Multiple sequence alignment - TraesCS1A01G138900

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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 TraesCS1A01G138900 chr1A 100.000 2987 0 0 1 2987 234153513 234150527 0.000000e+00 5517
1 TraesCS1A01G138900 chr1A 90.974 986 76 8 1078 2061 234106420 234105446 0.000000e+00 1315
2 TraesCS1A01G138900 chr1D 91.974 2118 149 10 584 2699 180837637 180835539 0.000000e+00 2950
3 TraesCS1A01G138900 chr1D 89.554 1972 168 11 690 2656 180827472 180825534 0.000000e+00 2466
4 TraesCS1A01G138900 chr1D 86.223 421 54 4 1218 1635 379997408 379996989 1.260000e-123 453
5 TraesCS1A01G138900 chr1D 79.676 556 65 25 2162 2693 485184914 485185445 1.020000e-94 357
6 TraesCS1A01G138900 chr6A 98.789 578 7 0 1 578 162090710 162090133 0.000000e+00 1029
7 TraesCS1A01G138900 chr6A 85.761 611 73 10 1033 1637 530607749 530608351 4.200000e-178 634
8 TraesCS1A01G138900 chr3B 97.815 595 9 2 1 592 90155675 90156268 0.000000e+00 1024
9 TraesCS1A01G138900 chr3B 83.570 986 141 18 1561 2535 182209677 182210652 0.000000e+00 904
10 TraesCS1A01G138900 chr5B 98.110 582 10 1 1 581 224614053 224614634 0.000000e+00 1013
11 TraesCS1A01G138900 chr5B 97.288 590 12 4 1 589 229136921 229136335 0.000000e+00 998
12 TraesCS1A01G138900 chr5B 79.070 1204 213 39 1332 2518 470784192 470785373 0.000000e+00 791
13 TraesCS1A01G138900 chr5B 78.460 1221 223 37 1332 2535 470813562 470814759 0.000000e+00 761
14 TraesCS1A01G138900 chr7B 98.107 581 10 1 1 580 741260081 741260661 0.000000e+00 1011
15 TraesCS1A01G138900 chr4A 97.945 584 10 2 1 583 16029092 16029674 0.000000e+00 1011
16 TraesCS1A01G138900 chr4A 97.288 590 14 2 1 589 24089564 24088976 0.000000e+00 1000
17 TraesCS1A01G138900 chr4A 80.769 1170 174 37 1563 2694 585251825 585252981 0.000000e+00 867
18 TraesCS1A01G138900 chr4A 79.240 1079 183 38 1472 2533 493059935 493058881 0.000000e+00 713
19 TraesCS1A01G138900 chr4A 96.309 298 9 2 2692 2987 112558561 112558264 3.460000e-134 488
20 TraesCS1A01G138900 chr4A 96.599 294 9 1 2695 2987 477172478 477172185 1.240000e-133 486
21 TraesCS1A01G138900 chr4A 96.897 290 7 2 2695 2983 196680780 196681068 4.480000e-133 484
22 TraesCS1A01G138900 chr4A 96.587 293 9 1 2695 2986 467211962 467211670 4.480000e-133 484
23 TraesCS1A01G138900 chr7A 98.103 580 10 1 1 579 317173601 317174180 0.000000e+00 1009
24 TraesCS1A01G138900 chr7A 78.641 1133 208 31 1421 2535 445187171 445186055 0.000000e+00 721
25 TraesCS1A01G138900 chr7A 96.599 294 9 1 2695 2987 148525683 148525390 1.240000e-133 486
26 TraesCS1A01G138900 chr7A 96.259 294 10 1 2695 2987 248444053 248444346 5.790000e-132 481
27 TraesCS1A01G138900 chr7A 96.259 294 10 1 2695 2987 622591936 622592229 5.790000e-132 481
28 TraesCS1A01G138900 chr6B 97.458 590 13 2 1 589 204158189 204158777 0.000000e+00 1005
29 TraesCS1A01G138900 chr6B 85.034 441 58 7 1200 1637 576461425 576461860 2.730000e-120 442
30 TraesCS1A01G138900 chr5D 81.266 1185 176 36 1479 2629 227594989 227596161 0.000000e+00 917
31 TraesCS1A01G138900 chr5D 83.002 653 79 19 2071 2699 209221918 209221274 2.010000e-156 562
32 TraesCS1A01G138900 chr5D 83.549 541 56 17 2177 2691 261640606 261641139 2.690000e-130 475
33 TraesCS1A01G138900 chr3A 84.240 882 124 14 1661 2535 617559045 617559918 0.000000e+00 845
34 TraesCS1A01G138900 chr5A 78.051 1221 233 31 1337 2538 159402163 159400959 0.000000e+00 737
35 TraesCS1A01G138900 chr5A 95.652 299 11 2 2687 2983 343606956 343607254 2.080000e-131 479
36 TraesCS1A01G138900 chr2A 77.157 1182 196 52 1563 2699 314992336 314991184 1.180000e-173 619
37 TraesCS1A01G138900 chr2A 96.599 294 9 1 2695 2987 503765175 503764882 1.240000e-133 486
38 TraesCS1A01G138900 chr6D 84.013 613 72 15 1033 1637 386084039 386084633 1.550000e-157 566
39 TraesCS1A01G138900 chr6D 81.216 559 55 29 2162 2694 289651139 289650605 3.590000e-109 405
40 TraesCS1A01G138900 chr6D 80.859 559 57 29 2162 2694 289672601 289672067 7.760000e-106 394
41 TraesCS1A01G138900 chr2B 81.353 665 110 13 1479 2138 434086653 434085998 2.040000e-146 529
42 TraesCS1A01G138900 chr1B 81.449 566 67 17 2162 2699 607678327 607677772 2.130000e-116 429
43 TraesCS1A01G138900 chr7D 79.781 549 65 32 2177 2699 83360602 83360074 1.020000e-94 357
44 TraesCS1A01G138900 chr4B 89.474 209 17 5 1276 1481 143876789 143876995 2.950000e-65 259


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 TraesCS1A01G138900 chr1A 234150527 234153513 2986 True 5517 5517 100.000 1 2987 1 chr1A.!!$R2 2986
1 TraesCS1A01G138900 chr1A 234105446 234106420 974 True 1315 1315 90.974 1078 2061 1 chr1A.!!$R1 983
2 TraesCS1A01G138900 chr1D 180835539 180837637 2098 True 2950 2950 91.974 584 2699 1 chr1D.!!$R2 2115
3 TraesCS1A01G138900 chr1D 180825534 180827472 1938 True 2466 2466 89.554 690 2656 1 chr1D.!!$R1 1966
4 TraesCS1A01G138900 chr1D 485184914 485185445 531 False 357 357 79.676 2162 2693 1 chr1D.!!$F1 531
5 TraesCS1A01G138900 chr6A 162090133 162090710 577 True 1029 1029 98.789 1 578 1 chr6A.!!$R1 577
6 TraesCS1A01G138900 chr6A 530607749 530608351 602 False 634 634 85.761 1033 1637 1 chr6A.!!$F1 604
7 TraesCS1A01G138900 chr3B 90155675 90156268 593 False 1024 1024 97.815 1 592 1 chr3B.!!$F1 591
8 TraesCS1A01G138900 chr3B 182209677 182210652 975 False 904 904 83.570 1561 2535 1 chr3B.!!$F2 974
9 TraesCS1A01G138900 chr5B 224614053 224614634 581 False 1013 1013 98.110 1 581 1 chr5B.!!$F1 580
10 TraesCS1A01G138900 chr5B 229136335 229136921 586 True 998 998 97.288 1 589 1 chr5B.!!$R1 588
11 TraesCS1A01G138900 chr5B 470784192 470785373 1181 False 791 791 79.070 1332 2518 1 chr5B.!!$F2 1186
12 TraesCS1A01G138900 chr5B 470813562 470814759 1197 False 761 761 78.460 1332 2535 1 chr5B.!!$F3 1203
13 TraesCS1A01G138900 chr7B 741260081 741260661 580 False 1011 1011 98.107 1 580 1 chr7B.!!$F1 579
14 TraesCS1A01G138900 chr4A 16029092 16029674 582 False 1011 1011 97.945 1 583 1 chr4A.!!$F1 582
15 TraesCS1A01G138900 chr4A 24088976 24089564 588 True 1000 1000 97.288 1 589 1 chr4A.!!$R1 588
16 TraesCS1A01G138900 chr4A 585251825 585252981 1156 False 867 867 80.769 1563 2694 1 chr4A.!!$F3 1131
17 TraesCS1A01G138900 chr4A 493058881 493059935 1054 True 713 713 79.240 1472 2533 1 chr4A.!!$R5 1061
18 TraesCS1A01G138900 chr7A 317173601 317174180 579 False 1009 1009 98.103 1 579 1 chr7A.!!$F2 578
19 TraesCS1A01G138900 chr7A 445186055 445187171 1116 True 721 721 78.641 1421 2535 1 chr7A.!!$R2 1114
20 TraesCS1A01G138900 chr6B 204158189 204158777 588 False 1005 1005 97.458 1 589 1 chr6B.!!$F1 588
21 TraesCS1A01G138900 chr5D 227594989 227596161 1172 False 917 917 81.266 1479 2629 1 chr5D.!!$F1 1150
22 TraesCS1A01G138900 chr5D 209221274 209221918 644 True 562 562 83.002 2071 2699 1 chr5D.!!$R1 628
23 TraesCS1A01G138900 chr5D 261640606 261641139 533 False 475 475 83.549 2177 2691 1 chr5D.!!$F2 514
24 TraesCS1A01G138900 chr3A 617559045 617559918 873 False 845 845 84.240 1661 2535 1 chr3A.!!$F1 874
25 TraesCS1A01G138900 chr5A 159400959 159402163 1204 True 737 737 78.051 1337 2538 1 chr5A.!!$R1 1201
26 TraesCS1A01G138900 chr2A 314991184 314992336 1152 True 619 619 77.157 1563 2699 1 chr2A.!!$R1 1136
27 TraesCS1A01G138900 chr6D 386084039 386084633 594 False 566 566 84.013 1033 1637 1 chr6D.!!$F1 604
28 TraesCS1A01G138900 chr6D 289650605 289651139 534 True 405 405 81.216 2162 2694 1 chr6D.!!$R1 532
29 TraesCS1A01G138900 chr6D 289672067 289672601 534 True 394 394 80.859 2162 2694 1 chr6D.!!$R2 532
30 TraesCS1A01G138900 chr2B 434085998 434086653 655 True 529 529 81.353 1479 2138 1 chr2B.!!$R1 659
31 TraesCS1A01G138900 chr1B 607677772 607678327 555 True 429 429 81.449 2162 2699 1 chr1B.!!$R1 537
32 TraesCS1A01G138900 chr7D 83360074 83360602 528 True 357 357 79.781 2177 2699 1 chr7D.!!$R1 522

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
930 935 0.108662 AGTTGCAGACATCGATGCGA 60.109 50.0 25.11 9.98 45.54 5.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2889 3060 0.036671 ATTCCGTGGAGTTTCGGGAC 60.037 55.0 3.85 0.0 45.79 4.46 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
581 586 7.593273 CAGAAGCTATACATAGTCTAACACTGC 59.407 40.741 0.00 0.00 36.43 4.40
582 587 6.003234 AGCTATACATAGTCTAACACTGCG 57.997 41.667 0.00 0.00 36.43 5.18
638 643 4.790962 CAGGCTGTGGCGGCTCAT 62.791 66.667 14.40 0.00 37.76 2.90
682 687 3.123620 GGAGCGTGGCAAGCAGAG 61.124 66.667 26.47 0.00 37.01 3.35
683 688 3.797546 GAGCGTGGCAAGCAGAGC 61.798 66.667 26.47 9.60 37.01 4.09
684 689 4.326507 AGCGTGGCAAGCAGAGCT 62.327 61.111 26.47 10.11 42.56 4.09
685 690 3.797546 GCGTGGCAAGCAGAGCTC 61.798 66.667 20.52 5.27 38.25 4.09
686 691 2.047465 CGTGGCAAGCAGAGCTCT 60.047 61.111 11.45 11.45 38.25 4.09
687 692 1.216444 CGTGGCAAGCAGAGCTCTA 59.784 57.895 17.75 0.00 38.25 2.43
688 693 0.805322 CGTGGCAAGCAGAGCTCTAG 60.805 60.000 17.75 12.07 38.25 2.43
742 747 3.183754 TGCGGTATACTGTGACAAATCG 58.816 45.455 13.23 0.55 0.00 3.34
753 758 1.078426 ACAAATCGAAGCGGGGGAG 60.078 57.895 0.00 0.00 0.00 4.30
755 760 1.090052 CAAATCGAAGCGGGGGAGAC 61.090 60.000 0.00 0.00 0.00 3.36
829 834 2.043852 GAGGCTCCGGAGAGGTCA 60.044 66.667 35.69 0.00 40.79 4.02
843 848 2.026822 AGAGGTCAAATCACAGGCGAAT 60.027 45.455 0.00 0.00 0.00 3.34
873 878 1.805869 CCCTCGGATGAAGATGATGC 58.194 55.000 0.00 0.00 0.00 3.91
902 907 1.377994 CTGCAGAGGTTCCTGGCTT 59.622 57.895 8.42 0.00 34.82 4.35
921 926 1.301716 GAGCCGGAAGTTGCAGACA 60.302 57.895 5.05 0.00 0.00 3.41
922 927 0.674895 GAGCCGGAAGTTGCAGACAT 60.675 55.000 5.05 0.00 0.00 3.06
930 935 0.108662 AGTTGCAGACATCGATGCGA 60.109 50.000 25.11 9.98 45.54 5.10
945 950 2.490217 CGATCGACGGTGGAGCTT 59.510 61.111 10.26 0.00 38.46 3.74
952 957 2.377628 GACGGTGGAGCTTGTGGACA 62.378 60.000 0.00 0.00 0.00 4.02
1164 1170 0.332632 CATCCATGGTTGTGGGAGGT 59.667 55.000 12.58 0.00 39.80 3.85
1172 1178 0.889186 GTTGTGGGAGGTTGCACGAT 60.889 55.000 0.00 0.00 0.00 3.73
1204 1210 4.100373 GCCCCTGATGAATAGAGGTAGAT 58.900 47.826 0.00 0.00 0.00 1.98
1259 1265 1.768275 TGACTTGAAGCCCAGAAGTGA 59.232 47.619 0.00 0.00 30.01 3.41
1287 1293 3.324846 ACCTCTGGCCTTTTCAAATTTCC 59.675 43.478 3.32 0.00 0.00 3.13
1376 1384 4.582656 TGGGATTTGGCTCAATAAATACCG 59.417 41.667 0.00 0.00 46.03 4.02
1379 1387 5.067283 GGATTTGGCTCAATAAATACCGTGT 59.933 40.000 0.00 0.00 0.00 4.49
1386 1394 9.999660 TGGCTCAATAAATACCGTGTAATATTA 57.000 29.630 0.00 0.00 0.00 0.98
1497 1506 7.930325 GCACTAGTTTAAATAGGTTAGGGGTAG 59.070 40.741 4.48 0.00 0.00 3.18
1643 1658 6.421377 AATTGAGCTTGGTTTGAAACAAAC 57.579 33.333 10.53 15.97 0.00 2.93
1644 1659 4.527509 TGAGCTTGGTTTGAAACAAACA 57.472 36.364 22.60 10.70 32.04 2.83
1727 1748 6.481134 CATGATTCTCGAGGTGTTACAAATG 58.519 40.000 13.56 1.63 0.00 2.32
1730 1751 4.866508 TCTCGAGGTGTTACAAATGTCT 57.133 40.909 13.56 0.00 0.00 3.41
1782 1805 3.786213 AGAGGTGGAGTAAGGGAGAAT 57.214 47.619 0.00 0.00 0.00 2.40
1866 1892 6.479990 TCGATCCATTACATTGATGTCTTCAC 59.520 38.462 0.00 0.00 41.97 3.18
2004 2056 1.697432 TGACGGTGAACTCAGGGAAAT 59.303 47.619 0.00 0.00 0.00 2.17
2014 2081 3.891049 ACTCAGGGAAATAGGCATGAAC 58.109 45.455 0.00 0.00 0.00 3.18
2210 2343 4.109766 CGTGATCTACATACGAAGCCAAA 58.890 43.478 0.00 0.00 40.01 3.28
2363 2507 1.912043 AGGCATGTCATAGGATAGCCC 59.088 52.381 12.20 0.71 41.45 5.19
2505 2652 7.545362 AGAATGTCATCACAATAGTAACAGC 57.455 36.000 0.00 0.00 35.64 4.40
2518 2665 4.785511 AGTAACAGCGTCTTACTGACAT 57.214 40.909 0.00 0.00 45.60 3.06
2694 2865 3.494626 CGAGGGAATTCATGATGTTACCG 59.505 47.826 13.97 3.59 30.88 4.02
2699 2870 5.120208 GGGAATTCATGATGTTACCGATACG 59.880 44.000 7.93 0.00 0.00 3.06
2700 2871 5.694910 GGAATTCATGATGTTACCGATACGT 59.305 40.000 7.93 0.00 0.00 3.57
2701 2872 6.128902 GGAATTCATGATGTTACCGATACGTC 60.129 42.308 7.93 0.00 33.20 4.34
2702 2873 4.233123 TCATGATGTTACCGATACGTCC 57.767 45.455 0.00 0.00 31.89 4.79
2703 2874 3.633065 TCATGATGTTACCGATACGTCCA 59.367 43.478 0.00 0.00 31.89 4.02
2704 2875 4.279922 TCATGATGTTACCGATACGTCCAT 59.720 41.667 0.00 0.00 31.89 3.41
2705 2876 4.659111 TGATGTTACCGATACGTCCATT 57.341 40.909 0.00 0.00 31.89 3.16
2706 2877 5.013568 TGATGTTACCGATACGTCCATTT 57.986 39.130 0.00 0.00 31.89 2.32
2707 2878 5.421277 TGATGTTACCGATACGTCCATTTT 58.579 37.500 0.00 0.00 31.89 1.82
2708 2879 5.292345 TGATGTTACCGATACGTCCATTTTG 59.708 40.000 0.00 0.00 31.89 2.44
2709 2880 3.371591 TGTTACCGATACGTCCATTTTGC 59.628 43.478 0.00 0.00 0.00 3.68
2710 2881 2.102070 ACCGATACGTCCATTTTGCA 57.898 45.000 0.00 0.00 0.00 4.08
2711 2882 2.639065 ACCGATACGTCCATTTTGCAT 58.361 42.857 0.00 0.00 0.00 3.96
2712 2883 2.612212 ACCGATACGTCCATTTTGCATC 59.388 45.455 0.00 0.00 0.00 3.91
2713 2884 2.611751 CCGATACGTCCATTTTGCATCA 59.388 45.455 0.00 0.00 0.00 3.07
2714 2885 3.250762 CCGATACGTCCATTTTGCATCAT 59.749 43.478 0.00 0.00 0.00 2.45
2715 2886 4.213674 CGATACGTCCATTTTGCATCATG 58.786 43.478 0.00 0.00 0.00 3.07
2716 2887 2.282701 ACGTCCATTTTGCATCATGC 57.717 45.000 1.35 1.35 45.29 4.06
2717 2888 1.820519 ACGTCCATTTTGCATCATGCT 59.179 42.857 11.84 0.00 45.31 3.79
2718 2889 2.231964 ACGTCCATTTTGCATCATGCTT 59.768 40.909 11.84 0.00 45.31 3.91
2719 2890 3.255725 CGTCCATTTTGCATCATGCTTT 58.744 40.909 11.84 0.00 45.31 3.51
2720 2891 3.680937 CGTCCATTTTGCATCATGCTTTT 59.319 39.130 11.84 0.00 45.31 2.27
2721 2892 4.863689 CGTCCATTTTGCATCATGCTTTTA 59.136 37.500 11.84 0.00 45.31 1.52
2722 2893 5.521010 CGTCCATTTTGCATCATGCTTTTAT 59.479 36.000 11.84 0.00 45.31 1.40
2723 2894 6.696583 CGTCCATTTTGCATCATGCTTTTATA 59.303 34.615 11.84 0.00 45.31 0.98
2724 2895 7.383029 CGTCCATTTTGCATCATGCTTTTATAT 59.617 33.333 11.84 0.00 45.31 0.86
2725 2896 8.706035 GTCCATTTTGCATCATGCTTTTATATC 58.294 33.333 11.84 0.00 45.31 1.63
2726 2897 8.422566 TCCATTTTGCATCATGCTTTTATATCA 58.577 29.630 11.84 0.00 45.31 2.15
2727 2898 9.047371 CCATTTTGCATCATGCTTTTATATCAA 57.953 29.630 11.84 0.00 45.31 2.57
2757 2928 9.593134 TTATTGCATTATGGGTTGTTATTTCAC 57.407 29.630 0.00 0.00 0.00 3.18
2758 2929 6.596309 TGCATTATGGGTTGTTATTTCACA 57.404 33.333 0.00 0.00 0.00 3.58
2759 2930 7.180322 TGCATTATGGGTTGTTATTTCACAT 57.820 32.000 0.00 0.00 0.00 3.21
2760 2931 7.619050 TGCATTATGGGTTGTTATTTCACATT 58.381 30.769 0.00 0.00 0.00 2.71
2761 2932 8.753133 TGCATTATGGGTTGTTATTTCACATTA 58.247 29.630 0.00 0.00 0.00 1.90
2762 2933 9.762933 GCATTATGGGTTGTTATTTCACATTAT 57.237 29.630 0.00 0.00 0.00 1.28
2766 2937 7.767250 TGGGTTGTTATTTCACATTATGTCA 57.233 32.000 0.00 0.00 0.00 3.58
2767 2938 7.598278 TGGGTTGTTATTTCACATTATGTCAC 58.402 34.615 0.00 0.00 0.00 3.67
2768 2939 7.231519 TGGGTTGTTATTTCACATTATGTCACA 59.768 33.333 0.00 0.00 0.00 3.58
2769 2940 8.085296 GGGTTGTTATTTCACATTATGTCACAA 58.915 33.333 0.00 0.00 0.00 3.33
2770 2941 9.638239 GGTTGTTATTTCACATTATGTCACAAT 57.362 29.630 0.00 0.00 0.00 2.71
2779 2950 9.898152 TTCACATTATGTCACAATACTTATGGA 57.102 29.630 0.00 0.00 0.00 3.41
2815 2986 9.689501 TTATTTACAAGGTTTACATAAGGAGGG 57.310 33.333 0.00 0.00 0.00 4.30
2816 2987 6.956102 TTACAAGGTTTACATAAGGAGGGA 57.044 37.500 0.00 0.00 0.00 4.20
2817 2988 5.437191 ACAAGGTTTACATAAGGAGGGAG 57.563 43.478 0.00 0.00 0.00 4.30
2818 2989 5.098663 ACAAGGTTTACATAAGGAGGGAGA 58.901 41.667 0.00 0.00 0.00 3.71
2819 2990 5.550403 ACAAGGTTTACATAAGGAGGGAGAA 59.450 40.000 0.00 0.00 0.00 2.87
2820 2991 6.217693 ACAAGGTTTACATAAGGAGGGAGAAT 59.782 38.462 0.00 0.00 0.00 2.40
2821 2992 6.253946 AGGTTTACATAAGGAGGGAGAATG 57.746 41.667 0.00 0.00 0.00 2.67
2822 2993 4.822350 GGTTTACATAAGGAGGGAGAATGC 59.178 45.833 0.00 0.00 0.00 3.56
2830 3001 2.512896 GGGAGAATGCCGGCATCT 59.487 61.111 40.38 34.06 36.28 2.90
2831 3002 1.895707 GGGAGAATGCCGGCATCTG 60.896 63.158 40.38 0.00 36.28 2.90
2832 3003 1.895707 GGAGAATGCCGGCATCTGG 60.896 63.158 40.38 0.00 35.31 3.86
2833 3004 1.146930 GAGAATGCCGGCATCTGGA 59.853 57.895 40.38 14.16 35.31 3.86
2834 3005 0.464373 GAGAATGCCGGCATCTGGAA 60.464 55.000 40.38 13.30 35.31 3.53
2835 3006 0.184451 AGAATGCCGGCATCTGGAAT 59.816 50.000 40.38 25.04 35.31 3.01
2836 3007 1.035139 GAATGCCGGCATCTGGAATT 58.965 50.000 40.38 24.93 37.45 2.17
2837 3008 1.000938 GAATGCCGGCATCTGGAATTC 60.001 52.381 40.38 28.24 42.78 2.17
2838 3009 0.184451 ATGCCGGCATCTGGAATTCT 59.816 50.000 36.10 11.49 29.42 2.40
2839 3010 0.749091 TGCCGGCATCTGGAATTCTG 60.749 55.000 29.03 0.00 0.00 3.02
2840 3011 1.450531 GCCGGCATCTGGAATTCTGG 61.451 60.000 24.80 0.00 0.00 3.86
2841 3012 0.820891 CCGGCATCTGGAATTCTGGG 60.821 60.000 5.23 0.00 0.00 4.45
2842 3013 1.450531 CGGCATCTGGAATTCTGGGC 61.451 60.000 5.23 6.69 0.00 5.36
2843 3014 0.106318 GGCATCTGGAATTCTGGGCT 60.106 55.000 5.23 0.00 0.00 5.19
2844 3015 1.030457 GCATCTGGAATTCTGGGCTG 58.970 55.000 5.23 0.00 0.00 4.85
2845 3016 1.688772 CATCTGGAATTCTGGGCTGG 58.311 55.000 5.23 0.00 0.00 4.85
2846 3017 1.213678 CATCTGGAATTCTGGGCTGGA 59.786 52.381 5.23 0.00 0.00 3.86
2847 3018 1.371467 TCTGGAATTCTGGGCTGGAA 58.629 50.000 5.23 0.00 0.00 3.53
2848 3019 1.710244 TCTGGAATTCTGGGCTGGAAA 59.290 47.619 5.23 0.00 0.00 3.13
2849 3020 2.109834 TCTGGAATTCTGGGCTGGAAAA 59.890 45.455 5.23 0.00 0.00 2.29
2850 3021 2.494870 CTGGAATTCTGGGCTGGAAAAG 59.505 50.000 5.23 0.00 0.00 2.27
2851 3022 1.827344 GGAATTCTGGGCTGGAAAAGG 59.173 52.381 5.23 0.00 0.00 3.11
2852 3023 2.557452 GGAATTCTGGGCTGGAAAAGGA 60.557 50.000 5.23 0.00 0.00 3.36
2853 3024 2.521547 ATTCTGGGCTGGAAAAGGAG 57.478 50.000 0.00 0.00 0.00 3.69
2854 3025 0.251341 TTCTGGGCTGGAAAAGGAGC 60.251 55.000 0.00 0.00 34.23 4.70
2855 3026 1.075482 CTGGGCTGGAAAAGGAGCA 59.925 57.895 0.00 0.00 36.90 4.26
2856 3027 0.540365 CTGGGCTGGAAAAGGAGCAA 60.540 55.000 0.00 0.00 36.90 3.91
2857 3028 0.105760 TGGGCTGGAAAAGGAGCAAA 60.106 50.000 0.00 0.00 36.90 3.68
2858 3029 1.269958 GGGCTGGAAAAGGAGCAAAT 58.730 50.000 0.00 0.00 36.90 2.32
2859 3030 2.225242 TGGGCTGGAAAAGGAGCAAATA 60.225 45.455 0.00 0.00 36.90 1.40
2860 3031 3.033909 GGGCTGGAAAAGGAGCAAATAT 58.966 45.455 0.00 0.00 36.90 1.28
2861 3032 3.452264 GGGCTGGAAAAGGAGCAAATATT 59.548 43.478 0.00 0.00 36.90 1.28
2862 3033 4.649218 GGGCTGGAAAAGGAGCAAATATTA 59.351 41.667 0.00 0.00 36.90 0.98
2863 3034 5.221322 GGGCTGGAAAAGGAGCAAATATTAG 60.221 44.000 0.00 0.00 36.90 1.73
2864 3035 5.594317 GGCTGGAAAAGGAGCAAATATTAGA 59.406 40.000 0.00 0.00 36.90 2.10
2865 3036 6.238869 GGCTGGAAAAGGAGCAAATATTAGAG 60.239 42.308 0.00 0.00 36.90 2.43
2866 3037 6.543831 GCTGGAAAAGGAGCAAATATTAGAGA 59.456 38.462 0.00 0.00 35.15 3.10
2867 3038 7.467947 GCTGGAAAAGGAGCAAATATTAGAGAC 60.468 40.741 0.00 0.00 35.15 3.36
2868 3039 6.828785 TGGAAAAGGAGCAAATATTAGAGACC 59.171 38.462 0.00 0.00 0.00 3.85
2869 3040 7.057264 GGAAAAGGAGCAAATATTAGAGACCT 58.943 38.462 0.00 0.00 0.00 3.85
2870 3041 8.211629 GGAAAAGGAGCAAATATTAGAGACCTA 58.788 37.037 0.00 0.00 0.00 3.08
2871 3042 9.785982 GAAAAGGAGCAAATATTAGAGACCTAT 57.214 33.333 0.00 0.00 0.00 2.57
2876 3047 9.103861 GGAGCAAATATTAGAGACCTATTATGC 57.896 37.037 0.00 0.00 0.00 3.14
2877 3048 9.658799 GAGCAAATATTAGAGACCTATTATGCA 57.341 33.333 0.00 0.00 30.29 3.96
2878 3049 9.442047 AGCAAATATTAGAGACCTATTATGCAC 57.558 33.333 0.00 0.00 30.29 4.57
2879 3050 9.219603 GCAAATATTAGAGACCTATTATGCACA 57.780 33.333 0.00 0.00 0.00 4.57
2884 3055 5.283457 AGAGACCTATTATGCACAACTCC 57.717 43.478 0.00 0.00 0.00 3.85
2885 3056 4.716784 AGAGACCTATTATGCACAACTCCA 59.283 41.667 0.00 0.00 0.00 3.86
2886 3057 5.189736 AGAGACCTATTATGCACAACTCCAA 59.810 40.000 0.00 0.00 0.00 3.53
2887 3058 5.815581 AGACCTATTATGCACAACTCCAAA 58.184 37.500 0.00 0.00 0.00 3.28
2888 3059 6.245408 AGACCTATTATGCACAACTCCAAAA 58.755 36.000 0.00 0.00 0.00 2.44
2889 3060 6.375455 AGACCTATTATGCACAACTCCAAAAG 59.625 38.462 0.00 0.00 0.00 2.27
2890 3061 6.010219 ACCTATTATGCACAACTCCAAAAGT 58.990 36.000 0.00 0.00 41.10 2.66
2891 3062 6.151144 ACCTATTATGCACAACTCCAAAAGTC 59.849 38.462 0.00 0.00 37.17 3.01
2892 3063 4.846779 TTATGCACAACTCCAAAAGTCC 57.153 40.909 0.00 0.00 37.17 3.85
2893 3064 1.398692 TGCACAACTCCAAAAGTCCC 58.601 50.000 0.00 0.00 37.17 4.46
2894 3065 0.310854 GCACAACTCCAAAAGTCCCG 59.689 55.000 0.00 0.00 37.17 5.14
2895 3066 1.961793 CACAACTCCAAAAGTCCCGA 58.038 50.000 0.00 0.00 37.17 5.14
2896 3067 2.294074 CACAACTCCAAAAGTCCCGAA 58.706 47.619 0.00 0.00 37.17 4.30
2897 3068 2.685897 CACAACTCCAAAAGTCCCGAAA 59.314 45.455 0.00 0.00 37.17 3.46
2898 3069 2.686405 ACAACTCCAAAAGTCCCGAAAC 59.314 45.455 0.00 0.00 37.17 2.78
2899 3070 2.949644 CAACTCCAAAAGTCCCGAAACT 59.050 45.455 0.00 0.00 37.17 2.66
2900 3071 2.847441 ACTCCAAAAGTCCCGAAACTC 58.153 47.619 0.00 0.00 30.02 3.01
2901 3072 2.152016 CTCCAAAAGTCCCGAAACTCC 58.848 52.381 0.00 0.00 0.00 3.85
2902 3073 1.491332 TCCAAAAGTCCCGAAACTCCA 59.509 47.619 0.00 0.00 0.00 3.86
2903 3074 1.607148 CCAAAAGTCCCGAAACTCCAC 59.393 52.381 0.00 0.00 0.00 4.02
2904 3075 1.263217 CAAAAGTCCCGAAACTCCACG 59.737 52.381 0.00 0.00 0.00 4.94
2912 3083 2.667473 CGAAACTCCACGGAATACCT 57.333 50.000 0.00 0.00 0.00 3.08
2913 3084 2.968675 CGAAACTCCACGGAATACCTT 58.031 47.619 0.00 0.00 0.00 3.50
2914 3085 4.114058 CGAAACTCCACGGAATACCTTA 57.886 45.455 0.00 0.00 0.00 2.69
2915 3086 4.690122 CGAAACTCCACGGAATACCTTAT 58.310 43.478 0.00 0.00 0.00 1.73
2916 3087 5.835257 CGAAACTCCACGGAATACCTTATA 58.165 41.667 0.00 0.00 0.00 0.98
2917 3088 6.275335 CGAAACTCCACGGAATACCTTATAA 58.725 40.000 0.00 0.00 0.00 0.98
2918 3089 6.927381 CGAAACTCCACGGAATACCTTATAAT 59.073 38.462 0.00 0.00 0.00 1.28
2919 3090 8.084073 CGAAACTCCACGGAATACCTTATAATA 58.916 37.037 0.00 0.00 0.00 0.98
2920 3091 9.768662 GAAACTCCACGGAATACCTTATAATAA 57.231 33.333 0.00 0.00 0.00 1.40
2942 3113 9.883142 AATAAATAATGAAAAATCCTCGCCAAA 57.117 25.926 0.00 0.00 0.00 3.28
2943 3114 7.832503 AAATAATGAAAAATCCTCGCCAAAG 57.167 32.000 0.00 0.00 0.00 2.77
2944 3115 6.773976 ATAATGAAAAATCCTCGCCAAAGA 57.226 33.333 0.00 0.00 0.00 2.52
2945 3116 5.665916 AATGAAAAATCCTCGCCAAAGAT 57.334 34.783 0.00 0.00 0.00 2.40
2946 3117 5.665916 ATGAAAAATCCTCGCCAAAGATT 57.334 34.783 0.00 0.00 0.00 2.40
2947 3118 6.773976 ATGAAAAATCCTCGCCAAAGATTA 57.226 33.333 0.00 0.00 30.21 1.75
2948 3119 6.582677 TGAAAAATCCTCGCCAAAGATTAA 57.417 33.333 0.00 0.00 30.21 1.40
2949 3120 6.620678 TGAAAAATCCTCGCCAAAGATTAAG 58.379 36.000 0.00 0.00 30.21 1.85
2950 3121 6.432783 TGAAAAATCCTCGCCAAAGATTAAGA 59.567 34.615 0.00 0.00 30.21 2.10
2951 3122 5.819825 AAATCCTCGCCAAAGATTAAGAC 57.180 39.130 0.00 0.00 30.21 3.01
2952 3123 3.261981 TCCTCGCCAAAGATTAAGACC 57.738 47.619 0.00 0.00 0.00 3.85
2953 3124 2.569853 TCCTCGCCAAAGATTAAGACCA 59.430 45.455 0.00 0.00 0.00 4.02
2954 3125 2.939103 CCTCGCCAAAGATTAAGACCAG 59.061 50.000 0.00 0.00 0.00 4.00
2955 3126 2.939103 CTCGCCAAAGATTAAGACCAGG 59.061 50.000 0.00 0.00 0.00 4.45
2956 3127 2.017049 CGCCAAAGATTAAGACCAGGG 58.983 52.381 0.00 0.00 0.00 4.45
2957 3128 2.379005 GCCAAAGATTAAGACCAGGGG 58.621 52.381 0.00 0.00 0.00 4.79
2958 3129 2.950418 GCCAAAGATTAAGACCAGGGGG 60.950 54.545 0.00 0.00 41.29 5.40
2959 3130 2.379005 CAAAGATTAAGACCAGGGGGC 58.621 52.381 0.00 0.00 37.90 5.80
2960 3131 0.927029 AAGATTAAGACCAGGGGGCC 59.073 55.000 0.00 0.00 37.90 5.80
2961 3132 0.994050 AGATTAAGACCAGGGGGCCC 60.994 60.000 15.76 15.76 37.90 5.80
2962 3133 1.230482 ATTAAGACCAGGGGGCCCA 60.230 57.895 26.86 0.00 38.92 5.36
2963 3134 1.580994 ATTAAGACCAGGGGGCCCAC 61.581 60.000 26.86 23.59 38.92 4.61
2964 3135 3.508786 TAAGACCAGGGGGCCCACA 62.509 63.158 30.24 0.00 38.92 4.17
2974 3145 3.661648 GGCCCACACCCTGTCCAT 61.662 66.667 0.00 0.00 0.00 3.41
2975 3146 2.361610 GCCCACACCCTGTCCATG 60.362 66.667 0.00 0.00 0.00 3.66
2976 3147 2.905996 GCCCACACCCTGTCCATGA 61.906 63.158 0.00 0.00 0.00 3.07
2977 3148 1.300963 CCCACACCCTGTCCATGAG 59.699 63.158 0.00 0.00 0.00 2.90
2978 3149 1.300963 CCACACCCTGTCCATGAGG 59.699 63.158 0.00 0.00 0.00 3.86
2982 3153 3.001514 CCCTGTCCATGAGGGTGG 58.998 66.667 9.42 0.00 44.85 4.61
2983 3154 2.273449 CCTGTCCATGAGGGTGGC 59.727 66.667 0.00 0.00 39.19 5.01
2984 3155 2.124983 CTGTCCATGAGGGTGGCG 60.125 66.667 0.00 0.00 39.19 5.69
2985 3156 3.687321 CTGTCCATGAGGGTGGCGG 62.687 68.421 0.00 0.00 39.19 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
260 261 2.596851 GGCTCTGCTCAACCTCCCA 61.597 63.158 0.00 0.00 0.00 4.37
582 587 4.468689 GTACCCGCCCCTGTGCTC 62.469 72.222 0.00 0.00 0.00 4.26
659 664 4.695993 TTGCCACGCTCCGCATCA 62.696 61.111 0.00 0.00 34.35 3.07
665 670 3.123620 CTCTGCTTGCCACGCTCC 61.124 66.667 0.00 0.00 0.00 4.70
675 680 0.540923 CTTGCCCTAGAGCTCTGCTT 59.459 55.000 26.78 1.99 39.88 3.91
676 681 1.970352 GCTTGCCCTAGAGCTCTGCT 61.970 60.000 26.78 2.40 43.88 4.24
677 682 1.523484 GCTTGCCCTAGAGCTCTGC 60.523 63.158 26.78 20.69 36.01 4.26
678 683 0.179078 CTGCTTGCCCTAGAGCTCTG 60.179 60.000 26.78 15.29 39.60 3.35
679 684 0.325110 TCTGCTTGCCCTAGAGCTCT 60.325 55.000 22.17 22.17 39.60 4.09
680 685 0.104671 CTCTGCTTGCCCTAGAGCTC 59.895 60.000 5.27 5.27 39.60 4.09
681 686 2.210424 CTCTGCTTGCCCTAGAGCT 58.790 57.895 0.00 0.00 39.60 4.09
682 687 4.852962 CTCTGCTTGCCCTAGAGC 57.147 61.111 0.00 0.00 39.33 4.09
683 688 0.104671 GAGCTCTGCTTGCCCTAGAG 59.895 60.000 6.43 0.00 39.88 2.43
684 689 1.333636 GGAGCTCTGCTTGCCCTAGA 61.334 60.000 14.64 0.00 39.88 2.43
685 690 1.145819 GGAGCTCTGCTTGCCCTAG 59.854 63.158 14.64 0.00 39.88 3.02
686 691 1.613332 TGGAGCTCTGCTTGCCCTA 60.613 57.895 14.64 0.00 39.88 3.53
687 692 2.932194 TGGAGCTCTGCTTGCCCT 60.932 61.111 14.64 0.00 39.88 5.19
688 693 2.438075 CTGGAGCTCTGCTTGCCC 60.438 66.667 14.64 0.00 39.88 5.36
720 725 3.615056 CGATTTGTCACAGTATACCGCAA 59.385 43.478 0.00 0.00 0.00 4.85
765 770 4.154347 CGCAGTGAGCCCCTCCTC 62.154 72.222 0.00 0.00 41.38 3.71
857 862 3.405831 GATTGGCATCATCTTCATCCGA 58.594 45.455 0.00 0.00 0.00 4.55
858 863 2.486982 GGATTGGCATCATCTTCATCCG 59.513 50.000 0.00 0.00 0.00 4.18
873 878 2.046023 TCTGCAGTGCCGGATTGG 60.046 61.111 14.67 0.00 42.50 3.16
902 907 1.301716 GTCTGCAACTTCCGGCTCA 60.302 57.895 0.00 0.00 0.00 4.26
930 935 1.079819 CACAAGCTCCACCGTCGAT 60.080 57.895 0.00 0.00 0.00 3.59
1008 1013 3.767630 AAGTTCACCAGCCGCCGTT 62.768 57.895 0.00 0.00 0.00 4.44
1017 1022 1.227823 CACCTCCGCAAGTTCACCA 60.228 57.895 0.00 0.00 0.00 4.17
1076 1081 3.162154 CCCTCCCGAACCCTAGCC 61.162 72.222 0.00 0.00 0.00 3.93
1155 1161 1.302431 CATCGTGCAACCTCCCACA 60.302 57.895 0.00 0.00 32.37 4.17
1161 1167 2.672996 GTGGCCATCGTGCAACCT 60.673 61.111 9.72 0.00 0.00 3.50
1164 1170 4.321966 TCGGTGGCCATCGTGCAA 62.322 61.111 35.86 16.15 36.14 4.08
1204 1210 3.238497 CCACCACCGACACCCTCA 61.238 66.667 0.00 0.00 0.00 3.86
1259 1265 0.106015 AAAAGGCCAGAGGTGCACTT 60.106 50.000 17.98 9.59 0.00 3.16
1300 1308 9.507329 AAACAATTAGCAACTGAGAGAGATTAA 57.493 29.630 0.00 0.00 0.00 1.40
1346 1354 8.961294 TTTATTGAGCCAAATCCCATATTTTG 57.039 30.769 0.00 0.00 33.58 2.44
1386 1394 3.701040 CCAACCATTTTATAGCAGTGCCT 59.299 43.478 12.58 1.80 0.00 4.75
1556 1566 7.699566 ACAGTAAAACAAAAATGTTCGCTAGA 58.300 30.769 0.00 0.00 0.00 2.43
1727 1748 5.471257 ACGAGATTTCTTGTAGTGGAAGAC 58.529 41.667 0.00 0.00 38.76 3.01
1730 1751 4.322499 GGGACGAGATTTCTTGTAGTGGAA 60.322 45.833 0.37 0.00 40.54 3.53
1782 1805 6.215121 TCGTTAGAATTTCGTAACCAGAACA 58.785 36.000 10.49 0.00 0.00 3.18
1866 1892 6.416631 TCATGATGACCTGAAATAGAGGAG 57.583 41.667 0.00 0.00 34.37 3.69
2004 2056 5.450818 ACTTGGGAAATAGTTCATGCCTA 57.549 39.130 5.15 0.00 35.25 3.93
2014 2081 5.648092 CCCTGAGTTACAACTTGGGAAATAG 59.352 44.000 20.50 2.71 46.72 1.73
2021 2089 2.270352 TGCCCTGAGTTACAACTTGG 57.730 50.000 0.00 2.74 39.88 3.61
2083 2160 2.229792 GGGCATCGAATGATTGCCTAA 58.770 47.619 22.59 0.00 42.99 2.69
2210 2343 6.209391 CCTGTTTCCAAAGTTATTCCTCATGT 59.791 38.462 0.00 0.00 0.00 3.21
2290 2427 6.387465 GCCCTTTCTACTTTTAAACCACATC 58.613 40.000 0.00 0.00 0.00 3.06
2363 2507 1.206578 GTTGCCAACATGACCGACG 59.793 57.895 1.91 0.00 0.00 5.12
2466 2612 2.276201 CATTCTTGTAACCGCCGATGA 58.724 47.619 0.00 0.00 0.00 2.92
2576 2747 8.482128 TGTTTAAACACATTTTCCTCTCCATTT 58.518 29.630 17.01 0.00 33.17 2.32
2694 2865 3.976942 GCATGATGCAAAATGGACGTATC 59.023 43.478 13.36 0.00 44.26 2.24
2731 2902 9.593134 GTGAAATAACAACCCATAATGCAATAA 57.407 29.630 0.00 0.00 0.00 1.40
2732 2903 8.753133 TGTGAAATAACAACCCATAATGCAATA 58.247 29.630 0.00 0.00 0.00 1.90
2733 2904 7.619050 TGTGAAATAACAACCCATAATGCAAT 58.381 30.769 0.00 0.00 0.00 3.56
2734 2905 6.997655 TGTGAAATAACAACCCATAATGCAA 58.002 32.000 0.00 0.00 0.00 4.08
2735 2906 6.596309 TGTGAAATAACAACCCATAATGCA 57.404 33.333 0.00 0.00 0.00 3.96
2736 2907 9.762933 ATAATGTGAAATAACAACCCATAATGC 57.237 29.630 0.00 0.00 32.81 3.56
2740 2911 9.467796 TGACATAATGTGAAATAACAACCCATA 57.532 29.630 0.00 0.00 32.81 2.74
2741 2912 8.250332 GTGACATAATGTGAAATAACAACCCAT 58.750 33.333 0.00 0.00 32.81 4.00
2742 2913 7.231519 TGTGACATAATGTGAAATAACAACCCA 59.768 33.333 0.00 0.00 32.81 4.51
2743 2914 7.598278 TGTGACATAATGTGAAATAACAACCC 58.402 34.615 0.00 0.00 32.81 4.11
2744 2915 9.638239 ATTGTGACATAATGTGAAATAACAACC 57.362 29.630 0.00 0.00 32.81 3.77
2753 2924 9.898152 TCCATAAGTATTGTGACATAATGTGAA 57.102 29.630 7.62 0.00 39.84 3.18
2789 2960 9.689501 CCCTCCTTATGTAAACCTTGTAAATAA 57.310 33.333 0.00 0.00 0.00 1.40
2790 2961 9.060137 TCCCTCCTTATGTAAACCTTGTAAATA 57.940 33.333 0.00 0.00 0.00 1.40
2791 2962 7.935405 TCCCTCCTTATGTAAACCTTGTAAAT 58.065 34.615 0.00 0.00 0.00 1.40
2792 2963 7.238096 TCTCCCTCCTTATGTAAACCTTGTAAA 59.762 37.037 0.00 0.00 0.00 2.01
2793 2964 6.731919 TCTCCCTCCTTATGTAAACCTTGTAA 59.268 38.462 0.00 0.00 0.00 2.41
2794 2965 6.266080 TCTCCCTCCTTATGTAAACCTTGTA 58.734 40.000 0.00 0.00 0.00 2.41
2795 2966 5.098663 TCTCCCTCCTTATGTAAACCTTGT 58.901 41.667 0.00 0.00 0.00 3.16
2796 2967 5.693769 TCTCCCTCCTTATGTAAACCTTG 57.306 43.478 0.00 0.00 0.00 3.61
2797 2968 6.663734 CATTCTCCCTCCTTATGTAAACCTT 58.336 40.000 0.00 0.00 0.00 3.50
2798 2969 5.398012 GCATTCTCCCTCCTTATGTAAACCT 60.398 44.000 0.00 0.00 0.00 3.50
2799 2970 4.822350 GCATTCTCCCTCCTTATGTAAACC 59.178 45.833 0.00 0.00 0.00 3.27
2800 2971 4.822350 GGCATTCTCCCTCCTTATGTAAAC 59.178 45.833 0.00 0.00 0.00 2.01
2801 2972 4.444306 CGGCATTCTCCCTCCTTATGTAAA 60.444 45.833 0.00 0.00 0.00 2.01
2802 2973 3.071023 CGGCATTCTCCCTCCTTATGTAA 59.929 47.826 0.00 0.00 0.00 2.41
2803 2974 2.632996 CGGCATTCTCCCTCCTTATGTA 59.367 50.000 0.00 0.00 0.00 2.29
2804 2975 1.417890 CGGCATTCTCCCTCCTTATGT 59.582 52.381 0.00 0.00 0.00 2.29
2805 2976 1.271054 CCGGCATTCTCCCTCCTTATG 60.271 57.143 0.00 0.00 0.00 1.90
2806 2977 1.059913 CCGGCATTCTCCCTCCTTAT 58.940 55.000 0.00 0.00 0.00 1.73
2807 2978 1.696097 GCCGGCATTCTCCCTCCTTA 61.696 60.000 24.80 0.00 0.00 2.69
2808 2979 3.049080 GCCGGCATTCTCCCTCCTT 62.049 63.158 24.80 0.00 0.00 3.36
2809 2980 3.483869 GCCGGCATTCTCCCTCCT 61.484 66.667 24.80 0.00 0.00 3.69
2810 2981 3.125376 ATGCCGGCATTCTCCCTCC 62.125 63.158 36.10 0.00 31.82 4.30
2811 2982 1.599240 GATGCCGGCATTCTCCCTC 60.599 63.158 40.56 24.48 36.70 4.30
2812 2983 2.074948 AGATGCCGGCATTCTCCCT 61.075 57.895 40.56 29.14 36.70 4.20
2813 2984 1.895707 CAGATGCCGGCATTCTCCC 60.896 63.158 40.56 27.42 36.70 4.30
2814 2985 1.895707 CCAGATGCCGGCATTCTCC 60.896 63.158 40.56 27.79 36.70 3.71
2815 2986 0.464373 TTCCAGATGCCGGCATTCTC 60.464 55.000 40.56 29.44 36.70 2.87
2816 2987 0.184451 ATTCCAGATGCCGGCATTCT 59.816 50.000 40.56 32.18 36.70 2.40
2817 2988 1.000938 GAATTCCAGATGCCGGCATTC 60.001 52.381 40.56 30.69 36.70 2.67
2818 2989 1.035139 GAATTCCAGATGCCGGCATT 58.965 50.000 40.56 26.91 36.70 3.56
2819 2990 0.184451 AGAATTCCAGATGCCGGCAT 59.816 50.000 41.16 41.16 39.69 4.40
2820 2991 0.749091 CAGAATTCCAGATGCCGGCA 60.749 55.000 34.80 34.80 0.00 5.69
2821 2992 1.450531 CCAGAATTCCAGATGCCGGC 61.451 60.000 22.73 22.73 0.00 6.13
2822 2993 0.820891 CCCAGAATTCCAGATGCCGG 60.821 60.000 0.65 0.00 0.00 6.13
2823 2994 1.450531 GCCCAGAATTCCAGATGCCG 61.451 60.000 0.65 0.00 0.00 5.69
2824 2995 0.106318 AGCCCAGAATTCCAGATGCC 60.106 55.000 0.65 0.00 0.00 4.40
2825 2996 1.030457 CAGCCCAGAATTCCAGATGC 58.970 55.000 0.65 2.44 0.00 3.91
2826 2997 1.213678 TCCAGCCCAGAATTCCAGATG 59.786 52.381 0.65 0.10 0.00 2.90
2827 2998 1.600058 TCCAGCCCAGAATTCCAGAT 58.400 50.000 0.65 0.00 0.00 2.90
2828 2999 1.371467 TTCCAGCCCAGAATTCCAGA 58.629 50.000 0.65 0.00 0.00 3.86
2829 3000 2.220653 TTTCCAGCCCAGAATTCCAG 57.779 50.000 0.65 0.00 0.00 3.86
2830 3001 2.528564 CTTTTCCAGCCCAGAATTCCA 58.471 47.619 0.65 0.00 0.00 3.53
2831 3002 1.827344 CCTTTTCCAGCCCAGAATTCC 59.173 52.381 0.65 0.00 0.00 3.01
2832 3003 2.757314 CTCCTTTTCCAGCCCAGAATTC 59.243 50.000 0.00 0.00 0.00 2.17
2833 3004 2.812658 CTCCTTTTCCAGCCCAGAATT 58.187 47.619 0.00 0.00 0.00 2.17
2834 3005 1.618074 GCTCCTTTTCCAGCCCAGAAT 60.618 52.381 0.00 0.00 0.00 2.40
2835 3006 0.251341 GCTCCTTTTCCAGCCCAGAA 60.251 55.000 0.00 0.00 0.00 3.02
2836 3007 1.380302 GCTCCTTTTCCAGCCCAGA 59.620 57.895 0.00 0.00 0.00 3.86
2837 3008 0.540365 TTGCTCCTTTTCCAGCCCAG 60.540 55.000 0.00 0.00 34.47 4.45
2838 3009 0.105760 TTTGCTCCTTTTCCAGCCCA 60.106 50.000 0.00 0.00 34.47 5.36
2839 3010 1.269958 ATTTGCTCCTTTTCCAGCCC 58.730 50.000 0.00 0.00 34.47 5.19
2840 3011 4.743057 AATATTTGCTCCTTTTCCAGCC 57.257 40.909 0.00 0.00 34.47 4.85
2841 3012 6.543831 TCTCTAATATTTGCTCCTTTTCCAGC 59.456 38.462 0.00 0.00 36.08 4.85
2842 3013 7.012799 GGTCTCTAATATTTGCTCCTTTTCCAG 59.987 40.741 0.00 0.00 0.00 3.86
2843 3014 6.828785 GGTCTCTAATATTTGCTCCTTTTCCA 59.171 38.462 0.00 0.00 0.00 3.53
2844 3015 7.057264 AGGTCTCTAATATTTGCTCCTTTTCC 58.943 38.462 0.00 0.00 0.00 3.13
2845 3016 9.785982 ATAGGTCTCTAATATTTGCTCCTTTTC 57.214 33.333 0.00 0.00 0.00 2.29
2850 3021 9.103861 GCATAATAGGTCTCTAATATTTGCTCC 57.896 37.037 0.00 0.00 0.00 4.70
2851 3022 9.658799 TGCATAATAGGTCTCTAATATTTGCTC 57.341 33.333 0.00 0.00 31.57 4.26
2852 3023 9.442047 GTGCATAATAGGTCTCTAATATTTGCT 57.558 33.333 0.00 0.00 31.57 3.91
2853 3024 9.219603 TGTGCATAATAGGTCTCTAATATTTGC 57.780 33.333 0.00 0.00 0.00 3.68
2858 3029 8.585881 GGAGTTGTGCATAATAGGTCTCTAATA 58.414 37.037 0.00 0.00 0.00 0.98
2859 3030 7.071196 TGGAGTTGTGCATAATAGGTCTCTAAT 59.929 37.037 0.00 0.00 0.00 1.73
2860 3031 6.382859 TGGAGTTGTGCATAATAGGTCTCTAA 59.617 38.462 0.00 0.00 0.00 2.10
2861 3032 5.897250 TGGAGTTGTGCATAATAGGTCTCTA 59.103 40.000 0.00 0.00 0.00 2.43
2862 3033 4.716784 TGGAGTTGTGCATAATAGGTCTCT 59.283 41.667 0.00 0.00 0.00 3.10
2863 3034 5.023533 TGGAGTTGTGCATAATAGGTCTC 57.976 43.478 0.00 0.86 0.00 3.36
2864 3035 5.435686 TTGGAGTTGTGCATAATAGGTCT 57.564 39.130 0.00 0.00 0.00 3.85
2865 3036 6.151144 ACTTTTGGAGTTGTGCATAATAGGTC 59.849 38.462 0.00 0.00 33.92 3.85
2866 3037 6.010219 ACTTTTGGAGTTGTGCATAATAGGT 58.990 36.000 0.00 0.00 33.92 3.08
2867 3038 6.404734 GGACTTTTGGAGTTGTGCATAATAGG 60.405 42.308 0.00 0.00 39.19 2.57
2868 3039 6.404734 GGGACTTTTGGAGTTGTGCATAATAG 60.405 42.308 0.00 0.00 39.19 1.73
2869 3040 5.417580 GGGACTTTTGGAGTTGTGCATAATA 59.582 40.000 0.00 0.00 39.19 0.98
2870 3041 4.220602 GGGACTTTTGGAGTTGTGCATAAT 59.779 41.667 0.00 0.00 39.19 1.28
2871 3042 3.572255 GGGACTTTTGGAGTTGTGCATAA 59.428 43.478 0.00 0.00 39.19 1.90
2872 3043 3.153919 GGGACTTTTGGAGTTGTGCATA 58.846 45.455 0.00 0.00 39.19 3.14
2873 3044 1.963515 GGGACTTTTGGAGTTGTGCAT 59.036 47.619 0.00 0.00 39.19 3.96
2874 3045 1.398692 GGGACTTTTGGAGTTGTGCA 58.601 50.000 0.00 0.00 39.19 4.57
2875 3046 0.310854 CGGGACTTTTGGAGTTGTGC 59.689 55.000 0.00 0.00 39.19 4.57
2876 3047 1.961793 TCGGGACTTTTGGAGTTGTG 58.038 50.000 0.00 0.00 39.19 3.33
2877 3048 2.686405 GTTTCGGGACTTTTGGAGTTGT 59.314 45.455 0.00 0.00 39.19 3.32
2878 3049 2.949644 AGTTTCGGGACTTTTGGAGTTG 59.050 45.455 0.00 0.00 39.19 3.16
2879 3050 3.211865 GAGTTTCGGGACTTTTGGAGTT 58.788 45.455 0.00 0.00 39.19 3.01
2880 3051 2.486727 GGAGTTTCGGGACTTTTGGAGT 60.487 50.000 0.00 0.00 42.70 3.85
2881 3052 2.152016 GGAGTTTCGGGACTTTTGGAG 58.848 52.381 0.00 0.00 0.00 3.86
2882 3053 1.491332 TGGAGTTTCGGGACTTTTGGA 59.509 47.619 0.00 0.00 0.00 3.53
2883 3054 1.607148 GTGGAGTTTCGGGACTTTTGG 59.393 52.381 0.00 0.00 0.00 3.28
2884 3055 1.263217 CGTGGAGTTTCGGGACTTTTG 59.737 52.381 0.00 0.00 0.00 2.44
2885 3056 1.589803 CGTGGAGTTTCGGGACTTTT 58.410 50.000 0.00 0.00 0.00 2.27
2886 3057 0.250166 CCGTGGAGTTTCGGGACTTT 60.250 55.000 0.00 0.00 42.61 2.66
2887 3058 1.117142 TCCGTGGAGTTTCGGGACTT 61.117 55.000 3.85 0.00 45.79 3.01
2888 3059 1.117142 TTCCGTGGAGTTTCGGGACT 61.117 55.000 3.85 0.00 45.79 3.85
2889 3060 0.036671 ATTCCGTGGAGTTTCGGGAC 60.037 55.000 3.85 0.00 45.79 4.46
2890 3061 1.205417 GTATTCCGTGGAGTTTCGGGA 59.795 52.381 3.85 0.00 45.79 5.14
2891 3062 1.648504 GTATTCCGTGGAGTTTCGGG 58.351 55.000 3.85 0.00 45.79 5.14
2892 3063 1.206371 AGGTATTCCGTGGAGTTTCGG 59.794 52.381 0.00 0.00 46.93 4.30
2893 3064 2.667473 AGGTATTCCGTGGAGTTTCG 57.333 50.000 0.00 0.00 39.05 3.46
2894 3065 9.768662 TTATTATAAGGTATTCCGTGGAGTTTC 57.231 33.333 0.00 0.00 39.05 2.78
2916 3087 9.883142 TTTGGCGAGGATTTTTCATTATTTATT 57.117 25.926 0.00 0.00 0.00 1.40
2917 3088 9.533253 CTTTGGCGAGGATTTTTCATTATTTAT 57.467 29.630 0.00 0.00 0.00 1.40
2918 3089 8.744652 TCTTTGGCGAGGATTTTTCATTATTTA 58.255 29.630 0.00 0.00 0.00 1.40
2919 3090 7.610865 TCTTTGGCGAGGATTTTTCATTATTT 58.389 30.769 0.00 0.00 0.00 1.40
2920 3091 7.169158 TCTTTGGCGAGGATTTTTCATTATT 57.831 32.000 0.00 0.00 0.00 1.40
2921 3092 6.773976 TCTTTGGCGAGGATTTTTCATTAT 57.226 33.333 0.00 0.00 0.00 1.28
2922 3093 6.773976 ATCTTTGGCGAGGATTTTTCATTA 57.226 33.333 0.00 0.00 0.00 1.90
2923 3094 5.665916 ATCTTTGGCGAGGATTTTTCATT 57.334 34.783 0.00 0.00 0.00 2.57
2924 3095 5.665916 AATCTTTGGCGAGGATTTTTCAT 57.334 34.783 6.28 0.00 0.00 2.57
2925 3096 6.432783 TCTTAATCTTTGGCGAGGATTTTTCA 59.567 34.615 16.26 0.00 32.78 2.69
2926 3097 6.747739 GTCTTAATCTTTGGCGAGGATTTTTC 59.252 38.462 16.26 3.61 32.78 2.29
2927 3098 6.350194 GGTCTTAATCTTTGGCGAGGATTTTT 60.350 38.462 16.26 0.00 32.78 1.94
2928 3099 5.125578 GGTCTTAATCTTTGGCGAGGATTTT 59.874 40.000 16.26 0.00 32.78 1.82
2929 3100 4.640647 GGTCTTAATCTTTGGCGAGGATTT 59.359 41.667 16.26 2.89 32.78 2.17
2930 3101 4.200092 GGTCTTAATCTTTGGCGAGGATT 58.800 43.478 15.49 15.49 34.59 3.01
2931 3102 3.199946 TGGTCTTAATCTTTGGCGAGGAT 59.800 43.478 0.00 0.00 0.00 3.24
2932 3103 2.569853 TGGTCTTAATCTTTGGCGAGGA 59.430 45.455 0.00 0.00 0.00 3.71
2933 3104 2.939103 CTGGTCTTAATCTTTGGCGAGG 59.061 50.000 0.00 0.00 0.00 4.63
2934 3105 2.939103 CCTGGTCTTAATCTTTGGCGAG 59.061 50.000 0.00 0.00 0.00 5.03
2935 3106 2.355716 CCCTGGTCTTAATCTTTGGCGA 60.356 50.000 0.00 0.00 0.00 5.54
2936 3107 2.017049 CCCTGGTCTTAATCTTTGGCG 58.983 52.381 0.00 0.00 0.00 5.69
2937 3108 2.379005 CCCCTGGTCTTAATCTTTGGC 58.621 52.381 0.00 0.00 0.00 4.52
2938 3109 2.950418 GCCCCCTGGTCTTAATCTTTGG 60.950 54.545 0.00 0.00 0.00 3.28
2939 3110 2.379005 GCCCCCTGGTCTTAATCTTTG 58.621 52.381 0.00 0.00 0.00 2.77
2940 3111 1.288037 GGCCCCCTGGTCTTAATCTTT 59.712 52.381 0.00 0.00 31.67 2.52
2941 3112 0.927029 GGCCCCCTGGTCTTAATCTT 59.073 55.000 0.00 0.00 31.67 2.40
2942 3113 0.994050 GGGCCCCCTGGTCTTAATCT 60.994 60.000 12.23 0.00 36.12 2.40
2943 3114 1.286305 TGGGCCCCCTGGTCTTAATC 61.286 60.000 22.27 0.00 36.12 1.75
2944 3115 1.230482 TGGGCCCCCTGGTCTTAAT 60.230 57.895 22.27 0.00 36.12 1.40
2945 3116 2.211575 TGGGCCCCCTGGTCTTAA 59.788 61.111 22.27 0.00 36.12 1.85
2946 3117 2.612746 GTGGGCCCCCTGGTCTTA 60.613 66.667 22.27 0.00 36.12 2.10
2947 3118 4.938756 TGTGGGCCCCCTGGTCTT 62.939 66.667 22.27 0.00 36.12 3.01
2957 3128 3.661648 ATGGACAGGGTGTGGGCC 61.662 66.667 0.00 0.00 0.00 5.80
2958 3129 2.361610 CATGGACAGGGTGTGGGC 60.362 66.667 0.00 0.00 0.00 5.36
2959 3130 1.300963 CTCATGGACAGGGTGTGGG 59.699 63.158 0.00 0.00 0.00 4.61
2960 3131 1.300963 CCTCATGGACAGGGTGTGG 59.699 63.158 0.00 0.00 34.57 4.17
2961 3132 1.300963 CCCTCATGGACAGGGTGTG 59.699 63.158 9.42 0.00 45.35 3.82
2962 3133 3.826282 CCCTCATGGACAGGGTGT 58.174 61.111 9.42 0.00 45.35 4.16
2966 3137 2.273449 GCCACCCTCATGGACAGG 59.727 66.667 0.00 0.00 43.02 4.00
2967 3138 2.124983 CGCCACCCTCATGGACAG 60.125 66.667 0.00 0.00 43.02 3.51
2968 3139 3.716195 CCGCCACCCTCATGGACA 61.716 66.667 0.00 0.00 43.02 4.02


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

AutoCloner maintained by Alex Coulton.