Multiple sequence alignment - TraesCS5D01G277900

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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 TraesCS5D01G277900 chr5D 100.000 4161 0 0 1 4161 379837185 379841345 0.000000e+00 7685.0
1 TraesCS5D01G277900 chr5D 86.813 91 9 3 273 361 60244168 60244257 9.520000e-17 99.0
2 TraesCS5D01G277900 chr5D 76.800 125 20 6 2561 2679 379839462 379839583 1.250000e-05 62.1
3 TraesCS5D01G277900 chr5A 93.610 2598 116 17 731 3295 480334825 480337405 0.000000e+00 3832.0
4 TraesCS5D01G277900 chr5A 89.617 626 54 7 3396 4016 480344066 480344685 0.000000e+00 785.0
5 TraesCS5D01G277900 chr5A 91.852 135 10 1 4028 4161 480344745 480344879 1.980000e-43 187.0
6 TraesCS5D01G277900 chr5A 94.937 79 3 1 652 730 688723542 688723465 5.650000e-24 122.0
7 TraesCS5D01G277900 chr5A 97.917 48 1 0 3351 3398 480342256 480342303 2.670000e-12 84.2
8 TraesCS5D01G277900 chr5B 88.799 1857 148 20 2182 4024 455748104 455749914 0.000000e+00 2222.0
9 TraesCS5D01G277900 chr5B 91.301 1506 73 31 731 2182 455746570 455748071 0.000000e+00 2002.0
10 TraesCS5D01G277900 chr5B 78.006 341 49 14 3691 4018 26043525 26043852 1.530000e-44 191.0
11 TraesCS5D01G277900 chr2D 98.198 555 9 1 1 554 338703030 338702476 0.000000e+00 968.0
12 TraesCS5D01G277900 chr2D 80.519 154 28 1 3818 3969 517257580 517257427 2.630000e-22 117.0
13 TraesCS5D01G277900 chr1B 78.341 434 64 15 3616 4027 644303898 644303473 1.920000e-63 254.0
14 TraesCS5D01G277900 chr7B 77.322 366 60 12 3671 4019 55862685 55863044 1.180000e-45 195.0
15 TraesCS5D01G277900 chr7A 76.562 384 65 14 3660 4027 107087100 107086726 1.980000e-43 187.0
16 TraesCS5D01G277900 chr7A 86.585 82 3 8 652 731 688669915 688669990 2.670000e-12 84.2
17 TraesCS5D01G277900 chr7A 86.420 81 3 8 652 730 688676614 688676688 9.590000e-12 82.4
18 TraesCS5D01G277900 chr7D 78.481 316 44 11 3721 4024 100304642 100304945 7.100000e-43 185.0
19 TraesCS5D01G277900 chr2B 77.193 342 58 12 3689 4019 139917136 139917468 9.190000e-42 182.0
20 TraesCS5D01G277900 chr2B 83.824 136 21 1 4027 4161 135085210 135085075 1.210000e-25 128.0
21 TraesCS5D01G277900 chr2B 94.286 35 0 2 2555 2588 680446215 680446182 8.000000e-03 52.8
22 TraesCS5D01G277900 chr3D 98.750 80 1 0 652 731 135179987 135179908 4.340000e-30 143.0
23 TraesCS5D01G277900 chr3D 97.500 80 2 0 652 731 574281676 574281755 2.020000e-28 137.0
24 TraesCS5D01G277900 chr3D 97.468 79 2 0 652 730 574292450 574292528 7.260000e-28 135.0
25 TraesCS5D01G277900 chr3D 94.595 37 2 0 3 39 27887849 27887885 1.620000e-04 58.4
26 TraesCS5D01G277900 chr2A 74.286 315 50 15 3720 4019 598165214 598165512 2.050000e-18 104.0
27 TraesCS5D01G277900 chr3B 84.259 108 14 3 273 378 190895601 190895707 7.360000e-18 102.0
28 TraesCS5D01G277900 chr3B 100.000 29 0 0 2557 2585 22460679 22460651 2.000000e-03 54.7
29 TraesCS5D01G277900 chr3A 85.185 81 6 6 652 731 13830802 13830727 1.240000e-10 78.7
30 TraesCS5D01G277900 chr1A 91.228 57 3 2 652 706 13743471 13743527 4.460000e-10 76.8
31 TraesCS5D01G277900 chr1A 85.714 70 8 2 652 720 516384381 516384313 5.770000e-09 73.1


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 TraesCS5D01G277900 chr5D 379837185 379841345 4160 False 3873.550000 7685 88.400000 1 4161 2 chr5D.!!$F2 4160
1 TraesCS5D01G277900 chr5A 480334825 480337405 2580 False 3832.000000 3832 93.610000 731 3295 1 chr5A.!!$F1 2564
2 TraesCS5D01G277900 chr5A 480342256 480344879 2623 False 352.066667 785 93.128667 3351 4161 3 chr5A.!!$F2 810
3 TraesCS5D01G277900 chr5B 455746570 455749914 3344 False 2112.000000 2222 90.050000 731 4024 2 chr5B.!!$F2 3293
4 TraesCS5D01G277900 chr2D 338702476 338703030 554 True 968.000000 968 98.198000 1 554 1 chr2D.!!$R1 553

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
575 577 0.034059 CAGTCCAGTCAGACGCCTTT 59.966 55.0 0.00 0.00 41.83 3.11 F
627 629 0.034616 AATATCGAGCTCAGCTGGGC 59.965 55.0 31.79 31.79 39.88 5.36 F
1778 1820 0.160182 CAAGTAAACACGTCGACGCC 59.840 55.0 35.92 17.11 44.43 5.68 F
2486 2616 0.035739 GGTACGAAGGGTTGAAGCCA 59.964 55.0 16.56 0.00 38.48 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1777 1819 0.245539 TGGTTCGAAAGAGGTAGCGG 59.754 55.0 0.00 0.00 43.69 5.52 R
2462 2592 0.320374 TCAACCCTTCGTACCTGCAG 59.680 55.0 6.78 6.78 0.00 4.41 R
2984 3118 0.179029 ATTGGTACCTGGCGTATGGC 60.179 55.0 14.36 0.56 42.51 4.40 R
3324 3461 0.373716 GCTGTTTGCGGGTATTCTCG 59.626 55.0 0.00 0.00 0.00 4.04 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
424 426 3.680786 GGGCCGGCAAGTGTTTCC 61.681 66.667 30.85 13.99 0.00 3.13
433 435 2.540973 GGCAAGTGTTTCCAGAACGAAC 60.541 50.000 0.00 0.00 0.00 3.95
441 443 0.391597 TCCAGAACGAACCAGACCAC 59.608 55.000 0.00 0.00 0.00 4.16
505 507 2.561956 CGGACCAGACCACACGACT 61.562 63.158 0.00 0.00 0.00 4.18
520 522 4.675029 ACTGTTTCCGTCGCCCCG 62.675 66.667 0.00 0.00 0.00 5.73
541 543 2.602676 GCTTGACCTAGGGCCCACA 61.603 63.158 27.56 10.69 0.00 4.17
554 556 1.597742 GCCCACATATGCCTACTGTG 58.402 55.000 1.58 0.00 39.93 3.66
564 566 2.366469 CCTACTGTGGCAGTCCAGT 58.634 57.895 12.99 12.99 41.21 4.00
565 567 0.247736 CCTACTGTGGCAGTCCAGTC 59.752 60.000 11.95 0.00 41.21 3.51
566 568 0.969149 CTACTGTGGCAGTCCAGTCA 59.031 55.000 11.95 0.00 41.21 3.41
567 569 0.969149 TACTGTGGCAGTCCAGTCAG 59.031 55.000 11.95 5.13 41.21 3.51
568 570 0.760567 ACTGTGGCAGTCCAGTCAGA 60.761 55.000 3.60 0.00 41.21 3.27
569 571 0.320247 CTGTGGCAGTCCAGTCAGAC 60.320 60.000 0.00 0.00 44.48 3.51
570 572 1.373497 GTGGCAGTCCAGTCAGACG 60.373 63.158 0.00 0.00 44.48 4.18
571 573 2.433318 GGCAGTCCAGTCAGACGC 60.433 66.667 0.00 0.00 41.83 5.19
572 574 2.433318 GCAGTCCAGTCAGACGCC 60.433 66.667 0.00 0.00 41.83 5.68
573 575 2.936912 GCAGTCCAGTCAGACGCCT 61.937 63.158 0.00 0.00 41.83 5.52
574 576 1.668294 CAGTCCAGTCAGACGCCTT 59.332 57.895 0.00 0.00 41.83 4.35
575 577 0.034059 CAGTCCAGTCAGACGCCTTT 59.966 55.000 0.00 0.00 41.83 3.11
576 578 0.759346 AGTCCAGTCAGACGCCTTTT 59.241 50.000 0.00 0.00 41.83 2.27
577 579 1.149148 GTCCAGTCAGACGCCTTTTC 58.851 55.000 0.00 0.00 0.00 2.29
578 580 0.756294 TCCAGTCAGACGCCTTTTCA 59.244 50.000 0.00 0.00 0.00 2.69
579 581 1.347707 TCCAGTCAGACGCCTTTTCAT 59.652 47.619 0.00 0.00 0.00 2.57
580 582 1.466167 CCAGTCAGACGCCTTTTCATG 59.534 52.381 0.00 0.00 0.00 3.07
581 583 1.466167 CAGTCAGACGCCTTTTCATGG 59.534 52.381 0.00 0.00 0.00 3.66
582 584 1.347707 AGTCAGACGCCTTTTCATGGA 59.652 47.619 0.00 0.00 0.00 3.41
583 585 2.026822 AGTCAGACGCCTTTTCATGGAT 60.027 45.455 0.00 0.00 0.00 3.41
584 586 2.352960 GTCAGACGCCTTTTCATGGATC 59.647 50.000 0.00 0.00 0.00 3.36
585 587 1.672881 CAGACGCCTTTTCATGGATCC 59.327 52.381 4.20 4.20 0.00 3.36
586 588 1.025041 GACGCCTTTTCATGGATCCC 58.975 55.000 9.90 0.00 0.00 3.85
587 589 0.331278 ACGCCTTTTCATGGATCCCA 59.669 50.000 9.90 0.00 38.19 4.37
588 590 1.272425 ACGCCTTTTCATGGATCCCAA 60.272 47.619 9.90 0.00 36.95 4.12
589 591 1.406539 CGCCTTTTCATGGATCCCAAG 59.593 52.381 9.90 3.76 36.95 3.61
590 592 1.137675 GCCTTTTCATGGATCCCAAGC 59.862 52.381 9.90 0.00 36.95 4.01
591 593 2.459644 CCTTTTCATGGATCCCAAGCA 58.540 47.619 9.90 0.00 36.95 3.91
592 594 2.167075 CCTTTTCATGGATCCCAAGCAC 59.833 50.000 9.90 0.00 36.95 4.40
593 595 2.601240 TTTCATGGATCCCAAGCACA 57.399 45.000 9.90 0.00 36.95 4.57
594 596 2.133281 TTCATGGATCCCAAGCACAG 57.867 50.000 9.90 0.00 36.95 3.66
595 597 1.288188 TCATGGATCCCAAGCACAGA 58.712 50.000 9.90 0.00 36.95 3.41
596 598 1.634973 TCATGGATCCCAAGCACAGAA 59.365 47.619 9.90 0.00 36.95 3.02
597 599 1.747355 CATGGATCCCAAGCACAGAAC 59.253 52.381 9.90 0.00 36.95 3.01
598 600 0.321564 TGGATCCCAAGCACAGAACG 60.322 55.000 9.90 0.00 0.00 3.95
599 601 0.321653 GGATCCCAAGCACAGAACGT 60.322 55.000 0.00 0.00 0.00 3.99
612 614 4.846779 ACAGAACGTGTGGCAAAAATAT 57.153 36.364 0.00 0.00 38.28 1.28
613 615 4.794169 ACAGAACGTGTGGCAAAAATATC 58.206 39.130 0.00 0.00 38.28 1.63
614 616 3.845775 CAGAACGTGTGGCAAAAATATCG 59.154 43.478 0.00 0.00 0.00 2.92
615 617 3.749088 AGAACGTGTGGCAAAAATATCGA 59.251 39.130 0.00 0.00 0.00 3.59
616 618 3.740044 ACGTGTGGCAAAAATATCGAG 57.260 42.857 0.00 0.00 0.00 4.04
617 619 2.159572 ACGTGTGGCAAAAATATCGAGC 60.160 45.455 0.00 0.00 0.00 5.03
618 620 2.095853 CGTGTGGCAAAAATATCGAGCT 59.904 45.455 0.00 0.00 0.00 4.09
619 621 3.685058 GTGTGGCAAAAATATCGAGCTC 58.315 45.455 2.73 2.73 0.00 4.09
620 622 3.126858 GTGTGGCAAAAATATCGAGCTCA 59.873 43.478 15.40 1.08 0.00 4.26
621 623 3.374988 TGTGGCAAAAATATCGAGCTCAG 59.625 43.478 15.40 6.88 0.00 3.35
622 624 2.355756 TGGCAAAAATATCGAGCTCAGC 59.644 45.455 15.40 0.00 0.00 4.26
623 625 2.615912 GGCAAAAATATCGAGCTCAGCT 59.384 45.455 15.40 0.00 43.88 4.24
624 626 3.547613 GGCAAAAATATCGAGCTCAGCTG 60.548 47.826 2.14 7.63 39.88 4.24
625 627 3.547613 GCAAAAATATCGAGCTCAGCTGG 60.548 47.826 15.13 1.71 39.88 4.85
626 628 2.540265 AAATATCGAGCTCAGCTGGG 57.460 50.000 15.13 12.70 39.88 4.45
627 629 0.034616 AATATCGAGCTCAGCTGGGC 59.965 55.000 31.79 31.79 39.88 5.36
628 630 0.831288 ATATCGAGCTCAGCTGGGCT 60.831 55.000 40.75 40.75 39.88 5.19
631 633 4.527583 GAGCTCAGCTGGGCTCGG 62.528 72.222 43.88 15.84 44.01 4.63
648 650 2.746277 GGCACCGAAACGCCTCAT 60.746 61.111 0.00 0.00 45.29 2.90
649 651 2.750888 GGCACCGAAACGCCTCATC 61.751 63.158 0.00 0.00 45.29 2.92
650 652 2.750888 GCACCGAAACGCCTCATCC 61.751 63.158 0.00 0.00 0.00 3.51
651 653 2.125673 ACCGAAACGCCTCATCCG 60.126 61.111 0.00 0.00 0.00 4.18
652 654 2.125673 CCGAAACGCCTCATCCGT 60.126 61.111 0.00 0.00 41.24 4.69
653 655 1.140161 CCGAAACGCCTCATCCGTA 59.860 57.895 0.00 0.00 38.06 4.02
654 656 0.249322 CCGAAACGCCTCATCCGTAT 60.249 55.000 0.00 0.00 38.06 3.06
655 657 1.001048 CCGAAACGCCTCATCCGTATA 60.001 52.381 0.00 0.00 38.06 1.47
656 658 2.544277 CCGAAACGCCTCATCCGTATAA 60.544 50.000 0.00 0.00 38.06 0.98
657 659 3.117794 CGAAACGCCTCATCCGTATAAA 58.882 45.455 0.00 0.00 38.06 1.40
658 660 3.739300 CGAAACGCCTCATCCGTATAAAT 59.261 43.478 0.00 0.00 38.06 1.40
659 661 4.919168 CGAAACGCCTCATCCGTATAAATA 59.081 41.667 0.00 0.00 38.06 1.40
660 662 5.164119 CGAAACGCCTCATCCGTATAAATAC 60.164 44.000 0.00 0.00 38.06 1.89
661 663 4.184079 ACGCCTCATCCGTATAAATACC 57.816 45.455 0.00 0.00 37.12 2.73
662 664 3.056322 ACGCCTCATCCGTATAAATACCC 60.056 47.826 0.00 0.00 37.12 3.69
663 665 3.677976 CGCCTCATCCGTATAAATACCCC 60.678 52.174 0.00 0.00 0.00 4.95
664 666 3.262405 GCCTCATCCGTATAAATACCCCA 59.738 47.826 0.00 0.00 0.00 4.96
665 667 4.263156 GCCTCATCCGTATAAATACCCCAA 60.263 45.833 0.00 0.00 0.00 4.12
666 668 5.572885 GCCTCATCCGTATAAATACCCCAAT 60.573 44.000 0.00 0.00 0.00 3.16
667 669 6.113411 CCTCATCCGTATAAATACCCCAATC 58.887 44.000 0.00 0.00 0.00 2.67
668 670 6.070194 CCTCATCCGTATAAATACCCCAATCT 60.070 42.308 0.00 0.00 0.00 2.40
669 671 7.324388 TCATCCGTATAAATACCCCAATCTT 57.676 36.000 0.00 0.00 0.00 2.40
670 672 7.391620 TCATCCGTATAAATACCCCAATCTTC 58.608 38.462 0.00 0.00 0.00 2.87
671 673 6.750660 TCCGTATAAATACCCCAATCTTCA 57.249 37.500 0.00 0.00 0.00 3.02
672 674 7.139287 TCCGTATAAATACCCCAATCTTCAA 57.861 36.000 0.00 0.00 0.00 2.69
673 675 7.751646 TCCGTATAAATACCCCAATCTTCAAT 58.248 34.615 0.00 0.00 0.00 2.57
674 676 7.881232 TCCGTATAAATACCCCAATCTTCAATC 59.119 37.037 0.00 0.00 0.00 2.67
675 677 7.663905 CCGTATAAATACCCCAATCTTCAATCA 59.336 37.037 0.00 0.00 0.00 2.57
676 678 9.062524 CGTATAAATACCCCAATCTTCAATCAA 57.937 33.333 0.00 0.00 0.00 2.57
681 683 9.713684 AAATACCCCAATCTTCAATCAATAGAA 57.286 29.630 0.00 0.00 0.00 2.10
682 684 9.887862 AATACCCCAATCTTCAATCAATAGAAT 57.112 29.630 0.00 0.00 0.00 2.40
684 686 8.930846 ACCCCAATCTTCAATCAATAGAATAG 57.069 34.615 0.00 0.00 0.00 1.73
685 687 7.449704 ACCCCAATCTTCAATCAATAGAATAGC 59.550 37.037 0.00 0.00 0.00 2.97
686 688 7.668886 CCCCAATCTTCAATCAATAGAATAGCT 59.331 37.037 0.00 0.00 0.00 3.32
687 689 8.512956 CCCAATCTTCAATCAATAGAATAGCTG 58.487 37.037 0.00 0.00 0.00 4.24
688 690 9.064706 CCAATCTTCAATCAATAGAATAGCTGT 57.935 33.333 0.00 0.00 0.00 4.40
691 693 9.842775 ATCTTCAATCAATAGAATAGCTGTTCA 57.157 29.630 23.17 10.96 0.00 3.18
692 694 9.842775 TCTTCAATCAATAGAATAGCTGTTCAT 57.157 29.630 23.17 12.54 0.00 2.57
694 696 8.613060 TCAATCAATAGAATAGCTGTTCATCC 57.387 34.615 23.17 0.00 0.00 3.51
695 697 8.212995 TCAATCAATAGAATAGCTGTTCATCCA 58.787 33.333 23.17 7.46 0.00 3.41
696 698 9.011095 CAATCAATAGAATAGCTGTTCATCCAT 57.989 33.333 23.17 9.22 0.00 3.41
697 699 9.584008 AATCAATAGAATAGCTGTTCATCCATT 57.416 29.630 23.17 13.73 0.00 3.16
703 705 8.845413 AGAATAGCTGTTCATCCATTATTCTC 57.155 34.615 23.17 0.00 31.94 2.87
704 706 8.658619 AGAATAGCTGTTCATCCATTATTCTCT 58.341 33.333 23.17 0.00 31.94 3.10
705 707 8.845413 AATAGCTGTTCATCCATTATTCTCTC 57.155 34.615 0.00 0.00 0.00 3.20
706 708 6.497624 AGCTGTTCATCCATTATTCTCTCT 57.502 37.500 0.00 0.00 0.00 3.10
707 709 6.289834 AGCTGTTCATCCATTATTCTCTCTG 58.710 40.000 0.00 0.00 0.00 3.35
708 710 5.049543 GCTGTTCATCCATTATTCTCTCTGC 60.050 44.000 0.00 0.00 0.00 4.26
709 711 6.244552 TGTTCATCCATTATTCTCTCTGCT 57.755 37.500 0.00 0.00 0.00 4.24
710 712 6.286758 TGTTCATCCATTATTCTCTCTGCTC 58.713 40.000 0.00 0.00 0.00 4.26
711 713 6.099413 TGTTCATCCATTATTCTCTCTGCTCT 59.901 38.462 0.00 0.00 0.00 4.09
712 714 6.099159 TCATCCATTATTCTCTCTGCTCTG 57.901 41.667 0.00 0.00 0.00 3.35
713 715 5.601729 TCATCCATTATTCTCTCTGCTCTGT 59.398 40.000 0.00 0.00 0.00 3.41
714 716 5.528043 TCCATTATTCTCTCTGCTCTGTC 57.472 43.478 0.00 0.00 0.00 3.51
715 717 5.207354 TCCATTATTCTCTCTGCTCTGTCT 58.793 41.667 0.00 0.00 0.00 3.41
716 718 5.660417 TCCATTATTCTCTCTGCTCTGTCTT 59.340 40.000 0.00 0.00 0.00 3.01
717 719 6.155910 TCCATTATTCTCTCTGCTCTGTCTTT 59.844 38.462 0.00 0.00 0.00 2.52
718 720 6.822676 CCATTATTCTCTCTGCTCTGTCTTTT 59.177 38.462 0.00 0.00 0.00 2.27
719 721 7.011295 CCATTATTCTCTCTGCTCTGTCTTTTC 59.989 40.741 0.00 0.00 0.00 2.29
720 722 3.951775 TCTCTCTGCTCTGTCTTTTCC 57.048 47.619 0.00 0.00 0.00 3.13
721 723 3.234353 TCTCTCTGCTCTGTCTTTTCCA 58.766 45.455 0.00 0.00 0.00 3.53
722 724 3.837146 TCTCTCTGCTCTGTCTTTTCCAT 59.163 43.478 0.00 0.00 0.00 3.41
723 725 4.081752 TCTCTCTGCTCTGTCTTTTCCATC 60.082 45.833 0.00 0.00 0.00 3.51
724 726 3.837146 TCTCTGCTCTGTCTTTTCCATCT 59.163 43.478 0.00 0.00 0.00 2.90
725 727 4.285517 TCTCTGCTCTGTCTTTTCCATCTT 59.714 41.667 0.00 0.00 0.00 2.40
726 728 4.978099 TCTGCTCTGTCTTTTCCATCTTT 58.022 39.130 0.00 0.00 0.00 2.52
727 729 6.014242 TCTCTGCTCTGTCTTTTCCATCTTTA 60.014 38.462 0.00 0.00 0.00 1.85
728 730 5.934625 TCTGCTCTGTCTTTTCCATCTTTAC 59.065 40.000 0.00 0.00 0.00 2.01
729 731 5.620206 TGCTCTGTCTTTTCCATCTTTACA 58.380 37.500 0.00 0.00 0.00 2.41
883 888 1.006688 CGTCGGACACCACACATCA 60.007 57.895 9.10 0.00 0.00 3.07
1337 1371 2.719354 GCAGTTTGCGGTTCCGTT 59.281 55.556 12.81 0.00 31.71 4.44
1338 1372 1.657181 GCAGTTTGCGGTTCCGTTG 60.657 57.895 12.81 5.58 31.71 4.10
1662 1704 3.740397 CGACTACGTGGCCACCGA 61.740 66.667 29.95 16.72 34.56 4.69
1747 1789 1.452108 CACCAGATTCGGCTTCCCC 60.452 63.158 0.00 0.00 0.00 4.81
1771 1813 1.270678 GCCCTCCTCAAGTAAACACGT 60.271 52.381 0.00 0.00 0.00 4.49
1776 1818 1.712350 CCTCAAGTAAACACGTCGACG 59.288 52.381 34.58 34.58 46.33 5.12
1777 1819 1.121967 CTCAAGTAAACACGTCGACGC 59.878 52.381 35.92 19.28 44.43 5.19
1778 1820 0.160182 CAAGTAAACACGTCGACGCC 59.840 55.000 35.92 17.11 44.43 5.68
1779 1821 1.270777 AAGTAAACACGTCGACGCCG 61.271 55.000 35.92 28.41 44.43 6.46
1802 1857 3.840124 ACCTCTTTCGAACCAGACTTT 57.160 42.857 0.00 0.00 0.00 2.66
2276 2385 2.113774 CACCAGCAGCACCTCCAA 59.886 61.111 0.00 0.00 0.00 3.53
2399 2526 1.012486 GGCGTAAGTGAACCGACTGG 61.012 60.000 0.00 0.00 40.26 4.00
2404 2531 0.393077 AAGTGAACCGACTGGACTGG 59.607 55.000 0.00 0.00 39.21 4.00
2412 2542 1.685180 CCGACTGGACTGGTATCCTGA 60.685 57.143 5.78 0.00 39.46 3.86
2413 2543 2.311463 CGACTGGACTGGTATCCTGAT 58.689 52.381 5.78 0.00 39.46 2.90
2414 2544 2.035193 CGACTGGACTGGTATCCTGATG 59.965 54.545 5.78 0.00 39.46 3.07
2415 2545 2.366916 GACTGGACTGGTATCCTGATGG 59.633 54.545 5.78 0.00 39.46 3.51
2417 2547 2.366916 CTGGACTGGTATCCTGATGGAC 59.633 54.545 0.00 0.00 46.51 4.02
2418 2548 2.023015 TGGACTGGTATCCTGATGGACT 60.023 50.000 0.00 0.00 46.51 3.85
2419 2549 2.366916 GGACTGGTATCCTGATGGACTG 59.633 54.545 0.00 0.00 46.51 3.51
2428 2558 6.440647 GGTATCCTGATGGACTGATGGTAATA 59.559 42.308 0.00 0.00 46.51 0.98
2486 2616 0.035739 GGTACGAAGGGTTGAAGCCA 59.964 55.000 16.56 0.00 38.48 4.75
2492 2622 0.779997 AAGGGTTGAAGCCACCATCT 59.220 50.000 16.56 0.00 38.48 2.90
2558 2688 4.803426 GAGTCGCCTCCTGCACCG 62.803 72.222 0.00 0.00 41.33 4.94
2682 2812 3.103793 CGTAAGCAAACCAACTGATCG 57.896 47.619 0.00 0.00 0.00 3.69
2683 2813 2.734606 CGTAAGCAAACCAACTGATCGA 59.265 45.455 0.00 0.00 0.00 3.59
2712 2843 3.415212 TCCTTGGCATTTGAGTGAAGAG 58.585 45.455 0.00 0.00 0.00 2.85
2715 2846 4.038402 CCTTGGCATTTGAGTGAAGAGTTT 59.962 41.667 0.00 0.00 0.00 2.66
2786 2917 2.852075 AAGCCACCGTCTTCCCCA 60.852 61.111 0.00 0.00 0.00 4.96
2837 2968 0.839277 ATGCCGGTGATTCTCCATCA 59.161 50.000 1.90 2.78 39.82 3.07
2873 3004 2.125552 TCTCCGGATGCAGCAACG 60.126 61.111 3.57 14.13 0.00 4.10
2936 3070 1.088269 TGGATTCCAACCCCAATGGA 58.912 50.000 1.94 0.00 45.09 3.41
3000 3134 2.279918 CGCCATACGCCAGGTACC 60.280 66.667 2.73 2.73 32.95 3.34
3015 3149 2.576648 AGGTACCAATTTCTCCCTGTCC 59.423 50.000 15.94 0.00 0.00 4.02
3022 3156 4.741239 TCTCCCTGTCCCCCTGCC 62.741 72.222 0.00 0.00 0.00 4.85
3055 3189 2.159212 TGGCAATGGCATTCGAATTCAG 60.159 45.455 10.36 0.00 43.71 3.02
3069 3206 3.124128 CGAATTCAGGCGTATGATCCATG 59.876 47.826 6.22 0.00 0.00 3.66
3129 3266 2.224305 ACGAAGACCTGAAACCTCCAAG 60.224 50.000 0.00 0.00 0.00 3.61
3252 3389 2.194271 GAGCTCAAGGCACGTGTATAC 58.806 52.381 18.38 5.53 44.79 1.47
3296 3433 5.712217 AATACAAATGTACACGACGATGG 57.288 39.130 0.00 0.00 32.72 3.51
3398 3535 4.873817 TGCACTAAAGAGCGTACAACTTA 58.126 39.130 0.00 0.00 34.29 2.24
3400 3537 4.326548 GCACTAAAGAGCGTACAACTTAGG 59.673 45.833 0.00 0.00 0.00 2.69
3401 3538 5.467705 CACTAAAGAGCGTACAACTTAGGT 58.532 41.667 0.00 0.00 0.00 3.08
3534 5436 2.443016 CCCTCCTCCTCCCTCGTG 60.443 72.222 0.00 0.00 0.00 4.35
3548 5450 2.030562 CGTGTTCGCCAGAGGGTT 59.969 61.111 0.00 0.00 36.17 4.11
3671 5573 4.980805 TCCGGACACTGTTGCCGC 62.981 66.667 0.00 0.00 39.60 6.53
3705 5607 1.202382 GCAGTACGTCCGGCTATTCTT 60.202 52.381 0.00 0.00 0.00 2.52
3709 5611 0.460311 ACGTCCGGCTATTCTTGGAG 59.540 55.000 0.00 0.00 0.00 3.86
3727 5629 1.452108 GTGCGCCTTGCCCTCTATT 60.452 57.895 4.18 0.00 45.60 1.73
3778 5684 6.642707 TTGTGATTCGTTTGTAGGGAAAAT 57.357 33.333 0.00 0.00 0.00 1.82
3787 5693 9.463902 TTCGTTTGTAGGGAAAATAATGGATTA 57.536 29.630 0.00 0.00 0.00 1.75
3788 5694 9.463902 TCGTTTGTAGGGAAAATAATGGATTAA 57.536 29.630 0.00 0.00 0.00 1.40
3841 5747 7.332557 TGGAGCTTGATGAATTAATGCAAAAT 58.667 30.769 0.00 0.00 0.00 1.82
3857 5764 5.830912 TGCAAAATGAGTTCTTGATTCGTT 58.169 33.333 0.00 0.00 0.00 3.85
4024 5931 9.398538 CTACTCTACAAGTACTACTTTGATCCT 57.601 37.037 0.00 0.00 36.03 3.24
4056 6011 1.990060 CGTGGTGGAGGGAGTGGAT 60.990 63.158 0.00 0.00 0.00 3.41
4061 6016 2.187946 GGAGGGAGTGGATGCACG 59.812 66.667 12.02 0.00 0.00 5.34
4076 6031 0.737715 GCACGTGCTCCCTACTTCAG 60.738 60.000 32.55 0.00 38.21 3.02
4082 6037 1.127343 GCTCCCTACTTCAGGCTCAT 58.873 55.000 0.00 0.00 43.98 2.90
4106 6062 1.197721 GGATTGTTGTGGCAACTCTCG 59.802 52.381 12.36 0.00 37.61 4.04
4121 6077 4.792521 ACTCTCGTTCTCTGTTAAGCAT 57.207 40.909 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 3.268965 GACGAGGTCTGCGCAGTCA 62.269 63.158 34.70 16.24 0.00 3.41
248 250 1.851658 GCTTCTTTTCTTTTGCCGCA 58.148 45.000 0.00 0.00 0.00 5.69
390 392 1.944676 CCGCGTATCCGTCTTGCTC 60.945 63.158 4.92 0.00 36.15 4.26
424 426 1.217882 GTGTGGTCTGGTTCGTTCTG 58.782 55.000 0.00 0.00 0.00 3.02
433 435 1.445942 ACCAGAACGTGTGGTCTGG 59.554 57.895 25.60 25.60 45.74 3.86
441 443 1.003355 AGCCATGGACCAGAACGTG 60.003 57.895 18.40 0.00 0.00 4.49
520 522 4.858680 GGCCCTAGGTCAAGCGGC 62.859 72.222 8.29 1.41 38.96 6.53
554 556 2.433318 GCGTCTGACTGGACTGCC 60.433 66.667 6.21 0.00 34.38 4.85
555 557 2.433318 GGCGTCTGACTGGACTGC 60.433 66.667 6.21 0.52 36.14 4.40
556 558 0.034059 AAAGGCGTCTGACTGGACTG 59.966 55.000 6.21 0.00 29.56 3.51
557 559 0.759346 AAAAGGCGTCTGACTGGACT 59.241 50.000 6.21 0.00 29.56 3.85
558 560 1.149148 GAAAAGGCGTCTGACTGGAC 58.851 55.000 6.21 0.00 29.56 4.02
559 561 0.756294 TGAAAAGGCGTCTGACTGGA 59.244 50.000 6.21 0.00 29.56 3.86
560 562 1.466167 CATGAAAAGGCGTCTGACTGG 59.534 52.381 6.21 0.00 29.56 4.00
561 563 1.466167 CCATGAAAAGGCGTCTGACTG 59.534 52.381 6.21 1.03 29.56 3.51
562 564 1.347707 TCCATGAAAAGGCGTCTGACT 59.652 47.619 6.21 0.00 31.31 3.41
563 565 1.808411 TCCATGAAAAGGCGTCTGAC 58.192 50.000 0.00 0.00 0.00 3.51
564 566 2.632377 GATCCATGAAAAGGCGTCTGA 58.368 47.619 0.00 0.00 0.00 3.27
565 567 1.672881 GGATCCATGAAAAGGCGTCTG 59.327 52.381 6.95 0.00 0.00 3.51
566 568 1.408822 GGGATCCATGAAAAGGCGTCT 60.409 52.381 15.23 0.00 0.00 4.18
567 569 1.025041 GGGATCCATGAAAAGGCGTC 58.975 55.000 15.23 0.00 0.00 5.19
568 570 0.331278 TGGGATCCATGAAAAGGCGT 59.669 50.000 15.23 0.00 0.00 5.68
569 571 1.406539 CTTGGGATCCATGAAAAGGCG 59.593 52.381 15.23 0.00 31.53 5.52
570 572 1.137675 GCTTGGGATCCATGAAAAGGC 59.862 52.381 15.23 2.30 31.53 4.35
571 573 2.167075 GTGCTTGGGATCCATGAAAAGG 59.833 50.000 15.23 0.00 31.53 3.11
572 574 2.827322 TGTGCTTGGGATCCATGAAAAG 59.173 45.455 15.23 9.61 31.53 2.27
573 575 2.827322 CTGTGCTTGGGATCCATGAAAA 59.173 45.455 15.23 0.00 31.53 2.29
574 576 2.041485 TCTGTGCTTGGGATCCATGAAA 59.959 45.455 15.23 1.20 31.53 2.69
575 577 1.634973 TCTGTGCTTGGGATCCATGAA 59.365 47.619 15.23 1.93 31.53 2.57
576 578 1.288188 TCTGTGCTTGGGATCCATGA 58.712 50.000 15.23 0.00 31.53 3.07
577 579 1.747355 GTTCTGTGCTTGGGATCCATG 59.253 52.381 15.23 3.75 31.53 3.66
578 580 1.679944 CGTTCTGTGCTTGGGATCCAT 60.680 52.381 15.23 0.00 31.53 3.41
579 581 0.321564 CGTTCTGTGCTTGGGATCCA 60.322 55.000 15.23 0.00 0.00 3.41
580 582 0.321653 ACGTTCTGTGCTTGGGATCC 60.322 55.000 1.92 1.92 0.00 3.36
581 583 0.798776 CACGTTCTGTGCTTGGGATC 59.201 55.000 0.00 0.00 42.70 3.36
582 584 2.932663 CACGTTCTGTGCTTGGGAT 58.067 52.632 0.00 0.00 42.70 3.85
583 585 4.454948 CACGTTCTGTGCTTGGGA 57.545 55.556 0.00 0.00 42.70 4.37
591 593 4.612712 CGATATTTTTGCCACACGTTCTGT 60.613 41.667 0.00 0.00 0.00 3.41
592 594 3.845775 CGATATTTTTGCCACACGTTCTG 59.154 43.478 0.00 0.00 0.00 3.02
593 595 3.749088 TCGATATTTTTGCCACACGTTCT 59.251 39.130 0.00 0.00 0.00 3.01
594 596 4.073169 TCGATATTTTTGCCACACGTTC 57.927 40.909 0.00 0.00 0.00 3.95
595 597 3.669557 GCTCGATATTTTTGCCACACGTT 60.670 43.478 0.00 0.00 0.00 3.99
596 598 2.159572 GCTCGATATTTTTGCCACACGT 60.160 45.455 0.00 0.00 0.00 4.49
597 599 2.095853 AGCTCGATATTTTTGCCACACG 59.904 45.455 0.00 0.00 0.00 4.49
598 600 3.126858 TGAGCTCGATATTTTTGCCACAC 59.873 43.478 9.64 0.00 0.00 3.82
599 601 3.342719 TGAGCTCGATATTTTTGCCACA 58.657 40.909 9.64 0.00 0.00 4.17
600 602 3.790123 GCTGAGCTCGATATTTTTGCCAC 60.790 47.826 9.64 0.00 0.00 5.01
601 603 2.355756 GCTGAGCTCGATATTTTTGCCA 59.644 45.455 9.64 0.00 0.00 4.92
602 604 2.615912 AGCTGAGCTCGATATTTTTGCC 59.384 45.455 9.64 0.00 30.62 4.52
603 605 3.547613 CCAGCTGAGCTCGATATTTTTGC 60.548 47.826 17.39 2.34 36.40 3.68
604 606 3.003068 CCCAGCTGAGCTCGATATTTTTG 59.997 47.826 17.39 0.00 36.40 2.44
605 607 3.209410 CCCAGCTGAGCTCGATATTTTT 58.791 45.455 17.39 0.00 36.40 1.94
606 608 2.843701 CCCAGCTGAGCTCGATATTTT 58.156 47.619 17.39 0.00 36.40 1.82
607 609 1.542108 GCCCAGCTGAGCTCGATATTT 60.542 52.381 17.39 0.00 36.40 1.40
608 610 0.034616 GCCCAGCTGAGCTCGATATT 59.965 55.000 17.39 0.00 36.40 1.28
609 611 0.831288 AGCCCAGCTGAGCTCGATAT 60.831 55.000 18.14 0.00 37.57 1.63
610 612 1.456518 AGCCCAGCTGAGCTCGATA 60.457 57.895 18.14 0.00 37.57 2.92
611 613 2.763292 AGCCCAGCTGAGCTCGAT 60.763 61.111 18.14 0.00 37.57 3.59
612 614 3.456365 GAGCCCAGCTGAGCTCGA 61.456 66.667 30.94 0.00 45.44 4.04
632 634 2.750888 GGATGAGGCGTTTCGGTGC 61.751 63.158 0.00 0.00 0.00 5.01
633 635 2.452813 CGGATGAGGCGTTTCGGTG 61.453 63.158 0.00 0.00 0.00 4.94
634 636 1.597797 TACGGATGAGGCGTTTCGGT 61.598 55.000 0.00 8.03 0.00 4.69
635 637 0.249322 ATACGGATGAGGCGTTTCGG 60.249 55.000 0.00 0.00 0.00 4.30
636 638 2.410785 TATACGGATGAGGCGTTTCG 57.589 50.000 0.00 0.00 0.00 3.46
637 639 5.119743 GGTATTTATACGGATGAGGCGTTTC 59.880 44.000 0.00 0.00 34.11 2.78
638 640 4.992951 GGTATTTATACGGATGAGGCGTTT 59.007 41.667 0.00 0.00 34.11 3.60
639 641 4.562143 GGGTATTTATACGGATGAGGCGTT 60.562 45.833 0.00 0.00 34.11 4.84
640 642 3.056322 GGGTATTTATACGGATGAGGCGT 60.056 47.826 0.00 0.00 34.11 5.68
641 643 3.518590 GGGTATTTATACGGATGAGGCG 58.481 50.000 0.00 0.00 34.11 5.52
642 644 3.262405 TGGGGTATTTATACGGATGAGGC 59.738 47.826 0.00 0.00 34.11 4.70
643 645 5.492855 TTGGGGTATTTATACGGATGAGG 57.507 43.478 0.00 0.00 34.11 3.86
644 646 6.947464 AGATTGGGGTATTTATACGGATGAG 58.053 40.000 0.00 0.00 34.11 2.90
645 647 6.945636 AGATTGGGGTATTTATACGGATGA 57.054 37.500 0.00 0.00 34.11 2.92
646 648 7.165485 TGAAGATTGGGGTATTTATACGGATG 58.835 38.462 0.00 0.00 34.11 3.51
647 649 7.324388 TGAAGATTGGGGTATTTATACGGAT 57.676 36.000 0.00 0.00 34.11 4.18
648 650 6.750660 TGAAGATTGGGGTATTTATACGGA 57.249 37.500 0.00 0.00 34.11 4.69
649 651 7.663905 TGATTGAAGATTGGGGTATTTATACGG 59.336 37.037 0.00 0.00 34.11 4.02
650 652 8.615878 TGATTGAAGATTGGGGTATTTATACG 57.384 34.615 0.00 0.00 34.11 3.06
655 657 9.713684 TTCTATTGATTGAAGATTGGGGTATTT 57.286 29.630 0.00 0.00 0.00 1.40
656 658 9.887862 ATTCTATTGATTGAAGATTGGGGTATT 57.112 29.630 0.00 0.00 0.00 1.89
659 661 7.449704 GCTATTCTATTGATTGAAGATTGGGGT 59.550 37.037 0.00 0.00 0.00 4.95
660 662 7.668886 AGCTATTCTATTGATTGAAGATTGGGG 59.331 37.037 0.00 0.00 0.00 4.96
661 663 8.512956 CAGCTATTCTATTGATTGAAGATTGGG 58.487 37.037 0.00 0.00 0.00 4.12
662 664 9.064706 ACAGCTATTCTATTGATTGAAGATTGG 57.935 33.333 0.00 0.00 0.00 3.16
665 667 9.842775 TGAACAGCTATTCTATTGATTGAAGAT 57.157 29.630 6.26 0.00 0.00 2.40
666 668 9.842775 ATGAACAGCTATTCTATTGATTGAAGA 57.157 29.630 6.26 0.00 0.00 2.87
668 670 9.060347 GGATGAACAGCTATTCTATTGATTGAA 57.940 33.333 6.26 0.00 0.00 2.69
669 671 8.212995 TGGATGAACAGCTATTCTATTGATTGA 58.787 33.333 6.26 0.00 0.00 2.57
670 672 8.387190 TGGATGAACAGCTATTCTATTGATTG 57.613 34.615 6.26 0.00 0.00 2.67
671 673 9.584008 AATGGATGAACAGCTATTCTATTGATT 57.416 29.630 6.26 0.00 0.00 2.57
677 679 9.935241 GAGAATAATGGATGAACAGCTATTCTA 57.065 33.333 6.26 0.00 38.37 2.10
678 680 8.658619 AGAGAATAATGGATGAACAGCTATTCT 58.341 33.333 6.26 3.14 39.56 2.40
679 681 8.845413 AGAGAATAATGGATGAACAGCTATTC 57.155 34.615 0.00 0.00 33.54 1.75
680 682 8.658619 AGAGAGAATAATGGATGAACAGCTATT 58.341 33.333 6.84 6.84 32.73 1.73
681 683 8.095792 CAGAGAGAATAATGGATGAACAGCTAT 58.904 37.037 0.00 0.00 0.00 2.97
682 684 7.440198 CAGAGAGAATAATGGATGAACAGCTA 58.560 38.462 0.00 0.00 0.00 3.32
683 685 6.289834 CAGAGAGAATAATGGATGAACAGCT 58.710 40.000 0.00 0.00 0.00 4.24
684 686 5.049543 GCAGAGAGAATAATGGATGAACAGC 60.050 44.000 0.00 0.00 0.00 4.40
685 687 6.289834 AGCAGAGAGAATAATGGATGAACAG 58.710 40.000 0.00 0.00 0.00 3.16
686 688 6.099413 AGAGCAGAGAGAATAATGGATGAACA 59.901 38.462 0.00 0.00 0.00 3.18
687 689 6.424509 CAGAGCAGAGAGAATAATGGATGAAC 59.575 42.308 0.00 0.00 0.00 3.18
688 690 6.099413 ACAGAGCAGAGAGAATAATGGATGAA 59.901 38.462 0.00 0.00 0.00 2.57
689 691 5.601729 ACAGAGCAGAGAGAATAATGGATGA 59.398 40.000 0.00 0.00 0.00 2.92
690 692 5.856156 ACAGAGCAGAGAGAATAATGGATG 58.144 41.667 0.00 0.00 0.00 3.51
691 693 5.840149 AGACAGAGCAGAGAGAATAATGGAT 59.160 40.000 0.00 0.00 0.00 3.41
692 694 5.207354 AGACAGAGCAGAGAGAATAATGGA 58.793 41.667 0.00 0.00 0.00 3.41
693 695 5.534207 AGACAGAGCAGAGAGAATAATGG 57.466 43.478 0.00 0.00 0.00 3.16
694 696 7.011295 GGAAAAGACAGAGCAGAGAGAATAATG 59.989 40.741 0.00 0.00 0.00 1.90
695 697 7.047271 GGAAAAGACAGAGCAGAGAGAATAAT 58.953 38.462 0.00 0.00 0.00 1.28
696 698 6.014242 TGGAAAAGACAGAGCAGAGAGAATAA 60.014 38.462 0.00 0.00 0.00 1.40
697 699 5.481824 TGGAAAAGACAGAGCAGAGAGAATA 59.518 40.000 0.00 0.00 0.00 1.75
698 700 4.285517 TGGAAAAGACAGAGCAGAGAGAAT 59.714 41.667 0.00 0.00 0.00 2.40
699 701 3.643320 TGGAAAAGACAGAGCAGAGAGAA 59.357 43.478 0.00 0.00 0.00 2.87
700 702 3.234353 TGGAAAAGACAGAGCAGAGAGA 58.766 45.455 0.00 0.00 0.00 3.10
701 703 3.674528 TGGAAAAGACAGAGCAGAGAG 57.325 47.619 0.00 0.00 0.00 3.20
702 704 3.837146 AGATGGAAAAGACAGAGCAGAGA 59.163 43.478 0.00 0.00 0.00 3.10
703 705 4.205065 AGATGGAAAAGACAGAGCAGAG 57.795 45.455 0.00 0.00 0.00 3.35
704 706 4.630644 AAGATGGAAAAGACAGAGCAGA 57.369 40.909 0.00 0.00 0.00 4.26
705 707 5.702670 TGTAAAGATGGAAAAGACAGAGCAG 59.297 40.000 0.00 0.00 0.00 4.24
706 708 5.470098 GTGTAAAGATGGAAAAGACAGAGCA 59.530 40.000 0.00 0.00 0.00 4.26
707 709 5.106515 GGTGTAAAGATGGAAAAGACAGAGC 60.107 44.000 0.00 0.00 0.00 4.09
708 710 5.412904 GGGTGTAAAGATGGAAAAGACAGAG 59.587 44.000 0.00 0.00 0.00 3.35
709 711 5.313712 GGGTGTAAAGATGGAAAAGACAGA 58.686 41.667 0.00 0.00 0.00 3.41
710 712 4.154195 CGGGTGTAAAGATGGAAAAGACAG 59.846 45.833 0.00 0.00 0.00 3.51
711 713 4.069304 CGGGTGTAAAGATGGAAAAGACA 58.931 43.478 0.00 0.00 0.00 3.41
712 714 3.119955 GCGGGTGTAAAGATGGAAAAGAC 60.120 47.826 0.00 0.00 0.00 3.01
713 715 3.078837 GCGGGTGTAAAGATGGAAAAGA 58.921 45.455 0.00 0.00 0.00 2.52
714 716 2.159572 CGCGGGTGTAAAGATGGAAAAG 60.160 50.000 0.00 0.00 0.00 2.27
715 717 1.807742 CGCGGGTGTAAAGATGGAAAA 59.192 47.619 0.00 0.00 0.00 2.29
716 718 1.270947 ACGCGGGTGTAAAGATGGAAA 60.271 47.619 12.47 0.00 0.00 3.13
717 719 0.322322 ACGCGGGTGTAAAGATGGAA 59.678 50.000 12.47 0.00 0.00 3.53
718 720 0.108520 GACGCGGGTGTAAAGATGGA 60.109 55.000 10.96 0.00 0.00 3.41
719 721 1.418342 CGACGCGGGTGTAAAGATGG 61.418 60.000 10.96 0.00 0.00 3.51
720 722 1.995991 CGACGCGGGTGTAAAGATG 59.004 57.895 10.96 0.00 0.00 2.90
721 723 1.808390 GCGACGCGGGTGTAAAGAT 60.808 57.895 10.96 0.00 0.00 2.40
722 724 2.431260 GCGACGCGGGTGTAAAGA 60.431 61.111 10.96 0.00 0.00 2.52
723 725 3.484547 GGCGACGCGGGTGTAAAG 61.485 66.667 10.96 0.00 0.00 1.85
724 726 3.592856 ATGGCGACGCGGGTGTAAA 62.593 57.895 10.96 0.00 0.00 2.01
725 727 3.993376 GATGGCGACGCGGGTGTAA 62.993 63.158 10.96 0.00 0.00 2.41
726 728 4.501714 GATGGCGACGCGGGTGTA 62.502 66.667 10.96 0.00 0.00 2.90
883 888 3.580193 CGTATCGCGTCGAGGGGT 61.580 66.667 19.74 11.03 39.91 4.95
1216 1250 4.379243 CTGCTCCTTCACCGGCGT 62.379 66.667 6.01 0.00 0.00 5.68
1299 1333 2.103143 CGGCGATCGAGCAGAGTT 59.897 61.111 21.57 0.00 42.43 3.01
1337 1371 1.750018 ATTACGCATGCAGCAGCCA 60.750 52.632 19.57 0.00 46.13 4.75
1338 1372 1.298863 CATTACGCATGCAGCAGCC 60.299 57.895 19.57 0.00 46.13 4.85
1366 1404 1.298863 GCACACGCATGGCATCATC 60.299 57.895 0.00 0.00 38.36 2.92
1496 1538 4.200283 CTCCAGCCTCGAGTCCGC 62.200 72.222 12.31 7.90 35.37 5.54
1500 1542 3.073735 CCAGCTCCAGCCTCGAGT 61.074 66.667 12.31 0.00 43.38 4.18
1711 1753 4.083862 GTGCCGAGGGAGGTGACC 62.084 72.222 0.00 0.00 0.00 4.02
1747 1789 2.515996 TTTACTTGAGGAGGGCGGCG 62.516 60.000 0.51 0.51 0.00 6.46
1771 1813 2.262471 GAAAGAGGTAGCGGCGTCGA 62.262 60.000 16.53 0.00 39.00 4.20
1776 1818 1.082679 GGTTCGAAAGAGGTAGCGGC 61.083 60.000 0.00 0.00 43.69 6.53
1777 1819 0.245539 TGGTTCGAAAGAGGTAGCGG 59.754 55.000 0.00 0.00 43.69 5.52
1778 1820 1.201647 TCTGGTTCGAAAGAGGTAGCG 59.798 52.381 0.00 0.00 43.69 4.26
1779 1821 2.231721 AGTCTGGTTCGAAAGAGGTAGC 59.768 50.000 0.00 0.00 43.69 3.58
1802 1857 2.302445 CCATCAATCCTTGGCCAAAACA 59.698 45.455 20.91 6.37 0.00 2.83
1819 1874 5.332883 CGATCGATCATGTGAAAACTCCATC 60.333 44.000 24.40 0.00 0.00 3.51
1912 1967 3.604202 CGCACGATCGTGTACGGC 61.604 66.667 39.58 27.82 46.90 5.68
2263 2351 2.113986 GGTGTTGGAGGTGCTGCT 59.886 61.111 0.00 0.00 0.00 4.24
2412 2542 5.775195 TGATCGTCTATTACCATCAGTCCAT 59.225 40.000 0.00 0.00 31.63 3.41
2413 2543 5.137551 TGATCGTCTATTACCATCAGTCCA 58.862 41.667 0.00 0.00 31.63 4.02
2414 2544 5.707242 TGATCGTCTATTACCATCAGTCC 57.293 43.478 0.00 0.00 31.63 3.85
2415 2545 7.359598 GCAAATGATCGTCTATTACCATCAGTC 60.360 40.741 0.00 0.00 38.81 3.51
2416 2546 6.425114 GCAAATGATCGTCTATTACCATCAGT 59.575 38.462 0.00 0.00 38.81 3.41
2417 2547 6.648310 AGCAAATGATCGTCTATTACCATCAG 59.352 38.462 0.00 0.00 38.81 2.90
2418 2548 6.424812 CAGCAAATGATCGTCTATTACCATCA 59.575 38.462 0.00 0.00 39.59 3.07
2419 2549 6.646653 TCAGCAAATGATCGTCTATTACCATC 59.353 38.462 0.00 0.00 31.12 3.51
2460 2590 1.764571 AACCCTTCGTACCTGCAGCA 61.765 55.000 8.66 0.00 0.00 4.41
2461 2591 1.003718 AACCCTTCGTACCTGCAGC 60.004 57.895 8.66 0.00 0.00 5.25
2462 2592 0.320374 TCAACCCTTCGTACCTGCAG 59.680 55.000 6.78 6.78 0.00 4.41
2486 2616 1.071314 TGGGTGTTGGGGAAGATGGT 61.071 55.000 0.00 0.00 0.00 3.55
2492 2622 0.854218 TAAAGCTGGGTGTTGGGGAA 59.146 50.000 0.00 0.00 0.00 3.97
2668 2798 5.605564 TGTAACATCGATCAGTTGGTTTG 57.394 39.130 10.50 0.00 0.00 2.93
2669 2799 5.354234 GGATGTAACATCGATCAGTTGGTTT 59.646 40.000 10.50 0.00 0.00 3.27
2680 2810 3.558931 ATGCCAAGGATGTAACATCGA 57.441 42.857 0.00 0.00 0.00 3.59
2681 2811 4.096231 TCAAATGCCAAGGATGTAACATCG 59.904 41.667 0.00 0.00 0.00 3.84
2682 2812 5.126061 ACTCAAATGCCAAGGATGTAACATC 59.874 40.000 0.00 0.00 0.00 3.06
2683 2813 5.018809 ACTCAAATGCCAAGGATGTAACAT 58.981 37.500 0.00 0.00 0.00 2.71
2712 2843 1.064463 TGGATCCATCAGAGGCCAAAC 60.064 52.381 11.44 0.00 31.79 2.93
2715 2846 1.526315 AATGGATCCATCAGAGGCCA 58.474 50.000 27.45 0.00 37.31 5.36
2786 2917 4.335647 CCGCTCCTGCTGGGTGTT 62.336 66.667 10.07 0.00 36.97 3.32
2802 2933 1.648504 GCATCCATTTTCTTGCTGCC 58.351 50.000 0.00 0.00 32.41 4.85
2815 2946 1.271127 TGGAGAATCACCGGCATCCA 61.271 55.000 0.00 3.37 36.25 3.41
2954 3088 2.672908 CCTGGATCAGCAGTGGCA 59.327 61.111 0.00 0.00 44.61 4.92
2984 3118 0.179029 ATTGGTACCTGGCGTATGGC 60.179 55.000 14.36 0.56 42.51 4.40
3000 3134 1.002857 AGGGGGACAGGGAGAAATTG 58.997 55.000 0.00 0.00 0.00 2.32
3015 3149 1.132554 ATGAGCTAGATGGGCAGGGG 61.133 60.000 0.00 0.00 0.00 4.79
3022 3156 2.160205 CCATTGCCATGAGCTAGATGG 58.840 52.381 16.81 16.81 44.23 3.51
3055 3189 1.089920 GGATGCATGGATCATACGCC 58.910 55.000 26.07 7.04 0.00 5.68
3069 3206 4.679373 TTAATCAGACAGAGAGGGATGC 57.321 45.455 0.00 0.00 0.00 3.91
3129 3266 3.499737 CGGATGGAGTTGGCGTGC 61.500 66.667 0.00 0.00 0.00 5.34
3252 3389 2.742053 TCTCGAAGAAGGAAAATTGGCG 59.258 45.455 0.00 0.00 34.09 5.69
3324 3461 0.373716 GCTGTTTGCGGGTATTCTCG 59.626 55.000 0.00 0.00 0.00 4.04
3330 3467 2.357760 GTCGGCTGTTTGCGGGTA 60.358 61.111 0.00 0.00 44.05 3.69
3398 3535 2.622942 CACCTTGCATTGTACACAACCT 59.377 45.455 0.00 0.00 38.86 3.50
3400 3537 2.393764 GCACCTTGCATTGTACACAAC 58.606 47.619 0.00 0.00 44.26 3.32
3401 3538 2.791383 GCACCTTGCATTGTACACAA 57.209 45.000 0.00 0.00 44.26 3.33
3499 5401 1.704704 GTGGGTAGAGGAGGGAGGT 59.295 63.158 0.00 0.00 0.00 3.85
3534 5436 2.434359 CGGAACCCTCTGGCGAAC 60.434 66.667 0.00 0.00 33.59 3.95
3727 5629 2.349438 GCTCGAGCAATTTGTCGAACAA 60.349 45.455 31.91 0.00 44.19 2.83
3778 5684 7.941790 TGATGAACCATCCGAATTAATCCATTA 59.058 33.333 4.69 0.00 39.87 1.90
3787 5693 5.039920 TCATCTGATGAACCATCCGAATT 57.960 39.130 17.56 0.00 39.87 2.17
3788 5694 4.504514 CCTCATCTGATGAACCATCCGAAT 60.505 45.833 19.95 0.00 39.87 3.34
3789 5695 3.181462 CCTCATCTGATGAACCATCCGAA 60.181 47.826 19.95 0.00 39.87 4.30
3790 5696 2.366590 CCTCATCTGATGAACCATCCGA 59.633 50.000 19.95 4.37 39.87 4.55
3841 5747 5.391449 CGACTCTAACGAATCAAGAACTCA 58.609 41.667 0.00 0.00 0.00 3.41
3857 5764 1.931841 CGACATCTTCGTCCGACTCTA 59.068 52.381 0.00 0.00 43.24 2.43
3902 5809 0.548510 CTCCCTGTCCATTTCCTCCC 59.451 60.000 0.00 0.00 0.00 4.30
4024 5931 2.292016 CCACCACGCACAAGAACAATTA 59.708 45.455 0.00 0.00 0.00 1.40
4056 6011 1.292223 GAAGTAGGGAGCACGTGCA 59.708 57.895 39.21 18.32 45.16 4.57
4076 6031 2.689983 CCACAACAATCCCTAATGAGCC 59.310 50.000 0.00 0.00 0.00 4.70
4082 6037 3.153919 GAGTTGCCACAACAATCCCTAA 58.846 45.455 12.56 0.00 0.00 2.69
4121 6077 6.456853 GCATTCTCATAGTTGTCGTGCATTTA 60.457 38.462 0.00 0.00 0.00 1.40
4129 6085 3.371898 TGCAAGCATTCTCATAGTTGTCG 59.628 43.478 0.00 0.00 0.00 4.35
4133 6089 5.121811 CCTAGTGCAAGCATTCTCATAGTT 58.878 41.667 0.00 0.00 0.00 2.24
4134 6090 4.163078 ACCTAGTGCAAGCATTCTCATAGT 59.837 41.667 0.00 0.00 0.00 2.12
4138 6094 3.369471 GGTACCTAGTGCAAGCATTCTCA 60.369 47.826 4.06 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.