Multiple sequence alignment - TraesCS4B01G125500

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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 TraesCS4B01G125500 chr4B 100.000 4415 0 0 1 4415 155381099 155376685 0.000000e+00 8154.0
1 TraesCS4B01G125500 chr4B 85.714 84 12 0 1769 1852 103773369 103773452 6.080000e-14 89.8
2 TraesCS4B01G125500 chr4B 87.302 63 5 2 2862 2923 536927821 536927881 7.920000e-08 69.4
3 TraesCS4B01G125500 chr4D 96.895 2351 49 9 545 2873 168195913 168198261 0.000000e+00 3916.0
4 TraesCS4B01G125500 chr4D 90.762 1548 71 25 2877 4415 168198755 168200239 0.000000e+00 2001.0
5 TraesCS4B01G125500 chr4D 96.063 254 8 2 1 253 168176771 168177023 3.180000e-111 412.0
6 TraesCS4B01G125500 chr4D 87.624 202 6 10 371 554 168177335 168177535 2.670000e-52 217.0
7 TraesCS4B01G125500 chr4D 88.525 122 10 3 252 372 168177185 168177303 1.280000e-30 145.0
8 TraesCS4B01G125500 chr4D 85.714 84 12 0 1769 1852 70119509 70119592 6.080000e-14 89.8
9 TraesCS4B01G125500 chr4A 93.514 1403 55 15 1472 2859 363711558 363712939 0.000000e+00 2054.0
10 TraesCS4B01G125500 chr4A 89.549 842 40 22 2974 3791 363712965 363713782 0.000000e+00 1024.0
11 TraesCS4B01G125500 chr4A 89.413 699 20 8 639 1312 363710225 363710894 0.000000e+00 832.0
12 TraesCS4B01G125500 chr4A 85.307 456 66 1 3956 4410 363719102 363719557 1.860000e-128 470.0
13 TraesCS4B01G125500 chr4A 92.188 320 20 4 1 319 363709353 363709668 8.710000e-122 448.0
14 TraesCS4B01G125500 chr4A 91.667 276 16 5 375 649 363709779 363710048 4.170000e-100 375.0
15 TraesCS4B01G125500 chr4A 97.340 188 5 0 1303 1490 363711358 363711545 1.980000e-83 320.0
16 TraesCS4B01G125500 chr4A 95.876 97 4 0 3799 3895 363714716 363714812 1.640000e-34 158.0
17 TraesCS4B01G125500 chr4A 91.919 99 5 2 274 372 363709655 363709750 7.700000e-28 135.0
18 TraesCS4B01G125500 chr4A 85.714 84 12 0 1769 1852 522294541 522294624 6.080000e-14 89.8
19 TraesCS4B01G125500 chr6D 74.400 500 103 19 1733 2218 335375780 335375292 1.620000e-44 191.0
20 TraesCS4B01G125500 chr6D 90.164 61 2 3 2863 2923 108554028 108554084 4.740000e-10 76.8
21 TraesCS4B01G125500 chr6B 82.609 207 34 2 1734 1939 485292909 485293114 9.750000e-42 182.0
22 TraesCS4B01G125500 chr6A 82.464 211 29 7 1733 1939 475000348 475000142 1.260000e-40 178.0
23 TraesCS4B01G125500 chr6A 88.571 70 2 5 2864 2930 58376600 58376534 3.660000e-11 80.5
24 TraesCS4B01G125500 chr2D 81.250 208 35 4 1734 1939 509942710 509942915 9.820000e-37 165.0
25 TraesCS4B01G125500 chr2D 88.525 61 4 3 2877 2935 630947874 630947815 2.200000e-08 71.3
26 TraesCS4B01G125500 chr3D 91.667 60 4 1 2865 2923 256985609 256985668 1.020000e-11 82.4
27 TraesCS4B01G125500 chr3D 88.525 61 4 3 2865 2923 576885414 576885473 2.200000e-08 71.3
28 TraesCS4B01G125500 chr1A 96.000 50 1 1 2877 2925 175176177 175176128 3.660000e-11 80.5
29 TraesCS4B01G125500 chr7B 88.525 61 5 2 2864 2923 609013683 609013742 6.130000e-09 73.1
30 TraesCS4B01G125500 chr5B 84.000 75 3 7 2854 2923 548098953 548099023 3.690000e-06 63.9


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 TraesCS4B01G125500 chr4B 155376685 155381099 4414 True 8154.00 8154 100.000000 1 4415 1 chr4B.!!$R1 4414
1 TraesCS4B01G125500 chr4D 168195913 168200239 4326 False 2958.50 3916 93.828500 545 4415 2 chr4D.!!$F3 3870
2 TraesCS4B01G125500 chr4D 168176771 168177535 764 False 258.00 412 90.737333 1 554 3 chr4D.!!$F2 553
3 TraesCS4B01G125500 chr4A 363709353 363714812 5459 False 668.25 2054 92.683250 1 3895 8 chr4A.!!$F3 3894

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
757 1188 0.539986 AACCACAGCCGGTACCTATG 59.46 55.0 10.90 8.24 38.76 2.23 F
1700 2682 0.809636 CATGGTCCATTCGCGCACTA 60.81 55.0 8.75 0.00 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2377 3367 0.653636 GACGTGACGTTTTGAAGCCA 59.346 50.0 13.44 0.0 41.37 4.75 R
3438 4942 0.168348 GTTGCAGTGCATCAGCTCAG 59.832 55.0 20.50 0.0 42.74 3.35 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
68 69 9.871299 AAAAAGTTGACAAAAACATGTTAACAC 57.129 25.926 12.39 3.92 46.44 3.32
69 70 8.594881 AAAGTTGACAAAAACATGTTAACACA 57.405 26.923 12.39 6.43 46.44 3.72
245 247 1.676916 CCCCATAGATATGTGGCGCTG 60.677 57.143 7.64 0.00 34.08 5.18
348 539 6.560361 TGCTCCTAGATTTCTCTATCTCCAT 58.440 40.000 0.00 0.00 36.34 3.41
363 554 8.094284 TCTATCTCCATCCCATAATGTAATGG 57.906 38.462 3.31 3.31 45.20 3.16
457 698 3.723772 GGGCAGCCCAAATTTTTGT 57.276 47.368 27.33 0.00 44.65 2.83
592 833 4.057432 ACAAATAATGCAAAAGCGCAGTT 58.943 34.783 11.47 0.00 46.99 3.16
611 855 6.459573 CGCAGTTGTAATGTATTTTAGGGCAT 60.460 38.462 0.00 0.00 0.00 4.40
745 1176 2.011222 ACAAACACACGGTAACCACAG 58.989 47.619 0.00 0.00 0.00 3.66
746 1177 1.018910 AAACACACGGTAACCACAGC 58.981 50.000 0.00 0.00 0.00 4.40
747 1178 0.816421 AACACACGGTAACCACAGCC 60.816 55.000 0.00 0.00 0.00 4.85
751 1182 2.972267 CGGTAACCACAGCCGGTA 59.028 61.111 1.90 0.00 38.76 4.02
752 1183 1.446618 CGGTAACCACAGCCGGTAC 60.447 63.158 1.90 0.00 38.76 3.34
753 1184 1.078918 GGTAACCACAGCCGGTACC 60.079 63.158 1.90 0.16 38.76 3.34
754 1185 1.547472 GGTAACCACAGCCGGTACCT 61.547 60.000 10.90 0.00 38.76 3.08
755 1186 1.185315 GTAACCACAGCCGGTACCTA 58.815 55.000 10.90 0.00 38.76 3.08
756 1187 1.758862 GTAACCACAGCCGGTACCTAT 59.241 52.381 10.90 0.00 38.76 2.57
757 1188 0.539986 AACCACAGCCGGTACCTATG 59.460 55.000 10.90 8.24 38.76 2.23
853 1290 5.929697 TCATCAAGCCGTATTGATCAATC 57.070 39.130 23.95 14.29 44.68 2.67
963 1403 4.545610 TCCTTTCGTTGATGCATTTGTTC 58.454 39.130 0.00 0.00 0.00 3.18
964 1404 4.278170 TCCTTTCGTTGATGCATTTGTTCT 59.722 37.500 0.00 0.00 0.00 3.01
965 1405 4.984161 CCTTTCGTTGATGCATTTGTTCTT 59.016 37.500 0.00 0.00 0.00 2.52
969 1409 4.975502 TCGTTGATGCATTTGTTCTTGTTC 59.024 37.500 0.00 0.00 0.00 3.18
1700 2682 0.809636 CATGGTCCATTCGCGCACTA 60.810 55.000 8.75 0.00 0.00 2.74
1709 2691 3.058708 CCATTCGCGCACTATCATTCATT 60.059 43.478 8.75 0.00 0.00 2.57
1866 2848 2.586357 GCCTTCATCGGCGTCCTC 60.586 66.667 6.85 0.00 40.79 3.71
2039 3029 2.692041 GGAAGGAAGATTTGATGCAGGG 59.308 50.000 0.00 0.00 0.00 4.45
2345 3335 5.335191 CGTCTGGTGAGATCAATATCGATCA 60.335 44.000 0.00 0.00 43.61 2.92
2850 3844 2.224042 GCTAGTTTTGCTTGCCTTGGTT 60.224 45.455 0.00 0.00 39.49 3.67
2898 4380 1.584724 TTGAGAAGGAGGATGACCCC 58.415 55.000 0.00 0.00 36.73 4.95
2899 4381 0.687757 TGAGAAGGAGGATGACCCCG 60.688 60.000 0.00 0.00 36.73 5.73
2900 4382 1.383248 AGAAGGAGGATGACCCCGG 60.383 63.158 0.00 0.00 36.73 5.73
2964 4446 6.122277 AGAGGTTGTTGATTTGTCTTCTTCA 58.878 36.000 0.00 0.00 0.00 3.02
2965 4447 6.774656 AGAGGTTGTTGATTTGTCTTCTTCAT 59.225 34.615 0.00 0.00 0.00 2.57
2966 4448 6.974965 AGGTTGTTGATTTGTCTTCTTCATC 58.025 36.000 0.00 0.00 0.00 2.92
2967 4449 6.774656 AGGTTGTTGATTTGTCTTCTTCATCT 59.225 34.615 0.00 0.00 0.00 2.90
2968 4450 7.286316 AGGTTGTTGATTTGTCTTCTTCATCTT 59.714 33.333 0.00 0.00 0.00 2.40
2969 4451 7.592903 GGTTGTTGATTTGTCTTCTTCATCTTC 59.407 37.037 0.00 0.00 0.00 2.87
2970 4452 8.348507 GTTGTTGATTTGTCTTCTTCATCTTCT 58.651 33.333 0.00 0.00 0.00 2.85
2971 4453 8.455903 TGTTGATTTGTCTTCTTCATCTTCTT 57.544 30.769 0.00 0.00 0.00 2.52
2972 4454 8.562892 TGTTGATTTGTCTTCTTCATCTTCTTC 58.437 33.333 0.00 0.00 0.00 2.87
3138 4620 1.474677 CCTGACAAGCTAGCTGATGGG 60.475 57.143 20.16 13.10 0.00 4.00
3139 4621 1.209019 CTGACAAGCTAGCTGATGGGT 59.791 52.381 20.16 11.65 0.00 4.51
3140 4622 1.065926 TGACAAGCTAGCTGATGGGTG 60.066 52.381 20.16 14.08 0.00 4.61
3141 4623 0.254178 ACAAGCTAGCTGATGGGTGG 59.746 55.000 20.16 3.44 0.00 4.61
3207 4689 3.822192 GACCGGATTTTGCGCCCC 61.822 66.667 9.46 0.00 0.00 5.80
3249 4731 1.333931 GATGACATCGACGTCCTGCTA 59.666 52.381 9.43 1.48 34.88 3.49
3418 4906 5.470098 GCAACTTCTTCTGAGGTGTGAAATA 59.530 40.000 0.00 0.00 32.63 1.40
3419 4907 6.150140 GCAACTTCTTCTGAGGTGTGAAATAT 59.850 38.462 0.00 0.00 32.63 1.28
3438 4942 7.658982 TGAAATATAATGGTGAGTGAGATGAGC 59.341 37.037 0.00 0.00 0.00 4.26
3441 4945 1.928868 TGGTGAGTGAGATGAGCTGA 58.071 50.000 0.00 0.00 0.00 4.26
3637 5141 3.255969 TCTACGTACCATTTTCTGCCC 57.744 47.619 0.00 0.00 0.00 5.36
3993 6431 1.198867 CATCACGAAAATGCGACCCAA 59.801 47.619 0.00 0.00 34.83 4.12
4010 6448 0.029300 CAACTGCACACCTCAAACCG 59.971 55.000 0.00 0.00 0.00 4.44
4013 6451 2.904866 GCACACCTCAAACCGGCA 60.905 61.111 0.00 0.00 0.00 5.69
4023 6461 3.131396 CTCAAACCGGCACTATACATCC 58.869 50.000 0.00 0.00 0.00 3.51
4055 6494 2.297033 CACCTTTCAAACCCAGTCCATG 59.703 50.000 0.00 0.00 0.00 3.66
4094 6533 4.129737 CCCGGACGCGTCTGTCAT 62.130 66.667 37.95 4.94 40.72 3.06
4112 6551 3.736252 GTCATATCAGATCCGACAAACCG 59.264 47.826 7.09 0.00 0.00 4.44
4125 6564 1.686110 AAACCGGCCACACCCAAAA 60.686 52.632 0.00 0.00 33.26 2.44
4126 6565 1.051556 AAACCGGCCACACCCAAAAT 61.052 50.000 0.00 0.00 33.26 1.82
4127 6566 1.468506 AACCGGCCACACCCAAAATC 61.469 55.000 0.00 0.00 33.26 2.17
4128 6567 2.645192 CCGGCCACACCCAAAATCC 61.645 63.158 2.24 0.00 33.26 3.01
4129 6568 2.645192 CGGCCACACCCAAAATCCC 61.645 63.158 2.24 0.00 33.26 3.85
4130 6569 1.229177 GGCCACACCCAAAATCCCT 60.229 57.895 0.00 0.00 0.00 4.20
4131 6570 1.257750 GGCCACACCCAAAATCCCTC 61.258 60.000 0.00 0.00 0.00 4.30
4132 6571 1.595093 GCCACACCCAAAATCCCTCG 61.595 60.000 0.00 0.00 0.00 4.63
4133 6572 0.037590 CCACACCCAAAATCCCTCGA 59.962 55.000 0.00 0.00 0.00 4.04
4134 6573 1.546773 CCACACCCAAAATCCCTCGAA 60.547 52.381 0.00 0.00 0.00 3.71
4135 6574 2.235016 CACACCCAAAATCCCTCGAAA 58.765 47.619 0.00 0.00 0.00 3.46
4136 6575 2.030274 CACACCCAAAATCCCTCGAAAC 60.030 50.000 0.00 0.00 0.00 2.78
4137 6576 2.158519 ACACCCAAAATCCCTCGAAACT 60.159 45.455 0.00 0.00 0.00 2.66
4138 6577 2.228822 CACCCAAAATCCCTCGAAACTG 59.771 50.000 0.00 0.00 0.00 3.16
4139 6578 2.107552 ACCCAAAATCCCTCGAAACTGA 59.892 45.455 0.00 0.00 0.00 3.41
4140 6579 2.488153 CCCAAAATCCCTCGAAACTGAC 59.512 50.000 0.00 0.00 0.00 3.51
4141 6580 2.488153 CCAAAATCCCTCGAAACTGACC 59.512 50.000 0.00 0.00 0.00 4.02
4221 6660 3.763897 ACCTAGTCCACCAAATTGAATGC 59.236 43.478 0.00 0.00 0.00 3.56
4236 6675 2.198304 AATGCCCTCTTCCCGTGTCC 62.198 60.000 0.00 0.00 0.00 4.02
4240 6679 2.572284 CTCTTCCCGTGTCCGTCC 59.428 66.667 0.00 0.00 0.00 4.79
4255 6694 0.822164 CGTCCTCCATTTCCTACCGT 59.178 55.000 0.00 0.00 0.00 4.83
4256 6695 1.206371 CGTCCTCCATTTCCTACCGTT 59.794 52.381 0.00 0.00 0.00 4.44
4267 6706 0.608640 CCTACCGTTGAGCCTTCACT 59.391 55.000 0.00 0.00 31.71 3.41
4268 6707 1.822990 CCTACCGTTGAGCCTTCACTA 59.177 52.381 0.00 0.00 31.71 2.74
4289 6728 2.852075 TCCGCCCTTGGTCCTGTT 60.852 61.111 0.00 0.00 0.00 3.16
4291 6730 2.429930 CGCCCTTGGTCCTGTTCA 59.570 61.111 0.00 0.00 0.00 3.18
4298 6737 2.045926 GGTCCTGTTCATGCCGCT 60.046 61.111 0.00 0.00 0.00 5.52
4314 6753 0.384309 CGCTGCCCTCGTAGATAACA 59.616 55.000 0.00 0.00 33.89 2.41
4334 6773 1.757340 CTCCGAGTACCCTGTCCCC 60.757 68.421 0.00 0.00 0.00 4.81
4391 6830 2.070650 GGCTCCCATCCGTAGGGTT 61.071 63.158 0.53 0.00 39.56 4.11
4400 6839 2.936498 CATCCGTAGGGTTAGTTGCAAG 59.064 50.000 0.00 0.00 39.56 4.01
4404 6843 0.978151 TAGGGTTAGTTGCAAGGCGA 59.022 50.000 0.00 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 6.261826 GGTGGGATCTTCAAAACTAGATCATG 59.738 42.308 12.56 0.00 38.98 3.07
69 70 6.360618 GGTGGGATCTTCAAAACTAGATCAT 58.639 40.000 12.56 0.00 38.98 2.45
203 205 4.141620 GGGCTCAATTCTCTTCTATCCACA 60.142 45.833 0.00 0.00 0.00 4.17
293 458 4.287766 AGGTAAAGTTCCTCGCAGAAAT 57.712 40.909 0.00 0.00 34.09 2.17
297 488 3.371285 GCTTAAGGTAAAGTTCCTCGCAG 59.629 47.826 4.29 0.00 33.76 5.18
302 493 4.367039 TGCAGCTTAAGGTAAAGTTCCT 57.633 40.909 6.90 0.00 36.81 3.36
348 539 7.130285 CCCCCTATTATCCATTACATTATGGGA 59.870 40.741 0.00 0.00 44.32 4.37
457 698 3.961849 TGTATATTTGCAGCACTTGGGA 58.038 40.909 0.00 0.00 0.00 4.37
592 833 8.588290 AAAGTGATGCCCTAAAATACATTACA 57.412 30.769 0.00 0.00 32.99 2.41
611 855 3.367395 CGTAGCAGATCAGGTGAAAGTGA 60.367 47.826 0.00 0.00 0.00 3.41
644 888 3.130516 TGGAGATACGAGATGACAACACC 59.869 47.826 0.00 0.00 0.00 4.16
750 1181 5.579753 AGAGGAGAATCGGTACATAGGTA 57.420 43.478 0.00 0.00 34.37 3.08
751 1182 4.456662 AGAGGAGAATCGGTACATAGGT 57.543 45.455 0.00 0.00 34.37 3.08
752 1183 5.074115 AGAAGAGGAGAATCGGTACATAGG 58.926 45.833 0.00 0.00 34.37 2.57
753 1184 5.182380 GGAGAAGAGGAGAATCGGTACATAG 59.818 48.000 0.00 0.00 34.37 2.23
754 1185 5.071370 GGAGAAGAGGAGAATCGGTACATA 58.929 45.833 0.00 0.00 34.37 2.29
755 1186 3.892588 GGAGAAGAGGAGAATCGGTACAT 59.107 47.826 0.00 0.00 34.37 2.29
756 1187 3.288964 GGAGAAGAGGAGAATCGGTACA 58.711 50.000 0.00 0.00 34.37 2.90
757 1188 2.624364 GGGAGAAGAGGAGAATCGGTAC 59.376 54.545 0.00 0.00 34.37 3.34
853 1290 3.099267 GGTATGATCAGACCGAAGTGG 57.901 52.381 22.99 0.00 46.41 4.00
963 1403 3.476552 TCAAGGCCTACAACAGAACAAG 58.523 45.455 5.16 0.00 0.00 3.16
964 1404 3.569194 TCAAGGCCTACAACAGAACAA 57.431 42.857 5.16 0.00 0.00 2.83
965 1405 3.674997 GATCAAGGCCTACAACAGAACA 58.325 45.455 5.16 0.00 0.00 3.18
969 1409 2.672961 TCGATCAAGGCCTACAACAG 57.327 50.000 5.16 0.00 0.00 3.16
1700 2682 6.201044 GGACGTAAACGAGATCAATGAATGAT 59.799 38.462 9.86 0.00 46.37 2.45
1709 2691 3.507786 CACATGGACGTAAACGAGATCA 58.492 45.455 9.86 2.48 43.02 2.92
1866 2848 4.821589 GGGAGCTTGACGGAGCCG 62.822 72.222 7.48 7.48 43.74 5.52
2015 3005 4.465305 CCTGCATCAAATCTTCCTTCCTTT 59.535 41.667 0.00 0.00 0.00 3.11
2039 3029 2.057922 ACCTCCATCATGTACATCCCC 58.942 52.381 5.07 0.00 0.00 4.81
2345 3335 2.154462 CAAAGTCTGACGGCCAATCTT 58.846 47.619 2.24 0.00 0.00 2.40
2377 3367 0.653636 GACGTGACGTTTTGAAGCCA 59.346 50.000 13.44 0.00 41.37 4.75
2581 3574 1.152989 CTCCTCCTCGTACGACTCCG 61.153 65.000 15.28 4.43 42.50 4.63
2708 3701 4.873129 GAGAAGATCGCCGCCGCA 62.873 66.667 0.00 0.00 34.03 5.69
2873 4355 6.187682 GGGTCATCCTCCTTCTCAAAAATTA 58.812 40.000 0.00 0.00 0.00 1.40
2874 4356 5.019470 GGGTCATCCTCCTTCTCAAAAATT 58.981 41.667 0.00 0.00 0.00 1.82
2875 4357 4.570719 GGGGTCATCCTCCTTCTCAAAAAT 60.571 45.833 0.00 0.00 35.33 1.82
2883 4365 3.108288 GCCGGGGTCATCCTCCTTC 62.108 68.421 2.18 0.00 35.33 3.46
2887 4369 3.551407 GAGGCCGGGGTCATCCTC 61.551 72.222 2.18 5.59 38.40 3.71
2898 4380 0.602106 ATCGATTGATGCAGAGGCCG 60.602 55.000 0.00 0.00 40.13 6.13
2899 4381 0.873054 CATCGATTGATGCAGAGGCC 59.127 55.000 10.05 0.00 45.06 5.19
2925 4407 4.813161 ACAACCTCTCTTCGCATCATTATG 59.187 41.667 0.00 0.00 36.09 1.90
2928 4410 3.340814 ACAACCTCTCTTCGCATCATT 57.659 42.857 0.00 0.00 0.00 2.57
2964 4446 6.042552 TCACACCTGAAGAAGAAGAAGAAGAT 59.957 38.462 0.00 0.00 0.00 2.40
2965 4447 5.363868 TCACACCTGAAGAAGAAGAAGAAGA 59.636 40.000 0.00 0.00 0.00 2.87
2966 4448 5.605534 TCACACCTGAAGAAGAAGAAGAAG 58.394 41.667 0.00 0.00 0.00 2.85
2967 4449 5.614324 TCACACCTGAAGAAGAAGAAGAA 57.386 39.130 0.00 0.00 0.00 2.52
2968 4450 5.614324 TTCACACCTGAAGAAGAAGAAGA 57.386 39.130 0.00 0.00 32.33 2.87
3138 4620 3.264845 ATCCACCCACCCACCCAC 61.265 66.667 0.00 0.00 0.00 4.61
3139 4621 2.938798 GATCCACCCACCCACCCA 60.939 66.667 0.00 0.00 0.00 4.51
3140 4622 2.938798 TGATCCACCCACCCACCC 60.939 66.667 0.00 0.00 0.00 4.61
3141 4623 2.677228 CTGATCCACCCACCCACC 59.323 66.667 0.00 0.00 0.00 4.61
3207 4689 3.432051 GAGGATCACCGTGCCCTCG 62.432 68.421 18.09 0.00 41.83 4.63
3249 4731 4.265056 GCCACCTTGTCCACCCGT 62.265 66.667 0.00 0.00 0.00 5.28
3418 4906 4.652881 TCAGCTCATCTCACTCACCATTAT 59.347 41.667 0.00 0.00 0.00 1.28
3419 4907 4.026052 TCAGCTCATCTCACTCACCATTA 58.974 43.478 0.00 0.00 0.00 1.90
3438 4942 0.168348 GTTGCAGTGCATCAGCTCAG 59.832 55.000 20.50 0.00 42.74 3.35
3441 4945 0.250597 TGAGTTGCAGTGCATCAGCT 60.251 50.000 24.31 17.16 42.74 4.24
3637 5141 5.348418 ACAACATTCTTGAATCTGTGACG 57.652 39.130 6.75 0.00 0.00 4.35
3769 5277 1.472480 CCCCAGGCGTTGTTATTCAAG 59.528 52.381 0.00 0.00 36.66 3.02
3825 6259 1.835494 ATGATGCCTGCTATCATGCC 58.165 50.000 12.88 0.00 42.15 4.40
3895 6329 3.893813 TGCAGATGCTCTAAGATGCTCTA 59.106 43.478 6.35 0.00 42.66 2.43
3896 6330 2.699321 TGCAGATGCTCTAAGATGCTCT 59.301 45.455 6.35 0.00 42.66 4.09
3899 6333 2.290093 GGTTGCAGATGCTCTAAGATGC 59.710 50.000 6.35 0.00 42.66 3.91
3926 6364 0.387112 ACGTTTGCGGACGATACGAA 60.387 50.000 17.04 0.00 45.47 3.85
3950 6388 4.142038 GTTCACTAAACCTGGTTGTCCAT 58.858 43.478 13.79 0.00 43.43 3.41
3979 6417 0.313672 TGCAGTTGGGTCGCATTTTC 59.686 50.000 0.00 0.00 0.00 2.29
3981 6419 1.106351 TGTGCAGTTGGGTCGCATTT 61.106 50.000 0.00 0.00 38.07 2.32
3993 6431 1.525995 CCGGTTTGAGGTGTGCAGT 60.526 57.895 0.00 0.00 0.00 4.40
4010 6448 2.480845 GACAACCGGATGTATAGTGCC 58.519 52.381 18.29 0.00 32.57 5.01
4055 6494 1.622811 CTCCCCATATCAGCTCCAGAC 59.377 57.143 0.00 0.00 0.00 3.51
4089 6528 4.693283 GGTTTGTCGGATCTGATATGACA 58.307 43.478 16.18 16.18 37.76 3.58
4112 6551 1.229177 AGGGATTTTGGGTGTGGCC 60.229 57.895 0.00 0.00 0.00 5.36
4116 6555 2.158519 AGTTTCGAGGGATTTTGGGTGT 60.159 45.455 0.00 0.00 0.00 4.16
4125 6564 3.025262 GACTAGGTCAGTTTCGAGGGAT 58.975 50.000 0.00 0.00 37.72 3.85
4126 6565 2.444421 GACTAGGTCAGTTTCGAGGGA 58.556 52.381 0.00 0.00 37.72 4.20
4127 6566 1.477295 GGACTAGGTCAGTTTCGAGGG 59.523 57.143 0.00 0.00 37.72 4.30
4128 6567 2.094649 GTGGACTAGGTCAGTTTCGAGG 60.095 54.545 0.00 0.00 37.72 4.63
4129 6568 2.094649 GGTGGACTAGGTCAGTTTCGAG 60.095 54.545 0.00 0.00 37.72 4.04
4130 6569 1.891150 GGTGGACTAGGTCAGTTTCGA 59.109 52.381 0.00 0.00 37.72 3.71
4131 6570 1.616865 TGGTGGACTAGGTCAGTTTCG 59.383 52.381 0.00 0.00 37.72 3.46
4132 6571 3.764237 TTGGTGGACTAGGTCAGTTTC 57.236 47.619 0.00 0.00 37.72 2.78
4133 6572 4.513406 TTTTGGTGGACTAGGTCAGTTT 57.487 40.909 0.00 0.00 37.72 2.66
4134 6573 4.513406 TTTTTGGTGGACTAGGTCAGTT 57.487 40.909 0.00 0.00 37.72 3.16
4158 6597 5.183904 GGTGAGCAATTCAAACTAGTCCATT 59.816 40.000 0.00 0.00 37.61 3.16
4159 6598 4.702131 GGTGAGCAATTCAAACTAGTCCAT 59.298 41.667 0.00 0.00 37.61 3.41
4164 6603 5.633830 ATGTGGTGAGCAATTCAAACTAG 57.366 39.130 0.00 0.00 37.61 2.57
4221 6660 2.995574 ACGGACACGGGAAGAGGG 60.996 66.667 0.00 0.00 46.48 4.30
4236 6675 0.822164 ACGGTAGGAAATGGAGGACG 59.178 55.000 0.00 0.00 0.00 4.79
4240 6679 2.280628 GCTCAACGGTAGGAAATGGAG 58.719 52.381 0.00 0.00 0.00 3.86
4255 6694 1.275291 CGGAGGTTAGTGAAGGCTCAA 59.725 52.381 0.00 0.00 31.88 3.02
4256 6695 0.895530 CGGAGGTTAGTGAAGGCTCA 59.104 55.000 0.00 0.00 0.00 4.26
4267 6706 2.295602 GGACCAAGGGCGGAGGTTA 61.296 63.158 0.00 0.00 35.36 2.85
4268 6707 3.647771 GGACCAAGGGCGGAGGTT 61.648 66.667 0.00 0.00 35.36 3.50
4291 6730 4.227134 CTACGAGGGCAGCGGCAT 62.227 66.667 11.88 0.00 43.71 4.40
4298 6737 2.891580 GGAGATGTTATCTACGAGGGCA 59.108 50.000 0.00 0.00 40.38 5.36
4305 6744 5.181622 CAGGGTACTCGGAGATGTTATCTAC 59.818 48.000 12.86 1.03 40.38 2.59
4314 6753 0.106116 GGGACAGGGTACTCGGAGAT 60.106 60.000 12.86 0.00 33.89 2.75
4334 6773 4.201679 CATGCATGCTGGCGGTGG 62.202 66.667 20.33 0.00 36.28 4.61
4358 6797 1.229625 AGCCCCACAGACTCCATCA 60.230 57.895 0.00 0.00 0.00 3.07
4386 6825 0.109723 TTCGCCTTGCAACTAACCCT 59.890 50.000 0.00 0.00 0.00 4.34
4391 6830 2.742053 GACATTCTTCGCCTTGCAACTA 59.258 45.455 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.