Multiple sequence alignment - TraesCS6D01G067900

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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 TraesCS6D01G067900 chr6D 100.000 6995 0 0 1 6995 34079010 34086004 0.000000e+00 12918.0
1 TraesCS6D01G067900 chr6D 86.866 3746 302 86 2018 5661 8545351 8541694 0.000000e+00 4017.0
2 TraesCS6D01G067900 chr6D 90.870 1632 102 17 4067 5661 8809377 8810998 0.000000e+00 2145.0
3 TraesCS6D01G067900 chr6D 85.337 1930 156 48 2248 4128 8807528 8809379 0.000000e+00 1879.0
4 TraesCS6D01G067900 chr6D 86.311 1220 88 23 2697 3866 8561403 8560213 0.000000e+00 1254.0
5 TraesCS6D01G067900 chr6D 90.236 594 28 9 4623 5188 8560053 8559462 0.000000e+00 749.0
6 TraesCS6D01G067900 chr6D 92.259 478 31 5 5186 5661 8559338 8558865 0.000000e+00 673.0
7 TraesCS6D01G067900 chr6D 81.277 689 67 29 2018 2696 8562383 8561747 1.050000e-137 501.0
8 TraesCS6D01G067900 chr6D 82.582 488 44 19 5799 6255 8558628 8558151 6.580000e-105 392.0
9 TraesCS6D01G067900 chr6D 95.431 197 7 2 5963 6157 8811324 8811520 5.270000e-81 313.0
10 TraesCS6D01G067900 chr6D 93.909 197 10 2 5963 6157 8541368 8541172 5.310000e-76 296.0
11 TraesCS6D01G067900 chr6D 92.899 169 8 2 4415 4583 8560216 8560052 7.010000e-60 243.0
12 TraesCS6D01G067900 chr6D 93.548 93 6 0 1042 1134 8654259 8654167 9.460000e-29 139.0
13 TraesCS6D01G067900 chr6D 83.846 130 14 3 5807 5935 8811202 8811325 4.430000e-22 117.0
14 TraesCS6D01G067900 chr6D 83.077 130 15 3 5807 5935 8541490 8541367 2.060000e-20 111.0
15 TraesCS6D01G067900 chr5B 91.311 3510 199 55 1721 5188 556786844 556783399 0.000000e+00 4695.0
16 TraesCS6D01G067900 chr5B 92.027 1179 62 14 1 1170 556789361 556788206 0.000000e+00 1628.0
17 TraesCS6D01G067900 chr5B 92.687 547 27 7 1175 1711 556787465 556786922 0.000000e+00 776.0
18 TraesCS6D01G067900 chr5B 88.062 645 51 10 5186 5805 556783276 556782633 0.000000e+00 741.0
19 TraesCS6D01G067900 chr5B 81.494 589 58 29 5805 6354 17672849 17673425 3.000000e-118 436.0
20 TraesCS6D01G067900 chr5B 91.195 318 24 3 5493 5806 17666640 17666957 5.010000e-116 429.0
21 TraesCS6D01G067900 chr5B 86.601 306 21 8 5856 6160 556782366 556782080 3.150000e-83 320.0
22 TraesCS6D01G067900 chr5B 92.473 93 7 0 1042 1134 37063591 37063683 4.400000e-27 134.0
23 TraesCS6D01G067900 chr6B 86.854 3849 318 74 1917 5661 16439937 16443701 0.000000e+00 4132.0
24 TraesCS6D01G067900 chr6B 86.807 3790 302 76 1959 5641 15210746 15207048 0.000000e+00 4047.0
25 TraesCS6D01G067900 chr6B 90.738 637 41 9 534 1170 15384143 15383525 0.000000e+00 833.0
26 TraesCS6D01G067900 chr6B 90.815 577 37 9 430 1005 670529477 670528916 0.000000e+00 758.0
27 TraesCS6D01G067900 chr6B 82.771 859 94 37 5810 6633 16443915 16444754 0.000000e+00 717.0
28 TraesCS6D01G067900 chr6B 91.117 394 24 4 2 387 670530761 670530371 2.240000e-144 523.0
29 TraesCS6D01G067900 chr6B 91.282 195 12 4 1 193 15384331 15384140 1.940000e-65 261.0
30 TraesCS6D01G067900 chr6B 89.831 59 2 2 1081 1135 55722606 55722548 9.730000e-09 73.1
31 TraesCS6D01G067900 chr6A 86.539 3395 255 85 1917 5188 9481832 9485147 0.000000e+00 3552.0
32 TraesCS6D01G067900 chr6A 93.082 477 31 2 5186 5661 9485271 9485746 0.000000e+00 697.0
33 TraesCS6D01G067900 chr6A 81.855 733 74 22 5799 6485 9485965 9486684 4.740000e-156 562.0
34 TraesCS6D01G067900 chr6A 85.677 384 26 8 6505 6882 9486674 9487034 1.840000e-100 377.0
35 TraesCS6D01G067900 chr6A 90.816 98 9 0 1070 1167 9480082 9480179 1.580000e-26 132.0
36 TraesCS6D01G067900 chr6A 95.946 74 3 0 6868 6941 9488890 9488963 3.430000e-23 121.0
37 TraesCS6D01G067900 chr5D 89.339 469 35 8 5352 5806 42078790 42079257 6.090000e-160 575.0
38 TraesCS6D01G067900 chr4A 78.750 400 60 13 752 1139 16975791 16976177 1.950000e-60 244.0
39 TraesCS6D01G067900 chr4A 89.831 59 5 1 1175 1232 16978441 16978499 2.710000e-09 75.0
40 TraesCS6D01G067900 chr4A 92.857 42 1 1 1191 1232 17035505 17035466 7.580000e-05 60.2
41 TraesCS6D01G067900 chrUn 93.182 132 9 0 5675 5806 65761429 65761298 1.990000e-45 195.0
42 TraesCS6D01G067900 chr1B 86.957 115 10 3 1025 1135 664763161 664763274 2.650000e-24 124.0
43 TraesCS6D01G067900 chr1A 86.087 115 10 3 1025 1134 573207674 573207787 1.230000e-22 119.0
44 TraesCS6D01G067900 chr4D 89.831 59 3 2 1175 1232 449971911 449971855 9.730000e-09 73.1
45 TraesCS6D01G067900 chr4D 92.857 42 1 1 1191 1232 449851586 449851625 7.580000e-05 60.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G067900 chr6D 34079010 34086004 6994 False 12918.000000 12918 100.000000 1 6995 1 chr6D.!!$F1 6994
1 TraesCS6D01G067900 chr6D 8541172 8545351 4179 True 1474.666667 4017 87.950667 2018 6157 3 chr6D.!!$R2 4139
2 TraesCS6D01G067900 chr6D 8807528 8811520 3992 False 1113.500000 2145 88.871000 2248 6157 4 chr6D.!!$F2 3909
3 TraesCS6D01G067900 chr6D 8558151 8562383 4232 True 635.333333 1254 87.594000 2018 6255 6 chr6D.!!$R3 4237
4 TraesCS6D01G067900 chr5B 556782080 556789361 7281 True 1632.000000 4695 90.137600 1 6160 5 chr5B.!!$R1 6159
5 TraesCS6D01G067900 chr5B 17672849 17673425 576 False 436.000000 436 81.494000 5805 6354 1 chr5B.!!$F2 549
6 TraesCS6D01G067900 chr6B 15207048 15210746 3698 True 4047.000000 4047 86.807000 1959 5641 1 chr6B.!!$R1 3682
7 TraesCS6D01G067900 chr6B 16439937 16444754 4817 False 2424.500000 4132 84.812500 1917 6633 2 chr6B.!!$F1 4716
8 TraesCS6D01G067900 chr6B 670528916 670530761 1845 True 640.500000 758 90.966000 2 1005 2 chr6B.!!$R4 1003
9 TraesCS6D01G067900 chr6B 15383525 15384331 806 True 547.000000 833 91.010000 1 1170 2 chr6B.!!$R3 1169
10 TraesCS6D01G067900 chr6A 9480082 9488963 8881 False 906.833333 3552 88.985833 1070 6941 6 chr6A.!!$F1 5871

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
114 115 0.893270 TTTCCATTGACAGGCCACCG 60.893 55.000 5.01 0.0 0.00 4.94 F
1011 1872 1.177401 GGGGAGCAATGTTGGACTTC 58.823 55.000 0.00 0.0 0.00 3.01 F
1635 3983 0.035056 ACTGCATGCCTAGTTGGTCC 60.035 55.000 16.68 0.0 38.35 4.46 F
2416 4896 0.181350 ACTCCCATTCCATCTTCGCC 59.819 55.000 0.00 0.0 0.00 5.54 F
2417 4897 0.536006 CTCCCATTCCATCTTCGCCC 60.536 60.000 0.00 0.0 0.00 6.13 F
4037 7501 0.391130 TAGCACTTCACATCGTGGGC 60.391 55.000 0.00 0.0 33.87 5.36 F
4759 8303 2.435805 AGTGTTGTCAGGAGAAGAGCAA 59.564 45.455 0.00 0.0 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1016 1877 0.250510 TGTTCAACATACCGCAGCCA 60.251 50.000 0.00 0.0 0.00 4.75 R
2928 5815 0.036022 ACTGCTTCCCTTGAGCTGAC 59.964 55.000 9.47 0.0 40.30 3.51 R
3605 6515 2.093973 ACAACGGCCAAACAATTTGTCA 60.094 40.909 2.24 0.0 38.98 3.58 R
3691 6601 1.007721 ACAGAGGGTCCAGAGCAGTAT 59.992 52.381 0.00 0.0 0.00 2.12 R
4274 7804 1.273327 CAAGGGAACAGTTTGGGCATC 59.727 52.381 0.00 0.0 0.00 3.91 R
5109 8692 0.899720 AATTGGGGCATTGCTGTCAG 59.100 50.000 8.82 0.0 0.00 3.51 R
6278 10436 0.242825 ACCACCACAGTCGATACACG 59.757 55.000 0.00 0.0 44.09 4.49 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
109 110 8.947055 ATTATTTACATTTTCCATTGACAGGC 57.053 30.769 0.00 0.00 0.00 4.85
114 115 0.893270 TTTCCATTGACAGGCCACCG 60.893 55.000 5.01 0.00 0.00 4.94
587 1448 6.595716 GTCTAGGCATAGTTGAAATCACAGTT 59.404 38.462 5.15 0.00 0.00 3.16
607 1468 3.492421 TGACCGTCGGTTATACACTTC 57.508 47.619 19.95 2.52 35.25 3.01
686 1547 5.353678 CCATTTTTGCAAAAACAGTGGAGAA 59.646 36.000 33.10 15.75 40.33 2.87
761 1622 4.965814 AGTCCTTATATGTGGCATGTCTG 58.034 43.478 0.00 0.00 0.00 3.51
981 1842 4.463539 CCATTTGGATGACAATTCTGGACA 59.536 41.667 0.00 0.00 39.21 4.02
1011 1872 1.177401 GGGGAGCAATGTTGGACTTC 58.823 55.000 0.00 0.00 0.00 3.01
1016 1877 3.760684 GGAGCAATGTTGGACTTCTTGAT 59.239 43.478 0.00 0.00 0.00 2.57
1020 1881 2.957402 TGTTGGACTTCTTGATGGCT 57.043 45.000 0.00 0.00 0.00 4.75
1021 1882 2.507484 TGTTGGACTTCTTGATGGCTG 58.493 47.619 0.00 0.00 0.00 4.85
1022 1883 1.200948 GTTGGACTTCTTGATGGCTGC 59.799 52.381 0.00 0.00 0.00 5.25
1040 1901 1.156736 GCGGTATGTTGAACACTGCT 58.843 50.000 11.22 0.00 40.62 4.24
1043 1904 3.002791 CGGTATGTTGAACACTGCTGAT 58.997 45.455 0.00 0.00 0.00 2.90
1068 1929 5.772825 TGCAGTTTTGATCTAGTTTGCTT 57.227 34.783 11.39 0.00 0.00 3.91
1170 2032 4.984146 AAGACTAAGCCTCCTCTGTTTT 57.016 40.909 0.00 0.00 0.00 2.43
1172 2034 4.164204 AGACTAAGCCTCCTCTGTTTTCT 58.836 43.478 0.00 0.00 0.00 2.52
1174 2036 4.164204 ACTAAGCCTCCTCTGTTTTCTCT 58.836 43.478 0.00 0.00 0.00 3.10
1176 2038 5.961421 ACTAAGCCTCCTCTGTTTTCTCTAT 59.039 40.000 0.00 0.00 0.00 1.98
1177 2039 7.126733 ACTAAGCCTCCTCTGTTTTCTCTATA 58.873 38.462 0.00 0.00 0.00 1.31
1180 3518 4.202274 GCCTCCTCTGTTTTCTCTATACCC 60.202 50.000 0.00 0.00 0.00 3.69
1205 3543 5.371115 TTGTGCTATTGTTAGACTTTGGC 57.629 39.130 0.00 0.00 0.00 4.52
1219 3557 5.876357 AGACTTTGGCTGTATACCTTTTGA 58.124 37.500 0.00 0.00 0.00 2.69
1240 3578 6.741992 TGAAATCGTGAGCACAAGATAAAT 57.258 33.333 12.36 3.48 42.47 1.40
1307 3650 9.591792 CTGACTCAGATCACATATAAGAACAAA 57.408 33.333 0.00 0.00 32.44 2.83
1407 3750 4.262808 GCATCTGGGCTGTCTATCAGTTAT 60.263 45.833 0.00 0.00 45.23 1.89
1457 3800 2.036604 GCTCCCTCATGTTAGTAGAGGC 59.963 54.545 0.00 0.00 45.99 4.70
1458 3801 3.300388 CTCCCTCATGTTAGTAGAGGCA 58.700 50.000 0.00 0.00 45.99 4.75
1486 3829 4.597004 AGTTGACTCTTCACCCGTATAGA 58.403 43.478 0.00 0.00 0.00 1.98
1530 3873 9.265901 TGCAATCATAGTATAAAGCTCTCTTTC 57.734 33.333 0.00 0.00 41.34 2.62
1544 3887 6.892691 AGCTCTCTTTCTATTTTGTCAAACG 58.107 36.000 0.00 0.00 0.00 3.60
1548 3891 7.636326 TCTCTTTCTATTTTGTCAAACGGTTC 58.364 34.615 0.00 0.00 0.00 3.62
1635 3983 0.035056 ACTGCATGCCTAGTTGGTCC 60.035 55.000 16.68 0.00 38.35 4.46
1663 4011 4.202121 GGTGTGACAAGAACAGTCAGTAGA 60.202 45.833 0.00 0.00 45.77 2.59
1684 4033 9.739276 AGTAGAACCATGATATTTCAGTTTTCA 57.261 29.630 0.00 0.00 34.73 2.69
1711 4060 9.686683 ATCTTAGCAAATCTGTAGGTTAACAAT 57.313 29.630 8.10 0.00 0.00 2.71
1715 4064 8.225603 AGCAAATCTGTAGGTTAACAATATGG 57.774 34.615 8.10 0.00 0.00 2.74
1716 4065 7.834181 AGCAAATCTGTAGGTTAACAATATGGT 59.166 33.333 8.10 0.00 0.00 3.55
1718 4067 8.405531 CAAATCTGTAGGTTAACAATATGGTGG 58.594 37.037 8.10 0.00 0.00 4.61
1748 4165 9.970395 TTTTGCCATTGCTCTTATTCTTATATG 57.030 29.630 0.00 0.00 38.71 1.78
1765 4182 0.464373 ATGCTGCCATTACTCCCACG 60.464 55.000 0.00 0.00 0.00 4.94
1806 4237 1.134280 CCACTAACCATGCCTCTCAGG 60.134 57.143 0.00 0.00 38.80 3.86
1809 4240 2.503356 ACTAACCATGCCTCTCAGGAAG 59.497 50.000 0.00 0.00 37.67 3.46
1816 4247 4.521146 CATGCCTCTCAGGAAGTATTGTT 58.479 43.478 0.00 0.00 37.67 2.83
1821 4252 5.649831 GCCTCTCAGGAAGTATTGTTCATTT 59.350 40.000 0.00 0.00 37.67 2.32
1830 4261 7.043565 GGAAGTATTGTTCATTTTCATGCCAT 58.956 34.615 0.00 0.00 0.00 4.40
1845 4276 5.932455 TCATGCCATCTGACAAGATAATGA 58.068 37.500 0.00 0.00 41.43 2.57
1849 4280 5.819379 TGCCATCTGACAAGATAATGAACTC 59.181 40.000 0.00 0.00 41.43 3.01
1917 4348 7.899973 AGGTCAGAAACAAAAGATGCAATTAT 58.100 30.769 0.00 0.00 0.00 1.28
1945 4376 1.520342 CAGAGCTTAGCTGTCCGGC 60.520 63.158 13.01 0.00 39.88 6.13
1973 4404 5.184864 TGCATATAGACAAAACCAACAAGGG 59.815 40.000 0.00 0.00 43.89 3.95
1976 4407 2.384828 AGACAAAACCAACAAGGGTCC 58.615 47.619 0.00 0.00 41.32 4.46
1978 4409 0.756294 CAAAACCAACAAGGGTCCCC 59.244 55.000 3.51 0.00 41.32 4.81
2400 4880 3.881688 CACCAATCTCCATCCATTCACTC 59.118 47.826 0.00 0.00 0.00 3.51
2401 4881 3.117738 ACCAATCTCCATCCATTCACTCC 60.118 47.826 0.00 0.00 0.00 3.85
2402 4882 3.484407 CAATCTCCATCCATTCACTCCC 58.516 50.000 0.00 0.00 0.00 4.30
2403 4883 2.268796 TCTCCATCCATTCACTCCCA 57.731 50.000 0.00 0.00 0.00 4.37
2404 4884 2.780414 TCTCCATCCATTCACTCCCAT 58.220 47.619 0.00 0.00 0.00 4.00
2405 4885 3.125656 TCTCCATCCATTCACTCCCATT 58.874 45.455 0.00 0.00 0.00 3.16
2406 4886 3.137176 TCTCCATCCATTCACTCCCATTC 59.863 47.826 0.00 0.00 0.00 2.67
2407 4887 2.175499 TCCATCCATTCACTCCCATTCC 59.825 50.000 0.00 0.00 0.00 3.01
2408 4888 2.091720 CCATCCATTCACTCCCATTCCA 60.092 50.000 0.00 0.00 0.00 3.53
2409 4889 3.437491 CCATCCATTCACTCCCATTCCAT 60.437 47.826 0.00 0.00 0.00 3.41
2410 4890 3.582998 TCCATTCACTCCCATTCCATC 57.417 47.619 0.00 0.00 0.00 3.51
2411 4891 3.125656 TCCATTCACTCCCATTCCATCT 58.874 45.455 0.00 0.00 0.00 2.90
2412 4892 3.528905 TCCATTCACTCCCATTCCATCTT 59.471 43.478 0.00 0.00 0.00 2.40
2413 4893 3.887716 CCATTCACTCCCATTCCATCTTC 59.112 47.826 0.00 0.00 0.00 2.87
2414 4894 2.988010 TCACTCCCATTCCATCTTCG 57.012 50.000 0.00 0.00 0.00 3.79
2415 4895 1.134401 TCACTCCCATTCCATCTTCGC 60.134 52.381 0.00 0.00 0.00 4.70
2416 4896 0.181350 ACTCCCATTCCATCTTCGCC 59.819 55.000 0.00 0.00 0.00 5.54
2417 4897 0.536006 CTCCCATTCCATCTTCGCCC 60.536 60.000 0.00 0.00 0.00 6.13
2418 4898 0.988145 TCCCATTCCATCTTCGCCCT 60.988 55.000 0.00 0.00 0.00 5.19
2419 4899 0.536006 CCCATTCCATCTTCGCCCTC 60.536 60.000 0.00 0.00 0.00 4.30
2581 5083 9.664332 ATTTACTATTTTTGTGCCAATTATGCA 57.336 25.926 0.00 0.00 36.12 3.96
2588 5090 7.507733 TTTTGTGCCAATTATGCAGAAATTT 57.492 28.000 18.82 0.00 46.87 1.82
2600 5102 5.643379 TGCAGAAATTTATTGAGGTGGAC 57.357 39.130 6.40 0.00 0.00 4.02
2782 5627 0.598562 AGCGTATCATCGGCGAGATT 59.401 50.000 17.22 4.56 37.52 2.40
2899 5786 3.955145 CAGGGACAAGCCATGTGTA 57.045 52.632 0.00 0.00 44.12 2.90
2928 5815 1.671901 AAGGTGGGTGGTTTTGTGCG 61.672 55.000 0.00 0.00 0.00 5.34
3115 6005 5.231552 TCATCTTGGGGGAATTATGGTCTA 58.768 41.667 0.00 0.00 0.00 2.59
3279 6185 6.241645 AGTGATCTATCATGTAGATCCGACA 58.758 40.000 25.84 15.00 45.68 4.35
3363 6269 1.741028 TTTGGGGAGAGGTGACATCA 58.259 50.000 0.00 0.00 0.00 3.07
3364 6270 1.279496 TTGGGGAGAGGTGACATCAG 58.721 55.000 0.00 0.00 0.00 2.90
3371 6277 1.701847 AGAGGTGACATCAGTTTGGCT 59.298 47.619 0.00 0.00 0.00 4.75
3453 6360 2.093658 AGATACGACAAACCGATTGGCT 60.094 45.455 0.00 0.00 45.55 4.75
3673 6583 6.938596 TGACAAATATGATCTGCTTCCCATAG 59.061 38.462 0.00 0.00 0.00 2.23
3691 6601 0.976641 AGACCGGACAGCTCAATGAA 59.023 50.000 9.46 0.00 0.00 2.57
3699 6609 3.559242 GGACAGCTCAATGAATACTGCTC 59.441 47.826 7.30 5.27 31.46 4.26
3754 6668 3.937706 GACCTCCATTCAGTCATTGTCAG 59.062 47.826 0.00 0.00 0.00 3.51
3819 6743 2.821969 ACATCAAGCGGCTCAAAGAATT 59.178 40.909 1.45 0.00 0.00 2.17
3869 6793 7.010160 TGGGAGCTCTTATAATTAATTTGGGG 58.990 38.462 14.64 0.00 0.00 4.96
3913 6837 9.825109 TCTATTTTATCGTCACAACATTCCATA 57.175 29.630 0.00 0.00 0.00 2.74
3922 6846 8.862085 TCGTCACAACATTCCATAACCTATATA 58.138 33.333 0.00 0.00 0.00 0.86
3923 6847 9.653287 CGTCACAACATTCCATAACCTATATAT 57.347 33.333 0.00 0.00 0.00 0.86
3946 6870 9.685276 ATATATTGGAGAAACATGTCTGTTCAA 57.315 29.630 10.56 2.26 44.83 2.69
4037 7501 0.391130 TAGCACTTCACATCGTGGGC 60.391 55.000 0.00 0.00 33.87 5.36
4093 7558 5.160607 TCCCTTTATCGTCACAACATTCT 57.839 39.130 0.00 0.00 0.00 2.40
4118 7643 7.492524 TGTGACATAGATAGGAGAAACATGTC 58.507 38.462 0.00 0.00 40.60 3.06
4122 7647 3.375699 AGATAGGAGAAACATGTCCCGT 58.624 45.455 0.00 0.00 32.70 5.28
4154 7679 6.599244 CACATTACTTGGATGGTTCTGTACAT 59.401 38.462 0.00 0.00 0.00 2.29
4156 7681 7.121168 ACATTACTTGGATGGTTCTGTACATTG 59.879 37.037 0.00 0.00 0.00 2.82
4159 7684 3.950397 TGGATGGTTCTGTACATTGGAC 58.050 45.455 0.00 0.00 0.00 4.02
4331 7866 7.687941 AAGTCCATGTATGTTTTTGGTCTAG 57.312 36.000 0.00 0.00 29.38 2.43
4334 7869 5.872617 TCCATGTATGTTTTTGGTCTAGACG 59.127 40.000 16.56 0.00 0.00 4.18
4344 7881 4.761235 TTGGTCTAGACGTGTAGTTCTG 57.239 45.455 18.24 0.00 0.00 3.02
4517 8060 6.090129 TGGTGAAATAAATCGCTTTGCTTAC 58.910 36.000 0.00 0.00 0.00 2.34
4518 8061 6.090129 GGTGAAATAAATCGCTTTGCTTACA 58.910 36.000 0.00 0.00 0.00 2.41
4519 8062 6.033513 GGTGAAATAAATCGCTTTGCTTACAC 59.966 38.462 0.00 0.00 0.00 2.90
4583 8126 9.087871 ACTCAGATACAGATAATCATAGTGCTT 57.912 33.333 0.00 0.00 0.00 3.91
4584 8127 9.926158 CTCAGATACAGATAATCATAGTGCTTT 57.074 33.333 0.00 0.00 0.00 3.51
4662 8205 3.843999 TCATTAAAGCGATTTTGTGGGC 58.156 40.909 3.03 0.00 0.00 5.36
4705 8249 3.567164 GCATATTGCAGTATTGGTGCTCT 59.433 43.478 0.00 0.00 44.26 4.09
4712 8256 3.618507 GCAGTATTGGTGCTCTGAGAGTT 60.619 47.826 11.64 0.00 37.96 3.01
4759 8303 2.435805 AGTGTTGTCAGGAGAAGAGCAA 59.564 45.455 0.00 0.00 0.00 3.91
4827 8371 9.743057 TTTTCGATCATTGTGTTTACTGAAATT 57.257 25.926 0.00 0.00 0.00 1.82
4874 8438 8.982091 AGTGTGCTCTACTCATCTACTATTAA 57.018 34.615 0.00 0.00 0.00 1.40
4935 8500 7.955864 GCCTTTGTAAACTACTCATTTTACTCG 59.044 37.037 5.96 0.00 38.48 4.18
5009 8584 8.764524 ACTGCTCTAGTACAATTTTCTAGTTG 57.235 34.615 0.00 0.00 38.04 3.16
5114 8697 3.494398 GGGTTCTCTTTACAGCACTGACA 60.494 47.826 4.31 0.00 0.00 3.58
5145 8728 7.147391 TGCCCCAATTATCATAGTGTTTAGAGA 60.147 37.037 0.00 0.00 0.00 3.10
5217 8926 8.837788 TGTTAGATTATTGTCTATGGATGCAG 57.162 34.615 0.00 0.00 31.19 4.41
5220 8930 7.559335 AGATTATTGTCTATGGATGCAGGTA 57.441 36.000 0.00 0.00 0.00 3.08
5221 8931 7.390027 AGATTATTGTCTATGGATGCAGGTAC 58.610 38.462 0.00 0.00 0.00 3.34
5472 9210 2.218603 ACTGTTTTCCTTGTAGGTGCG 58.781 47.619 0.00 0.00 36.53 5.34
5530 9268 2.300433 TCTGTGCAGCATGTTCAAACT 58.700 42.857 0.00 0.00 39.31 2.66
5587 9326 8.234546 CGTCTTAAAACCTTTGTAGCATTACAT 58.765 33.333 0.00 0.00 39.43 2.29
5657 9397 6.147492 GCTTGATATGCAAAACATTGAACCAA 59.853 34.615 0.00 0.00 40.38 3.67
5695 9435 9.982651 GATGCTATGGATTCAGTTAGTTTACTA 57.017 33.333 0.00 0.00 0.00 1.82
5742 9483 7.475015 TGTTAATGAAATGAATGCAGCTAGTC 58.525 34.615 0.00 0.00 0.00 2.59
5764 9505 6.426980 TCTGCATGTCAGACATTGAATAAC 57.573 37.500 13.79 0.00 46.34 1.89
5821 9712 2.612212 TGTTTCGCTTTCTTGTCTGGAC 59.388 45.455 0.00 0.00 0.00 4.02
5836 9727 4.221924 TGTCTGGACGATGGACATCTTTAA 59.778 41.667 10.28 0.00 35.44 1.52
5846 9737 7.276218 ACGATGGACATCTTTAATTTGCAATTG 59.724 33.333 0.00 0.00 35.72 2.32
5854 9962 7.551035 TCTTTAATTTGCAATTGCTTTGTGT 57.449 28.000 29.37 13.15 42.66 3.72
5870 9978 5.407407 TTTGTGTTTTAACTCTTTGGGCA 57.593 34.783 0.00 0.00 0.00 5.36
5886 9995 8.189119 TCTTTGGGCATTTGTTCTTACTAAAT 57.811 30.769 0.00 0.00 0.00 1.40
5990 10099 3.352648 GTGCAGGCCTTAATCCTAAACA 58.647 45.455 0.00 0.00 31.52 2.83
6068 10179 3.006967 AGTCGTAGAACATGCTCAACCTT 59.993 43.478 0.00 0.00 39.69 3.50
6241 10399 1.810151 TCGGTTTGTAGAAATGCAGCC 59.190 47.619 0.00 0.00 0.00 4.85
6266 10424 8.181573 CCGCAGTGTAATCTTTACAATATTGTT 58.818 33.333 25.31 9.64 42.35 2.83
6267 10425 9.554724 CGCAGTGTAATCTTTACAATATTGTTT 57.445 29.630 25.31 15.39 42.35 2.83
6278 10436 9.490663 CTTTACAATATTGTTTCTCGTTGATCC 57.509 33.333 25.31 0.00 42.35 3.36
6284 10442 4.182693 TGTTTCTCGTTGATCCGTGTAT 57.817 40.909 0.00 0.00 0.00 2.29
6305 10463 4.811969 TCGACTGTGGTGGTATATTGTT 57.188 40.909 0.00 0.00 0.00 2.83
6362 10521 3.831715 ATTAAGACGAGGCAAACAAGC 57.168 42.857 0.00 0.00 0.00 4.01
6374 10533 2.618442 AAACAAGCCACCATGTTTGG 57.382 45.000 6.28 6.28 45.34 3.28
6397 10556 8.288689 TGGTAAACTAAATAATTTCCTCTGCC 57.711 34.615 0.00 0.00 0.00 4.85
6442 10601 9.744468 ATTATAGTGGATGATTTTTAAAACCGC 57.256 29.630 0.00 5.17 0.00 5.68
6460 10619 5.587033 ACCGCTAAAAACTAAAGAGAACG 57.413 39.130 0.00 0.00 0.00 3.95
6490 10650 6.898041 TGAGTGTTTGTGTTAGAATACATGC 58.102 36.000 0.00 0.00 30.00 4.06
6493 10653 4.155099 TGTTTGTGTTAGAATACATGCCCG 59.845 41.667 0.00 0.00 30.00 6.13
6495 10655 3.266636 TGTGTTAGAATACATGCCCGTG 58.733 45.455 0.00 0.00 0.00 4.94
6515 10675 4.731961 CGTGTATTTGCTTGCATCAGAATC 59.268 41.667 0.00 0.00 0.00 2.52
6517 10677 4.635324 TGTATTTGCTTGCATCAGAATCGA 59.365 37.500 0.00 0.00 0.00 3.59
6563 10723 7.056635 ACTAATCATCCATTCTTACCAACCTG 58.943 38.462 0.00 0.00 0.00 4.00
6575 10735 0.798776 CCAACCTGCTAACTCAAGCG 59.201 55.000 0.00 0.00 45.85 4.68
6645 10805 4.279420 GTCAAATTGGAGCCTCAACTTCTT 59.721 41.667 0.00 0.00 0.00 2.52
6651 10811 4.579869 TGGAGCCTCAACTTCTTAACATC 58.420 43.478 0.00 0.00 0.00 3.06
6652 10812 4.287067 TGGAGCCTCAACTTCTTAACATCT 59.713 41.667 0.00 0.00 0.00 2.90
6653 10813 4.633565 GGAGCCTCAACTTCTTAACATCTG 59.366 45.833 0.00 0.00 0.00 2.90
6654 10814 5.234466 AGCCTCAACTTCTTAACATCTGT 57.766 39.130 0.00 0.00 0.00 3.41
6655 10815 5.625150 AGCCTCAACTTCTTAACATCTGTT 58.375 37.500 0.69 0.69 41.73 3.16
6656 10816 5.471456 AGCCTCAACTTCTTAACATCTGTTG 59.529 40.000 5.84 0.00 38.90 3.33
6657 10817 5.693814 CCTCAACTTCTTAACATCTGTTGC 58.306 41.667 5.84 0.00 38.90 4.17
6658 10818 5.471456 CCTCAACTTCTTAACATCTGTTGCT 59.529 40.000 5.84 0.00 38.90 3.91
6659 10819 6.016777 CCTCAACTTCTTAACATCTGTTGCTT 60.017 38.462 5.84 0.00 38.90 3.91
6660 10820 7.333528 TCAACTTCTTAACATCTGTTGCTTT 57.666 32.000 5.84 0.00 38.90 3.51
6661 10821 8.445275 TCAACTTCTTAACATCTGTTGCTTTA 57.555 30.769 5.84 0.00 38.90 1.85
6662 10822 8.898761 TCAACTTCTTAACATCTGTTGCTTTAA 58.101 29.630 5.84 0.00 38.90 1.52
6663 10823 8.958043 CAACTTCTTAACATCTGTTGCTTTAAC 58.042 33.333 5.84 0.00 38.90 2.01
6664 10824 8.220755 ACTTCTTAACATCTGTTGCTTTAACA 57.779 30.769 5.84 0.00 46.62 2.41
6665 10825 8.129211 ACTTCTTAACATCTGTTGCTTTAACAC 58.871 33.333 5.84 0.00 44.07 3.32
6686 10846 5.221601 ACACGGAGATATTCTACTCTCGGTA 60.222 44.000 10.99 0.00 45.03 4.02
6733 10897 0.801251 GCAGTTAGCTGGAGCAACAG 59.199 55.000 8.78 3.53 45.16 3.16
6753 10917 8.417884 GCAACAGGAATTTACTATAGAGAGAGT 58.582 37.037 6.78 0.00 0.00 3.24
6790 10955 5.965033 TCCTCTCTTGGCTTCAGATTAAT 57.035 39.130 0.00 0.00 0.00 1.40
6799 10964 3.627577 GGCTTCAGATTAATTGCTTCCGA 59.372 43.478 0.00 0.00 0.00 4.55
6806 10971 4.636206 AGATTAATTGCTTCCGACCTCAAC 59.364 41.667 0.00 0.00 0.00 3.18
6812 10977 4.015872 TGCTTCCGACCTCAACTTTTAT 57.984 40.909 0.00 0.00 0.00 1.40
6854 11019 9.821662 AAATGAACTAAGTTCGCATAAAAGTAC 57.178 29.630 0.00 0.00 44.55 2.73
6869 11034 7.919091 GCATAAAAGTACATTTAAAGGGCTACC 59.081 37.037 7.32 0.00 0.00 3.18
6919 12954 5.927954 ATGTTCATGCATTTGGTTTTGTC 57.072 34.783 0.00 0.00 0.00 3.18
6941 12976 4.340950 TCACCCCACAAGTTTGATTTCTTC 59.659 41.667 0.00 0.00 0.00 2.87
6942 12977 4.099266 CACCCCACAAGTTTGATTTCTTCA 59.901 41.667 0.00 0.00 0.00 3.02
6943 12978 4.342092 ACCCCACAAGTTTGATTTCTTCAG 59.658 41.667 0.00 0.00 35.27 3.02
6944 12979 4.584325 CCCCACAAGTTTGATTTCTTCAGA 59.416 41.667 0.00 0.00 35.27 3.27
6945 12980 5.244626 CCCCACAAGTTTGATTTCTTCAGAT 59.755 40.000 0.00 0.00 35.27 2.90
6946 12981 6.434028 CCCCACAAGTTTGATTTCTTCAGATA 59.566 38.462 0.00 0.00 35.27 1.98
6947 12982 7.123247 CCCCACAAGTTTGATTTCTTCAGATAT 59.877 37.037 0.00 0.00 35.27 1.63
6948 12983 8.526147 CCCACAAGTTTGATTTCTTCAGATATT 58.474 33.333 0.00 0.00 35.27 1.28
6949 12984 9.565213 CCACAAGTTTGATTTCTTCAGATATTC 57.435 33.333 0.00 0.00 35.27 1.75
6957 12992 8.964476 TGATTTCTTCAGATATTCTACCAACC 57.036 34.615 0.00 0.00 0.00 3.77
6958 12993 8.772250 TGATTTCTTCAGATATTCTACCAACCT 58.228 33.333 0.00 0.00 0.00 3.50
6961 12996 8.603898 TTCTTCAGATATTCTACCAACCTACA 57.396 34.615 0.00 0.00 0.00 2.74
6962 12997 8.239038 TCTTCAGATATTCTACCAACCTACAG 57.761 38.462 0.00 0.00 0.00 2.74
6963 12998 7.839705 TCTTCAGATATTCTACCAACCTACAGT 59.160 37.037 0.00 0.00 0.00 3.55
6964 12999 9.132923 CTTCAGATATTCTACCAACCTACAGTA 57.867 37.037 0.00 0.00 0.00 2.74
6965 13000 8.461249 TCAGATATTCTACCAACCTACAGTAC 57.539 38.462 0.00 0.00 0.00 2.73
6966 13001 8.280084 TCAGATATTCTACCAACCTACAGTACT 58.720 37.037 0.00 0.00 0.00 2.73
6967 13002 8.915036 CAGATATTCTACCAACCTACAGTACTT 58.085 37.037 0.00 0.00 0.00 2.24
6971 13006 6.521151 TCTACCAACCTACAGTACTTAAGC 57.479 41.667 1.29 0.00 0.00 3.09
6972 13007 6.012113 TCTACCAACCTACAGTACTTAAGCA 58.988 40.000 1.29 0.00 0.00 3.91
6973 13008 4.891260 ACCAACCTACAGTACTTAAGCAC 58.109 43.478 1.29 0.00 0.00 4.40
6974 13009 4.251268 CCAACCTACAGTACTTAAGCACC 58.749 47.826 1.29 0.00 0.00 5.01
6975 13010 4.262721 CCAACCTACAGTACTTAAGCACCA 60.263 45.833 1.29 0.00 0.00 4.17
6976 13011 5.302360 CAACCTACAGTACTTAAGCACCAA 58.698 41.667 1.29 0.00 0.00 3.67
6977 13012 5.148651 ACCTACAGTACTTAAGCACCAAG 57.851 43.478 1.29 0.00 0.00 3.61
6978 13013 4.591924 ACCTACAGTACTTAAGCACCAAGT 59.408 41.667 1.29 2.28 39.50 3.16
6979 13014 5.071384 ACCTACAGTACTTAAGCACCAAGTT 59.929 40.000 1.29 0.00 37.42 2.66
6980 13015 5.995897 CCTACAGTACTTAAGCACCAAGTTT 59.004 40.000 1.29 0.00 37.42 2.66
6981 13016 5.751243 ACAGTACTTAAGCACCAAGTTTG 57.249 39.130 1.29 0.00 37.42 2.93
6982 13017 5.433526 ACAGTACTTAAGCACCAAGTTTGA 58.566 37.500 1.29 0.00 37.42 2.69
6983 13018 6.062095 ACAGTACTTAAGCACCAAGTTTGAT 58.938 36.000 1.29 0.00 37.42 2.57
6984 13019 6.204882 ACAGTACTTAAGCACCAAGTTTGATC 59.795 38.462 1.29 0.00 37.42 2.92
6985 13020 6.428159 CAGTACTTAAGCACCAAGTTTGATCT 59.572 38.462 1.29 0.00 37.42 2.75
6986 13021 5.695851 ACTTAAGCACCAAGTTTGATCTG 57.304 39.130 1.29 0.00 32.28 2.90
6987 13022 5.376625 ACTTAAGCACCAAGTTTGATCTGA 58.623 37.500 1.29 0.00 32.28 3.27
6988 13023 5.827797 ACTTAAGCACCAAGTTTGATCTGAA 59.172 36.000 1.29 0.00 32.28 3.02
6989 13024 4.574599 AAGCACCAAGTTTGATCTGAAC 57.425 40.909 0.00 0.00 0.00 3.18
6990 13025 3.825328 AGCACCAAGTTTGATCTGAACT 58.175 40.909 8.62 8.62 38.92 3.01
6991 13026 4.973168 AGCACCAAGTTTGATCTGAACTA 58.027 39.130 13.15 0.00 36.38 2.24
6992 13027 4.757149 AGCACCAAGTTTGATCTGAACTAC 59.243 41.667 13.15 4.53 36.38 2.73
6993 13028 4.515191 GCACCAAGTTTGATCTGAACTACA 59.485 41.667 13.15 0.00 36.38 2.74
6994 13029 5.334414 GCACCAAGTTTGATCTGAACTACAG 60.334 44.000 13.15 8.91 46.97 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 110 1.380403 TTGCAAGACAACCACGGTGG 61.380 55.000 25.21 25.21 45.02 4.61
114 115 3.119708 GGATGATCTTGCAAGACAACCAC 60.120 47.826 30.71 21.57 37.98 4.16
170 171 2.886913 TGCCCACAGATTCCAAATTCA 58.113 42.857 0.00 0.00 0.00 2.57
173 174 1.483415 GCATGCCCACAGATTCCAAAT 59.517 47.619 6.36 0.00 0.00 2.32
208 210 2.227388 CAGAAGGGTGATTGCTTGTCAC 59.773 50.000 7.79 7.79 44.01 3.67
318 327 4.951094 CCCCCGATTTCAAAAGGTATACAA 59.049 41.667 5.01 0.00 0.00 2.41
587 1448 2.164219 GGAAGTGTATAACCGACGGTCA 59.836 50.000 22.00 6.02 33.12 4.02
607 1468 0.670162 CCACCAGCTCAAACAACAGG 59.330 55.000 0.00 0.00 0.00 4.00
701 1562 1.027357 AGTGCAACAACTCTTGGCTG 58.973 50.000 0.00 0.00 41.43 4.85
745 1606 3.711190 AGTCCACAGACATGCCACATATA 59.289 43.478 0.00 0.00 46.15 0.86
761 1622 2.568623 ACAGGGATGAACAAGTCCAC 57.431 50.000 0.00 0.00 36.19 4.02
886 1747 1.004745 GATTGAGGGCCTTCCTTCACA 59.995 52.381 13.07 0.00 46.58 3.58
887 1748 1.283321 AGATTGAGGGCCTTCCTTCAC 59.717 52.381 13.07 0.00 46.58 3.18
989 1850 3.451894 CCAACATTGCTCCCCCGC 61.452 66.667 0.00 0.00 0.00 6.13
990 1851 2.046285 GTCCAACATTGCTCCCCCG 61.046 63.158 0.00 0.00 0.00 5.73
1011 1872 1.064505 CAACATACCGCAGCCATCAAG 59.935 52.381 0.00 0.00 0.00 3.02
1016 1877 0.250510 TGTTCAACATACCGCAGCCA 60.251 50.000 0.00 0.00 0.00 4.75
1020 1881 0.871722 GCAGTGTTCAACATACCGCA 59.128 50.000 0.00 0.00 0.00 5.69
1021 1882 1.135972 CAGCAGTGTTCAACATACCGC 60.136 52.381 0.00 0.00 0.00 5.68
1022 1883 2.412870 TCAGCAGTGTTCAACATACCG 58.587 47.619 0.00 0.00 0.00 4.02
1040 1901 7.532571 CAAACTAGATCAAAACTGCATCATCA 58.467 34.615 0.00 0.00 0.00 3.07
1043 1904 5.474532 AGCAAACTAGATCAAAACTGCATCA 59.525 36.000 0.00 0.00 0.00 3.07
1068 1929 4.689612 ACAAGAACTAGAGCAAGGAACA 57.310 40.909 0.00 0.00 0.00 3.18
1170 2032 7.195374 ACAATAGCACAAAAGGGTATAGAGA 57.805 36.000 0.00 0.00 0.00 3.10
1172 2034 8.764558 TCTAACAATAGCACAAAAGGGTATAGA 58.235 33.333 0.00 0.00 0.00 1.98
1174 2036 8.545472 AGTCTAACAATAGCACAAAAGGGTATA 58.455 33.333 0.00 0.00 0.00 1.47
1176 2038 6.775708 AGTCTAACAATAGCACAAAAGGGTA 58.224 36.000 0.00 0.00 0.00 3.69
1177 2039 5.631119 AGTCTAACAATAGCACAAAAGGGT 58.369 37.500 0.00 0.00 0.00 4.34
1180 3518 6.363357 GCCAAAGTCTAACAATAGCACAAAAG 59.637 38.462 0.00 0.00 0.00 2.27
1205 3543 6.092122 TGCTCACGATTTCAAAAGGTATACAG 59.908 38.462 5.01 0.00 0.00 2.74
1219 3557 9.906660 TTAAAATTTATCTTGTGCTCACGATTT 57.093 25.926 12.26 5.00 34.95 2.17
1272 3615 6.410942 TGTGATCTGAGTCAGAAAGAAAGA 57.589 37.500 26.06 6.76 44.04 2.52
1273 3616 8.945481 ATATGTGATCTGAGTCAGAAAGAAAG 57.055 34.615 26.06 0.00 44.04 2.62
1307 3650 6.096705 TGACTGTTCATGTCTCCAAAAACAAT 59.903 34.615 0.00 0.00 35.63 2.71
1310 3653 5.499139 TGACTGTTCATGTCTCCAAAAAC 57.501 39.130 0.00 0.00 35.63 2.43
1349 3692 6.757237 TGTAATCATTGCTTTGAACCATGTT 58.243 32.000 0.00 0.00 0.00 2.71
1431 3774 4.830046 TCTACTAACATGAGGGAGCTCATC 59.170 45.833 17.19 13.32 41.65 2.92
1446 3789 7.097834 AGTCAACTAAATGTGCCTCTACTAAC 58.902 38.462 0.00 0.00 0.00 2.34
1452 3795 4.899352 AGAGTCAACTAAATGTGCCTCT 57.101 40.909 0.00 0.00 0.00 3.69
1457 3800 4.152402 CGGGTGAAGAGTCAACTAAATGTG 59.848 45.833 0.00 0.00 41.62 3.21
1458 3801 4.202326 ACGGGTGAAGAGTCAACTAAATGT 60.202 41.667 0.00 0.00 41.62 2.71
1527 3870 5.834169 GGGAACCGTTTGACAAAATAGAAA 58.166 37.500 1.27 0.00 40.86 2.52
1611 3959 5.110814 ACCAACTAGGCATGCAGTAAATA 57.889 39.130 21.36 1.26 43.14 1.40
1614 3962 2.355716 GGACCAACTAGGCATGCAGTAA 60.356 50.000 21.36 0.00 43.14 2.24
1635 3983 4.096231 TGACTGTTCTTGTCACACCATTTG 59.904 41.667 0.00 0.00 39.23 2.32
1684 4033 9.515226 TTGTTAACCTACAGATTTGCTAAGATT 57.485 29.630 2.48 0.00 0.00 2.40
1692 4041 8.405531 CCACCATATTGTTAACCTACAGATTTG 58.594 37.037 2.48 0.00 0.00 2.32
1711 4060 4.019501 AGCAATGGCAAAATTTCCACCATA 60.020 37.500 15.90 0.00 40.20 2.74
1712 4061 3.083293 GCAATGGCAAAATTTCCACCAT 58.917 40.909 11.75 11.75 42.89 3.55
1713 4062 2.106166 AGCAATGGCAAAATTTCCACCA 59.894 40.909 8.67 8.67 44.61 4.17
1714 4063 2.743664 GAGCAATGGCAAAATTTCCACC 59.256 45.455 0.91 0.00 44.61 4.61
1715 4064 3.667360 AGAGCAATGGCAAAATTTCCAC 58.333 40.909 0.91 0.00 44.61 4.02
1716 4065 4.354893 AAGAGCAATGGCAAAATTTCCA 57.645 36.364 0.00 1.38 44.61 3.53
1718 4067 7.838771 AGAATAAGAGCAATGGCAAAATTTC 57.161 32.000 0.00 0.00 44.61 2.17
1748 4165 2.472909 GCGTGGGAGTAATGGCAGC 61.473 63.158 0.00 0.00 0.00 5.25
1765 4182 1.722011 TTTAGGACTTGCTACAGCGC 58.278 50.000 0.00 0.00 45.83 5.92
1806 4237 7.977853 AGATGGCATGAAAATGAACAATACTTC 59.022 33.333 3.81 0.00 0.00 3.01
1809 4240 7.221452 GTCAGATGGCATGAAAATGAACAATAC 59.779 37.037 3.81 0.00 0.00 1.89
1816 4247 5.011586 TCTTGTCAGATGGCATGAAAATGA 58.988 37.500 3.81 0.00 32.04 2.57
1821 4252 6.358991 TCATTATCTTGTCAGATGGCATGAA 58.641 36.000 3.81 0.00 40.28 2.57
1830 4261 6.100004 GGTTCGAGTTCATTATCTTGTCAGA 58.900 40.000 0.00 0.00 0.00 3.27
1929 4360 2.202946 GGCCGGACAGCTAAGCTC 60.203 66.667 5.05 0.00 36.40 4.09
1945 4376 4.955925 TGGTTTTGTCTATATGCAACGG 57.044 40.909 0.00 0.00 0.00 4.44
1976 4407 3.373565 GTTGGAGCAAAGGCCGGG 61.374 66.667 2.18 0.00 42.56 5.73
1978 4409 1.508088 GATGTTGGAGCAAAGGCCG 59.492 57.895 0.00 0.00 42.56 6.13
1981 4412 1.962807 TGTTGGATGTTGGAGCAAAGG 59.037 47.619 0.00 0.00 0.00 3.11
2099 4545 6.584942 CAGCTATGTGACGTTTTCTAGTAACA 59.415 38.462 0.00 0.00 36.29 2.41
2254 4732 9.799106 ATTTCCTCTTTTGTTCTTTCTCATCTA 57.201 29.630 0.00 0.00 0.00 1.98
2266 4744 8.414629 AGCTCTCATTTATTTCCTCTTTTGTT 57.585 30.769 0.00 0.00 0.00 2.83
2302 4780 0.810031 CAATGGACGGCTACCCTTCG 60.810 60.000 0.00 0.00 30.38 3.79
2400 4880 0.536006 GAGGGCGAAGATGGAATGGG 60.536 60.000 0.00 0.00 0.00 4.00
2401 4881 0.536006 GGAGGGCGAAGATGGAATGG 60.536 60.000 0.00 0.00 0.00 3.16
2402 4882 0.536006 GGGAGGGCGAAGATGGAATG 60.536 60.000 0.00 0.00 0.00 2.67
2403 4883 1.709994 GGGGAGGGCGAAGATGGAAT 61.710 60.000 0.00 0.00 0.00 3.01
2404 4884 2.375345 GGGGAGGGCGAAGATGGAA 61.375 63.158 0.00 0.00 0.00 3.53
2405 4885 2.768344 GGGGAGGGCGAAGATGGA 60.768 66.667 0.00 0.00 0.00 3.41
2406 4886 2.770048 AGGGGAGGGCGAAGATGG 60.770 66.667 0.00 0.00 0.00 3.51
2407 4887 2.317149 GACAGGGGAGGGCGAAGATG 62.317 65.000 0.00 0.00 0.00 2.90
2408 4888 2.041265 ACAGGGGAGGGCGAAGAT 59.959 61.111 0.00 0.00 0.00 2.40
2409 4889 2.683933 GACAGGGGAGGGCGAAGA 60.684 66.667 0.00 0.00 0.00 2.87
2410 4890 3.787001 GGACAGGGGAGGGCGAAG 61.787 72.222 0.00 0.00 0.00 3.79
2411 4891 4.332543 AGGACAGGGGAGGGCGAA 62.333 66.667 0.00 0.00 0.00 4.70
2412 4892 4.779733 GAGGACAGGGGAGGGCGA 62.780 72.222 0.00 0.00 0.00 5.54
2413 4893 4.787280 AGAGGACAGGGGAGGGCG 62.787 72.222 0.00 0.00 0.00 6.13
2414 4894 2.766229 GAGAGGACAGGGGAGGGC 60.766 72.222 0.00 0.00 0.00 5.19
2415 4895 2.041405 GGAGAGGACAGGGGAGGG 60.041 72.222 0.00 0.00 0.00 4.30
2416 4896 1.075600 GAGGAGAGGACAGGGGAGG 60.076 68.421 0.00 0.00 0.00 4.30
2417 4897 0.106217 GAGAGGAGAGGACAGGGGAG 60.106 65.000 0.00 0.00 0.00 4.30
2418 4898 1.585651 GGAGAGGAGAGGACAGGGGA 61.586 65.000 0.00 0.00 0.00 4.81
2419 4899 1.075600 GGAGAGGAGAGGACAGGGG 60.076 68.421 0.00 0.00 0.00 4.79
2567 5068 8.039538 TCAATAAATTTCTGCATAATTGGCACA 58.960 29.630 0.00 0.00 36.11 4.57
2581 5083 5.892348 ACCTGTCCACCTCAATAAATTTCT 58.108 37.500 0.00 0.00 0.00 2.52
2588 5090 3.056393 CACGTTACCTGTCCACCTCAATA 60.056 47.826 0.00 0.00 0.00 1.90
2600 5102 6.330278 TCTCTGACAAATATCACGTTACCTG 58.670 40.000 0.00 0.00 0.00 4.00
2782 5627 0.465278 TTGTGTACAGCAGCTTGGCA 60.465 50.000 0.00 0.00 35.83 4.92
2899 5786 1.909302 CCACCCACCTTGTCATAGTCT 59.091 52.381 0.00 0.00 0.00 3.24
2928 5815 0.036022 ACTGCTTCCCTTGAGCTGAC 59.964 55.000 9.47 0.00 40.30 3.51
3027 5915 3.685139 TTGCACACCAAGAACCAAAAA 57.315 38.095 0.00 0.00 0.00 1.94
3028 5916 3.685139 TTTGCACACCAAGAACCAAAA 57.315 38.095 0.00 0.00 34.34 2.44
3029 5917 3.902881 ATTTGCACACCAAGAACCAAA 57.097 38.095 0.00 0.00 34.34 3.28
3030 5918 3.902881 AATTTGCACACCAAGAACCAA 57.097 38.095 0.00 0.00 34.34 3.67
3031 5919 3.320541 CCTAATTTGCACACCAAGAACCA 59.679 43.478 0.00 0.00 34.34 3.67
3041 5929 5.592688 GGGAGCTAAATACCTAATTTGCACA 59.407 40.000 0.00 0.00 38.29 4.57
3144 6035 6.666546 AGGAAATTGACCATCATTGTCAGATT 59.333 34.615 5.02 0.00 43.14 2.40
3154 6045 3.196039 CCAATGCAGGAAATTGACCATCA 59.804 43.478 0.00 2.92 37.22 3.07
3363 6269 8.732746 ATCTAAACGAATATAACAGCCAAACT 57.267 30.769 0.00 0.00 0.00 2.66
3364 6270 9.783256 AAATCTAAACGAATATAACAGCCAAAC 57.217 29.630 0.00 0.00 0.00 2.93
3605 6515 2.093973 ACAACGGCCAAACAATTTGTCA 60.094 40.909 2.24 0.00 38.98 3.58
3673 6583 2.029838 ATTCATTGAGCTGTCCGGTC 57.970 50.000 0.00 0.00 40.53 4.79
3691 6601 1.007721 ACAGAGGGTCCAGAGCAGTAT 59.992 52.381 0.00 0.00 0.00 2.12
3699 6609 2.289694 CCACTTAACACAGAGGGTCCAG 60.290 54.545 0.00 0.00 0.00 3.86
3819 6743 2.325583 AAAAGGAGACGTGAAGTGCA 57.674 45.000 0.00 0.00 0.00 4.57
3884 6808 9.309516 GGAATGTTGTGACGATAAAATAGAGTA 57.690 33.333 0.00 0.00 0.00 2.59
3885 6809 7.822334 TGGAATGTTGTGACGATAAAATAGAGT 59.178 33.333 0.00 0.00 0.00 3.24
4037 7501 7.461182 TCCACACCAAATTAATTGTAAGAGG 57.539 36.000 0.39 1.58 37.32 3.69
4093 7558 7.417911 GGACATGTTTCTCCTATCTATGTCACA 60.418 40.741 14.13 0.00 42.69 3.58
4118 7643 3.500982 CAAGTAATGTGAATGCAACGGG 58.499 45.455 0.00 0.00 0.00 5.28
4122 7647 4.771577 ACCATCCAAGTAATGTGAATGCAA 59.228 37.500 0.00 0.00 0.00 4.08
4154 7679 9.177608 CAATTGACCTGAATAAGATAAGTCCAA 57.822 33.333 0.00 0.00 0.00 3.53
4156 7681 8.964476 TCAATTGACCTGAATAAGATAAGTCC 57.036 34.615 3.38 0.00 0.00 3.85
4159 7684 9.007901 GGGATCAATTGACCTGAATAAGATAAG 57.992 37.037 11.07 0.00 0.00 1.73
4256 7786 8.150827 TGGGCATCATAATATTAGCTTCTAGT 57.849 34.615 0.00 0.00 0.00 2.57
4257 7787 9.453572 TTTGGGCATCATAATATTAGCTTCTAG 57.546 33.333 0.00 0.00 0.00 2.43
4263 7793 7.219484 ACAGTTTGGGCATCATAATATTAGC 57.781 36.000 1.02 0.00 0.00 3.09
4274 7804 1.273327 CAAGGGAACAGTTTGGGCATC 59.727 52.381 0.00 0.00 0.00 3.91
4331 7866 4.744570 TGATTCCATCAGAACTACACGTC 58.255 43.478 0.00 0.00 37.29 4.34
4344 7881 4.202398 TGGCTTACATCCTCTGATTCCATC 60.202 45.833 0.00 0.00 0.00 3.51
4517 8060 0.035439 ACTATGAAAGCCCGGTGGTG 60.035 55.000 0.00 0.00 0.00 4.17
4518 8061 0.696501 AACTATGAAAGCCCGGTGGT 59.303 50.000 0.00 0.00 0.00 4.16
4519 8062 1.094785 CAACTATGAAAGCCCGGTGG 58.905 55.000 0.00 0.00 0.00 4.61
4593 8136 7.732222 ATCTCTTCACTTCAGAATCCTAAGT 57.268 36.000 0.00 0.00 33.82 2.24
4705 8249 6.054941 TGAATGCAACTGTTCTTAACTCTCA 58.945 36.000 0.00 0.00 0.00 3.27
4712 8256 5.129634 TGGAACTGAATGCAACTGTTCTTA 58.870 37.500 27.69 20.50 37.66 2.10
4935 8500 5.532779 CCCAAAATCTGTCTCTATAAAGGCC 59.467 44.000 0.00 0.00 0.00 5.19
5076 8657 3.636764 AGAACCCAGCTTTTCGTTTCAAT 59.363 39.130 0.00 0.00 0.00 2.57
5109 8692 0.899720 AATTGGGGCATTGCTGTCAG 59.100 50.000 8.82 0.00 0.00 3.51
5114 8697 4.525487 CACTATGATAATTGGGGCATTGCT 59.475 41.667 8.82 0.00 0.00 3.91
5145 8728 9.755122 AGACAAAACTTAGCTTCCCTTTTATAT 57.245 29.630 0.00 0.00 0.00 0.86
5213 8922 5.739959 TGCTTAACAAGATATGTACCTGCA 58.260 37.500 0.00 0.00 42.99 4.41
5245 8955 8.010697 TCTTATGAATATCACCCTGGAGTTCTA 58.989 37.037 0.00 0.00 0.00 2.10
5281 8991 6.561614 TCTGGTAGAATTATCGTGACAGTTC 58.438 40.000 0.00 0.00 0.00 3.01
5472 9210 3.995199 TCACAGAATCCAGTGAGTTCAC 58.005 45.455 4.09 4.09 46.77 3.18
5530 9268 9.781633 TTTAAAAAGTAGTACCTGAAGCATGTA 57.218 29.630 0.00 0.00 0.00 2.29
5587 9326 5.155278 TCCTTCGCATTCCAGTTTACTAA 57.845 39.130 0.00 0.00 0.00 2.24
5657 9397 8.380867 TGAATCCATAGCATCATATCTTCTGTT 58.619 33.333 0.00 0.00 0.00 3.16
5695 9435 8.491331 AACAAGCTTTTCATTTGTTGTTATGT 57.509 26.923 0.00 0.00 41.85 2.29
5742 9483 6.432607 AGTTATTCAATGTCTGACATGCAG 57.567 37.500 22.91 15.66 46.31 4.41
5821 9712 7.614908 CAATTGCAAATTAAAGATGTCCATCG 58.385 34.615 1.71 0.00 42.48 3.84
5836 9727 7.760437 AGTTAAAACACAAAGCAATTGCAAAT 58.240 26.923 30.89 14.65 43.13 2.32
5846 9737 4.270084 GCCCAAAGAGTTAAAACACAAAGC 59.730 41.667 0.00 0.00 0.00 3.51
5854 9962 6.883744 AGAACAAATGCCCAAAGAGTTAAAA 58.116 32.000 0.00 0.00 0.00 1.52
5886 9995 8.755696 AAAAGCTTGCATTATACGAAAATGAA 57.244 26.923 0.00 0.96 36.61 2.57
5895 10004 8.197439 ACCCATTAAGAAAAGCTTGCATTATAC 58.803 33.333 0.00 0.00 37.42 1.47
5935 10044 3.548587 CTGCATCAGAAACAGAACAACG 58.451 45.455 0.00 0.00 32.44 4.10
5971 10080 3.621558 ACTGTTTAGGATTAAGGCCTGC 58.378 45.455 5.69 0.00 36.96 4.85
5990 10099 4.440802 CCAGCTTTATCGCTCAAGTCTACT 60.441 45.833 0.00 0.00 38.41 2.57
6189 10328 3.119990 AGACACCAATAATCCGCAAAACG 60.120 43.478 0.00 0.00 43.15 3.60
6241 10399 9.554724 AAACAATATTGTAAAGATTACACTGCG 57.445 29.630 21.07 0.00 35.19 5.18
6266 10424 2.679336 TCGATACACGGATCAACGAGAA 59.321 45.455 0.00 0.00 42.82 2.87
6267 10425 2.031314 GTCGATACACGGATCAACGAGA 59.969 50.000 0.00 0.00 42.82 4.04
6278 10436 0.242825 ACCACCACAGTCGATACACG 59.757 55.000 0.00 0.00 44.09 4.49
6284 10442 4.221041 TCAACAATATACCACCACAGTCGA 59.779 41.667 0.00 0.00 0.00 4.20
6362 10521 9.936759 AATTATTTAGTTTACCAAACATGGTGG 57.063 29.630 14.45 14.45 43.79 4.61
6373 10532 7.281549 TCGGCAGAGGAAATTATTTAGTTTACC 59.718 37.037 0.00 0.00 0.00 2.85
6374 10533 8.205131 TCGGCAGAGGAAATTATTTAGTTTAC 57.795 34.615 0.00 0.00 0.00 2.01
6423 10582 8.766151 GTTTTTAGCGGTTTTAAAAATCATCCA 58.234 29.630 1.31 0.00 40.24 3.41
6442 10601 8.443160 TCATGCATCGTTCTCTTTAGTTTTTAG 58.557 33.333 0.00 0.00 0.00 1.85
6454 10613 3.187227 ACAAACACTCATGCATCGTTCTC 59.813 43.478 0.00 0.00 0.00 2.87
6456 10615 3.228749 CACAAACACTCATGCATCGTTC 58.771 45.455 0.00 0.00 0.00 3.95
6460 10619 5.611796 TCTAACACAAACACTCATGCATC 57.388 39.130 0.00 0.00 0.00 3.91
6490 10650 1.472082 TGATGCAAGCAAATACACGGG 59.528 47.619 0.00 0.00 0.00 5.28
6493 10653 4.731961 CGATTCTGATGCAAGCAAATACAC 59.268 41.667 0.00 0.00 0.00 2.90
6495 10655 5.160699 TCGATTCTGATGCAAGCAAATAC 57.839 39.130 0.00 0.00 0.00 1.89
6500 10660 2.813172 TGTTTCGATTCTGATGCAAGCA 59.187 40.909 0.00 0.00 0.00 3.91
6515 10675 4.764679 TGGATCAACTTCCATTGTTTCG 57.235 40.909 0.00 0.00 40.90 3.46
6517 10677 6.484364 AGTTTGGATCAACTTCCATTGTTT 57.516 33.333 0.00 0.00 45.08 2.83
6563 10723 1.007580 GCTTACCCGCTTGAGTTAGC 58.992 55.000 0.00 0.00 37.80 3.09
6575 10735 1.134431 CCCCAAAATGCATGCTTACCC 60.134 52.381 20.33 0.00 0.00 3.69
6577 10737 2.620242 CACCCCAAAATGCATGCTTAC 58.380 47.619 20.33 0.00 0.00 2.34
6617 10777 2.373169 TGAGGCTCCAATTTGACTCACT 59.627 45.455 12.86 0.00 30.75 3.41
6652 10812 6.170506 AGAATATCTCCGTGTTAAAGCAACA 58.829 36.000 0.00 0.00 44.97 3.33
6653 10813 6.663944 AGAATATCTCCGTGTTAAAGCAAC 57.336 37.500 0.00 0.00 37.67 4.17
6654 10814 7.553334 AGTAGAATATCTCCGTGTTAAAGCAA 58.447 34.615 0.00 0.00 0.00 3.91
6655 10815 7.068348 AGAGTAGAATATCTCCGTGTTAAAGCA 59.932 37.037 0.00 0.00 0.00 3.91
6656 10816 7.427214 AGAGTAGAATATCTCCGTGTTAAAGC 58.573 38.462 0.00 0.00 0.00 3.51
6657 10817 7.799447 CGAGAGTAGAATATCTCCGTGTTAAAG 59.201 40.741 0.00 0.00 39.02 1.85
6658 10818 7.255035 CCGAGAGTAGAATATCTCCGTGTTAAA 60.255 40.741 0.00 0.00 39.02 1.52
6659 10819 6.204301 CCGAGAGTAGAATATCTCCGTGTTAA 59.796 42.308 0.00 0.00 39.02 2.01
6660 10820 5.699915 CCGAGAGTAGAATATCTCCGTGTTA 59.300 44.000 0.00 0.00 39.02 2.41
6661 10821 4.515944 CCGAGAGTAGAATATCTCCGTGTT 59.484 45.833 0.00 0.00 39.02 3.32
6662 10822 4.066490 CCGAGAGTAGAATATCTCCGTGT 58.934 47.826 0.00 0.00 39.02 4.49
6663 10823 4.066490 ACCGAGAGTAGAATATCTCCGTG 58.934 47.826 0.00 0.00 39.02 4.94
6664 10824 4.354893 ACCGAGAGTAGAATATCTCCGT 57.645 45.455 0.00 0.00 39.02 4.69
6701 10861 2.743183 GCTAACTGCCATTCAGATCCGT 60.743 50.000 0.00 0.00 45.72 4.69
6715 10879 1.002430 TCCTGTTGCTCCAGCTAACTG 59.998 52.381 0.00 6.88 44.05 3.16
6790 10955 2.341846 AAAGTTGAGGTCGGAAGCAA 57.658 45.000 0.00 0.00 0.00 3.91
6799 10964 7.410174 TCCATGTGGATTATAAAAGTTGAGGT 58.590 34.615 0.00 0.00 39.78 3.85
6830 10995 8.542497 TGTACTTTTATGCGAACTTAGTTCAT 57.458 30.769 22.70 13.56 42.05 2.57
6848 11013 6.433093 CACTGGTAGCCCTTTAAATGTACTTT 59.567 38.462 0.00 0.00 0.00 2.66
6854 11019 8.514330 TTAATACACTGGTAGCCCTTTAAATG 57.486 34.615 0.00 0.00 31.88 2.32
6900 12935 4.125703 GGTGACAAAACCAAATGCATGAA 58.874 39.130 0.00 0.00 40.22 2.57
6919 12954 4.099266 TGAAGAAATCAAACTTGTGGGGTG 59.901 41.667 0.00 0.00 34.30 4.61
6941 12976 8.466617 AGTACTGTAGGTTGGTAGAATATCTG 57.533 38.462 0.00 0.00 0.00 2.90
6945 12980 8.689972 GCTTAAGTACTGTAGGTTGGTAGAATA 58.310 37.037 4.02 0.00 0.00 1.75
6946 12981 7.179694 TGCTTAAGTACTGTAGGTTGGTAGAAT 59.820 37.037 4.02 0.00 0.00 2.40
6947 12982 6.494491 TGCTTAAGTACTGTAGGTTGGTAGAA 59.506 38.462 4.02 0.00 0.00 2.10
6948 12983 6.012113 TGCTTAAGTACTGTAGGTTGGTAGA 58.988 40.000 4.02 0.00 0.00 2.59
6949 12984 6.098017 GTGCTTAAGTACTGTAGGTTGGTAG 58.902 44.000 15.60 0.00 0.00 3.18
6950 12985 5.047092 GGTGCTTAAGTACTGTAGGTTGGTA 60.047 44.000 20.97 0.00 0.00 3.25
6951 12986 4.262765 GGTGCTTAAGTACTGTAGGTTGGT 60.263 45.833 20.97 0.00 0.00 3.67
6952 12987 4.251268 GGTGCTTAAGTACTGTAGGTTGG 58.749 47.826 20.97 0.00 0.00 3.77
6953 12988 4.890088 TGGTGCTTAAGTACTGTAGGTTG 58.110 43.478 20.97 0.00 0.00 3.77
6954 12989 5.071384 ACTTGGTGCTTAAGTACTGTAGGTT 59.929 40.000 20.97 2.10 36.66 3.50
6955 12990 4.591924 ACTTGGTGCTTAAGTACTGTAGGT 59.408 41.667 20.97 12.31 36.66 3.08
6956 12991 5.148651 ACTTGGTGCTTAAGTACTGTAGG 57.851 43.478 20.97 11.79 36.66 3.18
6957 12992 6.704493 TCAAACTTGGTGCTTAAGTACTGTAG 59.296 38.462 20.97 16.88 37.39 2.74
6958 12993 6.584488 TCAAACTTGGTGCTTAAGTACTGTA 58.416 36.000 20.97 7.50 37.39 2.74
6959 12994 5.433526 TCAAACTTGGTGCTTAAGTACTGT 58.566 37.500 20.97 14.78 37.39 3.55
6960 12995 6.428159 AGATCAAACTTGGTGCTTAAGTACTG 59.572 38.462 20.97 11.63 37.39 2.74
6961 12996 6.428159 CAGATCAAACTTGGTGCTTAAGTACT 59.572 38.462 20.97 0.88 37.39 2.73
6962 12997 6.426937 TCAGATCAAACTTGGTGCTTAAGTAC 59.573 38.462 14.67 14.67 37.39 2.73
6963 12998 6.530120 TCAGATCAAACTTGGTGCTTAAGTA 58.470 36.000 4.02 0.00 37.39 2.24
6964 12999 5.376625 TCAGATCAAACTTGGTGCTTAAGT 58.623 37.500 4.02 0.00 39.92 2.24
6965 13000 5.947228 TCAGATCAAACTTGGTGCTTAAG 57.053 39.130 0.00 0.00 0.00 1.85
6966 13001 5.827797 AGTTCAGATCAAACTTGGTGCTTAA 59.172 36.000 7.49 0.00 33.19 1.85
6967 13002 5.376625 AGTTCAGATCAAACTTGGTGCTTA 58.623 37.500 7.49 0.00 33.19 3.09
6968 13003 4.210331 AGTTCAGATCAAACTTGGTGCTT 58.790 39.130 7.49 0.00 33.19 3.91
6969 13004 3.825328 AGTTCAGATCAAACTTGGTGCT 58.175 40.909 7.49 0.00 33.19 4.40
6970 13005 4.515191 TGTAGTTCAGATCAAACTTGGTGC 59.485 41.667 15.95 5.92 38.00 5.01
6971 13006 6.233430 CTGTAGTTCAGATCAAACTTGGTG 57.767 41.667 15.95 4.64 46.27 4.17


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

AutoCloner maintained by Alex Coulton.