Multiple sequence alignment - TraesCS7A01G556600

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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 TraesCS7A01G556600 chr7A 100.000 2486 0 0 1 2486 727799887 727802372 0.000000e+00 4591.0
1 TraesCS7A01G556600 chr7D 90.248 1333 68 27 916 2213 638274434 638273129 0.000000e+00 1685.0
2 TraesCS7A01G556600 chr7D 94.255 557 23 6 1 551 638275332 638274779 0.000000e+00 843.0
3 TraesCS7A01G556600 chr7D 96.341 246 6 1 2214 2456 638271763 638271518 3.850000e-108 401.0
4 TraesCS7A01G556600 chr7D 95.588 136 6 0 568 703 638274792 638274657 4.160000e-53 219.0
5 TraesCS7A01G556600 chr7B 85.908 738 55 19 916 1627 734426487 734427201 0.000000e+00 741.0
6 TraesCS7A01G556600 chr7B 85.536 560 38 16 1893 2450 734427224 734427742 1.680000e-151 545.0
7 TraesCS7A01G556600 chr7B 81.502 546 48 15 1241 1767 734417016 734417527 1.390000e-107 399.0
8 TraesCS7A01G556600 chr7B 78.342 591 79 30 916 1467 734379435 734380015 1.100000e-88 337.0
9 TraesCS7A01G556600 chr7B 86.018 329 26 5 1893 2213 734417512 734417828 3.960000e-88 335.0
10 TraesCS7A01G556600 chr7B 90.090 222 21 1 2220 2440 734417949 734418170 1.130000e-73 287.0
11 TraesCS7A01G556600 chr7B 94.000 50 1 2 729 777 329924898 329924850 9.540000e-10 75.0
12 TraesCS7A01G556600 chr7B 92.157 51 4 0 720 770 372023822 372023772 3.430000e-09 73.1
13 TraesCS7A01G556600 chr4D 81.452 124 21 2 1265 1387 483041293 483041171 1.570000e-17 100.0
14 TraesCS7A01G556600 chr6B 94.545 55 2 1 723 777 679732997 679732944 1.580000e-12 84.2
15 TraesCS7A01G556600 chr6B 95.918 49 0 2 728 775 472233679 472233632 7.370000e-11 78.7
16 TraesCS7A01G556600 chr5D 91.667 60 3 1 729 786 356692158 356692099 5.700000e-12 82.4
17 TraesCS7A01G556600 chr2B 92.857 56 2 1 728 781 568734084 568734139 2.050000e-11 80.5
18 TraesCS7A01G556600 chr3D 97.778 45 1 0 729 773 275776957 275776913 7.370000e-11 78.7
19 TraesCS7A01G556600 chr4A 95.745 47 2 0 729 775 30311144 30311098 2.650000e-10 76.8
20 TraesCS7A01G556600 chr2A 89.831 59 6 0 729 787 32367635 32367693 2.650000e-10 76.8
21 TraesCS7A01G556600 chr1B 89.583 48 5 0 1841 1888 25238621 25238668 7.420000e-06 62.1


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 TraesCS7A01G556600 chr7A 727799887 727802372 2485 False 4591.000000 4591 100.000 1 2486 1 chr7A.!!$F1 2485
1 TraesCS7A01G556600 chr7D 638271518 638275332 3814 True 787.000000 1685 94.108 1 2456 4 chr7D.!!$R1 2455
2 TraesCS7A01G556600 chr7B 734426487 734427742 1255 False 643.000000 741 85.722 916 2450 2 chr7B.!!$F3 1534
3 TraesCS7A01G556600 chr7B 734417016 734418170 1154 False 340.333333 399 85.870 1241 2440 3 chr7B.!!$F2 1199
4 TraesCS7A01G556600 chr7B 734379435 734380015 580 False 337.000000 337 78.342 916 1467 1 chr7B.!!$F1 551

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
897 940 0.320374 CACGGCCAGAGTCAAAGGTA 59.68 55.0 2.24 0.0 0.0 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2009 2149 1.076727 TCCGAAGAGGACTGCCAGA 59.923 57.895 0.0 0.0 45.98 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
23 24 6.690194 AATGATGGAGTCAACTTAGCAATC 57.310 37.500 0.00 0.00 40.97 2.67
48 49 8.181573 TCGGATTTGTTGTTTTTGCTCTATATC 58.818 33.333 0.00 0.00 0.00 1.63
178 179 8.783660 AATATGTTATCACTTAGTCCTCTCCA 57.216 34.615 0.00 0.00 0.00 3.86
238 240 7.797121 ACCTTCATAAATGTTCCCTTTTCAT 57.203 32.000 0.00 0.00 0.00 2.57
320 322 4.026407 GCGCACGGATCAAATAAGTTAAC 58.974 43.478 0.30 0.00 0.00 2.01
321 323 4.584394 CGCACGGATCAAATAAGTTAACC 58.416 43.478 0.88 0.00 0.00 2.85
322 324 4.093703 CGCACGGATCAAATAAGTTAACCA 59.906 41.667 0.88 0.00 0.00 3.67
334 339 7.898014 AATAAGTTAACCATTTCCCCTCATC 57.102 36.000 0.88 0.00 0.00 2.92
369 374 3.940209 ATTTCGCATGCTCCAAGAAAA 57.060 38.095 17.13 5.22 34.97 2.29
371 376 3.940209 TTCGCATGCTCCAAGAAAATT 57.060 38.095 17.13 0.00 0.00 1.82
372 377 3.492421 TCGCATGCTCCAAGAAAATTC 57.508 42.857 17.13 0.00 0.00 2.17
411 417 4.049186 GCATCTTTCCATAATGCAAGCAG 58.951 43.478 0.00 0.00 44.07 4.24
413 419 3.025978 TCTTTCCATAATGCAAGCAGGG 58.974 45.455 0.00 0.07 0.00 4.45
523 529 3.388024 TCAGGCCACTAATATCTTTCGCT 59.612 43.478 5.01 0.00 0.00 4.93
536 542 4.265904 TCTTTCGCTGATCCACTTTACA 57.734 40.909 0.00 0.00 0.00 2.41
552 558 9.787435 TCCACTTTACAATAAGAAATGTGTACT 57.213 29.630 0.00 0.00 0.00 2.73
560 566 9.502091 ACAATAAGAAATGTGTACTAGCTTCAA 57.498 29.630 0.00 0.00 0.00 2.69
666 672 3.910862 TCTTTTCACACACACGTTACG 57.089 42.857 2.19 2.19 0.00 3.18
678 684 1.083657 CGTTACGCGCACATATGGC 60.084 57.895 5.73 6.87 0.00 4.40
703 709 1.829222 CTCCAGGAAGGTAGGCGTTTA 59.171 52.381 0.00 0.00 39.02 2.01
704 710 1.829222 TCCAGGAAGGTAGGCGTTTAG 59.171 52.381 0.00 0.00 39.02 1.85
705 711 1.553704 CCAGGAAGGTAGGCGTTTAGT 59.446 52.381 0.00 0.00 0.00 2.24
706 712 2.762327 CCAGGAAGGTAGGCGTTTAGTA 59.238 50.000 0.00 0.00 0.00 1.82
707 713 3.387050 CCAGGAAGGTAGGCGTTTAGTAT 59.613 47.826 0.00 0.00 0.00 2.12
708 714 4.141779 CCAGGAAGGTAGGCGTTTAGTATT 60.142 45.833 0.00 0.00 0.00 1.89
733 753 7.049133 TCTACAGTGTCACTAGATCCTACTTC 58.951 42.308 4.85 0.00 0.00 3.01
734 754 4.951094 ACAGTGTCACTAGATCCTACTTCC 59.049 45.833 4.85 0.00 0.00 3.46
735 755 5.197451 CAGTGTCACTAGATCCTACTTCCT 58.803 45.833 4.85 0.00 0.00 3.36
736 756 5.654650 CAGTGTCACTAGATCCTACTTCCTT 59.345 44.000 4.85 0.00 0.00 3.36
737 757 5.889289 AGTGTCACTAGATCCTACTTCCTTC 59.111 44.000 2.87 0.00 0.00 3.46
738 758 4.882427 TGTCACTAGATCCTACTTCCTTCG 59.118 45.833 0.00 0.00 0.00 3.79
739 759 4.883006 GTCACTAGATCCTACTTCCTTCGT 59.117 45.833 0.00 0.00 0.00 3.85
740 760 5.357596 GTCACTAGATCCTACTTCCTTCGTT 59.642 44.000 0.00 0.00 0.00 3.85
741 761 5.950549 TCACTAGATCCTACTTCCTTCGTTT 59.049 40.000 0.00 0.00 0.00 3.60
742 762 6.095160 TCACTAGATCCTACTTCCTTCGTTTC 59.905 42.308 0.00 0.00 0.00 2.78
743 763 5.950549 ACTAGATCCTACTTCCTTCGTTTCA 59.049 40.000 0.00 0.00 0.00 2.69
744 764 5.740290 AGATCCTACTTCCTTCGTTTCAA 57.260 39.130 0.00 0.00 0.00 2.69
745 765 6.110411 AGATCCTACTTCCTTCGTTTCAAA 57.890 37.500 0.00 0.00 0.00 2.69
746 766 6.531021 AGATCCTACTTCCTTCGTTTCAAAA 58.469 36.000 0.00 0.00 0.00 2.44
747 767 7.168905 AGATCCTACTTCCTTCGTTTCAAAAT 58.831 34.615 0.00 0.00 0.00 1.82
748 768 8.319146 AGATCCTACTTCCTTCGTTTCAAAATA 58.681 33.333 0.00 0.00 0.00 1.40
749 769 8.857694 ATCCTACTTCCTTCGTTTCAAAATAA 57.142 30.769 0.00 0.00 0.00 1.40
750 770 8.680039 TCCTACTTCCTTCGTTTCAAAATAAA 57.320 30.769 0.00 0.00 0.00 1.40
751 771 9.292195 TCCTACTTCCTTCGTTTCAAAATAAAT 57.708 29.630 0.00 0.00 0.00 1.40
752 772 9.341899 CCTACTTCCTTCGTTTCAAAATAAATG 57.658 33.333 0.00 0.00 0.00 2.32
754 774 8.797266 ACTTCCTTCGTTTCAAAATAAATGAC 57.203 30.769 0.00 0.00 34.83 3.06
755 775 7.865889 ACTTCCTTCGTTTCAAAATAAATGACC 59.134 33.333 0.00 0.00 34.83 4.02
756 776 6.683715 TCCTTCGTTTCAAAATAAATGACCC 58.316 36.000 0.00 0.00 34.83 4.46
757 777 6.265649 TCCTTCGTTTCAAAATAAATGACCCA 59.734 34.615 0.00 0.00 34.83 4.51
758 778 6.926272 CCTTCGTTTCAAAATAAATGACCCAA 59.074 34.615 0.00 0.00 34.83 4.12
759 779 7.095816 CCTTCGTTTCAAAATAAATGACCCAAC 60.096 37.037 0.00 0.00 34.83 3.77
760 780 7.045126 TCGTTTCAAAATAAATGACCCAACT 57.955 32.000 0.00 0.00 31.13 3.16
761 781 7.493367 TCGTTTCAAAATAAATGACCCAACTT 58.507 30.769 0.00 0.00 31.13 2.66
762 782 7.982354 TCGTTTCAAAATAAATGACCCAACTTT 59.018 29.630 0.00 0.00 31.13 2.66
763 783 9.250624 CGTTTCAAAATAAATGACCCAACTTTA 57.749 29.630 0.00 0.00 0.00 1.85
817 837 4.003788 CGTGGGCGTCACCTTCCT 62.004 66.667 0.00 0.00 43.23 3.36
820 840 1.072505 TGGGCGTCACCTTCCTTTC 59.927 57.895 0.00 0.00 39.10 2.62
825 845 1.512926 CGTCACCTTCCTTTCCACAG 58.487 55.000 0.00 0.00 0.00 3.66
841 861 4.988598 AGCACCACGGCCACTTCG 62.989 66.667 2.24 0.00 0.00 3.79
874 894 0.873312 CTACGCAGAGCATCGCACAT 60.873 55.000 0.00 0.00 42.67 3.21
877 897 1.147557 CGCAGAGCATCGCACATACA 61.148 55.000 0.00 0.00 42.67 2.29
897 940 0.320374 CACGGCCAGAGTCAAAGGTA 59.680 55.000 2.24 0.00 0.00 3.08
923 988 0.901827 TCAGACACCATACCATGCGT 59.098 50.000 0.00 0.00 0.00 5.24
952 1017 4.767255 CCTCCTGCACCGAGCCAC 62.767 72.222 1.16 0.00 44.83 5.01
1239 1328 3.250323 CCAGCGCAGTCATCGTCG 61.250 66.667 11.47 0.00 0.00 5.12
1241 1330 2.202492 AGCGCAGTCATCGTCGTC 60.202 61.111 11.47 0.00 0.00 4.20
1242 1331 3.598562 GCGCAGTCATCGTCGTCG 61.599 66.667 0.30 0.00 38.55 5.12
1257 1346 1.202568 GTCGTCGTCGTCGTCAGAA 59.797 57.895 11.41 0.00 38.33 3.02
1262 1351 2.497092 CGTCGTCGTCAGAATGCGG 61.497 63.158 0.00 0.00 36.53 5.69
1470 1583 3.889044 GAGAGGTGCGGCGATCGA 61.889 66.667 21.57 0.00 42.43 3.59
1471 1584 3.815569 GAGAGGTGCGGCGATCGAG 62.816 68.421 21.57 13.01 42.43 4.04
1472 1585 3.889044 GAGGTGCGGCGATCGAGA 61.889 66.667 21.57 0.00 42.43 4.04
1515 1631 1.831736 CGAGAACATGTCCTTACCCCT 59.168 52.381 0.00 0.00 0.00 4.79
1570 1686 3.316588 GGCTGTCGATCTGATGTCTCTTA 59.683 47.826 0.00 0.00 0.00 2.10
1701 1840 3.003480 GCCATGAACAAGTCACCTACTC 58.997 50.000 0.00 0.00 39.72 2.59
1730 1869 3.601443 ATTCACCTCTTGTCCTCTTCG 57.399 47.619 0.00 0.00 0.00 3.79
1755 1894 2.046285 GGCCGGGACAAATCACCAG 61.046 63.158 2.18 0.00 0.00 4.00
1758 1897 1.612199 GCCGGGACAAATCACCAGTTA 60.612 52.381 2.18 0.00 0.00 2.24
1768 1907 7.362142 GGACAAATCACCAGTTAATCTTCTTCC 60.362 40.741 0.00 0.00 0.00 3.46
1770 1909 7.725844 ACAAATCACCAGTTAATCTTCTTCCTT 59.274 33.333 0.00 0.00 0.00 3.36
1773 1912 8.712228 ATCACCAGTTAATCTTCTTCCTTTTT 57.288 30.769 0.00 0.00 0.00 1.94
1774 1913 8.166422 TCACCAGTTAATCTTCTTCCTTTTTC 57.834 34.615 0.00 0.00 0.00 2.29
1775 1914 7.998964 TCACCAGTTAATCTTCTTCCTTTTTCT 59.001 33.333 0.00 0.00 0.00 2.52
1782 1921 4.932146 TCTTCTTCCTTTTTCTTTTGCGG 58.068 39.130 0.00 0.00 0.00 5.69
1815 1954 7.336931 ACAATGTATTACTCATCACCAAGGTTC 59.663 37.037 0.00 0.00 0.00 3.62
1962 2101 8.420189 GTTCAATTGAAAATAGCTTCAGTTTCG 58.580 33.333 22.07 0.00 34.20 3.46
2009 2149 1.699634 CATCGACCATGGATTAGGGGT 59.300 52.381 21.47 0.00 33.51 4.95
2026 2166 1.216710 GTCTGGCAGTCCTCTTCGG 59.783 63.158 15.27 0.00 0.00 4.30
2091 2239 1.784062 GTGTCTGATCACACGCAGC 59.216 57.895 9.49 0.00 37.53 5.25
2092 2240 1.734117 TGTCTGATCACACGCAGCG 60.734 57.895 14.82 14.82 32.27 5.18
2093 2241 2.810887 TCTGATCACACGCAGCGC 60.811 61.111 16.61 0.00 32.27 5.92
2094 2242 3.113979 CTGATCACACGCAGCGCA 61.114 61.111 16.61 2.15 0.00 6.09
2234 3778 3.797039 ACACGGGATTGATCATACACAG 58.203 45.455 0.00 0.00 0.00 3.66
2259 3806 2.514458 AGTTGCTACTTTCCATGGGG 57.486 50.000 13.02 5.34 0.00 4.96
2419 3967 3.007979 TCATACGAAATCGATGGTCCG 57.992 47.619 10.16 3.09 43.02 4.79
2450 3998 3.546616 GCATCACAAAGCAAAGGCAAAAC 60.547 43.478 0.00 0.00 44.61 2.43
2451 3999 3.325293 TCACAAAGCAAAGGCAAAACA 57.675 38.095 0.00 0.00 44.61 2.83
2456 4004 2.399916 AGCAAAGGCAAAACAAAGCA 57.600 40.000 0.00 0.00 44.61 3.91
2457 4005 2.709213 AGCAAAGGCAAAACAAAGCAA 58.291 38.095 0.00 0.00 44.61 3.91
2458 4006 3.080319 AGCAAAGGCAAAACAAAGCAAA 58.920 36.364 0.00 0.00 44.61 3.68
2459 4007 3.127376 AGCAAAGGCAAAACAAAGCAAAG 59.873 39.130 0.00 0.00 44.61 2.77
2460 4008 3.731565 GCAAAGGCAAAACAAAGCAAAGG 60.732 43.478 0.00 0.00 40.72 3.11
2461 4009 3.625649 AAGGCAAAACAAAGCAAAGGA 57.374 38.095 0.00 0.00 0.00 3.36
2462 4010 3.843893 AGGCAAAACAAAGCAAAGGAT 57.156 38.095 0.00 0.00 0.00 3.24
2463 4011 4.953940 AGGCAAAACAAAGCAAAGGATA 57.046 36.364 0.00 0.00 0.00 2.59
2464 4012 4.886579 AGGCAAAACAAAGCAAAGGATAG 58.113 39.130 0.00 0.00 0.00 2.08
2465 4013 4.588528 AGGCAAAACAAAGCAAAGGATAGA 59.411 37.500 0.00 0.00 0.00 1.98
2466 4014 4.925646 GGCAAAACAAAGCAAAGGATAGAG 59.074 41.667 0.00 0.00 0.00 2.43
2467 4015 5.278957 GGCAAAACAAAGCAAAGGATAGAGA 60.279 40.000 0.00 0.00 0.00 3.10
2468 4016 6.393171 GCAAAACAAAGCAAAGGATAGAGAT 58.607 36.000 0.00 0.00 0.00 2.75
2469 4017 6.309737 GCAAAACAAAGCAAAGGATAGAGATG 59.690 38.462 0.00 0.00 0.00 2.90
2470 4018 6.521151 AAACAAAGCAAAGGATAGAGATGG 57.479 37.500 0.00 0.00 0.00 3.51
2471 4019 5.184892 ACAAAGCAAAGGATAGAGATGGT 57.815 39.130 0.00 0.00 0.00 3.55
2472 4020 5.574188 ACAAAGCAAAGGATAGAGATGGTT 58.426 37.500 0.00 0.00 33.57 3.67
2473 4021 6.721318 ACAAAGCAAAGGATAGAGATGGTTA 58.279 36.000 0.00 0.00 32.07 2.85
2474 4022 7.175104 ACAAAGCAAAGGATAGAGATGGTTAA 58.825 34.615 0.00 0.00 32.07 2.01
2475 4023 7.669722 ACAAAGCAAAGGATAGAGATGGTTAAA 59.330 33.333 0.00 0.00 32.07 1.52
2476 4024 8.689972 CAAAGCAAAGGATAGAGATGGTTAAAT 58.310 33.333 0.00 0.00 32.07 1.40
2477 4025 9.920946 AAAGCAAAGGATAGAGATGGTTAAATA 57.079 29.630 0.00 0.00 32.07 1.40
2479 4027 9.512588 AGCAAAGGATAGAGATGGTTAAATATG 57.487 33.333 0.00 0.00 0.00 1.78
2480 4028 8.239998 GCAAAGGATAGAGATGGTTAAATATGC 58.760 37.037 0.00 0.00 0.00 3.14
2481 4029 9.288576 CAAAGGATAGAGATGGTTAAATATGCA 57.711 33.333 0.00 0.00 0.00 3.96
2482 4030 9.512588 AAAGGATAGAGATGGTTAAATATGCAG 57.487 33.333 0.00 0.00 0.00 4.41
2483 4031 8.212259 AGGATAGAGATGGTTAAATATGCAGT 57.788 34.615 0.00 0.00 0.00 4.40
2484 4032 8.317679 AGGATAGAGATGGTTAAATATGCAGTC 58.682 37.037 0.00 0.00 0.00 3.51
2485 4033 8.097038 GGATAGAGATGGTTAAATATGCAGTCA 58.903 37.037 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 5.122396 ACAAATCCGATTGCTAAGTTGACTC 59.878 40.000 0.00 0.00 33.52 3.36
23 24 8.184192 AGATATAGAGCAAAAACAACAAATCCG 58.816 33.333 0.00 0.00 0.00 4.18
71 72 7.796958 AAAAGCGAATTTTGTGCTAGATAAC 57.203 32.000 0.00 0.00 39.67 1.89
80 81 9.368921 GGAAAGAAATAAAAAGCGAATTTTGTG 57.631 29.630 8.36 0.00 40.27 3.33
83 84 8.773645 CCTGGAAAGAAATAAAAAGCGAATTTT 58.226 29.630 0.00 0.00 43.04 1.82
85 86 7.666623 TCCTGGAAAGAAATAAAAAGCGAATT 58.333 30.769 0.00 0.00 0.00 2.17
178 179 4.168101 TGTCTGGAACTAGGGACAAAGAT 58.832 43.478 0.00 0.00 36.04 2.40
296 298 0.042188 CTTATTTGATCCGTGCGCCG 60.042 55.000 4.18 8.27 0.00 6.46
320 322 7.896383 TTTATTGTAAGATGAGGGGAAATGG 57.104 36.000 0.00 0.00 0.00 3.16
321 323 9.807649 CTTTTTATTGTAAGATGAGGGGAAATG 57.192 33.333 0.00 0.00 0.00 2.32
322 324 9.768215 TCTTTTTATTGTAAGATGAGGGGAAAT 57.232 29.630 0.00 0.00 0.00 2.17
334 339 8.863049 AGCATGCGAAATTCTTTTTATTGTAAG 58.137 29.630 13.01 0.00 0.00 2.34
383 389 4.373527 GCATTATGGAAAGATGCATGCAA 58.626 39.130 26.68 6.44 44.18 4.08
411 417 1.718757 GCCAAGCACGATCATCACCC 61.719 60.000 0.00 0.00 0.00 4.61
413 419 1.594862 GTAGCCAAGCACGATCATCAC 59.405 52.381 0.00 0.00 0.00 3.06
486 492 2.076863 GCCTGACTAAAATCACGTGCT 58.923 47.619 11.67 0.00 0.00 4.40
489 495 2.038557 AGTGGCCTGACTAAAATCACGT 59.961 45.455 3.32 0.00 0.00 4.49
523 529 9.295825 ACACATTTCTTATTGTAAAGTGGATCA 57.704 29.630 0.00 0.00 0.00 2.92
576 582 0.028374 AAAAGTTGCGGTGCGTACAC 59.972 50.000 5.86 0.00 46.66 2.90
577 583 0.305313 GAAAAGTTGCGGTGCGTACA 59.695 50.000 5.86 0.00 0.00 2.90
578 584 0.584876 AGAAAAGTTGCGGTGCGTAC 59.415 50.000 0.00 0.00 0.00 3.67
579 585 1.262151 GAAGAAAAGTTGCGGTGCGTA 59.738 47.619 0.00 0.00 0.00 4.42
580 586 0.028902 GAAGAAAAGTTGCGGTGCGT 59.971 50.000 0.00 0.00 0.00 5.24
581 587 0.307760 AGAAGAAAAGTTGCGGTGCG 59.692 50.000 0.00 0.00 0.00 5.34
582 588 2.033424 AGAAGAAGAAAAGTTGCGGTGC 59.967 45.455 0.00 0.00 0.00 5.01
583 589 3.971032 AGAAGAAGAAAAGTTGCGGTG 57.029 42.857 0.00 0.00 0.00 4.94
666 672 1.502163 GAGACCAGCCATATGTGCGC 61.502 60.000 0.00 0.00 0.00 6.09
668 674 0.181114 TGGAGACCAGCCATATGTGC 59.819 55.000 1.24 5.09 0.00 4.57
692 698 5.975939 CACTGTAGAATACTAAACGCCTACC 59.024 44.000 0.00 0.00 43.54 3.18
703 709 7.579105 AGGATCTAGTGACACTGTAGAATACT 58.421 38.462 18.58 10.16 43.54 2.12
704 710 7.811117 AGGATCTAGTGACACTGTAGAATAC 57.189 40.000 18.58 8.33 43.42 1.89
705 711 8.715842 AGTAGGATCTAGTGACACTGTAGAATA 58.284 37.037 18.58 6.36 0.00 1.75
706 712 7.579105 AGTAGGATCTAGTGACACTGTAGAAT 58.421 38.462 18.58 7.20 0.00 2.40
707 713 6.959904 AGTAGGATCTAGTGACACTGTAGAA 58.040 40.000 18.58 0.00 0.00 2.10
708 714 6.563037 AGTAGGATCTAGTGACACTGTAGA 57.437 41.667 18.58 13.82 0.00 2.59
733 753 6.451393 TGGGTCATTTATTTTGAAACGAAGG 58.549 36.000 0.00 0.00 0.00 3.46
734 754 7.651704 AGTTGGGTCATTTATTTTGAAACGAAG 59.348 33.333 0.00 0.00 0.00 3.79
735 755 7.493367 AGTTGGGTCATTTATTTTGAAACGAA 58.507 30.769 0.00 0.00 0.00 3.85
736 756 7.045126 AGTTGGGTCATTTATTTTGAAACGA 57.955 32.000 0.00 0.00 0.00 3.85
737 757 7.707774 AAGTTGGGTCATTTATTTTGAAACG 57.292 32.000 0.00 0.00 0.00 3.60
768 788 9.442033 GCTCGTGTTTAGTACAAAATTAAAGTT 57.558 29.630 0.00 0.00 38.80 2.66
769 789 8.071967 GGCTCGTGTTTAGTACAAAATTAAAGT 58.928 33.333 0.00 0.00 38.80 2.66
770 790 8.071368 TGGCTCGTGTTTAGTACAAAATTAAAG 58.929 33.333 0.00 0.00 38.80 1.85
771 791 7.928103 TGGCTCGTGTTTAGTACAAAATTAAA 58.072 30.769 0.00 0.00 38.80 1.52
772 792 7.493743 TGGCTCGTGTTTAGTACAAAATTAA 57.506 32.000 0.00 0.00 38.80 1.40
773 793 7.675962 ATGGCTCGTGTTTAGTACAAAATTA 57.324 32.000 0.00 0.00 38.80 1.40
774 794 6.569179 ATGGCTCGTGTTTAGTACAAAATT 57.431 33.333 0.00 0.00 38.80 1.82
775 795 6.093082 GGTATGGCTCGTGTTTAGTACAAAAT 59.907 38.462 0.00 0.00 38.80 1.82
776 796 5.409214 GGTATGGCTCGTGTTTAGTACAAAA 59.591 40.000 0.00 0.00 38.80 2.44
777 797 4.931002 GGTATGGCTCGTGTTTAGTACAAA 59.069 41.667 0.00 0.00 38.80 2.83
778 798 4.497300 GGTATGGCTCGTGTTTAGTACAA 58.503 43.478 0.00 0.00 38.80 2.41
779 799 3.427909 CGGTATGGCTCGTGTTTAGTACA 60.428 47.826 0.00 0.00 0.00 2.90
780 800 3.111098 CGGTATGGCTCGTGTTTAGTAC 58.889 50.000 0.00 0.00 0.00 2.73
781 801 2.754552 ACGGTATGGCTCGTGTTTAGTA 59.245 45.455 0.00 0.00 38.25 1.82
782 802 1.547372 ACGGTATGGCTCGTGTTTAGT 59.453 47.619 0.00 0.00 38.25 2.24
783 803 2.288961 ACGGTATGGCTCGTGTTTAG 57.711 50.000 0.00 0.00 38.25 1.85
809 829 0.954452 GTGCTGTGGAAAGGAAGGTG 59.046 55.000 0.00 0.00 0.00 4.00
817 837 2.904866 GCCGTGGTGCTGTGGAAA 60.905 61.111 0.00 0.00 0.00 3.13
825 845 4.980805 TCGAAGTGGCCGTGGTGC 62.981 66.667 0.00 0.00 0.00 5.01
854 874 1.517257 GTGCGATGCTCTGCGTAGT 60.517 57.895 0.00 0.00 0.00 2.73
863 883 1.083806 CCGTGTGTATGTGCGATGCT 61.084 55.000 0.00 0.00 0.00 3.79
874 894 0.753867 TTTGACTCTGGCCGTGTGTA 59.246 50.000 0.00 0.00 0.00 2.90
877 897 1.071471 CCTTTGACTCTGGCCGTGT 59.929 57.895 0.00 0.00 0.00 4.49
897 940 3.239449 TGGTATGGTGTCTGAACTCTGT 58.761 45.455 0.00 0.00 0.00 3.41
1048 1113 0.984230 ACCACCATGTCCGAGTTCAT 59.016 50.000 0.00 0.00 0.00 2.57
1139 1216 1.627297 GGGAGGAGGAGAATTGGCGT 61.627 60.000 0.00 0.00 0.00 5.68
1239 1328 0.179230 ATTCTGACGACGACGACGAC 60.179 55.000 25.15 19.21 42.66 4.34
1241 1330 1.721257 GCATTCTGACGACGACGACG 61.721 60.000 17.60 17.60 42.66 5.12
1242 1331 1.721257 CGCATTCTGACGACGACGAC 61.721 60.000 15.32 8.68 42.66 4.34
1257 1346 4.575973 GCCAGGCAGATCCCGCAT 62.576 66.667 6.55 0.00 34.51 4.73
1262 1351 2.932130 GAACTCGGCCAGGCAGATCC 62.932 65.000 15.36 3.71 31.76 3.36
1329 1418 2.180518 TCGACGCATGCGACATGA 59.819 55.556 43.72 29.41 42.83 3.07
1408 1521 2.357517 CACCACAGTGGGAGTCGC 60.358 66.667 24.13 0.00 43.37 5.19
1416 1529 0.319555 CCACTACGACCACCACAGTG 60.320 60.000 0.00 0.00 44.12 3.66
1515 1631 9.846248 GCTAAAAAGCAGAGAATGAAGAAAATA 57.154 29.630 0.00 0.00 34.41 1.40
1570 1686 5.291905 AGTAAACACAAGTCTAGCCTGTT 57.708 39.130 0.00 0.00 0.00 3.16
1701 1840 4.047822 GACAAGAGGTGAATATCGCAGAG 58.952 47.826 0.00 0.00 43.63 3.35
1730 1869 1.332686 GATTTGTCCCGGCCGATAAAC 59.667 52.381 30.73 18.52 0.00 2.01
1755 1894 8.480066 CGCAAAAGAAAAAGGAAGAAGATTAAC 58.520 33.333 0.00 0.00 0.00 2.01
1758 1897 5.985530 CCGCAAAAGAAAAAGGAAGAAGATT 59.014 36.000 0.00 0.00 0.00 2.40
1768 1907 4.390297 TGTTTTCACCCGCAAAAGAAAAAG 59.610 37.500 0.00 0.00 40.41 2.27
1770 1909 3.926616 TGTTTTCACCCGCAAAAGAAAA 58.073 36.364 0.00 0.00 37.56 2.29
1773 1912 3.118956 ACATTGTTTTCACCCGCAAAAGA 60.119 39.130 0.00 0.00 0.00 2.52
1774 1913 3.194062 ACATTGTTTTCACCCGCAAAAG 58.806 40.909 0.00 0.00 0.00 2.27
1775 1914 3.252974 ACATTGTTTTCACCCGCAAAA 57.747 38.095 0.00 0.00 0.00 2.44
1782 1921 7.968405 GGTGATGAGTAATACATTGTTTTCACC 59.032 37.037 9.35 9.35 32.42 4.02
1815 1954 5.990386 AGAGCTAGCTGTGATTGATTGTATG 59.010 40.000 24.99 0.00 0.00 2.39
2009 2149 1.076727 TCCGAAGAGGACTGCCAGA 59.923 57.895 0.00 0.00 45.98 3.86
2026 2166 9.472361 TGCACGATACTTAGGATTATTTTAGTC 57.528 33.333 0.00 0.00 0.00 2.59
2092 2240 1.880340 CACTAGCTAGTGCGGCTGC 60.880 63.158 34.51 11.65 46.03 5.25
2093 2241 4.409342 CACTAGCTAGTGCGGCTG 57.591 61.111 34.51 15.33 46.03 4.85
2234 3778 5.992217 CCCATGGAAAGTAGCAACTATCTAC 59.008 44.000 15.22 0.00 33.75 2.59
2259 3806 3.679389 ACTCCATTGGTTGAGACATGAC 58.321 45.455 0.00 0.00 32.84 3.06
2419 3967 1.400242 GCTTTGTGATGCACTCCGAAC 60.400 52.381 0.00 0.00 35.11 3.95
2450 3998 7.630242 TTAACCATCTCTATCCTTTGCTTTG 57.370 36.000 0.00 0.00 0.00 2.77
2451 3999 8.829373 ATTTAACCATCTCTATCCTTTGCTTT 57.171 30.769 0.00 0.00 0.00 3.51
2456 4004 9.512588 CTGCATATTTAACCATCTCTATCCTTT 57.487 33.333 0.00 0.00 0.00 3.11
2457 4005 8.664079 ACTGCATATTTAACCATCTCTATCCTT 58.336 33.333 0.00 0.00 0.00 3.36
2458 4006 8.212259 ACTGCATATTTAACCATCTCTATCCT 57.788 34.615 0.00 0.00 0.00 3.24
2459 4007 8.097038 TGACTGCATATTTAACCATCTCTATCC 58.903 37.037 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.