Multiple sequence alignment - TraesCS7D01G422000

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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 TraesCS7D01G422000 chr7D 100.000 5383 0 0 1 5383 541501102 541495720 0.000000e+00 9941.0
1 TraesCS7D01G422000 chr7D 92.622 1274 64 8 994 2239 540711141 540712412 0.000000e+00 1805.0
2 TraesCS7D01G422000 chr7D 89.803 814 60 13 4577 5383 540714687 540715484 0.000000e+00 1022.0
3 TraesCS7D01G422000 chr7D 88.629 642 52 13 1095 1716 542096395 542095755 0.000000e+00 761.0
4 TraesCS7D01G422000 chr7D 88.704 540 26 6 4629 5156 540791714 540792230 1.270000e-175 627.0
5 TraesCS7D01G422000 chr7D 92.910 409 27 2 1020 1428 541963133 541962727 1.290000e-165 593.0
6 TraesCS7D01G422000 chr7D 86.355 535 44 17 2646 3156 556706919 556706390 1.690000e-154 556.0
7 TraesCS7D01G422000 chr7D 83.929 504 55 12 2661 3142 540712860 540713359 4.910000e-125 459.0
8 TraesCS7D01G422000 chr7D 85.271 387 50 5 4138 4524 540714308 540714687 5.050000e-105 392.0
9 TraesCS7D01G422000 chr7D 86.431 339 37 5 1902 2239 556708543 556708213 3.960000e-96 363.0
10 TraesCS7D01G422000 chr7D 89.493 276 28 1 1 275 541965552 541965277 1.110000e-91 348.0
11 TraesCS7D01G422000 chr7D 93.133 233 14 2 5152 5383 540792301 540792532 1.860000e-89 340.0
12 TraesCS7D01G422000 chr7D 87.004 277 33 3 1 275 542098452 542098177 5.240000e-80 309.0
13 TraesCS7D01G422000 chr7D 90.769 195 16 1 3340 3534 540713616 540713808 5.350000e-65 259.0
14 TraesCS7D01G422000 chr7D 88.272 162 13 2 3763 3924 378322133 378322288 7.120000e-44 189.0
15 TraesCS7D01G422000 chr7D 91.892 111 9 0 3169 3279 540713481 540713591 7.220000e-34 156.0
16 TraesCS7D01G422000 chr7D 76.628 261 55 5 16 274 543562287 543562031 7.270000e-29 139.0
17 TraesCS7D01G422000 chr7D 80.142 141 20 7 4995 5128 421789962 421790101 1.230000e-16 99.0
18 TraesCS7D01G422000 chr7A 91.456 3043 172 36 2413 5383 624811325 624808299 0.000000e+00 4098.0
19 TraesCS7D01G422000 chr7A 93.485 1274 55 7 994 2239 622368114 622369387 0.000000e+00 1868.0
20 TraesCS7D01G422000 chr7A 88.943 814 53 9 4577 5383 622371741 622372524 0.000000e+00 970.0
21 TraesCS7D01G422000 chr7A 89.460 759 55 14 1684 2422 624819382 624818629 0.000000e+00 935.0
22 TraesCS7D01G422000 chr7A 91.071 672 36 8 1020 1668 624820037 624819367 0.000000e+00 887.0
23 TraesCS7D01G422000 chr7A 85.894 397 48 8 4134 4524 622371347 622371741 3.000000e-112 416.0
24 TraesCS7D01G422000 chr7A 80.399 602 70 28 1626 2195 642323305 642322720 1.080000e-111 414.0
25 TraesCS7D01G422000 chr7A 90.604 298 26 2 4861 5156 623321774 623322071 1.410000e-105 394.0
26 TraesCS7D01G422000 chr7A 91.923 260 21 0 2883 3142 622370197 622370456 1.100000e-96 364.0
27 TraesCS7D01G422000 chr7A 93.562 233 13 2 5152 5383 623322142 623322373 3.990000e-91 346.0
28 TraesCS7D01G422000 chr7A 89.286 252 15 5 4629 4869 623321416 623321666 6.770000e-79 305.0
29 TraesCS7D01G422000 chr7A 83.969 262 35 7 18 275 642326082 642325824 1.500000e-60 244.0
30 TraesCS7D01G422000 chr7A 81.746 252 21 8 4209 4437 623297718 623297967 2.560000e-43 187.0
31 TraesCS7D01G422000 chr7A 88.125 160 9 4 3765 3924 206939267 206939118 1.190000e-41 182.0
32 TraesCS7D01G422000 chr7A 87.898 157 14 1 3767 3923 193561494 193561343 4.280000e-41 180.0
33 TraesCS7D01G422000 chr7A 90.090 111 10 1 3169 3279 622370573 622370682 5.620000e-30 143.0
34 TraesCS7D01G422000 chr7A 84.921 126 9 4 2241 2364 642322626 642322509 9.470000e-23 119.0
35 TraesCS7D01G422000 chr7A 85.185 81 8 4 2294 2371 622369587 622369666 4.470000e-11 80.5
36 TraesCS7D01G422000 chr7A 100.000 30 0 0 4423 4452 623320815 623320844 7.530000e-04 56.5
37 TraesCS7D01G422000 chr7B 92.103 2963 145 34 2469 5383 585490750 585487829 0.000000e+00 4093.0
38 TraesCS7D01G422000 chr7B 90.109 1284 88 13 994 2239 584031726 584033008 0.000000e+00 1631.0
39 TraesCS7D01G422000 chr7B 88.267 1125 82 27 918 2017 585499540 585498441 0.000000e+00 1301.0
40 TraesCS7D01G422000 chr7B 91.074 605 44 2 4789 5383 584035392 584035996 0.000000e+00 809.0
41 TraesCS7D01G422000 chr7B 95.445 461 19 1 2004 2462 585491451 585490991 0.000000e+00 734.0
42 TraesCS7D01G422000 chr7B 90.959 542 33 7 4629 5156 584268538 584269077 0.000000e+00 715.0
43 TraesCS7D01G422000 chr7B 84.294 503 54 12 2661 3142 584033440 584033938 8.160000e-128 468.0
44 TraesCS7D01G422000 chr7B 86.181 398 45 7 4134 4524 584034837 584035231 6.450000e-114 422.0
45 TraesCS7D01G422000 chr7B 91.667 276 21 2 1 275 585513821 585513547 1.090000e-101 381.0
46 TraesCS7D01G422000 chr7B 93.133 233 14 2 5152 5383 584269148 584269379 1.860000e-89 340.0
47 TraesCS7D01G422000 chr7B 87.043 301 32 6 4138 4436 584262455 584262750 3.110000e-87 333.0
48 TraesCS7D01G422000 chr7B 90.306 196 17 1 3339 3534 584034190 584034383 6.920000e-64 255.0
49 TraesCS7D01G422000 chr7B 93.243 148 9 1 4583 4729 584035239 584035386 3.260000e-52 217.0
50 TraesCS7D01G422000 chr7B 81.061 264 43 7 16 275 604099459 604099199 2.540000e-48 204.0
51 TraesCS7D01G422000 chr7B 81.455 275 13 8 372 617 585502434 585502169 1.980000e-44 191.0
52 TraesCS7D01G422000 chr7B 89.172 157 12 1 3767 3923 712253798 712253647 1.980000e-44 191.0
53 TraesCS7D01G422000 chr7B 92.793 111 8 0 3169 3279 584034056 584034166 1.550000e-35 161.0
54 TraesCS7D01G422000 chr7B 91.089 101 9 0 1 101 585620696 585620596 2.610000e-28 137.0
55 TraesCS7D01G422000 chr7B 82.759 145 18 5 2504 2645 332806607 332806467 7.320000e-24 122.0
56 TraesCS7D01G422000 chrUn 81.455 275 44 7 1 271 88865478 88865749 9.080000e-53 219.0
57 TraesCS7D01G422000 chrUn 81.091 275 45 7 1 271 88844408 88844679 4.220000e-51 213.0
58 TraesCS7D01G422000 chrUn 80.608 263 46 5 16 275 365696115 365695855 1.180000e-46 198.0
59 TraesCS7D01G422000 chr5B 86.387 191 19 1 715 898 466648076 466648266 9.140000e-48 202.0
60 TraesCS7D01G422000 chr5B 87.013 154 20 0 718 871 249556123 249555970 1.990000e-39 174.0
61 TraesCS7D01G422000 chr5D 83.810 210 29 1 713 917 513525465 513525674 1.530000e-45 195.0
62 TraesCS7D01G422000 chr4A 88.957 163 10 4 3763 3924 573322288 573322443 1.530000e-45 195.0
63 TraesCS7D01G422000 chr3B 89.172 157 12 1 3767 3923 449811430 449811279 1.980000e-44 191.0
64 TraesCS7D01G422000 chr3B 83.065 124 21 0 2504 2627 263273425 263273548 4.410000e-21 113.0
65 TraesCS7D01G422000 chr3D 83.412 211 23 3 717 920 136776665 136776460 9.210000e-43 185.0
66 TraesCS7D01G422000 chr3D 87.671 146 18 0 2504 2649 305629450 305629595 2.580000e-38 171.0
67 TraesCS7D01G422000 chr3D 82.258 124 21 1 2504 2627 184600177 184600299 7.370000e-19 106.0
68 TraesCS7D01G422000 chr3D 78.704 108 13 7 2499 2596 147458520 147458413 4.500000e-06 63.9
69 TraesCS7D01G422000 chr4D 86.503 163 17 3 3763 3925 293386209 293386052 1.990000e-39 174.0
70 TraesCS7D01G422000 chr1B 86.420 162 15 2 3763 3924 68073320 68073474 2.580000e-38 171.0
71 TraesCS7D01G422000 chr6B 86.250 160 15 4 713 871 274061152 274061305 3.330000e-37 167.0
72 TraesCS7D01G422000 chr2A 82.741 197 25 4 713 901 149199675 149199480 3.330000e-37 167.0
73 TraesCS7D01G422000 chr2A 82.653 196 21 5 713 901 182038287 182038098 1.550000e-35 161.0
74 TraesCS7D01G422000 chr2A 82.234 197 26 3 713 901 773857989 773858184 1.550000e-35 161.0
75 TraesCS7D01G422000 chr2A 82.456 114 20 0 2533 2646 174426006 174426119 3.430000e-17 100.0
76 TraesCS7D01G422000 chr2A 96.970 33 0 1 671 703 739298327 739298296 3.000000e-03 54.7
77 TraesCS7D01G422000 chr4B 85.000 160 17 4 717 875 16879527 16879374 7.220000e-34 156.0
78 TraesCS7D01G422000 chr4B 89.873 79 5 3 854 930 529301156 529301079 1.230000e-16 99.0
79 TraesCS7D01G422000 chr3A 83.766 154 15 4 2504 2649 423678205 423678356 2.610000e-28 137.0
80 TraesCS7D01G422000 chr3A 77.108 166 25 6 675 839 711423064 711422911 3.460000e-12 84.2
81 TraesCS7D01G422000 chr5A 86.538 104 14 0 2505 2608 640679435 640679538 1.230000e-21 115.0
82 TraesCS7D01G422000 chr2D 95.714 70 3 0 851 920 118470154 118470223 4.410000e-21 113.0
83 TraesCS7D01G422000 chr1D 80.986 142 23 3 2506 2645 477208402 477208263 5.700000e-20 110.0
84 TraesCS7D01G422000 chr6A 92.500 40 3 0 666 705 433958496 433958535 2.090000e-04 58.4


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 TraesCS7D01G422000 chr7D 541495720 541501102 5382 True 9941.000000 9941 100.000000 1 5383 1 chr7D.!!$R1 5382
1 TraesCS7D01G422000 chr7D 540711141 540715484 4343 False 682.166667 1805 89.047667 994 5383 6 chr7D.!!$F3 4389
2 TraesCS7D01G422000 chr7D 542095755 542098452 2697 True 535.000000 761 87.816500 1 1716 2 chr7D.!!$R4 1715
3 TraesCS7D01G422000 chr7D 540791714 540792532 818 False 483.500000 627 90.918500 4629 5383 2 chr7D.!!$F4 754
4 TraesCS7D01G422000 chr7D 541962727 541965552 2825 True 470.500000 593 91.201500 1 1428 2 chr7D.!!$R3 1427
5 TraesCS7D01G422000 chr7D 556706390 556708543 2153 True 459.500000 556 86.393000 1902 3156 2 chr7D.!!$R5 1254
6 TraesCS7D01G422000 chr7A 624808299 624811325 3026 True 4098.000000 4098 91.456000 2413 5383 1 chr7A.!!$R3 2970
7 TraesCS7D01G422000 chr7A 624818629 624820037 1408 True 911.000000 935 90.265500 1020 2422 2 chr7A.!!$R4 1402
8 TraesCS7D01G422000 chr7A 622368114 622372524 4410 False 640.250000 1868 89.253333 994 5383 6 chr7A.!!$F2 4389
9 TraesCS7D01G422000 chr7A 623320815 623322373 1558 False 275.375000 394 93.363000 4423 5383 4 chr7A.!!$F3 960
10 TraesCS7D01G422000 chr7A 642322509 642326082 3573 True 259.000000 414 83.096333 18 2364 3 chr7A.!!$R5 2346
11 TraesCS7D01G422000 chr7B 585487829 585491451 3622 True 2413.500000 4093 93.774000 2004 5383 2 chr7B.!!$R6 3379
12 TraesCS7D01G422000 chr7B 585498441 585502434 3993 True 746.000000 1301 84.861000 372 2017 2 chr7B.!!$R7 1645
13 TraesCS7D01G422000 chr7B 584031726 584035996 4270 False 566.142857 1631 89.714286 994 5383 7 chr7B.!!$F2 4389
14 TraesCS7D01G422000 chr7B 584268538 584269379 841 False 527.500000 715 92.046000 4629 5383 2 chr7B.!!$F3 754

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
802 5314 0.026285 GCTCGTCATATTTGCGCGTT 59.974 50.0 8.43 0.0 0.00 4.84 F
889 5943 0.033228 TTTGCATCGGGCTTTGGTTG 59.967 50.0 0.00 0.0 45.15 3.77 F
1904 7086 0.526211 CAGCGGGCCTAACTTTTTCC 59.474 55.0 0.84 0.0 0.00 3.13 F
2097 7288 1.598882 TACTTGATGCGTGTTGCCAA 58.401 45.0 0.00 0.0 45.60 4.52 F
3408 10316 2.289945 ACTGGTGGATGAGCTTGTTCTC 60.290 50.0 0.00 0.0 0.00 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2390 8794 1.638529 AAATGTGGATTTTCCGGGCA 58.361 45.000 0.00 0.0 40.17 5.36 R
2747 9404 2.235898 CCTAGCTTTCCACTCTTCAGCT 59.764 50.000 0.00 0.0 43.33 4.24 R
3616 10639 0.037975 GAATGGCAGCCAACAAGGTG 60.038 55.000 20.84 0.0 36.95 4.00 R
3617 10640 0.178953 AGAATGGCAGCCAACAAGGT 60.179 50.000 20.84 0.0 36.95 3.50 R
4932 12762 1.804372 GCCACAGATACTCAGCTTCCG 60.804 57.143 0.00 0.0 0.00 4.30 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
45 46 7.853299 TGTAATTGGTACAGGTATTTCTGCTA 58.147 34.615 0.00 0.00 42.39 3.49
94 95 8.082242 CCTACTAATGGTTTGGAGAAACAAAAG 58.918 37.037 0.00 0.00 42.95 2.27
95 96 7.654022 ACTAATGGTTTGGAGAAACAAAAGA 57.346 32.000 0.00 0.00 42.95 2.52
103 104 7.416326 GGTTTGGAGAAACAAAAGAAAGAGCTA 60.416 37.037 0.00 0.00 42.95 3.32
116 117 8.814038 AAAGAAAGAGCTATGGTCAAATACAT 57.186 30.769 0.00 0.00 31.89 2.29
121 122 9.632638 AAAGAGCTATGGTCAAATACATAATGT 57.367 29.630 0.00 0.00 31.89 2.71
141 142 6.653526 ATGTATCTGAAGTCTCTGATGGAG 57.346 41.667 5.15 0.00 39.71 3.86
143 144 5.954752 TGTATCTGAAGTCTCTGATGGAGTT 59.045 40.000 5.15 0.00 39.71 3.01
204 206 9.777008 AAATTATTTTACAGATAAGTTGGGGGA 57.223 29.630 0.00 0.00 29.30 4.81
275 278 3.701205 TTGCAGTGAAGAGGCTTGATA 57.299 42.857 0.00 0.00 0.00 2.15
276 279 3.920231 TGCAGTGAAGAGGCTTGATAT 57.080 42.857 0.00 0.00 0.00 1.63
277 280 3.801698 TGCAGTGAAGAGGCTTGATATC 58.198 45.455 0.00 0.00 0.00 1.63
278 281 3.137533 GCAGTGAAGAGGCTTGATATCC 58.862 50.000 0.00 0.00 0.00 2.59
279 282 3.388308 CAGTGAAGAGGCTTGATATCCG 58.612 50.000 0.00 0.00 0.00 4.18
280 283 3.068732 CAGTGAAGAGGCTTGATATCCGA 59.931 47.826 0.00 0.00 0.00 4.55
282 285 3.993081 GTGAAGAGGCTTGATATCCGATG 59.007 47.826 0.00 0.00 0.00 3.84
283 286 3.007290 TGAAGAGGCTTGATATCCGATGG 59.993 47.826 0.00 0.00 0.00 3.51
287 2930 2.975489 AGGCTTGATATCCGATGGAGTT 59.025 45.455 0.00 0.00 34.05 3.01
288 2931 3.007398 AGGCTTGATATCCGATGGAGTTC 59.993 47.826 0.00 0.00 34.05 3.01
292 2935 0.243907 ATATCCGATGGAGTTCCGCG 59.756 55.000 0.00 0.00 39.43 6.46
309 2952 2.125512 GCTGTGACGCGAAGGGAT 60.126 61.111 15.93 0.00 46.37 3.85
311 2954 1.215382 CTGTGACGCGAAGGGATCA 59.785 57.895 15.93 0.73 46.37 2.92
313 2956 1.080093 GTGACGCGAAGGGATCACA 60.080 57.895 15.93 0.00 46.37 3.58
314 2957 1.080093 TGACGCGAAGGGATCACAC 60.080 57.895 15.93 0.00 46.37 3.82
315 2958 2.126071 ACGCGAAGGGATCACACG 60.126 61.111 15.93 9.62 46.37 4.49
316 2959 2.180769 CGCGAAGGGATCACACGA 59.819 61.111 16.50 0.00 46.37 4.35
338 2983 1.003355 CACCAGTGAGGGCAATCGT 60.003 57.895 0.00 0.00 43.89 3.73
340 2985 1.450312 CCAGTGAGGGCAATCGTCC 60.450 63.158 0.00 0.00 37.05 4.79
361 3006 2.989824 CGGCGGGGGACTCGATAT 60.990 66.667 0.00 0.00 0.00 1.63
369 3014 1.964223 GGGGACTCGATATCAAGCTCA 59.036 52.381 3.12 0.00 0.00 4.26
370 3015 2.365617 GGGGACTCGATATCAAGCTCAA 59.634 50.000 3.12 0.00 0.00 3.02
371 3016 3.181465 GGGGACTCGATATCAAGCTCAAA 60.181 47.826 3.12 0.00 0.00 2.69
372 3017 4.054671 GGGACTCGATATCAAGCTCAAAG 58.945 47.826 3.12 0.00 0.00 2.77
373 3018 4.054671 GGACTCGATATCAAGCTCAAAGG 58.945 47.826 3.12 0.00 0.00 3.11
375 3020 5.510520 GGACTCGATATCAAGCTCAAAGGAT 60.511 44.000 3.12 0.00 0.00 3.24
376 3021 5.537188 ACTCGATATCAAGCTCAAAGGATC 58.463 41.667 3.12 0.00 0.00 3.36
381 3075 2.109126 AAGCTCAAAGGATCGCCGC 61.109 57.895 0.00 0.00 39.96 6.53
451 3145 1.524621 CGCGGATGAATTGCCCTCT 60.525 57.895 0.00 0.00 0.00 3.69
455 3149 0.469917 GGATGAATTGCCCTCTCCGA 59.530 55.000 0.00 0.00 0.00 4.55
459 3168 2.852495 GAATTGCCCTCTCCGACGCA 62.852 60.000 0.00 0.00 0.00 5.24
486 3203 3.382803 GAGCAGGCATGAGCGGAGT 62.383 63.158 0.62 0.00 43.41 3.85
589 3312 2.035940 AAGGAGGCCTCTCGTCGT 59.964 61.111 31.36 10.90 40.85 4.34
666 3431 3.122971 GTGGAAGCGGCGTAACCC 61.123 66.667 9.37 5.79 33.26 4.11
669 3434 2.046604 GAAGCGGCGTAACCCCTT 60.047 61.111 9.37 1.19 33.26 3.95
675 3440 0.247185 CGGCGTAACCCCTTCAACTA 59.753 55.000 0.00 0.00 33.26 2.24
677 3442 1.551883 GGCGTAACCCCTTCAACTAGA 59.448 52.381 0.00 0.00 0.00 2.43
681 3446 3.368116 CGTAACCCCTTCAACTAGACCTG 60.368 52.174 0.00 0.00 0.00 4.00
682 3447 1.657804 ACCCCTTCAACTAGACCTGG 58.342 55.000 0.00 0.00 0.00 4.45
683 3448 0.253327 CCCCTTCAACTAGACCTGGC 59.747 60.000 0.00 0.00 0.00 4.85
686 3451 1.561542 CCTTCAACTAGACCTGGCCAT 59.438 52.381 5.51 0.00 0.00 4.40
688 3453 0.911769 TCAACTAGACCTGGCCATGG 59.088 55.000 5.51 13.05 0.00 3.66
689 3454 0.107017 CAACTAGACCTGGCCATGGG 60.107 60.000 20.97 16.10 0.00 4.00
725 3490 2.728397 AAAAAGCCCGACCTTGTCC 58.272 52.632 0.00 0.00 0.00 4.02
726 3491 0.106419 AAAAAGCCCGACCTTGTCCA 60.106 50.000 0.00 0.00 0.00 4.02
727 3492 0.112412 AAAAGCCCGACCTTGTCCAT 59.888 50.000 0.00 0.00 0.00 3.41
728 3493 0.609131 AAAGCCCGACCTTGTCCATG 60.609 55.000 0.00 0.00 0.00 3.66
729 3494 2.438434 GCCCGACCTTGTCCATGG 60.438 66.667 4.97 4.97 0.00 3.66
730 3495 2.272146 CCCGACCTTGTCCATGGG 59.728 66.667 13.02 0.00 0.00 4.00
731 3496 2.438434 CCGACCTTGTCCATGGGC 60.438 66.667 10.20 10.20 0.00 5.36
753 5265 3.780624 GCTCGGGCCTAGATTTCAA 57.219 52.632 9.63 0.00 0.00 2.69
754 5266 1.587547 GCTCGGGCCTAGATTTCAAG 58.412 55.000 9.63 0.00 0.00 3.02
755 5267 1.587547 CTCGGGCCTAGATTTCAAGC 58.412 55.000 0.84 0.00 0.00 4.01
756 5268 0.180406 TCGGGCCTAGATTTCAAGCC 59.820 55.000 0.84 0.00 43.09 4.35
758 5270 2.707902 GGCCTAGATTTCAAGCCCG 58.292 57.895 0.00 0.00 37.66 6.13
759 5271 0.180406 GGCCTAGATTTCAAGCCCGA 59.820 55.000 0.00 0.00 37.66 5.14
760 5272 1.300481 GCCTAGATTTCAAGCCCGAC 58.700 55.000 0.00 0.00 0.00 4.79
761 5273 1.571919 CCTAGATTTCAAGCCCGACG 58.428 55.000 0.00 0.00 0.00 5.12
762 5274 1.134788 CCTAGATTTCAAGCCCGACGT 60.135 52.381 0.00 0.00 0.00 4.34
763 5275 2.194271 CTAGATTTCAAGCCCGACGTC 58.806 52.381 5.18 5.18 0.00 4.34
764 5276 0.391263 AGATTTCAAGCCCGACGTCC 60.391 55.000 10.58 0.00 0.00 4.79
765 5277 1.693083 GATTTCAAGCCCGACGTCCG 61.693 60.000 10.58 3.03 38.18 4.79
791 5303 4.129737 CGGACCCGTGCTCGTCAT 62.130 66.667 7.47 0.00 35.01 3.06
792 5304 2.767445 CGGACCCGTGCTCGTCATA 61.767 63.158 7.47 0.00 35.01 2.15
793 5305 1.740285 GGACCCGTGCTCGTCATAT 59.260 57.895 7.47 0.00 35.01 1.78
794 5306 0.104304 GGACCCGTGCTCGTCATATT 59.896 55.000 7.47 0.00 35.01 1.28
795 5307 1.472728 GGACCCGTGCTCGTCATATTT 60.473 52.381 7.47 0.00 35.01 1.40
796 5308 1.593006 GACCCGTGCTCGTCATATTTG 59.407 52.381 7.47 0.00 35.01 2.32
797 5309 0.304705 CCCGTGCTCGTCATATTTGC 59.695 55.000 7.47 0.00 35.01 3.68
798 5310 0.043053 CCGTGCTCGTCATATTTGCG 60.043 55.000 7.47 0.00 35.01 4.85
799 5311 0.651610 CGTGCTCGTCATATTTGCGC 60.652 55.000 0.00 0.00 0.00 6.09
800 5312 0.651610 GTGCTCGTCATATTTGCGCG 60.652 55.000 0.00 0.00 0.00 6.86
801 5313 1.081556 TGCTCGTCATATTTGCGCGT 61.082 50.000 8.43 0.00 0.00 6.01
802 5314 0.026285 GCTCGTCATATTTGCGCGTT 59.974 50.000 8.43 0.00 0.00 4.84
803 5315 1.256895 GCTCGTCATATTTGCGCGTTA 59.743 47.619 8.43 0.00 0.00 3.18
804 5316 2.285371 GCTCGTCATATTTGCGCGTTAA 60.285 45.455 8.43 2.27 0.00 2.01
805 5317 3.269310 CTCGTCATATTTGCGCGTTAAC 58.731 45.455 8.43 0.00 0.00 2.01
806 5318 2.017208 CGTCATATTTGCGCGTTAACG 58.983 47.619 23.40 23.40 43.27 3.18
807 5319 2.284571 CGTCATATTTGCGCGTTAACGA 60.285 45.455 31.03 10.52 43.02 3.85
808 5320 3.661819 GTCATATTTGCGCGTTAACGAA 58.338 40.909 31.03 16.39 43.02 3.85
809 5321 3.712572 GTCATATTTGCGCGTTAACGAAG 59.287 43.478 31.03 22.74 43.02 3.79
810 5322 3.613299 TCATATTTGCGCGTTAACGAAGA 59.387 39.130 31.03 13.86 43.02 2.87
811 5323 2.503943 ATTTGCGCGTTAACGAAGAG 57.496 45.000 31.03 18.07 43.02 2.85
812 5324 0.509499 TTTGCGCGTTAACGAAGAGG 59.491 50.000 31.03 14.14 43.02 3.69
813 5325 1.893168 TTGCGCGTTAACGAAGAGGC 61.893 55.000 31.03 22.13 43.02 4.70
814 5326 3.078560 CGCGTTAACGAAGAGGCC 58.921 61.111 31.03 10.53 43.02 5.19
815 5327 1.445582 CGCGTTAACGAAGAGGCCT 60.446 57.895 31.03 3.86 43.02 5.19
816 5328 1.683790 CGCGTTAACGAAGAGGCCTG 61.684 60.000 31.03 0.00 43.02 4.85
817 5329 1.359459 GCGTTAACGAAGAGGCCTGG 61.359 60.000 31.03 0.00 43.02 4.45
818 5330 1.359459 CGTTAACGAAGAGGCCTGGC 61.359 60.000 23.35 11.05 43.02 4.85
844 5898 4.160635 CGGCGGGCTTTTAGCGTG 62.161 66.667 0.00 0.00 43.62 5.34
845 5899 2.744709 GGCGGGCTTTTAGCGTGA 60.745 61.111 0.00 0.00 43.62 4.35
853 5907 1.202031 GCTTTTAGCGTGATGTTCCGG 60.202 52.381 0.00 0.00 0.00 5.14
855 5909 1.022451 TTTAGCGTGATGTTCCGGGC 61.022 55.000 0.00 0.00 0.00 6.13
856 5910 2.173758 TTAGCGTGATGTTCCGGGCA 62.174 55.000 0.00 1.02 0.00 5.36
857 5911 2.845752 TAGCGTGATGTTCCGGGCAC 62.846 60.000 0.00 0.00 0.00 5.01
858 5912 3.487202 CGTGATGTTCCGGGCACG 61.487 66.667 0.00 0.00 46.25 5.34
886 5940 3.603144 TTTTTGCATCGGGCTTTGG 57.397 47.368 0.00 0.00 45.15 3.28
888 5942 0.755686 TTTTGCATCGGGCTTTGGTT 59.244 45.000 0.00 0.00 45.15 3.67
889 5943 0.033228 TTTGCATCGGGCTTTGGTTG 59.967 50.000 0.00 0.00 45.15 3.77
890 5944 1.814772 TTGCATCGGGCTTTGGTTGG 61.815 55.000 0.00 0.00 45.15 3.77
891 5945 2.573340 CATCGGGCTTTGGTTGGC 59.427 61.111 0.00 0.00 0.00 4.52
892 5946 2.679996 ATCGGGCTTTGGTTGGCC 60.680 61.111 0.00 0.00 46.89 5.36
913 5967 3.402681 CCCGACAGATGGCCAGGT 61.403 66.667 13.05 9.65 0.00 4.00
914 5968 2.063979 CCCGACAGATGGCCAGGTA 61.064 63.158 13.05 0.00 0.00 3.08
915 5969 1.410850 CCCGACAGATGGCCAGGTAT 61.411 60.000 13.05 0.00 0.00 2.73
916 5970 1.338107 CCGACAGATGGCCAGGTATA 58.662 55.000 13.05 0.00 0.00 1.47
931 6006 4.514401 CAGGTATACCTTCAACCCTCAAC 58.486 47.826 22.36 0.00 46.09 3.18
932 6007 4.019681 CAGGTATACCTTCAACCCTCAACA 60.020 45.833 22.36 0.00 46.09 3.33
933 6008 4.600111 AGGTATACCTTCAACCCTCAACAA 59.400 41.667 19.27 0.00 46.09 2.83
944 6019 4.192453 TCAACAAACGGGCCGGGT 62.192 61.111 31.78 21.68 0.00 5.28
954 6029 3.961414 GGCCGGGTCCAAAGGTGA 61.961 66.667 2.18 0.00 0.00 4.02
956 6031 2.358247 CCGGGTCCAAAGGTGACG 60.358 66.667 0.00 0.00 33.46 4.35
960 6035 1.395635 GGGTCCAAAGGTGACGTTTT 58.604 50.000 0.00 0.00 33.46 2.43
961 6036 1.752498 GGGTCCAAAGGTGACGTTTTT 59.248 47.619 0.00 0.00 33.46 1.94
1440 6528 5.641709 GCCAATGATGACATGATGATGATC 58.358 41.667 0.00 0.00 36.79 2.92
1506 6594 2.112297 TTCCGGTGGCTGTTGTCC 59.888 61.111 0.00 0.00 0.00 4.02
1558 6652 5.947443 AGCATCATTCTCTTTGCAAAGTAC 58.053 37.500 32.46 11.46 37.56 2.73
1559 6653 5.709164 AGCATCATTCTCTTTGCAAAGTACT 59.291 36.000 32.46 16.91 37.56 2.73
1560 6654 6.881065 AGCATCATTCTCTTTGCAAAGTACTA 59.119 34.615 32.46 19.30 37.56 1.82
1561 6655 7.065563 AGCATCATTCTCTTTGCAAAGTACTAG 59.934 37.037 32.46 23.85 37.56 2.57
1562 6656 7.678218 GCATCATTCTCTTTGCAAAGTACTAGG 60.678 40.741 32.46 20.48 37.31 3.02
1563 6657 6.173339 TCATTCTCTTTGCAAAGTACTAGGG 58.827 40.000 32.46 19.19 37.31 3.53
1564 6658 3.939066 TCTCTTTGCAAAGTACTAGGGC 58.061 45.455 32.46 0.75 37.31 5.19
1573 6686 5.424252 TGCAAAGTACTAGGGCTGTAGTAAT 59.576 40.000 12.68 5.62 37.27 1.89
1668 6827 5.364778 TGTGTTGCAGTAACTACTTGTGAT 58.635 37.500 2.84 0.00 40.05 3.06
1693 6852 3.743396 CACCAGAAGCTTCAGTCACTAAC 59.257 47.826 27.57 0.00 0.00 2.34
1866 7044 5.772825 TTTTGGTTTCTCTGTTGAGGATG 57.227 39.130 0.00 0.00 40.58 3.51
1904 7086 0.526211 CAGCGGGCCTAACTTTTTCC 59.474 55.000 0.84 0.00 0.00 3.13
2097 7288 1.598882 TACTTGATGCGTGTTGCCAA 58.401 45.000 0.00 0.00 45.60 4.52
2321 8672 7.323049 ACAGTGTACTACTCATCTGACATAC 57.677 40.000 0.00 0.00 37.60 2.39
2390 8794 6.394345 AAGGGTCCTGATACTTTCTTGATT 57.606 37.500 0.00 0.00 0.00 2.57
2397 8801 3.054728 TGATACTTTCTTGATTGCCCGGA 60.055 43.478 0.73 0.00 0.00 5.14
2411 8815 3.370104 TGCCCGGAAAATCCACATTTAT 58.630 40.909 0.73 0.00 35.91 1.40
2483 9122 5.606348 AGACTGTTACATCATCTTCTCCC 57.394 43.478 0.00 0.00 0.00 4.30
2740 9397 7.570982 TGGGGGAATCTGAGATTAACAGTTATA 59.429 37.037 7.82 0.00 36.81 0.98
2742 9399 8.652290 GGGGAATCTGAGATTAACAGTTATAGT 58.348 37.037 7.82 0.00 36.81 2.12
2743 9400 9.699703 GGGAATCTGAGATTAACAGTTATAGTC 57.300 37.037 7.82 0.00 36.81 2.59
2979 9778 3.302870 CCACTAAACAAAGAACGTCGTGG 60.303 47.826 0.00 0.00 34.21 4.94
3009 9808 4.439968 CTTACCCTTATCGGACCAGTTTC 58.560 47.826 0.00 0.00 33.16 2.78
3061 9862 5.477291 ACATTTTCGTCTCCTGTTCTCTCTA 59.523 40.000 0.00 0.00 0.00 2.43
3104 9905 7.108194 TGCTGATGATGATAGAACAGTTCTTT 58.892 34.615 21.05 13.37 41.14 2.52
3362 10263 5.566230 GCACTTGCTGAATCTGGAAATTTCT 60.566 40.000 17.42 0.00 38.21 2.52
3370 10271 7.627300 GCTGAATCTGGAAATTTCTAACTCACC 60.627 40.741 17.42 0.00 0.00 4.02
3371 10272 7.461749 TGAATCTGGAAATTTCTAACTCACCT 58.538 34.615 17.42 0.00 0.00 4.00
3375 10276 8.166422 TCTGGAAATTTCTAACTCACCTTTTC 57.834 34.615 17.42 0.00 0.00 2.29
3408 10316 2.289945 ACTGGTGGATGAGCTTGTTCTC 60.290 50.000 0.00 0.00 0.00 2.87
3555 10560 7.817418 TTCCTATTAAATGGCTGTTGGATAC 57.183 36.000 0.00 0.00 0.00 2.24
3620 10643 2.907892 TCAGAATGAGTCCTTCCACCT 58.092 47.619 4.70 0.00 42.56 4.00
3621 10644 3.251484 TCAGAATGAGTCCTTCCACCTT 58.749 45.455 4.70 0.00 42.56 3.50
3622 10645 3.008375 TCAGAATGAGTCCTTCCACCTTG 59.992 47.826 4.70 0.00 42.56 3.61
3623 10646 2.982488 AGAATGAGTCCTTCCACCTTGT 59.018 45.455 4.70 0.00 0.00 3.16
3645 10668 4.342862 TGGCTGCCATTCTACTATCTTC 57.657 45.455 19.30 0.00 0.00 2.87
3789 10846 1.269723 CGCAGTGGTCAAGTACTCTCA 59.730 52.381 0.00 0.00 0.00 3.27
3815 10872 1.296715 CCAAGAGGTCCTGGGTTCG 59.703 63.158 0.00 0.00 30.82 3.95
4010 11090 7.616528 TCTTATGATACTGGAATGGTGATCA 57.383 36.000 0.00 0.00 0.00 2.92
4023 11103 8.328758 TGGAATGGTGATCAGAGTAAAGTATTT 58.671 33.333 0.00 0.00 43.42 1.40
4041 11123 9.630098 AAAGTATTTTGATGTTTAGAGTGCATG 57.370 29.630 0.00 0.00 31.62 4.06
4046 11128 5.050644 TGATGTTTAGAGTGCATGCAAAG 57.949 39.130 24.58 0.00 0.00 2.77
4062 11144 3.111098 GCAAAGCAAGTCAGTTTCTGTG 58.889 45.455 0.00 0.00 32.61 3.66
4069 11153 3.498774 AGTCAGTTTCTGTGCAGGAAT 57.501 42.857 3.34 0.00 32.61 3.01
4073 11157 4.036734 GTCAGTTTCTGTGCAGGAATCAAA 59.963 41.667 10.88 0.00 32.61 2.69
4076 11160 3.581024 TTCTGTGCAGGAATCAAATGC 57.419 42.857 0.00 0.00 40.40 3.56
4101 11185 0.749818 TTCTGTTGGTTTCTGCCGCA 60.750 50.000 0.00 0.00 0.00 5.69
4110 11194 1.406539 GTTTCTGCCGCATGGATTCAT 59.593 47.619 0.00 0.00 37.49 2.57
4130 11214 3.872511 TGGGCAAATTGCTGTTATCTG 57.127 42.857 18.04 0.00 44.28 2.90
4166 11386 0.758734 CATATCTGGCCCGAACTCCA 59.241 55.000 0.00 0.00 0.00 3.86
4168 11388 1.507140 TATCTGGCCCGAACTCCAAT 58.493 50.000 0.00 0.00 30.98 3.16
4173 11393 1.272425 TGGCCCGAACTCCAATTTGAT 60.272 47.619 0.00 0.00 0.00 2.57
4176 11396 3.445805 GGCCCGAACTCCAATTTGATTTA 59.554 43.478 0.00 0.00 0.00 1.40
4180 11400 6.593770 GCCCGAACTCCAATTTGATTTATTTT 59.406 34.615 0.00 0.00 0.00 1.82
4204 11429 8.746922 TTTTCTACTTCTTATTGCTGCATTTG 57.253 30.769 1.84 0.00 0.00 2.32
4228 11453 5.021033 TCATTTCTTCCTCTGAGATCTGC 57.979 43.478 6.17 0.00 0.00 4.26
4265 11490 5.365605 TCATGGTAAGATGTACCCTTGTAGG 59.634 44.000 7.60 0.00 36.79 3.18
4359 11584 2.989840 CGTTTCAAACAACTTTGCACCA 59.010 40.909 0.22 0.00 37.31 4.17
4414 11639 8.758829 ACTGGTATTCTCAATGTACATAGTTGA 58.241 33.333 9.21 9.34 0.00 3.18
4415 11640 9.599866 CTGGTATTCTCAATGTACATAGTTGAA 57.400 33.333 9.21 11.39 32.08 2.69
4751 12443 0.322456 TGTACCCTGCTCAACATGCC 60.322 55.000 0.00 0.00 0.00 4.40
4752 12444 0.322456 GTACCCTGCTCAACATGCCA 60.322 55.000 0.00 0.00 0.00 4.92
4911 12738 5.003096 AGGGGAGAATCAAACAGTTCATT 57.997 39.130 0.00 0.00 36.25 2.57
4932 12762 0.620556 TGTCTGCCCATTCTTCTCCC 59.379 55.000 0.00 0.00 0.00 4.30
5241 13147 2.728817 GGTATGACGCCCGGAGAG 59.271 66.667 0.73 0.00 0.00 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 5.461078 CCAATTACAACTCCGGTAACTATCG 59.539 44.000 0.00 0.00 33.89 2.92
14 15 3.934068 ACCTGTACCAATTACAACTCCG 58.066 45.455 0.00 0.00 40.33 4.63
45 46 6.064717 GGAGGATGAGTGCAAATAAACCTAT 58.935 40.000 0.00 0.00 0.00 2.57
95 96 9.632638 ACATTATGTATTTGACCATAGCTCTTT 57.367 29.630 0.00 0.00 0.00 2.52
116 117 7.782168 ACTCCATCAGAGACTTCAGATACATTA 59.218 37.037 0.00 0.00 46.50 1.90
121 122 7.284261 CAGTAACTCCATCAGAGACTTCAGATA 59.716 40.741 0.00 0.00 46.50 1.98
133 134 8.893219 TTATCTAAATGCAGTAACTCCATCAG 57.107 34.615 0.00 0.00 0.00 2.90
169 171 7.740519 ATCTGTAAAATAATTTGTTGCTCGC 57.259 32.000 0.00 0.00 0.00 5.03
204 206 4.892934 TGAATACAGAACCAAAACTGCCTT 59.107 37.500 0.00 0.00 37.61 4.35
256 259 3.432749 GGATATCAAGCCTCTTCACTGCA 60.433 47.826 4.83 0.00 0.00 4.41
275 278 2.417516 CGCGGAACTCCATCGGAT 59.582 61.111 0.00 0.00 35.14 4.18
276 279 4.508128 GCGCGGAACTCCATCGGA 62.508 66.667 8.83 0.00 33.90 4.55
277 280 4.514577 AGCGCGGAACTCCATCGG 62.515 66.667 8.83 0.00 33.90 4.18
278 281 3.257561 CAGCGCGGAACTCCATCG 61.258 66.667 8.83 0.20 35.59 3.84
279 282 2.125512 ACAGCGCGGAACTCCATC 60.126 61.111 16.26 0.00 35.14 3.51
280 283 2.434884 CACAGCGCGGAACTCCAT 60.435 61.111 16.26 0.00 35.14 3.41
282 285 3.112709 GTCACAGCGCGGAACTCC 61.113 66.667 16.26 0.00 0.00 3.85
283 286 3.470567 CGTCACAGCGCGGAACTC 61.471 66.667 16.26 0.85 0.00 3.01
292 2935 2.125512 ATCCCTTCGCGTCACAGC 60.126 61.111 5.77 0.00 0.00 4.40
305 2948 1.153549 GGTGAGCTCGTGTGATCCC 60.154 63.158 9.64 0.00 0.00 3.85
309 2952 1.106944 TCACTGGTGAGCTCGTGTGA 61.107 55.000 19.63 19.63 34.14 3.58
311 2954 3.856309 TCACTGGTGAGCTCGTGT 58.144 55.556 16.06 7.03 34.14 4.49
344 2989 2.989824 ATATCGAGTCCCCCGCCG 60.990 66.667 0.00 0.00 0.00 6.46
347 2992 0.038159 GCTTGATATCGAGTCCCCCG 60.038 60.000 19.24 0.00 0.00 5.73
360 3005 1.673168 GGCGATCCTTTGAGCTTGAT 58.327 50.000 0.00 0.00 0.00 2.57
361 3006 0.740868 CGGCGATCCTTTGAGCTTGA 60.741 55.000 0.00 0.00 0.00 3.02
402 3096 0.249073 CGTGATCTGGTCGCCTTAGG 60.249 60.000 0.00 0.00 33.71 2.69
405 3099 2.125512 GCGTGATCTGGTCGCCTT 60.126 61.111 11.69 0.00 43.41 4.35
417 3111 4.337060 CGTGGTCTGGACGCGTGA 62.337 66.667 20.70 4.67 0.00 4.35
451 3145 3.733960 CGACCTGTCTGCGTCGGA 61.734 66.667 1.80 0.00 46.21 4.55
455 3149 3.274455 CTGCTCGACCTGTCTGCGT 62.274 63.158 0.00 0.00 32.29 5.24
459 3168 1.986757 ATGCCTGCTCGACCTGTCT 60.987 57.895 0.00 0.00 0.00 3.41
611 3334 4.722700 CACCCCCAACCTCGGCAG 62.723 72.222 0.00 0.00 0.00 4.85
615 3368 4.029809 GACCCACCCCCAACCTCG 62.030 72.222 0.00 0.00 0.00 4.63
650 3415 4.397832 GGGGTTACGCCGCTTCCA 62.398 66.667 1.91 0.00 45.76 3.53
660 3425 3.055312 CCAGGTCTAGTTGAAGGGGTTAC 60.055 52.174 0.00 0.00 0.00 2.50
663 3428 1.657804 CCAGGTCTAGTTGAAGGGGT 58.342 55.000 0.00 0.00 0.00 4.95
666 3431 0.984230 TGGCCAGGTCTAGTTGAAGG 59.016 55.000 0.00 0.00 0.00 3.46
669 3434 0.911769 CCATGGCCAGGTCTAGTTGA 59.088 55.000 17.55 0.00 0.00 3.18
707 3472 0.106419 TGGACAAGGTCGGGCTTTTT 60.106 50.000 0.00 0.00 32.65 1.94
708 3473 0.112412 ATGGACAAGGTCGGGCTTTT 59.888 50.000 0.00 0.00 32.65 2.27
711 3476 2.671070 CATGGACAAGGTCGGGCT 59.329 61.111 0.00 0.00 32.65 5.19
713 3478 2.272146 CCCATGGACAAGGTCGGG 59.728 66.667 15.22 0.00 32.65 5.14
714 3479 2.438434 GCCCATGGACAAGGTCGG 60.438 66.667 15.22 0.00 32.65 4.79
715 3480 2.438434 GGCCCATGGACAAGGTCG 60.438 66.667 15.22 0.00 32.65 4.79
718 3483 4.820744 CCCGGCCCATGGACAAGG 62.821 72.222 15.22 9.16 0.00 3.61
743 5255 2.194271 GACGTCGGGCTTGAAATCTAG 58.806 52.381 0.00 0.00 0.00 2.43
744 5256 1.134907 GGACGTCGGGCTTGAAATCTA 60.135 52.381 9.92 0.00 0.00 1.98
747 5259 1.740296 CGGACGTCGGGCTTGAAAT 60.740 57.895 14.86 0.00 34.75 2.17
748 5260 2.356553 CGGACGTCGGGCTTGAAA 60.357 61.111 14.86 0.00 34.75 2.69
774 5286 2.071844 ATATGACGAGCACGGGTCCG 62.072 60.000 8.74 7.97 44.46 4.79
775 5287 0.104304 AATATGACGAGCACGGGTCC 59.896 55.000 8.74 0.00 44.46 4.46
776 5288 1.593006 CAAATATGACGAGCACGGGTC 59.407 52.381 8.74 0.00 44.46 4.46
777 5289 1.651987 CAAATATGACGAGCACGGGT 58.348 50.000 8.74 0.00 44.46 5.28
778 5290 0.304705 GCAAATATGACGAGCACGGG 59.695 55.000 8.74 0.00 44.46 5.28
779 5291 0.043053 CGCAAATATGACGAGCACGG 60.043 55.000 8.74 0.00 44.46 4.94
780 5292 0.651610 GCGCAAATATGACGAGCACG 60.652 55.000 0.30 0.76 45.75 5.34
781 5293 0.651610 CGCGCAAATATGACGAGCAC 60.652 55.000 8.75 0.00 31.58 4.40
782 5294 1.081556 ACGCGCAAATATGACGAGCA 61.082 50.000 5.73 0.00 32.46 4.26
783 5295 0.026285 AACGCGCAAATATGACGAGC 59.974 50.000 5.73 0.00 32.46 5.03
784 5296 3.269310 GTTAACGCGCAAATATGACGAG 58.731 45.455 5.73 0.00 34.23 4.18
785 5297 2.284571 CGTTAACGCGCAAATATGACGA 60.285 45.455 16.05 0.00 33.47 4.20
786 5298 2.017208 CGTTAACGCGCAAATATGACG 58.983 47.619 16.05 4.20 34.84 4.35
787 5299 3.292624 TCGTTAACGCGCAAATATGAC 57.707 42.857 22.96 0.00 39.60 3.06
788 5300 3.613299 TCTTCGTTAACGCGCAAATATGA 59.387 39.130 22.96 8.77 39.60 2.15
789 5301 3.918635 TCTTCGTTAACGCGCAAATATG 58.081 40.909 22.96 6.64 39.60 1.78
790 5302 3.000925 CCTCTTCGTTAACGCGCAAATAT 59.999 43.478 22.96 0.00 39.60 1.28
791 5303 2.346244 CCTCTTCGTTAACGCGCAAATA 59.654 45.455 22.96 0.87 39.60 1.40
792 5304 1.127951 CCTCTTCGTTAACGCGCAAAT 59.872 47.619 22.96 0.00 39.60 2.32
793 5305 0.509499 CCTCTTCGTTAACGCGCAAA 59.491 50.000 22.96 11.00 39.60 3.68
794 5306 1.893168 GCCTCTTCGTTAACGCGCAA 61.893 55.000 22.96 11.35 39.60 4.85
795 5307 2.377310 GCCTCTTCGTTAACGCGCA 61.377 57.895 22.96 8.47 39.60 6.09
796 5308 2.394524 GCCTCTTCGTTAACGCGC 59.605 61.111 22.96 14.00 39.60 6.86
797 5309 1.445582 AGGCCTCTTCGTTAACGCG 60.446 57.895 22.96 15.60 39.60 6.01
798 5310 1.359459 CCAGGCCTCTTCGTTAACGC 61.359 60.000 22.96 7.70 39.60 4.84
799 5311 1.359459 GCCAGGCCTCTTCGTTAACG 61.359 60.000 21.85 21.85 41.45 3.18
800 5312 1.025113 GGCCAGGCCTCTTCGTTAAC 61.025 60.000 24.99 0.00 46.69 2.01
801 5313 1.298667 GGCCAGGCCTCTTCGTTAA 59.701 57.895 24.99 0.00 46.69 2.01
802 5314 2.987125 GGCCAGGCCTCTTCGTTA 59.013 61.111 24.99 0.00 46.69 3.18
827 5339 4.160635 CACGCTAAAAGCCCGCCG 62.161 66.667 0.00 0.00 38.18 6.46
828 5340 2.112815 ATCACGCTAAAAGCCCGCC 61.113 57.895 0.00 0.00 38.18 6.13
829 5341 1.062525 CATCACGCTAAAAGCCCGC 59.937 57.895 0.00 0.00 38.18 6.13
830 5342 0.802494 AACATCACGCTAAAAGCCCG 59.198 50.000 0.00 0.00 38.18 6.13
831 5343 1.132453 GGAACATCACGCTAAAAGCCC 59.868 52.381 0.00 0.00 38.18 5.19
834 5888 1.396996 CCCGGAACATCACGCTAAAAG 59.603 52.381 0.73 0.00 0.00 2.27
838 5892 2.185867 GCCCGGAACATCACGCTA 59.814 61.111 0.73 0.00 0.00 4.26
841 5895 3.487202 CGTGCCCGGAACATCACG 61.487 66.667 0.73 10.69 44.62 4.35
869 5923 0.755686 AACCAAAGCCCGATGCAAAA 59.244 45.000 0.00 0.00 44.83 2.44
870 5924 0.033228 CAACCAAAGCCCGATGCAAA 59.967 50.000 0.00 0.00 44.83 3.68
871 5925 1.664873 CAACCAAAGCCCGATGCAA 59.335 52.632 0.00 0.00 44.83 4.08
872 5926 2.274645 CCAACCAAAGCCCGATGCA 61.275 57.895 0.00 0.00 44.83 3.96
873 5927 2.573340 CCAACCAAAGCCCGATGC 59.427 61.111 0.00 0.00 41.71 3.91
874 5928 2.573340 GCCAACCAAAGCCCGATG 59.427 61.111 0.00 0.00 0.00 3.84
896 5950 1.410850 ATACCTGGCCATCTGTCGGG 61.411 60.000 5.51 4.26 0.00 5.14
897 5951 1.000955 GTATACCTGGCCATCTGTCGG 59.999 57.143 5.51 5.16 0.00 4.79
898 5952 1.000955 GGTATACCTGGCCATCTGTCG 59.999 57.143 15.09 0.00 0.00 4.35
899 5953 2.330216 AGGTATACCTGGCCATCTGTC 58.670 52.381 24.01 0.00 46.55 3.51
900 5954 2.496679 AGGTATACCTGGCCATCTGT 57.503 50.000 24.01 6.94 46.55 3.41
911 5965 4.563140 TGTTGAGGGTTGAAGGTATACC 57.437 45.455 14.54 14.54 0.00 2.73
913 5967 4.998672 CGTTTGTTGAGGGTTGAAGGTATA 59.001 41.667 0.00 0.00 0.00 1.47
914 5968 3.818773 CGTTTGTTGAGGGTTGAAGGTAT 59.181 43.478 0.00 0.00 0.00 2.73
915 5969 3.207778 CGTTTGTTGAGGGTTGAAGGTA 58.792 45.455 0.00 0.00 0.00 3.08
916 5970 2.021457 CGTTTGTTGAGGGTTGAAGGT 58.979 47.619 0.00 0.00 0.00 3.50
931 6006 4.958897 TTGGACCCGGCCCGTTTG 62.959 66.667 0.85 0.00 0.00 2.93
932 6007 4.206943 TTTGGACCCGGCCCGTTT 62.207 61.111 0.85 0.00 0.00 3.60
933 6008 4.653888 CTTTGGACCCGGCCCGTT 62.654 66.667 0.85 0.00 0.00 4.44
960 6035 2.490903 GTCGAGCACCTCCTACTGTAAA 59.509 50.000 0.00 0.00 0.00 2.01
961 6036 2.089980 GTCGAGCACCTCCTACTGTAA 58.910 52.381 0.00 0.00 0.00 2.41
962 6037 1.681166 GGTCGAGCACCTCCTACTGTA 60.681 57.143 10.30 0.00 42.84 2.74
963 6038 0.966370 GGTCGAGCACCTCCTACTGT 60.966 60.000 10.30 0.00 42.84 3.55
964 6039 1.810532 GGTCGAGCACCTCCTACTG 59.189 63.158 10.30 0.00 42.84 2.74
965 6040 1.749638 CGGTCGAGCACCTCCTACT 60.750 63.158 15.89 0.00 44.21 2.57
967 6042 3.138798 GCGGTCGAGCACCTCCTA 61.139 66.667 15.89 0.00 44.21 2.94
1506 6594 0.107508 ATCATGGAGCACGAACCTGG 60.108 55.000 0.00 0.00 0.00 4.45
1558 6652 6.963083 AACTACTCATTACTACAGCCCTAG 57.037 41.667 0.00 0.00 0.00 3.02
1559 6653 9.430399 AATAAACTACTCATTACTACAGCCCTA 57.570 33.333 0.00 0.00 0.00 3.53
1560 6654 7.916077 ATAAACTACTCATTACTACAGCCCT 57.084 36.000 0.00 0.00 0.00 5.19
1561 6655 8.959705 AAATAAACTACTCATTACTACAGCCC 57.040 34.615 0.00 0.00 0.00 5.19
1668 6827 1.970640 TGACTGAAGCTTCTGGTGCTA 59.029 47.619 29.77 13.17 40.22 3.49
1693 6852 9.132521 CACCTTTAATGCTGAAATACTTCAAAG 57.867 33.333 0.00 0.00 41.05 2.77
1857 7035 4.272018 GCACATACTGATGTCATCCTCAAC 59.728 45.833 10.36 0.00 44.82 3.18
1866 7044 3.063180 GCTGTTCAGCACATACTGATGTC 59.937 47.826 18.26 0.00 44.82 3.06
1904 7086 3.820467 TGGTCAAGCTGAATGTGGTTAAG 59.180 43.478 0.00 0.00 0.00 1.85
2097 7288 4.597004 ACTCATCATCTGCAGGAATGTTT 58.403 39.130 15.13 1.35 0.00 2.83
2321 8672 4.744795 AAGGCTATACCACAGTTCTCAG 57.255 45.455 0.00 0.00 43.14 3.35
2390 8794 1.638529 AAATGTGGATTTTCCGGGCA 58.361 45.000 0.00 0.00 40.17 5.36
2397 8801 9.341078 GGCATTCCATTTATAAATGTGGATTTT 57.659 29.630 28.10 12.27 43.24 1.82
2411 8815 6.662865 TTCAGTTTTCAGGCATTCCATTTA 57.337 33.333 0.00 0.00 33.74 1.40
2422 8826 2.363359 AGGCAGCTTTTCAGTTTTCAGG 59.637 45.455 0.00 0.00 0.00 3.86
2483 9122 7.202526 ACAATGGTGACTATTGACAAACAAAG 58.797 34.615 25.29 0.00 42.03 2.77
2699 9342 6.506770 AGATTCCCCCATGAATATGATGTACT 59.493 38.462 0.00 0.00 35.15 2.73
2710 9353 5.193527 TGTTAATCTCAGATTCCCCCATGAA 59.806 40.000 2.18 0.00 0.00 2.57
2740 9397 5.486526 CTTTCCACTCTTCAGCTAATGACT 58.513 41.667 0.00 0.00 37.77 3.41
2742 9399 4.019860 AGCTTTCCACTCTTCAGCTAATGA 60.020 41.667 0.00 0.00 39.08 2.57
2743 9400 4.260170 AGCTTTCCACTCTTCAGCTAATG 58.740 43.478 0.00 0.00 39.08 1.90
2744 9401 4.566426 AGCTTTCCACTCTTCAGCTAAT 57.434 40.909 0.00 0.00 39.08 1.73
2745 9402 4.081420 CCTAGCTTTCCACTCTTCAGCTAA 60.081 45.833 0.00 0.00 41.42 3.09
2746 9403 3.449018 CCTAGCTTTCCACTCTTCAGCTA 59.551 47.826 0.00 0.00 41.18 3.32
2747 9404 2.235898 CCTAGCTTTCCACTCTTCAGCT 59.764 50.000 0.00 0.00 43.33 4.24
2870 9655 5.893824 ACTGAAGTTGAAGGAAAAGGACAAT 59.106 36.000 0.00 0.00 0.00 2.71
2979 9778 1.873591 CGATAAGGGTAAGCCATGCAC 59.126 52.381 0.00 0.00 36.17 4.57
3061 9862 4.080807 TCAGCATGCATCCATTGGAAAAAT 60.081 37.500 21.98 0.67 32.42 1.82
3104 9905 4.993705 ATCAGGACAACCTTCTTACCAA 57.006 40.909 0.00 0.00 45.36 3.67
3370 10271 8.391075 TCCACCAGTCTAAATACAAAGAAAAG 57.609 34.615 0.00 0.00 0.00 2.27
3371 10272 8.792633 CATCCACCAGTCTAAATACAAAGAAAA 58.207 33.333 0.00 0.00 0.00 2.29
3375 10276 6.037610 GCTCATCCACCAGTCTAAATACAAAG 59.962 42.308 0.00 0.00 0.00 2.77
3408 10316 3.130516 TCGTGGCTGACTCCTTATACAAG 59.869 47.826 0.00 0.00 0.00 3.16
3555 10560 5.105473 TCCGAACCTAATTTACTCTGACAGG 60.105 44.000 1.81 0.00 0.00 4.00
3611 10634 1.809567 GCAGCCAACAAGGTGGAAGG 61.810 60.000 8.65 0.00 41.65 3.46
3612 10635 1.662044 GCAGCCAACAAGGTGGAAG 59.338 57.895 8.65 0.00 41.65 3.46
3613 10636 1.832167 GGCAGCCAACAAGGTGGAA 60.832 57.895 8.65 0.00 41.65 3.53
3614 10637 2.203480 GGCAGCCAACAAGGTGGA 60.203 61.111 8.65 0.00 41.65 4.02
3615 10638 1.474332 AATGGCAGCCAACAAGGTGG 61.474 55.000 20.84 0.00 42.05 4.61
3616 10639 0.037975 GAATGGCAGCCAACAAGGTG 60.038 55.000 20.84 0.00 36.95 4.00
3617 10640 0.178953 AGAATGGCAGCCAACAAGGT 60.179 50.000 20.84 0.00 36.95 3.50
3618 10641 1.474077 GTAGAATGGCAGCCAACAAGG 59.526 52.381 20.84 0.00 36.95 3.61
3619 10642 2.440409 AGTAGAATGGCAGCCAACAAG 58.560 47.619 20.84 0.00 36.95 3.16
3620 10643 2.584835 AGTAGAATGGCAGCCAACAA 57.415 45.000 20.84 1.12 36.95 2.83
3621 10644 3.455910 AGATAGTAGAATGGCAGCCAACA 59.544 43.478 20.84 0.30 36.95 3.33
3622 10645 4.078639 AGATAGTAGAATGGCAGCCAAC 57.921 45.455 20.84 15.78 36.95 3.77
3623 10646 4.708177 GAAGATAGTAGAATGGCAGCCAA 58.292 43.478 20.84 0.00 36.95 4.52
3645 10668 7.316544 AGAATAACTAATTTAACTGCCCACG 57.683 36.000 0.00 0.00 0.00 4.94
3815 10872 1.078848 AATGCAGAGAGGCCACGTC 60.079 57.895 5.01 0.00 0.00 4.34
3940 11000 5.873146 ACCCTAGCTAGAAGTATTGTTCC 57.127 43.478 22.70 0.00 0.00 3.62
3987 11067 7.674120 TCTGATCACCATTCCAGTATCATAAG 58.326 38.462 0.00 0.00 0.00 1.73
4001 11081 9.911788 ATCAAAATACTTTACTCTGATCACCAT 57.088 29.630 0.00 0.00 0.00 3.55
4023 11103 5.450592 TTTGCATGCACTCTAAACATCAA 57.549 34.783 22.58 4.23 0.00 2.57
4040 11122 2.754552 ACAGAAACTGACTTGCTTTGCA 59.245 40.909 5.76 0.00 35.18 4.08
4041 11123 3.111098 CACAGAAACTGACTTGCTTTGC 58.889 45.455 5.76 0.00 35.18 3.68
4046 11128 1.002033 CCTGCACAGAAACTGACTTGC 60.002 52.381 5.76 5.95 35.18 4.01
4062 11144 4.400567 AGAAGGTAAGCATTTGATTCCTGC 59.599 41.667 0.00 0.00 36.15 4.85
4069 11153 4.469657 ACCAACAGAAGGTAAGCATTTGA 58.530 39.130 0.00 0.00 37.67 2.69
4073 11157 4.520492 CAGAAACCAACAGAAGGTAAGCAT 59.480 41.667 0.00 0.00 38.76 3.79
4076 11160 3.253432 GGCAGAAACCAACAGAAGGTAAG 59.747 47.826 0.00 0.00 38.76 2.34
4101 11185 2.775384 AGCAATTTGCCCATGAATCCAT 59.225 40.909 17.51 0.00 46.52 3.41
4110 11194 3.429492 TCAGATAACAGCAATTTGCCCA 58.571 40.909 17.51 1.40 46.52 5.36
4153 11373 0.111446 TCAAATTGGAGTTCGGGCCA 59.889 50.000 4.39 0.00 0.00 5.36
4154 11374 1.474330 ATCAAATTGGAGTTCGGGCC 58.526 50.000 0.00 0.00 0.00 5.80
4180 11400 8.109705 TCAAATGCAGCAATAAGAAGTAGAAA 57.890 30.769 0.00 0.00 0.00 2.52
4185 11405 6.519679 TGATCAAATGCAGCAATAAGAAGT 57.480 33.333 0.00 0.00 0.00 3.01
4186 11406 8.420374 AAATGATCAAATGCAGCAATAAGAAG 57.580 30.769 0.00 0.00 0.00 2.85
4204 11429 5.697633 GCAGATCTCAGAGGAAGAAATGATC 59.302 44.000 0.00 0.00 0.00 2.92
4228 11453 5.500234 TCTTACCATGAGAAGACCAAATGG 58.500 41.667 0.00 0.00 42.88 3.16
4359 11584 4.100653 TCAGAATTCTGGCGAATGATCTCT 59.899 41.667 30.33 3.06 43.91 3.10
4414 11639 7.002879 ACAGCCTTGATTTGATCTATGCTATT 58.997 34.615 0.00 0.00 34.90 1.73
4415 11640 6.540995 ACAGCCTTGATTTGATCTATGCTAT 58.459 36.000 0.00 0.00 34.90 2.97
4666 12357 6.680874 TTTTACGTGTTGATTTGGTACACT 57.319 33.333 0.00 0.00 39.29 3.55
4911 12738 2.439507 GGGAGAAGAATGGGCAGACATA 59.560 50.000 0.00 0.00 0.00 2.29
4932 12762 1.804372 GCCACAGATACTCAGCTTCCG 60.804 57.143 0.00 0.00 0.00 4.30
5210 13116 2.742116 ATACCCTGACGCGGCCATT 61.742 57.895 10.82 0.00 0.00 3.16
5222 13128 2.838225 CTCCGGGCGTCATACCCT 60.838 66.667 0.00 0.00 46.04 4.34
5337 13243 1.920734 TACCTCACCGCAATGGCCAT 61.921 55.000 14.09 14.09 43.94 4.40
5345 13251 3.449227 CCGAGCTACCTCACCGCA 61.449 66.667 0.00 0.00 38.00 5.69


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

AutoCloner maintained by Alex Coulton.