Multiple sequence alignment - TraesCS5A01G101000

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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 TraesCS5A01G101000 chr5A 100.000 4241 0 0 1 4241 146533350 146537590 0.000000e+00 7832.0
1 TraesCS5A01G101000 chr5B 93.669 3917 160 32 157 4021 142243781 142247661 0.000000e+00 5779.0
2 TraesCS5A01G101000 chr5B 91.803 61 5 0 1 61 142243343 142243403 7.560000e-13 86.1
3 TraesCS5A01G101000 chr5D 93.546 3889 163 41 152 4021 130187106 130190925 0.000000e+00 5710.0
4 TraesCS5A01G101000 chr5D 91.129 124 10 1 1 123 130186731 130186854 2.620000e-37 167.0
5 TraesCS5A01G101000 chr4B 97.748 222 5 0 4020 4241 34861582 34861803 2.390000e-102 383.0
6 TraesCS5A01G101000 chr4B 97.748 222 5 0 4020 4241 34864189 34864410 2.390000e-102 383.0
7 TraesCS5A01G101000 chr4B 97.748 222 5 0 4020 4241 34866795 34867016 2.390000e-102 383.0
8 TraesCS5A01G101000 chr4B 97.748 222 5 0 4020 4241 34870039 34870260 2.390000e-102 383.0
9 TraesCS5A01G101000 chr2A 97.748 222 5 0 4020 4241 157532902 157532681 2.390000e-102 383.0
10 TraesCS5A01G101000 chr2A 85.211 142 19 2 1183 1323 696219351 696219491 1.230000e-30 145.0
11 TraesCS5A01G101000 chr2A 85.211 142 19 2 1183 1323 696825381 696825521 1.230000e-30 145.0
12 TraesCS5A01G101000 chr7A 95.000 220 11 0 4022 4241 463447723 463447942 3.140000e-91 346.0
13 TraesCS5A01G101000 chr7A 93.665 221 14 0 4021 4241 317907255 317907475 8.790000e-87 331.0
14 TraesCS5A01G101000 chr7A 81.818 88 15 1 390 476 442965773 442965860 5.880000e-09 73.1
15 TraesCS5A01G101000 chr3D 81.193 218 40 1 4024 4241 562533372 562533156 1.570000e-39 174.0
16 TraesCS5A01G101000 chr3D 80.723 83 14 2 2386 2467 253340073 253339992 3.540000e-06 63.9
17 TraesCS5A01G101000 chr1D 79.339 242 44 6 1085 1323 449674683 449674921 9.430000e-37 165.0
18 TraesCS5A01G101000 chr1D 86.029 136 19 0 1184 1319 449752774 449752909 3.420000e-31 147.0
19 TraesCS5A01G101000 chr1A 86.486 148 20 0 1183 1330 544927973 544928120 3.390000e-36 163.0
20 TraesCS5A01G101000 chr1A 86.131 137 19 0 1183 1319 544748433 544748569 9.500000e-32 148.0
21 TraesCS5A01G101000 chr1A 77.959 245 42 8 1085 1323 545000221 545000459 4.420000e-30 143.0
22 TraesCS5A01G101000 chr1B 87.500 136 17 0 1184 1319 615581874 615582009 1.580000e-34 158.0
23 TraesCS5A01G101000 chr1B 97.059 34 1 0 2417 2450 659780216 659780183 1.650000e-04 58.4
24 TraesCS5A01G101000 chr6A 87.342 79 9 1 393 470 7301529 7301451 5.840000e-14 89.8
25 TraesCS5A01G101000 chr6A 94.872 39 2 0 2414 2452 554716476 554716514 1.270000e-05 62.1
26 TraesCS5A01G101000 chr3B 89.231 65 7 0 4102 4166 795810541 795810605 9.770000e-12 82.4
27 TraesCS5A01G101000 chr3B 80.723 83 14 2 2386 2467 304277893 304277974 3.540000e-06 63.9
28 TraesCS5A01G101000 chr3A 80.723 83 14 2 2386 2467 330698718 330698799 3.540000e-06 63.9
29 TraesCS5A01G101000 chr6D 94.872 39 2 0 2414 2452 408946016 408946054 1.270000e-05 62.1
30 TraesCS5A01G101000 chr6B 92.308 39 3 0 2414 2452 613610630 613610668 5.920000e-04 56.5


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 TraesCS5A01G101000 chr5A 146533350 146537590 4240 False 7832.00 7832 100.0000 1 4241 1 chr5A.!!$F1 4240
1 TraesCS5A01G101000 chr5B 142243343 142247661 4318 False 2932.55 5779 92.7360 1 4021 2 chr5B.!!$F1 4020
2 TraesCS5A01G101000 chr5D 130186731 130190925 4194 False 2938.50 5710 92.3375 1 4021 2 chr5D.!!$F1 4020
3 TraesCS5A01G101000 chr4B 34861582 34870260 8678 False 383.00 383 97.7480 4020 4241 4 chr4B.!!$F1 221

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
391 731 0.032952 TATCGGCTTATCGGTGTGGC 59.967 55.000 0.0 0.0 0.00 5.01 F
926 1274 0.034670 ACTTGCAGCCTTGGAGATCC 60.035 55.000 0.0 0.0 0.00 3.36 F
1323 1671 1.005394 CCTCGGCAACAGGTACGTT 60.005 57.895 0.0 0.0 32.28 3.99 F
2868 3229 0.394899 CAATGGAAGGAGGAGGTGGC 60.395 60.000 0.0 0.0 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1323 1671 1.663379 CTGGCACGGAGTATGGACGA 61.663 60.000 0.0 0.0 41.61 4.20 R
2628 2986 1.679153 GATGACGAAGAGGAGGAGGAC 59.321 57.143 0.0 0.0 0.00 3.85 R
2927 3288 1.455217 TCTAGTAGAGGGGGCACGC 60.455 63.158 0.0 0.0 42.17 5.34 R
4066 4462 0.665835 TCCAACGCAACACACAATCC 59.334 50.000 0.0 0.0 0.00 3.01 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
36 37 6.940298 TCAAGTGGTAAGTTTTGAAGGATAGG 59.060 38.462 0.00 0.00 0.00 2.57
39 40 6.272558 AGTGGTAAGTTTTGAAGGATAGGTCT 59.727 38.462 0.00 0.00 0.00 3.85
101 103 5.420725 GGGCTTGATTCCCTAAACATTTT 57.579 39.130 0.00 0.00 40.66 1.82
105 107 7.710907 GGGCTTGATTCCCTAAACATTTTTATC 59.289 37.037 0.00 0.00 40.66 1.75
128 130 1.416772 GGGAATAAAGTCTCCCCCTCG 59.583 57.143 0.00 0.00 45.03 4.63
129 131 2.395619 GGAATAAAGTCTCCCCCTCGA 58.604 52.381 0.00 0.00 0.00 4.04
130 132 2.973406 GGAATAAAGTCTCCCCCTCGAT 59.027 50.000 0.00 0.00 0.00 3.59
131 133 4.158015 GGAATAAAGTCTCCCCCTCGATA 58.842 47.826 0.00 0.00 0.00 2.92
132 134 4.778427 GGAATAAAGTCTCCCCCTCGATAT 59.222 45.833 0.00 0.00 0.00 1.63
133 135 5.248705 GGAATAAAGTCTCCCCCTCGATATT 59.751 44.000 0.00 0.00 0.00 1.28
134 136 6.239915 GGAATAAAGTCTCCCCCTCGATATTT 60.240 42.308 0.00 0.00 0.00 1.40
135 137 4.423625 AAAGTCTCCCCCTCGATATTTG 57.576 45.455 0.00 0.00 0.00 2.32
136 138 3.047695 AGTCTCCCCCTCGATATTTGT 57.952 47.619 0.00 0.00 0.00 2.83
137 139 2.966516 AGTCTCCCCCTCGATATTTGTC 59.033 50.000 0.00 0.00 0.00 3.18
138 140 1.961394 TCTCCCCCTCGATATTTGTCG 59.039 52.381 0.00 0.00 42.74 4.35
139 141 1.000955 CTCCCCCTCGATATTTGTCGG 59.999 57.143 0.00 0.00 41.74 4.79
141 143 0.944311 CCCCTCGATATTTGTCGGCG 60.944 60.000 0.00 0.00 41.74 6.46
143 145 1.409412 CCTCGATATTTGTCGGCGAG 58.591 55.000 11.20 0.00 45.67 5.03
144 146 0.778815 CTCGATATTTGTCGGCGAGC 59.221 55.000 11.20 6.16 41.35 5.03
145 147 0.596600 TCGATATTTGTCGGCGAGCC 60.597 55.000 11.20 3.59 41.74 4.70
146 148 1.557443 CGATATTTGTCGGCGAGCCC 61.557 60.000 11.20 0.00 37.94 5.19
147 149 0.531974 GATATTTGTCGGCGAGCCCA 60.532 55.000 11.20 1.18 0.00 5.36
148 150 0.108585 ATATTTGTCGGCGAGCCCAT 59.891 50.000 11.20 2.75 0.00 4.00
149 151 0.531974 TATTTGTCGGCGAGCCCATC 60.532 55.000 11.20 0.00 0.00 3.51
150 152 2.535485 ATTTGTCGGCGAGCCCATCA 62.535 55.000 11.20 0.00 0.00 3.07
155 495 2.885676 CGGCGAGCCCATCAATTCG 61.886 63.158 0.00 0.00 36.23 3.34
165 505 3.120086 ATCAATTCGCCCCCTCCCG 62.120 63.158 0.00 0.00 0.00 5.14
175 515 4.351054 CCCTCCCGTTTGCCTGCT 62.351 66.667 0.00 0.00 0.00 4.24
180 520 1.745489 CCCGTTTGCCTGCTACTCC 60.745 63.158 0.00 0.00 0.00 3.85
235 575 4.160626 GCCTTGACTCCGGCTAATAGATAT 59.839 45.833 0.00 0.00 42.98 1.63
317 657 2.027625 CGGTCGTTTGGGCTCTGAC 61.028 63.158 0.00 0.00 0.00 3.51
322 662 0.034059 CGTTTGGGCTCTGACACTCT 59.966 55.000 0.00 0.00 0.00 3.24
324 664 2.147150 GTTTGGGCTCTGACACTCTTC 58.853 52.381 0.00 0.00 0.00 2.87
337 677 2.358267 ACACTCTTCGAGTTCGTCAGTT 59.642 45.455 1.07 0.00 41.37 3.16
339 679 2.617308 ACTCTTCGAGTTCGTCAGTTGA 59.383 45.455 1.07 0.00 40.28 3.18
342 682 3.502595 TCTTCGAGTTCGTCAGTTGAGAT 59.497 43.478 1.07 0.00 40.80 2.75
351 691 6.097554 AGTTCGTCAGTTGAGATGGATTAGAT 59.902 38.462 0.00 0.00 0.00 1.98
359 699 8.149647 CAGTTGAGATGGATTAGATAAAGCTCT 58.850 37.037 0.00 0.00 0.00 4.09
360 700 8.367156 AGTTGAGATGGATTAGATAAAGCTCTC 58.633 37.037 0.00 0.00 0.00 3.20
366 706 6.736123 TGGATTAGATAAAGCTCTCGTGTAC 58.264 40.000 0.00 0.00 0.00 2.90
371 711 6.208988 AGATAAAGCTCTCGTGTACATTCA 57.791 37.500 0.00 0.00 0.00 2.57
386 726 4.537135 ACATTCATATCGGCTTATCGGT 57.463 40.909 0.00 0.00 0.00 4.69
388 728 4.245660 CATTCATATCGGCTTATCGGTGT 58.754 43.478 0.00 0.00 0.00 4.16
391 731 0.032952 TATCGGCTTATCGGTGTGGC 59.967 55.000 0.00 0.00 0.00 5.01
399 739 1.405872 TATCGGTGTGGCGAGGTTAT 58.594 50.000 0.00 0.00 0.00 1.89
436 777 2.930826 ACGCAAGGGGATATTAGGTG 57.069 50.000 0.00 0.00 46.39 4.00
460 801 4.566759 TGCGGTTCTTTAGATCGATTCAAG 59.433 41.667 0.00 2.69 0.00 3.02
461 802 4.804139 GCGGTTCTTTAGATCGATTCAAGA 59.196 41.667 0.00 5.13 0.00 3.02
473 818 8.327941 AGATCGATTCAAGAATTCAAAGACAA 57.672 30.769 8.44 0.00 0.00 3.18
496 841 5.068234 TGGTCATTAGTGGTTTAGAGACG 57.932 43.478 0.00 0.00 0.00 4.18
509 854 6.987992 TGGTTTAGAGACGTCAATGTAACTTT 59.012 34.615 19.50 0.00 0.00 2.66
510 855 8.143193 TGGTTTAGAGACGTCAATGTAACTTTA 58.857 33.333 19.50 4.21 0.00 1.85
536 881 8.788325 ATTATGTTTGGACTACCTTGTACTTC 57.212 34.615 0.00 0.00 37.04 3.01
537 882 4.964593 TGTTTGGACTACCTTGTACTTCC 58.035 43.478 0.00 0.00 37.04 3.46
549 894 4.322801 CCTTGTACTTCCGGTGAATCTTCT 60.323 45.833 0.00 0.00 0.00 2.85
550 895 4.884668 TGTACTTCCGGTGAATCTTCTT 57.115 40.909 0.00 0.00 0.00 2.52
558 903 8.145122 ACTTCCGGTGAATCTTCTTAATAGATC 58.855 37.037 0.00 0.00 31.28 2.75
655 1001 0.106669 GTGGACCTAGCAATTCCCCC 60.107 60.000 0.00 0.00 0.00 5.40
656 1002 1.148498 GGACCTAGCAATTCCCCCG 59.852 63.158 0.00 0.00 0.00 5.73
659 1005 0.702316 ACCTAGCAATTCCCCCGTTT 59.298 50.000 0.00 0.00 0.00 3.60
660 1006 1.340697 ACCTAGCAATTCCCCCGTTTC 60.341 52.381 0.00 0.00 0.00 2.78
661 1007 1.064685 CCTAGCAATTCCCCCGTTTCT 60.065 52.381 0.00 0.00 0.00 2.52
662 1008 2.289565 CTAGCAATTCCCCCGTTTCTC 58.710 52.381 0.00 0.00 0.00 2.87
663 1009 0.698818 AGCAATTCCCCCGTTTCTCT 59.301 50.000 0.00 0.00 0.00 3.10
664 1010 1.095600 GCAATTCCCCCGTTTCTCTC 58.904 55.000 0.00 0.00 0.00 3.20
665 1011 1.340114 GCAATTCCCCCGTTTCTCTCT 60.340 52.381 0.00 0.00 0.00 3.10
800 1146 1.222387 CTCCTCTCGTCGTCCTCCT 59.778 63.158 0.00 0.00 0.00 3.69
801 1147 0.812412 CTCCTCTCGTCGTCCTCCTC 60.812 65.000 0.00 0.00 0.00 3.71
802 1148 1.820481 CCTCTCGTCGTCCTCCTCC 60.820 68.421 0.00 0.00 0.00 4.30
803 1149 1.078356 CTCTCGTCGTCCTCCTCCA 60.078 63.158 0.00 0.00 0.00 3.86
809 1155 0.461961 GTCGTCCTCCTCCATTCCTG 59.538 60.000 0.00 0.00 0.00 3.86
819 1165 1.153289 CCATTCCTGCCCTCACTCG 60.153 63.158 0.00 0.00 0.00 4.18
855 1203 9.489084 ACATACACATCATATATAACACACACC 57.511 33.333 0.00 0.00 0.00 4.16
867 1215 1.079621 ACACACCCCCGAGTCCATA 59.920 57.895 0.00 0.00 0.00 2.74
877 1225 2.826725 CCCGAGTCCATATCTCCCTTAC 59.173 54.545 0.00 0.00 0.00 2.34
884 1232 7.993758 CGAGTCCATATCTCCCTTACATATAGA 59.006 40.741 0.00 0.00 0.00 1.98
885 1233 9.349713 GAGTCCATATCTCCCTTACATATAGAG 57.650 40.741 0.00 0.00 0.00 2.43
926 1274 0.034670 ACTTGCAGCCTTGGAGATCC 60.035 55.000 0.00 0.00 0.00 3.36
1149 1497 2.509336 GCGTACATGCTGCGGAGT 60.509 61.111 5.62 0.00 0.00 3.85
1242 1590 1.006758 TGGATCAACTACCTCCGTCCT 59.993 52.381 0.00 0.00 31.36 3.85
1323 1671 1.005394 CCTCGGCAACAGGTACGTT 60.005 57.895 0.00 0.00 32.28 3.99
1345 1693 2.203070 CATACTCCGTGCCAGCCC 60.203 66.667 0.00 0.00 0.00 5.19
1346 1694 2.687200 ATACTCCGTGCCAGCCCA 60.687 61.111 0.00 0.00 0.00 5.36
1444 1796 3.067439 TTGCGGGGATGCGCAAAT 61.067 55.556 17.11 0.00 46.14 2.32
1445 1797 3.353770 TTGCGGGGATGCGCAAATG 62.354 57.895 17.11 3.94 46.14 2.32
1446 1798 3.825611 GCGGGGATGCGCAAATGT 61.826 61.111 17.11 0.00 0.00 2.71
1448 1800 2.807622 GGGGATGCGCAAATGTCC 59.192 61.111 17.11 17.44 0.00 4.02
1533 1886 7.397221 TGTAGGAGGATATAATTGGATTGCTG 58.603 38.462 0.00 0.00 0.00 4.41
1554 1907 7.989826 TGCTGCCTTCTTCTTTATTCTATTTC 58.010 34.615 0.00 0.00 0.00 2.17
1730 2083 2.175878 ACACACTGTGATTCTCTGCC 57.824 50.000 16.30 0.00 36.96 4.85
1750 2104 3.670627 GCCGGTGTGCTAAAAGATGAAAG 60.671 47.826 1.90 0.00 0.00 2.62
1849 2204 8.118607 CCTTTCTTTGATTTGTCTTTTTGCTTC 58.881 33.333 0.00 0.00 0.00 3.86
1942 2297 6.054860 AGCATAGTTGGATGACTAAAGTGT 57.945 37.500 0.00 0.00 35.86 3.55
2097 2452 9.032624 ACAGAGGTAGTAGTAGCAAATAAAAGA 57.967 33.333 9.37 0.00 0.00 2.52
2132 2487 9.520204 CAAGAAGTGAAAGTGATACATGTTTTT 57.480 29.630 2.30 0.00 0.00 1.94
2218 2573 6.092670 ACCAGAAATTGTGATTACGACATCAG 59.907 38.462 0.00 0.00 33.69 2.90
2333 2691 2.228582 TGCGCATGTAGCTTTTTGACAT 59.771 40.909 5.66 0.00 42.61 3.06
2339 2697 5.576774 GCATGTAGCTTTTTGACATAAACCC 59.423 40.000 0.00 0.00 41.15 4.11
2348 2706 4.561500 TTGACATAAACCCCTCGATTGA 57.438 40.909 0.00 0.00 0.00 2.57
2520 2878 2.726691 GACCACGGAATGTGCGTCG 61.727 63.158 0.00 0.00 41.66 5.12
2865 3226 0.846427 TGGCAATGGAAGGAGGAGGT 60.846 55.000 0.00 0.00 0.00 3.85
2868 3229 0.394899 CAATGGAAGGAGGAGGTGGC 60.395 60.000 0.00 0.00 0.00 5.01
2927 3288 3.182967 GCGAACATAGTGTCCTCTTCAG 58.817 50.000 0.00 0.00 0.00 3.02
3084 3445 3.671433 GCTGCAACATCAATGACGACAAT 60.671 43.478 0.00 0.00 0.00 2.71
3126 3487 0.963962 GTGTGGTCTCGTACTGGGAA 59.036 55.000 0.00 0.00 0.00 3.97
3186 3547 1.850755 GGGGGAGTGGGACTTGGAA 60.851 63.158 0.00 0.00 0.00 3.53
3514 3910 4.679662 AGTTATATGGTCTTCAACGGTCG 58.320 43.478 0.00 0.00 0.00 4.79
3535 3931 3.699067 GTCACAAAGCCATGCATGTATC 58.301 45.455 24.58 13.27 31.61 2.24
3653 4049 2.885135 TCATGGCAAAGTGACATCCT 57.115 45.000 0.00 0.00 44.20 3.24
3896 4292 4.315803 CGATTAGAGGCCGTTAATTGGAT 58.684 43.478 16.18 0.00 0.00 3.41
3923 4319 1.864435 GCCGTGCGATTAGACTACAGG 60.864 57.143 0.00 0.00 0.00 4.00
4005 4401 5.121811 CAACCAGTCAATATCTCTCCTTGG 58.878 45.833 0.00 0.00 0.00 3.61
4066 4462 1.215244 CACATGATACGCTGCTCCAG 58.785 55.000 0.00 0.00 34.12 3.86
4172 4568 1.017387 GCACCCTCGAAAATAGCCTG 58.983 55.000 0.00 0.00 0.00 4.85
4198 4594 9.034544 GTTTTTGCAAACTCATAACAGATTTCT 57.965 29.630 12.39 0.00 39.49 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 4.718276 CCCCTAGTACCTTTAGTGCCTAAA 59.282 45.833 7.05 7.05 35.12 1.85
60 61 2.660556 CCCTATCATCCCCCTAGTACCT 59.339 54.545 0.00 0.00 0.00 3.08
65 66 1.912043 CAAGCCCTATCATCCCCCTAG 59.088 57.143 0.00 0.00 0.00 3.02
112 114 5.607171 ACAAATATCGAGGGGGAGACTTTAT 59.393 40.000 0.00 0.00 0.00 1.40
119 121 1.000955 CCGACAAATATCGAGGGGGAG 59.999 57.143 0.00 0.00 45.13 4.30
123 125 0.031585 TCGCCGACAAATATCGAGGG 59.968 55.000 0.00 0.00 45.13 4.30
124 126 1.409412 CTCGCCGACAAATATCGAGG 58.591 55.000 0.00 0.00 45.13 4.63
125 127 0.778815 GCTCGCCGACAAATATCGAG 59.221 55.000 5.69 5.69 45.13 4.04
126 128 0.596600 GGCTCGCCGACAAATATCGA 60.597 55.000 0.00 0.00 45.13 3.59
127 129 1.557443 GGGCTCGCCGACAAATATCG 61.557 60.000 1.24 0.00 41.89 2.92
128 130 0.531974 TGGGCTCGCCGACAAATATC 60.532 55.000 1.24 0.00 36.85 1.63
129 131 0.108585 ATGGGCTCGCCGACAAATAT 59.891 50.000 1.24 0.00 36.85 1.28
130 132 0.531974 GATGGGCTCGCCGACAAATA 60.532 55.000 1.24 0.00 36.85 1.40
131 133 1.819632 GATGGGCTCGCCGACAAAT 60.820 57.895 1.24 0.00 36.85 2.32
132 134 2.435938 GATGGGCTCGCCGACAAA 60.436 61.111 1.24 0.00 36.85 2.83
133 135 2.535485 ATTGATGGGCTCGCCGACAA 62.535 55.000 12.57 12.57 36.85 3.18
134 136 2.535485 AATTGATGGGCTCGCCGACA 62.535 55.000 1.24 0.00 36.85 4.35
135 137 1.776034 GAATTGATGGGCTCGCCGAC 61.776 60.000 1.24 0.00 36.85 4.79
136 138 1.523711 GAATTGATGGGCTCGCCGA 60.524 57.895 1.24 0.00 36.85 5.54
137 139 2.885676 CGAATTGATGGGCTCGCCG 61.886 63.158 1.24 0.00 36.85 6.46
138 140 3.025619 CGAATTGATGGGCTCGCC 58.974 61.111 0.00 0.00 0.00 5.54
141 143 2.196245 GGGGCGAATTGATGGGCTC 61.196 63.158 0.00 0.00 0.00 4.70
143 145 3.226537 GGGGGCGAATTGATGGGC 61.227 66.667 0.00 0.00 0.00 5.36
144 146 1.529244 GAGGGGGCGAATTGATGGG 60.529 63.158 0.00 0.00 0.00 4.00
145 147 1.529244 GGAGGGGGCGAATTGATGG 60.529 63.158 0.00 0.00 0.00 3.51
146 148 1.529244 GGGAGGGGGCGAATTGATG 60.529 63.158 0.00 0.00 0.00 3.07
147 149 2.927056 GGGAGGGGGCGAATTGAT 59.073 61.111 0.00 0.00 0.00 2.57
148 150 3.792736 CGGGAGGGGGCGAATTGA 61.793 66.667 0.00 0.00 0.00 2.57
149 151 3.638592 AACGGGAGGGGGCGAATTG 62.639 63.158 0.00 0.00 0.00 2.32
150 152 2.914310 AAACGGGAGGGGGCGAATT 61.914 57.895 0.00 0.00 0.00 2.17
180 520 3.309436 TTCCCGTCACCATCCGCTG 62.309 63.158 0.00 0.00 0.00 5.18
184 524 2.590092 CCCTTCCCGTCACCATCC 59.410 66.667 0.00 0.00 0.00 3.51
187 527 1.540367 ATTCCCCTTCCCGTCACCA 60.540 57.895 0.00 0.00 0.00 4.17
192 532 0.342313 ACTAGGATTCCCCTTCCCGT 59.658 55.000 0.00 0.00 44.85 5.28
235 575 5.397899 CCCTGTGATGATTTAAGCCCTAAGA 60.398 44.000 0.00 0.00 0.00 2.10
266 606 0.822532 GCATCTCCATCTGCCCAAGG 60.823 60.000 0.00 0.00 32.15 3.61
300 640 1.070786 TGTCAGAGCCCAAACGACC 59.929 57.895 0.00 0.00 0.00 4.79
322 662 3.565516 CATCTCAACTGACGAACTCGAA 58.434 45.455 6.05 0.00 43.02 3.71
324 664 2.095212 TCCATCTCAACTGACGAACTCG 60.095 50.000 0.00 0.00 46.33 4.18
337 677 6.491745 ACGAGAGCTTTATCTAATCCATCTCA 59.508 38.462 0.00 0.00 32.16 3.27
339 679 6.266558 ACACGAGAGCTTTATCTAATCCATCT 59.733 38.462 0.00 0.00 0.00 2.90
342 682 5.854010 ACACGAGAGCTTTATCTAATCCA 57.146 39.130 0.00 0.00 0.00 3.41
351 691 6.856426 CGATATGAATGTACACGAGAGCTTTA 59.144 38.462 0.00 0.00 0.00 1.85
359 699 4.316205 AAGCCGATATGAATGTACACGA 57.684 40.909 0.00 0.00 0.00 4.35
360 700 5.003496 CGATAAGCCGATATGAATGTACACG 59.997 44.000 0.00 0.00 0.00 4.49
366 706 4.091945 CACACCGATAAGCCGATATGAATG 59.908 45.833 0.00 0.00 0.00 2.67
371 711 1.337823 GCCACACCGATAAGCCGATAT 60.338 52.381 0.00 0.00 0.00 1.63
386 726 1.349688 AGAAACCATAACCTCGCCACA 59.650 47.619 0.00 0.00 0.00 4.17
388 728 1.404986 CGAGAAACCATAACCTCGCCA 60.405 52.381 0.00 0.00 41.31 5.69
399 739 1.336517 CGTACTCAAGGCGAGAAACCA 60.337 52.381 0.00 0.00 45.45 3.67
436 777 3.863424 TGAATCGATCTAAAGAACCGCAC 59.137 43.478 0.00 0.00 0.00 5.34
460 801 7.756722 CCACTAATGACCATTGTCTTTGAATTC 59.243 37.037 7.97 0.00 42.28 2.17
461 802 7.233348 ACCACTAATGACCATTGTCTTTGAATT 59.767 33.333 7.97 0.00 42.28 2.17
468 809 7.016153 TCTAAACCACTAATGACCATTGTCT 57.984 36.000 5.56 0.00 42.28 3.41
473 818 5.187186 ACGTCTCTAAACCACTAATGACCAT 59.813 40.000 0.00 0.00 0.00 3.55
510 855 9.227777 GAAGTACAAGGTAGTCCAAACATAATT 57.772 33.333 0.00 0.00 35.89 1.40
521 866 2.821969 TCACCGGAAGTACAAGGTAGTC 59.178 50.000 9.46 0.00 34.83 2.59
523 868 3.947910 TTCACCGGAAGTACAAGGTAG 57.052 47.619 9.46 0.00 34.83 3.18
526 871 3.611766 AGATTCACCGGAAGTACAAGG 57.388 47.619 9.46 0.00 36.25 3.61
527 872 4.822026 AGAAGATTCACCGGAAGTACAAG 58.178 43.478 9.46 0.00 36.25 3.16
536 881 7.661968 TCAGATCTATTAAGAAGATTCACCGG 58.338 38.462 0.00 0.00 33.82 5.28
537 882 8.356657 ACTCAGATCTATTAAGAAGATTCACCG 58.643 37.037 0.00 0.00 33.82 4.94
549 894 7.272244 TGCCGAAAATGACTCAGATCTATTAA 58.728 34.615 0.00 0.00 0.00 1.40
550 895 6.816136 TGCCGAAAATGACTCAGATCTATTA 58.184 36.000 0.00 0.00 0.00 0.98
580 925 3.686241 GCAGTCATGTCACATGCTTCTTA 59.314 43.478 13.41 0.00 34.10 2.10
581 926 2.486982 GCAGTCATGTCACATGCTTCTT 59.513 45.455 13.41 0.00 34.10 2.52
582 927 2.082231 GCAGTCATGTCACATGCTTCT 58.918 47.619 13.41 8.29 34.10 2.85
583 928 1.808343 TGCAGTCATGTCACATGCTTC 59.192 47.619 13.41 8.60 37.76 3.86
593 938 2.224606 CAAGTGGACTTGCAGTCATGT 58.775 47.619 15.22 0.00 46.79 3.21
612 957 5.362717 CACACAATCTACCATCTACCCTACA 59.637 44.000 0.00 0.00 0.00 2.74
687 1033 2.428890 GCAGGATCGGAGAGAGAGAAAA 59.571 50.000 0.00 0.00 43.63 2.29
800 1146 1.617018 CGAGTGAGGGCAGGAATGGA 61.617 60.000 0.00 0.00 0.00 3.41
801 1147 1.153289 CGAGTGAGGGCAGGAATGG 60.153 63.158 0.00 0.00 0.00 3.16
802 1148 0.460987 GTCGAGTGAGGGCAGGAATG 60.461 60.000 0.00 0.00 0.00 2.67
803 1149 0.904865 TGTCGAGTGAGGGCAGGAAT 60.905 55.000 0.00 0.00 0.00 3.01
809 1155 0.586802 GTTTTGTGTCGAGTGAGGGC 59.413 55.000 0.00 0.00 0.00 5.19
855 1203 0.115349 AGGGAGATATGGACTCGGGG 59.885 60.000 0.00 0.00 35.49 5.73
926 1274 2.738587 TCCTAGCTAGAGACCAGGTG 57.261 55.000 22.70 1.98 0.00 4.00
1116 1464 3.386237 GCCACCAGCCTCTCGTCT 61.386 66.667 0.00 0.00 34.35 4.18
1323 1671 1.663379 CTGGCACGGAGTATGGACGA 61.663 60.000 0.00 0.00 41.61 4.20
1444 1796 9.656323 ACCTCAGTTAGTCAATTATATAGGACA 57.344 33.333 11.49 0.15 32.79 4.02
1533 1886 9.995957 GTTGAGAAATAGAATAAAGAAGAAGGC 57.004 33.333 0.00 0.00 0.00 4.35
1554 1907 9.630098 AATATGTGTTTCTAAAGCAATGTTGAG 57.370 29.630 0.00 0.00 0.00 3.02
1730 2083 4.749245 ACTTTCATCTTTTAGCACACCG 57.251 40.909 0.00 0.00 0.00 4.94
1750 2104 8.922676 ACGGTGATAATCGTTTGATCAATATAC 58.077 33.333 9.40 3.79 36.04 1.47
1942 2297 5.183713 CAGTCTGTAATTTTGAGAATGCCCA 59.816 40.000 0.00 0.00 0.00 5.36
1983 2338 7.496591 ACAAAAACGTCTCATAGTTAGGAACAA 59.503 33.333 0.00 0.00 0.00 2.83
2097 2452 5.073144 TCACTTTCACTTCTTGATAAGGGGT 59.927 40.000 0.00 0.00 32.84 4.95
2203 2558 7.576750 TTTAGTTCACTGATGTCGTAATCAC 57.423 36.000 0.00 0.00 33.08 3.06
2333 2691 4.082463 GCAAACATTCAATCGAGGGGTTTA 60.082 41.667 0.00 0.00 0.00 2.01
2339 2697 4.092821 TCGTAAGCAAACATTCAATCGAGG 59.907 41.667 0.00 0.00 37.18 4.63
2628 2986 1.679153 GATGACGAAGAGGAGGAGGAC 59.321 57.143 0.00 0.00 0.00 3.85
2821 3182 2.908796 GGGGTAGTAGCCACCAGC 59.091 66.667 19.76 0.00 37.54 4.85
2865 3226 4.020617 CCCGTGAAGCAGGAGCCA 62.021 66.667 0.00 0.00 43.56 4.75
2927 3288 1.455217 TCTAGTAGAGGGGGCACGC 60.455 63.158 0.00 0.00 42.17 5.34
2994 3355 2.805671 TCTATGGTTGTTGTCGCTGTTG 59.194 45.455 0.00 0.00 0.00 3.33
3084 3445 5.356751 ACTGTTGATGTTGTTCTTGCTGTTA 59.643 36.000 0.00 0.00 0.00 2.41
3126 3487 4.289101 TGCTGGTGGCCATGCTGT 62.289 61.111 22.61 0.00 40.92 4.40
3186 3547 2.297315 TGACACGTCTTTCATCAGCTCT 59.703 45.455 0.00 0.00 0.00 4.09
3351 3716 7.915293 ACATCACGTAAAATAATGTCAAGGA 57.085 32.000 0.00 0.00 0.00 3.36
3387 3752 3.467803 AGTGAAGTAGTGGCTGTTGAAC 58.532 45.455 0.00 0.00 0.00 3.18
3460 3825 7.043565 ACTTTGCTTGAATTATTTGCATAGGG 58.956 34.615 15.95 6.53 37.15 3.53
3507 3903 0.534203 ATGGCTTTGTGACGACCGTT 60.534 50.000 0.00 0.00 0.00 4.44
3514 3910 3.699067 GATACATGCATGGCTTTGTGAC 58.301 45.455 29.41 7.45 30.92 3.67
3535 3931 5.683743 GCTAGCTTCTTCTACAATGTACTCG 59.316 44.000 7.70 0.00 0.00 4.18
3653 4049 6.867662 TGAAGCAAAGGAACAAAACAAAAA 57.132 29.167 0.00 0.00 0.00 1.94
3785 4181 2.835431 ATCCCCCTCACTCGCTCG 60.835 66.667 0.00 0.00 0.00 5.03
3923 4319 3.201045 GCCTCCCCCTCCATTATATTCTC 59.799 52.174 0.00 0.00 0.00 2.87
4005 4401 3.055719 CCCCATCACACCACACGC 61.056 66.667 0.00 0.00 0.00 5.34
4066 4462 0.665835 TCCAACGCAACACACAATCC 59.334 50.000 0.00 0.00 0.00 3.01
4172 4568 9.034544 AGAAATCTGTTATGAGTTTGCAAAAAC 57.965 29.630 14.67 14.31 0.00 2.43
4198 4594 1.066143 GGGATTTTGAGGAGAGACGCA 60.066 52.381 0.00 0.00 0.00 5.24
4199 4595 1.066143 TGGGATTTTGAGGAGAGACGC 60.066 52.381 0.00 0.00 0.00 5.19
4201 4597 5.995446 ACTATTGGGATTTTGAGGAGAGAC 58.005 41.667 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.