Multiple sequence alignment - TraesCS4A01G086200

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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 TraesCS4A01G086200 chr4A 100.000 3709 0 0 1 3709 90438116 90441824 0.000000e+00 6850.0
1 TraesCS4A01G086200 chr4A 84.470 2009 211 45 876 2830 478190956 478192917 0.000000e+00 1888.0
2 TraesCS4A01G086200 chr4A 92.316 885 58 9 2827 3709 556922143 556921267 0.000000e+00 1249.0
3 TraesCS4A01G086200 chr4A 77.764 1610 295 36 1158 2736 36607969 36606392 0.000000e+00 931.0
4 TraesCS4A01G086200 chr4B 91.125 1938 144 16 903 2830 460157061 460155142 0.000000e+00 2601.0
5 TraesCS4A01G086200 chr4B 85.081 1917 219 30 874 2742 139594124 139592227 0.000000e+00 1893.0
6 TraesCS4A01G086200 chr4B 78.593 1649 291 41 1115 2736 535331732 535330119 0.000000e+00 1033.0
7 TraesCS4A01G086200 chr4B 98.214 56 1 0 840 895 460157402 460157347 8.480000e-17 99.0
8 TraesCS4A01G086200 chr4D 85.513 1912 215 30 874 2742 98015885 98013993 0.000000e+00 1940.0
9 TraesCS4A01G086200 chr4D 93.297 1268 68 5 1549 2813 374041175 374039922 0.000000e+00 1855.0
10 TraesCS4A01G086200 chr4D 78.911 1598 279 38 1165 2736 435198935 435197370 0.000000e+00 1031.0
11 TraesCS4A01G086200 chr4D 89.450 673 59 7 898 1558 374049670 374048998 0.000000e+00 839.0
12 TraesCS4A01G086200 chr4D 76.842 1425 254 44 1117 2497 505358918 505357526 0.000000e+00 734.0
13 TraesCS4A01G086200 chr4D 95.283 106 3 1 2684 2787 374039922 374039817 2.290000e-37 167.0
14 TraesCS4A01G086200 chr7A 93.115 886 51 9 2827 3707 31867330 31868210 0.000000e+00 1290.0
15 TraesCS4A01G086200 chr7A 92.421 884 56 8 2828 3709 639642874 639643748 0.000000e+00 1251.0
16 TraesCS4A01G086200 chr7A 83.492 315 42 6 31 345 123238947 123238643 6.060000e-73 285.0
17 TraesCS4A01G086200 chr3A 92.768 885 55 8 2829 3709 173975953 173976832 0.000000e+00 1271.0
18 TraesCS4A01G086200 chr3A 92.525 883 54 11 2831 3709 619547028 619546154 0.000000e+00 1254.0
19 TraesCS4A01G086200 chr3A 92.308 884 57 8 2828 3709 490178928 490178054 0.000000e+00 1245.0
20 TraesCS4A01G086200 chr3A 79.773 1320 209 34 1434 2723 149716588 149715297 0.000000e+00 905.0
21 TraesCS4A01G086200 chr2A 92.325 886 59 9 2828 3709 371984594 371985474 0.000000e+00 1251.0
22 TraesCS4A01G086200 chr5A 92.212 886 57 10 2829 3709 447494633 447493755 0.000000e+00 1243.0
23 TraesCS4A01G086200 chr5A 92.072 883 65 4 2828 3709 409300933 409300055 0.000000e+00 1238.0
24 TraesCS4A01G086200 chr3B 79.887 1417 240 24 1142 2525 706028910 706027506 0.000000e+00 996.0
25 TraesCS4A01G086200 chr3B 78.121 1426 232 42 1146 2512 706754685 706756089 0.000000e+00 832.0
26 TraesCS4A01G086200 chr3D 79.619 1418 239 23 1142 2525 533960108 533958707 0.000000e+00 972.0
27 TraesCS4A01G086200 chr3D 78.279 1418 242 34 1146 2513 535399957 535401358 0.000000e+00 852.0
28 TraesCS4A01G086200 chr3D 89.118 680 66 7 28 704 496064472 496063798 0.000000e+00 839.0
29 TraesCS4A01G086200 chr3D 89.019 683 61 10 27 704 68435623 68434950 0.000000e+00 833.0
30 TraesCS4A01G086200 chr6D 90.290 690 60 5 28 711 163341832 163341144 0.000000e+00 896.0
31 TraesCS4A01G086200 chr6D 88.856 682 66 8 28 704 377817522 377816846 0.000000e+00 830.0
32 TraesCS4A01G086200 chr6D 79.765 425 74 4 2300 2723 61004179 61004592 7.790000e-77 298.0
33 TraesCS4A01G086200 chr1D 90.588 680 58 6 28 704 442054650 442055326 0.000000e+00 896.0
34 TraesCS4A01G086200 chr1D 89.412 680 66 6 30 706 332942653 332941977 0.000000e+00 852.0
35 TraesCS4A01G086200 chr1D 84.088 685 93 13 31 704 30589288 30589967 0.000000e+00 647.0
36 TraesCS4A01G086200 chr5D 89.665 687 63 4 28 706 104149574 104148888 0.000000e+00 869.0
37 TraesCS4A01G086200 chr5D 82.653 686 92 19 32 707 444854125 444853457 1.920000e-162 582.0
38 TraesCS4A01G086200 chr7D 88.842 708 66 8 1 704 140764362 140765060 0.000000e+00 857.0
39 TraesCS4A01G086200 chr7D 77.848 1422 263 33 1115 2499 63462315 63463721 0.000000e+00 833.0
40 TraesCS4A01G086200 chr2D 87.712 708 78 7 1 704 43753606 43754308 0.000000e+00 817.0
41 TraesCS4A01G086200 chr1A 76.955 1189 213 37 1376 2512 463219047 463220226 4.070000e-174 621.0
42 TraesCS4A01G086200 chrUn 82.301 678 93 22 40 707 31231113 31230453 2.500000e-156 562.0
43 TraesCS4A01G086200 chrUn 79.680 438 56 23 1 420 460715086 460715508 6.060000e-73 285.0
44 TraesCS4A01G086200 chr2B 100.000 34 0 0 1 34 87541460 87541493 3.090000e-06 63.9


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 TraesCS4A01G086200 chr4A 90438116 90441824 3708 False 6850 6850 100.0000 1 3709 1 chr4A.!!$F1 3708
1 TraesCS4A01G086200 chr4A 478190956 478192917 1961 False 1888 1888 84.4700 876 2830 1 chr4A.!!$F2 1954
2 TraesCS4A01G086200 chr4A 556921267 556922143 876 True 1249 1249 92.3160 2827 3709 1 chr4A.!!$R2 882
3 TraesCS4A01G086200 chr4A 36606392 36607969 1577 True 931 931 77.7640 1158 2736 1 chr4A.!!$R1 1578
4 TraesCS4A01G086200 chr4B 139592227 139594124 1897 True 1893 1893 85.0810 874 2742 1 chr4B.!!$R1 1868
5 TraesCS4A01G086200 chr4B 460155142 460157402 2260 True 1350 2601 94.6695 840 2830 2 chr4B.!!$R3 1990
6 TraesCS4A01G086200 chr4B 535330119 535331732 1613 True 1033 1033 78.5930 1115 2736 1 chr4B.!!$R2 1621
7 TraesCS4A01G086200 chr4D 98013993 98015885 1892 True 1940 1940 85.5130 874 2742 1 chr4D.!!$R1 1868
8 TraesCS4A01G086200 chr4D 435197370 435198935 1565 True 1031 1031 78.9110 1165 2736 1 chr4D.!!$R3 1571
9 TraesCS4A01G086200 chr4D 374039817 374041175 1358 True 1011 1855 94.2900 1549 2813 2 chr4D.!!$R5 1264
10 TraesCS4A01G086200 chr4D 374048998 374049670 672 True 839 839 89.4500 898 1558 1 chr4D.!!$R2 660
11 TraesCS4A01G086200 chr4D 505357526 505358918 1392 True 734 734 76.8420 1117 2497 1 chr4D.!!$R4 1380
12 TraesCS4A01G086200 chr7A 31867330 31868210 880 False 1290 1290 93.1150 2827 3707 1 chr7A.!!$F1 880
13 TraesCS4A01G086200 chr7A 639642874 639643748 874 False 1251 1251 92.4210 2828 3709 1 chr7A.!!$F2 881
14 TraesCS4A01G086200 chr3A 173975953 173976832 879 False 1271 1271 92.7680 2829 3709 1 chr3A.!!$F1 880
15 TraesCS4A01G086200 chr3A 619546154 619547028 874 True 1254 1254 92.5250 2831 3709 1 chr3A.!!$R3 878
16 TraesCS4A01G086200 chr3A 490178054 490178928 874 True 1245 1245 92.3080 2828 3709 1 chr3A.!!$R2 881
17 TraesCS4A01G086200 chr3A 149715297 149716588 1291 True 905 905 79.7730 1434 2723 1 chr3A.!!$R1 1289
18 TraesCS4A01G086200 chr2A 371984594 371985474 880 False 1251 1251 92.3250 2828 3709 1 chr2A.!!$F1 881
19 TraesCS4A01G086200 chr5A 447493755 447494633 878 True 1243 1243 92.2120 2829 3709 1 chr5A.!!$R2 880
20 TraesCS4A01G086200 chr5A 409300055 409300933 878 True 1238 1238 92.0720 2828 3709 1 chr5A.!!$R1 881
21 TraesCS4A01G086200 chr3B 706027506 706028910 1404 True 996 996 79.8870 1142 2525 1 chr3B.!!$R1 1383
22 TraesCS4A01G086200 chr3B 706754685 706756089 1404 False 832 832 78.1210 1146 2512 1 chr3B.!!$F1 1366
23 TraesCS4A01G086200 chr3D 533958707 533960108 1401 True 972 972 79.6190 1142 2525 1 chr3D.!!$R3 1383
24 TraesCS4A01G086200 chr3D 535399957 535401358 1401 False 852 852 78.2790 1146 2513 1 chr3D.!!$F1 1367
25 TraesCS4A01G086200 chr3D 496063798 496064472 674 True 839 839 89.1180 28 704 1 chr3D.!!$R2 676
26 TraesCS4A01G086200 chr3D 68434950 68435623 673 True 833 833 89.0190 27 704 1 chr3D.!!$R1 677
27 TraesCS4A01G086200 chr6D 163341144 163341832 688 True 896 896 90.2900 28 711 1 chr6D.!!$R1 683
28 TraesCS4A01G086200 chr6D 377816846 377817522 676 True 830 830 88.8560 28 704 1 chr6D.!!$R2 676
29 TraesCS4A01G086200 chr1D 442054650 442055326 676 False 896 896 90.5880 28 704 1 chr1D.!!$F2 676
30 TraesCS4A01G086200 chr1D 332941977 332942653 676 True 852 852 89.4120 30 706 1 chr1D.!!$R1 676
31 TraesCS4A01G086200 chr1D 30589288 30589967 679 False 647 647 84.0880 31 704 1 chr1D.!!$F1 673
32 TraesCS4A01G086200 chr5D 104148888 104149574 686 True 869 869 89.6650 28 706 1 chr5D.!!$R1 678
33 TraesCS4A01G086200 chr5D 444853457 444854125 668 True 582 582 82.6530 32 707 1 chr5D.!!$R2 675
34 TraesCS4A01G086200 chr7D 140764362 140765060 698 False 857 857 88.8420 1 704 1 chr7D.!!$F2 703
35 TraesCS4A01G086200 chr7D 63462315 63463721 1406 False 833 833 77.8480 1115 2499 1 chr7D.!!$F1 1384
36 TraesCS4A01G086200 chr2D 43753606 43754308 702 False 817 817 87.7120 1 704 1 chr2D.!!$F1 703
37 TraesCS4A01G086200 chr1A 463219047 463220226 1179 False 621 621 76.9550 1376 2512 1 chr1A.!!$F1 1136
38 TraesCS4A01G086200 chrUn 31230453 31231113 660 True 562 562 82.3010 40 707 1 chrUn.!!$R1 667

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
783 813 0.172578 ATCGACGATCTTTGTGCGGA 59.827 50.0 4.05 0.0 0.00 5.54 F
1718 2081 0.098905 GCTCGAGACGCTATGTGTCA 59.901 55.0 18.75 0.0 44.42 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2518 3052 0.250467 AGAGGCAGCGTCAAACACAT 60.250 50.0 17.21 0.0 0.00 3.21 R
3516 4066 0.178912 AGAGGGGTGTTACCGGAACT 60.179 55.0 9.46 0.0 39.83 3.01 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
68 72 9.312904 AGGAAATTATGGAAAAAGAACTCATCA 57.687 29.630 0.00 0.00 0.00 3.07
86 90 5.941733 TCATCAATGAAGTCCATTTTCGTG 58.058 37.500 0.00 0.00 42.55 4.35
114 118 3.036084 CCGTCGAACAGCTTGCGT 61.036 61.111 0.00 0.00 0.00 5.24
341 352 4.770362 TGATGGAGGGGGCGACGA 62.770 66.667 0.00 0.00 0.00 4.20
351 364 2.750637 GGCGACGAGGGAGTGAGA 60.751 66.667 0.00 0.00 0.00 3.27
364 377 1.484240 GAGTGAGAGGCATTGCTAGGT 59.516 52.381 8.82 0.00 0.00 3.08
406 420 2.863153 CAGAGTCGCCGGCAAAAG 59.137 61.111 28.98 10.38 0.00 2.27
585 613 3.782443 GGTCGGGAATGGGTCGCT 61.782 66.667 0.00 0.00 37.05 4.93
596 624 2.278013 GGTCGCTCGCGGACTAAG 60.278 66.667 6.13 0.00 40.25 2.18
606 634 1.880894 CGGACTAAGAGCGGACACA 59.119 57.895 0.00 0.00 0.00 3.72
645 674 1.676006 CGTTGGGCTGACTTTTCTGTT 59.324 47.619 0.00 0.00 0.00 3.16
649 678 0.944386 GGCTGACTTTTCTGTTCGCA 59.056 50.000 0.00 0.00 0.00 5.10
651 680 1.599542 GCTGACTTTTCTGTTCGCACT 59.400 47.619 0.00 0.00 0.00 4.40
707 737 2.025887 CCCCATTGGAGTTGCTCTTAGT 60.026 50.000 3.62 0.00 35.39 2.24
708 738 3.199946 CCCCATTGGAGTTGCTCTTAGTA 59.800 47.826 3.62 0.00 35.39 1.82
710 740 5.440610 CCCATTGGAGTTGCTCTTAGTATT 58.559 41.667 3.62 0.00 0.00 1.89
711 741 5.529060 CCCATTGGAGTTGCTCTTAGTATTC 59.471 44.000 3.62 0.00 0.00 1.75
712 742 6.115446 CCATTGGAGTTGCTCTTAGTATTCA 58.885 40.000 0.00 0.00 0.00 2.57
713 743 6.769822 CCATTGGAGTTGCTCTTAGTATTCAT 59.230 38.462 0.00 0.00 0.00 2.57
714 744 7.255035 CCATTGGAGTTGCTCTTAGTATTCATG 60.255 40.741 0.00 0.00 0.00 3.07
715 745 6.299805 TGGAGTTGCTCTTAGTATTCATGT 57.700 37.500 0.00 0.00 0.00 3.21
716 746 6.711277 TGGAGTTGCTCTTAGTATTCATGTT 58.289 36.000 0.00 0.00 0.00 2.71
717 747 7.847096 TGGAGTTGCTCTTAGTATTCATGTTA 58.153 34.615 0.00 0.00 0.00 2.41
718 748 8.318412 TGGAGTTGCTCTTAGTATTCATGTTAA 58.682 33.333 0.00 0.00 0.00 2.01
719 749 8.821894 GGAGTTGCTCTTAGTATTCATGTTAAG 58.178 37.037 0.00 0.00 0.00 1.85
720 750 9.372369 GAGTTGCTCTTAGTATTCATGTTAAGT 57.628 33.333 0.00 0.00 0.00 2.24
721 751 9.155975 AGTTGCTCTTAGTATTCATGTTAAGTG 57.844 33.333 0.00 0.00 0.00 3.16
722 752 8.936864 GTTGCTCTTAGTATTCATGTTAAGTGT 58.063 33.333 0.00 0.00 0.00 3.55
747 777 4.981806 TTTTAACATCTGGGCTGCATAC 57.018 40.909 0.50 0.00 0.00 2.39
748 778 2.638480 TAACATCTGGGCTGCATACC 57.362 50.000 0.50 0.00 0.00 2.73
755 785 3.996614 GGCTGCATACCCACGTTT 58.003 55.556 0.50 0.00 0.00 3.60
756 786 3.162448 GGCTGCATACCCACGTTTA 57.838 52.632 0.50 0.00 0.00 2.01
757 787 1.455248 GGCTGCATACCCACGTTTAA 58.545 50.000 0.50 0.00 0.00 1.52
758 788 1.813786 GGCTGCATACCCACGTTTAAA 59.186 47.619 0.50 0.00 0.00 1.52
759 789 2.229302 GGCTGCATACCCACGTTTAAAA 59.771 45.455 0.50 0.00 0.00 1.52
760 790 3.119280 GGCTGCATACCCACGTTTAAAAT 60.119 43.478 0.50 0.00 0.00 1.82
761 791 4.490743 GCTGCATACCCACGTTTAAAATT 58.509 39.130 0.00 0.00 0.00 1.82
762 792 5.393243 GGCTGCATACCCACGTTTAAAATTA 60.393 40.000 0.50 0.00 0.00 1.40
763 793 5.513849 GCTGCATACCCACGTTTAAAATTAC 59.486 40.000 0.00 0.00 0.00 1.89
764 794 6.570672 TGCATACCCACGTTTAAAATTACA 57.429 33.333 0.00 0.00 0.00 2.41
765 795 7.159322 TGCATACCCACGTTTAAAATTACAT 57.841 32.000 0.00 0.00 0.00 2.29
766 796 7.251994 TGCATACCCACGTTTAAAATTACATC 58.748 34.615 0.00 0.00 0.00 3.06
767 797 6.412653 GCATACCCACGTTTAAAATTACATCG 59.587 38.462 0.00 0.00 0.00 3.84
768 798 7.676807 GCATACCCACGTTTAAAATTACATCGA 60.677 37.037 0.00 0.00 0.00 3.59
769 799 5.930405 ACCCACGTTTAAAATTACATCGAC 58.070 37.500 0.00 0.00 0.00 4.20
770 800 5.016985 CCCACGTTTAAAATTACATCGACG 58.983 41.667 0.00 0.00 35.59 5.12
771 801 5.163972 CCCACGTTTAAAATTACATCGACGA 60.164 40.000 0.00 0.00 33.86 4.20
772 802 6.455913 CCCACGTTTAAAATTACATCGACGAT 60.456 38.462 4.05 4.05 33.86 3.73
773 803 6.622183 CCACGTTTAAAATTACATCGACGATC 59.378 38.462 7.54 0.00 33.86 3.69
774 804 7.388712 CACGTTTAAAATTACATCGACGATCT 58.611 34.615 7.54 0.00 33.86 2.75
775 805 7.896274 CACGTTTAAAATTACATCGACGATCTT 59.104 33.333 7.54 0.34 33.86 2.40
776 806 8.437742 ACGTTTAAAATTACATCGACGATCTTT 58.562 29.630 7.54 5.68 33.86 2.52
777 807 8.712609 CGTTTAAAATTACATCGACGATCTTTG 58.287 33.333 7.54 0.50 0.00 2.77
778 808 9.537848 GTTTAAAATTACATCGACGATCTTTGT 57.462 29.630 7.54 7.22 0.00 2.83
779 809 9.536558 TTTAAAATTACATCGACGATCTTTGTG 57.463 29.630 7.54 0.00 0.00 3.33
780 810 4.778842 ATTACATCGACGATCTTTGTGC 57.221 40.909 7.54 0.00 0.00 4.57
781 811 0.992072 ACATCGACGATCTTTGTGCG 59.008 50.000 7.54 0.00 0.00 5.34
782 812 0.298707 CATCGACGATCTTTGTGCGG 59.701 55.000 7.54 0.00 0.00 5.69
783 813 0.172578 ATCGACGATCTTTGTGCGGA 59.827 50.000 4.05 0.00 0.00 5.54
784 814 0.172578 TCGACGATCTTTGTGCGGAT 59.827 50.000 0.00 0.00 0.00 4.18
785 815 1.402613 TCGACGATCTTTGTGCGGATA 59.597 47.619 0.00 0.00 0.00 2.59
786 816 1.781429 CGACGATCTTTGTGCGGATAG 59.219 52.381 0.00 0.00 0.00 2.08
787 817 2.128035 GACGATCTTTGTGCGGATAGG 58.872 52.381 0.00 0.00 0.00 2.57
788 818 1.754803 ACGATCTTTGTGCGGATAGGA 59.245 47.619 0.00 0.00 0.00 2.94
789 819 2.128035 CGATCTTTGTGCGGATAGGAC 58.872 52.381 0.00 0.00 41.99 3.85
793 823 3.706855 TGTGCGGATAGGACAGCA 58.293 55.556 0.00 0.00 46.44 4.41
794 824 1.517361 TGTGCGGATAGGACAGCAG 59.483 57.895 0.00 0.00 46.44 4.24
795 825 0.970427 TGTGCGGATAGGACAGCAGA 60.970 55.000 0.00 0.00 46.44 4.26
796 826 0.249238 GTGCGGATAGGACAGCAGAG 60.249 60.000 0.00 0.00 40.97 3.35
797 827 1.365633 GCGGATAGGACAGCAGAGG 59.634 63.158 0.00 0.00 0.00 3.69
798 828 1.365633 CGGATAGGACAGCAGAGGC 59.634 63.158 0.00 0.00 41.61 4.70
816 846 3.902086 GGGCGCGTCCTCTAGGTC 61.902 72.222 25.46 0.00 36.34 3.85
817 847 2.829458 GGCGCGTCCTCTAGGTCT 60.829 66.667 8.43 0.00 36.34 3.85
818 848 1.525535 GGCGCGTCCTCTAGGTCTA 60.526 63.158 8.43 0.00 36.34 2.59
819 849 1.648174 GCGCGTCCTCTAGGTCTAC 59.352 63.158 8.43 0.00 36.34 2.59
820 850 1.094073 GCGCGTCCTCTAGGTCTACA 61.094 60.000 8.43 0.00 36.34 2.74
821 851 0.656785 CGCGTCCTCTAGGTCTACAC 59.343 60.000 0.00 0.00 36.34 2.90
822 852 1.023502 GCGTCCTCTAGGTCTACACC 58.976 60.000 0.00 0.00 44.19 4.16
823 853 1.681166 GCGTCCTCTAGGTCTACACCA 60.681 57.143 0.00 0.00 46.68 4.17
824 854 2.719739 CGTCCTCTAGGTCTACACCAA 58.280 52.381 0.00 0.00 46.68 3.67
825 855 2.683867 CGTCCTCTAGGTCTACACCAAG 59.316 54.545 0.00 0.00 46.68 3.61
826 856 3.699413 GTCCTCTAGGTCTACACCAAGT 58.301 50.000 0.00 0.00 46.68 3.16
827 857 3.444388 GTCCTCTAGGTCTACACCAAGTG 59.556 52.174 0.00 0.00 46.68 3.16
828 858 2.761208 CCTCTAGGTCTACACCAAGTGG 59.239 54.545 0.00 0.00 46.68 4.00
829 859 6.056736 TCCTCTAGGTCTACACCAAGTGGT 62.057 50.000 0.00 0.00 46.68 4.16
830 860 7.475205 TCCTCTAGGTCTACACCAAGTGGTT 62.475 48.000 0.00 0.00 46.68 3.67
831 861 8.180394 TCCTCTAGGTCTACACCAAGTGGTTA 62.180 46.154 0.00 0.00 46.68 2.85
832 862 9.867552 TCCTCTAGGTCTACACCAAGTGGTTAG 62.868 48.148 0.00 6.77 46.68 2.34
936 1252 1.665916 CTGCTCCAGTCCACACACG 60.666 63.158 0.00 0.00 0.00 4.49
1009 1328 2.278596 CGGCGACCATGGAGTACG 60.279 66.667 21.47 18.00 0.00 3.67
1043 1362 2.725008 CCTTTTCGCCCGTTTGCA 59.275 55.556 0.00 0.00 0.00 4.08
1048 1367 2.343163 TTTCGCCCGTTTGCACAAGG 62.343 55.000 0.00 0.00 0.00 3.61
1055 1374 1.081442 GTTTGCACAAGGTAGCGGC 60.081 57.895 0.00 0.00 0.00 6.53
1062 1381 2.100631 CAAGGTAGCGGCCGAGTTG 61.101 63.158 33.48 18.93 0.00 3.16
1079 1398 4.090057 GCTCCGCAACAAGGACGC 62.090 66.667 0.00 0.00 33.58 5.19
1108 1427 1.660575 CTATTCCACCGCGCCTACG 60.661 63.158 0.00 0.00 44.07 3.51
1147 1466 2.636412 CCCGACTCGCTTGTCTCCA 61.636 63.158 0.00 0.00 35.00 3.86
1173 1492 2.190488 CTTGCCTCTTCGCCCTCCTT 62.190 60.000 0.00 0.00 0.00 3.36
1186 1510 2.203523 TCCTTCCCCACGACGACA 60.204 61.111 0.00 0.00 0.00 4.35
1233 1558 1.129437 GCGCTTCTTCACAACATCTCC 59.871 52.381 0.00 0.00 0.00 3.71
1357 1688 4.155733 CGCCACCTCCGCCATGTA 62.156 66.667 0.00 0.00 0.00 2.29
1368 1699 1.218047 GCCATGTACAGCGTCCTCA 59.782 57.895 0.33 0.00 0.00 3.86
1374 1706 1.002250 GTACAGCGTCCTCACACACG 61.002 60.000 0.00 0.00 39.09 4.49
1379 1711 3.986006 GTCCTCACACACGCCCGA 61.986 66.667 0.00 0.00 0.00 5.14
1396 1728 3.682292 GAGGCCCTTCCGATGCGTT 62.682 63.158 0.00 0.00 40.77 4.84
1412 1744 1.227943 GTTCACCTCACCAGCTGCA 60.228 57.895 8.66 0.00 0.00 4.41
1440 1772 1.063492 TGAATTCCATGCCCTGCTCAT 60.063 47.619 2.27 0.00 0.00 2.90
1534 1887 4.154347 GCTCTCCCCGCCACTCTG 62.154 72.222 0.00 0.00 0.00 3.35
1627 1986 1.816572 GCCACCTGTTTCCGTAACCTT 60.817 52.381 0.00 0.00 35.81 3.50
1638 1997 1.604693 CCGTAACCTTTGTGAGCTCGT 60.605 52.381 9.64 0.00 0.00 4.18
1641 2000 0.463654 AACCTTTGTGAGCTCGTGCA 60.464 50.000 12.58 5.29 42.74 4.57
1711 2074 3.506096 CCCGTGCTCGAGACGCTA 61.506 66.667 18.75 0.00 39.71 4.26
1718 2081 0.098905 GCTCGAGACGCTATGTGTCA 59.901 55.000 18.75 0.00 44.42 3.58
1765 2129 1.466851 GCCTTGTCAGCCAAAGCCTT 61.467 55.000 0.00 0.00 41.25 4.35
1961 2343 1.313812 CGTCCTAGAGGTCGGCAACT 61.314 60.000 7.25 0.00 41.75 3.16
1966 2348 1.482593 CTAGAGGTCGGCAACTCCATT 59.517 52.381 0.00 0.00 34.27 3.16
2034 2450 6.032956 AGTGATCAATGCAAATGTGTGATT 57.967 33.333 0.00 0.00 0.00 2.57
2107 2550 0.478072 TGAGTCCAAGCACCATGGTT 59.522 50.000 16.84 0.00 38.82 3.67
2131 2574 1.005450 GGTGTGGGAATCCTGGCTTTA 59.995 52.381 0.00 0.00 0.00 1.85
2184 2627 0.914417 ATGGTTCCCGGTGTCCTCAT 60.914 55.000 0.00 0.00 0.00 2.90
2197 2640 3.309954 GTGTCCTCATATGCTTTCCGAAC 59.690 47.826 0.00 0.00 0.00 3.95
2200 2643 4.024556 GTCCTCATATGCTTTCCGAACATG 60.025 45.833 0.00 0.00 0.00 3.21
2224 2667 1.003580 ACGCTCCACATCAAGGTGAAT 59.996 47.619 0.00 0.00 41.32 2.57
2233 2676 1.741028 TCAAGGTGAATCCCCTGACA 58.259 50.000 0.00 0.00 36.75 3.58
2238 2681 0.108138 GTGAATCCCCTGACACCTCG 60.108 60.000 0.00 0.00 0.00 4.63
2258 2703 1.994779 GTTTGGCTTCCATTTGCATCG 59.005 47.619 0.00 0.00 31.53 3.84
2339 2873 7.519032 AATTTTCAGTCTGGAAAAACCGATA 57.481 32.000 10.40 0.00 46.39 2.92
2340 2874 6.945938 TTTTCAGTCTGGAAAAACCGATAA 57.054 33.333 3.64 0.00 42.15 1.75
2341 2875 6.945938 TTTCAGTCTGGAAAAACCGATAAA 57.054 33.333 0.00 0.00 42.61 1.40
2342 2876 7.519032 TTTCAGTCTGGAAAAACCGATAAAT 57.481 32.000 0.00 0.00 42.61 1.40
2343 2877 6.737254 TCAGTCTGGAAAAACCGATAAATC 57.263 37.500 0.00 0.00 42.61 2.17
2344 2878 5.646360 TCAGTCTGGAAAAACCGATAAATCC 59.354 40.000 0.00 0.00 42.61 3.01
2345 2879 5.648092 CAGTCTGGAAAAACCGATAAATCCT 59.352 40.000 0.00 0.00 42.61 3.24
2346 2880 5.880887 AGTCTGGAAAAACCGATAAATCCTC 59.119 40.000 0.00 0.00 42.61 3.71
2347 2881 5.646360 GTCTGGAAAAACCGATAAATCCTCA 59.354 40.000 0.00 0.00 42.61 3.86
2348 2882 6.318900 GTCTGGAAAAACCGATAAATCCTCAT 59.681 38.462 0.00 0.00 42.61 2.90
2502 3036 1.159285 CTTTGAGAGCGCATTGGTGA 58.841 50.000 11.47 0.00 0.00 4.02
2513 3047 1.843368 CATTGGTGATGCAGGAGGTT 58.157 50.000 0.00 0.00 0.00 3.50
2515 3049 0.770499 TTGGTGATGCAGGAGGTTGA 59.230 50.000 0.00 0.00 0.00 3.18
2518 3052 1.003580 GGTGATGCAGGAGGTTGAGAA 59.996 52.381 0.00 0.00 0.00 2.87
2537 3071 0.250467 ATGTGTTTGACGCTGCCTCT 60.250 50.000 0.00 0.00 0.00 3.69
2611 3145 1.383523 GCCAGTGAAACCTCCATAGC 58.616 55.000 0.00 0.00 37.80 2.97
2632 3166 2.811317 GGTCGCTGCGAGTTCTGG 60.811 66.667 26.68 0.00 36.23 3.86
2635 3169 2.049156 CGCTGCGAGTTCTGGTCA 60.049 61.111 18.66 0.00 0.00 4.02
2679 3213 7.163001 AGCTTCAAAATAGGATCTGGTTTTC 57.837 36.000 0.00 0.00 0.00 2.29
2707 3241 4.040217 TGCCGACCCTTTTGTAAACTACTA 59.960 41.667 0.00 0.00 0.00 1.82
2744 3278 3.467803 GCCTATGTACTTCGGAATGCTT 58.532 45.455 3.72 0.00 0.00 3.91
2764 3298 6.872920 TGCTTTGGAAGTTGTTAATGTTCTT 58.127 32.000 0.00 0.00 0.00 2.52
2789 3328 7.530010 TCTGCTTGCAAGACTGTTTAATATTC 58.470 34.615 30.39 7.28 0.00 1.75
2926 3466 1.662044 GTGTCGTCCACGTACCCTT 59.338 57.895 0.00 0.00 40.80 3.95
2934 3474 1.203038 TCCACGTACCCTTGTAGACCA 60.203 52.381 0.00 0.00 0.00 4.02
3003 3543 2.224137 ACGATCGACCGATCCTAGTACA 60.224 50.000 24.34 0.00 45.95 2.90
3041 3581 1.284297 CGATCTGCACACGTTCAGCA 61.284 55.000 6.22 6.22 36.72 4.41
3063 3603 0.249155 GTGACGTCCCACGAACTCAA 60.249 55.000 14.12 0.00 46.05 3.02
3174 3714 0.873054 CCGCTACGATATGACCGAGT 59.127 55.000 0.00 0.00 0.00 4.18
3237 3778 4.717877 TCAATGATCAACTTGTGTGTCCT 58.282 39.130 0.00 0.00 0.00 3.85
3295 3839 2.123382 GGCTAGCCGTCCCTAGGT 60.123 66.667 20.16 0.00 36.23 3.08
3333 3877 1.501604 GAGTCCTCCTCCTAGTGGGAT 59.498 57.143 0.00 0.00 44.15 3.85
3394 3938 0.547954 GGAGTGGGAGAGGGGAAAGT 60.548 60.000 0.00 0.00 0.00 2.66
3443 3993 2.667470 CTATTCGGACTCAAGGGAGGA 58.333 52.381 0.00 0.00 45.81 3.71
3498 4048 2.022428 TCTCCACTAGGGCCCATTAAGA 60.022 50.000 27.56 15.53 36.21 2.10
3516 4066 2.040254 CCCATTAGTCCCCGGGGA 60.040 66.667 39.67 39.67 41.49 4.81
3543 4094 0.472925 TAACACCCCTCTGGCACTCA 60.473 55.000 0.00 0.00 37.83 3.41
3569 4120 1.974957 TCTCCGAGATCACCCAAAACA 59.025 47.619 0.00 0.00 0.00 2.83
3647 4198 1.339610 GAGACTCCTCATCATGTCCGG 59.660 57.143 0.00 0.00 39.24 5.14
3697 4248 8.407064 ACCTTCGTTACATCAAAACACATAAAA 58.593 29.630 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 74 2.270352 AGGCACGAAAATGGACTTCA 57.730 45.000 0.00 0.00 0.00 3.02
72 76 1.613437 CCAAGGCACGAAAATGGACTT 59.387 47.619 0.00 0.00 32.82 3.01
86 90 2.548295 TTCGACGGTTTGCCAAGGC 61.548 57.895 3.61 3.61 42.35 4.35
114 118 1.209383 CGTCTCCTTCTTCGACGCA 59.791 57.895 0.00 0.00 43.02 5.24
287 297 0.395173 AGCAAACTGTTTCCCACCGT 60.395 50.000 2.13 0.00 0.00 4.83
341 352 0.913451 AGCAATGCCTCTCACTCCCT 60.913 55.000 0.00 0.00 0.00 4.20
351 364 0.921896 ACATCCACCTAGCAATGCCT 59.078 50.000 0.00 0.00 0.00 4.75
420 434 2.282462 CCGCCTCCTTTGTTGCCT 60.282 61.111 0.00 0.00 0.00 4.75
424 441 3.901797 CTCGCCCGCCTCCTTTGTT 62.902 63.158 0.00 0.00 0.00 2.83
496 523 4.465446 CGCCTCCTCCTCTCCCCA 62.465 72.222 0.00 0.00 0.00 4.96
633 662 2.607635 GTCAGTGCGAACAGAAAAGTCA 59.392 45.455 0.00 0.00 0.00 3.41
645 674 2.280524 CCGTTTGGGTCAGTGCGA 60.281 61.111 0.00 0.00 0.00 5.10
651 680 2.280524 CGCTGTCCGTTTGGGTCA 60.281 61.111 0.00 0.00 37.00 4.02
725 755 4.159506 GGTATGCAGCCCAGATGTTAAAAA 59.840 41.667 0.00 0.00 0.00 1.94
726 756 3.699038 GGTATGCAGCCCAGATGTTAAAA 59.301 43.478 0.00 0.00 0.00 1.52
727 757 3.287222 GGTATGCAGCCCAGATGTTAAA 58.713 45.455 0.00 0.00 0.00 1.52
728 758 2.422803 GGGTATGCAGCCCAGATGTTAA 60.423 50.000 20.64 0.00 45.40 2.01
729 759 1.142870 GGGTATGCAGCCCAGATGTTA 59.857 52.381 20.64 0.00 45.40 2.41
730 760 0.106519 GGGTATGCAGCCCAGATGTT 60.107 55.000 20.64 0.00 45.40 2.71
731 761 1.533711 GGGTATGCAGCCCAGATGT 59.466 57.895 20.64 0.00 45.40 3.06
732 762 4.488790 GGGTATGCAGCCCAGATG 57.511 61.111 20.64 0.00 45.40 2.90
737 767 0.393267 TAAACGTGGGTATGCAGCCC 60.393 55.000 19.22 19.22 46.26 5.19
738 768 1.455248 TTAAACGTGGGTATGCAGCC 58.545 50.000 0.00 0.00 43.07 4.85
739 769 3.562567 TTTTAAACGTGGGTATGCAGC 57.437 42.857 0.00 0.00 0.00 5.25
740 770 6.613233 TGTAATTTTAAACGTGGGTATGCAG 58.387 36.000 0.00 0.00 0.00 4.41
741 771 6.570672 TGTAATTTTAAACGTGGGTATGCA 57.429 33.333 0.00 0.00 0.00 3.96
742 772 6.412653 CGATGTAATTTTAAACGTGGGTATGC 59.587 38.462 0.00 0.00 0.00 3.14
743 773 7.637132 GTCGATGTAATTTTAAACGTGGGTATG 59.363 37.037 0.00 0.00 0.00 2.39
744 774 7.464444 CGTCGATGTAATTTTAAACGTGGGTAT 60.464 37.037 0.00 0.00 0.00 2.73
745 775 6.183360 CGTCGATGTAATTTTAAACGTGGGTA 60.183 38.462 0.00 0.00 0.00 3.69
746 776 5.389725 CGTCGATGTAATTTTAAACGTGGGT 60.390 40.000 0.00 0.00 0.00 4.51
747 777 5.016985 CGTCGATGTAATTTTAAACGTGGG 58.983 41.667 0.00 0.00 0.00 4.61
748 778 5.845576 TCGTCGATGTAATTTTAAACGTGG 58.154 37.500 4.21 0.00 0.00 4.94
749 779 7.388712 AGATCGTCGATGTAATTTTAAACGTG 58.611 34.615 13.54 0.00 0.00 4.49
750 780 7.515957 AGATCGTCGATGTAATTTTAAACGT 57.484 32.000 13.54 0.00 0.00 3.99
751 781 8.712609 CAAAGATCGTCGATGTAATTTTAAACG 58.287 33.333 13.54 0.00 0.00 3.60
752 782 9.537848 ACAAAGATCGTCGATGTAATTTTAAAC 57.462 29.630 13.54 0.00 0.00 2.01
753 783 9.536558 CACAAAGATCGTCGATGTAATTTTAAA 57.463 29.630 13.54 0.00 0.00 1.52
754 784 7.690637 GCACAAAGATCGTCGATGTAATTTTAA 59.309 33.333 13.54 0.00 0.00 1.52
755 785 7.177407 GCACAAAGATCGTCGATGTAATTTTA 58.823 34.615 13.54 0.00 0.00 1.52
756 786 6.021596 GCACAAAGATCGTCGATGTAATTTT 58.978 36.000 13.54 0.00 0.00 1.82
757 787 5.560148 GCACAAAGATCGTCGATGTAATTT 58.440 37.500 13.54 5.60 0.00 1.82
758 788 4.259810 CGCACAAAGATCGTCGATGTAATT 60.260 41.667 13.54 0.00 0.00 1.40
759 789 3.242944 CGCACAAAGATCGTCGATGTAAT 59.757 43.478 13.54 0.00 0.00 1.89
760 790 2.596862 CGCACAAAGATCGTCGATGTAA 59.403 45.455 13.54 0.00 0.00 2.41
761 791 2.182014 CGCACAAAGATCGTCGATGTA 58.818 47.619 13.54 0.00 0.00 2.29
762 792 0.992072 CGCACAAAGATCGTCGATGT 59.008 50.000 13.54 5.61 0.00 3.06
763 793 0.298707 CCGCACAAAGATCGTCGATG 59.701 55.000 13.54 1.88 0.00 3.84
764 794 0.172578 TCCGCACAAAGATCGTCGAT 59.827 50.000 7.63 7.63 0.00 3.59
765 795 0.172578 ATCCGCACAAAGATCGTCGA 59.827 50.000 0.00 0.00 0.00 4.20
766 796 1.781429 CTATCCGCACAAAGATCGTCG 59.219 52.381 0.00 0.00 0.00 5.12
767 797 2.128035 CCTATCCGCACAAAGATCGTC 58.872 52.381 0.00 0.00 0.00 4.20
768 798 1.754803 TCCTATCCGCACAAAGATCGT 59.245 47.619 0.00 0.00 0.00 3.73
769 799 2.128035 GTCCTATCCGCACAAAGATCG 58.872 52.381 0.00 0.00 0.00 3.69
770 800 3.126831 CTGTCCTATCCGCACAAAGATC 58.873 50.000 0.00 0.00 0.00 2.75
771 801 2.743183 GCTGTCCTATCCGCACAAAGAT 60.743 50.000 0.00 0.00 0.00 2.40
772 802 1.405526 GCTGTCCTATCCGCACAAAGA 60.406 52.381 0.00 0.00 0.00 2.52
773 803 1.009829 GCTGTCCTATCCGCACAAAG 58.990 55.000 0.00 0.00 0.00 2.77
774 804 0.323302 TGCTGTCCTATCCGCACAAA 59.677 50.000 0.00 0.00 0.00 2.83
775 805 0.108186 CTGCTGTCCTATCCGCACAA 60.108 55.000 0.00 0.00 0.00 3.33
776 806 0.970427 TCTGCTGTCCTATCCGCACA 60.970 55.000 0.00 0.00 0.00 4.57
777 807 0.249238 CTCTGCTGTCCTATCCGCAC 60.249 60.000 0.00 0.00 0.00 5.34
778 808 1.395045 CCTCTGCTGTCCTATCCGCA 61.395 60.000 0.00 0.00 0.00 5.69
779 809 1.365633 CCTCTGCTGTCCTATCCGC 59.634 63.158 0.00 0.00 0.00 5.54
780 810 1.365633 GCCTCTGCTGTCCTATCCG 59.634 63.158 0.00 0.00 33.53 4.18
781 811 1.365633 CGCCTCTGCTGTCCTATCC 59.634 63.158 0.00 0.00 34.43 2.59
782 812 1.365633 CCGCCTCTGCTGTCCTATC 59.634 63.158 0.00 0.00 34.43 2.08
783 813 2.136878 CCCGCCTCTGCTGTCCTAT 61.137 63.158 0.00 0.00 34.43 2.57
784 814 2.759973 CCCGCCTCTGCTGTCCTA 60.760 66.667 0.00 0.00 34.43 2.94
799 829 2.955022 TAGACCTAGAGGACGCGCCC 62.955 65.000 5.73 3.78 38.94 6.13
800 830 1.525535 TAGACCTAGAGGACGCGCC 60.526 63.158 5.73 9.03 38.94 6.53
801 831 1.094073 TGTAGACCTAGAGGACGCGC 61.094 60.000 5.73 0.00 38.94 6.86
802 832 0.656785 GTGTAGACCTAGAGGACGCG 59.343 60.000 3.53 3.53 38.94 6.01
803 833 1.023502 GGTGTAGACCTAGAGGACGC 58.976 60.000 0.76 0.00 39.47 5.19
804 834 2.414994 TGGTGTAGACCTAGAGGACG 57.585 55.000 10.86 0.00 43.58 4.79
805 835 3.444388 CACTTGGTGTAGACCTAGAGGAC 59.556 52.174 23.89 0.00 45.21 3.85
806 836 3.698289 CACTTGGTGTAGACCTAGAGGA 58.302 50.000 23.89 0.00 45.21 3.71
807 837 2.761208 CCACTTGGTGTAGACCTAGAGG 59.239 54.545 23.89 21.13 45.21 3.69
821 851 5.348164 CAAAAACCTGAACTAACCACTTGG 58.652 41.667 0.00 0.00 42.17 3.61
822 852 4.803613 GCAAAAACCTGAACTAACCACTTG 59.196 41.667 0.00 0.00 0.00 3.16
823 853 4.464597 TGCAAAAACCTGAACTAACCACTT 59.535 37.500 0.00 0.00 0.00 3.16
824 854 4.020543 TGCAAAAACCTGAACTAACCACT 58.979 39.130 0.00 0.00 0.00 4.00
825 855 4.379339 TGCAAAAACCTGAACTAACCAC 57.621 40.909 0.00 0.00 0.00 4.16
826 856 5.105146 ACATTGCAAAAACCTGAACTAACCA 60.105 36.000 1.71 0.00 0.00 3.67
827 857 5.234116 CACATTGCAAAAACCTGAACTAACC 59.766 40.000 1.71 0.00 0.00 2.85
828 858 5.234116 CCACATTGCAAAAACCTGAACTAAC 59.766 40.000 1.71 0.00 0.00 2.34
829 859 5.127845 TCCACATTGCAAAAACCTGAACTAA 59.872 36.000 1.71 0.00 0.00 2.24
830 860 4.646945 TCCACATTGCAAAAACCTGAACTA 59.353 37.500 1.71 0.00 0.00 2.24
831 861 3.450457 TCCACATTGCAAAAACCTGAACT 59.550 39.130 1.71 0.00 0.00 3.01
832 862 3.791245 TCCACATTGCAAAAACCTGAAC 58.209 40.909 1.71 0.00 0.00 3.18
833 863 4.478206 TTCCACATTGCAAAAACCTGAA 57.522 36.364 1.71 0.00 0.00 3.02
834 864 4.686191 ATTCCACATTGCAAAAACCTGA 57.314 36.364 1.71 0.00 0.00 3.86
835 865 5.528320 AGAAATTCCACATTGCAAAAACCTG 59.472 36.000 1.71 0.00 0.00 4.00
836 866 5.683681 AGAAATTCCACATTGCAAAAACCT 58.316 33.333 1.71 0.00 0.00 3.50
837 867 5.526846 TGAGAAATTCCACATTGCAAAAACC 59.473 36.000 1.71 0.00 0.00 3.27
838 868 6.601741 TGAGAAATTCCACATTGCAAAAAC 57.398 33.333 1.71 0.00 0.00 2.43
870 900 0.318441 GCCCCTCAGCTTTTTCAACC 59.682 55.000 0.00 0.00 0.00 3.77
953 1269 2.150719 TGGGGACGAGGGCTTTGAA 61.151 57.895 0.00 0.00 0.00 2.69
997 1313 1.183549 GACAGGTCGTACTCCATGGT 58.816 55.000 12.58 0.00 0.00 3.55
1009 1328 3.703127 GGGACACCGGGACAGGTC 61.703 72.222 6.32 5.16 43.89 3.85
1043 1362 2.580601 AACTCGGCCGCTACCTTGT 61.581 57.895 23.51 7.16 0.00 3.16
1048 1367 2.886124 GAGCAACTCGGCCGCTAC 60.886 66.667 23.51 7.87 35.75 3.58
1079 1398 1.153647 TGGAATAGCTGTCGCACCG 60.154 57.895 0.00 0.00 39.10 4.94
1085 1404 2.526120 GCGCGGTGGAATAGCTGTC 61.526 63.158 8.83 0.00 0.00 3.51
1135 1454 4.373116 GGCGGTGGAGACAAGCGA 62.373 66.667 1.92 0.00 46.06 4.93
1139 1458 2.852075 AAGGGGCGGTGGAGACAA 60.852 61.111 0.00 0.00 46.06 3.18
1140 1459 3.636231 CAAGGGGCGGTGGAGACA 61.636 66.667 0.00 0.00 38.70 3.41
1147 1466 4.035102 GAAGAGGCAAGGGGCGGT 62.035 66.667 0.00 0.00 46.16 5.68
1314 1639 3.210528 GCCGGAGTCGACGAGGAT 61.211 66.667 24.21 2.72 39.00 3.24
1353 1684 0.966179 TGTGTGAGGACGCTGTACAT 59.034 50.000 0.00 0.00 33.42 2.29
1357 1688 2.027605 CGTGTGTGAGGACGCTGT 59.972 61.111 0.00 0.00 33.42 4.40
1379 1711 3.682292 GAACGCATCGGAAGGGCCT 62.682 63.158 0.00 0.00 0.00 5.19
1440 1772 3.092511 GGATCTGGAGCCAGCCCA 61.093 66.667 11.68 0.00 43.31 5.36
1627 1986 2.246739 GCAGTGCACGAGCTCACAA 61.247 57.895 24.12 0.00 42.74 3.33
1638 1997 0.518195 CATGATGACGTTGCAGTGCA 59.482 50.000 15.37 15.37 36.47 4.57
1641 2000 1.276138 TCTCCATGATGACGTTGCAGT 59.724 47.619 0.00 0.00 0.00 4.40
1711 2074 4.728772 TCAACAGATTCCCTTTGACACAT 58.271 39.130 0.00 0.00 0.00 3.21
1718 2081 3.532641 AAGCCTCAACAGATTCCCTTT 57.467 42.857 0.00 0.00 0.00 3.11
1765 2129 1.519234 GATGATCTGCACGCACCGA 60.519 57.895 0.00 0.00 0.00 4.69
1839 2206 1.612462 GGGTAAAACCTTCGGACTGGG 60.612 57.143 0.00 0.00 38.64 4.45
1961 2343 3.718434 AGATGAGGCACCTTGATAATGGA 59.282 43.478 0.00 0.00 0.00 3.41
1966 2348 3.523157 TGGAAAGATGAGGCACCTTGATA 59.477 43.478 0.00 0.00 0.00 2.15
2034 2450 4.339814 ACGCACCCAATTAAGACAAGAAAA 59.660 37.500 0.00 0.00 0.00 2.29
2107 2550 2.386864 CAGGATTCCCACACCTGGA 58.613 57.895 0.00 0.00 44.96 3.86
2131 2574 0.680061 GGACTCCGAAACACACCTCT 59.320 55.000 0.00 0.00 0.00 3.69
2184 2627 3.531538 GTCTCCATGTTCGGAAAGCATA 58.468 45.455 0.00 0.00 33.65 3.14
2224 2667 1.752198 CAAACGAGGTGTCAGGGGA 59.248 57.895 0.00 0.00 0.00 4.81
2233 2676 1.613437 CAAATGGAAGCCAAACGAGGT 59.387 47.619 0.00 0.00 36.95 3.85
2238 2681 1.994779 CGATGCAAATGGAAGCCAAAC 59.005 47.619 0.00 0.00 36.95 2.93
2339 2873 3.203710 TGCCAGAGGATTGATGAGGATTT 59.796 43.478 0.00 0.00 0.00 2.17
2340 2874 2.781757 TGCCAGAGGATTGATGAGGATT 59.218 45.455 0.00 0.00 0.00 3.01
2341 2875 2.415624 TGCCAGAGGATTGATGAGGAT 58.584 47.619 0.00 0.00 0.00 3.24
2342 2876 1.883678 TGCCAGAGGATTGATGAGGA 58.116 50.000 0.00 0.00 0.00 3.71
2343 2877 2.573369 CTTGCCAGAGGATTGATGAGG 58.427 52.381 0.00 0.00 0.00 3.86
2344 2878 1.948145 GCTTGCCAGAGGATTGATGAG 59.052 52.381 0.00 0.00 0.00 2.90
2345 2879 1.562942 AGCTTGCCAGAGGATTGATGA 59.437 47.619 0.00 0.00 0.00 2.92
2346 2880 1.676529 CAGCTTGCCAGAGGATTGATG 59.323 52.381 0.00 0.00 0.00 3.07
2347 2881 1.562942 TCAGCTTGCCAGAGGATTGAT 59.437 47.619 0.00 0.00 0.00 2.57
2348 2882 0.986527 TCAGCTTGCCAGAGGATTGA 59.013 50.000 0.00 0.00 0.00 2.57
2474 3008 6.365789 CCAATGCGCTCTCAAAGAAAAATTTA 59.634 34.615 9.73 0.00 0.00 1.40
2502 3036 2.040813 ACACATTCTCAACCTCCTGCAT 59.959 45.455 0.00 0.00 0.00 3.96
2513 3047 1.264020 GCAGCGTCAAACACATTCTCA 59.736 47.619 0.00 0.00 0.00 3.27
2515 3049 0.593128 GGCAGCGTCAAACACATTCT 59.407 50.000 0.00 0.00 0.00 2.40
2518 3052 0.250467 AGAGGCAGCGTCAAACACAT 60.250 50.000 17.21 0.00 0.00 3.21
2537 3071 5.065731 GGATTCTACCTCTTCGAACGAACTA 59.934 44.000 5.53 0.00 0.00 2.24
2625 3159 2.770802 CTCCTCCATGATGACCAGAACT 59.229 50.000 0.00 0.00 0.00 3.01
2632 3166 3.881688 CCAAATGTCTCCTCCATGATGAC 59.118 47.826 0.00 0.00 0.00 3.06
2635 3169 3.434739 GCTCCAAATGTCTCCTCCATGAT 60.435 47.826 0.00 0.00 0.00 2.45
2679 3213 1.675641 CAAAAGGGTCGGCAGGAGG 60.676 63.158 0.00 0.00 0.00 4.30
2744 3278 6.321181 AGCAGAAGAACATTAACAACTTCCAA 59.679 34.615 0.00 0.00 38.04 3.53
2764 3298 7.452880 AATATTAAACAGTCTTGCAAGCAGA 57.547 32.000 21.99 1.37 0.00 4.26
2789 3328 4.672413 GCAAGTCTTCAAACACTGAAATCG 59.328 41.667 0.00 0.00 43.54 3.34
2926 3466 2.496070 ACGCTTCTGCTTATGGTCTACA 59.504 45.455 0.00 0.00 36.97 2.74
2934 3474 4.032900 CGTTGTCATAACGCTTCTGCTTAT 59.967 41.667 0.00 0.00 36.82 1.73
3003 3543 2.968206 GGAGGTGCCGTACGTTCT 59.032 61.111 15.21 5.62 0.00 3.01
3063 3603 3.649023 TCCCTCGAAGCTCTACTAGATCT 59.351 47.826 0.00 0.00 0.00 2.75
3174 3714 1.231018 CCCCCTCCACCATAATCCAA 58.769 55.000 0.00 0.00 0.00 3.53
3295 3839 4.020617 CTCCTCTTGGCGCACCCA 62.021 66.667 10.83 0.00 43.51 4.51
3498 4048 2.367784 CCCCGGGGACTAATGGGT 60.368 66.667 38.41 0.00 40.20 4.51
3516 4066 0.178912 AGAGGGGTGTTACCGGAACT 60.179 55.000 9.46 0.00 39.83 3.01
3543 4094 1.555533 GGGTGATCTCGGAGAAAACCT 59.444 52.381 27.82 9.40 35.37 3.50
3585 4136 8.498054 AAAGATTGATATATTGGATGGCTACG 57.502 34.615 0.00 0.00 0.00 3.51
3647 4198 1.749033 GGAGTCCCGGATGTGATCC 59.251 63.158 0.73 0.00 46.22 3.36


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

AutoCloner maintained by Alex Coulton.