Multiple sequence alignment - TraesCS4A01G374100

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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 TraesCS4A01G374100 chr4A 100.000 3829 0 0 1 3829 649000400 648996572 0.000000e+00 7071.0
1 TraesCS4A01G374100 chr4A 88.198 1110 95 14 1743 2832 649021464 649020371 0.000000e+00 1291.0
2 TraesCS4A01G374100 chr4A 96.889 675 21 0 1 675 649050899 649050225 0.000000e+00 1131.0
3 TraesCS4A01G374100 chr4A 92.944 496 17 5 1255 1747 649024107 649023627 0.000000e+00 706.0
4 TraesCS4A01G374100 chr7A 88.201 2746 215 45 362 3034 41469814 41467105 0.000000e+00 3175.0
5 TraesCS4A01G374100 chr7A 78.841 794 131 27 1336 2118 90453960 90454727 5.710000e-138 501.0
6 TraesCS4A01G374100 chr7D 90.809 1545 109 11 1210 2747 41933117 41934635 0.000000e+00 2036.0
7 TraesCS4A01G374100 chr7D 88.707 1647 107 23 1210 2832 41831832 41830241 0.000000e+00 1938.0
8 TraesCS4A01G374100 chr7D 86.267 1733 151 38 1210 2928 42238484 42236825 0.000000e+00 1801.0
9 TraesCS4A01G374100 chr7D 91.515 990 53 11 26 989 41812019 41811035 0.000000e+00 1334.0
10 TraesCS4A01G374100 chr7D 89.868 908 78 5 1211 2111 41810372 41809472 0.000000e+00 1155.0
11 TraesCS4A01G374100 chr7D 88.968 843 60 12 2121 2949 41808529 41807706 0.000000e+00 1011.0
12 TraesCS4A01G374100 chr7D 79.567 832 129 26 1336 2154 89274248 89275051 1.200000e-154 556.0
13 TraesCS4A01G374100 chr7D 84.837 521 65 10 239 748 41930930 41931447 2.640000e-141 512.0
14 TraesCS4A01G374100 chr7D 83.810 525 63 18 239 748 41871378 41871895 2.680000e-131 479.0
15 TraesCS4A01G374100 chr7D 92.237 219 12 1 994 1212 41810854 41810641 4.810000e-79 305.0
16 TraesCS4A01G374100 chr5B 92.459 610 40 4 3033 3640 470394839 470394234 0.000000e+00 867.0
17 TraesCS4A01G374100 chrUn 90.926 540 29 3 673 1212 49809886 49810405 0.000000e+00 708.0
18 TraesCS4A01G374100 chr5A 77.081 829 149 27 1336 2154 666944658 666943861 1.260000e-119 440.0
19 TraesCS4A01G374100 chr6D 93.182 44 3 0 3786 3829 413025255 413025212 8.880000e-07 65.8


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 TraesCS4A01G374100 chr4A 648996572 649000400 3828 True 7071.00 7071 100.000 1 3829 1 chr4A.!!$R1 3828
1 TraesCS4A01G374100 chr4A 649050225 649050899 674 True 1131.00 1131 96.889 1 675 1 chr4A.!!$R2 674
2 TraesCS4A01G374100 chr4A 649020371 649024107 3736 True 998.50 1291 90.571 1255 2832 2 chr4A.!!$R3 1577
3 TraesCS4A01G374100 chr7A 41467105 41469814 2709 True 3175.00 3175 88.201 362 3034 1 chr7A.!!$R1 2672
4 TraesCS4A01G374100 chr7A 90453960 90454727 767 False 501.00 501 78.841 1336 2118 1 chr7A.!!$F1 782
5 TraesCS4A01G374100 chr7D 41830241 41831832 1591 True 1938.00 1938 88.707 1210 2832 1 chr7D.!!$R1 1622
6 TraesCS4A01G374100 chr7D 42236825 42238484 1659 True 1801.00 1801 86.267 1210 2928 1 chr7D.!!$R2 1718
7 TraesCS4A01G374100 chr7D 41930930 41934635 3705 False 1274.00 2036 87.823 239 2747 2 chr7D.!!$F3 2508
8 TraesCS4A01G374100 chr7D 41807706 41812019 4313 True 951.25 1334 90.647 26 2949 4 chr7D.!!$R3 2923
9 TraesCS4A01G374100 chr7D 89274248 89275051 803 False 556.00 556 79.567 1336 2154 1 chr7D.!!$F2 818
10 TraesCS4A01G374100 chr7D 41871378 41871895 517 False 479.00 479 83.810 239 748 1 chr7D.!!$F1 509
11 TraesCS4A01G374100 chr5B 470394234 470394839 605 True 867.00 867 92.459 3033 3640 1 chr5B.!!$R1 607
12 TraesCS4A01G374100 chrUn 49809886 49810405 519 False 708.00 708 90.926 673 1212 1 chrUn.!!$F1 539
13 TraesCS4A01G374100 chr5A 666943861 666944658 797 True 440.00 440 77.081 1336 2154 1 chr5A.!!$R1 818

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
973 1328 0.321996 GTTGAGAAAGGAGCGAGGGT 59.678 55.0 0.00 0.00 0.00 4.34 F
1093 2543 0.179145 CGTCCATGGACACGAGGTAC 60.179 60.0 37.42 14.05 44.77 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2237 7162 0.038892 TCTTTTCGGGAAGACGACGG 60.039 55.0 0.0 0.0 43.37 4.79 R
2890 7844 0.107456 AATAGGTCCATCAGCCTGCG 59.893 55.0 0.0 0.0 36.38 5.18 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 3.386726 CCATCATGATGTTCCCAAATGCT 59.613 43.478 29.23 0.00 37.11 3.79
43 44 6.602410 TGCTGGGAATAAAATTGTCATCAA 57.398 33.333 0.00 0.00 37.98 2.57
126 127 2.112297 GCAGGGACGGAACACCAA 59.888 61.111 0.00 0.00 0.00 3.67
128 129 1.450211 CAGGGACGGAACACCAACT 59.550 57.895 0.00 0.00 0.00 3.16
158 159 7.777910 TCTTCCCTTTTGAACATCTTTGAACTA 59.222 33.333 0.00 0.00 0.00 2.24
162 163 9.546428 CCCTTTTGAACATCTTTGAACTAAAAT 57.454 29.630 0.00 0.00 0.00 1.82
217 218 3.061831 GCGCATACAGAGCATATCATCAC 59.938 47.826 0.30 0.00 43.16 3.06
273 280 7.226523 ACCCACAAACAAATAAAATCTCAAAGC 59.773 33.333 0.00 0.00 0.00 3.51
459 468 4.020396 CCATGGTAGAAGAGATCCCATCAG 60.020 50.000 2.57 0.00 33.70 2.90
562 576 5.084519 AGGTTGTACTCCTAGTTGATGTCA 58.915 41.667 8.10 0.00 33.04 3.58
644 665 5.984926 GTGATCACACATCCATTTGTTGTTT 59.015 36.000 21.07 0.00 45.32 2.83
730 751 4.024472 CACAACATGTGTCGTGGATGTTTA 60.024 41.667 0.00 0.00 43.08 2.01
780 840 9.291664 CAACCATCGACAAAGTAAACTTTAAAA 57.708 29.630 7.73 0.00 43.72 1.52
926 1281 6.715280 AGATAGATGTTCTGTTGTTGTCCAT 58.285 36.000 0.00 0.00 0.00 3.41
973 1328 0.321996 GTTGAGAAAGGAGCGAGGGT 59.678 55.000 0.00 0.00 0.00 4.34
1093 2543 0.179145 CGTCCATGGACACGAGGTAC 60.179 60.000 37.42 14.05 44.77 3.34
1098 2548 2.159282 CCATGGACACGAGGTACAGTAC 60.159 54.545 5.56 1.59 45.57 2.73
1178 2629 5.466393 GTGAGCTTGTGTGGCAAAATTTAAT 59.534 36.000 0.00 0.00 36.53 1.40
1179 2630 6.018016 GTGAGCTTGTGTGGCAAAATTTAATT 60.018 34.615 0.00 0.00 36.53 1.40
1180 2631 6.018098 TGAGCTTGTGTGGCAAAATTTAATTG 60.018 34.615 0.00 0.00 36.53 2.32
1181 2632 6.054295 AGCTTGTGTGGCAAAATTTAATTGA 58.946 32.000 0.00 0.00 36.53 2.57
1182 2633 6.203338 AGCTTGTGTGGCAAAATTTAATTGAG 59.797 34.615 0.00 0.00 36.53 3.02
1435 3223 2.173669 CCGCAACATAGCCCACGAG 61.174 63.158 0.00 0.00 0.00 4.18
1821 5788 2.246761 CTGGTCGCGTTCCCCCATAA 62.247 60.000 5.77 0.00 0.00 1.90
1933 5903 1.079819 CTTCATGTCGTCACCGGCT 60.080 57.895 0.00 0.00 40.05 5.52
2257 7182 1.603678 CCGTCGTCTTCCCGAAAAGAA 60.604 52.381 1.64 0.00 38.80 2.52
2337 7262 3.004354 TTTCCCGCCGGGCTTCTA 61.004 61.111 19.91 0.00 43.94 2.10
2353 7278 2.241281 TCTACCCACATCTCCGGAAA 57.759 50.000 5.23 0.00 0.00 3.13
2382 7307 1.443872 CCACTACGACCACGAGCAC 60.444 63.158 0.00 0.00 42.66 4.40
2421 7346 2.125512 CGGCGAAGAAGGGGACAG 60.126 66.667 0.00 0.00 0.00 3.51
2533 7458 2.576317 GCGTCGAGCTACGTGTCC 60.576 66.667 10.52 0.00 44.64 4.02
2556 7486 5.253330 CCTGCTCCAGGTGAATTTACTTAA 58.747 41.667 3.09 0.00 45.82 1.85
2570 7500 9.919416 TGAATTTACTTAAGAATCATCCATCCA 57.081 29.630 10.09 0.00 0.00 3.41
2581 7515 1.534163 CATCCATCCATTAGCTGTGCG 59.466 52.381 0.00 0.00 0.00 5.34
2726 7674 2.757917 GAGAGGCTGAGGGACGCT 60.758 66.667 0.00 0.00 35.22 5.07
2890 7844 0.892755 TGGTGTCTCCACGGTGATAC 59.107 55.000 10.28 6.51 42.80 2.24
2976 7933 7.826690 GTGTCACCATTTCACCAAATTACTAT 58.173 34.615 0.00 0.00 28.97 2.12
2978 7935 8.865090 TGTCACCATTTCACCAAATTACTATTT 58.135 29.630 0.00 0.00 34.29 1.40
3018 7975 2.604046 ATTTATCTTCGAGCTGCGGT 57.396 45.000 0.00 0.00 41.33 5.68
3096 8053 1.896183 CCACCACATGTCGGCAACA 60.896 57.895 12.53 0.00 43.51 3.33
3101 8058 1.269174 CCACATGTCGGCAACATTGAA 59.731 47.619 0.00 0.00 46.73 2.69
3102 8059 2.288091 CCACATGTCGGCAACATTGAAA 60.288 45.455 0.00 0.00 46.73 2.69
3104 8061 3.989167 CACATGTCGGCAACATTGAAATT 59.011 39.130 0.00 0.00 46.73 1.82
3109 8066 2.363680 TCGGCAACATTGAAATTGGTGT 59.636 40.909 0.00 0.00 0.00 4.16
3161 8118 8.845227 TCATTTTTGCACTAGAATACACAAAGA 58.155 29.630 0.00 0.00 0.00 2.52
3181 8138 6.478512 AAGAAATACAAAATGGTGTGTGGT 57.521 33.333 0.00 0.00 32.75 4.16
3198 8155 1.001641 GTCCCCTCTGCATGCACTT 60.002 57.895 18.46 0.00 0.00 3.16
3202 8159 0.322277 CCCTCTGCATGCACTTCAGT 60.322 55.000 18.46 0.00 0.00 3.41
3220 8177 8.517878 CACTTCAGTTTTTGTCAGAATATGGAT 58.482 33.333 0.00 0.00 0.00 3.41
3227 8184 4.442401 TGTCAGAATATGGATGCATGGT 57.558 40.909 10.37 0.00 0.00 3.55
3262 8219 7.229581 ACGTTAACTCTCTCTCCACTAAAAT 57.770 36.000 3.71 0.00 0.00 1.82
3265 8222 5.489792 AACTCTCTCTCCACTAAAATGCA 57.510 39.130 0.00 0.00 0.00 3.96
3323 8280 7.320443 TGATATCTTCTGAACCAAAATTCCG 57.680 36.000 3.98 0.00 0.00 4.30
3327 8284 6.215495 TCTTCTGAACCAAAATTCCGTTTT 57.785 33.333 0.00 0.00 40.59 2.43
3481 8438 3.964909 ACGGCTTTCACTCATTTTGAAC 58.035 40.909 0.00 0.00 32.65 3.18
3503 8460 4.524328 ACTAGATTCCACCCTTTGCAAAAG 59.476 41.667 13.84 7.10 0.00 2.27
3509 8467 2.430332 CCACCCTTTGCAAAAGAACTGA 59.570 45.455 13.84 0.00 0.00 3.41
3685 8644 7.982761 AATAACAAGTTACCCGTATTTCACA 57.017 32.000 0.00 0.00 0.00 3.58
3686 8645 5.678132 AACAAGTTACCCGTATTTCACAC 57.322 39.130 0.00 0.00 0.00 3.82
3687 8646 4.067192 ACAAGTTACCCGTATTTCACACC 58.933 43.478 0.00 0.00 0.00 4.16
3688 8647 4.066490 CAAGTTACCCGTATTTCACACCA 58.934 43.478 0.00 0.00 0.00 4.17
3689 8648 4.354893 AGTTACCCGTATTTCACACCAA 57.645 40.909 0.00 0.00 0.00 3.67
3690 8649 4.716794 AGTTACCCGTATTTCACACCAAA 58.283 39.130 0.00 0.00 0.00 3.28
3691 8650 5.131784 AGTTACCCGTATTTCACACCAAAA 58.868 37.500 0.00 0.00 0.00 2.44
3692 8651 5.593502 AGTTACCCGTATTTCACACCAAAAA 59.406 36.000 0.00 0.00 0.00 1.94
3739 8698 9.048446 ACAGATTTCACTCATTTCAAAAATTGG 57.952 29.630 0.00 0.00 0.00 3.16
3740 8699 9.048446 CAGATTTCACTCATTTCAAAAATTGGT 57.952 29.630 0.00 0.00 0.00 3.67
3741 8700 9.617523 AGATTTCACTCATTTCAAAAATTGGTT 57.382 25.926 0.00 0.00 0.00 3.67
3742 8701 9.868389 GATTTCACTCATTTCAAAAATTGGTTC 57.132 29.630 0.00 0.00 0.00 3.62
3743 8702 9.617523 ATTTCACTCATTTCAAAAATTGGTTCT 57.382 25.926 0.00 0.00 0.00 3.01
3744 8703 8.647143 TTCACTCATTTCAAAAATTGGTTCTC 57.353 30.769 0.00 0.00 0.00 2.87
3745 8704 7.780064 TCACTCATTTCAAAAATTGGTTCTCA 58.220 30.769 0.00 0.00 0.00 3.27
3746 8705 8.256605 TCACTCATTTCAAAAATTGGTTCTCAA 58.743 29.630 0.00 0.00 40.01 3.02
3780 8739 5.509716 AAACTTTTACTTCAGGAAACCGG 57.490 39.130 0.00 0.00 0.00 5.28
3781 8740 4.160642 ACTTTTACTTCAGGAAACCGGT 57.839 40.909 0.00 0.00 0.00 5.28
3782 8741 4.529897 ACTTTTACTTCAGGAAACCGGTT 58.470 39.130 15.86 15.86 0.00 4.44
3783 8742 4.951715 ACTTTTACTTCAGGAAACCGGTTT 59.048 37.500 32.08 32.08 35.14 3.27
3784 8743 5.066893 ACTTTTACTTCAGGAAACCGGTTTC 59.933 40.000 40.16 40.16 46.03 2.78
3810 8769 8.677148 ACTGTTATAGTGATTGGCGATTTTAT 57.323 30.769 0.00 0.00 38.49 1.40
3811 8770 8.559536 ACTGTTATAGTGATTGGCGATTTTATG 58.440 33.333 0.00 0.00 38.49 1.90
3812 8771 8.669946 TGTTATAGTGATTGGCGATTTTATGA 57.330 30.769 0.00 0.00 0.00 2.15
3813 8772 8.773645 TGTTATAGTGATTGGCGATTTTATGAG 58.226 33.333 0.00 0.00 0.00 2.90
3814 8773 4.558538 AGTGATTGGCGATTTTATGAGC 57.441 40.909 0.00 0.00 0.00 4.26
3822 8781 4.088823 GCGATTTTATGAGCCATCCATC 57.911 45.455 0.00 0.00 0.00 3.51
3823 8782 3.119708 GCGATTTTATGAGCCATCCATCC 60.120 47.826 0.00 0.00 0.00 3.51
3824 8783 4.074259 CGATTTTATGAGCCATCCATCCA 58.926 43.478 0.00 0.00 0.00 3.41
3825 8784 4.083110 CGATTTTATGAGCCATCCATCCAC 60.083 45.833 0.00 0.00 0.00 4.02
3826 8785 4.524802 TTTTATGAGCCATCCATCCACT 57.475 40.909 0.00 0.00 0.00 4.00
3827 8786 3.777106 TTATGAGCCATCCATCCACTC 57.223 47.619 0.00 0.00 0.00 3.51
3828 8787 1.817087 ATGAGCCATCCATCCACTCT 58.183 50.000 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 4.695928 GCTCGAGGAGGACAACTTTAAATT 59.304 41.667 15.58 0.00 0.00 1.82
126 127 5.893824 AGATGTTCAAAAGGGAAGACAAAGT 59.106 36.000 0.00 0.00 0.00 2.66
128 129 6.790232 AAGATGTTCAAAAGGGAAGACAAA 57.210 33.333 0.00 0.00 0.00 2.83
165 166 4.367450 GCACTGTTTTGCATCCAAGTAAA 58.633 39.130 0.00 0.00 42.49 2.01
440 447 4.651503 TGAACTGATGGGATCTCTTCTACC 59.348 45.833 9.68 0.00 0.00 3.18
459 468 1.197721 CGAAATGTGGTGGCTCTGAAC 59.802 52.381 0.00 0.00 0.00 3.18
644 665 1.738830 GCGGCTACTTACAACGGCA 60.739 57.895 0.00 0.00 0.00 5.69
730 751 6.015519 TGTGCCACTATTGCTCTTTTAAATGT 60.016 34.615 0.00 0.00 0.00 2.71
800 860 5.184479 GGCCTATTATATGTGTCGACACCTA 59.816 44.000 38.12 32.97 45.88 3.08
926 1281 4.039124 TGAGTCGATCAAAGCATGGCTATA 59.961 41.667 0.00 0.00 33.56 1.31
985 1340 1.134907 CATCATTGTTGGCTTGAGGGC 60.135 52.381 0.00 0.00 41.27 5.19
1042 1573 2.359900 CTCTTCCACCATGGTTACAGC 58.640 52.381 16.84 0.00 39.03 4.40
1159 2610 7.481275 ACTCAATTAAATTTTGCCACACAAG 57.519 32.000 0.00 0.00 40.06 3.16
1274 3046 6.707440 ACAAAGTTGTGTATGTGGAAATGA 57.293 33.333 0.00 0.00 40.49 2.57
1282 3054 2.685897 ACGGCAACAAAGTTGTGTATGT 59.314 40.909 11.09 1.68 41.31 2.29
1416 3195 2.125310 CGTGGGCTATGTTGCGGA 60.125 61.111 0.00 0.00 0.00 5.54
1488 3285 3.414700 CTTCGACACTGCGCACCC 61.415 66.667 5.66 0.00 0.00 4.61
1489 3286 4.077188 GCTTCGACACTGCGCACC 62.077 66.667 5.66 0.00 0.00 5.01
1783 5747 0.741221 GCGAGAAGAAGTGCCGGAAT 60.741 55.000 5.05 0.00 0.00 3.01
1821 5788 1.525077 CCGCGGAGAGAGTAGAGCT 60.525 63.158 24.07 0.00 0.00 4.09
1966 5936 2.742116 GGCGGACCTGAATGGCCTA 61.742 63.158 3.32 0.00 40.59 3.93
2055 6025 2.049985 CCGTGAGATCGATCGGGC 60.050 66.667 19.33 13.21 39.41 6.13
2176 7086 2.680352 GTGGACTCCTCCGCTGGA 60.680 66.667 0.00 0.00 43.05 3.86
2230 7155 3.470567 GAAGACGACGGCGCACTG 61.471 66.667 12.58 0.00 42.48 3.66
2231 7156 4.719369 GGAAGACGACGGCGCACT 62.719 66.667 12.58 8.12 42.48 4.40
2235 7160 3.902162 TTTCGGGAAGACGACGGCG 62.902 63.158 10.39 10.39 43.37 6.46
2236 7161 1.623973 CTTTTCGGGAAGACGACGGC 61.624 60.000 0.00 0.00 43.37 5.68
2237 7162 0.038892 TCTTTTCGGGAAGACGACGG 60.039 55.000 0.00 0.00 43.37 4.79
2238 7163 1.774639 TTCTTTTCGGGAAGACGACG 58.225 50.000 0.00 0.00 43.37 5.12
2239 7164 3.805971 TCTTTTCTTTTCGGGAAGACGAC 59.194 43.478 0.00 0.00 43.37 4.34
2240 7165 4.062677 TCTTTTCTTTTCGGGAAGACGA 57.937 40.909 0.00 0.00 41.76 4.20
2241 7166 4.773510 CTTCTTTTCTTTTCGGGAAGACG 58.226 43.478 0.00 0.00 35.50 4.18
2242 7167 4.537965 GCTTCTTTTCTTTTCGGGAAGAC 58.462 43.478 0.00 0.00 35.50 3.01
2245 7170 2.292292 CCGCTTCTTTTCTTTTCGGGAA 59.708 45.455 0.00 0.00 32.55 3.97
2257 7182 2.328099 CGGCAGCTTCCGCTTCTTT 61.328 57.895 12.92 0.00 46.47 2.52
2271 7196 4.657408 TTGCATGGTGCTCCGGCA 62.657 61.111 16.97 16.97 45.31 5.69
2302 7227 1.249407 AAGAGAGATATCCCGACGCC 58.751 55.000 0.00 0.00 0.00 5.68
2337 7262 1.299976 GCTTTCCGGAGATGTGGGT 59.700 57.895 3.34 0.00 0.00 4.51
2353 7278 2.927580 CGTAGTGGTGGTCCGTGCT 61.928 63.158 0.00 0.00 36.30 4.40
2382 7307 2.267351 TGGCATTGCTTCCCGTGTG 61.267 57.895 8.82 0.00 0.00 3.82
2456 7381 4.794439 CTCCGGCGTGACGATGCA 62.794 66.667 10.10 0.00 35.60 3.96
2515 7440 2.576317 GACACGTAGCTCGACGCC 60.576 66.667 8.91 0.00 46.87 5.68
2518 7443 1.136984 CAGGGACACGTAGCTCGAC 59.863 63.158 11.64 0.00 42.86 4.20
2556 7486 5.314529 CACAGCTAATGGATGGATGATTCT 58.685 41.667 0.00 0.00 35.35 2.40
2568 7498 1.290203 ATCGAACGCACAGCTAATGG 58.710 50.000 0.00 0.00 0.00 3.16
2570 7500 1.588404 CGAATCGAACGCACAGCTAAT 59.412 47.619 0.00 0.00 0.00 1.73
2571 7501 0.989164 CGAATCGAACGCACAGCTAA 59.011 50.000 0.00 0.00 0.00 3.09
2572 7502 0.169451 TCGAATCGAACGCACAGCTA 59.831 50.000 1.57 0.00 31.06 3.32
2573 7503 1.073216 CTCGAATCGAACGCACAGCT 61.073 55.000 6.84 0.00 34.74 4.24
2581 7515 4.264543 ACAAATCATGCTCGAATCGAAC 57.735 40.909 6.84 2.45 34.74 3.95
2645 7593 1.703438 CCGTCTACAGGACTCGGTCG 61.703 65.000 0.00 0.00 42.44 4.79
2747 7695 4.697756 TCGGCCTTCACCTTGCGG 62.698 66.667 0.00 0.00 0.00 5.69
2861 7815 1.267574 GGAGACACCAGGAGCCATGA 61.268 60.000 0.00 0.00 38.79 3.07
2890 7844 0.107456 AATAGGTCCATCAGCCTGCG 59.893 55.000 0.00 0.00 36.38 5.18
2989 7946 9.204570 GCAGCTCGAAGATAAATAAATAGGTAA 57.795 33.333 0.00 0.00 33.89 2.85
3009 7966 3.764885 AAATATGTCAAACCGCAGCTC 57.235 42.857 0.00 0.00 0.00 4.09
3018 7975 8.556213 AAACTTAGTCGCCTAAATATGTCAAA 57.444 30.769 0.00 0.00 32.86 2.69
3057 8014 2.610438 TCTTTCACCGGTACCTACCT 57.390 50.000 6.87 0.00 44.25 3.08
3059 8016 2.762327 TGGATCTTTCACCGGTACCTAC 59.238 50.000 6.87 0.00 0.00 3.18
3071 8028 2.009774 CCGACATGTGGTGGATCTTTC 58.990 52.381 1.15 0.00 0.00 2.62
3089 8046 2.753296 ACACCAATTTCAATGTTGCCG 58.247 42.857 0.00 0.00 0.00 5.69
3096 8053 7.791029 ACTCTAAAACCAACACCAATTTCAAT 58.209 30.769 0.00 0.00 0.00 2.57
3102 8059 9.582648 AGTTTATACTCTAAAACCAACACCAAT 57.417 29.630 0.00 0.00 36.46 3.16
3104 8061 9.715121 CTAGTTTATACTCTAAAACCAACACCA 57.285 33.333 0.00 0.00 36.46 4.17
3161 8118 4.039852 GGGACCACACACCATTTTGTATTT 59.960 41.667 0.00 0.00 0.00 1.40
3181 8138 1.300963 GAAGTGCATGCAGAGGGGA 59.699 57.895 23.41 0.00 0.00 4.81
3198 8155 6.433716 TGCATCCATATTCTGACAAAAACTGA 59.566 34.615 0.00 0.00 0.00 3.41
3202 8159 6.154877 ACCATGCATCCATATTCTGACAAAAA 59.845 34.615 0.00 0.00 0.00 1.94
3227 8184 6.598457 AGAGAGAGTTAACGTACTGAGCATAA 59.402 38.462 0.00 0.00 0.00 1.90
3262 8219 7.652524 TTTGCTATGGAAATTTATAGGTGCA 57.347 32.000 9.14 5.52 0.00 4.57
3308 8265 6.843069 ATTGAAAACGGAATTTTGGTTCAG 57.157 33.333 0.00 0.00 40.73 3.02
3462 8419 6.560253 TCTAGTTCAAAATGAGTGAAAGCC 57.440 37.500 0.00 0.00 36.77 4.35
3481 8438 4.766891 TCTTTTGCAAAGGGTGGAATCTAG 59.233 41.667 19.84 7.05 37.41 2.43
3571 8530 9.696917 GTCCAAAATCTGTTTTATGAAATGAGT 57.303 29.630 0.00 0.00 35.83 3.41
3659 8618 8.848182 TGTGAAATACGGGTAACTTGTTATTTT 58.152 29.630 0.00 0.00 0.00 1.82
3660 8619 8.291740 GTGTGAAATACGGGTAACTTGTTATTT 58.708 33.333 0.00 0.00 0.00 1.40
3661 8620 7.094677 GGTGTGAAATACGGGTAACTTGTTATT 60.095 37.037 0.00 0.00 0.00 1.40
3662 8621 6.372381 GGTGTGAAATACGGGTAACTTGTTAT 59.628 38.462 0.00 0.00 0.00 1.89
3663 8622 5.700373 GGTGTGAAATACGGGTAACTTGTTA 59.300 40.000 0.00 0.00 0.00 2.41
3664 8623 4.516321 GGTGTGAAATACGGGTAACTTGTT 59.484 41.667 0.00 0.00 0.00 2.83
3665 8624 4.067192 GGTGTGAAATACGGGTAACTTGT 58.933 43.478 0.00 0.00 0.00 3.16
3666 8625 4.066490 TGGTGTGAAATACGGGTAACTTG 58.934 43.478 0.00 0.00 0.00 3.16
3667 8626 4.354893 TGGTGTGAAATACGGGTAACTT 57.645 40.909 0.00 0.00 0.00 2.66
3668 8627 4.354893 TTGGTGTGAAATACGGGTAACT 57.645 40.909 0.00 0.00 0.00 2.24
3669 8628 5.435820 TTTTGGTGTGAAATACGGGTAAC 57.564 39.130 0.00 0.00 0.00 2.50
3699 8658 9.941664 GAGTGAAATCTGTTTTCCATACATATG 57.058 33.333 0.00 0.00 42.63 1.78
3700 8659 9.685276 TGAGTGAAATCTGTTTTCCATACATAT 57.315 29.630 8.33 0.00 42.63 1.78
3701 8660 9.685276 ATGAGTGAAATCTGTTTTCCATACATA 57.315 29.630 8.33 0.00 42.63 2.29
3702 8661 8.585471 ATGAGTGAAATCTGTTTTCCATACAT 57.415 30.769 8.33 6.60 42.63 2.29
3703 8662 8.408043 AATGAGTGAAATCTGTTTTCCATACA 57.592 30.769 8.33 5.05 42.63 2.29
3704 8663 9.346725 GAAATGAGTGAAATCTGTTTTCCATAC 57.653 33.333 8.33 1.86 42.63 2.39
3705 8664 9.076781 TGAAATGAGTGAAATCTGTTTTCCATA 57.923 29.630 8.33 0.00 42.63 2.74
3706 8665 7.954835 TGAAATGAGTGAAATCTGTTTTCCAT 58.045 30.769 8.33 3.34 42.63 3.41
3707 8666 7.345422 TGAAATGAGTGAAATCTGTTTTCCA 57.655 32.000 8.33 1.47 42.63 3.53
3708 8667 8.647143 TTTGAAATGAGTGAAATCTGTTTTCC 57.353 30.769 8.33 1.79 42.63 3.13
3713 8672 9.048446 CCAATTTTTGAAATGAGTGAAATCTGT 57.952 29.630 0.00 0.00 0.00 3.41
3714 8673 9.048446 ACCAATTTTTGAAATGAGTGAAATCTG 57.952 29.630 0.00 0.00 0.00 2.90
3715 8674 9.617523 AACCAATTTTTGAAATGAGTGAAATCT 57.382 25.926 0.00 0.00 0.00 2.40
3716 8675 9.868389 GAACCAATTTTTGAAATGAGTGAAATC 57.132 29.630 0.00 0.00 0.00 2.17
3717 8676 9.617523 AGAACCAATTTTTGAAATGAGTGAAAT 57.382 25.926 0.00 0.00 0.00 2.17
3718 8677 9.097257 GAGAACCAATTTTTGAAATGAGTGAAA 57.903 29.630 0.00 0.00 0.00 2.69
3719 8678 8.256605 TGAGAACCAATTTTTGAAATGAGTGAA 58.743 29.630 0.00 0.00 0.00 3.18
3720 8679 7.780064 TGAGAACCAATTTTTGAAATGAGTGA 58.220 30.769 0.00 0.00 0.00 3.41
3721 8680 8.422973 TTGAGAACCAATTTTTGAAATGAGTG 57.577 30.769 0.00 0.00 0.00 3.51
3756 8715 6.071221 ACCGGTTTCCTGAAGTAAAAGTTTTT 60.071 34.615 0.00 0.00 0.00 1.94
3757 8716 5.419788 ACCGGTTTCCTGAAGTAAAAGTTTT 59.580 36.000 0.00 6.06 0.00 2.43
3758 8717 4.951715 ACCGGTTTCCTGAAGTAAAAGTTT 59.048 37.500 0.00 0.00 0.00 2.66
3759 8718 4.529897 ACCGGTTTCCTGAAGTAAAAGTT 58.470 39.130 0.00 0.00 0.00 2.66
3760 8719 4.160642 ACCGGTTTCCTGAAGTAAAAGT 57.839 40.909 0.00 0.00 0.00 2.66
3761 8720 5.066764 TGAAACCGGTTTCCTGAAGTAAAAG 59.933 40.000 42.37 0.00 46.15 2.27
3762 8721 4.948621 TGAAACCGGTTTCCTGAAGTAAAA 59.051 37.500 42.37 25.16 46.15 1.52
3763 8722 4.336153 GTGAAACCGGTTTCCTGAAGTAAA 59.664 41.667 42.37 25.78 46.15 2.01
3764 8723 3.878699 GTGAAACCGGTTTCCTGAAGTAA 59.121 43.478 42.37 26.39 46.15 2.24
3765 8724 3.135167 AGTGAAACCGGTTTCCTGAAGTA 59.865 43.478 42.37 27.01 46.15 2.24
3766 8725 2.092592 AGTGAAACCGGTTTCCTGAAGT 60.093 45.455 42.37 29.36 46.15 3.01
3767 8726 2.290641 CAGTGAAACCGGTTTCCTGAAG 59.709 50.000 40.60 29.51 46.15 3.02
3768 8727 2.294074 CAGTGAAACCGGTTTCCTGAA 58.706 47.619 40.60 29.73 46.15 3.02
3769 8728 1.210967 ACAGTGAAACCGGTTTCCTGA 59.789 47.619 44.40 32.85 46.15 3.86
3770 8729 1.675552 ACAGTGAAACCGGTTTCCTG 58.324 50.000 40.84 40.84 46.15 3.86
3771 8730 2.430248 AACAGTGAAACCGGTTTCCT 57.570 45.000 42.37 35.70 46.15 3.36
3772 8731 4.999311 ACTATAACAGTGAAACCGGTTTCC 59.001 41.667 42.37 34.51 46.15 3.13
3785 8744 8.559536 CATAAAATCGCCAATCACTATAACAGT 58.440 33.333 0.00 0.00 38.32 3.55
3786 8745 8.773645 TCATAAAATCGCCAATCACTATAACAG 58.226 33.333 0.00 0.00 0.00 3.16
3787 8746 8.669946 TCATAAAATCGCCAATCACTATAACA 57.330 30.769 0.00 0.00 0.00 2.41
3788 8747 7.746475 GCTCATAAAATCGCCAATCACTATAAC 59.254 37.037 0.00 0.00 0.00 1.89
3789 8748 7.094805 GGCTCATAAAATCGCCAATCACTATAA 60.095 37.037 0.00 0.00 42.06 0.98
3790 8749 6.371548 GGCTCATAAAATCGCCAATCACTATA 59.628 38.462 0.00 0.00 42.06 1.31
3791 8750 5.182001 GGCTCATAAAATCGCCAATCACTAT 59.818 40.000 0.00 0.00 42.06 2.12
3792 8751 4.515191 GGCTCATAAAATCGCCAATCACTA 59.485 41.667 0.00 0.00 42.06 2.74
3793 8752 3.316308 GGCTCATAAAATCGCCAATCACT 59.684 43.478 0.00 0.00 42.06 3.41
3794 8753 3.632189 GGCTCATAAAATCGCCAATCAC 58.368 45.455 0.00 0.00 42.06 3.06
3795 8754 3.988379 GGCTCATAAAATCGCCAATCA 57.012 42.857 0.00 0.00 42.06 2.57
3800 8759 2.229792 TGGATGGCTCATAAAATCGCC 58.770 47.619 0.00 0.00 42.78 5.54
3801 8760 3.119708 GGATGGATGGCTCATAAAATCGC 60.120 47.826 0.00 0.00 0.00 4.58
3802 8761 4.074259 TGGATGGATGGCTCATAAAATCG 58.926 43.478 0.00 0.00 0.00 3.34
3803 8762 5.075493 AGTGGATGGATGGCTCATAAAATC 58.925 41.667 0.00 0.00 0.00 2.17
3804 8763 5.070823 AGTGGATGGATGGCTCATAAAAT 57.929 39.130 0.00 0.00 0.00 1.82
3805 8764 4.166725 AGAGTGGATGGATGGCTCATAAAA 59.833 41.667 0.00 0.00 0.00 1.52
3806 8765 3.718434 AGAGTGGATGGATGGCTCATAAA 59.282 43.478 0.00 0.00 0.00 1.40
3807 8766 3.321039 AGAGTGGATGGATGGCTCATAA 58.679 45.455 0.00 0.00 0.00 1.90
3808 8767 2.981921 AGAGTGGATGGATGGCTCATA 58.018 47.619 0.00 0.00 0.00 2.15
3809 8768 1.817087 AGAGTGGATGGATGGCTCAT 58.183 50.000 0.00 0.00 0.00 2.90
3810 8769 3.329497 AGAGTGGATGGATGGCTCA 57.671 52.632 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.