Multiple sequence alignment - TraesCS6D01G346600

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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 TraesCS6D01G346600 chr6D 100.000 4685 0 0 1 4685 445826820 445822136 0.000000e+00 8652.0
1 TraesCS6D01G346600 chr6D 85.772 1497 172 18 2103 3580 445956250 445957724 0.000000e+00 1546.0
2 TraesCS6D01G346600 chr6D 88.145 911 101 6 2158 3065 445839183 445840089 0.000000e+00 1077.0
3 TraesCS6D01G346600 chr6D 80.143 841 109 27 703 1512 445837804 445838617 4.070000e-160 575.0
4 TraesCS6D01G346600 chr6D 84.766 512 71 6 3144 3650 445810802 445810293 1.500000e-139 507.0
5 TraesCS6D01G346600 chr6D 86.177 463 52 9 1057 1519 445812953 445812503 1.510000e-134 490.0
6 TraesCS6D01G346600 chr6D 84.431 501 66 8 1066 1557 445800046 445799549 2.540000e-132 483.0
7 TraesCS6D01G346600 chr6D 81.975 405 52 7 1605 1999 445838671 445839064 1.630000e-84 324.0
8 TraesCS6D01G346600 chr6D 76.389 504 64 27 4154 4610 445796795 445796300 2.190000e-53 220.0
9 TraesCS6D01G346600 chr6D 90.789 76 7 0 4535 4610 445846699 445846774 8.290000e-18 102.0
10 TraesCS6D01G346600 chr6D 91.525 59 4 1 363 420 445814084 445814026 3.890000e-11 80.5
11 TraesCS6D01G346600 chr6D 100.000 28 0 0 598 625 445850304 445850331 8.000000e-03 52.8
12 TraesCS6D01G346600 chr6B 96.192 2994 76 12 1053 4024 672636463 672633486 0.000000e+00 4863.0
13 TraesCS6D01G346600 chr6B 95.321 3099 80 15 854 3927 673675418 673678476 0.000000e+00 4859.0
14 TraesCS6D01G346600 chr6B 85.211 1447 193 14 1598 3029 672680764 672682204 0.000000e+00 1467.0
15 TraesCS6D01G346600 chr6B 85.977 1198 140 16 2103 3273 673365678 673364482 0.000000e+00 1256.0
16 TraesCS6D01G346600 chr6B 88.372 989 108 6 2105 3089 672506946 672505961 0.000000e+00 1182.0
17 TraesCS6D01G346600 chr6B 88.217 959 98 9 2115 3060 673757580 673758536 0.000000e+00 1131.0
18 TraesCS6D01G346600 chr6B 85.774 963 126 9 2103 3058 672894335 672895293 0.000000e+00 1009.0
19 TraesCS6D01G346600 chr6B 85.318 974 131 11 2103 3069 672944911 672945879 0.000000e+00 996.0
20 TraesCS6D01G346600 chr6B 85.893 957 96 19 3142 4083 672505967 672505035 0.000000e+00 983.0
21 TraesCS6D01G346600 chr6B 85.324 879 121 8 2760 3633 673821153 673822028 0.000000e+00 902.0
22 TraesCS6D01G346600 chr6B 91.291 643 29 15 389 1010 672637100 672636464 0.000000e+00 852.0
23 TraesCS6D01G346600 chr6B 79.722 1297 156 54 779 1999 672882999 672884264 0.000000e+00 839.0
24 TraesCS6D01G346600 chr6B 91.327 565 34 11 292 843 673670706 673671268 0.000000e+00 758.0
25 TraesCS6D01G346600 chr6B 91.717 495 34 3 4192 4685 673681520 673682008 0.000000e+00 680.0
26 TraesCS6D01G346600 chr6B 88.395 517 35 11 4184 4680 672633446 672632935 2.410000e-167 599.0
27 TraesCS6D01G346600 chr6B 84.766 512 71 6 3144 3650 672619507 672618998 1.500000e-139 507.0
28 TraesCS6D01G346600 chr6B 87.191 445 55 2 1064 1507 672507960 672507517 5.410000e-139 505.0
29 TraesCS6D01G346600 chr6B 86.199 442 61 0 1071 1512 672680276 672680717 3.280000e-131 479.0
30 TraesCS6D01G346600 chr6B 85.776 464 52 11 1057 1519 673696411 673696861 3.280000e-131 479.0
31 TraesCS6D01G346600 chr6B 82.990 388 55 6 1605 1982 673757083 673757469 1.610000e-89 340.0
32 TraesCS6D01G346600 chr6B 75.071 706 106 39 3842 4522 672503223 672502563 1.000000e-66 265.0
33 TraesCS6D01G346600 chr6B 91.160 181 11 3 4018 4194 673678474 673678653 1.680000e-59 241.0
34 TraesCS6D01G346600 chr6B 78.920 389 50 15 4154 4519 673759630 673760009 7.840000e-58 235.0
35 TraesCS6D01G346600 chr6B 78.462 390 56 15 1605 1981 673025462 673025836 3.650000e-56 230.0
36 TraesCS6D01G346600 chr6B 97.170 106 3 0 138 243 450083730 450083835 3.720000e-41 180.0
37 TraesCS6D01G346600 chr6B 89.256 121 9 3 264 383 672637542 672637425 1.050000e-31 148.0
38 TraesCS6D01G346600 chr6B 83.544 158 14 5 4535 4681 672947299 672947455 2.270000e-28 137.0
39 TraesCS6D01G346600 chr6B 82.911 158 15 6 4535 4681 673606497 673606341 1.060000e-26 132.0
40 TraesCS6D01G346600 chr6B 83.846 130 11 5 16 137 673670540 673670667 1.070000e-21 115.0
41 TraesCS6D01G346600 chr6B 81.538 130 14 9 4540 4665 673760066 673760189 1.070000e-16 99.0
42 TraesCS6D01G346600 chr6B 80.882 136 11 12 4540 4665 672502509 672502379 4.990000e-15 93.5
43 TraesCS6D01G346600 chr6B 97.826 46 1 0 363 408 673695645 673695690 3.890000e-11 80.5
44 TraesCS6D01G346600 chr6A 89.459 1461 149 3 1605 3064 592501351 592499895 0.000000e+00 1840.0
45 TraesCS6D01G346600 chr6A 85.409 514 62 11 3147 3650 592492964 592492454 5.370000e-144 521.0
46 TraesCS6D01G346600 chr6A 85.950 484 60 6 3164 3646 592499759 592499283 1.160000e-140 510.0
47 TraesCS6D01G346600 chr6A 86.384 448 61 0 1066 1513 592478564 592478117 1.510000e-134 490.0
48 TraesCS6D01G346600 chr6A 81.041 538 49 23 4136 4636 592498970 592498449 3.420000e-101 379.0
49 TraesCS6D01G346600 chr6A 79.231 390 66 9 1605 1982 592477977 592477591 1.670000e-64 257.0
50 TraesCS6D01G346600 chr6A 97.170 106 3 0 138 243 53810381 53810486 3.720000e-41 180.0
51 TraesCS6D01G346600 chr6A 76.955 243 34 10 3842 4079 592610767 592610992 8.240000e-23 119.0
52 TraesCS6D01G346600 chr6A 97.826 46 1 0 363 408 592496018 592495973 3.890000e-11 80.5
53 TraesCS6D01G346600 chr6A 96.970 33 1 0 593 625 592535269 592535301 6.550000e-04 56.5
54 TraesCS6D01G346600 chr7D 83.065 372 57 4 1067 1438 94116045 94115680 2.700000e-87 333.0
55 TraesCS6D01G346600 chr7D 97.170 106 3 0 138 243 231569783 231569678 3.720000e-41 180.0
56 TraesCS6D01G346600 chr7D 97.170 106 3 0 138 243 231570328 231570223 3.720000e-41 180.0
57 TraesCS6D01G346600 chrUn 97.170 106 3 0 138 243 422172855 422172750 3.720000e-41 180.0
58 TraesCS6D01G346600 chr7B 97.170 106 3 0 138 243 662730842 662730947 3.720000e-41 180.0
59 TraesCS6D01G346600 chr4D 97.170 106 3 0 138 243 322005861 322005756 3.720000e-41 180.0
60 TraesCS6D01G346600 chr1D 97.170 106 3 0 138 243 254529534 254529639 3.720000e-41 180.0
61 TraesCS6D01G346600 chr1B 97.170 106 3 0 138 243 673308224 673308329 3.720000e-41 180.0


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 TraesCS6D01G346600 chr6D 445822136 445826820 4684 True 8652.000000 8652 100.000000 1 4685 1 chr6D.!!$R1 4684
1 TraesCS6D01G346600 chr6D 445956250 445957724 1474 False 1546.000000 1546 85.772000 2103 3580 1 chr6D.!!$F1 1477
2 TraesCS6D01G346600 chr6D 445837804 445840089 2285 False 658.666667 1077 83.421000 703 3065 3 chr6D.!!$F2 2362
3 TraesCS6D01G346600 chr6D 445810293 445814084 3791 True 359.166667 507 87.489333 363 3650 3 chr6D.!!$R3 3287
4 TraesCS6D01G346600 chr6D 445796300 445800046 3746 True 351.500000 483 80.410000 1066 4610 2 chr6D.!!$R2 3544
5 TraesCS6D01G346600 chr6B 673675418 673682008 6590 False 1926.666667 4859 92.732667 854 4685 3 chr6B.!!$F9 3831
6 TraesCS6D01G346600 chr6B 672632935 672637542 4607 True 1615.500000 4863 91.283500 264 4680 4 chr6B.!!$R5 4416
7 TraesCS6D01G346600 chr6B 673364482 673365678 1196 True 1256.000000 1256 85.977000 2103 3273 1 chr6B.!!$R2 1170
8 TraesCS6D01G346600 chr6B 672894335 672895293 958 False 1009.000000 1009 85.774000 2103 3058 1 chr6B.!!$F3 955
9 TraesCS6D01G346600 chr6B 672680276 672682204 1928 False 973.000000 1467 85.705000 1071 3029 2 chr6B.!!$F6 1958
10 TraesCS6D01G346600 chr6B 673821153 673822028 875 False 902.000000 902 85.324000 2760 3633 1 chr6B.!!$F5 873
11 TraesCS6D01G346600 chr6B 672882999 672884264 1265 False 839.000000 839 79.722000 779 1999 1 chr6B.!!$F2 1220
12 TraesCS6D01G346600 chr6B 672502379 672507960 5581 True 605.700000 1182 83.481800 1064 4665 5 chr6B.!!$R4 3601
13 TraesCS6D01G346600 chr6B 672944911 672947455 2544 False 566.500000 996 84.431000 2103 4681 2 chr6B.!!$F7 2578
14 TraesCS6D01G346600 chr6B 672618998 672619507 509 True 507.000000 507 84.766000 3144 3650 1 chr6B.!!$R1 506
15 TraesCS6D01G346600 chr6B 673757083 673760189 3106 False 451.250000 1131 82.916250 1605 4665 4 chr6B.!!$F11 3060
16 TraesCS6D01G346600 chr6B 673670540 673671268 728 False 436.500000 758 87.586500 16 843 2 chr6B.!!$F8 827
17 TraesCS6D01G346600 chr6B 673695645 673696861 1216 False 279.750000 479 91.801000 363 1519 2 chr6B.!!$F10 1156
18 TraesCS6D01G346600 chr6A 592492454 592501351 8897 True 666.100000 1840 87.937000 363 4636 5 chr6A.!!$R2 4273
19 TraesCS6D01G346600 chr6A 592477591 592478564 973 True 373.500000 490 82.807500 1066 1982 2 chr6A.!!$R1 916

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
248 257 0.036388 TTGGGATGTTCGCCTCTGTC 60.036 55.000 0.00 0.0 0.00 3.51 F
625 1304 0.804364 TGACATTCGCCATTCTGCAC 59.196 50.000 0.00 0.0 0.00 4.57 F
1514 2559 1.140816 GTCGTCAAGTTGCTGGACTC 58.859 55.000 0.00 0.0 32.58 3.36 F
1524 2572 1.448013 GCTGGACTCGTGGCTTACC 60.448 63.158 0.00 0.0 0.00 2.85 F
2685 4011 0.741221 GGTTGCTCCTCTTCGCGATT 60.741 55.000 10.88 0.0 0.00 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1449 2488 1.080772 CAGCACCGCGAAGTAGACA 60.081 57.895 8.23 0.00 0.00 3.41 R
2095 3354 2.039879 TGCTAACAGGGGAAAGGAAGAC 59.960 50.000 0.00 0.00 0.00 3.01 R
2685 4011 0.179004 AGGTGATGGTTGCGGTCAAA 60.179 50.000 0.00 0.00 33.37 2.69 R
3486 11919 0.608130 TCGTCCAGTTCATCACCCTG 59.392 55.000 0.00 0.00 0.00 4.45 R
3800 12341 0.107752 GCAAGGAAGCAGAGCTAGCT 60.108 55.000 19.45 19.45 45.97 3.32 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
48 57 1.001158 GAGAATCGATCGGTCCAGGAC 60.001 57.143 16.41 11.70 0.00 3.85
105 114 5.407502 TCATGACGAATTTCACTGACGTAT 58.592 37.500 0.00 0.00 37.32 3.06
106 115 5.288472 TCATGACGAATTTCACTGACGTATG 59.712 40.000 0.00 0.00 37.32 2.39
115 124 3.253230 TCACTGACGTATGCAACATGAG 58.747 45.455 0.00 0.00 0.00 2.90
118 127 2.416202 CTGACGTATGCAACATGAGCAA 59.584 45.455 18.45 8.10 46.27 3.91
121 130 2.551887 ACGTATGCAACATGAGCAAACA 59.448 40.909 18.45 7.19 46.27 2.83
124 133 3.945981 ATGCAACATGAGCAAACATCA 57.054 38.095 18.45 0.00 46.27 3.07
125 134 3.015934 TGCAACATGAGCAAACATCAC 57.984 42.857 13.66 0.00 39.39 3.06
126 135 1.980844 GCAACATGAGCAAACATCACG 59.019 47.619 0.00 0.00 0.00 4.35
127 136 2.605338 GCAACATGAGCAAACATCACGT 60.605 45.455 0.00 0.00 0.00 4.49
130 139 2.224079 ACATGAGCAAACATCACGTCAC 59.776 45.455 0.00 0.00 0.00 3.67
131 140 1.946745 TGAGCAAACATCACGTCACA 58.053 45.000 0.00 0.00 0.00 3.58
132 141 1.866601 TGAGCAAACATCACGTCACAG 59.133 47.619 0.00 0.00 0.00 3.66
133 142 0.588252 AGCAAACATCACGTCACAGC 59.412 50.000 0.00 0.00 0.00 4.40
134 143 0.588252 GCAAACATCACGTCACAGCT 59.412 50.000 0.00 0.00 0.00 4.24
135 144 1.661178 GCAAACATCACGTCACAGCTG 60.661 52.381 13.48 13.48 0.00 4.24
136 145 1.069703 CAAACATCACGTCACAGCTGG 60.070 52.381 19.93 7.28 0.00 4.85
137 146 0.603707 AACATCACGTCACAGCTGGG 60.604 55.000 19.93 15.69 0.00 4.45
138 147 1.742880 CATCACGTCACAGCTGGGG 60.743 63.158 17.80 8.84 0.00 4.96
139 148 3.612247 ATCACGTCACAGCTGGGGC 62.612 63.158 17.80 14.80 39.06 5.80
149 158 4.249513 GCTGGGGCTGATCTTTCC 57.750 61.111 0.00 0.00 35.22 3.13
150 159 1.611965 GCTGGGGCTGATCTTTCCT 59.388 57.895 0.00 0.00 35.22 3.36
151 160 0.839946 GCTGGGGCTGATCTTTCCTA 59.160 55.000 0.00 0.00 35.22 2.94
152 161 1.212935 GCTGGGGCTGATCTTTCCTAA 59.787 52.381 0.00 0.00 35.22 2.69
153 162 2.747799 GCTGGGGCTGATCTTTCCTAAG 60.748 54.545 0.00 0.00 35.22 2.18
154 163 2.774234 CTGGGGCTGATCTTTCCTAAGA 59.226 50.000 0.00 0.00 44.16 2.10
155 164 2.774234 TGGGGCTGATCTTTCCTAAGAG 59.226 50.000 0.00 0.00 43.33 2.85
156 165 2.774809 GGGGCTGATCTTTCCTAAGAGT 59.225 50.000 0.00 0.00 43.33 3.24
157 166 3.181459 GGGGCTGATCTTTCCTAAGAGTC 60.181 52.174 0.00 0.00 43.33 3.36
158 167 3.181459 GGGCTGATCTTTCCTAAGAGTCC 60.181 52.174 0.00 0.00 43.33 3.85
159 168 3.452627 GGCTGATCTTTCCTAAGAGTCCA 59.547 47.826 0.00 0.00 43.33 4.02
160 169 4.438148 GCTGATCTTTCCTAAGAGTCCAC 58.562 47.826 0.00 0.00 43.33 4.02
161 170 4.081420 GCTGATCTTTCCTAAGAGTCCACA 60.081 45.833 0.00 0.00 43.33 4.17
162 171 5.396213 GCTGATCTTTCCTAAGAGTCCACAT 60.396 44.000 0.00 0.00 43.33 3.21
163 172 6.227298 TGATCTTTCCTAAGAGTCCACATC 57.773 41.667 0.00 0.00 43.33 3.06
164 173 4.720649 TCTTTCCTAAGAGTCCACATCG 57.279 45.455 0.00 0.00 35.49 3.84
165 174 4.341487 TCTTTCCTAAGAGTCCACATCGA 58.659 43.478 0.00 0.00 35.49 3.59
166 175 4.158025 TCTTTCCTAAGAGTCCACATCGAC 59.842 45.833 0.00 0.00 35.49 4.20
167 176 2.014857 TCCTAAGAGTCCACATCGACG 58.985 52.381 0.00 0.00 37.85 5.12
168 177 1.065701 CCTAAGAGTCCACATCGACGG 59.934 57.143 0.00 0.00 37.85 4.79
169 178 1.065701 CTAAGAGTCCACATCGACGGG 59.934 57.143 0.00 0.00 37.85 5.28
170 179 0.611062 AAGAGTCCACATCGACGGGA 60.611 55.000 0.00 0.00 37.85 5.14
171 180 0.611062 AGAGTCCACATCGACGGGAA 60.611 55.000 3.35 0.00 37.85 3.97
172 181 0.179134 GAGTCCACATCGACGGGAAG 60.179 60.000 3.35 0.00 37.85 3.46
173 182 1.153628 GTCCACATCGACGGGAAGG 60.154 63.158 3.35 0.00 31.32 3.46
174 183 1.608336 TCCACATCGACGGGAAGGT 60.608 57.895 0.00 0.00 0.00 3.50
175 184 1.189524 TCCACATCGACGGGAAGGTT 61.190 55.000 0.00 0.00 0.00 3.50
176 185 0.321298 CCACATCGACGGGAAGGTTT 60.321 55.000 0.00 0.00 0.00 3.27
177 186 0.796312 CACATCGACGGGAAGGTTTG 59.204 55.000 0.00 0.00 0.00 2.93
178 187 0.321298 ACATCGACGGGAAGGTTTGG 60.321 55.000 0.00 0.00 0.00 3.28
179 188 1.376812 ATCGACGGGAAGGTTTGGC 60.377 57.895 0.00 0.00 0.00 4.52
180 189 2.119484 ATCGACGGGAAGGTTTGGCA 62.119 55.000 0.00 0.00 0.00 4.92
181 190 2.613506 CGACGGGAAGGTTTGGCAC 61.614 63.158 0.00 0.00 0.00 5.01
189 198 4.397348 GGTTTGGCACCTCGATGT 57.603 55.556 0.00 0.00 43.29 3.06
190 199 2.171635 GGTTTGGCACCTCGATGTC 58.828 57.895 0.00 0.00 43.29 3.06
191 200 1.635663 GGTTTGGCACCTCGATGTCG 61.636 60.000 0.00 0.00 43.29 4.35
192 201 1.375396 TTTGGCACCTCGATGTCGG 60.375 57.895 2.25 0.00 40.29 4.79
193 202 3.950794 TTGGCACCTCGATGTCGGC 62.951 63.158 2.25 8.83 40.29 5.54
194 203 4.148825 GGCACCTCGATGTCGGCT 62.149 66.667 2.25 0.00 40.29 5.52
195 204 2.583593 GCACCTCGATGTCGGCTC 60.584 66.667 2.25 0.00 40.29 4.70
196 205 3.069980 GCACCTCGATGTCGGCTCT 62.070 63.158 2.25 0.00 40.29 4.09
197 206 1.513158 CACCTCGATGTCGGCTCTT 59.487 57.895 2.25 0.00 40.29 2.85
198 207 0.526524 CACCTCGATGTCGGCTCTTC 60.527 60.000 2.25 0.00 40.29 2.87
199 208 1.298713 CCTCGATGTCGGCTCTTCG 60.299 63.158 2.25 0.00 40.29 3.79
200 209 1.941734 CTCGATGTCGGCTCTTCGC 60.942 63.158 2.25 0.00 40.29 4.70
209 218 2.125350 GCTCTTCGCCACCTGGAG 60.125 66.667 0.00 0.00 37.39 3.86
210 219 2.125350 CTCTTCGCCACCTGGAGC 60.125 66.667 0.00 1.58 37.39 4.70
211 220 2.604686 TCTTCGCCACCTGGAGCT 60.605 61.111 0.00 0.00 37.39 4.09
212 221 2.435586 CTTCGCCACCTGGAGCTG 60.436 66.667 0.00 0.31 37.39 4.24
213 222 3.241530 TTCGCCACCTGGAGCTGT 61.242 61.111 0.00 0.00 37.39 4.40
214 223 1.888436 CTTCGCCACCTGGAGCTGTA 61.888 60.000 0.00 0.00 37.39 2.74
215 224 1.888436 TTCGCCACCTGGAGCTGTAG 61.888 60.000 0.00 0.00 37.39 2.74
216 225 2.586792 GCCACCTGGAGCTGTAGG 59.413 66.667 10.57 10.57 40.01 3.18
219 228 4.136978 ACCTGGAGCTGTAGGTGG 57.863 61.111 15.79 1.32 45.30 4.61
220 229 1.158705 ACCTGGAGCTGTAGGTGGT 59.841 57.895 15.79 1.89 45.30 4.16
221 230 0.473886 ACCTGGAGCTGTAGGTGGTT 60.474 55.000 15.79 0.00 45.30 3.67
222 231 0.250513 CCTGGAGCTGTAGGTGGTTC 59.749 60.000 0.00 0.00 0.00 3.62
223 232 0.250513 CTGGAGCTGTAGGTGGTTCC 59.749 60.000 0.00 0.00 34.19 3.62
224 233 0.472925 TGGAGCTGTAGGTGGTTCCA 60.473 55.000 0.00 0.00 39.78 3.53
225 234 0.690762 GGAGCTGTAGGTGGTTCCAA 59.309 55.000 0.00 0.00 39.02 3.53
226 235 1.339151 GGAGCTGTAGGTGGTTCCAAG 60.339 57.143 0.00 0.00 39.02 3.61
227 236 0.693049 AGCTGTAGGTGGTTCCAAGG 59.307 55.000 0.00 0.00 39.02 3.61
228 237 0.322546 GCTGTAGGTGGTTCCAAGGG 60.323 60.000 0.00 0.00 39.02 3.95
229 238 1.064825 CTGTAGGTGGTTCCAAGGGT 58.935 55.000 0.00 0.00 39.02 4.34
230 239 1.423921 CTGTAGGTGGTTCCAAGGGTT 59.576 52.381 0.00 0.00 39.02 4.11
231 240 1.144093 TGTAGGTGGTTCCAAGGGTTG 59.856 52.381 0.00 0.00 39.02 3.77
241 250 1.883021 CAAGGGTTGGGATGTTCGC 59.117 57.895 0.00 0.00 0.00 4.70
244 253 1.749258 GGGTTGGGATGTTCGCCTC 60.749 63.158 0.00 0.00 0.00 4.70
248 257 0.036388 TTGGGATGTTCGCCTCTGTC 60.036 55.000 0.00 0.00 0.00 3.51
249 258 1.153349 GGGATGTTCGCCTCTGTCC 60.153 63.158 0.00 0.00 0.00 4.02
260 269 1.130561 GCCTCTGTCCGTTGCAAATAC 59.869 52.381 0.00 0.00 0.00 1.89
261 270 2.422597 CCTCTGTCCGTTGCAAATACA 58.577 47.619 0.00 5.14 0.00 2.29
262 271 2.416547 CCTCTGTCCGTTGCAAATACAG 59.583 50.000 22.09 22.09 36.13 2.74
277 286 8.319143 TGCAAATACAGTAGTTTTTCCTAGTC 57.681 34.615 0.00 0.00 28.32 2.59
280 289 8.936864 CAAATACAGTAGTTTTTCCTAGTCCTG 58.063 37.037 0.00 0.00 28.32 3.86
281 290 5.485209 ACAGTAGTTTTTCCTAGTCCTGG 57.515 43.478 0.00 0.00 0.00 4.45
282 291 4.906060 ACAGTAGTTTTTCCTAGTCCTGGT 59.094 41.667 0.00 0.00 0.00 4.00
283 292 6.080009 ACAGTAGTTTTTCCTAGTCCTGGTA 58.920 40.000 0.00 0.00 0.00 3.25
284 293 6.210984 ACAGTAGTTTTTCCTAGTCCTGGTAG 59.789 42.308 0.00 0.00 0.00 3.18
285 294 6.436532 CAGTAGTTTTTCCTAGTCCTGGTAGA 59.563 42.308 0.00 0.00 0.00 2.59
286 295 7.124448 CAGTAGTTTTTCCTAGTCCTGGTAGAT 59.876 40.741 0.00 0.00 0.00 1.98
287 296 8.342270 AGTAGTTTTTCCTAGTCCTGGTAGATA 58.658 37.037 0.00 0.00 0.00 1.98
288 297 8.975295 GTAGTTTTTCCTAGTCCTGGTAGATAA 58.025 37.037 0.00 0.00 0.00 1.75
424 752 2.374184 CTTCTCCGATGACCTGACTCT 58.626 52.381 0.00 0.00 0.00 3.24
426 754 1.282157 TCTCCGATGACCTGACTCTGA 59.718 52.381 0.00 0.00 0.00 3.27
431 759 2.223688 CGATGACCTGACTCTGATCACC 60.224 54.545 0.00 0.00 0.00 4.02
500 833 5.852250 ACCTTAAAGATAGGATATGCAGGGT 59.148 40.000 0.00 0.00 36.58 4.34
530 864 2.947532 CGGCAGCTTCCTCCAGACA 61.948 63.158 0.00 0.00 0.00 3.41
538 872 1.613925 CTTCCTCCAGACAACGACTCA 59.386 52.381 0.00 0.00 0.00 3.41
625 1304 0.804364 TGACATTCGCCATTCTGCAC 59.196 50.000 0.00 0.00 0.00 4.57
852 1750 2.097038 CGCTCCGTCAGGCTTTGAG 61.097 63.158 0.00 0.00 36.21 3.02
1449 2488 2.286523 CCGGGACAAGAGCTCCACT 61.287 63.158 10.93 0.00 0.00 4.00
1514 2559 1.140816 GTCGTCAAGTTGCTGGACTC 58.859 55.000 0.00 0.00 32.58 3.36
1524 2572 1.448013 GCTGGACTCGTGGCTTACC 60.448 63.158 0.00 0.00 0.00 2.85
1602 2829 6.237154 CCTCAAGGAACTGAAAGAGAAAGAT 58.763 40.000 0.00 0.00 40.86 2.40
1782 3009 3.957497 TGAGGGTGTTTTTACACTGCAAT 59.043 39.130 8.18 0.00 40.28 3.56
2095 3354 4.211374 ACGAAACTGAACTGAAAATCCTCG 59.789 41.667 0.00 0.00 0.00 4.63
2238 3558 1.738350 TCTCTTGTTCTACTCCTCGCG 59.262 52.381 0.00 0.00 0.00 5.87
2604 3924 2.415491 CCATGTCGTCTTCTTCACGCTA 60.415 50.000 0.00 0.00 37.18 4.26
2685 4011 0.741221 GGTTGCTCCTCTTCGCGATT 60.741 55.000 10.88 0.00 0.00 3.34
3096 4596 4.597079 ACATAAATAGCAACAATTCGGCG 58.403 39.130 0.00 0.00 0.00 6.46
3162 4668 1.512926 CACCCAAAGAACAGGACGAG 58.487 55.000 0.00 0.00 0.00 4.18
3327 11760 1.301087 CAGTGGCAACGGGTACGAA 60.301 57.895 0.00 0.00 44.60 3.85
3347 11780 4.457496 AGGCGACCCAGTGATGCG 62.457 66.667 0.00 0.00 0.00 4.73
3486 11919 0.250513 AATGGGAGGAACAGTCGCTC 59.749 55.000 0.00 0.00 0.00 5.03
3680 12113 1.722034 TCCAAAGAGAGACCTGCAGT 58.278 50.000 13.81 0.11 0.00 4.40
3716 12149 2.902065 TATCTGCAGCGTCGCTATAG 57.098 50.000 21.25 19.68 36.40 1.31
3717 12150 0.955178 ATCTGCAGCGTCGCTATAGT 59.045 50.000 21.25 8.82 36.40 2.12
3718 12151 0.029433 TCTGCAGCGTCGCTATAGTG 59.971 55.000 21.25 9.33 36.40 2.74
3719 12152 1.543941 CTGCAGCGTCGCTATAGTGC 61.544 60.000 21.25 19.53 36.40 4.40
3720 12153 1.299468 GCAGCGTCGCTATAGTGCT 60.299 57.895 21.25 6.74 36.40 4.40
3721 12154 0.040336 GCAGCGTCGCTATAGTGCTA 60.040 55.000 21.25 0.00 36.40 3.49
3722 12155 1.401670 GCAGCGTCGCTATAGTGCTAT 60.402 52.381 21.25 0.00 36.40 2.97
3800 12341 9.303116 CTTTAGATCTCTAATCAGCTTACCCTA 57.697 37.037 0.00 0.00 38.16 3.53
3892 12445 5.749596 TGTAATTGGATGAATAACCTGCG 57.250 39.130 0.00 0.00 0.00 5.18
3900 12454 1.899814 TGAATAACCTGCGTCCACTCT 59.100 47.619 0.00 0.00 0.00 3.24
3969 12533 8.179615 GCATCTTAATCGAATGAATATGCATGA 58.820 33.333 10.16 0.00 37.67 3.07
3998 12562 1.737793 GTTTTCCTGACCCTATGTGCG 59.262 52.381 0.00 0.00 0.00 5.34
3999 12563 0.392461 TTTCCTGACCCTATGTGCGC 60.392 55.000 0.00 0.00 0.00 6.09
4028 12592 5.500234 TGTCTCATAAGAACTTGAATGGGG 58.500 41.667 0.00 0.00 31.93 4.96
4113 14754 8.536175 TGAAACATATGTCACTTGGTATAGTCA 58.464 33.333 9.23 0.00 0.00 3.41
4114 14755 8.948631 AAACATATGTCACTTGGTATAGTCAG 57.051 34.615 9.23 0.00 0.00 3.51
4115 14756 7.898014 ACATATGTCACTTGGTATAGTCAGA 57.102 36.000 1.41 0.00 0.00 3.27
4116 14757 8.306313 ACATATGTCACTTGGTATAGTCAGAA 57.694 34.615 1.41 0.00 0.00 3.02
4117 14758 8.417106 ACATATGTCACTTGGTATAGTCAGAAG 58.583 37.037 1.41 0.00 0.00 2.85
4118 14759 6.859112 ATGTCACTTGGTATAGTCAGAAGT 57.141 37.500 0.00 0.00 0.00 3.01
4119 14760 6.665992 TGTCACTTGGTATAGTCAGAAGTT 57.334 37.500 0.00 0.00 0.00 2.66
4120 14761 6.455647 TGTCACTTGGTATAGTCAGAAGTTG 58.544 40.000 0.00 0.00 0.00 3.16
4121 14762 6.041637 TGTCACTTGGTATAGTCAGAAGTTGT 59.958 38.462 0.00 0.00 0.00 3.32
4123 14764 6.041637 TCACTTGGTATAGTCAGAAGTTGTGT 59.958 38.462 0.00 0.00 0.00 3.72
4124 14765 6.146184 CACTTGGTATAGTCAGAAGTTGTGTG 59.854 42.308 0.00 0.00 0.00 3.82
4125 14766 4.566004 TGGTATAGTCAGAAGTTGTGTGC 58.434 43.478 0.00 0.00 0.00 4.57
4126 14767 4.039852 TGGTATAGTCAGAAGTTGTGTGCA 59.960 41.667 0.00 0.00 0.00 4.57
4127 14768 4.994852 GGTATAGTCAGAAGTTGTGTGCAA 59.005 41.667 0.00 0.00 0.00 4.08
4128 14769 5.643777 GGTATAGTCAGAAGTTGTGTGCAAT 59.356 40.000 0.00 0.00 36.92 3.56
4129 14770 5.869753 ATAGTCAGAAGTTGTGTGCAATC 57.130 39.130 0.00 0.00 36.92 2.67
4130 14771 2.880890 AGTCAGAAGTTGTGTGCAATCC 59.119 45.455 0.00 0.00 36.92 3.01
4132 14773 2.880268 TCAGAAGTTGTGTGCAATCCTG 59.120 45.455 0.00 0.00 36.92 3.86
4143 14784 2.840296 GCAATCCTGCTAGCTTTGTC 57.160 50.000 17.23 7.37 45.74 3.18
4145 14786 3.535561 GCAATCCTGCTAGCTTTGTCTA 58.464 45.455 17.23 0.00 45.74 2.59
4146 14787 3.559242 GCAATCCTGCTAGCTTTGTCTAG 59.441 47.826 17.23 2.46 45.74 2.43
4177 14876 6.590068 TGTCACTAGGTATAGTCTGGAGTAC 58.410 44.000 0.00 0.00 40.38 2.73
4182 14881 4.794334 AGGTATAGTCTGGAGTACTGTGG 58.206 47.826 0.00 0.00 0.00 4.17
4196 17830 7.092444 TGGAGTACTGTGGAATCCTGATAATTT 60.092 37.037 0.00 0.00 0.00 1.82
4197 17831 8.429641 GGAGTACTGTGGAATCCTGATAATTTA 58.570 37.037 0.00 0.00 0.00 1.40
4230 17865 5.073311 TCGAGAGGAAACATACCTTGAAG 57.927 43.478 0.00 0.00 37.93 3.02
4232 17867 4.579869 GAGAGGAAACATACCTTGAAGCA 58.420 43.478 0.00 0.00 37.93 3.91
4472 18137 1.375908 GAGGCGTGAATGCAGGTGA 60.376 57.895 0.00 0.00 36.28 4.02
4672 18424 2.203437 GGAAACCGGCAACCTGGT 60.203 61.111 0.00 0.00 41.20 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 9.398170 CGATTCTCAATCTAAAACAACATTGTT 57.602 29.630 4.13 4.13 42.96 2.83
10 11 8.783093 TCGATTCTCAATCTAAAACAACATTGT 58.217 29.630 0.00 0.00 38.19 2.71
11 12 9.778993 ATCGATTCTCAATCTAAAACAACATTG 57.221 29.630 0.00 0.00 35.73 2.82
12 13 9.994432 GATCGATTCTCAATCTAAAACAACATT 57.006 29.630 0.00 0.00 35.73 2.71
13 14 8.331022 CGATCGATTCTCAATCTAAAACAACAT 58.669 33.333 10.26 0.00 35.73 2.71
14 15 7.201522 CCGATCGATTCTCAATCTAAAACAACA 60.202 37.037 18.66 0.00 35.73 3.33
24 25 3.312828 CTGGACCGATCGATTCTCAATC 58.687 50.000 18.66 0.35 34.52 2.67
26 27 1.409064 CCTGGACCGATCGATTCTCAA 59.591 52.381 18.66 0.00 0.00 3.02
30 31 0.744874 TGTCCTGGACCGATCGATTC 59.255 55.000 23.42 12.27 0.00 2.52
38 39 0.240945 GCAAACAATGTCCTGGACCG 59.759 55.000 23.42 14.21 0.00 4.79
40 41 2.227388 CTCTGCAAACAATGTCCTGGAC 59.773 50.000 19.96 19.96 0.00 4.02
43 44 1.542915 CCCTCTGCAAACAATGTCCTG 59.457 52.381 0.00 0.00 0.00 3.86
48 57 1.444895 GCGCCCTCTGCAAACAATG 60.445 57.895 0.00 0.00 41.33 2.82
74 83 4.616802 GTGAAATTCGTCATGAAATTGCGT 59.383 37.500 0.00 0.00 40.71 5.24
105 114 2.605097 CGTGATGTTTGCTCATGTTGCA 60.605 45.455 11.00 11.00 38.80 4.08
106 115 1.980844 CGTGATGTTTGCTCATGTTGC 59.019 47.619 6.53 6.53 0.00 4.17
115 124 0.588252 AGCTGTGACGTGATGTTTGC 59.412 50.000 0.00 0.00 0.00 3.68
118 127 0.603707 CCCAGCTGTGACGTGATGTT 60.604 55.000 13.81 0.00 0.00 2.71
121 130 2.665000 CCCCAGCTGTGACGTGAT 59.335 61.111 13.81 0.00 0.00 3.06
131 140 5.025509 CTTAGGAAAGATCAGCCCCAGCT 62.026 52.174 0.00 0.00 42.32 4.24
132 141 0.839946 TAGGAAAGATCAGCCCCAGC 59.160 55.000 0.00 0.00 40.32 4.85
133 142 2.774234 TCTTAGGAAAGATCAGCCCCAG 59.226 50.000 0.00 0.00 36.80 4.45
134 143 2.774234 CTCTTAGGAAAGATCAGCCCCA 59.226 50.000 0.00 0.00 40.92 4.96
135 144 2.774809 ACTCTTAGGAAAGATCAGCCCC 59.225 50.000 0.00 0.00 40.92 5.80
136 145 3.181459 GGACTCTTAGGAAAGATCAGCCC 60.181 52.174 0.00 0.00 40.92 5.19
137 146 3.452627 TGGACTCTTAGGAAAGATCAGCC 59.547 47.826 0.00 0.00 40.92 4.85
138 147 4.081420 TGTGGACTCTTAGGAAAGATCAGC 60.081 45.833 0.00 0.00 40.92 4.26
139 148 5.667539 TGTGGACTCTTAGGAAAGATCAG 57.332 43.478 0.00 0.00 40.92 2.90
140 149 5.163509 CGATGTGGACTCTTAGGAAAGATCA 60.164 44.000 0.00 0.00 40.92 2.92
141 150 5.067936 TCGATGTGGACTCTTAGGAAAGATC 59.932 44.000 0.00 0.00 40.92 2.75
142 151 4.956700 TCGATGTGGACTCTTAGGAAAGAT 59.043 41.667 0.00 0.00 40.92 2.40
143 152 4.158025 GTCGATGTGGACTCTTAGGAAAGA 59.842 45.833 0.00 0.00 39.47 2.52
144 153 4.425520 GTCGATGTGGACTCTTAGGAAAG 58.574 47.826 0.00 0.00 34.09 2.62
145 154 3.119602 CGTCGATGTGGACTCTTAGGAAA 60.120 47.826 0.00 0.00 34.75 3.13
146 155 2.422479 CGTCGATGTGGACTCTTAGGAA 59.578 50.000 0.00 0.00 34.75 3.36
147 156 2.014857 CGTCGATGTGGACTCTTAGGA 58.985 52.381 0.00 0.00 34.75 2.94
148 157 1.065701 CCGTCGATGTGGACTCTTAGG 59.934 57.143 3.52 0.00 34.75 2.69
149 158 1.065701 CCCGTCGATGTGGACTCTTAG 59.934 57.143 3.52 0.00 34.75 2.18
150 159 1.100510 CCCGTCGATGTGGACTCTTA 58.899 55.000 3.52 0.00 34.75 2.10
151 160 0.611062 TCCCGTCGATGTGGACTCTT 60.611 55.000 9.90 0.00 34.75 2.85
152 161 0.611062 TTCCCGTCGATGTGGACTCT 60.611 55.000 12.69 0.00 34.75 3.24
153 162 0.179134 CTTCCCGTCGATGTGGACTC 60.179 60.000 12.69 0.00 34.75 3.36
154 163 1.605058 CCTTCCCGTCGATGTGGACT 61.605 60.000 12.69 0.00 34.75 3.85
155 164 1.153628 CCTTCCCGTCGATGTGGAC 60.154 63.158 12.69 0.00 0.00 4.02
156 165 1.189524 AACCTTCCCGTCGATGTGGA 61.190 55.000 9.90 9.90 0.00 4.02
157 166 0.321298 AAACCTTCCCGTCGATGTGG 60.321 55.000 3.52 4.93 0.00 4.17
158 167 0.796312 CAAACCTTCCCGTCGATGTG 59.204 55.000 3.52 0.00 0.00 3.21
159 168 0.321298 CCAAACCTTCCCGTCGATGT 60.321 55.000 3.52 0.00 0.00 3.06
160 169 1.644786 GCCAAACCTTCCCGTCGATG 61.645 60.000 0.00 0.00 0.00 3.84
161 170 1.376812 GCCAAACCTTCCCGTCGAT 60.377 57.895 0.00 0.00 0.00 3.59
162 171 2.031465 GCCAAACCTTCCCGTCGA 59.969 61.111 0.00 0.00 0.00 4.20
163 172 2.281208 TGCCAAACCTTCCCGTCG 60.281 61.111 0.00 0.00 0.00 5.12
164 173 2.265904 GGTGCCAAACCTTCCCGTC 61.266 63.158 0.00 0.00 46.55 4.79
165 174 2.203437 GGTGCCAAACCTTCCCGT 60.203 61.111 0.00 0.00 46.55 5.28
173 182 1.635663 CCGACATCGAGGTGCCAAAC 61.636 60.000 7.79 0.00 43.02 2.93
174 183 1.375396 CCGACATCGAGGTGCCAAA 60.375 57.895 7.79 0.00 43.02 3.28
175 184 2.264480 CCGACATCGAGGTGCCAA 59.736 61.111 7.79 0.00 43.02 4.52
176 185 4.451150 GCCGACATCGAGGTGCCA 62.451 66.667 7.79 0.00 43.02 4.92
177 186 4.148825 AGCCGACATCGAGGTGCC 62.149 66.667 7.79 0.00 43.02 5.01
178 187 2.564553 AAGAGCCGACATCGAGGTGC 62.565 60.000 7.79 5.85 43.02 5.01
179 188 0.526524 GAAGAGCCGACATCGAGGTG 60.527 60.000 7.79 0.00 43.02 4.00
180 189 1.810532 GAAGAGCCGACATCGAGGT 59.189 57.895 0.50 0.50 43.02 3.85
181 190 1.298713 CGAAGAGCCGACATCGAGG 60.299 63.158 2.09 0.00 43.02 4.63
182 191 1.941734 GCGAAGAGCCGACATCGAG 60.942 63.158 2.09 0.00 40.81 4.04
183 192 2.102357 GCGAAGAGCCGACATCGA 59.898 61.111 2.09 0.00 40.81 3.59
193 202 2.125350 GCTCCAGGTGGCGAAGAG 60.125 66.667 0.00 0.00 34.44 2.85
194 203 2.604686 AGCTCCAGGTGGCGAAGA 60.605 61.111 0.00 0.00 34.44 2.87
195 204 1.888436 TACAGCTCCAGGTGGCGAAG 61.888 60.000 10.41 0.00 46.90 3.79
196 205 1.888436 CTACAGCTCCAGGTGGCGAA 61.888 60.000 10.41 0.00 46.90 4.70
197 206 2.283604 TACAGCTCCAGGTGGCGA 60.284 61.111 10.41 0.00 46.90 5.54
198 207 2.185350 CTACAGCTCCAGGTGGCG 59.815 66.667 10.41 0.00 46.90 5.69
199 208 2.294078 ACCTACAGCTCCAGGTGGC 61.294 63.158 13.84 0.00 46.90 5.01
200 209 4.136978 ACCTACAGCTCCAGGTGG 57.863 61.111 13.84 0.00 46.90 4.61
202 211 0.473886 AACCACCTACAGCTCCAGGT 60.474 55.000 9.57 9.57 46.29 4.00
203 212 0.250513 GAACCACCTACAGCTCCAGG 59.749 60.000 8.35 8.35 37.97 4.45
204 213 0.250513 GGAACCACCTACAGCTCCAG 59.749 60.000 0.00 0.00 35.41 3.86
205 214 0.472925 TGGAACCACCTACAGCTCCA 60.473 55.000 0.00 0.00 39.86 3.86
206 215 0.690762 TTGGAACCACCTACAGCTCC 59.309 55.000 0.00 0.00 39.86 4.70
207 216 1.339151 CCTTGGAACCACCTACAGCTC 60.339 57.143 0.00 0.00 39.86 4.09
208 217 0.693049 CCTTGGAACCACCTACAGCT 59.307 55.000 0.00 0.00 39.86 4.24
209 218 0.322546 CCCTTGGAACCACCTACAGC 60.323 60.000 0.00 0.00 39.86 4.40
210 219 1.064825 ACCCTTGGAACCACCTACAG 58.935 55.000 0.00 0.00 39.86 2.74
211 220 1.144093 CAACCCTTGGAACCACCTACA 59.856 52.381 0.00 0.00 39.86 2.74
212 221 1.905637 CAACCCTTGGAACCACCTAC 58.094 55.000 0.00 0.00 39.86 3.18
223 232 1.595093 GGCGAACATCCCAACCCTTG 61.595 60.000 0.00 0.00 0.00 3.61
224 233 1.304134 GGCGAACATCCCAACCCTT 60.304 57.895 0.00 0.00 0.00 3.95
225 234 2.198304 GAGGCGAACATCCCAACCCT 62.198 60.000 0.00 0.00 0.00 4.34
226 235 1.749258 GAGGCGAACATCCCAACCC 60.749 63.158 0.00 0.00 0.00 4.11
227 236 1.026718 CAGAGGCGAACATCCCAACC 61.027 60.000 0.00 0.00 0.00 3.77
228 237 0.321653 ACAGAGGCGAACATCCCAAC 60.322 55.000 0.00 0.00 0.00 3.77
229 238 0.036388 GACAGAGGCGAACATCCCAA 60.036 55.000 0.00 0.00 0.00 4.12
230 239 1.596934 GACAGAGGCGAACATCCCA 59.403 57.895 0.00 0.00 0.00 4.37
231 240 1.153349 GGACAGAGGCGAACATCCC 60.153 63.158 0.00 0.00 0.00 3.85
232 241 1.519455 CGGACAGAGGCGAACATCC 60.519 63.158 0.00 0.00 0.00 3.51
233 242 0.389948 AACGGACAGAGGCGAACATC 60.390 55.000 0.00 0.00 0.00 3.06
234 243 0.670546 CAACGGACAGAGGCGAACAT 60.671 55.000 0.00 0.00 0.00 2.71
235 244 1.300620 CAACGGACAGAGGCGAACA 60.301 57.895 0.00 0.00 0.00 3.18
236 245 2.668280 GCAACGGACAGAGGCGAAC 61.668 63.158 0.00 0.00 0.00 3.95
237 246 2.357034 GCAACGGACAGAGGCGAA 60.357 61.111 0.00 0.00 0.00 4.70
239 248 1.577328 ATTTGCAACGGACAGAGGCG 61.577 55.000 0.00 0.00 0.00 5.52
241 250 2.416547 CTGTATTTGCAACGGACAGAGG 59.583 50.000 21.73 4.20 39.94 3.69
244 253 3.994392 ACTACTGTATTTGCAACGGACAG 59.006 43.478 23.38 23.38 42.58 3.51
248 257 5.627780 GGAAAAACTACTGTATTTGCAACGG 59.372 40.000 0.00 0.00 0.00 4.44
249 258 6.435428 AGGAAAAACTACTGTATTTGCAACG 58.565 36.000 0.00 0.00 0.00 4.10
260 269 5.485209 ACCAGGACTAGGAAAAACTACTG 57.515 43.478 0.00 0.00 0.00 2.74
261 270 6.559429 TCTACCAGGACTAGGAAAAACTACT 58.441 40.000 0.00 0.00 0.00 2.57
262 271 6.847421 TCTACCAGGACTAGGAAAAACTAC 57.153 41.667 0.00 0.00 0.00 2.73
305 314 2.362760 TGAGGGGCGCCGTAGTTA 60.363 61.111 22.54 0.96 0.00 2.24
424 752 1.337384 CCCCGATGTCCAGGTGATCA 61.337 60.000 0.00 0.00 0.00 2.92
426 754 1.002921 TCCCCGATGTCCAGGTGAT 59.997 57.895 0.00 0.00 0.00 3.06
431 759 1.617018 TTGCTCTCCCCGATGTCCAG 61.617 60.000 0.00 0.00 0.00 3.86
500 833 2.999485 GCTGCCGAGTCTCTCTGCA 61.999 63.158 13.31 13.31 45.54 4.41
530 864 2.132762 CTTAACTTGGCGTGAGTCGTT 58.867 47.619 0.00 0.00 39.79 3.85
538 872 3.202829 TGGAAAGACTTAACTTGGCGT 57.797 42.857 0.00 0.00 0.00 5.68
567 901 6.593759 AGGAAGGGAGAGTGATTACTAGTA 57.406 41.667 0.00 0.00 37.25 1.82
569 903 6.265876 GGTTAGGAAGGGAGAGTGATTACTAG 59.734 46.154 0.00 0.00 37.25 2.57
570 904 6.068379 AGGTTAGGAAGGGAGAGTGATTACTA 60.068 42.308 0.00 0.00 37.25 1.82
588 1267 1.091771 CATGGCAGCGACAGGTTAGG 61.092 60.000 0.00 0.00 0.00 2.69
625 1304 5.649395 TCTTCTTTTCTGGCTATTGTGATGG 59.351 40.000 0.00 0.00 0.00 3.51
677 1495 0.664767 GATGTAGTCCGAGCGCCATC 60.665 60.000 2.29 3.26 0.00 3.51
678 1496 1.364171 GATGTAGTCCGAGCGCCAT 59.636 57.895 2.29 0.00 0.00 4.40
679 1497 2.805546 GATGTAGTCCGAGCGCCA 59.194 61.111 2.29 0.00 0.00 5.69
680 1498 2.353607 CGATGTAGTCCGAGCGCC 60.354 66.667 2.29 0.00 0.00 6.53
684 1502 1.360551 CTGGCCGATGTAGTCCGAG 59.639 63.158 0.00 0.00 0.00 4.63
685 1503 2.782222 GCTGGCCGATGTAGTCCGA 61.782 63.158 0.00 0.00 0.00 4.55
1449 2488 1.080772 CAGCACCGCGAAGTAGACA 60.081 57.895 8.23 0.00 0.00 3.41
1514 2559 3.799755 GCTTGCCGGTAAGCCACG 61.800 66.667 38.22 14.32 45.62 4.94
2047 3304 2.689471 TGTGCTGAGTTGCATCAGTTTT 59.311 40.909 16.63 0.00 46.93 2.43
2095 3354 2.039879 TGCTAACAGGGGAAAGGAAGAC 59.960 50.000 0.00 0.00 0.00 3.01
2238 3558 2.045926 ATGGTGGCGGCAAGAGTC 60.046 61.111 15.50 0.00 0.00 3.36
2604 3924 5.280654 TGTTTTCCGTAACCTTGTAGTCT 57.719 39.130 0.00 0.00 0.00 3.24
2685 4011 0.179004 AGGTGATGGTTGCGGTCAAA 60.179 50.000 0.00 0.00 33.37 2.69
3096 4596 1.679153 TCTTCGTCCTTTGTTTTGGGC 59.321 47.619 0.00 0.00 0.00 5.36
3162 4668 4.642466 TTCTTCCTTCTTCCCTTCTTCC 57.358 45.455 0.00 0.00 0.00 3.46
3327 11760 3.005539 ATCACTGGGTCGCCTGCT 61.006 61.111 0.00 0.00 0.00 4.24
3347 11780 2.991540 GGGGCCTCCTGTTGTTGC 60.992 66.667 0.84 0.00 0.00 4.17
3486 11919 0.608130 TCGTCCAGTTCATCACCCTG 59.392 55.000 0.00 0.00 0.00 4.45
3716 12149 4.750952 TCGCTCTCACATAGTATAGCAC 57.249 45.455 3.43 0.00 0.00 4.40
3717 12150 5.703876 CAATCGCTCTCACATAGTATAGCA 58.296 41.667 3.43 0.00 0.00 3.49
3718 12151 4.560819 GCAATCGCTCTCACATAGTATAGC 59.439 45.833 0.00 0.00 34.30 2.97
3800 12341 0.107752 GCAAGGAAGCAGAGCTAGCT 60.108 55.000 19.45 19.45 45.97 3.32
3892 12445 1.085091 CAAGCATGCTCAGAGTGGAC 58.915 55.000 22.93 0.00 0.00 4.02
3998 12562 5.105554 TCAAGTTCTTATGAGACAGAGAGGC 60.106 44.000 0.00 0.00 0.00 4.70
3999 12563 6.522625 TCAAGTTCTTATGAGACAGAGAGG 57.477 41.667 0.00 0.00 0.00 3.69
4110 14751 2.880890 AGGATTGCACACAACTTCTGAC 59.119 45.455 0.00 0.00 38.99 3.51
4111 14752 2.880268 CAGGATTGCACACAACTTCTGA 59.120 45.455 0.00 0.00 38.99 3.27
4136 14777 5.897050 AGTGACATACTAGCTAGACAAAGC 58.103 41.667 27.45 11.54 38.04 3.51
4150 14849 7.225725 ACTCCAGACTATACCTAGTGACATAC 58.774 42.308 0.00 0.00 38.33 2.39
4151 14850 7.390013 ACTCCAGACTATACCTAGTGACATA 57.610 40.000 0.00 0.00 38.33 2.29
4165 14864 4.017407 AGGATTCCACAGTACTCCAGACTA 60.017 45.833 5.29 0.00 0.00 2.59
4196 17830 7.582667 TGTTTCCTCTCGATCAGTGATTATA 57.417 36.000 7.16 0.00 0.00 0.98
4197 17831 6.471233 TGTTTCCTCTCGATCAGTGATTAT 57.529 37.500 7.16 0.00 0.00 1.28
4277 17920 2.031012 TGCAGGTGCTCGGTGAAG 59.969 61.111 3.18 0.00 42.66 3.02
4299 17942 4.854924 TGCATGCGTGGATCGGGG 62.855 66.667 14.09 0.00 40.26 5.73
4400 18063 0.673437 GAGGAATCCTCTCCGAGCAG 59.327 60.000 21.48 0.00 46.41 4.24
4472 18137 1.557269 AACCAGCTGGATTCGAGCCT 61.557 55.000 39.19 10.61 37.12 4.58
4627 18363 1.126846 GTTTCTGAATGCCACGAGACG 59.873 52.381 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.