Multiple sequence alignment - TraesCS4B01G187700

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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 TraesCS4B01G187700 chr4B 100.000 3269 0 0 439 3707 408949291 408952559 0.000000e+00 6037.0
1 TraesCS4B01G187700 chr4B 100.000 218 0 0 1 218 408948853 408949070 1.600000e-108 403.0
2 TraesCS4B01G187700 chr4B 94.483 145 6 2 2958 3100 373995780 373995924 4.820000e-54 222.0
3 TraesCS4B01G187700 chr4B 93.103 145 9 1 2958 3102 545764428 545764571 1.040000e-50 211.0
4 TraesCS4B01G187700 chr4B 82.692 156 24 3 515 669 653736829 653736982 6.460000e-28 135.0
5 TraesCS4B01G187700 chr4D 94.935 2547 79 23 439 2953 328996733 328999261 0.000000e+00 3943.0
6 TraesCS4B01G187700 chr4D 84.615 559 52 21 3164 3707 328999421 328999960 3.280000e-145 525.0
7 TraesCS4B01G187700 chr4D 94.595 37 1 1 3104 3139 328999277 328999313 5.170000e-04 56.5
8 TraesCS4B01G187700 chr1B 95.544 2334 64 15 655 2953 135964762 135962434 0.000000e+00 3698.0
9 TraesCS4B01G187700 chr1B 91.246 297 18 4 3417 3707 135961342 135961048 7.460000e-107 398.0
10 TraesCS4B01G187700 chr1B 85.350 157 19 4 515 669 681008282 681008128 3.830000e-35 159.0
11 TraesCS4B01G187700 chr1B 97.059 34 0 1 3107 3139 135962415 135962382 5.170000e-04 56.5
12 TraesCS4B01G187700 chr4A 95.435 2300 66 14 688 2953 141132266 141129972 0.000000e+00 3629.0
13 TraesCS4B01G187700 chr4A 84.946 558 51 17 3164 3707 141125671 141125133 5.450000e-148 534.0
14 TraesCS4B01G187700 chr4A 92.544 228 5 2 688 903 141142601 141142374 2.150000e-82 316.0
15 TraesCS4B01G187700 chr4A 87.671 73 4 4 3107 3174 141125796 141125724 3.070000e-11 80.5
16 TraesCS4B01G187700 chr4A 90.385 52 5 0 613 664 656740286 656740235 6.640000e-08 69.4
17 TraesCS4B01G187700 chr2D 95.747 1975 58 14 995 2953 407227417 407225453 0.000000e+00 3158.0
18 TraesCS4B01G187700 chr2D 78.332 983 187 20 998 1970 43799877 43798911 2.450000e-171 612.0
19 TraesCS4B01G187700 chr2D 80.170 706 126 13 1970 2668 43798685 43797987 1.970000e-142 516.0
20 TraesCS4B01G187700 chr2D 84.258 559 54 20 3164 3707 407225292 407224753 7.100000e-142 514.0
21 TraesCS4B01G187700 chr2D 72.376 543 126 19 2015 2545 413778647 413778117 2.310000e-32 150.0
22 TraesCS4B01G187700 chr2D 97.059 34 0 1 3107 3139 407225434 407225401 5.170000e-04 56.5
23 TraesCS4B01G187700 chr2B 78.760 984 178 24 998 1970 68424478 68423515 6.760000e-177 630.0
24 TraesCS4B01G187700 chr2B 80.142 705 128 11 1970 2668 68423274 68422576 1.970000e-142 516.0
25 TraesCS4B01G187700 chr2B 72.560 543 125 19 2015 2545 486986804 486986274 4.960000e-34 156.0
26 TraesCS4B01G187700 chr2A 77.744 984 188 23 1001 1970 46115598 46114632 3.210000e-160 575.0
27 TraesCS4B01G187700 chr2A 79.915 707 126 14 1970 2668 46114418 46113720 4.270000e-139 505.0
28 TraesCS4B01G187700 chr2A 93.151 146 8 2 2958 3101 226553861 226553716 2.900000e-51 213.0
29 TraesCS4B01G187700 chrUn 91.246 297 18 4 3417 3707 377051861 377051567 7.460000e-107 398.0
30 TraesCS4B01G187700 chr7D 84.818 303 30 6 3405 3707 113715524 113715238 1.300000e-74 291.0
31 TraesCS4B01G187700 chr7B 85.821 268 30 3 3440 3707 73331919 73331660 1.010000e-70 278.0
32 TraesCS4B01G187700 chr7B 83.498 303 35 5 3405 3707 73234419 73234132 6.100000e-68 268.0
33 TraesCS4B01G187700 chr7B 91.333 150 10 2 2958 3104 367495882 367495733 6.280000e-48 202.0
34 TraesCS4B01G187700 chr3B 94.595 148 5 2 2958 3102 443348945 443348798 3.730000e-55 226.0
35 TraesCS4B01G187700 chr7A 80.573 314 37 10 3398 3707 118574718 118574425 1.730000e-53 220.0
36 TraesCS4B01G187700 chr6B 93.793 145 7 2 2958 3100 664459170 664459026 2.240000e-52 217.0
37 TraesCS4B01G187700 chr1A 93.289 149 7 2 2958 3103 530170114 530169966 2.240000e-52 217.0
38 TraesCS4B01G187700 chr1A 93.103 145 9 1 2958 3101 12264422 12264566 1.040000e-50 211.0
39 TraesCS4B01G187700 chr5B 93.197 147 7 2 2958 3101 440262809 440262955 2.900000e-51 213.0


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 TraesCS4B01G187700 chr4B 408948853 408952559 3706 False 3220.000000 6037 100.000000 1 3707 2 chr4B.!!$F4 3706
1 TraesCS4B01G187700 chr4D 328996733 328999960 3227 False 1508.166667 3943 91.381667 439 3707 3 chr4D.!!$F1 3268
2 TraesCS4B01G187700 chr1B 135961048 135964762 3714 True 1384.166667 3698 94.616333 655 3707 3 chr1B.!!$R2 3052
3 TraesCS4B01G187700 chr4A 141129972 141132266 2294 True 3629.000000 3629 95.435000 688 2953 1 chr4A.!!$R1 2265
4 TraesCS4B01G187700 chr4A 141125133 141125796 663 True 307.250000 534 86.308500 3107 3707 2 chr4A.!!$R4 600
5 TraesCS4B01G187700 chr2D 407224753 407227417 2664 True 1242.833333 3158 92.354667 995 3707 3 chr2D.!!$R3 2712
6 TraesCS4B01G187700 chr2D 43797987 43799877 1890 True 564.000000 612 79.251000 998 2668 2 chr2D.!!$R2 1670
7 TraesCS4B01G187700 chr2B 68422576 68424478 1902 True 573.000000 630 79.451000 998 2668 2 chr2B.!!$R2 1670
8 TraesCS4B01G187700 chr2A 46113720 46115598 1878 True 540.000000 575 78.829500 1001 2668 2 chr2A.!!$R2 1667

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
493 503 0.179171 CGAAAGGACTCGCGCTAAGA 60.179 55.0 5.56 0.0 31.04 2.10 F
2212 2504 0.465460 GGTGGTGTTCCAGAACTGCA 60.465 55.0 11.56 0.0 45.24 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2329 2621 1.197721 CATGTGGTCTTTGAACTCCGC 59.802 52.381 0.0 0.0 0.00 5.54 R
3373 3798 0.037590 TCCTCATGGGTTTTCACGGG 59.962 55.000 0.0 0.0 36.25 5.28 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
31 32 9.872721 AAAATTGGCTGAACATTTTCAAAAATT 57.127 22.222 0.00 0.75 41.34 1.82
35 36 7.583230 TGGCTGAACATTTTCAAAAATTATGC 58.417 30.769 0.00 0.00 41.34 3.14
36 37 7.228108 TGGCTGAACATTTTCAAAAATTATGCA 59.772 29.630 0.00 0.00 41.34 3.96
37 38 8.238631 GGCTGAACATTTTCAAAAATTATGCAT 58.761 29.630 3.79 3.79 41.34 3.96
148 149 8.989653 AAGAAAAACAAAGAATAAAACGGTGA 57.010 26.923 0.00 0.00 0.00 4.02
149 150 9.594478 AAGAAAAACAAAGAATAAAACGGTGAT 57.406 25.926 0.00 0.00 0.00 3.06
150 151 9.030301 AGAAAAACAAAGAATAAAACGGTGATG 57.970 29.630 0.00 0.00 0.00 3.07
151 152 8.934507 AAAAACAAAGAATAAAACGGTGATGA 57.065 26.923 0.00 0.00 0.00 2.92
152 153 8.934507 AAAACAAAGAATAAAACGGTGATGAA 57.065 26.923 0.00 0.00 0.00 2.57
153 154 8.574196 AAACAAAGAATAAAACGGTGATGAAG 57.426 30.769 0.00 0.00 0.00 3.02
154 155 7.504924 ACAAAGAATAAAACGGTGATGAAGA 57.495 32.000 0.00 0.00 0.00 2.87
155 156 7.936584 ACAAAGAATAAAACGGTGATGAAGAA 58.063 30.769 0.00 0.00 0.00 2.52
156 157 8.076178 ACAAAGAATAAAACGGTGATGAAGAAG 58.924 33.333 0.00 0.00 0.00 2.85
157 158 7.979444 AAGAATAAAACGGTGATGAAGAAGA 57.021 32.000 0.00 0.00 0.00 2.87
158 159 7.979444 AGAATAAAACGGTGATGAAGAAGAA 57.021 32.000 0.00 0.00 0.00 2.52
159 160 8.034058 AGAATAAAACGGTGATGAAGAAGAAG 57.966 34.615 0.00 0.00 0.00 2.85
160 161 7.661847 AGAATAAAACGGTGATGAAGAAGAAGT 59.338 33.333 0.00 0.00 0.00 3.01
161 162 7.745620 ATAAAACGGTGATGAAGAAGAAGTT 57.254 32.000 0.00 0.00 0.00 2.66
162 163 8.842358 ATAAAACGGTGATGAAGAAGAAGTTA 57.158 30.769 0.00 0.00 0.00 2.24
163 164 7.562454 AAAACGGTGATGAAGAAGAAGTTAA 57.438 32.000 0.00 0.00 0.00 2.01
164 165 7.562454 AAACGGTGATGAAGAAGAAGTTAAA 57.438 32.000 0.00 0.00 0.00 1.52
165 166 7.562454 AACGGTGATGAAGAAGAAGTTAAAA 57.438 32.000 0.00 0.00 0.00 1.52
166 167 7.745620 ACGGTGATGAAGAAGAAGTTAAAAT 57.254 32.000 0.00 0.00 0.00 1.82
167 168 8.166422 ACGGTGATGAAGAAGAAGTTAAAATT 57.834 30.769 0.00 0.00 0.00 1.82
168 169 9.280174 ACGGTGATGAAGAAGAAGTTAAAATTA 57.720 29.630 0.00 0.00 0.00 1.40
462 469 6.319141 GATTATTGATCCAGCTTTGGTACC 57.681 41.667 4.43 4.43 0.00 3.34
464 471 0.251916 TGATCCAGCTTTGGTACCGG 59.748 55.000 7.57 0.00 0.00 5.28
480 487 1.136984 CGGAGGTCGAGACGAAAGG 59.863 63.158 0.00 0.00 42.43 3.11
493 503 0.179171 CGAAAGGACTCGCGCTAAGA 60.179 55.000 5.56 0.00 31.04 2.10
496 506 0.818296 AAGGACTCGCGCTAAGATGT 59.182 50.000 5.56 0.00 0.00 3.06
506 516 6.528423 ACTCGCGCTAAGATGTATCAATAATC 59.472 38.462 5.56 0.00 0.00 1.75
509 519 6.237675 CGCGCTAAGATGTATCAATAATCCTG 60.238 42.308 5.56 0.00 0.00 3.86
539 549 2.817665 AGAGGCTACGTAAACCTTCCT 58.182 47.619 15.90 8.41 32.67 3.36
582 596 2.772622 CTATTCGGGGGTGGGCCT 60.773 66.667 4.53 0.00 34.45 5.19
584 598 3.644465 TATTCGGGGGTGGGCCTCA 62.644 63.158 4.53 0.00 36.82 3.86
602 616 1.985159 TCACCTCTGCCTAACACCAAT 59.015 47.619 0.00 0.00 0.00 3.16
603 617 2.375174 TCACCTCTGCCTAACACCAATT 59.625 45.455 0.00 0.00 0.00 2.32
609 623 6.152831 ACCTCTGCCTAACACCAATTAAAATC 59.847 38.462 0.00 0.00 0.00 2.17
769 795 1.447838 CGTGCGGCTGTCCTGTAAT 60.448 57.895 0.00 0.00 0.00 1.89
839 865 1.539388 CTTGTCCCAAATTAGCACGCA 59.461 47.619 0.00 0.00 0.00 5.24
867 893 4.760530 AAATGACGAATCCTCATCTCCA 57.239 40.909 0.00 0.00 0.00 3.86
957 983 5.074115 TCGTAAACACCTCCCATTTGATTT 58.926 37.500 0.00 0.00 0.00 2.17
1076 1108 2.502080 CGTCTGCGTCGTGTCCTC 60.502 66.667 0.00 0.00 0.00 3.71
1077 1109 2.643272 GTCTGCGTCGTGTCCTCA 59.357 61.111 0.00 0.00 0.00 3.86
1079 1111 1.004277 GTCTGCGTCGTGTCCTCAAG 61.004 60.000 0.00 0.00 0.00 3.02
1089 1121 3.191581 TCGTGTCCTCAAGAGAAGCTAAG 59.808 47.826 0.00 0.00 0.00 2.18
1107 1139 0.908198 AGAATGAGGAGGACAGCACC 59.092 55.000 0.00 0.00 0.00 5.01
1273 1313 2.107141 GGATCGAGAAGGCCGTGG 59.893 66.667 0.00 0.00 0.00 4.94
1373 1413 1.712018 TACGCCATCGACGACCTCAG 61.712 60.000 0.00 0.00 39.41 3.35
1593 1633 2.707849 CGTGGACGAGTTCGGGGAT 61.708 63.158 6.48 0.00 44.95 3.85
1769 1815 1.641577 GGCGACTACAAGACCATCAC 58.358 55.000 0.00 0.00 0.00 3.06
2007 2299 2.513666 TTCATGCGCGGGATCACC 60.514 61.111 8.83 0.00 0.00 4.02
2212 2504 0.465460 GGTGGTGTTCCAGAACTGCA 60.465 55.000 11.56 0.00 45.24 4.41
2430 2722 3.209812 TCGGAGATCGGCGACCTG 61.210 66.667 11.66 10.01 39.77 4.00
2688 2987 4.415150 CAGGCCGGCCACACTGAT 62.415 66.667 45.13 22.35 38.92 2.90
2689 2988 4.415150 AGGCCGGCCACACTGATG 62.415 66.667 45.13 0.00 38.92 3.07
2690 2989 4.408821 GGCCGGCCACACTGATGA 62.409 66.667 40.73 0.00 35.81 2.92
2724 3023 4.766088 CGTTCGTCCGGGGTCGAC 62.766 72.222 7.13 7.13 39.00 4.20
2733 3048 2.412323 CGGGGTCGACGAAGATGGA 61.412 63.158 9.92 0.00 39.00 3.41
2756 3072 8.649591 TGGATTGTTAATTTTATGGATGGATGG 58.350 33.333 0.00 0.00 0.00 3.51
2757 3073 8.869109 GGATTGTTAATTTTATGGATGGATGGA 58.131 33.333 0.00 0.00 0.00 3.41
2760 3076 8.192743 TGTTAATTTTATGGATGGATGGATGG 57.807 34.615 0.00 0.00 0.00 3.51
2761 3077 8.009513 TGTTAATTTTATGGATGGATGGATGGA 58.990 33.333 0.00 0.00 0.00 3.41
2762 3078 9.039165 GTTAATTTTATGGATGGATGGATGGAT 57.961 33.333 0.00 0.00 0.00 3.41
2865 3191 7.210174 AGAATGTAGAATGTATGTGCGTGTAT 58.790 34.615 0.00 0.00 0.00 2.29
2885 3211 1.376037 CTGCTCTTTCGGACACCCC 60.376 63.158 0.00 0.00 0.00 4.95
2900 3226 0.038744 ACCCCTGCTCACAATTGGAG 59.961 55.000 10.83 13.78 35.47 3.86
2903 3229 2.517959 CCCTGCTCACAATTGGAGAAA 58.482 47.619 21.24 11.30 34.24 2.52
2913 3239 5.347635 TCACAATTGGAGAAATTACGACTCG 59.652 40.000 10.83 0.00 36.28 4.18
2921 3247 7.194278 TGGAGAAATTACGACTCGAATAGAAG 58.806 38.462 5.20 0.00 0.00 2.85
2933 3259 8.293867 CGACTCGAATAGAAGAGGATTTAAGAT 58.706 37.037 0.00 0.00 38.72 2.40
2953 3283 9.863845 TTAAGATAGTTTACGACATGTTGATCA 57.136 29.630 20.26 0.00 0.00 2.92
2968 3298 7.891782 CATGTTGATCATGTAAATCACAAAGC 58.108 34.615 0.00 0.00 46.18 3.51
2969 3299 6.979465 TGTTGATCATGTAAATCACAAAGCA 58.021 32.000 0.00 0.00 41.55 3.91
2970 3300 7.604549 TGTTGATCATGTAAATCACAAAGCAT 58.395 30.769 0.00 0.00 41.55 3.79
2971 3301 7.756272 TGTTGATCATGTAAATCACAAAGCATC 59.244 33.333 0.00 0.00 41.55 3.91
2972 3302 7.634671 TGATCATGTAAATCACAAAGCATCT 57.365 32.000 0.00 0.00 41.55 2.90
2973 3303 8.735692 TGATCATGTAAATCACAAAGCATCTA 57.264 30.769 0.00 0.00 41.55 1.98
2974 3304 9.176460 TGATCATGTAAATCACAAAGCATCTAA 57.824 29.630 0.00 0.00 41.55 2.10
2977 3307 9.399797 TCATGTAAATCACAAAGCATCTAATCT 57.600 29.630 0.00 0.00 41.55 2.40
2978 3308 9.661187 CATGTAAATCACAAAGCATCTAATCTC 57.339 33.333 0.00 0.00 41.55 2.75
2979 3309 9.624373 ATGTAAATCACAAAGCATCTAATCTCT 57.376 29.630 0.00 0.00 41.55 3.10
2980 3310 9.453572 TGTAAATCACAAAGCATCTAATCTCTT 57.546 29.630 0.00 0.00 32.95 2.85
2981 3311 9.928236 GTAAATCACAAAGCATCTAATCTCTTC 57.072 33.333 0.00 0.00 0.00 2.87
2982 3312 7.565323 AATCACAAAGCATCTAATCTCTTCC 57.435 36.000 0.00 0.00 0.00 3.46
2983 3313 5.431765 TCACAAAGCATCTAATCTCTTCCC 58.568 41.667 0.00 0.00 0.00 3.97
2984 3314 4.578105 CACAAAGCATCTAATCTCTTCCCC 59.422 45.833 0.00 0.00 0.00 4.81
2985 3315 4.140536 CAAAGCATCTAATCTCTTCCCCC 58.859 47.826 0.00 0.00 0.00 5.40
2999 3329 2.275418 CCCCCGATTTCAGGTGGG 59.725 66.667 0.00 0.00 41.56 4.61
3001 3331 3.087065 CCCGATTTCAGGTGGGGT 58.913 61.111 0.00 0.00 38.03 4.95
3002 3332 1.378514 CCCGATTTCAGGTGGGGTG 60.379 63.158 0.00 0.00 38.03 4.61
3003 3333 1.682849 CCGATTTCAGGTGGGGTGA 59.317 57.895 0.00 0.00 0.00 4.02
3004 3334 0.392998 CCGATTTCAGGTGGGGTGAG 60.393 60.000 0.00 0.00 0.00 3.51
3005 3335 0.392998 CGATTTCAGGTGGGGTGAGG 60.393 60.000 0.00 0.00 0.00 3.86
3006 3336 0.698818 GATTTCAGGTGGGGTGAGGT 59.301 55.000 0.00 0.00 0.00 3.85
3007 3337 0.405585 ATTTCAGGTGGGGTGAGGTG 59.594 55.000 0.00 0.00 0.00 4.00
3008 3338 1.715019 TTTCAGGTGGGGTGAGGTGG 61.715 60.000 0.00 0.00 0.00 4.61
3009 3339 2.529136 CAGGTGGGGTGAGGTGGA 60.529 66.667 0.00 0.00 0.00 4.02
3010 3340 1.925455 CAGGTGGGGTGAGGTGGAT 60.925 63.158 0.00 0.00 0.00 3.41
3011 3341 1.925455 AGGTGGGGTGAGGTGGATG 60.925 63.158 0.00 0.00 0.00 3.51
3012 3342 2.044946 GTGGGGTGAGGTGGATGC 60.045 66.667 0.00 0.00 0.00 3.91
3013 3343 2.204136 TGGGGTGAGGTGGATGCT 60.204 61.111 0.00 0.00 0.00 3.79
3014 3344 1.852157 TGGGGTGAGGTGGATGCTT 60.852 57.895 0.00 0.00 0.00 3.91
3015 3345 1.384191 GGGGTGAGGTGGATGCTTT 59.616 57.895 0.00 0.00 0.00 3.51
3016 3346 0.967380 GGGGTGAGGTGGATGCTTTG 60.967 60.000 0.00 0.00 0.00 2.77
3017 3347 0.251341 GGGTGAGGTGGATGCTTTGT 60.251 55.000 0.00 0.00 0.00 2.83
3018 3348 0.883833 GGTGAGGTGGATGCTTTGTG 59.116 55.000 0.00 0.00 0.00 3.33
3019 3349 1.545428 GGTGAGGTGGATGCTTTGTGA 60.545 52.381 0.00 0.00 0.00 3.58
3020 3350 2.440409 GTGAGGTGGATGCTTTGTGAT 58.560 47.619 0.00 0.00 0.00 3.06
3021 3351 2.821969 GTGAGGTGGATGCTTTGTGATT 59.178 45.455 0.00 0.00 0.00 2.57
3022 3352 3.256631 GTGAGGTGGATGCTTTGTGATTT 59.743 43.478 0.00 0.00 0.00 2.17
3023 3353 3.256383 TGAGGTGGATGCTTTGTGATTTG 59.744 43.478 0.00 0.00 0.00 2.32
3024 3354 3.233507 AGGTGGATGCTTTGTGATTTGT 58.766 40.909 0.00 0.00 0.00 2.83
3025 3355 3.006110 AGGTGGATGCTTTGTGATTTGTG 59.994 43.478 0.00 0.00 0.00 3.33
3026 3356 3.319755 GTGGATGCTTTGTGATTTGTGG 58.680 45.455 0.00 0.00 0.00 4.17
3027 3357 2.299582 TGGATGCTTTGTGATTTGTGGG 59.700 45.455 0.00 0.00 0.00 4.61
3028 3358 2.299867 GGATGCTTTGTGATTTGTGGGT 59.700 45.455 0.00 0.00 0.00 4.51
3029 3359 2.886862 TGCTTTGTGATTTGTGGGTG 57.113 45.000 0.00 0.00 0.00 4.61
3030 3360 1.202510 TGCTTTGTGATTTGTGGGTGC 60.203 47.619 0.00 0.00 0.00 5.01
3031 3361 1.873486 GCTTTGTGATTTGTGGGTGCC 60.873 52.381 0.00 0.00 0.00 5.01
3032 3362 1.411977 CTTTGTGATTTGTGGGTGCCA 59.588 47.619 0.00 0.00 0.00 4.92
3040 3370 2.281484 GTGGGTGCCACGTGTCAT 60.281 61.111 15.65 0.00 44.95 3.06
3041 3371 2.031919 TGGGTGCCACGTGTCATC 59.968 61.111 15.65 8.29 0.00 2.92
3042 3372 2.746277 GGGTGCCACGTGTCATCC 60.746 66.667 13.90 13.90 0.00 3.51
3043 3373 2.031919 GGTGCCACGTGTCATCCA 59.968 61.111 15.65 0.55 0.00 3.41
3044 3374 1.377202 GGTGCCACGTGTCATCCAT 60.377 57.895 15.65 0.00 0.00 3.41
3045 3375 0.960364 GGTGCCACGTGTCATCCATT 60.960 55.000 15.65 0.00 0.00 3.16
3046 3376 1.677518 GGTGCCACGTGTCATCCATTA 60.678 52.381 15.65 0.00 0.00 1.90
3047 3377 1.665679 GTGCCACGTGTCATCCATTAG 59.334 52.381 15.65 0.00 0.00 1.73
3048 3378 1.299541 GCCACGTGTCATCCATTAGG 58.700 55.000 15.65 0.00 0.00 2.69
3062 3392 3.482156 CATTAGGATGGGTCTCACCTG 57.518 52.381 0.00 0.00 38.64 4.00
3063 3393 1.204146 TTAGGATGGGTCTCACCTGC 58.796 55.000 0.00 0.00 38.64 4.85
3064 3394 0.339859 TAGGATGGGTCTCACCTGCT 59.660 55.000 0.00 0.00 38.64 4.24
3065 3395 0.339859 AGGATGGGTCTCACCTGCTA 59.660 55.000 0.00 0.00 38.64 3.49
3066 3396 1.204146 GGATGGGTCTCACCTGCTAA 58.796 55.000 0.00 0.00 38.64 3.09
3067 3397 1.771255 GGATGGGTCTCACCTGCTAAT 59.229 52.381 0.00 0.00 38.64 1.73
3068 3398 2.224402 GGATGGGTCTCACCTGCTAATC 60.224 54.545 0.00 0.00 38.64 1.75
3069 3399 1.204146 TGGGTCTCACCTGCTAATCC 58.796 55.000 0.00 0.00 38.64 3.01
3070 3400 0.105039 GGGTCTCACCTGCTAATCCG 59.895 60.000 0.00 0.00 38.64 4.18
3071 3401 0.824759 GGTCTCACCTGCTAATCCGT 59.175 55.000 0.00 0.00 34.73 4.69
3072 3402 1.471676 GGTCTCACCTGCTAATCCGTG 60.472 57.143 0.00 0.00 34.73 4.94
3073 3403 1.476891 GTCTCACCTGCTAATCCGTGA 59.523 52.381 0.00 0.00 34.26 4.35
3074 3404 2.215907 CTCACCTGCTAATCCGTGAG 57.784 55.000 2.01 2.01 44.38 3.51
3075 3405 1.847328 TCACCTGCTAATCCGTGAGA 58.153 50.000 0.00 0.00 31.80 3.27
3076 3406 1.476891 TCACCTGCTAATCCGTGAGAC 59.523 52.381 0.00 0.00 31.80 3.36
3077 3407 0.824759 ACCTGCTAATCCGTGAGACC 59.175 55.000 0.00 0.00 0.00 3.85
3078 3408 1.115467 CCTGCTAATCCGTGAGACCT 58.885 55.000 0.00 0.00 0.00 3.85
3079 3409 1.202463 CCTGCTAATCCGTGAGACCTG 60.202 57.143 0.00 0.00 0.00 4.00
3080 3410 0.824109 TGCTAATCCGTGAGACCTGG 59.176 55.000 0.00 0.00 0.00 4.45
3081 3411 0.824759 GCTAATCCGTGAGACCTGGT 59.175 55.000 0.00 0.00 0.00 4.00
3082 3412 1.207329 GCTAATCCGTGAGACCTGGTT 59.793 52.381 0.00 0.00 0.00 3.67
3083 3413 2.354805 GCTAATCCGTGAGACCTGGTTT 60.355 50.000 0.00 0.00 0.00 3.27
3084 3414 2.474410 AATCCGTGAGACCTGGTTTC 57.526 50.000 10.29 10.29 0.00 2.78
3085 3415 1.348064 ATCCGTGAGACCTGGTTTCA 58.652 50.000 15.44 15.44 0.00 2.69
3086 3416 1.348064 TCCGTGAGACCTGGTTTCAT 58.652 50.000 21.29 0.00 29.77 2.57
3087 3417 2.531771 TCCGTGAGACCTGGTTTCATA 58.468 47.619 21.29 9.08 29.77 2.15
3088 3418 2.496070 TCCGTGAGACCTGGTTTCATAG 59.504 50.000 21.29 17.42 29.77 2.23
3089 3419 2.496070 CCGTGAGACCTGGTTTCATAGA 59.504 50.000 21.29 0.00 29.77 1.98
3090 3420 3.056107 CCGTGAGACCTGGTTTCATAGAA 60.056 47.826 21.29 0.00 29.77 2.10
3091 3421 4.383118 CCGTGAGACCTGGTTTCATAGAAT 60.383 45.833 21.29 0.00 29.77 2.40
3092 3422 5.178797 CGTGAGACCTGGTTTCATAGAATT 58.821 41.667 21.29 0.00 29.77 2.17
3093 3423 5.643777 CGTGAGACCTGGTTTCATAGAATTT 59.356 40.000 21.29 0.00 29.77 1.82
3094 3424 6.149474 CGTGAGACCTGGTTTCATAGAATTTT 59.851 38.462 21.29 0.00 29.77 1.82
3095 3425 7.308589 CGTGAGACCTGGTTTCATAGAATTTTT 60.309 37.037 21.29 0.00 29.77 1.94
3170 3531 4.277423 TCCTGATTTTCTTTTCGAACACCC 59.723 41.667 0.00 0.00 0.00 4.61
3183 3607 4.647611 TCGAACACCCACTTGTAAATGAT 58.352 39.130 0.00 0.00 0.00 2.45
3186 3610 3.343617 ACACCCACTTGTAAATGATCCG 58.656 45.455 0.00 0.00 0.00 4.18
3188 3612 3.374058 CACCCACTTGTAAATGATCCGAC 59.626 47.826 0.00 0.00 0.00 4.79
3287 3712 1.792949 CAACACACTGTCGCTTCCTAC 59.207 52.381 0.00 0.00 0.00 3.18
3318 3743 5.062308 AGAGCGAACGAAATTATGTTCAGTC 59.938 40.000 17.76 13.86 43.59 3.51
3319 3744 4.013397 GCGAACGAAATTATGTTCAGTCG 58.987 43.478 17.76 6.87 43.59 4.18
3329 3754 3.885484 ATGTTCAGTCGAGCAAACAAG 57.115 42.857 9.62 0.00 35.84 3.16
3330 3755 2.899976 TGTTCAGTCGAGCAAACAAGA 58.100 42.857 4.45 0.00 28.24 3.02
3331 3756 2.607635 TGTTCAGTCGAGCAAACAAGAC 59.392 45.455 4.45 0.00 28.24 3.01
3332 3757 2.595124 TCAGTCGAGCAAACAAGACA 57.405 45.000 0.00 0.00 36.18 3.41
3333 3758 3.111853 TCAGTCGAGCAAACAAGACAT 57.888 42.857 0.00 0.00 36.18 3.06
3334 3759 3.466836 TCAGTCGAGCAAACAAGACATT 58.533 40.909 0.00 0.00 36.18 2.71
3335 3760 3.494626 TCAGTCGAGCAAACAAGACATTC 59.505 43.478 0.00 0.00 36.18 2.67
3336 3761 3.496130 CAGTCGAGCAAACAAGACATTCT 59.504 43.478 0.00 0.00 36.18 2.40
3337 3762 3.743396 AGTCGAGCAAACAAGACATTCTC 59.257 43.478 0.00 0.00 36.18 2.87
3338 3763 2.731451 TCGAGCAAACAAGACATTCTCG 59.269 45.455 0.00 0.00 42.04 4.04
3339 3764 2.159787 CGAGCAAACAAGACATTCTCGG 60.160 50.000 0.00 0.00 38.48 4.63
3340 3765 2.808543 GAGCAAACAAGACATTCTCGGT 59.191 45.455 0.00 0.00 0.00 4.69
3341 3766 2.808543 AGCAAACAAGACATTCTCGGTC 59.191 45.455 0.00 0.00 35.50 4.79
3342 3767 2.095718 GCAAACAAGACATTCTCGGTCC 60.096 50.000 0.00 0.00 35.89 4.46
3343 3768 3.138304 CAAACAAGACATTCTCGGTCCA 58.862 45.455 0.00 0.00 35.89 4.02
3344 3769 2.457366 ACAAGACATTCTCGGTCCAC 57.543 50.000 0.00 0.00 35.89 4.02
3345 3770 1.691976 ACAAGACATTCTCGGTCCACA 59.308 47.619 0.00 0.00 35.89 4.17
3346 3771 2.289072 ACAAGACATTCTCGGTCCACAG 60.289 50.000 0.00 0.00 35.89 3.66
3347 3772 1.924731 AGACATTCTCGGTCCACAGA 58.075 50.000 0.00 0.00 35.89 3.41
3348 3773 1.546476 AGACATTCTCGGTCCACAGAC 59.454 52.381 0.00 0.00 42.73 3.51
3349 3774 1.546476 GACATTCTCGGTCCACAGACT 59.454 52.381 0.00 0.00 43.05 3.24
3350 3775 1.971357 ACATTCTCGGTCCACAGACTT 59.029 47.619 0.00 0.00 43.05 3.01
3351 3776 2.028930 ACATTCTCGGTCCACAGACTTC 60.029 50.000 0.00 0.00 43.05 3.01
3352 3777 0.966920 TTCTCGGTCCACAGACTTCC 59.033 55.000 0.00 0.00 43.05 3.46
3353 3778 0.178973 TCTCGGTCCACAGACTTCCA 60.179 55.000 0.00 0.00 43.05 3.53
3354 3779 0.679505 CTCGGTCCACAGACTTCCAA 59.320 55.000 0.00 0.00 43.05 3.53
3355 3780 1.276421 CTCGGTCCACAGACTTCCAAT 59.724 52.381 0.00 0.00 43.05 3.16
3356 3781 1.697432 TCGGTCCACAGACTTCCAATT 59.303 47.619 0.00 0.00 43.05 2.32
3357 3782 2.076863 CGGTCCACAGACTTCCAATTC 58.923 52.381 0.00 0.00 43.05 2.17
3358 3783 2.437413 GGTCCACAGACTTCCAATTCC 58.563 52.381 0.00 0.00 43.05 3.01
3359 3784 2.224769 GGTCCACAGACTTCCAATTCCA 60.225 50.000 0.00 0.00 43.05 3.53
3360 3785 3.486383 GTCCACAGACTTCCAATTCCAA 58.514 45.455 0.00 0.00 40.10 3.53
3361 3786 3.888930 GTCCACAGACTTCCAATTCCAAA 59.111 43.478 0.00 0.00 40.10 3.28
3373 3798 9.725019 ACTTCCAATTCCAAATTCCTTTTATTC 57.275 29.630 0.00 0.00 0.00 1.75
3377 3802 6.867519 ATTCCAAATTCCTTTTATTCCCGT 57.132 33.333 0.00 0.00 0.00 5.28
3379 3804 5.326069 TCCAAATTCCTTTTATTCCCGTGA 58.674 37.500 0.00 0.00 0.00 4.35
3383 3808 7.095397 CCAAATTCCTTTTATTCCCGTGAAAAC 60.095 37.037 0.00 0.00 33.32 2.43
3413 4525 5.587844 AGGAAGATACATAAGCAAGCAACAG 59.412 40.000 0.00 0.00 0.00 3.16
3415 4527 3.629398 AGATACATAAGCAAGCAACAGCC 59.371 43.478 0.00 0.00 0.00 4.85
3484 4617 1.072159 GCCCACACTCTGCTCAGTT 59.928 57.895 0.00 0.00 0.00 3.16
3488 4621 1.617850 CCACACTCTGCTCAGTTCTCT 59.382 52.381 0.00 0.00 0.00 3.10
3502 4635 3.124806 CAGTTCTCTCGCGTCACTACTTA 59.875 47.826 5.77 0.00 0.00 2.24
3503 4636 3.940221 AGTTCTCTCGCGTCACTACTTAT 59.060 43.478 5.77 0.00 0.00 1.73
3504 4637 3.946308 TCTCTCGCGTCACTACTTATG 57.054 47.619 5.77 0.00 0.00 1.90
3531 4664 1.002087 AGCGGCTTTATTAGATCGGGG 59.998 52.381 0.00 0.00 0.00 5.73
3533 4666 2.931320 GCGGCTTTATTAGATCGGGGAG 60.931 54.545 0.00 0.00 0.00 4.30
3560 4693 4.743348 GCACACAAAAATCAAACCAGGGAT 60.743 41.667 0.00 0.00 0.00 3.85
3597 4736 2.115427 TGTGTGTTCCCTCTCAACTGA 58.885 47.619 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.872721 AATTTTTGAAAATGTTCAGCCAATTTT 57.127 22.222 0.00 0.00 44.49 1.82
9 10 8.074972 GCATAATTTTTGAAAATGTTCAGCCAA 58.925 29.630 0.00 0.00 44.49 4.52
10 11 7.228108 TGCATAATTTTTGAAAATGTTCAGCCA 59.772 29.630 0.00 0.00 44.49 4.75
11 12 7.583230 TGCATAATTTTTGAAAATGTTCAGCC 58.417 30.769 0.00 0.00 44.49 4.85
122 123 9.425577 TCACCGTTTTATTCTTTGTTTTTCTTT 57.574 25.926 0.00 0.00 0.00 2.52
123 124 8.989653 TCACCGTTTTATTCTTTGTTTTTCTT 57.010 26.923 0.00 0.00 0.00 2.52
124 125 9.030301 CATCACCGTTTTATTCTTTGTTTTTCT 57.970 29.630 0.00 0.00 0.00 2.52
125 126 9.026074 TCATCACCGTTTTATTCTTTGTTTTTC 57.974 29.630 0.00 0.00 0.00 2.29
126 127 8.934507 TCATCACCGTTTTATTCTTTGTTTTT 57.065 26.923 0.00 0.00 0.00 1.94
127 128 8.934507 TTCATCACCGTTTTATTCTTTGTTTT 57.065 26.923 0.00 0.00 0.00 2.43
128 129 8.410141 TCTTCATCACCGTTTTATTCTTTGTTT 58.590 29.630 0.00 0.00 0.00 2.83
129 130 7.936584 TCTTCATCACCGTTTTATTCTTTGTT 58.063 30.769 0.00 0.00 0.00 2.83
130 131 7.504924 TCTTCATCACCGTTTTATTCTTTGT 57.495 32.000 0.00 0.00 0.00 2.83
131 132 8.289618 TCTTCTTCATCACCGTTTTATTCTTTG 58.710 33.333 0.00 0.00 0.00 2.77
132 133 8.391075 TCTTCTTCATCACCGTTTTATTCTTT 57.609 30.769 0.00 0.00 0.00 2.52
133 134 7.979444 TCTTCTTCATCACCGTTTTATTCTT 57.021 32.000 0.00 0.00 0.00 2.52
134 135 7.661847 ACTTCTTCTTCATCACCGTTTTATTCT 59.338 33.333 0.00 0.00 0.00 2.40
135 136 7.807680 ACTTCTTCTTCATCACCGTTTTATTC 58.192 34.615 0.00 0.00 0.00 1.75
136 137 7.745620 ACTTCTTCTTCATCACCGTTTTATT 57.254 32.000 0.00 0.00 0.00 1.40
137 138 7.745620 AACTTCTTCTTCATCACCGTTTTAT 57.254 32.000 0.00 0.00 0.00 1.40
138 139 8.665643 TTAACTTCTTCTTCATCACCGTTTTA 57.334 30.769 0.00 0.00 0.00 1.52
139 140 7.562454 TTAACTTCTTCTTCATCACCGTTTT 57.438 32.000 0.00 0.00 0.00 2.43
140 141 7.562454 TTTAACTTCTTCTTCATCACCGTTT 57.438 32.000 0.00 0.00 0.00 3.60
141 142 7.562454 TTTTAACTTCTTCTTCATCACCGTT 57.438 32.000 0.00 0.00 0.00 4.44
142 143 7.745620 ATTTTAACTTCTTCTTCATCACCGT 57.254 32.000 0.00 0.00 0.00 4.83
462 469 1.136984 CCTTTCGTCTCGACCTCCG 59.863 63.158 0.00 0.00 34.89 4.63
464 471 1.130938 GAGTCCTTTCGTCTCGACCTC 59.869 57.143 0.00 0.00 34.89 3.85
480 487 3.269486 TGATACATCTTAGCGCGAGTC 57.731 47.619 12.10 0.00 0.00 3.36
493 503 6.521162 TGTACGTGCAGGATTATTGATACAT 58.479 36.000 14.38 0.00 0.00 2.29
496 506 7.269316 TCTTTGTACGTGCAGGATTATTGATA 58.731 34.615 14.38 0.00 0.00 2.15
506 516 0.320771 AGCCTCTTTGTACGTGCAGG 60.321 55.000 6.41 4.53 0.00 4.85
509 519 0.989890 CGTAGCCTCTTTGTACGTGC 59.010 55.000 0.00 0.00 35.83 5.34
565 575 2.772622 AGGCCCACCCCCGAATAG 60.773 66.667 0.00 0.00 36.11 1.73
566 576 2.770904 GAGGCCCACCCCCGAATA 60.771 66.667 0.00 0.00 36.11 1.75
582 596 1.429930 TTGGTGTTAGGCAGAGGTGA 58.570 50.000 0.00 0.00 0.00 4.02
584 598 4.650972 TTAATTGGTGTTAGGCAGAGGT 57.349 40.909 0.00 0.00 0.00 3.85
609 623 9.745880 AATGTTACGTGATTAGGTAGTTGATAG 57.254 33.333 0.00 0.00 0.00 2.08
650 664 3.935203 GCTTGAGCAATGCTACACTTAGA 59.065 43.478 8.12 0.00 39.88 2.10
769 795 2.317609 GCTCGCAAACAAGCCGAGA 61.318 57.895 12.76 0.00 37.35 4.04
839 865 9.482627 GAGATGAGGATTCGTCATTTTATAAGT 57.517 33.333 19.69 0.00 41.03 2.24
867 893 5.763876 ACAAGTTGGACTAAATAGGAGCT 57.236 39.130 7.96 0.00 0.00 4.09
936 962 9.719355 AATTAAAATCAAATGGGAGGTGTTTAC 57.281 29.630 0.00 0.00 0.00 2.01
957 983 7.228507 CACCTCCCGATCAATTGATACAATTAA 59.771 37.037 20.75 3.15 34.37 1.40
1076 1108 5.128499 TCCTCCTCATTCTTAGCTTCTCTTG 59.872 44.000 0.00 0.00 0.00 3.02
1077 1109 5.128663 GTCCTCCTCATTCTTAGCTTCTCTT 59.871 44.000 0.00 0.00 0.00 2.85
1079 1111 4.404073 TGTCCTCCTCATTCTTAGCTTCTC 59.596 45.833 0.00 0.00 0.00 2.87
1089 1121 0.460987 CGGTGCTGTCCTCCTCATTC 60.461 60.000 0.00 0.00 0.00 2.67
1107 1139 4.471726 ACCGACGCCGTAAGCTCG 62.472 66.667 0.00 0.00 39.96 5.03
1113 1145 2.562912 GACTTCACCGACGCCGTA 59.437 61.111 0.00 0.00 0.00 4.02
1117 1149 0.731514 TTGATCGACTTCACCGACGC 60.732 55.000 0.00 0.00 38.97 5.19
1177 1209 4.135153 CGTCTCCCCCAGCGTCTG 62.135 72.222 0.52 0.52 0.00 3.51
1273 1313 1.548357 TTGAGCAGGCTGGACTCCTC 61.548 60.000 17.64 13.69 0.00 3.71
1373 1413 2.047179 GCTGGTCGAAGGTGGTCC 60.047 66.667 0.00 0.00 0.00 4.46
1593 1633 1.600107 GTCCAGGTTGGCGATGGTA 59.400 57.895 0.00 0.00 37.47 3.25
2212 2504 2.270205 CTTGCGCACCTGGAGGAT 59.730 61.111 11.12 0.00 38.94 3.24
2329 2621 1.197721 CATGTGGTCTTTGAACTCCGC 59.802 52.381 0.00 0.00 0.00 5.54
2340 2632 2.937689 AGCCTGCCCATGTGGTCT 60.938 61.111 0.00 0.00 36.04 3.85
2678 2977 1.436600 CTCAGTGTCATCAGTGTGGC 58.563 55.000 3.53 0.00 43.31 5.01
2688 2987 0.109086 GCTAGCTTCGCTCAGTGTCA 60.109 55.000 7.70 0.00 40.44 3.58
2689 2988 1.136872 CGCTAGCTTCGCTCAGTGTC 61.137 60.000 13.93 0.00 40.44 3.67
2690 2989 1.153939 CGCTAGCTTCGCTCAGTGT 60.154 57.895 13.93 0.00 40.44 3.55
2751 3066 0.987294 ACCGATCCATCCATCCATCC 59.013 55.000 0.00 0.00 0.00 3.51
2754 3070 1.212375 ACAACCGATCCATCCATCCA 58.788 50.000 0.00 0.00 0.00 3.41
2755 3071 2.767505 GTACAACCGATCCATCCATCC 58.232 52.381 0.00 0.00 0.00 3.51
2756 3072 2.223971 ACGTACAACCGATCCATCCATC 60.224 50.000 0.00 0.00 0.00 3.51
2757 3073 1.760613 ACGTACAACCGATCCATCCAT 59.239 47.619 0.00 0.00 0.00 3.41
2758 3074 1.187974 ACGTACAACCGATCCATCCA 58.812 50.000 0.00 0.00 0.00 3.41
2759 3075 2.099592 TGTACGTACAACCGATCCATCC 59.900 50.000 25.54 0.00 32.40 3.51
2760 3076 3.111098 GTGTACGTACAACCGATCCATC 58.889 50.000 28.89 9.65 38.04 3.51
2761 3077 2.756760 AGTGTACGTACAACCGATCCAT 59.243 45.455 28.89 5.16 38.04 3.41
2762 3078 2.095110 CAGTGTACGTACAACCGATCCA 60.095 50.000 28.89 1.10 38.04 3.41
2865 3191 0.606604 GGGTGTCCGAAAGAGCAGTA 59.393 55.000 0.00 0.00 0.00 2.74
2885 3211 5.122239 TCGTAATTTCTCCAATTGTGAGCAG 59.878 40.000 15.30 0.89 35.71 4.24
2900 3226 7.416022 TCCTCTTCTATTCGAGTCGTAATTTC 58.584 38.462 13.12 0.00 0.00 2.17
2903 3229 7.513371 AATCCTCTTCTATTCGAGTCGTAAT 57.487 36.000 13.12 12.79 0.00 1.89
2921 3247 9.530633 ACATGTCGTAAACTATCTTAAATCCTC 57.469 33.333 0.00 0.00 0.00 3.71
2953 3283 9.624373 AGAGATTAGATGCTTTGTGATTTACAT 57.376 29.630 0.00 0.00 39.48 2.29
2955 3285 9.928236 GAAGAGATTAGATGCTTTGTGATTTAC 57.072 33.333 0.00 0.00 0.00 2.01
2957 3287 7.067981 GGGAAGAGATTAGATGCTTTGTGATTT 59.932 37.037 0.00 0.00 0.00 2.17
2958 3288 6.545298 GGGAAGAGATTAGATGCTTTGTGATT 59.455 38.462 0.00 0.00 0.00 2.57
2959 3289 6.060788 GGGAAGAGATTAGATGCTTTGTGAT 58.939 40.000 0.00 0.00 0.00 3.06
2961 3291 4.578105 GGGGAAGAGATTAGATGCTTTGTG 59.422 45.833 0.00 0.00 0.00 3.33
2962 3292 4.385754 GGGGGAAGAGATTAGATGCTTTGT 60.386 45.833 0.00 0.00 0.00 2.83
2963 3293 4.140536 GGGGGAAGAGATTAGATGCTTTG 58.859 47.826 0.00 0.00 0.00 2.77
2964 3294 4.445557 GGGGGAAGAGATTAGATGCTTT 57.554 45.455 0.00 0.00 0.00 3.51
2982 3312 2.275418 CCCACCTGAAATCGGGGG 59.725 66.667 12.76 8.38 46.75 5.40
2985 3315 0.392998 CTCACCCCACCTGAAATCGG 60.393 60.000 0.00 0.00 0.00 4.18
2986 3316 0.392998 CCTCACCCCACCTGAAATCG 60.393 60.000 0.00 0.00 0.00 3.34
2987 3317 0.698818 ACCTCACCCCACCTGAAATC 59.301 55.000 0.00 0.00 0.00 2.17
2988 3318 0.405585 CACCTCACCCCACCTGAAAT 59.594 55.000 0.00 0.00 0.00 2.17
2989 3319 1.715019 CCACCTCACCCCACCTGAAA 61.715 60.000 0.00 0.00 0.00 2.69
2990 3320 2.153401 CCACCTCACCCCACCTGAA 61.153 63.158 0.00 0.00 0.00 3.02
2991 3321 2.415962 ATCCACCTCACCCCACCTGA 62.416 60.000 0.00 0.00 0.00 3.86
2992 3322 1.925455 ATCCACCTCACCCCACCTG 60.925 63.158 0.00 0.00 0.00 4.00
2993 3323 1.925455 CATCCACCTCACCCCACCT 60.925 63.158 0.00 0.00 0.00 4.00
2994 3324 2.677228 CATCCACCTCACCCCACC 59.323 66.667 0.00 0.00 0.00 4.61
2995 3325 2.044946 GCATCCACCTCACCCCAC 60.045 66.667 0.00 0.00 0.00 4.61
2996 3326 1.434513 AAAGCATCCACCTCACCCCA 61.435 55.000 0.00 0.00 0.00 4.96
2997 3327 0.967380 CAAAGCATCCACCTCACCCC 60.967 60.000 0.00 0.00 0.00 4.95
2998 3328 0.251341 ACAAAGCATCCACCTCACCC 60.251 55.000 0.00 0.00 0.00 4.61
2999 3329 0.883833 CACAAAGCATCCACCTCACC 59.116 55.000 0.00 0.00 0.00 4.02
3000 3330 1.896220 TCACAAAGCATCCACCTCAC 58.104 50.000 0.00 0.00 0.00 3.51
3001 3331 2.885135 ATCACAAAGCATCCACCTCA 57.115 45.000 0.00 0.00 0.00 3.86
3002 3332 3.256631 ACAAATCACAAAGCATCCACCTC 59.743 43.478 0.00 0.00 0.00 3.85
3003 3333 3.006110 CACAAATCACAAAGCATCCACCT 59.994 43.478 0.00 0.00 0.00 4.00
3004 3334 3.319755 CACAAATCACAAAGCATCCACC 58.680 45.455 0.00 0.00 0.00 4.61
3005 3335 3.319755 CCACAAATCACAAAGCATCCAC 58.680 45.455 0.00 0.00 0.00 4.02
3006 3336 2.299582 CCCACAAATCACAAAGCATCCA 59.700 45.455 0.00 0.00 0.00 3.41
3007 3337 2.299867 ACCCACAAATCACAAAGCATCC 59.700 45.455 0.00 0.00 0.00 3.51
3008 3338 3.319755 CACCCACAAATCACAAAGCATC 58.680 45.455 0.00 0.00 0.00 3.91
3009 3339 2.548493 GCACCCACAAATCACAAAGCAT 60.548 45.455 0.00 0.00 0.00 3.79
3010 3340 1.202510 GCACCCACAAATCACAAAGCA 60.203 47.619 0.00 0.00 0.00 3.91
3011 3341 1.501169 GCACCCACAAATCACAAAGC 58.499 50.000 0.00 0.00 0.00 3.51
3012 3342 1.411977 TGGCACCCACAAATCACAAAG 59.588 47.619 0.00 0.00 0.00 2.77
3013 3343 1.489481 TGGCACCCACAAATCACAAA 58.511 45.000 0.00 0.00 0.00 2.83
3014 3344 3.214023 TGGCACCCACAAATCACAA 57.786 47.368 0.00 0.00 0.00 3.33
3024 3354 2.031919 GATGACACGTGGCACCCA 59.968 61.111 29.77 12.45 34.80 4.51
3025 3355 2.746277 GGATGACACGTGGCACCC 60.746 66.667 29.77 25.95 34.80 4.61
3026 3356 0.960364 AATGGATGACACGTGGCACC 60.960 55.000 29.77 27.79 34.80 5.01
3027 3357 1.665679 CTAATGGATGACACGTGGCAC 59.334 52.381 29.77 20.04 34.80 5.01
3028 3358 1.406751 CCTAATGGATGACACGTGGCA 60.407 52.381 29.28 29.28 37.54 4.92
3029 3359 1.134521 TCCTAATGGATGACACGTGGC 60.135 52.381 21.57 19.24 37.46 5.01
3030 3360 2.979814 TCCTAATGGATGACACGTGG 57.020 50.000 21.57 1.66 37.46 4.94
3042 3372 2.486191 GCAGGTGAGACCCATCCTAATG 60.486 54.545 0.00 0.00 39.75 1.90
3043 3373 1.771255 GCAGGTGAGACCCATCCTAAT 59.229 52.381 0.00 0.00 39.75 1.73
3044 3374 1.204146 GCAGGTGAGACCCATCCTAA 58.796 55.000 0.00 0.00 39.75 2.69
3045 3375 0.339859 AGCAGGTGAGACCCATCCTA 59.660 55.000 0.00 0.00 39.75 2.94
3046 3376 0.339859 TAGCAGGTGAGACCCATCCT 59.660 55.000 0.00 0.00 39.75 3.24
3047 3377 1.204146 TTAGCAGGTGAGACCCATCC 58.796 55.000 0.00 0.00 39.75 3.51
3048 3378 2.224402 GGATTAGCAGGTGAGACCCATC 60.224 54.545 0.00 0.00 39.75 3.51
3049 3379 1.771255 GGATTAGCAGGTGAGACCCAT 59.229 52.381 0.00 0.00 39.75 4.00
3050 3380 1.204146 GGATTAGCAGGTGAGACCCA 58.796 55.000 0.00 0.00 39.75 4.51
3051 3381 0.105039 CGGATTAGCAGGTGAGACCC 59.895 60.000 0.00 0.00 39.75 4.46
3052 3382 0.824759 ACGGATTAGCAGGTGAGACC 59.175 55.000 0.00 0.00 38.99 3.85
3053 3383 1.476891 TCACGGATTAGCAGGTGAGAC 59.523 52.381 0.00 0.00 34.71 3.36
3054 3384 1.847328 TCACGGATTAGCAGGTGAGA 58.153 50.000 0.00 0.00 34.71 3.27
3056 3386 1.476891 GTCTCACGGATTAGCAGGTGA 59.523 52.381 0.00 0.00 37.77 4.02
3057 3387 1.471676 GGTCTCACGGATTAGCAGGTG 60.472 57.143 0.00 0.00 0.00 4.00
3058 3388 0.824759 GGTCTCACGGATTAGCAGGT 59.175 55.000 0.00 0.00 0.00 4.00
3059 3389 1.115467 AGGTCTCACGGATTAGCAGG 58.885 55.000 0.00 0.00 0.00 4.85
3060 3390 1.202463 CCAGGTCTCACGGATTAGCAG 60.202 57.143 0.00 0.00 0.00 4.24
3061 3391 0.824109 CCAGGTCTCACGGATTAGCA 59.176 55.000 0.00 0.00 0.00 3.49
3062 3392 0.824759 ACCAGGTCTCACGGATTAGC 59.175 55.000 0.00 0.00 0.00 3.09
3063 3393 3.056107 TGAAACCAGGTCTCACGGATTAG 60.056 47.826 0.00 0.00 0.00 1.73
3064 3394 2.901192 TGAAACCAGGTCTCACGGATTA 59.099 45.455 0.00 0.00 0.00 1.75
3065 3395 1.697432 TGAAACCAGGTCTCACGGATT 59.303 47.619 0.00 0.00 0.00 3.01
3066 3396 1.348064 TGAAACCAGGTCTCACGGAT 58.652 50.000 0.00 0.00 0.00 4.18
3067 3397 1.348064 ATGAAACCAGGTCTCACGGA 58.652 50.000 0.00 0.00 0.00 4.69
3068 3398 2.496070 TCTATGAAACCAGGTCTCACGG 59.504 50.000 0.00 0.00 0.00 4.94
3069 3399 3.868757 TCTATGAAACCAGGTCTCACG 57.131 47.619 0.00 0.00 0.00 4.35
3070 3400 7.454260 AAAATTCTATGAAACCAGGTCTCAC 57.546 36.000 0.00 0.00 0.00 3.51
3093 3423 7.782049 AGACGTCTAGATACATCATGGAAAAA 58.218 34.615 18.46 0.00 0.00 1.94
3094 3424 7.348080 AGACGTCTAGATACATCATGGAAAA 57.652 36.000 18.46 0.00 0.00 2.29
3095 3425 6.961360 AGACGTCTAGATACATCATGGAAA 57.039 37.500 18.46 0.00 0.00 3.13
3096 3426 6.735968 GCAAGACGTCTAGATACATCATGGAA 60.736 42.308 20.39 0.00 0.00 3.53
3097 3427 5.278512 GCAAGACGTCTAGATACATCATGGA 60.279 44.000 20.39 0.00 0.00 3.41
3098 3428 4.920340 GCAAGACGTCTAGATACATCATGG 59.080 45.833 20.39 0.00 0.00 3.66
3099 3429 5.523369 TGCAAGACGTCTAGATACATCATG 58.477 41.667 20.39 10.25 0.00 3.07
3100 3430 5.300539 ACTGCAAGACGTCTAGATACATCAT 59.699 40.000 20.39 0.00 37.43 2.45
3101 3431 4.640647 ACTGCAAGACGTCTAGATACATCA 59.359 41.667 20.39 7.08 37.43 3.07
3102 3432 4.973051 CACTGCAAGACGTCTAGATACATC 59.027 45.833 20.39 2.81 37.43 3.06
3103 3433 4.734989 GCACTGCAAGACGTCTAGATACAT 60.735 45.833 20.39 0.00 37.43 2.29
3104 3434 3.427638 GCACTGCAAGACGTCTAGATACA 60.428 47.826 20.39 11.50 37.43 2.29
3105 3435 3.109619 GCACTGCAAGACGTCTAGATAC 58.890 50.000 20.39 7.34 37.43 2.24
3170 3531 4.094887 CCAAGGTCGGATCATTTACAAGTG 59.905 45.833 0.00 0.00 0.00 3.16
3183 3607 0.976073 GATCCAGGTCCAAGGTCGGA 60.976 60.000 0.00 0.00 0.00 4.55
3186 3610 0.833949 GAGGATCCAGGTCCAAGGTC 59.166 60.000 15.82 0.00 40.90 3.85
3188 3612 1.826024 CGAGGATCCAGGTCCAAGG 59.174 63.158 15.82 0.00 40.90 3.61
3216 3640 4.001652 CTGGCAAGTGCATCTATCTATGG 58.998 47.826 5.52 0.00 44.36 2.74
3221 3645 4.970662 TTTTCTGGCAAGTGCATCTATC 57.029 40.909 5.52 0.00 44.36 2.08
3287 3712 6.797033 ACATAATTTCGTTCGCTCTTTTCAAG 59.203 34.615 0.00 0.00 0.00 3.02
3299 3724 5.163992 TGCTCGACTGAACATAATTTCGTTC 60.164 40.000 11.01 11.01 41.53 3.95
3318 3743 2.159787 CCGAGAATGTCTTGTTTGCTCG 60.160 50.000 0.00 0.00 42.22 5.03
3319 3744 2.808543 ACCGAGAATGTCTTGTTTGCTC 59.191 45.455 0.00 0.00 0.00 4.26
3329 3754 1.546476 AGTCTGTGGACCGAGAATGTC 59.454 52.381 0.00 0.00 43.05 3.06
3330 3755 1.633774 AGTCTGTGGACCGAGAATGT 58.366 50.000 0.00 0.00 43.05 2.71
3331 3756 2.611518 GAAGTCTGTGGACCGAGAATG 58.388 52.381 0.00 0.00 43.05 2.67
3332 3757 1.550976 GGAAGTCTGTGGACCGAGAAT 59.449 52.381 0.00 0.00 43.05 2.40
3333 3758 0.966920 GGAAGTCTGTGGACCGAGAA 59.033 55.000 0.00 0.00 43.05 2.87
3334 3759 0.178973 TGGAAGTCTGTGGACCGAGA 60.179 55.000 0.00 0.00 43.05 4.04
3335 3760 0.679505 TTGGAAGTCTGTGGACCGAG 59.320 55.000 0.00 0.00 43.05 4.63
3336 3761 1.348064 ATTGGAAGTCTGTGGACCGA 58.652 50.000 0.00 0.00 43.05 4.69
3337 3762 2.076863 GAATTGGAAGTCTGTGGACCG 58.923 52.381 0.00 0.00 43.05 4.79
3338 3763 2.224769 TGGAATTGGAAGTCTGTGGACC 60.225 50.000 0.00 0.00 43.05 4.46
3339 3764 3.140325 TGGAATTGGAAGTCTGTGGAC 57.860 47.619 0.00 0.00 42.41 4.02
3340 3765 3.874383 TTGGAATTGGAAGTCTGTGGA 57.126 42.857 0.00 0.00 0.00 4.02
3341 3766 5.473039 GAATTTGGAATTGGAAGTCTGTGG 58.527 41.667 0.00 0.00 0.00 4.17
3342 3767 5.244626 AGGAATTTGGAATTGGAAGTCTGTG 59.755 40.000 0.00 0.00 0.00 3.66
3343 3768 5.397360 AGGAATTTGGAATTGGAAGTCTGT 58.603 37.500 0.00 0.00 0.00 3.41
3344 3769 5.990120 AGGAATTTGGAATTGGAAGTCTG 57.010 39.130 0.00 0.00 0.00 3.51
3345 3770 7.379059 AAAAGGAATTTGGAATTGGAAGTCT 57.621 32.000 0.00 0.00 0.00 3.24
3346 3771 9.725019 AATAAAAGGAATTTGGAATTGGAAGTC 57.275 29.630 0.00 0.00 32.27 3.01
3347 3772 9.725019 GAATAAAAGGAATTTGGAATTGGAAGT 57.275 29.630 0.00 0.00 32.27 3.01
3348 3773 9.166173 GGAATAAAAGGAATTTGGAATTGGAAG 57.834 33.333 0.00 0.00 32.27 3.46
3349 3774 8.106462 GGGAATAAAAGGAATTTGGAATTGGAA 58.894 33.333 0.00 0.00 32.27 3.53
3350 3775 7.580495 CGGGAATAAAAGGAATTTGGAATTGGA 60.580 37.037 0.00 0.00 32.27 3.53
3351 3776 6.538381 CGGGAATAAAAGGAATTTGGAATTGG 59.462 38.462 0.00 0.00 32.27 3.16
3352 3777 7.064490 CACGGGAATAAAAGGAATTTGGAATTG 59.936 37.037 0.00 0.00 32.27 2.32
3353 3778 7.038658 TCACGGGAATAAAAGGAATTTGGAATT 60.039 33.333 0.00 0.00 32.27 2.17
3354 3779 6.439058 TCACGGGAATAAAAGGAATTTGGAAT 59.561 34.615 0.00 0.00 32.27 3.01
3355 3780 5.775701 TCACGGGAATAAAAGGAATTTGGAA 59.224 36.000 0.00 0.00 32.27 3.53
3356 3781 5.326069 TCACGGGAATAAAAGGAATTTGGA 58.674 37.500 0.00 0.00 32.27 3.53
3357 3782 5.652994 TCACGGGAATAAAAGGAATTTGG 57.347 39.130 0.00 0.00 32.27 3.28
3358 3783 7.095397 GGTTTTCACGGGAATAAAAGGAATTTG 60.095 37.037 0.00 0.00 31.93 2.32
3359 3784 6.932400 GGTTTTCACGGGAATAAAAGGAATTT 59.068 34.615 0.00 0.00 31.93 1.82
3360 3785 6.460781 GGTTTTCACGGGAATAAAAGGAATT 58.539 36.000 0.00 0.00 31.93 2.17
3361 3786 5.046878 GGGTTTTCACGGGAATAAAAGGAAT 60.047 40.000 0.00 0.00 31.93 3.01
3373 3798 0.037590 TCCTCATGGGTTTTCACGGG 59.962 55.000 0.00 0.00 36.25 5.28
3377 3802 5.512942 TGTATCTTCCTCATGGGTTTTCA 57.487 39.130 0.00 0.00 36.25 2.69
3379 3804 6.547510 GCTTATGTATCTTCCTCATGGGTTTT 59.452 38.462 0.00 0.00 36.25 2.43
3383 3808 5.233083 TGCTTATGTATCTTCCTCATGGG 57.767 43.478 0.00 0.00 0.00 4.00
3413 4525 6.039382 CAGTATTTGTAACTATCAAAGGGGGC 59.961 42.308 0.00 0.00 38.02 5.80
3415 4527 8.801882 TTCAGTATTTGTAACTATCAAAGGGG 57.198 34.615 0.00 0.00 38.02 4.79
3455 4588 2.972713 AGAGTGTGGGCTTGAGAAGTTA 59.027 45.455 0.00 0.00 0.00 2.24
3457 4590 1.071385 CAGAGTGTGGGCTTGAGAAGT 59.929 52.381 0.00 0.00 0.00 3.01
3458 4591 1.805869 CAGAGTGTGGGCTTGAGAAG 58.194 55.000 0.00 0.00 0.00 2.85
3460 4593 1.123861 AGCAGAGTGTGGGCTTGAGA 61.124 55.000 0.00 0.00 33.21 3.27
3461 4594 0.673022 GAGCAGAGTGTGGGCTTGAG 60.673 60.000 0.00 0.00 38.15 3.02
3467 4600 0.683973 AGAACTGAGCAGAGTGTGGG 59.316 55.000 4.21 0.00 0.00 4.61
3484 4617 2.612672 CCATAAGTAGTGACGCGAGAGA 59.387 50.000 15.93 0.00 0.00 3.10
3488 4621 3.247442 CAAACCATAAGTAGTGACGCGA 58.753 45.455 15.93 0.00 0.00 5.87
3502 4635 2.143876 ATAAAGCCGCTCCAAACCAT 57.856 45.000 0.00 0.00 0.00 3.55
3503 4636 1.917872 AATAAAGCCGCTCCAAACCA 58.082 45.000 0.00 0.00 0.00 3.67
3504 4637 3.275999 TCTAATAAAGCCGCTCCAAACC 58.724 45.455 0.00 0.00 0.00 3.27
3531 4664 5.580297 TGGTTTGATTTTTGTGTGCTTTCTC 59.420 36.000 0.00 0.00 0.00 2.87
3533 4666 5.220643 CCTGGTTTGATTTTTGTGTGCTTTC 60.221 40.000 0.00 0.00 0.00 2.62
3560 4693 7.228507 GGAACACACATGGTTATGATTATGCTA 59.771 37.037 0.00 0.00 37.73 3.49
3597 4736 0.108329 CCGGACGCCTACAACTGAAT 60.108 55.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.