Multiple sequence alignment - TraesCS1A01G255000

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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 TraesCS1A01G255000 chr1A 100.000 7573 0 0 1 7573 446549055 446541483 0.000000e+00 13985.0
1 TraesCS1A01G255000 chr1B 95.250 4821 155 38 835 5623 463525959 463530737 0.000000e+00 7566.0
2 TraesCS1A01G255000 chr1B 91.633 1255 56 12 6325 7573 463531430 463532641 0.000000e+00 1690.0
3 TraesCS1A01G255000 chr1B 93.272 654 37 5 5680 6328 463530738 463531389 0.000000e+00 957.0
4 TraesCS1A01G255000 chr1B 93.796 274 17 0 254 527 463525516 463525789 5.470000e-111 412.0
5 TraesCS1A01G255000 chr1B 91.837 147 11 1 1 146 463525044 463525190 3.580000e-48 204.0
6 TraesCS1A01G255000 chr1B 86.813 91 10 2 6159 6248 159205721 159205810 4.840000e-17 100.0
7 TraesCS1A01G255000 chr1D 97.738 4112 49 14 1820 5906 346398809 346394717 0.000000e+00 7038.0
8 TraesCS1A01G255000 chr1D 96.720 1677 50 5 165 1838 346401277 346399603 0.000000e+00 2787.0
9 TraesCS1A01G255000 chr1D 93.865 1255 59 11 6325 7573 346394324 346393082 0.000000e+00 1875.0
10 TraesCS1A01G255000 chr1D 91.294 425 22 2 5904 6328 346394774 346394365 3.970000e-157 566.0
11 TraesCS1A01G255000 chr1D 89.333 150 9 2 1 147 346401580 346401435 1.680000e-41 182.0
12 TraesCS1A01G255000 chr1D 90.000 90 9 0 6160 6249 122770170 122770081 4.800000e-22 117.0
13 TraesCS1A01G255000 chr1D 95.918 49 2 0 243 291 393121325 393121373 6.300000e-11 80.5
14 TraesCS1A01G255000 chr1D 95.918 49 2 0 243 291 475305017 475304969 6.300000e-11 80.5
15 TraesCS1A01G255000 chr6A 91.949 236 14 2 526 757 230651628 230651394 7.330000e-85 326.0
16 TraesCS1A01G255000 chr6A 91.880 234 14 2 528 757 230642128 230641896 9.480000e-84 322.0
17 TraesCS1A01G255000 chr6A 91.880 234 14 2 528 757 230646036 230645804 9.480000e-84 322.0
18 TraesCS1A01G255000 chr6D 91.880 234 14 2 528 757 423454565 423454797 9.480000e-84 322.0
19 TraesCS1A01G255000 chr6D 97.872 47 1 0 6849 6895 363180571 363180525 1.750000e-11 82.4
20 TraesCS1A01G255000 chr6B 90.830 229 14 3 529 757 295973260 295973039 4.440000e-77 300.0
21 TraesCS1A01G255000 chr6B 89.565 230 13 2 528 757 638471252 638471470 1.610000e-71 281.0
22 TraesCS1A01G255000 chr6B 90.625 96 9 0 243 338 81247198 81247103 2.220000e-25 128.0
23 TraesCS1A01G255000 chr2D 90.094 212 18 3 546 757 19508335 19508543 9.680000e-69 272.0
24 TraesCS1A01G255000 chr2B 92.701 137 10 0 548 684 592565678 592565542 1.670000e-46 198.0
25 TraesCS1A01G255000 chr4A 92.708 96 7 0 243 338 175693424 175693329 1.020000e-28 139.0
26 TraesCS1A01G255000 chr7B 87.500 88 11 0 6158 6245 603560303 603560390 1.340000e-17 102.0
27 TraesCS1A01G255000 chr7A 87.778 90 7 3 6158 6245 49190918 49191005 1.340000e-17 102.0
28 TraesCS1A01G255000 chr2A 87.356 87 10 1 6160 6245 697303955 697303869 1.740000e-16 99.0
29 TraesCS1A01G255000 chr2A 97.059 34 0 1 4762 4794 43144087 43144120 1.000000e-03 56.5
30 TraesCS1A01G255000 chrUn 86.517 89 11 1 6161 6249 416910952 416910865 6.250000e-16 97.1
31 TraesCS1A01G255000 chr3D 85.870 92 11 2 6163 6253 611499114 611499024 6.250000e-16 97.1
32 TraesCS1A01G255000 chr4D 95.918 49 2 0 243 291 466649676 466649724 6.300000e-11 80.5
33 TraesCS1A01G255000 chr4B 95.918 49 2 0 243 291 57249915 57249867 6.300000e-11 80.5
34 TraesCS1A01G255000 chr4B 95.918 49 2 0 243 291 506591199 506591151 6.300000e-11 80.5


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 TraesCS1A01G255000 chr1A 446541483 446549055 7572 True 13985.0 13985 100.0000 1 7573 1 chr1A.!!$R1 7572
1 TraesCS1A01G255000 chr1B 463525044 463532641 7597 False 2165.8 7566 93.1576 1 7573 5 chr1B.!!$F2 7572
2 TraesCS1A01G255000 chr1D 346393082 346401580 8498 True 2489.6 7038 93.7900 1 7573 5 chr1D.!!$R3 7572
3 TraesCS1A01G255000 chr6A 230641896 230646036 4140 True 322.0 322 91.8800 528 757 2 chr6A.!!$R2 229

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
158 162 0.103208 CGGCTTAGTCCTCGCTGATT 59.897 55.000 0.00 0.0 31.83 2.57 F
327 550 0.366871 GCAGAGAACATGTACGTGCG 59.633 55.000 15.12 0.0 0.00 5.34 F
741 969 4.425520 CTTCGTCACCTCCTTTATCTCAC 58.574 47.826 0.00 0.0 0.00 3.51 F
1906 4733 1.618343 GGAAACATTGTGAGGGTTGGG 59.382 52.381 0.00 0.0 0.00 4.12 F
3056 5889 1.073284 GGGCAGAAGGTGTGGAAACTA 59.927 52.381 0.00 0.0 0.00 2.24 F
3403 6237 2.233271 CTGATGCCAAACTGACTTGGT 58.767 47.619 12.56 0.0 46.53 3.67 F
4855 8706 6.775142 TGTCAAGAATTCCTATGTGGTTTTGA 59.225 34.615 0.65 0.0 37.07 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1290 3281 2.035449 TGAATCCATCGTATCCACCGTC 59.965 50.000 0.00 0.00 0.00 4.79 R
1819 3834 5.751586 TGTTCCCCAAATCAGATACCTTAC 58.248 41.667 0.00 0.00 0.00 2.34 R
2464 5295 4.320714 GCATCTTTGTGCAGAGAACAATCA 60.321 41.667 0.00 0.00 44.43 2.57 R
3172 6005 2.293122 TGTCTTGTCGAAAATTGGGCAG 59.707 45.455 0.00 0.00 0.00 4.85 R
4795 8646 1.338769 GCTTGTCCGGTTGTCCACTAT 60.339 52.381 0.00 0.00 0.00 2.12 R
5133 8984 2.557056 CCCATCAGCATTGGATGTCATC 59.443 50.000 4.06 4.06 40.38 2.92 R
6714 10621 0.818938 CATATGCACTTGGCTTGGCA 59.181 50.000 0.00 0.00 45.15 4.92 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
115 119 3.384789 TCCTGCTATATATGCTAAGCCGG 59.615 47.826 0.00 0.00 39.79 6.13
148 152 2.006772 CGATGTTGCCGGCTTAGTC 58.993 57.895 29.70 18.62 0.00 2.59
150 154 0.107654 GATGTTGCCGGCTTAGTCCT 60.108 55.000 29.70 5.51 0.00 3.85
151 155 0.107654 ATGTTGCCGGCTTAGTCCTC 60.108 55.000 29.70 9.10 0.00 3.71
152 156 1.810030 GTTGCCGGCTTAGTCCTCG 60.810 63.158 29.70 0.00 0.00 4.63
153 157 3.659089 TTGCCGGCTTAGTCCTCGC 62.659 63.158 29.70 0.00 0.00 5.03
155 159 2.105128 CCGGCTTAGTCCTCGCTG 59.895 66.667 0.00 0.00 0.00 5.18
156 160 2.415608 CCGGCTTAGTCCTCGCTGA 61.416 63.158 0.00 0.00 31.83 4.26
157 161 1.736586 CGGCTTAGTCCTCGCTGAT 59.263 57.895 0.00 0.00 31.83 2.90
158 162 0.103208 CGGCTTAGTCCTCGCTGATT 59.897 55.000 0.00 0.00 31.83 2.57
159 163 1.471676 CGGCTTAGTCCTCGCTGATTT 60.472 52.381 0.00 0.00 31.83 2.17
160 164 2.633488 GGCTTAGTCCTCGCTGATTTT 58.367 47.619 0.00 0.00 0.00 1.82
161 165 2.352960 GGCTTAGTCCTCGCTGATTTTG 59.647 50.000 0.00 0.00 0.00 2.44
162 166 3.003480 GCTTAGTCCTCGCTGATTTTGT 58.997 45.455 0.00 0.00 0.00 2.83
168 315 1.536766 CCTCGCTGATTTTGTGCTGAA 59.463 47.619 0.00 0.00 0.00 3.02
172 319 2.225019 CGCTGATTTTGTGCTGAAGAGT 59.775 45.455 0.00 0.00 0.00 3.24
173 320 3.433274 CGCTGATTTTGTGCTGAAGAGTA 59.567 43.478 0.00 0.00 0.00 2.59
185 332 7.161404 TGTGCTGAAGAGTATATGTTGAAGTT 58.839 34.615 0.00 0.00 0.00 2.66
225 372 4.098044 TCGAAATTGGTAGGAGTAGCTCAG 59.902 45.833 0.00 0.00 31.08 3.35
250 397 3.161866 TGCCTGAAACAAGGGAAATACC 58.838 45.455 0.00 0.00 34.26 2.73
327 550 0.366871 GCAGAGAACATGTACGTGCG 59.633 55.000 15.12 0.00 0.00 5.34
422 645 6.122277 CCTCCTTCATAGGACATTGCTAAAA 58.878 40.000 0.00 0.00 45.82 1.52
700 924 8.975439 CCTATTCTGTAAACGACCAATATGTAC 58.025 37.037 0.00 0.00 0.00 2.90
723 951 4.803088 CACATAAAAGCTCTCTCTCCTTCG 59.197 45.833 0.00 0.00 0.00 3.79
741 969 4.425520 CTTCGTCACCTCCTTTATCTCAC 58.574 47.826 0.00 0.00 0.00 3.51
1397 3410 8.087982 TGCTATGCTCTAATGCAATAGTAAAC 57.912 34.615 8.63 0.00 46.61 2.01
1423 3436 7.488471 CGTTTTACTAAGCTCTAGTAAGCACAT 59.512 37.037 19.04 0.00 45.00 3.21
1439 3452 6.594788 AAGCACATGTACAATTTCCTGAAT 57.405 33.333 0.00 0.00 0.00 2.57
1456 3471 6.242396 TCCTGAATTTTCGGTTTCCTAATCA 58.758 36.000 0.00 0.00 31.55 2.57
1819 3834 4.153117 CCGAAGAGGATGAACTGAACTTTG 59.847 45.833 0.00 0.00 45.00 2.77
1906 4733 1.618343 GGAAACATTGTGAGGGTTGGG 59.382 52.381 0.00 0.00 0.00 4.12
2032 4859 5.960113 TGGAACATATTGGAAAAACGGATG 58.040 37.500 0.00 0.00 0.00 3.51
2033 4860 4.803613 GGAACATATTGGAAAAACGGATGC 59.196 41.667 0.00 0.00 0.00 3.91
2464 5295 3.090790 TGTAGCACATCCACATGCATTT 58.909 40.909 0.00 0.00 44.59 2.32
2732 5563 1.140852 TGCCTGCCCATACAGTATGAC 59.859 52.381 20.55 12.86 39.69 3.06
3056 5889 1.073284 GGGCAGAAGGTGTGGAAACTA 59.927 52.381 0.00 0.00 0.00 2.24
3163 5996 7.698163 ATCTCTGACCTTTTTATATGGGTCT 57.302 36.000 11.44 0.00 45.85 3.85
3172 6005 3.788227 TTATATGGGTCTGCCATGGTC 57.212 47.619 14.67 6.41 36.17 4.02
3243 6076 5.745312 TGTACCTTTGATGTGTCTCTGAT 57.255 39.130 0.00 0.00 0.00 2.90
3403 6237 2.233271 CTGATGCCAAACTGACTTGGT 58.767 47.619 12.56 0.00 46.53 3.67
3465 6302 9.825109 ATGTATAAAAAGCTAGGAAGTTCTCTC 57.175 33.333 2.25 0.00 0.00 3.20
3736 6575 8.895141 TGTATAGGATATTTTAGCTAGCCTGA 57.105 34.615 12.13 0.00 35.79 3.86
4855 8706 6.775142 TGTCAAGAATTCCTATGTGGTTTTGA 59.225 34.615 0.65 0.00 37.07 2.69
5133 8984 3.386543 GATGTGGGACATCCGGAAG 57.613 57.895 9.01 6.72 46.99 3.46
5391 9242 4.802039 TCAGTTCTCCGTACATTAATTCGC 59.198 41.667 0.00 0.00 0.00 4.70
5449 9301 1.005097 TGCTCAGGAACTTGGCATCAT 59.995 47.619 0.00 0.00 38.17 2.45
5605 9463 1.140161 CAACATGCCAGCCCATTCG 59.860 57.895 0.00 0.00 0.00 3.34
5634 9492 9.880157 TTCTTTTGTTCTTGTTGTACTACTACT 57.120 29.630 8.88 0.00 0.00 2.57
5640 9498 9.784531 TGTTCTTGTTGTACTACTACTACTACT 57.215 33.333 8.88 0.00 31.88 2.57
5898 9757 7.918076 TGGAGAAGATACTTGAAGTACCATTT 58.082 34.615 7.28 0.28 32.84 2.32
5917 9778 3.328382 TTATTGCACAGTCTACGGCTT 57.672 42.857 0.00 0.00 0.00 4.35
5920 9781 2.363788 TGCACAGTCTACGGCTTTAG 57.636 50.000 0.00 0.00 0.00 1.85
5927 9788 4.038883 ACAGTCTACGGCTTTAGAAAGTGT 59.961 41.667 4.05 5.79 38.28 3.55
5932 9793 3.139077 ACGGCTTTAGAAAGTGTTGGAG 58.861 45.455 4.05 0.00 38.28 3.86
5953 9814 8.547967 TGGAGAACATACTTGAAGTACAATTC 57.452 34.615 7.28 11.08 37.88 2.17
5985 9846 7.425606 TGCATTTCCTTTTACTTGTTCTCTTC 58.574 34.615 0.00 0.00 0.00 2.87
6081 9942 6.755141 ACCATATGACAACATTACTACGTGAC 59.245 38.462 3.65 0.00 37.87 3.67
6111 9972 4.505313 TGGATCTCATACATAGACGCAC 57.495 45.455 0.00 0.00 0.00 5.34
6253 10115 2.817665 ACGGAGGGAGTAGCTTTTAGT 58.182 47.619 0.00 0.00 0.00 2.24
6546 10453 3.827898 GGTCCAGGACTCGCTCCG 61.828 72.222 19.57 0.00 45.10 4.63
6568 10475 3.535561 AGCAAGATACTTGTGAATCCGG 58.464 45.455 12.07 0.00 0.00 5.14
6649 10556 1.272816 TGGGTCACAAGGGATACTCGA 60.273 52.381 0.00 0.00 0.00 4.04
6653 10560 2.230508 GTCACAAGGGATACTCGACACA 59.769 50.000 0.00 0.00 0.00 3.72
6661 10568 2.915463 GGATACTCGACACAGTTTGACG 59.085 50.000 0.00 0.00 43.63 4.35
6693 10600 7.446001 AGAAAATGAAAAGGAACTCTAGCTG 57.554 36.000 0.00 0.00 38.49 4.24
6848 10755 1.487482 GGTTGTTTTTGCTCTTCCGC 58.513 50.000 0.00 0.00 0.00 5.54
6901 10808 4.209288 CAGAACTGTTTGTACTTCGTGAGG 59.791 45.833 0.00 0.00 0.00 3.86
6912 10819 6.289834 TGTACTTCGTGAGGGAAATTTGTTA 58.710 36.000 0.00 0.00 0.00 2.41
6913 10820 6.938030 TGTACTTCGTGAGGGAAATTTGTTAT 59.062 34.615 0.00 0.00 0.00 1.89
6916 10823 7.391620 ACTTCGTGAGGGAAATTTGTTATAGA 58.608 34.615 0.00 0.00 0.00 1.98
6943 10850 9.681062 AAAAGCACTGTATATTTGTACCTATGT 57.319 29.630 0.00 0.00 0.00 2.29
7044 10951 2.004583 TAAGTTGTTCATCGCGGAGG 57.995 50.000 6.13 0.00 0.00 4.30
7095 11019 5.635549 GAAAAACTTTTCCGGTGACATTG 57.364 39.130 0.00 0.00 40.41 2.82
7096 11020 4.729227 AAAACTTTTCCGGTGACATTGT 57.271 36.364 0.00 0.00 0.00 2.71
7097 11021 5.838531 AAAACTTTTCCGGTGACATTGTA 57.161 34.783 0.00 0.00 0.00 2.41
7098 11022 6.399639 AAAACTTTTCCGGTGACATTGTAT 57.600 33.333 0.00 0.00 0.00 2.29
7099 11023 7.513371 AAAACTTTTCCGGTGACATTGTATA 57.487 32.000 0.00 0.00 0.00 1.47
7100 11024 6.490566 AACTTTTCCGGTGACATTGTATAC 57.509 37.500 0.00 0.00 0.00 1.47
7124 11048 3.564511 GCAACATGTTCTGCGTATTTGT 58.435 40.909 8.48 0.00 0.00 2.83
7142 11066 7.530525 CGTATTTGTGACTATGTTGTTTCTGTG 59.469 37.037 0.00 0.00 0.00 3.66
7209 11133 6.094719 TGTTTGAAGCAGAAATATGATGCAC 58.905 36.000 9.07 4.51 42.45 4.57
7251 11175 0.723414 CGCCTTACTGCATGTGACTG 59.277 55.000 0.00 0.00 0.00 3.51
7266 11190 3.641436 TGTGACTGTAGTTCTGTGGATGT 59.359 43.478 0.00 0.00 0.00 3.06
7379 11304 6.161855 TGGGCTTATGTGACTATAGTTGAG 57.838 41.667 6.88 0.00 0.00 3.02
7384 11309 2.876091 TGTGACTATAGTTGAGTGCGC 58.124 47.619 6.88 0.00 0.00 6.09
7397 11322 2.223900 TGAGTGCGCAAGAGGATATCTG 60.224 50.000 14.00 0.00 38.67 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 76 1.863454 GCGATGGCTGTTGATCTACTG 59.137 52.381 8.74 9.03 35.83 2.74
128 132 3.155470 CTAAGCCGGCAACATCGCG 62.155 63.158 31.54 0.00 0.00 5.87
148 152 1.159285 TCAGCACAAAATCAGCGAGG 58.841 50.000 0.00 0.00 0.00 4.63
150 154 2.481568 CTCTTCAGCACAAAATCAGCGA 59.518 45.455 0.00 0.00 0.00 4.93
151 155 2.225019 ACTCTTCAGCACAAAATCAGCG 59.775 45.455 0.00 0.00 0.00 5.18
152 156 3.911661 ACTCTTCAGCACAAAATCAGC 57.088 42.857 0.00 0.00 0.00 4.26
153 157 8.206325 ACATATACTCTTCAGCACAAAATCAG 57.794 34.615 0.00 0.00 0.00 2.90
155 159 8.668353 TCAACATATACTCTTCAGCACAAAATC 58.332 33.333 0.00 0.00 0.00 2.17
156 160 8.565896 TCAACATATACTCTTCAGCACAAAAT 57.434 30.769 0.00 0.00 0.00 1.82
157 161 7.977789 TCAACATATACTCTTCAGCACAAAA 57.022 32.000 0.00 0.00 0.00 2.44
158 162 7.661437 ACTTCAACATATACTCTTCAGCACAAA 59.339 33.333 0.00 0.00 0.00 2.83
159 163 7.161404 ACTTCAACATATACTCTTCAGCACAA 58.839 34.615 0.00 0.00 0.00 3.33
160 164 6.701340 ACTTCAACATATACTCTTCAGCACA 58.299 36.000 0.00 0.00 0.00 4.57
161 165 7.602517 AACTTCAACATATACTCTTCAGCAC 57.397 36.000 0.00 0.00 0.00 4.40
162 166 7.361201 GCAAACTTCAACATATACTCTTCAGCA 60.361 37.037 0.00 0.00 0.00 4.41
168 315 8.798859 AATCAGCAAACTTCAACATATACTCT 57.201 30.769 0.00 0.00 0.00 3.24
172 319 8.087136 TGCAAAATCAGCAAACTTCAACATATA 58.913 29.630 0.00 0.00 39.39 0.86
173 320 6.930164 TGCAAAATCAGCAAACTTCAACATAT 59.070 30.769 0.00 0.00 39.39 1.78
185 332 5.369685 TTTCGATAGTGCAAAATCAGCAA 57.630 34.783 9.51 0.00 44.64 3.91
225 372 0.250901 TCCCTTGTTTCAGGCAGCTC 60.251 55.000 0.00 0.00 31.69 4.09
250 397 5.872617 ACAAACAATGAATCTTGCATCCATG 59.127 36.000 0.00 0.00 0.00 3.66
302 525 3.257375 ACGTACATGTTCTCTGCTTGGTA 59.743 43.478 2.30 0.00 0.00 3.25
422 645 0.254178 ACGCAGCTTGGAAGGATCAT 59.746 50.000 0.00 0.00 0.00 2.45
553 777 8.700644 GCGATTGTACAACTATTCCTACATAAG 58.299 37.037 11.22 0.00 0.00 1.73
598 822 1.210478 TGCAGGAGCCTCCAAATACTC 59.790 52.381 14.46 0.00 39.61 2.59
700 924 4.803088 CGAAGGAGAGAGAGCTTTTATGTG 59.197 45.833 0.00 0.00 0.00 3.21
723 951 4.382147 GGTGAGTGAGATAAAGGAGGTGAC 60.382 50.000 0.00 0.00 0.00 3.67
741 969 3.853355 AAGAATAGGCCATCTGGTGAG 57.147 47.619 5.01 0.00 37.57 3.51
1290 3281 2.035449 TGAATCCATCGTATCCACCGTC 59.965 50.000 0.00 0.00 0.00 4.79
1397 3410 6.805271 TGTGCTTACTAGAGCTTAGTAAAACG 59.195 38.462 19.77 13.74 43.11 3.60
1423 3436 6.642707 ACCGAAAATTCAGGAAATTGTACA 57.357 33.333 0.00 0.00 37.64 2.90
1439 3452 7.014808 ACAAAAGGATGATTAGGAAACCGAAAA 59.985 33.333 0.00 0.00 0.00 2.29
1456 3471 8.434589 TTCCCTGATAATGAAAACAAAAGGAT 57.565 30.769 0.00 0.00 0.00 3.24
1819 3834 5.751586 TGTTCCCCAAATCAGATACCTTAC 58.248 41.667 0.00 0.00 0.00 2.34
2464 5295 4.320714 GCATCTTTGTGCAGAGAACAATCA 60.321 41.667 0.00 0.00 44.43 2.57
3056 5889 7.781324 ACACCTAAGAAATCAACCAAATGAT 57.219 32.000 0.00 0.00 41.74 2.45
3172 6005 2.293122 TGTCTTGTCGAAAATTGGGCAG 59.707 45.455 0.00 0.00 0.00 4.85
3465 6302 2.438021 TGGATAAATTCCCGACTGGAGG 59.562 50.000 0.00 0.00 46.24 4.30
3932 6777 6.287525 TGTGTTGACATCAGACTGAAATGTA 58.712 36.000 9.70 0.00 33.91 2.29
4361 8191 9.632638 ACCATCTCATTTTATTTATGCACTAGT 57.367 29.630 0.00 0.00 0.00 2.57
4795 8646 1.338769 GCTTGTCCGGTTGTCCACTAT 60.339 52.381 0.00 0.00 0.00 2.12
4807 8658 6.183360 ACAAATGAATTATAGGTGCTTGTCCG 60.183 38.462 0.00 0.00 0.00 4.79
5133 8984 2.557056 CCCATCAGCATTGGATGTCATC 59.443 50.000 4.06 4.06 40.38 2.92
5391 9242 7.227156 ACCTATATGTGGGAGAAAAATAGCAG 58.773 38.462 0.00 0.00 0.00 4.24
5605 9463 8.880750 AGTAGTACAACAAGAACAAAAGAACTC 58.119 33.333 2.52 0.00 0.00 3.01
5634 9492 9.324008 AGGATGCAGATAGTAGTAGTAGTAGTA 57.676 37.037 0.00 2.65 0.00 1.82
5635 9493 8.209802 AGGATGCAGATAGTAGTAGTAGTAGT 57.790 38.462 0.00 0.00 0.00 2.73
5636 9494 9.509956 AAAGGATGCAGATAGTAGTAGTAGTAG 57.490 37.037 0.00 0.00 0.00 2.57
5637 9495 9.863650 AAAAGGATGCAGATAGTAGTAGTAGTA 57.136 33.333 0.00 0.00 0.00 1.82
5638 9496 8.770010 AAAAGGATGCAGATAGTAGTAGTAGT 57.230 34.615 0.00 0.00 0.00 2.73
5640 9498 9.863650 AGTAAAAGGATGCAGATAGTAGTAGTA 57.136 33.333 0.00 0.00 0.00 1.82
5641 9499 8.770010 AGTAAAAGGATGCAGATAGTAGTAGT 57.230 34.615 0.00 0.00 0.00 2.73
5642 9500 9.469807 CAAGTAAAAGGATGCAGATAGTAGTAG 57.530 37.037 0.00 0.00 0.00 2.57
5643 9501 7.926555 GCAAGTAAAAGGATGCAGATAGTAGTA 59.073 37.037 0.00 0.00 38.63 1.82
5644 9502 6.763610 GCAAGTAAAAGGATGCAGATAGTAGT 59.236 38.462 0.00 0.00 38.63 2.73
5645 9503 6.203723 GGCAAGTAAAAGGATGCAGATAGTAG 59.796 42.308 0.00 0.00 40.51 2.57
5646 9504 6.055588 GGCAAGTAAAAGGATGCAGATAGTA 58.944 40.000 0.00 0.00 40.51 1.82
5898 9757 3.328382 AAAGCCGTAGACTGTGCAATA 57.672 42.857 0.00 0.00 0.00 1.90
5917 9778 8.208224 TCAAGTATGTTCTCCAACACTTTCTAA 58.792 33.333 0.00 0.00 45.47 2.10
5920 9781 6.861065 TCAAGTATGTTCTCCAACACTTTC 57.139 37.500 0.00 0.00 45.47 2.62
5927 9788 8.918202 AATTGTACTTCAAGTATGTTCTCCAA 57.082 30.769 0.00 0.00 39.55 3.53
5932 9793 8.237267 CCAAGGAATTGTACTTCAAGTATGTTC 58.763 37.037 0.00 5.90 39.55 3.18
5953 9814 5.665916 AGTAAAAGGAAATGCATCCAAGG 57.334 39.130 9.02 0.00 42.27 3.61
6106 9967 1.736645 GCATGTCTACACCGTGCGT 60.737 57.895 0.00 0.00 0.00 5.24
6108 9969 1.079127 AGGCATGTCTACACCGTGC 60.079 57.895 0.00 0.00 34.16 5.34
6111 9972 1.204704 TCAAGAGGCATGTCTACACCG 59.795 52.381 0.00 0.00 0.00 4.94
6235 10097 3.770388 AGTGACTAAAAGCTACTCCCTCC 59.230 47.826 0.00 0.00 0.00 4.30
6253 10115 8.981659 TGAAAGATCTATGTTATCCAAGAGTGA 58.018 33.333 0.00 0.00 0.00 3.41
6524 10431 1.040339 AGCGAGTCCTGGACCATCTC 61.040 60.000 22.81 12.77 32.18 2.75
6546 10453 3.557595 CCGGATTCACAAGTATCTTGCTC 59.442 47.826 0.00 2.72 0.00 4.26
6568 10475 6.506513 CGAAGTATCTGCACACTCGATTTAAC 60.507 42.308 0.00 0.00 31.41 2.01
6649 10556 6.671614 TTCTATTGTTTCGTCAAACTGTGT 57.328 33.333 1.97 0.00 42.29 3.72
6653 10560 9.796120 TTTCATTTTCTATTGTTTCGTCAAACT 57.204 25.926 1.97 0.00 42.29 2.66
6693 10600 8.109705 TGGCATCCATTTTATATGTACATCAC 57.890 34.615 12.68 0.00 0.00 3.06
6714 10621 0.818938 CATATGCACTTGGCTTGGCA 59.181 50.000 0.00 0.00 45.15 4.92
6848 10755 1.467734 GGATGAACTGCAACTGCTCAG 59.532 52.381 2.95 0.00 42.66 3.35
6901 10808 9.476202 ACAGTGCTTTTTCTATAACAAATTTCC 57.524 29.630 0.00 0.00 0.00 3.13
6913 10820 9.953565 AGGTACAAATATACAGTGCTTTTTCTA 57.046 29.630 0.00 0.00 0.00 2.10
6941 10848 7.470935 TCTTGCAAAGTACAGGTAGTATACA 57.529 36.000 5.50 0.00 44.29 2.29
6942 10849 8.767478 TTTCTTGCAAAGTACAGGTAGTATAC 57.233 34.615 0.00 0.00 46.34 1.47
6943 10850 9.953565 AATTTCTTGCAAAGTACAGGTAGTATA 57.046 29.630 0.00 0.00 46.34 1.47
6944 10851 8.863872 AATTTCTTGCAAAGTACAGGTAGTAT 57.136 30.769 0.00 0.00 46.34 2.12
7021 10928 4.750098 CCTCCGCGATGAACAACTTATAAT 59.250 41.667 8.23 0.00 0.00 1.28
7025 10932 1.274167 ACCTCCGCGATGAACAACTTA 59.726 47.619 8.23 0.00 0.00 2.24
7026 10933 0.034896 ACCTCCGCGATGAACAACTT 59.965 50.000 8.23 0.00 0.00 2.66
7027 10934 0.670546 CACCTCCGCGATGAACAACT 60.671 55.000 8.23 0.00 0.00 3.16
7028 10935 1.635663 CCACCTCCGCGATGAACAAC 61.636 60.000 8.23 0.00 0.00 3.32
7029 10936 1.375396 CCACCTCCGCGATGAACAA 60.375 57.895 8.23 0.00 0.00 2.83
7031 10938 1.810030 GTCCACCTCCGCGATGAAC 60.810 63.158 8.23 0.00 0.00 3.18
7039 10946 2.027625 GTTCAAGCGTCCACCTCCG 61.028 63.158 0.00 0.00 0.00 4.63
7085 11009 0.228742 GCGCGTATACAATGTCACCG 59.771 55.000 8.43 0.00 0.00 4.94
7086 11010 1.282817 TGCGCGTATACAATGTCACC 58.717 50.000 8.43 0.00 0.00 4.02
7087 11011 2.092995 TGTTGCGCGTATACAATGTCAC 59.907 45.455 8.43 0.00 0.00 3.67
7088 11012 2.338500 TGTTGCGCGTATACAATGTCA 58.662 42.857 8.43 0.00 0.00 3.58
7089 11013 3.242284 ACATGTTGCGCGTATACAATGTC 60.242 43.478 8.43 0.00 0.00 3.06
7090 11014 2.675844 ACATGTTGCGCGTATACAATGT 59.324 40.909 8.43 8.23 0.00 2.71
7091 11015 3.317744 ACATGTTGCGCGTATACAATG 57.682 42.857 8.43 7.59 0.00 2.82
7092 11016 3.621268 AGAACATGTTGCGCGTATACAAT 59.379 39.130 17.58 1.49 0.00 2.71
7093 11017 2.997303 AGAACATGTTGCGCGTATACAA 59.003 40.909 17.58 0.00 0.00 2.41
7094 11018 2.347150 CAGAACATGTTGCGCGTATACA 59.653 45.455 17.58 11.11 0.00 2.29
7095 11019 2.845764 GCAGAACATGTTGCGCGTATAC 60.846 50.000 17.58 5.28 0.00 1.47
7096 11020 1.326245 GCAGAACATGTTGCGCGTATA 59.674 47.619 17.58 0.00 0.00 1.47
7097 11021 0.096976 GCAGAACATGTTGCGCGTAT 59.903 50.000 17.58 0.00 0.00 3.06
7098 11022 1.495509 GCAGAACATGTTGCGCGTA 59.504 52.632 17.58 0.00 0.00 4.42
7099 11023 2.252260 GCAGAACATGTTGCGCGT 59.748 55.556 17.58 0.00 0.00 6.01
7124 11048 4.960938 AGAGCACAGAAACAACATAGTCA 58.039 39.130 0.00 0.00 0.00 3.41
7142 11066 2.031682 AGCACAAATGTCAAACGAGAGC 60.032 45.455 0.00 0.00 0.00 4.09
7209 11133 3.373748 GGAAACACCTGCCAAACTTTTTG 59.626 43.478 0.00 0.00 35.41 2.44
7341 11266 8.849168 CACATAAGCCCATAAGATAAATTCACA 58.151 33.333 0.00 0.00 0.00 3.58
7379 11304 0.864455 GCAGATATCCTCTTGCGCAC 59.136 55.000 11.12 0.00 29.16 5.34
7384 11309 3.474600 CAACCCAGCAGATATCCTCTTG 58.525 50.000 0.00 0.00 29.16 3.02
7397 11322 3.255642 TCTTCTAAAATGTGCAACCCAGC 59.744 43.478 0.00 0.00 34.36 4.85


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

AutoCloner maintained by Alex Coulton.