Multiple sequence alignment - TraesCS3A01G106700

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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 TraesCS3A01G106700 chr3A 100.000 4502 0 0 1 4502 71145710 71150211 0.000000e+00 8314
1 TraesCS3A01G106700 chr3D 94.482 3842 117 40 317 4102 62067215 62071017 0.000000e+00 5832
2 TraesCS3A01G106700 chr3D 86.376 367 25 13 4137 4502 62071020 62071362 1.180000e-100 377
3 TraesCS3A01G106700 chr3D 88.976 127 9 4 8 132 62067070 62067193 7.800000e-33 152
4 TraesCS3A01G106700 chr3B 92.245 3572 170 49 2 3503 100964773 100968307 0.000000e+00 4963
5 TraesCS3A01G106700 chr3B 95.269 613 11 6 3492 4103 100968455 100969050 0.000000e+00 955
6 TraesCS3A01G106700 chr3B 88.285 239 12 4 4137 4361 100969052 100969288 5.740000e-69 272
7 TraesCS3A01G106700 chr2A 89.439 748 56 11 1815 2554 610179269 610178537 0.000000e+00 922
8 TraesCS3A01G106700 chr6B 86.684 751 70 10 1812 2552 661997952 661998682 0.000000e+00 806
9 TraesCS3A01G106700 chr6B 83.198 738 82 24 2563 3280 578650450 578651165 4.910000e-179 638
10 TraesCS3A01G106700 chr7B 82.464 211 35 2 3275 3484 492495887 492496096 2.770000e-42 183
11 TraesCS3A01G106700 chr7D 81.991 211 36 2 3275 3484 468937308 468937517 1.290000e-40 178
12 TraesCS3A01G106700 chr7A 81.643 207 36 2 3278 3483 531730459 531730254 2.150000e-38 171


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 TraesCS3A01G106700 chr3A 71145710 71150211 4501 False 8314.000000 8314 100.000000 1 4502 1 chr3A.!!$F1 4501
1 TraesCS3A01G106700 chr3D 62067070 62071362 4292 False 2120.333333 5832 89.944667 8 4502 3 chr3D.!!$F1 4494
2 TraesCS3A01G106700 chr3B 100964773 100969288 4515 False 2063.333333 4963 91.933000 2 4361 3 chr3B.!!$F1 4359
3 TraesCS3A01G106700 chr2A 610178537 610179269 732 True 922.000000 922 89.439000 1815 2554 1 chr2A.!!$R1 739
4 TraesCS3A01G106700 chr6B 661997952 661998682 730 False 806.000000 806 86.684000 1812 2552 1 chr6B.!!$F2 740
5 TraesCS3A01G106700 chr6B 578650450 578651165 715 False 638.000000 638 83.198000 2563 3280 1 chr6B.!!$F1 717

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
907 943 0.107214 AGGAGAGGAGACAGAGCGAG 60.107 60.0 0.00 0.0 0.00 5.03 F
908 944 0.107410 GGAGAGGAGACAGAGCGAGA 60.107 60.0 0.00 0.0 0.00 4.04 F
1348 1391 0.247185 CCATGGCGGAAACAGCAATT 59.753 50.0 0.00 0.0 36.56 2.32 F
1787 1857 0.593263 CGCTCATAACGTACCCGGAC 60.593 60.0 0.73 0.0 38.78 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1964 2035 2.046023 TCATGGCCTTGCGGAGTG 60.046 61.111 13.75 0.00 0.00 3.51 R
2304 2385 2.224329 TGCAAAGAGGGTAAGCACGTAA 60.224 45.455 0.00 0.00 0.00 3.18 R
2782 2867 3.507411 ACTTACACTTCTACAGGCCTGA 58.493 45.455 39.19 20.75 0.00 3.86 R
3570 3837 2.653448 CGTGCTCCGATCAGCTCG 60.653 66.667 13.01 13.01 46.36 5.03 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
55 58 1.285667 TGTCGTGGAGGTGGGTAGATA 59.714 52.381 0.00 0.00 0.00 1.98
65 68 0.341961 TGGGTAGATAGGCCACCACT 59.658 55.000 5.01 0.84 33.78 4.00
66 69 1.274184 TGGGTAGATAGGCCACCACTT 60.274 52.381 5.01 0.00 33.78 3.16
67 70 1.844497 GGGTAGATAGGCCACCACTTT 59.156 52.381 5.01 0.00 33.78 2.66
68 71 2.241430 GGGTAGATAGGCCACCACTTTT 59.759 50.000 5.01 0.00 33.78 2.27
69 72 3.308904 GGGTAGATAGGCCACCACTTTTT 60.309 47.826 5.01 0.00 33.78 1.94
136 139 6.461110 AGCTCCATAACCATTTGATCTTTG 57.539 37.500 0.00 0.00 0.00 2.77
140 144 6.866480 TCCATAACCATTTGATCTTTGAAGC 58.134 36.000 0.00 0.00 0.00 3.86
146 150 5.105997 ACCATTTGATCTTTGAAGCACTAGC 60.106 40.000 0.00 0.00 42.56 3.42
164 168 7.904094 GCACTAGCTTGTATATCTCATAATGC 58.096 38.462 0.00 0.00 37.91 3.56
165 169 7.763528 GCACTAGCTTGTATATCTCATAATGCT 59.236 37.037 0.00 0.00 37.91 3.79
174 178 9.569167 TGTATATCTCATAATGCTTAACTACGC 57.431 33.333 0.00 0.00 0.00 4.42
177 181 3.386486 TCATAATGCTTAACTACGCCCG 58.614 45.455 0.00 0.00 0.00 6.13
180 184 0.533491 ATGCTTAACTACGCCCGACA 59.467 50.000 0.00 0.00 0.00 4.35
183 190 2.004733 GCTTAACTACGCCCGACAAAT 58.995 47.619 0.00 0.00 0.00 2.32
198 205 6.270064 CCCGACAAATAATTCCATGGTAAAC 58.730 40.000 12.58 0.00 0.00 2.01
217 224 2.104967 ACATGCTAAGCAATGCCATGT 58.895 42.857 17.77 17.77 43.62 3.21
218 225 3.289836 ACATGCTAAGCAATGCCATGTA 58.710 40.909 20.62 4.55 43.62 2.29
219 226 3.893200 ACATGCTAAGCAATGCCATGTAT 59.107 39.130 20.62 6.43 43.62 2.29
220 227 5.072055 ACATGCTAAGCAATGCCATGTATA 58.928 37.500 20.62 0.00 43.62 1.47
221 228 5.535783 ACATGCTAAGCAATGCCATGTATAA 59.464 36.000 20.62 0.00 43.62 0.98
222 229 6.040729 ACATGCTAAGCAATGCCATGTATAAA 59.959 34.615 20.62 0.00 43.62 1.40
223 230 6.653526 TGCTAAGCAATGCCATGTATAAAT 57.346 33.333 0.00 0.00 34.76 1.40
224 231 7.757941 TGCTAAGCAATGCCATGTATAAATA 57.242 32.000 0.00 0.00 34.76 1.40
306 313 9.693739 AATACAATTACAGGACACATAATTCCA 57.306 29.630 0.00 0.00 33.92 3.53
513 549 8.569641 AGTACACAAACTTTTGAACTGTACAAA 58.430 29.630 22.87 0.00 43.36 2.83
514 550 9.182933 GTACACAAACTTTTGAACTGTACAAAA 57.817 29.630 19.34 0.00 42.07 2.44
555 591 1.991813 TCCCATTGACCATTGGACTGA 59.008 47.619 10.37 0.00 34.61 3.41
571 607 5.500645 GGACTGAAAAATAGGCCATGTAC 57.499 43.478 5.01 0.00 43.21 2.90
585 621 4.162131 GGCCATGTACTGAAAATTCCCAAT 59.838 41.667 0.00 0.00 0.00 3.16
587 623 5.337491 GCCATGTACTGAAAATTCCCAATGT 60.337 40.000 0.00 0.00 0.00 2.71
588 624 6.700352 CCATGTACTGAAAATTCCCAATGTT 58.300 36.000 0.00 0.00 0.00 2.71
632 668 2.367202 CCCGTAGCAGACCACCCAT 61.367 63.158 0.00 0.00 0.00 4.00
896 932 3.120191 GGGGGAAGGAGGAGAGGA 58.880 66.667 0.00 0.00 0.00 3.71
897 933 1.074850 GGGGGAAGGAGGAGAGGAG 60.075 68.421 0.00 0.00 0.00 3.69
899 935 0.397957 GGGGAAGGAGGAGAGGAGAC 60.398 65.000 0.00 0.00 0.00 3.36
900 936 0.336737 GGGAAGGAGGAGAGGAGACA 59.663 60.000 0.00 0.00 0.00 3.41
901 937 1.687996 GGGAAGGAGGAGAGGAGACAG 60.688 61.905 0.00 0.00 0.00 3.51
902 938 1.286553 GGAAGGAGGAGAGGAGACAGA 59.713 57.143 0.00 0.00 0.00 3.41
903 939 2.654863 GAAGGAGGAGAGGAGACAGAG 58.345 57.143 0.00 0.00 0.00 3.35
904 940 0.258774 AGGAGGAGAGGAGACAGAGC 59.741 60.000 0.00 0.00 0.00 4.09
906 942 0.107410 GAGGAGAGGAGACAGAGCGA 60.107 60.000 0.00 0.00 0.00 4.93
907 943 0.107214 AGGAGAGGAGACAGAGCGAG 60.107 60.000 0.00 0.00 0.00 5.03
908 944 0.107410 GGAGAGGAGACAGAGCGAGA 60.107 60.000 0.00 0.00 0.00 4.04
911 948 1.134401 AGAGGAGACAGAGCGAGAGAG 60.134 57.143 0.00 0.00 0.00 3.20
919 956 2.044848 AGCGAGAGAGCCGGAAGA 60.045 61.111 5.05 0.00 38.01 2.87
920 957 2.058829 GAGCGAGAGAGCCGGAAGAG 62.059 65.000 5.05 0.00 38.01 2.85
949 986 2.359602 AGCGACGACGAGGAGGAA 60.360 61.111 12.29 0.00 42.66 3.36
953 990 1.707239 CGACGACGAGGAGGAAGAGG 61.707 65.000 0.00 0.00 42.66 3.69
954 991 1.378124 GACGACGAGGAGGAAGAGGG 61.378 65.000 0.00 0.00 0.00 4.30
955 992 1.077644 CGACGAGGAGGAAGAGGGA 60.078 63.158 0.00 0.00 0.00 4.20
977 1014 1.441311 GTTGTTGGTGGGCTGTTGG 59.559 57.895 0.00 0.00 0.00 3.77
1082 1119 1.741770 GTGCTCGCATTCCGGTTCT 60.742 57.895 0.00 0.00 37.59 3.01
1083 1120 1.003839 TGCTCGCATTCCGGTTCTT 60.004 52.632 0.00 0.00 37.59 2.52
1084 1121 1.298157 TGCTCGCATTCCGGTTCTTG 61.298 55.000 0.00 0.00 37.59 3.02
1085 1122 1.019278 GCTCGCATTCCGGTTCTTGA 61.019 55.000 0.00 0.00 37.59 3.02
1089 1126 1.202177 CGCATTCCGGTTCTTGATTGG 60.202 52.381 0.00 0.00 0.00 3.16
1214 1254 1.063070 TCTGTTAGGGTGGTTGGGCA 61.063 55.000 0.00 0.00 0.00 5.36
1215 1255 0.609131 CTGTTAGGGTGGTTGGGCAG 60.609 60.000 0.00 0.00 0.00 4.85
1216 1256 1.304134 GTTAGGGTGGTTGGGCAGG 60.304 63.158 0.00 0.00 0.00 4.85
1217 1257 3.218386 TTAGGGTGGTTGGGCAGGC 62.218 63.158 0.00 0.00 0.00 4.85
1255 1298 3.701040 TGCTGATTTCTGCCCCTTTATTC 59.299 43.478 6.93 0.00 39.65 1.75
1260 1303 7.201947 GCTGATTTCTGCCCCTTTATTCTTATT 60.202 37.037 0.00 0.00 35.17 1.40
1261 1304 9.354673 CTGATTTCTGCCCCTTTATTCTTATTA 57.645 33.333 0.00 0.00 0.00 0.98
1262 1305 9.354673 TGATTTCTGCCCCTTTATTCTTATTAG 57.645 33.333 0.00 0.00 0.00 1.73
1341 1384 1.452108 CCTCCTCCATGGCGGAAAC 60.452 63.158 23.57 0.00 45.75 2.78
1342 1385 1.299648 CTCCTCCATGGCGGAAACA 59.700 57.895 23.57 2.29 45.75 2.83
1343 1386 0.745845 CTCCTCCATGGCGGAAACAG 60.746 60.000 23.57 8.98 45.75 3.16
1344 1387 2.409870 CCTCCATGGCGGAAACAGC 61.410 63.158 16.30 0.00 45.75 4.40
1345 1388 1.675310 CTCCATGGCGGAAACAGCA 60.675 57.895 6.96 0.00 45.75 4.41
1347 1390 0.611618 TCCATGGCGGAAACAGCAAT 60.612 50.000 6.96 0.00 42.52 3.56
1348 1391 0.247185 CCATGGCGGAAACAGCAATT 59.753 50.000 0.00 0.00 36.56 2.32
1351 1394 2.611225 TGGCGGAAACAGCAATTTTT 57.389 40.000 0.00 0.00 36.08 1.94
1401 1469 5.398169 TGCGTGGCTTGTTATTTATTCTTG 58.602 37.500 0.00 0.00 0.00 3.02
1582 1652 3.249080 GTGTGTTAAGCAACGTATGGTGT 59.751 43.478 1.14 0.00 40.33 4.16
1590 1660 3.630312 AGCAACGTATGGTGTCTGTTTTT 59.370 39.130 1.14 0.00 38.62 1.94
1598 1668 3.292460 TGGTGTCTGTTTTTACCAAGGG 58.708 45.455 0.00 0.00 40.05 3.95
1682 1752 7.068226 ACAGCTGTTACTAAATTTGTGTCCTTT 59.932 33.333 15.25 0.00 0.00 3.11
1695 1765 3.005684 TGTGTCCTTTTGCCATGTGATTC 59.994 43.478 0.00 0.00 0.00 2.52
1787 1857 0.593263 CGCTCATAACGTACCCGGAC 60.593 60.000 0.73 0.00 38.78 4.79
1809 1879 3.000674 CGTAGCTCTAAATTGTGAGTGCG 60.001 47.826 0.00 7.63 37.29 5.34
1864 1935 4.380531 TGCTATAACAAGGTAGCTCATGC 58.619 43.478 0.00 0.00 36.58 4.06
2332 2413 4.072839 GCTTACCCTCTTTGCAGTAAGTT 58.927 43.478 17.54 0.00 42.28 2.66
2501 2582 7.700656 GTGGTTGTATAACAAGGTAATGATTGC 59.299 37.037 4.65 0.00 39.00 3.56
2782 2867 5.301805 ACAAGAACCTGAATCGGAAATTGTT 59.698 36.000 0.00 0.00 0.00 2.83
2939 3033 5.294356 GCAGGGTGTTAATGTATGTCGATA 58.706 41.667 0.00 0.00 0.00 2.92
3255 3363 1.303155 AGCAAGGCAGGTTCTGAGC 60.303 57.895 0.00 0.00 32.44 4.26
3484 3592 1.910580 GAAGCCCATCAAGACCCGGA 61.911 60.000 0.73 0.00 0.00 5.14
3505 3772 4.508662 GACCTCCCTCATTGTCTAAACAG 58.491 47.826 0.00 0.00 36.57 3.16
3570 3837 4.683432 AGCGAAGACTGCTTGGTC 57.317 55.556 0.00 0.00 40.48 4.02
3635 3902 3.242897 TTCCGGTACCTTGGCACGG 62.243 63.158 10.90 8.71 45.52 4.94
3788 4055 3.507786 ACGGCTGTTTGTTTCTTTGTTC 58.492 40.909 0.00 0.00 0.00 3.18
3789 4056 3.057174 ACGGCTGTTTGTTTCTTTGTTCA 60.057 39.130 0.00 0.00 0.00 3.18
3790 4057 4.111916 CGGCTGTTTGTTTCTTTGTTCAT 58.888 39.130 0.00 0.00 0.00 2.57
3866 4133 8.514594 CATTTCACACGGGAAAGCAATATATAT 58.485 33.333 0.00 0.00 39.88 0.86
3867 4134 9.733556 ATTTCACACGGGAAAGCAATATATATA 57.266 29.630 0.00 0.00 39.88 0.86
3868 4135 9.733556 TTTCACACGGGAAAGCAATATATATAT 57.266 29.630 0.00 0.00 33.16 0.86
4103 4370 2.224426 TGTCACTTTCCGCTGTACCAAT 60.224 45.455 0.00 0.00 0.00 3.16
4104 4371 2.812011 GTCACTTTCCGCTGTACCAATT 59.188 45.455 0.00 0.00 0.00 2.32
4105 4372 3.998341 GTCACTTTCCGCTGTACCAATTA 59.002 43.478 0.00 0.00 0.00 1.40
4106 4373 4.634443 GTCACTTTCCGCTGTACCAATTAT 59.366 41.667 0.00 0.00 0.00 1.28
4107 4374 5.813672 GTCACTTTCCGCTGTACCAATTATA 59.186 40.000 0.00 0.00 0.00 0.98
4108 4375 6.482308 GTCACTTTCCGCTGTACCAATTATAT 59.518 38.462 0.00 0.00 0.00 0.86
4109 4376 7.012044 GTCACTTTCCGCTGTACCAATTATATT 59.988 37.037 0.00 0.00 0.00 1.28
4110 4377 7.011950 TCACTTTCCGCTGTACCAATTATATTG 59.988 37.037 0.00 0.00 0.00 1.90
4111 4378 6.262273 ACTTTCCGCTGTACCAATTATATTGG 59.738 38.462 15.14 15.14 44.91 3.16
4112 4379 5.554437 TCCGCTGTACCAATTATATTGGA 57.446 39.130 21.82 6.10 42.06 3.53
4113 4380 5.302360 TCCGCTGTACCAATTATATTGGAC 58.698 41.667 21.82 15.64 42.06 4.02
4114 4381 4.151689 CCGCTGTACCAATTATATTGGACG 59.848 45.833 21.82 15.73 42.06 4.79
4115 4382 4.377022 CGCTGTACCAATTATATTGGACGC 60.377 45.833 21.82 18.19 42.06 5.19
4116 4383 4.513692 GCTGTACCAATTATATTGGACGCA 59.486 41.667 21.82 15.41 42.06 5.24
4117 4384 5.181245 GCTGTACCAATTATATTGGACGCAT 59.819 40.000 21.82 4.96 42.06 4.73
4118 4385 6.620733 GCTGTACCAATTATATTGGACGCATC 60.621 42.308 21.82 10.65 42.06 3.91
4119 4386 6.292150 TGTACCAATTATATTGGACGCATCA 58.708 36.000 21.82 10.00 42.06 3.07
4120 4387 6.939730 TGTACCAATTATATTGGACGCATCAT 59.060 34.615 21.82 3.11 42.06 2.45
4121 4388 6.500684 ACCAATTATATTGGACGCATCATC 57.499 37.500 21.82 0.00 42.06 2.92
4122 4389 6.240894 ACCAATTATATTGGACGCATCATCT 58.759 36.000 21.82 0.00 42.06 2.90
4123 4390 6.372659 ACCAATTATATTGGACGCATCATCTC 59.627 38.462 21.82 0.00 42.06 2.75
4124 4391 6.372381 CCAATTATATTGGACGCATCATCTCA 59.628 38.462 12.08 0.00 42.06 3.27
4125 4392 7.094677 CCAATTATATTGGACGCATCATCTCAA 60.095 37.037 12.08 0.00 42.06 3.02
4126 4393 7.984422 ATTATATTGGACGCATCATCTCAAA 57.016 32.000 0.00 0.00 0.00 2.69
4127 4394 7.800155 TTATATTGGACGCATCATCTCAAAA 57.200 32.000 0.00 0.00 0.00 2.44
4128 4395 6.698008 ATATTGGACGCATCATCTCAAAAA 57.302 33.333 0.00 0.00 0.00 1.94
4209 4476 3.879295 GCTAACATAAATGGAGCTCAGCA 59.121 43.478 17.19 5.51 37.67 4.41
4228 4500 1.542472 CAGCAGCATCAACATTGGACA 59.458 47.619 0.00 0.00 0.00 4.02
4239 4511 2.318908 ACATTGGACACATGCAAAGGT 58.681 42.857 0.00 0.00 39.86 3.50
4241 4513 2.886862 TTGGACACATGCAAAGGTTG 57.113 45.000 0.00 0.00 32.51 3.77
4242 4514 1.774110 TGGACACATGCAAAGGTTGT 58.226 45.000 0.00 0.00 0.00 3.32
4243 4515 1.408340 TGGACACATGCAAAGGTTGTG 59.592 47.619 14.32 14.32 44.85 3.33
4246 4518 2.582728 CACATGCAAAGGTTGTGTGT 57.417 45.000 8.85 0.00 36.77 3.72
4255 4536 4.261031 GCAAAGGTTGTGTGTACTTAGTGG 60.261 45.833 0.00 0.00 0.00 4.00
4388 4669 3.449018 AGGAAGACTACGATGCTGTGATT 59.551 43.478 0.00 0.00 0.00 2.57
4394 4675 3.445450 ACTACGATGCTGTGATTGTCTCT 59.555 43.478 0.00 0.00 0.00 3.10
4395 4676 4.640647 ACTACGATGCTGTGATTGTCTCTA 59.359 41.667 0.00 0.00 0.00 2.43
4442 4724 3.413522 GCCAAAGCTGCACATCTTC 57.586 52.632 1.02 0.00 35.50 2.87
4459 4741 8.994170 GCACATCTTCCTTCTTCTATATAAACC 58.006 37.037 0.00 0.00 0.00 3.27
4460 4742 9.197694 CACATCTTCCTTCTTCTATATAAACCG 57.802 37.037 0.00 0.00 0.00 4.44
4490 4772 1.656652 CAAGCCATCCTTGTCGTAGG 58.343 55.000 0.00 0.00 44.74 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.483889 CCCTCTCCTCATTTACCGCTTC 60.484 54.545 0.00 0.00 0.00 3.86
140 144 9.650539 AAGCATTATGAGATATACAAGCTAGTG 57.349 33.333 0.00 0.00 0.00 2.74
149 153 9.021863 GGCGTAGTTAAGCATTATGAGATATAC 57.978 37.037 0.00 0.00 34.54 1.47
155 159 3.428870 CGGGCGTAGTTAAGCATTATGAG 59.571 47.826 0.00 0.00 34.54 2.90
164 168 5.978934 ATTATTTGTCGGGCGTAGTTAAG 57.021 39.130 0.00 0.00 0.00 1.85
165 169 5.294060 GGAATTATTTGTCGGGCGTAGTTAA 59.706 40.000 0.00 0.00 0.00 2.01
169 173 3.199677 TGGAATTATTTGTCGGGCGTAG 58.800 45.455 0.00 0.00 0.00 3.51
174 178 6.127591 TGTTTACCATGGAATTATTTGTCGGG 60.128 38.462 21.47 0.00 0.00 5.14
198 205 2.882927 ACATGGCATTGCTTAGCATG 57.117 45.000 8.05 18.29 38.76 4.06
269 276 9.916397 GTCCTGTAATTGTATTCAAATTACTCG 57.084 33.333 15.97 9.53 37.11 4.18
286 293 8.593945 ATTGTTGGAATTATGTGTCCTGTAAT 57.406 30.769 0.00 0.00 34.77 1.89
289 296 8.469200 CATTATTGTTGGAATTATGTGTCCTGT 58.531 33.333 0.00 0.00 34.77 4.00
376 385 8.274322 TCATAACTCATTCATGGATGTTTACCT 58.726 33.333 13.82 0.00 0.00 3.08
382 391 7.341256 AGCTTTTCATAACTCATTCATGGATGT 59.659 33.333 13.82 0.00 0.00 3.06
390 399 7.325660 TCATGGAGCTTTTCATAACTCATTC 57.674 36.000 0.00 0.00 0.00 2.67
391 400 7.363268 GGTTCATGGAGCTTTTCATAACTCATT 60.363 37.037 0.00 0.00 0.00 2.57
513 549 7.447238 TGGGATGTCGTCTATTTTTCTTCTTTT 59.553 33.333 0.00 0.00 0.00 2.27
514 550 6.940298 TGGGATGTCGTCTATTTTTCTTCTTT 59.060 34.615 0.00 0.00 0.00 2.52
537 573 4.870123 TTTTCAGTCCAATGGTCAATGG 57.130 40.909 0.00 0.00 38.09 3.16
555 591 8.040727 GGAATTTTCAGTACATGGCCTATTTTT 58.959 33.333 3.32 0.00 0.00 1.94
569 605 5.841237 TGGGAAACATTGGGAATTTTCAGTA 59.159 36.000 0.00 0.00 30.88 2.74
571 607 4.996758 GTGGGAAACATTGGGAATTTTCAG 59.003 41.667 0.00 0.00 30.88 3.02
617 653 3.118038 TGGATAAATGGGTGGTCTGCTAC 60.118 47.826 0.00 0.00 0.00 3.58
632 668 2.227865 GCCTTGTGAAAGCGTGGATAAA 59.772 45.455 0.00 0.00 0.00 1.40
821 857 1.401905 CCGCTGCCCAGAAATAAACTC 59.598 52.381 0.00 0.00 0.00 3.01
882 918 1.286553 TCTGTCTCCTCTCCTCCTTCC 59.713 57.143 0.00 0.00 0.00 3.46
883 919 2.654863 CTCTGTCTCCTCTCCTCCTTC 58.345 57.143 0.00 0.00 0.00 3.46
884 920 1.341976 GCTCTGTCTCCTCTCCTCCTT 60.342 57.143 0.00 0.00 0.00 3.36
885 921 0.258774 GCTCTGTCTCCTCTCCTCCT 59.741 60.000 0.00 0.00 0.00 3.69
886 922 1.101049 CGCTCTGTCTCCTCTCCTCC 61.101 65.000 0.00 0.00 0.00 4.30
887 923 0.107410 TCGCTCTGTCTCCTCTCCTC 60.107 60.000 0.00 0.00 0.00 3.71
888 924 0.107214 CTCGCTCTGTCTCCTCTCCT 60.107 60.000 0.00 0.00 0.00 3.69
895 931 1.727467 GGCTCTCTCGCTCTGTCTC 59.273 63.158 0.00 0.00 0.00 3.36
896 932 2.112198 CGGCTCTCTCGCTCTGTCT 61.112 63.158 0.00 0.00 0.00 3.41
897 933 2.407210 CGGCTCTCTCGCTCTGTC 59.593 66.667 0.00 0.00 0.00 3.51
899 935 2.335052 CTTCCGGCTCTCTCGCTCTG 62.335 65.000 0.00 0.00 0.00 3.35
900 936 2.044848 TTCCGGCTCTCTCGCTCT 60.045 61.111 0.00 0.00 0.00 4.09
901 937 2.058829 CTCTTCCGGCTCTCTCGCTC 62.059 65.000 0.00 0.00 0.00 5.03
902 938 2.044848 TCTTCCGGCTCTCTCGCT 60.045 61.111 0.00 0.00 0.00 4.93
903 939 2.058829 CTCTCTTCCGGCTCTCTCGC 62.059 65.000 0.00 0.00 0.00 5.03
904 940 1.444119 CCTCTCTTCCGGCTCTCTCG 61.444 65.000 0.00 0.00 0.00 4.04
906 942 0.333312 TTCCTCTCTTCCGGCTCTCT 59.667 55.000 0.00 0.00 0.00 3.10
907 943 0.744281 CTTCCTCTCTTCCGGCTCTC 59.256 60.000 0.00 0.00 0.00 3.20
908 944 0.333312 TCTTCCTCTCTTCCGGCTCT 59.667 55.000 0.00 0.00 0.00 4.09
911 948 1.819905 CCTCTTCCTCTCTTCCGGC 59.180 63.158 0.00 0.00 0.00 6.13
919 956 2.044848 TCGCTCGCCTCTTCCTCT 60.045 61.111 0.00 0.00 0.00 3.69
920 957 2.103340 GTCGCTCGCCTCTTCCTC 59.897 66.667 0.00 0.00 0.00 3.71
949 986 1.059913 CACCAACAACCTCTCCCTCT 58.940 55.000 0.00 0.00 0.00 3.69
953 990 1.603739 GCCCACCAACAACCTCTCC 60.604 63.158 0.00 0.00 0.00 3.71
954 991 0.890996 CAGCCCACCAACAACCTCTC 60.891 60.000 0.00 0.00 0.00 3.20
955 992 1.151450 CAGCCCACCAACAACCTCT 59.849 57.895 0.00 0.00 0.00 3.69
1082 1119 3.774216 GGGGGAATCAATCAACCAATCAA 59.226 43.478 0.00 0.00 0.00 2.57
1083 1120 3.373830 GGGGGAATCAATCAACCAATCA 58.626 45.455 0.00 0.00 0.00 2.57
1214 1254 1.063183 AAGAACAAGCTCCTCTGCCT 58.937 50.000 0.00 0.00 0.00 4.75
1215 1255 1.163554 CAAGAACAAGCTCCTCTGCC 58.836 55.000 0.00 0.00 0.00 4.85
1216 1256 0.520847 GCAAGAACAAGCTCCTCTGC 59.479 55.000 0.00 0.00 0.00 4.26
1217 1257 1.805345 CAGCAAGAACAAGCTCCTCTG 59.195 52.381 0.00 0.00 39.50 3.35
1255 1298 6.749036 AGAACAGGTGGGGATACTAATAAG 57.251 41.667 0.00 0.00 0.00 1.73
1260 1303 7.847848 ACTAATTAAGAACAGGTGGGGATACTA 59.152 37.037 0.00 0.00 0.00 1.82
1261 1304 6.677076 ACTAATTAAGAACAGGTGGGGATACT 59.323 38.462 0.00 0.00 0.00 2.12
1262 1305 6.896883 ACTAATTAAGAACAGGTGGGGATAC 58.103 40.000 0.00 0.00 0.00 2.24
1401 1469 2.736192 GCATTGCAACCACAACATAACC 59.264 45.455 0.00 0.00 31.03 2.85
1444 1512 5.921962 ACCAAATTCTAAGCCTGATTTCC 57.078 39.130 0.00 0.00 0.00 3.13
1582 1652 5.382664 ACTTCTCCCTTGGTAAAAACAGA 57.617 39.130 0.00 0.00 0.00 3.41
1590 1660 5.189145 GTCCAGAAATACTTCTCCCTTGGTA 59.811 44.000 0.00 0.00 40.05 3.25
1598 1668 5.186021 TGACCAGAGTCCAGAAATACTTCTC 59.814 44.000 0.00 0.00 42.81 2.87
1682 1752 3.284617 CTCCTGATGAATCACATGGCAA 58.715 45.455 0.00 0.00 39.56 4.52
1787 1857 3.000674 CGCACTCACAATTTAGAGCTACG 60.001 47.826 4.26 2.92 35.28 3.51
1809 1879 2.164827 ACCAACCACAAAGAAAACGACC 59.835 45.455 0.00 0.00 0.00 4.79
1864 1935 4.992319 TGTCTACCAAACAGGAATACAACG 59.008 41.667 0.00 0.00 41.22 4.10
1964 2035 2.046023 TCATGGCCTTGCGGAGTG 60.046 61.111 13.75 0.00 0.00 3.51
2304 2385 2.224329 TGCAAAGAGGGTAAGCACGTAA 60.224 45.455 0.00 0.00 0.00 3.18
2332 2413 6.646240 GCTTTGAAGGACTAATCATGCAAAAA 59.354 34.615 0.00 0.00 42.26 1.94
2336 2417 4.592942 AGCTTTGAAGGACTAATCATGCA 58.407 39.130 0.00 0.00 31.89 3.96
2340 2421 4.655963 AGCAAGCTTTGAAGGACTAATCA 58.344 39.130 0.00 0.00 0.00 2.57
2352 2433 5.410439 AGCCAAAATCAAATAGCAAGCTTTG 59.590 36.000 0.00 0.00 34.41 2.77
2501 2582 6.506500 AATTCATGGCTGAAACTGAAGTAG 57.493 37.500 0.00 0.00 44.29 2.57
2782 2867 3.507411 ACTTACACTTCTACAGGCCTGA 58.493 45.455 39.19 20.75 0.00 3.86
2939 3033 7.974482 ACTTACTCGTTTATTGCTTTAAGGT 57.026 32.000 0.00 0.00 0.00 3.50
3300 3408 4.459089 GGCTGCTCCTCGGTGACC 62.459 72.222 0.00 0.00 0.00 4.02
3484 3592 3.307762 GCTGTTTAGACAATGAGGGAGGT 60.308 47.826 0.00 0.00 34.85 3.85
3570 3837 2.653448 CGTGCTCCGATCAGCTCG 60.653 66.667 13.01 13.01 46.36 5.03
3635 3902 3.052745 TCTCGATCTATGCAATGCGTTC 58.947 45.455 4.87 0.00 0.00 3.95
3636 3903 3.097877 TCTCGATCTATGCAATGCGTT 57.902 42.857 4.87 0.00 0.00 4.84
3788 4055 9.144747 GATGTGGACTACTACAAAGCATATATG 57.855 37.037 8.45 8.45 40.59 1.78
3789 4056 8.870116 TGATGTGGACTACTACAAAGCATATAT 58.130 33.333 0.00 0.00 40.59 0.86
3790 4057 8.141909 GTGATGTGGACTACTACAAAGCATATA 58.858 37.037 0.00 0.00 40.59 0.86
3874 4141 9.326489 AGACAGGATTCTGCTTTACCATATATA 57.674 33.333 0.00 0.00 44.59 0.86
3875 4142 8.099537 CAGACAGGATTCTGCTTTACCATATAT 58.900 37.037 0.00 0.00 44.59 0.86
3996 4263 2.198827 TCACCCAATCCATGACACAC 57.801 50.000 0.00 0.00 0.00 3.82
4103 4370 7.800155 TTTTGAGATGATGCGTCCAATATAA 57.200 32.000 2.83 0.00 0.00 0.98
4104 4371 7.800155 TTTTTGAGATGATGCGTCCAATATA 57.200 32.000 2.83 0.00 0.00 0.86
4105 4372 6.698008 TTTTTGAGATGATGCGTCCAATAT 57.302 33.333 2.83 0.00 0.00 1.28
4127 4394 8.667463 GCTTTGCATGTGTCCAATATAATTTTT 58.333 29.630 0.00 0.00 0.00 1.94
4128 4395 7.823310 TGCTTTGCATGTGTCCAATATAATTTT 59.177 29.630 0.00 0.00 31.71 1.82
4129 4396 7.329499 TGCTTTGCATGTGTCCAATATAATTT 58.671 30.769 0.00 0.00 31.71 1.82
4130 4397 6.876155 TGCTTTGCATGTGTCCAATATAATT 58.124 32.000 0.00 0.00 31.71 1.40
4131 4398 6.468333 TGCTTTGCATGTGTCCAATATAAT 57.532 33.333 0.00 0.00 31.71 1.28
4132 4399 5.911378 TGCTTTGCATGTGTCCAATATAA 57.089 34.783 0.00 0.00 31.71 0.98
4209 4476 1.542915 GTGTCCAATGTTGATGCTGCT 59.457 47.619 0.00 0.00 0.00 4.24
4228 4500 3.287222 AGTACACACAACCTTTGCATGT 58.713 40.909 0.00 0.00 36.41 3.21
4239 4511 5.361571 TCTCTGTTCCACTAAGTACACACAA 59.638 40.000 0.00 0.00 0.00 3.33
4241 4513 5.449107 TCTCTGTTCCACTAAGTACACAC 57.551 43.478 0.00 0.00 0.00 3.82
4242 4514 5.831525 TCTTCTCTGTTCCACTAAGTACACA 59.168 40.000 0.00 0.00 0.00 3.72
4243 4515 6.151004 GTCTTCTCTGTTCCACTAAGTACAC 58.849 44.000 0.00 0.00 0.00 2.90
4245 4517 5.243283 TGGTCTTCTCTGTTCCACTAAGTAC 59.757 44.000 0.00 0.00 0.00 2.73
4246 4518 5.391256 TGGTCTTCTCTGTTCCACTAAGTA 58.609 41.667 0.00 0.00 0.00 2.24
4255 4536 4.201920 GGTGTTTGTTGGTCTTCTCTGTTC 60.202 45.833 0.00 0.00 0.00 3.18
4350 4631 7.589958 AGTCTTCCTACAGGTGTCTTATATG 57.410 40.000 0.00 0.00 36.34 1.78
4388 4669 2.566724 TCATGCACACACCATAGAGACA 59.433 45.455 0.00 0.00 0.00 3.41
4394 4675 4.582240 TCTGTTTTTCATGCACACACCATA 59.418 37.500 0.00 0.00 0.00 2.74
4395 4676 3.384146 TCTGTTTTTCATGCACACACCAT 59.616 39.130 0.00 0.00 0.00 3.55
4437 4719 7.039923 TCGCGGTTTATATAGAAGAAGGAAGAT 60.040 37.037 6.13 0.00 0.00 2.40
4442 4724 4.615961 CGTCGCGGTTTATATAGAAGAAGG 59.384 45.833 6.13 0.00 0.00 3.46
4459 4741 1.626654 ATGGCTTGAACTTCGTCGCG 61.627 55.000 0.00 0.00 0.00 5.87
4460 4742 0.095417 GATGGCTTGAACTTCGTCGC 59.905 55.000 0.00 0.00 0.00 5.19
4469 4751 2.354704 CCTACGACAAGGATGGCTTGAA 60.355 50.000 0.00 0.00 39.15 2.69


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

AutoCloner maintained by Alex Coulton.