Multiple sequence alignment - TraesCS7B01G280000

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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 TraesCS7B01G280000 chr7B 100.000 3917 0 0 1 3917 512760630 512756714 0.000000e+00 7234.0
1 TraesCS7B01G280000 chr7A 94.102 3713 159 26 50 3720 553391021 553387327 0.000000e+00 5589.0
2 TraesCS7B01G280000 chr7A 77.746 346 55 14 8 334 545480322 545480664 3.990000e-45 193.0
3 TraesCS7B01G280000 chr7A 91.304 46 3 1 3545 3590 724047485 724047441 1.180000e-05 62.1
4 TraesCS7B01G280000 chr7D 96.115 2703 91 7 450 3146 485104875 485102181 0.000000e+00 4397.0
5 TraesCS7B01G280000 chr7D 80.058 346 25 19 3156 3483 485102130 485101811 2.370000e-52 217.0
6 TraesCS7B01G280000 chr7D 82.353 221 29 6 3705 3917 289252177 289251959 2.400000e-42 183.0
7 TraesCS7B01G280000 chr7D 91.304 46 4 0 3545 3590 53265827 53265782 3.270000e-06 63.9
8 TraesCS7B01G280000 chr1D 89.736 341 27 3 1 333 435266602 435266942 2.800000e-116 429.0
9 TraesCS7B01G280000 chr1D 87.202 336 34 8 2 334 448389814 448390143 1.330000e-99 374.0
10 TraesCS7B01G280000 chr1D 85.223 291 28 9 55 333 61979969 61979682 6.410000e-73 285.0
11 TraesCS7B01G280000 chr6B 86.127 346 32 11 2 333 219219284 219218941 3.720000e-95 359.0
12 TraesCS7B01G280000 chr5B 84.570 337 43 7 3 333 247672045 247672378 3.770000e-85 326.0
13 TraesCS7B01G280000 chr5B 83.333 342 38 14 5 333 493598424 493598089 8.230000e-77 298.0
14 TraesCS7B01G280000 chr5B 78.250 400 65 9 3534 3911 270439001 270439400 1.820000e-58 237.0
15 TraesCS7B01G280000 chr6D 83.285 347 39 12 3 333 163134692 163134349 6.360000e-78 302.0
16 TraesCS7B01G280000 chr1B 87.004 277 25 7 58 331 466941956 466941688 6.360000e-78 302.0
17 TraesCS7B01G280000 chr2D 78.304 401 65 9 3533 3911 327964300 327964700 5.060000e-59 239.0
18 TraesCS7B01G280000 chr4B 77.451 408 64 12 3533 3917 407066753 407066351 6.590000e-53 219.0
19 TraesCS7B01G280000 chr6A 76.658 407 73 11 3533 3917 386109208 386108802 5.130000e-49 206.0
20 TraesCS7B01G280000 chr3B 76.559 401 72 11 3533 3911 417353235 417353635 2.390000e-47 200.0
21 TraesCS7B01G280000 chr3B 91.304 46 4 0 3545 3590 35385943 35385898 3.270000e-06 63.9
22 TraesCS7B01G280000 chr5A 75.980 408 74 13 3533 3917 666208666 666208260 5.170000e-44 189.0
23 TraesCS7B01G280000 chr5A 75.434 403 73 14 3533 3911 606887797 606888197 5.200000e-39 172.0
24 TraesCS7B01G280000 chr4D 75.573 393 74 10 3541 3911 108827292 108827684 1.450000e-39 174.0
25 TraesCS7B01G280000 chr3A 91.304 46 4 0 3545 3590 629017762 629017717 3.270000e-06 63.9
26 TraesCS7B01G280000 chr3A 91.304 46 4 0 3545 3590 696268679 696268634 3.270000e-06 63.9
27 TraesCS7B01G280000 chr3A 91.111 45 4 0 3545 3589 696252229 696252185 1.180000e-05 62.1


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 TraesCS7B01G280000 chr7B 512756714 512760630 3916 True 7234 7234 100.0000 1 3917 1 chr7B.!!$R1 3916
1 TraesCS7B01G280000 chr7A 553387327 553391021 3694 True 5589 5589 94.1020 50 3720 1 chr7A.!!$R1 3670
2 TraesCS7B01G280000 chr7D 485101811 485104875 3064 True 2307 4397 88.0865 450 3483 2 chr7D.!!$R3 3033

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
39 40 0.702383 CGCGTCCGCTTTTTCATTTG 59.298 50.000 10.21 0.0 39.32 2.32 F
42 43 1.000717 CGTCCGCTTTTTCATTTGGGT 60.001 47.619 0.00 0.0 0.00 4.51 F
47 48 1.000843 GCTTTTTCATTTGGGTCGGCT 59.999 47.619 0.00 0.0 0.00 5.52 F
1704 1732 0.034896 CAGCAACCTGTACTTCCGGT 59.965 55.000 0.00 0.0 35.16 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1530 1558 1.472878 CCAGATGGTCGACGAAGAGAA 59.527 52.381 9.92 0.0 0.00 2.87 R
1704 1732 3.064207 GCGATGTTGTGGACTAACAGAA 58.936 45.455 0.00 0.0 40.92 3.02 R
2193 2221 2.709125 TACAGTCAGGGTGCGTGCAC 62.709 60.000 16.40 16.4 45.49 4.57 R
3290 3370 0.167908 AACACACACACACAAGCACG 59.832 50.000 0.00 0.0 0.00 5.34 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
37 38 4.838959 CGCGTCCGCTTTTTCATT 57.161 50.000 10.21 0.00 39.32 2.57
38 39 3.086161 CGCGTCCGCTTTTTCATTT 57.914 47.368 10.21 0.00 39.32 2.32
39 40 0.702383 CGCGTCCGCTTTTTCATTTG 59.298 50.000 10.21 0.00 39.32 2.32
40 41 1.059942 GCGTCCGCTTTTTCATTTGG 58.940 50.000 4.10 0.00 38.26 3.28
41 42 1.696988 CGTCCGCTTTTTCATTTGGG 58.303 50.000 0.00 0.00 0.00 4.12
42 43 1.000717 CGTCCGCTTTTTCATTTGGGT 60.001 47.619 0.00 0.00 0.00 4.51
43 44 2.672714 GTCCGCTTTTTCATTTGGGTC 58.327 47.619 0.00 0.00 0.00 4.46
44 45 1.268352 TCCGCTTTTTCATTTGGGTCG 59.732 47.619 0.00 0.00 0.00 4.79
45 46 1.668628 CCGCTTTTTCATTTGGGTCGG 60.669 52.381 0.00 0.00 0.00 4.79
46 47 1.428448 GCTTTTTCATTTGGGTCGGC 58.572 50.000 0.00 0.00 0.00 5.54
47 48 1.000843 GCTTTTTCATTTGGGTCGGCT 59.999 47.619 0.00 0.00 0.00 5.52
48 49 2.676076 CTTTTTCATTTGGGTCGGCTG 58.324 47.619 0.00 0.00 0.00 4.85
53 54 3.505790 ATTTGGGTCGGCTGGTGCA 62.506 57.895 0.00 0.00 41.91 4.57
82 83 2.422945 GGAGGCCGATCCAAATTTACCT 60.423 50.000 6.15 0.00 39.34 3.08
137 140 6.801575 ACATAATAAAACATTAAGTGGCCGG 58.198 36.000 0.00 0.00 0.00 6.13
139 142 4.976224 ATAAAACATTAAGTGGCCGGTC 57.024 40.909 0.00 0.00 0.00 4.79
169 172 4.500716 CGGCCAAAGTCCACTTAAAACATT 60.501 41.667 2.24 0.00 34.61 2.71
268 278 2.202797 CAGCCGGTGAGGTCGATG 60.203 66.667 1.90 0.00 43.70 3.84
320 330 2.971598 GCTTGGTAGGCTGCCAGGA 61.972 63.158 32.46 15.84 37.31 3.86
403 426 9.525409 GATCGATGAAAATCATTTTGGAATTCT 57.475 29.630 0.54 0.00 37.20 2.40
426 449 9.778741 TTCTATTCTCTTTAATGACACAGTTGT 57.221 29.630 0.00 0.00 39.32 3.32
474 497 5.422331 TGCTTGCTAGTATTCAGTAAGAGGT 59.578 40.000 4.65 0.00 37.78 3.85
542 568 8.248253 ACCTACAATTCAAGTTTTTCTTTTCGT 58.752 29.630 0.00 0.00 33.63 3.85
574 600 5.215160 GCAATTCAAATCGTTGTCTTGTCT 58.785 37.500 0.00 0.00 36.07 3.41
618 644 2.430248 TATGTCTCAGGTGGTAGCGA 57.570 50.000 0.00 0.00 0.00 4.93
810 837 6.716628 TGATTCCTCTGAAGTTTAGCATTGTT 59.283 34.615 0.00 0.00 33.05 2.83
842 870 9.725019 TTTGAGAAGAAATAACTTATCTCTGCA 57.275 29.630 0.00 0.00 38.45 4.41
1095 1123 2.423898 CGTCCCCGTAGCCAGTCAT 61.424 63.158 0.00 0.00 0.00 3.06
1230 1258 2.110901 ACTCAGATTCCAGCAAGCAG 57.889 50.000 0.00 0.00 0.00 4.24
1269 1297 3.558109 GCACCATATCTTCTCCTAAGGGC 60.558 52.174 0.00 0.00 0.00 5.19
1530 1558 4.262079 CCAAGAGTTGACGAAGGTTCTACT 60.262 45.833 0.00 0.00 0.00 2.57
1545 1573 3.049708 TCTACTTCTCTTCGTCGACCA 57.950 47.619 10.58 0.00 0.00 4.02
1704 1732 0.034896 CAGCAACCTGTACTTCCGGT 59.965 55.000 0.00 0.00 35.16 5.28
2193 2221 2.345760 GCATGGTGGTGGCAGAAGG 61.346 63.158 0.00 0.00 0.00 3.46
2690 2718 4.329545 TCGGAGCCACCCTGCAAC 62.330 66.667 0.00 0.00 34.64 4.17
2739 2770 4.143740 CTTCCAGTGGAGGCTCCT 57.856 61.111 32.28 12.46 37.46 3.69
2742 2773 4.106925 CCAGTGGAGGCTCCTGGC 62.107 72.222 32.28 21.70 39.36 4.85
2955 2986 2.503375 CCGACCTCCGTTTCGACG 60.503 66.667 0.00 0.00 37.43 5.12
2999 3030 0.392336 CTCCTGCTCCTGTCCTATGC 59.608 60.000 0.00 0.00 0.00 3.14
3033 3065 2.029244 CGCGGTATGATTGTGTGAAGTC 59.971 50.000 0.00 0.00 0.00 3.01
3122 3155 2.546789 GGTTGGGTGTCGAAGTGTTAAG 59.453 50.000 0.00 0.00 0.00 1.85
3154 3228 3.438781 GTCTTGTGTTGAAGGTGTGTTCA 59.561 43.478 0.00 0.00 34.56 3.18
3174 3251 6.150641 TGTTCATAGTACAGTGGTCTACAGTC 59.849 42.308 0.00 0.00 30.97 3.51
3244 3322 5.385509 ACAGTTATACAACATTTGGGTGC 57.614 39.130 0.00 0.00 37.10 5.01
3290 3370 9.169468 GCTGTTGTATACAAACATATATTGTGC 57.831 33.333 19.63 12.16 40.95 4.57
3306 3386 2.037702 TGCGTGCTTGTGTGTGTGT 61.038 52.632 0.00 0.00 0.00 3.72
3307 3387 1.583451 GCGTGCTTGTGTGTGTGTG 60.583 57.895 0.00 0.00 0.00 3.82
3308 3388 1.793581 CGTGCTTGTGTGTGTGTGT 59.206 52.632 0.00 0.00 0.00 3.72
3309 3389 0.167908 CGTGCTTGTGTGTGTGTGTT 59.832 50.000 0.00 0.00 0.00 3.32
3310 3390 1.400888 CGTGCTTGTGTGTGTGTGTTT 60.401 47.619 0.00 0.00 0.00 2.83
3311 3391 1.984990 GTGCTTGTGTGTGTGTGTTTG 59.015 47.619 0.00 0.00 0.00 2.93
3312 3392 1.611006 TGCTTGTGTGTGTGTGTTTGT 59.389 42.857 0.00 0.00 0.00 2.83
3313 3393 1.984990 GCTTGTGTGTGTGTGTTTGTG 59.015 47.619 0.00 0.00 0.00 3.33
3314 3394 2.606795 GCTTGTGTGTGTGTGTTTGTGT 60.607 45.455 0.00 0.00 0.00 3.72
3315 3395 2.695613 TGTGTGTGTGTGTTTGTGTG 57.304 45.000 0.00 0.00 0.00 3.82
3316 3396 1.950216 TGTGTGTGTGTGTTTGTGTGT 59.050 42.857 0.00 0.00 0.00 3.72
3317 3397 2.031595 TGTGTGTGTGTGTTTGTGTGTC 60.032 45.455 0.00 0.00 0.00 3.67
3318 3398 2.225491 GTGTGTGTGTGTTTGTGTGTCT 59.775 45.455 0.00 0.00 0.00 3.41
3319 3399 2.225255 TGTGTGTGTGTTTGTGTGTCTG 59.775 45.455 0.00 0.00 0.00 3.51
3387 3468 5.762179 TGGTTGTTGTATCTCTCATCCTT 57.238 39.130 0.00 0.00 0.00 3.36
3389 3470 6.542821 TGGTTGTTGTATCTCTCATCCTTTT 58.457 36.000 0.00 0.00 0.00 2.27
3462 3554 1.202976 AGGCAGAGGCTGAATGTTTGT 60.203 47.619 0.00 0.00 40.87 2.83
3480 3572 7.364522 TGTTTGTTTCTCAGAAGATATTCCG 57.635 36.000 0.00 0.00 0.00 4.30
3483 3575 6.968131 TGTTTCTCAGAAGATATTCCGTTG 57.032 37.500 0.00 0.00 0.00 4.10
3523 3615 8.840321 ACATATTGAGATTTGTAAGGCATACAC 58.160 33.333 1.44 0.00 44.11 2.90
3528 3620 6.874664 TGAGATTTGTAAGGCATACACGTTTA 59.125 34.615 1.44 0.00 44.11 2.01
3538 3637 6.604930 AGGCATACACGTTTATTTACAACAC 58.395 36.000 0.00 0.00 0.00 3.32
3542 3641 7.149096 GCATACACGTTTATTTACAACACCAAC 60.149 37.037 0.00 0.00 0.00 3.77
3544 3643 6.618811 ACACGTTTATTTACAACACCAACAA 58.381 32.000 0.00 0.00 0.00 2.83
3547 3646 7.273815 CACGTTTATTTACAACACCAACAAAGT 59.726 33.333 0.00 0.00 0.00 2.66
3553 3652 8.920509 ATTTACAACACCAACAAAGTCTTTAC 57.079 30.769 0.00 0.00 0.00 2.01
3564 3663 8.129211 CCAACAAAGTCTTTACTCCTAAACAAG 58.871 37.037 0.00 0.00 33.75 3.16
3567 3666 8.674607 ACAAAGTCTTTACTCCTAAACAAGTTG 58.325 33.333 0.00 0.00 33.75 3.16
3569 3668 6.296803 AGTCTTTACTCCTAAACAAGTTGGG 58.703 40.000 7.96 0.00 39.23 4.12
3570 3669 5.472478 GTCTTTACTCCTAAACAAGTTGGGG 59.528 44.000 7.96 4.21 38.40 4.96
3574 3673 3.244805 ACTCCTAAACAAGTTGGGGTAGC 60.245 47.826 7.96 0.00 38.40 3.58
3580 3679 2.846950 ACAAGTTGGGGTAGCCTAGAT 58.153 47.619 11.48 0.00 0.00 1.98
3594 3693 7.256908 GGGTAGCCTAGATATGAAACCCATAAA 60.257 40.741 2.95 0.00 43.95 1.40
3598 3697 8.448008 AGCCTAGATATGAAACCCATAAAATCA 58.552 33.333 0.00 0.00 40.79 2.57
3599 3698 9.247861 GCCTAGATATGAAACCCATAAAATCAT 57.752 33.333 0.00 0.00 40.79 2.45
3624 3727 2.760650 ACTCATAGTTCTCGCACATGGA 59.239 45.455 0.00 0.00 0.00 3.41
3625 3728 3.386078 ACTCATAGTTCTCGCACATGGAT 59.614 43.478 0.00 0.00 0.00 3.41
3627 3730 5.069119 ACTCATAGTTCTCGCACATGGATAA 59.931 40.000 0.00 0.00 0.00 1.75
3631 3734 4.323417 AGTTCTCGCACATGGATAACAAA 58.677 39.130 0.00 0.00 0.00 2.83
3634 3737 4.323417 TCTCGCACATGGATAACAAACTT 58.677 39.130 0.00 0.00 0.00 2.66
3637 3740 3.845775 CGCACATGGATAACAAACTTTCG 59.154 43.478 0.00 0.00 0.00 3.46
3639 3742 4.615912 GCACATGGATAACAAACTTTCGCT 60.616 41.667 0.00 0.00 0.00 4.93
3642 3745 4.742438 TGGATAACAAACTTTCGCTCAC 57.258 40.909 0.00 0.00 0.00 3.51
3650 3753 2.693267 ACTTTCGCTCACCCCTATTC 57.307 50.000 0.00 0.00 0.00 1.75
3661 3764 5.367945 TCACCCCTATTCATGGTTAGTTC 57.632 43.478 0.00 0.00 0.00 3.01
3662 3765 4.785914 TCACCCCTATTCATGGTTAGTTCA 59.214 41.667 0.00 0.00 0.00 3.18
3694 3798 4.399934 ACTCAGATCTCTTTTACGGACTCC 59.600 45.833 0.00 0.00 0.00 3.85
3715 3819 8.934023 ACTCCTTTCATATCAAGTTTGGTTTA 57.066 30.769 0.00 0.00 0.00 2.01
3720 3824 8.698973 TTTCATATCAAGTTTGGTTTACCTCA 57.301 30.769 0.00 0.00 36.82 3.86
3721 3825 8.698973 TTCATATCAAGTTTGGTTTACCTCAA 57.301 30.769 0.00 0.00 36.82 3.02
3722 3826 8.106247 TCATATCAAGTTTGGTTTACCTCAAC 57.894 34.615 0.00 3.89 36.82 3.18
3723 3827 5.784578 ATCAAGTTTGGTTTACCTCAACC 57.215 39.130 0.00 0.00 45.88 3.77
3724 3828 4.862371 TCAAGTTTGGTTTACCTCAACCT 58.138 39.130 4.32 0.00 45.87 3.50
3725 3829 5.265989 TCAAGTTTGGTTTACCTCAACCTT 58.734 37.500 4.32 0.00 45.87 3.50
3726 3830 5.717654 TCAAGTTTGGTTTACCTCAACCTTT 59.282 36.000 4.32 0.00 45.87 3.11
3727 3831 5.847111 AGTTTGGTTTACCTCAACCTTTC 57.153 39.130 4.32 0.00 45.87 2.62
3728 3832 5.516044 AGTTTGGTTTACCTCAACCTTTCT 58.484 37.500 4.32 0.00 45.87 2.52
3729 3833 5.955959 AGTTTGGTTTACCTCAACCTTTCTT 59.044 36.000 4.32 0.00 45.87 2.52
3730 3834 7.120716 AGTTTGGTTTACCTCAACCTTTCTTA 58.879 34.615 4.32 0.00 45.87 2.10
3731 3835 7.616542 AGTTTGGTTTACCTCAACCTTTCTTAA 59.383 33.333 4.32 0.00 45.87 1.85
3732 3836 6.947644 TGGTTTACCTCAACCTTTCTTAAC 57.052 37.500 4.32 0.00 45.87 2.01
3733 3837 6.424883 TGGTTTACCTCAACCTTTCTTAACA 58.575 36.000 4.32 0.00 45.87 2.41
3734 3838 7.064229 TGGTTTACCTCAACCTTTCTTAACAT 58.936 34.615 4.32 0.00 45.87 2.71
3735 3839 7.562088 TGGTTTACCTCAACCTTTCTTAACATT 59.438 33.333 4.32 0.00 45.87 2.71
3736 3840 9.070179 GGTTTACCTCAACCTTTCTTAACATTA 57.930 33.333 0.00 0.00 42.79 1.90
3740 3844 8.934023 ACCTCAACCTTTCTTAACATTATCAA 57.066 30.769 0.00 0.00 0.00 2.57
3741 3845 8.793592 ACCTCAACCTTTCTTAACATTATCAAC 58.206 33.333 0.00 0.00 0.00 3.18
3742 3846 8.792633 CCTCAACCTTTCTTAACATTATCAACA 58.207 33.333 0.00 0.00 0.00 3.33
3743 3847 9.612620 CTCAACCTTTCTTAACATTATCAACAC 57.387 33.333 0.00 0.00 0.00 3.32
3744 3848 8.286800 TCAACCTTTCTTAACATTATCAACACG 58.713 33.333 0.00 0.00 0.00 4.49
3745 3849 7.739498 ACCTTTCTTAACATTATCAACACGT 57.261 32.000 0.00 0.00 0.00 4.49
3746 3850 8.161699 ACCTTTCTTAACATTATCAACACGTT 57.838 30.769 0.00 0.00 0.00 3.99
3747 3851 8.626526 ACCTTTCTTAACATTATCAACACGTTT 58.373 29.630 0.00 0.00 0.00 3.60
3748 3852 9.458374 CCTTTCTTAACATTATCAACACGTTTT 57.542 29.630 0.00 0.00 0.00 2.43
3751 3855 9.601971 TTCTTAACATTATCAACACGTTTTAGC 57.398 29.630 0.00 0.00 0.00 3.09
3752 3856 8.231837 TCTTAACATTATCAACACGTTTTAGCC 58.768 33.333 0.00 0.00 0.00 3.93
3753 3857 5.950758 ACATTATCAACACGTTTTAGCCA 57.049 34.783 0.00 0.00 0.00 4.75
3754 3858 6.509418 ACATTATCAACACGTTTTAGCCAT 57.491 33.333 0.00 0.00 0.00 4.40
3755 3859 6.919721 ACATTATCAACACGTTTTAGCCATT 58.080 32.000 0.00 0.00 0.00 3.16
3756 3860 7.027161 ACATTATCAACACGTTTTAGCCATTC 58.973 34.615 0.00 0.00 0.00 2.67
3757 3861 6.561737 TTATCAACACGTTTTAGCCATTCA 57.438 33.333 0.00 0.00 0.00 2.57
3758 3862 4.217754 TCAACACGTTTTAGCCATTCAC 57.782 40.909 0.00 0.00 0.00 3.18
3759 3863 3.880490 TCAACACGTTTTAGCCATTCACT 59.120 39.130 0.00 0.00 0.00 3.41
3760 3864 3.896648 ACACGTTTTAGCCATTCACTG 57.103 42.857 0.00 0.00 0.00 3.66
3761 3865 3.211045 ACACGTTTTAGCCATTCACTGT 58.789 40.909 0.00 0.00 0.00 3.55
3762 3866 4.382291 ACACGTTTTAGCCATTCACTGTA 58.618 39.130 0.00 0.00 0.00 2.74
3763 3867 4.451096 ACACGTTTTAGCCATTCACTGTAG 59.549 41.667 0.00 0.00 0.00 2.74
3764 3868 4.451096 CACGTTTTAGCCATTCACTGTAGT 59.549 41.667 0.00 0.00 0.00 2.73
3765 3869 5.049680 CACGTTTTAGCCATTCACTGTAGTT 60.050 40.000 0.00 0.00 0.00 2.24
3766 3870 5.529800 ACGTTTTAGCCATTCACTGTAGTTT 59.470 36.000 0.00 0.00 0.00 2.66
3767 3871 6.077838 CGTTTTAGCCATTCACTGTAGTTTC 58.922 40.000 0.00 0.00 0.00 2.78
3768 3872 6.073222 CGTTTTAGCCATTCACTGTAGTTTCT 60.073 38.462 0.00 0.00 0.00 2.52
3769 3873 6.801539 TTTAGCCATTCACTGTAGTTTCTG 57.198 37.500 0.00 0.00 0.00 3.02
3770 3874 3.679389 AGCCATTCACTGTAGTTTCTGG 58.321 45.455 0.00 0.00 0.00 3.86
3771 3875 3.327757 AGCCATTCACTGTAGTTTCTGGA 59.672 43.478 7.38 0.00 0.00 3.86
3772 3876 3.686726 GCCATTCACTGTAGTTTCTGGAG 59.313 47.826 7.38 0.00 0.00 3.86
3773 3877 4.256920 CCATTCACTGTAGTTTCTGGAGG 58.743 47.826 0.00 0.00 0.00 4.30
3774 3878 3.402628 TTCACTGTAGTTTCTGGAGGC 57.597 47.619 0.00 0.00 0.00 4.70
3775 3879 1.623811 TCACTGTAGTTTCTGGAGGCC 59.376 52.381 0.00 0.00 0.00 5.19
3776 3880 0.608640 ACTGTAGTTTCTGGAGGCCG 59.391 55.000 0.00 0.00 0.00 6.13
3777 3881 0.608640 CTGTAGTTTCTGGAGGCCGT 59.391 55.000 0.00 0.00 0.00 5.68
3778 3882 0.320374 TGTAGTTTCTGGAGGCCGTG 59.680 55.000 0.00 0.00 0.00 4.94
3779 3883 0.320697 GTAGTTTCTGGAGGCCGTGT 59.679 55.000 0.00 0.00 0.00 4.49
3780 3884 1.053424 TAGTTTCTGGAGGCCGTGTT 58.947 50.000 0.00 0.00 0.00 3.32
3781 3885 0.535102 AGTTTCTGGAGGCCGTGTTG 60.535 55.000 0.00 0.00 0.00 3.33
3782 3886 1.228124 TTTCTGGAGGCCGTGTTGG 60.228 57.895 0.00 0.00 42.50 3.77
3783 3887 1.701031 TTTCTGGAGGCCGTGTTGGA 61.701 55.000 0.00 0.00 42.00 3.53
3784 3888 1.488705 TTCTGGAGGCCGTGTTGGAT 61.489 55.000 0.00 0.00 42.00 3.41
3785 3889 0.616395 TCTGGAGGCCGTGTTGGATA 60.616 55.000 0.00 0.00 42.00 2.59
3786 3890 0.469917 CTGGAGGCCGTGTTGGATAT 59.530 55.000 0.00 0.00 42.00 1.63
3787 3891 1.691976 CTGGAGGCCGTGTTGGATATA 59.308 52.381 0.00 0.00 42.00 0.86
3788 3892 1.414919 TGGAGGCCGTGTTGGATATAC 59.585 52.381 0.00 0.00 42.00 1.47
3789 3893 1.692519 GGAGGCCGTGTTGGATATACT 59.307 52.381 0.00 0.00 42.00 2.12
3790 3894 2.288886 GGAGGCCGTGTTGGATATACTC 60.289 54.545 0.00 0.00 42.00 2.59
3791 3895 2.364324 GAGGCCGTGTTGGATATACTCA 59.636 50.000 0.00 0.00 42.00 3.41
3792 3896 2.769663 AGGCCGTGTTGGATATACTCAA 59.230 45.455 0.00 0.00 42.00 3.02
3793 3897 3.199071 AGGCCGTGTTGGATATACTCAAA 59.801 43.478 0.00 0.00 42.00 2.69
3794 3898 3.311596 GGCCGTGTTGGATATACTCAAAC 59.688 47.826 0.00 0.00 42.00 2.93
3795 3899 3.311596 GCCGTGTTGGATATACTCAAACC 59.688 47.826 0.00 0.00 42.00 3.27
3796 3900 3.554324 CCGTGTTGGATATACTCAAACCG 59.446 47.826 0.00 0.00 42.00 4.44
3797 3901 4.178540 CGTGTTGGATATACTCAAACCGT 58.821 43.478 0.00 0.00 37.03 4.83
3798 3902 4.266976 CGTGTTGGATATACTCAAACCGTC 59.733 45.833 0.00 0.00 37.03 4.79
3799 3903 5.416947 GTGTTGGATATACTCAAACCGTCT 58.583 41.667 0.00 0.00 37.03 4.18
3800 3904 5.519206 GTGTTGGATATACTCAAACCGTCTC 59.481 44.000 0.00 0.00 37.03 3.36
3801 3905 5.186215 TGTTGGATATACTCAAACCGTCTCA 59.814 40.000 0.00 0.00 37.03 3.27
3802 3906 5.515797 TGGATATACTCAAACCGTCTCAG 57.484 43.478 0.00 0.00 0.00 3.35
3803 3907 5.198207 TGGATATACTCAAACCGTCTCAGA 58.802 41.667 0.00 0.00 0.00 3.27
3804 3908 5.067413 TGGATATACTCAAACCGTCTCAGAC 59.933 44.000 0.00 0.00 0.00 3.51
3818 3922 5.000012 GTCTCAGACGATATTGGACAAGT 58.000 43.478 0.00 0.00 0.00 3.16
3819 3923 5.411781 GTCTCAGACGATATTGGACAAGTT 58.588 41.667 0.00 0.00 0.00 2.66
3820 3924 5.869888 GTCTCAGACGATATTGGACAAGTTT 59.130 40.000 0.00 0.00 0.00 2.66
3821 3925 6.035112 GTCTCAGACGATATTGGACAAGTTTC 59.965 42.308 0.00 0.00 0.00 2.78
3822 3926 6.037786 TCAGACGATATTGGACAAGTTTCT 57.962 37.500 0.00 0.00 0.00 2.52
3823 3927 6.100004 TCAGACGATATTGGACAAGTTTCTC 58.900 40.000 0.00 0.00 0.00 2.87
3824 3928 6.071334 TCAGACGATATTGGACAAGTTTCTCT 60.071 38.462 0.00 0.00 0.00 3.10
3825 3929 6.591834 CAGACGATATTGGACAAGTTTCTCTT 59.408 38.462 0.00 0.00 36.75 2.85
3826 3930 6.814146 AGACGATATTGGACAAGTTTCTCTTC 59.186 38.462 0.00 0.00 33.63 2.87
3827 3931 5.577164 ACGATATTGGACAAGTTTCTCTTCG 59.423 40.000 0.00 0.00 33.63 3.79
3828 3932 5.805486 CGATATTGGACAAGTTTCTCTTCGA 59.195 40.000 0.00 0.00 33.63 3.71
3829 3933 6.477033 CGATATTGGACAAGTTTCTCTTCGAT 59.523 38.462 0.00 0.00 33.63 3.59
3830 3934 7.306283 CGATATTGGACAAGTTTCTCTTCGATC 60.306 40.741 0.00 0.00 33.63 3.69
3831 3935 3.575630 TGGACAAGTTTCTCTTCGATCG 58.424 45.455 9.36 9.36 33.63 3.69
3832 3936 2.924290 GGACAAGTTTCTCTTCGATCGG 59.076 50.000 16.41 0.00 33.63 4.18
3833 3937 3.576648 GACAAGTTTCTCTTCGATCGGT 58.423 45.455 16.41 0.00 33.63 4.69
3834 3938 3.318017 ACAAGTTTCTCTTCGATCGGTG 58.682 45.455 16.41 8.55 33.63 4.94
3835 3939 1.997669 AGTTTCTCTTCGATCGGTGC 58.002 50.000 16.41 0.00 0.00 5.01
3836 3940 1.546476 AGTTTCTCTTCGATCGGTGCT 59.454 47.619 16.41 0.16 0.00 4.40
3837 3941 2.753452 AGTTTCTCTTCGATCGGTGCTA 59.247 45.455 16.41 0.00 0.00 3.49
3838 3942 2.846039 TTCTCTTCGATCGGTGCTAC 57.154 50.000 16.41 0.00 0.00 3.58
3839 3943 2.039818 TCTCTTCGATCGGTGCTACT 57.960 50.000 16.41 0.00 0.00 2.57
3840 3944 1.941294 TCTCTTCGATCGGTGCTACTC 59.059 52.381 16.41 0.00 0.00 2.59
3841 3945 1.002251 CTCTTCGATCGGTGCTACTCC 60.002 57.143 16.41 0.00 0.00 3.85
3842 3946 0.738975 CTTCGATCGGTGCTACTCCA 59.261 55.000 16.41 0.00 0.00 3.86
3843 3947 1.134367 CTTCGATCGGTGCTACTCCAA 59.866 52.381 16.41 0.00 0.00 3.53
3844 3948 1.399714 TCGATCGGTGCTACTCCAAT 58.600 50.000 16.41 0.00 0.00 3.16
3845 3949 1.754803 TCGATCGGTGCTACTCCAATT 59.245 47.619 16.41 0.00 0.00 2.32
3846 3950 2.128035 CGATCGGTGCTACTCCAATTC 58.872 52.381 7.38 0.00 0.00 2.17
3847 3951 2.223829 CGATCGGTGCTACTCCAATTCT 60.224 50.000 7.38 0.00 0.00 2.40
3848 3952 3.004419 CGATCGGTGCTACTCCAATTCTA 59.996 47.826 7.38 0.00 0.00 2.10
3849 3953 4.321304 CGATCGGTGCTACTCCAATTCTAT 60.321 45.833 7.38 0.00 0.00 1.98
3850 3954 4.585955 TCGGTGCTACTCCAATTCTATC 57.414 45.455 0.00 0.00 0.00 2.08
3851 3955 4.215908 TCGGTGCTACTCCAATTCTATCT 58.784 43.478 0.00 0.00 0.00 1.98
3852 3956 4.278669 TCGGTGCTACTCCAATTCTATCTC 59.721 45.833 0.00 0.00 0.00 2.75
3853 3957 4.551388 GGTGCTACTCCAATTCTATCTCG 58.449 47.826 0.00 0.00 0.00 4.04
3854 3958 4.038162 GGTGCTACTCCAATTCTATCTCGT 59.962 45.833 0.00 0.00 0.00 4.18
3855 3959 5.241064 GGTGCTACTCCAATTCTATCTCGTA 59.759 44.000 0.00 0.00 0.00 3.43
3856 3960 6.071840 GGTGCTACTCCAATTCTATCTCGTAT 60.072 42.308 0.00 0.00 0.00 3.06
3857 3961 7.120873 GGTGCTACTCCAATTCTATCTCGTATA 59.879 40.741 0.00 0.00 0.00 1.47
3858 3962 8.679100 GTGCTACTCCAATTCTATCTCGTATAT 58.321 37.037 0.00 0.00 0.00 0.86
3859 3963 8.894731 TGCTACTCCAATTCTATCTCGTATATC 58.105 37.037 0.00 0.00 0.00 1.63
3860 3964 8.894731 GCTACTCCAATTCTATCTCGTATATCA 58.105 37.037 0.00 0.00 0.00 2.15
3863 3967 9.467796 ACTCCAATTCTATCTCGTATATCATCA 57.532 33.333 0.00 0.00 0.00 3.07
3868 3972 9.958234 AATTCTATCTCGTATATCATCATTCCG 57.042 33.333 0.00 0.00 0.00 4.30
3869 3973 7.497925 TCTATCTCGTATATCATCATTCCGG 57.502 40.000 0.00 0.00 0.00 5.14
3870 3974 7.280356 TCTATCTCGTATATCATCATTCCGGA 58.720 38.462 0.00 0.00 0.00 5.14
3871 3975 6.968263 ATCTCGTATATCATCATTCCGGAT 57.032 37.500 4.15 0.00 0.00 4.18
3872 3976 6.378710 TCTCGTATATCATCATTCCGGATC 57.621 41.667 4.15 0.00 0.00 3.36
3873 3977 5.299531 TCTCGTATATCATCATTCCGGATCC 59.700 44.000 4.15 0.00 0.00 3.36
3874 3978 4.036380 TCGTATATCATCATTCCGGATCCG 59.964 45.833 27.65 27.65 39.44 4.18
3886 3990 2.094762 CGGATCCGGTTCTTTCTTGT 57.905 50.000 26.95 0.00 35.56 3.16
3887 3991 1.732259 CGGATCCGGTTCTTTCTTGTG 59.268 52.381 26.95 0.00 35.56 3.33
3888 3992 2.779506 GGATCCGGTTCTTTCTTGTGT 58.220 47.619 12.19 0.00 0.00 3.72
3889 3993 2.484264 GGATCCGGTTCTTTCTTGTGTG 59.516 50.000 12.19 0.00 0.00 3.82
3890 3994 1.961793 TCCGGTTCTTTCTTGTGTGG 58.038 50.000 0.00 0.00 0.00 4.17
3891 3995 0.310854 CCGGTTCTTTCTTGTGTGGC 59.689 55.000 0.00 0.00 0.00 5.01
3892 3996 0.310854 CGGTTCTTTCTTGTGTGGCC 59.689 55.000 0.00 0.00 0.00 5.36
3893 3997 1.398692 GGTTCTTTCTTGTGTGGCCA 58.601 50.000 0.00 0.00 0.00 5.36
3894 3998 1.067060 GGTTCTTTCTTGTGTGGCCAC 59.933 52.381 29.67 29.67 42.19 5.01
3904 4008 2.436109 GTGGCCACACATCCACCT 59.564 61.111 31.23 0.00 46.90 4.00
3905 4009 1.228552 GTGGCCACACATCCACCTT 60.229 57.895 31.23 0.00 46.90 3.50
3906 4010 0.037590 GTGGCCACACATCCACCTTA 59.962 55.000 31.23 0.00 46.90 2.69
3907 4011 0.774276 TGGCCACACATCCACCTTAA 59.226 50.000 0.00 0.00 0.00 1.85
3908 4012 1.173913 GGCCACACATCCACCTTAAC 58.826 55.000 0.00 0.00 0.00 2.01
3909 4013 1.546773 GGCCACACATCCACCTTAACA 60.547 52.381 0.00 0.00 0.00 2.41
3910 4014 2.446435 GCCACACATCCACCTTAACAT 58.554 47.619 0.00 0.00 0.00 2.71
3911 4015 2.164219 GCCACACATCCACCTTAACATG 59.836 50.000 0.00 0.00 0.00 3.21
3912 4016 3.420893 CCACACATCCACCTTAACATGT 58.579 45.455 0.00 0.00 0.00 3.21
3914 4018 2.819608 ACACATCCACCTTAACATGTGC 59.180 45.455 0.00 0.00 46.77 4.57
3915 4019 2.819019 CACATCCACCTTAACATGTGCA 59.181 45.455 0.00 0.00 39.66 4.57
3916 4020 3.444742 CACATCCACCTTAACATGTGCAT 59.555 43.478 0.00 0.00 39.66 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 1.059942 CCAAATGAAAAAGCGGACGC 58.940 50.000 8.91 8.91 42.33 5.19
22 23 1.000717 ACCCAAATGAAAAAGCGGACG 60.001 47.619 0.00 0.00 0.00 4.79
23 24 2.672714 GACCCAAATGAAAAAGCGGAC 58.327 47.619 0.00 0.00 0.00 4.79
24 25 1.268352 CGACCCAAATGAAAAAGCGGA 59.732 47.619 0.00 0.00 0.00 5.54
25 26 1.668628 CCGACCCAAATGAAAAAGCGG 60.669 52.381 0.00 0.00 0.00 5.52
26 27 1.696988 CCGACCCAAATGAAAAAGCG 58.303 50.000 0.00 0.00 0.00 4.68
27 28 1.000843 AGCCGACCCAAATGAAAAAGC 59.999 47.619 0.00 0.00 0.00 3.51
28 29 2.610232 CCAGCCGACCCAAATGAAAAAG 60.610 50.000 0.00 0.00 0.00 2.27
29 30 1.342819 CCAGCCGACCCAAATGAAAAA 59.657 47.619 0.00 0.00 0.00 1.94
30 31 0.965439 CCAGCCGACCCAAATGAAAA 59.035 50.000 0.00 0.00 0.00 2.29
31 32 0.178975 ACCAGCCGACCCAAATGAAA 60.179 50.000 0.00 0.00 0.00 2.69
32 33 0.893270 CACCAGCCGACCCAAATGAA 60.893 55.000 0.00 0.00 0.00 2.57
33 34 1.303236 CACCAGCCGACCCAAATGA 60.303 57.895 0.00 0.00 0.00 2.57
34 35 2.993471 GCACCAGCCGACCCAAATG 61.993 63.158 0.00 0.00 33.58 2.32
35 36 2.676471 GCACCAGCCGACCCAAAT 60.676 61.111 0.00 0.00 33.58 2.32
36 37 4.196778 TGCACCAGCCGACCCAAA 62.197 61.111 0.00 0.00 41.13 3.28
37 38 4.947147 GTGCACCAGCCGACCCAA 62.947 66.667 5.22 0.00 41.13 4.12
68 69 3.013921 TGGACGCAGGTAAATTTGGATC 58.986 45.455 0.00 0.00 0.00 3.36
70 71 2.570415 TGGACGCAGGTAAATTTGGA 57.430 45.000 0.00 0.00 0.00 3.53
137 140 4.038080 CTTTGGCCGGCGGTTGAC 62.038 66.667 28.82 15.69 0.00 3.18
139 142 4.038080 GACTTTGGCCGGCGGTTG 62.038 66.667 28.82 13.30 0.00 3.77
211 215 2.028190 CGGATGTCTAGGGCAGCG 59.972 66.667 0.00 0.00 0.00 5.18
288 298 3.936203 AAGCAGCGTTCGGGTGGA 61.936 61.111 0.00 0.00 44.32 4.02
289 299 3.726517 CAAGCAGCGTTCGGGTGG 61.727 66.667 0.00 0.00 44.32 4.61
320 330 0.259065 TAGTCATCGGAGGAGGCTGT 59.741 55.000 0.00 0.00 0.00 4.40
453 476 6.436218 TGACACCTCTTACTGAATACTAGCAA 59.564 38.462 0.00 0.00 0.00 3.91
454 477 5.949952 TGACACCTCTTACTGAATACTAGCA 59.050 40.000 0.00 0.00 0.00 3.49
474 497 8.842358 AAACTTAAGGAATCGAAAGTATGACA 57.158 30.769 7.53 0.00 32.09 3.58
542 568 7.089538 ACAACGATTTGAATTGCATGTCATTA 58.910 30.769 1.04 0.00 36.48 1.90
574 600 8.635765 AATGTCAACTTTTGCTAAAGGATAGA 57.364 30.769 21.83 12.08 44.10 1.98
618 644 7.432148 TGTAGGGTACTGTTCAATCATGTAT 57.568 36.000 0.00 0.00 0.00 2.29
810 837 6.639632 AAGTTATTTCTTCTCAAAGCAGCA 57.360 33.333 0.00 0.00 32.18 4.41
840 868 3.282021 TCCATTTTCCAGTGCTCTATGC 58.718 45.455 0.00 0.00 43.25 3.14
842 870 4.141620 ACGATCCATTTTCCAGTGCTCTAT 60.142 41.667 0.00 0.00 0.00 1.98
1095 1123 2.730382 TGACTATTACTGTCTGCGGGA 58.270 47.619 0.00 0.00 35.63 5.14
1230 1258 2.817423 GCAGCCAGCACGCATACTC 61.817 63.158 0.00 0.00 44.79 2.59
1269 1297 5.059161 TCAACAGAAGAACCTTCATCACTG 58.941 41.667 9.10 0.00 33.19 3.66
1501 1529 3.367498 CCTTCGTCAACTCTTGGGACTAG 60.367 52.174 0.00 0.00 0.00 2.57
1530 1558 1.472878 CCAGATGGTCGACGAAGAGAA 59.527 52.381 9.92 0.00 0.00 2.87
1545 1573 5.520748 AATTAAGGAACTGACCACCAGAT 57.479 39.130 0.00 0.00 45.78 2.90
1583 1611 3.913799 TGGAGAAAACCCAGTCATCCTTA 59.086 43.478 0.00 0.00 0.00 2.69
1704 1732 3.064207 GCGATGTTGTGGACTAACAGAA 58.936 45.455 0.00 0.00 40.92 3.02
2193 2221 2.709125 TACAGTCAGGGTGCGTGCAC 62.709 60.000 16.40 16.40 45.49 4.57
2425 2453 1.065854 GCTCTTATCACACCCAGCAGT 60.066 52.381 0.00 0.00 0.00 4.40
2538 2566 4.643387 GCAAGGCGGTCACAGGGT 62.643 66.667 0.00 0.00 0.00 4.34
2690 2718 2.747855 GCCTGCTGGTTTCCGAGG 60.748 66.667 11.69 0.00 35.27 4.63
2778 2809 3.631144 AGCAAACATTGACACGATGTTG 58.369 40.909 15.22 11.38 44.55 3.33
2955 2986 2.851104 CCAGACGAAACGAACCGC 59.149 61.111 0.00 0.00 0.00 5.68
2999 3030 2.501223 TACCGCGGCCTTCTTCACAG 62.501 60.000 28.58 0.00 0.00 3.66
3122 3155 7.860872 CACCTTCAACACAAGACCTAAAATTAC 59.139 37.037 0.00 0.00 0.00 1.89
3154 3228 5.067936 GCATGACTGTAGACCACTGTACTAT 59.932 44.000 0.00 0.00 39.22 2.12
3174 3251 3.635373 ACAGGGCTAATTCTTCATGCATG 59.365 43.478 21.07 21.07 0.00 4.06
3244 3322 6.558009 ACAGCAGCAACATCAATATTTACTG 58.442 36.000 0.00 0.00 0.00 2.74
3290 3370 0.167908 AACACACACACACAAGCACG 59.832 50.000 0.00 0.00 0.00 5.34
3306 3386 3.331150 ACGAACTTCAGACACACAAACA 58.669 40.909 0.00 0.00 0.00 2.83
3307 3387 4.092968 AGAACGAACTTCAGACACACAAAC 59.907 41.667 0.00 0.00 0.00 2.93
3308 3388 4.092821 CAGAACGAACTTCAGACACACAAA 59.907 41.667 0.00 0.00 0.00 2.83
3309 3389 3.616821 CAGAACGAACTTCAGACACACAA 59.383 43.478 0.00 0.00 0.00 3.33
3310 3390 3.186909 CAGAACGAACTTCAGACACACA 58.813 45.455 0.00 0.00 0.00 3.72
3311 3391 3.187700 ACAGAACGAACTTCAGACACAC 58.812 45.455 0.00 0.00 0.00 3.82
3312 3392 3.444916 GACAGAACGAACTTCAGACACA 58.555 45.455 0.00 0.00 0.00 3.72
3313 3393 2.795470 GGACAGAACGAACTTCAGACAC 59.205 50.000 0.00 0.00 0.00 3.67
3314 3394 2.429250 TGGACAGAACGAACTTCAGACA 59.571 45.455 0.00 0.00 0.00 3.41
3315 3395 3.093717 TGGACAGAACGAACTTCAGAC 57.906 47.619 0.00 0.00 0.00 3.51
3316 3396 3.574396 AGATGGACAGAACGAACTTCAGA 59.426 43.478 0.00 0.00 0.00 3.27
3317 3397 3.677121 CAGATGGACAGAACGAACTTCAG 59.323 47.826 0.00 0.00 0.00 3.02
3318 3398 3.320826 TCAGATGGACAGAACGAACTTCA 59.679 43.478 0.00 0.00 0.00 3.02
3319 3399 3.914312 TCAGATGGACAGAACGAACTTC 58.086 45.455 0.00 0.00 0.00 3.01
3387 3468 6.377146 GGATAAAATCACTAGCCCTGACAAAA 59.623 38.462 0.00 0.00 0.00 2.44
3389 3470 5.191722 AGGATAAAATCACTAGCCCTGACAA 59.808 40.000 0.00 0.00 0.00 3.18
3462 3554 6.934645 ACAACAACGGAATATCTTCTGAGAAA 59.065 34.615 6.66 0.00 39.72 2.52
3509 3601 8.320396 TGTAAATAAACGTGTATGCCTTACAA 57.680 30.769 14.81 4.27 42.37 2.41
3523 3615 7.698970 AGACTTTGTTGGTGTTGTAAATAAACG 59.301 33.333 0.00 0.00 0.00 3.60
3528 3620 8.745590 AGTAAAGACTTTGTTGGTGTTGTAAAT 58.254 29.630 10.80 0.00 28.61 1.40
3538 3637 7.562454 TGTTTAGGAGTAAAGACTTTGTTGG 57.438 36.000 10.80 0.00 35.45 3.77
3542 3641 8.129211 CCAACTTGTTTAGGAGTAAAGACTTTG 58.871 37.037 10.80 0.00 35.45 2.77
3544 3643 6.771267 CCCAACTTGTTTAGGAGTAAAGACTT 59.229 38.462 0.00 0.00 35.45 3.01
3547 3646 5.133153 ACCCCAACTTGTTTAGGAGTAAAGA 59.867 40.000 5.79 0.00 0.00 2.52
3553 3652 3.344515 GCTACCCCAACTTGTTTAGGAG 58.655 50.000 5.79 0.00 0.00 3.69
3564 3663 5.306394 GTTTCATATCTAGGCTACCCCAAC 58.694 45.833 0.00 0.00 35.39 3.77
3567 3666 3.263681 GGGTTTCATATCTAGGCTACCCC 59.736 52.174 5.22 0.00 38.39 4.95
3569 3668 5.763876 ATGGGTTTCATATCTAGGCTACC 57.236 43.478 0.00 0.00 33.61 3.18
3570 3669 9.740710 ATTTTATGGGTTTCATATCTAGGCTAC 57.259 33.333 0.00 0.00 38.08 3.58
3580 3679 8.837099 AGTTCCATGATTTTATGGGTTTCATA 57.163 30.769 0.00 0.00 46.16 2.15
3606 3709 5.049828 TGTTATCCATGTGCGAGAACTATG 58.950 41.667 8.68 0.00 33.60 2.23
3609 3712 3.610040 TGTTATCCATGTGCGAGAACT 57.390 42.857 8.68 0.00 33.60 3.01
3613 3716 4.685169 AAGTTTGTTATCCATGTGCGAG 57.315 40.909 0.00 0.00 0.00 5.03
3624 3727 2.817844 GGGGTGAGCGAAAGTTTGTTAT 59.182 45.455 0.00 0.00 0.00 1.89
3625 3728 2.158726 AGGGGTGAGCGAAAGTTTGTTA 60.159 45.455 0.00 0.00 0.00 2.41
3627 3730 0.182775 AGGGGTGAGCGAAAGTTTGT 59.817 50.000 0.00 0.00 0.00 2.83
3631 3734 1.906574 TGAATAGGGGTGAGCGAAAGT 59.093 47.619 0.00 0.00 0.00 2.66
3634 3737 1.140852 CCATGAATAGGGGTGAGCGAA 59.859 52.381 0.00 0.00 0.00 4.70
3637 3740 2.736670 AACCATGAATAGGGGTGAGC 57.263 50.000 0.00 0.00 34.51 4.26
3639 3742 4.785914 TGAACTAACCATGAATAGGGGTGA 59.214 41.667 0.00 0.00 34.51 4.02
3642 3745 5.536161 CCAATGAACTAACCATGAATAGGGG 59.464 44.000 0.00 0.00 30.18 4.79
3650 3753 4.761739 AGTGTCACCAATGAACTAACCATG 59.238 41.667 0.00 0.00 36.31 3.66
3661 3764 4.468765 AGAGATCTGAGTGTCACCAATG 57.531 45.455 0.00 0.00 0.00 2.82
3662 3765 5.495926 AAAGAGATCTGAGTGTCACCAAT 57.504 39.130 0.00 0.00 0.00 3.16
3694 3798 8.792633 TGAGGTAAACCAAACTTGATATGAAAG 58.207 33.333 1.26 0.00 38.89 2.62
3715 3819 8.793592 GTTGATAATGTTAAGAAAGGTTGAGGT 58.206 33.333 0.00 0.00 0.00 3.85
3720 3824 8.161699 ACGTGTTGATAATGTTAAGAAAGGTT 57.838 30.769 0.00 0.00 0.00 3.50
3721 3825 7.739498 ACGTGTTGATAATGTTAAGAAAGGT 57.261 32.000 0.00 0.00 0.00 3.50
3722 3826 9.458374 AAAACGTGTTGATAATGTTAAGAAAGG 57.542 29.630 0.00 0.00 0.00 3.11
3725 3829 9.601971 GCTAAAACGTGTTGATAATGTTAAGAA 57.398 29.630 0.00 0.00 0.00 2.52
3726 3830 8.231837 GGCTAAAACGTGTTGATAATGTTAAGA 58.768 33.333 0.00 0.00 0.00 2.10
3727 3831 8.018520 TGGCTAAAACGTGTTGATAATGTTAAG 58.981 33.333 0.00 0.00 0.00 1.85
3728 3832 7.872881 TGGCTAAAACGTGTTGATAATGTTAA 58.127 30.769 0.00 0.00 0.00 2.01
3729 3833 7.436430 TGGCTAAAACGTGTTGATAATGTTA 57.564 32.000 0.00 0.00 0.00 2.41
3730 3834 6.320494 TGGCTAAAACGTGTTGATAATGTT 57.680 33.333 0.00 0.00 0.00 2.71
3731 3835 5.950758 TGGCTAAAACGTGTTGATAATGT 57.049 34.783 0.00 0.00 0.00 2.71
3732 3836 7.008266 GTGAATGGCTAAAACGTGTTGATAATG 59.992 37.037 0.00 0.00 0.00 1.90
3733 3837 7.027161 GTGAATGGCTAAAACGTGTTGATAAT 58.973 34.615 0.00 0.00 0.00 1.28
3734 3838 6.205853 AGTGAATGGCTAAAACGTGTTGATAA 59.794 34.615 0.00 0.00 0.00 1.75
3735 3839 5.703592 AGTGAATGGCTAAAACGTGTTGATA 59.296 36.000 0.00 0.00 0.00 2.15
3736 3840 4.518970 AGTGAATGGCTAAAACGTGTTGAT 59.481 37.500 0.00 0.00 0.00 2.57
3737 3841 3.880490 AGTGAATGGCTAAAACGTGTTGA 59.120 39.130 0.00 0.00 0.00 3.18
3738 3842 3.974401 CAGTGAATGGCTAAAACGTGTTG 59.026 43.478 0.00 0.00 0.00 3.33
3739 3843 3.630312 ACAGTGAATGGCTAAAACGTGTT 59.370 39.130 0.00 0.00 0.00 3.32
3740 3844 3.211045 ACAGTGAATGGCTAAAACGTGT 58.789 40.909 0.00 0.00 0.00 4.49
3741 3845 3.896648 ACAGTGAATGGCTAAAACGTG 57.103 42.857 0.00 0.00 0.00 4.49
3742 3846 4.638304 ACTACAGTGAATGGCTAAAACGT 58.362 39.130 0.00 0.00 0.00 3.99
3743 3847 5.607119 AACTACAGTGAATGGCTAAAACG 57.393 39.130 0.00 0.00 0.00 3.60
3744 3848 7.078228 CAGAAACTACAGTGAATGGCTAAAAC 58.922 38.462 0.00 0.00 0.00 2.43
3745 3849 6.206634 CCAGAAACTACAGTGAATGGCTAAAA 59.793 38.462 0.00 0.00 0.00 1.52
3746 3850 5.705441 CCAGAAACTACAGTGAATGGCTAAA 59.295 40.000 0.00 0.00 0.00 1.85
3747 3851 5.012664 TCCAGAAACTACAGTGAATGGCTAA 59.987 40.000 0.00 0.00 0.00 3.09
3748 3852 4.530553 TCCAGAAACTACAGTGAATGGCTA 59.469 41.667 0.00 0.00 0.00 3.93
3749 3853 3.327757 TCCAGAAACTACAGTGAATGGCT 59.672 43.478 0.00 0.00 0.00 4.75
3750 3854 3.674997 TCCAGAAACTACAGTGAATGGC 58.325 45.455 0.00 0.00 0.00 4.40
3751 3855 4.256920 CCTCCAGAAACTACAGTGAATGG 58.743 47.826 0.00 0.00 0.00 3.16
3752 3856 3.686726 GCCTCCAGAAACTACAGTGAATG 59.313 47.826 0.00 0.00 0.00 2.67
3753 3857 3.307762 GGCCTCCAGAAACTACAGTGAAT 60.308 47.826 0.00 0.00 0.00 2.57
3754 3858 2.038557 GGCCTCCAGAAACTACAGTGAA 59.961 50.000 0.00 0.00 0.00 3.18
3755 3859 1.623811 GGCCTCCAGAAACTACAGTGA 59.376 52.381 0.00 0.00 0.00 3.41
3756 3860 1.673033 CGGCCTCCAGAAACTACAGTG 60.673 57.143 0.00 0.00 0.00 3.66
3757 3861 0.608640 CGGCCTCCAGAAACTACAGT 59.391 55.000 0.00 0.00 0.00 3.55
3758 3862 0.608640 ACGGCCTCCAGAAACTACAG 59.391 55.000 0.00 0.00 0.00 2.74
3759 3863 0.320374 CACGGCCTCCAGAAACTACA 59.680 55.000 0.00 0.00 0.00 2.74
3760 3864 0.320697 ACACGGCCTCCAGAAACTAC 59.679 55.000 0.00 0.00 0.00 2.73
3761 3865 1.053424 AACACGGCCTCCAGAAACTA 58.947 50.000 0.00 0.00 0.00 2.24
3762 3866 0.535102 CAACACGGCCTCCAGAAACT 60.535 55.000 0.00 0.00 0.00 2.66
3763 3867 1.515521 CCAACACGGCCTCCAGAAAC 61.516 60.000 0.00 0.00 0.00 2.78
3764 3868 1.228124 CCAACACGGCCTCCAGAAA 60.228 57.895 0.00 0.00 0.00 2.52
3765 3869 1.488705 ATCCAACACGGCCTCCAGAA 61.489 55.000 0.00 0.00 33.14 3.02
3766 3870 0.616395 TATCCAACACGGCCTCCAGA 60.616 55.000 0.00 0.00 33.14 3.86
3767 3871 0.469917 ATATCCAACACGGCCTCCAG 59.530 55.000 0.00 0.00 33.14 3.86
3768 3872 1.414919 GTATATCCAACACGGCCTCCA 59.585 52.381 0.00 0.00 33.14 3.86
3769 3873 1.692519 AGTATATCCAACACGGCCTCC 59.307 52.381 0.00 0.00 33.14 4.30
3770 3874 2.364324 TGAGTATATCCAACACGGCCTC 59.636 50.000 0.00 0.00 33.14 4.70
3771 3875 2.394632 TGAGTATATCCAACACGGCCT 58.605 47.619 0.00 0.00 33.14 5.19
3772 3876 2.902705 TGAGTATATCCAACACGGCC 57.097 50.000 0.00 0.00 33.14 6.13
3773 3877 3.311596 GGTTTGAGTATATCCAACACGGC 59.688 47.826 0.00 0.00 35.69 5.68
3774 3878 3.554324 CGGTTTGAGTATATCCAACACGG 59.446 47.826 0.00 0.00 35.69 4.94
3775 3879 4.178540 ACGGTTTGAGTATATCCAACACG 58.821 43.478 0.00 0.00 35.69 4.49
3776 3880 5.416947 AGACGGTTTGAGTATATCCAACAC 58.583 41.667 0.00 0.00 35.69 3.32
3777 3881 5.186215 TGAGACGGTTTGAGTATATCCAACA 59.814 40.000 0.00 0.00 35.69 3.33
3778 3882 5.657474 TGAGACGGTTTGAGTATATCCAAC 58.343 41.667 0.00 0.00 33.74 3.77
3779 3883 5.655090 TCTGAGACGGTTTGAGTATATCCAA 59.345 40.000 0.00 0.00 0.00 3.53
3780 3884 5.067413 GTCTGAGACGGTTTGAGTATATCCA 59.933 44.000 0.00 0.00 0.00 3.41
3781 3885 5.521544 GTCTGAGACGGTTTGAGTATATCC 58.478 45.833 0.00 0.00 0.00 2.59
3796 3900 5.000012 ACTTGTCCAATATCGTCTGAGAC 58.000 43.478 1.65 1.65 0.00 3.36
3797 3901 5.661056 AACTTGTCCAATATCGTCTGAGA 57.339 39.130 0.00 0.00 0.00 3.27
3798 3902 6.102663 AGAAACTTGTCCAATATCGTCTGAG 58.897 40.000 0.00 0.00 0.00 3.35
3799 3903 6.037786 AGAAACTTGTCCAATATCGTCTGA 57.962 37.500 0.00 0.00 0.00 3.27
3800 3904 6.102663 AGAGAAACTTGTCCAATATCGTCTG 58.897 40.000 0.00 0.00 0.00 3.51
3801 3905 6.287589 AGAGAAACTTGTCCAATATCGTCT 57.712 37.500 0.00 0.00 0.00 4.18
3802 3906 6.237595 CGAAGAGAAACTTGTCCAATATCGTC 60.238 42.308 0.00 0.00 39.13 4.20
3803 3907 5.577164 CGAAGAGAAACTTGTCCAATATCGT 59.423 40.000 0.00 0.00 39.13 3.73
3804 3908 5.805486 TCGAAGAGAAACTTGTCCAATATCG 59.195 40.000 0.00 0.00 39.13 2.92
3805 3909 7.306283 CGATCGAAGAGAAACTTGTCCAATATC 60.306 40.741 10.26 0.00 43.63 1.63
3806 3910 6.477033 CGATCGAAGAGAAACTTGTCCAATAT 59.523 38.462 10.26 0.00 43.63 1.28
3807 3911 5.805486 CGATCGAAGAGAAACTTGTCCAATA 59.195 40.000 10.26 0.00 43.63 1.90
3808 3912 4.627467 CGATCGAAGAGAAACTTGTCCAAT 59.373 41.667 10.26 0.00 43.63 3.16
3809 3913 3.987868 CGATCGAAGAGAAACTTGTCCAA 59.012 43.478 10.26 0.00 43.63 3.53
3810 3914 3.575630 CGATCGAAGAGAAACTTGTCCA 58.424 45.455 10.26 0.00 43.63 4.02
3811 3915 2.924290 CCGATCGAAGAGAAACTTGTCC 59.076 50.000 18.66 0.00 43.63 4.02
3812 3916 3.365220 CACCGATCGAAGAGAAACTTGTC 59.635 47.826 18.66 0.00 43.63 3.18
3813 3917 3.318017 CACCGATCGAAGAGAAACTTGT 58.682 45.455 18.66 0.00 43.63 3.16
3814 3918 2.092838 GCACCGATCGAAGAGAAACTTG 59.907 50.000 18.66 0.00 43.63 3.16
3815 3919 2.028930 AGCACCGATCGAAGAGAAACTT 60.029 45.455 18.66 0.00 43.63 2.66
3816 3920 1.546476 AGCACCGATCGAAGAGAAACT 59.454 47.619 18.66 0.00 43.63 2.66
3817 3921 1.997669 AGCACCGATCGAAGAGAAAC 58.002 50.000 18.66 0.00 43.63 2.78
3818 3922 2.753452 AGTAGCACCGATCGAAGAGAAA 59.247 45.455 18.66 0.00 43.63 2.52
3819 3923 2.355132 GAGTAGCACCGATCGAAGAGAA 59.645 50.000 18.66 0.00 43.63 2.87
3820 3924 1.941294 GAGTAGCACCGATCGAAGAGA 59.059 52.381 18.66 0.00 43.63 3.10
3821 3925 1.002251 GGAGTAGCACCGATCGAAGAG 60.002 57.143 18.66 1.54 43.63 2.85
3822 3926 1.022735 GGAGTAGCACCGATCGAAGA 58.977 55.000 18.66 0.00 45.75 2.87
3823 3927 0.738975 TGGAGTAGCACCGATCGAAG 59.261 55.000 18.66 9.60 0.00 3.79
3824 3928 1.179152 TTGGAGTAGCACCGATCGAA 58.821 50.000 18.66 0.00 0.00 3.71
3825 3929 1.399714 ATTGGAGTAGCACCGATCGA 58.600 50.000 18.66 0.00 0.00 3.59
3826 3930 2.128035 GAATTGGAGTAGCACCGATCG 58.872 52.381 8.51 8.51 31.76 3.69
3827 3931 3.460857 AGAATTGGAGTAGCACCGATC 57.539 47.619 0.00 0.00 31.76 3.69
3828 3932 4.835615 AGATAGAATTGGAGTAGCACCGAT 59.164 41.667 0.00 0.00 33.39 4.18
3829 3933 4.215908 AGATAGAATTGGAGTAGCACCGA 58.784 43.478 0.00 0.00 0.00 4.69
3830 3934 4.551388 GAGATAGAATTGGAGTAGCACCG 58.449 47.826 0.00 0.00 0.00 4.94
3831 3935 4.038162 ACGAGATAGAATTGGAGTAGCACC 59.962 45.833 0.00 0.00 0.00 5.01
3832 3936 5.189659 ACGAGATAGAATTGGAGTAGCAC 57.810 43.478 0.00 0.00 0.00 4.40
3833 3937 8.809468 ATATACGAGATAGAATTGGAGTAGCA 57.191 34.615 0.00 0.00 0.00 3.49
3834 3938 8.894731 TGATATACGAGATAGAATTGGAGTAGC 58.105 37.037 0.00 0.00 0.00 3.58
3837 3941 9.467796 TGATGATATACGAGATAGAATTGGAGT 57.532 33.333 0.00 0.00 0.00 3.85
3842 3946 9.958234 CGGAATGATGATATACGAGATAGAATT 57.042 33.333 0.00 0.00 0.00 2.17
3843 3947 8.572185 CCGGAATGATGATATACGAGATAGAAT 58.428 37.037 0.00 0.00 0.00 2.40
3844 3948 7.773690 TCCGGAATGATGATATACGAGATAGAA 59.226 37.037 0.00 0.00 0.00 2.10
3845 3949 7.280356 TCCGGAATGATGATATACGAGATAGA 58.720 38.462 0.00 0.00 0.00 1.98
3846 3950 7.497925 TCCGGAATGATGATATACGAGATAG 57.502 40.000 0.00 0.00 0.00 2.08
3847 3951 7.175119 GGATCCGGAATGATGATATACGAGATA 59.825 40.741 9.01 0.00 0.00 1.98
3848 3952 6.015856 GGATCCGGAATGATGATATACGAGAT 60.016 42.308 9.01 0.00 0.00 2.75
3849 3953 5.299531 GGATCCGGAATGATGATATACGAGA 59.700 44.000 9.01 0.00 0.00 4.04
3850 3954 5.524284 GGATCCGGAATGATGATATACGAG 58.476 45.833 9.01 0.00 0.00 4.18
3851 3955 4.036380 CGGATCCGGAATGATGATATACGA 59.964 45.833 26.95 0.00 35.56 3.43
3852 3956 4.290969 CGGATCCGGAATGATGATATACG 58.709 47.826 26.95 0.00 35.56 3.06
3867 3971 1.732259 CACAAGAAAGAACCGGATCCG 59.268 52.381 27.65 27.65 39.44 4.18
3868 3972 2.484264 CACACAAGAAAGAACCGGATCC 59.516 50.000 9.46 0.00 0.00 3.36
3869 3973 2.484264 CCACACAAGAAAGAACCGGATC 59.516 50.000 9.46 5.83 0.00 3.36
3870 3974 2.504367 CCACACAAGAAAGAACCGGAT 58.496 47.619 9.46 0.00 0.00 4.18
3871 3975 1.961793 CCACACAAGAAAGAACCGGA 58.038 50.000 9.46 0.00 0.00 5.14
3872 3976 0.310854 GCCACACAAGAAAGAACCGG 59.689 55.000 0.00 0.00 0.00 5.28
3873 3977 0.310854 GGCCACACAAGAAAGAACCG 59.689 55.000 0.00 0.00 0.00 4.44
3874 3978 1.067060 GTGGCCACACAAGAAAGAACC 59.933 52.381 31.23 0.00 46.90 3.62
3875 3979 2.492019 GTGGCCACACAAGAAAGAAC 57.508 50.000 31.23 0.00 46.90 3.01
3888 3992 0.774276 TTAAGGTGGATGTGTGGCCA 59.226 50.000 0.00 0.00 0.00 5.36
3889 3993 1.173913 GTTAAGGTGGATGTGTGGCC 58.826 55.000 0.00 0.00 0.00 5.36
3890 3994 1.904287 TGTTAAGGTGGATGTGTGGC 58.096 50.000 0.00 0.00 0.00 5.01
3891 3995 3.191162 CACATGTTAAGGTGGATGTGTGG 59.809 47.826 0.00 0.00 40.45 4.17
3892 3996 3.366273 GCACATGTTAAGGTGGATGTGTG 60.366 47.826 0.00 0.00 44.94 3.82
3893 3997 2.819608 GCACATGTTAAGGTGGATGTGT 59.180 45.455 0.00 0.00 44.94 3.72
3894 3998 2.819019 TGCACATGTTAAGGTGGATGTG 59.181 45.455 0.00 0.00 45.60 3.21
3895 3999 3.153369 TGCACATGTTAAGGTGGATGT 57.847 42.857 0.00 0.00 38.53 3.06


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

AutoCloner maintained by Alex Coulton.