Multiple sequence alignment - TraesCS6B01G046500

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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 TraesCS6B01G046500 chr6B 100.000 3524 0 0 1 3524 27684301 27687824 0.000000e+00 6508.0
1 TraesCS6B01G046500 chr6B 87.050 278 15 5 2875 3136 27694065 27694337 9.570000e-76 294.0
2 TraesCS6B01G046500 chr6B 97.059 34 1 0 3150 3183 27694337 27694370 1.370000e-04 58.4
3 TraesCS6B01G046500 chr6D 93.512 2466 124 11 331 2785 15657708 15660148 0.000000e+00 3635.0
4 TraesCS6B01G046500 chr6D 81.998 2222 307 53 378 2543 15799902 15797718 0.000000e+00 1801.0
5 TraesCS6B01G046500 chr6D 81.699 2213 315 55 378 2543 15809467 15807298 0.000000e+00 1760.0
6 TraesCS6B01G046500 chr6D 86.821 1510 195 3 1046 2552 15747924 15746416 0.000000e+00 1683.0
7 TraesCS6B01G046500 chr6D 85.379 1621 217 11 945 2552 15419665 15418052 0.000000e+00 1663.0
8 TraesCS6B01G046500 chr6D 83.890 509 42 23 2875 3358 15667907 15668400 1.930000e-122 449.0
9 TraesCS6B01G046500 chr6D 92.398 171 7 3 1 165 15656796 15656966 4.550000e-59 239.0
10 TraesCS6B01G046500 chr6D 90.960 177 12 1 247 423 15652581 15652753 5.880000e-58 235.0
11 TraesCS6B01G046500 chr6D 84.541 207 13 6 2875 3065 15666410 15666613 1.670000e-43 187.0
12 TraesCS6B01G046500 chr6D 89.773 88 9 0 247 334 15656970 15657057 2.880000e-21 113.0
13 TraesCS6B01G046500 chr6A 92.416 2479 152 16 331 2785 16357191 16359657 0.000000e+00 3504.0
14 TraesCS6B01G046500 chr6A 81.822 2217 311 54 378 2543 16410652 16408477 0.000000e+00 1777.0
15 TraesCS6B01G046500 chr6A 81.744 2202 316 56 392 2543 16401315 16399150 0.000000e+00 1760.0
16 TraesCS6B01G046500 chr6A 85.515 1650 209 17 1046 2667 16388139 16386492 0.000000e+00 1696.0
17 TraesCS6B01G046500 chr6A 84.512 523 33 19 2875 3358 16362164 16362677 1.140000e-129 473.0
18 TraesCS6B01G046500 chr6A 85.139 323 26 5 2875 3183 16366845 16367159 9.500000e-81 311.0
19 TraesCS6B01G046500 chr6A 91.358 162 14 0 4 165 16355379 16355540 4.580000e-54 222.0
20 TraesCS6B01G046500 chr6A 85.000 180 21 2 3179 3358 16367193 16367366 1.010000e-40 178.0
21 TraesCS6B01G046500 chr2D 92.000 75 6 0 174 248 649609816 649609890 4.810000e-19 106.0
22 TraesCS6B01G046500 chr4D 83.333 114 18 1 3412 3524 502422063 502421950 1.730000e-18 104.0
23 TraesCS6B01G046500 chr5D 84.000 100 16 0 3420 3519 5478989 5479088 2.900000e-16 97.1
24 TraesCS6B01G046500 chr7A 91.837 49 1 2 203 248 179422018 179422066 8.170000e-07 65.8
25 TraesCS6B01G046500 chr4B 94.872 39 2 0 166 204 27175046 27175008 1.060000e-05 62.1
26 TraesCS6B01G046500 chr4B 92.308 39 3 0 166 204 630349604 630349566 4.910000e-04 56.5
27 TraesCS6B01G046500 chr3D 89.583 48 5 0 203 250 582188224 582188271 1.060000e-05 62.1
28 TraesCS6B01G046500 chr2B 100.000 30 0 0 219 248 138112014 138112043 4.910000e-04 56.5


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 TraesCS6B01G046500 chr6B 27684301 27687824 3523 False 6508.000000 6508 100.000000 1 3524 1 chr6B.!!$F1 3523
1 TraesCS6B01G046500 chr6D 15797718 15799902 2184 True 1801.000000 1801 81.998000 378 2543 1 chr6D.!!$R3 2165
2 TraesCS6B01G046500 chr6D 15807298 15809467 2169 True 1760.000000 1760 81.699000 378 2543 1 chr6D.!!$R4 2165
3 TraesCS6B01G046500 chr6D 15746416 15747924 1508 True 1683.000000 1683 86.821000 1046 2552 1 chr6D.!!$R2 1506
4 TraesCS6B01G046500 chr6D 15418052 15419665 1613 True 1663.000000 1663 85.379000 945 2552 1 chr6D.!!$R1 1607
5 TraesCS6B01G046500 chr6D 15656796 15660148 3352 False 1329.000000 3635 91.894333 1 2785 3 chr6D.!!$F2 2784
6 TraesCS6B01G046500 chr6D 15666410 15668400 1990 False 318.000000 449 84.215500 2875 3358 2 chr6D.!!$F3 483
7 TraesCS6B01G046500 chr6A 16408477 16410652 2175 True 1777.000000 1777 81.822000 378 2543 1 chr6A.!!$R3 2165
8 TraesCS6B01G046500 chr6A 16399150 16401315 2165 True 1760.000000 1760 81.744000 392 2543 1 chr6A.!!$R2 2151
9 TraesCS6B01G046500 chr6A 16386492 16388139 1647 True 1696.000000 1696 85.515000 1046 2667 1 chr6A.!!$R1 1621
10 TraesCS6B01G046500 chr6A 16355379 16362677 7298 False 1399.666667 3504 89.428667 4 3358 3 chr6A.!!$F1 3354
11 TraesCS6B01G046500 chr6A 16366845 16367366 521 False 244.500000 311 85.069500 2875 3358 2 chr6A.!!$F2 483

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
617 2604 0.771127 AAGTAGTTTGGCAGCCCTGA 59.229 50.0 9.64 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2564 4590 0.960364 CACCACAGGGCCATGTACAC 60.96 60.0 24.77 0.0 37.9 2.9 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
67 68 3.097877 TCCAGAATATAGCAGCACACG 57.902 47.619 0.00 0.00 0.00 4.49
92 93 2.978156 TATCCCATCCAAATCCTGCC 57.022 50.000 0.00 0.00 0.00 4.85
131 135 5.698545 GTGCAAGAGAGGCTAATAGTATTGG 59.301 44.000 5.61 3.74 0.00 3.16
156 163 2.354821 GTCAACTCTCTGCACGGTTTTT 59.645 45.455 0.00 0.00 0.00 1.94
165 172 5.000012 TCTGCACGGTTTTTAACAACAAT 58.000 34.783 6.81 0.00 0.00 2.71
166 173 5.038033 TCTGCACGGTTTTTAACAACAATC 58.962 37.500 6.81 0.00 0.00 2.67
168 175 4.142138 TGCACGGTTTTTAACAACAATCCT 60.142 37.500 6.81 0.00 0.00 3.24
169 176 4.806775 GCACGGTTTTTAACAACAATCCTT 59.193 37.500 6.81 0.00 0.00 3.36
170 177 5.051307 GCACGGTTTTTAACAACAATCCTTC 60.051 40.000 6.81 0.00 0.00 3.46
171 178 5.460748 CACGGTTTTTAACAACAATCCTTCC 59.539 40.000 6.81 0.00 0.00 3.46
172 179 5.127356 ACGGTTTTTAACAACAATCCTTCCA 59.873 36.000 6.81 0.00 0.00 3.53
173 180 6.183360 ACGGTTTTTAACAACAATCCTTCCAT 60.183 34.615 6.81 0.00 0.00 3.41
174 181 6.704050 CGGTTTTTAACAACAATCCTTCCATT 59.296 34.615 6.81 0.00 0.00 3.16
175 182 7.225734 CGGTTTTTAACAACAATCCTTCCATTT 59.774 33.333 6.81 0.00 0.00 2.32
176 183 8.556194 GGTTTTTAACAACAATCCTTCCATTTC 58.444 33.333 6.81 0.00 0.00 2.17
177 184 9.103861 GTTTTTAACAACAATCCTTCCATTTCA 57.896 29.630 0.00 0.00 0.00 2.69
178 185 9.672673 TTTTTAACAACAATCCTTCCATTTCAA 57.327 25.926 0.00 0.00 0.00 2.69
179 186 9.672673 TTTTAACAACAATCCTTCCATTTCAAA 57.327 25.926 0.00 0.00 0.00 2.69
180 187 9.672673 TTTAACAACAATCCTTCCATTTCAAAA 57.327 25.926 0.00 0.00 0.00 2.44
181 188 9.844257 TTAACAACAATCCTTCCATTTCAAAAT 57.156 25.926 0.00 0.00 0.00 1.82
183 190 9.492973 AACAACAATCCTTCCATTTCAAAATAG 57.507 29.630 0.00 0.00 0.00 1.73
184 191 8.869109 ACAACAATCCTTCCATTTCAAAATAGA 58.131 29.630 0.00 0.00 0.00 1.98
185 192 9.880157 CAACAATCCTTCCATTTCAAAATAGAT 57.120 29.630 0.00 0.00 0.00 1.98
186 193 9.880157 AACAATCCTTCCATTTCAAAATAGATG 57.120 29.630 0.00 0.00 0.00 2.90
187 194 9.258629 ACAATCCTTCCATTTCAAAATAGATGA 57.741 29.630 0.00 0.00 0.00 2.92
188 195 9.525409 CAATCCTTCCATTTCAAAATAGATGAC 57.475 33.333 0.00 0.00 0.00 3.06
189 196 9.484806 AATCCTTCCATTTCAAAATAGATGACT 57.515 29.630 0.00 0.00 0.00 3.41
190 197 8.511604 TCCTTCCATTTCAAAATAGATGACTC 57.488 34.615 0.00 0.00 0.00 3.36
191 198 8.108999 TCCTTCCATTTCAAAATAGATGACTCA 58.891 33.333 0.00 0.00 0.00 3.41
192 199 8.742777 CCTTCCATTTCAAAATAGATGACTCAA 58.257 33.333 0.00 0.00 0.00 3.02
193 200 9.565213 CTTCCATTTCAAAATAGATGACTCAAC 57.435 33.333 0.00 0.00 0.00 3.18
194 201 7.751732 TCCATTTCAAAATAGATGACTCAACG 58.248 34.615 0.00 0.00 0.00 4.10
195 202 7.390440 TCCATTTCAAAATAGATGACTCAACGT 59.610 33.333 0.00 0.00 0.00 3.99
196 203 8.023128 CCATTTCAAAATAGATGACTCAACGTT 58.977 33.333 0.00 0.00 0.00 3.99
197 204 8.843733 CATTTCAAAATAGATGACTCAACGTTG 58.156 33.333 22.35 22.35 0.00 4.10
198 205 7.490962 TTCAAAATAGATGACTCAACGTTGT 57.509 32.000 26.47 9.72 0.00 3.32
199 206 8.596271 TTCAAAATAGATGACTCAACGTTGTA 57.404 30.769 26.47 13.16 0.00 2.41
200 207 8.771920 TCAAAATAGATGACTCAACGTTGTAT 57.228 30.769 26.47 16.31 0.00 2.29
201 208 9.214957 TCAAAATAGATGACTCAACGTTGTATT 57.785 29.630 26.47 17.42 0.00 1.89
206 213 9.871238 ATAGATGACTCAACGTTGTATTAAAGT 57.129 29.630 26.47 20.57 0.00 2.66
207 214 8.603242 AGATGACTCAACGTTGTATTAAAGTT 57.397 30.769 26.47 8.52 0.00 2.66
208 215 9.701098 AGATGACTCAACGTTGTATTAAAGTTA 57.299 29.630 26.47 17.76 0.00 2.24
227 234 8.854614 AAAGTTAATACAAAGCTGAGTCATCT 57.145 30.769 0.00 0.00 0.00 2.90
228 235 9.944376 AAAGTTAATACAAAGCTGAGTCATCTA 57.056 29.630 0.00 0.00 0.00 1.98
234 241 9.453572 AATACAAAGCTGAGTCATCTATTTTCA 57.546 29.630 0.00 0.00 0.00 2.69
235 242 7.750229 ACAAAGCTGAGTCATCTATTTTCAA 57.250 32.000 0.00 0.00 0.00 2.69
236 243 8.169977 ACAAAGCTGAGTCATCTATTTTCAAA 57.830 30.769 0.00 0.00 0.00 2.69
237 244 8.078596 ACAAAGCTGAGTCATCTATTTTCAAAC 58.921 33.333 0.00 0.00 0.00 2.93
238 245 6.414408 AGCTGAGTCATCTATTTTCAAACG 57.586 37.500 0.00 0.00 0.00 3.60
239 246 5.352569 AGCTGAGTCATCTATTTTCAAACGG 59.647 40.000 0.00 0.00 0.00 4.44
240 247 5.351465 GCTGAGTCATCTATTTTCAAACGGA 59.649 40.000 0.00 0.00 0.00 4.69
241 248 6.456181 GCTGAGTCATCTATTTTCAAACGGAG 60.456 42.308 0.00 0.00 0.00 4.63
242 249 5.874810 TGAGTCATCTATTTTCAAACGGAGG 59.125 40.000 0.00 0.00 0.00 4.30
243 250 5.186198 AGTCATCTATTTTCAAACGGAGGG 58.814 41.667 0.00 0.00 0.00 4.30
244 251 5.045869 AGTCATCTATTTTCAAACGGAGGGA 60.046 40.000 0.00 0.00 0.00 4.20
245 252 5.294552 GTCATCTATTTTCAAACGGAGGGAG 59.705 44.000 0.00 0.00 0.00 4.30
298 1476 9.970395 TCGATCAAACTTGTAGTACTAAAGAAA 57.030 29.630 21.50 8.95 0.00 2.52
356 2256 3.258225 CCGTCAACTCGATGGCTAG 57.742 57.895 0.00 0.00 43.93 3.42
483 2390 3.675228 CGTAGAAGTACGTTTGGGATGCT 60.675 47.826 0.00 0.00 45.84 3.79
581 2488 3.743521 TGCAACAACTAATGCAGTCTCT 58.256 40.909 0.00 0.00 46.87 3.10
582 2489 3.748048 TGCAACAACTAATGCAGTCTCTC 59.252 43.478 0.00 0.00 46.87 3.20
583 2490 3.999663 GCAACAACTAATGCAGTCTCTCT 59.000 43.478 0.00 0.00 42.12 3.10
587 2494 5.233988 ACAACTAATGCAGTCTCTCTCAAC 58.766 41.667 0.00 0.00 36.04 3.18
589 2496 5.474578 ACTAATGCAGTCTCTCTCAACAA 57.525 39.130 0.00 0.00 28.33 2.83
617 2604 0.771127 AAGTAGTTTGGCAGCCCTGA 59.229 50.000 9.64 0.00 0.00 3.86
618 2605 0.995024 AGTAGTTTGGCAGCCCTGAT 59.005 50.000 9.64 0.00 0.00 2.90
619 2606 2.196595 AGTAGTTTGGCAGCCCTGATA 58.803 47.619 9.64 0.00 0.00 2.15
620 2607 2.576191 AGTAGTTTGGCAGCCCTGATAA 59.424 45.455 9.64 0.00 0.00 1.75
621 2608 2.134789 AGTTTGGCAGCCCTGATAAG 57.865 50.000 9.64 0.00 0.00 1.73
622 2609 1.355720 AGTTTGGCAGCCCTGATAAGT 59.644 47.619 9.64 0.00 0.00 2.24
623 2610 2.171003 GTTTGGCAGCCCTGATAAGTT 58.829 47.619 9.64 0.00 0.00 2.66
624 2611 2.128771 TTGGCAGCCCTGATAAGTTC 57.871 50.000 9.64 0.00 0.00 3.01
625 2612 0.991146 TGGCAGCCCTGATAAGTTCA 59.009 50.000 9.64 0.00 0.00 3.18
682 2669 2.423446 TAGTTGGGCCCCGTTAATTC 57.577 50.000 22.27 0.30 0.00 2.17
695 2686 3.127030 CCGTTAATTCAGGAACAGAAGCC 59.873 47.826 0.00 0.00 37.25 4.35
790 2792 3.901797 AAAGGAAGCCACGGGAGCG 62.902 63.158 0.00 0.00 34.64 5.03
798 2800 1.731433 GCCACGGGAGCGTGTAGATA 61.731 60.000 0.00 0.00 38.12 1.98
853 2856 6.926272 TGCACGCTATAAATACACATCACATA 59.074 34.615 0.00 0.00 0.00 2.29
855 2858 7.448228 CACGCTATAAATACACATCACATAGC 58.552 38.462 0.00 0.00 37.23 2.97
943 2947 1.208052 TGCATCTTAGTCCACAGCTCC 59.792 52.381 0.00 0.00 0.00 4.70
1133 3140 3.567797 GCGTGCCTTCCATCTCGC 61.568 66.667 0.00 0.00 37.88 5.03
1257 3264 3.319198 GGGGTTGCCTCCGTCTCA 61.319 66.667 0.00 0.00 0.00 3.27
1416 3423 0.389166 CTATCCGCTTCCTCATCGGC 60.389 60.000 0.00 0.00 42.65 5.54
1626 3633 0.184933 TTGCCTACTTTGTGCCAGGT 59.815 50.000 0.00 0.00 0.00 4.00
1875 3882 1.446272 CTTCCACCTCGACCTTCGC 60.446 63.158 0.00 0.00 40.21 4.70
2001 4008 1.688735 CGCCTCTGGAACATCTGGATA 59.311 52.381 0.00 0.00 38.20 2.59
2139 4146 0.815213 ATGGCGTCATCCCATTCGTG 60.815 55.000 0.00 0.00 40.06 4.35
2144 4151 1.674519 CGTCATCCCATTCGTGTCCAA 60.675 52.381 0.00 0.00 0.00 3.53
2160 4167 4.394712 AAACGCTCCCTCGGCCTG 62.395 66.667 0.00 0.00 0.00 4.85
2343 4350 1.074623 CTCCATGCTCCTCCCTCCT 60.075 63.158 0.00 0.00 0.00 3.69
2518 4525 0.256177 TAACAACACACCCCAGCACA 59.744 50.000 0.00 0.00 0.00 4.57
2553 4564 6.563222 TTTTTCTTACCTCATGTAAACCCG 57.437 37.500 0.00 0.00 38.91 5.28
2554 4565 4.895668 TTCTTACCTCATGTAAACCCGT 57.104 40.909 0.00 0.00 38.91 5.28
2564 4590 5.929278 TCATGTAAACCCGTTATGAAAACG 58.071 37.500 3.41 3.41 42.74 3.60
2650 4686 1.173043 TTGTGGGCGCCTATCAAAAG 58.827 50.000 28.56 0.00 0.00 2.27
2669 4706 2.844839 CCCTTAGAGGAGGCCCCG 60.845 72.222 0.00 0.00 37.67 5.73
2674 4711 1.144503 CTTAGAGGAGGCCCCGTAGTA 59.855 57.143 0.00 0.00 40.87 1.82
2676 4713 1.453633 AGAGGAGGCCCCGTAGTATA 58.546 55.000 0.00 0.00 40.87 1.47
2697 4738 1.482182 TGTGTACATGGAGGCTAGCTG 59.518 52.381 15.72 7.04 0.00 4.24
2727 4768 6.408869 TGCTTGTATCATGTGATGAGAAGAA 58.591 36.000 5.78 0.00 43.53 2.52
2740 4781 7.148188 TGTGATGAGAAGAAATCAATAAGTGGC 60.148 37.037 0.00 0.00 34.70 5.01
2741 4782 6.319658 TGATGAGAAGAAATCAATAAGTGGCC 59.680 38.462 0.00 0.00 29.97 5.36
2742 4783 4.635765 TGAGAAGAAATCAATAAGTGGCCG 59.364 41.667 0.00 0.00 0.00 6.13
2743 4784 3.947834 AGAAGAAATCAATAAGTGGCCGG 59.052 43.478 0.00 0.00 0.00 6.13
2785 4826 4.034975 GCTTGCCATTTGTGTTTGCTTTTA 59.965 37.500 0.00 0.00 0.00 1.52
2787 4828 5.921004 TGCCATTTGTGTTTGCTTTTATC 57.079 34.783 0.00 0.00 0.00 1.75
2788 4829 4.754114 TGCCATTTGTGTTTGCTTTTATCC 59.246 37.500 0.00 0.00 0.00 2.59
2789 4830 4.996758 GCCATTTGTGTTTGCTTTTATCCT 59.003 37.500 0.00 0.00 0.00 3.24
2790 4831 6.162777 GCCATTTGTGTTTGCTTTTATCCTA 58.837 36.000 0.00 0.00 0.00 2.94
2791 4832 6.818142 GCCATTTGTGTTTGCTTTTATCCTAT 59.182 34.615 0.00 0.00 0.00 2.57
2793 4834 8.872845 CCATTTGTGTTTGCTTTTATCCTATTC 58.127 33.333 0.00 0.00 0.00 1.75
2794 4835 9.421806 CATTTGTGTTTGCTTTTATCCTATTCA 57.578 29.630 0.00 0.00 0.00 2.57
2795 4836 8.810652 TTTGTGTTTGCTTTTATCCTATTCAC 57.189 30.769 0.00 0.00 0.00 3.18
2797 4838 7.816640 TGTGTTTGCTTTTATCCTATTCACTC 58.183 34.615 0.00 0.00 0.00 3.51
2798 4839 7.446931 TGTGTTTGCTTTTATCCTATTCACTCA 59.553 33.333 0.00 0.00 0.00 3.41
2832 4884 0.303493 TGAAGACTTTCGCAACACGC 59.697 50.000 0.00 0.00 43.23 5.34
2836 4888 2.425124 CTTTCGCAACACGCCGTG 60.425 61.111 16.94 16.94 43.23 4.94
2849 4901 1.072391 CGCCGTGCAAGTACACAATA 58.928 50.000 0.00 0.00 40.73 1.90
2851 4903 2.861335 CGCCGTGCAAGTACACAATATA 59.139 45.455 0.00 0.00 40.73 0.86
2856 4908 6.452242 CCGTGCAAGTACACAATATATCCTA 58.548 40.000 0.00 0.00 40.73 2.94
2857 4909 7.097192 CCGTGCAAGTACACAATATATCCTAT 58.903 38.462 0.00 0.00 40.73 2.57
2860 4912 9.489084 GTGCAAGTACACAATATATCCTATTCA 57.511 33.333 0.00 0.00 40.40 2.57
2861 4913 9.489084 TGCAAGTACACAATATATCCTATTCAC 57.511 33.333 0.00 0.00 0.00 3.18
2862 4914 9.712305 GCAAGTACACAATATATCCTATTCACT 57.288 33.333 0.00 0.00 0.00 3.41
2945 7405 5.069119 ACTCCGTACTTGATGATCTTGCATA 59.931 40.000 0.00 0.00 0.00 3.14
2980 8954 1.667236 TTATCTTGGAGTGCCGCATG 58.333 50.000 0.00 0.00 36.79 4.06
2985 8959 0.179048 TTGGAGTGCCGCATGATAGG 60.179 55.000 0.00 0.00 36.79 2.57
2987 8961 0.106708 GGAGTGCCGCATGATAGGAA 59.893 55.000 0.00 0.00 0.00 3.36
3041 9018 4.426416 CTTTGACCAACCGTACATCGATA 58.574 43.478 0.00 0.00 42.86 2.92
3098 9077 1.856629 ATGCACCTCCCCATTTTCAG 58.143 50.000 0.00 0.00 0.00 3.02
3116 9095 1.134965 CAGGGGACGTCATTCAGACTC 60.135 57.143 18.91 0.00 45.32 3.36
3118 9097 1.134965 GGGGACGTCATTCAGACTCTG 60.135 57.143 18.91 0.00 45.32 3.35
3192 9209 5.060506 TCTTTGAGCTTGGATTTCGTAACA 58.939 37.500 0.00 0.00 0.00 2.41
3212 9229 4.778415 CGACTGACGAGCCCACGG 62.778 72.222 0.00 0.00 45.77 4.94
3262 9283 5.253330 TGCATTGCTTACTATATAAGGGGC 58.747 41.667 10.49 0.00 0.00 5.80
3265 9286 6.434340 GCATTGCTTACTATATAAGGGGCTTT 59.566 38.462 0.16 0.00 0.00 3.51
3272 9293 6.441088 ACTATATAAGGGGCTTTGAGAAGG 57.559 41.667 0.00 0.00 33.34 3.46
3275 9296 2.363018 GGGGCTTTGAGAAGGGCC 60.363 66.667 0.00 0.00 43.68 5.80
3276 9297 2.766660 GGGCTTTGAGAAGGGCCT 59.233 61.111 0.00 0.00 43.62 5.19
3277 9298 1.571773 GGGGCTTTGAGAAGGGCCTA 61.572 60.000 6.41 0.00 43.62 3.93
3278 9299 0.394488 GGGCTTTGAGAAGGGCCTAC 60.394 60.000 6.41 2.00 43.62 3.18
3282 9303 2.290323 GCTTTGAGAAGGGCCTACTGAA 60.290 50.000 6.41 0.00 33.34 3.02
3294 9315 4.040461 GGGCCTACTGAATACAGCTTCATA 59.960 45.833 0.84 0.00 46.95 2.15
3305 9326 9.679661 TGAATACAGCTTCATAAAGGAACATAA 57.320 29.630 0.00 0.00 32.79 1.90
3316 9337 2.790433 AGGAACATAAGGCGCAAAAGA 58.210 42.857 10.83 0.00 0.00 2.52
3340 9362 1.227556 ACGCAAAGGAGCACGTCTT 60.228 52.632 0.00 0.00 32.37 3.01
3354 9376 3.059800 GCACGTCTTTCTACTCAACAACC 60.060 47.826 0.00 0.00 0.00 3.77
3358 9380 5.465724 ACGTCTTTCTACTCAACAACCATTC 59.534 40.000 0.00 0.00 0.00 2.67
3359 9381 5.465390 CGTCTTTCTACTCAACAACCATTCA 59.535 40.000 0.00 0.00 0.00 2.57
3360 9382 6.346919 CGTCTTTCTACTCAACAACCATTCAG 60.347 42.308 0.00 0.00 0.00 3.02
3361 9383 6.706270 GTCTTTCTACTCAACAACCATTCAGA 59.294 38.462 0.00 0.00 0.00 3.27
3362 9384 6.706270 TCTTTCTACTCAACAACCATTCAGAC 59.294 38.462 0.00 0.00 0.00 3.51
3363 9385 4.894784 TCTACTCAACAACCATTCAGACC 58.105 43.478 0.00 0.00 0.00 3.85
3364 9386 3.576078 ACTCAACAACCATTCAGACCA 57.424 42.857 0.00 0.00 0.00 4.02
3365 9387 3.480470 ACTCAACAACCATTCAGACCAG 58.520 45.455 0.00 0.00 0.00 4.00
3366 9388 2.816087 CTCAACAACCATTCAGACCAGG 59.184 50.000 0.00 0.00 0.00 4.45
3367 9389 2.441375 TCAACAACCATTCAGACCAGGA 59.559 45.455 0.00 0.00 0.00 3.86
3368 9390 2.816087 CAACAACCATTCAGACCAGGAG 59.184 50.000 0.00 0.00 0.00 3.69
3369 9391 2.338809 ACAACCATTCAGACCAGGAGA 58.661 47.619 0.00 0.00 0.00 3.71
3370 9392 2.304180 ACAACCATTCAGACCAGGAGAG 59.696 50.000 0.00 0.00 0.00 3.20
3371 9393 2.568956 CAACCATTCAGACCAGGAGAGA 59.431 50.000 0.00 0.00 0.00 3.10
3372 9394 2.907892 ACCATTCAGACCAGGAGAGAA 58.092 47.619 0.00 0.00 0.00 2.87
3373 9395 3.458831 ACCATTCAGACCAGGAGAGAAT 58.541 45.455 0.00 0.00 0.00 2.40
3374 9396 4.624913 ACCATTCAGACCAGGAGAGAATA 58.375 43.478 0.00 0.00 0.00 1.75
3375 9397 5.222870 ACCATTCAGACCAGGAGAGAATAT 58.777 41.667 0.00 0.00 0.00 1.28
3376 9398 5.669447 ACCATTCAGACCAGGAGAGAATATT 59.331 40.000 0.00 0.00 0.00 1.28
3377 9399 6.846505 ACCATTCAGACCAGGAGAGAATATTA 59.153 38.462 0.00 0.00 0.00 0.98
3378 9400 7.515514 ACCATTCAGACCAGGAGAGAATATTAT 59.484 37.037 0.00 0.00 0.00 1.28
3379 9401 9.040259 CCATTCAGACCAGGAGAGAATATTATA 57.960 37.037 0.00 0.00 0.00 0.98
3380 9402 9.868277 CATTCAGACCAGGAGAGAATATTATAC 57.132 37.037 0.00 0.00 0.00 1.47
3381 9403 7.689446 TCAGACCAGGAGAGAATATTATACG 57.311 40.000 0.00 0.00 0.00 3.06
3382 9404 6.659668 TCAGACCAGGAGAGAATATTATACGG 59.340 42.308 0.00 0.00 0.00 4.02
3383 9405 6.659668 CAGACCAGGAGAGAATATTATACGGA 59.340 42.308 0.00 0.00 0.00 4.69
3384 9406 7.176865 CAGACCAGGAGAGAATATTATACGGAA 59.823 40.741 0.00 0.00 0.00 4.30
3385 9407 7.728981 AGACCAGGAGAGAATATTATACGGAAA 59.271 37.037 0.00 0.00 0.00 3.13
3386 9408 7.668492 ACCAGGAGAGAATATTATACGGAAAC 58.332 38.462 0.00 0.00 0.00 2.78
3387 9409 7.097834 CCAGGAGAGAATATTATACGGAAACC 58.902 42.308 0.00 0.00 0.00 3.27
3388 9410 7.256190 CCAGGAGAGAATATTATACGGAAACCA 60.256 40.741 0.00 0.00 0.00 3.67
3389 9411 8.148351 CAGGAGAGAATATTATACGGAAACCAA 58.852 37.037 0.00 0.00 0.00 3.67
3390 9412 8.148999 AGGAGAGAATATTATACGGAAACCAAC 58.851 37.037 0.00 0.00 0.00 3.77
3391 9413 7.929785 GGAGAGAATATTATACGGAAACCAACA 59.070 37.037 0.00 0.00 0.00 3.33
3392 9414 9.490379 GAGAGAATATTATACGGAAACCAACAT 57.510 33.333 0.00 0.00 0.00 2.71
3393 9415 9.847224 AGAGAATATTATACGGAAACCAACATT 57.153 29.630 0.00 0.00 0.00 2.71
3395 9417 9.621629 AGAATATTATACGGAAACCAACATTCA 57.378 29.630 0.00 0.00 0.00 2.57
3399 9421 8.980143 ATTATACGGAAACCAACATTCAAAAG 57.020 30.769 0.00 0.00 0.00 2.27
3400 9422 4.993029 ACGGAAACCAACATTCAAAAGA 57.007 36.364 0.00 0.00 0.00 2.52
3401 9423 5.331876 ACGGAAACCAACATTCAAAAGAA 57.668 34.783 0.00 0.00 0.00 2.52
3402 9424 5.106442 ACGGAAACCAACATTCAAAAGAAC 58.894 37.500 0.00 0.00 0.00 3.01
3403 9425 4.506288 CGGAAACCAACATTCAAAAGAACC 59.494 41.667 0.00 0.00 0.00 3.62
3404 9426 5.670485 GGAAACCAACATTCAAAAGAACCT 58.330 37.500 0.00 0.00 0.00 3.50
3405 9427 5.753438 GGAAACCAACATTCAAAAGAACCTC 59.247 40.000 0.00 0.00 0.00 3.85
3406 9428 4.937201 ACCAACATTCAAAAGAACCTCC 57.063 40.909 0.00 0.00 0.00 4.30
3407 9429 3.317993 ACCAACATTCAAAAGAACCTCCG 59.682 43.478 0.00 0.00 0.00 4.63
3408 9430 3.317993 CCAACATTCAAAAGAACCTCCGT 59.682 43.478 0.00 0.00 0.00 4.69
3409 9431 4.290155 CAACATTCAAAAGAACCTCCGTG 58.710 43.478 0.00 0.00 0.00 4.94
3410 9432 2.884639 ACATTCAAAAGAACCTCCGTGG 59.115 45.455 0.00 0.00 42.93 4.94
3411 9433 3.146066 CATTCAAAAGAACCTCCGTGGA 58.854 45.455 0.00 0.00 39.71 4.02
3412 9434 3.284793 TTCAAAAGAACCTCCGTGGAA 57.715 42.857 0.00 0.00 39.71 3.53
3413 9435 3.284793 TCAAAAGAACCTCCGTGGAAA 57.715 42.857 0.00 0.00 39.71 3.13
3414 9436 3.622630 TCAAAAGAACCTCCGTGGAAAA 58.377 40.909 0.00 0.00 39.71 2.29
3415 9437 4.211920 TCAAAAGAACCTCCGTGGAAAAT 58.788 39.130 0.00 0.00 39.71 1.82
3416 9438 4.277423 TCAAAAGAACCTCCGTGGAAAATC 59.723 41.667 0.00 0.00 39.71 2.17
3417 9439 3.790089 AAGAACCTCCGTGGAAAATCT 57.210 42.857 0.00 0.00 39.71 2.40
3418 9440 4.903045 AAGAACCTCCGTGGAAAATCTA 57.097 40.909 0.00 0.00 39.71 1.98
3419 9441 4.903045 AGAACCTCCGTGGAAAATCTAA 57.097 40.909 0.00 0.00 39.71 2.10
3420 9442 5.237236 AGAACCTCCGTGGAAAATCTAAA 57.763 39.130 0.00 0.00 39.71 1.85
3421 9443 5.627135 AGAACCTCCGTGGAAAATCTAAAA 58.373 37.500 0.00 0.00 39.71 1.52
3422 9444 6.066032 AGAACCTCCGTGGAAAATCTAAAAA 58.934 36.000 0.00 0.00 39.71 1.94
3473 9495 9.606631 TTTTTATTGCCATGTGAAACTTTAAGT 57.393 25.926 0.00 0.00 38.04 2.24
3478 9500 9.606631 ATTGCCATGTGAAACTTTAAGTAAAAA 57.393 25.926 0.00 0.00 38.04 1.94
3479 9501 8.413899 TGCCATGTGAAACTTTAAGTAAAAAC 57.586 30.769 0.00 0.00 38.04 2.43
3480 9502 8.035394 TGCCATGTGAAACTTTAAGTAAAAACA 58.965 29.630 0.00 2.05 38.04 2.83
3481 9503 8.325282 GCCATGTGAAACTTTAAGTAAAAACAC 58.675 33.333 0.00 5.76 38.04 3.32
3482 9504 9.360093 CCATGTGAAACTTTAAGTAAAAACACA 57.640 29.630 17.16 17.16 38.04 3.72
3493 9515 9.601971 TTTAAGTAAAAACACAATACGAGATGC 57.398 29.630 0.00 0.00 0.00 3.91
3495 9517 5.636121 AGTAAAAACACAATACGAGATGCGA 59.364 36.000 0.00 0.00 44.57 5.10
3496 9518 5.351233 AAAAACACAATACGAGATGCGAA 57.649 34.783 0.00 0.00 44.57 4.70
3497 9519 3.991605 AACACAATACGAGATGCGAAC 57.008 42.857 0.00 0.00 44.57 3.95
3498 9520 3.232213 ACACAATACGAGATGCGAACT 57.768 42.857 0.00 0.00 44.57 3.01
3499 9521 4.365899 ACACAATACGAGATGCGAACTA 57.634 40.909 0.00 0.00 44.57 2.24
3500 9522 4.933330 ACACAATACGAGATGCGAACTAT 58.067 39.130 0.00 0.00 44.57 2.12
3501 9523 4.740205 ACACAATACGAGATGCGAACTATG 59.260 41.667 0.00 0.00 44.57 2.23
3502 9524 4.976116 CACAATACGAGATGCGAACTATGA 59.024 41.667 0.00 0.00 44.57 2.15
3503 9525 5.458779 CACAATACGAGATGCGAACTATGAA 59.541 40.000 0.00 0.00 44.57 2.57
3504 9526 6.019881 CACAATACGAGATGCGAACTATGAAA 60.020 38.462 0.00 0.00 44.57 2.69
3505 9527 6.533723 ACAATACGAGATGCGAACTATGAAAA 59.466 34.615 0.00 0.00 44.57 2.29
3506 9528 7.064134 ACAATACGAGATGCGAACTATGAAAAA 59.936 33.333 0.00 0.00 44.57 1.94
3507 9529 5.456192 ACGAGATGCGAACTATGAAAAAG 57.544 39.130 0.00 0.00 44.57 2.27
3508 9530 4.201724 ACGAGATGCGAACTATGAAAAAGC 60.202 41.667 0.00 0.00 44.57 3.51
3509 9531 4.592179 GAGATGCGAACTATGAAAAAGCC 58.408 43.478 0.00 0.00 0.00 4.35
3510 9532 4.009675 AGATGCGAACTATGAAAAAGCCA 58.990 39.130 0.00 0.00 0.00 4.75
3511 9533 4.458989 AGATGCGAACTATGAAAAAGCCAA 59.541 37.500 0.00 0.00 0.00 4.52
3512 9534 4.576216 TGCGAACTATGAAAAAGCCAAA 57.424 36.364 0.00 0.00 0.00 3.28
3513 9535 5.132897 TGCGAACTATGAAAAAGCCAAAT 57.867 34.783 0.00 0.00 0.00 2.32
3514 9536 5.537188 TGCGAACTATGAAAAAGCCAAATT 58.463 33.333 0.00 0.00 0.00 1.82
3515 9537 5.633182 TGCGAACTATGAAAAAGCCAAATTC 59.367 36.000 0.00 0.00 0.00 2.17
3516 9538 5.633182 GCGAACTATGAAAAAGCCAAATTCA 59.367 36.000 0.00 0.00 37.47 2.57
3517 9539 6.183360 GCGAACTATGAAAAAGCCAAATTCAG 60.183 38.462 0.00 0.00 36.59 3.02
3518 9540 6.183360 CGAACTATGAAAAAGCCAAATTCAGC 60.183 38.462 0.00 0.00 36.59 4.26
3519 9541 6.100404 ACTATGAAAAAGCCAAATTCAGCA 57.900 33.333 2.85 0.00 36.59 4.41
3520 9542 6.523840 ACTATGAAAAAGCCAAATTCAGCAA 58.476 32.000 2.85 0.00 36.59 3.91
3521 9543 7.163441 ACTATGAAAAAGCCAAATTCAGCAAT 58.837 30.769 2.85 0.00 36.59 3.56
3522 9544 5.676532 TGAAAAAGCCAAATTCAGCAATG 57.323 34.783 2.85 0.00 0.00 2.82
3523 9545 5.366460 TGAAAAAGCCAAATTCAGCAATGA 58.634 33.333 2.85 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 4.946157 CAGGATTTGGATGGGATATGCTAC 59.054 45.833 0.00 0.00 0.00 3.58
131 135 0.510359 CGTGCAGAGAGTTGACTTGC 59.490 55.000 0.00 0.52 0.00 4.01
165 172 8.108999 TGAGTCATCTATTTTGAAATGGAAGGA 58.891 33.333 6.61 5.45 38.98 3.36
166 173 8.284945 TGAGTCATCTATTTTGAAATGGAAGG 57.715 34.615 6.61 3.58 38.98 3.46
168 175 8.236586 CGTTGAGTCATCTATTTTGAAATGGAA 58.763 33.333 6.61 0.00 38.98 3.53
169 176 7.390440 ACGTTGAGTCATCTATTTTGAAATGGA 59.610 33.333 5.21 5.21 39.67 3.41
170 177 7.530010 ACGTTGAGTCATCTATTTTGAAATGG 58.470 34.615 0.00 0.00 0.00 3.16
171 178 8.843733 CAACGTTGAGTCATCTATTTTGAAATG 58.156 33.333 23.90 0.00 0.00 2.32
172 179 8.567948 ACAACGTTGAGTCATCTATTTTGAAAT 58.432 29.630 33.66 2.00 0.00 2.17
173 180 7.925993 ACAACGTTGAGTCATCTATTTTGAAA 58.074 30.769 33.66 0.00 0.00 2.69
174 181 7.490962 ACAACGTTGAGTCATCTATTTTGAA 57.509 32.000 33.66 0.00 0.00 2.69
175 182 8.771920 ATACAACGTTGAGTCATCTATTTTGA 57.228 30.769 33.66 0.00 0.00 2.69
180 187 9.871238 ACTTTAATACAACGTTGAGTCATCTAT 57.129 29.630 33.66 16.00 0.00 1.98
181 188 9.701098 AACTTTAATACAACGTTGAGTCATCTA 57.299 29.630 33.66 14.42 0.00 1.98
182 189 8.603242 AACTTTAATACAACGTTGAGTCATCT 57.397 30.769 33.66 12.61 0.00 2.90
201 208 9.944376 AGATGACTCAGCTTTGTATTAACTTTA 57.056 29.630 0.00 0.00 0.00 1.85
202 209 8.854614 AGATGACTCAGCTTTGTATTAACTTT 57.145 30.769 0.00 0.00 0.00 2.66
208 215 9.453572 TGAAAATAGATGACTCAGCTTTGTATT 57.546 29.630 1.33 0.00 30.76 1.89
209 216 9.453572 TTGAAAATAGATGACTCAGCTTTGTAT 57.546 29.630 1.33 0.00 30.76 2.29
210 217 8.846943 TTGAAAATAGATGACTCAGCTTTGTA 57.153 30.769 1.33 0.00 30.76 2.41
211 218 7.750229 TTGAAAATAGATGACTCAGCTTTGT 57.250 32.000 1.33 0.00 30.76 2.83
212 219 7.269937 CGTTTGAAAATAGATGACTCAGCTTTG 59.730 37.037 1.33 0.00 30.76 2.77
213 220 7.301054 CGTTTGAAAATAGATGACTCAGCTTT 58.699 34.615 1.33 0.00 30.76 3.51
214 221 6.128172 CCGTTTGAAAATAGATGACTCAGCTT 60.128 38.462 1.33 0.00 30.76 3.74
215 222 5.352569 CCGTTTGAAAATAGATGACTCAGCT 59.647 40.000 1.74 1.74 33.54 4.24
216 223 5.351465 TCCGTTTGAAAATAGATGACTCAGC 59.649 40.000 0.00 0.00 0.00 4.26
217 224 6.036517 CCTCCGTTTGAAAATAGATGACTCAG 59.963 42.308 0.00 0.00 0.00 3.35
218 225 5.874810 CCTCCGTTTGAAAATAGATGACTCA 59.125 40.000 0.00 0.00 0.00 3.41
219 226 5.294552 CCCTCCGTTTGAAAATAGATGACTC 59.705 44.000 0.00 0.00 0.00 3.36
220 227 5.045869 TCCCTCCGTTTGAAAATAGATGACT 60.046 40.000 0.00 0.00 0.00 3.41
221 228 5.183228 TCCCTCCGTTTGAAAATAGATGAC 58.817 41.667 0.00 0.00 0.00 3.06
222 229 5.045869 ACTCCCTCCGTTTGAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
223 230 5.186198 ACTCCCTCCGTTTGAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
224 231 5.437191 ACTCCCTCCGTTTGAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
225 232 4.903045 ACTCCCTCCGTTTGAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
226 233 4.571176 GCTACTCCCTCCGTTTGAAAATAG 59.429 45.833 0.00 0.00 0.00 1.73
227 234 4.224370 AGCTACTCCCTCCGTTTGAAAATA 59.776 41.667 0.00 0.00 0.00 1.40
228 235 3.009143 AGCTACTCCCTCCGTTTGAAAAT 59.991 43.478 0.00 0.00 0.00 1.82
229 236 2.370849 AGCTACTCCCTCCGTTTGAAAA 59.629 45.455 0.00 0.00 0.00 2.29
230 237 1.975680 AGCTACTCCCTCCGTTTGAAA 59.024 47.619 0.00 0.00 0.00 2.69
231 238 1.640917 AGCTACTCCCTCCGTTTGAA 58.359 50.000 0.00 0.00 0.00 2.69
232 239 1.275291 CAAGCTACTCCCTCCGTTTGA 59.725 52.381 0.00 0.00 0.00 2.69
233 240 1.002087 ACAAGCTACTCCCTCCGTTTG 59.998 52.381 0.00 0.00 0.00 2.93
234 241 1.349067 ACAAGCTACTCCCTCCGTTT 58.651 50.000 0.00 0.00 0.00 3.60
235 242 1.823610 GTACAAGCTACTCCCTCCGTT 59.176 52.381 0.00 0.00 0.00 4.44
236 243 1.005687 AGTACAAGCTACTCCCTCCGT 59.994 52.381 0.00 0.00 0.00 4.69
237 244 1.765230 AGTACAAGCTACTCCCTCCG 58.235 55.000 0.00 0.00 0.00 4.63
238 245 3.900971 AGTAGTACAAGCTACTCCCTCC 58.099 50.000 2.52 0.00 46.05 4.30
298 1476 9.995003 TGATTTTCACCTTATTTGCTTGTTAAT 57.005 25.926 0.00 0.00 0.00 1.40
304 1482 8.686334 ACGATATGATTTTCACCTTATTTGCTT 58.314 29.630 0.00 0.00 0.00 3.91
321 1499 2.729882 GACGGCGCTTAAACGATATGAT 59.270 45.455 6.90 0.00 34.06 2.45
353 2253 5.583854 ACTTCTCATTGCACATGTAAGCTAG 59.416 40.000 9.33 3.05 0.00 3.42
354 2254 5.491070 ACTTCTCATTGCACATGTAAGCTA 58.509 37.500 9.33 2.64 0.00 3.32
355 2255 4.330250 ACTTCTCATTGCACATGTAAGCT 58.670 39.130 9.33 0.00 0.00 3.74
356 2256 4.691860 ACTTCTCATTGCACATGTAAGC 57.308 40.909 0.00 0.00 0.00 3.09
481 2388 2.604462 CACAAAACTTGCAGGTTGAAGC 59.396 45.455 15.63 0.00 0.00 3.86
483 2390 2.676463 GCCACAAAACTTGCAGGTTGAA 60.676 45.455 15.63 0.00 33.22 2.69
566 2473 5.474578 TGTTGAGAGAGACTGCATTAGTT 57.525 39.130 0.00 0.00 40.53 2.24
567 2474 5.474578 TTGTTGAGAGAGACTGCATTAGT 57.525 39.130 0.00 0.00 44.02 2.24
587 2494 8.454106 GGCTGCCAAACTACTTATATGATATTG 58.546 37.037 15.17 0.00 0.00 1.90
589 2496 7.037297 AGGGCTGCCAAACTACTTATATGATAT 60.037 37.037 22.05 0.00 0.00 1.63
617 2604 4.833478 ACATCTGTCCTGCTGAACTTAT 57.167 40.909 0.00 0.00 0.00 1.73
618 2605 4.380550 CGTACATCTGTCCTGCTGAACTTA 60.381 45.833 0.00 0.00 0.00 2.24
619 2606 3.615110 CGTACATCTGTCCTGCTGAACTT 60.615 47.826 0.00 0.00 0.00 2.66
620 2607 2.094494 CGTACATCTGTCCTGCTGAACT 60.094 50.000 0.00 0.00 0.00 3.01
621 2608 2.094700 TCGTACATCTGTCCTGCTGAAC 60.095 50.000 0.00 0.00 0.00 3.18
622 2609 2.167662 TCGTACATCTGTCCTGCTGAA 58.832 47.619 0.00 0.00 0.00 3.02
623 2610 1.834188 TCGTACATCTGTCCTGCTGA 58.166 50.000 0.00 0.00 0.00 4.26
624 2611 2.544694 GGATCGTACATCTGTCCTGCTG 60.545 54.545 0.00 0.00 0.00 4.41
625 2612 1.683917 GGATCGTACATCTGTCCTGCT 59.316 52.381 0.00 0.00 0.00 4.24
626 2613 1.269831 GGGATCGTACATCTGTCCTGC 60.270 57.143 0.00 0.00 0.00 4.85
627 2614 2.035193 CAGGGATCGTACATCTGTCCTG 59.965 54.545 11.12 11.12 35.27 3.86
628 2615 2.311463 CAGGGATCGTACATCTGTCCT 58.689 52.381 0.00 0.00 0.00 3.85
629 2616 2.032620 ACAGGGATCGTACATCTGTCC 58.967 52.381 0.00 0.00 34.00 4.02
682 2669 0.250295 TTGACCGGCTTCTGTTCCTG 60.250 55.000 0.00 0.00 0.00 3.86
695 2686 5.235616 ACGCCATTAGTTATATGTTTGACCG 59.764 40.000 0.00 0.00 0.00 4.79
790 2792 6.073003 GCTGGCATATTCTTTGGTATCTACAC 60.073 42.308 0.00 0.00 0.00 2.90
791 2793 5.997746 GCTGGCATATTCTTTGGTATCTACA 59.002 40.000 0.00 0.00 0.00 2.74
798 2800 3.370840 TCAGCTGGCATATTCTTTGGT 57.629 42.857 15.13 0.00 0.00 3.67
853 2856 1.067495 GTTTGTGCTAGAGAGACCGCT 60.067 52.381 0.00 0.00 0.00 5.52
855 2858 1.272490 TGGTTTGTGCTAGAGAGACCG 59.728 52.381 0.00 0.00 0.00 4.79
856 2859 3.402628 TTGGTTTGTGCTAGAGAGACC 57.597 47.619 0.00 0.00 0.00 3.85
923 2927 1.208052 GGAGCTGTGGACTAAGATGCA 59.792 52.381 0.00 0.00 0.00 3.96
943 2947 1.357907 CTTGCTTCTTGGAGCTCTCG 58.642 55.000 14.64 2.41 43.11 4.04
1133 3140 3.276857 CAGGTGAAGAAGGACATCCATG 58.723 50.000 0.00 0.00 38.89 3.66
1257 3264 1.919600 GCCTGGAGAAGATGGCACCT 61.920 60.000 0.00 0.00 44.34 4.00
1293 3300 0.251341 GTGGGCCAAGAAGGTCACAT 60.251 55.000 8.40 0.00 46.80 3.21
1353 3360 4.060205 CGATGATGGACATGCAGAATACA 58.940 43.478 0.00 0.00 39.56 2.29
1416 3423 0.734253 CGAAGGTGGCAAGAGAGACG 60.734 60.000 0.00 0.00 0.00 4.18
1626 3633 1.548081 CCATCACCACCAGCATCAAA 58.452 50.000 0.00 0.00 0.00 2.69
1875 3882 2.180017 GCAATGGTTCCAGCAGCG 59.820 61.111 0.00 0.00 0.00 5.18
2001 4008 2.230664 TCCACCTGCAGTTTGGAGT 58.769 52.632 24.03 7.59 33.66 3.85
2139 4146 2.434359 CCGAGGGAGCGTTTGGAC 60.434 66.667 0.00 0.00 0.00 4.02
2160 4167 2.356793 CCGCTCATGCCGGAGATC 60.357 66.667 16.65 0.00 37.05 2.75
2181 4188 2.994699 CCTCCCACATTACCGCCA 59.005 61.111 0.00 0.00 0.00 5.69
2553 4564 4.408694 GGCCATGTACACGTTTTCATAAC 58.591 43.478 0.00 0.00 0.00 1.89
2554 4565 3.440872 GGGCCATGTACACGTTTTCATAA 59.559 43.478 4.39 0.00 0.00 1.90
2564 4590 0.960364 CACCACAGGGCCATGTACAC 60.960 60.000 24.77 0.00 37.90 2.90
2626 4662 1.429148 GATAGGCGCCCACAAAGTCG 61.429 60.000 26.15 0.00 0.00 4.18
2650 4686 1.766864 GGGGCCTCCTCTAAGGGTC 60.767 68.421 0.84 0.00 36.88 4.46
2669 4706 6.591750 AGCCTCCATGTACACATATACTAC 57.408 41.667 0.00 0.00 34.26 2.73
2674 4711 4.020751 CAGCTAGCCTCCATGTACACATAT 60.021 45.833 12.13 0.00 34.26 1.78
2676 4713 2.103771 CAGCTAGCCTCCATGTACACAT 59.896 50.000 12.13 0.00 36.96 3.21
2697 4738 7.226128 TCTCATCACATGATACAAGCAAAGATC 59.774 37.037 0.00 0.00 38.85 2.75
2727 4768 6.738453 GCATTAATTCCGGCCACTTATTGATT 60.738 38.462 2.24 0.00 0.00 2.57
2740 4781 5.208624 CATAGACGATGCATTAATTCCGG 57.791 43.478 0.00 0.00 0.00 5.14
2768 4809 9.421806 TGAATAGGATAAAAGCAAACACAAATG 57.578 29.630 0.00 0.00 0.00 2.32
2770 4811 8.637986 AGTGAATAGGATAAAAGCAAACACAAA 58.362 29.630 0.00 0.00 0.00 2.83
2801 4842 7.648142 TGCGAAAGTCTTCATCTTACATTTTT 58.352 30.769 0.00 0.00 0.00 1.94
2802 4843 7.202016 TGCGAAAGTCTTCATCTTACATTTT 57.798 32.000 0.00 0.00 0.00 1.82
2803 4844 6.801539 TGCGAAAGTCTTCATCTTACATTT 57.198 33.333 0.00 0.00 0.00 2.32
2804 4845 6.204688 TGTTGCGAAAGTCTTCATCTTACATT 59.795 34.615 0.00 0.00 0.00 2.71
2805 4846 5.700832 TGTTGCGAAAGTCTTCATCTTACAT 59.299 36.000 0.00 0.00 0.00 2.29
2806 4847 5.050363 GTGTTGCGAAAGTCTTCATCTTACA 60.050 40.000 0.00 0.00 0.00 2.41
2808 4849 4.149922 CGTGTTGCGAAAGTCTTCATCTTA 59.850 41.667 0.00 0.00 44.77 2.10
2809 4850 3.059597 CGTGTTGCGAAAGTCTTCATCTT 60.060 43.478 0.00 0.00 44.77 2.40
2832 4884 5.297547 AGGATATATTGTGTACTTGCACGG 58.702 41.667 0.00 0.00 41.94 4.94
2836 4888 9.712305 AGTGAATAGGATATATTGTGTACTTGC 57.288 33.333 0.00 0.00 0.00 4.01
2860 4912 9.955102 ATGCATTGTCATCATAATATACTGAGT 57.045 29.630 0.00 0.00 0.00 3.41
2862 4914 9.090692 CGATGCATTGTCATCATAATATACTGA 57.909 33.333 0.00 0.00 42.15 3.41
2863 4915 9.090692 TCGATGCATTGTCATCATAATATACTG 57.909 33.333 13.73 2.71 42.15 2.74
2866 4918 9.874205 TTCTCGATGCATTGTCATCATAATATA 57.126 29.630 13.73 0.00 42.15 0.86
2867 4919 8.782339 TTCTCGATGCATTGTCATCATAATAT 57.218 30.769 13.73 0.00 42.15 1.28
2868 4920 8.782339 ATTCTCGATGCATTGTCATCATAATA 57.218 30.769 13.73 0.00 42.15 0.98
2869 4921 7.683437 ATTCTCGATGCATTGTCATCATAAT 57.317 32.000 13.73 11.00 42.15 1.28
2870 4922 8.606040 TTATTCTCGATGCATTGTCATCATAA 57.394 30.769 13.73 7.85 42.15 1.90
2871 4923 8.782339 ATTATTCTCGATGCATTGTCATCATA 57.218 30.769 13.73 2.80 42.15 2.15
2872 4924 7.683437 ATTATTCTCGATGCATTGTCATCAT 57.317 32.000 13.73 3.63 42.15 2.45
2873 4925 7.656948 TGTATTATTCTCGATGCATTGTCATCA 59.343 33.333 13.73 0.00 42.15 3.07
2980 8954 4.320788 GGCTACAAGCATGCATTTCCTATC 60.321 45.833 21.98 0.03 44.75 2.08
2985 8959 2.533266 GTGGCTACAAGCATGCATTTC 58.467 47.619 21.98 3.35 44.75 2.17
2987 8961 0.819582 GGTGGCTACAAGCATGCATT 59.180 50.000 21.98 8.51 44.75 3.56
3192 9209 1.300697 GTGGGCTCGTCAGTCGTTT 60.301 57.895 0.00 0.00 40.80 3.60
3199 9216 1.379443 AGTATCCGTGGGCTCGTCA 60.379 57.895 2.69 0.00 0.00 4.35
3204 9221 1.221840 CTTGCAGTATCCGTGGGCT 59.778 57.895 0.00 0.00 0.00 5.19
3250 9270 5.804771 GCCCTTCTCAAAGCCCCTTATATAG 60.805 48.000 0.00 0.00 0.00 1.31
3251 9271 4.042934 GCCCTTCTCAAAGCCCCTTATATA 59.957 45.833 0.00 0.00 0.00 0.86
3258 9279 2.363018 GGCCCTTCTCAAAGCCCC 60.363 66.667 0.00 0.00 39.60 5.80
3262 9283 3.703001 TTCAGTAGGCCCTTCTCAAAG 57.297 47.619 0.00 0.00 0.00 2.77
3265 9286 3.706594 CTGTATTCAGTAGGCCCTTCTCA 59.293 47.826 0.00 0.00 36.97 3.27
3272 9293 3.543680 TGAAGCTGTATTCAGTAGGCC 57.456 47.619 0.00 0.00 43.05 5.19
3275 9296 8.821894 GTTCCTTTATGAAGCTGTATTCAGTAG 58.178 37.037 1.02 0.00 42.20 2.57
3276 9297 8.318412 TGTTCCTTTATGAAGCTGTATTCAGTA 58.682 33.333 1.02 0.00 42.20 2.74
3277 9298 7.168219 TGTTCCTTTATGAAGCTGTATTCAGT 58.832 34.615 1.02 0.00 42.20 3.41
3278 9299 7.615582 TGTTCCTTTATGAAGCTGTATTCAG 57.384 36.000 0.00 0.00 42.20 3.02
3282 9303 7.229506 GCCTTATGTTCCTTTATGAAGCTGTAT 59.770 37.037 0.00 0.00 0.00 2.29
3294 9315 3.572255 TCTTTTGCGCCTTATGTTCCTTT 59.428 39.130 4.18 0.00 0.00 3.11
3328 9350 2.515854 TGAGTAGAAAGACGTGCTCCT 58.484 47.619 0.00 0.00 0.00 3.69
3340 9362 5.163248 TGGTCTGAATGGTTGTTGAGTAGAA 60.163 40.000 0.00 0.00 0.00 2.10
3354 9376 9.868277 GTATAATATTCTCTCCTGGTCTGAATG 57.132 37.037 15.40 0.00 0.00 2.67
3358 9380 6.659668 TCCGTATAATATTCTCTCCTGGTCTG 59.340 42.308 0.00 0.00 0.00 3.51
3359 9381 6.791371 TCCGTATAATATTCTCTCCTGGTCT 58.209 40.000 0.00 0.00 0.00 3.85
3360 9382 7.463961 TTCCGTATAATATTCTCTCCTGGTC 57.536 40.000 0.00 0.00 0.00 4.02
3361 9383 7.256225 GGTTTCCGTATAATATTCTCTCCTGGT 60.256 40.741 0.00 0.00 0.00 4.00
3362 9384 7.097834 GGTTTCCGTATAATATTCTCTCCTGG 58.902 42.308 0.00 0.00 0.00 4.45
3363 9385 7.667557 TGGTTTCCGTATAATATTCTCTCCTG 58.332 38.462 0.00 0.00 0.00 3.86
3364 9386 7.850935 TGGTTTCCGTATAATATTCTCTCCT 57.149 36.000 0.00 0.00 0.00 3.69
3365 9387 7.929785 TGTTGGTTTCCGTATAATATTCTCTCC 59.070 37.037 0.00 0.00 0.00 3.71
3366 9388 8.882415 TGTTGGTTTCCGTATAATATTCTCTC 57.118 34.615 0.00 0.00 0.00 3.20
3367 9389 9.847224 AATGTTGGTTTCCGTATAATATTCTCT 57.153 29.630 0.00 0.00 0.00 3.10
3369 9391 9.621629 TGAATGTTGGTTTCCGTATAATATTCT 57.378 29.630 0.00 0.00 33.10 2.40
3374 9396 8.798402 TCTTTTGAATGTTGGTTTCCGTATAAT 58.202 29.630 0.00 0.00 0.00 1.28
3375 9397 8.167605 TCTTTTGAATGTTGGTTTCCGTATAA 57.832 30.769 0.00 0.00 0.00 0.98
3376 9398 7.747155 TCTTTTGAATGTTGGTTTCCGTATA 57.253 32.000 0.00 0.00 0.00 1.47
3377 9399 6.642707 TCTTTTGAATGTTGGTTTCCGTAT 57.357 33.333 0.00 0.00 0.00 3.06
3378 9400 6.267070 GTTCTTTTGAATGTTGGTTTCCGTA 58.733 36.000 0.00 0.00 40.94 4.02
3379 9401 4.993029 TCTTTTGAATGTTGGTTTCCGT 57.007 36.364 0.00 0.00 0.00 4.69
3380 9402 4.506288 GGTTCTTTTGAATGTTGGTTTCCG 59.494 41.667 0.00 0.00 40.94 4.30
3381 9403 5.670485 AGGTTCTTTTGAATGTTGGTTTCC 58.330 37.500 0.00 0.00 40.94 3.13
3382 9404 5.753438 GGAGGTTCTTTTGAATGTTGGTTTC 59.247 40.000 0.00 0.00 40.94 2.78
3383 9405 5.670485 GGAGGTTCTTTTGAATGTTGGTTT 58.330 37.500 0.00 0.00 40.94 3.27
3384 9406 4.202111 CGGAGGTTCTTTTGAATGTTGGTT 60.202 41.667 0.00 0.00 40.94 3.67
3385 9407 3.317993 CGGAGGTTCTTTTGAATGTTGGT 59.682 43.478 0.00 0.00 40.94 3.67
3386 9408 3.317993 ACGGAGGTTCTTTTGAATGTTGG 59.682 43.478 0.00 0.00 40.94 3.77
3387 9409 4.290155 CACGGAGGTTCTTTTGAATGTTG 58.710 43.478 0.00 0.00 40.94 3.33
3388 9410 3.317993 CCACGGAGGTTCTTTTGAATGTT 59.682 43.478 0.00 0.00 40.94 2.71
3389 9411 2.884639 CCACGGAGGTTCTTTTGAATGT 59.115 45.455 0.00 0.00 40.94 2.71
3390 9412 3.146066 TCCACGGAGGTTCTTTTGAATG 58.854 45.455 0.00 0.00 40.94 2.67
3391 9413 3.502123 TCCACGGAGGTTCTTTTGAAT 57.498 42.857 0.00 0.00 40.94 2.57
3392 9414 3.284793 TTCCACGGAGGTTCTTTTGAA 57.715 42.857 0.00 0.00 39.02 2.69
3393 9415 3.284793 TTTCCACGGAGGTTCTTTTGA 57.715 42.857 0.00 0.00 39.02 2.69
3394 9416 4.278419 AGATTTTCCACGGAGGTTCTTTTG 59.722 41.667 0.00 0.00 39.02 2.44
3395 9417 4.470602 AGATTTTCCACGGAGGTTCTTTT 58.529 39.130 0.00 0.00 39.02 2.27
3396 9418 4.100279 AGATTTTCCACGGAGGTTCTTT 57.900 40.909 0.00 0.00 39.02 2.52
3397 9419 3.790089 AGATTTTCCACGGAGGTTCTT 57.210 42.857 0.00 0.00 39.02 2.52
3398 9420 4.903045 TTAGATTTTCCACGGAGGTTCT 57.097 40.909 0.00 0.00 39.02 3.01
3399 9421 5.952526 TTTTAGATTTTCCACGGAGGTTC 57.047 39.130 0.00 0.00 39.02 3.62
3447 9469 9.606631 ACTTAAAGTTTCACATGGCAATAAAAA 57.393 25.926 0.00 0.00 0.00 1.94
3452 9474 9.606631 TTTTTACTTAAAGTTTCACATGGCAAT 57.393 25.926 0.00 0.00 0.00 3.56
3453 9475 8.874816 GTTTTTACTTAAAGTTTCACATGGCAA 58.125 29.630 0.00 0.00 0.00 4.52
3454 9476 8.035394 TGTTTTTACTTAAAGTTTCACATGGCA 58.965 29.630 0.00 0.00 0.00 4.92
3455 9477 8.325282 GTGTTTTTACTTAAAGTTTCACATGGC 58.675 33.333 0.00 0.00 0.00 4.40
3456 9478 9.360093 TGTGTTTTTACTTAAAGTTTCACATGG 57.640 29.630 0.00 0.00 0.00 3.66
3467 9489 9.601971 GCATCTCGTATTGTGTTTTTACTTAAA 57.398 29.630 0.00 0.00 0.00 1.52
3468 9490 7.953173 CGCATCTCGTATTGTGTTTTTACTTAA 59.047 33.333 0.00 0.00 0.00 1.85
3469 9491 7.328982 TCGCATCTCGTATTGTGTTTTTACTTA 59.671 33.333 0.00 0.00 39.67 2.24
3470 9492 6.146510 TCGCATCTCGTATTGTGTTTTTACTT 59.853 34.615 0.00 0.00 39.67 2.24
3471 9493 5.636121 TCGCATCTCGTATTGTGTTTTTACT 59.364 36.000 0.00 0.00 39.67 2.24
3472 9494 5.849858 TCGCATCTCGTATTGTGTTTTTAC 58.150 37.500 0.00 0.00 39.67 2.01
3473 9495 6.146510 AGTTCGCATCTCGTATTGTGTTTTTA 59.853 34.615 0.00 0.00 39.67 1.52
3474 9496 5.049680 AGTTCGCATCTCGTATTGTGTTTTT 60.050 36.000 0.00 0.00 39.67 1.94
3475 9497 4.451096 AGTTCGCATCTCGTATTGTGTTTT 59.549 37.500 0.00 0.00 39.67 2.43
3476 9498 3.994392 AGTTCGCATCTCGTATTGTGTTT 59.006 39.130 0.00 0.00 39.67 2.83
3477 9499 3.585862 AGTTCGCATCTCGTATTGTGTT 58.414 40.909 0.00 0.00 39.67 3.32
3478 9500 3.232213 AGTTCGCATCTCGTATTGTGT 57.768 42.857 0.00 0.00 39.67 3.72
3479 9501 4.976116 TCATAGTTCGCATCTCGTATTGTG 59.024 41.667 0.00 0.00 39.67 3.33
3480 9502 5.183014 TCATAGTTCGCATCTCGTATTGT 57.817 39.130 0.00 0.00 39.67 2.71
3481 9503 6.510746 TTTCATAGTTCGCATCTCGTATTG 57.489 37.500 0.00 0.00 39.67 1.90
3482 9504 7.534085 TTTTTCATAGTTCGCATCTCGTATT 57.466 32.000 0.00 0.00 39.67 1.89
3483 9505 6.292381 GCTTTTTCATAGTTCGCATCTCGTAT 60.292 38.462 0.00 0.00 39.67 3.06
3484 9506 5.005394 GCTTTTTCATAGTTCGCATCTCGTA 59.995 40.000 0.00 0.00 39.67 3.43
3485 9507 4.201724 GCTTTTTCATAGTTCGCATCTCGT 60.202 41.667 0.00 0.00 39.67 4.18
3486 9508 4.266945 GCTTTTTCATAGTTCGCATCTCG 58.733 43.478 0.00 0.00 40.15 4.04
3487 9509 4.094887 TGGCTTTTTCATAGTTCGCATCTC 59.905 41.667 0.00 0.00 0.00 2.75
3488 9510 4.009675 TGGCTTTTTCATAGTTCGCATCT 58.990 39.130 0.00 0.00 0.00 2.90
3489 9511 4.355543 TGGCTTTTTCATAGTTCGCATC 57.644 40.909 0.00 0.00 0.00 3.91
3490 9512 4.782019 TTGGCTTTTTCATAGTTCGCAT 57.218 36.364 0.00 0.00 0.00 4.73
3491 9513 4.576216 TTTGGCTTTTTCATAGTTCGCA 57.424 36.364 0.00 0.00 0.00 5.10
3492 9514 5.633182 TGAATTTGGCTTTTTCATAGTTCGC 59.367 36.000 0.00 0.00 0.00 4.70
3493 9515 6.183360 GCTGAATTTGGCTTTTTCATAGTTCG 60.183 38.462 0.00 0.00 0.00 3.95
3494 9516 6.646240 TGCTGAATTTGGCTTTTTCATAGTTC 59.354 34.615 5.45 0.00 0.00 3.01
3495 9517 6.523840 TGCTGAATTTGGCTTTTTCATAGTT 58.476 32.000 5.45 0.00 0.00 2.24
3496 9518 6.100404 TGCTGAATTTGGCTTTTTCATAGT 57.900 33.333 5.45 0.00 0.00 2.12
3497 9519 7.332430 TCATTGCTGAATTTGGCTTTTTCATAG 59.668 33.333 5.45 0.00 0.00 2.23
3498 9520 7.160049 TCATTGCTGAATTTGGCTTTTTCATA 58.840 30.769 5.45 0.00 0.00 2.15
3499 9521 5.998981 TCATTGCTGAATTTGGCTTTTTCAT 59.001 32.000 5.45 0.00 0.00 2.57
3500 9522 5.366460 TCATTGCTGAATTTGGCTTTTTCA 58.634 33.333 5.45 0.00 0.00 2.69
3501 9523 5.927954 TCATTGCTGAATTTGGCTTTTTC 57.072 34.783 5.45 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.