Multiple sequence alignment - TraesCS4D01G143200

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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 TraesCS4D01G143200 chr4D 100.000 6556 0 0 1 6556 130546373 130552928 0.000000e+00 12107.0
1 TraesCS4D01G143200 chr4D 87.037 108 10 2 633 739 111131657 111131761 1.150000e-22 119.0
2 TraesCS4D01G143200 chr4A 96.695 3419 90 13 3023 6430 436444373 436440967 0.000000e+00 5666.0
3 TraesCS4D01G143200 chr4A 93.017 1604 60 20 1458 3027 436451485 436449900 0.000000e+00 2294.0
4 TraesCS4D01G143200 chr4A 85.152 1017 94 26 335 1322 436452459 436451471 0.000000e+00 989.0
5 TraesCS4D01G143200 chr4A 89.904 208 18 3 123 328 436822100 436821894 1.400000e-66 265.0
6 TraesCS4D01G143200 chrUn 97.601 2876 51 8 654 3514 56079425 56076553 0.000000e+00 4913.0
7 TraesCS4D01G143200 chrUn 99.702 2013 6 0 2801 4813 358692917 358694929 0.000000e+00 3685.0
8 TraesCS4D01G143200 chrUn 99.012 1720 14 2 4221 5940 55721899 55723615 0.000000e+00 3079.0
9 TraesCS4D01G143200 chrUn 96.931 619 12 1 5937 6555 55723695 55724306 0.000000e+00 1031.0
10 TraesCS4D01G143200 chrUn 85.383 431 52 6 222 644 56089894 56089467 2.810000e-118 436.0
11 TraesCS4D01G143200 chrUn 89.520 229 20 4 1 227 53477511 53477285 2.990000e-73 287.0
12 TraesCS4D01G143200 chr5D 94.326 141 6 2 1317 1455 302711222 302711362 1.430000e-51 215.0
13 TraesCS4D01G143200 chr5D 85.227 88 12 1 656 742 114002241 114002154 9.050000e-14 89.8
14 TraesCS4D01G143200 chr1D 94.531 128 6 1 1332 1458 391284109 391284236 5.190000e-46 196.0
15 TraesCS4D01G143200 chr1D 85.981 107 10 5 632 735 459872381 459872485 6.950000e-20 110.0
16 TraesCS4D01G143200 chr1D 84.685 111 12 4 627 734 459867406 459867514 8.990000e-19 106.0
17 TraesCS4D01G143200 chr1B 93.023 129 8 1 1332 1459 16662414 16662286 3.120000e-43 187.0
18 TraesCS4D01G143200 chr6D 92.969 128 8 1 1332 1458 224799468 224799341 1.120000e-42 185.0
19 TraesCS4D01G143200 chr1A 90.625 128 11 1 1332 1458 22350637 22350510 1.130000e-37 169.0
20 TraesCS4D01G143200 chr5B 89.412 85 9 0 1357 1441 88703938 88703854 2.500000e-19 108.0
21 TraesCS4D01G143200 chr7D 89.024 82 9 0 653 734 82607783 82607864 1.160000e-17 102.0
22 TraesCS4D01G143200 chr7D 81.982 111 17 3 634 742 571276374 571276265 2.520000e-14 91.6
23 TraesCS4D01G143200 chr3B 88.095 84 9 1 655 737 46762811 46762894 1.500000e-16 99.0
24 TraesCS4D01G143200 chr3B 86.585 82 10 1 657 737 775823847 775823766 9.050000e-14 89.8
25 TraesCS4D01G143200 chr3D 86.585 82 10 1 657 737 580537748 580537667 9.050000e-14 89.8


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 TraesCS4D01G143200 chr4D 130546373 130552928 6555 False 12107.0 12107 100.0000 1 6556 1 chr4D.!!$F2 6555
1 TraesCS4D01G143200 chr4A 436440967 436444373 3406 True 5666.0 5666 96.6950 3023 6430 1 chr4A.!!$R1 3407
2 TraesCS4D01G143200 chr4A 436449900 436452459 2559 True 1641.5 2294 89.0845 335 3027 2 chr4A.!!$R3 2692
3 TraesCS4D01G143200 chrUn 56076553 56079425 2872 True 4913.0 4913 97.6010 654 3514 1 chrUn.!!$R2 2860
4 TraesCS4D01G143200 chrUn 358692917 358694929 2012 False 3685.0 3685 99.7020 2801 4813 1 chrUn.!!$F1 2012
5 TraesCS4D01G143200 chrUn 55721899 55724306 2407 False 2055.0 3079 97.9715 4221 6555 2 chrUn.!!$F2 2334

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
280 281 0.098376 GCGCTTGATGCAAGAGGAAG 59.902 55.000 11.08 0.00 43.42 3.46 F
281 282 0.098376 CGCTTGATGCAAGAGGAAGC 59.902 55.000 11.08 0.00 43.42 3.86 F
380 381 0.377203 TCACTCCGACGATGATGACG 59.623 55.000 0.00 0.00 0.00 4.35 F
408 409 0.527817 GACTATGAAGGTGCCGTCGG 60.528 60.000 6.99 6.99 0.00 4.79 F
1813 1868 1.000060 GATGCTTGGCTTCAGTTTGCA 60.000 47.619 0.00 0.00 33.71 4.08 F
2758 2823 1.129058 CCCTATAGAAACCGCCCACT 58.871 55.000 0.00 0.00 0.00 4.00 F
2759 2824 2.322658 CCCTATAGAAACCGCCCACTA 58.677 52.381 0.00 0.00 0.00 2.74 F
2760 2825 2.701951 CCCTATAGAAACCGCCCACTAA 59.298 50.000 0.00 0.00 0.00 2.24 F
3791 3860 3.060003 GCATGCTGAAGCTTATGACTACG 60.060 47.826 11.37 0.00 42.66 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1786 1841 0.674895 GAAGCCAAGCATCGTCCAGT 60.675 55.000 0.00 0.00 0.0 4.00 R
1922 1977 1.134189 GGTACCCTTTTCATCCCCTCG 60.134 57.143 0.00 0.00 0.0 4.63 R
2038 2093 1.493772 CAACATTGTGGCTGCAGTTG 58.506 50.000 16.64 6.19 0.0 3.16 R
2161 2216 4.340381 CCCTGGGCTTCTTATCATGAAAAG 59.660 45.833 0.00 2.99 0.0 2.27 R
2799 2868 6.071165 AGGAAAAAGGCAATAACATGAGAAGG 60.071 38.462 0.00 0.00 0.0 3.46 R
4095 4164 4.416516 TGCTATCGATGAAGGGGAATAGA 58.583 43.478 8.54 0.00 0.0 1.98 R
5016 5086 6.330278 TCAATATCTACCTGCATACATACGC 58.670 40.000 0.00 0.00 0.0 4.42 R
5499 5569 5.645067 CCTCAATGTAGTGAATCTTCTTGCA 59.355 40.000 0.00 0.00 0.0 4.08 R
6507 6670 0.394899 GCCAAACCATAGAGCCTGCT 60.395 55.000 0.00 0.00 0.0 4.24 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
17 18 3.003763 AGGAGGTTCCCCAGCGAC 61.004 66.667 0.00 0.00 37.19 5.19
18 19 4.097361 GGAGGTTCCCCAGCGACC 62.097 72.222 0.00 0.00 0.00 4.79
19 20 3.319198 GAGGTTCCCCAGCGACCA 61.319 66.667 0.00 0.00 35.89 4.02
20 21 3.607370 GAGGTTCCCCAGCGACCAC 62.607 68.421 0.00 0.00 35.89 4.16
22 23 3.998672 GTTCCCCAGCGACCACGA 61.999 66.667 0.00 0.00 42.66 4.35
23 24 3.235481 TTCCCCAGCGACCACGAA 61.235 61.111 0.00 0.00 42.66 3.85
24 25 3.234630 TTCCCCAGCGACCACGAAG 62.235 63.158 0.00 0.00 42.66 3.79
25 26 4.760047 CCCCAGCGACCACGAAGG 62.760 72.222 0.00 0.00 42.66 3.46
45 46 3.389206 CGCAAGCGCCTTCTCTAC 58.611 61.111 2.29 0.00 33.11 2.59
46 47 1.153745 CGCAAGCGCCTTCTCTACT 60.154 57.895 2.29 0.00 33.11 2.57
47 48 0.100682 CGCAAGCGCCTTCTCTACTA 59.899 55.000 2.29 0.00 33.11 1.82
48 49 1.562017 GCAAGCGCCTTCTCTACTAC 58.438 55.000 2.29 0.00 0.00 2.73
49 50 1.803252 GCAAGCGCCTTCTCTACTACC 60.803 57.143 2.29 0.00 0.00 3.18
50 51 1.751924 CAAGCGCCTTCTCTACTACCT 59.248 52.381 2.29 0.00 0.00 3.08
51 52 1.682740 AGCGCCTTCTCTACTACCTC 58.317 55.000 2.29 0.00 0.00 3.85
52 53 0.308376 GCGCCTTCTCTACTACCTCG 59.692 60.000 0.00 0.00 0.00 4.63
53 54 0.308376 CGCCTTCTCTACTACCTCGC 59.692 60.000 0.00 0.00 0.00 5.03
54 55 1.682740 GCCTTCTCTACTACCTCGCT 58.317 55.000 0.00 0.00 0.00 4.93
55 56 1.605232 GCCTTCTCTACTACCTCGCTC 59.395 57.143 0.00 0.00 0.00 5.03
56 57 1.868498 CCTTCTCTACTACCTCGCTCG 59.132 57.143 0.00 0.00 0.00 5.03
57 58 1.262151 CTTCTCTACTACCTCGCTCGC 59.738 57.143 0.00 0.00 0.00 5.03
58 59 0.875040 TCTCTACTACCTCGCTCGCG 60.875 60.000 0.00 0.00 41.35 5.87
59 60 1.152989 CTCTACTACCTCGCTCGCGT 61.153 60.000 5.77 0.00 40.74 6.01
60 61 0.742281 TCTACTACCTCGCTCGCGTT 60.742 55.000 5.77 0.16 40.74 4.84
61 62 0.589229 CTACTACCTCGCTCGCGTTG 60.589 60.000 5.77 1.17 40.74 4.10
62 63 1.985447 TACTACCTCGCTCGCGTTGG 61.985 60.000 5.77 18.49 40.74 3.77
63 64 3.338126 CTACCTCGCTCGCGTTGGT 62.338 63.158 24.77 24.77 44.07 3.67
64 65 3.620300 TACCTCGCTCGCGTTGGTG 62.620 63.158 27.39 4.86 42.80 4.17
70 71 4.988598 CTCGCGTTGGTGGTGGCT 62.989 66.667 5.77 0.00 0.00 4.75
71 72 4.980805 TCGCGTTGGTGGTGGCTC 62.981 66.667 5.77 0.00 0.00 4.70
73 74 4.643387 GCGTTGGTGGTGGCTCCT 62.643 66.667 7.19 0.00 37.07 3.69
74 75 2.113139 CGTTGGTGGTGGCTCCTT 59.887 61.111 7.19 0.00 37.07 3.36
75 76 2.260869 CGTTGGTGGTGGCTCCTTG 61.261 63.158 7.19 0.00 37.07 3.61
76 77 1.152756 GTTGGTGGTGGCTCCTTGT 60.153 57.895 7.19 0.00 37.07 3.16
77 78 1.150536 TTGGTGGTGGCTCCTTGTC 59.849 57.895 7.19 0.00 37.07 3.18
78 79 2.034221 GGTGGTGGCTCCTTGTCC 59.966 66.667 7.19 1.29 37.07 4.02
79 80 2.529744 GGTGGTGGCTCCTTGTCCT 61.530 63.158 7.19 0.00 37.07 3.85
80 81 1.302832 GTGGTGGCTCCTTGTCCTG 60.303 63.158 7.19 0.00 37.07 3.86
81 82 1.770110 TGGTGGCTCCTTGTCCTGT 60.770 57.895 7.19 0.00 37.07 4.00
82 83 1.302832 GGTGGCTCCTTGTCCTGTG 60.303 63.158 0.00 0.00 0.00 3.66
83 84 1.451936 GTGGCTCCTTGTCCTGTGT 59.548 57.895 0.00 0.00 0.00 3.72
84 85 0.603975 GTGGCTCCTTGTCCTGTGTC 60.604 60.000 0.00 0.00 0.00 3.67
85 86 1.003233 GGCTCCTTGTCCTGTGTCC 60.003 63.158 0.00 0.00 0.00 4.02
86 87 1.754745 GCTCCTTGTCCTGTGTCCA 59.245 57.895 0.00 0.00 0.00 4.02
87 88 0.321122 GCTCCTTGTCCTGTGTCCAG 60.321 60.000 0.00 0.00 38.50 3.86
95 96 3.148084 CTGTGTCCAGGACCGGTT 58.852 61.111 17.59 0.00 34.90 4.44
96 97 1.301716 CTGTGTCCAGGACCGGTTG 60.302 63.158 17.59 3.31 34.90 3.77
97 98 1.754380 CTGTGTCCAGGACCGGTTGA 61.754 60.000 17.59 0.04 34.90 3.18
98 99 1.125093 TGTGTCCAGGACCGGTTGAT 61.125 55.000 17.59 0.00 0.00 2.57
99 100 0.673644 GTGTCCAGGACCGGTTGATG 60.674 60.000 17.59 8.17 0.00 3.07
100 101 0.834261 TGTCCAGGACCGGTTGATGA 60.834 55.000 17.59 0.45 0.00 2.92
101 102 0.391263 GTCCAGGACCGGTTGATGAC 60.391 60.000 9.42 10.47 0.00 3.06
102 103 1.078426 CCAGGACCGGTTGATGACC 60.078 63.158 9.42 3.57 45.55 4.02
110 111 3.960237 GTTGATGACCACGGCGAA 58.040 55.556 16.62 0.00 0.00 4.70
111 112 1.787847 GTTGATGACCACGGCGAAG 59.212 57.895 16.62 6.64 0.00 3.79
112 113 0.669318 GTTGATGACCACGGCGAAGA 60.669 55.000 16.62 0.00 0.00 2.87
113 114 0.669318 TTGATGACCACGGCGAAGAC 60.669 55.000 16.62 5.11 0.00 3.01
147 148 4.598894 CGCAGCCTCGATGGGGAG 62.599 72.222 0.00 0.00 36.00 4.30
148 149 4.925861 GCAGCCTCGATGGGGAGC 62.926 72.222 0.00 0.00 36.00 4.70
149 150 3.160047 CAGCCTCGATGGGGAGCT 61.160 66.667 0.00 0.00 36.00 4.09
150 151 2.841988 AGCCTCGATGGGGAGCTC 60.842 66.667 4.71 4.71 36.00 4.09
151 152 3.157252 GCCTCGATGGGGAGCTCA 61.157 66.667 17.19 0.00 36.00 4.26
152 153 2.818132 CCTCGATGGGGAGCTCAC 59.182 66.667 17.19 12.85 32.57 3.51
153 154 2.801631 CCTCGATGGGGAGCTCACC 61.802 68.421 29.19 29.19 40.76 4.02
160 161 1.144936 GGGGAGCTCACCAAGATCG 59.855 63.158 30.79 0.00 41.51 3.69
161 162 1.144936 GGGAGCTCACCAAGATCGG 59.855 63.158 17.19 0.00 41.51 4.18
162 163 1.144936 GGAGCTCACCAAGATCGGG 59.855 63.158 17.19 5.06 41.51 5.14
163 164 1.144936 GAGCTCACCAAGATCGGGG 59.855 63.158 9.40 7.64 29.25 5.73
164 165 1.306141 AGCTCACCAAGATCGGGGA 60.306 57.895 12.00 2.26 35.55 4.81
166 167 4.050313 TCACCAAGATCGGGGAGG 57.950 61.111 12.00 2.18 31.82 4.30
167 168 1.080354 TCACCAAGATCGGGGAGGT 59.920 57.895 12.00 2.77 31.82 3.85
168 169 1.221840 CACCAAGATCGGGGAGGTG 59.778 63.158 12.00 10.62 43.14 4.00
169 170 1.229529 ACCAAGATCGGGGAGGTGT 60.230 57.895 12.00 0.00 0.00 4.16
170 171 1.221840 CCAAGATCGGGGAGGTGTG 59.778 63.158 0.00 0.00 0.00 3.82
171 172 1.221840 CAAGATCGGGGAGGTGTGG 59.778 63.158 0.00 0.00 0.00 4.17
172 173 1.229529 AAGATCGGGGAGGTGTGGT 60.230 57.895 0.00 0.00 0.00 4.16
173 174 1.265454 AAGATCGGGGAGGTGTGGTC 61.265 60.000 0.00 0.00 0.00 4.02
174 175 2.687566 ATCGGGGAGGTGTGGTCC 60.688 66.667 0.00 0.00 0.00 4.46
175 176 3.254035 ATCGGGGAGGTGTGGTCCT 62.254 63.158 0.00 0.00 40.97 3.85
176 177 1.882189 ATCGGGGAGGTGTGGTCCTA 61.882 60.000 0.00 0.00 38.02 2.94
177 178 1.611261 CGGGGAGGTGTGGTCCTAA 60.611 63.158 0.00 0.00 38.02 2.69
178 179 1.614241 CGGGGAGGTGTGGTCCTAAG 61.614 65.000 0.00 0.00 38.02 2.18
179 180 0.252558 GGGGAGGTGTGGTCCTAAGA 60.253 60.000 0.00 0.00 38.02 2.10
180 181 1.196012 GGGAGGTGTGGTCCTAAGAG 58.804 60.000 0.00 0.00 38.02 2.85
181 182 1.273098 GGGAGGTGTGGTCCTAAGAGA 60.273 57.143 0.00 0.00 38.02 3.10
182 183 2.104170 GGAGGTGTGGTCCTAAGAGAG 58.896 57.143 0.00 0.00 38.02 3.20
183 184 2.291670 GGAGGTGTGGTCCTAAGAGAGA 60.292 54.545 0.00 0.00 38.02 3.10
184 185 2.756207 GAGGTGTGGTCCTAAGAGAGAC 59.244 54.545 0.00 0.00 38.02 3.36
192 193 3.366396 GTCCTAAGAGAGACCACCATCA 58.634 50.000 0.00 0.00 0.00 3.07
193 194 3.131400 GTCCTAAGAGAGACCACCATCAC 59.869 52.174 0.00 0.00 0.00 3.06
194 195 2.432510 CCTAAGAGAGACCACCATCACC 59.567 54.545 0.00 0.00 0.00 4.02
195 196 0.898320 AAGAGAGACCACCATCACCG 59.102 55.000 0.00 0.00 0.00 4.94
196 197 0.251832 AGAGAGACCACCATCACCGT 60.252 55.000 0.00 0.00 0.00 4.83
197 198 0.173708 GAGAGACCACCATCACCGTC 59.826 60.000 0.00 0.00 0.00 4.79
198 199 1.153823 GAGACCACCATCACCGTCG 60.154 63.158 0.00 0.00 0.00 5.12
199 200 2.125673 GACCACCATCACCGTCGG 60.126 66.667 10.48 10.48 0.00 4.79
200 201 4.388499 ACCACCATCACCGTCGGC 62.388 66.667 12.28 0.00 0.00 5.54
201 202 4.386951 CCACCATCACCGTCGGCA 62.387 66.667 12.28 0.00 0.00 5.69
202 203 2.358125 CACCATCACCGTCGGCAA 60.358 61.111 12.28 0.00 0.00 4.52
203 204 2.047274 ACCATCACCGTCGGCAAG 60.047 61.111 12.28 1.48 0.00 4.01
204 205 2.819595 CCATCACCGTCGGCAAGG 60.820 66.667 12.28 4.65 0.00 3.61
205 206 2.819595 CATCACCGTCGGCAAGGG 60.820 66.667 12.28 0.00 38.94 3.95
206 207 4.778143 ATCACCGTCGGCAAGGGC 62.778 66.667 12.28 0.00 36.30 5.19
211 212 4.697756 CGTCGGCAAGGGCAAGGA 62.698 66.667 0.00 0.00 43.71 3.36
212 213 3.056328 GTCGGCAAGGGCAAGGAC 61.056 66.667 0.00 0.00 43.71 3.85
213 214 3.565214 TCGGCAAGGGCAAGGACA 61.565 61.111 0.00 0.00 43.71 4.02
214 215 2.597217 CGGCAAGGGCAAGGACAA 60.597 61.111 0.00 0.00 43.71 3.18
215 216 1.978617 CGGCAAGGGCAAGGACAAT 60.979 57.895 0.00 0.00 43.71 2.71
216 217 1.593265 GGCAAGGGCAAGGACAATG 59.407 57.895 0.00 0.00 43.71 2.82
217 218 1.593265 GCAAGGGCAAGGACAATGG 59.407 57.895 0.00 0.00 40.72 3.16
218 219 1.593265 CAAGGGCAAGGACAATGGC 59.407 57.895 0.00 0.00 42.20 4.40
221 222 3.291611 GGCAAGGACAATGGCCAG 58.708 61.111 13.05 0.00 45.70 4.85
222 223 2.353610 GGCAAGGACAATGGCCAGG 61.354 63.158 13.05 8.83 45.70 4.45
223 224 2.353610 GCAAGGACAATGGCCAGGG 61.354 63.158 13.05 8.41 0.00 4.45
224 225 2.037847 AAGGACAATGGCCAGGGC 59.962 61.111 13.05 8.25 41.06 5.19
225 226 2.551413 AAGGACAATGGCCAGGGCT 61.551 57.895 13.05 0.00 41.60 5.19
226 227 2.440980 GGACAATGGCCAGGGCTC 60.441 66.667 13.05 2.80 41.60 4.70
227 228 2.440980 GACAATGGCCAGGGCTCC 60.441 66.667 13.05 0.00 41.60 4.70
228 229 4.066139 ACAATGGCCAGGGCTCCC 62.066 66.667 13.05 0.00 41.60 4.30
244 245 3.314331 CCTGAGCAGGGTCGGTGT 61.314 66.667 8.69 0.00 44.87 4.16
245 246 2.743718 CTGAGCAGGGTCGGTGTT 59.256 61.111 0.00 0.00 0.00 3.32
246 247 1.669115 CTGAGCAGGGTCGGTGTTG 60.669 63.158 0.00 0.00 0.00 3.33
247 248 2.358737 GAGCAGGGTCGGTGTTGG 60.359 66.667 0.00 0.00 0.00 3.77
248 249 4.643387 AGCAGGGTCGGTGTTGGC 62.643 66.667 0.00 0.00 0.00 4.52
249 250 4.643387 GCAGGGTCGGTGTTGGCT 62.643 66.667 0.00 0.00 0.00 4.75
250 251 2.669569 CAGGGTCGGTGTTGGCTG 60.670 66.667 0.00 0.00 0.00 4.85
251 252 2.847234 AGGGTCGGTGTTGGCTGA 60.847 61.111 0.00 0.00 0.00 4.26
252 253 2.358737 GGGTCGGTGTTGGCTGAG 60.359 66.667 0.00 0.00 0.00 3.35
253 254 2.358737 GGTCGGTGTTGGCTGAGG 60.359 66.667 0.00 0.00 0.00 3.86
254 255 3.050275 GTCGGTGTTGGCTGAGGC 61.050 66.667 0.00 0.00 37.82 4.70
255 256 3.555324 TCGGTGTTGGCTGAGGCA 61.555 61.111 3.93 3.93 40.87 4.75
256 257 3.052082 CGGTGTTGGCTGAGGCAG 61.052 66.667 9.16 0.00 39.75 4.85
273 274 3.751246 GCCCTGCGCTTGATGCAA 61.751 61.111 9.73 0.00 42.70 4.08
274 275 2.488355 CCCTGCGCTTGATGCAAG 59.512 61.111 9.73 2.91 42.70 4.01
275 276 2.042259 CCCTGCGCTTGATGCAAGA 61.042 57.895 9.73 0.00 43.42 3.02
276 277 1.428219 CCTGCGCTTGATGCAAGAG 59.572 57.895 9.73 8.72 43.42 2.85
277 278 1.428219 CTGCGCTTGATGCAAGAGG 59.572 57.895 9.73 3.41 43.42 3.69
278 279 1.003476 TGCGCTTGATGCAAGAGGA 60.003 52.632 9.73 6.21 43.42 3.71
279 280 0.606130 TGCGCTTGATGCAAGAGGAA 60.606 50.000 9.73 0.00 43.42 3.36
280 281 0.098376 GCGCTTGATGCAAGAGGAAG 59.902 55.000 11.08 0.00 43.42 3.46
281 282 0.098376 CGCTTGATGCAAGAGGAAGC 59.902 55.000 11.08 0.00 43.42 3.86
282 283 1.461559 GCTTGATGCAAGAGGAAGCT 58.538 50.000 11.08 0.00 43.42 3.74
283 284 1.132643 GCTTGATGCAAGAGGAAGCTG 59.867 52.381 11.08 0.00 43.42 4.24
284 285 2.708051 CTTGATGCAAGAGGAAGCTGA 58.292 47.619 1.01 0.00 43.42 4.26
285 286 2.398252 TGATGCAAGAGGAAGCTGAG 57.602 50.000 0.00 0.00 0.00 3.35
286 287 1.015868 GATGCAAGAGGAAGCTGAGC 58.984 55.000 0.00 0.00 0.00 4.26
287 288 0.743701 ATGCAAGAGGAAGCTGAGCG 60.744 55.000 0.00 0.00 0.00 5.03
288 289 2.105466 GCAAGAGGAAGCTGAGCGG 61.105 63.158 0.00 0.00 0.00 5.52
289 290 2.105466 CAAGAGGAAGCTGAGCGGC 61.105 63.158 0.00 0.00 0.00 6.53
290 291 2.289532 AAGAGGAAGCTGAGCGGCT 61.290 57.895 0.00 0.00 45.30 5.52
291 292 2.202864 GAGGAAGCTGAGCGGCTC 60.203 66.667 22.78 22.78 42.24 4.70
292 293 3.731653 GAGGAAGCTGAGCGGCTCC 62.732 68.421 26.00 12.41 42.24 4.70
293 294 3.780173 GGAAGCTGAGCGGCTCCT 61.780 66.667 26.00 14.50 42.24 3.69
294 295 2.202864 GAAGCTGAGCGGCTCCTC 60.203 66.667 26.00 17.16 42.24 3.71
295 296 3.731653 GAAGCTGAGCGGCTCCTCC 62.732 68.421 26.00 14.22 42.24 4.30
297 298 4.828925 GCTGAGCGGCTCCTCCAC 62.829 72.222 26.00 8.10 34.01 4.02
298 299 3.385384 CTGAGCGGCTCCTCCACA 61.385 66.667 26.00 7.07 34.01 4.17
299 300 2.922503 TGAGCGGCTCCTCCACAA 60.923 61.111 26.00 3.64 34.01 3.33
300 301 2.125350 GAGCGGCTCCTCCACAAG 60.125 66.667 19.20 0.00 34.01 3.16
301 302 4.400961 AGCGGCTCCTCCACAAGC 62.401 66.667 0.00 0.00 37.80 4.01
303 304 4.379243 CGGCTCCTCCACAAGCGT 62.379 66.667 0.00 0.00 39.47 5.07
304 305 2.435059 GGCTCCTCCACAAGCGTC 60.435 66.667 0.00 0.00 39.47 5.19
305 306 2.811317 GCTCCTCCACAAGCGTCG 60.811 66.667 0.00 0.00 0.00 5.12
306 307 2.125912 CTCCTCCACAAGCGTCGG 60.126 66.667 0.00 0.00 0.00 4.79
307 308 3.649277 CTCCTCCACAAGCGTCGGG 62.649 68.421 0.00 0.00 0.00 5.14
370 371 3.181506 GCCATTGAAAGAATCACTCCGAC 60.182 47.826 0.00 0.00 37.92 4.79
380 381 0.377203 TCACTCCGACGATGATGACG 59.623 55.000 0.00 0.00 0.00 4.35
381 382 0.592500 CACTCCGACGATGATGACGG 60.593 60.000 0.00 0.00 46.23 4.79
390 391 1.599419 CGATGATGACGGCACATACGA 60.599 52.381 0.00 0.00 34.93 3.43
392 393 0.815095 TGATGACGGCACATACGACT 59.185 50.000 0.00 0.00 34.93 4.18
405 406 1.466856 TACGACTATGAAGGTGCCGT 58.533 50.000 0.00 0.00 0.00 5.68
408 409 0.527817 GACTATGAAGGTGCCGTCGG 60.528 60.000 6.99 6.99 0.00 4.79
437 438 4.988716 AGGCGGACGAGGTCACCA 62.989 66.667 0.00 0.00 34.23 4.17
440 441 2.494918 CGGACGAGGTCACCATCC 59.505 66.667 0.00 0.00 33.68 3.51
441 442 2.348104 CGGACGAGGTCACCATCCA 61.348 63.158 11.36 0.00 33.68 3.41
450 451 4.589908 GAGGTCACCATCCACTACAAATT 58.410 43.478 0.00 0.00 0.00 1.82
536 538 9.825972 AACTTTATGTTCGTCTACATGAATTTG 57.174 29.630 0.00 0.00 39.06 2.32
537 539 8.999431 ACTTTATGTTCGTCTACATGAATTTGT 58.001 29.630 0.00 0.00 39.06 2.83
541 544 6.426327 TGTTCGTCTACATGAATTTGTTGTG 58.574 36.000 0.00 0.00 30.00 3.33
584 587 8.885722 TCAAATTTACTTGTATATCGGTTGGAC 58.114 33.333 0.00 0.00 0.00 4.02
588 591 3.181483 ACTTGTATATCGGTTGGACGGTC 60.181 47.826 0.00 0.00 0.00 4.79
591 594 1.039233 ATATCGGTTGGACGGTCGGT 61.039 55.000 1.43 0.00 0.00 4.69
592 595 1.656818 TATCGGTTGGACGGTCGGTC 61.657 60.000 1.43 1.98 45.31 4.79
593 596 3.677648 CGGTTGGACGGTCGGTCT 61.678 66.667 10.07 0.00 45.35 3.85
600 608 4.648626 ACGGTCGGTCTCGGTCCA 62.649 66.667 0.00 0.00 36.95 4.02
612 620 3.621715 GTCTCGGTCCATGAACAAATACC 59.378 47.826 0.00 0.00 0.00 2.73
618 626 4.097892 GGTCCATGAACAAATACCATGTCC 59.902 45.833 0.00 0.00 36.77 4.02
625 633 5.067936 TGAACAAATACCATGTCCGTTTTGT 59.932 36.000 0.00 0.00 38.53 2.83
627 635 6.636562 ACAAATACCATGTCCGTTTTGTTA 57.363 33.333 0.00 0.00 34.60 2.41
630 638 3.217681 ACCATGTCCGTTTTGTTAGGT 57.782 42.857 0.00 0.00 0.00 3.08
631 639 2.882137 ACCATGTCCGTTTTGTTAGGTG 59.118 45.455 0.00 0.00 0.00 4.00
733 743 3.388024 TCCACATTCATAGACCACCTAGC 59.612 47.826 0.00 0.00 0.00 3.42
734 744 3.134623 CCACATTCATAGACCACCTAGCA 59.865 47.826 0.00 0.00 0.00 3.49
737 747 4.225042 ACATTCATAGACCACCTAGCAACA 59.775 41.667 0.00 0.00 0.00 3.33
738 748 4.901197 TTCATAGACCACCTAGCAACAA 57.099 40.909 0.00 0.00 0.00 2.83
739 749 5.435686 TTCATAGACCACCTAGCAACAAT 57.564 39.130 0.00 0.00 0.00 2.71
740 750 5.435686 TCATAGACCACCTAGCAACAATT 57.564 39.130 0.00 0.00 0.00 2.32
741 751 6.553953 TCATAGACCACCTAGCAACAATTA 57.446 37.500 0.00 0.00 0.00 1.40
742 752 6.953101 TCATAGACCACCTAGCAACAATTAA 58.047 36.000 0.00 0.00 0.00 1.40
743 753 7.047891 TCATAGACCACCTAGCAACAATTAAG 58.952 38.462 0.00 0.00 0.00 1.85
745 755 2.747446 ACCACCTAGCAACAATTAAGCG 59.253 45.455 0.00 0.00 0.00 4.68
747 757 3.063997 CCACCTAGCAACAATTAAGCGAG 59.936 47.826 0.00 0.00 0.00 5.03
748 758 2.678336 ACCTAGCAACAATTAAGCGAGC 59.322 45.455 0.00 0.00 30.93 5.03
749 759 2.032178 CCTAGCAACAATTAAGCGAGCC 59.968 50.000 0.00 0.00 30.93 4.70
750 760 1.533625 AGCAACAATTAAGCGAGCCA 58.466 45.000 0.00 0.00 0.00 4.75
753 763 2.663119 GCAACAATTAAGCGAGCCAAAG 59.337 45.455 0.00 0.00 0.00 2.77
758 785 4.982295 ACAATTAAGCGAGCCAAAGAAAAC 59.018 37.500 0.00 0.00 0.00 2.43
792 819 7.521509 AATCCACTAAAAACGATAAGTCTCG 57.478 36.000 0.00 0.00 44.14 4.04
866 894 1.959226 CCTGCTAACGCCACGTGTT 60.959 57.895 15.65 4.91 39.99 3.32
1302 1333 3.128068 GGTAACGATGAATTTGGTGGGTC 59.872 47.826 0.00 0.00 0.00 4.46
1357 1388 5.428253 TGAAACAGGGATGCTTGTAGTATC 58.572 41.667 1.55 0.67 36.72 2.24
1397 1428 7.946655 TCATTGTTCTGTAACTCTGTAACTG 57.053 36.000 0.00 0.00 36.51 3.16
1464 1495 6.183359 GCAATACTTTCGTCAAAAATGTCGTC 60.183 38.462 0.00 0.00 0.00 4.20
1565 1616 4.584518 TGCTGTGGGTGTGGCTGG 62.585 66.667 0.00 0.00 0.00 4.85
1567 1618 2.595463 CTGTGGGTGTGGCTGGTG 60.595 66.667 0.00 0.00 0.00 4.17
1575 1626 2.554344 GGGTGTGGCTGGTGAGATTTTA 60.554 50.000 0.00 0.00 0.00 1.52
1762 1817 2.529780 TTTTCTTCGGGTTAGCGACA 57.470 45.000 0.00 0.00 0.00 4.35
1786 1841 1.150827 CTGCGCATGTTGAAGACAGA 58.849 50.000 12.24 0.00 42.62 3.41
1813 1868 1.000060 GATGCTTGGCTTCAGTTTGCA 60.000 47.619 0.00 0.00 33.71 4.08
1930 1985 1.781529 TCTTCTAGGCTACGAGGGGAT 59.218 52.381 0.00 0.00 0.00 3.85
2038 2093 4.382147 GGTGAAGAATCTAGTGGTGGAGAC 60.382 50.000 0.00 0.00 0.00 3.36
2435 2500 5.372547 AAATAGAACGCCTTCTTTGTTCC 57.627 39.130 3.21 0.00 42.22 3.62
2673 2738 5.698089 GGATGTCACACACATATGGACTATG 59.302 44.000 7.80 0.00 46.53 2.23
2758 2823 1.129058 CCCTATAGAAACCGCCCACT 58.871 55.000 0.00 0.00 0.00 4.00
2759 2824 2.322658 CCCTATAGAAACCGCCCACTA 58.677 52.381 0.00 0.00 0.00 2.74
2760 2825 2.701951 CCCTATAGAAACCGCCCACTAA 59.298 50.000 0.00 0.00 0.00 2.24
2761 2826 3.326880 CCCTATAGAAACCGCCCACTAAT 59.673 47.826 0.00 0.00 0.00 1.73
3791 3860 3.060003 GCATGCTGAAGCTTATGACTACG 60.060 47.826 11.37 0.00 42.66 3.51
3955 4024 5.300034 TGAGTTCAATGCAAGAATGTGTTCT 59.700 36.000 8.02 0.72 46.50 3.01
4095 4164 6.701340 TGTCACAATAGCTAACTCAATGACT 58.299 36.000 17.42 0.00 35.93 3.41
4219 4288 7.056635 CCTGGTCCTCTATATGACAACATTTT 58.943 38.462 0.00 0.00 37.87 1.82
5016 5086 5.373812 ACAGGGAAGTAGATAAACATGGG 57.626 43.478 0.00 0.00 0.00 4.00
5100 5170 3.136626 GGATCTATAGGTGGTGGCTTGTT 59.863 47.826 0.00 0.00 0.00 2.83
5499 5569 1.333619 GCGTTATGCGACCATTTCCAT 59.666 47.619 0.00 0.00 44.77 3.41
5593 5664 7.195839 AGTTGCTATTCAAGTTCTGTTTCTC 57.804 36.000 0.00 0.00 34.81 2.87
5886 5959 7.589954 CCCAGAACGTCTAAACAAGTTAAATTG 59.410 37.037 13.78 13.78 36.22 2.32
6014 6171 0.801872 TTGATTGAACACGATGCCGG 59.198 50.000 0.00 0.00 40.78 6.13
6015 6172 0.321210 TGATTGAACACGATGCCGGT 60.321 50.000 1.90 0.00 40.78 5.28
6016 6173 0.096976 GATTGAACACGATGCCGGTG 59.903 55.000 1.90 0.00 40.78 4.94
6017 6174 0.321210 ATTGAACACGATGCCGGTGA 60.321 50.000 1.90 0.00 40.78 4.02
6018 6175 0.533085 TTGAACACGATGCCGGTGAA 60.533 50.000 1.90 0.00 40.78 3.18
6019 6176 0.533085 TGAACACGATGCCGGTGAAA 60.533 50.000 1.90 0.00 40.78 2.69
6020 6177 0.165944 GAACACGATGCCGGTGAAAG 59.834 55.000 1.90 0.00 40.78 2.62
6028 6185 0.394488 TGCCGGTGAAAGGTGAAACA 60.394 50.000 1.90 0.00 39.98 2.83
6447 6610 4.569966 GGATTTGACACTCATGTAGCTCAG 59.430 45.833 0.00 0.00 39.95 3.35
6454 6617 2.034878 CTCATGTAGCTCAGCAGGGTA 58.965 52.381 0.00 0.00 0.00 3.69
6503 6666 0.178938 TCGGGGTGGGTGTAGTGTAA 60.179 55.000 0.00 0.00 0.00 2.41
6507 6670 1.972795 GGGTGGGTGTAGTGTAAGTGA 59.027 52.381 0.00 0.00 0.00 3.41
6555 6718 1.487300 TGCATAGGCGTAACCACCTA 58.513 50.000 0.00 0.00 45.35 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.524648 TTCGTGGTCGCTGGGGAAC 62.525 63.158 0.00 0.00 36.96 3.62
6 7 3.234630 CTTCGTGGTCGCTGGGGAA 62.235 63.158 0.00 0.00 36.96 3.97
7 8 3.691342 CTTCGTGGTCGCTGGGGA 61.691 66.667 0.00 0.00 36.96 4.81
8 9 4.760047 CCTTCGTGGTCGCTGGGG 62.760 72.222 0.00 0.00 36.96 4.96
27 28 2.509336 TAGAGAAGGCGCTTGCGC 60.509 61.111 28.67 28.67 40.46 6.09
28 29 0.100682 TAGTAGAGAAGGCGCTTGCG 59.899 55.000 7.64 10.90 40.46 4.85
29 30 1.562017 GTAGTAGAGAAGGCGCTTGC 58.438 55.000 7.64 0.00 38.11 4.01
30 31 1.751924 AGGTAGTAGAGAAGGCGCTTG 59.248 52.381 7.64 0.00 0.00 4.01
31 32 2.025898 GAGGTAGTAGAGAAGGCGCTT 58.974 52.381 7.64 0.00 0.00 4.68
32 33 1.682740 GAGGTAGTAGAGAAGGCGCT 58.317 55.000 7.64 0.00 0.00 5.92
33 34 0.308376 CGAGGTAGTAGAGAAGGCGC 59.692 60.000 0.00 0.00 0.00 6.53
34 35 0.308376 GCGAGGTAGTAGAGAAGGCG 59.692 60.000 0.00 0.00 0.00 5.52
35 36 1.605232 GAGCGAGGTAGTAGAGAAGGC 59.395 57.143 0.00 0.00 0.00 4.35
36 37 1.868498 CGAGCGAGGTAGTAGAGAAGG 59.132 57.143 0.00 0.00 0.00 3.46
37 38 1.262151 GCGAGCGAGGTAGTAGAGAAG 59.738 57.143 0.00 0.00 0.00 2.85
38 39 1.297664 GCGAGCGAGGTAGTAGAGAA 58.702 55.000 0.00 0.00 0.00 2.87
39 40 0.875040 CGCGAGCGAGGTAGTAGAGA 60.875 60.000 12.58 0.00 42.83 3.10
40 41 1.152989 ACGCGAGCGAGGTAGTAGAG 61.153 60.000 24.72 0.00 42.83 2.43
41 42 0.742281 AACGCGAGCGAGGTAGTAGA 60.742 55.000 24.72 0.00 42.83 2.59
42 43 0.589229 CAACGCGAGCGAGGTAGTAG 60.589 60.000 24.72 0.92 42.83 2.57
43 44 1.426621 CAACGCGAGCGAGGTAGTA 59.573 57.895 24.72 0.00 42.83 1.82
44 45 2.178521 CAACGCGAGCGAGGTAGT 59.821 61.111 24.72 0.00 42.83 2.73
45 46 2.579787 CCAACGCGAGCGAGGTAG 60.580 66.667 24.72 8.18 42.83 3.18
46 47 3.367743 ACCAACGCGAGCGAGGTA 61.368 61.111 27.13 0.00 44.31 3.08
53 54 4.988598 AGCCACCACCAACGCGAG 62.989 66.667 15.93 4.40 0.00 5.03
54 55 4.980805 GAGCCACCACCAACGCGA 62.981 66.667 15.93 0.00 0.00 5.87
56 57 4.643387 AGGAGCCACCACCAACGC 62.643 66.667 0.47 0.00 42.04 4.84
57 58 2.113139 AAGGAGCCACCACCAACG 59.887 61.111 0.47 0.00 42.04 4.10
58 59 1.152756 ACAAGGAGCCACCACCAAC 60.153 57.895 0.47 0.00 42.04 3.77
59 60 1.150536 GACAAGGAGCCACCACCAA 59.849 57.895 0.47 0.00 42.04 3.67
60 61 2.829384 GGACAAGGAGCCACCACCA 61.829 63.158 0.47 0.00 42.04 4.17
61 62 2.034221 GGACAAGGAGCCACCACC 59.966 66.667 0.47 0.00 42.04 4.61
62 63 1.302832 CAGGACAAGGAGCCACCAC 60.303 63.158 0.47 0.00 42.04 4.16
63 64 1.770110 ACAGGACAAGGAGCCACCA 60.770 57.895 0.47 0.00 42.04 4.17
64 65 1.302832 CACAGGACAAGGAGCCACC 60.303 63.158 0.00 0.00 39.35 4.61
65 66 0.603975 GACACAGGACAAGGAGCCAC 60.604 60.000 0.00 0.00 0.00 5.01
66 67 1.754745 GACACAGGACAAGGAGCCA 59.245 57.895 0.00 0.00 0.00 4.75
67 68 1.003233 GGACACAGGACAAGGAGCC 60.003 63.158 0.00 0.00 0.00 4.70
68 69 0.321122 CTGGACACAGGACAAGGAGC 60.321 60.000 0.00 0.00 41.13 4.70
69 70 3.923354 CTGGACACAGGACAAGGAG 57.077 57.895 0.00 0.00 41.13 3.69
78 79 1.301716 CAACCGGTCCTGGACACAG 60.302 63.158 26.94 16.83 44.51 3.66
79 80 1.125093 ATCAACCGGTCCTGGACACA 61.125 55.000 26.94 5.29 33.68 3.72
80 81 0.673644 CATCAACCGGTCCTGGACAC 60.674 60.000 26.94 15.55 33.68 3.67
81 82 0.834261 TCATCAACCGGTCCTGGACA 60.834 55.000 26.94 6.95 33.68 4.02
82 83 0.391263 GTCATCAACCGGTCCTGGAC 60.391 60.000 18.65 18.65 0.00 4.02
83 84 1.550130 GGTCATCAACCGGTCCTGGA 61.550 60.000 8.04 3.86 38.58 3.86
84 85 1.078426 GGTCATCAACCGGTCCTGG 60.078 63.158 8.04 0.00 38.58 4.45
85 86 4.617875 GGTCATCAACCGGTCCTG 57.382 61.111 8.04 3.01 38.58 3.86
93 94 0.669318 TCTTCGCCGTGGTCATCAAC 60.669 55.000 0.00 0.00 0.00 3.18
94 95 0.669318 GTCTTCGCCGTGGTCATCAA 60.669 55.000 0.00 0.00 0.00 2.57
95 96 1.080093 GTCTTCGCCGTGGTCATCA 60.080 57.895 0.00 0.00 0.00 3.07
96 97 2.158959 CGTCTTCGCCGTGGTCATC 61.159 63.158 0.00 0.00 0.00 2.92
97 98 2.126071 CGTCTTCGCCGTGGTCAT 60.126 61.111 0.00 0.00 0.00 3.06
98 99 3.547249 GACGTCTTCGCCGTGGTCA 62.547 63.158 8.70 0.00 38.92 4.02
99 100 2.804090 GACGTCTTCGCCGTGGTC 60.804 66.667 8.70 0.00 38.92 4.02
100 101 4.353437 GGACGTCTTCGCCGTGGT 62.353 66.667 16.46 0.00 38.92 4.16
124 125 4.862092 ATCGAGGCTGCGCAGTCG 62.862 66.667 32.67 32.67 38.27 4.18
125 126 3.260483 CATCGAGGCTGCGCAGTC 61.260 66.667 34.01 34.01 0.00 3.51
126 127 4.827087 CCATCGAGGCTGCGCAGT 62.827 66.667 35.80 19.82 0.00 4.40
130 131 4.598894 CTCCCCATCGAGGCTGCG 62.599 72.222 0.00 0.00 35.39 5.18
131 132 4.925861 GCTCCCCATCGAGGCTGC 62.926 72.222 0.00 0.00 35.39 5.25
132 133 3.160047 AGCTCCCCATCGAGGCTG 61.160 66.667 0.00 0.00 35.39 4.85
133 134 2.841988 GAGCTCCCCATCGAGGCT 60.842 66.667 0.87 0.00 35.39 4.58
134 135 3.157252 TGAGCTCCCCATCGAGGC 61.157 66.667 12.15 0.00 35.39 4.70
135 136 2.801631 GGTGAGCTCCCCATCGAGG 61.802 68.421 10.75 0.00 37.03 4.63
136 137 1.617018 TTGGTGAGCTCCCCATCGAG 61.617 60.000 19.27 0.00 0.00 4.04
137 138 1.612146 TTGGTGAGCTCCCCATCGA 60.612 57.895 19.27 0.91 0.00 3.59
138 139 1.153289 CTTGGTGAGCTCCCCATCG 60.153 63.158 19.27 9.46 0.00 3.84
139 140 0.842635 ATCTTGGTGAGCTCCCCATC 59.157 55.000 19.27 0.00 0.00 3.51
140 141 0.842635 GATCTTGGTGAGCTCCCCAT 59.157 55.000 19.27 3.94 0.00 4.00
141 142 1.617018 CGATCTTGGTGAGCTCCCCA 61.617 60.000 14.59 14.59 0.00 4.96
142 143 1.144936 CGATCTTGGTGAGCTCCCC 59.855 63.158 12.15 10.28 0.00 4.81
143 144 1.144936 CCGATCTTGGTGAGCTCCC 59.855 63.158 12.15 12.55 0.00 4.30
144 145 1.144936 CCCGATCTTGGTGAGCTCC 59.855 63.158 12.15 2.19 0.00 4.70
145 146 1.144936 CCCCGATCTTGGTGAGCTC 59.855 63.158 6.82 6.82 0.00 4.09
146 147 1.306141 TCCCCGATCTTGGTGAGCT 60.306 57.895 0.00 0.00 0.00 4.09
147 148 1.144936 CTCCCCGATCTTGGTGAGC 59.855 63.158 0.00 0.00 0.00 4.26
148 149 0.978146 ACCTCCCCGATCTTGGTGAG 60.978 60.000 0.00 1.33 0.00 3.51
149 150 1.080354 ACCTCCCCGATCTTGGTGA 59.920 57.895 0.00 0.00 0.00 4.02
150 151 1.221840 CACCTCCCCGATCTTGGTG 59.778 63.158 0.00 0.00 41.50 4.17
151 152 1.229529 ACACCTCCCCGATCTTGGT 60.230 57.895 0.00 0.00 0.00 3.67
152 153 1.221840 CACACCTCCCCGATCTTGG 59.778 63.158 0.00 0.00 0.00 3.61
153 154 1.221840 CCACACCTCCCCGATCTTG 59.778 63.158 0.00 0.00 0.00 3.02
154 155 1.229529 ACCACACCTCCCCGATCTT 60.230 57.895 0.00 0.00 0.00 2.40
155 156 1.686110 GACCACACCTCCCCGATCT 60.686 63.158 0.00 0.00 0.00 2.75
156 157 2.732619 GGACCACACCTCCCCGATC 61.733 68.421 0.00 0.00 0.00 3.69
157 158 1.882189 TAGGACCACACCTCCCCGAT 61.882 60.000 0.00 0.00 41.00 4.18
158 159 2.096707 TTAGGACCACACCTCCCCGA 62.097 60.000 0.00 0.00 41.00 5.14
159 160 1.611261 TTAGGACCACACCTCCCCG 60.611 63.158 0.00 0.00 41.00 5.73
160 161 0.252558 TCTTAGGACCACACCTCCCC 60.253 60.000 0.00 0.00 41.00 4.81
161 162 1.196012 CTCTTAGGACCACACCTCCC 58.804 60.000 0.00 0.00 41.00 4.30
162 163 2.104170 CTCTCTTAGGACCACACCTCC 58.896 57.143 0.00 0.00 41.00 4.30
163 164 2.756207 GTCTCTCTTAGGACCACACCTC 59.244 54.545 0.00 0.00 41.00 3.85
164 165 2.810164 GTCTCTCTTAGGACCACACCT 58.190 52.381 0.00 0.00 43.32 4.00
171 172 3.131400 GTGATGGTGGTCTCTCTTAGGAC 59.869 52.174 0.00 0.00 0.00 3.85
172 173 3.366396 GTGATGGTGGTCTCTCTTAGGA 58.634 50.000 0.00 0.00 0.00 2.94
173 174 2.432510 GGTGATGGTGGTCTCTCTTAGG 59.567 54.545 0.00 0.00 0.00 2.69
174 175 2.099921 CGGTGATGGTGGTCTCTCTTAG 59.900 54.545 0.00 0.00 0.00 2.18
175 176 2.100197 CGGTGATGGTGGTCTCTCTTA 58.900 52.381 0.00 0.00 0.00 2.10
176 177 0.898320 CGGTGATGGTGGTCTCTCTT 59.102 55.000 0.00 0.00 0.00 2.85
177 178 0.251832 ACGGTGATGGTGGTCTCTCT 60.252 55.000 0.00 0.00 0.00 3.10
178 179 0.173708 GACGGTGATGGTGGTCTCTC 59.826 60.000 0.00 0.00 0.00 3.20
179 180 1.595993 CGACGGTGATGGTGGTCTCT 61.596 60.000 0.00 0.00 0.00 3.10
180 181 1.153823 CGACGGTGATGGTGGTCTC 60.154 63.158 0.00 0.00 0.00 3.36
181 182 2.646175 CCGACGGTGATGGTGGTCT 61.646 63.158 5.48 0.00 0.00 3.85
182 183 2.125673 CCGACGGTGATGGTGGTC 60.126 66.667 5.48 0.00 0.00 4.02
183 184 4.388499 GCCGACGGTGATGGTGGT 62.388 66.667 16.73 0.00 0.00 4.16
184 185 3.892740 TTGCCGACGGTGATGGTGG 62.893 63.158 16.73 0.00 0.00 4.61
185 186 2.358125 TTGCCGACGGTGATGGTG 60.358 61.111 16.73 0.00 0.00 4.17
186 187 2.047274 CTTGCCGACGGTGATGGT 60.047 61.111 16.73 0.00 0.00 3.55
187 188 2.819595 CCTTGCCGACGGTGATGG 60.820 66.667 16.73 10.23 0.00 3.51
188 189 2.819595 CCCTTGCCGACGGTGATG 60.820 66.667 16.73 5.00 0.00 3.07
189 190 4.778143 GCCCTTGCCGACGGTGAT 62.778 66.667 16.73 0.00 0.00 3.06
194 195 4.697756 TCCTTGCCCTTGCCGACG 62.698 66.667 0.00 0.00 36.33 5.12
195 196 3.056328 GTCCTTGCCCTTGCCGAC 61.056 66.667 0.00 0.00 36.33 4.79
196 197 2.424842 ATTGTCCTTGCCCTTGCCGA 62.425 55.000 0.00 0.00 36.33 5.54
197 198 1.978617 ATTGTCCTTGCCCTTGCCG 60.979 57.895 0.00 0.00 36.33 5.69
198 199 1.593265 CATTGTCCTTGCCCTTGCC 59.407 57.895 0.00 0.00 36.33 4.52
199 200 1.593265 CCATTGTCCTTGCCCTTGC 59.407 57.895 0.00 0.00 38.26 4.01
200 201 1.593265 GCCATTGTCCTTGCCCTTG 59.407 57.895 0.00 0.00 0.00 3.61
201 202 1.610379 GGCCATTGTCCTTGCCCTT 60.610 57.895 0.00 0.00 37.94 3.95
202 203 2.037847 GGCCATTGTCCTTGCCCT 59.962 61.111 0.00 0.00 37.94 5.19
203 204 2.283821 TGGCCATTGTCCTTGCCC 60.284 61.111 0.00 0.00 43.35 5.36
204 205 2.353610 CCTGGCCATTGTCCTTGCC 61.354 63.158 5.51 0.00 44.27 4.52
205 206 2.353610 CCCTGGCCATTGTCCTTGC 61.354 63.158 5.51 0.00 0.00 4.01
206 207 2.353610 GCCCTGGCCATTGTCCTTG 61.354 63.158 5.51 0.00 34.56 3.61
207 208 2.037847 GCCCTGGCCATTGTCCTT 59.962 61.111 5.51 0.00 34.56 3.36
208 209 2.943265 AGCCCTGGCCATTGTCCT 60.943 61.111 5.51 0.00 43.17 3.85
209 210 2.440980 GAGCCCTGGCCATTGTCC 60.441 66.667 5.51 0.00 43.17 4.02
210 211 2.440980 GGAGCCCTGGCCATTGTC 60.441 66.667 5.51 0.32 43.17 3.18
211 212 4.066139 GGGAGCCCTGGCCATTGT 62.066 66.667 5.51 0.00 43.17 2.71
212 213 3.747579 AGGGAGCCCTGGCCATTG 61.748 66.667 5.51 0.53 46.22 2.82
228 229 1.669115 CAACACCGACCCTGCTCAG 60.669 63.158 0.00 0.00 0.00 3.35
229 230 2.425592 CAACACCGACCCTGCTCA 59.574 61.111 0.00 0.00 0.00 4.26
230 231 2.358737 CCAACACCGACCCTGCTC 60.359 66.667 0.00 0.00 0.00 4.26
231 232 4.643387 GCCAACACCGACCCTGCT 62.643 66.667 0.00 0.00 0.00 4.24
232 233 4.643387 AGCCAACACCGACCCTGC 62.643 66.667 0.00 0.00 0.00 4.85
233 234 2.669569 CAGCCAACACCGACCCTG 60.670 66.667 0.00 0.00 0.00 4.45
234 235 2.847234 TCAGCCAACACCGACCCT 60.847 61.111 0.00 0.00 0.00 4.34
235 236 2.358737 CTCAGCCAACACCGACCC 60.359 66.667 0.00 0.00 0.00 4.46
236 237 2.358737 CCTCAGCCAACACCGACC 60.359 66.667 0.00 0.00 0.00 4.79
237 238 3.050275 GCCTCAGCCAACACCGAC 61.050 66.667 0.00 0.00 0.00 4.79
238 239 3.535629 CTGCCTCAGCCAACACCGA 62.536 63.158 0.00 0.00 38.69 4.69
239 240 3.052082 CTGCCTCAGCCAACACCG 61.052 66.667 0.00 0.00 38.69 4.94
263 264 1.132643 CAGCTTCCTCTTGCATCAAGC 59.867 52.381 1.90 0.00 40.84 4.01
264 265 2.678836 CTCAGCTTCCTCTTGCATCAAG 59.321 50.000 0.00 0.37 42.25 3.02
265 266 2.708051 CTCAGCTTCCTCTTGCATCAA 58.292 47.619 0.00 0.00 0.00 2.57
266 267 1.678123 GCTCAGCTTCCTCTTGCATCA 60.678 52.381 0.00 0.00 0.00 3.07
267 268 1.015868 GCTCAGCTTCCTCTTGCATC 58.984 55.000 0.00 0.00 0.00 3.91
268 269 0.743701 CGCTCAGCTTCCTCTTGCAT 60.744 55.000 0.00 0.00 0.00 3.96
269 270 1.375140 CGCTCAGCTTCCTCTTGCA 60.375 57.895 0.00 0.00 0.00 4.08
270 271 2.105466 CCGCTCAGCTTCCTCTTGC 61.105 63.158 0.00 0.00 0.00 4.01
271 272 2.105466 GCCGCTCAGCTTCCTCTTG 61.105 63.158 0.00 0.00 0.00 3.02
272 273 2.237534 GAGCCGCTCAGCTTCCTCTT 62.238 60.000 15.78 0.00 45.15 2.85
273 274 2.683212 AGCCGCTCAGCTTCCTCT 60.683 61.111 0.00 0.00 41.41 3.69
274 275 2.202864 GAGCCGCTCAGCTTCCTC 60.203 66.667 15.78 0.00 45.15 3.71
275 276 3.780173 GGAGCCGCTCAGCTTCCT 61.780 66.667 21.76 0.00 45.15 3.36
276 277 3.731653 GAGGAGCCGCTCAGCTTCC 62.732 68.421 21.76 4.36 45.15 3.46
277 278 2.202864 GAGGAGCCGCTCAGCTTC 60.203 66.667 21.76 9.62 45.15 3.86
278 279 3.780173 GGAGGAGCCGCTCAGCTT 61.780 66.667 21.76 4.34 45.15 3.74
280 281 4.828925 GTGGAGGAGCCGCTCAGC 62.829 72.222 21.76 12.20 44.03 4.26
286 287 4.379243 ACGCTTGTGGAGGAGCCG 62.379 66.667 0.00 0.00 40.66 5.52
287 288 2.435059 GACGCTTGTGGAGGAGCC 60.435 66.667 0.00 0.00 35.49 4.70
288 289 2.811317 CGACGCTTGTGGAGGAGC 60.811 66.667 0.00 0.00 35.58 4.70
289 290 2.125912 CCGACGCTTGTGGAGGAG 60.126 66.667 0.00 0.00 0.00 3.69
290 291 3.691342 CCCGACGCTTGTGGAGGA 61.691 66.667 0.00 0.00 0.00 3.71
349 350 3.062639 CGTCGGAGTGATTCTTTCAATGG 59.937 47.826 0.00 0.00 35.70 3.16
351 352 4.188247 TCGTCGGAGTGATTCTTTCAAT 57.812 40.909 0.00 0.00 35.70 2.57
355 356 3.868757 TCATCGTCGGAGTGATTCTTT 57.131 42.857 0.00 0.00 0.00 2.52
359 360 2.541794 CGTCATCATCGTCGGAGTGATT 60.542 50.000 6.12 0.00 30.57 2.57
370 371 0.778223 CGTATGTGCCGTCATCATCG 59.222 55.000 0.00 0.00 0.00 3.84
380 381 3.123804 CACCTTCATAGTCGTATGTGCC 58.876 50.000 0.00 0.00 37.81 5.01
381 382 2.540101 GCACCTTCATAGTCGTATGTGC 59.460 50.000 0.00 0.00 37.81 4.57
390 391 1.515954 CCGACGGCACCTTCATAGT 59.484 57.895 0.00 0.00 0.00 2.12
416 417 4.131088 GACCTCGTCCGCCTGACC 62.131 72.222 0.00 0.00 41.18 4.02
417 418 3.371063 TGACCTCGTCCGCCTGAC 61.371 66.667 0.00 0.00 40.81 3.51
418 419 3.371063 GTGACCTCGTCCGCCTGA 61.371 66.667 0.00 0.00 0.00 3.86
521 523 6.690957 ACAAACACAACAAATTCATGTAGACG 59.309 34.615 0.00 0.00 32.02 4.18
524 526 9.676195 TCATACAAACACAACAAATTCATGTAG 57.324 29.630 0.00 0.00 32.02 2.74
526 528 8.939201 TTCATACAAACACAACAAATTCATGT 57.061 26.923 0.00 0.00 34.24 3.21
567 570 3.378339 GACCGTCCAACCGATATACAAG 58.622 50.000 0.00 0.00 0.00 3.16
574 577 2.993264 ACCGACCGTCCAACCGAT 60.993 61.111 0.00 0.00 0.00 4.18
575 578 3.673484 GACCGACCGTCCAACCGA 61.673 66.667 0.00 0.00 35.23 4.69
576 579 3.621892 GAGACCGACCGTCCAACCG 62.622 68.421 0.00 0.00 43.08 4.44
584 587 3.138798 ATGGACCGAGACCGACCG 61.139 66.667 0.00 0.00 38.22 4.79
588 591 0.037697 TTGTTCATGGACCGAGACCG 60.038 55.000 0.46 0.00 0.00 4.79
591 594 3.262151 TGGTATTTGTTCATGGACCGAGA 59.738 43.478 0.46 0.00 0.00 4.04
592 595 3.605634 TGGTATTTGTTCATGGACCGAG 58.394 45.455 0.46 0.00 0.00 4.63
593 596 3.704800 TGGTATTTGTTCATGGACCGA 57.295 42.857 0.46 0.00 0.00 4.69
600 608 5.975693 AAACGGACATGGTATTTGTTCAT 57.024 34.783 0.00 0.00 0.00 2.57
612 620 4.561735 AACACCTAACAAAACGGACATG 57.438 40.909 0.00 0.00 0.00 3.21
709 718 5.455326 GCTAGGTGGTCTATGAATGTGGATT 60.455 44.000 0.00 0.00 0.00 3.01
713 722 4.406648 TGCTAGGTGGTCTATGAATGTG 57.593 45.455 0.00 0.00 0.00 3.21
719 729 6.238484 GCTTAATTGTTGCTAGGTGGTCTATG 60.238 42.308 0.00 0.00 0.00 2.23
733 743 4.159377 TCTTTGGCTCGCTTAATTGTTG 57.841 40.909 0.00 0.00 0.00 3.33
734 744 4.846779 TTCTTTGGCTCGCTTAATTGTT 57.153 36.364 0.00 0.00 0.00 2.83
737 747 5.195001 TGTTTTCTTTGGCTCGCTTAATT 57.805 34.783 0.00 0.00 0.00 1.40
738 748 4.846779 TGTTTTCTTTGGCTCGCTTAAT 57.153 36.364 0.00 0.00 0.00 1.40
739 749 4.320935 GGATGTTTTCTTTGGCTCGCTTAA 60.321 41.667 0.00 0.00 0.00 1.85
740 750 3.190535 GGATGTTTTCTTTGGCTCGCTTA 59.809 43.478 0.00 0.00 0.00 3.09
741 751 2.029918 GGATGTTTTCTTTGGCTCGCTT 60.030 45.455 0.00 0.00 0.00 4.68
742 752 1.541588 GGATGTTTTCTTTGGCTCGCT 59.458 47.619 0.00 0.00 0.00 4.93
743 753 1.269448 TGGATGTTTTCTTTGGCTCGC 59.731 47.619 0.00 0.00 0.00 5.03
866 894 1.650242 TTGGTTGAGGGCCCACAAGA 61.650 55.000 32.15 19.94 0.00 3.02
926 954 0.760945 ATAGGAGTGGCGGGAAGAGG 60.761 60.000 0.00 0.00 0.00 3.69
1302 1333 3.731216 GTCACCATAAGACGACATCGATG 59.269 47.826 23.68 23.68 43.02 3.84
1397 1428 7.596749 TTGATTAATCAGACGGAGAGAAAAC 57.403 36.000 17.28 0.00 38.19 2.43
1565 1616 4.083537 TGCATGACAACGGTAAAATCTCAC 60.084 41.667 0.00 0.00 0.00 3.51
1567 1618 4.437390 CCTGCATGACAACGGTAAAATCTC 60.437 45.833 0.00 0.00 0.00 2.75
1575 1626 2.487762 CAAATACCTGCATGACAACGGT 59.512 45.455 0.00 1.85 0.00 4.83
1786 1841 0.674895 GAAGCCAAGCATCGTCCAGT 60.675 55.000 0.00 0.00 0.00 4.00
1813 1868 2.482721 GTCATCAACGGATTGTTCGGTT 59.517 45.455 0.00 0.00 43.74 4.44
1888 1943 1.440893 CTGAGAGCCTCCATCACCG 59.559 63.158 0.00 0.00 0.00 4.94
1922 1977 1.134189 GGTACCCTTTTCATCCCCTCG 60.134 57.143 0.00 0.00 0.00 4.63
1930 1985 2.500098 CTCTCCATCGGTACCCTTTTCA 59.500 50.000 6.25 0.00 0.00 2.69
2038 2093 1.493772 CAACATTGTGGCTGCAGTTG 58.506 50.000 16.64 6.19 0.00 3.16
2131 2186 8.294577 GTCTTGGATTACAAAACCGAACTAAAT 58.705 33.333 0.00 0.00 38.91 1.40
2161 2216 4.340381 CCCTGGGCTTCTTATCATGAAAAG 59.660 45.833 0.00 2.99 0.00 2.27
2429 2494 4.764050 TGTTCTGTAGAAGTGGGAACAA 57.236 40.909 0.00 0.00 46.06 2.83
2435 2500 3.741344 CCGTCTTTGTTCTGTAGAAGTGG 59.259 47.826 0.00 0.00 34.27 4.00
2490 2555 5.649831 GCTAGAAACTGATCCCAATCTTTGT 59.350 40.000 0.00 0.00 32.75 2.83
2758 2823 9.569122 AGGCAAACTGAAGTACTTTCTTAATTA 57.431 29.630 10.02 0.00 36.71 1.40
2759 2824 8.465273 AGGCAAACTGAAGTACTTTCTTAATT 57.535 30.769 10.02 0.00 36.71 1.40
2760 2825 8.465273 AAGGCAAACTGAAGTACTTTCTTAAT 57.535 30.769 10.02 0.00 36.71 1.40
2761 2826 7.875327 AAGGCAAACTGAAGTACTTTCTTAA 57.125 32.000 10.02 0.00 36.71 1.85
2799 2868 6.071165 AGGAAAAAGGCAATAACATGAGAAGG 60.071 38.462 0.00 0.00 0.00 3.46
3791 3860 9.620259 AGATCCTATTTACCTTTCTGAATGAAC 57.380 33.333 4.98 0.00 33.88 3.18
4095 4164 4.416516 TGCTATCGATGAAGGGGAATAGA 58.583 43.478 8.54 0.00 0.00 1.98
5016 5086 6.330278 TCAATATCTACCTGCATACATACGC 58.670 40.000 0.00 0.00 0.00 4.42
5499 5569 5.645067 CCTCAATGTAGTGAATCTTCTTGCA 59.355 40.000 0.00 0.00 0.00 4.08
5705 5778 6.326583 TCCAGAGGAAATATTACCCTACACAG 59.673 42.308 8.76 0.16 0.00 3.66
5886 5959 4.082895 AGCTGCATCTTCAGTCAAATCAAC 60.083 41.667 1.02 0.00 36.49 3.18
6028 6185 5.622180 AGATGCTCATATGCTCAGTGAAAT 58.378 37.500 0.00 0.00 0.00 2.17
6259 6418 5.240713 AGAAACAGAACTGCTCAAAACTG 57.759 39.130 1.46 0.00 0.00 3.16
6417 6580 3.126001 TGAGTGTCAAATCCACTGTCC 57.874 47.619 0.00 0.00 43.00 4.02
6447 6610 5.652994 TTTATCCAACAAACATACCCTGC 57.347 39.130 0.00 0.00 0.00 4.85
6479 6642 3.471570 TACACCCACCCCGACAGGT 62.472 63.158 0.00 0.00 42.40 4.00
6503 6666 1.577736 AACCATAGAGCCTGCTCACT 58.422 50.000 20.38 4.19 44.99 3.41
6507 6670 0.394899 GCCAAACCATAGAGCCTGCT 60.395 55.000 0.00 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.