Multiple sequence alignment - TraesCS2D01G446000

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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 TraesCS2D01G446000 chr2D 100.000 3113 0 0 1 3113 556349549 556352661 0.000000e+00 5749.0
1 TraesCS2D01G446000 chr2D 89.224 1494 145 11 825 2307 556267051 556268539 0.000000e+00 1853.0
2 TraesCS2D01G446000 chr2D 82.728 1488 174 36 835 2300 556618970 556620396 0.000000e+00 1247.0
3 TraesCS2D01G446000 chr2D 82.094 1452 167 38 864 2300 556407908 556409281 0.000000e+00 1155.0
4 TraesCS2D01G446000 chr2D 87.857 980 98 9 1347 2306 556339260 556340238 0.000000e+00 1131.0
5 TraesCS2D01G446000 chr2D 81.916 1211 157 32 999 2164 556642397 556643590 0.000000e+00 966.0
6 TraesCS2D01G446000 chr2D 88.123 522 44 8 979 1491 556318394 556318906 3.430000e-169 604.0
7 TraesCS2D01G446000 chr2D 82.090 469 72 7 1487 1953 556333284 556333742 1.050000e-104 390.0
8 TraesCS2D01G446000 chr2D 83.586 396 50 11 2720 3108 556390056 556390443 1.060000e-94 357.0
9 TraesCS2D01G446000 chr2D 84.155 284 38 5 2302 2581 556340284 556340564 5.120000e-68 268.0
10 TraesCS2D01G446000 chr2D 81.333 300 27 18 249 522 556618323 556618619 1.880000e-52 217.0
11 TraesCS2D01G446000 chr2D 85.792 183 12 6 513 681 556265715 556265897 6.860000e-42 182.0
12 TraesCS2D01G446000 chr2D 74.942 431 45 25 269 676 556364678 556365068 4.190000e-29 139.0
13 TraesCS2D01G446000 chr2D 95.238 84 4 0 688 771 556265940 556266023 1.950000e-27 134.0
14 TraesCS2D01G446000 chr2D 81.111 180 15 10 55 220 556618052 556618226 3.260000e-25 126.0
15 TraesCS2D01G446000 chr2D 93.939 66 4 0 2166 2231 556643644 556643709 1.980000e-17 100.0
16 TraesCS2D01G446000 chr2D 90.667 75 5 1 56 128 556364002 556364076 7.100000e-17 99.0
17 TraesCS2D01G446000 chr2D 87.500 72 3 1 63 128 556265200 556265271 9.260000e-11 78.7
18 TraesCS2D01G446000 chr2A 90.068 1329 120 8 979 2306 696040411 696041728 0.000000e+00 1712.0
19 TraesCS2D01G446000 chr2A 85.912 1519 164 27 825 2306 695998938 696000443 0.000000e+00 1574.0
20 TraesCS2D01G446000 chr2A 87.632 760 69 15 864 1598 696306895 696307654 0.000000e+00 859.0
21 TraesCS2D01G446000 chr2A 91.353 266 19 3 2043 2306 696001156 696001419 8.210000e-96 361.0
22 TraesCS2D01G446000 chr2A 83.624 287 39 6 2302 2584 696041774 696042056 2.380000e-66 263.0
23 TraesCS2D01G446000 chr2A 90.714 140 13 0 687 826 695998769 695998908 1.470000e-43 187.0
24 TraesCS2D01G446000 chr2A 75.468 481 50 25 219 676 696218401 696218836 4.130000e-39 172.0
25 TraesCS2D01G446000 chr2A 84.328 134 14 2 2166 2292 696826489 696826622 1.170000e-24 124.0
26 TraesCS2D01G446000 chr2A 81.159 138 18 3 2166 2295 696316838 696316975 1.530000e-18 104.0
27 TraesCS2D01G446000 chr2A 88.571 70 2 2 65 128 695998112 695998181 2.570000e-11 80.5
28 TraesCS2D01G446000 chr2B 86.879 1509 157 23 825 2305 663828794 663830289 0.000000e+00 1652.0
29 TraesCS2D01G446000 chr2B 85.605 1438 147 27 864 2288 663837874 663839264 0.000000e+00 1454.0
30 TraesCS2D01G446000 chr2B 81.706 1454 160 51 866 2300 663885893 663887259 0.000000e+00 1114.0
31 TraesCS2D01G446000 chr2B 84.047 934 140 5 1380 2306 663180828 663179897 0.000000e+00 891.0
32 TraesCS2D01G446000 chr2B 90.698 387 32 4 242 626 663835082 663835466 2.140000e-141 512.0
33 TraesCS2D01G446000 chr2B 83.959 293 33 10 2829 3113 663831242 663831528 5.120000e-68 268.0
34 TraesCS2D01G446000 chr2B 92.143 140 11 0 687 826 663828625 663828764 6.810000e-47 198.0
35 TraesCS2D01G446000 chr2B 89.933 149 12 3 536 681 663828438 663828586 4.100000e-44 189.0
36 TraesCS2D01G446000 chr2B 86.335 161 7 2 17 168 663832920 663833074 8.930000e-36 161.0
37 TraesCS2D01G446000 chr2B 84.337 166 17 4 219 380 663885249 663885409 1.500000e-33 154.0
38 TraesCS2D01G446000 chr2B 85.065 154 11 7 219 369 663827866 663828010 2.500000e-31 147.0
39 TraesCS2D01G446000 chr2B 84.559 136 14 2 2166 2294 663899999 663900134 9.060000e-26 128.0
40 TraesCS2D01G446000 chr2B 94.118 68 1 2 153 220 663834480 663834544 1.980000e-17 100.0
41 TraesCS2D01G446000 chr2B 95.161 62 3 0 620 681 663837568 663837629 7.100000e-17 99.0
42 TraesCS2D01G446000 chr2B 88.889 72 2 2 63 128 663827682 663827753 1.990000e-12 84.2
43 TraesCS2D01G446000 chr1A 75.389 321 67 8 1811 2126 459441787 459441474 9.000000e-31 145.0
44 TraesCS2D01G446000 chr7D 86.765 68 9 0 2624 2691 80767084 80767017 3.330000e-10 76.8


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 TraesCS2D01G446000 chr2D 556349549 556352661 3112 False 5749.000 5749 100.000000 1 3113 1 chr2D.!!$F3 3112
1 TraesCS2D01G446000 chr2D 556407908 556409281 1373 False 1155.000 1155 82.094000 864 2300 1 chr2D.!!$F5 1436
2 TraesCS2D01G446000 chr2D 556339260 556340564 1304 False 699.500 1131 86.006000 1347 2581 2 chr2D.!!$F7 1234
3 TraesCS2D01G446000 chr2D 556318394 556318906 512 False 604.000 604 88.123000 979 1491 1 chr2D.!!$F1 512
4 TraesCS2D01G446000 chr2D 556265200 556268539 3339 False 561.925 1853 89.438500 63 2307 4 chr2D.!!$F6 2244
5 TraesCS2D01G446000 chr2D 556642397 556643709 1312 False 533.000 966 87.927500 999 2231 2 chr2D.!!$F10 1232
6 TraesCS2D01G446000 chr2D 556618052 556620396 2344 False 530.000 1247 81.724000 55 2300 3 chr2D.!!$F9 2245
7 TraesCS2D01G446000 chr2A 696040411 696042056 1645 False 987.500 1712 86.846000 979 2584 2 chr2A.!!$F6 1605
8 TraesCS2D01G446000 chr2A 696306895 696307654 759 False 859.000 859 87.632000 864 1598 1 chr2A.!!$F2 734
9 TraesCS2D01G446000 chr2A 695998112 696001419 3307 False 550.625 1574 89.137500 65 2306 4 chr2A.!!$F5 2241
10 TraesCS2D01G446000 chr2B 663179897 663180828 931 True 891.000 891 84.047000 1380 2306 1 chr2B.!!$R1 926
11 TraesCS2D01G446000 chr2B 663885249 663887259 2010 False 634.000 1114 83.021500 219 2300 2 chr2B.!!$F3 2081
12 TraesCS2D01G446000 chr2B 663827682 663839264 11582 False 442.200 1652 88.980455 17 3113 11 chr2B.!!$F2 3096

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
265 366 0.038166 CTGCCTAACCTTTGGGAGCA 59.962 55.0 0.00 0.0 35.19 4.26 F
267 368 0.038310 GCCTAACCTTTGGGAGCAGT 59.962 55.0 0.00 0.0 32.08 4.40 F
414 776 0.179134 CGTCGGATCCAGAGACCAAC 60.179 60.0 13.41 0.0 0.00 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1233 2729 0.179000 GGAGGTTGATGATGAGGCGT 59.821 55.0 0.0 0.0 0.00 5.68 R
2019 3634 0.179009 CCATCGTGGGCTCCATCAAT 60.179 55.0 0.0 0.0 35.28 2.57 R
2344 5050 0.958382 GCCACGCTCCAACCATAACA 60.958 55.0 0.0 0.0 0.00 2.41 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
29 30 3.830465 AAAAACCACGTCCGGGTG 58.170 55.556 0.00 2.09 39.01 4.61
30 31 2.483197 AAAAACCACGTCCGGGTGC 61.483 57.895 0.00 0.00 39.01 5.01
31 32 3.700831 AAAACCACGTCCGGGTGCA 62.701 57.895 0.00 0.00 39.01 4.57
32 33 2.969300 AAAACCACGTCCGGGTGCAT 62.969 55.000 0.00 0.00 39.01 3.96
33 34 4.697756 ACCACGTCCGGGTGCATG 62.698 66.667 0.00 0.00 37.23 4.06
53 54 4.111016 CACGGCTCGGCTACACGA 62.111 66.667 0.00 0.00 41.13 4.35
54 55 3.367743 ACGGCTCGGCTACACGAA 61.368 61.111 0.00 0.00 42.98 3.85
55 56 2.879462 CGGCTCGGCTACACGAAC 60.879 66.667 0.00 0.00 42.98 3.95
56 57 2.260434 GGCTCGGCTACACGAACA 59.740 61.111 0.00 0.00 42.98 3.18
57 58 2.092882 GGCTCGGCTACACGAACAC 61.093 63.158 0.00 0.00 42.98 3.32
58 59 2.434134 GCTCGGCTACACGAACACG 61.434 63.158 0.00 0.00 42.98 4.49
59 60 1.800315 CTCGGCTACACGAACACGG 60.800 63.158 0.00 0.00 42.98 4.94
60 61 2.807895 CGGCTACACGAACACGGG 60.808 66.667 0.00 0.00 35.47 5.28
61 62 2.341176 GGCTACACGAACACGGGT 59.659 61.111 2.66 2.66 45.70 5.28
166 195 0.455815 GCCATGTCCCGTGGAAAATC 59.544 55.000 6.66 0.00 42.73 2.17
170 199 2.178912 TGTCCCGTGGAAAATCTGAC 57.821 50.000 0.00 0.00 31.38 3.51
199 285 4.187056 GCTACAAGAGCCACGGTC 57.813 61.111 0.00 0.00 46.41 4.79
200 286 1.292223 GCTACAAGAGCCACGGTCA 59.708 57.895 0.00 0.00 46.41 4.02
201 287 0.108138 GCTACAAGAGCCACGGTCAT 60.108 55.000 0.00 0.00 46.41 3.06
203 289 1.204704 CTACAAGAGCCACGGTCATGA 59.795 52.381 3.39 0.00 33.79 3.07
204 290 0.615331 ACAAGAGCCACGGTCATGAT 59.385 50.000 0.00 0.00 33.79 2.45
205 291 1.012086 CAAGAGCCACGGTCATGATG 58.988 55.000 0.00 0.00 31.68 3.07
206 292 0.904649 AAGAGCCACGGTCATGATGA 59.095 50.000 0.00 0.00 31.89 2.92
207 293 0.463204 AGAGCCACGGTCATGATGAG 59.537 55.000 0.00 0.00 31.89 2.90
208 294 1.153289 AGCCACGGTCATGATGAGC 60.153 57.895 14.25 14.25 41.16 4.26
209 295 1.450134 GCCACGGTCATGATGAGCA 60.450 57.895 22.56 0.00 44.51 4.26
210 296 1.709147 GCCACGGTCATGATGAGCAC 61.709 60.000 22.56 6.78 44.51 4.40
212 298 1.284657 CACGGTCATGATGAGCACTC 58.715 55.000 22.56 0.00 44.51 3.51
213 299 0.897621 ACGGTCATGATGAGCACTCA 59.102 50.000 22.56 2.25 44.51 3.41
215 301 1.135721 CGGTCATGATGAGCACTCAGA 59.864 52.381 22.56 0.00 44.51 3.27
216 302 2.223994 CGGTCATGATGAGCACTCAGAT 60.224 50.000 22.56 0.00 44.51 2.90
217 303 3.740452 CGGTCATGATGAGCACTCAGATT 60.740 47.826 22.56 0.00 44.51 2.40
248 349 1.298157 TTTCATCGAACGCAGGCCTG 61.298 55.000 29.34 29.34 0.00 4.85
265 366 0.038166 CTGCCTAACCTTTGGGAGCA 59.962 55.000 0.00 0.00 35.19 4.26
267 368 0.038310 GCCTAACCTTTGGGAGCAGT 59.962 55.000 0.00 0.00 32.08 4.40
301 402 8.673711 CGAGTATTTTAATTGGATTCTTCACCA 58.326 33.333 0.00 0.00 0.00 4.17
311 413 4.010349 GGATTCTTCACCAAATTCCGACT 58.990 43.478 0.00 0.00 0.00 4.18
312 414 4.142600 GGATTCTTCACCAAATTCCGACTG 60.143 45.833 0.00 0.00 0.00 3.51
398 743 8.408743 AGTAGTAACATAAGAATTCTTGCGTC 57.591 34.615 27.37 13.93 37.40 5.19
399 744 6.332504 AGTAACATAAGAATTCTTGCGTCG 57.667 37.500 27.37 14.30 37.40 5.12
400 745 4.600012 AACATAAGAATTCTTGCGTCGG 57.400 40.909 27.37 13.59 37.40 4.79
404 766 1.941325 AGAATTCTTGCGTCGGATCC 58.059 50.000 0.88 0.00 0.00 3.36
414 776 0.179134 CGTCGGATCCAGAGACCAAC 60.179 60.000 13.41 0.00 0.00 3.77
433 800 4.722194 CAACACATGGACGTAATTTGGAG 58.278 43.478 0.00 0.00 0.00 3.86
439 806 3.191669 TGGACGTAATTTGGAGCATACG 58.808 45.455 0.00 2.96 44.82 3.06
494 864 1.069978 TGTGTCGATCAGCACTCCAAA 59.930 47.619 14.96 0.00 36.63 3.28
495 865 1.461127 GTGTCGATCAGCACTCCAAAC 59.539 52.381 8.80 0.00 33.22 2.93
497 867 0.389817 TCGATCAGCACTCCAAACGG 60.390 55.000 0.00 0.00 0.00 4.44
547 953 1.808390 GGCACAAGCTACGTACCCG 60.808 63.158 0.00 0.00 41.70 5.28
585 996 1.635487 TGGCTTGCTTACCAGATCCTT 59.365 47.619 0.00 0.00 0.00 3.36
658 1069 1.228367 AGCCTGCCACTTGTTGAGG 60.228 57.895 0.00 0.00 0.00 3.86
676 1087 5.102953 TGAGGGTGATCACTTTATTCCTG 57.897 43.478 24.50 0.00 0.00 3.86
677 1088 4.536090 TGAGGGTGATCACTTTATTCCTGT 59.464 41.667 24.50 2.31 0.00 4.00
679 1090 5.256474 AGGGTGATCACTTTATTCCTGTTG 58.744 41.667 24.50 0.00 0.00 3.33
680 1091 4.142381 GGGTGATCACTTTATTCCTGTTGC 60.142 45.833 24.50 3.36 0.00 4.17
681 1092 4.437390 GGTGATCACTTTATTCCTGTTGCG 60.437 45.833 24.50 0.00 0.00 4.85
684 1095 3.472652 TCACTTTATTCCTGTTGCGTGT 58.527 40.909 0.00 0.00 0.00 4.49
716 1196 1.407299 CCAGATCTCCGGACAATTGCA 60.407 52.381 0.00 0.00 0.00 4.08
718 1198 0.652592 GATCTCCGGACAATTGCACG 59.347 55.000 0.00 10.25 0.00 5.34
791 2219 1.865865 ACTGTTCAACACTAGTGGCG 58.134 50.000 26.12 16.30 34.19 5.69
793 2221 2.037251 ACTGTTCAACACTAGTGGCGAT 59.963 45.455 26.12 7.31 34.19 4.58
798 2226 2.036604 TCAACACTAGTGGCGATGACAA 59.963 45.455 26.12 2.71 34.19 3.18
804 2240 1.512926 AGTGGCGATGACAACAGAAC 58.487 50.000 0.00 0.00 0.00 3.01
839 2308 3.814577 GCTTCTGCTGGACTACGAA 57.185 52.632 0.00 0.00 36.03 3.85
844 2313 0.240145 CTGCTGGACTACGAACACGA 59.760 55.000 0.00 0.00 0.00 4.35
874 2345 5.120399 CGTGCCCTCTACTCCTCTATATAG 58.880 50.000 3.10 3.10 0.00 1.31
879 2350 6.069264 GCCCTCTACTCCTCTATATAGACCTT 60.069 46.154 8.44 0.00 0.00 3.50
974 2470 1.704582 GCTAGCAGAGCGTGTTTCG 59.295 57.895 10.63 0.00 42.62 3.46
975 2471 1.009389 GCTAGCAGAGCGTGTTTCGT 61.009 55.000 10.63 0.00 42.62 3.85
976 2472 1.731424 GCTAGCAGAGCGTGTTTCGTA 60.731 52.381 10.63 0.00 42.62 3.43
977 2473 1.912110 CTAGCAGAGCGTGTTTCGTAC 59.088 52.381 0.00 0.00 42.13 3.67
992 2488 1.195448 TCGTACAGTCGTCGAGGAAAC 59.805 52.381 9.78 5.42 0.00 2.78
994 2490 2.413112 CGTACAGTCGTCGAGGAAACTA 59.587 50.000 9.78 0.00 44.43 2.24
1030 2526 2.723746 CGTGCTGCTGCCAAAACT 59.276 55.556 13.47 0.00 38.71 2.66
1194 2690 2.484742 GGTGGACAAATTACCTCCGT 57.515 50.000 0.00 0.00 31.67 4.69
1233 2729 1.168407 ACTTCACCGACGACGAGGAA 61.168 55.000 18.00 10.57 42.66 3.36
1401 2950 7.498900 TGTTAGTCTTGAAATGACACTGACATT 59.501 33.333 1.42 1.42 42.90 2.71
1491 3044 5.564848 CGAGATCAAGAACTACTGGAACACA 60.565 44.000 0.00 0.00 31.69 3.72
1521 3074 3.687321 GAAGCTCCTGCGCATGGGA 62.687 63.158 17.39 17.00 45.42 4.37
1540 3093 3.220658 TCGACCCAGTGACGCACA 61.221 61.111 11.58 0.00 36.74 4.57
1590 3143 0.907704 ACCTCAACGCCACCTCCATA 60.908 55.000 0.00 0.00 0.00 2.74
1687 3240 0.661020 GGCGCAACTTGTACAACAGT 59.339 50.000 10.83 0.00 0.00 3.55
1770 3323 1.882912 ACGCAATGCTGAACTCAAGA 58.117 45.000 2.94 0.00 0.00 3.02
1833 3407 1.380302 CCTGCAGCTGGGTTACCTT 59.620 57.895 17.12 0.00 37.76 3.50
1845 3419 2.583143 GGTTACCTTTGCAACACCTCT 58.417 47.619 0.00 0.00 0.00 3.69
1852 3426 6.969993 ACCTTTGCAACACCTCTAATTTTA 57.030 33.333 0.00 0.00 0.00 1.52
1857 3431 6.554334 TGCAACACCTCTAATTTTACAGAC 57.446 37.500 0.00 0.00 0.00 3.51
1863 3437 5.882557 CACCTCTAATTTTACAGACCAGCAT 59.117 40.000 0.00 0.00 0.00 3.79
1920 3502 1.916697 GAACGAGCTCCTTTGCAGCC 61.917 60.000 8.47 0.00 37.63 4.85
1922 3504 3.130160 GAGCTCCTTTGCAGCCGG 61.130 66.667 0.87 0.00 37.63 6.13
1924 3506 3.435186 GCTCCTTTGCAGCCGGTC 61.435 66.667 1.90 0.00 0.00 4.79
1927 3509 1.580845 CTCCTTTGCAGCCGGTCAAG 61.581 60.000 1.90 0.00 0.00 3.02
1986 3577 2.703798 GCATGATGTTGCACCGGCT 61.704 57.895 0.00 0.00 42.31 5.52
2005 3620 4.980805 GTGACTGGTCGCCCGCAA 62.981 66.667 3.19 0.00 34.22 4.85
2007 3622 2.975799 GACTGGTCGCCCGCAAAA 60.976 61.111 0.00 0.00 0.00 2.44
2019 3634 1.227999 CCGCAAAAGAGTTCGCTGGA 61.228 55.000 0.00 0.00 0.00 3.86
2033 3648 1.105759 GCTGGATTGATGGAGCCCAC 61.106 60.000 0.00 0.00 35.80 4.61
2058 3676 2.584418 CTGCCCGATCTGTGCTCG 60.584 66.667 0.00 0.00 35.92 5.03
2091 3709 7.400339 AGTGATTCTTTCTGGAAGGACATACTA 59.600 37.037 0.00 0.00 35.98 1.82
2163 3833 7.066404 TGTGTTGTGTATGACAGTTTTGTACAT 59.934 33.333 0.00 0.00 37.76 2.29
2164 3834 7.375808 GTGTTGTGTATGACAGTTTTGTACATG 59.624 37.037 0.00 0.00 37.76 3.21
2273 4929 4.192317 GTCACTGAAGTTGAAGGTTGTCT 58.808 43.478 0.00 0.00 0.00 3.41
2277 4933 7.012421 GTCACTGAAGTTGAAGGTTGTCTATTT 59.988 37.037 0.00 0.00 0.00 1.40
2336 5042 4.647853 TGACCGTGGTGCTTATTAGATAGT 59.352 41.667 0.00 0.00 0.00 2.12
2337 5043 5.829391 TGACCGTGGTGCTTATTAGATAGTA 59.171 40.000 0.00 0.00 0.00 1.82
2338 5044 6.492429 TGACCGTGGTGCTTATTAGATAGTAT 59.508 38.462 0.00 0.00 0.00 2.12
2340 5046 8.053026 ACCGTGGTGCTTATTAGATAGTATAG 57.947 38.462 0.00 0.00 0.00 1.31
2359 5065 3.915437 AGTTTTGTTATGGTTGGAGCG 57.085 42.857 0.00 0.00 0.00 5.03
2361 5067 3.004315 AGTTTTGTTATGGTTGGAGCGTG 59.996 43.478 0.00 0.00 0.00 5.34
2375 5081 2.224066 GGAGCGTGGCAATAGATACTGT 60.224 50.000 0.00 0.00 0.00 3.55
2392 5098 8.948631 AGATACTGTAATGGAATGTTACACTG 57.051 34.615 0.00 0.00 37.19 3.66
2402 5108 5.886474 TGGAATGTTACACTGGTTTACACAA 59.114 36.000 0.00 0.00 0.00 3.33
2410 5117 3.004315 CACTGGTTTACACAACCCATGTC 59.996 47.826 1.30 0.00 41.46 3.06
2429 5136 5.276461 TGTCAGCTAATACATGAACGGAT 57.724 39.130 0.00 0.00 0.00 4.18
2434 5141 7.652105 GTCAGCTAATACATGAACGGATCTAAA 59.348 37.037 0.00 0.00 0.00 1.85
2436 5143 7.116948 CAGCTAATACATGAACGGATCTAAAGG 59.883 40.741 0.00 0.00 0.00 3.11
2440 5147 2.953466 TGAACGGATCTAAAGGGTCG 57.047 50.000 0.00 0.00 0.00 4.79
2441 5148 1.479323 TGAACGGATCTAAAGGGTCGG 59.521 52.381 0.00 0.00 0.00 4.79
2448 5155 4.586884 GGATCTAAAGGGTCGGAAAAAGT 58.413 43.478 0.00 0.00 0.00 2.66
2450 5157 5.106277 GGATCTAAAGGGTCGGAAAAAGTTG 60.106 44.000 0.00 0.00 0.00 3.16
2505 5212 1.218316 CCGGCAGGAACACTACCTC 59.782 63.158 0.00 0.00 41.02 3.85
2507 5214 0.608640 CGGCAGGAACACTACCTCTT 59.391 55.000 0.00 0.00 35.35 2.85
2541 5252 4.993705 AGGAGGAATTACAAAGGTGACA 57.006 40.909 0.00 0.00 0.00 3.58
2543 5254 5.701224 AGGAGGAATTACAAAGGTGACAAA 58.299 37.500 0.00 0.00 0.00 2.83
2571 5282 1.550976 AGAGAACTAGCCGAAACCCTG 59.449 52.381 0.00 0.00 0.00 4.45
2573 5284 2.494870 GAGAACTAGCCGAAACCCTGTA 59.505 50.000 0.00 0.00 0.00 2.74
2584 5295 5.803461 GCCGAAACCCTGTATTTTCAATAAC 59.197 40.000 0.00 0.00 32.21 1.89
2585 5296 6.025280 CCGAAACCCTGTATTTTCAATAACG 58.975 40.000 0.00 0.00 32.21 3.18
2587 5298 5.907866 AACCCTGTATTTTCAATAACGGG 57.092 39.130 8.70 8.70 37.99 5.28
2589 5300 5.762279 ACCCTGTATTTTCAATAACGGGAT 58.238 37.500 14.11 0.00 40.24 3.85
2590 5301 6.192044 ACCCTGTATTTTCAATAACGGGATT 58.808 36.000 14.11 0.00 40.24 3.01
2591 5302 6.096282 ACCCTGTATTTTCAATAACGGGATTG 59.904 38.462 14.11 5.44 40.24 2.67
2592 5303 5.977129 CCTGTATTTTCAATAACGGGATTGC 59.023 40.000 6.66 0.00 40.24 3.56
2593 5304 6.183360 CCTGTATTTTCAATAACGGGATTGCT 60.183 38.462 6.66 0.00 40.24 3.91
2594 5305 7.012894 CCTGTATTTTCAATAACGGGATTGCTA 59.987 37.037 6.66 0.00 40.24 3.49
2596 5307 8.740906 TGTATTTTCAATAACGGGATTGCTAAA 58.259 29.630 6.66 9.12 36.85 1.85
2597 5308 9.744468 GTATTTTCAATAACGGGATTGCTAAAT 57.256 29.630 17.74 17.74 36.85 1.40
2599 5310 7.639113 TTTCAATAACGGGATTGCTAAATCT 57.361 32.000 6.66 0.00 41.74 2.40
2601 5312 6.353323 TCAATAACGGGATTGCTAAATCTCA 58.647 36.000 6.66 0.00 42.61 3.27
2602 5313 6.826231 TCAATAACGGGATTGCTAAATCTCAA 59.174 34.615 6.66 0.00 42.61 3.02
2606 5317 3.187227 CGGGATTGCTAAATCTCAATCGG 59.813 47.826 8.33 1.41 45.69 4.18
2609 5320 4.320057 GGATTGCTAAATCTCAATCGGCTG 60.320 45.833 8.33 0.00 45.69 4.85
2610 5321 3.541996 TGCTAAATCTCAATCGGCTGA 57.458 42.857 0.00 0.00 0.00 4.26
2611 5322 3.461061 TGCTAAATCTCAATCGGCTGAG 58.539 45.455 0.00 8.01 43.62 3.35
2618 5329 4.111375 TCTCAATCGGCTGAGACTTAAC 57.889 45.455 11.82 0.00 45.45 2.01
2619 5330 3.119101 TCTCAATCGGCTGAGACTTAACC 60.119 47.826 11.82 0.00 45.45 2.85
2622 5333 3.695830 ATCGGCTGAGACTTAACCAAA 57.304 42.857 0.00 0.00 0.00 3.28
2623 5334 3.695830 TCGGCTGAGACTTAACCAAAT 57.304 42.857 0.00 0.00 0.00 2.32
2625 5336 3.260884 TCGGCTGAGACTTAACCAAATCT 59.739 43.478 0.00 0.00 0.00 2.40
2627 5338 4.579869 GGCTGAGACTTAACCAAATCTCA 58.420 43.478 3.03 3.03 44.05 3.27
2630 5341 4.579869 TGAGACTTAACCAAATCTCAGCC 58.420 43.478 0.00 0.00 41.99 4.85
2631 5342 4.287067 TGAGACTTAACCAAATCTCAGCCT 59.713 41.667 0.00 0.00 41.99 4.58
2633 5344 6.156949 TGAGACTTAACCAAATCTCAGCCTAT 59.843 38.462 0.00 0.00 41.99 2.57
2634 5345 6.352516 AGACTTAACCAAATCTCAGCCTATG 58.647 40.000 0.00 0.00 0.00 2.23
2635 5346 4.884164 ACTTAACCAAATCTCAGCCTATGC 59.116 41.667 0.00 0.00 37.95 3.14
2658 5369 9.809096 ATGCTATATTCATAAGATCTTACGTGG 57.191 33.333 17.35 7.90 0.00 4.94
2660 5371 9.509855 GCTATATTCATAAGATCTTACGTGGAG 57.490 37.037 17.35 9.89 0.00 3.86
2714 5425 9.929180 TTTATATGTTATGTGAGATCTAGCCAC 57.071 33.333 0.00 0.03 0.00 5.01
2715 5426 5.876651 ATGTTATGTGAGATCTAGCCACA 57.123 39.130 15.71 15.71 43.77 4.17
2717 5428 4.141937 TGTTATGTGAGATCTAGCCACACC 60.142 45.833 15.69 9.03 42.65 4.16
2718 5429 1.195115 TGTGAGATCTAGCCACACCC 58.805 55.000 10.77 0.00 36.07 4.61
2719 5430 1.273267 TGTGAGATCTAGCCACACCCT 60.273 52.381 10.77 0.00 36.07 4.34
2720 5431 1.834263 GTGAGATCTAGCCACACCCTT 59.166 52.381 7.89 0.00 0.00 3.95
2722 5433 2.501723 TGAGATCTAGCCACACCCTTTC 59.498 50.000 0.00 0.00 0.00 2.62
2723 5434 2.769095 GAGATCTAGCCACACCCTTTCT 59.231 50.000 0.00 0.00 0.00 2.52
2733 5853 6.911308 AGCCACACCCTTTCTATAATGTATT 58.089 36.000 0.00 0.00 0.00 1.89
2735 5855 6.998673 GCCACACCCTTTCTATAATGTATTCT 59.001 38.462 0.00 0.00 0.00 2.40
2742 5862 7.819900 CCCTTTCTATAATGTATTCTCCTTCCG 59.180 40.741 0.00 0.00 0.00 4.30
2746 5866 8.929260 TCTATAATGTATTCTCCTTCCGTACA 57.071 34.615 0.00 0.00 0.00 2.90
2750 5870 5.320549 TGTATTCTCCTTCCGTACAGTTC 57.679 43.478 0.00 0.00 0.00 3.01
2758 5878 3.992427 CCTTCCGTACAGTTCCTTGTAAC 59.008 47.826 0.00 0.00 35.47 2.50
2761 5881 5.376854 TCCGTACAGTTCCTTGTAACTAC 57.623 43.478 0.00 0.00 37.61 2.73
2762 5882 4.826733 TCCGTACAGTTCCTTGTAACTACA 59.173 41.667 0.00 0.00 37.61 2.74
2767 5887 7.383029 CGTACAGTTCCTTGTAACTACATTTGA 59.617 37.037 0.00 0.00 37.61 2.69
2769 5889 8.514330 ACAGTTCCTTGTAACTACATTTGAAA 57.486 30.769 0.00 0.00 37.61 2.69
2770 5890 9.131791 ACAGTTCCTTGTAACTACATTTGAAAT 57.868 29.630 0.00 0.00 37.61 2.17
2774 5894 9.959749 TTCCTTGTAACTACATTTGAAATGAAC 57.040 29.630 23.37 12.80 35.89 3.18
2775 5895 9.126151 TCCTTGTAACTACATTTGAAATGAACA 57.874 29.630 23.37 14.77 35.89 3.18
2785 5905 8.125728 ACATTTGAAATGAACAGTTTTAACCG 57.874 30.769 23.37 0.00 0.00 4.44
2788 5908 6.939132 TGAAATGAACAGTTTTAACCGGTA 57.061 33.333 8.00 0.00 0.00 4.02
2834 5954 6.909550 AATACCACAGAAATAGCAAAACCA 57.090 33.333 0.00 0.00 0.00 3.67
2836 5956 3.957497 ACCACAGAAATAGCAAAACCACA 59.043 39.130 0.00 0.00 0.00 4.17
2840 5960 6.482973 CCACAGAAATAGCAAAACCACATTTT 59.517 34.615 0.00 0.00 41.38 1.82
2851 5971 5.738118 AAACCACATTTTGCAATGACTTG 57.262 34.783 7.04 0.91 42.35 3.16
2859 5979 3.731652 TTGCAATGACTTGTTTCTGGG 57.268 42.857 0.00 0.00 34.69 4.45
2865 5985 6.045955 GCAATGACTTGTTTCTGGGTTAAAA 58.954 36.000 0.00 0.00 34.69 1.52
2868 5988 9.757227 CAATGACTTGTTTCTGGGTTAAAATTA 57.243 29.630 0.00 0.00 0.00 1.40
2869 5989 9.981114 AATGACTTGTTTCTGGGTTAAAATTAG 57.019 29.630 0.00 0.00 0.00 1.73
2871 5991 8.973182 TGACTTGTTTCTGGGTTAAAATTAGTT 58.027 29.630 0.00 0.00 0.00 2.24
2872 5992 9.459640 GACTTGTTTCTGGGTTAAAATTAGTTC 57.540 33.333 0.00 0.00 0.00 3.01
2873 5993 8.973182 ACTTGTTTCTGGGTTAAAATTAGTTCA 58.027 29.630 0.00 0.00 0.00 3.18
2874 5994 9.981114 CTTGTTTCTGGGTTAAAATTAGTTCAT 57.019 29.630 0.00 0.00 0.00 2.57
2875 5995 9.757227 TTGTTTCTGGGTTAAAATTAGTTCATG 57.243 29.630 0.00 0.00 0.00 3.07
2876 5996 9.137459 TGTTTCTGGGTTAAAATTAGTTCATGA 57.863 29.630 0.00 0.00 0.00 3.07
2911 6034 8.683615 CCTGTCTTAGTTTCCTAAAAACAGTTT 58.316 33.333 15.89 0.00 40.81 2.66
2912 6035 9.717892 CTGTCTTAGTTTCCTAAAAACAGTTTC 57.282 33.333 0.00 0.00 39.42 2.78
2959 6082 6.363357 AGCAACTTAATCGACAATTTTGAAGC 59.637 34.615 0.00 0.00 0.00 3.86
2963 6086 2.704725 TCGACAATTTTGAAGCCAGC 57.295 45.000 0.00 0.00 0.00 4.85
3001 6124 7.920682 ACCATTTTGAATAGAACAACACTTCAC 59.079 33.333 0.00 0.00 0.00 3.18
3002 6125 7.382218 CCATTTTGAATAGAACAACACTTCACC 59.618 37.037 0.00 0.00 0.00 4.02
3003 6126 5.666969 TTGAATAGAACAACACTTCACCG 57.333 39.130 0.00 0.00 0.00 4.94
3006 6129 5.007234 TGAATAGAACAACACTTCACCGTTG 59.993 40.000 0.00 0.00 46.31 4.10
3016 6139 4.081917 ACACTTCACCGTTGGACAATTTTT 60.082 37.500 0.00 0.00 0.00 1.94
3017 6140 4.267452 CACTTCACCGTTGGACAATTTTTG 59.733 41.667 0.00 0.00 0.00 2.44
3019 6142 4.035278 TCACCGTTGGACAATTTTTGAC 57.965 40.909 0.00 0.00 0.00 3.18
3020 6143 3.444034 TCACCGTTGGACAATTTTTGACA 59.556 39.130 0.00 0.00 0.00 3.58
3021 6144 4.098654 TCACCGTTGGACAATTTTTGACAT 59.901 37.500 0.00 0.00 0.00 3.06
3022 6145 4.208873 CACCGTTGGACAATTTTTGACATG 59.791 41.667 0.00 0.00 0.00 3.21
3023 6146 4.098654 ACCGTTGGACAATTTTTGACATGA 59.901 37.500 0.00 0.00 0.00 3.07
3024 6147 5.221422 ACCGTTGGACAATTTTTGACATGAT 60.221 36.000 0.00 0.00 0.00 2.45
3025 6148 5.118971 CCGTTGGACAATTTTTGACATGATG 59.881 40.000 0.00 0.00 0.00 3.07
3026 6149 5.388682 CGTTGGACAATTTTTGACATGATGC 60.389 40.000 0.00 0.00 0.00 3.91
3027 6150 4.567971 TGGACAATTTTTGACATGATGCC 58.432 39.130 0.00 0.00 0.00 4.40
3060 6183 0.676466 GACATGGTGCATCCGGTTGA 60.676 55.000 16.83 0.00 39.52 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.483197 GCACCCGGACGTGGTTTTT 61.483 57.895 0.73 0.00 32.46 1.94
13 14 2.903350 GCACCCGGACGTGGTTTT 60.903 61.111 0.73 0.00 32.46 2.43
14 15 3.485346 ATGCACCCGGACGTGGTTT 62.485 57.895 0.73 0.00 32.46 3.27
15 16 3.948719 ATGCACCCGGACGTGGTT 61.949 61.111 0.73 0.00 32.46 3.67
16 17 4.697756 CATGCACCCGGACGTGGT 62.698 66.667 0.73 0.00 36.21 4.16
36 37 3.620300 TTCGTGTAGCCGAGCCGTG 62.620 63.158 0.00 0.00 38.23 4.94
37 38 3.367743 TTCGTGTAGCCGAGCCGT 61.368 61.111 0.00 0.00 38.23 5.68
38 39 2.879462 GTTCGTGTAGCCGAGCCG 60.879 66.667 0.00 0.00 38.23 5.52
39 40 2.092882 GTGTTCGTGTAGCCGAGCC 61.093 63.158 0.00 0.00 37.28 4.70
40 41 2.434134 CGTGTTCGTGTAGCCGAGC 61.434 63.158 0.00 0.00 38.23 5.03
41 42 1.800315 CCGTGTTCGTGTAGCCGAG 60.800 63.158 0.00 0.00 38.23 4.63
42 43 2.256158 CCGTGTTCGTGTAGCCGA 59.744 61.111 0.00 0.00 35.01 5.54
43 44 2.807895 CCCGTGTTCGTGTAGCCG 60.808 66.667 0.00 0.00 35.01 5.52
44 45 1.287041 GAACCCGTGTTCGTGTAGCC 61.287 60.000 0.00 0.00 41.35 3.93
45 46 2.147820 GAACCCGTGTTCGTGTAGC 58.852 57.895 0.00 0.00 41.35 3.58
53 54 2.322658 TCCACTAGAAGAACCCGTGTT 58.677 47.619 0.00 0.00 37.42 3.32
54 55 2.005370 TCCACTAGAAGAACCCGTGT 57.995 50.000 0.00 0.00 0.00 4.49
55 56 2.496070 TGATCCACTAGAAGAACCCGTG 59.504 50.000 0.00 0.00 0.00 4.94
56 57 2.761208 CTGATCCACTAGAAGAACCCGT 59.239 50.000 0.00 0.00 0.00 5.28
57 58 2.101582 CCTGATCCACTAGAAGAACCCG 59.898 54.545 0.00 0.00 0.00 5.28
58 59 3.108376 ACCTGATCCACTAGAAGAACCC 58.892 50.000 0.00 0.00 0.00 4.11
59 60 3.118592 CCACCTGATCCACTAGAAGAACC 60.119 52.174 0.00 0.00 0.00 3.62
60 61 3.680196 GCCACCTGATCCACTAGAAGAAC 60.680 52.174 0.00 0.00 0.00 3.01
61 62 2.501723 GCCACCTGATCCACTAGAAGAA 59.498 50.000 0.00 0.00 0.00 2.52
116 125 0.253327 GACTCGGGGCCATTTCTTCT 59.747 55.000 4.39 0.00 0.00 2.85
166 195 0.720027 TAGCGTTCTCTCGTCGTCAG 59.280 55.000 0.00 0.00 0.00 3.51
170 199 1.128136 TCTTGTAGCGTTCTCTCGTCG 59.872 52.381 0.00 0.00 0.00 5.12
199 285 4.150804 CGATGAATCTGAGTGCTCATCATG 59.849 45.833 16.74 8.94 42.80 3.07
200 286 4.308265 CGATGAATCTGAGTGCTCATCAT 58.692 43.478 13.47 13.47 42.80 2.45
201 287 3.492137 CCGATGAATCTGAGTGCTCATCA 60.492 47.826 15.80 4.64 42.80 3.07
203 289 2.433604 ACCGATGAATCTGAGTGCTCAT 59.566 45.455 2.06 0.00 39.13 2.90
204 290 1.827344 ACCGATGAATCTGAGTGCTCA 59.173 47.619 1.69 1.69 38.06 4.26
205 291 2.159184 TGACCGATGAATCTGAGTGCTC 60.159 50.000 0.00 0.00 0.00 4.26
206 292 1.827344 TGACCGATGAATCTGAGTGCT 59.173 47.619 0.00 0.00 0.00 4.40
207 293 2.299993 TGACCGATGAATCTGAGTGC 57.700 50.000 0.00 0.00 0.00 4.40
208 294 5.808042 AAAATGACCGATGAATCTGAGTG 57.192 39.130 0.00 0.00 0.00 3.51
209 295 5.939883 TGAAAAATGACCGATGAATCTGAGT 59.060 36.000 0.00 0.00 0.00 3.41
210 296 6.426980 TGAAAAATGACCGATGAATCTGAG 57.573 37.500 0.00 0.00 0.00 3.35
212 298 5.905733 CGATGAAAAATGACCGATGAATCTG 59.094 40.000 0.00 0.00 0.00 2.90
213 299 5.817296 TCGATGAAAAATGACCGATGAATCT 59.183 36.000 0.00 0.00 0.00 2.40
215 301 6.258160 GTTCGATGAAAAATGACCGATGAAT 58.742 36.000 0.00 0.00 0.00 2.57
216 302 5.627172 GTTCGATGAAAAATGACCGATGAA 58.373 37.500 0.00 0.00 0.00 2.57
217 303 4.201676 CGTTCGATGAAAAATGACCGATGA 60.202 41.667 0.00 0.00 0.00 2.92
248 349 0.038310 ACTGCTCCCAAAGGTTAGGC 59.962 55.000 0.00 0.00 0.00 3.93
249 350 2.586648 AACTGCTCCCAAAGGTTAGG 57.413 50.000 0.00 0.00 0.00 2.69
250 351 4.262036 GGAAAAACTGCTCCCAAAGGTTAG 60.262 45.833 0.00 0.00 0.00 2.34
251 352 3.639561 GGAAAAACTGCTCCCAAAGGTTA 59.360 43.478 0.00 0.00 0.00 2.85
255 356 2.543653 CGTGGAAAAACTGCTCCCAAAG 60.544 50.000 0.00 0.00 0.00 2.77
265 366 8.852135 TCCAATTAAAATACTCGTGGAAAAACT 58.148 29.630 0.00 0.00 30.89 2.66
301 402 5.170748 GCCAAATGATTTCAGTCGGAATTT 58.829 37.500 0.00 0.00 34.91 1.82
311 413 3.571828 TGAGGTTTCGCCAAATGATTTCA 59.428 39.130 0.00 0.00 40.61 2.69
312 414 4.173036 TGAGGTTTCGCCAAATGATTTC 57.827 40.909 0.00 0.00 40.61 2.17
380 725 3.857052 TCCGACGCAAGAATTCTTATGT 58.143 40.909 20.07 19.49 43.62 2.29
381 726 4.084328 GGATCCGACGCAAGAATTCTTATG 60.084 45.833 20.07 16.68 43.62 1.90
390 735 0.679960 TCTCTGGATCCGACGCAAGA 60.680 55.000 7.39 2.03 43.62 3.02
393 738 2.415608 GGTCTCTGGATCCGACGCA 61.416 63.158 7.39 0.00 0.00 5.24
395 740 0.179134 GTTGGTCTCTGGATCCGACG 60.179 60.000 7.39 0.00 0.00 5.12
396 741 0.895530 TGTTGGTCTCTGGATCCGAC 59.104 55.000 7.39 8.45 36.48 4.79
398 743 0.608130 TGTGTTGGTCTCTGGATCCG 59.392 55.000 7.39 2.06 0.00 4.18
399 744 2.636830 CATGTGTTGGTCTCTGGATCC 58.363 52.381 4.20 4.20 0.00 3.36
400 745 2.237143 TCCATGTGTTGGTCTCTGGATC 59.763 50.000 0.00 0.00 46.52 3.36
404 766 1.270305 ACGTCCATGTGTTGGTCTCTG 60.270 52.381 0.00 0.00 46.52 3.35
414 776 2.746904 TGCTCCAAATTACGTCCATGTG 59.253 45.455 0.00 0.00 0.00 3.21
433 800 3.467043 CATGGCTGCAATCGTATGC 57.533 52.632 0.50 8.00 46.58 3.14
494 864 2.850695 ACCTTCCTCTATTCCTCCGT 57.149 50.000 0.00 0.00 0.00 4.69
495 865 2.365941 GGAACCTTCCTCTATTCCTCCG 59.634 54.545 0.00 0.00 44.11 4.63
547 953 6.460261 GCAAGCCAGGTAGATCCTTAATTTTC 60.460 42.308 0.00 0.00 45.67 2.29
569 975 7.054124 CCTGTAATTAAGGATCTGGTAAGCAA 58.946 38.462 7.54 0.00 36.91 3.91
585 996 8.756486 TCTATGTAGTGTAGCACCTGTAATTA 57.244 34.615 0.00 0.00 34.49 1.40
658 1069 4.437390 CGCAACAGGAATAAAGTGATCACC 60.437 45.833 22.21 5.17 0.00 4.02
676 1087 0.231279 CCACGTAAGACACACGCAAC 59.769 55.000 0.00 0.00 43.10 4.17
677 1088 1.492319 GCCACGTAAGACACACGCAA 61.492 55.000 0.00 0.00 43.10 4.85
679 1090 2.664436 GGCCACGTAAGACACACGC 61.664 63.158 0.00 0.00 43.10 5.34
680 1091 1.282248 CTGGCCACGTAAGACACACG 61.282 60.000 0.00 0.00 44.80 4.49
681 1092 0.032952 TCTGGCCACGTAAGACACAC 59.967 55.000 0.00 0.00 43.62 3.82
684 1095 1.476891 GAGATCTGGCCACGTAAGACA 59.523 52.381 0.00 0.00 43.62 3.41
716 1196 3.671928 GTGTACGATGTAAGTCAAAGCGT 59.328 43.478 0.00 0.00 36.73 5.07
718 1198 4.942765 GTGTGTACGATGTAAGTCAAAGC 58.057 43.478 0.00 0.00 0.00 3.51
791 2219 3.040147 TCCTTCCGTTCTGTTGTCATC 57.960 47.619 0.00 0.00 0.00 2.92
793 2221 2.992124 TTCCTTCCGTTCTGTTGTCA 57.008 45.000 0.00 0.00 0.00 3.58
798 2226 3.473625 ACGAATTTTCCTTCCGTTCTGT 58.526 40.909 0.00 0.00 0.00 3.41
804 2240 3.933332 AGAAGCTACGAATTTTCCTTCCG 59.067 43.478 0.00 0.00 31.49 4.30
829 2265 1.001048 CCAGTTCGTGTTCGTAGTCCA 60.001 52.381 0.00 0.00 38.33 4.02
831 2267 1.058404 GCCAGTTCGTGTTCGTAGTC 58.942 55.000 0.00 0.00 38.33 2.59
879 2350 2.040939 TGTTCGTGTCTTCCCTTGGTA 58.959 47.619 0.00 0.00 0.00 3.25
967 2463 1.967908 CTCGACGACTGTACGAAACAC 59.032 52.381 0.00 0.00 35.70 3.32
971 2467 1.511850 TTCCTCGACGACTGTACGAA 58.488 50.000 0.00 0.00 35.70 3.85
972 2468 1.195448 GTTTCCTCGACGACTGTACGA 59.805 52.381 0.00 0.00 37.03 3.43
973 2469 1.196354 AGTTTCCTCGACGACTGTACG 59.804 52.381 0.00 0.00 39.31 3.67
974 2470 2.985406 AGTTTCCTCGACGACTGTAC 57.015 50.000 0.00 0.00 0.00 2.90
975 2471 4.940046 AGATTAGTTTCCTCGACGACTGTA 59.060 41.667 0.00 0.00 0.00 2.74
976 2472 3.757493 AGATTAGTTTCCTCGACGACTGT 59.243 43.478 0.00 0.00 0.00 3.55
977 2473 4.099120 CAGATTAGTTTCCTCGACGACTG 58.901 47.826 0.00 0.00 0.00 3.51
992 2488 1.001406 GCGACCTCCCCATCAGATTAG 59.999 57.143 0.00 0.00 0.00 1.73
993 2489 1.048601 GCGACCTCCCCATCAGATTA 58.951 55.000 0.00 0.00 0.00 1.75
994 2490 1.700042 GGCGACCTCCCCATCAGATT 61.700 60.000 0.00 0.00 0.00 2.40
1026 2522 1.226746 CTTTCTTCACGCCGGAGTTT 58.773 50.000 8.62 0.00 0.00 2.66
1027 2523 0.602905 CCTTTCTTCACGCCGGAGTT 60.603 55.000 8.62 0.00 0.00 3.01
1030 2526 2.345991 CCCTTTCTTCACGCCGGA 59.654 61.111 5.05 0.00 0.00 5.14
1170 2666 2.235402 GAGGTAATTTGTCCACCGGAGA 59.765 50.000 9.46 0.40 37.42 3.71
1194 2690 4.812476 CCGCGCTTGATGTCGGGA 62.812 66.667 5.56 0.00 40.41 5.14
1233 2729 0.179000 GGAGGTTGATGATGAGGCGT 59.821 55.000 0.00 0.00 0.00 5.68
1247 2743 3.790437 CGAGGCTGGCATGGAGGT 61.790 66.667 3.38 0.00 0.00 3.85
1341 2863 3.054802 AGGTCCAGCTGTAGGAAATTGAG 60.055 47.826 13.81 0.00 36.80 3.02
1401 2950 6.183360 ACCTAACGCGCAACAATAATTTATCA 60.183 34.615 5.73 0.00 0.00 2.15
1455 3008 1.872679 GATCTCGTTGTCCGTCCGC 60.873 63.158 0.00 0.00 37.94 5.54
1491 3044 0.250513 GGAGCTTCTTCCGGATGTGT 59.749 55.000 16.29 1.02 0.00 3.72
1521 3074 2.910479 TGCGTCACTGGGTCGACT 60.910 61.111 16.46 0.00 0.00 4.18
1565 3118 4.947147 TGGCGTTGAGGTGGTGGC 62.947 66.667 0.00 0.00 0.00 5.01
1667 3220 0.660488 CTGTTGTACAAGTTGCGCCA 59.340 50.000 8.98 0.51 0.00 5.69
1678 3231 4.537135 TGATCTGGAGGAACTGTTGTAC 57.463 45.455 0.00 0.00 41.55 2.90
1687 3240 1.043816 GAGCCGATGATCTGGAGGAA 58.956 55.000 7.36 0.00 0.00 3.36
1770 3323 3.855159 GTTCGGAACCATGCTACCT 57.145 52.632 9.75 0.00 0.00 3.08
1833 3407 6.016610 GGTCTGTAAAATTAGAGGTGTTGCAA 60.017 38.462 0.00 0.00 0.00 4.08
1845 3419 5.895636 CCACATGCTGGTCTGTAAAATTA 57.104 39.130 0.00 0.00 34.90 1.40
1920 3502 3.359194 CTGATCAGCCTCTTGACCG 57.641 57.895 10.38 0.00 0.00 4.79
2005 3620 3.012518 CCATCAATCCAGCGAACTCTTT 58.987 45.455 0.00 0.00 0.00 2.52
2007 3622 1.833630 TCCATCAATCCAGCGAACTCT 59.166 47.619 0.00 0.00 0.00 3.24
2019 3634 0.179009 CCATCGTGGGCTCCATCAAT 60.179 55.000 0.00 0.00 35.28 2.57
2033 3648 2.356793 GATCGGGCAGCTCCATCG 60.357 66.667 0.00 0.00 36.21 3.84
2058 3676 3.055530 TCCAGAAAGAATCACTCTCCAGC 60.056 47.826 0.00 0.00 31.02 4.85
2091 3709 4.744795 CTACAAATGGTAGCTGTCCTCT 57.255 45.455 0.00 0.00 42.81 3.69
2118 3736 2.884639 ACATTTGTTTCAGTCGGAAGGG 59.115 45.455 0.00 0.00 36.72 3.95
2255 4910 7.442364 TCAGAAATAGACAACCTTCAACTTCAG 59.558 37.037 0.00 0.00 0.00 3.02
2273 4929 9.453572 AGCAAGAGTCACATTAAATCAGAAATA 57.546 29.630 0.00 0.00 0.00 1.40
2277 4933 5.877012 GGAGCAAGAGTCACATTAAATCAGA 59.123 40.000 0.00 0.00 0.00 3.27
2336 5042 6.092944 CACGCTCCAACCATAACAAAACTATA 59.907 38.462 0.00 0.00 0.00 1.31
2337 5043 5.007682 ACGCTCCAACCATAACAAAACTAT 58.992 37.500 0.00 0.00 0.00 2.12
2338 5044 4.214545 CACGCTCCAACCATAACAAAACTA 59.785 41.667 0.00 0.00 0.00 2.24
2340 5046 3.305110 CACGCTCCAACCATAACAAAAC 58.695 45.455 0.00 0.00 0.00 2.43
2344 5050 0.958382 GCCACGCTCCAACCATAACA 60.958 55.000 0.00 0.00 0.00 2.41
2345 5051 0.958382 TGCCACGCTCCAACCATAAC 60.958 55.000 0.00 0.00 0.00 1.89
2359 5065 7.445402 ACATTCCATTACAGTATCTATTGCCAC 59.555 37.037 0.00 0.00 0.00 5.01
2361 5067 7.986085 ACATTCCATTACAGTATCTATTGCC 57.014 36.000 0.00 0.00 0.00 4.52
2375 5081 7.720074 TGTGTAAACCAGTGTAACATTCCATTA 59.280 33.333 0.00 0.00 41.43 1.90
2392 5098 2.030274 GCTGACATGGGTTGTGTAAACC 60.030 50.000 0.00 0.00 44.35 3.27
2410 5117 7.116948 CCTTTAGATCCGTTCATGTATTAGCTG 59.883 40.741 0.00 0.00 0.00 4.24
2429 5136 5.038651 TCAACTTTTTCCGACCCTTTAGA 57.961 39.130 0.00 0.00 0.00 2.10
2434 5141 3.644738 TCTACTCAACTTTTTCCGACCCT 59.355 43.478 0.00 0.00 0.00 4.34
2436 5143 6.204108 TGAAATCTACTCAACTTTTTCCGACC 59.796 38.462 0.00 0.00 0.00 4.79
2484 5191 0.250597 GGTAGTGTTCCTGCCGGTTT 60.251 55.000 1.90 0.00 36.13 3.27
2541 5252 9.459640 GTTTCGGCTAGTTCTCTTTAAAAATTT 57.540 29.630 0.00 0.00 0.00 1.82
2543 5254 7.309012 GGGTTTCGGCTAGTTCTCTTTAAAAAT 60.309 37.037 0.00 0.00 0.00 1.82
2549 5260 2.638363 AGGGTTTCGGCTAGTTCTCTTT 59.362 45.455 0.00 0.00 0.00 2.52
2571 5282 9.744468 ATTTAGCAATCCCGTTATTGAAAATAC 57.256 29.630 10.27 0.00 38.84 1.89
2573 5284 8.695456 AGATTTAGCAATCCCGTTATTGAAAAT 58.305 29.630 10.27 12.53 39.95 1.82
2584 5295 3.187227 CCGATTGAGATTTAGCAATCCCG 59.813 47.826 0.00 0.00 44.59 5.14
2585 5296 3.057946 GCCGATTGAGATTTAGCAATCCC 60.058 47.826 0.00 0.00 44.59 3.85
2587 5298 4.512944 TCAGCCGATTGAGATTTAGCAATC 59.487 41.667 0.00 0.00 44.20 2.67
2589 5300 3.872696 TCAGCCGATTGAGATTTAGCAA 58.127 40.909 0.00 0.00 0.00 3.91
2590 5301 3.132824 TCTCAGCCGATTGAGATTTAGCA 59.867 43.478 12.86 0.00 46.42 3.49
2591 5302 3.722147 TCTCAGCCGATTGAGATTTAGC 58.278 45.455 12.86 0.00 46.42 3.09
2599 5310 2.565391 TGGTTAAGTCTCAGCCGATTGA 59.435 45.455 0.00 0.00 0.00 2.57
2601 5312 3.695830 TTGGTTAAGTCTCAGCCGATT 57.304 42.857 0.00 0.00 0.00 3.34
2602 5313 3.695830 TTTGGTTAAGTCTCAGCCGAT 57.304 42.857 0.00 0.00 0.00 4.18
2609 5320 4.837972 AGGCTGAGATTTGGTTAAGTCTC 58.162 43.478 5.82 5.82 45.07 3.36
2610 5321 4.917906 AGGCTGAGATTTGGTTAAGTCT 57.082 40.909 0.00 0.00 35.80 3.24
2611 5322 5.008118 GCATAGGCTGAGATTTGGTTAAGTC 59.992 44.000 0.00 0.00 36.96 3.01
2613 5324 5.429957 GCATAGGCTGAGATTTGGTTAAG 57.570 43.478 0.00 0.00 36.96 1.85
2633 5344 9.020731 TCCACGTAAGATCTTATGAATATAGCA 57.979 33.333 32.10 10.82 43.62 3.49
2634 5345 9.509855 CTCCACGTAAGATCTTATGAATATAGC 57.490 37.037 32.10 11.44 43.62 2.97
2638 5349 8.740906 GGATCTCCACGTAAGATCTTATGAATA 58.259 37.037 32.10 18.60 45.56 1.75
2640 5351 6.549736 TGGATCTCCACGTAAGATCTTATGAA 59.450 38.462 32.10 19.12 45.56 2.57
2641 5352 6.068670 TGGATCTCCACGTAAGATCTTATGA 58.931 40.000 32.10 18.64 45.56 2.15
2642 5353 6.332735 TGGATCTCCACGTAAGATCTTATG 57.667 41.667 26.36 26.36 45.56 1.90
2688 5399 9.929180 GTGGCTAGATCTCACATAACATATAAA 57.071 33.333 0.00 0.00 0.00 1.40
2689 5400 9.088987 TGTGGCTAGATCTCACATAACATATAA 57.911 33.333 10.77 0.00 36.61 0.98
2690 5401 8.523658 GTGTGGCTAGATCTCACATAACATATA 58.476 37.037 16.23 0.00 42.34 0.86
2692 5403 6.239317 GGTGTGGCTAGATCTCACATAACATA 60.239 42.308 16.23 0.00 42.34 2.29
2693 5404 5.453903 GGTGTGGCTAGATCTCACATAACAT 60.454 44.000 16.23 0.00 42.34 2.71
2694 5405 4.141937 GGTGTGGCTAGATCTCACATAACA 60.142 45.833 16.23 5.65 42.34 2.41
2695 5406 4.372656 GGTGTGGCTAGATCTCACATAAC 58.627 47.826 16.23 8.49 42.34 1.89
2696 5407 3.388024 GGGTGTGGCTAGATCTCACATAA 59.612 47.826 16.23 0.00 42.34 1.90
2697 5408 2.965831 GGGTGTGGCTAGATCTCACATA 59.034 50.000 16.23 3.47 42.34 2.29
2698 5409 1.765314 GGGTGTGGCTAGATCTCACAT 59.235 52.381 16.23 0.00 42.34 3.21
2699 5410 1.195115 GGGTGTGGCTAGATCTCACA 58.805 55.000 10.77 10.77 38.84 3.58
2702 5413 2.769095 AGAAAGGGTGTGGCTAGATCTC 59.231 50.000 0.00 0.00 0.00 2.75
2704 5415 4.965200 ATAGAAAGGGTGTGGCTAGATC 57.035 45.455 0.00 0.00 0.00 2.75
2707 5418 5.930135 ACATTATAGAAAGGGTGTGGCTAG 58.070 41.667 0.00 0.00 0.00 3.42
2708 5419 5.968676 ACATTATAGAAAGGGTGTGGCTA 57.031 39.130 0.00 0.00 0.00 3.93
2709 5420 4.862641 ACATTATAGAAAGGGTGTGGCT 57.137 40.909 0.00 0.00 0.00 4.75
2710 5421 6.998673 AGAATACATTATAGAAAGGGTGTGGC 59.001 38.462 0.00 0.00 0.00 5.01
2711 5422 7.661847 GGAGAATACATTATAGAAAGGGTGTGG 59.338 40.741 0.00 0.00 0.00 4.17
2712 5423 8.432805 AGGAGAATACATTATAGAAAGGGTGTG 58.567 37.037 0.00 0.00 0.00 3.82
2713 5424 8.568617 AGGAGAATACATTATAGAAAGGGTGT 57.431 34.615 0.00 0.00 0.00 4.16
2714 5425 9.495572 GAAGGAGAATACATTATAGAAAGGGTG 57.504 37.037 0.00 0.00 0.00 4.61
2715 5426 8.661345 GGAAGGAGAATACATTATAGAAAGGGT 58.339 37.037 0.00 0.00 0.00 4.34
2717 5428 8.368668 ACGGAAGGAGAATACATTATAGAAAGG 58.631 37.037 0.00 0.00 0.00 3.11
2720 5431 9.358406 TGTACGGAAGGAGAATACATTATAGAA 57.642 33.333 0.00 0.00 0.00 2.10
2722 5433 8.794553 ACTGTACGGAAGGAGAATACATTATAG 58.205 37.037 9.17 0.00 0.00 1.31
2723 5434 8.701908 ACTGTACGGAAGGAGAATACATTATA 57.298 34.615 9.17 0.00 0.00 0.98
2733 5853 2.561419 CAAGGAACTGTACGGAAGGAGA 59.439 50.000 9.17 0.00 40.86 3.71
2735 5855 2.322658 ACAAGGAACTGTACGGAAGGA 58.677 47.619 9.17 0.00 40.86 3.36
2742 5862 8.597662 TCAAATGTAGTTACAAGGAACTGTAC 57.402 34.615 7.93 0.04 40.86 2.90
2750 5870 9.398170 CTGTTCATTTCAAATGTAGTTACAAGG 57.602 33.333 9.98 0.00 39.99 3.61
2761 5881 7.223777 ACCGGTTAAAACTGTTCATTTCAAATG 59.776 33.333 0.00 3.46 33.38 2.32
2762 5882 7.269316 ACCGGTTAAAACTGTTCATTTCAAAT 58.731 30.769 0.00 0.00 33.38 2.32
2769 5889 9.287373 TCTAAATTACCGGTTAAAACTGTTCAT 57.713 29.630 15.04 0.00 33.38 2.57
2770 5890 8.674263 TCTAAATTACCGGTTAAAACTGTTCA 57.326 30.769 15.04 0.00 33.38 3.18
2807 5927 9.699703 GGTTTTGCTATTTCTGTGGTATTAAAA 57.300 29.630 0.00 0.00 0.00 1.52
2808 5928 8.861086 TGGTTTTGCTATTTCTGTGGTATTAAA 58.139 29.630 0.00 0.00 0.00 1.52
2809 5929 8.301002 GTGGTTTTGCTATTTCTGTGGTATTAA 58.699 33.333 0.00 0.00 0.00 1.40
2810 5930 7.448777 TGTGGTTTTGCTATTTCTGTGGTATTA 59.551 33.333 0.00 0.00 0.00 0.98
2811 5931 6.266558 TGTGGTTTTGCTATTTCTGTGGTATT 59.733 34.615 0.00 0.00 0.00 1.89
2812 5932 5.772672 TGTGGTTTTGCTATTTCTGTGGTAT 59.227 36.000 0.00 0.00 0.00 2.73
2813 5933 5.133941 TGTGGTTTTGCTATTTCTGTGGTA 58.866 37.500 0.00 0.00 0.00 3.25
2814 5934 3.957497 TGTGGTTTTGCTATTTCTGTGGT 59.043 39.130 0.00 0.00 0.00 4.16
2815 5935 4.582701 TGTGGTTTTGCTATTTCTGTGG 57.417 40.909 0.00 0.00 0.00 4.17
2816 5936 7.481275 AAAATGTGGTTTTGCTATTTCTGTG 57.519 32.000 0.00 0.00 38.56 3.66
2831 5951 4.405116 ACAAGTCATTGCAAAATGTGGT 57.595 36.364 1.71 0.00 40.27 4.16
2834 5954 5.524646 CCAGAAACAAGTCATTGCAAAATGT 59.475 36.000 1.71 1.65 40.27 2.71
2836 5956 5.058490 CCCAGAAACAAGTCATTGCAAAAT 58.942 37.500 1.71 0.00 40.27 1.82
2840 5960 2.665165 ACCCAGAAACAAGTCATTGCA 58.335 42.857 0.00 0.00 40.27 4.08
2842 5962 8.661352 AATTTTAACCCAGAAACAAGTCATTG 57.339 30.769 0.00 0.00 42.46 2.82
2845 5965 8.528044 ACTAATTTTAACCCAGAAACAAGTCA 57.472 30.769 0.00 0.00 0.00 3.41
2943 6066 2.821969 AGCTGGCTTCAAAATTGTCGAT 59.178 40.909 0.00 0.00 0.00 3.59
2944 6067 2.229792 AGCTGGCTTCAAAATTGTCGA 58.770 42.857 0.00 0.00 0.00 4.20
2945 6068 2.712057 AGCTGGCTTCAAAATTGTCG 57.288 45.000 0.00 0.00 0.00 4.35
2946 6069 4.386954 GCTAAAGCTGGCTTCAAAATTGTC 59.613 41.667 8.33 0.00 38.21 3.18
2947 6070 4.309933 GCTAAAGCTGGCTTCAAAATTGT 58.690 39.130 8.33 0.00 38.21 2.71
2948 6071 4.916099 GCTAAAGCTGGCTTCAAAATTG 57.084 40.909 8.33 0.00 38.21 2.32
2996 6119 4.502645 GTCAAAAATTGTCCAACGGTGAAG 59.497 41.667 0.00 0.00 0.00 3.02
2999 6122 3.775202 TGTCAAAAATTGTCCAACGGTG 58.225 40.909 0.00 0.00 0.00 4.94
3001 6124 4.615949 TCATGTCAAAAATTGTCCAACGG 58.384 39.130 0.00 0.00 0.00 4.44
3002 6125 5.388682 GCATCATGTCAAAAATTGTCCAACG 60.389 40.000 0.00 0.00 0.00 4.10
3003 6126 5.106987 GGCATCATGTCAAAAATTGTCCAAC 60.107 40.000 0.00 0.00 0.00 3.77
3006 6129 3.934579 GGGCATCATGTCAAAAATTGTCC 59.065 43.478 0.00 0.00 0.00 4.02
3016 6139 0.035152 GACTGTGGGGCATCATGTCA 60.035 55.000 0.00 0.00 0.00 3.58
3017 6140 0.035152 TGACTGTGGGGCATCATGTC 60.035 55.000 0.00 0.00 0.00 3.06
3019 6142 0.813184 GTTGACTGTGGGGCATCATG 59.187 55.000 0.00 0.00 30.17 3.07
3020 6143 0.405198 TGTTGACTGTGGGGCATCAT 59.595 50.000 0.00 0.00 30.17 2.45
3021 6144 0.405198 ATGTTGACTGTGGGGCATCA 59.595 50.000 0.00 0.00 37.11 3.07
3022 6145 0.813184 CATGTTGACTGTGGGGCATC 59.187 55.000 0.00 0.00 30.17 3.91
3023 6146 0.405198 TCATGTTGACTGTGGGGCAT 59.595 50.000 0.00 0.00 30.17 4.40
3024 6147 0.537143 GTCATGTTGACTGTGGGGCA 60.537 55.000 0.45 0.00 43.73 5.36
3025 6148 2.257353 GTCATGTTGACTGTGGGGC 58.743 57.895 0.45 0.00 43.73 5.80
3060 6183 3.322254 TGTTTCCAAACACAGTGGTTGTT 59.678 39.130 26.31 0.00 43.25 2.83


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

AutoCloner maintained by Alex Coulton.