Multiple sequence alignment - TraesCS1B01G289200

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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 TraesCS1B01G289200 chr1B 100.000 2727 0 0 2842 5568 504090497 504093223 0.000000e+00 5036.0
1 TraesCS1B01G289200 chr1B 100.000 2524 0 0 1 2524 504087656 504090179 0.000000e+00 4662.0
2 TraesCS1B01G289200 chr1D 93.866 1940 83 21 1 1924 377186712 377188631 0.000000e+00 2891.0
3 TraesCS1B01G289200 chr1D 89.709 1924 120 36 3191 5094 377189525 377191390 0.000000e+00 2385.0
4 TraesCS1B01G289200 chr1D 92.675 587 25 7 1914 2485 377188667 377189250 0.000000e+00 830.0
5 TraesCS1B01G289200 chr1D 84.211 418 34 12 5104 5506 377191432 377191832 1.460000e-100 377.0
6 TraesCS1B01G289200 chr1D 91.373 255 16 3 2878 3131 377189251 377189500 1.490000e-90 344.0
7 TraesCS1B01G289200 chr1A 91.612 1526 70 28 1025 2501 477730922 477732438 0.000000e+00 2056.0
8 TraesCS1B01G289200 chr1A 89.412 1020 66 24 3563 4551 477733646 477734654 0.000000e+00 1247.0
9 TraesCS1B01G289200 chr1A 93.415 653 37 4 2912 3564 477732919 477733565 0.000000e+00 963.0
10 TraesCS1B01G289200 chr1A 88.406 207 8 4 596 802 477730295 477730485 9.330000e-58 235.0
11 TraesCS1B01G289200 chr1A 86.957 184 15 7 5385 5568 477735387 477735561 1.220000e-46 198.0
12 TraesCS1B01G289200 chr1A 77.181 298 42 17 4700 4984 477734838 477735122 3.470000e-32 150.0
13 TraesCS1B01G289200 chr1A 92.857 84 0 2 788 866 477730503 477730585 3.520000e-22 117.0
14 TraesCS1B01G289200 chr1A 85.149 101 4 6 1820 1920 505525753 505525664 5.940000e-15 93.5
15 TraesCS1B01G289200 chr3D 82.243 428 54 9 1484 1909 471775891 471775484 3.190000e-92 350.0
16 TraesCS1B01G289200 chr3D 81.443 97 9 4 1820 1916 161403666 161403753 2.780000e-08 71.3
17 TraesCS1B01G289200 chr3D 80.412 97 10 4 1820 1916 161499700 161499787 1.290000e-06 65.8
18 TraesCS1B01G289200 chr3B 82.243 428 54 9 1484 1909 627213753 627213346 3.190000e-92 350.0
19 TraesCS1B01G289200 chr3A 81.628 430 59 7 1484 1909 614541161 614540748 6.910000e-89 339.0
20 TraesCS1B01G289200 chr4B 84.034 119 16 3 2086 2202 25484573 25484456 1.640000e-20 111.0
21 TraesCS1B01G289200 chr2A 84.483 116 15 3 2086 2199 195808063 195808177 1.640000e-20 111.0
22 TraesCS1B01G289200 chr4A 82.906 117 16 4 2086 2199 585663404 585663519 9.870000e-18 102.0
23 TraesCS1B01G289200 chr4A 86.139 101 3 6 1820 1920 16031336 16031425 1.280000e-16 99.0
24 TraesCS1B01G289200 chr6D 86.957 92 9 2 2084 2175 254167062 254167150 3.550000e-17 100.0
25 TraesCS1B01G289200 chr6A 88.889 81 8 1 2112 2192 364670027 364669948 1.280000e-16 99.0


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 TraesCS1B01G289200 chr1B 504087656 504093223 5567 False 4849.000000 5036 100.000000 1 5568 2 chr1B.!!$F1 5567
1 TraesCS1B01G289200 chr1D 377186712 377191832 5120 False 1365.400000 2891 90.366800 1 5506 5 chr1D.!!$F1 5505
2 TraesCS1B01G289200 chr1A 477730295 477735561 5266 False 709.428571 2056 88.548571 596 5568 7 chr1A.!!$F1 4972

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
196 198 0.035056 AGACTGCCACCCATGTTAGC 60.035 55.000 0.00 0.0 0.00 3.09 F
908 957 0.036875 CCAAACCCCTCCACAGTCTC 59.963 60.000 0.00 0.0 0.00 3.36 F
1382 1616 0.252927 AGGTTGAGGAAGAGGAGGGG 60.253 60.000 0.00 0.0 0.00 4.79 F
2210 2501 0.039618 GGGGCAGATGGTGAGGAAAA 59.960 55.000 0.00 0.0 0.00 2.29 F
3379 3765 1.594862 GCTTACCATGTGAAGCTAGCG 59.405 52.381 17.36 0.0 43.84 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2106 2394 0.322456 ACCATGTGTTCATCCACCCG 60.322 55.0 0.00 0.00 34.35 5.28 R
2210 2501 0.036732 TCGATCCAGCACTTTGCCTT 59.963 50.0 0.00 0.00 46.52 4.35 R
3294 3680 0.323360 TGGGGGAAATGTGCTGCTAC 60.323 55.0 0.00 0.00 0.00 3.58 R
3806 4294 0.326048 AGATCTCACAGGTCCTGGGG 60.326 60.0 21.40 13.31 35.28 4.96 R
4706 5246 0.106918 TCGCCCATATTGGTCCAACC 60.107 55.0 6.41 0.00 35.17 3.77 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
38 39 9.657419 ATGATTCATTTGAAGGAAAAACATACC 57.343 29.630 0.00 0.00 37.48 2.73
89 90 2.418628 TCTTTTCCGCGTCATGAAATCC 59.581 45.455 4.92 0.00 31.10 3.01
90 91 1.814793 TTTCCGCGTCATGAAATCCA 58.185 45.000 4.92 0.00 0.00 3.41
91 92 1.814793 TTCCGCGTCATGAAATCCAA 58.185 45.000 4.92 0.00 0.00 3.53
92 93 1.814793 TCCGCGTCATGAAATCCAAA 58.185 45.000 4.92 0.00 0.00 3.28
174 176 9.388506 TGATTTTGGAAATTACACAACATGTTT 57.611 25.926 8.77 0.00 43.19 2.83
196 198 0.035056 AGACTGCCACCCATGTTAGC 60.035 55.000 0.00 0.00 0.00 3.09
210 212 4.981674 CCATGTTAGCACACAAATTTCGTT 59.018 37.500 0.00 0.00 35.03 3.85
245 247 2.298610 GCTTCCTTATACCTTGTGGCC 58.701 52.381 0.00 0.00 36.63 5.36
267 269 1.435577 ACGAGCCAATTACCGAACAC 58.564 50.000 0.00 0.00 0.00 3.32
270 272 2.147958 GAGCCAATTACCGAACACACA 58.852 47.619 0.00 0.00 0.00 3.72
329 333 6.786207 TGTATGAAAACACATCAAACGACAA 58.214 32.000 0.00 0.00 0.00 3.18
333 337 7.588143 TGAAAACACATCAAACGACAATTTT 57.412 28.000 0.00 0.00 0.00 1.82
349 353 7.971168 ACGACAATTTTATGTTCAAACAAGTGA 59.029 29.630 0.00 0.00 43.03 3.41
380 384 6.424207 AGTTGTCTCGTCCTTATTTCAAGAAC 59.576 38.462 0.00 0.00 0.00 3.01
382 386 6.464222 TGTCTCGTCCTTATTTCAAGAACAT 58.536 36.000 0.00 0.00 0.00 2.71
383 387 7.608153 TGTCTCGTCCTTATTTCAAGAACATA 58.392 34.615 0.00 0.00 0.00 2.29
386 390 9.667107 TCTCGTCCTTATTTCAAGAACATAATT 57.333 29.630 0.00 0.00 0.00 1.40
398 407 8.697846 TCAAGAACATAATTTACTACCTCGTG 57.302 34.615 0.00 0.00 0.00 4.35
402 411 8.098912 AGAACATAATTTACTACCTCGTGGTTT 58.901 33.333 15.36 4.43 46.05 3.27
403 412 9.369904 GAACATAATTTACTACCTCGTGGTTTA 57.630 33.333 15.36 6.58 46.05 2.01
421 430 6.741358 GTGGTTTATTTTCGCTAGATTGTCAC 59.259 38.462 0.00 0.00 0.00 3.67
429 438 5.142061 TCGCTAGATTGTCACTGGTTAAA 57.858 39.130 0.00 0.00 0.00 1.52
488 497 1.581934 CACACGAGAGCTTGTTGGAA 58.418 50.000 0.00 0.00 0.00 3.53
491 500 2.549754 ACACGAGAGCTTGTTGGAAATG 59.450 45.455 0.00 0.00 0.00 2.32
500 509 5.321102 AGCTTGTTGGAAATGTATACACCA 58.679 37.500 7.96 8.64 0.00 4.17
548 558 6.265422 CCATATTTCCCAAAATGGAGTCTACC 59.735 42.308 0.00 0.00 40.96 3.18
549 559 4.733077 TTTCCCAAAATGGAGTCTACCA 57.267 40.909 0.00 0.00 40.96 3.25
552 562 3.396276 TCCCAAAATGGAGTCTACCACAA 59.604 43.478 0.00 0.00 40.96 3.33
589 599 6.628919 TGATCTCACAAGCAATTATCATGG 57.371 37.500 0.00 0.00 0.00 3.66
594 604 2.431782 ACAAGCAATTATCATGGCCCAC 59.568 45.455 0.00 0.00 0.00 4.61
628 638 8.827677 CCTAACAAAGCCTTACTATGTAATGAC 58.172 37.037 0.00 0.00 0.00 3.06
662 672 5.045942 TCACCAAGCAATATCCAACTACTCA 60.046 40.000 0.00 0.00 0.00 3.41
664 674 6.319658 CACCAAGCAATATCCAACTACTCATT 59.680 38.462 0.00 0.00 0.00 2.57
667 677 7.703621 CCAAGCAATATCCAACTACTCATTTTG 59.296 37.037 0.00 0.00 0.00 2.44
668 678 7.944729 AGCAATATCCAACTACTCATTTTGT 57.055 32.000 0.00 0.00 0.00 2.83
669 679 7.765307 AGCAATATCCAACTACTCATTTTGTG 58.235 34.615 0.00 0.00 0.00 3.33
670 680 7.394359 AGCAATATCCAACTACTCATTTTGTGT 59.606 33.333 0.00 0.00 0.00 3.72
671 681 8.673711 GCAATATCCAACTACTCATTTTGTGTA 58.326 33.333 0.00 0.00 0.00 2.90
803 847 1.280133 CCACAGATTCAGAGGAGGCAA 59.720 52.381 0.00 0.00 0.00 4.52
879 928 1.735920 CACGGTGAGCTGAGCTGAC 60.736 63.158 13.71 14.94 41.79 3.51
907 956 2.069165 GCCAAACCCCTCCACAGTCT 62.069 60.000 0.00 0.00 0.00 3.24
908 957 0.036875 CCAAACCCCTCCACAGTCTC 59.963 60.000 0.00 0.00 0.00 3.36
909 958 1.059913 CAAACCCCTCCACAGTCTCT 58.940 55.000 0.00 0.00 0.00 3.10
910 959 1.002544 CAAACCCCTCCACAGTCTCTC 59.997 57.143 0.00 0.00 0.00 3.20
956 1009 1.350019 TCGTCTTTTCCTTTCTCCCCC 59.650 52.381 0.00 0.00 0.00 5.40
1038 1265 0.546598 CACTCTTTATTCCCCCGGCT 59.453 55.000 0.00 0.00 0.00 5.52
1116 1343 2.027024 CGCCGCTTCAGCCGTATA 59.973 61.111 0.00 0.00 37.91 1.47
1141 1372 2.690881 ATTAGTCGGGGCCCAGCA 60.691 61.111 26.86 7.07 0.00 4.41
1191 1422 1.500108 CATGCGCTCTTCCTGATCTC 58.500 55.000 9.73 0.00 0.00 2.75
1265 1496 2.415357 CGCGGCATTTTGTCTGGTATTT 60.415 45.455 0.00 0.00 0.00 1.40
1266 1497 3.584834 GCGGCATTTTGTCTGGTATTTT 58.415 40.909 0.00 0.00 0.00 1.82
1267 1498 3.612423 GCGGCATTTTGTCTGGTATTTTC 59.388 43.478 0.00 0.00 0.00 2.29
1382 1616 0.252927 AGGTTGAGGAAGAGGAGGGG 60.253 60.000 0.00 0.00 0.00 4.79
1394 1628 4.424711 GAGGGGCAATGGTCGGCA 62.425 66.667 0.00 0.00 0.00 5.69
1912 2149 1.003696 AGAGGCAACAAGTAAGCTCCC 59.996 52.381 0.00 0.00 41.41 4.30
1913 2150 0.771127 AGGCAACAAGTAAGCTCCCA 59.229 50.000 0.00 0.00 41.41 4.37
1931 2214 4.731612 CTCTGTCAGTGCGCCGCT 62.732 66.667 11.67 0.00 0.00 5.52
1932 2215 3.342370 CTCTGTCAGTGCGCCGCTA 62.342 63.158 11.67 0.00 0.00 4.26
1938 2221 1.060937 CAGTGCGCCGCTACATTTC 59.939 57.895 11.67 0.00 0.00 2.17
1955 2238 6.759497 ACATTTCCTGCTCAGTAATTAACC 57.241 37.500 0.00 0.00 0.00 2.85
1971 2254 8.520351 AGTAATTAACCTGAATAAACTGCCAAC 58.480 33.333 0.00 0.00 0.00 3.77
2032 2315 0.465287 CAGTTGCAGGCAGGGTTTTT 59.535 50.000 0.00 0.00 0.00 1.94
2140 2428 8.106462 TGAACACATGGTTAAGGAATCTTATGA 58.894 33.333 0.00 0.00 40.63 2.15
2210 2501 0.039618 GGGGCAGATGGTGAGGAAAA 59.960 55.000 0.00 0.00 0.00 2.29
2312 2605 5.768164 GGTGAAAGTAGGATTGGTTCTTCAA 59.232 40.000 0.00 0.00 0.00 2.69
2391 2693 8.962679 AGTGTTGACCAAGTTTGTTTCTTAATA 58.037 29.630 0.00 0.00 0.00 0.98
2501 2807 5.042463 TGTTTTGATGGAACTGTAGGTGA 57.958 39.130 0.00 0.00 0.00 4.02
2503 2809 5.163248 TGTTTTGATGGAACTGTAGGTGAGA 60.163 40.000 0.00 0.00 0.00 3.27
2504 2810 5.560722 TTTGATGGAACTGTAGGTGAGAA 57.439 39.130 0.00 0.00 0.00 2.87
2505 2811 5.762179 TTGATGGAACTGTAGGTGAGAAT 57.238 39.130 0.00 0.00 0.00 2.40
2506 2812 5.344743 TGATGGAACTGTAGGTGAGAATC 57.655 43.478 0.00 0.00 0.00 2.52
2522 2846 5.922053 TGAGAATCATGACCTTGGTGATAG 58.078 41.667 0.00 0.00 42.56 2.08
2523 2847 5.163269 TGAGAATCATGACCTTGGTGATAGG 60.163 44.000 0.00 0.00 42.56 2.57
2865 3189 6.801575 GCTTCTGTTAGCTCAGAGTATTACT 58.198 40.000 5.38 0.00 43.85 2.24
2866 3190 6.695278 GCTTCTGTTAGCTCAGAGTATTACTG 59.305 42.308 0.00 0.00 43.85 2.74
2867 3191 7.415765 GCTTCTGTTAGCTCAGAGTATTACTGA 60.416 40.741 0.00 0.00 43.85 3.41
2868 3192 7.939784 TCTGTTAGCTCAGAGTATTACTGAA 57.060 36.000 0.00 0.00 42.58 3.02
2869 3193 8.526667 TCTGTTAGCTCAGAGTATTACTGAAT 57.473 34.615 0.00 0.00 42.58 2.57
2870 3194 8.625651 TCTGTTAGCTCAGAGTATTACTGAATC 58.374 37.037 0.00 0.00 42.58 2.52
2871 3195 8.293699 TGTTAGCTCAGAGTATTACTGAATCA 57.706 34.615 0.00 0.00 42.58 2.57
2872 3196 8.409371 TGTTAGCTCAGAGTATTACTGAATCAG 58.591 37.037 8.98 8.98 42.58 2.90
2874 3198 7.416964 AGCTCAGAGTATTACTGAATCAGTT 57.583 36.000 21.83 7.02 42.59 3.16
2875 3199 8.526667 AGCTCAGAGTATTACTGAATCAGTTA 57.473 34.615 21.83 13.10 42.59 2.24
2876 3200 8.410141 AGCTCAGAGTATTACTGAATCAGTTAC 58.590 37.037 21.83 17.40 42.59 2.50
2902 3226 2.464157 AAGTGTAGAAGGCACTCAGC 57.536 50.000 0.00 0.00 45.36 4.26
2903 3227 1.694150 AAGTGTAGAAGGCACTCAGCA 59.306 47.619 0.00 0.00 45.36 4.41
2904 3228 2.104792 AAGTGTAGAAGGCACTCAGCAA 59.895 45.455 0.00 0.00 45.36 3.91
2905 3229 4.052285 AAGTGTAGAAGGCACTCAGCAAC 61.052 47.826 0.00 0.00 45.36 4.17
2954 3330 4.271696 TCAAATGTCTGGTGATCGTTCT 57.728 40.909 0.00 0.00 0.00 3.01
2970 3346 3.697542 TCGTTCTTCATAGAATCGGTCCA 59.302 43.478 0.00 0.00 42.14 4.02
3080 3456 9.567776 TTATGCAAACTGCTAATAGGCTAATAA 57.432 29.630 0.00 0.00 45.31 1.40
3085 3461 6.115448 ACTGCTAATAGGCTAATAAGGGTG 57.885 41.667 0.00 0.00 0.00 4.61
3170 3555 8.451748 GGACAAGATGTTCCACTAAAATTAGTC 58.548 37.037 2.88 0.00 41.82 2.59
3192 3577 4.586421 TCAGACCACAACCAAATATTGCAA 59.414 37.500 0.00 0.00 0.00 4.08
3252 3637 3.350219 TGGCATTAACAGGAGGAGTTC 57.650 47.619 0.00 0.00 0.00 3.01
3294 3680 5.220472 GCATATTGGCATATAGTGTACAGCG 60.220 44.000 0.00 0.00 0.00 5.18
3324 3710 3.134081 ACATTTCCCCCATACTCGTACAG 59.866 47.826 0.00 0.00 0.00 2.74
3353 3739 5.716094 CTGTCATTCAAGGAATCATTGCAA 58.284 37.500 0.00 0.00 28.87 4.08
3379 3765 1.594862 GCTTACCATGTGAAGCTAGCG 59.405 52.381 17.36 0.00 43.84 4.26
3390 3776 3.000971 GTGAAGCTAGCGACGTAACATTC 60.001 47.826 9.55 4.90 0.00 2.67
3501 3887 4.151070 GTTGTGTGATTGCAACTACATCG 58.849 43.478 17.46 0.00 41.05 3.84
3519 3905 5.313712 ACATCGAAACTTACTGGGTTGATT 58.686 37.500 0.00 0.00 0.00 2.57
3520 3906 5.768164 ACATCGAAACTTACTGGGTTGATTT 59.232 36.000 0.00 0.00 0.00 2.17
3521 3907 6.264518 ACATCGAAACTTACTGGGTTGATTTT 59.735 34.615 0.00 0.00 0.00 1.82
3602 4073 7.962964 TGTTGTTCCTGTGTTAAGAGAATAG 57.037 36.000 0.00 0.00 0.00 1.73
3605 4076 7.311092 TGTTCCTGTGTTAAGAGAATAGGAA 57.689 36.000 0.00 0.00 39.71 3.36
3730 4215 8.908786 TTGATGATGACCCTGTAGAATTATTC 57.091 34.615 0.00 0.00 0.00 1.75
3731 4216 8.267620 TGATGATGACCCTGTAGAATTATTCT 57.732 34.615 12.39 12.39 43.72 2.40
3755 4242 7.119699 TCTGTTCAAGTGCAAAGATAACTATGG 59.880 37.037 0.00 0.00 0.00 2.74
3775 4262 3.055963 TGGGCAATTTGAATGTGGATGAC 60.056 43.478 0.00 0.00 0.00 3.06
3789 4276 6.918892 TGTGGATGACGAACCTAAAATATG 57.081 37.500 0.00 0.00 0.00 1.78
3797 4285 6.380274 TGACGAACCTAAAATATGTCTCTCCT 59.620 38.462 0.00 0.00 0.00 3.69
3801 4289 8.604890 CGAACCTAAAATATGTCTCTCCTTTTC 58.395 37.037 0.00 0.00 0.00 2.29
3802 4290 9.674068 GAACCTAAAATATGTCTCTCCTTTTCT 57.326 33.333 0.00 0.00 0.00 2.52
3806 4294 9.780413 CTAAAATATGTCTCTCCTTTTCTTTGC 57.220 33.333 0.00 0.00 0.00 3.68
3872 4360 0.899720 TGTTAGGCGATCCGGAGTTT 59.100 50.000 11.34 0.00 37.47 2.66
3908 4396 0.250467 AATCGAACACCACAGCAGCT 60.250 50.000 0.00 0.00 0.00 4.24
3915 4403 2.273123 CCACAGCAGCTGGGCATA 59.727 61.111 26.38 0.00 32.80 3.14
4040 4528 2.874664 CGTCCCGGGGTGAGTTTCA 61.875 63.158 23.50 0.00 0.00 2.69
4135 4623 4.141251 TCTGGAGAAACAGGCTAAAAGGTT 60.141 41.667 0.00 0.00 38.98 3.50
4208 4696 0.111446 TTTGCCTTGATCGGGGTTCA 59.889 50.000 6.66 0.00 0.00 3.18
4213 4701 1.473434 CCTTGATCGGGGTTCAGTAGC 60.473 57.143 0.00 0.00 0.00 3.58
4245 4733 1.255882 CTGATCAGGATCTCCTCCCG 58.744 60.000 15.38 0.00 46.65 5.14
4246 4734 0.829602 TGATCAGGATCTCCTCCCGC 60.830 60.000 10.38 0.00 46.65 6.13
4247 4735 1.535202 ATCAGGATCTCCTCCCGCC 60.535 63.158 0.00 0.00 46.65 6.13
4248 4736 3.237741 CAGGATCTCCTCCCGCCC 61.238 72.222 0.00 0.00 46.65 6.13
4249 4737 4.924187 AGGATCTCCTCCCGCCCG 62.924 72.222 0.00 0.00 44.77 6.13
4288 4783 2.219674 GTGAAGATAGCGGCGAAGAATG 59.780 50.000 12.98 0.00 0.00 2.67
4296 4791 1.656652 CGGCGAAGAATGGAAGATGT 58.343 50.000 0.00 0.00 0.00 3.06
4317 4813 1.088306 TTGTTGTTCGCTTGTTCCGT 58.912 45.000 0.00 0.00 0.00 4.69
4351 4847 3.632145 TCTTGGTTTGAAGAAGAACAGGC 59.368 43.478 0.00 0.00 0.00 4.85
4361 4857 5.643777 TGAAGAAGAACAGGCTTATGTTAGC 59.356 40.000 3.11 0.00 43.32 3.09
4379 4875 3.059352 AGCGTTGTCATTTCCTAGCTT 57.941 42.857 0.00 0.00 0.00 3.74
4380 4876 3.412386 AGCGTTGTCATTTCCTAGCTTT 58.588 40.909 0.00 0.00 0.00 3.51
4384 4880 4.382754 CGTTGTCATTTCCTAGCTTTTTGC 59.617 41.667 0.00 0.00 43.29 3.68
4409 4905 0.751277 TGCCTTGTGAGTTGGTGTGG 60.751 55.000 0.00 0.00 0.00 4.17
4429 4932 2.481952 GGTCTGTGTGTGCAGATTTCTC 59.518 50.000 0.00 0.00 45.81 2.87
4432 4935 4.387256 GTCTGTGTGTGCAGATTTCTCTAC 59.613 45.833 0.00 0.00 45.81 2.59
4437 4940 1.929836 GTGCAGATTTCTCTACGCCTG 59.070 52.381 0.00 0.00 0.00 4.85
4487 4990 2.124403 CAGGATGAGGTGGCAGCC 60.124 66.667 13.95 3.66 44.50 4.85
4488 4991 2.611800 AGGATGAGGTGGCAGCCA 60.612 61.111 11.22 11.22 46.51 4.75
4520 5023 2.094545 GCAAGGAAAATGTAGTGCCAGG 60.095 50.000 0.00 0.00 0.00 4.45
4526 5029 2.770164 AATGTAGTGCCAGGTCAGTC 57.230 50.000 0.00 0.00 0.00 3.51
4535 5038 0.107831 CCAGGTCAGTCCCGAACAAA 59.892 55.000 0.00 0.00 36.75 2.83
4547 5050 2.609244 CCCGAACAAATGTTGCCGAAAT 60.609 45.455 3.05 0.00 38.56 2.17
4548 5051 3.366476 CCCGAACAAATGTTGCCGAAATA 60.366 43.478 3.05 0.00 38.56 1.40
4550 5053 4.862018 CCGAACAAATGTTGCCGAAATAAT 59.138 37.500 3.05 0.00 38.56 1.28
4551 5054 5.004345 CCGAACAAATGTTGCCGAAATAATC 59.996 40.000 3.05 0.00 38.56 1.75
4552 5055 5.570973 CGAACAAATGTTGCCGAAATAATCA 59.429 36.000 3.05 0.00 38.56 2.57
4553 5056 6.253298 CGAACAAATGTTGCCGAAATAATCAT 59.747 34.615 3.05 0.00 38.56 2.45
4554 5057 6.890663 ACAAATGTTGCCGAAATAATCATG 57.109 33.333 0.00 0.00 0.00 3.07
4557 5060 4.898829 TGTTGCCGAAATAATCATGAGG 57.101 40.909 0.09 0.00 0.00 3.86
4561 5083 6.096705 TGTTGCCGAAATAATCATGAGGAAAT 59.903 34.615 0.09 0.00 0.00 2.17
4563 5085 7.815840 TGCCGAAATAATCATGAGGAAATTA 57.184 32.000 0.09 0.00 0.00 1.40
4587 5109 2.097142 GTGGAATGCTTGAGCTCACATC 59.903 50.000 18.03 8.96 42.66 3.06
4588 5110 2.026542 TGGAATGCTTGAGCTCACATCT 60.027 45.455 18.03 8.49 42.66 2.90
4593 5115 1.004679 TTGAGCTCACATCTGCGCA 60.005 52.632 18.03 10.98 37.23 6.09
4594 5116 1.293963 TTGAGCTCACATCTGCGCAC 61.294 55.000 18.03 0.00 38.59 5.34
4687 5220 7.773149 AGATATATACTCCTGGCGAATAACAC 58.227 38.462 0.00 0.00 0.00 3.32
4688 5221 5.801531 ATATACTCCTGGCGAATAACACA 57.198 39.130 0.00 0.00 0.00 3.72
4689 5222 2.851263 ACTCCTGGCGAATAACACAA 57.149 45.000 0.00 0.00 0.00 3.33
4690 5223 2.423577 ACTCCTGGCGAATAACACAAC 58.576 47.619 0.00 0.00 0.00 3.32
4692 5225 2.147958 TCCTGGCGAATAACACAACAC 58.852 47.619 0.00 0.00 0.00 3.32
4693 5226 1.876799 CCTGGCGAATAACACAACACA 59.123 47.619 0.00 0.00 0.00 3.72
4694 5227 2.292016 CCTGGCGAATAACACAACACAA 59.708 45.455 0.00 0.00 0.00 3.33
4696 5229 4.545610 CTGGCGAATAACACAACACAATT 58.454 39.130 0.00 0.00 0.00 2.32
4697 5230 4.541779 TGGCGAATAACACAACACAATTC 58.458 39.130 0.00 0.00 0.00 2.17
4701 5241 6.200097 GGCGAATAACACAACACAATTCTTTT 59.800 34.615 0.00 0.00 0.00 2.27
4706 5246 6.966435 AACACAACACAATTCTTTTCAAGG 57.034 33.333 0.00 0.00 0.00 3.61
4756 5299 2.223340 CCATAATTTGGTCGCTGTGAGC 60.223 50.000 13.11 13.11 45.46 4.26
4821 5374 0.250640 CCAGGCATAGGATCTGGTGC 60.251 60.000 8.47 7.81 42.17 5.01
4830 5383 1.596477 GATCTGGTGCGATGAGGCC 60.596 63.158 0.00 0.00 0.00 5.19
4867 5420 4.860150 GCAATGAATCGCGACGAG 57.140 55.556 12.93 0.00 39.91 4.18
4870 5423 1.396440 GCAATGAATCGCGACGAGATG 60.396 52.381 12.93 9.89 39.91 2.90
4871 5424 0.855349 AATGAATCGCGACGAGATGC 59.145 50.000 12.93 13.54 39.91 3.91
4872 5425 0.249031 ATGAATCGCGACGAGATGCA 60.249 50.000 22.31 22.31 39.91 3.96
4948 5501 2.522185 CTGGGCCAGCTATAATTGCAT 58.478 47.619 22.68 0.00 0.00 3.96
4954 5507 4.245660 GCCAGCTATAATTGCATACGAGA 58.754 43.478 0.00 0.00 0.00 4.04
5016 5569 0.911769 TGAGAGGTACCCTTGCATGG 59.088 55.000 8.74 11.68 31.76 3.66
5017 5570 1.204146 GAGAGGTACCCTTGCATGGA 58.796 55.000 19.85 0.00 31.76 3.41
5019 5572 1.492176 AGAGGTACCCTTGCATGGATG 59.508 52.381 19.85 6.76 31.76 3.51
5020 5573 2.087385 GAGGTACCCTTGCATGGATGC 61.087 57.143 19.85 6.35 43.87 3.91
5036 5589 1.734465 GATGCGTTTGTTCCTCTCCAG 59.266 52.381 0.00 0.00 0.00 3.86
5094 5651 2.484264 CAGAAGCGAAAACCCTACCAAG 59.516 50.000 0.00 0.00 0.00 3.61
5095 5652 1.810755 GAAGCGAAAACCCTACCAAGG 59.189 52.381 0.00 0.00 43.25 3.61
5096 5653 0.608308 AGCGAAAACCCTACCAAGGC 60.608 55.000 0.00 0.00 42.14 4.35
5098 5655 1.611519 CGAAAACCCTACCAAGGCAA 58.388 50.000 0.00 0.00 42.14 4.52
5100 5657 2.030274 CGAAAACCCTACCAAGGCAAAG 60.030 50.000 0.00 0.00 42.14 2.77
5108 5697 1.228988 CCAAGGCAAAGGGGAAGCT 60.229 57.895 0.00 0.00 0.00 3.74
5111 5700 3.752339 GGCAAAGGGGAAGCTGCG 61.752 66.667 0.00 0.00 35.60 5.18
5113 5702 3.752339 CAAAGGGGAAGCTGCGGC 61.752 66.667 10.33 10.33 39.06 6.53
5188 5780 0.961753 CAAGGCAAAGTGGAGGGAAC 59.038 55.000 0.00 0.00 0.00 3.62
5200 5792 3.487576 AGGGAACTCACACGCAAAA 57.512 47.368 0.00 0.00 32.90 2.44
5209 5801 1.068921 ACACGCAAAACCCAATGGC 59.931 52.632 0.00 0.00 33.59 4.40
5409 6027 5.251081 CGCTAACAGAATGAATGAAACTCG 58.749 41.667 0.00 0.00 39.69 4.18
5484 6102 9.310716 GAGAATCGATATGAATGCATCAATAGA 57.689 33.333 0.00 0.00 42.54 1.98
5507 6125 8.204903 AGATGATGATAGAATTAAGCTGGTCT 57.795 34.615 0.00 0.00 0.00 3.85
5510 6128 7.212976 TGATGATAGAATTAAGCTGGTCTGTC 58.787 38.462 0.00 0.00 0.00 3.51
5511 6129 5.592054 TGATAGAATTAAGCTGGTCTGTCG 58.408 41.667 0.00 0.00 32.61 4.35
5512 6130 3.252974 AGAATTAAGCTGGTCTGTCGG 57.747 47.619 0.00 0.00 0.00 4.79
5513 6131 2.567615 AGAATTAAGCTGGTCTGTCGGT 59.432 45.455 0.00 0.00 0.00 4.69
5514 6132 2.674796 ATTAAGCTGGTCTGTCGGTC 57.325 50.000 0.00 0.00 0.00 4.79
5515 6133 0.242825 TTAAGCTGGTCTGTCGGTCG 59.757 55.000 0.00 0.00 0.00 4.79
5516 6134 1.592400 TAAGCTGGTCTGTCGGTCGG 61.592 60.000 0.00 0.00 0.00 4.79
5517 6135 3.371063 GCTGGTCTGTCGGTCGGA 61.371 66.667 0.00 0.00 0.00 4.55
5547 6165 2.575735 ACATGTACACCCACATCCATCA 59.424 45.455 0.00 0.00 37.02 3.07
5554 6172 2.889045 CACCCACATCCATCATCAATCC 59.111 50.000 0.00 0.00 0.00 3.01
5559 6177 5.129815 CCCACATCCATCATCAATCCTTTTT 59.870 40.000 0.00 0.00 0.00 1.94
5561 6179 6.046593 CACATCCATCATCAATCCTTTTTGG 58.953 40.000 0.00 0.00 37.10 3.28
5562 6180 5.722923 ACATCCATCATCAATCCTTTTTGGT 59.277 36.000 0.00 0.00 37.07 3.67
5565 6183 5.543405 TCCATCATCAATCCTTTTTGGTGTT 59.457 36.000 0.00 0.00 38.57 3.32
5566 6184 5.640357 CCATCATCAATCCTTTTTGGTGTTG 59.360 40.000 0.00 0.00 38.57 3.33
5567 6185 5.867903 TCATCAATCCTTTTTGGTGTTGT 57.132 34.783 0.00 0.00 38.57 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 0.586319 ATTTTATCGATGCCGCGTGG 59.414 50.000 11.67 11.67 38.77 4.94
38 39 3.722555 ATATTTTATCGATGCCGCGTG 57.277 42.857 8.54 0.00 35.37 5.34
112 113 9.883142 ATGGTTTGTTGATTTTTCTTAAGTGAA 57.117 25.926 1.63 0.00 0.00 3.18
150 152 9.612066 AGAAACATGTTGTGTAATTTCCAAAAT 57.388 25.926 12.82 0.00 41.14 1.82
160 162 5.468746 GGCAGTCTAGAAACATGTTGTGTAA 59.531 40.000 12.82 0.00 41.14 2.41
165 167 3.189287 GGTGGCAGTCTAGAAACATGTTG 59.811 47.826 12.82 0.00 0.00 3.33
174 176 1.656587 AACATGGGTGGCAGTCTAGA 58.343 50.000 0.00 0.00 0.00 2.43
196 198 4.647964 CCGGAGATAACGAAATTTGTGTG 58.352 43.478 0.00 0.00 0.00 3.82
245 247 3.061697 GTGTTCGGTAATTGGCTCGTAAG 59.938 47.826 0.00 0.00 0.00 2.34
258 260 8.723311 CCTTTTATATTTCTTGTGTGTTCGGTA 58.277 33.333 0.00 0.00 0.00 4.02
260 262 7.812648 TCCTTTTATATTTCTTGTGTGTTCGG 58.187 34.615 0.00 0.00 0.00 4.30
308 312 7.769272 AAATTGTCGTTTGATGTGTTTTCAT 57.231 28.000 0.00 0.00 0.00 2.57
310 314 9.566624 CATAAAATTGTCGTTTGATGTGTTTTC 57.433 29.630 0.00 0.00 29.09 2.29
329 333 8.788806 TCGGTATCACTTGTTTGAACATAAAAT 58.211 29.630 0.00 0.00 38.95 1.82
333 337 6.460781 ACTCGGTATCACTTGTTTGAACATA 58.539 36.000 0.00 0.00 38.95 2.29
395 404 5.864986 ACAATCTAGCGAAAATAAACCACG 58.135 37.500 0.00 0.00 0.00 4.94
396 405 6.741358 GTGACAATCTAGCGAAAATAAACCAC 59.259 38.462 0.00 0.00 0.00 4.16
398 407 6.961554 CAGTGACAATCTAGCGAAAATAAACC 59.038 38.462 0.00 0.00 0.00 3.27
402 411 5.730550 ACCAGTGACAATCTAGCGAAAATA 58.269 37.500 0.00 0.00 0.00 1.40
403 412 4.579869 ACCAGTGACAATCTAGCGAAAAT 58.420 39.130 0.00 0.00 0.00 1.82
421 430 5.005094 TCGTTGAGGGGTTATTTTAACCAG 58.995 41.667 16.13 1.87 42.03 4.00
452 461 6.429078 TCTCGTGTGGTCTAGCGTAATATATT 59.571 38.462 2.97 2.97 0.00 1.28
488 497 9.290988 TCAACAATGTAGTTTGGTGTATACATT 57.709 29.630 9.18 4.12 45.20 2.71
523 533 6.265422 GGTAGACTCCATTTTGGGAAATATGG 59.735 42.308 0.00 0.00 38.32 2.74
527 537 5.016831 GTGGTAGACTCCATTTTGGGAAAT 58.983 41.667 0.00 0.00 39.81 2.17
561 571 7.755591 TGATAATTGCTTGTGAGATCAAACTC 58.244 34.615 0.00 0.00 37.42 3.01
589 599 3.502123 TTGTTAGGGCATATAGTGGGC 57.498 47.619 0.00 0.00 0.00 5.36
594 604 6.534634 AGTAAGGCTTTGTTAGGGCATATAG 58.465 40.000 4.45 0.00 0.00 1.31
628 638 2.886862 TGCTTGGTGATGTGGTTTTG 57.113 45.000 0.00 0.00 0.00 2.44
662 672 9.295825 TCTCCATACACAAAATCTACACAAAAT 57.704 29.630 0.00 0.00 0.00 1.82
664 674 8.729756 CATCTCCATACACAAAATCTACACAAA 58.270 33.333 0.00 0.00 0.00 2.83
667 677 6.540189 AGCATCTCCATACACAAAATCTACAC 59.460 38.462 0.00 0.00 0.00 2.90
668 678 6.653020 AGCATCTCCATACACAAAATCTACA 58.347 36.000 0.00 0.00 0.00 2.74
669 679 8.839310 ATAGCATCTCCATACACAAAATCTAC 57.161 34.615 0.00 0.00 0.00 2.59
671 681 9.445878 CATATAGCATCTCCATACACAAAATCT 57.554 33.333 0.00 0.00 0.00 2.40
672 682 9.440773 TCATATAGCATCTCCATACACAAAATC 57.559 33.333 0.00 0.00 0.00 2.17
803 847 1.907936 AGAGGAGTGCAGCTGAAGATT 59.092 47.619 20.43 0.00 0.00 2.40
879 928 2.736531 GGGTTTGGCTTGGCACTG 59.263 61.111 0.00 0.00 0.00 3.66
907 956 1.506907 TTGTCGGGAGGAGGAGGAGA 61.507 60.000 0.00 0.00 0.00 3.71
908 957 1.000486 TTGTCGGGAGGAGGAGGAG 60.000 63.158 0.00 0.00 0.00 3.69
909 958 1.000486 CTTGTCGGGAGGAGGAGGA 60.000 63.158 0.00 0.00 0.00 3.71
910 959 2.726351 GCTTGTCGGGAGGAGGAGG 61.726 68.421 0.00 0.00 0.00 4.30
956 1009 1.004862 GGTGAGGGGAAAAGAGGAAGG 59.995 57.143 0.00 0.00 0.00 3.46
958 1011 1.985895 GAGGTGAGGGGAAAAGAGGAA 59.014 52.381 0.00 0.00 0.00 3.36
959 1012 1.132527 TGAGGTGAGGGGAAAAGAGGA 60.133 52.381 0.00 0.00 0.00 3.71
1038 1265 2.664851 CGCAACGAGACAAGGGCA 60.665 61.111 0.00 0.00 0.00 5.36
1141 1372 1.139095 GAGAAACGATCCGGCGAGT 59.861 57.895 9.30 0.00 34.83 4.18
1244 1475 0.732571 ATACCAGACAAAATGCCGCG 59.267 50.000 0.00 0.00 0.00 6.46
1256 1487 8.432805 ACAGAAGAAGAAGAAGAAAATACCAGA 58.567 33.333 0.00 0.00 0.00 3.86
1265 1496 8.834465 CATCAAGAAACAGAAGAAGAAGAAGAA 58.166 33.333 0.00 0.00 0.00 2.52
1266 1497 7.443575 CCATCAAGAAACAGAAGAAGAAGAAGA 59.556 37.037 0.00 0.00 0.00 2.87
1267 1498 7.308469 CCCATCAAGAAACAGAAGAAGAAGAAG 60.308 40.741 0.00 0.00 0.00 2.85
1416 1650 3.701604 ATGTCTTCGACCTCCGCGC 62.702 63.158 0.00 0.00 38.37 6.86
1429 1663 2.824489 TCGCCGAGCTCGATGTCT 60.824 61.111 36.59 0.00 43.02 3.41
1470 1704 2.745100 CCTCCTCGTCGTCGTCCA 60.745 66.667 1.33 0.00 38.33 4.02
1930 2213 7.770897 AGGTTAATTACTGAGCAGGAAATGTAG 59.229 37.037 0.00 0.00 34.42 2.74
1931 2214 7.552687 CAGGTTAATTACTGAGCAGGAAATGTA 59.447 37.037 0.00 0.00 34.42 2.29
1932 2215 6.375455 CAGGTTAATTACTGAGCAGGAAATGT 59.625 38.462 0.00 0.00 34.42 2.71
1938 2221 8.398665 GTTTATTCAGGTTAATTACTGAGCAGG 58.601 37.037 2.20 0.00 43.84 4.85
1955 2238 6.801539 TTAGTGAGTTGGCAGTTTATTCAG 57.198 37.500 0.00 0.00 0.00 3.02
2032 2315 6.317642 CACCGAATACATAAATCCCTGAAACA 59.682 38.462 0.00 0.00 0.00 2.83
2097 2385 2.120909 CATCCACCCGAATGCACCC 61.121 63.158 0.00 0.00 0.00 4.61
2106 2394 0.322456 ACCATGTGTTCATCCACCCG 60.322 55.000 0.00 0.00 34.35 5.28
2140 2428 6.436218 ACAAAGAACTAAAGAAAACACCACCT 59.564 34.615 0.00 0.00 0.00 4.00
2210 2501 0.036732 TCGATCCAGCACTTTGCCTT 59.963 50.000 0.00 0.00 46.52 4.35
2391 2693 2.234661 TCGCATCAGACCAAGTCAATCT 59.765 45.455 0.00 0.00 34.60 2.40
2501 2807 5.301835 CCTATCACCAAGGTCATGATTCT 57.698 43.478 0.00 0.00 34.86 2.40
2841 3165 6.695278 CAGTAATACTCTGAGCTAACAGAAGC 59.305 42.308 4.19 0.00 44.62 3.86
2842 3166 7.990917 TCAGTAATACTCTGAGCTAACAGAAG 58.009 38.462 4.19 4.22 44.62 2.85
2843 3167 7.939784 TCAGTAATACTCTGAGCTAACAGAA 57.060 36.000 4.19 0.00 44.62 3.02
2844 3168 7.939784 TTCAGTAATACTCTGAGCTAACAGA 57.060 36.000 4.19 5.13 41.87 3.41
2845 3169 8.409371 TGATTCAGTAATACTCTGAGCTAACAG 58.591 37.037 4.19 0.00 41.87 3.16
2846 3170 8.293699 TGATTCAGTAATACTCTGAGCTAACA 57.706 34.615 4.19 0.00 41.87 2.41
2847 3171 8.410141 ACTGATTCAGTAATACTCTGAGCTAAC 58.590 37.037 17.63 0.00 43.46 2.34
2848 3172 8.526667 ACTGATTCAGTAATACTCTGAGCTAA 57.473 34.615 17.63 0.00 43.46 3.09
2849 3173 8.526667 AACTGATTCAGTAATACTCTGAGCTA 57.473 34.615 19.27 0.00 44.62 3.32
2850 3174 7.416964 AACTGATTCAGTAATACTCTGAGCT 57.583 36.000 19.27 0.00 44.62 4.09
2851 3175 8.191446 TGTAACTGATTCAGTAATACTCTGAGC 58.809 37.037 19.27 0.00 44.62 4.26
2868 3192 9.823647 CCTTCTACACTTTGATATGTAACTGAT 57.176 33.333 0.00 0.00 31.09 2.90
2869 3193 7.764443 GCCTTCTACACTTTGATATGTAACTGA 59.236 37.037 0.00 0.00 31.09 3.41
2870 3194 7.549134 TGCCTTCTACACTTTGATATGTAACTG 59.451 37.037 0.00 0.00 31.09 3.16
2871 3195 7.549488 GTGCCTTCTACACTTTGATATGTAACT 59.451 37.037 0.00 0.00 35.12 2.24
2872 3196 7.549488 AGTGCCTTCTACACTTTGATATGTAAC 59.451 37.037 0.00 0.00 46.01 2.50
2873 3197 7.620880 AGTGCCTTCTACACTTTGATATGTAA 58.379 34.615 0.00 0.00 46.01 2.41
2874 3198 7.182817 AGTGCCTTCTACACTTTGATATGTA 57.817 36.000 0.00 0.00 46.01 2.29
2875 3199 6.054860 AGTGCCTTCTACACTTTGATATGT 57.945 37.500 0.00 0.00 46.01 2.29
2902 3226 4.944962 TTTTCCATGATAGCTCGTGTTG 57.055 40.909 0.00 0.00 36.79 3.33
2903 3227 5.185454 TCATTTTCCATGATAGCTCGTGTT 58.815 37.500 0.00 0.00 36.79 3.32
2904 3228 4.769688 TCATTTTCCATGATAGCTCGTGT 58.230 39.130 0.00 0.00 36.79 4.49
2905 3229 5.739752 TTCATTTTCCATGATAGCTCGTG 57.260 39.130 0.00 0.00 38.02 4.35
3019 3395 5.748402 TCATATGATGAAGCTGTCAAACCT 58.252 37.500 0.00 0.00 40.50 3.50
3085 3461 5.344933 GCATAAACTTCATCGTTTGGGAAAC 59.655 40.000 0.00 0.00 37.63 2.78
3100 3477 6.014156 AGTGAGAACTCCTACAGCATAAACTT 60.014 38.462 0.00 0.00 0.00 2.66
3170 3555 4.517952 TGCAATATTTGGTTGTGGTCTG 57.482 40.909 0.00 0.00 0.00 3.51
3192 3577 3.508845 AGTAATGTTCCTGTTGCCAGT 57.491 42.857 0.00 0.00 36.95 4.00
3294 3680 0.323360 TGGGGGAAATGTGCTGCTAC 60.323 55.000 0.00 0.00 0.00 3.58
3324 3710 3.988379 TTCCTTGAATGACAGCAACAC 57.012 42.857 0.00 0.00 0.00 3.32
3353 3739 4.644103 GCTTCACATGGTAAGCATTGAT 57.356 40.909 22.36 0.00 45.89 2.57
3366 3752 2.094906 TGTTACGTCGCTAGCTTCACAT 60.095 45.455 13.93 0.00 0.00 3.21
3379 3765 9.690434 GAACTAAAATGATGAGAATGTTACGTC 57.310 33.333 0.00 0.00 0.00 4.34
3602 4073 1.134965 CATCACCGAGTCTGGTCTTCC 60.135 57.143 4.01 0.00 41.38 3.46
3605 4076 0.891373 CACATCACCGAGTCTGGTCT 59.109 55.000 4.01 0.00 41.38 3.85
3730 4215 7.246311 CCATAGTTATCTTTGCACTTGAACAG 58.754 38.462 0.00 0.00 0.00 3.16
3731 4216 6.150976 CCCATAGTTATCTTTGCACTTGAACA 59.849 38.462 0.00 0.00 0.00 3.18
3749 4236 4.352009 TCCACATTCAAATTGCCCATAGT 58.648 39.130 0.00 0.00 0.00 2.12
3755 4242 3.119531 TCGTCATCCACATTCAAATTGCC 60.120 43.478 0.00 0.00 0.00 4.52
3775 4262 8.494016 AAAAGGAGAGACATATTTTAGGTTCG 57.506 34.615 0.00 0.00 0.00 3.95
3789 4276 2.163509 GGGGCAAAGAAAAGGAGAGAC 58.836 52.381 0.00 0.00 0.00 3.36
3797 4285 0.560688 AGGTCCTGGGGCAAAGAAAA 59.439 50.000 0.00 0.00 0.00 2.29
3801 4289 1.604593 CACAGGTCCTGGGGCAAAG 60.605 63.158 23.06 0.00 35.51 2.77
3802 4290 2.067932 CTCACAGGTCCTGGGGCAAA 62.068 60.000 21.40 0.32 35.28 3.68
3805 4293 1.977293 GATCTCACAGGTCCTGGGGC 61.977 65.000 21.40 5.01 35.28 5.80
3806 4294 0.326048 AGATCTCACAGGTCCTGGGG 60.326 60.000 21.40 13.31 35.28 4.96
3908 4396 2.796557 TCGTTTGGAAATGTATGCCCA 58.203 42.857 0.00 0.00 0.00 5.36
3915 4403 3.292460 TCCTGGTTTCGTTTGGAAATGT 58.708 40.909 0.00 0.00 45.80 2.71
4042 4530 1.963464 TTATTGAGGGACCGTCCGCC 61.963 60.000 11.55 6.22 37.43 6.13
4135 4623 6.041182 TGTGTACCTCTTCACAGCTTAACTTA 59.959 38.462 0.00 0.00 39.23 2.24
4208 4696 1.002087 CAGGGTTCCTTTCGTGCTACT 59.998 52.381 0.00 0.00 0.00 2.57
4213 4701 2.350522 CTGATCAGGGTTCCTTTCGTG 58.649 52.381 15.38 0.00 0.00 4.35
4249 4737 1.244019 ACTCAAATCTTGGGGCACGC 61.244 55.000 0.00 0.00 43.69 5.34
4250 4738 0.523072 CACTCAAATCTTGGGGCACG 59.477 55.000 0.00 0.00 34.70 5.34
4251 4739 1.909700 TCACTCAAATCTTGGGGCAC 58.090 50.000 0.00 0.00 34.70 5.01
4288 4783 2.290641 AGCGAACAACAACACATCTTCC 59.709 45.455 0.00 0.00 0.00 3.46
4296 4791 1.202087 CGGAACAAGCGAACAACAACA 60.202 47.619 0.00 0.00 0.00 3.33
4317 4813 8.231692 TCTTCAAACCAAGACAACAATAATCA 57.768 30.769 0.00 0.00 0.00 2.57
4351 4847 6.422776 AGGAAATGACAACGCTAACATAAG 57.577 37.500 0.00 0.00 0.00 1.73
4361 4857 4.382754 GCAAAAAGCTAGGAAATGACAACG 59.617 41.667 0.00 0.00 41.15 4.10
4379 4875 1.066858 TCACAAGGCAAAACGGCAAAA 60.067 42.857 0.00 0.00 44.47 2.44
4380 4876 0.532573 TCACAAGGCAAAACGGCAAA 59.467 45.000 0.00 0.00 44.47 3.68
4384 4880 1.535860 CCAACTCACAAGGCAAAACGG 60.536 52.381 0.00 0.00 0.00 4.44
4429 4932 1.305930 GGAACAAAGGGCAGGCGTAG 61.306 60.000 0.00 0.00 0.00 3.51
4432 4935 2.597217 TGGAACAAAGGGCAGGCG 60.597 61.111 0.00 0.00 31.92 5.52
4437 4940 4.765339 ACTATAAACACTGGAACAAAGGGC 59.235 41.667 0.00 0.00 38.70 5.19
4495 4998 4.458989 TGGCACTACATTTTCCTTGCTAAG 59.541 41.667 0.00 0.00 0.00 2.18
4520 5023 2.604614 GCAACATTTGTTCGGGACTGAC 60.605 50.000 0.00 0.00 35.83 3.51
4526 5029 0.312416 TTCGGCAACATTTGTTCGGG 59.688 50.000 5.16 0.00 35.83 5.14
4535 5038 5.132502 TCCTCATGATTATTTCGGCAACAT 58.867 37.500 0.00 0.00 0.00 2.71
4548 5051 7.929785 GCATTCCACAATAATTTCCTCATGATT 59.070 33.333 0.00 0.00 0.00 2.57
4550 5053 6.608405 AGCATTCCACAATAATTTCCTCATGA 59.392 34.615 0.00 0.00 0.00 3.07
4551 5054 6.812998 AGCATTCCACAATAATTTCCTCATG 58.187 36.000 0.00 0.00 0.00 3.07
4552 5055 7.124599 TCAAGCATTCCACAATAATTTCCTCAT 59.875 33.333 0.00 0.00 0.00 2.90
4553 5056 6.436847 TCAAGCATTCCACAATAATTTCCTCA 59.563 34.615 0.00 0.00 0.00 3.86
4554 5057 6.866480 TCAAGCATTCCACAATAATTTCCTC 58.134 36.000 0.00 0.00 0.00 3.71
4557 5060 6.335777 AGCTCAAGCATTCCACAATAATTTC 58.664 36.000 4.59 0.00 45.16 2.17
4561 5083 4.156556 GTGAGCTCAAGCATTCCACAATAA 59.843 41.667 20.19 0.00 45.16 1.40
4563 5085 2.490903 GTGAGCTCAAGCATTCCACAAT 59.509 45.455 20.19 0.00 45.16 2.71
4587 5109 1.695893 ATCATCGTTTCCGTGCGCAG 61.696 55.000 12.22 4.91 35.01 5.18
4588 5110 0.458716 TATCATCGTTTCCGTGCGCA 60.459 50.000 5.66 5.66 35.01 6.09
4593 5115 6.140110 CACAAGTTTTTATCATCGTTTCCGT 58.860 36.000 0.00 0.00 35.01 4.69
4594 5116 6.140110 ACACAAGTTTTTATCATCGTTTCCG 58.860 36.000 0.00 0.00 0.00 4.30
4670 5203 2.224426 TGTTGTGTTATTCGCCAGGAGT 60.224 45.455 0.00 0.00 0.00 3.85
4671 5204 2.159627 GTGTTGTGTTATTCGCCAGGAG 59.840 50.000 0.00 0.00 0.00 3.69
4674 5207 3.617540 TTGTGTTGTGTTATTCGCCAG 57.382 42.857 0.00 0.00 0.00 4.85
4675 5208 4.277174 AGAATTGTGTTGTGTTATTCGCCA 59.723 37.500 0.00 0.00 32.05 5.69
4676 5209 4.794169 AGAATTGTGTTGTGTTATTCGCC 58.206 39.130 0.00 0.00 32.05 5.54
4677 5210 6.747659 AAAGAATTGTGTTGTGTTATTCGC 57.252 33.333 0.00 0.00 32.05 4.70
4678 5211 8.334016 TGAAAAGAATTGTGTTGTGTTATTCG 57.666 30.769 0.00 0.00 32.05 3.34
4690 5223 8.307927 TGGTCCAACCCTTGAAAAGAATTGTG 62.308 42.308 0.00 0.00 45.77 3.33
4692 5225 4.100808 TGGTCCAACCCTTGAAAAGAATTG 59.899 41.667 0.00 0.00 45.77 2.32
4693 5226 4.294347 TGGTCCAACCCTTGAAAAGAATT 58.706 39.130 0.00 0.00 45.77 2.17
4694 5227 3.922375 TGGTCCAACCCTTGAAAAGAAT 58.078 40.909 0.00 0.00 45.77 2.40
4696 5229 3.390175 TTGGTCCAACCCTTGAAAAGA 57.610 42.857 0.00 0.00 45.77 2.52
4697 5230 5.337491 CCATATTGGTCCAACCCTTGAAAAG 60.337 44.000 6.41 0.00 37.50 2.27
4701 5241 2.024464 CCCATATTGGTCCAACCCTTGA 60.024 50.000 6.41 0.00 37.50 3.02
4706 5246 0.106918 TCGCCCATATTGGTCCAACC 60.107 55.000 6.41 0.00 35.17 3.77
4756 5299 4.172512 AGAGCCATCTGCCCTGCG 62.173 66.667 0.00 0.00 42.71 5.18
4803 5356 0.602106 CGCACCAGATCCTATGCCTG 60.602 60.000 7.00 0.00 34.49 4.85
4821 5374 1.502163 GGAATTCTGCGGCCTCATCG 61.502 60.000 5.23 0.00 0.00 3.84
4830 5383 1.815421 CGGTCCTGGGAATTCTGCG 60.815 63.158 5.23 0.00 0.00 5.18
4867 5420 1.134699 TGCTACTACCACTGCTGCATC 60.135 52.381 1.31 0.00 0.00 3.91
4870 5423 0.532573 TCTGCTACTACCACTGCTGC 59.467 55.000 0.00 0.00 0.00 5.25
4871 5424 1.470632 GCTCTGCTACTACCACTGCTG 60.471 57.143 0.00 0.00 0.00 4.41
4872 5425 0.820871 GCTCTGCTACTACCACTGCT 59.179 55.000 0.00 0.00 0.00 4.24
4943 5496 2.951457 TCACCGATTCTCGTATGCAA 57.049 45.000 0.00 0.00 38.40 4.08
5016 5569 1.734465 CTGGAGAGGAACAAACGCATC 59.266 52.381 0.00 0.00 0.00 3.91
5017 5570 1.611673 CCTGGAGAGGAACAAACGCAT 60.612 52.381 0.00 0.00 42.93 4.73
5019 5572 0.955919 CCCTGGAGAGGAACAAACGC 60.956 60.000 0.00 0.00 42.93 4.84
5020 5573 0.955919 GCCCTGGAGAGGAACAAACG 60.956 60.000 0.00 0.00 42.93 3.60
5023 5576 2.592993 CGGCCCTGGAGAGGAACAA 61.593 63.158 0.00 0.00 42.93 2.83
5024 5577 3.003173 CGGCCCTGGAGAGGAACA 61.003 66.667 0.00 0.00 42.93 3.18
5094 5651 3.752339 CGCAGCTTCCCCTTTGCC 61.752 66.667 0.00 0.00 33.10 4.52
5095 5652 3.752339 CCGCAGCTTCCCCTTTGC 61.752 66.667 0.00 0.00 0.00 3.68
5096 5653 3.752339 GCCGCAGCTTCCCCTTTG 61.752 66.667 0.00 0.00 35.50 2.77
5132 5721 1.125093 TTTCGTGCTGGGGAGAAGGA 61.125 55.000 0.00 0.00 0.00 3.36
5177 5766 2.050269 CGTGTGAGTTCCCTCCACT 58.950 57.895 0.00 0.00 37.04 4.00
5179 5768 1.691195 TTGCGTGTGAGTTCCCTCCA 61.691 55.000 0.00 0.00 36.86 3.86
5188 5780 1.602668 CCATTGGGTTTTGCGTGTGAG 60.603 52.381 0.00 0.00 0.00 3.51
5381 5999 1.011968 TTCATTCTGTTAGCGCGCGT 61.012 50.000 32.35 20.00 0.00 6.01
5389 6007 6.227522 TGGACGAGTTTCATTCATTCTGTTA 58.772 36.000 0.00 0.00 0.00 2.41
5451 6069 0.243907 CATATCGATTCTCCGCCGGT 59.756 55.000 1.71 0.00 0.00 5.28
5484 6102 7.743749 ACAGACCAGCTTAATTCTATCATCAT 58.256 34.615 0.00 0.00 0.00 2.45
5489 6107 4.985409 CCGACAGACCAGCTTAATTCTATC 59.015 45.833 0.00 0.00 0.00 2.08
5507 6125 1.599071 GTACATATCGTCCGACCGACA 59.401 52.381 0.00 0.00 42.07 4.35
5510 6128 2.031420 ACATGTACATATCGTCCGACCG 60.031 50.000 8.32 0.00 0.00 4.79
5511 6129 3.637998 ACATGTACATATCGTCCGACC 57.362 47.619 8.32 0.00 0.00 4.79
5512 6130 4.908156 GTGTACATGTACATATCGTCCGAC 59.092 45.833 34.66 17.89 46.36 4.79
5513 6131 4.023792 GGTGTACATGTACATATCGTCCGA 60.024 45.833 34.66 10.94 46.36 4.55
5514 6132 4.224433 GGTGTACATGTACATATCGTCCG 58.776 47.826 34.66 0.00 46.36 4.79
5515 6133 4.038282 TGGGTGTACATGTACATATCGTCC 59.962 45.833 34.66 28.42 46.36 4.79
5516 6134 4.980434 GTGGGTGTACATGTACATATCGTC 59.020 45.833 34.66 22.64 46.36 4.20
5517 6135 4.403113 TGTGGGTGTACATGTACATATCGT 59.597 41.667 34.66 5.30 46.36 3.73
5524 6142 3.620427 TGGATGTGGGTGTACATGTAC 57.380 47.619 25.99 25.99 41.15 2.90
5542 6160 5.410355 ACACCAAAAAGGATTGATGATGG 57.590 39.130 0.00 0.00 41.22 3.51


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

AutoCloner maintained by Alex Coulton.