060 40.000 1.73 0.00 44.49 2.90
111 112 3.214328 GTGTGGTGACTTTGTCAATCCT 58.786 45.455 1.73 0.00 44.49 3.24
112 113 2.948979 TGTGTGGTGACTTTGTCAATCC 59.051 45.455 1.73 1.76 44.49 3.01
115 116 1.735018 CGTGTGTGGTGACTTTGTCAA 59.265 47.619 1.73 0.00 44.49 3.18
127 128 1.443872 GACTACGAGGCGTGTGTGG 60.444 63.158 2.33 0.00 41.39 4.17
143 144 3.191581 TGAGAGAAGATGTTCCTGTCGAC 59.808 47.826 9.11 9.11 32.48 4.20
149 150 4.321601 CGTTCAGTGAGAGAAGATGTTCCT 60.322 45.833 0.00 0.00 32.48 3.36
155 156 2.297315 TGTGCGTTCAGTGAGAGAAGAT 59.703 45.455 0.00 0.00 0.00 2.40
159 160 2.224042 ACAATGTGCGTTCAGTGAGAGA 60.224 45.455 13.97 0.00 36.97 3.10
163 164 0.858583 CGACAATGTGCGTTCAGTGA 59.141 50.000 13.97 0.00 36.97 3.41
204 205 5.064707 TCAAGTTCTGGCGCTTGTATTATTC 59.935 40.000 7.64 0.00 41.83 1.75
211 212 0.663153 GTTCAAGTTCTGGCGCTTGT 59.337 50.000 7.64 0.00 41.83 3.16
213 214 1.172812 GGGTTCAAGTTCTGGCGCTT 61.173 55.000 7.64 0.00 0.00 4.68
217 218 1.815003 CATCAGGGTTCAAGTTCTGGC 59.185 52.381 0.00 0.00 0.00 4.85
232 233 2.437281 AGGTGGTATCTCAAGCCATCAG 59.563 50.000 0.00 0.00 35.93 2.90
239 241 2.907042 GGGGGATAGGTGGTATCTCAAG 59.093 54.545 0.00 0.00 40.14 3.02
241 243 1.870327 TGGGGGATAGGTGGTATCTCA 59.130 52.381 0.00 0.00 40.14 3.27
243 245 2.699281 GGTTGGGGGATAGGTGGTATCT 60.699 54.545 0.00 0.00 38.14 1.98
251 253 0.178981 CTGCATGGTTGGGGGATAGG 60.179 60.000 0.00 0.00 0.00 2.57
255 257 1.928046 TAGCTGCATGGTTGGGGGA 60.928 57.895 1.02 0.00 0.00 4.81
267 270 1.128692 CGCAAACTAACCTGTAGCTGC 59.871 52.381 0.00 0.00 0.00 5.25
270 273 3.259064 TCATCGCAAACTAACCTGTAGC 58.741 45.455 0.00 0.00 0.00 3.58
277 280 6.975772 AGAATCTAGACTCATCGCAAACTAAC 59.024 38.462 3.70 0.00 0.00 2.34
280 283 5.126222 TCAGAATCTAGACTCATCGCAAACT 59.874 40.000 3.70 0.00 0.00 2.66
284 287 5.582689 TTTCAGAATCTAGACTCATCGCA 57.417 39.130 3.70 0.00 0.00 5.10
286 289 5.404968 GCCATTTCAGAATCTAGACTCATCG 59.595 44.000 3.70 0.00 0.00 3.84
318 321 2.425773 CAAGCACGCAACGCACTC 60.426 61.111 0.00 0.00 0.00 3.51
319 322 3.202001 ACAAGCACGCAACGCACT 61.202 55.556 0.00 0.00 0.00 4.40
320 323 3.018428 CACAAGCACGCAACGCAC 61.018 61.111 0.00 0.00 0.00 5.34
321 324 3.504273 ACACAAGCACGCAACGCA 61.504 55.556 0.00 0.00 0.00 5.24
322 325 3.018428 CACACAAGCACGCAACGC 61.018 61.111 0.00 0.00 0.00 4.84
323 326 3.018428 GCACACAAGCACGCAACG 61.018 61.111 0.00 0.00 0.00 4.10
324 327 2.101965 TGCACACAAGCACGCAAC 59.898 55.556 0.00 0.00 40.11 4.17
331 334 2.907910 AATCGAAGATGCACACAAGC 57.092 45.000 0.00 0.00 45.12 4.01
332 335 3.189080 TCCAAATCGAAGATGCACACAAG 59.811 43.478 0.00 0.00 45.12 3.16
333 336 3.145286 TCCAAATCGAAGATGCACACAA 58.855 40.909 0.00 0.00 45.12 3.33
334 337 2.777094 TCCAAATCGAAGATGCACACA 58.223 42.857 0.00 0.00 45.12 3.72
335 338 5.484173 TTATCCAAATCGAAGATGCACAC 57.516 39.130 0.00 0.00 45.12 3.82
336 339 6.698008 ATTTATCCAAATCGAAGATGCACA 57.302 33.333 0.00 0.00 45.12 4.57
337 340 7.800380 CACTATTTATCCAAATCGAAGATGCAC 59.200 37.037 0.00 0.00 45.12 4.57
338 341 7.714813 TCACTATTTATCCAAATCGAAGATGCA 59.285 33.333 0.00 0.00 45.12 3.96
339 342 8.087982 TCACTATTTATCCAAATCGAAGATGC 57.912 34.615 0.00 0.00 45.12 3.91
357 360 8.301002 GCTACTTCGAGAAGGATAATCACTATT 58.699 37.037 16.16 0.00 42.53 1.73
358 361 7.448777 TGCTACTTCGAGAAGGATAATCACTAT 59.551 37.037 16.16 0.00 42.53 2.12
359 362 6.771267 TGCTACTTCGAGAAGGATAATCACTA 59.229 38.462 16.16 0.00 42.53 2.74
360 363 5.594725 TGCTACTTCGAGAAGGATAATCACT 59.405 40.000 16.16 0.00 42.53 3.41
361 364 5.833082 TGCTACTTCGAGAAGGATAATCAC 58.167 41.667 16.16 0.00 42.53 3.06
362 365 6.040955 ACATGCTACTTCGAGAAGGATAATCA 59.959 38.462 16.16 5.26 42.53 2.57
363 366 6.451393 ACATGCTACTTCGAGAAGGATAATC 58.549 40.000 16.16 0.37 42.53 1.75
364 367 6.412362 ACATGCTACTTCGAGAAGGATAAT 57.588 37.500 16.16 3.02 42.53 1.28
365 368 5.854010 ACATGCTACTTCGAGAAGGATAA 57.146 39.130 16.16 0.87 42.53 1.75
366 369 5.854010 AACATGCTACTTCGAGAAGGATA 57.146 39.130 16.16 1.97 42.53 2.59
367 370 4.744795 AACATGCTACTTCGAGAAGGAT 57.255 40.909 16.16 0.26 42.53 3.24
368 371 4.245660 CAAACATGCTACTTCGAGAAGGA 58.754 43.478 16.16 7.63 42.53 3.36
369 372 3.997021 ACAAACATGCTACTTCGAGAAGG 59.003 43.478 16.16 1.98 42.53 3.46
370 373 4.667668 GCACAAACATGCTACTTCGAGAAG 60.668 45.833 10.97 10.97 42.62 2.85
371 374 3.186409 GCACAAACATGCTACTTCGAGAA 59.814 43.478 0.00 0.00 42.62 2.87
372 375 2.736721 GCACAAACATGCTACTTCGAGA 59.263 45.455 0.00 0.00 42.62 4.04
373 376 2.480037 TGCACAAACATGCTACTTCGAG 59.520 45.455 0.00 0.00 46.28 4.04
374 377 2.223144 GTGCACAAACATGCTACTTCGA 59.777 45.455 13.17 0.00 46.28 3.71
375 378 2.574322 GTGCACAAACATGCTACTTCG 58.426 47.619 13.17 0.00 46.28 3.79
376 379 2.223144 TCGTGCACAAACATGCTACTTC 59.777 45.455 18.64 0.00 46.28 3.01
377 380 2.217750 TCGTGCACAAACATGCTACTT 58.782 42.857 18.64 0.00 46.28 2.24
378 381 1.800586 CTCGTGCACAAACATGCTACT 59.199 47.619 18.64 0.00 46.28 2.57
379 382 1.798223 TCTCGTGCACAAACATGCTAC 59.202 47.619 18.64 0.00 46.28 3.58
380 383 2.162319 TCTCGTGCACAAACATGCTA 57.838 45.000 18.64 0.00 46.28 3.49
381 384 1.308047 TTCTCGTGCACAAACATGCT 58.692 45.000 18.64 0.00 46.28 3.79
382 385 1.980844 CATTCTCGTGCACAAACATGC 59.019 47.619 18.64 0.00 46.32 4.06
383 386 3.272439 ACATTCTCGTGCACAAACATG 57.728 42.857 18.64 14.81 0.00 3.21
384 387 4.065088 ACTACATTCTCGTGCACAAACAT 58.935 39.130 18.64 0.00 0.00 2.71
385 388 3.462982 ACTACATTCTCGTGCACAAACA 58.537 40.909 18.64 0.00 0.00 2.83
386 389 4.211374 AGAACTACATTCTCGTGCACAAAC 59.789 41.667 18.64 0.00 44.99 2.93
387 390 4.211164 CAGAACTACATTCTCGTGCACAAA 59.789 41.667 18.64 8.19 44.99 2.83
388 391 3.740832 CAGAACTACATTCTCGTGCACAA 59.259 43.478 18.64 3.87 44.99 3.33
389 392 3.317150 CAGAACTACATTCTCGTGCACA 58.683 45.455 18.64 3.15 44.99 4.57
390 393 2.092838 GCAGAACTACATTCTCGTGCAC 59.907 50.000 6.82 6.82 44.99 4.57
391 394 2.337583 GCAGAACTACATTCTCGTGCA 58.662 47.619 0.00 0.00 44.99 4.57
392 395 1.661112 GGCAGAACTACATTCTCGTGC 59.339 52.381 0.00 0.00 44.99 5.34
393 396 3.119316 AGAGGCAGAACTACATTCTCGTG 60.119 47.826 0.00 0.00 44.99 4.35
394 397 3.093057 AGAGGCAGAACTACATTCTCGT 58.907 45.455 0.00 0.00 44.99 4.18
395 398 3.701241 GAGAGGCAGAACTACATTCTCG 58.299 50.000 0.00 0.00 44.99 4.04
396 399 3.490078 CCGAGAGGCAGAACTACATTCTC 60.490 52.174 0.00 0.00 44.93 2.87
412 415 2.556189 AGTCATCATCCGATTCCGAGAG 59.444 50.000 0.00 0.00 38.22 3.20
413 416 2.587522 AGTCATCATCCGATTCCGAGA 58.412 47.619 0.00 0.00 38.22 4.04
414 417 3.377346 AAGTCATCATCCGATTCCGAG 57.623 47.619 0.00 0.00 38.22 4.63
415 418 3.118775 ACAAAGTCATCATCCGATTCCGA 60.119 43.478 0.00 0.00 38.22 4.55
416 419 3.198068 ACAAAGTCATCATCCGATTCCG 58.802 45.455 0.00 0.00 0.00 4.30
417 420 4.035675 GGAACAAAGTCATCATCCGATTCC 59.964 45.833 0.00 0.00 0.00 3.01
418 421 4.635765 TGGAACAAAGTCATCATCCGATTC 59.364 41.667 0.00 0.00 31.92 2.52
419 422 4.588899 TGGAACAAAGTCATCATCCGATT 58.411 39.130 0.00 0.00 31.92 3.34
420 423 4.220693 TGGAACAAAGTCATCATCCGAT 57.779 40.909 0.00 0.00 31.92 4.18
421 424 3.694043 TGGAACAAAGTCATCATCCGA 57.306 42.857 0.00 0.00 31.92 4.55
468 471 9.386010 TGAGCTACAAACTAAAGTTTTAACTCA 57.614 29.630 15.99 15.99 45.07 3.41
526 533 5.672321 GCGAAAATGAAAAACCAAGCACAAA 60.672 36.000 0.00 0.00 0.00 2.83
529 536 3.308323 TGCGAAAATGAAAAACCAAGCAC 59.692 39.130 0.00 0.00 0.00 4.40
530 537 3.525537 TGCGAAAATGAAAAACCAAGCA 58.474 36.364 0.00 0.00 0.00 3.91
532 539 3.803778 AGCTGCGAAAATGAAAAACCAAG 59.196 39.130 0.00 0.00 0.00 3.61
535 542 3.380142 TGAGCTGCGAAAATGAAAAACC 58.620 40.909 0.00 0.00 0.00 3.27
536 543 4.290155 TCTGAGCTGCGAAAATGAAAAAC 58.710 39.130 0.00 0.00 0.00 2.43
537 544 4.566545 TCTGAGCTGCGAAAATGAAAAA 57.433 36.364 0.00 0.00 0.00 1.94
543 563 4.022935 TGTTGATTTCTGAGCTGCGAAAAT 60.023 37.500 10.12 5.20 33.37 1.82
576 596 8.442605 TTTCGAAATCGTTCAATATTGTTTCC 57.557 30.769 14.97 1.75 40.80 3.13
616 636 4.795278 GCTCACCGCATTCTATTCTTTTTG 59.205 41.667 0.00 0.00 38.92 2.44
622 642 1.258982 CACGCTCACCGCATTCTATTC 59.741 52.381 0.00 0.00 41.76 1.75
625 645 1.153647 CCACGCTCACCGCATTCTA 60.154 57.895 0.00 0.00 41.76 2.10
705 736 8.344831 TCTGGAATTACAAATTATGAAGCATCG 58.655 33.333 0.00 0.00 0.00 3.84
780 816 3.901667 CGACGTAGGAGTTGCATTAAC 57.098 47.619 0.00 0.00 39.65 2.01
797 833 0.947180 TTGCTACGGGAAACTGCGAC 60.947 55.000 0.00 0.00 41.93 5.19
809 847 4.481930 TGATTCCAACTGTTTTGCTACG 57.518 40.909 0.00 0.00 0.00 3.51
863 901 3.424170 GCTTCAAGCGTCAATTGAGAGAC 60.424 47.826 8.80 0.00 37.91 3.36
879 917 2.957680 TGGCAATTCTGTGAAGCTTCAA 59.042 40.909 29.99 15.58 39.21 2.69
882 920 2.590821 AGTGGCAATTCTGTGAAGCTT 58.409 42.857 0.00 0.00 0.00 3.74
884 922 2.813754 TGTAGTGGCAATTCTGTGAAGC 59.186 45.455 0.00 0.00 0.00 3.86
1003 1043 4.218852 GTGAACCAGAGCTGAGTACTTACT 59.781 45.833 0.00 0.00 39.71 2.24
1004 1044 4.487019 GTGAACCAGAGCTGAGTACTTAC 58.513 47.826 0.00 0.00 0.00 2.34
1005 1045 3.510360 GGTGAACCAGAGCTGAGTACTTA 59.490 47.826 0.00 0.00 35.64 2.24
1006 1046 2.300437 GGTGAACCAGAGCTGAGTACTT 59.700 50.000 0.00 0.00 35.64 2.24
1345 1385 4.347453 GTCGTGGTGGGCGTACGT 62.347 66.667 17.90 0.00 38.80 3.57
1661 1701 3.064900 ACATGCTCAAGAAGGAGGAAC 57.935 47.619 0.00 0.00 38.78 3.62
1662 1702 3.072915 TCAACATGCTCAAGAAGGAGGAA 59.927 43.478 0.00 0.00 38.78 3.36
1812 1852 2.656069 GGGGTTCCTGAGCGTGCTA 61.656 63.158 0.00 0.00 0.00 3.49
1820 1860 2.853542 TGCAGCTGGGGTTCCTGA 60.854 61.111 17.12 0.00 34.32 3.86
2049 2089 4.367023 GGCGACACCACCGTGCTA 62.367 66.667 0.00 0.00 44.40 3.49
2133 2173 2.202440 CAGACGTACGACCGCCAG 60.202 66.667 24.41 0.00 0.00 4.85
2274 2318 0.830648 TGCTTGGACGAGGGATTAGG 59.169 55.000 0.00 0.00 0.00 2.69
2278 2322 0.909610 TTCCTGCTTGGACGAGGGAT 60.910 55.000 0.00 0.00 46.14 3.85
2279 2323 1.125093 TTTCCTGCTTGGACGAGGGA 61.125 55.000 0.00 0.00 46.14 4.20
2280 2324 0.250727 TTTTCCTGCTTGGACGAGGG 60.251 55.000 0.00 0.00 46.14 4.30
2282 2326 2.481952 CTCTTTTTCCTGCTTGGACGAG 59.518 50.000 0.00 0.97 46.14 4.18
2283 2327 2.104111 TCTCTTTTTCCTGCTTGGACGA 59.896 45.455 0.00 0.00 46.14 4.20
2323 2414 5.655090 TCTCGATGAGTTCTTGGTTGGTATA 59.345 40.000 0.00 0.00 0.00 1.47
2344 2435 3.664107 GCCATCTTTTTGGGGTTTTCTC 58.336 45.455 0.00 0.00 37.24 2.87
2355 2446 3.989817 GCAGATTTGTTCGCCATCTTTTT 59.010 39.130 0.00 0.00 0.00 1.94
2366 2457 0.449388 CCGGAGCTGCAGATTTGTTC 59.551 55.000 20.43 0.00 0.00 3.18
2451 2542 2.099756 CCAGCAGCCAGTTAAAATAGCC 59.900 50.000 0.00 0.00 0.00 3.93
2455 2546 1.273327 GTGCCAGCAGCCAGTTAAAAT 59.727 47.619 0.00 0.00 42.71 1.82
2460 2551 2.282040 GAGTGCCAGCAGCCAGTT 60.282 61.111 0.00 0.00 42.71 3.16
2462 2553 3.054503 GTGAGTGCCAGCAGCCAG 61.055 66.667 0.00 0.00 42.71 4.85
2463 2554 3.541950 GAGTGAGTGCCAGCAGCCA 62.542 63.158 0.00 0.00 42.71 4.75
2464 2555 2.745492 GAGTGAGTGCCAGCAGCC 60.745 66.667 0.00 0.00 42.71 4.85
2465 2556 2.745492 GGAGTGAGTGCCAGCAGC 60.745 66.667 0.00 0.00 44.14 5.25
2467 2558 2.848679 TGGGAGTGAGTGCCAGCA 60.849 61.111 0.00 0.00 42.96 4.41
2487 2593 3.117776 CCATGGATTCTTGATGGGAGTGA 60.118 47.826 5.56 0.00 34.14 3.41
2518 2624 1.136611 GTTTCGTCTGCTGCTGTTACG 60.137 52.381 12.40 12.40 34.99 3.18
2709 2831 2.378038 CTCTCTCTCCTCCAAGACAGG 58.622 57.143 0.00 0.00 0.00 4.00
2713 2835 0.633921 CCCCTCTCTCTCCTCCAAGA 59.366 60.000 0.00 0.00 0.00 3.02
2714 2836 0.633921 TCCCCTCTCTCTCCTCCAAG 59.366 60.000 0.00 0.00 0.00 3.61
2715 2837 0.633921 CTCCCCTCTCTCTCCTCCAA 59.366 60.000 0.00 0.00 0.00 3.53
2716 2838 0.253868 TCTCCCCTCTCTCTCCTCCA 60.254 60.000 0.00 0.00 0.00 3.86
2718 2840 0.478507 CCTCTCCCCTCTCTCTCCTC 59.521 65.000 0.00 0.00 0.00 3.71
2719 2841 0.047176 TCCTCTCCCCTCTCTCTCCT 59.953 60.000 0.00 0.00 0.00 3.69
2720 2842 0.478507 CTCCTCTCCCCTCTCTCTCC 59.521 65.000 0.00 0.00 0.00 3.71
2728 2850 3.024356 TCGCTCCTCCTCTCCCCT 61.024 66.667 0.00 0.00 0.00 4.79
2729 2851 2.520741 CTCGCTCCTCCTCTCCCC 60.521 72.222 0.00 0.00 0.00 4.81
2749 2871 0.622154 TCCTCCTCTCTCCCTCGTCT 60.622 60.000 0.00 0.00 0.00 4.18
2753 2875 0.106217 CACCTCCTCCTCTCTCCCTC 60.106 65.000 0.00 0.00 0.00 4.30
2754 2876 0.853586 ACACCTCCTCCTCTCTCCCT 60.854 60.000 0.00 0.00 0.00 4.20
2755 2877 0.686112 CACACCTCCTCCTCTCTCCC 60.686 65.000 0.00 0.00 0.00 4.30
2756 2878 0.040499 ACACACCTCCTCCTCTCTCC 59.960 60.000 0.00 0.00 0.00 3.71
2949 3074 0.749818 TTCCGTTCCAAGCTGCACAA 60.750 50.000 1.02 0.00 0.00 3.33
2967 3092 0.106918 TCAAGTTGAGGTTGGCCGTT 60.107 50.000 0.08 0.00 40.50 4.44
2968 3093 0.535102 CTCAAGTTGAGGTTGGCCGT 60.535 55.000 22.95 0.00 40.71 5.68
2969 3094 0.250295 TCTCAAGTTGAGGTTGGCCG 60.250 55.000 28.33 5.69 44.39 6.13
2970 3095 1.815003 CATCTCAAGTTGAGGTTGGCC 59.185 52.381 28.33 0.00 44.39 5.36
2971 3096 2.746362 CTCATCTCAAGTTGAGGTTGGC 59.254 50.000 28.33 0.00 44.39 4.52
2972 3097 4.252073 CTCTCATCTCAAGTTGAGGTTGG 58.748 47.826 28.33 17.61 44.39 3.77
2973 3098 4.252073 CCTCTCATCTCAAGTTGAGGTTG 58.748 47.826 28.33 24.37 44.39 3.77
2974 3099 3.307339 GCCTCTCATCTCAAGTTGAGGTT 60.307 47.826 28.33 15.99 44.39 3.50
2975 3100 2.235898 GCCTCTCATCTCAAGTTGAGGT 59.764 50.000 28.33 21.61 44.39 3.85
2976 3101 2.500910 AGCCTCTCATCTCAAGTTGAGG 59.499 50.000 28.33 15.94 44.39 3.86
2977 3102 3.523547 CAGCCTCTCATCTCAAGTTGAG 58.476 50.000 24.37 24.37 45.59 3.02
2978 3103 2.354503 GCAGCCTCTCATCTCAAGTTGA 60.355 50.000 5.25 5.25 0.00 3.18
3008 3133 7.014230 GCAGAACAGGCCTATTAATCCATTTTA 59.986 37.037 3.98 0.00 0.00 1.52
3233 3413 1.312371 ACTGCTGAGGAGTCGAGAGC 61.312 60.000 0.00 0.00 0.00 4.09
3239 3419 3.686916 AAGGTTTACTGCTGAGGAGTC 57.313 47.619 10.68 0.00 0.00 3.36
3244 3424 3.753797 GGAGGAAAAGGTTTACTGCTGAG 59.246 47.826 0.00 0.00 0.00 3.35
3253 3433 4.140782 ACCCATGTAAGGAGGAAAAGGTTT 60.141 41.667 0.00 0.00 0.00 3.27
3267 3447 4.991776 TGGAACAATCAAGACCCATGTAA 58.008 39.130 0.00 0.00 31.92 2.41
3340 3525 8.361889 TCATAATGTCAATTTGAGGCCATTATG 58.638 33.333 29.44 29.44 43.55 1.90
3347 3532 6.441093 TCTGTCATAATGTCAATTTGAGGC 57.559 37.500 0.00 0.00 0.00 4.70
3452 3638 2.815478 AGCATACACTTCTTAGCGAGC 58.185 47.619 0.00 0.00 0.00 5.03
3453 3639 4.033358 CCAAAGCATACACTTCTTAGCGAG 59.967 45.833 0.00 0.00 0.00 5.03
3458 3644 5.221843 ACTGGACCAAAGCATACACTTCTTA 60.222 40.000 0.00 0.00 0.00 2.10
3464 3650 3.317993 ACAAACTGGACCAAAGCATACAC 59.682 43.478 0.00 0.00 0.00 2.90
3465 3651 3.561143 ACAAACTGGACCAAAGCATACA 58.439 40.909 0.00 0.00 0.00 2.29
3478 3664 3.486841 CGCAACATTTTCTGACAAACTGG 59.513 43.478 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.