Multiple sequence alignment - TraesCS3B01G123000

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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 TraesCS3B01G123000 chr3B 100.000 3957 0 0 1 3957 94665367 94669323 0.000000e+00 7308
1 TraesCS3B01G123000 chr3B 85.974 606 54 14 1 579 602478637 602479238 1.560000e-173 619
2 TraesCS3B01G123000 chr3B 88.696 345 27 10 523 859 602479220 602479560 1.020000e-110 411
3 TraesCS3B01G123000 chr3D 93.405 2866 116 33 860 3709 58754906 58757714 0.000000e+00 4178
4 TraesCS3B01G123000 chr3A 93.261 1855 88 15 2070 3914 67912177 67914004 0.000000e+00 2699
5 TraesCS3B01G123000 chr3A 92.605 1217 51 18 862 2072 67910937 67912120 0.000000e+00 1712
6 TraesCS3B01G123000 chr3A 81.153 711 100 22 1613 2296 164279270 164278567 1.250000e-149 540
7 TraesCS3B01G123000 chr3A 88.571 105 8 4 3813 3914 217723379 217723276 1.490000e-24 124
8 TraesCS3B01G123000 chr7B 83.987 893 91 25 15 859 710734831 710733943 0.000000e+00 809
9 TraesCS3B01G123000 chr7B 86.822 129 13 4 3787 3914 477814817 477814942 1.480000e-29 141
10 TraesCS3B01G123000 chr5A 82.492 931 86 24 1 859 617905403 617906328 0.000000e+00 745
11 TraesCS3B01G123000 chr4B 87.888 644 46 14 1 616 57964786 57964147 0.000000e+00 728
12 TraesCS3B01G123000 chr4B 87.110 481 36 12 121 578 34451053 34450576 4.530000e-144 521
13 TraesCS3B01G123000 chr4B 81.440 625 88 22 3 617 488125777 488126383 1.650000e-133 486
14 TraesCS3B01G123000 chr4B 87.857 280 26 6 584 859 629050355 629050080 4.930000e-84 322
15 TraesCS3B01G123000 chr1B 87.092 643 49 16 1 616 182166960 182167595 0.000000e+00 697
16 TraesCS3B01G123000 chr1B 91.099 382 23 9 481 859 182167522 182167895 1.270000e-139 507
17 TraesCS3B01G123000 chr1B 85.496 131 16 3 3787 3914 646931262 646931132 2.480000e-27 134
18 TraesCS3B01G123000 chr1B 81.379 145 17 9 615 751 94543687 94543545 4.180000e-20 110
19 TraesCS3B01G123000 chr2B 89.306 533 20 10 1 498 641656472 641657002 5.580000e-178 634
20 TraesCS3B01G123000 chr2B 83.981 643 65 19 1 612 426887738 426888373 2.050000e-162 582
21 TraesCS3B01G123000 chr2B 89.844 384 32 5 481 860 130358200 130357820 1.650000e-133 486
22 TraesCS3B01G123000 chr2B 86.528 386 36 13 481 859 426888303 426888679 1.020000e-110 411
23 TraesCS3B01G123000 chr5D 83.494 624 86 15 1 617 231603654 231604267 2.060000e-157 566
24 TraesCS3B01G123000 chr5B 84.456 386 44 14 481 859 373477578 373477954 2.250000e-97 366
25 TraesCS3B01G123000 chr5B 85.588 340 22 12 523 859 480286405 480286090 8.200000e-87 331
26 TraesCS3B01G123000 chrUn 86.262 313 24 8 2683 2977 3120880 3120569 4.930000e-84 322
27 TraesCS3B01G123000 chr1A 85.366 123 13 4 3796 3914 297698236 297698357 5.370000e-24 122
28 TraesCS3B01G123000 chr2D 85.217 115 13 4 3803 3914 14772018 14772131 8.990000e-22 115
29 TraesCS3B01G123000 chr4A 85.455 110 13 3 3808 3914 742971362 742971471 1.160000e-20 111
30 TraesCS3B01G123000 chr1D 84.167 120 14 5 3796 3912 395850790 395850907 1.160000e-20 111
31 TraesCS3B01G123000 chr7A 81.890 127 20 3 3790 3913 674819305 674819431 1.950000e-18 104


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 TraesCS3B01G123000 chr3B 94665367 94669323 3956 False 7308.0 7308 100.0000 1 3957 1 chr3B.!!$F1 3956
1 TraesCS3B01G123000 chr3B 602478637 602479560 923 False 515.0 619 87.3350 1 859 2 chr3B.!!$F2 858
2 TraesCS3B01G123000 chr3D 58754906 58757714 2808 False 4178.0 4178 93.4050 860 3709 1 chr3D.!!$F1 2849
3 TraesCS3B01G123000 chr3A 67910937 67914004 3067 False 2205.5 2699 92.9330 862 3914 2 chr3A.!!$F1 3052
4 TraesCS3B01G123000 chr3A 164278567 164279270 703 True 540.0 540 81.1530 1613 2296 1 chr3A.!!$R1 683
5 TraesCS3B01G123000 chr7B 710733943 710734831 888 True 809.0 809 83.9870 15 859 1 chr7B.!!$R1 844
6 TraesCS3B01G123000 chr5A 617905403 617906328 925 False 745.0 745 82.4920 1 859 1 chr5A.!!$F1 858
7 TraesCS3B01G123000 chr4B 57964147 57964786 639 True 728.0 728 87.8880 1 616 1 chr4B.!!$R2 615
8 TraesCS3B01G123000 chr4B 488125777 488126383 606 False 486.0 486 81.4400 3 617 1 chr4B.!!$F1 614
9 TraesCS3B01G123000 chr1B 182166960 182167895 935 False 602.0 697 89.0955 1 859 2 chr1B.!!$F1 858
10 TraesCS3B01G123000 chr2B 641656472 641657002 530 False 634.0 634 89.3060 1 498 1 chr2B.!!$F1 497
11 TraesCS3B01G123000 chr2B 426887738 426888679 941 False 496.5 582 85.2545 1 859 2 chr2B.!!$F2 858
12 TraesCS3B01G123000 chr5D 231603654 231604267 613 False 566.0 566 83.4940 1 617 1 chr5D.!!$F1 616

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
836 980 1.154225 GCCCGACATTTTGACGCAG 60.154 57.895 0.0 0.0 34.45 5.18 F
1398 1543 0.178068 TCGTGCTTTGGCTATCTCCC 59.822 55.000 0.0 0.0 39.59 4.30 F
1400 1545 0.466372 GTGCTTTGGCTATCTCCCCC 60.466 60.000 0.0 0.0 39.59 5.40 F
1902 2076 0.879765 CTTGAGCTGAACCTGCCTTG 59.120 55.000 0.0 0.0 0.00 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2300 2537 0.096976 CGTGATGTGAACCCGAATGC 59.903 55.0 0.00 0.0 0.0 3.56 R
2308 2545 0.438830 GTCTTCCGCGTGATGTGAAC 59.561 55.0 4.92 0.0 0.0 3.18 R
2470 2711 0.890683 CCAGATCCCCACAAAGCAAC 59.109 55.0 0.00 0.0 0.0 4.17 R
3586 3833 0.307760 GGACCACAGCAACAACTTCG 59.692 55.0 0.00 0.0 0.0 3.79 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
115 131 3.444703 TTGGGACCACGAACAAATTTG 57.555 42.857 16.67 16.67 0.00 2.32
375 419 9.837525 CAAAATCCAGAACAAATTTTGAAAACA 57.162 25.926 15.81 0.00 46.15 2.83
707 847 3.329814 ACCGTCTAGAAGGTTCCCAAAAT 59.670 43.478 22.96 0.00 40.26 1.82
775 919 3.263261 TGTGTGAAGCGTGTTAAACAGA 58.737 40.909 0.00 0.00 0.00 3.41
836 980 1.154225 GCCCGACATTTTGACGCAG 60.154 57.895 0.00 0.00 34.45 5.18
853 997 1.640428 CAGCGAGCGTCAAATAGGAA 58.360 50.000 0.00 0.00 0.00 3.36
976 1120 1.347050 CGAGCATTCCCCATCAGATCT 59.653 52.381 0.00 0.00 0.00 2.75
1047 1191 2.881352 GTGCTCTACTGCGGCGTC 60.881 66.667 9.37 0.91 35.36 5.19
1166 1310 3.009714 GGCCTCCTCCTCCGGTTT 61.010 66.667 0.00 0.00 0.00 3.27
1172 1316 3.646715 CTCCTCCGGTTTGCCCCA 61.647 66.667 0.00 0.00 0.00 4.96
1173 1317 2.938798 TCCTCCGGTTTGCCCCAT 60.939 61.111 0.00 0.00 0.00 4.00
1174 1318 2.755469 CCTCCGGTTTGCCCCATG 60.755 66.667 0.00 0.00 0.00 3.66
1175 1319 2.354729 CTCCGGTTTGCCCCATGA 59.645 61.111 0.00 0.00 0.00 3.07
1176 1320 2.034999 TCCGGTTTGCCCCATGAC 59.965 61.111 0.00 0.00 0.00 3.06
1177 1321 3.068064 CCGGTTTGCCCCATGACC 61.068 66.667 0.00 0.00 0.00 4.02
1178 1322 2.035626 CGGTTTGCCCCATGACCT 59.964 61.111 0.00 0.00 0.00 3.85
1225 1369 1.296056 CCCCACTTCGTTTACGCCTG 61.296 60.000 0.00 0.00 39.60 4.85
1228 1372 0.949105 CACTTCGTTTACGCCTGCCT 60.949 55.000 0.00 0.00 39.60 4.75
1284 1428 3.139077 GGTTCGTTTGATCTGTGAAGGT 58.861 45.455 0.00 0.00 0.00 3.50
1381 1526 2.675056 GCAGGTTGCTGTGAGCTCG 61.675 63.158 9.64 0.00 42.97 5.03
1395 1540 3.071580 GCTCGTGCTTTGGCTATCT 57.928 52.632 1.41 0.00 39.59 1.98
1396 1541 0.933796 GCTCGTGCTTTGGCTATCTC 59.066 55.000 1.41 0.00 39.59 2.75
1397 1542 1.576356 CTCGTGCTTTGGCTATCTCC 58.424 55.000 0.00 0.00 39.59 3.71
1398 1543 0.178068 TCGTGCTTTGGCTATCTCCC 59.822 55.000 0.00 0.00 39.59 4.30
1399 1544 0.815615 CGTGCTTTGGCTATCTCCCC 60.816 60.000 0.00 0.00 39.59 4.81
1400 1545 0.466372 GTGCTTTGGCTATCTCCCCC 60.466 60.000 0.00 0.00 39.59 5.40
1562 1714 4.349663 TTGCACACTTTACACAGTTCAC 57.650 40.909 0.00 0.00 0.00 3.18
1567 1719 5.569413 CACACTTTACACAGTTCACTTTCC 58.431 41.667 0.00 0.00 0.00 3.13
1570 1722 4.881850 ACTTTACACAGTTCACTTTCCAGG 59.118 41.667 0.00 0.00 0.00 4.45
1583 1735 3.694566 ACTTTCCAGGTGTTTGACTTCAC 59.305 43.478 0.00 0.00 0.00 3.18
1649 1801 1.065551 GTTCGGGCCAATGTAGAATGC 59.934 52.381 4.39 0.00 0.00 3.56
1667 1819 3.540314 TGCCTGTCTTGCAATGTTTTT 57.460 38.095 0.00 0.00 35.40 1.94
1679 1831 3.915569 GCAATGTTTTTGAATGCCAATGC 59.084 39.130 0.00 0.00 34.23 3.56
1833 2007 8.787852 AGTGAAGTAAAAAGATTGGAGATGAAC 58.212 33.333 0.00 0.00 0.00 3.18
1902 2076 0.879765 CTTGAGCTGAACCTGCCTTG 59.120 55.000 0.00 0.00 0.00 3.61
1938 2112 9.694137 GATACTATCTGTTCGCTATTAAGGTTT 57.306 33.333 0.00 0.00 0.00 3.27
2211 2447 3.054434 ACTTCATTACAGCTACATGGCCA 60.054 43.478 8.56 8.56 0.00 5.36
2300 2537 5.950883 AGCATTCTGATCAACTTGACAATG 58.049 37.500 0.00 2.78 0.00 2.82
2308 2545 2.228582 TCAACTTGACAATGCATTCGGG 59.771 45.455 9.53 0.86 0.00 5.14
2470 2711 9.900710 GTATATATATAGGAATGGAGAGCAACG 57.099 37.037 2.53 0.00 0.00 4.10
2471 2712 6.859112 ATATATAGGAATGGAGAGCAACGT 57.141 37.500 0.00 0.00 0.00 3.99
2512 2754 2.949177 TCAGTTGGTGCTTACATGGT 57.051 45.000 0.00 0.00 0.00 3.55
2530 2772 9.581289 TTACATGGTTAATAGATAATGGGGTTG 57.419 33.333 0.00 0.00 0.00 3.77
2548 2790 3.123050 GTTGGCTCAATGGTGTTTTGAC 58.877 45.455 0.00 0.00 0.00 3.18
2629 2871 7.828223 TGGTTTACCTTCTGTACTTTACAAACA 59.172 33.333 0.00 0.00 36.08 2.83
2701 2943 9.832445 ATGAAATATGTTTCGTAATACTCTGGT 57.168 29.630 7.79 0.00 45.34 4.00
2717 2959 5.983540 ACTCTGGTTATTCTGGATCTCAAC 58.016 41.667 0.00 0.00 0.00 3.18
2718 2960 5.723887 ACTCTGGTTATTCTGGATCTCAACT 59.276 40.000 0.00 0.00 0.00 3.16
2731 2974 6.824553 TGGATCTCAACTAGGATTCATTCTG 58.175 40.000 0.00 0.00 0.00 3.02
2761 3004 8.941995 AGACTAATAGGTAGCACAATCTGATA 57.058 34.615 0.00 0.00 32.45 2.15
2835 3078 7.226720 CACCAGTTATTGACCTATCACCATAAC 59.773 40.741 0.00 0.00 38.10 1.89
2868 3111 7.573968 AGTTAGCAAGACTCTTTTTGTTCAT 57.426 32.000 0.00 0.00 0.00 2.57
2926 3169 4.695455 CCTGAATCGGCCGTATATTTCATT 59.305 41.667 27.15 14.70 0.00 2.57
2960 3203 0.599558 GGTTGCTGCTGCTTGATTGA 59.400 50.000 17.00 0.00 40.48 2.57
3071 3314 3.453353 TGGGTTCTTAATCCTTACTCCCG 59.547 47.826 0.00 0.00 35.59 5.14
3075 3318 5.304871 GGTTCTTAATCCTTACTCCCGAGAT 59.695 44.000 0.00 0.00 0.00 2.75
3078 3321 6.850234 TCTTAATCCTTACTCCCGAGATACT 58.150 40.000 0.00 0.00 0.00 2.12
3275 3519 7.004555 ACAATTCAGTACCAACTATCTGTGA 57.995 36.000 0.00 0.00 33.48 3.58
3349 3593 4.497291 AGGAACAGTCTGGTGTTTTGTA 57.503 40.909 4.53 0.00 40.83 2.41
3507 3754 6.100404 AGAAGCAAGATAGATCTGGATGAC 57.900 41.667 5.18 0.00 37.19 3.06
3586 3833 6.742718 CGTCATGATCATTAAACTTGTTCACC 59.257 38.462 5.16 0.00 0.00 4.02
3590 3837 6.898041 TGATCATTAAACTTGTTCACCGAAG 58.102 36.000 0.00 0.00 0.00 3.79
3634 3881 9.852091 AGCTGATTTGTTCTTTAATTCAGAATC 57.148 29.630 11.57 0.00 37.56 2.52
3640 3890 9.496873 TTTGTTCTTTAATTCAGAATCGGTCTA 57.503 29.630 0.00 0.00 33.56 2.59
3682 3936 1.736645 CACGCAAGGTTCGTCCGAT 60.737 57.895 0.00 0.00 46.39 4.18
3699 3954 3.756963 TCCGATGGAGACTTATATCACGG 59.243 47.826 0.00 0.00 38.31 4.94
3718 3973 0.819666 GCCTGGCACTATTGTAGGCC 60.820 60.000 15.17 0.00 43.73 5.19
3724 3979 1.134788 GCACTATTGTAGGCCGACACT 60.135 52.381 19.21 15.91 0.00 3.55
3728 3983 2.961526 ATTGTAGGCCGACACTGTAG 57.038 50.000 19.21 0.00 0.00 2.74
3730 3985 1.460504 TGTAGGCCGACACTGTAGAG 58.539 55.000 15.44 0.00 0.00 2.43
3731 3986 0.739561 GTAGGCCGACACTGTAGAGG 59.260 60.000 11.60 0.00 0.00 3.69
3805 4060 8.488651 AAACAAATACTATTACCTCCGTTCAG 57.511 34.615 0.00 0.00 0.00 3.02
3811 4066 9.978044 AATACTATTACCTCCGTTCAGAAATAC 57.022 33.333 0.00 0.00 0.00 1.89
3819 4074 5.751028 CCTCCGTTCAGAAATACAAGATCTC 59.249 44.000 0.00 0.00 0.00 2.75
3820 4075 6.406400 CCTCCGTTCAGAAATACAAGATCTCT 60.406 42.308 0.00 0.00 0.00 3.10
3841 4096 6.147821 TCTCTCAACTTTTTGTGAATCGGATC 59.852 38.462 0.00 0.00 35.38 3.36
3843 4098 7.158697 TCTCAACTTTTTGTGAATCGGATCTA 58.841 34.615 0.00 0.00 33.35 1.98
3847 4102 8.664798 CAACTTTTTGTGAATCGGATCTATGTA 58.335 33.333 0.00 0.00 0.00 2.29
3848 4103 8.425577 ACTTTTTGTGAATCGGATCTATGTAG 57.574 34.615 0.00 0.00 0.00 2.74
3849 4104 8.258007 ACTTTTTGTGAATCGGATCTATGTAGA 58.742 33.333 0.00 0.00 36.65 2.59
3850 4105 8.420374 TTTTTGTGAATCGGATCTATGTAGAC 57.580 34.615 0.00 0.00 34.72 2.59
3851 4106 6.709018 TTGTGAATCGGATCTATGTAGACA 57.291 37.500 0.00 0.00 34.72 3.41
3852 4107 6.073327 TGTGAATCGGATCTATGTAGACAC 57.927 41.667 0.00 0.00 34.72 3.67
3853 4108 5.592688 TGTGAATCGGATCTATGTAGACACA 59.407 40.000 0.00 0.00 39.52 3.72
3883 4138 8.682936 ATGTGTTTGTTCTCTAATTTCAGTCT 57.317 30.769 0.00 0.00 0.00 3.24
3916 4171 9.184523 AGTTCATATTGAAATATCCAAAACGGA 57.815 29.630 0.00 0.00 42.84 4.69
3917 4172 9.450807 GTTCATATTGAAATATCCAAAACGGAG 57.549 33.333 0.00 0.00 42.28 4.63
3918 4173 8.629158 TTCATATTGAAATATCCAAAACGGAGG 58.371 33.333 0.00 0.00 39.46 4.30
3926 4181 2.829023 TCCAAAACGGAGGGAGTATCT 58.171 47.619 0.00 0.00 39.64 1.98
3927 4182 3.178865 TCCAAAACGGAGGGAGTATCTT 58.821 45.455 0.00 0.00 39.64 2.40
3928 4183 4.355549 TCCAAAACGGAGGGAGTATCTTA 58.644 43.478 0.00 0.00 39.64 2.10
3929 4184 4.966805 TCCAAAACGGAGGGAGTATCTTAT 59.033 41.667 0.00 0.00 39.64 1.73
3930 4185 6.138263 TCCAAAACGGAGGGAGTATCTTATA 58.862 40.000 0.00 0.00 39.64 0.98
3931 4186 6.785963 TCCAAAACGGAGGGAGTATCTTATAT 59.214 38.462 0.00 0.00 39.64 0.86
3932 4187 7.291651 TCCAAAACGGAGGGAGTATCTTATATT 59.708 37.037 0.00 0.00 39.64 1.28
3933 4188 8.591072 CCAAAACGGAGGGAGTATCTTATATTA 58.409 37.037 0.00 0.00 36.56 0.98
3934 4189 9.991906 CAAAACGGAGGGAGTATCTTATATTAA 57.008 33.333 0.00 0.00 33.73 1.40
3938 4193 9.543231 ACGGAGGGAGTATCTTATATTAATTCA 57.457 33.333 0.00 0.00 33.73 2.57
3939 4194 9.804758 CGGAGGGAGTATCTTATATTAATTCAC 57.195 37.037 0.00 0.00 33.73 3.18
3943 4198 9.303537 GGGAGTATCTTATATTAATTCACTCGC 57.696 37.037 0.00 0.00 36.65 5.03
3944 4199 9.303537 GGAGTATCTTATATTAATTCACTCGCC 57.696 37.037 0.00 0.00 32.56 5.54
3947 4202 9.856488 GTATCTTATATTAATTCACTCGCCTCA 57.144 33.333 0.00 0.00 0.00 3.86
3949 4204 9.950496 ATCTTATATTAATTCACTCGCCTCATT 57.050 29.630 0.00 0.00 0.00 2.57
3950 4205 9.424319 TCTTATATTAATTCACTCGCCTCATTC 57.576 33.333 0.00 0.00 0.00 2.67
3951 4206 9.208022 CTTATATTAATTCACTCGCCTCATTCA 57.792 33.333 0.00 0.00 0.00 2.57
3952 4207 9.725019 TTATATTAATTCACTCGCCTCATTCAT 57.275 29.630 0.00 0.00 0.00 2.57
3953 4208 5.991328 TTAATTCACTCGCCTCATTCATC 57.009 39.130 0.00 0.00 0.00 2.92
3954 4209 3.834489 ATTCACTCGCCTCATTCATCT 57.166 42.857 0.00 0.00 0.00 2.90
3955 4210 4.944619 ATTCACTCGCCTCATTCATCTA 57.055 40.909 0.00 0.00 0.00 1.98
3956 4211 3.998099 TCACTCGCCTCATTCATCTAG 57.002 47.619 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
252 292 9.191995 ACGTTTATGAATTTGTTCAGGATTTTC 57.808 29.630 0.00 0.00 34.02 2.29
775 919 0.395173 AGCGATTTAAATGGGCCGGT 60.395 50.000 5.17 5.70 0.00 5.28
836 980 3.546218 GGAATTTCCTATTTGACGCTCGC 60.546 47.826 8.25 0.00 32.53 5.03
853 997 2.896685 TGGGTGCGATTTTTCTGGAATT 59.103 40.909 0.00 0.00 0.00 2.17
976 1120 4.942481 CGCCGCCGGATTCGATCA 62.942 66.667 7.68 0.00 39.00 2.92
1126 1270 1.451747 GCTCGTCGGGGTAGACTCT 60.452 63.158 0.00 0.00 38.90 3.24
1128 1272 1.451747 GAGCTCGTCGGGGTAGACT 60.452 63.158 0.00 0.00 38.90 3.24
1166 1310 0.693092 GGTAGGTAGGTCATGGGGCA 60.693 60.000 0.00 0.00 0.00 5.36
1172 1316 3.467863 AGAAGGCTAGGTAGGTAGGTCAT 59.532 47.826 0.00 0.00 0.00 3.06
1173 1317 2.857498 AGAAGGCTAGGTAGGTAGGTCA 59.143 50.000 0.00 0.00 0.00 4.02
1174 1318 3.489355 GAGAAGGCTAGGTAGGTAGGTC 58.511 54.545 0.00 0.00 0.00 3.85
1175 1319 2.158638 CGAGAAGGCTAGGTAGGTAGGT 60.159 54.545 0.00 0.00 0.00 3.08
1176 1320 2.506444 CGAGAAGGCTAGGTAGGTAGG 58.494 57.143 0.00 0.00 0.00 3.18
1177 1321 1.881324 GCGAGAAGGCTAGGTAGGTAG 59.119 57.143 0.00 0.00 0.00 3.18
1178 1322 1.493871 AGCGAGAAGGCTAGGTAGGTA 59.506 52.381 0.00 0.00 42.62 3.08
1228 1372 2.915659 AGAGCGGGACCGACACAA 60.916 61.111 15.99 0.00 42.83 3.33
1284 1428 0.104120 CCACGTCCTTATCATCGCCA 59.896 55.000 0.00 0.00 0.00 5.69
1381 1526 0.466372 GGGGGAGATAGCCAAAGCAC 60.466 60.000 0.00 0.00 43.56 4.40
1397 1542 6.965607 TCTAGGTTAAACAAATAAGAGGGGG 58.034 40.000 0.00 0.00 0.00 5.40
1398 1543 8.107729 AGTTCTAGGTTAAACAAATAAGAGGGG 58.892 37.037 0.00 0.00 0.00 4.79
1406 1551 9.449719 CATGTCCTAGTTCTAGGTTAAACAAAT 57.550 33.333 20.92 6.00 38.38 2.32
1407 1552 8.434392 ACATGTCCTAGTTCTAGGTTAAACAAA 58.566 33.333 20.92 1.75 38.38 2.83
1408 1553 7.970102 ACATGTCCTAGTTCTAGGTTAAACAA 58.030 34.615 20.92 2.41 38.38 2.83
1409 1554 7.549147 ACATGTCCTAGTTCTAGGTTAAACA 57.451 36.000 20.92 18.00 38.38 2.83
1410 1555 8.476657 GAACATGTCCTAGTTCTAGGTTAAAC 57.523 38.462 20.92 14.07 40.63 2.01
1429 1574 6.210796 ACACACATCAATTTGACAGAACATG 58.789 36.000 0.15 0.00 0.00 3.21
1431 1576 5.833406 ACACACATCAATTTGACAGAACA 57.167 34.783 0.15 0.00 0.00 3.18
1436 1581 5.321959 ACACAACACACATCAATTTGACA 57.678 34.783 0.15 0.00 0.00 3.58
1481 1626 3.491267 GTCGTTTCACCTCTTCAGTCTTG 59.509 47.826 0.00 0.00 0.00 3.02
1562 1714 4.292977 GTGAAGTCAAACACCTGGAAAG 57.707 45.455 0.00 0.00 0.00 2.62
1570 1722 3.764237 TCTAGGGGTGAAGTCAAACAC 57.236 47.619 0.00 0.00 36.44 3.32
1583 1735 5.070981 TCAATTTCAGACTAGCATCTAGGGG 59.929 44.000 5.92 0.00 0.00 4.79
1649 1801 5.559417 GCATTCAAAAACATTGCAAGACAGG 60.559 40.000 4.94 0.00 33.58 4.00
1667 1819 1.360185 AAAAGGGGCATTGGCATTCA 58.640 45.000 12.70 0.00 43.71 2.57
1679 1831 4.157840 GCTTGTCCTACACATAAAAAGGGG 59.842 45.833 0.00 0.00 33.90 4.79
1861 2035 3.193267 GCCTGGATCTAGCATCTACAGAG 59.807 52.174 0.00 0.00 0.00 3.35
1902 2076 7.436673 AGCGAACAGATAGTATCATCAAACTTC 59.563 37.037 12.66 2.06 0.00 3.01
2002 2176 4.742167 GCAAACTTCTTTCCAAGCTTCTTC 59.258 41.667 0.00 0.00 0.00 2.87
2300 2537 0.096976 CGTGATGTGAACCCGAATGC 59.903 55.000 0.00 0.00 0.00 3.56
2308 2545 0.438830 GTCTTCCGCGTGATGTGAAC 59.561 55.000 4.92 0.00 0.00 3.18
2441 2681 9.368416 TGCTCTCCATTCCTATATATATACACC 57.632 37.037 0.00 0.00 0.00 4.16
2470 2711 0.890683 CCAGATCCCCACAAAGCAAC 59.109 55.000 0.00 0.00 0.00 4.17
2471 2712 0.899717 GCCAGATCCCCACAAAGCAA 60.900 55.000 0.00 0.00 0.00 3.91
2482 2724 1.747355 CACCAACTGAATGCCAGATCC 59.253 52.381 0.00 0.00 45.78 3.36
2512 2754 6.523035 TGAGCCAACCCCATTATCTATTAA 57.477 37.500 0.00 0.00 0.00 1.40
2530 2772 2.438868 GGTCAAAACACCATTGAGCC 57.561 50.000 7.10 1.21 45.10 4.70
2548 2790 6.029346 ACCTTCTAAGCAAACATCAAATGG 57.971 37.500 0.00 0.00 33.60 3.16
2583 2825 6.078456 ACCATAGGAGATTGATTCCACAAA 57.922 37.500 0.00 0.00 37.18 2.83
2629 2871 7.553334 CAATTGATGAAGGATTGATGAGGTTT 58.447 34.615 0.00 0.00 33.67 3.27
2697 2939 6.325028 TCCTAGTTGAGATCCAGAATAACCAG 59.675 42.308 0.00 0.00 0.00 4.00
2701 2943 8.553085 TGAATCCTAGTTGAGATCCAGAATAA 57.447 34.615 0.00 0.00 0.00 1.40
2717 2959 9.995003 ATTAGTCTAAAGCAGAATGAATCCTAG 57.005 33.333 0.00 0.00 39.69 3.02
2731 2974 8.145122 AGATTGTGCTACCTATTAGTCTAAAGC 58.855 37.037 6.36 6.36 0.00 3.51
2761 3004 5.461737 CAGTGTTCAACCGCAAAAACATAAT 59.538 36.000 0.00 0.00 34.45 1.28
2835 3078 7.913674 AAGAGTCTTGCTAACTTTAATCAGG 57.086 36.000 4.10 0.00 0.00 3.86
2868 3111 4.338118 CAGAAAAGCAAGGAGTAACCAACA 59.662 41.667 0.00 0.00 42.04 3.33
2911 3154 5.705441 TCCATCTTCAATGAAATATACGGCC 59.295 40.000 0.00 0.00 0.00 6.13
2926 3169 2.376518 AGCAACCTTCCTTCCATCTTCA 59.623 45.455 0.00 0.00 0.00 3.02
2960 3203 6.665680 TGGTGTATTGCCTTGTAAACCATATT 59.334 34.615 0.00 0.00 34.12 1.28
3071 3314 5.688176 GTCAAAATGGAGCGAGTAGTATCTC 59.312 44.000 0.00 0.00 0.00 2.75
3075 3318 5.168569 CAAGTCAAAATGGAGCGAGTAGTA 58.831 41.667 0.00 0.00 0.00 1.82
3078 3321 3.745975 CACAAGTCAAAATGGAGCGAGTA 59.254 43.478 0.00 0.00 0.00 2.59
3235 3479 8.103948 ACTGAATTGTTCTGAAACTAGGATTG 57.896 34.615 0.00 0.00 36.30 2.67
3349 3593 8.807948 ACTTACTGGATGCAATACAAAGTAAT 57.192 30.769 0.00 0.00 36.15 1.89
3480 3727 7.714377 TCATCCAGATCTATCTTGCTTCTTTTC 59.286 37.037 0.00 0.00 34.22 2.29
3507 3754 2.287188 GGCCACACTAATTCATGATGCG 60.287 50.000 0.00 0.00 0.00 4.73
3586 3833 0.307760 GGACCACAGCAACAACTTCG 59.692 55.000 0.00 0.00 0.00 3.79
3682 3936 2.628178 CAGGCCGTGATATAAGTCTCCA 59.372 50.000 0.00 0.00 0.00 3.86
3699 3954 2.707902 GCCTACAATAGTGCCAGGC 58.292 57.895 17.45 17.45 44.57 4.85
3718 3973 3.692101 AGTGAAGATCCTCTACAGTGTCG 59.308 47.826 0.00 0.00 0.00 4.35
3724 3979 7.244886 TGATGAAAAGTGAAGATCCTCTACA 57.755 36.000 0.00 0.00 0.00 2.74
3728 3983 5.738909 TCCTGATGAAAAGTGAAGATCCTC 58.261 41.667 0.00 0.00 0.00 3.71
3730 3985 6.376581 ACAATCCTGATGAAAAGTGAAGATCC 59.623 38.462 0.00 0.00 0.00 3.36
3731 3986 7.336427 AGACAATCCTGATGAAAAGTGAAGATC 59.664 37.037 0.00 0.00 0.00 2.75
3782 4037 7.414222 TCTGAACGGAGGTAATAGTATTTGT 57.586 36.000 0.00 0.00 0.00 2.83
3783 4038 8.712285 TTTCTGAACGGAGGTAATAGTATTTG 57.288 34.615 0.00 0.00 0.00 2.32
3786 4041 9.139734 TGTATTTCTGAACGGAGGTAATAGTAT 57.860 33.333 0.00 0.00 0.00 2.12
3787 4042 8.523915 TGTATTTCTGAACGGAGGTAATAGTA 57.476 34.615 0.00 0.00 0.00 1.82
3788 4043 7.414222 TGTATTTCTGAACGGAGGTAATAGT 57.586 36.000 0.00 0.00 0.00 2.12
3789 4044 8.195436 TCTTGTATTTCTGAACGGAGGTAATAG 58.805 37.037 0.00 0.00 0.00 1.73
3790 4045 8.070034 TCTTGTATTTCTGAACGGAGGTAATA 57.930 34.615 0.00 0.00 0.00 0.98
3791 4046 6.942976 TCTTGTATTTCTGAACGGAGGTAAT 58.057 36.000 0.00 0.00 0.00 1.89
3792 4047 6.349243 TCTTGTATTTCTGAACGGAGGTAA 57.651 37.500 0.00 0.00 0.00 2.85
3793 4048 5.988310 TCTTGTATTTCTGAACGGAGGTA 57.012 39.130 0.00 0.00 0.00 3.08
3794 4049 4.884668 TCTTGTATTTCTGAACGGAGGT 57.115 40.909 0.00 0.00 0.00 3.85
3811 4066 7.533222 CGATTCACAAAAAGTTGAGAGATCTTG 59.467 37.037 0.00 0.00 36.01 3.02
3819 4074 6.246420 AGATCCGATTCACAAAAAGTTGAG 57.754 37.500 0.00 0.00 38.20 3.02
3820 4075 7.390440 ACATAGATCCGATTCACAAAAAGTTGA 59.610 33.333 0.00 0.00 38.20 3.18
3917 4172 9.303537 GCGAGTGAATTAATATAAGATACTCCC 57.696 37.037 0.00 0.00 30.95 4.30
3918 4173 9.303537 GGCGAGTGAATTAATATAAGATACTCC 57.696 37.037 0.00 0.00 30.95 3.85
3921 4176 9.856488 TGAGGCGAGTGAATTAATATAAGATAC 57.144 33.333 0.00 0.00 0.00 2.24
3923 4178 9.950496 AATGAGGCGAGTGAATTAATATAAGAT 57.050 29.630 0.00 0.00 0.00 2.40
3924 4179 9.424319 GAATGAGGCGAGTGAATTAATATAAGA 57.576 33.333 0.00 0.00 0.00 2.10
3925 4180 9.208022 TGAATGAGGCGAGTGAATTAATATAAG 57.792 33.333 0.00 0.00 0.00 1.73
3926 4181 9.725019 ATGAATGAGGCGAGTGAATTAATATAA 57.275 29.630 0.00 0.00 0.00 0.98
3927 4182 9.371136 GATGAATGAGGCGAGTGAATTAATATA 57.629 33.333 0.00 0.00 0.00 0.86
3928 4183 8.099537 AGATGAATGAGGCGAGTGAATTAATAT 58.900 33.333 0.00 0.00 0.00 1.28
3929 4184 7.445121 AGATGAATGAGGCGAGTGAATTAATA 58.555 34.615 0.00 0.00 0.00 0.98
3930 4185 6.294473 AGATGAATGAGGCGAGTGAATTAAT 58.706 36.000 0.00 0.00 0.00 1.40
3931 4186 5.674525 AGATGAATGAGGCGAGTGAATTAA 58.325 37.500 0.00 0.00 0.00 1.40
3932 4187 5.282055 AGATGAATGAGGCGAGTGAATTA 57.718 39.130 0.00 0.00 0.00 1.40
3933 4188 4.148128 AGATGAATGAGGCGAGTGAATT 57.852 40.909 0.00 0.00 0.00 2.17
3934 4189 3.834489 AGATGAATGAGGCGAGTGAAT 57.166 42.857 0.00 0.00 0.00 2.57
3935 4190 4.313277 CTAGATGAATGAGGCGAGTGAA 57.687 45.455 0.00 0.00 0.00 3.18
3936 4191 3.998099 CTAGATGAATGAGGCGAGTGA 57.002 47.619 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.