Multiple sequence alignment - TraesCS5A01G397800

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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 TraesCS5A01G397800 chr5A 100.000 4355 0 0 1 4355 592033012 592037366 0.000000e+00 8043
1 TraesCS5A01G397800 chr5A 87.117 947 103 11 1040 1969 592198228 592199172 0.000000e+00 1055
2 TraesCS5A01G397800 chr5A 86.828 949 108 8 1032 1964 592122407 592123354 0.000000e+00 1044
3 TraesCS5A01G397800 chr5A 97.932 532 8 2 3824 4355 645056887 645056359 0.000000e+00 918
4 TraesCS5A01G397800 chr5A 94.727 531 27 1 2781 3310 55273260 55273790 0.000000e+00 824
5 TraesCS5A01G397800 chr5A 93.447 412 14 6 1860 2271 55272861 55273259 2.240000e-167 599
6 TraesCS5A01G397800 chr5D 91.532 2905 154 38 999 3823 472520362 472523254 0.000000e+00 3917
7 TraesCS5A01G397800 chr5D 86.779 953 98 10 1040 1969 472626836 472627783 0.000000e+00 1037
8 TraesCS5A01G397800 chr5D 86.492 955 106 10 1032 1964 472568522 472569475 0.000000e+00 1027
9 TraesCS5A01G397800 chr5D 84.677 620 95 0 2643 3262 472570558 472571177 1.720000e-173 619
10 TraesCS5A01G397800 chr5D 84.194 639 99 1 2636 3274 472627860 472628496 1.720000e-173 619
11 TraesCS5A01G397800 chr5D 85.745 463 36 14 529 984 472519869 472520308 3.070000e-126 462
12 TraesCS5A01G397800 chr5D 81.696 448 78 4 2693 3138 472466708 472466263 1.910000e-98 370
13 TraesCS5A01G397800 chr5D 94.000 200 12 0 181 380 472519656 472519855 1.970000e-78 303
14 TraesCS5A01G397800 chr5D 95.683 139 5 1 46 184 472516805 472516942 5.670000e-54 222
15 TraesCS5A01G397800 chr5B 89.316 1797 96 38 587 2347 579519705 579521441 0.000000e+00 2167
16 TraesCS5A01G397800 chr5B 93.231 783 42 5 2570 3346 579521433 579522210 0.000000e+00 1142
17 TraesCS5A01G397800 chr5B 87.234 940 105 5 1040 1964 579590939 579591878 0.000000e+00 1057
18 TraesCS5A01G397800 chr5B 87.925 911 93 7 1040 1934 579807425 579808334 0.000000e+00 1057
19 TraesCS5A01G397800 chr5B 87.049 942 103 8 1040 1964 580073245 580074184 0.000000e+00 1046
20 TraesCS5A01G397800 chr5B 80.191 838 149 10 1135 1958 579406660 579405826 2.880000e-171 612
21 TraesCS5A01G397800 chr5B 90.364 467 41 3 3349 3814 579522296 579522759 1.040000e-170 610
22 TraesCS5A01G397800 chr5B 90.789 380 27 3 7 380 579517519 579517896 6.500000e-138 501
23 TraesCS5A01G397800 chr6B 94.400 625 16 7 1653 2271 650651148 650651759 0.000000e+00 942
24 TraesCS5A01G397800 chr6B 94.350 531 29 1 2781 3310 650651760 650652290 0.000000e+00 813
25 TraesCS5A01G397800 chr6B 90.244 164 9 7 2361 2520 664653845 664653685 1.590000e-49 207
26 TraesCS5A01G397800 chr6B 86.705 173 22 1 2349 2520 704027232 704027060 1.600000e-44 191
27 TraesCS5A01G397800 chr2A 94.240 625 17 7 1653 2271 469818939 469819550 0.000000e+00 937
28 TraesCS5A01G397800 chr2A 98.120 532 9 1 3824 4355 701912150 701911620 0.000000e+00 926
29 TraesCS5A01G397800 chr2A 97.932 532 9 2 3824 4355 738541164 738540635 0.000000e+00 920
30 TraesCS5A01G397800 chr2A 92.467 531 26 2 2781 3310 469819551 469820068 0.000000e+00 747
31 TraesCS5A01G397800 chr2A 75.711 844 168 26 1042 1863 763381429 763382257 5.280000e-104 388
32 TraesCS5A01G397800 chr2A 87.356 174 20 2 2349 2520 663629575 663629402 9.550000e-47 198
33 TraesCS5A01G397800 chr4A 98.308 532 8 1 3824 4355 83844037 83843507 0.000000e+00 931
34 TraesCS5A01G397800 chr4A 97.757 535 11 1 3821 4355 152031703 152032236 0.000000e+00 920
35 TraesCS5A01G397800 chr6A 98.120 532 9 1 3824 4355 470628315 470627785 0.000000e+00 926
36 TraesCS5A01G397800 chr1A 98.120 532 9 1 3824 4355 60712532 60713062 0.000000e+00 926
37 TraesCS5A01G397800 chr1A 97.936 533 9 2 3824 4355 328751259 328750728 0.000000e+00 922
38 TraesCS5A01G397800 chr1A 97.932 532 10 1 3824 4355 208749389 208749919 0.000000e+00 920
39 TraesCS5A01G397800 chr3A 91.049 648 41 4 2663 3310 497759564 497758934 0.000000e+00 859
40 TraesCS5A01G397800 chr3A 93.562 466 17 2 1653 2118 497760016 497759564 0.000000e+00 682
41 TraesCS5A01G397800 chr3A 90.244 164 15 1 2358 2520 596114428 596114591 3.410000e-51 213
42 TraesCS5A01G397800 chr1B 89.091 165 17 1 2357 2520 504744702 504744538 2.050000e-48 204
43 TraesCS5A01G397800 chr1B 88.485 165 18 1 2357 2520 426466016 426465852 9.550000e-47 198
44 TraesCS5A01G397800 chr2B 79.195 298 56 4 1570 1864 797636842 797637136 7.390000e-48 202
45 TraesCS5A01G397800 chr3B 88.415 164 18 1 2358 2520 150851038 150851201 3.440000e-46 196
46 TraesCS5A01G397800 chr2D 87.283 173 20 2 2349 2520 637678332 637678161 3.440000e-46 196


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 TraesCS5A01G397800 chr5A 592033012 592037366 4354 False 8043.0 8043 100.0000 1 4355 1 chr5A.!!$F1 4354
1 TraesCS5A01G397800 chr5A 592198228 592199172 944 False 1055.0 1055 87.1170 1040 1969 1 chr5A.!!$F3 929
2 TraesCS5A01G397800 chr5A 592122407 592123354 947 False 1044.0 1044 86.8280 1032 1964 1 chr5A.!!$F2 932
3 TraesCS5A01G397800 chr5A 645056359 645056887 528 True 918.0 918 97.9320 3824 4355 1 chr5A.!!$R1 531
4 TraesCS5A01G397800 chr5A 55272861 55273790 929 False 711.5 824 94.0870 1860 3310 2 chr5A.!!$F4 1450
5 TraesCS5A01G397800 chr5D 472516805 472523254 6449 False 1226.0 3917 91.7400 46 3823 4 chr5D.!!$F1 3777
6 TraesCS5A01G397800 chr5D 472626836 472628496 1660 False 828.0 1037 85.4865 1040 3274 2 chr5D.!!$F3 2234
7 TraesCS5A01G397800 chr5D 472568522 472571177 2655 False 823.0 1027 85.5845 1032 3262 2 chr5D.!!$F2 2230
8 TraesCS5A01G397800 chr5B 579517519 579522759 5240 False 1105.0 2167 90.9250 7 3814 4 chr5B.!!$F4 3807
9 TraesCS5A01G397800 chr5B 579590939 579591878 939 False 1057.0 1057 87.2340 1040 1964 1 chr5B.!!$F1 924
10 TraesCS5A01G397800 chr5B 579807425 579808334 909 False 1057.0 1057 87.9250 1040 1934 1 chr5B.!!$F2 894
11 TraesCS5A01G397800 chr5B 580073245 580074184 939 False 1046.0 1046 87.0490 1040 1964 1 chr5B.!!$F3 924
12 TraesCS5A01G397800 chr5B 579405826 579406660 834 True 612.0 612 80.1910 1135 1958 1 chr5B.!!$R1 823
13 TraesCS5A01G397800 chr6B 650651148 650652290 1142 False 877.5 942 94.3750 1653 3310 2 chr6B.!!$F1 1657
14 TraesCS5A01G397800 chr2A 701911620 701912150 530 True 926.0 926 98.1200 3824 4355 1 chr2A.!!$R2 531
15 TraesCS5A01G397800 chr2A 738540635 738541164 529 True 920.0 920 97.9320 3824 4355 1 chr2A.!!$R3 531
16 TraesCS5A01G397800 chr2A 469818939 469820068 1129 False 842.0 937 93.3535 1653 3310 2 chr2A.!!$F2 1657
17 TraesCS5A01G397800 chr2A 763381429 763382257 828 False 388.0 388 75.7110 1042 1863 1 chr2A.!!$F1 821
18 TraesCS5A01G397800 chr4A 83843507 83844037 530 True 931.0 931 98.3080 3824 4355 1 chr4A.!!$R1 531
19 TraesCS5A01G397800 chr4A 152031703 152032236 533 False 920.0 920 97.7570 3821 4355 1 chr4A.!!$F1 534
20 TraesCS5A01G397800 chr6A 470627785 470628315 530 True 926.0 926 98.1200 3824 4355 1 chr6A.!!$R1 531
21 TraesCS5A01G397800 chr1A 60712532 60713062 530 False 926.0 926 98.1200 3824 4355 1 chr1A.!!$F1 531
22 TraesCS5A01G397800 chr1A 328750728 328751259 531 True 922.0 922 97.9360 3824 4355 1 chr1A.!!$R1 531
23 TraesCS5A01G397800 chr1A 208749389 208749919 530 False 920.0 920 97.9320 3824 4355 1 chr1A.!!$F2 531
24 TraesCS5A01G397800 chr3A 497758934 497760016 1082 True 770.5 859 92.3055 1653 3310 2 chr3A.!!$R1 1657

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
513 3237 0.034574 TCACGTTAGGGCCATGCATT 60.035 50.0 6.18 0.0 0.0 3.56 F
514 3238 0.101040 CACGTTAGGGCCATGCATTG 59.899 55.0 6.18 0.0 0.0 2.82 F
861 5341 0.108138 AGACTGTCATGGGCGCTAAC 60.108 55.0 7.64 0.0 0.0 2.34 F
873 5353 0.530870 GCGCTAACCTCCATCTCCAC 60.531 60.0 0.00 0.0 0.0 4.02 F
2428 7870 0.798776 CTTTAGTTGCTGCGAGGTGG 59.201 55.0 0.00 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1949 6510 0.319555 GACTTACCGCACACAGAGCA 60.320 55.000 0.00 0.00 0.00 4.26 R
2363 7805 3.749088 TGACATGCTTAAATTCCGAACGT 59.251 39.130 0.00 0.00 0.00 3.99 R
2545 8004 4.013728 CCGGAACAGATAAATCCCAAACA 58.986 43.478 0.00 0.00 0.00 2.83 R
2796 8279 4.075793 AGGTAGCTGAGGCGGGGA 62.076 66.667 0.00 0.00 44.37 4.81 R
3793 9365 0.320771 GAGGGAACACGTGTGCTCAT 60.321 55.000 28.33 14.98 0.00 2.90 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
24 25 1.406069 CCATGTAGGAGTGTCAGCCAC 60.406 57.143 0.00 0.00 44.89 5.01
31 32 4.295119 GTGTCAGCCACGGTCGGT 62.295 66.667 0.00 0.00 33.61 4.69
34 35 4.293648 TCAGCCACGGTCGGTGTG 62.294 66.667 9.43 2.94 45.52 3.82
57 58 1.144298 ACGGGCCTTATGGATAAACCC 59.856 52.381 0.84 6.93 36.25 4.11
106 107 1.153745 GGAGAGCACACACTAGCGG 60.154 63.158 0.00 0.00 35.48 5.52
233 2951 1.000274 GATTGGCTTTCCGTTGCACTT 60.000 47.619 0.00 0.00 34.14 3.16
252 2970 1.619654 TGGTCCTGGCTGAAACAATG 58.380 50.000 0.00 0.00 0.00 2.82
277 2995 2.486982 TCGGTCAGCTGTGTAGACTAAC 59.513 50.000 14.67 0.36 32.98 2.34
280 2998 3.367498 GGTCAGCTGTGTAGACTAACAGG 60.367 52.174 14.67 9.08 43.29 4.00
363 3087 2.686915 GCTGGCTATGCATGAGAAAAGT 59.313 45.455 10.16 0.00 0.00 2.66
383 3107 3.726004 TCCATGCAGGACCGTGAT 58.274 55.556 0.00 0.00 43.07 3.06
384 3108 2.909140 TCCATGCAGGACCGTGATA 58.091 52.632 0.00 0.00 43.07 2.15
385 3109 1.199615 TCCATGCAGGACCGTGATAA 58.800 50.000 0.00 0.00 43.07 1.75
386 3110 1.768275 TCCATGCAGGACCGTGATAAT 59.232 47.619 0.00 0.00 43.07 1.28
387 3111 1.875514 CCATGCAGGACCGTGATAATG 59.124 52.381 0.00 0.00 41.22 1.90
388 3112 2.485302 CCATGCAGGACCGTGATAATGA 60.485 50.000 0.00 0.00 41.22 2.57
389 3113 3.405831 CATGCAGGACCGTGATAATGAT 58.594 45.455 0.00 0.00 0.00 2.45
391 3115 2.146342 GCAGGACCGTGATAATGATGG 58.854 52.381 0.00 0.00 0.00 3.51
393 3117 1.768275 AGGACCGTGATAATGATGGCA 59.232 47.619 0.00 0.00 0.00 4.92
394 3118 2.373169 AGGACCGTGATAATGATGGCAT 59.627 45.455 0.00 0.00 35.92 4.40
395 3119 3.582647 AGGACCGTGATAATGATGGCATA 59.417 43.478 0.00 0.00 33.44 3.14
397 3121 4.333649 GGACCGTGATAATGATGGCATATG 59.666 45.833 0.00 0.00 33.44 1.78
398 3122 4.264253 ACCGTGATAATGATGGCATATGG 58.736 43.478 0.00 0.00 33.44 2.74
399 3123 4.019411 ACCGTGATAATGATGGCATATGGA 60.019 41.667 0.00 0.00 33.44 3.41
400 3124 5.128205 CCGTGATAATGATGGCATATGGAT 58.872 41.667 0.00 0.00 33.44 3.41
401 3125 5.008316 CCGTGATAATGATGGCATATGGATG 59.992 44.000 0.00 0.00 33.44 3.51
418 3142 9.609346 CATATGGATGCAGATGTCTCATAATAA 57.391 33.333 13.14 0.00 0.00 1.40
420 3144 8.929260 ATGGATGCAGATGTCTCATAATAAAA 57.071 30.769 0.00 0.00 0.00 1.52
421 3145 8.750515 TGGATGCAGATGTCTCATAATAAAAA 57.249 30.769 0.00 0.00 0.00 1.94
443 3167 5.428184 AATAATAGTAGGCTGGATCCTGC 57.572 43.478 30.08 30.08 38.87 4.85
444 3168 2.405618 ATAGTAGGCTGGATCCTGCA 57.594 50.000 35.70 20.83 40.72 4.41
445 3169 2.405618 TAGTAGGCTGGATCCTGCAT 57.594 50.000 35.70 32.76 40.72 3.96
446 3170 1.055040 AGTAGGCTGGATCCTGCATC 58.945 55.000 35.70 25.83 40.72 3.91
447 3171 1.055040 GTAGGCTGGATCCTGCATCT 58.945 55.000 35.70 27.77 41.69 2.90
448 3172 1.419387 GTAGGCTGGATCCTGCATCTT 59.581 52.381 35.70 22.98 41.69 2.40
449 3173 0.183014 AGGCTGGATCCTGCATCTTG 59.817 55.000 35.70 9.29 41.69 3.02
450 3174 1.453762 GGCTGGATCCTGCATCTTGC 61.454 60.000 35.70 19.15 45.29 4.01
472 3196 3.634397 GAGGATCTGGTTGACATCCAA 57.366 47.619 6.70 0.00 34.35 3.53
473 3197 4.162040 GAGGATCTGGTTGACATCCAAT 57.838 45.455 6.70 3.97 37.08 3.16
474 3198 4.133078 GAGGATCTGGTTGACATCCAATC 58.867 47.826 6.70 11.08 37.08 2.67
475 3199 2.874701 GGATCTGGTTGACATCCAATCG 59.125 50.000 6.70 0.00 38.72 3.34
476 3200 3.535561 GATCTGGTTGACATCCAATCGT 58.464 45.455 6.70 0.00 38.72 3.73
477 3201 4.442893 GGATCTGGTTGACATCCAATCGTA 60.443 45.833 6.70 0.00 38.72 3.43
478 3202 3.857052 TCTGGTTGACATCCAATCGTAC 58.143 45.455 6.70 0.00 38.72 3.67
479 3203 3.259625 TCTGGTTGACATCCAATCGTACA 59.740 43.478 6.70 0.00 38.72 2.90
480 3204 4.081142 TCTGGTTGACATCCAATCGTACAT 60.081 41.667 6.70 0.00 38.72 2.29
481 3205 3.938334 TGGTTGACATCCAATCGTACATG 59.062 43.478 2.59 0.00 38.72 3.21
482 3206 3.312421 GGTTGACATCCAATCGTACATGG 59.688 47.826 0.00 3.52 37.08 3.66
483 3207 2.560504 TGACATCCAATCGTACATGGC 58.439 47.619 0.00 0.00 36.62 4.40
484 3208 2.093235 TGACATCCAATCGTACATGGCA 60.093 45.455 0.00 0.00 36.62 4.92
485 3209 3.141398 GACATCCAATCGTACATGGCAT 58.859 45.455 0.00 0.00 36.62 4.40
486 3210 4.202305 TGACATCCAATCGTACATGGCATA 60.202 41.667 0.00 0.00 36.62 3.14
487 3211 4.065088 ACATCCAATCGTACATGGCATAC 58.935 43.478 0.00 0.00 36.62 2.39
488 3212 4.202357 ACATCCAATCGTACATGGCATACT 60.202 41.667 0.00 0.00 36.62 2.12
489 3213 5.011635 ACATCCAATCGTACATGGCATACTA 59.988 40.000 0.00 0.00 36.62 1.82
490 3214 5.134202 TCCAATCGTACATGGCATACTAG 57.866 43.478 0.00 0.00 36.62 2.57
491 3215 4.830600 TCCAATCGTACATGGCATACTAGA 59.169 41.667 0.00 0.00 36.62 2.43
492 3216 4.923871 CCAATCGTACATGGCATACTAGAC 59.076 45.833 0.00 0.00 0.00 2.59
493 3217 5.508994 CCAATCGTACATGGCATACTAGACA 60.509 44.000 0.00 0.00 0.00 3.41
494 3218 5.984695 ATCGTACATGGCATACTAGACAT 57.015 39.130 0.00 0.00 37.88 3.06
495 3219 5.372547 TCGTACATGGCATACTAGACATC 57.627 43.478 0.00 0.00 34.20 3.06
496 3220 4.825085 TCGTACATGGCATACTAGACATCA 59.175 41.667 0.00 0.00 34.20 3.07
497 3221 4.917998 CGTACATGGCATACTAGACATCAC 59.082 45.833 0.00 0.00 34.20 3.06
498 3222 3.982475 ACATGGCATACTAGACATCACG 58.018 45.455 0.00 0.00 34.20 4.35
499 3223 3.384789 ACATGGCATACTAGACATCACGT 59.615 43.478 0.00 0.00 34.20 4.49
500 3224 4.141937 ACATGGCATACTAGACATCACGTT 60.142 41.667 0.00 0.00 34.20 3.99
501 3225 5.068591 ACATGGCATACTAGACATCACGTTA 59.931 40.000 0.00 0.00 34.20 3.18
502 3226 5.183014 TGGCATACTAGACATCACGTTAG 57.817 43.478 0.00 0.00 0.00 2.34
503 3227 4.037565 TGGCATACTAGACATCACGTTAGG 59.962 45.833 0.00 0.00 0.00 2.69
504 3228 4.547532 GCATACTAGACATCACGTTAGGG 58.452 47.826 0.00 0.00 0.00 3.53
505 3229 4.547532 CATACTAGACATCACGTTAGGGC 58.452 47.826 0.00 0.00 0.00 5.19
506 3230 1.755380 ACTAGACATCACGTTAGGGCC 59.245 52.381 0.00 0.00 0.00 5.80
507 3231 1.754803 CTAGACATCACGTTAGGGCCA 59.245 52.381 6.18 0.00 0.00 5.36
508 3232 1.204146 AGACATCACGTTAGGGCCAT 58.796 50.000 6.18 0.00 0.00 4.40
509 3233 1.134401 AGACATCACGTTAGGGCCATG 60.134 52.381 6.18 0.57 0.00 3.66
510 3234 0.748005 ACATCACGTTAGGGCCATGC 60.748 55.000 6.18 0.00 0.00 4.06
511 3235 0.747644 CATCACGTTAGGGCCATGCA 60.748 55.000 6.18 0.00 0.00 3.96
512 3236 0.183492 ATCACGTTAGGGCCATGCAT 59.817 50.000 6.18 0.00 0.00 3.96
513 3237 0.034574 TCACGTTAGGGCCATGCATT 60.035 50.000 6.18 0.00 0.00 3.56
514 3238 0.101040 CACGTTAGGGCCATGCATTG 59.899 55.000 6.18 0.00 0.00 2.82
515 3239 0.323360 ACGTTAGGGCCATGCATTGT 60.323 50.000 6.18 0.00 0.00 2.71
516 3240 1.065053 ACGTTAGGGCCATGCATTGTA 60.065 47.619 6.18 0.00 0.00 2.41
517 3241 1.333619 CGTTAGGGCCATGCATTGTAC 59.666 52.381 6.18 0.00 0.00 2.90
518 3242 2.374184 GTTAGGGCCATGCATTGTACA 58.626 47.619 6.18 0.00 0.00 2.90
519 3243 2.958355 GTTAGGGCCATGCATTGTACAT 59.042 45.455 6.18 0.00 0.00 2.29
520 3244 1.405872 AGGGCCATGCATTGTACATG 58.594 50.000 6.18 0.00 43.67 3.21
521 3245 0.249573 GGGCCATGCATTGTACATGC 60.250 55.000 17.91 17.91 42.89 4.06
522 3246 0.249573 GGCCATGCATTGTACATGCC 60.250 55.000 20.37 10.77 42.89 4.40
523 3247 0.249573 GCCATGCATTGTACATGCCC 60.250 55.000 20.37 8.54 42.89 5.36
524 3248 1.405872 CCATGCATTGTACATGCCCT 58.594 50.000 20.37 10.27 42.89 5.19
525 3249 1.758280 CCATGCATTGTACATGCCCTT 59.242 47.619 20.37 8.63 42.89 3.95
526 3250 2.168936 CCATGCATTGTACATGCCCTTT 59.831 45.455 20.37 6.90 42.89 3.11
527 3251 3.384146 CCATGCATTGTACATGCCCTTTA 59.616 43.478 20.37 8.07 42.89 1.85
539 3263 9.210329 TGTACATGCCCTTTATATACAATTACG 57.790 33.333 0.00 0.00 0.00 3.18
549 3273 8.556213 TTTATATACAATTACGGATGGGAAGC 57.444 34.615 0.00 0.00 0.00 3.86
573 3304 1.533625 GCATTTGCAGGAGGTACACA 58.466 50.000 0.00 0.00 41.59 3.72
574 3305 1.470098 GCATTTGCAGGAGGTACACAG 59.530 52.381 0.00 0.00 41.59 3.66
575 3306 2.783135 CATTTGCAGGAGGTACACAGT 58.217 47.619 0.00 0.00 0.00 3.55
585 3316 3.995048 GGAGGTACACAGTTCTGCTTAAC 59.005 47.826 0.00 0.00 0.00 2.01
623 5085 2.143925 ACTCTGCAAGTAAACGAAGCC 58.856 47.619 0.00 0.00 36.07 4.35
665 5128 3.429207 GGACAACTACGTCAGAGCTTTTC 59.571 47.826 0.00 0.00 37.66 2.29
666 5129 3.391049 ACAACTACGTCAGAGCTTTTCC 58.609 45.455 0.00 0.00 0.00 3.13
677 5140 7.393515 ACGTCAGAGCTTTTCCCTATTTTAATT 59.606 33.333 0.00 0.00 0.00 1.40
686 5149 9.741647 CTTTTCCCTATTTTAATTCATCAGAGC 57.258 33.333 0.00 0.00 0.00 4.09
717 5184 7.534400 TTTCGGAAGGAAAGGTCGCAAGATA 62.534 44.000 0.00 0.00 43.97 1.98
773 5240 1.999002 GGAAGGGGTCCGGATCCAA 60.999 63.158 34.48 0.00 36.40 3.53
776 5243 3.090532 GGGGTCCGGATCCAAGCT 61.091 66.667 34.48 0.00 31.60 3.74
806 5273 4.326255 CAAGACATGCCCACCTCC 57.674 61.111 0.00 0.00 0.00 4.30
807 5274 1.379044 CAAGACATGCCCACCTCCC 60.379 63.158 0.00 0.00 0.00 4.30
808 5275 1.852157 AAGACATGCCCACCTCCCA 60.852 57.895 0.00 0.00 0.00 4.37
809 5276 2.044946 GACATGCCCACCTCCCAC 60.045 66.667 0.00 0.00 0.00 4.61
810 5277 3.976701 GACATGCCCACCTCCCACG 62.977 68.421 0.00 0.00 0.00 4.94
815 5282 3.000819 CCCACCTCCCACGCAGTA 61.001 66.667 0.00 0.00 41.61 2.74
816 5283 2.264794 CCACCTCCCACGCAGTAC 59.735 66.667 0.00 0.00 41.61 2.73
835 5302 8.543071 GCAGTACGAACCAAATAATCAATAAC 57.457 34.615 0.00 0.00 0.00 1.89
843 5310 9.994432 GAACCAAATAATCAATAACTCTGTCAG 57.006 33.333 0.00 0.00 0.00 3.51
844 5311 9.739276 AACCAAATAATCAATAACTCTGTCAGA 57.261 29.630 1.78 1.78 0.00 3.27
845 5312 9.167311 ACCAAATAATCAATAACTCTGTCAGAC 57.833 33.333 0.00 0.00 0.00 3.51
846 5313 9.388506 CCAAATAATCAATAACTCTGTCAGACT 57.611 33.333 0.00 0.00 0.00 3.24
861 5341 0.108138 AGACTGTCATGGGCGCTAAC 60.108 55.000 7.64 0.00 0.00 2.34
869 5349 1.056700 ATGGGCGCTAACCTCCATCT 61.057 55.000 7.64 0.00 35.26 2.90
873 5353 0.530870 GCGCTAACCTCCATCTCCAC 60.531 60.000 0.00 0.00 0.00 4.02
917 5398 3.061848 GCTTAAGCTGCCCCGCAA 61.062 61.111 20.38 0.00 38.41 4.85
918 5399 3.056313 GCTTAAGCTGCCCCGCAAG 62.056 63.158 20.38 0.00 38.41 4.01
2017 7331 1.268899 ACCCGAGTACTTCAACTGTCG 59.731 52.381 0.00 0.00 0.00 4.35
2065 7399 7.279313 GCAATTTGGCATCATCAGTAGATTTTT 59.721 33.333 0.00 0.00 30.20 1.94
2384 7826 4.336532 ACGTTCGGAATTTAAGCATGTC 57.663 40.909 0.00 0.00 0.00 3.06
2385 7827 3.749088 ACGTTCGGAATTTAAGCATGTCA 59.251 39.130 0.00 0.00 0.00 3.58
2386 7828 4.394920 ACGTTCGGAATTTAAGCATGTCAT 59.605 37.500 0.00 0.00 0.00 3.06
2389 7831 4.780815 TCGGAATTTAAGCATGTCATCCT 58.219 39.130 0.00 0.00 0.00 3.24
2390 7832 5.924356 TCGGAATTTAAGCATGTCATCCTA 58.076 37.500 0.00 0.00 0.00 2.94
2428 7870 0.798776 CTTTAGTTGCTGCGAGGTGG 59.201 55.000 0.00 0.00 0.00 4.61
2432 7874 2.282391 TTGCTGCGAGGTGGCAAT 60.282 55.556 0.00 0.00 43.39 3.56
2446 7888 5.849510 AGGTGGCAATTTTAGTTGTTAACC 58.150 37.500 2.48 0.00 32.72 2.85
2450 7892 6.147000 GTGGCAATTTTAGTTGTTAACCCATG 59.853 38.462 2.48 0.00 0.00 3.66
2504 7946 4.420522 AATTGCCATGTTTGTCAACCTT 57.579 36.364 0.00 0.00 31.02 3.50
2505 7947 5.543507 AATTGCCATGTTTGTCAACCTTA 57.456 34.783 0.00 0.00 31.02 2.69
2506 7948 5.743636 ATTGCCATGTTTGTCAACCTTAT 57.256 34.783 0.00 0.00 31.02 1.73
2507 7949 4.782019 TGCCATGTTTGTCAACCTTATC 57.218 40.909 0.00 0.00 31.02 1.75
2521 7963 9.199982 TGTCAACCTTATCTTAACTAAAGTTCG 57.800 33.333 0.00 0.00 39.31 3.95
2522 7964 8.654215 GTCAACCTTATCTTAACTAAAGTTCGG 58.346 37.037 0.00 0.00 39.31 4.30
2525 7967 9.955102 AACCTTATCTTAACTAAAGTTCGGATT 57.045 29.630 12.47 0.00 39.31 3.01
2526 7968 9.379791 ACCTTATCTTAACTAAAGTTCGGATTG 57.620 33.333 12.47 8.38 39.31 2.67
2531 7990 4.701956 AACTAAAGTTCGGATTGCCATG 57.298 40.909 0.00 0.00 31.64 3.66
2545 8004 7.768120 TCGGATTGCCATGCTTAAAATTTAAAT 59.232 29.630 0.00 0.00 0.00 1.40
2796 8279 2.431942 GTCACCGCCGATGACGTT 60.432 61.111 0.00 0.00 37.34 3.99
2889 8372 3.518998 CACGAGTCCTCCGCCGAT 61.519 66.667 0.00 0.00 0.00 4.18
3017 8500 4.814294 GCGGTTCGAGGACGGCAT 62.814 66.667 13.15 0.00 43.07 4.40
3141 8624 1.006571 GTGCTTCGACTGGGAACGA 60.007 57.895 0.00 0.00 36.75 3.85
3148 8631 1.802337 CGACTGGGAACGAGTGGACA 61.802 60.000 0.00 0.00 0.00 4.02
3150 8633 1.293498 CTGGGAACGAGTGGACAGG 59.707 63.158 0.00 0.00 0.00 4.00
3266 8750 4.202503 TGTCCTTCAAAAGCTCTGAGGATT 60.203 41.667 6.83 0.00 0.00 3.01
3282 8766 4.012374 GAGGATTGAACTTCTTGGCATCA 58.988 43.478 0.00 0.00 0.00 3.07
3284 8768 3.760684 GGATTGAACTTCTTGGCATCACT 59.239 43.478 0.00 0.00 0.00 3.41
3286 8770 4.572985 TTGAACTTCTTGGCATCACTTG 57.427 40.909 0.00 0.00 0.00 3.16
3314 8798 3.510360 AGTAGTTTCCAGTAGCATCGTGT 59.490 43.478 0.00 0.00 0.00 4.49
3328 8812 0.108377 TCGTGTCGTATGCATGGCTT 60.108 50.000 10.16 0.00 0.00 4.35
3346 8913 5.189928 TGGCTTGATACCGTTTTGATGTAT 58.810 37.500 0.00 0.00 0.00 2.29
3347 8914 5.650266 TGGCTTGATACCGTTTTGATGTATT 59.350 36.000 0.00 0.00 0.00 1.89
3372 8939 3.951979 AAACTTGTTGCGACTTCAGAG 57.048 42.857 5.50 0.00 0.00 3.35
3426 8993 3.009033 TGCACAAGCTAGGGTCTTTGTAT 59.991 43.478 0.00 0.00 42.74 2.29
3427 8994 4.224147 TGCACAAGCTAGGGTCTTTGTATA 59.776 41.667 0.00 0.00 42.74 1.47
3515 9082 1.228552 AGAAACGCCAGCCCAATGT 60.229 52.632 0.00 0.00 0.00 2.71
3541 9109 1.198867 CGCAAATCCAAATCACGTCCA 59.801 47.619 0.00 0.00 0.00 4.02
3546 9114 2.465860 TCCAAATCACGTCCATTCGT 57.534 45.000 0.00 0.00 45.10 3.85
3558 9126 0.595053 CCATTCGTGATCCGTCCGAG 60.595 60.000 3.97 0.00 37.94 4.63
3573 9141 2.491621 GAGCGCATTTTCAGCCCC 59.508 61.111 11.47 0.00 0.00 5.80
3585 9153 4.456662 TTTCAGCCCCAACTTACCTTTA 57.543 40.909 0.00 0.00 0.00 1.85
3586 9154 4.456662 TTCAGCCCCAACTTACCTTTAA 57.543 40.909 0.00 0.00 0.00 1.52
3587 9155 3.758425 TCAGCCCCAACTTACCTTTAAC 58.242 45.455 0.00 0.00 0.00 2.01
3588 9156 2.823747 CAGCCCCAACTTACCTTTAACC 59.176 50.000 0.00 0.00 0.00 2.85
3590 9158 3.918270 AGCCCCAACTTACCTTTAACCTA 59.082 43.478 0.00 0.00 0.00 3.08
3591 9159 4.542931 AGCCCCAACTTACCTTTAACCTAT 59.457 41.667 0.00 0.00 0.00 2.57
3592 9160 4.643334 GCCCCAACTTACCTTTAACCTATG 59.357 45.833 0.00 0.00 0.00 2.23
3593 9161 5.808710 GCCCCAACTTACCTTTAACCTATGT 60.809 44.000 0.00 0.00 0.00 2.29
3594 9162 5.884232 CCCCAACTTACCTTTAACCTATGTC 59.116 44.000 0.00 0.00 0.00 3.06
3596 9164 7.092757 CCCCAACTTACCTTTAACCTATGTCTA 60.093 40.741 0.00 0.00 0.00 2.59
3597 9165 8.491958 CCCAACTTACCTTTAACCTATGTCTAT 58.508 37.037 0.00 0.00 0.00 1.98
3617 9189 1.198713 AAGGACATGAGATGGACGCT 58.801 50.000 0.00 0.00 33.60 5.07
3622 9194 1.737029 ACATGAGATGGACGCTTCACG 60.737 52.381 0.00 0.00 40.71 4.35
3640 9212 1.238439 CGCATCCTTTTGGTGTCTGT 58.762 50.000 0.00 0.00 41.38 3.41
3719 9291 2.990479 GGAATCGTCCAGGCCACT 59.010 61.111 5.01 0.00 44.26 4.00
3785 9357 4.324874 CCCATTTCTCCTTTCTCACTCCAT 60.325 45.833 0.00 0.00 0.00 3.41
3793 9365 6.213397 TCTCCTTTCTCACTCCATTCAACATA 59.787 38.462 0.00 0.00 0.00 2.29
3797 9369 7.012138 CCTTTCTCACTCCATTCAACATATGAG 59.988 40.741 10.38 1.52 39.77 2.90
3801 9373 4.637091 CACTCCATTCAACATATGAGCACA 59.363 41.667 10.38 0.00 39.77 4.57
3814 9386 3.712881 GCACACGTGTTCCCTCGC 61.713 66.667 20.79 14.67 0.00 5.03
4091 9663 6.687958 CGAAGACTTAGATCTTTCGTAGTTCC 59.312 42.308 15.24 0.00 39.08 3.62
4240 9813 2.254471 TCCAGAGTCGGACAAGTCG 58.746 57.895 11.27 0.00 0.00 4.18
4310 9883 1.395608 CGTTGGAACACGTGTCAGTTT 59.604 47.619 23.61 5.42 39.29 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.757118 GCTGACACTCCTACATGGCTA 59.243 52.381 0.00 0.00 35.26 3.93
2 3 0.539051 GCTGACACTCCTACATGGCT 59.461 55.000 0.00 0.00 35.26 4.75
3 4 0.462759 GGCTGACACTCCTACATGGC 60.463 60.000 0.00 0.00 35.26 4.40
4 5 0.904649 TGGCTGACACTCCTACATGG 59.095 55.000 0.00 0.00 37.10 3.66
31 32 1.202099 TCCATAAGGCCCGTTCCACA 61.202 55.000 0.00 0.00 33.74 4.17
34 35 2.882761 GTTTATCCATAAGGCCCGTTCC 59.117 50.000 0.00 0.00 33.74 3.62
36 37 2.423803 GGGTTTATCCATAAGGCCCGTT 60.424 50.000 0.00 0.00 38.11 4.44
39 40 1.905637 CGGGTTTATCCATAAGGCCC 58.094 55.000 0.00 9.40 36.63 5.80
57 58 0.872388 GGACCACCACAAGTTAAGCG 59.128 55.000 0.00 0.00 35.97 4.68
233 2951 1.144708 TCATTGTTTCAGCCAGGACCA 59.855 47.619 0.00 0.00 0.00 4.02
252 2970 1.540267 TCTACACAGCTGACCGAGTTC 59.460 52.381 23.35 0.00 0.00 3.01
277 2995 0.907486 TGGGACTCAATCTCTGCCTG 59.093 55.000 0.00 0.00 0.00 4.85
280 2998 0.908198 AGGTGGGACTCAATCTCTGC 59.092 55.000 0.00 0.00 0.00 4.26
395 3119 8.929260 TTTTATTATGAGACATCTGCATCCAT 57.071 30.769 0.00 0.00 0.00 3.41
418 3142 6.717084 GCAGGATCCAGCCTACTATTATTTTT 59.283 38.462 18.02 0.00 36.22 1.94
419 3143 6.183361 TGCAGGATCCAGCCTACTATTATTTT 60.183 38.462 24.79 0.00 36.22 1.82
420 3144 5.310594 TGCAGGATCCAGCCTACTATTATTT 59.689 40.000 24.79 0.00 36.22 1.40
421 3145 4.846367 TGCAGGATCCAGCCTACTATTATT 59.154 41.667 24.79 0.00 36.22 1.40
422 3146 4.429505 TGCAGGATCCAGCCTACTATTAT 58.570 43.478 24.79 0.00 36.22 1.28
423 3147 3.856900 TGCAGGATCCAGCCTACTATTA 58.143 45.455 24.79 2.10 36.22 0.98
424 3148 2.694397 TGCAGGATCCAGCCTACTATT 58.306 47.619 24.79 0.00 36.22 1.73
425 3149 2.405618 TGCAGGATCCAGCCTACTAT 57.594 50.000 24.79 0.00 36.22 2.12
426 3150 2.158249 AGATGCAGGATCCAGCCTACTA 60.158 50.000 24.79 7.58 36.22 1.82
427 3151 1.055040 GATGCAGGATCCAGCCTACT 58.945 55.000 24.79 8.29 36.22 2.57
428 3152 1.055040 AGATGCAGGATCCAGCCTAC 58.945 55.000 24.79 15.69 36.22 3.18
429 3153 1.419012 CAAGATGCAGGATCCAGCCTA 59.581 52.381 24.79 9.07 36.22 3.93
430 3154 0.183014 CAAGATGCAGGATCCAGCCT 59.817 55.000 24.79 16.27 39.37 4.58
431 3155 1.453762 GCAAGATGCAGGATCCAGCC 61.454 60.000 24.79 11.50 44.26 4.85
432 3156 2.031360 GCAAGATGCAGGATCCAGC 58.969 57.895 21.57 21.57 44.26 4.85
442 3166 1.134159 ACCAGATCCTCTGCAAGATGC 60.134 52.381 0.00 0.00 45.62 3.91
443 3167 2.943690 CAACCAGATCCTCTGCAAGATG 59.056 50.000 0.00 0.00 45.62 2.90
444 3168 2.842496 TCAACCAGATCCTCTGCAAGAT 59.158 45.455 0.00 0.00 45.62 2.40
445 3169 2.027745 GTCAACCAGATCCTCTGCAAGA 60.028 50.000 0.00 0.00 42.98 3.02
446 3170 2.289882 TGTCAACCAGATCCTCTGCAAG 60.290 50.000 0.00 0.00 42.98 4.01
447 3171 1.699083 TGTCAACCAGATCCTCTGCAA 59.301 47.619 0.00 0.00 42.98 4.08
448 3172 1.351076 TGTCAACCAGATCCTCTGCA 58.649 50.000 0.00 0.00 42.98 4.41
449 3173 2.559440 GATGTCAACCAGATCCTCTGC 58.441 52.381 0.00 0.00 42.98 4.26
450 3174 2.502947 TGGATGTCAACCAGATCCTCTG 59.497 50.000 0.00 0.00 43.91 3.35
451 3175 2.837947 TGGATGTCAACCAGATCCTCT 58.162 47.619 0.00 0.00 37.20 3.69
452 3176 3.634397 TTGGATGTCAACCAGATCCTC 57.366 47.619 1.70 0.00 38.70 3.71
453 3177 3.432749 CGATTGGATGTCAACCAGATCCT 60.433 47.826 1.70 0.00 38.31 3.24
454 3178 2.874701 CGATTGGATGTCAACCAGATCC 59.125 50.000 1.70 0.00 38.31 3.36
455 3179 3.535561 ACGATTGGATGTCAACCAGATC 58.464 45.455 1.70 7.73 38.31 2.75
456 3180 3.634397 ACGATTGGATGTCAACCAGAT 57.366 42.857 1.70 0.14 38.31 2.90
457 3181 3.259625 TGTACGATTGGATGTCAACCAGA 59.740 43.478 1.70 0.00 38.31 3.86
458 3182 3.595173 TGTACGATTGGATGTCAACCAG 58.405 45.455 1.70 0.00 38.31 4.00
459 3183 3.686916 TGTACGATTGGATGTCAACCA 57.313 42.857 0.00 0.00 38.31 3.67
460 3184 3.312421 CCATGTACGATTGGATGTCAACC 59.688 47.826 3.81 0.00 38.31 3.77
461 3185 3.242739 GCCATGTACGATTGGATGTCAAC 60.243 47.826 12.15 0.00 38.31 3.18
462 3186 2.942376 GCCATGTACGATTGGATGTCAA 59.058 45.455 12.15 0.00 40.01 3.18
463 3187 2.093235 TGCCATGTACGATTGGATGTCA 60.093 45.455 12.15 0.18 34.81 3.58
464 3188 2.560504 TGCCATGTACGATTGGATGTC 58.439 47.619 12.15 0.00 34.81 3.06
465 3189 2.708216 TGCCATGTACGATTGGATGT 57.292 45.000 12.15 0.00 34.81 3.06
466 3190 4.318332 AGTATGCCATGTACGATTGGATG 58.682 43.478 12.15 0.00 34.81 3.51
467 3191 4.623932 AGTATGCCATGTACGATTGGAT 57.376 40.909 12.15 6.52 34.81 3.41
468 3192 4.830600 TCTAGTATGCCATGTACGATTGGA 59.169 41.667 12.15 0.62 34.81 3.53
469 3193 4.923871 GTCTAGTATGCCATGTACGATTGG 59.076 45.833 5.23 5.23 36.03 3.16
470 3194 5.528870 TGTCTAGTATGCCATGTACGATTG 58.471 41.667 0.00 0.00 0.00 2.67
471 3195 5.784578 TGTCTAGTATGCCATGTACGATT 57.215 39.130 0.00 0.00 0.00 3.34
472 3196 5.476945 TGATGTCTAGTATGCCATGTACGAT 59.523 40.000 0.00 0.00 0.00 3.73
473 3197 4.825085 TGATGTCTAGTATGCCATGTACGA 59.175 41.667 0.00 0.00 0.00 3.43
474 3198 4.917998 GTGATGTCTAGTATGCCATGTACG 59.082 45.833 0.00 0.00 0.00 3.67
475 3199 4.917998 CGTGATGTCTAGTATGCCATGTAC 59.082 45.833 0.00 0.00 0.00 2.90
476 3200 4.583073 ACGTGATGTCTAGTATGCCATGTA 59.417 41.667 0.00 0.00 0.00 2.29
477 3201 3.384789 ACGTGATGTCTAGTATGCCATGT 59.615 43.478 0.00 0.00 0.00 3.21
478 3202 3.982475 ACGTGATGTCTAGTATGCCATG 58.018 45.455 0.00 0.00 0.00 3.66
479 3203 4.672587 AACGTGATGTCTAGTATGCCAT 57.327 40.909 0.00 0.00 0.00 4.40
480 3204 4.037565 CCTAACGTGATGTCTAGTATGCCA 59.962 45.833 0.00 0.00 0.00 4.92
481 3205 4.547532 CCTAACGTGATGTCTAGTATGCC 58.452 47.826 0.00 0.00 0.00 4.40
482 3206 4.547532 CCCTAACGTGATGTCTAGTATGC 58.452 47.826 0.00 0.00 0.00 3.14
483 3207 4.547532 GCCCTAACGTGATGTCTAGTATG 58.452 47.826 0.00 0.00 0.00 2.39
484 3208 3.573110 GGCCCTAACGTGATGTCTAGTAT 59.427 47.826 0.00 0.00 0.00 2.12
485 3209 2.954318 GGCCCTAACGTGATGTCTAGTA 59.046 50.000 0.00 0.00 0.00 1.82
486 3210 1.755380 GGCCCTAACGTGATGTCTAGT 59.245 52.381 0.00 0.00 0.00 2.57
487 3211 1.754803 TGGCCCTAACGTGATGTCTAG 59.245 52.381 0.00 0.00 0.00 2.43
488 3212 1.855295 TGGCCCTAACGTGATGTCTA 58.145 50.000 0.00 0.00 0.00 2.59
489 3213 1.134401 CATGGCCCTAACGTGATGTCT 60.134 52.381 0.00 0.00 0.00 3.41
490 3214 1.299541 CATGGCCCTAACGTGATGTC 58.700 55.000 0.00 0.00 0.00 3.06
491 3215 0.748005 GCATGGCCCTAACGTGATGT 60.748 55.000 0.00 0.00 0.00 3.06
492 3216 0.747644 TGCATGGCCCTAACGTGATG 60.748 55.000 0.00 0.00 0.00 3.07
493 3217 0.183492 ATGCATGGCCCTAACGTGAT 59.817 50.000 0.00 0.00 0.00 3.06
494 3218 0.034574 AATGCATGGCCCTAACGTGA 60.035 50.000 0.00 0.00 0.00 4.35
495 3219 0.101040 CAATGCATGGCCCTAACGTG 59.899 55.000 0.00 0.00 0.00 4.49
496 3220 0.323360 ACAATGCATGGCCCTAACGT 60.323 50.000 0.00 0.00 0.00 3.99
497 3221 1.333619 GTACAATGCATGGCCCTAACG 59.666 52.381 0.00 0.00 0.00 3.18
498 3222 2.374184 TGTACAATGCATGGCCCTAAC 58.626 47.619 0.00 0.00 0.00 2.34
499 3223 2.816777 TGTACAATGCATGGCCCTAA 57.183 45.000 0.00 0.00 0.00 2.69
500 3224 2.585330 CATGTACAATGCATGGCCCTA 58.415 47.619 0.00 0.00 39.82 3.53
501 3225 1.405872 CATGTACAATGCATGGCCCT 58.594 50.000 0.00 0.00 39.82 5.19
502 3226 0.249573 GCATGTACAATGCATGGCCC 60.250 55.000 19.12 0.00 44.00 5.80
503 3227 3.277652 GCATGTACAATGCATGGCC 57.722 52.632 19.12 0.00 44.00 5.36
505 3229 1.405872 AGGGCATGTACAATGCATGG 58.594 50.000 22.92 0.00 46.21 3.66
506 3230 3.530265 AAAGGGCATGTACAATGCATG 57.470 42.857 22.92 9.91 46.21 4.06
507 3231 7.669304 TGTATATAAAGGGCATGTACAATGCAT 59.331 33.333 22.92 14.12 46.21 3.96
508 3232 7.001073 TGTATATAAAGGGCATGTACAATGCA 58.999 34.615 22.92 7.69 46.21 3.96
509 3233 7.447374 TGTATATAAAGGGCATGTACAATGC 57.553 36.000 17.01 17.01 43.85 3.56
513 3237 9.210329 CGTAATTGTATATAAAGGGCATGTACA 57.790 33.333 0.00 0.00 30.84 2.90
514 3238 8.662141 CCGTAATTGTATATAAAGGGCATGTAC 58.338 37.037 0.00 0.00 0.00 2.90
515 3239 8.595421 TCCGTAATTGTATATAAAGGGCATGTA 58.405 33.333 0.00 0.00 0.00 2.29
516 3240 7.455058 TCCGTAATTGTATATAAAGGGCATGT 58.545 34.615 0.00 0.00 0.00 3.21
517 3241 7.915293 TCCGTAATTGTATATAAAGGGCATG 57.085 36.000 0.00 0.00 0.00 4.06
518 3242 7.556275 CCATCCGTAATTGTATATAAAGGGCAT 59.444 37.037 0.00 0.00 0.00 4.40
519 3243 6.882140 CCATCCGTAATTGTATATAAAGGGCA 59.118 38.462 0.00 0.00 0.00 5.36
520 3244 6.317893 CCCATCCGTAATTGTATATAAAGGGC 59.682 42.308 0.00 0.00 0.00 5.19
521 3245 7.626390 TCCCATCCGTAATTGTATATAAAGGG 58.374 38.462 0.00 0.00 0.00 3.95
522 3246 9.162764 CTTCCCATCCGTAATTGTATATAAAGG 57.837 37.037 0.00 0.00 0.00 3.11
523 3247 8.665685 GCTTCCCATCCGTAATTGTATATAAAG 58.334 37.037 0.00 0.00 0.00 1.85
524 3248 7.332430 CGCTTCCCATCCGTAATTGTATATAAA 59.668 37.037 0.00 0.00 0.00 1.40
525 3249 6.814644 CGCTTCCCATCCGTAATTGTATATAA 59.185 38.462 0.00 0.00 0.00 0.98
526 3250 6.153170 TCGCTTCCCATCCGTAATTGTATATA 59.847 38.462 0.00 0.00 0.00 0.86
527 3251 5.046878 TCGCTTCCCATCCGTAATTGTATAT 60.047 40.000 0.00 0.00 0.00 0.86
539 3263 1.035139 AATGCAATCGCTTCCCATCC 58.965 50.000 0.00 0.00 39.64 3.51
571 3302 5.359576 TGGTGAAATTGTTAAGCAGAACTGT 59.640 36.000 3.77 0.00 0.00 3.55
572 3303 5.687285 GTGGTGAAATTGTTAAGCAGAACTG 59.313 40.000 0.00 0.00 0.00 3.16
573 3304 5.594317 AGTGGTGAAATTGTTAAGCAGAACT 59.406 36.000 2.87 0.00 0.00 3.01
574 3305 5.831997 AGTGGTGAAATTGTTAAGCAGAAC 58.168 37.500 0.00 0.00 0.00 3.01
575 3306 6.127479 ACAAGTGGTGAAATTGTTAAGCAGAA 60.127 34.615 0.00 0.00 33.49 3.02
585 3316 6.149308 TGCAGAGTATACAAGTGGTGAAATTG 59.851 38.462 5.50 0.00 0.00 2.32
665 5128 8.688747 AGAAGCTCTGATGAATTAAAATAGGG 57.311 34.615 0.00 0.00 0.00 3.53
666 5129 9.947669 CAAGAAGCTCTGATGAATTAAAATAGG 57.052 33.333 0.00 0.00 0.00 2.57
677 5140 3.006859 TCCGAAACAAGAAGCTCTGATGA 59.993 43.478 0.00 0.00 0.00 2.92
686 5149 3.883489 ACCTTTCCTTCCGAAACAAGAAG 59.117 43.478 0.00 0.00 35.49 2.85
717 5184 2.504367 CAACTCGAATTGGGGTTCTGT 58.496 47.619 2.27 0.00 0.00 3.41
798 5265 3.000819 TACTGCGTGGGAGGTGGG 61.001 66.667 0.00 0.00 0.00 4.61
800 5267 2.126071 CGTACTGCGTGGGAGGTG 60.126 66.667 0.00 0.00 35.54 4.00
801 5268 1.904865 TTCGTACTGCGTGGGAGGT 60.905 57.895 0.00 0.00 42.13 3.85
802 5269 1.445582 GTTCGTACTGCGTGGGAGG 60.446 63.158 0.00 0.00 42.13 4.30
804 5271 1.746322 TTGGTTCGTACTGCGTGGGA 61.746 55.000 0.00 0.00 42.13 4.37
805 5272 0.881159 TTTGGTTCGTACTGCGTGGG 60.881 55.000 0.00 0.00 42.13 4.61
806 5273 1.153353 ATTTGGTTCGTACTGCGTGG 58.847 50.000 0.00 0.00 42.13 4.94
807 5274 4.092237 TGATTATTTGGTTCGTACTGCGTG 59.908 41.667 0.00 0.00 42.13 5.34
808 5275 4.247258 TGATTATTTGGTTCGTACTGCGT 58.753 39.130 0.00 0.00 42.13 5.24
809 5276 4.850859 TGATTATTTGGTTCGTACTGCG 57.149 40.909 0.00 0.00 43.01 5.18
810 5277 8.395633 AGTTATTGATTATTTGGTTCGTACTGC 58.604 33.333 0.00 0.00 0.00 4.40
811 5278 9.916397 GAGTTATTGATTATTTGGTTCGTACTG 57.084 33.333 0.00 0.00 0.00 2.74
812 5279 9.886132 AGAGTTATTGATTATTTGGTTCGTACT 57.114 29.630 0.00 0.00 0.00 2.73
813 5280 9.916397 CAGAGTTATTGATTATTTGGTTCGTAC 57.084 33.333 0.00 0.00 0.00 3.67
814 5281 9.661563 ACAGAGTTATTGATTATTTGGTTCGTA 57.338 29.630 0.00 0.00 0.00 3.43
815 5282 8.561738 ACAGAGTTATTGATTATTTGGTTCGT 57.438 30.769 0.00 0.00 0.00 3.85
816 5283 8.664798 TGACAGAGTTATTGATTATTTGGTTCG 58.335 33.333 0.00 0.00 0.00 3.95
817 5284 9.994432 CTGACAGAGTTATTGATTATTTGGTTC 57.006 33.333 0.00 0.00 0.00 3.62
818 5285 9.739276 TCTGACAGAGTTATTGATTATTTGGTT 57.261 29.630 0.00 0.00 0.00 3.67
819 5286 9.167311 GTCTGACAGAGTTATTGATTATTTGGT 57.833 33.333 5.10 0.00 0.00 3.67
820 5287 9.388506 AGTCTGACAGAGTTATTGATTATTTGG 57.611 33.333 5.10 0.00 0.00 3.28
822 5289 9.950496 ACAGTCTGACAGAGTTATTGATTATTT 57.050 29.630 10.22 0.00 0.00 1.40
823 5290 9.593134 GACAGTCTGACAGAGTTATTGATTATT 57.407 33.333 10.22 0.00 0.00 1.40
824 5291 8.753133 TGACAGTCTGACAGAGTTATTGATTAT 58.247 33.333 10.22 0.00 0.00 1.28
825 5292 8.122472 TGACAGTCTGACAGAGTTATTGATTA 57.878 34.615 10.22 0.00 0.00 1.75
826 5293 6.997655 TGACAGTCTGACAGAGTTATTGATT 58.002 36.000 10.22 0.00 0.00 2.57
827 5294 6.596309 TGACAGTCTGACAGAGTTATTGAT 57.404 37.500 10.22 0.00 0.00 2.57
828 5295 6.393171 CATGACAGTCTGACAGAGTTATTGA 58.607 40.000 10.22 0.00 0.00 2.57
829 5296 5.579904 CCATGACAGTCTGACAGAGTTATTG 59.420 44.000 10.22 6.26 0.00 1.90
835 5302 1.405256 GCCCATGACAGTCTGACAGAG 60.405 57.143 5.10 3.93 0.00 3.35
843 5310 1.090052 GGTTAGCGCCCATGACAGTC 61.090 60.000 2.29 0.00 0.00 3.51
844 5311 1.078426 GGTTAGCGCCCATGACAGT 60.078 57.895 2.29 0.00 0.00 3.55
845 5312 0.811616 GAGGTTAGCGCCCATGACAG 60.812 60.000 2.29 0.00 0.00 3.51
846 5313 1.220749 GAGGTTAGCGCCCATGACA 59.779 57.895 2.29 0.00 0.00 3.58
847 5314 1.523938 GGAGGTTAGCGCCCATGAC 60.524 63.158 2.29 0.00 0.00 3.06
861 5341 2.005960 GACGTCCGTGGAGATGGAGG 62.006 65.000 3.51 0.00 45.24 4.30
869 5349 2.994995 ATGCCTGACGTCCGTGGA 60.995 61.111 14.12 2.77 0.00 4.02
911 5392 4.060038 CTTGGCTTGCCTTGCGGG 62.060 66.667 13.18 0.00 38.36 6.13
919 5400 2.951101 ATGGCTTGGCTTGGCTTGC 61.951 57.895 5.64 0.31 0.00 4.01
949 5435 0.239082 TATACTGTATCACGCGCCGG 59.761 55.000 5.73 0.00 0.00 6.13
960 5446 2.608593 TGGCGGGCCTATATACTGTA 57.391 50.000 11.55 0.00 36.94 2.74
961 5447 1.555075 CATGGCGGGCCTATATACTGT 59.445 52.381 11.55 0.00 36.94 3.55
962 5448 1.743772 GCATGGCGGGCCTATATACTG 60.744 57.143 11.55 0.00 36.94 2.74
963 5449 0.541863 GCATGGCGGGCCTATATACT 59.458 55.000 11.55 0.00 36.94 2.12
964 5450 0.251916 TGCATGGCGGGCCTATATAC 59.748 55.000 11.55 0.00 36.94 1.47
1239 5771 4.116328 CCGCAGCGAGAAGACCGA 62.116 66.667 18.75 0.00 0.00 4.69
1779 6334 4.838152 CACCGTGGCCAGGATCCG 62.838 72.222 26.78 16.14 0.00 4.18
1949 6510 0.319555 GACTTACCGCACACAGAGCA 60.320 55.000 0.00 0.00 0.00 4.26
2017 7331 5.047377 TGCCAATGTCCTTAATGAAGAAACC 60.047 40.000 0.00 0.00 34.25 3.27
2197 7566 3.873952 GGATTCATCCAGCTAAGTGACAC 59.126 47.826 0.00 0.00 46.38 3.67
2345 7787 4.156455 ACGTTCGAGACCTATTAGGGTA 57.844 45.455 14.26 0.00 40.58 3.69
2363 7805 3.749088 TGACATGCTTAAATTCCGAACGT 59.251 39.130 0.00 0.00 0.00 3.99
2375 7817 7.967854 CGAAAAACATTTAGGATGACATGCTTA 59.032 33.333 15.16 2.91 31.56 3.09
2384 7826 8.184192 AGTTGCTATCGAAAAACATTTAGGATG 58.816 33.333 0.00 0.00 0.00 3.51
2385 7827 8.281212 AGTTGCTATCGAAAAACATTTAGGAT 57.719 30.769 0.00 0.00 0.00 3.24
2386 7828 7.681939 AGTTGCTATCGAAAAACATTTAGGA 57.318 32.000 0.00 0.00 0.00 2.94
2390 7832 9.744468 AACTAAAGTTGCTATCGAAAAACATTT 57.256 25.926 0.00 0.00 36.80 2.32
2428 7870 6.926272 TGTCATGGGTTAACAACTAAAATTGC 59.074 34.615 8.10 0.00 32.47 3.56
2476 7918 5.856156 TGACAAACATGGCAATTTTCTGAT 58.144 33.333 0.00 0.00 0.00 2.90
2504 7946 7.332557 TGGCAATCCGAACTTTAGTTAAGATA 58.667 34.615 0.00 0.00 38.56 1.98
2505 7947 6.177610 TGGCAATCCGAACTTTAGTTAAGAT 58.822 36.000 0.00 0.00 38.56 2.40
2506 7948 5.553123 TGGCAATCCGAACTTTAGTTAAGA 58.447 37.500 0.00 0.00 38.56 2.10
2507 7949 5.873179 TGGCAATCCGAACTTTAGTTAAG 57.127 39.130 0.00 0.00 38.56 1.85
2520 7962 6.900568 TTAAATTTTAAGCATGGCAATCCG 57.099 33.333 0.00 0.00 34.14 4.18
2521 7963 8.676401 ACATTTAAATTTTAAGCATGGCAATCC 58.324 29.630 13.95 0.00 0.00 3.01
2525 7967 8.295288 CCAAACATTTAAATTTTAAGCATGGCA 58.705 29.630 13.95 0.00 0.00 4.92
2526 7968 7.754475 CCCAAACATTTAAATTTTAAGCATGGC 59.246 33.333 13.95 0.00 0.00 4.40
2545 8004 4.013728 CCGGAACAGATAAATCCCAAACA 58.986 43.478 0.00 0.00 0.00 2.83
2796 8279 4.075793 AGGTAGCTGAGGCGGGGA 62.076 66.667 0.00 0.00 44.37 4.81
2889 8372 4.010224 TAGCCGCCGACCTTGCAA 62.010 61.111 0.00 0.00 0.00 4.08
2997 8480 3.441290 CCGTCCTCGAACCGCTCT 61.441 66.667 0.00 0.00 39.71 4.09
3141 8624 1.843376 CACCTCCACCCTGTCCACT 60.843 63.158 0.00 0.00 0.00 4.00
3148 8631 1.160870 TCATGTCCACCTCCACCCT 59.839 57.895 0.00 0.00 0.00 4.34
3150 8633 1.079127 CGTCATGTCCACCTCCACC 60.079 63.158 0.00 0.00 0.00 4.61
3266 8750 3.316029 CACAAGTGATGCCAAGAAGTTCA 59.684 43.478 5.50 0.00 0.00 3.18
3282 8766 5.609533 ACTGGAAACTACTGTACACAAGT 57.390 39.130 0.00 0.00 0.00 3.16
3284 8768 5.069383 TGCTACTGGAAACTACTGTACACAA 59.931 40.000 0.00 0.00 0.00 3.33
3286 8770 5.130292 TGCTACTGGAAACTACTGTACAC 57.870 43.478 0.00 0.00 0.00 2.90
3314 8798 2.766313 GGTATCAAGCCATGCATACGA 58.234 47.619 0.00 0.00 0.00 3.43
3346 8913 6.037720 TCTGAAGTCGCAACAAGTTTATTCAA 59.962 34.615 0.00 0.00 0.00 2.69
3347 8914 5.525745 TCTGAAGTCGCAACAAGTTTATTCA 59.474 36.000 0.00 0.00 0.00 2.57
3372 8939 5.242393 ACAGATGATGGCAAGGTTATTATGC 59.758 40.000 0.00 0.00 39.33 3.14
3427 8994 9.667607 CCCTAGGGATAATCATTATGATAGACT 57.332 37.037 24.99 5.78 34.83 3.24
3546 9114 2.572095 AAATGCGCTCGGACGGATCA 62.572 55.000 9.73 0.00 43.71 2.92
3547 9115 1.429148 AAAATGCGCTCGGACGGATC 61.429 55.000 9.73 0.00 43.71 3.36
3548 9116 1.429148 GAAAATGCGCTCGGACGGAT 61.429 55.000 9.73 0.00 46.64 4.18
3558 9126 1.737735 GTTGGGGCTGAAAATGCGC 60.738 57.895 0.00 0.00 41.70 6.09
3592 9160 5.704888 CGTCCATCTCATGTCCTTATAGAC 58.295 45.833 0.00 0.00 37.28 2.59
3593 9161 4.218635 GCGTCCATCTCATGTCCTTATAGA 59.781 45.833 0.00 0.00 0.00 1.98
3594 9162 4.219507 AGCGTCCATCTCATGTCCTTATAG 59.780 45.833 0.00 0.00 0.00 1.31
3596 9164 2.968574 AGCGTCCATCTCATGTCCTTAT 59.031 45.455 0.00 0.00 0.00 1.73
3597 9165 2.388735 AGCGTCCATCTCATGTCCTTA 58.611 47.619 0.00 0.00 0.00 2.69
3617 9189 1.606668 GACACCAAAAGGATGCGTGAA 59.393 47.619 0.00 0.00 0.00 3.18
3622 9194 2.485814 GAGACAGACACCAAAAGGATGC 59.514 50.000 0.00 0.00 0.00 3.91
3719 9291 4.054671 CACGCTTGCCATTTAAAAAGGAA 58.945 39.130 12.75 4.84 0.00 3.36
3756 9328 2.989571 AGAAAGGAGAAATGGGTGAGGT 59.010 45.455 0.00 0.00 0.00 3.85
3785 9357 3.398406 ACACGTGTGCTCATATGTTGAA 58.602 40.909 22.71 0.00 32.78 2.69
3793 9365 0.320771 GAGGGAACACGTGTGCTCAT 60.321 55.000 28.33 14.98 0.00 2.90
3797 9369 3.712881 GCGAGGGAACACGTGTGC 61.713 66.667 24.16 21.51 46.61 4.57
3801 9373 4.681978 GCTGGCGAGGGAACACGT 62.682 66.667 0.00 0.00 46.61 4.49
3814 9386 0.391661 ATGCACTTACAGTCGGCTGG 60.392 55.000 22.98 6.06 46.62 4.85
3847 9419 5.929992 TCGTCAATACTCCAAAACCAACTAG 59.070 40.000 0.00 0.00 0.00 2.57
4091 9663 8.383318 TCCTATGACTCAACAAAGAAGAAAAG 57.617 34.615 0.00 0.00 0.00 2.27
4162 9735 5.362430 AGGTTTTGGTTAAGCATCACTTCAA 59.638 36.000 8.40 0.00 39.97 2.69
4320 9893 2.940994 TTTGTCCGAAATGACCCTGA 57.059 45.000 0.00 0.00 34.25 3.86


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

AutoCloner maintained by Alex Coulton.