Multiple sequence alignment - TraesCS6A01G333900

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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 TraesCS6A01G333900 chr6A 100.000 4881 0 0 1 4881 564881756 564886636 0.000000e+00 9014
1 TraesCS6A01G333900 chr6A 90.438 251 20 3 986 1236 146494334 146494088 1.310000e-85 327
2 TraesCS6A01G333900 chr6D 93.191 3701 121 45 499 4099 422078126 422081795 0.000000e+00 5317
3 TraesCS6A01G333900 chr6D 94.602 352 14 4 153 502 422077751 422078099 1.550000e-149 540
4 TraesCS6A01G333900 chr6D 84.358 537 69 10 4357 4881 422081791 422082324 3.370000e-141 512
5 TraesCS6A01G333900 chr6D 91.667 168 9 5 1 167 293936930 293936767 1.370000e-55 228
6 TraesCS6A01G333900 chr6B 92.817 3592 156 50 584 4099 636392315 636395880 0.000000e+00 5110
7 TraesCS6A01G333900 chr6B 85.054 368 45 9 4357 4716 636395876 636396241 2.780000e-97 366
8 TraesCS6A01G333900 chr6B 90.837 251 19 2 986 1236 202352779 202353025 2.820000e-87 333
9 TraesCS6A01G333900 chr7A 94.717 265 13 1 4098 4361 736532403 736532139 1.260000e-110 411
10 TraesCS6A01G333900 chr7A 94.007 267 15 1 4095 4360 367140300 367140034 2.120000e-108 403
11 TraesCS6A01G333900 chr7A 93.657 268 16 1 4095 4361 589833216 589833483 2.740000e-107 399
12 TraesCS6A01G333900 chr4A 94.677 263 12 2 4098 4358 689648687 689648949 1.640000e-109 407
13 TraesCS6A01G333900 chr4A 93.631 157 7 3 1 155 32117180 32117025 1.060000e-56 231
14 TraesCS6A01G333900 chr4A 93.590 156 8 2 1 155 683963580 683963426 1.060000e-56 231
15 TraesCS6A01G333900 chr3A 94.052 269 15 1 4098 4365 726454341 726454073 1.640000e-109 407
16 TraesCS6A01G333900 chr3A 93.985 266 15 1 4093 4357 198424654 198424389 7.610000e-108 401
17 TraesCS6A01G333900 chr3A 92.527 281 17 4 4093 4370 545089969 545090248 2.740000e-107 399
18 TraesCS6A01G333900 chr1A 94.340 265 15 0 4096 4360 505332230 505331966 1.640000e-109 407
19 TraesCS6A01G333900 chr1A 92.800 125 8 1 1305 1429 565149774 565149897 3.880000e-41 180
20 TraesCS6A01G333900 chr5A 93.066 274 15 4 4087 4358 347015711 347015982 9.840000e-107 398
21 TraesCS6A01G333900 chr5A 94.400 125 5 2 1305 1429 137045045 137044923 1.790000e-44 191
22 TraesCS6A01G333900 chr1D 93.204 206 14 0 986 1191 414710838 414711043 2.210000e-78 303
23 TraesCS6A01G333900 chr1D 92.233 206 16 0 986 1191 428617769 428617564 4.780000e-75 292
24 TraesCS6A01G333900 chr1D 95.200 125 5 1 1305 1429 414711078 414711201 3.850000e-46 196
25 TraesCS6A01G333900 chr1D 95.200 125 5 1 1305 1429 428617529 428617406 3.850000e-46 196
26 TraesCS6A01G333900 chr3D 92.718 206 15 0 986 1191 572506362 572506157 1.030000e-76 298
27 TraesCS6A01G333900 chr3D 93.590 156 8 2 1 155 373600125 373600279 1.060000e-56 231
28 TraesCS6A01G333900 chr3D 93.038 158 9 2 1 157 603703322 603703166 3.800000e-56 230
29 TraesCS6A01G333900 chr3D 94.400 125 6 1 1305 1429 572506122 572505999 1.790000e-44 191
30 TraesCS6A01G333900 chr7D 92.233 206 16 0 986 1191 69450024 69449819 4.780000e-75 292
31 TraesCS6A01G333900 chr7D 94.231 156 8 1 1 156 439780623 439780777 2.270000e-58 237
32 TraesCS6A01G333900 chr7D 95.200 125 5 1 1305 1429 69449784 69449661 3.850000e-46 196
33 TraesCS6A01G333900 chr7B 84.375 256 23 10 986 1236 747327498 747327255 8.170000e-58 235
34 TraesCS6A01G333900 chr1B 93.631 157 8 2 1 156 212061697 212061542 2.940000e-57 233
35 TraesCS6A01G333900 chr1B 89.714 175 13 4 1 173 588156755 588156926 8.230000e-53 219
36 TraesCS6A01G333900 chr5D 93.590 156 8 2 1 155 126262795 126262949 1.060000e-56 231
37 TraesCS6A01G333900 chr5B 92.800 125 8 1 1305 1429 262568193 262568070 3.880000e-41 180


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 TraesCS6A01G333900 chr6A 564881756 564886636 4880 False 9014 9014 100.0000 1 4881 1 chr6A.!!$F1 4880
1 TraesCS6A01G333900 chr6D 422077751 422082324 4573 False 2123 5317 90.7170 153 4881 3 chr6D.!!$F1 4728
2 TraesCS6A01G333900 chr6B 636392315 636396241 3926 False 2738 5110 88.9355 584 4716 2 chr6B.!!$F2 4132

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
676 709 0.107459 CTGCCTGAGCCCTAGTTTCC 60.107 60.0 0.0 0.0 38.69 3.13 F
766 811 0.945813 TCTTGGCAAACGTAAACGGG 59.054 50.0 7.5 0.0 44.95 5.28 F
2281 2437 0.043053 CGAACTGAAGCGTGTGTGTG 60.043 55.0 0.0 0.0 0.00 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1672 1745 0.107312 CTCCCCACTGATTCTGCCAG 60.107 60.000 0.00 0.00 37.64 4.85 R
2670 2826 0.317799 GTCACCACCAATGCAATGCA 59.682 50.000 11.44 11.44 44.86 3.96 R
4058 4219 1.404583 CCCCTGTAACGTAACCGGAAG 60.405 57.143 9.46 0.00 38.78 3.46 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
29 30 9.778741 AATATTATCAGATACACCATGAAACGT 57.221 29.630 0.00 0.00 0.00 3.99
32 33 9.778741 ATTATCAGATACACCATGAAACGTATT 57.221 29.630 0.00 0.00 0.00 1.89
33 34 9.607988 TTATCAGATACACCATGAAACGTATTT 57.392 29.630 0.00 0.00 0.00 1.40
34 35 7.915293 TCAGATACACCATGAAACGTATTTT 57.085 32.000 0.00 0.00 0.00 1.82
35 36 7.970384 TCAGATACACCATGAAACGTATTTTC 58.030 34.615 0.00 0.00 43.63 2.29
115 116 6.190954 ACTTTGTGTAGTTTGACTTTGACC 57.809 37.500 0.00 0.00 0.00 4.02
116 117 5.708230 ACTTTGTGTAGTTTGACTTTGACCA 59.292 36.000 0.00 0.00 0.00 4.02
117 118 6.207810 ACTTTGTGTAGTTTGACTTTGACCAA 59.792 34.615 0.00 0.00 0.00 3.67
118 119 6.576662 TTGTGTAGTTTGACTTTGACCAAA 57.423 33.333 0.00 0.00 0.00 3.28
119 120 6.767524 TGTGTAGTTTGACTTTGACCAAAT 57.232 33.333 0.00 0.00 35.14 2.32
120 121 7.164230 TGTGTAGTTTGACTTTGACCAAATT 57.836 32.000 0.00 0.00 35.14 1.82
121 122 7.607250 TGTGTAGTTTGACTTTGACCAAATTT 58.393 30.769 0.00 0.00 35.14 1.82
122 123 8.091449 TGTGTAGTTTGACTTTGACCAAATTTT 58.909 29.630 0.00 0.00 35.14 1.82
123 124 9.575783 GTGTAGTTTGACTTTGACCAAATTTTA 57.424 29.630 0.00 0.00 35.14 1.52
129 130 9.770097 TTTGACTTTGACCAAATTTTATATGCA 57.230 25.926 0.00 0.00 0.00 3.96
130 131 9.770097 TTGACTTTGACCAAATTTTATATGCAA 57.230 25.926 0.00 0.00 0.00 4.08
131 132 9.770097 TGACTTTGACCAAATTTTATATGCAAA 57.230 25.926 0.00 0.00 0.00 3.68
133 134 9.777297 ACTTTGACCAAATTTTATATGCAAAGT 57.223 25.926 16.96 16.96 44.45 2.66
173 174 5.850128 GGAGTATGACTACGTATACTTTGCG 59.150 44.000 9.49 0.00 39.52 4.85
193 194 0.467804 ACAAAATGGTTGGGTGCACC 59.532 50.000 28.57 28.57 40.81 5.01
212 213 4.458989 GCACCATCCAATACAGAAGAAACA 59.541 41.667 0.00 0.00 0.00 2.83
270 272 2.871096 TGGTGGCGTTTAAGAGGATT 57.129 45.000 0.00 0.00 0.00 3.01
283 285 7.118680 CGTTTAAGAGGATTTAGCAAACCACTA 59.881 37.037 0.00 0.00 0.00 2.74
379 381 6.928492 GCATCCCTCATTTTTGTTTGTAGAAA 59.072 34.615 0.00 0.00 0.00 2.52
380 382 7.095649 GCATCCCTCATTTTTGTTTGTAGAAAC 60.096 37.037 8.49 8.49 41.72 2.78
385 387 7.700656 CCTCATTTTTGTTTGTAGAAACGTTCT 59.299 33.333 10.55 3.32 43.92 3.01
462 464 5.106475 TGTCCGAAATTACAATTGTAGGTGC 60.106 40.000 17.36 8.15 0.00 5.01
638 670 2.048503 GCGACTTAGCCGTGGTGT 60.049 61.111 0.00 0.00 0.00 4.16
639 671 1.213537 GCGACTTAGCCGTGGTGTA 59.786 57.895 0.00 0.00 0.00 2.90
655 687 6.594159 CCGTGGTGTATAGAAATCTCAAAACT 59.406 38.462 0.00 0.00 0.00 2.66
658 691 7.119846 GTGGTGTATAGAAATCTCAAAACTGCT 59.880 37.037 0.00 0.00 0.00 4.24
676 709 0.107459 CTGCCTGAGCCCTAGTTTCC 60.107 60.000 0.00 0.00 38.69 3.13
679 712 1.950954 GCCTGAGCCCTAGTTTCCAAC 60.951 57.143 0.00 0.00 0.00 3.77
685 718 4.103469 TGAGCCCTAGTTTCCAACTGTTAA 59.897 41.667 0.00 0.00 42.84 2.01
686 719 4.395625 AGCCCTAGTTTCCAACTGTTAAC 58.604 43.478 0.00 0.00 42.84 2.01
687 720 3.504906 GCCCTAGTTTCCAACTGTTAACC 59.495 47.826 2.48 0.00 42.84 2.85
688 721 4.721132 CCCTAGTTTCCAACTGTTAACCA 58.279 43.478 2.48 0.00 42.84 3.67
690 723 4.760204 CCTAGTTTCCAACTGTTAACCAGG 59.240 45.833 2.48 5.25 46.06 4.45
691 724 4.513406 AGTTTCCAACTGTTAACCAGGA 57.487 40.909 2.48 2.46 46.06 3.86
732 777 5.712917 TGATAAACTTCCCATTTTACGCCTT 59.287 36.000 0.00 0.00 0.00 4.35
766 811 0.945813 TCTTGGCAAACGTAAACGGG 59.054 50.000 7.50 0.00 44.95 5.28
929 974 3.364441 CACGCACCACACCCATGG 61.364 66.667 4.14 4.14 46.10 3.66
1003 1072 3.367743 CACAAGCAGCGGCCATGT 61.368 61.111 4.82 8.67 42.56 3.21
1430 1499 2.448542 TATGCCCCTCCCTCTGCC 60.449 66.667 0.00 0.00 0.00 4.85
1456 1525 2.097466 ACCATCGCAAAATCCATCGTTC 59.903 45.455 0.00 0.00 0.00 3.95
1494 1564 3.045601 TCTGTGCTTCAGCCTTTCTAC 57.954 47.619 0.00 0.00 43.32 2.59
1552 1623 3.645884 CATGCTCCCAAGTTTTTGTGAG 58.354 45.455 0.00 0.00 40.48 3.51
1609 1680 1.670811 CATGGGGAATGAACGTACTGC 59.329 52.381 0.00 0.00 38.72 4.40
1672 1745 4.742012 TCCTCCTAACCTCTACATGATCC 58.258 47.826 0.00 0.00 0.00 3.36
1689 1762 1.077212 CCTGGCAGAATCAGTGGGG 60.077 63.158 17.94 0.00 0.00 4.96
1726 1799 1.501169 TCTGCATGCATATCGAACCG 58.499 50.000 22.97 6.12 0.00 4.44
1748 1843 8.976986 ACCGTATTAGACTACAAGTTTTACTG 57.023 34.615 0.00 0.00 0.00 2.74
1750 1845 7.009907 CCGTATTAGACTACAAGTTTTACTGCC 59.990 40.741 0.00 0.00 0.00 4.85
1834 1946 1.354337 CTGTGATCCAACCGTCGCAG 61.354 60.000 2.08 2.08 43.81 5.18
1947 2059 4.221041 GGACTAGTCTGGGGTCATATTAGC 59.779 50.000 21.88 0.00 0.00 3.09
1951 2063 7.073854 ACTAGTCTGGGGTCATATTAGCTTTA 58.926 38.462 0.00 0.00 0.00 1.85
1985 2097 4.260538 CGGTATGTGGTACTAGTCGACTTC 60.261 50.000 25.44 11.67 33.64 3.01
1997 2110 7.040473 ACTAGTCGACTTCCTATTGGTTATG 57.960 40.000 25.44 0.00 34.23 1.90
2056 2169 2.802247 GGTGAAATTTGTTCCTTGCTGC 59.198 45.455 0.00 0.00 0.00 5.25
2060 2173 3.775261 AATTTGTTCCTTGCTGCCAAT 57.225 38.095 0.00 0.00 0.00 3.16
2085 2201 1.269998 ACAACAGAGTAGACCGAGCAC 59.730 52.381 0.00 0.00 0.00 4.40
2126 2250 4.218200 TGGCTTTTTATCAGACACACATGG 59.782 41.667 0.00 0.00 0.00 3.66
2186 2312 2.046292 CCCAAACCAGTGGTTCCAAAT 58.954 47.619 27.53 9.23 46.20 2.32
2193 2319 2.553904 CCAGTGGTTCCAAATCTGCTCT 60.554 50.000 0.00 0.00 0.00 4.09
2223 2363 2.589014 CATTCCTGCAAAAAGAGCGAC 58.411 47.619 0.00 0.00 33.85 5.19
2241 2381 3.365969 GCGACACATTTTTCTTACTGGGG 60.366 47.826 0.00 0.00 0.00 4.96
2249 2389 0.770557 TTCTTACTGGGGCCCACTGT 60.771 55.000 24.76 21.96 0.00 3.55
2281 2437 0.043053 CGAACTGAAGCGTGTGTGTG 60.043 55.000 0.00 0.00 0.00 3.82
2282 2438 1.006832 GAACTGAAGCGTGTGTGTGT 58.993 50.000 0.00 0.00 0.00 3.72
2283 2439 0.726827 AACTGAAGCGTGTGTGTGTG 59.273 50.000 0.00 0.00 0.00 3.82
2284 2440 1.010797 CTGAAGCGTGTGTGTGTGC 60.011 57.895 0.00 0.00 0.00 4.57
2670 2826 2.771089 ACGTCATGTTCATCTTGCACT 58.229 42.857 0.00 0.00 0.00 4.40
2708 2864 1.375396 CACGGTCGAGGATTGCCAA 60.375 57.895 0.00 0.00 36.29 4.52
2745 2901 1.135972 GCTGCCGTGTTATCTTGTGTG 60.136 52.381 0.00 0.00 0.00 3.82
2810 2966 2.184322 CTGTACGAGCACCCGCAT 59.816 61.111 0.00 0.00 42.27 4.73
3059 3215 1.218316 CGTAAGCTCCTCCCACACC 59.782 63.158 0.00 0.00 0.00 4.16
3079 3235 1.323534 CCTCGAAACGAAACGGCATAG 59.676 52.381 0.00 0.00 34.74 2.23
3095 3251 2.874701 GCATAGATCTTGGTTGATGCGT 59.125 45.455 0.00 0.00 31.33 5.24
3096 3252 4.058124 GCATAGATCTTGGTTGATGCGTA 58.942 43.478 0.00 0.00 31.33 4.42
3239 3395 2.493675 CTGATCGACAAGAAGTGGGAGA 59.506 50.000 0.00 0.00 0.00 3.71
3244 3400 1.122019 ACAAGAAGTGGGAGAGGCGT 61.122 55.000 0.00 0.00 0.00 5.68
4058 4219 0.591659 GTTGTCGGAGCCCAAAGTTC 59.408 55.000 0.00 0.00 0.00 3.01
4076 4237 2.989166 GTTCTTCCGGTTACGTTACAGG 59.011 50.000 16.36 16.36 38.78 4.00
4099 4260 7.121759 CAGGGGATGATTGAATTGGTGATATAC 59.878 40.741 0.00 0.00 0.00 1.47
4100 4261 7.018952 AGGGGATGATTGAATTGGTGATATACT 59.981 37.037 0.00 0.00 0.00 2.12
4102 4263 8.734386 GGGATGATTGAATTGGTGATATACTTC 58.266 37.037 0.00 0.00 0.00 3.01
4103 4264 8.734386 GGATGATTGAATTGGTGATATACTTCC 58.266 37.037 0.00 0.00 0.00 3.46
4104 4265 9.512588 GATGATTGAATTGGTGATATACTTCCT 57.487 33.333 0.00 0.00 0.00 3.36
4105 4266 8.908786 TGATTGAATTGGTGATATACTTCCTC 57.091 34.615 0.00 0.00 0.00 3.71
4106 4267 7.939039 TGATTGAATTGGTGATATACTTCCTCC 59.061 37.037 0.00 0.00 0.00 4.30
4107 4268 6.823286 TGAATTGGTGATATACTTCCTCCA 57.177 37.500 0.00 0.00 0.00 3.86
4108 4269 6.830912 TGAATTGGTGATATACTTCCTCCAG 58.169 40.000 0.00 0.00 0.00 3.86
4109 4270 6.386927 TGAATTGGTGATATACTTCCTCCAGT 59.613 38.462 0.00 0.00 0.00 4.00
4110 4271 5.871396 TTGGTGATATACTTCCTCCAGTC 57.129 43.478 0.00 0.00 0.00 3.51
4111 4272 5.144159 TGGTGATATACTTCCTCCAGTCT 57.856 43.478 0.00 0.00 0.00 3.24
4112 4273 5.529289 TGGTGATATACTTCCTCCAGTCTT 58.471 41.667 0.00 0.00 0.00 3.01
4113 4274 5.964477 TGGTGATATACTTCCTCCAGTCTTT 59.036 40.000 0.00 0.00 0.00 2.52
4114 4275 6.443849 TGGTGATATACTTCCTCCAGTCTTTT 59.556 38.462 0.00 0.00 0.00 2.27
4115 4276 7.037586 TGGTGATATACTTCCTCCAGTCTTTTT 60.038 37.037 0.00 0.00 0.00 1.94
4140 4301 9.594478 TTTAGTTCGCATATAAGATTTGACTGA 57.406 29.630 0.00 0.00 0.00 3.41
4141 4302 9.594478 TTAGTTCGCATATAAGATTTGACTGAA 57.406 29.630 0.00 0.00 0.00 3.02
4142 4303 8.136057 AGTTCGCATATAAGATTTGACTGAAG 57.864 34.615 0.00 0.00 0.00 3.02
4143 4304 7.766278 AGTTCGCATATAAGATTTGACTGAAGT 59.234 33.333 0.00 0.00 0.00 3.01
4144 4305 7.700322 TCGCATATAAGATTTGACTGAAGTC 57.300 36.000 3.41 3.41 44.97 3.01
4157 4318 5.196809 GACTGAAGTCAAGCATCGTAAAG 57.803 43.478 5.58 0.00 44.18 1.85
4158 4319 4.632153 ACTGAAGTCAAGCATCGTAAAGT 58.368 39.130 0.00 0.00 0.00 2.66
4159 4320 5.057149 ACTGAAGTCAAGCATCGTAAAGTT 58.943 37.500 0.00 0.00 0.00 2.66
4160 4321 5.527582 ACTGAAGTCAAGCATCGTAAAGTTT 59.472 36.000 0.00 0.00 0.00 2.66
4161 4322 5.747565 TGAAGTCAAGCATCGTAAAGTTTG 58.252 37.500 0.00 0.00 0.00 2.93
4162 4323 5.525745 TGAAGTCAAGCATCGTAAAGTTTGA 59.474 36.000 0.00 0.00 0.00 2.69
4163 4324 5.344207 AGTCAAGCATCGTAAAGTTTGAC 57.656 39.130 12.26 12.26 42.72 3.18
4164 4325 4.213482 AGTCAAGCATCGTAAAGTTTGACC 59.787 41.667 15.26 2.61 43.15 4.02
4165 4326 4.024387 GTCAAGCATCGTAAAGTTTGACCA 60.024 41.667 9.91 0.00 38.79 4.02
4166 4327 4.576873 TCAAGCATCGTAAAGTTTGACCAA 59.423 37.500 0.00 0.00 0.00 3.67
4167 4328 4.483476 AGCATCGTAAAGTTTGACCAAC 57.517 40.909 0.00 0.00 35.32 3.77
4235 4396 9.896645 ATCAATAGATGTGTCATGACTTAAAGT 57.103 29.630 25.55 9.39 31.91 2.66
4236 4397 9.725019 TCAATAGATGTGTCATGACTTAAAGTT 57.275 29.630 25.55 10.34 0.00 2.66
4239 4400 9.725019 ATAGATGTGTCATGACTTAAAGTTTCA 57.275 29.630 25.55 11.05 0.00 2.69
4240 4401 8.627208 AGATGTGTCATGACTTAAAGTTTCAT 57.373 30.769 25.55 14.42 0.00 2.57
4241 4402 9.725019 AGATGTGTCATGACTTAAAGTTTCATA 57.275 29.630 25.55 1.27 0.00 2.15
4267 4428 9.618890 ATTGTATAACTTTAGCATGACAGATGT 57.381 29.630 0.00 0.00 0.00 3.06
4268 4429 9.448438 TTGTATAACTTTAGCATGACAGATGTT 57.552 29.630 0.00 0.00 0.00 2.71
4269 4430 8.882736 TGTATAACTTTAGCATGACAGATGTTG 58.117 33.333 0.00 0.00 0.00 3.33
4270 4431 9.098355 GTATAACTTTAGCATGACAGATGTTGA 57.902 33.333 0.00 0.00 0.00 3.18
4271 4432 8.743085 ATAACTTTAGCATGACAGATGTTGAT 57.257 30.769 0.00 0.00 0.00 2.57
4272 4433 9.836864 ATAACTTTAGCATGACAGATGTTGATA 57.163 29.630 0.00 0.00 0.00 2.15
4273 4434 8.743085 AACTTTAGCATGACAGATGTTGATAT 57.257 30.769 0.00 0.00 0.00 1.63
4274 4435 8.743085 ACTTTAGCATGACAGATGTTGATATT 57.257 30.769 0.00 0.00 0.00 1.28
4275 4436 9.182214 ACTTTAGCATGACAGATGTTGATATTT 57.818 29.630 0.00 0.00 0.00 1.40
4334 4495 9.671279 TGACTTCAAAGAATTCTAATATGCAGA 57.329 29.630 8.75 0.00 0.00 4.26
4336 4497 9.678260 ACTTCAAAGAATTCTAATATGCAGAGT 57.322 29.630 8.75 7.81 0.00 3.24
4347 4508 8.818141 TCTAATATGCAGAGTAAAAAGGATCG 57.182 34.615 0.00 0.00 0.00 3.69
4348 4509 6.867662 AATATGCAGAGTAAAAAGGATCGG 57.132 37.500 0.00 0.00 0.00 4.18
4349 4510 3.973206 TGCAGAGTAAAAAGGATCGGA 57.027 42.857 0.00 0.00 0.00 4.55
4350 4511 3.861840 TGCAGAGTAAAAAGGATCGGAG 58.138 45.455 0.00 0.00 0.00 4.63
4351 4512 3.198872 GCAGAGTAAAAAGGATCGGAGG 58.801 50.000 0.00 0.00 0.00 4.30
4352 4513 3.118738 GCAGAGTAAAAAGGATCGGAGGA 60.119 47.826 0.00 0.00 0.00 3.71
4353 4514 4.623171 GCAGAGTAAAAAGGATCGGAGGAA 60.623 45.833 0.00 0.00 0.00 3.36
4354 4515 5.112686 CAGAGTAAAAAGGATCGGAGGAAG 58.887 45.833 0.00 0.00 0.00 3.46
4355 4516 4.778427 AGAGTAAAAAGGATCGGAGGAAGT 59.222 41.667 0.00 0.00 0.00 3.01
4356 4517 5.956563 AGAGTAAAAAGGATCGGAGGAAGTA 59.043 40.000 0.00 0.00 0.00 2.24
4357 4518 6.612049 AGAGTAAAAAGGATCGGAGGAAGTAT 59.388 38.462 0.00 0.00 0.00 2.12
4358 4519 7.783596 AGAGTAAAAAGGATCGGAGGAAGTATA 59.216 37.037 0.00 0.00 0.00 1.47
4359 4520 8.315220 AGTAAAAAGGATCGGAGGAAGTATAA 57.685 34.615 0.00 0.00 0.00 0.98
4360 4521 8.765517 AGTAAAAAGGATCGGAGGAAGTATAAA 58.234 33.333 0.00 0.00 0.00 1.40
4361 4522 9.387257 GTAAAAAGGATCGGAGGAAGTATAAAA 57.613 33.333 0.00 0.00 0.00 1.52
4394 4555 7.433719 GCAGATTATATGTAGCTGTTCCTATCG 59.566 40.741 0.00 0.00 0.00 2.92
4406 4570 5.414789 TGTTCCTATCGGTTCTTCAATCA 57.585 39.130 0.00 0.00 0.00 2.57
4528 4716 2.481795 GCACATCAACTTTGCCAAGTGT 60.482 45.455 3.60 0.00 42.89 3.55
4529 4717 3.784338 CACATCAACTTTGCCAAGTGTT 58.216 40.909 3.60 0.00 42.89 3.32
4530 4718 4.183101 CACATCAACTTTGCCAAGTGTTT 58.817 39.130 3.60 0.00 42.89 2.83
4531 4719 4.033129 CACATCAACTTTGCCAAGTGTTTG 59.967 41.667 3.60 4.98 42.89 2.93
4543 4731 4.729227 CAAGTGTTTGGTGTACCCTTTT 57.271 40.909 0.00 0.00 34.29 2.27
4544 4732 4.429108 CAAGTGTTTGGTGTACCCTTTTG 58.571 43.478 0.00 0.00 34.29 2.44
4545 4733 2.429250 AGTGTTTGGTGTACCCTTTTGC 59.571 45.455 0.00 0.00 34.29 3.68
4546 4734 1.757699 TGTTTGGTGTACCCTTTTGCC 59.242 47.619 0.00 0.00 34.29 4.52
4547 4735 1.757699 GTTTGGTGTACCCTTTTGCCA 59.242 47.619 0.00 0.00 34.29 4.92
4548 4736 2.160721 TTGGTGTACCCTTTTGCCAA 57.839 45.000 0.00 0.00 34.12 4.52
4549 4737 1.698506 TGGTGTACCCTTTTGCCAAG 58.301 50.000 0.00 0.00 34.29 3.61
4550 4738 1.063567 TGGTGTACCCTTTTGCCAAGT 60.064 47.619 0.00 0.00 34.29 3.16
4551 4739 1.339929 GGTGTACCCTTTTGCCAAGTG 59.660 52.381 0.00 0.00 0.00 3.16
4561 4749 0.948623 TTGCCAAGTGATCGGTGTCG 60.949 55.000 0.00 0.00 37.82 4.35
4598 4786 3.124921 CCCGGCGAGCACGATTTT 61.125 61.111 9.30 0.00 42.66 1.82
4650 4838 2.747799 GCTCCTTTCATGGTCAGATCCC 60.748 54.545 0.00 0.00 0.00 3.85
4663 4851 1.855599 CAGATCCCCTGAATCCCCTTT 59.144 52.381 0.00 0.00 45.78 3.11
4669 4857 3.120108 CCCCTGAATCCCCTTTGTACTA 58.880 50.000 0.00 0.00 0.00 1.82
4704 4893 1.827399 GAGGCGTTCCAACCCTCAGA 61.827 60.000 16.26 0.00 41.77 3.27
4721 4910 1.375523 GACCATCTCCAACGCCGTT 60.376 57.895 0.00 0.00 0.00 4.44
4741 4930 3.632643 TCATCAGAGCATTTACAGCCA 57.367 42.857 0.00 0.00 0.00 4.75
4745 4934 2.302733 TCAGAGCATTTACAGCCAGACA 59.697 45.455 0.00 0.00 0.00 3.41
4747 4936 1.394917 GAGCATTTACAGCCAGACACG 59.605 52.381 0.00 0.00 0.00 4.49
4748 4937 1.156736 GCATTTACAGCCAGACACGT 58.843 50.000 0.00 0.00 0.00 4.49
4749 4938 2.028476 AGCATTTACAGCCAGACACGTA 60.028 45.455 0.00 0.00 0.00 3.57
4750 4939 2.936498 GCATTTACAGCCAGACACGTAT 59.064 45.455 0.00 0.00 0.00 3.06
4753 4942 5.560148 CATTTACAGCCAGACACGTATTTC 58.440 41.667 0.00 0.00 0.00 2.17
4755 4944 1.623811 ACAGCCAGACACGTATTTCCT 59.376 47.619 0.00 0.00 0.00 3.36
4759 4948 2.354805 GCCAGACACGTATTTCCTTCCT 60.355 50.000 0.00 0.00 0.00 3.36
4760 4949 3.118884 GCCAGACACGTATTTCCTTCCTA 60.119 47.826 0.00 0.00 0.00 2.94
4762 4951 5.484715 CCAGACACGTATTTCCTTCCTAAA 58.515 41.667 0.00 0.00 0.00 1.85
4763 4952 5.350640 CCAGACACGTATTTCCTTCCTAAAC 59.649 44.000 0.00 0.00 0.00 2.01
4764 4953 5.061808 CAGACACGTATTTCCTTCCTAAACG 59.938 44.000 0.00 0.00 0.00 3.60
4765 4954 4.886579 ACACGTATTTCCTTCCTAAACGT 58.113 39.130 0.00 0.00 0.00 3.99
4766 4955 4.925646 ACACGTATTTCCTTCCTAAACGTC 59.074 41.667 0.00 0.00 0.00 4.34
4780 4974 1.007336 AACGTCCGTCTCGTCAATGC 61.007 55.000 0.00 0.00 40.69 3.56
4781 4975 2.158959 CGTCCGTCTCGTCAATGCC 61.159 63.158 0.00 0.00 0.00 4.40
4787 4981 1.078759 GTCTCGTCAATGCCCAGTCG 61.079 60.000 0.00 0.00 0.00 4.18
4793 4987 0.597568 TCAATGCCCAGTCGCAAAAG 59.402 50.000 0.00 0.00 43.24 2.27
4801 4995 2.154462 CCAGTCGCAAAAGATTGACCT 58.846 47.619 0.00 0.00 38.94 3.85
4805 4999 3.751698 AGTCGCAAAAGATTGACCTAACC 59.248 43.478 0.00 0.00 38.94 2.85
4806 5000 2.739913 TCGCAAAAGATTGACCTAACCG 59.260 45.455 0.00 0.00 38.94 4.44
4816 5010 0.690077 GACCTAACCGGACCCCTCAT 60.690 60.000 9.46 0.00 36.31 2.90
4823 5017 1.273666 ACCGGACCCCTCATTTAGTCT 60.274 52.381 9.46 0.00 0.00 3.24
4828 5022 3.642377 GGACCCCTCATTTAGTCTCCTAC 59.358 52.174 0.00 0.00 0.00 3.18
4833 5027 4.036971 CCCTCATTTAGTCTCCTACGTCTG 59.963 50.000 0.00 0.00 0.00 3.51
4834 5028 4.036971 CCTCATTTAGTCTCCTACGTCTGG 59.963 50.000 0.00 0.00 0.00 3.86
4839 5033 2.379972 AGTCTCCTACGTCTGGATTGG 58.620 52.381 10.14 1.01 32.56 3.16
4840 5034 1.112113 TCTCCTACGTCTGGATTGGC 58.888 55.000 10.14 0.00 32.56 4.52
4848 5042 4.431131 CTGGATTGGCCGGCACCT 62.431 66.667 30.85 11.65 40.66 4.00
4856 5050 1.344953 TGGCCGGCACCTCTCATATT 61.345 55.000 30.85 0.00 0.00 1.28
4861 5055 2.303022 CCGGCACCTCTCATATTGGTAT 59.697 50.000 0.00 0.00 32.13 2.73
4863 5057 3.589988 GGCACCTCTCATATTGGTATCG 58.410 50.000 0.00 0.00 32.13 2.92
4868 5062 6.459066 CACCTCTCATATTGGTATCGAATGT 58.541 40.000 0.00 0.00 32.13 2.71
4874 5068 6.931838 TCATATTGGTATCGAATGTAGGGAC 58.068 40.000 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.778741 ACGTTTCATGGTGTATCTGATAATATT 57.221 29.630 0.00 0.00 0.00 1.28
6 7 9.778741 AATACGTTTCATGGTGTATCTGATAAT 57.221 29.630 0.00 0.00 0.00 1.28
7 8 9.607988 AAATACGTTTCATGGTGTATCTGATAA 57.392 29.630 0.00 0.00 0.00 1.75
8 9 9.607988 AAAATACGTTTCATGGTGTATCTGATA 57.392 29.630 0.00 0.00 0.00 2.15
9 10 8.506168 AAAATACGTTTCATGGTGTATCTGAT 57.494 30.769 0.00 0.00 0.00 2.90
10 11 7.915293 AAAATACGTTTCATGGTGTATCTGA 57.085 32.000 0.00 0.00 0.00 3.27
91 92 6.207810 TGGTCAAAGTCAAACTACACAAAGTT 59.792 34.615 0.00 0.00 41.46 2.66
92 93 5.708230 TGGTCAAAGTCAAACTACACAAAGT 59.292 36.000 0.00 0.00 0.00 2.66
93 94 6.189677 TGGTCAAAGTCAAACTACACAAAG 57.810 37.500 0.00 0.00 0.00 2.77
94 95 6.576662 TTGGTCAAAGTCAAACTACACAAA 57.423 33.333 0.00 0.00 0.00 2.83
95 96 6.576662 TTTGGTCAAAGTCAAACTACACAA 57.423 33.333 0.00 0.00 0.00 3.33
96 97 6.767524 ATTTGGTCAAAGTCAAACTACACA 57.232 33.333 2.55 0.00 35.97 3.72
97 98 8.474006 AAAATTTGGTCAAAGTCAAACTACAC 57.526 30.769 0.00 0.00 35.97 2.90
103 104 9.770097 TGCATATAAAATTTGGTCAAAGTCAAA 57.230 25.926 0.00 0.00 37.29 2.69
104 105 9.770097 TTGCATATAAAATTTGGTCAAAGTCAA 57.230 25.926 0.00 0.00 33.32 3.18
105 106 9.770097 TTTGCATATAAAATTTGGTCAAAGTCA 57.230 25.926 0.00 0.00 33.32 3.41
107 108 9.777297 ACTTTGCATATAAAATTTGGTCAAAGT 57.223 25.926 18.17 18.17 43.26 2.66
139 140 5.245526 ACGTAGTCATACTCCCTCTGTTTTT 59.754 40.000 0.00 0.00 29.74 1.94
140 141 4.771054 ACGTAGTCATACTCCCTCTGTTTT 59.229 41.667 0.00 0.00 29.74 2.43
141 142 4.342359 ACGTAGTCATACTCCCTCTGTTT 58.658 43.478 0.00 0.00 29.74 2.83
142 143 3.965694 ACGTAGTCATACTCCCTCTGTT 58.034 45.455 0.00 0.00 29.74 3.16
143 144 3.648507 ACGTAGTCATACTCCCTCTGT 57.351 47.619 0.00 0.00 29.74 3.41
144 145 6.465948 AGTATACGTAGTCATACTCCCTCTG 58.534 44.000 0.08 0.00 43.93 3.35
145 146 6.684897 AGTATACGTAGTCATACTCCCTCT 57.315 41.667 0.08 0.00 43.93 3.69
146 147 7.583230 CAAAGTATACGTAGTCATACTCCCTC 58.417 42.308 8.73 0.00 43.93 4.30
147 148 6.016443 GCAAAGTATACGTAGTCATACTCCCT 60.016 42.308 8.73 0.00 43.93 4.20
148 149 6.148264 GCAAAGTATACGTAGTCATACTCCC 58.852 44.000 8.73 0.00 43.93 4.30
149 150 5.850128 CGCAAAGTATACGTAGTCATACTCC 59.150 44.000 8.73 2.09 43.93 3.85
150 151 6.572989 GTCGCAAAGTATACGTAGTCATACTC 59.427 42.308 8.73 0.00 43.93 2.59
151 152 6.037500 TGTCGCAAAGTATACGTAGTCATACT 59.962 38.462 0.08 2.04 43.93 2.12
173 174 1.540146 GGTGCACCCAACCATTTTGTC 60.540 52.381 26.31 0.00 0.00 3.18
193 194 4.701651 TGCCTGTTTCTTCTGTATTGGATG 59.298 41.667 0.00 0.00 0.00 3.51
263 265 6.313519 TGATAGTGGTTTGCTAAATCCTCT 57.686 37.500 0.00 0.00 0.00 3.69
298 300 7.876936 ATTTCATGCAGTGATAAACTCATCT 57.123 32.000 0.00 0.00 36.83 2.90
407 409 6.418057 TCAATTGGTTTTCAAGTTGGCTAT 57.582 33.333 5.42 0.00 38.95 2.97
408 410 5.860941 TCAATTGGTTTTCAAGTTGGCTA 57.139 34.783 5.42 0.00 38.95 3.93
409 411 4.751767 TCAATTGGTTTTCAAGTTGGCT 57.248 36.364 5.42 0.00 38.95 4.75
410 412 4.260743 GCTTCAATTGGTTTTCAAGTTGGC 60.261 41.667 5.42 0.00 38.95 4.52
412 414 4.803088 TCGCTTCAATTGGTTTTCAAGTTG 59.197 37.500 5.42 0.00 38.95 3.16
414 416 4.610945 CTCGCTTCAATTGGTTTTCAAGT 58.389 39.130 5.42 0.00 38.95 3.16
415 417 3.426525 GCTCGCTTCAATTGGTTTTCAAG 59.573 43.478 5.42 1.88 38.95 3.02
416 418 3.068024 AGCTCGCTTCAATTGGTTTTCAA 59.932 39.130 5.42 0.00 40.01 2.69
417 419 2.622942 AGCTCGCTTCAATTGGTTTTCA 59.377 40.909 5.42 0.00 0.00 2.69
418 420 2.982470 CAGCTCGCTTCAATTGGTTTTC 59.018 45.455 5.42 0.00 0.00 2.29
462 464 7.849804 ACATAGCTGACATTGTAACCTTAAG 57.150 36.000 0.00 0.00 0.00 1.85
597 629 6.473455 GCGCTGAATTTATTCTACATTTTGCT 59.527 34.615 0.00 0.00 37.67 3.91
638 670 6.317140 CAGGCAGCAGTTTTGAGATTTCTATA 59.683 38.462 0.00 0.00 0.00 1.31
639 671 5.125097 CAGGCAGCAGTTTTGAGATTTCTAT 59.875 40.000 0.00 0.00 0.00 1.98
658 691 0.840288 TGGAAACTAGGGCTCAGGCA 60.840 55.000 0.00 0.00 40.87 4.75
676 709 3.568430 GGGAAGTTCCTGGTTAACAGTTG 59.432 47.826 21.25 0.00 46.06 3.16
685 718 3.328535 AACAAATGGGAAGTTCCTGGT 57.671 42.857 21.25 7.72 36.57 4.00
686 719 3.897505 AGAAACAAATGGGAAGTTCCTGG 59.102 43.478 21.25 9.07 36.57 4.45
687 720 4.584325 TCAGAAACAAATGGGAAGTTCCTG 59.416 41.667 21.25 13.74 36.57 3.86
688 721 4.803452 TCAGAAACAAATGGGAAGTTCCT 58.197 39.130 21.25 0.00 36.57 3.36
689 722 5.728637 ATCAGAAACAAATGGGAAGTTCC 57.271 39.130 13.99 13.99 35.23 3.62
690 723 8.360390 AGTTTATCAGAAACAAATGGGAAGTTC 58.640 33.333 0.00 0.00 32.81 3.01
691 724 8.250143 AGTTTATCAGAAACAAATGGGAAGTT 57.750 30.769 0.00 0.00 32.81 2.66
732 777 2.205342 CCAAGAGAGGTTTATCCCCCA 58.795 52.381 0.00 0.00 36.75 4.96
1003 1072 2.364317 CAGGGAGGCCGAGGAAGA 60.364 66.667 0.00 0.00 0.00 2.87
1430 1499 1.226660 GATTTTGCGATGGTGCGGG 60.227 57.895 0.00 0.00 37.81 6.13
1494 1564 1.253800 CGAACGTGCATCGATCAAGAG 59.746 52.381 14.18 0.00 42.76 2.85
1538 1609 6.695245 CGATTGAAAACTCACAAAAACTTGG 58.305 36.000 0.00 0.00 0.00 3.61
1539 1610 6.177822 GCGATTGAAAACTCACAAAAACTTG 58.822 36.000 0.00 0.00 0.00 3.16
1552 1623 0.363178 GTGCATGCGCGATTGAAAAC 59.637 50.000 16.63 0.00 42.97 2.43
1609 1680 4.033932 TGGAGTGATTATTGAATGAACGCG 59.966 41.667 3.53 3.53 0.00 6.01
1672 1745 0.107312 CTCCCCACTGATTCTGCCAG 60.107 60.000 0.00 0.00 37.64 4.85
1689 1762 7.507304 CATGCAGAAACAAAATGTCAATTCTC 58.493 34.615 0.00 0.00 26.29 2.87
1726 1799 8.767478 TGGCAGTAAAACTTGTAGTCTAATAC 57.233 34.615 0.00 0.00 0.00 1.89
1748 1843 8.409358 AGTAGGAATATGAATACCAATTTGGC 57.591 34.615 15.49 0.00 42.67 4.52
1750 1845 9.573166 TGGAGTAGGAATATGAATACCAATTTG 57.427 33.333 0.00 0.00 0.00 2.32
1966 2078 3.965694 AGGAAGTCGACTAGTACCACAT 58.034 45.455 20.39 0.00 0.00 3.21
1971 2083 6.448207 AACCAATAGGAAGTCGACTAGTAC 57.552 41.667 20.39 4.70 38.69 2.73
1985 2097 3.876914 ACGTGTCATGCATAACCAATAGG 59.123 43.478 0.00 0.00 42.21 2.57
1997 2110 2.390288 CGTGCGTACGTGTCATGC 59.610 61.111 18.32 0.00 44.99 4.06
2056 2169 4.320494 GGTCTACTCTGTTGTTGCAATTGG 60.320 45.833 0.59 0.00 0.00 3.16
2060 2173 2.101750 TCGGTCTACTCTGTTGTTGCAA 59.898 45.455 0.00 0.00 0.00 4.08
2085 2201 8.882415 AAAAGCCATTATATTCTTGCAGAATG 57.118 30.769 16.76 1.93 44.14 2.67
2139 2263 5.574970 ACCCCAAAAGGAATATTTTGCAA 57.425 34.783 0.00 0.00 44.93 4.08
2223 2363 2.233676 GGGCCCCAGTAAGAAAAATGTG 59.766 50.000 12.23 0.00 0.00 3.21
2241 2381 1.340889 TCAGCATTTTTCACAGTGGGC 59.659 47.619 0.00 0.00 0.00 5.36
2249 2389 4.789481 GCTTCAGTTCGTCAGCATTTTTCA 60.789 41.667 0.00 0.00 32.17 2.69
2281 2437 4.564116 GCCCATCTGCATGCGCAC 62.564 66.667 14.90 0.12 45.36 5.34
2670 2826 0.317799 GTCACCACCAATGCAATGCA 59.682 50.000 11.44 11.44 44.86 3.96
2708 2864 0.321919 AGCAACGGCATGTCAGTCAT 60.322 50.000 0.00 0.00 44.61 3.06
2745 2901 1.205893 CCACTTCCTAGGACTGCTCAC 59.794 57.143 12.22 0.00 0.00 3.51
2810 2966 1.175654 TGTACGCCAGGTCGTTGATA 58.824 50.000 13.15 0.00 43.15 2.15
3059 3215 1.323534 CTATGCCGTTTCGTTTCGAGG 59.676 52.381 0.00 0.00 37.14 4.63
3079 3235 7.331934 ACATACATATACGCATCAACCAAGATC 59.668 37.037 0.00 0.00 0.00 2.75
3095 3251 8.204160 CCAGAAGTTCAGAACCACATACATATA 58.796 37.037 9.85 0.00 0.00 0.86
3096 3252 7.050377 CCAGAAGTTCAGAACCACATACATAT 58.950 38.462 9.85 0.00 0.00 1.78
3136 3292 2.114838 GCCTCCATCCCCTGCATC 59.885 66.667 0.00 0.00 0.00 3.91
3239 3395 3.450115 GCCGAGGTAGTCACGCCT 61.450 66.667 0.00 0.00 37.91 5.52
3244 3400 2.986979 TGCACGCCGAGGTAGTCA 60.987 61.111 0.00 0.00 0.00 3.41
3427 3583 4.711949 AGCAGCGCCTCCACCTTG 62.712 66.667 2.29 0.00 0.00 3.61
3461 3617 2.095252 GGTGCGCCGAGAACTTCTC 61.095 63.158 4.18 8.56 40.06 2.87
3910 4071 2.356665 TCGAGATCAGGAGAAGGAGG 57.643 55.000 0.00 0.00 0.00 4.30
4058 4219 1.404583 CCCCTGTAACGTAACCGGAAG 60.405 57.143 9.46 0.00 38.78 3.46
4076 4237 8.641498 AAGTATATCACCAATTCAATCATCCC 57.359 34.615 0.00 0.00 0.00 3.85
4114 4275 9.594478 TCAGTCAAATCTTATATGCGAACTAAA 57.406 29.630 0.00 0.00 0.00 1.85
4115 4276 9.594478 TTCAGTCAAATCTTATATGCGAACTAA 57.406 29.630 0.00 0.00 0.00 2.24
4116 4277 9.249457 CTTCAGTCAAATCTTATATGCGAACTA 57.751 33.333 0.00 0.00 0.00 2.24
4117 4278 7.766278 ACTTCAGTCAAATCTTATATGCGAACT 59.234 33.333 0.00 0.00 0.00 3.01
4118 4279 7.910304 ACTTCAGTCAAATCTTATATGCGAAC 58.090 34.615 0.00 0.00 0.00 3.95
4119 4280 8.131455 GACTTCAGTCAAATCTTATATGCGAA 57.869 34.615 1.86 0.00 44.18 4.70
4120 4281 7.700322 GACTTCAGTCAAATCTTATATGCGA 57.300 36.000 1.86 0.00 44.18 5.10
4135 4296 4.686554 ACTTTACGATGCTTGACTTCAGTC 59.313 41.667 0.00 0.00 44.97 3.51
4136 4297 4.632153 ACTTTACGATGCTTGACTTCAGT 58.368 39.130 0.00 0.00 0.00 3.41
4137 4298 5.597813 AACTTTACGATGCTTGACTTCAG 57.402 39.130 0.00 0.00 0.00 3.02
4138 4299 5.525745 TCAAACTTTACGATGCTTGACTTCA 59.474 36.000 0.00 0.00 0.00 3.02
4139 4300 5.846473 GTCAAACTTTACGATGCTTGACTTC 59.154 40.000 5.69 0.00 39.54 3.01
4140 4301 5.277828 GGTCAAACTTTACGATGCTTGACTT 60.278 40.000 11.30 0.00 41.40 3.01
4141 4302 4.213482 GGTCAAACTTTACGATGCTTGACT 59.787 41.667 11.30 0.00 41.40 3.41
4142 4303 4.024387 TGGTCAAACTTTACGATGCTTGAC 60.024 41.667 4.55 4.55 41.09 3.18
4143 4304 4.130857 TGGTCAAACTTTACGATGCTTGA 58.869 39.130 0.00 0.00 0.00 3.02
4144 4305 4.481930 TGGTCAAACTTTACGATGCTTG 57.518 40.909 0.00 0.00 0.00 4.01
4145 4306 4.855531 GTTGGTCAAACTTTACGATGCTT 58.144 39.130 0.00 0.00 35.75 3.91
4146 4307 4.483476 GTTGGTCAAACTTTACGATGCT 57.517 40.909 0.00 0.00 35.75 3.79
4209 4370 9.896645 ACTTTAAGTCATGACACATCTATTGAT 57.103 29.630 27.02 0.00 0.00 2.57
4210 4371 9.725019 AACTTTAAGTCATGACACATCTATTGA 57.275 29.630 27.02 5.47 0.00 2.57
4213 4374 9.725019 TGAAACTTTAAGTCATGACACATCTAT 57.275 29.630 27.02 7.36 0.00 1.98
4214 4375 9.725019 ATGAAACTTTAAGTCATGACACATCTA 57.275 29.630 27.02 7.86 30.84 1.98
4215 4376 8.627208 ATGAAACTTTAAGTCATGACACATCT 57.373 30.769 27.02 3.53 30.84 2.90
4241 4402 9.618890 ACATCTGTCATGCTAAAGTTATACAAT 57.381 29.630 0.00 0.00 0.00 2.71
4242 4403 9.448438 AACATCTGTCATGCTAAAGTTATACAA 57.552 29.630 0.00 0.00 0.00 2.41
4243 4404 8.882736 CAACATCTGTCATGCTAAAGTTATACA 58.117 33.333 0.00 0.00 0.00 2.29
4244 4405 9.098355 TCAACATCTGTCATGCTAAAGTTATAC 57.902 33.333 0.00 0.00 0.00 1.47
4245 4406 9.836864 ATCAACATCTGTCATGCTAAAGTTATA 57.163 29.630 0.00 0.00 0.00 0.98
4246 4407 8.743085 ATCAACATCTGTCATGCTAAAGTTAT 57.257 30.769 0.00 0.00 0.00 1.89
4247 4408 9.836864 ATATCAACATCTGTCATGCTAAAGTTA 57.163 29.630 0.00 0.00 0.00 2.24
4248 4409 8.743085 ATATCAACATCTGTCATGCTAAAGTT 57.257 30.769 0.00 0.00 0.00 2.66
4249 4410 8.743085 AATATCAACATCTGTCATGCTAAAGT 57.257 30.769 0.00 0.00 0.00 2.66
4280 4441 9.275398 ACTTCACAAAGTTTGACCGTATTTATA 57.725 29.630 22.23 0.00 43.28 0.98
4281 4442 8.161699 ACTTCACAAAGTTTGACCGTATTTAT 57.838 30.769 22.23 0.00 43.28 1.40
4282 4443 7.556733 ACTTCACAAAGTTTGACCGTATTTA 57.443 32.000 22.23 0.00 43.28 1.40
4283 4444 6.445357 ACTTCACAAAGTTTGACCGTATTT 57.555 33.333 22.23 0.00 43.28 1.40
4308 4469 9.671279 TCTGCATATTAGAATTCTTTGAAGTCA 57.329 29.630 14.36 3.90 0.00 3.41
4310 4471 9.678260 ACTCTGCATATTAGAATTCTTTGAAGT 57.322 29.630 14.36 8.33 0.00 3.01
4321 4482 9.261180 CGATCCTTTTTACTCTGCATATTAGAA 57.739 33.333 0.00 0.00 0.00 2.10
4322 4483 7.872993 CCGATCCTTTTTACTCTGCATATTAGA 59.127 37.037 0.00 0.00 0.00 2.10
4323 4484 7.872993 TCCGATCCTTTTTACTCTGCATATTAG 59.127 37.037 0.00 0.00 0.00 1.73
4324 4485 7.732025 TCCGATCCTTTTTACTCTGCATATTA 58.268 34.615 0.00 0.00 0.00 0.98
4325 4486 6.591935 TCCGATCCTTTTTACTCTGCATATT 58.408 36.000 0.00 0.00 0.00 1.28
4326 4487 6.174720 TCCGATCCTTTTTACTCTGCATAT 57.825 37.500 0.00 0.00 0.00 1.78
4327 4488 5.453339 CCTCCGATCCTTTTTACTCTGCATA 60.453 44.000 0.00 0.00 0.00 3.14
4328 4489 4.446371 CTCCGATCCTTTTTACTCTGCAT 58.554 43.478 0.00 0.00 0.00 3.96
4329 4490 3.369471 CCTCCGATCCTTTTTACTCTGCA 60.369 47.826 0.00 0.00 0.00 4.41
4330 4491 3.118738 TCCTCCGATCCTTTTTACTCTGC 60.119 47.826 0.00 0.00 0.00 4.26
4331 4492 4.737855 TCCTCCGATCCTTTTTACTCTG 57.262 45.455 0.00 0.00 0.00 3.35
4332 4493 4.778427 ACTTCCTCCGATCCTTTTTACTCT 59.222 41.667 0.00 0.00 0.00 3.24
4333 4494 5.087391 ACTTCCTCCGATCCTTTTTACTC 57.913 43.478 0.00 0.00 0.00 2.59
4334 4495 6.809976 ATACTTCCTCCGATCCTTTTTACT 57.190 37.500 0.00 0.00 0.00 2.24
4335 4496 8.953368 TTTATACTTCCTCCGATCCTTTTTAC 57.047 34.615 0.00 0.00 0.00 2.01
4339 4500 9.780186 CTTATTTTATACTTCCTCCGATCCTTT 57.220 33.333 0.00 0.00 0.00 3.11
4340 4501 9.155785 TCTTATTTTATACTTCCTCCGATCCTT 57.844 33.333 0.00 0.00 0.00 3.36
4341 4502 8.722622 TCTTATTTTATACTTCCTCCGATCCT 57.277 34.615 0.00 0.00 0.00 3.24
4342 4503 9.425577 CTTCTTATTTTATACTTCCTCCGATCC 57.574 37.037 0.00 0.00 0.00 3.36
4343 4504 8.927721 GCTTCTTATTTTATACTTCCTCCGATC 58.072 37.037 0.00 0.00 0.00 3.69
4344 4505 8.429641 TGCTTCTTATTTTATACTTCCTCCGAT 58.570 33.333 0.00 0.00 0.00 4.18
4345 4506 7.788026 TGCTTCTTATTTTATACTTCCTCCGA 58.212 34.615 0.00 0.00 0.00 4.55
4346 4507 7.926555 TCTGCTTCTTATTTTATACTTCCTCCG 59.073 37.037 0.00 0.00 0.00 4.63
4347 4508 9.785982 ATCTGCTTCTTATTTTATACTTCCTCC 57.214 33.333 0.00 0.00 0.00 4.30
4362 4523 9.698309 GAACAGCTACATATAATCTGCTTCTTA 57.302 33.333 0.00 0.00 0.00 2.10
4394 4555 4.697352 ACTGTAGCACATGATTGAAGAACC 59.303 41.667 0.00 0.00 0.00 3.62
4429 4593 3.476552 TCCCGATTGAACTGCATAATCC 58.523 45.455 0.00 0.00 0.00 3.01
4528 4716 2.160721 TGGCAAAAGGGTACACCAAA 57.839 45.000 0.00 0.00 43.89 3.28
4529 4717 2.035632 CTTGGCAAAAGGGTACACCAA 58.964 47.619 0.00 0.00 43.89 3.67
4530 4718 1.063567 ACTTGGCAAAAGGGTACACCA 60.064 47.619 0.00 0.00 43.89 4.17
4531 4719 1.339929 CACTTGGCAAAAGGGTACACC 59.660 52.381 0.00 0.00 40.67 4.16
4532 4720 2.303175 TCACTTGGCAAAAGGGTACAC 58.697 47.619 0.00 0.00 0.00 2.90
4533 4721 2.738587 TCACTTGGCAAAAGGGTACA 57.261 45.000 0.00 0.00 0.00 2.90
4534 4722 2.161609 CGATCACTTGGCAAAAGGGTAC 59.838 50.000 0.00 0.00 0.00 3.34
4535 4723 2.432444 CGATCACTTGGCAAAAGGGTA 58.568 47.619 0.00 0.00 0.00 3.69
4536 4724 1.247567 CGATCACTTGGCAAAAGGGT 58.752 50.000 0.00 0.00 0.00 4.34
4537 4725 0.527565 CCGATCACTTGGCAAAAGGG 59.472 55.000 0.00 0.00 0.00 3.95
4538 4726 1.068333 CACCGATCACTTGGCAAAAGG 60.068 52.381 0.00 1.39 0.00 3.11
4539 4727 1.608590 ACACCGATCACTTGGCAAAAG 59.391 47.619 0.00 0.00 0.00 2.27
4540 4728 1.606668 GACACCGATCACTTGGCAAAA 59.393 47.619 0.00 0.00 0.00 2.44
4541 4729 1.234821 GACACCGATCACTTGGCAAA 58.765 50.000 0.00 0.00 0.00 3.68
4542 4730 0.948623 CGACACCGATCACTTGGCAA 60.949 55.000 0.00 0.00 38.22 4.52
4543 4731 1.374125 CGACACCGATCACTTGGCA 60.374 57.895 0.00 0.00 38.22 4.92
4544 4732 2.100631 CCGACACCGATCACTTGGC 61.101 63.158 0.00 0.00 38.22 4.52
4545 4733 2.100631 GCCGACACCGATCACTTGG 61.101 63.158 0.00 0.00 38.22 3.61
4546 4734 2.444624 CGCCGACACCGATCACTTG 61.445 63.158 0.00 0.00 38.22 3.16
4547 4735 2.126071 CGCCGACACCGATCACTT 60.126 61.111 0.00 0.00 38.22 3.16
4548 4736 3.371063 ACGCCGACACCGATCACT 61.371 61.111 0.00 0.00 38.22 3.41
4549 4737 3.179265 CACGCCGACACCGATCAC 61.179 66.667 0.00 0.00 38.22 3.06
4550 4738 3.620300 GACACGCCGACACCGATCA 62.620 63.158 0.00 0.00 38.22 2.92
4551 4739 2.879462 GACACGCCGACACCGATC 60.879 66.667 0.00 0.00 38.22 3.69
4586 4774 0.516877 TTGCCTCAAAATCGTGCTCG 59.483 50.000 0.81 0.81 38.55 5.03
4594 4782 3.057315 CAGAACCGATGTTGCCTCAAAAT 60.057 43.478 0.00 0.00 33.97 1.82
4598 4786 0.684535 TCAGAACCGATGTTGCCTCA 59.315 50.000 0.00 0.00 33.97 3.86
4650 4838 4.200092 GCTTAGTACAAAGGGGATTCAGG 58.800 47.826 0.00 0.00 0.00 3.86
4663 4851 2.738643 GCTCGATGGCTTGCTTAGTACA 60.739 50.000 0.00 0.00 0.00 2.90
4669 4857 1.812922 CTCGCTCGATGGCTTGCTT 60.813 57.895 0.00 0.00 0.00 3.91
4704 4893 1.375523 GAACGGCGTTGGAGATGGT 60.376 57.895 31.90 1.43 0.00 3.55
4721 4910 3.198417 TCTGGCTGTAAATGCTCTGATGA 59.802 43.478 0.00 0.00 0.00 2.92
4741 4930 5.166398 CGTTTAGGAAGGAAATACGTGTCT 58.834 41.667 0.00 0.00 0.00 3.41
4745 4934 4.498241 GGACGTTTAGGAAGGAAATACGT 58.502 43.478 0.00 0.00 42.59 3.57
4747 4936 4.498241 ACGGACGTTTAGGAAGGAAATAC 58.502 43.478 0.00 0.00 0.00 1.89
4748 4937 4.463891 AGACGGACGTTTAGGAAGGAAATA 59.536 41.667 0.00 0.00 0.00 1.40
4749 4938 3.260128 AGACGGACGTTTAGGAAGGAAAT 59.740 43.478 0.00 0.00 0.00 2.17
4750 4939 2.629617 AGACGGACGTTTAGGAAGGAAA 59.370 45.455 0.00 0.00 0.00 3.13
4753 4942 1.467035 CGAGACGGACGTTTAGGAAGG 60.467 57.143 0.00 0.00 0.00 3.46
4755 4944 1.197721 GACGAGACGGACGTTTAGGAA 59.802 52.381 0.00 0.00 43.97 3.36
4759 4948 2.587956 CATTGACGAGACGGACGTTTA 58.412 47.619 0.00 0.00 43.97 2.01
4760 4949 1.415374 CATTGACGAGACGGACGTTT 58.585 50.000 0.00 0.00 43.97 3.60
4762 4951 1.443872 GCATTGACGAGACGGACGT 60.444 57.895 0.00 0.00 46.58 4.34
4763 4952 2.158959 GGCATTGACGAGACGGACG 61.159 63.158 0.00 0.00 0.00 4.79
4764 4953 1.810030 GGGCATTGACGAGACGGAC 60.810 63.158 0.00 0.00 0.00 4.79
4765 4954 2.225791 CTGGGCATTGACGAGACGGA 62.226 60.000 0.00 0.00 0.00 4.69
4766 4955 1.811266 CTGGGCATTGACGAGACGG 60.811 63.158 0.00 0.00 0.00 4.79
4780 4974 1.200020 GGTCAATCTTTTGCGACTGGG 59.800 52.381 0.00 0.00 32.61 4.45
4781 4975 2.154462 AGGTCAATCTTTTGCGACTGG 58.846 47.619 0.00 0.00 32.61 4.00
4787 4981 3.078837 TCCGGTTAGGTCAATCTTTTGC 58.921 45.455 0.00 0.00 41.99 3.68
4793 4987 0.179702 GGGGTCCGGTTAGGTCAATC 59.820 60.000 0.00 0.00 41.99 2.67
4801 4995 2.767960 GACTAAATGAGGGGTCCGGTTA 59.232 50.000 0.00 0.00 0.00 2.85
4805 4999 1.413077 GGAGACTAAATGAGGGGTCCG 59.587 57.143 0.00 0.00 0.00 4.79
4806 5000 2.765502 AGGAGACTAAATGAGGGGTCC 58.234 52.381 0.00 0.00 40.61 4.46
4816 5010 4.401519 CCAATCCAGACGTAGGAGACTAAA 59.598 45.833 13.86 0.00 46.54 1.85
4823 5017 1.672854 CGGCCAATCCAGACGTAGGA 61.673 60.000 11.23 11.23 39.97 2.94
4828 5022 4.776322 TGCCGGCCAATCCAGACG 62.776 66.667 26.77 0.00 34.01 4.18
4833 5027 4.115199 AGAGGTGCCGGCCAATCC 62.115 66.667 26.77 20.18 0.00 3.01
4834 5028 2.514824 GAGAGGTGCCGGCCAATC 60.515 66.667 26.77 18.48 0.00 2.67
4839 5033 0.886490 CCAATATGAGAGGTGCCGGC 60.886 60.000 22.73 22.73 0.00 6.13
4840 5034 0.469917 ACCAATATGAGAGGTGCCGG 59.530 55.000 0.00 0.00 33.57 6.13
4848 5042 6.951778 TCCCTACATTCGATACCAATATGAGA 59.048 38.462 0.00 0.00 0.00 3.27
4856 5050 2.934887 TCGTCCCTACATTCGATACCA 58.065 47.619 0.00 0.00 0.00 3.25


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

AutoCloner maintained by Alex Coulton.