Multiple sequence alignment - TraesCS3A01G291100

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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 TraesCS3A01G291100 chr3A 100.000 5719 0 0 1 5719 521309475 521303757 0.000000e+00 10562.0
1 TraesCS3A01G291100 chr3A 89.676 678 58 9 3 675 716376299 716376969 0.000000e+00 854.0
2 TraesCS3A01G291100 chr3A 87.874 701 49 10 1 678 728891964 728891277 0.000000e+00 791.0
3 TraesCS3A01G291100 chr3A 79.720 143 19 5 2336 2471 11941025 11940886 1.700000e-15 95.3
4 TraesCS3A01G291100 chr3A 87.500 80 8 2 2388 2467 575492153 575492076 2.190000e-14 91.6
5 TraesCS3A01G291100 chr3A 98.000 50 1 0 2331 2380 724371540 724371589 2.840000e-13 87.9
6 TraesCS3A01G291100 chr3D 95.309 2025 57 13 3722 5717 400994957 400992942 0.000000e+00 3179.0
7 TraesCS3A01G291100 chr3D 92.870 2146 100 23 1616 3724 400997115 400994986 0.000000e+00 3066.0
8 TraesCS3A01G291100 chr3D 83.540 322 20 13 701 993 400999237 400998920 2.630000e-68 270.0
9 TraesCS3A01G291100 chr3D 90.000 80 6 1 2388 2467 437486615 437486538 1.010000e-17 102.0
10 TraesCS3A01G291100 chr3D 98.077 52 1 0 2331 2382 593106489 593106540 2.190000e-14 91.6
11 TraesCS3A01G291100 chr3B 93.582 1823 70 23 2984 4786 526696815 526695020 0.000000e+00 2675.0
12 TraesCS3A01G291100 chr3B 92.434 1520 75 4 1460 2954 526698317 526696813 0.000000e+00 2134.0
13 TraesCS3A01G291100 chr3B 93.906 919 27 4 4825 5719 526694753 526693840 0.000000e+00 1360.0
14 TraesCS3A01G291100 chr3B 85.282 727 56 18 780 1475 526699041 526698335 0.000000e+00 702.0
15 TraesCS3A01G291100 chr3B 100.000 41 0 0 4786 4826 526694896 526694856 6.140000e-10 76.8
16 TraesCS3A01G291100 chr2A 90.355 705 42 6 1 680 758540439 758541142 0.000000e+00 902.0
17 TraesCS3A01G291100 chr2A 90.029 682 63 4 3 680 738120819 738120139 0.000000e+00 878.0
18 TraesCS3A01G291100 chr5A 90.511 685 58 6 1 680 509986825 509987507 0.000000e+00 898.0
19 TraesCS3A01G291100 chr5A 89.033 693 66 8 3 689 622105702 622105014 0.000000e+00 850.0
20 TraesCS3A01G291100 chr6A 89.474 703 46 8 1 678 80518846 80518147 0.000000e+00 863.0
21 TraesCS3A01G291100 chr6A 87.500 80 8 1 2388 2467 263886940 263887017 2.190000e-14 91.6
22 TraesCS3A01G291100 chr6A 87.719 57 5 2 2322 2378 110335386 110335332 1.330000e-06 65.8
23 TraesCS3A01G291100 chr7A 89.205 704 49 16 1 678 63408837 63408135 0.000000e+00 854.0
24 TraesCS3A01G291100 chr7A 88.427 674 51 12 33 681 272570742 272571413 0.000000e+00 787.0
25 TraesCS3A01G291100 chr7A 87.500 680 79 6 3 678 35982807 35982130 0.000000e+00 780.0
26 TraesCS3A01G291100 chr7A 80.519 154 9 9 2333 2467 701301359 701301510 1.310000e-16 99.0
27 TraesCS3A01G291100 chr1A 87.712 708 57 13 1 680 471935978 471936683 0.000000e+00 798.0
28 TraesCS3A01G291100 chr1A 88.889 45 5 0 2338 2382 361357561 361357517 8.010000e-04 56.5
29 TraesCS3A01G291100 chr2D 85.841 113 12 4 5146 5256 579594895 579595005 3.620000e-22 117.0
30 TraesCS3A01G291100 chr2D 96.000 50 2 0 2333 2382 102591825 102591874 1.320000e-11 82.4
31 TraesCS3A01G291100 chr6D 88.372 86 7 2 2392 2476 12492316 12492399 3.650000e-17 100.0
32 TraesCS3A01G291100 chr6D 89.474 57 4 2 2322 2378 91560272 91560218 2.860000e-08 71.3
33 TraesCS3A01G291100 chr4A 80.132 151 16 9 2328 2467 543368290 543368437 3.650000e-17 100.0
34 TraesCS3A01G291100 chr4D 79.730 148 16 9 2331 2467 53760138 53759994 1.700000e-15 95.3
35 TraesCS3A01G291100 chr6B 83.505 97 12 4 2354 2448 455419170 455419264 2.840000e-13 87.9
36 TraesCS3A01G291100 chr6B 87.719 57 5 2 2322 2378 175712769 175712715 1.330000e-06 65.8
37 TraesCS3A01G291100 chr4B 79.646 113 19 4 5146 5256 227095269 227095159 1.710000e-10 78.7


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 TraesCS3A01G291100 chr3A 521303757 521309475 5718 True 10562.000000 10562 100.0000 1 5719 1 chr3A.!!$R2 5718
1 TraesCS3A01G291100 chr3A 716376299 716376969 670 False 854.000000 854 89.6760 3 675 1 chr3A.!!$F1 672
2 TraesCS3A01G291100 chr3A 728891277 728891964 687 True 791.000000 791 87.8740 1 678 1 chr3A.!!$R4 677
3 TraesCS3A01G291100 chr3D 400992942 400999237 6295 True 2171.666667 3179 90.5730 701 5717 3 chr3D.!!$R2 5016
4 TraesCS3A01G291100 chr3B 526693840 526699041 5201 True 1389.560000 2675 93.0408 780 5719 5 chr3B.!!$R1 4939
5 TraesCS3A01G291100 chr2A 758540439 758541142 703 False 902.000000 902 90.3550 1 680 1 chr2A.!!$F1 679
6 TraesCS3A01G291100 chr2A 738120139 738120819 680 True 878.000000 878 90.0290 3 680 1 chr2A.!!$R1 677
7 TraesCS3A01G291100 chr5A 509986825 509987507 682 False 898.000000 898 90.5110 1 680 1 chr5A.!!$F1 679
8 TraesCS3A01G291100 chr5A 622105014 622105702 688 True 850.000000 850 89.0330 3 689 1 chr5A.!!$R1 686
9 TraesCS3A01G291100 chr6A 80518147 80518846 699 True 863.000000 863 89.4740 1 678 1 chr6A.!!$R1 677
10 TraesCS3A01G291100 chr7A 63408135 63408837 702 True 854.000000 854 89.2050 1 678 1 chr7A.!!$R2 677
11 TraesCS3A01G291100 chr7A 272570742 272571413 671 False 787.000000 787 88.4270 33 681 1 chr7A.!!$F1 648
12 TraesCS3A01G291100 chr7A 35982130 35982807 677 True 780.000000 780 87.5000 3 678 1 chr7A.!!$R1 675
13 TraesCS3A01G291100 chr1A 471935978 471936683 705 False 798.000000 798 87.7120 1 680 1 chr1A.!!$F1 679

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
598 648 0.038166 ATGGCTGGGAACGTGTTCAT 59.962 50.0 14.16 0.0 41.20 2.57 F
1081 1167 0.041576 TCTTCGTCGCGATATCACCG 60.042 55.0 14.06 10.5 35.23 4.94 F
1907 3284 0.537188 CCTGCCTCGAGGTTGTGTAT 59.463 55.0 31.43 0.0 37.57 2.29 F
3540 4970 2.608016 CGCTCTACACTCAGTGCTTCAA 60.608 50.0 4.13 0.0 36.98 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1555 1805 0.247814 GCTGAACATGACATTCGGCG 60.248 55.000 11.33 0.0 45.74 6.46 R
2862 4284 1.185618 TGAGTAGCAAGACCGGCAGT 61.186 55.000 0.00 0.0 0.00 4.40 R
3680 5111 3.689872 TCTGCCTTCCTCCTATGTAGT 57.310 47.619 0.00 0.0 0.00 2.73 R
5066 6776 1.130561 GTTTCGCTGCACATACTTCCC 59.869 52.381 0.00 0.0 0.00 3.97 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
67 69 3.792047 CCGACGTACGTGCTCCGA 61.792 66.667 28.16 0.00 40.70 4.55
140 143 0.458669 GAGACGCCCTATTTCCACGA 59.541 55.000 0.00 0.00 0.00 4.35
565 614 3.636231 CTGTGGGGGCGTCTGGAA 61.636 66.667 0.00 0.00 0.00 3.53
567 616 2.355115 GTGGGGGCGTCTGGAAAT 59.645 61.111 0.00 0.00 0.00 2.17
579 629 0.322456 CTGGAAATGACTTGGGGCGA 60.322 55.000 0.00 0.00 0.00 5.54
580 630 0.331278 TGGAAATGACTTGGGGCGAT 59.669 50.000 0.00 0.00 0.00 4.58
598 648 0.038166 ATGGCTGGGAACGTGTTCAT 59.962 50.000 14.16 0.00 41.20 2.57
682 736 2.355010 GGCTGAAGATGCCCTAATGT 57.645 50.000 0.00 0.00 44.32 2.71
683 737 1.952296 GGCTGAAGATGCCCTAATGTG 59.048 52.381 0.00 0.00 44.32 3.21
684 738 2.421952 GGCTGAAGATGCCCTAATGTGA 60.422 50.000 0.00 0.00 44.32 3.58
685 739 2.615912 GCTGAAGATGCCCTAATGTGAC 59.384 50.000 0.00 0.00 0.00 3.67
686 740 3.209410 CTGAAGATGCCCTAATGTGACC 58.791 50.000 0.00 0.00 0.00 4.02
687 741 2.575735 TGAAGATGCCCTAATGTGACCA 59.424 45.455 0.00 0.00 0.00 4.02
688 742 3.010027 TGAAGATGCCCTAATGTGACCAA 59.990 43.478 0.00 0.00 0.00 3.67
689 743 3.959495 AGATGCCCTAATGTGACCAAT 57.041 42.857 0.00 0.00 0.00 3.16
690 744 3.825328 AGATGCCCTAATGTGACCAATC 58.175 45.455 0.00 0.00 0.00 2.67
691 745 3.202818 AGATGCCCTAATGTGACCAATCA 59.797 43.478 0.00 0.00 0.00 2.57
692 746 3.448093 TGCCCTAATGTGACCAATCAA 57.552 42.857 0.00 0.00 36.31 2.57
693 747 3.772387 TGCCCTAATGTGACCAATCAAA 58.228 40.909 0.00 0.00 36.31 2.69
694 748 4.155709 TGCCCTAATGTGACCAATCAAAA 58.844 39.130 0.00 0.00 36.31 2.44
695 749 4.220382 TGCCCTAATGTGACCAATCAAAAG 59.780 41.667 0.00 0.00 36.31 2.27
696 750 4.747810 CCCTAATGTGACCAATCAAAAGC 58.252 43.478 0.00 0.00 36.31 3.51
697 751 4.414852 CCTAATGTGACCAATCAAAAGCG 58.585 43.478 0.00 0.00 36.31 4.68
698 752 4.082787 CCTAATGTGACCAATCAAAAGCGT 60.083 41.667 0.00 0.00 36.31 5.07
699 753 4.320608 AATGTGACCAATCAAAAGCGTT 57.679 36.364 0.00 0.00 36.31 4.84
700 754 3.347958 TGTGACCAATCAAAAGCGTTC 57.652 42.857 0.00 0.00 36.31 3.95
701 755 2.948979 TGTGACCAATCAAAAGCGTTCT 59.051 40.909 0.00 0.00 36.31 3.01
702 756 3.380004 TGTGACCAATCAAAAGCGTTCTT 59.620 39.130 0.00 0.00 36.31 2.52
703 757 3.730715 GTGACCAATCAAAAGCGTTCTTG 59.269 43.478 0.00 0.00 36.31 3.02
704 758 3.629855 TGACCAATCAAAAGCGTTCTTGA 59.370 39.130 0.00 0.00 36.08 3.02
705 759 4.278170 TGACCAATCAAAAGCGTTCTTGAT 59.722 37.500 0.00 0.00 42.67 2.57
706 760 4.549458 ACCAATCAAAAGCGTTCTTGATG 58.451 39.130 1.31 0.00 40.54 3.07
710 764 4.209452 TCAAAAGCGTTCTTGATGTGAC 57.791 40.909 0.00 0.00 31.78 3.67
725 779 0.580104 GTGACGAAACAAGTCCGTGG 59.420 55.000 5.55 0.00 37.80 4.94
734 788 2.786777 ACAAGTCCGTGGGAAAATACC 58.213 47.619 0.00 0.00 31.38 2.73
742 796 6.328148 AGTCCGTGGGAAAATACCTTCATATA 59.672 38.462 0.00 0.00 31.38 0.86
743 797 7.017254 AGTCCGTGGGAAAATACCTTCATATAT 59.983 37.037 0.00 0.00 31.38 0.86
751 805 9.232473 GGAAAATACCTTCATATATTCACTCCC 57.768 37.037 0.00 0.00 0.00 4.30
763 817 1.189524 TCACTCCCTGGTAACCCGTG 61.190 60.000 0.00 0.00 0.00 4.94
764 818 1.916777 ACTCCCTGGTAACCCGTGG 60.917 63.158 0.00 0.00 0.00 4.94
777 831 1.153249 CCGTGGCCGTGGACATATT 60.153 57.895 7.28 0.00 34.62 1.28
789 843 5.049060 CCGTGGACATATTTTCAGTTCAACA 60.049 40.000 0.00 0.00 0.00 3.33
811 865 2.639839 ACCCAGCTCAACAGTAGTCAAT 59.360 45.455 0.00 0.00 0.00 2.57
824 878 3.012722 TCAATCCCCGGTCCCCAC 61.013 66.667 0.00 0.00 0.00 4.61
825 879 3.015145 CAATCCCCGGTCCCCACT 61.015 66.667 0.00 0.00 0.00 4.00
911 994 1.705186 CCTTCTTCTTCCCTCCCACAA 59.295 52.381 0.00 0.00 0.00 3.33
963 1046 4.070552 GCCTCACCTCGCGACCTT 62.071 66.667 3.71 0.00 0.00 3.50
980 1063 3.135994 ACCTTGTACGCGTCAAAGAAAT 58.864 40.909 26.63 13.93 0.00 2.17
1008 1091 2.249535 CCGATTCGCCATGGCTCAG 61.250 63.158 33.07 18.78 39.32 3.35
1011 1094 0.883814 GATTCGCCATGGCTCAGGAG 60.884 60.000 33.07 17.27 39.32 3.69
1024 1107 1.213678 CTCAGGAGCAATCCAATCCCA 59.786 52.381 0.00 0.00 33.30 4.37
1035 1118 1.279846 TCCAATCCCAACGAGGTAACC 59.720 52.381 0.00 0.00 34.66 2.85
1036 1119 1.365699 CAATCCCAACGAGGTAACCG 58.634 55.000 0.00 0.00 34.66 4.44
1042 1125 0.316204 CAACGAGGTAACCGTCCAGT 59.684 55.000 0.00 0.00 41.56 4.00
1056 1139 2.541556 GTCCAGTACGATTCTTGGCTC 58.458 52.381 0.00 0.00 0.00 4.70
1070 1156 0.805614 TGGCTCTCTCTTCTTCGTCG 59.194 55.000 0.00 0.00 0.00 5.12
1072 1158 0.859788 GCTCTCTCTTCTTCGTCGCG 60.860 60.000 0.00 0.00 0.00 5.87
1073 1159 0.722282 CTCTCTCTTCTTCGTCGCGA 59.278 55.000 3.71 3.71 0.00 5.87
1074 1160 1.329292 CTCTCTCTTCTTCGTCGCGAT 59.671 52.381 14.06 0.00 35.23 4.58
1075 1161 2.540516 CTCTCTCTTCTTCGTCGCGATA 59.459 50.000 14.06 0.00 35.23 2.92
1076 1162 3.132160 TCTCTCTTCTTCGTCGCGATAT 58.868 45.455 14.06 0.00 35.23 1.63
1077 1163 3.184783 TCTCTCTTCTTCGTCGCGATATC 59.815 47.826 14.06 0.00 35.23 1.63
1078 1164 2.870411 TCTCTTCTTCGTCGCGATATCA 59.130 45.455 14.06 0.00 35.23 2.15
1080 1166 2.044860 CTTCTTCGTCGCGATATCACC 58.955 52.381 14.06 0.00 35.23 4.02
1081 1167 0.041576 TCTTCGTCGCGATATCACCG 60.042 55.000 14.06 10.50 35.23 4.94
1082 1168 0.997226 CTTCGTCGCGATATCACCGG 60.997 60.000 14.06 0.00 35.23 5.28
1083 1169 2.994143 TTCGTCGCGATATCACCGGC 62.994 60.000 14.06 9.36 35.23 6.13
1084 1170 2.335369 GTCGCGATATCACCGGCT 59.665 61.111 14.06 0.00 0.00 5.52
1127 1213 2.505777 CTCTCTGCGCAGGTCGTG 60.506 66.667 35.36 20.21 41.07 4.35
1212 1298 3.151958 AACGACAGAGTGGTGCGCT 62.152 57.895 9.73 0.00 0.00 5.92
1227 1314 1.519013 CGCTCTCTTGCTCTGGCTC 60.519 63.158 0.00 0.00 39.59 4.70
1238 1325 0.539051 CTCTGGCTCGGGAGATGTTT 59.461 55.000 0.00 0.00 38.80 2.83
1244 1331 2.872858 GGCTCGGGAGATGTTTGATTAC 59.127 50.000 0.00 0.00 38.80 1.89
1246 1333 3.938963 GCTCGGGAGATGTTTGATTACAA 59.061 43.478 0.00 0.00 38.80 2.41
1291 1485 2.096466 TCGCGACTGCTTATTTGTGTTG 60.096 45.455 3.71 0.00 39.65 3.33
1294 1488 2.668279 CGACTGCTTATTTGTGTTGGGC 60.668 50.000 0.00 0.00 0.00 5.36
1299 1493 4.402829 TGCTTATTTGTGTTGGGCTTCTA 58.597 39.130 0.00 0.00 0.00 2.10
1300 1494 4.830046 TGCTTATTTGTGTTGGGCTTCTAA 59.170 37.500 0.00 0.00 0.00 2.10
1301 1495 5.480073 TGCTTATTTGTGTTGGGCTTCTAAT 59.520 36.000 0.00 0.00 0.00 1.73
1302 1496 6.014669 TGCTTATTTGTGTTGGGCTTCTAATT 60.015 34.615 0.00 0.00 0.00 1.40
1304 1498 8.032451 GCTTATTTGTGTTGGGCTTCTAATTTA 58.968 33.333 0.00 0.00 0.00 1.40
1305 1499 9.921637 CTTATTTGTGTTGGGCTTCTAATTTAA 57.078 29.630 0.00 0.00 0.00 1.52
1308 1502 9.791801 ATTTGTGTTGGGCTTCTAATTTAATTT 57.208 25.926 0.00 0.00 0.00 1.82
1309 1503 8.600449 TTGTGTTGGGCTTCTAATTTAATTTG 57.400 30.769 0.00 0.00 0.00 2.32
1310 1504 7.731054 TGTGTTGGGCTTCTAATTTAATTTGT 58.269 30.769 0.00 0.00 0.00 2.83
1311 1505 7.655328 TGTGTTGGGCTTCTAATTTAATTTGTG 59.345 33.333 0.00 0.00 0.00 3.33
1331 1525 1.616374 GTGCAGGTCTATCTCCTAGCC 59.384 57.143 0.00 0.00 33.54 3.93
1360 1554 3.624777 TGGAGAAATGGGAGAAAGATGC 58.375 45.455 0.00 0.00 0.00 3.91
1362 1556 3.624777 GAGAAATGGGAGAAAGATGCCA 58.375 45.455 0.00 0.00 45.54 4.92
1393 1587 2.271800 GGTCATCTTCAAGGTGCGTAG 58.728 52.381 0.00 0.00 0.00 3.51
1396 1590 1.920574 CATCTTCAAGGTGCGTAGTCG 59.079 52.381 0.00 0.00 40.37 4.18
1404 1598 2.356553 TGCGTAGTCGTTGGCACC 60.357 61.111 0.00 0.00 39.49 5.01
1407 1601 1.736645 CGTAGTCGTTGGCACCTGG 60.737 63.158 0.00 0.00 0.00 4.45
1417 1611 2.546494 GGCACCTGGCGCATCATAC 61.546 63.158 10.83 0.00 46.16 2.39
1418 1612 1.819208 GCACCTGGCGCATCATACA 60.819 57.895 10.83 0.00 0.00 2.29
1421 1615 2.493035 CACCTGGCGCATCATACATTA 58.507 47.619 10.83 0.00 0.00 1.90
1422 1616 2.877786 CACCTGGCGCATCATACATTAA 59.122 45.455 10.83 0.00 0.00 1.40
1423 1617 3.058708 CACCTGGCGCATCATACATTAAG 60.059 47.826 10.83 0.00 0.00 1.85
1424 1618 2.095567 CCTGGCGCATCATACATTAAGC 60.096 50.000 10.83 0.00 0.00 3.09
1425 1619 2.810274 CTGGCGCATCATACATTAAGCT 59.190 45.455 10.83 0.00 0.00 3.74
1426 1620 2.549329 TGGCGCATCATACATTAAGCTG 59.451 45.455 10.83 0.00 0.00 4.24
1427 1621 2.578495 GCGCATCATACATTAAGCTGC 58.422 47.619 0.30 0.00 0.00 5.25
1428 1622 2.225019 GCGCATCATACATTAAGCTGCT 59.775 45.455 0.30 0.00 0.00 4.24
1429 1623 3.433274 GCGCATCATACATTAAGCTGCTA 59.567 43.478 0.90 0.00 0.00 3.49
1433 1627 7.342942 CGCATCATACATTAAGCTGCTATATG 58.657 38.462 17.37 17.37 0.00 1.78
1448 1642 1.884235 ATATGCTGCTTTAGGACGGC 58.116 50.000 0.00 0.00 38.70 5.68
1456 1650 1.302993 TTTAGGACGGCAACCAGGC 60.303 57.895 0.00 0.00 39.93 4.85
1457 1651 1.774894 TTTAGGACGGCAACCAGGCT 61.775 55.000 0.00 0.00 41.46 4.58
1458 1652 0.905809 TTAGGACGGCAACCAGGCTA 60.906 55.000 0.00 0.00 41.46 3.93
1481 1705 3.005554 CTGGTGCTTAAGAGTGTCATGG 58.994 50.000 6.67 0.00 0.00 3.66
1485 1709 4.320494 GGTGCTTAAGAGTGTCATGGTTTG 60.320 45.833 6.67 0.00 0.00 2.93
1555 1805 6.981722 TGCTTTTCTCTAATCCAAAGGAAAC 58.018 36.000 0.00 0.00 34.34 2.78
1694 3071 4.232221 CAAGTGCATGAATGTGAGGTTTC 58.768 43.478 0.00 0.00 0.00 2.78
1717 3094 1.194781 ATCAACAGGGAGCAGGACGT 61.195 55.000 0.00 0.00 0.00 4.34
1864 3241 2.692041 GCAAGGCTGCTTGGAGATATTT 59.308 45.455 0.00 0.00 45.74 1.40
1907 3284 0.537188 CCTGCCTCGAGGTTGTGTAT 59.463 55.000 31.43 0.00 37.57 2.29
1934 3311 2.906691 ACTGGCTCTGCTATCACATC 57.093 50.000 0.00 0.00 0.00 3.06
1975 3352 2.722094 GGTGATGCCCTTGTGACATAA 58.278 47.619 0.00 0.00 0.00 1.90
2131 3508 5.237344 GCAGTTGTCACAGAGAAAACAGTAT 59.763 40.000 3.97 0.00 45.31 2.12
2151 3528 7.122501 ACAGTATGAATCAATTTATGCCACACA 59.877 33.333 0.00 0.00 39.69 3.72
2175 3552 9.646522 ACATATGGCCTTTCTAGTGATAAATTT 57.353 29.630 3.32 0.00 0.00 1.82
2342 3744 7.282224 TCCAATCAAACTTGAATATTACCTCCG 59.718 37.037 0.00 0.00 41.13 4.63
2518 3940 5.874810 TGTTTGGAGTTTCTCATAAGGATCG 59.125 40.000 0.00 0.00 31.08 3.69
2641 4063 5.357032 AGGTAGGCATTGAGTTTAATTTCCG 59.643 40.000 0.00 0.00 0.00 4.30
2673 4095 7.286087 CACATCCCCAGAGAATAATTTGAATGA 59.714 37.037 0.00 0.00 0.00 2.57
2677 4099 7.340232 TCCCCAGAGAATAATTTGAATGACTTG 59.660 37.037 0.00 0.00 0.00 3.16
2681 4103 8.456471 CAGAGAATAATTTGAATGACTTGCTCA 58.544 33.333 0.00 0.00 0.00 4.26
2862 4284 7.223260 AGACTGAATGCAAAAGAAATGATCA 57.777 32.000 0.00 0.00 0.00 2.92
2954 4376 9.371136 TGTATTGTTTTGTTTGCAGTATTTTGA 57.629 25.926 0.00 0.00 0.00 2.69
2985 4407 7.063780 GGTTCCAAGCACAAAAATCTGATATTG 59.936 37.037 12.11 12.11 0.00 1.90
3291 4716 5.178809 ACGGTTTCTTTGAGTAATGTGCTAC 59.821 40.000 0.00 0.00 0.00 3.58
3330 4759 5.441500 TGGAAACAAACTGACACTGGAATA 58.558 37.500 0.00 0.00 37.44 1.75
3349 4778 8.099364 TGGAATATCGATTTTTGATAGGCTTC 57.901 34.615 1.71 0.00 32.21 3.86
3360 4789 5.808366 TTGATAGGCTTCCAACTATCGAT 57.192 39.130 2.16 2.16 45.35 3.59
3540 4970 2.608016 CGCTCTACACTCAGTGCTTCAA 60.608 50.000 4.13 0.00 36.98 2.69
3543 4973 5.171476 GCTCTACACTCAGTGCTTCAAATA 58.829 41.667 4.13 0.00 36.98 1.40
3669 5100 5.587388 ATTGGTTTATCATGCTGGTTCTG 57.413 39.130 0.00 0.00 0.00 3.02
3679 5110 2.665165 TGCTGGTTCTGTGGTTCATTT 58.335 42.857 0.00 0.00 0.00 2.32
3680 5111 3.826524 TGCTGGTTCTGTGGTTCATTTA 58.173 40.909 0.00 0.00 0.00 1.40
3681 5112 3.568007 TGCTGGTTCTGTGGTTCATTTAC 59.432 43.478 0.00 0.00 0.00 2.01
3717 5148 6.491714 AGGCAGAAATGATACACTCATACT 57.508 37.500 0.00 0.00 44.03 2.12
3727 5189 5.891551 TGATACACTCATACTCTTACTGCCA 59.108 40.000 0.00 0.00 0.00 4.92
3747 5209 4.245660 CCATGCCGTATAATGAGACGAAT 58.754 43.478 0.00 0.00 42.96 3.34
3911 5373 1.405821 CTGCGATCGGTAGGAACTCTT 59.594 52.381 18.30 0.00 41.75 2.85
3913 5375 1.134560 GCGATCGGTAGGAACTCTTGT 59.865 52.381 18.30 0.00 41.75 3.16
4085 5548 2.296073 TCTTTTTATGGGGTGCGGTT 57.704 45.000 0.00 0.00 0.00 4.44
4241 5705 5.614324 AACAATGAACATCCTCCGATCTA 57.386 39.130 0.00 0.00 0.00 1.98
4252 5716 3.764434 TCCTCCGATCTATCATTACTGGC 59.236 47.826 0.00 0.00 0.00 4.85
4261 5725 5.769367 TCTATCATTACTGGCGATGTGTAC 58.231 41.667 0.00 0.00 0.00 2.90
4394 5861 2.237392 ACAATGCACCTAAGGTCTCTCC 59.763 50.000 0.00 0.00 31.02 3.71
4414 5886 5.317262 TCTCCCTCCCTCTCTCAATACATAT 59.683 44.000 0.00 0.00 0.00 1.78
4463 5935 4.016479 TGGGGCCTAAATGGGTTTACATAA 60.016 41.667 0.84 0.00 36.00 1.90
4648 6122 5.715279 ACACCTAGCATAGACAGTTTACTCA 59.285 40.000 0.00 0.00 42.77 3.41
4723 6197 9.317936 CTATGCTAAATCTTCACAGTAATCACA 57.682 33.333 0.00 0.00 0.00 3.58
4894 6598 6.931840 AGTAAAACTCATCTCCTGTTCTTGTC 59.068 38.462 0.00 0.00 0.00 3.18
4895 6599 5.559148 AAACTCATCTCCTGTTCTTGTCT 57.441 39.130 0.00 0.00 0.00 3.41
4896 6600 5.559148 AACTCATCTCCTGTTCTTGTCTT 57.441 39.130 0.00 0.00 0.00 3.01
4897 6601 4.892433 ACTCATCTCCTGTTCTTGTCTTG 58.108 43.478 0.00 0.00 0.00 3.02
4898 6602 4.346418 ACTCATCTCCTGTTCTTGTCTTGT 59.654 41.667 0.00 0.00 0.00 3.16
4899 6603 4.635223 TCATCTCCTGTTCTTGTCTTGTG 58.365 43.478 0.00 0.00 0.00 3.33
4900 6604 4.344968 TCATCTCCTGTTCTTGTCTTGTGA 59.655 41.667 0.00 0.00 0.00 3.58
4902 6606 5.097742 TCTCCTGTTCTTGTCTTGTGAAA 57.902 39.130 0.00 0.00 0.00 2.69
4903 6607 5.496556 TCTCCTGTTCTTGTCTTGTGAAAA 58.503 37.500 0.00 0.00 0.00 2.29
4904 6608 5.354234 TCTCCTGTTCTTGTCTTGTGAAAAC 59.646 40.000 0.00 0.00 0.00 2.43
4905 6609 5.253330 TCCTGTTCTTGTCTTGTGAAAACT 58.747 37.500 0.00 0.00 0.00 2.66
4906 6610 6.411376 TCCTGTTCTTGTCTTGTGAAAACTA 58.589 36.000 0.00 0.00 0.00 2.24
4907 6611 6.315393 TCCTGTTCTTGTCTTGTGAAAACTAC 59.685 38.462 0.00 0.00 0.00 2.73
4908 6612 6.093495 CCTGTTCTTGTCTTGTGAAAACTACA 59.907 38.462 0.00 0.00 0.00 2.74
5066 6776 6.318900 AGTCAAGGACAAAAGTTCTACCAAAG 59.681 38.462 0.00 0.00 34.60 2.77
5488 7216 5.874093 ACATCTCTCAATGAACTGAAACCT 58.126 37.500 0.00 0.00 0.00 3.50
5589 7317 3.181516 GCTTCTGATTCACGCGAGAAATT 60.182 43.478 22.33 7.58 0.00 1.82
5639 7367 6.222389 CCTTCAAATGTAATTGGCAACTTCA 58.778 36.000 0.00 0.00 36.10 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.623542 GGGTAGTTGGCCTCGTGGAT 61.624 60.000 7.92 0.00 34.57 3.41
218 221 4.728102 CGAAGTACGCCGCCCACA 62.728 66.667 0.00 0.00 34.51 4.17
292 295 3.286751 GCCCTCGCTGTTGTTGCA 61.287 61.111 0.00 0.00 0.00 4.08
313 316 3.884774 GACACCCCACCACAGGCA 61.885 66.667 0.00 0.00 0.00 4.75
565 614 1.754234 GCCATCGCCCCAAGTCATT 60.754 57.895 0.00 0.00 0.00 2.57
567 616 3.329889 AGCCATCGCCCCAAGTCA 61.330 61.111 0.00 0.00 34.57 3.41
579 629 0.038166 ATGAACACGTTCCCAGCCAT 59.962 50.000 7.43 0.00 38.77 4.40
580 630 0.605319 GATGAACACGTTCCCAGCCA 60.605 55.000 7.43 0.00 38.77 4.75
681 735 3.626028 AGAACGCTTTTGATTGGTCAC 57.374 42.857 0.00 0.00 33.11 3.67
682 736 3.629855 TCAAGAACGCTTTTGATTGGTCA 59.370 39.130 0.00 0.00 30.14 4.02
683 737 4.223320 TCAAGAACGCTTTTGATTGGTC 57.777 40.909 0.00 0.00 30.14 4.02
684 738 4.037923 ACATCAAGAACGCTTTTGATTGGT 59.962 37.500 2.08 0.00 40.93 3.67
685 739 4.383649 CACATCAAGAACGCTTTTGATTGG 59.616 41.667 2.08 0.00 40.93 3.16
686 740 5.116074 GTCACATCAAGAACGCTTTTGATTG 59.884 40.000 2.08 5.35 40.93 2.67
687 741 5.215160 GTCACATCAAGAACGCTTTTGATT 58.785 37.500 2.08 0.00 40.93 2.57
688 742 4.611355 CGTCACATCAAGAACGCTTTTGAT 60.611 41.667 0.00 0.00 42.98 2.57
689 743 3.303066 CGTCACATCAAGAACGCTTTTGA 60.303 43.478 0.00 0.00 37.68 2.69
690 744 2.966708 CGTCACATCAAGAACGCTTTTG 59.033 45.455 0.00 0.00 30.14 2.44
691 745 2.869801 TCGTCACATCAAGAACGCTTTT 59.130 40.909 0.00 0.00 30.14 2.27
692 746 2.479837 TCGTCACATCAAGAACGCTTT 58.520 42.857 0.00 0.00 30.14 3.51
693 747 2.148916 TCGTCACATCAAGAACGCTT 57.851 45.000 0.00 0.00 33.74 4.68
694 748 2.148916 TTCGTCACATCAAGAACGCT 57.851 45.000 0.00 0.00 0.00 5.07
695 749 2.033236 TGTTTCGTCACATCAAGAACGC 60.033 45.455 0.00 0.00 0.00 4.84
696 750 3.852471 TGTTTCGTCACATCAAGAACG 57.148 42.857 0.00 0.00 0.00 3.95
697 751 5.156804 ACTTGTTTCGTCACATCAAGAAC 57.843 39.130 9.63 0.00 38.82 3.01
698 752 4.272504 GGACTTGTTTCGTCACATCAAGAA 59.727 41.667 9.63 0.00 38.82 2.52
699 753 3.807622 GGACTTGTTTCGTCACATCAAGA 59.192 43.478 9.63 0.00 38.82 3.02
700 754 3.362986 CGGACTTGTTTCGTCACATCAAG 60.363 47.826 0.00 0.00 40.54 3.02
701 755 2.542178 CGGACTTGTTTCGTCACATCAA 59.458 45.455 0.00 0.00 33.11 2.57
702 756 2.131972 CGGACTTGTTTCGTCACATCA 58.868 47.619 0.00 0.00 33.11 3.07
703 757 2.096909 CACGGACTTGTTTCGTCACATC 60.097 50.000 0.00 0.00 34.73 3.06
704 758 1.864711 CACGGACTTGTTTCGTCACAT 59.135 47.619 0.00 0.00 34.73 3.21
705 759 1.282817 CACGGACTTGTTTCGTCACA 58.717 50.000 0.00 0.00 34.73 3.58
706 760 0.580104 CCACGGACTTGTTTCGTCAC 59.420 55.000 0.00 0.00 34.73 3.67
710 764 1.301423 TTTCCCACGGACTTGTTTCG 58.699 50.000 0.00 0.00 0.00 3.46
725 779 9.232473 GGGAGTGAATATATGAAGGTATTTTCC 57.768 37.037 0.00 0.00 0.00 3.13
734 788 7.162082 GGTTACCAGGGAGTGAATATATGAAG 58.838 42.308 0.00 0.00 0.00 3.02
742 796 0.909623 CGGGTTACCAGGGAGTGAAT 59.090 55.000 2.98 0.00 36.13 2.57
743 797 0.472352 ACGGGTTACCAGGGAGTGAA 60.472 55.000 6.48 0.00 36.13 3.18
751 805 4.011517 ACGGCCACGGGTTACCAG 62.012 66.667 2.24 0.81 46.48 4.00
763 817 2.365582 ACTGAAAATATGTCCACGGCC 58.634 47.619 0.00 0.00 0.00 6.13
764 818 3.438781 TGAACTGAAAATATGTCCACGGC 59.561 43.478 0.00 0.00 0.00 5.68
777 831 2.687935 GAGCTGGGTTGTTGAACTGAAA 59.312 45.455 0.00 0.00 32.15 2.69
789 843 2.047061 TGACTACTGTTGAGCTGGGTT 58.953 47.619 0.00 0.00 0.00 4.11
960 1043 3.432252 AGATTTCTTTGACGCGTACAAGG 59.568 43.478 22.96 21.28 0.00 3.61
963 1046 2.991190 GGAGATTTCTTTGACGCGTACA 59.009 45.455 13.97 9.74 0.00 2.90
980 1063 2.786495 GCGAATCGGGAGCTGGAGA 61.786 63.158 4.35 0.00 0.00 3.71
1008 1091 0.740737 CGTTGGGATTGGATTGCTCC 59.259 55.000 0.00 0.00 42.45 4.70
1011 1094 0.740737 CCTCGTTGGGATTGGATTGC 59.259 55.000 0.00 0.00 0.00 3.56
1015 1098 1.279846 GGTTACCTCGTTGGGATTGGA 59.720 52.381 0.00 0.00 41.11 3.53
1024 1107 1.541588 GTACTGGACGGTTACCTCGTT 59.458 52.381 0.00 0.00 41.22 3.85
1036 1119 2.166664 AGAGCCAAGAATCGTACTGGAC 59.833 50.000 0.94 0.00 0.00 4.02
1042 1125 4.274147 AGAAGAGAGAGCCAAGAATCGTA 58.726 43.478 0.00 0.00 0.00 3.43
1049 1132 2.730715 CGACGAAGAAGAGAGAGCCAAG 60.731 54.545 0.00 0.00 0.00 3.61
1050 1133 1.200252 CGACGAAGAAGAGAGAGCCAA 59.800 52.381 0.00 0.00 0.00 4.52
1052 1135 0.524604 GCGACGAAGAAGAGAGAGCC 60.525 60.000 0.00 0.00 0.00 4.70
1053 1136 0.859788 CGCGACGAAGAAGAGAGAGC 60.860 60.000 0.00 0.00 0.00 4.09
1054 1137 0.722282 TCGCGACGAAGAAGAGAGAG 59.278 55.000 3.71 0.00 31.06 3.20
1056 1139 3.059529 TGATATCGCGACGAAGAAGAGAG 60.060 47.826 12.93 0.00 39.99 3.20
1070 1156 2.430921 CCGAGCCGGTGATATCGC 60.431 66.667 7.79 7.79 42.73 4.58
1102 1188 0.869454 CTGCGCAGAGAGTCGGATTC 60.869 60.000 33.66 0.00 0.00 2.52
1127 1213 1.522580 GTTGATCTCCTGCCCGAGC 60.523 63.158 0.00 0.00 40.48 5.03
1184 1270 0.439985 CTCTGTCGTTGATGCCGTTG 59.560 55.000 0.00 0.00 0.00 4.10
1212 1298 2.354401 CCCGAGCCAGAGCAAGAGA 61.354 63.158 0.00 0.00 43.56 3.10
1227 1314 4.094887 CCACTTGTAATCAAACATCTCCCG 59.905 45.833 0.00 0.00 32.87 5.14
1238 1325 4.406456 AGCATTCCAACCACTTGTAATCA 58.594 39.130 0.00 0.00 0.00 2.57
1244 1331 7.099266 TCATTATTAGCATTCCAACCACTTG 57.901 36.000 0.00 0.00 0.00 3.16
1246 1333 6.426587 ACTCATTATTAGCATTCCAACCACT 58.573 36.000 0.00 0.00 0.00 4.00
1291 1485 6.162777 TGCACACAAATTAAATTAGAAGCCC 58.837 36.000 0.00 0.00 0.00 5.19
1294 1488 8.299570 AGACCTGCACACAAATTAAATTAGAAG 58.700 33.333 0.00 0.00 0.00 2.85
1299 1493 8.353423 AGATAGACCTGCACACAAATTAAATT 57.647 30.769 0.00 0.00 0.00 1.82
1300 1494 7.067494 GGAGATAGACCTGCACACAAATTAAAT 59.933 37.037 0.00 0.00 0.00 1.40
1301 1495 6.374333 GGAGATAGACCTGCACACAAATTAAA 59.626 38.462 0.00 0.00 0.00 1.52
1302 1496 5.880332 GGAGATAGACCTGCACACAAATTAA 59.120 40.000 0.00 0.00 0.00 1.40
1304 1498 4.018960 AGGAGATAGACCTGCACACAAATT 60.019 41.667 0.00 0.00 36.30 1.82
1305 1499 3.521126 AGGAGATAGACCTGCACACAAAT 59.479 43.478 0.00 0.00 36.30 2.32
1306 1500 2.906389 AGGAGATAGACCTGCACACAAA 59.094 45.455 0.00 0.00 36.30 2.83
1307 1501 2.540383 AGGAGATAGACCTGCACACAA 58.460 47.619 0.00 0.00 36.30 3.33
1308 1502 2.238084 AGGAGATAGACCTGCACACA 57.762 50.000 0.00 0.00 36.30 3.72
1309 1503 2.035321 GCTAGGAGATAGACCTGCACAC 59.965 54.545 0.00 0.00 38.31 3.82
1310 1504 2.311463 GCTAGGAGATAGACCTGCACA 58.689 52.381 0.00 0.00 38.31 4.57
1311 1505 1.616374 GGCTAGGAGATAGACCTGCAC 59.384 57.143 0.00 0.00 38.31 4.57
1360 1554 0.458669 GATGACCAGCTTGGCATTGG 59.541 55.000 7.71 10.55 42.67 3.16
1362 1556 2.097825 GAAGATGACCAGCTTGGCATT 58.902 47.619 7.71 0.00 42.67 3.56
1396 1590 4.120331 GATGCGCCAGGTGCCAAC 62.120 66.667 22.68 9.69 38.39 3.77
1404 1598 2.810274 AGCTTAATGTATGATGCGCCAG 59.190 45.455 4.18 0.00 0.00 4.85
1407 1601 2.225019 AGCAGCTTAATGTATGATGCGC 59.775 45.455 0.00 0.00 46.01 6.09
1426 1620 2.996621 CCGTCCTAAAGCAGCATATAGC 59.003 50.000 0.00 0.00 46.19 2.97
1427 1621 2.996621 GCCGTCCTAAAGCAGCATATAG 59.003 50.000 0.00 0.00 0.00 1.31
1428 1622 2.367241 TGCCGTCCTAAAGCAGCATATA 59.633 45.455 0.00 0.00 31.65 0.86
1429 1623 1.140852 TGCCGTCCTAAAGCAGCATAT 59.859 47.619 0.00 0.00 31.65 1.78
1433 1627 1.502190 GTTGCCGTCCTAAAGCAGC 59.498 57.895 0.00 0.00 37.89 5.25
1445 1639 2.821366 CAGCTAGCCTGGTTGCCG 60.821 66.667 12.13 0.00 37.93 5.69
1466 1690 3.820467 TGGCAAACCATGACACTCTTAAG 59.180 43.478 0.00 0.00 44.10 1.85
1481 1705 5.938125 TGAAACTTCTCCTACTATGGCAAAC 59.062 40.000 0.00 0.00 0.00 2.93
1485 1709 4.406003 TCCTGAAACTTCTCCTACTATGGC 59.594 45.833 0.00 0.00 0.00 4.40
1529 1753 5.880901 TCCTTTGGATTAGAGAAAAGCAGT 58.119 37.500 0.00 0.00 0.00 4.40
1530 1754 6.824305 TTCCTTTGGATTAGAGAAAAGCAG 57.176 37.500 0.00 0.00 0.00 4.24
1531 1755 6.293955 CGTTTCCTTTGGATTAGAGAAAAGCA 60.294 38.462 0.00 0.00 0.00 3.91
1532 1756 6.086871 CGTTTCCTTTGGATTAGAGAAAAGC 58.913 40.000 0.00 0.00 0.00 3.51
1533 1757 6.086871 GCGTTTCCTTTGGATTAGAGAAAAG 58.913 40.000 0.00 0.00 0.00 2.27
1534 1758 5.048294 GGCGTTTCCTTTGGATTAGAGAAAA 60.048 40.000 0.00 0.00 0.00 2.29
1535 1759 4.457949 GGCGTTTCCTTTGGATTAGAGAAA 59.542 41.667 0.00 0.00 0.00 2.52
1539 1789 2.027929 TCGGCGTTTCCTTTGGATTAGA 60.028 45.455 6.85 0.00 0.00 2.10
1555 1805 0.247814 GCTGAACATGACATTCGGCG 60.248 55.000 11.33 0.00 45.74 6.46
1602 2969 0.454452 GCAGGACGCCGAATTTCAAC 60.454 55.000 0.00 0.00 32.94 3.18
1643 3012 9.979578 ACAATTGCTGAATATTAAAACACTTGA 57.020 25.926 5.05 0.00 0.00 3.02
1647 3016 9.190858 TGTGACAATTGCTGAATATTAAAACAC 57.809 29.630 5.05 0.00 0.00 3.32
1652 3021 7.541783 GCACTTGTGACAATTGCTGAATATTAA 59.458 33.333 26.74 0.00 0.00 1.40
1694 3071 1.211212 TCCTGCTCCCTGTTGATCATG 59.789 52.381 0.00 0.00 0.00 3.07
1732 3109 3.490419 CGTAGAACATCTTTAGGTCCCCG 60.490 52.174 0.00 0.00 0.00 5.73
1907 3284 2.461300 AGCAGAGCCAGTACATCCTA 57.539 50.000 0.00 0.00 0.00 2.94
1934 3311 6.764085 TCACCGTGGTTTTCTTATATGTATGG 59.236 38.462 0.00 0.00 0.00 2.74
1975 3352 6.151144 CAGTAAAACAGGGAATTTTCCTCGAT 59.849 38.462 9.13 0.00 46.72 3.59
2026 3403 3.084039 CCACCTGTATGAATGCACAAGT 58.916 45.455 0.00 0.00 0.00 3.16
2131 3508 7.435305 CCATATGTGTGGCATAAATTGATTCA 58.565 34.615 1.24 0.00 42.68 2.57
2151 3528 9.646522 ACAAATTTATCACTAGAAAGGCCATAT 57.353 29.630 5.01 0.00 0.00 1.78
2241 3624 6.658816 TCAATAGAAAGGCATTGAAGCTTACA 59.341 34.615 0.00 0.00 38.02 2.41
2450 3872 2.496899 TAGTACTCCTTCCGTTCCGT 57.503 50.000 0.00 0.00 0.00 4.69
2518 3940 5.062934 GGCAAAAACCTACACAAACAGAAAC 59.937 40.000 0.00 0.00 0.00 2.78
2641 4063 4.703379 ATTCTCTGGGGATGTGAGAATC 57.297 45.455 10.51 0.00 37.91 2.52
2673 4095 4.384647 GGACAATATCCCTCTTGAGCAAGT 60.385 45.833 9.79 0.00 42.46 3.16
2862 4284 1.185618 TGAGTAGCAAGACCGGCAGT 61.186 55.000 0.00 0.00 0.00 4.40
3234 4656 6.148811 TCAAATGAGTAAACGTGGAATCCTTC 59.851 38.462 0.00 0.00 0.00 3.46
3330 4759 5.888161 AGTTGGAAGCCTATCAAAAATCGAT 59.112 36.000 0.00 0.00 0.00 3.59
3349 4778 7.348201 GCTGAGAAACATTTATCGATAGTTGG 58.652 38.462 16.47 7.44 31.34 3.77
3470 4899 6.912051 TGAACAACAGATCAAGAAAATTGACG 59.088 34.615 0.00 0.00 0.00 4.35
3521 4950 7.547019 TGAATATTTGAAGCACTGAGTGTAGAG 59.453 37.037 14.82 0.00 35.75 2.43
3623 5054 9.905713 AATTACAACATTCTCCTAAGCTGAATA 57.094 29.630 0.00 0.00 0.00 1.75
3669 5100 7.120923 TCCTCCTATGTAGTAAATGAACCAC 57.879 40.000 0.00 0.00 0.00 4.16
3679 5110 4.808767 TCTGCCTTCCTCCTATGTAGTA 57.191 45.455 0.00 0.00 0.00 1.82
3680 5111 3.689872 TCTGCCTTCCTCCTATGTAGT 57.310 47.619 0.00 0.00 0.00 2.73
3681 5112 5.070981 TCATTTCTGCCTTCCTCCTATGTAG 59.929 44.000 0.00 0.00 0.00 2.74
3717 5148 4.039852 TCATTATACGGCATGGCAGTAAGA 59.960 41.667 20.37 13.74 41.75 2.10
3727 5189 5.134202 TCATTCGTCTCATTATACGGCAT 57.866 39.130 0.00 0.00 39.52 4.40
3784 5246 4.264253 TGAATCCTACATCCACAAGCAAG 58.736 43.478 0.00 0.00 0.00 4.01
3911 5373 2.769095 TCCACGGATAATGGATGACACA 59.231 45.455 0.00 0.00 41.47 3.72
4062 5525 3.023832 CCGCACCCCATAAAAAGATTCT 58.976 45.455 0.00 0.00 0.00 2.40
4077 5540 2.750237 CCCAGCCTAAACCGCACC 60.750 66.667 0.00 0.00 0.00 5.01
4085 5548 1.146982 AGCAAAAGAACCCCAGCCTAA 59.853 47.619 0.00 0.00 0.00 2.69
4195 5659 5.316987 AGTCCGAATTCCTTCTTCAAACAT 58.683 37.500 0.00 0.00 0.00 2.71
4241 5705 3.067601 TCGTACACATCGCCAGTAATGAT 59.932 43.478 0.00 0.00 0.00 2.45
4252 5716 2.804647 TGCAATACCTCGTACACATCG 58.195 47.619 0.00 0.00 0.00 3.84
4261 5725 1.999048 TGTACGGTTGCAATACCTCG 58.001 50.000 0.59 5.08 35.97 4.63
4394 5861 8.435982 AGAAAAATATGTATTGAGAGAGGGAGG 58.564 37.037 0.00 0.00 0.00 4.30
4414 5886 2.143122 AGAACAGATGCGCGAGAAAAA 58.857 42.857 12.10 0.00 0.00 1.94
4463 5935 3.808618 GCAGGACTCCACTGTTGAGATTT 60.809 47.826 15.03 0.00 38.22 2.17
4607 6079 3.953612 AGGTGTCTGAAATTCAAACAGCA 59.046 39.130 26.68 7.26 0.00 4.41
4894 6598 5.099575 GGGTTGTGTTGTAGTTTTCACAAG 58.900 41.667 9.32 0.00 46.48 3.16
4895 6599 4.523173 TGGGTTGTGTTGTAGTTTTCACAA 59.477 37.500 5.64 5.64 44.70 3.33
4896 6600 4.079970 TGGGTTGTGTTGTAGTTTTCACA 58.920 39.130 0.00 0.00 38.71 3.58
4897 6601 4.396790 TCTGGGTTGTGTTGTAGTTTTCAC 59.603 41.667 0.00 0.00 0.00 3.18
4898 6602 4.590918 TCTGGGTTGTGTTGTAGTTTTCA 58.409 39.130 0.00 0.00 0.00 2.69
4899 6603 5.767816 ATCTGGGTTGTGTTGTAGTTTTC 57.232 39.130 0.00 0.00 0.00 2.29
4900 6604 7.724061 AGAATATCTGGGTTGTGTTGTAGTTTT 59.276 33.333 0.00 0.00 0.00 2.43
4902 6606 6.779860 AGAATATCTGGGTTGTGTTGTAGTT 58.220 36.000 0.00 0.00 0.00 2.24
4903 6607 6.213600 AGAGAATATCTGGGTTGTGTTGTAGT 59.786 38.462 0.00 0.00 36.69 2.73
4904 6608 6.644347 AGAGAATATCTGGGTTGTGTTGTAG 58.356 40.000 0.00 0.00 36.69 2.74
4905 6609 6.620877 AGAGAATATCTGGGTTGTGTTGTA 57.379 37.500 0.00 0.00 36.69 2.41
4906 6610 5.505181 AGAGAATATCTGGGTTGTGTTGT 57.495 39.130 0.00 0.00 36.69 3.32
5066 6776 1.130561 GTTTCGCTGCACATACTTCCC 59.869 52.381 0.00 0.00 0.00 3.97
5329 7039 6.768381 GCCTAACTAATAGCCTGTTGAAGATT 59.232 38.462 0.00 0.00 0.00 2.40
5488 7216 6.659242 TCTCGGTATGCATCTTATCATCTACA 59.341 38.462 0.19 0.00 0.00 2.74
5589 7317 4.467438 TGAGGATATTGTCAGTGAGCTTGA 59.533 41.667 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.