Multiple sequence alignment - TraesCS3A01G512400

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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 TraesCS3A01G512400 chr3A 100.000 3704 0 0 938 4641 732045097 732041394 0.000000e+00 6841.0
1 TraesCS3A01G512400 chr3A 100.000 639 0 0 1 639 732046034 732045396 0.000000e+00 1181.0
2 TraesCS3A01G512400 chr3A 80.624 1378 232 28 2492 3854 730887986 730889343 0.000000e+00 1033.0
3 TraesCS3A01G512400 chr3A 80.282 142 23 3 1166 1304 730953009 730952870 8.220000e-18 102.0
4 TraesCS3A01G512400 chr3A 100.000 31 0 0 4429 4459 517660474 517660504 1.800000e-04 58.4
5 TraesCS3A01G512400 chr3D 89.435 2991 249 44 1698 4641 602276159 602273189 0.000000e+00 3711.0
6 TraesCS3A01G512400 chr3D 80.409 1368 239 23 2498 3852 602215902 602214551 0.000000e+00 1014.0
7 TraesCS3A01G512400 chr3D 78.788 1353 214 39 2519 3854 602241196 602239900 0.000000e+00 841.0
8 TraesCS3A01G512400 chr3D 88.764 356 23 10 1019 1365 602277087 602276740 2.000000e-113 420.0
9 TraesCS3A01G512400 chr3D 84.130 460 13 32 231 639 602277946 602277496 1.570000e-104 390.0
10 TraesCS3A01G512400 chr3D 92.188 128 9 1 98 225 602278167 602278041 3.690000e-41 180.0
11 TraesCS3A01G512400 chr3D 72.124 678 140 25 2866 3524 602253988 602253341 4.810000e-35 159.0
12 TraesCS3A01G512400 chr3D 87.770 139 6 3 98 236 602280773 602280646 8.040000e-33 152.0
13 TraesCS3A01G512400 chr3D 85.149 101 9 4 1797 1892 602276361 602276262 1.060000e-16 99.0
14 TraesCS3A01G512400 chr3B 88.405 2251 198 36 1749 3948 809541236 809538998 0.000000e+00 2652.0
15 TraesCS3A01G512400 chr3B 81.176 1360 214 26 2498 3831 809452228 809450885 0.000000e+00 1055.0
16 TraesCS3A01G512400 chr3B 80.247 1377 230 32 2498 3854 809362889 809361535 0.000000e+00 998.0
17 TraesCS3A01G512400 chr3B 79.611 1388 235 37 2492 3854 809233777 809235141 0.000000e+00 952.0
18 TraesCS3A01G512400 chr3B 87.025 447 20 13 231 639 809542399 809541953 1.950000e-128 470.0
19 TraesCS3A01G512400 chr3B 89.206 315 26 5 1023 1331 809541865 809541553 2.030000e-103 387.0
20 TraesCS3A01G512400 chr3B 74.684 474 84 21 3042 3497 809457830 809457375 1.330000e-40 178.0
21 TraesCS3A01G512400 chr3B 91.150 113 6 1 98 206 809589913 809589801 2.890000e-32 150.0
22 TraesCS3A01G512400 chr3B 90.265 113 7 1 98 206 809553899 809554011 1.350000e-30 145.0
23 TraesCS3A01G512400 chr7A 73.134 268 53 12 4325 4578 157219456 157219194 1.380000e-10 78.7
24 TraesCS3A01G512400 chr7B 97.143 35 0 1 4426 4459 662909345 662909311 1.800000e-04 58.4
25 TraesCS3A01G512400 chr1B 100.000 31 0 0 4429 4459 284490416 284490386 1.800000e-04 58.4
26 TraesCS3A01G512400 chr5B 100.000 28 0 0 4429 4456 655211476 655211449 8.000000e-03 52.8
27 TraesCS3A01G512400 chr4B 100.000 28 0 0 4429 4456 440918192 440918219 8.000000e-03 52.8


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 TraesCS3A01G512400 chr3A 732041394 732046034 4640 True 4011.000000 6841 100.000 1 4641 2 chr3A.!!$R2 4640
1 TraesCS3A01G512400 chr3A 730887986 730889343 1357 False 1033.000000 1033 80.624 2492 3854 1 chr3A.!!$F2 1362
2 TraesCS3A01G512400 chr3D 602214551 602215902 1351 True 1014.000000 1014 80.409 2498 3852 1 chr3D.!!$R1 1354
3 TraesCS3A01G512400 chr3D 602239900 602241196 1296 True 841.000000 841 78.788 2519 3854 1 chr3D.!!$R2 1335
4 TraesCS3A01G512400 chr3D 602273189 602280773 7584 True 825.333333 3711 87.906 98 4641 6 chr3D.!!$R4 4543
5 TraesCS3A01G512400 chr3B 809538998 809542399 3401 True 1169.666667 2652 88.212 231 3948 3 chr3B.!!$R5 3717
6 TraesCS3A01G512400 chr3B 809450885 809452228 1343 True 1055.000000 1055 81.176 2498 3831 1 chr3B.!!$R2 1333
7 TraesCS3A01G512400 chr3B 809361535 809362889 1354 True 998.000000 998 80.247 2498 3854 1 chr3B.!!$R1 1356
8 TraesCS3A01G512400 chr3B 809233777 809235141 1364 False 952.000000 952 79.611 2492 3854 1 chr3B.!!$F1 1362

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
221 2828 0.034616 CTAGGGCTAGCCATCTGTGC 59.965 60.0 34.09 15.49 37.98 4.57 F
456 3203 0.463654 ACGTGCATGTCACCAACAGT 60.464 50.0 5.51 4.21 42.37 3.55 F
1478 4592 0.171903 GTGGCGCTGCATGAGAATTT 59.828 50.0 7.64 0.00 0.00 1.82 F
2406 5910 0.031721 CACGGCCTATTAGTCGGGTC 59.968 60.0 0.00 0.00 0.00 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1107 4215 0.462047 GCAGACCATCAGTAACCGGG 60.462 60.0 6.32 0.00 0.00 5.73 R
2389 5893 0.314302 CTGACCCGACTAATAGGCCG 59.686 60.0 0.00 0.00 0.00 6.13 R
3403 6955 0.670546 CGAATGCCTCGTCTTGTGGT 60.671 55.0 0.00 0.00 42.89 4.16 R
3925 7492 1.538687 AACCAAGCATCAGGCCAAGC 61.539 55.0 5.01 2.59 46.50 4.01 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
22 23 5.420725 ACATGTGTATTACTGAGCCTTGA 57.579 39.130 0.00 0.00 0.00 3.02
23 24 5.423015 ACATGTGTATTACTGAGCCTTGAG 58.577 41.667 0.00 0.00 0.00 3.02
24 25 4.471904 TGTGTATTACTGAGCCTTGAGG 57.528 45.455 0.00 0.00 38.53 3.86
25 26 3.197766 TGTGTATTACTGAGCCTTGAGGG 59.802 47.826 0.00 0.00 35.18 4.30
34 35 1.115467 AGCCTTGAGGGTGAGTATCG 58.885 55.000 0.04 0.00 45.50 2.92
35 36 0.824759 GCCTTGAGGGTGAGTATCGT 59.175 55.000 0.00 0.00 34.36 3.73
36 37 2.029623 GCCTTGAGGGTGAGTATCGTA 58.970 52.381 0.00 0.00 34.36 3.43
37 38 2.429610 GCCTTGAGGGTGAGTATCGTAA 59.570 50.000 0.00 0.00 34.36 3.18
38 39 3.118884 GCCTTGAGGGTGAGTATCGTAAA 60.119 47.826 0.00 0.00 34.36 2.01
39 40 4.443034 GCCTTGAGGGTGAGTATCGTAAAT 60.443 45.833 0.00 0.00 34.36 1.40
40 41 5.671493 CCTTGAGGGTGAGTATCGTAAATT 58.329 41.667 0.00 0.00 38.61 1.82
41 42 6.684613 GCCTTGAGGGTGAGTATCGTAAATTA 60.685 42.308 0.00 0.00 34.36 1.40
42 43 6.700520 CCTTGAGGGTGAGTATCGTAAATTAC 59.299 42.308 0.00 0.00 38.61 1.89
43 44 6.778834 TGAGGGTGAGTATCGTAAATTACA 57.221 37.500 3.91 0.00 38.61 2.41
44 45 7.172868 TGAGGGTGAGTATCGTAAATTACAA 57.827 36.000 3.91 0.00 38.61 2.41
45 46 7.788026 TGAGGGTGAGTATCGTAAATTACAAT 58.212 34.615 3.91 0.00 38.61 2.71
46 47 8.916062 TGAGGGTGAGTATCGTAAATTACAATA 58.084 33.333 3.91 0.00 38.61 1.90
47 48 9.924650 GAGGGTGAGTATCGTAAATTACAATAT 57.075 33.333 3.91 0.00 38.61 1.28
56 57 7.266922 TCGTAAATTACAATATTTGGAGGGC 57.733 36.000 3.91 0.00 34.12 5.19
57 58 7.057894 TCGTAAATTACAATATTTGGAGGGCT 58.942 34.615 3.91 0.00 34.12 5.19
58 59 8.212312 TCGTAAATTACAATATTTGGAGGGCTA 58.788 33.333 3.91 0.00 34.12 3.93
59 60 8.842280 CGTAAATTACAATATTTGGAGGGCTAA 58.158 33.333 3.91 0.00 34.12 3.09
61 62 6.901081 ATTACAATATTTGGAGGGCTAAGC 57.099 37.500 0.00 0.00 34.12 3.09
62 63 4.526438 ACAATATTTGGAGGGCTAAGCT 57.474 40.909 0.00 0.00 34.12 3.74
63 64 5.646692 ACAATATTTGGAGGGCTAAGCTA 57.353 39.130 0.00 0.00 34.12 3.32
64 65 6.013554 ACAATATTTGGAGGGCTAAGCTAA 57.986 37.500 0.00 0.00 34.12 3.09
65 66 6.614657 ACAATATTTGGAGGGCTAAGCTAAT 58.385 36.000 0.00 0.00 34.12 1.73
66 67 7.069344 ACAATATTTGGAGGGCTAAGCTAATT 58.931 34.615 0.00 0.00 34.12 1.40
67 68 7.014615 ACAATATTTGGAGGGCTAAGCTAATTG 59.985 37.037 0.00 0.00 34.12 2.32
68 69 4.584638 TTTGGAGGGCTAAGCTAATTGA 57.415 40.909 0.00 0.00 0.00 2.57
69 70 3.560636 TGGAGGGCTAAGCTAATTGAC 57.439 47.619 0.00 0.00 0.00 3.18
70 71 2.158957 TGGAGGGCTAAGCTAATTGACG 60.159 50.000 0.00 0.00 0.00 4.35
71 72 2.102588 GGAGGGCTAAGCTAATTGACGA 59.897 50.000 0.00 0.00 0.00 4.20
72 73 3.385577 GAGGGCTAAGCTAATTGACGAG 58.614 50.000 0.00 0.00 0.00 4.18
73 74 2.766828 AGGGCTAAGCTAATTGACGAGT 59.233 45.455 0.00 0.00 0.00 4.18
74 75 3.197983 AGGGCTAAGCTAATTGACGAGTT 59.802 43.478 0.00 0.00 0.00 3.01
75 76 3.939592 GGGCTAAGCTAATTGACGAGTTT 59.060 43.478 0.00 0.00 0.00 2.66
76 77 4.034163 GGGCTAAGCTAATTGACGAGTTTC 59.966 45.833 0.00 0.00 0.00 2.78
77 78 4.630069 GGCTAAGCTAATTGACGAGTTTCA 59.370 41.667 0.00 0.00 0.00 2.69
78 79 5.294552 GGCTAAGCTAATTGACGAGTTTCAT 59.705 40.000 0.00 0.00 0.00 2.57
79 80 6.183360 GGCTAAGCTAATTGACGAGTTTCATT 60.183 38.462 0.00 0.00 0.00 2.57
80 81 6.684555 GCTAAGCTAATTGACGAGTTTCATTG 59.315 38.462 0.00 0.00 0.00 2.82
81 82 5.551760 AGCTAATTGACGAGTTTCATTGG 57.448 39.130 0.00 0.00 0.00 3.16
82 83 5.245531 AGCTAATTGACGAGTTTCATTGGA 58.754 37.500 0.00 0.00 0.00 3.53
83 84 5.122396 AGCTAATTGACGAGTTTCATTGGAC 59.878 40.000 0.00 0.00 0.00 4.02
84 85 4.404507 AATTGACGAGTTTCATTGGACG 57.595 40.909 0.00 0.00 0.00 4.79
85 86 2.804697 TGACGAGTTTCATTGGACGA 57.195 45.000 0.00 0.00 0.00 4.20
86 87 2.672714 TGACGAGTTTCATTGGACGAG 58.327 47.619 0.00 0.00 0.00 4.18
87 88 1.993370 GACGAGTTTCATTGGACGAGG 59.007 52.381 0.00 0.00 0.00 4.63
88 89 0.721718 CGAGTTTCATTGGACGAGGC 59.278 55.000 0.00 0.00 0.00 4.70
89 90 0.721718 GAGTTTCATTGGACGAGGCG 59.278 55.000 0.00 0.00 0.00 5.52
90 91 0.673644 AGTTTCATTGGACGAGGCGG 60.674 55.000 0.00 0.00 0.00 6.13
91 92 0.953960 GTTTCATTGGACGAGGCGGT 60.954 55.000 0.00 0.00 0.00 5.68
92 93 0.250553 TTTCATTGGACGAGGCGGTT 60.251 50.000 0.00 0.00 0.00 4.44
93 94 0.250553 TTCATTGGACGAGGCGGTTT 60.251 50.000 0.00 0.00 0.00 3.27
94 95 0.609151 TCATTGGACGAGGCGGTTTA 59.391 50.000 0.00 0.00 0.00 2.01
95 96 0.725117 CATTGGACGAGGCGGTTTAC 59.275 55.000 0.00 0.00 0.00 2.01
96 97 0.392060 ATTGGACGAGGCGGTTTACC 60.392 55.000 0.00 0.00 0.00 2.85
101 102 1.137675 GACGAGGCGGTTTACCCTAAT 59.862 52.381 0.00 0.00 0.00 1.73
120 121 0.821517 TGGTACCGATCGCAATCTGT 59.178 50.000 10.32 3.49 34.25 3.41
149 2756 2.789092 GCAGATACGACAAGCAATGTGC 60.789 50.000 0.00 0.00 44.12 4.57
174 2781 4.096003 CCTGGGTACAGCCGGGTG 62.096 72.222 31.30 31.30 43.53 4.61
209 2816 2.503061 CATGCGTGCTCTAGGGCT 59.497 61.111 17.26 0.00 0.00 5.19
210 2817 1.742146 CATGCGTGCTCTAGGGCTA 59.258 57.895 17.26 0.00 0.00 3.93
211 2818 0.319383 CATGCGTGCTCTAGGGCTAG 60.319 60.000 17.26 10.74 34.56 3.42
212 2819 2.028337 GCGTGCTCTAGGGCTAGC 59.972 66.667 17.26 16.92 39.25 3.42
213 2820 2.731374 CGTGCTCTAGGGCTAGCC 59.269 66.667 26.55 26.55 37.97 3.93
214 2821 2.127869 CGTGCTCTAGGGCTAGCCA 61.128 63.158 34.09 14.89 37.97 4.75
216 2823 0.320050 GTGCTCTAGGGCTAGCCATC 59.680 60.000 34.09 18.51 37.97 3.51
217 2824 0.189574 TGCTCTAGGGCTAGCCATCT 59.810 55.000 34.09 24.33 37.97 2.90
218 2825 0.607620 GCTCTAGGGCTAGCCATCTG 59.392 60.000 34.09 22.74 37.98 2.90
219 2826 2.008242 CTCTAGGGCTAGCCATCTGT 57.992 55.000 34.09 15.34 37.98 3.41
220 2827 1.617850 CTCTAGGGCTAGCCATCTGTG 59.382 57.143 34.09 19.54 37.98 3.66
221 2828 0.034616 CTAGGGCTAGCCATCTGTGC 59.965 60.000 34.09 15.49 37.98 4.57
222 2829 1.748329 TAGGGCTAGCCATCTGTGCG 61.748 60.000 34.09 0.00 37.98 5.34
223 2830 2.187946 GGCTAGCCATCTGTGCGT 59.812 61.111 29.33 0.00 35.81 5.24
225 2832 2.233654 GCTAGCCATCTGTGCGTCG 61.234 63.158 2.29 0.00 0.00 5.12
226 2833 2.202743 TAGCCATCTGTGCGTCGC 60.203 61.111 11.10 11.10 0.00 5.19
321 3039 3.721575 TGGCATCTCCACCTAATTACCAT 59.278 43.478 0.00 0.00 40.72 3.55
324 3042 5.598417 GGCATCTCCACCTAATTACCATTTT 59.402 40.000 0.00 0.00 34.01 1.82
456 3203 0.463654 ACGTGCATGTCACCAACAGT 60.464 50.000 5.51 4.21 42.37 3.55
464 3211 1.202639 TGTCACCAACAGTAGGCAGTG 60.203 52.381 0.00 0.00 32.81 3.66
964 3728 6.493802 TCTCTCATACTACTGTTTTGAGGTGT 59.506 38.462 0.00 0.00 36.61 4.16
979 4060 2.434185 TGTTGATCGAGTGGCGCC 60.434 61.111 22.73 22.73 40.61 6.53
1017 4098 3.620821 GCAAGATGGTAGAGAAGAACAGC 59.379 47.826 0.00 0.00 0.00 4.40
1021 4123 1.819288 TGGTAGAGAAGAACAGCGAGG 59.181 52.381 0.00 0.00 0.00 4.63
1035 4137 2.496817 GAGGTGCTGGTAGGCTCG 59.503 66.667 0.00 0.00 0.00 5.03
1107 4215 2.668550 GTCAGCGGTGTTGTCCCC 60.669 66.667 15.22 0.00 0.00 4.81
1127 4235 0.537188 CCGGTTACTGATGGTCTGCT 59.463 55.000 0.00 0.00 0.00 4.24
1137 4248 2.359230 GGTCTGCTGCAGGTGGTC 60.359 66.667 27.79 13.52 31.51 4.02
1142 4253 2.815647 GCTGCAGGTGGTCGTAGC 60.816 66.667 17.12 0.00 0.00 3.58
1278 4389 1.672356 CTTCGCCCAACACCTCCAG 60.672 63.158 0.00 0.00 0.00 3.86
1310 4421 4.096003 CCACCTGGGTACGGCCAG 62.096 72.222 2.24 10.39 39.65 4.85
1317 4431 2.590092 GGTACGGCCAGCTCCATT 59.410 61.111 2.24 0.00 37.17 3.16
1333 4447 1.154197 CATTGATCTGCATCGGCGAT 58.846 50.000 18.14 18.14 45.35 4.58
1335 4449 0.601046 TTGATCTGCATCGGCGATCC 60.601 55.000 21.25 12.51 43.26 3.36
1348 4462 1.858041 CGATCCGATCATGCTGCAC 59.142 57.895 3.57 0.00 0.00 4.57
1368 4482 3.518003 GCTCCGGCTTGCATTGAT 58.482 55.556 0.00 0.00 35.22 2.57
1369 4483 2.706636 GCTCCGGCTTGCATTGATA 58.293 52.632 0.00 0.00 35.22 2.15
1370 4484 1.242076 GCTCCGGCTTGCATTGATAT 58.758 50.000 0.00 0.00 35.22 1.63
1371 4485 1.068748 GCTCCGGCTTGCATTGATATG 60.069 52.381 0.00 0.00 35.22 1.78
1372 4486 4.829140 GCTCCGGCTTGCATTGATATGC 62.829 54.545 0.00 3.26 44.96 3.14
1444 4558 1.780806 CATGCATGCTCCTAGTCTCG 58.219 55.000 20.33 0.00 0.00 4.04
1445 4559 1.068281 CATGCATGCTCCTAGTCTCGT 59.932 52.381 20.33 0.00 0.00 4.18
1453 4567 0.596577 TCCTAGTCTCGTGTGTGTGC 59.403 55.000 0.00 0.00 0.00 4.57
1476 4590 2.466982 CGTGGCGCTGCATGAGAAT 61.467 57.895 7.64 0.00 0.00 2.40
1477 4591 1.805254 GTGGCGCTGCATGAGAATT 59.195 52.632 7.64 0.00 0.00 2.17
1478 4592 0.171903 GTGGCGCTGCATGAGAATTT 59.828 50.000 7.64 0.00 0.00 1.82
1479 4593 0.889994 TGGCGCTGCATGAGAATTTT 59.110 45.000 7.64 0.00 0.00 1.82
1530 4644 9.893634 TTAAAAATATTACAGTGGAAGATCGGA 57.106 29.630 0.00 0.00 0.00 4.55
1541 4655 6.647067 CAGTGGAAGATCGGAATAAATAGGTC 59.353 42.308 0.00 0.00 0.00 3.85
1547 4661 9.884465 GAAGATCGGAATAAATAGGTCAAATTG 57.116 33.333 0.00 0.00 0.00 2.32
1552 4666 2.959507 AAATAGGTCAAATTGCCGCC 57.040 45.000 0.00 0.00 0.00 6.13
1553 4667 2.143876 AATAGGTCAAATTGCCGCCT 57.856 45.000 8.19 8.19 0.00 5.52
1559 4673 2.230266 GGTCAAATTGCCGCCTTAAGAA 59.770 45.455 3.36 0.00 0.00 2.52
1560 4674 3.242518 GTCAAATTGCCGCCTTAAGAAC 58.757 45.455 3.36 0.00 0.00 3.01
1562 4676 2.986479 CAAATTGCCGCCTTAAGAACAC 59.014 45.455 3.36 0.00 0.00 3.32
1569 4683 3.181500 GCCGCCTTAAGAACACCAAATAG 60.181 47.826 3.36 0.00 0.00 1.73
1570 4684 4.258543 CCGCCTTAAGAACACCAAATAGA 58.741 43.478 3.36 0.00 0.00 1.98
1571 4685 4.698304 CCGCCTTAAGAACACCAAATAGAA 59.302 41.667 3.36 0.00 0.00 2.10
1572 4686 5.391629 CCGCCTTAAGAACACCAAATAGAAC 60.392 44.000 3.36 0.00 0.00 3.01
1573 4687 5.628134 GCCTTAAGAACACCAAATAGAACG 58.372 41.667 3.36 0.00 0.00 3.95
1574 4688 5.410439 GCCTTAAGAACACCAAATAGAACGA 59.590 40.000 3.36 0.00 0.00 3.85
1575 4689 6.093633 GCCTTAAGAACACCAAATAGAACGAT 59.906 38.462 3.36 0.00 0.00 3.73
1576 4690 7.464358 CCTTAAGAACACCAAATAGAACGATG 58.536 38.462 3.36 0.00 0.00 3.84
1577 4691 7.333423 CCTTAAGAACACCAAATAGAACGATGA 59.667 37.037 3.36 0.00 0.00 2.92
1578 4692 8.786826 TTAAGAACACCAAATAGAACGATGAT 57.213 30.769 0.00 0.00 0.00 2.45
1579 4693 6.668541 AGAACACCAAATAGAACGATGATG 57.331 37.500 0.00 0.00 0.00 3.07
1580 4694 6.173339 AGAACACCAAATAGAACGATGATGT 58.827 36.000 0.00 0.00 0.00 3.06
1581 4695 6.313905 AGAACACCAAATAGAACGATGATGTC 59.686 38.462 0.00 0.00 0.00 3.06
1582 4696 4.876107 ACACCAAATAGAACGATGATGTCC 59.124 41.667 0.00 0.00 0.00 4.02
1583 4697 5.118990 CACCAAATAGAACGATGATGTCCT 58.881 41.667 0.00 0.00 0.00 3.85
1584 4698 6.127168 ACACCAAATAGAACGATGATGTCCTA 60.127 38.462 0.00 0.00 0.00 2.94
1585 4699 6.422100 CACCAAATAGAACGATGATGTCCTAG 59.578 42.308 0.00 0.00 0.00 3.02
1586 4700 6.323996 ACCAAATAGAACGATGATGTCCTAGA 59.676 38.462 0.00 0.00 0.00 2.43
1587 4701 6.642950 CCAAATAGAACGATGATGTCCTAGAC 59.357 42.308 0.00 0.00 0.00 2.59
1588 4702 7.429633 CAAATAGAACGATGATGTCCTAGACT 58.570 38.462 0.00 0.00 33.15 3.24
1589 4703 7.589958 AATAGAACGATGATGTCCTAGACTT 57.410 36.000 0.00 0.00 33.15 3.01
1590 4704 5.923733 AGAACGATGATGTCCTAGACTTT 57.076 39.130 0.00 0.00 33.15 2.66
1591 4705 6.287589 AGAACGATGATGTCCTAGACTTTT 57.712 37.500 0.00 0.00 33.15 2.27
1592 4706 6.702329 AGAACGATGATGTCCTAGACTTTTT 58.298 36.000 0.00 0.00 33.15 1.94
1629 4744 2.025605 TGTCCTAGACTTCGGGAAGCTA 60.026 50.000 8.29 9.45 41.99 3.32
1632 4747 3.053842 TCCTAGACTTCGGGAAGCTAGAA 60.054 47.826 25.00 13.56 41.82 2.10
1640 4755 1.562672 GGGAAGCTAGAACCCTGCCA 61.563 60.000 10.69 0.00 40.39 4.92
1650 4765 4.388577 AGAACCCTGCCAAAATAGAACT 57.611 40.909 0.00 0.00 0.00 3.01
1696 5162 3.901844 AGAACCAGTAGCAACAGGTAGAA 59.098 43.478 0.00 0.00 44.17 2.10
1714 5180 9.307121 CAGGTAGAATGACTAAGTGAGTTAATG 57.693 37.037 0.00 0.00 39.06 1.90
1715 5181 8.478877 AGGTAGAATGACTAAGTGAGTTAATGG 58.521 37.037 0.00 0.00 39.06 3.16
1741 5207 9.611284 GATTTTCCAAAACAAAAGGATTAATGC 57.389 29.630 0.00 0.00 0.00 3.56
1744 5210 7.961325 TCCAAAACAAAAGGATTAATGCTTC 57.039 32.000 20.83 0.00 37.48 3.86
1746 5212 6.709846 CCAAAACAAAAGGATTAATGCTTCCA 59.290 34.615 20.83 0.00 37.48 3.53
1800 5275 7.595502 TCTCAAAAGAAGATCGTCTAACAACTC 59.404 37.037 11.75 0.00 0.00 3.01
1809 5284 3.123804 CGTCTAACAACTCTGCACACTT 58.876 45.455 0.00 0.00 0.00 3.16
1816 5291 3.118629 ACAACTCTGCACACTTCTTCTCA 60.119 43.478 0.00 0.00 0.00 3.27
1823 5298 4.923893 TGCACACTTCTTCTCAAATTGTG 58.076 39.130 0.00 0.00 39.16 3.33
1826 5301 6.094742 TGCACACTTCTTCTCAAATTGTGTAA 59.905 34.615 0.00 0.00 38.69 2.41
1860 5343 4.765339 GGTTGGCTAACAGTGGTAGAATTT 59.235 41.667 19.68 0.00 38.58 1.82
1916 5399 4.746729 TGCCAACAAAAGTCATGCATATC 58.253 39.130 0.00 0.00 0.00 1.63
1922 5405 8.437742 CCAACAAAAGTCATGCATATCTTTTTC 58.562 33.333 25.13 4.37 37.81 2.29
1923 5406 9.199982 CAACAAAAGTCATGCATATCTTTTTCT 57.800 29.630 25.13 17.39 37.81 2.52
1924 5407 8.752766 ACAAAAGTCATGCATATCTTTTTCTG 57.247 30.769 25.13 20.38 37.81 3.02
1926 5409 6.461110 AAGTCATGCATATCTTTTTCTGGG 57.539 37.500 0.00 0.00 0.00 4.45
1935 5421 3.039252 TCTTTTTCTGGGAAAAGGCCA 57.961 42.857 5.01 0.00 43.49 5.36
2080 5572 1.270947 CCATTGCCAGCACCACAAAAT 60.271 47.619 0.00 0.00 0.00 1.82
2095 5597 8.392612 GCACCACAAAATAAATACATACGTACT 58.607 33.333 0.00 0.00 0.00 2.73
2134 5638 8.392612 TCATCATGCAATTTATACTATCATGCG 58.607 33.333 0.00 0.00 35.18 4.73
2137 5641 5.930405 TGCAATTTATACTATCATGCGCAG 58.070 37.500 18.32 8.46 35.18 5.18
2138 5642 5.700373 TGCAATTTATACTATCATGCGCAGA 59.300 36.000 18.32 14.05 35.18 4.26
2165 5669 3.940209 TCTCATGCAAATGTTTGTCCC 57.060 42.857 7.26 0.00 40.24 4.46
2195 5699 2.414612 ACCCTTACAACCTGGACTTCA 58.585 47.619 0.00 0.00 0.00 3.02
2239 5743 5.246981 TCCAGAACTTCTCCATCAACAAT 57.753 39.130 0.00 0.00 0.00 2.71
2257 5761 0.541863 ATCTCGGCGACCCTTTCATT 59.458 50.000 4.99 0.00 0.00 2.57
2293 5797 0.843309 TCCACTCCAGGCAGTTTGAA 59.157 50.000 0.00 0.00 0.00 2.69
2305 5809 1.102978 AGTTTGAAGTTGCCGTGCTT 58.897 45.000 0.00 0.00 0.00 3.91
2308 5812 0.380378 TTGAAGTTGCCGTGCTTGAC 59.620 50.000 0.00 0.00 0.00 3.18
2314 5818 1.034838 TTGCCGTGCTTGACTGGTTT 61.035 50.000 0.00 0.00 0.00 3.27
2338 5842 1.986413 CCTCTGGGACCTCCAACAG 59.014 63.158 0.00 0.00 46.51 3.16
2374 5878 0.895100 ACATCACCAATTGCGGCACT 60.895 50.000 0.05 0.00 0.00 4.40
2406 5910 0.031721 CACGGCCTATTAGTCGGGTC 59.968 60.000 0.00 0.00 0.00 4.46
2415 5919 5.123661 GCCTATTAGTCGGGTCAGTATCTAC 59.876 48.000 0.00 0.00 0.00 2.59
2417 5921 4.508551 TTAGTCGGGTCAGTATCTACCA 57.491 45.455 0.00 0.00 37.51 3.25
2418 5922 2.933573 AGTCGGGTCAGTATCTACCAG 58.066 52.381 0.00 0.00 37.51 4.00
2419 5923 2.508716 AGTCGGGTCAGTATCTACCAGA 59.491 50.000 0.00 0.00 37.59 3.86
2420 5924 3.138653 AGTCGGGTCAGTATCTACCAGAT 59.861 47.826 0.00 0.00 41.12 2.90
2421 5925 4.350225 AGTCGGGTCAGTATCTACCAGATA 59.650 45.833 0.00 0.00 41.12 1.98
2422 5926 5.014333 AGTCGGGTCAGTATCTACCAGATAT 59.986 44.000 0.00 0.00 41.12 1.63
2423 5927 5.354792 GTCGGGTCAGTATCTACCAGATATC 59.645 48.000 0.00 0.00 41.12 1.63
2424 5928 4.641094 CGGGTCAGTATCTACCAGATATCC 59.359 50.000 0.00 1.91 39.21 2.59
2425 5929 4.957327 GGGTCAGTATCTACCAGATATCCC 59.043 50.000 0.00 6.22 39.21 3.85
2426 5930 5.281821 GGGTCAGTATCTACCAGATATCCCT 60.282 48.000 0.00 2.48 39.21 4.20
2427 5931 6.257586 GGTCAGTATCTACCAGATATCCCTT 58.742 44.000 0.00 0.00 39.21 3.95
2428 5932 7.411808 GGTCAGTATCTACCAGATATCCCTTA 58.588 42.308 0.00 0.00 39.21 2.69
2464 5970 7.859377 GCATACATTTTTCACATGATCGAGAAT 59.141 33.333 0.00 0.00 0.00 2.40
2472 5978 7.704789 TTCACATGATCGAGAATGTATCTTG 57.295 36.000 13.64 5.21 38.96 3.02
2473 5979 5.693555 TCACATGATCGAGAATGTATCTTGC 59.306 40.000 13.64 0.00 38.96 4.01
2474 5980 5.464389 CACATGATCGAGAATGTATCTTGCA 59.536 40.000 13.64 0.00 38.96 4.08
2479 6010 6.865205 TGATCGAGAATGTATCTTGCATACTG 59.135 38.462 0.00 0.00 38.96 2.74
2496 6028 8.518430 TGCATACTGGTTGTGATTTTATATGT 57.482 30.769 0.00 0.00 0.00 2.29
2514 6046 2.344592 TGTAGGAGGGAGCTTTTTCCA 58.655 47.619 12.19 0.00 39.09 3.53
2556 6088 0.454620 GTGAGTCGCACTACTCCGTG 60.455 60.000 0.00 0.00 44.40 4.94
2586 6120 5.186797 GGCAGCTAGGATGTATAGAGTTGAT 59.813 44.000 0.00 0.00 0.00 2.57
2728 6262 5.063060 GCTTTCACATTTTCATCAGAATGGC 59.937 40.000 0.00 0.00 37.53 4.40
2732 6266 5.124936 TCACATTTTCATCAGAATGGCTCAG 59.875 40.000 0.00 0.00 37.53 3.35
2748 6283 3.922850 GGCTCAGAAAATGCTTTGCTTAC 59.077 43.478 0.00 0.00 0.00 2.34
2763 6298 6.128526 GCTTTGCTTACGTGTCTCTCTTTATT 60.129 38.462 0.00 0.00 0.00 1.40
2847 6386 3.491619 CCATCGACGATCTTGACAGGATT 60.492 47.826 7.54 0.00 0.00 3.01
2874 6413 3.535280 ACGCTTGAAAAATGTGGGTTT 57.465 38.095 0.00 0.00 0.00 3.27
2951 6490 4.782019 TTATCAAACAAGTGGGTCATGC 57.218 40.909 0.00 0.00 0.00 4.06
2952 6491 2.064434 TCAAACAAGTGGGTCATGCA 57.936 45.000 0.00 0.00 0.00 3.96
2953 6492 1.680735 TCAAACAAGTGGGTCATGCAC 59.319 47.619 0.00 0.00 0.00 4.57
2954 6493 1.682854 CAAACAAGTGGGTCATGCACT 59.317 47.619 0.00 0.00 0.00 4.40
2990 6531 5.567138 AAGGACATTTAGTTAGCACATGC 57.433 39.130 0.00 0.00 42.49 4.06
2993 6534 4.438744 GGACATTTAGTTAGCACATGCCAC 60.439 45.833 0.00 0.00 43.38 5.01
2999 6540 2.034558 AGTTAGCACATGCCACAACAAC 59.965 45.455 13.08 4.59 43.38 3.32
3032 6584 7.661536 ATCTAGAGAACAACATAGCTAACCA 57.338 36.000 0.00 0.00 0.00 3.67
3035 6587 5.865085 AGAGAACAACATAGCTAACCAACA 58.135 37.500 0.00 0.00 0.00 3.33
3082 6634 2.206576 AGGTGACATTCAAGAAGCCC 57.793 50.000 0.00 0.00 0.00 5.19
3127 6679 2.291153 CCACAAGTTCATGGGATGTCCT 60.291 50.000 0.00 0.00 36.20 3.85
3136 6688 0.546122 TGGGATGTCCTGTACCATGC 59.454 55.000 0.00 0.00 36.20 4.06
3263 6815 2.882137 CCAATGTTCCTTTGGTACACGT 59.118 45.455 0.00 0.00 39.29 4.49
3277 6829 3.377798 GGTACACGTTGAACAAAAAGGGA 59.622 43.478 0.00 0.00 0.00 4.20
3341 6893 2.881074 CTCATCATCTCGTGAACCGTT 58.119 47.619 0.00 0.00 40.97 4.44
3343 6895 4.421058 CTCATCATCTCGTGAACCGTTTA 58.579 43.478 0.00 0.00 40.97 2.01
3403 6955 1.658114 CACGGTGGTGTTCGAGAGA 59.342 57.895 0.00 0.00 39.38 3.10
3502 7054 1.203523 GTGAGTGTGGAGAAGCTCGAT 59.796 52.381 0.00 0.00 0.00 3.59
3509 7061 3.509967 TGTGGAGAAGCTCGATGACTTTA 59.490 43.478 0.00 0.00 0.00 1.85
3512 7064 4.402474 TGGAGAAGCTCGATGACTTTATCA 59.598 41.667 0.00 0.00 43.13 2.15
3526 7078 5.091261 ACTTTATCAAAGAGCTCATCGGT 57.909 39.130 17.77 1.67 41.02 4.69
3669 7221 2.640316 AGGAGTGGAGAACAACAACC 57.360 50.000 0.00 0.00 0.00 3.77
3870 7436 2.839486 TTGTCTCGCCAACTCTGATT 57.161 45.000 0.00 0.00 0.00 2.57
3875 7441 4.021456 TGTCTCGCCAACTCTGATTCTAAA 60.021 41.667 0.00 0.00 0.00 1.85
3880 7446 5.705441 TCGCCAACTCTGATTCTAAAACAAT 59.295 36.000 0.00 0.00 0.00 2.71
3881 7447 6.206634 TCGCCAACTCTGATTCTAAAACAATT 59.793 34.615 0.00 0.00 0.00 2.32
3882 7448 7.389330 TCGCCAACTCTGATTCTAAAACAATTA 59.611 33.333 0.00 0.00 0.00 1.40
3883 7449 8.020819 CGCCAACTCTGATTCTAAAACAATTAA 58.979 33.333 0.00 0.00 0.00 1.40
3908 7475 7.979115 TTACACAAAGTTGCATTGACTAAAC 57.021 32.000 5.55 0.00 0.00 2.01
3972 7539 3.850740 GCACGGTAGTTTGCTGTAAAACC 60.851 47.826 2.97 2.97 40.26 3.27
3974 7541 4.751098 CACGGTAGTTTGCTGTAAAACCTA 59.249 41.667 9.42 0.00 40.26 3.08
4005 7572 7.721399 ACTTGACAAAGACTATCCTTGATGTTT 59.279 33.333 0.00 0.00 36.84 2.83
4010 7577 3.944015 AGACTATCCTTGATGTTTGCTGC 59.056 43.478 0.00 0.00 0.00 5.25
4088 7656 5.749596 TGTTGTTGTGACAATCTTAGTGG 57.250 39.130 0.00 0.00 46.63 4.00
4091 7659 5.029807 TGTTGTGACAATCTTAGTGGTCA 57.970 39.130 0.00 0.00 37.89 4.02
4096 7664 7.202016 TGTGACAATCTTAGTGGTCATTTTC 57.798 36.000 0.00 0.00 41.73 2.29
4098 7666 7.041167 TGTGACAATCTTAGTGGTCATTTTCTG 60.041 37.037 0.00 0.00 41.73 3.02
4131 7699 3.982516 TGATGACTCTTGGTAGTAGGCT 58.017 45.455 0.00 0.00 0.00 4.58
4168 7736 7.699812 ACACTCTTTCCTTTATAATACGACGTC 59.300 37.037 2.43 5.18 0.00 4.34
4208 7776 6.238402 GGTTCCAAAGAGAGTGTTCACTTTAC 60.238 42.308 6.91 2.80 40.69 2.01
4273 7842 4.976540 AGCTGTCTTGGTAGTAGGTTTT 57.023 40.909 0.00 0.00 0.00 2.43
4274 7843 4.642429 AGCTGTCTTGGTAGTAGGTTTTG 58.358 43.478 0.00 0.00 0.00 2.44
4302 7871 3.943671 TCCAAAAGGTTCTCTGAACCA 57.056 42.857 25.39 6.56 42.69 3.67
4311 7880 6.544928 AGGTTCTCTGAACCATTTGTTTTT 57.455 33.333 25.39 4.73 42.69 1.94
4461 8033 7.595819 TGTTCCTGTATTCAAATTTTGTCCT 57.404 32.000 8.89 0.00 0.00 3.85
4607 8180 8.933653 TGGGATTTTGAAAGATAGTTCCTTTTT 58.066 29.630 0.00 0.00 34.33 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.420725 TCAAGGCTCAGTAATACACATGT 57.579 39.130 0.00 0.00 0.00 3.21
1 2 4.813161 CCTCAAGGCTCAGTAATACACATG 59.187 45.833 0.00 0.00 0.00 3.21
2 3 4.141620 CCCTCAAGGCTCAGTAATACACAT 60.142 45.833 0.00 0.00 0.00 3.21
3 4 3.197766 CCCTCAAGGCTCAGTAATACACA 59.802 47.826 0.00 0.00 0.00 3.72
4 5 3.197983 ACCCTCAAGGCTCAGTAATACAC 59.802 47.826 0.00 0.00 40.58 2.90
6 7 3.451178 TCACCCTCAAGGCTCAGTAATAC 59.549 47.826 0.00 0.00 40.58 1.89
7 8 3.706594 CTCACCCTCAAGGCTCAGTAATA 59.293 47.826 0.00 0.00 40.58 0.98
8 9 2.503356 CTCACCCTCAAGGCTCAGTAAT 59.497 50.000 0.00 0.00 40.58 1.89
9 10 1.902508 CTCACCCTCAAGGCTCAGTAA 59.097 52.381 0.00 0.00 40.58 2.24
10 11 1.203187 ACTCACCCTCAAGGCTCAGTA 60.203 52.381 0.00 0.00 40.58 2.74
11 12 0.472734 ACTCACCCTCAAGGCTCAGT 60.473 55.000 0.00 0.00 40.58 3.41
12 13 1.561643 TACTCACCCTCAAGGCTCAG 58.438 55.000 0.00 0.00 40.58 3.35
13 14 2.111384 GATACTCACCCTCAAGGCTCA 58.889 52.381 0.00 0.00 40.58 4.26
14 15 1.067821 CGATACTCACCCTCAAGGCTC 59.932 57.143 0.00 0.00 40.58 4.70
15 16 1.115467 CGATACTCACCCTCAAGGCT 58.885 55.000 0.00 0.00 40.58 4.58
16 17 0.824759 ACGATACTCACCCTCAAGGC 59.175 55.000 0.00 0.00 40.58 4.35
17 18 4.730949 TTTACGATACTCACCCTCAAGG 57.269 45.455 0.00 0.00 43.78 3.61
18 19 7.262772 TGTAATTTACGATACTCACCCTCAAG 58.737 38.462 2.30 0.00 0.00 3.02
19 20 7.172868 TGTAATTTACGATACTCACCCTCAA 57.827 36.000 2.30 0.00 0.00 3.02
20 21 6.778834 TGTAATTTACGATACTCACCCTCA 57.221 37.500 2.30 0.00 0.00 3.86
21 22 9.924650 ATATTGTAATTTACGATACTCACCCTC 57.075 33.333 15.63 0.00 37.74 4.30
30 31 9.005777 GCCCTCCAAATATTGTAATTTACGATA 57.994 33.333 15.65 15.65 38.90 2.92
31 32 7.724061 AGCCCTCCAAATATTGTAATTTACGAT 59.276 33.333 12.77 12.77 36.73 3.73
32 33 7.057894 AGCCCTCCAAATATTGTAATTTACGA 58.942 34.615 0.00 0.00 0.00 3.43
33 34 7.272037 AGCCCTCCAAATATTGTAATTTACG 57.728 36.000 2.30 0.00 0.00 3.18
35 36 8.856103 GCTTAGCCCTCCAAATATTGTAATTTA 58.144 33.333 0.00 0.00 0.00 1.40
36 37 7.565029 AGCTTAGCCCTCCAAATATTGTAATTT 59.435 33.333 0.00 0.00 0.00 1.82
37 38 7.069344 AGCTTAGCCCTCCAAATATTGTAATT 58.931 34.615 0.00 0.00 0.00 1.40
38 39 6.614657 AGCTTAGCCCTCCAAATATTGTAAT 58.385 36.000 0.00 0.00 0.00 1.89
39 40 6.013554 AGCTTAGCCCTCCAAATATTGTAA 57.986 37.500 0.00 0.00 0.00 2.41
40 41 5.646692 AGCTTAGCCCTCCAAATATTGTA 57.353 39.130 0.00 0.00 0.00 2.41
41 42 4.526438 AGCTTAGCCCTCCAAATATTGT 57.474 40.909 0.00 0.00 0.00 2.71
42 43 7.231317 TCAATTAGCTTAGCCCTCCAAATATTG 59.769 37.037 0.00 0.00 0.00 1.90
43 44 7.231519 GTCAATTAGCTTAGCCCTCCAAATATT 59.768 37.037 0.00 0.00 0.00 1.28
44 45 6.717084 GTCAATTAGCTTAGCCCTCCAAATAT 59.283 38.462 0.00 0.00 0.00 1.28
45 46 6.062095 GTCAATTAGCTTAGCCCTCCAAATA 58.938 40.000 0.00 0.00 0.00 1.40
46 47 4.889995 GTCAATTAGCTTAGCCCTCCAAAT 59.110 41.667 0.00 0.00 0.00 2.32
47 48 4.270008 GTCAATTAGCTTAGCCCTCCAAA 58.730 43.478 0.00 0.00 0.00 3.28
48 49 3.681594 CGTCAATTAGCTTAGCCCTCCAA 60.682 47.826 0.00 0.00 0.00 3.53
49 50 2.158957 CGTCAATTAGCTTAGCCCTCCA 60.159 50.000 0.00 0.00 0.00 3.86
50 51 2.102588 TCGTCAATTAGCTTAGCCCTCC 59.897 50.000 0.00 0.00 0.00 4.30
51 52 3.181474 ACTCGTCAATTAGCTTAGCCCTC 60.181 47.826 0.00 0.00 0.00 4.30
52 53 2.766828 ACTCGTCAATTAGCTTAGCCCT 59.233 45.455 0.00 0.00 0.00 5.19
53 54 3.180891 ACTCGTCAATTAGCTTAGCCC 57.819 47.619 0.00 0.00 0.00 5.19
54 55 4.630069 TGAAACTCGTCAATTAGCTTAGCC 59.370 41.667 0.00 0.00 0.00 3.93
55 56 5.779806 TGAAACTCGTCAATTAGCTTAGC 57.220 39.130 0.00 0.00 0.00 3.09
56 57 7.064609 TCCAATGAAACTCGTCAATTAGCTTAG 59.935 37.037 0.00 0.00 0.00 2.18
57 58 6.876789 TCCAATGAAACTCGTCAATTAGCTTA 59.123 34.615 0.00 0.00 0.00 3.09
58 59 5.705441 TCCAATGAAACTCGTCAATTAGCTT 59.295 36.000 0.00 0.00 0.00 3.74
59 60 5.122396 GTCCAATGAAACTCGTCAATTAGCT 59.878 40.000 0.00 0.00 0.00 3.32
60 61 5.324697 GTCCAATGAAACTCGTCAATTAGC 58.675 41.667 0.00 0.00 0.00 3.09
61 62 5.347635 TCGTCCAATGAAACTCGTCAATTAG 59.652 40.000 0.00 0.00 0.00 1.73
62 63 5.231702 TCGTCCAATGAAACTCGTCAATTA 58.768 37.500 0.00 0.00 0.00 1.40
63 64 4.062293 TCGTCCAATGAAACTCGTCAATT 58.938 39.130 0.00 0.00 0.00 2.32
64 65 3.659786 TCGTCCAATGAAACTCGTCAAT 58.340 40.909 0.00 0.00 0.00 2.57
65 66 3.057019 CTCGTCCAATGAAACTCGTCAA 58.943 45.455 0.00 0.00 0.00 3.18
66 67 2.609491 CCTCGTCCAATGAAACTCGTCA 60.609 50.000 0.00 0.00 0.00 4.35
67 68 1.993370 CCTCGTCCAATGAAACTCGTC 59.007 52.381 0.00 0.00 0.00 4.20
68 69 1.939838 GCCTCGTCCAATGAAACTCGT 60.940 52.381 0.00 0.00 0.00 4.18
69 70 0.721718 GCCTCGTCCAATGAAACTCG 59.278 55.000 0.00 0.00 0.00 4.18
70 71 0.721718 CGCCTCGTCCAATGAAACTC 59.278 55.000 0.00 0.00 0.00 3.01
71 72 0.673644 CCGCCTCGTCCAATGAAACT 60.674 55.000 0.00 0.00 0.00 2.66
72 73 0.953960 ACCGCCTCGTCCAATGAAAC 60.954 55.000 0.00 0.00 0.00 2.78
73 74 0.250553 AACCGCCTCGTCCAATGAAA 60.251 50.000 0.00 0.00 0.00 2.69
74 75 0.250553 AAACCGCCTCGTCCAATGAA 60.251 50.000 0.00 0.00 0.00 2.57
75 76 0.609151 TAAACCGCCTCGTCCAATGA 59.391 50.000 0.00 0.00 0.00 2.57
76 77 0.725117 GTAAACCGCCTCGTCCAATG 59.275 55.000 0.00 0.00 0.00 2.82
77 78 0.392060 GGTAAACCGCCTCGTCCAAT 60.392 55.000 0.00 0.00 0.00 3.16
78 79 1.004679 GGTAAACCGCCTCGTCCAA 60.005 57.895 0.00 0.00 0.00 3.53
79 80 2.658422 GGTAAACCGCCTCGTCCA 59.342 61.111 0.00 0.00 0.00 4.02
80 81 1.322538 TAGGGTAAACCGCCTCGTCC 61.323 60.000 0.00 0.00 46.96 4.79
81 82 0.532115 TTAGGGTAAACCGCCTCGTC 59.468 55.000 0.00 0.00 46.96 4.20
82 83 1.134610 CATTAGGGTAAACCGCCTCGT 60.135 52.381 0.00 0.00 46.96 4.18
83 84 1.578583 CATTAGGGTAAACCGCCTCG 58.421 55.000 0.00 0.00 46.96 4.63
84 85 1.963172 CCATTAGGGTAAACCGCCTC 58.037 55.000 0.00 0.00 46.96 4.70
95 96 0.677288 TGCGATCGGTACCATTAGGG 59.323 55.000 18.30 0.00 44.81 3.53
96 97 2.519377 TTGCGATCGGTACCATTAGG 57.481 50.000 18.30 0.00 42.21 2.69
101 102 0.821517 ACAGATTGCGATCGGTACCA 59.178 50.000 17.04 2.85 38.64 3.25
120 121 3.447742 CTTGTCGTATCTGCACTGCATA 58.552 45.455 3.64 0.00 38.13 3.14
174 2781 0.249447 TGCACCATGTCGATCGATCC 60.249 55.000 22.50 10.03 0.00 3.36
206 2813 1.884926 GACGCACAGATGGCTAGCC 60.885 63.158 27.71 27.71 0.00 3.93
207 2814 2.233654 CGACGCACAGATGGCTAGC 61.234 63.158 6.04 6.04 0.00 3.42
208 2815 2.233654 GCGACGCACAGATGGCTAG 61.234 63.158 16.42 0.00 0.00 3.42
209 2816 2.202743 GCGACGCACAGATGGCTA 60.203 61.111 16.42 0.00 0.00 3.93
308 3026 9.226606 TCAGTTGACTAAAATGGTAATTAGGTG 57.773 33.333 0.00 0.00 34.59 4.00
321 3039 5.929992 CGGTCCATTACTCAGTTGACTAAAA 59.070 40.000 0.00 0.00 0.00 1.52
324 3042 4.157289 GTCGGTCCATTACTCAGTTGACTA 59.843 45.833 0.00 0.00 0.00 2.59
456 3203 1.632948 CTCGTCGACGTCACTGCCTA 61.633 60.000 34.40 13.41 40.80 3.93
464 3211 4.517703 CCTCGCCTCGTCGACGTC 62.518 72.222 34.40 23.09 40.80 4.34
614 3378 2.107366 GAGAGAGAGGTGGAAGAAGGG 58.893 57.143 0.00 0.00 0.00 3.95
937 3701 6.948886 ACCTCAAAACAGTAGTATGAGAGAGA 59.051 38.462 10.91 0.00 41.09 3.10
938 3702 7.032580 CACCTCAAAACAGTAGTATGAGAGAG 58.967 42.308 10.91 0.00 41.09 3.20
939 3703 6.493802 ACACCTCAAAACAGTAGTATGAGAGA 59.506 38.462 10.91 0.00 41.09 3.10
940 3704 6.692486 ACACCTCAAAACAGTAGTATGAGAG 58.308 40.000 10.91 0.00 41.09 3.20
945 3709 6.590292 CGATCAACACCTCAAAACAGTAGTAT 59.410 38.462 0.00 0.00 0.00 2.12
946 3710 5.924254 CGATCAACACCTCAAAACAGTAGTA 59.076 40.000 0.00 0.00 0.00 1.82
947 3711 4.750098 CGATCAACACCTCAAAACAGTAGT 59.250 41.667 0.00 0.00 0.00 2.73
949 3713 4.951254 TCGATCAACACCTCAAAACAGTA 58.049 39.130 0.00 0.00 0.00 2.74
952 3716 3.559655 CACTCGATCAACACCTCAAAACA 59.440 43.478 0.00 0.00 0.00 2.83
953 3717 3.058914 CCACTCGATCAACACCTCAAAAC 60.059 47.826 0.00 0.00 0.00 2.43
964 3728 3.583276 AACGGCGCCACTCGATCAA 62.583 57.895 28.98 0.00 41.67 2.57
1017 4098 2.496817 GAGCCTACCAGCACCTCG 59.503 66.667 0.00 0.00 34.23 4.63
1050 4152 1.451504 CTTCTGGTGGCAGTGGTGA 59.548 57.895 0.00 0.00 0.00 4.02
1107 4215 0.462047 GCAGACCATCAGTAACCGGG 60.462 60.000 6.32 0.00 0.00 5.73
1127 4235 1.906333 TCTGCTACGACCACCTGCA 60.906 57.895 0.00 0.00 0.00 4.41
1137 4248 2.048597 TTGCCCGTGTCTGCTACG 60.049 61.111 0.00 0.00 40.98 3.51
1142 4253 3.716006 CGTGCTTGCCCGTGTCTG 61.716 66.667 0.00 0.00 0.00 3.51
1278 4389 2.203938 TGGTGGGTGGTCCTCTCC 60.204 66.667 0.00 0.00 36.20 3.71
1310 4421 0.873054 CCGATGCAGATCAATGGAGC 59.127 55.000 0.00 0.00 0.00 4.70
1317 4431 1.005748 GGATCGCCGATGCAGATCA 60.006 57.895 14.01 0.00 43.26 2.92
1333 4447 1.227060 CTCGTGCAGCATGATCGGA 60.227 57.895 17.88 0.00 39.69 4.55
1389 4503 4.170062 CATGCACGCAAGCCGGAG 62.170 66.667 5.05 0.00 42.52 4.63
1394 4508 4.824166 CGAGGCATGCACGCAAGC 62.824 66.667 21.36 10.60 45.62 4.01
1442 4556 3.919386 CGTTGCGCACACACACGA 61.919 61.111 23.24 0.00 0.00 4.35
1443 4557 4.217111 ACGTTGCGCACACACACG 62.217 61.111 25.17 25.17 0.00 4.49
1444 4558 2.647481 CACGTTGCGCACACACAC 60.647 61.111 11.12 3.85 0.00 3.82
1445 4559 3.870422 CCACGTTGCGCACACACA 61.870 61.111 11.12 0.00 0.00 3.72
1515 4629 6.099845 ACCTATTTATTCCGATCTTCCACTGT 59.900 38.462 0.00 0.00 0.00 3.55
1517 4631 6.326583 TGACCTATTTATTCCGATCTTCCACT 59.673 38.462 0.00 0.00 0.00 4.00
1520 4634 8.622948 ATTTGACCTATTTATTCCGATCTTCC 57.377 34.615 0.00 0.00 0.00 3.46
1521 4635 9.884465 CAATTTGACCTATTTATTCCGATCTTC 57.116 33.333 0.00 0.00 0.00 2.87
1522 4636 8.352942 GCAATTTGACCTATTTATTCCGATCTT 58.647 33.333 0.00 0.00 0.00 2.40
1524 4638 7.084486 GGCAATTTGACCTATTTATTCCGATC 58.916 38.462 0.00 0.00 0.00 3.69
1526 4640 5.008217 CGGCAATTTGACCTATTTATTCCGA 59.992 40.000 0.00 0.00 33.21 4.55
1528 4642 4.982295 GCGGCAATTTGACCTATTTATTCC 59.018 41.667 0.00 0.00 0.00 3.01
1530 4644 4.649218 AGGCGGCAATTTGACCTATTTATT 59.351 37.500 13.08 0.00 0.00 1.40
1541 4655 2.986479 GTGTTCTTAAGGCGGCAATTTG 59.014 45.455 13.08 0.00 0.00 2.32
1547 4661 0.955905 TTTGGTGTTCTTAAGGCGGC 59.044 50.000 0.00 0.00 0.00 6.53
1552 4666 8.251750 TCATCGTTCTATTTGGTGTTCTTAAG 57.748 34.615 0.00 0.00 0.00 1.85
1553 4667 8.664798 CATCATCGTTCTATTTGGTGTTCTTAA 58.335 33.333 0.00 0.00 0.00 1.85
1559 4673 4.876107 GGACATCATCGTTCTATTTGGTGT 59.124 41.667 0.00 0.00 36.19 4.16
1560 4674 5.118990 AGGACATCATCGTTCTATTTGGTG 58.881 41.667 0.00 0.00 0.00 4.17
1562 4676 6.642950 GTCTAGGACATCATCGTTCTATTTGG 59.357 42.308 0.00 0.00 32.09 3.28
1569 4683 6.969828 AAAAAGTCTAGGACATCATCGTTC 57.030 37.500 0.52 0.00 34.60 3.95
1594 4708 2.859165 AGGACATCCTCTCGCAAAAA 57.141 45.000 0.00 0.00 44.77 1.94
1595 4709 3.096852 TCTAGGACATCCTCTCGCAAAA 58.903 45.455 2.97 0.00 44.77 2.44
1596 4710 2.427453 GTCTAGGACATCCTCTCGCAAA 59.573 50.000 2.97 0.00 44.77 3.68
1597 4711 2.025155 GTCTAGGACATCCTCTCGCAA 58.975 52.381 2.97 0.00 44.77 4.85
1598 4712 1.213182 AGTCTAGGACATCCTCTCGCA 59.787 52.381 2.97 0.00 44.77 5.10
1599 4713 1.975660 AGTCTAGGACATCCTCTCGC 58.024 55.000 2.97 0.00 44.77 5.03
1600 4714 2.546368 CGAAGTCTAGGACATCCTCTCG 59.454 54.545 2.97 3.28 44.77 4.04
1601 4715 2.882137 CCGAAGTCTAGGACATCCTCTC 59.118 54.545 2.97 0.00 44.77 3.20
1613 4727 3.022406 GGTTCTAGCTTCCCGAAGTCTA 58.978 50.000 6.34 7.19 40.45 2.59
1615 4729 1.134759 GGGTTCTAGCTTCCCGAAGTC 60.135 57.143 6.34 0.00 40.45 3.01
1629 4744 4.082125 CAGTTCTATTTTGGCAGGGTTCT 58.918 43.478 0.00 0.00 0.00 3.01
1632 4747 3.525800 ACAGTTCTATTTTGGCAGGGT 57.474 42.857 0.00 0.00 0.00 4.34
1688 5118 9.307121 CATTAACTCACTTAGTCATTCTACCTG 57.693 37.037 0.00 0.00 37.50 4.00
1696 5162 9.178758 GGAAAATCCATTAACTCACTTAGTCAT 57.821 33.333 0.00 0.00 35.07 3.06
1715 5181 9.611284 GCATTAATCCTTTTGTTTTGGAAAATC 57.389 29.630 0.00 0.00 33.20 2.17
1733 5199 5.432157 CGTAATCACGTGGAAGCATTAATC 58.568 41.667 17.00 0.92 43.31 1.75
1734 5200 5.403897 CGTAATCACGTGGAAGCATTAAT 57.596 39.130 17.00 0.00 43.31 1.40
1769 5236 8.979574 GTTAGACGATCTTCTTTTGAGAGAAAA 58.020 33.333 7.08 0.00 35.38 2.29
1782 5249 4.324936 GTGCAGAGTTGTTAGACGATCTTC 59.675 45.833 0.00 0.00 0.00 2.87
1789 5264 4.372656 AGAAGTGTGCAGAGTTGTTAGAC 58.627 43.478 8.93 0.00 0.00 2.59
1800 5275 4.974275 CACAATTTGAGAAGAAGTGTGCAG 59.026 41.667 2.79 0.00 43.24 4.41
1809 5284 8.378565 AGAGAGGAATTACACAATTTGAGAAGA 58.621 33.333 2.79 0.00 34.44 2.87
1816 5291 7.255942 CCAACCAAGAGAGGAATTACACAATTT 60.256 37.037 0.00 0.00 34.44 1.82
1823 5298 3.956744 AGCCAACCAAGAGAGGAATTAC 58.043 45.455 0.00 0.00 0.00 1.89
1826 5301 3.330701 TGTTAGCCAACCAAGAGAGGAAT 59.669 43.478 0.00 0.00 33.41 3.01
1860 5343 4.208746 CTGGTACCCCAACAAAACTACAA 58.791 43.478 10.07 0.00 41.27 2.41
1916 5399 4.283212 TGTATGGCCTTTTCCCAGAAAAAG 59.717 41.667 3.32 2.22 43.02 2.27
1922 5405 7.781324 ATAAATATGTATGGCCTTTTCCCAG 57.219 36.000 3.32 0.00 35.48 4.45
1923 5406 9.836179 ATAATAAATATGTATGGCCTTTTCCCA 57.164 29.630 3.32 0.00 36.66 4.37
2134 5638 5.810587 ACATTTGCATGAGAAATCAATCTGC 59.189 36.000 0.00 0.00 34.11 4.26
2137 5641 8.025243 ACAAACATTTGCATGAGAAATCAATC 57.975 30.769 0.00 0.00 41.79 2.67
2138 5642 7.118680 GGACAAACATTTGCATGAGAAATCAAT 59.881 33.333 0.00 0.00 41.79 2.57
2195 5699 2.969821 TGGGCCATCACACTAAAGTT 57.030 45.000 0.00 0.00 0.00 2.66
2239 5743 0.391130 CAATGAAAGGGTCGCCGAGA 60.391 55.000 0.00 0.00 0.00 4.04
2257 5761 1.211969 GACGCCGTAGTTGCTCTCA 59.788 57.895 0.00 0.00 0.00 3.27
2293 5797 1.893808 CCAGTCAAGCACGGCAACT 60.894 57.895 0.00 0.00 0.00 3.16
2305 5809 3.842925 GAGGCGGGCAAACCAGTCA 62.843 63.158 3.78 0.00 38.36 3.41
2308 5812 3.058160 CAGAGGCGGGCAAACCAG 61.058 66.667 3.78 0.00 40.22 4.00
2338 5842 4.935808 GTGATGTATCCCCAATATTCGTCC 59.064 45.833 0.00 0.00 0.00 4.79
2365 5869 1.896660 GTTCCCTTCAGTGCCGCAA 60.897 57.895 0.00 0.00 0.00 4.85
2374 5878 2.890766 GCCGTGGAGGTTCCCTTCA 61.891 63.158 0.00 0.00 43.70 3.02
2389 5893 0.314302 CTGACCCGACTAATAGGCCG 59.686 60.000 0.00 0.00 0.00 6.13
2406 5910 9.707957 AGATTAAGGGATATCTGGTAGATACTG 57.292 37.037 2.05 0.00 39.76 2.74
2415 5919 7.855375 TGCAAGATAGATTAAGGGATATCTGG 58.145 38.462 2.05 0.00 35.64 3.86
2422 5926 9.866655 AAAATGTATGCAAGATAGATTAAGGGA 57.133 29.630 0.00 0.00 0.00 4.20
2443 5947 9.378597 GATACATTCTCGATCATGTGAAAAATG 57.621 33.333 16.29 5.83 35.24 2.32
2444 5950 9.334947 AGATACATTCTCGATCATGTGAAAAAT 57.665 29.630 16.29 5.01 35.24 1.82
2464 5970 5.159273 TCACAACCAGTATGCAAGATACA 57.841 39.130 0.00 0.00 31.97 2.29
2479 6010 7.514721 TCCCTCCTACATATAAAATCACAACC 58.485 38.462 0.00 0.00 0.00 3.77
2496 6028 2.915869 TCTGGAAAAAGCTCCCTCCTA 58.084 47.619 8.82 0.00 34.22 2.94
2514 6046 3.357203 AGACGCGTATATGATCCCATCT 58.643 45.455 13.97 0.00 34.31 2.90
2556 6088 2.409948 ACATCCTAGCTGCCTTGAAC 57.590 50.000 0.00 0.00 0.00 3.18
2586 6120 2.239400 AGAGTGTCGATCTCCACACAA 58.761 47.619 17.06 0.00 44.60 3.33
2608 6142 3.529533 CGCAGTTCATCTCTCCAGAAAT 58.470 45.455 0.00 0.00 30.24 2.17
2728 6262 4.614284 CACGTAAGCAAAGCATTTTCTGAG 59.386 41.667 0.00 0.00 45.62 3.35
2732 6266 4.537015 AGACACGTAAGCAAAGCATTTTC 58.463 39.130 0.00 0.00 45.62 2.29
2748 6283 8.282592 TCAAAATCAACAATAAAGAGAGACACG 58.717 33.333 0.00 0.00 0.00 4.49
2847 6386 6.207810 ACCCACATTTTTCAAGCGTTCTTATA 59.792 34.615 0.00 0.00 0.00 0.98
2973 6512 4.700268 TGTGGCATGTGCTAACTAAATG 57.300 40.909 4.84 0.00 41.70 2.32
2979 6518 2.034558 AGTTGTTGTGGCATGTGCTAAC 59.965 45.455 4.84 8.62 41.70 2.34
3025 6577 9.489084 AGGAAAATAAAGAAAATGTTGGTTAGC 57.511 29.630 0.00 0.00 0.00 3.09
3032 6584 9.088987 TGCCTAGAGGAAAATAAAGAAAATGTT 57.911 29.630 0.00 0.00 37.39 2.71
3035 6587 7.673926 TGGTGCCTAGAGGAAAATAAAGAAAAT 59.326 33.333 0.00 0.00 37.39 1.82
3082 6634 1.723542 GATATGCTCACGCTTCCGATG 59.276 52.381 0.00 0.00 38.29 3.84
3263 6815 6.489603 TGCCTCTATATCCCTTTTTGTTCAA 58.510 36.000 0.00 0.00 0.00 2.69
3277 6829 3.055530 CCTCTTTGCGGATGCCTCTATAT 60.056 47.826 0.00 0.00 41.78 0.86
3341 6893 0.976073 CTCACTCCCGCCTCCCTTAA 60.976 60.000 0.00 0.00 0.00 1.85
3343 6895 2.685380 CTCACTCCCGCCTCCCTT 60.685 66.667 0.00 0.00 0.00 3.95
3403 6955 0.670546 CGAATGCCTCGTCTTGTGGT 60.671 55.000 0.00 0.00 42.89 4.16
3502 7054 5.111989 CCGATGAGCTCTTTGATAAAGTCA 58.888 41.667 16.19 0.00 39.52 3.41
3509 7061 3.176552 CTCACCGATGAGCTCTTTGAT 57.823 47.619 16.19 0.00 45.83 2.57
3526 7078 2.664398 TGCCAGCGCAATCTCTCA 59.336 55.556 11.47 0.00 43.74 3.27
3669 7221 9.010029 TGTGCCCTTAAGAACTCTAATTTTTAG 57.990 33.333 3.36 0.00 0.00 1.85
3882 7448 9.030301 GTTTAGTCAATGCAACTTTGTGTAATT 57.970 29.630 0.00 0.00 0.00 1.40
3883 7449 8.194104 TGTTTAGTCAATGCAACTTTGTGTAAT 58.806 29.630 0.00 0.00 0.00 1.89
3925 7492 1.538687 AACCAAGCATCAGGCCAAGC 61.539 55.000 5.01 2.59 46.50 4.01
3972 7539 6.322712 AGGATAGTCTTTGTCAAGTAGCCTAG 59.677 42.308 0.00 0.00 29.66 3.02
3974 7541 5.026790 AGGATAGTCTTTGTCAAGTAGCCT 58.973 41.667 0.00 0.00 27.54 4.58
4072 7640 6.998074 AGAAAATGACCACTAAGATTGTCACA 59.002 34.615 0.00 0.00 40.24 3.58
4088 7656 5.984926 TCAAATGCCAAAGACAGAAAATGAC 59.015 36.000 0.00 0.00 0.00 3.06
4091 7659 6.647895 GTCATCAAATGCCAAAGACAGAAAAT 59.352 34.615 0.00 0.00 0.00 1.82
4096 7664 4.458295 AGAGTCATCAAATGCCAAAGACAG 59.542 41.667 0.00 0.00 0.00 3.51
4098 7666 5.159209 CAAGAGTCATCAAATGCCAAAGAC 58.841 41.667 0.00 0.00 0.00 3.01
4168 7736 3.869065 TGGAACCATAAGAAAGCTACGG 58.131 45.455 0.00 0.00 0.00 4.02
4246 7815 5.103601 ACCTACTACCAAGACAGCTACCTAT 60.104 44.000 0.00 0.00 0.00 2.57
4249 7818 3.363627 ACCTACTACCAAGACAGCTACC 58.636 50.000 0.00 0.00 0.00 3.18
4256 7825 4.628963 TCCCAAAACCTACTACCAAGAC 57.371 45.455 0.00 0.00 0.00 3.01
4311 7880 7.611213 AAGAAACAGAAACGAGAGAAAAGAA 57.389 32.000 0.00 0.00 0.00 2.52
4437 8008 7.595819 AGGACAAAATTTGAATACAGGAACA 57.404 32.000 13.19 0.00 0.00 3.18
4440 8011 9.527157 TGATTAGGACAAAATTTGAATACAGGA 57.473 29.630 13.19 0.00 0.00 3.86
4579 8152 8.670521 AAGGAACTATCTTTCAAAATCCCAAT 57.329 30.769 0.00 0.00 38.49 3.16


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

AutoCloner maintained by Alex Coulton.