Multiple sequence alignment - TraesCS1B01G280200

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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 TraesCS1B01G280200 chr1B 100.000 2255 0 0 1 2255 488473138 488475392 0.000000e+00 4165.0
1 TraesCS1B01G280200 chr1B 100.000 28 0 0 311 338 616319653 616319626 4.000000e-03 52.8
2 TraesCS1B01G280200 chr1D 93.813 1697 73 21 580 2255 365082014 365083699 0.000000e+00 2523.0
3 TraesCS1B01G280200 chr1D 77.320 194 31 11 87 273 377030403 377030590 3.960000e-18 102.0
4 TraesCS1B01G280200 chr1D 80.159 126 17 8 141 262 228022671 228022550 1.110000e-13 87.9
5 TraesCS1B01G280200 chr1D 82.222 90 12 4 133 219 208190462 208190550 8.640000e-10 75.0
6 TraesCS1B01G280200 chr1A 94.891 1566 72 2 689 2254 463958524 463960081 0.000000e+00 2442.0
7 TraesCS1B01G280200 chr1A 84.559 680 70 18 1 662 463948338 463949000 1.890000e-180 641.0
8 TraesCS1B01G280200 chr1A 85.938 128 13 5 250 377 474429058 474428936 5.050000e-27 132.0
9 TraesCS1B01G280200 chr3B 80.258 699 122 15 778 1468 651427238 651426548 1.540000e-141 512.0
10 TraesCS1B01G280200 chr3B 85.366 328 37 9 1741 2064 651426299 651425979 1.670000e-86 329.0
11 TraesCS1B01G280200 chr3B 84.756 328 39 9 1741 2064 489350602 489350282 3.610000e-83 318.0
12 TraesCS1B01G280200 chr3B 85.057 87 7 6 250 336 367834968 367835048 1.440000e-12 84.2
13 TraesCS1B01G280200 chr3A 79.857 700 123 17 778 1468 632041222 632040532 1.560000e-136 496.0
14 TraesCS1B01G280200 chr3A 85.366 328 37 9 1741 2064 632040292 632039972 1.670000e-86 329.0
15 TraesCS1B01G280200 chr3A 77.226 584 105 23 799 1365 632295260 632294688 1.300000e-82 316.0
16 TraesCS1B01G280200 chr4B 79.913 687 122 15 790 1468 46934226 46933548 7.240000e-135 490.0
17 TraesCS1B01G280200 chr4B 83.841 328 42 9 1741 2064 46933299 46932979 3.640000e-78 302.0
18 TraesCS1B01G280200 chr4B 89.655 58 6 0 779 836 672128282 672128339 8.640000e-10 75.0
19 TraesCS1B01G280200 chr3D 79.881 671 121 12 778 1441 488950102 488950765 1.570000e-131 479.0
20 TraesCS1B01G280200 chr3D 78.700 554 96 18 772 1314 488893876 488894418 1.280000e-92 350.0
21 TraesCS1B01G280200 chr3D 85.075 335 37 11 1735 2064 488951035 488951361 1.670000e-86 329.0
22 TraesCS1B01G280200 chr2B 79.506 688 125 14 789 1468 254626190 254626869 2.030000e-130 475.0
23 TraesCS1B01G280200 chr2B 85.030 334 39 9 1735 2064 254627112 254627438 1.670000e-86 329.0
24 TraesCS1B01G280200 chr7D 85.666 293 38 3 1741 2031 89311908 89312198 2.810000e-79 305.0
25 TraesCS1B01G280200 chr5D 88.462 78 8 1 140 216 482561527 482561604 2.380000e-15 93.5
26 TraesCS1B01G280200 chr2D 91.837 49 3 1 299 346 13525834 13525882 1.450000e-07 67.6
27 TraesCS1B01G280200 chr5B 91.489 47 4 0 306 352 74781351 74781397 5.200000e-07 65.8
28 TraesCS1B01G280200 chr5B 91.489 47 4 0 306 352 74803472 74803518 5.200000e-07 65.8
29 TraesCS1B01G280200 chr7A 100.000 30 0 0 188 217 135450942 135450971 3.130000e-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 TraesCS1B01G280200 chr1B 488473138 488475392 2254 False 4165.0 4165 100.0000 1 2255 1 chr1B.!!$F1 2254
1 TraesCS1B01G280200 chr1D 365082014 365083699 1685 False 2523.0 2523 93.8130 580 2255 1 chr1D.!!$F2 1675
2 TraesCS1B01G280200 chr1A 463958524 463960081 1557 False 2442.0 2442 94.8910 689 2254 1 chr1A.!!$F2 1565
3 TraesCS1B01G280200 chr1A 463948338 463949000 662 False 641.0 641 84.5590 1 662 1 chr1A.!!$F1 661
4 TraesCS1B01G280200 chr3B 651425979 651427238 1259 True 420.5 512 82.8120 778 2064 2 chr3B.!!$R2 1286
5 TraesCS1B01G280200 chr3A 632039972 632041222 1250 True 412.5 496 82.6115 778 2064 2 chr3A.!!$R2 1286
6 TraesCS1B01G280200 chr3A 632294688 632295260 572 True 316.0 316 77.2260 799 1365 1 chr3A.!!$R1 566
7 TraesCS1B01G280200 chr4B 46932979 46934226 1247 True 396.0 490 81.8770 790 2064 2 chr4B.!!$R1 1274
8 TraesCS1B01G280200 chr3D 488950102 488951361 1259 False 404.0 479 82.4780 778 2064 2 chr3D.!!$F2 1286
9 TraesCS1B01G280200 chr3D 488893876 488894418 542 False 350.0 350 78.7000 772 1314 1 chr3D.!!$F1 542
10 TraesCS1B01G280200 chr2B 254626190 254627438 1248 False 402.0 475 82.2680 789 2064 2 chr2B.!!$F1 1275

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
233 234 0.180406 CCCGGACCGATGGAGATTTT 59.82 55.0 17.49 0.0 0.0 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1556 1595 0.987715 CAGCGTGTTCAGTCGATGAG 59.012 55.0 0.0 0.0 44.4 2.9 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
43 44 1.089481 CATATGACGGGCACAACGCT 61.089 55.000 0.00 0.00 41.91 5.07
44 45 1.089481 ATATGACGGGCACAACGCTG 61.089 55.000 0.00 0.00 41.91 5.18
81 82 2.361230 CCTTCTTCCAACCGCCCC 60.361 66.667 0.00 0.00 0.00 5.80
82 83 2.361230 CTTCTTCCAACCGCCCCC 60.361 66.667 0.00 0.00 0.00 5.40
83 84 3.179339 TTCTTCCAACCGCCCCCA 61.179 61.111 0.00 0.00 0.00 4.96
84 85 2.499303 CTTCTTCCAACCGCCCCCAT 62.499 60.000 0.00 0.00 0.00 4.00
98 99 4.358841 CCATGGACCACCGGCCAA 62.359 66.667 5.56 0.00 39.42 4.52
99 100 2.282816 CATGGACCACCGGCCAAA 60.283 61.111 0.00 0.00 39.42 3.28
100 101 2.282887 ATGGACCACCGGCCAAAC 60.283 61.111 0.00 0.00 39.42 2.93
102 103 4.589675 GGACCACCGGCCAAACCA 62.590 66.667 0.00 0.00 39.03 3.67
103 104 2.282887 GACCACCGGCCAAACCAT 60.283 61.111 0.00 0.00 39.03 3.55
105 106 3.068064 CCACCGGCCAAACCATCC 61.068 66.667 0.00 0.00 39.03 3.51
106 107 3.068064 CACCGGCCAAACCATCCC 61.068 66.667 0.00 0.00 39.03 3.85
107 108 3.585428 ACCGGCCAAACCATCCCA 61.585 61.111 0.00 0.00 39.03 4.37
108 109 3.068064 CCGGCCAAACCATCCCAC 61.068 66.667 2.24 0.00 39.03 4.61
109 110 3.068064 CGGCCAAACCATCCCACC 61.068 66.667 2.24 0.00 39.03 4.61
110 111 2.119391 GGCCAAACCATCCCACCA 59.881 61.111 0.00 0.00 38.86 4.17
111 112 1.306056 GGCCAAACCATCCCACCAT 60.306 57.895 0.00 0.00 38.86 3.55
112 113 1.329913 GGCCAAACCATCCCACCATC 61.330 60.000 0.00 0.00 38.86 3.51
113 114 1.666209 GCCAAACCATCCCACCATCG 61.666 60.000 0.00 0.00 0.00 3.84
116 117 2.854300 AAACCATCCCACCATCGCCC 62.854 60.000 0.00 0.00 0.00 6.13
169 170 1.353394 CCCACCCTCCCCATAACCTC 61.353 65.000 0.00 0.00 0.00 3.85
180 181 1.306654 ATAACCTCCTCCCACCGCA 60.307 57.895 0.00 0.00 0.00 5.69
213 214 3.631046 CCGGCCATCCCTCTAGCC 61.631 72.222 2.24 0.00 42.18 3.93
216 217 3.253061 GCCATCCCTCTAGCCCCC 61.253 72.222 0.00 0.00 0.00 5.40
217 218 2.925170 CCATCCCTCTAGCCCCCG 60.925 72.222 0.00 0.00 0.00 5.73
218 219 2.925170 CATCCCTCTAGCCCCCGG 60.925 72.222 0.00 0.00 0.00 5.73
224 225 3.811807 CTCTAGCCCCCGGACCGAT 62.812 68.421 17.49 0.00 0.00 4.18
225 226 3.616721 CTAGCCCCCGGACCGATG 61.617 72.222 17.49 5.89 0.00 3.84
233 234 0.180406 CCCGGACCGATGGAGATTTT 59.820 55.000 17.49 0.00 0.00 1.82
235 236 1.583054 CGGACCGATGGAGATTTTCC 58.417 55.000 8.64 0.00 46.98 3.13
237 238 1.477014 GGACCGATGGAGATTTTCCCC 60.477 57.143 0.00 0.00 46.19 4.81
238 239 1.490910 GACCGATGGAGATTTTCCCCT 59.509 52.381 0.00 0.00 46.19 4.79
239 240 1.212935 ACCGATGGAGATTTTCCCCTG 59.787 52.381 0.00 0.00 46.19 4.45
243 244 0.918983 TGGAGATTTTCCCCTGCGAT 59.081 50.000 0.00 0.00 46.19 4.58
244 245 1.284785 TGGAGATTTTCCCCTGCGATT 59.715 47.619 0.00 0.00 46.19 3.34
248 249 3.165071 AGATTTTCCCCTGCGATTTTGT 58.835 40.909 0.00 0.00 0.00 2.83
257 258 1.127951 CTGCGATTTTGTACCACCGTC 59.872 52.381 0.00 0.00 0.00 4.79
287 288 4.060667 CCACCCCCACCACCCATC 62.061 72.222 0.00 0.00 0.00 3.51
288 289 3.264052 CACCCCCACCACCCATCA 61.264 66.667 0.00 0.00 0.00 3.07
289 290 2.453497 ACCCCCACCACCCATCAA 60.453 61.111 0.00 0.00 0.00 2.57
291 292 2.361104 CCCCACCACCCATCAACG 60.361 66.667 0.00 0.00 0.00 4.10
292 293 2.361104 CCCACCACCCATCAACGG 60.361 66.667 0.00 0.00 0.00 4.44
331 348 1.219393 CGGTGAGCTCCTTCCTTCC 59.781 63.158 12.15 1.78 0.00 3.46
333 350 0.912006 GGTGAGCTCCTTCCTTCCCT 60.912 60.000 12.15 0.00 0.00 4.20
334 351 0.539518 GTGAGCTCCTTCCTTCCCTC 59.460 60.000 12.15 0.00 0.00 4.30
335 352 0.618968 TGAGCTCCTTCCTTCCCTCC 60.619 60.000 12.15 0.00 0.00 4.30
336 353 1.681486 GAGCTCCTTCCTTCCCTCCG 61.681 65.000 0.87 0.00 0.00 4.63
337 354 2.736826 GCTCCTTCCTTCCCTCCGG 61.737 68.421 0.00 0.00 0.00 5.14
338 355 2.687566 TCCTTCCTTCCCTCCGGC 60.688 66.667 0.00 0.00 0.00 6.13
339 356 3.798511 CCTTCCTTCCCTCCGGCC 61.799 72.222 0.00 0.00 0.00 6.13
375 392 4.083802 ACTTCTTCGCCTTTCTCAAAATCG 60.084 41.667 0.00 0.00 0.00 3.34
381 398 3.423645 CGCCTTTCTCAAAATCGACTGAC 60.424 47.826 0.00 0.00 0.00 3.51
383 400 4.065088 CCTTTCTCAAAATCGACTGACCA 58.935 43.478 0.00 0.00 0.00 4.02
392 409 8.335532 TCAAAATCGACTGACCAAAATTAGAT 57.664 30.769 0.00 0.00 0.00 1.98
404 421 5.102313 CCAAAATTAGATTTTCAGGCGACC 58.898 41.667 0.00 0.00 40.27 4.79
405 422 4.616181 AAATTAGATTTTCAGGCGACCG 57.384 40.909 0.00 0.00 0.00 4.79
407 424 2.288961 TAGATTTTCAGGCGACCGAC 57.711 50.000 0.00 0.00 0.00 4.79
413 430 0.664166 TTCAGGCGACCGACGTTTAC 60.664 55.000 0.00 0.00 44.60 2.01
414 431 1.372004 CAGGCGACCGACGTTTACA 60.372 57.895 0.00 0.00 44.60 2.41
455 472 6.184789 TCCACCTAAATCCCTACAACAAATC 58.815 40.000 0.00 0.00 0.00 2.17
481 498 8.747666 CGCACTTAAATTTACTTGCTTTTTACA 58.252 29.630 20.29 0.00 0.00 2.41
482 499 9.843874 GCACTTAAATTTACTTGCTTTTTACAC 57.156 29.630 17.44 0.00 0.00 2.90
498 515 1.104577 ACACAACCGCGTGGGAAATT 61.105 50.000 21.14 0.67 41.38 1.82
547 564 1.751351 CGACAGAGCTATGTTCTCCCA 59.249 52.381 16.38 0.00 32.25 4.37
551 568 4.327680 ACAGAGCTATGTTCTCCCAAAAC 58.672 43.478 8.51 0.00 0.00 2.43
552 569 3.691609 CAGAGCTATGTTCTCCCAAAACC 59.308 47.826 0.00 0.00 0.00 3.27
554 571 2.649816 AGCTATGTTCTCCCAAAACCCT 59.350 45.455 0.00 0.00 0.00 4.34
615 634 1.605712 GGATCGAAGTGGGGAATAGCG 60.606 57.143 0.00 0.00 0.00 4.26
677 696 2.505405 TCCTATGCCTAGCACGAGTAG 58.495 52.381 0.00 0.00 43.04 2.57
679 698 2.486203 CCTATGCCTAGCACGAGTAGAG 59.514 54.545 0.00 0.00 43.04 2.43
680 699 2.060050 ATGCCTAGCACGAGTAGAGT 57.940 50.000 0.00 0.00 43.04 3.24
681 700 2.704464 TGCCTAGCACGAGTAGAGTA 57.296 50.000 0.00 0.00 31.71 2.59
682 701 3.210232 TGCCTAGCACGAGTAGAGTAT 57.790 47.619 0.00 0.00 31.71 2.12
683 702 4.347360 TGCCTAGCACGAGTAGAGTATA 57.653 45.455 0.00 0.00 31.71 1.47
684 703 4.907809 TGCCTAGCACGAGTAGAGTATAT 58.092 43.478 0.00 0.00 31.71 0.86
685 704 6.046290 TGCCTAGCACGAGTAGAGTATATA 57.954 41.667 0.00 0.00 31.71 0.86
686 705 5.873712 TGCCTAGCACGAGTAGAGTATATAC 59.126 44.000 4.60 4.60 31.71 1.47
687 706 6.108015 GCCTAGCACGAGTAGAGTATATACT 58.892 44.000 15.37 15.37 39.71 2.12
741 760 4.275936 GCTGCCTTCTTCTTGTACTTGAAA 59.724 41.667 0.00 0.00 0.00 2.69
858 877 2.860971 AACCAGCTCTGCCCCCTT 60.861 61.111 0.00 0.00 0.00 3.95
987 1006 2.820787 CACCTGGTCGTAGAAGAACTCT 59.179 50.000 0.00 0.00 39.69 3.24
1008 1027 1.746615 CAGGCCGACCATGGTGAAG 60.747 63.158 25.52 13.25 39.06 3.02
1520 1547 1.796459 CTGAGCACTGCAAATTTTGGC 59.204 47.619 10.96 5.76 0.00 4.52
1550 1577 1.808390 AATGGCTACGTCGCGTTCC 60.808 57.895 5.77 11.57 41.54 3.62
1556 1595 1.472276 CTACGTCGCGTTCCTGCATC 61.472 60.000 5.77 0.00 41.54 3.91
1557 1596 1.929806 TACGTCGCGTTCCTGCATCT 61.930 55.000 5.77 0.00 41.54 2.90
1565 1604 1.202348 CGTTCCTGCATCTCATCGACT 60.202 52.381 0.00 0.00 0.00 4.18
1606 1649 3.452990 TCTGAATTACCTGTATTCCGGCA 59.547 43.478 0.00 0.00 0.00 5.69
1660 1703 2.530151 AGGCTGCAAGGGGACTCA 60.530 61.111 0.50 0.00 42.68 3.41
1675 1718 2.668212 TCAACTTCCGCCGCTTGG 60.668 61.111 0.00 0.00 0.00 3.61
1738 1981 4.742201 GCTGCTTGCCGTCGGAGA 62.742 66.667 17.49 0.57 35.15 3.71
2158 2401 1.893808 CCCTGCACGCAGTTTCAGT 60.894 57.895 17.31 0.00 41.61 3.41
2159 2402 1.571460 CCTGCACGCAGTTTCAGTC 59.429 57.895 17.31 0.00 41.61 3.51
2161 2404 2.127609 GCACGCAGTTTCAGTCGC 60.128 61.111 0.00 0.00 41.61 5.19
2166 2409 2.892334 GCAGTTTCAGTCGCGCCAA 61.892 57.895 0.00 0.00 0.00 4.52
2167 2410 1.868997 CAGTTTCAGTCGCGCCAAT 59.131 52.632 0.00 0.00 0.00 3.16
2186 2429 7.487829 GCGCCAATTGAGAAATTTAGAAATGTA 59.512 33.333 7.12 0.00 0.00 2.29
2203 2446 7.441836 AGAAATGTAATGCATACGATCCTGTA 58.558 34.615 0.00 0.00 36.67 2.74
2254 2497 2.493675 CAGAGTGAAATCTCGTCCTCCA 59.506 50.000 0.00 0.00 39.21 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.149981 TGTGCCCGTCATATGTTTTCAA 58.850 40.909 1.90 0.00 0.00 2.69
19 20 3.498082 GTTGTGCCCGTCATATGTTTTC 58.502 45.455 1.90 0.00 0.00 2.29
43 44 1.139654 CATCGGGAGGAAGAAGATGCA 59.860 52.381 0.00 0.00 33.41 3.96
44 45 1.876322 CATCGGGAGGAAGAAGATGC 58.124 55.000 0.00 0.00 33.41 3.91
81 82 3.877344 TTTGGCCGGTGGTCCATGG 62.877 63.158 4.97 4.97 31.26 3.66
82 83 2.282816 TTTGGCCGGTGGTCCATG 60.283 61.111 1.90 0.00 31.26 3.66
83 84 2.282887 GTTTGGCCGGTGGTCCAT 60.283 61.111 1.90 0.00 31.26 3.41
84 85 4.589675 GGTTTGGCCGGTGGTCCA 62.590 66.667 1.90 0.00 0.00 4.02
90 91 3.585428 TGGGATGGTTTGGCCGGT 61.585 61.111 1.90 0.00 41.21 5.28
98 99 2.275418 GGCGATGGTGGGATGGTT 59.725 61.111 0.00 0.00 0.00 3.67
99 100 3.809013 GGGCGATGGTGGGATGGT 61.809 66.667 0.00 0.00 0.00 3.55
100 101 4.935495 CGGGCGATGGTGGGATGG 62.935 72.222 0.00 0.00 0.00 3.51
152 153 0.327576 AGGAGGTTATGGGGAGGGTG 60.328 60.000 0.00 0.00 0.00 4.61
153 154 0.029989 GAGGAGGTTATGGGGAGGGT 60.030 60.000 0.00 0.00 0.00 4.34
154 155 0.768609 GGAGGAGGTTATGGGGAGGG 60.769 65.000 0.00 0.00 0.00 4.30
156 157 0.030092 TGGGAGGAGGTTATGGGGAG 60.030 60.000 0.00 0.00 0.00 4.30
157 158 0.327191 GTGGGAGGAGGTTATGGGGA 60.327 60.000 0.00 0.00 0.00 4.81
159 160 1.696097 CGGTGGGAGGAGGTTATGGG 61.696 65.000 0.00 0.00 0.00 4.00
160 161 1.830145 CGGTGGGAGGAGGTTATGG 59.170 63.158 0.00 0.00 0.00 2.74
161 162 1.146263 GCGGTGGGAGGAGGTTATG 59.854 63.158 0.00 0.00 0.00 1.90
162 163 1.306654 TGCGGTGGGAGGAGGTTAT 60.307 57.895 0.00 0.00 0.00 1.89
163 164 1.987855 CTGCGGTGGGAGGAGGTTA 60.988 63.158 0.00 0.00 0.00 2.85
193 194 4.574614 TAGAGGGATGGCCGGGGG 62.575 72.222 2.18 0.00 33.83 5.40
199 200 3.253061 GGGGGCTAGAGGGATGGC 61.253 72.222 0.00 0.00 0.00 4.40
213 214 1.696097 AAATCTCCATCGGTCCGGGG 61.696 60.000 12.29 13.66 0.00 5.73
216 217 1.583054 GGAAAATCTCCATCGGTCCG 58.417 55.000 4.39 4.39 44.67 4.79
225 226 2.058593 AATCGCAGGGGAAAATCTCC 57.941 50.000 0.00 0.00 44.54 3.71
233 234 0.693622 TGGTACAAAATCGCAGGGGA 59.306 50.000 0.00 0.00 31.92 4.81
235 236 0.808755 GGTGGTACAAAATCGCAGGG 59.191 55.000 0.00 0.00 44.16 4.45
237 238 1.127951 GACGGTGGTACAAAATCGCAG 59.872 52.381 0.00 0.00 44.16 5.18
238 239 1.149987 GACGGTGGTACAAAATCGCA 58.850 50.000 0.00 0.00 44.16 5.10
239 240 0.094046 CGACGGTGGTACAAAATCGC 59.906 55.000 0.00 0.00 44.16 4.58
243 244 2.309326 GCACGACGGTGGTACAAAA 58.691 52.632 0.00 0.00 44.16 2.44
244 245 4.030821 GCACGACGGTGGTACAAA 57.969 55.556 0.00 0.00 44.16 2.83
271 272 2.851121 TTGATGGGTGGTGGGGGTG 61.851 63.158 0.00 0.00 0.00 4.61
272 273 2.453497 TTGATGGGTGGTGGGGGT 60.453 61.111 0.00 0.00 0.00 4.95
274 275 2.361104 CGTTGATGGGTGGTGGGG 60.361 66.667 0.00 0.00 0.00 4.96
277 278 0.611200 TCTACCGTTGATGGGTGGTG 59.389 55.000 0.00 0.00 38.50 4.17
278 279 1.209504 CATCTACCGTTGATGGGTGGT 59.790 52.381 13.35 0.00 38.50 4.16
280 281 2.979814 TCATCTACCGTTGATGGGTG 57.020 50.000 18.87 0.29 41.01 4.61
281 282 3.038280 TCATCATCTACCGTTGATGGGT 58.962 45.455 18.87 8.73 45.94 4.51
282 283 3.555795 CCTCATCATCTACCGTTGATGGG 60.556 52.174 18.87 12.14 46.10 4.00
283 284 3.070159 ACCTCATCATCTACCGTTGATGG 59.930 47.826 18.87 8.35 45.94 3.51
284 285 4.327982 ACCTCATCATCTACCGTTGATG 57.672 45.455 14.61 14.61 46.83 3.07
285 286 4.021894 GCTACCTCATCATCTACCGTTGAT 60.022 45.833 0.00 0.00 32.87 2.57
287 288 3.553096 GGCTACCTCATCATCTACCGTTG 60.553 52.174 0.00 0.00 0.00 4.10
288 289 2.628657 GGCTACCTCATCATCTACCGTT 59.371 50.000 0.00 0.00 0.00 4.44
289 290 2.240279 GGCTACCTCATCATCTACCGT 58.760 52.381 0.00 0.00 0.00 4.83
291 292 2.896039 AGGGCTACCTCATCATCTACC 58.104 52.381 0.00 0.00 46.95 3.18
314 331 0.912006 AGGGAAGGAAGGAGCTCACC 60.912 60.000 17.19 15.03 0.00 4.02
316 333 0.618968 GGAGGGAAGGAAGGAGCTCA 60.619 60.000 17.19 0.00 0.00 4.26
336 353 4.475135 GTTCGCTGGAGGGAGGCC 62.475 72.222 0.00 0.00 38.26 5.19
337 354 2.860972 GAAGTTCGCTGGAGGGAGGC 62.861 65.000 0.00 0.00 38.26 4.70
338 355 1.219393 GAAGTTCGCTGGAGGGAGG 59.781 63.158 0.00 0.00 38.26 4.30
339 356 0.610687 AAGAAGTTCGCTGGAGGGAG 59.389 55.000 0.00 0.00 38.26 4.30
363 380 6.443934 TTTTGGTCAGTCGATTTTGAGAAA 57.556 33.333 0.00 0.00 0.00 2.52
375 392 6.808704 GCCTGAAAATCTAATTTTGGTCAGTC 59.191 38.462 2.56 0.00 42.15 3.51
381 398 5.102313 GGTCGCCTGAAAATCTAATTTTGG 58.898 41.667 2.56 0.96 42.15 3.28
383 400 4.698304 TCGGTCGCCTGAAAATCTAATTTT 59.302 37.500 0.00 0.00 44.56 1.82
392 409 0.810823 AAACGTCGGTCGCCTGAAAA 60.811 50.000 0.00 0.00 44.19 2.29
430 447 5.586155 TTGTTGTAGGGATTTAGGTGGAA 57.414 39.130 0.00 0.00 0.00 3.53
449 466 7.145323 AGCAAGTAAATTTAAGTGCGATTTGT 58.855 30.769 20.41 7.02 37.09 2.83
455 472 8.747666 TGTAAAAAGCAAGTAAATTTAAGTGCG 58.252 29.630 20.41 3.93 37.09 5.34
481 498 1.657556 CAATTTCCCACGCGGTTGT 59.342 52.632 12.47 0.00 0.00 3.32
482 499 1.080839 CCAATTTCCCACGCGGTTG 60.081 57.895 12.47 0.00 0.00 3.77
498 515 5.697633 CCTAACTTTAAGTAACGTTGAGCCA 59.302 40.000 11.99 0.00 31.39 4.75
536 553 5.076873 CAAAGAGGGTTTTGGGAGAACATA 58.923 41.667 0.00 0.00 35.03 2.29
547 564 0.744281 CACGCCACAAAGAGGGTTTT 59.256 50.000 0.00 0.00 0.00 2.43
551 568 1.966451 GGACACGCCACAAAGAGGG 60.966 63.158 0.00 0.00 36.34 4.30
552 569 1.227823 TGGACACGCCACAAAGAGG 60.228 57.895 0.00 0.00 43.33 3.69
615 634 9.503427 GGTGTACATGCTTACATTTTTAAGATC 57.497 33.333 0.00 0.00 34.50 2.75
682 701 9.740239 CGTTGGTTAGAATTAGCAGTAAGTATA 57.260 33.333 0.00 0.00 0.00 1.47
683 702 7.709613 CCGTTGGTTAGAATTAGCAGTAAGTAT 59.290 37.037 0.00 0.00 0.00 2.12
684 703 7.037438 CCGTTGGTTAGAATTAGCAGTAAGTA 58.963 38.462 0.00 0.00 0.00 2.24
685 704 5.873164 CCGTTGGTTAGAATTAGCAGTAAGT 59.127 40.000 0.00 0.00 0.00 2.24
686 705 5.873164 ACCGTTGGTTAGAATTAGCAGTAAG 59.127 40.000 0.00 0.00 27.29 2.34
687 706 5.797051 ACCGTTGGTTAGAATTAGCAGTAA 58.203 37.500 0.00 0.00 27.29 2.24
741 760 0.595095 ACGTCTTCTTCGCCGTAACT 59.405 50.000 0.00 0.00 0.00 2.24
987 1006 3.965258 ACCATGGTCGGCCTGCAA 61.965 61.111 13.00 0.00 35.27 4.08
1520 1547 2.537529 CGTAGCCATTGATGTGCTTTCG 60.538 50.000 10.68 11.50 36.32 3.46
1528 1555 1.145759 ACGCGACGTAGCCATTGATG 61.146 55.000 15.93 1.60 38.73 3.07
1536 1563 3.542742 GCAGGAACGCGACGTAGC 61.543 66.667 15.93 10.95 39.99 3.58
1538 1565 1.515519 GATGCAGGAACGCGACGTA 60.516 57.895 15.93 0.00 39.99 3.57
1550 1577 2.602211 GTGTTCAGTCGATGAGATGCAG 59.398 50.000 0.00 0.00 39.68 4.41
1556 1595 0.987715 CAGCGTGTTCAGTCGATGAG 59.012 55.000 0.00 0.00 44.40 2.90
1557 1596 1.008875 GCAGCGTGTTCAGTCGATGA 61.009 55.000 6.98 0.00 44.40 2.92
1565 1604 1.029408 AGTGTTTGGCAGCGTGTTCA 61.029 50.000 0.00 0.00 0.00 3.18
1606 1649 3.950794 ATCGTGCGGCAACATCGGT 62.951 57.895 3.23 0.00 0.00 4.69
1619 1662 1.001624 TTCGCATGAAGCTCATCGTG 58.998 50.000 0.00 3.61 42.61 4.35
1620 1663 1.863454 GATTCGCATGAAGCTCATCGT 59.137 47.619 0.00 0.00 42.61 3.73
1660 1703 2.668550 GACCAAGCGGCGGAAGTT 60.669 61.111 9.78 0.00 34.57 2.66
2001 2244 2.066999 CCTCTACCTGGTGGCCCTC 61.067 68.421 10.23 0.00 36.63 4.30
2085 2328 1.079875 CCGGCAATCACAAATGCAGC 61.080 55.000 0.00 0.00 44.32 5.25
2158 2401 3.687212 TCTAAATTTCTCAATTGGCGCGA 59.313 39.130 12.10 0.00 32.57 5.87
2159 2402 4.014847 TCTAAATTTCTCAATTGGCGCG 57.985 40.909 0.00 0.00 32.57 6.86
2161 2404 7.816945 ACATTTCTAAATTTCTCAATTGGCG 57.183 32.000 5.42 0.00 32.57 5.69
2203 2446 4.123497 TCTCCGATGTTTGATTCACGAT 57.877 40.909 0.00 0.00 0.00 3.73


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

AutoCloner maintained by Alex Coulton.