Multiple sequence alignment - TraesCS1A01G036400

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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 TraesCS1A01G036400 chr1A 100.000 3688 0 0 1 3688 20239224 20235537 0.000000e+00 6811.0
1 TraesCS1A01G036400 chr1A 84.923 2202 231 50 1240 3402 20246161 20244022 0.000000e+00 2134.0
2 TraesCS1A01G036400 chr1A 84.436 257 20 12 3379 3627 20243824 20243580 6.160000e-58 235.0
3 TraesCS1A01G036400 chr1A 77.089 371 70 11 1549 1916 570374456 570374098 2.250000e-47 200.0
4 TraesCS1A01G036400 chr1A 78.201 289 59 4 1549 1835 570414102 570413816 8.140000e-42 182.0
5 TraesCS1A01G036400 chr1A 96.875 64 2 0 168 231 20238999 20238936 1.400000e-19 108.0
6 TraesCS1A01G036400 chr1A 96.875 64 2 0 226 289 20239057 20238994 1.400000e-19 108.0
7 TraesCS1A01G036400 chr1D 85.937 2439 244 51 1240 3627 18243481 18241091 0.000000e+00 2512.0
8 TraesCS1A01G036400 chr1D 88.906 1316 75 22 862 2162 18223978 18222719 0.000000e+00 1555.0
9 TraesCS1A01G036400 chr1D 94.301 930 48 2 2764 3688 18222022 18221093 0.000000e+00 1419.0
10 TraesCS1A01G036400 chr1D 94.087 575 30 2 2192 2766 18222725 18222155 0.000000e+00 870.0
11 TraesCS1A01G036400 chr1D 87.230 509 57 2 226 727 18226029 18225522 1.150000e-159 573.0
12 TraesCS1A01G036400 chr1D 86.131 411 56 1 419 829 18225094 18224685 3.380000e-120 442.0
13 TraesCS1A01G036400 chr1D 82.927 246 28 5 1 233 18226208 18225964 3.730000e-50 209.0
14 TraesCS1A01G036400 chr1D 76.738 374 66 15 1549 1916 474900553 474900195 4.860000e-44 189.0
15 TraesCS1A01G036400 chr1D 75.884 311 62 10 2324 2632 18079276 18078977 2.970000e-31 147.0
16 TraesCS1A01G036400 chr1D 72.857 490 109 17 2145 2628 81178340 81178811 2.970000e-31 147.0
17 TraesCS1A01G036400 chr1D 80.435 230 11 13 852 1054 18225380 18225158 1.070000e-30 145.0
18 TraesCS1A01G036400 chr1D 72.653 490 110 16 2145 2628 81287827 81288298 1.380000e-29 141.0
19 TraesCS1A01G036400 chr1D 72.010 393 86 14 2221 2607 469811057 469811431 1.090000e-15 95.3
20 TraesCS1A01G036400 chr1D 95.238 42 2 0 2907 2948 18241765 18241724 2.380000e-07 67.6
21 TraesCS1A01G036400 chr6D 73.333 1365 294 50 1551 2883 319244389 319245715 1.220000e-119 440.0
22 TraesCS1A01G036400 chr6D 75.368 475 100 12 1560 2027 7567547 7567083 2.890000e-51 213.0
23 TraesCS1A01G036400 chr6A 72.821 1354 312 37 1558 2882 457072526 457073852 9.530000e-111 411.0
24 TraesCS1A01G036400 chr6A 76.471 476 95 12 1560 2028 7732966 7732501 3.680000e-60 243.0
25 TraesCS1A01G036400 chr1B 73.745 1036 219 34 1540 2553 660013011 660012007 1.260000e-94 357.0
26 TraesCS1A01G036400 chr1B 72.414 493 106 21 2145 2628 134437452 134437923 2.990000e-26 130.0
27 TraesCS1A01G036400 chr1B 72.245 490 112 16 2145 2628 134575480 134575951 2.990000e-26 130.0
28 TraesCS1A01G036400 chr1B 79.268 82 17 0 261 342 535397661 535397580 1.430000e-04 58.4
29 TraesCS1A01G036400 chr6B 76.730 477 92 14 1560 2028 14251802 14251337 7.910000e-62 248.0
30 TraesCS1A01G036400 chr6B 76.520 477 93 14 1560 2028 13960172 13960637 3.680000e-60 243.0
31 TraesCS1A01G036400 chr3D 73.962 530 115 12 251 769 397775492 397774975 3.760000e-45 193.0
32 TraesCS1A01G036400 chr3D 86.275 102 14 0 251 352 64345309 64345208 1.080000e-20 111.0
33 TraesCS1A01G036400 chr3D 95.122 41 2 0 193 233 64345309 64345269 8.550000e-07 65.8
34 TraesCS1A01G036400 chr3D 95.122 41 2 0 193 233 397775492 397775452 8.550000e-07 65.8
35 TraesCS1A01G036400 chr7D 77.586 290 46 11 1558 1839 113117894 113118172 1.370000e-34 158.0
36 TraesCS1A01G036400 chr7D 70.609 558 136 22 1999 2542 113118377 113118920 3.030000e-16 97.1
37 TraesCS1A01G036400 chr7D 85.246 61 8 1 1970 2030 113158921 113158980 1.110000e-05 62.1
38 TraesCS1A01G036400 chr7B 73.976 415 94 14 2135 2545 72509143 72509547 4.930000e-34 156.0
39 TraesCS1A01G036400 chr7A 72.506 411 104 8 2135 2542 118241033 118241437 1.390000e-24 124.0
40 TraesCS1A01G036400 chr5B 72.885 461 85 16 251 685 224328147 224327701 5.000000e-24 122.0
41 TraesCS1A01G036400 chr5B 95.000 40 2 0 193 232 224328147 224328108 3.070000e-06 63.9
42 TraesCS1A01G036400 chr5A 78.981 157 33 0 251 407 690180702 690180858 1.400000e-19 108.0
43 TraesCS1A01G036400 chr5A 95.122 41 2 0 193 233 690180702 690180742 8.550000e-07 65.8
44 TraesCS1A01G036400 chr3B 77.457 173 32 6 251 420 70086687 70086855 3.030000e-16 97.1
45 TraesCS1A01G036400 chr3B 90.741 54 2 2 178 231 70086675 70086725 6.610000e-08 69.4
46 TraesCS1A01G036400 chr3A 83.333 102 16 1 251 352 74773525 74773425 3.920000e-15 93.5
47 TraesCS1A01G036400 chr3A 94.872 39 2 0 193 231 74773525 74773487 1.110000e-05 62.1
48 TraesCS1A01G036400 chr4A 80.702 114 22 0 251 364 164512678 164512791 5.070000e-14 89.8
49 TraesCS1A01G036400 chr4A 92.308 39 3 0 193 231 164512678 164512716 5.150000e-04 56.5


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 TraesCS1A01G036400 chr1A 20235537 20239224 3687 True 2342.333333 6811 97.916667 1 3688 3 chr1A.!!$R3 3687
1 TraesCS1A01G036400 chr1A 20243580 20246161 2581 True 1184.500000 2134 84.679500 1240 3627 2 chr1A.!!$R4 2387
2 TraesCS1A01G036400 chr1D 18241091 18243481 2390 True 1289.800000 2512 90.587500 1240 3627 2 chr1D.!!$R4 2387
3 TraesCS1A01G036400 chr1D 18221093 18226208 5115 True 744.714286 1555 87.716714 1 3688 7 chr1D.!!$R3 3687
4 TraesCS1A01G036400 chr6D 319244389 319245715 1326 False 440.000000 440 73.333000 1551 2883 1 chr6D.!!$F1 1332
5 TraesCS1A01G036400 chr6A 457072526 457073852 1326 False 411.000000 411 72.821000 1558 2882 1 chr6A.!!$F1 1324
6 TraesCS1A01G036400 chr1B 660012007 660013011 1004 True 357.000000 357 73.745000 1540 2553 1 chr1B.!!$R2 1013

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
675 1431 0.031585 TCTGTGTCCTGTCCGTTTCG 59.968 55.0 0.00 0.00 0.00 3.46 F
852 2224 0.034337 TTTGTAGGTGGTCGGTCAGC 59.966 55.0 0.97 0.97 35.58 4.26 F
1394 2841 0.109086 CACCGATGAAGCGTCTGACT 60.109 55.0 6.21 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1916 3380 0.105039 CCTCTTCGTCCAGCCATACC 59.895 60.0 0.0 0.0 0.0 2.73 R
2359 3832 0.537371 GGTCCAGTTTCCACCACCAG 60.537 60.0 0.0 0.0 0.0 4.00 R
2770 4395 1.949465 AGACGTTGAGGACACAAACC 58.051 50.0 0.0 0.0 0.0 3.27 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
21 22 4.947147 GCGACACCCAACCCAGCA 62.947 66.667 0.00 0.00 0.00 4.41
32 33 0.179032 AACCCAGCACGTGACATTGA 60.179 50.000 22.23 0.00 0.00 2.57
42 43 1.920574 CGTGACATTGAGGTCGATGAC 59.079 52.381 13.25 8.16 39.56 3.06
45 46 0.895530 ACATTGAGGTCGATGACGGT 59.104 50.000 13.25 0.00 39.56 4.83
48 49 1.929806 TTGAGGTCGATGACGGTCGG 61.930 60.000 3.34 0.00 41.74 4.79
49 50 3.753070 GAGGTCGATGACGGTCGGC 62.753 68.421 3.34 5.43 44.95 5.54
67 68 4.856801 GGCACGGGGCGATCATGT 62.857 66.667 0.00 0.00 46.16 3.21
68 69 2.824041 GCACGGGGCGATCATGTT 60.824 61.111 0.00 0.00 0.00 2.71
69 70 3.101209 CACGGGGCGATCATGTTG 58.899 61.111 0.00 0.00 0.00 3.33
70 71 2.824041 ACGGGGCGATCATGTTGC 60.824 61.111 0.00 0.00 36.42 4.17
108 119 2.176546 CGGTTTGCACCATGCTCG 59.823 61.111 2.02 0.00 45.31 5.03
120 133 2.224606 CCATGCTCGTGCCAGATAAAT 58.775 47.619 7.05 0.00 38.71 1.40
121 134 2.031420 CCATGCTCGTGCCAGATAAATG 60.031 50.000 7.05 2.19 38.71 2.32
123 136 0.308993 GCTCGTGCCAGATAAATGCC 59.691 55.000 0.00 0.00 0.00 4.40
127 140 0.746659 GTGCCAGATAAATGCCACCC 59.253 55.000 0.00 0.00 0.00 4.61
133 146 2.491693 CAGATAAATGCCACCCGTTTGT 59.508 45.455 0.00 0.00 34.58 2.83
134 147 2.491693 AGATAAATGCCACCCGTTTGTG 59.508 45.455 0.00 0.00 34.58 3.33
141 154 2.483441 CACCCGTTTGTGGTGTTGA 58.517 52.632 1.27 0.00 46.62 3.18
148 161 2.222027 GTTTGTGGTGTTGAGGAGGAG 58.778 52.381 0.00 0.00 0.00 3.69
152 165 0.471780 TGGTGTTGAGGAGGAGCTCA 60.472 55.000 17.19 0.00 31.08 4.26
154 167 1.280421 GGTGTTGAGGAGGAGCTCATT 59.720 52.381 17.19 2.37 31.08 2.57
155 168 2.354259 GTGTTGAGGAGGAGCTCATTG 58.646 52.381 17.19 0.00 31.08 2.82
196 209 3.589881 GCCGATGAGCATGTGGCC 61.590 66.667 0.00 0.00 46.50 5.36
197 210 3.274586 CCGATGAGCATGTGGCCG 61.275 66.667 0.00 0.00 46.50 6.13
198 211 3.274586 CGATGAGCATGTGGCCGG 61.275 66.667 0.00 0.00 46.50 6.13
199 212 2.124570 GATGAGCATGTGGCCGGT 60.125 61.111 1.90 0.00 46.50 5.28
200 213 2.438975 ATGAGCATGTGGCCGGTG 60.439 61.111 1.90 0.00 46.50 4.94
213 226 4.745751 CGGTGCGGGTCGGCTAAA 62.746 66.667 2.43 0.00 0.00 1.85
214 227 3.122971 GGTGCGGGTCGGCTAAAC 61.123 66.667 2.43 0.00 0.00 2.01
215 228 3.122971 GTGCGGGTCGGCTAAACC 61.123 66.667 2.43 0.00 35.97 3.27
220 233 4.850822 GGTCGGCTAAACCCTAGC 57.149 61.111 0.00 0.00 39.70 3.42
221 234 1.902556 GGTCGGCTAAACCCTAGCA 59.097 57.895 6.14 0.00 42.06 3.49
222 235 0.468648 GGTCGGCTAAACCCTAGCAT 59.531 55.000 6.14 0.00 42.06 3.79
223 236 1.583054 GTCGGCTAAACCCTAGCATG 58.417 55.000 6.14 0.00 42.06 4.06
224 237 1.138266 GTCGGCTAAACCCTAGCATGA 59.862 52.381 0.00 0.97 42.06 3.07
225 238 1.412710 TCGGCTAAACCCTAGCATGAG 59.587 52.381 0.00 0.00 42.06 2.90
226 239 1.541233 CGGCTAAACCCTAGCATGAGG 60.541 57.143 0.00 0.00 42.06 3.86
227 240 1.768870 GGCTAAACCCTAGCATGAGGA 59.231 52.381 0.00 0.00 42.06 3.71
228 241 2.224402 GGCTAAACCCTAGCATGAGGAG 60.224 54.545 0.00 0.00 42.06 3.69
229 242 2.224402 GCTAAACCCTAGCATGAGGAGG 60.224 54.545 0.00 0.00 39.15 4.30
231 244 3.155750 CCCTAGCATGAGGAGGGC 58.844 66.667 12.57 0.00 43.55 5.19
232 245 2.739784 CCTAGCATGAGGAGGGCG 59.260 66.667 0.00 0.00 39.15 6.13
233 246 1.834378 CCTAGCATGAGGAGGGCGA 60.834 63.158 0.00 0.00 39.15 5.54
234 247 1.402896 CCTAGCATGAGGAGGGCGAA 61.403 60.000 0.00 0.00 39.15 4.70
235 248 0.249657 CTAGCATGAGGAGGGCGAAC 60.250 60.000 0.00 0.00 0.00 3.95
236 249 2.016393 TAGCATGAGGAGGGCGAACG 62.016 60.000 0.00 0.00 0.00 3.95
237 250 2.202932 CATGAGGAGGGCGAACGG 60.203 66.667 0.00 0.00 0.00 4.44
238 251 4.162690 ATGAGGAGGGCGAACGGC 62.163 66.667 12.10 12.10 42.51 5.68
240 253 4.821589 GAGGAGGGCGAACGGCTG 62.822 72.222 18.90 0.00 42.94 4.85
242 255 4.162690 GGAGGGCGAACGGCTGAT 62.163 66.667 18.90 6.99 42.94 2.90
243 256 2.892425 GAGGGCGAACGGCTGATG 60.892 66.667 18.90 0.00 42.94 3.07
244 257 3.371097 GAGGGCGAACGGCTGATGA 62.371 63.158 18.90 0.00 42.94 2.92
245 258 2.892425 GGGCGAACGGCTGATGAG 60.892 66.667 18.90 0.00 42.94 2.90
246 259 3.567797 GGCGAACGGCTGATGAGC 61.568 66.667 13.15 0.00 45.40 4.26
293 306 1.690845 CCTAGCATGAGGAGGGAGTGT 60.691 57.143 0.00 0.00 39.15 3.55
295 308 1.222936 GCATGAGGAGGGAGTGTGG 59.777 63.158 0.00 0.00 0.00 4.17
298 311 2.997897 GAGGAGGGAGTGTGGCGT 60.998 66.667 0.00 0.00 0.00 5.68
299 312 2.526873 AGGAGGGAGTGTGGCGTT 60.527 61.111 0.00 0.00 0.00 4.84
300 313 2.358737 GGAGGGAGTGTGGCGTTG 60.359 66.667 0.00 0.00 0.00 4.10
301 314 2.426023 GAGGGAGTGTGGCGTTGT 59.574 61.111 0.00 0.00 0.00 3.32
336 349 2.027625 GCGACAAGGGACTCGTTGG 61.028 63.158 0.00 0.00 38.49 3.77
393 406 2.590007 GAGCATACTGGGCTGCGG 60.590 66.667 0.00 0.00 42.78 5.69
408 421 2.047274 CGGCTTTCCTCTCCGCAA 60.047 61.111 0.00 0.00 36.53 4.85
409 422 2.391389 CGGCTTTCCTCTCCGCAAC 61.391 63.158 0.00 0.00 36.53 4.17
444 464 6.118170 TCCTCTTGGATGATTCTTGAATGAC 58.882 40.000 0.09 0.00 37.46 3.06
446 466 6.260493 CCTCTTGGATGATTCTTGAATGACTC 59.740 42.308 0.09 0.00 34.57 3.36
448 468 4.445453 TGGATGATTCTTGAATGACTCGG 58.555 43.478 0.09 0.00 0.00 4.63
483 503 0.179163 GGCTTCTTTTTCATCGCGGG 60.179 55.000 6.13 0.00 0.00 6.13
500 520 3.771160 GACGGGTGGAGATGGCGT 61.771 66.667 0.00 0.00 0.00 5.68
503 523 3.399181 GGGTGGAGATGGCGTCCA 61.399 66.667 2.37 0.62 42.06 4.02
504 524 2.668632 GGTGGAGATGGCGTCCAA 59.331 61.111 2.37 0.00 45.85 3.53
595 1351 4.080807 GGTTTTTGGGAAAGAAGGTGGAAA 60.081 41.667 0.00 0.00 0.00 3.13
625 1381 4.380945 GTTCCCCATGGGCTGGCA 62.381 66.667 26.87 0.00 44.46 4.92
632 1388 3.275271 ATGGGCTGGCAAGGGGAA 61.275 61.111 2.88 0.00 0.00 3.97
645 1401 2.436824 GGGAAGACAAGGGCTCGC 60.437 66.667 0.00 0.00 0.00 5.03
647 1403 2.048127 GAAGACAAGGGCTCGCGT 60.048 61.111 5.77 0.00 0.00 6.01
662 1418 3.667282 CGTCCCGTCCGTCTGTGT 61.667 66.667 0.00 0.00 0.00 3.72
664 1420 2.987547 TCCCGTCCGTCTGTGTCC 60.988 66.667 0.00 0.00 0.00 4.02
669 1425 1.289380 GTCCGTCTGTGTCCTGTCC 59.711 63.158 0.00 0.00 0.00 4.02
675 1431 0.031585 TCTGTGTCCTGTCCGTTTCG 59.968 55.000 0.00 0.00 0.00 3.46
683 1439 0.382636 CTGTCCGTTTCGACGCAAAC 60.383 55.000 10.80 10.80 35.40 2.93
700 1456 3.304190 GCAAACGTGAACTAATTTCGGGT 60.304 43.478 0.00 0.00 36.97 5.28
701 1457 4.790444 GCAAACGTGAACTAATTTCGGGTT 60.790 41.667 0.00 0.00 36.97 4.11
703 1459 3.731089 ACGTGAACTAATTTCGGGTTGA 58.269 40.909 0.00 0.00 36.97 3.18
713 1469 2.366640 TTCGGGTTGAAAATGGGTCA 57.633 45.000 0.00 0.00 32.37 4.02
722 1478 2.875933 TGAAAATGGGTCACAGACGAAC 59.124 45.455 0.00 0.00 32.65 3.95
727 1483 1.691976 TGGGTCACAGACGAACAGAAT 59.308 47.619 0.00 0.00 32.65 2.40
729 1485 3.513912 TGGGTCACAGACGAACAGAATAT 59.486 43.478 0.00 0.00 32.65 1.28
730 1486 3.865745 GGGTCACAGACGAACAGAATATG 59.134 47.826 0.00 0.00 32.65 1.78
735 1491 2.535984 CAGACGAACAGAATATGGACGC 59.464 50.000 0.00 0.00 35.85 5.19
751 1507 2.594592 GCCTGTCTGTTTGCGGGT 60.595 61.111 0.00 0.00 33.78 5.28
781 1537 1.332904 GCCGCGATAATCCAAACGAAG 60.333 52.381 8.23 0.00 0.00 3.79
783 1539 2.285602 CCGCGATAATCCAAACGAAGTG 60.286 50.000 8.23 0.00 45.00 3.16
784 1540 2.347452 CGCGATAATCCAAACGAAGTGT 59.653 45.455 0.00 0.00 45.00 3.55
810 1566 3.746108 CGAAATGGGTCGTGTGTTG 57.254 52.632 0.00 0.00 36.26 3.33
825 1581 2.158534 TGTGTTGGAGTTGGCCTAACAT 60.159 45.455 16.93 5.65 41.88 2.71
834 2206 3.081804 GTTGGCCTAACATGTAGCAGTT 58.918 45.455 3.32 0.00 39.16 3.16
837 2209 3.081804 GGCCTAACATGTAGCAGTTTGT 58.918 45.455 15.00 0.00 0.00 2.83
841 2213 5.488341 CCTAACATGTAGCAGTTTGTAGGT 58.512 41.667 0.00 0.00 0.00 3.08
852 2224 0.034337 TTTGTAGGTGGTCGGTCAGC 59.966 55.000 0.97 0.97 35.58 4.26
860 2232 1.278637 GGTCGGTCAGCACAAAACG 59.721 57.895 0.00 0.00 0.00 3.60
879 2309 9.634163 ACAAAACGTTTTCATTTCTTTTCTACT 57.366 25.926 22.90 0.00 0.00 2.57
881 2311 8.543071 AAACGTTTTCATTTCTTTTCTACTCG 57.457 30.769 7.96 0.00 0.00 4.18
882 2312 7.473027 ACGTTTTCATTTCTTTTCTACTCGA 57.527 32.000 0.00 0.00 0.00 4.04
883 2313 8.084590 ACGTTTTCATTTCTTTTCTACTCGAT 57.915 30.769 0.00 0.00 0.00 3.59
916 2346 1.089920 CGCCCATTCCACTTCTCAAG 58.910 55.000 0.00 0.00 0.00 3.02
917 2347 1.467920 GCCCATTCCACTTCTCAAGG 58.532 55.000 0.00 0.00 0.00 3.61
1003 2435 2.038329 CCTAGGACGACCCACCCA 59.962 66.667 1.05 0.00 37.41 4.51
1007 2439 1.797018 TAGGACGACCCACCCAGTCT 61.797 60.000 0.00 0.00 37.41 3.24
1049 2483 1.153745 CGCAAGGAAGACGAGGAGG 60.154 63.158 0.00 0.00 0.00 4.30
1050 2484 1.448717 GCAAGGAAGACGAGGAGGC 60.449 63.158 0.00 0.00 0.00 4.70
1095 2529 2.434884 CATGCTCCGGCGACTGTT 60.435 61.111 9.30 0.00 42.25 3.16
1107 2541 1.600916 GACTGTTCACCCAGGCCAC 60.601 63.158 5.01 0.00 34.17 5.01
1162 2596 0.981277 CCCCATCACCGAGGTAGGTT 60.981 60.000 0.00 0.00 43.00 3.50
1172 2606 2.094130 CCGAGGTAGGTTCAGAGGTTTC 60.094 54.545 0.00 0.00 0.00 2.78
1204 2638 9.822727 TTTTTAACTATTCCTTCTCCCAATCTT 57.177 29.630 0.00 0.00 0.00 2.40
1205 2639 9.462606 TTTTAACTATTCCTTCTCCCAATCTTC 57.537 33.333 0.00 0.00 0.00 2.87
1206 2640 6.899892 AACTATTCCTTCTCCCAATCTTCT 57.100 37.500 0.00 0.00 0.00 2.85
1207 2641 7.996758 AACTATTCCTTCTCCCAATCTTCTA 57.003 36.000 0.00 0.00 0.00 2.10
1208 2642 7.610580 ACTATTCCTTCTCCCAATCTTCTAG 57.389 40.000 0.00 0.00 0.00 2.43
1223 2657 9.672673 CCAATCTTCTAGTTCTATCCAAGAAAA 57.327 33.333 0.00 0.00 45.78 2.29
1302 2743 4.847367 GGCCAGCCTTCCCCATGG 62.847 72.222 4.14 4.14 35.84 3.66
1307 2754 4.453892 GCCTTCCCCATGGCTGCT 62.454 66.667 6.09 0.00 45.26 4.24
1393 2840 1.078759 CCACCGATGAAGCGTCTGAC 61.079 60.000 0.31 0.00 0.00 3.51
1394 2841 0.109086 CACCGATGAAGCGTCTGACT 60.109 55.000 6.21 0.00 0.00 3.41
1395 2842 0.171455 ACCGATGAAGCGTCTGACTC 59.829 55.000 6.21 0.00 0.00 3.36
1396 2843 0.453793 CCGATGAAGCGTCTGACTCT 59.546 55.000 6.21 0.00 0.00 3.24
1397 2844 1.543614 CGATGAAGCGTCTGACTCTG 58.456 55.000 6.21 0.00 0.00 3.35
1398 2845 1.131315 CGATGAAGCGTCTGACTCTGA 59.869 52.381 6.21 0.00 0.00 3.27
1415 2869 1.967066 CTGAGGTATGCTCCCCTACAG 59.033 57.143 0.00 0.00 0.00 2.74
1451 2906 6.645790 ATCTTGAATCCAATCCAATACAGC 57.354 37.500 0.00 0.00 0.00 4.40
1477 2935 6.073602 GGACGTTAAACTGAACCTAAACGAAT 60.074 38.462 11.79 0.00 41.48 3.34
1556 3014 0.257039 ATCTTCCTGAAGGCGCCATT 59.743 50.000 31.54 19.82 38.88 3.16
1640 3098 3.160047 CTGGCCCTCTGCTCCGAT 61.160 66.667 0.00 0.00 40.92 4.18
1759 3220 0.609957 TTAGTCGACCCTTCGCTCCA 60.610 55.000 13.01 0.00 45.46 3.86
1771 3232 2.739704 CGCTCCATTTCTTGCGCGA 61.740 57.895 12.10 0.00 42.61 5.87
1916 3380 0.886490 GGACTGTGTTGCCTCCTGTG 60.886 60.000 0.00 0.00 0.00 3.66
1989 3453 4.224147 TGGATATCTTCTTGGGTTTCGACA 59.776 41.667 2.05 0.00 0.00 4.35
2129 3593 5.182570 GTGGGGTTACAAAACTATTCTGGTC 59.817 44.000 0.00 0.00 35.81 4.02
2192 3659 2.874701 GGCTACACATTATGCCTCAGTG 59.125 50.000 0.00 0.00 41.92 3.66
2359 3832 6.173339 TCTATGTGTGGGTTCTTGAAGATTC 58.827 40.000 0.00 0.00 0.00 2.52
2372 3845 3.486383 TGAAGATTCTGGTGGTGGAAAC 58.514 45.455 0.00 0.00 0.00 2.78
2572 4045 5.776744 CACTTTTTCTCAAGAATTCCAGGG 58.223 41.667 0.65 0.00 33.54 4.45
2608 4081 4.686191 TTCCATGTTTTGCTGAATGGTT 57.314 36.364 0.00 0.00 40.44 3.67
2609 4082 3.992643 TCCATGTTTTGCTGAATGGTTG 58.007 40.909 0.00 0.00 40.44 3.77
2610 4083 3.387374 TCCATGTTTTGCTGAATGGTTGT 59.613 39.130 0.00 0.00 40.44 3.32
2611 4084 4.128643 CCATGTTTTGCTGAATGGTTGTT 58.871 39.130 0.00 0.00 35.78 2.83
2706 4188 3.222603 GGTATGGGCCTAATCTTGTTGG 58.777 50.000 4.53 0.00 0.00 3.77
2719 4201 0.108424 TTGTTGGTTTGTGGCACTGC 60.108 50.000 19.83 8.50 0.00 4.40
2770 4395 7.646130 GTCTAGTTCAGTTTGATCTTCCTATCG 59.354 40.741 0.00 0.00 29.96 2.92
2782 4415 3.194968 TCTTCCTATCGGTTTGTGTCCTC 59.805 47.826 0.00 0.00 0.00 3.71
2786 4419 1.508632 ATCGGTTTGTGTCCTCAACG 58.491 50.000 0.00 0.00 0.00 4.10
2865 4506 6.102615 AGGTGCCCTCTAATTGGTCATTATTA 59.897 38.462 0.00 0.00 0.00 0.98
2869 4510 7.039784 TGCCCTCTAATTGGTCATTATTAATGC 60.040 37.037 10.92 6.84 38.77 3.56
2883 4524 2.889170 TAATGCCACCTTGTTAGCCA 57.111 45.000 0.00 0.00 0.00 4.75
3096 4763 9.679661 TCAATTTAGTAATAGAACATGGCAGAA 57.320 29.630 0.00 0.00 0.00 3.02
3153 4822 4.116747 TGGTGTTCCATTGTTGTTTCAC 57.883 40.909 0.00 0.00 39.03 3.18
3213 4882 8.467598 AGACAAACTACCTTTTCTTTCCTTTTC 58.532 33.333 0.00 0.00 0.00 2.29
3324 5018 5.183140 GGGTAATGATGCACACAAGTTAGTT 59.817 40.000 0.00 0.00 0.00 2.24
3386 5082 5.727515 GCTCCACTGTTCATTTTTGTTTTGC 60.728 40.000 0.00 0.00 0.00 3.68
3630 5557 6.793349 AGAGTGATTTGCTTCATAATTGCTC 58.207 36.000 0.00 0.00 0.00 4.26
3634 5561 6.252869 GTGATTTGCTTCATAATTGCTCACTG 59.747 38.462 0.00 0.00 31.31 3.66
3643 5570 8.437360 TTCATAATTGCTCACTGTTACCTATG 57.563 34.615 0.00 0.00 0.00 2.23
3648 5575 7.792374 ATTGCTCACTGTTACCTATGTATTG 57.208 36.000 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 1.544246 TCATCGACCTCAATGTCACGT 59.456 47.619 0.00 0.00 34.88 4.49
32 33 3.823330 GCCGACCGTCATCGACCT 61.823 66.667 0.00 0.00 45.13 3.85
52 53 3.101209 CAACATGATCGCCCCGTG 58.899 61.111 0.00 0.00 0.00 4.94
53 54 2.824041 GCAACATGATCGCCCCGT 60.824 61.111 0.00 0.00 0.00 5.28
54 55 3.585990 GGCAACATGATCGCCCCG 61.586 66.667 0.00 0.00 40.07 5.73
59 60 3.409856 GGGACGGCAACATGATCG 58.590 61.111 0.00 0.00 0.00 3.69
79 90 0.169009 GCAAACCGCTTCTCCATGTC 59.831 55.000 0.00 0.00 37.77 3.06
86 97 1.959085 CATGGTGCAAACCGCTTCT 59.041 52.632 0.00 0.00 43.06 2.85
111 122 1.762708 AACGGGTGGCATTTATCTGG 58.237 50.000 0.00 0.00 0.00 3.86
127 140 0.944386 CCTCCTCAACACCACAAACG 59.056 55.000 0.00 0.00 0.00 3.60
133 146 0.471780 TGAGCTCCTCCTCAACACCA 60.472 55.000 12.15 0.00 38.81 4.17
134 147 0.908198 ATGAGCTCCTCCTCAACACC 59.092 55.000 12.15 0.00 44.34 4.16
141 154 1.202330 CCAGTCAATGAGCTCCTCCT 58.798 55.000 12.15 0.00 0.00 3.69
148 161 1.001641 ACAGGGCCAGTCAATGAGC 60.002 57.895 6.18 0.00 0.00 4.26
152 165 1.687612 CTCCACAGGGCCAGTCAAT 59.312 57.895 6.18 0.00 0.00 2.57
154 167 2.930019 CCTCCACAGGGCCAGTCA 60.930 66.667 6.18 0.00 35.89 3.41
196 209 4.745751 TTTAGCCGACCCGCACCG 62.746 66.667 0.00 0.00 0.00 4.94
197 210 3.122971 GTTTAGCCGACCCGCACC 61.123 66.667 0.00 0.00 0.00 5.01
198 211 3.122971 GGTTTAGCCGACCCGCAC 61.123 66.667 0.00 0.00 0.00 5.34
199 212 4.397832 GGGTTTAGCCGACCCGCA 62.398 66.667 4.23 0.00 46.71 5.69
203 216 0.468648 ATGCTAGGGTTTAGCCGACC 59.531 55.000 3.94 0.00 39.69 4.79
204 217 1.138266 TCATGCTAGGGTTTAGCCGAC 59.862 52.381 3.94 0.00 39.69 4.79
205 218 1.412710 CTCATGCTAGGGTTTAGCCGA 59.587 52.381 3.94 0.78 39.69 5.54
206 219 1.541233 CCTCATGCTAGGGTTTAGCCG 60.541 57.143 3.94 0.00 39.69 5.52
207 220 1.768870 TCCTCATGCTAGGGTTTAGCC 59.231 52.381 0.82 0.00 39.69 3.93
208 221 2.224402 CCTCCTCATGCTAGGGTTTAGC 60.224 54.545 0.82 0.00 40.76 3.09
209 222 2.370189 CCCTCCTCATGCTAGGGTTTAG 59.630 54.545 15.25 0.92 44.34 1.85
210 223 2.408565 CCCTCCTCATGCTAGGGTTTA 58.591 52.381 15.25 0.00 44.34 2.01
211 224 1.216990 CCCTCCTCATGCTAGGGTTT 58.783 55.000 15.25 0.00 44.34 3.27
212 225 2.936823 CCCTCCTCATGCTAGGGTT 58.063 57.895 15.25 0.00 44.34 4.11
213 226 4.737346 CCCTCCTCATGCTAGGGT 57.263 61.111 15.25 0.00 44.34 4.34
215 228 1.402896 TTCGCCCTCCTCATGCTAGG 61.403 60.000 0.00 0.00 38.06 3.02
216 229 0.249657 GTTCGCCCTCCTCATGCTAG 60.250 60.000 0.00 0.00 0.00 3.42
217 230 1.823295 GTTCGCCCTCCTCATGCTA 59.177 57.895 0.00 0.00 0.00 3.49
218 231 2.586792 GTTCGCCCTCCTCATGCT 59.413 61.111 0.00 0.00 0.00 3.79
219 232 2.892425 CGTTCGCCCTCCTCATGC 60.892 66.667 0.00 0.00 0.00 4.06
220 233 2.202932 CCGTTCGCCCTCCTCATG 60.203 66.667 0.00 0.00 0.00 3.07
221 234 4.162690 GCCGTTCGCCCTCCTCAT 62.163 66.667 0.00 0.00 0.00 2.90
223 236 4.821589 CAGCCGTTCGCCCTCCTC 62.822 72.222 0.00 0.00 38.78 3.71
225 238 4.162690 ATCAGCCGTTCGCCCTCC 62.163 66.667 0.00 0.00 38.78 4.30
226 239 2.892425 CATCAGCCGTTCGCCCTC 60.892 66.667 0.00 0.00 38.78 4.30
227 240 3.376935 CTCATCAGCCGTTCGCCCT 62.377 63.158 0.00 0.00 38.78 5.19
228 241 2.892425 CTCATCAGCCGTTCGCCC 60.892 66.667 0.00 0.00 38.78 6.13
229 242 3.567797 GCTCATCAGCCGTTCGCC 61.568 66.667 0.00 0.00 40.14 5.54
230 243 2.176273 ATGCTCATCAGCCGTTCGC 61.176 57.895 0.00 0.00 46.26 4.70
231 244 1.086067 ACATGCTCATCAGCCGTTCG 61.086 55.000 0.00 0.00 46.26 3.95
232 245 0.376152 CACATGCTCATCAGCCGTTC 59.624 55.000 0.00 0.00 46.26 3.95
233 246 1.028330 CCACATGCTCATCAGCCGTT 61.028 55.000 0.00 0.00 46.26 4.44
234 247 1.450848 CCACATGCTCATCAGCCGT 60.451 57.895 0.00 0.00 46.26 5.68
235 248 2.831366 GCCACATGCTCATCAGCCG 61.831 63.158 0.00 0.00 46.26 5.52
236 249 2.487532 GGCCACATGCTCATCAGCC 61.488 63.158 0.00 0.00 46.26 4.85
238 251 2.184830 CCGGCCACATGCTCATCAG 61.185 63.158 2.24 0.00 40.92 2.90
239 252 2.124612 CCGGCCACATGCTCATCA 60.125 61.111 2.24 0.00 40.92 3.07
240 253 3.589881 GCCGGCCACATGCTCATC 61.590 66.667 18.11 0.00 40.92 2.92
265 278 1.768870 TCCTCATGCTAGGGTTTAGCC 59.231 52.381 0.82 0.00 39.69 3.93
273 286 1.047002 CACTCCCTCCTCATGCTAGG 58.953 60.000 0.00 0.00 38.06 3.02
295 308 2.026014 CCACACAGGCAACAACGC 59.974 61.111 0.00 0.00 41.41 4.84
318 331 2.027625 CCAACGAGTCCCTTGTCGC 61.028 63.158 0.00 0.00 39.89 5.19
344 357 3.595758 GCACAACACAAGGCCGCT 61.596 61.111 0.00 0.00 0.00 5.52
372 385 0.107508 GCAGCCCAGTATGCTCTCAA 60.108 55.000 0.00 0.00 39.38 3.02
377 390 4.864334 GCCGCAGCCCAGTATGCT 62.864 66.667 0.00 0.00 40.34 3.79
378 391 4.864334 AGCCGCAGCCCAGTATGC 62.864 66.667 0.00 0.00 41.25 3.14
393 406 1.916697 GCTGTTGCGGAGAGGAAAGC 61.917 60.000 0.00 0.00 31.67 3.51
408 421 3.914551 AAGAGGAGAGGGCCGCTGT 62.915 63.158 16.70 0.50 38.15 4.40
409 422 3.080121 AAGAGGAGAGGGCCGCTG 61.080 66.667 16.70 0.00 38.15 5.18
446 466 4.016706 AAAGGTGGGGCTCGACCG 62.017 66.667 12.63 0.00 45.06 4.79
448 468 2.359975 CCAAAGGTGGGGCTCGAC 60.360 66.667 0.00 0.00 41.77 4.20
483 503 3.718210 GACGCCATCTCCACCCGTC 62.718 68.421 0.00 0.00 40.92 4.79
500 520 1.752198 CCACCGTTGTCCTCTTGGA 59.248 57.895 0.00 0.00 40.69 3.53
503 523 0.179029 CAACCCACCGTTGTCCTCTT 60.179 55.000 0.00 0.00 45.79 2.85
504 524 1.450211 CAACCCACCGTTGTCCTCT 59.550 57.895 0.00 0.00 45.79 3.69
532 552 4.047125 CCCAGTTCCATGGCCGGT 62.047 66.667 6.96 0.00 39.17 5.28
533 553 3.280938 TTCCCAGTTCCATGGCCGG 62.281 63.158 6.96 0.00 39.17 6.13
562 582 0.187361 CCCAAAAACCCTCTCACCCA 59.813 55.000 0.00 0.00 0.00 4.51
566 586 3.963476 TCTTTCCCAAAAACCCTCTCA 57.037 42.857 0.00 0.00 0.00 3.27
595 1351 3.524095 TGGGGAACACAACATTCTCAT 57.476 42.857 0.00 0.00 0.00 2.90
625 1381 1.842381 CGAGCCCTTGTCTTCCCCTT 61.842 60.000 0.00 0.00 0.00 3.95
632 1388 4.070552 GGACGCGAGCCCTTGTCT 62.071 66.667 15.93 0.00 0.00 3.41
647 1403 2.987547 GGACACAGACGGACGGGA 60.988 66.667 0.00 0.00 0.00 5.14
656 1412 0.031585 CGAAACGGACAGGACACAGA 59.968 55.000 0.00 0.00 0.00 3.41
658 1414 0.249155 GTCGAAACGGACAGGACACA 60.249 55.000 0.00 0.00 36.91 3.72
683 1439 4.735662 TTCAACCCGAAATTAGTTCACG 57.264 40.909 0.00 0.00 35.83 4.35
685 1441 6.451393 CCATTTTCAACCCGAAATTAGTTCA 58.549 36.000 0.00 0.00 43.12 3.18
700 1456 3.201353 TCGTCTGTGACCCATTTTCAA 57.799 42.857 0.00 0.00 0.00 2.69
701 1457 2.875933 GTTCGTCTGTGACCCATTTTCA 59.124 45.455 0.00 0.00 0.00 2.69
703 1459 2.878406 CTGTTCGTCTGTGACCCATTTT 59.122 45.455 0.00 0.00 0.00 1.82
709 1465 3.865745 CCATATTCTGTTCGTCTGTGACC 59.134 47.826 0.00 0.00 0.00 4.02
713 1469 3.770666 CGTCCATATTCTGTTCGTCTGT 58.229 45.455 0.00 0.00 0.00 3.41
722 1478 2.159043 ACAGACAGGCGTCCATATTCTG 60.159 50.000 5.98 0.00 43.73 3.02
727 1483 1.943968 GCAAACAGACAGGCGTCCATA 60.944 52.381 5.98 0.00 43.73 2.74
729 1485 1.891919 GCAAACAGACAGGCGTCCA 60.892 57.895 5.98 0.00 43.73 4.02
730 1486 2.946762 GCAAACAGACAGGCGTCC 59.053 61.111 5.98 0.00 43.73 4.79
735 1491 2.908073 GCACCCGCAAACAGACAGG 61.908 63.158 0.00 0.00 38.36 4.00
755 1511 2.604174 GGATTATCGCGGCCCAACG 61.604 63.158 6.13 0.00 0.00 4.10
756 1512 1.098712 TTGGATTATCGCGGCCCAAC 61.099 55.000 6.13 0.00 32.51 3.77
758 1514 1.098712 GTTTGGATTATCGCGGCCCA 61.099 55.000 6.13 3.94 0.00 5.36
764 1520 3.485216 CCACACTTCGTTTGGATTATCGC 60.485 47.826 0.00 0.00 35.60 4.58
781 1537 2.686816 CCATTTCGTCCGGCCACAC 61.687 63.158 2.24 0.00 0.00 3.82
782 1538 2.359354 CCATTTCGTCCGGCCACA 60.359 61.111 2.24 0.00 0.00 4.17
783 1539 3.131478 CCCATTTCGTCCGGCCAC 61.131 66.667 2.24 0.00 0.00 5.01
784 1540 3.615509 GACCCATTTCGTCCGGCCA 62.616 63.158 2.24 0.00 0.00 5.36
805 1561 1.975660 TGTTAGGCCAACTCCAACAC 58.024 50.000 5.01 0.00 38.05 3.32
807 1563 2.514803 ACATGTTAGGCCAACTCCAAC 58.485 47.619 5.01 0.00 38.05 3.77
810 1566 2.289565 GCTACATGTTAGGCCAACTCC 58.710 52.381 5.01 0.00 38.05 3.85
825 1581 2.288579 CGACCACCTACAAACTGCTACA 60.289 50.000 0.00 0.00 0.00 2.74
834 2206 1.116536 TGCTGACCGACCACCTACAA 61.117 55.000 0.00 0.00 0.00 2.41
837 2209 1.116536 TTGTGCTGACCGACCACCTA 61.117 55.000 0.00 0.00 0.00 3.08
841 2213 1.433053 CGTTTTGTGCTGACCGACCA 61.433 55.000 0.00 0.00 0.00 4.02
852 2224 9.670180 GTAGAAAAGAAATGAAAACGTTTTGTG 57.330 29.630 29.67 0.00 0.00 3.33
917 2347 1.749063 CTTTATGGCTTCGTTTCCCCC 59.251 52.381 0.00 0.00 0.00 5.40
1080 2514 3.611674 TGAACAGTCGCCGGAGCA 61.612 61.111 5.05 0.00 39.83 4.26
1082 2516 2.432628 GGTGAACAGTCGCCGGAG 60.433 66.667 5.05 0.00 44.36 4.63
1107 2541 4.796231 CAGGGAACGTCCTCGCCG 62.796 72.222 0.00 0.00 41.18 6.46
1116 2550 3.508840 GGCGAATGGCAGGGAACG 61.509 66.667 0.00 0.00 46.16 3.95
1151 2585 1.558233 AACCTCTGAACCTACCTCGG 58.442 55.000 0.00 0.00 0.00 4.63
1181 2615 8.393959 AGAAGATTGGGAGAAGGAATAGTTAA 57.606 34.615 0.00 0.00 0.00 2.01
1203 2637 8.881262 AGGTTCTTTTCTTGGATAGAACTAGAA 58.119 33.333 12.04 0.00 42.50 2.10
1204 2638 8.314751 CAGGTTCTTTTCTTGGATAGAACTAGA 58.685 37.037 12.04 0.00 42.50 2.43
1205 2639 8.097662 ACAGGTTCTTTTCTTGGATAGAACTAG 58.902 37.037 12.04 8.35 42.50 2.57
1206 2640 7.974504 ACAGGTTCTTTTCTTGGATAGAACTA 58.025 34.615 12.04 0.00 42.50 2.24
1207 2641 6.842676 ACAGGTTCTTTTCTTGGATAGAACT 58.157 36.000 12.04 0.00 42.50 3.01
1208 2642 8.669243 CATACAGGTTCTTTTCTTGGATAGAAC 58.331 37.037 0.00 0.00 42.50 3.01
1223 2657 3.513912 TGGACACGATTCATACAGGTTCT 59.486 43.478 0.00 0.00 0.00 3.01
1307 2754 1.068083 GCGAATGATCCTGCTCCGA 59.932 57.895 0.00 0.00 0.00 4.55
1393 2840 2.243810 GTAGGGGAGCATACCTCAGAG 58.756 57.143 0.00 0.00 42.62 3.35
1394 2841 1.573857 TGTAGGGGAGCATACCTCAGA 59.426 52.381 0.00 0.00 42.62 3.27
1395 2842 1.967066 CTGTAGGGGAGCATACCTCAG 59.033 57.143 0.00 2.26 42.62 3.35
1396 2843 1.291033 ACTGTAGGGGAGCATACCTCA 59.709 52.381 0.00 0.00 42.62 3.86
1397 2844 1.689273 CACTGTAGGGGAGCATACCTC 59.311 57.143 0.00 0.00 38.30 3.85
1398 2845 1.794714 CACTGTAGGGGAGCATACCT 58.205 55.000 0.00 0.00 40.89 3.08
1415 2869 4.142293 GGATTCAAGATTGGAAGAAGGCAC 60.142 45.833 0.00 0.00 0.00 5.01
1451 2906 4.375305 CGTTTAGGTTCAGTTTAACGTCCG 60.375 45.833 0.00 0.00 35.11 4.79
1477 2935 4.590647 TGTTACAAATGGATCCAAAGGCAA 59.409 37.500 20.67 7.90 0.00 4.52
1527 2985 2.550277 TCAGGAAGATCTGTAGGGCA 57.450 50.000 0.00 0.00 36.25 5.36
1528 2986 2.103941 CCTTCAGGAAGATCTGTAGGGC 59.896 54.545 10.52 0.00 43.93 5.19
1529 2987 2.103941 GCCTTCAGGAAGATCTGTAGGG 59.896 54.545 15.75 7.49 46.15 3.53
1531 2989 2.801342 GCGCCTTCAGGAAGATCTGTAG 60.801 54.545 10.52 0.00 40.79 2.74
1532 2990 1.137086 GCGCCTTCAGGAAGATCTGTA 59.863 52.381 10.52 0.00 40.79 2.74
1533 2991 0.107945 GCGCCTTCAGGAAGATCTGT 60.108 55.000 10.52 0.00 40.79 3.41
1534 2992 0.813210 GGCGCCTTCAGGAAGATCTG 60.813 60.000 22.15 0.00 40.79 2.90
1535 2993 1.267574 TGGCGCCTTCAGGAAGATCT 61.268 55.000 29.70 0.00 40.79 2.75
1556 3014 0.748367 CCCTCGACAGGATCTCGACA 60.748 60.000 1.73 0.00 43.65 4.35
1640 3098 0.471211 ACCTCTTGTGGACTTCCGGA 60.471 55.000 0.00 0.00 39.43 5.14
1646 3104 2.932234 CGGCGACCTCTTGTGGACT 61.932 63.158 0.00 0.00 0.00 3.85
1651 3109 3.303135 TCTGCGGCGACCTCTTGT 61.303 61.111 12.98 0.00 0.00 3.16
1759 3220 1.281899 GTAGCTCTCGCGCAAGAAAT 58.718 50.000 8.75 0.00 42.32 2.17
1771 3232 3.929610 GACAGAAAAGCAATCGTAGCTCT 59.070 43.478 0.00 0.00 42.53 4.09
1916 3380 0.105039 CCTCTTCGTCCAGCCATACC 59.895 60.000 0.00 0.00 0.00 2.73
2129 3593 3.375299 GGAAGACACATTCTGAATTCCCG 59.625 47.826 2.27 0.00 34.50 5.14
2177 3644 2.677902 CGTGACCACTGAGGCATAATGT 60.678 50.000 0.00 0.00 43.14 2.71
2359 3832 0.537371 GGTCCAGTTTCCACCACCAG 60.537 60.000 0.00 0.00 0.00 4.00
2372 3845 4.023980 TGACAGTATACTTGAGGGTCCAG 58.976 47.826 14.42 0.00 0.00 3.86
2572 4045 4.361451 CATGGAATGTAAGGCAGAACAC 57.639 45.455 0.00 0.00 40.20 3.32
2608 4081 5.192927 ACTTTCAGTGACCATCAGAAAACA 58.807 37.500 0.00 0.00 0.00 2.83
2609 4082 5.757850 ACTTTCAGTGACCATCAGAAAAC 57.242 39.130 0.00 0.00 0.00 2.43
2610 4083 6.483307 CAGTACTTTCAGTGACCATCAGAAAA 59.517 38.462 0.00 0.00 0.00 2.29
2611 4084 5.991606 CAGTACTTTCAGTGACCATCAGAAA 59.008 40.000 0.00 0.00 0.00 2.52
2639 4112 3.521560 CACGCTAAGGACATTAAGCTGA 58.478 45.455 0.00 0.00 0.00 4.26
2719 4201 7.180051 ACATAGAAAGCTAGGAGATATCCAAGG 59.820 40.741 9.50 0.00 32.90 3.61
2729 4211 7.284489 ACTGAACTAGACATAGAAAGCTAGGAG 59.716 40.741 0.00 0.00 35.74 3.69
2770 4395 1.949465 AGACGTTGAGGACACAAACC 58.051 50.000 0.00 0.00 0.00 3.27
2786 4419 2.989422 AGCCACAAAACGCATTAGAC 57.011 45.000 0.00 0.00 0.00 2.59
2844 4477 7.315890 GCATTAATAATGACCAATTAGAGGGC 58.684 38.462 16.45 0.00 41.46 5.19
2865 4506 2.236489 ATGGCTAACAAGGTGGCATT 57.764 45.000 0.00 0.00 42.94 3.56
2883 4524 6.271857 ACATCTCTTAGATTCACCCAGCATAT 59.728 38.462 0.00 0.00 31.32 1.78
2992 4659 4.661649 GCACGACATCGATATTTGACATCG 60.662 45.833 8.54 0.00 45.17 3.84
3005 4672 2.285256 GCAGAATAACAGCACGACATCG 60.285 50.000 0.00 0.00 46.33 3.84
3045 4712 4.843728 ACTTTCCTAATCAGGCGAATGAA 58.156 39.130 0.00 0.00 42.30 2.57
3096 4763 2.297701 CCCTGTAAATGCAGCGGTTAT 58.702 47.619 0.00 0.00 35.28 1.89
3194 4863 7.825331 AAGGAGAAAAGGAAAGAAAAGGTAG 57.175 36.000 0.00 0.00 0.00 3.18
3197 4866 8.914011 TCTAAAAGGAGAAAAGGAAAGAAAAGG 58.086 33.333 0.00 0.00 0.00 3.11
3213 4882 8.154203 GGAAATCCTCTTCCTATCTAAAAGGAG 58.846 40.741 0.00 0.00 43.90 3.69
3299 4993 3.153369 ACTTGTGTGCATCATTACCCA 57.847 42.857 0.00 0.00 0.00 4.51
3386 5082 9.323985 GAAGATATTAGCCATGGATAGCTTAAG 57.676 37.037 18.40 0.00 40.56 1.85


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

AutoCloner maintained by Alex Coulton.