Multiple sequence alignment - TraesCS2B01G310200

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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 TraesCS2B01G310200 chr2B 100.000 6069 0 0 1 6069 443159913 443153845 0.000000e+00 11208.0
1 TraesCS2B01G310200 chr2B 99.333 600 4 0 3947 4546 102413333 102413932 0.000000e+00 1086.0
2 TraesCS2B01G310200 chr2B 98.988 593 6 0 3953 4545 146999291 146999883 0.000000e+00 1062.0
3 TraesCS2B01G310200 chr2B 77.778 171 38 0 5882 6052 685935369 685935539 8.320000e-19 106.0
4 TraesCS2B01G310200 chr2D 96.335 2128 47 11 1847 3949 373677158 373675037 0.000000e+00 3469.0
5 TraesCS2B01G310200 chr2D 95.726 1872 55 11 1 1852 373678986 373677120 0.000000e+00 2990.0
6 TraesCS2B01G310200 chr2D 90.945 1005 27 14 4535 5527 373675054 373674102 0.000000e+00 1293.0
7 TraesCS2B01G310200 chr2D 91.685 445 24 2 5527 5958 373674066 373673622 6.730000e-169 604.0
8 TraesCS2B01G310200 chr2D 92.727 110 8 0 5960 6069 373656827 373656718 6.300000e-35 159.0
9 TraesCS2B01G310200 chr2D 80.597 201 25 7 5548 5744 561825708 561825518 6.340000e-30 143.0
10 TraesCS2B01G310200 chr2D 77.637 237 39 2 5772 5996 201822613 201822847 1.370000e-26 132.0
11 TraesCS2B01G310200 chr2D 78.882 161 34 0 5892 6052 144553057 144553217 6.430000e-20 110.0
12 TraesCS2B01G310200 chr2D 100.000 32 0 0 5491 5522 186866863 186866832 6.570000e-05 60.2
13 TraesCS2B01G310200 chr2A 94.837 1840 61 16 27 1842 505085889 505084060 0.000000e+00 2841.0
14 TraesCS2B01G310200 chr2A 85.890 815 61 29 3159 3949 505082054 505081270 0.000000e+00 819.0
15 TraesCS2B01G310200 chr2A 88.889 414 20 13 4806 5213 505081120 505080727 2.540000e-133 486.0
16 TraesCS2B01G310200 chr2A 92.434 304 22 1 1903 2205 505084036 505083733 3.360000e-117 433.0
17 TraesCS2B01G310200 chr2A 89.815 216 21 1 2564 2778 505082790 505082575 5.990000e-70 276.0
18 TraesCS2B01G310200 chr2A 93.407 182 9 2 2790 2968 505082534 505082353 3.610000e-67 267.0
19 TraesCS2B01G310200 chr2A 91.573 178 11 4 2994 3170 505082282 505082108 6.080000e-60 243.0
20 TraesCS2B01G310200 chr2A 88.742 151 15 2 4554 4702 505081276 505081126 3.740000e-42 183.0
21 TraesCS2B01G310200 chr2A 77.778 225 42 7 5550 5769 590825595 590825374 1.370000e-26 132.0
22 TraesCS2B01G310200 chr2A 76.991 226 40 8 5550 5769 54854172 54853953 1.070000e-22 119.0
23 TraesCS2B01G310200 chr2A 78.365 208 28 11 5247 5453 505080725 505080534 1.070000e-22 119.0
24 TraesCS2B01G310200 chr2A 94.444 36 2 0 5487 5522 693434524 693434559 8.500000e-04 56.5
25 TraesCS2B01G310200 chr6B 99.496 595 3 0 3952 4546 398851780 398851186 0.000000e+00 1083.0
26 TraesCS2B01G310200 chr6B 99.327 594 4 0 3952 4545 720459627 720460220 0.000000e+00 1075.0
27 TraesCS2B01G310200 chr6B 99.158 594 5 0 3952 4545 545655350 545655943 0.000000e+00 1070.0
28 TraesCS2B01G310200 chr1A 99.495 594 3 0 3952 4545 241745486 241746079 0.000000e+00 1081.0
29 TraesCS2B01G310200 chr3B 98.990 594 6 0 3952 4545 9896308 9895715 0.000000e+00 1064.0
30 TraesCS2B01G310200 chr3B 88.963 299 31 2 2272 2568 154190618 154190320 9.610000e-98 368.0
31 TraesCS2B01G310200 chr3B 74.419 301 64 8 5772 6069 689157498 689157208 3.840000e-22 117.0
32 TraesCS2B01G310200 chr1B 98.824 595 7 0 3952 4546 198646501 198645907 0.000000e+00 1061.0
33 TraesCS2B01G310200 chr1B 97.980 594 12 0 3952 4545 284046841 284046248 0.000000e+00 1031.0
34 TraesCS2B01G310200 chr1B 88.158 304 30 6 2272 2572 50558326 50558626 2.080000e-94 357.0
35 TraesCS2B01G310200 chr1B 79.651 172 24 10 5604 5769 349083000 349083166 4.970000e-21 113.0
36 TraesCS2B01G310200 chr6A 91.935 310 25 0 4233 4542 35548455 35548764 9.340000e-118 435.0
37 TraesCS2B01G310200 chr6A 88.487 304 28 6 2269 2568 522884212 522884512 1.610000e-95 361.0
38 TraesCS2B01G310200 chr6A 80.447 179 34 1 5892 6069 509567258 509567436 1.060000e-27 135.0
39 TraesCS2B01G310200 chr7D 90.667 300 26 2 2272 2569 274697441 274697740 1.230000e-106 398.0
40 TraesCS2B01G310200 chr7D 78.882 161 34 0 5892 6052 259300600 259300440 6.430000e-20 110.0
41 TraesCS2B01G310200 chr7D 96.875 32 1 0 5772 5803 26555300 26555331 3.000000e-03 54.7
42 TraesCS2B01G310200 chr7A 90.136 294 26 3 2279 2569 307959909 307960202 4.440000e-101 379.0
43 TraesCS2B01G310200 chr4D 89.632 299 29 2 2272 2568 98888409 98888111 4.440000e-101 379.0
44 TraesCS2B01G310200 chr4D 89.011 182 17 3 3612 3792 463340052 463339873 7.920000e-54 222.0
45 TraesCS2B01G310200 chr3D 88.963 299 31 2 2272 2568 469481524 469481226 9.610000e-98 368.0
46 TraesCS2B01G310200 chr5D 88.449 303 30 5 2270 2567 287426940 287426638 1.610000e-95 361.0
47 TraesCS2B01G310200 chr5D 84.878 205 28 3 3574 3776 189266485 189266282 2.870000e-48 204.0
48 TraesCS2B01G310200 chr5D 83.333 138 18 5 5610 5744 73503961 73503826 8.260000e-24 122.0
49 TraesCS2B01G310200 chr5D 80.473 169 26 7 5605 5769 504813868 504813703 8.260000e-24 122.0
50 TraesCS2B01G310200 chr4B 87.678 211 23 3 3583 3792 578675615 578675407 6.080000e-60 243.0
51 TraesCS2B01G310200 chr4B 82.938 211 28 6 3584 3792 578445185 578444981 3.740000e-42 183.0
52 TraesCS2B01G310200 chr4B 82.938 211 28 6 3584 3792 578490718 578490514 3.740000e-42 183.0
53 TraesCS2B01G310200 chr4B 81.991 211 30 6 3584 3792 578360914 578360710 8.090000e-39 172.0
54 TraesCS2B01G310200 chr4B 97.297 37 1 0 2982 3018 646237568 646237604 5.080000e-06 63.9
55 TraesCS2B01G310200 chr4A 86.730 211 25 3 3583 3792 6343101 6343309 1.320000e-56 231.0
56 TraesCS2B01G310200 chr4A 85.096 208 24 6 3584 3789 6489985 6490187 7.970000e-49 206.0
57 TraesCS2B01G310200 chr5A 85.366 205 28 2 3574 3776 231299118 231299322 1.710000e-50 211.0
58 TraesCS2B01G310200 chr1D 81.778 225 31 5 5547 5769 95870771 95870987 4.830000e-41 180.0
59 TraesCS2B01G310200 chr1D 81.915 94 14 2 5772 5865 92964562 92964652 6.520000e-10 76.8
60 TraesCS2B01G310200 chr6D 80.838 167 26 5 5600 5762 388217032 388217196 6.390000e-25 126.0
61 TraesCS2B01G310200 chr7B 78.090 178 39 0 5892 6069 379495310 379495133 4.970000e-21 113.0


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 TraesCS2B01G310200 chr2B 443153845 443159913 6068 True 11208.000000 11208 100.00000 1 6069 1 chr2B.!!$R1 6068
1 TraesCS2B01G310200 chr2B 102413333 102413932 599 False 1086.000000 1086 99.33300 3947 4546 1 chr2B.!!$F1 599
2 TraesCS2B01G310200 chr2B 146999291 146999883 592 False 1062.000000 1062 98.98800 3953 4545 1 chr2B.!!$F2 592
3 TraesCS2B01G310200 chr2D 373673622 373678986 5364 True 2089.000000 3469 93.67275 1 5958 4 chr2D.!!$R4 5957
4 TraesCS2B01G310200 chr2A 505080534 505085889 5355 True 629.666667 2841 89.32800 27 5453 9 chr2A.!!$R3 5426
5 TraesCS2B01G310200 chr6B 398851186 398851780 594 True 1083.000000 1083 99.49600 3952 4546 1 chr6B.!!$R1 594
6 TraesCS2B01G310200 chr6B 720459627 720460220 593 False 1075.000000 1075 99.32700 3952 4545 1 chr6B.!!$F2 593
7 TraesCS2B01G310200 chr6B 545655350 545655943 593 False 1070.000000 1070 99.15800 3952 4545 1 chr6B.!!$F1 593
8 TraesCS2B01G310200 chr1A 241745486 241746079 593 False 1081.000000 1081 99.49500 3952 4545 1 chr1A.!!$F1 593
9 TraesCS2B01G310200 chr3B 9895715 9896308 593 True 1064.000000 1064 98.99000 3952 4545 1 chr3B.!!$R1 593
10 TraesCS2B01G310200 chr1B 198645907 198646501 594 True 1061.000000 1061 98.82400 3952 4546 1 chr1B.!!$R1 594
11 TraesCS2B01G310200 chr1B 284046248 284046841 593 True 1031.000000 1031 97.98000 3952 4545 1 chr1B.!!$R2 593

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
707 717 0.034186 GATGGAATGGTGGCTGTGGA 60.034 55.000 0.00 0.00 0.00 4.02 F
1104 1129 4.020039 AGTGGTGGATCGTGGTTTAATACA 60.020 41.667 0.00 0.00 0.00 2.29 F
1884 1914 0.837272 TATAACTGACCCTGCTGGCC 59.163 55.000 3.63 0.00 37.83 5.36 F
3525 4598 0.964358 GGAGCTTGCATGGACAGCTT 60.964 55.000 19.27 8.34 35.83 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1865 1895 0.837272 GGCCAGCAGGGTCAGTTATA 59.163 55.000 0.00 0.0 42.53 0.98 R
2781 3700 4.010349 GGCAAGCTTAGACAACCAAGTAT 58.990 43.478 0.00 0.0 0.00 2.12 R
3581 4655 0.385390 ACCAAGGCTCAAAGCAAACG 59.615 50.000 0.86 0.0 44.75 3.60 R
5458 6580 0.465460 AGAAAACTTGCAGGTCGCCA 60.465 50.000 0.32 0.0 41.33 5.69 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
23 24 4.158949 AGCAACTATCAGATTTGCATTGCA 59.841 37.500 18.15 7.38 46.62 4.08
174 175 3.015312 GCGAGTAAGGGGCTCCGTT 62.015 63.158 0.00 0.00 38.33 4.44
364 370 6.802834 GCTGCTACCTCGTCTACTAAAATATC 59.197 42.308 0.00 0.00 0.00 1.63
365 371 7.521748 GCTGCTACCTCGTCTACTAAAATATCA 60.522 40.741 0.00 0.00 0.00 2.15
367 373 6.802834 GCTACCTCGTCTACTAAAATATCAGC 59.197 42.308 0.00 0.00 0.00 4.26
370 376 5.010719 CCTCGTCTACTAAAATATCAGCCCA 59.989 44.000 0.00 0.00 0.00 5.36
371 377 6.085555 TCGTCTACTAAAATATCAGCCCAG 57.914 41.667 0.00 0.00 0.00 4.45
372 378 5.597182 TCGTCTACTAAAATATCAGCCCAGT 59.403 40.000 0.00 0.00 0.00 4.00
376 382 9.609346 GTCTACTAAAATATCAGCCCAGTTTAA 57.391 33.333 0.00 0.00 0.00 1.52
384 390 8.831715 AATATCAGCCCAGTTTAAAAGTTTTG 57.168 30.769 11.18 0.00 0.00 2.44
423 431 0.462047 CTAGGCCCAGCAACCGTTAG 60.462 60.000 0.00 0.00 0.00 2.34
448 456 3.057315 CGTGTTTCAATGAGAAAGCCCAT 60.057 43.478 0.00 0.00 46.34 4.00
451 459 4.588106 TGTTTCAATGAGAAAGCCCATGAA 59.412 37.500 0.00 0.00 46.34 2.57
455 463 4.400251 TCAATGAGAAAGCCCATGAATGTC 59.600 41.667 0.00 0.00 0.00 3.06
707 717 0.034186 GATGGAATGGTGGCTGTGGA 60.034 55.000 0.00 0.00 0.00 4.02
1104 1129 4.020039 AGTGGTGGATCGTGGTTTAATACA 60.020 41.667 0.00 0.00 0.00 2.29
1108 1133 7.066043 GTGGTGGATCGTGGTTTAATACAAATA 59.934 37.037 0.00 0.00 0.00 1.40
1266 1294 4.518211 GCATCCTAGTAATGCTTCATTGCT 59.482 41.667 16.26 13.14 45.67 3.91
1336 1364 7.319380 CACATTGAATTGCGTTTTTCATTTCTG 59.681 33.333 0.00 0.00 32.27 3.02
1346 1374 7.168972 TGCGTTTTTCATTTCTGGAAACAATAG 59.831 33.333 0.00 0.00 42.06 1.73
1441 1471 8.539770 TTCTCATTTCTTCAGTTTGCTACTAG 57.460 34.615 0.00 0.00 34.56 2.57
1860 1890 7.800300 ACTATTCTCTAGAAAAGGGTCAGTT 57.200 36.000 0.00 0.00 37.61 3.16
1861 1891 8.896722 ACTATTCTCTAGAAAAGGGTCAGTTA 57.103 34.615 0.00 0.00 37.61 2.24
1882 1912 7.680730 AGTTATATTATAACTGACCCTGCTGG 58.319 38.462 22.47 1.89 36.51 4.85
1883 1913 2.710096 TTATAACTGACCCTGCTGGC 57.290 50.000 3.63 0.00 37.83 4.85
1884 1914 0.837272 TATAACTGACCCTGCTGGCC 59.163 55.000 3.63 0.00 37.83 5.36
1885 1915 2.257409 ATAACTGACCCTGCTGGCCG 62.257 60.000 3.63 0.00 37.83 6.13
1968 1998 6.158169 AGGATAAGGAAATAAGGGAACGACTT 59.842 38.462 0.00 0.00 0.00 3.01
1980 2010 3.181485 GGGAACGACTTCAGGATAGTGAG 60.181 52.174 0.00 0.00 0.00 3.51
2085 2115 2.111582 GCCTTAGTGCTGCTGCTCC 61.112 63.158 17.00 7.36 40.48 4.70
2440 3358 5.426833 AGGAACATTAGCCTAGACTCAATGT 59.573 40.000 0.00 0.18 40.56 2.71
2446 3364 8.947115 ACATTAGCCTAGACTCAATGTAAAAAC 58.053 33.333 10.12 0.00 37.89 2.43
2456 3374 9.268282 AGACTCAATGTAAAAACTCCTATCCTA 57.732 33.333 0.00 0.00 0.00 2.94
2478 3396 7.228108 TCCTATGCATCAAATGACATCTCTTTC 59.772 37.037 0.19 0.00 32.25 2.62
2485 3403 9.117183 CATCAAATGACATCTCTTTCCTTATGA 57.883 33.333 0.00 0.00 0.00 2.15
2499 3417 8.627403 TCTTTCCTTATGAAATTGAGATGCATC 58.373 33.333 19.37 19.37 41.96 3.91
2629 3547 7.764443 CCTCCTTCGTATCTCAACTATTTGAAA 59.236 37.037 0.00 0.00 41.34 2.69
2674 3592 7.792374 TTTACAAGCATCCAGTCTTCATATC 57.208 36.000 0.00 0.00 0.00 1.63
2702 3621 9.229784 CATCTTGTTTTCTCATTTCATTATCGG 57.770 33.333 0.00 0.00 0.00 4.18
2752 3671 2.079158 CTATTGCCATGATAGTGCCCG 58.921 52.381 0.00 0.00 0.00 6.13
2778 3697 5.958955 AGTACTGAACGGTGTAATAACCTC 58.041 41.667 0.00 0.00 38.14 3.85
2779 3698 4.198028 ACTGAACGGTGTAATAACCTCC 57.802 45.455 0.00 0.00 38.14 4.30
2780 3699 3.836562 ACTGAACGGTGTAATAACCTCCT 59.163 43.478 0.00 0.00 38.14 3.69
2781 3700 5.018809 ACTGAACGGTGTAATAACCTCCTA 58.981 41.667 0.00 0.00 38.14 2.94
2846 3794 7.201652 CCTCAGCAGCTAAGGTTATTTTAGTTC 60.202 40.741 2.87 0.00 32.09 3.01
2989 3978 3.015327 CTCTGTAGTACCTGGTAGCGTT 58.985 50.000 6.84 0.00 0.00 4.84
3127 4124 8.496707 AAAGTTCATGCAAAAGACTTTCAATT 57.503 26.923 0.00 0.00 0.00 2.32
3198 4260 2.940083 GCAGTAGTTTGTTAGGCCTCCC 60.940 54.545 9.68 0.36 0.00 4.30
3227 4289 2.668457 CTCGTGTTCCACTGCTTATGAC 59.332 50.000 0.00 0.00 31.34 3.06
3525 4598 0.964358 GGAGCTTGCATGGACAGCTT 60.964 55.000 19.27 8.34 35.83 3.74
3838 4932 5.712446 AGCCAAGGAGGAAAATTTTCTAGTC 59.288 40.000 25.86 19.64 41.22 2.59
3941 5036 5.603596 TCGCTGTTGTCTCCTTAAAAGTAA 58.396 37.500 0.00 0.00 0.00 2.24
3942 5037 6.050432 TCGCTGTTGTCTCCTTAAAAGTAAA 58.950 36.000 0.00 0.00 0.00 2.01
3943 5038 6.018507 TCGCTGTTGTCTCCTTAAAAGTAAAC 60.019 38.462 0.00 0.00 0.00 2.01
3944 5039 6.018180 CGCTGTTGTCTCCTTAAAAGTAAACT 60.018 38.462 0.00 0.00 0.00 2.66
3945 5040 7.466860 CGCTGTTGTCTCCTTAAAAGTAAACTT 60.467 37.037 0.00 0.00 37.91 2.66
3950 5045 7.571025 TGTCTCCTTAAAAGTAAACTTGACCT 58.429 34.615 0.00 0.00 36.12 3.85
4244 5339 1.203523 AGTGAAGCTCGATTTCTCGCT 59.796 47.619 10.13 0.71 44.65 4.93
4703 5800 8.099537 CCATAGTCTATATCTGCAGTGGAATTT 58.900 37.037 14.67 0.00 0.00 1.82
4755 5858 3.313249 GCAATTTGATTATTTGCAGGGGC 59.687 43.478 0.00 0.00 43.95 5.80
4875 5982 8.593945 ATTCTCAGTATTTCAAGGGCAAAATA 57.406 30.769 0.00 0.00 0.00 1.40
4879 5986 7.957002 TCAGTATTTCAAGGGCAAAATAAACA 58.043 30.769 0.00 0.00 31.17 2.83
5123 6233 6.462073 ACGTTGTAACTAATGCTGTGTTAG 57.538 37.500 0.00 0.00 35.72 2.34
5155 6266 2.944129 TCCACTCTTTCTTGGTTTGGG 58.056 47.619 0.00 0.00 34.19 4.12
5171 6283 2.127651 TGGGGTTCTACCTCCAAAGT 57.872 50.000 4.28 0.00 38.22 2.66
5277 6392 7.093509 ACCTTGAACATACCATTTGAATTACCC 60.094 37.037 0.00 0.00 0.00 3.69
5278 6393 7.093552 CCTTGAACATACCATTTGAATTACCCA 60.094 37.037 0.00 0.00 0.00 4.51
5281 6396 5.502079 ACATACCATTTGAATTACCCACGA 58.498 37.500 0.00 0.00 0.00 4.35
5348 6470 4.753107 GGACAGTCTGGATTGTTTTCGTTA 59.247 41.667 4.53 0.00 31.12 3.18
5349 6471 5.411669 GGACAGTCTGGATTGTTTTCGTTAT 59.588 40.000 4.53 0.00 31.12 1.89
5350 6472 6.241207 ACAGTCTGGATTGTTTTCGTTATG 57.759 37.500 4.53 0.00 0.00 1.90
5351 6473 5.995282 ACAGTCTGGATTGTTTTCGTTATGA 59.005 36.000 4.53 0.00 0.00 2.15
5352 6474 6.147821 ACAGTCTGGATTGTTTTCGTTATGAG 59.852 38.462 4.53 0.00 0.00 2.90
5353 6475 6.147821 CAGTCTGGATTGTTTTCGTTATGAGT 59.852 38.462 0.00 0.00 0.00 3.41
5354 6476 6.147821 AGTCTGGATTGTTTTCGTTATGAGTG 59.852 38.462 0.00 0.00 0.00 3.51
5355 6477 5.411361 TCTGGATTGTTTTCGTTATGAGTGG 59.589 40.000 0.00 0.00 0.00 4.00
5356 6478 5.309638 TGGATTGTTTTCGTTATGAGTGGA 58.690 37.500 0.00 0.00 0.00 4.02
5357 6479 5.411361 TGGATTGTTTTCGTTATGAGTGGAG 59.589 40.000 0.00 0.00 0.00 3.86
5358 6480 5.411669 GGATTGTTTTCGTTATGAGTGGAGT 59.588 40.000 0.00 0.00 0.00 3.85
5359 6481 6.592607 GGATTGTTTTCGTTATGAGTGGAGTA 59.407 38.462 0.00 0.00 0.00 2.59
5360 6482 7.118680 GGATTGTTTTCGTTATGAGTGGAGTAA 59.881 37.037 0.00 0.00 0.00 2.24
5361 6483 7.416154 TTGTTTTCGTTATGAGTGGAGTAAG 57.584 36.000 0.00 0.00 0.00 2.34
5362 6484 6.518493 TGTTTTCGTTATGAGTGGAGTAAGT 58.482 36.000 0.00 0.00 0.00 2.24
5363 6485 6.987992 TGTTTTCGTTATGAGTGGAGTAAGTT 59.012 34.615 0.00 0.00 0.00 2.66
5364 6486 7.496591 TGTTTTCGTTATGAGTGGAGTAAGTTT 59.503 33.333 0.00 0.00 0.00 2.66
5365 6487 8.340443 GTTTTCGTTATGAGTGGAGTAAGTTTT 58.660 33.333 0.00 0.00 0.00 2.43
5366 6488 7.647907 TTCGTTATGAGTGGAGTAAGTTTTC 57.352 36.000 0.00 0.00 0.00 2.29
5367 6489 5.860182 TCGTTATGAGTGGAGTAAGTTTTCG 59.140 40.000 0.00 0.00 0.00 3.46
5368 6490 5.632347 CGTTATGAGTGGAGTAAGTTTTCGT 59.368 40.000 0.00 0.00 0.00 3.85
5369 6491 6.145048 CGTTATGAGTGGAGTAAGTTTTCGTT 59.855 38.462 0.00 0.00 0.00 3.85
5383 6505 9.148104 GTAAGTTTTCGTTATCAGTGGAGTAAT 57.852 33.333 0.00 0.00 0.00 1.89
5437 6559 5.255710 CTGTAGAAGCTGCTATGTGTACT 57.744 43.478 4.26 0.00 0.00 2.73
5458 6580 3.910627 CTGTAGGATAGGGTTTAGGGCAT 59.089 47.826 0.00 0.00 0.00 4.40
5484 6606 1.270550 CCTGCAAGTTTTCTCCGCATT 59.729 47.619 0.00 0.00 37.53 3.56
5488 6610 2.158841 GCAAGTTTTCTCCGCATTCGTA 59.841 45.455 0.00 0.00 0.00 3.43
5545 6703 2.166459 TGCGGAATTTGGTCAAACACAA 59.834 40.909 0.00 0.00 32.51 3.33
5546 6704 3.181471 TGCGGAATTTGGTCAAACACAAT 60.181 39.130 0.00 0.00 32.51 2.71
5609 6768 3.565482 CACACATGAACTAAGTGGTGCTT 59.435 43.478 0.00 0.00 41.05 3.91
5614 6773 1.798813 GAACTAAGTGGTGCTTGTCCG 59.201 52.381 0.00 0.00 38.05 4.79
5621 6780 1.896660 GGTGCTTGTCCGGCTTTGA 60.897 57.895 0.00 0.00 0.00 2.69
5639 6798 7.148306 CGGCTTTGAAGGTATAATTAACACACT 60.148 37.037 0.00 0.00 0.00 3.55
5674 6833 4.629523 TGCCCGTTCCCCGTGTTC 62.630 66.667 0.00 0.00 33.66 3.18
5699 6858 0.034896 TGAGCCCCGAGAACTGAAAC 59.965 55.000 0.00 0.00 0.00 2.78
5709 6868 3.394719 GAGAACTGAAACTTCGCCTTCT 58.605 45.455 0.00 0.00 0.00 2.85
5725 6884 0.104304 TTCTAATTCCTCCTCGGCGC 59.896 55.000 0.00 0.00 0.00 6.53
5730 6889 2.920076 ATTCCTCCTCGGCGCTCTCT 62.920 60.000 7.64 0.00 0.00 3.10
5741 6900 2.122167 CGCTCTCTACCTCCGCCTT 61.122 63.158 0.00 0.00 0.00 4.35
5744 6903 0.464013 CTCTCTACCTCCGCCTTCGA 60.464 60.000 0.00 0.00 38.10 3.71
5750 6909 2.352032 CCTCCGCCTTCGAAGACCT 61.352 63.158 26.61 0.00 38.10 3.85
5765 6924 1.202818 AGACCTGGGAAGTGAAGTTGC 60.203 52.381 0.00 0.00 0.00 4.17
5770 6929 0.955919 GGGAAGTGAAGTTGCCCGAG 60.956 60.000 0.00 0.00 31.86 4.63
5779 6938 4.351938 TTGCCCGAGTCGTGGTCG 62.352 66.667 12.31 0.00 37.17 4.79
5823 6982 1.149148 GAACCGACTTTGTCCTCTGC 58.851 55.000 0.00 0.00 0.00 4.26
5883 7054 0.472471 TTGGCGGTCTCCAGTTTTCT 59.528 50.000 0.00 0.00 37.44 2.52
5953 7124 2.486982 GAGTTGTAGGACTCGTGTAGCA 59.513 50.000 0.00 0.00 36.97 3.49
5958 7129 0.896019 AGGACTCGTGTAGCACAGCT 60.896 55.000 0.00 0.00 43.41 4.24
5959 7130 0.038159 GGACTCGTGTAGCACAGCTT 60.038 55.000 0.00 0.00 40.44 3.74
5960 7131 1.063806 GACTCGTGTAGCACAGCTTG 58.936 55.000 0.00 0.00 40.44 4.01
5969 7140 3.485431 CACAGCTTGCTCCGCGAG 61.485 66.667 8.23 4.18 42.54 5.03
5970 7141 3.684990 ACAGCTTGCTCCGCGAGA 61.685 61.111 8.23 1.68 42.27 4.04
5971 7142 2.202851 CAGCTTGCTCCGCGAGAT 60.203 61.111 8.23 0.00 42.27 2.75
5972 7143 2.105930 AGCTTGCTCCGCGAGATC 59.894 61.111 8.23 0.00 42.27 2.75
5973 7144 2.964389 GCTTGCTCCGCGAGATCC 60.964 66.667 8.23 0.00 42.27 3.36
5974 7145 2.656651 CTTGCTCCGCGAGATCCG 60.657 66.667 8.23 0.00 42.27 4.18
5984 7155 4.148825 GAGATCCGCGCCTGGTGT 62.149 66.667 9.31 0.00 0.00 4.16
5985 7156 4.457496 AGATCCGCGCCTGGTGTG 62.457 66.667 13.73 13.73 0.00 3.82
5986 7157 4.451150 GATCCGCGCCTGGTGTGA 62.451 66.667 21.68 12.49 0.00 3.58
5987 7158 3.740128 GATCCGCGCCTGGTGTGAT 62.740 63.158 21.68 16.40 0.00 3.06
5988 7159 2.363711 GATCCGCGCCTGGTGTGATA 62.364 60.000 21.68 9.94 0.00 2.15
5989 7160 2.369257 ATCCGCGCCTGGTGTGATAG 62.369 60.000 21.68 5.84 0.00 2.08
5990 7161 3.264897 CGCGCCTGGTGTGATAGC 61.265 66.667 15.50 0.00 0.00 2.97
5991 7162 2.897350 GCGCCTGGTGTGATAGCC 60.897 66.667 9.31 0.00 0.00 3.93
5992 7163 2.203070 CGCCTGGTGTGATAGCCC 60.203 66.667 0.00 0.00 0.00 5.19
5993 7164 2.735772 CGCCTGGTGTGATAGCCCT 61.736 63.158 0.00 0.00 0.00 5.19
5994 7165 1.153086 GCCTGGTGTGATAGCCCTG 60.153 63.158 0.00 0.00 0.00 4.45
5995 7166 1.153086 CCTGGTGTGATAGCCCTGC 60.153 63.158 0.00 0.00 0.00 4.85
5996 7167 1.153086 CTGGTGTGATAGCCCTGCC 60.153 63.158 0.00 0.00 0.00 4.85
5997 7168 1.913951 CTGGTGTGATAGCCCTGCCA 61.914 60.000 0.00 0.00 0.00 4.92
5998 7169 1.153086 GGTGTGATAGCCCTGCCAG 60.153 63.158 0.00 0.00 0.00 4.85
5999 7170 1.604378 GTGTGATAGCCCTGCCAGT 59.396 57.895 0.00 0.00 0.00 4.00
6000 7171 0.745845 GTGTGATAGCCCTGCCAGTG 60.746 60.000 0.00 0.00 0.00 3.66
6001 7172 1.153086 GTGATAGCCCTGCCAGTGG 60.153 63.158 4.20 4.20 0.00 4.00
6012 7183 4.625800 CCAGTGGCAAGCTACTCC 57.374 61.111 8.17 0.00 35.55 3.85
6013 7184 1.986413 CCAGTGGCAAGCTACTCCT 59.014 57.895 8.17 0.00 35.55 3.69
6014 7185 1.195115 CCAGTGGCAAGCTACTCCTA 58.805 55.000 8.17 0.00 35.55 2.94
6015 7186 1.134670 CCAGTGGCAAGCTACTCCTAC 60.135 57.143 8.17 0.00 35.55 3.18
6016 7187 0.818296 AGTGGCAAGCTACTCCTACG 59.182 55.000 5.16 0.00 32.12 3.51
6017 7188 0.806492 GTGGCAAGCTACTCCTACGC 60.806 60.000 0.98 0.00 0.00 4.42
6018 7189 1.227292 GGCAAGCTACTCCTACGCC 60.227 63.158 0.00 0.00 0.00 5.68
6019 7190 1.677637 GGCAAGCTACTCCTACGCCT 61.678 60.000 0.00 0.00 33.17 5.52
6020 7191 0.528684 GCAAGCTACTCCTACGCCTG 60.529 60.000 0.00 0.00 0.00 4.85
6021 7192 1.103803 CAAGCTACTCCTACGCCTGA 58.896 55.000 0.00 0.00 0.00 3.86
6022 7193 1.104630 AAGCTACTCCTACGCCTGAC 58.895 55.000 0.00 0.00 0.00 3.51
6032 7203 3.114616 CGCCTGACGGTGCTCTTG 61.115 66.667 0.00 0.00 38.44 3.02
6033 7204 2.743928 GCCTGACGGTGCTCTTGG 60.744 66.667 0.00 0.00 0.00 3.61
6034 7205 3.059982 CCTGACGGTGCTCTTGGA 58.940 61.111 0.00 0.00 0.00 3.53
6035 7206 1.079543 CCTGACGGTGCTCTTGGAG 60.080 63.158 0.00 0.00 0.00 3.86
6036 7207 1.536073 CCTGACGGTGCTCTTGGAGA 61.536 60.000 0.00 0.00 0.00 3.71
6037 7208 0.318441 CTGACGGTGCTCTTGGAGAA 59.682 55.000 0.00 0.00 0.00 2.87
6038 7209 0.318441 TGACGGTGCTCTTGGAGAAG 59.682 55.000 0.00 0.00 0.00 2.85
6039 7210 1.004440 ACGGTGCTCTTGGAGAAGC 60.004 57.895 0.00 0.00 32.77 3.86
6040 7211 1.294780 CGGTGCTCTTGGAGAAGCT 59.705 57.895 3.67 0.00 33.86 3.74
6041 7212 1.018226 CGGTGCTCTTGGAGAAGCTG 61.018 60.000 0.00 0.00 33.86 4.24
6042 7213 0.676151 GGTGCTCTTGGAGAAGCTGG 60.676 60.000 0.00 0.00 33.30 4.85
6043 7214 0.036022 GTGCTCTTGGAGAAGCTGGT 59.964 55.000 0.00 0.00 0.00 4.00
6044 7215 0.035881 TGCTCTTGGAGAAGCTGGTG 59.964 55.000 0.00 0.00 0.00 4.17
6045 7216 0.676151 GCTCTTGGAGAAGCTGGTGG 60.676 60.000 0.00 0.00 0.00 4.61
6046 7217 0.689623 CTCTTGGAGAAGCTGGTGGT 59.310 55.000 0.00 0.00 0.00 4.16
6047 7218 1.072965 CTCTTGGAGAAGCTGGTGGTT 59.927 52.381 0.00 0.00 36.51 3.67
6048 7219 1.202806 TCTTGGAGAAGCTGGTGGTTG 60.203 52.381 0.00 0.00 33.64 3.77
6049 7220 0.550914 TTGGAGAAGCTGGTGGTTGT 59.449 50.000 0.00 0.00 33.64 3.32
6050 7221 1.429930 TGGAGAAGCTGGTGGTTGTA 58.570 50.000 0.00 0.00 33.64 2.41
6051 7222 1.347707 TGGAGAAGCTGGTGGTTGTAG 59.652 52.381 0.00 0.00 33.64 2.74
6052 7223 1.339151 GGAGAAGCTGGTGGTTGTAGG 60.339 57.143 0.00 0.00 33.64 3.18
6053 7224 0.036875 AGAAGCTGGTGGTTGTAGGC 59.963 55.000 0.00 0.00 33.64 3.93
6054 7225 0.036875 GAAGCTGGTGGTTGTAGGCT 59.963 55.000 0.00 0.00 33.64 4.58
6055 7226 0.036875 AAGCTGGTGGTTGTAGGCTC 59.963 55.000 0.00 0.00 32.09 4.70
6056 7227 1.377333 GCTGGTGGTTGTAGGCTCC 60.377 63.158 0.00 0.00 0.00 4.70
6057 7228 1.079127 CTGGTGGTTGTAGGCTCCG 60.079 63.158 0.00 0.00 0.00 4.63
6058 7229 1.534476 TGGTGGTTGTAGGCTCCGA 60.534 57.895 0.00 0.00 0.00 4.55
6059 7230 1.079336 GGTGGTTGTAGGCTCCGAC 60.079 63.158 0.00 0.00 0.00 4.79
6060 7231 1.445582 GTGGTTGTAGGCTCCGACG 60.446 63.158 0.00 0.00 0.00 5.12
6061 7232 2.183555 GGTTGTAGGCTCCGACGG 59.816 66.667 7.84 7.84 0.00 4.79
6062 7233 2.508663 GTTGTAGGCTCCGACGGC 60.509 66.667 9.66 0.00 0.00 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.436015 CCGTCCGTCGATATGATCTTACT 59.564 47.826 0.00 0.00 42.86 2.24
137 138 1.808133 GCAGAAACCCTAGCAGATCGG 60.808 57.143 0.00 0.00 0.00 4.18
364 370 5.983118 CCTACAAAACTTTTAAACTGGGCTG 59.017 40.000 0.00 0.00 0.00 4.85
365 371 5.452776 GCCTACAAAACTTTTAAACTGGGCT 60.453 40.000 0.00 0.00 0.00 5.19
367 373 6.156748 AGCCTACAAAACTTTTAAACTGGG 57.843 37.500 0.00 0.00 0.00 4.45
370 376 9.366216 CTCAAAAGCCTACAAAACTTTTAAACT 57.634 29.630 0.00 0.00 40.63 2.66
371 377 9.146984 ACTCAAAAGCCTACAAAACTTTTAAAC 57.853 29.630 0.00 0.00 40.63 2.01
372 378 9.361315 GACTCAAAAGCCTACAAAACTTTTAAA 57.639 29.630 0.00 0.00 40.63 1.52
376 382 5.124936 ACGACTCAAAAGCCTACAAAACTTT 59.875 36.000 0.00 0.00 35.20 2.66
379 385 4.547406 ACGACTCAAAAGCCTACAAAAC 57.453 40.909 0.00 0.00 0.00 2.43
384 390 5.575995 CCTAGTAAACGACTCAAAAGCCTAC 59.424 44.000 0.00 0.00 39.81 3.18
423 431 3.555518 GCTTTCTCATTGAAACACGGAC 58.444 45.455 0.00 0.00 39.50 4.79
448 456 4.009675 GGTTTATGCCTCAGTGACATTCA 58.990 43.478 1.92 0.00 0.00 2.57
451 459 2.357154 GGGGTTTATGCCTCAGTGACAT 60.357 50.000 2.20 2.20 0.00 3.06
455 463 0.625849 AGGGGGTTTATGCCTCAGTG 59.374 55.000 0.00 0.00 0.00 3.66
707 717 1.271762 ACTGCACAGACCAATCAGCAT 60.272 47.619 4.31 0.00 31.68 3.79
857 881 2.969990 CGAAGCAGCAGATATGCCTAT 58.030 47.619 9.09 0.00 44.97 2.57
1266 1294 4.101119 AGTTCCCTCTTCTTTTCTCGTTGA 59.899 41.667 0.00 0.00 0.00 3.18
1346 1374 9.912634 TCACAGATTTTCAATCTTTCCATTTAC 57.087 29.630 0.00 0.00 0.00 2.01
1441 1471 3.255642 TGAAAAATAGGCAGGAGCACAAC 59.744 43.478 0.00 0.00 44.61 3.32
1858 1888 6.371825 GCCAGCAGGGTCAGTTATAATATAAC 59.628 42.308 13.70 13.70 39.65 1.89
1860 1890 5.045869 GGCCAGCAGGGTCAGTTATAATATA 60.046 44.000 0.00 0.00 42.53 0.86
1861 1891 4.263506 GGCCAGCAGGGTCAGTTATAATAT 60.264 45.833 0.00 0.00 42.53 1.28
1863 1893 2.158608 GGCCAGCAGGGTCAGTTATAAT 60.159 50.000 0.00 0.00 42.53 1.28
1865 1895 0.837272 GGCCAGCAGGGTCAGTTATA 59.163 55.000 0.00 0.00 42.53 0.98
1866 1896 1.609783 GGCCAGCAGGGTCAGTTAT 59.390 57.895 0.00 0.00 42.53 1.89
1867 1897 2.954684 CGGCCAGCAGGGTCAGTTA 61.955 63.158 2.24 0.00 43.46 2.24
1868 1898 4.335647 CGGCCAGCAGGGTCAGTT 62.336 66.667 2.24 0.00 43.46 3.16
1874 1904 3.561120 TTTACACCGGCCAGCAGGG 62.561 63.158 13.47 5.65 35.57 4.45
1875 1905 1.602323 TTTTACACCGGCCAGCAGG 60.602 57.895 0.00 7.31 37.31 4.85
1876 1906 1.579429 GTTTTACACCGGCCAGCAG 59.421 57.895 0.00 0.00 0.00 4.24
1877 1907 1.899534 GGTTTTACACCGGCCAGCA 60.900 57.895 0.00 0.00 35.12 4.41
1878 1908 2.959372 GGTTTTACACCGGCCAGC 59.041 61.111 0.00 0.00 35.12 4.85
1886 1916 2.956333 ACAGGAGCCTTTGGTTTTACAC 59.044 45.455 0.00 0.00 0.00 2.90
1887 1917 3.306472 ACAGGAGCCTTTGGTTTTACA 57.694 42.857 0.00 0.00 0.00 2.41
1888 1918 4.665833 AAACAGGAGCCTTTGGTTTTAC 57.334 40.909 0.00 0.00 0.00 2.01
1889 1919 5.069383 GGTTAAACAGGAGCCTTTGGTTTTA 59.931 40.000 8.25 0.00 34.00 1.52
1980 2010 6.148976 GGGGCATCGAGAAACCTAATTTATAC 59.851 42.308 0.00 0.00 0.00 1.47
2417 3335 5.675538 ACATTGAGTCTAGGCTAATGTTCC 58.324 41.667 18.49 0.00 38.42 3.62
2440 3358 9.866655 ATTTGATGCATAGGATAGGAGTTTTTA 57.133 29.630 0.00 0.00 0.00 1.52
2446 3364 6.470278 TGTCATTTGATGCATAGGATAGGAG 58.530 40.000 0.00 0.00 0.00 3.69
2456 3374 5.892119 AGGAAAGAGATGTCATTTGATGCAT 59.108 36.000 0.00 0.00 32.43 3.96
2499 3417 7.507829 AGGAAAATCATAGGAAGTGAGATGAG 58.492 38.462 0.00 0.00 32.12 2.90
2702 3621 5.830000 AAGTGTACAAACTGACCCTTTTC 57.170 39.130 0.00 0.00 0.00 2.29
2752 3671 7.315890 AGGTTATTACACCGTTCAGTACTTAC 58.684 38.462 0.00 0.00 42.33 2.34
2778 3697 5.294552 GCAAGCTTAGACAACCAAGTATAGG 59.705 44.000 0.00 0.00 0.00 2.57
2779 3698 5.294552 GGCAAGCTTAGACAACCAAGTATAG 59.705 44.000 0.00 0.00 0.00 1.31
2780 3699 5.045869 AGGCAAGCTTAGACAACCAAGTATA 60.046 40.000 0.00 0.00 0.00 1.47
2781 3700 4.010349 GGCAAGCTTAGACAACCAAGTAT 58.990 43.478 0.00 0.00 0.00 2.12
2846 3794 8.545420 CCAAATGACTTCAACAGAAGAATTTTG 58.455 33.333 11.79 14.32 40.97 2.44
2989 3978 4.027674 TGACTGCTAAGCAATTAACCCA 57.972 40.909 0.00 0.00 38.41 4.51
3127 4124 5.372343 AATATGGGAGCACTGATGTGTAA 57.628 39.130 0.00 0.00 45.44 2.41
3198 4260 3.642938 TGGAACACGAGAAATGGGG 57.357 52.632 0.00 0.00 0.00 4.96
3227 4289 3.260884 TCCTTTTGGAGTACTAGTGCTGG 59.739 47.826 18.92 11.78 45.19 4.85
3258 4320 3.517901 AGAATGGTCACGAGGTAATCCAA 59.482 43.478 0.00 0.00 35.89 3.53
3423 4496 5.000012 AGAAGTACACGATCAGATTGGAC 58.000 43.478 2.51 0.00 0.00 4.02
3581 4655 0.385390 ACCAAGGCTCAAAGCAAACG 59.615 50.000 0.86 0.00 44.75 3.60
3838 4932 8.370940 TGAATATCCTATCTCCTAAACTGCAAG 58.629 37.037 0.00 0.00 42.29 4.01
3943 5038 3.433615 CGCCTTCTTGAACTTAGGTCAAG 59.566 47.826 28.51 28.51 41.39 3.02
3944 5039 3.399330 CGCCTTCTTGAACTTAGGTCAA 58.601 45.455 12.46 12.46 0.00 3.18
3945 5040 2.870435 GCGCCTTCTTGAACTTAGGTCA 60.870 50.000 0.00 0.00 0.00 4.02
3950 5045 1.610624 CCCAGCGCCTTCTTGAACTTA 60.611 52.381 2.29 0.00 0.00 2.24
4244 5339 0.755079 CGAGGGATCAAGCATCTCCA 59.245 55.000 0.00 0.00 31.16 3.86
4751 5854 1.515521 GCGGTATGCTACATTGCCCC 61.516 60.000 0.00 0.00 41.73 5.80
4755 5858 2.533266 AGAGGCGGTATGCTACATTG 57.467 50.000 0.00 0.00 45.43 2.82
5155 6266 6.602410 AGTAGTTACTTTGGAGGTAGAACC 57.398 41.667 0.00 0.00 33.37 3.62
5277 6392 4.985413 AGTTGCATATCACCATTTTCGTG 58.015 39.130 0.00 0.00 0.00 4.35
5278 6393 4.096382 GGAGTTGCATATCACCATTTTCGT 59.904 41.667 0.00 0.00 0.00 3.85
5281 6396 4.646492 GGAGGAGTTGCATATCACCATTTT 59.354 41.667 0.00 0.00 0.00 1.82
5348 6470 7.383687 TGATAACGAAAACTTACTCCACTCAT 58.616 34.615 0.00 0.00 0.00 2.90
5349 6471 6.751157 TGATAACGAAAACTTACTCCACTCA 58.249 36.000 0.00 0.00 0.00 3.41
5350 6472 6.867293 ACTGATAACGAAAACTTACTCCACTC 59.133 38.462 0.00 0.00 0.00 3.51
5351 6473 6.645415 CACTGATAACGAAAACTTACTCCACT 59.355 38.462 0.00 0.00 0.00 4.00
5352 6474 6.128634 CCACTGATAACGAAAACTTACTCCAC 60.129 42.308 0.00 0.00 0.00 4.02
5353 6475 5.929992 CCACTGATAACGAAAACTTACTCCA 59.070 40.000 0.00 0.00 0.00 3.86
5354 6476 6.161381 TCCACTGATAACGAAAACTTACTCC 58.839 40.000 0.00 0.00 0.00 3.85
5355 6477 6.867293 ACTCCACTGATAACGAAAACTTACTC 59.133 38.462 0.00 0.00 0.00 2.59
5356 6478 6.756221 ACTCCACTGATAACGAAAACTTACT 58.244 36.000 0.00 0.00 0.00 2.24
5357 6479 8.524870 TTACTCCACTGATAACGAAAACTTAC 57.475 34.615 0.00 0.00 0.00 2.34
5358 6480 9.715121 AATTACTCCACTGATAACGAAAACTTA 57.285 29.630 0.00 0.00 0.00 2.24
5359 6481 8.617290 AATTACTCCACTGATAACGAAAACTT 57.383 30.769 0.00 0.00 0.00 2.66
5360 6482 8.504005 CAAATTACTCCACTGATAACGAAAACT 58.496 33.333 0.00 0.00 0.00 2.66
5361 6483 7.749126 CCAAATTACTCCACTGATAACGAAAAC 59.251 37.037 0.00 0.00 0.00 2.43
5362 6484 7.574217 GCCAAATTACTCCACTGATAACGAAAA 60.574 37.037 0.00 0.00 0.00 2.29
5363 6485 6.128117 GCCAAATTACTCCACTGATAACGAAA 60.128 38.462 0.00 0.00 0.00 3.46
5364 6486 5.353123 GCCAAATTACTCCACTGATAACGAA 59.647 40.000 0.00 0.00 0.00 3.85
5365 6487 4.873827 GCCAAATTACTCCACTGATAACGA 59.126 41.667 0.00 0.00 0.00 3.85
5366 6488 4.035208 GGCCAAATTACTCCACTGATAACG 59.965 45.833 0.00 0.00 0.00 3.18
5367 6489 4.035208 CGGCCAAATTACTCCACTGATAAC 59.965 45.833 2.24 0.00 0.00 1.89
5368 6490 4.080807 TCGGCCAAATTACTCCACTGATAA 60.081 41.667 2.24 0.00 0.00 1.75
5369 6491 3.452990 TCGGCCAAATTACTCCACTGATA 59.547 43.478 2.24 0.00 0.00 2.15
5383 6505 1.202114 GAATTGAGTGCATCGGCCAAA 59.798 47.619 2.24 0.00 40.13 3.28
5437 6559 3.424724 TGCCCTAAACCCTATCCTACA 57.575 47.619 0.00 0.00 0.00 2.74
5458 6580 0.465460 AGAAAACTTGCAGGTCGCCA 60.465 50.000 0.32 0.00 41.33 5.69
5484 6606 3.126879 ATCCGTGTCCGCGTACGA 61.127 61.111 21.65 13.00 43.93 3.43
5492 6614 4.530857 CCTCCCGCATCCGTGTCC 62.531 72.222 0.00 0.00 0.00 4.02
5515 6637 2.288763 ACCAAATTCCGCAATGTTGGAC 60.289 45.455 15.52 0.00 41.05 4.02
5521 6643 3.184178 GTGTTTGACCAAATTCCGCAATG 59.816 43.478 0.00 0.00 32.36 2.82
5545 6703 9.438163 AACCCTTCATGTTTATATGAAATCCAT 57.562 29.630 0.00 0.00 44.06 3.41
5546 6704 8.837099 AACCCTTCATGTTTATATGAAATCCA 57.163 30.769 0.00 0.00 44.06 3.41
5575 6734 6.899393 AGTTCATGTGTGTCCAAAATGTAT 57.101 33.333 0.00 0.00 0.00 2.29
5609 6768 3.985019 TTATACCTTCAAAGCCGGACA 57.015 42.857 5.05 0.00 0.00 4.02
5614 6773 7.968405 CAGTGTGTTAATTATACCTTCAAAGCC 59.032 37.037 0.00 0.00 0.00 4.35
5639 6798 3.466836 GGCACCGACAATCATAGATTCA 58.533 45.455 0.00 0.00 0.00 2.57
5681 6840 0.321996 AGTTTCAGTTCTCGGGGCTC 59.678 55.000 0.00 0.00 0.00 4.70
5699 6858 3.723260 GAGGAGGAATTAGAAGGCGAAG 58.277 50.000 0.00 0.00 0.00 3.79
5709 6868 0.755698 AGAGCGCCGAGGAGGAATTA 60.756 55.000 2.29 0.00 45.00 1.40
5725 6884 0.464013 TCGAAGGCGGAGGTAGAGAG 60.464 60.000 0.00 0.00 38.28 3.20
5730 6889 1.318158 GGTCTTCGAAGGCGGAGGTA 61.318 60.000 24.37 0.00 43.48 3.08
5741 6900 1.618837 CTTCACTTCCCAGGTCTTCGA 59.381 52.381 0.00 0.00 0.00 3.71
5744 6903 2.749800 GCAACTTCACTTCCCAGGTCTT 60.750 50.000 0.00 0.00 0.00 3.01
5750 6909 1.228124 CGGGCAACTTCACTTCCCA 60.228 57.895 0.00 0.00 36.79 4.37
5765 6924 4.415332 CCACGACCACGACTCGGG 62.415 72.222 2.98 0.00 42.66 5.14
5823 6982 1.427020 GGTAAGACCGACGACGAGG 59.573 63.158 9.28 7.24 42.66 4.63
5967 7138 4.148825 ACACCAGGCGCGGATCTC 62.149 66.667 8.83 0.00 0.00 2.75
5968 7139 4.457496 CACACCAGGCGCGGATCT 62.457 66.667 8.83 0.00 0.00 2.75
5969 7140 2.363711 TATCACACCAGGCGCGGATC 62.364 60.000 8.83 0.00 0.00 3.36
5970 7141 2.369257 CTATCACACCAGGCGCGGAT 62.369 60.000 8.83 1.46 0.00 4.18
5971 7142 3.071837 TATCACACCAGGCGCGGA 61.072 61.111 8.83 0.00 0.00 5.54
5972 7143 2.586079 CTATCACACCAGGCGCGG 60.586 66.667 8.83 0.00 0.00 6.46
5973 7144 3.264897 GCTATCACACCAGGCGCG 61.265 66.667 0.00 0.00 0.00 6.86
5974 7145 2.897350 GGCTATCACACCAGGCGC 60.897 66.667 0.00 0.00 0.00 6.53
5975 7146 2.203070 GGGCTATCACACCAGGCG 60.203 66.667 0.00 0.00 38.18 5.52
5976 7147 1.153086 CAGGGCTATCACACCAGGC 60.153 63.158 0.00 0.00 36.65 4.85
5977 7148 1.153086 GCAGGGCTATCACACCAGG 60.153 63.158 0.00 0.00 0.00 4.45
5978 7149 1.153086 GGCAGGGCTATCACACCAG 60.153 63.158 0.00 0.00 0.00 4.00
5979 7150 1.913951 CTGGCAGGGCTATCACACCA 61.914 60.000 6.61 0.00 0.00 4.17
5980 7151 1.153086 CTGGCAGGGCTATCACACC 60.153 63.158 6.61 0.00 0.00 4.16
5981 7152 0.745845 CACTGGCAGGGCTATCACAC 60.746 60.000 20.34 0.00 0.00 3.82
5982 7153 1.603842 CACTGGCAGGGCTATCACA 59.396 57.895 20.34 0.00 0.00 3.58
5983 7154 1.153086 CCACTGGCAGGGCTATCAC 60.153 63.158 20.34 0.00 0.00 3.06
5984 7155 3.323622 CCACTGGCAGGGCTATCA 58.676 61.111 20.34 0.00 0.00 2.15
5995 7166 1.134670 GTAGGAGTAGCTTGCCACTGG 60.135 57.143 0.00 0.00 0.00 4.00
5996 7167 1.469940 CGTAGGAGTAGCTTGCCACTG 60.470 57.143 0.00 0.00 0.00 3.66
5997 7168 0.818296 CGTAGGAGTAGCTTGCCACT 59.182 55.000 0.00 0.00 0.00 4.00
5998 7169 0.806492 GCGTAGGAGTAGCTTGCCAC 60.806 60.000 0.00 0.00 0.00 5.01
5999 7170 1.515954 GCGTAGGAGTAGCTTGCCA 59.484 57.895 0.00 0.00 0.00 4.92
6000 7171 1.227292 GGCGTAGGAGTAGCTTGCC 60.227 63.158 0.00 0.00 0.00 4.52
6001 7172 0.528684 CAGGCGTAGGAGTAGCTTGC 60.529 60.000 0.00 0.00 31.61 4.01
6002 7173 1.103803 TCAGGCGTAGGAGTAGCTTG 58.896 55.000 0.00 0.00 38.99 4.01
6003 7174 1.104630 GTCAGGCGTAGGAGTAGCTT 58.895 55.000 0.00 0.00 0.00 3.74
6004 7175 1.096386 CGTCAGGCGTAGGAGTAGCT 61.096 60.000 0.00 0.00 35.54 3.32
6005 7176 1.355916 CGTCAGGCGTAGGAGTAGC 59.644 63.158 0.00 0.00 35.54 3.58
6006 7177 0.747283 ACCGTCAGGCGTAGGAGTAG 60.747 60.000 0.00 0.00 42.76 2.57
6007 7178 1.028330 CACCGTCAGGCGTAGGAGTA 61.028 60.000 0.00 0.00 42.76 2.59
6008 7179 2.035312 ACCGTCAGGCGTAGGAGT 59.965 61.111 0.00 0.00 42.76 3.85
6009 7180 2.490217 CACCGTCAGGCGTAGGAG 59.510 66.667 0.00 0.00 42.76 3.69
6010 7181 3.755628 GCACCGTCAGGCGTAGGA 61.756 66.667 0.00 0.00 42.76 2.94
6011 7182 3.701604 GAGCACCGTCAGGCGTAGG 62.702 68.421 0.00 0.00 42.76 3.18
6012 7183 2.202623 GAGCACCGTCAGGCGTAG 60.203 66.667 0.00 0.00 42.76 3.51
6013 7184 2.273179 AAGAGCACCGTCAGGCGTA 61.273 57.895 0.00 0.00 42.76 4.42
6014 7185 3.616721 AAGAGCACCGTCAGGCGT 61.617 61.111 0.00 0.00 42.76 5.68
6015 7186 3.114616 CAAGAGCACCGTCAGGCG 61.115 66.667 0.00 0.00 42.76 5.52
6016 7187 2.743928 CCAAGAGCACCGTCAGGC 60.744 66.667 0.00 0.00 42.76 4.85
6017 7188 1.079543 CTCCAAGAGCACCGTCAGG 60.080 63.158 0.00 0.00 45.13 3.86
6018 7189 0.318441 TTCTCCAAGAGCACCGTCAG 59.682 55.000 0.00 0.00 0.00 3.51
6019 7190 0.318441 CTTCTCCAAGAGCACCGTCA 59.682 55.000 0.00 0.00 0.00 4.35
6020 7191 1.016653 GCTTCTCCAAGAGCACCGTC 61.017 60.000 0.00 0.00 0.00 4.79
6021 7192 1.004440 GCTTCTCCAAGAGCACCGT 60.004 57.895 0.00 0.00 0.00 4.83
6022 7193 1.018226 CAGCTTCTCCAAGAGCACCG 61.018 60.000 0.00 0.00 0.00 4.94
6023 7194 0.676151 CCAGCTTCTCCAAGAGCACC 60.676 60.000 0.00 0.00 0.00 5.01
6024 7195 0.036022 ACCAGCTTCTCCAAGAGCAC 59.964 55.000 0.00 0.00 0.00 4.40
6025 7196 0.035881 CACCAGCTTCTCCAAGAGCA 59.964 55.000 0.00 0.00 0.00 4.26
6026 7197 0.676151 CCACCAGCTTCTCCAAGAGC 60.676 60.000 0.00 0.00 0.00 4.09
6027 7198 0.689623 ACCACCAGCTTCTCCAAGAG 59.310 55.000 0.00 0.00 0.00 2.85
6028 7199 1.140312 AACCACCAGCTTCTCCAAGA 58.860 50.000 0.00 0.00 0.00 3.02
6029 7200 1.242076 CAACCACCAGCTTCTCCAAG 58.758 55.000 0.00 0.00 0.00 3.61
6030 7201 0.550914 ACAACCACCAGCTTCTCCAA 59.449 50.000 0.00 0.00 0.00 3.53
6031 7202 1.347707 CTACAACCACCAGCTTCTCCA 59.652 52.381 0.00 0.00 0.00 3.86
6032 7203 1.339151 CCTACAACCACCAGCTTCTCC 60.339 57.143 0.00 0.00 0.00 3.71
6033 7204 1.946283 GCCTACAACCACCAGCTTCTC 60.946 57.143 0.00 0.00 0.00 2.87
6034 7205 0.036875 GCCTACAACCACCAGCTTCT 59.963 55.000 0.00 0.00 0.00 2.85
6035 7206 0.036875 AGCCTACAACCACCAGCTTC 59.963 55.000 0.00 0.00 0.00 3.86
6036 7207 0.036875 GAGCCTACAACCACCAGCTT 59.963 55.000 0.00 0.00 0.00 3.74
6037 7208 1.679898 GAGCCTACAACCACCAGCT 59.320 57.895 0.00 0.00 0.00 4.24
6038 7209 1.377333 GGAGCCTACAACCACCAGC 60.377 63.158 0.00 0.00 0.00 4.85
6039 7210 1.079127 CGGAGCCTACAACCACCAG 60.079 63.158 0.00 0.00 0.00 4.00
6040 7211 1.534476 TCGGAGCCTACAACCACCA 60.534 57.895 0.00 0.00 0.00 4.17
6041 7212 1.079336 GTCGGAGCCTACAACCACC 60.079 63.158 0.00 0.00 0.00 4.61
6042 7213 1.445582 CGTCGGAGCCTACAACCAC 60.446 63.158 0.00 0.00 0.00 4.16
6043 7214 2.642254 CCGTCGGAGCCTACAACCA 61.642 63.158 4.91 0.00 0.00 3.67
6044 7215 2.183555 CCGTCGGAGCCTACAACC 59.816 66.667 4.91 0.00 0.00 3.77
6045 7216 2.508663 GCCGTCGGAGCCTACAAC 60.509 66.667 17.49 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.