Multiple sequence alignment - TraesCS7A01G310700

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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 TraesCS7A01G310700 chr7A 100.000 8109 0 0 1 8109 439636499 439628391 0.000000e+00 14975.0
1 TraesCS7A01G310700 chr7A 98.605 430 4 2 6032 6460 692756670 692756242 0.000000e+00 760.0
2 TraesCS7A01G310700 chr7A 77.095 179 27 6 2504 2669 17689827 17690004 3.120000e-14 91.6
3 TraesCS7A01G310700 chr7D 95.420 2511 65 18 2454 4957 388998170 388995703 0.000000e+00 3954.0
4 TraesCS7A01G310700 chr7D 93.775 2474 121 18 1 2463 389000726 388998275 0.000000e+00 3685.0
5 TraesCS7A01G310700 chr7D 90.730 2330 156 37 5814 8109 388994467 388992164 0.000000e+00 3051.0
6 TraesCS7A01G310700 chr7D 93.626 910 29 13 4956 5837 388995640 388994732 0.000000e+00 1332.0
7 TraesCS7A01G310700 chr7D 81.758 603 91 15 1812 2404 387917531 387916938 3.400000e-133 486.0
8 TraesCS7A01G310700 chr7D 90.722 97 5 3 4983 5079 88984973 88984881 8.540000e-25 126.0
9 TraesCS7A01G310700 chr7D 77.222 180 30 10 2440 2616 553806885 553807056 2.410000e-15 95.3
10 TraesCS7A01G310700 chr7B 93.842 1559 66 14 2457 3998 384201855 384200310 0.000000e+00 2320.0
11 TraesCS7A01G310700 chr7B 92.336 1644 100 8 834 2457 384203607 384201970 0.000000e+00 2314.0
12 TraesCS7A01G310700 chr7B 96.057 989 26 4 7121 8109 384190595 384189620 0.000000e+00 1598.0
13 TraesCS7A01G310700 chr7B 92.902 1113 38 10 4957 6031 384192320 384191211 0.000000e+00 1580.0
14 TraesCS7A01G310700 chr7B 91.748 921 54 12 4059 4957 384193305 384192385 0.000000e+00 1260.0
15 TraesCS7A01G310700 chr7B 96.825 630 17 2 6455 7084 384191219 384190593 0.000000e+00 1050.0
16 TraesCS7A01G310700 chr7B 82.283 920 116 14 1533 2425 510763587 510762688 0.000000e+00 752.0
17 TraesCS7A01G310700 chr7B 87.480 623 58 11 1 612 384204219 384203606 0.000000e+00 701.0
18 TraesCS7A01G310700 chr7B 77.299 511 93 14 4155 4655 458793422 458793919 6.200000e-71 279.0
19 TraesCS7A01G310700 chr7B 95.294 85 4 0 3979 4063 384200130 384200046 1.420000e-27 135.0
20 TraesCS7A01G310700 chr3B 83.507 958 126 14 1526 2455 187885395 187884442 0.000000e+00 865.0
21 TraesCS7A01G310700 chr3B 99.291 423 2 1 6032 6454 176923950 176924371 0.000000e+00 763.0
22 TraesCS7A01G310700 chr3B 82.220 928 113 25 1533 2444 1478975 1479866 0.000000e+00 752.0
23 TraesCS7A01G310700 chr3B 81.301 123 11 4 2554 2664 160277934 160277812 1.120000e-13 89.8
24 TraesCS7A01G310700 chr3D 83.368 956 116 23 1533 2457 108838436 108837493 0.000000e+00 845.0
25 TraesCS7A01G310700 chr3D 81.763 828 98 28 1533 2345 393010447 393009658 1.910000e-180 643.0
26 TraesCS7A01G310700 chr3D 78.327 526 100 9 4157 4672 67035254 67034733 2.180000e-85 327.0
27 TraesCS7A01G310700 chr3D 85.714 70 6 3 555 620 592853061 592853130 4.060000e-08 71.3
28 TraesCS7A01G310700 chr2A 83.721 903 99 14 1522 2404 771348850 771349724 0.000000e+00 809.0
29 TraesCS7A01G310700 chr2A 99.527 423 1 1 6032 6454 688238428 688238849 0.000000e+00 769.0
30 TraesCS7A01G310700 chr2A 89.385 179 18 1 3473 3651 203280021 203279844 2.950000e-54 224.0
31 TraesCS7A01G310700 chr6A 81.895 950 148 17 1525 2457 115336714 115337656 0.000000e+00 780.0
32 TraesCS7A01G310700 chr6A 84.109 258 34 5 3007 3259 577867687 577867432 8.130000e-60 243.0
33 TraesCS7A01G310700 chr6A 94.231 52 3 0 2616 2667 614852452 614852503 6.750000e-11 80.5
34 TraesCS7A01G310700 chr1A 99.764 424 0 1 6031 6454 37618817 37619239 0.000000e+00 776.0
35 TraesCS7A01G310700 chr1A 98.840 431 1 4 6028 6458 147685085 147684659 0.000000e+00 765.0
36 TraesCS7A01G310700 chr1A 83.571 420 51 8 1533 1951 575873498 575873900 2.140000e-100 377.0
37 TraesCS7A01G310700 chr1A 81.481 108 19 1 2510 2616 3947265 3947158 4.030000e-13 87.9
38 TraesCS7A01G310700 chr5A 99.527 423 1 1 6032 6454 450435624 450436045 0.000000e+00 769.0
39 TraesCS7A01G310700 chr5A 77.432 514 103 6 4160 4664 632276818 632277327 2.210000e-75 294.0
40 TraesCS7A01G310700 chr5A 87.448 239 25 3 3006 3240 589296693 589296930 3.730000e-68 270.0
41 TraesCS7A01G310700 chr4A 98.398 437 5 2 6022 6457 737301678 737302113 0.000000e+00 767.0
42 TraesCS7A01G310700 chr4A 83.408 223 22 5 2454 2662 574847806 574848027 8.310000e-45 193.0
43 TraesCS7A01G310700 chr6B 99.063 427 2 2 6028 6454 35812902 35813326 0.000000e+00 765.0
44 TraesCS7A01G310700 chr6B 78.416 505 95 8 4161 4655 348687461 348686961 4.720000e-82 316.0
45 TraesCS7A01G310700 chr6B 78.615 491 92 7 4175 4655 348659111 348659598 6.110000e-81 313.0
46 TraesCS7A01G310700 chr1B 99.059 425 2 2 6030 6454 626586269 626585847 0.000000e+00 761.0
47 TraesCS7A01G310700 chr1B 90.566 53 2 3 5025 5077 394875882 394875931 5.250000e-07 67.6
48 TraesCS7A01G310700 chr1D 81.170 940 125 26 1533 2443 479597288 479598204 0.000000e+00 708.0
49 TraesCS7A01G310700 chr1D 79.548 973 123 38 1533 2463 401437491 401438429 6.910000e-175 625.0
50 TraesCS7A01G310700 chr1D 86.611 239 25 6 3007 3240 366857401 366857637 2.900000e-64 257.0
51 TraesCS7A01G310700 chr2D 85.962 520 71 2 1940 2457 318582048 318582567 9.190000e-154 555.0
52 TraesCS7A01G310700 chr2D 89.268 205 20 2 3473 3677 189370066 189369864 1.040000e-63 255.0
53 TraesCS7A01G310700 chr2D 90.244 123 9 3 4957 5079 70636672 70636791 3.030000e-34 158.0
54 TraesCS7A01G310700 chr2D 88.430 121 7 5 4957 5077 56324155 56324042 1.100000e-28 139.0
55 TraesCS7A01G310700 chr2B 82.101 676 88 16 1808 2457 165109701 165110369 1.540000e-151 547.0
56 TraesCS7A01G310700 chr2B 86.719 256 28 5 2990 3240 273869752 273870006 6.200000e-71 279.0
57 TraesCS7A01G310700 chr2B 88.780 205 22 1 3473 3677 245686812 245686609 4.860000e-62 250.0
58 TraesCS7A01G310700 chr6D 81.053 665 107 12 1533 2184 373825006 373824348 5.610000e-141 512.0
59 TraesCS7A01G310700 chr4D 78.384 458 79 13 4177 4630 80830670 80830229 6.200000e-71 279.0
60 TraesCS7A01G310700 chr4D 76.091 481 95 16 4162 4634 423383030 423383498 4.890000e-57 233.0
61 TraesCS7A01G310700 chr4B 86.853 251 23 9 2997 3240 87400955 87400708 1.040000e-68 272.0
62 TraesCS7A01G310700 chr4B 87.395 238 25 4 3007 3240 183524986 183525222 1.340000e-67 268.0
63 TraesCS7A01G310700 chr4B 85.535 159 18 4 2462 2616 41190317 41190160 2.340000e-35 161.0
64 TraesCS7A01G310700 chr5D 87.395 238 24 5 3007 3240 4030140 4029905 1.340000e-67 268.0
65 TraesCS7A01G310700 chr5D 79.447 253 19 15 4957 5181 511950564 511950317 1.820000e-31 148.0
66 TraesCS7A01G310700 chr5D 80.269 223 15 13 2459 2666 11210416 11210208 3.050000e-29 141.0
67 TraesCS7A01G310700 chr5D 88.462 78 8 1 5000 5077 456624173 456624097 8.670000e-15 93.5
68 TraesCS7A01G310700 chr5B 86.290 124 12 5 4957 5079 53739022 53739141 6.600000e-26 130.0
69 TraesCS7A01G310700 chr5B 81.287 171 18 6 2509 2666 672470291 672470460 8.540000e-25 126.0
70 TraesCS7A01G310700 chr5B 95.000 40 1 1 4870 4909 268294024 268293986 2.440000e-05 62.1
71 TraesCS7A01G310700 chrUn 81.287 171 18 6 2509 2666 67314050 67313881 8.540000e-25 126.0
72 TraesCS7A01G310700 chrUn 81.287 171 18 6 2509 2666 248992595 248992426 8.540000e-25 126.0
73 TraesCS7A01G310700 chrUn 81.287 171 18 6 2509 2666 315257255 315257424 8.540000e-25 126.0
74 TraesCS7A01G310700 chr3A 96.875 32 0 1 560 591 22223042 22223012 1.500000e-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 TraesCS7A01G310700 chr7A 439628391 439636499 8108 True 14975.0 14975 100.00000 1 8109 1 chr7A.!!$R1 8108
1 TraesCS7A01G310700 chr7D 388992164 389000726 8562 True 3005.5 3954 93.38775 1 8109 4 chr7D.!!$R3 8108
2 TraesCS7A01G310700 chr7D 387916938 387917531 593 True 486.0 486 81.75800 1812 2404 1 chr7D.!!$R2 592
3 TraesCS7A01G310700 chr7B 384189620 384193305 3685 True 1372.0 1598 94.38300 4059 8109 4 chr7B.!!$R2 4050
4 TraesCS7A01G310700 chr7B 384200046 384204219 4173 True 1367.5 2320 92.23800 1 4063 4 chr7B.!!$R3 4062
5 TraesCS7A01G310700 chr7B 510762688 510763587 899 True 752.0 752 82.28300 1533 2425 1 chr7B.!!$R1 892
6 TraesCS7A01G310700 chr3B 187884442 187885395 953 True 865.0 865 83.50700 1526 2455 1 chr3B.!!$R2 929
7 TraesCS7A01G310700 chr3B 1478975 1479866 891 False 752.0 752 82.22000 1533 2444 1 chr3B.!!$F1 911
8 TraesCS7A01G310700 chr3D 108837493 108838436 943 True 845.0 845 83.36800 1533 2457 1 chr3D.!!$R2 924
9 TraesCS7A01G310700 chr3D 393009658 393010447 789 True 643.0 643 81.76300 1533 2345 1 chr3D.!!$R3 812
10 TraesCS7A01G310700 chr3D 67034733 67035254 521 True 327.0 327 78.32700 4157 4672 1 chr3D.!!$R1 515
11 TraesCS7A01G310700 chr2A 771348850 771349724 874 False 809.0 809 83.72100 1522 2404 1 chr2A.!!$F2 882
12 TraesCS7A01G310700 chr6A 115336714 115337656 942 False 780.0 780 81.89500 1525 2457 1 chr6A.!!$F1 932
13 TraesCS7A01G310700 chr5A 632276818 632277327 509 False 294.0 294 77.43200 4160 4664 1 chr5A.!!$F3 504
14 TraesCS7A01G310700 chr6B 348686961 348687461 500 True 316.0 316 78.41600 4161 4655 1 chr6B.!!$R1 494
15 TraesCS7A01G310700 chr1D 479597288 479598204 916 False 708.0 708 81.17000 1533 2443 1 chr1D.!!$F3 910
16 TraesCS7A01G310700 chr1D 401437491 401438429 938 False 625.0 625 79.54800 1533 2463 1 chr1D.!!$F2 930
17 TraesCS7A01G310700 chr2D 318582048 318582567 519 False 555.0 555 85.96200 1940 2457 1 chr2D.!!$F2 517
18 TraesCS7A01G310700 chr2B 165109701 165110369 668 False 547.0 547 82.10100 1808 2457 1 chr2B.!!$F1 649
19 TraesCS7A01G310700 chr6D 373824348 373825006 658 True 512.0 512 81.05300 1533 2184 1 chr6D.!!$R1 651

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
894 913 0.802607 CCAGAACGCGACTAGGAAGC 60.803 60.000 15.93 0.00 0.00 3.86 F
1586 1629 0.107848 ATCCGGCCGAGTAAACCTTG 60.108 55.000 30.73 5.39 0.00 3.61 F
1874 1947 0.394488 CTCGGTGAGAGCTGGGTCTA 60.394 60.000 0.00 0.00 40.54 2.59 F
1927 2003 0.827925 TGCTTCACCACTCCTCGACT 60.828 55.000 0.00 0.00 0.00 4.18 F
2497 2781 1.000993 GAGGCAGAGGAGAGGGACA 59.999 63.158 0.00 0.00 0.00 4.02 F
3920 4227 0.321671 ATCTGGACGGTTCTGGTGTG 59.678 55.000 0.00 0.00 0.00 3.82 F
4354 4875 0.251077 CTTGCTGTCTTCTTGGGGCT 60.251 55.000 0.00 0.00 0.00 5.19 F
4867 5402 0.804989 CACGTGGGAAGAGGATTTGC 59.195 55.000 7.95 0.00 0.00 3.68 F
6267 7208 1.056700 ATTCATCCTCCCGGACCAGG 61.057 60.000 0.73 5.22 43.51 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2547 2839 1.303091 ATTACTCGGCCGCCACAAAC 61.303 55.000 23.51 0.00 0.00 2.93 R
3003 3304 0.033796 CCAGGACGGAGGTGGTACTA 60.034 60.000 0.00 0.00 36.56 1.82 R
3004 3305 1.305046 CCAGGACGGAGGTGGTACT 60.305 63.158 0.00 0.00 36.56 2.73 R
3889 4196 1.082019 TCCAGATACAGGGGGTGCA 59.918 57.895 0.00 0.00 0.00 4.57 R
4354 4875 0.245539 CGAGAAACCCTAACCTCGCA 59.754 55.000 0.00 0.00 41.31 5.10 R
5349 5982 0.249238 CGCACAGGGAGAGTATGAGC 60.249 60.000 0.00 0.00 0.00 4.26 R
6255 7196 0.328258 ACAAATTCCTGGTCCGGGAG 59.672 55.000 19.25 10.52 40.34 4.30 R
6755 7719 1.071471 CGCCACCAAGGACAAGAGT 59.929 57.895 0.00 0.00 41.22 3.24 R
7609 8573 1.538047 AATGGTGGTGCAGCAGTTAG 58.462 50.000 20.85 0.00 45.01 2.34 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
29 30 1.878102 GCGGACATGAGACAAACTGGT 60.878 52.381 0.00 0.00 0.00 4.00
71 75 6.573664 AGATCAAATTCATGTTCGTTTGGA 57.426 33.333 0.00 0.00 33.55 3.53
76 80 2.465860 TCATGTTCGTTTGGATCGGT 57.534 45.000 0.00 0.00 0.00 4.69
154 158 7.477494 TGTTGTGCCTAGTTTACTTCTTTTTC 58.523 34.615 0.00 0.00 0.00 2.29
179 183 6.080648 TCTTCTTCAACTACAACGCTAAGA 57.919 37.500 0.00 0.00 0.00 2.10
184 188 4.543692 TCAACTACAACGCTAAGAGACAC 58.456 43.478 0.00 0.00 0.00 3.67
197 201 2.457598 AGAGACACAGCGATTTCCCTA 58.542 47.619 0.00 0.00 0.00 3.53
264 275 9.723447 TTTTGTGTTTTTCTTTTTCTTTTCACC 57.277 25.926 0.00 0.00 0.00 4.02
651 667 5.349270 GCAATTTTAAAATTACCGTGGACCC 59.651 40.000 22.44 0.00 36.52 4.46
661 677 3.801307 ACCGTGGACCCTTTCTAATTT 57.199 42.857 0.00 0.00 0.00 1.82
663 679 4.582869 ACCGTGGACCCTTTCTAATTTAC 58.417 43.478 0.00 0.00 0.00 2.01
668 684 5.936372 GTGGACCCTTTCTAATTTACGAACT 59.064 40.000 0.00 0.00 0.00 3.01
894 913 0.802607 CCAGAACGCGACTAGGAAGC 60.803 60.000 15.93 0.00 0.00 3.86
1020 1057 3.071602 CGATGGAACCACCTCTAATGGAT 59.928 47.826 0.00 0.00 39.87 3.41
1491 1528 5.523916 TCTGCTCTAAGCGAATTGGATTAAC 59.476 40.000 0.00 0.00 46.26 2.01
1586 1629 0.107848 ATCCGGCCGAGTAAACCTTG 60.108 55.000 30.73 5.39 0.00 3.61
1602 1645 8.270030 AGTAAACCTTGGTGGAGTATTTATACC 58.730 37.037 0.00 0.00 39.71 2.73
1874 1947 0.394488 CTCGGTGAGAGCTGGGTCTA 60.394 60.000 0.00 0.00 40.54 2.59
1927 2003 0.827925 TGCTTCACCACTCCTCGACT 60.828 55.000 0.00 0.00 0.00 4.18
2496 2780 1.760480 GGAGGCAGAGGAGAGGGAC 60.760 68.421 0.00 0.00 0.00 4.46
2497 2781 1.000993 GAGGCAGAGGAGAGGGACA 59.999 63.158 0.00 0.00 0.00 4.02
2498 2782 1.001503 AGGCAGAGGAGAGGGACAG 59.998 63.158 0.00 0.00 0.00 3.51
2499 2783 2.063378 GGCAGAGGAGAGGGACAGG 61.063 68.421 0.00 0.00 0.00 4.00
2500 2784 2.063378 GCAGAGGAGAGGGACAGGG 61.063 68.421 0.00 0.00 0.00 4.45
2501 2785 1.700368 CAGAGGAGAGGGACAGGGA 59.300 63.158 0.00 0.00 0.00 4.20
2547 2839 3.805207 CGGTGGAGTAAAAATAGGGAGG 58.195 50.000 0.00 0.00 0.00 4.30
2552 2844 6.008331 GTGGAGTAAAAATAGGGAGGTTTGT 58.992 40.000 0.00 0.00 0.00 2.83
2567 2859 1.302383 TTTGTGGCGGCCGAGTAATG 61.302 55.000 33.48 0.00 0.00 1.90
2569 2861 2.125310 TGGCGGCCGAGTAATGTG 60.125 61.111 33.48 0.00 0.00 3.21
2616 2909 1.117994 GGTTAGGTCCCGGTTAGAGG 58.882 60.000 0.00 0.00 0.00 3.69
2727 3028 4.647853 GGTACAGTGTGATATGGGTACTCA 59.352 45.833 5.88 0.00 33.47 3.41
2978 3279 6.747280 GCTGACTTGACAATAATTGCGTATTT 59.253 34.615 0.00 0.00 0.00 1.40
3139 3444 8.059798 ACCTCTTTCAAATATGAATCCAACAG 57.940 34.615 0.00 0.00 44.70 3.16
3448 3754 6.643770 GCTTTTGGTGATATGGCAGATTTATG 59.356 38.462 0.00 0.00 0.00 1.90
3843 4150 4.116961 CCAATGCATGTTGCTTTCCATAG 58.883 43.478 0.00 0.00 45.31 2.23
3889 4196 1.002134 CTTTGGCTCCGGGTGATGT 60.002 57.895 0.00 0.00 0.00 3.06
3920 4227 0.321671 ATCTGGACGGTTCTGGTGTG 59.678 55.000 0.00 0.00 0.00 3.82
4023 4529 5.401531 AGTTGAATACGGTAGAAGCAAGA 57.598 39.130 0.00 0.00 0.00 3.02
4084 4590 1.158007 TTGGCTTTCCTTCCCCTCTT 58.842 50.000 0.00 0.00 0.00 2.85
4147 4654 1.144936 GAGCCCGTGGAATCTCCTG 59.855 63.158 0.00 0.00 37.46 3.86
4159 4666 2.611964 ATCTCCTGCCCTCCGATGGT 62.612 60.000 0.00 0.00 0.00 3.55
4221 4728 7.549141 AGATAGGTTAGGGTCTTAATCCTCAT 58.451 38.462 0.00 0.00 34.75 2.90
4279 4800 0.968393 GAGTCAGTCTTCCGGGCTCT 60.968 60.000 0.00 0.00 0.00 4.09
4281 4802 1.228894 TCAGTCTTCCGGGCTCTGT 60.229 57.895 0.00 0.00 0.00 3.41
4354 4875 0.251077 CTTGCTGTCTTCTTGGGGCT 60.251 55.000 0.00 0.00 0.00 5.19
4387 4908 3.557595 GGTTTCTCGTCTTGCATATGAGG 59.442 47.826 6.97 8.06 31.99 3.86
4440 4961 2.188062 TTTAAGGGTTCAACGGCGAT 57.812 45.000 16.62 0.00 0.00 4.58
4814 5349 7.281040 ACATTTAATCATGTTGCCTATGAGG 57.719 36.000 0.00 0.00 37.91 3.86
4867 5402 0.804989 CACGTGGGAAGAGGATTTGC 59.195 55.000 7.95 0.00 0.00 3.68
5105 5738 9.918630 ACTTCATAGTCCAAGATTTCATTTTTG 57.081 29.630 0.00 0.00 0.00 2.44
5256 5889 4.392940 CAAGATATCGCCCCAGAGATTTT 58.607 43.478 0.00 0.00 34.10 1.82
5308 5941 7.819644 TGTGGTTCATATGTTTCTGAATTGAG 58.180 34.615 1.90 0.00 34.18 3.02
5349 5982 9.844790 TTTTCTCTGCATGTATATTGTTTTCAG 57.155 29.630 0.00 0.00 0.00 3.02
5393 6026 7.096640 CGTCGTGAATTTTATGAAATTATGCCC 60.097 37.037 8.07 0.00 43.61 5.36
5433 6066 4.500499 AGACAAGCTATTGGAGAATGCT 57.500 40.909 0.00 0.00 40.97 3.79
5713 6346 6.544038 GCAGTTGCAAAACCAGAATTAAAT 57.456 33.333 0.00 0.00 41.59 1.40
5807 6456 4.564782 ATGTATGGGTGCTCATGATAGG 57.435 45.455 0.00 0.00 0.00 2.57
5837 6774 9.804758 GAGTAAGCTACACTGTAGAAATATGTT 57.195 33.333 18.78 4.02 0.00 2.71
5919 6856 7.093596 TGACAGTAGATCAGTGATCATTCAGTT 60.094 37.037 30.05 13.47 41.12 3.16
6082 7023 5.017294 TGGAGCTCGGTTTTGAAAAATTT 57.983 34.783 7.83 0.00 0.00 1.82
6083 7024 4.808364 TGGAGCTCGGTTTTGAAAAATTTG 59.192 37.500 7.83 0.00 0.00 2.32
6088 7029 7.984391 AGCTCGGTTTTGAAAAATTTGAATTT 58.016 26.923 0.00 0.00 40.15 1.82
6090 7031 8.522661 GCTCGGTTTTGAAAAATTTGAATTTTG 58.477 29.630 13.45 1.84 45.16 2.44
6091 7032 9.553418 CTCGGTTTTGAAAAATTTGAATTTTGT 57.447 25.926 13.45 6.00 45.16 2.83
6093 7034 9.934641 CGGTTTTGAAAAATTTGAATTTTGTTG 57.065 25.926 13.45 0.00 45.16 3.33
6159 7100 7.973402 ACACACATATATATGAAGGCCTAACA 58.027 34.615 26.05 10.71 37.15 2.41
6164 7105 7.878127 ACATATATATGAAGGCCTAACACACAC 59.122 37.037 26.05 0.00 37.15 3.82
6182 7123 4.286910 CACACGTGTGTAAATTTTCAGGG 58.713 43.478 35.03 9.31 42.83 4.45
6183 7124 3.243267 ACACGTGTGTAAATTTTCAGGGC 60.243 43.478 22.71 0.00 42.90 5.19
6184 7125 2.952978 ACGTGTGTAAATTTTCAGGGCA 59.047 40.909 0.00 0.00 0.00 5.36
6190 7131 7.169982 CGTGTGTAAATTTTCAGGGCAAAATAA 59.830 33.333 0.00 0.00 35.35 1.40
6191 7132 8.495148 GTGTGTAAATTTTCAGGGCAAAATAAG 58.505 33.333 0.00 0.00 35.35 1.73
6197 7138 8.744568 AATTTTCAGGGCAAAATAAGTTGAAA 57.255 26.923 0.00 0.00 35.35 2.69
6200 7141 6.662865 TCAGGGCAAAATAAGTTGAAATGA 57.337 33.333 0.00 0.00 0.00 2.57
6202 7143 5.870978 CAGGGCAAAATAAGTTGAAATGAGG 59.129 40.000 0.00 0.00 0.00 3.86
6203 7144 5.046376 AGGGCAAAATAAGTTGAAATGAGGG 60.046 40.000 0.00 0.00 0.00 4.30
6208 7149 5.649782 AATAAGTTGAAATGAGGGCTGTG 57.350 39.130 0.00 0.00 0.00 3.66
6237 7178 8.648557 AAAAGACAAATCTGAGGCTTTTTAAC 57.351 30.769 3.80 0.00 34.48 2.01
6239 7180 6.739112 AGACAAATCTGAGGCTTTTTAACAC 58.261 36.000 0.00 0.00 32.29 3.32
6240 7181 6.321181 AGACAAATCTGAGGCTTTTTAACACA 59.679 34.615 0.00 0.00 32.29 3.72
6241 7182 7.014615 AGACAAATCTGAGGCTTTTTAACACAT 59.985 33.333 0.00 0.00 32.29 3.21
6242 7183 6.925165 ACAAATCTGAGGCTTTTTAACACATG 59.075 34.615 0.00 0.00 0.00 3.21
6243 7184 6.899393 AATCTGAGGCTTTTTAACACATGA 57.101 33.333 0.00 0.00 0.00 3.07
6244 7185 5.689383 TCTGAGGCTTTTTAACACATGAC 57.311 39.130 0.00 0.00 0.00 3.06
6245 7186 5.129634 TCTGAGGCTTTTTAACACATGACA 58.870 37.500 0.00 0.00 0.00 3.58
6246 7187 5.008613 TCTGAGGCTTTTTAACACATGACAC 59.991 40.000 0.00 0.00 0.00 3.67
6247 7188 4.887071 TGAGGCTTTTTAACACATGACACT 59.113 37.500 0.00 0.00 0.00 3.55
6248 7189 6.058833 TGAGGCTTTTTAACACATGACACTA 58.941 36.000 0.00 0.00 0.00 2.74
6249 7190 6.714810 TGAGGCTTTTTAACACATGACACTAT 59.285 34.615 0.00 0.00 0.00 2.12
6250 7191 7.230510 TGAGGCTTTTTAACACATGACACTATT 59.769 33.333 0.00 0.00 0.00 1.73
6251 7192 7.593825 AGGCTTTTTAACACATGACACTATTC 58.406 34.615 0.00 0.00 0.00 1.75
6252 7193 7.230510 AGGCTTTTTAACACATGACACTATTCA 59.769 33.333 0.00 0.00 0.00 2.57
6254 7195 9.065871 GCTTTTTAACACATGACACTATTCATC 57.934 33.333 0.00 0.00 33.74 2.92
6255 7196 9.559958 CTTTTTAACACATGACACTATTCATCC 57.440 33.333 0.00 0.00 33.74 3.51
6257 7198 8.492673 TTTAACACATGACACTATTCATCCTC 57.507 34.615 0.00 0.00 33.74 3.71
6258 7199 5.028549 ACACATGACACTATTCATCCTCC 57.971 43.478 0.00 0.00 33.74 4.30
6259 7200 4.141620 ACACATGACACTATTCATCCTCCC 60.142 45.833 0.00 0.00 33.74 4.30
6260 7201 3.070159 ACATGACACTATTCATCCTCCCG 59.930 47.826 0.00 0.00 33.74 5.14
6261 7202 2.039418 TGACACTATTCATCCTCCCGG 58.961 52.381 0.00 0.00 0.00 5.73
6262 7203 2.317040 GACACTATTCATCCTCCCGGA 58.683 52.381 0.73 0.00 45.16 5.14
6265 7206 1.062428 ACTATTCATCCTCCCGGACCA 60.062 52.381 0.73 0.00 43.51 4.02
6266 7207 1.620819 CTATTCATCCTCCCGGACCAG 59.379 57.143 0.73 0.00 43.51 4.00
6267 7208 1.056700 ATTCATCCTCCCGGACCAGG 61.057 60.000 0.73 5.22 43.51 4.45
6268 7209 2.041922 CATCCTCCCGGACCAGGA 60.042 66.667 16.50 16.50 43.51 3.86
6303 7244 7.499321 TTTGTATAGGTCACATTTCAACGTT 57.501 32.000 0.00 0.00 0.00 3.99
6307 7248 8.071368 TGTATAGGTCACATTTCAACGTTTTTC 58.929 33.333 0.00 0.00 0.00 2.29
6308 7249 5.317733 AGGTCACATTTCAACGTTTTTCA 57.682 34.783 0.00 0.00 0.00 2.69
6309 7250 5.901552 AGGTCACATTTCAACGTTTTTCAT 58.098 33.333 0.00 0.00 0.00 2.57
6310 7251 6.337356 AGGTCACATTTCAACGTTTTTCATT 58.663 32.000 0.00 0.00 0.00 2.57
6317 7258 9.097257 ACATTTCAACGTTTTTCATTCTGAAAT 57.903 25.926 11.37 11.37 44.75 2.17
6332 7273 8.243426 TCATTCTGAAATTTTACACACATAGGC 58.757 33.333 0.00 0.00 0.00 3.93
6333 7274 7.517614 TTCTGAAATTTTACACACATAGGCA 57.482 32.000 0.00 0.00 0.00 4.75
6335 7276 8.800370 TCTGAAATTTTACACACATAGGCATA 57.200 30.769 0.00 0.00 0.00 3.14
6337 7278 9.289303 CTGAAATTTTACACACATAGGCATAAC 57.711 33.333 0.00 0.00 0.00 1.89
6338 7279 8.797438 TGAAATTTTACACACATAGGCATAACA 58.203 29.630 0.00 0.00 0.00 2.41
6339 7280 9.801873 GAAATTTTACACACATAGGCATAACAT 57.198 29.630 0.00 0.00 0.00 2.71
6343 7284 9.456147 TTTTACACACATAGGCATAACATACTT 57.544 29.630 0.00 0.00 0.00 2.24
6344 7285 6.925610 ACACACATAGGCATAACATACTTG 57.074 37.500 0.00 0.00 0.00 3.16
6349 7290 8.889717 ACACATAGGCATAACATACTTGTTTAC 58.110 33.333 0.00 0.00 43.57 2.01
6350 7291 9.109393 CACATAGGCATAACATACTTGTTTACT 57.891 33.333 0.00 0.00 43.57 2.24
6351 7292 9.681062 ACATAGGCATAACATACTTGTTTACTT 57.319 29.630 0.00 0.00 43.57 2.24
6352 7293 9.935682 CATAGGCATAACATACTTGTTTACTTG 57.064 33.333 0.00 0.00 43.57 3.16
6353 7294 6.852664 AGGCATAACATACTTGTTTACTTGC 58.147 36.000 0.00 2.98 43.57 4.01
6354 7295 6.432783 AGGCATAACATACTTGTTTACTTGCA 59.567 34.615 0.00 0.00 43.57 4.08
6355 7296 6.526674 GGCATAACATACTTGTTTACTTGCAC 59.473 38.462 0.00 0.00 43.57 4.57
6356 7297 7.081349 GCATAACATACTTGTTTACTTGCACA 58.919 34.615 0.00 0.00 43.57 4.57
6357 7298 7.593273 GCATAACATACTTGTTTACTTGCACAA 59.407 33.333 0.00 0.00 43.57 3.33
6402 7343 8.940952 TGAAACCGAAAAGTTTGAATTTTGATT 58.059 25.926 0.00 0.00 40.01 2.57
6403 7344 9.767684 GAAACCGAAAAGTTTGAATTTTGATTT 57.232 25.926 0.00 0.00 40.01 2.17
6404 7345 9.553418 AAACCGAAAAGTTTGAATTTTGATTTG 57.447 25.926 0.00 0.00 38.51 2.32
6405 7346 8.262715 ACCGAAAAGTTTGAATTTTGATTTGT 57.737 26.923 0.00 0.00 30.22 2.83
6445 7386 4.016706 CTCCCGGGAGCCAAACGT 62.017 66.667 36.90 0.00 35.31 3.99
6449 7390 4.675029 CGGGAGCCAAACGTCCGT 62.675 66.667 1.73 0.00 35.14 4.69
6450 7391 2.281276 GGGAGCCAAACGTCCGTT 60.281 61.111 0.00 0.00 40.45 4.44
6451 7392 2.322830 GGGAGCCAAACGTCCGTTC 61.323 63.158 5.44 0.00 37.35 3.95
6452 7393 1.301479 GGAGCCAAACGTCCGTTCT 60.301 57.895 5.44 0.00 37.35 3.01
6453 7394 1.289800 GGAGCCAAACGTCCGTTCTC 61.290 60.000 5.44 8.11 37.35 2.87
6545 7495 2.290514 ACACCAGTGCTATGAACTGCAT 60.291 45.455 0.00 0.00 43.06 3.96
6554 7504 5.634439 GTGCTATGAACTGCATGATCTAGAG 59.366 44.000 0.00 0.00 41.45 2.43
6755 7719 5.699458 GGATTAGTTCTTCGGTCTGAACAAA 59.301 40.000 8.28 0.00 43.38 2.83
6777 7741 3.783362 TTGTCCTTGGTGGCGTGGG 62.783 63.158 0.00 0.00 35.26 4.61
6980 7944 3.586470 TGTTGGCTGGTAGGAAGAAAA 57.414 42.857 0.00 0.00 0.00 2.29
7009 7973 7.613022 TGAATATTCTGAAGATGCTTTTGGACT 59.387 33.333 16.24 0.00 0.00 3.85
7058 8022 4.724399 TCTTGGTCTAAACAATGAAGCCA 58.276 39.130 0.00 0.00 0.00 4.75
7059 8023 5.136828 TCTTGGTCTAAACAATGAAGCCAA 58.863 37.500 0.00 0.00 34.19 4.52
7134 8098 6.864360 ACAAATGATTTGAAACATGTTGGG 57.136 33.333 23.37 0.00 43.26 4.12
7140 8104 6.648192 TGATTTGAAACATGTTGGGTTCTTT 58.352 32.000 12.82 0.00 0.00 2.52
7386 8350 3.691498 GTTGTGAACCAAAGCTGTACAC 58.309 45.455 0.00 0.00 34.07 2.90
7586 8550 5.238214 GGATTTCAAGGAGATGAGCATACAC 59.762 44.000 0.00 0.00 0.00 2.90
7609 8573 5.183904 ACAAGAAGGTTCCATTCATGCTAAC 59.816 40.000 0.00 0.00 30.49 2.34
7619 8583 4.497006 CCATTCATGCTAACTAACTGCTGC 60.497 45.833 0.00 0.00 0.00 5.25
7620 8584 3.333029 TCATGCTAACTAACTGCTGCA 57.667 42.857 0.88 0.88 34.88 4.41
7621 8585 3.002791 TCATGCTAACTAACTGCTGCAC 58.997 45.455 0.00 0.00 33.16 4.57
7725 8689 1.915769 GGAGCCACTCCTGGTCAGT 60.916 63.158 6.38 0.00 46.41 3.41
7863 8827 0.106918 TTGCGGGGTTCTTGTTCTGT 60.107 50.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 75 1.315257 GCCAACTCCAATGCACCGAT 61.315 55.000 0.00 0.00 0.00 4.18
76 80 1.075374 ACTAAGGCCAACTCCAATGCA 59.925 47.619 5.01 0.00 0.00 3.96
154 158 6.641314 TCTTAGCGTTGTAGTTGAAGAAGAAG 59.359 38.462 0.00 0.00 0.00 2.85
179 183 3.914426 AATAGGGAAATCGCTGTGTCT 57.086 42.857 9.97 0.00 39.60 3.41
184 188 4.399303 AGAAACCAAATAGGGAAATCGCTG 59.601 41.667 9.97 0.00 43.89 5.18
330 341 7.923344 TCGTGGATTTAAAAAGCATTCAAAAGA 59.077 29.630 0.00 0.00 0.00 2.52
631 645 6.550481 AGAAAGGGTCCACGGTAATTTTAAAA 59.450 34.615 2.51 2.51 0.00 1.52
635 649 4.108501 AGAAAGGGTCCACGGTAATTTT 57.891 40.909 0.00 0.00 0.00 1.82
675 691 9.587772 TCAACTTTTAAAAATTCACATTTCGGA 57.412 25.926 1.66 0.00 30.80 4.55
787 806 2.921374 TTGACCGATCAACCGTTGG 58.079 52.632 11.35 0.00 40.01 3.77
813 832 1.796151 CATTGGTTCGCATCGCACT 59.204 52.632 0.00 0.00 0.00 4.40
894 913 1.304464 GGGACAAAAGAGCAGGGGG 60.304 63.158 0.00 0.00 0.00 5.40
1020 1057 1.198094 TGGTGGGAAGATCGAAGCCA 61.198 55.000 0.00 0.00 0.00 4.75
1131 1168 1.812922 CTCGCACCTGTCAGGATGC 60.813 63.158 26.18 25.41 37.67 3.91
1247 1284 3.247056 TTGAGGCGGTCAATGGCGA 62.247 57.895 0.00 0.00 40.45 5.54
1360 1397 2.434884 AAGACGAGCCCGCACATG 60.435 61.111 0.00 0.00 39.95 3.21
1514 1551 2.760650 TGCCGTTAGATCAGTCAGATGT 59.239 45.455 0.00 0.00 37.00 3.06
1602 1645 2.265589 ACCGACCAAAACTTAGTGGG 57.734 50.000 0.00 0.00 39.39 4.61
1675 1718 3.673338 GCAAGTTTCGGTTGAAATTAGGC 59.327 43.478 0.00 0.00 45.31 3.93
1927 2003 1.313812 GCGAGGAGGAGGAGTTCGAA 61.314 60.000 0.00 0.00 33.38 3.71
2138 2302 2.060383 CACCTCATCCTGCCGGAGA 61.060 63.158 5.05 0.00 44.06 3.71
2547 2839 1.303091 ATTACTCGGCCGCCACAAAC 61.303 55.000 23.51 0.00 0.00 2.93
2552 2844 2.125310 CACATTACTCGGCCGCCA 60.125 61.111 23.51 2.44 0.00 5.69
2567 2859 6.281405 CCAATAGACCATAGTGGAGTAACAC 58.719 44.000 2.45 0.00 40.96 3.32
2569 2861 5.221661 CCCCAATAGACCATAGTGGAGTAAC 60.222 48.000 2.45 0.00 40.96 2.50
2616 2909 4.904895 ACCAGTTAGAGGAGTAAAACCC 57.095 45.455 0.00 0.00 0.00 4.11
2617 2910 7.336176 CCAATAACCAGTTAGAGGAGTAAAACC 59.664 40.741 5.54 0.00 0.00 3.27
2618 2911 7.336176 CCCAATAACCAGTTAGAGGAGTAAAAC 59.664 40.741 10.87 0.00 0.00 2.43
2893 3194 4.942944 TCATAAGTACTCCCTCTGTTCCA 58.057 43.478 0.00 0.00 0.00 3.53
2937 3238 3.256631 AGTCAGCCATGCCACTTAAAAAG 59.743 43.478 0.00 0.00 0.00 2.27
2997 3298 5.415077 CAGGACGGAGGTGGTACTATTATAG 59.585 48.000 0.00 0.00 0.00 1.31
2998 3299 5.319453 CAGGACGGAGGTGGTACTATTATA 58.681 45.833 0.00 0.00 0.00 0.98
2999 3300 4.150359 CAGGACGGAGGTGGTACTATTAT 58.850 47.826 0.00 0.00 0.00 1.28
3000 3301 3.559069 CAGGACGGAGGTGGTACTATTA 58.441 50.000 0.00 0.00 0.00 0.98
3001 3302 2.385803 CAGGACGGAGGTGGTACTATT 58.614 52.381 0.00 0.00 0.00 1.73
3002 3303 1.411216 CCAGGACGGAGGTGGTACTAT 60.411 57.143 0.00 0.00 36.56 2.12
3003 3304 0.033796 CCAGGACGGAGGTGGTACTA 60.034 60.000 0.00 0.00 36.56 1.82
3004 3305 1.305046 CCAGGACGGAGGTGGTACT 60.305 63.158 0.00 0.00 36.56 2.73
3050 3351 8.626526 TGGTAGTTAAAATCAGGTCAAAGTTTC 58.373 33.333 0.00 0.00 0.00 2.78
3209 3514 2.237893 TCTCGGTTTATTGGTCCCCTTC 59.762 50.000 0.00 0.00 0.00 3.46
3843 4150 4.563786 GCTACCCATATAGGTCCTGCTTTC 60.564 50.000 0.00 0.00 41.58 2.62
3889 4196 1.082019 TCCAGATACAGGGGGTGCA 59.918 57.895 0.00 0.00 0.00 4.57
3920 4227 6.773685 ACCACTACTCTATGTCCTGATCTTAC 59.226 42.308 0.00 0.00 0.00 2.34
4023 4529 2.254546 TTTGATGGCGTCACAGAAGT 57.745 45.000 9.35 0.00 36.32 3.01
4032 4538 2.229792 ACACTCATGTTTTGATGGCGT 58.770 42.857 0.00 0.00 34.46 5.68
4084 4590 4.451150 CGCCCTACTCGCCTTGCA 62.451 66.667 0.00 0.00 0.00 4.08
4147 4654 2.801631 CTCTCCACCATCGGAGGGC 61.802 68.421 8.91 0.00 46.60 5.19
4159 4666 1.289160 CACCAAGATTCCCCTCTCCA 58.711 55.000 0.00 0.00 0.00 3.86
4221 4728 4.853142 ATCCGAGCGCCACCCCTA 62.853 66.667 2.29 0.00 0.00 3.53
4279 4800 1.343465 GGACGAACTTGAGGAGGAACA 59.657 52.381 0.00 0.00 0.00 3.18
4281 4802 0.601558 CGGACGAACTTGAGGAGGAA 59.398 55.000 0.00 0.00 0.00 3.36
4354 4875 0.245539 CGAGAAACCCTAACCTCGCA 59.754 55.000 0.00 0.00 41.31 5.10
4672 5203 1.658409 GCAAAACACCTGCACGCTC 60.658 57.895 0.00 0.00 39.69 5.03
4675 5206 2.027460 GGGCAAAACACCTGCACG 59.973 61.111 0.00 0.00 41.78 5.34
4684 5216 1.063321 CCGCAAACAAAAGGGCAAAAC 59.937 47.619 0.00 0.00 0.00 2.43
4814 5349 1.401552 TGCAAGCACGATAAGCAATCC 59.598 47.619 0.00 0.00 31.42 3.01
5079 5690 9.918630 CAAAAATGAAATCTTGGACTATGAAGT 57.081 29.630 0.00 0.00 39.21 3.01
5134 5767 3.529734 TGCTCCAACCCCCTATATGAAAA 59.470 43.478 0.00 0.00 0.00 2.29
5308 5941 6.255453 TGCAGAGAAAAATAACAACACAAAGC 59.745 34.615 0.00 0.00 0.00 3.51
5349 5982 0.249238 CGCACAGGGAGAGTATGAGC 60.249 60.000 0.00 0.00 0.00 4.26
5393 6026 4.756642 TGTCTAGTTCTGCAGAAACCAATG 59.243 41.667 29.99 16.25 35.58 2.82
5433 6066 0.761702 GTGCTATTACCGGGGAGGGA 60.762 60.000 6.32 0.00 46.96 4.20
5559 6192 5.346822 GTGAATAGTACCACTTGTAACACCG 59.653 44.000 0.00 0.00 0.00 4.94
5612 6245 0.945099 TATCTGAGCCGAGTAGTGCG 59.055 55.000 0.00 0.00 0.00 5.34
5713 6346 7.007723 ACCAAAGTAATGTACCTCAATCCAAA 58.992 34.615 0.00 0.00 0.00 3.28
5807 6456 3.695060 TCTACAGTGTAGCTTACTCAGGC 59.305 47.826 23.14 0.00 0.00 4.85
5837 6774 7.295322 AGATTCAGACTATCGAAATCCATCA 57.705 36.000 0.00 0.00 0.00 3.07
5919 6856 5.759506 GCTAGATGCTACAACTCTACTGA 57.240 43.478 0.00 0.00 38.95 3.41
6031 6968 2.222027 GGCCTCCAAAGACAATATCCG 58.778 52.381 0.00 0.00 0.00 4.18
6033 6970 3.134458 CTCGGCCTCCAAAGACAATATC 58.866 50.000 0.00 0.00 0.00 1.63
6034 6971 2.746472 GCTCGGCCTCCAAAGACAATAT 60.746 50.000 0.00 0.00 0.00 1.28
6035 6972 1.406887 GCTCGGCCTCCAAAGACAATA 60.407 52.381 0.00 0.00 0.00 1.90
6038 6975 2.172483 GAGCTCGGCCTCCAAAGACA 62.172 60.000 0.00 0.00 0.00 3.41
6040 6977 2.982130 GAGCTCGGCCTCCAAAGA 59.018 61.111 0.00 0.00 0.00 2.52
6066 7004 9.899226 AACAAAATTCAAATTTTTCAAAACCGA 57.101 22.222 10.05 0.00 43.91 4.69
6135 7076 7.877612 TGTGTTAGGCCTTCATATATATGTGTG 59.122 37.037 12.58 11.45 35.26 3.82
6137 7078 7.877612 TGTGTGTTAGGCCTTCATATATATGTG 59.122 37.037 12.58 14.19 35.26 3.21
6138 7079 7.878127 GTGTGTGTTAGGCCTTCATATATATGT 59.122 37.037 12.58 4.89 35.26 2.29
6140 7081 7.097192 CGTGTGTGTTAGGCCTTCATATATAT 58.903 38.462 12.58 0.00 0.00 0.86
6146 7087 1.071699 ACGTGTGTGTTAGGCCTTCAT 59.928 47.619 12.58 0.00 0.00 2.57
6148 7089 0.865769 CACGTGTGTGTTAGGCCTTC 59.134 55.000 12.58 5.51 41.34 3.46
6150 7091 4.771127 CACGTGTGTGTTAGGCCT 57.229 55.556 11.78 11.78 41.34 5.19
6164 7105 3.634568 TGCCCTGAAAATTTACACACG 57.365 42.857 0.00 0.00 0.00 4.49
6174 7115 7.989741 TCATTTCAACTTATTTTGCCCTGAAAA 59.010 29.630 0.00 0.00 35.59 2.29
6175 7116 7.504403 TCATTTCAACTTATTTTGCCCTGAAA 58.496 30.769 0.00 0.00 36.19 2.69
6180 7121 5.178061 CCCTCATTTCAACTTATTTTGCCC 58.822 41.667 0.00 0.00 0.00 5.36
6182 7123 5.349543 CAGCCCTCATTTCAACTTATTTTGC 59.650 40.000 0.00 0.00 0.00 3.68
6183 7124 6.366877 CACAGCCCTCATTTCAACTTATTTTG 59.633 38.462 0.00 0.00 0.00 2.44
6184 7125 6.458210 CACAGCCCTCATTTCAACTTATTTT 58.542 36.000 0.00 0.00 0.00 1.82
6190 7131 1.251251 GCACAGCCCTCATTTCAACT 58.749 50.000 0.00 0.00 0.00 3.16
6191 7132 0.961019 TGCACAGCCCTCATTTCAAC 59.039 50.000 0.00 0.00 0.00 3.18
6223 7164 5.009010 AGTGTCATGTGTTAAAAAGCCTCAG 59.991 40.000 0.00 0.00 0.00 3.35
6224 7165 4.887071 AGTGTCATGTGTTAAAAAGCCTCA 59.113 37.500 0.00 0.00 0.00 3.86
6225 7166 5.438761 AGTGTCATGTGTTAAAAAGCCTC 57.561 39.130 0.00 0.00 0.00 4.70
6226 7167 7.230510 TGAATAGTGTCATGTGTTAAAAAGCCT 59.769 33.333 0.00 0.00 0.00 4.58
6230 7171 9.295825 AGGATGAATAGTGTCATGTGTTAAAAA 57.704 29.630 0.00 0.00 38.38 1.94
6232 7173 7.552687 GGAGGATGAATAGTGTCATGTGTTAAA 59.447 37.037 0.00 0.00 38.38 1.52
6233 7174 7.047891 GGAGGATGAATAGTGTCATGTGTTAA 58.952 38.462 0.00 0.00 38.38 2.01
6234 7175 6.408092 GGGAGGATGAATAGTGTCATGTGTTA 60.408 42.308 0.00 0.00 38.38 2.41
6236 7177 4.141620 GGGAGGATGAATAGTGTCATGTGT 60.142 45.833 0.00 0.00 38.38 3.72
6237 7178 4.384056 GGGAGGATGAATAGTGTCATGTG 58.616 47.826 0.00 0.00 38.38 3.21
6239 7180 3.657634 CGGGAGGATGAATAGTGTCATG 58.342 50.000 0.00 0.00 38.38 3.07
6255 7196 0.328258 ACAAATTCCTGGTCCGGGAG 59.672 55.000 19.25 10.52 40.34 4.30
6257 7198 0.328258 AGACAAATTCCTGGTCCGGG 59.672 55.000 10.99 10.99 31.99 5.73
6258 7199 2.200373 AAGACAAATTCCTGGTCCGG 57.800 50.000 0.00 0.00 31.99 5.14
6259 7200 4.584327 AAAAAGACAAATTCCTGGTCCG 57.416 40.909 0.00 0.00 31.99 4.79
6283 7224 8.155821 TGAAAAACGTTGAAATGTGACCTATA 57.844 30.769 0.00 0.00 0.00 1.31
6285 7226 6.438259 TGAAAAACGTTGAAATGTGACCTA 57.562 33.333 0.00 0.00 0.00 3.08
6288 7229 7.219917 TCAGAATGAAAAACGTTGAAATGTGAC 59.780 33.333 0.00 0.00 45.97 3.67
6289 7230 7.254137 TCAGAATGAAAAACGTTGAAATGTGA 58.746 30.769 0.00 0.00 45.97 3.58
6307 7248 8.028354 TGCCTATGTGTGTAAAATTTCAGAATG 58.972 33.333 0.00 0.00 37.54 2.67
6308 7249 8.121305 TGCCTATGTGTGTAAAATTTCAGAAT 57.879 30.769 0.00 0.00 0.00 2.40
6309 7250 7.517614 TGCCTATGTGTGTAAAATTTCAGAA 57.482 32.000 0.00 0.00 0.00 3.02
6310 7251 7.701539 ATGCCTATGTGTGTAAAATTTCAGA 57.298 32.000 0.00 0.00 0.00 3.27
6317 7258 9.456147 AAGTATGTTATGCCTATGTGTGTAAAA 57.544 29.630 0.00 0.00 0.00 1.52
6420 7361 3.554342 CTCCCGGGAGCCATGGAG 61.554 72.222 36.90 12.91 36.38 3.86
6432 7373 4.675029 ACGGACGTTTGGCTCCCG 62.675 66.667 7.93 7.93 45.09 5.14
6433 7374 2.281276 AACGGACGTTTGGCTCCC 60.281 61.111 3.99 0.00 34.22 4.30
6439 7380 6.583912 ACATTATATGAGAACGGACGTTTG 57.416 37.500 11.67 5.25 38.60 2.93
6440 7381 7.760794 TGTAACATTATATGAGAACGGACGTTT 59.239 33.333 11.67 2.17 38.60 3.60
6441 7382 7.259882 TGTAACATTATATGAGAACGGACGTT 58.740 34.615 10.13 10.13 41.54 3.99
6442 7383 6.798482 TGTAACATTATATGAGAACGGACGT 58.202 36.000 0.00 0.00 0.00 4.34
6443 7384 7.869016 ATGTAACATTATATGAGAACGGACG 57.131 36.000 0.00 0.00 0.00 4.79
6554 7504 2.031870 GGGCAACACAGGAAATATCCC 58.968 52.381 0.00 0.00 43.24 3.85
6755 7719 1.071471 CGCCACCAAGGACAAGAGT 59.929 57.895 0.00 0.00 41.22 3.24
6777 7741 3.120060 ACATCTGAAGCGCATTTCACTTC 60.120 43.478 11.47 2.87 40.17 3.01
6890 7854 7.498570 ACAGTTATTCCAAATTTGCACAACATT 59.501 29.630 12.92 2.87 0.00 2.71
6980 7944 6.992063 AAAGCATCTTCAGAATATTCACGT 57.008 33.333 17.56 0.00 0.00 4.49
7134 8098 8.048534 TCTTCAGAATTGGATCATGAAAGAAC 57.951 34.615 0.00 0.00 30.10 3.01
7140 8104 9.027202 TGATTTTTCTTCAGAATTGGATCATGA 57.973 29.630 0.00 0.00 33.54 3.07
7386 8350 2.434702 ACAGAAAACTAGATAGGGGCCG 59.565 50.000 0.00 0.00 0.00 6.13
7586 8550 5.416952 AGTTAGCATGAATGGAACCTTCTTG 59.583 40.000 0.00 0.00 33.33 3.02
7609 8573 1.538047 AATGGTGGTGCAGCAGTTAG 58.462 50.000 20.85 0.00 45.01 2.34
7619 8583 3.826157 ACATCACAGGTAAAATGGTGGTG 59.174 43.478 0.00 0.00 45.45 4.17
7620 8584 4.112634 ACATCACAGGTAAAATGGTGGT 57.887 40.909 0.00 0.00 32.29 4.16
7621 8585 4.522405 TGAACATCACAGGTAAAATGGTGG 59.478 41.667 0.00 0.00 32.29 4.61
7863 8827 2.033448 GGTGTGCCATGGACCGAA 59.967 61.111 18.40 0.00 34.09 4.30


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

AutoCloner maintained by Alex Coulton.