Multiple sequence alignment - TraesCS2D01G492200

Loading Multiple Alignment...

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 TraesCS2D01G492200 chr2D 100.000 6344 0 0 1 6344 590154070 590147727 0.000000e+00 11716.0
1 TraesCS2D01G492200 chr2D 94.712 208 9 2 1788 1995 590152084 590151879 7.930000e-84 322.0
2 TraesCS2D01G492200 chr2D 94.712 208 9 2 1987 2192 590152283 590152076 7.930000e-84 322.0
3 TraesCS2D01G492200 chr2A 89.552 2680 174 54 3 2621 724521676 724519042 0.000000e+00 3301.0
4 TraesCS2D01G492200 chr2A 91.438 876 58 10 3903 4775 516091255 516092116 0.000000e+00 1186.0
5 TraesCS2D01G492200 chr2A 92.994 785 34 9 2953 3727 724518682 724517909 0.000000e+00 1125.0
6 TraesCS2D01G492200 chr2A 90.704 753 49 8 2493 3229 485200630 485201377 0.000000e+00 983.0
7 TraesCS2D01G492200 chr2A 90.571 753 50 8 2493 3229 485221194 485221941 0.000000e+00 977.0
8 TraesCS2D01G492200 chr2A 90.571 753 50 7 2493 3229 687890764 687891511 0.000000e+00 977.0
9 TraesCS2D01G492200 chr2A 91.443 596 39 7 5143 5733 724516411 724515823 0.000000e+00 808.0
10 TraesCS2D01G492200 chr2A 85.806 620 80 3 4527 5139 96437601 96438219 0.000000e+00 651.0
11 TraesCS2D01G492200 chr2A 96.632 386 10 3 1429 1813 687890385 687890768 6.940000e-179 638.0
12 TraesCS2D01G492200 chr2A 96.114 386 12 3 1429 1813 485200251 485200634 1.500000e-175 627.0
13 TraesCS2D01G492200 chr2A 95.855 386 13 3 1429 1813 485220815 485221198 6.990000e-174 621.0
14 TraesCS2D01G492200 chr2A 91.189 454 29 7 941 1383 687889939 687890392 1.960000e-169 606.0
15 TraesCS2D01G492200 chr2A 90.529 454 32 8 941 1383 485199805 485200258 1.970000e-164 590.0
16 TraesCS2D01G492200 chr2A 89.348 460 37 9 941 1389 485220369 485220827 9.230000e-158 568.0
17 TraesCS2D01G492200 chr2A 86.506 541 35 16 5734 6258 724515453 724514935 1.540000e-155 560.0
18 TraesCS2D01G492200 chr2A 95.324 278 13 0 2625 2902 724518955 724518678 5.840000e-120 442.0
19 TraesCS2D01G492200 chr2A 95.652 207 8 1 1788 1994 724519670 724519465 1.320000e-86 331.0
20 TraesCS2D01G492200 chr2A 95.337 193 6 3 3711 3902 724516596 724516406 2.870000e-78 303.0
21 TraesCS2D01G492200 chr2A 92.788 208 13 2 1987 2192 724519869 724519662 3.720000e-77 300.0
22 TraesCS2D01G492200 chr2A 88.889 72 2 1 6272 6337 724514943 724514872 4.080000e-12 84.2
23 TraesCS2D01G492200 chr3D 91.273 1249 92 10 3903 5151 139988710 139989941 0.000000e+00 1687.0
24 TraesCS2D01G492200 chr7D 91.347 1225 90 10 3903 5124 31478011 31476800 0.000000e+00 1661.0
25 TraesCS2D01G492200 chr7D 89.011 91 8 1 3403 3493 119897077 119896989 1.870000e-20 111.0
26 TraesCS2D01G492200 chr7D 86.517 89 10 1 3402 3490 119896991 119897077 5.240000e-16 97.1
27 TraesCS2D01G492200 chr6B 89.719 1245 100 11 3902 5143 597314540 597313321 0.000000e+00 1565.0
28 TraesCS2D01G492200 chr6B 90.173 753 53 8 2493 3229 95970724 95971471 0.000000e+00 961.0
29 TraesCS2D01G492200 chr6B 84.548 919 94 25 3904 4810 509569133 509570015 0.000000e+00 867.0
30 TraesCS2D01G492200 chr6B 96.632 386 10 3 1429 1813 95970345 95970728 6.940000e-179 638.0
31 TraesCS2D01G492200 chr6B 90.969 454 30 8 941 1383 95969899 95970352 9.100000e-168 601.0
32 TraesCS2D01G492200 chr6B 92.857 308 22 0 4832 5139 509569998 509570305 1.250000e-121 448.0
33 TraesCS2D01G492200 chr6B 88.235 85 8 1 3402 3486 503544573 503544655 4.050000e-17 100.0
34 TraesCS2D01G492200 chr1D 89.120 1250 114 14 3903 5144 172166649 172167884 0.000000e+00 1535.0
35 TraesCS2D01G492200 chr2B 85.561 1489 140 44 3 1450 714783605 714782151 0.000000e+00 1489.0
36 TraesCS2D01G492200 chr2B 91.888 752 41 8 2493 3229 263833246 263833992 0.000000e+00 1033.0
37 TraesCS2D01G492200 chr2B 90.837 753 48 11 2493 3229 772923017 772922270 0.000000e+00 989.0
38 TraesCS2D01G492200 chr2B 91.618 513 22 13 5843 6344 714779454 714778952 0.000000e+00 689.0
39 TraesCS2D01G492200 chr2B 92.070 454 25 8 941 1383 263832423 263832876 4.170000e-176 628.0
40 TraesCS2D01G492200 chr2B 92.018 451 25 8 944 1383 772923831 772923381 1.940000e-174 623.0
41 TraesCS2D01G492200 chr2B 95.596 386 12 4 1429 1813 263832869 263833250 1.170000e-171 614.0
42 TraesCS2D01G492200 chr2B 94.459 379 12 2 1436 1813 772923383 772923013 5.520000e-160 575.0
43 TraesCS2D01G492200 chr2B 82.045 440 52 14 3489 3902 714780692 714780254 3.640000e-92 350.0
44 TraesCS2D01G492200 chr2B 79.644 393 31 21 5143 5510 714780259 714779891 2.960000e-58 237.0
45 TraesCS2D01G492200 chr3B 87.030 1249 119 18 3903 5139 199505774 199506991 0.000000e+00 1369.0
46 TraesCS2D01G492200 chr3B 83.973 443 67 3 4706 5145 787187552 787187111 7.600000e-114 422.0
47 TraesCS2D01G492200 chr4A 86.093 1244 101 24 3903 5139 114125009 114126187 0.000000e+00 1273.0
48 TraesCS2D01G492200 chr4A 88.296 487 45 9 3903 4389 518337329 518336855 1.980000e-159 573.0
49 TraesCS2D01G492200 chr4A 89.130 92 7 2 3403 3494 16469323 16469411 1.870000e-20 111.0
50 TraesCS2D01G492200 chr5B 87.295 732 84 7 3895 4624 460726911 460726187 0.000000e+00 828.0
51 TraesCS2D01G492200 chr7B 86.505 741 66 14 4401 5139 53631541 53632249 0.000000e+00 784.0
52 TraesCS2D01G492200 chr7B 89.139 488 41 9 3902 4389 53630963 53631438 1.180000e-166 597.0
53 TraesCS2D01G492200 chr4B 88.780 615 53 6 4527 5139 253713504 253714104 0.000000e+00 739.0
54 TraesCS2D01G492200 chr4B 87.103 504 42 13 3903 4405 253712981 253713462 3.340000e-152 549.0
55 TraesCS2D01G492200 chr1A 87.202 336 40 2 4711 5044 586509305 586508971 4.640000e-101 379.0
56 TraesCS2D01G492200 chr4D 88.043 92 8 2 3403 3494 450203791 450203703 8.700000e-19 106.0
57 TraesCS2D01G492200 chr6D 87.097 93 7 1 3403 3490 96747893 96747801 4.050000e-17 100.0
58 TraesCS2D01G492200 chr6A 85.714 98 11 3 3404 3499 609314535 609314439 4.050000e-17 100.0
59 TraesCS2D01G492200 chr1B 86.316 95 10 2 3403 3496 493871880 493871972 4.050000e-17 100.0
60 TraesCS2D01G492200 chr1B 83.654 104 13 2 3403 3504 493871965 493871864 1.880000e-15 95.3


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 TraesCS2D01G492200 chr2D 590147727 590154070 6343 True 4120.000000 11716 96.474667 1 6344 3 chr2D.!!$R1 6343
1 TraesCS2D01G492200 chr2A 516091255 516092116 861 False 1186.000000 1186 91.438000 3903 4775 1 chr2A.!!$F2 872
2 TraesCS2D01G492200 chr2A 724514872 724521676 6804 True 806.022222 3301 92.053889 3 6337 9 chr2A.!!$R1 6334
3 TraesCS2D01G492200 chr2A 687889939 687891511 1572 False 740.333333 977 92.797333 941 3229 3 chr2A.!!$F5 2288
4 TraesCS2D01G492200 chr2A 485199805 485201377 1572 False 733.333333 983 92.449000 941 3229 3 chr2A.!!$F3 2288
5 TraesCS2D01G492200 chr2A 485220369 485221941 1572 False 722.000000 977 91.924667 941 3229 3 chr2A.!!$F4 2288
6 TraesCS2D01G492200 chr2A 96437601 96438219 618 False 651.000000 651 85.806000 4527 5139 1 chr2A.!!$F1 612
7 TraesCS2D01G492200 chr3D 139988710 139989941 1231 False 1687.000000 1687 91.273000 3903 5151 1 chr3D.!!$F1 1248
8 TraesCS2D01G492200 chr7D 31476800 31478011 1211 True 1661.000000 1661 91.347000 3903 5124 1 chr7D.!!$R1 1221
9 TraesCS2D01G492200 chr6B 597313321 597314540 1219 True 1565.000000 1565 89.719000 3902 5143 1 chr6B.!!$R1 1241
10 TraesCS2D01G492200 chr6B 95969899 95971471 1572 False 733.333333 961 92.591333 941 3229 3 chr6B.!!$F2 2288
11 TraesCS2D01G492200 chr6B 509569133 509570305 1172 False 657.500000 867 88.702500 3904 5139 2 chr6B.!!$F3 1235
12 TraesCS2D01G492200 chr1D 172166649 172167884 1235 False 1535.000000 1535 89.120000 3903 5144 1 chr1D.!!$F1 1241
13 TraesCS2D01G492200 chr2B 263832423 263833992 1569 False 758.333333 1033 93.184667 941 3229 3 chr2B.!!$F1 2288
14 TraesCS2D01G492200 chr2B 772922270 772923831 1561 True 729.000000 989 92.438000 944 3229 3 chr2B.!!$R2 2285
15 TraesCS2D01G492200 chr2B 714778952 714783605 4653 True 691.250000 1489 84.717000 3 6344 4 chr2B.!!$R1 6341
16 TraesCS2D01G492200 chr3B 199505774 199506991 1217 False 1369.000000 1369 87.030000 3903 5139 1 chr3B.!!$F1 1236
17 TraesCS2D01G492200 chr4A 114125009 114126187 1178 False 1273.000000 1273 86.093000 3903 5139 1 chr4A.!!$F2 1236
18 TraesCS2D01G492200 chr5B 460726187 460726911 724 True 828.000000 828 87.295000 3895 4624 1 chr5B.!!$R1 729
19 TraesCS2D01G492200 chr7B 53630963 53632249 1286 False 690.500000 784 87.822000 3902 5139 2 chr7B.!!$F1 1237
20 TraesCS2D01G492200 chr4B 253712981 253714104 1123 False 644.000000 739 87.941500 3903 5139 2 chr4B.!!$F1 1236

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
117 124 0.033796 ATGTGTTCCAGCCATCCAGG 60.034 55.0 0.00 0.0 41.84 4.45 F
135 142 0.175760 GGTCACTCGAGCCAGCATAA 59.824 55.0 13.61 0.0 33.34 1.90 F
1266 1312 0.178958 ACCCCGCCCACATTTTTGTA 60.179 50.0 0.00 0.0 0.00 2.41 F
1952 2277 0.249676 CTCAGAGTGCATGAGCCTGT 59.750 55.0 2.98 0.0 37.93 4.00 F
2419 2745 2.036475 ACTCATGATCCACGATAGGTGC 59.964 50.0 0.00 0.0 45.62 5.01 F
3273 3839 2.514458 AGTTCCAAAGCATCGGGATT 57.486 45.0 0.00 0.0 0.00 3.01 F
4468 6516 0.742505 GATGGGTACACGATGACGGA 59.257 55.0 0.00 0.0 44.46 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1273 1319 1.027357 GGGATAGACGCACGGTAAGA 58.973 55.000 0.00 0.0 0.00 2.10 R
1328 1385 2.244382 GTGTTCAACACCGCGACG 59.756 61.111 9.76 0.0 43.05 5.12 R
2332 2658 1.066929 GGCGGCATTTTGGAGAACATT 60.067 47.619 3.07 0.0 0.00 2.71 R
3401 3972 1.228533 TTTTGAAACGGCGGGAGTAC 58.771 50.000 13.24 0.0 0.00 2.73 R
3403 3974 2.188062 TATTTTGAAACGGCGGGAGT 57.812 45.000 13.24 0.0 0.00 3.85 R
4533 6584 2.107750 CCGCGCCACTCATCAGAT 59.892 61.111 0.00 0.0 0.00 2.90 R
6107 8773 0.109342 AGGAGGCAGAACTGTGGTTG 59.891 55.000 3.77 0.0 35.58 3.77 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
38 39 6.097412 CAGCATACATATAGGAGATACCAGCA 59.903 42.308 0.00 0.00 42.04 4.41
44 45 8.243961 ACATATAGGAGATACCAGCATATGAC 57.756 38.462 6.97 0.00 38.45 3.06
51 54 8.609483 AGGAGATACCAGCATATGACATTAATT 58.391 33.333 6.97 0.00 42.04 1.40
81 84 2.561478 TTGCTACTTCAGTTCCCACC 57.439 50.000 0.00 0.00 0.00 4.61
85 88 3.181434 TGCTACTTCAGTTCCCACCAAAT 60.181 43.478 0.00 0.00 0.00 2.32
94 97 9.942850 CTTCAGTTCCCACCAAATAAATTTTAT 57.057 29.630 0.00 0.00 0.00 1.40
97 100 9.313118 CAGTTCCCACCAAATAAATTTTATAGC 57.687 33.333 0.00 0.00 0.00 2.97
98 101 9.041354 AGTTCCCACCAAATAAATTTTATAGCA 57.959 29.630 0.00 0.00 0.00 3.49
99 102 9.830975 GTTCCCACCAAATAAATTTTATAGCAT 57.169 29.630 0.00 0.00 0.00 3.79
111 118 3.643199 TTATAGCATGTGTTCCAGCCA 57.357 42.857 0.00 0.00 0.00 4.75
117 124 0.033796 ATGTGTTCCAGCCATCCAGG 60.034 55.000 0.00 0.00 41.84 4.45
121 128 0.678048 GTTCCAGCCATCCAGGTCAC 60.678 60.000 0.00 0.00 40.61 3.67
123 130 1.222936 CCAGCCATCCAGGTCACTC 59.777 63.158 0.00 0.00 40.61 3.51
124 131 1.153489 CAGCCATCCAGGTCACTCG 60.153 63.158 0.00 0.00 40.61 4.18
125 132 1.305297 AGCCATCCAGGTCACTCGA 60.305 57.895 0.00 0.00 40.61 4.04
126 133 1.142748 GCCATCCAGGTCACTCGAG 59.857 63.158 11.84 11.84 40.61 4.04
127 134 1.142748 CCATCCAGGTCACTCGAGC 59.857 63.158 13.61 0.00 40.07 5.03
128 135 1.142748 CATCCAGGTCACTCGAGCC 59.857 63.158 13.61 5.84 40.69 4.70
129 136 1.305297 ATCCAGGTCACTCGAGCCA 60.305 57.895 13.61 0.00 40.69 4.75
130 137 1.326213 ATCCAGGTCACTCGAGCCAG 61.326 60.000 13.61 2.54 40.69 4.85
131 138 2.125753 CAGGTCACTCGAGCCAGC 60.126 66.667 13.61 8.85 40.69 4.85
132 139 2.601666 AGGTCACTCGAGCCAGCA 60.602 61.111 13.61 0.00 40.69 4.41
133 140 1.986757 AGGTCACTCGAGCCAGCAT 60.987 57.895 13.61 0.00 40.69 3.79
134 141 0.684479 AGGTCACTCGAGCCAGCATA 60.684 55.000 13.61 0.00 40.69 3.14
135 142 0.175760 GGTCACTCGAGCCAGCATAA 59.824 55.000 13.61 0.00 33.34 1.90
136 143 1.202580 GGTCACTCGAGCCAGCATAAT 60.203 52.381 13.61 0.00 33.34 1.28
137 144 1.863454 GTCACTCGAGCCAGCATAATG 59.137 52.381 13.61 0.00 0.00 1.90
138 145 1.482182 TCACTCGAGCCAGCATAATGT 59.518 47.619 13.61 0.00 0.00 2.71
140 147 3.132111 TCACTCGAGCCAGCATAATGTAA 59.868 43.478 13.61 0.00 0.00 2.41
146 153 2.360165 AGCCAGCATAATGTAAGCAAGC 59.640 45.455 0.00 0.00 0.00 4.01
147 154 2.099592 GCCAGCATAATGTAAGCAAGCA 59.900 45.455 0.00 0.00 0.00 3.91
152 159 5.287752 CAGCATAATGTAAGCAAGCACAAAG 59.712 40.000 0.00 0.00 0.00 2.77
169 176 5.178067 GCACAAAGCAAATAGCATTTGTTCT 59.822 36.000 17.25 8.57 44.52 3.01
173 180 7.809806 ACAAAGCAAATAGCATTTGTTCTAGTC 59.190 33.333 17.25 5.10 44.52 2.59
175 182 5.582550 GCAAATAGCATTTGTTCTAGTCCC 58.417 41.667 17.25 1.56 44.79 4.46
176 183 5.125417 GCAAATAGCATTTGTTCTAGTCCCA 59.875 40.000 17.25 0.00 44.79 4.37
177 184 6.678900 GCAAATAGCATTTGTTCTAGTCCCAG 60.679 42.308 17.25 0.00 44.79 4.45
178 185 5.700402 ATAGCATTTGTTCTAGTCCCAGT 57.300 39.130 0.00 0.00 0.00 4.00
179 186 4.373156 AGCATTTGTTCTAGTCCCAGTT 57.627 40.909 0.00 0.00 0.00 3.16
180 187 4.327680 AGCATTTGTTCTAGTCCCAGTTC 58.672 43.478 0.00 0.00 0.00 3.01
207 216 5.080337 CCTCCTAGATCACTAGCCAACATA 58.920 45.833 0.00 0.00 43.23 2.29
219 228 9.104965 TCACTAGCCAACATAACATAAATGTAC 57.895 33.333 0.00 0.00 40.80 2.90
224 233 9.109393 AGCCAACATAACATAAATGTACTACTG 57.891 33.333 0.00 0.00 40.80 2.74
225 234 8.889717 GCCAACATAACATAAATGTACTACTGT 58.110 33.333 0.00 0.00 40.80 3.55
291 300 2.831685 AGTTACAGATGACACCGCAA 57.168 45.000 0.00 0.00 0.00 4.85
302 311 0.743688 ACACCGCAAATTGCTTGTGA 59.256 45.000 30.29 0.00 46.63 3.58
304 313 0.317770 ACCGCAAATTGCTTGTGACG 60.318 50.000 16.42 0.00 46.63 4.35
376 385 1.151413 TGGAGAACAGGACCCCTACTT 59.849 52.381 0.00 0.00 29.64 2.24
380 389 1.838073 AACAGGACCCCTACTTGCCG 61.838 60.000 0.00 0.00 29.64 5.69
382 391 3.007323 GGACCCCTACTTGCCGGT 61.007 66.667 1.90 0.00 0.00 5.28
383 392 2.267961 GACCCCTACTTGCCGGTG 59.732 66.667 1.90 0.00 0.00 4.94
384 393 3.971109 GACCCCTACTTGCCGGTGC 62.971 68.421 1.90 0.00 38.26 5.01
385 394 3.717294 CCCCTACTTGCCGGTGCT 61.717 66.667 1.90 0.00 38.71 4.40
387 396 1.600107 CCCTACTTGCCGGTGCTTA 59.400 57.895 1.90 0.00 38.71 3.09
400 409 0.179043 GTGCTTAAGAGGGCTAGGGC 60.179 60.000 6.67 0.00 37.82 5.19
412 421 1.222936 CTAGGGCTGGTGCAGAAGG 59.777 63.158 0.00 0.00 41.91 3.46
415 424 2.743928 GGCTGGTGCAGAAGGACG 60.744 66.667 0.00 0.00 41.91 4.79
458 467 3.072468 TGGCCTAAGGGTCGACGG 61.072 66.667 9.92 5.74 40.80 4.79
462 471 2.783288 CCTAAGGGTCGACGGGAGC 61.783 68.421 9.92 0.00 42.48 4.70
464 473 2.005960 CTAAGGGTCGACGGGAGCAG 62.006 65.000 9.92 0.00 45.03 4.24
467 476 4.803426 GGTCGACGGGAGCAGCAG 62.803 72.222 9.92 0.00 42.75 4.24
531 540 2.306805 CCTAGGGGATGCATATGCTTCA 59.693 50.000 32.54 18.34 44.21 3.02
540 549 1.667236 CATATGCTTCAAGTGGCGGA 58.333 50.000 0.00 0.00 0.00 5.54
580 590 2.070639 AAGCTCCAGGGTTCAGTCC 58.929 57.895 0.00 0.00 0.00 3.85
744 763 3.686726 AGAAGCTTGCAGATAAAAGACGG 59.313 43.478 2.10 0.00 0.00 4.79
752 771 3.190874 CAGATAAAAGACGGAGAGGTGC 58.809 50.000 0.00 0.00 0.00 5.01
755 774 3.591254 AAAGACGGAGAGGTGCGCC 62.591 63.158 8.71 8.71 42.15 6.53
785 804 3.986006 GCCGTCCATATCGCCCGA 61.986 66.667 0.00 0.00 0.00 5.14
786 805 2.970639 CCGTCCATATCGCCCGAT 59.029 61.111 8.34 8.34 38.54 4.18
811 830 1.379443 ATCGGACGGCTACCAGTGA 60.379 57.895 0.00 0.00 0.00 3.41
814 833 1.982938 GGACGGCTACCAGTGACCT 60.983 63.158 0.00 0.00 0.00 3.85
839 858 1.666189 GGTCCAGCGTATTTTGCTCTC 59.334 52.381 0.00 0.00 41.72 3.20
878 897 0.951040 GTCGGCCTCTCAACACCTTG 60.951 60.000 0.00 0.00 0.00 3.61
882 901 1.380302 CCTCTCAACACCTTGGGGG 59.620 63.158 0.00 0.00 41.89 5.40
896 915 3.925470 GGGGTCCCCTGTTAACCA 58.075 61.111 21.13 0.00 41.34 3.67
897 916 1.381463 GGGGTCCCCTGTTAACCAC 59.619 63.158 21.13 0.00 41.34 4.16
898 917 1.138228 GGGGTCCCCTGTTAACCACT 61.138 60.000 21.13 0.00 41.34 4.00
899 918 0.775542 GGGTCCCCTGTTAACCACTT 59.224 55.000 2.48 0.00 34.62 3.16
900 919 1.987368 GGGTCCCCTGTTAACCACTTA 59.013 52.381 2.48 0.00 34.62 2.24
901 920 2.376181 GGGTCCCCTGTTAACCACTTAA 59.624 50.000 2.48 0.00 34.62 1.85
902 921 3.415212 GGTCCCCTGTTAACCACTTAAC 58.585 50.000 2.48 0.00 41.52 2.01
903 922 3.415212 GTCCCCTGTTAACCACTTAACC 58.585 50.000 2.48 0.00 40.76 2.85
904 923 2.376181 TCCCCTGTTAACCACTTAACCC 59.624 50.000 2.48 0.00 40.76 4.11
905 924 2.555892 CCCCTGTTAACCACTTAACCCC 60.556 54.545 2.48 0.00 40.76 4.95
939 958 4.161295 CATCTTCCCCGAGCGCCA 62.161 66.667 2.29 0.00 0.00 5.69
1266 1312 0.178958 ACCCCGCCCACATTTTTGTA 60.179 50.000 0.00 0.00 0.00 2.41
1273 1319 5.415221 CCGCCCACATTTTTGTACAAATAT 58.585 37.500 21.17 18.25 0.00 1.28
1286 1332 4.799949 TGTACAAATATCTTACCGTGCGTC 59.200 41.667 0.00 0.00 0.00 5.19
1306 1353 4.561105 GTCTATCCCCATCTCAATTCGTC 58.439 47.826 0.00 0.00 0.00 4.20
1309 1356 6.015350 GTCTATCCCCATCTCAATTCGTCTTA 60.015 42.308 0.00 0.00 0.00 2.10
1328 1385 6.308282 CGTCTTACTCTTGTGGTGATAAAGAC 59.692 42.308 0.00 0.00 37.83 3.01
1403 1460 7.563188 AGGAAGAAGATAACTGAGATAGAGCAA 59.437 37.037 0.00 0.00 0.00 3.91
1471 1528 7.805071 CAGATTTATTTGTCTGAAACTGTGGAC 59.195 37.037 0.00 0.00 43.50 4.02
1638 1948 6.313658 CCAAAATTTGCTTAGTTTAGATGGGC 59.686 38.462 0.00 0.00 0.00 5.36
1923 2248 3.942130 AACTGCTGACTAAATTTGCCC 57.058 42.857 0.00 0.00 0.00 5.36
1952 2277 0.249676 CTCAGAGTGCATGAGCCTGT 59.750 55.000 2.98 0.00 37.93 4.00
1956 2281 3.054875 TCAGAGTGCATGAGCCTGTTATT 60.055 43.478 0.00 0.00 41.13 1.40
1969 2294 6.072112 AGCCTGTTATTTGTACACTGTTTG 57.928 37.500 0.00 0.00 0.00 2.93
2015 2340 5.198602 AGCCTGTTTGAATTAGATTCCCT 57.801 39.130 0.00 0.00 38.50 4.20
2050 2376 9.832445 TGTCTTCAGTTAAACTAAAGAGAACAT 57.168 29.630 0.00 0.00 33.36 2.71
2126 2452 3.438781 TGCTGACTAAATTTGCCTTACGG 59.561 43.478 0.00 0.00 0.00 4.02
2154 2480 3.054875 TCAGAGTGCATGAGCCTGTTATT 60.055 43.478 0.00 0.00 41.13 1.40
2157 2483 3.424703 AGTGCATGAGCCTGTTATTTGT 58.575 40.909 0.00 0.00 41.13 2.83
2167 2493 6.072112 AGCCTGTTATTTGTACACTGTTTG 57.928 37.500 0.00 0.00 0.00 2.93
2191 2517 7.537715 TGCATCAACACCTACAAATTATCAAG 58.462 34.615 0.00 0.00 0.00 3.02
2192 2518 7.392953 TGCATCAACACCTACAAATTATCAAGA 59.607 33.333 0.00 0.00 0.00 3.02
2193 2519 8.243426 GCATCAACACCTACAAATTATCAAGAA 58.757 33.333 0.00 0.00 0.00 2.52
2194 2520 9.559958 CATCAACACCTACAAATTATCAAGAAC 57.440 33.333 0.00 0.00 0.00 3.01
2195 2521 8.684386 TCAACACCTACAAATTATCAAGAACA 57.316 30.769 0.00 0.00 0.00 3.18
2196 2522 9.295825 TCAACACCTACAAATTATCAAGAACAT 57.704 29.630 0.00 0.00 0.00 2.71
2197 2523 9.912634 CAACACCTACAAATTATCAAGAACATT 57.087 29.630 0.00 0.00 0.00 2.71
2199 2525 9.520515 ACACCTACAAATTATCAAGAACATTCT 57.479 29.630 0.00 0.00 39.74 2.40
2332 2658 3.580895 TCCTGGCATTGACAGTACACTTA 59.419 43.478 18.12 0.00 36.87 2.24
2336 2662 5.312895 TGGCATTGACAGTACACTTAATGT 58.687 37.500 0.00 0.00 46.06 2.71
2340 2666 7.237173 GCATTGACAGTACACTTAATGTTCTC 58.763 38.462 0.00 0.00 43.19 2.87
2349 2675 5.783111 ACACTTAATGTTCTCCAAAATGCC 58.217 37.500 0.00 0.00 38.98 4.40
2387 2713 9.631257 TTTGATATTTAATCTCTGCCAAGATGA 57.369 29.630 0.00 0.00 36.14 2.92
2389 2715 9.803507 TGATATTTAATCTCTGCCAAGATGATT 57.196 29.630 0.00 0.00 36.14 2.57
2419 2745 2.036475 ACTCATGATCCACGATAGGTGC 59.964 50.000 0.00 0.00 45.62 5.01
2489 2815 5.230306 CGAATTCTGAATTACCTCGAGACAC 59.770 44.000 15.71 0.00 0.00 3.67
2570 2897 6.663944 CCTGTTTGGTATTGACTAGCTAAC 57.336 41.667 0.00 0.93 41.15 2.34
2621 2950 9.555727 CATTCGAATTAAGGTCCCTATCTTAAA 57.444 33.333 8.21 0.00 40.74 1.52
2732 3146 8.362464 TGTCTCTAAGATGTTACACTGGTATT 57.638 34.615 0.00 0.00 0.00 1.89
2787 3201 4.008330 CTCCATGAAGCTTCAGTCATGTT 58.992 43.478 31.14 12.52 46.41 2.71
2793 3207 6.882610 TGAAGCTTCAGTCATGTTGTTATT 57.117 33.333 25.16 0.00 32.50 1.40
2844 3258 4.036852 CCTGTCTGATATAACGAGAGCACA 59.963 45.833 0.00 0.00 0.00 4.57
2930 3344 4.553330 TTTTCATCCGAGAAAGGCTACT 57.447 40.909 0.00 0.00 38.60 2.57
2931 3345 3.526931 TTCATCCGAGAAAGGCTACTG 57.473 47.619 0.00 0.00 0.00 2.74
2951 3365 8.932945 CTACTGTGTGTAGTATGATGATTGTT 57.067 34.615 0.00 0.00 42.68 2.83
3198 3759 3.995199 GCTGTATAATAGCTGACAGGCA 58.005 45.455 4.26 0.00 39.76 4.75
3268 3830 7.015226 TGAATTATGTAGTTCCAAAGCATCG 57.985 36.000 0.00 0.00 0.00 3.84
3273 3839 2.514458 AGTTCCAAAGCATCGGGATT 57.486 45.000 0.00 0.00 0.00 3.01
3296 3862 5.940192 TGGTTCTTAGCACAAGTTGTATG 57.060 39.130 8.49 0.00 0.00 2.39
3401 3972 8.879342 ATCCATTTCTCTATTAAGAACTGACG 57.121 34.615 5.79 0.00 37.86 4.35
3403 3974 8.963725 TCCATTTCTCTATTAAGAACTGACGTA 58.036 33.333 5.79 0.00 37.86 3.57
3409 3980 3.837213 TTAAGAACTGACGTACTCCCG 57.163 47.619 0.00 0.00 0.00 5.14
3444 4015 5.883503 AAGTGTCGTGGTTTTAGTTCAAA 57.116 34.783 0.00 0.00 0.00 2.69
3445 4016 5.883503 AGTGTCGTGGTTTTAGTTCAAAA 57.116 34.783 0.00 0.00 33.66 2.44
3446 4017 6.256912 AGTGTCGTGGTTTTAGTTCAAAAA 57.743 33.333 0.00 0.00 37.85 1.94
3447 4018 6.859017 AGTGTCGTGGTTTTAGTTCAAAAAT 58.141 32.000 0.00 0.00 37.85 1.82
3448 4019 7.317390 AGTGTCGTGGTTTTAGTTCAAAAATT 58.683 30.769 0.00 0.00 37.85 1.82
3449 4020 7.815549 AGTGTCGTGGTTTTAGTTCAAAAATTT 59.184 29.630 0.00 0.00 37.85 1.82
3450 4021 7.895767 GTGTCGTGGTTTTAGTTCAAAAATTTG 59.104 33.333 0.00 0.00 37.85 2.32
3451 4022 7.813148 TGTCGTGGTTTTAGTTCAAAAATTTGA 59.187 29.630 4.52 4.52 44.78 2.69
3471 4042 9.965824 AATTTGAACTAAAACCATGACACTTAG 57.034 29.630 0.00 0.00 0.00 2.18
3479 4050 9.965824 CTAAAACCATGACACTTAGTTTGAAAT 57.034 29.630 0.00 0.00 31.39 2.17
3486 4057 5.061721 ACACTTAGTTTGAAATGGAGGGT 57.938 39.130 0.00 0.00 0.00 4.34
3487 4058 4.827284 ACACTTAGTTTGAAATGGAGGGTG 59.173 41.667 0.00 0.00 0.00 4.61
3527 4100 9.565213 CATCTCAACCTTTTCTTTGTCAATATC 57.435 33.333 0.00 0.00 0.00 1.63
3564 4140 5.952347 GGATACCAAGAATTTCCAAACTCCT 59.048 40.000 0.00 0.00 0.00 3.69
3893 5818 9.628500 ATTACCAAATAAGATAGTTTGACCTCC 57.372 33.333 0.00 0.00 37.48 4.30
3895 5820 6.884836 ACCAAATAAGATAGTTTGACCTCCAC 59.115 38.462 0.00 0.00 37.48 4.02
3896 5821 7.112779 CCAAATAAGATAGTTTGACCTCCACT 58.887 38.462 0.00 0.00 37.48 4.00
3897 5822 7.066284 CCAAATAAGATAGTTTGACCTCCACTG 59.934 40.741 0.00 0.00 37.48 3.66
3898 5823 3.618690 AGATAGTTTGACCTCCACTGC 57.381 47.619 0.00 0.00 0.00 4.40
3899 5824 2.906389 AGATAGTTTGACCTCCACTGCA 59.094 45.455 0.00 0.00 0.00 4.41
3900 5825 3.521126 AGATAGTTTGACCTCCACTGCAT 59.479 43.478 0.00 0.00 0.00 3.96
4011 5936 7.817478 TCAGTTTATATATATGTCAGCCCAACG 59.183 37.037 5.44 0.00 0.00 4.10
4056 5982 3.387699 CCACCCAAATTGAACTGAAACCT 59.612 43.478 0.00 0.00 0.00 3.50
4162 6092 0.902531 CCCCGCCTCTTCTTCAACTA 59.097 55.000 0.00 0.00 0.00 2.24
4181 6126 2.797278 CCTTATCACCGCCGCCTCT 61.797 63.158 0.00 0.00 0.00 3.69
4468 6516 0.742505 GATGGGTACACGATGACGGA 59.257 55.000 0.00 0.00 44.46 4.69
4912 7028 0.826715 TGAGAAGAATGGGCTCGAGG 59.173 55.000 15.58 0.00 0.00 4.63
4918 7034 1.906574 AGAATGGGCTCGAGGTTTACA 59.093 47.619 15.58 0.00 0.00 2.41
4984 7100 1.691196 TTTTGGAGCTGGACCTGTTG 58.309 50.000 0.00 0.00 0.00 3.33
5169 7291 6.770746 TCCACTTACAGAGATAGTGTTACC 57.229 41.667 0.00 0.00 38.04 2.85
5187 7309 5.069119 TGTTACCAGATATGTCAGGTAGCAG 59.931 44.000 20.57 0.00 45.78 4.24
5238 7361 1.620819 TGACTCTGTTTCTGCCCTCTC 59.379 52.381 0.00 0.00 0.00 3.20
5277 7400 2.880879 CCGCACGTCATGTCGAGG 60.881 66.667 19.02 13.84 35.56 4.63
5280 7403 2.094659 GCACGTCATGTCGAGGGTG 61.095 63.158 19.02 7.71 34.07 4.61
5336 7459 1.899437 TTCCACGGGCTTAGCAGGAG 61.899 60.000 6.53 0.00 0.00 3.69
5360 7483 2.009774 GTGATCCCACCTCGTGATTTG 58.990 52.381 0.00 0.00 37.33 2.32
5366 7489 1.660607 CCACCTCGTGATTTGTGATCG 59.339 52.381 0.00 0.00 35.23 3.69
5368 7491 1.548719 ACCTCGTGATTTGTGATCGGA 59.451 47.619 0.00 0.00 0.00 4.55
5378 7502 0.250234 TGTGATCGGAGAAGCCCTTG 59.750 55.000 0.00 0.00 43.58 3.61
5380 7504 1.884926 GATCGGAGAAGCCCTTGCG 60.885 63.158 0.00 0.00 43.58 4.85
5381 7505 2.298158 GATCGGAGAAGCCCTTGCGA 62.298 60.000 0.00 0.00 43.58 5.10
5402 7550 0.460987 CAGTGGGGAGCGATCACTTC 60.461 60.000 1.57 0.00 39.43 3.01
5404 7552 1.612146 TGGGGAGCGATCACTTCCA 60.612 57.895 10.33 6.54 37.00 3.53
5532 7706 0.940991 GCGCTTGGGAAAAGCAGTTG 60.941 55.000 0.00 0.00 43.15 3.16
5589 7766 5.761234 TGTTGTAAATTCGAAGCTACTGGTT 59.239 36.000 16.22 0.00 36.51 3.67
5619 7805 0.469705 ATTTGCCAGTGGGAAGTGCA 60.470 50.000 16.28 1.88 33.87 4.57
5652 7838 8.752005 ATATGTTGTAATGCACTTCAGGTTAT 57.248 30.769 0.00 0.00 0.00 1.89
5698 7885 4.399618 CAGCTAGCTCTGGTAAACTACTGA 59.600 45.833 16.15 0.00 0.00 3.41
5730 7917 3.319137 TTGGTTCAGAGGATCAAGTCG 57.681 47.619 0.00 0.00 37.82 4.18
5788 8344 2.287188 CGCATAGTAATTGCAGCCCTTG 60.287 50.000 0.00 0.00 40.14 3.61
5799 8355 1.813513 CAGCCCTTGGTGTTCTACAG 58.186 55.000 0.00 0.00 35.25 2.74
5814 8466 3.684908 TCTACAGCAGCCAATTAAGCAA 58.315 40.909 2.79 0.00 0.00 3.91
5815 8467 4.078537 TCTACAGCAGCCAATTAAGCAAA 58.921 39.130 2.79 0.00 0.00 3.68
5816 8468 3.967332 ACAGCAGCCAATTAAGCAAAT 57.033 38.095 2.79 0.00 0.00 2.32
5888 8540 7.657354 GGTTTGTAAGATGAAAATTTCAAGCCT 59.343 33.333 12.75 7.51 43.95 4.58
5995 8648 3.365265 CCCAGCAACTCAACCGGC 61.365 66.667 0.00 0.00 0.00 6.13
6038 8703 2.559668 ACACACATCCCAAATGCTGAAG 59.440 45.455 0.00 0.00 0.00 3.02
6069 8734 2.300433 GGCATGCATGACTGTAATGGA 58.700 47.619 30.64 4.51 31.49 3.41
6107 8773 0.543749 AGTATGCCCCAGCTGAAGAC 59.456 55.000 17.39 5.35 40.80 3.01
6113 8779 0.890996 CCCCAGCTGAAGACAACCAC 60.891 60.000 17.39 0.00 0.00 4.16
6115 8781 1.233019 CCAGCTGAAGACAACCACAG 58.767 55.000 17.39 0.00 0.00 3.66
6119 8785 2.171448 AGCTGAAGACAACCACAGTTCT 59.829 45.455 0.00 0.00 32.45 3.01
6120 8786 2.289002 GCTGAAGACAACCACAGTTCTG 59.711 50.000 0.00 0.00 32.45 3.02
6121 8787 2.288666 TGAAGACAACCACAGTTCTGC 58.711 47.619 0.00 0.00 32.45 4.26
6122 8788 1.604278 GAAGACAACCACAGTTCTGCC 59.396 52.381 0.00 0.00 32.45 4.85
6123 8789 0.839946 AGACAACCACAGTTCTGCCT 59.160 50.000 0.00 0.00 32.45 4.75
6124 8790 1.202698 AGACAACCACAGTTCTGCCTC 60.203 52.381 0.00 0.00 32.45 4.70
6125 8791 0.179018 ACAACCACAGTTCTGCCTCC 60.179 55.000 0.00 0.00 32.45 4.30
6126 8792 0.109342 CAACCACAGTTCTGCCTCCT 59.891 55.000 0.00 0.00 32.45 3.69
6127 8793 0.398318 AACCACAGTTCTGCCTCCTC 59.602 55.000 0.00 0.00 0.00 3.71
6129 8795 1.197430 CCACAGTTCTGCCTCCTCCT 61.197 60.000 0.00 0.00 0.00 3.69
6130 8796 0.248843 CACAGTTCTGCCTCCTCCTC 59.751 60.000 0.00 0.00 0.00 3.71
6131 8797 0.178921 ACAGTTCTGCCTCCTCCTCA 60.179 55.000 0.00 0.00 0.00 3.86
6132 8798 1.202330 CAGTTCTGCCTCCTCCTCAT 58.798 55.000 0.00 0.00 0.00 2.90
6134 8800 0.908198 GTTCTGCCTCCTCCTCATGT 59.092 55.000 0.00 0.00 0.00 3.21
6135 8801 0.907486 TTCTGCCTCCTCCTCATGTG 59.093 55.000 0.00 0.00 0.00 3.21
6136 8802 0.041684 TCTGCCTCCTCCTCATGTGA 59.958 55.000 0.00 0.00 0.00 3.58
6137 8803 0.907486 CTGCCTCCTCCTCATGTGAA 59.093 55.000 0.00 0.00 0.00 3.18
6143 8809 3.433314 CCTCCTCCTCATGTGAAATCAGG 60.433 52.174 0.00 0.00 0.00 3.86
6145 8811 2.092538 CCTCCTCATGTGAAATCAGGCT 60.093 50.000 0.00 0.00 0.00 4.58
6196 8866 0.679505 CACCAACGGGAGAGACAAGA 59.320 55.000 0.00 0.00 38.05 3.02
6197 8867 0.680061 ACCAACGGGAGAGACAAGAC 59.320 55.000 0.00 0.00 38.05 3.01
6198 8868 0.679505 CCAACGGGAGAGACAAGACA 59.320 55.000 0.00 0.00 35.59 3.41
6199 8869 1.070134 CCAACGGGAGAGACAAGACAA 59.930 52.381 0.00 0.00 35.59 3.18
6200 8870 2.408050 CAACGGGAGAGACAAGACAAG 58.592 52.381 0.00 0.00 0.00 3.16
6262 8932 4.369182 GCTAGTACTCACACACACTTTGT 58.631 43.478 0.00 0.00 39.97 2.83
6266 8936 1.280710 ACTCACACACACTTTGTCCCA 59.719 47.619 0.00 0.00 35.67 4.37
6280 8952 2.124362 CCCAGGCACACACACACA 60.124 61.111 0.00 0.00 0.00 3.72
6294 8966 2.099405 ACACACACTTTGGACTTTGGG 58.901 47.619 0.00 0.00 0.00 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 9.874215 CAGTGAAGTAATTAATGTCATATGCTG 57.126 33.333 0.00 0.00 0.00 4.41
42 43 9.922305 GTAGCAATCAGTGAAGTAATTAATGTC 57.078 33.333 0.00 0.00 0.00 3.06
43 44 9.672673 AGTAGCAATCAGTGAAGTAATTAATGT 57.327 29.630 0.00 0.00 0.00 2.71
85 88 7.123397 TGGCTGGAACACATGCTATAAAATTTA 59.877 33.333 0.00 0.00 0.00 1.40
94 97 1.408683 GGATGGCTGGAACACATGCTA 60.409 52.381 0.00 0.00 32.14 3.49
96 99 0.966875 TGGATGGCTGGAACACATGC 60.967 55.000 0.00 0.00 34.63 4.06
97 100 1.100510 CTGGATGGCTGGAACACATG 58.899 55.000 0.00 0.00 0.00 3.21
98 101 0.033796 CCTGGATGGCTGGAACACAT 60.034 55.000 0.00 0.00 0.00 3.21
99 102 1.379916 CCTGGATGGCTGGAACACA 59.620 57.895 0.00 0.00 0.00 3.72
111 118 1.305297 TGGCTCGAGTGACCTGGAT 60.305 57.895 15.13 0.00 0.00 3.41
117 124 1.863454 CATTATGCTGGCTCGAGTGAC 59.137 52.381 15.13 5.65 0.00 3.67
121 128 2.478134 GCTTACATTATGCTGGCTCGAG 59.522 50.000 8.45 8.45 0.00 4.04
123 130 2.212652 TGCTTACATTATGCTGGCTCG 58.787 47.619 0.00 0.00 0.00 5.03
124 131 3.549625 GCTTGCTTACATTATGCTGGCTC 60.550 47.826 0.00 0.00 0.00 4.70
125 132 2.360165 GCTTGCTTACATTATGCTGGCT 59.640 45.455 0.00 0.00 0.00 4.75
126 133 2.099592 TGCTTGCTTACATTATGCTGGC 59.900 45.455 0.00 0.00 0.00 4.85
127 134 3.129113 TGTGCTTGCTTACATTATGCTGG 59.871 43.478 0.00 0.00 0.00 4.85
128 135 4.359971 TGTGCTTGCTTACATTATGCTG 57.640 40.909 0.00 0.00 0.00 4.41
129 136 5.389859 TTTGTGCTTGCTTACATTATGCT 57.610 34.783 0.00 0.00 0.00 3.79
130 137 4.032104 GCTTTGTGCTTGCTTACATTATGC 59.968 41.667 0.00 0.00 38.95 3.14
131 138 5.162794 TGCTTTGTGCTTGCTTACATTATG 58.837 37.500 0.00 0.00 43.37 1.90
132 139 5.389859 TGCTTTGTGCTTGCTTACATTAT 57.610 34.783 0.00 0.00 43.37 1.28
133 140 4.844998 TGCTTTGTGCTTGCTTACATTA 57.155 36.364 0.00 0.00 43.37 1.90
134 141 3.731652 TGCTTTGTGCTTGCTTACATT 57.268 38.095 0.00 0.00 43.37 2.71
135 142 3.731652 TTGCTTTGTGCTTGCTTACAT 57.268 38.095 0.00 0.00 43.37 2.29
136 143 3.516981 TTTGCTTTGTGCTTGCTTACA 57.483 38.095 0.00 0.00 43.37 2.41
137 144 4.090498 GCTATTTGCTTTGTGCTTGCTTAC 59.910 41.667 0.00 0.00 43.37 2.34
138 145 4.236935 GCTATTTGCTTTGTGCTTGCTTA 58.763 39.130 0.00 0.00 43.37 3.09
140 147 2.036217 TGCTATTTGCTTTGTGCTTGCT 59.964 40.909 0.00 0.00 43.37 3.91
146 153 6.774354 AGAACAAATGCTATTTGCTTTGTG 57.226 33.333 16.55 8.83 44.27 3.33
147 154 7.661040 ACTAGAACAAATGCTATTTGCTTTGT 58.339 30.769 16.55 11.59 45.51 2.83
152 159 5.125417 TGGGACTAGAACAAATGCTATTTGC 59.875 40.000 16.55 6.42 43.25 3.68
159 166 3.440522 GGAACTGGGACTAGAACAAATGC 59.559 47.826 0.00 0.00 0.00 3.56
163 170 2.038557 GCTGGAACTGGGACTAGAACAA 59.961 50.000 0.00 0.00 0.00 2.83
165 172 1.066071 GGCTGGAACTGGGACTAGAAC 60.066 57.143 0.00 0.00 0.00 3.01
169 176 0.617820 GGAGGCTGGAACTGGGACTA 60.618 60.000 0.00 0.00 0.00 2.59
173 180 0.325671 TCTAGGAGGCTGGAACTGGG 60.326 60.000 0.00 0.00 0.00 4.45
174 181 1.691434 GATCTAGGAGGCTGGAACTGG 59.309 57.143 0.00 0.00 0.00 4.00
175 182 2.102252 GTGATCTAGGAGGCTGGAACTG 59.898 54.545 0.00 0.00 0.00 3.16
176 183 2.023501 AGTGATCTAGGAGGCTGGAACT 60.024 50.000 0.00 0.00 0.00 3.01
177 184 2.393646 AGTGATCTAGGAGGCTGGAAC 58.606 52.381 0.00 0.00 0.00 3.62
178 185 2.856760 AGTGATCTAGGAGGCTGGAA 57.143 50.000 0.00 0.00 0.00 3.53
179 186 2.489985 GCTAGTGATCTAGGAGGCTGGA 60.490 54.545 0.00 0.00 42.66 3.86
180 187 1.892474 GCTAGTGATCTAGGAGGCTGG 59.108 57.143 0.00 0.00 42.66 4.85
228 237 8.412220 AGGTTTAGGGGGCTATAATACTGTATA 58.588 37.037 0.00 0.00 0.00 1.47
232 241 5.785940 AGAGGTTTAGGGGGCTATAATACTG 59.214 44.000 0.00 0.00 0.00 2.74
233 242 5.990943 AGAGGTTTAGGGGGCTATAATACT 58.009 41.667 0.00 0.00 0.00 2.12
234 243 5.105432 CGAGAGGTTTAGGGGGCTATAATAC 60.105 48.000 0.00 0.00 0.00 1.89
235 244 5.021458 CGAGAGGTTTAGGGGGCTATAATA 58.979 45.833 0.00 0.00 0.00 0.98
291 300 2.425312 TGAAACACCGTCACAAGCAATT 59.575 40.909 0.00 0.00 0.00 2.32
302 311 0.596341 GCCGCAAATTGAAACACCGT 60.596 50.000 0.00 0.00 0.00 4.83
304 313 0.249657 TGGCCGCAAATTGAAACACC 60.250 50.000 0.00 0.00 0.00 4.16
376 385 2.668632 CCCTCTTAAGCACCGGCA 59.331 61.111 0.00 0.00 44.61 5.69
380 389 0.470341 CCCTAGCCCTCTTAAGCACC 59.530 60.000 0.00 0.00 0.00 5.01
382 391 0.326618 AGCCCTAGCCCTCTTAAGCA 60.327 55.000 0.00 0.00 41.25 3.91
383 392 0.107643 CAGCCCTAGCCCTCTTAAGC 59.892 60.000 0.00 0.00 41.25 3.09
384 393 0.761802 CCAGCCCTAGCCCTCTTAAG 59.238 60.000 0.00 0.00 41.25 1.85
385 394 0.044244 ACCAGCCCTAGCCCTCTTAA 59.956 55.000 0.00 0.00 41.25 1.85
387 396 1.997874 CACCAGCCCTAGCCCTCTT 60.998 63.158 0.00 0.00 41.25 2.85
400 409 3.114616 CGCGTCCTTCTGCACCAG 61.115 66.667 0.00 0.00 0.00 4.00
419 428 4.748144 CCAGAGCTTGGGGGTGGC 62.748 72.222 6.96 0.00 43.75 5.01
439 448 2.348888 CGTCGACCCTTAGGCCAGT 61.349 63.158 10.58 0.00 36.11 4.00
458 467 2.749441 GCTTGTCCCTGCTGCTCC 60.749 66.667 0.00 0.00 0.00 4.70
531 540 4.324991 GGTCCCGTTCCGCCACTT 62.325 66.667 0.00 0.00 0.00 3.16
540 549 3.117246 TCTCCTGTATCTATGGTCCCGTT 60.117 47.826 0.00 0.00 0.00 4.44
576 586 3.690745 CGAAGGTACGTGGGGACT 58.309 61.111 0.00 0.00 0.00 3.85
656 674 1.080907 TCTCGTCGACGTCGTCTCT 60.081 57.895 34.40 0.00 40.80 3.10
744 763 2.887568 CATCGTGGCGCACCTCTC 60.888 66.667 10.83 0.00 36.63 3.20
827 846 2.424956 CAGCCCAAGGAGAGCAAAATAC 59.575 50.000 0.00 0.00 0.00 1.89
882 901 3.415212 GGTTAAGTGGTTAACAGGGGAC 58.585 50.000 8.10 0.00 46.87 4.46
894 913 1.985895 ACTGGAGAAGGGGTTAAGTGG 59.014 52.381 0.00 0.00 0.00 4.00
896 915 1.985895 CCACTGGAGAAGGGGTTAAGT 59.014 52.381 0.00 0.00 45.57 2.24
897 916 2.789409 CCACTGGAGAAGGGGTTAAG 57.211 55.000 0.00 0.00 45.57 1.85
903 922 2.352805 GGTGCCACTGGAGAAGGG 59.647 66.667 0.00 0.00 0.00 3.95
904 923 2.046892 CGGTGCCACTGGAGAAGG 60.047 66.667 0.00 0.00 0.00 3.46
905 924 2.743928 GCGGTGCCACTGGAGAAG 60.744 66.667 5.69 0.00 0.00 2.85
1017 1063 2.754658 TCCTCCTCGGCCTTCGAC 60.755 66.667 0.00 0.00 43.74 4.20
1266 1312 4.119442 AGACGCACGGTAAGATATTTGT 57.881 40.909 0.00 0.00 0.00 2.83
1273 1319 1.027357 GGGATAGACGCACGGTAAGA 58.973 55.000 0.00 0.00 0.00 2.10
1286 1332 4.881019 AGACGAATTGAGATGGGGATAG 57.119 45.455 0.00 0.00 0.00 2.08
1306 1353 6.157211 ACGTCTTTATCACCACAAGAGTAAG 58.843 40.000 0.00 0.00 0.00 2.34
1309 1356 4.557205 GACGTCTTTATCACCACAAGAGT 58.443 43.478 8.70 0.00 0.00 3.24
1328 1385 2.244382 GTGTTCAACACCGCGACG 59.756 61.111 9.76 0.00 43.05 5.12
1638 1948 7.155328 ACCCTCAGCTTATTTAGATAATCACG 58.845 38.462 0.00 0.00 0.00 4.35
1895 2220 7.436376 GCAAATTTAGTCAGCAGTTTCTTTCTT 59.564 33.333 0.00 0.00 0.00 2.52
1898 2223 5.985530 GGCAAATTTAGTCAGCAGTTTCTTT 59.014 36.000 0.00 0.00 0.00 2.52
1923 2248 6.006759 TCATGCACTCTGAGATAATCGTAG 57.993 41.667 12.44 0.00 0.00 3.51
1952 2277 7.433719 GTGTTGATGCAAACAGTGTACAAATAA 59.566 33.333 4.20 0.00 40.60 1.40
1956 2281 4.439426 GGTGTTGATGCAAACAGTGTACAA 60.439 41.667 4.20 0.00 40.60 2.41
1969 2294 7.009540 GCTTGAATAATTTGTAGGTGTTGATGC 59.990 37.037 0.00 0.00 0.00 3.91
2012 2337 8.718734 GTTTAACTGAAGACACTAATACAAGGG 58.281 37.037 0.00 0.00 0.00 3.95
2094 2420 6.920210 GCAAATTTAGTCAGCAGTTTCTTTCT 59.080 34.615 0.00 0.00 0.00 2.52
2126 2452 3.129871 GGCTCATGCACTCTGAGATAAC 58.870 50.000 17.93 2.17 42.22 1.89
2154 2480 4.439426 GGTGTTGATGCAAACAGTGTACAA 60.439 41.667 4.20 0.00 40.60 2.41
2157 2483 3.550820 AGGTGTTGATGCAAACAGTGTA 58.449 40.909 4.20 0.00 40.60 2.90
2167 2493 7.761409 TCTTGATAATTTGTAGGTGTTGATGC 58.239 34.615 0.00 0.00 0.00 3.91
2193 2519 9.547279 AGAAAATGGGGTCTTAATTTAGAATGT 57.453 29.630 0.00 0.00 0.00 2.71
2194 2520 9.807649 CAGAAAATGGGGTCTTAATTTAGAATG 57.192 33.333 0.00 0.00 0.00 2.67
2195 2521 8.981659 CCAGAAAATGGGGTCTTAATTTAGAAT 58.018 33.333 0.00 0.00 46.36 2.40
2196 2522 8.361169 CCAGAAAATGGGGTCTTAATTTAGAA 57.639 34.615 0.00 0.00 46.36 2.10
2197 2523 7.954666 CCAGAAAATGGGGTCTTAATTTAGA 57.045 36.000 0.00 0.00 46.36 2.10
2332 2658 1.066929 GGCGGCATTTTGGAGAACATT 60.067 47.619 3.07 0.00 0.00 2.71
2336 2662 1.067000 CATTGGCGGCATTTTGGAGAA 60.067 47.619 14.32 0.00 0.00 2.87
2340 2666 2.101249 AGATACATTGGCGGCATTTTGG 59.899 45.455 14.32 3.35 0.00 3.28
2378 2704 4.197750 AGTGTCTGATCAATCATCTTGGC 58.802 43.478 0.00 0.00 36.02 4.52
2382 2708 6.481434 TCATGAGTGTCTGATCAATCATCT 57.519 37.500 15.23 0.29 45.65 2.90
2387 2713 5.366460 GTGGATCATGAGTGTCTGATCAAT 58.634 41.667 12.93 0.00 46.22 2.57
2389 2715 3.181483 CGTGGATCATGAGTGTCTGATCA 60.181 47.826 12.93 0.00 46.22 2.92
2390 2716 3.067320 TCGTGGATCATGAGTGTCTGATC 59.933 47.826 0.09 4.36 44.54 2.92
2410 2736 2.549064 TTGGATCATGGCACCTATCG 57.451 50.000 0.00 0.00 0.00 2.92
2419 2745 4.891756 ACCTTCAGCTTATTTGGATCATGG 59.108 41.667 0.00 0.00 0.00 3.66
2568 2895 5.347620 TGACTAACCTTGTGTACACAGTT 57.652 39.130 26.97 26.97 42.94 3.16
2570 2897 6.044512 GTTTGACTAACCTTGTGTACACAG 57.955 41.667 26.52 19.11 42.94 3.66
2623 3035 9.656323 TTCTCCCTAGCTTAACTGAAATAGATA 57.344 33.333 0.00 0.00 0.00 1.98
2643 3056 8.608844 ACAATCTTCGAACATTATATTCTCCC 57.391 34.615 0.00 0.00 0.00 4.30
2708 3121 8.688151 AGAATACCAGTGTAACATCTTAGAGAC 58.312 37.037 0.00 0.00 41.43 3.36
2815 3229 5.985530 TCTCGTTATATCAGACAGGCAAATG 59.014 40.000 0.00 0.00 0.00 2.32
2844 3258 1.678101 GCCAAGAACTCTTTGCAGTGT 59.322 47.619 9.91 0.00 42.26 3.55
2913 3327 2.093973 ACACAGTAGCCTTTCTCGGATG 60.094 50.000 0.00 0.00 0.00 3.51
2914 3328 2.093973 CACACAGTAGCCTTTCTCGGAT 60.094 50.000 0.00 0.00 0.00 4.18
2930 3344 6.128309 GCACAACAATCATCATACTACACACA 60.128 38.462 0.00 0.00 0.00 3.72
2931 3345 6.092670 AGCACAACAATCATCATACTACACAC 59.907 38.462 0.00 0.00 0.00 3.82
3040 3468 5.077564 ACAGAACTCATATATGGGCTCGTA 58.922 41.667 12.75 0.00 0.00 3.43
3086 3548 8.839343 GGTAGGATCTCTACTAGTTTTACACTC 58.161 40.741 0.00 0.00 45.78 3.51
3192 3753 3.299503 GGGGAATTCAATACATGCCTGT 58.700 45.455 7.93 0.00 39.49 4.00
3198 3759 5.338300 GGCACTTTTGGGGAATTCAATACAT 60.338 40.000 7.93 0.00 0.00 2.29
3268 3830 3.826729 ACTTGTGCTAAGAACCAAATCCC 59.173 43.478 8.05 0.00 0.00 3.85
3273 3839 5.825679 ACATACAACTTGTGCTAAGAACCAA 59.174 36.000 4.57 0.00 0.00 3.67
3296 3862 5.551760 AATGTTGCACATGTAGCTTAGAC 57.448 39.130 17.30 12.19 37.97 2.59
3401 3972 1.228533 TTTTGAAACGGCGGGAGTAC 58.771 50.000 13.24 0.00 0.00 2.73
3403 3974 2.188062 TATTTTGAAACGGCGGGAGT 57.812 45.000 13.24 0.00 0.00 3.85
3409 3980 3.662186 CACGACACTTATTTTGAAACGGC 59.338 43.478 0.00 0.00 0.00 5.68
3445 4016 9.965824 CTAAGTGTCATGGTTTTAGTTCAAATT 57.034 29.630 0.00 0.00 0.00 1.82
3446 4017 9.131791 ACTAAGTGTCATGGTTTTAGTTCAAAT 57.868 29.630 0.00 0.00 32.30 2.32
3447 4018 8.514330 ACTAAGTGTCATGGTTTTAGTTCAAA 57.486 30.769 0.00 0.00 32.30 2.69
3448 4019 8.514330 AACTAAGTGTCATGGTTTTAGTTCAA 57.486 30.769 14.31 0.00 39.19 2.69
3449 4020 8.402472 CAAACTAAGTGTCATGGTTTTAGTTCA 58.598 33.333 17.61 0.00 41.27 3.18
3450 4021 8.617809 TCAAACTAAGTGTCATGGTTTTAGTTC 58.382 33.333 17.61 0.00 41.27 3.01
3451 4022 8.514330 TCAAACTAAGTGTCATGGTTTTAGTT 57.486 30.769 14.31 14.31 42.92 2.24
3471 4042 5.784578 AAAGTACACCCTCCATTTCAAAC 57.215 39.130 0.00 0.00 0.00 2.93
3479 4050 3.761897 CCATGAAAAAGTACACCCTCCA 58.238 45.455 0.00 0.00 0.00 3.86
3486 4057 5.048083 GGTTGAGATGCCATGAAAAAGTACA 60.048 40.000 0.00 0.00 0.00 2.90
3487 4058 5.183904 AGGTTGAGATGCCATGAAAAAGTAC 59.816 40.000 0.00 0.00 0.00 2.73
3527 4100 7.938140 TTCTTGGTATCCTTAACAAATGGAG 57.062 36.000 0.00 0.00 34.66 3.86
3564 4140 7.827236 CCTGGGTCAAACATTAATACTTACAGA 59.173 37.037 0.00 0.00 0.00 3.41
3576 4152 2.380064 TGCTTCCTGGGTCAAACATT 57.620 45.000 0.00 0.00 0.00 2.71
3757 5672 2.661718 TGTTCCCCAAAGAGGTTTCAC 58.338 47.619 0.00 0.00 34.66 3.18
3834 5759 5.004448 ACTAGGCCAACTTAAGAAAGAAGC 58.996 41.667 10.09 3.13 36.50 3.86
3893 5818 7.375106 ACTTTTCTCAGATTTAGATGCAGTG 57.625 36.000 0.00 0.00 0.00 3.66
3895 5820 8.509690 TCAAACTTTTCTCAGATTTAGATGCAG 58.490 33.333 0.00 0.00 0.00 4.41
3896 5821 8.394971 TCAAACTTTTCTCAGATTTAGATGCA 57.605 30.769 0.00 0.00 0.00 3.96
3897 5822 8.725148 TCTCAAACTTTTCTCAGATTTAGATGC 58.275 33.333 0.00 0.00 0.00 3.91
3900 5825 9.838339 AGTTCTCAAACTTTTCTCAGATTTAGA 57.162 29.630 0.00 0.00 43.28 2.10
4011 5936 5.350365 GGAAAGTCAAGTTGGTTTGGTTTTC 59.650 40.000 2.34 3.82 34.18 2.29
4056 5982 3.244422 CCTTCAACCACAGGTAAGCACTA 60.244 47.826 0.00 0.00 33.12 2.74
4113 6039 9.295825 TGCCATAGGACAATGGTTATTATTTAG 57.704 33.333 4.89 0.00 46.93 1.85
4162 6092 3.081409 AGGCGGCGGTGATAAGGT 61.081 61.111 9.78 0.00 0.00 3.50
4181 6126 3.003173 CAGGGGTGCGAGGAGGAA 61.003 66.667 0.00 0.00 0.00 3.36
4533 6584 2.107750 CCGCGCCACTCATCAGAT 59.892 61.111 0.00 0.00 0.00 2.90
4780 6857 4.569023 CGGAGCTACCATCGCGCA 62.569 66.667 8.75 0.00 38.90 6.09
4912 7028 4.972201 TGACGTTGGTTCTGTTTGTAAAC 58.028 39.130 0.00 0.65 39.33 2.01
4918 7034 3.128068 GGTTCTTGACGTTGGTTCTGTTT 59.872 43.478 0.00 0.00 0.00 2.83
4984 7100 2.233186 GGTATGGTCGGTTATAGGCCTC 59.767 54.545 9.68 0.00 33.78 4.70
5139 7261 3.876274 TCTCTGTAAGTGGATGCAGTC 57.124 47.619 0.00 0.00 34.96 3.51
5169 7291 5.459536 TTAGCTGCTACCTGACATATCTG 57.540 43.478 9.27 0.00 0.00 2.90
5277 7400 2.877168 CCTAGAATGCTTCTGATGCACC 59.123 50.000 18.87 13.82 43.59 5.01
5280 7403 4.333913 TCTCCTAGAATGCTTCTGATGC 57.666 45.455 8.46 8.46 40.94 3.91
5360 7483 1.092345 GCAAGGGCTTCTCCGATCAC 61.092 60.000 0.00 0.00 36.96 3.06
5366 7489 2.436824 GGTCGCAAGGGCTTCTCC 60.437 66.667 0.00 0.00 38.10 3.71
5368 7491 2.348998 CTGGTCGCAAGGGCTTCT 59.651 61.111 0.00 0.00 38.10 2.85
5380 7504 2.359169 TGATCGCTCCCCACTGGTC 61.359 63.158 0.00 0.00 34.77 4.02
5381 7505 2.284625 TGATCGCTCCCCACTGGT 60.285 61.111 0.00 0.00 34.77 4.00
5402 7550 3.253188 TCTTGGAGCATTCTTCGTTTTGG 59.747 43.478 0.00 0.00 0.00 3.28
5404 7552 5.712152 AATCTTGGAGCATTCTTCGTTTT 57.288 34.783 0.00 0.00 0.00 2.43
5514 7688 0.318955 CCAACTGCTTTTCCCAAGCG 60.319 55.000 2.31 0.64 45.80 4.68
5547 7724 0.443869 CACACATTAGCTGACGTGCC 59.556 55.000 4.44 0.00 32.53 5.01
5589 7766 2.292016 CACTGGCAAATTACACGACCAA 59.708 45.455 0.00 0.00 0.00 3.67
5633 7819 7.928167 CAGATAGATAACCTGAAGTGCATTACA 59.072 37.037 0.00 0.00 0.00 2.41
5634 7820 7.095439 GCAGATAGATAACCTGAAGTGCATTAC 60.095 40.741 0.00 0.00 0.00 1.89
5635 7821 6.931281 GCAGATAGATAACCTGAAGTGCATTA 59.069 38.462 0.00 0.00 0.00 1.90
5698 7885 4.038402 CCTCTGAACCAAAAATGAAGCAGT 59.962 41.667 0.00 0.00 0.00 4.40
5730 7917 6.520792 TTGAGTAAAAACGAGCAGAGTTAC 57.479 37.500 0.00 0.00 0.00 2.50
5788 8344 1.826385 ATTGGCTGCTGTAGAACACC 58.174 50.000 0.00 0.00 0.00 4.16
5827 8479 4.114058 ACCATTGCTATGTTTGCATGAC 57.886 40.909 7.37 0.00 40.34 3.06
5857 8509 8.149647 TGAAATTTTCATCTTACAAACCATGCT 58.850 29.630 7.74 0.00 34.08 3.79
5858 8510 8.309163 TGAAATTTTCATCTTACAAACCATGC 57.691 30.769 7.74 0.00 34.08 4.06
5868 8520 6.646240 GCACAAGGCTTGAAATTTTCATCTTA 59.354 34.615 32.50 0.00 39.84 2.10
5874 8526 2.807967 GGGCACAAGGCTTGAAATTTTC 59.192 45.455 32.50 13.66 44.01 2.29
5888 8540 1.205893 GTCTGTTGGTTTTGGGCACAA 59.794 47.619 0.00 0.00 34.07 3.33
6038 8703 4.107622 GTCATGCATGCCAGTTTTATCAC 58.892 43.478 22.25 6.41 0.00 3.06
6069 8734 6.540189 GCATACTTTTCTCTGTCCATATGTGT 59.460 38.462 1.24 0.00 0.00 3.72
6107 8773 0.109342 AGGAGGCAGAACTGTGGTTG 59.891 55.000 3.77 0.00 35.58 3.77
6113 8779 1.134461 CATGAGGAGGAGGCAGAACTG 60.134 57.143 0.00 0.00 0.00 3.16
6115 8781 0.908198 ACATGAGGAGGAGGCAGAAC 59.092 55.000 0.00 0.00 0.00 3.01
6119 8785 1.361204 TTTCACATGAGGAGGAGGCA 58.639 50.000 0.00 0.00 0.00 4.75
6120 8786 2.092753 TGATTTCACATGAGGAGGAGGC 60.093 50.000 0.00 0.00 0.00 4.70
6121 8787 3.433314 CCTGATTTCACATGAGGAGGAGG 60.433 52.174 0.00 0.00 0.00 4.30
6122 8788 3.806380 CCTGATTTCACATGAGGAGGAG 58.194 50.000 0.00 0.00 0.00 3.69
6123 8789 2.092753 GCCTGATTTCACATGAGGAGGA 60.093 50.000 0.00 0.00 0.00 3.71
6124 8790 2.092538 AGCCTGATTTCACATGAGGAGG 60.093 50.000 0.00 0.00 0.00 4.30
6125 8791 2.943690 CAGCCTGATTTCACATGAGGAG 59.056 50.000 0.00 0.00 0.00 3.69
6126 8792 2.356432 CCAGCCTGATTTCACATGAGGA 60.356 50.000 0.00 0.00 0.00 3.71
6127 8793 2.022195 CCAGCCTGATTTCACATGAGG 58.978 52.381 0.00 0.00 0.00 3.86
6129 8795 2.356432 CCTCCAGCCTGATTTCACATGA 60.356 50.000 0.00 0.00 0.00 3.07
6130 8796 2.022195 CCTCCAGCCTGATTTCACATG 58.978 52.381 0.00 0.00 0.00 3.21
6131 8797 1.918262 TCCTCCAGCCTGATTTCACAT 59.082 47.619 0.00 0.00 0.00 3.21
6132 8798 1.361204 TCCTCCAGCCTGATTTCACA 58.639 50.000 0.00 0.00 0.00 3.58
6134 8800 3.782523 AGTTATCCTCCAGCCTGATTTCA 59.217 43.478 0.00 0.00 0.00 2.69
6135 8801 4.429854 AGTTATCCTCCAGCCTGATTTC 57.570 45.455 0.00 0.00 0.00 2.17
6136 8802 4.870021 AAGTTATCCTCCAGCCTGATTT 57.130 40.909 0.00 0.00 0.00 2.17
6137 8803 4.870021 AAAGTTATCCTCCAGCCTGATT 57.130 40.909 0.00 0.00 0.00 2.57
6262 8932 2.191908 GTGTGTGTGTGCCTGGGA 59.808 61.111 0.00 0.00 0.00 4.37
6266 8936 0.810648 CAAAGTGTGTGTGTGTGCCT 59.189 50.000 0.00 0.00 0.00 4.75
6280 8952 3.293337 GGTTGTACCCAAAGTCCAAAGT 58.707 45.455 0.00 0.00 30.94 2.66
6294 8966 3.119280 ACTGTTTGGTTGCTTGGTTGTAC 60.119 43.478 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.