Multiple sequence alignment - TraesCS7A01G518500

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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 TraesCS7A01G518500 chr7A 100.000 5299 0 0 1 5299 702400343 702405641 0.000000e+00 9786.0
1 TraesCS7A01G518500 chr7A 84.528 1493 166 28 2959 4427 702227586 702229037 0.000000e+00 1417.0
2 TraesCS7A01G518500 chr7A 84.774 532 46 16 2184 2715 702225078 702225574 7.920000e-138 501.0
3 TraesCS7A01G518500 chr7A 84.244 476 66 9 2559 3031 702967325 702966856 6.260000e-124 455.0
4 TraesCS7A01G518500 chr7A 86.176 340 28 11 983 1319 702218831 702219154 3.040000e-92 350.0
5 TraesCS7A01G518500 chr7A 84.052 232 30 6 1399 1625 702219198 702219427 3.210000e-52 217.0
6 TraesCS7A01G518500 chr7A 77.119 354 72 8 4007 4359 702963837 702963492 4.190000e-46 196.0
7 TraesCS7A01G518500 chr7A 86.310 168 19 3 1681 1846 702224326 702224491 4.220000e-41 180.0
8 TraesCS7A01G518500 chr7A 90.625 96 4 5 5200 5293 726894340 726894248 7.210000e-24 122.0
9 TraesCS7A01G518500 chr7D 94.838 3584 130 20 847 4427 612317796 612321327 0.000000e+00 5542.0
10 TraesCS7A01G518500 chr7D 83.311 1498 179 34 2959 4427 612047945 612049400 0.000000e+00 1315.0
11 TraesCS7A01G518500 chr7D 92.584 863 60 3 4433 5291 612323204 612324066 0.000000e+00 1236.0
12 TraesCS7A01G518500 chr7D 84.663 815 98 15 3623 4427 611875409 611874612 0.000000e+00 787.0
13 TraesCS7A01G518500 chr7D 78.746 1021 170 27 2536 3547 612442541 612443523 1.610000e-179 640.0
14 TraesCS7A01G518500 chr7D 83.673 539 46 19 2187 2716 611863464 611862959 2.230000e-128 470.0
15 TraesCS7A01G518500 chr7D 90.747 281 14 6 967 1239 611878511 611878235 1.080000e-96 364.0
16 TraesCS7A01G518500 chr7D 82.775 418 55 11 2959 3372 611875816 611875412 1.810000e-94 357.0
17 TraesCS7A01G518500 chr7D 89.850 266 24 3 1 265 612315847 612316110 6.570000e-89 339.0
18 TraesCS7A01G518500 chr7D 81.250 288 44 5 2196 2479 554520579 554520860 1.920000e-54 224.0
19 TraesCS7A01G518500 chr7D 80.634 284 43 5 2196 2479 554477632 554477903 5.380000e-50 209.0
20 TraesCS7A01G518500 chr7D 78.462 325 64 4 4010 4334 612444020 612444338 1.930000e-49 207.0
21 TraesCS7A01G518500 chr7D 78.549 317 60 6 4471 4781 612402014 612402328 9.000000e-48 202.0
22 TraesCS7A01G518500 chr7D 83.700 227 23 9 2247 2468 612426674 612426891 9.000000e-48 202.0
23 TraesCS7A01G518500 chr7D 81.915 188 32 2 1399 1584 611878136 611877949 1.980000e-34 158.0
24 TraesCS7A01G518500 chr7D 86.364 110 13 2 2763 2872 611861627 611861520 9.320000e-23 119.0
25 TraesCS7A01G518500 chr7D 89.552 67 7 0 616 682 612316261 612316327 9.460000e-13 86.1
26 TraesCS7A01G518500 chr7D 97.500 40 1 0 2841 2880 612427529 612427568 9.520000e-08 69.4
27 TraesCS7A01G518500 chr7B 96.171 2507 70 7 1926 4427 701639049 701641534 0.000000e+00 4074.0
28 TraesCS7A01G518500 chr7B 91.715 869 57 10 4433 5289 701642027 701642892 0.000000e+00 1192.0
29 TraesCS7A01G518500 chr7B 95.094 530 16 1 1397 1926 701637892 701638411 0.000000e+00 826.0
30 TraesCS7A01G518500 chr7B 88.023 693 40 17 800 1485 701637151 701637807 0.000000e+00 780.0
31 TraesCS7A01G518500 chr7B 78.942 1021 165 30 2536 3547 701875101 701876080 0.000000e+00 649.0
32 TraesCS7A01G518500 chr7B 87.687 268 30 3 1 266 701474174 701474440 5.150000e-80 309.0
33 TraesCS7A01G518500 chr7B 82.645 242 26 6 3452 3690 701430621 701430849 3.240000e-47 200.0
34 TraesCS7A01G518500 chr7B 97.500 40 1 0 2557 2596 701875045 701875084 9.520000e-08 69.4
35 TraesCS7A01G518500 chr6A 92.000 150 11 1 478 626 222571269 222571418 5.380000e-50 209.0
36 TraesCS7A01G518500 chr5B 93.571 140 9 0 478 617 663232190 663232329 5.380000e-50 209.0
37 TraesCS7A01G518500 chr5A 91.781 146 12 0 478 623 206730877 206731022 2.500000e-48 204.0
38 TraesCS7A01G518500 chr2B 92.414 145 8 3 478 621 248103683 248103541 2.500000e-48 204.0
39 TraesCS7A01G518500 chr2A 91.781 146 12 0 478 623 600917743 600917598 2.500000e-48 204.0
40 TraesCS7A01G518500 chr2A 91.892 148 9 3 478 623 691479935 691479789 2.500000e-48 204.0
41 TraesCS7A01G518500 chr3B 91.781 146 11 1 478 622 749713665 749713520 9.000000e-48 202.0
42 TraesCS7A01G518500 chr3B 85.625 160 22 1 79 237 654338829 654338988 3.280000e-37 167.0
43 TraesCS7A01G518500 chrUn 82.645 242 26 6 3452 3690 87710992 87711220 3.240000e-47 200.0
44 TraesCS7A01G518500 chr5D 91.156 147 11 2 478 623 321901939 321902084 1.160000e-46 198.0
45 TraesCS7A01G518500 chr5D 73.204 362 76 15 4537 4888 436362502 436362852 1.560000e-20 111.0
46 TraesCS7A01G518500 chr1A 89.241 158 16 1 478 634 84438451 84438294 4.190000e-46 196.0
47 TraesCS7A01G518500 chr1A 80.508 118 16 7 4827 4937 479821033 479820916 3.400000e-12 84.2
48 TraesCS7A01G518500 chr2D 87.059 170 19 3 69 237 567968821 567968988 7.010000e-44 189.0
49 TraesCS7A01G518500 chr2D 91.579 95 5 3 5198 5291 19380927 19381019 1.550000e-25 128.0
50 TraesCS7A01G518500 chr4D 73.634 421 85 19 4464 4877 115539623 115540024 7.160000e-29 139.0
51 TraesCS7A01G518500 chr4D 89.130 92 7 3 5194 5285 490421891 490421979 1.560000e-20 111.0
52 TraesCS7A01G518500 chr3D 88.660 97 8 2 5196 5291 54975148 54975054 1.210000e-21 115.0
53 TraesCS7A01G518500 chr3D 87.755 98 8 4 5199 5293 562355630 562355534 1.560000e-20 111.0
54 TraesCS7A01G518500 chr6D 87.500 104 6 7 5190 5291 101208095 101207997 4.340000e-21 113.0
55 TraesCS7A01G518500 chr1D 87.629 97 8 4 5200 5293 203875907 203875812 5.610000e-20 110.0


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 TraesCS7A01G518500 chr7A 702400343 702405641 5298 False 9786.000000 9786 100.00000 1 5299 1 chr7A.!!$F1 5298
1 TraesCS7A01G518500 chr7A 702224326 702229037 4711 False 699.333333 1417 85.20400 1681 4427 3 chr7A.!!$F3 2746
2 TraesCS7A01G518500 chr7A 702963492 702967325 3833 True 325.500000 455 80.68150 2559 4359 2 chr7A.!!$R2 1800
3 TraesCS7A01G518500 chr7A 702218831 702219427 596 False 283.500000 350 85.11400 983 1625 2 chr7A.!!$F2 642
4 TraesCS7A01G518500 chr7D 612315847 612324066 8219 False 1800.775000 5542 91.70600 1 5291 4 chr7D.!!$F5 5290
5 TraesCS7A01G518500 chr7D 612047945 612049400 1455 False 1315.000000 1315 83.31100 2959 4427 1 chr7D.!!$F3 1468
6 TraesCS7A01G518500 chr7D 612442541 612444338 1797 False 423.500000 640 78.60400 2536 4334 2 chr7D.!!$F7 1798
7 TraesCS7A01G518500 chr7D 611874612 611878511 3899 True 416.500000 787 85.02500 967 4427 4 chr7D.!!$R2 3460
8 TraesCS7A01G518500 chr7D 611861520 611863464 1944 True 294.500000 470 85.01850 2187 2872 2 chr7D.!!$R1 685
9 TraesCS7A01G518500 chr7B 701637151 701642892 5741 False 1718.000000 4074 92.75075 800 5289 4 chr7B.!!$F3 4489
10 TraesCS7A01G518500 chr7B 701875045 701876080 1035 False 359.200000 649 88.22100 2536 3547 2 chr7B.!!$F4 1011

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
901 2233 0.250901 AAACTCAGCCCATTCGCACT 60.251 50.0 0.00 0.00 0.00 4.40 F
1847 3536 0.528249 CTTTTGCGGCAGTGCTTGTT 60.528 50.0 16.11 0.00 35.36 2.83 F
2534 5147 0.040067 GCAAGGCAAGAGTTCGGTTG 60.040 55.0 0.00 0.00 0.00 3.77 F
4059 12080 0.324091 ATTCAAGGCTGCCAAGGGAG 60.324 55.0 22.65 2.91 36.62 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2515 5128 0.040067 CAACCGAACTCTTGCCTTGC 60.040 55.0 0.0 0.0 0.00 4.01 R
2995 8714 0.030705 AGGCCTCTAGCATCCAAGGA 60.031 55.0 0.0 0.0 46.50 3.36 R
4099 12127 0.737367 GCCGCCAGCAATTTTCCTTC 60.737 55.0 0.0 0.0 42.97 3.46 R
4905 14856 1.104577 GTTTTGTTCCCCTGGCGACA 61.105 55.0 0.0 0.0 39.59 4.35 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
35 36 5.324409 ACAATTCCTCTGTTGCCATAGAAA 58.676 37.500 0.00 0.00 0.00 2.52
39 40 7.573968 ATTCCTCTGTTGCCATAGAAAATAC 57.426 36.000 0.00 0.00 0.00 1.89
66 67 6.258507 ACAAGATGGTTGTTGCAGAAAAATTC 59.741 34.615 0.00 0.00 29.38 2.17
67 68 6.165700 AGATGGTTGTTGCAGAAAAATTCT 57.834 33.333 0.00 0.00 41.70 2.40
121 122 4.853924 AAAATTCCGCAACAAGATGTCT 57.146 36.364 0.00 0.00 0.00 3.41
146 147 2.476241 GCCAGAAATTTTCGCAACAAGG 59.524 45.455 3.57 1.14 34.02 3.61
173 174 6.422333 TCTGTTGCAATAATGGATAGGAACA 58.578 36.000 0.59 0.00 0.00 3.18
229 230 1.202256 GCCCGGCCGATCTTTTAAAAG 60.202 52.381 30.73 19.91 37.36 2.27
243 244 0.468226 TAAAAGATCAGCCCGCGGAT 59.532 50.000 30.73 12.66 33.77 4.18
246 247 4.916293 GATCAGCCCGCGGATGCA 62.916 66.667 30.73 14.61 39.19 3.96
258 259 1.447643 GGATGCATAGCGTGTCCCT 59.552 57.895 0.00 0.00 0.00 4.20
261 262 1.331756 GATGCATAGCGTGTCCCTTTG 59.668 52.381 0.00 0.00 0.00 2.77
262 263 0.323302 TGCATAGCGTGTCCCTTTGA 59.677 50.000 0.00 0.00 0.00 2.69
263 264 1.065491 TGCATAGCGTGTCCCTTTGAT 60.065 47.619 0.00 0.00 0.00 2.57
264 265 2.017049 GCATAGCGTGTCCCTTTGATT 58.983 47.619 0.00 0.00 0.00 2.57
265 266 3.202906 GCATAGCGTGTCCCTTTGATTA 58.797 45.455 0.00 0.00 0.00 1.75
266 267 3.815401 GCATAGCGTGTCCCTTTGATTAT 59.185 43.478 0.00 0.00 0.00 1.28
267 268 4.275936 GCATAGCGTGTCCCTTTGATTATT 59.724 41.667 0.00 0.00 0.00 1.40
268 269 5.221048 GCATAGCGTGTCCCTTTGATTATTT 60.221 40.000 0.00 0.00 0.00 1.40
269 270 4.701956 AGCGTGTCCCTTTGATTATTTG 57.298 40.909 0.00 0.00 0.00 2.32
270 271 4.079253 AGCGTGTCCCTTTGATTATTTGT 58.921 39.130 0.00 0.00 0.00 2.83
271 272 4.156008 AGCGTGTCCCTTTGATTATTTGTC 59.844 41.667 0.00 0.00 0.00 3.18
272 273 4.156008 GCGTGTCCCTTTGATTATTTGTCT 59.844 41.667 0.00 0.00 0.00 3.41
273 274 5.335661 GCGTGTCCCTTTGATTATTTGTCTT 60.336 40.000 0.00 0.00 0.00 3.01
332 333 5.873179 TTTTTGCGAGGGTTAGTCATTAG 57.127 39.130 0.00 0.00 0.00 1.73
333 334 4.546829 TTTGCGAGGGTTAGTCATTAGT 57.453 40.909 0.00 0.00 0.00 2.24
334 335 4.546829 TTGCGAGGGTTAGTCATTAGTT 57.453 40.909 0.00 0.00 0.00 2.24
335 336 4.546829 TGCGAGGGTTAGTCATTAGTTT 57.453 40.909 0.00 0.00 0.00 2.66
336 337 5.664294 TGCGAGGGTTAGTCATTAGTTTA 57.336 39.130 0.00 0.00 0.00 2.01
337 338 6.229936 TGCGAGGGTTAGTCATTAGTTTAT 57.770 37.500 0.00 0.00 0.00 1.40
338 339 6.646267 TGCGAGGGTTAGTCATTAGTTTATT 58.354 36.000 0.00 0.00 0.00 1.40
339 340 6.537301 TGCGAGGGTTAGTCATTAGTTTATTG 59.463 38.462 0.00 0.00 0.00 1.90
340 341 6.537660 GCGAGGGTTAGTCATTAGTTTATTGT 59.462 38.462 0.00 0.00 0.00 2.71
341 342 7.065443 GCGAGGGTTAGTCATTAGTTTATTGTT 59.935 37.037 0.00 0.00 0.00 2.83
342 343 9.590451 CGAGGGTTAGTCATTAGTTTATTGTTA 57.410 33.333 0.00 0.00 0.00 2.41
366 367 5.009854 AGAACAACCAAAGAAACACATGG 57.990 39.130 0.00 0.00 38.91 3.66
370 371 5.600696 ACAACCAAAGAAACACATGGATTC 58.399 37.500 0.00 0.00 36.75 2.52
374 375 6.888105 ACCAAAGAAACACATGGATTCTTTT 58.112 32.000 22.29 12.91 45.99 2.27
378 379 4.284234 AGAAACACATGGATTCTTTTGGGG 59.716 41.667 0.00 0.00 29.35 4.96
379 380 2.539302 ACACATGGATTCTTTTGGGGG 58.461 47.619 0.00 0.00 0.00 5.40
409 410 2.293399 CACTTTAAGGTTCCACACAGCC 59.707 50.000 0.00 0.00 0.00 4.85
433 439 2.408050 GCACAGTAAGATCCATAGGCG 58.592 52.381 0.00 0.00 0.00 5.52
436 442 4.799678 CACAGTAAGATCCATAGGCGTAG 58.200 47.826 0.00 0.00 0.00 3.51
452 458 1.867233 CGTAGATTGCCGCAGCTTATT 59.133 47.619 3.53 0.00 40.80 1.40
454 460 3.604772 CGTAGATTGCCGCAGCTTATTTC 60.605 47.826 3.53 0.00 40.80 2.17
457 463 0.525761 TTGCCGCAGCTTATTTCCAC 59.474 50.000 0.00 0.00 40.80 4.02
458 464 0.322456 TGCCGCAGCTTATTTCCACT 60.322 50.000 0.00 0.00 40.80 4.00
465 471 4.572389 CGCAGCTTATTTCCACTATGAGTT 59.428 41.667 0.00 0.00 0.00 3.01
466 472 5.753438 CGCAGCTTATTTCCACTATGAGTTA 59.247 40.000 0.00 0.00 0.00 2.24
467 473 6.292381 CGCAGCTTATTTCCACTATGAGTTAC 60.292 42.308 0.00 0.00 0.00 2.50
468 474 6.763610 GCAGCTTATTTCCACTATGAGTTACT 59.236 38.462 0.00 0.00 0.00 2.24
469 475 7.281100 GCAGCTTATTTCCACTATGAGTTACTT 59.719 37.037 0.00 0.00 0.00 2.24
470 476 8.821894 CAGCTTATTTCCACTATGAGTTACTTC 58.178 37.037 0.00 0.00 0.00 3.01
471 477 7.988028 AGCTTATTTCCACTATGAGTTACTTCC 59.012 37.037 0.00 0.00 0.00 3.46
472 478 7.988028 GCTTATTTCCACTATGAGTTACTTCCT 59.012 37.037 0.00 0.00 0.00 3.36
475 481 6.446781 TTCCACTATGAGTTACTTCCTACG 57.553 41.667 0.00 0.00 0.00 3.51
476 482 5.503927 TCCACTATGAGTTACTTCCTACGT 58.496 41.667 0.00 0.00 0.00 3.57
477 483 5.948162 TCCACTATGAGTTACTTCCTACGTT 59.052 40.000 0.00 0.00 0.00 3.99
478 484 6.094603 TCCACTATGAGTTACTTCCTACGTTC 59.905 42.308 0.00 0.00 0.00 3.95
479 485 6.095160 CCACTATGAGTTACTTCCTACGTTCT 59.905 42.308 0.00 0.00 0.00 3.01
480 486 7.362747 CCACTATGAGTTACTTCCTACGTTCTT 60.363 40.741 0.00 0.00 0.00 2.52
481 487 8.027771 CACTATGAGTTACTTCCTACGTTCTTT 58.972 37.037 0.00 0.00 0.00 2.52
482 488 8.583296 ACTATGAGTTACTTCCTACGTTCTTTT 58.417 33.333 0.00 0.00 0.00 2.27
483 489 9.420551 CTATGAGTTACTTCCTACGTTCTTTTT 57.579 33.333 0.00 0.00 0.00 1.94
485 491 8.807667 TGAGTTACTTCCTACGTTCTTTTTAG 57.192 34.615 0.00 0.00 0.00 1.85
486 492 8.632679 TGAGTTACTTCCTACGTTCTTTTTAGA 58.367 33.333 0.00 0.00 0.00 2.10
487 493 9.127006 GAGTTACTTCCTACGTTCTTTTTAGAG 57.873 37.037 0.00 0.00 0.00 2.43
488 494 8.854117 AGTTACTTCCTACGTTCTTTTTAGAGA 58.146 33.333 0.00 0.00 0.00 3.10
489 495 9.636879 GTTACTTCCTACGTTCTTTTTAGAGAT 57.363 33.333 0.00 0.00 0.00 2.75
492 498 9.557061 ACTTCCTACGTTCTTTTTAGAGATTTT 57.443 29.630 0.00 0.00 0.00 1.82
558 564 9.768662 AGAGTGTAAATTCATTCATTTTGCTTT 57.231 25.926 0.00 0.00 0.00 3.51
559 565 9.801714 GAGTGTAAATTCATTCATTTTGCTTTG 57.198 29.630 0.00 0.00 0.00 2.77
560 566 9.328845 AGTGTAAATTCATTCATTTTGCTTTGT 57.671 25.926 0.00 0.00 0.00 2.83
568 574 9.624697 TTCATTCATTTTGCTTTGTATGTAGTC 57.375 29.630 0.00 0.00 0.00 2.59
569 575 8.791675 TCATTCATTTTGCTTTGTATGTAGTCA 58.208 29.630 0.00 0.00 0.00 3.41
570 576 8.853345 CATTCATTTTGCTTTGTATGTAGTCAC 58.147 33.333 0.00 0.00 0.00 3.67
571 577 7.744087 TCATTTTGCTTTGTATGTAGTCACT 57.256 32.000 0.00 0.00 0.00 3.41
572 578 8.165239 TCATTTTGCTTTGTATGTAGTCACTT 57.835 30.769 0.00 0.00 0.00 3.16
573 579 8.075574 TCATTTTGCTTTGTATGTAGTCACTTG 58.924 33.333 0.00 0.00 0.00 3.16
574 580 6.935741 TTTGCTTTGTATGTAGTCACTTGT 57.064 33.333 0.00 0.00 0.00 3.16
575 581 6.935741 TTGCTTTGTATGTAGTCACTTGTT 57.064 33.333 0.00 0.00 0.00 2.83
576 582 6.299023 TGCTTTGTATGTAGTCACTTGTTG 57.701 37.500 0.00 0.00 0.00 3.33
577 583 6.052360 TGCTTTGTATGTAGTCACTTGTTGA 58.948 36.000 0.00 0.00 0.00 3.18
578 584 6.540551 TGCTTTGTATGTAGTCACTTGTTGAA 59.459 34.615 0.00 0.00 35.39 2.69
579 585 7.066404 TGCTTTGTATGTAGTCACTTGTTGAAA 59.934 33.333 0.00 0.00 35.39 2.69
580 586 8.076178 GCTTTGTATGTAGTCACTTGTTGAAAT 58.924 33.333 0.00 0.00 35.39 2.17
581 587 9.599322 CTTTGTATGTAGTCACTTGTTGAAATC 57.401 33.333 0.00 0.00 35.39 2.17
582 588 8.902540 TTGTATGTAGTCACTTGTTGAAATCT 57.097 30.769 0.00 0.00 35.39 2.40
583 589 8.534333 TGTATGTAGTCACTTGTTGAAATCTC 57.466 34.615 0.00 0.00 35.39 2.75
584 590 8.367911 TGTATGTAGTCACTTGTTGAAATCTCT 58.632 33.333 0.00 0.00 35.39 3.10
585 591 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
587 593 9.778741 ATGTAGTCACTTGTTGAAATCTCTAAA 57.221 29.630 0.00 0.00 35.39 1.85
588 594 9.607988 TGTAGTCACTTGTTGAAATCTCTAAAA 57.392 29.630 0.00 0.00 35.39 1.52
591 597 8.624776 AGTCACTTGTTGAAATCTCTAAAAAGG 58.375 33.333 0.00 0.00 35.39 3.11
592 598 7.379797 GTCACTTGTTGAAATCTCTAAAAAGGC 59.620 37.037 0.00 0.00 35.39 4.35
593 599 7.068103 TCACTTGTTGAAATCTCTAAAAAGGCA 59.932 33.333 0.00 0.00 0.00 4.75
594 600 7.706179 CACTTGTTGAAATCTCTAAAAAGGCAA 59.294 33.333 0.00 0.00 0.00 4.52
595 601 8.257306 ACTTGTTGAAATCTCTAAAAAGGCAAA 58.743 29.630 0.00 0.00 0.00 3.68
596 602 9.264719 CTTGTTGAAATCTCTAAAAAGGCAAAT 57.735 29.630 0.00 0.00 0.00 2.32
607 613 9.503427 CTCTAAAAAGGCAAATATTTAGGAACG 57.497 33.333 0.00 0.00 36.48 3.95
608 614 8.463607 TCTAAAAAGGCAAATATTTAGGAACGG 58.536 33.333 0.00 0.00 36.48 4.44
609 615 6.844097 AAAAGGCAAATATTTAGGAACGGA 57.156 33.333 0.00 0.00 0.00 4.69
610 616 6.844097 AAAGGCAAATATTTAGGAACGGAA 57.156 33.333 0.00 0.00 0.00 4.30
611 617 6.451064 AAGGCAAATATTTAGGAACGGAAG 57.549 37.500 0.00 0.00 0.00 3.46
612 618 5.751586 AGGCAAATATTTAGGAACGGAAGA 58.248 37.500 0.00 0.00 0.00 2.87
613 619 6.184789 AGGCAAATATTTAGGAACGGAAGAA 58.815 36.000 0.00 0.00 0.00 2.52
614 620 6.318900 AGGCAAATATTTAGGAACGGAAGAAG 59.681 38.462 0.00 0.00 0.00 2.85
633 639 4.763793 AGAAGTAGTTCTTGTGCATGCATT 59.236 37.500 25.64 9.72 40.35 3.56
635 641 6.600822 AGAAGTAGTTCTTGTGCATGCATTAT 59.399 34.615 25.64 4.07 40.35 1.28
645 651 6.466308 TGTGCATGCATTATAAGTACGATC 57.534 37.500 25.64 5.93 0.00 3.69
646 652 5.988561 TGTGCATGCATTATAAGTACGATCA 59.011 36.000 25.64 8.73 0.00 2.92
647 653 6.146021 TGTGCATGCATTATAAGTACGATCAG 59.854 38.462 25.64 0.00 0.00 2.90
676 682 2.991190 GACATGACAGCCTGCATTTTTG 59.009 45.455 0.00 0.00 0.00 2.44
682 688 5.423015 TGACAGCCTGCATTTTTGTTTTTA 58.577 33.333 0.00 0.00 0.00 1.52
683 689 5.293079 TGACAGCCTGCATTTTTGTTTTTAC 59.707 36.000 0.00 0.00 0.00 2.01
684 690 5.181748 ACAGCCTGCATTTTTGTTTTTACA 58.818 33.333 0.00 0.00 0.00 2.41
687 693 7.025963 CAGCCTGCATTTTTGTTTTTACAAAA 58.974 30.769 11.04 11.04 44.71 2.44
700 706 4.744795 TTTACAAAAACATGGCAGGTGT 57.255 36.364 5.20 0.00 0.00 4.16
701 707 4.744795 TTACAAAAACATGGCAGGTGTT 57.255 36.364 5.20 2.98 41.28 3.32
710 901 4.666512 ACATGGCAGGTGTTTTTAGATCT 58.333 39.130 3.00 0.00 0.00 2.75
711 902 5.815581 ACATGGCAGGTGTTTTTAGATCTA 58.184 37.500 3.00 0.00 0.00 1.98
765 2066 6.476378 AGACAGTCAGGCTTTATTAACACAT 58.524 36.000 2.66 0.00 20.59 3.21
777 2078 4.852134 ATTAACACATGACAGCTTGCAA 57.148 36.364 0.00 0.00 0.00 4.08
778 2079 2.497107 AACACATGACAGCTTGCAAC 57.503 45.000 0.00 0.00 0.00 4.17
779 2080 0.670162 ACACATGACAGCTTGCAACC 59.330 50.000 0.00 0.00 0.00 3.77
780 2081 0.669619 CACATGACAGCTTGCAACCA 59.330 50.000 0.00 0.00 0.00 3.67
781 2082 1.067364 CACATGACAGCTTGCAACCAA 59.933 47.619 0.00 0.00 0.00 3.67
782 2083 1.755959 ACATGACAGCTTGCAACCAAA 59.244 42.857 0.00 0.00 0.00 3.28
783 2084 2.168106 ACATGACAGCTTGCAACCAAAA 59.832 40.909 0.00 0.00 0.00 2.44
784 2085 3.181463 ACATGACAGCTTGCAACCAAAAT 60.181 39.130 0.00 0.00 0.00 1.82
785 2086 3.540314 TGACAGCTTGCAACCAAAATT 57.460 38.095 0.00 0.00 0.00 1.82
786 2087 3.871485 TGACAGCTTGCAACCAAAATTT 58.129 36.364 0.00 0.00 0.00 1.82
787 2088 3.870419 TGACAGCTTGCAACCAAAATTTC 59.130 39.130 0.00 0.00 0.00 2.17
788 2089 4.122046 GACAGCTTGCAACCAAAATTTCT 58.878 39.130 0.00 0.00 0.00 2.52
789 2090 4.516323 ACAGCTTGCAACCAAAATTTCTT 58.484 34.783 0.00 0.00 0.00 2.52
790 2091 4.943093 ACAGCTTGCAACCAAAATTTCTTT 59.057 33.333 0.00 0.00 0.00 2.52
791 2092 5.415389 ACAGCTTGCAACCAAAATTTCTTTT 59.585 32.000 0.00 0.00 34.90 2.27
792 2093 6.072008 ACAGCTTGCAACCAAAATTTCTTTTT 60.072 30.769 0.00 0.00 38.05 1.94
901 2233 0.250901 AAACTCAGCCCATTCGCACT 60.251 50.000 0.00 0.00 0.00 4.40
902 2234 0.250901 AACTCAGCCCATTCGCACTT 60.251 50.000 0.00 0.00 0.00 3.16
908 2240 3.451894 CCATTCGCACTTGGGGCC 61.452 66.667 0.00 0.00 0.00 5.80
909 2241 3.451894 CATTCGCACTTGGGGCCC 61.452 66.667 18.17 18.17 0.00 5.80
958 2298 1.004080 CCTGCCTGTCTGACACTGG 60.004 63.158 6.36 8.98 45.12 4.00
1011 2351 4.796495 GCGGGGATGCCGGAACTT 62.796 66.667 15.29 0.00 0.00 2.66
1269 2617 1.227438 ACCACACGACAGTTTCCCG 60.227 57.895 0.00 0.00 0.00 5.14
1351 2706 1.477700 GGTGCATTAGCTTGATTGGCA 59.522 47.619 0.00 0.00 42.74 4.92
1383 2738 3.244561 GCTCGATTCCCATAGAAATCCCA 60.245 47.826 0.00 0.00 38.21 4.37
1385 2740 4.910195 TCGATTCCCATAGAAATCCCATG 58.090 43.478 0.00 0.00 38.21 3.66
1395 2750 6.260936 CCATAGAAATCCCATGTAGTGTCAAC 59.739 42.308 0.00 0.00 0.00 3.18
1451 2956 3.698029 ATGACAATTGCTGCCGATTAC 57.302 42.857 5.05 0.00 0.00 1.89
1601 3272 5.054477 GTCACAAAGTACAAGAGGCAAGTA 58.946 41.667 0.00 0.00 0.00 2.24
1675 3363 3.257375 TGTACAGTTGGAGCTCATAACGT 59.743 43.478 17.19 20.09 0.00 3.99
1710 3398 4.314121 GTTTCAGATCAGCTGTCAACTCT 58.686 43.478 14.67 6.65 45.14 3.24
1847 3536 0.528249 CTTTTGCGGCAGTGCTTGTT 60.528 50.000 16.11 0.00 35.36 2.83
1889 3578 2.473235 GTGAGCTCACGAGTTGAAAGTC 59.527 50.000 29.84 3.71 37.10 3.01
1997 4328 5.065218 CAGTAGCCCATATCTTTCAACACAC 59.935 44.000 0.00 0.00 0.00 3.82
2006 4337 7.148018 CCATATCTTTCAACACACCAAGCTTAT 60.148 37.037 0.00 0.00 0.00 1.73
2007 4338 8.892723 CATATCTTTCAACACACCAAGCTTATA 58.107 33.333 0.00 0.00 0.00 0.98
2227 4820 7.523293 AATTATATCATCAATCGTTGGCCAA 57.477 32.000 16.05 16.05 0.00 4.52
2230 4823 2.513753 TCATCAATCGTTGGCCAAGTT 58.486 42.857 21.21 11.62 0.00 2.66
2387 4997 8.160106 TGATGTGCCCAACCTTTTAAAATTTAT 58.840 29.630 0.09 0.00 0.00 1.40
2515 5128 9.231297 TCAAGTTCAGTTTAAATTATCTGGAGG 57.769 33.333 4.31 0.00 0.00 4.30
2534 5147 0.040067 GCAAGGCAAGAGTTCGGTTG 60.040 55.000 0.00 0.00 0.00 3.77
2822 7249 9.859427 AATACCATAATTGACATCTTGTGTTTG 57.141 29.630 0.00 0.00 42.36 2.93
2909 7336 7.040062 CCAGGTATTGGTACAGAAATTTGTGAA 60.040 37.037 21.09 6.05 42.39 3.18
2994 8713 1.975680 GGACTAAGGGTTGGACACTCA 59.024 52.381 0.00 0.00 24.25 3.41
2995 8714 2.572104 GGACTAAGGGTTGGACACTCAT 59.428 50.000 0.00 0.00 24.25 2.90
3031 8751 1.408822 GCCTGATTGTACAAGAGGGGG 60.409 57.143 26.56 18.45 0.00 5.40
3139 10889 8.547173 CCTAAGCAATCTGATCTTATCCCTAAT 58.453 37.037 0.00 0.00 0.00 1.73
3334 11093 2.611518 GAGAGTTGTGAAGCGCTACAT 58.388 47.619 12.05 0.00 0.00 2.29
3349 11108 3.374988 CGCTACATCAAAGCATCCAAGAA 59.625 43.478 0.00 0.00 40.08 2.52
3354 11113 6.506500 ACATCAAAGCATCCAAGAAGTTAG 57.493 37.500 0.00 0.00 0.00 2.34
3429 11195 5.530915 CAGAATACTTGTGTCTTGACCCAAA 59.469 40.000 0.94 0.00 0.00 3.28
3584 11362 4.494484 TGATAGTCTTGAACATGGTCACG 58.506 43.478 14.43 12.47 0.00 4.35
3596 11374 3.694072 ACATGGTCACGTCCATTATTTGG 59.306 43.478 6.05 0.00 44.75 3.28
3613 11395 2.323999 TGGGAAAATTGGCCACTGAT 57.676 45.000 3.88 0.00 0.00 2.90
3802 11606 3.106552 GTGAGCAACACGCCAACA 58.893 55.556 0.00 0.00 44.04 3.33
3803 11607 1.298339 GTGAGCAACACGCCAACAC 60.298 57.895 0.00 0.00 44.04 3.32
3984 12002 1.304282 GATGCCAAGGAAGCAGGGA 59.696 57.895 0.00 0.00 44.90 4.20
4059 12080 0.324091 ATTCAAGGCTGCCAAGGGAG 60.324 55.000 22.65 2.91 36.62 4.30
4099 12127 5.656416 TCATAAGTGCCCCTTCCAAAATAAG 59.344 40.000 0.00 0.00 34.46 1.73
4115 12143 6.128200 CCAAAATAAGAAGGAAAATTGCTGGC 60.128 38.462 0.00 0.00 0.00 4.85
4137 12165 3.182972 CGGCAAGAAGAAACAAAGCATTG 59.817 43.478 0.00 0.00 42.46 2.82
4427 12460 9.439500 CCAGTGATTATGAAACCATTTGAAATT 57.561 29.630 0.00 0.00 0.00 1.82
4447 14387 4.986054 TTACTAGGCCTTGTTCTTTCCA 57.014 40.909 24.94 2.24 0.00 3.53
4457 14397 7.035612 GGCCTTGTTCTTTCCATTAATTGTAG 58.964 38.462 0.00 0.00 0.00 2.74
4480 14420 3.202906 CTGTCCACTCGAGGTTGAAAAA 58.797 45.455 18.41 0.00 0.00 1.94
4602 14542 3.476552 AGAAGTTGCCGAAGAAACATCA 58.523 40.909 0.00 0.00 28.88 3.07
4645 14594 0.949397 CATCCTGCAATCCATCACCG 59.051 55.000 0.00 0.00 0.00 4.94
4669 14618 2.175202 GAGCAGAGAGTTGGAGAAGGA 58.825 52.381 0.00 0.00 0.00 3.36
4723 14674 2.205307 AAGCCGTCGCACTAATAGAC 57.795 50.000 0.00 0.00 37.52 2.59
4724 14675 1.100510 AGCCGTCGCACTAATAGACA 58.899 50.000 0.00 0.00 37.52 3.41
4808 14759 4.212214 ACAGATCTTGCGACAAAAACTCTC 59.788 41.667 0.00 0.00 0.00 3.20
4886 14837 3.417101 ACCTTATTTCAACACGCCATCA 58.583 40.909 0.00 0.00 0.00 3.07
4902 14853 2.174210 CCATCATCTCCACCACCTCATT 59.826 50.000 0.00 0.00 0.00 2.57
4905 14856 3.117745 TCATCTCCACCACCTCATTGAT 58.882 45.455 0.00 0.00 0.00 2.57
4958 14909 6.853490 AGATAAAAGAAATAGATGGGTCCCC 58.147 40.000 5.13 0.00 0.00 4.81
4969 14920 3.412408 GGTCCCCCTCCTCTTGCC 61.412 72.222 0.00 0.00 0.00 4.52
4998 14949 2.914289 GAGGCTGTCAGATGGGGG 59.086 66.667 3.32 0.00 0.00 5.40
5082 15033 1.064825 AATCTGGTCGAACCCCAAGT 58.935 50.000 0.00 0.00 37.50 3.16
5112 15063 2.642129 CGACGCCCATTTGTGCAA 59.358 55.556 0.00 0.00 0.00 4.08
5135 15086 0.313672 TTGGTTGCCAACGATTCTGC 59.686 50.000 0.74 0.00 38.75 4.26
5137 15088 0.169009 GGTTGCCAACGATTCTGCTC 59.831 55.000 0.74 0.00 0.00 4.26
5169 15120 7.243604 TGGTTAATGGAATGAGCAAATTTCT 57.756 32.000 0.00 0.00 0.00 2.52
5291 15244 1.540797 GCAGCACATCAAGCCCAAAAA 60.541 47.619 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 9.729023 CGGACATCTTGTTGCATAATATTTTTA 57.271 29.630 0.00 0.00 0.00 1.52
127 128 3.122297 TGCCTTGTTGCGAAAATTTCTG 58.878 40.909 4.09 0.00 0.00 3.02
160 161 1.141053 GGCCGAGTGTTCCTATCCATT 59.859 52.381 0.00 0.00 0.00 3.16
161 162 0.759346 GGCCGAGTGTTCCTATCCAT 59.241 55.000 0.00 0.00 0.00 3.41
224 225 0.468226 ATCCGCGGGCTGATCTTTTA 59.532 50.000 27.83 0.12 0.00 1.52
229 230 2.786539 TATGCATCCGCGGGCTGATC 62.787 60.000 27.83 11.64 42.97 2.92
230 231 2.793160 CTATGCATCCGCGGGCTGAT 62.793 60.000 27.83 18.25 42.97 2.90
231 232 3.519973 CTATGCATCCGCGGGCTGA 62.520 63.158 27.83 5.87 42.97 4.26
232 233 3.046087 CTATGCATCCGCGGGCTG 61.046 66.667 27.83 23.28 42.97 4.85
233 234 4.996434 GCTATGCATCCGCGGGCT 62.996 66.667 27.83 10.71 42.97 5.19
238 239 2.598632 GGACACGCTATGCATCCGC 61.599 63.158 16.70 13.48 39.24 5.54
243 244 0.323302 TCAAAGGGACACGCTATGCA 59.677 50.000 0.00 0.00 0.00 3.96
246 247 5.885912 ACAAATAATCAAAGGGACACGCTAT 59.114 36.000 0.00 0.00 0.00 2.97
254 255 9.594936 TTAGGAAAAGACAAATAATCAAAGGGA 57.405 29.630 0.00 0.00 0.00 4.20
310 311 5.310451 ACTAATGACTAACCCTCGCAAAAA 58.690 37.500 0.00 0.00 0.00 1.94
311 312 4.901868 ACTAATGACTAACCCTCGCAAAA 58.098 39.130 0.00 0.00 0.00 2.44
312 313 4.546829 ACTAATGACTAACCCTCGCAAA 57.453 40.909 0.00 0.00 0.00 3.68
313 314 4.546829 AACTAATGACTAACCCTCGCAA 57.453 40.909 0.00 0.00 0.00 4.85
314 315 4.546829 AAACTAATGACTAACCCTCGCA 57.453 40.909 0.00 0.00 0.00 5.10
315 316 6.537660 ACAATAAACTAATGACTAACCCTCGC 59.462 38.462 0.00 0.00 0.00 5.03
316 317 8.488651 AACAATAAACTAATGACTAACCCTCG 57.511 34.615 0.00 0.00 0.00 4.63
338 339 7.434492 TGTGTTTCTTTGGTTGTTCTTTAACA 58.566 30.769 0.00 0.00 43.85 2.41
339 340 7.876896 TGTGTTTCTTTGGTTGTTCTTTAAC 57.123 32.000 0.00 0.00 36.07 2.01
340 341 7.547370 CCATGTGTTTCTTTGGTTGTTCTTTAA 59.453 33.333 0.00 0.00 0.00 1.52
341 342 7.038659 CCATGTGTTTCTTTGGTTGTTCTTTA 58.961 34.615 0.00 0.00 0.00 1.85
342 343 5.874261 CCATGTGTTTCTTTGGTTGTTCTTT 59.126 36.000 0.00 0.00 0.00 2.52
355 356 4.284234 CCCCAAAAGAATCCATGTGTTTCT 59.716 41.667 0.00 0.00 0.00 2.52
383 384 0.113580 TGGAACCTTAAAGTGCCCCC 59.886 55.000 0.00 0.00 34.01 5.40
384 385 1.254026 GTGGAACCTTAAAGTGCCCC 58.746 55.000 0.00 0.00 34.01 5.80
385 386 1.611977 GTGTGGAACCTTAAAGTGCCC 59.388 52.381 0.00 0.00 34.01 5.36
386 387 2.293399 CTGTGTGGAACCTTAAAGTGCC 59.707 50.000 0.00 0.00 35.77 5.01
387 388 2.287608 GCTGTGTGGAACCTTAAAGTGC 60.288 50.000 0.00 0.00 34.36 4.40
388 389 2.293399 GGCTGTGTGGAACCTTAAAGTG 59.707 50.000 0.00 0.00 34.36 3.16
409 410 0.469917 ATGGATCTTACTGTGCCCCG 59.530 55.000 0.00 0.00 0.00 5.73
413 414 2.224066 ACGCCTATGGATCTTACTGTGC 60.224 50.000 0.00 0.00 0.00 4.57
414 415 3.735237 ACGCCTATGGATCTTACTGTG 57.265 47.619 0.00 0.00 0.00 3.66
418 419 4.865365 GCAATCTACGCCTATGGATCTTAC 59.135 45.833 0.00 0.00 0.00 2.34
433 439 3.304057 GGAAATAAGCTGCGGCAATCTAC 60.304 47.826 21.93 6.73 41.70 2.59
436 442 1.405105 TGGAAATAAGCTGCGGCAATC 59.595 47.619 21.93 9.65 41.70 2.67
446 452 7.988028 AGGAAGTAACTCATAGTGGAAATAAGC 59.012 37.037 0.00 0.00 0.00 3.09
452 458 5.948162 ACGTAGGAAGTAACTCATAGTGGAA 59.052 40.000 0.00 0.00 0.00 3.53
454 460 5.831702 ACGTAGGAAGTAACTCATAGTGG 57.168 43.478 0.00 0.00 0.00 4.00
457 463 8.983307 AAAAGAACGTAGGAAGTAACTCATAG 57.017 34.615 0.00 0.00 0.00 2.23
466 472 9.557061 AAAATCTCTAAAAAGAACGTAGGAAGT 57.443 29.630 0.00 0.00 0.00 3.01
532 538 9.768662 AAAGCAAAATGAATGAATTTACACTCT 57.231 25.926 0.00 0.00 0.00 3.24
533 539 9.801714 CAAAGCAAAATGAATGAATTTACACTC 57.198 29.630 0.00 0.00 0.00 3.51
534 540 9.328845 ACAAAGCAAAATGAATGAATTTACACT 57.671 25.926 0.00 0.00 0.00 3.55
542 548 9.624697 GACTACATACAAAGCAAAATGAATGAA 57.375 29.630 0.00 0.00 0.00 2.57
543 549 8.791675 TGACTACATACAAAGCAAAATGAATGA 58.208 29.630 0.00 0.00 0.00 2.57
544 550 8.853345 GTGACTACATACAAAGCAAAATGAATG 58.147 33.333 0.00 0.00 0.00 2.67
545 551 8.796475 AGTGACTACATACAAAGCAAAATGAAT 58.204 29.630 0.00 0.00 0.00 2.57
546 552 8.165239 AGTGACTACATACAAAGCAAAATGAA 57.835 30.769 0.00 0.00 0.00 2.57
547 553 7.744087 AGTGACTACATACAAAGCAAAATGA 57.256 32.000 0.00 0.00 0.00 2.57
548 554 7.862372 ACAAGTGACTACATACAAAGCAAAATG 59.138 33.333 0.00 0.00 0.00 2.32
549 555 7.940850 ACAAGTGACTACATACAAAGCAAAAT 58.059 30.769 0.00 0.00 0.00 1.82
550 556 7.328277 ACAAGTGACTACATACAAAGCAAAA 57.672 32.000 0.00 0.00 0.00 2.44
551 557 6.935741 ACAAGTGACTACATACAAAGCAAA 57.064 33.333 0.00 0.00 0.00 3.68
552 558 6.540551 TCAACAAGTGACTACATACAAAGCAA 59.459 34.615 0.00 0.00 0.00 3.91
553 559 6.052360 TCAACAAGTGACTACATACAAAGCA 58.948 36.000 0.00 0.00 0.00 3.91
554 560 6.539649 TCAACAAGTGACTACATACAAAGC 57.460 37.500 0.00 0.00 0.00 3.51
555 561 9.599322 GATTTCAACAAGTGACTACATACAAAG 57.401 33.333 0.00 0.00 35.39 2.77
556 562 9.337396 AGATTTCAACAAGTGACTACATACAAA 57.663 29.630 0.00 0.00 35.39 2.83
557 563 8.902540 AGATTTCAACAAGTGACTACATACAA 57.097 30.769 0.00 0.00 35.39 2.41
558 564 8.367911 AGAGATTTCAACAAGTGACTACATACA 58.632 33.333 0.00 0.00 35.39 2.29
559 565 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
561 567 9.778741 TTTAGAGATTTCAACAAGTGACTACAT 57.221 29.630 0.00 0.00 35.39 2.29
562 568 9.607988 TTTTAGAGATTTCAACAAGTGACTACA 57.392 29.630 0.00 0.00 35.39 2.74
565 571 8.624776 CCTTTTTAGAGATTTCAACAAGTGACT 58.375 33.333 0.00 0.00 35.39 3.41
566 572 7.379797 GCCTTTTTAGAGATTTCAACAAGTGAC 59.620 37.037 0.00 0.00 35.39 3.67
567 573 7.068103 TGCCTTTTTAGAGATTTCAACAAGTGA 59.932 33.333 0.00 0.00 0.00 3.41
568 574 7.202526 TGCCTTTTTAGAGATTTCAACAAGTG 58.797 34.615 0.00 0.00 0.00 3.16
569 575 7.346751 TGCCTTTTTAGAGATTTCAACAAGT 57.653 32.000 0.00 0.00 0.00 3.16
570 576 8.647143 TTTGCCTTTTTAGAGATTTCAACAAG 57.353 30.769 0.00 0.00 0.00 3.16
581 587 9.503427 CGTTCCTAAATATTTGCCTTTTTAGAG 57.497 33.333 11.05 0.00 34.90 2.43
582 588 8.463607 CCGTTCCTAAATATTTGCCTTTTTAGA 58.536 33.333 11.05 0.00 34.90 2.10
583 589 8.463607 TCCGTTCCTAAATATTTGCCTTTTTAG 58.536 33.333 11.05 0.00 33.47 1.85
584 590 8.350852 TCCGTTCCTAAATATTTGCCTTTTTA 57.649 30.769 11.05 0.00 0.00 1.52
585 591 7.234661 TCCGTTCCTAAATATTTGCCTTTTT 57.765 32.000 11.05 0.00 0.00 1.94
586 592 6.844097 TCCGTTCCTAAATATTTGCCTTTT 57.156 33.333 11.05 0.00 0.00 2.27
587 593 6.661805 TCTTCCGTTCCTAAATATTTGCCTTT 59.338 34.615 11.05 0.00 0.00 3.11
588 594 6.184789 TCTTCCGTTCCTAAATATTTGCCTT 58.815 36.000 11.05 0.00 0.00 4.35
589 595 5.751586 TCTTCCGTTCCTAAATATTTGCCT 58.248 37.500 11.05 0.00 0.00 4.75
590 596 6.095021 ACTTCTTCCGTTCCTAAATATTTGCC 59.905 38.462 11.05 0.00 0.00 4.52
591 597 7.085052 ACTTCTTCCGTTCCTAAATATTTGC 57.915 36.000 11.05 0.00 0.00 3.68
592 598 9.379791 ACTACTTCTTCCGTTCCTAAATATTTG 57.620 33.333 11.05 1.40 0.00 2.32
593 599 9.955102 AACTACTTCTTCCGTTCCTAAATATTT 57.045 29.630 5.89 5.89 0.00 1.40
594 600 9.597170 GAACTACTTCTTCCGTTCCTAAATATT 57.403 33.333 0.00 0.00 31.89 1.28
595 601 8.979534 AGAACTACTTCTTCCGTTCCTAAATAT 58.020 33.333 0.00 0.00 37.15 1.28
596 602 8.358582 AGAACTACTTCTTCCGTTCCTAAATA 57.641 34.615 0.00 0.00 37.15 1.40
597 603 7.242322 AGAACTACTTCTTCCGTTCCTAAAT 57.758 36.000 0.00 0.00 37.15 1.40
598 604 6.661304 AGAACTACTTCTTCCGTTCCTAAA 57.339 37.500 0.00 0.00 37.15 1.85
599 605 6.041296 ACAAGAACTACTTCTTCCGTTCCTAA 59.959 38.462 0.00 0.00 43.70 2.69
600 606 5.537674 ACAAGAACTACTTCTTCCGTTCCTA 59.462 40.000 0.00 0.00 43.70 2.94
601 607 4.344390 ACAAGAACTACTTCTTCCGTTCCT 59.656 41.667 0.00 0.00 43.70 3.36
602 608 4.448060 CACAAGAACTACTTCTTCCGTTCC 59.552 45.833 0.00 0.00 43.70 3.62
603 609 4.084485 GCACAAGAACTACTTCTTCCGTTC 60.084 45.833 0.00 0.00 43.70 3.95
604 610 3.808174 GCACAAGAACTACTTCTTCCGTT 59.192 43.478 0.00 0.00 43.70 4.44
605 611 3.181469 TGCACAAGAACTACTTCTTCCGT 60.181 43.478 0.00 0.00 43.70 4.69
606 612 3.390135 TGCACAAGAACTACTTCTTCCG 58.610 45.455 0.00 0.00 43.70 4.30
607 613 4.378874 GCATGCACAAGAACTACTTCTTCC 60.379 45.833 14.21 0.00 43.70 3.46
608 614 4.214119 TGCATGCACAAGAACTACTTCTTC 59.786 41.667 18.46 0.00 43.70 2.87
609 615 4.136796 TGCATGCACAAGAACTACTTCTT 58.863 39.130 18.46 0.00 46.01 2.52
610 616 3.743521 TGCATGCACAAGAACTACTTCT 58.256 40.909 18.46 0.00 38.49 2.85
611 617 4.691860 ATGCATGCACAAGAACTACTTC 57.308 40.909 25.37 0.00 36.61 3.01
612 618 6.764308 ATAATGCATGCACAAGAACTACTT 57.236 33.333 25.37 11.72 39.70 2.24
613 619 7.554118 ACTTATAATGCATGCACAAGAACTACT 59.446 33.333 25.37 0.00 0.00 2.57
614 620 7.697691 ACTTATAATGCATGCACAAGAACTAC 58.302 34.615 25.37 0.00 0.00 2.73
645 651 5.732528 GCAGGCTGTCATGTCATAAATTCTG 60.733 44.000 17.16 0.00 0.00 3.02
646 652 4.337555 GCAGGCTGTCATGTCATAAATTCT 59.662 41.667 17.16 0.00 0.00 2.40
647 653 4.096833 TGCAGGCTGTCATGTCATAAATTC 59.903 41.667 17.16 0.00 0.00 2.17
682 688 3.625649 AAACACCTGCCATGTTTTTGT 57.374 38.095 4.69 0.00 45.71 2.83
687 693 5.079643 AGATCTAAAAACACCTGCCATGTT 58.920 37.500 0.00 0.00 42.07 2.71
688 694 4.666512 AGATCTAAAAACACCTGCCATGT 58.333 39.130 0.00 0.00 0.00 3.21
689 695 6.757897 TTAGATCTAAAAACACCTGCCATG 57.242 37.500 12.87 0.00 0.00 3.66
690 696 7.775053 TTTTAGATCTAAAAACACCTGCCAT 57.225 32.000 29.79 0.00 40.74 4.40
691 697 7.589958 TTTTTAGATCTAAAAACACCTGCCA 57.410 32.000 34.21 18.74 44.98 4.92
733 924 4.706842 AAGCCTGACTGTCTTTCCTAAA 57.293 40.909 9.51 0.00 0.00 1.85
735 926 6.374417 AATAAAGCCTGACTGTCTTTCCTA 57.626 37.500 9.51 0.00 32.85 2.94
736 927 4.917906 ATAAAGCCTGACTGTCTTTCCT 57.082 40.909 9.51 0.00 32.85 3.36
738 929 7.041372 TGTGTTAATAAAGCCTGACTGTCTTTC 60.041 37.037 9.51 0.00 32.85 2.62
742 933 6.371548 TCATGTGTTAATAAAGCCTGACTGTC 59.628 38.462 0.00 0.00 0.00 3.51
746 937 6.494893 TGTCATGTGTTAATAAAGCCTGAC 57.505 37.500 0.00 0.00 0.00 3.51
747 938 5.123820 GCTGTCATGTGTTAATAAAGCCTGA 59.876 40.000 0.00 0.00 0.00 3.86
748 939 5.124457 AGCTGTCATGTGTTAATAAAGCCTG 59.876 40.000 0.00 0.00 0.00 4.85
749 940 5.256474 AGCTGTCATGTGTTAATAAAGCCT 58.744 37.500 0.00 0.00 0.00 4.58
750 941 5.567138 AGCTGTCATGTGTTAATAAAGCC 57.433 39.130 0.00 0.00 0.00 4.35
751 942 5.287035 GCAAGCTGTCATGTGTTAATAAAGC 59.713 40.000 0.00 0.00 0.00 3.51
754 945 5.956068 TGCAAGCTGTCATGTGTTAATAA 57.044 34.783 0.00 0.00 0.00 1.40
756 947 4.549458 GTTGCAAGCTGTCATGTGTTAAT 58.451 39.130 0.00 0.00 0.00 1.40
765 2066 3.540314 AATTTTGGTTGCAAGCTGTCA 57.460 38.095 27.31 10.82 0.00 3.58
777 2078 9.163931 TGGGTCACCTCAAAAAGAAATTTTGGT 62.164 37.037 12.24 2.81 44.76 3.67
778 2079 6.855065 TGGGTCACCTCAAAAAGAAATTTTGG 60.855 38.462 12.24 2.27 44.76 3.28
779 2080 6.112058 TGGGTCACCTCAAAAAGAAATTTTG 58.888 36.000 7.21 7.21 45.33 2.44
780 2081 6.306643 TGGGTCACCTCAAAAAGAAATTTT 57.693 33.333 0.00 0.00 38.57 1.82
781 2082 5.948742 TGGGTCACCTCAAAAAGAAATTT 57.051 34.783 0.00 0.00 37.76 1.82
782 2083 7.610580 TTATGGGTCACCTCAAAAAGAAATT 57.389 32.000 0.00 0.00 37.76 1.82
783 2084 7.797121 ATTATGGGTCACCTCAAAAAGAAAT 57.203 32.000 0.00 0.00 37.76 2.17
784 2085 8.713708 TTATTATGGGTCACCTCAAAAAGAAA 57.286 30.769 0.00 0.00 37.76 2.52
785 2086 8.713708 TTTATTATGGGTCACCTCAAAAAGAA 57.286 30.769 0.00 0.00 37.76 2.52
786 2087 8.748412 CATTTATTATGGGTCACCTCAAAAAGA 58.252 33.333 0.00 0.00 37.76 2.52
787 2088 8.531146 ACATTTATTATGGGTCACCTCAAAAAG 58.469 33.333 0.00 0.00 37.76 2.27
788 2089 8.310382 CACATTTATTATGGGTCACCTCAAAAA 58.690 33.333 0.00 0.00 37.76 1.94
789 2090 7.453126 ACACATTTATTATGGGTCACCTCAAAA 59.547 33.333 0.00 0.00 37.76 2.44
790 2091 6.951198 ACACATTTATTATGGGTCACCTCAAA 59.049 34.615 0.00 0.00 37.76 2.69
791 2092 6.489603 ACACATTTATTATGGGTCACCTCAA 58.510 36.000 0.00 0.00 37.76 3.02
792 2093 6.073447 ACACATTTATTATGGGTCACCTCA 57.927 37.500 0.00 0.00 37.76 3.86
793 2094 6.601613 TGAACACATTTATTATGGGTCACCTC 59.398 38.462 0.00 0.00 34.01 3.85
794 2095 6.377146 GTGAACACATTTATTATGGGTCACCT 59.623 38.462 0.00 0.00 34.01 4.00
795 2096 6.151985 TGTGAACACATTTATTATGGGTCACC 59.848 38.462 15.39 0.00 34.01 4.02
796 2097 7.151999 TGTGAACACATTTATTATGGGTCAC 57.848 36.000 3.39 13.06 34.01 3.67
908 2240 2.435938 CGTGTCCATCCCAACCGG 60.436 66.667 0.00 0.00 0.00 5.28
909 2241 3.124921 GCGTGTCCATCCCAACCG 61.125 66.667 0.00 0.00 0.00 4.44
910 2242 1.745489 GAGCGTGTCCATCCCAACC 60.745 63.158 0.00 0.00 0.00 3.77
911 2243 2.100631 CGAGCGTGTCCATCCCAAC 61.101 63.158 0.00 0.00 0.00 3.77
912 2244 2.264480 CGAGCGTGTCCATCCCAA 59.736 61.111 0.00 0.00 0.00 4.12
913 2245 4.451150 GCGAGCGTGTCCATCCCA 62.451 66.667 0.00 0.00 0.00 4.37
916 2248 4.796231 ACGGCGAGCGTGTCCATC 62.796 66.667 16.62 0.00 0.00 3.51
958 2298 4.200283 CTGAGTCCTCTCCGGCGC 62.200 72.222 0.00 0.00 39.75 6.53
1269 2617 2.736826 GCAGAGGCAGGGTAGGTCC 61.737 68.421 0.00 0.00 40.72 4.46
1351 2706 3.804036 TGGGAATCGAGCATAAATCGTT 58.196 40.909 0.00 0.00 40.95 3.85
1383 2738 4.937620 AGCGAATTCATGTTGACACTACAT 59.062 37.500 6.22 0.00 36.70 2.29
1385 2740 4.928661 AGCGAATTCATGTTGACACTAC 57.071 40.909 6.22 0.00 0.00 2.73
1395 2750 3.419922 GCGAGCAATTAAGCGAATTCATG 59.580 43.478 6.22 0.00 35.45 3.07
1601 3272 6.144080 CAGTGAGATACGAAACGAAAAAGAGT 59.856 38.462 0.00 0.00 0.00 3.24
1609 3280 4.233123 ACAACAGTGAGATACGAAACGA 57.767 40.909 0.00 0.00 0.00 3.85
1653 3341 3.257375 ACGTTATGAGCTCCAACTGTACA 59.743 43.478 20.05 0.00 0.00 2.90
1675 3363 6.499106 TGATCTGAAACCATCCATAAGCTA 57.501 37.500 0.00 0.00 0.00 3.32
1710 3398 2.680352 GAGGGCCACTCGTCCTCA 60.680 66.667 6.18 0.00 44.72 3.86
1847 3536 4.097741 CACACCTGAAGTTCACCATTTTGA 59.902 41.667 0.08 0.00 0.00 2.69
1889 3578 1.392853 GCAAGAGAAGTGACTCATGCG 59.607 52.381 9.44 0.00 46.20 4.73
1997 4328 8.450578 TGTCCATGAGTTTATTATAAGCTTGG 57.549 34.615 9.86 11.10 0.00 3.61
2120 4462 2.260481 GTTTCCGTGTGCTAGCTCTAC 58.740 52.381 17.23 10.90 0.00 2.59
2227 4820 3.751518 ACTAGTGCGGAAATTCCAAACT 58.248 40.909 17.32 17.32 35.91 2.66
2230 4823 4.901868 ACTAACTAGTGCGGAAATTCCAA 58.098 39.130 13.04 0.00 33.56 3.53
2241 4843 2.736347 TCAGGAGGGACTAACTAGTGC 58.264 52.381 0.00 0.04 41.55 4.40
2387 4997 3.379057 CCATCATCAAGCTGTACAATGCA 59.621 43.478 9.50 0.00 0.00 3.96
2515 5128 0.040067 CAACCGAACTCTTGCCTTGC 60.040 55.000 0.00 0.00 0.00 4.01
2557 5170 5.455392 CCAACAATACTTGAGTGAGCAAAG 58.545 41.667 0.00 0.00 0.00 2.77
2817 7244 5.772825 AGCTCTGCTCATAAAAACAAACA 57.227 34.783 0.00 0.00 30.62 2.83
2818 7245 6.208644 TGAAGCTCTGCTCATAAAAACAAAC 58.791 36.000 0.00 0.00 38.25 2.93
2822 7249 7.923888 TGATATGAAGCTCTGCTCATAAAAAC 58.076 34.615 9.34 4.13 38.25 2.43
2898 7325 3.456280 TGGTGCAAGCTTCACAAATTTC 58.544 40.909 22.19 10.38 36.22 2.17
2909 7336 2.030274 GGTATTTCGTTTGGTGCAAGCT 60.030 45.455 0.00 0.00 33.76 3.74
2994 8713 1.063183 GGCCTCTAGCATCCAAGGAT 58.937 55.000 0.00 0.00 46.50 3.24
2995 8714 0.030705 AGGCCTCTAGCATCCAAGGA 60.031 55.000 0.00 0.00 46.50 3.36
3031 8751 3.578282 ACAAAATGAATTCCTGGTCCCAC 59.422 43.478 2.27 0.00 0.00 4.61
3139 10889 4.010667 AGGTGTGTGTTAGCCGAAATTA 57.989 40.909 0.00 0.00 0.00 1.40
3334 11093 5.869579 AGACTAACTTCTTGGATGCTTTGA 58.130 37.500 0.00 0.00 0.00 2.69
3596 11374 2.178580 TCCATCAGTGGCCAATTTTCC 58.821 47.619 7.24 0.00 45.63 3.13
3613 11395 3.132160 TGCAAAATTACGACGAGTTCCA 58.868 40.909 0.00 0.00 0.00 3.53
3796 11600 4.389077 GTGTGATAGTGAAGTAGTGTTGGC 59.611 45.833 0.00 0.00 0.00 4.52
3797 11601 5.784177 AGTGTGATAGTGAAGTAGTGTTGG 58.216 41.667 0.00 0.00 0.00 3.77
3798 11602 7.653713 AGAAAGTGTGATAGTGAAGTAGTGTTG 59.346 37.037 0.00 0.00 0.00 3.33
3799 11603 7.653713 CAGAAAGTGTGATAGTGAAGTAGTGTT 59.346 37.037 0.00 0.00 0.00 3.32
3800 11604 7.148641 CAGAAAGTGTGATAGTGAAGTAGTGT 58.851 38.462 0.00 0.00 0.00 3.55
3801 11605 6.090088 GCAGAAAGTGTGATAGTGAAGTAGTG 59.910 42.308 0.00 0.00 0.00 2.74
3802 11606 6.159988 GCAGAAAGTGTGATAGTGAAGTAGT 58.840 40.000 0.00 0.00 0.00 2.73
3803 11607 5.578727 GGCAGAAAGTGTGATAGTGAAGTAG 59.421 44.000 0.00 0.00 0.00 2.57
3984 12002 3.898123 TCAGCTTCCACTTCTACTTCTGT 59.102 43.478 0.00 0.00 0.00 3.41
4059 12080 6.088824 CACTTATGACATCCTTGTTTTGCTC 58.911 40.000 0.00 0.00 35.79 4.26
4099 12127 0.737367 GCCGCCAGCAATTTTCCTTC 60.737 55.000 0.00 0.00 42.97 3.46
4115 12143 2.490328 TGCTTTGTTTCTTCTTGCCG 57.510 45.000 0.00 0.00 0.00 5.69
4137 12165 3.119245 ACATCATCTTTGCTGCCATGTTC 60.119 43.478 0.00 0.00 0.00 3.18
4427 12460 5.514500 AATGGAAAGAACAAGGCCTAGTA 57.486 39.130 5.16 0.00 0.00 1.82
4428 12461 4.388577 AATGGAAAGAACAAGGCCTAGT 57.611 40.909 5.16 0.00 0.00 2.57
4430 12463 6.723977 ACAATTAATGGAAAGAACAAGGCCTA 59.276 34.615 5.16 0.00 0.00 3.93
4431 12464 5.543790 ACAATTAATGGAAAGAACAAGGCCT 59.456 36.000 0.00 0.00 0.00 5.19
4447 14387 6.405953 CCTCGAGTGGACAGTCTACAATTAAT 60.406 42.308 18.49 0.00 29.47 1.40
4457 14397 0.959553 TCAACCTCGAGTGGACAGTC 59.040 55.000 12.31 0.00 0.00 3.51
4480 14420 4.136796 TCTTTACTGTTGCTTCAGTGCAT 58.863 39.130 19.21 1.43 46.36 3.96
4495 14435 4.532834 TGCAGGTGTCCTTTTTCTTTACT 58.467 39.130 0.00 0.00 0.00 2.24
4506 14446 1.607467 GGGCATTTGCAGGTGTCCT 60.607 57.895 14.69 0.00 44.36 3.85
4602 14542 0.745845 GCGTGAGGTGATGCTCCAAT 60.746 55.000 0.00 0.00 0.00 3.16
4645 14594 0.108233 CTCCAACTCTCTGCTCTGGC 60.108 60.000 0.00 0.00 39.26 4.85
4669 14618 2.363306 TTGTTCTGCAACATGGTCCT 57.637 45.000 0.00 0.00 42.28 3.85
4723 14674 1.250328 TCAAGGAGTGCAATTGGCTG 58.750 50.000 7.72 0.00 45.15 4.85
4724 14675 2.226962 ATCAAGGAGTGCAATTGGCT 57.773 45.000 7.72 0.00 45.15 4.75
4808 14759 0.875059 GCCTCGAAGAAGGGTTTGTG 59.125 55.000 0.00 0.00 34.09 3.33
4886 14837 2.848694 ACATCAATGAGGTGGTGGAGAT 59.151 45.455 0.00 0.00 33.66 2.75
4902 14853 1.773856 TTGTTCCCCTGGCGACATCA 61.774 55.000 0.00 0.00 41.51 3.07
4905 14856 1.104577 GTTTTGTTCCCCTGGCGACA 61.105 55.000 0.00 0.00 39.59 4.35
4958 14909 4.821589 GTCGGCGGCAAGAGGAGG 62.822 72.222 6.63 0.00 0.00 4.30
4998 14949 4.461198 CATTGGTATTGGAACCCTCCTAC 58.539 47.826 0.00 0.00 42.94 3.18
5082 15033 4.201679 CGTCGCCAGGCCATACGA 62.202 66.667 19.21 7.84 35.66 3.43
5135 15086 3.887621 TCCATTAACCAAGGAGTCGAG 57.112 47.619 0.00 0.00 0.00 4.04
5137 15088 4.513442 TCATTCCATTAACCAAGGAGTCG 58.487 43.478 0.00 0.00 32.11 4.18
5239 15191 4.289342 CATTTGCTTGTGATCGTTGTTGA 58.711 39.130 0.00 0.00 0.00 3.18
5264 15217 3.258228 TTGATGTGCTGCTCGCCCT 62.258 57.895 0.00 0.00 38.05 5.19


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

AutoCloner maintained by Alex Coulton.