Multiple sequence alignment - TraesCS7A01G557700

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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 TraesCS7A01G557700 chr7A 100.000 5276 0 0 1 5276 730435251 730429976 0.000000e+00 9744.0
1 TraesCS7A01G557700 chr7D 96.206 3585 106 13 874 4439 635579857 635583430 0.000000e+00 5840.0
2 TraesCS7A01G557700 chr7D 94.026 703 32 5 4579 5276 635584105 635584802 0.000000e+00 1057.0
3 TraesCS7A01G557700 chr7D 81.985 544 41 18 245 746 635579086 635579614 4.920000e-110 409.0
4 TraesCS7A01G557700 chr7D 96.491 57 2 0 162 218 635579034 635579090 1.560000e-15 95.3
5 TraesCS7A01G557700 chr7B 95.355 3617 121 23 862 4439 740041570 740037962 0.000000e+00 5705.0
6 TraesCS7A01G557700 chr7B 94.431 844 22 10 4435 5276 740037921 740037101 0.000000e+00 1275.0
7 TraesCS7A01G557700 chr7B 79.499 439 22 15 391 797 740042127 740041725 3.150000e-62 250.0
8 TraesCS7A01G557700 chr7B 79.935 309 25 12 1 294 740042579 740042293 5.390000e-45 193.0


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 TraesCS7A01G557700 chr7A 730429976 730435251 5275 True 9744.000 9744 100.000 1 5276 1 chr7A.!!$R1 5275
1 TraesCS7A01G557700 chr7D 635579034 635584802 5768 False 1850.325 5840 92.177 162 5276 4 chr7D.!!$F1 5114
2 TraesCS7A01G557700 chr7B 740037101 740042579 5478 True 1855.750 5705 87.305 1 5276 4 chr7B.!!$R1 5275

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
811 1030 0.036388 TTCCTGTGTCGGCCTGATTC 60.036 55.0 0.00 0.0 0.00 2.52 F
1475 1768 0.039618 GCCAGGAGGGATTGGTTCAA 59.960 55.0 0.00 0.0 40.01 2.69 F
1552 1845 0.109039 GACGCAGGTCCAGAAGTCTC 60.109 60.0 0.00 0.0 37.19 3.36 F
2074 2367 0.540923 AGAGGAGATCCAAGCACTGC 59.459 55.0 0.92 0.0 38.89 4.40 F
2790 3083 0.698818 AGGCTCTCCCAAAATCCGTT 59.301 50.0 0.00 0.0 35.39 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2062 2355 0.330604 ACATCCTGCAGTGCTTGGAT 59.669 50.0 26.52 26.52 40.73 3.41 R
2908 3201 1.528129 GACCAAGGGAGTTTCTGCAG 58.472 55.0 7.63 7.63 0.00 4.41 R
2991 3284 2.341846 TCAGTTCACCCACACCTTTC 57.658 50.0 0.00 0.00 0.00 2.62 R
3780 4073 0.608130 CACCCTCGACATGAAGGTCA 59.392 55.0 0.00 0.00 39.51 4.02 R
4435 4741 0.907486 CTCATTCCTCAGGCCTCACA 59.093 55.0 0.00 0.00 0.00 3.58 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
26 27 7.026562 TGTGATTAACTGAAATTTGTATGGCG 58.973 34.615 0.00 0.00 0.00 5.69
35 36 6.378582 TGAAATTTGTATGGCGAAGAAAGTC 58.621 36.000 0.00 0.00 0.00 3.01
48 49 4.610680 CGAAGAAAGTCCACACCGAATTTC 60.611 45.833 3.94 3.94 43.65 2.17
55 56 5.127491 AGTCCACACCGAATTTCAAAAGTA 58.873 37.500 0.00 0.00 0.00 2.24
56 57 5.591067 AGTCCACACCGAATTTCAAAAGTAA 59.409 36.000 0.00 0.00 0.00 2.24
57 58 6.095720 AGTCCACACCGAATTTCAAAAGTAAA 59.904 34.615 0.00 0.00 0.00 2.01
58 59 6.197655 GTCCACACCGAATTTCAAAAGTAAAC 59.802 38.462 0.00 0.00 0.00 2.01
62 63 7.895767 CACACCGAATTTCAAAAGTAAACAAAC 59.104 33.333 0.00 0.00 0.00 2.93
64 65 7.063544 CACCGAATTTCAAAAGTAAACAAACCA 59.936 33.333 0.00 0.00 0.00 3.67
67 68 9.980780 CGAATTTCAAAAGTAAACAAACCATTT 57.019 25.926 0.00 0.00 0.00 2.32
77 78 8.956533 AGTAAACAAACCATTTTATTTGCACT 57.043 26.923 0.00 0.00 39.03 4.40
85 86 4.330620 CCATTTTATTTGCACTGTCCATGC 59.669 41.667 0.00 0.00 43.68 4.06
87 88 2.212812 TATTTGCACTGTCCATGCCA 57.787 45.000 0.00 0.00 42.69 4.92
90 91 0.675083 TTGCACTGTCCATGCCAAAG 59.325 50.000 0.00 0.00 42.69 2.77
91 92 0.467844 TGCACTGTCCATGCCAAAGT 60.468 50.000 0.00 0.00 42.69 2.66
92 93 1.202867 TGCACTGTCCATGCCAAAGTA 60.203 47.619 0.00 0.00 42.69 2.24
94 95 2.493278 GCACTGTCCATGCCAAAGTAAT 59.507 45.455 0.00 0.00 37.08 1.89
99 100 3.096092 GTCCATGCCAAAGTAATTCCCA 58.904 45.455 0.00 0.00 0.00 4.37
100 101 3.706086 GTCCATGCCAAAGTAATTCCCAT 59.294 43.478 0.00 0.00 0.00 4.00
101 102 4.162131 GTCCATGCCAAAGTAATTCCCATT 59.838 41.667 0.00 0.00 0.00 3.16
102 103 4.782156 TCCATGCCAAAGTAATTCCCATTT 59.218 37.500 0.00 0.00 0.00 2.32
103 104 5.250313 TCCATGCCAAAGTAATTCCCATTTT 59.750 36.000 0.00 0.00 0.00 1.82
104 105 5.945191 CCATGCCAAAGTAATTCCCATTTTT 59.055 36.000 0.00 0.00 0.00 1.94
125 126 3.467374 TGCTCCCCAAAACATGTTTTC 57.533 42.857 29.21 18.79 40.45 2.29
184 198 0.953727 TGTTGCTGTCCATTGCTGTC 59.046 50.000 0.00 0.00 0.00 3.51
219 233 1.212375 TAGCCTGCCCAATTCTGCTA 58.788 50.000 0.00 0.00 0.00 3.49
220 234 0.554792 AGCCTGCCCAATTCTGCTAT 59.445 50.000 0.00 0.00 0.00 2.97
221 235 0.672342 GCCTGCCCAATTCTGCTATG 59.328 55.000 0.00 0.00 0.00 2.23
222 236 0.672342 CCTGCCCAATTCTGCTATGC 59.328 55.000 0.00 0.00 0.00 3.14
223 237 1.688772 CTGCCCAATTCTGCTATGCT 58.311 50.000 0.00 0.00 0.00 3.79
243 257 1.535444 TGTTCTCCCCTCTTCGCCA 60.535 57.895 0.00 0.00 0.00 5.69
252 266 3.764160 CTCTTCGCCATCTGCCCCC 62.764 68.421 0.00 0.00 36.24 5.40
294 308 2.129555 AACGTCCCTGCCAAGCTCAT 62.130 55.000 0.00 0.00 0.00 2.90
295 309 1.817099 CGTCCCTGCCAAGCTCATC 60.817 63.158 0.00 0.00 0.00 2.92
296 310 1.452833 GTCCCTGCCAAGCTCATCC 60.453 63.158 0.00 0.00 0.00 3.51
298 312 1.229359 CCCTGCCAAGCTCATCCAT 59.771 57.895 0.00 0.00 0.00 3.41
300 314 1.107538 CCTGCCAAGCTCATCCATGG 61.108 60.000 4.97 4.97 36.00 3.66
302 316 3.851955 CCAAGCTCATCCATGGCC 58.148 61.111 6.96 0.00 0.00 5.36
303 317 1.831286 CCAAGCTCATCCATGGCCC 60.831 63.158 6.96 0.00 0.00 5.80
305 319 3.426309 AAGCTCATCCATGGCCCGG 62.426 63.158 6.96 0.00 0.00 5.73
327 363 1.154112 GCGCCCATTTTGTACCACG 60.154 57.895 0.00 0.00 0.00 4.94
345 381 2.360191 GCAATCTTCCAGGGGCCA 59.640 61.111 4.39 0.00 0.00 5.36
354 390 2.285668 CAGGGGCCAGGAGGAGAA 60.286 66.667 4.39 0.00 36.89 2.87
356 392 1.925972 AGGGGCCAGGAGGAGAAAC 60.926 63.158 4.39 0.00 36.89 2.78
358 395 2.291043 GGGCCAGGAGGAGAAACGA 61.291 63.158 4.39 0.00 36.89 3.85
377 414 2.733552 CGAGAGATGTGACAGGTTGTTG 59.266 50.000 0.00 0.00 0.00 3.33
378 415 3.733337 GAGAGATGTGACAGGTTGTTGT 58.267 45.455 0.00 0.00 0.00 3.32
379 416 3.470709 AGAGATGTGACAGGTTGTTGTG 58.529 45.455 0.00 0.00 0.00 3.33
380 417 1.949525 AGATGTGACAGGTTGTTGTGC 59.050 47.619 0.00 0.00 0.00 4.57
384 452 0.106268 TGACAGGTTGTTGTGCCCAT 60.106 50.000 0.00 0.00 0.00 4.00
466 561 3.117851 GTGGAGAAATTAGGGGGAGGAAG 60.118 52.174 0.00 0.00 0.00 3.46
471 566 1.054978 ATTAGGGGGAGGAAGGCGTC 61.055 60.000 0.00 0.00 0.00 5.19
472 567 2.177529 TTAGGGGGAGGAAGGCGTCT 62.178 60.000 0.00 0.00 0.00 4.18
475 570 2.269241 GGGAGGAAGGCGTCTTGG 59.731 66.667 7.19 0.00 32.52 3.61
476 571 2.269241 GGAGGAAGGCGTCTTGGG 59.731 66.667 7.19 0.00 32.52 4.12
477 572 2.291043 GGAGGAAGGCGTCTTGGGA 61.291 63.158 7.19 0.00 32.52 4.37
478 573 1.079057 GAGGAAGGCGTCTTGGGAC 60.079 63.158 7.19 0.00 38.97 4.46
635 757 3.393941 CCTCTTGCTCCAATAATCCTCCT 59.606 47.826 0.00 0.00 0.00 3.69
636 758 4.504689 CCTCTTGCTCCAATAATCCTCCTC 60.505 50.000 0.00 0.00 0.00 3.71
637 759 3.392616 TCTTGCTCCAATAATCCTCCTCC 59.607 47.826 0.00 0.00 0.00 4.30
639 761 2.057922 GCTCCAATAATCCTCCTCCCA 58.942 52.381 0.00 0.00 0.00 4.37
640 762 2.443255 GCTCCAATAATCCTCCTCCCAA 59.557 50.000 0.00 0.00 0.00 4.12
641 763 3.075134 GCTCCAATAATCCTCCTCCCAAT 59.925 47.826 0.00 0.00 0.00 3.16
642 764 4.809007 GCTCCAATAATCCTCCTCCCAATC 60.809 50.000 0.00 0.00 0.00 2.67
643 765 4.581233 TCCAATAATCCTCCTCCCAATCT 58.419 43.478 0.00 0.00 0.00 2.40
693 827 7.892609 TCATCAATCAATCAATCCATCAATCC 58.107 34.615 0.00 0.00 0.00 3.01
695 829 7.849322 TCAATCAATCAATCCATCAATCCAT 57.151 32.000 0.00 0.00 0.00 3.41
696 830 8.257602 TCAATCAATCAATCCATCAATCCATT 57.742 30.769 0.00 0.00 0.00 3.16
697 831 9.369672 TCAATCAATCAATCCATCAATCCATTA 57.630 29.630 0.00 0.00 0.00 1.90
698 832 9.639601 CAATCAATCAATCCATCAATCCATTAG 57.360 33.333 0.00 0.00 0.00 1.73
699 833 8.951614 ATCAATCAATCCATCAATCCATTAGT 57.048 30.769 0.00 0.00 0.00 2.24
700 834 8.400184 TCAATCAATCCATCAATCCATTAGTC 57.600 34.615 0.00 0.00 0.00 2.59
701 835 8.000127 TCAATCAATCCATCAATCCATTAGTCA 59.000 33.333 0.00 0.00 0.00 3.41
702 836 7.997773 ATCAATCCATCAATCCATTAGTCAG 57.002 36.000 0.00 0.00 0.00 3.51
710 844 2.550277 TCCATTAGTCAGGGAGCAGA 57.450 50.000 0.00 0.00 0.00 4.26
714 848 3.118112 CCATTAGTCAGGGAGCAGATTGT 60.118 47.826 0.00 0.00 0.00 2.71
752 886 0.980423 AGTTCCAGCTCCTCAAGGAC 59.020 55.000 0.00 0.00 39.78 3.85
772 906 1.532090 CGCGCTCCCGATCTGATATAC 60.532 57.143 5.56 0.00 36.29 1.47
805 1024 0.534203 TGTTCTTTCCTGTGTCGGCC 60.534 55.000 0.00 0.00 0.00 6.13
811 1030 0.036388 TTCCTGTGTCGGCCTGATTC 60.036 55.000 0.00 0.00 0.00 2.52
821 1040 1.587547 GGCCTGATTCGATCCTCAAC 58.412 55.000 0.00 0.00 0.00 3.18
823 1042 2.365617 GGCCTGATTCGATCCTCAACTA 59.634 50.000 0.00 0.00 0.00 2.24
824 1043 3.181465 GGCCTGATTCGATCCTCAACTAA 60.181 47.826 0.00 0.00 0.00 2.24
831 1050 6.697455 TGATTCGATCCTCAACTAAAATCGAG 59.303 38.462 5.97 0.00 46.00 4.04
842 1061 7.570132 TCAACTAAAATCGAGATAAATGGGGA 58.430 34.615 0.00 0.00 0.00 4.81
845 1064 8.451908 ACTAAAATCGAGATAAATGGGGAAAG 57.548 34.615 0.00 0.00 0.00 2.62
848 1067 8.539117 AAAATCGAGATAAATGGGGAAAGAAT 57.461 30.769 0.00 0.00 0.00 2.40
849 1068 7.751768 AATCGAGATAAATGGGGAAAGAATC 57.248 36.000 0.00 0.00 0.00 2.52
914 1185 5.748630 GCCGTTGAAAGGATCCAATTTTATC 59.251 40.000 15.82 2.39 0.00 1.75
918 1192 5.848004 TGAAAGGATCCAATTTTATCCCCA 58.152 37.500 15.82 0.00 42.32 4.96
926 1200 2.491693 CAATTTTATCCCCACGTGCTGT 59.508 45.455 10.91 0.00 0.00 4.40
927 1201 3.637911 ATTTTATCCCCACGTGCTGTA 57.362 42.857 10.91 0.00 0.00 2.74
932 1206 0.902984 TCCCCACGTGCTGTACTGAT 60.903 55.000 10.91 0.00 0.00 2.90
940 1214 5.579119 CCACGTGCTGTACTGATACAAATTA 59.421 40.000 10.91 0.00 40.84 1.40
941 1215 6.257849 CCACGTGCTGTACTGATACAAATTAT 59.742 38.462 10.91 0.00 40.84 1.28
942 1216 7.201609 CCACGTGCTGTACTGATACAAATTATT 60.202 37.037 10.91 0.00 40.84 1.40
943 1217 7.635973 CACGTGCTGTACTGATACAAATTATTG 59.364 37.037 0.82 0.00 40.84 1.90
1398 1682 2.833582 ATCGACATCCGGCTCCGT 60.834 61.111 7.59 0.00 39.14 4.69
1475 1768 0.039618 GCCAGGAGGGATTGGTTCAA 59.960 55.000 0.00 0.00 40.01 2.69
1476 1769 1.342374 GCCAGGAGGGATTGGTTCAAT 60.342 52.381 0.00 0.00 40.01 2.57
1527 1820 4.742201 GTGAAGCCTCGCTCCGCA 62.742 66.667 0.00 0.00 38.25 5.69
1551 1844 1.968310 GACGCAGGTCCAGAAGTCT 59.032 57.895 0.00 0.00 37.19 3.24
1552 1845 0.109039 GACGCAGGTCCAGAAGTCTC 60.109 60.000 0.00 0.00 37.19 3.36
1612 1905 2.430382 GAAGGTGGACGTCTTCGCCA 62.430 60.000 21.54 7.86 41.18 5.69
2051 2344 1.908483 AGGTCTTCCTGGAATCCGC 59.092 57.895 10.03 0.85 43.33 5.54
2062 2355 1.115467 GGAATCCGCTTCAGAGGAGA 58.885 55.000 5.48 0.00 46.89 3.71
2070 2363 1.209019 GCTTCAGAGGAGATCCAAGCA 59.791 52.381 13.82 0.00 41.19 3.91
2074 2367 0.540923 AGAGGAGATCCAAGCACTGC 59.459 55.000 0.92 0.00 38.89 4.40
2136 2429 3.387962 TCCTCTGGCTATCAAGGTCATT 58.612 45.455 0.00 0.00 0.00 2.57
2172 2465 1.519719 GAGAGGCACGAGCAAGGAT 59.480 57.895 7.26 0.00 44.61 3.24
2179 2472 1.078848 ACGAGCAAGGATGAGTGGC 60.079 57.895 0.00 0.00 0.00 5.01
2199 2492 2.636830 CAGATGGTCCTGAAAAGCGAT 58.363 47.619 0.00 0.00 36.29 4.58
2226 2519 2.983030 ATGCGGCCGTTGCTTCAA 60.983 55.556 28.70 2.71 37.74 2.69
2328 2621 0.745845 CAGAAGACTGCCCCATTCGG 60.746 60.000 0.00 0.00 37.33 4.30
2790 3083 0.698818 AGGCTCTCCCAAAATCCGTT 59.301 50.000 0.00 0.00 35.39 4.44
2953 3246 5.494724 TCAGTGAATTGCAAGAGCTTAGAT 58.505 37.500 4.94 0.00 42.74 1.98
2991 3284 1.952296 ACTTCCCTACGCTATGTACCG 59.048 52.381 0.00 0.00 0.00 4.02
3120 3413 6.627087 TCTGAATTGAGGTACCTTCAGATT 57.373 37.500 28.67 19.88 45.17 2.40
3144 3437 4.219919 AGAGACTTGATAGGGCTACTTCC 58.780 47.826 0.00 0.00 0.00 3.46
3277 3570 3.809832 CGCAGAGAAAGAAGAAAAGGACA 59.190 43.478 0.00 0.00 0.00 4.02
3293 3586 9.586435 AGAAAAGGACAAACATGAAGTAAAAAG 57.414 29.630 0.00 0.00 0.00 2.27
3437 3730 1.858739 ATGGCGGGTCCCAAGCTAAA 61.859 55.000 9.12 0.00 38.61 1.85
3525 3818 2.985847 GGCCGCCTGAAACAGCTT 60.986 61.111 0.71 0.00 0.00 3.74
3597 3890 1.003355 CCTCGGCACCACTGTGATT 60.003 57.895 9.86 0.00 45.76 2.57
3612 3905 3.395858 GTGATTTCACAAGCCATCTCG 57.604 47.619 5.84 0.00 45.75 4.04
3708 4001 1.884579 CAGACATTGCTGCCTTGTCTT 59.115 47.619 23.71 12.12 45.88 3.01
3780 4073 0.679505 TAAAGGACGCTGCTCTGTGT 59.320 50.000 0.00 0.00 0.00 3.72
3788 4081 0.250038 GCTGCTCTGTGTGACCTTCA 60.250 55.000 0.00 0.00 0.00 3.02
4230 4523 1.058284 TAAGGTACAACAAGGCCCGT 58.942 50.000 0.00 0.00 0.00 5.28
4245 4538 1.712018 CCCGTCGCATCTACGAGACA 61.712 60.000 0.00 0.00 43.89 3.41
4291 4584 7.988028 AGTCTACCTAAAAATCTTGGTATGCTC 59.012 37.037 0.00 0.00 34.93 4.26
4318 4611 6.131544 TCTTTTCCACTTTTCAGTACTTGC 57.868 37.500 0.00 0.00 0.00 4.01
4319 4612 4.911514 TTTCCACTTTTCAGTACTTGCC 57.088 40.909 0.00 0.00 0.00 4.52
4355 4648 9.967451 TCTTATCCTTAATCTCTCGAGTGATAT 57.033 33.333 25.65 18.19 0.00 1.63
4409 4715 0.997196 GTAGACATGTTTCGGTCCGC 59.003 55.000 6.34 0.00 34.58 5.54
4427 4733 3.691342 CCGTCCCGACTGCTCCAA 61.691 66.667 0.00 0.00 0.00 3.53
4435 4741 1.066573 CCGACTGCTCCAAGAGATGTT 60.067 52.381 0.00 0.00 0.00 2.71
4556 4908 5.812642 ACCAATACTCGATGTGTGATTCTTC 59.187 40.000 0.00 0.00 0.00 2.87
4766 5608 9.918630 CTGAAATTGGATACTCTCAATTTGTTT 57.081 29.630 15.71 0.00 46.88 2.83
4792 5634 2.885266 CCTTGAATGGAGATGGATGCTG 59.115 50.000 0.00 0.00 0.00 4.41
4801 5643 3.478509 GAGATGGATGCTGCAATCTCTT 58.521 45.455 25.00 3.58 33.67 2.85
4928 5771 5.319453 TCTTCATTTGATGCTCTGGAGTTT 58.681 37.500 0.00 0.00 0.00 2.66
4990 5833 5.586243 GTCTTTTGCTTCATATCAGGTAGCA 59.414 40.000 0.00 0.00 39.85 3.49
4997 5840 5.009410 GCTTCATATCAGGTAGCAAGCAATT 59.991 40.000 6.15 0.00 33.83 2.32
5017 5860 4.859304 TTTGCTGTGCATCTTCTGAAAT 57.141 36.364 0.00 0.00 38.76 2.17
5060 5903 5.367302 AGCTCCAAGAGAGAATATGCTTTC 58.633 41.667 0.00 0.00 46.50 2.62
5105 5948 2.026822 AGTTCTTGGCCTAGTGTGGATG 60.027 50.000 14.12 0.00 0.00 3.51
5129 5972 6.098409 TGTCCAATGGCAAAAAGTTTACCTAA 59.902 34.615 0.00 0.00 0.00 2.69
5144 5987 1.349688 ACCTAATGCCTCACGTTTGGA 59.650 47.619 7.69 0.00 41.21 3.53
5206 6053 7.039011 ACAAGTCATGAGGAATCTTACAGTGTA 60.039 37.037 0.00 0.00 0.00 2.90
5240 6087 1.269257 GCCTTTCTTGCCTTGTGTGTC 60.269 52.381 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 8.181573 TCTTCGCCATACAAATTTCAGTTAATC 58.818 33.333 0.00 0.00 0.00 1.75
9 10 5.957842 TTCTTCGCCATACAAATTTCAGT 57.042 34.783 0.00 0.00 0.00 3.41
26 27 4.274950 TGAAATTCGGTGTGGACTTTCTTC 59.725 41.667 6.85 0.00 36.85 2.87
35 36 6.037098 TGTTTACTTTTGAAATTCGGTGTGG 58.963 36.000 0.00 0.00 0.00 4.17
55 56 7.201688 GGACAGTGCAAATAAAATGGTTTGTTT 60.202 33.333 0.00 0.00 38.23 2.83
56 57 6.259829 GGACAGTGCAAATAAAATGGTTTGTT 59.740 34.615 0.00 0.00 37.57 2.83
57 58 5.757808 GGACAGTGCAAATAAAATGGTTTGT 59.242 36.000 0.00 0.00 37.57 2.83
58 59 5.757320 TGGACAGTGCAAATAAAATGGTTTG 59.243 36.000 0.00 0.00 38.13 2.93
62 63 4.330620 GCATGGACAGTGCAAATAAAATGG 59.669 41.667 0.00 0.00 42.08 3.16
64 65 4.020396 TGGCATGGACAGTGCAAATAAAAT 60.020 37.500 0.00 0.00 44.25 1.82
67 68 2.523245 TGGCATGGACAGTGCAAATAA 58.477 42.857 0.00 0.00 44.25 1.40
68 69 2.212812 TGGCATGGACAGTGCAAATA 57.787 45.000 0.00 0.00 44.25 1.40
77 78 3.096092 GGGAATTACTTTGGCATGGACA 58.904 45.455 0.00 0.00 0.00 4.02
101 102 3.922171 ACATGTTTTGGGGAGCAAAAA 57.078 38.095 0.00 0.00 33.94 1.94
102 103 3.922171 AACATGTTTTGGGGAGCAAAA 57.078 38.095 4.92 0.00 0.00 2.44
103 104 3.922171 AAACATGTTTTGGGGAGCAAA 57.078 38.095 18.13 0.00 0.00 3.68
104 105 3.198635 TGAAAACATGTTTTGGGGAGCAA 59.801 39.130 34.88 11.79 42.26 3.91
105 106 2.768527 TGAAAACATGTTTTGGGGAGCA 59.231 40.909 34.88 23.53 42.26 4.26
106 107 3.467374 TGAAAACATGTTTTGGGGAGC 57.533 42.857 34.88 21.57 42.26 4.70
107 108 5.277925 GCAAATGAAAACATGTTTTGGGGAG 60.278 40.000 34.88 22.85 42.26 4.30
108 109 4.578105 GCAAATGAAAACATGTTTTGGGGA 59.422 37.500 34.88 18.72 42.26 4.81
109 110 4.337555 TGCAAATGAAAACATGTTTTGGGG 59.662 37.500 34.88 21.20 42.26 4.96
110 111 5.066246 AGTGCAAATGAAAACATGTTTTGGG 59.934 36.000 34.88 20.91 42.26 4.12
111 112 5.966503 CAGTGCAAATGAAAACATGTTTTGG 59.033 36.000 34.88 20.64 42.26 3.28
112 113 6.544622 ACAGTGCAAATGAAAACATGTTTTG 58.455 32.000 34.88 23.60 42.26 2.44
113 114 6.740411 ACAGTGCAAATGAAAACATGTTTT 57.260 29.167 31.40 31.40 44.59 2.43
114 115 6.370994 TGAACAGTGCAAATGAAAACATGTTT 59.629 30.769 18.13 18.13 34.17 2.83
115 116 5.873712 TGAACAGTGCAAATGAAAACATGTT 59.126 32.000 4.92 4.92 34.17 2.71
116 117 5.417811 TGAACAGTGCAAATGAAAACATGT 58.582 33.333 7.15 0.00 34.17 3.21
117 118 5.970140 TGAACAGTGCAAATGAAAACATG 57.030 34.783 7.15 0.00 34.17 3.21
118 119 5.049954 GCATGAACAGTGCAAATGAAAACAT 60.050 36.000 7.15 4.54 42.08 2.71
119 120 4.270566 GCATGAACAGTGCAAATGAAAACA 59.729 37.500 7.15 2.74 42.08 2.83
120 121 4.318974 GGCATGAACAGTGCAAATGAAAAC 60.319 41.667 7.15 0.00 44.25 2.43
125 126 2.736144 AGGCATGAACAGTGCAAATG 57.264 45.000 0.00 0.00 44.25 2.32
155 156 6.680810 CAATGGACAGCAACATCTAAAAAGA 58.319 36.000 0.00 0.00 0.00 2.52
156 157 5.346822 GCAATGGACAGCAACATCTAAAAAG 59.653 40.000 0.00 0.00 0.00 2.27
157 158 5.010922 AGCAATGGACAGCAACATCTAAAAA 59.989 36.000 0.00 0.00 0.00 1.94
184 198 5.039333 GCAGGCTATTTTTGTAATCAGCTG 58.961 41.667 7.63 7.63 0.00 4.24
219 233 1.836802 GAAGAGGGGAGAACAGAGCAT 59.163 52.381 0.00 0.00 0.00 3.79
220 234 1.270907 GAAGAGGGGAGAACAGAGCA 58.729 55.000 0.00 0.00 0.00 4.26
221 235 0.174617 CGAAGAGGGGAGAACAGAGC 59.825 60.000 0.00 0.00 0.00 4.09
222 236 0.174617 GCGAAGAGGGGAGAACAGAG 59.825 60.000 0.00 0.00 0.00 3.35
223 237 1.258445 GGCGAAGAGGGGAGAACAGA 61.258 60.000 0.00 0.00 0.00 3.41
277 291 1.817099 GATGAGCTTGGCAGGGACG 60.817 63.158 0.00 0.00 0.00 4.79
302 316 3.146913 AAAATGGGCGCCATCCGG 61.147 61.111 30.85 0.00 44.40 5.14
303 317 1.380403 TACAAAATGGGCGCCATCCG 61.380 55.000 30.85 13.42 44.40 4.18
305 319 0.102300 GGTACAAAATGGGCGCCATC 59.898 55.000 30.85 12.89 44.40 3.51
311 338 1.214325 GCCGTGGTACAAAATGGGC 59.786 57.895 0.00 0.00 44.16 5.36
327 363 2.442830 GGCCCCTGGAAGATTGCC 60.443 66.667 0.00 0.00 35.23 4.52
345 381 2.757868 CACATCTCTCGTTTCTCCTCCT 59.242 50.000 0.00 0.00 0.00 3.69
354 390 2.365617 ACAACCTGTCACATCTCTCGTT 59.634 45.455 0.00 0.00 0.00 3.85
356 392 2.732412 ACAACCTGTCACATCTCTCG 57.268 50.000 0.00 0.00 0.00 4.04
358 395 3.470709 CACAACAACCTGTCACATCTCT 58.529 45.455 0.00 0.00 0.00 3.10
377 414 0.038166 TTCTTCTGGTGGATGGGCAC 59.962 55.000 0.00 0.00 0.00 5.01
378 415 0.329261 CTTCTTCTGGTGGATGGGCA 59.671 55.000 0.00 0.00 0.00 5.36
379 416 0.620556 TCTTCTTCTGGTGGATGGGC 59.379 55.000 0.00 0.00 0.00 5.36
380 417 3.285484 CATTCTTCTTCTGGTGGATGGG 58.715 50.000 0.00 0.00 0.00 4.00
384 452 3.251484 ACTCCATTCTTCTTCTGGTGGA 58.749 45.455 0.00 0.00 34.77 4.02
466 561 3.319198 TCCCTGTCCCAAGACGCC 61.319 66.667 0.00 0.00 46.74 5.68
471 566 1.522569 GATCCGTCCCTGTCCCAAG 59.477 63.158 0.00 0.00 0.00 3.61
472 567 1.993391 GGATCCGTCCCTGTCCCAA 60.993 63.158 0.00 0.00 38.69 4.12
475 570 0.546598 AAATGGATCCGTCCCTGTCC 59.453 55.000 7.01 0.00 44.41 4.02
476 571 2.698797 TCTAAATGGATCCGTCCCTGTC 59.301 50.000 7.01 0.00 44.41 3.51
477 572 2.700897 CTCTAAATGGATCCGTCCCTGT 59.299 50.000 7.01 0.00 44.41 4.00
478 573 2.037772 CCTCTAAATGGATCCGTCCCTG 59.962 54.545 7.01 0.00 44.41 4.45
635 757 4.305539 TGAAGATTGCTGAAGATTGGGA 57.694 40.909 0.00 0.00 0.00 4.37
636 758 4.643334 TGATGAAGATTGCTGAAGATTGGG 59.357 41.667 0.00 0.00 0.00 4.12
637 759 5.830000 TGATGAAGATTGCTGAAGATTGG 57.170 39.130 0.00 0.00 0.00 3.16
639 761 6.127703 CCTGTTGATGAAGATTGCTGAAGATT 60.128 38.462 0.00 0.00 0.00 2.40
640 762 5.357314 CCTGTTGATGAAGATTGCTGAAGAT 59.643 40.000 0.00 0.00 0.00 2.40
641 763 4.698780 CCTGTTGATGAAGATTGCTGAAGA 59.301 41.667 0.00 0.00 0.00 2.87
642 764 4.458295 ACCTGTTGATGAAGATTGCTGAAG 59.542 41.667 0.00 0.00 0.00 3.02
643 765 4.401022 ACCTGTTGATGAAGATTGCTGAA 58.599 39.130 0.00 0.00 0.00 3.02
693 827 4.125703 GACAATCTGCTCCCTGACTAATG 58.874 47.826 0.00 0.00 0.00 1.90
695 829 3.173151 TGACAATCTGCTCCCTGACTAA 58.827 45.455 0.00 0.00 0.00 2.24
696 830 2.762887 CTGACAATCTGCTCCCTGACTA 59.237 50.000 0.00 0.00 0.00 2.59
697 831 1.554160 CTGACAATCTGCTCCCTGACT 59.446 52.381 0.00 0.00 0.00 3.41
698 832 1.277557 ACTGACAATCTGCTCCCTGAC 59.722 52.381 0.00 0.00 0.00 3.51
699 833 1.649321 ACTGACAATCTGCTCCCTGA 58.351 50.000 0.00 0.00 0.00 3.86
700 834 2.486472 AACTGACAATCTGCTCCCTG 57.514 50.000 0.00 0.00 0.00 4.45
701 835 4.851639 AATAACTGACAATCTGCTCCCT 57.148 40.909 0.00 0.00 0.00 4.20
702 836 7.067494 ACAATAAATAACTGACAATCTGCTCCC 59.933 37.037 0.00 0.00 0.00 4.30
714 848 8.856153 TGGAACTAAGCACAATAAATAACTGA 57.144 30.769 0.00 0.00 0.00 3.41
752 886 0.733150 TATATCAGATCGGGAGCGCG 59.267 55.000 0.00 0.00 0.00 6.86
772 906 7.175641 ACAGGAAAGAACAAAATCCATCTACTG 59.824 37.037 0.00 0.00 34.30 2.74
805 1024 6.697455 TCGATTTTAGTTGAGGATCGAATCAG 59.303 38.462 4.49 0.00 43.65 2.90
811 1030 8.575565 TTTATCTCGATTTTAGTTGAGGATCG 57.424 34.615 0.00 0.00 40.51 3.69
821 1040 8.677148 TCTTTCCCCATTTATCTCGATTTTAG 57.323 34.615 0.00 0.00 0.00 1.85
823 1042 7.954666 TTCTTTCCCCATTTATCTCGATTTT 57.045 32.000 0.00 0.00 0.00 1.82
824 1043 7.231519 GGATTCTTTCCCCATTTATCTCGATTT 59.768 37.037 0.00 0.00 38.75 2.17
869 1105 3.044986 CGATTAGGGCGCAAATTGATTG 58.955 45.455 10.83 0.00 42.21 2.67
870 1106 3.354089 CGATTAGGGCGCAAATTGATT 57.646 42.857 10.83 0.00 0.00 2.57
881 1152 0.377203 CTTTCAACGGCGATTAGGGC 59.623 55.000 16.62 0.00 0.00 5.19
914 1185 0.821517 TATCAGTACAGCACGTGGGG 59.178 55.000 18.88 0.00 0.00 4.96
918 1192 7.333423 ACAATAATTTGTATCAGTACAGCACGT 59.667 33.333 0.00 0.00 44.22 4.49
927 1201 9.638239 AAATGCGAAACAATAATTTGTATCAGT 57.362 25.926 0.00 0.00 45.30 3.41
932 1206 7.006653 CGACGAAATGCGAAACAATAATTTGTA 59.993 33.333 0.00 0.00 43.40 2.41
940 1214 2.720590 CGACGACGAAATGCGAAACAAT 60.721 45.455 0.00 0.00 44.57 2.71
941 1215 1.396192 CGACGACGAAATGCGAAACAA 60.396 47.619 0.00 0.00 44.57 2.83
942 1216 0.159973 CGACGACGAAATGCGAAACA 59.840 50.000 0.00 0.00 44.57 2.83
943 1217 0.160182 ACGACGACGAAATGCGAAAC 59.840 50.000 15.32 0.00 44.57 2.78
948 1222 0.785708 CAGCAACGACGACGAAATGC 60.786 55.000 15.32 19.00 42.26 3.56
957 1231 0.232303 GACCTTCAACAGCAACGACG 59.768 55.000 0.00 0.00 0.00 5.12
1398 1682 0.947960 GCATCTCGTCCTCGATCTCA 59.052 55.000 0.00 0.00 45.21 3.27
1475 1768 3.683847 GCAGCTCCTGGACATTTCACTAT 60.684 47.826 0.00 0.00 31.21 2.12
1476 1769 2.355108 GCAGCTCCTGGACATTTCACTA 60.355 50.000 0.00 0.00 31.21 2.74
1545 1838 3.378399 GAGGCCGCCCAGAGACTTC 62.378 68.421 5.55 0.00 0.00 3.01
1953 2246 4.269523 TTCAAGCCTGCCGCCACT 62.270 61.111 0.00 0.00 38.78 4.00
2051 2344 2.500910 AGTGCTTGGATCTCCTCTGAAG 59.499 50.000 0.00 0.00 36.82 3.02
2062 2355 0.330604 ACATCCTGCAGTGCTTGGAT 59.669 50.000 26.52 26.52 40.73 3.41
2070 2363 0.977627 TCATCCCGACATCCTGCAGT 60.978 55.000 13.81 0.00 0.00 4.40
2074 2367 2.608998 CGATCTTCATCCCGACATCCTG 60.609 54.545 0.00 0.00 0.00 3.86
2124 2417 3.609853 GACACCTGCAATGACCTTGATA 58.390 45.455 4.68 0.00 36.97 2.15
2172 2465 0.545071 TCAGGACCATCTGCCACTCA 60.545 55.000 0.00 0.00 34.91 3.41
2179 2472 2.099141 TCGCTTTTCAGGACCATCTG 57.901 50.000 0.00 0.00 36.17 2.90
2208 2501 3.266230 TTGAAGCAACGGCCGCATG 62.266 57.895 28.58 25.38 42.56 4.06
2328 2621 2.020559 CGCACGAGATCAAAGCGC 59.979 61.111 0.00 0.00 41.95 5.92
2532 2825 6.127101 TCTCTCCTGACCGTCAATTAAGATA 58.873 40.000 2.19 0.00 0.00 1.98
2790 3083 1.672030 CAGATGTCGCAAGGTGCCA 60.672 57.895 0.00 0.00 41.12 4.92
2908 3201 1.528129 GACCAAGGGAGTTTCTGCAG 58.472 55.000 7.63 7.63 0.00 4.41
2953 3246 2.525124 TTCCCTCGAGGCAAAGGCA 61.525 57.895 26.87 0.00 43.71 4.75
2991 3284 2.341846 TCAGTTCACCCACACCTTTC 57.658 50.000 0.00 0.00 0.00 2.62
3120 3413 4.528076 AGTAGCCCTATCAAGTCTCTCA 57.472 45.455 0.00 0.00 0.00 3.27
3144 3437 3.184683 GCGAGTGCAGAAGCTCCG 61.185 66.667 0.00 0.00 42.74 4.63
3277 3570 6.974622 CACTGAGCACTTTTTACTTCATGTTT 59.025 34.615 0.00 0.00 0.00 2.83
3293 3586 4.662468 TCATCTCTAATCCACTGAGCAC 57.338 45.455 0.00 0.00 0.00 4.40
3437 3730 2.936032 GGGCAGGGAAGGAGGTGT 60.936 66.667 0.00 0.00 0.00 4.16
3525 3818 4.949856 GCATTTGAGATTTCCAGGGACTTA 59.050 41.667 0.00 0.00 34.60 2.24
3597 3890 1.610624 GGGAACGAGATGGCTTGTGAA 60.611 52.381 0.00 0.00 38.76 3.18
3780 4073 0.608130 CACCCTCGACATGAAGGTCA 59.392 55.000 0.00 0.00 39.51 4.02
3788 4081 1.308069 GCAATGTGCACCCTCGACAT 61.308 55.000 15.69 0.00 44.26 3.06
4230 4523 2.159240 AGCATTTGTCTCGTAGATGCGA 60.159 45.455 0.00 0.00 45.69 5.10
4245 4538 4.712476 ACTTCTCTTCACACTGAGCATTT 58.288 39.130 0.00 0.00 0.00 2.32
4291 4584 7.793927 AGTACTGAAAAGTGGAAAAGAAGAG 57.206 36.000 0.00 0.00 0.00 2.85
4318 4611 8.970859 AGATTAAGGATAAGATGACAACTTGG 57.029 34.615 8.14 0.00 0.00 3.61
4319 4612 9.829507 AGAGATTAAGGATAAGATGACAACTTG 57.170 33.333 8.14 0.00 0.00 3.16
4366 4659 6.183360 ACCAAACAGCTGCAAGTACTTAAAAT 60.183 34.615 15.27 0.00 35.30 1.82
4367 4660 5.126384 ACCAAACAGCTGCAAGTACTTAAAA 59.874 36.000 15.27 0.00 35.30 1.52
4417 4723 2.740981 CACAACATCTCTTGGAGCAGTC 59.259 50.000 0.00 0.00 0.00 3.51
4427 4733 1.554160 CTCAGGCCTCACAACATCTCT 59.446 52.381 0.00 0.00 0.00 3.10
4435 4741 0.907486 CTCATTCCTCAGGCCTCACA 59.093 55.000 0.00 0.00 0.00 3.58
4556 4908 0.955919 GCCAGAACCAGGAAACGGAG 60.956 60.000 0.00 0.00 0.00 4.63
4766 5608 6.044754 AGCATCCATCTCCATTCAAGGTATTA 59.955 38.462 0.00 0.00 0.00 0.98
4792 5634 5.684626 CAGAACACAAACTTCAAGAGATTGC 59.315 40.000 0.00 0.00 40.66 3.56
4928 5771 5.178096 TGCAATCTCAATACCAGAAAGGA 57.822 39.130 0.00 0.00 41.22 3.36
4997 5840 4.859304 AATTTCAGAAGATGCACAGCAA 57.141 36.364 0.00 0.00 43.62 3.91
5060 5903 5.381174 TCAGAAGATCACAAAAGGCAATG 57.619 39.130 0.00 0.00 0.00 2.82
5105 5948 4.956085 AGGTAAACTTTTTGCCATTGGAC 58.044 39.130 6.95 0.00 0.00 4.02
5129 5972 1.271325 TGACATCCAAACGTGAGGCAT 60.271 47.619 0.00 0.00 0.00 4.40
5144 5987 2.224113 CCTTTGCCAGCAGTTTTGACAT 60.224 45.455 0.00 0.00 0.00 3.06
5206 6053 3.290710 AGAAAGGCGGCATTACATCATT 58.709 40.909 13.08 0.00 0.00 2.57
5240 6087 5.189180 CCTGGGAGAAGTTATTCCAAAGAG 58.811 45.833 0.00 0.00 35.94 2.85


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

AutoCloner maintained by Alex Coulton.