Multiple sequence alignment - TraesCS3A01G268500

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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 TraesCS3A01G268500 chr3A 100.000 8637 0 0 1 8637 494717657 494726293 0.000000e+00 15950.0
1 TraesCS3A01G268500 chr3A 85.845 1201 145 13 1769 2950 48667019 48668213 0.000000e+00 1253.0
2 TraesCS3A01G268500 chr3A 100.000 449 0 0 8931 9379 494726587 494727035 0.000000e+00 830.0
3 TraesCS3A01G268500 chr3A 85.926 810 76 12 6210 7007 644923121 644923904 0.000000e+00 830.0
4 TraesCS3A01G268500 chr3D 93.232 6974 308 48 1752 8637 373319137 373326034 0.000000e+00 10113.0
5 TraesCS3A01G268500 chr3D 96.979 960 20 3 744 1699 373317922 373318876 0.000000e+00 1604.0
6 TraesCS3A01G268500 chr3D 87.860 486 38 9 1 482 373317402 373317870 1.380000e-152 551.0
7 TraesCS3A01G268500 chr3D 92.683 205 6 2 8931 9135 373326114 373326309 4.290000e-73 287.0
8 TraesCS3A01G268500 chr3D 87.111 225 27 2 6210 6433 20936251 20936028 4.350000e-63 254.0
9 TraesCS3A01G268500 chr3D 86.667 225 28 2 6210 6433 20928509 20928286 2.020000e-61 248.0
10 TraesCS3A01G268500 chr3D 93.966 116 7 0 9264 9379 373326332 373326447 9.680000e-40 176.0
11 TraesCS3A01G268500 chr3D 79.762 252 39 11 1771 2015 169472162 169471916 1.250000e-38 172.0
12 TraesCS3A01G268500 chr3D 84.768 151 20 2 3827 3974 84928655 84928505 2.110000e-31 148.0
13 TraesCS3A01G268500 chr3D 87.356 87 10 1 7566 7651 505776983 505777069 2.160000e-16 99.0
14 TraesCS3A01G268500 chr4D 87.953 2233 223 26 1769 3974 132209748 132207535 0.000000e+00 2591.0
15 TraesCS3A01G268500 chr4D 88.076 1585 151 12 2422 3981 314637161 314635590 0.000000e+00 1845.0
16 TraesCS3A01G268500 chr4D 80.153 262 36 10 1769 2027 498102828 498102580 2.080000e-41 182.0
17 TraesCS3A01G268500 chr3B 93.207 1634 94 11 1 1625 487028990 487030615 0.000000e+00 2386.0
18 TraesCS3A01G268500 chr3B 94.906 1492 63 8 7150 8637 487045065 487046547 0.000000e+00 2322.0
19 TraesCS3A01G268500 chr3B 86.776 1883 217 18 2117 3974 60370432 60372307 0.000000e+00 2069.0
20 TraesCS3A01G268500 chr3B 91.153 1492 74 18 5681 7137 487043620 487045088 0.000000e+00 1971.0
21 TraesCS3A01G268500 chr3B 88.321 411 35 7 8970 9378 487047000 487047399 1.830000e-131 481.0
22 TraesCS3A01G268500 chr3B 87.209 86 10 1 7566 7650 667642461 667642546 7.750000e-16 97.1
23 TraesCS3A01G268500 chr3B 95.349 43 2 0 1734 1776 487043010 487043052 1.690000e-07 69.4
24 TraesCS3A01G268500 chr4B 85.746 2245 262 39 1769 3980 392652415 392650196 0.000000e+00 2320.0
25 TraesCS3A01G268500 chr4B 87.243 2046 192 41 1769 3793 165264072 165266069 0.000000e+00 2268.0
26 TraesCS3A01G268500 chr4B 81.818 187 31 3 1769 1953 414226902 414226717 4.540000e-33 154.0
27 TraesCS3A01G268500 chr4B 84.354 147 17 5 3840 3980 95690593 95690739 1.270000e-28 139.0
28 TraesCS3A01G268500 chr1B 85.480 2252 242 43 1769 3974 216485487 216487699 0.000000e+00 2268.0
29 TraesCS3A01G268500 chr1B 84.843 2263 280 32 1769 3977 677536660 677534407 0.000000e+00 2220.0
30 TraesCS3A01G268500 chr1B 86.262 808 71 18 6211 7008 8688611 8689388 0.000000e+00 841.0
31 TraesCS3A01G268500 chr1B 86.015 808 73 16 6211 7008 8968763 8967986 0.000000e+00 830.0
32 TraesCS3A01G268500 chr1B 81.168 839 116 21 4521 5331 27149023 27148199 3.690000e-178 636.0
33 TraesCS3A01G268500 chr1B 81.311 717 105 19 4492 5198 270312946 270313643 1.060000e-153 555.0
34 TraesCS3A01G268500 chr1B 78.046 952 153 30 4413 5337 13366275 13367197 4.950000e-152 549.0
35 TraesCS3A01G268500 chr1B 88.028 426 40 9 7764 8186 8690658 8691075 2.350000e-135 494.0
36 TraesCS3A01G268500 chr1B 87.793 426 41 10 7764 8186 8966330 8965913 1.090000e-133 488.0
37 TraesCS3A01G268500 chr1B 89.157 166 14 4 7408 7570 8966539 8966375 4.440000e-48 204.0
38 TraesCS3A01G268500 chr1B 91.304 138 11 1 7201 7337 8690350 8690487 4.470000e-43 187.0
39 TraesCS3A01G268500 chr1B 76.991 226 43 8 5455 5678 60270854 60271072 4.600000e-23 121.0
40 TraesCS3A01G268500 chr1B 87.640 89 9 2 7564 7650 529393059 529393147 1.670000e-17 102.0
41 TraesCS3A01G268500 chr5B 82.754 2244 297 51 1769 3970 580757431 580755236 0.000000e+00 1917.0
42 TraesCS3A01G268500 chr5B 85.432 810 76 16 6211 7008 693099449 693100228 0.000000e+00 804.0
43 TraesCS3A01G268500 chr5B 90.972 144 12 1 7195 7337 693101177 693101320 9.610000e-45 193.0
44 TraesCS3A01G268500 chr5B 81.579 152 21 5 1626 1775 382085061 382085207 1.650000e-22 119.0
45 TraesCS3A01G268500 chr4A 86.878 1669 177 28 1828 3475 161285179 161286826 0.000000e+00 1831.0
46 TraesCS3A01G268500 chr4A 82.264 1060 133 27 1769 2821 521521504 521522515 0.000000e+00 865.0
47 TraesCS3A01G268500 chr4A 96.377 138 4 1 9132 9269 726659441 726659577 9.480000e-55 226.0
48 TraesCS3A01G268500 chr4A 92.537 67 5 0 1673 1739 46084424 46084358 7.750000e-16 97.1
49 TraesCS3A01G268500 chr1A 85.287 1672 191 24 2333 3974 337304802 337303156 0.000000e+00 1674.0
50 TraesCS3A01G268500 chr1A 96.324 136 3 2 9128 9263 35530965 35531098 1.230000e-53 222.0
51 TraesCS3A01G268500 chr1A 82.237 152 23 4 1798 1947 541649498 541649349 2.750000e-25 128.0
52 TraesCS3A01G268500 chr1A 92.683 82 5 1 7566 7646 255486760 255486679 5.950000e-22 117.0
53 TraesCS3A01G268500 chr1A 84.112 107 15 2 5533 5638 20368206 20368101 1.670000e-17 102.0
54 TraesCS3A01G268500 chr6B 86.068 1536 173 23 1759 3272 316603923 316602407 0.000000e+00 1613.0
55 TraesCS3A01G268500 chr6B 82.615 719 96 22 4490 5198 680802515 680801816 8.050000e-170 608.0
56 TraesCS3A01G268500 chr6B 82.312 718 98 21 4490 5198 258004710 258004013 6.270000e-166 595.0
57 TraesCS3A01G268500 chr6B 82.158 723 88 29 4426 5141 172463024 172463712 4.880000e-162 582.0
58 TraesCS3A01G268500 chr6B 81.860 215 17 10 5470 5679 172463714 172463911 2.710000e-35 161.0
59 TraesCS3A01G268500 chr6B 78.481 158 31 3 591 746 26157430 26157274 5.990000e-17 100.0
60 TraesCS3A01G268500 chr6A 84.992 1266 142 17 1942 3189 259273022 259274257 0.000000e+00 1242.0
61 TraesCS3A01G268500 chr6A 80.234 855 127 22 4499 5329 108256008 108256844 1.040000e-168 604.0
62 TraesCS3A01G268500 chr6A 80.164 852 132 22 4515 5346 74672669 74671835 3.750000e-168 603.0
63 TraesCS3A01G268500 chr6A 97.015 134 2 2 9129 9262 617047908 617047777 3.410000e-54 224.0
64 TraesCS3A01G268500 chr6D 86.403 809 73 11 6210 7007 360610530 360611312 0.000000e+00 850.0
65 TraesCS3A01G268500 chr6D 88.312 385 34 10 7805 8186 28648463 28648087 1.440000e-122 451.0
66 TraesCS3A01G268500 chr6D 88.052 385 35 10 7805 8186 289620645 289621021 6.680000e-121 446.0
67 TraesCS3A01G268500 chr2A 85.393 801 76 14 6211 7001 80997436 80998205 0.000000e+00 793.0
68 TraesCS3A01G268500 chr2A 87.822 427 40 11 7764 8186 80999511 80999929 3.040000e-134 490.0
69 TraesCS3A01G268500 chr2A 90.210 143 13 1 7196 7337 80999164 80999306 1.610000e-42 185.0
70 TraesCS3A01G268500 chr2A 77.612 268 50 9 1769 2028 38396099 38396364 4.540000e-33 154.0
71 TraesCS3A01G268500 chr2D 82.033 718 100 22 4490 5198 552108885 552109582 1.360000e-162 584.0
72 TraesCS3A01G268500 chr2D 88.312 385 34 10 7805 8186 375659702 375659326 1.440000e-122 451.0
73 TraesCS3A01G268500 chr7D 81.641 719 100 25 4490 5198 631647580 631648276 1.370000e-157 568.0
74 TraesCS3A01G268500 chr7D 81.931 321 51 6 4902 5220 561394743 561395058 2.010000e-66 265.0
75 TraesCS3A01G268500 chr7D 81.875 320 51 6 4903 5220 561253334 561253648 7.220000e-66 263.0
76 TraesCS3A01G268500 chr7D 81.875 320 51 6 4903 5220 561302228 561302542 7.220000e-66 263.0
77 TraesCS3A01G268500 chr7D 81.818 275 36 11 5415 5680 631648478 631648747 1.590000e-52 219.0
78 TraesCS3A01G268500 chr7D 83.516 182 30 0 1769 1950 149178982 149179163 4.500000e-38 171.0
79 TraesCS3A01G268500 chr7D 86.000 150 19 2 1628 1776 171597948 171597800 9.750000e-35 159.0
80 TraesCS3A01G268500 chr7D 78.355 231 43 6 1769 1994 292242586 292242358 9.820000e-30 143.0
81 TraesCS3A01G268500 chr7D 87.209 86 11 0 7566 7651 380628602 380628687 2.160000e-16 99.0
82 TraesCS3A01G268500 chr7D 97.727 44 1 0 5286 5329 5504749 5504706 1.010000e-09 76.8
83 TraesCS3A01G268500 chr7B 81.259 731 106 21 4480 5198 23418325 23417614 6.360000e-156 562.0
84 TraesCS3A01G268500 chr7B 80.841 214 35 6 1769 1978 417690820 417691031 7.540000e-36 163.0
85 TraesCS3A01G268500 chr7B 85.333 150 20 2 1628 1776 137909613 137909465 4.540000e-33 154.0
86 TraesCS3A01G268500 chr7B 91.549 71 6 0 7566 7636 375386586 375386656 2.160000e-16 99.0
87 TraesCS3A01G268500 chrUn 78.128 951 154 30 4413 5337 327075707 327076629 1.060000e-153 555.0
88 TraesCS3A01G268500 chrUn 77.941 952 154 30 4413 5337 377662738 377663660 2.300000e-150 544.0
89 TraesCS3A01G268500 chr1D 88.312 385 34 10 7805 8186 464635923 464636299 1.440000e-122 451.0
90 TraesCS3A01G268500 chr1D 84.615 104 14 2 5536 5638 18392680 18392578 1.670000e-17 102.0
91 TraesCS3A01G268500 chr5A 98.485 132 1 1 9133 9264 154345660 154345530 2.040000e-56 231.0
92 TraesCS3A01G268500 chr5A 97.015 134 2 2 9129 9261 688512214 688512346 3.410000e-54 224.0
93 TraesCS3A01G268500 chr7A 96.992 133 3 1 9137 9269 77440664 77440533 1.230000e-53 222.0
94 TraesCS3A01G268500 chr7A 95.652 138 5 1 9133 9270 671503035 671503171 4.410000e-53 220.0
95 TraesCS3A01G268500 chr7A 92.857 70 5 0 7566 7635 428916347 428916416 1.670000e-17 102.0
96 TraesCS3A01G268500 chr5D 77.513 378 79 3 3974 4347 27859062 27858687 1.230000e-53 222.0
97 TraesCS3A01G268500 chr5D 80.645 155 24 6 1626 1776 27857165 27857013 2.140000e-21 115.0
98 TraesCS3A01G268500 chr5D 79.221 154 29 3 1626 1776 28026121 28026274 4.630000e-18 104.0
99 TraesCS3A01G268500 chr2B 95.714 140 3 3 9123 9261 627325236 627325099 1.230000e-53 222.0
100 TraesCS3A01G268500 chr2B 75.309 162 29 8 5820 5979 656515329 656515481 6.080000e-07 67.6


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 TraesCS3A01G268500 chr3A 494717657 494727035 9378 False 8390.000000 15950 100.000000 1 9379 2 chr3A.!!$F3 9378
1 TraesCS3A01G268500 chr3A 48667019 48668213 1194 False 1253.000000 1253 85.845000 1769 2950 1 chr3A.!!$F1 1181
2 TraesCS3A01G268500 chr3A 644923121 644923904 783 False 830.000000 830 85.926000 6210 7007 1 chr3A.!!$F2 797
3 TraesCS3A01G268500 chr3D 373317402 373326447 9045 False 2546.200000 10113 92.944000 1 9379 5 chr3D.!!$F2 9378
4 TraesCS3A01G268500 chr4D 132207535 132209748 2213 True 2591.000000 2591 87.953000 1769 3974 1 chr4D.!!$R1 2205
5 TraesCS3A01G268500 chr4D 314635590 314637161 1571 True 1845.000000 1845 88.076000 2422 3981 1 chr4D.!!$R2 1559
6 TraesCS3A01G268500 chr3B 487028990 487030615 1625 False 2386.000000 2386 93.207000 1 1625 1 chr3B.!!$F2 1624
7 TraesCS3A01G268500 chr3B 60370432 60372307 1875 False 2069.000000 2069 86.776000 2117 3974 1 chr3B.!!$F1 1857
8 TraesCS3A01G268500 chr3B 487043010 487047399 4389 False 1210.850000 2322 92.432250 1734 9378 4 chr3B.!!$F4 7644
9 TraesCS3A01G268500 chr4B 392650196 392652415 2219 True 2320.000000 2320 85.746000 1769 3980 1 chr4B.!!$R1 2211
10 TraesCS3A01G268500 chr4B 165264072 165266069 1997 False 2268.000000 2268 87.243000 1769 3793 1 chr4B.!!$F2 2024
11 TraesCS3A01G268500 chr1B 216485487 216487699 2212 False 2268.000000 2268 85.480000 1769 3974 1 chr1B.!!$F3 2205
12 TraesCS3A01G268500 chr1B 677534407 677536660 2253 True 2220.000000 2220 84.843000 1769 3977 1 chr1B.!!$R2 2208
13 TraesCS3A01G268500 chr1B 27148199 27149023 824 True 636.000000 636 81.168000 4521 5331 1 chr1B.!!$R1 810
14 TraesCS3A01G268500 chr1B 270312946 270313643 697 False 555.000000 555 81.311000 4492 5198 1 chr1B.!!$F4 706
15 TraesCS3A01G268500 chr1B 13366275 13367197 922 False 549.000000 549 78.046000 4413 5337 1 chr1B.!!$F1 924
16 TraesCS3A01G268500 chr1B 8688611 8691075 2464 False 507.333333 841 88.531333 6211 8186 3 chr1B.!!$F6 1975
17 TraesCS3A01G268500 chr1B 8965913 8968763 2850 True 507.333333 830 87.655000 6211 8186 3 chr1B.!!$R3 1975
18 TraesCS3A01G268500 chr5B 580755236 580757431 2195 True 1917.000000 1917 82.754000 1769 3970 1 chr5B.!!$R1 2201
19 TraesCS3A01G268500 chr5B 693099449 693101320 1871 False 498.500000 804 88.202000 6211 7337 2 chr5B.!!$F2 1126
20 TraesCS3A01G268500 chr4A 161285179 161286826 1647 False 1831.000000 1831 86.878000 1828 3475 1 chr4A.!!$F1 1647
21 TraesCS3A01G268500 chr4A 521521504 521522515 1011 False 865.000000 865 82.264000 1769 2821 1 chr4A.!!$F2 1052
22 TraesCS3A01G268500 chr1A 337303156 337304802 1646 True 1674.000000 1674 85.287000 2333 3974 1 chr1A.!!$R3 1641
23 TraesCS3A01G268500 chr6B 316602407 316603923 1516 True 1613.000000 1613 86.068000 1759 3272 1 chr6B.!!$R3 1513
24 TraesCS3A01G268500 chr6B 680801816 680802515 699 True 608.000000 608 82.615000 4490 5198 1 chr6B.!!$R4 708
25 TraesCS3A01G268500 chr6B 258004013 258004710 697 True 595.000000 595 82.312000 4490 5198 1 chr6B.!!$R2 708
26 TraesCS3A01G268500 chr6B 172463024 172463911 887 False 371.500000 582 82.009000 4426 5679 2 chr6B.!!$F1 1253
27 TraesCS3A01G268500 chr6A 259273022 259274257 1235 False 1242.000000 1242 84.992000 1942 3189 1 chr6A.!!$F2 1247
28 TraesCS3A01G268500 chr6A 108256008 108256844 836 False 604.000000 604 80.234000 4499 5329 1 chr6A.!!$F1 830
29 TraesCS3A01G268500 chr6A 74671835 74672669 834 True 603.000000 603 80.164000 4515 5346 1 chr6A.!!$R1 831
30 TraesCS3A01G268500 chr6D 360610530 360611312 782 False 850.000000 850 86.403000 6210 7007 1 chr6D.!!$F2 797
31 TraesCS3A01G268500 chr2A 80997436 80999929 2493 False 489.333333 793 87.808333 6211 8186 3 chr2A.!!$F2 1975
32 TraesCS3A01G268500 chr2D 552108885 552109582 697 False 584.000000 584 82.033000 4490 5198 1 chr2D.!!$F1 708
33 TraesCS3A01G268500 chr7D 631647580 631648747 1167 False 393.500000 568 81.729500 4490 5680 2 chr7D.!!$F6 1190
34 TraesCS3A01G268500 chr7B 23417614 23418325 711 True 562.000000 562 81.259000 4480 5198 1 chr7B.!!$R1 718
35 TraesCS3A01G268500 chrUn 327075707 327076629 922 False 555.000000 555 78.128000 4413 5337 1 chrUn.!!$F1 924
36 TraesCS3A01G268500 chrUn 377662738 377663660 922 False 544.000000 544 77.941000 4413 5337 1 chrUn.!!$F2 924

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
672 679 0.319211 TCGGTGTAAGAAGGCACACG 60.319 55.000 0.00 0.0 44.80 4.49 F
1706 1721 0.029834 GTGCTGTGCTTTGTGGAGTG 59.970 55.000 0.00 0.0 0.00 3.51 F
1707 1722 0.107263 TGCTGTGCTTTGTGGAGTGA 60.107 50.000 0.00 0.0 0.00 3.41 F
1723 1738 0.465097 GTGATCTGCTGATGGGTGGG 60.465 60.000 11.21 0.0 32.19 4.61 F
2198 2500 0.522180 CGGTGTGAGAGAAGCTACGT 59.478 55.000 0.00 0.0 0.00 3.57 F
2474 2778 0.527565 CTTGTGGTGGCTACATTGGC 59.472 55.000 1.52 0.0 0.00 4.52 F
3183 3519 0.551131 AGAAGGCCATTCCCCAGAGT 60.551 55.000 5.01 0.0 38.84 3.24 F
4757 5320 0.684479 TCCTGGATCGGAGGACACTG 60.684 60.000 7.82 0.0 34.49 3.66 F
4908 5471 0.035152 AGGCATCAACTCGGCATCAA 60.035 50.000 0.00 0.0 0.00 2.57 F
4909 5472 0.099436 GGCATCAACTCGGCATCAAC 59.901 55.000 0.00 0.0 0.00 3.18 F
5378 6025 0.959553 ACGTGATTCTCGACTGTGGT 59.040 50.000 14.43 0.0 0.00 4.16 F
6909 7646 1.205417 GCCAAATGTCATGGTTCCAGG 59.795 52.381 0.00 0.0 40.23 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1741 1756 0.319040 CTCATATCGCTCCACCACGG 60.319 60.000 0.00 0.00 0.00 4.94 R
3620 3969 1.140652 TGAGTCCACATGTGCTCAACA 59.859 47.619 25.05 16.06 44.79 3.33 R
4034 4567 2.426023 GGTCAACACCGGCTGACT 59.574 61.111 23.56 5.23 41.43 3.41 R
4262 4799 1.018910 CCAACCGGAAAAGACGTTGT 58.981 50.000 9.46 0.00 0.00 3.32 R
4631 5184 0.320771 CTGCAGCGGTTCACTACCTT 60.321 55.000 0.00 0.00 45.40 3.50 R
4900 5463 0.592637 TGCAGTTGAAGTTGATGCCG 59.407 50.000 0.00 0.00 36.04 5.69 R
4908 5471 0.666913 CAGCTGCTTGCAGTTGAAGT 59.333 50.000 27.39 4.36 45.94 3.01 R
6869 7596 0.103208 GGGCCGACACTCTGTATCAG 59.897 60.000 0.00 0.00 0.00 2.90 R
6871 7598 1.065928 CGGGCCGACACTCTGTATC 59.934 63.158 24.41 0.00 0.00 2.24 R
7141 7904 2.919666 ATGATTTTGTTTCTCCCGCG 57.080 45.000 0.00 0.00 0.00 6.46 R
7529 9405 2.892374 ACCAAAGAAAAGTTGCTGCAC 58.108 42.857 0.00 0.00 0.00 4.57 R
9246 11251 0.324091 TCACCTACTCCCTCCGTTCC 60.324 60.000 0.00 0.00 0.00 3.62 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
166 169 5.702266 AGGGTTTAATTTCTATAGTGCCCC 58.298 41.667 0.00 0.00 33.16 5.80
196 199 8.086522 ACACTAATATGGTCCATCGTTATGTAC 58.913 37.037 7.92 0.00 0.00 2.90
242 245 6.417191 TCTACGCATGAAAGATTACCAAAC 57.583 37.500 0.00 0.00 0.00 2.93
260 263 2.620251 ACGTGTGGGTCATATGGATG 57.380 50.000 2.13 0.00 0.00 3.51
368 372 3.759815 TTAGAAGCTAGAGGTGGAGGT 57.240 47.619 0.00 0.00 0.00 3.85
412 416 5.163301 ACGAGATTTATGGCACTTATGAGGT 60.163 40.000 0.00 0.00 0.00 3.85
601 608 5.348724 ACTGTATGTGTTTAGAACGATGCTG 59.651 40.000 0.00 0.00 0.00 4.41
611 618 1.385743 GAACGATGCTGTACACACGAC 59.614 52.381 17.65 11.72 35.99 4.34
615 622 2.174764 GATGCTGTACACACGACGTAG 58.825 52.381 0.00 0.00 0.00 3.51
628 635 2.159156 ACGACGTAGGCTGCATGATTTA 60.159 45.455 0.00 0.00 0.00 1.40
654 661 5.177696 GGACGATGTTGTTAATCTAGCCATC 59.822 44.000 0.00 0.00 0.00 3.51
660 667 5.105269 TGTTGTTAATCTAGCCATCGGTGTA 60.105 40.000 0.00 0.00 0.00 2.90
672 679 0.319211 TCGGTGTAAGAAGGCACACG 60.319 55.000 0.00 0.00 44.80 4.49
673 680 1.289109 CGGTGTAAGAAGGCACACGG 61.289 60.000 0.00 0.00 44.80 4.94
685 692 0.989890 GCACACGGTAGAACATCGTC 59.010 55.000 0.00 0.00 34.73 4.20
689 696 1.065102 CACGGTAGAACATCGTCCGAT 59.935 52.381 17.69 0.00 38.81 4.18
711 718 1.369689 GCATCGTGCATGAATCGGC 60.370 57.895 13.65 10.66 44.26 5.54
713 720 1.153188 ATCGTGCATGAATCGGCCA 60.153 52.632 13.65 0.00 0.00 5.36
718 725 1.065273 GCATGAATCGGCCAAGCAG 59.935 57.895 2.24 0.00 0.00 4.24
719 726 1.660560 GCATGAATCGGCCAAGCAGT 61.661 55.000 2.24 0.00 0.00 4.40
758 765 3.756933 TCGTAGTGTGTTTTAAGGGCT 57.243 42.857 0.00 0.00 0.00 5.19
886 896 3.311596 GGTAATAAATGTCCACGACCTGC 59.688 47.826 0.00 0.00 0.00 4.85
890 900 1.779061 AATGTCCACGACCTGCCCTT 61.779 55.000 0.00 0.00 0.00 3.95
1229 1240 0.611896 AATGCGGTCCAAAGGAAGGG 60.612 55.000 0.00 0.00 31.38 3.95
1372 1383 5.929992 AGTGTTTGCTAATTAACTAGCGTGA 59.070 36.000 11.03 0.00 46.13 4.35
1527 1538 4.548991 GCTGTAGCAGATTCCAATCTTG 57.451 45.455 0.00 0.00 42.96 3.02
1539 1550 2.356135 CCAATCTTGGTGTAGGTTCCG 58.644 52.381 0.55 0.00 43.43 4.30
1545 1556 1.956297 TGGTGTAGGTTCCGTTTGTG 58.044 50.000 0.00 0.00 0.00 3.33
1606 1621 5.841957 ACTGAATTGTAGAATGGCCAATC 57.158 39.130 10.96 12.30 0.00 2.67
1647 1662 4.260170 AGCTCTCTCAATCAATTGGTGTC 58.740 43.478 5.42 0.00 38.30 3.67
1651 1666 5.868454 TCTCTCAATCAATTGGTGTCTTCA 58.132 37.500 5.42 0.00 38.30 3.02
1699 1714 1.067364 TGGTCAATGTGCTGTGCTTTG 59.933 47.619 0.00 0.00 0.00 2.77
1700 1715 1.067516 GGTCAATGTGCTGTGCTTTGT 59.932 47.619 0.00 0.00 0.00 2.83
1701 1716 2.121786 GTCAATGTGCTGTGCTTTGTG 58.878 47.619 0.00 0.00 0.00 3.33
1702 1717 1.067364 TCAATGTGCTGTGCTTTGTGG 59.933 47.619 0.00 0.00 0.00 4.17
1703 1718 1.067364 CAATGTGCTGTGCTTTGTGGA 59.933 47.619 0.00 0.00 0.00 4.02
1704 1719 0.956633 ATGTGCTGTGCTTTGTGGAG 59.043 50.000 0.00 0.00 0.00 3.86
1705 1720 0.394216 TGTGCTGTGCTTTGTGGAGT 60.394 50.000 0.00 0.00 0.00 3.85
1706 1721 0.029834 GTGCTGTGCTTTGTGGAGTG 59.970 55.000 0.00 0.00 0.00 3.51
1707 1722 0.107263 TGCTGTGCTTTGTGGAGTGA 60.107 50.000 0.00 0.00 0.00 3.41
1708 1723 1.242076 GCTGTGCTTTGTGGAGTGAT 58.758 50.000 0.00 0.00 0.00 3.06
1709 1724 1.198637 GCTGTGCTTTGTGGAGTGATC 59.801 52.381 0.00 0.00 0.00 2.92
1710 1725 2.775890 CTGTGCTTTGTGGAGTGATCT 58.224 47.619 0.00 0.00 0.00 2.75
1711 1726 2.483106 CTGTGCTTTGTGGAGTGATCTG 59.517 50.000 0.00 0.00 0.00 2.90
1712 1727 1.198637 GTGCTTTGTGGAGTGATCTGC 59.801 52.381 0.00 0.00 0.00 4.26
1713 1728 1.072806 TGCTTTGTGGAGTGATCTGCT 59.927 47.619 0.00 0.00 33.13 4.24
1714 1729 1.467734 GCTTTGTGGAGTGATCTGCTG 59.532 52.381 0.00 0.00 33.13 4.41
1715 1730 2.873245 GCTTTGTGGAGTGATCTGCTGA 60.873 50.000 0.00 0.00 33.13 4.26
1716 1731 3.607741 CTTTGTGGAGTGATCTGCTGAT 58.392 45.455 5.69 5.69 35.26 2.90
1717 1732 2.685850 TGTGGAGTGATCTGCTGATG 57.314 50.000 11.21 0.00 32.19 3.07
1718 1733 1.208776 TGTGGAGTGATCTGCTGATGG 59.791 52.381 11.21 0.00 32.19 3.51
1719 1734 0.835276 TGGAGTGATCTGCTGATGGG 59.165 55.000 11.21 0.00 32.19 4.00
1720 1735 0.835941 GGAGTGATCTGCTGATGGGT 59.164 55.000 11.21 0.00 32.19 4.51
1721 1736 1.474677 GGAGTGATCTGCTGATGGGTG 60.475 57.143 11.21 0.00 32.19 4.61
1722 1737 0.545171 AGTGATCTGCTGATGGGTGG 59.455 55.000 11.21 0.00 32.19 4.61
1723 1738 0.465097 GTGATCTGCTGATGGGTGGG 60.465 60.000 11.21 0.00 32.19 4.61
1724 1739 1.527844 GATCTGCTGATGGGTGGGC 60.528 63.158 11.21 0.00 32.19 5.36
1725 1740 2.972892 GATCTGCTGATGGGTGGGCC 62.973 65.000 11.21 0.00 32.19 5.80
1726 1741 3.736224 CTGCTGATGGGTGGGCCT 61.736 66.667 4.53 0.00 34.45 5.19
1727 1742 4.051167 TGCTGATGGGTGGGCCTG 62.051 66.667 4.53 0.00 34.45 4.85
1728 1743 4.052518 GCTGATGGGTGGGCCTGT 62.053 66.667 4.53 0.00 34.45 4.00
1729 1744 2.765969 CTGATGGGTGGGCCTGTT 59.234 61.111 4.53 0.00 34.45 3.16
1730 1745 1.679977 CTGATGGGTGGGCCTGTTG 60.680 63.158 4.53 0.00 34.45 3.33
1731 1746 2.362889 GATGGGTGGGCCTGTTGG 60.363 66.667 4.53 0.00 34.45 3.77
1741 1756 3.359002 CCTGTTGGCAAGTGGCTC 58.641 61.111 0.00 0.80 44.01 4.70
1742 1757 2.270986 CCTGTTGGCAAGTGGCTCC 61.271 63.158 0.00 0.00 44.01 4.70
1824 2052 0.961857 GCGTCCGTTTGGGGGTAAAT 60.962 55.000 0.00 0.00 36.01 1.40
1830 2058 2.240279 CGTTTGGGGGTAAATGGACAA 58.760 47.619 0.00 0.00 0.00 3.18
1898 2126 0.672401 GTCCGCTTTCGACCCATTCA 60.672 55.000 0.00 0.00 38.10 2.57
1910 2138 1.595093 CCCATTCACGGCCCAACTTC 61.595 60.000 0.00 0.00 0.00 3.01
2137 2437 1.915078 ATAGCTGTCCCACACCTGCC 61.915 60.000 0.00 0.00 0.00 4.85
2173 2475 1.949257 CCAGCGTTTGTGGTTCCTC 59.051 57.895 0.00 0.00 0.00 3.71
2198 2500 0.522180 CGGTGTGAGAGAAGCTACGT 59.478 55.000 0.00 0.00 0.00 3.57
2201 2503 1.540267 GTGTGAGAGAAGCTACGTCCA 59.460 52.381 0.00 0.00 0.00 4.02
2234 2537 1.227734 CGACCCCAACAACTTCCGT 60.228 57.895 0.00 0.00 0.00 4.69
2284 2588 1.074072 CCACCATCGACCCCAAACA 59.926 57.895 0.00 0.00 0.00 2.83
2434 2738 4.514441 ACTTCATTTGCTCATCGGATGATC 59.486 41.667 20.21 16.65 38.85 2.92
2474 2778 0.527565 CTTGTGGTGGCTACATTGGC 59.472 55.000 1.52 0.00 0.00 4.52
2671 2979 2.623535 TGTGTTCAATCGTATTCGGGG 58.376 47.619 0.00 0.00 37.69 5.73
2747 3066 4.579869 TCTCTTCTTACCAGAAATGCACC 58.420 43.478 0.00 0.00 38.63 5.01
2784 3109 3.316308 GGTTGCATATGGAATCACTGGTC 59.684 47.826 14.72 0.00 0.00 4.02
2948 3279 2.426023 CGATAGGGGCTTTCCGGG 59.574 66.667 0.00 0.00 36.01 5.73
2949 3280 2.113351 GATAGGGGCTTTCCGGGC 59.887 66.667 0.00 0.00 36.01 6.13
3017 3348 1.614226 ATTTGCTTGGCAGGGGCAT 60.614 52.632 11.40 0.00 40.61 4.40
3037 3372 3.517296 TTACAAGGGGCATGTGAAAGA 57.483 42.857 0.00 0.00 32.27 2.52
3063 3398 2.037251 ACTGTCATACTTGAAGCGGTGT 59.963 45.455 0.00 0.00 32.48 4.16
3183 3519 0.551131 AGAAGGCCATTCCCCAGAGT 60.551 55.000 5.01 0.00 38.84 3.24
3366 3705 6.336842 AGTGTGCTTTTATGCTTCAATCTT 57.663 33.333 0.00 0.00 0.00 2.40
3395 3734 2.459060 TCGTTCGAAACCCTGCATTA 57.541 45.000 0.00 0.00 0.00 1.90
3500 3848 1.207329 AGCATCTACGACCAAGGGTTC 59.793 52.381 0.00 0.00 35.25 3.62
3525 3873 2.151202 TCGAGGGTGAAAATGTTGAGC 58.849 47.619 0.00 0.00 0.00 4.26
3591 3940 1.802069 TCGTGAAATGCGTGATTGGA 58.198 45.000 0.00 0.00 0.00 3.53
3609 3958 1.467734 GGAAGACTCATGTGCAGCTTG 59.532 52.381 0.00 0.00 0.00 4.01
3612 3961 1.622312 AGACTCATGTGCAGCTTGAGA 59.378 47.619 25.01 3.61 46.40 3.27
3613 3962 2.236644 AGACTCATGTGCAGCTTGAGAT 59.763 45.455 25.01 16.16 46.40 2.75
3620 3969 3.216800 TGTGCAGCTTGAGATTGACTTT 58.783 40.909 0.00 0.00 0.00 2.66
3718 4070 8.279970 TGATTGGGTTGTAAGACTATTTGATG 57.720 34.615 0.00 0.00 0.00 3.07
3835 4200 4.500116 GCCTCTGGCGGACGAGAC 62.500 72.222 0.00 0.00 39.62 3.36
4034 4567 3.850752 TGTTTTGCTCCTTTCCCCATTA 58.149 40.909 0.00 0.00 0.00 1.90
4061 4594 1.462731 GGTGTTGACCATGCCTTGCA 61.463 55.000 0.00 0.00 42.59 4.08
4089 4622 1.066430 GCCCAGGTGAAGTCAATCGTA 60.066 52.381 0.00 0.00 0.00 3.43
4103 4636 2.396590 ATCGTACCATGTGTTCCCAC 57.603 50.000 0.00 0.00 42.19 4.61
4174 4707 1.593196 TGGACAAGGAAAAGACAGCG 58.407 50.000 0.00 0.00 0.00 5.18
4262 4799 2.232892 TAGGCGGCTTGAGGGGAGTA 62.233 60.000 19.76 0.00 0.00 2.59
4264 4801 2.656069 GCGGCTTGAGGGGAGTACA 61.656 63.158 0.00 0.00 0.00 2.90
4273 4810 2.701951 TGAGGGGAGTACAACGTCTTTT 59.298 45.455 0.00 0.00 0.00 2.27
4367 4904 3.064324 GCAGGCGGCTGGATGTTT 61.064 61.111 36.25 0.00 40.25 2.83
4424 4961 1.676006 CTGGCAGTTGACGAAAAAGGT 59.324 47.619 6.28 0.00 0.00 3.50
4461 5003 3.799281 AAAACAACCACCACATCACAG 57.201 42.857 0.00 0.00 0.00 3.66
4523 5073 7.873739 AAAGAGAAGAAACACAAACAACAAG 57.126 32.000 0.00 0.00 0.00 3.16
4631 5184 1.977188 CACACGATGCGACTAAGACA 58.023 50.000 0.00 0.00 0.00 3.41
4640 5193 3.151554 TGCGACTAAGACAAGGTAGTGA 58.848 45.455 0.00 0.00 30.65 3.41
4641 5194 3.570975 TGCGACTAAGACAAGGTAGTGAA 59.429 43.478 0.00 0.00 30.65 3.18
4757 5320 0.684479 TCCTGGATCGGAGGACACTG 60.684 60.000 7.82 0.00 34.49 3.66
4846 5409 2.906897 CAACAAGCACGGCCACCT 60.907 61.111 2.24 0.00 0.00 4.00
4852 5415 4.722700 GCACGGCCACCTCACCAT 62.723 66.667 2.24 0.00 0.00 3.55
4900 5463 1.421485 CGTTCGCAGGCATCAACTC 59.579 57.895 0.00 0.00 0.00 3.01
4901 5464 1.421485 GTTCGCAGGCATCAACTCG 59.579 57.895 0.00 0.00 0.00 4.18
4902 5465 1.741401 TTCGCAGGCATCAACTCGG 60.741 57.895 0.00 0.00 0.00 4.63
4903 5466 3.869272 CGCAGGCATCAACTCGGC 61.869 66.667 0.00 0.00 0.00 5.54
4904 5467 2.747460 GCAGGCATCAACTCGGCA 60.747 61.111 0.00 0.00 0.00 5.69
4905 5468 2.117156 GCAGGCATCAACTCGGCAT 61.117 57.895 0.00 0.00 0.00 4.40
4906 5469 2.020131 CAGGCATCAACTCGGCATC 58.980 57.895 0.00 0.00 0.00 3.91
4907 5470 0.745486 CAGGCATCAACTCGGCATCA 60.745 55.000 0.00 0.00 0.00 3.07
4908 5471 0.035152 AGGCATCAACTCGGCATCAA 60.035 50.000 0.00 0.00 0.00 2.57
4909 5472 0.099436 GGCATCAACTCGGCATCAAC 59.901 55.000 0.00 0.00 0.00 3.18
4910 5473 1.089920 GCATCAACTCGGCATCAACT 58.910 50.000 0.00 0.00 0.00 3.16
5066 5636 1.638589 ACCCAATCCGGAGATTTTGGA 59.361 47.619 28.55 0.00 40.89 3.53
5070 5640 3.378427 CCAATCCGGAGATTTTGGACTTC 59.622 47.826 24.45 0.00 40.89 3.01
5205 5776 2.352371 CCCAATCCATCCCTACCAGAT 58.648 52.381 0.00 0.00 0.00 2.90
5302 5897 1.836166 CTTCAGATCTGCTCCAAGGGA 59.164 52.381 18.36 0.00 0.00 4.20
5378 6025 0.959553 ACGTGATTCTCGACTGTGGT 59.040 50.000 14.43 0.00 0.00 4.16
5595 6276 4.101448 CGGCAAGGGGAGAGGTGG 62.101 72.222 0.00 0.00 0.00 4.61
5596 6277 3.732849 GGCAAGGGGAGAGGTGGG 61.733 72.222 0.00 0.00 0.00 4.61
5597 6278 3.732849 GCAAGGGGAGAGGTGGGG 61.733 72.222 0.00 0.00 0.00 4.96
5783 6466 5.187772 TGTGGTAATGATCAGCTGTAGTTCT 59.812 40.000 14.67 0.00 0.00 3.01
5789 6472 3.578282 TGATCAGCTGTAGTTCTTCCACA 59.422 43.478 14.67 0.00 0.00 4.17
5815 6498 2.512692 TGCTGGAGTATTGTTGCCAT 57.487 45.000 0.00 0.00 0.00 4.40
5905 6589 2.420022 GGTTGATGTATGTCTGTGCACC 59.580 50.000 15.69 0.00 0.00 5.01
5935 6619 1.547372 AGGTTGTTCCTGCGTATACGT 59.453 47.619 25.04 0.00 46.19 3.57
6003 6714 4.537015 GTCAGATTGGAAGAAAACGTTGG 58.463 43.478 0.00 0.00 0.00 3.77
6036 6747 3.737559 TGCCATGTTGGGATTTAGAGT 57.262 42.857 0.00 0.00 38.19 3.24
6130 6846 4.280174 GTGTACACTGGTTCTAGGTCAGAA 59.720 45.833 18.92 0.00 41.10 3.02
6206 6922 8.480501 GGTTATACCCTTGTACTAGATGTTTCA 58.519 37.037 5.85 0.00 30.04 2.69
6245 6961 4.152938 TGCGAGATGTTTTTCTGTCATGAG 59.847 41.667 0.00 0.00 0.00 2.90
6419 7135 5.065914 CCATGATAAATCACTCCCGAATGT 58.934 41.667 0.00 0.00 40.03 2.71
6494 7210 2.212652 TGTAACTGTGCAGTCTGCTTG 58.787 47.619 24.76 16.22 45.31 4.01
6715 7442 6.036191 GCTACTTTCTATTACAGGTTGCAGAC 59.964 42.308 0.00 0.00 0.00 3.51
6819 7546 7.332557 TCTGTTCCCTTTTCGCATATACTTTA 58.667 34.615 0.00 0.00 0.00 1.85
6869 7596 4.082463 TCCCAATTTCGTTTAGCATGGAAC 60.082 41.667 0.00 0.00 0.00 3.62
6871 7598 4.858692 CCAATTTCGTTTAGCATGGAACTG 59.141 41.667 0.00 0.00 0.00 3.16
6872 7599 5.335583 CCAATTTCGTTTAGCATGGAACTGA 60.336 40.000 0.00 0.00 0.00 3.41
6873 7600 6.324819 CAATTTCGTTTAGCATGGAACTGAT 58.675 36.000 0.00 0.00 0.00 2.90
6874 7601 7.415095 CCAATTTCGTTTAGCATGGAACTGATA 60.415 37.037 0.00 0.00 0.00 2.15
6875 7602 6.417191 TTTCGTTTAGCATGGAACTGATAC 57.583 37.500 0.00 0.00 0.00 2.24
6909 7646 1.205417 GCCAAATGTCATGGTTCCAGG 59.795 52.381 0.00 0.00 40.23 4.45
6982 7719 6.170506 CCACCTTACTGTCTTTGCAACTATA 58.829 40.000 0.00 0.00 0.00 1.31
7016 7753 2.863809 ACAACCTAGCAGAAAACTGGG 58.136 47.619 0.00 0.00 41.33 4.45
7044 7781 4.789095 AGTTACAGCAAACACTACAACG 57.211 40.909 0.00 0.00 0.00 4.10
7529 9405 7.096640 CGAAAAACAGGTAAGTTGCTTACAATG 60.097 37.037 17.40 16.38 45.57 2.82
7591 9467 5.906772 ACCTCCGTCCCAAAATATAAGAT 57.093 39.130 0.00 0.00 0.00 2.40
7655 9532 7.504926 TTTTGGGACAGAGGTAGTATTGTAT 57.495 36.000 0.00 0.00 42.39 2.29
7656 9533 8.612486 TTTTGGGACAGAGGTAGTATTGTATA 57.388 34.615 0.00 0.00 42.39 1.47
7878 9756 8.331022 CAGTTGCAACTAAGCTGTAACATATAG 58.669 37.037 30.67 9.26 40.57 1.31
7933 9811 3.956199 ACTCTGGCATTCCCATGTTTATG 59.044 43.478 0.00 0.00 44.33 1.90
7981 9859 7.115947 AGCAACGTAGATTAGAACAAACAGTAC 59.884 37.037 0.00 0.00 0.00 2.73
7982 9860 7.620806 GCAACGTAGATTAGAACAAACAGTACC 60.621 40.741 0.00 0.00 0.00 3.34
8495 10378 9.152595 GAAAACTTGACCTAGTTTATAGGACAG 57.847 37.037 7.92 5.12 45.13 3.51
8567 10450 3.641906 TGCCTAGCAGGTTATTAGGTCTC 59.358 47.826 4.45 0.00 37.80 3.36
8598 10481 8.483758 AGATGATTCATATATGTGCTGCTATGA 58.516 33.333 12.42 2.88 0.00 2.15
8620 10504 2.698855 ACATTGATAGCAGCTTCGGT 57.301 45.000 0.00 0.00 0.00 4.69
8981 10985 1.202615 CGCATCCCTGATCAGTGTCAT 60.203 52.381 21.11 4.77 0.00 3.06
8982 10986 2.219458 GCATCCCTGATCAGTGTCATG 58.781 52.381 21.11 16.10 0.00 3.07
8983 10987 2.158856 GCATCCCTGATCAGTGTCATGA 60.159 50.000 21.11 8.07 0.00 3.07
8984 10988 3.683564 GCATCCCTGATCAGTGTCATGAA 60.684 47.826 21.11 0.00 31.76 2.57
8985 10989 3.900966 TCCCTGATCAGTGTCATGAAG 57.099 47.619 21.11 2.66 31.76 3.02
8986 10990 2.502947 TCCCTGATCAGTGTCATGAAGG 59.497 50.000 21.11 11.54 31.76 3.46
9006 11010 3.445096 AGGTGAAGGTATGCAAATTGCTC 59.555 43.478 19.34 7.54 45.31 4.26
9135 11139 3.624777 AGCTGCATTTGCTACTTGGTAT 58.375 40.909 1.02 0.00 42.66 2.73
9145 11149 2.169978 GCTACTTGGTATTCCCTCCGTT 59.830 50.000 0.00 0.00 0.00 4.44
9147 11151 2.547990 ACTTGGTATTCCCTCCGTTCT 58.452 47.619 0.00 0.00 0.00 3.01
9148 11152 2.236395 ACTTGGTATTCCCTCCGTTCTG 59.764 50.000 0.00 0.00 0.00 3.02
9151 11155 3.112263 TGGTATTCCCTCCGTTCTGAAT 58.888 45.455 0.00 0.00 0.00 2.57
9160 11164 4.322801 CCCTCCGTTCTGAATTACTTGTCT 60.323 45.833 0.00 0.00 0.00 3.41
9162 11166 6.395629 CCTCCGTTCTGAATTACTTGTCTTA 58.604 40.000 0.00 0.00 0.00 2.10
9165 11169 7.837863 TCCGTTCTGAATTACTTGTCTTAGAT 58.162 34.615 0.00 0.00 0.00 1.98
9166 11170 8.311836 TCCGTTCTGAATTACTTGTCTTAGATT 58.688 33.333 0.00 0.00 0.00 2.40
9181 11186 8.155821 TGTCTTAGATTTGTCTAGATACGGAG 57.844 38.462 0.00 0.00 0.00 4.63
9199 11204 5.844004 ACGGAGGTATCTAGCACTAAAATG 58.156 41.667 0.00 0.00 0.00 2.32
9200 11205 5.597182 ACGGAGGTATCTAGCACTAAAATGA 59.403 40.000 0.00 0.00 0.00 2.57
9214 11219 8.364142 AGCACTAAAATGAGTCTAGATACATCC 58.636 37.037 12.66 0.00 0.00 3.51
9215 11220 7.327275 GCACTAAAATGAGTCTAGATACATCCG 59.673 40.741 12.66 6.68 0.00 4.18
9216 11221 8.353684 CACTAAAATGAGTCTAGATACATCCGT 58.646 37.037 12.66 7.10 0.00 4.69
9217 11222 9.570468 ACTAAAATGAGTCTAGATACATCCGTA 57.430 33.333 12.66 6.93 0.00 4.02
9232 11237 6.479972 ACATCCGTATCTAGACAAATCCAA 57.520 37.500 0.00 0.00 0.00 3.53
9233 11238 6.884832 ACATCCGTATCTAGACAAATCCAAA 58.115 36.000 0.00 0.00 0.00 3.28
9246 11251 7.584987 AGACAAATCCAAAGACAAGTAATTCG 58.415 34.615 0.00 0.00 0.00 3.34
9248 11253 6.488683 ACAAATCCAAAGACAAGTAATTCGGA 59.511 34.615 0.00 0.00 0.00 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
166 169 5.601662 ACGATGGACCATATTAGTGTTGAG 58.398 41.667 7.05 0.00 0.00 3.02
242 245 2.620251 ACATCCATATGACCCACACG 57.380 50.000 3.65 0.00 36.54 4.49
356 359 2.025226 CCTCACTACACCTCCACCTCTA 60.025 54.545 0.00 0.00 0.00 2.43
412 416 2.313317 CTAGGTAACGGTGATGCCCTA 58.687 52.381 0.00 0.00 46.39 3.53
601 608 1.069378 GCAGCCTACGTCGTGTGTAC 61.069 60.000 8.47 0.00 0.00 2.90
611 618 3.187227 GTCCATAAATCATGCAGCCTACG 59.813 47.826 0.00 0.00 32.84 3.51
615 622 2.221169 TCGTCCATAAATCATGCAGCC 58.779 47.619 0.00 0.00 32.84 4.85
628 635 5.057149 GGCTAGATTAACAACATCGTCCAT 58.943 41.667 0.00 0.00 0.00 3.41
654 661 1.289109 CCGTGTGCCTTCTTACACCG 61.289 60.000 0.00 0.00 43.15 4.94
660 667 1.414919 TGTTCTACCGTGTGCCTTCTT 59.585 47.619 0.00 0.00 0.00 2.52
672 679 3.673809 GCATAATCGGACGATGTTCTACC 59.326 47.826 8.09 0.00 34.70 3.18
673 680 4.295870 TGCATAATCGGACGATGTTCTAC 58.704 43.478 8.09 0.00 34.70 2.59
711 718 0.817634 TTCGGAACCACACTGCTTGG 60.818 55.000 0.00 0.00 40.32 3.61
713 720 1.308998 CTTTCGGAACCACACTGCTT 58.691 50.000 0.00 0.00 0.00 3.91
718 725 4.463515 GAAACTACTTTCGGAACCACAC 57.536 45.455 0.00 0.00 0.00 3.82
743 750 7.870445 TGATTCAAATAAGCCCTTAAAACACAC 59.130 33.333 0.00 0.00 0.00 3.82
744 751 7.957002 TGATTCAAATAAGCCCTTAAAACACA 58.043 30.769 0.00 0.00 0.00 3.72
745 752 8.825667 TTGATTCAAATAAGCCCTTAAAACAC 57.174 30.769 0.00 0.00 0.00 3.32
890 900 6.742559 AGTACTGTAACTTTCAAGGAGGAA 57.257 37.500 0.00 0.00 0.00 3.36
1182 1193 2.417787 GCTGCATCAATCAAGAAACCCC 60.418 50.000 0.00 0.00 0.00 4.95
1229 1240 0.034863 TTTATCCGGGTCAACAGCCC 60.035 55.000 0.00 0.00 42.68 5.19
1372 1383 2.787723 GCAATATATGCGCGACGAAT 57.212 45.000 12.10 0.00 46.87 3.34
1527 1538 1.202675 TCCACAAACGGAACCTACACC 60.203 52.381 0.00 0.00 29.93 4.16
1539 1550 2.030274 CCGACAAAATCCCTCCACAAAC 60.030 50.000 0.00 0.00 0.00 2.93
1545 1556 2.781681 TTCTCCGACAAAATCCCTCC 57.218 50.000 0.00 0.00 0.00 4.30
1606 1621 2.159028 GCTCCTGCACCTTCTAACCTAG 60.159 54.545 0.00 0.00 39.41 3.02
1647 1662 5.059161 TGTGGACTGAATCTCAACTTGAAG 58.941 41.667 0.00 0.00 0.00 3.02
1651 1666 6.547141 TCAAATTGTGGACTGAATCTCAACTT 59.453 34.615 0.00 0.00 0.00 2.66
1699 1714 1.474677 CCCATCAGCAGATCACTCCAC 60.475 57.143 0.00 0.00 30.20 4.02
1700 1715 0.835276 CCCATCAGCAGATCACTCCA 59.165 55.000 0.00 0.00 30.20 3.86
1701 1716 0.835941 ACCCATCAGCAGATCACTCC 59.164 55.000 0.00 0.00 30.20 3.85
1702 1717 1.474677 CCACCCATCAGCAGATCACTC 60.475 57.143 0.00 0.00 30.20 3.51
1703 1718 0.545171 CCACCCATCAGCAGATCACT 59.455 55.000 0.00 0.00 30.20 3.41
1704 1719 0.465097 CCCACCCATCAGCAGATCAC 60.465 60.000 0.00 0.00 30.20 3.06
1705 1720 1.917495 CCCACCCATCAGCAGATCA 59.083 57.895 0.00 0.00 30.20 2.92
1706 1721 1.527844 GCCCACCCATCAGCAGATC 60.528 63.158 0.00 0.00 30.20 2.75
1707 1722 2.599597 GCCCACCCATCAGCAGAT 59.400 61.111 0.00 0.00 33.87 2.90
1708 1723 3.731728 GGCCCACCCATCAGCAGA 61.732 66.667 0.00 0.00 0.00 4.26
1709 1724 3.736224 AGGCCCACCCATCAGCAG 61.736 66.667 0.00 0.00 36.11 4.24
1710 1725 4.051167 CAGGCCCACCCATCAGCA 62.051 66.667 0.00 0.00 36.11 4.41
1711 1726 3.590466 AACAGGCCCACCCATCAGC 62.590 63.158 0.00 0.00 36.11 4.26
1712 1727 1.679977 CAACAGGCCCACCCATCAG 60.680 63.158 0.00 0.00 36.11 2.90
1713 1728 2.440147 CAACAGGCCCACCCATCA 59.560 61.111 0.00 0.00 36.11 3.07
1714 1729 2.362889 CCAACAGGCCCACCCATC 60.363 66.667 0.00 0.00 36.11 3.51
1715 1730 4.702274 GCCAACAGGCCCACCCAT 62.702 66.667 0.00 0.00 42.80 4.00
1724 1739 2.270986 GGAGCCACTTGCCAACAGG 61.271 63.158 0.00 0.00 42.71 4.00
1725 1740 2.620112 CGGAGCCACTTGCCAACAG 61.620 63.158 0.00 0.00 42.71 3.16
1726 1741 2.594303 CGGAGCCACTTGCCAACA 60.594 61.111 0.00 0.00 42.71 3.33
1727 1742 2.594592 ACGGAGCCACTTGCCAAC 60.595 61.111 0.00 0.00 42.71 3.77
1728 1743 2.594303 CACGGAGCCACTTGCCAA 60.594 61.111 0.00 0.00 42.71 4.52
1729 1744 4.641645 CCACGGAGCCACTTGCCA 62.642 66.667 0.00 0.00 42.71 4.92
1730 1745 4.643387 ACCACGGAGCCACTTGCC 62.643 66.667 0.00 0.00 42.71 4.52
1731 1746 3.357079 CACCACGGAGCCACTTGC 61.357 66.667 0.00 0.00 41.71 4.01
1732 1747 2.669569 CCACCACGGAGCCACTTG 60.670 66.667 0.00 0.00 36.56 3.16
1741 1756 0.319040 CTCATATCGCTCCACCACGG 60.319 60.000 0.00 0.00 0.00 4.94
1742 1757 0.385751 ACTCATATCGCTCCACCACG 59.614 55.000 0.00 0.00 0.00 4.94
1791 2013 3.636313 GACGCGGACGGACCATTCA 62.636 63.158 12.47 0.00 46.04 2.57
1792 2020 2.884207 GACGCGGACGGACCATTC 60.884 66.667 12.47 0.00 46.04 2.67
1824 2052 1.527380 GGGCCGTCTGTTTTGTCCA 60.527 57.895 0.00 0.00 0.00 4.02
1830 2058 3.284449 GCGTTGGGCCGTCTGTTT 61.284 61.111 0.00 0.00 34.80 2.83
2137 2437 1.068434 TGGCAAAAAGCTTTCCGGAAG 59.932 47.619 17.97 12.59 44.79 3.46
2234 2537 2.741985 CCGCAATGCACGACCTGA 60.742 61.111 5.91 0.00 0.00 3.86
2272 2575 1.339610 CAAAGCAATGTTTGGGGTCGA 59.660 47.619 0.00 0.00 34.34 4.20
2284 2588 2.209064 CTCGCAGGCAGCAAAGCAAT 62.209 55.000 1.96 0.00 46.13 3.56
2474 2778 2.691409 ACTAATGTGGTCATGGACGG 57.309 50.000 0.00 0.00 34.19 4.79
2526 2830 3.329889 AAGGACGGAGCATGGCCA 61.330 61.111 8.56 8.56 0.00 5.36
2671 2979 2.258109 GGTCATATCCTACCACTCCCC 58.742 57.143 0.00 0.00 35.73 4.81
2948 3279 5.760253 ACAATCTATACTACCAAGCATGTGC 59.240 40.000 0.00 0.00 42.49 4.57
2949 3280 8.929746 CATACAATCTATACTACCAAGCATGTG 58.070 37.037 0.00 0.00 0.00 3.21
3017 3348 3.517296 TCTTTCACATGCCCCTTGTAA 57.483 42.857 0.00 0.00 0.00 2.41
3037 3372 3.012518 GCTTCAAGTATGACAGTGGCAT 58.987 45.455 17.42 17.42 34.61 4.40
3173 3509 3.458118 TCTCAAAGTTGAACTCTGGGGAA 59.542 43.478 0.00 0.00 36.64 3.97
3183 3519 4.022068 GTGGCCATTGATCTCAAAGTTGAA 60.022 41.667 9.72 0.00 39.55 2.69
3366 3705 2.419021 GGTTTCGAACGATACCCCATCA 60.419 50.000 20.23 0.00 39.34 3.07
3395 3734 1.350351 AGCTTCTGAGTGCTCCATGTT 59.650 47.619 2.15 0.00 33.90 2.71
3500 3848 4.083537 TCAACATTTTCACCCTCGAAATCG 60.084 41.667 0.00 0.00 34.94 3.34
3525 3873 1.821936 CAGGAGGTAGCTGCTCAGG 59.178 63.158 13.55 0.00 0.00 3.86
3591 3940 2.038164 TCTCAAGCTGCACATGAGTCTT 59.962 45.455 21.40 0.00 41.04 3.01
3609 3958 4.818534 TGTGCTCAACAAAGTCAATCTC 57.181 40.909 0.00 0.00 35.24 2.75
3612 3961 4.500205 CCACATGTGCTCAACAAAGTCAAT 60.500 41.667 20.81 0.00 43.61 2.57
3613 3962 3.181488 CCACATGTGCTCAACAAAGTCAA 60.181 43.478 20.81 0.00 43.61 3.18
3620 3969 1.140652 TGAGTCCACATGTGCTCAACA 59.859 47.619 25.05 16.06 44.79 3.33
4034 4567 2.426023 GGTCAACACCGGCTGACT 59.574 61.111 23.56 5.23 41.43 3.41
4262 4799 1.018910 CCAACCGGAAAAGACGTTGT 58.981 50.000 9.46 0.00 0.00 3.32
4264 4801 1.449726 GCCCAACCGGAAAAGACGTT 61.450 55.000 9.46 0.00 0.00 3.99
4318 4855 3.574074 ATGACCGGCAGGCAAAGCT 62.574 57.895 0.00 0.00 42.76 3.74
4324 4861 3.512516 GCTGAATGACCGGCAGGC 61.513 66.667 0.00 0.00 42.76 4.85
4424 4961 8.171400 TGGTTGTTTTATAATACAAAGAGGGGA 58.829 33.333 19.05 0.00 36.15 4.81
4461 5003 6.417930 GCTCTTTGTTTTGACTTGTATGAACC 59.582 38.462 0.00 0.00 0.00 3.62
4523 5073 4.006319 GGCTCCTTTGCTATCATGTATCC 58.994 47.826 0.00 0.00 0.00 2.59
4631 5184 0.320771 CTGCAGCGGTTCACTACCTT 60.321 55.000 0.00 0.00 45.40 3.50
4640 5193 1.377725 CAATCCTCCTGCAGCGGTT 60.378 57.895 8.66 3.12 0.00 4.44
4641 5194 2.270205 CAATCCTCCTGCAGCGGT 59.730 61.111 8.66 0.00 0.00 5.68
4822 5385 1.166531 GCCGTGCTTGTTGTCCTCTT 61.167 55.000 0.00 0.00 0.00 2.85
4900 5463 0.592637 TGCAGTTGAAGTTGATGCCG 59.407 50.000 0.00 0.00 36.04 5.69
4901 5464 2.669364 CTTGCAGTTGAAGTTGATGCC 58.331 47.619 0.00 0.00 36.04 4.40
4902 5465 2.056577 GCTTGCAGTTGAAGTTGATGC 58.943 47.619 0.00 0.00 37.40 3.91
4903 5466 3.305964 CTGCTTGCAGTTGAAGTTGATG 58.694 45.455 13.89 0.00 0.00 3.07
4904 5467 2.288030 GCTGCTTGCAGTTGAAGTTGAT 60.288 45.455 21.55 0.00 42.31 2.57
4905 5468 1.066002 GCTGCTTGCAGTTGAAGTTGA 59.934 47.619 21.55 0.00 42.31 3.18
4906 5469 1.066605 AGCTGCTTGCAGTTGAAGTTG 59.933 47.619 21.55 0.00 45.94 3.16
4907 5470 1.066605 CAGCTGCTTGCAGTTGAAGTT 59.933 47.619 27.39 0.00 45.94 2.66
4908 5471 0.666913 CAGCTGCTTGCAGTTGAAGT 59.333 50.000 27.39 4.36 45.94 3.01
4909 5472 0.949397 TCAGCTGCTTGCAGTTGAAG 59.051 50.000 30.05 12.53 45.94 3.02
4910 5473 0.949397 CTCAGCTGCTTGCAGTTGAA 59.051 50.000 30.93 19.92 45.94 2.69
5081 5651 1.394151 CCCTCACCCTCTCCTTCCT 59.606 63.158 0.00 0.00 0.00 3.36
5205 5776 3.256960 GGTTGGTGGGGCTGAGGA 61.257 66.667 0.00 0.00 0.00 3.71
5378 6025 2.594303 CCAGAGTTGTGGCGGCAA 60.594 61.111 15.50 0.79 0.00 4.52
5500 6180 2.279069 CCCCCGCTCGATGATAGCT 61.279 63.158 0.00 0.00 37.85 3.32
5596 6277 2.974435 CTTAGGGCCCCTCCTCCTCC 62.974 70.000 21.43 0.00 38.30 4.30
5597 6278 1.460497 CTTAGGGCCCCTCCTCCTC 60.460 68.421 21.43 0.00 38.30 3.71
5783 6466 6.747414 ATACTCCAGCATAATACTGTGGAA 57.253 37.500 0.00 0.00 36.86 3.53
5789 6472 5.765182 GGCAACAATACTCCAGCATAATACT 59.235 40.000 0.00 0.00 0.00 2.12
5815 6498 3.901844 GCCCCCTACTGTGATAGTATTGA 59.098 47.826 0.00 0.00 40.94 2.57
5925 6609 3.120442 CGACATCCTCATACGTATACGCA 60.120 47.826 24.64 13.28 44.43 5.24
5935 6619 4.279420 CAGATGGACTTCGACATCCTCATA 59.721 45.833 13.87 0.00 43.42 2.15
6003 6714 2.094675 ACATGGCATCAAGCTAACCAC 58.905 47.619 0.00 0.00 44.79 4.16
6036 6747 8.271458 ACATCATTTGTAATGTCACCTACCATA 58.729 33.333 0.00 0.00 36.57 2.74
6130 6846 6.073222 ACGAAATTTCTATCAACGCAACTTCT 60.073 34.615 15.92 0.00 0.00 2.85
6206 6922 4.385825 TCTCGCATCAAAAAGGTTACAGT 58.614 39.130 0.00 0.00 0.00 3.55
6245 6961 7.165812 CAGTGTGTTAGCAATTCAAGTTTACAC 59.834 37.037 0.00 0.00 35.25 2.90
6494 7210 0.723981 GGATGCTCTTCGTGCTTCAC 59.276 55.000 0.00 0.00 36.65 3.18
6826 7553 4.440663 GGGAGCCATGCTTCTTAATTCAAC 60.441 45.833 0.00 0.00 39.88 3.18
6869 7596 0.103208 GGGCCGACACTCTGTATCAG 59.897 60.000 0.00 0.00 0.00 2.90
6871 7598 1.065928 CGGGCCGACACTCTGTATC 59.934 63.158 24.41 0.00 0.00 2.24
6872 7599 3.077519 GCGGGCCGACACTCTGTAT 62.078 63.158 33.44 0.00 0.00 2.29
6873 7600 3.755628 GCGGGCCGACACTCTGTA 61.756 66.667 33.44 0.00 0.00 2.74
6909 7646 6.021596 CGTGTGGATGTTTGTAATAAGCTTC 58.978 40.000 0.00 0.00 0.00 3.86
7016 7753 5.030874 AGTGTTTGCTGTAACTTAATCGC 57.969 39.130 0.00 0.00 0.00 4.58
7044 7781 4.870363 TGACATTTAGCTTTGGTTTCAGC 58.130 39.130 0.00 0.00 36.16 4.26
7141 7904 2.919666 ATGATTTTGTTTCTCCCGCG 57.080 45.000 0.00 0.00 0.00 6.46
7529 9405 2.892374 ACCAAAGAAAAGTTGCTGCAC 58.108 42.857 0.00 0.00 0.00 4.57
7664 9541 6.691508 TCATCAGGAGATATCAAATACACCG 58.308 40.000 5.32 0.00 31.88 4.94
7878 9756 6.583562 AGTACAAGGGTGATCTAAATACAGC 58.416 40.000 0.00 0.00 0.00 4.40
7933 9811 2.888594 TGCTACGTTAGGTCAGCAATC 58.111 47.619 5.98 0.00 40.87 2.67
7981 9859 5.689383 ACAATTTATAGTAGCGCCATTGG 57.311 39.130 2.29 0.00 0.00 3.16
7982 9860 7.094805 ACCATACAATTTATAGTAGCGCCATTG 60.095 37.037 2.29 2.95 0.00 2.82
8173 10055 2.270352 AATGGGCAAACTTCGAGTCA 57.730 45.000 0.00 0.00 0.00 3.41
8237 10119 5.620738 AGGAGCTCAAACTGCTAATATGA 57.379 39.130 17.19 0.00 41.30 2.15
8251 10133 2.111384 GGACATCTGGTTAGGAGCTCA 58.889 52.381 17.19 0.00 0.00 4.26
8331 10213 3.447918 TCCTATGCTGTTACGCCTTAC 57.552 47.619 0.00 0.00 0.00 2.34
8429 10312 4.708726 ACATAGCTGTGCAAAAGAATCC 57.291 40.909 10.79 0.00 33.22 3.01
8567 10450 8.766151 GCAGCACATATATGAATCATCTATCTG 58.234 37.037 19.63 5.46 0.00 2.90
8581 10464 9.070179 TCAATGTTTTCATAGCAGCACATATAT 57.930 29.630 0.00 0.00 39.94 0.86
8598 10481 3.758554 ACCGAAGCTGCTATCAATGTTTT 59.241 39.130 0.90 0.00 0.00 2.43
8930 10814 2.305405 GCACCGAGCATCACTCATC 58.695 57.895 0.00 0.00 46.63 2.92
8931 10815 4.528674 GCACCGAGCATCACTCAT 57.471 55.556 0.00 0.00 46.63 2.90
8981 10985 4.321899 GCAATTTGCATACCTTCACCTTCA 60.322 41.667 16.35 0.00 44.26 3.02
8982 10986 4.176271 GCAATTTGCATACCTTCACCTTC 58.824 43.478 16.35 0.00 44.26 3.46
8983 10987 4.192429 GCAATTTGCATACCTTCACCTT 57.808 40.909 16.35 0.00 44.26 3.50
8984 10988 3.874392 GCAATTTGCATACCTTCACCT 57.126 42.857 16.35 0.00 44.26 4.00
9006 11010 2.002586 CTGATTACACAGGCAAGGTCG 58.997 52.381 0.00 0.00 34.64 4.79
9135 11139 4.041198 ACAAGTAATTCAGAACGGAGGGAA 59.959 41.667 0.00 0.00 0.00 3.97
9160 11164 9.228949 GATACCTCCGTATCTAGACAAATCTAA 57.771 37.037 0.00 0.00 45.11 2.10
9162 11166 7.690952 GATACCTCCGTATCTAGACAAATCT 57.309 40.000 0.00 0.00 45.11 2.40
9175 11179 6.774170 TCATTTTAGTGCTAGATACCTCCGTA 59.226 38.462 0.00 0.00 0.00 4.02
9177 11181 6.085555 TCATTTTAGTGCTAGATACCTCCG 57.914 41.667 0.00 0.00 0.00 4.63
9181 11186 9.069082 TCTAGACTCATTTTAGTGCTAGATACC 57.931 37.037 0.00 0.00 34.69 2.73
9190 11195 8.353684 ACGGATGTATCTAGACTCATTTTAGTG 58.646 37.037 11.25 3.85 0.00 2.74
9214 11219 7.545965 ACTTGTCTTTGGATTTGTCTAGATACG 59.454 37.037 0.00 0.00 0.00 3.06
9215 11220 8.779354 ACTTGTCTTTGGATTTGTCTAGATAC 57.221 34.615 0.00 0.00 0.00 2.24
9217 11222 9.965902 ATTACTTGTCTTTGGATTTGTCTAGAT 57.034 29.630 0.00 0.00 0.00 1.98
9222 11227 6.801862 CCGAATTACTTGTCTTTGGATTTGTC 59.198 38.462 0.00 0.00 0.00 3.18
9223 11228 6.488683 TCCGAATTACTTGTCTTTGGATTTGT 59.511 34.615 0.00 0.00 29.31 2.83
9226 11231 6.348213 CGTTCCGAATTACTTGTCTTTGGATT 60.348 38.462 6.06 0.00 33.47 3.01
9227 11232 5.121768 CGTTCCGAATTACTTGTCTTTGGAT 59.878 40.000 6.06 0.00 33.47 3.41
9229 11234 4.378046 CCGTTCCGAATTACTTGTCTTTGG 60.378 45.833 0.00 0.00 0.00 3.28
9230 11235 4.449743 TCCGTTCCGAATTACTTGTCTTTG 59.550 41.667 0.00 0.00 0.00 2.77
9232 11237 4.243270 CTCCGTTCCGAATTACTTGTCTT 58.757 43.478 0.00 0.00 0.00 3.01
9233 11238 3.368116 CCTCCGTTCCGAATTACTTGTCT 60.368 47.826 0.00 0.00 0.00 3.41
9242 11247 1.400737 CTACTCCCTCCGTTCCGAAT 58.599 55.000 0.00 0.00 0.00 3.34
9246 11251 0.324091 TCACCTACTCCCTCCGTTCC 60.324 60.000 0.00 0.00 0.00 3.62
9248 11253 3.393426 TTATCACCTACTCCCTCCGTT 57.607 47.619 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.