Multiple sequence alignment - TraesCS4A01G376400

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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 TraesCS4A01G376400 chr4A 100.000 3344 0 0 1 3344 650848661 650845318 0.000000e+00 6176.0
1 TraesCS4A01G376400 chr4A 98.974 682 7 0 1 682 650857039 650856358 0.000000e+00 1221.0
2 TraesCS4A01G376400 chr4A 97.127 557 9 4 678 1233 650856257 650855707 0.000000e+00 933.0
3 TraesCS4A01G376400 chr4A 93.176 381 13 1 264 631 728534587 728534207 6.310000e-152 547.0
4 TraesCS4A01G376400 chr4A 86.325 117 14 1 37 151 667192509 667192625 3.500000e-25 126.0
5 TraesCS4A01G376400 chr7A 92.826 1840 104 11 867 2701 42976415 42978231 0.000000e+00 2641.0
6 TraesCS4A01G376400 chr7A 92.890 436 26 2 2784 3218 42978483 42978914 2.190000e-176 628.0
7 TraesCS4A01G376400 chr7A 92.366 262 15 2 2728 2988 42978229 42978486 5.270000e-98 368.0
8 TraesCS4A01G376400 chr7A 88.930 271 29 1 1 270 42974028 42974298 1.920000e-87 333.0
9 TraesCS4A01G376400 chr7A 78.178 527 65 22 2411 2935 42979862 42980340 1.170000e-74 291.0
10 TraesCS4A01G376400 chr7A 92.126 127 9 1 3218 3344 410726653 410726528 9.530000e-41 178.0
11 TraesCS4A01G376400 chr7D 95.440 1557 66 4 837 2390 43131714 43133268 0.000000e+00 2477.0
12 TraesCS4A01G376400 chr7D 89.519 811 33 11 2410 3214 43133761 43134525 0.000000e+00 979.0
13 TraesCS4A01G376400 chr1B 95.628 366 15 1 266 630 344376441 344376076 1.340000e-163 586.0
14 TraesCS4A01G376400 chr1B 91.228 342 29 1 295 635 138736616 138736275 6.530000e-127 464.0
15 TraesCS4A01G376400 chr2B 95.509 334 15 0 295 628 691048882 691048549 4.910000e-148 534.0
16 TraesCS4A01G376400 chr2B 93.255 341 23 0 292 632 620858810 620859150 1.380000e-138 503.0
17 TraesCS4A01G376400 chr3D 94.048 336 20 0 295 630 218313281 218312946 8.280000e-141 510.0
18 TraesCS4A01G376400 chr6B 89.267 382 28 2 263 631 19762448 19762829 1.820000e-127 466.0
19 TraesCS4A01G376400 chr6B 88.556 367 38 4 266 630 372971931 372972295 3.060000e-120 442.0
20 TraesCS4A01G376400 chr6B 95.238 126 6 0 3218 3343 578943320 578943445 2.030000e-47 200.0
21 TraesCS4A01G376400 chr6B 81.250 112 17 3 42 151 46691062 46691171 1.650000e-13 87.9
22 TraesCS4A01G376400 chr7B 89.062 256 28 0 1668 1923 710696862 710697117 5.380000e-83 318.0
23 TraesCS4A01G376400 chr7B 88.281 256 30 0 1668 1923 710339275 710339530 1.170000e-79 307.0
24 TraesCS4A01G376400 chr7B 96.063 127 5 0 3218 3344 3923502 3923376 1.220000e-49 207.0
25 TraesCS4A01G376400 chr1D 97.581 124 3 0 3221 3344 432545982 432545859 2.610000e-51 213.0
26 TraesCS4A01G376400 chr4B 94.030 134 8 0 3211 3344 22177997 22178130 1.570000e-48 204.0
27 TraesCS4A01G376400 chr4B 100.000 37 0 0 267 303 25849240 25849276 5.990000e-08 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G376400 chr4A 650845318 650848661 3343 True 6176.0 6176 100.0000 1 3344 1 chr4A.!!$R1 3343
1 TraesCS4A01G376400 chr4A 650855707 650857039 1332 True 1077.0 1221 98.0505 1 1233 2 chr4A.!!$R3 1232
2 TraesCS4A01G376400 chr7A 42974028 42980340 6312 False 852.2 2641 89.0380 1 3218 5 chr7A.!!$F1 3217
3 TraesCS4A01G376400 chr7D 43131714 43134525 2811 False 1728.0 2477 92.4795 837 3214 2 chr7D.!!$F1 2377

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
627 629 0.392998 CTAAACGCTGTGGATGCCCT 60.393 55.000 0.0 0.0 0.0 5.19 F
1899 3873 1.300963 GCTGCTGGAGTGGATGGAA 59.699 57.895 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2169 4143 0.038744 ACCAGGGCCAATCAAGTGAG 59.961 55.0 6.18 0.0 0.00 3.51 R
3313 5993 0.033699 AGAGGGCTCCTTTTGCATCC 60.034 55.0 0.00 0.0 31.76 3.51 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
71 72 1.945387 CAGACGGCAGAGCACATAAT 58.055 50.000 0.00 0.00 0.00 1.28
168 169 1.081892 CAAGCATCGCTGTTACTGCT 58.918 50.000 12.10 1.60 46.41 4.24
184 185 2.970639 CTCCGGAACCGAAGAGCA 59.029 61.111 15.07 0.00 42.83 4.26
420 422 7.980662 TGTCCATGCAATAAAATAATTCACTGG 59.019 33.333 0.00 0.00 0.00 4.00
485 487 2.379907 AGGATGAAAAAGAGCCCCTTGA 59.620 45.455 0.00 0.00 34.79 3.02
627 629 0.392998 CTAAACGCTGTGGATGCCCT 60.393 55.000 0.00 0.00 0.00 5.19
698 805 9.053472 TCTCCAATAAGTTAATAAACCCTCAGA 57.947 33.333 0.00 0.00 36.15 3.27
700 807 8.050930 TCCAATAAGTTAATAAACCCTCAGACC 58.949 37.037 0.00 0.00 36.15 3.85
701 808 7.012044 CCAATAAGTTAATAAACCCTCAGACCG 59.988 40.741 0.00 0.00 36.15 4.79
702 809 5.750352 AAGTTAATAAACCCTCAGACCGA 57.250 39.130 0.00 0.00 36.15 4.69
715 822 4.355437 CTCAGACCGAGAATACACATCAC 58.645 47.826 0.00 0.00 45.45 3.06
716 823 3.761752 TCAGACCGAGAATACACATCACA 59.238 43.478 0.00 0.00 0.00 3.58
873 2844 4.521130 TCGTCTGCTCTTGTTATTCTGT 57.479 40.909 0.00 0.00 0.00 3.41
1450 3424 2.362632 CCTTCCTCCCCGACGACT 60.363 66.667 0.00 0.00 0.00 4.18
1885 3859 4.117661 GCTGCTTCTGCTGGCTGC 62.118 66.667 9.67 9.67 43.58 5.25
1899 3873 1.300963 GCTGCTGGAGTGGATGGAA 59.699 57.895 0.00 0.00 0.00 3.53
1937 3911 2.509336 CGGCGCGATGGAGTTCTT 60.509 61.111 12.10 0.00 0.00 2.52
1938 3912 2.802667 CGGCGCGATGGAGTTCTTG 61.803 63.158 12.10 0.00 0.00 3.02
2016 3990 3.145551 GGCAGGATTGGGCTGCTG 61.146 66.667 0.00 0.00 43.02 4.41
2076 4050 2.432972 CCTGGCAAACGCAATGGC 60.433 61.111 2.80 2.80 43.15 4.40
2169 4143 1.494960 ACTTGCTCCTCAGAGGGATC 58.505 55.000 17.10 6.60 40.79 3.36
2190 4164 1.133199 TCACTTGATTGGCCCTGGTTT 60.133 47.619 0.00 0.00 0.00 3.27
2578 5030 2.091333 TCTTTCCAAGGAGGCAAGGTTT 60.091 45.455 0.00 0.00 40.57 3.27
2622 5074 7.352079 AGTTTTGGGCATAATAGGAAATCTG 57.648 36.000 0.00 0.00 0.00 2.90
2623 5075 6.324770 AGTTTTGGGCATAATAGGAAATCTGG 59.675 38.462 0.00 0.00 0.00 3.86
2624 5076 5.661503 TTGGGCATAATAGGAAATCTGGA 57.338 39.130 0.00 0.00 0.00 3.86
2673 5129 5.069516 ACTGAGCACATTGAAGGACAAAAAT 59.930 36.000 0.00 0.00 42.03 1.82
2675 5131 5.984926 TGAGCACATTGAAGGACAAAAATTC 59.015 36.000 0.00 0.00 42.03 2.17
2685 5141 6.836527 TGAAGGACAAAAATTCCCTAAGTGAA 59.163 34.615 0.00 0.00 33.01 3.18
2722 5178 8.008513 TCTAAGGGAGTAATTAACTAGCTGTG 57.991 38.462 0.00 0.00 39.07 3.66
2769 5225 4.046286 AGTTCCTACATGGGCATTTTCA 57.954 40.909 0.00 0.00 36.20 2.69
2817 5273 8.362639 ACAAATCCATGCCAAAGATATATCAAC 58.637 33.333 15.08 0.43 0.00 3.18
2827 5283 8.819974 GCCAAAGATATATCAACAAAAATGGTG 58.180 33.333 15.08 0.00 0.00 4.17
2850 5306 4.517285 CTGGTGCCATTTACATACTCTGT 58.483 43.478 0.00 0.00 42.13 3.41
2851 5307 4.917385 TGGTGCCATTTACATACTCTGTT 58.083 39.130 0.00 0.00 39.39 3.16
2852 5308 5.321102 TGGTGCCATTTACATACTCTGTTT 58.679 37.500 0.00 0.00 39.39 2.83
2853 5309 5.772672 TGGTGCCATTTACATACTCTGTTTT 59.227 36.000 0.00 0.00 39.39 2.43
2939 5619 5.462034 TGTTTTTGCAAACATACAAGCAC 57.538 34.783 12.39 0.00 46.06 4.40
2941 5621 3.808466 TTTGCAAACATACAAGCACCA 57.192 38.095 8.05 0.00 36.62 4.17
2942 5622 2.791383 TGCAAACATACAAGCACCAC 57.209 45.000 0.00 0.00 31.05 4.16
2943 5623 1.339610 TGCAAACATACAAGCACCACC 59.660 47.619 0.00 0.00 31.05 4.61
2944 5624 1.339610 GCAAACATACAAGCACCACCA 59.660 47.619 0.00 0.00 0.00 4.17
2945 5625 2.029110 GCAAACATACAAGCACCACCAT 60.029 45.455 0.00 0.00 0.00 3.55
2946 5626 3.554752 GCAAACATACAAGCACCACCATT 60.555 43.478 0.00 0.00 0.00 3.16
2947 5627 3.940209 AACATACAAGCACCACCATTG 57.060 42.857 0.00 0.00 0.00 2.82
2948 5628 2.875296 ACATACAAGCACCACCATTGT 58.125 42.857 0.00 0.00 40.17 2.71
2949 5629 2.819608 ACATACAAGCACCACCATTGTC 59.180 45.455 0.00 0.00 38.14 3.18
2950 5630 2.949177 TACAAGCACCACCATTGTCT 57.051 45.000 0.00 0.00 38.14 3.41
2951 5631 2.071778 ACAAGCACCACCATTGTCTT 57.928 45.000 0.00 0.00 31.72 3.01
2952 5632 1.682854 ACAAGCACCACCATTGTCTTG 59.317 47.619 0.00 0.00 31.72 3.02
2953 5633 1.682854 CAAGCACCACCATTGTCTTGT 59.317 47.619 0.00 0.00 0.00 3.16
2954 5634 2.071778 AGCACCACCATTGTCTTGTT 57.928 45.000 0.00 0.00 0.00 2.83
2955 5635 1.682854 AGCACCACCATTGTCTTGTTG 59.317 47.619 0.00 0.00 0.00 3.33
2956 5636 1.408702 GCACCACCATTGTCTTGTTGT 59.591 47.619 0.00 0.00 0.00 3.32
2957 5637 2.621055 GCACCACCATTGTCTTGTTGTA 59.379 45.455 0.00 0.00 0.00 2.41
2958 5638 3.067461 GCACCACCATTGTCTTGTTGTAA 59.933 43.478 0.00 0.00 0.00 2.41
2959 5639 4.606961 CACCACCATTGTCTTGTTGTAAC 58.393 43.478 0.00 0.00 0.00 2.50
2960 5640 4.338118 CACCACCATTGTCTTGTTGTAACT 59.662 41.667 0.00 0.00 0.00 2.24
2961 5641 4.578928 ACCACCATTGTCTTGTTGTAACTC 59.421 41.667 0.00 0.00 0.00 3.01
2962 5642 4.578516 CCACCATTGTCTTGTTGTAACTCA 59.421 41.667 0.00 0.00 0.00 3.41
2963 5643 5.241506 CCACCATTGTCTTGTTGTAACTCAT 59.758 40.000 0.00 0.00 0.00 2.90
2964 5644 6.239008 CCACCATTGTCTTGTTGTAACTCATT 60.239 38.462 0.00 0.00 0.00 2.57
2965 5645 7.040755 CCACCATTGTCTTGTTGTAACTCATTA 60.041 37.037 0.00 0.00 0.00 1.90
3023 5703 5.862924 TGAGAACTGCTAATTTGCACTAC 57.137 39.130 10.62 5.18 38.12 2.73
3189 5869 7.120432 AGTGAGCAAATGGAGAGAGTTTTAATC 59.880 37.037 0.00 0.00 0.00 1.75
3200 5880 9.491934 GGAGAGAGTTTTAATCGATTTTAAAGC 57.508 33.333 17.19 13.11 33.78 3.51
3214 5894 8.902806 TCGATTTTAAAGCAATGTTCAGGATAT 58.097 29.630 0.00 0.00 0.00 1.63
3218 5898 5.603170 AAAGCAATGTTCAGGATATTGGG 57.397 39.130 0.62 0.00 33.54 4.12
3219 5899 3.569491 AGCAATGTTCAGGATATTGGGG 58.431 45.455 0.62 0.00 33.54 4.96
3220 5900 2.036346 GCAATGTTCAGGATATTGGGGC 59.964 50.000 0.62 0.00 33.54 5.80
3221 5901 2.276732 ATGTTCAGGATATTGGGGCG 57.723 50.000 0.00 0.00 0.00 6.13
3224 5904 0.916086 TTCAGGATATTGGGGCGTGT 59.084 50.000 0.00 0.00 0.00 4.49
3226 5906 1.283613 TCAGGATATTGGGGCGTGTTT 59.716 47.619 0.00 0.00 0.00 2.83
3227 5907 1.405105 CAGGATATTGGGGCGTGTTTG 59.595 52.381 0.00 0.00 0.00 2.93
3228 5908 0.744281 GGATATTGGGGCGTGTTTGG 59.256 55.000 0.00 0.00 0.00 3.28
3229 5909 1.470051 GATATTGGGGCGTGTTTGGT 58.530 50.000 0.00 0.00 0.00 3.67
3231 5911 1.705873 TATTGGGGCGTGTTTGGTTT 58.294 45.000 0.00 0.00 0.00 3.27
3232 5912 0.391228 ATTGGGGCGTGTTTGGTTTC 59.609 50.000 0.00 0.00 0.00 2.78
3234 5914 1.830847 GGGGCGTGTTTGGTTTCCT 60.831 57.895 0.00 0.00 0.00 3.36
3236 5916 1.362355 GGCGTGTTTGGTTTCCTGG 59.638 57.895 0.00 0.00 0.00 4.45
3237 5917 1.362355 GCGTGTTTGGTTTCCTGGG 59.638 57.895 0.00 0.00 0.00 4.45
3238 5918 1.362355 CGTGTTTGGTTTCCTGGGC 59.638 57.895 0.00 0.00 0.00 5.36
3239 5919 1.745890 GTGTTTGGTTTCCTGGGCC 59.254 57.895 0.00 0.00 0.00 5.80
3241 5921 2.915137 TTTGGTTTCCTGGGCCGC 60.915 61.111 0.00 0.00 0.00 6.53
3242 5922 3.740495 TTTGGTTTCCTGGGCCGCA 62.740 57.895 0.00 0.00 0.00 5.69
3267 5947 4.397090 CGCATCCGCCGTGCAAAA 62.397 61.111 0.61 0.00 42.62 2.44
3268 5948 2.181525 GCATCCGCCGTGCAAAAT 59.818 55.556 0.00 0.00 42.08 1.82
3269 5949 1.873572 GCATCCGCCGTGCAAAATC 60.874 57.895 0.00 0.00 42.08 2.17
3270 5950 1.583451 CATCCGCCGTGCAAAATCG 60.583 57.895 0.00 0.00 0.00 3.34
3271 5951 1.743623 ATCCGCCGTGCAAAATCGA 60.744 52.632 0.00 0.00 0.00 3.59
3274 5954 1.133363 CCGCCGTGCAAAATCGAATG 61.133 55.000 0.00 0.00 0.00 2.67
3276 5956 0.984109 GCCGTGCAAAATCGAATGTG 59.016 50.000 0.00 0.00 0.00 3.21
3277 5957 1.665735 GCCGTGCAAAATCGAATGTGT 60.666 47.619 0.00 0.00 0.00 3.72
3278 5958 2.660490 CCGTGCAAAATCGAATGTGTT 58.340 42.857 0.00 0.00 0.00 3.32
3281 5961 3.121396 CGTGCAAAATCGAATGTGTTTGG 60.121 43.478 0.00 0.00 32.73 3.28
3282 5962 3.801594 GTGCAAAATCGAATGTGTTTGGT 59.198 39.130 0.00 0.00 32.73 3.67
3283 5963 3.801050 TGCAAAATCGAATGTGTTTGGTG 59.199 39.130 0.00 0.00 32.73 4.17
3285 5965 4.085107 GCAAAATCGAATGTGTTTGGTGTC 60.085 41.667 0.00 0.00 32.73 3.67
3286 5966 3.915437 AATCGAATGTGTTTGGTGTCC 57.085 42.857 0.00 0.00 0.00 4.02
3288 5968 2.217750 TCGAATGTGTTTGGTGTCCTG 58.782 47.619 0.00 0.00 0.00 3.86
3289 5969 1.946768 CGAATGTGTTTGGTGTCCTGT 59.053 47.619 0.00 0.00 0.00 4.00
3291 5971 1.032014 ATGTGTTTGGTGTCCTGTGC 58.968 50.000 0.00 0.00 0.00 4.57
3294 5974 2.904866 TTTGGTGTCCTGTGCGGC 60.905 61.111 0.00 0.00 0.00 6.53
3323 6003 4.496927 GGCCCGCGGATGCAAAAG 62.497 66.667 30.73 8.26 42.97 2.27
3324 6004 4.496927 GCCCGCGGATGCAAAAGG 62.497 66.667 30.73 7.40 42.97 3.11
3325 6005 2.749839 CCCGCGGATGCAAAAGGA 60.750 61.111 30.73 0.00 42.97 3.36
3327 6007 2.100991 CGCGGATGCAAAAGGAGC 59.899 61.111 0.00 0.00 42.97 4.70
3328 6008 2.491621 GCGGATGCAAAAGGAGCC 59.508 61.111 0.00 0.00 42.15 4.70
3329 6009 3.068729 GCGGATGCAAAAGGAGCCC 62.069 63.158 0.00 0.00 42.15 5.19
3331 6011 1.379642 CGGATGCAAAAGGAGCCCTC 61.380 60.000 0.00 0.00 30.89 4.30
3332 6012 0.033699 GGATGCAAAAGGAGCCCTCT 60.034 55.000 0.00 0.00 30.89 3.69
3334 6014 0.700564 ATGCAAAAGGAGCCCTCTCA 59.299 50.000 0.00 0.00 41.13 3.27
3335 6015 0.037303 TGCAAAAGGAGCCCTCTCAG 59.963 55.000 0.00 0.00 41.13 3.35
3336 6016 1.311651 GCAAAAGGAGCCCTCTCAGC 61.312 60.000 0.00 0.00 41.13 4.26
3337 6017 0.679321 CAAAAGGAGCCCTCTCAGCC 60.679 60.000 0.00 0.00 41.13 4.85
3338 6018 1.136329 AAAAGGAGCCCTCTCAGCCA 61.136 55.000 0.00 0.00 41.13 4.75
3339 6019 1.560866 AAAGGAGCCCTCTCAGCCAG 61.561 60.000 0.00 0.00 41.13 4.85
3340 6020 3.478274 GGAGCCCTCTCAGCCAGG 61.478 72.222 0.00 0.00 41.13 4.45
3341 6021 4.173924 GAGCCCTCTCAGCCAGGC 62.174 72.222 1.84 1.84 46.13 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 1.083806 GCTGCATCGTGTCGGAATCA 61.084 55.000 0.00 0.00 0.00 2.57
168 169 1.595993 CTCTGCTCTTCGGTTCCGGA 61.596 60.000 0.00 0.00 0.00 5.14
184 185 0.390472 GCCGCTTTGCTACAGTCTCT 60.390 55.000 0.00 0.00 0.00 3.10
420 422 5.069781 ACTCTTCTTCTATGACATGTAGGGC 59.930 44.000 0.00 0.00 0.00 5.19
627 629 2.025155 GGCAGATGTCCTCTCGTCTAA 58.975 52.381 0.00 0.00 33.10 2.10
696 803 3.509967 TGTGTGATGTGTATTCTCGGTCT 59.490 43.478 0.00 0.00 0.00 3.85
698 805 3.006430 TGTGTGTGATGTGTATTCTCGGT 59.994 43.478 0.00 0.00 0.00 4.69
700 807 3.987220 TGTGTGTGTGATGTGTATTCTCG 59.013 43.478 0.00 0.00 0.00 4.04
701 808 4.749598 TGTGTGTGTGTGATGTGTATTCTC 59.250 41.667 0.00 0.00 0.00 2.87
702 809 4.511454 GTGTGTGTGTGTGATGTGTATTCT 59.489 41.667 0.00 0.00 0.00 2.40
715 822 2.503331 ACCATACCATGTGTGTGTGTG 58.497 47.619 9.17 1.19 34.50 3.82
716 823 2.884012 CAACCATACCATGTGTGTGTGT 59.116 45.455 9.17 5.47 34.50 3.72
861 2832 4.572389 CCCAGATCCGAACAGAATAACAAG 59.428 45.833 0.00 0.00 0.00 3.16
873 2844 1.043816 GCTCTCATCCCAGATCCGAA 58.956 55.000 0.00 0.00 0.00 4.30
1885 3859 2.089980 CAGCTTTTCCATCCACTCCAG 58.910 52.381 0.00 0.00 0.00 3.86
1899 3873 1.357258 CGTCGAGCATGAGCAGCTTT 61.357 55.000 0.00 0.00 43.58 3.51
1937 3911 2.577059 GCGGGAGGTCGACAATCA 59.423 61.111 18.91 0.00 0.00 2.57
1938 3912 2.202892 GGCGGGAGGTCGACAATC 60.203 66.667 18.91 14.22 38.21 2.67
2016 3990 5.067805 GTCCAATGTGTTCCTCCCAATATTC 59.932 44.000 0.00 0.00 0.00 1.75
2076 4050 1.083657 CGTTTCGTGTTGCCACTCG 60.084 57.895 6.08 6.08 39.55 4.18
2160 4134 3.806380 CCAATCAAGTGAGATCCCTCTG 58.194 50.000 0.00 0.00 40.10 3.35
2169 4143 0.038744 ACCAGGGCCAATCAAGTGAG 59.961 55.000 6.18 0.00 0.00 3.51
2190 4164 3.074369 TCCGATGAAGCGCTCCCA 61.074 61.111 12.06 13.08 0.00 4.37
2331 4305 5.805728 AGTTTACCAGTTCATAGAGTTGGG 58.194 41.667 0.00 0.00 33.20 4.12
2395 4370 3.691049 TTCAAAGCAACGGAAACTCTG 57.309 42.857 0.00 0.00 0.00 3.35
2512 4964 6.204495 GGAGCAAGAGAAAGGAATGATGATAC 59.796 42.308 0.00 0.00 0.00 2.24
2578 5030 3.780294 ACTATTACTCCCATGAACCAGCA 59.220 43.478 0.00 0.00 0.00 4.41
2582 5034 5.359860 CCCAAAACTATTACTCCCATGAACC 59.640 44.000 0.00 0.00 0.00 3.62
2620 5072 1.561643 TGTAGGCACTTCTCCTCCAG 58.438 55.000 0.00 0.00 41.75 3.86
2622 5074 3.418684 TTTTGTAGGCACTTCTCCTCC 57.581 47.619 0.00 0.00 41.75 4.30
2623 5075 4.762251 ACAATTTTGTAGGCACTTCTCCTC 59.238 41.667 0.00 0.00 40.16 3.71
2624 5076 4.729868 ACAATTTTGTAGGCACTTCTCCT 58.270 39.130 0.00 0.00 40.16 3.69
2673 5129 7.996644 AGAAACAAATGTAGTTCACTTAGGGAA 59.003 33.333 0.00 0.00 0.00 3.97
2675 5131 7.745620 AGAAACAAATGTAGTTCACTTAGGG 57.254 36.000 1.99 0.00 0.00 3.53
2722 5178 5.895928 AGAAAAGAAAAAGGAGAAGTGCAC 58.104 37.500 9.40 9.40 0.00 4.57
2769 5225 2.030007 GTGTTACATGTGTTGCAGCCAT 60.030 45.455 9.11 0.00 0.00 4.40
2817 5273 0.106335 TGGCACCAGCACCATTTTTG 59.894 50.000 0.00 0.00 44.61 2.44
2827 5283 3.313526 CAGAGTATGTAAATGGCACCAGC 59.686 47.826 0.00 0.00 41.10 4.85
2937 5617 4.338118 AGTTACAACAAGACAATGGTGGTG 59.662 41.667 0.00 0.00 42.42 4.17
2938 5618 4.532834 AGTTACAACAAGACAATGGTGGT 58.467 39.130 0.00 0.00 42.42 4.16
2939 5619 4.578516 TGAGTTACAACAAGACAATGGTGG 59.421 41.667 0.00 0.00 42.42 4.61
2941 5621 6.959639 AATGAGTTACAACAAGACAATGGT 57.040 33.333 0.00 0.00 0.00 3.55
2942 5622 9.345517 CAATAATGAGTTACAACAAGACAATGG 57.654 33.333 0.00 0.00 0.00 3.16
2943 5623 9.897744 ACAATAATGAGTTACAACAAGACAATG 57.102 29.630 0.00 0.00 0.00 2.82
2990 5670 2.040813 AGCAGTTCTCAACCATGGATGT 59.959 45.455 21.47 0.00 0.00 3.06
3189 5869 9.520204 AATATCCTGAACATTGCTTTAAAATCG 57.480 29.630 0.00 0.00 0.00 3.34
3200 5880 2.294233 CGCCCCAATATCCTGAACATTG 59.706 50.000 0.00 0.00 0.00 2.82
3214 5894 1.677637 GGAAACCAAACACGCCCCAA 61.678 55.000 0.00 0.00 0.00 4.12
3218 5898 1.362355 CCAGGAAACCAAACACGCC 59.638 57.895 0.00 0.00 0.00 5.68
3219 5899 1.362355 CCCAGGAAACCAAACACGC 59.638 57.895 0.00 0.00 0.00 5.34
3220 5900 1.362355 GCCCAGGAAACCAAACACG 59.638 57.895 0.00 0.00 0.00 4.49
3221 5901 1.745890 GGCCCAGGAAACCAAACAC 59.254 57.895 0.00 0.00 0.00 3.32
3224 5904 2.915137 GCGGCCCAGGAAACCAAA 60.915 61.111 0.00 0.00 0.00 3.28
3226 5906 4.966787 GTGCGGCCCAGGAAACCA 62.967 66.667 0.00 0.00 0.00 3.67
3250 5930 3.681961 ATTTTGCACGGCGGATGCG 62.682 57.895 13.24 0.65 46.49 4.73
3252 5932 1.583451 CGATTTTGCACGGCGGATG 60.583 57.895 13.24 1.72 0.00 3.51
3255 5935 1.133363 CATTCGATTTTGCACGGCGG 61.133 55.000 13.24 0.66 0.00 6.13
3256 5936 0.454285 ACATTCGATTTTGCACGGCG 60.454 50.000 4.80 4.80 0.00 6.46
3257 5937 0.984109 CACATTCGATTTTGCACGGC 59.016 50.000 0.00 0.00 0.00 5.68
3258 5938 2.330231 ACACATTCGATTTTGCACGG 57.670 45.000 0.00 0.00 0.00 4.94
3259 5939 3.121396 CCAAACACATTCGATTTTGCACG 60.121 43.478 0.00 0.00 0.00 5.34
3261 5941 3.801050 CACCAAACACATTCGATTTTGCA 59.199 39.130 0.00 0.00 0.00 4.08
3262 5942 3.801594 ACACCAAACACATTCGATTTTGC 59.198 39.130 0.00 0.00 0.00 3.68
3263 5943 4.444056 GGACACCAAACACATTCGATTTTG 59.556 41.667 0.00 0.00 0.00 2.44
3266 5946 3.253188 CAGGACACCAAACACATTCGATT 59.747 43.478 0.00 0.00 0.00 3.34
3267 5947 2.813754 CAGGACACCAAACACATTCGAT 59.186 45.455 0.00 0.00 0.00 3.59
3268 5948 2.217750 CAGGACACCAAACACATTCGA 58.782 47.619 0.00 0.00 0.00 3.71
3269 5949 1.946768 ACAGGACACCAAACACATTCG 59.053 47.619 0.00 0.00 0.00 3.34
3270 5950 2.543653 GCACAGGACACCAAACACATTC 60.544 50.000 0.00 0.00 0.00 2.67
3271 5951 1.408702 GCACAGGACACCAAACACATT 59.591 47.619 0.00 0.00 0.00 2.71
3274 5954 1.355210 CGCACAGGACACCAAACAC 59.645 57.895 0.00 0.00 0.00 3.32
3276 5956 3.030652 CCGCACAGGACACCAAAC 58.969 61.111 0.00 0.00 45.00 2.93
3277 5957 2.904866 GCCGCACAGGACACCAAA 60.905 61.111 0.00 0.00 45.00 3.28
3306 5986 4.496927 CTTTTGCATCCGCGGGCC 62.497 66.667 27.83 14.33 42.97 5.80
3307 5987 4.496927 CCTTTTGCATCCGCGGGC 62.497 66.667 27.83 22.46 42.97 6.13
3308 5988 2.749839 TCCTTTTGCATCCGCGGG 60.750 61.111 27.83 11.74 42.97 6.13
3309 5989 2.793946 CTCCTTTTGCATCCGCGG 59.206 61.111 22.12 22.12 42.97 6.46
3311 5991 2.491621 GGCTCCTTTTGCATCCGC 59.508 61.111 0.00 0.00 39.24 5.54
3312 5992 1.379044 AGGGCTCCTTTTGCATCCG 60.379 57.895 0.00 0.00 0.00 4.18
3313 5993 0.033699 AGAGGGCTCCTTTTGCATCC 60.034 55.000 0.00 0.00 31.76 3.51
3314 5994 1.340405 TGAGAGGGCTCCTTTTGCATC 60.340 52.381 0.00 0.00 40.55 3.91
3315 5995 0.700564 TGAGAGGGCTCCTTTTGCAT 59.299 50.000 0.00 0.00 40.55 3.96
3316 5996 0.037303 CTGAGAGGGCTCCTTTTGCA 59.963 55.000 0.00 0.00 40.55 4.08
3317 5997 1.311651 GCTGAGAGGGCTCCTTTTGC 61.312 60.000 0.00 0.00 40.55 3.68
3318 5998 0.679321 GGCTGAGAGGGCTCCTTTTG 60.679 60.000 0.00 0.00 40.55 2.44
3319 5999 1.136329 TGGCTGAGAGGGCTCCTTTT 61.136 55.000 0.00 0.00 40.55 2.27
3321 6001 1.994507 CTGGCTGAGAGGGCTCCTT 60.995 63.158 0.00 0.00 40.55 3.36
3322 6002 2.365370 CTGGCTGAGAGGGCTCCT 60.365 66.667 0.00 0.00 40.55 3.69
3323 6003 3.478274 CCTGGCTGAGAGGGCTCC 61.478 72.222 0.00 0.00 40.55 4.70
3324 6004 4.173924 GCCTGGCTGAGAGGGCTC 62.174 72.222 12.43 0.00 41.20 4.70


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

AutoCloner maintained by Alex Coulton.