Multiple sequence alignment - TraesCS3B01G381100

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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 TraesCS3B01G381100 chr3B 100.000 4169 0 0 1 4169 598907462 598911630 0.000000e+00 7699.0
1 TraesCS3B01G381100 chr3B 90.936 1004 86 4 3170 4169 770107239 770106237 0.000000e+00 1345.0
2 TraesCS3B01G381100 chr3A 93.064 1586 75 17 1000 2558 597849297 597850874 0.000000e+00 2287.0
3 TraesCS3B01G381100 chr3A 92.295 623 30 11 2551 3170 597850913 597851520 0.000000e+00 869.0
4 TraesCS3B01G381100 chr3A 98.182 55 1 0 926 980 597836490 597836544 3.430000e-16 97.1
5 TraesCS3B01G381100 chr3D 93.394 1529 79 15 799 2318 455593768 455595283 0.000000e+00 2244.0
6 TraesCS3B01G381100 chr3D 90.708 452 27 12 2551 2998 455595506 455595946 4.640000e-164 588.0
7 TraesCS3B01G381100 chr3D 94.241 191 8 1 2983 3170 455595960 455596150 5.270000e-74 289.0
8 TraesCS3B01G381100 chr3D 95.758 165 7 0 2394 2558 455595303 455595467 2.470000e-67 267.0
9 TraesCS3B01G381100 chr4D 91.525 1003 75 7 3171 4169 450004289 450005285 0.000000e+00 1373.0
10 TraesCS3B01G381100 chr4D 84.978 679 73 10 4 667 137889166 137888502 0.000000e+00 662.0
11 TraesCS3B01G381100 chr5D 89.133 1003 105 3 3171 4169 448717695 448718697 0.000000e+00 1245.0
12 TraesCS3B01G381100 chr5D 88.358 1005 108 8 3171 4169 318871198 318872199 0.000000e+00 1199.0
13 TraesCS3B01G381100 chr5D 81.844 694 82 24 1 653 65899997 65900687 1.020000e-150 544.0
14 TraesCS3B01G381100 chr5D 81.991 633 95 16 4 617 390739395 390738763 1.720000e-143 520.0
15 TraesCS3B01G381100 chr6A 88.911 1019 100 11 3160 4169 578542860 578543874 0.000000e+00 1243.0
16 TraesCS3B01G381100 chr7A 88.780 1025 95 17 3154 4169 533499889 533500902 0.000000e+00 1238.0
17 TraesCS3B01G381100 chr7A 89.452 986 91 9 3171 4152 85071984 85071008 0.000000e+00 1232.0
18 TraesCS3B01G381100 chr5B 88.922 1011 99 11 3164 4169 427963051 427964053 0.000000e+00 1234.0
19 TraesCS3B01G381100 chr5B 85.872 453 53 6 4 448 65193376 65192927 4.880000e-129 472.0
20 TraesCS3B01G381100 chr2A 88.714 1019 101 12 3160 4169 1649598 1648585 0.000000e+00 1232.0
21 TraesCS3B01G381100 chr5A 81.492 697 87 27 4 661 565622543 565623236 6.130000e-148 534.0
22 TraesCS3B01G381100 chr4A 81.481 702 83 28 4 661 29089176 29088478 2.210000e-147 532.0
23 TraesCS3B01G381100 chr2B 81.832 655 81 23 1 645 384340722 384341348 2.220000e-142 516.0
24 TraesCS3B01G381100 chr6B 89.487 390 37 3 1 386 352072633 352073022 1.350000e-134 490.0
25 TraesCS3B01G381100 chr6B 82.051 195 13 8 2935 3129 656486325 656486153 3.360000e-31 147.0
26 TraesCS3B01G381100 chr6B 81.026 195 15 7 2935 3129 681681478 681681306 7.270000e-28 135.0
27 TraesCS3B01G381100 chr6B 95.652 46 2 0 839 884 478904148 478904193 1.610000e-09 75.0
28 TraesCS3B01G381100 chr1D 86.323 446 56 2 1 442 398243138 398243582 8.110000e-132 481.0
29 TraesCS3B01G381100 chr1D 85.619 452 61 3 1 448 398243755 398244206 4.880000e-129 472.0
30 TraesCS3B01G381100 chr1D 84.127 63 10 0 837 899 445245575 445245637 1.250000e-05 62.1
31 TraesCS3B01G381100 chr7D 84.270 89 10 2 582 666 197146067 197146155 2.670000e-12 84.2


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 TraesCS3B01G381100 chr3B 598907462 598911630 4168 False 7699.0 7699 100.00000 1 4169 1 chr3B.!!$F1 4168
1 TraesCS3B01G381100 chr3B 770106237 770107239 1002 True 1345.0 1345 90.93600 3170 4169 1 chr3B.!!$R1 999
2 TraesCS3B01G381100 chr3A 597849297 597851520 2223 False 1578.0 2287 92.67950 1000 3170 2 chr3A.!!$F2 2170
3 TraesCS3B01G381100 chr3D 455593768 455596150 2382 False 847.0 2244 93.52525 799 3170 4 chr3D.!!$F1 2371
4 TraesCS3B01G381100 chr4D 450004289 450005285 996 False 1373.0 1373 91.52500 3171 4169 1 chr4D.!!$F1 998
5 TraesCS3B01G381100 chr4D 137888502 137889166 664 True 662.0 662 84.97800 4 667 1 chr4D.!!$R1 663
6 TraesCS3B01G381100 chr5D 448717695 448718697 1002 False 1245.0 1245 89.13300 3171 4169 1 chr5D.!!$F3 998
7 TraesCS3B01G381100 chr5D 318871198 318872199 1001 False 1199.0 1199 88.35800 3171 4169 1 chr5D.!!$F2 998
8 TraesCS3B01G381100 chr5D 65899997 65900687 690 False 544.0 544 81.84400 1 653 1 chr5D.!!$F1 652
9 TraesCS3B01G381100 chr5D 390738763 390739395 632 True 520.0 520 81.99100 4 617 1 chr5D.!!$R1 613
10 TraesCS3B01G381100 chr6A 578542860 578543874 1014 False 1243.0 1243 88.91100 3160 4169 1 chr6A.!!$F1 1009
11 TraesCS3B01G381100 chr7A 533499889 533500902 1013 False 1238.0 1238 88.78000 3154 4169 1 chr7A.!!$F1 1015
12 TraesCS3B01G381100 chr7A 85071008 85071984 976 True 1232.0 1232 89.45200 3171 4152 1 chr7A.!!$R1 981
13 TraesCS3B01G381100 chr5B 427963051 427964053 1002 False 1234.0 1234 88.92200 3164 4169 1 chr5B.!!$F1 1005
14 TraesCS3B01G381100 chr2A 1648585 1649598 1013 True 1232.0 1232 88.71400 3160 4169 1 chr2A.!!$R1 1009
15 TraesCS3B01G381100 chr5A 565622543 565623236 693 False 534.0 534 81.49200 4 661 1 chr5A.!!$F1 657
16 TraesCS3B01G381100 chr4A 29088478 29089176 698 True 532.0 532 81.48100 4 661 1 chr4A.!!$R1 657
17 TraesCS3B01G381100 chr2B 384340722 384341348 626 False 516.0 516 81.83200 1 645 1 chr2B.!!$F1 644
18 TraesCS3B01G381100 chr1D 398243138 398244206 1068 False 476.5 481 85.97100 1 448 2 chr1D.!!$F2 447

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
48 49 0.466555 CAAGGGGGAAACGACACCAA 60.467 55.0 0.00 0.00 34.56 3.67 F
625 684 0.468648 CGGGATGGAGGTTAGGGTTC 59.531 60.0 0.00 0.00 0.00 3.62 F
1896 2033 0.251077 CTCAAAAGAGGGCTGGCTGT 60.251 55.0 0.00 0.00 0.00 4.40 F
2617 2832 0.389025 GGTTGCCTGTTGAAACTGGG 59.611 55.0 17.62 10.11 45.14 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1859 1996 0.259938 AGCTCATTGGATTCACCCCC 59.740 55.000 0.00 0.0 38.00 5.40 R
2597 2811 1.110442 CCAGTTTCAACAGGCAACCA 58.890 50.000 0.00 0.0 37.17 3.67 R
2811 3029 0.467290 TCCTTGCTTGACACAACCCC 60.467 55.000 0.00 0.0 0.00 4.95 R
3497 3754 2.890474 CACGTAGCCCGGATGTGC 60.890 66.667 0.73 0.0 42.24 4.57 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
48 49 0.466555 CAAGGGGGAAACGACACCAA 60.467 55.000 0.00 0.00 34.56 3.67
126 131 3.119602 CCTTGAACTTCTCCACGACGATA 60.120 47.826 0.00 0.00 0.00 2.92
157 162 1.641677 GAACGACGCAAACAGCACT 59.358 52.632 0.00 0.00 46.13 4.40
199 204 2.946947 CCGATGGCAGGTTTTCACT 58.053 52.632 0.00 0.00 0.00 3.41
214 219 6.094881 AGGTTTTCACTCAGATTTGTTCGAAA 59.905 34.615 0.00 0.00 0.00 3.46
220 225 6.094881 TCACTCAGATTTGTTCGAAAAACCTT 59.905 34.615 0.00 0.00 0.00 3.50
297 302 1.339631 CCGCTACCAGATCCCAACAAA 60.340 52.381 0.00 0.00 0.00 2.83
304 311 3.395941 ACCAGATCCCAACAAAGAGAAGT 59.604 43.478 0.00 0.00 0.00 3.01
410 419 2.449518 TCCAGAGCCAACCCCACA 60.450 61.111 0.00 0.00 0.00 4.17
504 561 2.125147 TCGTGCTACAGCCATGCC 60.125 61.111 0.00 0.00 41.18 4.40
507 564 1.821332 GTGCTACAGCCATGCCCTC 60.821 63.158 0.00 0.00 41.18 4.30
603 662 2.675371 GGGGGTGTAGGAGGCAAC 59.325 66.667 0.00 0.00 0.00 4.17
604 663 2.675371 GGGGTGTAGGAGGCAACC 59.325 66.667 0.00 0.00 42.75 3.77
605 664 2.267961 GGGTGTAGGAGGCAACCG 59.732 66.667 0.00 0.00 33.65 4.44
606 665 2.436115 GGTGTAGGAGGCAACCGC 60.436 66.667 0.00 0.00 34.73 5.68
607 666 2.813908 GTGTAGGAGGCAACCGCG 60.814 66.667 0.00 0.00 39.92 6.46
608 667 4.077184 TGTAGGAGGCAACCGCGG 62.077 66.667 26.86 26.86 39.92 6.46
609 668 4.832608 GTAGGAGGCAACCGCGGG 62.833 72.222 31.76 14.21 39.92 6.13
617 676 4.096003 CAACCGCGGGATGGAGGT 62.096 66.667 31.76 1.49 42.25 3.85
618 677 3.327404 AACCGCGGGATGGAGGTT 61.327 61.111 31.76 9.04 43.94 3.50
619 678 1.991167 AACCGCGGGATGGAGGTTA 60.991 57.895 31.76 0.00 46.35 2.85
620 679 1.968050 AACCGCGGGATGGAGGTTAG 61.968 60.000 31.76 0.00 46.35 2.34
621 680 2.421739 CGCGGGATGGAGGTTAGG 59.578 66.667 0.00 0.00 0.00 2.69
622 681 2.829592 GCGGGATGGAGGTTAGGG 59.170 66.667 0.00 0.00 0.00 3.53
623 682 2.070650 GCGGGATGGAGGTTAGGGT 61.071 63.158 0.00 0.00 0.00 4.34
624 683 1.632965 GCGGGATGGAGGTTAGGGTT 61.633 60.000 0.00 0.00 0.00 4.11
625 684 0.468648 CGGGATGGAGGTTAGGGTTC 59.531 60.000 0.00 0.00 0.00 3.62
626 685 0.844660 GGGATGGAGGTTAGGGTTCC 59.155 60.000 0.00 0.00 0.00 3.62
627 686 0.844660 GGATGGAGGTTAGGGTTCCC 59.155 60.000 0.00 0.00 0.00 3.97
628 687 0.844660 GATGGAGGTTAGGGTTCCCC 59.155 60.000 4.02 0.00 45.90 4.81
658 717 4.116328 CGAGAGCGACGCAAGGGA 62.116 66.667 23.70 0.00 46.39 4.20
659 718 2.507324 GAGAGCGACGCAAGGGAC 60.507 66.667 23.70 5.90 46.39 4.46
669 728 3.702048 CAAGGGACGCGAGGGGAA 61.702 66.667 15.93 0.00 0.00 3.97
679 738 3.002371 GAGGGGAAGGGGCAGAAG 58.998 66.667 0.00 0.00 0.00 2.85
680 739 2.615288 AGGGGAAGGGGCAGAAGG 60.615 66.667 0.00 0.00 0.00 3.46
681 740 3.744155 GGGGAAGGGGCAGAAGGG 61.744 72.222 0.00 0.00 0.00 3.95
682 741 4.448976 GGGAAGGGGCAGAAGGGC 62.449 72.222 0.00 0.00 42.44 5.19
692 751 0.548510 GCAGAAGGGCCAGATTAGGT 59.451 55.000 6.18 0.00 0.00 3.08
693 752 1.768870 GCAGAAGGGCCAGATTAGGTA 59.231 52.381 6.18 0.00 0.00 3.08
694 753 2.485657 GCAGAAGGGCCAGATTAGGTAC 60.486 54.545 6.18 0.00 0.00 3.34
697 756 3.456277 AGAAGGGCCAGATTAGGTACTTG 59.544 47.826 6.18 0.00 41.75 3.16
698 757 2.127708 AGGGCCAGATTAGGTACTTGG 58.872 52.381 6.18 0.00 41.75 3.61
700 759 1.490910 GGCCAGATTAGGTACTTGGCT 59.509 52.381 12.88 0.04 41.75 4.75
701 760 2.704065 GGCCAGATTAGGTACTTGGCTA 59.296 50.000 12.88 0.00 41.75 3.93
702 761 3.244249 GGCCAGATTAGGTACTTGGCTAG 60.244 52.174 12.88 0.00 41.75 3.42
703 762 3.641906 GCCAGATTAGGTACTTGGCTAGA 59.358 47.826 2.20 0.00 41.75 2.43
704 763 4.284746 GCCAGATTAGGTACTTGGCTAGAT 59.715 45.833 2.20 0.00 41.75 1.98
705 764 5.788450 CCAGATTAGGTACTTGGCTAGATG 58.212 45.833 2.20 0.00 41.75 2.90
706 765 5.305644 CCAGATTAGGTACTTGGCTAGATGT 59.694 44.000 2.20 0.00 41.75 3.06
707 766 6.493802 CCAGATTAGGTACTTGGCTAGATGTA 59.506 42.308 2.20 0.00 41.75 2.29
708 767 7.179338 CCAGATTAGGTACTTGGCTAGATGTAT 59.821 40.741 2.20 0.00 41.75 2.29
709 768 9.244292 CAGATTAGGTACTTGGCTAGATGTATA 57.756 37.037 2.20 0.00 41.75 1.47
710 769 9.824216 AGATTAGGTACTTGGCTAGATGTATAA 57.176 33.333 2.20 0.00 41.75 0.98
713 772 5.780793 AGGTACTTGGCTAGATGTATAAGGG 59.219 44.000 2.20 0.00 27.25 3.95
714 773 5.778750 GGTACTTGGCTAGATGTATAAGGGA 59.221 44.000 2.20 0.00 0.00 4.20
717 776 5.308237 ACTTGGCTAGATGTATAAGGGAAGG 59.692 44.000 2.20 0.00 0.00 3.46
719 778 4.140543 TGGCTAGATGTATAAGGGAAGGGA 60.141 45.833 0.00 0.00 0.00 4.20
721 780 4.838986 GCTAGATGTATAAGGGAAGGGACA 59.161 45.833 0.00 0.00 0.00 4.02
722 781 5.279556 GCTAGATGTATAAGGGAAGGGACAC 60.280 48.000 0.00 0.00 0.00 3.67
723 782 3.641906 AGATGTATAAGGGAAGGGACACG 59.358 47.826 0.00 0.00 0.00 4.49
724 783 3.104519 TGTATAAGGGAAGGGACACGA 57.895 47.619 0.00 0.00 0.00 4.35
725 784 3.649843 TGTATAAGGGAAGGGACACGAT 58.350 45.455 0.00 0.00 0.00 3.73
726 785 4.035112 TGTATAAGGGAAGGGACACGATT 58.965 43.478 0.00 0.00 0.00 3.34
727 786 4.472108 TGTATAAGGGAAGGGACACGATTT 59.528 41.667 0.00 0.00 0.00 2.17
728 787 5.662208 TGTATAAGGGAAGGGACACGATTTA 59.338 40.000 0.00 0.00 0.00 1.40
730 789 7.510001 TGTATAAGGGAAGGGACACGATTTATA 59.490 37.037 0.00 0.00 0.00 0.98
732 791 5.906772 AGGGAAGGGACACGATTTATATT 57.093 39.130 0.00 0.00 0.00 1.28
733 792 7.383156 AAGGGAAGGGACACGATTTATATTA 57.617 36.000 0.00 0.00 0.00 0.98
734 793 6.766429 AGGGAAGGGACACGATTTATATTAC 58.234 40.000 0.00 0.00 0.00 1.89
735 794 6.557633 AGGGAAGGGACACGATTTATATTACT 59.442 38.462 0.00 0.00 0.00 2.24
736 795 7.072076 AGGGAAGGGACACGATTTATATTACTT 59.928 37.037 0.00 0.00 0.00 2.24
738 797 7.713942 GGAAGGGACACGATTTATATTACTTGT 59.286 37.037 0.00 0.00 0.00 3.16
739 798 8.658499 AAGGGACACGATTTATATTACTTGTC 57.342 34.615 0.00 0.00 32.98 3.18
740 799 6.921857 AGGGACACGATTTATATTACTTGTCG 59.078 38.462 0.00 0.00 34.27 4.35
741 800 6.346359 GGGACACGATTTATATTACTTGTCGC 60.346 42.308 0.00 0.00 38.15 5.19
742 801 6.420008 GGACACGATTTATATTACTTGTCGCT 59.580 38.462 0.00 0.00 34.27 4.93
743 802 7.161829 ACACGATTTATATTACTTGTCGCTG 57.838 36.000 0.00 0.00 0.00 5.18
747 806 7.011109 ACGATTTATATTACTTGTCGCTGCTTT 59.989 33.333 0.00 0.00 0.00 3.51
750 809 8.712285 TTTATATTACTTGTCGCTGCTTTAGT 57.288 30.769 0.00 0.00 0.00 2.24
752 811 7.695869 ATATTACTTGTCGCTGCTTTAGTAC 57.304 36.000 0.00 0.00 0.00 2.73
753 812 3.380479 ACTTGTCGCTGCTTTAGTACA 57.620 42.857 0.00 0.00 0.00 2.90
754 813 3.926616 ACTTGTCGCTGCTTTAGTACAT 58.073 40.909 0.00 0.00 0.00 2.29
755 814 5.068234 ACTTGTCGCTGCTTTAGTACATA 57.932 39.130 0.00 0.00 0.00 2.29
756 815 5.103000 ACTTGTCGCTGCTTTAGTACATAG 58.897 41.667 0.00 0.00 0.00 2.23
757 816 4.713824 TGTCGCTGCTTTAGTACATAGT 57.286 40.909 0.00 0.00 0.00 2.12
758 817 5.823209 TGTCGCTGCTTTAGTACATAGTA 57.177 39.130 0.00 0.00 0.00 1.82
759 818 5.817988 TGTCGCTGCTTTAGTACATAGTAG 58.182 41.667 0.00 0.00 0.00 2.57
760 819 5.587443 TGTCGCTGCTTTAGTACATAGTAGA 59.413 40.000 9.88 0.00 0.00 2.59
761 820 6.094464 TGTCGCTGCTTTAGTACATAGTAGAA 59.906 38.462 9.88 0.00 0.00 2.10
762 821 7.140048 GTCGCTGCTTTAGTACATAGTAGAAT 58.860 38.462 9.88 0.00 0.00 2.40
763 822 7.113684 GTCGCTGCTTTAGTACATAGTAGAATG 59.886 40.741 9.88 0.00 0.00 2.67
764 823 6.918569 CGCTGCTTTAGTACATAGTAGAATGT 59.081 38.462 9.88 0.00 42.62 2.71
765 824 7.113684 CGCTGCTTTAGTACATAGTAGAATGTC 59.886 40.741 9.88 0.00 40.52 3.06
766 825 7.921214 GCTGCTTTAGTACATAGTAGAATGTCA 59.079 37.037 9.88 0.00 40.52 3.58
767 826 9.973450 CTGCTTTAGTACATAGTAGAATGTCAT 57.027 33.333 0.00 0.00 40.52 3.06
768 827 9.750125 TGCTTTAGTACATAGTAGAATGTCATG 57.250 33.333 0.00 0.00 40.52 3.07
769 828 9.197694 GCTTTAGTACATAGTAGAATGTCATGG 57.802 37.037 0.00 0.00 40.52 3.66
770 829 9.197694 CTTTAGTACATAGTAGAATGTCATGGC 57.802 37.037 0.00 0.00 40.52 4.40
771 830 6.731292 AGTACATAGTAGAATGTCATGGCA 57.269 37.500 0.60 0.60 40.52 4.92
772 831 6.516718 AGTACATAGTAGAATGTCATGGCAC 58.483 40.000 0.00 0.00 40.52 5.01
773 832 4.371786 ACATAGTAGAATGTCATGGCACG 58.628 43.478 0.00 0.00 35.08 5.34
774 833 4.141937 ACATAGTAGAATGTCATGGCACGT 60.142 41.667 0.00 0.00 35.08 4.49
775 834 2.621338 AGTAGAATGTCATGGCACGTG 58.379 47.619 12.28 12.28 0.00 4.49
776 835 2.233676 AGTAGAATGTCATGGCACGTGA 59.766 45.455 22.23 0.00 0.00 4.35
777 836 1.442769 AGAATGTCATGGCACGTGAC 58.557 50.000 22.23 19.45 44.77 3.67
781 840 3.143675 GTCATGGCACGTGACATCT 57.856 52.632 33.78 13.53 43.11 2.90
782 841 1.002366 GTCATGGCACGTGACATCTC 58.998 55.000 33.78 23.73 43.11 2.75
783 842 0.607620 TCATGGCACGTGACATCTCA 59.392 50.000 33.78 17.73 43.11 3.27
784 843 1.001860 TCATGGCACGTGACATCTCAA 59.998 47.619 33.78 16.52 43.11 3.02
785 844 2.011947 CATGGCACGTGACATCTCAAT 58.988 47.619 33.78 10.94 43.11 2.57
786 845 2.183478 TGGCACGTGACATCTCAATT 57.817 45.000 23.03 0.00 0.00 2.32
787 846 2.076100 TGGCACGTGACATCTCAATTC 58.924 47.619 23.03 0.00 0.00 2.17
788 847 2.289631 TGGCACGTGACATCTCAATTCT 60.290 45.455 23.03 0.00 0.00 2.40
789 848 2.094894 GGCACGTGACATCTCAATTCTG 59.905 50.000 22.23 0.00 0.00 3.02
790 849 2.475187 GCACGTGACATCTCAATTCTGC 60.475 50.000 22.23 0.00 0.00 4.26
791 850 1.995484 ACGTGACATCTCAATTCTGCG 59.005 47.619 0.00 0.00 0.00 5.18
792 851 1.995484 CGTGACATCTCAATTCTGCGT 59.005 47.619 0.00 0.00 0.00 5.24
793 852 2.413112 CGTGACATCTCAATTCTGCGTT 59.587 45.455 0.00 0.00 0.00 4.84
794 853 3.120546 CGTGACATCTCAATTCTGCGTTT 60.121 43.478 0.00 0.00 0.00 3.60
795 854 4.611355 CGTGACATCTCAATTCTGCGTTTT 60.611 41.667 0.00 0.00 0.00 2.43
796 855 5.215160 GTGACATCTCAATTCTGCGTTTTT 58.785 37.500 0.00 0.00 0.00 1.94
797 856 5.340667 GTGACATCTCAATTCTGCGTTTTTC 59.659 40.000 0.00 0.00 0.00 2.29
809 868 6.677781 TCTGCGTTTTTCCTATTTCTATGG 57.322 37.500 0.00 0.00 0.00 2.74
839 899 1.281867 TGATAACCCAAGAGGCTGGTG 59.718 52.381 0.00 0.00 40.58 4.17
850 910 5.476945 CCAAGAGGCTGGTGTAATTTTTACT 59.523 40.000 0.00 0.00 0.00 2.24
871 931 8.726870 TTACTTTTAGTGTTCTTTGTACTGCT 57.273 30.769 0.00 0.00 0.00 4.24
880 940 5.064707 TGTTCTTTGTACTGCTTTGACAGAC 59.935 40.000 0.00 0.00 40.25 3.51
890 950 3.126831 GCTTTGACAGACGATGGATAGG 58.873 50.000 0.00 0.00 0.00 2.57
894 954 1.267261 GACAGACGATGGATAGGTCGG 59.733 57.143 0.00 0.00 41.87 4.79
903 964 5.070047 ACGATGGATAGGTCGGAAGTAAAAT 59.930 40.000 0.00 0.00 41.87 1.82
913 974 7.971455 AGGTCGGAAGTAAAATAAATCGAAAG 58.029 34.615 0.00 0.00 0.00 2.62
1016 1077 2.423538 AGTGGCAAAATTCGGATAGCAC 59.576 45.455 0.00 0.00 0.00 4.40
1024 1085 1.622607 TTCGGATAGCACCCACCAGG 61.623 60.000 0.00 0.00 43.78 4.45
1489 1626 2.859273 AAGGCGACATCCTGAAGCCG 62.859 60.000 0.00 0.00 43.79 5.52
1675 1812 2.278013 GACGGCGTGGAGATCGAC 60.278 66.667 21.19 0.00 0.00 4.20
1800 1937 3.190535 CGCTACAACAGGTAAAGCCATTT 59.809 43.478 0.00 0.00 40.61 2.32
1822 1959 3.447586 TGTCCATTCCTAGTGTCTACTGC 59.552 47.826 0.00 0.00 37.78 4.40
1859 1996 7.950124 ACCATTGGGGATTATATTTAGGAACAG 59.050 37.037 7.78 0.00 41.15 3.16
1889 2026 1.475682 CCAATGAGCTCAAAAGAGGGC 59.524 52.381 22.50 0.00 0.00 5.19
1896 2033 0.251077 CTCAAAAGAGGGCTGGCTGT 60.251 55.000 0.00 0.00 0.00 4.40
1903 2040 4.645809 GGGCTGGCTGTCCTTTAG 57.354 61.111 7.88 0.00 37.49 1.85
1929 2066 4.263905 TGGCTTTGGTATCCAGATTCACTT 60.264 41.667 0.00 0.00 33.81 3.16
2112 2252 3.058708 CGGGTGTGTGAATCATATCATGC 60.059 47.826 0.00 0.00 0.00 4.06
2123 2263 6.758416 TGAATCATATCATGCTTACTATCCGC 59.242 38.462 0.00 0.00 0.00 5.54
2135 2275 5.450137 GCTTACTATCCGCTTAACTCTGACA 60.450 44.000 0.00 0.00 0.00 3.58
2138 2278 2.672961 TCCGCTTAACTCTGACATGG 57.327 50.000 0.00 0.00 0.00 3.66
2159 2300 6.817765 TGGTTCTCTGCTAATTTAACAAGG 57.182 37.500 0.00 0.00 0.00 3.61
2276 2417 3.879295 TGCTGTTCTTGAGAGGAAACAAG 59.121 43.478 0.00 0.00 43.03 3.16
2344 2485 2.302733 TGTATCTGCACACACATGAGGT 59.697 45.455 0.00 0.00 0.00 3.85
2355 2496 6.502652 CACACACATGAGGTTTATTGTTTGA 58.497 36.000 0.00 0.00 0.00 2.69
2358 2499 7.080099 CACACATGAGGTTTATTGTTTGAGAG 58.920 38.462 0.00 0.00 0.00 3.20
2375 2516 5.755409 TGAGAGGCTAAAGGTGACAATTA 57.245 39.130 0.00 0.00 0.00 1.40
2381 2522 5.487845 AGGCTAAAGGTGACAATTAGTAGGT 59.512 40.000 7.96 0.00 35.57 3.08
2382 2523 5.816258 GGCTAAAGGTGACAATTAGTAGGTC 59.184 44.000 7.96 0.00 35.57 3.85
2384 2525 3.521947 AGGTGACAATTAGTAGGTCGC 57.478 47.619 0.00 0.00 40.39 5.19
2396 2563 3.858247 AGTAGGTCGCACATCTTTTACC 58.142 45.455 0.00 0.00 0.00 2.85
2406 2573 4.641396 CACATCTTTTACCCACTCTGACA 58.359 43.478 0.00 0.00 0.00 3.58
2424 2591 7.230510 ACTCTGACAGTATCTGATTATGGTCTC 59.769 40.741 1.59 0.00 35.00 3.36
2427 2594 6.040955 TGACAGTATCTGATTATGGTCTCCAC 59.959 42.308 3.70 0.00 33.87 4.02
2617 2832 0.389025 GGTTGCCTGTTGAAACTGGG 59.611 55.000 17.62 10.11 45.14 4.45
2661 2879 5.012458 TGTTCTCTGACATTTGATCCTCTGT 59.988 40.000 0.00 0.00 0.00 3.41
2723 2941 2.143876 GAGAAGAGGCTGAGTCTCCT 57.856 55.000 10.98 1.04 34.41 3.69
2732 2950 4.873010 AGGCTGAGTCTCCTAGTTTGATA 58.127 43.478 0.00 0.00 0.00 2.15
2735 2953 5.988561 GGCTGAGTCTCCTAGTTTGATAATG 59.011 44.000 0.00 0.00 0.00 1.90
2738 2956 8.364142 GCTGAGTCTCCTAGTTTGATAATGTAT 58.636 37.037 0.00 0.00 0.00 2.29
2742 2960 9.647918 AGTCTCCTAGTTTGATAATGTATCTGA 57.352 33.333 0.00 0.00 36.17 3.27
2763 2981 5.674525 TGAATAAGATGCGAAAGAGGACAT 58.325 37.500 0.00 0.00 0.00 3.06
2858 3076 7.253950 GGTGTGACAACAAACATGTATTTTGAC 60.254 37.037 14.21 10.73 38.27 3.18
2924 3143 9.866936 GTATATTCTCAGTTTCTAGTACTGTCG 57.133 37.037 19.84 14.72 42.77 4.35
2925 3144 6.821031 ATTCTCAGTTTCTAGTACTGTCGT 57.179 37.500 19.84 8.51 42.77 4.34
2926 3145 7.918536 ATTCTCAGTTTCTAGTACTGTCGTA 57.081 36.000 19.84 11.27 42.77 3.43
2927 3146 6.718454 TCTCAGTTTCTAGTACTGTCGTAC 57.282 41.667 19.84 0.00 45.04 3.67
3286 3537 6.560711 ACTAATTTTTCTTTCACGTGCACTT 58.439 32.000 16.19 1.59 0.00 3.16
3291 3542 2.899976 TCTTTCACGTGCACTTCTTCA 58.100 42.857 16.19 0.00 0.00 3.02
3343 3595 6.599638 AGGACAAAAAGCTGATGTTATCCTAC 59.400 38.462 0.87 0.00 0.00 3.18
3347 3599 8.806146 ACAAAAAGCTGATGTTATCCTACATTT 58.194 29.630 0.00 0.00 38.80 2.32
3390 3642 8.909708 TCAAAATATTTTGTAGCTCAAATCGG 57.090 30.769 30.50 9.04 45.77 4.18
3409 3661 1.974343 CGCCCCGATTGAAAACCCA 60.974 57.895 0.00 0.00 0.00 4.51
3544 3801 7.387119 TCACGTCTGTCATACATAAGTTACT 57.613 36.000 0.00 0.00 0.00 2.24
3717 3977 8.243426 TCAATAATTTTCATTCCCTCGTTCAAG 58.757 33.333 0.00 0.00 0.00 3.02
3762 4022 3.691118 TGAGTTATCAGCTTTCATGTGCC 59.309 43.478 0.00 0.00 0.00 5.01
3801 4061 6.127758 TGTTTACACATGAGTTATTGGGATGC 60.128 38.462 0.00 0.00 0.00 3.91
3912 4176 6.701400 ACGTAAAGTTATCGTGGTGTTTTACT 59.299 34.615 4.81 0.00 36.46 2.24
3933 4197 2.249309 AAGTTATCAGGACCGGGAGT 57.751 50.000 6.32 0.00 0.00 3.85
3934 4198 2.249309 AGTTATCAGGACCGGGAGTT 57.751 50.000 6.32 0.00 0.00 3.01
3999 4264 6.372103 TGTTTTCAGTAACTTTTCTTCACGGA 59.628 34.615 0.00 0.00 0.00 4.69
4038 4303 7.822334 TGGTGTTTGTACCTAAGTTATCAGATG 59.178 37.037 0.00 0.00 41.43 2.90
4055 4322 7.667575 ATCAGATGCGGAATCCTATATTACT 57.332 36.000 0.00 0.00 35.72 2.24
4156 4424 5.476614 ACCTAAGTTATCAAGTCCGACAAC 58.523 41.667 0.40 0.00 0.00 3.32
4158 4426 3.928727 AGTTATCAAGTCCGACAACGA 57.071 42.857 0.40 0.00 42.66 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 4.514577 CGGATGACGGCGGCTCTT 62.515 66.667 16.45 0.00 39.42 2.85
199 204 6.443934 TGAAGGTTTTTCGAACAAATCTGA 57.556 33.333 14.91 6.64 0.00 3.27
214 219 2.549754 CGTGCACAAGAGATGAAGGTTT 59.450 45.455 18.64 0.00 0.00 3.27
220 225 0.037326 GGTCCGTGCACAAGAGATGA 60.037 55.000 18.64 0.00 0.00 2.92
297 302 1.686741 GGTCTCGATGGGGACTTCTCT 60.687 57.143 7.73 0.00 33.46 3.10
348 357 3.083997 GGATCTGGTCCTGCGGGT 61.084 66.667 12.43 0.00 44.16 5.28
393 402 1.852157 ATGTGGGGTTGGCTCTGGA 60.852 57.895 0.00 0.00 0.00 3.86
410 419 4.666253 AGGCTGTGGCGGTTGCAT 62.666 61.111 0.00 0.00 45.35 3.96
490 547 2.591753 GAGGGCATGGCTGTAGCA 59.408 61.111 19.78 0.00 44.36 3.49
504 561 1.528309 GCTCCTCTCTCCTCCGAGG 60.528 68.421 8.30 8.30 46.52 4.63
507 564 2.520741 GGGCTCCTCTCTCCTCCG 60.521 72.222 0.00 0.00 0.00 4.63
587 646 2.675371 GGTTGCCTCCTACACCCC 59.325 66.667 0.00 0.00 0.00 4.95
589 648 2.436115 GCGGTTGCCTCCTACACC 60.436 66.667 0.00 0.00 33.98 4.16
591 650 4.077184 CCGCGGTTGCCTCCTACA 62.077 66.667 19.50 0.00 38.08 2.74
592 651 4.832608 CCCGCGGTTGCCTCCTAC 62.833 72.222 26.12 0.00 38.08 3.18
600 659 2.246761 TAACCTCCATCCCGCGGTTG 62.247 60.000 26.12 20.45 39.85 3.77
602 661 2.364579 TAACCTCCATCCCGCGGT 60.365 61.111 26.12 2.55 0.00 5.68
603 662 2.421739 CTAACCTCCATCCCGCGG 59.578 66.667 21.04 21.04 0.00 6.46
604 663 2.421739 CCTAACCTCCATCCCGCG 59.578 66.667 0.00 0.00 0.00 6.46
605 664 1.632965 AACCCTAACCTCCATCCCGC 61.633 60.000 0.00 0.00 0.00 6.13
606 665 0.468648 GAACCCTAACCTCCATCCCG 59.531 60.000 0.00 0.00 0.00 5.14
607 666 0.844660 GGAACCCTAACCTCCATCCC 59.155 60.000 0.00 0.00 0.00 3.85
642 701 2.507324 GTCCCTTGCGTCGCTCTC 60.507 66.667 19.50 0.00 0.00 3.20
653 712 3.391382 CTTCCCCTCGCGTCCCTT 61.391 66.667 5.77 0.00 0.00 3.95
661 720 3.009115 TTCTGCCCCTTCCCCTCG 61.009 66.667 0.00 0.00 0.00 4.63
665 724 4.448976 GCCCTTCTGCCCCTTCCC 62.449 72.222 0.00 0.00 0.00 3.97
666 725 4.448976 GGCCCTTCTGCCCCTTCC 62.449 72.222 0.00 0.00 46.11 3.46
673 732 0.548510 ACCTAATCTGGCCCTTCTGC 59.451 55.000 0.00 0.00 0.00 4.26
674 733 3.041946 AGTACCTAATCTGGCCCTTCTG 58.958 50.000 0.00 0.00 0.00 3.02
675 734 3.423058 AGTACCTAATCTGGCCCTTCT 57.577 47.619 0.00 0.00 0.00 2.85
676 735 3.433740 CCAAGTACCTAATCTGGCCCTTC 60.434 52.174 0.00 0.00 0.00 3.46
677 736 2.509964 CCAAGTACCTAATCTGGCCCTT 59.490 50.000 0.00 0.00 0.00 3.95
679 738 1.477014 GCCAAGTACCTAATCTGGCCC 60.477 57.143 0.00 0.00 35.15 5.80
680 739 1.490910 AGCCAAGTACCTAATCTGGCC 59.509 52.381 7.74 0.00 41.46 5.36
681 740 3.641906 TCTAGCCAAGTACCTAATCTGGC 59.358 47.826 3.16 3.16 40.90 4.85
682 741 5.305644 ACATCTAGCCAAGTACCTAATCTGG 59.694 44.000 0.00 0.00 0.00 3.86
683 742 6.412362 ACATCTAGCCAAGTACCTAATCTG 57.588 41.667 0.00 0.00 0.00 2.90
684 743 9.824216 TTATACATCTAGCCAAGTACCTAATCT 57.176 33.333 0.00 0.00 0.00 2.40
688 747 6.952358 CCCTTATACATCTAGCCAAGTACCTA 59.048 42.308 0.00 0.00 0.00 3.08
689 748 5.780793 CCCTTATACATCTAGCCAAGTACCT 59.219 44.000 0.00 0.00 0.00 3.08
690 749 5.778750 TCCCTTATACATCTAGCCAAGTACC 59.221 44.000 0.00 0.00 0.00 3.34
692 751 6.497259 CCTTCCCTTATACATCTAGCCAAGTA 59.503 42.308 0.00 0.00 0.00 2.24
693 752 5.308237 CCTTCCCTTATACATCTAGCCAAGT 59.692 44.000 0.00 0.00 0.00 3.16
694 753 5.280215 CCCTTCCCTTATACATCTAGCCAAG 60.280 48.000 0.00 0.00 0.00 3.61
697 756 4.223255 GTCCCTTCCCTTATACATCTAGCC 59.777 50.000 0.00 0.00 0.00 3.93
698 757 4.838986 TGTCCCTTCCCTTATACATCTAGC 59.161 45.833 0.00 0.00 0.00 3.42
700 759 4.831155 CGTGTCCCTTCCCTTATACATCTA 59.169 45.833 0.00 0.00 0.00 1.98
701 760 3.641906 CGTGTCCCTTCCCTTATACATCT 59.358 47.826 0.00 0.00 0.00 2.90
702 761 3.640029 TCGTGTCCCTTCCCTTATACATC 59.360 47.826 0.00 0.00 0.00 3.06
703 762 3.649843 TCGTGTCCCTTCCCTTATACAT 58.350 45.455 0.00 0.00 0.00 2.29
704 763 3.104519 TCGTGTCCCTTCCCTTATACA 57.895 47.619 0.00 0.00 0.00 2.29
705 764 4.684484 AATCGTGTCCCTTCCCTTATAC 57.316 45.455 0.00 0.00 0.00 1.47
706 765 8.674925 ATATAAATCGTGTCCCTTCCCTTATA 57.325 34.615 0.00 0.00 0.00 0.98
707 766 5.906772 ATAAATCGTGTCCCTTCCCTTAT 57.093 39.130 0.00 0.00 0.00 1.73
708 767 7.383156 AATATAAATCGTGTCCCTTCCCTTA 57.617 36.000 0.00 0.00 0.00 2.69
709 768 5.906772 ATATAAATCGTGTCCCTTCCCTT 57.093 39.130 0.00 0.00 0.00 3.95
710 769 5.906772 AATATAAATCGTGTCCCTTCCCT 57.093 39.130 0.00 0.00 0.00 4.20
711 770 6.766429 AGTAATATAAATCGTGTCCCTTCCC 58.234 40.000 0.00 0.00 0.00 3.97
713 772 8.658499 ACAAGTAATATAAATCGTGTCCCTTC 57.342 34.615 0.00 0.00 0.00 3.46
714 773 7.437267 CGACAAGTAATATAAATCGTGTCCCTT 59.563 37.037 0.00 0.00 36.50 3.95
717 776 6.420008 AGCGACAAGTAATATAAATCGTGTCC 59.580 38.462 0.00 0.00 36.50 4.02
719 778 6.292168 GCAGCGACAAGTAATATAAATCGTGT 60.292 38.462 0.00 0.00 0.00 4.49
721 780 5.983720 AGCAGCGACAAGTAATATAAATCGT 59.016 36.000 0.00 0.00 0.00 3.73
722 781 6.453643 AGCAGCGACAAGTAATATAAATCG 57.546 37.500 0.00 0.00 0.00 3.34
723 782 9.798885 CTAAAGCAGCGACAAGTAATATAAATC 57.201 33.333 0.00 0.00 0.00 2.17
724 783 9.326413 ACTAAAGCAGCGACAAGTAATATAAAT 57.674 29.630 0.00 0.00 0.00 1.40
725 784 8.712285 ACTAAAGCAGCGACAAGTAATATAAA 57.288 30.769 0.00 0.00 0.00 1.40
726 785 9.241317 GTACTAAAGCAGCGACAAGTAATATAA 57.759 33.333 0.00 0.00 0.00 0.98
727 786 8.407832 TGTACTAAAGCAGCGACAAGTAATATA 58.592 33.333 0.00 0.00 0.00 0.86
728 787 7.262772 TGTACTAAAGCAGCGACAAGTAATAT 58.737 34.615 0.00 0.00 0.00 1.28
730 789 5.475719 TGTACTAAAGCAGCGACAAGTAAT 58.524 37.500 0.00 0.00 0.00 1.89
732 791 4.508461 TGTACTAAAGCAGCGACAAGTA 57.492 40.909 0.00 0.00 0.00 2.24
733 792 3.380479 TGTACTAAAGCAGCGACAAGT 57.620 42.857 0.00 0.00 0.00 3.16
734 793 5.103000 ACTATGTACTAAAGCAGCGACAAG 58.897 41.667 0.00 0.00 29.74 3.16
735 794 5.068234 ACTATGTACTAAAGCAGCGACAA 57.932 39.130 0.00 0.00 29.74 3.18
736 795 4.713824 ACTATGTACTAAAGCAGCGACA 57.286 40.909 0.00 0.00 0.00 4.35
738 797 6.688637 TTCTACTATGTACTAAAGCAGCGA 57.311 37.500 0.00 0.00 0.00 4.93
739 798 6.918569 ACATTCTACTATGTACTAAAGCAGCG 59.081 38.462 0.00 0.00 36.99 5.18
740 799 7.921214 TGACATTCTACTATGTACTAAAGCAGC 59.079 37.037 0.00 0.00 38.80 5.25
741 800 9.973450 ATGACATTCTACTATGTACTAAAGCAG 57.027 33.333 0.00 0.00 38.80 4.24
742 801 9.750125 CATGACATTCTACTATGTACTAAAGCA 57.250 33.333 0.00 0.00 38.80 3.91
743 802 9.197694 CCATGACATTCTACTATGTACTAAAGC 57.802 37.037 0.00 0.00 38.80 3.51
747 806 7.521585 CGTGCCATGACATTCTACTATGTACTA 60.522 40.741 0.00 0.00 38.80 1.82
750 809 5.068591 ACGTGCCATGACATTCTACTATGTA 59.931 40.000 0.00 0.00 38.80 2.29
752 811 4.209911 CACGTGCCATGACATTCTACTATG 59.790 45.833 0.82 0.00 0.00 2.23
753 812 4.099419 TCACGTGCCATGACATTCTACTAT 59.901 41.667 11.67 0.00 0.00 2.12
754 813 3.445805 TCACGTGCCATGACATTCTACTA 59.554 43.478 11.67 0.00 0.00 1.82
755 814 2.233676 TCACGTGCCATGACATTCTACT 59.766 45.455 11.67 0.00 0.00 2.57
756 815 2.348666 GTCACGTGCCATGACATTCTAC 59.651 50.000 11.67 0.00 44.87 2.59
757 816 2.616960 GTCACGTGCCATGACATTCTA 58.383 47.619 11.67 0.00 44.87 2.10
758 817 1.442769 GTCACGTGCCATGACATTCT 58.557 50.000 11.67 0.00 44.87 2.40
759 818 3.975992 GTCACGTGCCATGACATTC 57.024 52.632 11.67 0.00 44.87 2.67
763 822 1.002366 GAGATGTCACGTGCCATGAC 58.998 55.000 17.99 7.11 45.58 3.06
764 823 0.607620 TGAGATGTCACGTGCCATGA 59.392 50.000 17.99 0.00 0.00 3.07
765 824 1.441738 TTGAGATGTCACGTGCCATG 58.558 50.000 17.99 0.00 30.10 3.66
766 825 2.408271 ATTGAGATGTCACGTGCCAT 57.592 45.000 12.59 12.59 30.10 4.40
767 826 2.076100 GAATTGAGATGTCACGTGCCA 58.924 47.619 11.67 6.09 30.10 4.92
768 827 2.094894 CAGAATTGAGATGTCACGTGCC 59.905 50.000 11.67 0.00 30.10 5.01
769 828 2.475187 GCAGAATTGAGATGTCACGTGC 60.475 50.000 11.67 6.86 30.10 5.34
770 829 2.222663 CGCAGAATTGAGATGTCACGTG 60.223 50.000 9.94 9.94 30.10 4.49
771 830 1.995484 CGCAGAATTGAGATGTCACGT 59.005 47.619 0.00 0.00 30.10 4.49
772 831 1.995484 ACGCAGAATTGAGATGTCACG 59.005 47.619 0.00 0.00 30.10 4.35
773 832 4.410492 AAACGCAGAATTGAGATGTCAC 57.590 40.909 0.00 0.00 30.10 3.67
774 833 5.437289 AAAAACGCAGAATTGAGATGTCA 57.563 34.783 0.00 0.00 0.00 3.58
775 834 4.853743 GGAAAAACGCAGAATTGAGATGTC 59.146 41.667 0.00 0.00 0.00 3.06
776 835 4.520492 AGGAAAAACGCAGAATTGAGATGT 59.480 37.500 0.00 0.00 0.00 3.06
777 836 5.051891 AGGAAAAACGCAGAATTGAGATG 57.948 39.130 0.00 0.00 0.00 2.90
778 837 7.396540 AATAGGAAAAACGCAGAATTGAGAT 57.603 32.000 0.00 0.00 0.00 2.75
779 838 6.817765 AATAGGAAAAACGCAGAATTGAGA 57.182 33.333 0.00 0.00 0.00 3.27
780 839 7.308435 AGAAATAGGAAAAACGCAGAATTGAG 58.692 34.615 0.00 0.00 0.00 3.02
781 840 7.214467 AGAAATAGGAAAAACGCAGAATTGA 57.786 32.000 0.00 0.00 0.00 2.57
782 841 9.013490 CATAGAAATAGGAAAAACGCAGAATTG 57.987 33.333 0.00 0.00 0.00 2.32
783 842 8.190784 CCATAGAAATAGGAAAAACGCAGAATT 58.809 33.333 0.00 0.00 0.00 2.17
784 843 7.339466 ACCATAGAAATAGGAAAAACGCAGAAT 59.661 33.333 0.00 0.00 0.00 2.40
785 844 6.657541 ACCATAGAAATAGGAAAAACGCAGAA 59.342 34.615 0.00 0.00 0.00 3.02
786 845 6.177610 ACCATAGAAATAGGAAAAACGCAGA 58.822 36.000 0.00 0.00 0.00 4.26
787 846 6.436843 ACCATAGAAATAGGAAAAACGCAG 57.563 37.500 0.00 0.00 0.00 5.18
788 847 6.827586 AACCATAGAAATAGGAAAAACGCA 57.172 33.333 0.00 0.00 0.00 5.24
809 868 8.914011 AGCCTCTTGGGTTATCAAAATATAAAC 58.086 33.333 0.00 0.00 42.12 2.01
819 879 1.281867 CACCAGCCTCTTGGGTTATCA 59.718 52.381 0.00 0.00 43.07 2.15
820 880 1.282157 ACACCAGCCTCTTGGGTTATC 59.718 52.381 0.00 0.00 43.07 1.75
822 882 2.032965 TACACCAGCCTCTTGGGTTA 57.967 50.000 0.00 0.00 43.07 2.85
850 910 7.966204 GTCAAAGCAGTACAAAGAACACTAAAA 59.034 33.333 0.00 0.00 0.00 1.52
860 920 3.802139 TCGTCTGTCAAAGCAGTACAAAG 59.198 43.478 0.00 0.00 37.70 2.77
871 931 3.181490 CGACCTATCCATCGTCTGTCAAA 60.181 47.826 0.00 0.00 33.63 2.69
880 940 4.579454 TTTACTTCCGACCTATCCATCG 57.421 45.455 0.00 0.00 38.08 3.84
890 950 9.815936 TTTCTTTCGATTTATTTTACTTCCGAC 57.184 29.630 0.00 0.00 0.00 4.79
903 964 7.066887 TGCTGGATATGCTTTTCTTTCGATTTA 59.933 33.333 0.00 0.00 0.00 1.40
913 974 6.874288 AGAATACTGCTGGATATGCTTTTC 57.126 37.500 0.00 0.00 0.00 2.29
919 980 8.442632 TGAGAAAAAGAATACTGCTGGATATG 57.557 34.615 0.00 0.00 0.00 1.78
920 981 9.466497 TTTGAGAAAAAGAATACTGCTGGATAT 57.534 29.630 0.00 0.00 0.00 1.63
921 982 8.862325 TTTGAGAAAAAGAATACTGCTGGATA 57.138 30.769 0.00 0.00 0.00 2.59
922 983 7.765695 TTTGAGAAAAAGAATACTGCTGGAT 57.234 32.000 0.00 0.00 0.00 3.41
923 984 7.502226 TCTTTTGAGAAAAAGAATACTGCTGGA 59.498 33.333 10.40 0.00 43.49 3.86
924 985 7.651808 TCTTTTGAGAAAAAGAATACTGCTGG 58.348 34.615 10.40 0.00 43.49 4.85
959 1020 2.907696 TCCCCTCTCACCGTTGAATTTA 59.092 45.455 0.00 0.00 0.00 1.40
1489 1626 1.681486 CCCGCTCTTCCTCCTCCTTC 61.681 65.000 0.00 0.00 0.00 3.46
1535 1672 2.657237 CGTCTTCTGCTCCCCGTT 59.343 61.111 0.00 0.00 0.00 4.44
1612 1749 1.579626 GTCGAAGTACTCCGACGCG 60.580 63.158 19.03 3.53 44.23 6.01
1675 1812 1.324005 GGTCGACCTCTCCTTCCCAG 61.324 65.000 27.64 0.00 0.00 4.45
1800 1937 3.447586 GCAGTAGACACTAGGAATGGACA 59.552 47.826 0.00 0.00 32.21 4.02
1822 1959 3.897239 TCCCCAATGGTTTACAGCTATG 58.103 45.455 0.00 0.00 34.77 2.23
1859 1996 0.259938 AGCTCATTGGATTCACCCCC 59.740 55.000 0.00 0.00 38.00 5.40
1889 2026 2.019984 GCCAATCTAAAGGACAGCCAG 58.980 52.381 0.00 0.00 36.29 4.85
1896 2033 5.044476 TGGATACCAAAGCCAATCTAAAGGA 60.044 40.000 0.00 0.00 0.00 3.36
1903 2040 4.889409 TGAATCTGGATACCAAAGCCAATC 59.111 41.667 0.00 0.00 30.80 2.67
1929 2066 4.713553 TCTCTGAGGCAACACAAAACATA 58.286 39.130 4.59 0.00 36.48 2.29
1963 2100 8.528643 ACACTACATCTGTAAACAGTGCTAATA 58.471 33.333 9.81 0.00 44.12 0.98
2052 2192 9.708092 GATCTTTTGTATCCCAGTATACCTTAC 57.292 37.037 0.00 0.00 32.36 2.34
2112 2252 6.132791 TGTCAGAGTTAAGCGGATAGTAAG 57.867 41.667 0.00 0.00 0.00 2.34
2123 2263 4.629200 GCAGAGAACCATGTCAGAGTTAAG 59.371 45.833 0.00 0.00 0.00 1.85
2135 2275 6.378280 CCCTTGTTAAATTAGCAGAGAACCAT 59.622 38.462 0.00 0.00 0.00 3.55
2138 2278 5.416013 AGCCCTTGTTAAATTAGCAGAGAAC 59.584 40.000 0.00 0.00 0.00 3.01
2222 2363 4.503741 TTCTTTTGCTTGGAGTGCATAC 57.496 40.909 0.00 0.00 40.34 2.39
2249 2390 4.356405 TCCTCTCAAGAACAGCAATTGA 57.644 40.909 10.34 0.00 0.00 2.57
2276 2417 9.752961 GACTAACCTTTTTCTCTGTATAGGATC 57.247 37.037 0.00 0.00 0.00 3.36
2344 2485 7.001674 TCACCTTTAGCCTCTCAAACAATAAA 58.998 34.615 0.00 0.00 0.00 1.40
2355 2496 5.763876 ACTAATTGTCACCTTTAGCCTCT 57.236 39.130 0.00 0.00 0.00 3.69
2358 2499 5.742063 ACCTACTAATTGTCACCTTTAGCC 58.258 41.667 0.00 0.00 0.00 3.93
2375 2516 3.369157 GGGTAAAAGATGTGCGACCTACT 60.369 47.826 0.00 0.00 0.00 2.57
2381 2522 2.301870 AGAGTGGGTAAAAGATGTGCGA 59.698 45.455 0.00 0.00 0.00 5.10
2382 2523 2.416547 CAGAGTGGGTAAAAGATGTGCG 59.583 50.000 0.00 0.00 0.00 5.34
2384 2525 4.641396 TGTCAGAGTGGGTAAAAGATGTG 58.359 43.478 0.00 0.00 0.00 3.21
2396 2563 6.041409 ACCATAATCAGATACTGTCAGAGTGG 59.959 42.308 6.91 2.43 35.96 4.00
2406 2573 4.524714 CCGTGGAGACCATAATCAGATACT 59.475 45.833 0.00 0.00 35.28 2.12
2424 2591 8.141909 TCTTATCTCTGTAAATACAATCCGTGG 58.858 37.037 0.00 0.00 35.50 4.94
2427 2594 9.529325 TGTTCTTATCTCTGTAAATACAATCCG 57.471 33.333 0.00 0.00 35.50 4.18
2597 2811 1.110442 CCAGTTTCAACAGGCAACCA 58.890 50.000 0.00 0.00 37.17 3.67
2622 2837 4.391216 CAGAGAACAATAACCAGCACTCTG 59.609 45.833 0.00 0.00 42.10 3.35
2732 2950 8.893219 TCTTTCGCATCTTATTCAGATACATT 57.107 30.769 0.00 0.00 40.67 2.71
2735 2953 7.115663 GTCCTCTTTCGCATCTTATTCAGATAC 59.884 40.741 0.00 0.00 40.67 2.24
2738 2956 5.105351 TGTCCTCTTTCGCATCTTATTCAGA 60.105 40.000 0.00 0.00 35.33 3.27
2742 2960 7.396540 AAAATGTCCTCTTTCGCATCTTATT 57.603 32.000 0.00 0.00 0.00 1.40
2763 2981 5.656416 CCTTTCCACTATAGGCATCCAAAAA 59.344 40.000 4.43 0.00 0.00 1.94
2811 3029 0.467290 TCCTTGCTTGACACAACCCC 60.467 55.000 0.00 0.00 0.00 4.95
2858 3076 6.560253 ACACTACAAAAGACTGCCTTAATG 57.440 37.500 0.00 0.00 34.00 1.90
2862 3080 7.582667 AAATTACACTACAAAAGACTGCCTT 57.417 32.000 0.00 0.00 36.47 4.35
2919 3138 6.706716 TCCTATCTAGAACATCAGTACGACAG 59.293 42.308 0.00 0.00 0.00 3.51
2920 3139 6.482641 GTCCTATCTAGAACATCAGTACGACA 59.517 42.308 0.00 0.00 0.00 4.35
2921 3140 6.073112 GGTCCTATCTAGAACATCAGTACGAC 60.073 46.154 0.00 0.00 0.00 4.34
2922 3141 5.996513 GGTCCTATCTAGAACATCAGTACGA 59.003 44.000 0.00 0.00 0.00 3.43
2923 3142 5.763698 TGGTCCTATCTAGAACATCAGTACG 59.236 44.000 0.00 0.00 0.00 3.67
2924 3143 6.773685 ACTGGTCCTATCTAGAACATCAGTAC 59.226 42.308 0.00 0.00 28.68 2.73
2925 3144 6.773200 CACTGGTCCTATCTAGAACATCAGTA 59.227 42.308 0.00 0.00 28.68 2.74
2926 3145 5.596361 CACTGGTCCTATCTAGAACATCAGT 59.404 44.000 0.00 4.01 28.68 3.41
2927 3146 5.010516 CCACTGGTCCTATCTAGAACATCAG 59.989 48.000 0.00 3.39 28.68 2.90
2971 3190 4.776795 AAAACGTAGCTAACCCCAAATG 57.223 40.909 0.00 0.00 0.00 2.32
3107 3355 3.229276 AGAAGATGAAGCTGTCACTCG 57.771 47.619 0.00 0.00 39.72 4.18
3176 3427 7.529880 AAATCCGAACGTTTGGTAGTTATAG 57.470 36.000 29.59 5.52 33.22 1.31
3390 3642 2.180769 GGTTTTCAATCGGGGCGC 59.819 61.111 0.00 0.00 0.00 6.53
3435 3688 6.553100 AGATGGGATCTAGTTTCGAAGATCTT 59.447 38.462 19.29 7.95 44.94 2.40
3497 3754 2.890474 CACGTAGCCCGGATGTGC 60.890 66.667 0.73 0.00 42.24 4.57
3717 3977 9.901724 CTCATATACAAATATCGCGGTAATTTC 57.098 33.333 1.77 0.00 0.00 2.17
3753 4013 6.602803 ACAACATGATAATACAGGCACATGAA 59.397 34.615 0.00 0.00 38.55 2.57
3912 4176 3.716431 ACTCCCGGTCCTGATAACTTAA 58.284 45.455 0.00 0.00 0.00 1.85
3982 4246 6.956047 ACTTTGATCCGTGAAGAAAAGTTAC 58.044 36.000 0.00 0.00 35.00 2.50
3986 4251 6.955963 CGATAACTTTGATCCGTGAAGAAAAG 59.044 38.462 0.00 0.00 0.00 2.27
3991 4256 4.032900 CCACGATAACTTTGATCCGTGAAG 59.967 45.833 15.43 6.19 33.52 3.02
3999 4264 6.072893 GGTACAAACACCACGATAACTTTGAT 60.073 38.462 0.00 0.00 38.55 2.57
4055 4322 9.508642 TCCAGTAACATTTGTGTCAATAACATA 57.491 29.630 0.00 0.00 40.80 2.29


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

AutoCloner maintained by Alex Coulton.