Multiple sequence alignment - TraesCS4A01G047700

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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 TraesCS4A01G047700 chr4A 100.000 3457 0 0 1 3457 38720244 38716788 0.000000e+00 6384.0
1 TraesCS4A01G047700 chr4D 92.697 1602 55 22 657 2238 426844016 426845575 0.000000e+00 2254.0
2 TraesCS4A01G047700 chr4D 88.394 629 41 11 37 658 426843381 426843984 0.000000e+00 728.0
3 TraesCS4A01G047700 chr4D 88.013 317 27 6 2406 2711 426845757 426846073 7.050000e-97 364.0
4 TraesCS4A01G047700 chr4D 94.928 138 6 1 2331 2467 426845619 426845756 7.510000e-52 215.0
5 TraesCS4A01G047700 chr4B 92.224 1466 60 22 655 2108 522503250 522504673 0.000000e+00 2026.0
6 TraesCS4A01G047700 chr4B 89.242 660 36 11 7 656 522502583 522503217 0.000000e+00 793.0
7 TraesCS4A01G047700 chr4B 88.542 672 50 9 2809 3457 116740612 116739945 0.000000e+00 789.0
8 TraesCS4A01G047700 chr4B 86.557 305 24 10 2406 2693 522504951 522505255 1.550000e-83 320.0
9 TraesCS4A01G047700 chr4B 99.123 114 1 0 2354 2467 522504837 522504950 4.520000e-49 206.0
10 TraesCS4A01G047700 chr4B 91.837 98 7 1 2141 2238 522504673 522504769 6.020000e-28 135.0
11 TraesCS4A01G047700 chr7A 98.592 639 9 0 2819 3457 676279410 676280048 0.000000e+00 1131.0
12 TraesCS4A01G047700 chr3D 96.367 633 21 2 2820 3451 65433047 65433678 0.000000e+00 1040.0
13 TraesCS4A01G047700 chr5D 95.801 643 22 4 2819 3457 80215270 80214629 0.000000e+00 1033.0
14 TraesCS4A01G047700 chr5D 100.000 36 0 0 2691 2726 66292120 66292085 2.230000e-07 67.6
15 TraesCS4A01G047700 chr1D 95.918 637 24 2 2819 3454 6254383 6255018 0.000000e+00 1031.0
16 TraesCS4A01G047700 chr2A 95.893 633 25 1 2819 3451 628521999 628522630 0.000000e+00 1024.0
17 TraesCS4A01G047700 chr2D 95.469 640 21 3 2819 3457 25806213 25805581 0.000000e+00 1014.0
18 TraesCS4A01G047700 chr2D 92.779 637 36 8 2819 3454 602378842 602379469 0.000000e+00 913.0
19 TraesCS4A01G047700 chr2D 83.824 68 5 2 2697 2764 150381044 150381105 3.730000e-05 60.2
20 TraesCS4A01G047700 chr1B 86.867 632 55 13 2848 3455 610964134 610963507 0.000000e+00 682.0
21 TraesCS4A01G047700 chr5B 90.295 474 35 7 2992 3457 576801424 576800954 8.200000e-171 610.0
22 TraesCS4A01G047700 chr7D 92.754 69 2 3 2698 2764 46702661 46702728 2.840000e-16 97.1
23 TraesCS4A01G047700 chr6B 85.135 74 7 4 2693 2764 113712208 113712279 4.790000e-09 73.1
24 TraesCS4A01G047700 chr2B 85.507 69 8 2 2698 2764 545261384 545261452 1.720000e-08 71.3
25 TraesCS4A01G047700 chr7B 84.286 70 8 3 2696 2764 18081138 18081205 8.010000e-07 65.8
26 TraesCS4A01G047700 chr5A 81.690 71 10 3 2698 2767 41166059 41165991 4.820000e-04 56.5
27 TraesCS4A01G047700 chr5A 86.538 52 5 2 2699 2748 539948750 539948801 4.820000e-04 56.5


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 TraesCS4A01G047700 chr4A 38716788 38720244 3456 True 6384.00 6384 100.0000 1 3457 1 chr4A.!!$R1 3456
1 TraesCS4A01G047700 chr4D 426843381 426846073 2692 False 890.25 2254 91.0080 37 2711 4 chr4D.!!$F1 2674
2 TraesCS4A01G047700 chr4B 116739945 116740612 667 True 789.00 789 88.5420 2809 3457 1 chr4B.!!$R1 648
3 TraesCS4A01G047700 chr4B 522502583 522505255 2672 False 696.00 2026 91.7966 7 2693 5 chr4B.!!$F1 2686
4 TraesCS4A01G047700 chr7A 676279410 676280048 638 False 1131.00 1131 98.5920 2819 3457 1 chr7A.!!$F1 638
5 TraesCS4A01G047700 chr3D 65433047 65433678 631 False 1040.00 1040 96.3670 2820 3451 1 chr3D.!!$F1 631
6 TraesCS4A01G047700 chr5D 80214629 80215270 641 True 1033.00 1033 95.8010 2819 3457 1 chr5D.!!$R2 638
7 TraesCS4A01G047700 chr1D 6254383 6255018 635 False 1031.00 1031 95.9180 2819 3454 1 chr1D.!!$F1 635
8 TraesCS4A01G047700 chr2A 628521999 628522630 631 False 1024.00 1024 95.8930 2819 3451 1 chr2A.!!$F1 632
9 TraesCS4A01G047700 chr2D 25805581 25806213 632 True 1014.00 1014 95.4690 2819 3457 1 chr2D.!!$R1 638
10 TraesCS4A01G047700 chr2D 602378842 602379469 627 False 913.00 913 92.7790 2819 3454 1 chr2D.!!$F2 635
11 TraesCS4A01G047700 chr1B 610963507 610964134 627 True 682.00 682 86.8670 2848 3455 1 chr1B.!!$R1 607

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
967 1018 0.024746 CGTCTTCGTCTAGTCGTCCG 59.975 60.0 9.17 4.38 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2754 2918 0.539986 TGGCTGTTATTCCCTCCGTC 59.46 55.0 0.0 0.0 0.0 4.79 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
72 73 1.708341 AGTTGCTGTTCCTTTGCCAT 58.292 45.000 0.00 0.00 0.00 4.40
73 74 2.041701 AGTTGCTGTTCCTTTGCCATT 58.958 42.857 0.00 0.00 0.00 3.16
91 92 4.743151 GCCATTGTGAACAGATAATGCATG 59.257 41.667 0.00 0.00 31.03 4.06
121 127 3.574826 ACAGAGAGACTACCAGACAAACC 59.425 47.826 0.00 0.00 0.00 3.27
131 137 1.806542 CCAGACAAACCCACGAATGAG 59.193 52.381 0.00 0.00 0.00 2.90
148 154 5.411361 CGAATGAGACCACACTAATCCAAAA 59.589 40.000 0.00 0.00 0.00 2.44
152 158 6.126409 TGAGACCACACTAATCCAAAACTTT 58.874 36.000 0.00 0.00 0.00 2.66
159 165 7.860872 CCACACTAATCCAAAACTTTCACTAAC 59.139 37.037 0.00 0.00 0.00 2.34
179 185 0.165944 CACGAACTGCCGACCAAATC 59.834 55.000 0.00 0.00 0.00 2.17
224 230 6.015434 CCTCCAATTTTAGCCAACAAACTAGT 60.015 38.462 0.00 0.00 0.00 2.57
225 231 7.175990 CCTCCAATTTTAGCCAACAAACTAGTA 59.824 37.037 0.00 0.00 0.00 1.82
226 232 7.878036 TCCAATTTTAGCCAACAAACTAGTAC 58.122 34.615 0.00 0.00 0.00 2.73
328 336 6.740411 TTGAAAGCAGCAAAAACAGAAAAT 57.260 29.167 0.00 0.00 0.00 1.82
335 343 2.601979 GCAAAAACAGAAAATTGCCCGC 60.602 45.455 0.00 0.00 41.67 6.13
339 347 1.137404 CAGAAAATTGCCCGCGGAG 59.863 57.895 30.73 18.40 0.00 4.63
399 407 1.097547 CCCCTGCACAACCATCGATC 61.098 60.000 0.00 0.00 0.00 3.69
428 436 3.750501 TTCTTTAATCCCCAAGTCCCC 57.249 47.619 0.00 0.00 0.00 4.81
491 500 1.323534 GTCGTCATCCGGTTCAAATCG 59.676 52.381 0.00 0.00 37.11 3.34
498 507 0.643820 CCGGTTCAAATCGCTCGTAC 59.356 55.000 0.00 0.00 0.00 3.67
502 511 2.512885 GTTCAAATCGCTCGTACGAGA 58.487 47.619 41.42 26.13 46.69 4.04
503 512 2.169663 TCAAATCGCTCGTACGAGAC 57.830 50.000 41.42 30.72 46.69 3.36
536 545 1.571919 CCGCTGCACATTACTCTACC 58.428 55.000 0.00 0.00 0.00 3.18
539 548 1.571919 CTGCACATTACTCTACCGGC 58.428 55.000 0.00 0.00 0.00 6.13
575 584 5.191522 TCATGATCCTGATTGTTTACTCCCA 59.808 40.000 0.00 0.00 0.00 4.37
600 613 8.900781 CACCATTATTCTTATGATCATCATCCC 58.099 37.037 12.53 0.00 38.26 3.85
609 622 0.683973 ATCATCATCCCGCACTCCTC 59.316 55.000 0.00 0.00 0.00 3.71
629 642 5.184864 TCCTCTTCTCAGTTTCTCACTCATC 59.815 44.000 0.00 0.00 30.92 2.92
645 658 0.179129 CATCGCACCCTTTCAATGGC 60.179 55.000 0.00 0.00 0.00 4.40
839 886 2.233305 ACCCCAAGATCACGAGTAGT 57.767 50.000 0.00 0.00 0.00 2.73
840 887 2.100989 ACCCCAAGATCACGAGTAGTC 58.899 52.381 0.00 0.00 0.00 2.59
841 888 1.409427 CCCCAAGATCACGAGTAGTCC 59.591 57.143 0.00 0.00 0.00 3.85
842 889 1.409427 CCCAAGATCACGAGTAGTCCC 59.591 57.143 0.00 0.00 0.00 4.46
843 890 2.100197 CCAAGATCACGAGTAGTCCCA 58.900 52.381 0.00 0.00 0.00 4.37
844 891 2.159226 CCAAGATCACGAGTAGTCCCAC 60.159 54.545 0.00 0.00 0.00 4.61
845 892 2.755655 CAAGATCACGAGTAGTCCCACT 59.244 50.000 0.00 0.00 0.00 4.00
871 918 6.205464 CCCACATTCAGCTACTGGTATAAATG 59.795 42.308 0.00 0.51 31.51 2.32
894 941 2.153945 CACACGCGCATTGGCAATC 61.154 57.895 10.36 4.79 41.24 2.67
927 978 7.627298 ACAAGAGATACAACATACGTACTCT 57.373 36.000 0.00 0.00 33.05 3.24
953 1004 0.723790 CGTCGAACAGCGTACGTCTT 60.724 55.000 17.90 5.55 41.80 3.01
966 1017 3.873828 CGTCTTCGTCTAGTCGTCC 57.126 57.895 9.17 0.00 0.00 4.79
967 1018 0.024746 CGTCTTCGTCTAGTCGTCCG 59.975 60.000 9.17 4.38 0.00 4.79
968 1019 1.074752 GTCTTCGTCTAGTCGTCCGT 58.925 55.000 9.17 0.00 0.00 4.69
969 1020 2.263077 GTCTTCGTCTAGTCGTCCGTA 58.737 52.381 9.17 0.00 0.00 4.02
970 1021 2.281234 GTCTTCGTCTAGTCGTCCGTAG 59.719 54.545 9.17 1.91 0.00 3.51
971 1022 2.094494 TCTTCGTCTAGTCGTCCGTAGT 60.094 50.000 9.17 0.00 0.00 2.73
972 1023 1.633561 TCGTCTAGTCGTCCGTAGTG 58.366 55.000 9.17 0.00 0.00 2.74
973 1024 0.026027 CGTCTAGTCGTCCGTAGTGC 59.974 60.000 0.93 0.00 0.00 4.40
974 1025 0.376502 GTCTAGTCGTCCGTAGTGCC 59.623 60.000 0.00 0.00 0.00 5.01
975 1026 0.036105 TCTAGTCGTCCGTAGTGCCA 60.036 55.000 0.00 0.00 0.00 4.92
976 1027 0.377554 CTAGTCGTCCGTAGTGCCAG 59.622 60.000 0.00 0.00 0.00 4.85
977 1028 1.028330 TAGTCGTCCGTAGTGCCAGG 61.028 60.000 0.00 0.00 0.00 4.45
978 1029 2.034532 TCGTCCGTAGTGCCAGGA 59.965 61.111 0.00 0.00 0.00 3.86
979 1030 2.044555 TCGTCCGTAGTGCCAGGAG 61.045 63.158 0.00 0.00 34.29 3.69
980 1031 2.044555 CGTCCGTAGTGCCAGGAGA 61.045 63.158 0.00 0.00 34.29 3.71
981 1032 1.810532 GTCCGTAGTGCCAGGAGAG 59.189 63.158 0.00 0.00 34.29 3.20
982 1033 0.680280 GTCCGTAGTGCCAGGAGAGA 60.680 60.000 0.00 0.00 34.29 3.10
983 1034 0.394488 TCCGTAGTGCCAGGAGAGAG 60.394 60.000 0.00 0.00 0.00 3.20
984 1035 0.394488 CCGTAGTGCCAGGAGAGAGA 60.394 60.000 0.00 0.00 0.00 3.10
985 1036 1.686355 CGTAGTGCCAGGAGAGAGAT 58.314 55.000 0.00 0.00 0.00 2.75
986 1037 1.606668 CGTAGTGCCAGGAGAGAGATC 59.393 57.143 0.00 0.00 0.00 2.75
987 1038 1.606668 GTAGTGCCAGGAGAGAGATCG 59.393 57.143 0.00 0.00 0.00 3.69
988 1039 0.257328 AGTGCCAGGAGAGAGATCGA 59.743 55.000 0.00 0.00 0.00 3.59
989 1040 1.133513 AGTGCCAGGAGAGAGATCGAT 60.134 52.381 0.00 0.00 0.00 3.59
990 1041 1.269448 GTGCCAGGAGAGAGATCGATC 59.731 57.143 17.91 17.91 0.00 3.69
991 1042 0.521291 GCCAGGAGAGAGATCGATCG 59.479 60.000 19.33 9.36 0.00 3.69
1438 1489 3.898627 AACGGCACTCAGAGCGACG 62.899 63.158 12.33 12.33 0.00 5.12
1503 1575 2.462889 GTACGTGAAAACGTGTCCTGA 58.537 47.619 13.71 0.00 46.53 3.86
1504 1576 1.567504 ACGTGAAAACGTGTCCTGAG 58.432 50.000 2.69 0.00 45.30 3.35
1505 1577 1.134907 ACGTGAAAACGTGTCCTGAGT 60.135 47.619 2.69 0.00 45.30 3.41
1506 1578 1.931172 CGTGAAAACGTGTCCTGAGTT 59.069 47.619 0.00 0.00 0.00 3.01
1507 1579 2.034001 CGTGAAAACGTGTCCTGAGTTC 60.034 50.000 0.00 0.00 0.00 3.01
1508 1580 2.287103 GTGAAAACGTGTCCTGAGTTCC 59.713 50.000 0.00 0.00 0.00 3.62
1509 1581 2.169769 TGAAAACGTGTCCTGAGTTCCT 59.830 45.455 0.00 0.00 0.00 3.36
1510 1582 2.240493 AAACGTGTCCTGAGTTCCTG 57.760 50.000 0.00 0.00 0.00 3.86
1871 1950 4.369182 CTCTACGCCAGGGTAAGTTAATG 58.631 47.826 0.00 0.00 0.00 1.90
1872 1951 2.413310 ACGCCAGGGTAAGTTAATGG 57.587 50.000 5.92 5.92 0.00 3.16
1878 1957 4.080186 GCCAGGGTAAGTTAATGGGTAGAA 60.080 45.833 10.49 0.00 0.00 2.10
1880 1959 5.191124 CCAGGGTAAGTTAATGGGTAGAAGT 59.809 44.000 3.22 0.00 0.00 3.01
1905 1984 2.029073 CAGTCGGCCACAACGTCT 59.971 61.111 2.24 0.00 0.00 4.18
2011 2090 2.911484 CTGCAGAACCTCATCCCTAAC 58.089 52.381 8.42 0.00 0.00 2.34
2025 2104 3.183801 TCCCTAACGGAACCAAGGTAAT 58.816 45.455 0.00 0.00 37.88 1.89
2065 2145 1.460504 TCGAGCTACGACTGGAACAT 58.539 50.000 4.47 0.00 46.45 2.71
2068 2148 2.345641 CGAGCTACGACTGGAACATTTG 59.654 50.000 0.00 0.00 45.77 2.32
2076 2156 7.703621 GCTACGACTGGAACATTTGTTATACTA 59.296 37.037 0.00 0.00 36.91 1.82
2079 2159 8.879759 ACGACTGGAACATTTGTTATACTAATG 58.120 33.333 10.84 10.84 43.55 1.90
2080 2160 7.850982 CGACTGGAACATTTGTTATACTAATGC 59.149 37.037 11.89 0.78 42.35 3.56
2104 2184 6.014840 GCAAATATCTGGGGAAATGATGATGT 60.015 38.462 0.00 0.00 0.00 3.06
2107 2187 2.582172 TCTGGGGAAATGATGATGTGGT 59.418 45.455 0.00 0.00 0.00 4.16
2109 2189 4.229353 TCTGGGGAAATGATGATGTGGTTA 59.771 41.667 0.00 0.00 0.00 2.85
2110 2190 5.103558 TCTGGGGAAATGATGATGTGGTTAT 60.104 40.000 0.00 0.00 0.00 1.89
2111 2191 6.102468 TCTGGGGAAATGATGATGTGGTTATA 59.898 38.462 0.00 0.00 0.00 0.98
2112 2192 6.677552 TGGGGAAATGATGATGTGGTTATAA 58.322 36.000 0.00 0.00 0.00 0.98
2113 2193 7.128751 TGGGGAAATGATGATGTGGTTATAAA 58.871 34.615 0.00 0.00 0.00 1.40
2114 2194 7.788867 TGGGGAAATGATGATGTGGTTATAAAT 59.211 33.333 0.00 0.00 0.00 1.40
2115 2195 8.650490 GGGGAAATGATGATGTGGTTATAAATT 58.350 33.333 0.00 0.00 0.00 1.82
2218 2298 1.827969 CTCCAGATCAAGGTCGGTTCT 59.172 52.381 0.00 0.00 0.00 3.01
2219 2299 1.550524 TCCAGATCAAGGTCGGTTCTG 59.449 52.381 0.00 0.00 33.76 3.02
2227 2307 1.301479 GGTCGGTTCTGGCGAAACT 60.301 57.895 5.78 0.00 34.63 2.66
2229 2309 1.005394 TCGGTTCTGGCGAAACTCC 60.005 57.895 5.78 0.00 34.63 3.85
2238 2318 3.452990 TCTGGCGAAACTCCAACCATATA 59.547 43.478 0.00 0.00 32.41 0.86
2240 2320 4.787551 TGGCGAAACTCCAACCATATATT 58.212 39.130 0.00 0.00 0.00 1.28
2242 2322 6.358178 TGGCGAAACTCCAACCATATATTAA 58.642 36.000 0.00 0.00 0.00 1.40
2243 2323 6.261381 TGGCGAAACTCCAACCATATATTAAC 59.739 38.462 0.00 0.00 0.00 2.01
2244 2324 6.293790 GGCGAAACTCCAACCATATATTAACC 60.294 42.308 0.00 0.00 0.00 2.85
2245 2325 6.293790 GCGAAACTCCAACCATATATTAACCC 60.294 42.308 0.00 0.00 0.00 4.11
2247 2327 7.501225 CGAAACTCCAACCATATATTAACCCTT 59.499 37.037 0.00 0.00 0.00 3.95
2248 2328 9.197306 GAAACTCCAACCATATATTAACCCTTT 57.803 33.333 0.00 0.00 0.00 3.11
2277 2357 7.651027 AGAAATCTATGGATGTTTTTCAGGG 57.349 36.000 0.00 0.00 31.75 4.45
2278 2358 5.859205 AATCTATGGATGTTTTTCAGGGC 57.141 39.130 0.00 0.00 31.75 5.19
2279 2359 4.591321 TCTATGGATGTTTTTCAGGGCT 57.409 40.909 0.00 0.00 0.00 5.19
2280 2360 4.272489 TCTATGGATGTTTTTCAGGGCTG 58.728 43.478 0.00 0.00 0.00 4.85
2281 2361 0.968405 TGGATGTTTTTCAGGGCTGC 59.032 50.000 0.00 0.00 0.00 5.25
2282 2362 0.968405 GGATGTTTTTCAGGGCTGCA 59.032 50.000 0.50 0.00 0.00 4.41
2283 2363 1.337167 GGATGTTTTTCAGGGCTGCAC 60.337 52.381 0.50 0.00 0.00 4.57
2284 2364 1.615392 GATGTTTTTCAGGGCTGCACT 59.385 47.619 0.00 0.00 0.00 4.40
2285 2365 1.484038 TGTTTTTCAGGGCTGCACTT 58.516 45.000 0.00 0.00 0.00 3.16
2286 2366 1.830477 TGTTTTTCAGGGCTGCACTTT 59.170 42.857 0.00 0.00 0.00 2.66
2287 2367 2.235898 TGTTTTTCAGGGCTGCACTTTT 59.764 40.909 0.00 0.00 0.00 2.27
2288 2368 3.449018 TGTTTTTCAGGGCTGCACTTTTA 59.551 39.130 0.00 0.00 0.00 1.52
2289 2369 4.100808 TGTTTTTCAGGGCTGCACTTTTAT 59.899 37.500 0.00 0.00 0.00 1.40
2290 2370 4.519540 TTTTCAGGGCTGCACTTTTATC 57.480 40.909 0.00 0.00 0.00 1.75
2291 2371 3.439857 TTCAGGGCTGCACTTTTATCT 57.560 42.857 0.00 0.00 0.00 1.98
2292 2372 3.439857 TCAGGGCTGCACTTTTATCTT 57.560 42.857 0.00 0.00 0.00 2.40
2293 2373 3.347216 TCAGGGCTGCACTTTTATCTTC 58.653 45.455 0.00 0.00 0.00 2.87
2294 2374 3.084039 CAGGGCTGCACTTTTATCTTCA 58.916 45.455 0.00 0.00 0.00 3.02
2295 2375 3.128242 CAGGGCTGCACTTTTATCTTCAG 59.872 47.826 0.00 0.00 0.00 3.02
2296 2376 3.009473 AGGGCTGCACTTTTATCTTCAGA 59.991 43.478 0.00 0.00 0.00 3.27
2297 2377 3.758554 GGGCTGCACTTTTATCTTCAGAA 59.241 43.478 0.50 0.00 0.00 3.02
2298 2378 4.142513 GGGCTGCACTTTTATCTTCAGAAG 60.143 45.833 3.45 3.45 0.00 2.85
2299 2379 4.697352 GGCTGCACTTTTATCTTCAGAAGA 59.303 41.667 15.44 15.44 42.69 2.87
2301 2381 6.127786 GGCTGCACTTTTATCTTCAGAAGATT 60.128 38.462 27.23 13.68 45.75 2.40
2302 2382 7.066284 GGCTGCACTTTTATCTTCAGAAGATTA 59.934 37.037 27.23 17.64 45.75 1.75
2303 2383 8.454106 GCTGCACTTTTATCTTCAGAAGATTAA 58.546 33.333 27.23 21.87 45.75 1.40
2342 2426 5.302568 TGTTTTGAGCAAATTGATCCTGACT 59.697 36.000 8.86 0.00 30.48 3.41
2349 2433 4.219288 GCAAATTGATCCTGACTGTTTCCT 59.781 41.667 0.00 0.00 0.00 3.36
2411 2496 2.960129 CCGATCGCCTACAACGGC 60.960 66.667 10.32 0.00 46.68 5.68
2487 2634 2.383527 CCAACGAGGCTCGAGCAAC 61.384 63.158 40.35 26.59 43.74 4.17
2529 2687 3.057386 TGCATTCGTGCACAATGATTCTT 60.057 39.130 29.81 5.25 40.23 2.52
2586 2744 7.359262 TCAGTCATAAATTACAGACAAACGG 57.641 36.000 9.21 0.00 33.56 4.44
2629 2791 8.971321 TGAACGATATTTTACCTTATTACGCTC 58.029 33.333 0.00 0.00 0.00 5.03
2675 2839 0.665369 CGACGGACGCCAGTAGTTTT 60.665 55.000 0.00 0.00 34.51 2.43
2676 2840 1.066136 GACGGACGCCAGTAGTTTTC 58.934 55.000 0.00 0.00 0.00 2.29
2682 2846 0.323629 CGCCAGTAGTTTTCCCCTCA 59.676 55.000 0.00 0.00 0.00 3.86
2697 2861 8.560374 GTTTTCCCCTCATTTTCTCGATATTAG 58.440 37.037 0.00 0.00 0.00 1.73
2711 2875 4.999950 TCGATATTAGTTACTCCCTCCGTC 59.000 45.833 0.00 0.00 0.00 4.79
2712 2876 4.155644 CGATATTAGTTACTCCCTCCGTCC 59.844 50.000 0.00 0.00 0.00 4.79
2713 2877 2.149973 TTAGTTACTCCCTCCGTCCC 57.850 55.000 0.00 0.00 0.00 4.46
2714 2878 1.002069 TAGTTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
2715 2879 0.338814 AGTTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
2716 2880 1.572415 AGTTACTCCCTCCGTCCCATA 59.428 52.381 0.00 0.00 0.00 2.74
2717 2881 2.023695 AGTTACTCCCTCCGTCCCATAA 60.024 50.000 0.00 0.00 0.00 1.90
2718 2882 2.970640 GTTACTCCCTCCGTCCCATAAT 59.029 50.000 0.00 0.00 0.00 1.28
2719 2883 4.140853 AGTTACTCCCTCCGTCCCATAATA 60.141 45.833 0.00 0.00 0.00 0.98
2720 2884 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2721 2885 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2722 2886 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2723 2887 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2724 2888 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2725 2889 5.021458 TCCCTCCGTCCCATAATATAAGAC 58.979 45.833 0.00 0.00 0.00 3.01
2726 2890 5.024118 CCCTCCGTCCCATAATATAAGACT 58.976 45.833 0.00 0.00 0.00 3.24
2727 2891 6.011362 TCCCTCCGTCCCATAATATAAGACTA 60.011 42.308 0.00 0.00 0.00 2.59
2728 2892 6.321690 CCCTCCGTCCCATAATATAAGACTAG 59.678 46.154 0.00 0.00 0.00 2.57
2729 2893 6.890814 CCTCCGTCCCATAATATAAGACTAGT 59.109 42.308 0.00 0.00 0.00 2.57
2730 2894 7.148052 CCTCCGTCCCATAATATAAGACTAGTG 60.148 44.444 0.00 0.00 0.00 2.74
2731 2895 7.236529 TCCGTCCCATAATATAAGACTAGTGT 58.763 38.462 0.00 0.00 0.00 3.55
2732 2896 7.392673 TCCGTCCCATAATATAAGACTAGTGTC 59.607 40.741 0.00 0.00 43.22 3.67
2733 2897 7.176165 CCGTCCCATAATATAAGACTAGTGTCA 59.824 40.741 0.00 0.00 45.20 3.58
2734 2898 8.573885 CGTCCCATAATATAAGACTAGTGTCAA 58.426 37.037 0.00 0.00 45.20 3.18
2753 2917 8.996988 GTGTCAAAACACGTCTTATTTTATGA 57.003 30.769 0.00 0.00 45.84 2.15
2754 2918 9.103048 GTGTCAAAACACGTCTTATTTTATGAG 57.897 33.333 0.00 0.00 45.84 2.90
2755 2919 9.047371 TGTCAAAACACGTCTTATTTTATGAGA 57.953 29.630 0.00 0.00 0.00 3.27
2756 2920 9.314501 GTCAAAACACGTCTTATTTTATGAGAC 57.685 33.333 0.00 0.00 41.11 3.36
2763 2927 6.158023 GTCTTATTTTATGAGACGGAGGGA 57.842 41.667 0.00 0.00 36.39 4.20
2764 2928 6.579865 GTCTTATTTTATGAGACGGAGGGAA 58.420 40.000 0.00 0.00 36.39 3.97
2765 2929 7.217906 GTCTTATTTTATGAGACGGAGGGAAT 58.782 38.462 0.00 0.00 36.39 3.01
2766 2930 8.365647 GTCTTATTTTATGAGACGGAGGGAATA 58.634 37.037 0.00 0.00 36.39 1.75
2767 2931 8.930527 TCTTATTTTATGAGACGGAGGGAATAA 58.069 33.333 0.00 0.00 0.00 1.40
2768 2932 8.897872 TTATTTTATGAGACGGAGGGAATAAC 57.102 34.615 0.00 0.00 0.00 1.89
2769 2933 5.943349 TTTATGAGACGGAGGGAATAACA 57.057 39.130 0.00 0.00 0.00 2.41
2770 2934 5.531122 TTATGAGACGGAGGGAATAACAG 57.469 43.478 0.00 0.00 0.00 3.16
2771 2935 1.480954 TGAGACGGAGGGAATAACAGC 59.519 52.381 0.00 0.00 0.00 4.40
2772 2936 0.831307 AGACGGAGGGAATAACAGCC 59.169 55.000 0.00 0.00 0.00 4.85
2773 2937 0.539986 GACGGAGGGAATAACAGCCA 59.460 55.000 0.00 0.00 0.00 4.75
2774 2938 0.988832 ACGGAGGGAATAACAGCCAA 59.011 50.000 0.00 0.00 0.00 4.52
2775 2939 1.564348 ACGGAGGGAATAACAGCCAAT 59.436 47.619 0.00 0.00 0.00 3.16
2776 2940 2.222027 CGGAGGGAATAACAGCCAATC 58.778 52.381 0.00 0.00 0.00 2.67
2777 2941 2.421388 CGGAGGGAATAACAGCCAATCA 60.421 50.000 0.00 0.00 0.00 2.57
2778 2942 3.631250 GGAGGGAATAACAGCCAATCAA 58.369 45.455 0.00 0.00 0.00 2.57
2779 2943 4.218312 GGAGGGAATAACAGCCAATCAAT 58.782 43.478 0.00 0.00 0.00 2.57
2780 2944 5.385198 GGAGGGAATAACAGCCAATCAATA 58.615 41.667 0.00 0.00 0.00 1.90
2781 2945 5.474876 GGAGGGAATAACAGCCAATCAATAG 59.525 44.000 0.00 0.00 0.00 1.73
2782 2946 5.388654 AGGGAATAACAGCCAATCAATAGG 58.611 41.667 0.00 0.00 0.00 2.57
2783 2947 5.103515 AGGGAATAACAGCCAATCAATAGGT 60.104 40.000 0.00 0.00 0.00 3.08
2784 2948 5.241728 GGGAATAACAGCCAATCAATAGGTC 59.758 44.000 0.00 0.00 0.00 3.85
2785 2949 5.827797 GGAATAACAGCCAATCAATAGGTCA 59.172 40.000 0.00 0.00 0.00 4.02
2786 2950 6.491403 GGAATAACAGCCAATCAATAGGTCAT 59.509 38.462 0.00 0.00 0.00 3.06
2787 2951 7.665559 GGAATAACAGCCAATCAATAGGTCATA 59.334 37.037 0.00 0.00 0.00 2.15
2788 2952 8.627208 AATAACAGCCAATCAATAGGTCATAG 57.373 34.615 0.00 0.00 0.00 2.23
2789 2953 4.978099 ACAGCCAATCAATAGGTCATAGG 58.022 43.478 0.00 0.00 0.00 2.57
2790 2954 4.413520 ACAGCCAATCAATAGGTCATAGGT 59.586 41.667 0.00 0.00 0.00 3.08
2791 2955 4.758674 CAGCCAATCAATAGGTCATAGGTG 59.241 45.833 0.00 0.00 0.00 4.00
2792 2956 4.413520 AGCCAATCAATAGGTCATAGGTGT 59.586 41.667 0.00 0.00 0.00 4.16
2793 2957 5.606749 AGCCAATCAATAGGTCATAGGTGTA 59.393 40.000 0.00 0.00 0.00 2.90
2794 2958 6.101150 AGCCAATCAATAGGTCATAGGTGTAA 59.899 38.462 0.00 0.00 0.00 2.41
2795 2959 6.204882 GCCAATCAATAGGTCATAGGTGTAAC 59.795 42.308 0.00 0.00 0.00 2.50
2796 2960 7.509546 CCAATCAATAGGTCATAGGTGTAACT 58.490 38.462 0.00 0.00 36.74 2.24
2797 2961 7.993183 CCAATCAATAGGTCATAGGTGTAACTT 59.007 37.037 0.00 0.00 36.74 2.66
2801 2965 8.701895 TCAATAGGTCATAGGTGTAACTTAAGG 58.298 37.037 7.53 0.00 36.74 2.69
2802 2966 8.483758 CAATAGGTCATAGGTGTAACTTAAGGT 58.516 37.037 7.53 2.03 36.74 3.50
2803 2967 6.295719 AGGTCATAGGTGTAACTTAAGGTG 57.704 41.667 2.38 0.00 36.74 4.00
2804 2968 5.783875 AGGTCATAGGTGTAACTTAAGGTGT 59.216 40.000 2.38 0.00 36.74 4.16
2805 2969 6.955851 AGGTCATAGGTGTAACTTAAGGTGTA 59.044 38.462 2.38 0.00 36.74 2.90
2806 2970 7.622479 AGGTCATAGGTGTAACTTAAGGTGTAT 59.378 37.037 2.38 0.00 36.74 2.29
2807 2971 8.917088 GGTCATAGGTGTAACTTAAGGTGTATA 58.083 37.037 2.38 0.00 36.74 1.47
2946 3125 1.133407 GCCATAAAACATCGCCCGAAA 59.867 47.619 0.00 0.00 0.00 3.46
3014 3193 6.349694 CCAAGGGTCTTCAAGCTATTCTTTTC 60.350 42.308 0.00 0.00 31.27 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 5.008980 TGTCCATGCATTATCTGTTCACAA 58.991 37.500 0.00 0.00 0.00 3.33
73 74 4.587891 TGTCCATGCATTATCTGTTCACA 58.412 39.130 0.00 0.00 0.00 3.58
91 92 3.764434 TGGTAGTCTCTCTGTTCATGTCC 59.236 47.826 0.00 0.00 0.00 4.02
121 127 3.313012 TTAGTGTGGTCTCATTCGTGG 57.687 47.619 0.00 0.00 0.00 4.94
131 137 6.039382 AGTGAAAGTTTTGGATTAGTGTGGTC 59.961 38.462 0.00 0.00 0.00 4.02
148 154 2.870411 GCAGTTCGTGGTTAGTGAAAGT 59.130 45.455 0.00 0.00 0.00 2.66
152 158 0.319211 CGGCAGTTCGTGGTTAGTGA 60.319 55.000 0.00 0.00 0.00 3.41
159 165 1.234615 ATTTGGTCGGCAGTTCGTGG 61.235 55.000 0.00 0.00 0.00 4.94
179 185 9.632638 TTGGAGGGAAGAGAGAATAAATAAATG 57.367 33.333 0.00 0.00 0.00 2.32
328 336 2.037902 TCATTATAATCTCCGCGGGCAA 59.962 45.455 27.83 11.65 0.00 4.52
332 340 3.254060 CCTGTCATTATAATCTCCGCGG 58.746 50.000 22.12 22.12 0.00 6.46
335 343 6.015010 AGAGTTCCCTGTCATTATAATCTCCG 60.015 42.308 0.00 0.00 0.00 4.63
339 347 7.971183 GGAAGAGTTCCCTGTCATTATAATC 57.029 40.000 0.00 0.00 44.30 1.75
399 407 3.761752 TGGGGATTAAAGAAAGAAAGGCG 59.238 43.478 0.00 0.00 0.00 5.52
428 436 2.758979 ACGGATGGTAGGACTGTAGTTG 59.241 50.000 0.00 0.00 0.00 3.16
498 507 2.479650 GGTGGTCTCGACGTCTCG 59.520 66.667 14.70 1.54 41.65 4.04
536 545 1.069765 ATGATTAGGGTGAGCGCCG 59.930 57.895 2.29 0.00 0.00 6.46
539 548 2.301296 AGGATCATGATTAGGGTGAGCG 59.699 50.000 10.14 0.00 0.00 5.03
575 584 7.772292 CGGGATGATGATCATAAGAATAATGGT 59.228 37.037 8.54 0.00 37.20 3.55
600 613 2.029470 AGAAACTGAGAAGAGGAGTGCG 60.029 50.000 0.00 0.00 0.00 5.34
609 622 3.611986 GCGATGAGTGAGAAACTGAGAAG 59.388 47.826 0.00 0.00 40.07 2.85
629 642 1.937546 GAGGCCATTGAAAGGGTGCG 61.938 60.000 5.01 0.00 31.15 5.34
724 770 0.110419 TTAACACACGCAGCATTCGC 60.110 50.000 0.00 0.00 38.99 4.70
763 809 2.256174 CCATTGCGCTTTCAACATCAG 58.744 47.619 9.73 0.00 0.00 2.90
839 886 0.842030 AGCTGAATGTGGGAGTGGGA 60.842 55.000 0.00 0.00 0.00 4.37
840 887 0.911769 TAGCTGAATGTGGGAGTGGG 59.088 55.000 0.00 0.00 0.00 4.61
841 888 1.556911 AGTAGCTGAATGTGGGAGTGG 59.443 52.381 0.00 0.00 0.00 4.00
842 889 2.625737 CAGTAGCTGAATGTGGGAGTG 58.374 52.381 0.00 0.00 32.44 3.51
843 890 1.556911 CCAGTAGCTGAATGTGGGAGT 59.443 52.381 0.00 0.00 32.44 3.85
844 891 1.556911 ACCAGTAGCTGAATGTGGGAG 59.443 52.381 0.00 0.00 32.44 4.30
845 892 1.656587 ACCAGTAGCTGAATGTGGGA 58.343 50.000 0.00 0.00 32.44 4.37
894 941 5.664457 TGTTGTATCTCTTGTAGATGCCAG 58.336 41.667 0.00 0.00 44.33 4.85
953 1004 1.633561 CACTACGGACGACTAGACGA 58.366 55.000 21.04 0.00 37.03 4.20
966 1017 1.606668 GATCTCTCTCCTGGCACTACG 59.393 57.143 0.00 0.00 0.00 3.51
967 1018 1.606668 CGATCTCTCTCCTGGCACTAC 59.393 57.143 0.00 0.00 0.00 2.73
968 1019 1.490910 TCGATCTCTCTCCTGGCACTA 59.509 52.381 0.00 0.00 0.00 2.74
969 1020 0.257328 TCGATCTCTCTCCTGGCACT 59.743 55.000 0.00 0.00 0.00 4.40
970 1021 1.269448 GATCGATCTCTCTCCTGGCAC 59.731 57.143 18.29 0.00 0.00 5.01
971 1022 1.614996 GATCGATCTCTCTCCTGGCA 58.385 55.000 18.29 0.00 0.00 4.92
972 1023 0.521291 CGATCGATCTCTCTCCTGGC 59.479 60.000 22.43 0.00 0.00 4.85
973 1024 2.177394 TCGATCGATCTCTCTCCTGG 57.823 55.000 22.43 4.50 0.00 4.45
987 1038 1.795286 GCCTCCATTGTTCGATCGATC 59.205 52.381 20.18 18.57 0.00 3.69
988 1039 1.541233 GGCCTCCATTGTTCGATCGAT 60.541 52.381 20.18 0.00 0.00 3.59
989 1040 0.179084 GGCCTCCATTGTTCGATCGA 60.179 55.000 15.15 15.15 0.00 3.59
990 1041 0.179073 AGGCCTCCATTGTTCGATCG 60.179 55.000 9.36 9.36 0.00 3.69
991 1042 1.587547 GAGGCCTCCATTGTTCGATC 58.412 55.000 23.19 0.00 0.00 3.69
1086 1137 0.878961 GGTCGTTGCCGAAGAACTGT 60.879 55.000 0.00 0.00 46.26 3.55
1104 1155 3.207669 GCCGGATGCTGCTTCTGG 61.208 66.667 29.50 29.50 41.76 3.86
1227 1278 1.595357 GTGGCTGTAGTAACCCGCT 59.405 57.895 0.00 0.00 0.00 5.52
1444 1495 2.663196 CTTCTTCTTCGGGGCGGT 59.337 61.111 0.00 0.00 0.00 5.68
1495 1546 0.321122 CTGCCAGGAACTCAGGACAC 60.321 60.000 0.00 0.00 34.60 3.67
1503 1575 0.036022 GTCAAGAGCTGCCAGGAACT 59.964 55.000 0.00 0.00 43.88 3.01
1504 1576 0.250467 TGTCAAGAGCTGCCAGGAAC 60.250 55.000 0.00 0.00 0.00 3.62
1505 1577 0.694771 ATGTCAAGAGCTGCCAGGAA 59.305 50.000 0.00 0.00 0.00 3.36
1506 1578 1.571955 TATGTCAAGAGCTGCCAGGA 58.428 50.000 0.00 0.00 0.00 3.86
1507 1579 2.408271 TTATGTCAAGAGCTGCCAGG 57.592 50.000 0.00 0.00 0.00 4.45
1508 1580 5.061853 ACATATTATGTCAAGAGCTGCCAG 58.938 41.667 3.40 0.00 39.92 4.85
1509 1581 5.039920 ACATATTATGTCAAGAGCTGCCA 57.960 39.130 3.40 0.00 39.92 4.92
1557 1629 3.674410 GCATCGATCAGACAGACACTCAA 60.674 47.826 0.00 0.00 0.00 3.02
1676 1749 1.571460 GAGCTCTGCACGTTGTTGG 59.429 57.895 6.43 0.00 0.00 3.77
1871 1950 1.298859 CTGCGTTGGCACTTCTACCC 61.299 60.000 0.00 0.00 46.21 3.69
1872 1951 0.602905 ACTGCGTTGGCACTTCTACC 60.603 55.000 0.00 0.00 46.21 3.18
2050 2130 5.796350 ATAACAAATGTTCCAGTCGTAGC 57.204 39.130 1.37 0.00 39.31 3.58
2068 2148 9.515226 TTCCCCAGATATTTGCATTAGTATAAC 57.485 33.333 0.00 0.00 0.00 1.89
2076 2156 6.555738 TCATCATTTCCCCAGATATTTGCATT 59.444 34.615 0.00 0.00 0.00 3.56
2079 2159 6.014840 ACATCATCATTTCCCCAGATATTTGC 60.015 38.462 0.00 0.00 0.00 3.68
2080 2160 7.375834 CACATCATCATTTCCCCAGATATTTG 58.624 38.462 0.00 0.00 0.00 2.32
2104 2184 7.935520 TCGCATGCATTAGAAATTTATAACCA 58.064 30.769 19.57 8.37 0.00 3.67
2109 2189 9.188588 CAAATCTCGCATGCATTAGAAATTTAT 57.811 29.630 19.57 0.00 0.00 1.40
2110 2190 7.648908 CCAAATCTCGCATGCATTAGAAATTTA 59.351 33.333 19.57 0.00 0.00 1.40
2111 2191 6.477688 CCAAATCTCGCATGCATTAGAAATTT 59.522 34.615 19.57 8.47 0.00 1.82
2112 2192 5.981315 CCAAATCTCGCATGCATTAGAAATT 59.019 36.000 19.57 12.68 0.00 1.82
2113 2193 5.526115 CCAAATCTCGCATGCATTAGAAAT 58.474 37.500 19.57 7.80 0.00 2.17
2114 2194 4.734402 GCCAAATCTCGCATGCATTAGAAA 60.734 41.667 19.57 0.00 0.00 2.52
2115 2195 3.243168 GCCAAATCTCGCATGCATTAGAA 60.243 43.478 19.57 2.97 0.00 2.10
2116 2196 2.291465 GCCAAATCTCGCATGCATTAGA 59.709 45.455 19.57 16.66 0.00 2.10
2117 2197 2.292569 AGCCAAATCTCGCATGCATTAG 59.707 45.455 19.57 11.69 0.00 1.73
2176 2256 3.686241 GCTGCATGAACTTGATGTAGTGA 59.314 43.478 7.85 0.00 36.30 3.41
2218 2298 2.799126 ATATGGTTGGAGTTTCGCCA 57.201 45.000 0.00 0.00 0.00 5.69
2219 2299 6.293790 GGTTAATATATGGTTGGAGTTTCGCC 60.294 42.308 0.00 0.00 0.00 5.54
2251 2331 9.189156 CCCTGAAAAACATCCATAGATTTCTAA 57.811 33.333 0.00 0.00 31.39 2.10
2252 2332 7.285401 GCCCTGAAAAACATCCATAGATTTCTA 59.715 37.037 0.00 0.00 0.00 2.10
2254 2334 6.097412 AGCCCTGAAAAACATCCATAGATTTC 59.903 38.462 0.00 0.00 0.00 2.17
2256 2336 5.361857 CAGCCCTGAAAAACATCCATAGATT 59.638 40.000 0.00 0.00 0.00 2.40
2257 2337 4.891756 CAGCCCTGAAAAACATCCATAGAT 59.108 41.667 0.00 0.00 0.00 1.98
2258 2338 4.272489 CAGCCCTGAAAAACATCCATAGA 58.728 43.478 0.00 0.00 0.00 1.98
2259 2339 3.181483 GCAGCCCTGAAAAACATCCATAG 60.181 47.826 0.00 0.00 0.00 2.23
2260 2340 2.760092 GCAGCCCTGAAAAACATCCATA 59.240 45.455 0.00 0.00 0.00 2.74
2261 2341 1.551883 GCAGCCCTGAAAAACATCCAT 59.448 47.619 0.00 0.00 0.00 3.41
2262 2342 0.968405 GCAGCCCTGAAAAACATCCA 59.032 50.000 0.00 0.00 0.00 3.41
2263 2343 0.968405 TGCAGCCCTGAAAAACATCC 59.032 50.000 0.00 0.00 0.00 3.51
2265 2345 1.708341 AGTGCAGCCCTGAAAAACAT 58.292 45.000 0.00 0.00 0.00 2.71
2266 2346 1.484038 AAGTGCAGCCCTGAAAAACA 58.516 45.000 0.00 0.00 0.00 2.83
2267 2347 2.602257 AAAGTGCAGCCCTGAAAAAC 57.398 45.000 0.00 0.00 0.00 2.43
2268 2348 4.588528 AGATAAAAGTGCAGCCCTGAAAAA 59.411 37.500 0.00 0.00 0.00 1.94
2269 2349 4.151883 AGATAAAAGTGCAGCCCTGAAAA 58.848 39.130 0.00 0.00 0.00 2.29
2270 2350 3.766545 AGATAAAAGTGCAGCCCTGAAA 58.233 40.909 0.00 0.00 0.00 2.69
2271 2351 3.439857 AGATAAAAGTGCAGCCCTGAA 57.560 42.857 0.00 0.00 0.00 3.02
2272 2352 3.244875 TGAAGATAAAAGTGCAGCCCTGA 60.245 43.478 0.00 0.00 0.00 3.86
2273 2353 3.084039 TGAAGATAAAAGTGCAGCCCTG 58.916 45.455 0.00 0.00 0.00 4.45
2274 2354 3.009473 TCTGAAGATAAAAGTGCAGCCCT 59.991 43.478 0.00 0.00 0.00 5.19
2275 2355 3.347216 TCTGAAGATAAAAGTGCAGCCC 58.653 45.455 0.00 0.00 0.00 5.19
2276 2356 4.697352 TCTTCTGAAGATAAAAGTGCAGCC 59.303 41.667 15.82 0.00 31.20 4.85
2277 2357 5.869753 TCTTCTGAAGATAAAAGTGCAGC 57.130 39.130 15.82 0.00 31.20 5.25
2302 2382 9.555727 TGCTCAAAACAGTTTCTACTAGTTATT 57.444 29.630 0.00 0.00 31.96 1.40
2303 2383 9.555727 TTGCTCAAAACAGTTTCTACTAGTTAT 57.444 29.630 0.00 0.00 31.96 1.89
2304 2384 8.951787 TTGCTCAAAACAGTTTCTACTAGTTA 57.048 30.769 0.00 0.00 31.96 2.24
2305 2385 7.859325 TTGCTCAAAACAGTTTCTACTAGTT 57.141 32.000 0.00 0.00 31.96 2.24
2306 2386 7.859325 TTTGCTCAAAACAGTTTCTACTAGT 57.141 32.000 0.00 0.00 31.96 2.57
2307 2387 9.173939 CAATTTGCTCAAAACAGTTTCTACTAG 57.826 33.333 0.00 0.00 33.56 2.57
2308 2388 8.898761 TCAATTTGCTCAAAACAGTTTCTACTA 58.101 29.630 0.00 0.00 33.56 1.82
2309 2389 7.771183 TCAATTTGCTCAAAACAGTTTCTACT 58.229 30.769 0.00 0.00 33.56 2.57
2310 2390 7.985634 TCAATTTGCTCAAAACAGTTTCTAC 57.014 32.000 0.00 0.00 33.56 2.59
2311 2391 7.867403 GGATCAATTTGCTCAAAACAGTTTCTA 59.133 33.333 0.00 0.00 33.56 2.10
2312 2392 6.703165 GGATCAATTTGCTCAAAACAGTTTCT 59.297 34.615 0.00 0.00 33.56 2.52
2313 2393 6.703165 AGGATCAATTTGCTCAAAACAGTTTC 59.297 34.615 0.00 0.00 33.56 2.78
2314 2394 6.480981 CAGGATCAATTTGCTCAAAACAGTTT 59.519 34.615 2.95 0.00 33.56 2.66
2315 2395 5.987347 CAGGATCAATTTGCTCAAAACAGTT 59.013 36.000 2.95 0.00 33.56 3.16
2316 2396 5.302568 TCAGGATCAATTTGCTCAAAACAGT 59.697 36.000 2.95 0.00 33.56 3.55
2317 2397 5.632347 GTCAGGATCAATTTGCTCAAAACAG 59.368 40.000 2.95 0.00 33.56 3.16
2326 2406 4.219288 AGGAAACAGTCAGGATCAATTTGC 59.781 41.667 0.00 0.00 0.00 3.68
2349 2433 1.469595 GCTCAAAAGCTGTGCACAACA 60.470 47.619 21.98 0.00 45.55 3.33
2411 2496 2.257371 TCGAGGCCGACGTTGAAG 59.743 61.111 20.74 0.00 40.30 3.02
2487 2634 3.242543 GCACATATGAACTGCCGAGAAAG 60.243 47.826 10.38 0.00 0.00 2.62
2613 2771 7.107542 AGGACAAATGAGCGTAATAAGGTAAA 58.892 34.615 0.00 0.00 0.00 2.01
2619 2777 5.001237 TCGAGGACAAATGAGCGTAATAA 57.999 39.130 0.00 0.00 0.00 1.40
2621 2779 3.130516 TCTCGAGGACAAATGAGCGTAAT 59.869 43.478 13.56 0.00 0.00 1.89
2623 2781 2.089201 TCTCGAGGACAAATGAGCGTA 58.911 47.619 13.56 0.00 0.00 4.42
2626 2788 3.170791 TCATCTCGAGGACAAATGAGC 57.829 47.619 13.56 0.00 0.00 4.26
2629 2791 4.510711 CAGGATTCATCTCGAGGACAAATG 59.489 45.833 13.56 8.61 0.00 2.32
2675 2839 6.996180 ACTAATATCGAGAAAATGAGGGGA 57.004 37.500 0.00 0.00 0.00 4.81
2676 2840 8.368668 AGTAACTAATATCGAGAAAATGAGGGG 58.631 37.037 0.00 0.00 0.00 4.79
2682 2846 8.586744 GGAGGGAGTAACTAATATCGAGAAAAT 58.413 37.037 0.00 0.00 0.00 1.82
2697 2861 2.077687 TATGGGACGGAGGGAGTAAC 57.922 55.000 0.00 0.00 0.00 2.50
2716 2880 9.136952 GACGTGTTTTGACACTAGTCTTATATT 57.863 33.333 0.00 0.00 45.20 1.28
2717 2881 8.521176 AGACGTGTTTTGACACTAGTCTTATAT 58.479 33.333 11.75 0.00 45.20 0.86
2718 2882 7.879070 AGACGTGTTTTGACACTAGTCTTATA 58.121 34.615 11.75 0.00 45.20 0.98
2719 2883 6.746120 AGACGTGTTTTGACACTAGTCTTAT 58.254 36.000 11.75 0.00 45.20 1.73
2720 2884 6.140303 AGACGTGTTTTGACACTAGTCTTA 57.860 37.500 11.75 0.00 45.20 2.10
2721 2885 5.007385 AGACGTGTTTTGACACTAGTCTT 57.993 39.130 11.75 0.00 45.20 3.01
2722 2886 4.650754 AGACGTGTTTTGACACTAGTCT 57.349 40.909 11.75 11.75 45.20 3.24
2723 2887 7.404139 AATAAGACGTGTTTTGACACTAGTC 57.596 36.000 2.22 8.33 45.19 2.59
2724 2888 7.781548 AAATAAGACGTGTTTTGACACTAGT 57.218 32.000 2.22 0.00 38.40 2.57
2727 2891 8.832521 TCATAAAATAAGACGTGTTTTGACACT 58.167 29.630 2.22 0.00 38.40 3.55
2728 2892 8.996988 TCATAAAATAAGACGTGTTTTGACAC 57.003 30.769 2.22 0.00 33.17 3.67
2729 2893 9.047371 TCTCATAAAATAAGACGTGTTTTGACA 57.953 29.630 2.22 0.00 33.17 3.58
2730 2894 9.314501 GTCTCATAAAATAAGACGTGTTTTGAC 57.685 33.333 2.22 1.62 33.17 3.18
2740 2904 6.158023 TCCCTCCGTCTCATAAAATAAGAC 57.842 41.667 0.00 0.00 36.82 3.01
2741 2905 6.801718 TTCCCTCCGTCTCATAAAATAAGA 57.198 37.500 0.00 0.00 0.00 2.10
2742 2906 8.989980 GTTATTCCCTCCGTCTCATAAAATAAG 58.010 37.037 0.00 0.00 0.00 1.73
2743 2907 8.487848 TGTTATTCCCTCCGTCTCATAAAATAA 58.512 33.333 0.00 0.00 0.00 1.40
2744 2908 8.025270 TGTTATTCCCTCCGTCTCATAAAATA 57.975 34.615 0.00 0.00 0.00 1.40
2745 2909 6.895782 TGTTATTCCCTCCGTCTCATAAAAT 58.104 36.000 0.00 0.00 0.00 1.82
2746 2910 6.302535 TGTTATTCCCTCCGTCTCATAAAA 57.697 37.500 0.00 0.00 0.00 1.52
2747 2911 5.684030 GCTGTTATTCCCTCCGTCTCATAAA 60.684 44.000 0.00 0.00 0.00 1.40
2748 2912 4.202223 GCTGTTATTCCCTCCGTCTCATAA 60.202 45.833 0.00 0.00 0.00 1.90
2749 2913 3.321111 GCTGTTATTCCCTCCGTCTCATA 59.679 47.826 0.00 0.00 0.00 2.15
2750 2914 2.103263 GCTGTTATTCCCTCCGTCTCAT 59.897 50.000 0.00 0.00 0.00 2.90
2751 2915 1.480954 GCTGTTATTCCCTCCGTCTCA 59.519 52.381 0.00 0.00 0.00 3.27
2752 2916 1.202545 GGCTGTTATTCCCTCCGTCTC 60.203 57.143 0.00 0.00 0.00 3.36
2753 2917 0.831307 GGCTGTTATTCCCTCCGTCT 59.169 55.000 0.00 0.00 0.00 4.18
2754 2918 0.539986 TGGCTGTTATTCCCTCCGTC 59.460 55.000 0.00 0.00 0.00 4.79
2755 2919 0.988832 TTGGCTGTTATTCCCTCCGT 59.011 50.000 0.00 0.00 0.00 4.69
2756 2920 2.222027 GATTGGCTGTTATTCCCTCCG 58.778 52.381 0.00 0.00 0.00 4.63
2757 2921 3.297134 TGATTGGCTGTTATTCCCTCC 57.703 47.619 0.00 0.00 0.00 4.30
2758 2922 5.474876 CCTATTGATTGGCTGTTATTCCCTC 59.525 44.000 0.00 0.00 0.00 4.30
2759 2923 5.103515 ACCTATTGATTGGCTGTTATTCCCT 60.104 40.000 0.00 0.00 0.00 4.20
2760 2924 5.140454 ACCTATTGATTGGCTGTTATTCCC 58.860 41.667 0.00 0.00 0.00 3.97
2761 2925 5.827797 TGACCTATTGATTGGCTGTTATTCC 59.172 40.000 0.00 0.00 0.00 3.01
2762 2926 6.942532 TGACCTATTGATTGGCTGTTATTC 57.057 37.500 0.00 0.00 0.00 1.75
2763 2927 7.667219 CCTATGACCTATTGATTGGCTGTTATT 59.333 37.037 0.00 0.00 0.00 1.40
2764 2928 7.170965 CCTATGACCTATTGATTGGCTGTTAT 58.829 38.462 0.00 0.00 0.00 1.89
2765 2929 6.101150 ACCTATGACCTATTGATTGGCTGTTA 59.899 38.462 0.00 0.00 0.00 2.41
2766 2930 5.103940 ACCTATGACCTATTGATTGGCTGTT 60.104 40.000 0.00 0.00 0.00 3.16
2767 2931 4.413520 ACCTATGACCTATTGATTGGCTGT 59.586 41.667 0.00 0.00 0.00 4.40
2768 2932 4.758674 CACCTATGACCTATTGATTGGCTG 59.241 45.833 0.00 0.00 0.00 4.85
2769 2933 4.413520 ACACCTATGACCTATTGATTGGCT 59.586 41.667 0.00 0.00 0.00 4.75
2770 2934 4.718961 ACACCTATGACCTATTGATTGGC 58.281 43.478 0.00 0.00 0.00 4.52
2771 2935 7.509546 AGTTACACCTATGACCTATTGATTGG 58.490 38.462 0.00 0.00 0.00 3.16
2772 2936 8.964476 AAGTTACACCTATGACCTATTGATTG 57.036 34.615 0.00 0.00 0.00 2.67
2775 2939 8.701895 CCTTAAGTTACACCTATGACCTATTGA 58.298 37.037 0.97 0.00 0.00 2.57
2776 2940 8.483758 ACCTTAAGTTACACCTATGACCTATTG 58.516 37.037 0.97 0.00 0.00 1.90
2777 2941 8.483758 CACCTTAAGTTACACCTATGACCTATT 58.516 37.037 0.97 0.00 0.00 1.73
2778 2942 7.622479 ACACCTTAAGTTACACCTATGACCTAT 59.378 37.037 0.97 0.00 0.00 2.57
2779 2943 6.955851 ACACCTTAAGTTACACCTATGACCTA 59.044 38.462 0.97 0.00 0.00 3.08
2780 2944 5.783875 ACACCTTAAGTTACACCTATGACCT 59.216 40.000 0.97 0.00 0.00 3.85
2781 2945 6.046290 ACACCTTAAGTTACACCTATGACC 57.954 41.667 0.97 0.00 0.00 4.02
2806 2970 8.667463 GGGCGTTTTACTAGTCATGTTTAATTA 58.333 33.333 0.00 0.00 0.00 1.40
2807 2971 7.532571 GGGCGTTTTACTAGTCATGTTTAATT 58.467 34.615 0.00 0.00 0.00 1.40
2808 2972 6.183360 CGGGCGTTTTACTAGTCATGTTTAAT 60.183 38.462 0.00 0.00 0.00 1.40
2809 2973 5.120519 CGGGCGTTTTACTAGTCATGTTTAA 59.879 40.000 0.00 0.00 0.00 1.52
2810 2974 4.626604 CGGGCGTTTTACTAGTCATGTTTA 59.373 41.667 0.00 0.00 0.00 2.01
2811 2975 3.434299 CGGGCGTTTTACTAGTCATGTTT 59.566 43.478 0.00 0.00 0.00 2.83
2812 2976 2.997986 CGGGCGTTTTACTAGTCATGTT 59.002 45.455 0.00 0.00 0.00 2.71
2813 2977 2.028748 ACGGGCGTTTTACTAGTCATGT 60.029 45.455 0.00 0.00 0.00 3.21
2816 2980 1.936203 GCACGGGCGTTTTACTAGTCA 60.936 52.381 0.00 0.00 0.00 3.41
2817 2981 0.717784 GCACGGGCGTTTTACTAGTC 59.282 55.000 0.00 0.00 0.00 2.59
2946 3125 2.024369 ACACCTTCCAAAGACAAGGGTT 60.024 45.455 2.88 0.00 43.25 4.11
3014 3193 3.629058 AGATGAATTATGTCGACGTCCG 58.371 45.455 14.83 5.50 40.25 4.79


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

AutoCloner maintained by Alex Coulton.