Multiple sequence alignment - TraesCS2D01G336800

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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 TraesCS2D01G336800 chr2D 100.000 3512 0 0 1 3512 430435175 430431664 0.000000e+00 6486.0
1 TraesCS2D01G336800 chr2D 88.972 1070 82 14 1546 2584 430022363 430021299 0.000000e+00 1290.0
2 TraesCS2D01G336800 chr2D 93.832 843 48 4 2672 3512 187943483 187944323 0.000000e+00 1266.0
3 TraesCS2D01G336800 chr2D 93.609 845 50 4 2670 3512 245441490 245440648 0.000000e+00 1258.0
4 TraesCS2D01G336800 chr2D 92.517 735 52 3 1873 2605 430440481 430439748 0.000000e+00 1050.0
5 TraesCS2D01G336800 chr2D 91.721 761 28 13 798 1542 430023191 430022450 0.000000e+00 1024.0
6 TraesCS2D01G336800 chr2D 88.745 693 45 13 823 1499 430442142 430441467 0.000000e+00 817.0
7 TraesCS2D01G336800 chr2D 86.424 302 24 3 1537 1838 430440999 430440715 7.320000e-82 315.0
8 TraesCS2D01G336800 chr2A 94.572 3298 121 17 261 3512 555886670 555889955 0.000000e+00 5046.0
9 TraesCS2D01G336800 chr2A 92.181 1036 75 5 2479 3512 556379105 556380136 0.000000e+00 1459.0
10 TraesCS2D01G336800 chr2A 86.815 1077 92 23 1533 2576 556986957 556988016 0.000000e+00 1157.0
11 TraesCS2D01G336800 chr2A 92.070 744 55 4 1863 2605 555884393 555885133 0.000000e+00 1044.0
12 TraesCS2D01G336800 chr2A 91.345 751 28 16 798 1533 556986180 556986908 0.000000e+00 992.0
13 TraesCS2D01G336800 chr2A 91.911 717 37 6 823 1533 555883165 555883866 0.000000e+00 983.0
14 TraesCS2D01G336800 chr2A 91.202 341 25 1 2040 2380 556378770 556379105 3.190000e-125 459.0
15 TraesCS2D01G336800 chr2A 89.911 337 23 5 1537 1862 555883989 555884325 1.170000e-114 424.0
16 TraesCS2D01G336800 chr2A 88.618 123 9 2 623 744 556972081 556972199 1.020000e-30 145.0
17 TraesCS2D01G336800 chr2A 79.048 210 32 6 1336 1533 451013338 451013129 2.200000e-27 134.0
18 TraesCS2D01G336800 chr2B 87.540 1854 119 36 802 2584 507912788 507910976 0.000000e+00 2041.0
19 TraesCS2D01G336800 chr2B 94.275 1083 56 4 1578 2659 508183220 508182143 0.000000e+00 1652.0
20 TraesCS2D01G336800 chr2B 89.959 986 59 10 908 1862 508215231 508214255 0.000000e+00 1236.0
21 TraesCS2D01G336800 chr2B 91.962 734 53 3 1873 2605 508214180 508213452 0.000000e+00 1024.0
22 TraesCS2D01G336800 chr2B 93.750 640 25 2 958 1582 508193399 508192760 0.000000e+00 946.0
23 TraesCS2D01G336800 chr2B 94.231 572 24 5 363 931 508194457 508193892 0.000000e+00 865.0
24 TraesCS2D01G336800 chr2B 85.950 242 30 2 996 1233 406098738 406098979 4.500000e-64 255.0
25 TraesCS2D01G336800 chr2B 93.396 106 3 2 635 740 507914374 507914273 1.690000e-33 154.0
26 TraesCS2D01G336800 chr2B 91.509 106 7 2 75 179 508212057 508211953 1.020000e-30 145.0
27 TraesCS2D01G336800 chr4D 94.687 847 40 4 2669 3512 500812987 500812143 0.000000e+00 1310.0
28 TraesCS2D01G336800 chr3D 93.846 845 49 3 2670 3512 234832933 234833776 0.000000e+00 1269.0
29 TraesCS2D01G336800 chr5D 93.728 845 48 5 2670 3512 112404616 112403775 0.000000e+00 1262.0
30 TraesCS2D01G336800 chr4B 93.506 847 50 5 2664 3506 600126793 600127638 0.000000e+00 1254.0
31 TraesCS2D01G336800 chr1A 93.491 845 51 4 2670 3512 122471072 122470230 0.000000e+00 1253.0
32 TraesCS2D01G336800 chr1B 87.603 121 7 4 452 564 645376391 645376511 2.200000e-27 134.0
33 TraesCS2D01G336800 chr1B 92.647 68 4 1 622 688 645486001 645486068 2.890000e-16 97.1
34 TraesCS2D01G336800 chr1B 85.333 75 6 3 670 743 645376668 645376738 4.860000e-09 73.1
35 TraesCS2D01G336800 chr1D 88.496 113 8 4 448 555 467535785 467535897 7.910000e-27 132.0
36 TraesCS2D01G336800 chr1D 92.754 69 4 1 621 688 467594982 467595050 8.020000e-17 99.0
37 TraesCS2D01G336800 chr3A 90.909 55 5 0 229 283 244484144 244484090 1.350000e-09 75.0
38 TraesCS2D01G336800 chr3B 80.000 95 13 5 190 283 264165363 264165274 8.140000e-07 65.8


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 TraesCS2D01G336800 chr2D 430431664 430435175 3511 True 6486.000000 6486 100.000000 1 3512 1 chr2D.!!$R2 3511
1 TraesCS2D01G336800 chr2D 187943483 187944323 840 False 1266.000000 1266 93.832000 2672 3512 1 chr2D.!!$F1 840
2 TraesCS2D01G336800 chr2D 245440648 245441490 842 True 1258.000000 1258 93.609000 2670 3512 1 chr2D.!!$R1 842
3 TraesCS2D01G336800 chr2D 430021299 430023191 1892 True 1157.000000 1290 90.346500 798 2584 2 chr2D.!!$R3 1786
4 TraesCS2D01G336800 chr2D 430439748 430442142 2394 True 727.333333 1050 89.228667 823 2605 3 chr2D.!!$R4 1782
5 TraesCS2D01G336800 chr2A 555883165 555889955 6790 False 1874.250000 5046 92.116000 261 3512 4 chr2A.!!$F2 3251
6 TraesCS2D01G336800 chr2A 556986180 556988016 1836 False 1074.500000 1157 89.080000 798 2576 2 chr2A.!!$F4 1778
7 TraesCS2D01G336800 chr2A 556378770 556380136 1366 False 959.000000 1459 91.691500 2040 3512 2 chr2A.!!$F3 1472
8 TraesCS2D01G336800 chr2B 508182143 508183220 1077 True 1652.000000 1652 94.275000 1578 2659 1 chr2B.!!$R1 1081
9 TraesCS2D01G336800 chr2B 507910976 507914374 3398 True 1097.500000 2041 90.468000 635 2584 2 chr2B.!!$R2 1949
10 TraesCS2D01G336800 chr2B 508192760 508194457 1697 True 905.500000 946 93.990500 363 1582 2 chr2B.!!$R3 1219
11 TraesCS2D01G336800 chr2B 508211953 508215231 3278 True 801.666667 1236 91.143333 75 2605 3 chr2B.!!$R4 2530
12 TraesCS2D01G336800 chr4D 500812143 500812987 844 True 1310.000000 1310 94.687000 2669 3512 1 chr4D.!!$R1 843
13 TraesCS2D01G336800 chr3D 234832933 234833776 843 False 1269.000000 1269 93.846000 2670 3512 1 chr3D.!!$F1 842
14 TraesCS2D01G336800 chr5D 112403775 112404616 841 True 1262.000000 1262 93.728000 2670 3512 1 chr5D.!!$R1 842
15 TraesCS2D01G336800 chr4B 600126793 600127638 845 False 1254.000000 1254 93.506000 2664 3506 1 chr4B.!!$F1 842
16 TraesCS2D01G336800 chr1A 122470230 122471072 842 True 1253.000000 1253 93.491000 2670 3512 1 chr1A.!!$R1 842

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
313 314 0.030638 AGTTTGCCACACACGAATGC 59.969 50.0 0.0 0.0 0.00 3.56 F
326 327 0.104120 CGAATGCCTCCGTGTATGGA 59.896 55.0 0.0 0.0 36.37 3.41 F
870 2303 0.108945 GGCAGCTCATTCAAACCAGC 60.109 55.0 0.0 0.0 0.00 4.85 F
1507 3772 0.167470 CAGCACCGCATTGACAAGAG 59.833 55.0 0.0 0.0 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1507 3772 0.797249 CGTGATCTCGACGGGAACAC 60.797 60.000 23.81 23.81 34.58 3.32 R
1703 8091 1.338105 TGTGCCCTTCTGATTGTCGAG 60.338 52.381 0.00 0.00 0.00 4.04 R
1745 8133 1.428869 AAGACCACTCCAGCTGAACT 58.571 50.000 17.39 0.60 0.00 3.01 R
3365 10887 1.340248 TCCTCACCGAGTGACAAAGTC 59.660 52.381 3.02 0.00 37.67 3.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.582728 TCACAAAGCAAAACTGCTGG 57.417 45.000 0.00 0.00 45.54 4.85
27 28 1.824230 TCACAAAGCAAAACTGCTGGT 59.176 42.857 0.00 0.00 45.54 4.00
28 29 3.020274 TCACAAAGCAAAACTGCTGGTA 58.980 40.909 0.00 0.00 45.54 3.25
29 30 3.066621 TCACAAAGCAAAACTGCTGGTAG 59.933 43.478 0.00 0.00 45.54 3.18
30 31 2.362077 ACAAAGCAAAACTGCTGGTAGG 59.638 45.455 0.00 0.00 45.54 3.18
31 32 2.362077 CAAAGCAAAACTGCTGGTAGGT 59.638 45.455 0.00 0.00 45.54 3.08
32 33 3.502123 AAGCAAAACTGCTGGTAGGTA 57.498 42.857 0.00 0.00 45.54 3.08
33 34 3.059352 AGCAAAACTGCTGGTAGGTAG 57.941 47.619 0.00 0.00 44.44 3.18
34 35 2.372172 AGCAAAACTGCTGGTAGGTAGT 59.628 45.455 0.00 0.00 44.44 2.73
35 36 3.146847 GCAAAACTGCTGGTAGGTAGTT 58.853 45.455 0.00 0.00 42.27 2.24
36 37 4.041198 AGCAAAACTGCTGGTAGGTAGTTA 59.959 41.667 0.00 0.00 44.44 2.24
37 38 4.941873 GCAAAACTGCTGGTAGGTAGTTAT 59.058 41.667 0.00 0.00 40.27 1.89
38 39 5.163754 GCAAAACTGCTGGTAGGTAGTTATG 60.164 44.000 0.00 0.00 40.27 1.90
39 40 5.757099 AAACTGCTGGTAGGTAGTTATGT 57.243 39.130 0.00 0.00 40.27 2.29
40 41 5.757099 AACTGCTGGTAGGTAGTTATGTT 57.243 39.130 0.00 0.00 39.60 2.71
41 42 6.862469 AACTGCTGGTAGGTAGTTATGTTA 57.138 37.500 0.00 0.00 39.60 2.41
42 43 6.862469 ACTGCTGGTAGGTAGTTATGTTAA 57.138 37.500 0.00 0.00 0.00 2.01
43 44 7.248743 ACTGCTGGTAGGTAGTTATGTTAAA 57.751 36.000 0.00 0.00 0.00 1.52
44 45 7.328737 ACTGCTGGTAGGTAGTTATGTTAAAG 58.671 38.462 0.00 0.00 0.00 1.85
45 46 7.179694 ACTGCTGGTAGGTAGTTATGTTAAAGA 59.820 37.037 0.00 0.00 0.00 2.52
46 47 7.325694 TGCTGGTAGGTAGTTATGTTAAAGAC 58.674 38.462 0.00 0.00 0.00 3.01
47 48 7.038870 TGCTGGTAGGTAGTTATGTTAAAGACA 60.039 37.037 0.00 0.00 43.71 3.41
48 49 7.820872 GCTGGTAGGTAGTTATGTTAAAGACAA 59.179 37.037 0.00 0.00 42.62 3.18
49 50 9.886132 CTGGTAGGTAGTTATGTTAAAGACAAT 57.114 33.333 0.00 0.00 42.62 2.71
102 103 5.205565 GCTTATTTAGCCTAACAATGACGC 58.794 41.667 0.00 0.00 44.48 5.19
103 104 5.007724 GCTTATTTAGCCTAACAATGACGCT 59.992 40.000 0.00 0.00 44.48 5.07
104 105 6.202188 GCTTATTTAGCCTAACAATGACGCTA 59.798 38.462 0.00 0.00 44.48 4.26
105 106 7.254658 GCTTATTTAGCCTAACAATGACGCTAA 60.255 37.037 0.00 0.00 44.48 3.09
106 107 5.789710 TTTAGCCTAACAATGACGCTAAC 57.210 39.130 0.00 0.00 40.66 2.34
107 108 3.611766 AGCCTAACAATGACGCTAACT 57.388 42.857 0.00 0.00 0.00 2.24
108 109 4.730949 AGCCTAACAATGACGCTAACTA 57.269 40.909 0.00 0.00 0.00 2.24
109 110 5.277857 AGCCTAACAATGACGCTAACTAT 57.722 39.130 0.00 0.00 0.00 2.12
110 111 5.671493 AGCCTAACAATGACGCTAACTATT 58.329 37.500 0.00 0.00 0.00 1.73
111 112 5.753921 AGCCTAACAATGACGCTAACTATTC 59.246 40.000 0.00 0.00 0.00 1.75
112 113 5.050295 GCCTAACAATGACGCTAACTATTCC 60.050 44.000 0.00 0.00 0.00 3.01
113 114 6.281405 CCTAACAATGACGCTAACTATTCCT 58.719 40.000 0.00 0.00 0.00 3.36
114 115 7.431249 CCTAACAATGACGCTAACTATTCCTA 58.569 38.462 0.00 0.00 0.00 2.94
115 116 7.924412 CCTAACAATGACGCTAACTATTCCTAA 59.076 37.037 0.00 0.00 0.00 2.69
116 117 7.535489 AACAATGACGCTAACTATTCCTAAC 57.465 36.000 0.00 0.00 0.00 2.34
117 118 6.636705 ACAATGACGCTAACTATTCCTAACA 58.363 36.000 0.00 0.00 0.00 2.41
118 119 7.101054 ACAATGACGCTAACTATTCCTAACAA 58.899 34.615 0.00 0.00 0.00 2.83
119 120 7.604927 ACAATGACGCTAACTATTCCTAACAAA 59.395 33.333 0.00 0.00 0.00 2.83
120 121 6.956299 TGACGCTAACTATTCCTAACAAAC 57.044 37.500 0.00 0.00 0.00 2.93
121 122 6.694447 TGACGCTAACTATTCCTAACAAACT 58.306 36.000 0.00 0.00 0.00 2.66
122 123 7.829725 TGACGCTAACTATTCCTAACAAACTA 58.170 34.615 0.00 0.00 0.00 2.24
123 124 8.472413 TGACGCTAACTATTCCTAACAAACTAT 58.528 33.333 0.00 0.00 0.00 2.12
124 125 8.644318 ACGCTAACTATTCCTAACAAACTATG 57.356 34.615 0.00 0.00 0.00 2.23
125 126 8.472413 ACGCTAACTATTCCTAACAAACTATGA 58.528 33.333 0.00 0.00 0.00 2.15
126 127 9.477484 CGCTAACTATTCCTAACAAACTATGAT 57.523 33.333 0.00 0.00 0.00 2.45
149 150 9.388506 TGATGATTTTCTATCAGAAGAGGAAAC 57.611 33.333 0.00 0.00 35.37 2.78
150 151 9.388506 GATGATTTTCTATCAGAAGAGGAAACA 57.611 33.333 0.00 0.00 35.37 2.83
151 152 9.745018 ATGATTTTCTATCAGAAGAGGAAACAA 57.255 29.630 0.00 0.00 35.37 2.83
152 153 9.003658 TGATTTTCTATCAGAAGAGGAAACAAC 57.996 33.333 0.00 0.00 35.37 3.32
153 154 8.924511 ATTTTCTATCAGAAGAGGAAACAACA 57.075 30.769 0.00 0.00 35.37 3.33
154 155 8.746052 TTTTCTATCAGAAGAGGAAACAACAA 57.254 30.769 0.00 0.00 35.37 2.83
155 156 8.924511 TTTCTATCAGAAGAGGAAACAACAAT 57.075 30.769 0.00 0.00 35.37 2.71
156 157 7.912056 TCTATCAGAAGAGGAAACAACAATG 57.088 36.000 0.00 0.00 0.00 2.82
157 158 4.836125 TCAGAAGAGGAAACAACAATGC 57.164 40.909 0.00 0.00 0.00 3.56
158 159 3.569701 TCAGAAGAGGAAACAACAATGCC 59.430 43.478 0.00 0.00 0.00 4.40
159 160 2.893489 AGAAGAGGAAACAACAATGCCC 59.107 45.455 0.00 0.00 0.00 5.36
160 161 1.632589 AGAGGAAACAACAATGCCCC 58.367 50.000 0.00 0.00 0.00 5.80
161 162 0.243636 GAGGAAACAACAATGCCCCG 59.756 55.000 0.00 0.00 0.00 5.73
162 163 0.178975 AGGAAACAACAATGCCCCGA 60.179 50.000 0.00 0.00 0.00 5.14
163 164 0.676736 GGAAACAACAATGCCCCGAA 59.323 50.000 0.00 0.00 0.00 4.30
164 165 1.604438 GGAAACAACAATGCCCCGAAC 60.604 52.381 0.00 0.00 0.00 3.95
165 166 0.031449 AAACAACAATGCCCCGAACG 59.969 50.000 0.00 0.00 0.00 3.95
166 167 0.820074 AACAACAATGCCCCGAACGA 60.820 50.000 0.00 0.00 0.00 3.85
167 168 1.234615 ACAACAATGCCCCGAACGAG 61.235 55.000 0.00 0.00 0.00 4.18
168 169 0.953471 CAACAATGCCCCGAACGAGA 60.953 55.000 0.00 0.00 0.00 4.04
169 170 0.035439 AACAATGCCCCGAACGAGAT 60.035 50.000 0.00 0.00 0.00 2.75
170 171 0.828022 ACAATGCCCCGAACGAGATA 59.172 50.000 0.00 0.00 0.00 1.98
171 172 1.202533 ACAATGCCCCGAACGAGATAG 60.203 52.381 0.00 0.00 0.00 2.08
172 173 0.249911 AATGCCCCGAACGAGATAGC 60.250 55.000 0.00 0.00 0.00 2.97
173 174 1.115930 ATGCCCCGAACGAGATAGCT 61.116 55.000 0.00 0.00 0.00 3.32
174 175 1.327690 TGCCCCGAACGAGATAGCTT 61.328 55.000 0.00 0.00 0.00 3.74
175 176 0.876342 GCCCCGAACGAGATAGCTTG 60.876 60.000 0.00 0.00 0.00 4.01
176 177 0.249489 CCCCGAACGAGATAGCTTGG 60.249 60.000 0.00 0.00 0.00 3.61
177 178 0.876342 CCCGAACGAGATAGCTTGGC 60.876 60.000 0.00 0.00 0.00 4.52
178 179 0.103208 CCGAACGAGATAGCTTGGCT 59.897 55.000 0.00 0.00 43.41 4.75
179 180 1.482278 CGAACGAGATAGCTTGGCTC 58.518 55.000 0.00 0.00 40.44 4.70
180 181 1.202302 CGAACGAGATAGCTTGGCTCA 60.202 52.381 0.00 0.00 40.44 4.26
181 182 2.197577 GAACGAGATAGCTTGGCTCAC 58.802 52.381 0.00 0.00 40.44 3.51
182 183 1.186200 ACGAGATAGCTTGGCTCACA 58.814 50.000 0.00 0.00 40.44 3.58
183 184 1.134965 ACGAGATAGCTTGGCTCACAC 60.135 52.381 0.00 0.00 40.44 3.82
184 185 1.565305 GAGATAGCTTGGCTCACACG 58.435 55.000 0.00 0.00 40.44 4.49
185 186 0.460987 AGATAGCTTGGCTCACACGC 60.461 55.000 0.00 0.00 44.08 5.34
197 198 5.091910 GGCTCACACGCCTTAATAATTAC 57.908 43.478 0.00 0.00 46.63 1.89
198 199 4.814771 GGCTCACACGCCTTAATAATTACT 59.185 41.667 0.00 0.00 46.63 2.24
199 200 5.296035 GGCTCACACGCCTTAATAATTACTT 59.704 40.000 0.00 0.00 46.63 2.24
200 201 6.419771 GCTCACACGCCTTAATAATTACTTC 58.580 40.000 0.00 0.00 0.00 3.01
201 202 6.511282 GCTCACACGCCTTAATAATTACTTCC 60.511 42.308 0.00 0.00 0.00 3.46
202 203 6.646267 TCACACGCCTTAATAATTACTTCCT 58.354 36.000 0.00 0.00 0.00 3.36
203 204 6.759827 TCACACGCCTTAATAATTACTTCCTC 59.240 38.462 0.00 0.00 0.00 3.71
204 205 6.018180 CACACGCCTTAATAATTACTTCCTCC 60.018 42.308 0.00 0.00 0.00 4.30
205 206 5.176958 CACGCCTTAATAATTACTTCCTCCG 59.823 44.000 0.00 0.00 0.00 4.63
206 207 5.163374 ACGCCTTAATAATTACTTCCTCCGT 60.163 40.000 0.00 0.00 0.00 4.69
207 208 5.404667 CGCCTTAATAATTACTTCCTCCGTC 59.595 44.000 0.00 0.00 0.00 4.79
208 209 6.522946 GCCTTAATAATTACTTCCTCCGTCT 58.477 40.000 0.00 0.00 0.00 4.18
209 210 6.645827 GCCTTAATAATTACTTCCTCCGTCTC 59.354 42.308 0.00 0.00 0.00 3.36
210 211 7.686127 GCCTTAATAATTACTTCCTCCGTCTCA 60.686 40.741 0.00 0.00 0.00 3.27
211 212 7.652507 CCTTAATAATTACTTCCTCCGTCTCAC 59.347 40.741 0.00 0.00 0.00 3.51
212 213 6.540438 AATAATTACTTCCTCCGTCTCACA 57.460 37.500 0.00 0.00 0.00 3.58
213 214 4.884668 AATTACTTCCTCCGTCTCACAA 57.115 40.909 0.00 0.00 0.00 3.33
214 215 5.422214 AATTACTTCCTCCGTCTCACAAT 57.578 39.130 0.00 0.00 0.00 2.71
215 216 2.751166 ACTTCCTCCGTCTCACAATG 57.249 50.000 0.00 0.00 0.00 2.82
216 217 1.971357 ACTTCCTCCGTCTCACAATGT 59.029 47.619 0.00 0.00 0.00 2.71
217 218 3.162666 ACTTCCTCCGTCTCACAATGTA 58.837 45.455 0.00 0.00 0.00 2.29
218 219 3.576982 ACTTCCTCCGTCTCACAATGTAA 59.423 43.478 0.00 0.00 0.00 2.41
219 220 4.223032 ACTTCCTCCGTCTCACAATGTAAT 59.777 41.667 0.00 0.00 0.00 1.89
220 221 5.421056 ACTTCCTCCGTCTCACAATGTAATA 59.579 40.000 0.00 0.00 0.00 0.98
221 222 6.098409 ACTTCCTCCGTCTCACAATGTAATAT 59.902 38.462 0.00 0.00 0.00 1.28
222 223 7.287005 ACTTCCTCCGTCTCACAATGTAATATA 59.713 37.037 0.00 0.00 0.00 0.86
223 224 7.591421 TCCTCCGTCTCACAATGTAATATAA 57.409 36.000 0.00 0.00 0.00 0.98
224 225 8.190326 TCCTCCGTCTCACAATGTAATATAAT 57.810 34.615 0.00 0.00 0.00 1.28
225 226 9.304335 TCCTCCGTCTCACAATGTAATATAATA 57.696 33.333 0.00 0.00 0.00 0.98
226 227 9.574458 CCTCCGTCTCACAATGTAATATAATAG 57.426 37.037 0.00 0.00 0.00 1.73
227 228 8.981724 TCCGTCTCACAATGTAATATAATAGC 57.018 34.615 0.00 0.00 0.00 2.97
228 229 7.753580 TCCGTCTCACAATGTAATATAATAGCG 59.246 37.037 0.00 0.00 0.00 4.26
229 230 7.541091 CCGTCTCACAATGTAATATAATAGCGT 59.459 37.037 0.00 0.00 0.00 5.07
230 231 8.912658 CGTCTCACAATGTAATATAATAGCGTT 58.087 33.333 0.00 0.00 0.00 4.84
251 252 8.941977 AGCGTTTTTGATATTAATGTAGTGTCA 58.058 29.630 0.00 0.00 0.00 3.58
252 253 9.549509 GCGTTTTTGATATTAATGTAGTGTCAA 57.450 29.630 0.00 0.00 0.00 3.18
272 273 9.248291 GTGTCAAAAACATGCTTATATTATGGG 57.752 33.333 0.00 0.00 40.80 4.00
273 274 9.194972 TGTCAAAAACATGCTTATATTATGGGA 57.805 29.630 0.00 0.00 31.20 4.37
276 277 9.426837 CAAAAACATGCTTATATTATGGGATGG 57.573 33.333 13.22 0.00 33.03 3.51
277 278 8.954834 AAAACATGCTTATATTATGGGATGGA 57.045 30.769 13.22 0.00 33.03 3.41
278 279 8.585471 AAACATGCTTATATTATGGGATGGAG 57.415 34.615 13.22 0.00 33.03 3.86
279 280 6.666678 ACATGCTTATATTATGGGATGGAGG 58.333 40.000 13.22 0.00 33.03 4.30
280 281 5.715439 TGCTTATATTATGGGATGGAGGG 57.285 43.478 0.00 0.00 0.00 4.30
281 282 5.358306 TGCTTATATTATGGGATGGAGGGA 58.642 41.667 0.00 0.00 0.00 4.20
282 283 5.429762 TGCTTATATTATGGGATGGAGGGAG 59.570 44.000 0.00 0.00 0.00 4.30
283 284 5.163152 GCTTATATTATGGGATGGAGGGAGG 60.163 48.000 0.00 0.00 0.00 4.30
284 285 1.376649 ATTATGGGATGGAGGGAGGC 58.623 55.000 0.00 0.00 0.00 4.70
285 286 0.271927 TTATGGGATGGAGGGAGGCT 59.728 55.000 0.00 0.00 0.00 4.58
286 287 0.271927 TATGGGATGGAGGGAGGCTT 59.728 55.000 0.00 0.00 0.00 4.35
287 288 0.628668 ATGGGATGGAGGGAGGCTTT 60.629 55.000 0.00 0.00 0.00 3.51
288 289 1.281925 TGGGATGGAGGGAGGCTTTC 61.282 60.000 0.00 0.00 0.00 2.62
289 290 1.534203 GGATGGAGGGAGGCTTTCC 59.466 63.158 6.68 6.68 46.00 3.13
296 297 3.715015 GGAGGCTTTCCCGAGAGT 58.285 61.111 0.00 0.00 40.37 3.24
297 298 1.984020 GGAGGCTTTCCCGAGAGTT 59.016 57.895 0.00 0.00 40.37 3.01
298 299 0.325272 GGAGGCTTTCCCGAGAGTTT 59.675 55.000 0.00 0.00 40.37 2.66
299 300 1.443802 GAGGCTTTCCCGAGAGTTTG 58.556 55.000 0.00 0.00 39.21 2.93
300 301 0.606673 AGGCTTTCCCGAGAGTTTGC 60.607 55.000 0.00 0.00 39.21 3.68
301 302 1.587043 GGCTTTCCCGAGAGTTTGCC 61.587 60.000 0.00 0.00 0.00 4.52
302 303 0.889186 GCTTTCCCGAGAGTTTGCCA 60.889 55.000 0.00 0.00 0.00 4.92
303 304 0.875059 CTTTCCCGAGAGTTTGCCAC 59.125 55.000 0.00 0.00 0.00 5.01
304 305 0.181587 TTTCCCGAGAGTTTGCCACA 59.818 50.000 0.00 0.00 0.00 4.17
305 306 0.534203 TTCCCGAGAGTTTGCCACAC 60.534 55.000 0.00 0.00 0.00 3.82
306 307 1.227823 CCCGAGAGTTTGCCACACA 60.228 57.895 0.00 0.00 0.00 3.72
307 308 1.507141 CCCGAGAGTTTGCCACACAC 61.507 60.000 0.00 0.00 0.00 3.82
308 309 1.564622 CGAGAGTTTGCCACACACG 59.435 57.895 0.00 0.00 0.00 4.49
309 310 0.874175 CGAGAGTTTGCCACACACGA 60.874 55.000 0.00 0.00 33.09 4.35
310 311 1.295792 GAGAGTTTGCCACACACGAA 58.704 50.000 0.00 0.00 0.00 3.85
311 312 1.873591 GAGAGTTTGCCACACACGAAT 59.126 47.619 0.00 0.00 0.00 3.34
312 313 1.603802 AGAGTTTGCCACACACGAATG 59.396 47.619 0.00 0.00 0.00 2.67
313 314 0.030638 AGTTTGCCACACACGAATGC 59.969 50.000 0.00 0.00 0.00 3.56
314 315 0.939106 GTTTGCCACACACGAATGCC 60.939 55.000 0.00 0.00 0.00 4.40
315 316 1.106351 TTTGCCACACACGAATGCCT 61.106 50.000 0.00 0.00 0.00 4.75
316 317 1.514678 TTGCCACACACGAATGCCTC 61.515 55.000 0.00 0.00 0.00 4.70
317 318 2.690778 GCCACACACGAATGCCTCC 61.691 63.158 0.00 0.00 0.00 4.30
318 319 2.390599 CCACACACGAATGCCTCCG 61.391 63.158 0.00 0.00 0.00 4.63
319 320 1.667830 CACACACGAATGCCTCCGT 60.668 57.895 0.00 0.00 39.88 4.69
324 325 3.362581 ACGAATGCCTCCGTGTATG 57.637 52.632 0.00 0.00 37.64 2.39
325 326 0.179084 ACGAATGCCTCCGTGTATGG 60.179 55.000 0.00 0.00 37.64 2.74
326 327 0.104120 CGAATGCCTCCGTGTATGGA 59.896 55.000 0.00 0.00 36.37 3.41
327 328 1.583054 GAATGCCTCCGTGTATGGAC 58.417 55.000 0.00 0.00 33.48 4.02
328 329 0.908910 AATGCCTCCGTGTATGGACA 59.091 50.000 0.00 0.00 33.48 4.02
329 330 0.908910 ATGCCTCCGTGTATGGACAA 59.091 50.000 0.00 0.00 37.31 3.18
330 331 0.908910 TGCCTCCGTGTATGGACAAT 59.091 50.000 0.00 0.00 37.31 2.71
331 332 1.134521 TGCCTCCGTGTATGGACAATC 60.135 52.381 0.00 0.00 37.31 2.67
332 333 1.139058 GCCTCCGTGTATGGACAATCT 59.861 52.381 0.00 0.00 37.31 2.40
333 334 2.803492 GCCTCCGTGTATGGACAATCTC 60.803 54.545 0.00 0.00 37.31 2.75
334 335 2.224066 CCTCCGTGTATGGACAATCTCC 60.224 54.545 0.00 0.00 37.31 3.71
335 336 2.695666 CTCCGTGTATGGACAATCTCCT 59.304 50.000 0.00 0.00 40.26 3.69
336 337 3.104512 TCCGTGTATGGACAATCTCCTT 58.895 45.455 0.00 0.00 40.26 3.36
337 338 3.118775 TCCGTGTATGGACAATCTCCTTG 60.119 47.826 0.00 0.00 40.26 3.61
338 339 3.198068 CGTGTATGGACAATCTCCTTGG 58.802 50.000 0.00 0.00 40.26 3.61
339 340 3.118775 CGTGTATGGACAATCTCCTTGGA 60.119 47.826 0.00 0.00 40.26 3.53
340 341 4.443457 CGTGTATGGACAATCTCCTTGGAT 60.443 45.833 0.00 0.00 40.26 3.41
341 342 5.059833 GTGTATGGACAATCTCCTTGGATC 58.940 45.833 0.00 0.00 40.26 3.36
342 343 2.988010 TGGACAATCTCCTTGGATCG 57.012 50.000 0.00 0.00 40.26 3.69
343 344 1.134401 TGGACAATCTCCTTGGATCGC 60.134 52.381 0.00 0.00 40.26 4.58
344 345 1.587547 GACAATCTCCTTGGATCGCC 58.412 55.000 0.00 0.00 39.30 5.54
345 346 1.139853 GACAATCTCCTTGGATCGCCT 59.860 52.381 0.00 0.00 39.30 5.52
346 347 1.139853 ACAATCTCCTTGGATCGCCTC 59.860 52.381 0.00 0.00 39.30 4.70
347 348 0.390860 AATCTCCTTGGATCGCCTCG 59.609 55.000 0.00 0.00 34.31 4.63
348 349 0.757188 ATCTCCTTGGATCGCCTCGT 60.757 55.000 0.00 0.00 34.31 4.18
349 350 1.066587 CTCCTTGGATCGCCTCGTC 59.933 63.158 0.00 0.00 34.31 4.20
350 351 1.667154 CTCCTTGGATCGCCTCGTCA 61.667 60.000 0.00 0.00 34.31 4.35
351 352 1.519455 CCTTGGATCGCCTCGTCAC 60.519 63.158 0.00 0.00 34.31 3.67
352 353 1.513158 CTTGGATCGCCTCGTCACT 59.487 57.895 0.00 0.00 34.31 3.41
353 354 0.526524 CTTGGATCGCCTCGTCACTC 60.527 60.000 0.00 0.00 34.31 3.51
354 355 1.248101 TTGGATCGCCTCGTCACTCA 61.248 55.000 0.00 0.00 34.31 3.41
355 356 1.226717 GGATCGCCTCGTCACTCAC 60.227 63.158 0.00 0.00 0.00 3.51
356 357 1.658686 GGATCGCCTCGTCACTCACT 61.659 60.000 0.00 0.00 0.00 3.41
357 358 0.248296 GATCGCCTCGTCACTCACTC 60.248 60.000 0.00 0.00 0.00 3.51
358 359 1.983196 ATCGCCTCGTCACTCACTCG 61.983 60.000 0.00 0.00 0.00 4.18
359 360 2.677979 CGCCTCGTCACTCACTCGA 61.678 63.158 0.00 0.00 0.00 4.04
360 361 1.154188 GCCTCGTCACTCACTCGAC 60.154 63.158 0.00 0.00 0.00 4.20
361 362 1.853114 GCCTCGTCACTCACTCGACA 61.853 60.000 0.00 0.00 32.24 4.35
365 366 1.283181 GTCACTCACTCGACACGCT 59.717 57.895 0.00 0.00 32.24 5.07
390 391 0.457337 ATCGTACGTCCGAGCCAAAC 60.457 55.000 16.05 0.00 40.68 2.93
403 404 0.817654 GCCAAACCTATCCACAAGCC 59.182 55.000 0.00 0.00 0.00 4.35
410 411 0.254178 CTATCCACAAGCCAGCCAGT 59.746 55.000 0.00 0.00 0.00 4.00
573 576 1.862806 GGCAGTCACTTCGCACTTC 59.137 57.895 0.00 0.00 0.00 3.01
576 579 1.006102 AGTCACTTCGCACTTCGGG 60.006 57.895 0.00 0.00 39.05 5.14
596 599 3.287222 GGGTCCATCATCGGATTTTTCA 58.713 45.455 0.00 0.00 37.41 2.69
701 706 3.196207 ATCCGTTGCACCAGCCAGT 62.196 57.895 0.00 0.00 41.13 4.00
747 2122 3.314331 CCCCGCCACTCACTCACT 61.314 66.667 0.00 0.00 0.00 3.41
748 2123 2.262915 CCCGCCACTCACTCACTC 59.737 66.667 0.00 0.00 0.00 3.51
749 2124 2.574018 CCCGCCACTCACTCACTCA 61.574 63.158 0.00 0.00 0.00 3.41
772 2147 3.361786 TGTCATGGAGTACGAGGAATCA 58.638 45.455 0.00 0.00 0.00 2.57
870 2303 0.108945 GGCAGCTCATTCAAACCAGC 60.109 55.000 0.00 0.00 0.00 4.85
1339 3281 1.899814 TCTCCGTGTGATAAAGCAGGT 59.100 47.619 0.00 0.00 0.00 4.00
1507 3772 0.167470 CAGCACCGCATTGACAAGAG 59.833 55.000 0.00 0.00 0.00 2.85
1542 4015 0.731417 CACGGTCAGTCCCTACTACG 59.269 60.000 0.00 0.00 33.48 3.51
1574 7953 6.358030 CACTTGTTCAGCTTCGTTTCATTTAG 59.642 38.462 0.00 0.00 0.00 1.85
1703 8091 4.388499 TTGTCGGAAGCCTCGGCC 62.388 66.667 3.92 0.00 43.17 6.13
1745 8133 0.460109 CAGTTCATCCGATCACCGCA 60.460 55.000 0.00 0.00 36.84 5.69
1885 8495 6.956047 ACTTATGAAACGTCCTCAAAAAGAC 58.044 36.000 20.89 0.00 0.00 3.01
2007 8617 4.223032 ACACATTACCAGAGGACGATTTCT 59.777 41.667 0.00 0.00 0.00 2.52
2310 8940 0.032130 AGAACGTGAGAGCGCTTTCA 59.968 50.000 25.28 25.28 35.82 2.69
2382 9012 1.899437 ATGCGGTCCAAGGTGATCGT 61.899 55.000 0.00 0.00 40.92 3.73
2454 9095 3.440522 GTCATCCTGGAAAGCCACTTAAC 59.559 47.826 0.00 0.00 39.92 2.01
2468 9109 3.386726 CCACTTAACTGGGTATCATCGGA 59.613 47.826 0.00 0.00 0.00 4.55
2469 9110 4.141801 CCACTTAACTGGGTATCATCGGAA 60.142 45.833 0.00 0.00 0.00 4.30
2470 9111 5.454755 CCACTTAACTGGGTATCATCGGAAT 60.455 44.000 0.00 0.00 0.00 3.01
2471 9112 5.696724 CACTTAACTGGGTATCATCGGAATC 59.303 44.000 0.00 0.00 0.00 2.52
2501 9150 4.186856 TGTTGATGCTTCGTATCACTGA 57.813 40.909 0.00 0.00 34.66 3.41
2512 9161 6.848296 GCTTCGTATCACTGATTTGAAATAGC 59.152 38.462 0.00 0.00 0.00 2.97
2557 9206 3.205338 CACTCCGTGCATGGATGAAATA 58.795 45.455 27.70 4.03 37.41 1.40
2737 9386 5.931146 GGGTGATGCATCAAAGTAGAGATAG 59.069 44.000 30.24 0.00 38.75 2.08
2972 10175 6.352016 TGCAGCAAGATATTTTTGGGTTTA 57.648 33.333 0.00 0.00 0.00 2.01
3121 10328 4.621991 AGCGCAAAGTTATGACGATATCT 58.378 39.130 11.47 0.00 0.00 1.98
3317 10524 5.954150 ACTCAAGCAATATGATGAAAACCCT 59.046 36.000 0.00 0.00 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 5.938125 ACATAACTACCTACCAGCAGTTTTG 59.062 40.000 0.00 0.00 36.58 2.44
16 17 6.123045 ACATAACTACCTACCAGCAGTTTT 57.877 37.500 0.00 0.00 33.47 2.43
17 18 5.757099 ACATAACTACCTACCAGCAGTTT 57.243 39.130 0.00 0.00 33.47 2.66
18 19 5.757099 AACATAACTACCTACCAGCAGTT 57.243 39.130 0.00 0.00 35.50 3.16
19 20 6.862469 TTAACATAACTACCTACCAGCAGT 57.138 37.500 0.00 0.00 0.00 4.40
20 21 7.491696 GTCTTTAACATAACTACCTACCAGCAG 59.508 40.741 0.00 0.00 0.00 4.24
21 22 7.038870 TGTCTTTAACATAACTACCTACCAGCA 60.039 37.037 0.00 0.00 31.20 4.41
22 23 7.325694 TGTCTTTAACATAACTACCTACCAGC 58.674 38.462 0.00 0.00 31.20 4.85
23 24 9.886132 ATTGTCTTTAACATAACTACCTACCAG 57.114 33.333 0.00 0.00 37.82 4.00
63 64 1.404843 AAGCAGTTACCCCGCAAAAA 58.595 45.000 0.00 0.00 0.00 1.94
64 65 2.273538 TAAGCAGTTACCCCGCAAAA 57.726 45.000 0.00 0.00 0.00 2.44
65 66 2.500392 ATAAGCAGTTACCCCGCAAA 57.500 45.000 0.00 0.00 0.00 3.68
66 67 2.500392 AATAAGCAGTTACCCCGCAA 57.500 45.000 0.00 0.00 0.00 4.85
67 68 2.500392 AAATAAGCAGTTACCCCGCA 57.500 45.000 0.00 0.00 0.00 5.69
80 81 6.604735 AGCGTCATTGTTAGGCTAAATAAG 57.395 37.500 8.86 0.40 36.38 1.73
81 82 7.767198 AGTTAGCGTCATTGTTAGGCTAAATAA 59.233 33.333 8.86 7.99 46.12 1.40
82 83 7.270047 AGTTAGCGTCATTGTTAGGCTAAATA 58.730 34.615 8.86 0.14 46.12 1.40
83 84 6.113411 AGTTAGCGTCATTGTTAGGCTAAAT 58.887 36.000 8.86 9.26 46.12 1.40
84 85 5.484715 AGTTAGCGTCATTGTTAGGCTAAA 58.515 37.500 8.86 0.00 46.12 1.85
85 86 5.080969 AGTTAGCGTCATTGTTAGGCTAA 57.919 39.130 2.04 2.04 43.94 3.09
86 87 4.730949 AGTTAGCGTCATTGTTAGGCTA 57.269 40.909 0.00 0.00 38.82 3.93
87 88 3.611766 AGTTAGCGTCATTGTTAGGCT 57.388 42.857 0.00 0.00 40.81 4.58
88 89 5.050295 GGAATAGTTAGCGTCATTGTTAGGC 60.050 44.000 0.00 0.00 0.00 3.93
89 90 6.281405 AGGAATAGTTAGCGTCATTGTTAGG 58.719 40.000 0.00 0.00 0.00 2.69
90 91 8.753175 GTTAGGAATAGTTAGCGTCATTGTTAG 58.247 37.037 0.00 0.00 0.00 2.34
91 92 8.252417 TGTTAGGAATAGTTAGCGTCATTGTTA 58.748 33.333 0.00 0.00 0.00 2.41
92 93 7.101054 TGTTAGGAATAGTTAGCGTCATTGTT 58.899 34.615 0.00 0.00 0.00 2.83
93 94 6.636705 TGTTAGGAATAGTTAGCGTCATTGT 58.363 36.000 0.00 0.00 0.00 2.71
94 95 7.534085 TTGTTAGGAATAGTTAGCGTCATTG 57.466 36.000 0.00 0.00 0.00 2.82
95 96 7.822822 AGTTTGTTAGGAATAGTTAGCGTCATT 59.177 33.333 0.00 0.00 0.00 2.57
96 97 7.328737 AGTTTGTTAGGAATAGTTAGCGTCAT 58.671 34.615 0.00 0.00 0.00 3.06
97 98 6.694447 AGTTTGTTAGGAATAGTTAGCGTCA 58.306 36.000 0.00 0.00 0.00 4.35
98 99 8.753175 CATAGTTTGTTAGGAATAGTTAGCGTC 58.247 37.037 0.00 0.00 0.00 5.19
99 100 8.472413 TCATAGTTTGTTAGGAATAGTTAGCGT 58.528 33.333 0.00 0.00 0.00 5.07
100 101 8.867112 TCATAGTTTGTTAGGAATAGTTAGCG 57.133 34.615 0.00 0.00 0.00 4.26
123 124 9.388506 GTTTCCTCTTCTGATAGAAAATCATCA 57.611 33.333 0.00 0.00 33.19 3.07
124 125 9.388506 TGTTTCCTCTTCTGATAGAAAATCATC 57.611 33.333 0.00 0.00 33.19 2.92
125 126 9.745018 TTGTTTCCTCTTCTGATAGAAAATCAT 57.255 29.630 0.00 0.00 33.19 2.45
126 127 9.003658 GTTGTTTCCTCTTCTGATAGAAAATCA 57.996 33.333 0.00 0.00 33.19 2.57
127 128 9.003658 TGTTGTTTCCTCTTCTGATAGAAAATC 57.996 33.333 0.00 0.00 33.19 2.17
128 129 8.924511 TGTTGTTTCCTCTTCTGATAGAAAAT 57.075 30.769 0.00 0.00 33.19 1.82
129 130 8.746052 TTGTTGTTTCCTCTTCTGATAGAAAA 57.254 30.769 0.00 0.00 33.19 2.29
130 131 8.786898 CATTGTTGTTTCCTCTTCTGATAGAAA 58.213 33.333 0.00 0.00 33.19 2.52
131 132 7.094634 GCATTGTTGTTTCCTCTTCTGATAGAA 60.095 37.037 0.00 0.00 32.50 2.10
132 133 6.372659 GCATTGTTGTTTCCTCTTCTGATAGA 59.627 38.462 0.00 0.00 0.00 1.98
133 134 6.404074 GGCATTGTTGTTTCCTCTTCTGATAG 60.404 42.308 0.00 0.00 0.00 2.08
134 135 5.415701 GGCATTGTTGTTTCCTCTTCTGATA 59.584 40.000 0.00 0.00 0.00 2.15
135 136 4.219288 GGCATTGTTGTTTCCTCTTCTGAT 59.781 41.667 0.00 0.00 0.00 2.90
136 137 3.569701 GGCATTGTTGTTTCCTCTTCTGA 59.430 43.478 0.00 0.00 0.00 3.27
137 138 3.305608 GGGCATTGTTGTTTCCTCTTCTG 60.306 47.826 0.00 0.00 0.00 3.02
138 139 2.893489 GGGCATTGTTGTTTCCTCTTCT 59.107 45.455 0.00 0.00 0.00 2.85
139 140 2.029020 GGGGCATTGTTGTTTCCTCTTC 60.029 50.000 0.00 0.00 0.00 2.87
140 141 1.970640 GGGGCATTGTTGTTTCCTCTT 59.029 47.619 0.00 0.00 0.00 2.85
141 142 1.632589 GGGGCATTGTTGTTTCCTCT 58.367 50.000 0.00 0.00 0.00 3.69
142 143 0.243636 CGGGGCATTGTTGTTTCCTC 59.756 55.000 0.00 0.00 0.00 3.71
143 144 0.178975 TCGGGGCATTGTTGTTTCCT 60.179 50.000 0.00 0.00 0.00 3.36
144 145 0.676736 TTCGGGGCATTGTTGTTTCC 59.323 50.000 0.00 0.00 0.00 3.13
145 146 1.778334 GTTCGGGGCATTGTTGTTTC 58.222 50.000 0.00 0.00 0.00 2.78
146 147 0.031449 CGTTCGGGGCATTGTTGTTT 59.969 50.000 0.00 0.00 0.00 2.83
147 148 0.820074 TCGTTCGGGGCATTGTTGTT 60.820 50.000 0.00 0.00 0.00 2.83
148 149 1.228003 TCGTTCGGGGCATTGTTGT 60.228 52.632 0.00 0.00 0.00 3.32
149 150 0.953471 TCTCGTTCGGGGCATTGTTG 60.953 55.000 0.00 0.00 0.00 3.33
150 151 0.035439 ATCTCGTTCGGGGCATTGTT 60.035 50.000 0.00 0.00 0.00 2.83
151 152 0.828022 TATCTCGTTCGGGGCATTGT 59.172 50.000 0.00 0.00 0.00 2.71
152 153 1.502231 CTATCTCGTTCGGGGCATTG 58.498 55.000 0.00 0.00 0.00 2.82
153 154 0.249911 GCTATCTCGTTCGGGGCATT 60.250 55.000 0.00 0.00 0.00 3.56
154 155 1.115930 AGCTATCTCGTTCGGGGCAT 61.116 55.000 0.00 0.00 0.00 4.40
155 156 1.327690 AAGCTATCTCGTTCGGGGCA 61.328 55.000 0.00 0.00 0.00 5.36
156 157 0.876342 CAAGCTATCTCGTTCGGGGC 60.876 60.000 0.00 0.00 0.00 5.80
157 158 0.249489 CCAAGCTATCTCGTTCGGGG 60.249 60.000 0.00 0.00 0.00 5.73
158 159 0.876342 GCCAAGCTATCTCGTTCGGG 60.876 60.000 0.00 0.00 0.00 5.14
159 160 0.103208 AGCCAAGCTATCTCGTTCGG 59.897 55.000 0.00 0.00 36.99 4.30
160 161 1.202302 TGAGCCAAGCTATCTCGTTCG 60.202 52.381 0.00 0.00 39.88 3.95
161 162 2.197577 GTGAGCCAAGCTATCTCGTTC 58.802 52.381 0.00 0.00 39.88 3.95
162 163 1.550524 TGTGAGCCAAGCTATCTCGTT 59.449 47.619 0.00 0.00 39.88 3.85
163 164 1.134965 GTGTGAGCCAAGCTATCTCGT 60.135 52.381 0.00 0.00 39.88 4.18
164 165 1.565305 GTGTGAGCCAAGCTATCTCG 58.435 55.000 0.00 0.00 39.88 4.04
165 166 1.565305 CGTGTGAGCCAAGCTATCTC 58.435 55.000 0.00 0.00 39.88 2.75
166 167 0.460987 GCGTGTGAGCCAAGCTATCT 60.461 55.000 0.00 0.00 44.08 1.98
167 168 2.009888 GCGTGTGAGCCAAGCTATC 58.990 57.895 0.00 0.00 44.08 2.08
168 169 4.208632 GCGTGTGAGCCAAGCTAT 57.791 55.556 0.00 0.00 44.08 2.97
176 177 5.986004 AGTAATTATTAAGGCGTGTGAGC 57.014 39.130 0.00 0.00 0.00 4.26
177 178 6.761714 AGGAAGTAATTATTAAGGCGTGTGAG 59.238 38.462 0.00 0.00 0.00 3.51
178 179 6.646267 AGGAAGTAATTATTAAGGCGTGTGA 58.354 36.000 0.00 0.00 0.00 3.58
179 180 6.018180 GGAGGAAGTAATTATTAAGGCGTGTG 60.018 42.308 0.00 0.00 0.00 3.82
180 181 6.053650 GGAGGAAGTAATTATTAAGGCGTGT 58.946 40.000 0.00 0.00 0.00 4.49
181 182 5.176958 CGGAGGAAGTAATTATTAAGGCGTG 59.823 44.000 0.00 0.00 0.00 5.34
182 183 5.163374 ACGGAGGAAGTAATTATTAAGGCGT 60.163 40.000 0.00 0.00 0.00 5.68
183 184 5.295152 ACGGAGGAAGTAATTATTAAGGCG 58.705 41.667 0.00 0.00 0.00 5.52
184 185 6.522946 AGACGGAGGAAGTAATTATTAAGGC 58.477 40.000 0.00 0.00 0.00 4.35
185 186 7.652507 GTGAGACGGAGGAAGTAATTATTAAGG 59.347 40.741 0.00 0.00 0.00 2.69
186 187 8.195436 TGTGAGACGGAGGAAGTAATTATTAAG 58.805 37.037 0.00 0.00 0.00 1.85
187 188 8.070034 TGTGAGACGGAGGAAGTAATTATTAA 57.930 34.615 0.00 0.00 0.00 1.40
188 189 7.649533 TGTGAGACGGAGGAAGTAATTATTA 57.350 36.000 0.00 0.00 0.00 0.98
189 190 6.540438 TGTGAGACGGAGGAAGTAATTATT 57.460 37.500 0.00 0.00 0.00 1.40
190 191 6.540438 TTGTGAGACGGAGGAAGTAATTAT 57.460 37.500 0.00 0.00 0.00 1.28
191 192 5.988310 TTGTGAGACGGAGGAAGTAATTA 57.012 39.130 0.00 0.00 0.00 1.40
192 193 4.884668 TTGTGAGACGGAGGAAGTAATT 57.115 40.909 0.00 0.00 0.00 1.40
193 194 4.223032 ACATTGTGAGACGGAGGAAGTAAT 59.777 41.667 0.00 0.00 0.00 1.89
194 195 3.576982 ACATTGTGAGACGGAGGAAGTAA 59.423 43.478 0.00 0.00 0.00 2.24
195 196 3.162666 ACATTGTGAGACGGAGGAAGTA 58.837 45.455 0.00 0.00 0.00 2.24
196 197 1.971357 ACATTGTGAGACGGAGGAAGT 59.029 47.619 0.00 0.00 0.00 3.01
197 198 2.751166 ACATTGTGAGACGGAGGAAG 57.249 50.000 0.00 0.00 0.00 3.46
198 199 4.819105 ATTACATTGTGAGACGGAGGAA 57.181 40.909 0.00 0.00 0.00 3.36
199 200 7.591421 TTATATTACATTGTGAGACGGAGGA 57.409 36.000 0.00 0.00 0.00 3.71
200 201 9.574458 CTATTATATTACATTGTGAGACGGAGG 57.426 37.037 0.00 0.00 0.00 4.30
201 202 9.077674 GCTATTATATTACATTGTGAGACGGAG 57.922 37.037 0.00 0.00 0.00 4.63
202 203 7.753580 CGCTATTATATTACATTGTGAGACGGA 59.246 37.037 0.00 0.00 0.00 4.69
203 204 7.541091 ACGCTATTATATTACATTGTGAGACGG 59.459 37.037 0.00 0.00 0.00 4.79
204 205 8.449085 ACGCTATTATATTACATTGTGAGACG 57.551 34.615 0.00 0.00 0.00 4.18
225 226 8.941977 TGACACTACATTAATATCAAAAACGCT 58.058 29.630 0.00 0.00 0.00 5.07
226 227 9.549509 TTGACACTACATTAATATCAAAAACGC 57.450 29.630 0.00 0.00 0.00 4.84
246 247 9.248291 CCCATAATATAAGCATGTTTTTGACAC 57.752 33.333 0.00 0.00 42.04 3.67
247 248 9.194972 TCCCATAATATAAGCATGTTTTTGACA 57.805 29.630 0.00 0.00 43.71 3.58
250 251 9.426837 CCATCCCATAATATAAGCATGTTTTTG 57.573 33.333 0.00 0.00 0.00 2.44
251 252 9.378504 TCCATCCCATAATATAAGCATGTTTTT 57.621 29.630 0.00 0.00 0.00 1.94
252 253 8.954834 TCCATCCCATAATATAAGCATGTTTT 57.045 30.769 0.00 0.00 0.00 2.43
253 254 7.616935 CCTCCATCCCATAATATAAGCATGTTT 59.383 37.037 0.00 0.00 0.00 2.83
254 255 7.121382 CCTCCATCCCATAATATAAGCATGTT 58.879 38.462 0.00 0.00 0.00 2.71
255 256 6.354213 CCCTCCATCCCATAATATAAGCATGT 60.354 42.308 0.00 0.00 0.00 3.21
256 257 6.066690 CCCTCCATCCCATAATATAAGCATG 58.933 44.000 0.00 0.00 0.00 4.06
257 258 5.978752 TCCCTCCATCCCATAATATAAGCAT 59.021 40.000 0.00 0.00 0.00 3.79
258 259 5.358306 TCCCTCCATCCCATAATATAAGCA 58.642 41.667 0.00 0.00 0.00 3.91
259 260 5.163152 CCTCCCTCCATCCCATAATATAAGC 60.163 48.000 0.00 0.00 0.00 3.09
260 261 5.163152 GCCTCCCTCCATCCCATAATATAAG 60.163 48.000 0.00 0.00 0.00 1.73
261 262 4.726825 GCCTCCCTCCATCCCATAATATAA 59.273 45.833 0.00 0.00 0.00 0.98
262 263 4.014306 AGCCTCCCTCCATCCCATAATATA 60.014 45.833 0.00 0.00 0.00 0.86
263 264 3.126453 GCCTCCCTCCATCCCATAATAT 58.874 50.000 0.00 0.00 0.00 1.28
264 265 2.116158 AGCCTCCCTCCATCCCATAATA 59.884 50.000 0.00 0.00 0.00 0.98
265 266 1.131937 AGCCTCCCTCCATCCCATAAT 60.132 52.381 0.00 0.00 0.00 1.28
266 267 0.271927 AGCCTCCCTCCATCCCATAA 59.728 55.000 0.00 0.00 0.00 1.90
267 268 0.271927 AAGCCTCCCTCCATCCCATA 59.728 55.000 0.00 0.00 0.00 2.74
268 269 0.628668 AAAGCCTCCCTCCATCCCAT 60.629 55.000 0.00 0.00 0.00 4.00
269 270 1.230281 AAAGCCTCCCTCCATCCCA 60.230 57.895 0.00 0.00 0.00 4.37
270 271 1.534203 GAAAGCCTCCCTCCATCCC 59.466 63.158 0.00 0.00 0.00 3.85
271 272 1.534203 GGAAAGCCTCCCTCCATCC 59.466 63.158 0.00 0.00 38.44 3.51
279 280 0.325272 AAACTCTCGGGAAAGCCTCC 59.675 55.000 0.00 0.00 44.54 4.30
280 281 1.443802 CAAACTCTCGGGAAAGCCTC 58.556 55.000 0.00 0.00 0.00 4.70
281 282 0.606673 GCAAACTCTCGGGAAAGCCT 60.607 55.000 0.00 0.00 0.00 4.58
282 283 1.587043 GGCAAACTCTCGGGAAAGCC 61.587 60.000 1.82 1.82 0.00 4.35
283 284 0.889186 TGGCAAACTCTCGGGAAAGC 60.889 55.000 0.00 0.00 0.00 3.51
284 285 0.875059 GTGGCAAACTCTCGGGAAAG 59.125 55.000 0.00 0.00 0.00 2.62
285 286 0.181587 TGTGGCAAACTCTCGGGAAA 59.818 50.000 0.00 0.00 0.00 3.13
286 287 0.534203 GTGTGGCAAACTCTCGGGAA 60.534 55.000 0.00 0.00 0.00 3.97
287 288 1.070786 GTGTGGCAAACTCTCGGGA 59.929 57.895 0.00 0.00 0.00 5.14
288 289 1.227823 TGTGTGGCAAACTCTCGGG 60.228 57.895 9.62 0.00 0.00 5.14
289 290 1.831389 CGTGTGTGGCAAACTCTCGG 61.831 60.000 9.62 0.00 36.27 4.63
290 291 0.874175 TCGTGTGTGGCAAACTCTCG 60.874 55.000 9.62 11.04 39.41 4.04
291 292 1.295792 TTCGTGTGTGGCAAACTCTC 58.704 50.000 9.62 0.00 0.00 3.20
292 293 1.603802 CATTCGTGTGTGGCAAACTCT 59.396 47.619 9.62 0.00 0.00 3.24
293 294 1.925946 GCATTCGTGTGTGGCAAACTC 60.926 52.381 9.62 4.47 0.00 3.01
294 295 0.030638 GCATTCGTGTGTGGCAAACT 59.969 50.000 9.62 0.00 0.00 2.66
295 296 0.939106 GGCATTCGTGTGTGGCAAAC 60.939 55.000 0.00 0.00 40.30 2.93
296 297 1.106351 AGGCATTCGTGTGTGGCAAA 61.106 50.000 0.00 0.00 42.73 3.68
297 298 1.514678 GAGGCATTCGTGTGTGGCAA 61.515 55.000 0.00 0.00 42.73 4.52
298 299 1.965930 GAGGCATTCGTGTGTGGCA 60.966 57.895 1.85 0.00 42.73 4.92
299 300 2.690778 GGAGGCATTCGTGTGTGGC 61.691 63.158 0.00 0.00 40.82 5.01
300 301 2.390599 CGGAGGCATTCGTGTGTGG 61.391 63.158 0.00 0.00 0.00 4.17
301 302 1.667830 ACGGAGGCATTCGTGTGTG 60.668 57.895 2.71 0.00 38.25 3.82
302 303 2.741092 ACGGAGGCATTCGTGTGT 59.259 55.556 2.71 0.00 38.25 3.72
306 307 0.179084 CCATACACGGAGGCATTCGT 60.179 55.000 0.00 0.00 40.49 3.85
307 308 0.104120 TCCATACACGGAGGCATTCG 59.896 55.000 0.00 0.00 0.00 3.34
308 309 1.134521 TGTCCATACACGGAGGCATTC 60.135 52.381 0.00 0.00 35.10 2.67
309 310 0.908910 TGTCCATACACGGAGGCATT 59.091 50.000 0.00 0.00 35.10 3.56
310 311 0.908910 TTGTCCATACACGGAGGCAT 59.091 50.000 0.00 0.00 35.10 4.40
311 312 0.908910 ATTGTCCATACACGGAGGCA 59.091 50.000 0.00 0.00 35.10 4.75
312 313 1.139058 AGATTGTCCATACACGGAGGC 59.861 52.381 0.00 0.00 35.10 4.70
313 314 2.224066 GGAGATTGTCCATACACGGAGG 60.224 54.545 0.00 0.00 46.10 4.30
314 315 3.099267 GGAGATTGTCCATACACGGAG 57.901 52.381 0.00 0.00 46.10 4.63
324 325 4.131040 AGGCGATCCAAGGAGATTGTCC 62.131 54.545 0.00 0.00 39.41 4.02
325 326 1.139853 AGGCGATCCAAGGAGATTGTC 59.860 52.381 0.00 0.00 37.17 3.18
326 327 1.139853 GAGGCGATCCAAGGAGATTGT 59.860 52.381 0.00 0.00 37.17 2.71
327 328 1.871408 CGAGGCGATCCAAGGAGATTG 60.871 57.143 0.00 0.00 38.74 2.67
328 329 0.390860 CGAGGCGATCCAAGGAGATT 59.609 55.000 0.00 0.00 33.74 2.40
329 330 0.757188 ACGAGGCGATCCAAGGAGAT 60.757 55.000 0.00 0.00 33.74 2.75
330 331 1.379977 ACGAGGCGATCCAAGGAGA 60.380 57.895 0.00 0.00 33.74 3.71
331 332 1.066587 GACGAGGCGATCCAAGGAG 59.933 63.158 0.00 0.00 33.74 3.69
332 333 1.680989 TGACGAGGCGATCCAAGGA 60.681 57.895 0.00 0.00 33.74 3.36
333 334 1.519455 GTGACGAGGCGATCCAAGG 60.519 63.158 0.00 0.00 33.74 3.61
334 335 0.526524 GAGTGACGAGGCGATCCAAG 60.527 60.000 0.00 0.00 33.74 3.61
335 336 1.248101 TGAGTGACGAGGCGATCCAA 61.248 55.000 0.00 0.00 33.74 3.53
336 337 1.677633 TGAGTGACGAGGCGATCCA 60.678 57.895 0.00 0.00 33.74 3.41
337 338 1.226717 GTGAGTGACGAGGCGATCC 60.227 63.158 0.00 0.00 0.00 3.36
338 339 0.248296 GAGTGAGTGACGAGGCGATC 60.248 60.000 0.00 0.00 0.00 3.69
339 340 1.803943 GAGTGAGTGACGAGGCGAT 59.196 57.895 0.00 0.00 0.00 4.58
340 341 2.677979 CGAGTGAGTGACGAGGCGA 61.678 63.158 0.00 0.00 0.00 5.54
341 342 2.202362 CGAGTGAGTGACGAGGCG 60.202 66.667 0.00 0.00 0.00 5.52
342 343 1.154188 GTCGAGTGAGTGACGAGGC 60.154 63.158 0.00 0.00 36.74 4.70
343 344 0.110147 GTGTCGAGTGAGTGACGAGG 60.110 60.000 0.00 0.00 37.94 4.63
344 345 0.451299 CGTGTCGAGTGAGTGACGAG 60.451 60.000 0.00 0.00 37.94 4.18
345 346 1.568025 CGTGTCGAGTGAGTGACGA 59.432 57.895 0.00 0.00 37.94 4.20
346 347 2.075489 GCGTGTCGAGTGAGTGACG 61.075 63.158 0.00 0.00 37.94 4.35
347 348 0.999228 CAGCGTGTCGAGTGAGTGAC 60.999 60.000 0.00 0.00 35.67 3.67
348 349 1.282875 CAGCGTGTCGAGTGAGTGA 59.717 57.895 0.00 0.00 0.00 3.41
349 350 0.999228 GACAGCGTGTCGAGTGAGTG 60.999 60.000 0.00 0.00 37.67 3.51
350 351 1.283181 GACAGCGTGTCGAGTGAGT 59.717 57.895 0.00 0.00 37.67 3.41
351 352 4.138722 GACAGCGTGTCGAGTGAG 57.861 61.111 0.00 0.00 37.67 3.51
377 378 0.529992 GGATAGGTTTGGCTCGGACG 60.530 60.000 0.00 0.00 0.00 4.79
390 391 0.465097 CTGGCTGGCTTGTGGATAGG 60.465 60.000 2.00 0.00 0.00 2.57
403 404 2.281970 TGCTGGCTTGACTGGCTG 60.282 61.111 0.00 0.00 35.24 4.85
410 411 0.038251 CTGTCTACGTGCTGGCTTGA 60.038 55.000 0.00 0.00 0.00 3.02
460 463 3.399181 GGACGGGTCTGGCATCCA 61.399 66.667 10.27 0.00 0.00 3.41
560 563 2.342279 CCCCGAAGTGCGAAGTGA 59.658 61.111 0.00 0.00 44.57 3.41
573 576 0.108585 AAATCCGATGATGGACCCCG 59.891 55.000 0.00 0.00 41.85 5.73
576 579 4.339247 ACATGAAAAATCCGATGATGGACC 59.661 41.667 0.00 0.00 41.85 4.46
746 2121 2.098280 CCTCGTACTCCATGACAGTGAG 59.902 54.545 0.00 0.30 0.00 3.51
747 2122 2.092323 CCTCGTACTCCATGACAGTGA 58.908 52.381 0.00 0.00 0.00 3.41
748 2123 2.092323 TCCTCGTACTCCATGACAGTG 58.908 52.381 0.00 0.00 0.00 3.66
749 2124 2.509166 TCCTCGTACTCCATGACAGT 57.491 50.000 0.00 0.00 0.00 3.55
772 2147 5.646215 TCACTCTTCTAAGGTCCTCTTCTT 58.354 41.667 0.00 0.00 36.93 2.52
847 2278 2.633967 TGGTTTGAATGAGCTGCCAAAT 59.366 40.909 0.00 0.00 32.16 2.32
870 2303 0.321653 GGTCACCACTTACCAGGCTG 60.322 60.000 7.75 7.75 35.73 4.85
1109 3033 2.596851 ATGTCCTGCTCGGGCTTGT 61.597 57.895 9.62 0.00 38.58 3.16
1371 3313 2.485122 GCCGAATTTCGTGGCCAG 59.515 61.111 5.11 0.00 43.06 4.85
1507 3772 0.797249 CGTGATCTCGACGGGAACAC 60.797 60.000 23.81 23.81 34.58 3.32
1542 4015 3.365220 CGAAGCTGAACAAGTGCTACTAC 59.635 47.826 0.00 0.00 35.85 2.73
1574 7953 2.237392 ACCTACAAGCCCTCAATCTGTC 59.763 50.000 0.00 0.00 0.00 3.51
1677 8065 2.019951 CTTCCGACAACCCGACGTG 61.020 63.158 0.00 0.00 0.00 4.49
1703 8091 1.338105 TGTGCCCTTCTGATTGTCGAG 60.338 52.381 0.00 0.00 0.00 4.04
1745 8133 1.428869 AAGACCACTCCAGCTGAACT 58.571 50.000 17.39 0.60 0.00 3.01
1917 8527 1.472480 GTACGCCACAATTCCAATGCT 59.528 47.619 0.00 0.00 0.00 3.79
2007 8617 2.243810 GGGTGGTTCATTTACCTTGCA 58.756 47.619 0.00 0.00 39.04 4.08
2382 9012 3.181464 TGTTGAGGAACGTGATGTGGTAA 60.181 43.478 0.00 0.00 34.49 2.85
2454 9095 4.692625 GTGATTGATTCCGATGATACCCAG 59.307 45.833 0.00 0.00 0.00 4.45
2468 9109 6.317140 ACGAAGCATCAACATAGTGATTGATT 59.683 34.615 0.00 0.00 41.69 2.57
2469 9110 5.819379 ACGAAGCATCAACATAGTGATTGAT 59.181 36.000 0.00 0.00 44.52 2.57
2470 9111 5.178061 ACGAAGCATCAACATAGTGATTGA 58.822 37.500 0.00 0.00 36.04 2.57
2471 9112 5.475273 ACGAAGCATCAACATAGTGATTG 57.525 39.130 0.00 0.00 36.04 2.67
2512 9161 6.759356 TGCTCATGGAATTATTTGATTTGCAG 59.241 34.615 0.00 0.00 0.00 4.41
2557 9206 3.136260 AGCAAACAATTGGTGGTTCCATT 59.864 39.130 10.83 0.00 45.12 3.16
2659 9308 3.646162 TCAAGAAGTAGCAAACTCCCAGA 59.354 43.478 0.00 0.00 37.50 3.86
2665 9314 4.260784 CGCAAGTTCAAGAAGTAGCAAACT 60.261 41.667 0.00 0.00 41.49 2.66
2737 9386 7.094334 CCTTGGTTCTTAACTGAAGGAAATACC 60.094 40.741 12.21 0.00 40.47 2.73
3121 10328 9.925545 ATGCCTATATTCATAATCATTGCCTTA 57.074 29.630 0.00 0.00 0.00 2.69
3248 10455 2.643933 ACTTAAGGCGTTACTCCGTC 57.356 50.000 7.53 0.00 0.00 4.79
3365 10887 1.340248 TCCTCACCGAGTGACAAAGTC 59.660 52.381 3.02 0.00 37.67 3.01


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

AutoCloner maintained by Alex Coulton.