Multiple sequence alignment - TraesCS4A01G301900

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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 TraesCS4A01G301900 chr4A 100.000 5579 0 0 1 5579 598717142 598711564 0.000000e+00 10303
1 TraesCS4A01G301900 chr4A 94.839 155 6 2 5253 5406 597929381 597929534 2.010000e-59 241
2 TraesCS4A01G301900 chr4A 95.333 150 6 1 5253 5401 37605412 37605561 2.600000e-58 237
3 TraesCS4A01G301900 chr4D 94.783 4926 174 31 339 5227 4764689 4759810 0.000000e+00 7596
4 TraesCS4A01G301900 chr4D 87.755 294 22 9 7 289 4765064 4764774 1.160000e-86 331
5 TraesCS4A01G301900 chr4D 93.532 201 10 1 3814 4014 5034844 5035041 4.230000e-76 296
6 TraesCS4A01G301900 chr4D 88.889 153 13 3 5401 5551 4759461 4759311 9.540000e-43 185
7 TraesCS4A01G301900 chr4B 94.770 4474 175 28 715 5155 7812471 7808024 0.000000e+00 6911
8 TraesCS4A01G301900 chr4B 93.968 315 15 2 4901 5215 8411966 8412276 1.820000e-129 473
9 TraesCS4A01G301900 chr4B 86.911 382 31 4 289 669 7812817 7812454 1.450000e-110 411
10 TraesCS4A01G301900 chr1A 95.364 151 5 2 5253 5401 241680342 241680492 7.220000e-59 239
11 TraesCS4A01G301900 chr1A 94.079 152 7 2 5253 5403 541703642 541703792 4.350000e-56 230
12 TraesCS4A01G301900 chr7A 95.918 147 4 2 5253 5397 23346926 23346780 2.600000e-58 237
13 TraesCS4A01G301900 chr6A 95.918 147 4 2 5253 5397 76526006 76526152 2.600000e-58 237
14 TraesCS4A01G301900 chr2A 94.268 157 5 4 5253 5406 66217108 66217263 2.600000e-58 237
15 TraesCS4A01G301900 chr5A 94.156 154 8 1 5253 5405 463798451 463798298 3.360000e-57 233
16 TraesCS4A01G301900 chr5A 94.702 151 7 1 5253 5402 464193305 464193455 3.360000e-57 233
17 TraesCS4A01G301900 chr3D 83.495 206 26 6 1454 1654 147821782 147821984 9.540000e-43 185
18 TraesCS4A01G301900 chr3B 82.843 204 29 4 1454 1654 214559682 214559482 1.600000e-40 178


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 TraesCS4A01G301900 chr4A 598711564 598717142 5578 True 10303 10303 100.000000 1 5579 1 chr4A.!!$R1 5578
1 TraesCS4A01G301900 chr4D 4759311 4765064 5753 True 2704 7596 90.475667 7 5551 3 chr4D.!!$R1 5544
2 TraesCS4A01G301900 chr4B 7808024 7812817 4793 True 3661 6911 90.840500 289 5155 2 chr4B.!!$R1 4866


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
239 250 0.674534 CCCCTCTTCCCGTATCTTCG 59.325 60.000 0.0 0.0 0.00 3.79 F
284 295 1.068474 GTTCGCTGCTTGTGTACGAT 58.932 50.000 0.0 0.0 32.13 3.73 F
729 787 1.208293 GAACCCTGGACCTCTGATGTC 59.792 57.143 4.7 4.7 0.00 3.06 F
2069 2149 1.480954 GATAAAGGCACAGGGAGACGA 59.519 52.381 0.0 0.0 0.00 4.20 F
3897 3983 0.037697 CTTCACCGTCCACCGATTCA 60.038 55.000 0.0 0.0 39.56 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1908 1988 0.179029 ACGGTGTTCAACAGAAGGGG 60.179 55.000 0.00 0.00 0.00 4.79 R
2252 2336 1.692042 AGGGCCCCTCACATCTCTG 60.692 63.158 21.43 0.00 0.00 3.35 R
2417 2501 0.319211 TGTCCAAACGTACAGAGCCG 60.319 55.000 0.00 0.00 0.00 5.52 R
3969 4055 0.036010 CTGAAGGCTGGACGATTGGT 60.036 55.000 0.00 0.00 0.00 3.67 R
5559 5839 0.032952 ATGCCTTGCAAACACAGCTG 59.967 50.000 13.48 13.48 43.62 4.24 R


All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 32 8.267894 ACATGAATGAATGGTAGCTAGTTAGTT 58.732 33.333 0.00 0.00 31.46 2.24
72 74 4.555709 TGTCAAGGGCGGCGTTGT 62.556 61.111 33.93 7.15 0.00 3.32
113 115 4.379813 CGAGAGTAAATTTGCAGTGCCAAT 60.380 41.667 13.72 10.90 0.00 3.16
137 139 7.243604 TGGCATTGGAAAAATAGAGTGAATT 57.756 32.000 0.00 0.00 0.00 2.17
157 159 1.064003 TGCTTTGCCCAGTCTCCTTA 58.936 50.000 0.00 0.00 0.00 2.69
162 164 1.153549 GCCCAGTCTCCTTACGCAG 60.154 63.158 0.00 0.00 0.00 5.18
163 165 1.605058 GCCCAGTCTCCTTACGCAGA 61.605 60.000 0.00 0.00 0.00 4.26
177 179 1.446272 GCAGAGTGTACGGTGCCTC 60.446 63.158 6.61 6.61 0.00 4.70
198 209 2.280971 CGTTCTGATTCTGTCGATGCTG 59.719 50.000 0.00 0.00 0.00 4.41
210 221 4.445453 TGTCGATGCTGATGAATAAAGCT 58.555 39.130 0.00 0.00 37.82 3.74
212 223 5.203370 GTCGATGCTGATGAATAAAGCTTG 58.797 41.667 0.00 0.00 37.82 4.01
213 224 3.973135 CGATGCTGATGAATAAAGCTTGC 59.027 43.478 0.00 0.00 37.82 4.01
217 228 3.294214 CTGATGAATAAAGCTTGCCCCT 58.706 45.455 0.00 0.00 0.00 4.79
218 229 3.290710 TGATGAATAAAGCTTGCCCCTC 58.709 45.455 0.00 0.00 0.00 4.30
239 250 0.674534 CCCCTCTTCCCGTATCTTCG 59.325 60.000 0.00 0.00 0.00 3.79
264 275 3.864686 CGGTGCCTGTGTATGCGC 61.865 66.667 0.00 0.00 37.27 6.09
283 294 2.513159 GTTCGCTGCTTGTGTACGA 58.487 52.632 0.00 0.00 0.00 3.43
284 295 1.068474 GTTCGCTGCTTGTGTACGAT 58.932 50.000 0.00 0.00 32.13 3.73
294 305 4.875536 TGCTTGTGTACGATGCTATCATTT 59.124 37.500 0.00 0.00 31.96 2.32
295 306 5.200454 GCTTGTGTACGATGCTATCATTTG 58.800 41.667 0.00 0.00 31.96 2.32
310 366 7.226325 TGCTATCATTTGTTTTTCTTTTGGGTG 59.774 33.333 0.00 0.00 0.00 4.61
331 387 2.212900 TACGAGTGCTGCAGCGATGT 62.213 55.000 32.11 26.90 45.83 3.06
332 388 2.385875 CGAGTGCTGCAGCGATGTT 61.386 57.895 32.11 16.03 45.83 2.71
350 406 3.386486 TGTTCAGTCACGCTAAATCGTT 58.614 40.909 0.00 0.00 41.21 3.85
368 424 2.156117 CGTTGAAAGATTACCGTTGCGA 59.844 45.455 0.00 0.00 0.00 5.10
407 463 2.740981 GACTGTCTCATTCCTGCTGTTG 59.259 50.000 0.00 0.00 0.00 3.33
424 480 5.764686 TGCTGTTGAGTCACACTAAATCATT 59.235 36.000 0.00 0.00 0.00 2.57
441 498 7.789273 AAATCATTGAAAGATTGTTGTTGCA 57.211 28.000 0.00 0.00 35.96 4.08
442 499 7.789273 AATCATTGAAAGATTGTTGTTGCAA 57.211 28.000 0.00 0.00 34.59 4.08
453 510 4.139183 TGTTGTTGCAAAAACAAACAGC 57.861 36.364 28.81 11.85 41.23 4.40
457 514 3.152232 GTTGCAAAAACAAACAGCGTTG 58.848 40.909 0.00 0.00 34.52 4.10
469 526 1.308998 CAGCGTTGGGAACTGTTTCT 58.691 50.000 0.00 0.00 31.71 2.52
541 598 5.688621 CCTGCACGGAAAAATGATTCATATG 59.311 40.000 0.00 0.00 33.16 1.78
549 606 6.703165 GGAAAAATGATTCATATGCCTGAACC 59.297 38.462 0.00 0.00 37.93 3.62
571 629 7.385778 ACCGCTTATCTATATCTGAACTCTC 57.614 40.000 0.00 0.00 0.00 3.20
586 644 4.627035 TGAACTCTCTGATATGTTTGCACG 59.373 41.667 0.00 0.00 0.00 5.34
658 716 3.135530 CCTCTTTTATAGCTGGGCTCTGT 59.864 47.826 0.00 0.00 40.44 3.41
679 737 8.795786 TCTGTTATGTTTGCACAAAGATTAAC 57.204 30.769 10.55 12.03 36.05 2.01
683 741 9.040939 GTTATGTTTGCACAAAGATTAACCTTT 57.959 29.630 10.55 0.00 36.05 3.11
729 787 1.208293 GAACCCTGGACCTCTGATGTC 59.792 57.143 4.70 4.70 0.00 3.06
795 853 6.945435 TCTGGCACTTAAATCACTTCCATTTA 59.055 34.615 0.00 0.00 0.00 1.40
923 981 3.690139 TCGTTAGACTTCTACAGAGGCAG 59.310 47.826 0.00 0.00 0.00 4.85
1016 1074 5.476599 TGTAAAACATGCAGCTATTGGTTCT 59.523 36.000 0.00 0.00 0.00 3.01
1017 1075 4.708726 AAACATGCAGCTATTGGTTCTC 57.291 40.909 0.00 0.00 0.00 2.87
1029 1087 4.640771 ATTGGTTCTCCTTTGTCTAGCA 57.359 40.909 0.00 0.00 34.23 3.49
1078 1136 6.313905 CCGAAAGAATTAGTGTAGCAGATTGT 59.686 38.462 0.00 0.00 0.00 2.71
1079 1137 7.148407 CCGAAAGAATTAGTGTAGCAGATTGTT 60.148 37.037 0.00 0.00 0.00 2.83
1080 1138 8.230486 CGAAAGAATTAGTGTAGCAGATTGTTT 58.770 33.333 0.00 0.00 0.00 2.83
1146 1221 2.959030 GGGCCTCTGAAAGTTTTTGAGT 59.041 45.455 0.84 0.00 33.76 3.41
1299 1374 4.593206 TGTAGGTTCCAAGTGATCAGAAGT 59.407 41.667 0.00 0.00 0.00 3.01
1301 1376 4.392940 AGGTTCCAAGTGATCAGAAGTTG 58.607 43.478 0.00 0.00 0.00 3.16
1432 1507 4.115516 CGACATAACCCTCTTCATGACAG 58.884 47.826 0.00 0.00 0.00 3.51
1499 1577 4.899457 TGACATCCTAATGACGTTATCCCT 59.101 41.667 0.00 0.00 36.67 4.20
1641 1719 5.072055 TCACTGCAAATGATTGAGAAGGAA 58.928 37.500 0.00 0.00 38.94 3.36
1668 1746 7.880160 TGGTTTTCAATCATCTACTAATGGG 57.120 36.000 0.00 0.00 0.00 4.00
1789 1867 3.494048 CCAACAACCAAATAAGGCAAGCA 60.494 43.478 0.00 0.00 0.00 3.91
1908 1988 3.708563 TGGTGTTGTAGCTGCTTTTTC 57.291 42.857 7.79 0.00 0.00 2.29
2045 2125 4.300345 TCGAAAGGGGTAATAGGATTGGA 58.700 43.478 0.00 0.00 0.00 3.53
2069 2149 1.480954 GATAAAGGCACAGGGAGACGA 59.519 52.381 0.00 0.00 0.00 4.20
2252 2336 2.167075 CCCCATTCATGAAAAGCCAGAC 59.833 50.000 13.09 0.00 0.00 3.51
2330 2414 1.560505 GCCAAGATGGAATTGTGGGT 58.439 50.000 0.00 0.00 40.96 4.51
2331 2415 1.901833 GCCAAGATGGAATTGTGGGTT 59.098 47.619 0.00 0.00 40.96 4.11
2397 2481 2.754552 AGACGCAACCATTTGTATGCAT 59.245 40.909 3.79 3.79 38.69 3.96
2417 2501 3.802948 TCTAAGGATGTTCGCTCTTCC 57.197 47.619 4.34 4.34 33.54 3.46
2456 2540 0.951040 GTGCACTTCTCCCAACTCCG 60.951 60.000 10.32 0.00 0.00 4.63
2484 2568 9.607333 TCAGTAATTCTGATAGGATTGGTAGAT 57.393 33.333 4.18 0.00 46.77 1.98
2726 2810 1.541588 GGACATCCAACAAGCCAAGAC 59.458 52.381 0.00 0.00 35.64 3.01
2740 2824 1.528586 CCAAGACAGAAGACTTGCACG 59.471 52.381 0.00 0.00 43.23 5.34
2872 2956 8.586570 TTCAACTTTGCAACCTATAATGTTTG 57.413 30.769 0.00 0.00 0.00 2.93
2875 2959 8.487176 CAACTTTGCAACCTATAATGTTTGTTC 58.513 33.333 0.00 0.00 0.00 3.18
2891 2976 8.871686 ATGTTTGTTCTAAACCTTGTGATTTC 57.128 30.769 0.00 0.00 0.00 2.17
2911 2996 6.678568 TTTCCCATGTACCATGTTGAATTT 57.321 33.333 3.75 0.00 0.00 1.82
2918 3003 7.329226 CCATGTACCATGTTGAATTTTCTTCAC 59.671 37.037 3.75 0.00 0.00 3.18
2934 3019 5.437289 TCTTCACACATGCCTTTAAACTG 57.563 39.130 0.00 0.00 0.00 3.16
3123 3209 3.178611 GGGCGGGATCCCAGGATT 61.179 66.667 30.42 0.00 45.82 3.01
3141 3227 7.039082 CCCAGGATTTCAAGGTTTTCTAATCAA 60.039 37.037 0.00 0.00 0.00 2.57
3182 3268 5.023533 TCTGTACCTGTTGGATTATCAGC 57.976 43.478 0.00 0.00 37.04 4.26
3184 3270 1.668419 ACCTGTTGGATTATCAGCGC 58.332 50.000 0.00 0.00 37.04 5.92
3306 3392 3.973657 GCATGACATTTATGCTTCCAGG 58.026 45.455 0.00 0.00 45.64 4.45
3329 3415 3.244491 CCATTTCTGCCATTGGGTCAAAA 60.244 43.478 4.53 0.45 36.17 2.44
3378 3464 4.400567 GCTCATACCTTGCCTCAAAATTCT 59.599 41.667 0.00 0.00 0.00 2.40
3412 3498 1.812922 CGGCCTAGTCTGCAAGCAG 60.813 63.158 15.67 15.67 44.86 4.24
3451 3537 0.595095 GCAGACTCAAAAGCACCCTG 59.405 55.000 0.00 0.00 0.00 4.45
3519 3605 5.487433 TCACAAGAAAATTCCTCATCGCTA 58.513 37.500 0.00 0.00 0.00 4.26
3568 3654 1.482593 CTACCGGAATGGAAGAGCAGT 59.517 52.381 9.46 0.00 42.00 4.40
3595 3681 1.152756 GTGTCCTTGCCCAGTGGTT 60.153 57.895 8.74 0.00 0.00 3.67
3642 3728 4.783764 AAGTGCTAGTAATTTGTTGGCC 57.216 40.909 0.00 0.00 0.00 5.36
3684 3770 5.940192 TCATACCAAACACAAGTGATCAC 57.060 39.130 18.47 18.47 0.00 3.06
3729 3815 2.705127 GGCATCTCTTCCATCTTCCTCT 59.295 50.000 0.00 0.00 0.00 3.69
3749 3835 1.512694 CCAGCGAAAATGCCCCTTC 59.487 57.895 0.00 0.00 34.65 3.46
3870 3956 0.315251 GTTCTCTGGTTGCAAAGGGC 59.685 55.000 0.00 0.00 45.13 5.19
3897 3983 0.037697 CTTCACCGTCCACCGATTCA 60.038 55.000 0.00 0.00 39.56 2.57
3919 4005 1.741525 GCTGTTGCAAGAAAGCCCA 59.258 52.632 14.81 1.25 39.41 5.36
3932 4018 5.248380 AGAAAGCCCAGTAAATCAAGTCT 57.752 39.130 0.00 0.00 0.00 3.24
3969 4055 1.842920 TGCTTCAGCTCCACCTCCA 60.843 57.895 0.00 0.00 42.66 3.86
4040 4126 0.032615 TTGTTGCCCAAACCTCCTGT 60.033 50.000 0.00 0.00 38.06 4.00
4151 4237 1.065102 CCAAAGCCATCGATGCAGAAG 59.935 52.381 20.25 7.05 0.00 2.85
4269 4355 1.227292 GTACCCTAGCAAGAGCCGC 60.227 63.158 0.00 0.00 43.56 6.53
4349 4435 2.436824 GGGAACCGCAGAGGAAGC 60.437 66.667 0.00 0.00 45.00 3.86
4463 4549 1.672881 GTGGATGTACAAGGATGCTGC 59.327 52.381 0.00 0.00 0.00 5.25
4503 4598 2.156098 AGAAGGTGGCAGCTCCCAA 61.156 57.895 20.86 0.00 36.46 4.12
4567 4662 2.542411 GGAATCTCAAACGATGGCATGC 60.542 50.000 9.90 9.90 0.00 4.06
4584 4679 3.415212 CATGCAGGTGGATTAGTATGGG 58.585 50.000 0.00 0.00 0.00 4.00
4682 4777 2.338785 GCCCAGCAGAGCCTCAAAC 61.339 63.158 0.00 0.00 0.00 2.93
4795 4891 0.991920 GGTCCCTTGATCTCCACCAA 59.008 55.000 0.00 0.00 0.00 3.67
4809 4905 5.875224 TCTCCACCAATTGTCATGTAGAAA 58.125 37.500 4.43 0.00 0.00 2.52
4853 4949 3.093717 ACATACCGAGCCAATTAGTCG 57.906 47.619 0.00 0.00 0.00 4.18
4886 4984 1.879380 CAGCGAGTCAACATTTTGGGA 59.121 47.619 0.00 0.00 33.06 4.37
5000 5103 3.479269 GCGAGCGAAACGGGTGAG 61.479 66.667 0.00 0.00 0.00 3.51
5122 5226 4.114015 ACTTCATCATGGATGGATGCAT 57.886 40.909 0.00 0.00 41.46 3.96
5164 5268 0.950116 GCTCTTGCTTGCTTGTCTGT 59.050 50.000 0.00 0.00 36.03 3.41
5166 5270 2.492012 CTCTTGCTTGCTTGTCTGTCT 58.508 47.619 0.00 0.00 0.00 3.41
5167 5271 2.216046 TCTTGCTTGCTTGTCTGTCTG 58.784 47.619 0.00 0.00 0.00 3.51
5168 5272 1.945394 CTTGCTTGCTTGTCTGTCTGT 59.055 47.619 0.00 0.00 0.00 3.41
5169 5273 1.586422 TGCTTGCTTGTCTGTCTGTC 58.414 50.000 0.00 0.00 0.00 3.51
5170 5274 1.134431 TGCTTGCTTGTCTGTCTGTCA 60.134 47.619 0.00 0.00 0.00 3.58
5171 5275 2.149578 GCTTGCTTGTCTGTCTGTCAT 58.850 47.619 0.00 0.00 0.00 3.06
5172 5276 2.551459 GCTTGCTTGTCTGTCTGTCATT 59.449 45.455 0.00 0.00 0.00 2.57
5173 5277 3.608707 GCTTGCTTGTCTGTCTGTCATTG 60.609 47.826 0.00 0.00 0.00 2.82
5174 5278 3.198409 TGCTTGTCTGTCTGTCATTGT 57.802 42.857 0.00 0.00 0.00 2.71
5175 5279 4.335400 TGCTTGTCTGTCTGTCATTGTA 57.665 40.909 0.00 0.00 0.00 2.41
5176 5280 4.898320 TGCTTGTCTGTCTGTCATTGTAT 58.102 39.130 0.00 0.00 0.00 2.29
5177 5281 4.931601 TGCTTGTCTGTCTGTCATTGTATC 59.068 41.667 0.00 0.00 0.00 2.24
5178 5282 5.174395 GCTTGTCTGTCTGTCATTGTATCT 58.826 41.667 0.00 0.00 0.00 1.98
5179 5283 5.063186 GCTTGTCTGTCTGTCATTGTATCTG 59.937 44.000 0.00 0.00 0.00 2.90
5180 5284 4.498241 TGTCTGTCTGTCATTGTATCTGC 58.502 43.478 0.00 0.00 0.00 4.26
5181 5285 3.868077 GTCTGTCTGTCATTGTATCTGCC 59.132 47.826 0.00 0.00 0.00 4.85
5182 5286 3.515104 TCTGTCTGTCATTGTATCTGCCA 59.485 43.478 0.00 0.00 0.00 4.92
5183 5287 3.599343 TGTCTGTCATTGTATCTGCCAC 58.401 45.455 0.00 0.00 0.00 5.01
5227 5331 9.590451 CCATTCTGTTATTTCTGTTATTTGCAT 57.410 29.630 0.00 0.00 0.00 3.96
5246 5350 7.637631 TTGCATACATTCTTTAATAGTGGCA 57.362 32.000 0.00 0.00 0.00 4.92
5247 5351 7.637631 TGCATACATTCTTTAATAGTGGCAA 57.362 32.000 0.00 0.00 0.00 4.52
5248 5352 8.060931 TGCATACATTCTTTAATAGTGGCAAA 57.939 30.769 0.00 0.00 0.00 3.68
5249 5353 8.526978 TGCATACATTCTTTAATAGTGGCAAAA 58.473 29.630 0.00 0.00 0.00 2.44
5250 5354 9.364989 GCATACATTCTTTAATAGTGGCAAAAA 57.635 29.630 0.00 0.00 0.00 1.94
5255 5359 9.585099 CATTCTTTAATAGTGGCAAAAATAGCA 57.415 29.630 0.00 0.00 0.00 3.49
5256 5360 8.980143 TTCTTTAATAGTGGCAAAAATAGCAC 57.020 30.769 0.00 0.00 0.00 4.40
5257 5361 8.348285 TCTTTAATAGTGGCAAAAATAGCACT 57.652 30.769 0.00 0.00 0.00 4.40
5258 5362 8.243426 TCTTTAATAGTGGCAAAAATAGCACTG 58.757 33.333 0.00 0.00 0.00 3.66
5259 5363 2.730550 AGTGGCAAAAATAGCACTGC 57.269 45.000 0.00 0.00 0.00 4.40
5262 5366 3.763360 AGTGGCAAAAATAGCACTGCATA 59.237 39.130 3.30 0.00 36.50 3.14
5264 5368 5.593909 AGTGGCAAAAATAGCACTGCATATA 59.406 36.000 3.30 0.00 36.50 0.86
5265 5369 6.266103 AGTGGCAAAAATAGCACTGCATATAT 59.734 34.615 3.30 0.00 36.50 0.86
5268 5372 6.306356 GGCAAAAATAGCACTGCATATATTCG 59.694 38.462 3.30 0.00 36.50 3.34
5270 5374 8.015087 GCAAAAATAGCACTGCATATATTCGTA 58.985 33.333 3.30 0.00 34.87 3.43
5273 5377 8.777865 AAATAGCACTGCATATATTCGTATGT 57.222 30.769 3.30 0.00 35.09 2.29
5274 5378 7.761651 ATAGCACTGCATATATTCGTATGTG 57.238 36.000 3.30 0.00 35.09 3.21
5276 5380 6.223120 AGCACTGCATATATTCGTATGTGAA 58.777 36.000 3.30 0.00 35.09 3.18
5277 5381 6.705825 AGCACTGCATATATTCGTATGTGAAA 59.294 34.615 3.30 0.00 35.09 2.69
5278 5382 7.011773 GCACTGCATATATTCGTATGTGAAAG 58.988 38.462 0.00 0.00 35.09 2.62
5279 5383 7.513132 CACTGCATATATTCGTATGTGAAAGG 58.487 38.462 0.00 0.00 35.09 3.11
5280 5384 7.384932 CACTGCATATATTCGTATGTGAAAGGA 59.615 37.037 0.00 0.00 35.09 3.36
5281 5385 7.600375 ACTGCATATATTCGTATGTGAAAGGAG 59.400 37.037 0.00 0.00 35.09 3.69
5282 5386 6.368791 TGCATATATTCGTATGTGAAAGGAGC 59.631 38.462 0.00 0.00 35.09 4.70
5285 5389 8.993121 CATATATTCGTATGTGAAAGGAGCTTT 58.007 33.333 0.00 0.00 36.29 3.51
5321 5425 9.524106 AATTTTCACATTATGCATGTCATGTAG 57.476 29.630 10.16 9.56 43.17 2.74
5322 5426 7.628769 TTTCACATTATGCATGTCATGTAGT 57.371 32.000 10.16 1.63 43.17 2.73
5323 5427 8.729805 TTTCACATTATGCATGTCATGTAGTA 57.270 30.769 10.16 2.89 43.17 1.82
5325 5429 8.907222 TCACATTATGCATGTCATGTAGTATT 57.093 30.769 10.16 0.00 43.17 1.89
5326 5430 9.995003 TCACATTATGCATGTCATGTAGTATTA 57.005 29.630 10.16 0.00 43.17 0.98
5349 5453 9.965824 ATTAATTTTATCAATAGTCAAAGGCGG 57.034 29.630 0.00 0.00 0.00 6.13
5350 5454 7.404671 AATTTTATCAATAGTCAAAGGCGGT 57.595 32.000 0.00 0.00 0.00 5.68
5351 5455 6.431198 TTTTATCAATAGTCAAAGGCGGTC 57.569 37.500 0.00 0.00 0.00 4.79
5352 5456 3.914426 ATCAATAGTCAAAGGCGGTCT 57.086 42.857 0.00 0.00 0.00 3.85
5354 5458 3.334691 TCAATAGTCAAAGGCGGTCTTG 58.665 45.455 0.00 0.00 35.55 3.02
5355 5459 3.007506 TCAATAGTCAAAGGCGGTCTTGA 59.992 43.478 0.00 0.00 35.55 3.02
5356 5460 2.450609 TAGTCAAAGGCGGTCTTGAC 57.549 50.000 13.46 13.46 35.55 3.18
5357 5461 0.468226 AGTCAAAGGCGGTCTTGACA 59.532 50.000 19.55 0.00 36.68 3.58
5358 5462 1.134220 AGTCAAAGGCGGTCTTGACAA 60.134 47.619 19.55 0.00 36.68 3.18
5359 5463 1.673920 GTCAAAGGCGGTCTTGACAAA 59.326 47.619 15.31 0.00 35.52 2.83
5360 5464 1.673920 TCAAAGGCGGTCTTGACAAAC 59.326 47.619 0.00 0.00 35.55 2.93
5361 5465 0.661020 AAAGGCGGTCTTGACAAACG 59.339 50.000 0.00 0.00 35.55 3.60
5367 5471 3.103793 CGGTCTTGACAAACGCATTAG 57.896 47.619 3.08 0.00 0.00 1.73
5369 5473 2.414161 GGTCTTGACAAACGCATTAGGC 60.414 50.000 3.08 0.00 39.90 3.93
5370 5474 1.810151 TCTTGACAAACGCATTAGGCC 59.190 47.619 0.00 0.00 40.31 5.19
5371 5475 0.885196 TTGACAAACGCATTAGGCCC 59.115 50.000 0.00 0.00 40.31 5.80
5372 5476 0.037590 TGACAAACGCATTAGGCCCT 59.962 50.000 0.00 0.00 40.31 5.19
5373 5477 1.279558 TGACAAACGCATTAGGCCCTA 59.720 47.619 0.00 0.00 40.31 3.53
5374 5478 2.092646 TGACAAACGCATTAGGCCCTAT 60.093 45.455 0.00 0.00 40.31 2.57
5375 5479 3.134985 TGACAAACGCATTAGGCCCTATA 59.865 43.478 0.00 0.00 40.31 1.31
5376 5480 4.202419 TGACAAACGCATTAGGCCCTATAT 60.202 41.667 0.00 0.00 40.31 0.86
5377 5481 5.012251 TGACAAACGCATTAGGCCCTATATA 59.988 40.000 0.00 0.00 40.31 0.86
5379 5483 5.247564 ACAAACGCATTAGGCCCTATATAGA 59.752 40.000 11.53 0.00 40.31 1.98
5380 5484 6.070194 ACAAACGCATTAGGCCCTATATAGAT 60.070 38.462 11.53 0.00 40.31 1.98
5381 5485 5.537300 ACGCATTAGGCCCTATATAGATG 57.463 43.478 11.53 6.87 40.31 2.90
5382 5486 4.345257 ACGCATTAGGCCCTATATAGATGG 59.655 45.833 11.53 6.04 40.31 3.51
5384 5488 5.070446 CGCATTAGGCCCTATATAGATGGAA 59.930 44.000 11.53 0.00 40.31 3.53
5386 5490 6.465035 GCATTAGGCCCTATATAGATGGAAGG 60.465 46.154 11.53 3.94 36.11 3.46
5388 5492 4.889780 AGGCCCTATATAGATGGAAGGAG 58.110 47.826 11.53 0.00 0.00 3.69
5389 5493 3.970640 GGCCCTATATAGATGGAAGGAGG 59.029 52.174 11.53 1.87 0.00 4.30
5390 5494 3.970640 GCCCTATATAGATGGAAGGAGGG 59.029 52.174 11.53 3.52 44.52 4.30
5391 5495 4.327010 GCCCTATATAGATGGAAGGAGGGA 60.327 50.000 11.53 0.00 44.48 4.20
5392 5496 5.463154 CCCTATATAGATGGAAGGAGGGAG 58.537 50.000 11.53 0.00 44.48 4.30
5393 5497 5.042979 CCCTATATAGATGGAAGGAGGGAGT 60.043 48.000 11.53 0.00 44.48 3.85
5394 5498 5.896678 CCTATATAGATGGAAGGAGGGAGTG 59.103 48.000 11.53 0.00 0.00 3.51
5397 5677 0.179936 GATGGAAGGAGGGAGTGCTG 59.820 60.000 0.00 0.00 0.00 4.41
5403 5683 0.853530 AGGAGGGAGTGCTGGTTTTT 59.146 50.000 0.00 0.00 0.00 1.94
5404 5684 0.961753 GGAGGGAGTGCTGGTTTTTG 59.038 55.000 0.00 0.00 0.00 2.44
5409 5689 1.341209 GGAGTGCTGGTTTTTGAAGGG 59.659 52.381 0.00 0.00 0.00 3.95
5412 5692 3.103742 AGTGCTGGTTTTTGAAGGGAAA 58.896 40.909 0.00 0.00 0.00 3.13
5416 5696 5.007626 GTGCTGGTTTTTGAAGGGAAATTTC 59.992 40.000 9.83 9.83 0.00 2.17
5417 5697 4.515191 GCTGGTTTTTGAAGGGAAATTTCC 59.485 41.667 26.41 26.41 46.82 3.13
5436 5716 1.283029 CCATCCACCTCAACCTCATGT 59.717 52.381 0.00 0.00 0.00 3.21
5461 5741 7.707035 GTGAAGAATCCTACGTATTGAAGATGT 59.293 37.037 0.00 0.00 0.00 3.06
5467 5747 5.049828 CCTACGTATTGAAGATGTCATGCA 58.950 41.667 0.00 0.00 35.70 3.96
5477 5757 4.978083 AGATGTCATGCAACTCCATTTC 57.022 40.909 0.00 0.00 0.00 2.17
5482 5762 3.254166 GTCATGCAACTCCATTTCTGTGT 59.746 43.478 0.00 0.00 0.00 3.72
5495 5775 8.924511 TCCATTTCTGTGTTTTTCTCTATTCT 57.075 30.769 0.00 0.00 0.00 2.40
5525 5805 6.757897 TTACAAATCCTGCGAATCAAAGAT 57.242 33.333 0.00 0.00 0.00 2.40
5526 5806 4.990257 ACAAATCCTGCGAATCAAAGATG 58.010 39.130 0.00 0.00 0.00 2.90
5528 5808 1.382522 TCCTGCGAATCAAAGATGCC 58.617 50.000 0.00 0.00 0.00 4.40
5544 5824 3.382546 AGATGCCCTGAATGTTTGTATGC 59.617 43.478 0.00 0.00 0.00 3.14
5551 5831 4.930405 CCTGAATGTTTGTATGCATGCAAA 59.070 37.500 31.20 31.20 39.48 3.68
5552 5832 5.583061 CCTGAATGTTTGTATGCATGCAAAT 59.417 36.000 35.09 24.29 42.66 2.32
5553 5833 6.757478 CCTGAATGTTTGTATGCATGCAAATA 59.243 34.615 35.09 32.92 42.66 1.40
5554 5834 7.278203 CCTGAATGTTTGTATGCATGCAAATAA 59.722 33.333 35.09 27.99 42.66 1.40
5555 5835 8.187354 TGAATGTTTGTATGCATGCAAATAAG 57.813 30.769 35.09 0.00 42.66 1.73
5556 5836 7.818446 TGAATGTTTGTATGCATGCAAATAAGT 59.182 29.630 35.09 27.20 42.66 2.24
5557 5837 6.947903 TGTTTGTATGCATGCAAATAAGTG 57.052 33.333 35.09 0.00 42.66 3.16
5558 5838 6.685657 TGTTTGTATGCATGCAAATAAGTGA 58.314 32.000 35.09 16.50 42.66 3.41
5559 5839 6.585702 TGTTTGTATGCATGCAAATAAGTGAC 59.414 34.615 35.09 24.84 42.66 3.67
5560 5840 5.893897 TGTATGCATGCAAATAAGTGACA 57.106 34.783 26.68 14.60 0.00 3.58
5561 5841 5.882553 TGTATGCATGCAAATAAGTGACAG 58.117 37.500 26.68 0.00 0.00 3.51
5562 5842 3.220507 TGCATGCAAATAAGTGACAGC 57.779 42.857 20.30 0.00 0.00 4.40
5563 5843 2.821378 TGCATGCAAATAAGTGACAGCT 59.179 40.909 20.30 0.00 0.00 4.24
5564 5844 3.176708 GCATGCAAATAAGTGACAGCTG 58.823 45.455 14.21 13.48 0.00 4.24
5565 5845 3.366679 GCATGCAAATAAGTGACAGCTGT 60.367 43.478 21.88 21.88 0.00 4.40
5566 5846 3.902261 TGCAAATAAGTGACAGCTGTG 57.098 42.857 27.27 7.50 0.00 3.66
5567 5847 3.213506 TGCAAATAAGTGACAGCTGTGT 58.786 40.909 27.27 9.11 40.71 3.72
5568 5848 3.631686 TGCAAATAAGTGACAGCTGTGTT 59.368 39.130 27.27 16.65 36.88 3.32
5569 5849 4.097741 TGCAAATAAGTGACAGCTGTGTTT 59.902 37.500 27.27 17.00 36.88 2.83
5570 5850 4.442073 GCAAATAAGTGACAGCTGTGTTTG 59.558 41.667 27.27 21.85 36.88 2.93
5571 5851 3.904136 ATAAGTGACAGCTGTGTTTGC 57.096 42.857 27.27 10.06 36.88 3.68
5572 5852 1.462616 AAGTGACAGCTGTGTTTGCA 58.537 45.000 27.27 12.96 36.88 4.08
5573 5853 1.462616 AGTGACAGCTGTGTTTGCAA 58.537 45.000 27.27 0.00 36.88 4.08
5574 5854 1.402968 AGTGACAGCTGTGTTTGCAAG 59.597 47.619 27.27 0.00 36.88 4.01
5575 5855 0.740149 TGACAGCTGTGTTTGCAAGG 59.260 50.000 27.27 0.00 36.88 3.61
5576 5856 0.595825 GACAGCTGTGTTTGCAAGGC 60.596 55.000 27.27 0.95 36.88 4.35
5577 5857 1.321805 ACAGCTGTGTTTGCAAGGCA 61.322 50.000 20.97 0.00 36.47 4.75
5578 5858 0.032952 CAGCTGTGTTTGCAAGGCAT 59.967 50.000 5.25 0.00 38.76 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.949754 AGCTACCATTCATTCATGTGGTG 59.050 43.478 12.42 5.30 44.27 4.17
1 2 4.240881 AGCTACCATTCATTCATGTGGT 57.759 40.909 8.33 8.33 46.16 4.16
2 3 5.371526 ACTAGCTACCATTCATTCATGTGG 58.628 41.667 0.00 0.00 37.74 4.17
3 4 6.932356 AACTAGCTACCATTCATTCATGTG 57.068 37.500 0.00 0.00 0.00 3.21
4 5 7.796054 ACTAACTAGCTACCATTCATTCATGT 58.204 34.615 0.00 0.00 0.00 3.21
5 6 8.668510 AACTAACTAGCTACCATTCATTCATG 57.331 34.615 0.00 0.00 0.00 3.07
17 18 5.469084 ACAGCAAACCAAACTAACTAGCTAC 59.531 40.000 0.00 0.00 0.00 3.58
54 56 3.726517 CAACGCCGCCCTTGACAG 61.727 66.667 0.00 0.00 0.00 3.51
83 85 5.124457 ACTGCAAATTTACTCTCGCAATGAT 59.876 36.000 0.00 0.00 0.00 2.45
113 115 6.855763 ATTCACTCTATTTTTCCAATGCCA 57.144 33.333 0.00 0.00 0.00 4.92
122 124 6.427853 GGGCAAAGCAAATTCACTCTATTTTT 59.572 34.615 0.00 0.00 0.00 1.94
137 139 0.185901 AAGGAGACTGGGCAAAGCAA 59.814 50.000 0.00 0.00 42.68 3.91
157 159 2.049433 GCACCGTACACTCTGCGT 60.049 61.111 0.00 0.00 0.00 5.24
162 164 0.731855 GAACGAGGCACCGTACACTC 60.732 60.000 5.44 0.00 42.54 3.51
163 165 1.177256 AGAACGAGGCACCGTACACT 61.177 55.000 5.44 3.94 42.54 3.55
177 179 2.280971 CAGCATCGACAGAATCAGAACG 59.719 50.000 0.00 0.00 0.00 3.95
198 209 2.625314 GGAGGGGCAAGCTTTATTCATC 59.375 50.000 0.00 0.00 0.00 2.92
224 235 2.681848 GAGACACGAAGATACGGGAAGA 59.318 50.000 0.00 0.00 39.16 2.87
225 236 2.683867 AGAGACACGAAGATACGGGAAG 59.316 50.000 0.00 0.00 39.16 3.46
226 237 2.681848 GAGAGACACGAAGATACGGGAA 59.318 50.000 0.00 0.00 39.16 3.97
231 242 2.791849 GCACCGAGAGACACGAAGATAC 60.792 54.545 0.00 0.00 0.00 2.24
232 243 1.400846 GCACCGAGAGACACGAAGATA 59.599 52.381 0.00 0.00 0.00 1.98
233 244 0.171455 GCACCGAGAGACACGAAGAT 59.829 55.000 0.00 0.00 0.00 2.40
234 245 1.579932 GCACCGAGAGACACGAAGA 59.420 57.895 0.00 0.00 0.00 2.87
236 247 1.901948 AGGCACCGAGAGACACGAA 60.902 57.895 0.00 0.00 0.00 3.85
239 250 1.373497 CACAGGCACCGAGAGACAC 60.373 63.158 0.00 0.00 0.00 3.67
264 275 1.127817 CGTACACAAGCAGCGAACG 59.872 57.895 0.00 0.00 0.00 3.95
283 294 7.938490 ACCCAAAAGAAAAACAAATGATAGCAT 59.062 29.630 0.00 0.00 35.92 3.79
284 295 7.226325 CACCCAAAAGAAAAACAAATGATAGCA 59.774 33.333 0.00 0.00 0.00 3.49
294 305 5.591067 ACTCGTATCACCCAAAAGAAAAACA 59.409 36.000 0.00 0.00 0.00 2.83
295 306 5.912955 CACTCGTATCACCCAAAAGAAAAAC 59.087 40.000 0.00 0.00 0.00 2.43
310 366 0.596083 ATCGCTGCAGCACTCGTATC 60.596 55.000 36.03 5.81 42.21 2.24
331 387 3.644823 TCAACGATTTAGCGTGACTGAA 58.355 40.909 0.00 0.00 44.86 3.02
332 388 3.291809 TCAACGATTTAGCGTGACTGA 57.708 42.857 0.00 0.00 44.86 3.41
350 406 4.035324 TGTTTTCGCAACGGTAATCTTTCA 59.965 37.500 0.00 0.00 0.00 2.69
368 424 2.024369 AGTCCCAAACCCTGTCTGTTTT 60.024 45.455 0.00 0.00 33.82 2.43
407 463 9.552114 CAATCTTTCAATGATTTAGTGTGACTC 57.448 33.333 0.00 0.00 32.47 3.36
424 480 6.791887 TGTTTTTGCAACAACAATCTTTCA 57.208 29.167 24.84 3.25 29.81 2.69
441 498 2.997303 GTTCCCAACGCTGTTTGTTTTT 59.003 40.909 0.00 0.00 0.00 1.94
442 499 2.232696 AGTTCCCAACGCTGTTTGTTTT 59.767 40.909 0.00 0.00 36.23 2.43
453 510 3.349488 GGAAAGAAACAGTTCCCAACG 57.651 47.619 0.00 0.00 37.87 4.10
469 526 2.159014 CGGATAGTGGAACATCGGGAAA 60.159 50.000 0.00 0.00 44.52 3.13
476 533 2.236146 TGCTGAACGGATAGTGGAACAT 59.764 45.455 0.00 0.00 44.52 2.71
541 598 5.105716 TCAGATATAGATAAGCGGTTCAGGC 60.106 44.000 1.59 0.00 0.00 4.85
549 606 8.262715 TCAGAGAGTTCAGATATAGATAAGCG 57.737 38.462 0.00 0.00 0.00 4.68
571 629 4.627035 TCAGTCTTCGTGCAAACATATCAG 59.373 41.667 0.00 0.00 0.00 2.90
586 644 7.117812 TCGTTCCATTCATAAAGTTCAGTCTTC 59.882 37.037 0.00 0.00 0.00 2.87
679 737 8.229253 TCCACTCATCATTCAATTCATAAAGG 57.771 34.615 0.00 0.00 0.00 3.11
683 741 6.717997 CCCATCCACTCATCATTCAATTCATA 59.282 38.462 0.00 0.00 0.00 2.15
717 775 0.528017 TGTCTGCGACATCAGAGGTC 59.472 55.000 5.06 5.06 43.10 3.85
795 853 6.942532 TGTTACAGAGAAGAAGCAAACAAT 57.057 33.333 0.00 0.00 0.00 2.71
883 941 7.431668 GTCTAACGACGTTTCTCTTATAAGCAT 59.568 37.037 19.71 0.00 0.00 3.79
884 942 6.744537 GTCTAACGACGTTTCTCTTATAAGCA 59.255 38.462 19.71 0.00 0.00 3.91
900 958 3.439476 TGCCTCTGTAGAAGTCTAACGAC 59.561 47.826 0.00 0.00 40.54 4.34
923 981 3.835395 CTGATATCAGGAGGAGTTACCCC 59.165 52.174 22.89 0.00 40.20 4.95
961 1019 3.761218 TCTGGACACAACAACACAATGTT 59.239 39.130 0.00 0.00 44.08 2.71
962 1020 3.351740 TCTGGACACAACAACACAATGT 58.648 40.909 0.00 0.00 34.24 2.71
1004 1062 4.917906 AGACAAAGGAGAACCAATAGCT 57.082 40.909 0.00 0.00 38.94 3.32
1029 1087 7.260603 GGCAAGAGTAATCAACAGCAAATATT 58.739 34.615 0.00 0.00 0.00 1.28
1078 1136 6.589523 CCATTGACAACAGAACAAACAGAAAA 59.410 34.615 0.00 0.00 0.00 2.29
1079 1137 6.071672 TCCATTGACAACAGAACAAACAGAAA 60.072 34.615 0.00 0.00 0.00 2.52
1080 1138 5.417266 TCCATTGACAACAGAACAAACAGAA 59.583 36.000 0.00 0.00 0.00 3.02
1146 1221 8.748412 CAAGGAAATGGTATCATAAGGAAACAA 58.252 33.333 0.00 0.00 32.44 2.83
1299 1374 4.637534 GTCAAGCAGATAAAGAGATGGCAA 59.362 41.667 0.00 0.00 0.00 4.52
1301 1376 4.194640 TGTCAAGCAGATAAAGAGATGGC 58.805 43.478 0.00 0.00 0.00 4.40
1372 1447 5.395435 GGGTCAAGACTAACCTCAGGTAATC 60.395 48.000 0.00 0.00 33.12 1.75
1410 1485 4.115516 CTGTCATGAAGAGGGTTATGTCG 58.884 47.826 0.00 0.00 0.00 4.35
1420 1495 5.529060 GGGTTTATTAGGCTGTCATGAAGAG 59.471 44.000 0.00 0.00 0.00 2.85
1432 1507 3.977312 AGGAAACTGGGGTTTATTAGGC 58.023 45.455 0.00 0.00 44.58 3.93
1530 1608 1.765314 ACCTGTCTATAGGCCTTGCAG 59.235 52.381 12.58 12.21 41.75 4.41
1614 1692 3.192001 TCTCAATCATTTGCAGTGAAGCC 59.808 43.478 7.79 0.00 32.61 4.35
1641 1719 8.960591 CCATTAGTAGATGATTGAAAACCAAGT 58.039 33.333 0.00 0.00 38.31 3.16
1660 1738 2.092753 CAGCACCTGATGACCCATTAGT 60.093 50.000 0.00 0.00 32.44 2.24
1716 1794 4.207165 GGTTTACATGTATGCTGTGGGAT 58.793 43.478 6.36 0.00 0.00 3.85
1908 1988 0.179029 ACGGTGTTCAACAGAAGGGG 60.179 55.000 0.00 0.00 0.00 4.79
2045 2125 4.273318 GTCTCCCTGTGCCTTTATCAATT 58.727 43.478 0.00 0.00 0.00 2.32
2069 2149 4.211920 GCCTAGAGTTCAGAGTATCCAGT 58.788 47.826 0.00 0.00 33.66 4.00
2132 2216 5.423931 AGAAAAACAAAGGAGGCCAAGTAAA 59.576 36.000 5.01 0.00 0.00 2.01
2140 2224 9.489084 AAATACATAAAGAAAAACAAAGGAGGC 57.511 29.630 0.00 0.00 0.00 4.70
2182 2266 4.260375 GCTGTAAGTTTGGCAGATCATACG 60.260 45.833 0.00 0.00 35.30 3.06
2252 2336 1.692042 AGGGCCCCTCACATCTCTG 60.692 63.158 21.43 0.00 0.00 3.35
2397 2481 2.099263 CGGAAGAGCGAACATCCTTAGA 59.901 50.000 0.00 0.00 0.00 2.10
2407 2491 0.963856 TACAGAGCCGGAAGAGCGAA 60.964 55.000 5.05 0.00 34.64 4.70
2417 2501 0.319211 TGTCCAAACGTACAGAGCCG 60.319 55.000 0.00 0.00 0.00 5.52
2484 2568 6.417258 TCCAGCTTTTATCAGATGATGACAA 58.583 36.000 5.58 0.00 41.91 3.18
2656 2740 2.214216 TCAGGGTCCAACGGGTCTG 61.214 63.158 0.00 0.00 34.93 3.51
2726 2810 2.148916 TGTACCGTGCAAGTCTTCTG 57.851 50.000 0.00 0.00 0.00 3.02
2740 2824 3.275617 TTGCTCCACATACCATGTACC 57.724 47.619 0.00 0.00 42.70 3.34
2780 2864 2.496871 TCCCATGGCAAAAATAGCACTG 59.503 45.455 6.09 0.00 0.00 3.66
2827 2911 2.381911 AGGCATCCCAGCAGTTAAATG 58.618 47.619 0.00 0.00 35.83 2.32
2872 2956 6.015434 ACATGGGAAATCACAAGGTTTAGAAC 60.015 38.462 0.00 0.00 30.29 3.01
2875 2959 5.982890 ACATGGGAAATCACAAGGTTTAG 57.017 39.130 0.00 0.00 30.29 1.85
2911 2996 5.359576 ACAGTTTAAAGGCATGTGTGAAGAA 59.640 36.000 0.00 0.00 0.00 2.52
2918 3003 9.507280 CATAGAAATACAGTTTAAAGGCATGTG 57.493 33.333 0.00 0.00 0.00 3.21
2959 3044 3.341823 ACTCTGCATGATCCTGAACAAC 58.658 45.455 0.00 0.00 0.00 3.32
3000 3086 2.158460 CCTATCAATTCTTGGGTCCCCC 60.158 54.545 5.13 0.00 45.71 5.40
3044 3130 1.898154 CCACGAGATTCCGGGAACT 59.102 57.895 12.53 11.23 34.30 3.01
3123 3209 7.831691 TGGTGATTGATTAGAAAACCTTGAA 57.168 32.000 0.00 0.00 0.00 2.69
3141 3227 3.945921 CAGATGAAGTGATGCTTGGTGAT 59.054 43.478 0.00 0.00 37.59 3.06
3184 3270 1.875576 GCTTGATCGTCCAGCATAGGG 60.876 57.143 6.31 0.00 0.00 3.53
3306 3392 0.176449 GACCCAATGGCAGAAATGGC 59.824 55.000 0.00 0.00 33.59 4.40
3329 3415 1.777272 GGTTATGCTCTTCCTGGGGAT 59.223 52.381 0.00 0.00 0.00 3.85
3361 3447 1.270550 CGCAGAATTTTGAGGCAAGGT 59.729 47.619 0.00 0.00 0.00 3.50
3378 3464 1.218047 CCGACCCTGAGAATTCGCA 59.782 57.895 11.56 11.56 0.00 5.10
3412 3498 0.319728 TGAGAAGCCTGTGACAGAGC 59.680 55.000 15.33 15.30 32.44 4.09
3451 3537 1.008079 GTGGCTTTGACTGCACAGC 60.008 57.895 0.00 0.00 44.97 4.40
3510 3596 4.222886 CAGACGGTCTAAATAGCGATGAG 58.777 47.826 10.87 0.00 42.76 2.90
3519 3605 3.430929 GCAGATGGACAGACGGTCTAAAT 60.431 47.826 10.87 2.32 46.16 1.40
3568 3654 0.687354 GGCAAGGACACCTCTTCAGA 59.313 55.000 0.00 0.00 30.89 3.27
3595 3681 0.250252 TCTGACTTTGCATGTGCGGA 60.250 50.000 0.01 0.00 45.83 5.54
3642 3728 4.076394 TGAATCCACCCTTAAAAAGACCG 58.924 43.478 0.00 0.00 0.00 4.79
3684 3770 0.448990 CATGTGAATGTGGGACAGCG 59.551 55.000 0.00 0.00 41.80 5.18
3729 3815 3.381136 GGGGCATTTTCGCTGGCA 61.381 61.111 0.00 0.00 40.70 4.92
3749 3835 0.109597 GTTTGGTGCATGAGGCTTCG 60.110 55.000 0.00 0.00 45.15 3.79
3870 3956 3.007635 GGTGGACGGTGAAGAAATTAGG 58.992 50.000 0.00 0.00 0.00 2.69
3897 3983 1.271656 GGCTTTCTTGCAACAGCAGAT 59.728 47.619 17.91 0.00 39.82 2.90
3919 4005 5.798132 TGATGTGCTCAGACTTGATTTACT 58.202 37.500 0.00 0.00 31.68 2.24
3932 4018 2.968675 CACTGACATCTGATGTGCTCA 58.031 47.619 26.71 17.03 45.03 4.26
3969 4055 0.036010 CTGAAGGCTGGACGATTGGT 60.036 55.000 0.00 0.00 0.00 3.67
4040 4126 3.292492 TTAGGTCAGCCATCTCGACTA 57.708 47.619 0.00 0.00 37.19 2.59
4068 4154 1.845809 GCACCACTGGCTTGAACTCG 61.846 60.000 0.00 0.00 0.00 4.18
4142 4228 6.690194 ATCTTAAACCACATCTTCTGCATC 57.310 37.500 0.00 0.00 0.00 3.91
4151 4237 7.672983 TCAAGTCTGAATCTTAAACCACATC 57.327 36.000 0.00 0.00 0.00 3.06
4269 4355 4.878397 GGTTCAGGTAATCTGTCAATCCAG 59.122 45.833 0.00 0.00 43.76 3.86
4349 4435 2.749621 GCAGGGACCATAAACTCACAAG 59.250 50.000 0.00 0.00 0.00 3.16
4463 4549 3.740832 TGCCTTTGAGCGATCATAATACG 59.259 43.478 3.25 0.00 34.65 3.06
4503 4598 0.685097 TGGGTGCGAGCTCTTTACTT 59.315 50.000 12.85 0.00 0.00 2.24
4515 4610 0.747644 TTGCATGGACTATGGGTGCG 60.748 55.000 0.57 0.00 39.22 5.34
4567 4662 4.080582 TGACAACCCATACTAATCCACCTG 60.081 45.833 0.00 0.00 0.00 4.00
4584 4679 5.052481 TCTGCTGCTATATGACATGACAAC 58.948 41.667 0.00 0.00 0.00 3.32
4682 4777 1.314534 TGTTTGCCTCCATGCCATCG 61.315 55.000 0.00 0.00 0.00 3.84
4795 4891 7.823745 AAGAACACCTTTTCTACATGACAAT 57.176 32.000 0.00 0.00 34.60 2.71
4853 4949 0.383231 CTCGCTGGGATCAAAATGCC 59.617 55.000 0.00 0.00 43.46 4.40
4886 4984 0.253347 ATGTCATCTGACCCCACCCT 60.253 55.000 7.81 0.00 44.15 4.34
5122 5226 7.221450 AGCTAACAACACTGGTAGTTCAAATA 58.779 34.615 0.00 0.00 43.74 1.40
5164 5268 3.261643 ACAGTGGCAGATACAATGACAGA 59.738 43.478 0.00 0.00 36.02 3.41
5166 5270 3.701205 ACAGTGGCAGATACAATGACA 57.299 42.857 0.00 0.00 37.37 3.58
5167 5271 6.316140 TGAATAACAGTGGCAGATACAATGAC 59.684 38.462 0.00 0.00 37.37 3.06
5168 5272 6.413892 TGAATAACAGTGGCAGATACAATGA 58.586 36.000 0.00 0.00 37.37 2.57
5169 5273 6.682423 TGAATAACAGTGGCAGATACAATG 57.318 37.500 0.00 0.00 39.58 2.82
5170 5274 6.932356 CTGAATAACAGTGGCAGATACAAT 57.068 37.500 0.00 0.00 41.30 2.71
5229 5333 9.585099 TGCTATTTTTGCCACTATTAAAGAATG 57.415 29.630 0.00 0.00 0.00 2.67
5230 5334 9.586435 GTGCTATTTTTGCCACTATTAAAGAAT 57.414 29.630 0.00 0.00 0.00 2.40
5232 5336 8.243426 CAGTGCTATTTTTGCCACTATTAAAGA 58.757 33.333 0.00 0.00 0.00 2.52
5233 5337 7.009540 GCAGTGCTATTTTTGCCACTATTAAAG 59.990 37.037 8.18 0.00 0.00 1.85
5234 5338 6.811170 GCAGTGCTATTTTTGCCACTATTAAA 59.189 34.615 8.18 0.00 0.00 1.52
5236 5340 5.417266 TGCAGTGCTATTTTTGCCACTATTA 59.583 36.000 17.60 0.00 35.75 0.98
5237 5341 4.220382 TGCAGTGCTATTTTTGCCACTATT 59.780 37.500 17.60 0.00 35.75 1.73
5239 5343 3.153130 TGCAGTGCTATTTTTGCCACTA 58.847 40.909 17.60 0.00 35.75 2.74
5241 5345 2.437200 TGCAGTGCTATTTTTGCCAC 57.563 45.000 17.60 0.00 35.75 5.01
5242 5346 6.653526 ATATATGCAGTGCTATTTTTGCCA 57.346 33.333 17.60 0.00 35.75 4.92
5247 5351 9.219603 ACATACGAATATATGCAGTGCTATTTT 57.780 29.630 17.60 11.98 36.21 1.82
5248 5352 8.659491 CACATACGAATATATGCAGTGCTATTT 58.341 33.333 17.60 6.25 36.21 1.40
5249 5353 8.034804 TCACATACGAATATATGCAGTGCTATT 58.965 33.333 17.60 11.89 36.21 1.73
5250 5354 7.547227 TCACATACGAATATATGCAGTGCTAT 58.453 34.615 17.60 13.31 36.21 2.97
5252 5356 5.783111 TCACATACGAATATATGCAGTGCT 58.217 37.500 17.60 4.48 36.21 4.40
5253 5357 6.466308 TTCACATACGAATATATGCAGTGC 57.534 37.500 8.58 8.58 36.21 4.40
5255 5359 7.441836 TCCTTTCACATACGAATATATGCAGT 58.558 34.615 0.00 0.00 36.21 4.40
5256 5360 7.412346 GCTCCTTTCACATACGAATATATGCAG 60.412 40.741 0.00 0.00 36.21 4.41
5257 5361 6.368791 GCTCCTTTCACATACGAATATATGCA 59.631 38.462 0.00 0.00 36.21 3.96
5258 5362 6.591834 AGCTCCTTTCACATACGAATATATGC 59.408 38.462 0.00 0.00 36.21 3.14
5259 5363 8.539770 AAGCTCCTTTCACATACGAATATATG 57.460 34.615 0.00 0.00 38.34 1.78
5262 5366 7.484035 GAAAGCTCCTTTCACATACGAATAT 57.516 36.000 11.65 0.00 46.23 1.28
5264 5368 5.803020 GAAAGCTCCTTTCACATACGAAT 57.197 39.130 11.65 0.00 46.23 3.34
5323 5427 9.965824 CCGCCTTTGACTATTGATAAAATTAAT 57.034 29.630 0.00 0.00 0.00 1.40
5325 5429 8.514330 ACCGCCTTTGACTATTGATAAAATTA 57.486 30.769 0.00 0.00 0.00 1.40
5326 5430 7.339466 AGACCGCCTTTGACTATTGATAAAATT 59.661 33.333 0.00 0.00 0.00 1.82
5330 5434 5.353394 AGACCGCCTTTGACTATTGATAA 57.647 39.130 0.00 0.00 0.00 1.75
5331 5435 5.105106 TCAAGACCGCCTTTGACTATTGATA 60.105 40.000 0.00 0.00 31.42 2.15
5334 5438 3.125316 GTCAAGACCGCCTTTGACTATTG 59.875 47.826 13.50 0.00 33.79 1.90
5335 5439 3.244422 TGTCAAGACCGCCTTTGACTATT 60.244 43.478 18.47 0.00 35.67 1.73
5337 5441 1.689813 TGTCAAGACCGCCTTTGACTA 59.310 47.619 18.47 8.06 35.67 2.59
5339 5443 1.305201 TTGTCAAGACCGCCTTTGAC 58.695 50.000 13.75 13.75 35.45 3.18
5340 5444 1.673920 GTTTGTCAAGACCGCCTTTGA 59.326 47.619 0.00 0.00 31.42 2.69
5341 5445 1.596954 CGTTTGTCAAGACCGCCTTTG 60.597 52.381 0.00 0.00 31.42 2.77
5342 5446 0.661020 CGTTTGTCAAGACCGCCTTT 59.339 50.000 0.00 0.00 31.42 3.11
5343 5447 1.782028 GCGTTTGTCAAGACCGCCTT 61.782 55.000 12.60 0.00 34.84 4.35
5344 5448 2.251642 GCGTTTGTCAAGACCGCCT 61.252 57.895 12.60 0.00 34.84 5.52
5345 5449 1.852067 ATGCGTTTGTCAAGACCGCC 61.852 55.000 17.90 6.46 38.24 6.13
5346 5450 0.040425 AATGCGTTTGTCAAGACCGC 60.040 50.000 15.32 15.32 39.04 5.68
5347 5451 2.159707 CCTAATGCGTTTGTCAAGACCG 60.160 50.000 0.00 0.00 0.00 4.79
5348 5452 2.414161 GCCTAATGCGTTTGTCAAGACC 60.414 50.000 0.00 0.00 0.00 3.85
5349 5453 2.414161 GGCCTAATGCGTTTGTCAAGAC 60.414 50.000 0.00 0.00 42.61 3.01
5350 5454 1.810151 GGCCTAATGCGTTTGTCAAGA 59.190 47.619 0.00 0.00 42.61 3.02
5351 5455 1.135402 GGGCCTAATGCGTTTGTCAAG 60.135 52.381 0.84 0.00 42.61 3.02
5352 5456 0.885196 GGGCCTAATGCGTTTGTCAA 59.115 50.000 0.84 0.00 42.61 3.18
5354 5458 2.032680 TAGGGCCTAATGCGTTTGTC 57.967 50.000 11.78 0.00 42.61 3.18
5355 5459 2.729028 ATAGGGCCTAATGCGTTTGT 57.271 45.000 18.91 0.00 42.61 2.83
5356 5460 5.730550 TCTATATAGGGCCTAATGCGTTTG 58.269 41.667 18.91 3.25 42.61 2.93
5357 5461 6.349300 CATCTATATAGGGCCTAATGCGTTT 58.651 40.000 18.91 1.12 42.61 3.60
5358 5462 5.163301 CCATCTATATAGGGCCTAATGCGTT 60.163 44.000 18.91 1.94 42.61 4.84
5359 5463 4.345257 CCATCTATATAGGGCCTAATGCGT 59.655 45.833 18.91 2.76 42.61 5.24
5360 5464 4.588951 TCCATCTATATAGGGCCTAATGCG 59.411 45.833 18.91 10.04 42.61 4.73
5361 5465 6.465035 CCTTCCATCTATATAGGGCCTAATGC 60.465 46.154 18.91 0.00 40.16 3.56
5362 5466 6.846505 TCCTTCCATCTATATAGGGCCTAATG 59.153 42.308 18.91 15.42 0.00 1.90
5363 5467 7.009960 TCCTTCCATCTATATAGGGCCTAAT 57.990 40.000 18.91 14.19 0.00 1.73
5364 5468 6.432190 TCCTTCCATCTATATAGGGCCTAA 57.568 41.667 18.91 7.61 0.00 2.69
5366 5470 4.327332 CCTCCTTCCATCTATATAGGGCCT 60.327 50.000 12.58 12.58 0.00 5.19
5367 5471 3.970640 CCTCCTTCCATCTATATAGGGCC 59.029 52.174 9.89 0.00 0.00 5.80
5369 5473 5.042979 ACTCCCTCCTTCCATCTATATAGGG 60.043 48.000 9.89 4.49 43.23 3.53
5370 5474 5.896678 CACTCCCTCCTTCCATCTATATAGG 59.103 48.000 9.89 0.00 0.00 2.57
5371 5475 5.362430 GCACTCCCTCCTTCCATCTATATAG 59.638 48.000 3.10 3.10 0.00 1.31
5372 5476 5.016782 AGCACTCCCTCCTTCCATCTATATA 59.983 44.000 0.00 0.00 0.00 0.86
5373 5477 4.100373 GCACTCCCTCCTTCCATCTATAT 58.900 47.826 0.00 0.00 0.00 0.86
5374 5478 3.142977 AGCACTCCCTCCTTCCATCTATA 59.857 47.826 0.00 0.00 0.00 1.31
5375 5479 2.090267 AGCACTCCCTCCTTCCATCTAT 60.090 50.000 0.00 0.00 0.00 1.98
5376 5480 1.292242 AGCACTCCCTCCTTCCATCTA 59.708 52.381 0.00 0.00 0.00 1.98
5377 5481 0.043940 AGCACTCCCTCCTTCCATCT 59.956 55.000 0.00 0.00 0.00 2.90
5379 5483 1.277580 CCAGCACTCCCTCCTTCCAT 61.278 60.000 0.00 0.00 0.00 3.41
5380 5484 1.920325 CCAGCACTCCCTCCTTCCA 60.920 63.158 0.00 0.00 0.00 3.53
5381 5485 1.492993 AACCAGCACTCCCTCCTTCC 61.493 60.000 0.00 0.00 0.00 3.46
5382 5486 0.402121 AAACCAGCACTCCCTCCTTC 59.598 55.000 0.00 0.00 0.00 3.46
5384 5488 0.853530 AAAAACCAGCACTCCCTCCT 59.146 50.000 0.00 0.00 0.00 3.69
5386 5490 1.981256 TCAAAAACCAGCACTCCCTC 58.019 50.000 0.00 0.00 0.00 4.30
5388 5492 1.341209 CCTTCAAAAACCAGCACTCCC 59.659 52.381 0.00 0.00 0.00 4.30
5389 5493 1.341209 CCCTTCAAAAACCAGCACTCC 59.659 52.381 0.00 0.00 0.00 3.85
5390 5494 2.306847 TCCCTTCAAAAACCAGCACTC 58.693 47.619 0.00 0.00 0.00 3.51
5391 5495 2.452600 TCCCTTCAAAAACCAGCACT 57.547 45.000 0.00 0.00 0.00 4.40
5392 5496 3.535280 TTTCCCTTCAAAAACCAGCAC 57.465 42.857 0.00 0.00 0.00 4.40
5393 5497 4.769345 AATTTCCCTTCAAAAACCAGCA 57.231 36.364 0.00 0.00 0.00 4.41
5394 5498 4.515191 GGAAATTTCCCTTCAAAAACCAGC 59.485 41.667 24.44 0.00 41.62 4.85
5409 5689 4.089361 AGGTTGAGGTGGATGGAAATTTC 58.911 43.478 9.83 9.83 0.00 2.17
5412 5692 2.649312 TGAGGTTGAGGTGGATGGAAAT 59.351 45.455 0.00 0.00 0.00 2.17
5416 5696 1.283029 ACATGAGGTTGAGGTGGATGG 59.717 52.381 0.00 0.00 0.00 3.51
5417 5697 2.026915 TCACATGAGGTTGAGGTGGATG 60.027 50.000 0.00 0.00 0.00 3.51
5418 5698 2.269023 TCACATGAGGTTGAGGTGGAT 58.731 47.619 0.00 0.00 0.00 3.41
5419 5699 1.728323 TCACATGAGGTTGAGGTGGA 58.272 50.000 0.00 0.00 0.00 4.02
5420 5700 2.038952 TCTTCACATGAGGTTGAGGTGG 59.961 50.000 0.00 0.00 0.00 4.61
5422 5702 4.566488 GGATTCTTCACATGAGGTTGAGGT 60.566 45.833 0.00 0.00 0.00 3.85
5423 5703 3.944015 GGATTCTTCACATGAGGTTGAGG 59.056 47.826 0.00 0.00 0.00 3.86
5427 5707 4.223032 ACGTAGGATTCTTCACATGAGGTT 59.777 41.667 0.00 0.00 0.00 3.50
5436 5716 7.782049 ACATCTTCAATACGTAGGATTCTTCA 58.218 34.615 0.08 0.00 0.00 3.02
5461 5741 3.489355 ACACAGAAATGGAGTTGCATGA 58.511 40.909 0.00 0.00 0.00 3.07
5467 5747 8.697507 ATAGAGAAAAACACAGAAATGGAGTT 57.302 30.769 0.00 0.00 0.00 3.01
5495 5775 8.219546 TGATTCGCAGGATTTGTAAAATATGA 57.780 30.769 0.00 0.00 0.00 2.15
5525 5805 2.523245 TGCATACAAACATTCAGGGCA 58.477 42.857 0.00 0.00 0.00 5.36
5526 5806 3.450578 CATGCATACAAACATTCAGGGC 58.549 45.455 0.00 0.00 0.00 5.19
5528 5808 4.112716 TGCATGCATACAAACATTCAGG 57.887 40.909 18.46 0.00 0.00 3.86
5544 5824 4.163552 CACAGCTGTCACTTATTTGCATG 58.836 43.478 18.64 0.00 0.00 4.06
5551 5831 3.213506 TGCAAACACAGCTGTCACTTAT 58.786 40.909 18.64 0.00 0.00 1.73
5552 5832 2.637947 TGCAAACACAGCTGTCACTTA 58.362 42.857 18.64 0.00 0.00 2.24
5553 5833 1.462616 TGCAAACACAGCTGTCACTT 58.537 45.000 18.64 7.59 0.00 3.16
5554 5834 1.402968 CTTGCAAACACAGCTGTCACT 59.597 47.619 18.64 0.56 0.00 3.41
5555 5835 1.534595 CCTTGCAAACACAGCTGTCAC 60.535 52.381 18.64 5.28 0.00 3.67
5556 5836 0.740149 CCTTGCAAACACAGCTGTCA 59.260 50.000 18.64 8.91 0.00 3.58
5557 5837 0.595825 GCCTTGCAAACACAGCTGTC 60.596 55.000 18.64 5.91 0.00 3.51
5558 5838 1.321805 TGCCTTGCAAACACAGCTGT 61.322 50.000 15.25 15.25 34.76 4.40
5559 5839 0.032952 ATGCCTTGCAAACACAGCTG 59.967 50.000 13.48 13.48 43.62 4.24
5560 5840 2.433217 ATGCCTTGCAAACACAGCT 58.567 47.368 0.00 0.00 43.62 4.24



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

AutoCloner maintained by Alex Coulton.