Multiple sequence alignment - TraesCS6A01G223200

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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 TraesCS6A01G223200 chr6A 100.000 3685 0 0 1 3685 418543070 418546754 0.000000e+00 6806
1 TraesCS6A01G223200 chr6A 97.133 1988 55 1 1700 3685 40242265 40244252 0.000000e+00 3354
2 TraesCS6A01G223200 chr6A 97.035 1990 50 6 1701 3685 418589248 418587263 0.000000e+00 3339
3 TraesCS6A01G223200 chr6A 97.318 1864 44 5 1824 3685 418599699 418601558 0.000000e+00 3160
4 TraesCS6A01G223200 chr6A 81.772 395 65 6 916 1306 18566051 18565660 1.280000e-84 324
5 TraesCS6A01G223200 chr6A 85.959 292 33 5 1412 1695 18565222 18564931 4.620000e-79 305
6 TraesCS6A01G223200 chr6A 87.826 115 13 1 1582 1695 11456072 11455958 2.310000e-27 134
7 TraesCS6A01G223200 chr3A 97.386 1989 43 6 1701 3685 547257695 547259678 0.000000e+00 3376
8 TraesCS6A01G223200 chr3A 97.134 1989 52 3 1701 3685 691700327 691698340 0.000000e+00 3352
9 TraesCS6A01G223200 chr3A 95.315 1985 82 9 1710 3685 497204947 497202965 0.000000e+00 3140
10 TraesCS6A01G223200 chr3A 85.366 574 61 13 1145 1701 697763896 697763329 1.150000e-159 573
11 TraesCS6A01G223200 chr3A 86.435 317 34 9 3374 3685 20187004 20186692 4.560000e-89 339
12 TraesCS6A01G223200 chr3A 80.531 452 40 18 1 408 697772102 697771655 1.660000e-78 303
13 TraesCS6A01G223200 chr3A 75.506 494 58 31 1 457 149080503 149080036 2.260000e-42 183
14 TraesCS6A01G223200 chr4A 97.134 1989 54 2 1700 3685 615427648 615425660 0.000000e+00 3354
15 TraesCS6A01G223200 chr4A 80.443 542 58 24 1 505 667372822 667373352 1.620000e-98 370
16 TraesCS6A01G223200 chr4A 89.000 300 23 6 1412 1701 667375607 667375906 2.700000e-96 363
17 TraesCS6A01G223200 chr4A 94.030 67 4 0 669 735 667373349 667373415 6.510000e-18 102
18 TraesCS6A01G223200 chr5A 96.687 1992 58 5 1699 3685 77885543 77887531 0.000000e+00 3306
19 TraesCS6A01G223200 chr1A 96.241 1809 51 11 1701 3500 474217351 474215551 0.000000e+00 2948
20 TraesCS6A01G223200 chr1A 92.357 157 11 1 502 657 580955988 580955832 4.790000e-54 222
21 TraesCS6A01G223200 chr1A 90.361 166 15 1 493 657 84012556 84012391 2.230000e-52 217
22 TraesCS6A01G223200 chr3B 83.302 533 50 16 1 505 750319455 750318934 4.340000e-124 455
23 TraesCS6A01G223200 chr3B 89.632 299 22 6 1412 1701 750316386 750316088 4.490000e-99 372
24 TraesCS6A01G223200 chr3B 82.522 452 41 16 1 419 750324272 750323826 2.700000e-96 363
25 TraesCS6A01G223200 chr3B 94.690 113 6 0 669 781 750318937 750318825 3.780000e-40 176
26 TraesCS6A01G223200 chr7B 80.901 555 97 7 803 1352 641378475 641377925 2.630000e-116 429
27 TraesCS6A01G223200 chr7B 81.041 269 43 4 1435 1695 641377879 641377611 1.340000e-49 207
28 TraesCS6A01G223200 chr7A 79.857 561 94 9 803 1352 670215856 670215304 3.450000e-105 392
29 TraesCS6A01G223200 chr6B 75.058 862 157 29 835 1658 9179772 9180613 7.570000e-92 348
30 TraesCS6A01G223200 chrUn 82.368 380 60 6 910 1285 772601 772977 1.280000e-84 324
31 TraesCS6A01G223200 chrUn 85.959 292 33 5 1412 1695 773436 773727 4.620000e-79 305
32 TraesCS6A01G223200 chr2D 78.616 477 56 29 19 457 616651336 616650868 1.300000e-69 274
33 TraesCS6A01G223200 chr2B 91.667 168 13 1 491 657 115381514 115381681 7.960000e-57 231
34 TraesCS6A01G223200 chr5D 92.357 157 11 1 502 657 198954907 198955063 4.790000e-54 222
35 TraesCS6A01G223200 chr5D 92.715 151 9 2 502 651 2310926 2311075 2.230000e-52 217
36 TraesCS6A01G223200 chr5D 82.105 190 30 3 796 983 547534572 547534385 3.810000e-35 159
37 TraesCS6A01G223200 chr1B 91.411 163 12 2 493 654 141294109 141293948 4.790000e-54 222
38 TraesCS6A01G223200 chr3D 91.824 159 10 2 502 657 292030886 292031044 6.200000e-53 219
39 TraesCS6A01G223200 chr1D 92.258 155 11 1 504 657 483951534 483951380 6.200000e-53 219
40 TraesCS6A01G223200 chr1D 92.715 151 9 2 502 651 220076855 220077004 2.230000e-52 217
41 TraesCS6A01G223200 chr5B 80.903 288 40 5 1412 1684 691020009 691019722 2.880000e-51 213


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 TraesCS6A01G223200 chr6A 418543070 418546754 3684 False 6806.000000 6806 100.000000 1 3685 1 chr6A.!!$F2 3684
1 TraesCS6A01G223200 chr6A 40242265 40244252 1987 False 3354.000000 3354 97.133000 1700 3685 1 chr6A.!!$F1 1985
2 TraesCS6A01G223200 chr6A 418587263 418589248 1985 True 3339.000000 3339 97.035000 1701 3685 1 chr6A.!!$R2 1984
3 TraesCS6A01G223200 chr6A 418599699 418601558 1859 False 3160.000000 3160 97.318000 1824 3685 1 chr6A.!!$F3 1861
4 TraesCS6A01G223200 chr6A 18564931 18566051 1120 True 314.500000 324 83.865500 916 1695 2 chr6A.!!$R3 779
5 TraesCS6A01G223200 chr3A 547257695 547259678 1983 False 3376.000000 3376 97.386000 1701 3685 1 chr3A.!!$F1 1984
6 TraesCS6A01G223200 chr3A 691698340 691700327 1987 True 3352.000000 3352 97.134000 1701 3685 1 chr3A.!!$R4 1984
7 TraesCS6A01G223200 chr3A 497202965 497204947 1982 True 3140.000000 3140 95.315000 1710 3685 1 chr3A.!!$R3 1975
8 TraesCS6A01G223200 chr3A 697763329 697763896 567 True 573.000000 573 85.366000 1145 1701 1 chr3A.!!$R5 556
9 TraesCS6A01G223200 chr4A 615425660 615427648 1988 True 3354.000000 3354 97.134000 1700 3685 1 chr4A.!!$R1 1985
10 TraesCS6A01G223200 chr4A 667372822 667375906 3084 False 278.333333 370 87.824333 1 1701 3 chr4A.!!$F1 1700
11 TraesCS6A01G223200 chr5A 77885543 77887531 1988 False 3306.000000 3306 96.687000 1699 3685 1 chr5A.!!$F1 1986
12 TraesCS6A01G223200 chr1A 474215551 474217351 1800 True 2948.000000 2948 96.241000 1701 3500 1 chr1A.!!$R2 1799
13 TraesCS6A01G223200 chr3B 750316088 750319455 3367 True 334.333333 455 89.208000 1 1701 3 chr3B.!!$R2 1700
14 TraesCS6A01G223200 chr7B 641377611 641378475 864 True 318.000000 429 80.971000 803 1695 2 chr7B.!!$R1 892
15 TraesCS6A01G223200 chr7A 670215304 670215856 552 True 392.000000 392 79.857000 803 1352 1 chr7A.!!$R1 549
16 TraesCS6A01G223200 chr6B 9179772 9180613 841 False 348.000000 348 75.058000 835 1658 1 chr6B.!!$F1 823
17 TraesCS6A01G223200 chrUn 772601 773727 1126 False 314.500000 324 84.163500 910 1695 2 chrUn.!!$F1 785

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
711 751 1.070445 GAGCAGCACTGTGGTCTGT 59.930 57.895 9.92 0.0 40.98 3.41 F
1723 3915 0.458889 GCCGATAACTGCCACACGTA 60.459 55.000 0.00 0.0 0.00 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1899 4094 0.535335 CGAGAAAGGGGACGGATCAA 59.465 55.0 0.00 0.0 0.0 2.57 R
3540 5749 0.600557 TTGGTCAAATCGCGGCAAAT 59.399 45.0 6.13 0.0 0.0 2.32 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
54 56 1.529226 TAACCGACCAAATGCTGTGG 58.471 50.000 0.03 0.03 42.28 4.17
88 90 3.735591 TGTTCTTCCTTCCTTGGTTACG 58.264 45.455 0.00 0.00 0.00 3.18
114 131 3.065925 GTGCTTGCTTTCTCTTGTTGTCT 59.934 43.478 0.00 0.00 0.00 3.41
118 135 5.049129 GCTTGCTTTCTCTTGTTGTCTATGT 60.049 40.000 0.00 0.00 0.00 2.29
121 138 6.054941 TGCTTTCTCTTGTTGTCTATGTCAA 58.945 36.000 0.00 0.00 0.00 3.18
161 181 6.448369 TTTATCCTTGTCTCTTCCAGGAAA 57.552 37.500 2.72 0.00 0.00 3.13
167 187 4.778213 TGTCTCTTCCAGGAAATATGGG 57.222 45.455 2.72 0.00 38.44 4.00
171 191 6.216662 TGTCTCTTCCAGGAAATATGGGTTAA 59.783 38.462 2.72 0.00 38.44 2.01
175 195 7.475299 TCTTCCAGGAAATATGGGTTAACTTT 58.525 34.615 2.72 0.00 38.44 2.66
177 197 8.817092 TTCCAGGAAATATGGGTTAACTTTAG 57.183 34.615 0.00 0.00 38.44 1.85
219 239 2.223377 GTGTTAGTGCCCACTTCTTTCG 59.777 50.000 6.21 0.00 42.54 3.46
222 242 2.052782 AGTGCCCACTTCTTTCGTTT 57.947 45.000 0.00 0.00 38.83 3.60
234 254 3.486383 TCTTTCGTTTGATTCCCTGCTT 58.514 40.909 0.00 0.00 0.00 3.91
238 258 2.038426 TCGTTTGATTCCCTGCTTCTGA 59.962 45.455 0.00 0.00 0.00 3.27
307 330 2.166870 TCTTGCACCATTCATGATTGCC 59.833 45.455 11.35 3.95 36.42 4.52
339 362 8.713708 TTTATTTATTTTGTGTTGAGGGAGGA 57.286 30.769 0.00 0.00 0.00 3.71
340 363 8.713708 TTATTTATTTTGTGTTGAGGGAGGAA 57.286 30.769 0.00 0.00 0.00 3.36
341 364 6.399639 TTTATTTTGTGTTGAGGGAGGAAC 57.600 37.500 0.00 0.00 0.00 3.62
342 365 3.374042 TTTTGTGTTGAGGGAGGAACA 57.626 42.857 0.00 0.00 0.00 3.18
343 366 3.593442 TTTGTGTTGAGGGAGGAACAT 57.407 42.857 0.00 0.00 34.69 2.71
391 427 8.409358 AATAATTGAGAGGCTAACACAACTTT 57.591 30.769 0.00 0.00 0.00 2.66
393 429 4.415881 TGAGAGGCTAACACAACTTTCA 57.584 40.909 0.00 0.00 0.00 2.69
394 430 4.973168 TGAGAGGCTAACACAACTTTCAT 58.027 39.130 0.00 0.00 0.00 2.57
396 432 4.327680 AGAGGCTAACACAACTTTCATCC 58.672 43.478 0.00 0.00 0.00 3.51
397 433 4.072131 GAGGCTAACACAACTTTCATCCA 58.928 43.478 0.00 0.00 0.00 3.41
398 434 4.666512 AGGCTAACACAACTTTCATCCAT 58.333 39.130 0.00 0.00 0.00 3.41
401 437 6.891908 AGGCTAACACAACTTTCATCCATAAT 59.108 34.615 0.00 0.00 0.00 1.28
402 438 7.397192 AGGCTAACACAACTTTCATCCATAATT 59.603 33.333 0.00 0.00 0.00 1.40
403 439 7.702348 GGCTAACACAACTTTCATCCATAATTC 59.298 37.037 0.00 0.00 0.00 2.17
404 440 8.462016 GCTAACACAACTTTCATCCATAATTCT 58.538 33.333 0.00 0.00 0.00 2.40
424 462 7.716799 ATTCTAAATGTACCCTTGATGCAAA 57.283 32.000 0.00 0.00 0.00 3.68
427 465 3.806625 ATGTACCCTTGATGCAAATGC 57.193 42.857 0.00 0.00 42.50 3.56
448 488 3.810373 CATGCACGTCCAAAACTACTTC 58.190 45.455 0.00 0.00 0.00 3.01
457 497 6.485648 ACGTCCAAAACTACTTCTGCTAAATT 59.514 34.615 0.00 0.00 0.00 1.82
458 498 7.658575 ACGTCCAAAACTACTTCTGCTAAATTA 59.341 33.333 0.00 0.00 0.00 1.40
459 499 8.500773 CGTCCAAAACTACTTCTGCTAAATTAA 58.499 33.333 0.00 0.00 0.00 1.40
461 501 9.569122 TCCAAAACTACTTCTGCTAAATTAAGT 57.431 29.630 0.00 0.00 36.26 2.24
477 517 9.261180 CTAAATTAAGTATCATGTCATCGGTGT 57.739 33.333 0.00 0.00 0.00 4.16
481 521 5.592104 AGTATCATGTCATCGGTGTAACA 57.408 39.130 0.00 0.00 39.98 2.41
482 522 5.592054 AGTATCATGTCATCGGTGTAACAG 58.408 41.667 0.00 0.00 39.98 3.16
485 525 2.736144 TGTCATCGGTGTAACAGGAC 57.264 50.000 0.00 0.00 39.98 3.85
493 533 3.890756 TCGGTGTAACAGGACTTCTAACA 59.109 43.478 0.00 0.00 39.98 2.41
504 544 7.736893 ACAGGACTTCTAACAAATCAGTTACT 58.263 34.615 0.00 0.00 33.07 2.24
505 545 7.873505 ACAGGACTTCTAACAAATCAGTTACTC 59.126 37.037 0.00 0.00 33.07 2.59
506 546 7.332182 CAGGACTTCTAACAAATCAGTTACTCC 59.668 40.741 0.00 0.00 33.07 3.85
507 547 6.594547 GGACTTCTAACAAATCAGTTACTCCC 59.405 42.308 0.00 0.00 33.07 4.30
508 548 7.317722 ACTTCTAACAAATCAGTTACTCCCT 57.682 36.000 0.00 0.00 33.07 4.20
509 549 7.387643 ACTTCTAACAAATCAGTTACTCCCTC 58.612 38.462 0.00 0.00 33.07 4.30
510 550 6.295719 TCTAACAAATCAGTTACTCCCTCC 57.704 41.667 0.00 0.00 33.07 4.30
511 551 3.611766 ACAAATCAGTTACTCCCTCCG 57.388 47.619 0.00 0.00 0.00 4.63
512 552 2.904434 ACAAATCAGTTACTCCCTCCGT 59.096 45.455 0.00 0.00 0.00 4.69
513 553 3.326880 ACAAATCAGTTACTCCCTCCGTT 59.673 43.478 0.00 0.00 0.00 4.44
514 554 3.889520 AATCAGTTACTCCCTCCGTTC 57.110 47.619 0.00 0.00 0.00 3.95
515 555 1.553706 TCAGTTACTCCCTCCGTTCC 58.446 55.000 0.00 0.00 0.00 3.62
516 556 1.076677 TCAGTTACTCCCTCCGTTCCT 59.923 52.381 0.00 0.00 0.00 3.36
517 557 2.309755 TCAGTTACTCCCTCCGTTCCTA 59.690 50.000 0.00 0.00 0.00 2.94
518 558 3.094572 CAGTTACTCCCTCCGTTCCTAA 58.905 50.000 0.00 0.00 0.00 2.69
519 559 3.512724 CAGTTACTCCCTCCGTTCCTAAA 59.487 47.826 0.00 0.00 0.00 1.85
520 560 4.161754 CAGTTACTCCCTCCGTTCCTAAAT 59.838 45.833 0.00 0.00 0.00 1.40
521 561 4.161754 AGTTACTCCCTCCGTTCCTAAATG 59.838 45.833 0.00 0.00 0.00 2.32
522 562 2.547990 ACTCCCTCCGTTCCTAAATGT 58.452 47.619 0.00 0.00 0.00 2.71
523 563 3.716431 ACTCCCTCCGTTCCTAAATGTA 58.284 45.455 0.00 0.00 0.00 2.29
524 564 4.098894 ACTCCCTCCGTTCCTAAATGTAA 58.901 43.478 0.00 0.00 0.00 2.41
525 565 4.161754 ACTCCCTCCGTTCCTAAATGTAAG 59.838 45.833 0.00 0.00 0.00 2.34
526 566 4.355549 TCCCTCCGTTCCTAAATGTAAGA 58.644 43.478 0.00 0.00 0.00 2.10
527 567 4.161001 TCCCTCCGTTCCTAAATGTAAGAC 59.839 45.833 0.00 0.00 0.00 3.01
528 568 4.439968 CCTCCGTTCCTAAATGTAAGACC 58.560 47.826 0.00 0.00 0.00 3.85
529 569 4.161754 CCTCCGTTCCTAAATGTAAGACCT 59.838 45.833 0.00 0.00 0.00 3.85
530 570 5.338137 CCTCCGTTCCTAAATGTAAGACCTT 60.338 44.000 0.00 0.00 0.00 3.50
531 571 6.117975 TCCGTTCCTAAATGTAAGACCTTT 57.882 37.500 0.00 0.00 0.00 3.11
532 572 6.536447 TCCGTTCCTAAATGTAAGACCTTTT 58.464 36.000 0.00 0.00 0.00 2.27
533 573 7.678837 TCCGTTCCTAAATGTAAGACCTTTTA 58.321 34.615 0.00 0.00 0.00 1.52
534 574 7.820872 TCCGTTCCTAAATGTAAGACCTTTTAG 59.179 37.037 0.00 0.00 34.38 1.85
535 575 7.065443 CCGTTCCTAAATGTAAGACCTTTTAGG 59.935 40.741 12.11 12.11 45.08 2.69
539 579 9.901172 TCCTAAATGTAAGACCTTTTAGGATTC 57.099 33.333 15.51 0.00 46.09 2.52
540 580 9.121658 CCTAAATGTAAGACCTTTTAGGATTCC 57.878 37.037 12.75 0.00 45.79 3.01
541 581 9.681062 CTAAATGTAAGACCTTTTAGGATTCCA 57.319 33.333 5.29 0.00 37.67 3.53
542 582 7.939784 AATGTAAGACCTTTTAGGATTCCAC 57.060 36.000 5.29 0.00 37.67 4.02
543 583 6.697641 TGTAAGACCTTTTAGGATTCCACT 57.302 37.500 5.29 0.00 37.67 4.00
544 584 7.801893 TGTAAGACCTTTTAGGATTCCACTA 57.198 36.000 5.29 0.00 37.67 2.74
545 585 7.618137 TGTAAGACCTTTTAGGATTCCACTAC 58.382 38.462 5.29 0.00 37.67 2.73
546 586 6.697641 AAGACCTTTTAGGATTCCACTACA 57.302 37.500 5.29 0.00 37.67 2.74
547 587 6.301169 AGACCTTTTAGGATTCCACTACAG 57.699 41.667 5.29 0.00 37.67 2.74
548 588 6.023603 AGACCTTTTAGGATTCCACTACAGA 58.976 40.000 5.29 0.00 37.67 3.41
549 589 6.051179 ACCTTTTAGGATTCCACTACAGAC 57.949 41.667 5.29 0.00 37.67 3.51
550 590 5.785940 ACCTTTTAGGATTCCACTACAGACT 59.214 40.000 5.29 0.00 37.67 3.24
551 591 6.958192 ACCTTTTAGGATTCCACTACAGACTA 59.042 38.462 5.29 0.00 37.67 2.59
552 592 7.093421 ACCTTTTAGGATTCCACTACAGACTAC 60.093 40.741 5.29 0.00 37.67 2.73
553 593 7.093465 CCTTTTAGGATTCCACTACAGACTACA 60.093 40.741 5.29 0.00 37.67 2.74
554 594 7.973048 TTTAGGATTCCACTACAGACTACAT 57.027 36.000 5.29 0.00 0.00 2.29
555 595 9.483489 TTTTAGGATTCCACTACAGACTACATA 57.517 33.333 5.29 0.00 0.00 2.29
556 596 6.963083 AGGATTCCACTACAGACTACATAC 57.037 41.667 5.29 0.00 0.00 2.39
557 597 5.531659 AGGATTCCACTACAGACTACATACG 59.468 44.000 5.29 0.00 0.00 3.06
558 598 5.278364 GGATTCCACTACAGACTACATACGG 60.278 48.000 0.00 0.00 0.00 4.02
559 599 4.492494 TCCACTACAGACTACATACGGA 57.508 45.455 0.00 0.00 0.00 4.69
560 600 4.449131 TCCACTACAGACTACATACGGAG 58.551 47.826 0.00 0.00 0.00 4.63
561 601 3.003482 CCACTACAGACTACATACGGAGC 59.997 52.174 0.00 0.00 0.00 4.70
562 602 3.626217 CACTACAGACTACATACGGAGCA 59.374 47.826 0.00 0.00 0.00 4.26
563 603 4.095932 CACTACAGACTACATACGGAGCAA 59.904 45.833 0.00 0.00 0.00 3.91
564 604 4.703575 ACTACAGACTACATACGGAGCAAA 59.296 41.667 0.00 0.00 0.00 3.68
565 605 4.530710 ACAGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
566 606 5.086104 ACAGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
567 607 4.870426 ACAGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
568 608 5.109210 CAGACTACATACGGAGCAAAATGA 58.891 41.667 0.00 0.00 0.00 2.57
569 609 5.233050 CAGACTACATACGGAGCAAAATGAG 59.767 44.000 0.00 0.00 0.00 2.90
570 610 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
571 611 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
572 612 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
573 613 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
574 614 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
575 615 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
576 616 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
577 617 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
578 618 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
579 619 4.259970 CGGAGCAAAATGAGTGAATCTACG 60.260 45.833 0.00 0.00 0.00 3.51
580 620 4.494855 GGAGCAAAATGAGTGAATCTACGC 60.495 45.833 0.00 0.00 0.00 4.42
581 621 4.256920 AGCAAAATGAGTGAATCTACGCT 58.743 39.130 0.00 0.00 0.00 5.07
582 622 4.331168 AGCAAAATGAGTGAATCTACGCTC 59.669 41.667 0.00 0.00 44.55 5.03
583 623 4.331168 GCAAAATGAGTGAATCTACGCTCT 59.669 41.667 0.00 0.00 44.58 4.09
584 624 5.520288 GCAAAATGAGTGAATCTACGCTCTA 59.480 40.000 0.00 0.00 44.58 2.43
585 625 6.036083 GCAAAATGAGTGAATCTACGCTCTAA 59.964 38.462 0.00 0.00 44.58 2.10
586 626 7.413000 GCAAAATGAGTGAATCTACGCTCTAAA 60.413 37.037 0.00 0.00 44.58 1.85
587 627 7.763172 AAATGAGTGAATCTACGCTCTAAAG 57.237 36.000 0.00 0.00 44.58 1.85
588 628 5.899120 TGAGTGAATCTACGCTCTAAAGT 57.101 39.130 0.00 0.00 44.58 2.66
589 629 5.641709 TGAGTGAATCTACGCTCTAAAGTG 58.358 41.667 0.00 0.00 44.58 3.16
590 630 4.425520 AGTGAATCTACGCTCTAAAGTGC 58.574 43.478 0.00 0.00 36.42 4.40
603 643 7.728580 GCTCTAAAGTGCGTCTATATACATC 57.271 40.000 0.00 0.00 0.00 3.06
604 644 6.748198 GCTCTAAAGTGCGTCTATATACATCC 59.252 42.308 0.00 0.00 0.00 3.51
605 645 6.839033 TCTAAAGTGCGTCTATATACATCCG 58.161 40.000 0.00 0.00 0.00 4.18
606 646 5.449107 AAAGTGCGTCTATATACATCCGT 57.551 39.130 0.00 0.00 0.00 4.69
607 647 6.564709 AAAGTGCGTCTATATACATCCGTA 57.435 37.500 0.00 0.00 0.00 4.02
608 648 6.754702 AAGTGCGTCTATATACATCCGTAT 57.245 37.500 0.00 0.00 41.34 3.06
609 649 6.120378 AGTGCGTCTATATACATCCGTATG 57.880 41.667 0.00 0.00 38.79 2.39
622 662 6.085555 ACATCCGTATGTAGTTCATAGTGG 57.914 41.667 0.00 2.99 44.66 4.00
623 663 5.831525 ACATCCGTATGTAGTTCATAGTGGA 59.168 40.000 11.01 11.01 44.66 4.02
624 664 6.322969 ACATCCGTATGTAGTTCATAGTGGAA 59.677 38.462 12.08 0.00 44.66 3.53
625 665 6.971726 TCCGTATGTAGTTCATAGTGGAAT 57.028 37.500 7.73 0.00 39.60 3.01
626 666 6.978338 TCCGTATGTAGTTCATAGTGGAATC 58.022 40.000 7.73 0.00 39.60 2.52
627 667 6.776116 TCCGTATGTAGTTCATAGTGGAATCT 59.224 38.462 7.73 0.00 39.60 2.40
628 668 7.040617 TCCGTATGTAGTTCATAGTGGAATCTC 60.041 40.741 7.73 0.00 39.60 2.75
629 669 7.040340 CCGTATGTAGTTCATAGTGGAATCTCT 60.040 40.741 3.20 0.00 39.36 3.10
630 670 9.000486 CGTATGTAGTTCATAGTGGAATCTCTA 58.000 37.037 0.00 0.00 39.36 2.43
635 675 9.535878 GTAGTTCATAGTGGAATCTCTAAAAGG 57.464 37.037 0.00 0.00 0.00 3.11
636 676 8.152023 AGTTCATAGTGGAATCTCTAAAAGGT 57.848 34.615 0.00 0.00 0.00 3.50
637 677 8.261522 AGTTCATAGTGGAATCTCTAAAAGGTC 58.738 37.037 0.00 0.00 0.00 3.85
638 678 7.979786 TCATAGTGGAATCTCTAAAAGGTCT 57.020 36.000 0.00 0.00 0.00 3.85
639 679 8.380742 TCATAGTGGAATCTCTAAAAGGTCTT 57.619 34.615 0.00 0.00 0.00 3.01
640 680 9.488762 TCATAGTGGAATCTCTAAAAGGTCTTA 57.511 33.333 0.00 0.00 0.00 2.10
644 684 9.495382 AGTGGAATCTCTAAAAGGTCTTATACT 57.505 33.333 0.00 0.00 0.00 2.12
659 699 7.726738 AGGTCTTATACTTAGGAACTGAGGATC 59.273 40.741 0.00 0.00 42.41 3.36
660 700 7.308710 GGTCTTATACTTAGGAACTGAGGATCG 60.309 44.444 0.00 0.00 42.41 3.69
661 701 6.715718 TCTTATACTTAGGAACTGAGGATCGG 59.284 42.308 0.00 0.00 42.41 4.18
662 702 5.063017 ATACTTAGGAACTGAGGATCGGA 57.937 43.478 0.00 0.00 42.41 4.55
663 703 5.074115 ATACTTAGGAACTGAGGATCGGAG 58.926 45.833 0.00 0.00 42.41 4.63
664 704 5.983488 ATACTTAGGAACTGAGGATCGGAGG 60.983 48.000 0.00 0.00 42.41 4.30
665 705 8.897525 ATACTTAGGAACTGAGGATCGGAGGG 62.898 50.000 0.00 0.00 42.41 4.30
670 710 3.823369 TGAGGATCGGAGGGAGTAC 57.177 57.895 0.00 0.00 38.61 2.73
676 716 2.297597 GGATCGGAGGGAGTACTTGATG 59.702 54.545 0.00 0.00 0.00 3.07
711 751 1.070445 GAGCAGCACTGTGGTCTGT 59.930 57.895 9.92 0.00 40.98 3.41
715 755 1.096967 CAGCACTGTGGTCTGTTGCA 61.097 55.000 9.92 0.00 0.00 4.08
750 790 9.905713 TCTCATTACCTTGCTTTATGAACTTAT 57.094 29.630 0.00 0.00 0.00 1.73
792 848 9.186323 CTAGTATTTGATGAAGGTTCTATCGTG 57.814 37.037 0.00 0.00 0.00 4.35
807 863 8.457261 GGTTCTATCGTGACGGTTAAGATATAT 58.543 37.037 4.70 0.00 0.00 0.86
831 2659 2.435069 ACTGAATCAGCATCCTCTCCTG 59.565 50.000 10.62 0.00 34.37 3.86
856 2684 7.436376 TGATTGAGAGACACGACATGATAATTC 59.564 37.037 0.00 0.00 0.00 2.17
865 2693 8.587952 ACACGACATGATAATTCATTAATCGA 57.412 30.769 0.00 0.00 40.70 3.59
887 2715 3.731652 TCTTTTTGCCACTGAACATGG 57.268 42.857 0.00 0.00 40.50 3.66
908 2738 8.906867 ACATGGTCATCCTTGTTTATATCTTTG 58.093 33.333 0.00 0.00 45.74 2.77
967 2797 1.745087 ACAAGTCCAGCGCCATTAATG 59.255 47.619 2.29 8.58 0.00 1.90
1026 2856 0.976641 TGAACTGTCGCTTCCCTGAT 59.023 50.000 0.00 0.00 0.00 2.90
1162 2997 6.597280 GCTGTGACTTCTTCCAGAAAATAGAT 59.403 38.462 0.00 0.00 33.19 1.98
1234 3069 1.165907 TGCGAAGTTTGGTGCCTGAG 61.166 55.000 0.00 0.00 0.00 3.35
1237 3072 1.528129 GAAGTTTGGTGCCTGAGGAG 58.472 55.000 0.65 0.00 0.00 3.69
1271 3106 3.991536 GAAGCTGACCGTCTCCCGC 62.992 68.421 0.00 0.00 34.38 6.13
1285 3120 1.141254 CTCCCGCTGAGTCTAGGACTA 59.859 57.143 0.00 0.00 43.53 2.59
1295 3130 7.571613 CGCTGAGTCTAGGACTACAATATGTAC 60.572 44.444 0.00 0.00 43.53 2.90
1319 3442 3.461061 AGTCATTATGGCTGTGATGTCG 58.539 45.455 0.00 0.00 26.79 4.35
1358 3485 9.781633 TGAGTTAACTAGTTACCATGCTTTTTA 57.218 29.630 14.96 0.00 0.00 1.52
1383 3513 6.569127 TTTATAGCTCCCTGTCATTTGGTA 57.431 37.500 0.00 0.00 0.00 3.25
1407 3537 4.578871 TGCACTGTATGATAGCTTGTGTT 58.421 39.130 0.00 0.00 0.00 3.32
1408 3538 5.729510 TGCACTGTATGATAGCTTGTGTTA 58.270 37.500 0.00 0.00 0.00 2.41
1472 3653 6.010294 AGTGATGAAGCAATCTTCTTTGTG 57.990 37.500 6.60 0.00 46.81 3.33
1585 3769 5.366477 TGCAGGTGATCTCATTAAGGATGTA 59.634 40.000 0.00 0.00 37.06 2.29
1618 3804 2.559668 CTGTGAGGGTTGGACGTTACTA 59.440 50.000 0.00 0.00 0.00 1.82
1629 3815 6.476053 GGTTGGACGTTACTAAAAATTGCAAA 59.524 34.615 1.71 0.00 0.00 3.68
1671 3860 1.066152 GCCTGAATTTGGCGATTCCTC 59.934 52.381 7.51 0.00 41.03 3.71
1681 3870 2.093658 TGGCGATTCCTCTGAGGTAAAC 60.094 50.000 22.50 12.93 36.53 2.01
1697 3889 9.245962 CTGAGGTAAACTGTAATACTATTTCGG 57.754 37.037 0.00 0.00 0.00 4.30
1723 3915 0.458889 GCCGATAACTGCCACACGTA 60.459 55.000 0.00 0.00 0.00 3.57
1883 4077 3.760035 CCGCTGCCTGTACGACCT 61.760 66.667 0.00 0.00 0.00 3.85
1895 4090 2.535485 TACGACCTAGCCGTTCCCGA 62.535 60.000 12.46 0.00 40.95 5.14
1899 4094 2.356780 CCTAGCCGTTCCCGACCTT 61.357 63.158 0.00 0.00 35.63 3.50
1900 4095 1.595357 CTAGCCGTTCCCGACCTTT 59.405 57.895 0.00 0.00 35.63 3.11
1913 4108 0.618981 GACCTTTGATCCGTCCCCTT 59.381 55.000 0.00 0.00 0.00 3.95
2171 4371 4.759183 GGGCAGAAAATTGCAAAATTACCA 59.241 37.500 1.71 0.00 45.86 3.25
2273 4473 8.657387 AATACACTAGATCTGCCATGTAGTAT 57.343 34.615 5.18 0.43 0.00 2.12
2430 4632 3.061322 GTGTATAACGTCAGTTGCCACA 58.939 45.455 0.00 0.00 41.35 4.17
2452 4654 1.806542 GTCATTGTCGTCAACTGCCAT 59.193 47.619 0.00 0.00 36.33 4.40
2619 4822 5.176958 GTGATAGCACTGACGTGTTAACTTT 59.823 40.000 3.28 0.00 43.16 2.66
2633 4836 5.977129 GTGTTAACTTTTACATGCAAGCAGT 59.023 36.000 7.22 2.04 0.00 4.40
2794 5001 1.656818 CCGCCACCTTTCGATGCATT 61.657 55.000 0.00 0.00 0.00 3.56
3158 5365 3.547746 TGGCAAAAGGACTTACGAGTTT 58.452 40.909 0.00 0.00 35.88 2.66
3202 5409 3.654201 GTGCAGCACGTGGAATCA 58.346 55.556 18.88 0.00 0.00 2.57
3350 5559 7.633193 TCTACGGTTGCCATGTATTAAAAAT 57.367 32.000 0.00 0.00 0.00 1.82
3591 5800 2.483014 TTGCAGGTTATTACGCTGGT 57.517 45.000 0.00 0.00 0.00 4.00
3597 5806 2.504175 AGGTTATTACGCTGGTGGTGAT 59.496 45.455 0.00 0.00 0.00 3.06
3670 5879 3.788227 ATGGTGTAACAGACCACACAT 57.212 42.857 7.12 0.00 46.30 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 39 0.606401 CTCCACAGCATTTGGTCGGT 60.606 55.000 0.00 0.00 35.42 4.69
54 56 7.288158 AGGAAGGAAGAACATATAGTACACCTC 59.712 40.741 0.00 0.00 0.00 3.85
88 90 2.555757 ACAAGAGAAAGCAAGCACATCC 59.444 45.455 0.00 0.00 0.00 3.51
152 172 8.395605 ACTAAAGTTAACCCATATTTCCTGGAA 58.604 33.333 4.68 4.68 35.70 3.53
161 181 8.365647 CCGACTATCACTAAAGTTAACCCATAT 58.634 37.037 0.88 0.00 0.00 1.78
167 187 6.255237 GCCTTCCGACTATCACTAAAGTTAAC 59.745 42.308 0.00 0.00 0.00 2.01
171 191 3.767673 TGCCTTCCGACTATCACTAAAGT 59.232 43.478 0.00 0.00 0.00 2.66
175 195 4.501071 GTTTTGCCTTCCGACTATCACTA 58.499 43.478 0.00 0.00 0.00 2.74
177 197 2.093783 CGTTTTGCCTTCCGACTATCAC 59.906 50.000 0.00 0.00 0.00 3.06
182 202 0.463116 ACACGTTTTGCCTTCCGACT 60.463 50.000 0.00 0.00 0.00 4.18
184 204 1.868498 CTAACACGTTTTGCCTTCCGA 59.132 47.619 0.00 0.00 0.00 4.55
219 239 4.219288 ACAATCAGAAGCAGGGAATCAAAC 59.781 41.667 0.00 0.00 0.00 2.93
222 242 3.726557 ACAATCAGAAGCAGGGAATCA 57.273 42.857 0.00 0.00 0.00 2.57
238 258 7.272515 CGGCGAACAACATAAGAAAATAACAAT 59.727 33.333 0.00 0.00 0.00 2.71
260 283 2.218603 AGTAGGATTAATTTGGCGGCG 58.781 47.619 0.51 0.51 0.00 6.46
326 349 5.010282 ACAATAATGTTCCTCCCTCAACAC 58.990 41.667 0.00 0.00 35.91 3.32
358 394 9.959721 TGTTAGCCTCTCAATTATTTAAGAAGT 57.040 29.630 0.00 0.00 0.00 3.01
391 427 9.573166 CAAGGGTACATTTAGAATTATGGATGA 57.427 33.333 0.00 0.00 0.00 2.92
394 430 9.573166 CATCAAGGGTACATTTAGAATTATGGA 57.427 33.333 0.00 0.00 0.00 3.41
396 432 8.849168 TGCATCAAGGGTACATTTAGAATTATG 58.151 33.333 0.00 0.00 0.00 1.90
397 433 8.995027 TGCATCAAGGGTACATTTAGAATTAT 57.005 30.769 0.00 0.00 0.00 1.28
398 434 8.815565 TTGCATCAAGGGTACATTTAGAATTA 57.184 30.769 0.00 0.00 0.00 1.40
401 437 7.546358 CATTTGCATCAAGGGTACATTTAGAA 58.454 34.615 0.00 0.00 0.00 2.10
402 438 6.405731 GCATTTGCATCAAGGGTACATTTAGA 60.406 38.462 0.00 0.00 41.59 2.10
403 439 5.750067 GCATTTGCATCAAGGGTACATTTAG 59.250 40.000 0.00 0.00 41.59 1.85
404 440 5.659463 GCATTTGCATCAAGGGTACATTTA 58.341 37.500 0.00 0.00 41.59 1.40
424 462 0.961019 AGTTTTGGACGTGCATGCAT 59.039 45.000 25.64 8.94 0.00 3.96
427 465 3.498397 AGAAGTAGTTTTGGACGTGCATG 59.502 43.478 11.62 3.82 0.00 4.06
428 466 3.498397 CAGAAGTAGTTTTGGACGTGCAT 59.502 43.478 11.62 0.00 0.00 3.96
429 467 2.869801 CAGAAGTAGTTTTGGACGTGCA 59.130 45.455 5.33 5.33 0.00 4.57
430 468 2.349532 GCAGAAGTAGTTTTGGACGTGC 60.350 50.000 0.00 0.00 0.00 5.34
435 473 9.569122 ACTTAATTTAGCAGAAGTAGTTTTGGA 57.431 29.630 3.25 0.00 30.45 3.53
448 488 8.438513 CCGATGACATGATACTTAATTTAGCAG 58.561 37.037 0.00 0.00 0.00 4.24
457 497 7.102847 TGTTACACCGATGACATGATACTTA 57.897 36.000 0.00 0.00 0.00 2.24
458 498 5.972935 TGTTACACCGATGACATGATACTT 58.027 37.500 0.00 0.00 0.00 2.24
459 499 5.451937 CCTGTTACACCGATGACATGATACT 60.452 44.000 0.00 0.00 0.00 2.12
461 501 4.647399 TCCTGTTACACCGATGACATGATA 59.353 41.667 0.00 0.00 0.00 2.15
462 502 3.450817 TCCTGTTACACCGATGACATGAT 59.549 43.478 0.00 0.00 0.00 2.45
463 503 2.829120 TCCTGTTACACCGATGACATGA 59.171 45.455 0.00 0.00 0.00 3.07
464 504 2.930040 GTCCTGTTACACCGATGACATG 59.070 50.000 0.00 0.00 0.00 3.21
465 505 2.832129 AGTCCTGTTACACCGATGACAT 59.168 45.455 0.00 0.00 0.00 3.06
466 506 2.244695 AGTCCTGTTACACCGATGACA 58.755 47.619 0.00 0.00 0.00 3.58
472 512 4.247267 TGTTAGAAGTCCTGTTACACCG 57.753 45.455 0.00 0.00 0.00 4.94
477 517 9.485206 GTAACTGATTTGTTAGAAGTCCTGTTA 57.515 33.333 0.00 0.00 33.67 2.41
481 521 7.387643 GGAGTAACTGATTTGTTAGAAGTCCT 58.612 38.462 0.00 0.00 33.67 3.85
482 522 6.594547 GGGAGTAACTGATTTGTTAGAAGTCC 59.405 42.308 0.00 0.00 33.67 3.85
485 525 6.819146 GGAGGGAGTAACTGATTTGTTAGAAG 59.181 42.308 0.00 0.00 33.67 2.85
493 533 3.055312 GGAACGGAGGGAGTAACTGATTT 60.055 47.826 0.00 0.00 0.00 2.17
504 544 4.161001 GTCTTACATTTAGGAACGGAGGGA 59.839 45.833 0.00 0.00 0.00 4.20
505 545 4.439968 GTCTTACATTTAGGAACGGAGGG 58.560 47.826 0.00 0.00 0.00 4.30
506 546 4.161754 AGGTCTTACATTTAGGAACGGAGG 59.838 45.833 0.00 0.00 0.00 4.30
507 547 5.340439 AGGTCTTACATTTAGGAACGGAG 57.660 43.478 0.00 0.00 0.00 4.63
508 548 5.750352 AAGGTCTTACATTTAGGAACGGA 57.250 39.130 0.00 0.00 0.00 4.69
509 549 6.812879 AAAAGGTCTTACATTTAGGAACGG 57.187 37.500 0.00 0.00 30.13 4.44
515 555 9.681062 TGGAATCCTAAAAGGTCTTACATTTAG 57.319 33.333 0.00 0.00 36.53 1.85
516 556 9.457436 GTGGAATCCTAAAAGGTCTTACATTTA 57.543 33.333 0.00 0.00 36.53 1.40
517 557 8.170730 AGTGGAATCCTAAAAGGTCTTACATTT 58.829 33.333 0.00 0.00 36.53 2.32
518 558 7.699878 AGTGGAATCCTAAAAGGTCTTACATT 58.300 34.615 0.00 0.00 36.53 2.71
519 559 7.272144 AGTGGAATCCTAAAAGGTCTTACAT 57.728 36.000 0.00 0.00 36.53 2.29
520 560 6.697641 AGTGGAATCCTAAAAGGTCTTACA 57.302 37.500 0.00 0.00 36.53 2.41
521 561 7.618137 TGTAGTGGAATCCTAAAAGGTCTTAC 58.382 38.462 0.00 0.00 36.53 2.34
522 562 7.676893 TCTGTAGTGGAATCCTAAAAGGTCTTA 59.323 37.037 0.00 0.00 36.53 2.10
523 563 6.500751 TCTGTAGTGGAATCCTAAAAGGTCTT 59.499 38.462 0.00 0.00 36.53 3.01
524 564 6.023603 TCTGTAGTGGAATCCTAAAAGGTCT 58.976 40.000 0.00 0.00 36.53 3.85
525 565 6.070710 AGTCTGTAGTGGAATCCTAAAAGGTC 60.071 42.308 0.00 0.00 36.53 3.85
526 566 5.785940 AGTCTGTAGTGGAATCCTAAAAGGT 59.214 40.000 0.00 0.00 36.53 3.50
527 567 6.301169 AGTCTGTAGTGGAATCCTAAAAGG 57.699 41.667 0.00 0.00 36.46 3.11
528 568 7.837863 TGTAGTCTGTAGTGGAATCCTAAAAG 58.162 38.462 0.00 0.00 0.00 2.27
529 569 7.786046 TGTAGTCTGTAGTGGAATCCTAAAA 57.214 36.000 0.00 0.00 0.00 1.52
530 570 7.973048 ATGTAGTCTGTAGTGGAATCCTAAA 57.027 36.000 0.00 0.00 0.00 1.85
531 571 7.228108 CGTATGTAGTCTGTAGTGGAATCCTAA 59.772 40.741 0.00 0.00 0.00 2.69
532 572 6.709397 CGTATGTAGTCTGTAGTGGAATCCTA 59.291 42.308 0.00 0.00 0.00 2.94
533 573 5.531659 CGTATGTAGTCTGTAGTGGAATCCT 59.468 44.000 0.00 0.00 0.00 3.24
534 574 5.278364 CCGTATGTAGTCTGTAGTGGAATCC 60.278 48.000 0.00 0.00 0.00 3.01
535 575 5.530171 TCCGTATGTAGTCTGTAGTGGAATC 59.470 44.000 0.00 0.00 0.00 2.52
536 576 5.443283 TCCGTATGTAGTCTGTAGTGGAAT 58.557 41.667 0.00 0.00 0.00 3.01
537 577 4.847198 TCCGTATGTAGTCTGTAGTGGAA 58.153 43.478 0.00 0.00 0.00 3.53
538 578 4.449131 CTCCGTATGTAGTCTGTAGTGGA 58.551 47.826 0.00 0.00 0.00 4.02
539 579 3.003482 GCTCCGTATGTAGTCTGTAGTGG 59.997 52.174 0.00 0.00 0.00 4.00
540 580 3.626217 TGCTCCGTATGTAGTCTGTAGTG 59.374 47.826 0.00 0.00 0.00 2.74
541 581 3.882444 TGCTCCGTATGTAGTCTGTAGT 58.118 45.455 0.00 0.00 0.00 2.73
542 582 4.895224 TTGCTCCGTATGTAGTCTGTAG 57.105 45.455 0.00 0.00 0.00 2.74
543 583 5.648178 TTTTGCTCCGTATGTAGTCTGTA 57.352 39.130 0.00 0.00 0.00 2.74
544 584 4.530710 TTTTGCTCCGTATGTAGTCTGT 57.469 40.909 0.00 0.00 0.00 3.41
545 585 5.109210 TCATTTTGCTCCGTATGTAGTCTG 58.891 41.667 0.00 0.00 0.00 3.51
546 586 5.105310 ACTCATTTTGCTCCGTATGTAGTCT 60.105 40.000 0.00 0.00 0.00 3.24
547 587 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
548 588 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
549 589 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
550 590 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
551 591 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
552 592 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
553 593 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
554 594 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
555 595 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
556 596 4.259970 CGTAGATTCACTCATTTTGCTCCG 60.260 45.833 0.00 0.00 0.00 4.63
557 597 4.494855 GCGTAGATTCACTCATTTTGCTCC 60.495 45.833 0.00 0.00 0.00 4.70
558 598 4.331168 AGCGTAGATTCACTCATTTTGCTC 59.669 41.667 0.00 0.00 0.00 4.26
559 599 4.256920 AGCGTAGATTCACTCATTTTGCT 58.743 39.130 0.00 0.00 0.00 3.91
560 600 4.331168 AGAGCGTAGATTCACTCATTTTGC 59.669 41.667 0.00 0.00 0.00 3.68
561 601 7.525688 TTAGAGCGTAGATTCACTCATTTTG 57.474 36.000 0.00 0.00 0.00 2.44
562 602 7.819900 ACTTTAGAGCGTAGATTCACTCATTTT 59.180 33.333 0.00 0.00 0.00 1.82
563 603 7.276658 CACTTTAGAGCGTAGATTCACTCATTT 59.723 37.037 0.00 0.00 0.00 2.32
564 604 6.754209 CACTTTAGAGCGTAGATTCACTCATT 59.246 38.462 0.00 0.00 0.00 2.57
565 605 6.269315 CACTTTAGAGCGTAGATTCACTCAT 58.731 40.000 0.00 0.00 0.00 2.90
566 606 5.641709 CACTTTAGAGCGTAGATTCACTCA 58.358 41.667 0.00 0.00 0.00 3.41
567 607 4.501198 GCACTTTAGAGCGTAGATTCACTC 59.499 45.833 0.00 0.00 0.00 3.51
568 608 4.425520 GCACTTTAGAGCGTAGATTCACT 58.574 43.478 0.00 0.00 0.00 3.41
569 609 3.240861 CGCACTTTAGAGCGTAGATTCAC 59.759 47.826 12.41 0.00 46.99 3.18
570 610 3.435566 CGCACTTTAGAGCGTAGATTCA 58.564 45.455 12.41 0.00 46.99 2.57
579 619 6.748198 GGATGTATATAGACGCACTTTAGAGC 59.252 42.308 0.00 0.00 0.00 4.09
580 620 6.962116 CGGATGTATATAGACGCACTTTAGAG 59.038 42.308 0.00 0.00 0.00 2.43
581 621 6.429078 ACGGATGTATATAGACGCACTTTAGA 59.571 38.462 0.00 0.00 0.00 2.10
582 622 6.609533 ACGGATGTATATAGACGCACTTTAG 58.390 40.000 0.00 0.00 0.00 1.85
583 623 6.564709 ACGGATGTATATAGACGCACTTTA 57.435 37.500 0.00 0.00 0.00 1.85
584 624 5.449107 ACGGATGTATATAGACGCACTTT 57.551 39.130 0.00 0.00 0.00 2.66
585 625 6.150641 ACATACGGATGTATATAGACGCACTT 59.849 38.462 12.79 0.00 44.77 3.16
586 626 5.646793 ACATACGGATGTATATAGACGCACT 59.353 40.000 12.79 0.00 44.77 4.40
587 627 5.877031 ACATACGGATGTATATAGACGCAC 58.123 41.667 12.79 0.00 44.77 5.34
588 628 6.820152 ACTACATACGGATGTATATAGACGCA 59.180 38.462 20.64 0.00 45.42 5.24
589 629 7.244166 ACTACATACGGATGTATATAGACGC 57.756 40.000 20.64 0.00 45.42 5.19
590 630 8.876790 TGAACTACATACGGATGTATATAGACG 58.123 37.037 20.64 9.79 45.42 4.18
596 636 8.953313 CCACTATGAACTACATACGGATGTATA 58.047 37.037 20.64 10.04 45.42 1.47
597 637 7.668469 TCCACTATGAACTACATACGGATGTAT 59.332 37.037 20.64 7.28 45.42 2.29
598 638 6.999871 TCCACTATGAACTACATACGGATGTA 59.000 38.462 19.32 19.32 44.77 2.29
600 640 6.327279 TCCACTATGAACTACATACGGATG 57.673 41.667 5.94 5.94 40.07 3.51
601 641 6.971726 TTCCACTATGAACTACATACGGAT 57.028 37.500 0.00 0.00 37.58 4.18
602 642 6.776116 AGATTCCACTATGAACTACATACGGA 59.224 38.462 0.00 0.00 40.07 4.69
603 643 6.982852 AGATTCCACTATGAACTACATACGG 58.017 40.000 0.00 0.00 40.07 4.02
604 644 7.877003 AGAGATTCCACTATGAACTACATACG 58.123 38.462 0.00 0.00 40.07 3.06
609 649 9.535878 CCTTTTAGAGATTCCACTATGAACTAC 57.464 37.037 0.00 0.00 0.00 2.73
610 650 9.268282 ACCTTTTAGAGATTCCACTATGAACTA 57.732 33.333 0.00 0.00 0.00 2.24
611 651 8.152023 ACCTTTTAGAGATTCCACTATGAACT 57.848 34.615 0.00 0.00 0.00 3.01
612 652 8.261522 AGACCTTTTAGAGATTCCACTATGAAC 58.738 37.037 0.00 0.00 0.00 3.18
613 653 8.380742 AGACCTTTTAGAGATTCCACTATGAA 57.619 34.615 0.00 0.00 0.00 2.57
614 654 7.979786 AGACCTTTTAGAGATTCCACTATGA 57.020 36.000 0.00 0.00 0.00 2.15
618 658 9.495382 AGTATAAGACCTTTTAGAGATTCCACT 57.505 33.333 0.00 0.00 0.00 4.00
630 670 8.541234 CCTCAGTTCCTAAGTATAAGACCTTTT 58.459 37.037 0.00 0.00 0.00 2.27
631 671 7.899709 TCCTCAGTTCCTAAGTATAAGACCTTT 59.100 37.037 0.00 0.00 0.00 3.11
632 672 7.420029 TCCTCAGTTCCTAAGTATAAGACCTT 58.580 38.462 0.00 0.00 0.00 3.50
633 673 6.982899 TCCTCAGTTCCTAAGTATAAGACCT 58.017 40.000 0.00 0.00 0.00 3.85
634 674 7.308710 CGATCCTCAGTTCCTAAGTATAAGACC 60.309 44.444 0.00 0.00 0.00 3.85
635 675 7.308710 CCGATCCTCAGTTCCTAAGTATAAGAC 60.309 44.444 0.00 0.00 0.00 3.01
636 676 6.715718 CCGATCCTCAGTTCCTAAGTATAAGA 59.284 42.308 0.00 0.00 0.00 2.10
637 677 6.715718 TCCGATCCTCAGTTCCTAAGTATAAG 59.284 42.308 0.00 0.00 0.00 1.73
638 678 6.607970 TCCGATCCTCAGTTCCTAAGTATAA 58.392 40.000 0.00 0.00 0.00 0.98
639 679 6.196918 TCCGATCCTCAGTTCCTAAGTATA 57.803 41.667 0.00 0.00 0.00 1.47
640 680 5.063017 TCCGATCCTCAGTTCCTAAGTAT 57.937 43.478 0.00 0.00 0.00 2.12
641 681 4.462133 CTCCGATCCTCAGTTCCTAAGTA 58.538 47.826 0.00 0.00 0.00 2.24
642 682 3.292460 CTCCGATCCTCAGTTCCTAAGT 58.708 50.000 0.00 0.00 0.00 2.24
643 683 2.625790 CCTCCGATCCTCAGTTCCTAAG 59.374 54.545 0.00 0.00 0.00 2.18
644 684 2.667470 CCTCCGATCCTCAGTTCCTAA 58.333 52.381 0.00 0.00 0.00 2.69
645 685 1.133450 CCCTCCGATCCTCAGTTCCTA 60.133 57.143 0.00 0.00 0.00 2.94
646 686 0.397816 CCCTCCGATCCTCAGTTCCT 60.398 60.000 0.00 0.00 0.00 3.36
647 687 0.397254 TCCCTCCGATCCTCAGTTCC 60.397 60.000 0.00 0.00 0.00 3.62
648 688 1.036707 CTCCCTCCGATCCTCAGTTC 58.963 60.000 0.00 0.00 0.00 3.01
649 689 0.336737 ACTCCCTCCGATCCTCAGTT 59.663 55.000 0.00 0.00 0.00 3.16
650 690 1.133730 GTACTCCCTCCGATCCTCAGT 60.134 57.143 0.00 0.00 0.00 3.41
651 691 1.144093 AGTACTCCCTCCGATCCTCAG 59.856 57.143 0.00 0.00 0.00 3.35
652 692 1.223501 AGTACTCCCTCCGATCCTCA 58.776 55.000 0.00 0.00 0.00 3.86
653 693 1.957877 CAAGTACTCCCTCCGATCCTC 59.042 57.143 0.00 0.00 0.00 3.71
654 694 1.569548 TCAAGTACTCCCTCCGATCCT 59.430 52.381 0.00 0.00 0.00 3.24
655 695 2.068834 TCAAGTACTCCCTCCGATCC 57.931 55.000 0.00 0.00 0.00 3.36
656 696 2.959707 ACATCAAGTACTCCCTCCGATC 59.040 50.000 0.00 0.00 0.00 3.69
657 697 2.695666 CACATCAAGTACTCCCTCCGAT 59.304 50.000 0.00 0.00 0.00 4.18
658 698 2.100197 CACATCAAGTACTCCCTCCGA 58.900 52.381 0.00 0.00 0.00 4.55
659 699 1.471676 GCACATCAAGTACTCCCTCCG 60.472 57.143 0.00 0.00 0.00 4.63
660 700 1.834263 AGCACATCAAGTACTCCCTCC 59.166 52.381 0.00 0.00 0.00 4.30
661 701 2.898705 CAGCACATCAAGTACTCCCTC 58.101 52.381 0.00 0.00 0.00 4.30
662 702 1.065854 GCAGCACATCAAGTACTCCCT 60.066 52.381 0.00 0.00 0.00 4.20
663 703 1.065854 AGCAGCACATCAAGTACTCCC 60.066 52.381 0.00 0.00 0.00 4.30
664 704 2.393271 AGCAGCACATCAAGTACTCC 57.607 50.000 0.00 0.00 0.00 3.85
665 705 4.116747 AGTAGCAGCACATCAAGTACTC 57.883 45.455 0.00 0.00 0.00 2.59
666 706 5.860941 ATAGTAGCAGCACATCAAGTACT 57.139 39.130 0.00 0.00 0.00 2.73
667 707 6.042777 TCAATAGTAGCAGCACATCAAGTAC 58.957 40.000 0.00 0.00 0.00 2.73
668 708 6.220726 TCAATAGTAGCAGCACATCAAGTA 57.779 37.500 0.00 0.00 0.00 2.24
669 709 5.089970 TCAATAGTAGCAGCACATCAAGT 57.910 39.130 0.00 0.00 0.00 3.16
670 710 5.814188 TCTTCAATAGTAGCAGCACATCAAG 59.186 40.000 0.00 0.00 0.00 3.02
676 716 3.525537 TGCTCTTCAATAGTAGCAGCAC 58.474 45.455 0.00 0.00 39.92 4.40
711 751 7.592938 CAAGGTAATGAGATGTAGTTTTGCAA 58.407 34.615 0.00 0.00 0.00 4.08
715 755 8.409358 AAAGCAAGGTAATGAGATGTAGTTTT 57.591 30.769 0.00 0.00 0.00 2.43
781 821 4.361451 TCTTAACCGTCACGATAGAACC 57.639 45.455 0.00 0.00 41.38 3.62
783 823 9.445878 AGATATATCTTAACCGTCACGATAGAA 57.554 33.333 9.57 0.00 34.52 2.10
807 863 3.894427 GGAGAGGATGCTGATTCAGTAGA 59.106 47.826 14.90 0.70 33.43 2.59
831 2659 7.436376 TGAATTATCATGTCGTGTCTCTCAATC 59.564 37.037 0.00 0.00 0.00 2.67
856 2684 7.028962 TCAGTGGCAAAAAGAATCGATTAATG 58.971 34.615 11.38 7.12 0.00 1.90
863 2691 3.963665 TGTTCAGTGGCAAAAAGAATCG 58.036 40.909 0.00 0.00 0.00 3.34
865 2693 4.101430 ACCATGTTCAGTGGCAAAAAGAAT 59.899 37.500 0.00 0.00 40.49 2.40
877 2705 3.795688 ACAAGGATGACCATGTTCAGT 57.204 42.857 0.00 0.00 44.25 3.41
887 2715 8.616076 CCTGACAAAGATATAAACAAGGATGAC 58.384 37.037 0.00 0.00 0.00 3.06
897 2725 7.039784 AGCAAAACAGCCTGACAAAGATATAAA 60.040 33.333 0.00 0.00 34.23 1.40
902 2732 2.961062 AGCAAAACAGCCTGACAAAGAT 59.039 40.909 0.00 0.00 34.23 2.40
908 2738 1.000938 CTTCCAGCAAAACAGCCTGAC 60.001 52.381 0.00 0.00 34.23 3.51
967 2797 4.261197 CCTTTTGCTGACACCAGTACTTTC 60.261 45.833 0.00 0.00 42.35 2.62
995 2825 5.664457 AGCGACAGTTCATGATCATCTTAA 58.336 37.500 4.86 0.00 0.00 1.85
1026 2856 3.243839 GCTTTCCAACAGCCATTTTCTGA 60.244 43.478 0.00 0.00 35.61 3.27
1118 2953 7.809331 GTCACAGCAAAAATGATGATGAAAGTA 59.191 33.333 0.59 0.00 37.61 2.24
1124 2959 6.387465 AGAAGTCACAGCAAAAATGATGATG 58.613 36.000 0.59 0.00 39.95 3.07
1129 2964 4.644234 TGGAAGAAGTCACAGCAAAAATGA 59.356 37.500 0.00 0.00 0.00 2.57
1162 2997 8.268605 TCCATTACAGTTGTATTATACAGGCAA 58.731 33.333 5.17 0.00 40.24 4.52
1178 3013 3.202151 CCCCACATTACCTCCATTACAGT 59.798 47.826 0.00 0.00 0.00 3.55
1234 3069 1.093159 CAGCCAGCTGTGATTTCTCC 58.907 55.000 13.81 0.00 39.10 3.71
1237 3072 1.135460 GCTTCAGCCAGCTGTGATTTC 60.135 52.381 18.61 0.00 43.96 2.17
1271 3106 8.779303 CAGTACATATTGTAGTCCTAGACTCAG 58.221 40.741 0.00 0.00 42.40 3.35
1285 3120 7.658982 CAGCCATAATGACTCAGTACATATTGT 59.341 37.037 0.00 0.00 0.00 2.71
1295 3130 4.449131 ACATCACAGCCATAATGACTCAG 58.551 43.478 0.00 0.00 0.00 3.35
1346 3473 7.565029 AGGGAGCTATAAAATAAAAAGCATGGT 59.435 33.333 0.00 0.00 35.63 3.55
1358 3485 6.435164 ACCAAATGACAGGGAGCTATAAAAT 58.565 36.000 0.00 0.00 0.00 1.82
1383 3513 5.188434 ACACAAGCTATCATACAGTGCAAT 58.812 37.500 0.00 0.00 0.00 3.56
1472 3653 2.079925 GATTTGCTCACTGACCTGGAC 58.920 52.381 0.00 0.00 0.00 4.02
1585 3769 1.064906 CCCTCACAGTTGATGCCAGAT 60.065 52.381 0.00 0.00 0.00 2.90
1629 3815 4.746089 GCCACCATATCATCTTCAGAGCTT 60.746 45.833 0.00 0.00 0.00 3.74
1671 3860 9.245962 CCGAAATAGTATTACAGTTTACCTCAG 57.754 37.037 0.00 0.00 0.00 3.35
1681 3870 6.424207 GGCTTCCTTCCGAAATAGTATTACAG 59.576 42.308 0.00 0.00 0.00 2.74
1697 3889 1.300481 GGCAGTTATCGGCTTCCTTC 58.700 55.000 0.00 0.00 35.25 3.46
1723 3915 4.740822 GGTTGCCCTCCACGCCAT 62.741 66.667 0.00 0.00 0.00 4.40
1874 4068 1.315257 GGGAACGGCTAGGTCGTACA 61.315 60.000 0.00 0.00 45.33 2.90
1876 4070 3.924507 GGGAACGGCTAGGTCGTA 58.075 61.111 0.00 0.00 45.33 3.43
1895 4090 1.004394 GAAAGGGGACGGATCAAAGGT 59.996 52.381 0.00 0.00 0.00 3.50
1899 4094 0.535335 CGAGAAAGGGGACGGATCAA 59.465 55.000 0.00 0.00 0.00 2.57
1900 4095 0.613853 ACGAGAAAGGGGACGGATCA 60.614 55.000 0.00 0.00 0.00 2.92
1913 4108 4.116328 CGAGGGCGCAGACGAGAA 62.116 66.667 10.83 0.00 43.93 2.87
2171 4371 5.733620 TGGATCTAGTTACCAACTTCGTT 57.266 39.130 0.00 0.00 42.81 3.85
2182 4382 5.681494 ACCCTGTAGGATGGATCTAGTTA 57.319 43.478 0.00 0.00 39.89 2.24
2273 4473 4.270834 AGAACTCACGGTTATCTCTAGCA 58.729 43.478 0.00 0.00 38.41 3.49
2352 4552 9.933240 ATTCCAAATTTATCAATTCTCTCTCCT 57.067 29.630 0.00 0.00 30.80 3.69
2430 4632 1.806542 GGCAGTTGACGACAATGACAT 59.193 47.619 3.18 0.00 38.32 3.06
2452 4654 3.825585 TGGCAAGCAATAAGTTGACATGA 59.174 39.130 0.00 0.00 36.75 3.07
2619 4822 7.622893 TTATCATTGTACTGCTTGCATGTAA 57.377 32.000 1.14 0.00 0.00 2.41
2794 5001 5.122519 CAGAGATGAGCTGACTGTACTCTA 58.877 45.833 0.00 0.00 35.39 2.43
2991 5198 0.679321 TTGTGACTGCACTTGCCACA 60.679 50.000 7.45 7.45 45.36 4.17
3097 5304 8.291191 TCATTTTTCATGTCCACAGCATTATA 57.709 30.769 0.00 0.00 0.00 0.98
3150 5357 3.724508 TTACACCCGTGAAAACTCGTA 57.275 42.857 0.96 0.00 0.00 3.43
3158 5365 2.811431 CTCTGCATTTTACACCCGTGAA 59.189 45.455 0.96 0.00 0.00 3.18
3202 5409 1.925455 AGGTACATGGGTGCTGCCT 60.925 57.895 0.00 0.00 37.43 4.75
3350 5559 4.455533 GGTGTGCAGAGATGACAAATGTTA 59.544 41.667 0.00 0.00 0.00 2.41
3540 5749 0.600557 TTGGTCAAATCGCGGCAAAT 59.399 45.000 6.13 0.00 0.00 2.32
3591 5800 1.669760 GACGTTTGCCGGATCACCA 60.670 57.895 5.05 0.00 42.24 4.17
3597 5806 2.342279 CAGGAGACGTTTGCCGGA 59.658 61.111 5.05 0.00 42.24 5.14


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

AutoCloner maintained by Alex Coulton.