Multiple sequence alignment - TraesCS2A01G057400

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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 TraesCS2A01G057400 chr2A 100.000 4057 0 0 1 4057 24166690 24162634 0.000000e+00 7492.0
1 TraesCS2A01G057400 chr2A 100.000 2416 0 0 4370 6785 24162321 24159906 0.000000e+00 4462.0
2 TraesCS2A01G057400 chr2A 90.481 935 73 11 2901 3830 32529831 32530754 0.000000e+00 1219.0
3 TraesCS2A01G057400 chr2A 81.006 1232 157 38 4682 5871 32530991 32532187 0.000000e+00 907.0
4 TraesCS2A01G057400 chr2A 81.641 719 97 18 2090 2781 32528572 32529282 1.280000e-156 564.0
5 TraesCS2A01G057400 chr2A 77.268 893 139 45 2965 3830 32542999 32543854 3.710000e-127 466.0
6 TraesCS2A01G057400 chr2A 86.286 350 47 1 5936 6285 32532414 32532762 4.970000e-101 379.0
7 TraesCS2A01G057400 chr2A 78.108 539 80 24 5372 5887 32544349 32544872 2.380000e-79 307.0
8 TraesCS2A01G057400 chr2A 77.846 492 62 28 970 1443 32527950 32528412 1.880000e-65 261.0
9 TraesCS2A01G057400 chr2D 88.145 2151 123 56 804 2877 22463676 22465771 0.000000e+00 2438.0
10 TraesCS2A01G057400 chr2D 93.991 1581 64 19 4374 5940 22467142 22468705 0.000000e+00 2364.0
11 TraesCS2A01G057400 chr2D 90.013 1572 104 20 4411 5940 22430547 22428987 0.000000e+00 1984.0
12 TraesCS2A01G057400 chr2D 86.519 1810 150 42 302 2060 22434672 22432906 0.000000e+00 1905.0
13 TraesCS2A01G057400 chr2D 94.996 1139 47 7 2880 4013 22466011 22467144 0.000000e+00 1779.0
14 TraesCS2A01G057400 chr2D 94.216 1141 55 8 2880 4013 22431694 22430558 0.000000e+00 1731.0
15 TraesCS2A01G057400 chr2D 92.491 839 45 6 2060 2886 22432757 22431925 0.000000e+00 1184.0
16 TraesCS2A01G057400 chr2D 89.519 935 82 12 2901 3830 30549031 30549954 0.000000e+00 1170.0
17 TraesCS2A01G057400 chr2D 90.421 856 44 16 5936 6778 22468810 22469640 0.000000e+00 1092.0
18 TraesCS2A01G057400 chr2D 89.708 855 54 16 5936 6781 22428888 22428059 0.000000e+00 1061.0
19 TraesCS2A01G057400 chr2D 82.800 750 83 21 2090 2799 30547934 30548677 4.470000e-176 628.0
20 TraesCS2A01G057400 chr2D 88.327 514 54 4 5362 5871 30550399 30550910 4.500000e-171 612.0
21 TraesCS2A01G057400 chr2D 84.646 508 56 9 296 793 22463217 22463712 2.840000e-133 486.0
22 TraesCS2A01G057400 chr2D 77.441 891 141 45 2965 3830 30586481 30587336 1.710000e-130 477.0
23 TraesCS2A01G057400 chr2D 85.429 350 50 1 5936 6285 30551055 30551403 5.000000e-96 363.0
24 TraesCS2A01G057400 chr2D 78.937 527 81 25 5372 5887 30587923 30588430 1.410000e-86 331.0
25 TraesCS2A01G057400 chr2D 79.324 503 49 30 970 1443 30547301 30547777 1.110000e-77 302.0
26 TraesCS2A01G057400 chr2D 84.667 300 42 3 1 299 22462861 22463157 5.150000e-76 296.0
27 TraesCS2A01G057400 chr2D 79.487 156 23 8 4681 4830 30550185 30550337 1.200000e-17 102.0
28 TraesCS2A01G057400 chr2D 97.368 38 1 0 844 881 335545946 335545909 1.580000e-06 65.8
29 TraesCS2A01G057400 chr2D 94.737 38 2 0 4372 4409 22430562 22430525 7.350000e-05 60.2
30 TraesCS2A01G057400 chr2B 84.307 1848 150 50 296 2060 39366054 39367844 0.000000e+00 1677.0
31 TraesCS2A01G057400 chr2B 92.436 1137 45 17 2880 4013 39369023 39370121 0.000000e+00 1585.0
32 TraesCS2A01G057400 chr2B 94.118 918 43 8 4374 5285 39370119 39371031 0.000000e+00 1386.0
33 TraesCS2A01G057400 chr2B 89.840 935 80 10 2901 3830 50288654 50289578 0.000000e+00 1186.0
34 TraesCS2A01G057400 chr2B 91.882 850 38 9 2057 2877 39367992 39368839 0.000000e+00 1158.0
35 TraesCS2A01G057400 chr2B 89.110 854 56 10 5936 6778 39371856 39372683 0.000000e+00 1027.0
36 TraesCS2A01G057400 chr2B 93.363 663 30 7 5287 5940 39371094 39371751 0.000000e+00 968.0
37 TraesCS2A01G057400 chr2B 80.308 1234 151 45 4682 5871 50289809 50290994 0.000000e+00 848.0
38 TraesCS2A01G057400 chr2B 85.150 734 70 24 804 1511 39206622 39205902 0.000000e+00 715.0
39 TraesCS2A01G057400 chr2B 86.337 505 53 9 301 793 39207086 39206586 2.780000e-148 536.0
40 TraesCS2A01G057400 chr2B 88.785 428 43 3 2377 2799 50287888 50288315 2.800000e-143 520.0
41 TraesCS2A01G057400 chr2B 77.278 845 139 36 3008 3830 50347574 50348387 1.340000e-121 448.0
42 TraesCS2A01G057400 chr2B 81.674 442 60 17 5372 5803 50348986 50349416 1.400000e-91 348.0
43 TraesCS2A01G057400 chr2B 83.934 305 42 5 1 299 39207458 39207155 1.110000e-72 285.0
44 TraesCS2A01G057400 chr2B 77.670 515 46 29 970 1443 50286933 50287419 4.060000e-62 250.0
45 TraesCS2A01G057400 chr5B 89.076 357 23 8 3489 3839 123212501 123212155 4.860000e-116 429.0
46 TraesCS2A01G057400 chr5B 88.515 357 25 8 3489 3839 123429819 123429473 1.050000e-112 418.0
47 TraesCS2A01G057400 chr3B 77.574 544 94 15 4706 5223 35054626 35054085 3.070000e-78 303.0
48 TraesCS2A01G057400 chr3B 77.574 544 94 15 4706 5223 35138626 35138085 3.070000e-78 303.0
49 TraesCS2A01G057400 chr4B 83.590 195 27 5 2494 2687 658574251 658574441 1.940000e-40 178.0
50 TraesCS2A01G057400 chr4B 95.122 41 0 2 844 883 6064564 6064525 5.680000e-06 63.9
51 TraesCS2A01G057400 chr6D 95.238 42 2 0 841 882 448416091 448416132 4.390000e-07 67.6
52 TraesCS2A01G057400 chr7B 90.909 44 4 0 844 887 702428903 702428860 7.350000e-05 60.2
53 TraesCS2A01G057400 chr1D 92.683 41 3 0 841 881 232142858 232142898 7.350000e-05 60.2
54 TraesCS2A01G057400 chr1A 94.737 38 2 0 844 881 316902592 316902555 7.350000e-05 60.2
55 TraesCS2A01G057400 chr3D 97.059 34 0 1 844 877 11821463 11821431 1.000000e-03 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 TraesCS2A01G057400 chr2A 24159906 24166690 6784 True 5977.000000 7492 100.000000 1 6785 2 chr2A.!!$R1 6784
1 TraesCS2A01G057400 chr2A 32527950 32532762 4812 False 666.000000 1219 83.452000 970 6285 5 chr2A.!!$F1 5315
2 TraesCS2A01G057400 chr2A 32542999 32544872 1873 False 386.500000 466 77.688000 2965 5887 2 chr2A.!!$F2 2922
3 TraesCS2A01G057400 chr2D 22462861 22469640 6779 False 1409.166667 2438 89.477667 1 6778 6 chr2D.!!$F1 6777
4 TraesCS2A01G057400 chr2D 22428059 22434672 6613 True 1320.866667 1984 91.280667 302 6781 6 chr2D.!!$R2 6479
5 TraesCS2A01G057400 chr2D 30547301 30551403 4102 False 529.500000 1170 84.147667 970 6285 6 chr2D.!!$F2 5315
6 TraesCS2A01G057400 chr2D 30586481 30588430 1949 False 404.000000 477 78.189000 2965 5887 2 chr2D.!!$F3 2922
7 TraesCS2A01G057400 chr2B 39366054 39372683 6629 False 1300.166667 1677 90.869333 296 6778 6 chr2B.!!$F1 6482
8 TraesCS2A01G057400 chr2B 50286933 50290994 4061 False 701.000000 1186 84.150750 970 5871 4 chr2B.!!$F2 4901
9 TraesCS2A01G057400 chr2B 39205902 39207458 1556 True 512.000000 715 85.140333 1 1511 3 chr2B.!!$R1 1510
10 TraesCS2A01G057400 chr2B 50347574 50349416 1842 False 398.000000 448 79.476000 3008 5803 2 chr2B.!!$F3 2795
11 TraesCS2A01G057400 chr3B 35054085 35054626 541 True 303.000000 303 77.574000 4706 5223 1 chr3B.!!$R1 517
12 TraesCS2A01G057400 chr3B 35138085 35138626 541 True 303.000000 303 77.574000 4706 5223 1 chr3B.!!$R2 517

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
765 909 0.038343 CTGGTTGGGACATTTTGCCG 60.038 55.0 0.00 0.00 39.06 5.69 F
766 910 0.468214 TGGTTGGGACATTTTGCCGA 60.468 50.0 0.00 0.00 39.06 5.54 F
1985 2279 0.678950 TGATGCCTCGTCAGTTCACA 59.321 50.0 0.00 0.00 0.00 3.58 F
3031 4122 0.319900 CCCACGAAGGCCTCATATCG 60.320 60.0 20.38 20.38 40.90 2.92 F
3587 4693 0.246086 GTGGCAGTGTCCAGAGAGAG 59.754 60.0 6.54 0.00 36.67 3.20 F
4056 5180 0.266152 ACAAGAGGATCGGAGGGGAT 59.734 55.0 0.00 0.00 42.67 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2095 2543 1.143684 AGTGGGAAACAGTGCAGTGAT 59.856 47.619 28.02 13.93 0.00 3.06 R
2342 2821 2.390599 CCAACACCGCGATGACTGG 61.391 63.158 7.92 10.00 0.00 4.00 R
3368 4474 1.025113 TCTCCGCGAGTTCGTCTGAT 61.025 55.000 8.23 0.00 42.22 2.90 R
4037 5161 0.266152 ATCCCCTCCGATCCTCTTGT 59.734 55.000 0.00 0.00 0.00 3.16 R
4973 6177 2.423446 CTACGGCTCCTCCATGCC 59.577 66.667 0.00 0.00 45.25 4.40 R
5958 7568 2.103042 GCGCACCTCCTTGTAGCAG 61.103 63.158 0.30 0.00 0.00 4.24 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
54 55 1.500474 TGGAGCACAATAGGAGAGGG 58.500 55.000 0.00 0.00 0.00 4.30
90 93 0.611714 GGTGTACACCCTGGTACCTG 59.388 60.000 31.39 12.94 45.68 4.00
96 99 1.423921 ACACCCTGGTACCTGGAAAAG 59.576 52.381 33.32 20.88 37.23 2.27
123 130 0.255890 TCTTAGCCCCTGGATGCAAC 59.744 55.000 10.19 0.00 0.00 4.17
143 150 3.736720 ACTGGACGATTGGATCATCATG 58.263 45.455 0.00 0.00 0.00 3.07
154 161 7.012704 CGATTGGATCATCATGTTAAACCTCTT 59.987 37.037 0.00 0.00 0.00 2.85
160 167 6.711277 TCATCATGTTAAACCTCTTAGCTGT 58.289 36.000 0.00 0.00 0.00 4.40
161 168 6.595326 TCATCATGTTAAACCTCTTAGCTGTG 59.405 38.462 0.00 0.00 0.00 3.66
204 211 1.091771 CGCGCAAGTCTTCCATCCAT 61.092 55.000 8.75 0.00 41.68 3.41
205 212 1.098050 GCGCAAGTCTTCCATCCATT 58.902 50.000 0.30 0.00 41.68 3.16
209 216 2.424956 GCAAGTCTTCCATCCATTGACC 59.575 50.000 0.00 0.00 0.00 4.02
226 233 1.683917 GACCTGTCGCACTCTATCCAT 59.316 52.381 0.00 0.00 0.00 3.41
239 246 4.016666 ACTCTATCCATCTATCTCCCCCTG 60.017 50.000 0.00 0.00 0.00 4.45
287 294 1.154016 CGCACCACCTCGTCACTAG 60.154 63.158 0.00 0.00 0.00 2.57
290 297 1.535833 CACCACCTCGTCACTAGACT 58.464 55.000 0.00 0.00 42.73 3.24
299 306 5.711036 ACCTCGTCACTAGACTAGATTTTGT 59.289 40.000 16.55 2.10 42.73 2.83
300 307 6.208994 ACCTCGTCACTAGACTAGATTTTGTT 59.791 38.462 16.55 0.00 42.73 2.83
302 309 7.210718 TCGTCACTAGACTAGATTTTGTTCA 57.789 36.000 16.55 0.00 42.73 3.18
303 310 7.827701 TCGTCACTAGACTAGATTTTGTTCAT 58.172 34.615 16.55 0.00 42.73 2.57
304 311 7.968956 TCGTCACTAGACTAGATTTTGTTCATC 59.031 37.037 16.55 0.00 42.73 2.92
340 414 1.915141 CTTGCAATCCTTCACCACCT 58.085 50.000 0.00 0.00 0.00 4.00
354 430 2.505407 CACCACCTGTCCATAGGATTGA 59.495 50.000 0.00 0.00 40.42 2.57
374 450 1.741770 GAAACCGAGTCATGCCGCT 60.742 57.895 0.00 0.00 0.00 5.52
375 451 0.459585 GAAACCGAGTCATGCCGCTA 60.460 55.000 0.00 0.00 0.00 4.26
385 465 4.513442 AGTCATGCCGCTAAGTAAATTGA 58.487 39.130 0.00 0.00 0.00 2.57
386 466 4.941263 AGTCATGCCGCTAAGTAAATTGAA 59.059 37.500 0.00 0.00 0.00 2.69
387 467 5.414454 AGTCATGCCGCTAAGTAAATTGAAA 59.586 36.000 0.00 0.00 0.00 2.69
411 491 2.754946 GGGTCTAAATCACGACACCA 57.245 50.000 0.00 0.00 31.88 4.17
445 525 5.591877 ACCATTGCTTCTCTTGATTGATACC 59.408 40.000 0.00 0.00 0.00 2.73
446 526 5.277683 CCATTGCTTCTCTTGATTGATACCG 60.278 44.000 0.00 0.00 0.00 4.02
451 531 5.343593 GCTTCTCTTGATTGATACCGATACG 59.656 44.000 0.00 0.00 0.00 3.06
504 585 2.580783 ACCTGGCAACACATATACCCTT 59.419 45.455 0.00 0.00 46.17 3.95
513 594 4.770795 ACACATATACCCTTGCAACTCTC 58.229 43.478 0.00 0.00 0.00 3.20
516 597 1.276622 ATACCCTTGCAACTCTCCGT 58.723 50.000 0.00 0.00 0.00 4.69
520 601 1.373497 CTTGCAACTCTCCGTCGCT 60.373 57.895 0.00 0.00 0.00 4.93
552 633 0.386113 GTCGTGATGTAGGGAGAGGC 59.614 60.000 0.00 0.00 0.00 4.70
568 649 6.100714 AGGGAGAGGCCGAAAATACTTTATTA 59.899 38.462 0.00 0.00 37.63 0.98
586 667 2.034048 TATAACGGGCCATCGCTGCA 62.034 55.000 4.39 0.00 34.44 4.41
624 705 5.012354 TGTCGTTAGGGAAACAGAACCTAAT 59.988 40.000 5.78 0.00 45.57 1.73
645 729 9.410556 CCTAATGAAAACAATGACCTACAAAAG 57.589 33.333 0.00 0.00 0.00 2.27
718 814 3.157949 GAGGAAGGGAGGCCGAGG 61.158 72.222 0.00 0.00 0.00 4.63
757 901 1.140852 CTTGAGTGACTGGTTGGGACA 59.859 52.381 0.00 0.00 0.00 4.02
758 902 1.434188 TGAGTGACTGGTTGGGACAT 58.566 50.000 0.00 0.00 39.30 3.06
759 903 1.774254 TGAGTGACTGGTTGGGACATT 59.226 47.619 0.00 0.00 39.30 2.71
760 904 2.174639 TGAGTGACTGGTTGGGACATTT 59.825 45.455 0.00 0.00 39.30 2.32
761 905 3.222603 GAGTGACTGGTTGGGACATTTT 58.777 45.455 0.00 0.00 39.30 1.82
762 906 2.958355 AGTGACTGGTTGGGACATTTTG 59.042 45.455 0.00 0.00 39.30 2.44
763 907 1.686052 TGACTGGTTGGGACATTTTGC 59.314 47.619 0.00 0.00 39.30 3.68
764 908 1.000843 GACTGGTTGGGACATTTTGCC 59.999 52.381 0.00 0.00 39.30 4.52
765 909 0.038343 CTGGTTGGGACATTTTGCCG 60.038 55.000 0.00 0.00 39.06 5.69
766 910 0.468214 TGGTTGGGACATTTTGCCGA 60.468 50.000 0.00 0.00 39.06 5.54
767 911 0.894835 GGTTGGGACATTTTGCCGAT 59.105 50.000 0.00 0.00 39.06 4.18
768 912 2.096248 GGTTGGGACATTTTGCCGATA 58.904 47.619 0.00 0.00 39.06 2.92
769 913 2.159296 GGTTGGGACATTTTGCCGATAC 60.159 50.000 0.00 0.00 39.06 2.24
770 914 2.490115 GTTGGGACATTTTGCCGATACA 59.510 45.455 0.00 0.00 39.06 2.29
771 915 2.088423 TGGGACATTTTGCCGATACAC 58.912 47.619 0.00 0.00 39.06 2.90
772 916 2.290641 TGGGACATTTTGCCGATACACT 60.291 45.455 0.00 0.00 39.06 3.55
773 917 2.354821 GGGACATTTTGCCGATACACTC 59.645 50.000 0.00 0.00 0.00 3.51
774 918 3.270877 GGACATTTTGCCGATACACTCT 58.729 45.455 0.00 0.00 0.00 3.24
775 919 3.309954 GGACATTTTGCCGATACACTCTC 59.690 47.826 0.00 0.00 0.00 3.20
776 920 2.930040 ACATTTTGCCGATACACTCTCG 59.070 45.455 0.00 0.00 35.92 4.04
777 921 2.736144 TTTTGCCGATACACTCTCGT 57.264 45.000 0.00 0.00 34.36 4.18
778 922 3.853831 TTTTGCCGATACACTCTCGTA 57.146 42.857 0.00 0.00 34.36 3.43
779 923 2.838386 TTGCCGATACACTCTCGTAC 57.162 50.000 0.00 0.00 34.36 3.67
780 924 1.019673 TGCCGATACACTCTCGTACC 58.980 55.000 0.00 0.00 34.36 3.34
781 925 1.019673 GCCGATACACTCTCGTACCA 58.980 55.000 0.00 0.00 34.36 3.25
782 926 1.607628 GCCGATACACTCTCGTACCAT 59.392 52.381 0.00 0.00 34.36 3.55
783 927 2.604855 GCCGATACACTCTCGTACCATG 60.605 54.545 0.00 0.00 34.36 3.66
784 928 2.617308 CCGATACACTCTCGTACCATGT 59.383 50.000 0.00 0.00 34.36 3.21
785 929 3.811497 CCGATACACTCTCGTACCATGTA 59.189 47.826 0.00 0.00 34.36 2.29
786 930 4.083961 CCGATACACTCTCGTACCATGTAG 60.084 50.000 0.00 0.00 34.36 2.74
787 931 4.748600 CGATACACTCTCGTACCATGTAGA 59.251 45.833 0.00 0.00 0.00 2.59
788 932 5.107414 CGATACACTCTCGTACCATGTAGAG 60.107 48.000 0.00 0.00 41.03 2.43
790 934 3.940221 ACACTCTCGTACCATGTAGAGTC 59.060 47.826 0.00 0.00 45.24 3.36
791 935 3.939592 CACTCTCGTACCATGTAGAGTCA 59.060 47.826 0.00 0.00 45.24 3.41
792 936 3.940221 ACTCTCGTACCATGTAGAGTCAC 59.060 47.826 0.00 0.00 44.03 3.67
793 937 3.939592 CTCTCGTACCATGTAGAGTCACA 59.060 47.826 0.00 0.00 32.54 3.58
794 938 3.688185 TCTCGTACCATGTAGAGTCACAC 59.312 47.826 0.00 0.00 32.90 3.82
795 939 2.751259 TCGTACCATGTAGAGTCACACC 59.249 50.000 0.00 0.00 0.00 4.16
796 940 2.753452 CGTACCATGTAGAGTCACACCT 59.247 50.000 0.00 0.00 0.00 4.00
797 941 3.181499 CGTACCATGTAGAGTCACACCTC 60.181 52.174 0.00 0.00 0.00 3.85
798 942 2.889512 ACCATGTAGAGTCACACCTCA 58.110 47.619 0.00 0.00 33.75 3.86
799 943 3.445008 ACCATGTAGAGTCACACCTCAT 58.555 45.455 0.00 0.00 33.75 2.90
800 944 3.449018 ACCATGTAGAGTCACACCTCATC 59.551 47.826 0.00 0.00 33.75 2.92
801 945 3.181471 CCATGTAGAGTCACACCTCATCC 60.181 52.174 0.00 0.00 33.75 3.51
802 946 3.458044 TGTAGAGTCACACCTCATCCT 57.542 47.619 0.00 0.00 33.75 3.24
803 947 3.357203 TGTAGAGTCACACCTCATCCTC 58.643 50.000 0.00 0.00 33.75 3.71
813 957 2.426024 CACCTCATCCTCAATTTGCTGG 59.574 50.000 0.00 0.00 0.00 4.85
844 988 6.773200 TCTCCTACCATGTAGAGTCACTAATG 59.227 42.308 2.88 0.00 32.49 1.90
911 1058 5.148502 AGATATCTACTGTACCACTTGGGG 58.851 45.833 2.53 0.00 42.91 4.96
1119 1319 4.137615 TCGCCCTCCCTCGATCCA 62.138 66.667 0.00 0.00 0.00 3.41
1120 1320 2.919856 CGCCCTCCCTCGATCCAT 60.920 66.667 0.00 0.00 0.00 3.41
1197 1397 1.625616 CCATCGTCAAGTACACGGTC 58.374 55.000 4.61 0.00 37.85 4.79
1237 1438 2.028876 GCTTCCTCCTGTAGTCTCCTC 58.971 57.143 0.00 0.00 0.00 3.71
1240 1449 1.104577 CCTCCTGTAGTCTCCTCGGC 61.105 65.000 0.00 0.00 0.00 5.54
1262 1476 2.359850 GGTGATGGTTGCTCGGCA 60.360 61.111 0.00 0.00 36.47 5.69
1288 1513 3.066342 ACTTCTCCGAAATCTCGCGATTA 59.934 43.478 10.36 0.38 44.04 1.75
1402 1639 2.879462 GATCGGGTGTCGTCGCAC 60.879 66.667 10.20 10.20 40.32 5.34
1411 1648 2.121786 GTGTCGTCGCACTTCAGTTAA 58.878 47.619 11.08 0.00 36.51 2.01
1464 1701 4.407296 TGTACTTTTTGCCTTGTTGGGAAT 59.593 37.500 0.00 0.00 45.65 3.01
1483 1720 4.378770 GGAATATGGATTGCGTGTATGCTG 60.379 45.833 0.00 0.00 35.36 4.41
1486 1723 1.356624 GATTGCGTGTATGCTGGCC 59.643 57.895 0.00 0.00 35.36 5.36
1521 1758 5.424121 AATTTCGTGATGCCTTATGTAGC 57.576 39.130 0.00 0.00 0.00 3.58
1549 1788 8.588472 CCTGAATTCTTTTGTAAAGGGAAAGAT 58.412 33.333 7.05 0.00 30.65 2.40
1551 1790 8.923270 TGAATTCTTTTGTAAAGGGAAAGATGT 58.077 29.630 7.05 0.00 30.65 3.06
1554 1793 8.990163 TTCTTTTGTAAAGGGAAAGATGTACT 57.010 30.769 0.00 0.00 30.65 2.73
1688 1931 7.327032 GCAAGATAACTGAAAACTGTTGGATTC 59.673 37.037 0.00 0.00 0.00 2.52
1698 1941 2.447047 ACTGTTGGATTCCCCTCTGTTT 59.553 45.455 0.00 0.00 35.38 2.83
1780 2031 7.041848 GCATTTGCTCTGGAAAGTGTTTATTTT 60.042 33.333 0.00 0.00 38.21 1.82
1903 2197 4.947388 TGTGTTCCTTTGCTGTTAGTTCTT 59.053 37.500 0.00 0.00 0.00 2.52
1904 2198 6.116806 TGTGTTCCTTTGCTGTTAGTTCTTA 58.883 36.000 0.00 0.00 0.00 2.10
1912 2206 8.660373 CCTTTGCTGTTAGTTCTTATAGTTCAG 58.340 37.037 0.00 0.00 0.00 3.02
1981 2275 2.499289 AGAGAATGATGCCTCGTCAGTT 59.501 45.455 0.00 0.00 32.64 3.16
1982 2276 2.863137 GAGAATGATGCCTCGTCAGTTC 59.137 50.000 0.00 1.00 32.64 3.01
1983 2277 2.234661 AGAATGATGCCTCGTCAGTTCA 59.765 45.455 10.65 0.00 32.64 3.18
1984 2278 2.015736 ATGATGCCTCGTCAGTTCAC 57.984 50.000 0.00 0.00 32.64 3.18
1985 2279 0.678950 TGATGCCTCGTCAGTTCACA 59.321 50.000 0.00 0.00 0.00 3.58
1991 2285 1.721389 CCTCGTCAGTTCACAATCACG 59.279 52.381 0.00 0.00 0.00 4.35
2033 2327 5.873179 ACTTGTTGATTGTATACGTTGGG 57.127 39.130 0.00 0.00 0.00 4.12
2047 2343 3.143728 ACGTTGGGGTGAATAAGTTGTC 58.856 45.455 0.00 0.00 0.00 3.18
2055 2351 3.551551 GTGAATAAGTTGTCGTGGTTGC 58.448 45.455 0.00 0.00 0.00 4.17
2071 2518 2.742589 GGTTGCTACTACACTTGCCTTC 59.257 50.000 0.00 0.00 0.00 3.46
2095 2543 6.945435 TCTGTTTTTCTAATGATGCCTGGTTA 59.055 34.615 0.00 0.00 0.00 2.85
2106 2554 1.089920 GCCTGGTTATCACTGCACTG 58.910 55.000 0.00 0.00 0.00 3.66
2112 2561 2.488153 GGTTATCACTGCACTGTTTCCC 59.512 50.000 0.00 0.00 0.00 3.97
2116 2565 1.765904 TCACTGCACTGTTTCCCACTA 59.234 47.619 0.00 0.00 0.00 2.74
2119 2568 3.569701 CACTGCACTGTTTCCCACTATTT 59.430 43.478 0.00 0.00 0.00 1.40
2257 2715 3.831323 TGCAAGAGGATGAGGTGAAAAA 58.169 40.909 0.00 0.00 0.00 1.94
2340 2819 1.699083 TGAACACAGAGAAGGATGCCA 59.301 47.619 0.00 0.00 0.00 4.92
2342 2821 0.326264 ACACAGAGAAGGATGCCACC 59.674 55.000 0.00 0.00 0.00 4.61
2348 2828 0.842030 AGAAGGATGCCACCCAGTCA 60.842 55.000 0.00 0.00 0.00 3.41
2426 2970 9.577003 GAATCAGTTGTTTTAGTTGTTACTACG 57.423 33.333 0.00 0.00 36.61 3.51
2428 2972 5.837191 CAGTTGTTTTAGTTGTTACTACGCG 59.163 40.000 3.53 3.53 36.61 6.01
2498 3047 8.391106 CCTTTACAACTATCTGTCTGCAATTAC 58.609 37.037 0.00 0.00 0.00 1.89
2712 3263 2.263077 CGTATTCTCAGTGTCAGTGGC 58.737 52.381 7.82 0.00 0.00 5.01
2755 3306 1.410083 GCCCAAGGACATTAGGATGCA 60.410 52.381 0.00 0.00 36.72 3.96
2844 3589 4.104102 AGTTAACACCATCTGACCTTTCCA 59.896 41.667 8.61 0.00 0.00 3.53
2848 3593 3.074390 ACACCATCTGACCTTTCCAATGA 59.926 43.478 0.00 0.00 0.00 2.57
2867 3612 7.175990 TCCAATGACCTACAATAAACTTTCACC 59.824 37.037 0.00 0.00 0.00 4.02
2885 3973 9.113838 ACTTTCACCAGATATTCATGTGATAAC 57.886 33.333 0.00 0.00 36.00 1.89
2915 4003 6.371548 TGTGTCTCAAGTCTTACCAATAATGC 59.628 38.462 0.00 0.00 0.00 3.56
2943 4031 7.342541 AGTTAGGGTACAGGAGAAGTTCTTATC 59.657 40.741 6.88 0.61 0.00 1.75
2989 4078 3.009026 CACATTGTGACCGATGATCCAA 58.991 45.455 11.45 0.00 36.18 3.53
3031 4122 0.319900 CCCACGAAGGCCTCATATCG 60.320 60.000 20.38 20.38 40.90 2.92
3033 4124 1.603172 CCACGAAGGCCTCATATCGTC 60.603 57.143 23.87 7.70 45.78 4.20
3368 4474 1.233919 TTGTCAGCGCTATTTGCACA 58.766 45.000 10.99 3.40 43.06 4.57
3443 4549 9.765295 TCTCCTACTTGGTAACTATCTAAGTTT 57.235 33.333 0.00 0.00 40.24 2.66
3555 4661 2.678324 AGTCAAGCTGAAGTTACTCGC 58.322 47.619 0.00 0.00 0.00 5.03
3587 4693 0.246086 GTGGCAGTGTCCAGAGAGAG 59.754 60.000 6.54 0.00 36.67 3.20
3672 4778 6.595716 GTGTTGCTTCTGTATGTATTCTCCTT 59.404 38.462 0.00 0.00 0.00 3.36
3723 4835 6.100714 TCTGACCTTGTAACCCTAGTTCTTTT 59.899 38.462 0.00 0.00 37.42 2.27
3724 4836 6.059484 TGACCTTGTAACCCTAGTTCTTTTG 58.941 40.000 0.00 0.00 37.42 2.44
3725 4837 6.009908 ACCTTGTAACCCTAGTTCTTTTGT 57.990 37.500 0.00 0.00 37.42 2.83
3727 4839 7.576403 ACCTTGTAACCCTAGTTCTTTTGTAA 58.424 34.615 0.00 0.00 37.42 2.41
3728 4840 8.222637 ACCTTGTAACCCTAGTTCTTTTGTAAT 58.777 33.333 0.00 0.00 37.42 1.89
3729 4841 9.729281 CCTTGTAACCCTAGTTCTTTTGTAATA 57.271 33.333 0.00 0.00 37.42 0.98
3872 4991 2.143925 GTAATCCTAGCGGGTTGATGC 58.856 52.381 0.00 0.00 33.62 3.91
3917 5037 2.485266 GCTCGAGCCTCTTCTCTTAC 57.515 55.000 27.22 0.00 34.31 2.34
4016 5140 9.569122 TTTGATACAGAATAATACCTTAAGGCC 57.431 33.333 21.92 0.00 39.32 5.19
4017 5141 8.506196 TGATACAGAATAATACCTTAAGGCCT 57.494 34.615 21.92 0.00 39.32 5.19
4019 5143 9.220767 GATACAGAATAATACCTTAAGGCCTTG 57.779 37.037 28.77 14.05 39.32 3.61
4024 5148 7.775561 AGAATAATACCTTAAGGCCTTGTTCAG 59.224 37.037 28.46 16.81 39.32 3.02
4025 5149 4.929146 ATACCTTAAGGCCTTGTTCAGT 57.071 40.909 28.77 18.53 39.32 3.41
4027 5151 4.717279 ACCTTAAGGCCTTGTTCAGTTA 57.283 40.909 28.77 1.62 39.32 2.24
4029 5153 4.141344 ACCTTAAGGCCTTGTTCAGTTACA 60.141 41.667 28.77 0.00 39.32 2.41
4030 5154 4.215613 CCTTAAGGCCTTGTTCAGTTACAC 59.784 45.833 28.77 0.00 0.00 2.90
4032 5156 1.202891 AGGCCTTGTTCAGTTACACCC 60.203 52.381 0.00 0.00 0.00 4.61
4035 5159 2.779506 CCTTGTTCAGTTACACCCCTC 58.220 52.381 0.00 0.00 0.00 4.30
4036 5160 2.552373 CCTTGTTCAGTTACACCCCTCC 60.552 54.545 0.00 0.00 0.00 4.30
4037 5161 1.809133 TGTTCAGTTACACCCCTCCA 58.191 50.000 0.00 0.00 0.00 3.86
4038 5162 1.418637 TGTTCAGTTACACCCCTCCAC 59.581 52.381 0.00 0.00 0.00 4.02
4039 5163 1.418637 GTTCAGTTACACCCCTCCACA 59.581 52.381 0.00 0.00 0.00 4.17
4040 5164 1.809133 TCAGTTACACCCCTCCACAA 58.191 50.000 0.00 0.00 0.00 3.33
4041 5165 1.697432 TCAGTTACACCCCTCCACAAG 59.303 52.381 0.00 0.00 0.00 3.16
4042 5166 1.697432 CAGTTACACCCCTCCACAAGA 59.303 52.381 0.00 0.00 0.00 3.02
4043 5167 1.978580 AGTTACACCCCTCCACAAGAG 59.021 52.381 0.00 0.00 42.83 2.85
4052 5176 0.749649 CTCCACAAGAGGATCGGAGG 59.250 60.000 0.00 0.00 42.67 4.30
4053 5177 0.687757 TCCACAAGAGGATCGGAGGG 60.688 60.000 0.00 0.00 42.67 4.30
4054 5178 1.690219 CCACAAGAGGATCGGAGGGG 61.690 65.000 0.00 0.00 42.67 4.79
4055 5179 0.687757 CACAAGAGGATCGGAGGGGA 60.688 60.000 0.00 0.00 42.67 4.81
4056 5180 0.266152 ACAAGAGGATCGGAGGGGAT 59.734 55.000 0.00 0.00 42.67 3.85
4428 5552 6.650120 AGAAACTGTTTTTCTGTCCTCTGTA 58.350 36.000 7.28 0.00 37.37 2.74
4429 5553 7.110155 AGAAACTGTTTTTCTGTCCTCTGTAA 58.890 34.615 7.28 0.00 37.37 2.41
4564 5690 4.273969 CGGGCCATCGTAAAAGCTAAAATA 59.726 41.667 4.39 0.00 0.00 1.40
4567 5693 7.303261 GGGCCATCGTAAAAGCTAAAATATAC 58.697 38.462 4.39 0.00 0.00 1.47
4568 5694 7.174426 GGGCCATCGTAAAAGCTAAAATATACT 59.826 37.037 4.39 0.00 0.00 2.12
4610 5738 4.451096 ACACATCTTTGCTTACTGTTACGG 59.549 41.667 0.00 0.00 0.00 4.02
4732 5895 4.851639 AGAATAGCATGAGGTTCCAAGT 57.148 40.909 0.00 0.00 0.00 3.16
4872 6051 0.548682 AGGGCTGTGGAGTTCTCCAT 60.549 55.000 22.05 4.92 42.41 3.41
4973 6177 7.259290 AGTTGAAGTAGTTTTGGTACATGTG 57.741 36.000 9.11 0.00 39.30 3.21
5011 6215 6.694844 CGTAGCTGCTATATGAATAGTGGATG 59.305 42.308 13.20 0.00 37.90 3.51
5014 6219 8.316497 AGCTGCTATATGAATAGTGGATGTAT 57.684 34.615 0.00 0.00 37.90 2.29
5199 6417 5.525378 GTCTGTCATCATATTCCACTTGACC 59.475 44.000 0.00 0.00 34.11 4.02
5226 6487 6.959639 AACTCCACTTTTCATTCTTGCTAA 57.040 33.333 0.00 0.00 0.00 3.09
5276 6576 7.856145 AGTTTCCTGAAATAGCATTCACTAG 57.144 36.000 0.00 0.00 35.55 2.57
5297 6659 4.518249 AGAAAAGTAGTGGAGCATTAGGC 58.482 43.478 0.00 0.00 45.30 3.93
5358 6720 4.455533 CACACCATTACAACTGCTGTATGT 59.544 41.667 13.14 13.14 40.27 2.29
5492 6864 6.759497 ATGGGTATGAGCTTTTAACTTGAC 57.241 37.500 0.00 0.00 0.00 3.18
5515 6887 8.777413 TGACATTTTGTAGTGATTTTCTCTGAG 58.223 33.333 0.00 0.00 0.00 3.35
5522 6894 5.815233 AGTGATTTTCTCTGAGAGGACAA 57.185 39.130 9.97 0.72 0.00 3.18
5527 6899 3.857549 TTCTCTGAGAGGACAATGACG 57.142 47.619 9.97 0.00 0.00 4.35
5579 6966 7.578169 TGTTGTTACGTTTGGGTTTTAAAAG 57.422 32.000 0.00 0.00 0.00 2.27
5905 7301 7.148355 TCCTTTGTCTTTGTCGTAAAAGTTT 57.852 32.000 10.79 0.00 38.16 2.66
5906 7302 8.266392 TCCTTTGTCTTTGTCGTAAAAGTTTA 57.734 30.769 10.79 0.00 38.16 2.01
5907 7303 8.895737 TCCTTTGTCTTTGTCGTAAAAGTTTAT 58.104 29.630 10.79 0.00 38.16 1.40
5908 7304 9.511144 CCTTTGTCTTTGTCGTAAAAGTTTATT 57.489 29.630 10.79 0.00 38.16 1.40
5958 7568 8.034804 AGAATTTTATGGTTTTGGCATCAGTAC 58.965 33.333 0.00 0.00 0.00 2.73
5976 7586 2.047274 TGCTACAAGGAGGTGCGC 60.047 61.111 0.00 0.00 0.00 6.09
6016 7626 1.188863 GATGTTGGCAATGAGGGCTT 58.811 50.000 1.92 0.00 0.00 4.35
6044 7654 4.349503 ACTTGGCATCCCGCTGCA 62.350 61.111 0.00 0.00 44.12 4.41
6057 7667 2.322161 CCGCTGCAACTTGAAATTCTG 58.678 47.619 0.00 0.00 0.00 3.02
6212 7822 2.158385 TGGGAAGTGGCAACCTGTTATT 60.158 45.455 0.00 0.00 0.00 1.40
6285 7895 5.163953 CGACATTCTTTATCGCAAGTGAACT 60.164 40.000 0.00 0.00 39.48 3.01
6286 7896 5.931532 ACATTCTTTATCGCAAGTGAACTG 58.068 37.500 0.00 0.00 39.48 3.16
6287 7897 5.470098 ACATTCTTTATCGCAAGTGAACTGT 59.530 36.000 0.00 0.00 39.48 3.55
6288 7898 4.990543 TCTTTATCGCAAGTGAACTGTG 57.009 40.909 0.00 0.00 39.48 3.66
6289 7899 3.186409 TCTTTATCGCAAGTGAACTGTGC 59.814 43.478 7.25 7.25 39.48 4.57
6290 7900 2.162319 TATCGCAAGTGAACTGTGCA 57.838 45.000 13.94 0.00 38.19 4.57
6291 7901 0.870393 ATCGCAAGTGAACTGTGCAG 59.130 50.000 13.94 0.00 38.19 4.41
6292 7902 1.159713 TCGCAAGTGAACTGTGCAGG 61.160 55.000 13.94 0.00 38.19 4.85
6293 7903 1.439353 CGCAAGTGAACTGTGCAGGT 61.439 55.000 13.94 0.00 38.19 4.00
6294 7904 1.593196 GCAAGTGAACTGTGCAGGTA 58.407 50.000 4.11 0.00 38.19 3.08
6295 7905 2.154462 GCAAGTGAACTGTGCAGGTAT 58.846 47.619 4.11 0.00 38.19 2.73
6296 7906 2.554032 GCAAGTGAACTGTGCAGGTATT 59.446 45.455 4.11 0.00 38.19 1.89
6297 7907 3.004734 GCAAGTGAACTGTGCAGGTATTT 59.995 43.478 4.11 0.00 38.19 1.40
6298 7908 4.215399 GCAAGTGAACTGTGCAGGTATTTA 59.785 41.667 4.11 0.00 38.19 1.40
6299 7909 5.106157 GCAAGTGAACTGTGCAGGTATTTAT 60.106 40.000 4.11 0.00 38.19 1.40
6300 7910 6.570378 GCAAGTGAACTGTGCAGGTATTTATT 60.570 38.462 4.11 0.00 38.19 1.40
6301 7911 7.370383 CAAGTGAACTGTGCAGGTATTTATTT 58.630 34.615 4.11 0.00 0.00 1.40
6302 7912 8.511321 CAAGTGAACTGTGCAGGTATTTATTTA 58.489 33.333 4.11 0.00 0.00 1.40
6303 7913 8.630054 AGTGAACTGTGCAGGTATTTATTTAA 57.370 30.769 4.11 0.00 0.00 1.52
6304 7914 9.073475 AGTGAACTGTGCAGGTATTTATTTAAA 57.927 29.630 4.11 0.00 0.00 1.52
6305 7915 9.685828 GTGAACTGTGCAGGTATTTATTTAAAA 57.314 29.630 4.11 0.00 0.00 1.52
6345 7957 6.861065 TTCTGTAGGCTACTTGACAAAAAG 57.139 37.500 24.07 10.69 0.00 2.27
6353 7965 5.183140 GGCTACTTGACAAAAAGCATTCCTA 59.817 40.000 18.24 0.00 34.85 2.94
6356 7968 6.566197 ACTTGACAAAAAGCATTCCTAGAG 57.434 37.500 0.00 0.00 0.00 2.43
6439 8060 6.279123 GCATCTGATCTCAATCTACTTGTGA 58.721 40.000 0.00 0.00 40.54 3.58
6596 8223 9.654663 ATTTGTTACTGATACTGTACTCCTTTC 57.345 33.333 0.00 0.00 0.00 2.62
6611 8238 4.081586 ACTCCTTTCCTTCTGTATTCGGAC 60.082 45.833 0.00 0.00 0.00 4.79
6671 8298 5.006386 AGATGTTTTCCAGCTTCCTTGTAG 58.994 41.667 0.00 0.00 36.00 2.74
6695 8323 6.540189 AGTCGGGTGAAATTGAATCTTGATAG 59.460 38.462 0.00 0.00 0.00 2.08
6700 8328 7.970614 GGGTGAAATTGAATCTTGATAGACAAC 59.029 37.037 0.00 0.00 34.56 3.32
6703 8331 9.897744 TGAAATTGAATCTTGATAGACAACAAC 57.102 29.630 0.00 0.00 34.56 3.32
6778 8408 6.942005 TCTGTTTCCATGATTTGTGTAGTCAT 59.058 34.615 0.00 0.00 33.08 3.06
6781 8411 7.663493 TGTTTCCATGATTTGTGTAGTCATACA 59.337 33.333 0.00 0.00 39.63 2.29
6782 8412 8.511321 GTTTCCATGATTTGTGTAGTCATACAA 58.489 33.333 0.00 0.00 43.42 2.41
6783 8413 7.609760 TCCATGATTTGTGTAGTCATACAAC 57.390 36.000 0.00 0.00 43.42 3.32
6784 8414 7.394016 TCCATGATTTGTGTAGTCATACAACT 58.606 34.615 0.00 0.00 43.42 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.868172 ATCCACTTTCTCATCCCATTGA 57.132 40.909 0.00 0.00 0.00 2.57
74 77 1.648116 TTCCAGGTACCAGGGTGTAC 58.352 55.000 22.27 0.00 40.29 2.90
96 99 5.825151 GCATCCAGGGGCTAAGATATTAATC 59.175 44.000 0.00 0.00 0.00 1.75
112 119 0.107508 ATCGTCCAGTTGCATCCAGG 60.108 55.000 0.00 0.00 0.00 4.45
123 130 3.736720 ACATGATGATCCAATCGTCCAG 58.263 45.455 0.00 2.81 43.16 3.86
143 150 6.706716 AGAAGAACACAGCTAAGAGGTTTAAC 59.293 38.462 0.00 0.00 0.00 2.01
154 161 1.623811 GTGGGGAGAAGAACACAGCTA 59.376 52.381 0.00 0.00 34.16 3.32
160 167 1.003118 CCATTCGTGGGGAGAAGAACA 59.997 52.381 0.00 0.00 0.00 3.18
161 168 1.278127 TCCATTCGTGGGGAGAAGAAC 59.722 52.381 0.00 0.00 0.00 3.01
204 211 1.476891 GGATAGAGTGCGACAGGTCAA 59.523 52.381 0.00 0.00 0.00 3.18
205 212 1.103803 GGATAGAGTGCGACAGGTCA 58.896 55.000 0.00 0.00 0.00 4.02
209 216 4.699735 AGATAGATGGATAGAGTGCGACAG 59.300 45.833 0.00 0.00 0.00 3.51
226 233 1.549297 GAGGGCAGGGGGAGATAGA 59.451 63.158 0.00 0.00 0.00 1.98
283 290 7.038302 TGGGTGATGAACAAAATCTAGTCTAGT 60.038 37.037 6.77 0.00 0.00 2.57
287 294 5.705441 TGTGGGTGATGAACAAAATCTAGTC 59.295 40.000 0.00 0.00 0.00 2.59
290 297 5.380900 TGTGTGGGTGATGAACAAAATCTA 58.619 37.500 0.00 0.00 0.00 1.98
299 306 0.464554 TGCGTTGTGTGGGTGATGAA 60.465 50.000 0.00 0.00 0.00 2.57
300 307 0.884259 CTGCGTTGTGTGGGTGATGA 60.884 55.000 0.00 0.00 0.00 2.92
302 309 1.600636 CCTGCGTTGTGTGGGTGAT 60.601 57.895 0.00 0.00 0.00 3.06
303 310 2.203139 CCTGCGTTGTGTGGGTGA 60.203 61.111 0.00 0.00 0.00 4.02
304 311 3.964875 GCCTGCGTTGTGTGGGTG 61.965 66.667 0.00 0.00 0.00 4.61
340 414 4.224147 TCGGTTTCTTCAATCCTATGGACA 59.776 41.667 0.00 0.00 32.98 4.02
354 430 1.298859 GCGGCATGACTCGGTTTCTT 61.299 55.000 0.00 0.00 0.00 2.52
386 466 4.517832 GTGTCGTGATTTAGACCCCTTTTT 59.482 41.667 0.00 0.00 36.61 1.94
387 467 4.070009 GTGTCGTGATTTAGACCCCTTTT 58.930 43.478 0.00 0.00 36.61 2.27
405 485 0.033504 TGGTCTCGCTCTTTGGTGTC 59.966 55.000 0.00 0.00 0.00 3.67
411 491 2.079925 GAAGCAATGGTCTCGCTCTTT 58.920 47.619 0.00 0.00 34.11 2.52
445 525 4.557690 CGGATCTTAATAGTTGGCGTATCG 59.442 45.833 0.00 0.00 0.00 2.92
446 526 5.706916 TCGGATCTTAATAGTTGGCGTATC 58.293 41.667 0.00 0.00 0.00 2.24
451 531 5.844004 TCTCTTCGGATCTTAATAGTTGGC 58.156 41.667 0.00 0.00 0.00 4.52
516 597 2.355445 GACATCCGATCTGGCAGCGA 62.355 60.000 10.34 2.75 37.80 4.93
520 601 1.141665 CACGACATCCGATCTGGCA 59.858 57.895 0.00 0.00 41.76 4.92
552 633 7.041235 TGGCCCGTTATAATAAAGTATTTTCGG 60.041 37.037 0.00 0.00 40.09 4.30
568 649 2.591715 GCAGCGATGGCCCGTTAT 60.592 61.111 1.46 0.00 41.24 1.89
586 667 5.395324 CCCTAACGACATTGATGAGGTAGTT 60.395 44.000 0.00 0.00 40.23 2.24
624 705 7.411486 TTCCTTTTGTAGGTCATTGTTTTCA 57.589 32.000 0.00 0.00 45.03 2.69
645 729 6.101296 TCCTCTCCCCTATCTTTACATTTTCC 59.899 42.308 0.00 0.00 0.00 3.13
718 814 4.344865 TCCCTTTCAGGCCGCCAC 62.345 66.667 13.15 0.00 32.73 5.01
733 829 1.517242 CAACCAGTCACTCAAGCTCC 58.483 55.000 0.00 0.00 0.00 4.70
757 901 3.247006 ACGAGAGTGTATCGGCAAAAT 57.753 42.857 0.00 0.00 46.97 1.82
758 902 2.736144 ACGAGAGTGTATCGGCAAAA 57.264 45.000 0.00 0.00 46.97 2.44
764 908 7.448904 ACTCTACATGGTACGAGAGTGTATCG 61.449 46.154 12.72 0.00 45.36 2.92
765 909 5.759273 ACTCTACATGGTACGAGAGTGTATC 59.241 44.000 12.72 0.00 45.36 2.24
766 910 5.682659 ACTCTACATGGTACGAGAGTGTAT 58.317 41.667 12.72 0.00 45.36 2.29
767 911 5.095145 ACTCTACATGGTACGAGAGTGTA 57.905 43.478 12.72 2.32 45.36 2.90
768 912 3.940221 GACTCTACATGGTACGAGAGTGT 59.060 47.826 16.34 3.60 46.68 3.55
769 913 3.939592 TGACTCTACATGGTACGAGAGTG 59.060 47.826 16.34 0.00 46.68 3.51
771 915 3.939592 TGTGACTCTACATGGTACGAGAG 59.060 47.826 0.00 3.73 41.06 3.20
772 916 3.688185 GTGTGACTCTACATGGTACGAGA 59.312 47.826 0.00 0.00 32.43 4.04
773 917 3.181499 GGTGTGACTCTACATGGTACGAG 60.181 52.174 0.00 0.00 32.43 4.18
774 918 2.751259 GGTGTGACTCTACATGGTACGA 59.249 50.000 0.00 0.00 32.43 3.43
775 919 2.753452 AGGTGTGACTCTACATGGTACG 59.247 50.000 0.00 0.00 32.43 3.67
776 920 3.762288 TGAGGTGTGACTCTACATGGTAC 59.238 47.826 0.00 0.00 38.32 3.34
777 921 4.042271 TGAGGTGTGACTCTACATGGTA 57.958 45.455 0.00 0.00 38.32 3.25
778 922 2.889512 TGAGGTGTGACTCTACATGGT 58.110 47.619 0.00 0.00 38.32 3.55
779 923 3.181471 GGATGAGGTGTGACTCTACATGG 60.181 52.174 0.00 0.00 38.32 3.66
780 924 3.703556 AGGATGAGGTGTGACTCTACATG 59.296 47.826 0.00 0.00 38.32 3.21
781 925 3.957497 GAGGATGAGGTGTGACTCTACAT 59.043 47.826 0.00 0.00 38.32 2.29
782 926 3.245264 TGAGGATGAGGTGTGACTCTACA 60.245 47.826 0.00 0.00 38.32 2.74
783 927 3.357203 TGAGGATGAGGTGTGACTCTAC 58.643 50.000 0.00 0.00 38.32 2.59
784 928 3.739401 TGAGGATGAGGTGTGACTCTA 57.261 47.619 0.00 0.00 38.32 2.43
785 929 2.612285 TGAGGATGAGGTGTGACTCT 57.388 50.000 0.00 0.00 38.32 3.24
786 930 3.902881 ATTGAGGATGAGGTGTGACTC 57.097 47.619 0.00 0.00 37.99 3.36
787 931 4.330250 CAAATTGAGGATGAGGTGTGACT 58.670 43.478 0.00 0.00 0.00 3.41
788 932 3.119708 GCAAATTGAGGATGAGGTGTGAC 60.120 47.826 0.00 0.00 0.00 3.67
789 933 3.084039 GCAAATTGAGGATGAGGTGTGA 58.916 45.455 0.00 0.00 0.00 3.58
790 934 3.087031 AGCAAATTGAGGATGAGGTGTG 58.913 45.455 0.00 0.00 0.00 3.82
791 935 3.087031 CAGCAAATTGAGGATGAGGTGT 58.913 45.455 0.00 0.00 0.00 4.16
792 936 2.426024 CCAGCAAATTGAGGATGAGGTG 59.574 50.000 0.00 0.00 0.00 4.00
793 937 2.042162 ACCAGCAAATTGAGGATGAGGT 59.958 45.455 11.04 0.00 0.00 3.85
794 938 2.731572 ACCAGCAAATTGAGGATGAGG 58.268 47.619 11.04 0.00 0.00 3.86
795 939 4.095483 GTGTACCAGCAAATTGAGGATGAG 59.905 45.833 11.04 0.00 0.00 2.90
796 940 4.009675 GTGTACCAGCAAATTGAGGATGA 58.990 43.478 11.04 0.00 0.00 2.92
797 941 4.012374 AGTGTACCAGCAAATTGAGGATG 58.988 43.478 11.04 0.00 0.00 3.51
798 942 4.018960 AGAGTGTACCAGCAAATTGAGGAT 60.019 41.667 11.04 0.49 0.00 3.24
799 943 3.327757 AGAGTGTACCAGCAAATTGAGGA 59.672 43.478 11.04 0.00 0.00 3.71
800 944 3.679389 AGAGTGTACCAGCAAATTGAGG 58.321 45.455 0.00 0.00 0.00 3.86
801 945 3.686726 GGAGAGTGTACCAGCAAATTGAG 59.313 47.826 0.00 0.00 0.00 3.02
802 946 3.327757 AGGAGAGTGTACCAGCAAATTGA 59.672 43.478 0.00 0.00 0.00 2.57
803 947 3.679389 AGGAGAGTGTACCAGCAAATTG 58.321 45.455 0.00 0.00 0.00 2.32
813 957 5.438833 ACTCTACATGGTAGGAGAGTGTAC 58.561 45.833 7.99 0.00 45.36 2.90
895 1042 0.178885 AGGCCCCAAGTGGTACAGTA 60.179 55.000 0.00 0.00 43.84 2.74
897 1044 0.609131 CAAGGCCCCAAGTGGTACAG 60.609 60.000 0.00 0.00 41.80 2.74
898 1045 1.458486 CAAGGCCCCAAGTGGTACA 59.542 57.895 0.00 0.00 0.00 2.90
899 1046 1.977009 GCAAGGCCCCAAGTGGTAC 60.977 63.158 0.00 0.00 0.00 3.34
911 1058 0.109735 GTAGCGGTCTTTTGCAAGGC 60.110 55.000 0.00 0.00 33.39 4.35
954 1101 2.029288 CTGCTTCTTTCGGCTCGCA 61.029 57.895 0.00 0.00 0.00 5.10
993 1160 8.668653 ACCTTGAATTTTATCCCCATTTCTTTT 58.331 29.630 0.00 0.00 0.00 2.27
1116 1316 2.046700 GTGGAAACCGCCGATGGA 60.047 61.111 0.00 0.00 0.00 3.41
1237 1438 2.740826 AACCATCACCGTTCGCCG 60.741 61.111 0.00 0.00 0.00 6.46
1240 1449 1.787847 GAGCAACCATCACCGTTCG 59.212 57.895 0.00 0.00 0.00 3.95
1262 1476 3.190874 GCGAGATTTCGGAGAAGTGATT 58.809 45.455 7.84 0.00 46.76 2.57
1266 1480 0.809385 TCGCGAGATTTCGGAGAAGT 59.191 50.000 3.71 0.00 46.76 3.01
1402 1639 5.403466 GCAGCCAAGAAAATGTTAACTGAAG 59.597 40.000 7.22 0.00 0.00 3.02
1411 1648 1.956477 AGAACGCAGCCAAGAAAATGT 59.044 42.857 0.00 0.00 0.00 2.71
1464 1701 2.493035 CCAGCATACACGCAATCCATA 58.507 47.619 0.00 0.00 0.00 2.74
1483 1720 1.793414 AATTAATTGGAGGGCTGGCC 58.207 50.000 13.15 13.15 0.00 5.36
1486 1723 3.694072 TCACGAAATTAATTGGAGGGCTG 59.306 43.478 0.39 0.00 0.00 4.85
1521 1758 6.648879 TCCCTTTACAAAAGAATTCAGGTG 57.351 37.500 8.44 4.60 0.00 4.00
1549 1788 3.642848 AGAAACCCCAACGAACTAGTACA 59.357 43.478 0.00 0.00 0.00 2.90
1551 1790 3.642848 ACAGAAACCCCAACGAACTAGTA 59.357 43.478 0.00 0.00 0.00 1.82
1552 1791 2.436911 ACAGAAACCCCAACGAACTAGT 59.563 45.455 0.00 0.00 0.00 2.57
1553 1792 3.121738 ACAGAAACCCCAACGAACTAG 57.878 47.619 0.00 0.00 0.00 2.57
1554 1793 3.118334 TGAACAGAAACCCCAACGAACTA 60.118 43.478 0.00 0.00 0.00 2.24
1631 1870 9.092876 GAAATATCCAATCTATCTAGCTTTCCG 57.907 37.037 0.00 0.00 0.00 4.30
1688 1931 1.407437 CCGATCCAGAAAACAGAGGGG 60.407 57.143 0.00 0.00 0.00 4.79
1698 1941 1.489481 ACAGAGCATCCGATCCAGAA 58.511 50.000 0.00 0.00 33.66 3.02
1780 2031 1.333177 AAACGGCAGGGCATTGTAAA 58.667 45.000 0.00 0.00 0.00 2.01
1796 2047 3.197116 TCCGGTCCTTCATCCTAGAAAAC 59.803 47.826 0.00 0.00 0.00 2.43
1874 2168 6.756542 ACTAACAGCAAAGGAACACAAATTTC 59.243 34.615 0.00 0.00 0.00 2.17
1981 2275 2.559698 ATCCAACACCGTGATTGTGA 57.440 45.000 5.28 6.53 37.18 3.58
1982 2276 3.641437 AAATCCAACACCGTGATTGTG 57.359 42.857 5.28 0.00 39.63 3.33
1983 2277 3.888930 AGAAAATCCAACACCGTGATTGT 59.111 39.130 5.28 0.00 0.00 2.71
1984 2278 4.503741 AGAAAATCCAACACCGTGATTG 57.496 40.909 5.28 6.24 0.00 2.67
1985 2279 5.529581 AAAGAAAATCCAACACCGTGATT 57.470 34.783 5.28 0.00 0.00 2.57
1991 2285 7.489160 ACAAGTAGAAAAGAAAATCCAACACC 58.511 34.615 0.00 0.00 0.00 4.16
2026 2320 3.143728 GACAACTTATTCACCCCAACGT 58.856 45.455 0.00 0.00 0.00 3.99
2033 2327 3.608474 GCAACCACGACAACTTATTCACC 60.608 47.826 0.00 0.00 0.00 4.02
2047 2343 1.459592 GCAAGTGTAGTAGCAACCACG 59.540 52.381 0.00 0.00 33.14 4.94
2055 2351 6.483640 AGAAAAACAGAAGGCAAGTGTAGTAG 59.516 38.462 0.00 0.00 0.00 2.57
2071 2518 5.649782 ACCAGGCATCATTAGAAAAACAG 57.350 39.130 0.00 0.00 0.00 3.16
2095 2543 1.143684 AGTGGGAAACAGTGCAGTGAT 59.856 47.619 28.02 13.93 0.00 3.06
2106 2554 6.146021 CACAAATGCAGAAAATAGTGGGAAAC 59.854 38.462 0.00 0.00 0.00 2.78
2161 2610 3.527253 TCCTTGATCCTAGAAAATGGCCA 59.473 43.478 8.56 8.56 0.00 5.36
2257 2715 4.373156 ACTAGCAGGAAAGGAACACAAT 57.627 40.909 0.00 0.00 0.00 2.71
2340 2819 2.879233 AACACCGCGATGACTGGGT 61.879 57.895 7.92 0.00 0.00 4.51
2342 2821 2.390599 CCAACACCGCGATGACTGG 61.391 63.158 7.92 10.00 0.00 4.00
2348 2828 4.712122 AAATTAATTCCAACACCGCGAT 57.288 36.364 8.23 0.00 0.00 4.58
2498 3047 7.234371 TCTCCTCATCTGGTAATTCATCCTAAG 59.766 40.741 0.00 0.00 0.00 2.18
2736 3287 2.734755 TGCATCCTAATGTCCTTGGG 57.265 50.000 0.00 0.00 36.84 4.12
2755 3306 3.584848 AGGAGCTACAATGTTCTCACCTT 59.415 43.478 14.19 0.00 0.00 3.50
2844 3589 7.942341 TCTGGTGAAAGTTTATTGTAGGTCATT 59.058 33.333 0.00 0.00 0.00 2.57
2848 3593 9.975218 AATATCTGGTGAAAGTTTATTGTAGGT 57.025 29.630 0.00 0.00 0.00 3.08
2867 3612 8.219105 CACATGACGTTATCACATGAATATCTG 58.781 37.037 17.99 4.24 41.24 2.90
2877 3622 4.513198 TGAGACACATGACGTTATCACA 57.487 40.909 0.00 0.00 41.24 3.58
2885 3973 3.921021 GGTAAGACTTGAGACACATGACG 59.079 47.826 0.00 0.00 0.00 4.35
2915 4003 3.354467 ACTTCTCCTGTACCCTAACTCG 58.646 50.000 0.00 0.00 0.00 4.18
2959 4048 5.384063 TCGGTCACAATGTGCAAAATTAT 57.616 34.783 8.78 0.00 32.98 1.28
2962 4051 3.255395 TCATCGGTCACAATGTGCAAAAT 59.745 39.130 8.78 0.00 32.98 1.82
2978 4067 7.728847 TGTTACATTAGATTTGGATCATCGG 57.271 36.000 0.00 0.00 34.60 4.18
2989 4078 8.340757 TGGGGAAAACCTATGTTACATTAGATT 58.659 33.333 2.23 0.00 40.03 2.40
3164 4261 7.865706 ATAAGTATCACAAAAAGGGCACTAG 57.134 36.000 0.00 0.00 0.00 2.57
3368 4474 1.025113 TCTCCGCGAGTTCGTCTGAT 61.025 55.000 8.23 0.00 42.22 2.90
3483 4589 8.387354 TGTTTACAAGCATAGTCATATCAAACG 58.613 33.333 0.00 0.00 0.00 3.60
3555 4661 2.424601 CACTGCCACATGTTCCATTAGG 59.575 50.000 0.00 0.00 0.00 2.69
3587 4693 3.186613 GTCCCATTTCAGACGACAGAAAC 59.813 47.826 7.51 0.00 35.13 2.78
3932 5054 1.891150 CAAAGCAGATTCAGCAAGGGT 59.109 47.619 3.76 0.00 0.00 4.34
4013 5137 1.244816 GGGTGTAACTGAACAAGGCC 58.755 55.000 0.00 0.00 36.74 5.19
4014 5138 1.202891 AGGGGTGTAACTGAACAAGGC 60.203 52.381 0.00 0.00 36.74 4.35
4015 5139 2.552373 GGAGGGGTGTAACTGAACAAGG 60.552 54.545 0.00 0.00 36.74 3.61
4016 5140 2.105821 TGGAGGGGTGTAACTGAACAAG 59.894 50.000 0.00 0.00 36.74 3.16
4017 5141 2.128535 TGGAGGGGTGTAACTGAACAA 58.871 47.619 0.00 0.00 36.74 2.83
4019 5143 1.418637 TGTGGAGGGGTGTAACTGAAC 59.581 52.381 0.00 0.00 36.74 3.18
4024 5148 2.474410 CTCTTGTGGAGGGGTGTAAC 57.526 55.000 0.00 0.00 38.35 2.50
4035 5159 1.690219 CCCCTCCGATCCTCTTGTGG 61.690 65.000 0.00 0.00 0.00 4.17
4036 5160 0.687757 TCCCCTCCGATCCTCTTGTG 60.688 60.000 0.00 0.00 0.00 3.33
4037 5161 0.266152 ATCCCCTCCGATCCTCTTGT 59.734 55.000 0.00 0.00 0.00 3.16
4038 5162 3.155897 ATCCCCTCCGATCCTCTTG 57.844 57.895 0.00 0.00 0.00 3.02
4369 5493 8.560355 AGAAAAACACAAAAACATTTTAGGCT 57.440 26.923 0.00 0.00 0.00 4.58
4370 5494 9.619316 AAAGAAAAACACAAAAACATTTTAGGC 57.381 25.926 0.00 0.00 0.00 3.93
4374 5498 9.891828 GAGGAAAGAAAAACACAAAAACATTTT 57.108 25.926 0.00 0.00 0.00 1.82
4375 5499 9.283768 AGAGGAAAGAAAAACACAAAAACATTT 57.716 25.926 0.00 0.00 0.00 2.32
4466 5590 3.963428 ACGACCTTGCATCTACTTCTT 57.037 42.857 0.00 0.00 0.00 2.52
4610 5738 8.584600 CGCTACATATATTTCATACTCGGAAAC 58.415 37.037 0.00 0.00 37.10 2.78
4715 5878 6.808321 AATACTACTTGGAACCTCATGCTA 57.192 37.500 0.00 0.00 0.00 3.49
4732 5895 7.340232 TCGCTAAGACCAAGGAGTTTAATACTA 59.660 37.037 0.00 0.00 37.17 1.82
4973 6177 2.423446 CTACGGCTCCTCCATGCC 59.577 66.667 0.00 0.00 45.25 4.40
5011 6215 7.220741 TCCATGTCAGAGCTAATACTGATAC 57.779 40.000 6.17 0.00 43.46 2.24
5014 6219 6.544928 TTTCCATGTCAGAGCTAATACTGA 57.455 37.500 0.00 0.00 40.22 3.41
5113 6329 4.228895 TGTAGACCAGTACTCTCCACCATA 59.771 45.833 0.00 0.00 0.00 2.74
5199 6417 6.536224 AGCAAGAATGAAAAGTGGAGTTTTTG 59.464 34.615 0.00 0.00 29.58 2.44
5276 6576 3.309954 CGCCTAATGCTCCACTACTTTTC 59.690 47.826 0.00 0.00 38.05 2.29
5492 6864 8.449397 CCTCTCAGAGAAAATCACTACAAAATG 58.551 37.037 2.09 0.00 0.00 2.32
5515 6887 5.917541 TGAAACTTAACGTCATTGTCCTC 57.082 39.130 0.00 0.00 0.00 3.71
5522 6894 5.805728 AGGGATCTTGAAACTTAACGTCAT 58.194 37.500 0.00 0.00 0.00 3.06
5527 6899 6.332735 AGCAAAGGGATCTTGAAACTTAAC 57.667 37.500 0.00 0.00 32.75 2.01
5579 6966 8.642020 CAGACTGCAAAAGATAAAAGCAAATAC 58.358 33.333 0.00 0.00 34.45 1.89
5809 7205 9.383519 GAAACTCTAACCTGATTGACATTCATA 57.616 33.333 0.71 0.00 0.00 2.15
5958 7568 2.103042 GCGCACCTCCTTGTAGCAG 61.103 63.158 0.30 0.00 0.00 4.24
5976 7586 2.176045 GTTGGTTTAACATCCAGGGGG 58.824 52.381 0.00 0.00 39.16 5.40
6044 7654 2.560105 GCTCTGCCCAGAATTTCAAGTT 59.440 45.455 0.00 0.00 36.94 2.66
6228 7838 1.242076 GACACAGCAAGGTCAGCAAT 58.758 50.000 0.00 0.00 34.22 3.56
6306 7916 6.515035 GCCTACAGAATACTTGCACAGTTTTT 60.515 38.462 6.82 3.04 36.88 1.94
6307 7917 5.048713 GCCTACAGAATACTTGCACAGTTTT 60.049 40.000 6.82 5.87 36.88 2.43
6308 7918 4.455877 GCCTACAGAATACTTGCACAGTTT 59.544 41.667 6.82 0.00 36.88 2.66
6353 7965 7.520798 TCAATAGATTTAATGTGCCATCCTCT 58.479 34.615 0.00 0.00 0.00 3.69
6356 7968 9.236006 ACTATCAATAGATTTAATGTGCCATCC 57.764 33.333 4.07 0.00 35.67 3.51
6439 8060 6.942532 TTCTCAAATGAGTAAGCACAACTT 57.057 33.333 10.06 0.00 42.60 2.66
6596 8223 2.810650 CTTCCGTCCGAATACAGAAGG 58.189 52.381 0.00 0.00 32.55 3.46
6611 8238 6.479990 TGTTCTCATCAATTATGTAGCTTCCG 59.520 38.462 0.00 0.00 36.89 4.30
6671 8298 5.567138 ATCAAGATTCAATTTCACCCGAC 57.433 39.130 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.