Multiple sequence alignment - TraesCS4B01G053200

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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 TraesCS4B01G053200 chr4B 100.000 4071 0 0 1 4071 41847942 41843872 0.000000e+00 7518
1 TraesCS4B01G053200 chr4B 83.676 1899 238 43 1051 2919 9942490 9944346 0.000000e+00 1724
2 TraesCS4B01G053200 chr4B 90.865 416 28 9 1 411 134826887 134827297 2.140000e-152 549
3 TraesCS4B01G053200 chr4B 82.268 485 50 19 3058 3530 9944696 9945156 1.770000e-103 387
4 TraesCS4B01G053200 chr4B 94.505 182 10 0 454 635 63952900 63952719 8.620000e-72 281
5 TraesCS4B01G053200 chr4B 95.652 69 3 0 4002 4070 9947510 9947578 1.200000e-20 111
6 TraesCS4B01G053200 chr4B 87.255 102 7 4 482 581 63931458 63931361 1.200000e-20 111
7 TraesCS4B01G053200 chr4B 81.208 149 11 11 2916 3060 9944458 9944593 2.000000e-18 104
8 TraesCS4B01G053200 chr4A 93.457 4096 173 39 39 4071 573658922 573662985 0.000000e+00 5991
9 TraesCS4B01G053200 chr4A 83.096 2532 318 72 1051 3530 597870724 597868251 0.000000e+00 2204
10 TraesCS4B01G053200 chr4A 93.778 225 14 0 411 635 555808208 555808432 5.040000e-89 339
11 TraesCS4B01G053200 chr4A 93.182 220 12 2 418 635 555969566 555969784 1.830000e-83 320
12 TraesCS4B01G053200 chr4A 88.938 226 15 6 3685 3903 597868228 597868006 1.860000e-68 270
13 TraesCS4B01G053200 chr4A 94.643 112 5 1 524 635 555935369 555935479 5.410000e-39 172
14 TraesCS4B01G053200 chr4A 85.882 170 13 7 3798 3956 597888950 597888781 1.950000e-38 171
15 TraesCS4B01G053200 chr4A 90.179 112 11 0 411 522 555934876 555934987 3.280000e-31 147
16 TraesCS4B01G053200 chr4A 98.571 70 1 0 4002 4071 597887017 597886948 1.540000e-24 124
17 TraesCS4B01G053200 chr4A 91.209 91 0 5 3688 3777 653076767 653076850 2.570000e-22 117
18 TraesCS4B01G053200 chr4A 95.714 70 3 0 4002 4071 597848809 597848740 3.330000e-21 113
19 TraesCS4B01G053200 chr4A 82.609 138 14 5 3617 3744 597889083 597888946 3.330000e-21 113
20 TraesCS4B01G053200 chr4A 87.000 100 8 3 484 581 556163249 556163345 1.550000e-19 108
21 TraesCS4B01G053200 chr4D 96.807 2662 61 11 1427 4071 29415084 29412430 0.000000e+00 4423
22 TraesCS4B01G053200 chr4D 84.812 2186 254 43 1513 3645 5670300 5672460 0.000000e+00 2126
23 TraesCS4B01G053200 chr4D 82.770 1834 234 44 1772 3543 5658633 5660446 0.000000e+00 1561
24 TraesCS4B01G053200 chr4D 83.333 714 105 13 1051 1763 5642992 5643692 0.000000e+00 647
25 TraesCS4B01G053200 chr4D 93.833 227 12 2 412 638 44050727 44050503 1.400000e-89 340
26 TraesCS4B01G053200 chr4D 93.694 222 14 0 414 635 43850477 43850256 2.350000e-87 333
27 TraesCS4B01G053200 chr4D 93.939 99 6 0 3971 4069 5672617 5672715 2.530000e-32 150
28 TraesCS4B01G053200 chr4D 94.203 69 4 0 4003 4071 5662345 5662413 5.570000e-19 106
29 TraesCS4B01G053200 chr7A 88.204 2238 222 28 1318 3521 708657999 708660228 0.000000e+00 2632
30 TraesCS4B01G053200 chr7A 94.006 317 18 1 1062 1378 708657681 708657996 2.850000e-131 479
31 TraesCS4B01G053200 chr7A 83.592 451 47 18 1062 1512 708630722 708631145 8.200000e-107 398
32 TraesCS4B01G053200 chr7A 72.766 1186 258 49 1442 2595 45982058 45980906 1.400000e-89 340
33 TraesCS4B01G053200 chr7A 95.714 70 3 0 4002 4071 708656297 708656366 3.330000e-21 113
34 TraesCS4B01G053200 chr7A 86.735 98 2 5 3688 3780 45855297 45855206 9.310000e-17 99
35 TraesCS4B01G053200 chr6B 88.028 1988 176 35 1611 3566 625875722 625877679 0.000000e+00 2296
36 TraesCS4B01G053200 chr6B 83.513 1019 141 17 1634 2629 625827793 625828807 0.000000e+00 926
37 TraesCS4B01G053200 chr6B 89.688 417 35 7 1 412 63231781 63231368 3.600000e-145 525
38 TraesCS4B01G053200 chr6B 89.688 417 35 7 1 412 63262034 63261621 3.600000e-145 525
39 TraesCS4B01G053200 chr6B 91.483 317 26 1 1062 1378 625848982 625849297 6.250000e-118 435
40 TraesCS4B01G053200 chr6B 89.789 284 29 0 1052 1335 625827505 625827788 8.320000e-97 364
41 TraesCS4B01G053200 chr6B 81.452 372 23 23 3726 4071 625883767 625884118 3.120000e-66 263
42 TraesCS4B01G053200 chr6B 92.373 118 6 2 3604 3721 625883051 625883165 9.050000e-37 165
43 TraesCS4B01G053200 chr6B 97.727 44 0 1 3817 3859 625883821 625883864 1.570000e-09 75
44 TraesCS4B01G053200 chrUn 84.237 2176 269 39 1417 3543 52140801 52142951 0.000000e+00 2050
45 TraesCS4B01G053200 chrUn 90.071 282 22 4 1051 1332 52140459 52140734 1.080000e-95 361
46 TraesCS4B01G053200 chr2D 90.954 409 31 5 1 404 552574913 552575320 2.770000e-151 545
47 TraesCS4B01G053200 chr1B 90.647 417 29 9 1 411 636256847 636256435 2.770000e-151 545
48 TraesCS4B01G053200 chr7D 90.071 423 33 7 1 419 51754796 51754379 1.290000e-149 540
49 TraesCS4B01G053200 chr7D 90.261 421 25 14 1 414 164538191 164538602 1.670000e-148 536
50 TraesCS4B01G053200 chr7D 72.991 1170 260 40 1440 2584 43634228 43633090 3.870000e-95 359
51 TraesCS4B01G053200 chr3A 90.191 418 35 5 1 414 56965624 56965209 1.290000e-149 540


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 TraesCS4B01G053200 chr4B 41843872 41847942 4070 True 7518.000000 7518 100.000000 1 4071 1 chr4B.!!$R1 4070
1 TraesCS4B01G053200 chr4B 9942490 9947578 5088 False 581.500000 1724 85.701000 1051 4070 4 chr4B.!!$F2 3019
2 TraesCS4B01G053200 chr4A 573658922 573662985 4063 False 5991.000000 5991 93.457000 39 4071 1 chr4A.!!$F4 4032
3 TraesCS4B01G053200 chr4A 597868006 597870724 2718 True 1237.000000 2204 86.017000 1051 3903 2 chr4A.!!$R2 2852
4 TraesCS4B01G053200 chr4D 29412430 29415084 2654 True 4423.000000 4423 96.807000 1427 4071 1 chr4D.!!$R1 2644
5 TraesCS4B01G053200 chr4D 5670300 5672715 2415 False 1138.000000 2126 89.375500 1513 4069 2 chr4D.!!$F3 2556
6 TraesCS4B01G053200 chr4D 5658633 5662413 3780 False 833.500000 1561 88.486500 1772 4071 2 chr4D.!!$F2 2299
7 TraesCS4B01G053200 chr4D 5642992 5643692 700 False 647.000000 647 83.333000 1051 1763 1 chr4D.!!$F1 712
8 TraesCS4B01G053200 chr7A 708656297 708660228 3931 False 1074.666667 2632 92.641333 1062 4071 3 chr7A.!!$F2 3009
9 TraesCS4B01G053200 chr7A 45980906 45982058 1152 True 340.000000 340 72.766000 1442 2595 1 chr7A.!!$R2 1153
10 TraesCS4B01G053200 chr6B 625875722 625877679 1957 False 2296.000000 2296 88.028000 1611 3566 1 chr6B.!!$F2 1955
11 TraesCS4B01G053200 chr6B 625827505 625828807 1302 False 645.000000 926 86.651000 1052 2629 2 chr6B.!!$F3 1577
12 TraesCS4B01G053200 chrUn 52140459 52142951 2492 False 1205.500000 2050 87.154000 1051 3543 2 chrUn.!!$F1 2492
13 TraesCS4B01G053200 chr7D 43633090 43634228 1138 True 359.000000 359 72.991000 1440 2584 1 chr7D.!!$R1 1144

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
58 59 0.035317 TGGCAACTGCAGTAGACCAG 59.965 55.0 22.01 7.33 44.36 4.00 F
1744 2179 0.109226 CGACCTCGACCTCTTCAACC 60.109 60.0 0.00 0.00 43.02 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1853 2297 0.244721 GACAACCAGCCCATCTTTGC 59.755 55.0 0.00 0.0 0.0 3.68 R
3377 4185 0.447406 TCCTTGCGCAAATCATGTCG 59.553 50.0 25.01 9.5 0.0 4.35 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
20 21 3.402628 CTAGTGTTAGTGGTGGCAACT 57.597 47.619 3.27 0.00 37.61 3.16
21 22 2.256117 AGTGTTAGTGGTGGCAACTC 57.744 50.000 3.27 0.00 37.61 3.01
30 31 2.956333 GTGGTGGCAACTCCTAAAGTTT 59.044 45.455 3.27 0.00 46.26 2.66
31 32 3.383505 GTGGTGGCAACTCCTAAAGTTTT 59.616 43.478 3.27 0.00 46.26 2.43
32 33 3.383185 TGGTGGCAACTCCTAAAGTTTTG 59.617 43.478 3.27 0.00 46.26 2.44
33 34 3.634910 GGTGGCAACTCCTAAAGTTTTGA 59.365 43.478 0.00 0.00 46.26 2.69
34 35 4.098807 GGTGGCAACTCCTAAAGTTTTGAA 59.901 41.667 0.00 0.00 46.26 2.69
35 36 5.394773 GGTGGCAACTCCTAAAGTTTTGAAA 60.395 40.000 0.00 0.00 46.26 2.69
36 37 6.280643 GTGGCAACTCCTAAAGTTTTGAAAT 58.719 36.000 0.00 0.00 46.26 2.17
37 38 6.420903 GTGGCAACTCCTAAAGTTTTGAAATC 59.579 38.462 0.00 0.00 46.26 2.17
52 53 3.419943 TGAAATCATGGCAACTGCAGTA 58.580 40.909 22.01 4.30 44.36 2.74
55 56 2.099141 TCATGGCAACTGCAGTAGAC 57.901 50.000 22.01 13.35 44.36 2.59
58 59 0.035317 TGGCAACTGCAGTAGACCAG 59.965 55.000 22.01 7.33 44.36 4.00
59 60 0.321671 GGCAACTGCAGTAGACCAGA 59.678 55.000 22.01 0.00 44.36 3.86
61 62 1.941668 GCAACTGCAGTAGACCAGACC 60.942 57.143 22.01 0.00 41.59 3.85
62 63 1.344438 CAACTGCAGTAGACCAGACCA 59.656 52.381 22.01 0.00 33.40 4.02
63 64 1.944177 ACTGCAGTAGACCAGACCAT 58.056 50.000 20.16 0.00 33.40 3.55
128 129 4.142687 GCGACATGGCAACTACAGTTAAAT 60.143 41.667 0.00 0.00 36.32 1.40
132 133 6.677913 ACATGGCAACTACAGTTAAATGAAC 58.322 36.000 10.35 0.00 36.32 3.18
321 324 2.853731 TTACTTGTTTTGCCCACACG 57.146 45.000 0.00 0.00 0.00 4.49
327 330 1.876799 TGTTTTGCCCACACGTAGATG 59.123 47.619 0.00 0.00 0.00 2.90
471 474 2.032924 CGTGTGTCCAGCTATCGTCATA 59.967 50.000 0.00 0.00 0.00 2.15
488 491 2.435805 TCATAGGCAAAGGAGCGAGATT 59.564 45.455 0.00 0.00 34.64 2.40
490 493 2.611225 AGGCAAAGGAGCGAGATTAG 57.389 50.000 0.00 0.00 34.64 1.73
511 514 2.537401 GGATTCCGGAGTACTGAAACG 58.463 52.381 3.34 0.00 0.00 3.60
717 720 2.145865 CCATGTGGGCCTAGGTAGG 58.854 63.158 11.31 0.00 46.42 3.18
718 721 0.399949 CCATGTGGGCCTAGGTAGGA 60.400 60.000 11.31 0.00 46.63 2.94
719 722 1.051812 CATGTGGGCCTAGGTAGGAG 58.948 60.000 11.31 0.00 46.63 3.69
720 723 0.941963 ATGTGGGCCTAGGTAGGAGA 59.058 55.000 11.31 0.00 46.63 3.71
721 724 0.714180 TGTGGGCCTAGGTAGGAGAA 59.286 55.000 11.31 0.00 46.63 2.87
722 725 1.343075 TGTGGGCCTAGGTAGGAGAAG 60.343 57.143 11.31 0.00 46.63 2.85
735 766 3.952628 GAGAAGGGCGGTTGGTCGG 62.953 68.421 0.00 0.00 0.00 4.79
842 875 1.261238 AAGGAGGCCGAGTCAAGGAG 61.261 60.000 0.00 0.00 0.00 3.69
850 883 0.734253 CGAGTCAAGGAGGCAAGTCG 60.734 60.000 0.00 0.00 0.00 4.18
851 884 1.004440 AGTCAAGGAGGCAAGTCGC 60.004 57.895 0.00 0.00 41.28 5.19
852 885 2.048222 TCAAGGAGGCAAGTCGCG 60.048 61.111 0.00 0.00 43.84 5.87
855 888 3.591254 AAGGAGGCAAGTCGCGACC 62.591 63.158 34.08 20.08 43.84 4.79
857 890 2.357034 GAGGCAAGTCGCGACCAA 60.357 61.111 34.08 0.00 43.84 3.67
858 891 1.959226 GAGGCAAGTCGCGACCAAA 60.959 57.895 34.08 0.00 43.84 3.28
859 892 1.503818 GAGGCAAGTCGCGACCAAAA 61.504 55.000 34.08 0.00 43.84 2.44
860 893 1.082104 GGCAAGTCGCGACCAAAAG 60.082 57.895 34.08 20.07 43.84 2.27
862 895 0.384353 GCAAGTCGCGACCAAAAGAC 60.384 55.000 34.08 14.02 0.00 3.01
866 899 0.111398 GTCGCGACCAAAAGACGAAC 60.111 55.000 28.61 0.00 35.57 3.95
867 900 0.249155 TCGCGACCAAAAGACGAACT 60.249 50.000 3.71 0.00 35.57 3.01
868 901 0.161024 CGCGACCAAAAGACGAACTC 59.839 55.000 0.00 0.00 35.57 3.01
870 903 1.798813 GCGACCAAAAGACGAACTCAT 59.201 47.619 0.00 0.00 35.57 2.90
871 904 2.159827 GCGACCAAAAGACGAACTCATC 60.160 50.000 0.00 0.00 35.57 2.92
872 905 2.412089 CGACCAAAAGACGAACTCATCC 59.588 50.000 0.00 0.00 35.57 3.51
873 906 2.742589 GACCAAAAGACGAACTCATCCC 59.257 50.000 0.00 0.00 0.00 3.85
874 907 2.105821 ACCAAAAGACGAACTCATCCCA 59.894 45.455 0.00 0.00 0.00 4.37
875 908 2.484264 CCAAAAGACGAACTCATCCCAC 59.516 50.000 0.00 0.00 0.00 4.61
876 909 3.403038 CAAAAGACGAACTCATCCCACT 58.597 45.455 0.00 0.00 0.00 4.00
877 910 3.320673 AAAGACGAACTCATCCCACTC 57.679 47.619 0.00 0.00 0.00 3.51
911 944 2.599408 TATCTCCCCACCCTATCGAC 57.401 55.000 0.00 0.00 0.00 4.20
912 945 0.178929 ATCTCCCCACCCTATCGACC 60.179 60.000 0.00 0.00 0.00 4.79
913 946 2.123597 TCCCCACCCTATCGACCG 60.124 66.667 0.00 0.00 0.00 4.79
973 1006 2.258013 CGCCCAGAGAAAAACGCCA 61.258 57.895 0.00 0.00 0.00 5.69
1193 1526 1.446099 GCAAGCTCATCGTCGGTCA 60.446 57.895 0.00 0.00 0.00 4.02
1270 1603 3.695606 GCCTCCTCAGCACCGACA 61.696 66.667 0.00 0.00 0.00 4.35
1279 1612 4.687215 GCACCGACAGCCTCTGCA 62.687 66.667 0.00 0.00 41.13 4.41
1365 1731 1.176619 TCGAAGTCGAGGCCAAGACA 61.177 55.000 25.77 8.35 44.22 3.41
1423 1852 2.297597 AGGTCCAAGAGAAAGAGACACG 59.702 50.000 0.00 0.00 0.00 4.49
1652 2087 2.282462 CAAGGCCGCCCTCAAGTT 60.282 61.111 5.55 0.00 41.90 2.66
1744 2179 0.109226 CGACCTCGACCTCTTCAACC 60.109 60.000 0.00 0.00 43.02 3.77
2174 2649 0.169672 CAGGCCTTCAAGATGTTGCG 59.830 55.000 0.00 0.00 33.23 4.85
2597 3095 0.733729 CTGCTGCTCAATCCTGAAGC 59.266 55.000 0.00 0.00 36.39 3.86
2780 3302 2.516448 CCTTGAGGCGGGTATCAGA 58.484 57.895 0.00 0.00 0.00 3.27
2782 3304 0.824109 CTTGAGGCGGGTATCAGACA 59.176 55.000 0.00 0.00 0.00 3.41
2800 3322 5.890419 TCAGACATGAGATCACAGTATGAGT 59.110 40.000 0.00 0.89 41.91 3.41
3044 3693 4.133078 GGATCAAAGACAGGAAGGCTATG 58.867 47.826 0.00 0.00 30.53 2.23
3352 4156 5.667466 TCATCTTACTGATCCGGGTTTTAC 58.333 41.667 0.00 0.00 32.05 2.01
3377 4185 7.543520 ACTTTGTTAATAGGACGTTGCTACTAC 59.456 37.037 0.00 0.00 0.00 2.73
3468 4282 2.746277 GAACCCGCAGCGTGGATT 60.746 61.111 24.08 15.63 34.74 3.01
3469 4283 2.282180 AACCCGCAGCGTGGATTT 60.282 55.556 24.08 9.88 34.74 2.17
3636 4459 3.456280 GATTCAGAGGATGAGTCTGTGC 58.544 50.000 0.31 0.00 40.55 4.57
3656 4479 2.235898 GCCTCTGGATGAGTGAGTCTTT 59.764 50.000 0.00 0.00 41.11 2.52
3673 4500 1.415672 TTTTCTCCTCCGTGGCCACT 61.416 55.000 32.28 0.00 35.26 4.00
3793 4677 1.878775 GCCATCAGCAAGTGGACAC 59.121 57.895 5.56 0.00 42.97 3.67
3810 4694 0.165295 CACTGCGCTGTGACATTCTG 59.835 55.000 35.56 11.62 40.12 3.02
3956 4844 4.946160 TTCCCCCTTCTGTTGACATATT 57.054 40.909 0.00 0.00 0.00 1.28
3960 4848 3.954258 CCCCTTCTGTTGACATATTTCCC 59.046 47.826 0.00 0.00 0.00 3.97
3961 4849 3.954258 CCCTTCTGTTGACATATTTCCCC 59.046 47.826 0.00 0.00 0.00 4.81
3962 4850 3.954258 CCTTCTGTTGACATATTTCCCCC 59.046 47.826 0.00 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.326747 GAGTTGCCACCACTAACACTAG 58.673 50.000 0.00 0.00 0.00 2.57
2 3 1.202770 GGAGTTGCCACCACTAACACT 60.203 52.381 0.00 0.00 36.34 3.55
4 5 1.136828 AGGAGTTGCCACCACTAACA 58.863 50.000 0.00 0.00 40.02 2.41
5 6 3.412237 TTAGGAGTTGCCACCACTAAC 57.588 47.619 0.00 0.00 40.02 2.34
6 7 3.393278 ACTTTAGGAGTTGCCACCACTAA 59.607 43.478 0.00 0.00 40.02 2.24
7 8 2.976882 ACTTTAGGAGTTGCCACCACTA 59.023 45.455 0.00 0.00 40.02 2.74
8 9 1.774856 ACTTTAGGAGTTGCCACCACT 59.225 47.619 0.00 0.00 40.02 4.00
9 10 2.271944 ACTTTAGGAGTTGCCACCAC 57.728 50.000 0.00 0.00 40.02 4.16
18 19 6.267471 TGCCATGATTTCAAAACTTTAGGAGT 59.733 34.615 0.00 0.00 41.47 3.85
19 20 6.690530 TGCCATGATTTCAAAACTTTAGGAG 58.309 36.000 0.00 0.00 0.00 3.69
20 21 6.662865 TGCCATGATTTCAAAACTTTAGGA 57.337 33.333 0.00 0.00 0.00 2.94
21 22 6.930722 AGTTGCCATGATTTCAAAACTTTAGG 59.069 34.615 0.00 0.00 0.00 2.69
22 23 7.569957 GCAGTTGCCATGATTTCAAAACTTTAG 60.570 37.037 0.00 0.00 34.31 1.85
23 24 6.202570 GCAGTTGCCATGATTTCAAAACTTTA 59.797 34.615 0.00 0.00 34.31 1.85
24 25 5.007921 GCAGTTGCCATGATTTCAAAACTTT 59.992 36.000 0.00 0.00 34.31 2.66
25 26 4.512571 GCAGTTGCCATGATTTCAAAACTT 59.487 37.500 0.00 0.00 34.31 2.66
26 27 4.060205 GCAGTTGCCATGATTTCAAAACT 58.940 39.130 0.00 0.00 34.31 2.66
27 28 3.808726 TGCAGTTGCCATGATTTCAAAAC 59.191 39.130 1.06 0.00 41.18 2.43
28 29 4.059511 CTGCAGTTGCCATGATTTCAAAA 58.940 39.130 5.25 0.00 41.18 2.44
29 30 3.069872 ACTGCAGTTGCCATGATTTCAAA 59.930 39.130 15.25 0.00 41.18 2.69
30 31 2.629137 ACTGCAGTTGCCATGATTTCAA 59.371 40.909 15.25 0.00 41.18 2.69
31 32 2.241160 ACTGCAGTTGCCATGATTTCA 58.759 42.857 15.25 0.00 41.18 2.69
32 33 3.691118 TCTACTGCAGTTGCCATGATTTC 59.309 43.478 27.06 0.00 41.18 2.17
33 34 3.441572 GTCTACTGCAGTTGCCATGATTT 59.558 43.478 27.06 0.00 41.18 2.17
34 35 3.012518 GTCTACTGCAGTTGCCATGATT 58.987 45.455 27.06 0.00 41.18 2.57
35 36 2.636830 GTCTACTGCAGTTGCCATGAT 58.363 47.619 27.06 0.00 41.18 2.45
36 37 1.339055 GGTCTACTGCAGTTGCCATGA 60.339 52.381 27.06 10.89 41.18 3.07
37 38 1.089920 GGTCTACTGCAGTTGCCATG 58.910 55.000 27.06 8.76 41.18 3.66
128 129 0.608130 CAGACCCTCGTCCATGTTCA 59.392 55.000 0.00 0.00 40.12 3.18
132 133 1.517832 GTCCAGACCCTCGTCCATG 59.482 63.158 0.00 0.00 40.12 3.66
155 156 3.049674 CACGCATCCCGCAGTTGT 61.050 61.111 0.00 0.00 42.60 3.32
171 172 4.293648 CCCGCGTGACAGTCACCA 62.294 66.667 25.11 0.00 44.20 4.17
198 199 2.279517 GGCCTCGTACCTCATGCG 60.280 66.667 0.00 0.00 37.84 4.73
261 264 1.028905 CCTCTCGATCCCTCTCACAC 58.971 60.000 0.00 0.00 0.00 3.82
290 293 5.566627 GCAAAACAAGTAATGCCCACATACT 60.567 40.000 0.00 0.00 34.62 2.12
321 324 3.008049 AGAGGAACAACCCACACATCTAC 59.992 47.826 0.00 0.00 40.05 2.59
327 330 4.694037 GTGTATAAGAGGAACAACCCACAC 59.306 45.833 0.00 0.00 40.05 3.82
329 332 4.259356 GGTGTATAAGAGGAACAACCCAC 58.741 47.826 0.00 0.00 40.05 4.61
330 333 3.911260 TGGTGTATAAGAGGAACAACCCA 59.089 43.478 0.00 0.00 40.05 4.51
334 337 5.554437 TGTGTGGTGTATAAGAGGAACAA 57.446 39.130 0.00 0.00 0.00 2.83
336 339 6.870971 TTTTGTGTGGTGTATAAGAGGAAC 57.129 37.500 0.00 0.00 0.00 3.62
363 366 2.696187 GGGAGTTAGGAGATCTGTCCAC 59.304 54.545 0.00 0.00 39.34 4.02
373 376 0.966920 ACACGTGTGGGAGTTAGGAG 59.033 55.000 22.71 0.00 34.19 3.69
374 377 0.677288 CACACGTGTGGGAGTTAGGA 59.323 55.000 35.65 0.00 42.10 2.94
375 378 3.210857 CACACGTGTGGGAGTTAGG 57.789 57.895 35.65 11.35 42.10 2.69
471 474 1.139853 CCTAATCTCGCTCCTTTGCCT 59.860 52.381 0.00 0.00 0.00 4.75
488 491 3.675348 TTCAGTACTCCGGAATCCCTA 57.325 47.619 5.23 0.00 0.00 3.53
490 493 2.737679 CGTTTCAGTACTCCGGAATCCC 60.738 54.545 5.23 0.00 0.00 3.85
511 514 3.685058 GCCACGAGCTGAATTGTTAATC 58.315 45.455 0.00 0.00 38.99 1.75
717 720 2.434359 CGACCAACCGCCCTTCTC 60.434 66.667 0.00 0.00 0.00 2.87
718 721 4.016706 CCGACCAACCGCCCTTCT 62.017 66.667 0.00 0.00 0.00 2.85
719 722 4.324991 ACCGACCAACCGCCCTTC 62.325 66.667 0.00 0.00 0.00 3.46
720 723 4.324991 GACCGACCAACCGCCCTT 62.325 66.667 0.00 0.00 0.00 3.95
735 766 0.964358 TCCTTCCTTCCTCGACCGAC 60.964 60.000 0.00 0.00 0.00 4.79
817 850 2.272471 CTCGGCCTCCTTTTCCCC 59.728 66.667 0.00 0.00 0.00 4.81
842 875 1.082104 CTTTTGGTCGCGACTTGCC 60.082 57.895 35.50 21.61 42.08 4.52
844 877 0.111266 CGTCTTTTGGTCGCGACTTG 60.111 55.000 35.50 20.97 0.00 3.16
845 878 0.249155 TCGTCTTTTGGTCGCGACTT 60.249 50.000 35.50 0.00 0.00 3.01
846 879 0.249155 TTCGTCTTTTGGTCGCGACT 60.249 50.000 35.50 0.00 0.00 4.18
850 883 1.214367 TGAGTTCGTCTTTTGGTCGC 58.786 50.000 0.00 0.00 0.00 5.19
851 884 2.412089 GGATGAGTTCGTCTTTTGGTCG 59.588 50.000 1.72 0.00 32.61 4.79
852 885 2.742589 GGGATGAGTTCGTCTTTTGGTC 59.257 50.000 1.72 0.00 32.61 4.02
855 888 3.403038 AGTGGGATGAGTTCGTCTTTTG 58.597 45.455 1.72 0.00 32.61 2.44
857 890 2.028020 GGAGTGGGATGAGTTCGTCTTT 60.028 50.000 1.72 0.00 32.61 2.52
858 891 1.550976 GGAGTGGGATGAGTTCGTCTT 59.449 52.381 1.72 0.00 32.61 3.01
859 892 1.187087 GGAGTGGGATGAGTTCGTCT 58.813 55.000 1.72 0.00 32.61 4.18
860 893 0.895530 TGGAGTGGGATGAGTTCGTC 59.104 55.000 0.00 0.00 0.00 4.20
862 895 5.667539 ATATATGGAGTGGGATGAGTTCG 57.332 43.478 0.00 0.00 0.00 3.95
891 924 2.292323 GGTCGATAGGGTGGGGAGATAT 60.292 54.545 0.00 0.00 0.00 1.63
892 925 1.076677 GGTCGATAGGGTGGGGAGATA 59.923 57.143 0.00 0.00 0.00 1.98
893 926 0.178929 GGTCGATAGGGTGGGGAGAT 60.179 60.000 0.00 0.00 0.00 2.75
894 927 1.232216 GGTCGATAGGGTGGGGAGA 59.768 63.158 0.00 0.00 0.00 3.71
895 928 2.201022 CGGTCGATAGGGTGGGGAG 61.201 68.421 0.00 0.00 0.00 4.30
896 929 2.123597 CGGTCGATAGGGTGGGGA 60.124 66.667 0.00 0.00 0.00 4.81
897 930 2.123597 TCGGTCGATAGGGTGGGG 60.124 66.667 0.00 0.00 0.00 4.96
898 931 1.453762 GAGTCGGTCGATAGGGTGGG 61.454 65.000 0.00 0.00 0.00 4.61
899 932 2.031360 GAGTCGGTCGATAGGGTGG 58.969 63.158 0.00 0.00 0.00 4.61
913 946 2.548057 AGAAGAGCAGATCGATCGAGTC 59.452 50.000 23.84 18.86 34.30 3.36
1193 1526 2.873288 GGAACGCCTCGTCGTAGT 59.127 61.111 0.00 0.00 42.46 2.73
1744 2179 0.597568 TTGGCCGAAAACAGATGCTG 59.402 50.000 0.00 0.00 37.52 4.41
1791 2235 1.175983 GCAACCCACGGTGGATTTCA 61.176 55.000 28.36 0.00 40.96 2.69
1853 2297 0.244721 GACAACCAGCCCATCTTTGC 59.755 55.000 0.00 0.00 0.00 3.68
2597 3095 0.685097 TGAGACCAGGAGTTTTCGGG 59.315 55.000 0.00 0.00 0.00 5.14
2696 3194 1.327303 CCAGGGTGCTGCTTTGTAAA 58.673 50.000 0.00 0.00 0.00 2.01
2779 3301 7.598118 CCAATACTCATACTGTGATCTCATGTC 59.402 40.741 0.00 0.00 35.97 3.06
2780 3302 7.288621 TCCAATACTCATACTGTGATCTCATGT 59.711 37.037 0.00 2.24 35.97 3.21
2782 3304 7.039152 CCTCCAATACTCATACTGTGATCTCAT 60.039 40.741 0.00 0.00 35.97 2.90
2800 3322 1.528824 GCAGCCAGCTCCTCCAATA 59.471 57.895 0.00 0.00 41.15 1.90
2823 3345 3.190118 CCTTGAGCACCTGTTCAATCTTC 59.810 47.826 5.19 0.00 42.76 2.87
3021 3661 1.065854 AGCCTTCCTGTCTTTGATCCG 60.066 52.381 0.00 0.00 0.00 4.18
3044 3693 1.090052 GCACGTATCAGTGAAGGGGC 61.090 60.000 0.00 1.82 44.43 5.80
3352 4156 6.963049 AGTAGCAACGTCCTATTAACAAAG 57.037 37.500 0.00 0.00 0.00 2.77
3377 4185 0.447406 TCCTTGCGCAAATCATGTCG 59.553 50.000 25.01 9.50 0.00 4.35
3468 4282 2.625314 CGAGGTCCATCTCTAGCATGAA 59.375 50.000 0.00 0.00 0.00 2.57
3469 4283 2.234143 CGAGGTCCATCTCTAGCATGA 58.766 52.381 0.00 0.00 0.00 3.07
3636 4459 8.519029 GGAGAAAAGACTCACTCATCCAGAGG 62.519 50.000 0.00 0.00 39.72 3.69
3656 4479 2.203788 AGTGGCCACGGAGGAGAA 60.204 61.111 29.68 0.00 41.22 2.87
3673 4500 3.489229 GCATCACACACTCGTATCTAGCA 60.489 47.826 0.00 0.00 0.00 3.49
3810 4694 1.937899 ACCAAACGTGCTTCAGTACAC 59.062 47.619 0.00 0.00 0.00 2.90
3956 4844 3.589542 CCCAGCACCAAGGGGGAA 61.590 66.667 0.00 0.00 43.57 3.97
3960 4848 0.609662 CAAAATCCCAGCACCAAGGG 59.390 55.000 0.00 0.00 46.90 3.95
3961 4849 1.341080 ACAAAATCCCAGCACCAAGG 58.659 50.000 0.00 0.00 0.00 3.61
3962 4850 2.548493 CCAACAAAATCCCAGCACCAAG 60.548 50.000 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.