Multiple sequence alignment - TraesCS5A01G033300

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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 TraesCS5A01G033300 chr5A 100.000 4151 0 0 1 4151 30403522 30407672 0.000000e+00 7666
1 TraesCS5A01G033300 chr5A 93.330 3583 180 34 593 4151 555770318 555773865 0.000000e+00 5238
2 TraesCS5A01G033300 chr5D 92.622 4012 222 45 153 4151 42016029 42019979 0.000000e+00 5701
3 TraesCS5A01G033300 chr5D 92.633 3760 219 30 423 4151 440159793 440163525 0.000000e+00 5356
4 TraesCS5A01G033300 chr5D 88.133 1559 138 19 285 1808 42054072 42052526 0.000000e+00 1810
5 TraesCS5A01G033300 chr5D 94.839 620 23 4 1833 2452 42052528 42051918 0.000000e+00 959
6 TraesCS5A01G033300 chr5B 92.100 3747 229 36 437 4151 535110725 535114436 0.000000e+00 5217
7 TraesCS5A01G033300 chr5B 90.355 4054 245 56 163 4151 36719637 36723609 0.000000e+00 5186
8 TraesCS5A01G033300 chr5B 93.106 2379 111 16 818 3195 36767815 36765489 0.000000e+00 3435
9 TraesCS5A01G033300 chr5B 82.183 623 97 8 176 791 36771844 36771229 1.320000e-144 523
10 TraesCS5A01G033300 chr5B 95.973 149 4 2 3778 3926 36765233 36765087 1.490000e-59 241
11 TraesCS5A01G033300 chr5B 98.473 131 2 0 3952 4082 36765090 36764960 8.970000e-57 231
12 TraesCS5A01G033300 chr5B 91.150 113 10 0 1 113 36773090 36772978 2.000000e-33 154
13 TraesCS5A01G033300 chr5B 91.150 113 10 0 1 113 36813996 36813884 2.000000e-33 154
14 TraesCS5A01G033300 chr5B 91.150 113 9 1 1 113 36697271 36697382 7.190000e-33 152
15 TraesCS5A01G033300 chr3A 91.803 122 10 0 291 412 695634639 695634518 1.980000e-38 171
16 TraesCS5A01G033300 chr3A 91.803 122 10 0 291 412 695644623 695644502 1.980000e-38 171
17 TraesCS5A01G033300 chrUn 90.984 122 11 0 291 412 392770448 392770327 9.230000e-37 165
18 TraesCS5A01G033300 chrUn 91.150 113 10 0 1 113 65848605 65848717 2.000000e-33 154
19 TraesCS5A01G033300 chrUn 91.150 113 10 0 1 113 340279376 340279488 2.000000e-33 154
20 TraesCS5A01G033300 chrUn 91.150 113 10 0 1 113 340337903 340338015 2.000000e-33 154
21 TraesCS5A01G033300 chr7B 90.984 122 11 0 291 412 622433732 622433853 9.230000e-37 165
22 TraesCS5A01G033300 chr2D 90.984 122 11 0 291 412 591988847 591988726 9.230000e-37 165


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 TraesCS5A01G033300 chr5A 30403522 30407672 4150 False 7666.0 7666 100.000 1 4151 1 chr5A.!!$F1 4150
1 TraesCS5A01G033300 chr5A 555770318 555773865 3547 False 5238.0 5238 93.330 593 4151 1 chr5A.!!$F2 3558
2 TraesCS5A01G033300 chr5D 42016029 42019979 3950 False 5701.0 5701 92.622 153 4151 1 chr5D.!!$F1 3998
3 TraesCS5A01G033300 chr5D 440159793 440163525 3732 False 5356.0 5356 92.633 423 4151 1 chr5D.!!$F2 3728
4 TraesCS5A01G033300 chr5D 42051918 42054072 2154 True 1384.5 1810 91.486 285 2452 2 chr5D.!!$R1 2167
5 TraesCS5A01G033300 chr5B 535110725 535114436 3711 False 5217.0 5217 92.100 437 4151 1 chr5B.!!$F3 3714
6 TraesCS5A01G033300 chr5B 36719637 36723609 3972 False 5186.0 5186 90.355 163 4151 1 chr5B.!!$F2 3988
7 TraesCS5A01G033300 chr5B 36764960 36773090 8130 True 916.8 3435 92.177 1 4082 5 chr5B.!!$R2 4081

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
174 1254 0.182537 CTCTGAACCCCAACACCACA 59.817 55.0 0.0 0.0 0.00 4.17 F
340 1426 0.322322 CCGTACTTGGCTACCCAACA 59.678 55.0 0.0 0.0 46.01 3.33 F
738 1835 0.790207 TGCTCTTAAAAGACAGCGCG 59.210 50.0 0.0 0.0 31.10 6.86 F
1956 6453 0.035152 ATGCAGATGAGGCGTTGGAA 60.035 50.0 0.0 0.0 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1930 6427 0.251033 GCCTCATCTGCATGCCCATA 60.251 55.000 16.68 0.0 0.00 2.74 R
1956 6453 2.476199 CCCTCTGACTCCCTCAAGAAT 58.524 52.381 0.00 0.0 0.00 2.40 R
2673 7170 1.342819 AGCTCTGTCGCTTCTTTCAGT 59.657 47.619 0.00 0.0 36.74 3.41 R
3709 8330 0.889186 GGTGGCCAACGAACATCTGT 60.889 55.000 7.24 0.0 0.00 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 39 9.920133 GACTAGATGATCAATCTAAGCAATGTA 57.080 33.333 0.00 0.00 45.34 2.29
80 81 5.775195 AGCCTTTAGGAATATATTGTTGCCC 59.225 40.000 1.78 0.00 37.39 5.36
113 114 2.282391 TTGGCCTCATGCGCAACT 60.282 55.556 17.11 0.00 42.61 3.16
117 1197 0.740737 GGCCTCATGCGCAACTATTT 59.259 50.000 17.11 0.00 42.61 1.40
118 1198 1.268743 GGCCTCATGCGCAACTATTTC 60.269 52.381 17.11 0.09 42.61 2.17
122 1202 4.039703 CCTCATGCGCAACTATTTCATTG 58.960 43.478 17.11 3.67 0.00 2.82
124 1204 3.693578 TCATGCGCAACTATTTCATTGGA 59.306 39.130 17.11 0.00 0.00 3.53
126 1206 3.081061 TGCGCAACTATTTCATTGGACT 58.919 40.909 8.16 0.00 0.00 3.85
129 1209 3.941483 CGCAACTATTTCATTGGACTCCT 59.059 43.478 0.00 0.00 0.00 3.69
138 1218 2.622942 TCATTGGACTCCTTGCACAAAC 59.377 45.455 0.00 0.00 0.00 2.93
140 1220 0.257328 TGGACTCCTTGCACAAACCA 59.743 50.000 0.00 0.00 0.00 3.67
142 1222 1.754226 GGACTCCTTGCACAAACCAAA 59.246 47.619 0.00 0.00 0.00 3.28
143 1223 2.167487 GGACTCCTTGCACAAACCAAAA 59.833 45.455 0.00 0.00 0.00 2.44
144 1224 3.186909 GACTCCTTGCACAAACCAAAAC 58.813 45.455 0.00 0.00 0.00 2.43
145 1225 2.093711 ACTCCTTGCACAAACCAAAACC 60.094 45.455 0.00 0.00 0.00 3.27
146 1226 1.902508 TCCTTGCACAAACCAAAACCA 59.097 42.857 0.00 0.00 0.00 3.67
148 1228 2.613133 CCTTGCACAAACCAAAACCATG 59.387 45.455 0.00 0.00 0.00 3.66
149 1229 3.529533 CTTGCACAAACCAAAACCATGA 58.470 40.909 0.00 0.00 0.00 3.07
150 1230 3.176552 TGCACAAACCAAAACCATGAG 57.823 42.857 0.00 0.00 0.00 2.90
151 1231 1.866601 GCACAAACCAAAACCATGAGC 59.133 47.619 0.00 0.00 0.00 4.26
157 1237 0.804989 CCAAAACCATGAGCCGTCTC 59.195 55.000 0.00 0.00 39.78 3.36
161 1241 0.976641 AACCATGAGCCGTCTCTGAA 59.023 50.000 0.00 0.00 40.03 3.02
168 1248 1.671379 GCCGTCTCTGAACCCCAAC 60.671 63.158 0.00 0.00 0.00 3.77
169 1249 1.752198 CCGTCTCTGAACCCCAACA 59.248 57.895 0.00 0.00 0.00 3.33
172 1252 0.472471 GTCTCTGAACCCCAACACCA 59.528 55.000 0.00 0.00 0.00 4.17
174 1254 0.182537 CTCTGAACCCCAACACCACA 59.817 55.000 0.00 0.00 0.00 4.17
194 1274 1.137479 AGAGGTAGTCGTCGGAGAGAG 59.863 57.143 0.00 0.00 36.95 3.20
199 1279 0.614294 AGTCGTCGGAGAGAGAGGAA 59.386 55.000 0.00 0.00 36.95 3.36
223 1303 7.682787 AAAGTACCTCCTTCATCATCATAGT 57.317 36.000 0.00 0.00 0.00 2.12
239 1319 1.179174 TAGTCGGGAGGGCATCATCG 61.179 60.000 0.08 4.63 0.00 3.84
240 1320 2.443952 TCGGGAGGGCATCATCGT 60.444 61.111 12.28 0.00 0.00 3.73
247 1327 0.904649 AGGGCATCATCGTTGTCAGA 59.095 50.000 0.00 0.00 0.00 3.27
257 1337 2.473816 TCGTTGTCAGAGCTTTGTGAG 58.526 47.619 3.90 0.00 0.00 3.51
258 1338 2.100749 TCGTTGTCAGAGCTTTGTGAGA 59.899 45.455 3.90 0.00 0.00 3.27
264 1350 2.435805 TCAGAGCTTTGTGAGACAAGGT 59.564 45.455 3.90 0.00 39.53 3.50
269 1355 1.876156 CTTTGTGAGACAAGGTCTGCC 59.124 52.381 3.21 0.00 43.53 4.85
306 1392 9.681062 ACACACATAAACTACCTATATGCTTTT 57.319 29.630 0.00 0.00 31.66 2.27
340 1426 0.322322 CCGTACTTGGCTACCCAACA 59.678 55.000 0.00 0.00 46.01 3.33
369 1455 2.176889 AGGCACGATAACTGGTACACT 58.823 47.619 0.00 0.00 0.00 3.55
380 1466 3.490348 ACTGGTACACTAGTGGTACGTT 58.510 45.455 26.12 7.21 41.53 3.99
419 1505 5.126707 CGTACTAGGGAAAGGTCATGTTAGT 59.873 44.000 0.00 0.00 0.00 2.24
421 1507 5.091552 ACTAGGGAAAGGTCATGTTAGTCA 58.908 41.667 0.00 0.00 0.00 3.41
424 1510 3.010420 GGAAAGGTCATGTTAGTCAGGC 58.990 50.000 0.00 0.00 0.00 4.85
519 1613 2.275547 CTTGCGCCTCTTTCCATGCC 62.276 60.000 4.18 0.00 0.00 4.40
526 1620 1.409802 CCTCTTTCCATGCCTCATGCT 60.410 52.381 1.47 0.00 40.20 3.79
530 1624 3.054139 TCTTTCCATGCCTCATGCTAACT 60.054 43.478 1.47 0.00 40.20 2.24
538 1632 6.883217 CCATGCCTCATGCTAACTATCTTATT 59.117 38.462 1.47 0.00 40.20 1.40
549 1643 5.552870 AACTATCTTATTCCACGAGCCAT 57.447 39.130 0.00 0.00 0.00 4.40
563 1657 1.001020 GCCATCACCACCACCATGA 60.001 57.895 0.00 0.00 0.00 3.07
595 1690 1.284408 GCCATCCGCGAACACAAAA 59.716 52.632 8.23 0.00 0.00 2.44
622 1717 2.499693 TGCTCCTCAACCACGATTATGA 59.500 45.455 0.00 0.00 0.00 2.15
629 1724 4.269183 TCAACCACGATTATGAAGGCAAT 58.731 39.130 0.00 0.00 0.00 3.56
631 1726 5.295787 TCAACCACGATTATGAAGGCAATAC 59.704 40.000 0.00 0.00 0.00 1.89
640 1736 8.393366 CGATTATGAAGGCAATACATATGAAGG 58.607 37.037 10.38 0.00 0.00 3.46
651 1747 9.273016 GCAATACATATGAAGGCTCTAAGTTTA 57.727 33.333 10.38 0.00 0.00 2.01
696 1792 3.700538 TCATAAGCATTTGGAGGCTGTT 58.299 40.909 0.00 0.00 43.08 3.16
738 1835 0.790207 TGCTCTTAAAAGACAGCGCG 59.210 50.000 0.00 0.00 31.10 6.86
798 1897 3.129287 AGAAGCCTGGTATTGCAAAATCG 59.871 43.478 1.71 0.00 0.00 3.34
802 1904 3.377172 GCCTGGTATTGCAAAATCGTACT 59.623 43.478 1.71 0.00 0.00 2.73
807 5173 7.656137 CCTGGTATTGCAAAATCGTACTACTAT 59.344 37.037 1.71 0.00 0.00 2.12
839 5325 2.099405 GCAAAAAGGCTATGTGGGCTA 58.901 47.619 0.00 0.00 41.31 3.93
969 5462 1.254026 GCCTTCCTAACCACCAAACC 58.746 55.000 0.00 0.00 0.00 3.27
1042 5539 1.081174 ACCCATTTCTCCTCCTCCTCA 59.919 52.381 0.00 0.00 0.00 3.86
1047 5544 2.723530 TTCTCCTCCTCCTCAAACCT 57.276 50.000 0.00 0.00 0.00 3.50
1134 5631 2.040178 GTCAAGGAGATACCCCACGAT 58.960 52.381 0.00 0.00 40.05 3.73
1563 6060 1.003355 CATGCAGAAGGACGGGTGT 60.003 57.895 0.00 0.00 0.00 4.16
1601 6098 1.806758 GCAATGTGGCGGTGAATGC 60.807 57.895 0.00 0.00 0.00 3.56
1608 6105 2.202349 GCGGTGAATGCGCTTGTC 60.202 61.111 9.73 3.59 0.00 3.18
1737 6234 2.429930 CGGAGGGTTGTTGAGGCA 59.570 61.111 0.00 0.00 0.00 4.75
1749 6246 5.181748 GTTGTTGAGGCACTAGAGATGATT 58.818 41.667 0.00 0.00 41.55 2.57
1751 6248 4.467438 TGTTGAGGCACTAGAGATGATTGA 59.533 41.667 0.00 0.00 41.55 2.57
1865 6362 1.342374 GGGTTTGCTTGGGAGGATGAT 60.342 52.381 0.00 0.00 0.00 2.45
1956 6453 0.035152 ATGCAGATGAGGCGTTGGAA 60.035 50.000 0.00 0.00 0.00 3.53
2060 6557 2.830370 GATGGCCGAGGCAAAGGG 60.830 66.667 16.65 0.00 42.43 3.95
2526 7023 8.811994 AGCAAAGGTTGTACCATTAATGTTATT 58.188 29.630 14.25 0.00 41.95 1.40
2610 7107 5.745312 TGTTGGATGACTTGTATCTCAGT 57.255 39.130 0.00 0.00 0.00 3.41
2673 7170 2.227194 GCTTTGGGAAAGAAAGGTCGA 58.773 47.619 0.16 0.00 41.02 4.20
2733 7230 6.487299 AATAGAGGAATTGTCCCTACACTC 57.513 41.667 0.00 0.00 46.30 3.51
3118 7615 7.771183 TGCTGGGAAGCTTATAATTAAGTTTG 58.229 34.615 0.00 0.00 38.50 2.93
3175 7679 2.785540 TGCTGTCTGGCATGTTGATA 57.214 45.000 0.00 0.00 37.29 2.15
3239 7826 8.741603 ATTTGATCTGACATGTTGATGTATCA 57.258 30.769 16.58 10.14 43.22 2.15
3240 7827 8.741603 TTTGATCTGACATGTTGATGTATCAT 57.258 30.769 16.58 0.00 43.22 2.45
3241 7828 7.724305 TGATCTGACATGTTGATGTATCATG 57.276 36.000 16.58 0.00 43.22 3.07
3326 7917 4.756135 GGGTTCAGTTGGTAACGTTTCATA 59.244 41.667 5.91 0.00 42.51 2.15
3337 7928 1.591248 CGTTTCATACGTTGTGCTGC 58.409 50.000 0.00 0.00 45.14 5.25
3339 7930 2.349438 CGTTTCATACGTTGTGCTGCTT 60.349 45.455 0.00 0.00 45.14 3.91
3340 7931 3.120820 CGTTTCATACGTTGTGCTGCTTA 60.121 43.478 0.00 0.00 45.14 3.09
3341 7932 4.394795 GTTTCATACGTTGTGCTGCTTAG 58.605 43.478 0.00 0.00 0.00 2.18
3342 7933 3.313012 TCATACGTTGTGCTGCTTAGT 57.687 42.857 0.00 0.00 0.00 2.24
3343 7934 3.659786 TCATACGTTGTGCTGCTTAGTT 58.340 40.909 0.00 0.00 0.00 2.24
3344 7935 4.811908 TCATACGTTGTGCTGCTTAGTTA 58.188 39.130 0.00 0.00 0.00 2.24
3363 7975 3.967886 GCTGCCAGCGAATAGACTA 57.032 52.632 0.00 0.00 0.00 2.59
3398 8010 3.375299 CCTGAATGTTAGTTAGCTGCCAC 59.625 47.826 0.00 0.00 0.00 5.01
3399 8011 4.256920 CTGAATGTTAGTTAGCTGCCACT 58.743 43.478 0.00 7.22 0.00 4.00
3400 8012 4.253685 TGAATGTTAGTTAGCTGCCACTC 58.746 43.478 5.42 0.00 0.00 3.51
3401 8013 3.981071 ATGTTAGTTAGCTGCCACTCA 57.019 42.857 5.42 0.47 0.00 3.41
3402 8014 3.762407 TGTTAGTTAGCTGCCACTCAA 57.238 42.857 5.42 0.00 0.00 3.02
3403 8015 4.079980 TGTTAGTTAGCTGCCACTCAAA 57.920 40.909 5.42 0.00 0.00 2.69
3404 8016 4.065088 TGTTAGTTAGCTGCCACTCAAAG 58.935 43.478 5.42 0.00 0.00 2.77
3405 8017 2.191128 AGTTAGCTGCCACTCAAAGG 57.809 50.000 0.00 0.00 0.00 3.11
3406 8018 1.168714 GTTAGCTGCCACTCAAAGGG 58.831 55.000 0.00 0.00 0.00 3.95
3484 8105 7.038302 TCCATAATGAACTAGACCAAGTGAAGT 60.038 37.037 0.00 0.00 0.00 3.01
3517 8138 2.122768 GAGACAATGGAGGGAGATGGT 58.877 52.381 0.00 0.00 0.00 3.55
3565 8186 1.037579 TCATCGATGACCGGTCAGCT 61.038 55.000 40.49 27.70 43.26 4.24
3605 8226 4.424711 GGGAGCCGGTGCCATTCA 62.425 66.667 15.24 0.00 36.40 2.57
3709 8330 0.537371 TCACTCTCAGCCTCGTCACA 60.537 55.000 0.00 0.00 0.00 3.58
3739 8360 2.674380 GGCCACCTTGGTGAGCTG 60.674 66.667 20.27 5.52 40.46 4.24
3812 8433 2.564771 GCATCATGGTAACTAGCTGCA 58.435 47.619 1.02 0.00 34.74 4.41
3816 8437 2.831526 TCATGGTAACTAGCTGCACTCA 59.168 45.455 1.02 0.00 37.61 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 8.830201 ACATTGCTTAGATTGATCATCTAGTC 57.170 34.615 0.00 3.43 44.04 2.59
51 52 9.566432 CAACAATATATTCCTAAAGGCTTCTCT 57.434 33.333 0.00 0.00 34.44 3.10
54 55 7.371159 GGCAACAATATATTCCTAAAGGCTTC 58.629 38.462 0.00 0.00 34.44 3.86
55 56 6.267699 GGGCAACAATATATTCCTAAAGGCTT 59.732 38.462 0.00 0.00 39.74 4.35
59 60 6.293955 CGTGGGGCAACAATATATTCCTAAAG 60.294 42.308 0.00 0.00 39.74 1.85
113 114 4.661222 TGTGCAAGGAGTCCAATGAAATA 58.339 39.130 12.86 0.00 0.00 1.40
117 1197 2.622942 GTTTGTGCAAGGAGTCCAATGA 59.377 45.455 12.86 0.00 0.00 2.57
118 1198 2.288395 GGTTTGTGCAAGGAGTCCAATG 60.288 50.000 12.86 11.15 0.00 2.82
122 1202 1.398692 TTGGTTTGTGCAAGGAGTCC 58.601 50.000 0.00 0.00 0.00 3.85
124 1204 2.093711 GGTTTTGGTTTGTGCAAGGAGT 60.094 45.455 0.00 0.00 0.00 3.85
126 1206 1.902508 TGGTTTTGGTTTGTGCAAGGA 59.097 42.857 0.00 0.00 0.00 3.36
129 1209 3.529533 CTCATGGTTTTGGTTTGTGCAA 58.470 40.909 0.00 0.00 0.00 4.08
138 1218 0.804989 GAGACGGCTCATGGTTTTGG 59.195 55.000 15.11 0.00 40.96 3.28
140 1220 1.347707 TCAGAGACGGCTCATGGTTTT 59.652 47.619 22.94 0.00 43.81 2.43
142 1222 0.976641 TTCAGAGACGGCTCATGGTT 59.023 50.000 22.94 0.00 43.81 3.67
143 1223 0.247736 GTTCAGAGACGGCTCATGGT 59.752 55.000 22.94 0.00 43.81 3.55
144 1224 0.460987 GGTTCAGAGACGGCTCATGG 60.461 60.000 22.94 9.78 43.81 3.66
145 1225 0.460987 GGGTTCAGAGACGGCTCATG 60.461 60.000 22.94 15.65 43.81 3.07
146 1226 1.617947 GGGGTTCAGAGACGGCTCAT 61.618 60.000 22.94 2.25 43.81 2.90
148 1228 1.827399 TTGGGGTTCAGAGACGGCTC 61.827 60.000 11.39 11.39 41.62 4.70
149 1229 1.841556 TTGGGGTTCAGAGACGGCT 60.842 57.895 0.00 0.00 0.00 5.52
150 1230 1.671379 GTTGGGGTTCAGAGACGGC 60.671 63.158 0.00 0.00 0.00 5.68
151 1231 0.602905 GTGTTGGGGTTCAGAGACGG 60.603 60.000 0.00 0.00 0.00 4.79
157 1237 0.182537 TCTGTGGTGTTGGGGTTCAG 59.817 55.000 0.00 0.00 0.00 3.02
161 1241 3.250847 CCTCTGTGGTGTTGGGGT 58.749 61.111 0.00 0.00 0.00 4.95
172 1252 0.612229 TCTCCGACGACTACCTCTGT 59.388 55.000 0.00 0.00 0.00 3.41
174 1254 1.137479 CTCTCTCCGACGACTACCTCT 59.863 57.143 0.00 0.00 0.00 3.69
185 1265 3.010361 AGGTACTTTTCCTCTCTCTCCGA 59.990 47.826 0.00 0.00 27.25 4.55
199 1279 7.470702 CGACTATGATGATGAAGGAGGTACTTT 60.471 40.741 0.00 0.00 41.55 2.66
223 1303 2.063979 AACGATGATGCCCTCCCGA 61.064 57.895 0.00 0.00 0.00 5.14
239 1319 3.198068 TGTCTCACAAAGCTCTGACAAC 58.802 45.455 0.00 0.00 32.50 3.32
240 1320 3.541996 TGTCTCACAAAGCTCTGACAA 57.458 42.857 0.00 0.00 32.50 3.18
247 1327 2.843701 CAGACCTTGTCTCACAAAGCT 58.156 47.619 0.00 0.00 41.37 3.74
257 1337 3.414700 CGTGCGGCAGACCTTGTC 61.415 66.667 1.18 0.00 0.00 3.18
277 1363 7.715249 AGCATATAGGTAGTTTATGTGTGTTGG 59.285 37.037 0.00 0.00 0.00 3.77
280 1366 9.681062 AAAAGCATATAGGTAGTTTATGTGTGT 57.319 29.630 0.00 0.00 0.00 3.72
306 1392 6.682113 GCCAAGTACGGAGATGATAACTGTTA 60.682 42.308 2.26 2.26 0.00 2.41
308 1394 4.441634 GCCAAGTACGGAGATGATAACTGT 60.442 45.833 0.00 0.00 0.00 3.55
317 1403 1.342674 TGGGTAGCCAAGTACGGAGAT 60.343 52.381 12.23 0.00 0.00 2.75
369 1455 1.176527 CCGGGAAGAACGTACCACTA 58.823 55.000 0.00 0.00 0.00 2.74
380 1466 0.393537 GTACGAGAGGACCGGGAAGA 60.394 60.000 6.32 0.00 39.75 2.87
419 1505 3.733960 CACGAGGACGACGCCTGA 61.734 66.667 14.30 0.00 42.66 3.86
424 1510 2.579787 GATGGCACGAGGACGACG 60.580 66.667 0.00 0.00 42.66 5.12
483 1569 1.480212 AAGGACGGCATGACTGGTCA 61.480 55.000 8.61 5.87 44.59 4.02
519 1613 7.371159 TCGTGGAATAAGATAGTTAGCATGAG 58.629 38.462 0.00 0.00 0.00 2.90
526 1620 6.266786 TGATGGCTCGTGGAATAAGATAGTTA 59.733 38.462 0.00 0.00 0.00 2.24
530 1624 4.262463 GGTGATGGCTCGTGGAATAAGATA 60.262 45.833 0.00 0.00 0.00 1.98
538 1632 2.662596 GTGGTGATGGCTCGTGGA 59.337 61.111 0.00 0.00 0.00 4.02
549 1643 1.376086 CTGCTCATGGTGGTGGTGA 59.624 57.895 0.00 0.00 0.00 4.02
563 1657 3.650298 ATGGCCGATGGTTGCTGCT 62.650 57.895 0.00 0.00 0.00 4.24
584 1679 0.913876 GCAGTGTGTTTTGTGTTCGC 59.086 50.000 0.00 0.00 0.00 4.70
595 1690 0.179045 GTGGTTGAGGAGCAGTGTGT 60.179 55.000 0.00 0.00 36.22 3.72
622 1717 5.316158 AGAGCCTTCATATGTATTGCCTT 57.684 39.130 1.90 0.00 0.00 4.35
629 1724 6.921857 GCGTAAACTTAGAGCCTTCATATGTA 59.078 38.462 1.90 0.00 0.00 2.29
631 1726 5.753438 TGCGTAAACTTAGAGCCTTCATATG 59.247 40.000 0.00 0.00 0.00 1.78
640 1736 3.522553 AGATGGTGCGTAAACTTAGAGC 58.477 45.455 0.00 0.00 0.00 4.09
651 1747 0.532573 AATCTGTCGAGATGGTGCGT 59.467 50.000 0.00 0.00 39.04 5.24
696 1792 9.565090 AGCAACTCTAGCAAAATCATCATATTA 57.435 29.630 0.00 0.00 0.00 0.98
738 1835 1.216710 CTGGCTTCACCCTCGTCTC 59.783 63.158 0.00 0.00 37.83 3.36
798 1897 4.336433 TGCTACGGTGTCCAATAGTAGTAC 59.664 45.833 0.00 0.00 37.63 2.73
802 1904 4.804868 TTTGCTACGGTGTCCAATAGTA 57.195 40.909 0.00 0.00 0.00 1.82
807 5173 1.950909 CCTTTTTGCTACGGTGTCCAA 59.049 47.619 0.00 0.00 0.00 3.53
839 5325 3.626924 GGGTCACAGCGTCAGGGT 61.627 66.667 0.00 0.00 0.00 4.34
878 5365 3.770040 TCACTGGCCGACGATGGG 61.770 66.667 0.00 0.00 0.00 4.00
969 5462 3.508840 GTGCGCGGGAGGAAATGG 61.509 66.667 8.83 0.00 0.00 3.16
1563 6060 2.743664 GCATATCAATATGTCAGGCGCA 59.256 45.455 10.83 0.00 41.63 6.09
1601 6098 4.404654 GCCCGGCAAAGACAAGCG 62.405 66.667 3.91 0.00 0.00 4.68
1737 6234 6.224584 CAGCATCACATCAATCATCTCTAGT 58.775 40.000 0.00 0.00 0.00 2.57
1749 6246 2.093921 CCCATTTTGCAGCATCACATCA 60.094 45.455 0.00 0.00 0.00 3.07
1751 6248 1.903860 ACCCATTTTGCAGCATCACAT 59.096 42.857 0.00 0.00 0.00 3.21
1865 6362 3.118075 TGGAAATAGACCCGCATCATTCA 60.118 43.478 0.00 0.00 0.00 2.57
1930 6427 0.251033 GCCTCATCTGCATGCCCATA 60.251 55.000 16.68 0.00 0.00 2.74
1956 6453 2.476199 CCCTCTGACTCCCTCAAGAAT 58.524 52.381 0.00 0.00 0.00 2.40
1992 6489 4.240888 CTGCACTATATCCAACCTCATCG 58.759 47.826 0.00 0.00 0.00 3.84
2060 6557 4.329462 GAGATCATCTCACCTACAACCC 57.671 50.000 10.02 0.00 42.90 4.11
2331 6828 4.578105 CCTTCTCTTCTAAACCCATGCATC 59.422 45.833 0.00 0.00 0.00 3.91
2532 7029 8.331022 CGAGAAAATCCATGAATTACAGTAGTG 58.669 37.037 0.00 0.00 0.00 2.74
2610 7107 3.719268 ACAACATCTGGATGCCTGTTA 57.281 42.857 10.13 0.00 42.39 2.41
2673 7170 1.342819 AGCTCTGTCGCTTCTTTCAGT 59.657 47.619 0.00 0.00 36.74 3.41
2733 7230 5.886992 TGTATCACTGTCCTGTATGTAACG 58.113 41.667 0.00 0.00 0.00 3.18
3109 7606 9.495572 CAGAAGACCTCTTTCTACAAACTTAAT 57.504 33.333 0.00 0.00 36.11 1.40
3118 7615 7.210873 TCTTGTTTCAGAAGACCTCTTTCTAC 58.789 38.462 0.00 0.00 36.11 2.59
3175 7679 5.507817 CCAGTTGCCAATAAACGCATGATAT 60.508 40.000 0.00 0.00 34.35 1.63
3183 7687 2.288152 ACTTGCCAGTTGCCAATAAACG 60.288 45.455 0.00 0.00 40.16 3.60
3238 7825 3.922240 GCTTTCCAGCATGTAAACACATG 59.078 43.478 12.34 12.34 46.49 3.21
3239 7826 4.178545 GCTTTCCAGCATGTAAACACAT 57.821 40.909 0.00 0.00 46.49 3.21
3240 7827 3.641437 GCTTTCCAGCATGTAAACACA 57.359 42.857 0.00 0.00 46.49 3.72
3337 7928 2.010145 TTCGCTGGCAGCTAACTAAG 57.990 50.000 34.17 18.49 39.60 2.18
3339 7930 2.956333 TCTATTCGCTGGCAGCTAACTA 59.044 45.455 34.17 20.97 39.60 2.24
3340 7931 1.757118 TCTATTCGCTGGCAGCTAACT 59.243 47.619 34.17 20.98 39.60 2.24
3341 7932 1.861575 GTCTATTCGCTGGCAGCTAAC 59.138 52.381 34.17 16.54 39.60 2.34
3342 7933 1.757118 AGTCTATTCGCTGGCAGCTAA 59.243 47.619 34.17 29.97 39.60 3.09
3343 7934 1.403814 AGTCTATTCGCTGGCAGCTA 58.596 50.000 34.17 23.45 39.60 3.32
3344 7935 1.339610 CTAGTCTATTCGCTGGCAGCT 59.660 52.381 34.17 20.17 39.60 4.24
3347 7938 2.885266 CCTACTAGTCTATTCGCTGGCA 59.115 50.000 0.00 0.00 0.00 4.92
3354 7966 6.270156 GGTGCCATACCTACTAGTCTATTC 57.730 45.833 0.00 0.00 46.51 1.75
3398 8010 3.409026 ACTGTTCAGTAGCCCTTTGAG 57.591 47.619 3.47 0.00 0.00 3.02
3399 8011 3.644265 TGTACTGTTCAGTAGCCCTTTGA 59.356 43.478 12.19 0.00 0.00 2.69
3400 8012 3.746492 GTGTACTGTTCAGTAGCCCTTTG 59.254 47.826 12.19 0.00 0.00 2.77
3401 8013 3.389983 TGTGTACTGTTCAGTAGCCCTTT 59.610 43.478 12.19 0.00 0.00 3.11
3402 8014 2.969950 TGTGTACTGTTCAGTAGCCCTT 59.030 45.455 12.19 0.00 0.00 3.95
3403 8015 2.605257 TGTGTACTGTTCAGTAGCCCT 58.395 47.619 12.19 0.00 0.00 5.19
3404 8016 3.262420 CATGTGTACTGTTCAGTAGCCC 58.738 50.000 12.19 3.28 0.00 5.19
3405 8017 3.926616 ACATGTGTACTGTTCAGTAGCC 58.073 45.455 12.19 7.21 0.00 3.93
3484 8105 4.037927 CCATTGTCTCCTCCCCTTAAGTA 58.962 47.826 0.97 0.00 0.00 2.24
3517 8138 4.961511 GGCGCCGTCACAGTGTCA 62.962 66.667 12.58 0.00 0.00 3.58
3709 8330 0.889186 GGTGGCCAACGAACATCTGT 60.889 55.000 7.24 0.00 0.00 3.41
3812 8433 5.730296 ACTACATAGTGCAAGAACTGAGT 57.270 39.130 0.00 0.00 34.72 3.41
3816 8437 7.780745 AGGACTATACTACATAGTGCAAGAACT 59.219 37.037 15.41 0.00 42.86 3.01
4013 8634 4.221041 GCCAGAGTACCAGTAGAAGAAAGT 59.779 45.833 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.