Multiple sequence alignment - TraesCS5B01G154100

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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 TraesCS5B01G154100 chr5B 100.000 4287 0 0 1 4287 283626483 283622197 0.000000e+00 7917
1 TraesCS5B01G154100 chr5A 91.283 4038 262 39 6 3992 334267458 334263460 0.000000e+00 5424
2 TraesCS5B01G154100 chr5A 94.771 306 15 1 3983 4287 334263274 334262969 3.880000e-130 475
3 TraesCS5B01G154100 chr5D 91.531 2834 178 23 1480 4287 251065107 251062310 0.000000e+00 3847
4 TraesCS5B01G154100 chr5D 93.501 1508 78 10 1 1492 251066676 251065173 0.000000e+00 2224
5 TraesCS5B01G154100 chr6B 87.591 137 17 0 2434 2570 539727679 539727543 4.440000e-35 159
6 TraesCS5B01G154100 chr6B 84.375 160 23 2 2412 2570 564993598 564993440 5.740000e-34 156
7 TraesCS5B01G154100 chr6D 84.375 160 23 2 2412 2570 378379440 378379282 5.740000e-34 156
8 TraesCS5B01G154100 chr6A 84.375 160 23 2 2412 2570 520355710 520355552 5.740000e-34 156
9 TraesCS5B01G154100 chr7D 83.544 158 26 0 2412 2569 174992614 174992771 9.600000e-32 148
10 TraesCS5B01G154100 chr7B 83.544 158 26 0 2412 2569 140652907 140653064 9.600000e-32 148
11 TraesCS5B01G154100 chr7A 83.544 158 26 0 2412 2569 177136164 177136321 9.600000e-32 148


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 TraesCS5B01G154100 chr5B 283622197 283626483 4286 True 7917.0 7917 100.000 1 4287 1 chr5B.!!$R1 4286
1 TraesCS5B01G154100 chr5A 334262969 334267458 4489 True 2949.5 5424 93.027 6 4287 2 chr5A.!!$R1 4281
2 TraesCS5B01G154100 chr5D 251062310 251066676 4366 True 3035.5 3847 92.516 1 4287 2 chr5D.!!$R1 4286

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
718 740 0.393673 CACACAACCACTCCACCACA 60.394 55.000 0.00 0.00 0.00 4.17 F
1661 1761 1.196581 TGTTCGTGTGTACATGCATGC 59.803 47.619 26.53 11.82 33.05 4.06 F
2835 2952 0.323725 GGAGGGCTTCTTGATGGCAA 60.324 55.000 11.06 0.00 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1837 1937 0.953471 TGGTAACGGCTGTGTGCATC 60.953 55.000 0.00 0.0 45.15 3.91 R
3177 3300 0.239347 GTTGTCATCACTGTGGCTGC 59.761 55.000 8.11 0.0 0.00 5.25 R
3662 3789 1.142060 ACCCACAAAAGACCACGATGA 59.858 47.619 0.00 0.0 0.00 2.92 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
20 21 3.303351 CCATATTTTCCAGGCTGAGGT 57.697 47.619 17.94 0.00 0.00 3.85
167 185 6.493802 GTCCCATGGATCAACTGTAGTAGATA 59.506 42.308 15.22 0.00 32.73 1.98
209 227 8.891671 AGATTGTGTTGCTTTGTGATATTTTT 57.108 26.923 0.00 0.00 0.00 1.94
270 288 9.651913 GGTGACAATGGTTTGTTTCATTATTAT 57.348 29.630 0.00 0.00 46.01 1.28
438 456 6.317140 GTCAGATATCTGCCATGACTTTTTCA 59.683 38.462 25.27 2.72 43.46 2.69
444 462 5.350633 TCTGCCATGACTTTTTCAAAACAG 58.649 37.500 0.00 0.00 37.92 3.16
666 688 3.701532 TCTAAAACGGTGTGCCAAAAG 57.298 42.857 0.00 0.00 34.09 2.27
679 701 3.381590 GTGCCAAAAGAGAGTTCACCTTT 59.618 43.478 0.00 0.00 0.00 3.11
718 740 0.393673 CACACAACCACTCCACCACA 60.394 55.000 0.00 0.00 0.00 4.17
764 786 1.406477 CCTACCCCGTGTTTTCTAGCC 60.406 57.143 0.00 0.00 0.00 3.93
872 894 4.262808 GCTGTTCATACCCATGCTATCTCT 60.263 45.833 0.00 0.00 31.73 3.10
894 916 1.618837 GAGACAGGTGTGTGAAGGCTA 59.381 52.381 0.00 0.00 36.88 3.93
909 931 1.216175 AGGCTATGTGGTCCATGCATT 59.784 47.619 0.00 0.00 34.86 3.56
952 974 3.707102 TCCGTCCATCCATGTGTGTATAA 59.293 43.478 0.00 0.00 0.00 0.98
955 977 5.056480 CGTCCATCCATGTGTGTATAACAT 58.944 41.667 0.00 0.00 41.97 2.71
985 1007 9.811995 AAATATAATATACACATACGTCCGCAT 57.188 29.630 0.00 0.00 0.00 4.73
1026 1048 1.685224 CTGTTGGCCCCAAGCTCTA 59.315 57.895 0.00 0.00 43.05 2.43
1188 1210 1.550976 CCTCTAGCCGTTTTGTCCTCT 59.449 52.381 0.00 0.00 0.00 3.69
1189 1211 2.417515 CCTCTAGCCGTTTTGTCCTCTC 60.418 54.545 0.00 0.00 0.00 3.20
1332 1354 6.205853 TCATTCTGCGGTAGTGTTTAAACATT 59.794 34.615 23.11 20.80 41.59 2.71
1344 1366 5.405269 GTGTTTAAACATTTGGCTAGCCTTG 59.595 40.000 33.07 26.89 41.59 3.61
1346 1368 1.631405 AACATTTGGCTAGCCTTGCA 58.369 45.000 33.07 11.61 36.94 4.08
1347 1369 1.631405 ACATTTGGCTAGCCTTGCAA 58.369 45.000 33.07 20.18 36.94 4.08
1359 1381 5.357032 GCTAGCCTTGCAAGTATAAAAAGGA 59.643 40.000 24.35 0.00 39.88 3.36
1400 1422 4.565652 CCCATAGCACTAGACCAAACAACT 60.566 45.833 0.00 0.00 0.00 3.16
1446 1468 2.439507 TCACCTGGTGAGCTTCTTCTTT 59.560 45.455 25.12 0.00 37.67 2.52
1454 1476 5.829924 TGGTGAGCTTCTTCTTTCTTTGATT 59.170 36.000 0.00 0.00 0.00 2.57
1478 1500 7.648039 TTCTATCACTTACTCTTTCTCCCTC 57.352 40.000 0.00 0.00 0.00 4.30
1499 1599 2.613977 CCTTCTTCTTCCTCGTGCATGT 60.614 50.000 5.68 0.00 0.00 3.21
1508 1608 1.603802 CCTCGTGCATGTGACTTTTGT 59.396 47.619 9.53 0.00 0.00 2.83
1522 1622 7.685481 TGTGACTTTTGTTAGATAATCTCCCA 58.315 34.615 0.00 0.00 0.00 4.37
1525 1625 8.328758 TGACTTTTGTTAGATAATCTCCCACAT 58.671 33.333 0.00 0.00 0.00 3.21
1534 1634 5.481824 AGATAATCTCCCACATTATCGCTCA 59.518 40.000 6.73 0.00 43.61 4.26
1535 1635 4.422073 AATCTCCCACATTATCGCTCAA 57.578 40.909 0.00 0.00 0.00 3.02
1536 1636 4.630644 ATCTCCCACATTATCGCTCAAT 57.369 40.909 0.00 0.00 0.00 2.57
1543 1643 2.033801 ACATTATCGCTCAATGCAAGCC 59.966 45.455 3.34 0.00 43.06 4.35
1607 1707 6.742559 AATACCCGTTGTAGATCTAACCAT 57.257 37.500 3.40 0.00 31.61 3.55
1622 1722 4.953579 TCTAACCATGGGCTATTCCAAAAC 59.046 41.667 18.09 0.00 40.62 2.43
1646 1746 2.730183 TTCTCTTGTTTGCGTGTTCG 57.270 45.000 0.00 0.00 40.37 3.95
1661 1761 1.196581 TGTTCGTGTGTACATGCATGC 59.803 47.619 26.53 11.82 33.05 4.06
1681 1781 7.078851 GCATGCATCTAGATCTTGATTTTGAG 58.921 38.462 15.82 6.93 0.00 3.02
1722 1822 4.345854 TGACCTACCTTGTTTGGTTTGTT 58.654 39.130 0.00 0.00 41.22 2.83
1741 1841 9.484326 GGTTTGTTTAATTTTGATGTTGTTGTC 57.516 29.630 0.00 0.00 0.00 3.18
1756 1856 8.891671 ATGTTGTTGTCTCAATTTTAGCAAAT 57.108 26.923 0.00 0.00 33.72 2.32
1757 1857 8.715191 TGTTGTTGTCTCAATTTTAGCAAATT 57.285 26.923 0.00 0.00 42.37 1.82
1837 1937 2.110967 CCAGGCTCTGCATCGGTTG 61.111 63.158 0.00 0.00 0.00 3.77
1889 1989 1.145119 ACTGATCCATGGATGCATGCT 59.855 47.619 32.05 6.73 34.60 3.79
1891 1991 3.010250 ACTGATCCATGGATGCATGCTAT 59.990 43.478 32.05 15.60 34.60 2.97
1898 1998 6.483405 TCCATGGATGCATGCTATATTTACA 58.517 36.000 20.86 7.00 0.00 2.41
1905 2005 9.185192 GGATGCATGCTATATTTACAAGTTTTC 57.815 33.333 20.33 0.00 0.00 2.29
1953 2070 8.889717 TGAAAAATTGGATCGGTATAGTTCTTC 58.110 33.333 0.00 0.00 0.00 2.87
1965 2082 8.358148 TCGGTATAGTTCTTCTTTATCCATGTC 58.642 37.037 0.00 0.00 0.00 3.06
2021 2138 6.877611 ATTTTGTCTCGGTTTCTTACATGT 57.122 33.333 2.69 2.69 0.00 3.21
2024 2141 5.970317 TGTCTCGGTTTCTTACATGTCTA 57.030 39.130 0.00 0.00 0.00 2.59
2081 2198 9.974980 CTTTCAAGGAATCCTAATACTAGAGAC 57.025 37.037 0.46 0.00 31.13 3.36
2093 2210 7.183112 CCTAATACTAGAGACTATGGGGAGAGA 59.817 44.444 0.00 0.00 0.00 3.10
2103 2220 4.591072 ACTATGGGGAGAGACAGCTTATTC 59.409 45.833 0.00 0.00 0.00 1.75
2147 2264 4.441079 GGGCGCTTAGAGTTGTAGTTGATA 60.441 45.833 7.64 0.00 0.00 2.15
2205 2322 7.512130 AGACCTGATTATGCACTTATCATGAA 58.488 34.615 0.00 0.00 0.00 2.57
2338 2455 1.143684 TCAAACTCCAAGAGCAAGGCT 59.856 47.619 0.00 0.00 43.88 4.58
2530 2647 3.009115 CATGGTGGGTCCCTCCGT 61.009 66.667 21.67 19.36 39.80 4.69
2619 2736 3.379445 GGCCTCCTCGTCGGAACA 61.379 66.667 0.00 0.00 42.53 3.18
2668 2785 3.055891 GCACAGGGATAAACTTTGCCAAT 60.056 43.478 0.00 0.00 36.04 3.16
2710 2827 3.822735 CTGCTGGTTTTGAGATTCCAAGA 59.177 43.478 0.00 0.00 0.00 3.02
2726 2843 1.149101 AAGAAGCCTTTCCCTGACCA 58.851 50.000 0.00 0.00 33.64 4.02
2812 2929 1.859841 TAGACGTGCTGAGAGGGGGA 61.860 60.000 0.00 0.00 0.00 4.81
2813 2930 2.203788 ACGTGCTGAGAGGGGGAA 60.204 61.111 0.00 0.00 0.00 3.97
2835 2952 0.323725 GGAGGGCTTCTTGATGGCAA 60.324 55.000 11.06 0.00 0.00 4.52
2840 2957 0.449388 GCTTCTTGATGGCAACCTCG 59.551 55.000 0.00 0.00 33.32 4.63
2870 2987 2.860817 TGGCTACTACTATGGTGGGT 57.139 50.000 0.00 0.00 0.00 4.51
2873 2990 3.464456 TGGCTACTACTATGGTGGGTCTA 59.536 47.826 0.00 0.00 0.00 2.59
2932 3055 1.076841 TCATTTGGCATTCCAGGTCCA 59.923 47.619 0.00 0.00 44.53 4.02
2954 3077 1.523032 CAGCAGCATGGCGATCTCA 60.523 57.895 0.00 0.00 39.27 3.27
3034 3157 1.964223 GAGGAAGGAGATGACGGCATA 59.036 52.381 2.12 0.00 34.11 3.14
3039 3162 1.004440 GAGATGACGGCATAGGGGC 60.004 63.158 2.12 0.00 34.11 5.80
3067 3190 2.056223 GCTCCAATGGCAGCCACAT 61.056 57.895 19.10 5.91 35.80 3.21
3158 3281 2.887783 ACGATGGGCAACAACAACATAA 59.112 40.909 0.00 0.00 39.74 1.90
3166 3289 5.295540 GGGCAACAACAACATAAACAACAAT 59.704 36.000 0.00 0.00 39.74 2.71
3182 3305 5.418676 ACAACAATAACAATAATGGCAGCC 58.581 37.500 3.66 3.66 0.00 4.85
3183 3306 5.046735 ACAACAATAACAATAATGGCAGCCA 60.047 36.000 18.99 18.99 38.19 4.75
3185 3308 4.465660 ACAATAACAATAATGGCAGCCACA 59.534 37.500 19.10 8.36 35.80 4.17
3198 3321 1.265095 CAGCCACAGTGATGACAACAC 59.735 52.381 7.72 7.72 38.38 3.32
3232 3355 3.244353 CGAGGGATTGCTACTGGATCAAT 60.244 47.826 0.00 0.00 33.57 2.57
3256 3379 0.107214 GAGGATCGAACCCATGGCAA 60.107 55.000 6.09 0.00 0.00 4.52
3303 3426 6.151691 TGATGTAAGTGCAAGAAGAAAATGC 58.848 36.000 0.00 0.00 40.45 3.56
3313 3436 5.702865 CAAGAAGAAAATGCGAAATGGAGA 58.297 37.500 0.00 0.00 0.00 3.71
3347 3470 3.813166 GAGAAGTGGGTCAATCGTTTTCA 59.187 43.478 0.00 0.00 0.00 2.69
3447 3573 6.426633 GGGGATTGTTTTGTTTATTTGAGTGG 59.573 38.462 0.00 0.00 0.00 4.00
3467 3593 3.214328 GGAACTCCAGACAATGTGTGTT 58.786 45.455 9.68 0.14 36.87 3.32
3468 3594 3.003689 GGAACTCCAGACAATGTGTGTTG 59.996 47.826 9.68 4.45 36.87 3.33
3606 3733 4.086457 GTTGGTTTACCCACTGATCCAAT 58.914 43.478 0.00 0.00 45.19 3.16
3637 3764 4.585581 CCATGGATTGTATTTCAGCATCCA 59.414 41.667 5.56 1.76 43.39 3.41
3662 3789 8.621286 CAAAACCTCATTTGTAGAAACACTAGT 58.379 33.333 0.00 0.00 35.93 2.57
3667 3794 7.009631 CCTCATTTGTAGAAACACTAGTCATCG 59.990 40.741 0.00 0.00 34.61 3.84
3736 3863 7.264294 ACTAGATCTTTCCCACTCTTGAAAT 57.736 36.000 0.00 0.00 30.67 2.17
3751 3878 9.626045 CACTCTTGAAATGGAGGTTTTATTTAC 57.374 33.333 0.00 0.00 34.22 2.01
3778 3905 7.693952 TCAATTCAACCTTCTATTAACATCGC 58.306 34.615 0.00 0.00 0.00 4.58
3798 3925 3.245284 CGCGAGATTTTTACATCGTCCAT 59.755 43.478 0.00 0.00 37.49 3.41
3799 3926 4.443063 CGCGAGATTTTTACATCGTCCATA 59.557 41.667 0.00 0.00 37.49 2.74
3800 3927 5.387444 CGCGAGATTTTTACATCGTCCATAG 60.387 44.000 0.00 0.00 37.49 2.23
3812 3939 3.552875 TCGTCCATAGAAGAGGGTACAG 58.447 50.000 0.00 0.00 0.00 2.74
3822 3949 5.026790 AGAAGAGGGTACAGCAGAATTAGT 58.973 41.667 0.00 0.00 0.00 2.24
3839 3966 9.793252 CAGAATTAGTTGGTTTATCCATCAAAG 57.207 33.333 0.00 0.00 46.60 2.77
3875 4002 7.224557 GCATTTTTCTTCTTTCAGGCAGTTTTA 59.775 33.333 0.00 0.00 0.00 1.52
3880 4007 3.412386 TCTTTCAGGCAGTTTTAGCTCC 58.588 45.455 0.00 0.00 0.00 4.70
3887 4014 4.096984 CAGGCAGTTTTAGCTCCCAATAAG 59.903 45.833 0.00 0.00 0.00 1.73
3888 4015 4.017126 GGCAGTTTTAGCTCCCAATAAGT 58.983 43.478 0.00 0.00 0.00 2.24
3893 4020 7.556844 CAGTTTTAGCTCCCAATAAGTCTAGA 58.443 38.462 0.00 0.00 0.00 2.43
4003 4325 2.964464 TGGTTCTTCCACATTTGCATGT 59.036 40.909 0.00 0.00 45.18 3.21
4051 4373 8.514330 TTTAGAAAACTTGAAAGGTTGCTCTA 57.486 30.769 4.54 2.04 36.94 2.43
4054 4376 8.011844 AGAAAACTTGAAAGGTTGCTCTATTT 57.988 30.769 0.00 0.00 36.94 1.40
4111 4434 4.623932 ACTCACTCTTTCAAGGTGCATA 57.376 40.909 0.00 0.00 31.50 3.14
4243 4566 4.065088 GCCATCACACACACTCTTAAAGA 58.935 43.478 0.00 0.00 0.00 2.52
4247 4570 7.134815 CCATCACACACACTCTTAAAGAAAAG 58.865 38.462 0.00 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.281867 CAACCTCTCTACCATTGGCCA 59.718 52.381 0.00 0.00 0.00 5.36
70 71 3.826729 AGCCAACCAAAAGTCAAGTATCC 59.173 43.478 0.00 0.00 0.00 2.59
137 138 6.844388 ACTACAGTTGATCCATGGGACTATAA 59.156 38.462 13.02 0.00 32.98 0.98
141 142 3.454858 ACTACAGTTGATCCATGGGACT 58.545 45.455 13.02 8.41 32.98 3.85
142 143 3.914426 ACTACAGTTGATCCATGGGAC 57.086 47.619 13.02 7.02 32.98 4.46
143 144 4.878968 TCTACTACAGTTGATCCATGGGA 58.121 43.478 13.02 0.00 35.55 4.37
181 199 7.928307 ATATCACAAAGCAACACAATCTAGT 57.072 32.000 0.00 0.00 0.00 2.57
220 238 8.041323 ACCAAAGTCCATAGAGTAGTTTGTATG 58.959 37.037 0.00 0.00 0.00 2.39
270 288 7.817962 CCTCTTTAGTGAGGTTCGAATTTTCTA 59.182 37.037 0.00 0.00 46.33 2.10
334 352 8.821817 ACCCCTATTTTTGTTGCACTATATTTT 58.178 29.630 0.00 0.00 0.00 1.82
438 456 4.201657 AGTAACTTGGTAACGCCTGTTTT 58.798 39.130 0.00 0.00 39.54 2.43
444 462 6.966435 TTTGTATAGTAACTTGGTAACGCC 57.034 37.500 0.00 0.00 42.51 5.68
481 499 8.217115 CGAATCGATATTTGTATTTCCTCACAG 58.783 37.037 0.00 0.00 0.00 3.66
501 519 5.696270 TCATTAATTCTCCACCATCGAATCG 59.304 40.000 0.00 0.00 0.00 3.34
509 527 5.836705 TCCCATTTCATTAATTCTCCACCA 58.163 37.500 0.00 0.00 0.00 4.17
653 675 1.264288 GAACTCTCTTTTGGCACACCG 59.736 52.381 0.00 0.00 39.29 4.94
657 679 2.576615 AGGTGAACTCTCTTTTGGCAC 58.423 47.619 0.00 0.00 0.00 5.01
666 688 2.680339 GCATAGGCAAAGGTGAACTCTC 59.320 50.000 0.00 0.00 40.72 3.20
718 740 1.656652 GCATTCACGTGTCATAGCCT 58.343 50.000 16.51 0.00 0.00 4.58
749 771 2.736682 CGCGGCTAGAAAACACGGG 61.737 63.158 0.00 0.00 0.00 5.28
764 786 1.550065 CTATCTTGTCAGTGACCGCG 58.450 55.000 20.43 0.00 0.00 6.46
872 894 1.475034 GCCTTCACACACCTGTCTCAA 60.475 52.381 0.00 0.00 0.00 3.02
894 916 4.795469 TCTATGAAATGCATGGACCACAT 58.205 39.130 0.00 0.00 39.27 3.21
909 931 2.730382 TGCACTCTACGGGTCTATGAA 58.270 47.619 0.00 0.00 0.00 2.57
962 984 8.071967 GCTATGCGGACGTATGTGTATATTATA 58.928 37.037 5.56 0.00 0.00 0.98
1026 1048 0.472471 TCCTCCTTCCGTTGCTTGTT 59.528 50.000 0.00 0.00 0.00 2.83
1088 1110 6.989759 GGAAACAGAAAAGAGAGAGAAAGACT 59.010 38.462 0.00 0.00 0.00 3.24
1137 1159 5.684704 CACACTAGAGAGAGAGAGAAGGAT 58.315 45.833 0.00 0.00 0.00 3.24
1188 1210 2.112297 GTTGGCCTGTTGTCCCGA 59.888 61.111 3.32 0.00 0.00 5.14
1189 1211 2.203280 TGTTGGCCTGTTGTCCCG 60.203 61.111 3.32 0.00 0.00 5.14
1332 1354 2.806945 ATACTTGCAAGGCTAGCCAA 57.193 45.000 34.70 19.14 35.00 4.52
1344 1366 4.462834 AGTTGCCCTCCTTTTTATACTTGC 59.537 41.667 0.00 0.00 0.00 4.01
1346 1368 6.208797 GTGAAGTTGCCCTCCTTTTTATACTT 59.791 38.462 0.00 0.00 0.00 2.24
1347 1369 5.710567 GTGAAGTTGCCCTCCTTTTTATACT 59.289 40.000 0.00 0.00 0.00 2.12
1400 1422 6.791847 TGAAGGGTAGTATGGAGTATAGGA 57.208 41.667 0.00 0.00 0.00 2.94
1454 1476 6.608002 GGAGGGAGAAAGAGTAAGTGATAGAA 59.392 42.308 0.00 0.00 0.00 2.10
1478 1500 2.005451 CATGCACGAGGAAGAAGAAGG 58.995 52.381 0.00 0.00 0.00 3.46
1499 1599 7.685481 TGTGGGAGATTATCTAACAAAAGTCA 58.315 34.615 0.00 0.00 0.00 3.41
1508 1608 7.178451 TGAGCGATAATGTGGGAGATTATCTAA 59.822 37.037 0.00 0.00 39.29 2.10
1556 1656 3.254470 AGATCGCTAGCTAGATCGCTA 57.746 47.619 25.15 2.04 45.68 4.26
1557 1657 2.107950 AGATCGCTAGCTAGATCGCT 57.892 50.000 25.15 10.65 45.68 4.93
1558 1658 2.160615 TGAAGATCGCTAGCTAGATCGC 59.839 50.000 25.15 15.45 45.68 4.58
1559 1659 3.435327 AGTGAAGATCGCTAGCTAGATCG 59.565 47.826 25.15 18.29 45.68 3.69
1560 1660 5.371115 AAGTGAAGATCGCTAGCTAGATC 57.629 43.478 25.15 18.08 42.52 2.75
1561 1661 5.782893 AAAGTGAAGATCGCTAGCTAGAT 57.217 39.130 25.15 10.07 35.97 1.98
1562 1662 6.694877 TTAAAGTGAAGATCGCTAGCTAGA 57.305 37.500 25.15 4.93 35.97 2.43
1607 1707 7.125391 AGAGAAATATGTTTTGGAATAGCCCA 58.875 34.615 0.00 0.00 34.97 5.36
1622 1722 5.281376 CGAACACGCAAACAAGAGAAATATG 59.719 40.000 0.00 0.00 0.00 1.78
1646 1746 4.122046 TCTAGATGCATGCATGTACACAC 58.878 43.478 36.73 20.03 36.70 3.82
1692 1792 5.414765 CCAAACAAGGTAGGTCAGGAATTAC 59.585 44.000 0.00 0.00 0.00 1.89
1699 1799 3.951680 ACAAACCAAACAAGGTAGGTCAG 59.048 43.478 0.00 0.00 42.25 3.51
1756 1856 5.221067 CCTCTATTGTTCTAGCTACGAGCAA 60.221 44.000 17.79 17.79 45.56 3.91
1757 1857 4.276183 CCTCTATTGTTCTAGCTACGAGCA 59.724 45.833 9.09 0.00 45.56 4.26
1837 1937 0.953471 TGGTAACGGCTGTGTGCATC 60.953 55.000 0.00 0.00 45.15 3.91
1943 2056 8.473358 TCCGACATGGATAAAGAAGAACTATA 57.527 34.615 0.00 0.00 43.74 1.31
1944 2057 7.361457 TCCGACATGGATAAAGAAGAACTAT 57.639 36.000 0.00 0.00 43.74 2.12
1965 2082 4.196626 TGGGTACAAAGTAGTGAATCCG 57.803 45.455 0.00 0.00 0.00 4.18
2081 2198 4.837860 AGAATAAGCTGTCTCTCCCCATAG 59.162 45.833 0.00 0.00 0.00 2.23
2114 2231 1.472480 TCTAAGCGCCCATTCTTTTGC 59.528 47.619 2.29 0.00 0.00 3.68
2147 2264 8.812513 TCAGATCCATACAACAGATTCAATTT 57.187 30.769 0.00 0.00 0.00 1.82
2338 2455 4.731853 TCCCCCGCCATCTGACCA 62.732 66.667 0.00 0.00 0.00 4.02
2521 2638 2.714991 GGGGACGTTACGGAGGGAC 61.715 68.421 10.20 0.00 0.00 4.46
2530 2647 3.301070 CCACCGATGGGGACGTTA 58.699 61.111 0.00 0.00 43.04 3.18
2656 2773 1.970640 GGGAGGACATTGGCAAAGTTT 59.029 47.619 9.70 1.64 0.00 2.66
2668 2785 1.203052 GACATAAACGTCGGGAGGACA 59.797 52.381 0.00 0.00 46.42 4.02
2710 2827 1.068352 AGGTGGTCAGGGAAAGGCTT 61.068 55.000 0.00 0.00 0.00 4.35
2726 2843 3.673515 CGACGACGATGACCCAAAGGT 62.674 57.143 0.00 0.00 46.27 3.50
2756 2873 2.607750 AGGGGACATCACAGCCGT 60.608 61.111 0.00 0.00 0.00 5.68
2761 2878 3.494506 CCACCAGGGGACATCACA 58.505 61.111 0.00 0.00 0.00 3.58
2788 2905 2.159310 CCCTCTCAGCACGTCTAGAAAG 60.159 54.545 0.00 0.00 0.00 2.62
2812 2929 1.005215 CCATCAAGAAGCCCTCCTGTT 59.995 52.381 0.00 0.00 0.00 3.16
2813 2930 0.622665 CCATCAAGAAGCCCTCCTGT 59.377 55.000 0.00 0.00 0.00 4.00
2835 2952 0.321653 GCCATTGTTCTGACCGAGGT 60.322 55.000 0.00 0.00 0.00 3.85
2840 2957 4.473477 AGTAGTAGCCATTGTTCTGACC 57.527 45.455 0.00 0.00 0.00 4.02
2954 3077 4.264804 ACCTATTCCATTTCCACCAACCAT 60.265 41.667 0.00 0.00 0.00 3.55
3013 3136 0.614697 TGCCGTCATCTCCTTCCTCA 60.615 55.000 0.00 0.00 0.00 3.86
3039 3162 0.830444 CCATTGGAGCCCCATCATGG 60.830 60.000 3.76 3.76 41.77 3.66
3041 3164 1.152398 GCCATTGGAGCCCCATCAT 60.152 57.895 6.95 0.00 43.12 2.45
3067 3190 1.074727 CCACCTCCACCATTACCAACA 59.925 52.381 0.00 0.00 0.00 3.33
3073 3196 0.695924 CACCACCACCTCCACCATTA 59.304 55.000 0.00 0.00 0.00 1.90
3158 3281 5.874261 GGCTGCCATTATTGTTATTGTTGTT 59.126 36.000 15.17 0.00 0.00 2.83
3166 3289 3.443329 CACTGTGGCTGCCATTATTGTTA 59.557 43.478 26.22 0.00 35.28 2.41
3175 3298 1.302752 GTCATCACTGTGGCTGCCA 60.303 57.895 19.30 19.30 0.00 4.92
3177 3300 0.239347 GTTGTCATCACTGTGGCTGC 59.761 55.000 8.11 0.00 0.00 5.25
3185 3308 1.202806 CCCACCAGTGTTGTCATCACT 60.203 52.381 10.24 10.24 45.43 3.41
3198 3321 1.050988 ATCCCTCGATGACCCACCAG 61.051 60.000 0.00 0.00 0.00 4.00
3232 3355 2.371841 CCATGGGTTCGATCCTCCATTA 59.628 50.000 12.19 0.00 37.86 1.90
3256 3379 1.140652 GAGCTGCTATTGAGGAGGCTT 59.859 52.381 0.15 0.00 41.32 4.35
3268 3391 2.432146 CACTTACATCAGGGAGCTGCTA 59.568 50.000 0.15 0.00 0.00 3.49
3303 3426 6.261603 TCTCCAATTCAATGATCTCCATTTCG 59.738 38.462 0.00 0.00 42.55 3.46
3313 3436 4.939255 ACCCACTTCTCCAATTCAATGAT 58.061 39.130 0.00 0.00 0.00 2.45
3347 3470 6.803154 AAAAAGAAGCGCTGAAACTAGTAT 57.197 33.333 12.58 0.00 0.00 2.12
3371 3497 7.095355 GGAGCGAAATAAGTCAAGAAAGTAACA 60.095 37.037 0.00 0.00 0.00 2.41
3372 3498 7.095355 TGGAGCGAAATAAGTCAAGAAAGTAAC 60.095 37.037 0.00 0.00 0.00 2.50
3379 3505 5.084818 TGATGGAGCGAAATAAGTCAAGA 57.915 39.130 0.00 0.00 0.00 3.02
3447 3573 3.627577 ACAACACACATTGTCTGGAGTTC 59.372 43.478 0.00 0.00 38.44 3.01
3467 3593 8.240682 ACAATACTTAATTAAGCATCGCAAACA 58.759 29.630 22.45 0.00 36.79 2.83
3468 3594 8.614994 ACAATACTTAATTAAGCATCGCAAAC 57.385 30.769 22.45 0.00 36.79 2.93
3637 3764 8.747538 ACTAGTGTTTCTACAAATGAGGTTTT 57.252 30.769 0.00 0.00 35.69 2.43
3662 3789 1.142060 ACCCACAAAAGACCACGATGA 59.858 47.619 0.00 0.00 0.00 2.92
3667 3794 6.584185 ATGTTATAACCCACAAAAGACCAC 57.416 37.500 13.01 0.00 0.00 4.16
3714 3841 6.215431 TCCATTTCAAGAGTGGGAAAGATCTA 59.785 38.462 0.00 0.00 36.55 1.98
3736 3863 9.974980 GTTGAATTGAAGTAAATAAAACCTCCA 57.025 29.630 0.00 0.00 0.00 3.86
3751 3878 9.708222 CGATGTTAATAGAAGGTTGAATTGAAG 57.292 33.333 0.00 0.00 0.00 3.02
3754 3881 6.628856 CGCGATGTTAATAGAAGGTTGAATTG 59.371 38.462 0.00 0.00 0.00 2.32
3776 3903 2.601314 TGGACGATGTAAAAATCTCGCG 59.399 45.455 0.00 0.00 34.60 5.87
3778 3905 7.648112 TCTTCTATGGACGATGTAAAAATCTCG 59.352 37.037 0.00 0.00 37.17 4.04
3785 3912 4.960469 ACCCTCTTCTATGGACGATGTAAA 59.040 41.667 0.00 0.00 0.00 2.01
3798 3925 6.195700 ACTAATTCTGCTGTACCCTCTTCTA 58.804 40.000 0.00 0.00 0.00 2.10
3799 3926 5.026790 ACTAATTCTGCTGTACCCTCTTCT 58.973 41.667 0.00 0.00 0.00 2.85
3800 3927 5.346181 ACTAATTCTGCTGTACCCTCTTC 57.654 43.478 0.00 0.00 0.00 2.87
3875 4002 5.137412 AGACTCTAGACTTATTGGGAGCT 57.863 43.478 0.00 0.00 0.00 4.09
4051 4373 6.567050 CGAACCTTGATGATGGAAATGAAAT 58.433 36.000 0.00 0.00 0.00 2.17
4054 4376 3.378112 GCGAACCTTGATGATGGAAATGA 59.622 43.478 0.00 0.00 0.00 2.57
4120 4443 5.782893 AATGGCTAGTGTTGCTTTAAACA 57.217 34.783 0.00 0.00 37.71 2.83
4132 4455 9.319143 GTATAATTAGCTCCATAATGGCTAGTG 57.681 37.037 0.00 0.00 39.30 2.74
4220 4543 3.483808 TTAAGAGTGTGTGTGATGGCA 57.516 42.857 0.00 0.00 0.00 4.92
4221 4544 4.065088 TCTTTAAGAGTGTGTGTGATGGC 58.935 43.478 0.00 0.00 0.00 4.40
4227 4550 6.415573 ACTCCTTTTCTTTAAGAGTGTGTGT 58.584 36.000 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.