Multiple sequence alignment - TraesCS7D01G520600

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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 TraesCS7D01G520600 chr7D 100.000 1543 0 0 1 1543 618167486 618165944 0.000000e+00 2850.0
1 TraesCS7D01G520600 chr7D 100.000 642 0 0 1824 2465 618165663 618165022 0.000000e+00 1186.0
2 TraesCS7D01G520600 chr7D 75.090 558 85 36 978 1525 618178413 618177900 6.910000e-51 211.0
3 TraesCS7D01G520600 chr7B 95.446 549 25 0 976 1524 712495383 712494835 0.000000e+00 876.0
4 TraesCS7D01G520600 chr7B 86.064 653 69 15 1824 2464 712494769 712494127 0.000000e+00 682.0
5 TraesCS7D01G520600 chr7B 83.467 375 48 3 17 390 712502086 712501725 1.090000e-88 337.0
6 TraesCS7D01G520600 chr7B 94.444 216 9 1 735 947 712495585 712495370 1.830000e-86 329.0
7 TraesCS7D01G520600 chr7B 75.556 315 51 14 2026 2320 559536833 559537141 5.530000e-27 132.0
8 TraesCS7D01G520600 chr7B 78.333 180 29 7 2033 2203 531799993 531799815 9.320000e-20 108.0
9 TraesCS7D01G520600 chr7A 93.127 582 31 4 967 1540 711900320 711899740 0.000000e+00 845.0
10 TraesCS7D01G520600 chr7A 82.292 672 93 15 6 668 711901201 711900547 2.140000e-155 558.0
11 TraesCS7D01G520600 chr7A 88.937 461 34 8 1824 2272 711899701 711899246 9.960000e-154 553.0
12 TraesCS7D01G520600 chr7A 92.394 355 20 1 979 1326 711907201 711906847 1.320000e-137 499.0
13 TraesCS7D01G520600 chr7A 91.509 212 17 1 2255 2465 711895946 711895735 8.620000e-75 291.0
14 TraesCS7D01G520600 chr7A 73.936 564 83 43 978 1525 711924299 711923784 4.220000e-38 169.0
15 TraesCS7D01G520600 chr7A 90.476 126 9 3 735 858 711900537 711900413 1.960000e-36 163.0
16 TraesCS7D01G520600 chr7A 78.333 180 26 8 2035 2202 690777620 690777442 1.210000e-18 104.0
17 TraesCS7D01G520600 chr7A 91.228 57 5 0 2137 2193 711895887 711895943 7.310000e-11 78.7
18 TraesCS7D01G520600 chr2D 81.159 276 36 10 2034 2298 577685346 577685616 8.930000e-50 207.0
19 TraesCS7D01G520600 chr2D 84.112 107 13 4 2030 2134 105433131 105433235 1.560000e-17 100.0
20 TraesCS7D01G520600 chr5A 80.357 280 36 12 2034 2297 578827361 578827085 6.960000e-46 195.0
21 TraesCS7D01G520600 chr5A 82.609 115 10 5 2095 2200 578827019 578827132 2.610000e-15 93.5
22 TraesCS7D01G520600 chr2B 82.051 156 19 6 2034 2180 776232297 776232452 9.260000e-25 124.0
23 TraesCS7D01G520600 chr1A 78.453 181 26 8 2034 2202 10145063 10144884 3.350000e-19 106.0
24 TraesCS7D01G520600 chr3D 93.478 46 3 0 2149 2194 458315075 458315030 4.400000e-08 69.4


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 TraesCS7D01G520600 chr7D 618165022 618167486 2464 True 2018 2850 100.000000 1 2465 2 chr7D.!!$R2 2464
1 TraesCS7D01G520600 chr7D 618177900 618178413 513 True 211 211 75.090000 978 1525 1 chr7D.!!$R1 547
2 TraesCS7D01G520600 chr7B 712494127 712495585 1458 True 629 876 91.984667 735 2464 3 chr7B.!!$R3 1729
3 TraesCS7D01G520600 chr7A 711895735 711901201 5466 True 482 845 89.268200 6 2465 5 chr7A.!!$R4 2459

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
189 190 0.105964 TTCAGGGTGGTGTGAACTCG 59.894 55.0 0.0 0.0 0.00 4.18 F
538 543 0.106708 ATCCCTACGAATGCACGCAT 59.893 50.0 0.0 0.0 38.46 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1019 1064 0.654683 GCAGATGATCCTCGTGTTGC 59.345 55.0 0.00 0.00 0.00 4.17 R
2439 5836 2.799412 CGGTTCTGCATGAGATAGAAGC 59.201 50.0 15.52 15.52 42.44 3.86 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 4.157607 CAGTGTTTTCAGGGCGGT 57.842 55.556 0.00 0.00 0.00 5.68
19 20 1.101049 CAGTGTTTTCAGGGCGGTGT 61.101 55.000 0.00 0.00 0.00 4.16
26 27 1.407656 TTCAGGGCGGTGTGAACTCT 61.408 55.000 0.00 0.00 0.00 3.24
37 38 1.190643 GTGAACTCTCCTCCTCAGGG 58.809 60.000 0.00 0.00 40.80 4.45
65 66 7.050377 AGGTACATGACAATCCTACATTGAAG 58.950 38.462 0.00 0.00 33.51 3.02
66 67 6.823689 GGTACATGACAATCCTACATTGAAGT 59.176 38.462 0.00 0.00 33.51 3.01
67 68 7.985184 GGTACATGACAATCCTACATTGAAGTA 59.015 37.037 0.00 0.00 33.51 2.24
72 73 6.032956 ACAATCCTACATTGAAGTACGACA 57.967 37.500 1.36 0.00 33.51 4.35
77 78 3.040147 ACATTGAAGTACGACAGTGGG 57.960 47.619 16.75 0.00 0.00 4.61
78 79 1.732259 CATTGAAGTACGACAGTGGGC 59.268 52.381 0.00 0.00 0.00 5.36
82 83 2.488087 AAGTACGACAGTGGGCGAGC 62.488 60.000 13.52 6.44 0.00 5.03
95 96 1.817099 GCGAGCTGGGATTGTGGAG 60.817 63.158 0.00 0.00 0.00 3.86
102 103 0.620556 TGGGATTGTGGAGAAGAGGC 59.379 55.000 0.00 0.00 0.00 4.70
110 111 0.772124 TGGAGAAGAGGCTTTGGGGT 60.772 55.000 0.00 0.00 0.00 4.95
112 113 0.322906 GAGAAGAGGCTTTGGGGTGG 60.323 60.000 0.00 0.00 0.00 4.61
164 165 1.081892 CACAAGATGGGCTTCTGACG 58.918 55.000 0.00 0.00 33.60 4.35
172 173 0.591659 GGGCTTCTGACGGTGTTTTC 59.408 55.000 0.00 0.00 0.00 2.29
173 174 1.305201 GGCTTCTGACGGTGTTTTCA 58.695 50.000 0.00 0.00 0.00 2.69
189 190 0.105964 TTCAGGGTGGTGTGAACTCG 59.894 55.000 0.00 0.00 0.00 4.18
190 191 1.961277 CAGGGTGGTGTGAACTCGC 60.961 63.158 0.00 0.00 0.00 5.03
206 208 4.809513 GCCTCCTTAGGGGTCAGA 57.190 61.111 0.00 0.00 43.87 3.27
208 210 1.051556 GCCTCCTTAGGGGTCAGAGG 61.052 65.000 0.00 0.00 45.74 3.69
240 242 3.716195 CTGGATGGTGGCGGTGGA 61.716 66.667 0.00 0.00 0.00 4.02
241 243 3.014538 TGGATGGTGGCGGTGGAT 61.015 61.111 0.00 0.00 0.00 3.41
270 272 2.487265 GGTTGTTGAGGAGAGGCTTTGA 60.487 50.000 0.00 0.00 0.00 2.69
272 274 1.349026 TGTTGAGGAGAGGCTTTGAGG 59.651 52.381 0.00 0.00 0.00 3.86
278 280 2.264120 GAGAGGCTTTGAGGAGGGCC 62.264 65.000 0.00 0.00 44.38 5.80
302 304 0.179034 GAGGCAGGCTACAATGGGAG 60.179 60.000 0.00 0.00 0.00 4.30
315 317 3.228017 GGGAGCCTAGGAGACGGC 61.228 72.222 14.75 0.00 46.65 5.68
319 321 3.541713 GCCTAGGAGACGGCAGGG 61.542 72.222 14.75 0.00 45.59 4.45
321 323 1.381327 CCTAGGAGACGGCAGGGAA 60.381 63.158 1.05 0.00 0.00 3.97
322 324 1.395826 CCTAGGAGACGGCAGGGAAG 61.396 65.000 1.05 0.00 0.00 3.46
325 327 1.079057 GGAGACGGCAGGGAAGAAC 60.079 63.158 0.00 0.00 0.00 3.01
330 332 1.201429 ACGGCAGGGAAGAACTGGAT 61.201 55.000 0.00 0.00 36.48 3.41
331 333 0.745845 CGGCAGGGAAGAACTGGATG 60.746 60.000 0.00 0.00 36.48 3.51
339 341 3.009584 GGGAAGAACTGGATGGAAGAAGT 59.990 47.826 0.00 0.00 0.00 3.01
342 344 5.495640 GAAGAACTGGATGGAAGAAGTCAT 58.504 41.667 0.00 0.00 0.00 3.06
345 347 2.915604 ACTGGATGGAAGAAGTCATGGT 59.084 45.455 0.00 0.00 0.00 3.55
349 351 2.655090 TGGAAGAAGTCATGGTTGCA 57.345 45.000 0.00 0.00 0.00 4.08
356 358 2.486472 AGTCATGGTTGCAGAGGAAG 57.514 50.000 0.00 0.00 0.00 3.46
360 362 1.841302 ATGGTTGCAGAGGAAGGCGA 61.841 55.000 0.00 0.00 0.00 5.54
362 364 1.293498 GTTGCAGAGGAAGGCGAGA 59.707 57.895 0.00 0.00 0.00 4.04
375 378 3.191078 AGGCGAGAGATGAGAATTTGG 57.809 47.619 0.00 0.00 0.00 3.28
384 387 0.109532 TGAGAATTTGGCGGTGGTCA 59.890 50.000 0.00 0.00 0.00 4.02
387 390 1.545582 AGAATTTGGCGGTGGTCATTG 59.454 47.619 0.00 0.00 0.00 2.82
389 392 0.887933 ATTTGGCGGTGGTCATTGTC 59.112 50.000 0.00 0.00 0.00 3.18
392 395 1.003839 GGCGGTGGTCATTGTCTCA 60.004 57.895 0.00 0.00 0.00 3.27
401 404 2.012673 GTCATTGTCTCACTGGCATCC 58.987 52.381 0.00 0.00 0.00 3.51
421 424 1.603455 CCTCGGCCATTGTGGTTGT 60.603 57.895 2.24 0.00 40.46 3.32
423 426 2.049248 CGGCCATTGTGGTTGTGC 60.049 61.111 2.24 0.00 40.46 4.57
426 429 2.650196 CCATTGTGGTTGTGCGGG 59.350 61.111 0.00 0.00 31.35 6.13
433 436 2.426023 GGTTGTGCGGGAGTGAGT 59.574 61.111 0.00 0.00 0.00 3.41
442 445 0.753262 CGGGAGTGAGTGGGATAAGG 59.247 60.000 0.00 0.00 0.00 2.69
448 451 1.134788 GTGAGTGGGATAAGGTGGTCG 60.135 57.143 0.00 0.00 0.00 4.79
459 462 1.164041 AGGTGGTCGGCGACTTTTTG 61.164 55.000 35.42 0.00 32.47 2.44
516 521 3.756434 CCCCCTAACAAATACACACACAG 59.244 47.826 0.00 0.00 0.00 3.66
520 525 5.705441 CCCTAACAAATACACACACAGTCAT 59.295 40.000 0.00 0.00 0.00 3.06
530 535 2.832129 ACACACAGTCATCCCTACGAAT 59.168 45.455 0.00 0.00 0.00 3.34
531 536 3.190079 CACACAGTCATCCCTACGAATG 58.810 50.000 0.00 0.00 33.61 2.67
532 537 2.205074 CACAGTCATCCCTACGAATGC 58.795 52.381 0.00 0.00 30.59 3.56
534 539 2.205074 CAGTCATCCCTACGAATGCAC 58.795 52.381 0.00 0.00 0.00 4.57
538 543 0.106708 ATCCCTACGAATGCACGCAT 59.893 50.000 0.00 0.00 38.46 4.73
626 637 0.820226 TGGCTCCTCATTCTGTCTCG 59.180 55.000 0.00 0.00 0.00 4.04
642 654 0.174845 CTCGTGGCCGGTCAGAAATA 59.825 55.000 10.28 0.00 33.95 1.40
652 664 1.141053 GGTCAGAAATAGGGCCGTGAT 59.859 52.381 8.57 0.00 0.00 3.06
653 665 2.213499 GTCAGAAATAGGGCCGTGATG 58.787 52.381 8.57 0.00 0.00 3.07
665 677 1.308069 CCGTGATGACCCAAAGGCTG 61.308 60.000 0.00 0.00 36.11 4.85
668 680 1.815003 GTGATGACCCAAAGGCTGAAG 59.185 52.381 0.00 0.00 36.11 3.02
669 681 0.813821 GATGACCCAAAGGCTGAAGC 59.186 55.000 0.00 0.00 41.14 3.86
688 700 3.322466 CACACGGGAGGGCCTCTT 61.322 66.667 31.39 14.53 35.95 2.85
689 701 3.003763 ACACGGGAGGGCCTCTTC 61.004 66.667 31.39 22.00 35.95 2.87
690 702 3.787001 CACGGGAGGGCCTCTTCC 61.787 72.222 31.39 23.51 37.81 3.46
691 703 4.012721 ACGGGAGGGCCTCTTCCT 62.013 66.667 31.39 12.85 39.11 3.36
692 704 2.282446 CGGGAGGGCCTCTTCCTA 59.718 66.667 31.39 0.00 39.11 2.94
693 705 1.382695 CGGGAGGGCCTCTTCCTAA 60.383 63.158 31.39 0.00 39.11 2.69
694 706 0.981277 CGGGAGGGCCTCTTCCTAAA 60.981 60.000 31.39 0.00 39.11 1.85
695 707 1.296002 GGGAGGGCCTCTTCCTAAAA 58.704 55.000 31.39 0.00 38.18 1.52
696 708 1.639108 GGGAGGGCCTCTTCCTAAAAA 59.361 52.381 31.39 0.00 38.18 1.94
877 920 7.309621 GGCACGTATCTCCCTCTATATAAACAA 60.310 40.741 0.00 0.00 0.00 2.83
880 923 8.574737 ACGTATCTCCCTCTATATAAACAACAC 58.425 37.037 0.00 0.00 0.00 3.32
890 933 7.562135 TCTATATAAACAACACCAGGAGAACC 58.438 38.462 0.00 0.00 0.00 3.62
899 942 0.807667 CCAGGAGAACCGAATCGCAG 60.808 60.000 0.00 0.00 41.83 5.18
935 980 1.375013 GCCCCGTAGAACAAGCGAA 60.375 57.895 0.00 0.00 0.00 4.70
936 981 1.359459 GCCCCGTAGAACAAGCGAAG 61.359 60.000 0.00 0.00 0.00 3.79
937 982 0.245539 CCCCGTAGAACAAGCGAAGA 59.754 55.000 0.00 0.00 0.00 2.87
938 983 1.337447 CCCCGTAGAACAAGCGAAGAA 60.337 52.381 0.00 0.00 0.00 2.52
939 984 1.993370 CCCGTAGAACAAGCGAAGAAG 59.007 52.381 0.00 0.00 0.00 2.85
940 985 2.352421 CCCGTAGAACAAGCGAAGAAGA 60.352 50.000 0.00 0.00 0.00 2.87
941 986 3.314553 CCGTAGAACAAGCGAAGAAGAA 58.685 45.455 0.00 0.00 0.00 2.52
942 987 3.365220 CCGTAGAACAAGCGAAGAAGAAG 59.635 47.826 0.00 0.00 0.00 2.85
943 988 4.227538 CGTAGAACAAGCGAAGAAGAAGA 58.772 43.478 0.00 0.00 0.00 2.87
944 989 4.680110 CGTAGAACAAGCGAAGAAGAAGAA 59.320 41.667 0.00 0.00 0.00 2.52
945 990 5.164138 CGTAGAACAAGCGAAGAAGAAGAAG 60.164 44.000 0.00 0.00 0.00 2.85
946 991 4.950050 AGAACAAGCGAAGAAGAAGAAGA 58.050 39.130 0.00 0.00 0.00 2.87
947 992 5.360591 AGAACAAGCGAAGAAGAAGAAGAA 58.639 37.500 0.00 0.00 0.00 2.52
948 993 5.465056 AGAACAAGCGAAGAAGAAGAAGAAG 59.535 40.000 0.00 0.00 0.00 2.85
949 994 4.950050 ACAAGCGAAGAAGAAGAAGAAGA 58.050 39.130 0.00 0.00 0.00 2.87
950 995 5.360591 ACAAGCGAAGAAGAAGAAGAAGAA 58.639 37.500 0.00 0.00 0.00 2.52
951 996 5.465056 ACAAGCGAAGAAGAAGAAGAAGAAG 59.535 40.000 0.00 0.00 0.00 2.85
952 997 5.461032 AGCGAAGAAGAAGAAGAAGAAGA 57.539 39.130 0.00 0.00 0.00 2.87
953 998 5.848406 AGCGAAGAAGAAGAAGAAGAAGAA 58.152 37.500 0.00 0.00 0.00 2.52
954 999 5.925969 AGCGAAGAAGAAGAAGAAGAAGAAG 59.074 40.000 0.00 0.00 0.00 2.85
955 1000 5.923684 GCGAAGAAGAAGAAGAAGAAGAAGA 59.076 40.000 0.00 0.00 0.00 2.87
956 1001 6.422400 GCGAAGAAGAAGAAGAAGAAGAAGAA 59.578 38.462 0.00 0.00 0.00 2.52
957 1002 7.359181 GCGAAGAAGAAGAAGAAGAAGAAGAAG 60.359 40.741 0.00 0.00 0.00 2.85
958 1003 7.865385 CGAAGAAGAAGAAGAAGAAGAAGAAGA 59.135 37.037 0.00 0.00 0.00 2.87
959 1004 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
960 1005 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
961 1006 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
962 1007 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
963 1008 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
964 1009 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
965 1010 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
966 1011 9.898152 AAGAAGAAGAAGAAGAAGAAGAAGAAA 57.102 29.630 0.00 0.00 0.00 2.52
967 1012 9.898152 AGAAGAAGAAGAAGAAGAAGAAGAAAA 57.102 29.630 0.00 0.00 0.00 2.29
970 1015 9.898152 AGAAGAAGAAGAAGAAGAAGAAAAAGA 57.102 29.630 0.00 0.00 0.00 2.52
973 1018 9.898152 AGAAGAAGAAGAAGAAGAAAAAGAAGA 57.102 29.630 0.00 0.00 0.00 2.87
976 1021 9.898152 AGAAGAAGAAGAAGAAAAAGAAGAAGA 57.102 29.630 0.00 0.00 0.00 2.87
1019 1064 2.133553 CATGGCAGCTATGAAGACGAG 58.866 52.381 13.41 0.00 0.00 4.18
1113 1161 4.451435 CGTTAGTCAAAGTCCTCCTTTTCC 59.549 45.833 0.00 0.00 41.51 3.13
1166 1214 3.587797 TCGTAGGCAGAGAATTTCGTT 57.412 42.857 0.00 0.00 0.00 3.85
1526 1584 5.304101 TCTGAACTACTACCCGTTTTGGTAA 59.696 40.000 0.00 0.00 40.30 2.85
1527 1585 5.296748 TGAACTACTACCCGTTTTGGTAAC 58.703 41.667 0.00 0.00 40.30 2.50
1529 1587 2.168326 ACTACCCGTTTTGGTAACCG 57.832 50.000 0.00 0.00 40.30 4.44
1854 1923 6.892658 ATATGTGTTGTCTGGTGCTTAAAA 57.107 33.333 0.00 0.00 0.00 1.52
1903 1972 8.842358 ACGAATGGTCTAGAAACTATGAAAAA 57.158 30.769 0.00 0.00 0.00 1.94
1932 2001 5.793026 TTTTTCTTTCATGTTTTGCGCTT 57.207 30.435 9.73 0.00 0.00 4.68
1943 2012 0.941542 TTTGCGCTTGTGTACCTGAC 59.058 50.000 9.73 0.00 0.00 3.51
1945 2014 2.380410 GCGCTTGTGTACCTGACCG 61.380 63.158 0.00 0.00 0.00 4.79
2146 2228 7.536895 TTTTGAGACATCCACAAATGTTTTG 57.463 32.000 0.00 0.00 39.93 2.44
2154 2236 5.250235 TCCACAAATGTTTTGCGTTCTTA 57.750 34.783 0.06 0.00 0.00 2.10
2167 2249 8.539674 GTTTTGCGTTCTTACAAAATTTCATCT 58.460 29.630 4.43 0.00 44.81 2.90
2310 5707 9.974750 TGAAATTTTGGAAAAACGTAAAACATC 57.025 25.926 0.00 0.00 0.00 3.06
2319 5716 7.807907 GGAAAAACGTAAAACATCTGATCATGT 59.192 33.333 0.00 0.00 38.74 3.21
2348 5745 4.108336 CACATGTCTCTGATACGTCCAAG 58.892 47.826 0.00 0.00 0.00 3.61
2362 5759 7.598869 TGATACGTCCAAGAATATTATGCAGAC 59.401 37.037 0.00 0.00 0.00 3.51
2439 5836 7.881142 TGTCCAATACAAAAATAAGACACCAG 58.119 34.615 0.00 0.00 34.29 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.101049 ACACCGCCCTGAAAACACTG 61.101 55.000 0.00 0.00 0.00 3.66
1 2 1.101049 CACACCGCCCTGAAAACACT 61.101 55.000 0.00 0.00 0.00 3.55
2 3 1.098712 TCACACCGCCCTGAAAACAC 61.099 55.000 0.00 0.00 0.00 3.32
3 4 0.394488 TTCACACCGCCCTGAAAACA 60.394 50.000 0.00 0.00 0.00 2.83
4 5 0.030235 GTTCACACCGCCCTGAAAAC 59.970 55.000 0.00 0.00 0.00 2.43
9 10 1.374758 GAGAGTTCACACCGCCCTG 60.375 63.158 0.00 0.00 0.00 4.45
14 15 0.528470 GAGGAGGAGAGTTCACACCG 59.472 60.000 0.00 0.00 0.00 4.94
17 18 1.551099 CCCTGAGGAGGAGAGTTCACA 60.551 57.143 0.00 0.00 42.93 3.58
19 20 0.041833 CCCCTGAGGAGGAGAGTTCA 59.958 60.000 0.00 0.00 42.93 3.18
37 38 3.709653 TGTAGGATTGTCATGTACCTCCC 59.290 47.826 0.00 0.00 32.00 4.30
44 45 6.535150 CGTACTTCAATGTAGGATTGTCATGT 59.465 38.462 0.00 0.00 32.07 3.21
47 48 6.097356 GTCGTACTTCAATGTAGGATTGTCA 58.903 40.000 0.00 0.00 38.82 3.58
65 66 2.506438 GCTCGCCCACTGTCGTAC 60.506 66.667 0.00 0.00 0.00 3.67
66 67 2.675423 AGCTCGCCCACTGTCGTA 60.675 61.111 0.00 0.00 0.00 3.43
67 68 4.363990 CAGCTCGCCCACTGTCGT 62.364 66.667 0.00 0.00 0.00 4.34
72 73 3.011517 AATCCCAGCTCGCCCACT 61.012 61.111 0.00 0.00 0.00 4.00
77 78 1.817099 CTCCACAATCCCAGCTCGC 60.817 63.158 0.00 0.00 0.00 5.03
78 79 0.250234 TTCTCCACAATCCCAGCTCG 59.750 55.000 0.00 0.00 0.00 5.03
82 83 1.407989 GCCTCTTCTCCACAATCCCAG 60.408 57.143 0.00 0.00 0.00 4.45
85 86 2.751806 CAAAGCCTCTTCTCCACAATCC 59.248 50.000 0.00 0.00 0.00 3.01
95 96 1.304464 CCCACCCCAAAGCCTCTTC 60.304 63.158 0.00 0.00 0.00 2.87
102 103 2.036256 CTCAGGCCCACCCCAAAG 59.964 66.667 0.00 0.00 36.11 2.77
110 111 2.368594 CCTACCTCCTCAGGCCCA 59.631 66.667 0.00 0.00 45.05 5.36
136 137 1.450312 CCATCTTGTGGGCTCCGAC 60.450 63.158 0.00 0.00 44.79 4.79
161 162 0.464916 ACCACCCTGAAAACACCGTC 60.465 55.000 0.00 0.00 0.00 4.79
164 165 0.744281 CACACCACCCTGAAAACACC 59.256 55.000 0.00 0.00 0.00 4.16
172 173 1.961277 GCGAGTTCACACCACCCTG 60.961 63.158 0.00 0.00 0.00 4.45
173 174 2.426023 GCGAGTTCACACCACCCT 59.574 61.111 0.00 0.00 0.00 4.34
189 190 1.051556 CCTCTGACCCCTAAGGAGGC 61.052 65.000 0.00 0.00 42.21 4.70
190 191 0.637195 TCCTCTGACCCCTAAGGAGG 59.363 60.000 0.00 0.00 43.35 4.30
204 206 3.370104 CAGTGTAGGAATGTCCTCCTCT 58.630 50.000 0.00 0.00 45.66 3.69
206 208 2.044492 TCCAGTGTAGGAATGTCCTCCT 59.956 50.000 0.00 0.00 45.66 3.69
208 210 3.181461 CCATCCAGTGTAGGAATGTCCTC 60.181 52.174 0.00 0.00 45.66 3.71
225 227 2.516930 CATCCACCGCCACCATCC 60.517 66.667 0.00 0.00 0.00 3.51
240 242 2.240667 CTCCTCAACAACCCCATCTCAT 59.759 50.000 0.00 0.00 0.00 2.90
241 243 1.630369 CTCCTCAACAACCCCATCTCA 59.370 52.381 0.00 0.00 0.00 3.27
278 280 0.835941 ATTGTAGCCTGCCTCCTCAG 59.164 55.000 0.00 0.00 0.00 3.35
290 292 1.346068 CTCCTAGGCTCCCATTGTAGC 59.654 57.143 2.96 0.75 38.03 3.58
306 308 1.229209 TTCTTCCCTGCCGTCTCCT 60.229 57.895 0.00 0.00 0.00 3.69
315 317 2.573462 TCTTCCATCCAGTTCTTCCCTG 59.427 50.000 0.00 0.00 0.00 4.45
319 321 4.899502 TGACTTCTTCCATCCAGTTCTTC 58.100 43.478 0.00 0.00 0.00 2.87
321 323 4.324099 CCATGACTTCTTCCATCCAGTTCT 60.324 45.833 0.00 0.00 0.00 3.01
322 324 3.944015 CCATGACTTCTTCCATCCAGTTC 59.056 47.826 0.00 0.00 0.00 3.01
325 327 3.641434 ACCATGACTTCTTCCATCCAG 57.359 47.619 0.00 0.00 0.00 3.86
330 332 2.106338 TCTGCAACCATGACTTCTTCCA 59.894 45.455 0.00 0.00 0.00 3.53
331 333 2.746362 CTCTGCAACCATGACTTCTTCC 59.254 50.000 0.00 0.00 0.00 3.46
339 341 0.322816 GCCTTCCTCTGCAACCATGA 60.323 55.000 0.00 0.00 0.00 3.07
342 344 2.032528 CGCCTTCCTCTGCAACCA 59.967 61.111 0.00 0.00 0.00 3.67
345 347 0.900182 TCTCTCGCCTTCCTCTGCAA 60.900 55.000 0.00 0.00 0.00 4.08
349 351 1.214175 TCTCATCTCTCGCCTTCCTCT 59.786 52.381 0.00 0.00 0.00 3.69
356 358 1.601430 GCCAAATTCTCATCTCTCGCC 59.399 52.381 0.00 0.00 0.00 5.54
360 362 2.636830 CACCGCCAAATTCTCATCTCT 58.363 47.619 0.00 0.00 0.00 3.10
362 364 1.004745 ACCACCGCCAAATTCTCATCT 59.995 47.619 0.00 0.00 0.00 2.90
375 378 0.320771 AGTGAGACAATGACCACCGC 60.321 55.000 0.00 0.00 0.00 5.68
384 387 0.745845 GCGGATGCCAGTGAGACAAT 60.746 55.000 0.00 0.00 33.98 2.71
407 410 2.049248 CGCACAACCACAATGGCC 60.049 61.111 0.00 0.00 42.67 5.36
408 411 2.049248 CCGCACAACCACAATGGC 60.049 61.111 0.00 0.00 42.67 4.40
421 424 0.616395 TTATCCCACTCACTCCCGCA 60.616 55.000 0.00 0.00 0.00 5.69
423 426 0.753262 CCTTATCCCACTCACTCCCG 59.247 60.000 0.00 0.00 0.00 5.14
426 429 2.168728 GACCACCTTATCCCACTCACTC 59.831 54.545 0.00 0.00 0.00 3.51
433 436 2.727392 CGCCGACCACCTTATCCCA 61.727 63.158 0.00 0.00 0.00 4.37
442 445 1.193874 CTACAAAAAGTCGCCGACCAC 59.806 52.381 14.60 0.00 32.18 4.16
448 451 0.240145 GCCACCTACAAAAAGTCGCC 59.760 55.000 0.00 0.00 0.00 5.54
494 497 3.756434 CTGTGTGTGTATTTGTTAGGGGG 59.244 47.826 0.00 0.00 0.00 5.40
499 504 5.703592 GGGATGACTGTGTGTGTATTTGTTA 59.296 40.000 0.00 0.00 0.00 2.41
500 505 4.518970 GGGATGACTGTGTGTGTATTTGTT 59.481 41.667 0.00 0.00 0.00 2.83
504 509 4.381612 CGTAGGGATGACTGTGTGTGTATT 60.382 45.833 0.00 0.00 0.00 1.89
505 510 3.130516 CGTAGGGATGACTGTGTGTGTAT 59.869 47.826 0.00 0.00 0.00 2.29
516 521 1.209128 CGTGCATTCGTAGGGATGAC 58.791 55.000 7.91 2.81 0.00 3.06
520 525 0.809636 CATGCGTGCATTCGTAGGGA 60.810 55.000 4.24 0.00 33.90 4.20
582 593 6.823497 AGTGCTAGTCACCTGTTACTAAAAA 58.177 36.000 11.98 0.00 46.81 1.94
583 594 6.415206 AGTGCTAGTCACCTGTTACTAAAA 57.585 37.500 11.98 0.00 46.81 1.52
584 595 6.220930 CAAGTGCTAGTCACCTGTTACTAAA 58.779 40.000 11.98 0.00 46.81 1.85
585 596 5.279306 CCAAGTGCTAGTCACCTGTTACTAA 60.279 44.000 11.98 0.00 46.81 2.24
586 597 4.219944 CCAAGTGCTAGTCACCTGTTACTA 59.780 45.833 11.98 0.00 46.81 1.82
587 598 3.006967 CCAAGTGCTAGTCACCTGTTACT 59.993 47.826 11.98 0.00 46.81 2.24
588 599 3.326747 CCAAGTGCTAGTCACCTGTTAC 58.673 50.000 11.98 0.00 46.81 2.50
589 600 2.289444 GCCAAGTGCTAGTCACCTGTTA 60.289 50.000 11.98 0.00 46.81 2.41
590 601 1.543429 GCCAAGTGCTAGTCACCTGTT 60.543 52.381 11.98 0.92 46.81 3.16
591 602 0.035458 GCCAAGTGCTAGTCACCTGT 59.965 55.000 11.98 0.00 46.81 4.00
592 603 2.846371 GCCAAGTGCTAGTCACCTG 58.154 57.895 11.98 10.01 46.81 4.00
619 630 3.633094 CTGACCGGCCACGAGACAG 62.633 68.421 0.00 0.19 44.60 3.51
626 637 0.463833 CCCTATTTCTGACCGGCCAC 60.464 60.000 0.00 0.00 0.00 5.01
642 654 2.484287 CTTTGGGTCATCACGGCCCT 62.484 60.000 2.99 0.00 42.77 5.19
652 664 4.500265 GCTTCAGCCTTTGGGTCA 57.500 55.556 0.00 0.00 34.31 4.02
671 683 3.316573 GAAGAGGCCCTCCCGTGTG 62.317 68.421 7.26 0.00 39.21 3.82
672 684 3.003763 GAAGAGGCCCTCCCGTGT 61.004 66.667 7.26 0.00 39.21 4.49
673 685 2.873557 TAGGAAGAGGCCCTCCCGTG 62.874 65.000 7.26 0.00 39.21 4.94
674 686 2.177529 TTAGGAAGAGGCCCTCCCGT 62.178 60.000 7.26 4.23 39.21 5.28
676 688 1.296002 TTTTAGGAAGAGGCCCTCCC 58.704 55.000 7.26 2.09 35.30 4.30
877 920 0.246635 CGATTCGGTTCTCCTGGTGT 59.753 55.000 0.00 0.00 0.00 4.16
880 923 0.807667 CTGCGATTCGGTTCTCCTGG 60.808 60.000 8.34 0.00 0.00 4.45
890 933 1.253116 CAATGTGTTGCTGCGATTCG 58.747 50.000 0.62 0.62 0.00 3.34
935 980 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
936 981 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
937 982 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
938 983 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
939 984 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
940 985 9.898152 TTTCTTCTTCTTCTTCTTCTTCTTCTT 57.102 29.630 0.00 0.00 0.00 2.52
941 986 9.898152 TTTTCTTCTTCTTCTTCTTCTTCTTCT 57.102 29.630 0.00 0.00 0.00 2.85
944 989 9.898152 TCTTTTTCTTCTTCTTCTTCTTCTTCT 57.102 29.630 0.00 0.00 0.00 2.85
947 992 9.898152 TCTTCTTTTTCTTCTTCTTCTTCTTCT 57.102 29.630 0.00 0.00 0.00 2.85
950 995 9.898152 TCTTCTTCTTTTTCTTCTTCTTCTTCT 57.102 29.630 0.00 0.00 0.00 2.85
953 998 9.898152 TCTTCTTCTTCTTTTTCTTCTTCTTCT 57.102 29.630 0.00 0.00 0.00 2.85
956 1001 9.898152 TCTTCTTCTTCTTCTTTTTCTTCTTCT 57.102 29.630 0.00 0.00 0.00 2.85
959 1004 9.898152 TCTTCTTCTTCTTCTTCTTTTTCTTCT 57.102 29.630 0.00 0.00 0.00 2.85
962 1007 9.898152 TCTTCTTCTTCTTCTTCTTCTTTTTCT 57.102 29.630 0.00 0.00 0.00 2.52
963 1008 9.929722 GTCTTCTTCTTCTTCTTCTTCTTTTTC 57.070 33.333 0.00 0.00 0.00 2.29
964 1009 9.454859 TGTCTTCTTCTTCTTCTTCTTCTTTTT 57.545 29.630 0.00 0.00 0.00 1.94
965 1010 8.888716 GTGTCTTCTTCTTCTTCTTCTTCTTTT 58.111 33.333 0.00 0.00 0.00 2.27
966 1011 7.497579 GGTGTCTTCTTCTTCTTCTTCTTCTTT 59.502 37.037 0.00 0.00 0.00 2.52
967 1012 6.989759 GGTGTCTTCTTCTTCTTCTTCTTCTT 59.010 38.462 0.00 0.00 0.00 2.52
968 1013 6.521162 GGTGTCTTCTTCTTCTTCTTCTTCT 58.479 40.000 0.00 0.00 0.00 2.85
969 1014 5.404066 CGGTGTCTTCTTCTTCTTCTTCTTC 59.596 44.000 0.00 0.00 0.00 2.87
970 1015 5.293560 CGGTGTCTTCTTCTTCTTCTTCTT 58.706 41.667 0.00 0.00 0.00 2.52
971 1016 4.262249 CCGGTGTCTTCTTCTTCTTCTTCT 60.262 45.833 0.00 0.00 0.00 2.85
972 1017 3.991121 CCGGTGTCTTCTTCTTCTTCTTC 59.009 47.826 0.00 0.00 0.00 2.87
973 1018 3.804063 GCCGGTGTCTTCTTCTTCTTCTT 60.804 47.826 1.90 0.00 0.00 2.52
974 1019 2.289133 GCCGGTGTCTTCTTCTTCTTCT 60.289 50.000 1.90 0.00 0.00 2.85
975 1020 2.070028 GCCGGTGTCTTCTTCTTCTTC 58.930 52.381 1.90 0.00 0.00 2.87
976 1021 1.605712 CGCCGGTGTCTTCTTCTTCTT 60.606 52.381 6.91 0.00 0.00 2.52
1019 1064 0.654683 GCAGATGATCCTCGTGTTGC 59.345 55.000 0.00 0.00 0.00 4.17
1056 1101 3.083997 ATGAGGAGGGTGGCCGTC 61.084 66.667 0.00 0.00 37.65 4.79
1166 1214 1.107114 TCAGGTTGGCGCAAAAAGAA 58.893 45.000 10.83 0.00 0.00 2.52
1424 1482 3.594775 CACCAGCAGGCGCAACAA 61.595 61.111 10.83 0.00 42.27 2.83
1832 1901 6.892658 ATTTTAAGCACCAGACAACACATA 57.107 33.333 0.00 0.00 0.00 2.29
1839 1908 5.772672 ACCACAATATTTTAAGCACCAGACA 59.227 36.000 0.00 0.00 0.00 3.41
1854 1923 4.277174 TCAAGCAAAACACGACCACAATAT 59.723 37.500 0.00 0.00 0.00 1.28
1910 1979 5.121454 ACAAGCGCAAAACATGAAAGAAAAA 59.879 32.000 11.47 0.00 0.00 1.94
1932 2001 3.827876 TGAAAGATACGGTCAGGTACACA 59.172 43.478 0.00 0.00 0.00 3.72
1988 2057 5.891551 GGGGAGCCTTTAGAACATTTTCATA 59.108 40.000 0.00 0.00 33.72 2.15
2111 2186 9.076781 TGTGGATGTCTCAAAATTTCAGAATTA 57.923 29.630 0.00 0.00 34.44 1.40
2134 2209 5.940603 TGTAAGAACGCAAAACATTTGTG 57.059 34.783 13.21 13.21 36.12 3.33
2146 2228 8.722342 TTGTAGATGAAATTTTGTAAGAACGC 57.278 30.769 0.00 0.00 0.00 4.84
2167 2249 6.127451 TGAGAGCTCCTCGAATGTTATTTGTA 60.127 38.462 10.93 0.00 44.92 2.41
2245 2328 3.066760 ACGAGCCCTCAACAAAAGAAAAG 59.933 43.478 0.00 0.00 0.00 2.27
2246 2329 3.020984 ACGAGCCCTCAACAAAAGAAAA 58.979 40.909 0.00 0.00 0.00 2.29
2294 5691 8.629986 CACATGATCAGATGTTTTACGTTTTTC 58.370 33.333 0.00 0.00 34.18 2.29
2297 5694 6.429692 TCCACATGATCAGATGTTTTACGTTT 59.570 34.615 0.00 0.00 34.18 3.60
2437 5834 3.808726 GGTTCTGCATGAGATAGAAGCTG 59.191 47.826 17.04 0.00 42.53 4.24
2439 5836 2.799412 CGGTTCTGCATGAGATAGAAGC 59.201 50.000 15.52 15.52 42.44 3.86


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

AutoCloner maintained by Alex Coulton.