Multiple sequence alignment - TraesCS2A01G128500

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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 TraesCS2A01G128500 chr2A 100.000 8192 0 0 1 8192 76360311 76368502 0.000000e+00 15128.0
1 TraesCS2A01G128500 chr2D 93.206 6638 354 36 333 6898 76545001 76551613 0.000000e+00 9670.0
2 TraesCS2A01G128500 chr2D 88.419 544 41 9 7635 8165 646136193 646135659 3.220000e-178 636.0
3 TraesCS2A01G128500 chr2D 91.453 468 30 6 7211 7676 646136683 646136224 1.160000e-177 634.0
4 TraesCS2A01G128500 chr2D 88.841 233 23 3 6974 7205 76551634 76551864 4.840000e-72 283.0
5 TraesCS2A01G128500 chr2D 89.394 66 0 1 121 179 76544715 76544780 8.820000e-10 76.8
6 TraesCS2A01G128500 chr2B 94.505 3949 164 23 3292 7204 117628859 117632790 0.000000e+00 6041.0
7 TraesCS2A01G128500 chr2B 91.656 2301 154 18 975 3250 117626259 117628546 0.000000e+00 3151.0
8 TraesCS2A01G128500 chr2B 92.814 1002 49 16 7196 8192 23475560 23474577 0.000000e+00 1430.0
9 TraesCS2A01G128500 chr2B 88.770 187 11 4 653 829 117625776 117625962 3.850000e-53 220.0
10 TraesCS2A01G128500 chr2B 92.742 124 5 3 1 120 117621919 117622042 8.450000e-40 176.0
11 TraesCS2A01G128500 chr5B 92.230 991 51 12 7206 8191 82138249 82139218 0.000000e+00 1380.0
12 TraesCS2A01G128500 chr5B 87.332 742 67 15 7464 8191 648730367 648731095 0.000000e+00 824.0
13 TraesCS2A01G128500 chr5B 87.455 550 42 13 7603 8135 644609253 644609792 7.030000e-170 608.0
14 TraesCS2A01G128500 chr5B 87.500 144 15 3 7241 7383 644608708 644608849 6.580000e-36 163.0
15 TraesCS2A01G128500 chr5D 87.190 1007 71 21 7207 8192 445302033 445303002 0.000000e+00 1092.0
16 TraesCS2A01G128500 chr6B 89.218 742 56 11 7464 8192 574472134 574472864 0.000000e+00 905.0
17 TraesCS2A01G128500 chr7B 89.113 744 56 11 7463 8192 710157013 710157745 0.000000e+00 902.0
18 TraesCS2A01G128500 chr7B 77.229 1357 270 25 3947 5273 14996797 14998144 0.000000e+00 758.0
19 TraesCS2A01G128500 chr7B 75.482 1505 267 72 3360 4829 12807713 12809150 6.930000e-180 641.0
20 TraesCS2A01G128500 chr7B 82.444 712 99 18 5312 6013 12182995 12182300 4.230000e-167 599.0
21 TraesCS2A01G128500 chr7B 77.446 1073 191 34 3783 4829 12536848 12535801 1.970000e-165 593.0
22 TraesCS2A01G128500 chr7B 82.244 704 100 16 5312 6004 12396888 12396199 1.180000e-162 584.0
23 TraesCS2A01G128500 chr7B 83.622 635 86 11 5362 5993 14065771 14065152 1.530000e-161 580.0
24 TraesCS2A01G128500 chr7B 78.208 904 178 14 3930 4829 13625963 13625075 2.000000e-155 560.0
25 TraesCS2A01G128500 chr7B 74.225 1420 326 27 1837 3243 13810431 13809039 7.180000e-155 558.0
26 TraesCS2A01G128500 chr7B 79.447 579 76 30 6225 6787 12396045 12395494 3.610000e-98 370.0
27 TraesCS2A01G128500 chr7B 78.887 521 89 14 3360 3880 12185247 12184748 4.740000e-87 333.0
28 TraesCS2A01G128500 chr7B 84.967 306 46 0 4971 5276 13115376 13115071 2.220000e-80 311.0
29 TraesCS2A01G128500 chr7B 85.563 284 41 0 4970 5253 13624973 13624690 1.730000e-76 298.0
30 TraesCS2A01G128500 chr7B 83.439 157 20 4 6147 6301 12182243 12182091 3.080000e-29 141.0
31 TraesCS2A01G128500 chr7B 85.366 123 16 2 6219 6340 12819147 12819268 8.630000e-25 126.0
32 TraesCS2A01G128500 chr1B 88.425 743 60 14 7464 8192 443569 444299 0.000000e+00 872.0
33 TraesCS2A01G128500 chr3B 87.349 743 66 15 7464 8192 129248838 129249566 0.000000e+00 826.0
34 TraesCS2A01G128500 chr6D 86.405 765 52 21 7463 8192 353640904 353641651 0.000000e+00 789.0
35 TraesCS2A01G128500 chr6D 85.714 70 10 0 7205 7274 61766530 61766599 3.170000e-09 75.0
36 TraesCS2A01G128500 chr1A 76.190 1386 309 15 1838 3218 21831808 21830439 0.000000e+00 712.0
37 TraesCS2A01G128500 chr7D 76.219 1497 254 68 3367 4829 70232046 70233474 0.000000e+00 699.0
38 TraesCS2A01G128500 chr7D 77.446 1073 191 34 3783 4829 70749189 70750236 1.970000e-165 593.0
39 TraesCS2A01G128500 chr7D 91.647 431 25 3 7463 7883 105262807 105263236 3.290000e-163 586.0
40 TraesCS2A01G128500 chr7D 81.767 713 102 19 5312 6013 69659928 69659233 9.220000e-159 571.0
41 TraesCS2A01G128500 chr7D 76.679 1072 201 35 3783 4829 69941219 69940172 4.320000e-152 549.0
42 TraesCS2A01G128500 chr7D 82.233 636 96 12 5362 5993 71316316 71315694 4.350000e-147 532.0
43 TraesCS2A01G128500 chr7D 77.547 913 176 19 3931 4829 71337255 71336358 2.620000e-144 523.0
44 TraesCS2A01G128500 chr7D 80.531 565 75 21 6227 6787 70827617 70827084 1.280000e-107 401.0
45 TraesCS2A01G128500 chr7D 89.769 303 22 5 7895 8192 105264311 105264609 6.000000e-101 379.0
46 TraesCS2A01G128500 chr7D 79.038 582 91 23 6221 6787 69816546 69815981 3.610000e-98 370.0
47 TraesCS2A01G128500 chr7D 86.025 322 39 6 6510 6829 72173761 72174078 2.830000e-89 340.0
48 TraesCS2A01G128500 chr7D 84.273 337 49 4 3360 3694 70831039 70830705 7.930000e-85 326.0
49 TraesCS2A01G128500 chr7D 85.065 308 46 0 4975 5282 69660573 69660266 1.720000e-81 315.0
50 TraesCS2A01G128500 chr7D 84.466 103 14 2 7206 7307 74059428 74059529 5.230000e-17 100.0
51 TraesCS2A01G128500 chr7A 82.517 715 96 21 5312 6013 76488155 76487457 1.180000e-167 601.0
52 TraesCS2A01G128500 chr7A 82.849 688 93 16 5312 5990 76191480 76190809 1.970000e-165 593.0
53 TraesCS2A01G128500 chr7A 77.207 895 175 20 3949 4829 77074340 77073461 5.710000e-136 496.0
54 TraesCS2A01G128500 chr7A 81.579 570 84 17 6227 6785 76939093 76938534 1.250000e-122 451.0
55 TraesCS2A01G128500 chr7A 86.025 322 39 6 6510 6829 77163854 77164171 2.830000e-89 340.0
56 TraesCS2A01G128500 chr7A 85.668 307 44 0 4970 5276 76983544 76983238 2.850000e-84 324.0
57 TraesCS2A01G128500 chr7A 84.553 123 18 1 6221 6343 76487320 76487199 4.020000e-23 121.0
58 TraesCS2A01G128500 chr7A 78.325 203 32 10 6219 6417 77006776 77006582 4.020000e-23 121.0
59 TraesCS2A01G128500 chr7A 89.873 79 7 1 7208 7286 51347966 51348043 5.230000e-17 100.0
60 TraesCS2A01G128500 chrUn 78.540 904 175 14 3930 4829 84286020 84285132 1.980000e-160 577.0
61 TraesCS2A01G128500 chrUn 78.540 904 175 14 3930 4829 226939345 226938457 1.980000e-160 577.0
62 TraesCS2A01G128500 chrUn 90.253 277 25 2 6505 6780 329448602 329448877 2.170000e-95 361.0
63 TraesCS2A01G128500 chrUn 86.319 307 42 0 4970 5276 84285030 84284724 1.320000e-87 335.0
64 TraesCS2A01G128500 chrUn 86.319 307 42 0 4970 5276 226938355 226938049 1.320000e-87 335.0
65 TraesCS2A01G128500 chrUn 82.000 150 23 3 6219 6368 329448186 329448331 3.100000e-24 124.0
66 TraesCS2A01G128500 chr3A 94.286 70 3 1 7197 7265 682274589 682274520 1.120000e-18 106.0
67 TraesCS2A01G128500 chr1D 89.024 82 9 0 7206 7287 437689157 437689076 1.450000e-17 102.0
68 TraesCS2A01G128500 chr1D 89.474 76 6 2 7198 7271 466009143 466009068 2.430000e-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 TraesCS2A01G128500 chr2A 76360311 76368502 8191 False 15128.000000 15128 100.000000 1 8192 1 chr2A.!!$F1 8191
1 TraesCS2A01G128500 chr2D 76544715 76551864 7149 False 3343.266667 9670 90.480333 121 7205 3 chr2D.!!$F1 7084
2 TraesCS2A01G128500 chr2D 646135659 646136683 1024 True 635.000000 636 89.936000 7211 8165 2 chr2D.!!$R1 954
3 TraesCS2A01G128500 chr2B 117621919 117632790 10871 False 2397.000000 6041 91.918250 1 7204 4 chr2B.!!$F1 7203
4 TraesCS2A01G128500 chr2B 23474577 23475560 983 True 1430.000000 1430 92.814000 7196 8192 1 chr2B.!!$R1 996
5 TraesCS2A01G128500 chr5B 82138249 82139218 969 False 1380.000000 1380 92.230000 7206 8191 1 chr5B.!!$F1 985
6 TraesCS2A01G128500 chr5B 648730367 648731095 728 False 824.000000 824 87.332000 7464 8191 1 chr5B.!!$F2 727
7 TraesCS2A01G128500 chr5B 644608708 644609792 1084 False 385.500000 608 87.477500 7241 8135 2 chr5B.!!$F3 894
8 TraesCS2A01G128500 chr5D 445302033 445303002 969 False 1092.000000 1092 87.190000 7207 8192 1 chr5D.!!$F1 985
9 TraesCS2A01G128500 chr6B 574472134 574472864 730 False 905.000000 905 89.218000 7464 8192 1 chr6B.!!$F1 728
10 TraesCS2A01G128500 chr7B 710157013 710157745 732 False 902.000000 902 89.113000 7463 8192 1 chr7B.!!$F4 729
11 TraesCS2A01G128500 chr7B 14996797 14998144 1347 False 758.000000 758 77.229000 3947 5273 1 chr7B.!!$F3 1326
12 TraesCS2A01G128500 chr7B 12807713 12809150 1437 False 641.000000 641 75.482000 3360 4829 1 chr7B.!!$F1 1469
13 TraesCS2A01G128500 chr7B 12535801 12536848 1047 True 593.000000 593 77.446000 3783 4829 1 chr7B.!!$R1 1046
14 TraesCS2A01G128500 chr7B 14065152 14065771 619 True 580.000000 580 83.622000 5362 5993 1 chr7B.!!$R4 631
15 TraesCS2A01G128500 chr7B 13809039 13810431 1392 True 558.000000 558 74.225000 1837 3243 1 chr7B.!!$R3 1406
16 TraesCS2A01G128500 chr7B 12395494 12396888 1394 True 477.000000 584 80.845500 5312 6787 2 chr7B.!!$R6 1475
17 TraesCS2A01G128500 chr7B 13624690 13625963 1273 True 429.000000 560 81.885500 3930 5253 2 chr7B.!!$R7 1323
18 TraesCS2A01G128500 chr7B 12182091 12185247 3156 True 357.666667 599 81.590000 3360 6301 3 chr7B.!!$R5 2941
19 TraesCS2A01G128500 chr1B 443569 444299 730 False 872.000000 872 88.425000 7464 8192 1 chr1B.!!$F1 728
20 TraesCS2A01G128500 chr3B 129248838 129249566 728 False 826.000000 826 87.349000 7464 8192 1 chr3B.!!$F1 728
21 TraesCS2A01G128500 chr6D 353640904 353641651 747 False 789.000000 789 86.405000 7463 8192 1 chr6D.!!$F2 729
22 TraesCS2A01G128500 chr1A 21830439 21831808 1369 True 712.000000 712 76.190000 1838 3218 1 chr1A.!!$R1 1380
23 TraesCS2A01G128500 chr7D 70232046 70233474 1428 False 699.000000 699 76.219000 3367 4829 1 chr7D.!!$F1 1462
24 TraesCS2A01G128500 chr7D 70749189 70750236 1047 False 593.000000 593 77.446000 3783 4829 1 chr7D.!!$F2 1046
25 TraesCS2A01G128500 chr7D 69940172 69941219 1047 True 549.000000 549 76.679000 3783 4829 1 chr7D.!!$R2 1046
26 TraesCS2A01G128500 chr7D 71315694 71316316 622 True 532.000000 532 82.233000 5362 5993 1 chr7D.!!$R3 631
27 TraesCS2A01G128500 chr7D 71336358 71337255 897 True 523.000000 523 77.547000 3931 4829 1 chr7D.!!$R4 898
28 TraesCS2A01G128500 chr7D 105262807 105264609 1802 False 482.500000 586 90.708000 7463 8192 2 chr7D.!!$F5 729
29 TraesCS2A01G128500 chr7D 69659233 69660573 1340 True 443.000000 571 83.416000 4975 6013 2 chr7D.!!$R5 1038
30 TraesCS2A01G128500 chr7D 69815981 69816546 565 True 370.000000 370 79.038000 6221 6787 1 chr7D.!!$R1 566
31 TraesCS2A01G128500 chr7D 70827084 70831039 3955 True 363.500000 401 82.402000 3360 6787 2 chr7D.!!$R6 3427
32 TraesCS2A01G128500 chr7A 76190809 76191480 671 True 593.000000 593 82.849000 5312 5990 1 chr7A.!!$R1 678
33 TraesCS2A01G128500 chr7A 77073461 77074340 879 True 496.000000 496 77.207000 3949 4829 1 chr7A.!!$R5 880
34 TraesCS2A01G128500 chr7A 76938534 76939093 559 True 451.000000 451 81.579000 6227 6785 1 chr7A.!!$R2 558
35 TraesCS2A01G128500 chr7A 76487199 76488155 956 True 361.000000 601 83.535000 5312 6343 2 chr7A.!!$R6 1031
36 TraesCS2A01G128500 chrUn 84284724 84286020 1296 True 456.000000 577 82.429500 3930 5276 2 chrUn.!!$R1 1346
37 TraesCS2A01G128500 chrUn 226938049 226939345 1296 True 456.000000 577 82.429500 3930 5276 2 chrUn.!!$R2 1346
38 TraesCS2A01G128500 chrUn 329448186 329448877 691 False 242.500000 361 86.126500 6219 6780 2 chrUn.!!$F1 561

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
596 1517 0.109342 CAGATGGGTATGGGGCAGAC 59.891 60.000 0.00 0.0 0.00 3.51 F
1411 4878 0.249447 GCTGCTTGGGGTTGTTTCAC 60.249 55.000 0.00 0.0 0.00 3.18 F
1948 5439 0.037697 ACGACAAAGACATGCCGCTA 60.038 50.000 0.00 0.0 28.49 4.26 F
2192 5689 0.474273 AACCGGGAAAGTGACCCCTA 60.474 55.000 6.32 0.0 44.09 3.53 F
2875 6373 0.603569 ACGTCTTCACCTTCATCGCT 59.396 50.000 0.00 0.0 0.00 4.93 F
3621 7424 1.002366 GCTGTACCAAGACGCAGATG 58.998 55.000 0.00 0.0 0.00 2.90 F
4356 8301 1.160329 CGGCGAATGTCCAAGATCCC 61.160 60.000 0.00 0.0 0.00 3.85 F
5282 9263 1.195115 TAGCCCTGGTGAGTAGCTTG 58.805 55.000 0.00 0.0 35.03 4.01 F
6653 11488 1.538419 GCCACGGCCTCTATAGACAAC 60.538 57.143 0.00 0.0 34.56 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1582 5052 0.037326 TCAGCAAGACCGACCATGAC 60.037 55.000 0.00 0.00 0.00 3.06 R
3121 6626 0.786435 AAATGGCAACCTTCTCCCCT 59.214 50.000 0.00 0.00 0.00 4.79 R
3539 7342 1.834822 CACTCCCCTCTCCCCGATC 60.835 68.421 0.00 0.00 0.00 3.69 R
3563 7366 2.031012 TGCTTCTGACCGCCACTG 59.969 61.111 0.00 0.00 0.00 3.66 R
4609 8564 2.162608 TGGCCCATCATTAAAAACGTCG 59.837 45.455 0.00 0.00 0.00 5.12 R
5168 9149 3.058016 CGTTGAATCAGCCATTCTGTTGT 60.058 43.478 7.36 0.00 41.58 3.32 R
5699 10351 0.618458 TCCATGCAGTACAAGGGGAC 59.382 55.000 0.00 0.00 37.74 4.46 R
6930 11771 1.767759 AGCATCCACTAATTGGTGCC 58.232 50.000 15.96 4.62 45.96 5.01 R
7559 12641 1.321474 CCAGGACTGAGCAAAGCAAA 58.679 50.000 0.00 0.00 0.00 3.68 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
24 25 2.090967 CGATGCAGCCGTTTTGAAATTG 59.909 45.455 0.00 0.00 0.00 2.32
39 41 4.753233 TGAAATTGTGGAGTTTGTGGTTG 58.247 39.130 0.00 0.00 0.00 3.77
48 50 0.249031 GTTTGTGGTTGCACTGGCTC 60.249 55.000 0.00 0.00 41.91 4.70
179 246 8.081633 CCAAATTTGAAGTTGATAGCACTACAA 58.918 33.333 19.86 0.00 36.17 2.41
180 247 9.121517 CAAATTTGAAGTTGATAGCACTACAAG 57.878 33.333 13.08 0.00 36.17 3.16
182 249 4.253685 TGAAGTTGATAGCACTACAAGGC 58.746 43.478 0.00 0.00 0.00 4.35
183 250 2.893637 AGTTGATAGCACTACAAGGCG 58.106 47.619 0.00 0.00 34.54 5.52
184 251 1.327764 GTTGATAGCACTACAAGGCGC 59.672 52.381 0.00 0.00 34.54 6.53
185 252 0.824109 TGATAGCACTACAAGGCGCT 59.176 50.000 7.64 0.00 38.51 5.92
186 253 1.202417 TGATAGCACTACAAGGCGCTC 60.202 52.381 7.64 0.00 35.93 5.03
200 317 3.780173 GCTCCTGCGCTCCCTTCT 61.780 66.667 9.73 0.00 0.00 2.85
241 453 2.642311 TGGAGGAGCTGTGTGGATTTTA 59.358 45.455 0.00 0.00 0.00 1.52
269 873 1.646189 GCTTGGGTGATTCTCTCGTC 58.354 55.000 0.00 0.00 0.00 4.20
284 888 0.537188 TCGTCCTCCCTTCTTGCATC 59.463 55.000 0.00 0.00 0.00 3.91
305 1136 4.110493 CGATGCTCCTTCGGGTTC 57.890 61.111 0.00 0.00 36.28 3.62
309 1140 0.250513 ATGCTCCTTCGGGTTCTGTC 59.749 55.000 0.00 0.00 36.28 3.51
310 1141 1.079057 GCTCCTTCGGGTTCTGTCC 60.079 63.158 0.00 0.00 36.28 4.02
318 1149 3.386543 GGGTTCTGTCCGATCCATG 57.613 57.895 0.00 0.00 33.85 3.66
319 1150 0.179045 GGGTTCTGTCCGATCCATGG 60.179 60.000 4.97 4.97 33.85 3.66
320 1151 0.541863 GGTTCTGTCCGATCCATGGT 59.458 55.000 12.58 0.00 32.68 3.55
321 1152 1.473434 GGTTCTGTCCGATCCATGGTC 60.473 57.143 12.58 7.90 32.68 4.02
323 1154 2.693591 GTTCTGTCCGATCCATGGTCTA 59.306 50.000 12.58 0.00 0.00 2.59
324 1155 3.244887 TCTGTCCGATCCATGGTCTAT 57.755 47.619 12.58 0.00 0.00 1.98
327 1158 0.976641 TCCGATCCATGGTCTATGCC 59.023 55.000 12.58 0.00 35.37 4.40
328 1159 0.686789 CCGATCCATGGTCTATGCCA 59.313 55.000 12.58 0.00 43.48 4.92
329 1160 1.072173 CCGATCCATGGTCTATGCCAA 59.928 52.381 12.58 0.00 42.48 4.52
330 1161 2.146342 CGATCCATGGTCTATGCCAAC 58.854 52.381 12.58 0.00 42.48 3.77
331 1162 2.485302 CGATCCATGGTCTATGCCAACA 60.485 50.000 12.58 0.00 42.48 3.33
332 1163 2.715749 TCCATGGTCTATGCCAACAG 57.284 50.000 12.58 0.00 42.48 3.16
422 1259 4.873010 TGCTTAGGATCCTCTTGTAGACT 58.127 43.478 20.22 0.00 0.00 3.24
503 1424 1.070175 GTTGGATGTGTTCGTCGGTTG 60.070 52.381 0.00 0.00 0.00 3.77
520 1441 0.185416 TTGGCTCCGGGTTTTGGTTA 59.815 50.000 0.00 0.00 0.00 2.85
595 1516 1.061905 CCAGATGGGTATGGGGCAGA 61.062 60.000 0.00 0.00 32.96 4.26
596 1517 0.109342 CAGATGGGTATGGGGCAGAC 59.891 60.000 0.00 0.00 0.00 3.51
620 1541 2.034053 CCTTCCTCTCTGTATCTGCGTC 59.966 54.545 0.00 0.00 0.00 5.19
633 1554 0.520404 CTGCGTCTCATGCTTTGCTT 59.480 50.000 0.00 0.00 0.00 3.91
844 4109 3.279116 GTGCCACTGTTGCTCGCA 61.279 61.111 5.42 0.00 0.00 5.10
902 4334 0.460109 TGGGATCGAATCGTGCAGTG 60.460 55.000 1.52 0.00 0.00 3.66
933 4383 3.289834 CCTGTTTGCGGCTGCTGT 61.290 61.111 20.27 0.00 43.34 4.40
973 4423 1.039068 CAGGACTCTGCTCGATCCAT 58.961 55.000 3.47 0.00 33.86 3.41
983 4433 1.747956 CTCGATCCATCTGTTCGTCG 58.252 55.000 0.00 0.00 34.60 5.12
1015 4465 1.067749 CAGATGAGCTCCCTCGCAG 59.932 63.158 12.15 0.94 41.13 5.18
1021 4484 2.202946 GCTCCCTCGCAGGTAAGC 60.203 66.667 9.44 9.44 35.84 3.09
1040 4503 2.152016 GCACTGTACTTTTCTCACCCC 58.848 52.381 0.00 0.00 0.00 4.95
1050 4514 1.852157 TTCTCACCCCTCCCATGCAC 61.852 60.000 0.00 0.00 0.00 4.57
1059 4523 4.764336 CCCATGCACGTTGCTGCG 62.764 66.667 10.54 0.00 45.31 5.18
1062 4526 1.225827 CATGCACGTTGCTGCGTAG 60.226 57.895 10.54 0.00 45.31 3.51
1063 4527 1.667830 ATGCACGTTGCTGCGTAGT 60.668 52.632 1.53 0.00 45.31 2.73
1064 4528 0.389296 ATGCACGTTGCTGCGTAGTA 60.389 50.000 1.53 0.00 45.31 1.82
1105 4569 1.195115 TGCTACTACAAGAGCTGGGG 58.805 55.000 0.00 0.00 39.54 4.96
1129 4593 3.121030 ACTGCGACGCAATGCTCC 61.121 61.111 24.51 0.00 38.41 4.70
1141 4605 2.033801 GCAATGCTCCGTGATTTATGCT 59.966 45.455 0.00 0.00 0.00 3.79
1201 4665 2.594592 GCTTGTTGCGACCAGGGT 60.595 61.111 7.27 0.00 0.00 4.34
1266 4730 2.433664 GGAAACCGGCATCGTCGT 60.434 61.111 0.00 0.00 33.95 4.34
1324 4788 2.757508 CTCCCCGAGAGCAGAGCA 60.758 66.667 0.00 0.00 35.31 4.26
1357 4824 3.710722 CGGCTTCTCAGGCCCTGT 61.711 66.667 11.27 0.00 46.24 4.00
1360 4827 1.743252 GCTTCTCAGGCCCTGTTCG 60.743 63.158 11.27 0.90 32.61 3.95
1408 4875 0.763986 ATGGCTGCTTGGGGTTGTTT 60.764 50.000 0.00 0.00 0.00 2.83
1411 4878 0.249447 GCTGCTTGGGGTTGTTTCAC 60.249 55.000 0.00 0.00 0.00 3.18
1457 4924 0.534203 GGGGAGCAACTTCGACAACA 60.534 55.000 0.00 0.00 0.00 3.33
1462 4929 2.548057 GAGCAACTTCGACAACAATCCA 59.452 45.455 0.00 0.00 0.00 3.41
1501 4971 1.355210 GCACTGGTGGTTTGTGACG 59.645 57.895 2.84 0.00 33.95 4.35
1507 4977 1.092921 GGTGGTTTGTGACGCTGTCA 61.093 55.000 7.20 7.20 40.50 3.58
1516 4986 0.396435 TGACGCTGTCACAGGGATTT 59.604 50.000 27.50 6.00 45.41 2.17
1528 4998 2.310052 ACAGGGATTTAGCTTGCTCCTT 59.690 45.455 0.00 0.00 0.00 3.36
1544 5014 2.281484 TTGCCGGCTTCGCTTTCT 60.281 55.556 29.70 0.00 0.00 2.52
1546 5016 2.435059 GCCGGCTTCGCTTTCTCT 60.435 61.111 22.15 0.00 0.00 3.10
1658 5128 2.555123 GCCATTGTTGCGGAGAAGA 58.445 52.632 0.00 0.00 0.00 2.87
1674 5144 3.228453 AGAAGACGGTCACTGTTAAGGA 58.772 45.455 11.27 0.00 0.00 3.36
1678 5148 1.270147 ACGGTCACTGTTAAGGACTGC 60.270 52.381 5.11 0.00 40.71 4.40
1695 5165 1.274703 TGCTTGGATCTCCTGTCCCC 61.275 60.000 0.00 0.00 34.76 4.81
1729 5199 7.518052 GCAGTTATGTTTCTCATCTACAGCATC 60.518 40.741 0.00 0.00 35.70 3.91
1789 5268 5.426833 AGGATTATACAAGCCACTGAAGACT 59.573 40.000 0.00 0.00 43.02 3.24
1791 5270 2.169832 TACAAGCCACTGAAGACTGC 57.830 50.000 0.00 0.00 0.00 4.40
1813 5304 4.752146 CTGATACAGCTGACAGTGATCAA 58.248 43.478 23.35 3.94 0.00 2.57
1891 5382 2.286872 CAGATGACATTCTGGTGGCTC 58.713 52.381 0.00 0.00 39.58 4.70
1948 5439 0.037697 ACGACAAAGACATGCCGCTA 60.038 50.000 0.00 0.00 28.49 4.26
2003 5494 2.562738 TCGATGTTCTTGGAGAAGCTGA 59.437 45.455 0.00 0.00 34.42 4.26
2004 5495 2.670414 CGATGTTCTTGGAGAAGCTGAC 59.330 50.000 0.00 0.00 34.42 3.51
2005 5496 2.550830 TGTTCTTGGAGAAGCTGACC 57.449 50.000 0.00 0.00 34.42 4.02
2006 5497 1.768275 TGTTCTTGGAGAAGCTGACCA 59.232 47.619 3.18 3.18 34.42 4.02
2007 5498 2.172505 TGTTCTTGGAGAAGCTGACCAA 59.827 45.455 15.41 15.41 40.68 3.67
2008 5499 2.550180 GTTCTTGGAGAAGCTGACCAAC 59.450 50.000 13.20 4.34 38.52 3.77
2067 5564 0.681733 TCAATCCTCTGGGCTATCGC 59.318 55.000 0.00 0.00 0.00 4.58
2098 5595 1.592669 GTGCGGGATCATGGTCTCG 60.593 63.158 24.12 24.12 44.74 4.04
2189 5686 0.887836 GTCAACCGGGAAAGTGACCC 60.888 60.000 6.32 0.00 43.57 4.46
2192 5689 0.474273 AACCGGGAAAGTGACCCCTA 60.474 55.000 6.32 0.00 44.09 3.53
2245 5742 3.427098 CGCTCATGTTCATCTGCAAATGT 60.427 43.478 0.00 0.00 0.00 2.71
2875 6373 0.603569 ACGTCTTCACCTTCATCGCT 59.396 50.000 0.00 0.00 0.00 4.93
3087 6592 2.749621 GGTGCGAAGATCCATCAAAACT 59.250 45.455 0.00 0.00 0.00 2.66
3121 6626 6.268847 AGGATGTAAATTTGGTGGTTAAAGCA 59.731 34.615 0.00 0.00 0.00 3.91
3225 6730 2.942376 CTCAAGGCACGGTAATAATGCA 59.058 45.455 0.00 0.00 41.27 3.96
3226 6731 3.550820 TCAAGGCACGGTAATAATGCAT 58.449 40.909 0.00 0.00 41.27 3.96
3230 6735 6.095580 TCAAGGCACGGTAATAATGCATTTTA 59.904 34.615 18.75 12.56 40.15 1.52
3231 6736 6.072112 AGGCACGGTAATAATGCATTTTAG 57.928 37.500 18.75 6.39 41.27 1.85
3284 6795 6.001449 TGAGGACCTAGGTTTATCAAATGG 57.999 41.667 17.53 0.00 0.00 3.16
3289 6800 7.615757 AGGACCTAGGTTTATCAAATGGAAAAG 59.384 37.037 17.53 0.00 0.00 2.27
3320 6831 8.764524 ATTTATCAGTTCATAAGGCTACGATC 57.235 34.615 0.00 0.00 0.00 3.69
3338 7137 4.504461 ACGATCGATGTGACAATAAGCTTC 59.496 41.667 24.34 0.00 0.00 3.86
3363 7166 8.245491 TCAATCATGTGTAAAATGTTCATCAGG 58.755 33.333 0.00 0.00 31.84 3.86
3448 7251 3.669251 GGAGAATATCCTCTTCGGGTG 57.331 52.381 0.00 0.00 45.64 4.61
3509 7312 1.216710 CTCGCTGGTGAAGGACCTC 59.783 63.158 0.00 0.00 46.32 3.85
3539 7342 3.507622 TGCCATATGGAGACGATACTCAG 59.492 47.826 26.47 0.00 38.51 3.35
3621 7424 1.002366 GCTGTACCAAGACGCAGATG 58.998 55.000 0.00 0.00 0.00 2.90
3690 7493 2.025887 ACCAGCCTCTTCAATGTAAGGG 60.026 50.000 0.00 0.00 0.00 3.95
3695 7498 3.610911 CCTCTTCAATGTAAGGGTCACC 58.389 50.000 0.00 0.00 0.00 4.02
3704 7523 5.708736 ATGTAAGGGTCACCATTATCACA 57.291 39.130 3.82 0.64 40.13 3.58
3724 7543 3.066760 ACAAGGTTTGCAGAGTGCTTAAC 59.933 43.478 0.00 5.00 45.31 2.01
3734 7553 6.160684 TGCAGAGTGCTTAACGATTTTAGTA 58.839 36.000 0.00 0.00 45.31 1.82
3736 7555 6.697152 CAGAGTGCTTAACGATTTTAGTAGC 58.303 40.000 0.00 0.00 0.00 3.58
3742 7561 7.477733 GTGCTTAACGATTTTAGTAGCAAACTC 59.522 37.037 0.00 0.00 38.69 3.01
3747 7566 6.888430 ACGATTTTAGTAGCAAACTCTTGTG 58.112 36.000 0.00 0.00 39.80 3.33
3759 7578 8.856490 AGCAAACTCTTGTGTAAATTAAGTTG 57.144 30.769 0.00 0.00 34.79 3.16
3829 7653 5.253330 TCAGACAAGACTGTTCTTTTGGTT 58.747 37.500 0.00 0.00 40.34 3.67
3869 7693 1.843368 ACCCGTCTTCGACTCCATTA 58.157 50.000 0.00 0.00 39.71 1.90
3880 7704 4.537751 TCGACTCCATTATGGTCTCTCTT 58.462 43.478 11.39 0.00 39.03 2.85
3903 7846 9.764363 TCTTTCACACACATATCTATAATGGTC 57.236 33.333 0.00 0.00 0.00 4.02
3904 7847 9.770097 CTTTCACACACATATCTATAATGGTCT 57.230 33.333 0.00 0.00 0.00 3.85
3905 7848 9.764363 TTTCACACACATATCTATAATGGTCTC 57.236 33.333 0.00 0.00 0.00 3.36
3906 7849 8.712228 TCACACACATATCTATAATGGTCTCT 57.288 34.615 0.00 0.00 0.00 3.10
3923 7866 5.522460 TGGTCTCTCTGTAAGTTTTTGTTCG 59.478 40.000 0.00 0.00 33.76 3.95
3945 7888 6.270815 TCGTGTTATCATCTAAACTAGTGGC 58.729 40.000 0.00 0.00 0.00 5.01
4009 7952 4.156922 CGGCACCTTATCGAGATCTATTCT 59.843 45.833 0.00 0.00 37.41 2.40
4095 8039 5.711506 TGTTGATAACAATGTTGCTCCTCAT 59.288 36.000 9.15 0.00 38.72 2.90
4129 8073 5.415701 GGAACATCAACAAAGGAGAAGCATA 59.584 40.000 0.00 0.00 0.00 3.14
4356 8301 1.160329 CGGCGAATGTCCAAGATCCC 61.160 60.000 0.00 0.00 0.00 3.85
4542 8487 7.730784 TCCTTTTATGATTCTACTCCTCTAGGG 59.269 40.741 0.00 0.00 35.41 3.53
4609 8564 7.951530 ATGTTGAAATTCTGTTTCACATTCC 57.048 32.000 2.94 0.00 38.05 3.01
5168 9149 5.626142 TCCCATACTTCTACAACTTTGCAA 58.374 37.500 0.00 0.00 0.00 4.08
5282 9263 1.195115 TAGCCCTGGTGAGTAGCTTG 58.805 55.000 0.00 0.00 35.03 4.01
5474 10122 2.710096 AATATCTGTGGAACGGGTGG 57.290 50.000 0.00 0.00 45.47 4.61
5535 10183 3.785122 AAGAAAACCGGCCGGCACT 62.785 57.895 43.58 30.80 39.32 4.40
5699 10351 6.127054 TGTCAGATTAGGTACAGAAAGGATGG 60.127 42.308 0.00 0.00 0.00 3.51
5809 10462 2.999507 AATTGGCGCATTGTTTCGTA 57.000 40.000 10.83 0.00 0.00 3.43
6368 11063 5.763204 TCTGTTCCTAAGAAACTGCGAAAAT 59.237 36.000 0.00 0.00 32.58 1.82
6386 11081 5.107298 CGAAAATAGCAAGCTATACCTCAGC 60.107 44.000 14.42 0.00 38.20 4.26
6478 11312 7.319646 GCACTAGATATATCTGTTTGCTAGCT 58.680 38.462 23.03 0.00 37.76 3.32
6503 11337 7.648142 TCAATTTCTGAAACTGTGTAATGGTC 58.352 34.615 10.88 0.00 0.00 4.02
6653 11488 1.538419 GCCACGGCCTCTATAGACAAC 60.538 57.143 0.00 0.00 34.56 3.32
6688 11523 6.340962 TGTTCTTCAGAAGACTATCCGAAA 57.659 37.500 12.75 0.00 37.23 3.46
6701 11536 8.391075 AGACTATCCGAAAAGAATTCAAACAA 57.609 30.769 8.44 0.00 0.00 2.83
6866 11706 9.010029 AGGGCACAAAATTAATACGGAATATAG 57.990 33.333 0.00 0.00 0.00 1.31
6881 11722 6.885376 ACGGAATATAGATCATACTCGGAACT 59.115 38.462 0.00 0.00 0.00 3.01
6890 11731 6.480320 AGATCATACTCGGAACTAAAATGCAC 59.520 38.462 0.00 0.00 0.00 4.57
6898 11739 4.082787 CGGAACTAAAATGCACTGTGGATT 60.083 41.667 19.97 19.97 40.20 3.01
6908 11749 2.893489 GCACTGTGGATTCTTTTTCCCT 59.107 45.455 10.21 0.00 31.87 4.20
6918 11759 7.119407 GTGGATTCTTTTTCCCTAACACTACTC 59.881 40.741 0.00 0.00 31.87 2.59
6986 11829 0.182775 ACAGTGACCCGCCTTTTTCT 59.817 50.000 0.00 0.00 0.00 2.52
6998 11841 5.263185 CCGCCTTTTTCTGTTGTATTATCG 58.737 41.667 0.00 0.00 0.00 2.92
7020 11863 7.444558 TCGTAGTCTTGCAAAAACATTTTTC 57.555 32.000 12.65 0.00 38.23 2.29
7027 11870 9.853921 GTCTTGCAAAAACATTTTTCTAAGATG 57.146 29.630 18.59 4.48 39.12 2.90
7152 11995 1.151668 CTTTCTTCCGTGAGCTGGTG 58.848 55.000 0.00 0.00 0.00 4.17
7193 12036 7.979444 ACACATCAAACGGAAATATATAGGG 57.021 36.000 0.00 0.00 0.00 3.53
7328 12174 5.243060 CCTTCCTCCGTTTCCAACTTTATTT 59.757 40.000 0.00 0.00 0.00 1.40
7334 12180 6.731164 TCCGTTTCCAACTTTATTTCTTCAC 58.269 36.000 0.00 0.00 0.00 3.18
7407 12487 2.543797 CCCCAGCCTACCCCAAACA 61.544 63.158 0.00 0.00 0.00 2.83
7559 12641 3.243704 GCACGATCTAGAGAAGCAATCCT 60.244 47.826 0.00 0.00 0.00 3.24
7616 12703 4.472108 AGGTTTTGGAATGATGCATGGAAT 59.528 37.500 2.46 0.00 0.00 3.01
7657 12746 7.686438 TGTGTGCATATACAAGAGACAAAAT 57.314 32.000 0.00 0.00 31.36 1.82
7719 12891 4.745125 GCTAGCTATCTTTCATGTACGCAA 59.255 41.667 7.70 0.00 0.00 4.85
7720 12892 5.406780 GCTAGCTATCTTTCATGTACGCAAT 59.593 40.000 7.70 0.00 0.00 3.56
7721 12893 6.073548 GCTAGCTATCTTTCATGTACGCAATT 60.074 38.462 7.70 0.00 0.00 2.32
7722 12894 6.683974 AGCTATCTTTCATGTACGCAATTT 57.316 33.333 0.00 0.00 0.00 1.82
7723 12895 7.088589 AGCTATCTTTCATGTACGCAATTTT 57.911 32.000 0.00 0.00 0.00 1.82
7724 12896 7.538575 AGCTATCTTTCATGTACGCAATTTTT 58.461 30.769 0.00 0.00 0.00 1.94
7780 12952 5.449297 TGGATGGATGATAGTGTTTGGAA 57.551 39.130 0.00 0.00 0.00 3.53
7849 13022 7.730067 TTACGAATAACACTTCAGTACATCG 57.270 36.000 0.00 0.00 0.00 3.84
7889 14131 7.148407 GGACAATCATACCAAAGTTCAGTACAG 60.148 40.741 0.00 0.00 0.00 2.74
7890 14132 6.655003 ACAATCATACCAAAGTTCAGTACAGG 59.345 38.462 0.00 0.00 0.00 4.00
7891 14133 5.818678 TCATACCAAAGTTCAGTACAGGT 57.181 39.130 0.00 0.00 34.44 4.00
7893 14135 6.597562 TCATACCAAAGTTCAGTACAGGTTT 58.402 36.000 0.00 0.00 32.92 3.27
7894 14136 7.737869 TCATACCAAAGTTCAGTACAGGTTTA 58.262 34.615 0.00 0.00 32.92 2.01
7895 14137 8.380099 TCATACCAAAGTTCAGTACAGGTTTAT 58.620 33.333 0.00 0.00 32.92 1.40
7896 14138 8.665685 CATACCAAAGTTCAGTACAGGTTTATC 58.334 37.037 0.00 0.00 32.92 1.75
7897 14139 6.597562 ACCAAAGTTCAGTACAGGTTTATCA 58.402 36.000 0.00 0.00 0.00 2.15
7898 14140 7.231467 ACCAAAGTTCAGTACAGGTTTATCAT 58.769 34.615 0.00 0.00 0.00 2.45
7899 14141 8.380099 ACCAAAGTTCAGTACAGGTTTATCATA 58.620 33.333 0.00 0.00 0.00 2.15
7900 14142 9.396022 CCAAAGTTCAGTACAGGTTTATCATAT 57.604 33.333 0.00 0.00 0.00 1.78
7923 14165 1.606668 GGTTTCAGTTGGACATTGCGA 59.393 47.619 0.00 0.00 0.00 5.10
7928 14170 0.396435 AGTTGGACATTGCGACTCCA 59.604 50.000 0.00 0.00 24.21 3.86
7954 14196 7.285172 ACAGCAAAACATATATATGCAACAGGA 59.715 33.333 20.46 0.00 39.42 3.86
7956 14198 8.863086 AGCAAAACATATATATGCAACAGGATT 58.137 29.630 20.46 4.29 39.42 3.01
7960 14202 8.511604 AACATATATATGCAACAGGATTAGCC 57.488 34.615 20.46 0.00 37.19 3.93
7961 14203 7.632861 ACATATATATGCAACAGGATTAGCCA 58.367 34.615 20.46 0.00 36.76 4.75
7989 14233 3.046968 GGCTAATTCTGGTAGCTAGCC 57.953 52.381 19.78 11.33 45.70 3.93
7998 14242 8.846423 AATTCTGGTAGCTAGCCTATATACAT 57.154 34.615 19.78 0.00 0.00 2.29
8109 14367 5.607119 AAGTATCGACACAACATCAAACC 57.393 39.130 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.200067 CACAATTTCAAAACGGCTGCA 58.800 42.857 0.50 0.00 0.00 4.41
24 25 1.102978 AGTGCAACCACAAACTCCAC 58.897 50.000 0.00 0.00 44.53 4.02
61 66 2.357637 TCCAAGTTTACAGTGCAAGCAC 59.642 45.455 16.97 16.97 46.50 4.40
114 119 0.392998 AATGCTGTGACCCATCCGAC 60.393 55.000 0.00 0.00 0.00 4.79
183 250 3.780173 AGAAGGGAGCGCAGGAGC 61.780 66.667 11.47 0.00 37.42 4.70
184 251 2.186384 CAGAAGGGAGCGCAGGAG 59.814 66.667 11.47 0.00 0.00 3.69
185 252 2.604686 ACAGAAGGGAGCGCAGGA 60.605 61.111 11.47 0.00 0.00 3.86
186 253 2.125350 GACAGAAGGGAGCGCAGG 60.125 66.667 11.47 0.00 0.00 4.85
215 332 1.072159 ACACAGCTCCTCCAAGCAC 59.928 57.895 0.00 0.00 45.00 4.40
219 336 1.067295 AATCCACACAGCTCCTCCAA 58.933 50.000 0.00 0.00 0.00 3.53
220 337 1.067295 AAATCCACACAGCTCCTCCA 58.933 50.000 0.00 0.00 0.00 3.86
222 339 4.207891 TCTAAAATCCACACAGCTCCTC 57.792 45.455 0.00 0.00 0.00 3.71
223 340 4.384647 GGATCTAAAATCCACACAGCTCCT 60.385 45.833 0.00 0.00 38.09 3.69
241 453 1.274703 ATCACCCAAGCCACGGATCT 61.275 55.000 0.00 0.00 0.00 2.75
269 873 1.813092 CGGATGATGCAAGAAGGGAGG 60.813 57.143 0.00 0.00 0.00 4.30
305 1136 2.611473 GCATAGACCATGGATCGGACAG 60.611 54.545 21.47 1.35 34.97 3.51
309 1140 0.686789 TGGCATAGACCATGGATCGG 59.313 55.000 21.47 4.78 33.75 4.18
310 1141 2.146342 GTTGGCATAGACCATGGATCG 58.854 52.381 21.47 2.83 40.13 3.69
318 1149 1.661341 CAGCTCTGTTGGCATAGACC 58.339 55.000 0.00 0.00 0.00 3.85
319 1150 1.661341 CCAGCTCTGTTGGCATAGAC 58.339 55.000 0.00 0.00 0.00 2.59
327 1158 1.703438 GAGATGCGCCAGCTCTGTTG 61.703 60.000 4.18 0.00 42.72 3.33
328 1159 1.449246 GAGATGCGCCAGCTCTGTT 60.449 57.895 4.18 0.00 42.72 3.16
329 1160 1.969200 ATGAGATGCGCCAGCTCTGT 61.969 55.000 20.25 10.39 45.71 3.41
330 1161 1.222766 GATGAGATGCGCCAGCTCTG 61.223 60.000 20.25 0.00 45.71 3.35
331 1162 1.069427 GATGAGATGCGCCAGCTCT 59.931 57.895 20.25 11.29 45.71 4.09
332 1163 2.308769 CGATGAGATGCGCCAGCTC 61.309 63.158 15.21 15.21 45.72 4.09
503 1424 1.592400 GCTAACCAAAACCCGGAGCC 61.592 60.000 0.73 0.00 0.00 4.70
520 1441 4.642429 ACTACGAACAAAGAATCCAAGCT 58.358 39.130 0.00 0.00 0.00 3.74
595 1516 1.940957 AGATACAGAGAGGAAGGGGGT 59.059 52.381 0.00 0.00 0.00 4.95
596 1517 2.324541 CAGATACAGAGAGGAAGGGGG 58.675 57.143 0.00 0.00 0.00 5.40
599 1520 2.028130 ACGCAGATACAGAGAGGAAGG 58.972 52.381 0.00 0.00 0.00 3.46
633 1554 8.998277 AATCTCCTTGCTACTACTATTACTCA 57.002 34.615 0.00 0.00 0.00 3.41
844 4109 8.959676 TGGTTAGTTTATTATGGTTTTTCCCT 57.040 30.769 0.00 0.00 34.77 4.20
902 4334 2.749621 CAAACAGGGCATGGAGTAGAAC 59.250 50.000 3.46 0.00 0.00 3.01
933 4383 1.683943 AGCACTGCTTGAAGCTGAAA 58.316 45.000 27.15 2.94 41.94 2.69
983 4433 1.734477 ATCTGTGCGAGTGTGCGAC 60.734 57.895 0.00 0.00 37.81 5.19
1015 4465 4.451435 GGTGAGAAAAGTACAGTGCTTACC 59.549 45.833 4.09 4.60 0.00 2.85
1021 4484 3.557264 GGAGGGGTGAGAAAAGTACAGTG 60.557 52.174 0.00 0.00 0.00 3.66
1050 4514 1.189403 GTAGCTACTACGCAGCAACG 58.811 55.000 16.88 0.00 41.66 4.10
1105 4569 1.002366 ATTGCGTCGCAGTGAGATTC 58.998 50.000 20.65 0.00 40.61 2.52
1129 4593 3.941483 AGGAACCTGAAGCATAAATCACG 59.059 43.478 0.00 0.00 0.00 4.35
1141 4605 1.752198 CGTCACCCAGGAACCTGAA 59.248 57.895 20.79 2.48 46.30 3.02
1298 4762 3.507009 CTCGGGGAGTCGGACGAC 61.507 72.222 16.39 16.39 44.86 4.34
1324 4788 4.457496 CGCCGGTGTGCAGAGGAT 62.457 66.667 6.91 0.00 0.00 3.24
1372 4839 2.325082 ATTGAACGACACGGCTGCC 61.325 57.895 9.11 9.11 0.00 4.85
1375 4842 2.325082 GCCATTGAACGACACGGCT 61.325 57.895 14.54 0.00 36.58 5.52
1376 4843 2.175811 GCCATTGAACGACACGGC 59.824 61.111 0.00 0.33 0.00 5.68
1382 4849 1.243342 CCCAAGCAGCCATTGAACGA 61.243 55.000 0.00 0.00 0.00 3.85
1383 4850 1.213537 CCCAAGCAGCCATTGAACG 59.786 57.895 0.00 0.00 0.00 3.95
1457 4924 4.346418 CAGGTAAGTAGAGGCATCTGGATT 59.654 45.833 11.96 5.53 36.96 3.01
1462 4929 2.043227 GGCAGGTAAGTAGAGGCATCT 58.957 52.381 6.01 6.01 39.75 2.90
1501 4971 2.409948 AGCTAAATCCCTGTGACAGC 57.590 50.000 7.16 0.00 0.00 4.40
1507 4977 1.918957 AGGAGCAAGCTAAATCCCTGT 59.081 47.619 7.26 0.00 31.86 4.00
1582 5052 0.037326 TCAGCAAGACCGACCATGAC 60.037 55.000 0.00 0.00 0.00 3.06
1658 5128 1.270147 GCAGTCCTTAACAGTGACCGT 60.270 52.381 0.00 0.00 0.00 4.83
1674 5144 0.908198 GGACAGGAGATCCAAGCAGT 59.092 55.000 0.92 0.00 38.89 4.40
1678 5148 1.826024 CGGGGACAGGAGATCCAAG 59.174 63.158 0.92 0.00 38.06 3.61
1729 5199 1.078918 TTCGTCATGGCTGCTCTGG 60.079 57.895 0.00 0.00 0.00 3.86
1791 5270 4.382345 TGATCACTGTCAGCTGTATCAG 57.618 45.455 23.46 23.46 34.12 2.90
1811 5302 2.354259 GTGGGTGCTCTCTGAAGATTG 58.646 52.381 0.00 0.00 0.00 2.67
1813 5304 0.908198 GGTGGGTGCTCTCTGAAGAT 59.092 55.000 0.00 0.00 0.00 2.40
1861 5352 5.121105 CAGAATGTCATCTGGCTCAACATA 58.879 41.667 0.00 0.00 42.52 2.29
1948 5439 4.891727 CGGTCTGCGGCGCCTAAT 62.892 66.667 30.82 0.00 0.00 1.73
2003 5494 3.378427 GTCTGCTTCTTCTTGTTGTTGGT 59.622 43.478 0.00 0.00 0.00 3.67
2004 5495 3.546815 CGTCTGCTTCTTCTTGTTGTTGG 60.547 47.826 0.00 0.00 0.00 3.77
2005 5496 3.063997 ACGTCTGCTTCTTCTTGTTGTTG 59.936 43.478 0.00 0.00 0.00 3.33
2006 5497 3.270877 ACGTCTGCTTCTTCTTGTTGTT 58.729 40.909 0.00 0.00 0.00 2.83
2007 5498 2.866762 GACGTCTGCTTCTTCTTGTTGT 59.133 45.455 8.70 0.00 0.00 3.32
2008 5499 2.866156 TGACGTCTGCTTCTTCTTGTTG 59.134 45.455 17.92 0.00 0.00 3.33
2067 5564 1.081892 CCCGCACTTGTGATGAGAAG 58.918 55.000 4.79 0.00 0.00 2.85
2189 5686 3.294214 AGCCTTCATGCTTGGAATTAGG 58.706 45.455 0.00 0.00 38.85 2.69
2192 5689 5.047519 GCATATAGCCTTCATGCTTGGAATT 60.048 40.000 0.00 0.00 42.75 2.17
2222 5719 1.812235 TTGCAGATGAACATGAGCGT 58.188 45.000 0.00 0.00 0.00 5.07
3087 6592 8.748412 CCACCAAATTTACATCCTTCAGATTAA 58.252 33.333 0.00 0.00 30.59 1.40
3121 6626 0.786435 AAATGGCAACCTTCTCCCCT 59.214 50.000 0.00 0.00 0.00 4.79
3250 6759 5.782925 ACCTAGGTCCTCAACTGAAGATAT 58.217 41.667 9.21 0.00 0.00 1.63
3294 6805 8.764524 ATCGTAGCCTTATGAACTGATAAATC 57.235 34.615 0.00 0.00 0.00 2.17
3316 6827 4.504097 TGAAGCTTATTGTCACATCGATCG 59.496 41.667 9.36 9.36 0.00 3.69
3320 6831 6.110543 TGATTGAAGCTTATTGTCACATCG 57.889 37.500 0.00 0.00 0.00 3.84
3338 7137 8.030692 ACCTGATGAACATTTTACACATGATTG 58.969 33.333 0.00 0.00 0.00 2.67
3363 7166 3.426292 GCTATTTTCCCGCAGACTTGAAC 60.426 47.826 0.00 0.00 0.00 3.18
3448 7251 2.380084 TCTTTGGCTGTCCATACGAC 57.620 50.000 0.00 0.00 43.05 4.34
3539 7342 1.834822 CACTCCCCTCTCCCCGATC 60.835 68.421 0.00 0.00 0.00 3.69
3563 7366 2.031012 TGCTTCTGACCGCCACTG 59.969 61.111 0.00 0.00 0.00 3.66
3621 7424 3.149005 AGGGTCATCGAGGAGATAGAC 57.851 52.381 0.00 0.00 37.52 2.59
3690 7493 4.022416 TGCAAACCTTGTGATAATGGTGAC 60.022 41.667 0.00 0.00 32.53 3.67
3695 7498 5.396484 CACTCTGCAAACCTTGTGATAATG 58.604 41.667 0.00 0.00 0.00 1.90
3724 7543 6.888430 ACACAAGAGTTTGCTACTAAAATCG 58.112 36.000 0.00 0.00 39.04 3.34
3734 7553 7.435192 GCAACTTAATTTACACAAGAGTTTGCT 59.565 33.333 0.00 0.00 37.85 3.91
3736 7555 8.856490 AGCAACTTAATTTACACAAGAGTTTG 57.144 30.769 0.00 0.00 40.24 2.93
3759 7578 7.064371 CCTGCATCTCACATATAAGTCAATAGC 59.936 40.741 0.00 0.00 0.00 2.97
3767 7586 9.096160 GACATATTCCTGCATCTCACATATAAG 57.904 37.037 0.00 0.00 0.00 1.73
3769 7588 8.137745 TGACATATTCCTGCATCTCACATATA 57.862 34.615 0.00 0.00 0.00 0.86
3770 7589 7.012661 TGACATATTCCTGCATCTCACATAT 57.987 36.000 0.00 0.00 0.00 1.78
3774 7593 4.454847 CCATGACATATTCCTGCATCTCAC 59.545 45.833 0.00 0.00 0.00 3.51
3829 7653 4.322953 GGTAGAAAATCGACTTGGTGGGTA 60.323 45.833 0.00 0.00 0.00 3.69
3869 7693 4.630644 ATGTGTGTGAAAGAGAGACCAT 57.369 40.909 0.00 0.00 0.00 3.55
3880 7704 9.147732 AGAGACCATTATAGATATGTGTGTGAA 57.852 33.333 0.00 0.00 0.00 3.18
3903 7846 6.345920 ACACGAACAAAAACTTACAGAGAG 57.654 37.500 0.00 0.00 0.00 3.20
3904 7847 6.730960 AACACGAACAAAAACTTACAGAGA 57.269 33.333 0.00 0.00 0.00 3.10
3905 7848 8.332464 TGATAACACGAACAAAAACTTACAGAG 58.668 33.333 0.00 0.00 0.00 3.35
3906 7849 8.199176 TGATAACACGAACAAAAACTTACAGA 57.801 30.769 0.00 0.00 0.00 3.41
3923 7866 7.843490 TTGCCACTAGTTTAGATGATAACAC 57.157 36.000 0.00 0.00 0.00 3.32
3945 7888 6.303970 CGTCTGACATCAGCTGTTAAAAATTG 59.696 38.462 14.67 2.93 43.46 2.32
4009 7952 5.760253 GGTCTTTGAATTCTTGACAGTCAGA 59.240 40.000 19.53 1.22 0.00 3.27
4095 8039 3.734463 TGTTGATGTTCCGTTTGCTCTA 58.266 40.909 0.00 0.00 0.00 2.43
4129 8073 9.784531 CTTTGTGTATCCACTTCCATAGATATT 57.215 33.333 0.00 0.00 42.34 1.28
4609 8564 2.162608 TGGCCCATCATTAAAAACGTCG 59.837 45.455 0.00 0.00 0.00 5.12
4901 8882 4.517832 GGAAAACGGTTGACTAATTCACCT 59.482 41.667 0.00 0.00 32.26 4.00
5168 9149 3.058016 CGTTGAATCAGCCATTCTGTTGT 60.058 43.478 7.36 0.00 41.58 3.32
5474 10122 6.653320 TCACTTTTTATGTCCATGTACTGGTC 59.347 38.462 10.08 6.49 46.08 4.02
5535 10183 5.192927 CACTACCAATTTGAGGCCAATCTA 58.807 41.667 5.01 0.00 31.46 1.98
5676 10328 5.964477 ACCATCCTTTCTGTACCTAATCTGA 59.036 40.000 0.00 0.00 0.00 3.27
5699 10351 0.618458 TCCATGCAGTACAAGGGGAC 59.382 55.000 0.00 0.00 37.74 4.46
5809 10462 1.210478 CCCTCCAGATGGTTCGACAAT 59.790 52.381 0.00 0.00 36.34 2.71
5953 10608 2.627699 GTTGGTCTGAGAATTGCCCAAA 59.372 45.455 3.40 0.00 34.05 3.28
6108 10773 3.075148 TCAGTTTGACAACGTGGTGAAA 58.925 40.909 0.00 0.64 38.03 2.69
6368 11063 2.677914 TGGCTGAGGTATAGCTTGCTA 58.322 47.619 21.60 16.62 40.92 3.49
6386 11081 9.709495 TTCATCCTATTTTGAACTTTGAAATGG 57.291 29.630 0.00 0.00 0.00 3.16
6478 11312 7.255451 GGACCATTACACAGTTTCAGAAATTGA 60.255 37.037 21.75 3.26 32.98 2.57
6503 11337 9.498176 TGACAATGATCTTGATCAGTAATATGG 57.502 33.333 16.86 6.04 33.59 2.74
6688 11523 4.320608 ACGGTGCATTGTTTGAATTCTT 57.679 36.364 7.05 0.00 0.00 2.52
6866 11706 6.480320 AGTGCATTTTAGTTCCGAGTATGATC 59.520 38.462 0.00 0.00 0.00 2.92
6881 11722 6.928492 GGAAAAAGAATCCACAGTGCATTTTA 59.072 34.615 0.00 0.00 36.92 1.52
6890 11731 5.770162 AGTGTTAGGGAAAAAGAATCCACAG 59.230 40.000 0.00 0.00 38.80 3.66
6898 11739 5.995897 GCTTGAGTAGTGTTAGGGAAAAAGA 59.004 40.000 0.00 0.00 0.00 2.52
6930 11771 1.767759 AGCATCCACTAATTGGTGCC 58.232 50.000 15.96 4.62 45.96 5.01
6931 11772 3.947834 AGTTAGCATCCACTAATTGGTGC 59.052 43.478 15.96 5.30 46.97 5.01
6986 11829 7.892778 TTTGCAAGACTACGATAATACAACA 57.107 32.000 0.00 0.00 0.00 3.33
7143 11986 2.237143 CCAATACTCCTTCACCAGCTCA 59.763 50.000 0.00 0.00 0.00 4.26
7152 11995 6.582636 TGATGTGTATGACCAATACTCCTTC 58.417 40.000 0.00 0.00 41.62 3.46
7193 12036 2.131972 GACGGACCCAAAACAAAATGC 58.868 47.619 0.00 0.00 0.00 3.56
7291 12135 3.553922 CGGAGGAAGGAACAGATCATAGC 60.554 52.174 0.00 0.00 0.00 2.97
7328 12174 2.096819 GGACAAACAAACAGCGTGAAGA 59.903 45.455 0.00 0.00 0.00 2.87
7334 12180 0.738389 ACCAGGACAAACAAACAGCG 59.262 50.000 0.00 0.00 0.00 5.18
7407 12487 1.115326 GCCTTTTGTCCACAAGGGCT 61.115 55.000 21.33 0.00 44.85 5.19
7469 12550 5.256474 AGGAGGAATAATGTGACCAACAAG 58.744 41.667 0.00 0.00 43.61 3.16
7559 12641 1.321474 CCAGGACTGAGCAAAGCAAA 58.679 50.000 0.00 0.00 0.00 3.68
7616 12703 5.942826 TGCACACATATACAAACTTCATCCA 59.057 36.000 0.00 0.00 0.00 3.41
7657 12746 5.365619 TGATAGCACACGTCTCACTATCTA 58.634 41.667 18.08 8.15 39.81 1.98
7725 12897 9.675464 ACATCGGTATATAGAAGGTTTCAAAAA 57.325 29.630 0.00 0.00 0.00 1.94
7849 13022 2.543777 TTGTCCTACTGAACCTGCAC 57.456 50.000 0.00 0.00 0.00 4.57
7889 14131 7.496591 TCCAACTGAAACCGTATATGATAAACC 59.503 37.037 0.00 0.00 0.00 3.27
7890 14132 8.333186 GTCCAACTGAAACCGTATATGATAAAC 58.667 37.037 0.00 0.00 0.00 2.01
7891 14133 8.041919 TGTCCAACTGAAACCGTATATGATAAA 58.958 33.333 0.00 0.00 0.00 1.40
7893 14135 7.114866 TGTCCAACTGAAACCGTATATGATA 57.885 36.000 0.00 0.00 0.00 2.15
7894 14136 5.984725 TGTCCAACTGAAACCGTATATGAT 58.015 37.500 0.00 0.00 0.00 2.45
7895 14137 5.408880 TGTCCAACTGAAACCGTATATGA 57.591 39.130 0.00 0.00 0.00 2.15
7896 14138 6.486248 CAATGTCCAACTGAAACCGTATATG 58.514 40.000 0.00 0.00 0.00 1.78
7897 14139 5.065988 GCAATGTCCAACTGAAACCGTATAT 59.934 40.000 0.00 0.00 0.00 0.86
7898 14140 4.393680 GCAATGTCCAACTGAAACCGTATA 59.606 41.667 0.00 0.00 0.00 1.47
7899 14141 3.190535 GCAATGTCCAACTGAAACCGTAT 59.809 43.478 0.00 0.00 0.00 3.06
7900 14142 2.550606 GCAATGTCCAACTGAAACCGTA 59.449 45.455 0.00 0.00 0.00 4.02
7901 14143 1.336755 GCAATGTCCAACTGAAACCGT 59.663 47.619 0.00 0.00 0.00 4.83
7902 14144 1.662876 CGCAATGTCCAACTGAAACCG 60.663 52.381 0.00 0.00 0.00 4.44
7923 14165 6.772233 TGCATATATATGTTTTGCTGTGGAGT 59.228 34.615 21.10 0.00 36.11 3.85
7928 14170 7.285172 TCCTGTTGCATATATATGTTTTGCTGT 59.715 33.333 21.10 0.00 36.11 4.40
7989 14233 6.781138 ACACGTGTTTTTGCCATGTATATAG 58.219 36.000 17.22 0.00 31.07 1.31
7998 14242 1.460504 TGGTACACGTGTTTTTGCCA 58.539 45.000 28.55 21.89 0.00 4.92
8109 14367 2.227388 GACACATCAAGTTGAAGGCCTG 59.773 50.000 5.69 5.77 0.00 4.85


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

AutoCloner maintained by Alex Coulton.