Multiple sequence alignment - TraesCS7A01G546100

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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 TraesCS7A01G546100 chr7A 100.000 2306 0 0 1420 3725 721854515 721856820 0.000000e+00 4259
1 TraesCS7A01G546100 chr7A 95.882 2307 70 13 1420 3725 78697301 78699583 0.000000e+00 3711
2 TraesCS7A01G546100 chr7A 95.883 2016 76 5 1459 3470 711643384 711645396 0.000000e+00 3256
3 TraesCS7A01G546100 chr7A 100.000 1181 0 0 1 1181 721853096 721854276 0.000000e+00 2182
4 TraesCS7A01G546100 chr7A 93.080 737 43 2 1 736 78696556 78697285 0.000000e+00 1072
5 TraesCS7A01G546100 chr7A 98.858 438 4 1 742 1178 721853386 721853823 0.000000e+00 780
6 TraesCS7A01G546100 chr7A 98.858 438 4 1 291 728 721853837 721854273 0.000000e+00 780
7 TraesCS7A01G546100 chr7A 93.763 481 29 1 1 480 711642607 711643087 0.000000e+00 721
8 TraesCS7A01G546100 chr7A 94.379 427 21 1 3299 3725 18140198 18140621 0.000000e+00 652
9 TraesCS7A01G546100 chr7A 92.290 441 26 2 742 1181 78696847 78697280 1.470000e-173 619
10 TraesCS7A01G546100 chr7A 93.226 310 21 0 427 736 711643074 711643383 1.220000e-124 457
11 TraesCS7A01G546100 chr7A 93.115 305 21 0 877 1181 711643074 711643378 7.340000e-122 448
12 TraesCS7A01G546100 chr2A 96.246 2264 82 1 1462 3725 63985556 63987816 0.000000e+00 3707
13 TraesCS7A01G546100 chr2A 93.763 481 29 1 1 480 63984776 63985256 0.000000e+00 721
14 TraesCS7A01G546100 chr2A 92.787 305 22 0 877 1181 63985243 63985547 3.410000e-120 442
15 TraesCS7A01G546100 chr2A 91.987 312 25 0 427 738 63985243 63985554 4.420000e-119 438
16 TraesCS7A01G546100 chr2A 94.118 187 10 1 745 930 63985070 63985256 2.190000e-72 283
17 TraesCS7A01G546100 chr3B 94.599 2333 97 4 1420 3725 752768654 752766324 0.000000e+00 3583
18 TraesCS7A01G546100 chr3B 92.010 388 30 1 349 736 752769056 752768670 9.100000e-151 544
19 TraesCS7A01G546100 chr3B 92.388 381 28 1 799 1179 752769056 752768677 3.270000e-150 542
20 TraesCS7A01G546100 chr6B 94.256 2333 102 7 1420 3725 684054457 684052130 0.000000e+00 3537
21 TraesCS7A01G546100 chr6B 94.164 377 21 1 805 1181 684054854 684054479 1.160000e-159 573
22 TraesCS7A01G546100 chr6B 93.455 382 24 1 355 736 684054854 684054474 1.940000e-157 566
23 TraesCS7A01G546100 chr3D 94.951 2258 86 2 1494 3725 605102624 605100369 0.000000e+00 3513
24 TraesCS7A01G546100 chr6A 93.142 2333 130 4 1420 3725 2547200 2544871 0.000000e+00 3395
25 TraesCS7A01G546100 chr6A 95.550 427 18 1 3299 3725 567581266 567580841 0.000000e+00 682
26 TraesCS7A01G546100 chr6A 74.834 302 37 15 138 425 604353109 604353385 2.370000e-17 100
27 TraesCS7A01G546100 chr2B 93.518 1481 57 9 2264 3716 1499264 1497795 0.000000e+00 2167
28 TraesCS7A01G546100 chr2B 92.641 462 21 5 1420 1880 1499706 1499257 0.000000e+00 652
29 TraesCS7A01G546100 chr2B 91.688 397 33 0 785 1181 1500126 1499730 5.440000e-153 551
30 TraesCS7A01G546100 chr2B 91.045 402 36 0 335 736 1500126 1499725 9.100000e-151 544
31 TraesCS7A01G546100 chr4A 81.380 913 107 31 2587 3466 664034045 664033163 0.000000e+00 686
32 TraesCS7A01G546100 chr7D 87.572 346 37 5 2186 2528 553452304 553451962 2.700000e-106 396
33 TraesCS7A01G546100 chr3A 81.068 206 22 8 335 524 26786509 26786713 8.340000e-32 148
34 TraesCS7A01G546100 chr5A 85.366 123 17 1 335 456 434794004 434794126 3.910000e-25 126


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 TraesCS7A01G546100 chr7A 721853096 721856820 3724 False 2000.250000 4259 99.429000 1 3725 4 chr7A.!!$F4 3724
1 TraesCS7A01G546100 chr7A 78696556 78699583 3027 False 1800.666667 3711 93.750667 1 3725 3 chr7A.!!$F2 3724
2 TraesCS7A01G546100 chr7A 711642607 711645396 2789 False 1220.500000 3256 93.996750 1 3470 4 chr7A.!!$F3 3469
3 TraesCS7A01G546100 chr2A 63984776 63987816 3040 False 1118.200000 3707 93.780200 1 3725 5 chr2A.!!$F1 3724
4 TraesCS7A01G546100 chr3B 752766324 752769056 2732 True 1556.333333 3583 92.999000 349 3725 3 chr3B.!!$R1 3376
5 TraesCS7A01G546100 chr6B 684052130 684054854 2724 True 1558.666667 3537 93.958333 355 3725 3 chr6B.!!$R1 3370
6 TraesCS7A01G546100 chr3D 605100369 605102624 2255 True 3513.000000 3513 94.951000 1494 3725 1 chr3D.!!$R1 2231
7 TraesCS7A01G546100 chr6A 2544871 2547200 2329 True 3395.000000 3395 93.142000 1420 3725 1 chr6A.!!$R1 2305
8 TraesCS7A01G546100 chr2B 1497795 1500126 2331 True 978.500000 2167 92.223000 335 3716 4 chr2B.!!$R1 3381
9 TraesCS7A01G546100 chr4A 664033163 664034045 882 True 686.000000 686 81.380000 2587 3466 1 chr4A.!!$R1 879

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
602 686 0.031585 ACGTTGTGCTTGTCGCTAGA 59.968 50.0 0.00 0.00 40.11 2.43 F
646 730 0.033504 TCGCTTGACTGGGTCAACTC 59.966 55.0 8.75 4.18 45.88 3.01 F
849 933 0.035534 TCCATCCAATCCACACACGG 60.036 55.0 0.00 0.00 0.00 4.94 F
1995 2080 0.039165 TCAGTCAGTGTAGCAGCACG 60.039 55.0 0.00 0.00 43.61 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1490 1575 1.093159 GAACTCTAAGGCGAGGACGA 58.907 55.000 0.0 0.0 42.66 4.20 R
1632 1717 2.031516 CACTGGCACCTTCAGAGCG 61.032 63.158 0.0 0.0 36.22 5.03 R
2699 2789 1.632409 AGGTGATGAGCATTCCACTGT 59.368 47.619 0.0 0.0 0.00 3.55 R
3280 3433 0.179140 GCACCACAACACAACACAGG 60.179 55.000 0.0 0.0 0.00 4.00 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
73 75 5.574055 TGGCACTAGTAGTTTTTATCGAACG 59.426 40.000 0.00 0.00 32.38 3.95
75 77 5.287992 GCACTAGTAGTTTTTATCGAACGCT 59.712 40.000 0.00 0.00 32.38 5.07
150 152 1.372838 CGCGCCATATGTCCACCAAA 61.373 55.000 0.00 0.00 0.00 3.28
174 176 0.454957 CAGCTCGTGCCAAATTTCCG 60.455 55.000 5.73 0.00 40.80 4.30
283 285 1.234529 CTCCTCCCGAATCCCCTCT 59.765 63.158 0.00 0.00 0.00 3.69
286 288 0.188834 CCTCCCGAATCCCCTCTAGT 59.811 60.000 0.00 0.00 0.00 2.57
361 363 2.123640 CTCCCCTCCTCCTCGTCC 60.124 72.222 0.00 0.00 0.00 4.79
362 364 2.617538 TCCCCTCCTCCTCGTCCT 60.618 66.667 0.00 0.00 0.00 3.85
499 583 2.416547 CCTAGAATCGTTGTTGCACCAG 59.583 50.000 0.00 0.00 0.00 4.00
545 629 0.749454 GCTTGATGGATCACCGCCTT 60.749 55.000 0.00 0.00 39.42 4.35
548 632 2.124151 ATGGATCACCGCCTTGCC 60.124 61.111 0.00 0.00 39.42 4.52
549 633 4.776322 TGGATCACCGCCTTGCCG 62.776 66.667 0.00 0.00 39.42 5.69
550 634 4.467084 GGATCACCGCCTTGCCGA 62.467 66.667 0.00 0.00 0.00 5.54
551 635 2.203070 GATCACCGCCTTGCCGAT 60.203 61.111 0.00 0.00 0.00 4.18
552 636 2.514592 ATCACCGCCTTGCCGATG 60.515 61.111 0.00 0.00 0.00 3.84
553 637 3.329542 ATCACCGCCTTGCCGATGT 62.330 57.895 0.00 0.00 0.00 3.06
554 638 3.803082 CACCGCCTTGCCGATGTG 61.803 66.667 0.00 0.00 0.00 3.21
557 641 3.499737 CGCCTTGCCGATGTGGTC 61.500 66.667 0.00 0.00 41.21 4.02
588 672 3.777925 CCGGAGCAGCGAACGTTG 61.778 66.667 5.00 6.68 0.00 4.10
589 673 3.036084 CGGAGCAGCGAACGTTGT 61.036 61.111 5.00 0.00 0.00 3.32
590 674 2.551270 GGAGCAGCGAACGTTGTG 59.449 61.111 5.00 1.06 0.00 3.33
591 675 2.127609 GAGCAGCGAACGTTGTGC 60.128 61.111 5.00 12.12 36.10 4.57
592 676 2.588877 AGCAGCGAACGTTGTGCT 60.589 55.556 18.89 18.89 41.47 4.40
593 677 2.105960 GAGCAGCGAACGTTGTGCTT 62.106 55.000 23.16 11.72 46.21 3.91
594 678 2.005537 GCAGCGAACGTTGTGCTTG 61.006 57.895 19.01 15.41 36.69 4.01
595 679 1.351707 CAGCGAACGTTGTGCTTGT 59.648 52.632 19.01 0.18 36.69 3.16
596 680 0.654472 CAGCGAACGTTGTGCTTGTC 60.654 55.000 19.01 0.00 36.69 3.18
597 681 1.717728 GCGAACGTTGTGCTTGTCG 60.718 57.895 5.00 0.72 0.00 4.35
598 682 1.717728 CGAACGTTGTGCTTGTCGC 60.718 57.895 5.00 0.00 39.77 5.19
599 683 1.641677 GAACGTTGTGCTTGTCGCT 59.358 52.632 5.00 0.00 40.11 4.93
600 684 0.856641 GAACGTTGTGCTTGTCGCTA 59.143 50.000 5.00 0.00 40.11 4.26
601 685 0.859232 AACGTTGTGCTTGTCGCTAG 59.141 50.000 0.00 0.00 40.11 3.42
602 686 0.031585 ACGTTGTGCTTGTCGCTAGA 59.968 50.000 0.00 0.00 40.11 2.43
604 688 0.790814 GTTGTGCTTGTCGCTAGACC 59.209 55.000 0.00 0.00 46.51 3.85
605 689 0.391228 TTGTGCTTGTCGCTAGACCA 59.609 50.000 0.00 0.00 46.51 4.02
606 690 0.038251 TGTGCTTGTCGCTAGACCAG 60.038 55.000 0.00 0.00 46.51 4.00
633 717 3.869272 GGTGAGCCGCATCGCTTG 61.869 66.667 0.00 0.00 39.87 4.01
634 718 2.815211 GTGAGCCGCATCGCTTGA 60.815 61.111 0.00 0.00 39.87 3.02
635 719 2.815211 TGAGCCGCATCGCTTGAC 60.815 61.111 0.00 0.00 39.87 3.18
636 720 2.510238 GAGCCGCATCGCTTGACT 60.510 61.111 0.00 0.00 39.87 3.41
637 721 2.806856 GAGCCGCATCGCTTGACTG 61.807 63.158 0.00 0.00 39.87 3.51
638 722 3.869272 GCCGCATCGCTTGACTGG 61.869 66.667 0.00 0.00 0.00 4.00
639 723 3.197790 CCGCATCGCTTGACTGGG 61.198 66.667 0.00 0.00 0.00 4.45
640 724 2.434884 CGCATCGCTTGACTGGGT 60.435 61.111 0.00 0.00 0.00 4.51
641 725 2.456119 CGCATCGCTTGACTGGGTC 61.456 63.158 0.00 0.00 0.00 4.46
642 726 1.375908 GCATCGCTTGACTGGGTCA 60.376 57.895 0.00 0.00 41.09 4.02
644 728 0.798776 CATCGCTTGACTGGGTCAAC 59.201 55.000 8.75 6.13 45.88 3.18
645 729 0.687354 ATCGCTTGACTGGGTCAACT 59.313 50.000 8.75 0.00 45.88 3.16
646 730 0.033504 TCGCTTGACTGGGTCAACTC 59.966 55.000 8.75 4.18 45.88 3.01
647 731 0.951040 CGCTTGACTGGGTCAACTCC 60.951 60.000 8.75 1.52 45.88 3.85
648 732 0.108585 GCTTGACTGGGTCAACTCCA 59.891 55.000 8.75 0.00 45.88 3.86
649 733 1.476833 GCTTGACTGGGTCAACTCCAA 60.477 52.381 8.75 0.00 45.88 3.53
650 734 2.815589 GCTTGACTGGGTCAACTCCAAT 60.816 50.000 8.75 0.00 45.88 3.16
651 735 2.566833 TGACTGGGTCAACTCCAATG 57.433 50.000 0.00 0.00 39.78 2.82
652 736 1.073763 TGACTGGGTCAACTCCAATGG 59.926 52.381 0.00 0.00 39.78 3.16
653 737 0.251341 ACTGGGTCAACTCCAATGGC 60.251 55.000 0.00 0.00 33.36 4.40
654 738 0.967380 CTGGGTCAACTCCAATGGCC 60.967 60.000 0.00 0.00 41.95 5.36
655 739 1.076549 GGGTCAACTCCAATGGCCA 59.923 57.895 8.56 8.56 44.53 5.36
656 740 1.250840 GGGTCAACTCCAATGGCCAC 61.251 60.000 8.16 0.00 44.53 5.01
657 741 1.586154 GGTCAACTCCAATGGCCACG 61.586 60.000 8.16 1.14 42.25 4.94
658 742 1.303236 TCAACTCCAATGGCCACGG 60.303 57.895 8.16 12.98 0.00 4.94
659 743 2.676471 AACTCCAATGGCCACGGC 60.676 61.111 8.16 0.00 41.06 5.68
724 808 3.286751 GGTGCTCGCAGTGGCAAA 61.287 61.111 0.00 0.00 41.24 3.68
725 809 2.253452 GTGCTCGCAGTGGCAAAG 59.747 61.111 0.00 0.00 41.24 2.77
726 810 2.979676 TGCTCGCAGTGGCAAAGG 60.980 61.111 0.00 0.00 41.24 3.11
727 811 2.669569 GCTCGCAGTGGCAAAGGA 60.670 61.111 0.00 0.00 41.24 3.36
728 812 2.970974 GCTCGCAGTGGCAAAGGAC 61.971 63.158 0.00 0.00 41.24 3.85
729 813 1.597854 CTCGCAGTGGCAAAGGACA 60.598 57.895 0.00 0.00 41.24 4.02
730 814 0.957395 CTCGCAGTGGCAAAGGACAT 60.957 55.000 0.00 0.00 41.24 3.06
731 815 1.210931 CGCAGTGGCAAAGGACATG 59.789 57.895 0.00 0.00 41.24 3.21
732 816 1.080298 GCAGTGGCAAAGGACATGC 60.080 57.895 0.00 0.00 43.08 4.06
733 817 1.210931 CAGTGGCAAAGGACATGCG 59.789 57.895 0.00 0.00 44.75 4.73
734 818 1.228245 AGTGGCAAAGGACATGCGT 60.228 52.632 0.00 0.00 44.75 5.24
735 819 1.081242 GTGGCAAAGGACATGCGTG 60.081 57.895 3.82 3.82 44.75 5.34
736 820 1.528076 TGGCAAAGGACATGCGTGT 60.528 52.632 12.38 12.38 44.75 4.49
737 821 1.081242 GGCAAAGGACATGCGTGTG 60.081 57.895 18.17 2.38 44.75 3.82
738 822 1.730547 GCAAAGGACATGCGTGTGC 60.731 57.895 21.76 21.76 45.96 4.57
775 859 3.775654 CCCGGGTCTGGCACTCTC 61.776 72.222 14.18 0.00 0.00 3.20
776 860 3.775654 CCGGGTCTGGCACTCTCC 61.776 72.222 0.00 0.00 0.00 3.71
777 861 3.775654 CGGGTCTGGCACTCTCCC 61.776 72.222 0.00 0.00 35.22 4.30
778 862 2.607750 GGGTCTGGCACTCTCCCA 60.608 66.667 6.65 0.00 38.15 4.37
779 863 2.665603 GGTCTGGCACTCTCCCAC 59.334 66.667 0.00 0.00 0.00 4.61
780 864 2.262915 GTCTGGCACTCTCCCACG 59.737 66.667 0.00 0.00 0.00 4.94
781 865 2.117423 TCTGGCACTCTCCCACGA 59.883 61.111 0.00 0.00 0.00 4.35
782 866 1.979155 TCTGGCACTCTCCCACGAG 60.979 63.158 0.00 0.00 37.48 4.18
783 867 2.997315 TGGCACTCTCCCACGAGG 60.997 66.667 0.00 0.00 36.70 4.63
784 868 4.459089 GGCACTCTCCCACGAGGC 62.459 72.222 0.00 0.00 36.70 4.70
785 869 4.459089 GCACTCTCCCACGAGGCC 62.459 72.222 0.00 0.00 36.70 5.19
786 870 2.997315 CACTCTCCCACGAGGCCA 60.997 66.667 5.01 0.00 36.70 5.36
787 871 2.997897 ACTCTCCCACGAGGCCAC 60.998 66.667 5.01 0.00 36.70 5.01
788 872 4.135153 CTCTCCCACGAGGCCACG 62.135 72.222 21.59 21.59 36.70 4.94
789 873 4.671590 TCTCCCACGAGGCCACGA 62.672 66.667 29.67 5.50 36.70 4.35
790 874 4.436998 CTCCCACGAGGCCACGAC 62.437 72.222 29.67 4.36 37.03 4.34
804 888 4.862823 CGACCCCCTCCCCTCCTC 62.863 77.778 0.00 0.00 0.00 3.71
805 889 4.500826 GACCCCCTCCCCTCCTCC 62.501 77.778 0.00 0.00 0.00 4.30
807 891 4.179599 CCCCCTCCCCTCCTCCTC 62.180 77.778 0.00 0.00 0.00 3.71
808 892 4.548513 CCCCTCCCCTCCTCCTCG 62.549 77.778 0.00 0.00 0.00 4.63
809 893 3.756783 CCCTCCCCTCCTCCTCGT 61.757 72.222 0.00 0.00 0.00 4.18
810 894 2.123640 CCTCCCCTCCTCCTCGTC 60.124 72.222 0.00 0.00 0.00 4.20
811 895 2.517402 CTCCCCTCCTCCTCGTCG 60.517 72.222 0.00 0.00 0.00 5.12
812 896 3.336568 TCCCCTCCTCCTCGTCGT 61.337 66.667 0.00 0.00 0.00 4.34
813 897 3.141488 CCCCTCCTCCTCGTCGTG 61.141 72.222 0.00 0.00 0.00 4.35
814 898 3.827898 CCCTCCTCCTCGTCGTGC 61.828 72.222 0.00 0.00 0.00 5.34
815 899 3.827898 CCTCCTCCTCGTCGTGCC 61.828 72.222 0.00 0.00 0.00 5.01
816 900 2.752238 CTCCTCCTCGTCGTGCCT 60.752 66.667 0.00 0.00 0.00 4.75
817 901 2.750637 TCCTCCTCGTCGTGCCTC 60.751 66.667 0.00 0.00 0.00 4.70
818 902 4.180946 CCTCCTCGTCGTGCCTCG 62.181 72.222 0.00 0.00 41.41 4.63
819 903 3.125573 CTCCTCGTCGTGCCTCGA 61.126 66.667 0.00 0.00 46.83 4.04
837 921 3.269639 ATCTGGCCAGATCCATCCA 57.730 52.632 37.67 15.47 44.37 3.41
838 922 1.526315 ATCTGGCCAGATCCATCCAA 58.474 50.000 37.67 14.71 44.37 3.53
839 923 1.526315 TCTGGCCAGATCCATCCAAT 58.474 50.000 32.00 0.00 35.22 3.16
840 924 1.422781 TCTGGCCAGATCCATCCAATC 59.577 52.381 32.00 0.00 35.22 2.67
841 925 0.479815 TGGCCAGATCCATCCAATCC 59.520 55.000 0.00 0.00 0.00 3.01
842 926 0.479815 GGCCAGATCCATCCAATCCA 59.520 55.000 0.00 0.00 0.00 3.41
843 927 1.613836 GCCAGATCCATCCAATCCAC 58.386 55.000 0.00 0.00 0.00 4.02
844 928 1.133699 GCCAGATCCATCCAATCCACA 60.134 52.381 0.00 0.00 0.00 4.17
845 929 2.579873 CCAGATCCATCCAATCCACAC 58.420 52.381 0.00 0.00 0.00 3.82
846 930 2.092267 CCAGATCCATCCAATCCACACA 60.092 50.000 0.00 0.00 0.00 3.72
847 931 2.947652 CAGATCCATCCAATCCACACAC 59.052 50.000 0.00 0.00 0.00 3.82
848 932 1.942657 GATCCATCCAATCCACACACG 59.057 52.381 0.00 0.00 0.00 4.49
849 933 0.035534 TCCATCCAATCCACACACGG 60.036 55.000 0.00 0.00 0.00 4.94
850 934 0.035534 CCATCCAATCCACACACGGA 60.036 55.000 0.00 0.00 40.07 4.69
852 936 1.942657 CATCCAATCCACACACGGATC 59.057 52.381 0.00 0.00 45.39 3.36
853 937 1.275666 TCCAATCCACACACGGATCT 58.724 50.000 0.00 0.00 45.39 2.75
854 938 1.066215 TCCAATCCACACACGGATCTG 60.066 52.381 0.00 0.00 45.39 2.90
855 939 1.372582 CAATCCACACACGGATCTGG 58.627 55.000 6.47 0.00 45.39 3.86
856 940 0.392998 AATCCACACACGGATCTGGC 60.393 55.000 6.47 0.00 45.39 4.85
857 941 2.257409 ATCCACACACGGATCTGGCC 62.257 60.000 6.47 0.00 42.36 5.36
858 942 2.665000 CACACACGGATCTGGCCT 59.335 61.111 3.32 0.00 0.00 5.19
859 943 1.613317 CCACACACGGATCTGGCCTA 61.613 60.000 3.32 0.00 0.00 3.93
860 944 0.249120 CACACACGGATCTGGCCTAA 59.751 55.000 3.32 0.00 0.00 2.69
861 945 0.249398 ACACACGGATCTGGCCTAAC 59.751 55.000 3.32 0.00 0.00 2.34
862 946 0.462047 CACACGGATCTGGCCTAACC 60.462 60.000 3.32 0.00 39.84 2.85
870 954 2.589540 TGGCCTAACCATCCTGCG 59.410 61.111 3.32 0.00 46.36 5.18
871 955 2.203209 GGCCTAACCATCCTGCGG 60.203 66.667 0.00 0.00 38.86 5.69
872 956 2.902343 GCCTAACCATCCTGCGGC 60.902 66.667 0.00 0.00 0.00 6.53
873 957 2.911143 CCTAACCATCCTGCGGCT 59.089 61.111 0.00 0.00 0.00 5.52
874 958 1.524621 CCTAACCATCCTGCGGCTG 60.525 63.158 0.00 0.00 0.00 4.85
875 959 2.124736 TAACCATCCTGCGGCTGC 60.125 61.111 11.65 11.65 43.20 5.25
909 993 3.998672 GACGGCGGTGGGAACAGA 61.999 66.667 13.24 0.00 44.46 3.41
910 994 4.309950 ACGGCGGTGGGAACAGAC 62.310 66.667 13.24 0.00 44.46 3.51
912 996 3.637273 GGCGGTGGGAACAGACCT 61.637 66.667 0.00 0.00 44.46 3.85
913 997 2.047179 GCGGTGGGAACAGACCTC 60.047 66.667 0.00 0.00 44.46 3.85
914 998 2.261671 CGGTGGGAACAGACCTCG 59.738 66.667 0.00 0.00 44.46 4.63
915 999 2.273179 CGGTGGGAACAGACCTCGA 61.273 63.158 0.00 0.00 44.46 4.04
916 1000 1.292541 GGTGGGAACAGACCTCGAC 59.707 63.158 0.00 0.00 44.46 4.20
917 1001 1.080705 GTGGGAACAGACCTCGACG 60.081 63.158 0.00 0.00 44.46 5.12
918 1002 2.273179 TGGGAACAGACCTCGACGG 61.273 63.158 0.00 0.03 35.44 4.79
919 1003 2.126031 GGAACAGACCTCGACGGC 60.126 66.667 0.00 0.00 35.61 5.68
920 1004 2.504244 GAACAGACCTCGACGGCG 60.504 66.667 2.87 2.87 35.61 6.46
921 1005 3.966026 GAACAGACCTCGACGGCGG 62.966 68.421 12.58 0.27 38.28 6.13
945 1029 3.592059 GGTACCTAGAATCGTTGTTGCA 58.408 45.455 4.06 0.00 0.00 4.08
946 1030 3.370061 GGTACCTAGAATCGTTGTTGCAC 59.630 47.826 4.06 0.00 0.00 4.57
947 1031 2.423577 ACCTAGAATCGTTGTTGCACC 58.576 47.619 0.00 0.00 0.00 5.01
948 1032 2.224426 ACCTAGAATCGTTGTTGCACCA 60.224 45.455 0.00 0.00 0.00 4.17
949 1033 2.416547 CCTAGAATCGTTGTTGCACCAG 59.583 50.000 0.00 0.00 0.00 4.00
950 1034 0.593128 AGAATCGTTGTTGCACCAGC 59.407 50.000 0.00 0.00 42.57 4.85
951 1035 0.387239 GAATCGTTGTTGCACCAGCC 60.387 55.000 0.00 0.00 41.13 4.85
952 1036 2.128853 AATCGTTGTTGCACCAGCCG 62.129 55.000 0.00 0.00 41.13 5.52
953 1037 4.980903 CGTTGTTGCACCAGCCGC 62.981 66.667 0.00 0.00 41.13 6.53
954 1038 4.980903 GTTGTTGCACCAGCCGCG 62.981 66.667 0.00 0.00 41.13 6.46
983 1067 4.883354 GGAGGGCGGGGCTTGATG 62.883 72.222 0.00 0.00 0.00 3.07
984 1068 4.883354 GAGGGCGGGGCTTGATGG 62.883 72.222 0.00 0.00 0.00 3.51
986 1070 4.209866 GGGCGGGGCTTGATGGAT 62.210 66.667 0.00 0.00 0.00 3.41
987 1071 2.595754 GGCGGGGCTTGATGGATC 60.596 66.667 0.00 0.00 0.00 3.36
988 1072 2.192979 GCGGGGCTTGATGGATCA 59.807 61.111 0.00 0.00 34.44 2.92
989 1073 2.189499 GCGGGGCTTGATGGATCAC 61.189 63.158 0.00 0.00 36.36 3.06
990 1074 1.526917 CGGGGCTTGATGGATCACC 60.527 63.158 0.00 0.00 36.36 4.02
991 1075 1.526917 GGGGCTTGATGGATCACCG 60.527 63.158 0.00 0.00 39.42 4.94
992 1076 2.189499 GGGCTTGATGGATCACCGC 61.189 63.158 0.00 0.00 39.42 5.68
993 1077 2.189499 GGCTTGATGGATCACCGCC 61.189 63.158 11.39 11.39 42.56 6.13
994 1078 1.153086 GCTTGATGGATCACCGCCT 60.153 57.895 0.00 0.00 39.42 5.52
995 1079 0.749454 GCTTGATGGATCACCGCCTT 60.749 55.000 0.00 0.00 39.42 4.35
996 1080 1.019673 CTTGATGGATCACCGCCTTG 58.980 55.000 0.00 0.00 39.42 3.61
997 1081 0.327924 TTGATGGATCACCGCCTTGT 59.672 50.000 0.00 0.00 39.42 3.16
1105 1189 1.076549 GGGTCAACTCCAATGGCCA 59.923 57.895 8.56 8.56 44.53 5.36
1484 1569 4.838152 CCACGTCTGGGCCATCCG 62.838 72.222 19.64 19.64 38.76 4.18
1490 1575 1.766059 TCTGGGCCATCCGCACTAT 60.766 57.895 6.72 0.00 43.53 2.12
1585 1670 6.155827 GTGTTTGTGGCTGCTCAAATTAATA 58.844 36.000 19.46 7.85 36.25 0.98
1649 1734 2.345244 CGCTCTGAAGGTGCCAGT 59.655 61.111 0.00 0.00 33.57 4.00
1652 1737 0.536006 GCTCTGAAGGTGCCAGTGTT 60.536 55.000 0.00 0.00 33.57 3.32
1755 1840 4.887071 TGCCATTTTCTTAACTGTGTCACT 59.113 37.500 4.27 0.00 0.00 3.41
1761 1846 5.712217 TTCTTAACTGTGTCACTCGTTTG 57.288 39.130 13.75 9.26 0.00 2.93
1873 1958 3.666883 TTGCGTAATTATGCCTGAACG 57.333 42.857 23.58 7.85 37.41 3.95
1909 1994 9.471702 AGAACAAAATCCTGACTGATTATTGAT 57.528 29.630 0.00 0.00 33.91 2.57
1995 2080 0.039165 TCAGTCAGTGTAGCAGCACG 60.039 55.000 0.00 0.00 43.61 5.34
2315 2403 1.063031 GTCGAAATGCTTTTGGCTGC 58.937 50.000 1.76 0.00 42.39 5.25
2507 2595 1.749634 CTCAAGGGTTCCTCGTCGTAT 59.250 52.381 0.00 0.00 30.89 3.06
2652 2740 7.761038 ATTAGCTAAACTTGGCTTGTAGTTT 57.239 32.000 10.85 0.00 42.75 2.66
2823 2916 6.616237 ATTTTTCCTCCGGAGTTAGTCTAA 57.384 37.500 29.25 13.85 31.21 2.10
2895 2988 3.011144 TCCCCCACATCTTAATCTGCAAA 59.989 43.478 0.00 0.00 0.00 3.68
2942 3035 1.339631 CGGTCTTCATGGGGTTGCTTA 60.340 52.381 0.00 0.00 0.00 3.09
2950 3043 4.787551 TCATGGGGTTGCTTATTCGTATT 58.212 39.130 0.00 0.00 0.00 1.89
2997 3090 7.630082 TGTAATTCCAGTCAAGTAAAGGCTAT 58.370 34.615 0.00 0.00 0.00 2.97
3140 3240 5.301555 TCAACAATAAAGGTCGACATCACA 58.698 37.500 18.91 0.00 0.00 3.58
3142 3242 6.429692 TCAACAATAAAGGTCGACATCACAAT 59.570 34.615 18.91 0.00 0.00 2.71
3167 3267 6.784031 AGGAAATGGTTCTGATTGTTACTCT 58.216 36.000 0.00 0.00 33.92 3.24
3280 3433 5.708230 TGAGTTTGGTTTGGTGGTATATGAC 59.292 40.000 0.00 0.00 0.00 3.06
3456 3615 9.812347 TGAAATTTCTATGGGAGCATGTATTAT 57.188 29.630 18.64 0.00 0.00 1.28
3633 3792 9.689976 TGTTATGTGTGATCAACTAAAATTTGG 57.310 29.630 0.00 0.00 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 103 8.537728 TTTATTAGGAAATGAGTTGGCATGAT 57.462 30.769 0.00 0.00 0.00 2.45
150 152 3.665745 AATTTGGCACGAGCTGAAAAT 57.334 38.095 4.48 6.37 41.70 1.82
174 176 5.235305 TCGATTTGCAGAAAAATAGGCTC 57.765 39.130 0.00 0.00 29.89 4.70
532 616 4.776322 CGGCAAGGCGGTGATCCA 62.776 66.667 8.26 0.00 0.00 3.41
571 655 3.777925 CAACGTTCGCTGCTCCGG 61.778 66.667 0.00 0.00 0.00 5.14
572 656 3.036084 ACAACGTTCGCTGCTCCG 61.036 61.111 0.00 0.00 0.00 4.63
573 657 2.551270 CACAACGTTCGCTGCTCC 59.449 61.111 0.00 0.00 0.00 4.70
574 658 2.105960 AAGCACAACGTTCGCTGCTC 62.106 55.000 19.49 0.00 39.08 4.26
575 659 2.180204 AAGCACAACGTTCGCTGCT 61.180 52.632 19.49 17.46 41.83 4.24
576 660 2.005537 CAAGCACAACGTTCGCTGC 61.006 57.895 19.49 15.75 35.79 5.25
577 661 0.654472 GACAAGCACAACGTTCGCTG 60.654 55.000 19.49 15.63 35.79 5.18
578 662 1.641677 GACAAGCACAACGTTCGCT 59.358 52.632 14.47 14.47 37.68 4.93
579 663 1.717728 CGACAAGCACAACGTTCGC 60.718 57.895 10.55 10.55 0.00 4.70
580 664 4.471814 CGACAAGCACAACGTTCG 57.528 55.556 0.00 0.00 0.00 3.95
616 700 3.869272 CAAGCGATGCGGCTCACC 61.869 66.667 0.00 0.00 43.93 4.02
617 701 2.815211 TCAAGCGATGCGGCTCAC 60.815 61.111 0.00 0.00 43.93 3.51
618 702 2.815211 GTCAAGCGATGCGGCTCA 60.815 61.111 0.00 0.00 43.93 4.26
619 703 2.510238 AGTCAAGCGATGCGGCTC 60.510 61.111 0.00 0.00 43.93 4.70
621 705 3.869272 CCAGTCAAGCGATGCGGC 61.869 66.667 0.00 0.00 0.00 6.53
622 706 3.197790 CCCAGTCAAGCGATGCGG 61.198 66.667 0.00 0.00 0.00 5.69
623 707 2.434884 ACCCAGTCAAGCGATGCG 60.435 61.111 0.00 0.00 0.00 4.73
624 708 0.955428 TTGACCCAGTCAAGCGATGC 60.955 55.000 6.08 0.00 45.88 3.91
625 709 3.231734 TTGACCCAGTCAAGCGATG 57.768 52.632 6.08 0.00 45.88 3.84
632 716 1.073763 CCATTGGAGTTGACCCAGTCA 59.926 52.381 0.00 0.00 41.09 3.41
633 717 1.826385 CCATTGGAGTTGACCCAGTC 58.174 55.000 0.00 0.00 34.77 3.51
634 718 0.251341 GCCATTGGAGTTGACCCAGT 60.251 55.000 6.95 0.00 34.77 4.00
635 719 0.967380 GGCCATTGGAGTTGACCCAG 60.967 60.000 6.95 0.00 34.77 4.45
636 720 1.076549 GGCCATTGGAGTTGACCCA 59.923 57.895 6.95 0.00 0.00 4.51
637 721 1.076549 TGGCCATTGGAGTTGACCC 59.923 57.895 0.00 0.00 0.00 4.46
638 722 1.586154 CGTGGCCATTGGAGTTGACC 61.586 60.000 9.72 0.00 0.00 4.02
639 723 1.586154 CCGTGGCCATTGGAGTTGAC 61.586 60.000 19.58 0.00 0.00 3.18
640 724 1.303236 CCGTGGCCATTGGAGTTGA 60.303 57.895 19.58 0.00 0.00 3.18
641 725 2.993471 GCCGTGGCCATTGGAGTTG 61.993 63.158 26.43 4.38 34.56 3.16
642 726 2.676471 GCCGTGGCCATTGGAGTT 60.676 61.111 26.43 0.00 34.56 3.01
707 791 3.259425 CTTTGCCACTGCGAGCACC 62.259 63.158 0.00 0.00 39.10 5.01
708 792 2.253452 CTTTGCCACTGCGAGCAC 59.747 61.111 0.00 0.00 39.10 4.40
709 793 2.979676 CCTTTGCCACTGCGAGCA 60.980 61.111 0.00 0.00 41.78 4.26
710 794 2.669569 TCCTTTGCCACTGCGAGC 60.670 61.111 0.00 0.00 41.78 5.03
711 795 0.957395 ATGTCCTTTGCCACTGCGAG 60.957 55.000 0.00 0.00 41.78 5.03
712 796 1.073025 ATGTCCTTTGCCACTGCGA 59.927 52.632 0.00 0.00 41.78 5.10
713 797 1.210931 CATGTCCTTTGCCACTGCG 59.789 57.895 0.00 0.00 41.78 5.18
714 798 1.080298 GCATGTCCTTTGCCACTGC 60.080 57.895 0.00 0.00 33.95 4.40
715 799 1.210931 CGCATGTCCTTTGCCACTG 59.789 57.895 0.00 0.00 36.75 3.66
716 800 1.228245 ACGCATGTCCTTTGCCACT 60.228 52.632 0.00 0.00 36.75 4.00
717 801 1.081242 CACGCATGTCCTTTGCCAC 60.081 57.895 0.00 0.00 36.75 5.01
718 802 1.528076 ACACGCATGTCCTTTGCCA 60.528 52.632 0.00 0.00 36.75 4.92
719 803 1.081242 CACACGCATGTCCTTTGCC 60.081 57.895 0.00 0.00 36.72 4.52
720 804 1.730547 GCACACGCATGTCCTTTGC 60.731 57.895 0.00 0.00 36.72 3.68
721 805 1.653667 TGCACACGCATGTCCTTTG 59.346 52.632 0.00 0.00 45.36 2.77
722 806 4.155950 TGCACACGCATGTCCTTT 57.844 50.000 0.00 0.00 45.36 3.11
758 842 3.775654 GAGAGTGCCAGACCCGGG 61.776 72.222 22.25 22.25 0.00 5.73
759 843 3.775654 GGAGAGTGCCAGACCCGG 61.776 72.222 0.00 0.00 0.00 5.73
760 844 3.775654 GGGAGAGTGCCAGACCCG 61.776 72.222 0.00 0.00 0.00 5.28
761 845 2.607750 TGGGAGAGTGCCAGACCC 60.608 66.667 0.00 0.00 40.79 4.46
762 846 2.665603 GTGGGAGAGTGCCAGACC 59.334 66.667 0.00 0.00 39.03 3.85
763 847 2.219325 CTCGTGGGAGAGTGCCAGAC 62.219 65.000 0.00 0.00 39.03 3.51
764 848 1.979155 CTCGTGGGAGAGTGCCAGA 60.979 63.158 0.00 0.00 39.03 3.86
765 849 2.575993 CTCGTGGGAGAGTGCCAG 59.424 66.667 0.00 0.00 39.03 4.85
766 850 2.997315 CCTCGTGGGAGAGTGCCA 60.997 66.667 0.00 0.00 43.27 4.92
767 851 4.459089 GCCTCGTGGGAGAGTGCC 62.459 72.222 5.54 0.00 43.27 5.01
768 852 4.459089 GGCCTCGTGGGAGAGTGC 62.459 72.222 5.54 0.00 43.27 4.40
769 853 2.997315 TGGCCTCGTGGGAGAGTG 60.997 66.667 3.32 0.00 43.27 3.51
770 854 2.997897 GTGGCCTCGTGGGAGAGT 60.998 66.667 3.32 0.00 43.27 3.24
771 855 4.135153 CGTGGCCTCGTGGGAGAG 62.135 72.222 18.86 0.00 43.27 3.20
772 856 4.671590 TCGTGGCCTCGTGGGAGA 62.672 66.667 25.10 3.51 43.27 3.71
773 857 4.436998 GTCGTGGCCTCGTGGGAG 62.437 72.222 25.10 0.00 40.14 4.30
787 871 4.862823 GAGGAGGGGAGGGGGTCG 62.863 77.778 0.00 0.00 0.00 4.79
788 872 4.500826 GGAGGAGGGGAGGGGGTC 62.501 77.778 0.00 0.00 0.00 4.46
790 874 4.179599 GAGGAGGAGGGGAGGGGG 62.180 77.778 0.00 0.00 0.00 5.40
791 875 4.548513 CGAGGAGGAGGGGAGGGG 62.549 77.778 0.00 0.00 0.00 4.79
792 876 3.742248 GACGAGGAGGAGGGGAGGG 62.742 73.684 0.00 0.00 0.00 4.30
793 877 2.123640 GACGAGGAGGAGGGGAGG 60.124 72.222 0.00 0.00 0.00 4.30
794 878 2.517402 CGACGAGGAGGAGGGGAG 60.517 72.222 0.00 0.00 0.00 4.30
795 879 3.336568 ACGACGAGGAGGAGGGGA 61.337 66.667 0.00 0.00 0.00 4.81
796 880 3.141488 CACGACGAGGAGGAGGGG 61.141 72.222 0.00 0.00 0.00 4.79
797 881 3.827898 GCACGACGAGGAGGAGGG 61.828 72.222 0.00 0.00 0.00 4.30
798 882 3.827898 GGCACGACGAGGAGGAGG 61.828 72.222 0.00 0.00 0.00 4.30
799 883 2.752238 AGGCACGACGAGGAGGAG 60.752 66.667 0.00 0.00 0.00 3.69
800 884 2.750637 GAGGCACGACGAGGAGGA 60.751 66.667 0.00 0.00 0.00 3.71
801 885 4.180946 CGAGGCACGACGAGGAGG 62.181 72.222 0.00 0.00 45.77 4.30
802 886 3.125573 TCGAGGCACGACGAGGAG 61.126 66.667 2.07 0.00 46.45 3.69
820 904 1.422781 GATTGGATGGATCTGGCCAGA 59.577 52.381 36.73 36.73 42.15 3.86
821 905 1.547223 GGATTGGATGGATCTGGCCAG 60.547 57.143 27.87 27.87 42.15 4.85
822 906 0.479815 GGATTGGATGGATCTGGCCA 59.520 55.000 4.71 4.71 43.23 5.36
823 907 0.479815 TGGATTGGATGGATCTGGCC 59.520 55.000 0.00 0.00 0.00 5.36
824 908 1.133699 TGTGGATTGGATGGATCTGGC 60.134 52.381 0.00 0.00 0.00 4.85
825 909 2.092267 TGTGTGGATTGGATGGATCTGG 60.092 50.000 0.00 0.00 0.00 3.86
826 910 2.947652 GTGTGTGGATTGGATGGATCTG 59.052 50.000 0.00 0.00 0.00 2.90
827 911 2.420547 CGTGTGTGGATTGGATGGATCT 60.421 50.000 0.00 0.00 0.00 2.75
828 912 1.942657 CGTGTGTGGATTGGATGGATC 59.057 52.381 0.00 0.00 0.00 3.36
829 913 1.408683 CCGTGTGTGGATTGGATGGAT 60.409 52.381 0.00 0.00 0.00 3.41
830 914 0.035534 CCGTGTGTGGATTGGATGGA 60.036 55.000 0.00 0.00 0.00 3.41
831 915 0.035534 TCCGTGTGTGGATTGGATGG 60.036 55.000 0.00 0.00 31.53 3.51
832 916 2.042686 ATCCGTGTGTGGATTGGATG 57.957 50.000 0.00 0.00 46.74 3.51
839 923 2.662596 GCCAGATCCGTGTGTGGA 59.337 61.111 4.87 0.00 43.58 4.02
840 924 1.613317 TAGGCCAGATCCGTGTGTGG 61.613 60.000 5.01 0.00 35.72 4.17
841 925 0.249120 TTAGGCCAGATCCGTGTGTG 59.751 55.000 5.01 0.00 0.00 3.82
842 926 0.249398 GTTAGGCCAGATCCGTGTGT 59.751 55.000 5.01 0.00 0.00 3.72
843 927 0.462047 GGTTAGGCCAGATCCGTGTG 60.462 60.000 5.01 0.00 37.17 3.82
844 928 0.907704 TGGTTAGGCCAGATCCGTGT 60.908 55.000 5.01 0.00 43.61 4.49
845 929 1.904771 TGGTTAGGCCAGATCCGTG 59.095 57.895 5.01 0.00 43.61 4.94
846 930 4.472701 TGGTTAGGCCAGATCCGT 57.527 55.556 5.01 0.00 43.61 4.69
878 962 4.742201 CGTCCTGGTGACCTGCCG 62.742 72.222 2.11 3.86 41.18 5.69
879 963 4.394712 CCGTCCTGGTGACCTGCC 62.395 72.222 2.11 0.00 41.18 4.85
892 976 3.998672 TCTGTTCCCACCGCCGTC 61.999 66.667 0.00 0.00 0.00 4.79
893 977 4.309950 GTCTGTTCCCACCGCCGT 62.310 66.667 0.00 0.00 0.00 5.68
895 979 3.607370 GAGGTCTGTTCCCACCGCC 62.607 68.421 0.00 0.00 37.79 6.13
896 980 2.047179 GAGGTCTGTTCCCACCGC 60.047 66.667 0.00 0.00 37.79 5.68
897 981 2.261671 CGAGGTCTGTTCCCACCG 59.738 66.667 0.00 0.00 37.79 4.94
898 982 1.292541 GTCGAGGTCTGTTCCCACC 59.707 63.158 0.00 0.00 0.00 4.61
899 983 1.080705 CGTCGAGGTCTGTTCCCAC 60.081 63.158 0.00 0.00 0.00 4.61
900 984 2.273179 CCGTCGAGGTCTGTTCCCA 61.273 63.158 4.18 0.00 34.51 4.37
901 985 2.572284 CCGTCGAGGTCTGTTCCC 59.428 66.667 4.18 0.00 34.51 3.97
902 986 2.126031 GCCGTCGAGGTCTGTTCC 60.126 66.667 4.18 0.00 43.70 3.62
903 987 2.504244 CGCCGTCGAGGTCTGTTC 60.504 66.667 4.18 0.00 43.70 3.18
904 988 4.052229 CCGCCGTCGAGGTCTGTT 62.052 66.667 4.18 0.00 43.70 3.16
917 1001 2.431805 GATTCTAGGTACCCGCCGCC 62.432 65.000 8.74 0.00 0.00 6.13
918 1002 1.006454 GATTCTAGGTACCCGCCGC 60.006 63.158 8.74 0.00 0.00 6.53
919 1003 1.285023 CGATTCTAGGTACCCGCCG 59.715 63.158 8.74 0.29 0.00 6.46
920 1004 0.749049 AACGATTCTAGGTACCCGCC 59.251 55.000 8.74 0.00 0.00 6.13
921 1005 1.135721 ACAACGATTCTAGGTACCCGC 59.864 52.381 8.74 0.00 0.00 6.13
922 1006 3.184541 CAACAACGATTCTAGGTACCCG 58.815 50.000 8.74 6.35 0.00 5.28
923 1007 2.934553 GCAACAACGATTCTAGGTACCC 59.065 50.000 8.74 0.00 0.00 3.69
924 1008 3.370061 GTGCAACAACGATTCTAGGTACC 59.630 47.826 2.73 2.73 36.32 3.34
925 1009 3.370061 GGTGCAACAACGATTCTAGGTAC 59.630 47.826 0.00 0.00 39.98 3.34
926 1010 3.007074 TGGTGCAACAACGATTCTAGGTA 59.993 43.478 0.00 0.00 39.98 3.08
927 1011 2.224426 TGGTGCAACAACGATTCTAGGT 60.224 45.455 0.00 0.00 39.98 3.08
928 1012 2.416547 CTGGTGCAACAACGATTCTAGG 59.583 50.000 5.64 0.00 39.98 3.02
929 1013 2.159653 GCTGGTGCAACAACGATTCTAG 60.160 50.000 5.64 0.00 39.98 2.43
930 1014 1.804151 GCTGGTGCAACAACGATTCTA 59.196 47.619 5.64 0.00 39.98 2.10
931 1015 0.593128 GCTGGTGCAACAACGATTCT 59.407 50.000 5.64 0.00 39.98 2.40
932 1016 0.387239 GGCTGGTGCAACAACGATTC 60.387 55.000 5.64 0.00 39.98 2.52
933 1017 1.659794 GGCTGGTGCAACAACGATT 59.340 52.632 5.64 0.00 39.98 3.34
934 1018 2.616330 CGGCTGGTGCAACAACGAT 61.616 57.895 20.23 0.00 39.98 3.73
935 1019 3.276091 CGGCTGGTGCAACAACGA 61.276 61.111 20.23 0.00 39.98 3.85
936 1020 4.980903 GCGGCTGGTGCAACAACG 62.981 66.667 20.48 20.48 39.98 4.10
937 1021 4.980903 CGCGGCTGGTGCAACAAC 62.981 66.667 5.64 0.00 39.98 3.32
966 1050 4.883354 CATCAAGCCCCGCCCTCC 62.883 72.222 0.00 0.00 0.00 4.30
967 1051 4.883354 CCATCAAGCCCCGCCCTC 62.883 72.222 0.00 0.00 0.00 4.30
969 1053 4.209866 ATCCATCAAGCCCCGCCC 62.210 66.667 0.00 0.00 0.00 6.13
970 1054 2.595754 GATCCATCAAGCCCCGCC 60.596 66.667 0.00 0.00 0.00 6.13
971 1055 2.189499 GTGATCCATCAAGCCCCGC 61.189 63.158 0.00 0.00 38.75 6.13
972 1056 1.526917 GGTGATCCATCAAGCCCCG 60.527 63.158 0.00 0.00 38.75 5.73
973 1057 1.526917 CGGTGATCCATCAAGCCCC 60.527 63.158 0.00 0.00 38.75 5.80
974 1058 2.189499 GCGGTGATCCATCAAGCCC 61.189 63.158 6.90 0.00 38.75 5.19
975 1059 3.425422 GCGGTGATCCATCAAGCC 58.575 61.111 6.90 0.00 38.75 4.35
976 1060 0.749454 AAGGCGGTGATCCATCAAGC 60.749 55.000 8.86 8.86 38.75 4.01
977 1061 1.019673 CAAGGCGGTGATCCATCAAG 58.980 55.000 0.00 0.00 38.75 3.02
978 1062 0.327924 ACAAGGCGGTGATCCATCAA 59.672 50.000 0.00 0.00 38.75 2.57
979 1063 0.107703 GACAAGGCGGTGATCCATCA 60.108 55.000 0.00 0.00 0.00 3.07
980 1064 1.154205 CGACAAGGCGGTGATCCATC 61.154 60.000 0.00 0.00 0.00 3.51
981 1065 1.153369 CGACAAGGCGGTGATCCAT 60.153 57.895 0.00 0.00 0.00 3.41
982 1066 1.613317 ATCGACAAGGCGGTGATCCA 61.613 55.000 0.00 0.00 0.00 3.41
983 1067 1.144057 ATCGACAAGGCGGTGATCC 59.856 57.895 0.00 0.00 0.00 3.36
984 1068 0.460284 ACATCGACAAGGCGGTGATC 60.460 55.000 16.50 0.00 44.79 2.92
985 1069 0.740868 CACATCGACAAGGCGGTGAT 60.741 55.000 16.50 0.00 44.79 3.06
986 1070 1.374125 CACATCGACAAGGCGGTGA 60.374 57.895 16.50 0.00 44.79 4.02
988 1072 2.047274 CCACATCGACAAGGCGGT 60.047 61.111 0.00 0.00 0.00 5.68
989 1073 2.047274 ACCACATCGACAAGGCGG 60.047 61.111 0.00 0.00 0.00 6.13
990 1074 3.474806 GACCACATCGACAAGGCG 58.525 61.111 0.00 0.00 0.00 5.52
1424 1508 1.876714 CCGCGTACACAGGATTCCG 60.877 63.158 4.92 0.00 0.00 4.30
1490 1575 1.093159 GAACTCTAAGGCGAGGACGA 58.907 55.000 0.00 0.00 42.66 4.20
1585 1670 3.130516 CAGCAGATTTGGCACATTCAGAT 59.869 43.478 0.00 0.00 39.30 2.90
1632 1717 2.031516 CACTGGCACCTTCAGAGCG 61.032 63.158 0.00 0.00 36.22 5.03
1649 1734 5.421693 CCATTGATAAATTCCCTCACCAACA 59.578 40.000 0.00 0.00 0.00 3.33
1652 1737 4.955450 CACCATTGATAAATTCCCTCACCA 59.045 41.667 0.00 0.00 0.00 4.17
1755 1840 2.804697 TGTACACTAGCTGCAAACGA 57.195 45.000 1.02 0.00 0.00 3.85
1761 1846 4.545823 TGTTTGTTTGTACACTAGCTGC 57.454 40.909 0.00 0.00 32.98 5.25
1873 1958 5.048083 TCAGGATTTTGTTCTTACCATGCAC 60.048 40.000 0.00 0.00 0.00 4.57
1943 2028 5.984725 TGGAACACTCTCAACTAAACAAGA 58.015 37.500 0.00 0.00 0.00 3.02
1995 2080 6.763135 TGCAGAGAAGTTGATTATACATGTCC 59.237 38.462 0.00 0.00 0.00 4.02
2250 2338 3.946606 TCATCATGTGCTCACAGTTCAT 58.053 40.909 8.74 0.00 45.48 2.57
2315 2403 7.916450 GCATATAGGCTAAGGAATAGTAAGTCG 59.084 40.741 1.25 0.00 33.87 4.18
2507 2595 9.487790 AGATTGAACAAAAACAAGAACAAAAGA 57.512 25.926 0.00 0.00 0.00 2.52
2699 2789 1.632409 AGGTGATGAGCATTCCACTGT 59.368 47.619 0.00 0.00 0.00 3.55
2823 2916 6.839657 AGTAGTAGCATACAACCTGGATAGTT 59.160 38.462 0.00 0.00 46.26 2.24
2942 3035 8.458052 TGAAGCACATGAACAAATAATACGAAT 58.542 29.630 0.00 0.00 0.00 3.34
2950 3043 9.755804 TTACAAAATGAAGCACATGAACAAATA 57.244 25.926 0.00 0.00 39.39 1.40
2997 3090 5.012664 TCAGTTTGAGGGTAGCATGTTTCTA 59.987 40.000 0.00 0.00 0.00 2.10
3140 3240 9.178758 GAGTAACAATCAGAACCATTTCCTATT 57.821 33.333 0.00 0.00 31.28 1.73
3142 3242 7.918076 AGAGTAACAATCAGAACCATTTCCTA 58.082 34.615 0.00 0.00 31.28 2.94
3280 3433 0.179140 GCACCACAACACAACACAGG 60.179 55.000 0.00 0.00 0.00 4.00
3428 3585 4.340381 ACATGCTCCCATAGAAATTTCAGC 59.660 41.667 19.99 17.41 0.00 4.26
3456 3615 9.809096 TTTTACATTCAGCAATTAACACAAGAA 57.191 25.926 0.00 0.00 0.00 2.52
3633 3792 2.359900 ACAAAGATTGGACGAGATGGC 58.640 47.619 0.00 0.00 34.12 4.40


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

AutoCloner maintained by Alex Coulton.