Multiple sequence alignment - TraesCS6B01G143800

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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 TraesCS6B01G143800 chr6B 100.000 5977 0 0 1 5977 143453873 143459849 0.000000e+00 11038.0
1 TraesCS6B01G143800 chr6B 89.507 629 66 0 1 629 553420423 553421051 0.000000e+00 797.0
2 TraesCS6B01G143800 chr6B 88.034 117 11 3 3949 4063 646750051 646750166 1.040000e-27 135.0
3 TraesCS6B01G143800 chr6D 95.647 3308 104 10 690 3958 68354323 68357629 0.000000e+00 5275.0
4 TraesCS6B01G143800 chr6D 92.748 1310 69 14 4038 5342 68357626 68358914 0.000000e+00 1869.0
5 TraesCS6B01G143800 chr6D 92.308 143 10 1 5503 5645 302746332 302746473 1.020000e-47 202.0
6 TraesCS6B01G143800 chr6D 82.648 219 23 12 5631 5847 68358986 68359191 4.760000e-41 180.0
7 TraesCS6B01G143800 chr6A 93.306 1479 77 13 4038 5507 85757035 85758500 0.000000e+00 2163.0
8 TraesCS6B01G143800 chr6A 89.846 1556 115 20 1666 3207 85754669 85756195 0.000000e+00 1958.0
9 TraesCS6B01G143800 chr6A 95.616 844 36 1 3116 3958 85756195 85757038 0.000000e+00 1352.0
10 TraesCS6B01G143800 chr6A 82.716 810 62 27 698 1475 85753819 85754582 0.000000e+00 649.0
11 TraesCS6B01G143800 chr6A 87.772 368 20 7 5631 5977 85758499 85758862 2.010000e-109 407.0
12 TraesCS6B01G143800 chr6A 94.203 138 7 1 5498 5635 572398889 572398753 6.070000e-50 209.0
13 TraesCS6B01G143800 chr6A 98.851 87 1 0 3955 4041 134181054 134181140 8.020000e-34 156.0
14 TraesCS6B01G143800 chr6A 97.674 86 2 0 3956 4041 608997738 608997653 1.340000e-31 148.0
15 TraesCS6B01G143800 chr2B 96.645 626 20 1 66 690 798553182 798552557 0.000000e+00 1038.0
16 TraesCS6B01G143800 chr2B 86.869 693 89 2 1 692 512098304 512098995 0.000000e+00 774.0
17 TraesCS6B01G143800 chr2B 94.853 136 7 0 5497 5632 620596669 620596804 4.690000e-51 213.0
18 TraesCS6B01G143800 chr2B 100.000 28 0 0 4422 4449 75615361 75615334 1.100000e-02 52.8
19 TraesCS6B01G143800 chr3B 91.739 690 47 1 1 690 766060090 766059411 0.000000e+00 950.0
20 TraesCS6B01G143800 chr3B 95.489 133 5 1 5506 5638 62947365 62947234 1.690000e-50 211.0
21 TraesCS6B01G143800 chr3B 95.604 91 4 0 3955 4045 372246383 372246293 4.830000e-31 147.0
22 TraesCS6B01G143800 chr7A 86.502 689 93 0 1 689 98550365 98549677 0.000000e+00 758.0
23 TraesCS6B01G143800 chr7A 88.462 182 14 1 3500 3681 112567293 112567467 4.690000e-51 213.0
24 TraesCS6B01G143800 chr4A 86.087 690 96 0 1 690 87519951 87520640 0.000000e+00 743.0
25 TraesCS6B01G143800 chr4A 95.960 99 4 0 5846 5944 729681911 729682009 1.720000e-35 161.0
26 TraesCS6B01G143800 chr4A 93.617 94 6 0 3955 4048 511040572 511040479 2.250000e-29 141.0
27 TraesCS6B01G143800 chr3A 85.818 691 96 2 1 690 750312353 750313042 0.000000e+00 732.0
28 TraesCS6B01G143800 chrUn 100.000 387 0 0 1974 2360 480519759 480519373 0.000000e+00 715.0
29 TraesCS6B01G143800 chrUn 88.506 174 12 4 3508 3681 31970599 31970434 2.820000e-48 204.0
30 TraesCS6B01G143800 chrUn 88.506 174 12 2 3508 3681 403788043 403788208 2.820000e-48 204.0
31 TraesCS6B01G143800 chr1B 87.785 483 58 1 210 691 583845194 583844712 1.120000e-156 564.0
32 TraesCS6B01G143800 chr1B 93.706 143 9 0 5496 5638 543038766 543038908 1.300000e-51 215.0
33 TraesCS6B01G143800 chr1D 80.980 694 124 6 1 690 479395265 479395954 1.470000e-150 544.0
34 TraesCS6B01G143800 chr1D 90.230 174 9 2 3508 3681 47376013 47376178 2.800000e-53 220.0
35 TraesCS6B01G143800 chr1D 94.118 102 6 0 5846 5947 41754366 41754467 8.020000e-34 156.0
36 TraesCS6B01G143800 chr2A 89.655 174 10 2 3508 3681 767439816 767439981 1.300000e-51 215.0
37 TraesCS6B01G143800 chr4B 88.462 182 14 1 3506 3687 545464279 545464105 4.690000e-51 213.0
38 TraesCS6B01G143800 chr4B 93.662 142 7 2 5506 5645 398529204 398529345 1.690000e-50 211.0
39 TraesCS6B01G143800 chr4B 94.000 100 6 0 5846 5945 315065469 315065370 1.040000e-32 152.0
40 TraesCS6B01G143800 chr3D 96.154 130 5 0 5503 5632 67437062 67437191 4.690000e-51 213.0
41 TraesCS6B01G143800 chr3D 94.624 93 4 1 3955 4047 206978598 206978507 6.240000e-30 143.0
42 TraesCS6B01G143800 chr3D 95.506 89 3 1 3957 4045 436676984 436676897 2.250000e-29 141.0
43 TraesCS6B01G143800 chr7B 92.958 142 9 1 5499 5639 94758955 94759096 7.850000e-49 206.0
44 TraesCS6B01G143800 chr7B 93.617 94 6 0 3955 4048 639796285 639796192 2.250000e-29 141.0
45 TraesCS6B01G143800 chr4D 92.308 143 10 1 5503 5645 74225429 74225570 1.020000e-47 202.0
46 TraesCS6B01G143800 chr4D 94.000 100 6 0 5846 5945 155576785 155576686 1.040000e-32 152.0
47 TraesCS6B01G143800 chr4D 95.699 93 4 0 3956 4048 23320448 23320540 3.730000e-32 150.0
48 TraesCS6B01G143800 chr4D 93.204 103 5 2 5846 5946 122197768 122197870 3.730000e-32 150.0
49 TraesCS6B01G143800 chr7D 84.615 182 15 3 3500 3681 41051464 41051632 1.030000e-37 169.0
50 TraesCS6B01G143800 chr1A 95.098 102 5 0 5846 5947 313736119 313736220 1.720000e-35 161.0
51 TraesCS6B01G143800 chr5A 92.453 106 8 0 5846 5951 422874750 422874855 1.040000e-32 152.0
52 TraesCS6B01G143800 chr5A 94.059 101 5 1 5846 5946 554560574 554560673 1.040000e-32 152.0


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 TraesCS6B01G143800 chr6B 143453873 143459849 5976 False 11038.000000 11038 100.000000 1 5977 1 chr6B.!!$F1 5976
1 TraesCS6B01G143800 chr6B 553420423 553421051 628 False 797.000000 797 89.507000 1 629 1 chr6B.!!$F2 628
2 TraesCS6B01G143800 chr6D 68354323 68359191 4868 False 2441.333333 5275 90.347667 690 5847 3 chr6D.!!$F2 5157
3 TraesCS6B01G143800 chr6A 85753819 85758862 5043 False 1305.800000 2163 89.851200 698 5977 5 chr6A.!!$F2 5279
4 TraesCS6B01G143800 chr2B 798552557 798553182 625 True 1038.000000 1038 96.645000 66 690 1 chr2B.!!$R2 624
5 TraesCS6B01G143800 chr2B 512098304 512098995 691 False 774.000000 774 86.869000 1 692 1 chr2B.!!$F1 691
6 TraesCS6B01G143800 chr3B 766059411 766060090 679 True 950.000000 950 91.739000 1 690 1 chr3B.!!$R3 689
7 TraesCS6B01G143800 chr7A 98549677 98550365 688 True 758.000000 758 86.502000 1 689 1 chr7A.!!$R1 688
8 TraesCS6B01G143800 chr4A 87519951 87520640 689 False 743.000000 743 86.087000 1 690 1 chr4A.!!$F1 689
9 TraesCS6B01G143800 chr3A 750312353 750313042 689 False 732.000000 732 85.818000 1 690 1 chr3A.!!$F1 689
10 TraesCS6B01G143800 chr1D 479395265 479395954 689 False 544.000000 544 80.980000 1 690 1 chr1D.!!$F3 689

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
719 720 0.034756 AGCTGCATGTCGTTGTGGTA 59.965 50.0 1.02 0.0 0.00 3.25 F
1342 1385 0.669012 TGCGTGCGTTTAGATGAGCA 60.669 50.0 0.00 0.0 37.26 4.26 F
3098 3190 0.179108 AAAGCGAGATAGCCACCGTC 60.179 55.0 0.00 0.0 38.01 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1729 1807 0.737019 CAATTGGGGTTGCGCATCAC 60.737 55.0 12.75 12.53 0.00 3.06 R
3123 3215 0.461548 TAGCTCAAGCCAGACCATCG 59.538 55.0 0.00 0.00 43.38 3.84 R
5075 5266 1.246737 GCACCAAGGAGGCAAAGAGG 61.247 60.0 0.00 0.00 43.14 3.69 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
90 91 5.042463 TCCAATCACCAGTGACAGTTAAA 57.958 39.130 1.88 0.00 43.11 1.52
114 115 5.774690 AGGTTTTATCACAAGGCTGATTTCA 59.225 36.000 0.00 0.00 32.86 2.69
254 255 1.132849 TCGTCATGGAGGATATGGGGT 60.133 52.381 0.00 0.00 0.00 4.95
391 392 5.178096 TGCCCTTTCTGATGATCTTTACA 57.822 39.130 0.00 0.00 0.00 2.41
561 562 3.793492 GCTCAAACTTTGAAGCTCACAAC 59.207 43.478 5.72 0.00 39.58 3.32
719 720 0.034756 AGCTGCATGTCGTTGTGGTA 59.965 50.000 1.02 0.00 0.00 3.25
789 790 2.025418 CCGAGACCAAACCGAACCG 61.025 63.158 0.00 0.00 0.00 4.44
896 919 3.423154 GAGCGCAACCCTGAACCG 61.423 66.667 11.47 0.00 0.00 4.44
902 925 1.966451 CAACCCTGAACCGACTGCC 60.966 63.158 0.00 0.00 0.00 4.85
965 1007 2.040359 CTTCCCTCCCTCCCTCCC 60.040 72.222 0.00 0.00 0.00 4.30
969 1011 3.039526 CCTCCCTCCCTCCCTCCT 61.040 72.222 0.00 0.00 0.00 3.69
971 1013 3.036959 TCCCTCCCTCCCTCCTCC 61.037 72.222 0.00 0.00 0.00 4.30
972 1014 3.368501 CCCTCCCTCCCTCCTCCA 61.369 72.222 0.00 0.00 0.00 3.86
1279 1321 3.370231 GCCACCCACGCGGATTTT 61.370 61.111 12.47 0.00 34.64 1.82
1342 1385 0.669012 TGCGTGCGTTTAGATGAGCA 60.669 50.000 0.00 0.00 37.26 4.26
1431 1499 2.217750 GTTGCCAACAAAATTGGGGAC 58.782 47.619 1.91 3.36 39.90 4.46
1444 1513 1.301954 GGGGACTATTGGCGGTGTT 59.698 57.895 0.00 0.00 0.00 3.32
1449 1518 3.075884 GGACTATTGGCGGTGTTGTTAA 58.924 45.455 0.00 0.00 0.00 2.01
1479 1557 1.728490 GATGAGCGGGGGATGCAAAC 61.728 60.000 0.00 0.00 33.85 2.93
1500 1578 1.135960 GGAGCTTAATCCTGGGCTCT 58.864 55.000 17.55 0.00 46.98 4.09
1506 1584 2.494888 TAATCCTGGGCTCTGATGGA 57.505 50.000 0.00 0.00 0.00 3.41
1562 1640 7.661127 TTTAACATACACAGTAGAAATGCGT 57.339 32.000 0.00 0.00 0.00 5.24
1579 1657 1.732259 GCGTCTTGTTCATGGTGTAGG 59.268 52.381 0.00 0.00 0.00 3.18
1583 1661 3.008049 GTCTTGTTCATGGTGTAGGGACT 59.992 47.826 0.00 0.00 46.37 3.85
1600 1678 3.446516 GGGACTACCGTCAAGTAGAATGT 59.553 47.826 5.75 0.00 41.98 2.71
1609 1687 6.157211 CCGTCAAGTAGAATGTACAAGTTCT 58.843 40.000 14.48 14.48 38.22 3.01
1615 1693 2.092323 GAATGTACAAGTTCTGGGGGC 58.908 52.381 0.00 0.00 0.00 5.80
1620 1698 1.303643 CAAGTTCTGGGGGCCTGTC 60.304 63.158 0.84 0.00 0.00 3.51
1682 1760 2.493414 TCTAGCTACTATCCCCGAGC 57.507 55.000 0.00 0.00 35.07 5.03
1700 1778 3.367395 CGAGCAGAATGTACAGGTTCAGA 60.367 47.826 10.93 0.00 39.31 3.27
1716 1794 4.249661 GTTCAGAGGGTCTGTTGAGATTC 58.750 47.826 3.92 0.00 44.58 2.52
1729 1807 6.881065 TCTGTTGAGATTCATTTTAGGTCCTG 59.119 38.462 0.00 0.00 0.00 3.86
1764 1842 5.221925 CCCCAATTGCATACCTCTACTGTAT 60.222 44.000 0.00 0.00 0.00 2.29
1784 1862 8.540388 ACTGTATATCCTATTTGAGTTGTGTGT 58.460 33.333 0.00 0.00 0.00 3.72
1792 1870 8.304596 TCCTATTTGAGTTGTGTGTCTACTTAG 58.695 37.037 0.00 0.00 32.78 2.18
1868 1946 6.986817 GTGCTTGGTGTCTGATGTATATAGTT 59.013 38.462 0.00 0.00 0.00 2.24
1972 2050 3.008594 TCCAGCTTTCGAGGATTTTACCA 59.991 43.478 0.00 0.00 0.00 3.25
2360 2442 4.072131 GGAGGTAACATGCAAGACTTCAA 58.928 43.478 0.00 0.00 41.41 2.69
2375 2457 4.083643 AGACTTCAACTGCATTCAACGATG 60.084 41.667 0.00 0.00 0.00 3.84
2379 2461 4.725359 TCAACTGCATTCAACGATGATTG 58.275 39.130 11.81 11.81 39.06 2.67
2839 2924 5.365605 TCCTCTTCACTTTGACTTGGAAGTA 59.634 40.000 0.00 0.00 39.88 2.24
3038 3130 1.748122 GCACTGGCAGATGGAGGTG 60.748 63.158 23.66 9.03 40.72 4.00
3098 3190 0.179108 AAAGCGAGATAGCCACCGTC 60.179 55.000 0.00 0.00 38.01 4.79
3349 3532 6.631238 CGTTGTTAGTGGTGTTATTGTTCTTG 59.369 38.462 0.00 0.00 0.00 3.02
3445 3628 2.846206 TCATGGGAAGAGCATACCACTT 59.154 45.455 0.00 0.00 35.52 3.16
3447 3630 4.473196 TCATGGGAAGAGCATACCACTTAA 59.527 41.667 0.00 0.00 35.52 1.85
3606 3789 5.245531 TCAGATGAACGGCTTCTTTTATGT 58.754 37.500 0.00 0.00 0.00 2.29
3751 3934 5.542635 TCTCCTGCCGTTATATTTCAGGTAT 59.457 40.000 6.49 0.00 43.49 2.73
3927 4111 5.373812 TTTGATTCTCCTATGTCCTTCCC 57.626 43.478 0.00 0.00 0.00 3.97
3937 4121 2.118403 TGTCCTTCCCCACTCTCTTT 57.882 50.000 0.00 0.00 0.00 2.52
3958 4142 6.320418 TCTTTCCTTTTCCCTTTCAACAGTAC 59.680 38.462 0.00 0.00 0.00 2.73
3959 4143 5.382664 TCCTTTTCCCTTTCAACAGTACT 57.617 39.130 0.00 0.00 0.00 2.73
3960 4144 5.374071 TCCTTTTCCCTTTCAACAGTACTC 58.626 41.667 0.00 0.00 0.00 2.59
3961 4145 4.519350 CCTTTTCCCTTTCAACAGTACTCC 59.481 45.833 0.00 0.00 0.00 3.85
3962 4146 3.782656 TTCCCTTTCAACAGTACTCCC 57.217 47.619 0.00 0.00 0.00 4.30
3963 4147 2.986050 TCCCTTTCAACAGTACTCCCT 58.014 47.619 0.00 0.00 0.00 4.20
3964 4148 2.904434 TCCCTTTCAACAGTACTCCCTC 59.096 50.000 0.00 0.00 0.00 4.30
3965 4149 2.907042 CCCTTTCAACAGTACTCCCTCT 59.093 50.000 0.00 0.00 0.00 3.69
3966 4150 3.307059 CCCTTTCAACAGTACTCCCTCTG 60.307 52.174 0.00 0.00 37.65 3.35
3967 4151 3.325135 CCTTTCAACAGTACTCCCTCTGT 59.675 47.826 0.00 0.00 45.21 3.41
3968 4152 4.527038 CCTTTCAACAGTACTCCCTCTGTA 59.473 45.833 0.00 0.00 42.95 2.74
3969 4153 5.011738 CCTTTCAACAGTACTCCCTCTGTAA 59.988 44.000 0.00 0.00 42.95 2.41
3970 4154 6.463897 CCTTTCAACAGTACTCCCTCTGTAAA 60.464 42.308 0.00 0.00 42.95 2.01
3971 4155 5.723672 TCAACAGTACTCCCTCTGTAAAG 57.276 43.478 0.00 0.00 42.95 1.85
3972 4156 5.391256 TCAACAGTACTCCCTCTGTAAAGA 58.609 41.667 0.00 0.00 42.95 2.52
3973 4157 5.836898 TCAACAGTACTCCCTCTGTAAAGAA 59.163 40.000 0.00 0.00 42.95 2.52
3974 4158 6.325545 TCAACAGTACTCCCTCTGTAAAGAAA 59.674 38.462 0.00 0.00 42.95 2.52
3975 4159 6.936968 ACAGTACTCCCTCTGTAAAGAAAT 57.063 37.500 0.00 0.00 42.13 2.17
3976 4160 8.311836 CAACAGTACTCCCTCTGTAAAGAAATA 58.688 37.037 0.00 0.00 42.95 1.40
3977 4161 8.611051 ACAGTACTCCCTCTGTAAAGAAATAT 57.389 34.615 0.00 0.00 42.13 1.28
3978 4162 9.710818 ACAGTACTCCCTCTGTAAAGAAATATA 57.289 33.333 0.00 0.00 42.13 0.86
3983 4167 8.425703 ACTCCCTCTGTAAAGAAATATAAGAGC 58.574 37.037 0.00 0.00 0.00 4.09
3984 4168 8.319057 TCCCTCTGTAAAGAAATATAAGAGCA 57.681 34.615 0.00 0.00 0.00 4.26
3985 4169 8.938883 TCCCTCTGTAAAGAAATATAAGAGCAT 58.061 33.333 0.00 0.00 0.00 3.79
3986 4170 9.566432 CCCTCTGTAAAGAAATATAAGAGCATT 57.434 33.333 0.00 0.00 0.00 3.56
4035 4219 8.943909 AACACTCTTATATTTCTTTACGGAGG 57.056 34.615 0.00 0.00 0.00 4.30
4036 4220 7.498443 ACACTCTTATATTTCTTTACGGAGGG 58.502 38.462 0.00 0.00 0.00 4.30
4037 4221 7.343833 ACACTCTTATATTTCTTTACGGAGGGA 59.656 37.037 0.00 0.00 0.00 4.20
4038 4222 7.868415 CACTCTTATATTTCTTTACGGAGGGAG 59.132 40.741 0.00 0.00 0.00 4.30
4039 4223 7.564292 ACTCTTATATTTCTTTACGGAGGGAGT 59.436 37.037 0.00 0.00 0.00 3.85
4040 4224 9.075678 CTCTTATATTTCTTTACGGAGGGAGTA 57.924 37.037 0.00 0.00 0.00 2.59
4044 4228 5.593679 TTTCTTTACGGAGGGAGTATCTG 57.406 43.478 0.00 0.00 33.73 2.90
4090 4274 6.295249 TCTCCACAAATGTTCAACTATGTCA 58.705 36.000 0.00 0.00 0.00 3.58
4157 4341 1.295792 TGAACGCTTTCACTGACCAC 58.704 50.000 0.75 0.00 36.79 4.16
4214 4398 8.898792 GTGTGCTTTAGTACTTTTTATTTTCCG 58.101 33.333 0.00 0.00 0.00 4.30
4236 4420 9.661563 TTCCGTATTTTACATCTTTCACTGTAT 57.338 29.630 0.00 0.00 0.00 2.29
4258 4442 9.496873 TGTATGATATAACGTCTTTTATTGGGG 57.503 33.333 0.00 0.00 0.00 4.96
4259 4443 7.996098 ATGATATAACGTCTTTTATTGGGGG 57.004 36.000 0.00 0.00 0.00 5.40
4406 4590 3.136626 AGGTCCAGTGGCCTGTTAATATC 59.863 47.826 20.42 0.00 36.95 1.63
4407 4591 3.118038 GGTCCAGTGGCCTGTTAATATCA 60.118 47.826 3.51 0.00 36.95 2.15
4408 4592 4.446311 GGTCCAGTGGCCTGTTAATATCAT 60.446 45.833 3.51 0.00 36.95 2.45
4417 4601 8.754080 GTGGCCTGTTAATATCATCTACTCTAT 58.246 37.037 3.32 0.00 0.00 1.98
4442 4626 5.965918 GCCTTCTTCTAATACAAAATGACGC 59.034 40.000 0.00 0.00 0.00 5.19
4481 4667 4.949856 TCTGAGGAAAACAATCCCTATTGC 59.050 41.667 0.00 0.00 45.41 3.56
4489 4675 3.347216 ACAATCCCTATTGCACTGTGTC 58.653 45.455 9.86 2.63 45.41 3.67
4504 4690 7.049754 TGCACTGTGTCATATCTGATGTATTT 58.950 34.615 9.86 0.00 32.98 1.40
4580 4766 3.471680 GAGCAAGACAGGAAGTGAGTTT 58.528 45.455 0.00 0.00 0.00 2.66
4594 4781 8.414003 AGGAAGTGAGTTTGGTTTTCTTTATTC 58.586 33.333 0.00 0.00 0.00 1.75
4629 4816 1.462283 CACTTGTCCGCTGATCACTTG 59.538 52.381 0.00 0.00 0.00 3.16
4631 4818 2.146342 CTTGTCCGCTGATCACTTGTT 58.854 47.619 0.00 0.00 0.00 2.83
4632 4819 3.244078 ACTTGTCCGCTGATCACTTGTTA 60.244 43.478 0.00 0.00 0.00 2.41
4633 4820 3.610040 TGTCCGCTGATCACTTGTTAT 57.390 42.857 0.00 0.00 0.00 1.89
4634 4821 3.261580 TGTCCGCTGATCACTTGTTATG 58.738 45.455 0.00 0.00 0.00 1.90
4635 4822 2.030946 GTCCGCTGATCACTTGTTATGC 59.969 50.000 0.00 0.00 0.00 3.14
4647 4834 3.630312 ACTTGTTATGCGTGTTTTCCTGT 59.370 39.130 0.00 0.00 0.00 4.00
4649 4836 5.472137 ACTTGTTATGCGTGTTTTCCTGTAT 59.528 36.000 0.00 0.00 0.00 2.29
4714 4901 0.329261 TACTGGCAGCCTGCTCAATT 59.671 50.000 17.55 5.60 44.28 2.32
4715 4902 0.964358 ACTGGCAGCCTGCTCAATTC 60.964 55.000 17.55 0.00 44.28 2.17
4726 4913 2.483106 CTGCTCAATTCTGGTGACACTG 59.517 50.000 5.39 0.00 35.60 3.66
4785 4972 4.340617 TCCCTTAATTTCTTGCACCGAAT 58.659 39.130 0.00 0.00 0.00 3.34
4789 4976 3.747099 AATTTCTTGCACCGAATCGAG 57.253 42.857 3.36 0.00 0.00 4.04
4790 4977 1.438651 TTTCTTGCACCGAATCGAGG 58.561 50.000 3.36 0.00 0.00 4.63
4883 5072 2.014128 CACTGGTTGTCACTTTCGGTT 58.986 47.619 0.00 0.00 0.00 4.44
4992 5181 3.753272 TCTGTAAATGAAGAGCAACCTGC 59.247 43.478 0.00 0.00 45.46 4.85
5075 5266 5.731686 GCAAGGCAATAGCTAGTCATTTGAC 60.732 44.000 7.97 5.18 42.17 3.18
5188 5379 4.200874 CGGAGTACTTCAGTAGAGGACAT 58.799 47.826 1.17 0.00 0.00 3.06
5189 5380 4.273969 CGGAGTACTTCAGTAGAGGACATC 59.726 50.000 1.17 0.00 0.00 3.06
5190 5381 5.442391 GGAGTACTTCAGTAGAGGACATCT 58.558 45.833 0.00 0.00 42.47 2.90
5191 5382 5.889289 GGAGTACTTCAGTAGAGGACATCTT 59.111 44.000 0.00 0.00 39.64 2.40
5192 5383 6.378848 GGAGTACTTCAGTAGAGGACATCTTT 59.621 42.308 0.00 0.00 39.64 2.52
5197 5388 7.382898 ACTTCAGTAGAGGACATCTTTTCTTC 58.617 38.462 0.00 0.00 39.64 2.87
5300 5494 1.203052 CTTCTGTTGGGCGCATCAAAT 59.797 47.619 10.83 0.00 0.00 2.32
5301 5495 2.121291 TCTGTTGGGCGCATCAAATA 57.879 45.000 10.83 5.39 0.00 1.40
5375 5570 7.646130 TGTGAAAACCGTTGATTTTACAATCTC 59.354 33.333 3.41 0.00 39.81 2.75
5382 5577 4.963276 TGATTTTACAATCTCTTGGGCG 57.037 40.909 3.41 0.00 39.81 6.13
5389 5584 1.740025 CAATCTCTTGGGCGGAGAAAC 59.260 52.381 7.35 0.00 42.16 2.78
5401 5596 1.525619 CGGAGAAACGAAAGCGAAGTT 59.474 47.619 0.00 0.00 41.64 2.66
5427 5622 4.281941 GCCATCATTTCCCCCTTCTTTATC 59.718 45.833 0.00 0.00 0.00 1.75
5462 5657 4.127566 AGAACAATTGCAAAACAGCACT 57.872 36.364 1.71 0.00 45.61 4.40
5515 5710 9.899226 GCATAAGCTTAATTATTACTCCCTTTG 57.101 33.333 10.85 0.00 37.91 2.77
5518 5713 8.521170 AAGCTTAATTATTACTCCCTTTGTCC 57.479 34.615 0.00 0.00 0.00 4.02
5519 5714 6.766467 AGCTTAATTATTACTCCCTTTGTCCG 59.234 38.462 0.00 0.00 0.00 4.79
5520 5715 6.017357 GCTTAATTATTACTCCCTTTGTCCGG 60.017 42.308 0.00 0.00 0.00 5.14
5521 5716 5.703730 AATTATTACTCCCTTTGTCCGGA 57.296 39.130 0.00 0.00 0.00 5.14
5522 5717 5.703730 ATTATTACTCCCTTTGTCCGGAA 57.296 39.130 5.23 0.00 0.00 4.30
5523 5718 5.502089 TTATTACTCCCTTTGTCCGGAAA 57.498 39.130 5.23 0.00 0.00 3.13
5524 5719 4.586306 ATTACTCCCTTTGTCCGGAAAT 57.414 40.909 5.23 0.00 0.00 2.17
5525 5720 5.703730 ATTACTCCCTTTGTCCGGAAATA 57.296 39.130 5.23 0.00 0.00 1.40
5526 5721 5.703730 TTACTCCCTTTGTCCGGAAATAT 57.296 39.130 5.23 0.00 0.00 1.28
5527 5722 4.586306 ACTCCCTTTGTCCGGAAATATT 57.414 40.909 5.23 0.00 0.00 1.28
5528 5723 4.930696 ACTCCCTTTGTCCGGAAATATTT 58.069 39.130 5.23 0.00 0.00 1.40
5529 5724 4.705023 ACTCCCTTTGTCCGGAAATATTTG 59.295 41.667 5.23 0.00 0.00 2.32
5530 5725 4.668636 TCCCTTTGTCCGGAAATATTTGT 58.331 39.130 5.23 0.00 0.00 2.83
5531 5726 4.703093 TCCCTTTGTCCGGAAATATTTGTC 59.297 41.667 5.23 0.00 0.00 3.18
5532 5727 4.705023 CCCTTTGTCCGGAAATATTTGTCT 59.295 41.667 5.23 0.00 0.00 3.41
5533 5728 5.185056 CCCTTTGTCCGGAAATATTTGTCTT 59.815 40.000 5.23 0.00 0.00 3.01
5534 5729 6.322491 CCTTTGTCCGGAAATATTTGTCTTC 58.678 40.000 5.23 0.00 0.00 2.87
5535 5730 6.072175 CCTTTGTCCGGAAATATTTGTCTTCA 60.072 38.462 5.23 0.00 0.00 3.02
5536 5731 6.885952 TTGTCCGGAAATATTTGTCTTCAA 57.114 33.333 5.23 0.00 0.00 2.69
5537 5732 6.885952 TGTCCGGAAATATTTGTCTTCAAA 57.114 33.333 5.23 0.00 45.71 2.69
5538 5733 6.674066 TGTCCGGAAATATTTGTCTTCAAAC 58.326 36.000 5.23 0.00 44.69 2.93
5539 5734 6.488683 TGTCCGGAAATATTTGTCTTCAAACT 59.511 34.615 5.23 0.00 44.69 2.66
5540 5735 6.801862 GTCCGGAAATATTTGTCTTCAAACTG 59.198 38.462 5.23 0.00 44.69 3.16
5541 5736 6.072175 TCCGGAAATATTTGTCTTCAAACTGG 60.072 38.462 0.00 2.65 44.69 4.00
5542 5737 6.072175 CCGGAAATATTTGTCTTCAAACTGGA 60.072 38.462 5.17 0.00 44.69 3.86
5543 5738 7.362920 CCGGAAATATTTGTCTTCAAACTGGAT 60.363 37.037 5.17 0.00 44.69 3.41
5544 5739 8.673711 CGGAAATATTTGTCTTCAAACTGGATA 58.326 33.333 5.17 0.00 44.69 2.59
5550 5745 6.648879 TTGTCTTCAAACTGGATAAAAGGG 57.351 37.500 0.00 0.00 0.00 3.95
5551 5746 5.076873 TGTCTTCAAACTGGATAAAAGGGG 58.923 41.667 0.00 0.00 0.00 4.79
5552 5747 5.163034 TGTCTTCAAACTGGATAAAAGGGGA 60.163 40.000 0.00 0.00 0.00 4.81
5553 5748 5.952347 GTCTTCAAACTGGATAAAAGGGGAT 59.048 40.000 0.00 0.00 0.00 3.85
5554 5749 5.951747 TCTTCAAACTGGATAAAAGGGGATG 59.048 40.000 0.00 0.00 0.00 3.51
5555 5750 5.269554 TCAAACTGGATAAAAGGGGATGT 57.730 39.130 0.00 0.00 0.00 3.06
5556 5751 6.395780 TCAAACTGGATAAAAGGGGATGTA 57.604 37.500 0.00 0.00 0.00 2.29
5557 5752 6.980577 TCAAACTGGATAAAAGGGGATGTAT 58.019 36.000 0.00 0.00 0.00 2.29
5558 5753 7.060421 TCAAACTGGATAAAAGGGGATGTATC 58.940 38.462 0.00 0.00 0.00 2.24
5559 5754 6.848562 AACTGGATAAAAGGGGATGTATCT 57.151 37.500 0.00 0.00 0.00 1.98
5560 5755 7.947782 AACTGGATAAAAGGGGATGTATCTA 57.052 36.000 0.00 0.00 0.00 1.98
5561 5756 7.560796 ACTGGATAAAAGGGGATGTATCTAG 57.439 40.000 0.00 0.00 37.50 2.43
5562 5757 7.313731 ACTGGATAAAAGGGGATGTATCTAGA 58.686 38.462 9.13 0.00 35.96 2.43
5563 5758 7.964293 ACTGGATAAAAGGGGATGTATCTAGAT 59.036 37.037 10.73 10.73 35.96 1.98
5564 5759 8.150827 TGGATAAAAGGGGATGTATCTAGATG 57.849 38.462 15.79 0.00 0.00 2.90
5565 5760 7.739444 TGGATAAAAGGGGATGTATCTAGATGT 59.261 37.037 15.79 1.25 0.00 3.06
5566 5761 9.268282 GGATAAAAGGGGATGTATCTAGATGTA 57.732 37.037 15.79 4.44 0.00 2.29
5573 5768 9.845214 AGGGGATGTATCTAGATGTATTTTAGT 57.155 33.333 15.79 0.00 0.00 2.24
5611 5806 9.918630 CTCTTTTTATCCATTTTGATGACAAGT 57.081 29.630 0.00 0.00 37.32 3.16
5618 5813 8.915871 ATCCATTTTGATGACAAGTATTTTCG 57.084 30.769 0.00 0.00 37.32 3.46
5619 5814 7.312154 TCCATTTTGATGACAAGTATTTTCGG 58.688 34.615 0.00 0.00 37.32 4.30
5620 5815 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
5621 5816 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
5622 5817 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
5623 5818 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
5624 5819 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
5625 5820 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
5626 5821 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
5627 5822 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
5628 5823 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
5629 5824 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
5630 5825 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
5631 5826 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
5632 5827 1.631405 TTTTCGGACGGAGGGAGTAA 58.369 50.000 0.00 0.00 0.00 2.24
5633 5828 1.856629 TTTCGGACGGAGGGAGTAAT 58.143 50.000 0.00 0.00 0.00 1.89
5634 5829 1.856629 TTCGGACGGAGGGAGTAATT 58.143 50.000 0.00 0.00 0.00 1.40
5635 5830 2.734755 TCGGACGGAGGGAGTAATTA 57.265 50.000 0.00 0.00 0.00 1.40
5636 5831 2.301346 TCGGACGGAGGGAGTAATTAC 58.699 52.381 7.57 7.57 0.00 1.89
5637 5832 2.092212 TCGGACGGAGGGAGTAATTACT 60.092 50.000 18.05 18.05 39.71 2.24
5638 5833 3.136443 TCGGACGGAGGGAGTAATTACTA 59.864 47.826 18.03 0.00 36.50 1.82
5639 5834 3.501445 CGGACGGAGGGAGTAATTACTAG 59.499 52.174 18.03 8.21 36.50 2.57
5646 5841 6.127952 CGGAGGGAGTAATTACTAGCATAGAC 60.128 46.154 18.03 3.41 42.77 2.59
5823 6020 1.786937 ACCACTGACCATGGCAAAAA 58.213 45.000 13.04 0.00 41.31 1.94
5885 6099 6.794158 CGTTTAAGAGAGCTGAAATTGAACTG 59.206 38.462 0.00 0.00 27.41 3.16
5892 6106 6.974965 AGAGCTGAAATTGAACTGTTTTAGG 58.025 36.000 0.00 0.00 0.00 2.69
5897 6111 7.575414 TGAAATTGAACTGTTTTAGGTGCTA 57.425 32.000 0.00 0.00 0.00 3.49
5917 6134 8.613482 GGTGCTATCTTAAATGTCTAAAAGGTC 58.387 37.037 0.00 0.00 0.00 3.85
5933 6150 9.621629 TCTAAAAGGTCTTACAAAAGTGAATGA 57.378 29.630 0.00 0.00 34.13 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 91 5.774690 TGAAATCAGCCTTGTGATAAAACCT 59.225 36.000 0.00 0.00 36.07 3.50
114 115 4.381292 GGTGTATGTACCGCTTGTAGTTCT 60.381 45.833 0.00 0.00 0.00 3.01
171 172 3.325753 GGCTGCCACTGAGAGGGT 61.326 66.667 15.17 0.00 0.00 4.34
254 255 1.517361 CGACTGATGGCTGCCACTA 59.483 57.895 25.99 14.83 35.80 2.74
391 392 0.814010 GCCACGTGAATCCGCCTTAT 60.814 55.000 19.30 0.00 0.00 1.73
618 619 0.682292 GGACGGATGGAAGATCTCCC 59.318 60.000 0.00 0.00 44.69 4.30
695 696 0.453950 CAACGACATGCAGCTCAAGC 60.454 55.000 0.00 0.00 42.49 4.01
696 697 0.870393 ACAACGACATGCAGCTCAAG 59.130 50.000 0.00 0.00 0.00 3.02
703 704 0.682292 TCCTACCACAACGACATGCA 59.318 50.000 0.00 0.00 0.00 3.96
719 720 4.459089 GGCCGCTCGCTTCTTCCT 62.459 66.667 0.00 0.00 37.74 3.36
764 765 1.539496 CGGTTTGGTCTCGGTCAGAAA 60.539 52.381 0.00 0.00 30.72 2.52
789 790 0.318784 GGTGACTGACCACACGACTC 60.319 60.000 0.00 0.00 45.34 3.36
1270 1312 2.004583 TACACTCTGGAAAATCCGCG 57.995 50.000 0.00 0.00 40.17 6.46
1279 1321 4.039973 ACGAGACCAAATTTACACTCTGGA 59.960 41.667 12.46 0.00 0.00 3.86
1319 1362 3.345714 CTCATCTAAACGCACGCATTTC 58.654 45.455 0.00 0.00 0.00 2.17
1342 1385 4.070552 GAGCCTCGCTTCCGTGGT 62.071 66.667 6.14 0.00 46.77 4.16
1357 1400 4.267452 GTGCTAGAGATTTTTGCGAGAGAG 59.733 45.833 0.00 0.00 0.00 3.20
1431 1499 2.159435 GCCTTAACAACACCGCCAATAG 60.159 50.000 0.00 0.00 0.00 1.73
1444 1513 3.879295 GCTCATCTGCTATTGCCTTAACA 59.121 43.478 0.00 0.00 38.71 2.41
1449 1518 0.250209 CCGCTCATCTGCTATTGCCT 60.250 55.000 0.00 0.00 38.71 4.75
1500 1578 5.690865 AGGATTAAGCGGTAATTTCCATCA 58.309 37.500 1.75 0.00 32.26 3.07
1506 1584 5.644636 TCGAACAAGGATTAAGCGGTAATTT 59.355 36.000 0.00 0.00 32.26 1.82
1548 1626 4.377021 TGAACAAGACGCATTTCTACTGT 58.623 39.130 0.00 0.00 0.00 3.55
1562 1640 3.248024 AGTCCCTACACCATGAACAAGA 58.752 45.455 0.00 0.00 0.00 3.02
1579 1657 4.715527 ACATTCTACTTGACGGTAGTCC 57.284 45.455 0.00 0.00 46.51 3.85
1583 1661 6.579666 ACTTGTACATTCTACTTGACGGTA 57.420 37.500 0.00 0.00 0.00 4.02
1600 1678 0.770557 ACAGGCCCCCAGAACTTGTA 60.771 55.000 0.00 0.00 0.00 2.41
1609 1687 2.285368 AATCTCGACAGGCCCCCA 60.285 61.111 0.00 0.00 0.00 4.96
1615 1693 4.811557 GGACCTAAAATGAATCTCGACAGG 59.188 45.833 0.00 0.00 0.00 4.00
1620 1698 7.148507 GCATCATAGGACCTAAAATGAATCTCG 60.149 40.741 21.99 7.43 32.47 4.04
1664 1742 2.088423 CTGCTCGGGGATAGTAGCTAG 58.912 57.143 0.00 0.00 35.95 3.42
1682 1760 3.261897 ACCCTCTGAACCTGTACATTCTG 59.738 47.826 9.90 9.36 0.00 3.02
1700 1778 6.183347 CCTAAAATGAATCTCAACAGACCCT 58.817 40.000 0.00 0.00 0.00 4.34
1716 1794 2.223340 GCGCATCACAGGACCTAAAATG 60.223 50.000 0.30 0.00 0.00 2.32
1729 1807 0.737019 CAATTGGGGTTGCGCATCAC 60.737 55.000 12.75 12.53 0.00 3.06
1764 1842 8.362464 AGTAGACACACAACTCAAATAGGATA 57.638 34.615 0.00 0.00 0.00 2.59
1779 1857 7.430502 ACGCGATATAAAACTAAGTAGACACAC 59.569 37.037 15.93 0.00 0.00 3.82
1784 1862 9.793252 AAAAGACGCGATATAAAACTAAGTAGA 57.207 29.630 15.93 0.00 0.00 2.59
1792 1870 4.494410 GCCACAAAAGACGCGATATAAAAC 59.506 41.667 15.93 0.00 0.00 2.43
1827 1905 7.668052 ACACCAAGCACTAGGTTCAATTTTATA 59.332 33.333 0.00 0.00 35.52 0.98
1868 1946 3.724478 CACCTGGCCTGGAGGATATATA 58.276 50.000 33.43 0.00 37.39 0.86
1966 2044 4.599041 CTCCATTGGGATCTGTTGGTAAA 58.401 43.478 2.09 0.00 43.91 2.01
1972 2050 1.355381 TGTGCTCCATTGGGATCTGTT 59.645 47.619 2.09 0.00 43.91 3.16
3038 3130 2.257691 ATGCTCCTGATGATGCAGAC 57.742 50.000 0.00 0.00 38.87 3.51
3098 3190 9.329913 CGAAATAACAAAAACTCTACCTGAATG 57.670 33.333 0.00 0.00 0.00 2.67
3123 3215 0.461548 TAGCTCAAGCCAGACCATCG 59.538 55.000 0.00 0.00 43.38 3.84
3320 3503 6.228258 ACAATAACACCACTAACAACGAGAT 58.772 36.000 0.00 0.00 0.00 2.75
3331 3514 3.317993 GCACCAAGAACAATAACACCACT 59.682 43.478 0.00 0.00 0.00 4.00
3606 3789 7.938490 ACACATATGACAAATATCCAGTATGCA 59.062 33.333 10.38 0.00 31.97 3.96
3808 3991 4.037684 AGGCTGCAAAGCATAGATCAAATC 59.962 41.667 0.50 0.00 38.13 2.17
3927 4111 3.797559 AGGGAAAAGGAAAGAGAGTGG 57.202 47.619 0.00 0.00 0.00 4.00
3937 4121 5.374071 GAGTACTGTTGAAAGGGAAAAGGA 58.626 41.667 0.00 0.00 0.00 3.36
3958 4142 8.424918 TGCTCTTATATTTCTTTACAGAGGGAG 58.575 37.037 0.00 0.00 0.00 4.30
3959 4143 8.319057 TGCTCTTATATTTCTTTACAGAGGGA 57.681 34.615 0.00 0.00 0.00 4.20
3960 4144 9.566432 AATGCTCTTATATTTCTTTACAGAGGG 57.434 33.333 0.00 0.00 0.00 4.30
4009 4193 9.379791 CCTCCGTAAAGAAATATAAGAGTGTTT 57.620 33.333 0.00 0.00 0.00 2.83
4010 4194 7.985752 CCCTCCGTAAAGAAATATAAGAGTGTT 59.014 37.037 0.00 0.00 0.00 3.32
4011 4195 7.343833 TCCCTCCGTAAAGAAATATAAGAGTGT 59.656 37.037 0.00 0.00 0.00 3.55
4012 4196 7.723324 TCCCTCCGTAAAGAAATATAAGAGTG 58.277 38.462 0.00 0.00 0.00 3.51
4013 4197 7.564292 ACTCCCTCCGTAAAGAAATATAAGAGT 59.436 37.037 0.00 0.00 0.00 3.24
4014 4198 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
4015 4199 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
4016 4200 9.857957 GATACTCCCTCCGTAAAGAAATATAAG 57.142 37.037 0.00 0.00 0.00 1.73
4017 4201 9.597681 AGATACTCCCTCCGTAAAGAAATATAA 57.402 33.333 0.00 0.00 0.00 0.98
4018 4202 9.021807 CAGATACTCCCTCCGTAAAGAAATATA 57.978 37.037 0.00 0.00 0.00 0.86
4019 4203 7.509659 ACAGATACTCCCTCCGTAAAGAAATAT 59.490 37.037 0.00 0.00 0.00 1.28
4020 4204 6.837568 ACAGATACTCCCTCCGTAAAGAAATA 59.162 38.462 0.00 0.00 0.00 1.40
4021 4205 5.661759 ACAGATACTCCCTCCGTAAAGAAAT 59.338 40.000 0.00 0.00 0.00 2.17
4022 4206 5.021458 ACAGATACTCCCTCCGTAAAGAAA 58.979 41.667 0.00 0.00 0.00 2.52
4023 4207 4.607239 ACAGATACTCCCTCCGTAAAGAA 58.393 43.478 0.00 0.00 0.00 2.52
4024 4208 4.246712 ACAGATACTCCCTCCGTAAAGA 57.753 45.455 0.00 0.00 0.00 2.52
4025 4209 6.448006 CATAACAGATACTCCCTCCGTAAAG 58.552 44.000 0.00 0.00 0.00 1.85
4026 4210 5.221382 GCATAACAGATACTCCCTCCGTAAA 60.221 44.000 0.00 0.00 0.00 2.01
4027 4211 4.280174 GCATAACAGATACTCCCTCCGTAA 59.720 45.833 0.00 0.00 0.00 3.18
4028 4212 3.825014 GCATAACAGATACTCCCTCCGTA 59.175 47.826 0.00 0.00 0.00 4.02
4029 4213 2.628657 GCATAACAGATACTCCCTCCGT 59.371 50.000 0.00 0.00 0.00 4.69
4030 4214 2.028930 GGCATAACAGATACTCCCTCCG 60.029 54.545 0.00 0.00 0.00 4.63
4031 4215 2.972713 TGGCATAACAGATACTCCCTCC 59.027 50.000 0.00 0.00 0.00 4.30
4032 4216 4.101741 ACTTGGCATAACAGATACTCCCTC 59.898 45.833 0.00 0.00 0.00 4.30
4033 4217 4.040755 ACTTGGCATAACAGATACTCCCT 58.959 43.478 0.00 0.00 0.00 4.20
4034 4218 4.423625 ACTTGGCATAACAGATACTCCC 57.576 45.455 0.00 0.00 0.00 4.30
4035 4219 5.065218 CACAACTTGGCATAACAGATACTCC 59.935 44.000 0.00 0.00 0.00 3.85
4036 4220 5.447818 GCACAACTTGGCATAACAGATACTC 60.448 44.000 0.00 0.00 0.00 2.59
4037 4221 4.396166 GCACAACTTGGCATAACAGATACT 59.604 41.667 0.00 0.00 0.00 2.12
4038 4222 4.396166 AGCACAACTTGGCATAACAGATAC 59.604 41.667 0.00 0.00 0.00 2.24
4039 4223 4.588899 AGCACAACTTGGCATAACAGATA 58.411 39.130 0.00 0.00 0.00 1.98
4040 4224 3.424703 AGCACAACTTGGCATAACAGAT 58.575 40.909 0.00 0.00 0.00 2.90
4044 4228 3.855689 ATGAGCACAACTTGGCATAAC 57.144 42.857 0.00 0.00 0.00 1.89
4090 4274 4.380791 AGGGTATACTTCCCAAACCTGAT 58.619 43.478 2.25 0.00 46.82 2.90
4236 4420 6.902408 ACCCCCAATAAAAGACGTTATATCA 58.098 36.000 0.00 0.00 0.00 2.15
4257 4441 5.066593 AGAGTGAGAAATGACTGAAAACCC 58.933 41.667 0.00 0.00 0.00 4.11
4258 4442 6.625873 AAGAGTGAGAAATGACTGAAAACC 57.374 37.500 0.00 0.00 0.00 3.27
4259 4443 8.279103 CAGTAAGAGTGAGAAATGACTGAAAAC 58.721 37.037 0.00 0.00 36.07 2.43
4407 4591 9.815306 TGTATTAGAAGAAGGCATAGAGTAGAT 57.185 33.333 0.00 0.00 0.00 1.98
4408 4592 9.642343 TTGTATTAGAAGAAGGCATAGAGTAGA 57.358 33.333 0.00 0.00 0.00 2.59
4417 4601 6.403200 GCGTCATTTTGTATTAGAAGAAGGCA 60.403 38.462 0.00 0.00 0.00 4.75
4481 4667 9.322773 AGAAAATACATCAGATATGACACAGTG 57.677 33.333 0.00 0.00 0.00 3.66
4504 4690 2.673775 TGCCTGGGTTCAAATCAGAA 57.326 45.000 0.00 0.00 0.00 3.02
4514 4700 2.158415 CCCTATCATTGATGCCTGGGTT 60.158 50.000 9.46 0.00 0.00 4.11
4580 4766 6.140377 AGGACCAAAGGAATAAAGAAAACCA 58.860 36.000 0.00 0.00 0.00 3.67
4629 4816 5.695818 ACAATACAGGAAAACACGCATAAC 58.304 37.500 0.00 0.00 0.00 1.89
4631 4818 5.950758 AACAATACAGGAAAACACGCATA 57.049 34.783 0.00 0.00 0.00 3.14
4632 4819 4.846779 AACAATACAGGAAAACACGCAT 57.153 36.364 0.00 0.00 0.00 4.73
4633 4820 5.057819 TCTAACAATACAGGAAAACACGCA 58.942 37.500 0.00 0.00 0.00 5.24
4634 4821 5.407387 TCTCTAACAATACAGGAAAACACGC 59.593 40.000 0.00 0.00 0.00 5.34
4635 4822 7.416154 TTCTCTAACAATACAGGAAAACACG 57.584 36.000 0.00 0.00 0.00 4.49
4690 4877 1.449246 GCAGGCTGCCAGTACAGAG 60.449 63.158 28.87 1.08 40.25 3.35
4714 4901 2.698274 TGAAGCTAACAGTGTCACCAGA 59.302 45.455 0.00 0.00 0.00 3.86
4715 4902 3.111853 TGAAGCTAACAGTGTCACCAG 57.888 47.619 0.00 0.00 0.00 4.00
4726 4913 4.811557 AGAATGTATCCGCTTGAAGCTAAC 59.188 41.667 15.92 8.13 39.60 2.34
4883 5072 2.455674 ATAAGCTCAACGTCACAGCA 57.544 45.000 13.89 0.00 35.46 4.41
4992 5181 4.248859 CTCAAGGTCAGTTGGATGTACAG 58.751 47.826 0.33 0.00 0.00 2.74
5075 5266 1.246737 GCACCAAGGAGGCAAAGAGG 61.247 60.000 0.00 0.00 43.14 3.69
5188 5379 4.929808 GCTTCATCTGTACCGAAGAAAAGA 59.070 41.667 12.84 0.00 38.75 2.52
5189 5380 4.932200 AGCTTCATCTGTACCGAAGAAAAG 59.068 41.667 12.84 8.33 38.75 2.27
5190 5381 4.894784 AGCTTCATCTGTACCGAAGAAAA 58.105 39.130 12.84 0.20 38.75 2.29
5191 5382 4.220821 AGAGCTTCATCTGTACCGAAGAAA 59.779 41.667 12.84 0.00 38.75 2.52
5192 5383 3.764434 AGAGCTTCATCTGTACCGAAGAA 59.236 43.478 12.84 9.30 38.75 2.52
5197 5388 3.312828 GCATAGAGCTTCATCTGTACCG 58.687 50.000 0.00 0.00 41.15 4.02
5301 5495 9.376075 CACTCATCATTACTTCATACAACTCTT 57.624 33.333 0.00 0.00 0.00 2.85
5375 5570 0.517316 CTTTCGTTTCTCCGCCCAAG 59.483 55.000 0.00 0.00 0.00 3.61
5382 5577 2.542595 TCAACTTCGCTTTCGTTTCTCC 59.457 45.455 0.00 0.00 36.96 3.71
5389 5584 0.798776 ATGGCTCAACTTCGCTTTCG 59.201 50.000 0.00 0.00 0.00 3.46
5401 5596 1.009997 AAGGGGGAAATGATGGCTCA 58.990 50.000 0.00 0.00 35.41 4.26
5427 5622 5.385617 CAATTGTTCTACCTTCTTGCTTCG 58.614 41.667 0.00 0.00 0.00 3.79
5507 5702 4.705023 ACAAATATTTCCGGACAAAGGGAG 59.295 41.667 1.83 0.00 33.01 4.30
5509 5704 4.705023 AGACAAATATTTCCGGACAAAGGG 59.295 41.667 1.83 0.00 0.00 3.95
5510 5705 5.897377 AGACAAATATTTCCGGACAAAGG 57.103 39.130 1.83 0.00 0.00 3.11
5513 5708 6.885952 TTGAAGACAAATATTTCCGGACAA 57.114 33.333 1.83 2.11 32.73 3.18
5514 5709 6.488683 AGTTTGAAGACAAATATTTCCGGACA 59.511 34.615 1.83 0.00 45.71 4.02
5515 5710 6.801862 CAGTTTGAAGACAAATATTTCCGGAC 59.198 38.462 1.83 0.00 45.71 4.79
5516 5711 6.072175 CCAGTTTGAAGACAAATATTTCCGGA 60.072 38.462 0.00 0.00 45.71 5.14
5517 5712 6.072175 TCCAGTTTGAAGACAAATATTTCCGG 60.072 38.462 0.00 0.00 45.71 5.14
5518 5713 6.908825 TCCAGTTTGAAGACAAATATTTCCG 58.091 36.000 0.00 0.00 45.71 4.30
5524 5719 8.802267 CCCTTTTATCCAGTTTGAAGACAAATA 58.198 33.333 0.00 0.00 45.71 1.40
5525 5720 7.256296 CCCCTTTTATCCAGTTTGAAGACAAAT 60.256 37.037 0.00 0.00 45.71 2.32
5526 5721 6.041523 CCCCTTTTATCCAGTTTGAAGACAAA 59.958 38.462 0.00 0.00 42.66 2.83
5527 5722 5.538433 CCCCTTTTATCCAGTTTGAAGACAA 59.462 40.000 0.00 0.00 0.00 3.18
5528 5723 5.076873 CCCCTTTTATCCAGTTTGAAGACA 58.923 41.667 0.00 0.00 0.00 3.41
5529 5724 5.321927 TCCCCTTTTATCCAGTTTGAAGAC 58.678 41.667 0.00 0.00 0.00 3.01
5530 5725 5.592587 TCCCCTTTTATCCAGTTTGAAGA 57.407 39.130 0.00 0.00 0.00 2.87
5531 5726 5.716703 ACATCCCCTTTTATCCAGTTTGAAG 59.283 40.000 0.00 0.00 0.00 3.02
5532 5727 5.650283 ACATCCCCTTTTATCCAGTTTGAA 58.350 37.500 0.00 0.00 0.00 2.69
5533 5728 5.269554 ACATCCCCTTTTATCCAGTTTGA 57.730 39.130 0.00 0.00 0.00 2.69
5534 5729 7.062957 AGATACATCCCCTTTTATCCAGTTTG 58.937 38.462 0.00 0.00 0.00 2.93
5535 5730 7.226059 AGATACATCCCCTTTTATCCAGTTT 57.774 36.000 0.00 0.00 0.00 2.66
5536 5731 6.848562 AGATACATCCCCTTTTATCCAGTT 57.151 37.500 0.00 0.00 0.00 3.16
5537 5732 7.313731 TCTAGATACATCCCCTTTTATCCAGT 58.686 38.462 0.00 0.00 0.00 4.00
5538 5733 7.798710 TCTAGATACATCCCCTTTTATCCAG 57.201 40.000 0.00 0.00 0.00 3.86
5539 5734 7.739444 ACATCTAGATACATCCCCTTTTATCCA 59.261 37.037 4.54 0.00 0.00 3.41
5540 5735 8.152023 ACATCTAGATACATCCCCTTTTATCC 57.848 38.462 4.54 0.00 0.00 2.59
5547 5742 9.845214 ACTAAAATACATCTAGATACATCCCCT 57.155 33.333 4.54 0.00 0.00 4.79
5585 5780 9.918630 ACTTGTCATCAAAATGGATAAAAAGAG 57.081 29.630 0.00 0.00 33.42 2.85
5593 5788 7.975616 CCGAAAATACTTGTCATCAAAATGGAT 59.024 33.333 0.00 0.00 33.42 3.41
5594 5789 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
5595 5790 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
5596 5791 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
5597 5792 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
5598 5793 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
5599 5794 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
5600 5795 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
5601 5796 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
5602 5797 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
5603 5798 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
5604 5799 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
5605 5800 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
5606 5801 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
5607 5802 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
5608 5803 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
5609 5804 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
5610 5805 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
5611 5806 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
5612 5807 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
5613 5808 1.631405 TTACTCCCTCCGTCCGAAAA 58.369 50.000 0.00 0.00 0.00 2.29
5614 5809 1.856629 ATTACTCCCTCCGTCCGAAA 58.143 50.000 0.00 0.00 0.00 3.46
5615 5810 1.856629 AATTACTCCCTCCGTCCGAA 58.143 50.000 0.00 0.00 0.00 4.30
5616 5811 2.092212 AGTAATTACTCCCTCCGTCCGA 60.092 50.000 12.50 0.00 0.00 4.55
5617 5812 2.305009 AGTAATTACTCCCTCCGTCCG 58.695 52.381 12.50 0.00 0.00 4.79
5618 5813 3.255395 GCTAGTAATTACTCCCTCCGTCC 59.745 52.174 21.25 0.00 37.73 4.79
5619 5814 3.887716 TGCTAGTAATTACTCCCTCCGTC 59.112 47.826 21.25 4.45 37.73 4.79
5620 5815 3.907221 TGCTAGTAATTACTCCCTCCGT 58.093 45.455 21.25 0.00 37.73 4.69
5621 5816 5.944599 TCTATGCTAGTAATTACTCCCTCCG 59.055 44.000 21.25 8.13 37.73 4.63
5622 5817 6.153170 GGTCTATGCTAGTAATTACTCCCTCC 59.847 46.154 21.25 10.43 37.73 4.30
5623 5818 6.720288 TGGTCTATGCTAGTAATTACTCCCTC 59.280 42.308 21.25 9.68 37.73 4.30
5624 5819 6.621394 TGGTCTATGCTAGTAATTACTCCCT 58.379 40.000 21.25 9.58 37.73 4.20
5625 5820 6.912951 TGGTCTATGCTAGTAATTACTCCC 57.087 41.667 21.25 13.55 37.73 4.30
5732 5928 9.158233 TGCTAAGTAAGTAATTTTTGCTATCGT 57.842 29.630 0.00 0.00 0.00 3.73
5806 6003 3.663995 TGATTTTTGCCATGGTCAGTG 57.336 42.857 14.67 0.00 0.00 3.66
5810 6007 5.063817 GCTAATGTTGATTTTTGCCATGGTC 59.936 40.000 14.67 6.41 0.00 4.02
5823 6020 7.066284 GTGAATTCACCTACTGCTAATGTTGAT 59.934 37.037 25.26 0.00 40.85 2.57
5892 6106 9.384764 AGACCTTTTAGACATTTAAGATAGCAC 57.615 33.333 0.00 0.00 0.00 4.40
5917 6134 6.884280 ACTCCCTTCATTCACTTTTGTAAG 57.116 37.500 0.00 0.00 37.40 2.34


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

AutoCloner maintained by Alex Coulton.