Multiple sequence alignment - TraesCS3A01G497900

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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 TraesCS3A01G497900 chr3A 100.000 3965 0 0 1 3965 724027233 724023269 0.000000e+00 7323.0
1 TraesCS3A01G497900 chr3A 100.000 1807 0 0 4150 5956 724023084 724021278 0.000000e+00 3338.0
2 TraesCS3A01G497900 chr3A 87.099 1589 163 24 4266 5843 723661413 723659856 0.000000e+00 1760.0
3 TraesCS3A01G497900 chr3A 97.603 292 7 0 253 544 733914174 733914465 8.910000e-138 501.0
4 TraesCS3A01G497900 chr3A 96.689 302 7 3 243 543 733978315 733978016 3.210000e-137 499.0
5 TraesCS3A01G497900 chr3A 96.959 296 8 1 253 547 733909344 733909639 4.150000e-136 496.0
6 TraesCS3A01G497900 chr3A 89.492 295 28 3 3661 3955 723662068 723661777 2.620000e-98 370.0
7 TraesCS3A01G497900 chr3A 77.323 269 40 14 1339 1603 204861042 204861293 8.050000e-29 139.0
8 TraesCS3A01G497900 chr3D 90.534 3465 236 57 542 3955 592572551 592575974 0.000000e+00 4497.0
9 TraesCS3A01G497900 chr3D 94.353 1753 73 10 4172 5909 592576653 592578394 0.000000e+00 2665.0
10 TraesCS3A01G497900 chr3D 86.096 1647 173 34 4191 5826 592608366 592609967 0.000000e+00 1722.0
11 TraesCS3A01G497900 chr3D 89.456 294 25 4 3662 3955 592607784 592608071 3.390000e-97 366.0
12 TraesCS3A01G497900 chr3D 88.583 254 25 2 1 253 592572301 592572551 7.500000e-79 305.0
13 TraesCS3A01G497900 chr3D 75.380 329 41 24 1239 1552 471075403 471075100 8.110000e-24 122.0
14 TraesCS3A01G497900 chr3D 100.000 35 0 0 3157 3191 592575208 592575242 1.390000e-06 65.8
15 TraesCS3A01G497900 chr3B 89.085 3463 251 67 591 3955 794596817 794593384 0.000000e+00 4183.0
16 TraesCS3A01G497900 chr3B 89.698 2582 218 26 599 3156 794843951 794841394 0.000000e+00 3251.0
17 TraesCS3A01G497900 chr3B 94.010 1636 82 8 4172 5799 794840207 794838580 0.000000e+00 2464.0
18 TraesCS3A01G497900 chr3B 93.440 1433 67 10 4172 5597 794593173 794591761 0.000000e+00 2100.0
19 TraesCS3A01G497900 chr3B 88.528 985 95 12 4260 5240 794544101 794543131 0.000000e+00 1177.0
20 TraesCS3A01G497900 chr3B 93.196 779 30 10 3181 3955 794841177 794840418 0.000000e+00 1123.0
21 TraesCS3A01G497900 chr3B 88.449 303 31 3 3655 3955 794544761 794544461 4.390000e-96 363.0
22 TraesCS3A01G497900 chr3B 86.561 253 29 3 1 253 794844420 794844173 2.110000e-69 274.0
23 TraesCS3A01G497900 chr3B 83.133 83 10 4 2484 2564 794547703 794547623 8.280000e-09 73.1
24 TraesCS3A01G497900 chrUn 98.969 291 3 0 253 543 13405606 13405896 6.840000e-144 521.0
25 TraesCS3A01G497900 chr7A 97.595 291 7 0 253 543 134023841 134024131 3.210000e-137 499.0
26 TraesCS3A01G497900 chr6A 97.595 291 7 0 253 543 472393939 472393649 3.210000e-137 499.0
27 TraesCS3A01G497900 chr6A 96.656 299 10 0 245 543 207632848 207632550 1.150000e-136 497.0
28 TraesCS3A01G497900 chr6B 96.346 301 11 0 244 544 504368178 504367878 4.150000e-136 496.0
29 TraesCS3A01G497900 chr6B 80.612 196 28 9 1236 1424 239339208 239339400 6.220000e-30 143.0
30 TraesCS3A01G497900 chr1A 96.346 301 9 2 253 551 70115389 70115089 1.490000e-135 494.0
31 TraesCS3A01G497900 chr1A 83.770 191 24 4 1 185 466339639 466339828 2.210000e-39 174.0
32 TraesCS3A01G497900 chr1A 81.176 170 22 7 1320 1484 120023413 120023577 1.740000e-25 128.0
33 TraesCS3A01G497900 chr1A 86.765 68 9 0 122 189 272436279 272436212 6.400000e-10 76.8
34 TraesCS3A01G497900 chr7B 80.263 380 50 15 1239 1602 667288111 667287741 4.580000e-66 263.0
35 TraesCS3A01G497900 chr2D 81.004 279 37 11 1336 1610 611218644 611218910 2.180000e-49 207.0
36 TraesCS3A01G497900 chr1D 76.190 357 51 24 1258 1603 112871776 112872109 2.220000e-34 158.0
37 TraesCS3A01G497900 chr5A 79.191 173 25 7 1234 1402 549948810 549948645 6.310000e-20 110.0
38 TraesCS3A01G497900 chr7D 92.727 55 4 0 2604 2658 249952808 249952862 4.950000e-11 80.5
39 TraesCS3A01G497900 chr6D 100.000 29 0 0 1080 1108 108385384 108385356 3.000000e-03 54.7


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 TraesCS3A01G497900 chr3A 724021278 724027233 5955 True 5330.5 7323 100.000000 1 5956 2 chr3A.!!$R3 5955
1 TraesCS3A01G497900 chr3A 723659856 723662068 2212 True 1065.0 1760 88.295500 3661 5843 2 chr3A.!!$R2 2182
2 TraesCS3A01G497900 chr3D 592572301 592578394 6093 False 1883.2 4497 93.367500 1 5909 4 chr3D.!!$F1 5908
3 TraesCS3A01G497900 chr3D 592607784 592609967 2183 False 1044.0 1722 87.776000 3662 5826 2 chr3D.!!$F2 2164
4 TraesCS3A01G497900 chr3B 794591761 794596817 5056 True 3141.5 4183 91.262500 591 5597 2 chr3B.!!$R2 5006
5 TraesCS3A01G497900 chr3B 794838580 794844420 5840 True 1778.0 3251 90.866250 1 5799 4 chr3B.!!$R3 5798
6 TraesCS3A01G497900 chr3B 794543131 794547703 4572 True 537.7 1177 86.703333 2484 5240 3 chr3B.!!$R1 2756

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
287 288 0.030101 CACGTTGTTGCGGGAATGTT 59.970 50.0 0.0 0.0 37.48 2.71 F
1301 1472 0.251297 AGCCATGCAACTGCCACTTA 60.251 50.0 0.0 0.0 41.18 2.24 F
2292 2484 0.313672 TTGCGTTGCAGGATTTGGTC 59.686 50.0 0.0 0.0 40.61 4.02 F
3796 6616 0.746204 GCCTGCCTTTCTGGACTAGC 60.746 60.0 0.0 0.0 38.35 3.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1560 1731 0.034337 TCTGTGCGGACCTTGGTAAC 59.966 55.0 4.04 0.0 0.0 2.50 R
2370 2562 0.321671 TCCGAGCAAGAGTGAAAGGG 59.678 55.0 0.00 0.0 0.0 3.95 R
4154 6974 0.546267 ATCAGTGGCAGAGACAGGGT 60.546 55.0 0.00 0.0 0.0 4.34 R
5361 8731 0.323629 CCCTGCCTCCGTCTTTGTAA 59.676 55.0 0.00 0.0 0.0 2.41 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
32 33 2.733956 TGTTGTTTTTGTGAGGGCTCT 58.266 42.857 0.00 0.00 0.00 4.09
34 35 4.469657 TGTTGTTTTTGTGAGGGCTCTAT 58.530 39.130 0.00 0.00 0.00 1.98
52 53 6.055588 GCTCTATGAAGGTTATTTGTGCCTA 58.944 40.000 0.00 0.00 31.43 3.93
60 61 7.923878 TGAAGGTTATTTGTGCCTAAAACTTTC 59.076 33.333 0.00 0.00 31.43 2.62
100 101 9.312904 TCTTTGATAAAGTTTGATCCCTGAAAT 57.687 29.630 0.00 0.00 39.52 2.17
246 247 2.957902 ATCCGCGTCCCCTCCCATTA 62.958 60.000 4.92 0.00 0.00 1.90
252 253 2.546899 CGTCCCCTCCCATTATGGATA 58.453 52.381 13.63 0.00 40.96 2.59
253 254 2.236395 CGTCCCCTCCCATTATGGATAC 59.764 54.545 13.63 0.91 40.96 2.24
254 255 3.532102 GTCCCCTCCCATTATGGATACT 58.468 50.000 13.63 0.00 40.96 2.12
255 256 4.695606 GTCCCCTCCCATTATGGATACTA 58.304 47.826 13.63 0.00 40.96 1.82
256 257 4.717280 GTCCCCTCCCATTATGGATACTAG 59.283 50.000 13.63 2.22 40.96 2.57
257 258 4.615201 TCCCCTCCCATTATGGATACTAGA 59.385 45.833 13.63 0.00 40.96 2.43
258 259 5.261181 TCCCCTCCCATTATGGATACTAGAT 59.739 44.000 13.63 0.00 40.96 1.98
259 260 5.367937 CCCCTCCCATTATGGATACTAGATG 59.632 48.000 13.63 0.00 40.96 2.90
260 261 6.205298 CCCTCCCATTATGGATACTAGATGA 58.795 44.000 13.63 0.00 40.96 2.92
261 262 6.848631 CCCTCCCATTATGGATACTAGATGAT 59.151 42.308 13.63 0.00 40.96 2.45
262 263 7.202075 CCCTCCCATTATGGATACTAGATGATG 60.202 44.444 13.63 0.00 40.96 3.07
263 264 7.129457 TCCCATTATGGATACTAGATGATGC 57.871 40.000 13.63 0.00 40.96 3.91
264 265 6.100279 TCCCATTATGGATACTAGATGATGCC 59.900 42.308 13.63 0.00 40.96 4.40
265 266 6.294473 CCATTATGGATACTAGATGATGCCC 58.706 44.000 5.05 0.00 40.96 5.36
266 267 5.957771 TTATGGATACTAGATGATGCCCC 57.042 43.478 0.00 0.00 37.61 5.80
267 268 2.179427 TGGATACTAGATGATGCCCCG 58.821 52.381 0.00 0.00 37.61 5.73
268 269 1.134670 GGATACTAGATGATGCCCCGC 60.135 57.143 0.00 0.00 0.00 6.13
269 270 1.550524 GATACTAGATGATGCCCCGCA 59.449 52.381 0.00 0.00 44.86 5.69
270 271 0.679505 TACTAGATGATGCCCCGCAC 59.320 55.000 0.00 0.00 43.04 5.34
271 272 1.665916 CTAGATGATGCCCCGCACG 60.666 63.158 0.00 0.00 43.04 5.34
272 273 2.369257 CTAGATGATGCCCCGCACGT 62.369 60.000 0.00 0.00 43.04 4.49
273 274 1.966901 TAGATGATGCCCCGCACGTT 61.967 55.000 0.00 0.00 43.04 3.99
274 275 3.112126 GATGATGCCCCGCACGTTG 62.112 63.158 0.00 0.00 43.04 4.10
275 276 3.918253 ATGATGCCCCGCACGTTGT 62.918 57.895 0.00 0.00 43.04 3.32
276 277 3.361977 GATGCCCCGCACGTTGTT 61.362 61.111 0.00 0.00 43.04 2.83
277 278 3.609214 GATGCCCCGCACGTTGTTG 62.609 63.158 0.00 0.00 43.04 3.33
284 285 2.642700 GCACGTTGTTGCGGGAAT 59.357 55.556 0.00 0.00 37.48 3.01
285 286 1.729131 GCACGTTGTTGCGGGAATG 60.729 57.895 0.00 0.00 37.48 2.67
286 287 1.652012 CACGTTGTTGCGGGAATGT 59.348 52.632 0.00 0.00 37.48 2.71
287 288 0.030101 CACGTTGTTGCGGGAATGTT 59.970 50.000 0.00 0.00 37.48 2.71
288 289 0.741915 ACGTTGTTGCGGGAATGTTT 59.258 45.000 0.00 0.00 35.98 2.83
289 290 1.268845 ACGTTGTTGCGGGAATGTTTC 60.269 47.619 0.00 0.00 35.98 2.78
343 344 8.859090 TGGAACATGAATTCTTGAAACAATAGT 58.141 29.630 23.84 0.04 0.00 2.12
344 345 9.696917 GGAACATGAATTCTTGAAACAATAGTT 57.303 29.630 23.84 7.73 40.40 2.24
408 409 6.612247 AATGGAATTTTACATGCATGCATG 57.388 33.333 44.22 44.22 46.33 4.06
417 418 2.804647 CATGCATGCATGTTGTAGTGG 58.195 47.619 40.30 20.25 46.20 4.00
418 419 2.197283 TGCATGCATGTTGTAGTGGA 57.803 45.000 26.79 0.00 0.00 4.02
419 420 2.725637 TGCATGCATGTTGTAGTGGAT 58.274 42.857 26.79 0.00 0.00 3.41
420 421 3.090790 TGCATGCATGTTGTAGTGGATT 58.909 40.909 26.79 0.00 0.00 3.01
421 422 3.510753 TGCATGCATGTTGTAGTGGATTT 59.489 39.130 26.79 0.00 0.00 2.17
422 423 4.021280 TGCATGCATGTTGTAGTGGATTTT 60.021 37.500 26.79 0.00 0.00 1.82
423 424 4.931002 GCATGCATGTTGTAGTGGATTTTT 59.069 37.500 26.79 0.00 0.00 1.94
424 425 6.098679 GCATGCATGTTGTAGTGGATTTTTA 58.901 36.000 26.79 0.00 0.00 1.52
425 426 6.589523 GCATGCATGTTGTAGTGGATTTTTAA 59.410 34.615 26.79 0.00 0.00 1.52
426 427 7.278424 GCATGCATGTTGTAGTGGATTTTTAAT 59.722 33.333 26.79 0.00 0.00 1.40
427 428 9.800433 CATGCATGTTGTAGTGGATTTTTAATA 57.200 29.630 18.91 0.00 0.00 0.98
429 430 9.800433 TGCATGTTGTAGTGGATTTTTAATATG 57.200 29.630 0.00 0.00 0.00 1.78
430 431 8.755018 GCATGTTGTAGTGGATTTTTAATATGC 58.245 33.333 0.00 0.00 35.29 3.14
431 432 9.800433 CATGTTGTAGTGGATTTTTAATATGCA 57.200 29.630 0.00 0.00 0.00 3.96
450 451 3.770263 CATAGTTGCATGTTGAGGTGG 57.230 47.619 0.00 0.00 0.00 4.61
451 452 3.346315 CATAGTTGCATGTTGAGGTGGA 58.654 45.455 0.00 0.00 0.00 4.02
452 453 1.609208 AGTTGCATGTTGAGGTGGAC 58.391 50.000 0.00 0.00 0.00 4.02
453 454 0.598065 GTTGCATGTTGAGGTGGACC 59.402 55.000 0.00 0.00 0.00 4.46
465 466 3.806949 AGGTGGACCTTTTCTTATGCA 57.193 42.857 0.00 0.00 46.09 3.96
466 467 4.322057 AGGTGGACCTTTTCTTATGCAT 57.678 40.909 3.79 3.79 46.09 3.96
467 468 4.019174 AGGTGGACCTTTTCTTATGCATG 58.981 43.478 10.16 0.00 46.09 4.06
468 469 3.763897 GGTGGACCTTTTCTTATGCATGT 59.236 43.478 10.16 0.00 0.00 3.21
469 470 4.220602 GGTGGACCTTTTCTTATGCATGTT 59.779 41.667 10.16 0.00 0.00 2.71
470 471 5.163513 GTGGACCTTTTCTTATGCATGTTG 58.836 41.667 10.16 0.00 0.00 3.33
471 472 5.048083 GTGGACCTTTTCTTATGCATGTTGA 60.048 40.000 10.16 1.61 0.00 3.18
472 473 5.538053 TGGACCTTTTCTTATGCATGTTGAA 59.462 36.000 10.16 8.00 0.00 2.69
473 474 6.211184 TGGACCTTTTCTTATGCATGTTGAAT 59.789 34.615 10.16 0.00 0.00 2.57
474 475 6.532657 GGACCTTTTCTTATGCATGTTGAATG 59.467 38.462 10.16 6.97 0.00 2.67
475 476 7.230849 ACCTTTTCTTATGCATGTTGAATGA 57.769 32.000 10.16 0.00 0.00 2.57
476 477 7.844009 ACCTTTTCTTATGCATGTTGAATGAT 58.156 30.769 10.16 0.00 0.00 2.45
477 478 7.762615 ACCTTTTCTTATGCATGTTGAATGATG 59.237 33.333 10.16 3.61 0.00 3.07
478 479 7.977293 CCTTTTCTTATGCATGTTGAATGATGA 59.023 33.333 10.16 0.00 0.00 2.92
479 480 8.920509 TTTTCTTATGCATGTTGAATGATGAG 57.079 30.769 10.16 0.00 0.00 2.90
480 481 6.628919 TCTTATGCATGTTGAATGATGAGG 57.371 37.500 10.16 0.00 0.00 3.86
481 482 6.124340 TCTTATGCATGTTGAATGATGAGGT 58.876 36.000 10.16 0.00 0.00 3.85
482 483 4.649088 ATGCATGTTGAATGATGAGGTG 57.351 40.909 0.00 0.00 0.00 4.00
483 484 2.756207 TGCATGTTGAATGATGAGGTGG 59.244 45.455 0.00 0.00 0.00 4.61
484 485 2.480759 GCATGTTGAATGATGAGGTGGC 60.481 50.000 0.00 0.00 0.00 5.01
485 486 2.583024 TGTTGAATGATGAGGTGGCA 57.417 45.000 0.00 0.00 0.00 4.92
486 487 3.090210 TGTTGAATGATGAGGTGGCAT 57.910 42.857 0.00 0.00 0.00 4.40
487 488 2.756207 TGTTGAATGATGAGGTGGCATG 59.244 45.455 0.00 0.00 0.00 4.06
488 489 1.395635 TGAATGATGAGGTGGCATGC 58.604 50.000 9.90 9.90 0.00 4.06
489 490 1.064240 TGAATGATGAGGTGGCATGCT 60.064 47.619 18.92 0.00 0.00 3.79
490 491 2.029623 GAATGATGAGGTGGCATGCTT 58.970 47.619 18.92 0.00 0.00 3.91
491 492 1.399714 ATGATGAGGTGGCATGCTTG 58.600 50.000 18.92 0.00 0.00 4.01
504 505 3.842732 CATGCTTGCATGTTGAGAGAA 57.157 42.857 23.00 0.00 0.00 2.87
505 506 4.168922 CATGCTTGCATGTTGAGAGAAA 57.831 40.909 23.00 0.00 0.00 2.52
506 507 4.744570 CATGCTTGCATGTTGAGAGAAAT 58.255 39.130 23.00 0.00 0.00 2.17
507 508 5.886992 CATGCTTGCATGTTGAGAGAAATA 58.113 37.500 23.00 0.00 0.00 1.40
508 509 6.504398 CATGCTTGCATGTTGAGAGAAATAT 58.496 36.000 23.00 0.00 0.00 1.28
509 510 6.127810 TGCTTGCATGTTGAGAGAAATATC 57.872 37.500 1.14 0.00 0.00 1.63
510 511 5.884232 TGCTTGCATGTTGAGAGAAATATCT 59.116 36.000 1.14 0.00 39.10 1.98
511 512 6.376299 TGCTTGCATGTTGAGAGAAATATCTT 59.624 34.615 1.14 0.00 35.54 2.40
512 513 7.553760 TGCTTGCATGTTGAGAGAAATATCTTA 59.446 33.333 1.14 0.00 35.54 2.10
513 514 8.068977 GCTTGCATGTTGAGAGAAATATCTTAG 58.931 37.037 1.14 0.00 35.54 2.18
514 515 9.107177 CTTGCATGTTGAGAGAAATATCTTAGT 57.893 33.333 0.00 0.00 35.54 2.24
515 516 8.429493 TGCATGTTGAGAGAAATATCTTAGTG 57.571 34.615 0.00 0.00 35.54 2.74
516 517 7.496920 TGCATGTTGAGAGAAATATCTTAGTGG 59.503 37.037 0.00 0.00 35.54 4.00
517 518 7.041508 GCATGTTGAGAGAAATATCTTAGTGGG 60.042 40.741 0.00 0.00 35.54 4.61
518 519 6.889198 TGTTGAGAGAAATATCTTAGTGGGG 58.111 40.000 0.00 0.00 35.54 4.96
519 520 6.126768 TGTTGAGAGAAATATCTTAGTGGGGG 60.127 42.308 0.00 0.00 35.54 5.40
520 521 4.348168 TGAGAGAAATATCTTAGTGGGGGC 59.652 45.833 0.00 0.00 35.54 5.80
521 522 4.571951 AGAGAAATATCTTAGTGGGGGCT 58.428 43.478 0.00 0.00 35.54 5.19
522 523 5.727630 AGAGAAATATCTTAGTGGGGGCTA 58.272 41.667 0.00 0.00 35.54 3.93
523 524 5.782845 AGAGAAATATCTTAGTGGGGGCTAG 59.217 44.000 0.00 0.00 35.54 3.42
524 525 4.287326 AGAAATATCTTAGTGGGGGCTAGC 59.713 45.833 6.04 6.04 29.15 3.42
525 526 3.569135 ATATCTTAGTGGGGGCTAGCT 57.431 47.619 15.72 0.00 0.00 3.32
526 527 4.694280 ATATCTTAGTGGGGGCTAGCTA 57.306 45.455 15.72 0.00 0.00 3.32
527 528 3.569135 ATCTTAGTGGGGGCTAGCTAT 57.431 47.619 15.72 0.00 0.00 2.97
528 529 3.346146 TCTTAGTGGGGGCTAGCTATT 57.654 47.619 15.72 0.00 0.00 1.73
529 530 3.665443 TCTTAGTGGGGGCTAGCTATTT 58.335 45.455 15.72 0.00 0.00 1.40
530 531 4.823107 TCTTAGTGGGGGCTAGCTATTTA 58.177 43.478 15.72 0.00 0.00 1.40
531 532 4.838986 TCTTAGTGGGGGCTAGCTATTTAG 59.161 45.833 15.72 2.91 0.00 1.85
532 533 3.346146 AGTGGGGGCTAGCTATTTAGA 57.654 47.619 15.72 0.00 0.00 2.10
533 534 3.875571 AGTGGGGGCTAGCTATTTAGAT 58.124 45.455 15.72 0.00 0.00 1.98
534 535 5.024803 AGTGGGGGCTAGCTATTTAGATA 57.975 43.478 15.72 0.00 0.00 1.98
535 536 5.604752 AGTGGGGGCTAGCTATTTAGATAT 58.395 41.667 15.72 0.00 0.00 1.63
536 537 6.753134 AGTGGGGGCTAGCTATTTAGATATA 58.247 40.000 15.72 0.00 0.00 0.86
537 538 6.841755 AGTGGGGGCTAGCTATTTAGATATAG 59.158 42.308 15.72 0.00 0.00 1.31
538 539 6.839657 GTGGGGGCTAGCTATTTAGATATAGA 59.160 42.308 15.72 0.00 31.10 1.98
539 540 7.344871 GTGGGGGCTAGCTATTTAGATATAGAA 59.655 40.741 15.72 0.00 31.10 2.10
540 541 7.565398 TGGGGGCTAGCTATTTAGATATAGAAG 59.435 40.741 15.72 0.00 31.10 2.85
620 786 8.702819 TCATCCATATAATCCTCATCTCATGAC 58.297 37.037 0.00 0.00 35.06 3.06
643 809 7.064134 TGACGTATTTTGAGTGCCAATACTTAG 59.936 37.037 0.00 0.00 33.11 2.18
725 891 1.348696 TGGTTCCCTCCTTCGTAAACC 59.651 52.381 0.00 0.00 37.31 3.27
756 922 4.017130 ACCTGAAAATTATTCCTGCCTCCT 60.017 41.667 0.00 0.00 0.00 3.69
855 1021 2.695666 ACTCCATCAATCCACCGAGTAG 59.304 50.000 0.00 0.00 0.00 2.57
894 1062 6.266323 CGTAGTGACTAGTGATGCAATTAGT 58.734 40.000 0.00 0.00 0.00 2.24
1015 1184 2.448453 TGTTGAAACCGGAGTTTGGTT 58.552 42.857 9.46 0.00 46.25 3.67
1040 1209 2.163010 CCCGATGCATATCAATTCAGGC 59.837 50.000 0.00 0.00 32.67 4.85
1043 1212 4.331992 CCGATGCATATCAATTCAGGCTAG 59.668 45.833 0.00 0.00 32.67 3.42
1046 1215 5.557576 TGCATATCAATTCAGGCTAGTCT 57.442 39.130 0.00 0.00 0.00 3.24
1072 1243 4.392138 CCACGAAAGAGTGTATTCCCTTTC 59.608 45.833 0.00 0.00 40.33 2.62
1144 1315 2.431057 ACGGGTTGTCTATCTCATGTCC 59.569 50.000 0.00 0.00 0.00 4.02
1148 1319 4.649674 GGGTTGTCTATCTCATGTCCTGTA 59.350 45.833 0.00 0.00 0.00 2.74
1152 1323 5.847304 TGTCTATCTCATGTCCTGTATTGC 58.153 41.667 0.00 0.00 0.00 3.56
1167 1338 5.237996 CCTGTATTGCTGTATCAACCATCTG 59.762 44.000 0.00 0.00 0.00 2.90
1198 1369 5.236478 ACAACTCGTTTACAAGTCTTCATGG 59.764 40.000 0.00 0.00 0.00 3.66
1212 1383 3.507233 TCTTCATGGAAATGACAGGCAAC 59.493 43.478 0.00 0.00 0.00 4.17
1241 1412 4.212214 CGGCTTGCTCTTTAGAATGTATCC 59.788 45.833 0.00 0.00 0.00 2.59
1266 1437 7.391833 CCTCTATTCCTAAATTGCTACAATCCC 59.608 40.741 0.00 0.00 0.00 3.85
1301 1472 0.251297 AGCCATGCAACTGCCACTTA 60.251 50.000 0.00 0.00 41.18 2.24
1394 1565 8.735692 TCAATTCATGCATGTTAGTCATAAGA 57.264 30.769 25.43 8.81 34.67 2.10
1537 1708 8.028938 TGCTTTCCATTAGTTTTAGATGCTTTC 58.971 33.333 0.00 0.00 0.00 2.62
1560 1731 5.804473 TCGTGGCAACTATTTATGCATTTTG 59.196 36.000 3.54 0.83 44.32 2.44
1571 1742 9.301153 CTATTTATGCATTTTGTTACCAAGGTC 57.699 33.333 3.54 0.00 0.00 3.85
1574 1745 2.924880 GCATTTTGTTACCAAGGTCCGC 60.925 50.000 0.00 0.00 0.00 5.54
1575 1746 2.054232 TTTTGTTACCAAGGTCCGCA 57.946 45.000 0.00 0.00 0.00 5.69
1636 1807 1.203994 GACCGCAAACACTAGGAGCTA 59.796 52.381 0.00 0.00 0.00 3.32
1664 1835 4.230745 TCAATTAAGTAGGGGGAACTGC 57.769 45.455 0.00 0.00 0.00 4.40
1670 1841 1.710809 AGTAGGGGGAACTGCACATTT 59.289 47.619 0.00 0.00 0.00 2.32
1672 1843 0.542702 AGGGGGAACTGCACATTTGG 60.543 55.000 0.00 0.00 0.00 3.28
1782 1953 2.247267 GACGCGTCGGTGGTTTTG 59.753 61.111 25.19 0.00 0.00 2.44
1784 1973 2.039062 GACGCGTCGGTGGTTTTGTT 62.039 55.000 25.19 0.00 0.00 2.83
1787 1976 0.917939 GCGTCGGTGGTTTTGTTTTG 59.082 50.000 0.00 0.00 0.00 2.44
1799 1988 6.094742 GTGGTTTTGTTTTGGGTGATTCATTT 59.905 34.615 0.00 0.00 0.00 2.32
1851 2042 6.318648 TGGTGCTTTGTACTTATGATGAATCC 59.681 38.462 0.00 0.00 0.00 3.01
1861 2052 6.421485 ACTTATGATGAATCCTTGCAAGAGT 58.579 36.000 28.05 14.62 0.00 3.24
1907 2098 1.544724 GATGTTAGGCTTTGGGCACA 58.455 50.000 0.00 0.00 44.01 4.57
1908 2099 1.202348 GATGTTAGGCTTTGGGCACAC 59.798 52.381 0.00 0.00 44.01 3.82
1941 2133 3.698040 CTGGATTAAGCCAACATTCTGCT 59.302 43.478 14.45 0.00 37.52 4.24
1953 2145 2.196997 ATTCTGCTGGCGGGTTAGCA 62.197 55.000 0.00 0.00 46.79 3.49
1965 2157 2.741553 CGGGTTAGCATGTGCATGACTA 60.742 50.000 15.53 12.37 45.16 2.59
1992 2184 1.718280 AGTATCCCCATTCCGTCTCC 58.282 55.000 0.00 0.00 0.00 3.71
2062 2254 9.132923 CTTGTAATGGTACTACTCTATTCCTCA 57.867 37.037 0.00 0.00 0.00 3.86
2086 2278 5.160641 TGACAGTGAAAAGTGCAAACTTTC 58.839 37.500 0.00 6.21 38.82 2.62
2088 2280 4.220602 ACAGTGAAAAGTGCAAACTTTCCT 59.779 37.500 0.00 7.36 38.82 3.36
2194 2386 9.891828 GAAACATGTTCACACTATTTACATCAA 57.108 29.630 12.39 0.00 0.00 2.57
2201 2393 8.946085 GTTCACACTATTTACATCAAATCCTCA 58.054 33.333 0.00 0.00 37.93 3.86
2229 2421 6.695278 CGAAATCACAGAAAGAGATACTCTCC 59.305 42.308 1.71 0.00 44.42 3.71
2240 2432 0.535553 ATACTCTCCCGAGGCGTCTC 60.536 60.000 7.05 7.05 41.71 3.36
2260 2452 3.576982 CTCGGTGGAGGCTTATATTACCA 59.423 47.826 0.00 0.00 36.61 3.25
2276 2468 1.098050 ACCAAGAAGATCGCCATTGC 58.902 50.000 0.00 0.00 0.00 3.56
2292 2484 0.313672 TTGCGTTGCAGGATTTGGTC 59.686 50.000 0.00 0.00 40.61 4.02
2316 2508 3.746492 CCAAAGTCCTTCGATTTCGTTCT 59.254 43.478 0.00 0.00 40.80 3.01
2319 2511 4.252971 AGTCCTTCGATTTCGTTCTTGA 57.747 40.909 0.00 0.00 40.80 3.02
2412 2604 5.125100 CACCATGCAGTGTATTTTTCACT 57.875 39.130 0.00 0.00 45.43 3.41
2471 2663 2.416836 CGACAAGGTCCTTATGCTCGAA 60.417 50.000 3.08 0.00 0.00 3.71
2538 2732 5.803020 TTTTTGCGGTGCAGTTTTATTTT 57.197 30.435 0.00 0.00 40.61 1.82
2544 2738 4.794655 GCGGTGCAGTTTTATTTTTGAGGA 60.795 41.667 0.00 0.00 0.00 3.71
2570 2764 6.092122 TGACCTAGTTTGCTTATTCGAATGTG 59.908 38.462 20.87 13.31 0.00 3.21
2670 2866 1.070786 GGCCCAGACTGTTCGTGAA 59.929 57.895 0.93 0.00 0.00 3.18
2814 3013 5.182380 TGTTCGGTGTCTTTTCTTCAAAAGT 59.818 36.000 7.01 0.00 46.10 2.66
2997 3197 7.971183 TTTAAAAATCACCCTGCATTAAACC 57.029 32.000 0.00 0.00 0.00 3.27
3094 3322 3.709987 AGTTGCAGCAAAATCAGTGAAC 58.290 40.909 10.11 0.00 0.00 3.18
3112 3340 4.036380 GTGAACAGGGAAACAACGAGAAAT 59.964 41.667 0.00 0.00 0.00 2.17
3115 3343 3.146066 CAGGGAAACAACGAGAAATGGA 58.854 45.455 0.00 0.00 0.00 3.41
3116 3344 3.568007 CAGGGAAACAACGAGAAATGGAA 59.432 43.478 0.00 0.00 0.00 3.53
3137 3365 1.202639 TGAACTGAGCGAGAAAAGCCA 60.203 47.619 0.00 0.00 34.64 4.75
3515 6315 1.065102 CAGCCAAGCCATTCATCTTCG 59.935 52.381 0.00 0.00 0.00 3.79
3656 6476 7.068103 TCCTCATTAAAGATTTTGTGTGTGTGT 59.932 33.333 0.00 0.00 0.00 3.72
3796 6616 0.746204 GCCTGCCTTTCTGGACTAGC 60.746 60.000 0.00 0.00 38.35 3.42
3800 6620 1.699634 TGCCTTTCTGGACTAGCTGTT 59.300 47.619 0.00 0.00 38.35 3.16
3894 6714 1.752833 GCCCCATACCGTCCCTTAG 59.247 63.158 0.00 0.00 0.00 2.18
4166 6986 2.046507 CTGGCACCCTGTCTCTGC 60.047 66.667 0.00 0.00 0.00 4.26
4169 6989 2.359230 GCACCCTGTCTCTGCCAC 60.359 66.667 0.00 0.00 0.00 5.01
4298 7650 7.364522 TCTTTAGTGAAAAAGTGGATCGATG 57.635 36.000 0.54 0.00 37.65 3.84
4465 7817 6.371809 ACAGTTGTTTTTCTTAATGAGCGA 57.628 33.333 0.00 0.00 0.00 4.93
4571 7926 1.222936 CCATTCCGCTTCTGCTCCT 59.777 57.895 0.00 0.00 36.97 3.69
4711 8066 7.056635 GGAATCAAAGAGGATATGAGGACAAA 58.943 38.462 0.00 0.00 0.00 2.83
5062 8423 7.252708 TGATGTGTCTTCATTTGTAATGCATC 58.747 34.615 0.00 0.00 0.00 3.91
5175 8540 0.761187 GCATAGCAGAGGTGATGGGA 59.239 55.000 0.00 0.00 0.00 4.37
5185 8551 5.717119 CAGAGGTGATGGGAAAATTTTCTG 58.283 41.667 25.86 11.60 37.35 3.02
5287 8653 3.053170 GGAGGCCCCTACCTTTTCATTAA 60.053 47.826 0.00 0.00 41.32 1.40
5288 8654 4.387550 GGAGGCCCCTACCTTTTCATTAAT 60.388 45.833 0.00 0.00 41.32 1.40
5289 8655 5.208890 GAGGCCCCTACCTTTTCATTAATT 58.791 41.667 0.00 0.00 41.32 1.40
5290 8656 6.349897 AGGCCCCTACCTTTTCATTAATTA 57.650 37.500 0.00 0.00 36.28 1.40
5351 8719 4.592485 TTTTTACACGCACAATGGGAAT 57.408 36.364 0.00 0.00 34.12 3.01
5354 8722 2.489938 ACACGCACAATGGGAATAGT 57.510 45.000 0.00 0.00 34.12 2.12
5361 8731 6.650807 CACGCACAATGGGAATAGTATAGAAT 59.349 38.462 0.00 0.00 34.12 2.40
5394 8766 1.208293 GGCAGGGTAGGAGACAAGAAG 59.792 57.143 0.00 0.00 0.00 2.85
5508 8883 6.411376 TGATAGGTGGAATAAAGCTTTTCGA 58.589 36.000 18.47 4.18 0.00 3.71
5513 8888 3.823873 TGGAATAAAGCTTTTCGAAGCCA 59.176 39.130 18.47 13.16 46.61 4.75
5514 8889 4.462483 TGGAATAAAGCTTTTCGAAGCCAT 59.538 37.500 18.47 0.00 46.61 4.40
5515 8890 5.650266 TGGAATAAAGCTTTTCGAAGCCATA 59.350 36.000 18.47 0.00 46.61 2.74
5516 8891 6.321181 TGGAATAAAGCTTTTCGAAGCCATAT 59.679 34.615 18.47 0.00 46.61 1.78
5561 8936 2.814336 GCCACCAAAGTCGAAGATCTTT 59.186 45.455 9.87 0.00 40.67 2.52
5563 8938 3.815401 CCACCAAAGTCGAAGATCTTTGT 59.185 43.478 20.03 1.66 45.23 2.83
5577 8952 6.140303 AGATCTTTGTTTCATATGCGCAAT 57.860 33.333 17.11 6.72 0.00 3.56
5631 9006 2.515854 CTCCCCATCGCTACTTAGCTA 58.484 52.381 6.68 0.00 46.85 3.32
5849 9237 8.700439 TTTGTAAATATTTAGCCTGGGTATCC 57.300 34.615 8.18 0.00 0.00 2.59
5857 9245 6.368779 TTTAGCCTGGGTATCCATACATAC 57.631 41.667 6.42 0.00 43.11 2.39
5859 9247 4.438913 AGCCTGGGTATCCATACATACAT 58.561 43.478 0.00 0.00 43.11 2.29
5860 9248 5.599751 AGCCTGGGTATCCATACATACATA 58.400 41.667 0.00 0.00 43.11 2.29
5861 9249 5.425539 AGCCTGGGTATCCATACATACATAC 59.574 44.000 0.00 0.00 43.11 2.39
5863 9251 5.724370 CCTGGGTATCCATACATACATACCA 59.276 44.000 0.00 0.00 41.82 3.25
5864 9252 6.214615 CCTGGGTATCCATACATACATACCAA 59.785 42.308 0.00 0.00 41.82 3.67
5865 9253 7.092444 CCTGGGTATCCATACATACATACCAAT 60.092 40.741 0.00 0.00 41.82 3.16
5866 9254 8.919018 TGGGTATCCATACATACATACCAATA 57.081 34.615 8.78 0.00 41.82 1.90
5877 9265 8.446599 ACATACATACCAATAAAGTAAGGTGC 57.553 34.615 0.00 0.00 35.62 5.01
5892 9280 7.506328 AGTAAGGTGCGTTTCTCTTAATTTT 57.494 32.000 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 4.156739 CCTTCATAGAGCCCTCACAAAAAC 59.843 45.833 0.00 0.00 0.00 2.43
32 33 8.644374 AGTTTTAGGCACAAATAACCTTCATA 57.356 30.769 0.00 0.00 34.92 2.15
34 35 6.969993 AGTTTTAGGCACAAATAACCTTCA 57.030 33.333 0.00 0.00 34.92 3.02
52 53 9.671279 AAAGATTTGATGTTCTTGGAAAGTTTT 57.329 25.926 0.00 0.00 46.34 2.43
129 130 6.007076 TGCACCCTCATAAACAGTAAATTCA 58.993 36.000 0.00 0.00 0.00 2.57
142 143 2.286045 TGCCCCTGCACCCTCATA 60.286 61.111 0.00 0.00 44.23 2.15
163 164 6.567602 AATGAGAAAGGTGTAATAGCTCCT 57.432 37.500 0.00 0.00 35.72 3.69
246 247 2.768527 CGGGGCATCATCTAGTATCCAT 59.231 50.000 0.00 0.00 0.00 3.41
252 253 1.447643 GTGCGGGGCATCATCTAGT 59.552 57.895 0.00 0.00 41.91 2.57
253 254 1.665916 CGTGCGGGGCATCATCTAG 60.666 63.158 0.00 0.00 41.91 2.43
254 255 1.966901 AACGTGCGGGGCATCATCTA 61.967 55.000 0.00 0.00 41.91 1.98
255 256 3.329542 AACGTGCGGGGCATCATCT 62.330 57.895 0.00 0.00 41.91 2.90
256 257 2.824041 AACGTGCGGGGCATCATC 60.824 61.111 0.00 0.00 41.91 2.92
257 258 3.133464 CAACGTGCGGGGCATCAT 61.133 61.111 0.00 0.00 41.91 2.45
258 259 4.634703 ACAACGTGCGGGGCATCA 62.635 61.111 0.00 0.00 41.91 3.07
259 260 3.361977 AACAACGTGCGGGGCATC 61.362 61.111 0.00 0.00 41.91 3.91
260 261 3.669344 CAACAACGTGCGGGGCAT 61.669 61.111 0.00 0.00 41.91 4.40
267 268 1.729131 CATTCCCGCAACAACGTGC 60.729 57.895 0.00 0.00 41.32 5.34
268 269 0.030101 AACATTCCCGCAACAACGTG 59.970 50.000 0.00 0.00 0.00 4.49
269 270 0.741915 AAACATTCCCGCAACAACGT 59.258 45.000 0.00 0.00 0.00 3.99
270 271 1.404477 GAAACATTCCCGCAACAACG 58.596 50.000 0.00 0.00 0.00 4.10
271 272 1.778334 GGAAACATTCCCGCAACAAC 58.222 50.000 0.00 0.00 44.30 3.32
316 317 9.865321 CTATTGTTTCAAGAATTCATGTTCCAT 57.135 29.630 8.44 2.45 0.00 3.41
317 318 8.859090 ACTATTGTTTCAAGAATTCATGTTCCA 58.141 29.630 8.44 2.12 0.00 3.53
318 319 9.696917 AACTATTGTTTCAAGAATTCATGTTCC 57.303 29.630 8.44 0.00 31.37 3.62
380 381 9.175312 TGCATGCATGTAAAATTCCATTTTATT 57.825 25.926 26.79 0.00 43.98 1.40
381 382 8.734218 TGCATGCATGTAAAATTCCATTTTAT 57.266 26.923 26.79 0.00 43.98 1.40
382 383 8.613482 CATGCATGCATGTAAAATTCCATTTTA 58.387 29.630 40.30 7.89 46.20 1.52
383 384 7.476667 CATGCATGCATGTAAAATTCCATTTT 58.523 30.769 40.30 12.04 46.20 1.82
384 385 7.022055 CATGCATGCATGTAAAATTCCATTT 57.978 32.000 40.30 12.41 46.20 2.32
385 386 6.612247 CATGCATGCATGTAAAATTCCATT 57.388 33.333 40.30 13.05 46.20 3.16
398 399 2.725637 TCCACTACAACATGCATGCAT 58.274 42.857 27.46 27.46 37.08 3.96
399 400 2.197283 TCCACTACAACATGCATGCA 57.803 45.000 26.53 25.04 0.00 3.96
400 401 3.788333 AATCCACTACAACATGCATGC 57.212 42.857 26.53 11.82 0.00 4.06
401 402 8.706492 ATTAAAAATCCACTACAACATGCATG 57.294 30.769 25.09 25.09 0.00 4.06
403 404 9.800433 CATATTAAAAATCCACTACAACATGCA 57.200 29.630 0.00 0.00 0.00 3.96
404 405 8.755018 GCATATTAAAAATCCACTACAACATGC 58.245 33.333 0.00 0.00 0.00 4.06
405 406 9.800433 TGCATATTAAAAATCCACTACAACATG 57.200 29.630 0.00 0.00 0.00 3.21
430 431 3.127548 GTCCACCTCAACATGCAACTATG 59.872 47.826 0.00 0.00 0.00 2.23
431 432 3.347216 GTCCACCTCAACATGCAACTAT 58.653 45.455 0.00 0.00 0.00 2.12
432 433 2.552155 GGTCCACCTCAACATGCAACTA 60.552 50.000 0.00 0.00 0.00 2.24
433 434 1.609208 GTCCACCTCAACATGCAACT 58.391 50.000 0.00 0.00 0.00 3.16
434 435 0.598065 GGTCCACCTCAACATGCAAC 59.402 55.000 0.00 0.00 0.00 4.17
435 436 0.478072 AGGTCCACCTCAACATGCAA 59.522 50.000 0.00 0.00 44.77 4.08
436 437 2.154139 AGGTCCACCTCAACATGCA 58.846 52.632 0.00 0.00 44.77 3.96
446 447 3.763897 ACATGCATAAGAAAAGGTCCACC 59.236 43.478 0.00 0.00 0.00 4.61
447 448 5.048083 TCAACATGCATAAGAAAAGGTCCAC 60.048 40.000 0.00 0.00 0.00 4.02
448 449 5.076182 TCAACATGCATAAGAAAAGGTCCA 58.924 37.500 0.00 0.00 0.00 4.02
449 450 5.643379 TCAACATGCATAAGAAAAGGTCC 57.357 39.130 0.00 0.00 0.00 4.46
450 451 7.315142 TCATTCAACATGCATAAGAAAAGGTC 58.685 34.615 0.00 0.00 0.00 3.85
451 452 7.230849 TCATTCAACATGCATAAGAAAAGGT 57.769 32.000 0.00 0.00 0.00 3.50
452 453 7.977293 TCATCATTCAACATGCATAAGAAAAGG 59.023 33.333 0.00 0.02 0.00 3.11
453 454 8.920509 TCATCATTCAACATGCATAAGAAAAG 57.079 30.769 0.00 2.32 0.00 2.27
454 455 7.977293 CCTCATCATTCAACATGCATAAGAAAA 59.023 33.333 0.00 0.00 0.00 2.29
455 456 7.123098 ACCTCATCATTCAACATGCATAAGAAA 59.877 33.333 0.00 0.00 0.00 2.52
456 457 6.604396 ACCTCATCATTCAACATGCATAAGAA 59.396 34.615 0.00 4.45 0.00 2.52
457 458 6.038936 CACCTCATCATTCAACATGCATAAGA 59.961 38.462 0.00 0.00 0.00 2.10
458 459 6.206498 CACCTCATCATTCAACATGCATAAG 58.794 40.000 0.00 0.00 0.00 1.73
459 460 5.068067 CCACCTCATCATTCAACATGCATAA 59.932 40.000 0.00 0.00 0.00 1.90
460 461 4.581409 CCACCTCATCATTCAACATGCATA 59.419 41.667 0.00 0.00 0.00 3.14
461 462 3.383505 CCACCTCATCATTCAACATGCAT 59.616 43.478 0.00 0.00 0.00 3.96
462 463 2.756207 CCACCTCATCATTCAACATGCA 59.244 45.455 0.00 0.00 0.00 3.96
463 464 2.480759 GCCACCTCATCATTCAACATGC 60.481 50.000 0.00 0.00 0.00 4.06
464 465 2.756207 TGCCACCTCATCATTCAACATG 59.244 45.455 0.00 0.00 0.00 3.21
465 466 3.090210 TGCCACCTCATCATTCAACAT 57.910 42.857 0.00 0.00 0.00 2.71
466 467 2.583024 TGCCACCTCATCATTCAACA 57.417 45.000 0.00 0.00 0.00 3.33
467 468 2.480759 GCATGCCACCTCATCATTCAAC 60.481 50.000 6.36 0.00 0.00 3.18
468 469 1.752498 GCATGCCACCTCATCATTCAA 59.248 47.619 6.36 0.00 0.00 2.69
469 470 1.064240 AGCATGCCACCTCATCATTCA 60.064 47.619 15.66 0.00 0.00 2.57
470 471 1.688772 AGCATGCCACCTCATCATTC 58.311 50.000 15.66 0.00 0.00 2.67
471 472 1.754803 CAAGCATGCCACCTCATCATT 59.245 47.619 15.66 0.00 0.00 2.57
472 473 1.399714 CAAGCATGCCACCTCATCAT 58.600 50.000 15.66 0.00 0.00 2.45
473 474 2.876581 CAAGCATGCCACCTCATCA 58.123 52.632 15.66 0.00 0.00 3.07
485 486 6.546403 AGATATTTCTCTCAACATGCAAGCAT 59.454 34.615 0.86 0.86 37.08 3.79
486 487 5.884232 AGATATTTCTCTCAACATGCAAGCA 59.116 36.000 0.00 0.00 0.00 3.91
487 488 6.374565 AGATATTTCTCTCAACATGCAAGC 57.625 37.500 0.00 0.00 0.00 4.01
488 489 9.107177 ACTAAGATATTTCTCTCAACATGCAAG 57.893 33.333 0.00 0.00 0.00 4.01
489 490 8.886719 CACTAAGATATTTCTCTCAACATGCAA 58.113 33.333 0.00 0.00 0.00 4.08
490 491 7.496920 CCACTAAGATATTTCTCTCAACATGCA 59.503 37.037 0.00 0.00 0.00 3.96
491 492 7.041508 CCCACTAAGATATTTCTCTCAACATGC 60.042 40.741 0.00 0.00 0.00 4.06
492 493 7.443575 CCCCACTAAGATATTTCTCTCAACATG 59.556 40.741 0.00 0.00 0.00 3.21
493 494 7.420680 CCCCCACTAAGATATTTCTCTCAACAT 60.421 40.741 0.00 0.00 0.00 2.71
494 495 6.126768 CCCCCACTAAGATATTTCTCTCAACA 60.127 42.308 0.00 0.00 0.00 3.33
495 496 6.292150 CCCCCACTAAGATATTTCTCTCAAC 58.708 44.000 0.00 0.00 0.00 3.18
496 497 5.163195 GCCCCCACTAAGATATTTCTCTCAA 60.163 44.000 0.00 0.00 0.00 3.02
497 498 4.348168 GCCCCCACTAAGATATTTCTCTCA 59.652 45.833 0.00 0.00 0.00 3.27
498 499 4.595350 AGCCCCCACTAAGATATTTCTCTC 59.405 45.833 0.00 0.00 0.00 3.20
499 500 4.571951 AGCCCCCACTAAGATATTTCTCT 58.428 43.478 0.00 0.00 0.00 3.10
500 501 4.984146 AGCCCCCACTAAGATATTTCTC 57.016 45.455 0.00 0.00 0.00 2.87
501 502 4.287326 GCTAGCCCCCACTAAGATATTTCT 59.713 45.833 2.29 0.00 0.00 2.52
502 503 4.287326 AGCTAGCCCCCACTAAGATATTTC 59.713 45.833 12.13 0.00 0.00 2.17
503 504 4.243643 AGCTAGCCCCCACTAAGATATTT 58.756 43.478 12.13 0.00 0.00 1.40
504 505 3.875571 AGCTAGCCCCCACTAAGATATT 58.124 45.455 12.13 0.00 0.00 1.28
505 506 3.569135 AGCTAGCCCCCACTAAGATAT 57.431 47.619 12.13 0.00 0.00 1.63
506 507 4.694280 ATAGCTAGCCCCCACTAAGATA 57.306 45.455 12.13 0.00 0.00 1.98
507 508 3.569135 ATAGCTAGCCCCCACTAAGAT 57.431 47.619 12.13 0.00 0.00 2.40
508 509 3.346146 AATAGCTAGCCCCCACTAAGA 57.654 47.619 12.13 0.00 0.00 2.10
509 510 4.838986 TCTAAATAGCTAGCCCCCACTAAG 59.161 45.833 12.13 0.00 0.00 2.18
510 511 4.823107 TCTAAATAGCTAGCCCCCACTAA 58.177 43.478 12.13 0.00 0.00 2.24
511 512 4.480777 TCTAAATAGCTAGCCCCCACTA 57.519 45.455 12.13 0.00 0.00 2.74
512 513 3.346146 TCTAAATAGCTAGCCCCCACT 57.654 47.619 12.13 0.00 0.00 4.00
513 514 5.959583 ATATCTAAATAGCTAGCCCCCAC 57.040 43.478 12.13 0.00 0.00 4.61
514 515 6.993408 TCTATATCTAAATAGCTAGCCCCCA 58.007 40.000 12.13 0.00 30.79 4.96
515 516 7.785506 TCTTCTATATCTAAATAGCTAGCCCCC 59.214 40.741 12.13 0.00 30.79 5.40
516 517 8.770010 TCTTCTATATCTAAATAGCTAGCCCC 57.230 38.462 12.13 0.00 30.79 5.80
589 590 7.628234 AGATGAGGATTATATGGATGAACACC 58.372 38.462 0.00 0.00 0.00 4.16
593 594 9.275572 TCATGAGATGAGGATTATATGGATGAA 57.724 33.333 0.00 0.00 33.59 2.57
620 786 7.303634 ACTAAGTATTGGCACTCAAAATACG 57.696 36.000 0.00 0.00 40.25 3.06
725 891 4.142469 GGAATAATTTTCAGGTGTGACGGG 60.142 45.833 0.00 0.00 30.10 5.28
837 1003 1.762957 ACCTACTCGGTGGATTGATGG 59.237 52.381 0.00 0.00 46.80 3.51
838 1004 3.637229 ACTACCTACTCGGTGGATTGATG 59.363 47.826 1.35 0.00 46.55 3.07
855 1021 4.095036 GTCACTACGGTACTACCAACTACC 59.905 50.000 6.06 0.00 38.47 3.18
862 1028 4.759782 TCACTAGTCACTACGGTACTACC 58.240 47.826 0.00 0.00 34.05 3.18
1015 1184 0.324614 ATTGATATGCATCGGGGCGA 59.675 50.000 0.19 0.00 41.13 5.54
1040 1209 5.373981 ACACTCTTTCGTGGTAAGACTAG 57.626 43.478 0.00 0.00 39.19 2.57
1043 1212 5.575995 GGAATACACTCTTTCGTGGTAAGAC 59.424 44.000 0.00 0.00 39.19 3.01
1046 1215 4.529377 AGGGAATACACTCTTTCGTGGTAA 59.471 41.667 0.00 0.00 39.19 2.85
1144 1315 5.237996 CCAGATGGTTGATACAGCAATACAG 59.762 44.000 0.00 0.00 0.00 2.74
1167 1338 6.865205 AGACTTGTAAACGAGTTGTACATACC 59.135 38.462 4.52 0.00 40.54 2.73
1181 1352 7.648142 TGTCATTTCCATGAAGACTTGTAAAC 58.352 34.615 0.00 0.00 41.30 2.01
1218 1389 4.212214 GGATACATTCTAAAGAGCAAGCCG 59.788 45.833 0.00 0.00 0.00 5.52
1241 1412 8.160106 AGGGATTGTAGCAATTTAGGAATAGAG 58.840 37.037 0.00 0.00 0.00 2.43
1255 1426 3.951563 AATAGGCAAGGGATTGTAGCA 57.048 42.857 0.00 0.00 0.00 3.49
1263 1434 3.372675 GGCTAGGAAAAATAGGCAAGGGA 60.373 47.826 2.06 0.00 43.38 4.20
1394 1565 9.428097 GAAGGATGAACTCTAATGCAAAAATTT 57.572 29.630 0.00 0.00 0.00 1.82
1537 1708 5.576384 ACAAAATGCATAAATAGTTGCCACG 59.424 36.000 0.00 0.00 38.08 4.94
1560 1731 0.034337 TCTGTGCGGACCTTGGTAAC 59.966 55.000 4.04 0.00 0.00 2.50
1574 1745 2.568090 GCCCCGTGCATTTCTGTG 59.432 61.111 0.00 0.00 40.77 3.66
1636 1807 6.147437 TCCCCCTACTTAATTGAACAACAT 57.853 37.500 0.00 0.00 0.00 2.71
1670 1841 3.018856 CCTTGATGATAAGCACAAGCCA 58.981 45.455 0.00 0.00 43.56 4.75
1672 1843 3.314635 CCTCCTTGATGATAAGCACAAGC 59.685 47.826 0.00 0.00 42.56 4.01
1781 1952 5.048364 CGAGGTAAATGAATCACCCAAAACA 60.048 40.000 0.00 0.00 32.43 2.83
1782 1953 5.048294 ACGAGGTAAATGAATCACCCAAAAC 60.048 40.000 0.00 0.00 32.43 2.43
1784 1973 4.658063 ACGAGGTAAATGAATCACCCAAA 58.342 39.130 0.00 0.00 32.43 3.28
1787 1976 4.007659 ACAACGAGGTAAATGAATCACCC 58.992 43.478 0.00 0.00 32.43 4.61
1851 2042 6.566197 AAAAGGACATAGAACTCTTGCAAG 57.434 37.500 20.81 20.81 0.00 4.01
1907 2098 1.324740 TAATCCAGTAGCACCCGCGT 61.325 55.000 4.92 0.00 45.49 6.01
1908 2099 0.179094 TTAATCCAGTAGCACCCGCG 60.179 55.000 0.00 0.00 45.49 6.46
1941 2133 2.749839 GCACATGCTAACCCGCCA 60.750 61.111 0.00 0.00 38.21 5.69
1953 2145 1.806496 TAGCCCCTAGTCATGCACAT 58.194 50.000 0.00 0.00 0.00 3.21
2011 2203 2.892425 GATCCCCAAGAGCGCACG 60.892 66.667 11.47 0.00 0.00 5.34
2012 2204 2.109126 GTGATCCCCAAGAGCGCAC 61.109 63.158 11.47 2.25 41.13 5.34
2023 2215 5.016831 ACCATTACAAGGAAAAGTGATCCC 58.983 41.667 0.00 0.00 37.71 3.85
2062 2254 4.989279 AGTTTGCACTTTTCACTGTCAT 57.011 36.364 0.00 0.00 0.00 3.06
2194 2386 3.877559 TCTGTGATTTCGCATGAGGATT 58.122 40.909 0.00 0.00 35.63 3.01
2201 2393 6.344500 AGTATCTCTTTCTGTGATTTCGCAT 58.656 36.000 0.00 0.00 35.63 4.73
2240 2432 4.039973 TCTTGGTAATATAAGCCTCCACCG 59.960 45.833 0.00 0.00 0.00 4.94
2276 2468 0.804989 GGAGACCAAATCCTGCAACG 59.195 55.000 0.00 0.00 33.77 4.10
2292 2484 3.326747 ACGAAATCGAAGGACTTTGGAG 58.673 45.455 10.16 0.00 43.02 3.86
2370 2562 0.321671 TCCGAGCAAGAGTGAAAGGG 59.678 55.000 0.00 0.00 0.00 3.95
2412 2604 4.889995 TGTGACAACAATCAATGGTTGGTA 59.110 37.500 11.27 1.25 46.56 3.25
2471 2663 6.650390 CCCGTCAAATCCAAGAATTTTCAAAT 59.350 34.615 0.00 0.00 0.00 2.32
2522 2715 4.865776 TCCTCAAAAATAAAACTGCACCG 58.134 39.130 0.00 0.00 0.00 4.94
2538 2732 4.640771 AAGCAAACTAGGTCATCCTCAA 57.359 40.909 0.00 0.00 43.94 3.02
2544 2738 6.823689 ACATTCGAATAAGCAAACTAGGTCAT 59.176 34.615 10.97 0.00 0.00 3.06
2593 2788 8.338072 TCCTATTTTACGCAAATTGAAGGTTA 57.662 30.769 0.00 0.00 36.43 2.85
2658 2854 4.703899 AATAACACGTTCACGAACAGTC 57.296 40.909 6.30 0.00 43.02 3.51
2777 2975 8.797266 AAGACACCGAACAATTTTCTAAAATC 57.203 30.769 1.36 0.00 37.62 2.17
2859 3059 7.776464 CGACAGGCGTTTTTAAATATACGATA 58.224 34.615 17.06 0.00 36.16 2.92
2976 3176 5.823861 AGGTTTAATGCAGGGTGATTTTT 57.176 34.783 0.00 0.00 0.00 1.94
3056 3284 5.546526 TGCAACTTTTCTGTTGGTTTTCTT 58.453 33.333 9.04 0.00 45.19 2.52
3094 3322 3.146066 TCCATTTCTCGTTGTTTCCCTG 58.854 45.455 0.00 0.00 0.00 4.45
3112 3340 3.401033 TTTCTCGCTCAGTTCATTCCA 57.599 42.857 0.00 0.00 0.00 3.53
3115 3343 2.485814 GGCTTTTCTCGCTCAGTTCATT 59.514 45.455 0.00 0.00 0.00 2.57
3116 3344 2.079925 GGCTTTTCTCGCTCAGTTCAT 58.920 47.619 0.00 0.00 0.00 2.57
3137 3365 4.536765 AGACCTGTTGTTTTCCTGTTCAT 58.463 39.130 0.00 0.00 0.00 2.57
3515 6315 8.301730 TGAAAAATCAATGAGAATTTCTGCAC 57.698 30.769 3.03 0.00 37.19 4.57
3647 6467 3.082698 ACATTTCATGCACACACACAC 57.917 42.857 0.00 0.00 0.00 3.82
3649 6469 4.858692 GGAATACATTTCATGCACACACAC 59.141 41.667 0.00 0.00 0.00 3.82
3656 6476 8.432013 AGTACATCTAGGAATACATTTCATGCA 58.568 33.333 0.00 0.00 0.00 3.96
3796 6616 5.523438 TTTGTGGGGCTAAAAACTAACAG 57.477 39.130 0.00 0.00 0.00 3.16
3800 6620 4.218852 CGGAATTTGTGGGGCTAAAAACTA 59.781 41.667 0.00 0.00 0.00 2.24
3894 6714 5.475719 TGGACTACTATGTGTTGTGCTTAC 58.524 41.667 0.00 0.00 41.51 2.34
4149 6969 2.046507 GCAGAGACAGGGTGCCAG 60.047 66.667 0.00 0.00 0.00 4.85
4152 6972 2.359230 GTGGCAGAGACAGGGTGC 60.359 66.667 0.00 0.00 36.42 5.01
4153 6973 1.004080 CAGTGGCAGAGACAGGGTG 60.004 63.158 0.00 0.00 0.00 4.61
4154 6974 0.546267 ATCAGTGGCAGAGACAGGGT 60.546 55.000 0.00 0.00 0.00 4.34
4155 6975 0.617413 AATCAGTGGCAGAGACAGGG 59.383 55.000 0.00 0.00 0.00 4.45
4156 6976 3.464907 CATAATCAGTGGCAGAGACAGG 58.535 50.000 0.00 0.00 0.00 4.00
4157 6977 2.871022 GCATAATCAGTGGCAGAGACAG 59.129 50.000 0.00 0.00 0.00 3.51
4159 6979 2.910199 TGCATAATCAGTGGCAGAGAC 58.090 47.619 0.00 0.00 0.00 3.36
4160 6980 3.198417 TCTTGCATAATCAGTGGCAGAGA 59.802 43.478 0.00 0.00 37.59 3.10
4161 6981 3.538591 TCTTGCATAATCAGTGGCAGAG 58.461 45.455 0.00 0.00 37.59 3.35
4163 6983 3.276857 ACTCTTGCATAATCAGTGGCAG 58.723 45.455 0.00 0.00 37.59 4.85
4164 6984 3.354948 ACTCTTGCATAATCAGTGGCA 57.645 42.857 0.00 0.00 0.00 4.92
4166 6986 9.722056 GTAAAAATACTCTTGCATAATCAGTGG 57.278 33.333 0.00 0.00 0.00 4.00
4298 7650 3.880490 TGTTGGTCATGACACAAAGGTAC 59.120 43.478 26.47 15.50 0.00 3.34
4339 7691 2.691526 TGACGACCGCCTTATCTACAAT 59.308 45.455 0.00 0.00 0.00 2.71
4410 7762 9.176460 TGTTGATCACATATGTTTGTACATCAT 57.824 29.630 5.37 15.14 43.81 2.45
4450 7802 4.576873 TGTTGTGGTCGCTCATTAAGAAAA 59.423 37.500 0.00 0.00 0.00 2.29
4571 7926 1.874872 GTAGCTTACGTTGCAACCCAA 59.125 47.619 23.42 15.60 0.00 4.12
4711 8066 9.965902 AGTCAATAAAATCTCTAGTTGGAATGT 57.034 29.630 0.00 0.00 0.00 2.71
4818 8173 7.105588 GGAGATGGTTTTTCCTTGCAATAATT 58.894 34.615 0.00 0.00 37.07 1.40
5148 8513 3.057245 TCACCTCTGCTATGCATCGATAC 60.057 47.826 0.19 0.00 38.13 2.24
5149 8514 3.157087 TCACCTCTGCTATGCATCGATA 58.843 45.455 0.19 0.00 38.13 2.92
5212 8578 5.604758 ATGTTCTAGCAACATAGCTGAGA 57.395 39.130 14.87 0.00 46.11 3.27
5287 8653 2.653726 TGCATGCCATCCGTTTCTAAT 58.346 42.857 16.68 0.00 0.00 1.73
5288 8654 2.121291 TGCATGCCATCCGTTTCTAA 57.879 45.000 16.68 0.00 0.00 2.10
5289 8655 1.948834 CATGCATGCCATCCGTTTCTA 59.051 47.619 14.93 0.00 29.71 2.10
5290 8656 0.742505 CATGCATGCCATCCGTTTCT 59.257 50.000 14.93 0.00 29.71 2.52
5351 8719 7.286087 TGCCTCCGTCTTTGTAATTCTATACTA 59.714 37.037 0.00 0.00 0.00 1.82
5354 8722 6.462487 CCTGCCTCCGTCTTTGTAATTCTATA 60.462 42.308 0.00 0.00 0.00 1.31
5361 8731 0.323629 CCCTGCCTCCGTCTTTGTAA 59.676 55.000 0.00 0.00 0.00 2.41
5394 8766 8.757164 TTTTGTTGTTTCTTTCCTCTTTCTTC 57.243 30.769 0.00 0.00 0.00 2.87
5508 8883 7.821134 ATTTCCTGGACTCTATATATGGCTT 57.179 36.000 0.00 0.00 0.00 4.35
5515 8890 8.808092 GCTACAACTATTTCCTGGACTCTATAT 58.192 37.037 0.00 0.00 0.00 0.86
5516 8891 7.232941 GGCTACAACTATTTCCTGGACTCTATA 59.767 40.741 0.00 0.00 0.00 1.31
5577 8952 2.010497 TCAGTTTGTGTAGCGTGCAAA 58.990 42.857 0.00 0.00 0.00 3.68
5681 9060 3.758300 CAAGTGAAACAACCACACACTC 58.242 45.455 0.00 0.00 41.43 3.51
5857 9245 6.431198 AACGCACCTTACTTTATTGGTATG 57.569 37.500 0.00 0.00 0.00 2.39
5859 9247 6.232692 AGAAACGCACCTTACTTTATTGGTA 58.767 36.000 0.00 0.00 0.00 3.25
5860 9248 5.067954 AGAAACGCACCTTACTTTATTGGT 58.932 37.500 0.00 0.00 0.00 3.67
5861 9249 5.411669 AGAGAAACGCACCTTACTTTATTGG 59.588 40.000 0.00 0.00 0.00 3.16
5863 9251 8.611654 TTAAGAGAAACGCACCTTACTTTATT 57.388 30.769 0.00 0.00 0.00 1.40
5864 9252 8.788325 ATTAAGAGAAACGCACCTTACTTTAT 57.212 30.769 0.00 0.00 0.00 1.40
5865 9253 8.611654 AATTAAGAGAAACGCACCTTACTTTA 57.388 30.769 0.00 0.00 0.00 1.85
5866 9254 7.506328 AATTAAGAGAAACGCACCTTACTTT 57.494 32.000 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.