Multiple sequence alignment - TraesCS2B01G562100

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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 TraesCS2B01G562100 chr2B 100.000 6428 0 0 1 6428 754655686 754649259 0.000000e+00 11871.0
1 TraesCS2B01G562100 chr2B 86.248 1258 142 22 1117 2356 755150731 755149487 0.000000e+00 1336.0
2 TraesCS2B01G562100 chr2B 85.804 1275 140 26 1117 2360 708716245 708714981 0.000000e+00 1314.0
3 TraesCS2B01G562100 chr2B 92.844 559 35 3 4718 5275 754622629 754622075 0.000000e+00 806.0
4 TraesCS2B01G562100 chr2B 84.615 585 76 6 1780 2356 755009816 755010394 2.600000e-158 569.0
5 TraesCS2B01G562100 chr2B 86.458 480 29 14 3503 3950 754628672 754628197 1.610000e-135 494.0
6 TraesCS2B01G562100 chr2B 89.697 330 25 3 4270 4590 754628099 754627770 4.640000e-111 412.0
7 TraesCS2B01G562100 chr2B 75.701 749 155 27 2832 3563 755148952 755148214 3.690000e-92 350.0
8 TraesCS2B01G562100 chr2B 71.231 1227 286 53 1158 2341 707970184 707968982 1.380000e-61 248.0
9 TraesCS2B01G562100 chr2B 90.370 135 13 0 4586 4720 754623138 754623004 1.840000e-40 178.0
10 TraesCS2B01G562100 chr2A 90.272 6476 422 91 87 6426 748911521 748905118 0.000000e+00 8277.0
11 TraesCS2B01G562100 chr2A 86.054 1262 141 20 1117 2356 749385211 749386459 0.000000e+00 1323.0
12 TraesCS2B01G562100 chr2A 84.673 1344 160 28 1052 2360 721729595 721728263 0.000000e+00 1299.0
13 TraesCS2B01G562100 chr2A 78.951 1297 219 31 1097 2360 749874449 749875724 0.000000e+00 833.0
14 TraesCS2B01G562100 chr2A 84.685 444 53 5 3275 3705 748870446 748870005 4.600000e-116 429.0
15 TraesCS2B01G562100 chr2A 71.880 1202 280 48 1172 2341 721106797 721105622 1.750000e-75 294.0
16 TraesCS2B01G562100 chr2A 85.878 262 34 3 3950 4210 257805597 257805856 6.350000e-70 276.0
17 TraesCS2B01G562100 chr2A 83.103 290 48 1 3279 3568 749388091 749388379 4.940000e-66 263.0
18 TraesCS2B01G562100 chr2A 87.500 128 16 0 2393 2520 748871062 748870935 1.440000e-31 148.0
19 TraesCS2B01G562100 chr2A 100.000 33 0 0 5562 5594 499767923 499767891 1.940000e-05 62.1
20 TraesCS2B01G562100 chr2D 94.690 2561 104 18 3876 6428 618140286 618137750 0.000000e+00 3947.0
21 TraesCS2B01G562100 chr2D 88.984 3159 202 58 168 3212 618144105 618140979 0.000000e+00 3771.0
22 TraesCS2B01G562100 chr2D 85.070 1353 156 30 1043 2360 586961710 586960369 0.000000e+00 1338.0
23 TraesCS2B01G562100 chr2D 84.954 1316 149 24 1076 2356 618333434 618334735 0.000000e+00 1288.0
24 TraesCS2B01G562100 chr2D 82.140 1271 172 34 1131 2360 586846897 586845641 0.000000e+00 1038.0
25 TraesCS2B01G562100 chr2D 81.659 1254 186 30 1131 2354 618660281 618659042 0.000000e+00 1002.0
26 TraesCS2B01G562100 chr2D 89.511 696 41 7 3240 3904 618140986 618140292 0.000000e+00 852.0
27 TraesCS2B01G562100 chr2D 83.056 301 50 1 3268 3568 618336478 618336777 8.210000e-69 272.0
28 TraesCS2B01G562100 chr3D 87.405 262 30 3 3950 4210 341493338 341493079 1.350000e-76 298.0
29 TraesCS2B01G562100 chr6A 86.415 265 32 4 3947 4210 577623816 577624077 2.930000e-73 287.0
30 TraesCS2B01G562100 chr6A 97.059 34 1 0 5559 5592 579386617 579386650 2.500000e-04 58.4
31 TraesCS2B01G562100 chr1D 86.641 262 32 3 3950 4210 100461843 100462102 2.930000e-73 287.0
32 TraesCS2B01G562100 chr1A 86.090 266 34 3 3946 4210 537981148 537981411 3.790000e-72 283.0
33 TraesCS2B01G562100 chr1A 97.059 34 1 0 5559 5592 394602551 394602584 2.500000e-04 58.4
34 TraesCS2B01G562100 chr3A 86.154 260 33 3 3950 4208 468323485 468323742 1.770000e-70 278.0
35 TraesCS2B01G562100 chr3A 85.878 262 34 3 3949 4209 721830157 721830416 6.350000e-70 276.0
36 TraesCS2B01G562100 chr5A 85.496 262 35 3 3950 4210 371024464 371024723 2.950000e-68 270.0
37 TraesCS2B01G562100 chr5A 100.000 34 0 0 5559 5592 657242230 657242197 5.380000e-06 63.9
38 TraesCS2B01G562100 chr7A 100.000 31 0 0 5562 5592 36160048 36160018 2.500000e-04 58.4
39 TraesCS2B01G562100 chr7A 97.059 34 1 0 5559 5592 732148430 732148463 2.500000e-04 58.4
40 TraesCS2B01G562100 chr7A 97.059 34 1 0 5559 5592 732399667 732399700 2.500000e-04 58.4


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 TraesCS2B01G562100 chr2B 754649259 754655686 6427 True 11871.000000 11871 100.000000 1 6428 1 chr2B.!!$R3 6427
1 TraesCS2B01G562100 chr2B 708714981 708716245 1264 True 1314.000000 1314 85.804000 1117 2360 1 chr2B.!!$R2 1243
2 TraesCS2B01G562100 chr2B 755148214 755150731 2517 True 843.000000 1336 80.974500 1117 3563 2 chr2B.!!$R6 2446
3 TraesCS2B01G562100 chr2B 755009816 755010394 578 False 569.000000 569 84.615000 1780 2356 1 chr2B.!!$F1 576
4 TraesCS2B01G562100 chr2B 754622075 754623138 1063 True 492.000000 806 91.607000 4586 5275 2 chr2B.!!$R4 689
5 TraesCS2B01G562100 chr2B 754627770 754628672 902 True 453.000000 494 88.077500 3503 4590 2 chr2B.!!$R5 1087
6 TraesCS2B01G562100 chr2B 707968982 707970184 1202 True 248.000000 248 71.231000 1158 2341 1 chr2B.!!$R1 1183
7 TraesCS2B01G562100 chr2A 748905118 748911521 6403 True 8277.000000 8277 90.272000 87 6426 1 chr2A.!!$R4 6339
8 TraesCS2B01G562100 chr2A 721728263 721729595 1332 True 1299.000000 1299 84.673000 1052 2360 1 chr2A.!!$R3 1308
9 TraesCS2B01G562100 chr2A 749874449 749875724 1275 False 833.000000 833 78.951000 1097 2360 1 chr2A.!!$F2 1263
10 TraesCS2B01G562100 chr2A 749385211 749388379 3168 False 793.000000 1323 84.578500 1117 3568 2 chr2A.!!$F3 2451
11 TraesCS2B01G562100 chr2A 721105622 721106797 1175 True 294.000000 294 71.880000 1172 2341 1 chr2A.!!$R2 1169
12 TraesCS2B01G562100 chr2A 748870005 748871062 1057 True 288.500000 429 86.092500 2393 3705 2 chr2A.!!$R5 1312
13 TraesCS2B01G562100 chr2D 618137750 618144105 6355 True 2856.666667 3947 91.061667 168 6428 3 chr2D.!!$R4 6260
14 TraesCS2B01G562100 chr2D 586960369 586961710 1341 True 1338.000000 1338 85.070000 1043 2360 1 chr2D.!!$R2 1317
15 TraesCS2B01G562100 chr2D 586845641 586846897 1256 True 1038.000000 1038 82.140000 1131 2360 1 chr2D.!!$R1 1229
16 TraesCS2B01G562100 chr2D 618659042 618660281 1239 True 1002.000000 1002 81.659000 1131 2354 1 chr2D.!!$R3 1223
17 TraesCS2B01G562100 chr2D 618333434 618336777 3343 False 780.000000 1288 84.005000 1076 3568 2 chr2D.!!$F1 2492

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
22 23 0.109412 GGCTGAGCAAAGCACACATC 60.109 55.0 6.82 0.0 45.43 3.06 F
776 828 0.597568 TGCTCTTGAACGGCCAAATG 59.402 50.0 2.24 0.0 0.00 2.32 F
1543 1661 0.169672 CATGAAGCTGGGCAAGAACG 59.830 55.0 0.00 0.0 0.00 3.95 F
3210 5335 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.0 0.00 0.0 0.00 3.82 F
4221 6442 0.105778 GAGGGAGTGCCTCACATAGC 59.894 60.0 24.71 0.0 36.16 2.97 F
5227 7881 0.037877 AGATGATAGGCCAGCCATGC 59.962 55.0 12.03 0.0 38.92 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1085 1153 2.093021 AGGAAGAAGCAGATCAAGAGCC 60.093 50.000 0.00 0.00 0.00 4.70 R
2594 4614 2.220824 GCGACTGGTTCCAAAATTTTGC 59.779 45.455 22.90 11.38 36.86 3.68 R
3289 5424 0.457443 GCCAATGGCTGCTTTCCTAC 59.543 55.000 18.47 0.00 46.69 3.18 R
4773 7426 0.331278 ATCCCCTTCATGGAACGCAA 59.669 50.000 0.00 0.00 38.35 4.85 R
5359 8013 0.659957 GGCGATCTCACCTCAATTGC 59.340 55.000 0.00 0.00 0.00 3.56 R
6287 8946 1.691219 CTTTGCAGGAAGCCCCCTA 59.309 57.895 0.00 0.00 44.83 3.53 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
17 18 4.410743 GGCGGCTGAGCAAAGCAC 62.411 66.667 17.58 6.39 45.43 4.40
18 19 3.663176 GCGGCTGAGCAAAGCACA 61.663 61.111 6.82 0.00 45.43 4.57
19 20 2.253452 CGGCTGAGCAAAGCACAC 59.747 61.111 6.82 0.00 45.43 3.82
20 21 2.545596 CGGCTGAGCAAAGCACACA 61.546 57.895 6.82 0.00 45.43 3.72
21 22 1.859427 CGGCTGAGCAAAGCACACAT 61.859 55.000 6.82 0.00 45.43 3.21
22 23 0.109412 GGCTGAGCAAAGCACACATC 60.109 55.000 6.82 0.00 45.43 3.06
23 24 0.879765 GCTGAGCAAAGCACACATCT 59.120 50.000 0.00 0.00 43.01 2.90
24 25 1.401148 GCTGAGCAAAGCACACATCTG 60.401 52.381 0.00 0.00 43.01 2.90
25 26 1.199327 CTGAGCAAAGCACACATCTGG 59.801 52.381 0.00 0.00 0.00 3.86
26 27 0.109412 GAGCAAAGCACACATCTGGC 60.109 55.000 0.00 0.00 0.00 4.85
27 28 1.080298 GCAAAGCACACATCTGGCC 60.080 57.895 0.00 0.00 0.00 5.36
28 29 1.530013 GCAAAGCACACATCTGGCCT 61.530 55.000 3.32 0.00 0.00 5.19
29 30 0.963962 CAAAGCACACATCTGGCCTT 59.036 50.000 3.32 0.00 0.00 4.35
30 31 1.342174 CAAAGCACACATCTGGCCTTT 59.658 47.619 3.32 0.00 0.00 3.11
31 32 1.708341 AAGCACACATCTGGCCTTTT 58.292 45.000 3.32 0.00 0.00 2.27
32 33 1.251251 AGCACACATCTGGCCTTTTC 58.749 50.000 3.32 0.00 0.00 2.29
33 34 0.961019 GCACACATCTGGCCTTTTCA 59.039 50.000 3.32 0.00 0.00 2.69
34 35 1.340889 GCACACATCTGGCCTTTTCAA 59.659 47.619 3.32 0.00 0.00 2.69
35 36 2.863704 GCACACATCTGGCCTTTTCAAC 60.864 50.000 3.32 0.00 0.00 3.18
36 37 1.963515 ACACATCTGGCCTTTTCAACC 59.036 47.619 3.32 0.00 0.00 3.77
37 38 1.962807 CACATCTGGCCTTTTCAACCA 59.037 47.619 3.32 0.00 0.00 3.67
38 39 2.564062 CACATCTGGCCTTTTCAACCAT 59.436 45.455 3.32 0.00 31.79 3.55
39 40 2.564062 ACATCTGGCCTTTTCAACCATG 59.436 45.455 3.32 0.00 31.79 3.66
40 41 2.673775 TCTGGCCTTTTCAACCATGA 57.326 45.000 3.32 0.00 31.79 3.07
41 42 3.173953 TCTGGCCTTTTCAACCATGAT 57.826 42.857 3.32 0.00 34.96 2.45
42 43 3.091545 TCTGGCCTTTTCAACCATGATC 58.908 45.455 3.32 0.00 34.96 2.92
43 44 3.094572 CTGGCCTTTTCAACCATGATCT 58.905 45.455 3.32 0.00 34.96 2.75
44 45 3.509442 TGGCCTTTTCAACCATGATCTT 58.491 40.909 3.32 0.00 34.96 2.40
45 46 3.511146 TGGCCTTTTCAACCATGATCTTC 59.489 43.478 3.32 0.00 34.96 2.87
46 47 3.766051 GGCCTTTTCAACCATGATCTTCT 59.234 43.478 0.00 0.00 34.96 2.85
47 48 4.221482 GGCCTTTTCAACCATGATCTTCTT 59.779 41.667 0.00 0.00 34.96 2.52
48 49 5.279657 GGCCTTTTCAACCATGATCTTCTTT 60.280 40.000 0.00 0.00 34.96 2.52
49 50 6.226052 GCCTTTTCAACCATGATCTTCTTTT 58.774 36.000 0.00 0.00 34.96 2.27
50 51 6.707608 GCCTTTTCAACCATGATCTTCTTTTT 59.292 34.615 0.00 0.00 34.96 1.94
51 52 7.095481 GCCTTTTCAACCATGATCTTCTTTTTC 60.095 37.037 0.00 0.00 34.96 2.29
52 53 7.927629 CCTTTTCAACCATGATCTTCTTTTTCA 59.072 33.333 0.00 0.00 34.96 2.69
53 54 8.647143 TTTTCAACCATGATCTTCTTTTTCAC 57.353 30.769 0.00 0.00 34.96 3.18
54 55 7.587037 TTCAACCATGATCTTCTTTTTCACT 57.413 32.000 0.00 0.00 34.96 3.41
55 56 6.973843 TCAACCATGATCTTCTTTTTCACTG 58.026 36.000 0.00 0.00 0.00 3.66
56 57 6.547141 TCAACCATGATCTTCTTTTTCACTGT 59.453 34.615 0.00 0.00 0.00 3.55
57 58 6.323203 ACCATGATCTTCTTTTTCACTGTG 57.677 37.500 0.17 0.17 0.00 3.66
58 59 6.064060 ACCATGATCTTCTTTTTCACTGTGA 58.936 36.000 6.36 6.36 0.00 3.58
59 60 6.718454 ACCATGATCTTCTTTTTCACTGTGAT 59.282 34.615 11.86 0.00 0.00 3.06
60 61 7.232127 ACCATGATCTTCTTTTTCACTGTGATT 59.768 33.333 11.86 0.00 0.00 2.57
61 62 7.541091 CCATGATCTTCTTTTTCACTGTGATTG 59.459 37.037 11.86 2.85 0.00 2.67
62 63 7.806409 TGATCTTCTTTTTCACTGTGATTGA 57.194 32.000 11.86 5.10 0.00 2.57
63 64 8.400184 TGATCTTCTTTTTCACTGTGATTGAT 57.600 30.769 11.86 7.59 0.00 2.57
64 65 8.509690 TGATCTTCTTTTTCACTGTGATTGATC 58.490 33.333 11.86 14.76 0.00 2.92
65 66 8.632906 ATCTTCTTTTTCACTGTGATTGATCT 57.367 30.769 11.86 0.00 0.00 2.75
66 67 9.730705 ATCTTCTTTTTCACTGTGATTGATCTA 57.269 29.630 11.86 0.00 0.00 1.98
67 68 9.559732 TCTTCTTTTTCACTGTGATTGATCTAA 57.440 29.630 11.86 0.00 0.00 2.10
93 94 7.946655 TTATATAGGCTTCAACAGAATCACG 57.053 36.000 0.00 0.00 0.00 4.35
94 95 2.839486 AGGCTTCAACAGAATCACGA 57.161 45.000 0.00 0.00 0.00 4.35
103 104 8.272176 GCTTCAACAGAATCACGAATAATCTAG 58.728 37.037 0.00 0.00 0.00 2.43
112 113 6.222038 TCACGAATAATCTAGCAAGGAAGT 57.778 37.500 0.00 0.00 0.00 3.01
132 133 6.760770 GGAAGTCCTGATTCTTGAATCACTAG 59.239 42.308 18.67 11.29 35.51 2.57
144 145 9.653516 TTCTTGAATCACTAGAGAGGAGAATAT 57.346 33.333 0.00 0.00 32.69 1.28
158 159 8.655935 AGAGGAGAATATTCAACCAACAAAAT 57.344 30.769 23.83 9.37 0.00 1.82
192 193 5.864418 TTGTGTGTAGACTAACAAGGACT 57.136 39.130 0.00 0.00 0.00 3.85
220 221 4.322049 CGAATTGAACTGGTCTAGGACACT 60.322 45.833 0.00 0.00 33.68 3.55
221 222 5.105877 CGAATTGAACTGGTCTAGGACACTA 60.106 44.000 0.00 0.00 33.68 2.74
248 249 7.333423 CGGTTACATGACCTCTTCAAAGATTTA 59.667 37.037 0.00 0.00 37.92 1.40
251 252 9.793259 TTACATGACCTCTTCAAAGATTTAAGT 57.207 29.630 0.00 0.00 37.92 2.24
259 260 6.837312 TCTTCAAAGATTTAAGTGAGGGTCA 58.163 36.000 0.00 0.00 0.00 4.02
294 302 7.427989 TGAGTTACTCCCGAAAATATAAGGT 57.572 36.000 10.10 0.00 0.00 3.50
295 303 7.270047 TGAGTTACTCCCGAAAATATAAGGTG 58.730 38.462 10.10 0.00 0.00 4.00
489 531 5.875910 TCAAAAGTTCAGTACAAAAGGACGA 59.124 36.000 0.00 0.00 0.00 4.20
595 644 4.646040 TGGCAATTTGATCCAGTCTAATGG 59.354 41.667 0.00 0.00 42.11 3.16
607 656 7.531857 TCCAGTCTAATGGATTCATCTAGAC 57.468 40.000 18.95 18.95 44.56 2.59
611 660 7.021873 AGTCTAATGGATTCATCTAGACCCAT 58.978 38.462 21.00 0.80 40.26 4.00
762 813 3.233507 TCCTTGAAAAATTGGCTGCTCT 58.766 40.909 0.00 0.00 0.00 4.09
775 827 0.883833 CTGCTCTTGAACGGCCAAAT 59.116 50.000 2.24 0.00 0.00 2.32
776 828 0.597568 TGCTCTTGAACGGCCAAATG 59.402 50.000 2.24 0.00 0.00 2.32
780 832 2.493278 CTCTTGAACGGCCAAATGGAAT 59.507 45.455 2.24 0.00 37.39 3.01
804 856 8.885494 ATTGTTTGGATTTCAATCTCGAAAAA 57.115 26.923 0.00 0.00 38.33 1.94
809 861 8.574196 TTGGATTTCAATCTCGAAAAAGAAAC 57.426 30.769 5.31 1.93 38.33 2.78
810 862 7.940850 TGGATTTCAATCTCGAAAAAGAAACT 58.059 30.769 5.31 0.00 38.33 2.66
812 864 9.893305 GGATTTCAATCTCGAAAAAGAAACTAA 57.107 29.630 5.31 0.00 38.33 2.24
851 907 7.310299 CCCATCTCTATCAAGTATGTAGCACAT 60.310 40.741 6.93 6.93 42.35 3.21
852 908 8.093307 CCATCTCTATCAAGTATGTAGCACATT 58.907 37.037 7.02 0.00 39.88 2.71
867 923 8.712285 TGTAGCACATTAGTACTAACCAAATC 57.288 34.615 17.45 6.91 0.00 2.17
869 925 7.611213 AGCACATTAGTACTAACCAAATCAC 57.389 36.000 17.45 3.04 0.00 3.06
873 929 8.234546 CACATTAGTACTAACCAAATCACCAAC 58.765 37.037 17.45 0.00 0.00 3.77
876 932 9.886132 ATTAGTACTAACCAAATCACCAACTAG 57.114 33.333 17.45 0.00 0.00 2.57
878 934 5.836024 ACTAACCAAATCACCAACTAGGA 57.164 39.130 0.00 0.00 41.22 2.94
879 935 5.805728 ACTAACCAAATCACCAACTAGGAG 58.194 41.667 0.00 0.00 41.22 3.69
880 936 4.724279 AACCAAATCACCAACTAGGAGT 57.276 40.909 0.00 0.00 41.22 3.85
882 938 5.161943 ACCAAATCACCAACTAGGAGTAC 57.838 43.478 0.00 0.00 41.22 2.73
885 941 5.105635 CCAAATCACCAACTAGGAGTACGTA 60.106 44.000 0.00 0.00 41.22 3.57
886 942 5.573337 AATCACCAACTAGGAGTACGTAC 57.427 43.478 18.10 18.10 41.22 3.67
887 943 4.292186 TCACCAACTAGGAGTACGTACT 57.708 45.455 27.71 27.71 41.22 2.73
888 944 4.655963 TCACCAACTAGGAGTACGTACTT 58.344 43.478 27.96 16.37 41.22 2.24
889 945 4.456911 TCACCAACTAGGAGTACGTACTTG 59.543 45.833 27.96 19.94 41.22 3.16
890 946 4.456911 CACCAACTAGGAGTACGTACTTGA 59.543 45.833 27.96 15.42 41.22 3.02
891 947 5.048504 CACCAACTAGGAGTACGTACTTGAA 60.049 44.000 27.96 15.23 41.22 2.69
892 948 5.536161 ACCAACTAGGAGTACGTACTTGAAA 59.464 40.000 27.96 13.63 41.22 2.69
893 949 6.210185 ACCAACTAGGAGTACGTACTTGAAAT 59.790 38.462 27.96 14.81 41.22 2.17
894 950 6.530534 CCAACTAGGAGTACGTACTTGAAATG 59.469 42.308 27.96 20.41 41.22 2.32
915 971 3.384789 TGTTATGATCTCGGTCCAAGAGG 59.615 47.826 0.00 0.00 36.45 3.69
916 972 2.166907 ATGATCTCGGTCCAAGAGGT 57.833 50.000 0.00 0.00 36.45 3.85
919 975 1.550976 GATCTCGGTCCAAGAGGTGTT 59.449 52.381 0.00 0.00 36.45 3.32
961 1022 3.067833 GTCTAGCTTTGAAAAGGTCGCT 58.932 45.455 10.55 2.20 44.77 4.93
962 1023 3.123790 GTCTAGCTTTGAAAAGGTCGCTC 59.876 47.826 10.55 0.12 44.77 5.03
964 1025 1.604278 AGCTTTGAAAAGGTCGCTCAC 59.396 47.619 1.73 0.00 42.60 3.51
1085 1153 1.515088 CACGTCTCCTACTGCAGCG 60.515 63.158 15.27 9.92 0.00 5.18
1364 1473 2.663196 CCTCGTCTTGGGGGACAC 59.337 66.667 0.00 0.00 36.12 3.67
1543 1661 0.169672 CATGAAGCTGGGCAAGAACG 59.830 55.000 0.00 0.00 0.00 3.95
1575 1693 2.433318 GAGTGGCAGCTCACGTCC 60.433 66.667 10.81 0.00 42.10 4.79
1661 1779 2.398588 GGAGATCATCCTGTGGTACCA 58.601 52.381 11.60 11.60 45.64 3.25
1671 1789 3.271142 GTGGTACCACGACGTCAAA 57.729 52.632 28.55 0.00 37.19 2.69
1848 1975 4.514585 AACCACACCGGCAAGGCA 62.515 61.111 0.00 0.00 46.52 4.75
1938 2080 2.968206 GAGTACGGGAAGTGCGGT 59.032 61.111 0.00 0.00 40.57 5.68
2205 2382 4.704833 TGCCTCGCCAACTGCTCC 62.705 66.667 0.00 0.00 38.05 4.70
2367 2551 5.046591 CGGTATGTACAGATTATGGGTGGAT 60.047 44.000 0.33 0.00 0.00 3.41
2410 3241 7.929941 ATTTTCACTTCAGTCCTAATCCTTC 57.070 36.000 0.00 0.00 0.00 3.46
2633 4657 3.487574 GTCGCTCACATTCGGAGATTAAG 59.512 47.826 0.00 0.00 35.04 1.85
2644 4668 7.989741 ACATTCGGAGATTAAGTCAATGAGATT 59.010 33.333 0.00 0.00 35.04 2.40
2645 4669 8.494347 CATTCGGAGATTAAGTCAATGAGATTC 58.506 37.037 0.00 0.00 35.04 2.52
2752 4777 1.812571 CAAGTTTCTGGATGGGGAACG 59.187 52.381 0.00 0.00 0.00 3.95
2770 4795 8.040727 TGGGGAACGATGATTATATGACATAAG 58.959 37.037 0.00 0.00 0.00 1.73
2911 4965 3.062763 CACAACTCTACCTTCTGCTGTG 58.937 50.000 0.00 0.00 0.00 3.66
2982 5036 8.462016 CAGAATTATAGGTAAATTATGCCCTGC 58.538 37.037 0.00 0.00 33.53 4.85
2995 5049 1.283029 TGCCCTGCTAGCTCAATCTTT 59.717 47.619 17.23 0.00 0.00 2.52
2996 5050 1.674962 GCCCTGCTAGCTCAATCTTTG 59.325 52.381 17.23 0.00 0.00 2.77
2998 5052 3.350833 CCCTGCTAGCTCAATCTTTGTT 58.649 45.455 17.23 0.00 0.00 2.83
2999 5053 3.128242 CCCTGCTAGCTCAATCTTTGTTG 59.872 47.826 17.23 0.00 0.00 3.33
3001 5055 4.217118 CCTGCTAGCTCAATCTTTGTTGTT 59.783 41.667 17.23 0.00 0.00 2.83
3005 5076 8.201554 TGCTAGCTCAATCTTTGTTGTTATAG 57.798 34.615 17.23 0.00 0.00 1.31
3023 5099 8.546083 TGTTATAGGGAAATGCATGGTAAATT 57.454 30.769 0.00 0.00 0.00 1.82
3030 5106 6.258507 GGGAAATGCATGGTAAATTCAATGTC 59.741 38.462 0.00 0.00 0.00 3.06
3036 5112 7.371159 TGCATGGTAAATTCAATGTCGTAAAA 58.629 30.769 0.00 0.00 0.00 1.52
3069 5145 1.737838 TTTGCAGGTGCTATTCCTCG 58.262 50.000 3.18 0.00 42.66 4.63
3160 5237 1.279271 AGTAATATCATCGGGCAGGGC 59.721 52.381 0.00 0.00 0.00 5.19
3210 5335 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3211 5336 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3212 5337 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3213 5338 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3266 5393 4.402474 GTGTTATCCTTCATGGGGGAAAAG 59.598 45.833 10.67 0.00 35.08 2.27
3568 5706 9.988815 GAGTCTGAACATCTACATATTTGGTAT 57.011 33.333 0.00 0.00 0.00 2.73
3658 5808 6.755607 AGATCATACAGATATATTGCGTGCTG 59.244 38.462 0.00 0.00 37.00 4.41
3709 5859 3.739810 CACATGCATGATCTCCTAAGTCG 59.260 47.826 32.75 1.29 0.00 4.18
3719 5869 1.481363 CTCCTAAGTCGAAGTTCCCCC 59.519 57.143 0.00 0.00 0.00 5.40
3817 5993 9.719355 AAATCATACATATAGATTTGCGTGGTA 57.281 29.630 0.00 0.00 39.68 3.25
3837 6013 8.653338 CGTGGTATATATATGCAACTTTGGTAC 58.347 37.037 14.29 0.00 0.00 3.34
3975 6193 3.328050 CCCTCCTGTCCTTTTTAGTCTGT 59.672 47.826 0.00 0.00 0.00 3.41
3979 6197 7.418025 CCCTCCTGTCCTTTTTAGTCTGTATAG 60.418 44.444 0.00 0.00 0.00 1.31
3996 6215 7.062022 GTCTGTATAGAAGTTTTGTCCGAAGTC 59.938 40.741 0.00 0.00 34.01 3.01
4057 6277 5.925397 TGTATCAACATTCACAATGCCAAAC 59.075 36.000 0.00 0.00 42.69 2.93
4063 6283 5.777802 ACATTCACAATGCCAAACGAATAA 58.222 33.333 0.00 0.00 42.69 1.40
4190 6410 8.213518 ACTTGACACAAATCTAATATGCGAAT 57.786 30.769 0.00 0.00 0.00 3.34
4210 6431 4.576330 ATTAAAAGGACCAGAGGGAGTG 57.424 45.455 0.00 0.00 38.05 3.51
4220 6441 1.411977 CAGAGGGAGTGCCTCACATAG 59.588 57.143 30.04 11.99 36.16 2.23
4221 6442 0.105778 GAGGGAGTGCCTCACATAGC 59.894 60.000 24.71 0.00 36.16 2.97
4222 6443 1.147153 GGGAGTGCCTCACATAGCC 59.853 63.158 0.00 0.00 36.74 3.93
4223 6444 1.626356 GGGAGTGCCTCACATAGCCA 61.626 60.000 0.00 0.00 36.74 4.75
4224 6445 0.462759 GGAGTGCCTCACATAGCCAC 60.463 60.000 4.85 0.00 36.74 5.01
4225 6446 0.250234 GAGTGCCTCACATAGCCACA 59.750 55.000 0.00 0.00 36.74 4.17
4226 6447 0.914644 AGTGCCTCACATAGCCACAT 59.085 50.000 0.00 0.00 36.74 3.21
4227 6448 2.103094 GAGTGCCTCACATAGCCACATA 59.897 50.000 0.00 0.00 36.74 2.29
4228 6449 2.158900 AGTGCCTCACATAGCCACATAC 60.159 50.000 0.00 0.00 36.74 2.39
4238 6459 0.394762 AGCCACATACACCTGCATGG 60.395 55.000 0.00 0.00 42.93 3.66
4258 6479 6.683861 GCATGGTTTTCCTTCTTTCAAGTTCT 60.684 38.462 0.00 0.00 41.38 3.01
4262 6483 8.154203 TGGTTTTCCTTCTTTCAAGTTCTTTTT 58.846 29.630 0.00 0.00 41.38 1.94
4501 6776 1.451936 GTGCTTCACTGGACTGGGT 59.548 57.895 0.00 0.00 0.00 4.51
4664 6939 1.943693 CACCGCCAAACTGTTTGCG 60.944 57.895 27.36 27.36 39.31 4.85
4681 6956 1.745890 CGGATAATCGGACTGGGCA 59.254 57.895 0.00 0.00 0.00 5.36
4682 6957 0.600255 CGGATAATCGGACTGGGCAC 60.600 60.000 0.00 0.00 0.00 5.01
4703 6978 6.586082 GGCACGATCAAACAATTGTTATTTCT 59.414 34.615 23.53 5.45 37.25 2.52
4773 7426 3.383825 GGATCCGACATACCTAACACTGT 59.616 47.826 0.00 0.00 0.00 3.55
4982 7635 2.950975 TGCATGCACGGTTCATATTGAT 59.049 40.909 18.46 0.00 0.00 2.57
5003 7657 5.709631 TGATATTGGTGTTGCAAAGCTCTAA 59.290 36.000 0.00 0.00 0.00 2.10
5008 7662 6.398234 TGGTGTTGCAAAGCTCTAAATTTA 57.602 33.333 0.00 0.00 0.00 1.40
5114 7768 5.350504 AGGATCATTGAACTTCTCGACAT 57.649 39.130 0.00 0.00 0.00 3.06
5154 7808 2.428890 CAAGTCCGAGCCTGAGATACTT 59.571 50.000 0.00 0.00 0.00 2.24
5157 7811 1.215673 TCCGAGCCTGAGATACTTCCT 59.784 52.381 0.00 0.00 0.00 3.36
5178 7832 4.693566 CCTGAGCTAAAACGTTGTATCCAA 59.306 41.667 0.00 0.00 0.00 3.53
5227 7881 0.037877 AGATGATAGGCCAGCCATGC 59.962 55.000 12.03 0.00 38.92 4.06
5299 7953 5.004448 CCAGAAGATCGGTACTAGATAGCA 58.996 45.833 0.00 0.00 0.00 3.49
5306 7960 7.626390 AGATCGGTACTAGATAGCAGAATAGT 58.374 38.462 0.00 0.00 33.27 2.12
5321 7975 5.298777 GCAGAATAGTCATGCCTTTGAATCT 59.701 40.000 0.00 0.00 33.81 2.40
5337 7991 4.389374 TGAATCTGTCCCTTGAACTTGAC 58.611 43.478 0.00 0.00 0.00 3.18
5359 8013 2.224621 ACTGATCACTTGAACCCCACTG 60.225 50.000 0.00 0.00 0.00 3.66
5485 8140 4.712337 TGGTTGTGATGTTGGTACCTTTTT 59.288 37.500 14.36 0.00 0.00 1.94
5535 8190 5.991606 TCATTGTAGAAAGATGCGGAATAGG 59.008 40.000 0.00 0.00 0.00 2.57
5688 8343 5.932883 GGTGGAAGTTTGTAAGAGGTTAGAG 59.067 44.000 0.00 0.00 0.00 2.43
5743 8398 4.915667 CGACTCTAGTTCGTGATTCAAACA 59.084 41.667 7.96 0.00 0.00 2.83
5764 8419 3.076621 ACATTGCAAGAGAGCGAATTCA 58.923 40.909 4.94 0.00 37.31 2.57
5765 8420 3.503363 ACATTGCAAGAGAGCGAATTCAA 59.497 39.130 4.94 0.00 37.31 2.69
5794 8449 3.798202 ACGATCCATGCTCTTAGGAAAC 58.202 45.455 0.00 0.00 34.62 2.78
5839 8494 1.014564 GCGAGACTGGTACTTGGCAC 61.015 60.000 0.00 0.00 0.00 5.01
5900 8555 1.075536 CCTCCTTTTTGTAGGCCCACT 59.924 52.381 2.16 0.00 35.15 4.00
5902 8557 1.777878 TCCTTTTTGTAGGCCCACTGA 59.222 47.619 2.16 0.00 35.15 3.41
5935 8590 6.770785 TCTTTGGGTATTTATCCGGAATCAAG 59.229 38.462 9.01 0.00 0.00 3.02
6042 8697 9.818796 GAGATTGAGTGTTCAAGATTTTAACTC 57.181 33.333 0.00 0.00 45.89 3.01
6114 8769 4.217767 GGGAGGTTGTGTGGAAAGATTTAC 59.782 45.833 0.00 0.00 0.00 2.01
6287 8946 6.438763 GTTGTTTGACATAGTTAGCAAGCTT 58.561 36.000 0.00 0.00 0.00 3.74
6401 9060 2.424246 GGGTAAGGAGAAGAGTGAGACG 59.576 54.545 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.663176 TGTGCTTTGCTCAGCCGC 61.663 61.111 0.00 0.00 39.25 6.53
2 3 1.859427 ATGTGTGCTTTGCTCAGCCG 61.859 55.000 0.00 0.00 39.25 5.52
3 4 0.109412 GATGTGTGCTTTGCTCAGCC 60.109 55.000 0.00 0.00 39.25 4.85
4 5 0.879765 AGATGTGTGCTTTGCTCAGC 59.120 50.000 0.00 0.00 40.55 4.26
5 6 1.199327 CCAGATGTGTGCTTTGCTCAG 59.801 52.381 0.00 0.00 32.70 3.35
6 7 1.241165 CCAGATGTGTGCTTTGCTCA 58.759 50.000 0.00 0.00 0.00 4.26
7 8 0.109412 GCCAGATGTGTGCTTTGCTC 60.109 55.000 0.00 0.00 0.00 4.26
8 9 1.530013 GGCCAGATGTGTGCTTTGCT 61.530 55.000 0.00 0.00 0.00 3.91
9 10 1.080298 GGCCAGATGTGTGCTTTGC 60.080 57.895 0.00 0.00 0.00 3.68
10 11 0.963962 AAGGCCAGATGTGTGCTTTG 59.036 50.000 5.01 0.00 0.00 2.77
11 12 1.708341 AAAGGCCAGATGTGTGCTTT 58.292 45.000 5.01 0.00 0.00 3.51
12 13 1.615392 GAAAAGGCCAGATGTGTGCTT 59.385 47.619 5.01 0.00 0.00 3.91
13 14 1.251251 GAAAAGGCCAGATGTGTGCT 58.749 50.000 5.01 0.00 0.00 4.40
14 15 0.961019 TGAAAAGGCCAGATGTGTGC 59.039 50.000 5.01 0.00 0.00 4.57
15 16 2.288395 GGTTGAAAAGGCCAGATGTGTG 60.288 50.000 5.01 0.00 0.00 3.82
16 17 1.963515 GGTTGAAAAGGCCAGATGTGT 59.036 47.619 5.01 0.00 0.00 3.72
17 18 1.962807 TGGTTGAAAAGGCCAGATGTG 59.037 47.619 5.01 0.00 0.00 3.21
18 19 2.380064 TGGTTGAAAAGGCCAGATGT 57.620 45.000 5.01 0.00 0.00 3.06
19 20 2.827322 TCATGGTTGAAAAGGCCAGATG 59.173 45.455 5.01 0.00 35.56 2.90
20 21 3.173953 TCATGGTTGAAAAGGCCAGAT 57.826 42.857 5.01 0.00 35.56 2.90
21 22 2.673775 TCATGGTTGAAAAGGCCAGA 57.326 45.000 5.01 0.00 35.56 3.86
22 23 3.094572 AGATCATGGTTGAAAAGGCCAG 58.905 45.455 5.01 0.00 34.96 4.85
23 24 3.173953 AGATCATGGTTGAAAAGGCCA 57.826 42.857 5.01 0.00 34.96 5.36
24 25 3.766051 AGAAGATCATGGTTGAAAAGGCC 59.234 43.478 0.00 0.00 34.96 5.19
25 26 5.397142 AAGAAGATCATGGTTGAAAAGGC 57.603 39.130 0.00 0.00 34.96 4.35
26 27 7.927629 TGAAAAAGAAGATCATGGTTGAAAAGG 59.072 33.333 0.00 0.00 34.96 3.11
27 28 8.758715 GTGAAAAAGAAGATCATGGTTGAAAAG 58.241 33.333 0.00 0.00 34.96 2.27
28 29 8.477256 AGTGAAAAAGAAGATCATGGTTGAAAA 58.523 29.630 0.00 0.00 34.96 2.29
29 30 7.922278 CAGTGAAAAAGAAGATCATGGTTGAAA 59.078 33.333 0.00 0.00 34.96 2.69
30 31 7.068593 ACAGTGAAAAAGAAGATCATGGTTGAA 59.931 33.333 0.00 0.00 34.96 2.69
31 32 6.547141 ACAGTGAAAAAGAAGATCATGGTTGA 59.453 34.615 0.00 0.00 36.00 3.18
32 33 6.639686 CACAGTGAAAAAGAAGATCATGGTTG 59.360 38.462 0.00 0.00 0.00 3.77
33 34 6.547141 TCACAGTGAAAAAGAAGATCATGGTT 59.453 34.615 0.00 0.00 0.00 3.67
34 35 6.064060 TCACAGTGAAAAAGAAGATCATGGT 58.936 36.000 0.00 0.00 0.00 3.55
35 36 6.564709 TCACAGTGAAAAAGAAGATCATGG 57.435 37.500 0.00 0.00 0.00 3.66
36 37 8.294577 TCAATCACAGTGAAAAAGAAGATCATG 58.705 33.333 7.50 0.00 0.00 3.07
37 38 8.400184 TCAATCACAGTGAAAAAGAAGATCAT 57.600 30.769 7.50 0.00 0.00 2.45
38 39 7.806409 TCAATCACAGTGAAAAAGAAGATCA 57.194 32.000 7.50 0.00 0.00 2.92
39 40 8.728833 AGATCAATCACAGTGAAAAAGAAGATC 58.271 33.333 7.50 11.67 0.00 2.75
40 41 8.632906 AGATCAATCACAGTGAAAAAGAAGAT 57.367 30.769 7.50 3.78 0.00 2.40
41 42 9.559732 TTAGATCAATCACAGTGAAAAAGAAGA 57.440 29.630 7.50 0.00 0.00 2.87
67 68 8.993121 CGTGATTCTGTTGAAGCCTATATAATT 58.007 33.333 0.00 0.00 37.76 1.40
68 69 8.367911 TCGTGATTCTGTTGAAGCCTATATAAT 58.632 33.333 0.00 0.00 37.76 1.28
69 70 7.722363 TCGTGATTCTGTTGAAGCCTATATAA 58.278 34.615 0.00 0.00 37.76 0.98
70 71 7.284919 TCGTGATTCTGTTGAAGCCTATATA 57.715 36.000 0.00 0.00 37.76 0.86
71 72 6.161855 TCGTGATTCTGTTGAAGCCTATAT 57.838 37.500 0.00 0.00 37.76 0.86
72 73 5.592104 TCGTGATTCTGTTGAAGCCTATA 57.408 39.130 0.00 0.00 37.76 1.31
73 74 4.471904 TCGTGATTCTGTTGAAGCCTAT 57.528 40.909 0.00 0.00 37.76 2.57
74 75 3.953712 TCGTGATTCTGTTGAAGCCTA 57.046 42.857 0.00 0.00 37.76 3.93
75 76 2.839486 TCGTGATTCTGTTGAAGCCT 57.161 45.000 0.00 0.00 37.76 4.58
76 77 5.545658 TTATTCGTGATTCTGTTGAAGCC 57.454 39.130 0.00 0.00 37.76 4.35
77 78 7.009568 AGATTATTCGTGATTCTGTTGAAGC 57.990 36.000 0.00 0.00 38.90 3.86
78 79 8.272176 GCTAGATTATTCGTGATTCTGTTGAAG 58.728 37.037 0.00 0.00 35.44 3.02
79 80 7.763985 TGCTAGATTATTCGTGATTCTGTTGAA 59.236 33.333 0.00 0.00 36.54 2.69
80 81 7.264947 TGCTAGATTATTCGTGATTCTGTTGA 58.735 34.615 0.00 0.00 0.00 3.18
81 82 7.468922 TGCTAGATTATTCGTGATTCTGTTG 57.531 36.000 0.00 0.00 0.00 3.33
82 83 7.225538 CCTTGCTAGATTATTCGTGATTCTGTT 59.774 37.037 0.00 0.00 0.00 3.16
83 84 6.703607 CCTTGCTAGATTATTCGTGATTCTGT 59.296 38.462 0.00 0.00 0.00 3.41
84 85 6.925718 TCCTTGCTAGATTATTCGTGATTCTG 59.074 38.462 0.00 0.00 0.00 3.02
85 86 7.055667 TCCTTGCTAGATTATTCGTGATTCT 57.944 36.000 0.00 0.00 0.00 2.40
86 87 7.439655 ACTTCCTTGCTAGATTATTCGTGATTC 59.560 37.037 0.00 0.00 0.00 2.52
87 88 7.275920 ACTTCCTTGCTAGATTATTCGTGATT 58.724 34.615 0.00 0.00 0.00 2.57
88 89 6.821388 ACTTCCTTGCTAGATTATTCGTGAT 58.179 36.000 0.00 0.00 0.00 3.06
89 90 6.222038 ACTTCCTTGCTAGATTATTCGTGA 57.778 37.500 0.00 0.00 0.00 4.35
90 91 5.463724 GGACTTCCTTGCTAGATTATTCGTG 59.536 44.000 0.00 0.00 0.00 4.35
91 92 5.364157 AGGACTTCCTTGCTAGATTATTCGT 59.636 40.000 0.00 0.00 46.09 3.85
92 93 5.694006 CAGGACTTCCTTGCTAGATTATTCG 59.306 44.000 0.00 0.00 46.09 3.34
93 94 6.821388 TCAGGACTTCCTTGCTAGATTATTC 58.179 40.000 0.00 0.00 46.09 1.75
94 95 6.814954 TCAGGACTTCCTTGCTAGATTATT 57.185 37.500 0.00 0.00 46.09 1.40
103 104 3.679389 TCAAGAATCAGGACTTCCTTGC 58.321 45.455 0.00 0.00 46.09 4.01
116 117 7.581213 TCTCCTCTCTAGTGATTCAAGAATC 57.419 40.000 14.33 14.33 45.55 2.52
132 133 7.687941 TTTGTTGGTTGAATATTCTCCTCTC 57.312 36.000 21.62 15.19 0.00 3.20
171 172 5.138276 AGAGTCCTTGTTAGTCTACACACA 58.862 41.667 0.00 0.00 0.00 3.72
192 193 4.081642 CCTAGACCAGTTCAATTCGGAAGA 60.082 45.833 0.00 0.00 39.20 2.87
198 199 5.153950 AGTGTCCTAGACCAGTTCAATTC 57.846 43.478 0.00 0.00 0.00 2.17
201 202 3.504906 CGTAGTGTCCTAGACCAGTTCAA 59.495 47.826 0.00 0.00 0.00 2.69
220 221 5.244402 TCTTTGAAGAGGTCATGTAACCGTA 59.756 40.000 0.00 0.00 44.49 4.02
221 222 4.039973 TCTTTGAAGAGGTCATGTAACCGT 59.960 41.667 0.00 0.00 44.49 4.83
248 249 6.601332 TCAAAGTCTTAAATGACCCTCACTT 58.399 36.000 0.00 0.00 37.66 3.16
250 251 5.998363 ACTCAAAGTCTTAAATGACCCTCAC 59.002 40.000 0.00 0.00 37.66 3.51
251 252 6.187727 ACTCAAAGTCTTAAATGACCCTCA 57.812 37.500 0.00 0.00 37.66 3.86
259 260 7.001099 TCGGGAGTAACTCAAAGTCTTAAAT 57.999 36.000 0.00 0.00 31.08 1.40
489 531 0.740868 ATCGCTATGTGCACGTGCTT 60.741 50.000 37.59 24.91 43.06 3.91
501 543 0.248565 AGCATGGCATCGATCGCTAT 59.751 50.000 11.09 13.55 0.00 2.97
595 644 8.760980 AGCTATAGTATGGGTCTAGATGAATC 57.239 38.462 0.00 0.00 0.00 2.52
607 656 7.338703 TCGGAATAGTACAAGCTATAGTATGGG 59.661 40.741 0.84 1.56 31.94 4.00
611 660 7.154656 TCGTCGGAATAGTACAAGCTATAGTA 58.845 38.462 0.84 0.00 31.94 1.82
648 697 4.093115 CACAGTCATTGCAGAGATGAGAAC 59.907 45.833 0.00 0.00 34.41 3.01
678 727 0.180406 GCGTGTGGAGGGGATAACAT 59.820 55.000 0.00 0.00 0.00 2.71
762 813 2.366916 ACAATTCCATTTGGCCGTTCAA 59.633 40.909 0.00 0.00 34.44 2.69
771 823 9.005777 AGATTGAAATCCAAACAATTCCATTTG 57.994 29.630 0.00 0.00 38.43 2.32
775 827 6.208402 TCGAGATTGAAATCCAAACAATTCCA 59.792 34.615 0.00 0.00 38.43 3.53
776 828 6.620678 TCGAGATTGAAATCCAAACAATTCC 58.379 36.000 0.00 0.00 38.43 3.01
780 832 8.194104 TCTTTTTCGAGATTGAAATCCAAACAA 58.806 29.630 0.00 0.00 37.66 2.83
842 894 8.315482 TGATTTGGTTAGTACTAATGTGCTACA 58.685 33.333 18.03 10.60 40.24 2.74
851 907 8.316214 CCTAGTTGGTGATTTGGTTAGTACTAA 58.684 37.037 11.38 11.38 0.00 2.24
852 908 7.675195 TCCTAGTTGGTGATTTGGTTAGTACTA 59.325 37.037 0.00 0.00 37.07 1.82
853 909 6.499350 TCCTAGTTGGTGATTTGGTTAGTACT 59.501 38.462 0.00 0.00 37.07 2.73
854 910 6.704310 TCCTAGTTGGTGATTTGGTTAGTAC 58.296 40.000 0.00 0.00 37.07 2.73
867 923 4.456911 TCAAGTACGTACTCCTAGTTGGTG 59.543 45.833 27.51 18.01 34.99 4.17
869 925 5.633830 TTCAAGTACGTACTCCTAGTTGG 57.366 43.478 27.51 10.44 34.99 3.77
873 929 9.234384 CATAACATTTCAAGTACGTACTCCTAG 57.766 37.037 27.51 17.26 34.99 3.02
876 932 8.644318 ATCATAACATTTCAAGTACGTACTCC 57.356 34.615 27.51 0.69 34.99 3.85
878 934 9.517609 GAGATCATAACATTTCAAGTACGTACT 57.482 33.333 22.45 22.45 38.39 2.73
879 935 8.469902 CGAGATCATAACATTTCAAGTACGTAC 58.530 37.037 18.10 18.10 0.00 3.67
880 936 7.646526 CCGAGATCATAACATTTCAAGTACGTA 59.353 37.037 0.00 0.00 0.00 3.57
882 938 6.475727 ACCGAGATCATAACATTTCAAGTACG 59.524 38.462 0.00 0.00 0.00 3.67
885 941 5.817816 GGACCGAGATCATAACATTTCAAGT 59.182 40.000 0.00 0.00 0.00 3.16
886 942 5.817296 TGGACCGAGATCATAACATTTCAAG 59.183 40.000 0.00 0.00 0.00 3.02
887 943 5.739959 TGGACCGAGATCATAACATTTCAA 58.260 37.500 0.00 0.00 0.00 2.69
888 944 5.351948 TGGACCGAGATCATAACATTTCA 57.648 39.130 0.00 0.00 0.00 2.69
889 945 6.049149 TCTTGGACCGAGATCATAACATTTC 58.951 40.000 7.42 0.00 0.00 2.17
890 946 5.989477 TCTTGGACCGAGATCATAACATTT 58.011 37.500 7.42 0.00 0.00 2.32
891 947 5.453903 CCTCTTGGACCGAGATCATAACATT 60.454 44.000 12.12 0.00 34.57 2.71
892 948 4.039730 CCTCTTGGACCGAGATCATAACAT 59.960 45.833 12.12 0.00 34.57 2.71
893 949 3.384789 CCTCTTGGACCGAGATCATAACA 59.615 47.826 12.12 0.00 34.57 2.41
894 950 3.385111 ACCTCTTGGACCGAGATCATAAC 59.615 47.826 12.12 0.00 37.04 1.89
915 971 8.780249 ACTGGTCATGTAATTAAGTTGTAACAC 58.220 33.333 0.00 0.00 0.00 3.32
916 972 8.911918 ACTGGTCATGTAATTAAGTTGTAACA 57.088 30.769 0.00 0.00 0.00 2.41
961 1022 1.338973 GGATGTATACGGCCGAAGTGA 59.661 52.381 35.90 13.01 0.00 3.41
962 1023 1.604693 GGGATGTATACGGCCGAAGTG 60.605 57.143 35.90 1.49 0.00 3.16
964 1025 0.677288 TGGGATGTATACGGCCGAAG 59.323 55.000 35.90 2.46 0.00 3.79
1085 1153 2.093021 AGGAAGAAGCAGATCAAGAGCC 60.093 50.000 0.00 0.00 0.00 4.70
1543 1661 3.827898 CTCGCCTCCGGTCCAGAC 61.828 72.222 0.00 0.00 34.56 3.51
1848 1975 4.704103 TCCCACTCCAGCCGCTCT 62.704 66.667 0.00 0.00 0.00 4.09
2272 2449 3.138304 GGCGTAGATCAACAATGGCATA 58.862 45.455 0.00 0.00 0.00 3.14
2367 2551 5.986501 AAATTTGGGGCGAAAATGTAGTA 57.013 34.783 0.00 0.00 0.00 1.82
2591 4611 4.441792 GACTGGTTCCAAAATTTTGCAGT 58.558 39.130 27.56 27.56 39.09 4.40
2594 4614 2.220824 GCGACTGGTTCCAAAATTTTGC 59.779 45.455 22.90 11.38 36.86 3.68
2683 4707 8.531530 GTCTACTTGCAAAATGTTGTAAAACTG 58.468 33.333 0.00 0.00 38.63 3.16
2911 4965 7.481642 TCATAAAGACGACCAGAAGAATAGTC 58.518 38.462 0.00 0.00 0.00 2.59
2978 5032 3.755378 ACAACAAAGATTGAGCTAGCAGG 59.245 43.478 18.83 0.00 33.57 4.85
2982 5036 7.987458 TCCCTATAACAACAAAGATTGAGCTAG 59.013 37.037 0.00 0.00 33.57 3.42
2995 5049 5.268387 ACCATGCATTTCCCTATAACAACA 58.732 37.500 0.00 0.00 0.00 3.33
2996 5050 5.852282 ACCATGCATTTCCCTATAACAAC 57.148 39.130 0.00 0.00 0.00 3.32
2998 5052 8.546083 AATTTACCATGCATTTCCCTATAACA 57.454 30.769 0.00 0.00 0.00 2.41
2999 5053 8.637986 TGAATTTACCATGCATTTCCCTATAAC 58.362 33.333 0.00 0.00 0.00 1.89
3001 5055 8.774546 TTGAATTTACCATGCATTTCCCTATA 57.225 30.769 0.00 0.00 0.00 1.31
3005 5076 6.114767 ACATTGAATTTACCATGCATTTCCC 58.885 36.000 0.00 0.00 0.00 3.97
3036 5112 3.676091 GCAAAACGAGCTTGCGTAT 57.324 47.368 0.00 0.00 44.86 3.06
3069 5145 4.800554 CCGCCATGGTAGGATTCC 57.199 61.111 19.73 0.00 0.00 3.01
3160 5237 5.949735 ACCTTGTAAACAATGCTAAATCCG 58.050 37.500 0.00 0.00 35.02 4.18
3232 5357 1.131826 GATAACACACACGCCACGC 59.868 57.895 0.00 0.00 0.00 5.34
3233 5358 0.669318 AGGATAACACACACGCCACG 60.669 55.000 0.00 0.00 0.00 4.94
3234 5359 1.463444 GAAGGATAACACACACGCCAC 59.537 52.381 0.00 0.00 0.00 5.01
3235 5360 1.070914 TGAAGGATAACACACACGCCA 59.929 47.619 0.00 0.00 0.00 5.69
3236 5361 1.803334 TGAAGGATAACACACACGCC 58.197 50.000 0.00 0.00 0.00 5.68
3237 5362 2.095853 CCATGAAGGATAACACACACGC 59.904 50.000 0.00 0.00 41.22 5.34
3238 5363 2.677836 CCCATGAAGGATAACACACACG 59.322 50.000 0.00 0.00 41.22 4.49
3239 5364 3.016736 CCCCATGAAGGATAACACACAC 58.983 50.000 0.00 0.00 41.22 3.82
3240 5365 2.025416 CCCCCATGAAGGATAACACACA 60.025 50.000 0.00 0.00 41.22 3.72
3241 5366 2.241176 TCCCCCATGAAGGATAACACAC 59.759 50.000 0.00 0.00 41.22 3.82
3242 5367 2.567862 TCCCCCATGAAGGATAACACA 58.432 47.619 0.00 0.00 41.22 3.72
3243 5368 3.662759 TTCCCCCATGAAGGATAACAC 57.337 47.619 4.70 0.00 41.22 3.32
3244 5369 4.045334 ACTTTTCCCCCATGAAGGATAACA 59.955 41.667 4.70 0.00 41.22 2.41
3289 5424 0.457443 GCCAATGGCTGCTTTCCTAC 59.543 55.000 18.47 0.00 46.69 3.18
3322 5457 9.492973 CCTGGTGATTTTAGAATTTGAAATGTT 57.507 29.630 0.00 0.00 0.00 2.71
3658 5808 2.288961 TTAGCGAAACACGAGGATCC 57.711 50.000 2.48 2.48 45.77 3.36
3709 5859 3.557054 GCTGGAATTTTTGGGGGAACTTC 60.557 47.826 0.00 0.00 0.00 3.01
3823 5999 5.606348 TTCTTTTGGTACCAAAGTTGCAT 57.394 34.783 32.78 0.00 45.15 3.96
3911 6129 9.123709 GCATTTTCTTACAAAACATATGACGAA 57.876 29.630 10.38 0.00 0.00 3.85
3947 6165 4.576330 AAAAAGGACAGGAGGGAGTATG 57.424 45.455 0.00 0.00 0.00 2.39
3975 6193 7.095355 GCTTTGACTTCGGACAAAACTTCTATA 60.095 37.037 0.00 0.00 38.59 1.31
3979 6197 4.035684 GCTTTGACTTCGGACAAAACTTC 58.964 43.478 0.00 0.00 38.59 3.01
3987 6205 2.966050 AGAGATGCTTTGACTTCGGAC 58.034 47.619 0.00 0.00 0.00 4.79
3988 6206 3.764434 AGTAGAGATGCTTTGACTTCGGA 59.236 43.478 0.00 0.00 0.00 4.55
4164 6384 7.609760 TCGCATATTAGATTTGTGTCAAGTT 57.390 32.000 0.00 0.00 0.00 2.66
4184 6404 3.343617 CCTCTGGTCCTTTTAATTCGCA 58.656 45.455 0.00 0.00 0.00 5.10
4190 6410 2.039879 GCACTCCCTCTGGTCCTTTTAA 59.960 50.000 0.00 0.00 0.00 1.52
4220 6441 2.109431 CCATGCAGGTGTATGTGGC 58.891 57.895 7.20 0.00 36.58 5.01
4262 6483 9.874205 ATGAAAACTTCACTCTTGATTCAAAAA 57.126 25.926 0.01 0.00 43.48 1.94
4329 6595 6.591834 TCTCTGAAAGCTGCTTATAAACACTC 59.408 38.462 16.31 7.37 0.00 3.51
4501 6776 7.280876 TCTCGCGTAGTAATTCTAACCTTCTTA 59.719 37.037 5.77 0.00 0.00 2.10
4664 6939 0.600255 CGTGCCCAGTCCGATTATCC 60.600 60.000 0.00 0.00 0.00 2.59
4681 6956 7.021196 CGGAGAAATAACAATTGTTTGATCGT 58.979 34.615 27.66 9.80 39.31 3.73
4682 6957 7.021196 ACGGAGAAATAACAATTGTTTGATCG 58.979 34.615 27.66 21.36 39.31 3.69
4741 7394 0.871722 TGTCGGATCCGCAACTTTTG 59.128 50.000 29.62 0.00 39.59 2.44
4773 7426 0.331278 ATCCCCTTCATGGAACGCAA 59.669 50.000 0.00 0.00 38.35 4.85
4982 7635 6.588719 ATTTAGAGCTTTGCAACACCAATA 57.411 33.333 0.00 0.00 0.00 1.90
5040 7694 7.337938 ACCAAAAAGAATTGTCAAGTTCCATT 58.662 30.769 0.00 0.00 0.00 3.16
5114 7768 1.971167 GGGAGCGGCACAATTGTCA 60.971 57.895 8.48 0.00 0.00 3.58
5154 7808 4.501071 GGATACAACGTTTTAGCTCAGGA 58.499 43.478 9.34 0.00 0.00 3.86
5178 7832 3.077556 ACGCAGAGGAGCCCGATT 61.078 61.111 0.00 0.00 0.00 3.34
5227 7881 1.331214 AACATGGCCACAACTTCAGG 58.669 50.000 8.16 0.00 0.00 3.86
5299 7953 6.421485 ACAGATTCAAAGGCATGACTATTCT 58.579 36.000 0.00 0.00 0.00 2.40
5306 7960 2.309755 AGGGACAGATTCAAAGGCATGA 59.690 45.455 0.00 0.00 0.00 3.07
5321 7975 2.503765 TCAGTGTCAAGTTCAAGGGACA 59.496 45.455 0.00 0.00 37.89 4.02
5337 7991 2.154462 GTGGGGTTCAAGTGATCAGTG 58.846 52.381 3.18 1.71 0.00 3.66
5359 8013 0.659957 GGCGATCTCACCTCAATTGC 59.340 55.000 0.00 0.00 0.00 3.56
5439 8093 7.397192 ACCAAAAGGCTATGTGTAAATGATTCT 59.603 33.333 0.00 0.00 0.00 2.40
5454 8108 3.320541 CCAACATCACAACCAAAAGGCTA 59.679 43.478 0.00 0.00 0.00 3.93
5485 8140 8.995027 ATCAAGGTACCAATATATGCAAAAGA 57.005 30.769 15.94 0.00 0.00 2.52
5535 8190 8.598041 AGTCTTACCTCCATATATGTTGAATCC 58.402 37.037 11.73 0.00 0.00 3.01
5743 8398 3.076621 TGAATTCGCTCTCTTGCAATGT 58.923 40.909 0.00 0.00 0.00 2.71
5794 8449 6.453092 ACAATACTATCGTTAAAGGATCGGG 58.547 40.000 0.00 0.00 0.00 5.14
5839 8494 8.588290 ACCTTAGTCTATATATTGCTCTGAGG 57.412 38.462 17.94 17.94 34.73 3.86
6114 8769 9.868277 TTTGCCACAATGGTATTTATTTCTAAG 57.132 29.630 0.00 0.00 40.46 2.18
6180 8835 5.817296 TCCGAATGGTGAAATAAGAGATGTG 59.183 40.000 0.00 0.00 36.30 3.21
6185 8840 6.036517 CAGACTTCCGAATGGTGAAATAAGAG 59.963 42.308 0.00 0.00 36.30 2.85
6287 8946 1.691219 CTTTGCAGGAAGCCCCCTA 59.309 57.895 0.00 0.00 44.83 3.53
6387 9046 8.346300 TGTATATCAAATCGTCTCACTCTTCTC 58.654 37.037 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.