Multiple sequence alignment - TraesCS7D01G188100

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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 TraesCS7D01G188100 chr7D 100.000 2937 0 0 1 2937 140734081 140731145 0.000000e+00 5424
1 TraesCS7D01G188100 chr7D 79.017 529 104 5 1396 1921 140327717 140327193 3.600000e-94 355
2 TraesCS7D01G188100 chr7B 87.512 2146 173 51 4 2097 105831827 105829725 0.000000e+00 2390
3 TraesCS7D01G188100 chr7B 79.206 529 103 5 1396 1921 105559491 105558967 7.740000e-96 361
4 TraesCS7D01G188100 chr7A 84.567 1283 95 45 46 1263 142645500 142644256 0.000000e+00 1177
5 TraesCS7D01G188100 chr7A 93.273 773 46 4 1318 2090 142643983 142643217 0.000000e+00 1134
6 TraesCS7D01G188100 chr7A 85.326 736 95 9 2211 2936 612663626 612662894 0.000000e+00 749
7 TraesCS7D01G188100 chr7A 79.206 529 103 5 1396 1921 142158554 142158030 7.740000e-96 361
8 TraesCS7D01G188100 chr7A 86.937 222 17 6 1869 2088 142620951 142620740 3.780000e-59 239
9 TraesCS7D01G188100 chr7A 91.262 103 7 1 2065 2165 142643215 142643113 3.950000e-29 139
10 TraesCS7D01G188100 chr3B 86.277 736 91 5 2211 2937 112234574 112233840 0.000000e+00 791
11 TraesCS7D01G188100 chr3D 86.198 739 82 10 2211 2937 18306781 18306051 0.000000e+00 782
12 TraesCS7D01G188100 chr5D 86.043 738 83 11 2211 2937 410623323 410622595 0.000000e+00 774
13 TraesCS7D01G188100 chr5D 84.918 736 99 6 2211 2937 272965282 272966014 0.000000e+00 734
14 TraesCS7D01G188100 chr3A 85.675 733 97 3 2211 2935 724917633 724916901 0.000000e+00 765
15 TraesCS7D01G188100 chr2B 85.445 742 86 13 2211 2937 617029249 617029983 0.000000e+00 752
16 TraesCS7D01G188100 chr4D 85.115 739 92 10 2211 2937 203625814 203626546 0.000000e+00 739
17 TraesCS7D01G188100 chr5B 84.980 739 97 12 2211 2937 136657265 136656529 0.000000e+00 737


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 TraesCS7D01G188100 chr7D 140731145 140734081 2936 True 5424.000000 5424 100.000000 1 2937 1 chr7D.!!$R2 2936
1 TraesCS7D01G188100 chr7D 140327193 140327717 524 True 355.000000 355 79.017000 1396 1921 1 chr7D.!!$R1 525
2 TraesCS7D01G188100 chr7B 105829725 105831827 2102 True 2390.000000 2390 87.512000 4 2097 1 chr7B.!!$R2 2093
3 TraesCS7D01G188100 chr7B 105558967 105559491 524 True 361.000000 361 79.206000 1396 1921 1 chr7B.!!$R1 525
4 TraesCS7D01G188100 chr7A 142643113 142645500 2387 True 816.666667 1177 89.700667 46 2165 3 chr7A.!!$R4 2119
5 TraesCS7D01G188100 chr7A 612662894 612663626 732 True 749.000000 749 85.326000 2211 2936 1 chr7A.!!$R3 725
6 TraesCS7D01G188100 chr7A 142158030 142158554 524 True 361.000000 361 79.206000 1396 1921 1 chr7A.!!$R1 525
7 TraesCS7D01G188100 chr3B 112233840 112234574 734 True 791.000000 791 86.277000 2211 2937 1 chr3B.!!$R1 726
8 TraesCS7D01G188100 chr3D 18306051 18306781 730 True 782.000000 782 86.198000 2211 2937 1 chr3D.!!$R1 726
9 TraesCS7D01G188100 chr5D 410622595 410623323 728 True 774.000000 774 86.043000 2211 2937 1 chr5D.!!$R1 726
10 TraesCS7D01G188100 chr5D 272965282 272966014 732 False 734.000000 734 84.918000 2211 2937 1 chr5D.!!$F1 726
11 TraesCS7D01G188100 chr3A 724916901 724917633 732 True 765.000000 765 85.675000 2211 2935 1 chr3A.!!$R1 724
12 TraesCS7D01G188100 chr2B 617029249 617029983 734 False 752.000000 752 85.445000 2211 2937 1 chr2B.!!$F1 726
13 TraesCS7D01G188100 chr4D 203625814 203626546 732 False 739.000000 739 85.115000 2211 2937 1 chr4D.!!$F1 726
14 TraesCS7D01G188100 chr5B 136656529 136657265 736 True 737.000000 737 84.980000 2211 2937 1 chr5B.!!$R1 726

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
305 352 0.030101 CGATCTCTCCTCGTGAAGGC 59.970 60.0 0.00 0.0 45.78 4.35 F
971 1060 0.036164 TGCGCTGTAAACATCTGGGT 59.964 50.0 9.73 0.0 0.00 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1931 2270 0.963962 ACCAAACCAGCTGCTCAATG 59.036 50.0 8.66 2.33 0.00 2.82 R
2788 3180 0.037447 GATGGGGAGATTGCTAGGGC 59.963 60.0 0.00 0.00 39.26 5.19 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
41 42 9.549509 GTTAAGATCGCACACATGTTTATAAAA 57.450 29.630 0.00 0.00 0.00 1.52
132 135 2.478831 CTCCTAGCCTGCTCGATTTTC 58.521 52.381 0.00 0.00 0.00 2.29
146 156 1.063616 GATTTTCCTTTCGGCGGTAGC 59.936 52.381 7.21 0.00 44.18 3.58
196 206 2.641439 GATGGGCTGCCTGACTCGAG 62.641 65.000 19.68 11.84 0.00 4.04
200 210 1.153862 GCTGCCTGACTCGAGACTG 60.154 63.158 21.68 16.74 0.00 3.51
206 216 0.170116 CTGACTCGAGACTGGTGAGC 59.830 60.000 21.68 0.00 32.98 4.26
208 218 0.170116 GACTCGAGACTGGTGAGCAG 59.830 60.000 21.68 10.51 32.98 4.24
264 311 7.468141 TCATATGTCAGAGTTGTAGACTTGT 57.532 36.000 1.90 0.00 39.19 3.16
265 312 8.575649 TCATATGTCAGAGTTGTAGACTTGTA 57.424 34.615 1.90 0.00 39.19 2.41
266 313 8.678199 TCATATGTCAGAGTTGTAGACTTGTAG 58.322 37.037 1.90 0.00 39.19 2.74
267 314 6.902771 ATGTCAGAGTTGTAGACTTGTAGT 57.097 37.500 0.00 0.00 39.19 2.73
268 315 6.073327 TGTCAGAGTTGTAGACTTGTAGTG 57.927 41.667 0.00 0.00 39.19 2.74
269 316 4.918583 GTCAGAGTTGTAGACTTGTAGTGC 59.081 45.833 0.00 0.00 39.19 4.40
270 317 4.583073 TCAGAGTTGTAGACTTGTAGTGCA 59.417 41.667 0.00 0.00 39.19 4.57
271 318 4.681942 CAGAGTTGTAGACTTGTAGTGCAC 59.318 45.833 9.40 9.40 39.19 4.57
272 319 3.639538 AGTTGTAGACTTGTAGTGCACG 58.360 45.455 12.01 0.00 33.92 5.34
273 320 3.067742 AGTTGTAGACTTGTAGTGCACGT 59.932 43.478 12.01 2.10 33.92 4.49
274 321 4.276678 AGTTGTAGACTTGTAGTGCACGTA 59.723 41.667 12.01 1.42 33.92 3.57
275 322 4.151258 TGTAGACTTGTAGTGCACGTAC 57.849 45.455 12.01 14.15 29.12 3.67
278 325 2.621998 AGACTTGTAGTGCACGTACTGT 59.378 45.455 12.01 15.14 29.12 3.55
295 342 3.207778 ACTGTACTAGTGCGATCTCTCC 58.792 50.000 5.39 0.00 38.49 3.71
297 344 3.468770 TGTACTAGTGCGATCTCTCCTC 58.531 50.000 5.39 0.00 0.00 3.71
298 345 1.588674 ACTAGTGCGATCTCTCCTCG 58.411 55.000 0.00 0.00 39.11 4.63
299 346 1.134340 ACTAGTGCGATCTCTCCTCGT 60.134 52.381 0.00 0.00 38.37 4.18
302 349 0.452184 GTGCGATCTCTCCTCGTGAA 59.548 55.000 0.00 0.00 38.37 3.18
303 350 0.735471 TGCGATCTCTCCTCGTGAAG 59.265 55.000 0.00 0.00 38.37 3.02
305 352 0.030101 CGATCTCTCCTCGTGAAGGC 59.970 60.000 0.00 0.00 45.78 4.35
310 365 3.068691 TCCTCGTGAAGGCGGGAG 61.069 66.667 0.00 0.00 45.78 4.30
315 370 2.646175 CGTGAAGGCGGGAGGAGAA 61.646 63.158 0.00 0.00 0.00 2.87
319 374 2.854187 GAAGGCGGGAGGAGAAACGG 62.854 65.000 0.00 0.00 0.00 4.44
320 375 3.387947 GGCGGGAGGAGAAACGGA 61.388 66.667 0.00 0.00 0.00 4.69
326 381 0.253327 GGAGGAGAAACGGATTGGCT 59.747 55.000 0.00 0.00 0.00 4.75
403 474 3.619054 GCTCGATAGCTGCGGTTC 58.381 61.111 10.32 0.00 45.85 3.62
405 476 1.658717 CTCGATAGCTGCGGTTCCG 60.659 63.158 6.90 6.90 0.00 4.30
417 488 2.035449 TGCGGTTCCGTGGAATATCTAG 59.965 50.000 12.81 0.00 36.45 2.43
421 492 5.218139 CGGTTCCGTGGAATATCTAGTAAC 58.782 45.833 4.36 0.00 36.45 2.50
442 513 1.086696 CGTCGCTGACCAAATGGAAT 58.913 50.000 6.42 0.00 38.94 3.01
444 515 2.030457 CGTCGCTGACCAAATGGAATAC 59.970 50.000 6.42 0.00 38.94 1.89
472 546 5.193663 TCATTTCGAAATGCAAAGGTGAA 57.806 34.783 35.42 18.74 44.15 3.18
476 550 4.582701 TCGAAATGCAAAGGTGAAACAT 57.417 36.364 0.00 0.00 39.98 2.71
523 597 1.154301 CATTTTGTCGTTCCGCGGG 60.154 57.895 27.83 9.82 41.72 6.13
543 617 2.353208 GGAGTTGACGAAGCAGAGTCAT 60.353 50.000 8.57 0.00 45.40 3.06
574 648 2.017049 ACACTTGCAGAACACCAAGTC 58.983 47.619 3.28 0.00 46.22 3.01
581 655 1.666872 GAACACCAAGTCGGACCGG 60.667 63.158 15.25 0.00 38.63 5.28
582 656 3.819877 AACACCAAGTCGGACCGGC 62.820 63.158 11.44 11.44 38.63 6.13
583 657 4.308458 CACCAAGTCGGACCGGCA 62.308 66.667 22.54 0.00 38.63 5.69
584 658 4.003788 ACCAAGTCGGACCGGCAG 62.004 66.667 22.54 12.61 38.63 4.85
614 692 1.354337 CGTGCCGTTCCAGTGATCTG 61.354 60.000 0.00 0.00 41.01 2.90
617 695 1.296392 CCGTTCCAGTGATCTGCCA 59.704 57.895 0.00 0.00 40.09 4.92
620 698 1.609061 CGTTCCAGTGATCTGCCAAGT 60.609 52.381 0.00 0.00 40.09 3.16
621 699 2.353704 CGTTCCAGTGATCTGCCAAGTA 60.354 50.000 0.00 0.00 40.09 2.24
622 700 3.003480 GTTCCAGTGATCTGCCAAGTAC 58.997 50.000 0.00 0.00 40.09 2.73
623 701 1.204704 TCCAGTGATCTGCCAAGTACG 59.795 52.381 0.00 0.00 40.09 3.67
624 702 1.066858 CCAGTGATCTGCCAAGTACGT 60.067 52.381 0.00 0.00 40.09 3.57
634 715 1.545582 GCCAAGTACGTACACAGGGTA 59.454 52.381 26.55 0.00 0.00 3.69
651 732 4.636206 CAGGGTAAAAATAGCTGGACTGAC 59.364 45.833 0.00 0.00 0.00 3.51
664 745 1.630148 GACTGACCACATACGCTCAC 58.370 55.000 0.00 0.00 0.00 3.51
673 754 1.135199 ACATACGCTCACCCGTTACTG 60.135 52.381 0.00 0.00 42.20 2.74
708 789 1.461127 GTGATGTTTCTCTGGACACGC 59.539 52.381 0.00 0.00 0.00 5.34
768 850 3.868077 CACCCTAGCTTGAATTCTCTTCG 59.132 47.826 7.05 0.00 0.00 3.79
787 874 2.281070 CCCAAGCACGTGCAGAGT 60.281 61.111 39.21 18.73 45.16 3.24
816 905 4.728110 TTCTCCCCGGTCTCGCGA 62.728 66.667 9.26 9.26 34.56 5.87
875 964 0.400213 CCCCTATAAATGGCCGCTGA 59.600 55.000 0.00 0.00 0.00 4.26
898 987 2.584064 CAGCCGTGGCCTACATCA 59.416 61.111 7.39 0.00 43.17 3.07
899 988 1.078497 CAGCCGTGGCCTACATCAA 60.078 57.895 7.39 0.00 43.17 2.57
963 1052 1.135972 CCATCAGTGTGCGCTGTAAAC 60.136 52.381 9.73 0.00 37.70 2.01
971 1060 0.036164 TGCGCTGTAAACATCTGGGT 59.964 50.000 9.73 0.00 0.00 4.51
975 1064 2.159627 CGCTGTAAACATCTGGGTTGTC 59.840 50.000 0.00 0.00 0.00 3.18
985 1075 2.519780 GGGTTGTCGGGTTTGGCA 60.520 61.111 0.00 0.00 0.00 4.92
1005 1095 4.503817 GGCAACATACTGATCTAGATGGCA 60.504 45.833 10.74 1.75 0.00 4.92
1009 1099 6.047511 ACATACTGATCTAGATGGCATTCC 57.952 41.667 10.74 0.00 0.00 3.01
1215 1305 4.477975 GTCCAGGTCGCCGTCTCG 62.478 72.222 0.00 0.00 0.00 4.04
1237 1331 4.352887 GCTCATCGTCTTCAAGGTACTAC 58.647 47.826 0.00 0.00 38.49 2.73
1239 1333 5.393243 GCTCATCGTCTTCAAGGTACTACTT 60.393 44.000 0.00 0.00 38.49 2.24
1241 1335 4.675190 TCGTCTTCAAGGTACTACTTCG 57.325 45.455 0.00 0.00 38.49 3.79
1250 1344 2.158490 AGGTACTACTTCGATCCCCTCC 60.158 54.545 0.00 0.00 36.02 4.30
1260 1354 2.105806 GATCCCCTCCTCGTGCCATC 62.106 65.000 0.00 0.00 0.00 3.51
1279 1607 2.503331 TCCATGCACAAGTTGGTAGTG 58.497 47.619 7.96 0.00 36.39 2.74
1284 1612 3.462982 TGCACAAGTTGGTAGTGTAGTG 58.537 45.455 7.96 0.00 35.75 2.74
1287 1615 5.051816 GCACAAGTTGGTAGTGTAGTGTTA 58.948 41.667 7.96 0.00 35.75 2.41
1311 1639 9.896263 TTAAAAAGACGTTTTACATTATGGGAC 57.104 29.630 5.90 0.00 40.59 4.46
1336 1664 4.587891 AGTAGTAGGACGTAACTTCTGCT 58.412 43.478 9.78 9.78 0.00 4.24
1853 2192 1.079405 ACGTACATGCCCTTCACGG 60.079 57.895 0.00 0.00 36.95 4.94
1857 2196 0.907704 TACATGCCCTTCACGGTCCT 60.908 55.000 0.00 0.00 0.00 3.85
1931 2270 1.639298 GCACGAGCATCACAAGTCCC 61.639 60.000 0.00 0.00 41.58 4.46
1967 2306 8.527135 TGGTTTGGTTTCCCCTGATATATATA 57.473 34.615 0.00 0.00 0.00 0.86
1968 2307 9.134504 TGGTTTGGTTTCCCCTGATATATATAT 57.865 33.333 4.86 4.86 0.00 0.86
2011 2350 9.999660 AGATATATAGAACTTCACTACAGACGA 57.000 33.333 0.00 0.00 0.00 4.20
2097 2464 7.063898 CCCTTATGAATATGTATGTTCTGCTCG 59.936 40.741 3.57 0.00 0.00 5.03
2102 2469 6.040504 TGAATATGTATGTTCTGCTCGTACCT 59.959 38.462 3.57 0.00 0.00 3.08
2117 2484 7.497595 TGCTCGTACCTTAAGTTATTGATGAT 58.502 34.615 0.97 0.00 0.00 2.45
2152 2519 2.609427 AATGCTGCTCTCGCTTATGA 57.391 45.000 0.00 0.00 36.97 2.15
2154 2521 3.949842 ATGCTGCTCTCGCTTATGATA 57.050 42.857 0.00 0.00 36.97 2.15
2157 2524 3.241701 GCTGCTCTCGCTTATGATAGTC 58.758 50.000 0.00 0.00 36.97 2.59
2165 2532 7.618502 TCTCGCTTATGATAGTCCTATCTTC 57.381 40.000 13.84 0.00 41.80 2.87
2166 2533 7.168905 TCTCGCTTATGATAGTCCTATCTTCA 58.831 38.462 13.84 0.00 41.80 3.02
2167 2534 7.665974 TCTCGCTTATGATAGTCCTATCTTCAA 59.334 37.037 13.84 6.02 41.80 2.69
2168 2535 7.821652 TCGCTTATGATAGTCCTATCTTCAAG 58.178 38.462 13.84 13.45 41.80 3.02
2169 2536 7.665974 TCGCTTATGATAGTCCTATCTTCAAGA 59.334 37.037 13.84 0.00 41.80 3.02
2170 2537 8.300286 CGCTTATGATAGTCCTATCTTCAAGAA 58.700 37.037 13.84 0.00 41.80 2.52
2171 2538 9.988815 GCTTATGATAGTCCTATCTTCAAGAAA 57.011 33.333 13.84 1.14 41.80 2.52
2176 2543 9.935241 TGATAGTCCTATCTTCAAGAAATATGC 57.065 33.333 13.84 0.00 41.80 3.14
2187 2554 8.461222 TCTTCAAGAAATATGCTTATGTTGTGG 58.539 33.333 0.00 0.00 0.00 4.17
2188 2555 7.936496 TCAAGAAATATGCTTATGTTGTGGA 57.064 32.000 0.00 0.00 0.00 4.02
2189 2556 8.523915 TCAAGAAATATGCTTATGTTGTGGAT 57.476 30.769 0.00 0.00 0.00 3.41
2190 2557 8.970020 TCAAGAAATATGCTTATGTTGTGGATT 58.030 29.630 0.00 0.00 0.00 3.01
2198 2565 8.710749 ATGCTTATGTTGTGGATTATATTGGT 57.289 30.769 0.00 0.00 0.00 3.67
2199 2566 7.939782 TGCTTATGTTGTGGATTATATTGGTG 58.060 34.615 0.00 0.00 0.00 4.17
2200 2567 7.777440 TGCTTATGTTGTGGATTATATTGGTGA 59.223 33.333 0.00 0.00 0.00 4.02
2201 2568 8.629158 GCTTATGTTGTGGATTATATTGGTGAA 58.371 33.333 0.00 0.00 0.00 3.18
2205 2572 7.264221 TGTTGTGGATTATATTGGTGAATTGC 58.736 34.615 0.00 0.00 0.00 3.56
2206 2573 7.093596 TGTTGTGGATTATATTGGTGAATTGCA 60.094 33.333 0.00 0.00 0.00 4.08
2207 2574 7.415592 TGTGGATTATATTGGTGAATTGCAA 57.584 32.000 0.00 0.00 0.00 4.08
2208 2575 8.020777 TGTGGATTATATTGGTGAATTGCAAT 57.979 30.769 5.99 5.99 0.00 3.56
2209 2576 8.484575 TGTGGATTATATTGGTGAATTGCAATT 58.515 29.630 24.33 24.33 0.00 2.32
2229 2596 3.398318 TGGTAGTCCCTAGAAGCATCA 57.602 47.619 0.00 0.00 0.00 3.07
2289 2659 6.118170 TCTTTTAAGAGGATGATCTGGCAAG 58.882 40.000 0.00 0.00 0.00 4.01
2301 2672 5.065914 TGATCTGGCAAGGCATTAGTAATC 58.934 41.667 0.00 0.00 0.00 1.75
2309 2680 5.360591 CAAGGCATTAGTAATCGGAGAAGT 58.639 41.667 0.00 0.00 43.58 3.01
2311 2682 4.896482 AGGCATTAGTAATCGGAGAAGTCT 59.104 41.667 0.00 0.00 43.58 3.24
2341 2714 4.535692 AGCTTGAGGGAGATTCTCTTCTTT 59.464 41.667 13.22 0.00 32.78 2.52
2384 2758 6.648879 ATTTTCTGTAAGGCAGCTTGTTTA 57.351 33.333 0.00 0.00 44.66 2.01
2438 2814 9.884814 GTAATATATCATATCCTGGGGACTACT 57.115 37.037 0.00 0.00 32.98 2.57
2460 2836 1.212935 ACACAACCAGGAGCAAGAGTT 59.787 47.619 0.00 0.00 0.00 3.01
2562 2942 4.523943 TGAGCAAATATGGTGGCAATATCC 59.476 41.667 0.00 0.00 37.41 2.59
2564 2944 4.525487 AGCAAATATGGTGGCAATATCCTG 59.475 41.667 0.00 0.00 35.55 3.86
2628 3009 5.050490 CCATGAAAACGATCGGATTCTACT 58.950 41.667 25.48 13.82 0.00 2.57
2629 3010 5.050769 CCATGAAAACGATCGGATTCTACTG 60.051 44.000 25.48 20.47 0.00 2.74
2738 3126 8.408043 TTCTCCATCATAGCTTTTTCTTTCAA 57.592 30.769 0.00 0.00 0.00 2.69
2859 3251 6.202570 GCATTTCAAATCTAGTAGGAGAGCTG 59.797 42.308 0.00 0.00 0.00 4.24
2909 3301 5.801350 TCAGTTTCAACAGTCTCAAGTTG 57.199 39.130 0.00 0.00 44.84 3.16
2914 3306 8.020819 CAGTTTCAACAGTCTCAAGTTGTTTAA 58.979 33.333 2.11 0.00 44.08 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.079475 GCGATCTTAACTAGAGATAACCTGAC 58.921 42.308 0.00 0.00 36.02 3.51
1 2 6.771267 TGCGATCTTAACTAGAGATAACCTGA 59.229 38.462 0.00 0.00 36.02 3.86
2 3 6.858993 GTGCGATCTTAACTAGAGATAACCTG 59.141 42.308 0.00 0.00 36.02 4.00
11 12 5.324784 ACATGTGTGCGATCTTAACTAGA 57.675 39.130 0.00 0.00 37.28 2.43
15 16 9.549509 TTTTATAAACATGTGTGCGATCTTAAC 57.450 29.630 0.00 0.00 0.00 2.01
69 72 6.416455 CGATAACAAAAACTGTGCAAGCTTAA 59.584 34.615 0.00 0.00 38.67 1.85
146 156 1.597027 GTGGTCGGTGGTGTGGAAG 60.597 63.158 0.00 0.00 0.00 3.46
206 216 4.206375 TCAGAGAATAGGAGCTCTCACTG 58.794 47.826 14.64 16.01 39.36 3.66
208 218 5.789643 ATTCAGAGAATAGGAGCTCTCAC 57.210 43.478 14.64 1.80 39.36 3.51
239 256 8.072321 ACAAGTCTACAACTCTGACATATGAT 57.928 34.615 10.38 0.00 37.17 2.45
244 291 6.682746 CACTACAAGTCTACAACTCTGACAT 58.317 40.000 0.00 0.00 37.17 3.06
252 299 3.378339 ACGTGCACTACAAGTCTACAAC 58.622 45.455 16.19 0.00 36.06 3.32
257 304 2.621998 ACAGTACGTGCACTACAAGTCT 59.378 45.455 16.19 2.27 40.38 3.24
259 306 3.567164 AGTACAGTACGTGCACTACAAGT 59.433 43.478 16.19 17.81 43.76 3.16
260 307 4.156664 AGTACAGTACGTGCACTACAAG 57.843 45.455 16.19 13.85 30.21 3.16
261 308 4.756642 ACTAGTACAGTACGTGCACTACAA 59.243 41.667 16.19 4.23 34.36 2.41
262 309 4.152938 CACTAGTACAGTACGTGCACTACA 59.847 45.833 16.19 0.00 34.36 2.74
263 310 4.645956 CACTAGTACAGTACGTGCACTAC 58.354 47.826 16.19 15.33 34.36 2.73
264 311 4.934075 CACTAGTACAGTACGTGCACTA 57.066 45.455 16.19 4.40 34.36 2.74
265 312 3.826236 CACTAGTACAGTACGTGCACT 57.174 47.619 16.19 3.34 36.64 4.40
268 315 1.129251 TCGCACTAGTACAGTACGTGC 59.871 52.381 23.68 23.68 43.32 5.34
269 316 3.309138 AGATCGCACTAGTACAGTACGTG 59.691 47.826 12.20 12.20 43.32 4.49
270 317 3.529533 AGATCGCACTAGTACAGTACGT 58.470 45.455 13.89 0.00 43.32 3.57
271 318 3.803231 AGAGATCGCACTAGTACAGTACG 59.197 47.826 5.02 10.15 44.06 3.67
272 319 4.211794 GGAGAGATCGCACTAGTACAGTAC 59.788 50.000 2.05 2.05 34.98 2.73
273 320 4.101274 AGGAGAGATCGCACTAGTACAGTA 59.899 45.833 0.00 0.00 34.98 2.74
274 321 3.118186 AGGAGAGATCGCACTAGTACAGT 60.118 47.826 0.00 0.00 38.32 3.55
275 322 3.472652 AGGAGAGATCGCACTAGTACAG 58.527 50.000 0.00 0.00 0.00 2.74
278 325 2.102757 ACGAGGAGAGATCGCACTAGTA 59.897 50.000 0.00 0.00 43.91 1.82
295 342 3.068691 TCCTCCCGCCTTCACGAG 61.069 66.667 0.00 0.00 34.06 4.18
297 344 2.167398 TTTCTCCTCCCGCCTTCACG 62.167 60.000 0.00 0.00 0.00 4.35
298 345 0.673956 GTTTCTCCTCCCGCCTTCAC 60.674 60.000 0.00 0.00 0.00 3.18
299 346 1.677552 GTTTCTCCTCCCGCCTTCA 59.322 57.895 0.00 0.00 0.00 3.02
302 349 3.391382 CCGTTTCTCCTCCCGCCT 61.391 66.667 0.00 0.00 0.00 5.52
303 350 2.253403 AATCCGTTTCTCCTCCCGCC 62.253 60.000 0.00 0.00 0.00 6.13
304 351 1.090052 CAATCCGTTTCTCCTCCCGC 61.090 60.000 0.00 0.00 0.00 6.13
305 352 0.462047 CCAATCCGTTTCTCCTCCCG 60.462 60.000 0.00 0.00 0.00 5.14
310 365 1.130561 CGAAAGCCAATCCGTTTCTCC 59.869 52.381 0.00 0.00 0.00 3.71
326 381 0.941542 CTTGACCTTTCACGGCGAAA 59.058 50.000 16.62 3.32 41.40 3.46
332 387 2.135664 AGACGTCTTGACCTTTCACG 57.864 50.000 13.58 0.00 0.00 4.35
336 391 7.562454 TTTCAAATTAGACGTCTTGACCTTT 57.438 32.000 25.44 12.87 0.00 3.11
403 474 5.614231 CGACGAGTTACTAGATATTCCACGG 60.614 48.000 0.00 0.00 0.00 4.94
405 476 5.049543 AGCGACGAGTTACTAGATATTCCAC 60.050 44.000 0.00 0.00 0.00 4.02
417 488 1.774639 TTTGGTCAGCGACGAGTTAC 58.225 50.000 0.00 0.00 32.65 2.50
421 492 0.389817 TCCATTTGGTCAGCGACGAG 60.390 55.000 0.00 0.00 36.34 4.18
442 513 2.285083 CATTTCGAAATGAGCGGGGTA 58.715 47.619 36.48 2.60 46.72 3.69
444 515 0.248621 GCATTTCGAAATGAGCGGGG 60.249 55.000 41.10 21.68 46.72 5.73
472 546 8.251721 GTCCAACTCTATCTGTTAGTACATGTT 58.748 37.037 2.30 0.00 32.86 2.71
476 550 6.175471 TCGTCCAACTCTATCTGTTAGTACA 58.825 40.000 0.00 0.00 0.00 2.90
523 597 2.423926 TGACTCTGCTTCGTCAACTC 57.576 50.000 0.00 0.00 37.23 3.01
543 617 6.872020 GTGTTCTGCAAGTGTTCTAGGTTATA 59.128 38.462 0.00 0.00 33.76 0.98
573 647 4.069232 CTGAAGCTGCCGGTCCGA 62.069 66.667 14.39 0.00 0.00 4.55
598 672 2.109126 GGCAGATCACTGGAACGGC 61.109 63.158 0.00 0.00 43.62 5.68
599 673 0.321564 TTGGCAGATCACTGGAACGG 60.322 55.000 0.00 0.00 43.62 4.44
614 692 0.319405 ACCCTGTGTACGTACTTGGC 59.681 55.000 25.12 13.45 0.00 4.52
617 695 6.591448 GCTATTTTTACCCTGTGTACGTACTT 59.409 38.462 25.12 6.53 0.00 2.24
620 698 6.101332 CAGCTATTTTTACCCTGTGTACGTA 58.899 40.000 0.00 0.00 0.00 3.57
621 699 4.933400 CAGCTATTTTTACCCTGTGTACGT 59.067 41.667 0.00 0.00 0.00 3.57
622 700 4.331717 CCAGCTATTTTTACCCTGTGTACG 59.668 45.833 0.00 0.00 0.00 3.67
623 701 5.353400 GTCCAGCTATTTTTACCCTGTGTAC 59.647 44.000 0.00 0.00 0.00 2.90
624 702 5.249852 AGTCCAGCTATTTTTACCCTGTGTA 59.750 40.000 0.00 0.00 0.00 2.90
651 732 0.173935 TAACGGGTGAGCGTATGTGG 59.826 55.000 0.00 0.00 0.00 4.17
664 745 1.734163 GTCCATGGTTCAGTAACGGG 58.266 55.000 12.58 0.00 36.39 5.28
673 754 3.074412 ACATCACTTTCGTCCATGGTTC 58.926 45.455 12.58 5.65 0.00 3.62
708 789 1.866059 CATGCATGCAACACTCGCG 60.866 57.895 26.68 0.00 0.00 5.87
719 800 1.063006 CGACGGGAAAGCATGCATG 59.937 57.895 22.70 22.70 0.00 4.06
720 801 2.114670 CCGACGGGAAAGCATGCAT 61.115 57.895 21.98 4.57 34.06 3.96
747 829 3.680196 GCGAAGAGAATTCAAGCTAGGGT 60.680 47.826 8.44 0.00 0.00 4.34
787 874 2.025699 CCGGGGAGAAAACTTGGGATAA 60.026 50.000 0.00 0.00 0.00 1.75
816 905 3.459063 GGCGGGTCTACGAAGGCT 61.459 66.667 0.00 0.00 35.47 4.58
898 987 4.806892 TGGATAGATGCATGGATGGTTTT 58.193 39.130 2.46 0.00 0.00 2.43
899 988 4.458256 TGGATAGATGCATGGATGGTTT 57.542 40.909 2.46 0.00 0.00 3.27
963 1052 0.881118 CAAACCCGACAACCCAGATG 59.119 55.000 0.00 0.00 0.00 2.90
971 1060 1.609555 GTATGTTGCCAAACCCGACAA 59.390 47.619 0.00 0.00 35.25 3.18
975 1064 1.529226 TCAGTATGTTGCCAAACCCG 58.471 50.000 0.00 0.00 37.40 5.28
985 1075 6.471146 GGAATGCCATCTAGATCAGTATGTT 58.529 40.000 1.03 0.00 37.40 2.71
989 1079 3.511540 CGGGAATGCCATCTAGATCAGTA 59.488 47.826 1.03 0.00 35.15 2.74
993 1083 1.625818 ACCGGGAATGCCATCTAGATC 59.374 52.381 6.32 0.00 35.15 2.75
997 1087 1.048601 GAGACCGGGAATGCCATCTA 58.951 55.000 6.32 0.00 35.15 1.98
1215 1305 3.512033 AGTACCTTGAAGACGATGAGC 57.488 47.619 0.00 0.00 0.00 4.26
1237 1331 1.736586 CACGAGGAGGGGATCGAAG 59.263 63.158 1.13 0.00 41.40 3.79
1239 1333 2.833582 GCACGAGGAGGGGATCGA 60.834 66.667 1.13 0.00 41.40 3.59
1241 1335 2.105806 GATGGCACGAGGAGGGGATC 62.106 65.000 0.00 0.00 0.00 3.36
1260 1354 2.229792 ACACTACCAACTTGTGCATGG 58.770 47.619 1.63 1.63 40.16 3.66
1284 1612 9.896263 TCCCATAATGTAAAACGTCTTTTTAAC 57.104 29.630 0.00 0.00 40.59 2.01
1287 1615 7.041235 TCGTCCCATAATGTAAAACGTCTTTTT 60.041 33.333 0.00 0.00 40.65 1.94
1306 1634 1.003580 ACGTCCTACTACTTCGTCCCA 59.996 52.381 0.00 0.00 0.00 4.37
1311 1639 5.558307 CAGAAGTTACGTCCTACTACTTCG 58.442 45.833 0.00 0.00 45.71 3.79
1322 1650 6.088350 CAGAAAGTAAGAGCAGAAGTTACGTC 59.912 42.308 0.00 0.00 32.86 4.34
1325 1653 5.164041 CGCAGAAAGTAAGAGCAGAAGTTAC 60.164 44.000 0.00 0.00 0.00 2.50
1336 1664 3.812609 TGCATGTTTCGCAGAAAGTAAGA 59.187 39.130 4.35 0.00 45.90 2.10
1576 1915 3.092511 TCCATGAGCAGGCCCTCC 61.093 66.667 0.00 0.00 0.00 4.30
1617 1956 2.363795 TCATCCCGGAAGCGAGGT 60.364 61.111 0.73 0.00 0.00 3.85
1642 1981 2.208431 GAGATGAAGAAGATGGCGGTG 58.792 52.381 0.00 0.00 0.00 4.94
1921 2260 1.883638 GCTGCTCAATGGGACTTGTGA 60.884 52.381 0.00 0.00 0.00 3.58
1931 2270 0.963962 ACCAAACCAGCTGCTCAATG 59.036 50.000 8.66 2.33 0.00 2.82
2010 2349 3.003068 GCCAGAACATGAGCACATACATC 59.997 47.826 0.00 0.00 35.09 3.06
2011 2350 2.947652 GCCAGAACATGAGCACATACAT 59.052 45.455 0.00 0.00 35.09 2.29
2012 2351 2.290197 TGCCAGAACATGAGCACATACA 60.290 45.455 0.00 0.00 35.09 2.29
2063 2402 8.166061 ACATACATATTCATAAGGGAGCACAAT 58.834 33.333 0.00 0.00 0.00 2.71
2084 2423 5.648572 ACTTAAGGTACGAGCAGAACATAC 58.351 41.667 7.53 0.00 0.00 2.39
2117 2484 8.144478 AGAGCAGCATTATCTTTCGTATCTTTA 58.856 33.333 0.00 0.00 0.00 1.85
2172 2539 9.806448 ACCAATATAATCCACAACATAAGCATA 57.194 29.630 0.00 0.00 0.00 3.14
2173 2540 8.579006 CACCAATATAATCCACAACATAAGCAT 58.421 33.333 0.00 0.00 0.00 3.79
2174 2541 7.777440 TCACCAATATAATCCACAACATAAGCA 59.223 33.333 0.00 0.00 0.00 3.91
2175 2542 8.165239 TCACCAATATAATCCACAACATAAGC 57.835 34.615 0.00 0.00 0.00 3.09
2179 2546 7.927629 GCAATTCACCAATATAATCCACAACAT 59.072 33.333 0.00 0.00 0.00 2.71
2180 2547 7.093596 TGCAATTCACCAATATAATCCACAACA 60.094 33.333 0.00 0.00 0.00 3.33
2181 2548 7.264221 TGCAATTCACCAATATAATCCACAAC 58.736 34.615 0.00 0.00 0.00 3.32
2182 2549 7.415592 TGCAATTCACCAATATAATCCACAA 57.584 32.000 0.00 0.00 0.00 3.33
2183 2550 7.415592 TTGCAATTCACCAATATAATCCACA 57.584 32.000 0.00 0.00 0.00 4.17
2184 2551 8.767085 CAATTGCAATTCACCAATATAATCCAC 58.233 33.333 21.70 0.00 31.82 4.02
2185 2552 7.932491 CCAATTGCAATTCACCAATATAATCCA 59.068 33.333 21.70 0.00 31.82 3.41
2186 2553 7.933033 ACCAATTGCAATTCACCAATATAATCC 59.067 33.333 21.70 0.00 31.82 3.01
2187 2554 8.891671 ACCAATTGCAATTCACCAATATAATC 57.108 30.769 21.70 0.00 31.82 1.75
2188 2555 9.985730 CTACCAATTGCAATTCACCAATATAAT 57.014 29.630 21.70 0.00 31.82 1.28
2189 2556 8.976353 ACTACCAATTGCAATTCACCAATATAA 58.024 29.630 21.70 0.00 31.82 0.98
2190 2557 8.532186 ACTACCAATTGCAATTCACCAATATA 57.468 30.769 21.70 5.23 31.82 0.86
2191 2558 7.417797 GGACTACCAATTGCAATTCACCAATAT 60.418 37.037 21.70 3.39 35.97 1.28
2192 2559 6.127479 GGACTACCAATTGCAATTCACCAATA 60.127 38.462 21.70 7.36 35.97 1.90
2193 2560 5.337491 GGACTACCAATTGCAATTCACCAAT 60.337 40.000 21.70 6.40 35.97 3.16
2194 2561 4.021544 GGACTACCAATTGCAATTCACCAA 60.022 41.667 21.70 5.54 35.97 3.67
2195 2562 3.509575 GGACTACCAATTGCAATTCACCA 59.490 43.478 21.70 6.86 35.97 4.17
2196 2563 3.119137 GGGACTACCAATTGCAATTCACC 60.119 47.826 21.70 16.19 39.85 4.02
2197 2564 3.763897 AGGGACTACCAATTGCAATTCAC 59.236 43.478 21.70 10.95 43.89 3.18
2198 2565 4.046286 AGGGACTACCAATTGCAATTCA 57.954 40.909 21.70 9.22 43.89 2.57
2199 2566 5.437060 TCTAGGGACTACCAATTGCAATTC 58.563 41.667 21.70 9.66 43.89 2.17
2200 2567 5.450818 TCTAGGGACTACCAATTGCAATT 57.549 39.130 18.99 18.99 43.89 2.32
2201 2568 5.440610 CTTCTAGGGACTACCAATTGCAAT 58.559 41.667 5.99 5.99 43.89 3.56
2202 2569 4.843728 CTTCTAGGGACTACCAATTGCAA 58.156 43.478 0.00 0.00 43.89 4.08
2203 2570 3.370527 GCTTCTAGGGACTACCAATTGCA 60.371 47.826 0.00 0.00 43.89 4.08
2204 2571 3.206964 GCTTCTAGGGACTACCAATTGC 58.793 50.000 0.00 0.00 43.89 3.56
2205 2572 4.487714 TGCTTCTAGGGACTACCAATTG 57.512 45.455 0.00 0.00 43.89 2.32
2206 2573 4.721776 TGATGCTTCTAGGGACTACCAATT 59.278 41.667 0.88 0.00 43.89 2.32
2207 2574 4.298626 TGATGCTTCTAGGGACTACCAAT 58.701 43.478 0.88 0.00 43.89 3.16
2208 2575 3.706594 CTGATGCTTCTAGGGACTACCAA 59.293 47.826 0.88 0.00 43.89 3.67
2209 2576 3.300388 CTGATGCTTCTAGGGACTACCA 58.700 50.000 0.88 0.00 43.89 3.25
2261 2628 8.274322 TGCCAGATCATCCTCTTAAAAGAAATA 58.726 33.333 0.00 0.00 34.03 1.40
2268 2638 4.785301 CCTTGCCAGATCATCCTCTTAAA 58.215 43.478 0.00 0.00 0.00 1.52
2289 2659 5.203060 AGACTTCTCCGATTACTAATGCC 57.797 43.478 0.00 0.00 0.00 4.40
2438 2814 0.836606 TCTTGCTCCTGGTTGTGTGA 59.163 50.000 0.00 0.00 0.00 3.58
2460 2836 6.723977 AGGGTGATGCTAAAGAATGGTTTAAA 59.276 34.615 0.00 0.00 0.00 1.52
2501 2877 9.674824 TTCGCTACTACTATATCTTTAAGTTGC 57.325 33.333 0.00 0.00 34.06 4.17
2562 2942 2.484264 GGCACACCTTACTAAACTGCAG 59.516 50.000 13.48 13.48 0.00 4.41
2564 2944 2.500229 TGGCACACCTTACTAAACTGC 58.500 47.619 0.00 0.00 36.63 4.40
2614 2995 9.627395 ATTAATTACTTCAGTAGAATCCGATCG 57.373 33.333 8.51 8.51 32.31 3.69
2648 3029 8.523915 TGTTACCGATAAGGATTACTCTGTTA 57.476 34.615 0.00 0.00 45.00 2.41
2713 3100 8.299570 GTTGAAAGAAAAAGCTATGATGGAGAA 58.700 33.333 0.00 0.00 0.00 2.87
2788 3180 0.037447 GATGGGGAGATTGCTAGGGC 59.963 60.000 0.00 0.00 39.26 5.19
2790 3182 1.438469 TGGATGGGGAGATTGCTAGG 58.562 55.000 0.00 0.00 0.00 3.02
2859 3251 8.409358 AAAACTATGATTCACCTATTATGCCC 57.591 34.615 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.