Multiple sequence alignment - TraesCS5B01G469500

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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 TraesCS5B01G469500 chr5B 100.000 5386 0 0 1 5386 643166771 643172156 0.000000e+00 9947
1 TraesCS5B01G469500 chr5B 94.000 50 2 1 4841 4890 643171562 643171610 2.080000e-09 75
2 TraesCS5B01G469500 chr5B 94.000 50 2 1 4792 4840 643171611 643171660 2.080000e-09 75
3 TraesCS5B01G469500 chr5A 92.478 3124 128 42 911 3990 640600183 640603243 0.000000e+00 4368
4 TraesCS5B01G469500 chr5A 95.712 793 26 4 4053 4840 640603273 640604062 0.000000e+00 1269
5 TraesCS5B01G469500 chr5A 84.099 805 86 23 1 780 640598969 640599756 0.000000e+00 739
6 TraesCS5B01G469500 chr5A 83.063 555 50 22 4840 5386 640604013 640604531 1.060000e-126 464
7 TraesCS5B01G469500 chr5D 91.801 1732 83 30 1 1709 512199261 512200956 0.000000e+00 2357
8 TraesCS5B01G469500 chr5D 87.848 1399 97 30 1746 3101 512201116 512202484 0.000000e+00 1574
9 TraesCS5B01G469500 chr5D 95.839 793 24 6 4053 4840 512203419 512204207 0.000000e+00 1273
10 TraesCS5B01G469500 chr5D 83.971 418 29 20 3132 3517 512202569 512202980 3.070000e-97 366
11 TraesCS5B01G469500 chr5D 81.651 436 44 18 4840 5268 512204157 512204563 4.020000e-86 329
12 TraesCS5B01G469500 chr5D 94.690 113 4 2 4954 5064 56450152 56450264 1.990000e-39 174
13 TraesCS5B01G469500 chr1A 96.190 105 2 2 4959 5062 554280633 554280530 2.580000e-38 171
14 TraesCS5B01G469500 chr1A 96.190 105 2 2 4959 5062 554293060 554293163 2.580000e-38 171
15 TraesCS5B01G469500 chr6B 94.545 110 5 1 4954 5062 693317639 693317530 9.280000e-38 169
16 TraesCS5B01G469500 chr1B 96.154 104 2 2 4959 5061 637536974 637536872 9.280000e-38 169
17 TraesCS5B01G469500 chr6D 92.982 114 5 3 4954 5064 455911919 455911806 4.320000e-36 163
18 TraesCS5B01G469500 chr3A 94.393 107 4 2 4951 5055 744061689 744061795 4.320000e-36 163


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 TraesCS5B01G469500 chr5B 643166771 643172156 5385 False 3365.666667 9947 96.000 1 5386 3 chr5B.!!$F1 5385
1 TraesCS5B01G469500 chr5A 640598969 640604531 5562 False 1710.000000 4368 88.838 1 5386 4 chr5A.!!$F1 5385
2 TraesCS5B01G469500 chr5D 512199261 512204563 5302 False 1179.800000 2357 88.222 1 5268 5 chr5D.!!$F2 5267

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
435 452 0.169672 CGACCGACACCTACGACATT 59.830 55.000 0.0 0.0 0.00 2.71 F
1317 1673 0.316204 GCTTGCTGCTTGTGGTCATT 59.684 50.000 0.0 0.0 38.95 2.57 F
1602 1971 0.179092 CTCTGATGTCGCTGATGGCA 60.179 55.000 0.0 0.0 41.91 4.92 F
2659 3195 0.031994 GGCACAAACGAAATGCACCT 59.968 50.000 0.0 0.0 41.27 4.00 F
3437 4050 1.068250 GAGCATACCTGAGCCGTCC 59.932 63.158 0.0 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1461 1823 0.107831 GTAACCACCTGTGACCAGCA 59.892 55.0 0.00 0.00 37.38 4.41 R
2622 3158 0.390860 CCCCAATCAGCCTCGACTAG 59.609 60.0 0.00 0.00 0.00 2.57 R
2916 3456 0.978146 CGTTCTCCCATCCTCCCTGT 60.978 60.0 0.00 0.00 0.00 4.00 R
3702 4375 0.392327 CCACACACACACCTCACACA 60.392 55.0 0.00 0.00 0.00 3.72 R
5333 6046 0.034476 TGTCTTGAGCTCAGCCACTG 59.966 55.0 17.43 4.78 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
40 41 6.734104 TGCATGGCCATTAATTTTGTTAAC 57.266 33.333 17.92 0.00 0.00 2.01
96 97 2.372837 AGTTGGTAAGTAGCCGGGAAAA 59.627 45.455 2.18 0.00 0.00 2.29
98 99 3.724732 TGGTAAGTAGCCGGGAAAATT 57.275 42.857 2.18 0.00 0.00 1.82
103 104 6.060136 GGTAAGTAGCCGGGAAAATTCTAAT 58.940 40.000 2.18 0.00 0.00 1.73
134 136 0.751277 TGACACTTTGTGCACCCAGG 60.751 55.000 15.69 3.94 36.98 4.45
189 192 2.760634 TCGAAGCTTAGACCATTGCA 57.239 45.000 5.03 0.00 0.00 4.08
196 199 2.743183 GCTTAGACCATTGCATCCGACT 60.743 50.000 0.00 0.00 0.00 4.18
245 252 3.553828 TCGGTTCCATTATCAAGGGAC 57.446 47.619 0.00 0.00 41.77 4.46
303 310 7.440856 ACCCTATTTGCATAACAACAAAAAGTG 59.559 33.333 0.00 0.00 39.09 3.16
322 329 5.836024 AGTGAACCCCTAATTTACTCACA 57.164 39.130 0.00 0.00 35.32 3.58
323 330 6.195600 AGTGAACCCCTAATTTACTCACAA 57.804 37.500 0.00 0.00 35.32 3.33
327 334 3.591977 ACCCCTAATTTACTCACAAGCCT 59.408 43.478 0.00 0.00 0.00 4.58
334 341 2.654749 TACTCACAAGCCTCGTCATG 57.345 50.000 0.00 0.00 0.00 3.07
384 391 0.958091 CACCATTCTGCCGACCAAAA 59.042 50.000 0.00 0.00 0.00 2.44
426 443 2.019984 AGTTATACCTCGACCGACACC 58.980 52.381 0.00 0.00 0.00 4.16
428 445 3.118261 AGTTATACCTCGACCGACACCTA 60.118 47.826 0.00 0.00 0.00 3.08
433 450 1.293963 CTCGACCGACACCTACGACA 61.294 60.000 0.00 0.00 0.00 4.35
435 452 0.169672 CGACCGACACCTACGACATT 59.830 55.000 0.00 0.00 0.00 2.71
515 532 3.069443 CCAAGACCAAGGCTAAAGCAAAA 59.931 43.478 4.07 0.00 44.36 2.44
600 626 6.765989 GGATAAAACAAACCAAAAGCTTTCCT 59.234 34.615 13.10 0.00 0.00 3.36
603 629 7.987750 AAAACAAACCAAAAGCTTTCCTTTA 57.012 28.000 13.10 0.00 42.82 1.85
632 666 6.867519 AGAAAAGGAGAAGAAACCCAAAAA 57.132 33.333 0.00 0.00 0.00 1.94
665 702 4.641645 CCAAGCCAGCACGACCCA 62.642 66.667 0.00 0.00 0.00 4.51
694 731 4.877619 TGCGCCCGACCCAAAACA 62.878 61.111 4.18 0.00 0.00 2.83
1228 1583 1.672363 CGTATGTGATGCTGGCATTGT 59.328 47.619 9.52 0.12 36.70 2.71
1271 1626 4.389576 GCTGGAGTTTGCGCCGTG 62.390 66.667 4.18 0.00 37.39 4.94
1317 1673 0.316204 GCTTGCTGCTTGTGGTCATT 59.684 50.000 0.00 0.00 38.95 2.57
1318 1674 1.541147 GCTTGCTGCTTGTGGTCATTA 59.459 47.619 0.00 0.00 38.95 1.90
1491 1860 4.020543 ACAGGTGGTTACAACACACAAAT 58.979 39.130 12.59 0.94 40.54 2.32
1602 1971 0.179092 CTCTGATGTCGCTGATGGCA 60.179 55.000 0.00 0.00 41.91 4.92
1620 1989 7.147312 TGATGGCAAAGTTTTGATGACTTTAG 58.853 34.615 8.70 0.00 43.44 1.85
1621 1990 6.463995 TGGCAAAGTTTTGATGACTTTAGT 57.536 33.333 8.70 0.00 43.44 2.24
1652 2021 2.490509 TCTGATGCACATGCCTTTCAAG 59.509 45.455 0.49 0.00 41.18 3.02
1679 2048 9.168451 TCATTATGCGAAGTTTGTAAGGAATAA 57.832 29.630 0.00 0.00 0.00 1.40
1709 2078 5.511234 AACTGGCATCTGAAATATGAAGC 57.489 39.130 0.00 0.00 0.00 3.86
1718 2218 9.343103 GCATCTGAAATATGAAGCTATCATTTG 57.657 33.333 14.02 0.00 46.85 2.32
1743 2243 6.161855 TGGCAATACTACTTGGATGTAGAG 57.838 41.667 8.43 0.00 41.63 2.43
1744 2244 5.661312 TGGCAATACTACTTGGATGTAGAGT 59.339 40.000 8.43 0.00 41.63 3.24
1745 2245 6.156256 TGGCAATACTACTTGGATGTAGAGTT 59.844 38.462 8.43 1.22 41.63 3.01
1746 2246 6.480320 GGCAATACTACTTGGATGTAGAGTTG 59.520 42.308 8.43 11.61 41.63 3.16
1747 2247 7.042335 GCAATACTACTTGGATGTAGAGTTGT 58.958 38.462 8.43 0.00 41.63 3.32
1748 2248 8.195436 GCAATACTACTTGGATGTAGAGTTGTA 58.805 37.037 8.43 0.00 41.63 2.41
1749 2249 9.737427 CAATACTACTTGGATGTAGAGTTGTAG 57.263 37.037 8.43 0.00 41.63 2.74
1750 2250 9.696572 AATACTACTTGGATGTAGAGTTGTAGA 57.303 33.333 8.43 0.00 41.63 2.59
1767 2267 3.192001 TGTAGACCGCGTTTAGACATTCT 59.808 43.478 4.92 0.00 0.00 2.40
1917 2418 5.009410 GGAAAGCACCTTCCATGAATATGAG 59.991 44.000 0.00 0.00 43.84 2.90
2066 2575 8.827832 ATTTCTTTTGGTGATTCCTATGATGA 57.172 30.769 0.00 0.00 37.07 2.92
2067 2576 7.870509 TTCTTTTGGTGATTCCTATGATGAG 57.129 36.000 0.00 0.00 37.07 2.90
2068 2577 7.199167 TCTTTTGGTGATTCCTATGATGAGA 57.801 36.000 0.00 0.00 37.07 3.27
2069 2578 7.278135 TCTTTTGGTGATTCCTATGATGAGAG 58.722 38.462 0.00 0.00 37.07 3.20
2070 2579 6.566079 TTTGGTGATTCCTATGATGAGAGT 57.434 37.500 0.00 0.00 37.07 3.24
2128 2637 2.789409 ATCTTTGTAGACTGTGGGGC 57.211 50.000 0.00 0.00 31.99 5.80
2580 3116 4.141981 TGGTCATGCAACAAAGTTGTCAAT 60.142 37.500 11.09 1.62 41.31 2.57
2581 3117 4.445385 GGTCATGCAACAAAGTTGTCAATC 59.555 41.667 11.09 5.53 41.31 2.67
2582 3118 5.042593 GTCATGCAACAAAGTTGTCAATCA 58.957 37.500 11.09 1.59 41.31 2.57
2583 3119 5.693104 GTCATGCAACAAAGTTGTCAATCAT 59.307 36.000 11.09 3.64 41.31 2.45
2584 3120 5.692654 TCATGCAACAAAGTTGTCAATCATG 59.307 36.000 15.22 15.22 41.31 3.07
2654 3190 2.288702 TGATTGGGGCACAAACGAAATG 60.289 45.455 6.13 0.00 43.46 2.32
2659 3195 0.031994 GGCACAAACGAAATGCACCT 59.968 50.000 0.00 0.00 41.27 4.00
2730 3266 9.294030 GTAATGAATTTCTCTGCAAGTTTATGG 57.706 33.333 0.00 0.00 33.76 2.74
2841 3379 8.686334 AGTGTATTTTCTCTTTCATTGTGTGTT 58.314 29.630 0.00 0.00 0.00 3.32
2916 3456 6.832520 TTGTTATTTTGCTGCTTCCTATCA 57.167 33.333 0.00 0.00 0.00 2.15
3101 3649 4.535526 TGTATGCTACAAGCTGAGACAA 57.464 40.909 0.03 0.00 42.97 3.18
3268 3880 2.472695 TAGTGGCATCCAGTTGTGAC 57.527 50.000 0.00 0.00 38.30 3.67
3306 3918 5.293560 GCTAGTTATCTCACTGCTTTAGGG 58.706 45.833 0.00 0.00 0.00 3.53
3360 3972 3.568430 GGTTTATATGCTTTTCCCCCTCG 59.432 47.826 0.00 0.00 0.00 4.63
3437 4050 1.068250 GAGCATACCTGAGCCGTCC 59.932 63.158 0.00 0.00 0.00 4.79
3480 4114 4.604843 TTGTATACCGTACTCACAGACG 57.395 45.455 0.00 0.00 38.79 4.18
3567 4240 6.687105 GCTCTTTGTAAATTAACATACTGGCG 59.313 38.462 2.30 0.00 0.00 5.69
3660 4333 5.804692 TTAGTTCACACTTTGCTCGAAAA 57.195 34.783 0.00 0.00 34.06 2.29
3696 4369 3.947196 ACATTTCAGATGTGTGTGTGTGT 59.053 39.130 0.00 0.00 0.00 3.72
3698 4371 1.298602 TCAGATGTGTGTGTGTGTGC 58.701 50.000 0.00 0.00 0.00 4.57
3700 4373 1.369209 GATGTGTGTGTGTGTGCGC 60.369 57.895 0.00 0.00 0.00 6.09
3702 4375 3.860125 GTGTGTGTGTGTGCGCGT 61.860 61.111 8.43 0.00 0.00 6.01
3708 4381 3.559344 GTGTGTGCGCGTGTGTGA 61.559 61.111 8.43 0.00 0.00 3.58
3710 4383 4.000557 GTGTGCGCGTGTGTGAGG 62.001 66.667 8.43 0.00 0.00 3.86
3711 4384 4.522689 TGTGCGCGTGTGTGAGGT 62.523 61.111 8.43 0.00 0.00 3.85
3712 4385 4.000557 GTGCGCGTGTGTGAGGTG 62.001 66.667 8.43 0.00 0.00 4.00
3713 4386 4.522689 TGCGCGTGTGTGAGGTGT 62.523 61.111 8.43 0.00 0.00 4.16
3714 4387 4.000557 GCGCGTGTGTGAGGTGTG 62.001 66.667 8.43 0.00 0.00 3.82
3715 4388 2.584970 CGCGTGTGTGAGGTGTGT 60.585 61.111 0.00 0.00 0.00 3.72
3716 4389 2.870341 CGCGTGTGTGAGGTGTGTG 61.870 63.158 0.00 0.00 0.00 3.82
3717 4390 1.813753 GCGTGTGTGAGGTGTGTGT 60.814 57.895 0.00 0.00 0.00 3.72
3718 4391 2.005995 CGTGTGTGAGGTGTGTGTG 58.994 57.895 0.00 0.00 0.00 3.82
3719 4392 0.739462 CGTGTGTGAGGTGTGTGTGT 60.739 55.000 0.00 0.00 0.00 3.72
3720 4393 0.726827 GTGTGTGAGGTGTGTGTGTG 59.273 55.000 0.00 0.00 0.00 3.82
3784 4457 3.708403 TGACCAGCATCAGTGAAGAAT 57.292 42.857 0.00 0.00 0.00 2.40
3891 4582 6.273730 TCATAAGGGTTAGAACCTTTTCTGGA 59.726 38.462 13.34 4.98 44.92 3.86
3893 4584 5.965486 AAGGGTTAGAACCTTTTCTGGAAT 58.035 37.500 11.16 0.00 44.92 3.01
3942 4633 9.190317 GATATTAAACCTGTTTCCATCTTTCCT 57.810 33.333 0.00 0.00 34.23 3.36
3984 4676 5.305139 TGCAAGATCATTCATGAACTGTG 57.695 39.130 11.07 5.72 38.73 3.66
3990 4682 6.111382 AGATCATTCATGAACTGTGTACTGG 58.889 40.000 11.07 0.00 38.32 4.00
3992 4684 5.863965 TCATTCATGAACTGTGTACTGGAA 58.136 37.500 11.07 0.00 33.08 3.53
3993 4685 6.475504 TCATTCATGAACTGTGTACTGGAAT 58.524 36.000 11.07 0.00 33.08 3.01
3995 4687 7.549134 TCATTCATGAACTGTGTACTGGAATAC 59.451 37.037 11.07 0.00 33.08 1.89
3998 4690 8.306313 TCATGAACTGTGTACTGGAATACTAT 57.694 34.615 0.00 0.00 0.00 2.12
3999 4691 9.416284 TCATGAACTGTGTACTGGAATACTATA 57.584 33.333 0.00 0.00 0.00 1.31
4000 4692 9.464714 CATGAACTGTGTACTGGAATACTATAC 57.535 37.037 0.00 0.00 0.00 1.47
4003 4695 7.024340 ACTGTGTACTGGAATACTATACGTG 57.976 40.000 0.00 0.00 0.00 4.49
4004 4696 6.825213 ACTGTGTACTGGAATACTATACGTGA 59.175 38.462 0.00 0.00 0.00 4.35
4005 4697 7.501559 ACTGTGTACTGGAATACTATACGTGAT 59.498 37.037 0.00 0.00 0.00 3.06
4006 4698 8.229253 TGTGTACTGGAATACTATACGTGATT 57.771 34.615 0.00 0.00 0.00 2.57
4007 4699 9.341078 TGTGTACTGGAATACTATACGTGATTA 57.659 33.333 0.00 0.00 0.00 1.75
4008 4700 9.823098 GTGTACTGGAATACTATACGTGATTAG 57.177 37.037 0.00 0.00 0.00 1.73
4011 4703 7.948357 ACTGGAATACTATACGTGATTAGCAA 58.052 34.615 0.00 0.00 0.00 3.91
4012 4704 8.082852 ACTGGAATACTATACGTGATTAGCAAG 58.917 37.037 0.00 0.00 0.00 4.01
4013 4705 8.173542 TGGAATACTATACGTGATTAGCAAGA 57.826 34.615 0.00 0.00 0.00 3.02
4014 4706 8.803235 TGGAATACTATACGTGATTAGCAAGAT 58.197 33.333 0.00 0.00 0.00 2.40
4015 4707 9.291664 GGAATACTATACGTGATTAGCAAGATC 57.708 37.037 0.00 0.00 0.00 2.75
4016 4708 9.841880 GAATACTATACGTGATTAGCAAGATCA 57.158 33.333 0.00 0.00 0.00 2.92
4023 4715 7.849804 ACGTGATTAGCAAGATCATTTAACT 57.150 32.000 0.00 0.00 36.07 2.24
4024 4716 8.268850 ACGTGATTAGCAAGATCATTTAACTT 57.731 30.769 0.00 0.00 36.07 2.66
4025 4717 8.177663 ACGTGATTAGCAAGATCATTTAACTTG 58.822 33.333 0.00 0.00 42.33 3.16
4035 4727 9.582431 CAAGATCATTTAACTTGCAAGATCATT 57.418 29.630 32.50 18.02 35.43 2.57
4036 4728 9.798994 AAGATCATTTAACTTGCAAGATCATTC 57.201 29.630 32.50 16.43 34.40 2.67
4037 4729 8.963725 AGATCATTTAACTTGCAAGATCATTCA 58.036 29.630 32.50 11.49 34.40 2.57
4038 4730 9.745880 GATCATTTAACTTGCAAGATCATTCAT 57.254 29.630 32.50 15.45 32.74 2.57
4039 4731 8.920509 TCATTTAACTTGCAAGATCATTCATG 57.079 30.769 32.50 20.73 0.00 3.07
4040 4732 8.741841 TCATTTAACTTGCAAGATCATTCATGA 58.258 29.630 32.50 22.29 41.70 3.07
4045 4737 7.876936 ACTTGCAAGATCATTCATGATTACT 57.123 32.000 32.50 0.70 46.84 2.24
4046 4738 8.969260 ACTTGCAAGATCATTCATGATTACTA 57.031 30.769 32.50 0.00 46.84 1.82
4047 4739 9.570468 ACTTGCAAGATCATTCATGATTACTAT 57.430 29.630 32.50 0.00 46.84 2.12
4050 4742 9.440773 TGCAAGATCATTCATGATTACTATACC 57.559 33.333 3.78 0.00 46.84 2.73
4051 4743 9.440773 GCAAGATCATTCATGATTACTATACCA 57.559 33.333 3.78 0.00 46.84 3.25
4081 4775 0.709992 ATGCCCCCATTGTACTTGGT 59.290 50.000 12.56 0.00 31.99 3.67
4292 4987 0.249699 AAGCCACGTCACAATGTCGA 60.250 50.000 1.48 0.00 33.41 4.20
4331 5026 1.294780 CTTGCTGACGGGCTTCTCT 59.705 57.895 0.00 0.00 0.00 3.10
4418 5113 0.108089 TCCTCCTCTGTCGTCTCTCG 60.108 60.000 0.00 0.00 41.41 4.04
4447 5142 0.539518 GCCTTCTCCTCTGTTCTCCC 59.460 60.000 0.00 0.00 0.00 4.30
4616 5311 5.803020 ATTTTAAGTGTCTGATTCTCGCC 57.197 39.130 0.00 0.00 0.00 5.54
4671 5366 4.952262 TTGATTTCTTGCTCCTGATTCG 57.048 40.909 0.00 0.00 0.00 3.34
4757 5453 2.063979 CCGGTGCCTCTGGATACCA 61.064 63.158 0.00 0.00 45.09 3.25
4790 5489 8.889000 CAACTGTATTTTAAGCAGTAAAACGAC 58.111 33.333 7.31 8.88 42.94 4.34
4809 5508 9.880157 AAAACGACTTAGCTGGAAGTATATAAA 57.120 29.630 1.81 0.00 39.79 1.40
4829 5529 2.175878 ACACTGGCTCATGAAGTGAC 57.824 50.000 25.66 6.22 43.22 3.67
4834 5534 2.164422 CTGGCTCATGAAGTGACGAGTA 59.836 50.000 0.00 0.00 32.22 2.59
4835 5535 2.164422 TGGCTCATGAAGTGACGAGTAG 59.836 50.000 0.00 0.00 32.22 2.57
4836 5536 2.164624 GGCTCATGAAGTGACGAGTAGT 59.835 50.000 0.00 0.00 32.22 2.73
4848 5548 4.698583 GACGAGTAGTCTTTTAGCTGGA 57.301 45.455 0.00 0.00 46.13 3.86
4849 5549 5.056894 GACGAGTAGTCTTTTAGCTGGAA 57.943 43.478 0.00 0.00 46.13 3.53
4850 5550 5.061920 ACGAGTAGTCTTTTAGCTGGAAG 57.938 43.478 0.00 0.00 0.00 3.46
4851 5551 4.523558 ACGAGTAGTCTTTTAGCTGGAAGT 59.476 41.667 0.00 0.00 35.30 3.01
4852 5552 5.709164 ACGAGTAGTCTTTTAGCTGGAAGTA 59.291 40.000 0.00 0.00 35.30 2.24
4853 5553 6.377712 ACGAGTAGTCTTTTAGCTGGAAGTAT 59.622 38.462 0.00 0.00 35.30 2.12
4854 5554 7.555554 ACGAGTAGTCTTTTAGCTGGAAGTATA 59.444 37.037 0.00 0.00 35.30 1.47
4855 5555 8.569641 CGAGTAGTCTTTTAGCTGGAAGTATAT 58.430 37.037 0.00 0.00 35.30 0.86
4865 5565 8.958119 TTAGCTGGAAGTATATAAAACACTGG 57.042 34.615 0.00 0.00 35.30 4.00
4866 5566 5.823045 AGCTGGAAGTATATAAAACACTGGC 59.177 40.000 0.00 0.00 35.30 4.85
4867 5567 5.823045 GCTGGAAGTATATAAAACACTGGCT 59.177 40.000 0.00 0.00 35.30 4.75
4868 5568 6.017852 GCTGGAAGTATATAAAACACTGGCTC 60.018 42.308 0.00 0.00 35.30 4.70
4869 5569 6.953101 TGGAAGTATATAAAACACTGGCTCA 58.047 36.000 0.00 0.00 0.00 4.26
4870 5570 7.573710 TGGAAGTATATAAAACACTGGCTCAT 58.426 34.615 0.00 0.00 0.00 2.90
4871 5571 7.498900 TGGAAGTATATAAAACACTGGCTCATG 59.501 37.037 0.00 0.00 0.00 3.07
4872 5572 7.715249 GGAAGTATATAAAACACTGGCTCATGA 59.285 37.037 0.00 0.00 0.00 3.07
4873 5573 9.109393 GAAGTATATAAAACACTGGCTCATGAA 57.891 33.333 0.00 0.00 0.00 2.57
4874 5574 8.668510 AGTATATAAAACACTGGCTCATGAAG 57.331 34.615 0.00 0.00 0.00 3.02
4875 5575 8.267894 AGTATATAAAACACTGGCTCATGAAGT 58.732 33.333 0.00 0.00 0.00 3.01
4876 5576 3.996150 AAAACACTGGCTCATGAAGTG 57.004 42.857 19.81 19.81 45.46 3.16
4877 5577 2.936919 AACACTGGCTCATGAAGTGA 57.063 45.000 25.66 0.00 43.22 3.41
4878 5578 3.430042 AACACTGGCTCATGAAGTGAT 57.570 42.857 25.66 15.34 43.22 3.06
4879 5579 2.983229 ACACTGGCTCATGAAGTGATC 58.017 47.619 25.66 2.40 43.22 2.92
4880 5580 2.303890 ACACTGGCTCATGAAGTGATCA 59.696 45.455 25.66 0.00 43.22 2.92
4881 5581 2.937149 CACTGGCTCATGAAGTGATCAG 59.063 50.000 17.54 10.96 43.22 2.90
4882 5582 2.570752 ACTGGCTCATGAAGTGATCAGT 59.429 45.455 0.00 0.00 42.53 3.41
4883 5583 3.771479 ACTGGCTCATGAAGTGATCAGTA 59.229 43.478 2.79 0.00 43.33 2.74
4890 5590 6.035866 GCTCATGAAGTGATCAGTAAGTCTTG 59.964 42.308 2.79 6.83 42.53 3.02
4953 5656 5.897050 ACAAGAAAAAGAAATTACACGGCA 58.103 33.333 0.00 0.00 0.00 5.69
4954 5657 6.334202 ACAAGAAAAAGAAATTACACGGCAA 58.666 32.000 0.00 0.00 0.00 4.52
4955 5658 6.814146 ACAAGAAAAAGAAATTACACGGCAAA 59.186 30.769 0.00 0.00 0.00 3.68
4956 5659 7.494298 ACAAGAAAAAGAAATTACACGGCAAAT 59.506 29.630 0.00 0.00 0.00 2.32
4957 5660 8.334632 CAAGAAAAAGAAATTACACGGCAAATT 58.665 29.630 0.00 0.00 0.00 1.82
4958 5661 9.535878 AAGAAAAAGAAATTACACGGCAAATTA 57.464 25.926 0.00 0.00 0.00 1.40
5057 5763 4.966787 GCGCCACCACCCCTTTGA 62.967 66.667 0.00 0.00 0.00 2.69
5062 5768 1.256812 CCACCACCCCTTTGATGTTC 58.743 55.000 0.00 0.00 0.00 3.18
5066 5772 3.758554 CACCACCCCTTTGATGTTCTAAG 59.241 47.826 0.00 0.00 0.00 2.18
5074 5780 7.995488 ACCCCTTTGATGTTCTAAGAGATATTG 59.005 37.037 1.14 0.00 32.27 1.90
5075 5781 7.995488 CCCCTTTGATGTTCTAAGAGATATTGT 59.005 37.037 1.14 0.00 32.27 2.71
5097 5807 7.669438 TGTAAACTAATTATGACGAGCGTAC 57.331 36.000 0.00 0.00 0.00 3.67
5120 5830 9.509855 GTACTGTGATCTGTAGACTATTTTCAG 57.490 37.037 0.00 0.00 0.00 3.02
5140 5850 4.811024 TCAGCCTAAAACTCGCATCTATTG 59.189 41.667 0.00 0.00 0.00 1.90
5173 5883 6.723131 GGGGACGCATCTAGTATTTTAATC 57.277 41.667 0.00 0.00 0.00 1.75
5213 5926 8.630054 GATCAAGAGATCCTACAGTATACAGT 57.370 38.462 5.50 5.86 43.97 3.55
5254 5967 8.357402 ACTGGACATAAAAATGAACCTAAACAC 58.643 33.333 0.00 0.00 0.00 3.32
5267 5980 8.603898 TGAACCTAAACACAGAGGAGATTATA 57.396 34.615 0.00 0.00 36.61 0.98
5268 5981 9.213777 TGAACCTAAACACAGAGGAGATTATAT 57.786 33.333 0.00 0.00 36.61 0.86
5295 6008 8.574251 TTAAAATTCTTACTGAAGCCATAGCA 57.426 30.769 0.00 0.00 43.56 3.49
5299 6012 5.165961 TCTTACTGAAGCCATAGCAAACT 57.834 39.130 0.00 0.00 43.56 2.66
5314 6027 2.221055 GCAAACTCGTCATCGTTTCACT 59.779 45.455 0.00 0.00 38.33 3.41
5322 6035 3.486108 CGTCATCGTTTCACTACCATAGC 59.514 47.826 0.00 0.00 0.00 2.97
5332 6045 4.290093 TCACTACCATAGCTCTCACCAAT 58.710 43.478 0.00 0.00 0.00 3.16
5333 6046 4.342378 TCACTACCATAGCTCTCACCAATC 59.658 45.833 0.00 0.00 0.00 2.67
5334 6047 4.100035 CACTACCATAGCTCTCACCAATCA 59.900 45.833 0.00 0.00 0.00 2.57
5335 6048 3.834489 ACCATAGCTCTCACCAATCAG 57.166 47.619 0.00 0.00 0.00 2.90
5336 6049 3.110705 ACCATAGCTCTCACCAATCAGT 58.889 45.455 0.00 0.00 0.00 3.41
5337 6050 3.118482 ACCATAGCTCTCACCAATCAGTG 60.118 47.826 0.00 0.00 39.20 3.66
5356 6069 1.072806 TGGCTGAGCTCAAGACAATGT 59.927 47.619 18.85 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 104 6.934083 TGCACAAAGTGTCAGAGTTCATAATA 59.066 34.615 0.00 0.00 35.75 0.98
114 115 0.664761 CTGGGTGCACAAAGTGTCAG 59.335 55.000 20.43 9.69 35.75 3.51
134 136 1.066430 TGGCGGACTCAGGTTTATCAC 60.066 52.381 0.00 0.00 0.00 3.06
211 218 7.452880 AATGGAACCGATATAATGTTGGATG 57.547 36.000 0.00 0.00 0.00 3.51
221 228 6.499000 TGTCCCTTGATAATGGAACCGATATA 59.501 38.462 0.00 0.00 0.00 0.86
222 229 5.309543 TGTCCCTTGATAATGGAACCGATAT 59.690 40.000 0.00 0.00 0.00 1.63
270 277 5.754782 TGTTATGCAAATAGGGTCAGATGT 58.245 37.500 0.00 0.00 0.00 3.06
272 279 6.186957 TGTTGTTATGCAAATAGGGTCAGAT 58.813 36.000 0.00 0.00 39.03 2.90
275 282 6.656632 TTTGTTGTTATGCAAATAGGGTCA 57.343 33.333 0.00 0.00 39.03 4.02
303 310 4.398358 GGCTTGTGAGTAAATTAGGGGTTC 59.602 45.833 0.00 0.00 0.00 3.62
334 341 1.092348 GGGTGTTCTATTTGCCGTCC 58.908 55.000 0.00 0.00 0.00 4.79
384 391 4.199432 TGCCTCACATGTTTTGTTTTGT 57.801 36.364 0.00 0.00 36.00 2.83
419 436 1.201647 AGTCAATGTCGTAGGTGTCGG 59.798 52.381 0.00 0.00 0.00 4.79
426 443 9.653067 CTCTTACTTATACAGTCAATGTCGTAG 57.347 37.037 0.00 0.00 42.70 3.51
428 445 6.973474 GCTCTTACTTATACAGTCAATGTCGT 59.027 38.462 0.00 0.00 42.70 4.34
433 450 8.540388 TGGAAAGCTCTTACTTATACAGTCAAT 58.460 33.333 0.00 0.00 36.88 2.57
435 452 7.476540 TGGAAAGCTCTTACTTATACAGTCA 57.523 36.000 0.00 0.00 36.88 3.41
520 537 9.616156 TGTTGTTTTTATTCTGACCTTGTACTA 57.384 29.630 0.00 0.00 0.00 1.82
545 566 6.176183 TGGGTGCATTATTTGGGTTTTTATG 58.824 36.000 0.00 0.00 0.00 1.90
548 569 4.713792 TGGGTGCATTATTTGGGTTTTT 57.286 36.364 0.00 0.00 0.00 1.94
603 629 6.611236 TGGGTTTCTTCTCCTTTTCTTTTCAT 59.389 34.615 0.00 0.00 0.00 2.57
632 666 2.439156 GGCCGGCTGCTGAGATTT 60.439 61.111 28.56 0.00 40.92 2.17
684 721 1.679153 TCTCGGCTTTTGTTTTGGGTC 59.321 47.619 0.00 0.00 0.00 4.46
1228 1583 1.107114 AACGCCCACACACATCAAAA 58.893 45.000 0.00 0.00 0.00 2.44
1317 1673 4.399764 CCCTGGATGGCAGACCTA 57.600 61.111 13.25 1.84 36.63 3.08
1399 1759 5.798434 CGGTAATATTTGTCGCTATCATCGA 59.202 40.000 0.00 0.00 0.00 3.59
1461 1823 0.107831 GTAACCACCTGTGACCAGCA 59.892 55.000 0.00 0.00 37.38 4.41
1491 1860 5.762179 AACACCTGGATTATGAAGAGTGA 57.238 39.130 0.00 0.00 0.00 3.41
1602 1971 8.770438 TTGCAAACTAAAGTCATCAAAACTTT 57.230 26.923 0.00 6.50 46.04 2.66
1620 1989 5.276678 GCATGTGCATCAGATATTTGCAAAC 60.277 40.000 15.41 1.67 46.91 2.93
1621 1990 4.806775 GCATGTGCATCAGATATTTGCAAA 59.193 37.500 15.44 15.44 46.91 3.68
1630 1999 2.730382 TGAAAGGCATGTGCATCAGAT 58.270 42.857 7.36 0.00 44.36 2.90
1652 2021 6.417191 TCCTTACAAACTTCGCATAATGAC 57.583 37.500 0.00 0.00 0.00 3.06
1679 2048 3.354948 TCAGATGCCAGTTATTGCTGT 57.645 42.857 0.00 0.00 34.84 4.40
1709 2078 8.131100 CCAAGTAGTATTGCCAACAAATGATAG 58.869 37.037 0.00 0.00 39.77 2.08
1718 2218 6.346096 TCTACATCCAAGTAGTATTGCCAAC 58.654 40.000 0.00 0.00 41.68 3.77
1743 2243 2.664916 TGTCTAAACGCGGTCTACAAC 58.335 47.619 12.47 0.00 0.00 3.32
1744 2244 3.581024 ATGTCTAAACGCGGTCTACAA 57.419 42.857 12.47 0.00 0.00 2.41
1745 2245 3.192001 AGAATGTCTAAACGCGGTCTACA 59.808 43.478 12.47 10.00 0.00 2.74
1746 2246 3.546670 CAGAATGTCTAAACGCGGTCTAC 59.453 47.826 12.47 3.53 0.00 2.59
1747 2247 3.441222 TCAGAATGTCTAAACGCGGTCTA 59.559 43.478 12.47 0.00 37.40 2.59
1748 2248 2.230508 TCAGAATGTCTAAACGCGGTCT 59.769 45.455 12.47 0.00 37.40 3.85
1749 2249 2.344741 GTCAGAATGTCTAAACGCGGTC 59.655 50.000 12.47 0.00 37.40 4.79
1750 2250 2.334838 GTCAGAATGTCTAAACGCGGT 58.665 47.619 12.47 0.00 37.40 5.68
1767 2267 4.640771 AGCCTTAAGAAGTCAATGGTCA 57.359 40.909 3.36 0.00 0.00 4.02
2060 2569 7.070946 AGGAACAATGTCTCATACTCTCATCAT 59.929 37.037 0.00 0.00 0.00 2.45
2063 2572 6.610830 AGAGGAACAATGTCTCATACTCTCAT 59.389 38.462 5.14 0.00 0.00 2.90
2064 2573 5.954752 AGAGGAACAATGTCTCATACTCTCA 59.045 40.000 5.14 0.00 0.00 3.27
2065 2574 6.463995 AGAGGAACAATGTCTCATACTCTC 57.536 41.667 5.14 0.00 0.00 3.20
2066 2575 6.865834 AAGAGGAACAATGTCTCATACTCT 57.134 37.500 5.14 0.00 34.54 3.24
2067 2576 9.092876 CTTAAAGAGGAACAATGTCTCATACTC 57.907 37.037 5.14 0.00 0.00 2.59
2068 2577 7.550906 GCTTAAAGAGGAACAATGTCTCATACT 59.449 37.037 5.14 0.00 0.00 2.12
2069 2578 7.334421 TGCTTAAAGAGGAACAATGTCTCATAC 59.666 37.037 5.14 0.00 0.00 2.39
2070 2579 7.394016 TGCTTAAAGAGGAACAATGTCTCATA 58.606 34.615 5.14 0.00 0.00 2.15
2118 2627 2.488153 GTGAATGTTAAGCCCCACAGTC 59.512 50.000 1.40 1.40 38.26 3.51
2128 2637 6.774354 AAGCAGCAAAATGTGAATGTTAAG 57.226 33.333 0.00 0.00 0.00 1.85
2331 2840 7.881142 TGTTCCAAAACAACTTGGTATGATAG 58.119 34.615 2.48 0.00 45.29 2.08
2435 2950 4.934001 GTGCATCTCAATTTGTCTCAGAGA 59.066 41.667 0.00 0.00 39.41 3.10
2527 3063 2.655407 TGGCCATTCCCTTTAACCCTTA 59.345 45.455 0.00 0.00 0.00 2.69
2580 3116 3.091545 GGGCTTTCTTTGGATGACATGA 58.908 45.455 0.00 0.00 0.00 3.07
2581 3117 2.827322 TGGGCTTTCTTTGGATGACATG 59.173 45.455 0.00 0.00 0.00 3.21
2582 3118 3.173953 TGGGCTTTCTTTGGATGACAT 57.826 42.857 0.00 0.00 0.00 3.06
2583 3119 2.673775 TGGGCTTTCTTTGGATGACA 57.326 45.000 0.00 0.00 0.00 3.58
2584 3120 4.706962 ACTATTGGGCTTTCTTTGGATGAC 59.293 41.667 0.00 0.00 0.00 3.06
2622 3158 0.390860 CCCCAATCAGCCTCGACTAG 59.609 60.000 0.00 0.00 0.00 2.57
2654 3190 6.029607 CACATGTATGTTAATGTTCAGGTGC 58.970 40.000 0.00 0.00 39.39 5.01
2659 3195 8.560355 AGTAAGCACATGTATGTTAATGTTCA 57.440 30.769 0.00 0.00 39.39 3.18
2695 3231 8.077991 TGCAGAGAAATTCATTACAAGACAAAG 58.922 33.333 0.00 0.00 0.00 2.77
2756 3292 5.245301 TCTGATCGGACTTCCTTCTGTAAAA 59.755 40.000 0.00 0.00 0.00 1.52
2825 3363 9.897744 ACAATACAATAACACACAATGAAAGAG 57.102 29.630 0.00 0.00 0.00 2.85
2916 3456 0.978146 CGTTCTCCCATCCTCCCTGT 60.978 60.000 0.00 0.00 0.00 4.00
3152 3757 4.393062 CACTGGCAGTTTAGTACAATCAGG 59.607 45.833 19.43 0.00 0.00 3.86
3294 3906 1.815003 CTTTCAGGCCCTAAAGCAGTG 59.185 52.381 12.97 0.00 0.00 3.66
3306 3918 1.540580 GGTACGGGATAGCTTTCAGGC 60.541 57.143 6.50 0.00 0.00 4.85
3360 3972 7.823799 ACCAATACATGAAATTTGATGGGTTTC 59.176 33.333 19.75 0.00 33.58 2.78
3437 4050 2.825861 ATGCAGCAGGAAAAAGTTGG 57.174 45.000 0.00 0.00 0.00 3.77
3687 4360 3.860125 ACACGCGCACACACACAC 61.860 61.111 5.73 0.00 0.00 3.82
3696 4369 4.522689 ACACCTCACACACGCGCA 62.523 61.111 5.73 0.00 0.00 6.09
3698 4371 2.584970 ACACACCTCACACACGCG 60.585 61.111 3.53 3.53 0.00 6.01
3700 4373 0.739462 ACACACACACCTCACACACG 60.739 55.000 0.00 0.00 0.00 4.49
3702 4375 0.392327 CCACACACACACCTCACACA 60.392 55.000 0.00 0.00 0.00 3.72
3984 4676 8.509690 TGCTAATCACGTATAGTATTCCAGTAC 58.490 37.037 0.00 0.00 0.00 2.73
3990 4682 9.841880 TGATCTTGCTAATCACGTATAGTATTC 57.158 33.333 0.00 0.00 0.00 1.75
3998 4690 8.942338 AGTTAAATGATCTTGCTAATCACGTA 57.058 30.769 0.00 0.00 36.04 3.57
3999 4691 7.849804 AGTTAAATGATCTTGCTAATCACGT 57.150 32.000 0.00 0.00 36.04 4.49
4000 4692 8.539062 CAAGTTAAATGATCTTGCTAATCACG 57.461 34.615 0.00 0.00 36.04 4.35
4011 4703 8.963725 TGAATGATCTTGCAAGTTAAATGATCT 58.036 29.630 25.19 5.40 32.58 2.75
4012 4704 9.745880 ATGAATGATCTTGCAAGTTAAATGATC 57.254 29.630 25.19 18.26 0.00 2.92
4013 4705 9.529325 CATGAATGATCTTGCAAGTTAAATGAT 57.471 29.630 25.19 10.36 0.00 2.45
4014 4706 8.741841 TCATGAATGATCTTGCAAGTTAAATGA 58.258 29.630 25.19 20.01 32.29 2.57
4015 4707 8.920509 TCATGAATGATCTTGCAAGTTAAATG 57.079 30.769 25.19 18.45 32.29 2.32
4019 4711 9.399797 AGTAATCATGAATGATCTTGCAAGTTA 57.600 29.630 25.19 13.35 46.22 2.24
4020 4712 8.289939 AGTAATCATGAATGATCTTGCAAGTT 57.710 30.769 25.19 17.79 46.22 2.66
4021 4713 7.876936 AGTAATCATGAATGATCTTGCAAGT 57.123 32.000 25.19 13.20 46.22 3.16
4024 4716 9.440773 GGTATAGTAATCATGAATGATCTTGCA 57.559 33.333 0.00 0.00 46.22 4.08
4025 4717 9.440773 TGGTATAGTAATCATGAATGATCTTGC 57.559 33.333 0.00 0.00 46.22 4.01
4041 4733 6.934645 GGCATGCTGATTACTTGGTATAGTAA 59.065 38.462 18.92 0.00 42.87 2.24
4042 4734 6.464222 GGCATGCTGATTACTTGGTATAGTA 58.536 40.000 18.92 0.00 0.00 1.82
4043 4735 5.308825 GGCATGCTGATTACTTGGTATAGT 58.691 41.667 18.92 0.00 0.00 2.12
4044 4736 4.697352 GGGCATGCTGATTACTTGGTATAG 59.303 45.833 18.92 0.00 0.00 1.31
4045 4737 4.506625 GGGGCATGCTGATTACTTGGTATA 60.507 45.833 18.92 0.00 0.00 1.47
4046 4738 3.490348 GGGCATGCTGATTACTTGGTAT 58.510 45.455 18.92 0.00 0.00 2.73
4047 4739 2.422803 GGGGCATGCTGATTACTTGGTA 60.423 50.000 18.92 0.00 0.00 3.25
4048 4740 1.686115 GGGGCATGCTGATTACTTGGT 60.686 52.381 18.92 0.00 0.00 3.67
4049 4741 1.035139 GGGGCATGCTGATTACTTGG 58.965 55.000 18.92 0.00 0.00 3.61
4050 4742 1.035139 GGGGGCATGCTGATTACTTG 58.965 55.000 18.92 0.00 0.00 3.16
4051 4743 0.630673 TGGGGGCATGCTGATTACTT 59.369 50.000 18.92 0.00 0.00 2.24
4292 4987 1.133976 GCCTCTTGCATCCACTGGTAT 60.134 52.381 0.00 0.00 40.77 2.73
4331 5026 0.764271 TCCAGTTGTCATGCCACTCA 59.236 50.000 0.00 0.00 0.00 3.41
4401 5096 0.742990 AGCGAGAGACGACAGAGGAG 60.743 60.000 0.00 0.00 45.77 3.69
4404 5099 1.466697 GGAAAGCGAGAGACGACAGAG 60.467 57.143 0.00 0.00 45.77 3.35
4418 5113 1.815613 GAGGAGAAGGCAAAGGAAAGC 59.184 52.381 0.00 0.00 0.00 3.51
4447 5142 1.609783 CAAGGTTGGGGCCTAGAGG 59.390 63.158 0.84 0.00 38.03 3.69
4616 5311 8.766493 TGAAATTTGAGAAATAATATGACGCG 57.234 30.769 3.53 3.53 0.00 6.01
4779 5475 4.989168 ACTTCCAGCTAAGTCGTTTTACTG 59.011 41.667 0.00 0.00 34.60 2.74
4790 5489 9.046296 CCAGTGTTTTATATACTTCCAGCTAAG 57.954 37.037 0.00 0.00 0.00 2.18
4809 5508 2.498167 GTCACTTCATGAGCCAGTGTT 58.502 47.619 20.28 0.00 38.28 3.32
4829 5529 5.061920 ACTTCCAGCTAAAAGACTACTCG 57.938 43.478 12.81 0.00 0.00 4.18
4839 5539 9.391006 CCAGTGTTTTATATACTTCCAGCTAAA 57.609 33.333 0.00 0.00 0.00 1.85
4840 5540 7.497909 GCCAGTGTTTTATATACTTCCAGCTAA 59.502 37.037 0.00 0.00 0.00 3.09
4841 5541 6.990349 GCCAGTGTTTTATATACTTCCAGCTA 59.010 38.462 0.00 0.00 0.00 3.32
4842 5542 5.823045 GCCAGTGTTTTATATACTTCCAGCT 59.177 40.000 0.00 0.00 0.00 4.24
4843 5543 5.823045 AGCCAGTGTTTTATATACTTCCAGC 59.177 40.000 0.00 0.00 0.00 4.85
4844 5544 7.047891 TGAGCCAGTGTTTTATATACTTCCAG 58.952 38.462 0.00 0.00 0.00 3.86
4845 5545 6.953101 TGAGCCAGTGTTTTATATACTTCCA 58.047 36.000 0.00 0.00 0.00 3.53
4846 5546 7.715249 TCATGAGCCAGTGTTTTATATACTTCC 59.285 37.037 0.00 0.00 0.00 3.46
4847 5547 8.662781 TCATGAGCCAGTGTTTTATATACTTC 57.337 34.615 0.00 0.00 0.00 3.01
4848 5548 9.113838 CTTCATGAGCCAGTGTTTTATATACTT 57.886 33.333 0.00 0.00 0.00 2.24
4849 5549 8.267894 ACTTCATGAGCCAGTGTTTTATATACT 58.732 33.333 0.00 0.00 0.00 2.12
4850 5550 8.338259 CACTTCATGAGCCAGTGTTTTATATAC 58.662 37.037 15.14 0.00 34.39 1.47
4851 5551 8.264347 TCACTTCATGAGCCAGTGTTTTATATA 58.736 33.333 20.28 2.17 39.24 0.86
4852 5552 7.112122 TCACTTCATGAGCCAGTGTTTTATAT 58.888 34.615 20.28 0.00 39.24 0.86
4853 5553 6.472016 TCACTTCATGAGCCAGTGTTTTATA 58.528 36.000 20.28 3.33 39.24 0.98
4854 5554 5.316167 TCACTTCATGAGCCAGTGTTTTAT 58.684 37.500 20.28 0.00 39.24 1.40
4855 5555 4.713553 TCACTTCATGAGCCAGTGTTTTA 58.286 39.130 20.28 4.20 39.24 1.52
4856 5556 3.554934 TCACTTCATGAGCCAGTGTTTT 58.445 40.909 20.28 0.00 39.24 2.43
4857 5557 3.213206 TCACTTCATGAGCCAGTGTTT 57.787 42.857 20.28 0.00 39.24 2.83
4858 5558 2.936919 TCACTTCATGAGCCAGTGTT 57.063 45.000 20.28 0.00 39.24 3.32
4859 5559 2.303890 TGATCACTTCATGAGCCAGTGT 59.696 45.455 20.28 11.30 43.49 3.55
4860 5560 2.937149 CTGATCACTTCATGAGCCAGTG 59.063 50.000 16.66 16.66 43.49 3.66
4861 5561 2.570752 ACTGATCACTTCATGAGCCAGT 59.429 45.455 0.00 8.20 43.49 4.00
4862 5562 3.263489 ACTGATCACTTCATGAGCCAG 57.737 47.619 0.00 0.00 43.49 4.85
4863 5563 4.223700 ACTTACTGATCACTTCATGAGCCA 59.776 41.667 0.00 0.00 43.49 4.75
4864 5564 4.764172 ACTTACTGATCACTTCATGAGCC 58.236 43.478 0.00 0.00 43.49 4.70
4865 5565 5.659463 AGACTTACTGATCACTTCATGAGC 58.341 41.667 0.00 0.00 44.45 4.26
4866 5566 7.095910 ACAAGACTTACTGATCACTTCATGAG 58.904 38.462 0.00 0.00 41.91 2.90
4867 5567 6.997655 ACAAGACTTACTGATCACTTCATGA 58.002 36.000 0.00 0.00 43.13 3.07
4868 5568 7.095910 AGACAAGACTTACTGATCACTTCATG 58.904 38.462 0.00 0.00 32.72 3.07
4869 5569 7.238486 AGACAAGACTTACTGATCACTTCAT 57.762 36.000 0.00 0.00 32.72 2.57
4870 5570 6.656632 AGACAAGACTTACTGATCACTTCA 57.343 37.500 0.00 0.00 0.00 3.02
4871 5571 7.954788 AAAGACAAGACTTACTGATCACTTC 57.045 36.000 0.00 0.00 0.00 3.01
4872 5572 7.169982 CGAAAAGACAAGACTTACTGATCACTT 59.830 37.037 0.00 0.00 0.00 3.16
4873 5573 6.642950 CGAAAAGACAAGACTTACTGATCACT 59.357 38.462 0.00 0.00 0.00 3.41
4874 5574 6.641314 TCGAAAAGACAAGACTTACTGATCAC 59.359 38.462 0.00 0.00 0.00 3.06
4875 5575 6.745116 TCGAAAAGACAAGACTTACTGATCA 58.255 36.000 0.00 0.00 0.00 2.92
4876 5576 7.085116 TCTCGAAAAGACAAGACTTACTGATC 58.915 38.462 0.00 0.00 0.00 2.92
4877 5577 6.982852 TCTCGAAAAGACAAGACTTACTGAT 58.017 36.000 0.00 0.00 0.00 2.90
4878 5578 6.387041 TCTCGAAAAGACAAGACTTACTGA 57.613 37.500 0.00 0.00 0.00 3.41
4879 5579 6.918569 TCTTCTCGAAAAGACAAGACTTACTG 59.081 38.462 0.00 0.00 30.51 2.74
4880 5580 7.040473 TCTTCTCGAAAAGACAAGACTTACT 57.960 36.000 0.00 0.00 30.51 2.24
4881 5581 6.919115 ACTCTTCTCGAAAAGACAAGACTTAC 59.081 38.462 0.00 0.00 31.88 2.34
4882 5582 7.040473 ACTCTTCTCGAAAAGACAAGACTTA 57.960 36.000 0.00 0.00 31.88 2.24
4883 5583 5.908341 ACTCTTCTCGAAAAGACAAGACTT 58.092 37.500 0.00 0.00 31.88 3.01
4890 5590 8.485591 TCGAAAATTTACTCTTCTCGAAAAGAC 58.514 33.333 0.00 0.00 32.27 3.01
4965 5671 1.984570 CGAGCCTCTCTCACCCCAA 60.985 63.158 0.00 0.00 41.98 4.12
5074 5780 7.430502 ACAGTACGCTCGTCATAATTAGTTTAC 59.569 37.037 0.00 0.00 0.00 2.01
5075 5781 7.430211 CACAGTACGCTCGTCATAATTAGTTTA 59.570 37.037 0.00 0.00 0.00 2.01
5087 5793 1.130749 ACAGATCACAGTACGCTCGTC 59.869 52.381 0.00 0.00 0.00 4.20
5088 5794 1.166129 ACAGATCACAGTACGCTCGT 58.834 50.000 0.00 0.00 0.00 4.18
5090 5796 3.623960 AGTCTACAGATCACAGTACGCTC 59.376 47.826 0.00 0.00 0.00 5.03
5097 5807 6.478344 GGCTGAAAATAGTCTACAGATCACAG 59.522 42.308 0.00 0.00 0.00 3.66
5120 5830 3.878245 GCAATAGATGCGAGTTTTAGGC 58.122 45.455 0.00 0.00 46.87 3.93
5172 5882 6.156775 TCTCTTGATCCAGTACAAATCATGGA 59.843 38.462 2.10 2.10 45.48 3.41
5173 5883 6.351711 TCTCTTGATCCAGTACAAATCATGG 58.648 40.000 0.00 0.00 30.03 3.66
5232 5945 9.612620 CTCTGTGTTTAGGTTCATTTTTATGTC 57.387 33.333 0.00 0.00 0.00 3.06
5269 5982 9.189156 TGCTATGGCTTCAGTAAGAATTTTAAT 57.811 29.630 1.68 0.00 39.59 1.40
5270 5983 8.574251 TGCTATGGCTTCAGTAAGAATTTTAA 57.426 30.769 1.68 0.00 39.59 1.52
5271 5984 8.574251 TTGCTATGGCTTCAGTAAGAATTTTA 57.426 30.769 1.68 0.00 39.59 1.52
5273 5986 7.177392 AGTTTGCTATGGCTTCAGTAAGAATTT 59.823 33.333 1.68 0.00 39.59 1.82
5274 5987 6.660949 AGTTTGCTATGGCTTCAGTAAGAATT 59.339 34.615 1.68 0.00 39.59 2.17
5275 5988 6.183347 AGTTTGCTATGGCTTCAGTAAGAAT 58.817 36.000 1.68 0.00 39.59 2.40
5276 5989 5.560724 AGTTTGCTATGGCTTCAGTAAGAA 58.439 37.500 1.68 0.00 39.59 2.52
5277 5990 5.165961 AGTTTGCTATGGCTTCAGTAAGA 57.834 39.130 1.68 0.00 39.59 2.10
5278 5991 4.033358 CGAGTTTGCTATGGCTTCAGTAAG 59.967 45.833 1.68 0.00 39.59 2.34
5280 5993 3.056107 ACGAGTTTGCTATGGCTTCAGTA 60.056 43.478 1.68 0.00 39.59 2.74
5281 5994 2.289694 ACGAGTTTGCTATGGCTTCAGT 60.290 45.455 1.68 0.00 39.59 3.41
5282 5995 2.349886 GACGAGTTTGCTATGGCTTCAG 59.650 50.000 1.68 0.00 39.59 3.02
5283 5996 2.289382 TGACGAGTTTGCTATGGCTTCA 60.289 45.455 1.68 0.00 39.59 3.02
5284 5997 2.346803 TGACGAGTTTGCTATGGCTTC 58.653 47.619 1.68 0.00 39.59 3.86
5285 5998 2.472695 TGACGAGTTTGCTATGGCTT 57.527 45.000 1.68 0.00 39.59 4.35
5286 5999 2.555199 GATGACGAGTTTGCTATGGCT 58.445 47.619 1.68 0.00 39.59 4.75
5287 6000 1.258982 CGATGACGAGTTTGCTATGGC 59.741 52.381 0.00 0.00 42.66 4.40
5288 6001 2.540515 ACGATGACGAGTTTGCTATGG 58.459 47.619 0.00 0.00 42.66 2.74
5295 6008 3.985925 GGTAGTGAAACGATGACGAGTTT 59.014 43.478 0.00 0.00 45.86 2.66
5299 6012 3.861276 ATGGTAGTGAAACGATGACGA 57.139 42.857 0.00 0.00 45.86 4.20
5314 6027 4.100035 CACTGATTGGTGAGAGCTATGGTA 59.900 45.833 0.00 0.00 39.34 3.25
5332 6045 0.319728 GTCTTGAGCTCAGCCACTGA 59.680 55.000 17.43 6.96 38.25 3.41
5333 6046 0.034476 TGTCTTGAGCTCAGCCACTG 59.966 55.000 17.43 4.78 0.00 3.66
5334 6047 0.761187 TTGTCTTGAGCTCAGCCACT 59.239 50.000 17.43 0.00 0.00 4.00
5335 6048 1.467734 CATTGTCTTGAGCTCAGCCAC 59.532 52.381 17.43 14.51 0.00 5.01
5336 6049 1.072806 ACATTGTCTTGAGCTCAGCCA 59.927 47.619 17.43 11.77 0.00 4.75
5337 6050 1.467734 CACATTGTCTTGAGCTCAGCC 59.532 52.381 17.43 9.26 0.00 4.85
5338 6051 2.095869 CACACATTGTCTTGAGCTCAGC 60.096 50.000 17.43 11.72 0.00 4.26
5339 6052 3.136763 ACACACATTGTCTTGAGCTCAG 58.863 45.455 17.43 11.30 29.79 3.35
5340 6053 3.198409 ACACACATTGTCTTGAGCTCA 57.802 42.857 13.74 13.74 29.79 4.26
5341 6054 3.561310 TGAACACACATTGTCTTGAGCTC 59.439 43.478 6.82 6.82 37.51 4.09
5342 6055 3.544684 TGAACACACATTGTCTTGAGCT 58.455 40.909 0.00 0.00 37.51 4.09
5343 6056 3.969117 TGAACACACATTGTCTTGAGC 57.031 42.857 2.60 0.00 37.51 4.26
5356 6069 9.913310 TGTGATTAATAGGGAAATATGAACACA 57.087 29.630 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.