Multiple sequence alignment - TraesCS2B01G354000

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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 TraesCS2B01G354000 chr2B 100.000 3673 0 0 1 3673 504778200 504774528 0.000000e+00 6783
1 TraesCS2B01G354000 chr2B 92.988 1526 79 14 1542 3051 512350518 512352031 0.000000e+00 2200
2 TraesCS2B01G354000 chr2B 89.827 865 56 15 698 1549 512347156 512348001 0.000000e+00 1081
3 TraesCS2B01G354000 chr2B 95.362 345 7 1 3329 3673 512353725 512354060 1.160000e-149 540
4 TraesCS2B01G354000 chr2B 91.093 247 12 6 3051 3295 512353490 512353728 3.540000e-85 326
5 TraesCS2B01G354000 chr2D 90.935 1423 89 15 1421 2832 427955163 427953770 0.000000e+00 1877
6 TraesCS2B01G354000 chr2D 97.282 515 13 1 1 514 67463190 67462676 0.000000e+00 872
7 TraesCS2B01G354000 chr2D 97.282 515 13 1 1 514 309500527 309501041 0.000000e+00 872
8 TraesCS2B01G354000 chr2D 97.266 512 14 0 1 512 373406998 373407509 0.000000e+00 869
9 TraesCS2B01G354000 chr2D 88.399 681 50 11 749 1420 427955871 427955211 0.000000e+00 793
10 TraesCS2B01G354000 chr2D 83.465 635 30 26 3062 3673 427953373 427952791 4.200000e-144 521
11 TraesCS2B01G354000 chr2D 90.991 222 19 1 2831 3051 427953676 427953455 7.710000e-77 298
12 TraesCS2B01G354000 chr2A 87.154 1191 108 27 1886 3051 559667199 559668369 0.000000e+00 1310
13 TraesCS2B01G354000 chr2A 89.474 627 32 13 805 1417 559666033 559666639 0.000000e+00 761
14 TraesCS2B01G354000 chr2A 87.660 624 49 9 3051 3673 559668420 559669016 0.000000e+00 701
15 TraesCS2B01G354000 chr2A 83.726 467 55 9 1421 1871 559666689 559667150 4.390000e-114 422
16 TraesCS2B01G354000 chr2A 86.170 282 35 4 2773 3050 142329334 142329615 5.960000e-78 302
17 TraesCS2B01G354000 chr7D 97.466 513 12 1 1 512 55287515 55288027 0.000000e+00 874
18 TraesCS2B01G354000 chr6B 97.461 512 13 0 1 512 706834273 706833762 0.000000e+00 874
19 TraesCS2B01G354000 chr5B 97.461 512 13 0 1 512 610948873 610949384 0.000000e+00 874
20 TraesCS2B01G354000 chr5B 96.911 518 16 0 1 518 208545076 208544559 0.000000e+00 869
21 TraesCS2B01G354000 chr6D 97.266 512 14 0 1 512 363083086 363083597 0.000000e+00 869
22 TraesCS2B01G354000 chr6D 96.374 524 17 2 1 522 350280413 350279890 0.000000e+00 861
23 TraesCS2B01G354000 chr7A 89.236 288 28 2 2763 3050 734601281 734600997 1.250000e-94 357
24 TraesCS2B01G354000 chr5A 87.797 295 28 7 2762 3050 113587227 113586935 4.540000e-89 339
25 TraesCS2B01G354000 chr6A 87.943 282 30 4 2773 3050 79407322 79407041 2.730000e-86 329


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 TraesCS2B01G354000 chr2B 504774528 504778200 3672 True 6783.00 6783 100.0000 1 3673 1 chr2B.!!$R1 3672
1 TraesCS2B01G354000 chr2B 512347156 512354060 6904 False 1036.75 2200 92.3175 698 3673 4 chr2B.!!$F1 2975
2 TraesCS2B01G354000 chr2D 427952791 427955871 3080 True 872.25 1877 88.4475 749 3673 4 chr2D.!!$R2 2924
3 TraesCS2B01G354000 chr2D 67462676 67463190 514 True 872.00 872 97.2820 1 514 1 chr2D.!!$R1 513
4 TraesCS2B01G354000 chr2D 309500527 309501041 514 False 872.00 872 97.2820 1 514 1 chr2D.!!$F1 513
5 TraesCS2B01G354000 chr2D 373406998 373407509 511 False 869.00 869 97.2660 1 512 1 chr2D.!!$F2 511
6 TraesCS2B01G354000 chr2A 559666033 559669016 2983 False 798.50 1310 87.0035 805 3673 4 chr2A.!!$F2 2868
7 TraesCS2B01G354000 chr7D 55287515 55288027 512 False 874.00 874 97.4660 1 512 1 chr7D.!!$F1 511
8 TraesCS2B01G354000 chr6B 706833762 706834273 511 True 874.00 874 97.4610 1 512 1 chr6B.!!$R1 511
9 TraesCS2B01G354000 chr5B 610948873 610949384 511 False 874.00 874 97.4610 1 512 1 chr5B.!!$F1 511
10 TraesCS2B01G354000 chr5B 208544559 208545076 517 True 869.00 869 96.9110 1 518 1 chr5B.!!$R1 517
11 TraesCS2B01G354000 chr6D 363083086 363083597 511 False 869.00 869 97.2660 1 512 1 chr6D.!!$F1 511
12 TraesCS2B01G354000 chr6D 350279890 350280413 523 True 861.00 861 96.3740 1 522 1 chr6D.!!$R1 521

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
684 686 0.034186 GGCATCAATCCCACCACTGA 60.034 55.0 0.00 0.0 0.0 3.41 F
688 690 0.392863 TCAATCCCACCACTGATGCG 60.393 55.0 0.00 0.0 0.0 4.73 F
690 692 0.392998 AATCCCACCACTGATGCGAC 60.393 55.0 0.00 0.0 0.0 5.19 F
699 701 0.530744 ACTGATGCGACGCCTTTAGA 59.469 50.0 18.69 0.0 0.0 2.10 F
2649 5305 0.895530 TGACGAAGAGGAGGCGATTT 59.104 50.0 0.00 0.0 0.0 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2350 5006 0.322546 GCCAACCTCGGACCTCAATT 60.323 55.000 0.00 0.0 0.00 2.32 R
2643 5299 2.196295 ACTGCTCGAGTCTAAATCGC 57.804 50.000 15.13 0.0 39.98 4.58 R
2655 5311 4.307432 TCCTGTTAAGAAAGAACTGCTCG 58.693 43.478 0.00 0.0 0.00 5.03 R
2665 5321 5.417580 GGCCATACAACATCCTGTTAAGAAA 59.582 40.000 0.00 0.0 38.77 2.52 R
3505 7807 3.524648 TTCACGAAGCCGGTGGTCC 62.525 63.158 1.90 0.0 40.78 4.46 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
51 52 4.194640 CAAATCCCAGTCTCGATTCATGT 58.805 43.478 0.00 0.00 0.00 3.21
128 129 5.761234 AGTTACATTGTGACGTTTGGTACAT 59.239 36.000 6.11 0.00 39.30 2.29
145 146 3.627395 ACATCCAAAGCATTCCTACGA 57.373 42.857 0.00 0.00 0.00 3.43
152 153 4.556233 CAAAGCATTCCTACGATATCCGA 58.444 43.478 0.00 0.00 41.76 4.55
352 354 6.183360 ACCATCTATTGATCAACGAGCTAGTT 60.183 38.462 11.07 6.37 34.15 2.24
416 418 5.356751 TCACACATGTATTATGGTTTCCAGC 59.643 40.000 0.00 0.00 36.75 4.85
438 440 8.171196 CCAGCTAATACAATTATAGCATGAACG 58.829 37.037 0.00 0.00 36.33 3.95
519 521 4.705023 GGGCATATTTCCAACACTAACACT 59.295 41.667 0.00 0.00 0.00 3.55
520 522 5.393027 GGGCATATTTCCAACACTAACACTG 60.393 44.000 0.00 0.00 0.00 3.66
521 523 5.183140 GGCATATTTCCAACACTAACACTGT 59.817 40.000 0.00 0.00 0.00 3.55
522 524 6.314784 GCATATTTCCAACACTAACACTGTC 58.685 40.000 0.00 0.00 0.00 3.51
523 525 6.072728 GCATATTTCCAACACTAACACTGTCA 60.073 38.462 0.00 0.00 0.00 3.58
524 526 5.751243 ATTTCCAACACTAACACTGTCAC 57.249 39.130 0.00 0.00 0.00 3.67
525 527 4.481368 TTCCAACACTAACACTGTCACT 57.519 40.909 0.00 0.00 0.00 3.41
526 528 4.054780 TCCAACACTAACACTGTCACTC 57.945 45.455 0.00 0.00 0.00 3.51
527 529 2.794910 CCAACACTAACACTGTCACTCG 59.205 50.000 0.00 0.00 0.00 4.18
528 530 2.794910 CAACACTAACACTGTCACTCGG 59.205 50.000 0.00 0.00 0.00 4.63
529 531 2.304092 ACACTAACACTGTCACTCGGA 58.696 47.619 0.00 0.00 0.00 4.55
530 532 2.691526 ACACTAACACTGTCACTCGGAA 59.308 45.455 0.00 0.00 0.00 4.30
531 533 3.243434 ACACTAACACTGTCACTCGGAAG 60.243 47.826 0.00 0.00 0.00 3.46
532 534 2.296471 ACTAACACTGTCACTCGGAAGG 59.704 50.000 0.00 0.00 0.00 3.46
533 535 0.393077 AACACTGTCACTCGGAAGGG 59.607 55.000 0.00 0.00 37.84 3.95
534 536 1.374758 CACTGTCACTCGGAAGGGC 60.375 63.158 0.00 0.00 31.71 5.19
535 537 2.266055 CTGTCACTCGGAAGGGCC 59.734 66.667 0.00 0.00 31.71 5.80
536 538 2.525629 TGTCACTCGGAAGGGCCA 60.526 61.111 6.18 0.00 35.94 5.36
537 539 1.903877 CTGTCACTCGGAAGGGCCAT 61.904 60.000 6.18 0.00 35.94 4.40
538 540 1.450312 GTCACTCGGAAGGGCCATG 60.450 63.158 6.18 0.00 35.94 3.66
539 541 1.918293 TCACTCGGAAGGGCCATGT 60.918 57.895 6.18 0.00 35.94 3.21
540 542 0.616395 TCACTCGGAAGGGCCATGTA 60.616 55.000 6.18 0.00 35.94 2.29
541 543 0.469917 CACTCGGAAGGGCCATGTAT 59.530 55.000 6.18 0.00 35.94 2.29
542 544 0.469917 ACTCGGAAGGGCCATGTATG 59.530 55.000 6.18 0.00 35.94 2.39
543 545 0.886490 CTCGGAAGGGCCATGTATGC 60.886 60.000 6.18 0.00 35.94 3.14
550 552 3.595758 GCCATGTATGCCGGCCAC 61.596 66.667 26.77 22.07 40.07 5.01
551 553 2.906897 CCATGTATGCCGGCCACC 60.907 66.667 26.77 11.89 0.00 4.61
561 563 3.905678 CGGCCACCGCAACCAAAA 61.906 61.111 2.24 0.00 41.17 2.44
562 564 2.501610 GGCCACCGCAACCAAAAA 59.498 55.556 0.00 0.00 36.38 1.94
563 565 1.070615 GGCCACCGCAACCAAAAAT 59.929 52.632 0.00 0.00 36.38 1.82
564 566 0.318762 GGCCACCGCAACCAAAAATA 59.681 50.000 0.00 0.00 36.38 1.40
565 567 1.066502 GGCCACCGCAACCAAAAATAT 60.067 47.619 0.00 0.00 36.38 1.28
566 568 2.267426 GCCACCGCAACCAAAAATATC 58.733 47.619 0.00 0.00 34.03 1.63
567 569 2.525055 CCACCGCAACCAAAAATATCG 58.475 47.619 0.00 0.00 0.00 2.92
568 570 2.094957 CCACCGCAACCAAAAATATCGT 60.095 45.455 0.00 0.00 0.00 3.73
569 571 3.168193 CACCGCAACCAAAAATATCGTC 58.832 45.455 0.00 0.00 0.00 4.20
570 572 2.159626 ACCGCAACCAAAAATATCGTCG 60.160 45.455 0.00 0.00 0.00 5.12
571 573 2.094575 CCGCAACCAAAAATATCGTCGA 59.905 45.455 0.00 0.00 0.00 4.20
572 574 3.425094 CCGCAACCAAAAATATCGTCGAA 60.425 43.478 0.00 0.00 0.00 3.71
573 575 4.339429 CGCAACCAAAAATATCGTCGAAT 58.661 39.130 0.00 0.00 0.00 3.34
574 576 4.433304 CGCAACCAAAAATATCGTCGAATC 59.567 41.667 0.00 0.00 0.00 2.52
575 577 4.433304 GCAACCAAAAATATCGTCGAATCG 59.567 41.667 0.00 0.00 0.00 3.34
576 578 4.789095 ACCAAAAATATCGTCGAATCGG 57.211 40.909 1.76 0.00 0.00 4.18
577 579 4.435425 ACCAAAAATATCGTCGAATCGGA 58.565 39.130 1.76 0.00 0.00 4.55
578 580 5.054477 ACCAAAAATATCGTCGAATCGGAT 58.946 37.500 1.76 1.08 0.00 4.18
579 581 5.050363 ACCAAAAATATCGTCGAATCGGATG 60.050 40.000 1.76 0.00 0.00 3.51
580 582 4.647291 AAAATATCGTCGAATCGGATGC 57.353 40.909 1.76 0.00 0.00 3.91
581 583 2.279582 ATATCGTCGAATCGGATGCC 57.720 50.000 1.76 0.00 0.00 4.40
582 584 0.242825 TATCGTCGAATCGGATGCCC 59.757 55.000 1.76 0.00 0.00 5.36
583 585 1.744320 ATCGTCGAATCGGATGCCCA 61.744 55.000 1.76 0.00 0.00 5.36
584 586 1.520564 CGTCGAATCGGATGCCCAA 60.521 57.895 1.76 0.00 0.00 4.12
585 587 1.762222 CGTCGAATCGGATGCCCAAC 61.762 60.000 1.76 0.00 0.00 3.77
586 588 1.520564 TCGAATCGGATGCCCAACG 60.521 57.895 1.76 0.00 0.00 4.10
587 589 1.520564 CGAATCGGATGCCCAACGA 60.521 57.895 0.00 0.00 41.20 3.85
588 590 1.490693 CGAATCGGATGCCCAACGAG 61.491 60.000 0.00 0.00 40.21 4.18
589 591 1.153168 AATCGGATGCCCAACGAGG 60.153 57.895 0.00 0.00 40.21 4.63
598 600 3.365265 CCAACGAGGGGCAGTTGC 61.365 66.667 3.09 0.00 44.45 4.17
623 625 2.816958 CGCTGCCGACTGAAGCAT 60.817 61.111 0.00 0.00 38.56 3.79
624 626 2.806856 CGCTGCCGACTGAAGCATC 61.807 63.158 0.00 0.00 38.56 3.91
625 627 1.742880 GCTGCCGACTGAAGCATCA 60.743 57.895 0.00 0.00 38.56 3.07
626 628 1.094073 GCTGCCGACTGAAGCATCAT 61.094 55.000 0.00 0.00 38.56 2.45
627 629 0.935898 CTGCCGACTGAAGCATCATC 59.064 55.000 0.00 0.00 38.56 2.92
628 630 0.807275 TGCCGACTGAAGCATCATCG 60.807 55.000 13.28 13.28 36.86 3.84
629 631 2.598045 CCGACTGAAGCATCATCGG 58.402 57.895 20.29 20.29 43.51 4.18
630 632 0.877649 CCGACTGAAGCATCATCGGG 60.878 60.000 23.37 10.01 44.29 5.14
631 633 0.103026 CGACTGAAGCATCATCGGGA 59.897 55.000 12.73 0.00 35.17 5.14
632 634 1.269988 CGACTGAAGCATCATCGGGAT 60.270 52.381 12.73 0.00 35.17 3.85
641 643 3.946242 TCATCGGGATGAGGGAGAA 57.054 52.632 7.26 0.00 42.42 2.87
642 644 1.709578 TCATCGGGATGAGGGAGAAG 58.290 55.000 7.26 0.00 42.42 2.85
643 645 0.034616 CATCGGGATGAGGGAGAAGC 59.965 60.000 2.46 0.00 41.20 3.86
644 646 0.399091 ATCGGGATGAGGGAGAAGCA 60.399 55.000 0.00 0.00 0.00 3.91
645 647 0.617535 TCGGGATGAGGGAGAAGCAA 60.618 55.000 0.00 0.00 0.00 3.91
646 648 0.179062 CGGGATGAGGGAGAAGCAAG 60.179 60.000 0.00 0.00 0.00 4.01
647 649 1.207791 GGGATGAGGGAGAAGCAAGA 58.792 55.000 0.00 0.00 0.00 3.02
648 650 1.773653 GGGATGAGGGAGAAGCAAGAT 59.226 52.381 0.00 0.00 0.00 2.40
649 651 2.224499 GGGATGAGGGAGAAGCAAGATC 60.224 54.545 0.00 0.00 0.00 2.75
650 652 2.437281 GGATGAGGGAGAAGCAAGATCA 59.563 50.000 0.00 0.00 0.00 2.92
651 653 3.072768 GGATGAGGGAGAAGCAAGATCAT 59.927 47.826 0.00 0.00 0.00 2.45
652 654 3.834489 TGAGGGAGAAGCAAGATCATC 57.166 47.619 0.00 0.00 0.00 2.92
653 655 3.382278 TGAGGGAGAAGCAAGATCATCT 58.618 45.455 0.00 0.00 0.00 2.90
654 656 3.779183 TGAGGGAGAAGCAAGATCATCTT 59.221 43.478 0.00 0.00 37.14 2.40
655 657 4.964897 TGAGGGAGAAGCAAGATCATCTTA 59.035 41.667 0.00 0.00 33.78 2.10
656 658 5.605908 TGAGGGAGAAGCAAGATCATCTTAT 59.394 40.000 0.00 0.00 33.78 1.73
657 659 6.100859 TGAGGGAGAAGCAAGATCATCTTATT 59.899 38.462 0.00 0.00 33.78 1.40
658 660 6.532826 AGGGAGAAGCAAGATCATCTTATTC 58.467 40.000 13.31 13.31 33.78 1.75
659 661 5.704978 GGGAGAAGCAAGATCATCTTATTCC 59.295 44.000 15.97 11.17 33.78 3.01
660 662 5.407995 GGAGAAGCAAGATCATCTTATTCCG 59.592 44.000 15.97 0.54 33.78 4.30
661 663 6.166984 AGAAGCAAGATCATCTTATTCCGA 57.833 37.500 15.97 0.00 33.78 4.55
662 664 6.222389 AGAAGCAAGATCATCTTATTCCGAG 58.778 40.000 15.97 0.00 33.78 4.63
663 665 4.892433 AGCAAGATCATCTTATTCCGAGG 58.108 43.478 0.00 0.00 33.78 4.63
664 666 3.434984 GCAAGATCATCTTATTCCGAGGC 59.565 47.826 0.00 0.00 33.78 4.70
665 667 3.584406 AGATCATCTTATTCCGAGGCG 57.416 47.619 0.00 0.00 0.00 5.52
666 668 3.306364 AAGATCATCTTATTCCGAGGCGG 60.306 47.826 0.00 0.00 40.89 6.13
667 669 6.886034 AAGATCATCTTATTCCGAGGCGGC 62.886 50.000 0.00 0.00 39.99 6.53
675 677 2.974698 CCGAGGCGGCATCAATCC 60.975 66.667 15.44 0.00 41.17 3.01
676 678 2.974698 CGAGGCGGCATCAATCCC 60.975 66.667 15.44 0.00 0.00 3.85
677 679 2.192979 GAGGCGGCATCAATCCCA 59.807 61.111 13.08 0.00 0.00 4.37
678 680 2.124151 AGGCGGCATCAATCCCAC 60.124 61.111 13.08 0.00 0.00 4.61
679 681 3.219198 GGCGGCATCAATCCCACC 61.219 66.667 3.07 0.00 0.00 4.61
680 682 2.440065 GCGGCATCAATCCCACCA 60.440 61.111 0.00 0.00 0.00 4.17
681 683 2.774799 GCGGCATCAATCCCACCAC 61.775 63.158 0.00 0.00 0.00 4.16
682 684 1.077501 CGGCATCAATCCCACCACT 60.078 57.895 0.00 0.00 0.00 4.00
683 685 1.378882 CGGCATCAATCCCACCACTG 61.379 60.000 0.00 0.00 0.00 3.66
684 686 0.034186 GGCATCAATCCCACCACTGA 60.034 55.000 0.00 0.00 0.00 3.41
685 687 1.410648 GGCATCAATCCCACCACTGAT 60.411 52.381 0.00 0.00 0.00 2.90
686 688 1.679680 GCATCAATCCCACCACTGATG 59.320 52.381 6.55 6.55 45.18 3.07
687 689 1.679680 CATCAATCCCACCACTGATGC 59.320 52.381 0.00 0.00 38.91 3.91
688 690 0.392863 TCAATCCCACCACTGATGCG 60.393 55.000 0.00 0.00 0.00 4.73
689 691 0.392863 CAATCCCACCACTGATGCGA 60.393 55.000 0.00 0.00 0.00 5.10
690 692 0.392998 AATCCCACCACTGATGCGAC 60.393 55.000 0.00 0.00 0.00 5.19
691 693 2.578163 ATCCCACCACTGATGCGACG 62.578 60.000 0.00 0.00 0.00 5.12
692 694 3.490759 CCACCACTGATGCGACGC 61.491 66.667 14.19 14.19 0.00 5.19
693 695 3.490759 CACCACTGATGCGACGCC 61.491 66.667 18.69 2.90 0.00 5.68
694 696 3.695606 ACCACTGATGCGACGCCT 61.696 61.111 18.69 7.51 0.00 5.52
695 697 2.434884 CCACTGATGCGACGCCTT 60.435 61.111 18.69 4.50 0.00 4.35
696 698 2.034879 CCACTGATGCGACGCCTTT 61.035 57.895 18.69 1.56 0.00 3.11
697 699 0.739462 CCACTGATGCGACGCCTTTA 60.739 55.000 18.69 0.00 0.00 1.85
698 700 0.647410 CACTGATGCGACGCCTTTAG 59.353 55.000 18.69 13.04 0.00 1.85
699 701 0.530744 ACTGATGCGACGCCTTTAGA 59.469 50.000 18.69 0.00 0.00 2.10
705 707 1.269883 TGCGACGCCTTTAGAAAGACA 60.270 47.619 18.69 0.00 38.28 3.41
719 721 7.334671 CTTTAGAAAGACAAGGCCTTACCTAAG 59.665 40.741 20.00 13.01 42.94 2.18
745 747 3.513912 TCTTAGGAGTGAAATTGCCTCGA 59.486 43.478 0.00 0.00 32.04 4.04
759 761 2.123251 TCGATCCCTGGCCTCTCC 60.123 66.667 3.32 0.00 0.00 3.71
803 805 3.840666 AGGATCCAGACAAGCTAAAGACA 59.159 43.478 15.82 0.00 0.00 3.41
842 844 2.030363 CGGCTCAAATAGTGTGGCAAAA 60.030 45.455 0.00 0.00 44.29 2.44
860 862 9.860898 GTGGCAAAATAGAATGTATTCTTTTCT 57.139 29.630 11.95 0.00 44.28 2.52
872 874 9.965824 AATGTATTCTTTTCTTTTTCGACATGT 57.034 25.926 0.00 0.00 0.00 3.21
874 876 9.872757 TGTATTCTTTTCTTTTTCGACATGTAC 57.127 29.630 0.00 0.00 0.00 2.90
878 880 9.537192 TTCTTTTCTTTTTCGACATGTACTAGA 57.463 29.630 0.00 0.00 0.00 2.43
879 881 9.537192 TCTTTTCTTTTTCGACATGTACTAGAA 57.463 29.630 0.00 0.00 0.00 2.10
882 884 8.827177 TTCTTTTTCGACATGTACTAGAATGT 57.173 30.769 0.00 3.42 39.69 2.71
883 885 9.917129 TTCTTTTTCGACATGTACTAGAATGTA 57.083 29.630 0.00 0.00 37.15 2.29
991 998 8.718102 TTCCAATAAGAAAAATACTCTCTCCG 57.282 34.615 0.00 0.00 0.00 4.63
1020 1036 2.202919 TGATGCGCACCTCATCCG 60.203 61.111 14.90 0.00 39.54 4.18
1030 1046 1.203994 CACCTCATCCGAAACTACCGT 59.796 52.381 0.00 0.00 0.00 4.83
1085 1101 3.636231 CGCCTTCTCACCCCACCA 61.636 66.667 0.00 0.00 0.00 4.17
1102 1118 3.301811 ACCTAGCCCCTTCCCCCT 61.302 66.667 0.00 0.00 0.00 4.79
1104 1120 2.706071 CTAGCCCCTTCCCCCTCT 59.294 66.667 0.00 0.00 0.00 3.69
1383 1399 2.621055 ACAACCGTATTTGTGTGTGCAT 59.379 40.909 0.00 0.00 38.31 3.96
1545 4141 5.801350 TTGCACTGATTTATCACTACAGC 57.199 39.130 0.00 0.00 32.50 4.40
1560 4156 4.572389 CACTACAGCAAACCTAGGCTATTG 59.428 45.833 9.30 12.93 38.56 1.90
1707 4309 5.121380 AGGTGAGCCATAGATGACATTTT 57.879 39.130 0.00 0.00 37.19 1.82
1708 4310 5.513233 AGGTGAGCCATAGATGACATTTTT 58.487 37.500 0.00 0.00 37.19 1.94
1772 4374 8.375506 TGAATGTGGGTATAGTTCCTTATCATC 58.624 37.037 0.00 0.00 0.00 2.92
1789 4393 3.084039 TCATCCTTGCAACAAGCCTTAG 58.916 45.455 0.00 0.00 44.83 2.18
1831 4435 5.690857 GTCTACATTAAGAATGAGGTACGCC 59.309 44.000 6.21 0.00 41.46 5.68
1843 4447 3.502979 TGAGGTACGCCCAAAATTTACAC 59.497 43.478 0.00 0.00 34.66 2.90
1923 4561 1.377725 CGGAACATGCTGAAGCCCT 60.378 57.895 0.00 0.00 41.18 5.19
1946 4586 6.253727 CCTCATAAAACACGCTAACTACTGAG 59.746 42.308 0.00 0.00 0.00 3.35
1960 4600 1.452651 CTGAGATTGCGGCCCACAT 60.453 57.895 0.00 0.00 0.00 3.21
1961 4601 1.442526 CTGAGATTGCGGCCCACATC 61.443 60.000 0.00 0.00 0.00 3.06
2035 4683 2.119029 GCAGTAAACGGGGATGCCC 61.119 63.158 13.41 13.41 44.51 5.36
2126 4777 5.070770 TGCATGGCAATTTACTTTGTAGG 57.929 39.130 0.00 0.00 34.76 3.18
2127 4778 4.769488 TGCATGGCAATTTACTTTGTAGGA 59.231 37.500 0.00 0.00 34.76 2.94
2128 4779 5.105797 TGCATGGCAATTTACTTTGTAGGAG 60.106 40.000 0.00 0.00 34.76 3.69
2130 4781 6.094881 GCATGGCAATTTACTTTGTAGGAGTA 59.905 38.462 0.00 0.00 0.00 2.59
2131 4782 7.201821 GCATGGCAATTTACTTTGTAGGAGTAT 60.202 37.037 0.00 0.00 30.30 2.12
2132 4783 8.686334 CATGGCAATTTACTTTGTAGGAGTATT 58.314 33.333 0.00 0.00 30.30 1.89
2135 4786 8.903820 GGCAATTTACTTTGTAGGAGTATTCAT 58.096 33.333 0.00 0.00 30.30 2.57
2260 4916 5.235850 TGCCTCTTGTTTTGTCACCTATA 57.764 39.130 0.00 0.00 0.00 1.31
2300 4956 2.103432 TCGAAAGGAGCACTGGTACAAA 59.897 45.455 0.00 0.00 38.70 2.83
2612 5268 3.582647 TGGAAGCAGAAAGTGACTATGGA 59.417 43.478 0.00 0.00 0.00 3.41
2643 5299 3.580731 GACTTCTTTGACGAAGAGGAGG 58.419 50.000 18.79 7.93 44.80 4.30
2649 5305 0.895530 TGACGAAGAGGAGGCGATTT 59.104 50.000 0.00 0.00 0.00 2.17
2655 5311 3.549221 CGAAGAGGAGGCGATTTAGACTC 60.549 52.174 0.00 0.00 45.39 3.36
2665 5321 3.732471 GCGATTTAGACTCGAGCAGTTCT 60.732 47.826 13.61 10.40 38.38 3.01
2697 5353 0.407528 TGTTGTATGGCCATGTGGGT 59.592 50.000 29.04 3.59 39.65 4.51
2700 5356 0.182537 TGTATGGCCATGTGGGTAGC 59.817 55.000 29.04 8.19 39.65 3.58
2770 5426 2.103263 GTCCATAATCTTCGACCCAGCT 59.897 50.000 0.00 0.00 0.00 4.24
2840 5599 9.938280 ACCCGAGATTCATAAATATTATCGAAA 57.062 29.630 0.00 0.00 0.00 3.46
2853 5619 2.189191 ATCGAAAGGCTGCCTGCAGA 62.189 55.000 24.16 20.49 46.30 4.26
2872 5638 6.384224 TGCAGATTCATCAGTTCATGTTTTC 58.616 36.000 0.00 0.00 0.00 2.29
2890 5657 7.844493 TGTTTTCCTCTAGGAGTACAACTTA 57.156 36.000 10.94 0.00 46.36 2.24
3111 7364 6.096987 TCAGTACAAGATGACCATAGAAGGAC 59.903 42.308 0.00 0.00 0.00 3.85
3113 7366 5.762179 ACAAGATGACCATAGAAGGACAA 57.238 39.130 0.00 0.00 36.93 3.18
3131 7384 6.684686 AGGACAAACAGATCAAAATGTCATG 58.315 36.000 17.70 9.20 39.06 3.07
3203 7459 7.708752 ACAAGTTTCTTCACTTTCAGAGAGTAG 59.291 37.037 0.00 0.00 34.60 2.57
3234 7493 2.153366 ACAAAAATCCTTGCAAGGCG 57.847 45.000 36.24 21.90 46.06 5.52
3295 7573 1.073199 ACTGAAGAAACAGCCGGGG 59.927 57.895 2.18 0.00 41.06 5.73
3315 7593 2.026542 GGTAATTCCCTTCCGTGTTCCT 60.027 50.000 0.00 0.00 0.00 3.36
3316 7594 2.200373 AATTCCCTTCCGTGTTCCTG 57.800 50.000 0.00 0.00 0.00 3.86
3317 7595 0.322546 ATTCCCTTCCGTGTTCCTGC 60.323 55.000 0.00 0.00 0.00 4.85
3318 7596 1.701031 TTCCCTTCCGTGTTCCTGCA 61.701 55.000 0.00 0.00 0.00 4.41
3319 7597 1.228124 CCCTTCCGTGTTCCTGCAA 60.228 57.895 0.00 0.00 0.00 4.08
3321 7599 1.247567 CCTTCCGTGTTCCTGCAATT 58.752 50.000 0.00 0.00 0.00 2.32
3322 7600 1.068333 CCTTCCGTGTTCCTGCAATTG 60.068 52.381 0.00 0.00 0.00 2.32
3323 7601 1.608590 CTTCCGTGTTCCTGCAATTGT 59.391 47.619 7.40 0.00 0.00 2.71
3324 7602 0.950836 TCCGTGTTCCTGCAATTGTG 59.049 50.000 7.40 0.56 0.00 3.33
3325 7603 0.667993 CCGTGTTCCTGCAATTGTGT 59.332 50.000 7.40 0.00 0.00 3.72
3326 7604 1.066908 CCGTGTTCCTGCAATTGTGTT 59.933 47.619 7.40 0.00 0.00 3.32
3327 7605 2.481104 CCGTGTTCCTGCAATTGTGTTT 60.481 45.455 7.40 0.00 0.00 2.83
3443 7739 2.055633 TGAACTAGATCCGGCGCCA 61.056 57.895 28.98 8.41 0.00 5.69
3557 7859 1.075482 CAGGTCCATGTTGGCACCT 59.925 57.895 10.19 10.19 40.05 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 2.285083 CGAAAGTGTCTGTTGGGTTGA 58.715 47.619 0.00 0.00 0.00 3.18
128 129 4.560716 CGGATATCGTAGGAATGCTTTGGA 60.561 45.833 0.00 0.00 0.00 3.53
145 146 4.100035 TGAGATTGTGCAACTCTCGGATAT 59.900 41.667 13.63 0.00 38.59 1.63
152 153 3.008813 AGACCATGAGATTGTGCAACTCT 59.991 43.478 0.00 0.00 38.04 3.24
352 354 3.526430 TGTCCCTAGTGAGCCTCTAGTTA 59.474 47.826 0.00 0.00 34.72 2.24
519 521 1.918293 ATGGCCCTTCCGAGTGACA 60.918 57.895 0.00 0.00 37.80 3.58
520 522 1.450312 CATGGCCCTTCCGAGTGAC 60.450 63.158 0.00 0.00 37.80 3.67
521 523 0.616395 TACATGGCCCTTCCGAGTGA 60.616 55.000 0.00 0.00 37.80 3.41
522 524 0.469917 ATACATGGCCCTTCCGAGTG 59.530 55.000 0.00 0.00 37.80 3.51
523 525 0.469917 CATACATGGCCCTTCCGAGT 59.530 55.000 0.00 0.00 37.80 4.18
524 526 0.886490 GCATACATGGCCCTTCCGAG 60.886 60.000 0.00 0.00 37.80 4.63
525 527 1.148273 GCATACATGGCCCTTCCGA 59.852 57.895 0.00 0.00 37.80 4.55
526 528 1.898574 GGCATACATGGCCCTTCCG 60.899 63.158 0.00 0.00 45.87 4.30
527 529 4.181051 GGCATACATGGCCCTTCC 57.819 61.111 0.00 0.00 45.87 3.46
534 536 2.906897 GGTGGCCGGCATACATGG 60.907 66.667 30.85 0.00 0.00 3.66
535 537 3.279116 CGGTGGCCGGCATACATG 61.279 66.667 30.85 17.68 44.15 3.21
545 547 0.318762 TATTTTTGGTTGCGGTGGCC 59.681 50.000 0.00 0.00 38.85 5.36
546 548 2.267426 GATATTTTTGGTTGCGGTGGC 58.733 47.619 0.00 0.00 40.52 5.01
547 549 2.094957 ACGATATTTTTGGTTGCGGTGG 60.095 45.455 0.00 0.00 0.00 4.61
548 550 3.168193 GACGATATTTTTGGTTGCGGTG 58.832 45.455 0.00 0.00 0.00 4.94
549 551 2.159626 CGACGATATTTTTGGTTGCGGT 60.160 45.455 0.00 0.00 0.00 5.68
550 552 2.094575 TCGACGATATTTTTGGTTGCGG 59.905 45.455 0.00 0.00 0.00 5.69
551 553 3.377434 TCGACGATATTTTTGGTTGCG 57.623 42.857 0.00 0.00 0.00 4.85
552 554 4.433304 CGATTCGACGATATTTTTGGTTGC 59.567 41.667 0.00 0.00 35.09 4.17
553 555 4.961551 CCGATTCGACGATATTTTTGGTTG 59.038 41.667 7.83 0.00 35.09 3.77
554 556 4.871557 TCCGATTCGACGATATTTTTGGTT 59.128 37.500 7.83 0.00 35.09 3.67
555 557 4.435425 TCCGATTCGACGATATTTTTGGT 58.565 39.130 7.83 0.00 35.09 3.67
556 558 5.374080 CATCCGATTCGACGATATTTTTGG 58.626 41.667 7.83 0.00 35.09 3.28
557 559 4.840772 GCATCCGATTCGACGATATTTTTG 59.159 41.667 7.83 0.00 35.09 2.44
558 560 4.084013 GGCATCCGATTCGACGATATTTTT 60.084 41.667 7.83 0.00 35.09 1.94
559 561 3.432252 GGCATCCGATTCGACGATATTTT 59.568 43.478 7.83 0.00 35.09 1.82
560 562 2.993899 GGCATCCGATTCGACGATATTT 59.006 45.455 7.83 0.00 35.09 1.40
561 563 2.607187 GGCATCCGATTCGACGATATT 58.393 47.619 7.83 0.00 35.09 1.28
562 564 1.135083 GGGCATCCGATTCGACGATAT 60.135 52.381 7.83 0.00 35.09 1.63
563 565 0.242825 GGGCATCCGATTCGACGATA 59.757 55.000 7.83 0.00 35.09 2.92
564 566 1.006102 GGGCATCCGATTCGACGAT 60.006 57.895 7.83 0.00 35.09 3.73
565 567 1.950973 TTGGGCATCCGATTCGACGA 61.951 55.000 7.83 0.00 35.24 4.20
566 568 1.520564 TTGGGCATCCGATTCGACG 60.521 57.895 7.83 0.00 35.24 5.12
567 569 1.762222 CGTTGGGCATCCGATTCGAC 61.762 60.000 7.83 0.00 35.24 4.20
568 570 1.520564 CGTTGGGCATCCGATTCGA 60.521 57.895 7.83 0.00 35.24 3.71
569 571 1.490693 CTCGTTGGGCATCCGATTCG 61.491 60.000 0.00 0.00 35.24 3.34
570 572 1.160329 CCTCGTTGGGCATCCGATTC 61.160 60.000 0.00 0.00 35.24 2.52
571 573 1.153168 CCTCGTTGGGCATCCGATT 60.153 57.895 0.00 0.00 35.24 3.34
572 574 2.505982 CCTCGTTGGGCATCCGAT 59.494 61.111 0.00 0.00 35.24 4.18
581 583 3.365265 GCAACTGCCCCTCGTTGG 61.365 66.667 0.00 0.00 40.52 3.77
606 608 2.806856 GATGCTTCAGTCGGCAGCG 61.807 63.158 0.00 0.00 41.88 5.18
607 609 1.094073 ATGATGCTTCAGTCGGCAGC 61.094 55.000 8.40 0.00 43.90 5.25
608 610 0.935898 GATGATGCTTCAGTCGGCAG 59.064 55.000 8.40 0.00 41.88 4.85
609 611 0.807275 CGATGATGCTTCAGTCGGCA 60.807 55.000 18.20 0.00 42.80 5.69
610 612 1.493950 CCGATGATGCTTCAGTCGGC 61.494 60.000 25.47 8.68 41.56 5.54
611 613 0.877649 CCCGATGATGCTTCAGTCGG 60.878 60.000 27.54 27.54 44.18 4.79
612 614 0.103026 TCCCGATGATGCTTCAGTCG 59.897 55.000 18.65 18.65 34.73 4.18
613 615 2.141517 CATCCCGATGATGCTTCAGTC 58.858 52.381 8.40 5.49 44.16 3.51
614 616 2.251409 CATCCCGATGATGCTTCAGT 57.749 50.000 8.40 0.00 44.16 3.41
622 624 2.255406 CTTCTCCCTCATCCCGATGAT 58.745 52.381 7.81 0.00 45.74 2.45
623 625 1.709578 CTTCTCCCTCATCCCGATGA 58.290 55.000 7.17 7.17 44.83 2.92
624 626 0.034616 GCTTCTCCCTCATCCCGATG 59.965 60.000 0.00 0.00 40.09 3.84
625 627 0.399091 TGCTTCTCCCTCATCCCGAT 60.399 55.000 0.00 0.00 0.00 4.18
626 628 0.617535 TTGCTTCTCCCTCATCCCGA 60.618 55.000 0.00 0.00 0.00 5.14
627 629 0.179062 CTTGCTTCTCCCTCATCCCG 60.179 60.000 0.00 0.00 0.00 5.14
628 630 1.207791 TCTTGCTTCTCCCTCATCCC 58.792 55.000 0.00 0.00 0.00 3.85
629 631 2.437281 TGATCTTGCTTCTCCCTCATCC 59.563 50.000 0.00 0.00 0.00 3.51
630 632 3.834489 TGATCTTGCTTCTCCCTCATC 57.166 47.619 0.00 0.00 0.00 2.92
631 633 3.975312 AGATGATCTTGCTTCTCCCTCAT 59.025 43.478 0.00 0.00 0.00 2.90
632 634 3.382278 AGATGATCTTGCTTCTCCCTCA 58.618 45.455 0.00 0.00 0.00 3.86
633 635 4.420522 AAGATGATCTTGCTTCTCCCTC 57.579 45.455 6.93 0.00 34.98 4.30
634 636 6.465607 GGAATAAGATGATCTTGCTTCTCCCT 60.466 42.308 17.50 0.00 37.29 4.20
635 637 5.704978 GGAATAAGATGATCTTGCTTCTCCC 59.295 44.000 17.50 5.65 37.29 4.30
636 638 5.407995 CGGAATAAGATGATCTTGCTTCTCC 59.592 44.000 17.50 13.12 37.29 3.71
637 639 6.219473 TCGGAATAAGATGATCTTGCTTCTC 58.781 40.000 17.50 11.84 37.29 2.87
638 640 6.166984 TCGGAATAAGATGATCTTGCTTCT 57.833 37.500 17.50 0.00 37.29 2.85
639 641 5.407995 CCTCGGAATAAGATGATCTTGCTTC 59.592 44.000 17.50 17.31 37.29 3.86
640 642 5.303971 CCTCGGAATAAGATGATCTTGCTT 58.696 41.667 17.50 10.58 37.29 3.91
641 643 4.802248 GCCTCGGAATAAGATGATCTTGCT 60.802 45.833 17.50 4.39 37.29 3.91
642 644 3.434984 GCCTCGGAATAAGATGATCTTGC 59.565 47.826 17.50 6.08 37.29 4.01
643 645 3.677121 CGCCTCGGAATAAGATGATCTTG 59.323 47.826 17.50 0.74 37.29 3.02
644 646 3.919216 CGCCTCGGAATAAGATGATCTT 58.081 45.455 12.86 12.86 40.35 2.40
645 647 3.584406 CGCCTCGGAATAAGATGATCT 57.416 47.619 0.00 0.00 0.00 2.75
647 649 6.946173 GATGCCGCCTCGGAATAAGATGAT 62.946 50.000 9.70 0.00 46.60 2.45
648 650 5.723163 GATGCCGCCTCGGAATAAGATGA 62.723 52.174 9.70 0.00 46.60 2.92
649 651 3.501161 GATGCCGCCTCGGAATAAGATG 61.501 54.545 9.70 0.00 46.60 2.90
650 652 1.338200 GATGCCGCCTCGGAATAAGAT 60.338 52.381 9.70 0.00 46.60 2.40
651 653 0.033504 GATGCCGCCTCGGAATAAGA 59.966 55.000 9.70 0.00 46.60 2.10
652 654 0.249868 TGATGCCGCCTCGGAATAAG 60.250 55.000 9.70 0.00 46.60 1.73
653 655 0.179234 TTGATGCCGCCTCGGAATAA 59.821 50.000 9.70 0.00 46.60 1.40
654 656 0.396435 ATTGATGCCGCCTCGGAATA 59.604 50.000 9.70 0.00 46.60 1.75
659 661 2.974698 GGGATTGATGCCGCCTCG 60.975 66.667 0.00 0.00 0.00 4.63
660 662 2.189499 GTGGGATTGATGCCGCCTC 61.189 63.158 3.94 0.00 42.20 4.70
661 663 2.124151 GTGGGATTGATGCCGCCT 60.124 61.111 3.94 0.00 42.20 5.52
663 665 2.440065 TGGTGGGATTGATGCCGC 60.440 61.111 6.54 6.54 46.55 6.53
664 666 1.077501 AGTGGTGGGATTGATGCCG 60.078 57.895 0.00 0.00 41.80 5.69
665 667 0.034186 TCAGTGGTGGGATTGATGCC 60.034 55.000 0.00 0.00 38.98 4.40
666 668 1.679680 CATCAGTGGTGGGATTGATGC 59.320 52.381 0.00 0.00 40.08 3.91
667 669 1.679680 GCATCAGTGGTGGGATTGATG 59.320 52.381 5.34 8.53 46.00 3.07
668 670 1.748244 CGCATCAGTGGTGGGATTGAT 60.748 52.381 15.05 0.00 0.00 2.57
669 671 0.392863 CGCATCAGTGGTGGGATTGA 60.393 55.000 15.05 0.00 0.00 2.57
670 672 0.392863 TCGCATCAGTGGTGGGATTG 60.393 55.000 18.47 0.00 34.18 2.67
671 673 0.392998 GTCGCATCAGTGGTGGGATT 60.393 55.000 24.16 0.00 40.08 3.01
672 674 1.221840 GTCGCATCAGTGGTGGGAT 59.778 57.895 24.16 0.00 40.08 3.85
673 675 2.662596 GTCGCATCAGTGGTGGGA 59.337 61.111 18.47 18.47 36.37 4.37
674 676 2.815211 CGTCGCATCAGTGGTGGG 60.815 66.667 14.06 14.06 0.00 4.61
675 677 3.490759 GCGTCGCATCAGTGGTGG 61.491 66.667 13.44 0.00 0.00 4.61
676 678 3.490759 GGCGTCGCATCAGTGGTG 61.491 66.667 20.50 0.00 0.00 4.17
677 679 2.731691 AAAGGCGTCGCATCAGTGGT 62.732 55.000 20.50 0.00 0.00 4.16
678 680 0.739462 TAAAGGCGTCGCATCAGTGG 60.739 55.000 20.50 0.00 0.00 4.00
679 681 0.647410 CTAAAGGCGTCGCATCAGTG 59.353 55.000 20.50 0.00 0.00 3.66
680 682 0.530744 TCTAAAGGCGTCGCATCAGT 59.469 50.000 20.50 3.74 0.00 3.41
681 683 1.640428 TTCTAAAGGCGTCGCATCAG 58.360 50.000 20.50 12.83 0.00 2.90
682 684 1.999735 CTTTCTAAAGGCGTCGCATCA 59.000 47.619 20.50 2.64 32.40 3.07
683 685 2.029365 GTCTTTCTAAAGGCGTCGCATC 59.971 50.000 20.50 2.01 36.67 3.91
684 686 2.000447 GTCTTTCTAAAGGCGTCGCAT 59.000 47.619 20.50 9.64 36.67 4.73
685 687 1.269883 TGTCTTTCTAAAGGCGTCGCA 60.270 47.619 20.50 0.00 43.38 5.10
686 688 1.425412 TGTCTTTCTAAAGGCGTCGC 58.575 50.000 9.22 9.22 43.38 5.19
687 689 2.412089 CCTTGTCTTTCTAAAGGCGTCG 59.588 50.000 2.87 0.00 43.38 5.12
692 694 4.700692 GGTAAGGCCTTGTCTTTCTAAAGG 59.299 45.833 28.77 0.00 42.86 3.11
693 695 5.881777 GGTAAGGCCTTGTCTTTCTAAAG 57.118 43.478 28.77 0.00 37.36 1.85
725 727 3.973206 TCGAGGCAATTTCACTCCTAA 57.027 42.857 0.00 0.00 0.00 2.69
727 729 2.420687 GGATCGAGGCAATTTCACTCCT 60.421 50.000 0.00 0.00 0.00 3.69
732 734 1.408683 CCAGGGATCGAGGCAATTTCA 60.409 52.381 0.00 0.00 0.00 2.69
742 744 2.123251 GGAGAGGCCAGGGATCGA 60.123 66.667 5.01 0.00 36.34 3.59
743 745 3.237741 GGGAGAGGCCAGGGATCG 61.238 72.222 5.01 0.00 38.95 3.69
771 773 0.179026 TCTGGATCCTCCGTCTACCG 60.179 60.000 14.23 0.00 40.17 4.02
774 776 2.656002 CTTGTCTGGATCCTCCGTCTA 58.344 52.381 14.23 0.00 40.17 2.59
787 789 4.453819 CCTCCTTTGTCTTTAGCTTGTCTG 59.546 45.833 0.00 0.00 0.00 3.51
788 790 4.348168 TCCTCCTTTGTCTTTAGCTTGTCT 59.652 41.667 0.00 0.00 0.00 3.41
795 797 6.648725 CACTTCTCTTCCTCCTTTGTCTTTAG 59.351 42.308 0.00 0.00 0.00 1.85
797 799 5.372373 CACTTCTCTTCCTCCTTTGTCTTT 58.628 41.667 0.00 0.00 0.00 2.52
803 805 1.002544 CCGCACTTCTCTTCCTCCTTT 59.997 52.381 0.00 0.00 0.00 3.11
884 886 9.883142 AACCAAAATCAGACAAATACAAAAGAA 57.117 25.926 0.00 0.00 0.00 2.52
887 889 9.757227 CCTAACCAAAATCAGACAAATACAAAA 57.243 29.630 0.00 0.00 0.00 2.44
888 890 9.137459 TCCTAACCAAAATCAGACAAATACAAA 57.863 29.630 0.00 0.00 0.00 2.83
889 891 8.698973 TCCTAACCAAAATCAGACAAATACAA 57.301 30.769 0.00 0.00 0.00 2.41
890 892 7.942341 ACTCCTAACCAAAATCAGACAAATACA 59.058 33.333 0.00 0.00 0.00 2.29
896 898 6.361433 TGAAACTCCTAACCAAAATCAGACA 58.639 36.000 0.00 0.00 0.00 3.41
981 988 1.764134 GGAGAGAGGACGGAGAGAGTA 59.236 57.143 0.00 0.00 0.00 2.59
983 990 0.179029 GGGAGAGAGGACGGAGAGAG 60.179 65.000 0.00 0.00 0.00 3.20
984 991 0.622154 AGGGAGAGAGGACGGAGAGA 60.622 60.000 0.00 0.00 0.00 3.10
985 992 0.465460 CAGGGAGAGAGGACGGAGAG 60.465 65.000 0.00 0.00 0.00 3.20
987 994 0.184933 ATCAGGGAGAGAGGACGGAG 59.815 60.000 0.00 0.00 0.00 4.63
988 995 0.106469 CATCAGGGAGAGAGGACGGA 60.106 60.000 0.00 0.00 0.00 4.69
989 996 1.743321 GCATCAGGGAGAGAGGACGG 61.743 65.000 0.00 0.00 0.00 4.79
990 997 1.739049 GCATCAGGGAGAGAGGACG 59.261 63.158 0.00 0.00 0.00 4.79
991 998 1.739049 CGCATCAGGGAGAGAGGAC 59.261 63.158 0.00 0.00 0.00 3.85
1020 1036 1.633561 GGCGGAAGTACGGTAGTTTC 58.366 55.000 9.47 6.80 0.00 2.78
1085 1101 3.301811 AGGGGGAAGGGGCTAGGT 61.302 66.667 0.00 0.00 0.00 3.08
1383 1399 4.093743 TCAATACACTCTGCTCCCAGTAA 58.906 43.478 0.00 0.00 40.09 2.24
1545 4141 5.882557 ACAGTTCATCAATAGCCTAGGTTTG 59.117 40.000 11.31 12.01 0.00 2.93
1707 4309 1.466856 CTGCTGGCATGCTTAGGAAA 58.533 50.000 18.92 0.00 0.00 3.13
1708 4310 0.394762 CCTGCTGGCATGCTTAGGAA 60.395 55.000 18.92 0.00 30.40 3.36
1709 4311 1.225426 CCTGCTGGCATGCTTAGGA 59.775 57.895 18.92 15.86 30.40 2.94
1772 4374 3.065925 GCTATCTAAGGCTTGTTGCAAGG 59.934 47.826 10.69 0.00 45.15 3.61
1824 4428 2.483491 TCGTGTAAATTTTGGGCGTACC 59.517 45.455 0.00 0.00 40.81 3.34
1843 4447 7.481798 GGTTGCTTGAGTAAAATTTATCACTCG 59.518 37.037 16.52 8.98 40.23 4.18
1862 4466 3.605664 GCTGGTTGGCGGTTGCTT 61.606 61.111 0.00 0.00 42.25 3.91
1923 4561 6.916440 TCTCAGTAGTTAGCGTGTTTTATGA 58.084 36.000 0.00 0.00 0.00 2.15
1946 4586 2.484062 CCTGATGTGGGCCGCAATC 61.484 63.158 25.56 20.43 0.00 2.67
2035 4683 5.140177 GCAACAACAACAGACTAAATCTCG 58.860 41.667 0.00 0.00 34.41 4.04
2260 4916 4.026744 TCGAATCTCCTCAAAGACCTGAT 58.973 43.478 0.00 0.00 0.00 2.90
2300 4956 4.595781 TCAACATACCAGAACAACCTAGGT 59.404 41.667 9.21 9.21 36.40 3.08
2350 5006 0.322546 GCCAACCTCGGACCTCAATT 60.323 55.000 0.00 0.00 0.00 2.32
2533 5189 3.263425 GGATTCAAGACCCTTGACCAGTA 59.737 47.826 8.72 0.00 0.00 2.74
2612 5268 2.635427 GTCAAAGAAGTCCCAGAGGTCT 59.365 50.000 0.00 0.00 32.31 3.85
2643 5299 2.196295 ACTGCTCGAGTCTAAATCGC 57.804 50.000 15.13 0.00 39.98 4.58
2649 5305 6.016527 TGTTAAGAAAGAACTGCTCGAGTCTA 60.017 38.462 15.13 0.06 31.73 2.59
2655 5311 4.307432 TCCTGTTAAGAAAGAACTGCTCG 58.693 43.478 0.00 0.00 0.00 5.03
2665 5321 5.417580 GGCCATACAACATCCTGTTAAGAAA 59.582 40.000 0.00 0.00 38.77 2.52
2761 5417 2.664916 CACAAAAATTCAGCTGGGTCG 58.335 47.619 15.13 0.00 0.00 4.79
2770 5426 6.625362 TCACTACTTGTTGCACAAAAATTCA 58.375 32.000 0.00 0.00 37.69 2.57
2835 5594 2.189191 ATCTGCAGGCAGCCTTTCGA 62.189 55.000 12.86 8.55 44.83 3.71
2840 5599 0.465824 GATGAATCTGCAGGCAGCCT 60.466 55.000 15.13 8.70 44.83 4.58
2853 5619 7.555554 CCTAGAGGAAAACATGAACTGATGAAT 59.444 37.037 0.00 0.00 37.39 2.57
2918 5687 9.961265 CAGAAGCAACAATGTGATTGATTATAT 57.039 29.630 3.35 0.00 42.83 0.86
3018 5787 4.229096 ACATTTTCGCAAGCAAGTACATG 58.771 39.130 0.00 0.00 37.18 3.21
3083 7313 8.085296 CCTTCTATGGTCATCTTGTACTGATAC 58.915 40.741 0.00 0.00 0.00 2.24
3111 7364 8.752254 GCATATCATGACATTTTGATCTGTTTG 58.248 33.333 0.00 0.00 34.52 2.93
3113 7366 8.002984 TGCATATCATGACATTTTGATCTGTT 57.997 30.769 0.00 0.00 34.52 3.16
3131 7384 2.159393 TGCCGCTTGTTCTTTGCATATC 60.159 45.455 0.00 0.00 0.00 1.63
3203 7459 2.287644 GGATTTTTGTTGGCAACTGCAC 59.712 45.455 28.71 15.36 44.36 4.57
3234 7493 2.731976 ACGTTCACGAAGCTCTTGATTC 59.268 45.455 6.30 0.00 43.02 2.52
3274 7533 0.868406 CCGGCTGTTTCTTCAGTGAC 59.132 55.000 0.00 0.00 37.70 3.67
3295 7573 3.007635 CAGGAACACGGAAGGGAATTAC 58.992 50.000 0.00 0.00 38.45 1.89
3315 7593 1.393603 TCACCCGAAACACAATTGCA 58.606 45.000 5.05 0.00 0.00 4.08
3316 7594 2.030363 TGATCACCCGAAACACAATTGC 60.030 45.455 5.05 0.00 0.00 3.56
3317 7595 3.913548 TGATCACCCGAAACACAATTG 57.086 42.857 3.24 3.24 0.00 2.32
3318 7596 4.616953 GTTTGATCACCCGAAACACAATT 58.383 39.130 0.00 0.00 31.25 2.32
3319 7597 3.304391 CGTTTGATCACCCGAAACACAAT 60.304 43.478 7.28 0.00 31.25 2.71
3321 7599 1.600013 CGTTTGATCACCCGAAACACA 59.400 47.619 7.28 0.00 31.25 3.72
3322 7600 1.868498 TCGTTTGATCACCCGAAACAC 59.132 47.619 12.18 0.00 31.25 3.32
3323 7601 2.139917 CTCGTTTGATCACCCGAAACA 58.860 47.619 14.67 0.47 31.25 2.83
3324 7602 2.157085 GTCTCGTTTGATCACCCGAAAC 59.843 50.000 14.67 9.71 0.00 2.78
3325 7603 2.409975 GTCTCGTTTGATCACCCGAAA 58.590 47.619 14.67 2.03 0.00 3.46
3326 7604 1.337447 GGTCTCGTTTGATCACCCGAA 60.337 52.381 14.67 5.95 0.00 4.30
3327 7605 0.245539 GGTCTCGTTTGATCACCCGA 59.754 55.000 13.49 13.49 0.00 5.14
3443 7739 1.908483 GGAGAACCAGGCGAGGAAT 59.092 57.895 6.03 0.00 35.97 3.01
3505 7807 3.524648 TTCACGAAGCCGGTGGTCC 62.525 63.158 1.90 0.00 40.78 4.46


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

AutoCloner maintained by Alex Coulton.