Multiple sequence alignment - TraesCS3B01G311700

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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 TraesCS3B01G311700 chr3B 100.000 5916 0 0 1 5916 501112302 501106387 0.000000e+00 10925.0
1 TraesCS3B01G311700 chr3B 93.297 552 31 4 4917 5464 366143524 366144073 0.000000e+00 809.0
2 TraesCS3B01G311700 chr3B 92.453 477 34 2 5441 5916 366144202 366144677 0.000000e+00 680.0
3 TraesCS3B01G311700 chr3A 92.800 4014 174 39 952 4901 507303799 507299837 0.000000e+00 5705.0
4 TraesCS3B01G311700 chr3A 89.965 847 61 17 10 839 507304943 507304104 0.000000e+00 1072.0
5 TraesCS3B01G311700 chr3D 89.809 2090 124 26 880 2943 384855137 384853111 0.000000e+00 2597.0
6 TraesCS3B01G311700 chr3D 88.144 1476 105 28 3113 4548 384853027 384851582 0.000000e+00 1692.0
7 TraesCS3B01G311700 chr3D 91.954 870 54 13 1 861 384855983 384855121 0.000000e+00 1205.0
8 TraesCS3B01G311700 chr3D 92.614 352 17 6 4555 4901 384851516 384851169 1.140000e-136 497.0
9 TraesCS3B01G311700 chr3D 93.056 72 5 0 2998 3069 384853108 384853037 8.110000e-19 106.0
10 TraesCS3B01G311700 chr3D 95.000 40 1 1 4820 4858 446119112 446119151 1.780000e-05 62.1
11 TraesCS3B01G311700 chr3D 94.737 38 1 1 4820 4856 171386182 171386145 2.300000e-04 58.4
12 TraesCS3B01G311700 chr3D 92.500 40 2 1 4820 4858 84113381 84113420 8.280000e-04 56.5
13 TraesCS3B01G311700 chr3D 92.308 39 2 1 4819 4856 20751745 20751707 3.000000e-03 54.7
14 TraesCS3B01G311700 chr6B 85.366 1025 112 27 4917 5916 275769572 275768561 0.000000e+00 1027.0
15 TraesCS3B01G311700 chr5B 91.773 547 38 5 4916 5458 373764929 373764386 0.000000e+00 754.0
16 TraesCS3B01G311700 chr5B 92.340 470 35 1 5448 5916 180015585 180015116 0.000000e+00 667.0
17 TraesCS3B01G311700 chr5B 86.700 609 66 14 4917 5518 332411435 332410835 0.000000e+00 662.0
18 TraesCS3B01G311700 chr7B 90.476 567 44 9 4907 5466 498139667 498139104 0.000000e+00 739.0
19 TraesCS3B01G311700 chr7B 90.357 560 46 6 4914 5468 220159982 220160538 0.000000e+00 728.0
20 TraesCS3B01G311700 chr7B 91.966 473 37 1 5445 5916 498138961 498138489 0.000000e+00 662.0
21 TraesCS3B01G311700 chr7B 97.222 36 0 1 4820 4854 9685808 9685843 6.400000e-05 60.2
22 TraesCS3B01G311700 chr7B 86.538 52 5 2 4806 4856 371734282 371734232 8.280000e-04 56.5
23 TraesCS3B01G311700 chr4B 90.893 549 41 4 4913 5457 514580467 514579924 0.000000e+00 728.0
24 TraesCS3B01G311700 chr4B 92.389 473 35 1 5445 5916 618527420 618527892 0.000000e+00 673.0
25 TraesCS3B01G311700 chr4B 92.178 473 35 2 5444 5915 514579392 514578921 0.000000e+00 667.0
26 TraesCS3B01G311700 chr4D 89.081 577 55 7 4918 5490 430826992 430827564 0.000000e+00 710.0
27 TraesCS3B01G311700 chr2B 92.812 473 33 1 5445 5916 770088921 770089393 0.000000e+00 684.0
28 TraesCS3B01G311700 chr2B 97.436 39 0 1 4820 4858 166545934 166545897 1.380000e-06 65.8
29 TraesCS3B01G311700 chr2B 94.872 39 1 1 4820 4858 72524553 72524590 6.400000e-05 60.2
30 TraesCS3B01G311700 chr6D 87.734 587 57 11 4913 5494 462527635 462528211 0.000000e+00 671.0
31 TraesCS3B01G311700 chr6D 92.683 41 2 1 4819 4858 128257036 128257076 2.300000e-04 58.4
32 TraesCS3B01G311700 chr6D 96.970 33 1 0 4826 4858 7460248 7460280 8.280000e-04 56.5
33 TraesCS3B01G311700 chr6D 92.308 39 2 1 4820 4857 17316659 17316621 3.000000e-03 54.7
34 TraesCS3B01G311700 chr6D 92.308 39 2 1 4820 4857 78083131 78083169 3.000000e-03 54.7
35 TraesCS3B01G311700 chr6D 100.000 28 0 0 4830 4857 192112456 192112483 1.100000e-02 52.8
36 TraesCS3B01G311700 chr1B 92.178 473 36 1 5445 5916 623307907 623308379 0.000000e+00 667.0
37 TraesCS3B01G311700 chr1B 91.966 473 36 2 5445 5916 73882223 73882694 0.000000e+00 662.0
38 TraesCS3B01G311700 chr4A 93.182 44 2 1 4815 4857 642603581 642603538 4.950000e-06 63.9
39 TraesCS3B01G311700 chr6A 95.000 40 1 1 4820 4858 7373564 7373603 1.780000e-05 62.1
40 TraesCS3B01G311700 chr5D 93.023 43 2 1 4815 4856 491106984 491106942 1.780000e-05 62.1
41 TraesCS3B01G311700 chr5A 88.000 50 4 2 4820 4868 654619419 654619467 2.300000e-04 58.4
42 TraesCS3B01G311700 chr2D 92.500 40 2 1 4820 4858 378043146 378043185 8.280000e-04 56.5
43 TraesCS3B01G311700 chr1D 96.970 33 1 0 4829 4861 456133080 456133048 8.280000e-04 56.5
44 TraesCS3B01G311700 chr1D 100.000 29 0 0 4829 4857 6474078 6474106 3.000000e-03 54.7
45 TraesCS3B01G311700 chr1D 91.892 37 3 0 4820 4856 329740441 329740477 1.100000e-02 52.8
46 TraesCS3B01G311700 chr1D 92.105 38 2 1 4820 4856 471122969 471123006 1.100000e-02 52.8
47 TraesCS3B01G311700 chr1A 94.286 35 1 1 4820 4853 126545422 126545388 1.100000e-02 52.8


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 TraesCS3B01G311700 chr3B 501106387 501112302 5915 True 10925.0 10925 100.0000 1 5916 1 chr3B.!!$R1 5915
1 TraesCS3B01G311700 chr3B 366143524 366144677 1153 False 744.5 809 92.8750 4917 5916 2 chr3B.!!$F1 999
2 TraesCS3B01G311700 chr3A 507299837 507304943 5106 True 3388.5 5705 91.3825 10 4901 2 chr3A.!!$R1 4891
3 TraesCS3B01G311700 chr3D 384851169 384855983 4814 True 1219.4 2597 91.1154 1 4901 5 chr3D.!!$R3 4900
4 TraesCS3B01G311700 chr6B 275768561 275769572 1011 True 1027.0 1027 85.3660 4917 5916 1 chr6B.!!$R1 999
5 TraesCS3B01G311700 chr5B 373764386 373764929 543 True 754.0 754 91.7730 4916 5458 1 chr5B.!!$R3 542
6 TraesCS3B01G311700 chr5B 332410835 332411435 600 True 662.0 662 86.7000 4917 5518 1 chr5B.!!$R2 601
7 TraesCS3B01G311700 chr7B 220159982 220160538 556 False 728.0 728 90.3570 4914 5468 1 chr7B.!!$F2 554
8 TraesCS3B01G311700 chr7B 498138489 498139667 1178 True 700.5 739 91.2210 4907 5916 2 chr7B.!!$R2 1009
9 TraesCS3B01G311700 chr4B 514578921 514580467 1546 True 697.5 728 91.5355 4913 5915 2 chr4B.!!$R1 1002
10 TraesCS3B01G311700 chr4D 430826992 430827564 572 False 710.0 710 89.0810 4918 5490 1 chr4D.!!$F1 572
11 TraesCS3B01G311700 chr6D 462527635 462528211 576 False 671.0 671 87.7340 4913 5494 1 chr6D.!!$F5 581

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
946 968 0.113190 CTTCTCCTGGGGTTTTGCCT 59.887 55.0 0.0 0.0 37.43 4.75 F
948 970 0.178964 TCTCCTGGGGTTTTGCCTTG 60.179 55.0 0.0 0.0 37.43 3.61 F
1762 2022 0.040499 TGTTGGGAAAGGTATGGCCC 59.960 55.0 0.0 0.0 41.08 5.80 F
2803 3074 0.251341 GCCCCCATCCGAATAGCAAT 60.251 55.0 0.0 0.0 0.00 3.56 F
3396 3694 0.465278 TGCTGCTGCTGTGGTTGTAA 60.465 50.0 17.0 0.0 40.48 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1749 2009 0.035820 TCACACGGGCCATACCTTTC 60.036 55.0 4.39 0.00 39.10 2.62 R
2784 3055 0.251341 ATTGCTATTCGGATGGGGGC 60.251 55.0 0.00 0.00 0.00 5.80 R
3477 3775 0.941463 AACGTTCTGCAGACAGCTCG 60.941 55.0 18.03 17.24 44.10 5.03 R
4467 4793 0.459063 GCGAACCTCGGTAAATCGGT 60.459 55.0 9.82 0.00 40.84 4.69 R
5176 5586 0.394352 GGACGAACCCTAGGTACGGA 60.394 60.0 18.63 0.00 33.12 4.69 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
17 18 3.388841 CTCCCCGTGTACAAGGCT 58.611 61.111 21.11 0.00 0.00 4.58
21 22 1.741770 CCCGTGTACAAGGCTGCTC 60.742 63.158 21.11 0.00 0.00 4.26
24 25 0.737715 CGTGTACAAGGCTGCTCTCC 60.738 60.000 0.00 0.00 0.00 3.71
45 46 8.617290 TCTCCAACTGGTCTTTATTTTCTTAC 57.383 34.615 0.00 0.00 36.34 2.34
47 48 8.934023 TCCAACTGGTCTTTATTTTCTTACAT 57.066 30.769 0.00 0.00 36.34 2.29
79 81 6.049790 GCCACTCTTTTATAGTCAGGTTAGG 58.950 44.000 0.00 0.00 0.00 2.69
80 82 6.351966 GCCACTCTTTTATAGTCAGGTTAGGT 60.352 42.308 0.00 0.00 0.00 3.08
81 83 7.621796 CCACTCTTTTATAGTCAGGTTAGGTT 58.378 38.462 0.00 0.00 0.00 3.50
116 118 1.207593 GCGCCTTGTGTAAGCTGTG 59.792 57.895 0.00 0.00 32.40 3.66
140 150 2.540361 GCAATGTCATGATCCGTTCTGC 60.540 50.000 0.00 0.00 0.00 4.26
366 376 5.833406 TCTCTGCAAAAGAAATTGTCACA 57.167 34.783 0.00 0.00 33.37 3.58
396 406 6.538189 AAATCATAAAAAGTTTGTTGGCCG 57.462 33.333 0.00 0.00 0.00 6.13
414 424 2.879826 CCGGCATTCAAACCAAGAATC 58.120 47.619 0.00 0.00 33.64 2.52
415 425 2.417243 CCGGCATTCAAACCAAGAATCC 60.417 50.000 0.00 0.00 33.64 3.01
426 436 8.036273 TCAAACCAAGAATCCGTTATAAGAAC 57.964 34.615 0.00 0.00 0.00 3.01
436 446 4.095782 TCCGTTATAAGAACATTGCTTGCC 59.904 41.667 0.00 0.00 0.00 4.52
445 455 5.989477 AGAACATTGCTTGCCTACTATGTA 58.011 37.500 0.00 0.00 0.00 2.29
456 466 7.440505 TTGCCTACTATGTACAATCCCTTTA 57.559 36.000 0.00 0.00 0.00 1.85
457 467 7.626999 TGCCTACTATGTACAATCCCTTTAT 57.373 36.000 0.00 0.00 0.00 1.40
507 523 5.069914 TCTCGTTTAATAGGCTAATGGCTCA 59.930 40.000 0.00 0.00 46.86 4.26
530 546 8.697846 TCATTTCGTGAGTAAATATTCTTCGT 57.302 30.769 0.00 0.00 31.80 3.85
559 575 4.060900 CGCTCCAGACTACATTATGCATT 58.939 43.478 3.54 0.00 0.00 3.56
562 578 6.128715 CGCTCCAGACTACATTATGCATTTAG 60.129 42.308 3.54 3.77 0.00 1.85
701 721 0.253044 GCACCTACTCCCAAGCATGA 59.747 55.000 0.00 0.00 0.00 3.07
705 725 3.826157 CACCTACTCCCAAGCATGAAAAA 59.174 43.478 0.00 0.00 0.00 1.94
720 741 3.804036 TGAAAAAGAGGTCGCTCAGAAA 58.196 40.909 0.00 0.00 0.00 2.52
829 851 1.609210 CCCATCCCACCAACCAACC 60.609 63.158 0.00 0.00 0.00 3.77
846 868 3.370953 CCAACCAACAATCCACCCAAAAA 60.371 43.478 0.00 0.00 0.00 1.94
849 871 2.486370 CCAACAATCCACCCAAAAACCC 60.486 50.000 0.00 0.00 0.00 4.11
850 872 1.044611 ACAATCCACCCAAAAACCCG 58.955 50.000 0.00 0.00 0.00 5.28
851 873 0.320050 CAATCCACCCAAAAACCCGG 59.680 55.000 0.00 0.00 0.00 5.73
852 874 0.188834 AATCCACCCAAAAACCCGGA 59.811 50.000 0.73 0.00 0.00 5.14
853 875 0.541063 ATCCACCCAAAAACCCGGAC 60.541 55.000 0.73 0.00 0.00 4.79
854 876 2.204461 CCACCCAAAAACCCGGACC 61.204 63.158 0.73 0.00 0.00 4.46
855 877 1.455959 CACCCAAAAACCCGGACCA 60.456 57.895 0.73 0.00 0.00 4.02
856 878 0.830023 CACCCAAAAACCCGGACCAT 60.830 55.000 0.73 0.00 0.00 3.55
857 879 0.541063 ACCCAAAAACCCGGACCATC 60.541 55.000 0.73 0.00 0.00 3.51
858 880 0.540830 CCCAAAAACCCGGACCATCA 60.541 55.000 0.73 0.00 0.00 3.07
859 881 0.887933 CCAAAAACCCGGACCATCAG 59.112 55.000 0.73 0.00 0.00 2.90
860 882 0.243636 CAAAAACCCGGACCATCAGC 59.756 55.000 0.73 0.00 0.00 4.26
861 883 0.898326 AAAAACCCGGACCATCAGCC 60.898 55.000 0.73 0.00 0.00 4.85
862 884 2.781431 AAAACCCGGACCATCAGCCC 62.781 60.000 0.73 0.00 0.00 5.19
866 888 3.866582 CGGACCATCAGCCCCCTC 61.867 72.222 0.00 0.00 0.00 4.30
867 889 3.493303 GGACCATCAGCCCCCTCC 61.493 72.222 0.00 0.00 0.00 4.30
868 890 3.493303 GACCATCAGCCCCCTCCC 61.493 72.222 0.00 0.00 0.00 4.30
871 893 3.813724 CATCAGCCCCCTCCCCAC 61.814 72.222 0.00 0.00 0.00 4.61
872 894 4.044390 ATCAGCCCCCTCCCCACT 62.044 66.667 0.00 0.00 0.00 4.00
873 895 4.741239 TCAGCCCCCTCCCCACTC 62.741 72.222 0.00 0.00 0.00 3.51
879 901 4.825679 CCCTCCCCACTCCCCCTC 62.826 77.778 0.00 0.00 0.00 4.30
880 902 4.825679 CCTCCCCACTCCCCCTCC 62.826 77.778 0.00 0.00 0.00 4.30
881 903 4.825679 CTCCCCACTCCCCCTCCC 62.826 77.778 0.00 0.00 0.00 4.30
936 958 2.581354 CCCGCAGTCTTCTCCTGG 59.419 66.667 0.00 0.00 0.00 4.45
946 968 0.113190 CTTCTCCTGGGGTTTTGCCT 59.887 55.000 0.00 0.00 37.43 4.75
947 969 0.560688 TTCTCCTGGGGTTTTGCCTT 59.439 50.000 0.00 0.00 37.43 4.35
948 970 0.178964 TCTCCTGGGGTTTTGCCTTG 60.179 55.000 0.00 0.00 37.43 3.61
949 971 1.820010 CTCCTGGGGTTTTGCCTTGC 61.820 60.000 0.00 0.00 37.43 4.01
950 972 2.743060 CTGGGGTTTTGCCTTGCC 59.257 61.111 0.00 0.00 37.43 4.52
1047 1271 2.124293 CGATCCACGAATCTCCCCA 58.876 57.895 0.00 0.00 45.77 4.96
1123 1359 4.097863 GTGCGCGTAAGGTTGGGC 62.098 66.667 8.43 0.00 43.57 5.36
1140 1376 2.049433 CCGTCGAGCTGTTTCGGT 60.049 61.111 0.00 0.00 40.83 4.69
1220 1474 2.766229 GGGGAGGAGCAGGAGGAC 60.766 72.222 0.00 0.00 0.00 3.85
1429 1683 5.556915 TCGTGATTACTTTGTCTGGGATTT 58.443 37.500 0.00 0.00 0.00 2.17
1478 1736 7.169982 GGAGTATATTGACTGATTCTTGTTCGG 59.830 40.741 0.00 0.00 0.00 4.30
1521 1779 4.851540 TCCATAAGATTGGATGATAGGGCA 59.148 41.667 0.00 0.00 40.90 5.36
1522 1780 5.045359 TCCATAAGATTGGATGATAGGGCAG 60.045 44.000 0.00 0.00 40.90 4.85
1529 1787 4.518278 TGGATGATAGGGCAGCTTTTTA 57.482 40.909 0.00 0.00 0.00 1.52
1624 1883 3.055602 GGGGCCTGTATATAAGGGTTACG 60.056 52.174 0.84 0.00 35.17 3.18
1625 1884 3.055602 GGGCCTGTATATAAGGGTTACGG 60.056 52.174 0.84 0.00 35.17 4.02
1669 1929 1.080705 AGTGACGCTCCGCTGTTAC 60.081 57.895 0.00 0.00 0.00 2.50
1678 1938 1.873591 CTCCGCTGTTACTTTTGTGCT 59.126 47.619 0.00 0.00 0.00 4.40
1682 1942 3.291585 CGCTGTTACTTTTGTGCTGAAG 58.708 45.455 0.00 0.00 0.00 3.02
1693 1953 0.385223 GTGCTGAAGTGCTGCTTTCG 60.385 55.000 0.00 3.74 41.53 3.46
1741 2001 6.531439 AGTATTTCTTGTAATTGACGTTCGC 58.469 36.000 0.00 0.00 0.00 4.70
1749 2009 1.234615 ATTGACGTTCGCCTGTTGGG 61.235 55.000 0.00 0.00 38.36 4.12
1755 2015 0.822121 GTTCGCCTGTTGGGAAAGGT 60.822 55.000 0.00 0.00 46.17 3.50
1762 2022 0.040499 TGTTGGGAAAGGTATGGCCC 59.960 55.000 0.00 0.00 41.08 5.80
1763 2023 1.035385 GTTGGGAAAGGTATGGCCCG 61.035 60.000 0.00 0.00 43.70 6.13
1789 2049 2.358898 AGCAGTGATTGTTGTTGTGTCC 59.641 45.455 0.00 0.00 0.00 4.02
1820 2080 1.135575 GGCTCCATTTTCGAGTGCAAG 60.136 52.381 0.00 0.00 0.00 4.01
1822 2082 2.421424 GCTCCATTTTCGAGTGCAAGAT 59.579 45.455 0.00 0.00 0.00 2.40
1907 2167 1.620822 GTCTTCCATTTGGCACTGGT 58.379 50.000 13.42 0.00 34.03 4.00
1937 2197 4.464008 CATGTTTACATGCCTAGGACCAT 58.536 43.478 14.75 4.29 45.92 3.55
1942 2202 5.808366 TTACATGCCTAGGACCATAGAAG 57.192 43.478 14.75 0.00 0.00 2.85
1956 2216 5.189180 ACCATAGAAGCCTTCTGTTGATTC 58.811 41.667 17.22 0.00 40.94 2.52
2005 2265 0.742505 TAGCATGCCTTGATTGCTGC 59.257 50.000 15.66 0.00 45.76 5.25
2018 2278 0.667993 TTGCTGCTGTTAGGTGTTGC 59.332 50.000 0.00 0.00 0.00 4.17
2250 2512 7.394923 CCAATGTCCTTGTACCAGGTAAATTTA 59.605 37.037 12.50 0.00 35.15 1.40
2295 2557 7.936950 TGCATGATTTCGTTTGTATTTTGAA 57.063 28.000 0.00 0.00 0.00 2.69
2390 2653 3.316308 ACTGTGGCTTTTCAGTTAGCAAG 59.684 43.478 0.00 0.00 41.33 4.01
2536 2799 6.882140 TGATTTTATCCACCGTAAGTTCATGT 59.118 34.615 0.00 0.00 0.00 3.21
2554 2817 2.167662 TGTCATGTCCTAGACGCAAGA 58.832 47.619 0.00 0.00 43.62 3.02
2604 2867 6.726764 AGTTCTCCTGATGTCTTTAGTACCTT 59.273 38.462 0.00 0.00 0.00 3.50
2639 2903 5.631096 GTGCTTTTCTCCTGCAATAAGAAAC 59.369 40.000 14.16 7.56 38.40 2.78
2784 3055 7.872163 TTGCAACACTATCTTTTAATGCAAG 57.128 32.000 5.81 0.00 44.70 4.01
2794 3065 0.754957 TTAATGCAAGCCCCCATCCG 60.755 55.000 0.00 0.00 0.00 4.18
2797 3068 2.123726 GCAAGCCCCCATCCGAAT 60.124 61.111 0.00 0.00 0.00 3.34
2803 3074 0.251341 GCCCCCATCCGAATAGCAAT 60.251 55.000 0.00 0.00 0.00 3.56
2831 3102 1.090728 TTTGTTTGCTGTCGCTGTGA 58.909 45.000 0.00 0.00 36.97 3.58
2953 3224 8.424918 CAAGGATAGTACACTATGAAGGAATGT 58.575 37.037 6.62 0.00 39.14 2.71
2970 3249 8.443953 AAGGAATGTCTACATAATTCTTGAGC 57.556 34.615 0.00 0.00 35.10 4.26
3090 3369 9.467258 CACTTTTTGTGTATCATGATTTTCAGT 57.533 29.630 14.65 3.34 41.53 3.41
3181 3469 2.227388 GTCCATGAAGAAGTTGCACCTG 59.773 50.000 0.00 0.00 0.00 4.00
3349 3645 8.362639 TGTCAAGAAACGGTCTAGTACTAAAAT 58.637 33.333 3.76 0.00 34.56 1.82
3396 3694 0.465278 TGCTGCTGCTGTGGTTGTAA 60.465 50.000 17.00 0.00 40.48 2.41
3398 3696 2.083774 GCTGCTGCTGTGGTTGTAATA 58.916 47.619 8.53 0.00 36.03 0.98
3401 3699 4.731773 GCTGCTGCTGTGGTTGTAATAATC 60.732 45.833 8.53 0.00 36.03 1.75
3408 3706 7.872881 TGCTGTGGTTGTAATAATCGTTTTTA 58.127 30.769 0.00 0.00 0.00 1.52
3451 3749 7.773224 TGTCTTTCAGTTCTCTTGTTTTATCCA 59.227 33.333 0.00 0.00 0.00 3.41
3477 3775 4.545610 TGCCGAAATTTGAACTCAATGAC 58.454 39.130 0.00 0.00 35.55 3.06
3696 4022 9.736023 ACATATTTTCTCGAAATTTCAATAGGC 57.264 29.630 17.99 0.00 38.80 3.93
3706 4032 6.625532 AAATTTCAATAGGCCTCAAATGGT 57.374 33.333 9.68 0.00 0.00 3.55
3750 4076 2.159184 TGTTTTTCAGGCAATGCGTCAA 60.159 40.909 0.00 0.00 0.00 3.18
3767 4093 4.084171 GCGTCAAAAGGTGGAACTACTTAC 60.084 45.833 0.00 0.00 36.74 2.34
3928 4254 8.908786 TTCAGATCAAATATAGGAACATGACC 57.091 34.615 0.00 2.33 0.00 4.02
4105 4431 5.047164 TGACATGATTTTGCAGGCTGTTATT 60.047 36.000 17.16 0.00 0.00 1.40
4231 4557 3.525537 CTGCACTGTGGAGTTCGATTAT 58.474 45.455 19.70 0.00 30.66 1.28
4336 4662 1.977129 GAAGCAGATCTGGAGGGCTAT 59.023 52.381 23.89 5.78 33.80 2.97
4387 4713 5.176774 TGTTGTGTCATTTGAAGTAGTAGCG 59.823 40.000 0.00 0.00 0.00 4.26
4417 4743 5.022227 AGCCCATTATGAGGAGACTATCT 57.978 43.478 0.00 0.00 44.43 1.98
4444 4770 6.071952 GCCTCTTTGGATCATTGAAAGTTACA 60.072 38.462 0.00 0.00 38.35 2.41
4467 4793 0.032615 AACTGTGAACCAGCCCCAAA 60.033 50.000 0.00 0.00 45.68 3.28
4517 4843 1.123928 AGGCCTGCTACTCGCTTTAT 58.876 50.000 3.11 0.00 40.11 1.40
4783 5169 8.806429 ATCATGTTTGGTGTCAGTATATTTCA 57.194 30.769 0.00 0.00 0.00 2.69
4826 5212 9.487790 TGGAATAAAACAATCTTGGAAAATGTC 57.512 29.630 0.00 0.00 0.00 3.06
4827 5213 9.487790 GGAATAAAACAATCTTGGAAAATGTCA 57.512 29.630 0.00 0.00 0.00 3.58
4867 5263 6.674573 AGGGAGTAGTTTATTGCTCTCTCTA 58.325 40.000 0.00 0.00 33.95 2.43
4892 5288 3.330267 GTGAATCTGGTCACTTCAGTCC 58.670 50.000 0.00 0.00 43.82 3.85
4901 5297 1.968493 TCACTTCAGTCCGGCTTAGTT 59.032 47.619 0.00 0.00 0.00 2.24
4902 5298 3.057033 GTCACTTCAGTCCGGCTTAGTTA 60.057 47.826 0.00 0.00 0.00 2.24
4903 5299 3.192844 TCACTTCAGTCCGGCTTAGTTAG 59.807 47.826 0.00 0.00 0.00 2.34
4904 5300 3.056749 CACTTCAGTCCGGCTTAGTTAGT 60.057 47.826 0.00 0.00 0.00 2.24
4905 5301 3.193056 ACTTCAGTCCGGCTTAGTTAGTC 59.807 47.826 0.00 0.00 0.00 2.59
4906 5302 2.097825 TCAGTCCGGCTTAGTTAGTCC 58.902 52.381 0.00 0.00 0.00 3.85
4907 5303 1.822990 CAGTCCGGCTTAGTTAGTCCA 59.177 52.381 0.00 0.00 0.00 4.02
4908 5304 2.431057 CAGTCCGGCTTAGTTAGTCCAT 59.569 50.000 0.00 0.00 0.00 3.41
4909 5305 2.431057 AGTCCGGCTTAGTTAGTCCATG 59.569 50.000 0.00 0.00 0.00 3.66
4910 5306 1.760613 TCCGGCTTAGTTAGTCCATGG 59.239 52.381 4.97 4.97 0.00 3.66
4911 5307 1.202651 CCGGCTTAGTTAGTCCATGGG 60.203 57.143 13.02 0.00 0.00 4.00
5000 5398 5.339008 TGTACTCCAAGATGACCATGTAC 57.661 43.478 0.00 0.00 0.00 2.90
5001 5399 5.023452 TGTACTCCAAGATGACCATGTACT 58.977 41.667 0.00 0.00 32.76 2.73
5053 5460 9.173021 CAATACAACAACTATTCCACCAATCTA 57.827 33.333 0.00 0.00 0.00 1.98
5060 5467 6.926630 ACTATTCCACCAATCTATCTCTCC 57.073 41.667 0.00 0.00 0.00 3.71
5063 5470 4.286813 TCCACCAATCTATCTCTCCCTT 57.713 45.455 0.00 0.00 0.00 3.95
5064 5471 4.227197 TCCACCAATCTATCTCTCCCTTC 58.773 47.826 0.00 0.00 0.00 3.46
5078 5485 8.980832 ATCTCTCCCTTCTATAACATGGTATT 57.019 34.615 8.93 0.00 0.00 1.89
5107 5517 0.251073 GTTCTAAACCCTAGCCGCCA 59.749 55.000 0.00 0.00 0.00 5.69
5282 5692 0.757561 TCCCGCCGGTCATCTTGATA 60.758 55.000 1.90 0.00 0.00 2.15
5297 5707 8.932791 GTCATCTTGATAGTCGGTTTCTTTTTA 58.067 33.333 0.00 0.00 0.00 1.52
5331 5741 0.319211 TCTTGATCGGTTTGCGTCGT 60.319 50.000 0.00 0.00 0.00 4.34
5348 5758 3.527427 TCCATCGCAGCCGTCGAT 61.527 61.111 0.00 0.30 46.27 3.59
5403 5813 1.218047 CGGCTTCTTCATCGACCCA 59.782 57.895 0.00 0.00 0.00 4.51
5591 6546 2.595095 GGATTGATCACCCGCCCA 59.405 61.111 0.00 0.00 0.00 5.36
5615 6570 3.770589 CGATCCGCCTCATCTCCT 58.229 61.111 0.00 0.00 0.00 3.69
5616 6571 2.045280 CGATCCGCCTCATCTCCTT 58.955 57.895 0.00 0.00 0.00 3.36
5621 6576 1.513158 CGCCTCATCTCCTTCGTGT 59.487 57.895 0.00 0.00 0.00 4.49
5690 6645 4.373116 GTCCCCGAGTTCAGCGCA 62.373 66.667 11.47 0.00 0.00 6.09
5701 6656 4.100084 CAGCGCATCCCTCCACCA 62.100 66.667 11.47 0.00 0.00 4.17
5814 6769 2.738480 CGTCGTCCCTTTGGGTCA 59.262 61.111 2.25 0.00 44.74 4.02
5828 6783 2.494918 GTCATAGTGTCGCGGCCT 59.505 61.111 8.89 7.68 0.00 5.19
5830 6785 2.184322 CATAGTGTCGCGGCCTGT 59.816 61.111 8.89 0.00 0.00 4.00
5877 6842 3.622826 CTTGGTCGTCCCCGTGGT 61.623 66.667 0.00 0.00 35.01 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.741770 GAGCAGCCTTGTACACGGG 60.742 63.158 19.17 13.88 0.00 5.28
8 9 1.002544 AGTTGGAGAGCAGCCTTGTAC 59.997 52.381 0.00 0.00 0.00 2.90
16 17 2.557920 AAAGACCAGTTGGAGAGCAG 57.442 50.000 4.92 0.00 38.94 4.24
17 18 4.640771 AATAAAGACCAGTTGGAGAGCA 57.359 40.909 4.92 0.00 38.94 4.26
21 22 8.391075 TGTAAGAAAATAAAGACCAGTTGGAG 57.609 34.615 4.92 0.00 38.94 3.86
45 46 8.723942 ACTATAAAAGAGTGGCTCAAAGTATG 57.276 34.615 0.00 0.00 32.06 2.39
47 48 7.903145 TGACTATAAAAGAGTGGCTCAAAGTA 58.097 34.615 0.00 0.00 32.06 2.24
79 81 4.538917 GCGCTCAGGAAGACTATACTAAC 58.461 47.826 0.00 0.00 0.00 2.34
80 82 3.568853 GGCGCTCAGGAAGACTATACTAA 59.431 47.826 7.64 0.00 0.00 2.24
81 83 3.147629 GGCGCTCAGGAAGACTATACTA 58.852 50.000 7.64 0.00 0.00 1.82
87 89 1.294780 CAAGGCGCTCAGGAAGACT 59.705 57.895 7.64 0.00 0.00 3.24
116 118 1.959042 ACGGATCATGACATTGCCTC 58.041 50.000 0.00 0.00 0.00 4.70
140 150 4.701956 AAAGGATGTAAAGTTGGCATCG 57.298 40.909 11.44 0.00 39.71 3.84
384 394 1.112315 TGAATGCCGGCCAACAAACT 61.112 50.000 26.77 0.00 0.00 2.66
385 395 0.249657 TTGAATGCCGGCCAACAAAC 60.250 50.000 26.77 8.84 0.00 2.93
388 398 1.365633 GTTTGAATGCCGGCCAACA 59.634 52.632 26.77 17.83 0.00 3.33
389 399 1.374125 GGTTTGAATGCCGGCCAAC 60.374 57.895 26.77 17.56 0.00 3.77
391 401 1.814772 CTTGGTTTGAATGCCGGCCA 61.815 55.000 26.77 12.55 0.00 5.36
392 402 1.079888 CTTGGTTTGAATGCCGGCC 60.080 57.895 26.77 9.46 0.00 6.13
393 403 0.316841 TTCTTGGTTTGAATGCCGGC 59.683 50.000 22.73 22.73 0.00 6.13
394 404 2.417243 GGATTCTTGGTTTGAATGCCGG 60.417 50.000 0.00 0.00 36.63 6.13
395 405 2.731968 CGGATTCTTGGTTTGAATGCCG 60.732 50.000 0.00 0.00 38.47 5.69
396 406 2.231235 ACGGATTCTTGGTTTGAATGCC 59.769 45.455 0.00 0.00 38.47 4.40
414 424 4.096382 AGGCAAGCAATGTTCTTATAACGG 59.904 41.667 0.00 0.00 0.00 4.44
415 425 5.235305 AGGCAAGCAATGTTCTTATAACG 57.765 39.130 0.00 0.00 0.00 3.18
426 436 6.293626 GGATTGTACATAGTAGGCAAGCAATG 60.294 42.308 0.00 0.00 0.00 2.82
507 523 8.697846 TCACGAAGAATATTTACTCACGAAAT 57.302 30.769 0.00 0.00 0.00 2.17
559 575 0.036765 ATTTGCCACGGAGCGACTAA 60.037 50.000 0.00 0.00 34.65 2.24
562 578 1.573829 TTCATTTGCCACGGAGCGAC 61.574 55.000 0.00 0.00 34.65 5.19
829 851 2.804933 CGGGTTTTTGGGTGGATTGTTG 60.805 50.000 0.00 0.00 0.00 3.33
849 871 3.866582 GAGGGGGCTGATGGTCCG 61.867 72.222 0.00 0.00 41.51 4.79
850 872 3.493303 GGAGGGGGCTGATGGTCC 61.493 72.222 0.00 0.00 39.42 4.46
851 873 3.493303 GGGAGGGGGCTGATGGTC 61.493 72.222 0.00 0.00 0.00 4.02
854 876 3.813724 GTGGGGAGGGGGCTGATG 61.814 72.222 0.00 0.00 0.00 3.07
855 877 4.044390 AGTGGGGAGGGGGCTGAT 62.044 66.667 0.00 0.00 0.00 2.90
856 878 4.741239 GAGTGGGGAGGGGGCTGA 62.741 72.222 0.00 0.00 0.00 4.26
862 884 4.825679 GAGGGGGAGTGGGGAGGG 62.826 77.778 0.00 0.00 0.00 4.30
863 885 4.825679 GGAGGGGGAGTGGGGAGG 62.826 77.778 0.00 0.00 0.00 4.30
864 886 4.825679 GGGAGGGGGAGTGGGGAG 62.826 77.778 0.00 0.00 0.00 4.30
868 890 3.353689 ATCCAGGGAGGGGGAGTGG 62.354 68.421 0.00 0.00 36.45 4.00
869 891 1.768077 GATCCAGGGAGGGGGAGTG 60.768 68.421 0.00 0.00 36.45 3.51
870 892 2.706071 GATCCAGGGAGGGGGAGT 59.294 66.667 0.00 0.00 36.45 3.85
871 893 2.122189 GGATCCAGGGAGGGGGAG 60.122 72.222 6.95 0.00 36.45 4.30
872 894 4.172232 CGGATCCAGGGAGGGGGA 62.172 72.222 13.41 0.00 38.24 4.81
873 895 2.991167 AATCGGATCCAGGGAGGGGG 62.991 65.000 13.41 0.00 38.24 5.40
874 896 1.462238 AATCGGATCCAGGGAGGGG 60.462 63.158 13.41 0.00 38.24 4.79
875 897 0.764369 TGAATCGGATCCAGGGAGGG 60.764 60.000 13.41 0.00 38.24 4.30
876 898 0.683973 CTGAATCGGATCCAGGGAGG 59.316 60.000 13.41 0.00 39.47 4.30
877 899 0.034616 GCTGAATCGGATCCAGGGAG 59.965 60.000 13.41 1.57 0.00 4.30
878 900 0.690744 TGCTGAATCGGATCCAGGGA 60.691 55.000 13.41 0.85 0.00 4.20
879 901 0.250209 CTGCTGAATCGGATCCAGGG 60.250 60.000 13.41 0.00 0.00 4.45
880 902 0.755079 TCTGCTGAATCGGATCCAGG 59.245 55.000 13.41 0.00 0.00 4.45
881 903 1.411977 AGTCTGCTGAATCGGATCCAG 59.588 52.381 13.41 0.00 0.00 3.86
882 904 1.410517 GAGTCTGCTGAATCGGATCCA 59.589 52.381 13.41 0.00 0.00 3.41
936 958 3.636231 GGGGGCAAGGCAAAACCC 61.636 66.667 0.00 0.00 40.58 4.11
949 971 4.351054 GAGTGTGGGCTGTGGGGG 62.351 72.222 0.00 0.00 0.00 5.40
950 972 2.754664 GAAGAGTGTGGGCTGTGGGG 62.755 65.000 0.00 0.00 0.00 4.96
1047 1271 2.586792 GGAACCAGCAGATCCGCT 59.413 61.111 0.00 0.00 45.21 5.52
1310 1564 1.068472 AGGACGTTGTAGAGAAGCGTG 60.068 52.381 0.00 0.00 35.86 5.34
1478 1736 3.561503 GACGCCAAGTGAACCAATTTAC 58.438 45.455 0.00 0.00 0.00 2.01
1521 1779 6.462909 CCCTTCATCACCAGTTTTAAAAAGCT 60.463 38.462 1.31 0.00 0.00 3.74
1522 1780 5.696270 CCCTTCATCACCAGTTTTAAAAAGC 59.304 40.000 1.31 0.00 0.00 3.51
1529 1787 2.958355 CACACCCTTCATCACCAGTTTT 59.042 45.455 0.00 0.00 0.00 2.43
1605 1864 3.260128 AGCCGTAACCCTTATATACAGGC 59.740 47.826 0.00 0.00 38.41 4.85
1607 1866 4.282703 ACCAGCCGTAACCCTTATATACAG 59.717 45.833 0.00 0.00 0.00 2.74
1608 1867 4.225573 ACCAGCCGTAACCCTTATATACA 58.774 43.478 0.00 0.00 0.00 2.29
1609 1868 4.879197 ACCAGCCGTAACCCTTATATAC 57.121 45.455 0.00 0.00 0.00 1.47
1624 1883 1.068127 GATGCAATCATGGAACCAGCC 59.932 52.381 0.00 0.00 44.70 4.85
1625 1884 2.503920 GATGCAATCATGGAACCAGC 57.496 50.000 0.00 0.00 44.70 4.85
1669 1929 1.066605 AGCAGCACTTCAGCACAAAAG 59.933 47.619 0.00 0.00 36.85 2.27
1678 1938 1.867233 GAAGACGAAAGCAGCACTTCA 59.133 47.619 0.00 0.00 37.75 3.02
1682 1942 2.139118 AGAAGAAGACGAAAGCAGCAC 58.861 47.619 0.00 0.00 0.00 4.40
1714 1974 9.069078 CGAACGTCAATTACAAGAAATACTCTA 57.931 33.333 0.00 0.00 32.46 2.43
1741 2001 1.474330 GCCATACCTTTCCCAACAGG 58.526 55.000 0.00 0.00 36.10 4.00
1749 2009 0.035820 TCACACGGGCCATACCTTTC 60.036 55.000 4.39 0.00 39.10 2.62
1755 2015 2.290287 ACTGCTCACACGGGCCATA 61.290 57.895 4.39 0.00 0.00 2.74
1762 2022 1.599071 ACAACAATCACTGCTCACACG 59.401 47.619 0.00 0.00 0.00 4.49
1763 2023 3.181497 ACAACAACAATCACTGCTCACAC 60.181 43.478 0.00 0.00 0.00 3.82
1789 2049 1.755179 AATGGAGCCTGAAATGACCG 58.245 50.000 0.00 0.00 0.00 4.79
1822 2082 9.507329 AGATACTGAAGAAAAAGTGCTCAAATA 57.493 29.630 0.00 0.00 0.00 1.40
1937 2197 3.260884 ACCGAATCAACAGAAGGCTTCTA 59.739 43.478 28.15 14.25 38.11 2.10
1942 2202 0.804989 CCACCGAATCAACAGAAGGC 59.195 55.000 0.00 0.00 0.00 4.35
1956 2216 1.234615 AATGCGTCCTTTCACCACCG 61.235 55.000 0.00 0.00 0.00 4.94
2005 2265 3.425193 GCAAAAATCGCAACACCTAACAG 59.575 43.478 0.00 0.00 0.00 3.16
2018 2278 5.561125 GCTAAATTGTGCAAAGCAAAAATCG 59.439 36.000 0.00 0.00 39.34 3.34
2100 2362 0.617413 ACTGCAGATGGAGGTTGGAG 59.383 55.000 23.35 0.00 37.85 3.86
2250 2512 8.714179 CATGCAACAATGAAATCAAGTAATGTT 58.286 29.630 0.00 0.00 0.00 2.71
2390 2653 9.366216 TGTGTTACTCATCAGTACATATTTGTC 57.634 33.333 0.00 0.00 34.64 3.18
2536 2799 2.723273 TCTCTTGCGTCTAGGACATGA 58.277 47.619 0.00 0.00 32.09 3.07
2639 2903 5.595542 TCCTTGCATCCCAAATCTAAATCAG 59.404 40.000 0.00 0.00 31.94 2.90
2764 3035 5.105351 GGGGCTTGCATTAAAAGATAGTGTT 60.105 40.000 0.00 0.00 0.00 3.32
2784 3055 0.251341 ATTGCTATTCGGATGGGGGC 60.251 55.000 0.00 0.00 0.00 5.80
2794 3065 8.758715 GCAAACAAATCCTTCATATTGCTATTC 58.241 33.333 0.00 0.00 38.96 1.75
2803 3074 4.379394 GCGACAGCAAACAAATCCTTCATA 60.379 41.667 0.00 0.00 44.35 2.15
2831 3102 5.884232 ACTTACTGTCATGCATGATGTCATT 59.116 36.000 30.89 19.82 39.30 2.57
2943 3214 9.605275 CTCAAGAATTATGTAGACATTCCTTCA 57.395 33.333 0.00 0.00 37.76 3.02
2953 3224 5.600696 TCATGCGCTCAAGAATTATGTAGA 58.399 37.500 9.73 0.00 0.00 2.59
2970 3249 3.040795 GCTTCTGCACATAAATCATGCG 58.959 45.455 0.00 0.00 42.44 4.73
2987 3266 5.909610 GTGTAGTGTTGAGAAATGTTGCTTC 59.090 40.000 0.00 0.00 0.00 3.86
2989 3268 5.126067 AGTGTAGTGTTGAGAAATGTTGCT 58.874 37.500 0.00 0.00 0.00 3.91
3136 3415 2.592102 ATGCTTGTGACTGATGGGTT 57.408 45.000 0.00 0.00 0.00 4.11
3138 3417 3.376234 CACTTATGCTTGTGACTGATGGG 59.624 47.826 0.00 0.00 36.38 4.00
3141 3420 4.256920 GGACACTTATGCTTGTGACTGAT 58.743 43.478 0.00 0.00 37.59 2.90
3142 3421 3.070878 TGGACACTTATGCTTGTGACTGA 59.929 43.478 0.00 0.00 37.59 3.41
3143 3422 3.402110 TGGACACTTATGCTTGTGACTG 58.598 45.455 0.00 0.00 37.59 3.51
3181 3469 3.243636 GCCACATCATCATGAATTGGGAC 60.244 47.826 16.32 1.51 34.58 4.46
3226 3522 7.373180 GCGATTCTTTGGAATTTCAACAAAAAC 59.627 33.333 0.00 0.00 41.68 2.43
3304 3600 9.399797 TCTTGACATATTATCAAAGAACTGCAT 57.600 29.630 0.00 0.00 35.70 3.96
3333 3629 9.477484 AATGAGCAATATTTTAGTACTAGACCG 57.523 33.333 2.23 0.00 0.00 4.79
3398 3696 8.880750 GGACAAGCTCTAGTAATAAAAACGATT 58.119 33.333 0.00 0.00 0.00 3.34
3401 3699 7.331193 ACAGGACAAGCTCTAGTAATAAAAACG 59.669 37.037 0.00 0.00 0.00 3.60
3408 3706 6.211584 TGAAAGACAGGACAAGCTCTAGTAAT 59.788 38.462 0.00 0.00 0.00 1.89
3451 3749 4.582701 TGAGTTCAAATTTCGGCATTGT 57.417 36.364 0.00 0.00 0.00 2.71
3477 3775 0.941463 AACGTTCTGCAGACAGCTCG 60.941 55.000 18.03 17.24 44.10 5.03
3544 3843 8.198109 TCAAGGAAGCTTGAAGATAGTACATAC 58.802 37.037 2.10 0.00 40.00 2.39
3545 3844 8.198109 GTCAAGGAAGCTTGAAGATAGTACATA 58.802 37.037 2.10 0.00 43.84 2.29
3546 3845 7.044798 GTCAAGGAAGCTTGAAGATAGTACAT 58.955 38.462 2.10 0.00 43.84 2.29
3547 3846 6.211584 AGTCAAGGAAGCTTGAAGATAGTACA 59.788 38.462 2.10 0.00 43.84 2.90
3548 3847 6.533367 CAGTCAAGGAAGCTTGAAGATAGTAC 59.467 42.308 2.10 0.00 43.84 2.73
3549 3848 6.211584 ACAGTCAAGGAAGCTTGAAGATAGTA 59.788 38.462 2.10 0.00 43.84 1.82
3550 3849 5.012561 ACAGTCAAGGAAGCTTGAAGATAGT 59.987 40.000 2.10 0.00 43.84 2.12
3682 4004 6.643388 ACCATTTGAGGCCTATTGAAATTTC 58.357 36.000 4.42 11.41 0.00 2.17
3767 4093 3.390135 TCTTCCAGCTTTACAGTGAACG 58.610 45.455 0.00 0.00 0.00 3.95
3928 4254 1.101331 GATCCAAAGCTGCTTCAGGG 58.899 55.000 24.67 20.90 31.21 4.45
4010 4336 5.700832 TCACTTGTATAGAACACAAAGGCAG 59.299 40.000 0.00 0.00 38.00 4.85
4105 4431 4.322725 CCAGTGGTGAGAGTGCTAAATACA 60.323 45.833 0.00 0.00 0.00 2.29
4225 4551 6.100004 AGGTAAACCGCTATCATCATAATCG 58.900 40.000 0.00 0.00 42.08 3.34
4231 4557 5.116180 CAAAGAGGTAAACCGCTATCATCA 58.884 41.667 5.79 0.00 45.67 3.07
4336 4662 3.326297 TCCCGGTATCAACATATGCATCA 59.674 43.478 0.19 0.00 0.00 3.07
4387 4713 1.869767 CTCATAATGGGCTTGCGACTC 59.130 52.381 0.00 0.00 0.00 3.36
4417 4743 4.834496 ACTTTCAATGATCCAAAGAGGCAA 59.166 37.500 9.37 0.00 37.29 4.52
4467 4793 0.459063 GCGAACCTCGGTAAATCGGT 60.459 55.000 9.82 0.00 40.84 4.69
4517 4843 2.685388 TCACAACACGGAGAAAATTGCA 59.315 40.909 0.00 0.00 0.00 4.08
4571 4956 3.067091 CCTGACTGGCTGACTGCT 58.933 61.111 4.20 0.00 42.39 4.24
4703 5089 2.631160 ACCACATGTTTCCGAGTGAA 57.369 45.000 0.00 0.00 33.99 3.18
4704 5090 2.616376 CAAACCACATGTTTCCGAGTGA 59.384 45.455 0.00 0.00 45.35 3.41
4823 5209 4.714802 CCCTCCGTCCCATAATATATGACA 59.285 45.833 0.00 0.00 0.00 3.58
4826 5212 4.962995 ACTCCCTCCGTCCCATAATATATG 59.037 45.833 0.00 0.00 0.00 1.78
4827 5213 5.222278 ACTCCCTCCGTCCCATAATATAT 57.778 43.478 0.00 0.00 0.00 0.86
4828 5214 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
4829 5215 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
4840 5235 3.385111 AGAGCAATAAACTACTCCCTCCG 59.615 47.826 0.00 0.00 0.00 4.63
4867 5263 4.202503 ACTGAAGTGACCAGATTCACCATT 60.203 41.667 0.00 0.00 46.14 3.16
4892 5288 1.760613 TCCCATGGACTAACTAAGCCG 59.239 52.381 15.22 0.00 0.00 5.52
4901 5297 3.650942 ACTCAACACTTTCCCATGGACTA 59.349 43.478 15.22 0.00 0.00 2.59
4902 5298 2.443255 ACTCAACACTTTCCCATGGACT 59.557 45.455 15.22 0.00 0.00 3.85
4903 5299 2.863809 ACTCAACACTTTCCCATGGAC 58.136 47.619 15.22 0.00 0.00 4.02
4904 5300 4.927267 ATACTCAACACTTTCCCATGGA 57.073 40.909 15.22 0.00 0.00 3.41
4905 5301 6.603201 ACATTATACTCAACACTTTCCCATGG 59.397 38.462 4.14 4.14 0.00 3.66
4906 5302 7.630242 ACATTATACTCAACACTTTCCCATG 57.370 36.000 0.00 0.00 0.00 3.66
4907 5303 8.650143 AAACATTATACTCAACACTTTCCCAT 57.350 30.769 0.00 0.00 0.00 4.00
4908 5304 9.747898 ATAAACATTATACTCAACACTTTCCCA 57.252 29.630 0.00 0.00 0.00 4.37
4953 5351 6.721318 AGTCAAGGCAGAAACAAATCCTATA 58.279 36.000 0.00 0.00 0.00 1.31
4954 5352 5.574188 AGTCAAGGCAGAAACAAATCCTAT 58.426 37.500 0.00 0.00 0.00 2.57
4997 5395 6.771749 AGCCTCGTGGGTATATATATGAGTAC 59.228 42.308 6.40 0.00 43.12 2.73
4999 5397 5.767670 AGCCTCGTGGGTATATATATGAGT 58.232 41.667 6.40 0.00 43.12 3.41
5000 5398 5.828328 TGAGCCTCGTGGGTATATATATGAG 59.172 44.000 8.42 2.60 45.24 2.90
5001 5399 5.762279 TGAGCCTCGTGGGTATATATATGA 58.238 41.667 8.42 0.00 45.24 2.15
5053 5460 8.980832 AATACCATGTTATAGAAGGGAGAGAT 57.019 34.615 0.00 0.00 0.00 2.75
5060 5467 9.204570 CGGAAACTAATACCATGTTATAGAAGG 57.795 37.037 0.00 0.00 0.00 3.46
5063 5470 7.290714 ACCCGGAAACTAATACCATGTTATAGA 59.709 37.037 0.73 0.00 0.00 1.98
5064 5471 7.447594 ACCCGGAAACTAATACCATGTTATAG 58.552 38.462 0.73 0.00 0.00 1.31
5169 5579 3.511595 CTAGGTACGGACGGCGCA 61.512 66.667 10.83 0.00 0.00 6.09
5176 5586 0.394352 GGACGAACCCTAGGTACGGA 60.394 60.000 18.63 0.00 33.12 4.69
5282 5692 5.585844 TCGGAAAACTAAAAAGAAACCGACT 59.414 36.000 0.00 0.00 41.32 4.18
5331 5741 3.527427 ATCGACGGCTGCGATGGA 61.527 61.111 19.46 0.00 45.74 3.41
5348 5758 3.138798 GAGTAGAGGCGCACGGGA 61.139 66.667 10.83 0.00 0.00 5.14
5615 6570 2.732016 CCAGGTCGGTCACACGAA 59.268 61.111 0.00 0.00 45.38 3.85
5616 6571 3.986006 GCCAGGTCGGTCACACGA 61.986 66.667 0.00 0.00 41.13 4.35
5690 6645 0.982852 TGCTCGATTGGTGGAGGGAT 60.983 55.000 0.00 0.00 31.51 3.85
5814 6769 2.184322 CACAGGCCGCGACACTAT 59.816 61.111 8.23 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.