Multiple sequence alignment - TraesCS3D01G180100

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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 TraesCS3D01G180100 chr3D 100.000 3427 0 0 1 3427 161977310 161980736 0.000000e+00 6329.0
1 TraesCS3D01G180100 chr3D 91.841 1385 61 17 1146 2494 161938006 161939374 0.000000e+00 1884.0
2 TraesCS3D01G180100 chr3D 83.605 921 93 25 2527 3427 441369417 441370299 0.000000e+00 811.0
3 TraesCS3D01G180100 chr3D 85.515 787 72 28 2520 3281 475866249 475867018 0.000000e+00 784.0
4 TraesCS3D01G180100 chr3D 82.986 864 111 15 1 830 161931538 161932399 0.000000e+00 749.0
5 TraesCS3D01G180100 chr3D 94.371 302 16 1 849 1150 161932501 161932801 2.410000e-126 462.0
6 TraesCS3D01G180100 chr3A 92.679 1680 65 16 849 2499 191889403 191891053 0.000000e+00 2368.0
7 TraesCS3D01G180100 chr3A 93.966 1011 37 7 1508 2497 191884728 191885735 0.000000e+00 1507.0
8 TraesCS3D01G180100 chr3A 83.353 841 100 23 1 829 191888196 191889008 0.000000e+00 741.0
9 TraesCS3D01G180100 chr3A 88.211 492 23 14 1031 1510 191883599 191884067 3.860000e-154 555.0
10 TraesCS3D01G180100 chr3A 88.060 201 6 2 849 1048 191883107 191883290 4.450000e-54 222.0
11 TraesCS3D01G180100 chr3A 100.000 28 0 0 602 629 517337340 517337367 6.000000e-03 52.8
12 TraesCS3D01G180100 chr3B 92.684 1654 55 17 849 2471 238500943 238502561 0.000000e+00 2324.0
13 TraesCS3D01G180100 chr3B 88.161 397 32 10 462 849 238500511 238500901 3.120000e-125 459.0
14 TraesCS3D01G180100 chr3B 85.862 290 31 6 3144 3427 557163640 557163925 2.000000e-77 300.0
15 TraesCS3D01G180100 chr3B 87.755 49 5 1 588 636 48965490 48965537 4.780000e-04 56.5
16 TraesCS3D01G180100 chr2D 85.106 940 92 24 2520 3427 608381175 608382098 0.000000e+00 917.0
17 TraesCS3D01G180100 chr6D 84.132 939 100 27 2520 3427 445703705 445702785 0.000000e+00 863.0
18 TraesCS3D01G180100 chr6D 83.912 951 86 29 2522 3427 158982366 158981438 0.000000e+00 846.0
19 TraesCS3D01G180100 chr6D 84.498 787 84 28 2522 3281 62201455 62200680 0.000000e+00 743.0
20 TraesCS3D01G180100 chr5A 84.066 910 105 25 2526 3414 78922891 78922001 0.000000e+00 841.0
21 TraesCS3D01G180100 chr5A 82.013 745 93 29 2519 3239 662666544 662665817 2.280000e-166 595.0
22 TraesCS3D01G180100 chr2A 83.369 944 102 30 2522 3427 693440125 693439199 0.000000e+00 822.0
23 TraesCS3D01G180100 chr2A 84.032 620 75 22 2525 3125 19440329 19439715 2.970000e-160 575.0
24 TraesCS3D01G180100 chr1D 83.777 789 87 30 2522 3281 143961743 143960967 0.000000e+00 710.0
25 TraesCS3D01G180100 chr1D 80.055 366 45 15 14 364 486122982 486122630 2.640000e-61 246.0
26 TraesCS3D01G180100 chr4D 83.760 782 85 33 2522 3281 488605243 488604482 0.000000e+00 702.0
27 TraesCS3D01G180100 chr1A 82.157 779 105 23 2520 3273 548290215 548290984 3.730000e-179 638.0
28 TraesCS3D01G180100 chr7D 82.260 761 79 31 2524 3265 549132862 549132139 1.050000e-169 606.0
29 TraesCS3D01G180100 chr7D 84.483 58 4 2 602 654 221983940 221983883 6.000000e-03 52.8
30 TraesCS3D01G180100 chr7A 83.612 659 75 22 2522 3157 648893762 648893114 3.810000e-164 588.0
31 TraesCS3D01G180100 chr7A 87.500 264 24 9 3168 3425 20564054 20564314 2.590000e-76 296.0
32 TraesCS3D01G180100 chr2B 84.262 305 35 7 3132 3427 26025963 26026263 5.600000e-73 285.0
33 TraesCS3D01G180100 chr1B 94.118 51 3 0 314 364 640223061 640223011 1.020000e-10 78.7
34 TraesCS3D01G180100 chr4A 86.792 53 4 3 590 639 702147509 702147561 4.780000e-04 56.5
35 TraesCS3D01G180100 chr4A 96.875 32 0 1 609 639 636016423 636016454 6.000000e-03 52.8


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 TraesCS3D01G180100 chr3D 161977310 161980736 3426 False 6329.0 6329 100.0000 1 3427 1 chr3D.!!$F2 3426
1 TraesCS3D01G180100 chr3D 161938006 161939374 1368 False 1884.0 1884 91.8410 1146 2494 1 chr3D.!!$F1 1348
2 TraesCS3D01G180100 chr3D 441369417 441370299 882 False 811.0 811 83.6050 2527 3427 1 chr3D.!!$F3 900
3 TraesCS3D01G180100 chr3D 475866249 475867018 769 False 784.0 784 85.5150 2520 3281 1 chr3D.!!$F4 761
4 TraesCS3D01G180100 chr3D 161931538 161932801 1263 False 605.5 749 88.6785 1 1150 2 chr3D.!!$F5 1149
5 TraesCS3D01G180100 chr3A 191883107 191891053 7946 False 1078.6 2368 89.2538 1 2499 5 chr3A.!!$F2 2498
6 TraesCS3D01G180100 chr3B 238500511 238502561 2050 False 1391.5 2324 90.4225 462 2471 2 chr3B.!!$F3 2009
7 TraesCS3D01G180100 chr2D 608381175 608382098 923 False 917.0 917 85.1060 2520 3427 1 chr2D.!!$F1 907
8 TraesCS3D01G180100 chr6D 445702785 445703705 920 True 863.0 863 84.1320 2520 3427 1 chr6D.!!$R3 907
9 TraesCS3D01G180100 chr6D 158981438 158982366 928 True 846.0 846 83.9120 2522 3427 1 chr6D.!!$R2 905
10 TraesCS3D01G180100 chr6D 62200680 62201455 775 True 743.0 743 84.4980 2522 3281 1 chr6D.!!$R1 759
11 TraesCS3D01G180100 chr5A 78922001 78922891 890 True 841.0 841 84.0660 2526 3414 1 chr5A.!!$R1 888
12 TraesCS3D01G180100 chr5A 662665817 662666544 727 True 595.0 595 82.0130 2519 3239 1 chr5A.!!$R2 720
13 TraesCS3D01G180100 chr2A 693439199 693440125 926 True 822.0 822 83.3690 2522 3427 1 chr2A.!!$R2 905
14 TraesCS3D01G180100 chr2A 19439715 19440329 614 True 575.0 575 84.0320 2525 3125 1 chr2A.!!$R1 600
15 TraesCS3D01G180100 chr1D 143960967 143961743 776 True 710.0 710 83.7770 2522 3281 1 chr1D.!!$R1 759
16 TraesCS3D01G180100 chr4D 488604482 488605243 761 True 702.0 702 83.7600 2522 3281 1 chr4D.!!$R1 759
17 TraesCS3D01G180100 chr1A 548290215 548290984 769 False 638.0 638 82.1570 2520 3273 1 chr1A.!!$F1 753
18 TraesCS3D01G180100 chr7D 549132139 549132862 723 True 606.0 606 82.2600 2524 3265 1 chr7D.!!$R2 741
19 TraesCS3D01G180100 chr7A 648893114 648893762 648 True 588.0 588 83.6120 2522 3157 1 chr7A.!!$R1 635

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
978 6494 0.460284 CGGGCTGATCGTACAAGCTT 60.46 55.0 0.0 0.0 0.0 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2969 8858 0.233848 GACTCGCGCGAAAGGAAAAA 59.766 50.0 33.99 8.02 0.0 1.94 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
28 5118 9.755064 CGGACTTTGATACATTACTTACTTTTG 57.245 33.333 0.00 0.00 0.00 2.44
61 5151 8.568732 TGTTTACAATTTCGAAGAATTGTTCC 57.431 30.769 25.31 16.59 45.90 3.62
84 5174 9.691362 TTCCAATAAAATAAAGAAGTGTTGAGC 57.309 29.630 0.00 0.00 0.00 4.26
107 5197 3.118038 TCTGCCACTGTGGTTAGTTCTTT 60.118 43.478 26.48 0.00 40.46 2.52
117 5207 7.284489 ACTGTGGTTAGTTCTTTGAAATTAGCA 59.716 33.333 0.00 0.00 0.00 3.49
150 5240 3.553511 GTCACTTACAATCATCAGCTCCG 59.446 47.826 0.00 0.00 0.00 4.63
185 5275 4.442375 ACACTTCATTACTGAGAGGTCG 57.558 45.455 0.00 0.00 31.68 4.79
192 5282 5.250982 TCATTACTGAGAGGTCGTCTACAA 58.749 41.667 0.00 0.00 34.71 2.41
212 5302 1.002900 ACGTGGTGCTTTTTCGTGATG 60.003 47.619 0.00 0.00 33.55 3.07
223 5314 3.347958 TTTCGTGATGTTTCCTGTTGC 57.652 42.857 0.00 0.00 0.00 4.17
232 5323 1.602377 GTTTCCTGTTGCGCTACAGTT 59.398 47.619 37.29 0.00 43.17 3.16
236 5327 0.792640 CTGTTGCGCTACAGTTCCAG 59.207 55.000 34.22 15.97 40.48 3.86
238 5329 1.070615 TTGCGCTACAGTTCCAGCA 59.929 52.632 9.73 0.00 37.66 4.41
254 5345 2.586245 CAGGAGCTTCCCATCGCA 59.414 61.111 0.00 0.00 37.19 5.10
257 5348 2.586792 GAGCTTCCCATCGCACCT 59.413 61.111 0.00 0.00 0.00 4.00
259 5350 2.244117 GAGCTTCCCATCGCACCTGA 62.244 60.000 0.00 0.00 0.00 3.86
261 5352 0.749454 GCTTCCCATCGCACCTGATT 60.749 55.000 0.00 0.00 0.00 2.57
321 5412 2.189521 GGGGTGTATCCTGTGCGG 59.810 66.667 0.00 0.00 36.25 5.69
365 5480 2.809010 GGCGTGTAGGAGCTCCTC 59.191 66.667 38.44 27.33 44.77 3.71
406 5523 1.674322 CGCTTGAATCCCCGTTGGT 60.674 57.895 0.00 0.00 34.77 3.67
426 5543 2.124612 TCCCGCGGACGATAGACA 60.125 61.111 30.73 0.00 43.93 3.41
427 5544 1.721664 CTCCCGCGGACGATAGACAA 61.722 60.000 30.73 0.00 43.93 3.18
435 5552 1.067212 GGACGATAGACAAGCCGTGAT 59.933 52.381 0.00 0.00 41.38 3.06
437 5554 2.025155 ACGATAGACAAGCCGTGATCT 58.975 47.619 0.00 0.00 41.38 2.75
445 5562 4.827835 AGACAAGCCGTGATCTAATAGCTA 59.172 41.667 0.00 0.00 0.00 3.32
449 5566 6.992715 ACAAGCCGTGATCTAATAGCTATTTT 59.007 34.615 23.47 9.69 0.00 1.82
542 5663 5.925969 CAGGTATTGGTTCATGAACAAAACC 59.074 40.000 33.42 31.19 42.85 3.27
551 5672 0.658897 TGAACAAAACCGACTTCCGC 59.341 50.000 0.00 0.00 36.84 5.54
832 5959 4.081695 AGGGTTTTCCTCTATCTCCAGT 57.918 45.455 0.00 0.00 44.06 4.00
833 5960 4.034410 AGGGTTTTCCTCTATCTCCAGTC 58.966 47.826 0.00 0.00 44.06 3.51
835 5962 4.410555 GGGTTTTCCTCTATCTCCAGTCAT 59.589 45.833 0.00 0.00 40.46 3.06
858 6362 8.356657 TCATCAAAAGAAAAAGAATTTAGCCGA 58.643 29.630 0.00 0.00 37.28 5.54
978 6494 0.460284 CGGGCTGATCGTACAAGCTT 60.460 55.000 0.00 0.00 0.00 3.74
979 6495 1.202371 CGGGCTGATCGTACAAGCTTA 60.202 52.381 0.00 0.00 0.00 3.09
981 6497 2.474816 GGCTGATCGTACAAGCTTAGG 58.525 52.381 0.00 0.00 0.00 2.69
982 6498 2.159085 GGCTGATCGTACAAGCTTAGGT 60.159 50.000 0.00 0.00 0.00 3.08
983 6499 2.860735 GCTGATCGTACAAGCTTAGGTG 59.139 50.000 0.00 0.00 0.00 4.00
984 6500 3.428999 GCTGATCGTACAAGCTTAGGTGA 60.429 47.826 0.00 0.00 0.00 4.02
985 6501 4.355437 CTGATCGTACAAGCTTAGGTGAG 58.645 47.826 0.00 0.00 0.00 3.51
986 6502 4.014406 TGATCGTACAAGCTTAGGTGAGA 58.986 43.478 0.00 0.00 0.00 3.27
1072 6588 0.528466 GCTCGCTGGACATCGATTGA 60.528 55.000 0.00 0.00 33.98 2.57
1189 6708 3.020237 GCGGTCCTCCTCTTGTCCC 62.020 68.421 0.00 0.00 0.00 4.46
1322 6848 7.821595 TGTAGTACGTTAAATCCATCAACTG 57.178 36.000 0.00 0.00 0.00 3.16
1323 6849 7.380536 TGTAGTACGTTAAATCCATCAACTGT 58.619 34.615 0.00 0.00 0.00 3.55
1324 6850 8.522003 TGTAGTACGTTAAATCCATCAACTGTA 58.478 33.333 0.00 0.00 0.00 2.74
1415 6949 6.915349 AGATCGCCATCTTTGATAGTACTAC 58.085 40.000 4.31 0.35 35.67 2.73
1416 6950 6.717540 AGATCGCCATCTTTGATAGTACTACT 59.282 38.462 4.31 0.00 35.67 2.57
1417 6951 7.883833 AGATCGCCATCTTTGATAGTACTACTA 59.116 37.037 4.31 0.00 35.67 1.82
1519 7053 4.900684 TGTTGTCCAATACTTCCGATGAA 58.099 39.130 0.00 0.00 0.00 2.57
1607 7147 2.106166 GTGGAAGATGATCTCCAGCCAT 59.894 50.000 12.03 0.00 32.30 4.40
1608 7148 2.371179 TGGAAGATGATCTCCAGCCATC 59.629 50.000 8.81 0.00 37.53 3.51
1609 7149 2.612471 GGAAGATGATCTCCAGCCATCG 60.612 54.545 0.00 0.00 40.99 3.84
1610 7150 0.321021 AGATGATCTCCAGCCATCGC 59.679 55.000 0.00 0.00 40.99 4.58
1611 7151 0.034476 GATGATCTCCAGCCATCGCA 59.966 55.000 0.00 0.00 37.52 5.10
1612 7152 0.471191 ATGATCTCCAGCCATCGCAA 59.529 50.000 0.00 0.00 37.52 4.85
1653 7193 2.463752 ACCACGCTGTTCCCTCTAATA 58.536 47.619 0.00 0.00 0.00 0.98
1705 7265 3.300853 CAGTGTACACGATGACTTTAGCG 59.699 47.826 19.93 0.00 36.20 4.26
1714 7274 1.277326 TGACTTTAGCGCGCATACTG 58.723 50.000 35.10 20.26 0.00 2.74
1849 7418 0.941463 GCACCGATACCTGATCAGCG 60.941 60.000 17.76 14.45 33.73 5.18
1890 7459 3.009916 ACACAAGCCATGGAGATTCTTCT 59.990 43.478 18.40 0.00 33.88 2.85
1931 7500 4.166011 GTGCCAGAATGCGTCGGC 62.166 66.667 12.79 12.79 42.65 5.54
1977 7546 2.027625 CCGTCCTCGCAAAGTGACC 61.028 63.158 0.00 0.00 35.54 4.02
2528 8108 5.929058 AAGATGACATAGAGAGAGCAACA 57.071 39.130 0.00 0.00 0.00 3.33
2575 8155 3.787676 CAACGATCAGCGCGCCAA 61.788 61.111 30.33 17.38 46.04 4.52
2577 8157 4.742201 ACGATCAGCGCGCCAAGT 62.742 61.111 30.33 17.99 46.04 3.16
2578 8158 4.214383 CGATCAGCGCGCCAAGTG 62.214 66.667 30.33 20.03 0.00 3.16
2590 8170 2.047465 CAAGTGGCGCTCTCAGCT 60.047 61.111 7.64 0.00 39.60 4.24
2613 8193 2.126618 CCACGTGTCGCGCTCTAA 60.127 61.111 15.65 0.00 46.11 2.10
2625 8205 3.266282 GCTCTAAGCGCTCTCTTCC 57.734 57.895 12.06 0.00 0.00 3.46
2775 8543 0.677288 TTCCCTTTCGCGAGAGTCAA 59.323 50.000 23.28 13.28 43.69 3.18
2888 8660 2.502213 TTCTTTTCGCGAGAGTCACA 57.498 45.000 9.59 0.00 43.69 3.58
2900 8672 3.309682 CGAGAGTCACAGTTTTGCTTTCA 59.690 43.478 0.00 0.00 0.00 2.69
2901 8673 4.551603 CGAGAGTCACAGTTTTGCTTTCAG 60.552 45.833 0.00 0.00 0.00 3.02
2903 8675 2.099756 AGTCACAGTTTTGCTTTCAGGC 59.900 45.455 0.00 0.00 0.00 4.85
2904 8676 2.098614 TCACAGTTTTGCTTTCAGGCA 58.901 42.857 0.00 0.00 40.74 4.75
2905 8677 2.694628 TCACAGTTTTGCTTTCAGGCAT 59.305 40.909 0.00 0.00 42.09 4.40
2949 8838 1.019278 GCCATGCCTCTCGAAAACGA 61.019 55.000 0.00 0.00 0.00 3.85
2950 8839 1.438651 CCATGCCTCTCGAAAACGAA 58.561 50.000 0.00 0.00 0.00 3.85
2951 8840 1.804151 CCATGCCTCTCGAAAACGAAA 59.196 47.619 0.00 0.00 0.00 3.46
2952 8841 2.225491 CCATGCCTCTCGAAAACGAAAA 59.775 45.455 0.00 0.00 0.00 2.29
2953 8842 3.304391 CCATGCCTCTCGAAAACGAAAAA 60.304 43.478 0.00 0.00 0.00 1.94
2987 8876 2.313267 TTTTTCCTTTCGCGCGAGT 58.687 47.368 32.74 0.00 0.00 4.18
2988 8877 0.233848 TTTTTCCTTTCGCGCGAGTC 59.766 50.000 32.74 0.00 0.00 3.36
2989 8878 0.876777 TTTTCCTTTCGCGCGAGTCA 60.877 50.000 32.74 16.33 0.00 3.41
2990 8879 1.554042 TTTCCTTTCGCGCGAGTCAC 61.554 55.000 32.74 0.00 0.00 3.67
2991 8880 3.827784 CCTTTCGCGCGAGTCACG 61.828 66.667 32.74 15.73 45.66 4.35
2992 8881 3.827784 CTTTCGCGCGAGTCACGG 61.828 66.667 32.74 15.49 42.83 4.94
2993 8882 4.634133 TTTCGCGCGAGTCACGGT 62.634 61.111 32.74 0.00 42.83 4.83
2994 8883 4.634133 TTCGCGCGAGTCACGGTT 62.634 61.111 32.74 0.00 42.83 4.44
2995 8884 4.634133 TCGCGCGAGTCACGGTTT 62.634 61.111 31.40 0.00 42.83 3.27
2996 8885 3.698463 CGCGCGAGTCACGGTTTT 61.698 61.111 28.94 0.00 42.83 2.43
2997 8886 2.127758 GCGCGAGTCACGGTTTTG 60.128 61.111 12.10 0.00 42.83 2.44
2998 8887 2.127758 CGCGAGTCACGGTTTTGC 60.128 61.111 0.00 0.00 42.83 3.68
2999 8888 2.594962 CGCGAGTCACGGTTTTGCT 61.595 57.895 0.00 0.00 42.83 3.91
3000 8889 1.647084 GCGAGTCACGGTTTTGCTT 59.353 52.632 0.00 0.00 42.83 3.91
3001 8890 0.384353 GCGAGTCACGGTTTTGCTTC 60.384 55.000 0.00 0.00 42.83 3.86
3002 8891 0.234884 CGAGTCACGGTTTTGCTTCC 59.765 55.000 0.00 0.00 38.46 3.46
3007 8896 4.398598 CGGTTTTGCTTCCGCGGG 62.399 66.667 27.83 11.74 40.28 6.13
3008 8897 4.050934 GGTTTTGCTTCCGCGGGG 62.051 66.667 27.83 19.42 39.65 5.73
3009 8898 4.050934 GTTTTGCTTCCGCGGGGG 62.051 66.667 27.83 19.04 39.65 5.40
3037 8926 4.725758 GCTTTAGCAAGCGTCACG 57.274 55.556 0.00 0.00 46.06 4.35
3038 8927 1.132640 GCTTTAGCAAGCGTCACGG 59.867 57.895 0.00 0.00 46.06 4.94
3039 8928 1.132640 CTTTAGCAAGCGTCACGGC 59.867 57.895 0.00 0.00 0.00 5.68
3040 8929 2.240612 CTTTAGCAAGCGTCACGGCC 62.241 60.000 0.00 0.00 0.00 6.13
3165 9062 1.301716 GCCGTGCCTCTCAGAAACA 60.302 57.895 0.00 0.00 0.00 2.83
3262 9388 4.357947 GAGAGTCACGGCCGTGCA 62.358 66.667 45.55 32.86 45.04 4.57
3385 9634 1.228657 GCGTGCCTCTTTCGGAAAGT 61.229 55.000 25.21 0.00 39.52 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 5160 2.225467 GGCAGAGCTCAACACTTCTTT 58.775 47.619 17.77 0.00 0.00 2.52
73 5163 0.871057 GTGGCAGAGCTCAACACTTC 59.129 55.000 17.77 0.00 0.00 3.01
84 5174 2.037772 AGAACTAACCACAGTGGCAGAG 59.962 50.000 20.48 15.76 42.67 3.35
107 5197 4.323417 ACTGATTCGTGGTGCTAATTTCA 58.677 39.130 0.00 0.00 0.00 2.69
117 5207 4.330944 TTGTAAGTGACTGATTCGTGGT 57.669 40.909 0.00 0.00 0.00 4.16
150 5240 3.521560 TGAAGTGTTGTCGATAGCCATC 58.478 45.455 0.00 0.00 0.00 3.51
185 5275 3.614588 GAAAAAGCACCACGTTGTAGAC 58.385 45.455 0.00 0.00 0.00 2.59
192 5282 1.002900 CATCACGAAAAAGCACCACGT 60.003 47.619 0.00 0.00 37.68 4.49
195 5285 3.490078 GGAAACATCACGAAAAAGCACCA 60.490 43.478 0.00 0.00 0.00 4.17
196 5286 3.049912 GGAAACATCACGAAAAAGCACC 58.950 45.455 0.00 0.00 0.00 5.01
197 5287 3.730715 CAGGAAACATCACGAAAAAGCAC 59.269 43.478 0.00 0.00 0.00 4.40
223 5314 0.459237 CTCCTGCTGGAACTGTAGCG 60.459 60.000 13.89 0.00 42.66 4.26
236 5327 2.899339 GCGATGGGAAGCTCCTGC 60.899 66.667 0.00 0.00 36.57 4.85
238 5329 2.586792 GTGCGATGGGAAGCTCCT 59.413 61.111 0.00 0.00 36.57 3.69
283 5374 4.776322 TGAGCCGGTCCATTGCGG 62.776 66.667 1.90 0.00 0.00 5.69
298 5389 0.040646 ACAGGATACACCCCGACTGA 59.959 55.000 0.00 0.00 40.05 3.41
321 5412 2.464459 CGGCAAATGGACGCTCCTC 61.464 63.158 5.77 0.00 43.96 3.71
365 5480 6.489787 GCCTAAAGCACGCAAGGTATCTTG 62.490 50.000 11.61 11.61 46.07 3.02
384 5499 1.906105 AACGGGGATTCAAGCGCCTA 61.906 55.000 2.29 0.00 36.31 3.93
391 5506 0.608035 GAGCACCAACGGGGATTCAA 60.608 55.000 2.06 0.00 41.15 2.69
420 5537 5.478679 AGCTATTAGATCACGGCTTGTCTAT 59.521 40.000 0.00 0.00 0.00 1.98
449 5566 2.925306 GCGACTAAGCGAGAAGACCAAA 60.925 50.000 0.00 0.00 0.00 3.28
451 5568 0.170561 GCGACTAAGCGAGAAGACCA 59.829 55.000 0.00 0.00 0.00 4.02
504 5621 9.896263 GAACCAATACCTGTTCGTTTTTAATTA 57.104 29.630 0.00 0.00 32.40 1.40
520 5641 4.920927 CGGTTTTGTTCATGAACCAATACC 59.079 41.667 30.66 29.32 42.27 2.73
521 5642 5.627780 GTCGGTTTTGTTCATGAACCAATAC 59.372 40.000 30.66 25.11 42.27 1.89
542 5663 9.763465 TTTTTAATCTATAAAAAGCGGAAGTCG 57.237 29.630 2.83 0.00 35.63 4.18
790 5917 1.070289 ACCTTTCCACGACAAGGACTC 59.930 52.381 4.94 0.00 42.11 3.36
832 5959 8.356657 TCGGCTAAATTCTTTTTCTTTTGATGA 58.643 29.630 0.00 0.00 0.00 2.92
833 5960 8.519492 TCGGCTAAATTCTTTTTCTTTTGATG 57.481 30.769 0.00 0.00 0.00 3.07
835 5962 7.537306 CGATCGGCTAAATTCTTTTTCTTTTGA 59.463 33.333 7.38 0.00 0.00 2.69
858 6362 2.660670 ACTCCTCCTATTCGTCCGAT 57.339 50.000 0.00 0.00 0.00 4.18
1102 6618 2.012051 GCCAATGGGAACGACGAGAAT 61.012 52.381 0.00 0.00 35.59 2.40
1184 6703 2.447572 TGCTGGTGGTGAGGGACA 60.448 61.111 0.00 0.00 0.00 4.02
1189 6708 2.348998 GTCCCTGCTGGTGGTGAG 59.651 66.667 9.00 0.00 34.77 3.51
1350 6876 2.033299 CCTTGCTGCGTTATATGTTGGG 59.967 50.000 0.00 0.00 0.00 4.12
1415 6949 7.220683 CAGGCAACCGATCACAAATTTATTTAG 59.779 37.037 0.00 0.00 37.17 1.85
1416 6950 7.032580 CAGGCAACCGATCACAAATTTATTTA 58.967 34.615 0.00 0.00 37.17 1.40
1417 6951 5.868801 CAGGCAACCGATCACAAATTTATTT 59.131 36.000 0.00 0.00 37.17 1.40
1519 7053 6.770785 TGAGTTTGTAGGTCAGCAACTTTATT 59.229 34.615 0.00 0.00 30.23 1.40
1562 7096 3.248602 GCGACAGTGAATTCAGAGTTTGT 59.751 43.478 8.80 8.53 0.00 2.83
1607 7147 0.179004 ACCATGGTTTCACCTTGCGA 60.179 50.000 13.00 0.00 40.83 5.10
1608 7148 1.529226 TACCATGGTTTCACCTTGCG 58.471 50.000 25.38 0.00 40.83 4.85
1609 7149 2.231235 CCTTACCATGGTTTCACCTTGC 59.769 50.000 25.38 0.00 40.83 4.01
1610 7150 3.761897 TCCTTACCATGGTTTCACCTTG 58.238 45.455 25.38 3.75 41.56 3.61
1611 7151 4.675063 ATCCTTACCATGGTTTCACCTT 57.325 40.909 25.38 0.00 39.58 3.50
1612 7152 4.079958 GGTATCCTTACCATGGTTTCACCT 60.080 45.833 25.38 6.74 46.24 4.00
1653 7193 9.739276 TTCTTATGTCTTCCATTGTCTGTAAAT 57.261 29.630 0.00 0.00 34.86 1.40
1675 7222 4.982916 GTCATCGTGTACACTGACTTTCTT 59.017 41.667 28.19 10.53 35.14 2.52
1714 7274 3.396560 ACAACCAAGTAACGGTAGAAGC 58.603 45.455 0.00 0.00 34.99 3.86
1849 7418 0.599204 TGGTTCCGTTGCTTCGTCTC 60.599 55.000 0.00 0.00 0.00 3.36
1931 7500 1.655654 CACTATGAGCTCGTCGCCG 60.656 63.158 12.83 2.48 40.39 6.46
1932 7501 1.946650 GCACTATGAGCTCGTCGCC 60.947 63.158 12.83 0.00 40.39 5.54
1933 7502 1.226688 TGCACTATGAGCTCGTCGC 60.227 57.895 12.83 14.06 39.57 5.19
2002 7571 2.113243 GAAGGGGAGCTGTTGGTCGT 62.113 60.000 0.00 0.00 41.26 4.34
2499 8079 8.314021 TGCTCTCTCTATGTCATCTTTGTTTTA 58.686 33.333 0.00 0.00 0.00 1.52
2500 8080 7.164122 TGCTCTCTCTATGTCATCTTTGTTTT 58.836 34.615 0.00 0.00 0.00 2.43
2501 8081 6.705302 TGCTCTCTCTATGTCATCTTTGTTT 58.295 36.000 0.00 0.00 0.00 2.83
2502 8082 6.291648 TGCTCTCTCTATGTCATCTTTGTT 57.708 37.500 0.00 0.00 0.00 2.83
2503 8083 5.929058 TGCTCTCTCTATGTCATCTTTGT 57.071 39.130 0.00 0.00 0.00 2.83
2504 8084 6.104665 TGTTGCTCTCTCTATGTCATCTTTG 58.895 40.000 0.00 0.00 0.00 2.77
2505 8085 6.291648 TGTTGCTCTCTCTATGTCATCTTT 57.708 37.500 0.00 0.00 0.00 2.52
2506 8086 5.929058 TGTTGCTCTCTCTATGTCATCTT 57.071 39.130 0.00 0.00 0.00 2.40
2507 8087 5.421693 ACTTGTTGCTCTCTCTATGTCATCT 59.578 40.000 0.00 0.00 0.00 2.90
2508 8088 5.659463 ACTTGTTGCTCTCTCTATGTCATC 58.341 41.667 0.00 0.00 0.00 2.92
2509 8089 5.674052 ACTTGTTGCTCTCTCTATGTCAT 57.326 39.130 0.00 0.00 0.00 3.06
2510 8090 5.474578 AACTTGTTGCTCTCTCTATGTCA 57.525 39.130 0.00 0.00 0.00 3.58
2511 8091 6.034044 CGTTAACTTGTTGCTCTCTCTATGTC 59.966 42.308 3.71 0.00 0.00 3.06
2512 8092 5.864474 CGTTAACTTGTTGCTCTCTCTATGT 59.136 40.000 3.71 0.00 0.00 2.29
2513 8093 6.093404 TCGTTAACTTGTTGCTCTCTCTATG 58.907 40.000 3.71 0.00 0.00 2.23
2514 8094 6.268825 TCGTTAACTTGTTGCTCTCTCTAT 57.731 37.500 3.71 0.00 0.00 1.98
2515 8095 5.700722 TCGTTAACTTGTTGCTCTCTCTA 57.299 39.130 3.71 0.00 0.00 2.43
2516 8096 4.551388 CTCGTTAACTTGTTGCTCTCTCT 58.449 43.478 3.71 0.00 0.00 3.10
2517 8097 3.122111 GCTCGTTAACTTGTTGCTCTCTC 59.878 47.826 3.71 0.00 0.00 3.20
2528 8108 1.711206 GAAGGAGCGCTCGTTAACTT 58.289 50.000 36.96 28.89 37.75 2.66
2572 8152 3.123620 GCTGAGAGCGCCACTTGG 61.124 66.667 2.29 2.69 38.53 3.61
2697 8316 4.553330 ATCGAAAAGCTAAGGAAGACCA 57.447 40.909 0.00 0.00 38.94 4.02
2758 8520 0.737715 CCTTGACTCTCGCGAAAGGG 60.738 60.000 23.06 10.73 46.71 3.95
2872 8644 2.218953 AACTGTGACTCTCGCGAAAA 57.781 45.000 11.33 0.00 0.00 2.29
2903 8675 2.407090 TCTCGTGAAAGCACACTCATG 58.593 47.619 0.00 0.00 45.41 3.07
2904 8676 2.036475 ACTCTCGTGAAAGCACACTCAT 59.964 45.455 0.00 0.00 45.41 2.90
2905 8677 1.409064 ACTCTCGTGAAAGCACACTCA 59.591 47.619 0.00 0.00 45.41 3.41
2969 8858 0.233848 GACTCGCGCGAAAGGAAAAA 59.766 50.000 33.99 8.02 0.00 1.94
2970 8859 0.876777 TGACTCGCGCGAAAGGAAAA 60.877 50.000 33.99 12.06 0.00 2.29
2971 8860 1.300311 TGACTCGCGCGAAAGGAAA 60.300 52.632 33.99 13.16 0.00 3.13
2972 8861 2.019951 GTGACTCGCGCGAAAGGAA 61.020 57.895 33.99 14.63 0.00 3.36
2973 8862 2.430244 GTGACTCGCGCGAAAGGA 60.430 61.111 33.99 14.86 0.00 3.36
2980 8869 2.127758 CAAAACCGTGACTCGCGC 60.128 61.111 0.00 0.00 35.94 6.86
2981 8870 2.101209 AAGCAAAACCGTGACTCGCG 62.101 55.000 0.00 0.00 38.35 5.87
2982 8871 0.384353 GAAGCAAAACCGTGACTCGC 60.384 55.000 0.00 0.00 38.35 5.03
2983 8872 0.234884 GGAAGCAAAACCGTGACTCG 59.765 55.000 0.00 0.00 39.52 4.18
2984 8873 0.234884 CGGAAGCAAAACCGTGACTC 59.765 55.000 0.00 0.00 43.53 3.36
2985 8874 2.317230 CGGAAGCAAAACCGTGACT 58.683 52.632 0.00 0.00 43.53 3.41
2986 8875 4.914291 CGGAAGCAAAACCGTGAC 57.086 55.556 0.00 0.00 43.53 3.67
3021 8910 1.132640 GCCGTGACGCTTGCTAAAG 59.867 57.895 0.00 0.00 36.41 1.85
3022 8911 2.322081 GGCCGTGACGCTTGCTAAA 61.322 57.895 0.00 0.00 0.00 1.85
3023 8912 2.740826 GGCCGTGACGCTTGCTAA 60.741 61.111 0.00 0.00 0.00 3.09
3065 8959 6.183359 GCGAAAGAAAGAAAAACAGAAAACGT 60.183 34.615 0.00 0.00 0.00 3.99
3239 9365 1.810532 GGCCGTGACTCTCGAGAAT 59.189 57.895 17.36 6.27 0.00 2.40
3306 9443 0.250338 GCAAAACCGTGACTCTCCCT 60.250 55.000 0.00 0.00 0.00 4.20
3308 9445 1.531578 GAAGCAAAACCGTGACTCTCC 59.468 52.381 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.