Multiple sequence alignment - TraesCS3D01G501400

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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 TraesCS3D01G501400 chr3D 100.000 5387 0 0 1 5387 590305214 590310600 0.000000e+00 9949.0
1 TraesCS3D01G501400 chr3D 88.720 1445 124 22 3124 4543 590204047 590205477 0.000000e+00 1729.0
2 TraesCS3D01G501400 chr3D 84.496 1348 157 29 3116 4441 589000722 588999405 0.000000e+00 1284.0
3 TraesCS3D01G501400 chr3D 85.744 968 118 14 3082 4035 588977705 588976744 0.000000e+00 1005.0
4 TraesCS3D01G501400 chr3D 82.108 1034 145 22 880 1902 590238359 590239363 0.000000e+00 848.0
5 TraesCS3D01G501400 chr3D 82.811 925 116 28 2168 3078 590203054 590203949 0.000000e+00 787.0
6 TraesCS3D01G501400 chr3D 82.366 930 110 43 2168 3078 590239995 590240889 0.000000e+00 760.0
7 TraesCS3D01G501400 chr3D 85.052 582 66 11 881 1460 590200522 590201084 1.680000e-159 573.0
8 TraesCS3D01G501400 chr3D 87.342 316 25 1 4178 4478 590241624 590241939 1.110000e-91 348.0
9 TraesCS3D01G501400 chr3D 89.076 119 11 2 1939 2055 590239367 590239485 4.350000e-31 147.0
10 TraesCS3D01G501400 chr3D 75.449 334 50 23 2725 3037 589001523 589001201 3.380000e-27 134.0
11 TraesCS3D01G501400 chr3A 92.341 3917 201 41 881 4764 720075266 720079116 0.000000e+00 5480.0
12 TraesCS3D01G501400 chr3A 94.106 2528 121 15 2158 4676 720229844 720232352 0.000000e+00 3818.0
13 TraesCS3D01G501400 chr3A 85.889 2693 255 63 2169 4783 719995154 719997799 0.000000e+00 2752.0
14 TraesCS3D01G501400 chr3A 89.623 1619 111 22 3216 4783 720221841 720223453 0.000000e+00 2006.0
15 TraesCS3D01G501400 chr3A 86.253 1935 147 48 1 1869 720227212 720229093 0.000000e+00 1989.0
16 TraesCS3D01G501400 chr3A 88.997 1445 120 22 3124 4543 719935993 719937423 0.000000e+00 1751.0
17 TraesCS3D01G501400 chr3A 86.835 1185 124 14 881 2061 719991681 719992837 0.000000e+00 1295.0
18 TraesCS3D01G501400 chr3A 83.203 1280 165 30 880 2139 719932898 719934147 0.000000e+00 1127.0
19 TraesCS3D01G501400 chr3A 86.528 1054 99 19 831 1869 720214300 720215325 0.000000e+00 1120.0
20 TraesCS3D01G501400 chr3A 90.862 766 55 10 4630 5383 720232385 720233147 0.000000e+00 1013.0
21 TraesCS3D01G501400 chr3A 93.731 654 31 6 2158 2808 720216122 720216768 0.000000e+00 972.0
22 TraesCS3D01G501400 chr3A 84.000 925 102 32 2168 3078 719935005 719935897 0.000000e+00 846.0
23 TraesCS3D01G501400 chr3A 86.224 392 26 13 491 869 720074826 720075202 3.020000e-107 399.0
24 TraesCS3D01G501400 chr3A 80.846 402 39 16 366 746 720213119 720213503 1.140000e-71 281.0
25 TraesCS3D01G501400 chr3A 74.388 695 136 26 1121 1797 719835850 719836520 5.350000e-65 259.0
26 TraesCS3D01G501400 chr3A 92.949 156 11 0 197 352 720074665 720074820 1.510000e-55 228.0
27 TraesCS3D01G501400 chr3A 85.854 205 21 5 1 198 720064144 720064347 1.520000e-50 211.0
28 TraesCS3D01G501400 chr3A 96.842 95 3 0 3060 3154 720216956 720217050 5.580000e-35 159.0
29 TraesCS3D01G501400 chr3A 83.019 159 16 7 1922 2070 720229107 720229264 3.380000e-27 134.0
30 TraesCS3D01G501400 chr3A 93.750 64 3 1 771 834 720213575 720213637 1.600000e-15 95.3
31 TraesCS3D01G501400 chr3B 93.111 2671 131 26 2034 4676 789227915 789230560 0.000000e+00 3864.0
32 TraesCS3D01G501400 chr3B 84.821 2688 239 85 2168 4783 789220102 789222692 0.000000e+00 2547.0
33 TraesCS3D01G501400 chr3B 89.635 1399 106 21 3124 4497 789179642 789181026 0.000000e+00 1744.0
34 TraesCS3D01G501400 chr3B 84.532 1377 127 44 666 1981 789226573 789227924 0.000000e+00 1284.0
35 TraesCS3D01G501400 chr3B 86.043 1175 127 21 881 2051 789217823 789218964 0.000000e+00 1227.0
36 TraesCS3D01G501400 chr3B 83.373 1269 164 25 882 2139 789175935 789177167 0.000000e+00 1131.0
37 TraesCS3D01G501400 chr3B 87.556 675 52 16 1 667 789225892 789226542 0.000000e+00 752.0
38 TraesCS3D01G501400 chr3B 86.389 529 58 11 2168 2691 789177605 789178124 2.820000e-157 566.0
39 TraesCS3D01G501400 chr3B 73.606 538 108 22 1124 1650 788982528 788983042 5.550000e-40 176.0
40 TraesCS3D01G501400 chr3B 81.657 169 19 6 4630 4789 789230593 789230758 4.380000e-26 130.0
41 TraesCS3D01G501400 chr3B 85.714 126 14 1 4921 5046 789230821 789230942 4.380000e-26 130.0
42 TraesCS3D01G501400 chr3B 78.802 217 26 15 4592 4802 789181039 789181241 1.570000e-25 128.0
43 TraesCS3D01G501400 chr5D 84.848 99 10 5 5214 5308 63783846 63783943 1.600000e-15 95.3


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 TraesCS3D01G501400 chr3D 590305214 590310600 5386 False 9949.000000 9949 100.000000 1 5387 1 chr3D.!!$F1 5386
1 TraesCS3D01G501400 chr3D 590200522 590205477 4955 False 1029.666667 1729 85.527667 881 4543 3 chr3D.!!$F2 3662
2 TraesCS3D01G501400 chr3D 588976744 588977705 961 True 1005.000000 1005 85.744000 3082 4035 1 chr3D.!!$R1 953
3 TraesCS3D01G501400 chr3D 588999405 589001523 2118 True 709.000000 1284 79.972500 2725 4441 2 chr3D.!!$R2 1716
4 TraesCS3D01G501400 chr3D 590238359 590241939 3580 False 525.750000 848 85.223000 880 4478 4 chr3D.!!$F3 3598
5 TraesCS3D01G501400 chr3A 720074665 720079116 4451 False 2035.666667 5480 90.504667 197 4764 3 chr3A.!!$F5 4567
6 TraesCS3D01G501400 chr3A 719991681 719997799 6118 False 2023.500000 2752 86.362000 881 4783 2 chr3A.!!$F4 3902
7 TraesCS3D01G501400 chr3A 720221841 720233147 11306 False 1792.000000 3818 88.772600 1 5383 5 chr3A.!!$F7 5382
8 TraesCS3D01G501400 chr3A 719932898 719937423 4525 False 1241.333333 1751 85.400000 880 4543 3 chr3A.!!$F3 3663
9 TraesCS3D01G501400 chr3A 720213119 720217050 3931 False 525.460000 1120 90.339400 366 3154 5 chr3A.!!$F6 2788
10 TraesCS3D01G501400 chr3A 719835850 719836520 670 False 259.000000 259 74.388000 1121 1797 1 chr3A.!!$F1 676
11 TraesCS3D01G501400 chr3B 789217823 789230942 13119 False 1419.142857 3864 86.204857 1 5046 7 chr3B.!!$F3 5045
12 TraesCS3D01G501400 chr3B 789175935 789181241 5306 False 892.250000 1744 84.549750 882 4802 4 chr3B.!!$F2 3920

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
985 10843 0.321122 CCAGAGCTCCGCAGTTTCTT 60.321 55.000 10.93 0.0 0.00 2.52 F
1871 11776 0.033781 GTTACAGTGTACCCGCACCA 59.966 55.000 1.43 0.0 40.04 4.17 F
2462 16264 1.933181 CGATCAAGCTGCCACGAATAA 59.067 47.619 0.00 0.0 0.00 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1920 11837 1.148273 TTCTTGGGTGCTCGCTTGT 59.852 52.632 4.41 0.00 0.00 3.16 R
3268 18598 1.541588 GAAACCCTGTCCTGAATGTGC 59.458 52.381 0.00 0.00 0.00 4.57 R
4442 19836 2.119495 AGTTCACTTGACCTGGTCTGT 58.881 47.619 26.03 20.64 33.15 3.41 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
38 9027 6.732896 TCCTCATATCCTCTTTTGTACCTC 57.267 41.667 0.00 0.00 0.00 3.85
41 9030 7.182026 TCCTCATATCCTCTTTTGTACCTCAAA 59.818 37.037 0.00 0.00 43.24 2.69
50 9039 6.713276 TCTTTTGTACCTCAAATATTCCCGA 58.287 36.000 0.00 0.00 44.15 5.14
52 9041 7.497909 TCTTTTGTACCTCAAATATTCCCGATC 59.502 37.037 0.00 0.00 44.15 3.69
56 9045 4.569943 ACCTCAAATATTCCCGATCGATG 58.430 43.478 18.66 7.52 0.00 3.84
68 9057 6.091718 TCCCGATCGATGATACAAACATAA 57.908 37.500 18.66 0.00 0.00 1.90
149 9144 5.743026 TTGCGATGTAAGAAACACAAGAA 57.257 34.783 0.00 0.00 42.09 2.52
172 9167 6.515272 AGTGGTGACAAAATCATCCAATAC 57.485 37.500 0.00 0.00 46.06 1.89
209 9204 1.268625 TCGAATATATGTGCGGCGAGT 59.731 47.619 12.98 0.00 0.00 4.18
210 9205 1.386748 CGAATATATGTGCGGCGAGTG 59.613 52.381 12.98 0.00 0.00 3.51
211 9206 2.404215 GAATATATGTGCGGCGAGTGT 58.596 47.619 12.98 0.00 0.00 3.55
212 9207 2.526304 ATATATGTGCGGCGAGTGTT 57.474 45.000 12.98 0.00 0.00 3.32
213 9208 2.303163 TATATGTGCGGCGAGTGTTT 57.697 45.000 12.98 0.00 0.00 2.83
214 9209 1.006832 ATATGTGCGGCGAGTGTTTC 58.993 50.000 12.98 0.00 0.00 2.78
406 9419 4.338118 ACTTCTTGCATCTTCGGAAAAACA 59.662 37.500 0.00 0.00 0.00 2.83
489 9502 1.065418 GTATATATGCGGCCTGGGCTT 60.065 52.381 18.81 5.63 41.60 4.35
869 10648 3.071892 TCCACAGTTACTACAACTTGGGG 59.928 47.826 13.48 8.76 33.38 4.96
870 10649 3.181448 CCACAGTTACTACAACTTGGGGT 60.181 47.826 0.00 0.00 31.17 4.95
871 10650 4.040706 CCACAGTTACTACAACTTGGGGTA 59.959 45.833 0.00 0.00 31.17 3.69
872 10651 5.455040 CCACAGTTACTACAACTTGGGGTAA 60.455 44.000 0.00 0.29 31.17 2.85
873 10652 5.467735 CACAGTTACTACAACTTGGGGTAAC 59.532 44.000 20.08 20.08 38.45 2.50
874 10653 5.367644 ACAGTTACTACAACTTGGGGTAACT 59.632 40.000 22.36 22.36 43.36 2.24
876 10655 3.136009 ACTACAACTTGGGGTAACTGC 57.864 47.619 0.00 0.00 0.00 4.40
878 10657 2.675658 ACAACTTGGGGTAACTGCAT 57.324 45.000 0.00 0.00 0.00 3.96
951 10809 9.352784 TGTTCTTGTTCTGTAACATTCTTTTTG 57.647 29.630 0.00 0.00 44.85 2.44
952 10810 9.353999 GTTCTTGTTCTGTAACATTCTTTTTGT 57.646 29.630 0.00 0.00 44.85 2.83
953 10811 9.567848 TTCTTGTTCTGTAACATTCTTTTTGTC 57.432 29.630 0.00 0.00 44.85 3.18
954 10812 8.956426 TCTTGTTCTGTAACATTCTTTTTGTCT 58.044 29.630 0.00 0.00 44.85 3.41
985 10843 0.321122 CCAGAGCTCCGCAGTTTCTT 60.321 55.000 10.93 0.00 0.00 2.52
1080 10943 1.761667 CCTCCTCCTCCTGCTCCTG 60.762 68.421 0.00 0.00 0.00 3.86
1081 10944 2.364842 TCCTCCTCCTGCTCCTGC 60.365 66.667 0.00 0.00 40.20 4.85
1082 10945 3.478274 CCTCCTCCTGCTCCTGCC 61.478 72.222 0.00 0.00 38.71 4.85
1083 10946 3.478274 CTCCTCCTGCTCCTGCCC 61.478 72.222 0.00 0.00 38.71 5.36
1461 11339 4.320667 TGACAAAATACTCGTCATTGCG 57.679 40.909 0.00 0.00 34.83 4.85
1462 11340 3.991121 TGACAAAATACTCGTCATTGCGA 59.009 39.130 0.00 3.78 34.83 5.10
1463 11341 4.143200 TGACAAAATACTCGTCATTGCGAC 60.143 41.667 0.00 0.00 41.62 5.19
1464 11342 3.994392 ACAAAATACTCGTCATTGCGACT 59.006 39.130 0.00 0.00 42.98 4.18
1465 11343 4.451096 ACAAAATACTCGTCATTGCGACTT 59.549 37.500 0.00 0.00 42.98 3.01
1466 11344 5.049680 ACAAAATACTCGTCATTGCGACTTT 60.050 36.000 0.00 0.03 42.98 2.66
1504 11400 2.186076 CGCTCAACACCTCGATAAGAC 58.814 52.381 0.00 0.00 0.00 3.01
1871 11776 0.033781 GTTACAGTGTACCCGCACCA 59.966 55.000 1.43 0.00 40.04 4.17
2021 11947 9.430838 CTCGCTTCAGTTAGATTCATTAATTTG 57.569 33.333 0.00 0.00 0.00 2.32
2285 16078 7.066163 TCCATTACTGTCAATATTTCTGTGCTG 59.934 37.037 8.93 6.91 0.00 4.41
2338 16131 7.540299 ACGAAGAAAAGGTTTGTTGTTATCAA 58.460 30.769 0.00 0.00 0.00 2.57
2462 16264 1.933181 CGATCAAGCTGCCACGAATAA 59.067 47.619 0.00 0.00 0.00 1.40
2535 16337 7.924940 AGTTCACTCTCTTTGAATTTTCTGAC 58.075 34.615 0.00 0.00 35.47 3.51
2732 17592 3.188460 AGCGTTGTTTACAGTAGCCAATG 59.812 43.478 8.27 8.27 0.00 2.82
2760 17620 3.557185 TGAATCGTGCTATGATGTGCTTC 59.443 43.478 0.00 0.00 0.00 3.86
2852 17731 6.780457 AATTTATCTTGCAGCAACCTATGT 57.220 33.333 2.83 0.00 0.00 2.29
2887 17778 3.898482 AGCCACACCCTTTCCATTATAC 58.102 45.455 0.00 0.00 0.00 1.47
3268 18598 0.313672 TGCAGTTAAAAGGCTTGCCG 59.686 50.000 0.00 0.00 0.00 5.69
3291 18621 2.443255 ACATTCAGGACAGGGTTTCACT 59.557 45.455 0.00 0.00 0.00 3.41
3447 18777 8.121305 TCTTTATCTTTGGTATGCACAATGTT 57.879 30.769 0.00 0.00 0.00 2.71
3474 18804 7.427318 GGTTAACCATTATTTTCGATCGTGTTC 59.573 37.037 20.12 0.00 35.64 3.18
3498 18828 4.754618 TGGCCATACTATAAAATGCACTCG 59.245 41.667 0.00 0.00 0.00 4.18
3526 18856 3.250762 GTGCAGATGTTAGCAGAACAACA 59.749 43.478 8.12 0.24 42.14 3.33
3933 19283 3.824443 TGGTGTGTTACTTCTCGAGATCA 59.176 43.478 17.44 8.12 0.00 2.92
4143 19513 2.726821 TCAATTGCCAAGGAGATCCAC 58.273 47.619 0.00 0.00 38.89 4.02
4149 19519 1.220206 CAAGGAGATCCACGCAGCT 59.780 57.895 0.92 0.00 38.89 4.24
4442 19836 0.675837 GCAATCAGACAGCAGGCAGA 60.676 55.000 0.00 0.00 0.00 4.26
4813 20305 8.260818 GCCAGGCTAACTAGAATATTGATATGA 58.739 37.037 3.29 0.00 0.00 2.15
4873 20365 5.277250 TCCATAGAGTTGTCATGGTAAGGA 58.723 41.667 0.00 0.00 40.18 3.36
4883 20375 5.830457 TTGTCATGGTAAGGACAACATGAAA 59.170 36.000 5.46 0.00 46.95 2.69
4889 20381 5.763204 TGGTAAGGACAACATGAAAGAGTTC 59.237 40.000 0.00 0.00 0.00 3.01
4902 20394 5.505780 TGAAAGAGTTCTTCCTTTTGGTGA 58.494 37.500 0.00 0.00 36.41 4.02
4961 20453 6.552445 ATTACTCACTGCTAAGGACAGAAT 57.448 37.500 0.00 0.00 38.55 2.40
4962 20454 7.661536 ATTACTCACTGCTAAGGACAGAATA 57.338 36.000 0.00 0.00 38.55 1.75
5126 20618 3.370231 GTGCGGGCCGACCATTTT 61.370 61.111 33.44 0.00 40.22 1.82
5127 20619 2.598985 TGCGGGCCGACCATTTTT 60.599 55.556 33.44 0.00 40.22 1.94
5128 20620 2.180769 GCGGGCCGACCATTTTTC 59.819 61.111 33.44 4.02 40.22 2.29
5129 20621 2.882132 CGGGCCGACCATTTTTCC 59.118 61.111 24.41 0.00 40.22 3.13
5131 20623 2.706834 GGGCCGACCATTTTTCCCG 61.707 63.158 0.00 0.00 39.85 5.14
5133 20625 1.211709 GCCGACCATTTTTCCCGTG 59.788 57.895 0.00 0.00 0.00 4.94
5340 20838 8.853345 GCATTAGAAAACTGTTTGATGTGTATG 58.147 33.333 6.53 6.18 0.00 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.178068 GAGGATTGCACCGGCTAAGA 59.822 55.000 0.00 0.00 41.91 2.10
4 5 0.767375 ATATGAGGATTGCACCGGCT 59.233 50.000 0.00 0.00 41.91 5.52
14 9002 6.846505 TGAGGTACAAAAGAGGATATGAGGAT 59.153 38.462 0.00 0.00 0.00 3.24
38 9027 7.595311 TTGTATCATCGATCGGGAATATTTG 57.405 36.000 16.41 1.27 0.00 2.32
41 9030 6.697395 TGTTTGTATCATCGATCGGGAATAT 58.303 36.000 16.41 0.00 0.00 1.28
125 9117 5.688823 TCTTGTGTTTCTTACATCGCAATG 58.311 37.500 0.00 0.00 39.39 2.82
127 9119 5.295787 ACTTCTTGTGTTTCTTACATCGCAA 59.704 36.000 0.00 0.00 39.39 4.85
128 9120 4.814234 ACTTCTTGTGTTTCTTACATCGCA 59.186 37.500 0.00 0.00 39.39 5.10
129 9121 5.140177 CACTTCTTGTGTTTCTTACATCGC 58.860 41.667 0.00 0.00 41.53 4.58
149 9144 6.009589 TGTATTGGATGATTTTGTCACCACT 58.990 36.000 0.00 0.00 40.28 4.00
152 9147 7.425606 GGTATGTATTGGATGATTTTGTCACC 58.574 38.462 0.00 0.00 40.28 4.02
153 9148 7.285401 AGGGTATGTATTGGATGATTTTGTCAC 59.715 37.037 0.00 0.00 40.28 3.67
209 9204 7.778470 ATTAAAAGAACAATTTGGCGAAACA 57.222 28.000 0.00 0.00 0.00 2.83
210 9205 9.187455 TCTATTAAAAGAACAATTTGGCGAAAC 57.813 29.630 0.00 0.00 0.00 2.78
211 9206 9.751542 TTCTATTAAAAGAACAATTTGGCGAAA 57.248 25.926 0.00 0.00 30.54 3.46
285 9293 8.975295 GGTAAAATTGTAGAAGTACTCCCTCTA 58.025 37.037 0.00 0.00 0.00 2.43
293 9301 6.653740 AGCTGGTGGTAAAATTGTAGAAGTAC 59.346 38.462 0.00 0.00 0.00 2.73
298 9306 4.250464 CGAGCTGGTGGTAAAATTGTAGA 58.750 43.478 0.00 0.00 0.00 2.59
396 9409 6.803154 ATGGTTTTGTTTTTGTTTTTCCGA 57.197 29.167 0.00 0.00 0.00 4.55
398 9411 9.249457 TGAAAATGGTTTTGTTTTTGTTTTTCC 57.751 25.926 0.00 0.00 32.39 3.13
406 9419 4.697828 ACGGCTGAAAATGGTTTTGTTTTT 59.302 33.333 0.00 0.00 31.94 1.94
453 9466 9.661563 CGCATATATACCCCTAATAAAAAGACA 57.338 33.333 0.00 0.00 0.00 3.41
470 9483 1.065491 CAAGCCCAGGCCGCATATATA 60.065 52.381 4.70 0.00 43.17 0.86
471 9484 0.322816 CAAGCCCAGGCCGCATATAT 60.323 55.000 4.70 0.00 43.17 0.86
472 9485 1.073025 CAAGCCCAGGCCGCATATA 59.927 57.895 4.70 0.00 43.17 0.86
473 9486 2.203394 CAAGCCCAGGCCGCATAT 60.203 61.111 4.70 0.00 43.17 1.78
489 9502 2.280119 GACCGTGTCTGCTGTGCA 60.280 61.111 0.00 0.00 36.92 4.57
705 9772 1.889105 CGCTCGCCAGCCAATGTAT 60.889 57.895 0.00 0.00 43.56 2.29
770 9846 4.079665 GGAACTGCCTTAAAACGATGAC 57.920 45.455 0.00 0.00 0.00 3.06
873 10652 4.843220 AGAGAACTGGAAAACAATGCAG 57.157 40.909 0.00 0.00 43.62 4.41
874 10653 5.129634 TGTAGAGAACTGGAAAACAATGCA 58.870 37.500 0.00 0.00 0.00 3.96
876 10655 7.651808 ACAATGTAGAGAACTGGAAAACAATG 58.348 34.615 0.00 0.00 0.00 2.82
878 10657 7.639113 AACAATGTAGAGAACTGGAAAACAA 57.361 32.000 0.00 0.00 0.00 2.83
937 10776 8.942338 AAAAAGGGAGACAAAAAGAATGTTAC 57.058 30.769 0.00 0.00 0.00 2.50
976 10834 3.003793 GTCAGGGAACTTGAAGAAACTGC 59.996 47.826 0.00 0.00 40.21 4.40
985 10843 0.389817 CGCATCGTCAGGGAACTTGA 60.390 55.000 0.00 0.00 40.21 3.02
1054 10917 2.612251 GAGGAGGAGGGGGAGGAG 59.388 72.222 0.00 0.00 0.00 3.69
1354 11232 0.677842 ACGGTGGTGTCCTTACTGTC 59.322 55.000 0.00 0.00 28.15 3.51
1461 11339 2.704725 TTTCCATGCTCGCAAAAGTC 57.295 45.000 0.00 0.00 0.00 3.01
1462 11340 2.950433 CATTTCCATGCTCGCAAAAGT 58.050 42.857 0.00 0.00 0.00 2.66
1504 11400 2.224066 ACAAGAACCTGAAGGAGTCGTG 60.224 50.000 2.62 10.41 37.80 4.35
1715 11620 3.834231 CAGAATTTGACCACCTTTCCCAT 59.166 43.478 0.00 0.00 0.00 4.00
1920 11837 1.148273 TTCTTGGGTGCTCGCTTGT 59.852 52.632 4.41 0.00 0.00 3.16
2021 11947 3.612479 GCAAGATGTGTGACATGTTTCCC 60.612 47.826 0.00 0.00 38.72 3.97
2200 15992 4.819630 TGAGTTGCGTCCTAAAGAAAACAT 59.180 37.500 0.00 0.00 0.00 2.71
2207 15999 1.798813 GGTGTGAGTTGCGTCCTAAAG 59.201 52.381 0.00 0.00 0.00 1.85
2285 16078 6.260714 TGTCATCCATACAATGCAACAGATAC 59.739 38.462 0.00 0.00 0.00 2.24
2371 16167 9.807649 ACGTTAAGACCGACTACATTAATTAAT 57.192 29.630 4.81 4.81 0.00 1.40
2372 16168 9.638239 AACGTTAAGACCGACTACATTAATTAA 57.362 29.630 0.00 0.00 0.00 1.40
2373 16169 9.075519 CAACGTTAAGACCGACTACATTAATTA 57.924 33.333 0.00 0.00 0.00 1.40
2374 16170 7.599998 ACAACGTTAAGACCGACTACATTAATT 59.400 33.333 0.00 0.00 0.00 1.40
2378 16174 4.874970 ACAACGTTAAGACCGACTACATT 58.125 39.130 0.00 0.00 0.00 2.71
2462 16264 1.446907 CAATGCGTCTTCTTCCAGCT 58.553 50.000 0.00 0.00 0.00 4.24
2535 16337 6.317140 AGAAGTTGTGTGTAGCATGGAATATG 59.683 38.462 0.00 0.00 0.00 1.78
2541 16343 2.744202 GGAGAAGTTGTGTGTAGCATGG 59.256 50.000 0.00 0.00 0.00 3.66
2732 17592 7.063898 AGCACATCATAGCACGATTCATTATAC 59.936 37.037 0.00 0.00 0.00 1.47
2874 17753 5.817816 GGGCATCGATAGTATAATGGAAAGG 59.182 44.000 0.00 0.00 37.40 3.11
2887 17778 8.777865 TTATTTTCATTCTAGGGCATCGATAG 57.222 34.615 0.00 0.00 0.00 2.08
3199 18529 4.317488 TGGAAGTATGTACAAAACCGGAC 58.683 43.478 9.46 0.00 0.00 4.79
3268 18598 1.541588 GAAACCCTGTCCTGAATGTGC 59.458 52.381 0.00 0.00 0.00 4.57
3474 18804 5.106948 CGAGTGCATTTTATAGTATGGCCAG 60.107 44.000 13.05 0.00 0.00 4.85
3498 18828 3.873361 TCTGCTAACATCTGCACATTAGC 59.127 43.478 14.95 14.95 46.33 3.09
3526 18856 8.596293 ACACATCTTTTATTCCAATCAACCAAT 58.404 29.630 0.00 0.00 0.00 3.16
3933 19283 3.947834 CCAGAATTCCTTTGTCCGCTAAT 59.052 43.478 0.65 0.00 0.00 1.73
4149 19519 4.616553 TGTTAATGTACTCCCTAGCCTCA 58.383 43.478 0.00 0.00 0.00 3.86
4442 19836 2.119495 AGTTCACTTGACCTGGTCTGT 58.881 47.619 26.03 20.64 33.15 3.41
4517 19919 3.641439 CGAAAAACGGCTACAGAGATG 57.359 47.619 0.00 0.00 38.46 2.90
4601 20008 1.720852 GCGGTGCACAAAAGCTAAATG 59.279 47.619 20.43 0.00 34.99 2.32
4707 20199 3.274288 CTTTACCCAGCAGGATTCTGTC 58.726 50.000 2.16 0.00 42.78 3.51
4710 20202 5.717119 AATACTTTACCCAGCAGGATTCT 57.283 39.130 0.00 0.00 39.89 2.40
4836 20328 6.899393 ACTCTATGGAAATGCTTGTTTTCA 57.101 33.333 0.00 0.00 35.29 2.69
4873 20365 7.260603 CAAAAGGAAGAACTCTTTCATGTTGT 58.739 34.615 0.65 0.00 36.11 3.32
4883 20375 5.707764 GCTAATCACCAAAAGGAAGAACTCT 59.292 40.000 0.00 0.00 0.00 3.24
4889 20381 3.119352 GCAGGCTAATCACCAAAAGGAAG 60.119 47.826 0.00 0.00 0.00 3.46
4902 20394 7.025520 ACTTATCCATCATTAGCAGGCTAAT 57.974 36.000 18.30 18.30 46.58 1.73
4975 20467 8.134895 ACTTTCTAGATGAATTTTGCGTGAAAA 58.865 29.630 0.00 0.00 37.93 2.29
5048 20540 9.956720 ACTCTTGATAATTTTGAAGAAACACAG 57.043 29.630 0.20 0.00 0.00 3.66
5062 20554 7.549134 TGCACAACTCGATAACTCTTGATAATT 59.451 33.333 0.00 0.00 0.00 1.40
5077 20569 0.463654 AACTGCCTTGCACAACTCGA 60.464 50.000 0.00 0.00 33.79 4.04
5078 20570 0.381801 AAACTGCCTTGCACAACTCG 59.618 50.000 0.00 0.00 33.79 4.18
5114 20606 1.974875 ACGGGAAAAATGGTCGGCC 60.975 57.895 0.00 0.00 0.00 6.13
5115 20607 1.211709 CACGGGAAAAATGGTCGGC 59.788 57.895 0.00 0.00 0.00 5.54
5116 20608 0.802494 CTCACGGGAAAAATGGTCGG 59.198 55.000 0.00 0.00 0.00 4.79
5117 20609 0.168128 GCTCACGGGAAAAATGGTCG 59.832 55.000 0.00 0.00 0.00 4.79
5119 20611 1.247567 CAGCTCACGGGAAAAATGGT 58.752 50.000 0.00 0.00 0.00 3.55
5122 20614 4.099419 AGAAAAACAGCTCACGGGAAAAAT 59.901 37.500 0.00 0.00 0.00 1.82
5123 20615 3.445805 AGAAAAACAGCTCACGGGAAAAA 59.554 39.130 0.00 0.00 0.00 1.94
5124 20616 3.020984 AGAAAAACAGCTCACGGGAAAA 58.979 40.909 0.00 0.00 0.00 2.29
5125 20617 2.650322 AGAAAAACAGCTCACGGGAAA 58.350 42.857 0.00 0.00 0.00 3.13
5126 20618 2.341846 AGAAAAACAGCTCACGGGAA 57.658 45.000 0.00 0.00 0.00 3.97
5127 20619 2.158813 AGAAGAAAAACAGCTCACGGGA 60.159 45.455 0.00 0.00 0.00 5.14
5128 20620 2.222027 AGAAGAAAAACAGCTCACGGG 58.778 47.619 0.00 0.00 0.00 5.28
5129 20621 3.065371 ACAAGAAGAAAAACAGCTCACGG 59.935 43.478 0.00 0.00 0.00 4.94
5131 20623 6.808704 AGAAAACAAGAAGAAAAACAGCTCAC 59.191 34.615 0.00 0.00 0.00 3.51
5133 20625 7.254137 AGAGAAAACAAGAAGAAAAACAGCTC 58.746 34.615 0.00 0.00 0.00 4.09
5302 20800 5.761234 AGTTTTCTAATGCACGGTGAACTTA 59.239 36.000 13.29 5.02 0.00 2.24
5314 20812 8.853345 CATACACATCAAACAGTTTTCTAATGC 58.147 33.333 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.