Multiple sequence alignment - TraesCS3A01G125100

Loading Multiple Alignment...

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 TraesCS3A01G125100 chr3A 100.000 3827 0 0 1 3827 100880822 100876996 0.000000e+00 7068.0
1 TraesCS3A01G125100 chr3A 91.143 2676 186 22 242 2883 100843897 100841239 0.000000e+00 3581.0
2 TraesCS3A01G125100 chr3A 80.813 1944 325 35 975 2888 100976699 100974774 0.000000e+00 1480.0
3 TraesCS3A01G125100 chr3A 88.585 841 63 17 2864 3685 100840598 100839772 0.000000e+00 990.0
4 TraesCS3A01G125100 chr3A 97.222 36 1 0 3605 3640 547368888 547368853 1.150000e-05 62.1
5 TraesCS3A01G125100 chr3D 91.800 2805 178 20 114 2883 84499085 84496298 0.000000e+00 3858.0
6 TraesCS3A01G125100 chr3D 88.116 1969 168 29 946 2883 84565056 84563123 0.000000e+00 2279.0
7 TraesCS3A01G125100 chr3D 88.517 836 64 19 2870 3685 84495652 84494829 0.000000e+00 983.0
8 TraesCS3A01G125100 chr3D 85.115 524 70 8 1019 1538 84112450 84111931 2.620000e-146 529.0
9 TraesCS3A01G125100 chr3D 86.558 491 35 4 1 490 84503294 84502834 2.640000e-141 512.0
10 TraesCS3A01G125100 chr3D 86.165 412 30 12 3291 3685 84562595 84562194 1.640000e-113 420.0
11 TraesCS3A01G125100 chr3D 97.826 92 2 0 488 579 84502604 84502513 3.960000e-35 159.0
12 TraesCS3A01G125100 chr3D 94.737 76 4 0 1 76 84499161 84499086 6.720000e-23 119.0
13 TraesCS3A01G125100 chr3B 91.074 2812 185 26 114 2883 132007664 132010451 0.000000e+00 3742.0
14 TraesCS3A01G125100 chr3B 90.893 2811 180 27 114 2883 132904121 132901346 0.000000e+00 3703.0
15 TraesCS3A01G125100 chr3B 90.703 2291 149 29 1548 3827 133204220 133206457 0.000000e+00 2992.0
16 TraesCS3A01G125100 chr3B 88.953 1738 141 22 1178 2883 132089864 132091582 0.000000e+00 2098.0
17 TraesCS3A01G125100 chr3B 83.232 1974 269 43 943 2891 132005504 132007440 0.000000e+00 1755.0
18 TraesCS3A01G125100 chr3B 83.023 1932 272 38 988 2891 132906248 132904345 0.000000e+00 1700.0
19 TraesCS3A01G125100 chr3B 88.999 1009 96 6 534 1539 133203135 133204131 0.000000e+00 1234.0
20 TraesCS3A01G125100 chr3B 86.277 838 64 24 2864 3685 132092225 132093027 0.000000e+00 863.0
21 TraesCS3A01G125100 chr3B 83.750 640 69 20 3066 3685 132901167 132900543 1.190000e-159 573.0
22 TraesCS3A01G125100 chr3B 86.015 522 69 4 1019 1538 132518612 132519131 1.200000e-154 556.0
23 TraesCS3A01G125100 chr3B 86.069 524 33 14 3175 3685 132011582 132012078 9.420000e-146 527.0
24 TraesCS3A01G125100 chr3B 90.661 257 21 3 2864 3118 132011094 132011349 4.740000e-89 339.0
25 TraesCS3A01G125100 chr3B 79.650 457 63 17 1 449 133202276 133202710 6.210000e-78 302.0
26 TraesCS3A01G125100 chr3B 96.053 76 3 0 1 76 132904197 132904122 1.440000e-24 124.0
27 TraesCS3A01G125100 chr3B 94.737 76 4 0 1 76 132007588 132007663 6.720000e-23 119.0


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 TraesCS3A01G125100 chr3A 100876996 100880822 3826 True 7068.000000 7068 100.000000 1 3827 1 chr3A.!!$R1 3826
1 TraesCS3A01G125100 chr3A 100839772 100843897 4125 True 2285.500000 3581 89.864000 242 3685 2 chr3A.!!$R4 3443
2 TraesCS3A01G125100 chr3A 100974774 100976699 1925 True 1480.000000 1480 80.813000 975 2888 1 chr3A.!!$R2 1913
3 TraesCS3A01G125100 chr3D 84562194 84565056 2862 True 1349.500000 2279 87.140500 946 3685 2 chr3D.!!$R3 2739
4 TraesCS3A01G125100 chr3D 84494829 84503294 8465 True 1126.200000 3858 91.887600 1 3685 5 chr3D.!!$R2 3684
5 TraesCS3A01G125100 chr3D 84111931 84112450 519 True 529.000000 529 85.115000 1019 1538 1 chr3D.!!$R1 519
6 TraesCS3A01G125100 chr3B 132900543 132906248 5705 True 1525.000000 3703 88.429750 1 3685 4 chr3B.!!$R1 3684
7 TraesCS3A01G125100 chr3B 133202276 133206457 4181 False 1509.333333 2992 86.450667 1 3827 3 chr3B.!!$F4 3826
8 TraesCS3A01G125100 chr3B 132089864 132093027 3163 False 1480.500000 2098 87.615000 1178 3685 2 chr3B.!!$F3 2507
9 TraesCS3A01G125100 chr3B 132005504 132012078 6574 False 1296.400000 3742 89.154600 1 3685 5 chr3B.!!$F2 3684
10 TraesCS3A01G125100 chr3B 132518612 132519131 519 False 556.000000 556 86.015000 1019 1538 1 chr3B.!!$F1 519

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
832 5371 0.319469 TTGCATCGTCAGCTCGTCAA 60.319 50.0 0.00 0.0 0.00 3.18 F
1891 6539 0.103755 TGAGCTCATCACGATCAGGC 59.896 55.0 13.74 0.0 31.12 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2156 6805 0.250727 TTGCAAGTACTGGGCCTCAC 60.251 55.0 15.03 0.0 0.0 3.51 R
3042 8494 0.311790 ACAGCAATGAAACCGCACAG 59.688 50.0 0.00 0.0 0.0 3.66 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
47 4206 2.048222 GCTGCACGACTAGCCACA 60.048 61.111 0.00 0.00 33.89 4.17
76 4235 2.168728 GAGGTGTAGGACAATGACTCCC 59.831 54.545 0.00 0.00 0.00 4.30
77 4236 1.906574 GGTGTAGGACAATGACTCCCA 59.093 52.381 0.00 0.00 0.00 4.37
78 4237 2.505819 GGTGTAGGACAATGACTCCCAT 59.494 50.000 0.00 0.00 36.99 4.00
79 4238 3.535561 GTGTAGGACAATGACTCCCATG 58.464 50.000 0.00 0.00 35.24 3.66
80 4239 3.197766 GTGTAGGACAATGACTCCCATGA 59.802 47.826 0.00 0.00 35.24 3.07
81 4240 4.040047 TGTAGGACAATGACTCCCATGAT 58.960 43.478 0.00 0.00 35.24 2.45
82 4241 3.572632 AGGACAATGACTCCCATGATG 57.427 47.619 0.00 0.00 35.24 3.07
84 4243 2.092212 GGACAATGACTCCCATGATGGT 60.092 50.000 11.09 0.00 35.17 3.55
85 4244 2.947652 GACAATGACTCCCATGATGGTG 59.052 50.000 11.09 5.48 35.17 4.17
86 4245 1.679680 CAATGACTCCCATGATGGTGC 59.320 52.381 11.09 0.00 35.17 5.01
88 4247 1.524621 GACTCCCATGATGGTGCCG 60.525 63.158 11.09 0.00 35.17 5.69
90 4249 4.504596 TCCCATGATGGTGCCGCC 62.505 66.667 11.09 0.00 35.17 6.13
237 4398 5.502606 GCTGCGGTCTTGTATTAAATTCTC 58.497 41.667 0.00 0.00 0.00 2.87
454 4654 8.836413 CACTAACAAAACTCTGAAAGGATACAA 58.164 33.333 0.00 0.00 41.41 2.41
607 4822 2.676839 GACAAGTCAGCATCAGACATGG 59.323 50.000 0.00 0.00 38.59 3.66
682 4898 1.559682 GGTGGTTAATCTGAGCCCTCA 59.440 52.381 0.00 0.00 38.06 3.86
693 4909 2.169978 CTGAGCCCTCAATGTCTGATCA 59.830 50.000 0.00 0.00 39.39 2.92
796 5335 1.669115 CGTCACTGGCAAGAGGTGG 60.669 63.158 0.00 0.00 0.00 4.61
832 5371 0.319469 TTGCATCGTCAGCTCGTCAA 60.319 50.000 0.00 0.00 0.00 3.18
841 5380 2.221981 GTCAGCTCGTCAACTTTCCTTG 59.778 50.000 0.00 0.00 0.00 3.61
890 5433 4.651778 ACACACACTATAGTTGCCATTGT 58.348 39.130 1.56 3.65 0.00 2.71
901 5444 2.756760 GTTGCCATTGTGACCATCATCT 59.243 45.455 0.00 0.00 0.00 2.90
913 5456 3.875727 GACCATCATCTGATTGTGTCCAG 59.124 47.826 1.97 0.00 31.52 3.86
916 5459 2.981898 TCATCTGATTGTGTCCAGCAG 58.018 47.619 0.00 0.00 0.00 4.24
920 5463 2.568509 TCTGATTGTGTCCAGCAGATCA 59.431 45.455 0.00 0.00 32.36 2.92
944 5487 2.645838 ATCTTGCCAGTGTCACTGTT 57.354 45.000 27.20 6.20 44.50 3.16
1011 5556 1.860950 CGATTAGCCATGACCTTCACG 59.139 52.381 0.00 0.00 0.00 4.35
1095 5640 2.123726 GGGCACACCATCCCCATC 60.124 66.667 0.00 0.00 38.70 3.51
1318 5863 3.054065 GGATCTTCTCCCCAACTTCATGT 60.054 47.826 0.00 0.00 38.19 3.21
1331 5876 4.277515 ACTTCATGTATGCCATCGCTAT 57.722 40.909 0.00 0.00 35.36 2.97
1372 5917 1.140452 CATACCTCCATGAGCAGCAGT 59.860 52.381 0.00 0.00 0.00 4.40
1503 6048 2.304761 GTCCCTCATCAGGTACAACCAA 59.695 50.000 0.00 0.00 41.95 3.67
1514 6062 3.383505 AGGTACAACCAAAAGAGGCAAAC 59.616 43.478 0.00 0.00 41.95 2.93
1577 6205 4.718961 AGTGCTTTACTTCAACAGTGGAT 58.281 39.130 0.00 0.00 35.67 3.41
1603 6231 6.152831 GGGAAACTAGTGTAAATTGCTTCCAT 59.847 38.462 15.55 0.00 33.06 3.41
1617 6245 4.910195 TGCTTCCATAGAGAAGAAAGCAA 58.090 39.130 5.21 0.00 45.08 3.91
1626 6254 8.341173 CCATAGAGAAGAAAGCAATGAACATAC 58.659 37.037 0.00 0.00 0.00 2.39
1645 6273 7.466746 ACATACAAAATGCTACACCTGAAAT 57.533 32.000 0.00 0.00 0.00 2.17
1746 6386 3.081804 GAGCAAGTTTTTAGGCCAGCTA 58.918 45.455 5.01 0.00 0.00 3.32
1747 6387 3.696548 GAGCAAGTTTTTAGGCCAGCTAT 59.303 43.478 5.01 0.00 0.00 2.97
1749 6389 5.449553 AGCAAGTTTTTAGGCCAGCTATAT 58.550 37.500 5.01 0.00 0.00 0.86
1750 6390 5.532779 AGCAAGTTTTTAGGCCAGCTATATC 59.467 40.000 5.01 0.00 0.00 1.63
1751 6391 5.299279 GCAAGTTTTTAGGCCAGCTATATCA 59.701 40.000 5.01 0.00 0.00 2.15
1753 6393 7.588512 CAAGTTTTTAGGCCAGCTATATCATC 58.411 38.462 5.01 0.00 0.00 2.92
1789 6437 2.423926 TGTCGAAGAAGTCTGCACTC 57.576 50.000 0.00 0.00 39.69 3.51
1842 6490 4.826733 TGCAGGTACATCACTTTTCACAAT 59.173 37.500 0.00 0.00 0.00 2.71
1889 6537 4.317909 CGAAAATGAGCTCATCACGATCAG 60.318 45.833 28.83 11.53 41.91 2.90
1891 6539 0.103755 TGAGCTCATCACGATCAGGC 59.896 55.000 13.74 0.00 31.12 4.85
1893 6541 1.227089 GCTCATCACGATCAGGCGT 60.227 57.895 0.00 0.00 46.88 5.68
2005 6653 1.830477 AGGAGCTGAGAAGTGATGGTC 59.170 52.381 0.00 0.00 0.00 4.02
2025 6673 4.072131 GTCAGGTCATTAACAGCTTCCAA 58.928 43.478 0.00 0.00 0.00 3.53
2028 6676 4.761739 CAGGTCATTAACAGCTTCCAAGAA 59.238 41.667 0.00 0.00 0.00 2.52
2064 6712 3.760684 ACATTGAATCCTTTGAGCAGACC 59.239 43.478 0.00 0.00 0.00 3.85
2085 6733 1.494721 ACAAAGAAGAAGGTCTGGGCA 59.505 47.619 0.00 0.00 0.00 5.36
2111 6759 1.604308 CAATGTGCCTCTGCCACCA 60.604 57.895 0.00 0.00 36.33 4.17
2146 6795 0.889186 GGCCGCAAGAGGAAACAAGA 60.889 55.000 0.00 0.00 43.02 3.02
2156 6805 2.484264 GAGGAAACAAGACGTCAATGGG 59.516 50.000 19.50 4.44 0.00 4.00
2163 6812 1.745489 GACGTCAATGGGTGAGGCC 60.745 63.158 11.55 0.00 44.42 5.19
2214 6863 1.233019 CAGGCTCAGTGGTCTTTGTG 58.767 55.000 0.00 0.00 0.00 3.33
2308 6957 5.127031 AGGAAACCATTTATTTGGGTGATCG 59.873 40.000 0.00 0.00 41.35 3.69
2335 6984 4.081420 CAGGAGCTAAGCTTCCAGAAGTTA 60.081 45.833 0.00 5.98 39.88 2.24
2539 7188 1.923356 TGGGGAGCAGTTTTGGAATC 58.077 50.000 0.00 0.00 0.00 2.52
2547 7196 4.655963 AGCAGTTTTGGAATCAGAAGCTA 58.344 39.130 0.00 0.00 0.00 3.32
2569 7218 2.557924 GTGGTGGATGTGCTGAAAATCA 59.442 45.455 0.00 0.00 0.00 2.57
2636 7285 7.507616 TGAAAAACAGGAGGTTATGGTTACAAT 59.492 33.333 0.00 0.00 39.29 2.71
2637 7286 7.849322 AAAACAGGAGGTTATGGTTACAATT 57.151 32.000 0.00 0.00 39.29 2.32
2638 7287 8.943594 AAAACAGGAGGTTATGGTTACAATTA 57.056 30.769 0.00 0.00 39.29 1.40
2639 7288 7.933215 AACAGGAGGTTATGGTTACAATTAC 57.067 36.000 0.00 0.00 38.15 1.89
2640 7289 7.023171 ACAGGAGGTTATGGTTACAATTACA 57.977 36.000 0.00 0.00 0.00 2.41
2641 7290 7.463431 ACAGGAGGTTATGGTTACAATTACAA 58.537 34.615 0.00 0.00 0.00 2.41
2682 7331 2.026915 TGTGAACACCCTGATGGATGAG 60.027 50.000 2.46 0.00 38.00 2.90
2761 7411 1.283321 AGGCTTTTGATGAGGGAGGTC 59.717 52.381 0.00 0.00 0.00 3.85
2825 7475 3.719924 ACAAGACAAATGCATGTGGTTG 58.280 40.909 23.18 23.18 32.57 3.77
2827 7477 4.039488 ACAAGACAAATGCATGTGGTTGAT 59.961 37.500 28.17 16.21 32.57 2.57
2828 7478 5.243507 ACAAGACAAATGCATGTGGTTGATA 59.756 36.000 28.17 0.00 32.57 2.15
2829 7479 5.314923 AGACAAATGCATGTGGTTGATAC 57.685 39.130 20.95 8.83 32.57 2.24
2830 7480 4.766373 AGACAAATGCATGTGGTTGATACA 59.234 37.500 20.95 0.00 32.57 2.29
2831 7481 5.063180 ACAAATGCATGTGGTTGATACAG 57.937 39.130 20.95 0.00 30.82 2.74
2877 7536 7.946207 TGGTGTGAACATAAAATAAAAGAGCA 58.054 30.769 0.00 0.00 0.00 4.26
2915 8367 5.006386 CCTGTTGTCATTAGAAAGAGCCTT 58.994 41.667 0.00 0.00 0.00 4.35
2976 8428 2.170607 TCCTTGTATTAGGCTCACTGGC 59.829 50.000 0.00 0.00 42.15 4.85
2993 8445 3.743636 CGGGGGCGCGATTGTTTT 61.744 61.111 12.10 0.00 0.00 2.43
3042 8494 4.024556 AGCAATATCAATTGTCTACGCTGC 60.025 41.667 5.13 6.86 43.75 5.25
3056 8509 1.286880 GCTGCTGTGCGGTTTCATT 59.713 52.632 0.00 0.00 37.24 2.57
3059 8512 1.286880 GCTGTGCGGTTTCATTGCT 59.713 52.632 0.00 0.00 0.00 3.91
3074 8527 7.221452 GGTTTCATTGCTGTCAACATAATGATC 59.779 37.037 16.80 13.97 38.22 2.92
3090 8543 7.763528 ACATAATGATCACACAGTCTTCTTCTC 59.236 37.037 0.00 0.00 0.00 2.87
3112 8565 5.819991 TCCAGATGTTATGCTCTCCTTTTT 58.180 37.500 0.00 0.00 0.00 1.94
3126 8579 6.249035 TCTCCTTTTTATTTTGCTACCACG 57.751 37.500 0.00 0.00 0.00 4.94
3157 8611 6.954232 TCAGAGTTAAATAAGGGTTCGGAAT 58.046 36.000 0.00 0.00 0.00 3.01
3218 8847 8.439286 CAAACTGAAACTAAGAGTAAGAGATGC 58.561 37.037 0.00 0.00 0.00 3.91
3237 8867 5.525378 AGATGCTTCGAGGTGAATAATCAAC 59.475 40.000 0.00 0.00 44.01 3.18
3258 8888 3.328050 ACGGAAGAGAAGGAAATGGAACT 59.672 43.478 0.00 0.00 0.00 3.01
3269 8899 3.438781 GGAAATGGAACTCACATAACGCA 59.561 43.478 0.00 0.00 0.00 5.24
3288 8918 7.792374 AACGCACATATGACATTAGAATCTT 57.208 32.000 10.38 0.00 0.00 2.40
3289 8919 8.887036 AACGCACATATGACATTAGAATCTTA 57.113 30.769 10.38 0.00 0.00 2.10
3468 9104 3.628032 TGTTTTGAACGTGCTGGTTGATA 59.372 39.130 0.00 0.00 0.00 2.15
3504 9140 7.116805 GCCAAAATCAATCTAAACCTGAACTTG 59.883 37.037 0.00 0.00 0.00 3.16
3505 9141 8.143835 CCAAAATCAATCTAAACCTGAACTTGT 58.856 33.333 0.00 0.00 0.00 3.16
3506 9142 9.533253 CAAAATCAATCTAAACCTGAACTTGTT 57.467 29.630 0.00 0.00 0.00 2.83
3564 9208 2.677875 CTGGGGGCACAAAGAGGC 60.678 66.667 0.00 0.00 0.00 4.70
3631 9280 5.181748 ACAGATGACTTTCATAGGAAGTGC 58.818 41.667 0.00 0.00 37.20 4.40
3729 9378 3.686916 AAGCTGTAGACTGGAGGAAAC 57.313 47.619 0.00 0.00 0.00 2.78
3747 9396 3.775661 AACAGAACAAACCTGGTTTCG 57.224 42.857 21.49 17.93 33.10 3.46
3751 9400 3.502211 CAGAACAAACCTGGTTTCGCTAT 59.498 43.478 21.49 6.68 33.10 2.97
3765 9414 0.580578 CGCTATGCACTGATGACTGC 59.419 55.000 0.00 0.00 0.00 4.40
3791 9440 5.826737 CCTTCATCTGGAGCATTCTGTAAAT 59.173 40.000 0.00 0.00 0.00 1.40
3812 9461 3.445008 TCATATGGATAGCCTCCTCACC 58.555 50.000 2.13 0.00 45.21 4.02
3813 9462 3.078153 TCATATGGATAGCCTCCTCACCT 59.922 47.826 2.13 0.00 45.21 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 4206 1.349067 GTCCTACACCTCCACCAACT 58.651 55.000 0.00 0.00 0.00 3.16
59 4218 3.449918 TCATGGGAGTCATTGTCCTACA 58.550 45.455 0.00 0.00 32.92 2.74
106 4265 1.987855 CCCTAGTTGCTCCCACGGA 60.988 63.158 0.00 0.00 0.00 4.69
109 4268 1.627297 CCCTCCCTAGTTGCTCCCAC 61.627 65.000 0.00 0.00 0.00 4.61
166 4326 1.438814 GCCATGTACAATGCCTGGC 59.561 57.895 18.88 18.88 44.91 4.85
192 4352 5.551760 CGATTAGCATGAAACAAGGTCTT 57.448 39.130 0.00 0.00 0.00 3.01
276 4437 3.571571 CTTCATGCACACAGACCAAATG 58.428 45.455 0.00 0.00 0.00 2.32
402 4563 3.075148 GCTAAAAGGAACTCCCAGTGAC 58.925 50.000 0.00 0.00 38.49 3.67
454 4654 6.015434 GTGATAGTGGGTGGAATTTTCTTGTT 60.015 38.462 0.00 0.00 0.00 2.83
607 4822 6.790232 TTTTTACAGGATTTGGATGATCCC 57.210 37.500 9.36 0.00 43.36 3.85
682 4898 2.158652 CCAGGCCATCTGATCAGACATT 60.159 50.000 27.37 9.59 46.18 2.71
693 4909 0.467384 CGTCAGAATCCAGGCCATCT 59.533 55.000 5.01 0.00 0.00 2.90
722 4938 3.552875 AGCCATGTGGATGAATCTTCAG 58.447 45.455 2.55 0.00 36.75 3.02
762 5301 1.338011 TGACGCATGCTCTCACATCAA 60.338 47.619 17.13 0.00 0.00 2.57
796 5335 1.919918 GCAACAGCGTATCAAATTGGC 59.080 47.619 0.00 0.00 0.00 4.52
869 5410 4.694982 TCACAATGGCAACTATAGTGTGTG 59.305 41.667 6.06 13.03 36.96 3.82
878 5421 3.431673 TGATGGTCACAATGGCAACTA 57.568 42.857 0.00 0.00 37.61 2.24
890 5433 3.263937 TGGACACAATCAGATGATGGTCA 59.736 43.478 17.22 5.84 36.60 4.02
901 5444 3.275999 CATGATCTGCTGGACACAATCA 58.724 45.455 0.00 0.00 0.00 2.57
916 5459 3.474600 ACACTGGCAAGATAGCATGATC 58.525 45.455 0.00 0.00 35.83 2.92
920 5463 2.238144 AGTGACACTGGCAAGATAGCAT 59.762 45.455 7.47 0.00 35.83 3.79
944 5487 1.971357 GGAGTCAGTCAAACTGGGAGA 59.029 52.381 7.21 0.00 45.94 3.71
966 5509 4.771903 TGTTGTAGCAAAAGTACTGGTGA 58.228 39.130 9.66 0.00 0.00 4.02
1128 5673 0.392060 TGATGAAGCTGACATGCGCT 60.392 50.000 9.73 0.00 38.30 5.92
1134 5679 0.950555 GCGTGGTGATGAAGCTGACA 60.951 55.000 0.00 0.00 0.00 3.58
1201 5746 3.702048 CCGAACTTCCAGGCCCGA 61.702 66.667 0.00 0.00 0.00 5.14
1302 5847 2.092429 GGCATACATGAAGTTGGGGAGA 60.092 50.000 0.00 0.00 0.00 3.71
1318 5863 2.613725 CCTGAAGCATAGCGATGGCATA 60.614 50.000 8.97 0.00 43.41 3.14
1503 6048 3.018423 ACTCACAAGGTTTGCCTCTTT 57.982 42.857 0.00 0.00 46.33 2.52
1577 6205 5.475564 GGAAGCAATTTACACTAGTTTCCCA 59.524 40.000 0.00 0.00 34.67 4.37
1603 6231 8.846943 TTGTATGTTCATTGCTTTCTTCTCTA 57.153 30.769 0.00 0.00 0.00 2.43
1617 6245 6.658816 TCAGGTGTAGCATTTTGTATGTTCAT 59.341 34.615 0.00 0.00 0.00 2.57
1626 6254 7.712264 TTTTCATTTCAGGTGTAGCATTTTG 57.288 32.000 0.00 0.00 0.00 2.44
1680 6313 8.140628 TGTGATGCAGTGTAAATTACATGTTTT 58.859 29.630 9.22 1.74 41.34 2.43
1746 6386 7.933577 ACAAACGTCAACCAGATATGATGATAT 59.066 33.333 0.00 0.00 36.34 1.63
1747 6387 7.272244 ACAAACGTCAACCAGATATGATGATA 58.728 34.615 0.00 0.00 36.34 2.15
1749 6389 5.487433 ACAAACGTCAACCAGATATGATGA 58.513 37.500 0.00 0.00 36.34 2.92
1750 6390 5.500771 CGACAAACGTCAACCAGATATGATG 60.501 44.000 0.00 0.00 38.30 3.07
1751 6391 4.566759 CGACAAACGTCAACCAGATATGAT 59.433 41.667 0.00 0.00 37.22 2.45
1753 6393 3.924073 TCGACAAACGTCAACCAGATATG 59.076 43.478 0.00 0.00 43.13 1.78
1789 6437 8.661257 TGGTCGTAGTTGTTTCAAATACATATG 58.339 33.333 16.28 0.00 0.00 1.78
1891 6539 2.416972 GCTCTAGTGGTGTAGGGAAACG 60.417 54.545 0.00 0.00 0.00 3.60
1893 6541 2.832129 CAGCTCTAGTGGTGTAGGGAAA 59.168 50.000 14.34 0.00 0.00 3.13
2005 6653 4.326826 TCTTGGAAGCTGTTAATGACCTG 58.673 43.478 0.00 0.00 0.00 4.00
2025 6673 6.114187 TCAATGTACAATGTCTCCAGTTCT 57.886 37.500 10.64 0.00 0.00 3.01
2028 6676 5.882557 GGATTCAATGTACAATGTCTCCAGT 59.117 40.000 20.30 0.00 0.00 4.00
2064 6712 1.882623 GCCCAGACCTTCTTCTTTGTG 59.117 52.381 0.00 0.00 0.00 3.33
2085 6733 2.173519 CAGAGGCACATTGGTCCAATT 58.826 47.619 14.80 0.00 31.05 2.32
2111 6759 2.151202 CGGCCATAGTGTTGTTGTCTT 58.849 47.619 2.24 0.00 0.00 3.01
2146 6795 2.351276 GGCCTCACCCATTGACGT 59.649 61.111 0.00 0.00 0.00 4.34
2156 6805 0.250727 TTGCAAGTACTGGGCCTCAC 60.251 55.000 15.03 0.00 0.00 3.51
2163 6812 2.161855 TCAAGCCATTGCAAGTACTGG 58.838 47.619 11.71 11.71 41.13 4.00
2263 6912 0.980423 GAGGCTTCAAGTCCCAGTCT 59.020 55.000 0.00 0.00 0.00 3.24
2335 6984 1.448540 CGTCTGCGAGCCATTCCTT 60.449 57.895 0.00 0.00 41.33 3.36
2439 7088 2.740714 GCAGTGCGTCACGAATCCC 61.741 63.158 0.00 0.00 39.64 3.85
2461 7110 2.912956 TGCCCTCTATTGTTGAGTTCCT 59.087 45.455 0.00 0.00 0.00 3.36
2539 7188 2.625737 CACATCCACCACTAGCTTCTG 58.374 52.381 0.00 0.00 0.00 3.02
2547 7196 2.363306 TTTTCAGCACATCCACCACT 57.637 45.000 0.00 0.00 0.00 4.00
2569 7218 0.401395 TTCACTCCAACCTCCACCCT 60.401 55.000 0.00 0.00 0.00 4.34
2636 7285 5.569630 GCTTTCTCCACCTCATCTCTTGTAA 60.570 44.000 0.00 0.00 0.00 2.41
2637 7286 4.081420 GCTTTCTCCACCTCATCTCTTGTA 60.081 45.833 0.00 0.00 0.00 2.41
2638 7287 3.307339 GCTTTCTCCACCTCATCTCTTGT 60.307 47.826 0.00 0.00 0.00 3.16
2639 7288 3.055240 AGCTTTCTCCACCTCATCTCTTG 60.055 47.826 0.00 0.00 0.00 3.02
2640 7289 3.055240 CAGCTTTCTCCACCTCATCTCTT 60.055 47.826 0.00 0.00 0.00 2.85
2641 7290 2.500910 CAGCTTTCTCCACCTCATCTCT 59.499 50.000 0.00 0.00 0.00 3.10
2761 7411 4.012374 AGCCTTATGTTGTCATGTGAAGG 58.988 43.478 0.00 0.00 38.94 3.46
2798 7448 2.791383 TGCATTTGTCTTGTTTCCCG 57.209 45.000 0.00 0.00 0.00 5.14
2825 7475 6.702716 AAGAGAGCTTACTACCACTGTATC 57.297 41.667 0.00 0.00 31.07 2.24
2827 7477 6.912951 AAAAGAGAGCTTACTACCACTGTA 57.087 37.500 0.00 0.00 32.98 2.74
2828 7478 5.810080 AAAAGAGAGCTTACTACCACTGT 57.190 39.130 0.00 0.00 32.98 3.55
2956 8408 2.565841 GCCAGTGAGCCTAATACAAGG 58.434 52.381 0.00 0.00 39.87 3.61
2976 8428 3.743636 AAAACAATCGCGCCCCCG 61.744 61.111 0.00 0.00 37.57 5.73
2981 8433 4.258471 CGTTTAATCTCAAAACAATCGCGC 60.258 41.667 0.00 0.00 36.78 6.86
2984 8436 6.021596 CCCTCGTTTAATCTCAAAACAATCG 58.978 40.000 0.00 0.00 36.78 3.34
2993 8445 4.627284 TTTGGACCCTCGTTTAATCTCA 57.373 40.909 0.00 0.00 0.00 3.27
3042 8494 0.311790 ACAGCAATGAAACCGCACAG 59.688 50.000 0.00 0.00 0.00 3.66
3056 8509 5.002516 TGTGTGATCATTATGTTGACAGCA 58.997 37.500 0.00 0.00 0.00 4.41
3059 8512 6.466812 AGACTGTGTGATCATTATGTTGACA 58.533 36.000 0.00 0.00 0.00 3.58
3074 8527 4.244066 CATCTGGAGAAGAAGACTGTGTG 58.756 47.826 0.00 0.00 38.79 3.82
3090 8543 7.814264 ATAAAAAGGAGAGCATAACATCTGG 57.186 36.000 0.00 0.00 0.00 3.86
3112 8565 3.046968 TGAGCACGTGGTAGCAAAATA 57.953 42.857 21.92 0.00 0.00 1.40
3126 8579 6.116126 ACCCTTATTTAACTCTGATGAGCAC 58.884 40.000 0.00 0.00 43.85 4.40
3206 8835 3.378742 TCACCTCGAAGCATCTCTTACTC 59.621 47.826 0.00 0.00 34.56 2.59
3218 8847 4.430007 TCCGTTGATTATTCACCTCGAAG 58.570 43.478 0.00 0.00 36.95 3.79
3237 8867 3.935828 GAGTTCCATTTCCTTCTCTTCCG 59.064 47.826 0.00 0.00 0.00 4.30
3258 8888 7.206687 TCTAATGTCATATGTGCGTTATGTGA 58.793 34.615 1.90 1.96 0.00 3.58
3288 8918 7.842982 TGCCACACTACTAAGTCAAACATATA 58.157 34.615 0.00 0.00 31.97 0.86
3289 8919 6.707290 TGCCACACTACTAAGTCAAACATAT 58.293 36.000 0.00 0.00 31.97 1.78
3441 9077 3.004315 ACCAGCACGTTCAAAACAATAGG 59.996 43.478 0.00 0.00 0.00 2.57
3468 9104 5.574188 AGATTGATTTTGGCAACTAGGAGT 58.426 37.500 0.00 0.00 37.61 3.85
3529 9166 4.279169 CCCCAGTTGCCAGATAAATACATG 59.721 45.833 0.00 0.00 0.00 3.21
3564 9208 6.840780 ATGGTTTCTTTGAACTTATCCAGG 57.159 37.500 0.00 0.00 0.00 4.45
3631 9280 8.461222 TGTTCATAATTGCTCAGTAAATCTTGG 58.539 33.333 0.00 0.00 0.00 3.61
3686 9335 2.418334 CCCTTTGCCTAGTTCGTACTCC 60.418 54.545 0.00 0.00 35.78 3.85
3687 9336 2.494870 TCCCTTTGCCTAGTTCGTACTC 59.505 50.000 0.00 0.00 35.78 2.59
3688 9337 2.532843 TCCCTTTGCCTAGTTCGTACT 58.467 47.619 0.00 0.00 38.44 2.73
3689 9338 3.323751 TTCCCTTTGCCTAGTTCGTAC 57.676 47.619 0.00 0.00 0.00 3.67
3690 9339 3.867216 GCTTTCCCTTTGCCTAGTTCGTA 60.867 47.826 0.00 0.00 0.00 3.43
3691 9340 2.779506 CTTTCCCTTTGCCTAGTTCGT 58.220 47.619 0.00 0.00 0.00 3.85
3692 9341 1.468914 GCTTTCCCTTTGCCTAGTTCG 59.531 52.381 0.00 0.00 0.00 3.95
3729 9378 1.676006 AGCGAAACCAGGTTTGTTCTG 59.324 47.619 22.98 7.72 35.77 3.02
3765 9414 1.493871 AGAATGCTCCAGATGAAGGGG 59.506 52.381 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.