Multiple sequence alignment - TraesCS4D01G083700

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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 TraesCS4D01G083700 chr4D 100.000 3912 0 0 1 3912 57474075 57477986 0.000000e+00 7225.0
1 TraesCS4D01G083700 chr4A 91.082 3409 194 35 107 3445 539300506 539297138 0.000000e+00 4510.0
2 TraesCS4D01G083700 chr4A 78.962 366 35 26 3521 3874 539297136 539296801 1.100000e-50 211.0
3 TraesCS4D01G083700 chr4B 92.295 2336 107 24 1 2293 86060618 86062923 0.000000e+00 3249.0
4 TraesCS4D01G083700 chr4B 87.477 1110 76 31 2810 3874 86062917 86064008 0.000000e+00 1221.0
5 TraesCS4D01G083700 chr6B 94.542 1191 61 2 1272 2461 551792826 551794013 0.000000e+00 1836.0
6 TraesCS4D01G083700 chr6B 89.587 1018 47 21 1 967 551791439 551792448 0.000000e+00 1238.0
7 TraesCS4D01G083700 chr6B 89.174 896 55 20 3002 3874 551794570 551795446 0.000000e+00 1079.0
8 TraesCS4D01G083700 chr6B 94.813 482 22 2 2488 2967 551794010 551794490 0.000000e+00 749.0
9 TraesCS4D01G083700 chr6B 89.407 236 11 6 964 1197 551792606 551792829 6.400000e-73 285.0
10 TraesCS4D01G083700 chr6B 94.118 34 2 0 2965 2998 551794521 551794554 7.000000e-03 52.8
11 TraesCS4D01G083700 chr5B 97.959 98 2 0 5 102 599755870 599755967 1.870000e-38 171.0
12 TraesCS4D01G083700 chr3A 97.000 100 3 0 3 102 650012971 650012872 6.720000e-38 169.0
13 TraesCS4D01G083700 chr1D 96.000 100 4 0 3 102 68403208 68403307 3.130000e-36 163.0
14 TraesCS4D01G083700 chr1D 96.000 100 4 0 3 102 254527096 254527195 3.130000e-36 163.0
15 TraesCS4D01G083700 chr1D 96.000 100 4 0 3 102 298349140 298349041 3.130000e-36 163.0
16 TraesCS4D01G083700 chr1D 96.000 100 4 0 3 102 459903227 459903128 3.130000e-36 163.0
17 TraesCS4D01G083700 chr1A 96.000 100 4 0 3 102 532075181 532075280 3.130000e-36 163.0


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 TraesCS4D01G083700 chr4D 57474075 57477986 3911 False 7225.0 7225 100.000000 1 3912 1 chr4D.!!$F1 3911
1 TraesCS4D01G083700 chr4A 539296801 539300506 3705 True 2360.5 4510 85.022000 107 3874 2 chr4A.!!$R1 3767
2 TraesCS4D01G083700 chr4B 86060618 86064008 3390 False 2235.0 3249 89.886000 1 3874 2 chr4B.!!$F1 3873
3 TraesCS4D01G083700 chr6B 551791439 551795446 4007 False 873.3 1836 91.940167 1 3874 6 chr6B.!!$F1 3873

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
52 53 1.005097 TGAATCCATGAGCAGGCAAGT 59.995 47.619 0.00 0.0 0.00 3.16 F
64 65 1.827789 GGCAAGTGACAACCTGGCA 60.828 57.895 0.00 0.0 41.69 4.92 F
629 646 2.969300 TTCCCCGGCTCGTTTTTGCT 62.969 55.000 0.00 0.0 0.00 3.91 F
1890 2234 0.170784 CGCAATGTATGGCAAGTGCA 59.829 50.000 10.24 0.0 44.36 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1039 1295 0.393537 CATCTGTTGGACCTCAGGCC 60.394 60.0 14.17 0.0 33.13 5.19 R
1041 1297 0.393537 GGCATCTGTTGGACCTCAGG 60.394 60.0 14.17 0.0 33.13 3.86 R
2363 2707 0.602638 CACAAGCCACTAGAACCGCA 60.603 55.0 0.00 0.0 0.00 5.69 R
2998 3377 0.250793 TAATGCAACGGGTCATCGGT 59.749 50.0 0.00 0.0 0.00 4.69 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
52 53 1.005097 TGAATCCATGAGCAGGCAAGT 59.995 47.619 0.00 0.00 0.00 3.16
64 65 1.827789 GGCAAGTGACAACCTGGCA 60.828 57.895 0.00 0.00 41.69 4.92
87 88 3.754965 ACTGAAACATCTTAGCAGCCAA 58.245 40.909 0.00 0.00 0.00 4.52
109 110 6.930722 CCAAAGGAAAAGAAAGCATGTAACAT 59.069 34.615 0.00 0.00 0.00 2.71
216 217 3.305964 CTCTGTTCTTTGTGCATTGCTG 58.694 45.455 10.49 0.00 0.00 4.41
246 247 5.105756 GGGCATACATTTTCTACACTTTGCT 60.106 40.000 0.00 0.00 0.00 3.91
337 341 8.037166 CAGTTAGATAACAGGCAGCATATATCA 58.963 37.037 12.18 0.44 38.62 2.15
339 343 6.617782 AGATAACAGGCAGCATATATCAGT 57.382 37.500 12.18 0.00 0.00 3.41
403 411 5.736951 ATGTCTAAGCTGAGATGTATCCC 57.263 43.478 3.44 0.00 0.00 3.85
629 646 2.969300 TTCCCCGGCTCGTTTTTGCT 62.969 55.000 0.00 0.00 0.00 3.91
683 700 4.393062 GCAACACTAGTGTAACATGAGCAT 59.607 41.667 28.13 6.32 44.13 3.79
710 731 3.102972 TCCATGAGAAGTCCAGAGAAGG 58.897 50.000 0.00 0.00 0.00 3.46
957 1051 8.383619 CAAACCAAACAAATTTCGACATGTAAA 58.616 29.630 0.00 0.00 0.00 2.01
1031 1287 3.169155 AACTCAGTCAGCAGCGGCA 62.169 57.895 12.44 0.00 44.61 5.69
1033 1289 3.871248 CTCAGTCAGCAGCGGCACA 62.871 63.158 12.44 0.00 44.61 4.57
1034 1290 3.720193 CAGTCAGCAGCGGCACAC 61.720 66.667 12.44 6.84 44.61 3.82
1035 1291 4.996434 AGTCAGCAGCGGCACACC 62.996 66.667 12.44 0.00 44.61 4.16
1037 1293 4.334118 TCAGCAGCGGCACACCAT 62.334 61.111 12.44 0.00 44.61 3.55
1038 1294 3.807538 CAGCAGCGGCACACCATC 61.808 66.667 12.44 0.00 44.61 3.51
1069 1325 1.207791 CAACAGATGCCCCCTACTCT 58.792 55.000 0.00 0.00 0.00 3.24
1152 1417 4.824515 CCGGCGTCTCCTCCTCCT 62.825 72.222 6.01 0.00 0.00 3.69
1153 1418 3.213402 CGGCGTCTCCTCCTCCTC 61.213 72.222 0.00 0.00 0.00 3.71
1154 1419 3.213402 GGCGTCTCCTCCTCCTCG 61.213 72.222 0.00 0.00 0.00 4.63
1155 1420 2.438795 GCGTCTCCTCCTCCTCGT 60.439 66.667 0.00 0.00 0.00 4.18
1156 1421 2.474612 GCGTCTCCTCCTCCTCGTC 61.475 68.421 0.00 0.00 0.00 4.20
1157 1422 1.820481 CGTCTCCTCCTCCTCGTCC 60.820 68.421 0.00 0.00 0.00 4.79
1730 2074 2.933287 ACGATGGTTGCCCAGGGA 60.933 61.111 10.89 0.00 46.15 4.20
1769 2113 3.071457 TCACTCTGATCAGTTTCTTGCCA 59.929 43.478 21.92 0.00 0.00 4.92
1794 2138 1.993653 CAGGGGCAGGAATGTCTCA 59.006 57.895 0.00 0.00 0.00 3.27
1890 2234 0.170784 CGCAATGTATGGCAAGTGCA 59.829 50.000 10.24 0.00 44.36 4.57
1925 2269 1.200020 GCGAAGGAGTTGTTTGATGGG 59.800 52.381 0.00 0.00 0.00 4.00
2085 2429 2.203056 TGTCTGCTTGCACACGCT 60.203 55.556 0.67 0.00 39.64 5.07
2235 2579 0.529555 GGCTTTTGAAGGTTTGCGCA 60.530 50.000 5.66 5.66 0.00 6.09
2258 2602 0.318441 CTGGTGTCGTGTCATGGAGT 59.682 55.000 0.00 0.00 0.00 3.85
2335 2679 3.193263 TCTCTGCGATGAAAGATCAAGC 58.807 45.455 0.00 0.00 39.49 4.01
2363 2707 2.678190 GCCTAATTCCTTCACGCTCACT 60.678 50.000 0.00 0.00 0.00 3.41
2378 2722 1.185618 TCACTGCGGTTCTAGTGGCT 61.186 55.000 0.00 0.00 43.40 4.75
2465 2809 6.823689 ACCATATATCACCAACACTTGAGAAC 59.176 38.462 0.00 0.00 0.00 3.01
2567 2911 1.331214 CAGACAAGTGCATTTGGGGT 58.669 50.000 23.78 5.15 32.32 4.95
2651 2995 2.567615 TCTCTTCCAGTTGGGCTCTAAC 59.432 50.000 0.00 0.00 36.21 2.34
2711 3055 0.924823 AGGCTGGAATGCTGGAAGAT 59.075 50.000 0.00 0.00 34.07 2.40
2732 3076 1.511768 GGAAAGGACGAGGAGGACG 59.488 63.158 0.00 0.00 0.00 4.79
2840 3186 6.116126 AGCTAGATGCAAGTTTTAGGTTAGG 58.884 40.000 0.00 0.00 45.94 2.69
2877 3223 5.189736 AGCTATTTACACATGTTCTCTCCCA 59.810 40.000 0.00 0.00 0.00 4.37
2942 3288 6.556495 TCTTAGGCTCATGATAAACTGAGGAT 59.444 38.462 0.00 0.00 39.42 3.24
2969 3315 8.519492 AATGTTGTGTTTTCTGATAATTTCCG 57.481 30.769 0.00 0.00 0.00 4.30
2998 3377 0.331278 CTGTACAATGGGGAAGGCCA 59.669 55.000 5.01 0.00 35.15 5.36
3197 3604 7.287061 TCGGTGAGGAATAATGGTTTTCATAT 58.713 34.615 0.00 0.00 34.44 1.78
3257 3664 0.895100 TGTTTCATGGCTCAGGTGGC 60.895 55.000 0.00 0.00 0.00 5.01
3366 3774 4.202398 ACCGATGGCAGATGACTGATTAAT 60.202 41.667 0.00 0.00 46.03 1.40
3431 3844 4.729868 AGGTAGGACAAAGAAGTTGCAAT 58.270 39.130 0.59 0.00 41.31 3.56
3444 3857 6.395629 AGAAGTTGCAATCTGAAAATGATGG 58.604 36.000 0.59 0.00 0.00 3.51
3445 3858 5.733620 AGTTGCAATCTGAAAATGATGGT 57.266 34.783 0.59 0.00 0.00 3.55
3446 3859 6.839124 AGTTGCAATCTGAAAATGATGGTA 57.161 33.333 0.59 0.00 0.00 3.25
3538 3953 5.556665 CGAAGAACGAGAAAGTTTCAAATCG 59.443 40.000 17.65 18.28 45.77 3.34
3566 3982 7.360353 GCTTCCTGCATTTTTGAATTTTCTACC 60.360 37.037 0.00 0.00 42.31 3.18
3573 3989 8.825745 GCATTTTTGAATTTTCTACCAAGAACA 58.174 29.630 0.00 0.00 41.48 3.18
3584 4000 8.924511 TTTCTACCAAGAACAATTTCATCTCT 57.075 30.769 0.00 0.00 41.48 3.10
3586 4002 9.436957 TTCTACCAAGAACAATTTCATCTCTAC 57.563 33.333 0.00 0.00 36.80 2.59
3587 4003 8.593679 TCTACCAAGAACAATTTCATCTCTACA 58.406 33.333 0.00 0.00 33.72 2.74
3588 4004 9.219603 CTACCAAGAACAATTTCATCTCTACAA 57.780 33.333 0.00 0.00 33.72 2.41
3592 4008 9.350357 CAAGAACAATTTCATCTCTACAAATGG 57.650 33.333 0.00 0.00 33.72 3.16
3593 4009 8.059798 AGAACAATTTCATCTCTACAAATGGG 57.940 34.615 0.00 0.00 33.72 4.00
3607 4028 9.778741 CTCTACAAATGGGTTCTAGCATTTATA 57.221 33.333 5.93 0.56 0.00 0.98
3622 4043 5.483583 AGCATTTATAGCTCTCCTAGGAAGG 59.516 44.000 13.77 9.44 40.49 3.46
3739 4171 3.626028 AGTGTGCATTCGTTTTTCTCC 57.374 42.857 0.00 0.00 0.00 3.71
3795 4234 1.079543 GTGAGTCGATGCAGCAGGT 60.080 57.895 1.53 0.00 0.00 4.00
3830 4273 2.902705 TGACACGCAAAGTACCTCTT 57.097 45.000 0.00 0.00 38.10 2.85
3831 4274 3.188159 TGACACGCAAAGTACCTCTTT 57.812 42.857 0.00 0.00 45.96 2.52
3874 4317 8.198778 GGTAACATCTTTTAGGAGAAGAGGTAG 58.801 40.741 4.84 0.00 44.50 3.18
3875 4318 7.800300 AACATCTTTTAGGAGAAGAGGTAGT 57.200 36.000 4.84 0.00 44.50 2.73
3876 4319 8.896722 AACATCTTTTAGGAGAAGAGGTAGTA 57.103 34.615 4.84 0.00 44.50 1.82
3877 4320 8.296211 ACATCTTTTAGGAGAAGAGGTAGTAC 57.704 38.462 2.74 0.00 43.75 2.73
3878 4321 7.894364 ACATCTTTTAGGAGAAGAGGTAGTACA 59.106 37.037 2.06 0.00 43.75 2.90
3879 4322 8.750298 CATCTTTTAGGAGAAGAGGTAGTACAA 58.250 37.037 2.06 0.00 36.64 2.41
3880 4323 8.716674 TCTTTTAGGAGAAGAGGTAGTACAAA 57.283 34.615 2.06 0.00 0.00 2.83
3881 4324 9.151177 TCTTTTAGGAGAAGAGGTAGTACAAAA 57.849 33.333 2.06 0.00 0.00 2.44
3882 4325 9.425577 CTTTTAGGAGAAGAGGTAGTACAAAAG 57.574 37.037 2.06 2.42 0.00 2.27
3883 4326 7.477945 TTAGGAGAAGAGGTAGTACAAAAGG 57.522 40.000 2.06 0.00 0.00 3.11
3884 4327 4.778427 AGGAGAAGAGGTAGTACAAAAGGG 59.222 45.833 2.06 0.00 0.00 3.95
3885 4328 4.776308 GGAGAAGAGGTAGTACAAAAGGGA 59.224 45.833 2.06 0.00 0.00 4.20
3886 4329 5.247792 GGAGAAGAGGTAGTACAAAAGGGAA 59.752 44.000 2.06 0.00 0.00 3.97
3887 4330 6.361768 AGAAGAGGTAGTACAAAAGGGAAG 57.638 41.667 2.06 0.00 0.00 3.46
3888 4331 5.248705 AGAAGAGGTAGTACAAAAGGGAAGG 59.751 44.000 2.06 0.00 0.00 3.46
3889 4332 3.844804 AGAGGTAGTACAAAAGGGAAGGG 59.155 47.826 2.06 0.00 0.00 3.95
3890 4333 2.917600 AGGTAGTACAAAAGGGAAGGGG 59.082 50.000 2.06 0.00 0.00 4.79
3891 4334 2.025605 GGTAGTACAAAAGGGAAGGGGG 60.026 54.545 2.06 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 2.136298 TTCAGTTTGCCAGGTTGTCA 57.864 45.000 0.00 0.00 0.00 3.58
64 65 4.144297 TGGCTGCTAAGATGTTTCAGTTT 58.856 39.130 0.00 0.00 0.00 2.66
87 88 6.458210 CCATGTTACATGCTTTCTTTTCCTT 58.542 36.000 18.95 0.00 0.00 3.36
109 110 3.244946 TGAATAAATGACCACCGTTCCCA 60.245 43.478 0.00 0.00 0.00 4.37
216 217 8.051901 AGTGTAGAAAATGTATGCCCTTAAAC 57.948 34.615 0.00 0.00 0.00 2.01
246 247 5.661312 AGCTAGATGAAGTGTATGTAACCCA 59.339 40.000 0.00 0.00 0.00 4.51
337 341 6.624352 ATGATACAATAATTTGCGCTGACT 57.376 33.333 9.73 0.00 36.22 3.41
339 343 8.401709 TGTAAATGATACAATAATTTGCGCTGA 58.598 29.630 9.73 0.00 36.22 4.26
403 411 2.887152 CAACCTTTCCTGGAACAAGGAG 59.113 50.000 26.59 17.05 38.70 3.69
629 646 6.943146 ACTCTGGATAGATTCAGCTAACGATA 59.057 38.462 0.00 0.00 31.21 2.92
736 805 5.646362 CAAAAACAACGTTTGCAACATTG 57.354 34.783 0.00 6.80 40.17 2.82
791 862 7.977818 TGGCAAATTACAGAGACTATGGATAT 58.022 34.615 1.55 0.00 0.00 1.63
792 863 7.071196 ACTGGCAAATTACAGAGACTATGGATA 59.929 37.037 1.55 0.00 38.09 2.59
795 866 5.431765 ACTGGCAAATTACAGAGACTATGG 58.568 41.667 1.55 0.00 38.09 2.74
800 871 4.022849 AGCAAACTGGCAAATTACAGAGAC 60.023 41.667 10.57 0.42 38.09 3.36
957 1051 5.918576 GCTACGGCTTCTTTTGTACAAAAAT 59.081 36.000 28.52 13.83 36.40 1.82
993 1249 1.235724 GGGTTTCACCACGGAGAAAG 58.764 55.000 8.68 0.00 41.02 2.62
999 1255 0.464735 TGAGTTGGGTTTCACCACGG 60.465 55.000 0.00 0.00 41.02 4.94
1031 1287 2.607750 ACCTCAGGCCGATGGTGT 60.608 61.111 14.27 0.00 0.00 4.16
1033 1289 3.083997 GGACCTCAGGCCGATGGT 61.084 66.667 14.80 14.80 35.23 3.55
1034 1290 2.669133 TTGGACCTCAGGCCGATGG 61.669 63.158 0.00 2.90 0.00 3.51
1035 1291 1.450312 GTTGGACCTCAGGCCGATG 60.450 63.158 0.00 0.00 0.00 3.84
1036 1292 1.903877 CTGTTGGACCTCAGGCCGAT 61.904 60.000 0.00 0.00 0.00 4.18
1037 1293 2.525629 TGTTGGACCTCAGGCCGA 60.526 61.111 0.00 0.00 0.00 5.54
1038 1294 1.903877 ATCTGTTGGACCTCAGGCCG 61.904 60.000 14.17 0.00 33.13 6.13
1039 1295 0.393537 CATCTGTTGGACCTCAGGCC 60.394 60.000 14.17 0.00 33.13 5.19
1040 1296 1.028868 GCATCTGTTGGACCTCAGGC 61.029 60.000 14.17 8.95 33.13 4.85
1041 1297 0.393537 GGCATCTGTTGGACCTCAGG 60.394 60.000 14.17 0.00 33.13 3.86
1042 1298 0.393537 GGGCATCTGTTGGACCTCAG 60.394 60.000 9.84 9.84 0.00 3.35
1099 1355 2.955751 GATGTAGTGGCGGACGAGGC 62.956 65.000 0.00 0.00 37.19 4.70
1297 1640 2.588877 ACATGTAGGCATCGCGGC 60.589 61.111 6.13 1.57 41.61 6.53
1730 2074 0.965866 TGATCTCGTTCGGGAGCACT 60.966 55.000 8.94 0.00 33.98 4.40
1794 2138 2.610859 AACCATCTCCCCGGCAGT 60.611 61.111 0.00 0.00 0.00 4.40
1868 2212 1.094785 ACTTGCCATACATTGCGACC 58.905 50.000 0.00 0.00 0.00 4.79
1869 2213 1.795162 GCACTTGCCATACATTGCGAC 60.795 52.381 0.00 0.00 30.46 5.19
1910 2254 1.478105 GCCATCCCATCAAACAACTCC 59.522 52.381 0.00 0.00 0.00 3.85
2085 2429 3.997400 CTGTCTCGAGGGCTCCCGA 62.997 68.421 13.56 0.00 41.95 5.14
2096 2440 1.293498 CACCCACTTCCCTGTCTCG 59.707 63.158 0.00 0.00 0.00 4.04
2235 2579 0.603707 CATGACACGACACCAGGCTT 60.604 55.000 0.00 0.00 0.00 4.35
2258 2602 1.883926 GCATATGCACTGATCATGGCA 59.116 47.619 22.84 19.77 41.59 4.92
2335 2679 3.308866 CGTGAAGGAATTAGGCTTTACCG 59.691 47.826 0.00 0.00 46.52 4.02
2363 2707 0.602638 CACAAGCCACTAGAACCGCA 60.603 55.000 0.00 0.00 0.00 5.69
2465 2809 1.753930 TGTCAACCATGCAGGCATAG 58.246 50.000 6.42 2.01 43.14 2.23
2567 2911 3.364442 CAACCGCCAAGGAATGCA 58.636 55.556 0.00 0.00 45.00 3.96
2570 2914 1.978617 CCTGCAACCGCCAAGGAAT 60.979 57.895 0.00 0.00 45.00 3.01
2641 2985 1.582968 GTGACGTCGTTAGAGCCCA 59.417 57.895 11.62 0.00 0.00 5.36
2711 3055 2.646175 CCTCCTCGTCCTTTCCGCA 61.646 63.158 0.00 0.00 0.00 5.69
2732 3076 5.350504 TCTTGAGTTCCATCTCCTTCATC 57.649 43.478 0.00 0.00 33.93 2.92
2911 3257 9.553064 CAGTTTATCATGAGCCTAAGATAAAGT 57.447 33.333 0.09 10.78 42.69 2.66
2919 3265 6.753913 ATCCTCAGTTTATCATGAGCCTAA 57.246 37.500 0.09 0.00 41.33 2.69
2927 3273 9.466497 ACACAACATTTATCCTCAGTTTATCAT 57.534 29.630 0.00 0.00 0.00 2.45
2950 3296 5.310720 AGGCGGAAATTATCAGAAAACAC 57.689 39.130 0.00 0.00 0.00 3.32
2967 3313 3.119990 CCATTGTACAGTTAACAAGGCGG 60.120 47.826 8.61 0.00 40.00 6.13
2968 3314 3.119990 CCCATTGTACAGTTAACAAGGCG 60.120 47.826 8.61 0.00 40.00 5.52
2969 3315 3.192633 CCCCATTGTACAGTTAACAAGGC 59.807 47.826 8.61 0.00 40.00 4.35
2998 3377 0.250793 TAATGCAACGGGTCATCGGT 59.749 50.000 0.00 0.00 0.00 4.69
3096 3495 5.128499 AGAGGTCTGAACATCACATCCTAAG 59.872 44.000 0.00 0.00 38.66 2.18
3146 3546 3.115390 AGTCCAATACCTGTGCCATACT 58.885 45.455 0.00 0.00 0.00 2.12
3156 3556 4.480115 TCACCGATCATAGTCCAATACCT 58.520 43.478 0.00 0.00 0.00 3.08
3161 3561 3.026707 TCCTCACCGATCATAGTCCAA 57.973 47.619 0.00 0.00 0.00 3.53
3197 3604 9.197306 TCAACTTAGCATAGTATTCTCCTGTAA 57.803 33.333 0.00 0.00 0.00 2.41
3211 3618 8.696043 ATTTCTATGCCAATCAACTTAGCATA 57.304 30.769 0.00 0.00 39.91 3.14
3214 3621 7.761249 ACAAATTTCTATGCCAATCAACTTAGC 59.239 33.333 0.00 0.00 0.00 3.09
3257 3664 3.686726 GTGACTACAATTCTCTGCCCTTG 59.313 47.826 0.00 0.00 0.00 3.61
3343 3751 1.126488 ATCAGTCATCTGCCATCGGT 58.874 50.000 0.00 0.00 41.10 4.69
3366 3774 9.959721 ACTAGCATGAAGAAGGAAAAAGTATAA 57.040 29.630 0.00 0.00 0.00 0.98
3381 3789 3.834489 ACTCATCCCACTAGCATGAAG 57.166 47.619 0.00 0.00 0.00 3.02
3431 3844 6.597672 ACATAAACGCTACCATCATTTTCAGA 59.402 34.615 0.00 0.00 0.00 3.27
3444 3857 9.207042 GAAGTGCTTAAATTACATAAACGCTAC 57.793 33.333 0.00 0.00 0.00 3.58
3445 3858 8.937884 TGAAGTGCTTAAATTACATAAACGCTA 58.062 29.630 0.00 0.00 0.00 4.26
3446 3859 7.749126 GTGAAGTGCTTAAATTACATAAACGCT 59.251 33.333 0.00 0.00 0.00 5.07
3566 3982 9.350357 CCATTTGTAGAGATGAAATTGTTCTTG 57.650 33.333 0.00 0.00 34.60 3.02
3573 3989 9.401058 CTAGAACCCATTTGTAGAGATGAAATT 57.599 33.333 0.00 0.00 33.67 1.82
3577 3993 5.425217 TGCTAGAACCCATTTGTAGAGATGA 59.575 40.000 0.00 0.00 33.67 2.92
3578 3994 5.674525 TGCTAGAACCCATTTGTAGAGATG 58.325 41.667 0.00 0.00 33.67 2.90
3579 3995 5.957771 TGCTAGAACCCATTTGTAGAGAT 57.042 39.130 0.00 0.00 33.67 2.75
3580 3996 5.957771 ATGCTAGAACCCATTTGTAGAGA 57.042 39.130 0.00 0.00 33.67 3.10
3581 3997 8.682936 ATAAATGCTAGAACCCATTTGTAGAG 57.317 34.615 13.28 0.00 40.66 2.43
3582 3998 9.778741 CTATAAATGCTAGAACCCATTTGTAGA 57.221 33.333 20.39 4.82 45.68 2.59
3583 3999 8.507249 GCTATAAATGCTAGAACCCATTTGTAG 58.493 37.037 20.55 20.55 45.64 2.74
3584 4000 8.217799 AGCTATAAATGCTAGAACCCATTTGTA 58.782 33.333 13.28 10.79 40.66 2.41
3585 4001 7.062957 AGCTATAAATGCTAGAACCCATTTGT 58.937 34.615 13.28 10.36 40.66 2.83
3586 4002 7.446625 AGAGCTATAAATGCTAGAACCCATTTG 59.553 37.037 13.28 2.52 40.66 2.32
3587 4003 7.521669 AGAGCTATAAATGCTAGAACCCATTT 58.478 34.615 9.89 9.89 42.46 2.32
3588 4004 7.084268 AGAGCTATAAATGCTAGAACCCATT 57.916 36.000 0.00 0.00 41.30 3.16
3592 4008 6.353404 AGGAGAGCTATAAATGCTAGAACC 57.647 41.667 0.00 0.00 41.30 3.62
3593 4009 7.394923 TCCTAGGAGAGCTATAAATGCTAGAAC 59.605 40.741 7.62 0.00 41.30 3.01
3607 4028 0.689412 GCACCCTTCCTAGGAGAGCT 60.689 60.000 12.26 0.00 45.05 4.09
3757 4196 6.714810 ACTCACATTTTAAGGTATGCAGTGAA 59.285 34.615 0.00 0.00 33.67 3.18
3761 4200 5.580691 TCGACTCACATTTTAAGGTATGCAG 59.419 40.000 0.00 0.00 0.00 4.41
3766 4205 5.483811 TGCATCGACTCACATTTTAAGGTA 58.516 37.500 0.00 0.00 0.00 3.08
3817 4258 6.856895 AGCAATGAATAAAGAGGTACTTTGC 58.143 36.000 0.00 0.00 46.62 3.68
3830 4273 8.995027 ATGTTACCCTGATTAGCAATGAATAA 57.005 30.769 0.00 0.00 0.00 1.40
3831 4274 8.439971 AGATGTTACCCTGATTAGCAATGAATA 58.560 33.333 0.00 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.