Multiple sequence alignment - TraesCS3D01G338200

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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 TraesCS3D01G338200 chr3D 100.000 4043 0 0 1 4043 451225511 451229553 0.000000e+00 7467.0
1 TraesCS3D01G338200 chr3D 95.436 241 10 1 1264 1504 539500782 539500543 2.280000e-102 383.0
2 TraesCS3D01G338200 chr3D 91.983 237 10 3 1800 2036 372622925 372623152 1.400000e-84 324.0
3 TraesCS3D01G338200 chr3D 78.707 263 35 1 1546 1808 539500106 539499865 5.410000e-34 156.0
4 TraesCS3D01G338200 chr3D 100.000 33 0 0 2043 2075 451227520 451227552 1.210000e-05 62.1
5 TraesCS3D01G338200 chr3D 100.000 33 0 0 2010 2042 451227553 451227585 1.210000e-05 62.1
6 TraesCS3D01G338200 chr3B 95.749 1435 48 6 608 2042 592859812 592861233 0.000000e+00 2300.0
7 TraesCS3D01G338200 chr3B 94.498 1236 59 6 2146 3374 592861543 592862776 0.000000e+00 1897.0
8 TraesCS3D01G338200 chr3B 90.840 393 29 5 228 616 592859055 592859444 1.670000e-143 520.0
9 TraesCS3D01G338200 chr3B 90.878 296 18 5 3543 3836 592863245 592863533 4.900000e-104 388.0
10 TraesCS3D01G338200 chr3B 92.149 242 11 2 1801 2042 486804935 486805168 6.470000e-88 335.0
11 TraesCS3D01G338200 chr3B 92.891 211 13 1 2043 2251 486805136 486805346 5.080000e-79 305.0
12 TraesCS3D01G338200 chr3B 88.995 209 18 4 3837 4042 592863762 592863968 1.870000e-63 254.0
13 TraesCS3D01G338200 chr3B 95.192 104 5 0 2045 2148 592861203 592861306 8.990000e-37 165.0
14 TraesCS3D01G338200 chr3B 97.619 42 1 0 3395 3436 592862779 592862820 5.610000e-09 73.1
15 TraesCS3D01G338200 chr3A 94.422 1004 38 8 806 1799 615103178 615104173 0.000000e+00 1528.0
16 TraesCS3D01G338200 chr3A 89.942 686 51 13 2618 3293 615104496 615105173 0.000000e+00 869.0
17 TraesCS3D01G338200 chr3A 93.007 286 10 3 2459 2741 615104284 615104562 3.760000e-110 409.0
18 TraesCS3D01G338200 chr3A 91.983 237 10 3 1800 2036 494034248 494034475 1.400000e-84 324.0
19 TraesCS3D01G338200 chr3A 90.780 141 10 1 228 368 700002002 700001865 6.900000e-43 185.0
20 TraesCS3D01G338200 chr3A 92.405 79 5 1 3321 3398 615105172 615105250 1.190000e-20 111.0
21 TraesCS3D01G338200 chr5D 91.814 904 62 8 886 1781 510914245 510915144 0.000000e+00 1249.0
22 TraesCS3D01G338200 chr5D 85.426 446 49 11 2814 3246 510915662 510916104 2.220000e-122 449.0
23 TraesCS3D01G338200 chr5D 87.714 350 21 3 3504 3836 414024877 414024533 4.900000e-104 388.0
24 TraesCS3D01G338200 chr5D 89.270 233 15 8 1 229 371864661 371864435 2.380000e-72 283.0
25 TraesCS3D01G338200 chr5D 85.978 271 29 6 3044 3312 510918535 510918798 8.560000e-72 281.0
26 TraesCS3D01G338200 chr5D 88.444 225 21 3 6 229 78505680 78505460 2.400000e-67 267.0
27 TraesCS3D01G338200 chr5A 90.741 918 65 12 886 1796 639181264 639182168 0.000000e+00 1206.0
28 TraesCS3D01G338200 chr5A 88.707 549 45 11 2771 3312 639187663 639188201 0.000000e+00 654.0
29 TraesCS3D01G338200 chr5A 88.000 350 20 3 3504 3836 526577966 526577622 1.050000e-105 394.0
30 TraesCS3D01G338200 chr5A 80.784 510 65 20 2814 3308 639182626 639183117 6.380000e-98 368.0
31 TraesCS3D01G338200 chr5A 90.780 141 10 1 228 368 706172966 706173103 6.900000e-43 185.0
32 TraesCS3D01G338200 chr5A 91.743 109 4 3 115 221 512071740 512071635 3.260000e-31 147.0
33 TraesCS3D01G338200 chr5B 90.604 894 51 17 886 1773 641925878 641926744 0.000000e+00 1155.0
34 TraesCS3D01G338200 chr5B 84.184 392 53 7 2814 3196 641927255 641927646 4.940000e-99 372.0
35 TraesCS3D01G338200 chr5B 86.571 350 25 3 3504 3836 596460648 596460992 2.300000e-97 366.0
36 TraesCS3D01G338200 chr5B 86.744 347 24 4 3504 3833 596498449 596498790 2.300000e-97 366.0
37 TraesCS3D01G338200 chr5B 86.571 350 21 9 3504 3836 499082442 499082102 2.970000e-96 363.0
38 TraesCS3D01G338200 chr5B 86.455 347 25 8 3507 3836 596541550 596541891 1.070000e-95 361.0
39 TraesCS3D01G338200 chr5B 78.119 489 81 19 2252 2731 641926758 641927229 1.840000e-73 287.0
40 TraesCS3D01G338200 chr5B 93.182 176 12 0 1264 1439 7139562 7139737 4.010000e-65 259.0
41 TraesCS3D01G338200 chr5B 86.580 231 19 9 3026 3246 641928349 641928577 1.120000e-60 244.0
42 TraesCS3D01G338200 chr1B 88.811 429 35 11 228 646 563963431 563963006 7.750000e-142 514.0
43 TraesCS3D01G338200 chr1B 87.413 429 40 9 228 646 399000465 399000889 7.860000e-132 481.0
44 TraesCS3D01G338200 chr1B 91.928 223 16 2 7 229 399000285 399000505 1.090000e-80 311.0
45 TraesCS3D01G338200 chr1B 91.480 223 17 2 7 229 563963611 563963391 5.080000e-79 305.0
46 TraesCS3D01G338200 chr1B 92.045 176 14 0 1264 1439 374015113 374014938 8.680000e-62 248.0
47 TraesCS3D01G338200 chr1B 88.208 212 15 2 1831 2042 95308492 95308291 1.120000e-60 244.0
48 TraesCS3D01G338200 chr1B 90.647 139 10 3 664 802 563963018 563962883 8.930000e-42 182.0
49 TraesCS3D01G338200 chr1B 89.209 139 12 2 664 802 399000877 399001012 1.930000e-38 171.0
50 TraesCS3D01G338200 chr1B 87.387 111 14 0 1698 1808 532158571 532158461 1.180000e-25 128.0
51 TraesCS3D01G338200 chr1B 94.366 71 4 0 2181 2251 95306481 95306411 4.270000e-20 110.0
52 TraesCS3D01G338200 chr4B 92.523 214 9 5 3837 4043 386725291 386725078 2.360000e-77 300.0
53 TraesCS3D01G338200 chr4B 89.286 140 12 1 228 367 381138599 381138463 5.370000e-39 172.0
54 TraesCS3D01G338200 chr4B 79.921 254 29 2 1546 1799 602875883 602876114 2.500000e-37 167.0
55 TraesCS3D01G338200 chr4A 92.523 214 9 5 3837 4043 165379154 165379367 2.360000e-77 300.0
56 TraesCS3D01G338200 chr4A 90.950 221 14 4 7 225 646534755 646534971 3.950000e-75 292.0
57 TraesCS3D01G338200 chr4A 89.362 141 12 1 228 368 599533344 599533207 1.490000e-39 174.0
58 TraesCS3D01G338200 chr7A 88.841 233 16 8 1 229 635281992 635281766 1.110000e-70 278.0
59 TraesCS3D01G338200 chr7A 90.071 141 10 2 228 368 721274998 721275134 3.210000e-41 180.0
60 TraesCS3D01G338200 chr7A 89.362 141 12 1 228 368 676401058 676400921 1.490000e-39 174.0
61 TraesCS3D01G338200 chr2D 88.841 233 16 6 1 229 86075785 86076011 1.110000e-70 278.0
62 TraesCS3D01G338200 chr2A 88.696 230 16 6 1 226 5097892 5098115 5.150000e-69 272.0
63 TraesCS3D01G338200 chr2A 90.071 141 11 1 228 368 64502376 64502513 3.210000e-41 180.0
64 TraesCS3D01G338200 chr1A 87.398 246 17 7 1800 2042 58331193 58330959 1.850000e-68 270.0
65 TraesCS3D01G338200 chr1A 90.071 141 11 1 228 368 418292498 418292361 3.210000e-41 180.0
66 TraesCS3D01G338200 chr6A 93.793 145 8 1 1360 1504 74429029 74428886 2.450000e-52 217.0
67 TraesCS3D01G338200 chr7D 91.096 146 11 2 11 155 577780418 577780562 3.190000e-46 196.0
68 TraesCS3D01G338200 chr2B 80.315 254 28 2 1546 1799 648910904 648911135 5.370000e-39 172.0
69 TraesCS3D01G338200 chr7B 100.000 43 0 0 1264 1306 706745112 706745154 3.350000e-11 80.5


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 TraesCS3D01G338200 chr3D 451225511 451229553 4042 False 2530.400000 7467 100.000000 1 4043 3 chr3D.!!$F2 4042
1 TraesCS3D01G338200 chr3D 539499865 539500782 917 True 269.500000 383 87.071500 1264 1808 2 chr3D.!!$R1 544
2 TraesCS3D01G338200 chr3B 592859055 592863968 4913 False 799.585714 2300 93.395857 228 4042 7 chr3B.!!$F2 3814
3 TraesCS3D01G338200 chr3A 615103178 615105250 2072 False 729.250000 1528 92.444000 806 3398 4 chr3A.!!$F2 2592
4 TraesCS3D01G338200 chr5D 510914245 510918798 4553 False 659.666667 1249 87.739333 886 3312 3 chr5D.!!$F1 2426
5 TraesCS3D01G338200 chr5A 639181264 639183117 1853 False 787.000000 1206 85.762500 886 3308 2 chr5A.!!$F3 2422
6 TraesCS3D01G338200 chr5A 639187663 639188201 538 False 654.000000 654 88.707000 2771 3312 1 chr5A.!!$F1 541
7 TraesCS3D01G338200 chr5B 641925878 641928577 2699 False 514.500000 1155 84.871750 886 3246 4 chr5B.!!$F5 2360
8 TraesCS3D01G338200 chr1B 563962883 563963611 728 True 333.666667 514 90.312667 7 802 3 chr1B.!!$R4 795
9 TraesCS3D01G338200 chr1B 399000285 399001012 727 False 321.000000 481 89.516667 7 802 3 chr1B.!!$F1 795

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
470 475 0.631753 CCAGGTACTCTCCCCTCTCA 59.368 60.0 0.0 0.0 34.60 3.27 F
2001 2805 0.027194 CCGCTGACGCTGATGAAATG 59.973 55.0 0.0 0.0 38.22 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2322 3392 0.324091 ATCAGCAAAGCCCCTTCCAG 60.324 55.0 0.0 0.0 0.00 3.86 R
3436 7263 0.321298 AATAACGAACGCACCAGCCT 60.321 50.0 0.0 0.0 37.52 4.58 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
49 50 9.793259 TCTAATTTCCTAGTTTTCTGACAATGT 57.207 29.630 0.00 0.00 0.00 2.71
61 62 6.816134 TTCTGACAATGTAAATTGCAGCTA 57.184 33.333 18.07 10.35 36.53 3.32
69 70 7.970061 ACAATGTAAATTGCAGCTACATTACAG 59.030 33.333 20.64 14.77 41.87 2.74
70 71 7.630242 ATGTAAATTGCAGCTACATTACAGT 57.370 32.000 15.09 5.19 36.88 3.55
79 80 5.584649 GCAGCTACATTACAGTGTAATGGAA 59.415 40.000 39.55 30.66 38.77 3.53
105 106 8.820628 CACATATTTTTCATGTGTACTTACCG 57.179 34.615 7.19 0.00 45.32 4.02
149 150 9.760660 GTGTATTTACAATGCTTCTTAACTCTG 57.239 33.333 0.00 0.00 38.04 3.35
165 166 7.660208 TCTTAACTCTGTATTTCCTGTTGGTTC 59.340 37.037 0.00 0.00 34.23 3.62
166 167 5.304686 ACTCTGTATTTCCTGTTGGTTCA 57.695 39.130 0.00 0.00 34.23 3.18
178 179 4.401202 CCTGTTGGTTCACTGTTTTTACCT 59.599 41.667 0.00 0.00 0.00 3.08
235 236 9.436957 TCAGTCTGTTAGAACCTGATAAATTTC 57.563 33.333 0.00 0.00 0.00 2.17
338 342 6.706270 AGTTGATGTAAAAGGTGTCTGTACAG 59.294 38.462 17.17 17.17 35.91 2.74
373 377 1.945580 AAGGAGTTGGAGAGGTCCTC 58.054 55.000 11.31 11.31 44.30 3.71
376 380 0.899019 GAGTTGGAGAGGTCCTCACC 59.101 60.000 24.50 24.50 44.30 4.02
460 465 2.622942 CTGCTGATCTCTCCAGGTACTC 59.377 54.545 0.00 0.00 34.60 2.59
470 475 0.631753 CCAGGTACTCTCCCCTCTCA 59.368 60.000 0.00 0.00 34.60 3.27
476 481 4.920749 AGGTACTCTCCCCTCTCACATATA 59.079 45.833 0.00 0.00 0.00 0.86
565 581 3.243336 GTGTTACGTGAGATCTGTGGAC 58.757 50.000 0.00 0.00 0.00 4.02
596 612 1.064017 AGTTGAGTTTGGGTCCTTGCA 60.064 47.619 0.00 0.00 0.00 4.08
643 1035 6.479095 TGTTTCCTGTTTTTGCTCTTTTTG 57.521 33.333 0.00 0.00 0.00 2.44
644 1036 5.994668 TGTTTCCTGTTTTTGCTCTTTTTGT 59.005 32.000 0.00 0.00 0.00 2.83
645 1037 6.484977 TGTTTCCTGTTTTTGCTCTTTTTGTT 59.515 30.769 0.00 0.00 0.00 2.83
759 1151 3.249559 GCTCTGTTTTGGTTCAGTGAGAG 59.750 47.826 0.00 0.00 33.89 3.20
760 1152 3.808728 TCTGTTTTGGTTCAGTGAGAGG 58.191 45.455 0.00 0.00 33.89 3.69
761 1153 3.454447 TCTGTTTTGGTTCAGTGAGAGGA 59.546 43.478 0.00 0.00 33.89 3.71
762 1154 3.541632 TGTTTTGGTTCAGTGAGAGGAC 58.458 45.455 0.00 0.00 0.00 3.85
763 1155 3.199946 TGTTTTGGTTCAGTGAGAGGACT 59.800 43.478 0.00 0.00 0.00 3.85
792 1184 4.095932 AGAATTTTTAGCCCGATCCGTTTC 59.904 41.667 0.00 0.00 0.00 2.78
809 1201 2.803956 GTTTCGTTGGACATTTCGAGGA 59.196 45.455 0.00 0.00 33.98 3.71
943 1345 4.711949 AGCGCCACAGCCTCCAAG 62.712 66.667 2.29 0.00 38.01 3.61
976 1379 4.804420 ATCGGAGCTCCCTGCCCA 62.804 66.667 27.20 4.48 44.23 5.36
1711 2511 3.128589 TGCCTTTTTCCATATTCTGCGAC 59.871 43.478 0.00 0.00 0.00 5.19
1739 2541 6.657541 TCCCATCATTGGTACTTTACTTTCAC 59.342 38.462 0.00 0.00 41.91 3.18
1817 2621 5.571784 TGAAGCTGCAGATAAAAAGATGG 57.428 39.130 20.43 0.00 0.00 3.51
1823 2627 3.623060 TGCAGATAAAAAGATGGAGACGC 59.377 43.478 0.00 0.00 0.00 5.19
1878 2682 6.708054 GCTATGATAACAGCAACATACCTTCT 59.292 38.462 0.00 0.00 37.73 2.85
1884 2688 9.162764 GATAACAGCAACATACCTTCTTCTTTA 57.837 33.333 0.00 0.00 0.00 1.85
1918 2722 3.562567 TTTCTCAAAATTTACCCGCCG 57.437 42.857 0.00 0.00 0.00 6.46
1937 2741 3.849911 CCGAAGTACTTCATTCTCTGCA 58.150 45.455 29.95 0.00 39.46 4.41
1941 2745 6.456181 CCGAAGTACTTCATTCTCTGCAATTC 60.456 42.308 29.95 3.57 39.46 2.17
1958 2762 4.668686 GCAATTCTTGAGTTGAGCTCTTCG 60.669 45.833 16.19 0.00 44.41 3.79
1974 2778 2.231478 TCTTCGTCTACCTCAAAGGCTG 59.769 50.000 0.00 0.00 39.63 4.85
1975 2779 1.629043 TCGTCTACCTCAAAGGCTGT 58.371 50.000 0.00 0.00 39.63 4.40
1976 2780 1.272490 TCGTCTACCTCAAAGGCTGTG 59.728 52.381 0.00 0.00 39.63 3.66
1986 2790 0.751643 AAAGGCTGTGTGTTTCCGCT 60.752 50.000 0.00 0.00 0.00 5.52
1987 2791 1.447317 AAGGCTGTGTGTTTCCGCTG 61.447 55.000 0.00 0.00 0.00 5.18
1988 2792 1.891919 GGCTGTGTGTTTCCGCTGA 60.892 57.895 0.00 0.00 0.00 4.26
1989 2793 1.279840 GCTGTGTGTTTCCGCTGAC 59.720 57.895 0.00 0.00 0.00 3.51
1990 2794 1.564622 CTGTGTGTTTCCGCTGACG 59.435 57.895 0.00 0.00 39.67 4.35
1991 2795 2.248431 GTGTGTTTCCGCTGACGC 59.752 61.111 0.00 0.00 38.22 5.19
2001 2805 0.027194 CCGCTGACGCTGATGAAATG 59.973 55.000 0.00 0.00 38.22 2.32
2009 2813 1.726248 CGCTGATGAAATGACGACACA 59.274 47.619 0.00 0.00 0.00 3.72
2010 2814 2.222663 CGCTGATGAAATGACGACACAG 60.223 50.000 0.00 0.00 0.00 3.66
2032 2836 9.608617 CACAGAGAATTACATGATGATAAATGC 57.391 33.333 0.00 0.00 0.00 3.56
2033 2837 9.346005 ACAGAGAATTACATGATGATAAATGCA 57.654 29.630 0.00 0.00 0.00 3.96
2034 2838 9.827411 CAGAGAATTACATGATGATAAATGCAG 57.173 33.333 0.00 0.00 0.00 4.41
2035 2839 9.570468 AGAGAATTACATGATGATAAATGCAGT 57.430 29.630 0.00 0.00 0.00 4.40
2043 2847 9.961265 ACATGATGATAAATGCAGTTAATTGAG 57.039 29.630 11.05 1.41 0.00 3.02
2046 2850 9.617523 TGATGATAAATGCAGTTAATTGAGAGA 57.382 29.630 11.05 0.00 0.00 3.10
2055 2859 8.791327 TGCAGTTAATTGAGAGAATTACATGA 57.209 30.769 0.00 0.00 0.00 3.07
2056 2860 9.399797 TGCAGTTAATTGAGAGAATTACATGAT 57.600 29.630 0.00 0.00 0.00 2.45
2057 2861 9.661187 GCAGTTAATTGAGAGAATTACATGATG 57.339 33.333 0.00 0.00 0.00 3.07
2096 2900 3.527533 CATATTGTTGCTGCATTTGCCT 58.472 40.909 1.84 0.00 41.18 4.75
2105 2909 1.474077 CTGCATTTGCCTGTTCCTACC 59.526 52.381 0.00 0.00 41.18 3.18
2120 2924 7.611855 CCTGTTCCTACCAATACTTTCAGAAAT 59.388 37.037 0.00 0.00 0.00 2.17
2127 2931 6.691508 ACCAATACTTTCAGAAATTGCCTTC 58.308 36.000 0.00 0.00 0.00 3.46
2136 2940 3.859386 CAGAAATTGCCTTCGCCATTAAC 59.141 43.478 0.00 0.00 30.52 2.01
2153 3198 9.891828 CGCCATTAACAAACAATATACATATGT 57.108 29.630 13.93 13.93 0.00 2.29
2160 3205 9.801873 AACAAACAATATACATATGTCTTTGCC 57.198 29.630 12.68 0.00 0.00 4.52
2169 3214 5.245531 ACATATGTCTTTGCCTTTTCTCGA 58.754 37.500 1.41 0.00 0.00 4.04
2176 3221 6.038825 TGTCTTTGCCTTTTCTCGATTAACAA 59.961 34.615 0.00 0.00 0.00 2.83
2245 3290 5.653330 AGTCATTGCATAACATGGTGATGAA 59.347 36.000 0.00 0.00 33.36 2.57
2299 3366 9.448438 TGTGCATCTTGTGAACTATTATACTTT 57.552 29.630 0.00 0.00 37.27 2.66
2322 3392 6.764877 TTTAGATATAAGCTTGCGTACTGC 57.235 37.500 9.86 3.22 46.70 4.40
2733 3887 9.973450 GCATCTAATCTCTTCTCTGTTTATACA 57.027 33.333 0.00 0.00 0.00 2.29
2812 3973 5.016051 TGATGATCTTAACTCCTGTCAGC 57.984 43.478 0.00 0.00 0.00 4.26
2841 4004 5.218885 TGAATGTATTCTTGTTTGCGTTGG 58.781 37.500 6.21 0.00 37.67 3.77
2869 4036 2.615912 GCCAACATGAGCTGATAACTCC 59.384 50.000 0.00 0.00 32.98 3.85
3033 4200 0.179062 ATGCACCAGCCGAGAAGATC 60.179 55.000 0.00 0.00 41.13 2.75
3067 4236 4.521146 TGTCGGTGTAAAGGGTTTTTACA 58.479 39.130 8.06 8.06 41.11 2.41
3073 4242 5.068067 GGTGTAAAGGGTTTTTACAAGCTGA 59.932 40.000 12.49 0.00 43.77 4.26
3143 6958 3.406764 GTGCTGTTTCAGGATGTCTCTT 58.593 45.455 0.00 0.00 33.78 2.85
3200 7019 6.757010 GCTACTCTCTTTTATCGTCAATGGAA 59.243 38.462 0.00 0.00 0.00 3.53
3292 7118 1.351076 TGATGTTGTCCTCTGCCTCA 58.649 50.000 0.00 0.00 0.00 3.86
3326 7152 7.493743 TTGTTGCTTAATTTACTCCACGTTA 57.506 32.000 0.00 0.00 0.00 3.18
3345 7172 4.957296 GTTATGGACCTGATAACGATGGT 58.043 43.478 0.00 0.00 35.23 3.55
3385 7212 1.967319 TCACCAGTCACTGCCTTTTC 58.033 50.000 0.00 0.00 0.00 2.29
3424 7251 5.215252 TCTTTCATCCTCTTCGACTTGTT 57.785 39.130 0.00 0.00 0.00 2.83
3436 7263 7.367159 TCTTCGACTTGTTTTGTTTAGTTCA 57.633 32.000 0.00 0.00 0.00 3.18
3437 7264 7.461107 TCTTCGACTTGTTTTGTTTAGTTCAG 58.539 34.615 0.00 0.00 0.00 3.02
3438 7265 6.114221 TCGACTTGTTTTGTTTAGTTCAGG 57.886 37.500 0.00 0.00 0.00 3.86
3439 7266 4.733405 CGACTTGTTTTGTTTAGTTCAGGC 59.267 41.667 0.00 0.00 0.00 4.85
3440 7267 5.448632 CGACTTGTTTTGTTTAGTTCAGGCT 60.449 40.000 0.00 0.00 0.00 4.58
3441 7268 5.650543 ACTTGTTTTGTTTAGTTCAGGCTG 58.349 37.500 8.58 8.58 0.00 4.85
3443 7270 4.020543 TGTTTTGTTTAGTTCAGGCTGGT 58.979 39.130 15.73 2.34 0.00 4.00
3444 7271 4.142271 TGTTTTGTTTAGTTCAGGCTGGTG 60.142 41.667 15.73 0.00 0.00 4.17
3447 7274 0.107831 TTTAGTTCAGGCTGGTGCGT 59.892 50.000 15.73 0.00 40.82 5.24
3448 7275 0.107831 TTAGTTCAGGCTGGTGCGTT 59.892 50.000 15.73 0.00 40.82 4.84
3450 7277 2.664851 TTCAGGCTGGTGCGTTCG 60.665 61.111 15.73 0.00 40.82 3.95
3451 7278 3.454587 TTCAGGCTGGTGCGTTCGT 62.455 57.895 15.73 0.00 40.82 3.85
3452 7279 2.933878 TTCAGGCTGGTGCGTTCGTT 62.934 55.000 15.73 0.00 40.82 3.85
3453 7280 1.666553 CAGGCTGGTGCGTTCGTTA 60.667 57.895 6.61 0.00 40.82 3.18
3457 7284 1.937899 GGCTGGTGCGTTCGTTATTAT 59.062 47.619 0.00 0.00 40.82 1.28
3458 7285 2.353579 GGCTGGTGCGTTCGTTATTATT 59.646 45.455 0.00 0.00 40.82 1.40
3460 7287 3.062909 GCTGGTGCGTTCGTTATTATTCA 59.937 43.478 0.00 0.00 0.00 2.57
3461 7288 4.782195 GCTGGTGCGTTCGTTATTATTCAG 60.782 45.833 0.00 0.00 0.00 3.02
3462 7289 4.247258 TGGTGCGTTCGTTATTATTCAGT 58.753 39.130 0.00 0.00 0.00 3.41
3464 7291 5.179742 TGGTGCGTTCGTTATTATTCAGTTT 59.820 36.000 0.00 0.00 0.00 2.66
3465 7292 6.081693 GGTGCGTTCGTTATTATTCAGTTTT 58.918 36.000 0.00 0.00 0.00 2.43
3466 7293 6.579666 GGTGCGTTCGTTATTATTCAGTTTTT 59.420 34.615 0.00 0.00 0.00 1.94
3467 7294 7.408921 GGTGCGTTCGTTATTATTCAGTTTTTG 60.409 37.037 0.00 0.00 0.00 2.44
3468 7295 7.112426 GTGCGTTCGTTATTATTCAGTTTTTGT 59.888 33.333 0.00 0.00 0.00 2.83
3469 7296 7.644551 TGCGTTCGTTATTATTCAGTTTTTGTT 59.355 29.630 0.00 0.00 0.00 2.83
3470 7297 7.937294 GCGTTCGTTATTATTCAGTTTTTGTTG 59.063 33.333 0.00 0.00 0.00 3.33
3471 7298 9.160576 CGTTCGTTATTATTCAGTTTTTGTTGA 57.839 29.630 0.00 0.00 0.00 3.18
3491 7318 8.715191 TGTTGACAATATAATTTGATTTGCCC 57.285 30.769 0.00 0.00 0.00 5.36
3492 7319 8.316946 TGTTGACAATATAATTTGATTTGCCCA 58.683 29.630 0.00 0.00 0.00 5.36
3493 7320 9.160496 GTTGACAATATAATTTGATTTGCCCAA 57.840 29.630 0.00 0.00 0.00 4.12
3494 7321 8.715191 TGACAATATAATTTGATTTGCCCAAC 57.285 30.769 0.00 0.00 0.00 3.77
3496 7323 8.491331 ACAATATAATTTGATTTGCCCAACAC 57.509 30.769 0.00 0.00 0.00 3.32
3498 7325 8.605746 CAATATAATTTGATTTGCCCAACACAG 58.394 33.333 0.00 0.00 0.00 3.66
3499 7326 2.237393 TTTGATTTGCCCAACACAGC 57.763 45.000 0.00 0.00 0.00 4.40
3500 7327 1.117994 TTGATTTGCCCAACACAGCA 58.882 45.000 0.00 0.00 37.18 4.41
3501 7328 1.117994 TGATTTGCCCAACACAGCAA 58.882 45.000 0.00 0.00 46.74 3.91
3504 7331 3.682766 TTGCCCAACACAGCAAATG 57.317 47.368 0.00 0.00 45.51 2.32
3505 7332 0.532417 TTGCCCAACACAGCAAATGC 60.532 50.000 0.00 0.00 45.51 3.56
3507 7334 1.747145 CCCAACACAGCAAATGCCA 59.253 52.632 0.94 0.00 43.38 4.92
3510 7337 1.001068 CCAACACAGCAAATGCCATGA 59.999 47.619 12.04 0.00 43.38 3.07
3511 7338 2.354303 CCAACACAGCAAATGCCATGAT 60.354 45.455 12.04 0.00 43.38 2.45
3512 7339 3.119065 CCAACACAGCAAATGCCATGATA 60.119 43.478 12.04 0.00 43.38 2.15
3515 7342 3.630769 ACACAGCAAATGCCATGATAGAG 59.369 43.478 12.04 0.00 43.38 2.43
3517 7344 4.519350 CACAGCAAATGCCATGATAGAGAT 59.481 41.667 0.94 0.00 43.38 2.75
3545 7515 8.823220 ATGTTAACCTGAGCATAAAAAGGTAT 57.177 30.769 2.48 0.00 0.00 2.73
3546 7516 9.914834 ATGTTAACCTGAGCATAAAAAGGTATA 57.085 29.630 2.48 0.00 0.00 1.47
3547 7517 9.742144 TGTTAACCTGAGCATAAAAAGGTATAA 57.258 29.630 2.48 0.00 0.00 0.98
3587 7732 5.126061 TCCAAAGAATATCAAAGCAGGAAGC 59.874 40.000 0.00 0.00 46.19 3.86
3602 7747 5.183228 GCAGGAAGCTAAAGTATACCAACA 58.817 41.667 0.00 0.00 41.15 3.33
3626 7771 6.980978 CACAATTCATAGTAGAAGTCACCGAT 59.019 38.462 0.00 0.00 0.00 4.18
3627 7772 7.492669 CACAATTCATAGTAGAAGTCACCGATT 59.507 37.037 0.00 0.00 0.00 3.34
3628 7773 7.707035 ACAATTCATAGTAGAAGTCACCGATTC 59.293 37.037 0.00 0.00 0.00 2.52
3629 7774 5.769484 TCATAGTAGAAGTCACCGATTCC 57.231 43.478 0.00 0.00 0.00 3.01
3640 7785 3.058224 GTCACCGATTCCTTCCTTTGTTG 60.058 47.826 0.00 0.00 0.00 3.33
3656 7801 3.949586 TGTTGGATGCCAATGGATCTA 57.050 42.857 2.05 0.00 45.80 1.98
3661 7806 2.641815 GGATGCCAATGGATCTACTCCT 59.358 50.000 2.05 0.00 45.21 3.69
3666 7811 4.721776 TGCCAATGGATCTACTCCTACTTT 59.278 41.667 2.05 0.00 45.21 2.66
3680 7825 5.536161 ACTCCTACTTTTGCACACATTTCAT 59.464 36.000 0.00 0.00 0.00 2.57
3685 7830 6.348621 ACTTTTGCACACATTTCATGAAAC 57.651 33.333 22.71 9.79 32.51 2.78
3688 7833 3.382855 TGCACACATTTCATGAAACTGC 58.617 40.909 22.71 22.80 32.51 4.40
3705 7852 7.161404 TGAAACTGCTGTGTCTAAATACTGAT 58.839 34.615 14.29 0.00 31.78 2.90
3708 7855 7.986085 ACTGCTGTGTCTAAATACTGATTTT 57.014 32.000 0.00 0.00 36.62 1.82
3759 7906 5.183014 TCGTGTACATACCATTAGCAGAG 57.817 43.478 0.00 0.00 0.00 3.35
3782 7929 2.514205 ACTGAAATGTGCTTTGCCAC 57.486 45.000 0.00 0.00 36.28 5.01
3850 8225 5.683876 AATACCACTCATGCAACTCTACT 57.316 39.130 0.00 0.00 0.00 2.57
3859 8234 4.099113 TCATGCAACTCTACTGAGGATCTG 59.901 45.833 0.00 0.00 44.29 2.90
3868 8243 7.179269 ACTCTACTGAGGATCTGTAAAGACTT 58.821 38.462 4.72 0.00 46.60 3.01
3873 8248 6.493802 ACTGAGGATCTGTAAAGACTTGTGTA 59.506 38.462 0.00 0.00 45.90 2.90
3876 8251 6.926313 AGGATCTGTAAAGACTTGTGTACTC 58.074 40.000 0.00 0.00 0.00 2.59
3877 8252 6.493802 AGGATCTGTAAAGACTTGTGTACTCA 59.506 38.462 0.00 0.00 0.00 3.41
3932 8310 4.469657 TGCAGTTCCAAACTTGTAATCCT 58.530 39.130 0.00 0.00 40.46 3.24
3945 8323 5.248477 ACTTGTAATCCTGTTAGAAGCCTCA 59.752 40.000 5.05 0.00 30.95 3.86
3954 8332 4.985538 TGTTAGAAGCCTCAACTGGATTT 58.014 39.130 0.00 0.00 35.67 2.17
3956 8334 3.515602 AGAAGCCTCAACTGGATTTGT 57.484 42.857 0.00 0.00 35.67 2.83
3974 8352 8.825745 TGGATTTGTTTCAAGCAAATTAACTTC 58.174 29.630 12.87 1.28 43.87 3.01
3978 8356 8.856490 TTGTTTCAAGCAAATTAACTTCTCTC 57.144 30.769 0.00 0.00 0.00 3.20
3982 8360 7.664082 TCAAGCAAATTAACTTCTCTCTGAG 57.336 36.000 0.00 0.00 0.00 3.35
3987 8365 7.548780 AGCAAATTAACTTCTCTCTGAGATGAC 59.451 37.037 8.00 0.00 38.56 3.06
3993 8371 6.357579 ACTTCTCTCTGAGATGACACATTT 57.642 37.500 8.00 0.00 38.56 2.32
4022 8400 3.129638 GCTAGCTCCATTACTCTATCCCG 59.870 52.174 7.70 0.00 0.00 5.14
4042 8420 2.095161 CGTAGTCTCTGTTCTTCGGCTT 60.095 50.000 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 8.554835 TTACACTGTAATGTAGCTGCAATTTA 57.445 30.769 9.07 0.84 36.45 1.40
61 62 9.461312 AATATGTGTTCCATTACACTGTAATGT 57.539 29.630 28.41 16.94 46.67 2.71
69 70 9.638239 ACATGAAAAATATGTGTTCCATTACAC 57.362 29.630 0.00 0.00 46.71 2.90
70 71 9.636879 CACATGAAAAATATGTGTTCCATTACA 57.363 29.630 0.00 0.00 46.37 2.41
140 141 7.444183 TGAACCAACAGGAAATACAGAGTTAAG 59.556 37.037 0.00 0.00 0.00 1.85
149 150 5.767816 AACAGTGAACCAACAGGAAATAC 57.232 39.130 0.00 0.00 0.00 1.89
207 208 9.793259 AATTTATCAGGTTCTAACAGACTGAAA 57.207 29.630 10.08 0.00 41.03 2.69
208 209 9.793259 AAATTTATCAGGTTCTAACAGACTGAA 57.207 29.630 10.08 0.00 41.03 3.02
209 210 9.436957 GAAATTTATCAGGTTCTAACAGACTGA 57.563 33.333 10.08 0.00 41.79 3.41
210 211 9.219603 TGAAATTTATCAGGTTCTAACAGACTG 57.780 33.333 0.00 0.00 0.00 3.51
211 212 9.442047 CTGAAATTTATCAGGTTCTAACAGACT 57.558 33.333 0.00 0.00 42.52 3.24
247 248 6.419484 TCATCAGGTTCTAACAGACTGAAA 57.581 37.500 10.08 0.00 41.03 2.69
252 253 5.734720 TGGAATCATCAGGTTCTAACAGAC 58.265 41.667 0.00 0.00 0.00 3.51
282 286 9.283768 TGCAGAAAACATCAAAGAATCTAGTAA 57.716 29.630 0.00 0.00 0.00 2.24
283 287 8.846943 TGCAGAAAACATCAAAGAATCTAGTA 57.153 30.769 0.00 0.00 0.00 1.82
338 342 1.888512 TCCTTTTGCTCACCATTCTGC 59.111 47.619 0.00 0.00 0.00 4.26
344 348 1.214175 TCCAACTCCTTTTGCTCACCA 59.786 47.619 0.00 0.00 0.00 4.17
373 377 2.502947 TCCAAGAGATGATCCACAGGTG 59.497 50.000 0.00 0.00 0.00 4.00
442 446 3.486383 GGAGAGTACCTGGAGAGATCAG 58.514 54.545 0.00 0.00 0.00 2.90
460 465 7.353525 AGTCAGATATATATGTGAGAGGGGAG 58.646 42.308 19.89 0.00 36.76 4.30
565 581 3.332034 CAAACTCAACTACCCTAACCCG 58.668 50.000 0.00 0.00 0.00 5.28
596 612 1.487558 GCCCTTCAATTTGCATCCCAT 59.512 47.619 0.00 0.00 0.00 4.00
645 1037 1.458588 GCACCCCACCCCTCAAAAA 60.459 57.895 0.00 0.00 0.00 1.94
707 1099 1.389106 GCTCAACTACGCAACTAACCG 59.611 52.381 0.00 0.00 0.00 4.44
759 1151 3.444034 GGCTAAAAATTCTGACCCAGTCC 59.556 47.826 0.00 0.00 32.61 3.85
760 1152 3.444034 GGGCTAAAAATTCTGACCCAGTC 59.556 47.826 0.00 0.00 35.84 3.51
761 1153 3.431415 GGGCTAAAAATTCTGACCCAGT 58.569 45.455 0.00 0.00 35.84 4.00
762 1154 2.423538 CGGGCTAAAAATTCTGACCCAG 59.576 50.000 0.00 0.00 35.49 4.45
763 1155 2.040545 TCGGGCTAAAAATTCTGACCCA 59.959 45.455 0.00 0.00 35.49 4.51
792 1184 1.076332 GGTCCTCGAAATGTCCAACG 58.924 55.000 0.00 0.00 0.00 4.10
897 1299 0.392327 GAAGGGTGGAAGAGAGCTGC 60.392 60.000 0.00 0.00 0.00 5.25
943 1345 2.527875 ATGGGGGAGATCGAGGGC 60.528 66.667 0.00 0.00 0.00 5.19
1739 2541 7.096353 GCACACATAATGCAAGCAATTATGTAG 60.096 37.037 24.93 22.21 44.75 2.74
1865 2669 6.874134 TCTGTCTAAAGAAGAAGGTATGTTGC 59.126 38.462 0.00 0.00 35.47 4.17
1903 2707 3.437741 AGTACTTCGGCGGGTAAATTTTG 59.562 43.478 7.21 0.00 0.00 2.44
1909 2713 1.255882 TGAAGTACTTCGGCGGGTAA 58.744 50.000 26.35 7.41 42.28 2.85
1918 2722 7.608308 AGAATTGCAGAGAATGAAGTACTTC 57.392 36.000 25.73 25.73 39.91 3.01
1958 2762 2.224305 ACACACAGCCTTTGAGGTAGAC 60.224 50.000 0.00 0.00 37.80 2.59
1974 2778 2.248431 GCGTCAGCGGAAACACAC 59.752 61.111 0.00 0.00 38.78 3.82
1986 2790 1.992667 GTCGTCATTTCATCAGCGTCA 59.007 47.619 0.00 0.00 0.00 4.35
1987 2791 1.992667 TGTCGTCATTTCATCAGCGTC 59.007 47.619 0.00 0.00 0.00 5.19
1988 2792 1.726791 GTGTCGTCATTTCATCAGCGT 59.273 47.619 0.00 0.00 0.00 5.07
1989 2793 1.726248 TGTGTCGTCATTTCATCAGCG 59.274 47.619 0.00 0.00 0.00 5.18
1990 2794 2.995939 TCTGTGTCGTCATTTCATCAGC 59.004 45.455 0.00 0.00 0.00 4.26
1991 2795 4.488879 TCTCTGTGTCGTCATTTCATCAG 58.511 43.478 0.00 0.00 0.00 2.90
2001 2805 6.036470 TCATCATGTAATTCTCTGTGTCGTC 58.964 40.000 0.00 0.00 0.00 4.20
2009 2813 9.570468 ACTGCATTTATCATCATGTAATTCTCT 57.430 29.630 0.00 0.00 0.00 3.10
2040 2844 9.563748 TGCATTTATCATCATGTAATTCTCTCA 57.436 29.630 0.00 0.00 0.00 3.27
2042 2846 9.570468 ACTGCATTTATCATCATGTAATTCTCT 57.430 29.630 0.00 0.00 0.00 3.10
2049 2853 9.681692 GCAATTAACTGCATTTATCATCATGTA 57.318 29.630 3.59 0.00 42.17 2.29
2050 2854 8.583810 GCAATTAACTGCATTTATCATCATGT 57.416 30.769 3.59 0.00 42.17 3.21
2096 2900 8.792633 CAATTTCTGAAAGTATTGGTAGGAACA 58.207 33.333 8.95 0.00 35.20 3.18
2105 2909 5.287035 GCGAAGGCAATTTCTGAAAGTATTG 59.713 40.000 8.95 9.27 38.85 1.90
2127 2931 9.891828 ACATATGTATATTGTTTGTTAATGGCG 57.108 29.630 6.56 0.00 0.00 5.69
2150 3195 6.206634 TGTTAATCGAGAAAAGGCAAAGACAT 59.793 34.615 0.00 0.00 0.00 3.06
2152 3197 5.997385 TGTTAATCGAGAAAAGGCAAAGAC 58.003 37.500 0.00 0.00 0.00 3.01
2153 3198 6.038825 TGTTGTTAATCGAGAAAAGGCAAAGA 59.961 34.615 0.00 0.00 0.00 2.52
2157 3202 5.471797 TCATGTTGTTAATCGAGAAAAGGCA 59.528 36.000 0.00 0.00 0.00 4.75
2158 3203 5.938322 TCATGTTGTTAATCGAGAAAAGGC 58.062 37.500 0.00 0.00 0.00 4.35
2160 3205 6.470235 GCCATCATGTTGTTAATCGAGAAAAG 59.530 38.462 3.19 0.00 0.00 2.27
2169 3214 4.219507 TGTTTCGGCCATCATGTTGTTAAT 59.780 37.500 2.24 0.00 0.00 1.40
2176 3221 1.614996 TGTTGTTTCGGCCATCATGT 58.385 45.000 2.24 0.00 0.00 3.21
2245 3290 7.395489 AGCAATCACTTCCAAACAGAATTATCT 59.605 33.333 0.00 0.00 35.88 1.98
2299 3366 6.420903 CAGCAGTACGCAAGCTTATATCTAAA 59.579 38.462 0.00 0.00 46.13 1.85
2322 3392 0.324091 ATCAGCAAAGCCCCTTCCAG 60.324 55.000 0.00 0.00 0.00 3.86
2429 3502 6.815641 AGCAGATAGACACACAAAACATAGAG 59.184 38.462 0.00 0.00 0.00 2.43
2552 3636 6.086222 ACTCGAAAATGCATTACATGAACAC 58.914 36.000 13.39 0.00 39.60 3.32
2733 3887 2.537633 AACAGATCATGGCACCCATT 57.462 45.000 0.00 0.00 42.23 3.16
2812 3973 5.634859 GCAAACAAGAATACATTCAACCTGG 59.365 40.000 4.85 0.00 39.23 4.45
2841 4004 1.131883 CAGCTCATGTTGGCAACTAGC 59.868 52.381 29.11 29.11 44.65 3.42
2869 4036 2.543653 CGAAGGTTGCCTGGAAACAAAG 60.544 50.000 19.12 3.86 42.06 2.77
3033 4200 1.135083 ACACCGACATCCTAAGCTTCG 60.135 52.381 0.00 0.00 0.00 3.79
3073 4242 2.746362 GCAAAGTGCATTAGACAGCTCT 59.254 45.455 0.00 0.00 44.26 4.09
3143 6958 1.178276 ACCAACACTTGACGGCAAAA 58.822 45.000 4.62 0.00 32.73 2.44
3200 7019 7.456725 AGACTGATTGCCATAATTATGTAGCT 58.543 34.615 21.20 6.47 31.82 3.32
3292 7118 9.389755 AGTAAATTAAGCAACAAAACAAACCAT 57.610 25.926 0.00 0.00 0.00 3.55
3326 7152 2.771943 ACACCATCGTTATCAGGTCCAT 59.228 45.455 0.00 0.00 30.44 3.41
3345 7172 2.566833 ATCACAGCAGCCAAACTACA 57.433 45.000 0.00 0.00 0.00 2.74
3385 7212 9.100554 GGATGAAAGATATCTTCATCAGCATAG 57.899 37.037 31.84 0.00 39.48 2.23
3424 7251 2.360801 GCACCAGCCTGAACTAAACAAA 59.639 45.455 0.00 0.00 33.58 2.83
3436 7263 0.321298 AATAACGAACGCACCAGCCT 60.321 50.000 0.00 0.00 37.52 4.58
3437 7264 1.361793 TAATAACGAACGCACCAGCC 58.638 50.000 0.00 0.00 37.52 4.85
3438 7265 3.062909 TGAATAATAACGAACGCACCAGC 59.937 43.478 0.00 0.00 37.42 4.85
3439 7266 4.328983 ACTGAATAATAACGAACGCACCAG 59.671 41.667 0.00 0.00 0.00 4.00
3440 7267 4.247258 ACTGAATAATAACGAACGCACCA 58.753 39.130 0.00 0.00 0.00 4.17
3441 7268 4.852609 ACTGAATAATAACGAACGCACC 57.147 40.909 0.00 0.00 0.00 5.01
3443 7270 7.133513 ACAAAAACTGAATAATAACGAACGCA 58.866 30.769 0.00 0.00 0.00 5.24
3444 7271 7.543127 ACAAAAACTGAATAATAACGAACGC 57.457 32.000 0.00 0.00 0.00 4.84
3465 7292 9.160496 GGGCAAATCAAATTATATTGTCAACAA 57.840 29.630 0.00 0.00 40.51 2.83
3466 7293 8.316946 TGGGCAAATCAAATTATATTGTCAACA 58.683 29.630 0.00 0.00 0.00 3.33
3467 7294 8.715191 TGGGCAAATCAAATTATATTGTCAAC 57.285 30.769 0.00 0.00 0.00 3.18
3468 7295 9.160496 GTTGGGCAAATCAAATTATATTGTCAA 57.840 29.630 0.00 0.00 0.00 3.18
3469 7296 8.316946 TGTTGGGCAAATCAAATTATATTGTCA 58.683 29.630 0.00 0.00 0.00 3.58
3470 7297 8.603181 GTGTTGGGCAAATCAAATTATATTGTC 58.397 33.333 0.00 0.00 0.00 3.18
3471 7298 8.099537 TGTGTTGGGCAAATCAAATTATATTGT 58.900 29.630 0.00 0.00 0.00 2.71
3472 7299 8.489990 TGTGTTGGGCAAATCAAATTATATTG 57.510 30.769 0.00 0.00 0.00 1.90
3473 7300 7.280652 GCTGTGTTGGGCAAATCAAATTATATT 59.719 33.333 0.00 0.00 0.00 1.28
3474 7301 6.762661 GCTGTGTTGGGCAAATCAAATTATAT 59.237 34.615 0.00 0.00 0.00 0.86
3476 7303 4.937015 GCTGTGTTGGGCAAATCAAATTAT 59.063 37.500 0.00 0.00 0.00 1.28
3477 7304 4.202295 TGCTGTGTTGGGCAAATCAAATTA 60.202 37.500 0.00 0.00 35.40 1.40
3478 7305 3.140623 GCTGTGTTGGGCAAATCAAATT 58.859 40.909 0.00 0.00 0.00 1.82
3479 7306 2.104451 TGCTGTGTTGGGCAAATCAAAT 59.896 40.909 0.00 0.00 35.40 2.32
3480 7307 1.483827 TGCTGTGTTGGGCAAATCAAA 59.516 42.857 0.00 0.00 35.40 2.69
3481 7308 1.117994 TGCTGTGTTGGGCAAATCAA 58.882 45.000 0.00 0.00 35.40 2.57
3482 7309 1.117994 TTGCTGTGTTGGGCAAATCA 58.882 45.000 0.00 0.00 44.01 2.57
3483 7310 3.984838 TTGCTGTGTTGGGCAAATC 57.015 47.368 0.00 0.00 44.01 2.17
3487 7314 1.069427 GCATTTGCTGTGTTGGGCA 59.931 52.632 0.00 0.00 38.21 5.36
3488 7315 1.668793 GGCATTTGCTGTGTTGGGC 60.669 57.895 2.12 0.00 41.70 5.36
3489 7316 0.322322 ATGGCATTTGCTGTGTTGGG 59.678 50.000 0.00 0.00 41.70 4.12
3491 7318 2.442212 TCATGGCATTTGCTGTGTTG 57.558 45.000 0.00 0.00 41.70 3.33
3492 7319 4.018490 TCTATCATGGCATTTGCTGTGTT 58.982 39.130 0.00 0.76 41.70 3.32
3493 7320 3.623703 TCTATCATGGCATTTGCTGTGT 58.376 40.909 0.00 0.00 41.70 3.72
3494 7321 3.881089 TCTCTATCATGGCATTTGCTGTG 59.119 43.478 0.00 2.44 41.70 3.66
3496 7323 5.240844 TCAATCTCTATCATGGCATTTGCTG 59.759 40.000 0.00 0.00 41.70 4.41
3498 7325 5.700722 TCAATCTCTATCATGGCATTTGC 57.299 39.130 0.00 0.00 41.14 3.68
3499 7326 7.215719 ACATCAATCTCTATCATGGCATTTG 57.784 36.000 0.00 0.00 0.00 2.32
3500 7327 7.834881 AACATCAATCTCTATCATGGCATTT 57.165 32.000 0.00 0.00 0.00 2.32
3501 7328 8.790718 GTTAACATCAATCTCTATCATGGCATT 58.209 33.333 0.00 0.00 0.00 3.56
3504 7331 6.939163 AGGTTAACATCAATCTCTATCATGGC 59.061 38.462 8.10 0.00 0.00 4.40
3505 7332 8.152898 TCAGGTTAACATCAATCTCTATCATGG 58.847 37.037 8.10 0.00 0.00 3.66
3507 7334 7.877097 GCTCAGGTTAACATCAATCTCTATCAT 59.123 37.037 8.10 0.00 0.00 2.45
3510 7337 7.129457 TGCTCAGGTTAACATCAATCTCTAT 57.871 36.000 8.10 0.00 0.00 1.98
3511 7338 6.544928 TGCTCAGGTTAACATCAATCTCTA 57.455 37.500 8.10 0.00 0.00 2.43
3512 7339 5.426689 TGCTCAGGTTAACATCAATCTCT 57.573 39.130 8.10 0.00 0.00 3.10
3515 7342 9.294030 CTTTTTATGCTCAGGTTAACATCAATC 57.706 33.333 8.10 0.00 0.00 2.67
3517 7344 7.232534 ACCTTTTTATGCTCAGGTTAACATCAA 59.767 33.333 8.10 0.00 36.09 2.57
3602 7747 6.525578 TCGGTGACTTCTACTATGAATTGT 57.474 37.500 0.00 0.00 0.00 2.71
3614 7759 2.541466 AGGAAGGAATCGGTGACTTCT 58.459 47.619 11.12 0.00 39.33 2.85
3626 7771 2.247358 GGCATCCAACAAAGGAAGGAA 58.753 47.619 0.00 0.00 41.92 3.36
3627 7772 1.146774 TGGCATCCAACAAAGGAAGGA 59.853 47.619 0.00 0.00 41.92 3.36
3628 7773 1.631405 TGGCATCCAACAAAGGAAGG 58.369 50.000 0.00 0.00 41.92 3.46
3629 7774 3.592059 CATTGGCATCCAACAAAGGAAG 58.408 45.455 0.00 0.00 46.95 3.46
3656 7801 4.887071 TGAAATGTGTGCAAAAGTAGGAGT 59.113 37.500 0.00 0.00 0.00 3.85
3661 7806 7.222417 CAGTTTCATGAAATGTGTGCAAAAGTA 59.778 33.333 23.05 0.00 46.80 2.24
3666 7811 3.803231 GCAGTTTCATGAAATGTGTGCAA 59.197 39.130 26.41 5.19 46.80 4.08
3680 7825 6.521162 TCAGTATTTAGACACAGCAGTTTCA 58.479 36.000 0.00 0.00 0.00 2.69
3708 7855 4.607293 AGTGCAGAGTGACATCAGTAAA 57.393 40.909 0.00 0.00 0.00 2.01
3713 7860 1.895131 TGCTAGTGCAGAGTGACATCA 59.105 47.619 0.00 0.00 45.31 3.07
3714 7861 2.662006 TGCTAGTGCAGAGTGACATC 57.338 50.000 0.00 0.00 45.31 3.06
3759 7906 3.243704 TGGCAAAGCACATTTCAGTTACC 60.244 43.478 0.00 0.00 0.00 2.85
3771 7918 7.315890 AGAATAAATTTCTAGTGGCAAAGCAC 58.684 34.615 0.00 0.00 0.00 4.40
3850 8225 5.808366 ACACAAGTCTTTACAGATCCTCA 57.192 39.130 0.00 0.00 0.00 3.86
3873 8248 2.902486 TGATGAGCTGGAGAAAGTGAGT 59.098 45.455 0.00 0.00 0.00 3.41
3876 8251 4.259356 TGAATGATGAGCTGGAGAAAGTG 58.741 43.478 0.00 0.00 0.00 3.16
3877 8252 4.019501 ACTGAATGATGAGCTGGAGAAAGT 60.020 41.667 0.00 0.00 0.00 2.66
3909 8287 4.892934 AGGATTACAAGTTTGGAACTGCAA 59.107 37.500 0.00 0.00 41.91 4.08
3914 8292 7.739498 TCTAACAGGATTACAAGTTTGGAAC 57.261 36.000 0.00 0.00 32.99 3.62
3919 8297 6.543735 AGGCTTCTAACAGGATTACAAGTTT 58.456 36.000 0.00 0.00 0.00 2.66
3932 8310 4.640771 AATCCAGTTGAGGCTTCTAACA 57.359 40.909 11.60 0.00 0.00 2.41
3945 8323 8.611757 GTTAATTTGCTTGAAACAAATCCAGTT 58.388 29.630 6.97 0.00 44.76 3.16
3954 8332 8.131100 CAGAGAGAAGTTAATTTGCTTGAAACA 58.869 33.333 0.00 0.00 0.00 2.83
3956 8334 8.450578 TCAGAGAGAAGTTAATTTGCTTGAAA 57.549 30.769 0.00 0.00 0.00 2.69
3974 8352 4.936411 AGCAAAATGTGTCATCTCAGAGAG 59.064 41.667 6.24 0.00 0.00 3.20
3978 8356 4.672024 GCAGAGCAAAATGTGTCATCTCAG 60.672 45.833 0.00 0.00 0.00 3.35
3982 8360 3.844577 AGCAGAGCAAAATGTGTCATC 57.155 42.857 0.00 0.00 0.00 2.92
4008 8386 5.998981 ACAGAGACTACGGGATAGAGTAATG 59.001 44.000 0.00 0.00 34.65 1.90
4018 8396 2.082231 CGAAGAACAGAGACTACGGGA 58.918 52.381 0.00 0.00 0.00 5.14
4022 8400 3.579335 AAGCCGAAGAACAGAGACTAC 57.421 47.619 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.