Multiple sequence alignment - TraesCS5D01G451900

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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 TraesCS5D01G451900 chr5D 100.000 6325 0 0 1 6325 499877199 499870875 0.000000e+00 11681.0
1 TraesCS5D01G451900 chr5A 94.973 2248 81 15 1392 3622 624217618 624215386 0.000000e+00 3496.0
2 TraesCS5D01G451900 chr5A 96.323 1251 40 5 3623 4868 624215343 624214094 0.000000e+00 2050.0
3 TraesCS5D01G451900 chr5A 87.164 1488 105 35 4878 6323 624214116 624212673 0.000000e+00 1611.0
4 TraesCS5D01G451900 chr5A 91.104 1214 67 17 187 1380 624218858 624217666 0.000000e+00 1605.0
5 TraesCS5D01G451900 chr5A 88.021 192 21 2 1 191 624219078 624218888 6.380000e-55 226.0
6 TraesCS5D01G451900 chr5B 94.021 2241 85 20 1398 3622 621266971 621264764 0.000000e+00 3350.0
7 TraesCS5D01G451900 chr5B 94.453 1262 49 12 3623 4868 621264721 621263465 0.000000e+00 1923.0
8 TraesCS5D01G451900 chr5B 91.925 1226 59 14 187 1381 621268242 621267026 0.000000e+00 1679.0
9 TraesCS5D01G451900 chr5B 91.620 895 46 16 4878 5748 621263487 621262598 0.000000e+00 1210.0
10 TraesCS5D01G451900 chr5B 89.529 191 19 1 1 191 621268461 621268272 2.280000e-59 241.0
11 TraesCS5D01G451900 chr5B 76.797 487 63 30 5865 6323 621262533 621262069 1.770000e-55 228.0
12 TraesCS5D01G451900 chr5B 83.750 80 11 2 5801 5880 136413156 136413233 2.450000e-09 75.0
13 TraesCS5D01G451900 chr5B 93.750 48 1 2 5750 5796 699979072 699979026 3.160000e-08 71.3
14 TraesCS5D01G451900 chr7D 84.524 84 12 1 2984 3066 382475289 382475372 1.460000e-11 82.4
15 TraesCS5D01G451900 chr7D 86.301 73 6 3 5800 5872 139819000 139819068 6.800000e-10 76.8
16 TraesCS5D01G451900 chr7D 85.135 74 7 2 5801 5874 454519331 454519400 8.800000e-09 73.1
17 TraesCS5D01G451900 chr3B 84.524 84 12 1 2984 3066 113686379 113686462 1.460000e-11 82.4
18 TraesCS5D01G451900 chr3B 95.833 48 0 2 5750 5796 706856472 706856426 6.800000e-10 76.8
19 TraesCS5D01G451900 chr3B 91.667 48 2 2 5750 5796 747527265 747527311 1.470000e-06 65.8
20 TraesCS5D01G451900 chr3B 82.192 73 9 3 5802 5872 31865896 31865966 6.850000e-05 60.2
21 TraesCS5D01G451900 chr3B 83.871 62 5 4 5817 5875 52774010 52773951 3.000000e-03 54.7
22 TraesCS5D01G451900 chr2B 84.524 84 12 1 2984 3066 416749855 416749772 1.460000e-11 82.4
23 TraesCS5D01G451900 chr2B 84.932 73 8 3 5801 5872 796537064 796537134 3.160000e-08 71.3
24 TraesCS5D01G451900 chr2B 83.784 74 7 3 5804 5872 792996842 792996769 1.470000e-06 65.8
25 TraesCS5D01G451900 chr1A 84.706 85 9 4 2989 3071 376514832 376514914 1.460000e-11 82.4
26 TraesCS5D01G451900 chr3D 84.706 85 7 3 5791 5872 152486645 152486726 5.260000e-11 80.5
27 TraesCS5D01G451900 chr1D 83.133 83 14 0 2989 3071 301641885 301641967 6.800000e-10 76.8
28 TraesCS5D01G451900 chr1B 83.133 83 14 0 2989 3071 407309007 407309089 6.800000e-10 76.8
29 TraesCS5D01G451900 chr6B 93.750 48 1 2 5750 5796 34135372 34135326 3.160000e-08 71.3
30 TraesCS5D01G451900 chr3A 93.750 48 1 2 5750 5796 56783573 56783619 3.160000e-08 71.3
31 TraesCS5D01G451900 chr3A 96.875 32 1 0 5750 5781 68867163 68867194 3.000000e-03 54.7
32 TraesCS5D01G451900 chr4D 100.000 36 0 0 5842 5877 27383585 27383620 4.090000e-07 67.6
33 TraesCS5D01G451900 chr7B 79.000 100 18 2 3065 3163 602894589 602894686 1.470000e-06 65.8
34 TraesCS5D01G451900 chr7B 94.872 39 2 0 5796 5834 723957858 723957820 1.900000e-05 62.1
35 TraesCS5D01G451900 chr7B 96.970 33 0 1 5771 5802 164500714 164500746 3.000000e-03 54.7
36 TraesCS5D01G451900 chr2A 89.583 48 3 2 5750 5796 52057189 52057143 6.850000e-05 60.2


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 TraesCS5D01G451900 chr5D 499870875 499877199 6324 True 11681.0 11681 100.000000 1 6325 1 chr5D.!!$R1 6324
1 TraesCS5D01G451900 chr5A 624212673 624219078 6405 True 1797.6 3496 91.517000 1 6323 5 chr5A.!!$R1 6322
2 TraesCS5D01G451900 chr5B 621262069 621268461 6392 True 1438.5 3350 89.724167 1 6323 6 chr5B.!!$R2 6322

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
680 732 0.317160 CCTCCACTTACACGTGAGCA 59.683 55.000 25.01 3.65 37.06 4.26 F
685 737 1.037493 ACTTACACGTGAGCACTCCA 58.963 50.000 25.01 0.00 0.00 3.86 F
1082 1162 2.434331 CACCAAAGGGGCGGAGAA 59.566 61.111 0.00 0.00 42.05 2.87 F
2498 2629 0.669625 GCGAGGAAGTTGTTAGCGGT 60.670 55.000 0.00 0.00 0.00 5.68 F
2740 2871 0.038166 TCTGGTGGAGGAAATGGTGC 59.962 55.000 0.00 0.00 0.00 5.01 F
3440 3581 1.535833 AGAGTACTCTGGTGACACCG 58.464 55.000 24.62 14.01 42.58 4.94 F
4745 4939 1.002069 TGGATGGTGCTTTCCAGGAT 58.998 50.000 0.00 0.00 41.05 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1670 1795 0.187361 AACAGCCAAGGCCACCTAAA 59.813 50.000 5.01 0.0 43.17 1.85 R
1798 1923 0.653636 TTGACAACGCACGGAAGTTC 59.346 50.000 0.00 0.0 46.40 3.01 R
2627 2758 1.269723 GCCTTTGTTGGTGACTTAGGC 59.730 52.381 0.00 0.0 43.31 3.93 R
3482 3623 1.337071 GTCACTGAACAGGAGTCGTCA 59.663 52.381 6.76 0.0 0.00 4.35 R
4433 4618 2.787473 TGGCAGTAGCAAGCTGTTAT 57.213 45.000 4.53 0.0 44.61 1.89 R
5306 5503 0.179234 TTCAGCTCACGGGTTTCACA 59.821 50.000 0.00 0.0 0.00 3.58 R
6252 6516 0.261991 AAGGGACAGCGAGAGGGATA 59.738 55.000 0.00 0.0 0.00 2.59 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.381941 GGAAGGATCCCCTGCTGCT 61.382 63.158 8.55 0.00 43.48 4.24
88 89 3.713288 TCTCGCGAAATTGACCGATATT 58.287 40.909 11.33 0.00 0.00 1.28
94 95 6.018588 TCGCGAAATTGACCGATATTGTTAAT 60.019 34.615 6.20 0.00 0.00 1.40
166 168 6.582677 TTCTCGGCTCCAAAATTCAAATAA 57.417 33.333 0.00 0.00 0.00 1.40
169 171 6.866248 TCTCGGCTCCAAAATTCAAATAAAAC 59.134 34.615 0.00 0.00 0.00 2.43
220 256 5.488341 ACGGTTGCTTAGATACTTGTTGAT 58.512 37.500 0.00 0.00 0.00 2.57
225 261 5.925509 TGCTTAGATACTTGTTGATACCCC 58.074 41.667 0.00 0.00 0.00 4.95
248 284 0.534203 TTTTCACCTTCTTCGCCGCT 60.534 50.000 0.00 0.00 0.00 5.52
249 285 0.949105 TTTCACCTTCTTCGCCGCTC 60.949 55.000 0.00 0.00 0.00 5.03
256 292 2.386249 CTTCTTCGCCGCTCTACATAC 58.614 52.381 0.00 0.00 0.00 2.39
294 330 2.693591 TCTGACCATCTCCACCGTTATC 59.306 50.000 0.00 0.00 0.00 1.75
417 466 2.521105 AAAGAGGCGTCAACGTTACT 57.479 45.000 9.41 0.80 42.22 2.24
443 492 1.762471 CCACAGGTTAACCCCCGAA 59.238 57.895 21.30 0.00 36.42 4.30
472 521 4.507879 GGTACCAACCGTCCGATG 57.492 61.111 7.15 0.00 35.62 3.84
483 532 1.976728 CCGTCCGATGATTAACGATCG 59.023 52.381 14.88 14.88 40.94 3.69
485 534 1.719780 GTCCGATGATTAACGATCGCC 59.280 52.381 16.60 0.04 40.12 5.54
573 624 2.590575 CCAGTTGGCGTGAACCGT 60.591 61.111 0.00 0.00 39.32 4.83
626 678 4.030452 GCCAGCACTGCACGGTTC 62.030 66.667 3.30 0.00 0.00 3.62
642 694 1.897802 GGTTCTCTACGGAAAGGTCCA 59.102 52.381 0.00 0.00 45.26 4.02
680 732 0.317160 CCTCCACTTACACGTGAGCA 59.683 55.000 25.01 3.65 37.06 4.26
685 737 1.037493 ACTTACACGTGAGCACTCCA 58.963 50.000 25.01 0.00 0.00 3.86
748 811 3.897122 GAAGCACCCACCCACCCA 61.897 66.667 0.00 0.00 0.00 4.51
749 812 4.218686 AAGCACCCACCCACCCAC 62.219 66.667 0.00 0.00 0.00 4.61
754 817 4.299796 CCCACCCACCCACCCAAG 62.300 72.222 0.00 0.00 0.00 3.61
1082 1162 2.434331 CACCAAAGGGGCGGAGAA 59.566 61.111 0.00 0.00 42.05 2.87
1238 1319 3.000724 GCTAGATCTGTTTTAGCTGTGCG 59.999 47.826 5.18 0.00 37.43 5.34
1332 1414 3.385115 AGGGTTTCGTATTGGAGGAGAT 58.615 45.455 0.00 0.00 0.00 2.75
1343 1425 6.642950 CGTATTGGAGGAGATAGATTCAACAC 59.357 42.308 0.00 0.00 0.00 3.32
1348 1430 4.036518 AGGAGATAGATTCAACACAGCCT 58.963 43.478 0.00 0.00 0.00 4.58
1349 1431 4.472833 AGGAGATAGATTCAACACAGCCTT 59.527 41.667 0.00 0.00 0.00 4.35
1350 1432 4.813697 GGAGATAGATTCAACACAGCCTTC 59.186 45.833 0.00 0.00 0.00 3.46
1351 1433 5.423015 GAGATAGATTCAACACAGCCTTCA 58.577 41.667 0.00 0.00 0.00 3.02
1358 1440 3.554934 TCAACACAGCCTTCACTCAAAT 58.445 40.909 0.00 0.00 0.00 2.32
1360 1442 2.936202 ACACAGCCTTCACTCAAATGT 58.064 42.857 0.00 0.00 0.00 2.71
1374 1456 7.047891 TCACTCAAATGTCTTACACTGAACTT 58.952 34.615 0.00 0.00 0.00 2.66
1382 1464 4.451435 GTCTTACACTGAACTTAGGTTGCC 59.549 45.833 0.00 0.00 35.58 4.52
1383 1465 4.101898 TCTTACACTGAACTTAGGTTGCCA 59.898 41.667 0.00 0.00 35.58 4.92
1384 1466 3.290948 ACACTGAACTTAGGTTGCCAA 57.709 42.857 0.00 0.00 35.58 4.52
1387 1469 3.632145 CACTGAACTTAGGTTGCCAAACT 59.368 43.478 0.00 0.00 36.48 2.66
1388 1470 3.883489 ACTGAACTTAGGTTGCCAAACTC 59.117 43.478 0.00 0.00 36.48 3.01
1389 1471 3.882888 CTGAACTTAGGTTGCCAAACTCA 59.117 43.478 0.00 0.00 36.48 3.41
1390 1472 4.274147 TGAACTTAGGTTGCCAAACTCAA 58.726 39.130 0.00 0.00 36.48 3.02
1391 1473 4.338118 TGAACTTAGGTTGCCAAACTCAAG 59.662 41.667 0.00 4.39 36.48 3.02
1395 1515 5.186992 ACTTAGGTTGCCAAACTCAAGTTTT 59.813 36.000 0.00 0.00 45.07 2.43
1396 1516 4.551702 AGGTTGCCAAACTCAAGTTTTT 57.448 36.364 5.41 0.00 45.07 1.94
1415 1535 3.914426 TTTTAGGAGTCCAGCTCATCC 57.086 47.619 12.86 0.00 45.88 3.51
1586 1709 4.862018 CCACCGGCAAATTTTAGTTGTATG 59.138 41.667 0.00 0.00 0.00 2.39
1608 1731 4.263462 TGTCTTGGCACATCTTACAGGAAT 60.263 41.667 0.00 0.00 39.30 3.01
1609 1732 4.702131 GTCTTGGCACATCTTACAGGAATT 59.298 41.667 0.00 0.00 39.30 2.17
1670 1795 7.884877 TCCATGTGAAGATTTTGAGATAGTGTT 59.115 33.333 0.00 0.00 0.00 3.32
1765 1890 3.891366 TCGATATGCAGTTGAGATCTGGA 59.109 43.478 0.00 0.00 37.63 3.86
1788 1913 5.440610 AGATCTTTGTCAACAGTTCTTGGT 58.559 37.500 0.00 0.00 0.00 3.67
1798 1923 4.199432 ACAGTTCTTGGTCATCAGCTAG 57.801 45.455 0.00 0.00 0.00 3.42
1819 1944 1.157870 ACTTCCGTGCGTTGTCAAGG 61.158 55.000 0.77 0.77 37.02 3.61
1875 2000 4.063689 TGCTTGGCCACATATTTTTGTTG 58.936 39.130 3.88 0.00 0.00 3.33
1882 2007 4.685628 GCCACATATTTTTGTTGTCACAGG 59.314 41.667 0.00 0.00 33.22 4.00
1926 2057 5.653769 ACATTAAGACATAAACTGGCATGCT 59.346 36.000 18.92 0.00 34.10 3.79
1965 2096 6.971184 AGCAATTCGATTCAGATGTTCAATTC 59.029 34.615 0.00 0.00 0.00 2.17
2046 2177 6.995686 TGTCCAAATTTACAGAAGTGCTCTTA 59.004 34.615 0.04 0.00 33.64 2.10
2105 2236 8.695456 ACATATATATGTCGGCATTATGAGTCA 58.305 33.333 21.23 0.00 42.96 3.41
2156 2287 4.276926 CAGGTTAGAAGCCTATCATTTGCC 59.723 45.833 0.00 0.00 34.45 4.52
2162 2293 4.583489 AGAAGCCTATCATTTGCCTGAATG 59.417 41.667 0.00 0.00 38.16 2.67
2272 2403 4.876107 CCGAATAGTTTATGAGGTTGCACT 59.124 41.667 0.00 0.00 0.00 4.40
2324 2455 7.369434 TCCCCCAATGTTTATCCATTTATTCT 58.631 34.615 0.00 0.00 32.81 2.40
2420 2551 0.908198 AAGAGGCTGCGGAAATCTCT 59.092 50.000 0.00 0.00 36.49 3.10
2423 2554 1.137086 GAGGCTGCGGAAATCTCTACA 59.863 52.381 0.00 0.00 0.00 2.74
2426 2557 2.224161 GGCTGCGGAAATCTCTACAGAT 60.224 50.000 0.00 0.00 41.59 2.90
2495 2626 2.742053 TGATTGCGAGGAAGTTGTTAGC 59.258 45.455 0.00 0.00 0.00 3.09
2498 2629 0.669625 GCGAGGAAGTTGTTAGCGGT 60.670 55.000 0.00 0.00 0.00 5.68
2579 2710 2.155279 GAAACAGGGGAAGACAAGCTC 58.845 52.381 0.00 0.00 0.00 4.09
2627 2758 4.179298 TCGATCAAGAAATGTCTGCTCTG 58.821 43.478 0.00 0.00 33.05 3.35
2646 2777 2.554032 CTGCCTAAGTCACCAACAAAGG 59.446 50.000 0.00 0.00 35.92 3.11
2672 2803 4.892934 AGTATGTCTGGATCAGAGAAGTCC 59.107 45.833 0.00 0.00 41.46 3.85
2719 2850 3.796844 GCACTTTCAACTCAAAGAAGGGC 60.797 47.826 0.02 0.00 36.92 5.19
2720 2851 3.633986 CACTTTCAACTCAAAGAAGGGCT 59.366 43.478 0.02 0.00 36.92 5.19
2740 2871 0.038166 TCTGGTGGAGGAAATGGTGC 59.962 55.000 0.00 0.00 0.00 5.01
2786 2917 2.564504 AGAAAAATCTGGGCAAGGAAGC 59.435 45.455 0.00 0.00 0.00 3.86
2823 2954 7.227314 CAGCAAGCATGATAAAGAAGGTATGTA 59.773 37.037 0.00 0.00 0.00 2.29
2826 2957 7.618019 AGCATGATAAAGAAGGTATGTAGGA 57.382 36.000 0.00 0.00 0.00 2.94
2863 2994 6.312426 GCTCTATTACACTGTATCATGATGCC 59.688 42.308 18.72 9.12 0.00 4.40
2864 2995 6.701340 TCTATTACACTGTATCATGATGCCC 58.299 40.000 18.72 6.67 0.00 5.36
3192 3327 3.149196 GAGTTGGTGATGCTTGGAAGAA 58.851 45.455 0.00 0.00 0.00 2.52
3275 3410 6.898041 TGTCGTGGAACATCTTAAATTTCTG 58.102 36.000 0.00 0.00 44.52 3.02
3440 3581 1.535833 AGAGTACTCTGGTGACACCG 58.464 55.000 24.62 14.01 42.58 4.94
3456 3597 2.002586 CACCGAAGAAGATGTCGCAAT 58.997 47.619 0.00 0.00 35.93 3.56
3482 3623 4.706962 GGCCTTACATTTCAACCTCAAGAT 59.293 41.667 0.00 0.00 0.00 2.40
3685 3868 5.348179 CACAAGCTGTATCTTCTCAGTTGAG 59.652 44.000 2.69 2.69 43.36 3.02
4063 4248 7.210174 GCTGAAACAAGGAAAAAGGTAAGAAT 58.790 34.615 0.00 0.00 0.00 2.40
4342 4527 6.498538 TGGAGGTTTATTTGTACATTCCCAT 58.501 36.000 0.00 0.00 0.00 4.00
4433 4618 3.960755 TCTGAATTCGAGCCCTAGATTCA 59.039 43.478 0.04 6.34 0.00 2.57
4521 4706 8.236586 TGTTACTAACATTTCTGATGTTCATGC 58.763 33.333 7.59 0.00 41.81 4.06
4628 4813 4.635963 AGGGCCCCCTCCAAAGGT 62.636 66.667 21.43 0.00 44.43 3.50
4649 4834 5.875359 AGGTTGAGCTTAAGAAGGTAATTCG 59.125 40.000 6.67 0.00 43.16 3.34
4666 4851 8.881262 AGGTAATTCGGATATCTTGTATTTCCT 58.119 33.333 14.04 14.04 0.00 3.36
4740 4934 5.343307 ACATTTAATGGATGGTGCTTTCC 57.657 39.130 9.88 0.00 33.60 3.13
4745 4939 1.002069 TGGATGGTGCTTTCCAGGAT 58.998 50.000 0.00 0.00 41.05 3.24
4758 4952 8.725148 GTGCTTTCCAGGATAATTCTGTATATG 58.275 37.037 0.00 0.00 0.00 1.78
4764 4958 7.512402 TCCAGGATAATTCTGTATATGTCACCA 59.488 37.037 0.00 0.00 0.00 4.17
4772 4966 7.864108 TTCTGTATATGTCACCAAAATGAGG 57.136 36.000 0.00 0.00 0.00 3.86
4775 4969 6.128486 TGTATATGTCACCAAAATGAGGCAT 58.872 36.000 0.00 0.00 0.00 4.40
4776 4970 7.286313 TGTATATGTCACCAAAATGAGGCATA 58.714 34.615 0.00 0.00 0.00 3.14
4777 4971 7.777440 TGTATATGTCACCAAAATGAGGCATAA 59.223 33.333 0.00 0.00 0.00 1.90
4778 4972 5.999205 ATGTCACCAAAATGAGGCATAAA 57.001 34.783 0.00 0.00 0.00 1.40
4780 4974 4.021544 TGTCACCAAAATGAGGCATAAACC 60.022 41.667 0.00 0.00 0.00 3.27
4848 5045 4.141959 CCCCTAATACAAAAGCAACCCATG 60.142 45.833 0.00 0.00 0.00 3.66
4851 5048 4.806640 AATACAAAAGCAACCCATGGAG 57.193 40.909 15.22 5.95 0.00 3.86
4853 5050 1.688197 ACAAAAGCAACCCATGGAGTG 59.312 47.619 15.22 11.81 0.00 3.51
4854 5051 1.962807 CAAAAGCAACCCATGGAGTGA 59.037 47.619 15.22 0.00 0.00 3.41
4855 5052 2.564062 CAAAAGCAACCCATGGAGTGAT 59.436 45.455 15.22 6.43 0.00 3.06
4856 5053 3.737559 AAAGCAACCCATGGAGTGATA 57.262 42.857 15.22 0.00 0.00 2.15
4857 5054 3.959495 AAGCAACCCATGGAGTGATAT 57.041 42.857 15.22 0.00 0.00 1.63
4858 5055 3.498774 AGCAACCCATGGAGTGATATC 57.501 47.619 15.22 0.00 0.00 1.63
4859 5056 2.779430 AGCAACCCATGGAGTGATATCA 59.221 45.455 15.22 0.00 0.00 2.15
4860 5057 3.396946 AGCAACCCATGGAGTGATATCAT 59.603 43.478 15.22 0.00 0.00 2.45
4861 5058 4.598807 AGCAACCCATGGAGTGATATCATA 59.401 41.667 15.22 0.00 0.00 2.15
4862 5059 4.940046 GCAACCCATGGAGTGATATCATAG 59.060 45.833 15.22 0.00 0.00 2.23
4863 5060 5.494724 CAACCCATGGAGTGATATCATAGG 58.505 45.833 15.22 5.12 0.00 2.57
4864 5061 4.767908 ACCCATGGAGTGATATCATAGGT 58.232 43.478 15.22 5.70 30.22 3.08
4865 5062 4.533707 ACCCATGGAGTGATATCATAGGTG 59.466 45.833 15.22 5.13 33.04 4.00
4866 5063 4.533707 CCCATGGAGTGATATCATAGGTGT 59.466 45.833 15.22 0.00 0.00 4.16
4867 5064 5.721480 CCCATGGAGTGATATCATAGGTGTA 59.279 44.000 15.22 0.00 0.00 2.90
4868 5065 6.385176 CCCATGGAGTGATATCATAGGTGTAT 59.615 42.308 15.22 0.00 0.00 2.29
4869 5066 7.418368 CCCATGGAGTGATATCATAGGTGTATC 60.418 44.444 15.22 0.00 0.00 2.24
4870 5067 7.344093 CCATGGAGTGATATCATAGGTGTATCT 59.656 40.741 5.56 0.00 0.00 1.98
4871 5068 9.413734 CATGGAGTGATATCATAGGTGTATCTA 57.586 37.037 9.02 0.00 0.00 1.98
4878 5075 9.936329 TGATATCATAGGTGTATCTATAAGGCA 57.064 33.333 0.00 0.00 0.00 4.75
4882 5079 8.664669 TCATAGGTGTATCTATAAGGCATTGA 57.335 34.615 0.00 0.00 0.00 2.57
4883 5080 9.271921 TCATAGGTGTATCTATAAGGCATTGAT 57.728 33.333 0.00 0.00 34.17 2.57
4967 5164 9.703892 GTTATAGAGAGTAGATGTTGATGCATT 57.296 33.333 0.00 0.00 0.00 3.56
5065 5262 4.224370 ACACACCCGATGGACTAACTTTAT 59.776 41.667 0.00 0.00 34.81 1.40
5332 5533 2.435586 CGTGAGCTGAAGGCCCTG 60.436 66.667 0.00 0.00 43.05 4.45
5345 5546 1.599576 GCCCTGTGAGAAGGAGGAC 59.400 63.158 0.00 0.00 40.02 3.85
5405 5606 2.036862 ACCCTAACTCAACGTTGTCTCC 59.963 50.000 26.47 0.00 37.05 3.71
5573 5788 0.848648 TCCCATGTTCCATGACCCCA 60.849 55.000 5.80 0.00 0.00 4.96
5574 5789 0.262580 CCCATGTTCCATGACCCCAT 59.737 55.000 5.80 0.00 0.00 4.00
5621 5840 9.689976 TGTTTGTATTATTGTCATGGTTTGAAG 57.310 29.630 0.00 0.00 35.70 3.02
5634 5853 8.613830 GTCATGGTTTGAAGTTTGCAAATTTGC 61.614 37.037 31.67 31.67 44.67 3.68
5682 5901 1.547372 GCCACCATGATAATGGATGGC 59.453 52.381 26.88 26.88 44.39 4.40
5698 5917 3.245052 GGATGGCCCAGCTTTACATCTAT 60.245 47.826 0.00 0.00 38.33 1.98
5702 5921 5.130350 TGGCCCAGCTTTACATCTATAAAC 58.870 41.667 0.00 0.00 0.00 2.01
5720 5939 9.565090 TCTATAAACATGAAAGCATAAGCATCT 57.435 29.630 0.00 0.00 45.49 2.90
5732 5951 5.286295 GCATAAGCATCTCCATGACATGGT 61.286 45.833 29.44 14.10 45.25 3.55
5752 5971 3.436035 GGTCACCCCTGGGAAATAATACC 60.436 52.174 16.20 7.84 38.96 2.73
5759 5978 3.060611 CTGGGAAATAATACCCCCTCCA 58.939 50.000 0.00 0.00 45.01 3.86
5763 5982 3.011369 GGAAATAATACCCCCTCCATCCC 59.989 52.174 0.00 0.00 0.00 3.85
5764 5983 3.393782 AATAATACCCCCTCCATCCCA 57.606 47.619 0.00 0.00 0.00 4.37
5765 5984 3.621173 ATAATACCCCCTCCATCCCAT 57.379 47.619 0.00 0.00 0.00 4.00
5766 5985 4.746206 ATAATACCCCCTCCATCCCATA 57.254 45.455 0.00 0.00 0.00 2.74
5767 5986 3.393782 AATACCCCCTCCATCCCATAA 57.606 47.619 0.00 0.00 0.00 1.90
5768 5987 3.621173 ATACCCCCTCCATCCCATAAT 57.379 47.619 0.00 0.00 0.00 1.28
5769 5988 4.746206 ATACCCCCTCCATCCCATAATA 57.254 45.455 0.00 0.00 0.00 0.98
5770 5989 3.393782 ACCCCCTCCATCCCATAATAA 57.606 47.619 0.00 0.00 0.00 1.40
5816 6035 7.093421 ACACTAAATTTAGTACTCCCTCAGTCC 60.093 40.741 26.38 0.00 41.82 3.85
5823 6042 5.681494 AGTACTCCCTCAGTCCCATAATA 57.319 43.478 0.00 0.00 36.43 0.98
5827 6046 7.896496 AGTACTCCCTCAGTCCCATAATATAAG 59.104 40.741 0.00 0.00 36.43 1.73
5830 6049 5.721960 TCCCTCAGTCCCATAATATAAGAGC 59.278 44.000 0.00 0.00 0.00 4.09
5831 6050 5.485353 CCCTCAGTCCCATAATATAAGAGCA 59.515 44.000 0.00 0.00 0.00 4.26
5832 6051 6.157645 CCCTCAGTCCCATAATATAAGAGCAT 59.842 42.308 0.00 0.00 0.00 3.79
5835 6054 8.206126 TCAGTCCCATAATATAAGAGCATTGA 57.794 34.615 0.00 0.00 0.00 2.57
5836 6055 8.097038 TCAGTCCCATAATATAAGAGCATTGAC 58.903 37.037 0.00 0.00 0.00 3.18
5837 6056 8.099537 CAGTCCCATAATATAAGAGCATTGACT 58.900 37.037 0.00 0.00 0.00 3.41
5838 6057 8.099537 AGTCCCATAATATAAGAGCATTGACTG 58.900 37.037 0.00 0.00 0.00 3.51
5839 6058 7.880195 GTCCCATAATATAAGAGCATTGACTGT 59.120 37.037 0.00 0.00 0.00 3.55
5840 6059 8.097038 TCCCATAATATAAGAGCATTGACTGTC 58.903 37.037 0.00 0.00 0.00 3.51
5908 6131 6.018669 CGCCATATTAAAAGTCAGAGAAGGAC 60.019 42.308 0.00 0.00 35.50 3.85
5921 6151 6.092807 GTCAGAGAAGGACCATTCACATTTAC 59.907 42.308 0.00 0.00 0.00 2.01
6046 6291 2.403252 GACCCGGTGTCAGAAATGAT 57.597 50.000 15.65 0.00 43.85 2.45
6054 6299 6.095440 CCCGGTGTCAGAAATGATAAGAAAAT 59.905 38.462 0.00 0.00 0.00 1.82
6055 6300 7.362920 CCCGGTGTCAGAAATGATAAGAAAATT 60.363 37.037 0.00 0.00 0.00 1.82
6102 6354 8.256605 TGGGACACAATGACATATTTAAATTGG 58.743 33.333 5.91 1.86 33.50 3.16
6107 6359 9.153721 CACAATGACATATTTAAATTGGCAACT 57.846 29.630 17.27 0.00 30.89 3.16
6137 6389 2.092323 GAAAGCCACCACCCTGTTATC 58.908 52.381 0.00 0.00 0.00 1.75
6146 6399 5.359860 CCACCACCCTGTTATCTTTATTTCC 59.640 44.000 0.00 0.00 0.00 3.13
6189 6453 1.001406 CACCTGTCGCCTCTTCTTCTT 59.999 52.381 0.00 0.00 0.00 2.52
6190 6454 1.694696 ACCTGTCGCCTCTTCTTCTTT 59.305 47.619 0.00 0.00 0.00 2.52
6191 6455 2.897969 ACCTGTCGCCTCTTCTTCTTTA 59.102 45.455 0.00 0.00 0.00 1.85
6192 6456 3.515901 ACCTGTCGCCTCTTCTTCTTTAT 59.484 43.478 0.00 0.00 0.00 1.40
6193 6457 4.116238 CCTGTCGCCTCTTCTTCTTTATC 58.884 47.826 0.00 0.00 0.00 1.75
6194 6458 4.142049 CCTGTCGCCTCTTCTTCTTTATCT 60.142 45.833 0.00 0.00 0.00 1.98
6235 6499 4.447138 TCTGGTGTACATTTCCAACCTT 57.553 40.909 0.00 0.00 0.00 3.50
6236 6500 4.141287 TCTGGTGTACATTTCCAACCTTG 58.859 43.478 0.00 0.00 0.00 3.61
6238 6502 2.029380 GGTGTACATTTCCAACCTTGCC 60.029 50.000 0.00 0.00 0.00 4.52
6239 6503 2.625790 GTGTACATTTCCAACCTTGCCA 59.374 45.455 0.00 0.00 0.00 4.92
6240 6504 3.258123 GTGTACATTTCCAACCTTGCCAT 59.742 43.478 0.00 0.00 0.00 4.40
6241 6505 3.257873 TGTACATTTCCAACCTTGCCATG 59.742 43.478 0.00 0.00 0.00 3.66
6242 6506 2.607499 ACATTTCCAACCTTGCCATGA 58.393 42.857 0.00 0.00 0.00 3.07
6243 6507 2.299867 ACATTTCCAACCTTGCCATGAC 59.700 45.455 0.00 0.00 0.00 3.06
6244 6508 2.079170 TTTCCAACCTTGCCATGACA 57.921 45.000 0.00 0.00 0.00 3.58
6246 6510 0.770499 TCCAACCTTGCCATGACAGA 59.230 50.000 0.00 0.00 0.00 3.41
6247 6511 1.171308 CCAACCTTGCCATGACAGAG 58.829 55.000 0.00 0.00 0.00 3.35
6248 6512 1.546323 CCAACCTTGCCATGACAGAGT 60.546 52.381 0.00 0.00 0.00 3.24
6249 6513 2.233271 CAACCTTGCCATGACAGAGTT 58.767 47.619 0.00 0.00 0.00 3.01
6250 6514 2.191128 ACCTTGCCATGACAGAGTTC 57.809 50.000 0.00 0.00 0.00 3.01
6251 6515 1.421268 ACCTTGCCATGACAGAGTTCA 59.579 47.619 0.00 0.00 0.00 3.18
6252 6516 2.040813 ACCTTGCCATGACAGAGTTCAT 59.959 45.455 0.00 0.00 36.62 2.57
6278 6552 0.318441 CTCGCTGTCCCTTTGACTGA 59.682 55.000 3.76 0.00 44.75 3.41
6279 6553 0.033504 TCGCTGTCCCTTTGACTGAC 59.966 55.000 3.76 0.00 44.75 3.51
6280 6554 0.034059 CGCTGTCCCTTTGACTGACT 59.966 55.000 3.76 0.00 44.75 3.41
6281 6555 1.517242 GCTGTCCCTTTGACTGACTG 58.483 55.000 3.76 0.00 44.75 3.51
6323 6606 6.483405 AGAAATCTCTCTCAGCCTTCAATTT 58.517 36.000 0.00 0.00 0.00 1.82
6324 6607 6.947158 AGAAATCTCTCTCAGCCTTCAATTTT 59.053 34.615 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.627986 CAGCAGGGGATCCTTCCTTT 59.372 55.000 12.58 0.00 42.67 3.11
129 130 2.661979 GCCGAGAAACAAGCGTAAGTTG 60.662 50.000 0.00 0.00 41.68 3.16
166 168 3.337694 TCGACCAATATGGAACCGTTT 57.662 42.857 2.85 0.00 40.96 3.60
169 171 3.486875 GCTTTTCGACCAATATGGAACCG 60.487 47.826 2.85 4.18 40.96 4.44
220 256 0.037160 GAAGGTGAAAAGGCGGGGTA 59.963 55.000 0.00 0.00 0.00 3.69
225 261 0.110192 GCGAAGAAGGTGAAAAGGCG 60.110 55.000 0.00 0.00 0.00 5.52
294 330 1.273606 AGAGTGGAAGGTGACATGACG 59.726 52.381 0.00 0.00 0.00 4.35
427 476 2.028561 TACTTCGGGGGTTAACCTGT 57.971 50.000 23.69 14.32 40.03 4.00
443 492 3.640029 CGGTTGGTACCATGACCTATACT 59.360 47.826 26.26 0.00 45.31 2.12
470 519 1.935300 GCTCGGGCGATCGTTAATCAT 60.935 52.381 17.81 0.00 33.65 2.45
471 520 0.596600 GCTCGGGCGATCGTTAATCA 60.597 55.000 17.81 0.00 33.65 2.57
472 521 1.282930 GGCTCGGGCGATCGTTAATC 61.283 60.000 17.81 0.00 39.81 1.75
573 624 1.344438 GGTGTCGCAGGGATCATCATA 59.656 52.381 0.00 0.00 0.00 2.15
626 678 3.995048 GACTTTTGGACCTTTCCGTAGAG 59.005 47.826 0.00 0.00 46.37 2.43
642 694 2.031870 GGTGACTTGGCTTGGACTTTT 58.968 47.619 0.00 0.00 0.00 2.27
680 732 4.918360 TGGGCTGTGGGGTGGAGT 62.918 66.667 0.00 0.00 0.00 3.85
748 811 2.037677 AGGGGTTGGGTCTTGGGT 60.038 61.111 0.00 0.00 0.00 4.51
749 812 2.763902 GAGGGGTTGGGTCTTGGG 59.236 66.667 0.00 0.00 0.00 4.12
750 813 2.185310 CTCGAGGGGTTGGGTCTTGG 62.185 65.000 3.91 0.00 0.00 3.61
751 814 1.296715 CTCGAGGGGTTGGGTCTTG 59.703 63.158 3.91 0.00 0.00 3.02
752 815 2.593956 GCTCGAGGGGTTGGGTCTT 61.594 63.158 15.58 0.00 0.00 3.01
753 816 3.003763 GCTCGAGGGGTTGGGTCT 61.004 66.667 15.58 0.00 0.00 3.85
754 817 3.319198 TGCTCGAGGGGTTGGGTC 61.319 66.667 15.58 0.00 0.00 4.46
846 917 1.113517 CCAACCCCGCTAGCTAGCTA 61.114 60.000 36.02 22.85 46.85 3.32
850 921 2.363975 CCACCAACCCCGCTAGCTA 61.364 63.158 13.93 0.00 0.00 3.32
1082 1162 7.338710 ACTACTGTAAGAATGGCATTACATGT 58.661 34.615 13.65 14.50 40.19 3.21
1092 1172 6.459298 CGGTACTGGTACTACTGTAAGAATGG 60.459 46.154 10.19 0.00 35.42 3.16
1095 1175 5.560724 ACGGTACTGGTACTACTGTAAGAA 58.439 41.667 6.65 0.00 32.86 2.52
1204 1285 1.483424 GATCTAGCAGCACGCCGAAC 61.483 60.000 0.00 0.00 44.04 3.95
1206 1287 2.121538 AGATCTAGCAGCACGCCGA 61.122 57.895 0.00 0.00 44.04 5.54
1207 1288 1.948138 CAGATCTAGCAGCACGCCG 60.948 63.158 0.00 0.00 44.04 6.46
1215 1296 3.935203 GCACAGCTAAAACAGATCTAGCA 59.065 43.478 15.13 0.00 40.44 3.49
1238 1319 1.386412 CCAAAAACACGCATGAATCGC 59.614 47.619 0.00 0.00 0.00 4.58
1332 1414 4.040339 TGAGTGAAGGCTGTGTTGAATCTA 59.960 41.667 0.00 0.00 0.00 1.98
1343 1425 4.756642 TGTAAGACATTTGAGTGAAGGCTG 59.243 41.667 0.00 0.00 0.00 4.85
1348 1430 7.047891 AGTTCAGTGTAAGACATTTGAGTGAA 58.952 34.615 0.00 0.00 30.22 3.18
1349 1431 6.582636 AGTTCAGTGTAAGACATTTGAGTGA 58.417 36.000 0.00 0.00 30.22 3.41
1350 1432 6.851222 AGTTCAGTGTAAGACATTTGAGTG 57.149 37.500 0.00 0.00 30.22 3.51
1351 1433 7.657761 CCTAAGTTCAGTGTAAGACATTTGAGT 59.342 37.037 0.00 0.00 30.22 3.41
1358 1440 5.054477 GCAACCTAAGTTCAGTGTAAGACA 58.946 41.667 0.00 0.00 32.45 3.41
1360 1442 4.101898 TGGCAACCTAAGTTCAGTGTAAGA 59.898 41.667 0.00 0.00 32.45 2.10
1374 1456 5.669164 AAAAACTTGAGTTTGGCAACCTA 57.331 34.783 9.67 0.00 46.47 3.08
1395 1515 3.454858 AGGATGAGCTGGACTCCTAAAA 58.545 45.455 0.00 0.00 45.61 1.52
1396 1516 3.121929 AGGATGAGCTGGACTCCTAAA 57.878 47.619 0.00 0.00 45.61 1.85
1586 1709 3.334583 TCCTGTAAGATGTGCCAAGAC 57.665 47.619 0.00 0.00 34.07 3.01
1625 1748 3.454082 TGGAAAAGCTGGTGACCAAAAAT 59.546 39.130 5.53 0.00 30.80 1.82
1631 1754 1.270550 CACATGGAAAAGCTGGTGACC 59.729 52.381 0.00 0.00 0.00 4.02
1670 1795 0.187361 AACAGCCAAGGCCACCTAAA 59.813 50.000 5.01 0.00 43.17 1.85
1765 1890 5.440610 ACCAAGAACTGTTGACAAAGATCT 58.559 37.500 0.00 0.00 0.00 2.75
1788 1913 2.417379 GCACGGAAGTTCTAGCTGATGA 60.417 50.000 2.25 0.00 46.40 2.92
1798 1923 0.653636 TTGACAACGCACGGAAGTTC 59.346 50.000 0.00 0.00 46.40 3.01
1934 2065 6.577103 ACATCTGAATCGAATTGCTCTAGAA 58.423 36.000 0.00 0.00 0.00 2.10
1935 2066 6.154203 ACATCTGAATCGAATTGCTCTAGA 57.846 37.500 0.00 0.00 0.00 2.43
1965 2096 3.849911 TGCCACTTCTCATAACTCTTCG 58.150 45.455 0.00 0.00 0.00 3.79
2056 2187 8.669946 TGTGACAACTGACAATGAAGTATAAA 57.330 30.769 0.00 0.00 0.00 1.40
2057 2188 8.846943 ATGTGACAACTGACAATGAAGTATAA 57.153 30.769 0.00 0.00 0.00 0.98
2105 2236 6.672946 TTATGATAGCCAATCCCCCATAAT 57.327 37.500 0.00 0.00 33.22 1.28
2217 2348 3.365264 CGTGCAAGCAACTCAACACATAT 60.365 43.478 0.00 0.00 0.00 1.78
2224 2355 4.475028 CAAATATCGTGCAAGCAACTCAA 58.525 39.130 0.00 0.00 0.00 3.02
2324 2455 8.083828 AGCTTTCTAGGAATTGTAATGAGAGA 57.916 34.615 0.00 0.00 0.00 3.10
2420 2551 6.550938 ACACCATCTGATTCTTCATCTGTA 57.449 37.500 0.00 0.00 33.52 2.74
2423 2554 5.813383 ACAACACCATCTGATTCTTCATCT 58.187 37.500 0.00 0.00 32.34 2.90
2426 2557 9.112725 CATATAACAACACCATCTGATTCTTCA 57.887 33.333 0.00 0.00 0.00 3.02
2495 2626 5.241728 TGGAGAACTATCATGATCACTACCG 59.758 44.000 12.53 0.00 0.00 4.02
2498 2629 6.718912 CCTCTGGAGAACTATCATGATCACTA 59.281 42.308 12.53 0.00 0.00 2.74
2579 2710 7.874940 TCAACTTCAGTGAATCTTGGTTTATG 58.125 34.615 17.33 5.38 0.00 1.90
2627 2758 1.269723 GCCTTTGTTGGTGACTTAGGC 59.730 52.381 0.00 0.00 43.31 3.93
2646 2777 5.534654 ACTTCTCTGATCCAGACATACTAGC 59.465 44.000 0.00 0.00 35.39 3.42
2672 2803 1.798813 GGTTGAGGAACAGTACGCTTG 59.201 52.381 0.00 0.00 33.27 4.01
2719 2850 2.440409 CACCATTTCCTCCACCAGAAG 58.560 52.381 0.00 0.00 0.00 2.85
2720 2851 1.547675 GCACCATTTCCTCCACCAGAA 60.548 52.381 0.00 0.00 0.00 3.02
2786 2917 2.039405 GCTTGCTGGAGAGGCACTG 61.039 63.158 0.00 0.00 41.55 3.66
2823 2954 9.771534 GTGTAATAGAGCATAAAGAAATCTCCT 57.228 33.333 0.00 0.00 0.00 3.69
2846 2977 2.130193 AGGGGCATCATGATACAGTGT 58.870 47.619 8.15 0.00 0.00 3.55
2863 2994 5.719085 AGACTAGAGGCACATGATATTAGGG 59.281 44.000 0.00 0.00 0.00 3.53
2864 2995 6.849085 AGACTAGAGGCACATGATATTAGG 57.151 41.667 0.00 0.00 0.00 2.69
3123 3258 7.575414 TTGTGACCAAAGTGTACAATACAAT 57.425 32.000 0.00 0.00 40.93 2.71
3275 3410 5.501715 CGTGCATATGTTCAGGTTCATAAC 58.498 41.667 4.29 0.00 31.67 1.89
3440 3581 2.031437 GCCAGATTGCGACATCTTCTTC 59.969 50.000 0.00 0.00 0.00 2.87
3456 3597 3.073798 TGAGGTTGAAATGTAAGGCCAGA 59.926 43.478 5.01 0.00 0.00 3.86
3482 3623 1.337071 GTCACTGAACAGGAGTCGTCA 59.663 52.381 6.76 0.00 0.00 4.35
3596 3737 3.367703 CCTTGAGCCTTGGTATGCAAAAG 60.368 47.826 0.00 0.00 0.00 2.27
4063 4248 9.438228 TGTTCCATCATACGAAATAAAAGTACA 57.562 29.630 0.00 0.00 0.00 2.90
4072 4257 7.630242 ACTCAAATGTTCCATCATACGAAAT 57.370 32.000 0.00 0.00 0.00 2.17
4342 4527 3.054434 AGACATACACTGCTATGGCCAAA 60.054 43.478 10.96 0.00 33.07 3.28
4433 4618 2.787473 TGGCAGTAGCAAGCTGTTAT 57.213 45.000 4.53 0.00 44.61 1.89
4463 4648 8.934023 ACAACAAAAGGTTCAAGGATATCTTA 57.066 30.769 2.05 0.00 37.72 2.10
4521 4706 5.215255 GCTTCTTGCTCATCCTACAGGAAG 61.215 50.000 1.23 9.06 45.29 3.46
4628 4813 6.045072 TCCGAATTACCTTCTTAAGCTCAA 57.955 37.500 0.00 0.00 0.00 3.02
4740 4934 9.559732 TTTGGTGACATATACAGAATTATCCTG 57.440 33.333 0.00 0.00 42.32 3.86
4758 4952 4.220602 AGGTTTATGCCTCATTTTGGTGAC 59.779 41.667 0.00 0.00 32.39 3.67
4856 5053 9.271921 TCAATGCCTTATAGATACACCTATGAT 57.728 33.333 0.00 0.00 32.15 2.45
4857 5054 8.664669 TCAATGCCTTATAGATACACCTATGA 57.335 34.615 0.00 0.00 32.15 2.15
4860 5057 9.990868 TCTATCAATGCCTTATAGATACACCTA 57.009 33.333 0.00 0.00 29.42 3.08
4861 5058 8.901472 TCTATCAATGCCTTATAGATACACCT 57.099 34.615 0.00 0.00 29.42 4.00
4872 5069 9.271921 ACACCTATGATATCTATCAATGCCTTA 57.728 33.333 3.98 0.00 44.96 2.69
4873 5070 8.155620 ACACCTATGATATCTATCAATGCCTT 57.844 34.615 3.98 0.00 44.96 4.35
4874 5071 7.746243 ACACCTATGATATCTATCAATGCCT 57.254 36.000 3.98 0.00 44.96 4.75
4967 5164 9.243637 GTTAAATGTTCTGCTTGTCATAAAACA 57.756 29.630 0.00 0.00 0.00 2.83
5009 5206 7.988599 TCTTGCCAGTAGTCAGTAAACTAAAAA 59.011 33.333 0.00 0.00 33.68 1.94
5065 5262 5.358725 TGTAAATCCGTGACTGAGCATAGTA 59.641 40.000 0.00 0.00 0.00 1.82
5194 5391 1.443194 GATGCAGCGCTGGTGTTTG 60.443 57.895 36.47 12.94 33.19 2.93
5195 5392 1.580845 GAGATGCAGCGCTGGTGTTT 61.581 55.000 36.47 5.64 33.19 2.83
5207 5404 3.333899 ATGCGCCCTGTGAGATGCA 62.334 57.895 4.18 0.00 36.69 3.96
5306 5503 0.179234 TTCAGCTCACGGGTTTCACA 59.821 50.000 0.00 0.00 0.00 3.58
5332 5533 1.484240 CTCCATGGTCCTCCTTCTCAC 59.516 57.143 12.58 0.00 34.23 3.51
5345 5546 1.001764 TTGTCTGGCTGCTCCATGG 60.002 57.895 4.97 4.97 45.50 3.66
5360 5561 0.319900 ACAGCGACATTCGAGCTTGT 60.320 50.000 0.00 0.00 43.74 3.16
5405 5606 1.717728 GCGAAACACAACGACAGCG 60.718 57.895 0.00 0.00 44.79 5.18
5573 5788 2.158769 TGAGCACAACACCAGACAAGAT 60.159 45.455 0.00 0.00 0.00 2.40
5574 5789 1.209261 TGAGCACAACACCAGACAAGA 59.791 47.619 0.00 0.00 0.00 3.02
5634 5853 1.409427 GGAACCCACAGATACTCCGAG 59.591 57.143 0.00 0.00 0.00 4.63
5646 5865 2.668550 GCCACGTCTGGAACCCAC 60.669 66.667 0.00 0.00 40.55 4.61
5647 5866 3.948719 GGCCACGTCTGGAACCCA 61.949 66.667 0.00 0.00 40.55 4.51
5682 5901 8.450578 TTCATGTTTATAGATGTAAAGCTGGG 57.549 34.615 0.00 0.00 0.00 4.45
5698 5917 6.602803 TGGAGATGCTTATGCTTTCATGTTTA 59.397 34.615 1.96 0.00 40.48 2.01
5702 5921 5.240844 TCATGGAGATGCTTATGCTTTCATG 59.759 40.000 1.96 8.20 40.48 3.07
5732 5951 2.787035 GGGTATTATTTCCCAGGGGTGA 59.213 50.000 5.33 0.00 42.95 4.02
5789 6008 8.890410 ACTGAGGGAGTACTAAATTTAGTGTA 57.110 34.615 31.97 16.50 43.44 2.90
5793 6012 6.383147 TGGGACTGAGGGAGTACTAAATTTAG 59.617 42.308 21.21 21.21 35.54 1.85
5796 6015 4.695606 TGGGACTGAGGGAGTACTAAATT 58.304 43.478 0.00 0.00 35.54 1.82
5797 6016 4.348020 TGGGACTGAGGGAGTACTAAAT 57.652 45.455 0.00 0.00 35.54 1.40
5798 6017 3.839323 TGGGACTGAGGGAGTACTAAA 57.161 47.619 0.00 0.00 35.54 1.85
5800 6019 5.681494 ATTATGGGACTGAGGGAGTACTA 57.319 43.478 0.00 0.00 35.54 1.82
5802 6021 7.894364 TCTTATATTATGGGACTGAGGGAGTAC 59.106 40.741 0.00 0.00 33.83 2.73
5803 6022 8.008104 TCTTATATTATGGGACTGAGGGAGTA 57.992 38.462 0.00 0.00 33.83 2.59
5807 6026 5.485353 TGCTCTTATATTATGGGACTGAGGG 59.515 44.000 0.00 0.00 0.00 4.30
5812 6031 8.099537 CAGTCAATGCTCTTATATTATGGGACT 58.900 37.037 0.00 0.00 0.00 3.85
5816 6035 8.837788 TGACAGTCAATGCTCTTATATTATGG 57.162 34.615 0.00 0.00 0.00 2.74
5832 6051 9.276590 CCATAATATAAGAGCATTGACAGTCAA 57.723 33.333 18.42 18.42 41.09 3.18
5835 6054 7.880195 GTCCCATAATATAAGAGCATTGACAGT 59.120 37.037 0.00 0.00 0.00 3.55
5836 6055 7.063898 CGTCCCATAATATAAGAGCATTGACAG 59.936 40.741 0.00 0.00 0.00 3.51
5837 6056 6.873605 CGTCCCATAATATAAGAGCATTGACA 59.126 38.462 0.00 0.00 0.00 3.58
5838 6057 6.313905 CCGTCCCATAATATAAGAGCATTGAC 59.686 42.308 0.00 0.00 0.00 3.18
5839 6058 6.212589 TCCGTCCCATAATATAAGAGCATTGA 59.787 38.462 0.00 0.00 0.00 2.57
5840 6059 6.406370 TCCGTCCCATAATATAAGAGCATTG 58.594 40.000 0.00 0.00 0.00 2.82
5898 6121 6.176183 AGTAAATGTGAATGGTCCTTCTCTG 58.824 40.000 0.00 0.00 0.00 3.35
5908 6131 9.865321 AATGAATGAGAAAGTAAATGTGAATGG 57.135 29.630 0.00 0.00 0.00 3.16
5935 6165 8.985315 AATGCTCCATTCTGTTCTAATGAATA 57.015 30.769 0.00 0.00 36.61 1.75
5936 6166 7.893124 AATGCTCCATTCTGTTCTAATGAAT 57.107 32.000 0.00 0.00 36.61 2.57
5937 6167 8.985315 ATAATGCTCCATTCTGTTCTAATGAA 57.015 30.769 0.00 0.00 36.61 2.57
5938 6168 8.985315 AATAATGCTCCATTCTGTTCTAATGA 57.015 30.769 0.00 0.00 36.61 2.57
5941 6171 9.547753 GAGTAATAATGCTCCATTCTGTTCTAA 57.452 33.333 0.00 0.00 35.54 2.10
6054 6299 7.238933 TCCCATCTAAACCTTTTTCCTCTCTAA 59.761 37.037 0.00 0.00 0.00 2.10
6055 6300 6.733807 TCCCATCTAAACCTTTTTCCTCTCTA 59.266 38.462 0.00 0.00 0.00 2.43
6061 6312 4.830600 TGTGTCCCATCTAAACCTTTTTCC 59.169 41.667 0.00 0.00 0.00 3.13
6063 6314 6.553100 TCATTGTGTCCCATCTAAACCTTTTT 59.447 34.615 0.00 0.00 0.00 1.94
6102 6354 5.392057 GGTGGCTTTCTCAATTACTAGTTGC 60.392 44.000 0.00 0.00 0.00 4.17
6107 6359 4.566907 GGGTGGTGGCTTTCTCAATTACTA 60.567 45.833 0.00 0.00 0.00 1.82
6108 6360 3.421844 GGTGGTGGCTTTCTCAATTACT 58.578 45.455 0.00 0.00 0.00 2.24
6109 6361 2.492088 GGGTGGTGGCTTTCTCAATTAC 59.508 50.000 0.00 0.00 0.00 1.89
6146 6399 7.063074 GGTGAATGCTCATGATCTTTTCTTTTG 59.937 37.037 0.00 0.00 33.05 2.44
6162 6426 1.078848 AGGCGACAGGTGAATGCTC 60.079 57.895 0.00 0.00 0.00 4.26
6192 6456 8.717821 CCAGATTAGACGAAATAAACAACAAGA 58.282 33.333 0.00 0.00 0.00 3.02
6193 6457 8.504005 ACCAGATTAGACGAAATAAACAACAAG 58.496 33.333 0.00 0.00 0.00 3.16
6194 6458 8.286800 CACCAGATTAGACGAAATAAACAACAA 58.713 33.333 0.00 0.00 0.00 2.83
6217 6481 2.029380 GGCAAGGTTGGAAATGTACACC 60.029 50.000 0.00 0.00 0.00 4.16
6235 6499 3.181451 GGGATATGAACTCTGTCATGGCA 60.181 47.826 0.00 0.00 38.69 4.92
6236 6500 3.072184 AGGGATATGAACTCTGTCATGGC 59.928 47.826 0.00 0.00 38.69 4.40
6238 6502 5.564455 CGAGAGGGATATGAACTCTGTCATG 60.564 48.000 0.00 0.00 41.38 3.07
6239 6503 4.522405 CGAGAGGGATATGAACTCTGTCAT 59.478 45.833 0.00 0.00 41.38 3.06
6240 6504 3.885901 CGAGAGGGATATGAACTCTGTCA 59.114 47.826 0.00 0.00 41.38 3.58
6241 6505 3.305064 GCGAGAGGGATATGAACTCTGTC 60.305 52.174 0.00 0.00 41.38 3.51
6242 6506 2.625790 GCGAGAGGGATATGAACTCTGT 59.374 50.000 0.00 0.00 41.38 3.41
6243 6507 2.890311 AGCGAGAGGGATATGAACTCTG 59.110 50.000 0.00 0.00 41.38 3.35
6244 6508 2.890311 CAGCGAGAGGGATATGAACTCT 59.110 50.000 0.00 0.00 43.81 3.24
6246 6510 2.625790 GACAGCGAGAGGGATATGAACT 59.374 50.000 0.00 0.00 0.00 3.01
6247 6511 2.288518 GGACAGCGAGAGGGATATGAAC 60.289 54.545 0.00 0.00 0.00 3.18
6248 6512 1.964223 GGACAGCGAGAGGGATATGAA 59.036 52.381 0.00 0.00 0.00 2.57
6249 6513 1.621992 GGACAGCGAGAGGGATATGA 58.378 55.000 0.00 0.00 0.00 2.15
6250 6514 0.605589 GGGACAGCGAGAGGGATATG 59.394 60.000 0.00 0.00 0.00 1.78
6251 6515 0.485099 AGGGACAGCGAGAGGGATAT 59.515 55.000 0.00 0.00 0.00 1.63
6252 6516 0.261991 AAGGGACAGCGAGAGGGATA 59.738 55.000 0.00 0.00 0.00 2.59
6278 6552 6.080648 TCTACGCGTATCAATAATTCCAGT 57.919 37.500 20.91 0.00 0.00 4.00
6279 6553 7.402811 TTTCTACGCGTATCAATAATTCCAG 57.597 36.000 20.91 4.87 0.00 3.86
6280 6554 7.870954 AGATTTCTACGCGTATCAATAATTCCA 59.129 33.333 20.91 0.00 0.00 3.53
6281 6555 8.240883 AGATTTCTACGCGTATCAATAATTCC 57.759 34.615 20.91 8.36 0.00 3.01


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

AutoCloner maintained by Alex Coulton.