Multiple sequence alignment - TraesCS1B01G377800

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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 TraesCS1B01G377800 chr1B 100.000 5888 0 0 1 5888 610170353 610164466 0.000000e+00 10874.0
1 TraesCS1B01G377800 chr1B 85.714 63 6 2 5253 5312 606319261 606319323 4.930000e-06 63.9
2 TraesCS1B01G377800 chr1D 93.468 4118 149 52 1059 5149 446271457 446267433 0.000000e+00 6004.0
3 TraesCS1B01G377800 chr1D 91.440 736 28 12 307 1021 446272249 446271528 0.000000e+00 977.0
4 TraesCS1B01G377800 chr1D 90.150 599 33 15 5307 5888 446267346 446266757 0.000000e+00 756.0
5 TraesCS1B01G377800 chr1D 92.727 275 16 3 2 274 446272602 446272330 1.540000e-105 394.0
6 TraesCS1B01G377800 chr1A 94.519 3339 124 22 1068 4378 541997231 541993924 0.000000e+00 5097.0
7 TraesCS1B01G377800 chr1A 89.990 1039 47 23 2 1021 541998311 541997311 0.000000e+00 1290.0
8 TraesCS1B01G377800 chr1A 90.013 741 52 13 4414 5147 541993925 541993200 0.000000e+00 939.0
9 TraesCS1B01G377800 chr1A 87.858 593 35 18 5307 5888 541992684 541992118 0.000000e+00 662.0
10 TraesCS1B01G377800 chr3A 81.250 112 19 1 5204 5313 695051521 695051632 8.130000e-14 89.8
11 TraesCS1B01G377800 chr3A 87.500 56 6 1 5260 5314 491183719 491183664 4.930000e-06 63.9
12 TraesCS1B01G377800 chr2B 87.500 64 8 0 5241 5304 4941623 4941686 2.280000e-09 75.0
13 TraesCS1B01G377800 chr3B 87.692 65 4 3 5252 5314 482487831 482487893 8.180000e-09 73.1
14 TraesCS1B01G377800 chr3B 86.441 59 7 1 5266 5323 810609217 810609275 4.930000e-06 63.9
15 TraesCS1B01G377800 chr7A 89.286 56 6 0 5250 5305 229207050 229207105 2.940000e-08 71.3
16 TraesCS1B01G377800 chr5B 93.478 46 3 0 5260 5305 328226211 328226256 1.060000e-07 69.4
17 TraesCS1B01G377800 chr3D 93.478 46 3 0 5260 5305 537165496 537165541 1.060000e-07 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G377800 chr1B 610164466 610170353 5887 True 10874.00 10874 100.00000 1 5888 1 chr1B.!!$R1 5887
1 TraesCS1B01G377800 chr1D 446266757 446272602 5845 True 2032.75 6004 91.94625 2 5888 4 chr1D.!!$R1 5886
2 TraesCS1B01G377800 chr1A 541992118 541998311 6193 True 1997.00 5097 90.59500 2 5888 4 chr1A.!!$R1 5886

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
426 484 0.524816 TTTCGTCGAGCATCTACCGC 60.525 55.000 0.00 0.00 0.00 5.68 F
1017 1093 0.178861 AGATGGGGGTCAAGGTGAGT 60.179 55.000 0.00 0.00 0.00 3.41 F
1054 1179 0.609151 TGGATTTGTTCGGCGGAGTA 59.391 50.000 7.21 0.00 0.00 2.59 F
1254 1379 0.613777 CGTATAGCCCCCATTCTCCC 59.386 60.000 0.00 0.00 0.00 4.30 F
1255 1380 0.992695 GTATAGCCCCCATTCTCCCC 59.007 60.000 0.00 0.00 0.00 4.81 F
2577 2724 2.054799 TGTTAGGAGCCAACTGGTTCT 58.945 47.619 11.77 3.46 43.85 3.01 F
3641 3791 2.243221 AGCAGTGGCCCAAGATTTATCT 59.757 45.455 0.00 0.00 42.56 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1437 1568 0.243907 CACCACACGAGGGTCTACAG 59.756 60.000 0.0 0.0 36.19 2.74 R
2307 2450 0.814457 CTCTACTGCCTTCGTCAGCT 59.186 55.000 0.0 0.0 35.04 4.24 R
2898 3045 2.812358 TACAGCATCACGAACACACT 57.188 45.000 0.0 0.0 0.00 3.55 R
3026 3174 4.275196 GGTGAAAACAAGAAGGTAGTGGAC 59.725 45.833 0.0 0.0 0.00 4.02 R
3384 3532 2.093288 TGTGGGCAACAAAATGAAAGCA 60.093 40.909 0.0 0.0 35.24 3.91 R
3647 3797 0.807496 GCCAAGAGGTGCATGACTTC 59.193 55.000 0.0 0.0 37.19 3.01 R
5694 6337 0.674534 GGGCGGGAGATAGTACACAG 59.325 60.000 0.0 0.0 0.00 3.66 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
191 192 3.023119 AGCAACACACAATCAGGTGAAA 58.977 40.909 0.00 0.00 41.32 2.69
192 193 3.115554 GCAACACACAATCAGGTGAAAC 58.884 45.455 0.00 0.00 41.32 2.78
215 218 2.094894 CAGAGGCGATTTAAGCACACAG 59.905 50.000 0.00 0.00 36.08 3.66
219 222 2.484264 GGCGATTTAAGCACACAGAACT 59.516 45.455 0.00 0.00 36.08 3.01
270 273 4.966366 GCGATCTTCCGATTTTCAAATGAG 59.034 41.667 0.00 0.00 0.00 2.90
280 293 8.458843 TCCGATTTTCAAATGAGTTCCTAAATC 58.541 33.333 0.00 0.00 0.00 2.17
321 371 2.045524 GGAGATCAGAGGAATCTGGCA 58.954 52.381 5.48 0.00 38.23 4.92
325 375 2.775911 TCAGAGGAATCTGGCAAGTG 57.224 50.000 5.48 0.00 38.23 3.16
328 378 3.008330 CAGAGGAATCTGGCAAGTGAAG 58.992 50.000 0.00 0.00 34.28 3.02
331 381 4.018597 AGAGGAATCTGGCAAGTGAAGAAT 60.019 41.667 0.00 0.00 0.00 2.40
333 383 3.428589 GGAATCTGGCAAGTGAAGAATGC 60.429 47.826 0.00 0.00 39.33 3.56
335 385 2.585330 TCTGGCAAGTGAAGAATGCAA 58.415 42.857 0.00 0.00 41.80 4.08
336 386 2.957680 TCTGGCAAGTGAAGAATGCAAA 59.042 40.909 0.00 0.00 41.80 3.68
377 431 3.693578 TGGACAATTTTATGATGCGAGCA 59.306 39.130 0.00 0.00 0.00 4.26
378 432 4.037690 GGACAATTTTATGATGCGAGCAC 58.962 43.478 0.00 0.00 0.00 4.40
379 433 3.683989 ACAATTTTATGATGCGAGCACG 58.316 40.909 0.00 0.00 42.93 5.34
380 434 3.038017 CAATTTTATGATGCGAGCACGG 58.962 45.455 5.52 0.00 40.15 4.94
381 435 1.013596 TTTTATGATGCGAGCACGGG 58.986 50.000 5.52 0.00 40.15 5.28
382 436 1.436195 TTTATGATGCGAGCACGGGC 61.436 55.000 0.00 0.00 40.15 6.13
426 484 0.524816 TTTCGTCGAGCATCTACCGC 60.525 55.000 0.00 0.00 0.00 5.68
495 553 2.974489 GCGTCGGTCCGAGAGTGAA 61.974 63.158 15.95 0.00 36.23 3.18
810 873 2.747855 CTGGACGCTTTCCTGCCC 60.748 66.667 3.14 0.00 46.10 5.36
835 898 3.400599 CTATTTGAGCCCGCCCGGT 62.401 63.158 0.00 0.00 0.00 5.28
1017 1093 0.178861 AGATGGGGGTCAAGGTGAGT 60.179 55.000 0.00 0.00 0.00 3.41
1021 1097 3.050275 GGGTCAAGGTGAGTGCGC 61.050 66.667 0.00 0.00 0.00 6.09
1026 1102 1.672030 CAAGGTGAGTGCGCCATGA 60.672 57.895 4.18 0.00 44.06 3.07
1030 1155 1.084370 GGTGAGTGCGCCATGAGTAC 61.084 60.000 4.18 0.00 44.29 2.73
1041 1166 2.357154 GCCATGAGTACCCTGTGGATTT 60.357 50.000 0.00 0.00 34.81 2.17
1042 1167 3.282021 CCATGAGTACCCTGTGGATTTG 58.718 50.000 0.00 0.00 34.81 2.32
1043 1168 3.308402 CCATGAGTACCCTGTGGATTTGT 60.308 47.826 0.00 0.00 34.81 2.83
1044 1169 4.335416 CATGAGTACCCTGTGGATTTGTT 58.665 43.478 0.00 0.00 34.81 2.83
1045 1170 4.015872 TGAGTACCCTGTGGATTTGTTC 57.984 45.455 0.00 0.00 34.81 3.18
1046 1171 3.000727 GAGTACCCTGTGGATTTGTTCG 58.999 50.000 0.00 0.00 34.81 3.95
1047 1172 2.081462 GTACCCTGTGGATTTGTTCGG 58.919 52.381 0.00 0.00 34.81 4.30
1048 1173 0.893727 ACCCTGTGGATTTGTTCGGC 60.894 55.000 0.00 0.00 34.81 5.54
1049 1174 1.501741 CCTGTGGATTTGTTCGGCG 59.498 57.895 0.00 0.00 0.00 6.46
1050 1175 1.501741 CTGTGGATTTGTTCGGCGG 59.498 57.895 7.21 0.00 0.00 6.13
1051 1176 0.953471 CTGTGGATTTGTTCGGCGGA 60.953 55.000 7.21 0.00 0.00 5.54
1052 1177 0.953471 TGTGGATTTGTTCGGCGGAG 60.953 55.000 7.21 0.00 0.00 4.63
1053 1178 0.953960 GTGGATTTGTTCGGCGGAGT 60.954 55.000 7.21 0.00 0.00 3.85
1054 1179 0.609151 TGGATTTGTTCGGCGGAGTA 59.391 50.000 7.21 0.00 0.00 2.59
1055 1180 1.208535 TGGATTTGTTCGGCGGAGTAT 59.791 47.619 7.21 0.00 0.00 2.12
1056 1181 1.865340 GGATTTGTTCGGCGGAGTATC 59.135 52.381 7.21 1.12 0.00 2.24
1057 1182 2.483188 GGATTTGTTCGGCGGAGTATCT 60.483 50.000 7.21 0.00 33.73 1.98
1066 1191 2.857744 CGGAGTATCTGGGGACGCC 61.858 68.421 0.53 0.53 38.01 5.68
1133 1258 2.353406 GCTGTAGGGTTTGACGAAGCTA 60.353 50.000 4.67 0.00 36.04 3.32
1254 1379 0.613777 CGTATAGCCCCCATTCTCCC 59.386 60.000 0.00 0.00 0.00 4.30
1255 1380 0.992695 GTATAGCCCCCATTCTCCCC 59.007 60.000 0.00 0.00 0.00 4.81
1302 1431 8.025243 TCCATTTACTGTTTGTTTCTCGTATC 57.975 34.615 0.00 0.00 0.00 2.24
1437 1568 4.645863 TCTTAGGTTGGGTTTAGGGTTC 57.354 45.455 0.00 0.00 0.00 3.62
1537 1668 4.826274 AGAAGATTGTTGCAGTAGGCTA 57.174 40.909 0.00 0.00 45.15 3.93
1538 1669 4.508662 AGAAGATTGTTGCAGTAGGCTAC 58.491 43.478 16.93 16.93 46.54 3.58
1539 1670 4.223923 AGAAGATTGTTGCAGTAGGCTACT 59.776 41.667 21.30 21.30 46.50 2.57
1577 1708 4.724279 CCCCTTGGGCATATAAGTTAGT 57.276 45.455 0.00 0.00 35.35 2.24
1580 1711 5.063880 CCCTTGGGCATATAAGTTAGTGTC 58.936 45.833 0.00 0.00 0.00 3.67
1738 1869 5.939883 AGCAGTTGTGAGATAATAGCAAACA 59.060 36.000 0.00 0.00 0.00 2.83
1739 1870 6.430925 AGCAGTTGTGAGATAATAGCAAACAA 59.569 34.615 0.00 0.00 0.00 2.83
1849 1980 3.255725 CTTACAAACGAAGCCGGTGATA 58.744 45.455 1.90 0.00 40.78 2.15
1869 2000 5.538053 TGATATCACCAGGTTCAGATCTCTC 59.462 44.000 0.00 0.00 0.00 3.20
1892 2023 6.361433 TCTCTCTCTCTCCAACCATACTTAG 58.639 44.000 0.00 0.00 0.00 2.18
1947 2086 3.679980 CCTAGTATGTATGTTCATGCGGC 59.320 47.826 0.00 0.00 35.99 6.53
1963 2106 2.948979 TGCGGCTCTTTCTTTTTCTTGA 59.051 40.909 0.00 0.00 0.00 3.02
2196 2339 9.006215 CGAGCTTTTAAAAAGGTTATTTATCCG 57.994 33.333 1.66 0.00 0.00 4.18
2307 2450 4.630644 AGAGGAATGAAGCAACAGAAGA 57.369 40.909 0.00 0.00 0.00 2.87
2380 2526 3.764434 TCCACGTTCTTCTATGCTCTCTT 59.236 43.478 0.00 0.00 0.00 2.85
2512 2659 9.567848 GTTGTTTGTGATAAAGAGTCTTGAAAA 57.432 29.630 6.06 0.00 0.00 2.29
2559 2706 5.627499 ATGTAAGACGATTTGCATTGTGT 57.373 34.783 0.00 0.00 30.61 3.72
2577 2724 2.054799 TGTTAGGAGCCAACTGGTTCT 58.945 47.619 11.77 3.46 43.85 3.01
2586 2733 2.887152 GCCAACTGGTTCTTTCACTGAT 59.113 45.455 0.00 0.00 37.57 2.90
2590 2737 5.242393 CCAACTGGTTCTTTCACTGATCAAT 59.758 40.000 0.00 0.00 0.00 2.57
2674 2821 7.963981 TGCGATGAATTAGTTTTCAGAGTAAG 58.036 34.615 0.00 0.00 38.90 2.34
2675 2822 7.064609 TGCGATGAATTAGTTTTCAGAGTAAGG 59.935 37.037 0.00 0.00 38.90 2.69
3026 3174 8.882415 ACAAGGTAATATTAACATAGTGGACG 57.118 34.615 12.96 0.00 0.00 4.79
3214 3362 6.016693 TGGAATTTGAAGTTGCGAAAGTATGA 60.017 34.615 0.00 0.00 0.00 2.15
3216 3364 7.381139 GGAATTTGAAGTTGCGAAAGTATGAAA 59.619 33.333 0.00 0.00 0.00 2.69
3221 3369 9.906660 TTGAAGTTGCGAAAGTATGAAATATTT 57.093 25.926 0.00 0.00 29.14 1.40
3230 3378 9.559958 CGAAAGTATGAAATATTTTGTTGAGCT 57.440 29.630 1.43 0.00 38.61 4.09
3398 3546 7.548780 TGCTTACTCTTTTGCTTTCATTTTGTT 59.451 29.630 0.00 0.00 0.00 2.83
3400 3548 6.110543 ACTCTTTTGCTTTCATTTTGTTGC 57.889 33.333 0.00 0.00 0.00 4.17
3641 3791 2.243221 AGCAGTGGCCCAAGATTTATCT 59.757 45.455 0.00 0.00 42.56 1.98
3642 3792 3.459598 AGCAGTGGCCCAAGATTTATCTA 59.540 43.478 0.00 0.00 42.56 1.98
3647 3797 5.888161 AGTGGCCCAAGATTTATCTACTTTG 59.112 40.000 0.00 0.00 35.76 2.77
3694 3844 5.872070 TGAAATTCTGGTTTGTGTTGGTTTC 59.128 36.000 0.00 0.00 0.00 2.78
3695 3845 5.675684 AATTCTGGTTTGTGTTGGTTTCT 57.324 34.783 0.00 0.00 0.00 2.52
3696 3846 5.675684 ATTCTGGTTTGTGTTGGTTTCTT 57.324 34.783 0.00 0.00 0.00 2.52
3697 3847 5.476091 TTCTGGTTTGTGTTGGTTTCTTT 57.524 34.783 0.00 0.00 0.00 2.52
3698 3848 4.815269 TCTGGTTTGTGTTGGTTTCTTTG 58.185 39.130 0.00 0.00 0.00 2.77
3709 3859 9.495572 TGTGTTGGTTTCTTTGTTAATTTCTTT 57.504 25.926 0.00 0.00 0.00 2.52
4082 4233 8.713971 TGTTAGGCCATAGAGAAGATTAAATCA 58.286 33.333 5.01 0.00 0.00 2.57
4151 4305 9.832445 ATATTCACATACACGGTTCTTAAGAAT 57.168 29.630 20.41 7.28 36.33 2.40
4308 4472 3.711863 ACATACATCCACCAAAATGCCT 58.288 40.909 0.00 0.00 0.00 4.75
4431 4595 3.560896 GTGCATGCAATTCAAACTTTGGT 59.439 39.130 24.58 0.00 0.00 3.67
4435 4599 5.119125 GCATGCAATTCAAACTTTGGTCTAC 59.881 40.000 14.21 0.00 0.00 2.59
4441 4605 6.619801 ATTCAAACTTTGGTCTACTGTGTC 57.380 37.500 1.62 0.00 0.00 3.67
4500 4664 0.540365 ACCAATTCACCACCAGGCTG 60.540 55.000 7.75 7.75 39.06 4.85
4518 4682 0.251165 TGCCTGCCCTAGTTTGAACC 60.251 55.000 0.00 0.00 0.00 3.62
4522 4686 2.344025 CTGCCCTAGTTTGAACCGTAC 58.656 52.381 0.00 0.00 0.00 3.67
4568 4732 5.526479 CCTGATATCAACATCACCACAAGAG 59.474 44.000 6.90 0.00 31.67 2.85
4633 4797 4.280174 TCCCCGTAGATACAAATAGCAGAC 59.720 45.833 0.00 0.00 0.00 3.51
4634 4798 4.557205 CCCGTAGATACAAATAGCAGACC 58.443 47.826 0.00 0.00 0.00 3.85
4680 4845 2.438392 AGTAATTCCAGACGATTCCCCC 59.562 50.000 0.00 0.00 0.00 5.40
4694 4860 4.991798 CCCCCGGGACACCTATAT 57.008 61.111 26.32 0.00 37.50 0.86
4705 4871 7.391620 CCGGGACACCTATATATTGTGTTTAT 58.608 38.462 17.06 1.00 42.89 1.40
4728 4894 4.782156 TGTTGAATCGTGCACTAACAATG 58.218 39.130 16.19 0.00 0.00 2.82
4845 5014 2.914097 AAACCAGCCAGTGCAGCC 60.914 61.111 0.00 0.00 41.13 4.85
4892 5061 3.682858 CGCGGAAGGAAGAAATAAGTTGA 59.317 43.478 0.00 0.00 0.00 3.18
4903 5072 4.154195 AGAAATAAGTTGAATGCGCGAACT 59.846 37.500 12.10 7.41 0.00 3.01
4919 5088 0.512952 AACTAAAAGCTGCAGTCGCG 59.487 50.000 16.64 0.00 42.97 5.87
4921 5090 0.179240 CTAAAAGCTGCAGTCGCGTG 60.179 55.000 16.64 0.00 42.97 5.34
4938 5107 1.675483 CGTGCTCAGCTAGATCAGTCT 59.325 52.381 0.00 0.00 38.52 3.24
4979 5148 2.440539 TCTTTGTTCGGTGCTCTCTC 57.559 50.000 0.00 0.00 0.00 3.20
4994 5163 2.416893 CTCTCTCGTCGTCTCATGTTCA 59.583 50.000 0.00 0.00 0.00 3.18
5031 5200 2.879026 AGCGACTTGAGAAGGGAAAAAC 59.121 45.455 0.00 0.00 0.00 2.43
5032 5201 2.616842 GCGACTTGAGAAGGGAAAAACA 59.383 45.455 0.00 0.00 0.00 2.83
5033 5202 3.066203 GCGACTTGAGAAGGGAAAAACAA 59.934 43.478 0.00 0.00 0.00 2.83
5074 5244 5.422012 TGTTCATCTGCTGATAGTTGTAGGA 59.578 40.000 5.70 0.00 32.72 2.94
5089 5259 5.245526 AGTTGTAGGATCGTACTTTCCTGTT 59.754 40.000 22.37 1.65 42.38 3.16
5102 5272 7.495934 CGTACTTTCCTGTTATGGAGAATTCAT 59.504 37.037 8.44 0.00 38.41 2.57
5103 5273 9.178758 GTACTTTCCTGTTATGGAGAATTCATT 57.821 33.333 8.44 0.00 34.80 2.57
5104 5274 8.059798 ACTTTCCTGTTATGGAGAATTCATTG 57.940 34.615 8.44 0.00 34.80 2.82
5105 5275 7.671398 ACTTTCCTGTTATGGAGAATTCATTGT 59.329 33.333 8.44 0.00 34.80 2.71
5107 5277 7.395190 TCCTGTTATGGAGAATTCATTGTTG 57.605 36.000 8.44 0.00 34.80 3.33
5108 5278 6.038356 CCTGTTATGGAGAATTCATTGTTGC 58.962 40.000 8.44 0.00 34.80 4.17
5109 5279 6.350361 CCTGTTATGGAGAATTCATTGTTGCA 60.350 38.462 8.44 0.00 34.80 4.08
5110 5280 6.990798 TGTTATGGAGAATTCATTGTTGCAA 58.009 32.000 8.44 0.00 34.80 4.08
5114 5284 7.989416 ATGGAGAATTCATTGTTGCAATTTT 57.011 28.000 8.44 0.00 18.61 1.82
5118 5288 7.064966 GGAGAATTCATTGTTGCAATTTTAGGG 59.935 37.037 8.44 0.00 0.00 3.53
5122 5292 4.590647 TCATTGTTGCAATTTTAGGGTGGA 59.409 37.500 0.59 0.00 0.00 4.02
5133 5303 2.990740 TAGGGTGGATTGCTTTGGTT 57.009 45.000 0.00 0.00 0.00 3.67
5135 5305 1.133199 AGGGTGGATTGCTTTGGTTGA 60.133 47.619 0.00 0.00 0.00 3.18
5138 5308 3.328505 GGTGGATTGCTTTGGTTGATTG 58.671 45.455 0.00 0.00 0.00 2.67
5149 5319 5.764131 CTTTGGTTGATTGCATGCAATTTT 58.236 33.333 38.66 23.74 45.50 1.82
5150 5320 6.568081 GCTTTGGTTGATTGCATGCAATTTTA 60.568 34.615 38.66 26.96 45.50 1.52
5152 5322 5.549347 TGGTTGATTGCATGCAATTTTAGT 58.451 33.333 38.66 22.32 45.50 2.24
5153 5323 5.996513 TGGTTGATTGCATGCAATTTTAGTT 59.003 32.000 38.66 21.62 45.50 2.24
5154 5324 7.157347 TGGTTGATTGCATGCAATTTTAGTTA 58.843 30.769 38.66 22.26 45.50 2.24
5161 5344 5.182190 TGCATGCAATTTTAGTTAAGACGGA 59.818 36.000 20.30 0.00 0.00 4.69
5162 5345 5.739161 GCATGCAATTTTAGTTAAGACGGAG 59.261 40.000 14.21 0.00 0.00 4.63
5167 5350 7.227910 TGCAATTTTAGTTAAGACGGAGAAAGT 59.772 33.333 0.00 0.00 0.00 2.66
5175 5358 4.950205 AAGACGGAGAAAGTTTGGACTA 57.050 40.909 0.00 0.00 34.21 2.59
5176 5359 4.950205 AGACGGAGAAAGTTTGGACTAA 57.050 40.909 0.00 0.00 34.21 2.24
5185 5368 6.607019 AGAAAGTTTGGACTAATACCAACCA 58.393 36.000 0.00 0.00 45.38 3.67
5186 5369 7.238710 AGAAAGTTTGGACTAATACCAACCAT 58.761 34.615 0.00 0.00 45.38 3.55
5193 5803 4.593634 GGACTAATACCAACCATCTAGGCT 59.406 45.833 0.00 0.00 43.14 4.58
5220 5842 2.747446 CCACAAAATGGTACTTCCTCCG 59.253 50.000 0.00 0.00 44.46 4.63
5221 5843 2.747446 CACAAAATGGTACTTCCTCCGG 59.253 50.000 0.00 0.00 37.07 5.14
5222 5844 2.374170 ACAAAATGGTACTTCCTCCGGT 59.626 45.455 0.00 0.00 37.07 5.28
5223 5845 3.007635 CAAAATGGTACTTCCTCCGGTC 58.992 50.000 0.00 0.00 37.07 4.79
5224 5846 1.201424 AATGGTACTTCCTCCGGTCC 58.799 55.000 0.00 0.00 37.07 4.46
5225 5847 0.042131 ATGGTACTTCCTCCGGTCCA 59.958 55.000 0.00 0.00 37.07 4.02
5226 5848 0.178926 TGGTACTTCCTCCGGTCCAA 60.179 55.000 0.00 0.00 37.07 3.53
5227 5849 0.978907 GGTACTTCCTCCGGTCCAAA 59.021 55.000 0.00 0.00 0.00 3.28
5228 5850 1.558294 GGTACTTCCTCCGGTCCAAAT 59.442 52.381 0.00 0.00 0.00 2.32
5229 5851 2.026542 GGTACTTCCTCCGGTCCAAATT 60.027 50.000 0.00 0.00 0.00 1.82
5230 5852 3.198417 GGTACTTCCTCCGGTCCAAATTA 59.802 47.826 0.00 0.00 0.00 1.40
5231 5853 4.323715 GGTACTTCCTCCGGTCCAAATTAA 60.324 45.833 0.00 0.00 0.00 1.40
5232 5854 4.586306 ACTTCCTCCGGTCCAAATTAAT 57.414 40.909 0.00 0.00 0.00 1.40
5233 5855 4.930696 ACTTCCTCCGGTCCAAATTAATT 58.069 39.130 0.00 0.00 0.00 1.40
5234 5856 4.705023 ACTTCCTCCGGTCCAAATTAATTG 59.295 41.667 0.00 0.00 38.84 2.32
5235 5857 4.577988 TCCTCCGGTCCAAATTAATTGA 57.422 40.909 0.00 0.00 41.85 2.57
5236 5858 4.266714 TCCTCCGGTCCAAATTAATTGAC 58.733 43.478 0.00 5.85 41.85 3.18
5237 5859 4.013728 CCTCCGGTCCAAATTAATTGACA 58.986 43.478 16.30 1.21 41.85 3.58
5238 5860 4.142469 CCTCCGGTCCAAATTAATTGACAC 60.142 45.833 16.30 7.64 41.85 3.67
5239 5861 4.658063 TCCGGTCCAAATTAATTGACACT 58.342 39.130 16.30 0.00 41.85 3.55
5240 5862 5.074115 TCCGGTCCAAATTAATTGACACTT 58.926 37.500 16.30 0.00 41.85 3.16
5241 5863 5.536916 TCCGGTCCAAATTAATTGACACTTT 59.463 36.000 16.30 0.00 41.85 2.66
5242 5864 6.041069 TCCGGTCCAAATTAATTGACACTTTT 59.959 34.615 16.30 0.00 41.85 2.27
5243 5865 7.230913 TCCGGTCCAAATTAATTGACACTTTTA 59.769 33.333 16.30 0.00 41.85 1.52
5244 5866 7.540745 CCGGTCCAAATTAATTGACACTTTTAG 59.459 37.037 16.30 3.67 41.85 1.85
5245 5867 8.079809 CGGTCCAAATTAATTGACACTTTTAGT 58.920 33.333 16.30 0.00 41.85 2.24
5282 5904 9.632807 AATAAAATTGTATTAAAGCAGCGTCAA 57.367 25.926 0.00 0.00 0.00 3.18
5283 5905 9.801873 ATAAAATTGTATTAAAGCAGCGTCAAT 57.198 25.926 0.00 0.00 0.00 2.57
5284 5906 8.532977 AAAATTGTATTAAAGCAGCGTCAATT 57.467 26.923 0.00 0.00 36.34 2.32
5285 5907 9.632807 AAAATTGTATTAAAGCAGCGTCAATTA 57.367 25.926 5.69 0.00 34.60 1.40
5286 5908 9.632807 AAATTGTATTAAAGCAGCGTCAATTAA 57.367 25.926 5.69 1.10 34.60 1.40
5287 5909 9.801873 AATTGTATTAAAGCAGCGTCAATTAAT 57.198 25.926 3.98 6.05 34.16 1.40
5290 5912 9.877137 TGTATTAAAGCAGCGTCAATTAATATG 57.123 29.630 10.66 0.00 33.49 1.78
5291 5913 9.329913 GTATTAAAGCAGCGTCAATTAATATGG 57.670 33.333 10.66 0.00 33.49 2.74
5292 5914 7.561021 TTAAAGCAGCGTCAATTAATATGGA 57.439 32.000 0.00 0.00 0.00 3.41
5293 5915 6.639632 AAAGCAGCGTCAATTAATATGGAT 57.360 33.333 0.00 0.00 0.00 3.41
5294 5916 6.639632 AAGCAGCGTCAATTAATATGGATT 57.360 33.333 0.00 0.00 0.00 3.01
5295 5917 6.005583 AGCAGCGTCAATTAATATGGATTG 57.994 37.500 5.39 5.39 35.18 2.67
5296 5918 5.048504 AGCAGCGTCAATTAATATGGATTGG 60.049 40.000 9.98 0.21 34.74 3.16
5297 5919 5.048782 GCAGCGTCAATTAATATGGATTGGA 60.049 40.000 9.98 0.00 34.74 3.53
5298 5920 6.605849 CAGCGTCAATTAATATGGATTGGAG 58.394 40.000 9.98 6.87 34.74 3.86
5299 5921 5.707298 AGCGTCAATTAATATGGATTGGAGG 59.293 40.000 9.98 0.00 34.74 4.30
5300 5922 5.106157 GCGTCAATTAATATGGATTGGAGGG 60.106 44.000 9.98 2.10 34.74 4.30
5301 5923 6.237901 CGTCAATTAATATGGATTGGAGGGA 58.762 40.000 9.98 0.00 34.74 4.20
5302 5924 6.372659 CGTCAATTAATATGGATTGGAGGGAG 59.627 42.308 9.98 0.00 34.74 4.30
5303 5925 7.234355 GTCAATTAATATGGATTGGAGGGAGT 58.766 38.462 9.98 0.00 34.74 3.85
5304 5926 8.383175 GTCAATTAATATGGATTGGAGGGAGTA 58.617 37.037 9.98 0.00 34.74 2.59
5305 5927 8.383175 TCAATTAATATGGATTGGAGGGAGTAC 58.617 37.037 9.98 0.00 34.74 2.73
5321 5943 4.406003 GGGAGTACTAGAATTTCTCCTGCA 59.594 45.833 1.27 0.00 42.76 4.41
5378 6001 5.248248 TGTGAAACATCCAGATGAAGTCCTA 59.752 40.000 14.42 0.00 45.67 2.94
5380 6003 5.485353 TGAAACATCCAGATGAAGTCCTAGT 59.515 40.000 14.42 0.00 41.20 2.57
5387 6017 6.120905 TCCAGATGAAGTCCTAGTACTGTAC 58.879 44.000 9.93 9.93 0.00 2.90
5444 6076 6.449698 ACAAGTGCAAAAAGAACATCTATGG 58.550 36.000 0.00 0.00 0.00 2.74
5453 6085 9.196552 CAAAAAGAACATCTATGGGAAAAGAAC 57.803 33.333 0.00 0.00 0.00 3.01
5458 6093 5.745227 ACATCTATGGGAAAAGAACGACAT 58.255 37.500 0.00 0.00 0.00 3.06
5509 6145 1.339824 GCAGCTGGCCTATATGAGCAT 60.340 52.381 17.12 0.00 36.11 3.79
5516 6152 5.498393 CTGGCCTATATGAGCATTTGATCT 58.502 41.667 3.32 0.00 0.00 2.75
5526 6162 4.456911 TGAGCATTTGATCTCACAAGTTCC 59.543 41.667 0.00 0.00 34.69 3.62
5528 6164 4.458295 AGCATTTGATCTCACAAGTTCCTG 59.542 41.667 0.00 0.00 0.00 3.86
5532 6168 3.510459 TGATCTCACAAGTTCCTGGAGA 58.490 45.455 0.00 0.00 38.80 3.71
5534 6170 4.533707 TGATCTCACAAGTTCCTGGAGAAT 59.466 41.667 0.00 0.00 38.05 2.40
5535 6171 4.982241 TCTCACAAGTTCCTGGAGAATT 57.018 40.909 0.00 0.00 36.69 2.17
5536 6172 6.213397 TGATCTCACAAGTTCCTGGAGAATTA 59.787 38.462 0.00 0.00 38.05 1.40
5538 6174 5.780282 TCTCACAAGTTCCTGGAGAATTAGA 59.220 40.000 0.00 0.00 36.69 2.10
5539 6175 5.794894 TCACAAGTTCCTGGAGAATTAGAC 58.205 41.667 0.00 0.00 36.69 2.59
5540 6176 5.306937 TCACAAGTTCCTGGAGAATTAGACA 59.693 40.000 0.00 0.00 36.69 3.41
5541 6177 5.409826 CACAAGTTCCTGGAGAATTAGACAC 59.590 44.000 0.00 0.00 36.69 3.67
5543 6179 3.195825 AGTTCCTGGAGAATTAGACACCG 59.804 47.826 0.00 0.00 36.69 4.94
5545 6181 1.139058 CCTGGAGAATTAGACACCGGG 59.861 57.143 6.32 0.00 37.96 5.73
5546 6182 1.139058 CTGGAGAATTAGACACCGGGG 59.861 57.143 0.00 0.00 0.00 5.73
5547 6183 1.273381 TGGAGAATTAGACACCGGGGA 60.273 52.381 12.96 0.00 0.00 4.81
5548 6184 1.835531 GGAGAATTAGACACCGGGGAA 59.164 52.381 12.96 0.00 0.00 3.97
5549 6185 2.158943 GGAGAATTAGACACCGGGGAAG 60.159 54.545 12.96 0.00 0.00 3.46
5550 6186 2.764572 GAGAATTAGACACCGGGGAAGA 59.235 50.000 12.96 0.00 0.00 2.87
5555 6191 1.657804 AGACACCGGGGAAGAAGATT 58.342 50.000 12.96 0.00 0.00 2.40
5622 6262 5.731591 ACACTTCTACCAAGGTTATAGCAC 58.268 41.667 0.00 0.00 0.00 4.40
5663 6304 2.944409 TTCCCACGGGACCAACAACG 62.944 60.000 3.66 0.00 45.11 4.10
5694 6337 2.088950 AAGCATTTGCATCTGTTGGC 57.911 45.000 5.20 0.00 45.16 4.52
5714 6357 0.032912 TGTGTACTATCTCCCGCCCA 60.033 55.000 0.00 0.00 0.00 5.36
5754 6397 1.188863 ATTTGTCCCAGCCATCTTGC 58.811 50.000 0.00 0.00 0.00 4.01
5874 6517 2.043852 ATGGCGACCGAGGAGAGT 60.044 61.111 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.544903 GGCATAGAGCTCCTTCGAGTTC 60.545 54.545 10.93 0.00 44.41 3.01
3 4 1.410882 GGCATAGAGCTCCTTCGAGTT 59.589 52.381 10.93 0.00 44.79 3.01
4 5 1.036707 GGCATAGAGCTCCTTCGAGT 58.963 55.000 10.93 0.00 44.79 4.18
5 6 0.039617 CGGCATAGAGCTCCTTCGAG 60.040 60.000 10.93 0.00 44.79 4.04
6 7 1.456196 CCGGCATAGAGCTCCTTCGA 61.456 60.000 10.93 0.00 44.79 3.71
8 9 1.301322 GCCGGCATAGAGCTCCTTC 60.301 63.158 24.80 0.00 44.79 3.46
10 11 0.470080 TAAGCCGGCATAGAGCTCCT 60.470 55.000 31.54 0.00 44.79 3.69
11 12 0.037790 CTAAGCCGGCATAGAGCTCC 60.038 60.000 30.22 0.00 44.79 4.70
12 13 0.669012 GCTAAGCCGGCATAGAGCTC 60.669 60.000 36.10 18.25 44.79 4.09
13 14 1.118356 AGCTAAGCCGGCATAGAGCT 61.118 55.000 36.10 31.83 44.79 4.09
14 15 0.250081 AAGCTAAGCCGGCATAGAGC 60.250 55.000 36.10 30.41 44.65 4.09
15 16 1.606737 GGAAGCTAAGCCGGCATAGAG 60.607 57.143 36.10 23.58 0.00 2.43
191 192 0.618458 TGCTTAAATCGCCTCTGGGT 59.382 50.000 0.00 0.00 34.45 4.51
192 193 1.017387 GTGCTTAAATCGCCTCTGGG 58.983 55.000 0.00 0.00 0.00 4.45
215 218 2.941720 CTGCATTGGAGAGGCTTAGTTC 59.058 50.000 0.00 0.00 35.70 3.01
219 222 3.711190 TGATACTGCATTGGAGAGGCTTA 59.289 43.478 12.54 0.00 35.70 3.09
270 273 6.767902 TGATATGTGGCTTCAGATTTAGGAAC 59.232 38.462 0.00 0.00 0.00 3.62
280 293 2.315925 ACGGTGATATGTGGCTTCAG 57.684 50.000 0.00 0.00 0.00 3.02
310 360 3.795688 TTCTTCACTTGCCAGATTCCT 57.204 42.857 0.00 0.00 0.00 3.36
333 383 3.678921 CCAGCCATGGCATCATTTG 57.321 52.632 37.18 24.50 44.88 2.32
349 403 4.098349 GCATCATAAAATTGTCCAGCTCCA 59.902 41.667 0.00 0.00 0.00 3.86
377 431 1.680522 CTCAGGATAGCACAGCCCGT 61.681 60.000 0.00 0.00 30.64 5.28
378 432 1.068753 CTCAGGATAGCACAGCCCG 59.931 63.158 0.00 0.00 30.64 6.13
379 433 1.227793 GCTCAGGATAGCACAGCCC 60.228 63.158 0.00 0.00 42.30 5.19
380 434 4.453093 GCTCAGGATAGCACAGCC 57.547 61.111 0.00 0.00 42.30 4.85
495 553 0.543749 GCTCTACAAGGTCAGGCCAT 59.456 55.000 5.01 0.00 40.61 4.40
845 908 1.750341 CGTGGTACATATGGGCCGGA 61.750 60.000 5.05 0.00 44.52 5.14
1005 1081 3.050275 GGCGCACTCACCTTGACC 61.050 66.667 10.83 0.00 0.00 4.02
1017 1093 2.290287 ACAGGGTACTCATGGCGCA 61.290 57.895 10.83 0.00 0.00 6.09
1021 1097 3.282021 CAAATCCACAGGGTACTCATGG 58.718 50.000 9.34 9.34 33.20 3.66
1023 1099 4.589908 GAACAAATCCACAGGGTACTCAT 58.410 43.478 0.00 0.00 34.93 2.90
1024 1100 3.556213 CGAACAAATCCACAGGGTACTCA 60.556 47.826 0.00 0.00 34.93 3.41
1026 1102 2.290071 CCGAACAAATCCACAGGGTACT 60.290 50.000 0.00 0.00 34.93 2.73
1030 1155 1.883021 GCCGAACAAATCCACAGGG 59.117 57.895 0.00 0.00 0.00 4.45
1041 1166 1.672854 CCCAGATACTCCGCCGAACA 61.673 60.000 0.00 0.00 0.00 3.18
1042 1167 1.067582 CCCAGATACTCCGCCGAAC 59.932 63.158 0.00 0.00 0.00 3.95
1043 1168 2.131709 CCCCAGATACTCCGCCGAA 61.132 63.158 0.00 0.00 0.00 4.30
1044 1169 2.520982 CCCCAGATACTCCGCCGA 60.521 66.667 0.00 0.00 0.00 5.54
1045 1170 2.520982 TCCCCAGATACTCCGCCG 60.521 66.667 0.00 0.00 0.00 6.46
1046 1171 2.857744 CGTCCCCAGATACTCCGCC 61.858 68.421 0.00 0.00 0.00 6.13
1047 1172 2.728817 CGTCCCCAGATACTCCGC 59.271 66.667 0.00 0.00 0.00 5.54
1048 1173 2.728817 GCGTCCCCAGATACTCCG 59.271 66.667 0.00 0.00 0.00 4.63
1049 1174 1.049289 AAGGCGTCCCCAGATACTCC 61.049 60.000 0.00 0.00 35.39 3.85
1050 1175 0.831307 AAAGGCGTCCCCAGATACTC 59.169 55.000 0.00 0.00 35.39 2.59
1051 1176 0.831307 GAAAGGCGTCCCCAGATACT 59.169 55.000 0.00 0.00 35.39 2.12
1052 1177 0.179054 GGAAAGGCGTCCCCAGATAC 60.179 60.000 0.00 0.00 35.39 2.24
1053 1178 2.218066 GGAAAGGCGTCCCCAGATA 58.782 57.895 0.00 0.00 35.39 1.98
1054 1179 2.998949 GGAAAGGCGTCCCCAGAT 59.001 61.111 0.00 0.00 35.39 2.90
1066 1191 1.803334 TTCGAATGTGACGGGGAAAG 58.197 50.000 0.00 0.00 0.00 2.62
1267 1392 1.123928 AGTAAATGGAGGAGAGGCCG 58.876 55.000 0.00 0.00 43.43 6.13
1401 1530 5.753721 ACCTAAGAAAGCAGATCTTCTGT 57.246 39.130 0.00 0.00 45.94 3.41
1402 1531 5.353678 CCAACCTAAGAAAGCAGATCTTCTG 59.646 44.000 0.00 0.08 46.90 3.02
1437 1568 0.243907 CACCACACGAGGGTCTACAG 59.756 60.000 0.00 0.00 36.19 2.74
1468 1599 4.808649 GCACTAGGCGACCAGTAC 57.191 61.111 0.00 0.00 0.00 2.73
1537 1668 2.343387 GGGCGCAAATTTGGCAGT 59.657 55.556 23.93 0.00 0.00 4.40
1538 1669 2.028733 GTGGGCGCAAATTTGGCAG 61.029 57.895 23.93 13.09 0.00 4.85
1539 1670 2.030262 GTGGGCGCAAATTTGGCA 59.970 55.556 23.93 9.49 0.00 4.92
1575 1706 4.101741 ACTCAGGCAAACTAAGAAGACACT 59.898 41.667 0.00 0.00 0.00 3.55
1576 1707 4.381411 ACTCAGGCAAACTAAGAAGACAC 58.619 43.478 0.00 0.00 0.00 3.67
1577 1708 4.689612 ACTCAGGCAAACTAAGAAGACA 57.310 40.909 0.00 0.00 0.00 3.41
1580 1711 6.566197 AATCAACTCAGGCAAACTAAGAAG 57.434 37.500 0.00 0.00 0.00 2.85
1849 1980 3.960102 GAGAGAGATCTGAACCTGGTGAT 59.040 47.826 0.00 0.00 0.00 3.06
1860 1991 4.694760 TGGAGAGAGAGAGAGAGATCTG 57.305 50.000 0.00 0.00 0.00 2.90
1869 2000 6.126409 ACTAAGTATGGTTGGAGAGAGAGAG 58.874 44.000 0.00 0.00 0.00 3.20
1947 2086 9.578439 AAATGACTGTTCAAGAAAAAGAAAGAG 57.422 29.630 1.96 0.00 34.61 2.85
1963 2106 2.366266 ACATGCCTTGCAAATGACTGTT 59.634 40.909 14.91 0.00 43.62 3.16
2092 2235 5.623169 TGTGACCCCGTTAAAAATAGACTT 58.377 37.500 0.00 0.00 0.00 3.01
2106 2249 0.888736 TGAGCAATGTTGTGACCCCG 60.889 55.000 0.00 0.00 0.00 5.73
2196 2339 2.949644 AGTGTGCTAGGAAACAACCAAC 59.050 45.455 7.37 0.00 0.00 3.77
2307 2450 0.814457 CTCTACTGCCTTCGTCAGCT 59.186 55.000 0.00 0.00 35.04 4.24
2391 2537 5.248020 AGAACAACAAAATGCATTCCCCATA 59.752 36.000 13.38 0.00 0.00 2.74
2392 2538 4.041938 AGAACAACAAAATGCATTCCCCAT 59.958 37.500 13.38 0.00 0.00 4.00
2393 2539 3.390639 AGAACAACAAAATGCATTCCCCA 59.609 39.130 13.38 0.00 0.00 4.96
2394 2540 4.006780 AGAACAACAAAATGCATTCCCC 57.993 40.909 13.38 0.00 0.00 4.81
2396 2542 4.627035 GCCTAGAACAACAAAATGCATTCC 59.373 41.667 13.38 0.00 0.00 3.01
2512 2659 9.838339 ATTAAGGAGATTACGACTGATGAAAAT 57.162 29.630 0.00 0.00 0.00 1.82
2522 2669 7.412853 TCGTCTTACATTAAGGAGATTACGAC 58.587 38.462 0.00 0.00 34.68 4.34
2559 2706 3.137544 TGAAAGAACCAGTTGGCTCCTAA 59.862 43.478 0.00 0.00 39.32 2.69
2643 2790 9.764363 TCTGAAAACTAATTCATCGCATATACT 57.236 29.630 0.00 0.00 38.55 2.12
2664 2811 7.616150 AGATGTAAAGCTAGACCTTACTCTGAA 59.384 37.037 0.00 0.00 0.00 3.02
2674 2821 6.116126 ACATGGAAAGATGTAAAGCTAGACC 58.884 40.000 0.00 0.00 34.69 3.85
2675 2822 6.258947 GGACATGGAAAGATGTAAAGCTAGAC 59.741 42.308 0.00 0.00 36.67 2.59
2850 2997 4.881850 AGAAAGCGAATTTACCGATTCCAT 59.118 37.500 0.00 0.00 34.39 3.41
2857 3004 4.270084 TGCTGATAGAAAGCGAATTTACCG 59.730 41.667 0.00 0.00 43.88 4.02
2898 3045 2.812358 TACAGCATCACGAACACACT 57.188 45.000 0.00 0.00 0.00 3.55
3026 3174 4.275196 GGTGAAAACAAGAAGGTAGTGGAC 59.725 45.833 0.00 0.00 0.00 4.02
3384 3532 2.093288 TGTGGGCAACAAAATGAAAGCA 60.093 40.909 0.00 0.00 35.24 3.91
3398 3546 7.287466 AGCTACATAATTTGATAAATGTGGGCA 59.713 33.333 13.66 0.00 36.15 5.36
3427 3575 8.660295 TCCCATACAGTTAGAAAACTTCTCTA 57.340 34.615 0.00 0.00 43.60 2.43
3590 3738 3.244665 TGACATGTTGGATTCAGCTGAGT 60.245 43.478 17.43 14.80 0.00 3.41
3641 3791 4.623932 AGAGGTGCATGACTTCAAAGTA 57.376 40.909 0.00 0.00 39.88 2.24
3642 3792 3.498774 AGAGGTGCATGACTTCAAAGT 57.501 42.857 0.00 0.00 43.16 2.66
3647 3797 0.807496 GCCAAGAGGTGCATGACTTC 59.193 55.000 0.00 0.00 37.19 3.01
3694 3844 7.224362 TGGACACATGCAAAGAAATTAACAAAG 59.776 33.333 0.00 0.00 0.00 2.77
3695 3845 7.044181 TGGACACATGCAAAGAAATTAACAAA 58.956 30.769 0.00 0.00 0.00 2.83
3696 3846 6.577103 TGGACACATGCAAAGAAATTAACAA 58.423 32.000 0.00 0.00 0.00 2.83
3697 3847 6.154203 TGGACACATGCAAAGAAATTAACA 57.846 33.333 0.00 0.00 0.00 2.41
3698 3848 7.171337 ACAATGGACACATGCAAAGAAATTAAC 59.829 33.333 0.00 0.00 37.40 2.01
3709 3859 3.244526 ACAGTAGACAATGGACACATGCA 60.245 43.478 0.00 0.00 37.40 3.96
4046 4197 2.917713 TGGCCTAACATGAAACCCAT 57.082 45.000 3.32 0.00 35.44 4.00
4058 4209 7.880195 GCTGATTTAATCTTCTCTATGGCCTAA 59.120 37.037 3.32 0.00 0.00 2.69
4082 4233 4.823989 CCTTGGGATGATTTATTCTTCGCT 59.176 41.667 7.94 0.00 40.24 4.93
4138 4289 9.702726 CACACATGTATTAATTCTTAAGAACCG 57.297 33.333 19.94 4.33 36.80 4.44
4151 4305 5.356426 AGCGACTATGCACACATGTATTAA 58.644 37.500 0.00 0.00 37.04 1.40
4338 4502 2.461695 TGTTTCTGGACAAGGCCAAAA 58.538 42.857 5.01 0.00 37.52 2.44
4339 4503 2.151502 TGTTTCTGGACAAGGCCAAA 57.848 45.000 5.01 0.00 37.52 3.28
4400 4564 5.450592 TGAATTGCATGCACAGTTCTAAA 57.549 34.783 22.58 1.96 37.23 1.85
4431 4595 6.482641 GGTACGAATATCAGAGACACAGTAGA 59.517 42.308 0.00 0.00 0.00 2.59
4435 4599 5.066634 AGTGGTACGAATATCAGAGACACAG 59.933 44.000 0.00 0.00 0.00 3.66
4441 4605 7.875316 CCAAATAGTGGTACGAATATCAGAG 57.125 40.000 0.00 0.00 43.20 3.35
4500 4664 1.305930 CGGTTCAAACTAGGGCAGGC 61.306 60.000 0.00 0.00 0.00 4.85
4518 4682 3.789791 GCTGCACAATGGAATCATGTACG 60.790 47.826 0.00 0.00 33.18 3.67
4522 4686 1.835121 CGCTGCACAATGGAATCATG 58.165 50.000 0.00 0.00 33.18 3.07
4568 4732 2.821969 ACTGTTGGGAAATGTGCATCTC 59.178 45.455 0.00 0.00 0.00 2.75
4606 4770 5.305902 TGCTATTTGTATCTACGGGGATTGA 59.694 40.000 0.00 0.00 0.00 2.57
4610 4774 4.280174 GTCTGCTATTTGTATCTACGGGGA 59.720 45.833 0.00 0.00 0.00 4.81
4612 4776 4.557205 GGTCTGCTATTTGTATCTACGGG 58.443 47.826 0.00 0.00 0.00 5.28
4613 4777 4.281182 AGGGTCTGCTATTTGTATCTACGG 59.719 45.833 0.00 0.00 0.00 4.02
4614 4778 5.455056 AGGGTCTGCTATTTGTATCTACG 57.545 43.478 0.00 0.00 0.00 3.51
4680 4845 4.884668 ACACAATATATAGGTGTCCCGG 57.115 45.455 14.24 0.00 41.63 5.73
4694 4860 7.324856 GTGCACGATTCAACAATAAACACAATA 59.675 33.333 0.00 0.00 0.00 1.90
4705 4871 4.884458 TTGTTAGTGCACGATTCAACAA 57.116 36.364 21.58 21.58 34.49 2.83
4766 4935 3.181478 TGTGCTGAAATGTTGTCATGCAA 60.181 39.130 0.00 0.00 33.78 4.08
4845 5014 1.914700 GACTTCGTCTTCTTGCTAGCG 59.085 52.381 10.77 0.00 0.00 4.26
4892 5061 1.729149 GCAGCTTTTAGTTCGCGCATT 60.729 47.619 8.75 0.00 0.00 3.56
4903 5072 1.859398 CACGCGACTGCAGCTTTTA 59.141 52.632 15.93 0.00 42.97 1.52
4919 5088 2.034558 GGAGACTGATCTAGCTGAGCAC 59.965 54.545 7.39 0.00 36.01 4.40
4921 5090 2.554032 GAGGAGACTGATCTAGCTGAGC 59.446 54.545 0.00 0.00 44.43 4.26
4938 5107 4.764050 TTTGAGTTACACAACAGGAGGA 57.236 40.909 0.00 0.00 37.10 3.71
4979 5148 4.910746 AATCTTTGAACATGAGACGACG 57.089 40.909 0.00 0.00 0.00 5.12
4994 5163 9.099454 CTCAAGTCGCTAATTTACCTAATCTTT 57.901 33.333 0.00 0.00 0.00 2.52
5031 5200 6.554419 TGAACAAACATGAGACAGAGTTTTG 58.446 36.000 0.00 0.00 32.34 2.44
5032 5201 6.757897 TGAACAAACATGAGACAGAGTTTT 57.242 33.333 0.00 0.00 32.34 2.43
5033 5202 6.769822 AGATGAACAAACATGAGACAGAGTTT 59.230 34.615 0.00 0.00 34.78 2.66
5074 5244 6.540438 TTCTCCATAACAGGAAAGTACGAT 57.460 37.500 0.00 0.00 37.20 3.73
5102 5272 5.303971 CAATCCACCCTAAAATTGCAACAA 58.696 37.500 0.00 0.00 0.00 2.83
5103 5273 4.892433 CAATCCACCCTAAAATTGCAACA 58.108 39.130 0.00 0.00 0.00 3.33
5108 5278 4.937015 CCAAAGCAATCCACCCTAAAATTG 59.063 41.667 0.00 0.00 33.31 2.32
5109 5279 4.597075 ACCAAAGCAATCCACCCTAAAATT 59.403 37.500 0.00 0.00 0.00 1.82
5110 5280 4.167319 ACCAAAGCAATCCACCCTAAAAT 58.833 39.130 0.00 0.00 0.00 1.82
5114 5284 2.109128 TCAACCAAAGCAATCCACCCTA 59.891 45.455 0.00 0.00 0.00 3.53
5115 5285 1.133199 TCAACCAAAGCAATCCACCCT 60.133 47.619 0.00 0.00 0.00 4.34
5118 5288 2.738314 GCAATCAACCAAAGCAATCCAC 59.262 45.455 0.00 0.00 0.00 4.02
5122 5292 2.745281 GCATGCAATCAACCAAAGCAAT 59.255 40.909 14.21 0.00 38.85 3.56
5133 5303 7.273164 CGTCTTAACTAAAATTGCATGCAATCA 59.727 33.333 38.48 26.53 44.86 2.57
5138 5308 5.636837 TCCGTCTTAACTAAAATTGCATGC 58.363 37.500 11.82 11.82 0.00 4.06
5149 5319 6.041296 AGTCCAAACTTTCTCCGTCTTAACTA 59.959 38.462 0.00 0.00 28.74 2.24
5150 5320 5.055144 GTCCAAACTTTCTCCGTCTTAACT 58.945 41.667 0.00 0.00 0.00 2.24
5152 5322 5.286267 AGTCCAAACTTTCTCCGTCTTAA 57.714 39.130 0.00 0.00 28.74 1.85
5153 5323 4.950205 AGTCCAAACTTTCTCCGTCTTA 57.050 40.909 0.00 0.00 28.74 2.10
5154 5324 3.840124 AGTCCAAACTTTCTCCGTCTT 57.160 42.857 0.00 0.00 28.74 3.01
5167 5350 6.634039 GCCTAGATGGTTGGTATTAGTCCAAA 60.634 42.308 0.00 0.00 44.91 3.28
5175 5358 2.509548 TGCAGCCTAGATGGTTGGTATT 59.490 45.455 0.00 0.00 45.70 1.89
5176 5359 2.126882 TGCAGCCTAGATGGTTGGTAT 58.873 47.619 0.00 0.00 45.70 2.73
5209 5831 8.278919 TCAATTAATTTGGACCGGAGGAAGTAC 61.279 40.741 9.46 0.00 43.23 2.73
5210 5832 6.296547 TCAATTAATTTGGACCGGAGGAAGTA 60.297 38.462 9.46 0.00 43.23 2.24
5211 5833 5.515886 TCAATTAATTTGGACCGGAGGAAGT 60.516 40.000 9.46 0.00 43.23 3.01
5212 5834 4.947388 TCAATTAATTTGGACCGGAGGAAG 59.053 41.667 9.46 0.00 43.23 3.46
5213 5835 4.703093 GTCAATTAATTTGGACCGGAGGAA 59.297 41.667 9.46 0.00 43.23 3.36
5214 5836 4.263550 TGTCAATTAATTTGGACCGGAGGA 60.264 41.667 9.46 0.00 43.23 3.71
5215 5837 4.013728 TGTCAATTAATTTGGACCGGAGG 58.986 43.478 9.46 0.00 45.06 4.30
5216 5838 4.700213 AGTGTCAATTAATTTGGACCGGAG 59.300 41.667 9.46 0.00 35.92 4.63
5217 5839 4.658063 AGTGTCAATTAATTTGGACCGGA 58.342 39.130 9.46 0.00 35.92 5.14
5218 5840 5.385509 AAGTGTCAATTAATTTGGACCGG 57.614 39.130 13.31 0.00 35.92 5.28
5219 5841 8.079809 ACTAAAAGTGTCAATTAATTTGGACCG 58.920 33.333 13.31 0.00 35.92 4.79
5256 5878 9.632807 TTGACGCTGCTTTAATACAATTTTATT 57.367 25.926 0.00 2.60 0.00 1.40
5257 5879 9.801873 ATTGACGCTGCTTTAATACAATTTTAT 57.198 25.926 0.00 0.00 0.00 1.40
5258 5880 9.632807 AATTGACGCTGCTTTAATACAATTTTA 57.367 25.926 0.00 0.00 34.54 1.52
5259 5881 8.532977 AATTGACGCTGCTTTAATACAATTTT 57.467 26.923 0.00 0.00 34.54 1.82
5260 5882 9.632807 TTAATTGACGCTGCTTTAATACAATTT 57.367 25.926 0.00 0.00 37.67 1.82
5261 5883 9.801873 ATTAATTGACGCTGCTTTAATACAATT 57.198 25.926 0.00 0.00 39.14 2.32
5264 5886 9.877137 CATATTAATTGACGCTGCTTTAATACA 57.123 29.630 0.00 0.00 31.29 2.29
5265 5887 9.329913 CCATATTAATTGACGCTGCTTTAATAC 57.670 33.333 0.00 0.00 31.29 1.89
5266 5888 9.278978 TCCATATTAATTGACGCTGCTTTAATA 57.721 29.630 0.00 5.00 32.39 0.98
5267 5889 8.165239 TCCATATTAATTGACGCTGCTTTAAT 57.835 30.769 0.00 0.00 0.00 1.40
5268 5890 7.561021 TCCATATTAATTGACGCTGCTTTAA 57.439 32.000 0.00 0.00 0.00 1.52
5269 5891 7.744087 ATCCATATTAATTGACGCTGCTTTA 57.256 32.000 0.00 0.00 0.00 1.85
5270 5892 6.639632 ATCCATATTAATTGACGCTGCTTT 57.360 33.333 0.00 0.00 0.00 3.51
5271 5893 6.441274 CAATCCATATTAATTGACGCTGCTT 58.559 36.000 0.00 0.00 35.35 3.91
5272 5894 5.048504 CCAATCCATATTAATTGACGCTGCT 60.049 40.000 0.00 0.00 35.35 4.24
5273 5895 5.048782 TCCAATCCATATTAATTGACGCTGC 60.049 40.000 7.95 0.00 35.35 5.25
5274 5896 6.348786 CCTCCAATCCATATTAATTGACGCTG 60.349 42.308 7.95 0.00 35.35 5.18
5275 5897 5.707298 CCTCCAATCCATATTAATTGACGCT 59.293 40.000 7.95 0.00 35.35 5.07
5276 5898 5.106157 CCCTCCAATCCATATTAATTGACGC 60.106 44.000 7.95 0.00 35.35 5.19
5277 5899 6.237901 TCCCTCCAATCCATATTAATTGACG 58.762 40.000 7.95 0.00 35.35 4.35
5278 5900 7.234355 ACTCCCTCCAATCCATATTAATTGAC 58.766 38.462 7.95 0.00 35.35 3.18
5279 5901 7.406620 ACTCCCTCCAATCCATATTAATTGA 57.593 36.000 7.95 0.00 35.35 2.57
5280 5902 8.386264 AGTACTCCCTCCAATCCATATTAATTG 58.614 37.037 0.00 1.40 33.57 2.32
5281 5903 8.525729 AGTACTCCCTCCAATCCATATTAATT 57.474 34.615 0.00 0.00 0.00 1.40
5282 5904 9.273137 CTAGTACTCCCTCCAATCCATATTAAT 57.727 37.037 0.00 0.00 0.00 1.40
5283 5905 8.461854 TCTAGTACTCCCTCCAATCCATATTAA 58.538 37.037 0.00 0.00 0.00 1.40
5284 5906 8.008104 TCTAGTACTCCCTCCAATCCATATTA 57.992 38.462 0.00 0.00 0.00 0.98
5285 5907 6.875469 TCTAGTACTCCCTCCAATCCATATT 58.125 40.000 0.00 0.00 0.00 1.28
5286 5908 6.485388 TCTAGTACTCCCTCCAATCCATAT 57.515 41.667 0.00 0.00 0.00 1.78
5287 5909 5.942977 TCTAGTACTCCCTCCAATCCATA 57.057 43.478 0.00 0.00 0.00 2.74
5288 5910 4.834406 TCTAGTACTCCCTCCAATCCAT 57.166 45.455 0.00 0.00 0.00 3.41
5289 5911 4.620086 TTCTAGTACTCCCTCCAATCCA 57.380 45.455 0.00 0.00 0.00 3.41
5290 5912 6.327887 AGAAATTCTAGTACTCCCTCCAATCC 59.672 42.308 0.00 0.00 0.00 3.01
5291 5913 7.368198 AGAAATTCTAGTACTCCCTCCAATC 57.632 40.000 0.00 0.00 0.00 2.67
5292 5914 6.327887 GGAGAAATTCTAGTACTCCCTCCAAT 59.672 42.308 0.00 0.00 40.58 3.16
5293 5915 5.661759 GGAGAAATTCTAGTACTCCCTCCAA 59.338 44.000 0.00 0.00 40.58 3.53
5294 5916 5.043281 AGGAGAAATTCTAGTACTCCCTCCA 60.043 44.000 0.00 0.00 45.53 3.86
5295 5917 5.303333 CAGGAGAAATTCTAGTACTCCCTCC 59.697 48.000 0.00 6.35 45.53 4.30
5296 5918 5.221362 GCAGGAGAAATTCTAGTACTCCCTC 60.221 48.000 0.00 0.00 45.53 4.30
5297 5919 4.651962 GCAGGAGAAATTCTAGTACTCCCT 59.348 45.833 0.00 0.00 45.53 4.20
5298 5920 4.406003 TGCAGGAGAAATTCTAGTACTCCC 59.594 45.833 0.00 0.00 45.53 4.30
5299 5921 5.599999 TGCAGGAGAAATTCTAGTACTCC 57.400 43.478 0.00 0.00 44.97 3.85
5300 5922 5.517054 CGTTGCAGGAGAAATTCTAGTACTC 59.483 44.000 0.00 0.00 0.00 2.59
5301 5923 5.411781 CGTTGCAGGAGAAATTCTAGTACT 58.588 41.667 0.00 0.00 0.00 2.73
5302 5924 4.567159 CCGTTGCAGGAGAAATTCTAGTAC 59.433 45.833 0.00 0.00 0.00 2.73
5303 5925 4.755411 CCGTTGCAGGAGAAATTCTAGTA 58.245 43.478 0.00 0.00 0.00 1.82
5304 5926 3.600388 CCGTTGCAGGAGAAATTCTAGT 58.400 45.455 0.00 0.00 0.00 2.57
5305 5927 2.352960 GCCGTTGCAGGAGAAATTCTAG 59.647 50.000 0.00 0.00 37.47 2.43
5321 5943 2.140792 ACTGGAGTGGACTGCCGTT 61.141 57.895 0.00 0.00 36.79 4.44
5365 5987 7.575414 ATGTACAGTACTAGGACTTCATCTG 57.425 40.000 4.33 0.00 0.00 2.90
5373 5996 8.943909 ATTTTGCTTATGTACAGTACTAGGAC 57.056 34.615 12.07 0.00 0.00 3.85
5378 6001 7.119262 GGTGTGATTTTGCTTATGTACAGTACT 59.881 37.037 12.07 0.00 0.00 2.73
5380 6003 6.937465 TGGTGTGATTTTGCTTATGTACAGTA 59.063 34.615 0.33 0.00 0.00 2.74
5387 6017 8.531622 TTGTAAATGGTGTGATTTTGCTTATG 57.468 30.769 0.00 0.00 0.00 1.90
5444 6076 4.678509 TGTATGCATGTCGTTCTTTTCC 57.321 40.909 10.16 0.00 0.00 3.13
5453 6085 3.128415 TCAATTGGGTTGTATGCATGTCG 59.872 43.478 10.16 0.00 38.95 4.35
5458 6093 5.999205 AAGATTCAATTGGGTTGTATGCA 57.001 34.783 5.42 0.00 38.95 3.96
5509 6145 4.347876 TCTCCAGGAACTTGTGAGATCAAA 59.652 41.667 0.00 0.00 34.60 2.69
5516 6152 5.306937 TGTCTAATTCTCCAGGAACTTGTGA 59.693 40.000 0.00 0.00 34.60 3.58
5526 6162 1.139058 CCCCGGTGTCTAATTCTCCAG 59.861 57.143 0.00 0.00 0.00 3.86
5528 6164 1.492764 TCCCCGGTGTCTAATTCTCC 58.507 55.000 0.00 0.00 0.00 3.71
5532 6168 3.178865 TCTTCTTCCCCGGTGTCTAATT 58.821 45.455 0.00 0.00 0.00 1.40
5534 6170 2.314071 TCTTCTTCCCCGGTGTCTAA 57.686 50.000 0.00 0.00 0.00 2.10
5535 6171 2.544844 ATCTTCTTCCCCGGTGTCTA 57.455 50.000 0.00 0.00 0.00 2.59
5536 6172 1.657804 AATCTTCTTCCCCGGTGTCT 58.342 50.000 0.00 0.00 0.00 3.41
5538 6174 2.107552 TCAAAATCTTCTTCCCCGGTGT 59.892 45.455 0.00 0.00 0.00 4.16
5539 6175 2.790433 TCAAAATCTTCTTCCCCGGTG 58.210 47.619 0.00 0.00 0.00 4.94
5540 6176 3.267031 AGATCAAAATCTTCTTCCCCGGT 59.733 43.478 0.00 0.00 39.27 5.28
5541 6177 3.891049 AGATCAAAATCTTCTTCCCCGG 58.109 45.455 0.00 0.00 39.27 5.73
5543 6179 5.298026 GCAGTAGATCAAAATCTTCTTCCCC 59.702 44.000 0.00 0.00 42.39 4.81
5545 6181 6.597280 AGTGCAGTAGATCAAAATCTTCTTCC 59.403 38.462 0.00 0.00 42.39 3.46
5546 6182 7.548780 AGAGTGCAGTAGATCAAAATCTTCTTC 59.451 37.037 0.00 0.00 42.39 2.87
5547 6183 7.393216 AGAGTGCAGTAGATCAAAATCTTCTT 58.607 34.615 0.00 0.00 42.39 2.52
5548 6184 6.945218 AGAGTGCAGTAGATCAAAATCTTCT 58.055 36.000 0.00 0.00 42.39 2.85
5549 6185 7.437862 CCTAGAGTGCAGTAGATCAAAATCTTC 59.562 40.741 0.00 0.00 42.39 2.87
5550 6186 7.271511 CCTAGAGTGCAGTAGATCAAAATCTT 58.728 38.462 0.00 0.00 42.39 2.40
5555 6191 4.026744 AGCCTAGAGTGCAGTAGATCAAA 58.973 43.478 0.00 0.00 0.00 2.69
5595 6232 3.382048 AACCTTGGTAGAAGTGTCGTC 57.618 47.619 0.00 0.00 0.00 4.20
5596 6233 5.393896 GCTATAACCTTGGTAGAAGTGTCGT 60.394 44.000 0.00 0.00 0.00 4.34
5597 6234 5.041940 GCTATAACCTTGGTAGAAGTGTCG 58.958 45.833 0.00 0.00 0.00 4.35
5622 6262 1.243342 TTTGCAGCATGGGACGGAAG 61.243 55.000 0.00 0.00 35.86 3.46
5694 6337 0.674534 GGGCGGGAGATAGTACACAG 59.325 60.000 0.00 0.00 0.00 3.66
5714 6357 1.908793 CCCGGACTCTGGACAGTGT 60.909 63.158 0.73 6.73 37.80 3.55
5754 6397 3.944250 ATGGGAGTTTGGCAGGCGG 62.944 63.158 0.00 0.00 0.00 6.13
5865 6508 0.969894 ACACCTCCAAACTCTCCTCG 59.030 55.000 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.