Multiple sequence alignment - TraesCS2D01G317300

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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 TraesCS2D01G317300 chr2D 100.000 2711 0 0 1 2711 406732204 406734914 0.000000e+00 5007.0
1 TraesCS2D01G317300 chr2D 84.037 758 71 26 636 1365 406695195 406695930 0.000000e+00 684.0
2 TraesCS2D01G317300 chr2A 91.804 1635 98 13 2 1627 546342147 546343754 0.000000e+00 2244.0
3 TraesCS2D01G317300 chr2B 92.282 1218 56 15 421 1624 482709437 482710630 0.000000e+00 1694.0
4 TraesCS2D01G317300 chr2B 90.909 1100 82 12 1626 2711 482710741 482711836 0.000000e+00 1461.0
5 TraesCS2D01G317300 chr5B 82.031 128 21 1 2476 2603 406612585 406612460 1.030000e-19 108.0
6 TraesCS2D01G317300 chr3A 81.818 110 20 0 2481 2590 639750847 639750956 2.870000e-15 93.5


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 TraesCS2D01G317300 chr2D 406732204 406734914 2710 False 5007.0 5007 100.0000 1 2711 1 chr2D.!!$F2 2710
1 TraesCS2D01G317300 chr2D 406695195 406695930 735 False 684.0 684 84.0370 636 1365 1 chr2D.!!$F1 729
2 TraesCS2D01G317300 chr2A 546342147 546343754 1607 False 2244.0 2244 91.8040 2 1627 1 chr2A.!!$F1 1625
3 TraesCS2D01G317300 chr2B 482709437 482711836 2399 False 1577.5 1694 91.5955 421 2711 2 chr2B.!!$F1 2290

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
748 753 0.109086 AGTCAGGAACACGATCGCAG 60.109 55.0 16.6 10.96 0.0 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2202 2345 0.027979 CACAGGAGCAACAACACACG 59.972 55.0 0.0 0.0 0.0 4.49 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 0.672091 TATGAACGCGCCATGTGTGT 60.672 50.000 20.47 0.00 41.44 3.72
25 26 2.127270 GAACGCGCCATGTGTGTG 60.127 61.111 5.73 4.82 41.44 3.82
43 44 3.555547 GTGTGTGCGATTGCTACATGATA 59.444 43.478 15.52 0.00 43.34 2.15
60 61 2.569853 TGATAAAACTGAAGCCGGGAGA 59.430 45.455 2.18 0.00 0.00 3.71
65 66 3.933861 AACTGAAGCCGGGAGATTAAT 57.066 42.857 2.18 0.00 0.00 1.40
70 71 5.765182 ACTGAAGCCGGGAGATTAATATTTG 59.235 40.000 2.18 0.00 0.00 2.32
82 83 6.599445 AGATTAATATTTGTGGCTGAGAGCT 58.401 36.000 0.00 0.00 41.99 4.09
85 86 0.610174 ATTTGTGGCTGAGAGCTCGA 59.390 50.000 8.37 0.00 41.99 4.04
104 105 5.123979 GCTCGAAATCAGATTAAAAGTGGGT 59.876 40.000 0.00 0.00 0.00 4.51
109 110 4.028993 TCAGATTAAAAGTGGGTGGTCC 57.971 45.455 0.00 0.00 0.00 4.46
117 118 0.769247 AGTGGGTGGTCCTGGTTTAC 59.231 55.000 0.00 0.00 36.20 2.01
122 123 2.372837 GGGTGGTCCTGGTTTACAGTAA 59.627 50.000 0.00 0.00 46.06 2.24
123 124 3.009805 GGGTGGTCCTGGTTTACAGTAAT 59.990 47.826 0.00 0.00 46.06 1.89
124 125 4.225717 GGGTGGTCCTGGTTTACAGTAATA 59.774 45.833 0.00 0.00 46.06 0.98
168 169 3.373565 GCCGGGGGCTGAAAGTTG 61.374 66.667 2.18 0.00 46.69 3.16
199 200 0.320334 TACAGTGTGTGGATGCGTGG 60.320 55.000 5.88 0.00 0.00 4.94
212 213 0.519519 TGCGTGGGAAAACATAAGCG 59.480 50.000 0.00 0.00 0.00 4.68
213 214 0.796870 GCGTGGGAAAACATAAGCGC 60.797 55.000 0.00 0.00 36.97 5.92
224 225 2.797786 ACATAAGCGCCCTAACCAAAA 58.202 42.857 2.29 0.00 0.00 2.44
243 244 4.395959 AAAAAGACTGTCCTCACGTACA 57.604 40.909 3.76 0.00 0.00 2.90
244 245 4.602340 AAAAGACTGTCCTCACGTACAT 57.398 40.909 3.76 0.00 0.00 2.29
245 246 3.851976 AAGACTGTCCTCACGTACATC 57.148 47.619 3.76 0.00 0.00 3.06
246 247 2.791655 AGACTGTCCTCACGTACATCA 58.208 47.619 3.76 0.00 0.00 3.07
247 248 2.488545 AGACTGTCCTCACGTACATCAC 59.511 50.000 3.76 0.00 0.00 3.06
261 262 1.072806 ACATCACCGATGCCATGCTAT 59.927 47.619 3.90 0.00 43.15 2.97
267 268 2.040278 ACCGATGCCATGCTATTGGTAT 59.960 45.455 14.46 4.65 43.76 2.73
268 269 2.421073 CCGATGCCATGCTATTGGTATG 59.579 50.000 8.68 0.00 41.51 2.39
276 277 3.467374 TGCTATTGGTATGTCATGCGA 57.533 42.857 0.00 0.00 0.00 5.10
278 279 3.559655 TGCTATTGGTATGTCATGCGAAC 59.440 43.478 0.65 0.00 0.00 3.95
280 281 2.371910 TTGGTATGTCATGCGAACGA 57.628 45.000 0.00 0.00 0.00 3.85
295 296 3.861569 GAACGAATCGACAATGATCCC 57.138 47.619 10.55 0.00 0.00 3.85
296 297 1.852942 ACGAATCGACAATGATCCCG 58.147 50.000 10.55 0.00 33.43 5.14
307 308 3.071602 ACAATGATCCCGGTTCTAGATGG 59.928 47.826 0.00 0.00 0.00 3.51
310 311 1.344763 GATCCCGGTTCTAGATGGTGG 59.655 57.143 0.00 0.00 0.00 4.61
311 312 0.337082 TCCCGGTTCTAGATGGTGGA 59.663 55.000 0.00 0.00 0.00 4.02
312 313 1.200519 CCCGGTTCTAGATGGTGGAA 58.799 55.000 0.00 0.00 0.00 3.53
325 326 6.065976 AGATGGTGGAAAGTGATGACATTA 57.934 37.500 0.00 0.00 0.00 1.90
328 329 4.042809 TGGTGGAAAGTGATGACATTACCT 59.957 41.667 6.73 0.00 0.00 3.08
329 330 4.396166 GGTGGAAAGTGATGACATTACCTG 59.604 45.833 6.73 0.00 0.00 4.00
330 331 5.003804 GTGGAAAGTGATGACATTACCTGT 58.996 41.667 6.73 0.00 42.15 4.00
331 332 5.473504 GTGGAAAGTGATGACATTACCTGTT 59.526 40.000 6.73 0.00 38.54 3.16
332 333 6.653320 GTGGAAAGTGATGACATTACCTGTTA 59.347 38.462 6.73 0.00 38.54 2.41
333 334 7.336931 GTGGAAAGTGATGACATTACCTGTTAT 59.663 37.037 6.73 0.00 38.54 1.89
334 335 7.552687 TGGAAAGTGATGACATTACCTGTTATC 59.447 37.037 6.73 3.86 46.13 1.75
361 362 8.500753 TTTATCAAGTTTGTAAGTGTGAGTGT 57.499 30.769 0.00 0.00 0.00 3.55
363 364 6.811253 TCAAGTTTGTAAGTGTGAGTGTTT 57.189 33.333 0.00 0.00 0.00 2.83
364 365 6.607689 TCAAGTTTGTAAGTGTGAGTGTTTG 58.392 36.000 0.00 0.00 0.00 2.93
368 369 5.637006 TTGTAAGTGTGAGTGTTTGCTTT 57.363 34.783 0.00 0.00 0.00 3.51
370 371 4.697828 TGTAAGTGTGAGTGTTTGCTTTGA 59.302 37.500 0.00 0.00 0.00 2.69
383 384 5.348179 TGTTTGCTTTGAGTTGTTTGATGTG 59.652 36.000 0.00 0.00 0.00 3.21
385 386 4.422840 TGCTTTGAGTTGTTTGATGTGTG 58.577 39.130 0.00 0.00 0.00 3.82
390 392 7.571059 GCTTTGAGTTGTTTGATGTGTGTTTTT 60.571 33.333 0.00 0.00 0.00 1.94
489 493 4.890581 TGGATTTCAACCTCTTTTTCCGAA 59.109 37.500 0.00 0.00 0.00 4.30
491 495 5.920840 GGATTTCAACCTCTTTTTCCGAAAG 59.079 40.000 0.00 0.00 0.00 2.62
599 603 3.565764 ATGATCCACCACAGTACCATG 57.434 47.619 0.00 0.00 0.00 3.66
611 615 6.842280 ACCACAGTACCATGTAACCATATAGA 59.158 38.462 0.00 0.00 0.00 1.98
691 696 4.429212 TGTGATCCCGCGTGACCG 62.429 66.667 4.92 0.00 37.07 4.79
748 753 0.109086 AGTCAGGAACACGATCGCAG 60.109 55.000 16.60 10.96 0.00 5.18
917 940 1.003580 CCCATCGCCCATATGCTACTT 59.996 52.381 0.00 0.00 0.00 2.24
1096 1124 3.493334 TCATCCATCATGGCTTTGGATC 58.507 45.455 13.86 0.00 45.01 3.36
1205 1233 2.459710 GGAGGGGAGGGAAAGGGA 59.540 66.667 0.00 0.00 0.00 4.20
1396 1430 7.619965 TGGAGGAACCATGGATTTTTATTTTC 58.380 34.615 21.47 8.08 44.64 2.29
1397 1431 7.236432 TGGAGGAACCATGGATTTTTATTTTCA 59.764 33.333 21.47 0.00 44.64 2.69
1640 1783 4.007659 ACCATTGTAGCCGAAACCTTAAG 58.992 43.478 0.00 0.00 0.00 1.85
1666 1809 9.070179 GGGTTAACTACTCACCAAATTTTAAGA 57.930 33.333 5.42 0.00 31.50 2.10
1708 1851 7.698130 CCATTCCAACTCTCTTATTTTTAAGCG 59.302 37.037 0.00 0.00 0.00 4.68
1713 1856 5.007682 ACTCTCTTATTTTTAAGCGGCCAA 58.992 37.500 2.24 0.00 0.00 4.52
1730 1873 3.560105 GCCAAGATGCCTCTCCTAAAAT 58.440 45.455 0.00 0.00 0.00 1.82
1731 1874 4.718961 GCCAAGATGCCTCTCCTAAAATA 58.281 43.478 0.00 0.00 0.00 1.40
1759 1902 2.912690 TTTATGTGACGTGGGTGACA 57.087 45.000 0.00 0.00 44.36 3.58
1771 1914 1.353091 GGGTGACACCTTCTTCTCCT 58.647 55.000 23.72 0.00 38.64 3.69
1774 1917 3.435169 GGGTGACACCTTCTTCTCCTTTT 60.435 47.826 23.72 0.00 38.64 2.27
1777 1920 3.632145 TGACACCTTCTTCTCCTTTTTGC 59.368 43.478 0.00 0.00 0.00 3.68
1794 1937 3.084579 CTGATGTCGGCTGTTCGC 58.915 61.111 0.00 0.00 38.13 4.70
1813 1956 0.821711 CTGCCCTGGTGACCGAAAAA 60.822 55.000 0.00 0.00 0.00 1.94
1907 2050 1.305930 GGTGATTCACAACTCGGGCC 61.306 60.000 18.09 0.00 35.86 5.80
1958 2101 1.961277 GTGGCAGTGGACTGGAACG 60.961 63.158 8.82 0.00 43.94 3.95
1960 2103 1.961277 GGCAGTGGACTGGAACGTG 60.961 63.158 8.82 0.00 43.94 4.49
1963 2106 0.813610 CAGTGGACTGGAACGTGCAA 60.814 55.000 0.00 0.00 40.20 4.08
1983 2126 2.947852 ACTGATGTCGTTGCAGTAGTC 58.052 47.619 0.00 0.00 40.79 2.59
2002 2145 2.162716 GTGGACCATGAACACGAGC 58.837 57.895 0.00 0.00 0.00 5.03
2007 2150 3.499737 CATGAACACGAGCGCCCC 61.500 66.667 2.29 0.00 0.00 5.80
2095 2238 0.389296 CATCCGACGTGGTGCAGTAA 60.389 55.000 0.00 0.00 39.52 2.24
2105 2248 2.996621 GTGGTGCAGTAAGACATCTCAC 59.003 50.000 0.00 0.00 0.00 3.51
2152 2295 2.870372 GCCTCCATCGTTGTGTGC 59.130 61.111 0.00 0.00 0.00 4.57
2174 2317 1.728717 GCGTTGTTGTTGCGTGTGTG 61.729 55.000 0.00 0.00 0.00 3.82
2199 2342 3.967203 TGATGATTGTGTGTGTGTGTG 57.033 42.857 0.00 0.00 0.00 3.82
2200 2343 3.277715 TGATGATTGTGTGTGTGTGTGT 58.722 40.909 0.00 0.00 0.00 3.72
2201 2344 3.065095 TGATGATTGTGTGTGTGTGTGTG 59.935 43.478 0.00 0.00 0.00 3.82
2202 2345 1.132073 TGATTGTGTGTGTGTGTGTGC 59.868 47.619 0.00 0.00 0.00 4.57
2205 2348 1.225991 GTGTGTGTGTGTGTGCGTG 60.226 57.895 0.00 0.00 0.00 5.34
2232 2383 1.577922 CTCCTGTGTGTGCATGTGC 59.422 57.895 0.00 0.00 42.50 4.57
2250 2401 0.875474 GCCATGTGTGTGTTGTTGCC 60.875 55.000 0.00 0.00 0.00 4.52
2258 2409 1.237954 TGTGTTGTTGCCGTGTGTGT 61.238 50.000 0.00 0.00 0.00 3.72
2266 2417 4.589700 CCGTGTGTGTGCGTGTGC 62.590 66.667 0.00 0.00 43.20 4.57
2267 2418 3.563088 CGTGTGTGTGCGTGTGCT 61.563 61.111 0.00 0.00 43.34 4.40
2271 2422 2.588596 TGTGTGCGTGTGCTCTGG 60.589 61.111 0.00 0.00 43.34 3.86
2287 2440 0.036105 CTGGGTGTGTGCATGCTCTA 60.036 55.000 20.33 6.23 0.00 2.43
2319 2472 1.188219 TGCAGCCTCTCCTCGTCTTT 61.188 55.000 0.00 0.00 0.00 2.52
2320 2473 0.459411 GCAGCCTCTCCTCGTCTTTC 60.459 60.000 0.00 0.00 0.00 2.62
2322 2475 1.139947 GCCTCTCCTCGTCTTTCCG 59.860 63.158 0.00 0.00 0.00 4.30
2330 2483 0.521659 CTCGTCTTTCCGAGCGTCTC 60.522 60.000 0.00 0.00 46.64 3.36
2425 2580 2.836981 CAGAGACTTTCATGAGGGGTCT 59.163 50.000 19.84 19.84 39.54 3.85
2479 2634 1.834188 AGGTCCGGCCACAATTTAAG 58.166 50.000 15.92 0.00 40.61 1.85
2522 2677 3.383185 TCAAAACAGACACCCCAAACATC 59.617 43.478 0.00 0.00 0.00 3.06
2524 2679 0.850100 ACAGACACCCCAAACATCCA 59.150 50.000 0.00 0.00 0.00 3.41
2527 2682 1.228429 ACACCCCAAACATCCACGG 60.228 57.895 0.00 0.00 0.00 4.94
2616 2771 0.257039 CCCCTTGTCCAATGGAGAGG 59.743 60.000 19.51 19.51 36.52 3.69
2632 2787 0.105709 GAGGGGAGAGAGAAGGGAGG 60.106 65.000 0.00 0.00 0.00 4.30
2641 2796 1.725182 AGAGAAGGGAGGGAGAGGAAA 59.275 52.381 0.00 0.00 0.00 3.13
2665 2821 2.169561 GTGGTTTGTGTTGGGGTTCAAT 59.830 45.455 0.00 0.00 37.73 2.57
2673 2829 2.176798 TGTTGGGGTTCAATCTTGTCCT 59.823 45.455 6.78 0.00 37.73 3.85
2674 2830 3.230976 GTTGGGGTTCAATCTTGTCCTT 58.769 45.455 6.78 0.00 37.73 3.36
2677 2833 3.017442 GGGGTTCAATCTTGTCCTTAGC 58.983 50.000 6.78 0.00 0.00 3.09
2678 2834 3.561313 GGGGTTCAATCTTGTCCTTAGCA 60.561 47.826 0.00 0.00 0.00 3.49
2684 2840 5.181009 TCAATCTTGTCCTTAGCATGTCTG 58.819 41.667 0.00 0.00 0.00 3.51
2694 2850 2.903357 CATGTCTGGACTCCCCCG 59.097 66.667 2.38 0.00 0.00 5.73
2695 2851 1.685765 CATGTCTGGACTCCCCCGA 60.686 63.158 2.38 0.00 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 5.353956 AGTTTTATCATGTAGCAATCGCACA 59.646 36.000 0.00 0.00 42.27 4.57
25 26 5.678483 CAGTTTTATCATGTAGCAATCGCAC 59.322 40.000 0.00 0.00 42.27 5.34
43 44 2.586648 AATCTCCCGGCTTCAGTTTT 57.413 45.000 0.00 0.00 0.00 2.43
60 61 5.468072 CGAGCTCTCAGCCACAAATATTAAT 59.532 40.000 12.85 0.00 43.77 1.40
65 66 1.824852 TCGAGCTCTCAGCCACAAATA 59.175 47.619 12.85 0.00 43.77 1.40
70 71 1.285578 GATTTCGAGCTCTCAGCCAC 58.714 55.000 12.85 0.00 43.77 5.01
82 83 5.414454 CCACCCACTTTTAATCTGATTTCGA 59.586 40.000 8.38 0.00 0.00 3.71
85 86 5.480422 GGACCACCCACTTTTAATCTGATTT 59.520 40.000 8.38 0.00 34.14 2.17
104 105 7.778853 TGTTTTTATTACTGTAAACCAGGACCA 59.221 33.333 4.11 0.00 46.06 4.02
122 123 7.710475 CACCACCTCTTGTTTCATTGTTTTTAT 59.290 33.333 0.00 0.00 0.00 1.40
123 124 7.038659 CACCACCTCTTGTTTCATTGTTTTTA 58.961 34.615 0.00 0.00 0.00 1.52
124 125 5.874261 CACCACCTCTTGTTTCATTGTTTTT 59.126 36.000 0.00 0.00 0.00 1.94
134 135 0.178990 GGCTCCACCACCTCTTGTTT 60.179 55.000 0.00 0.00 38.86 2.83
156 157 1.594331 AACTCGACAACTTTCAGCCC 58.406 50.000 0.00 0.00 0.00 5.19
165 166 4.025979 CACACTGTAAGGAAACTCGACAAC 60.026 45.833 0.00 0.00 42.68 3.32
168 169 3.489785 CACACACTGTAAGGAAACTCGAC 59.510 47.826 0.00 0.00 42.68 4.20
199 200 2.098607 GGTTAGGGCGCTTATGTTTTCC 59.901 50.000 9.23 0.00 0.00 3.13
239 240 0.588252 GCATGGCATCGGTGATGTAC 59.412 55.000 0.00 3.40 41.60 2.90
241 242 0.469494 TAGCATGGCATCGGTGATGT 59.531 50.000 0.00 0.00 41.60 3.06
242 243 1.817357 ATAGCATGGCATCGGTGATG 58.183 50.000 0.00 0.00 42.37 3.07
243 244 2.156917 CAATAGCATGGCATCGGTGAT 58.843 47.619 0.00 0.00 0.00 3.06
244 245 1.596603 CAATAGCATGGCATCGGTGA 58.403 50.000 0.00 0.00 0.00 4.02
245 246 0.594602 CCAATAGCATGGCATCGGTG 59.405 55.000 0.00 0.00 32.78 4.94
246 247 0.183492 ACCAATAGCATGGCATCGGT 59.817 50.000 0.00 1.87 44.75 4.69
247 248 2.183478 TACCAATAGCATGGCATCGG 57.817 50.000 0.00 0.00 44.75 4.18
261 262 2.371910 TCGTTCGCATGACATACCAA 57.628 45.000 0.00 0.00 0.00 3.67
276 277 2.201732 CGGGATCATTGTCGATTCGTT 58.798 47.619 5.89 0.00 0.00 3.85
278 279 1.139989 CCGGGATCATTGTCGATTCG 58.860 55.000 0.00 0.00 0.00 3.34
280 281 2.170607 AGAACCGGGATCATTGTCGATT 59.829 45.455 6.32 0.00 0.00 3.34
286 287 3.071602 ACCATCTAGAACCGGGATCATTG 59.928 47.826 6.32 0.88 0.00 2.82
288 289 2.634940 CACCATCTAGAACCGGGATCAT 59.365 50.000 6.32 0.00 0.00 2.45
295 296 3.056107 TCACTTTCCACCATCTAGAACCG 60.056 47.826 0.00 0.00 0.00 4.44
296 297 4.553330 TCACTTTCCACCATCTAGAACC 57.447 45.455 0.00 0.00 0.00 3.62
307 308 5.003804 ACAGGTAATGTCATCACTTTCCAC 58.996 41.667 0.00 0.00 37.75 4.02
310 311 8.492673 TGATAACAGGTAATGTCATCACTTTC 57.507 34.615 0.00 0.00 40.93 2.62
333 334 9.337396 ACTCACACTTACAAACTTGATAAATGA 57.663 29.630 0.00 0.00 0.00 2.57
334 335 9.385902 CACTCACACTTACAAACTTGATAAATG 57.614 33.333 0.00 0.00 0.00 2.32
335 336 9.120538 ACACTCACACTTACAAACTTGATAAAT 57.879 29.630 0.00 0.00 0.00 1.40
336 337 8.500753 ACACTCACACTTACAAACTTGATAAA 57.499 30.769 0.00 0.00 0.00 1.40
351 352 3.347216 ACTCAAAGCAAACACTCACACT 58.653 40.909 0.00 0.00 0.00 3.55
358 359 5.348451 ACATCAAACAACTCAAAGCAAACAC 59.652 36.000 0.00 0.00 0.00 3.32
361 362 5.348179 CACACATCAAACAACTCAAAGCAAA 59.652 36.000 0.00 0.00 0.00 3.68
363 364 4.082300 ACACACATCAAACAACTCAAAGCA 60.082 37.500 0.00 0.00 0.00 3.91
364 365 4.423732 ACACACATCAAACAACTCAAAGC 58.576 39.130 0.00 0.00 0.00 3.51
489 493 1.935873 CGTGGCATCGATGATGTTCTT 59.064 47.619 29.20 0.00 41.60 2.52
491 495 1.570813 TCGTGGCATCGATGATGTTC 58.429 50.000 29.20 10.37 41.60 3.18
523 527 2.038557 AGTATGTGGACTGAGGCGTTTT 59.961 45.455 0.00 0.00 0.00 2.43
611 615 5.810587 CAGTGCCGTGAAACATATAGTACTT 59.189 40.000 0.00 0.00 35.74 2.24
646 650 6.106003 GCCTGGGTTTTAAATTATGGTTCAG 58.894 40.000 0.00 0.00 0.00 3.02
691 696 1.439679 GTTGGAACTGGGACATCGTC 58.560 55.000 0.00 0.00 38.20 4.20
748 753 1.386533 ATGTGCATTCAGGTGCTAGC 58.613 50.000 8.10 8.10 45.27 3.42
992 1016 3.196207 TTGGTGCTGCTGGGGAGTC 62.196 63.158 0.00 0.00 0.00 3.36
1065 1092 2.916702 TGATGGATGATGAGTTCGGG 57.083 50.000 0.00 0.00 0.00 5.14
1174 1202 2.092212 TCCCCTCCGTAGACGAATTAGT 60.092 50.000 3.07 0.00 43.02 2.24
1205 1233 2.903357 CGCTCCCCTGCAGTATGT 59.097 61.111 13.81 0.00 39.31 2.29
1391 1425 5.393027 CGATCCGTTCCCTTGAAATGAAAAT 60.393 40.000 0.00 0.00 30.79 1.82
1396 1430 2.627945 TCGATCCGTTCCCTTGAAATG 58.372 47.619 0.00 0.00 30.79 2.32
1397 1431 3.206150 CATCGATCCGTTCCCTTGAAAT 58.794 45.455 0.00 0.00 30.79 2.17
1401 1435 2.024176 AACATCGATCCGTTCCCTTG 57.976 50.000 0.00 0.00 0.00 3.61
1402 1436 2.781681 AAACATCGATCCGTTCCCTT 57.218 45.000 0.00 0.00 0.00 3.95
1409 1443 5.554636 CAGAAGAAGAAAAACATCGATCCG 58.445 41.667 0.00 0.00 0.00 4.18
1581 1615 3.614092 AGCACACGAGATCATGGAAAAT 58.386 40.909 0.00 0.00 0.00 1.82
1640 1783 9.070179 TCTTAAAATTTGGTGAGTAGTTAACCC 57.930 33.333 0.88 0.00 32.70 4.11
1653 1796 8.541899 TGGGAGTTAACTTCTTAAAATTTGGT 57.458 30.769 13.68 0.00 0.00 3.67
1666 1809 5.212745 TGGAATGGTTTTGGGAGTTAACTT 58.787 37.500 10.02 0.00 0.00 2.66
1713 1856 9.706529 AGAATTTTTATTTTAGGAGAGGCATCT 57.293 29.630 0.00 0.00 38.98 2.90
1753 1896 3.493767 AAAGGAGAAGAAGGTGTCACC 57.506 47.619 14.68 14.68 38.99 4.02
1759 1902 4.170468 TCAGCAAAAAGGAGAAGAAGGT 57.830 40.909 0.00 0.00 0.00 3.50
1771 1914 1.317613 ACAGCCGACATCAGCAAAAA 58.682 45.000 0.00 0.00 0.00 1.94
1774 1917 1.291184 CGAACAGCCGACATCAGCAA 61.291 55.000 0.00 0.00 0.00 3.91
1777 1920 3.084579 GCGAACAGCCGACATCAG 58.915 61.111 0.00 0.00 40.81 2.90
1789 1932 3.050275 GTCACCAGGGCAGCGAAC 61.050 66.667 0.00 0.00 0.00 3.95
1794 1937 0.821711 TTTTTCGGTCACCAGGGCAG 60.822 55.000 0.00 0.00 0.00 4.85
1849 1992 4.676986 CGACGAGAATATGACACCCAAGAA 60.677 45.833 0.00 0.00 0.00 2.52
1884 2027 2.226330 CCGAGTTGTGAATCACCCAAA 58.774 47.619 11.24 0.00 32.73 3.28
1890 2033 1.375396 CGGCCCGAGTTGTGAATCA 60.375 57.895 0.00 0.00 0.00 2.57
1943 2086 2.607892 GCACGTTCCAGTCCACTGC 61.608 63.158 0.76 0.00 42.47 4.40
1963 2106 2.668556 CGACTACTGCAACGACATCAGT 60.669 50.000 0.00 0.00 42.89 3.41
1977 2120 2.029290 GTGTTCATGGTCCACGACTACT 60.029 50.000 0.00 0.00 32.47 2.57
2095 2238 1.621072 GGAGTGGAGGGTGAGATGTCT 60.621 57.143 0.00 0.00 0.00 3.41
2125 2268 1.202903 ACGATGGAGGCGGAGTACTAT 60.203 52.381 0.00 0.00 0.00 2.12
2157 2300 0.455972 AGCACACACGCAACAACAAC 60.456 50.000 0.00 0.00 0.00 3.32
2174 2317 3.189910 ACACACACACAATCATCATCAGC 59.810 43.478 0.00 0.00 0.00 4.26
2199 2342 1.298339 GGAGCAACAACACACGCAC 60.298 57.895 0.00 0.00 0.00 5.34
2200 2343 1.451207 AGGAGCAACAACACACGCA 60.451 52.632 0.00 0.00 0.00 5.24
2201 2344 1.009675 CAGGAGCAACAACACACGC 60.010 57.895 0.00 0.00 0.00 5.34
2202 2345 0.027979 CACAGGAGCAACAACACACG 59.972 55.000 0.00 0.00 0.00 4.49
2205 2348 1.094785 ACACACAGGAGCAACAACAC 58.905 50.000 0.00 0.00 0.00 3.32
2232 2383 0.594540 CGGCAACAACACACACATGG 60.595 55.000 0.00 0.00 0.00 3.66
2250 2401 3.491508 GAGCACACGCACACACACG 62.492 63.158 0.00 0.00 42.27 4.49
2258 2409 3.860605 ACACCCAGAGCACACGCA 61.861 61.111 0.00 0.00 42.27 5.24
2266 2417 1.303074 AGCATGCACACACCCAGAG 60.303 57.895 21.98 0.00 0.00 3.35
2267 2418 1.302752 GAGCATGCACACACCCAGA 60.303 57.895 21.98 0.00 0.00 3.86
2271 2422 0.036010 ACCTAGAGCATGCACACACC 60.036 55.000 21.98 1.40 0.00 4.16
2287 2440 1.601759 GCTGCATGGACACACACCT 60.602 57.895 0.00 0.00 0.00 4.00
2322 2475 3.894947 GGGCCGAGAGAGACGCTC 61.895 72.222 0.00 0.00 44.29 5.03
2330 2483 1.417890 AGGACAATAATGGGCCGAGAG 59.582 52.381 0.00 0.00 32.28 3.20
2336 2489 1.134220 TGGACGAGGACAATAATGGGC 60.134 52.381 0.00 0.00 0.00 5.36
2387 2540 7.243604 AGTCTCTGTTCATCATCTTCTTTCT 57.756 36.000 0.00 0.00 0.00 2.52
2388 2541 7.903995 AAGTCTCTGTTCATCATCTTCTTTC 57.096 36.000 0.00 0.00 0.00 2.62
2391 2544 7.002250 TGAAAGTCTCTGTTCATCATCTTCT 57.998 36.000 0.00 0.00 0.00 2.85
2392 2545 7.548427 TCATGAAAGTCTCTGTTCATCATCTTC 59.452 37.037 0.00 0.00 41.44 2.87
2394 2547 6.944096 TCATGAAAGTCTCTGTTCATCATCT 58.056 36.000 0.00 0.00 41.44 2.90
2395 2548 6.258287 CCTCATGAAAGTCTCTGTTCATCATC 59.742 42.308 0.00 0.00 41.44 2.92
2397 2550 5.485620 CCTCATGAAAGTCTCTGTTCATCA 58.514 41.667 0.00 0.00 41.44 3.07
2398 2551 4.874966 CCCTCATGAAAGTCTCTGTTCATC 59.125 45.833 0.00 0.00 41.44 2.92
2401 2554 3.008485 ACCCCTCATGAAAGTCTCTGTTC 59.992 47.826 0.00 0.00 0.00 3.18
2402 2555 2.982488 ACCCCTCATGAAAGTCTCTGTT 59.018 45.455 0.00 0.00 0.00 3.16
2403 2556 2.569404 GACCCCTCATGAAAGTCTCTGT 59.431 50.000 10.64 0.00 0.00 3.41
2404 2557 2.836981 AGACCCCTCATGAAAGTCTCTG 59.163 50.000 13.50 0.00 32.42 3.35
2448 2603 2.947652 GGCCGGACCTAATTAAACCTTC 59.052 50.000 5.05 0.00 34.51 3.46
2457 2612 2.525105 AAATTGTGGCCGGACCTAAT 57.475 45.000 3.83 1.77 40.22 1.73
2485 2640 0.902048 TTTGATGGGCGGCATTGGAA 60.902 50.000 12.47 0.00 0.00 3.53
2487 2642 0.740516 GTTTTGATGGGCGGCATTGG 60.741 55.000 12.47 0.00 0.00 3.16
2548 2703 2.184579 GCTCCACTACCGCTGTCC 59.815 66.667 0.00 0.00 0.00 4.02
2556 2711 2.109181 GATGGCCGGCTCCACTAC 59.891 66.667 28.56 8.18 39.25 2.73
2578 2733 1.900981 TGGACATTTGGTGCACCGG 60.901 57.895 30.07 20.78 43.49 5.28
2616 2771 0.105709 CTCCCTCCCTTCTCTCTCCC 60.106 65.000 0.00 0.00 0.00 4.30
2632 2787 3.699538 ACACAAACCACTTTTTCCTCTCC 59.300 43.478 0.00 0.00 0.00 3.71
2641 2796 1.945580 ACCCCAACACAAACCACTTT 58.054 45.000 0.00 0.00 0.00 2.66
2665 2821 3.055819 GTCCAGACATGCTAAGGACAAGA 60.056 47.826 17.40 0.00 46.15 3.02
2673 2829 1.204146 GGGGAGTCCAGACATGCTAA 58.796 55.000 12.30 0.00 35.00 3.09
2674 2830 0.691078 GGGGGAGTCCAGACATGCTA 60.691 60.000 12.30 0.00 37.22 3.49
2677 2833 1.264749 TTCGGGGGAGTCCAGACATG 61.265 60.000 12.30 0.00 39.44 3.21
2678 2834 1.080354 TTCGGGGGAGTCCAGACAT 59.920 57.895 12.30 0.00 39.44 3.06
2684 2840 2.181445 GAAGTGGTTCGGGGGAGTCC 62.181 65.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.