Multiple sequence alignment - TraesCS2B01G206000

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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 TraesCS2B01G206000 chr2B 100.000 2702 0 0 1 2702 184898828 184901529 0.000000e+00 4990.0
1 TraesCS2B01G206000 chr2B 92.010 776 39 12 658 1416 184799867 184800636 0.000000e+00 1068.0
2 TraesCS2B01G206000 chr2B 83.064 803 91 29 808 1568 184909436 184910235 0.000000e+00 688.0
3 TraesCS2B01G206000 chr2B 79.100 1000 134 39 1121 2064 184800488 184801468 1.060000e-173 619.0
4 TraesCS2B01G206000 chr2B 85.379 554 54 2 998 1551 184930645 184931171 1.410000e-152 549.0
5 TraesCS2B01G206000 chr2B 84.211 570 77 5 1216 1782 184877316 184877875 2.370000e-150 542.0
6 TraesCS2B01G206000 chr2B 78.827 784 102 39 823 1568 184876821 184877578 1.130000e-128 470.0
7 TraesCS2B01G206000 chr2B 80.892 628 81 22 1174 1778 184789496 184790107 2.450000e-125 459.0
8 TraesCS2B01G206000 chr2B 81.319 546 76 15 997 1534 184789361 184789888 1.160000e-113 420.0
9 TraesCS2B01G206000 chr2B 84.346 428 63 2 1343 1770 184910094 184910517 1.500000e-112 416.0
10 TraesCS2B01G206000 chr2B 88.797 241 17 6 323 553 184798279 184798519 1.220000e-73 287.0
11 TraesCS2B01G206000 chr2B 80.420 286 23 13 599 871 184928095 184928360 1.280000e-43 187.0
12 TraesCS2B01G206000 chr2B 97.143 70 2 0 599 668 184798521 184798590 4.730000e-23 119.0
13 TraesCS2B01G206000 chr2A 86.466 1293 93 43 323 1568 137941643 137942900 0.000000e+00 1343.0
14 TraesCS2B01G206000 chr2A 80.948 992 130 38 614 1567 138083971 138084941 0.000000e+00 730.0
15 TraesCS2B01G206000 chr2A 90.257 544 39 7 1238 1774 137942702 137943238 0.000000e+00 699.0
16 TraesCS2B01G206000 chr2A 88.616 571 63 2 999 1568 137951272 137951841 0.000000e+00 693.0
17 TraesCS2B01G206000 chr2A 83.453 556 78 6 1216 1768 137936365 137936909 3.100000e-139 505.0
18 TraesCS2B01G206000 chr2A 78.367 735 127 24 1343 2064 137951700 137952415 5.310000e-122 448.0
19 TraesCS2B01G206000 chr2A 91.416 233 20 0 2470 2702 672289108 672288876 1.210000e-83 320.0
20 TraesCS2B01G206000 chr2A 81.769 373 51 7 1410 1770 138084868 138085235 2.030000e-76 296.0
21 TraesCS2B01G206000 chr2A 88.696 230 14 1 1847 2064 137944912 137945141 1.230000e-68 270.0
22 TraesCS2B01G206000 chr2A 84.375 160 12 9 808 956 137951039 137951196 7.800000e-31 145.0
23 TraesCS2B01G206000 chr2A 94.048 84 4 1 1 83 738968017 738967934 2.820000e-25 126.0
24 TraesCS2B01G206000 chr2A 76.419 229 30 11 103 321 348021944 348021730 4.760000e-18 102.0
25 TraesCS2B01G206000 chr2A 75.330 227 30 12 99 314 447894493 447894282 4.790000e-13 86.1
26 TraesCS2B01G206000 chr2A 94.545 55 3 0 2339 2393 672289161 672289107 4.790000e-13 86.1
27 TraesCS2B01G206000 chr7B 93.023 645 44 1 2059 2702 683940007 683940651 0.000000e+00 941.0
28 TraesCS2B01G206000 chr7B 92.308 39 0 2 835 870 604334387 604334425 5.000000e-03 52.8
29 TraesCS2B01G206000 chr5B 93.023 645 44 1 2059 2702 197203489 197202845 0.000000e+00 941.0
30 TraesCS2B01G206000 chr4B 92.248 645 49 1 2059 2702 454991498 454990854 0.000000e+00 913.0
31 TraesCS2B01G206000 chr3A 91.938 645 51 1 2059 2702 531900817 531901461 0.000000e+00 902.0
32 TraesCS2B01G206000 chr2D 88.275 597 68 2 972 1568 131316763 131317357 0.000000e+00 713.0
33 TraesCS2B01G206000 chr2D 81.898 801 84 33 599 1352 131359777 131360563 1.060000e-173 619.0
34 TraesCS2B01G206000 chr2D 88.865 458 19 13 691 1120 131294951 131295404 3.960000e-148 534.0
35 TraesCS2B01G206000 chr2D 79.754 731 111 20 1343 2064 131317216 131317918 1.870000e-136 496.0
36 TraesCS2B01G206000 chr2D 94.737 266 13 1 1799 2064 131308201 131308465 1.940000e-111 412.0
37 TraesCS2B01G206000 chr2D 81.452 248 33 5 1829 2064 131361131 131361377 9.870000e-45 191.0
38 TraesCS2B01G206000 chr2D 95.349 43 2 0 99 141 629575781 629575823 4.830000e-08 69.4
39 TraesCS2B01G206000 chr6A 89.939 328 33 0 2375 2702 6900929 6901256 8.940000e-115 424.0
40 TraesCS2B01G206000 chr1D 81.034 232 22 8 99 321 399159054 399158836 5.980000e-37 165.0
41 TraesCS2B01G206000 chrUn 95.294 85 3 1 1 84 22865778 22865694 1.690000e-27 134.0
42 TraesCS2B01G206000 chrUn 94.048 84 4 1 1 83 407847456 407847373 2.820000e-25 126.0
43 TraesCS2B01G206000 chrUn 94.048 84 4 1 1 83 407861658 407861741 2.820000e-25 126.0
44 TraesCS2B01G206000 chrUn 94.048 84 4 1 1 83 428313475 428313558 2.820000e-25 126.0
45 TraesCS2B01G206000 chrUn 93.023 86 5 1 1 85 244159591 244159676 1.020000e-24 124.0
46 TraesCS2B01G206000 chr5D 95.294 85 3 1 1 84 260097803 260097719 1.690000e-27 134.0
47 TraesCS2B01G206000 chr4A 93.258 89 5 1 1 88 666541599 666541511 2.180000e-26 130.0
48 TraesCS2B01G206000 chr4D 93.103 87 5 1 1 86 69477474 69477388 2.820000e-25 126.0
49 TraesCS2B01G206000 chr5A 85.149 101 9 5 165 260 547327398 547327299 6.160000e-17 99.0
50 TraesCS2B01G206000 chr5A 81.609 87 11 5 207 288 504758241 504758327 1.740000e-07 67.6
51 TraesCS2B01G206000 chr3B 83.824 68 9 2 218 283 305648459 305648392 2.250000e-06 63.9
52 TraesCS2B01G206000 chr3D 100.000 32 0 0 218 249 606621252 606621221 2.910000e-05 60.2
53 TraesCS2B01G206000 chr1B 96.875 32 1 0 99 130 484712741 484712710 1.000000e-03 54.7


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 TraesCS2B01G206000 chr2B 184898828 184901529 2701 False 4990.000000 4990 100.0000 1 2702 1 chr2B.!!$F1 2701
1 TraesCS2B01G206000 chr2B 184909436 184910517 1081 False 552.000000 688 83.7050 808 1770 2 chr2B.!!$F5 962
2 TraesCS2B01G206000 chr2B 184798279 184801468 3189 False 523.250000 1068 89.2625 323 2064 4 chr2B.!!$F3 1741
3 TraesCS2B01G206000 chr2B 184876821 184877875 1054 False 506.000000 542 81.5190 823 1782 2 chr2B.!!$F4 959
4 TraesCS2B01G206000 chr2B 184789361 184790107 746 False 439.500000 459 81.1055 997 1778 2 chr2B.!!$F2 781
5 TraesCS2B01G206000 chr2B 184928095 184931171 3076 False 368.000000 549 82.8995 599 1551 2 chr2B.!!$F6 952
6 TraesCS2B01G206000 chr2A 137941643 137945141 3498 False 770.666667 1343 88.4730 323 2064 3 chr2A.!!$F2 1741
7 TraesCS2B01G206000 chr2A 138083971 138085235 1264 False 513.000000 730 81.3585 614 1770 2 chr2A.!!$F4 1156
8 TraesCS2B01G206000 chr2A 137936365 137936909 544 False 505.000000 505 83.4530 1216 1768 1 chr2A.!!$F1 552
9 TraesCS2B01G206000 chr2A 137951039 137952415 1376 False 428.666667 693 83.7860 808 2064 3 chr2A.!!$F3 1256
10 TraesCS2B01G206000 chr7B 683940007 683940651 644 False 941.000000 941 93.0230 2059 2702 1 chr7B.!!$F2 643
11 TraesCS2B01G206000 chr5B 197202845 197203489 644 True 941.000000 941 93.0230 2059 2702 1 chr5B.!!$R1 643
12 TraesCS2B01G206000 chr4B 454990854 454991498 644 True 913.000000 913 92.2480 2059 2702 1 chr4B.!!$R1 643
13 TraesCS2B01G206000 chr3A 531900817 531901461 644 False 902.000000 902 91.9380 2059 2702 1 chr3A.!!$F1 643
14 TraesCS2B01G206000 chr2D 131316763 131317918 1155 False 604.500000 713 84.0145 972 2064 2 chr2D.!!$F4 1092
15 TraesCS2B01G206000 chr2D 131359777 131361377 1600 False 405.000000 619 81.6750 599 2064 2 chr2D.!!$F5 1465

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
575 617 0.177836 AACTTTGGTGCTTTGGTGGC 59.822 50.0 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2270 8011 0.04109 TCCCCAGCCCTCCAAAATTC 59.959 55.0 0.0 0.0 0.0 2.17 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
56 57 4.180946 CTCCACGCCGTCCTCGAG 62.181 72.222 5.13 5.13 39.71 4.04
58 59 3.129502 CCACGCCGTCCTCGAGTA 61.130 66.667 12.31 0.00 39.71 2.59
59 60 2.099831 CACGCCGTCCTCGAGTAC 59.900 66.667 12.31 4.63 39.71 2.73
60 61 3.130160 ACGCCGTCCTCGAGTACC 61.130 66.667 12.31 0.00 39.71 3.34
61 62 2.823147 CGCCGTCCTCGAGTACCT 60.823 66.667 12.31 0.00 39.71 3.08
62 63 2.821688 CGCCGTCCTCGAGTACCTC 61.822 68.421 12.31 0.00 39.71 3.85
71 72 3.902086 GAGTACCTCGAGGGCGGC 61.902 72.222 34.04 19.95 40.27 6.53
72 73 4.753662 AGTACCTCGAGGGCGGCA 62.754 66.667 34.04 11.69 40.27 5.69
73 74 3.766691 GTACCTCGAGGGCGGCAA 61.767 66.667 34.04 10.25 40.27 4.52
74 75 2.762459 TACCTCGAGGGCGGCAAT 60.762 61.111 34.04 14.70 40.27 3.56
75 76 3.088941 TACCTCGAGGGCGGCAATG 62.089 63.158 34.04 7.20 40.27 2.82
76 77 4.161295 CCTCGAGGGCGGCAATGA 62.161 66.667 24.62 3.55 38.28 2.57
77 78 2.109799 CTCGAGGGCGGCAATGAT 59.890 61.111 12.47 0.00 38.28 2.45
78 79 1.958205 CTCGAGGGCGGCAATGATC 60.958 63.158 12.47 0.00 38.28 2.92
79 80 2.974698 CGAGGGCGGCAATGATCC 60.975 66.667 12.47 0.00 0.00 3.36
86 87 2.715624 GGCAATGATCCGCCGTTC 59.284 61.111 2.50 0.00 38.82 3.95
87 88 1.819632 GGCAATGATCCGCCGTTCT 60.820 57.895 2.50 0.00 38.82 3.01
88 89 1.643832 GCAATGATCCGCCGTTCTC 59.356 57.895 0.00 0.00 0.00 2.87
89 90 0.811616 GCAATGATCCGCCGTTCTCT 60.812 55.000 0.00 0.00 0.00 3.10
90 91 1.538204 GCAATGATCCGCCGTTCTCTA 60.538 52.381 0.00 0.00 0.00 2.43
91 92 2.868044 GCAATGATCCGCCGTTCTCTAT 60.868 50.000 0.00 0.00 0.00 1.98
92 93 2.732412 ATGATCCGCCGTTCTCTATG 57.268 50.000 0.00 0.00 0.00 2.23
93 94 1.399714 TGATCCGCCGTTCTCTATGT 58.600 50.000 0.00 0.00 0.00 2.29
94 95 2.578786 TGATCCGCCGTTCTCTATGTA 58.421 47.619 0.00 0.00 0.00 2.29
95 96 2.953648 TGATCCGCCGTTCTCTATGTAA 59.046 45.455 0.00 0.00 0.00 2.41
96 97 3.382227 TGATCCGCCGTTCTCTATGTAAA 59.618 43.478 0.00 0.00 0.00 2.01
97 98 3.872511 TCCGCCGTTCTCTATGTAAAA 57.127 42.857 0.00 0.00 0.00 1.52
98 99 4.191033 TCCGCCGTTCTCTATGTAAAAA 57.809 40.909 0.00 0.00 0.00 1.94
119 120 7.739498 AAAAACACCTAATCTATGTCGTGTT 57.261 32.000 0.00 0.00 44.06 3.32
121 122 6.721571 AACACCTAATCTATGTCGTGTTTG 57.278 37.500 0.00 0.00 40.51 2.93
122 123 4.630069 ACACCTAATCTATGTCGTGTTTGC 59.370 41.667 0.00 0.00 30.59 3.68
123 124 4.034048 CACCTAATCTATGTCGTGTTTGCC 59.966 45.833 0.00 0.00 0.00 4.52
124 125 3.245284 CCTAATCTATGTCGTGTTTGCCG 59.755 47.826 0.00 0.00 0.00 5.69
125 126 2.665649 ATCTATGTCGTGTTTGCCGA 57.334 45.000 0.00 0.00 0.00 5.54
126 127 2.442212 TCTATGTCGTGTTTGCCGAA 57.558 45.000 0.00 0.00 35.89 4.30
127 128 2.967362 TCTATGTCGTGTTTGCCGAAT 58.033 42.857 0.00 0.00 35.89 3.34
128 129 3.331150 TCTATGTCGTGTTTGCCGAATT 58.669 40.909 0.00 0.00 35.89 2.17
129 130 3.749088 TCTATGTCGTGTTTGCCGAATTT 59.251 39.130 0.00 0.00 35.89 1.82
130 131 2.112475 TGTCGTGTTTGCCGAATTTG 57.888 45.000 0.00 0.00 35.89 2.32
131 132 1.402259 TGTCGTGTTTGCCGAATTTGT 59.598 42.857 0.00 0.00 35.89 2.83
132 133 1.778591 GTCGTGTTTGCCGAATTTGTG 59.221 47.619 0.00 0.00 35.89 3.33
133 134 1.127701 CGTGTTTGCCGAATTTGTGG 58.872 50.000 0.00 0.00 0.00 4.17
138 139 2.642700 GCCGAATTTGTGGCGTGT 59.357 55.556 2.12 0.00 42.22 4.49
139 140 1.007849 GCCGAATTTGTGGCGTGTT 60.008 52.632 2.12 0.00 42.22 3.32
140 141 0.596341 GCCGAATTTGTGGCGTGTTT 60.596 50.000 2.12 0.00 42.22 2.83
141 142 1.335142 GCCGAATTTGTGGCGTGTTTA 60.335 47.619 2.12 0.00 42.22 2.01
142 143 2.312348 CCGAATTTGTGGCGTGTTTAC 58.688 47.619 0.00 0.00 0.00 2.01
143 144 2.312348 CGAATTTGTGGCGTGTTTACC 58.688 47.619 0.00 0.00 0.00 2.85
144 145 2.312348 GAATTTGTGGCGTGTTTACCG 58.688 47.619 0.00 0.00 0.00 4.02
145 146 1.595466 ATTTGTGGCGTGTTTACCGA 58.405 45.000 0.00 0.00 0.00 4.69
146 147 1.376543 TTTGTGGCGTGTTTACCGAA 58.623 45.000 0.00 0.00 0.00 4.30
147 148 1.595466 TTGTGGCGTGTTTACCGAAT 58.405 45.000 0.00 0.00 0.00 3.34
148 149 1.149987 TGTGGCGTGTTTACCGAATC 58.850 50.000 0.00 0.00 0.00 2.52
149 150 1.270412 TGTGGCGTGTTTACCGAATCT 60.270 47.619 0.00 0.00 0.00 2.40
150 151 2.029200 TGTGGCGTGTTTACCGAATCTA 60.029 45.455 0.00 0.00 0.00 1.98
151 152 3.192466 GTGGCGTGTTTACCGAATCTAT 58.808 45.455 0.00 0.00 0.00 1.98
152 153 3.000925 GTGGCGTGTTTACCGAATCTATG 59.999 47.826 0.00 0.00 0.00 2.23
153 154 2.033151 GGCGTGTTTACCGAATCTATGC 60.033 50.000 0.00 0.00 0.00 3.14
154 155 2.033151 GCGTGTTTACCGAATCTATGCC 60.033 50.000 0.00 0.00 0.00 4.40
155 156 3.191669 CGTGTTTACCGAATCTATGCCA 58.808 45.455 0.00 0.00 0.00 4.92
156 157 3.619483 CGTGTTTACCGAATCTATGCCAA 59.381 43.478 0.00 0.00 0.00 4.52
157 158 4.093703 CGTGTTTACCGAATCTATGCCAAA 59.906 41.667 0.00 0.00 0.00 3.28
158 159 5.220777 CGTGTTTACCGAATCTATGCCAAAT 60.221 40.000 0.00 0.00 0.00 2.32
159 160 6.018588 CGTGTTTACCGAATCTATGCCAAATA 60.019 38.462 0.00 0.00 0.00 1.40
160 161 7.307751 CGTGTTTACCGAATCTATGCCAAATAT 60.308 37.037 0.00 0.00 0.00 1.28
161 162 8.995220 GTGTTTACCGAATCTATGCCAAATATA 58.005 33.333 0.00 0.00 0.00 0.86
162 163 9.733556 TGTTTACCGAATCTATGCCAAATATAT 57.266 29.630 0.00 0.00 0.00 0.86
163 164 9.988350 GTTTACCGAATCTATGCCAAATATATG 57.012 33.333 0.00 0.00 0.00 1.78
164 165 9.733556 TTTACCGAATCTATGCCAAATATATGT 57.266 29.630 0.00 0.00 0.00 2.29
165 166 7.849804 ACCGAATCTATGCCAAATATATGTC 57.150 36.000 0.00 0.00 0.00 3.06
166 167 7.394016 ACCGAATCTATGCCAAATATATGTCA 58.606 34.615 0.00 0.00 0.00 3.58
167 168 8.049117 ACCGAATCTATGCCAAATATATGTCAT 58.951 33.333 0.00 0.00 0.00 3.06
168 169 8.340443 CCGAATCTATGCCAAATATATGTCATG 58.660 37.037 0.00 0.00 0.00 3.07
169 170 8.886719 CGAATCTATGCCAAATATATGTCATGT 58.113 33.333 0.00 0.00 0.00 3.21
173 174 8.298854 TCTATGCCAAATATATGTCATGTTTGC 58.701 33.333 11.60 9.16 0.00 3.68
174 175 5.599732 TGCCAAATATATGTCATGTTTGCC 58.400 37.500 11.60 5.18 0.00 4.52
175 176 4.681025 GCCAAATATATGTCATGTTTGCCG 59.319 41.667 11.60 4.64 0.00 5.69
176 177 5.507149 GCCAAATATATGTCATGTTTGCCGA 60.507 40.000 11.60 0.00 0.00 5.54
177 178 6.502652 CCAAATATATGTCATGTTTGCCGAA 58.497 36.000 11.60 0.00 0.00 4.30
178 179 7.147312 CCAAATATATGTCATGTTTGCCGAAT 58.853 34.615 11.60 0.00 0.00 3.34
179 180 7.652909 CCAAATATATGTCATGTTTGCCGAATT 59.347 33.333 11.60 0.00 0.00 2.17
180 181 9.033481 CAAATATATGTCATGTTTGCCGAATTT 57.967 29.630 0.00 0.00 0.00 1.82
181 182 9.598517 AAATATATGTCATGTTTGCCGAATTTT 57.401 25.926 0.00 0.00 0.00 1.82
182 183 6.890663 ATATGTCATGTTTGCCGAATTTTG 57.109 33.333 0.00 0.00 0.00 2.44
183 184 4.313277 TGTCATGTTTGCCGAATTTTGA 57.687 36.364 0.00 0.00 0.00 2.69
184 185 4.047822 TGTCATGTTTGCCGAATTTTGAC 58.952 39.130 0.00 0.00 0.00 3.18
185 186 3.428534 GTCATGTTTGCCGAATTTTGACC 59.571 43.478 0.00 0.00 0.00 4.02
186 187 2.126914 TGTTTGCCGAATTTTGACCG 57.873 45.000 0.00 0.00 0.00 4.79
187 188 1.676529 TGTTTGCCGAATTTTGACCGA 59.323 42.857 0.00 0.00 0.00 4.69
188 189 2.099263 TGTTTGCCGAATTTTGACCGAA 59.901 40.909 0.00 0.00 0.00 4.30
189 190 3.243569 TGTTTGCCGAATTTTGACCGAAT 60.244 39.130 0.00 0.00 0.00 3.34
190 191 4.023107 TGTTTGCCGAATTTTGACCGAATA 60.023 37.500 0.00 0.00 0.00 1.75
191 192 4.974368 TTGCCGAATTTTGACCGAATAT 57.026 36.364 0.00 0.00 0.00 1.28
192 193 4.545823 TGCCGAATTTTGACCGAATATC 57.454 40.909 0.00 0.00 0.00 1.63
193 194 3.314080 TGCCGAATTTTGACCGAATATCC 59.686 43.478 0.00 0.00 0.00 2.59
194 195 3.564225 GCCGAATTTTGACCGAATATCCT 59.436 43.478 0.00 0.00 0.00 3.24
195 196 4.036380 GCCGAATTTTGACCGAATATCCTT 59.964 41.667 0.00 0.00 0.00 3.36
196 197 5.449999 GCCGAATTTTGACCGAATATCCTTT 60.450 40.000 0.00 0.00 0.00 3.11
197 198 6.560711 CCGAATTTTGACCGAATATCCTTTT 58.439 36.000 0.00 0.00 0.00 2.27
198 199 6.472163 CCGAATTTTGACCGAATATCCTTTTG 59.528 38.462 0.00 0.00 0.00 2.44
199 200 7.247728 CGAATTTTGACCGAATATCCTTTTGA 58.752 34.615 0.00 0.00 0.00 2.69
200 201 7.753132 CGAATTTTGACCGAATATCCTTTTGAA 59.247 33.333 0.00 0.00 0.00 2.69
201 202 9.418045 GAATTTTGACCGAATATCCTTTTGAAA 57.582 29.630 0.00 0.00 0.00 2.69
202 203 9.942850 AATTTTGACCGAATATCCTTTTGAAAT 57.057 25.926 0.00 0.00 0.00 2.17
203 204 9.942850 ATTTTGACCGAATATCCTTTTGAAATT 57.057 25.926 0.00 0.00 0.00 1.82
204 205 8.755696 TTTGACCGAATATCCTTTTGAAATTG 57.244 30.769 0.00 0.00 0.00 2.32
205 206 6.329496 TGACCGAATATCCTTTTGAAATTGC 58.671 36.000 0.00 0.00 0.00 3.56
206 207 6.152661 TGACCGAATATCCTTTTGAAATTGCT 59.847 34.615 0.00 0.00 0.00 3.91
207 208 6.935167 ACCGAATATCCTTTTGAAATTGCTT 58.065 32.000 0.00 0.00 0.00 3.91
208 209 8.062065 ACCGAATATCCTTTTGAAATTGCTTA 57.938 30.769 0.00 0.00 0.00 3.09
209 210 8.527810 ACCGAATATCCTTTTGAAATTGCTTAA 58.472 29.630 0.00 0.00 0.00 1.85
210 211 9.364989 CCGAATATCCTTTTGAAATTGCTTAAA 57.635 29.630 0.00 0.00 0.00 1.52
258 259 1.446366 GGCTAGGAACCCGATCACC 59.554 63.158 0.00 0.00 0.00 4.02
259 260 1.446366 GCTAGGAACCCGATCACCC 59.554 63.158 0.00 0.00 0.00 4.61
260 261 1.335132 GCTAGGAACCCGATCACCCA 61.335 60.000 0.00 0.00 0.00 4.51
261 262 0.464452 CTAGGAACCCGATCACCCAC 59.536 60.000 0.00 0.00 0.00 4.61
262 263 1.324740 TAGGAACCCGATCACCCACG 61.325 60.000 0.00 0.00 0.00 4.94
264 265 4.404098 AACCCGATCACCCACGGC 62.404 66.667 0.00 0.00 46.59 5.68
267 268 4.444838 CCGATCACCCACGGCGAA 62.445 66.667 16.62 0.00 42.55 4.70
268 269 2.433491 CGATCACCCACGGCGAAA 60.433 61.111 16.62 0.00 0.00 3.46
269 270 2.030401 CGATCACCCACGGCGAAAA 61.030 57.895 16.62 0.00 0.00 2.29
270 271 1.366111 CGATCACCCACGGCGAAAAT 61.366 55.000 16.62 0.00 0.00 1.82
271 272 1.658994 GATCACCCACGGCGAAAATA 58.341 50.000 16.62 0.00 0.00 1.40
272 273 2.218603 GATCACCCACGGCGAAAATAT 58.781 47.619 16.62 0.00 0.00 1.28
273 274 1.658994 TCACCCACGGCGAAAATATC 58.341 50.000 16.62 0.00 0.00 1.63
282 283 1.487231 CGAAAATATCGCCGGCTCG 59.513 57.895 26.68 20.74 45.89 5.03
283 284 1.204312 GAAAATATCGCCGGCTCGC 59.796 57.895 26.68 0.00 0.00 5.03
299 300 3.424859 GCGCCGGCGGTTTTTCTA 61.425 61.111 45.81 0.00 40.19 2.10
300 301 2.782615 CGCCGGCGGTTTTTCTAG 59.217 61.111 40.50 8.79 35.56 2.43
301 302 2.483745 GCCGGCGGTTTTTCTAGC 59.516 61.111 28.82 5.42 0.00 3.42
302 303 3.047718 GCCGGCGGTTTTTCTAGCC 62.048 63.158 28.82 1.99 45.67 3.93
303 304 2.404186 CCGGCGGTTTTTCTAGCCC 61.404 63.158 19.97 0.00 46.36 5.19
304 305 2.404186 CGGCGGTTTTTCTAGCCCC 61.404 63.158 0.00 0.00 46.36 5.80
305 306 1.001269 GGCGGTTTTTCTAGCCCCT 60.001 57.895 0.00 0.00 43.54 4.79
306 307 1.313091 GGCGGTTTTTCTAGCCCCTG 61.313 60.000 0.00 0.00 43.54 4.45
307 308 0.322187 GCGGTTTTTCTAGCCCCTGA 60.322 55.000 0.00 0.00 0.00 3.86
308 309 1.739067 CGGTTTTTCTAGCCCCTGAG 58.261 55.000 0.00 0.00 0.00 3.35
309 310 1.679032 CGGTTTTTCTAGCCCCTGAGG 60.679 57.143 0.00 0.00 39.47 3.86
391 392 2.359107 ACGACGGACGCTCCTACA 60.359 61.111 0.00 0.00 46.94 2.74
421 422 1.769098 CGCGCTCAATCCATCACCAG 61.769 60.000 5.56 0.00 0.00 4.00
432 439 1.673033 CCATCACCAGACGGTCAACTC 60.673 57.143 11.27 0.00 44.71 3.01
435 442 1.529948 ACCAGACGGTCAACTCGGA 60.530 57.895 11.27 0.00 44.71 4.55
436 443 1.080705 CCAGACGGTCAACTCGGAC 60.081 63.158 11.27 0.00 37.06 4.79
437 444 1.524863 CCAGACGGTCAACTCGGACT 61.525 60.000 11.27 0.00 37.91 3.85
438 445 1.162698 CAGACGGTCAACTCGGACTA 58.837 55.000 11.27 0.00 37.91 2.59
440 447 1.163554 GACGGTCAACTCGGACTAGT 58.836 55.000 2.62 0.00 37.91 2.57
441 448 0.879765 ACGGTCAACTCGGACTAGTG 59.120 55.000 0.00 0.00 37.91 2.74
442 449 1.162698 CGGTCAACTCGGACTAGTGA 58.837 55.000 0.00 0.00 37.91 3.41
443 450 1.135746 CGGTCAACTCGGACTAGTGAC 60.136 57.143 0.00 0.00 37.91 3.67
444 451 2.161030 GGTCAACTCGGACTAGTGACT 58.839 52.381 0.00 0.00 37.91 3.41
500 517 2.259818 CTGCAGAACCGAGCGACT 59.740 61.111 8.42 0.00 0.00 4.18
526 568 4.766404 ACCGAATCATCCAAAAACACTC 57.234 40.909 0.00 0.00 0.00 3.51
533 575 0.302288 TCCAAAAACACTCGCGTTCG 59.698 50.000 5.77 0.00 0.00 3.95
560 602 3.403936 GTGGCACAGGACTGAACTT 57.596 52.632 13.86 0.00 41.80 2.66
561 603 1.680338 GTGGCACAGGACTGAACTTT 58.320 50.000 13.86 0.00 41.80 2.66
562 604 1.334869 GTGGCACAGGACTGAACTTTG 59.665 52.381 13.86 0.00 41.80 2.77
563 605 0.954452 GGCACAGGACTGAACTTTGG 59.046 55.000 6.29 0.00 0.00 3.28
564 606 1.680338 GCACAGGACTGAACTTTGGT 58.320 50.000 6.29 0.00 0.00 3.67
565 607 1.334869 GCACAGGACTGAACTTTGGTG 59.665 52.381 6.29 0.00 0.00 4.17
566 608 1.334869 CACAGGACTGAACTTTGGTGC 59.665 52.381 6.29 0.00 0.00 5.01
567 609 1.212935 ACAGGACTGAACTTTGGTGCT 59.787 47.619 6.29 0.00 32.11 4.40
568 610 2.301346 CAGGACTGAACTTTGGTGCTT 58.699 47.619 0.00 0.00 29.59 3.91
569 611 2.689983 CAGGACTGAACTTTGGTGCTTT 59.310 45.455 0.00 0.00 29.59 3.51
570 612 2.689983 AGGACTGAACTTTGGTGCTTTG 59.310 45.455 0.00 0.00 0.00 2.77
571 613 2.223805 GGACTGAACTTTGGTGCTTTGG 60.224 50.000 0.00 0.00 0.00 3.28
572 614 2.427095 GACTGAACTTTGGTGCTTTGGT 59.573 45.455 0.00 0.00 0.00 3.67
573 615 2.166254 ACTGAACTTTGGTGCTTTGGTG 59.834 45.455 0.00 0.00 0.00 4.17
574 616 1.480137 TGAACTTTGGTGCTTTGGTGG 59.520 47.619 0.00 0.00 0.00 4.61
575 617 0.177836 AACTTTGGTGCTTTGGTGGC 59.822 50.000 0.00 0.00 0.00 5.01
576 618 1.069596 CTTTGGTGCTTTGGTGGCC 59.930 57.895 0.00 0.00 0.00 5.36
577 619 1.382420 TTTGGTGCTTTGGTGGCCT 60.382 52.632 3.32 0.00 0.00 5.19
578 620 1.684386 TTTGGTGCTTTGGTGGCCTG 61.684 55.000 3.32 0.00 0.00 4.85
579 621 3.305516 GGTGCTTTGGTGGCCTGG 61.306 66.667 3.32 0.00 0.00 4.45
580 622 2.521708 GTGCTTTGGTGGCCTGGT 60.522 61.111 3.32 0.00 0.00 4.00
581 623 1.228429 GTGCTTTGGTGGCCTGGTA 60.228 57.895 3.32 0.00 0.00 3.25
582 624 1.074775 TGCTTTGGTGGCCTGGTAG 59.925 57.895 3.32 0.00 0.00 3.18
583 625 1.074951 GCTTTGGTGGCCTGGTAGT 59.925 57.895 3.32 0.00 0.00 2.73
584 626 1.244019 GCTTTGGTGGCCTGGTAGTG 61.244 60.000 3.32 0.00 0.00 2.74
585 627 0.609131 CTTTGGTGGCCTGGTAGTGG 60.609 60.000 3.32 0.00 0.00 4.00
586 628 1.357272 TTTGGTGGCCTGGTAGTGGT 61.357 55.000 3.32 0.00 0.00 4.16
587 629 0.474079 TTGGTGGCCTGGTAGTGGTA 60.474 55.000 3.32 0.00 0.00 3.25
588 630 0.907704 TGGTGGCCTGGTAGTGGTAG 60.908 60.000 3.32 0.00 0.00 3.18
589 631 1.623542 GGTGGCCTGGTAGTGGTAGG 61.624 65.000 3.32 0.00 34.67 3.18
590 632 0.908180 GTGGCCTGGTAGTGGTAGGT 60.908 60.000 3.32 0.00 34.06 3.08
591 633 0.616679 TGGCCTGGTAGTGGTAGGTC 60.617 60.000 3.32 0.00 36.74 3.85
592 634 0.616679 GGCCTGGTAGTGGTAGGTCA 60.617 60.000 0.00 0.00 36.25 4.02
593 635 0.535797 GCCTGGTAGTGGTAGGTCAC 59.464 60.000 0.00 0.00 37.89 3.67
651 698 4.576053 TCATATGCTACATTTGGACAGCAC 59.424 41.667 0.00 0.00 46.02 4.40
740 2074 2.989166 CACCGACCATATCATGTCATCG 59.011 50.000 0.00 0.00 0.00 3.84
827 2175 5.337009 GGAAGAGTAAACAACCACCGAGATA 60.337 44.000 0.00 0.00 0.00 1.98
960 4452 6.734104 GCTATAAATACCAGCCTTCATCAG 57.266 41.667 0.00 0.00 0.00 2.90
962 4454 6.148480 GCTATAAATACCAGCCTTCATCAGTG 59.852 42.308 0.00 0.00 0.00 3.66
1408 5285 1.592743 CCACACCCAATCGTACCGA 59.407 57.895 0.00 0.00 41.13 4.69
1789 5870 2.099756 TGTGTGTGTGTGTGAGAGAGAG 59.900 50.000 0.00 0.00 0.00 3.20
1790 5871 2.359214 GTGTGTGTGTGTGAGAGAGAGA 59.641 50.000 0.00 0.00 0.00 3.10
1792 5873 2.881513 GTGTGTGTGTGAGAGAGAGAGA 59.118 50.000 0.00 0.00 0.00 3.10
1793 5874 3.058293 GTGTGTGTGTGAGAGAGAGAGAG 60.058 52.174 0.00 0.00 0.00 3.20
1796 5877 3.326297 TGTGTGTGAGAGAGAGAGAGAGA 59.674 47.826 0.00 0.00 0.00 3.10
1797 5878 3.935203 GTGTGTGAGAGAGAGAGAGAGAG 59.065 52.174 0.00 0.00 0.00 3.20
1798 5879 3.837731 TGTGTGAGAGAGAGAGAGAGAGA 59.162 47.826 0.00 0.00 0.00 3.10
1799 5880 4.081476 TGTGTGAGAGAGAGAGAGAGAGAG 60.081 50.000 0.00 0.00 0.00 3.20
1801 5882 4.403752 TGTGAGAGAGAGAGAGAGAGAGAG 59.596 50.000 0.00 0.00 0.00 3.20
1802 5883 4.646945 GTGAGAGAGAGAGAGAGAGAGAGA 59.353 50.000 0.00 0.00 0.00 3.10
1803 5884 4.892345 TGAGAGAGAGAGAGAGAGAGAGAG 59.108 50.000 0.00 0.00 0.00 3.20
1804 5885 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
1805 5886 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1806 5887 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1807 5888 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1808 5889 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1809 5890 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1810 5891 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1811 5892 5.714863 AGAGAGAGAGAGAGAGAGAGAGAT 58.285 45.833 0.00 0.00 0.00 2.75
1859 7569 4.235360 GTGTTGTACATGTCGTTAGAGCT 58.765 43.478 0.00 0.00 0.00 4.09
2273 8014 3.536956 CATCTTTGCAGGCCAATGAAT 57.463 42.857 5.01 0.00 39.92 2.57
2291 8032 1.619298 ATTTTGGAGGGCTGGGGATA 58.381 50.000 0.00 0.00 0.00 2.59
2293 8034 1.619298 TTTGGAGGGCTGGGGATAAT 58.381 50.000 0.00 0.00 0.00 1.28
2309 8050 0.323302 TAATGGACCTGAGTGCGCAA 59.677 50.000 14.00 0.00 37.08 4.85
2345 8086 0.817634 TGAGGTGGTTGTGGCTTTCG 60.818 55.000 0.00 0.00 0.00 3.46
2379 8120 1.600023 CAAAGCGTGGTTGGGACTAA 58.400 50.000 0.00 0.00 0.00 2.24
2381 8122 0.601841 AAGCGTGGTTGGGACTAACG 60.602 55.000 0.00 0.00 38.20 3.18
2404 8145 0.249120 CCAACCGATGCCAGAGTACA 59.751 55.000 0.00 0.00 0.00 2.90
2428 8169 2.478894 CGTTGTTCGTGGCTTCAGTTAT 59.521 45.455 0.00 0.00 34.52 1.89
2439 8180 3.055094 GGCTTCAGTTATCTTCCACCTCA 60.055 47.826 0.00 0.00 0.00 3.86
2448 8189 0.621571 CTTCCACCTCAGGGATGGGA 60.622 60.000 0.00 0.00 35.74 4.37
2464 8205 4.462483 GGATGGGAAACACATTTGCTTCTA 59.538 41.667 0.00 0.00 36.45 2.10
2594 8335 1.207791 GGACACATCATCTCAGGGGT 58.792 55.000 0.00 0.00 0.00 4.95
2596 8337 2.771943 GGACACATCATCTCAGGGGTAA 59.228 50.000 0.00 0.00 0.00 2.85
2603 8344 6.212187 CACATCATCTCAGGGGTAATCTCATA 59.788 42.308 0.00 0.00 0.00 2.15
2606 8347 4.552883 TCTCAGGGGTAATCTCATACCA 57.447 45.455 5.90 0.00 45.98 3.25
2633 8374 2.563179 GGTCAGAGAGTTCACTGCCTTA 59.437 50.000 2.21 0.00 35.07 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 4.180946 CTCGAGGACGGCGTGGAG 62.181 72.222 21.19 14.55 40.21 3.86
40 41 3.610619 TACTCGAGGACGGCGTGGA 62.611 63.158 21.19 8.42 40.21 4.02
41 42 3.129502 TACTCGAGGACGGCGTGG 61.130 66.667 21.19 3.68 40.21 4.94
42 43 2.099831 GTACTCGAGGACGGCGTG 59.900 66.667 21.19 3.78 40.21 5.34
43 44 3.130160 GGTACTCGAGGACGGCGT 61.130 66.667 21.39 14.65 40.21 5.68
44 45 2.823147 AGGTACTCGAGGACGGCG 60.823 66.667 21.39 4.80 40.21 6.46
56 57 3.090219 ATTGCCGCCCTCGAGGTAC 62.090 63.158 29.25 19.63 38.26 3.34
57 58 2.762459 ATTGCCGCCCTCGAGGTA 60.762 61.111 29.25 8.00 38.26 3.08
58 59 4.473520 CATTGCCGCCCTCGAGGT 62.474 66.667 29.25 6.70 38.26 3.85
59 60 3.466791 ATCATTGCCGCCCTCGAGG 62.467 63.158 25.36 25.36 38.10 4.63
60 61 1.958205 GATCATTGCCGCCCTCGAG 60.958 63.158 5.13 5.13 38.10 4.04
61 62 2.108976 GATCATTGCCGCCCTCGA 59.891 61.111 0.00 0.00 38.10 4.04
62 63 2.974698 GGATCATTGCCGCCCTCG 60.975 66.667 0.00 0.00 0.00 4.63
63 64 2.974698 CGGATCATTGCCGCCCTC 60.975 66.667 0.00 0.00 42.55 4.30
70 71 0.811616 AGAGAACGGCGGATCATTGC 60.812 55.000 13.24 0.00 0.00 3.56
71 72 2.509052 TAGAGAACGGCGGATCATTG 57.491 50.000 13.24 0.00 0.00 2.82
72 73 2.365617 ACATAGAGAACGGCGGATCATT 59.634 45.455 13.24 0.00 0.00 2.57
73 74 1.964223 ACATAGAGAACGGCGGATCAT 59.036 47.619 13.24 5.01 0.00 2.45
74 75 1.399714 ACATAGAGAACGGCGGATCA 58.600 50.000 13.24 0.00 0.00 2.92
75 76 3.637998 TTACATAGAGAACGGCGGATC 57.362 47.619 13.24 9.52 0.00 3.36
76 77 4.395959 TTTTACATAGAGAACGGCGGAT 57.604 40.909 13.24 0.00 0.00 4.18
77 78 3.872511 TTTTACATAGAGAACGGCGGA 57.127 42.857 13.24 0.00 0.00 5.54
95 96 7.739498 AACACGACATAGATTAGGTGTTTTT 57.261 32.000 1.86 0.00 43.69 1.94
98 99 5.121768 GCAAACACGACATAGATTAGGTGTT 59.878 40.000 1.86 1.86 46.87 3.32
99 100 4.630069 GCAAACACGACATAGATTAGGTGT 59.370 41.667 0.00 0.00 40.04 4.16
100 101 4.034048 GGCAAACACGACATAGATTAGGTG 59.966 45.833 0.00 0.00 0.00 4.00
101 102 4.189231 GGCAAACACGACATAGATTAGGT 58.811 43.478 0.00 0.00 0.00 3.08
102 103 3.245284 CGGCAAACACGACATAGATTAGG 59.755 47.826 0.00 0.00 0.00 2.69
103 104 4.109766 TCGGCAAACACGACATAGATTAG 58.890 43.478 0.00 0.00 35.12 1.73
104 105 4.112716 TCGGCAAACACGACATAGATTA 57.887 40.909 0.00 0.00 35.12 1.75
105 106 2.967362 TCGGCAAACACGACATAGATT 58.033 42.857 0.00 0.00 35.12 2.40
106 107 2.665649 TCGGCAAACACGACATAGAT 57.334 45.000 0.00 0.00 35.12 1.98
107 108 2.442212 TTCGGCAAACACGACATAGA 57.558 45.000 0.00 0.00 40.45 1.98
108 109 3.740044 AATTCGGCAAACACGACATAG 57.260 42.857 0.00 0.00 40.45 2.23
109 110 3.251245 ACAAATTCGGCAAACACGACATA 59.749 39.130 0.00 0.00 40.45 2.29
110 111 2.034053 ACAAATTCGGCAAACACGACAT 59.966 40.909 0.00 0.00 40.45 3.06
111 112 1.402259 ACAAATTCGGCAAACACGACA 59.598 42.857 0.00 0.00 40.45 4.35
112 113 1.778591 CACAAATTCGGCAAACACGAC 59.221 47.619 0.00 0.00 40.45 4.34
113 114 1.268794 CCACAAATTCGGCAAACACGA 60.269 47.619 0.00 0.00 38.78 4.35
114 115 1.127701 CCACAAATTCGGCAAACACG 58.872 50.000 0.00 0.00 0.00 4.49
121 122 0.596341 AAACACGCCACAAATTCGGC 60.596 50.000 3.91 3.91 45.28 5.54
122 123 2.312348 GTAAACACGCCACAAATTCGG 58.688 47.619 0.00 0.00 0.00 4.30
123 124 2.312348 GGTAAACACGCCACAAATTCG 58.688 47.619 0.00 0.00 0.00 3.34
124 125 2.031857 TCGGTAAACACGCCACAAATTC 60.032 45.455 0.00 0.00 0.00 2.17
125 126 1.948145 TCGGTAAACACGCCACAAATT 59.052 42.857 0.00 0.00 0.00 1.82
126 127 1.595466 TCGGTAAACACGCCACAAAT 58.405 45.000 0.00 0.00 0.00 2.32
127 128 1.376543 TTCGGTAAACACGCCACAAA 58.623 45.000 0.00 0.00 0.00 2.83
128 129 1.532007 GATTCGGTAAACACGCCACAA 59.468 47.619 0.00 0.00 0.00 3.33
129 130 1.149987 GATTCGGTAAACACGCCACA 58.850 50.000 0.00 0.00 0.00 4.17
130 131 1.435577 AGATTCGGTAAACACGCCAC 58.564 50.000 0.00 0.00 0.00 5.01
131 132 3.191669 CATAGATTCGGTAAACACGCCA 58.808 45.455 0.00 0.00 0.00 5.69
132 133 2.033151 GCATAGATTCGGTAAACACGCC 60.033 50.000 0.00 0.00 0.00 5.68
133 134 2.033151 GGCATAGATTCGGTAAACACGC 60.033 50.000 0.00 0.00 0.00 5.34
134 135 3.191669 TGGCATAGATTCGGTAAACACG 58.808 45.455 0.00 0.00 0.00 4.49
135 136 5.554822 TTTGGCATAGATTCGGTAAACAC 57.445 39.130 0.00 0.00 0.00 3.32
136 137 9.733556 ATATATTTGGCATAGATTCGGTAAACA 57.266 29.630 0.00 0.00 0.00 2.83
137 138 9.988350 CATATATTTGGCATAGATTCGGTAAAC 57.012 33.333 0.00 0.00 0.00 2.01
138 139 9.733556 ACATATATTTGGCATAGATTCGGTAAA 57.266 29.630 0.00 0.00 0.00 2.01
139 140 9.378551 GACATATATTTGGCATAGATTCGGTAA 57.621 33.333 0.00 0.00 0.00 2.85
140 141 8.536175 TGACATATATTTGGCATAGATTCGGTA 58.464 33.333 0.00 0.00 26.74 4.02
141 142 7.394016 TGACATATATTTGGCATAGATTCGGT 58.606 34.615 0.00 0.00 26.74 4.69
142 143 7.848223 TGACATATATTTGGCATAGATTCGG 57.152 36.000 0.00 0.00 26.74 4.30
143 144 8.886719 ACATGACATATATTTGGCATAGATTCG 58.113 33.333 13.42 4.20 43.61 3.34
147 148 8.298854 GCAAACATGACATATATTTGGCATAGA 58.701 33.333 13.42 0.00 43.61 1.98
148 149 7.543172 GGCAAACATGACATATATTTGGCATAG 59.457 37.037 25.11 10.65 43.61 2.23
149 150 7.377398 GGCAAACATGACATATATTTGGCATA 58.623 34.615 25.11 0.00 43.61 3.14
150 151 6.225318 GGCAAACATGACATATATTTGGCAT 58.775 36.000 25.11 8.56 46.42 4.40
152 153 4.681025 CGGCAAACATGACATATATTTGGC 59.319 41.667 22.63 22.63 46.55 4.52
153 154 6.070897 TCGGCAAACATGACATATATTTGG 57.929 37.500 0.00 5.63 32.17 3.28
154 155 8.578308 AATTCGGCAAACATGACATATATTTG 57.422 30.769 0.00 11.79 34.17 2.32
155 156 9.598517 AAAATTCGGCAAACATGACATATATTT 57.401 25.926 0.00 0.00 0.00 1.40
156 157 9.033481 CAAAATTCGGCAAACATGACATATATT 57.967 29.630 0.00 0.00 0.00 1.28
157 158 8.412456 TCAAAATTCGGCAAACATGACATATAT 58.588 29.630 0.00 0.00 0.00 0.86
158 159 7.700234 GTCAAAATTCGGCAAACATGACATATA 59.300 33.333 0.00 0.00 36.75 0.86
159 160 6.531240 GTCAAAATTCGGCAAACATGACATAT 59.469 34.615 0.00 0.00 36.75 1.78
160 161 5.861251 GTCAAAATTCGGCAAACATGACATA 59.139 36.000 0.00 0.00 36.75 2.29
161 162 4.685628 GTCAAAATTCGGCAAACATGACAT 59.314 37.500 0.00 0.00 36.75 3.06
162 163 4.047822 GTCAAAATTCGGCAAACATGACA 58.952 39.130 0.00 0.00 36.75 3.58
163 164 3.428534 GGTCAAAATTCGGCAAACATGAC 59.571 43.478 0.00 0.00 36.18 3.06
164 165 3.648009 GGTCAAAATTCGGCAAACATGA 58.352 40.909 0.00 0.00 0.00 3.07
165 166 2.408032 CGGTCAAAATTCGGCAAACATG 59.592 45.455 0.00 0.00 0.00 3.21
166 167 2.294791 TCGGTCAAAATTCGGCAAACAT 59.705 40.909 0.00 0.00 0.00 2.71
167 168 1.676529 TCGGTCAAAATTCGGCAAACA 59.323 42.857 0.00 0.00 0.00 2.83
168 169 2.409152 TCGGTCAAAATTCGGCAAAC 57.591 45.000 0.00 0.00 0.00 2.93
169 170 3.651803 ATTCGGTCAAAATTCGGCAAA 57.348 38.095 0.00 0.00 0.00 3.68
170 171 4.201970 GGATATTCGGTCAAAATTCGGCAA 60.202 41.667 0.00 0.00 0.00 4.52
171 172 3.314080 GGATATTCGGTCAAAATTCGGCA 59.686 43.478 0.00 0.00 0.00 5.69
172 173 3.564225 AGGATATTCGGTCAAAATTCGGC 59.436 43.478 0.00 0.00 0.00 5.54
173 174 5.751243 AAGGATATTCGGTCAAAATTCGG 57.249 39.130 0.00 0.00 0.00 4.30
174 175 7.247728 TCAAAAGGATATTCGGTCAAAATTCG 58.752 34.615 0.00 0.00 0.00 3.34
175 176 8.980143 TTCAAAAGGATATTCGGTCAAAATTC 57.020 30.769 0.00 0.00 0.00 2.17
176 177 9.942850 ATTTCAAAAGGATATTCGGTCAAAATT 57.057 25.926 0.00 0.00 0.00 1.82
177 178 9.942850 AATTTCAAAAGGATATTCGGTCAAAAT 57.057 25.926 0.00 0.00 0.00 1.82
178 179 9.202273 CAATTTCAAAAGGATATTCGGTCAAAA 57.798 29.630 0.00 0.00 0.00 2.44
179 180 7.330700 GCAATTTCAAAAGGATATTCGGTCAAA 59.669 33.333 0.00 0.00 0.00 2.69
180 181 6.811170 GCAATTTCAAAAGGATATTCGGTCAA 59.189 34.615 0.00 0.00 0.00 3.18
181 182 6.152661 AGCAATTTCAAAAGGATATTCGGTCA 59.847 34.615 0.00 0.00 0.00 4.02
182 183 6.564328 AGCAATTTCAAAAGGATATTCGGTC 58.436 36.000 0.00 0.00 0.00 4.79
183 184 6.530019 AGCAATTTCAAAAGGATATTCGGT 57.470 33.333 0.00 0.00 0.00 4.69
184 185 8.925161 TTAAGCAATTTCAAAAGGATATTCGG 57.075 30.769 0.00 0.00 0.00 4.30
211 212 0.112412 AGGTCGCCCCAGACATTTTT 59.888 50.000 0.00 0.00 42.62 1.94
212 213 0.112412 AAGGTCGCCCCAGACATTTT 59.888 50.000 0.00 0.00 41.58 1.82
213 214 0.609131 CAAGGTCGCCCCAGACATTT 60.609 55.000 0.00 0.00 41.58 2.32
214 215 1.002134 CAAGGTCGCCCCAGACATT 60.002 57.895 0.00 0.00 44.58 2.71
215 216 2.671070 CAAGGTCGCCCCAGACAT 59.329 61.111 0.00 0.00 42.62 3.06
216 217 3.636231 CCAAGGTCGCCCCAGACA 61.636 66.667 0.00 0.00 42.62 3.41
217 218 4.410400 CCCAAGGTCGCCCCAGAC 62.410 72.222 0.00 0.00 40.25 3.51
240 241 1.446366 GGTGATCGGGTTCCTAGCC 59.554 63.158 0.00 0.00 38.61 3.93
241 242 1.335132 TGGGTGATCGGGTTCCTAGC 61.335 60.000 0.00 0.00 0.00 3.42
242 243 0.464452 GTGGGTGATCGGGTTCCTAG 59.536 60.000 0.00 0.00 0.00 3.02
243 244 1.324740 CGTGGGTGATCGGGTTCCTA 61.325 60.000 0.00 0.00 0.00 2.94
244 245 2.656069 CGTGGGTGATCGGGTTCCT 61.656 63.158 0.00 0.00 0.00 3.36
245 246 2.125269 CGTGGGTGATCGGGTTCC 60.125 66.667 0.00 0.00 0.00 3.62
246 247 2.125269 CCGTGGGTGATCGGGTTC 60.125 66.667 0.00 0.00 42.61 3.62
247 248 4.404098 GCCGTGGGTGATCGGGTT 62.404 66.667 5.78 0.00 45.85 4.11
250 251 3.943479 TTTCGCCGTGGGTGATCGG 62.943 63.158 0.00 0.00 42.13 4.18
251 252 1.366111 ATTTTCGCCGTGGGTGATCG 61.366 55.000 0.00 0.00 42.13 3.69
252 253 1.658994 TATTTTCGCCGTGGGTGATC 58.341 50.000 0.00 0.00 42.13 2.92
253 254 2.218603 GATATTTTCGCCGTGGGTGAT 58.781 47.619 0.00 0.00 42.13 3.06
254 255 1.658994 GATATTTTCGCCGTGGGTGA 58.341 50.000 0.00 0.00 40.77 4.02
255 256 0.303493 CGATATTTTCGCCGTGGGTG 59.697 55.000 0.00 0.00 41.69 4.61
256 257 2.685364 CGATATTTTCGCCGTGGGT 58.315 52.632 0.00 0.00 41.69 4.51
265 266 1.204312 GCGAGCCGGCGATATTTTC 59.796 57.895 23.20 10.39 0.00 2.29
266 267 3.330275 GCGAGCCGGCGATATTTT 58.670 55.556 23.20 0.00 0.00 1.82
282 283 3.376914 CTAGAAAAACCGCCGGCGC 62.377 63.158 42.39 27.21 38.24 6.53
283 284 2.782615 CTAGAAAAACCGCCGGCG 59.217 61.111 41.00 41.00 39.44 6.46
284 285 2.483745 GCTAGAAAAACCGCCGGC 59.516 61.111 19.07 19.07 0.00 6.13
285 286 2.404186 GGGCTAGAAAAACCGCCGG 61.404 63.158 0.00 0.00 43.38 6.13
286 287 2.404186 GGGGCTAGAAAAACCGCCG 61.404 63.158 0.00 0.00 43.38 6.46
287 288 1.001269 AGGGGCTAGAAAAACCGCC 60.001 57.895 0.00 0.00 41.75 6.13
288 289 0.322187 TCAGGGGCTAGAAAAACCGC 60.322 55.000 0.00 0.00 36.70 5.68
289 290 1.679032 CCTCAGGGGCTAGAAAAACCG 60.679 57.143 0.00 0.00 0.00 4.44
290 291 2.130272 CCTCAGGGGCTAGAAAAACC 57.870 55.000 0.00 0.00 0.00 3.27
319 320 2.267961 CCTGGTACGGCAGGTTCC 59.732 66.667 9.40 0.00 36.67 3.62
374 375 2.359107 TGTAGGAGCGTCCGTCGT 60.359 61.111 0.00 0.00 42.75 4.34
421 422 1.135746 CACTAGTCCGAGTTGACCGTC 60.136 57.143 0.00 0.00 35.83 4.79
426 427 3.262660 TCCTAGTCACTAGTCCGAGTTGA 59.737 47.826 11.06 0.00 32.62 3.18
432 439 4.062293 CTGATCTCCTAGTCACTAGTCCG 58.938 52.174 11.06 0.00 32.62 4.79
435 442 3.203263 TGGCTGATCTCCTAGTCACTAGT 59.797 47.826 11.06 0.00 32.62 2.57
436 443 3.820467 CTGGCTGATCTCCTAGTCACTAG 59.180 52.174 4.66 4.66 34.16 2.57
437 444 3.435746 CCTGGCTGATCTCCTAGTCACTA 60.436 52.174 0.00 0.00 0.00 2.74
438 445 2.665165 CTGGCTGATCTCCTAGTCACT 58.335 52.381 0.00 0.00 0.00 3.41
440 447 1.289231 ACCTGGCTGATCTCCTAGTCA 59.711 52.381 0.00 0.00 0.00 3.41
441 448 1.960689 GACCTGGCTGATCTCCTAGTC 59.039 57.143 0.00 3.62 0.00 2.59
442 449 1.752436 CGACCTGGCTGATCTCCTAGT 60.752 57.143 0.00 0.00 0.00 2.57
443 450 0.958091 CGACCTGGCTGATCTCCTAG 59.042 60.000 0.00 0.00 0.00 3.02
444 451 0.551396 TCGACCTGGCTGATCTCCTA 59.449 55.000 0.00 0.00 0.00 2.94
500 517 8.343168 AGTGTTTTTGGATGATTCGGTAATTA 57.657 30.769 0.00 0.00 0.00 1.40
544 586 0.954452 CCAAAGTTCAGTCCTGTGCC 59.046 55.000 0.00 0.00 0.00 5.01
553 595 2.481795 CCACCAAAGCACCAAAGTTCAG 60.482 50.000 0.00 0.00 0.00 3.02
554 596 1.480137 CCACCAAAGCACCAAAGTTCA 59.520 47.619 0.00 0.00 0.00 3.18
555 597 1.806247 GCCACCAAAGCACCAAAGTTC 60.806 52.381 0.00 0.00 0.00 3.01
556 598 0.177836 GCCACCAAAGCACCAAAGTT 59.822 50.000 0.00 0.00 0.00 2.66
557 599 1.685355 GGCCACCAAAGCACCAAAGT 61.685 55.000 0.00 0.00 0.00 2.66
558 600 1.069596 GGCCACCAAAGCACCAAAG 59.930 57.895 0.00 0.00 0.00 2.77
559 601 1.382420 AGGCCACCAAAGCACCAAA 60.382 52.632 5.01 0.00 0.00 3.28
560 602 2.132996 CAGGCCACCAAAGCACCAA 61.133 57.895 5.01 0.00 0.00 3.67
561 603 2.521465 CAGGCCACCAAAGCACCA 60.521 61.111 5.01 0.00 0.00 4.17
562 604 2.706952 TACCAGGCCACCAAAGCACC 62.707 60.000 5.01 0.00 0.00 5.01
563 605 1.228429 TACCAGGCCACCAAAGCAC 60.228 57.895 5.01 0.00 0.00 4.40
564 606 1.074775 CTACCAGGCCACCAAAGCA 59.925 57.895 5.01 0.00 0.00 3.91
565 607 1.074951 ACTACCAGGCCACCAAAGC 59.925 57.895 5.01 0.00 0.00 3.51
566 608 0.609131 CCACTACCAGGCCACCAAAG 60.609 60.000 5.01 0.00 0.00 2.77
567 609 1.357272 ACCACTACCAGGCCACCAAA 61.357 55.000 5.01 0.00 0.00 3.28
568 610 0.474079 TACCACTACCAGGCCACCAA 60.474 55.000 5.01 0.00 0.00 3.67
569 611 0.907704 CTACCACTACCAGGCCACCA 60.908 60.000 5.01 0.00 0.00 4.17
570 612 1.623542 CCTACCACTACCAGGCCACC 61.624 65.000 5.01 0.00 0.00 4.61
571 613 0.908180 ACCTACCACTACCAGGCCAC 60.908 60.000 5.01 0.00 32.31 5.01
572 614 0.616679 GACCTACCACTACCAGGCCA 60.617 60.000 5.01 0.00 32.31 5.36
573 615 0.616679 TGACCTACCACTACCAGGCC 60.617 60.000 0.00 0.00 32.31 5.19
574 616 0.535797 GTGACCTACCACTACCAGGC 59.464 60.000 0.00 0.00 34.38 4.85
585 627 0.103208 CCGAGATGCAGGTGACCTAC 59.897 60.000 2.59 0.00 29.64 3.18
586 628 0.324368 ACCGAGATGCAGGTGACCTA 60.324 55.000 2.59 0.00 39.66 3.08
587 629 1.610673 ACCGAGATGCAGGTGACCT 60.611 57.895 0.00 0.00 39.66 3.85
588 630 2.982130 ACCGAGATGCAGGTGACC 59.018 61.111 0.00 0.00 39.66 4.02
592 634 0.532573 CTACACACCGAGATGCAGGT 59.467 55.000 0.00 0.00 42.34 4.00
593 635 0.179100 CCTACACACCGAGATGCAGG 60.179 60.000 0.00 0.00 0.00 4.85
594 636 0.807667 GCCTACACACCGAGATGCAG 60.808 60.000 0.00 0.00 0.00 4.41
595 637 1.218047 GCCTACACACCGAGATGCA 59.782 57.895 0.00 0.00 0.00 3.96
596 638 0.807667 CAGCCTACACACCGAGATGC 60.808 60.000 0.00 0.00 0.00 3.91
597 639 0.817654 TCAGCCTACACACCGAGATG 59.182 55.000 0.00 0.00 0.00 2.90
651 698 4.113354 GGCTCTAAGATTGTACCAGAACG 58.887 47.826 0.00 0.00 0.00 3.95
740 2074 4.965814 TGGAATATTGAGGAGACATGAGC 58.034 43.478 0.00 0.00 0.00 4.26
783 2117 5.708736 TCCTCTGCCTATCTATCTCTAGG 57.291 47.826 0.00 0.00 38.03 3.02
792 2126 5.273208 TGTTTACTCTTCCTCTGCCTATCT 58.727 41.667 0.00 0.00 0.00 1.98
827 2175 2.689573 TGGCCTGGTAGGTCACCTGT 62.690 60.000 6.61 0.00 43.71 4.00
960 4452 0.312102 GCTTCTGGTTCTTGGTGCAC 59.688 55.000 8.80 8.80 0.00 4.57
962 4454 0.312102 GTGCTTCTGGTTCTTGGTGC 59.688 55.000 0.00 0.00 0.00 5.01
1077 4615 1.108132 CCTCCTCTAGGTACCGTGCC 61.108 65.000 6.18 0.00 40.94 5.01
1097 4635 2.026262 GGATACTCCTTCTTGGGCACAA 60.026 50.000 0.00 0.00 36.20 3.33
1408 5285 1.528309 CGTGGTCCTTTGGCACCTT 60.528 57.895 0.00 0.00 33.36 3.50
1453 5369 1.302832 CTTCAGGCTCCTTTGGCGT 60.303 57.895 0.00 0.00 37.59 5.68
1454 5370 1.302832 ACTTCAGGCTCCTTTGGCG 60.303 57.895 0.00 0.00 37.59 5.69
1789 5870 6.418057 AATCTCTCTCTCTCTCTCTCTCTC 57.582 45.833 0.00 0.00 0.00 3.20
1790 5871 6.157645 ACAAATCTCTCTCTCTCTCTCTCTCT 59.842 42.308 0.00 0.00 0.00 3.10
1792 5873 6.319048 ACAAATCTCTCTCTCTCTCTCTCT 57.681 41.667 0.00 0.00 0.00 3.10
1793 5874 8.682936 ATAACAAATCTCTCTCTCTCTCTCTC 57.317 38.462 0.00 0.00 0.00 3.20
1796 5877 9.561069 GTCTATAACAAATCTCTCTCTCTCTCT 57.439 37.037 0.00 0.00 0.00 3.10
1797 5878 9.561069 AGTCTATAACAAATCTCTCTCTCTCTC 57.439 37.037 0.00 0.00 0.00 3.20
1798 5879 9.920946 AAGTCTATAACAAATCTCTCTCTCTCT 57.079 33.333 0.00 0.00 0.00 3.10
1811 5892 9.838975 CACACATGCAAATAAGTCTATAACAAA 57.161 29.630 0.00 0.00 0.00 2.83
1859 7569 1.214589 GTCGGGAACTAGAGCGCAA 59.785 57.895 11.47 0.00 0.00 4.85
1886 7596 1.667236 TGCAACACCACTCAGACTTG 58.333 50.000 0.00 0.00 0.00 3.16
1888 7598 1.544093 CCATGCAACACCACTCAGACT 60.544 52.381 0.00 0.00 0.00 3.24
1993 7718 9.311916 CACAACTCCAATATTGAAACTCAAAAA 57.688 29.630 17.23 0.00 40.12 1.94
1997 7722 7.581213 AACACAACTCCAATATTGAAACTCA 57.419 32.000 17.23 0.00 0.00 3.41
2270 8011 0.041090 TCCCCAGCCCTCCAAAATTC 59.959 55.000 0.00 0.00 0.00 2.17
2273 8014 1.388174 TTATCCCCAGCCCTCCAAAA 58.612 50.000 0.00 0.00 0.00 2.44
2291 8032 0.537143 TTTGCGCACTCAGGTCCATT 60.537 50.000 11.12 0.00 0.00 3.16
2293 8034 1.597854 CTTTGCGCACTCAGGTCCA 60.598 57.895 11.12 0.00 0.00 4.02
2345 8086 3.524648 TTTGCTCGGGTCCGTCCAC 62.525 63.158 9.36 0.00 40.74 4.02
2366 8107 1.574702 GCAGCGTTAGTCCCAACCAC 61.575 60.000 0.00 0.00 0.00 4.16
2404 8145 1.163420 TGAAGCCACGAACAACGCAT 61.163 50.000 0.00 0.00 46.94 4.73
2428 8169 0.621571 CCCATCCCTGAGGTGGAAGA 60.622 60.000 9.57 0.00 36.80 2.87
2439 8180 1.901833 GCAAATGTGTTTCCCATCCCT 59.098 47.619 0.00 0.00 0.00 4.20
2448 8189 6.238759 GGTTCAGTCTAGAAGCAAATGTGTTT 60.239 38.462 0.00 0.00 43.52 2.83
2464 8205 2.787994 CTTGCATCCAAGGTTCAGTCT 58.212 47.619 0.00 0.00 43.75 3.24
2524 8265 4.389576 GCCGCTTTCGTGTGCAGG 62.390 66.667 0.00 0.00 0.00 4.85
2534 8275 3.053896 GCCACCGTTAGCCGCTTT 61.054 61.111 0.00 0.00 34.38 3.51
2581 8322 5.723887 GGTATGAGATTACCCCTGAGATGAT 59.276 44.000 0.00 0.00 36.42 2.45
2606 8347 0.469331 TGAACTCTCTGACCACCCGT 60.469 55.000 0.00 0.00 0.00 5.28
2608 8349 1.001406 CAGTGAACTCTCTGACCACCC 59.999 57.143 3.22 0.00 39.17 4.61
2633 8374 3.641436 TGACGTCCTGTAATAGCATCCAT 59.359 43.478 14.12 0.00 0.00 3.41
2671 8412 1.595093 CCGCCAAGAAACCATGTCCC 61.595 60.000 0.00 0.00 0.00 4.46
2677 8418 1.527380 GTCCACCGCCAAGAAACCA 60.527 57.895 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.