Multiple sequence alignment - TraesCS7D01G170200

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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 TraesCS7D01G170200 chr7D 100.000 4749 0 0 1 4749 122842675 122847423 0.000000e+00 8770
1 TraesCS7D01G170200 chr7B 89.013 3222 155 101 1497 4662 83905337 83902259 0.000000e+00 3805
2 TraesCS7D01G170200 chr7B 88.423 1287 55 43 240 1463 83906586 83905331 0.000000e+00 1465
3 TraesCS7D01G170200 chr7B 85.000 240 19 6 1 223 83907303 83907064 1.330000e-55 228
4 TraesCS7D01G170200 chr7A 94.353 2497 56 31 2301 4749 125714203 125716662 0.000000e+00 3751
5 TraesCS7D01G170200 chr7A 87.831 2301 135 71 1 2232 125711957 125714181 0.000000e+00 2564
6 TraesCS7D01G170200 chr5B 92.308 91 4 1 2028 2118 325493409 325493496 4.990000e-25 126
7 TraesCS7D01G170200 chr5B 91.489 94 5 1 2028 2121 469466470 469466380 4.990000e-25 126
8 TraesCS7D01G170200 chr4B 92.308 91 4 1 2028 2118 649511517 649511604 4.990000e-25 126
9 TraesCS7D01G170200 chr3B 91.489 94 5 1 2028 2121 56840364 56840274 4.990000e-25 126
10 TraesCS7D01G170200 chr2B 92.308 91 4 2 2028 2118 76639095 76639182 4.990000e-25 126
11 TraesCS7D01G170200 chr2B 92.308 91 4 1 2028 2118 785018406 785018493 4.990000e-25 126
12 TraesCS7D01G170200 chr1B 91.209 91 5 1 2028 2118 681300961 681301048 2.320000e-23 121


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 TraesCS7D01G170200 chr7D 122842675 122847423 4748 False 8770.000000 8770 100.000000 1 4749 1 chr7D.!!$F1 4748
1 TraesCS7D01G170200 chr7B 83902259 83907303 5044 True 1832.666667 3805 87.478667 1 4662 3 chr7B.!!$R1 4661
2 TraesCS7D01G170200 chr7A 125711957 125716662 4705 False 3157.500000 3751 91.092000 1 4749 2 chr7A.!!$F1 4748

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
850 1394 0.180406 ACCACACACACCAACTCCTC 59.820 55.0 0.00 0.0 0.00 3.71 F
1449 2021 0.038983 TGTGCATGCATGTCAACTGC 60.039 50.0 25.64 13.6 40.10 4.40 F
1546 2129 0.179070 GCCTAGCCTAGCTTCCACAC 60.179 60.0 0.00 0.0 40.44 3.82 F
3033 3694 0.105039 CCAGTCGACCCCATTAGAGC 59.895 60.0 13.01 0.0 0.00 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2778 3422 0.167908 TTTGTGAGCGGCGCAATTAG 59.832 50.000 35.02 0.0 45.59 1.73 R
2876 3529 1.143838 CATCGAGCCGTTGATCCCA 59.856 57.895 0.00 0.0 0.00 4.37 R
3322 3983 2.029918 TCACACTGAGATGAGAACCACG 60.030 50.000 0.00 0.0 0.00 4.94 R
3970 4659 0.317854 GGACACGGCACTTTGCTTTC 60.318 55.000 0.00 0.0 44.28 2.62 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
65 66 1.798813 GCTCATTTTGGCGGTACATGC 60.799 52.381 0.00 0.00 0.00 4.06
114 136 3.799366 TGGCTGAAACGAACTTCTGTTA 58.201 40.909 0.00 0.00 36.39 2.41
140 162 3.117046 GACACCACTATTAAGAGCTCGC 58.883 50.000 8.37 0.00 0.00 5.03
149 171 1.739338 TAAGAGCTCGCCTAGGCTGC 61.739 60.000 30.55 30.02 39.05 5.25
207 229 1.526464 CTTTGGATTTGTTGGTTGCGC 59.474 47.619 0.00 0.00 0.00 6.09
213 235 3.870679 TTGTTGGTTGCGCGCATCG 62.871 57.895 36.83 0.00 42.12 3.84
230 255 4.230657 GCATCGTCTATTGGTACTAGCAG 58.769 47.826 0.00 0.00 0.00 4.24
235 260 4.216708 GTCTATTGGTACTAGCAGAGGGT 58.783 47.826 0.00 0.00 0.00 4.34
337 821 1.203563 CGTCTCGATACGGCTACGG 59.796 63.158 14.88 0.00 46.48 4.02
340 824 0.602106 TCTCGATACGGCTACGGGAG 60.602 60.000 0.00 0.00 46.48 4.30
350 834 1.291132 GCTACGGGAGTGAATGAAGC 58.709 55.000 0.00 0.00 46.80 3.86
354 857 1.915078 CGGGAGTGAATGAAGCCCCT 61.915 60.000 0.00 0.00 35.30 4.79
493 1007 5.699915 CCATTGATTGATGACTAGCCAGTAG 59.300 44.000 0.00 0.00 34.21 2.57
506 1020 2.572104 AGCCAGTAGAGTTTCGGGAAAT 59.428 45.455 0.00 0.00 32.36 2.17
559 1086 4.657824 CACTCCGTTGCCGTCGGT 62.658 66.667 13.94 0.00 46.86 4.69
640 1167 1.004080 GCACAGGAAGCAGAGCAGA 60.004 57.895 0.00 0.00 0.00 4.26
773 1307 3.243201 GGCGCCCTAATCAAATTGAAGAG 60.243 47.826 18.11 0.20 0.00 2.85
776 1310 5.118990 CGCCCTAATCAAATTGAAGAGAGA 58.881 41.667 0.00 0.00 0.00 3.10
779 1313 7.201767 CGCCCTAATCAAATTGAAGAGAGAAAT 60.202 37.037 0.00 0.00 0.00 2.17
832 1366 1.371389 GTCTCCGTCGACACCACAC 60.371 63.158 17.16 1.17 34.11 3.82
836 1380 2.105328 CGTCGACACCACACCACA 59.895 61.111 17.16 0.00 0.00 4.17
850 1394 0.180406 ACCACACACACCAACTCCTC 59.820 55.000 0.00 0.00 0.00 3.71
1040 1591 2.431683 GAGTTCAGCAGCCACCCA 59.568 61.111 0.00 0.00 0.00 4.51
1043 1594 3.177884 TTCAGCAGCCACCCACCT 61.178 61.111 0.00 0.00 0.00 4.00
1122 1677 2.029666 CGTGCCTCGATCCATCCC 59.970 66.667 0.00 0.00 42.86 3.85
1123 1678 2.502492 CGTGCCTCGATCCATCCCT 61.502 63.158 0.00 0.00 42.86 4.20
1124 1679 1.369321 GTGCCTCGATCCATCCCTC 59.631 63.158 0.00 0.00 0.00 4.30
1125 1680 1.075301 TGCCTCGATCCATCCCTCA 60.075 57.895 0.00 0.00 0.00 3.86
1134 1689 1.995626 CCATCCCTCAACCCTCCGT 60.996 63.158 0.00 0.00 0.00 4.69
1135 1690 1.221840 CATCCCTCAACCCTCCGTG 59.778 63.158 0.00 0.00 0.00 4.94
1136 1691 1.229529 ATCCCTCAACCCTCCGTGT 60.230 57.895 0.00 0.00 0.00 4.49
1140 1695 1.445942 CTCAACCCTCCGTGTGTGT 59.554 57.895 0.00 0.00 0.00 3.72
1145 1700 0.831966 ACCCTCCGTGTGTGTTTGTA 59.168 50.000 0.00 0.00 0.00 2.41
1146 1701 1.209990 ACCCTCCGTGTGTGTTTGTAA 59.790 47.619 0.00 0.00 0.00 2.41
1148 1703 1.871039 CCTCCGTGTGTGTTTGTAAGG 59.129 52.381 0.00 0.00 0.00 2.69
1149 1704 1.263217 CTCCGTGTGTGTTTGTAAGGC 59.737 52.381 0.00 0.00 0.00 4.35
1152 1707 1.596954 CGTGTGTGTTTGTAAGGCAGC 60.597 52.381 0.00 0.00 0.00 5.25
1154 1709 0.941542 GTGTGTTTGTAAGGCAGCGA 59.058 50.000 0.00 0.00 0.00 4.93
1371 1931 2.932614 TCGAGAAGTACGTACTGGCTAC 59.067 50.000 28.00 18.20 36.50 3.58
1383 1943 1.151899 TGGCTACCACCAACCTCCT 60.152 57.895 0.00 0.00 36.55 3.69
1402 1974 5.365314 CCTCCTAATCTCTACCTTGCTTCTT 59.635 44.000 0.00 0.00 0.00 2.52
1404 1976 5.364157 TCCTAATCTCTACCTTGCTTCTTCC 59.636 44.000 0.00 0.00 0.00 3.46
1411 1983 0.322906 CCTTGCTTCTTCCTCCACCC 60.323 60.000 0.00 0.00 0.00 4.61
1412 1984 0.695347 CTTGCTTCTTCCTCCACCCT 59.305 55.000 0.00 0.00 0.00 4.34
1446 2018 1.339235 GCGTGTGCATGCATGTCAAC 61.339 55.000 25.64 21.31 42.66 3.18
1447 2019 0.239082 CGTGTGCATGCATGTCAACT 59.761 50.000 25.64 0.00 0.00 3.16
1448 2020 1.693467 GTGTGCATGCATGTCAACTG 58.307 50.000 25.64 2.44 0.00 3.16
1449 2021 0.038983 TGTGCATGCATGTCAACTGC 60.039 50.000 25.64 13.60 40.10 4.40
1452 2024 1.336424 TGCATGCATGTCAACTGCTTG 60.336 47.619 26.79 9.03 43.71 4.01
1477 2060 1.998315 CATGCACTCTGTCGGAAAGAG 59.002 52.381 21.15 21.15 45.57 2.85
1495 2078 4.691860 AGAGAGTTTTACATGCATGCAC 57.308 40.909 25.37 16.89 0.00 4.57
1500 2083 0.454117 TTTACATGCATGCACGCACG 60.454 50.000 25.37 3.63 46.56 5.34
1545 2128 0.325671 AGCCTAGCCTAGCTTCCACA 60.326 55.000 0.00 0.00 40.44 4.17
1546 2129 0.179070 GCCTAGCCTAGCTTCCACAC 60.179 60.000 0.00 0.00 40.44 3.82
1547 2130 0.466124 CCTAGCCTAGCTTCCACACC 59.534 60.000 0.00 0.00 40.44 4.16
1561 2144 3.897239 TCCACACCAATGTTTCAGAAGT 58.103 40.909 0.00 0.00 36.72 3.01
1577 2160 4.331717 TCAGAAGTCCAGTTCGTTTTTGTC 59.668 41.667 0.00 0.00 0.00 3.18
1603 2192 9.653287 CTCATCAGTTCCAAGTGTAGTTATTAA 57.347 33.333 0.00 0.00 0.00 1.40
1604 2193 9.431887 TCATCAGTTCCAAGTGTAGTTATTAAC 57.568 33.333 0.00 0.00 0.00 2.01
1605 2194 9.436957 CATCAGTTCCAAGTGTAGTTATTAACT 57.563 33.333 13.36 13.36 45.40 2.24
1655 2247 6.358118 TGGTTATCAATGTTATCTGTTCGC 57.642 37.500 0.00 0.00 0.00 4.70
1664 2259 6.694877 ATGTTATCTGTTCGCACTAGTAGA 57.305 37.500 3.59 0.00 0.00 2.59
1676 2271 7.329588 TCGCACTAGTAGATAGTTTCAATCA 57.670 36.000 3.59 0.00 42.30 2.57
1754 2349 2.992089 CGCAAACCTATCGCATCCT 58.008 52.632 0.00 0.00 0.00 3.24
1755 2350 2.148916 CGCAAACCTATCGCATCCTA 57.851 50.000 0.00 0.00 0.00 2.94
1787 2382 3.656559 CATGCCCAGGTCTTTCTTTTTG 58.343 45.455 0.00 0.00 0.00 2.44
1797 2392 4.159693 GGTCTTTCTTTTTGAACCACAGGT 59.840 41.667 0.00 0.00 37.65 4.00
1837 2446 2.853235 TTCTCGACCCCTTTCCTTTC 57.147 50.000 0.00 0.00 0.00 2.62
1838 2447 0.981943 TCTCGACCCCTTTCCTTTCC 59.018 55.000 0.00 0.00 0.00 3.13
1839 2448 0.391263 CTCGACCCCTTTCCTTTCCG 60.391 60.000 0.00 0.00 0.00 4.30
1840 2449 1.376812 CGACCCCTTTCCTTTCCGG 60.377 63.158 0.00 0.00 0.00 5.14
1869 2478 1.599606 CGGTCAGTCAGGAGTCAGGG 61.600 65.000 0.00 0.00 0.00 4.45
1880 2489 4.459089 GTCAGGGCGCCTCTGGAC 62.459 72.222 31.68 25.50 33.36 4.02
1930 2543 0.537371 CCCCGACAACCTTTGCTTCT 60.537 55.000 0.00 0.00 0.00 2.85
1936 2549 3.120199 CGACAACCTTTGCTTCTATGTGG 60.120 47.826 0.00 0.00 0.00 4.17
1966 2584 4.508861 TGTAACCGCACTAAGTGTTCTTTC 59.491 41.667 0.00 0.00 35.75 2.62
1967 2585 3.188159 ACCGCACTAAGTGTTCTTTCA 57.812 42.857 0.00 0.00 35.75 2.69
2002 2621 7.170240 GCTTTTATTAGCTTGATGCCAATTC 57.830 36.000 0.00 0.00 44.23 2.17
2232 2860 4.946772 TGCCATGCATGCTTTTACTTACTA 59.053 37.500 21.69 0.00 31.71 1.82
2233 2861 5.066375 TGCCATGCATGCTTTTACTTACTAG 59.934 40.000 21.69 3.43 31.71 2.57
2234 2862 5.066505 GCCATGCATGCTTTTACTTACTAGT 59.933 40.000 21.69 0.00 38.44 2.57
2235 2863 6.260050 GCCATGCATGCTTTTACTTACTAGTA 59.740 38.462 21.69 0.00 35.78 1.82
2236 2864 7.630924 CCATGCATGCTTTTACTTACTAGTAC 58.369 38.462 21.69 0.00 36.61 2.73
2237 2865 7.495934 CCATGCATGCTTTTACTTACTAGTACT 59.504 37.037 21.69 0.00 36.61 2.73
2281 2909 1.037493 ACAACTACGACCAGCTGTCA 58.963 50.000 13.81 0.00 44.71 3.58
2285 2913 0.881796 CTACGACCAGCTGTCAGTCA 59.118 55.000 13.81 0.00 44.71 3.41
2286 2914 1.474478 CTACGACCAGCTGTCAGTCAT 59.526 52.381 13.81 4.17 44.71 3.06
2288 2916 1.893137 ACGACCAGCTGTCAGTCATTA 59.107 47.619 13.81 0.00 44.71 1.90
2289 2917 2.263077 CGACCAGCTGTCAGTCATTAC 58.737 52.381 13.81 0.00 44.71 1.89
2290 2918 2.094494 CGACCAGCTGTCAGTCATTACT 60.094 50.000 13.81 0.00 44.71 2.24
2314 2953 5.690409 TGTGCTACTAGCTAACAATATTCGC 59.310 40.000 9.49 0.00 42.97 4.70
2705 3344 1.303888 TTCGTCCTCCAGGTACGCT 60.304 57.895 10.84 0.00 38.06 5.07
2765 3409 2.420372 GCTAGTAGCTTTGTTCCCTTGC 59.580 50.000 15.16 0.00 38.45 4.01
2767 3411 3.160679 AGTAGCTTTGTTCCCTTGCAT 57.839 42.857 0.00 0.00 0.00 3.96
2769 3413 4.010349 AGTAGCTTTGTTCCCTTGCATAC 58.990 43.478 0.00 0.00 0.00 2.39
2770 3414 1.812571 AGCTTTGTTCCCTTGCATACG 59.187 47.619 0.00 0.00 0.00 3.06
2771 3415 1.539827 GCTTTGTTCCCTTGCATACGT 59.460 47.619 0.00 0.00 0.00 3.57
2772 3416 2.414161 GCTTTGTTCCCTTGCATACGTC 60.414 50.000 0.00 0.00 0.00 4.34
2773 3417 1.816074 TTGTTCCCTTGCATACGTCC 58.184 50.000 0.00 0.00 0.00 4.79
2774 3418 0.390603 TGTTCCCTTGCATACGTCCG 60.391 55.000 0.00 0.00 0.00 4.79
2775 3419 0.390735 GTTCCCTTGCATACGTCCGT 60.391 55.000 0.00 0.00 0.00 4.69
2776 3420 1.135024 GTTCCCTTGCATACGTCCGTA 60.135 52.381 1.60 1.60 34.87 4.02
2777 3421 0.457035 TCCCTTGCATACGTCCGTAC 59.543 55.000 1.07 0.00 33.01 3.67
2778 3422 0.529119 CCCTTGCATACGTCCGTACC 60.529 60.000 1.07 0.00 33.01 3.34
2793 3442 0.808453 GTACCTAATTGCGCCGCTCA 60.808 55.000 11.67 0.00 0.00 4.26
2801 3450 4.403137 GCGCCGCTCACAAATGCA 62.403 61.111 0.00 0.00 0.00 3.96
2802 3451 2.486504 CGCCGCTCACAAATGCAT 59.513 55.556 0.00 0.00 0.00 3.96
2803 3452 1.870458 CGCCGCTCACAAATGCATG 60.870 57.895 0.00 0.00 0.00 4.06
2804 3453 2.162754 GCCGCTCACAAATGCATGC 61.163 57.895 11.82 11.82 0.00 4.06
2876 3529 4.166888 ATCTGCGCGATGGGCACT 62.167 61.111 12.10 0.00 46.09 4.40
3033 3694 0.105039 CCAGTCGACCCCATTAGAGC 59.895 60.000 13.01 0.00 0.00 4.09
3040 3701 3.321111 TCGACCCCATTAGAGCAGTTATC 59.679 47.826 0.00 0.00 0.00 1.75
3067 3728 4.074259 AGCTAATGGATGAATTATGCGCA 58.926 39.130 14.96 14.96 0.00 6.09
3069 3730 5.184479 AGCTAATGGATGAATTATGCGCATT 59.816 36.000 30.42 12.04 0.00 3.56
3314 3975 4.441079 GCTGCAGGAGTAATCGGTTAACTA 60.441 45.833 17.12 0.00 0.00 2.24
3315 3976 5.657474 CTGCAGGAGTAATCGGTTAACTAA 58.343 41.667 5.57 0.00 0.00 2.24
3316 3977 6.229936 TGCAGGAGTAATCGGTTAACTAAT 57.770 37.500 5.42 0.00 0.00 1.73
3706 4386 1.398390 GGAAGTTGCATGTGTCGATCC 59.602 52.381 0.00 0.00 0.00 3.36
3766 4446 6.608610 ACTTTGAGCGACCACATAAATTTAC 58.391 36.000 0.00 0.00 0.00 2.01
3867 4552 0.029967 CTGCTTCGCTCTGCTATCGA 59.970 55.000 0.00 0.00 0.00 3.59
3933 4618 0.171455 GAGCACCGATCACTCGTCTT 59.829 55.000 0.00 0.00 43.49 3.01
3935 4620 1.816835 AGCACCGATCACTCGTCTTTA 59.183 47.619 0.00 0.00 43.49 1.85
3939 4628 3.975670 CACCGATCACTCGTCTTTATAGC 59.024 47.826 0.00 0.00 43.49 2.97
3970 4659 4.527038 TCCTAACACTAACTCCAGTTGAGG 59.473 45.833 2.01 0.66 46.01 3.86
4173 4874 1.000171 CTGCCTTTCTTTCCCTTGTGC 60.000 52.381 0.00 0.00 0.00 4.57
4174 4875 1.039856 GCCTTTCTTTCCCTTGTGCA 58.960 50.000 0.00 0.00 0.00 4.57
4175 4876 1.620323 GCCTTTCTTTCCCTTGTGCAT 59.380 47.619 0.00 0.00 0.00 3.96
4176 4877 2.611224 GCCTTTCTTTCCCTTGTGCATG 60.611 50.000 0.00 0.00 0.00 4.06
4318 5019 6.031471 CGATCGATCGTCTTATCTCTCTCTA 58.969 44.000 33.95 0.00 44.74 2.43
4386 5096 0.517755 GCTATAGTGCTCGCTCGCTA 59.482 55.000 0.84 0.73 34.07 4.26
4425 5135 2.990479 GCCGGGGATATGGCCTAG 59.010 66.667 3.32 0.00 45.73 3.02
4648 5372 0.529337 TGCGTACGTCCGTGGAAAAA 60.529 50.000 17.90 0.00 0.00 1.94
4653 5377 0.309612 ACGTCCGTGGAAAAATGCAC 59.690 50.000 0.00 0.00 0.00 4.57
4708 5433 3.378742 GCTCGATCCAGAAGTGTAGAAGA 59.621 47.826 0.00 0.00 0.00 2.87
4735 5460 2.697761 CGATCGGGTGGACGTGACT 61.698 63.158 7.38 0.00 34.94 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 136 7.148641 CGAGCTCTTAATAGTGGTGTCATAAT 58.851 38.462 12.85 0.00 0.00 1.28
140 162 2.202756 GTTCGGACGCAGCCTAGG 60.203 66.667 3.67 3.67 0.00 3.02
149 171 3.009301 AGTACAACAGAAGTTCGGACG 57.991 47.619 10.15 2.89 35.28 4.79
207 229 3.235195 GCTAGTACCAATAGACGATGCG 58.765 50.000 0.00 0.00 0.00 4.73
213 235 4.216708 ACCCTCTGCTAGTACCAATAGAC 58.783 47.826 0.00 0.00 0.00 2.59
230 255 8.459635 GTTACAAGAGAAAAATATCCAACCCTC 58.540 37.037 0.00 0.00 0.00 4.30
235 260 8.934023 AGTGGTTACAAGAGAAAAATATCCAA 57.066 30.769 0.00 0.00 0.00 3.53
337 821 2.222227 AAAGGGGCTTCATTCACTCC 57.778 50.000 0.00 0.00 0.00 3.85
340 824 3.157087 TCAGAAAAGGGGCTTCATTCAC 58.843 45.455 0.00 0.00 0.00 3.18
350 834 4.670896 ATGTGTGTTTTCAGAAAAGGGG 57.329 40.909 8.67 0.00 0.00 4.79
493 1007 1.402852 GCCAAGCATTTCCCGAAACTC 60.403 52.381 0.00 0.00 32.51 3.01
559 1086 3.770040 CCCGCCTGGATGTCGTCA 61.770 66.667 0.00 0.00 37.49 4.35
732 1266 1.153127 ACGAGCTCTAGCCTAGCGT 60.153 57.895 12.85 0.00 44.87 5.07
734 1268 1.657556 CCACGAGCTCTAGCCTAGC 59.342 63.158 12.85 0.00 43.38 3.42
735 1269 1.657556 GCCACGAGCTCTAGCCTAG 59.342 63.158 12.85 0.00 43.38 3.02
736 1270 2.187493 CGCCACGAGCTCTAGCCTA 61.187 63.158 12.85 0.00 43.38 3.93
737 1271 3.522731 CGCCACGAGCTCTAGCCT 61.523 66.667 12.85 0.00 43.38 4.58
773 1307 0.243636 CCCGTGCACCCAAATTTCTC 59.756 55.000 12.15 0.00 0.00 2.87
776 1310 0.757188 TCACCCGTGCACCCAAATTT 60.757 50.000 12.15 0.00 0.00 1.82
779 1313 2.517402 GTCACCCGTGCACCCAAA 60.517 61.111 12.15 0.00 0.00 3.28
832 1366 0.535102 GGAGGAGTTGGTGTGTGTGG 60.535 60.000 0.00 0.00 0.00 4.17
836 1380 2.249139 GAGTAGGAGGAGTTGGTGTGT 58.751 52.381 0.00 0.00 0.00 3.72
850 1394 1.320344 TGCGTGCTGGTAGGAGTAGG 61.320 60.000 0.00 0.00 0.00 3.18
1026 1577 3.177884 AGGTGGGTGGCTGCTGAA 61.178 61.111 0.00 0.00 0.00 3.02
1113 1668 0.767998 GGAGGGTTGAGGGATGGATC 59.232 60.000 0.00 0.00 0.00 3.36
1119 1674 2.203182 ACACGGAGGGTTGAGGGA 59.797 61.111 0.00 0.00 0.00 4.20
1122 1677 0.179056 AACACACACGGAGGGTTGAG 60.179 55.000 0.00 0.00 0.00 3.02
1123 1678 0.253610 AAACACACACGGAGGGTTGA 59.746 50.000 0.00 0.00 0.00 3.18
1124 1679 0.380378 CAAACACACACGGAGGGTTG 59.620 55.000 0.00 0.00 0.00 3.77
1125 1680 0.034863 ACAAACACACACGGAGGGTT 60.035 50.000 0.00 0.00 0.00 4.11
1134 1689 0.660488 CGCTGCCTTACAAACACACA 59.340 50.000 0.00 0.00 0.00 3.72
1135 1690 0.941542 TCGCTGCCTTACAAACACAC 59.058 50.000 0.00 0.00 0.00 3.82
1136 1691 1.202592 TCTCGCTGCCTTACAAACACA 60.203 47.619 0.00 0.00 0.00 3.72
1140 1695 0.034756 TGCTCTCGCTGCCTTACAAA 59.965 50.000 0.00 0.00 36.97 2.83
1149 1704 2.895865 CCATGGCTGCTCTCGCTG 60.896 66.667 0.00 0.00 38.05 5.18
1371 1931 3.388350 GGTAGAGATTAGGAGGTTGGTGG 59.612 52.174 0.00 0.00 0.00 4.61
1383 1943 5.364157 GGAGGAAGAAGCAAGGTAGAGATTA 59.636 44.000 0.00 0.00 0.00 1.75
1402 1974 2.218673 AGACTAGATGAGGGTGGAGGA 58.781 52.381 0.00 0.00 0.00 3.71
1404 1976 3.909732 AGAAGACTAGATGAGGGTGGAG 58.090 50.000 0.00 0.00 0.00 3.86
1411 1983 3.856521 CACACGCAAGAAGACTAGATGAG 59.143 47.826 0.00 0.00 43.62 2.90
1412 1984 3.838120 CACACGCAAGAAGACTAGATGA 58.162 45.455 0.00 0.00 43.62 2.92
1447 2019 2.599281 AGTGCATGCAGGCAAGCA 60.599 55.556 29.55 18.86 46.93 3.91
1448 2020 2.181021 GAGTGCATGCAGGCAAGC 59.819 61.111 29.55 18.75 46.93 4.01
1449 2021 1.241990 ACAGAGTGCATGCAGGCAAG 61.242 55.000 29.55 19.50 46.93 4.01
1452 2024 2.747822 CGACAGAGTGCATGCAGGC 61.748 63.158 23.41 18.05 0.00 4.85
1477 2060 1.913403 GCGTGCATGCATGTAAAACTC 59.087 47.619 34.08 16.55 35.52 3.01
1479 2062 1.695813 TGCGTGCATGCATGTAAAAC 58.304 45.000 34.08 20.79 40.62 2.43
1500 2083 2.263540 CCTTGCCCTTGTGCATGC 59.736 61.111 11.82 11.82 41.70 4.06
1502 2085 2.284112 CCCCTTGCCCTTGTGCAT 60.284 61.111 0.00 0.00 41.70 3.96
1512 2095 4.822628 GGCTACCCTGCCCCTTGC 62.823 72.222 0.00 0.00 46.82 4.01
1545 2128 4.170468 ACTGGACTTCTGAAACATTGGT 57.830 40.909 0.00 0.00 0.00 3.67
1546 2129 4.319766 CGAACTGGACTTCTGAAACATTGG 60.320 45.833 0.00 0.00 0.00 3.16
1547 2130 4.273480 ACGAACTGGACTTCTGAAACATTG 59.727 41.667 0.00 0.00 0.00 2.82
1561 2144 4.447290 TGATGAGACAAAAACGAACTGGA 58.553 39.130 0.00 0.00 0.00 3.86
1577 2160 9.653287 TTAATAACTACACTTGGAACTGATGAG 57.347 33.333 0.00 0.00 0.00 2.90
1609 2198 9.420118 ACCATTTTACTTTGGCTGATGATAATA 57.580 29.630 0.00 0.00 36.41 0.98
1610 2199 8.310122 ACCATTTTACTTTGGCTGATGATAAT 57.690 30.769 0.00 0.00 36.41 1.28
1676 2271 7.544622 TCTAGTGCTTGATTACGTAGTGATTT 58.455 34.615 0.00 0.00 45.73 2.17
1753 2348 0.671781 GGGCATGCATCGCTAGGTAG 60.672 60.000 21.36 0.00 0.00 3.18
1754 2349 1.371183 GGGCATGCATCGCTAGGTA 59.629 57.895 21.36 0.00 0.00 3.08
1755 2350 2.111878 GGGCATGCATCGCTAGGT 59.888 61.111 21.36 0.00 0.00 3.08
1787 2382 5.815740 ACGTGAATGAATATACCTGTGGTTC 59.184 40.000 0.00 0.00 37.09 3.62
1797 2392 6.046593 AGAAAAGCCGACGTGAATGAATATA 58.953 36.000 0.00 0.00 0.00 0.86
1869 2478 2.928731 GCATAGATTAGTCCAGAGGCGC 60.929 54.545 0.00 0.00 0.00 6.53
1880 2489 3.131396 GTGTCGGTTGGGCATAGATTAG 58.869 50.000 0.00 0.00 0.00 1.73
1930 2543 1.798283 GGTTACACGCACACCACATA 58.202 50.000 0.00 0.00 0.00 2.29
1992 2610 2.298163 CTGGGCATTAGGAATTGGCATC 59.702 50.000 0.00 0.00 0.00 3.91
2002 2621 3.702147 CTCAGAGCTGGGCATTAGG 57.298 57.895 0.00 0.00 0.00 2.69
2114 2737 0.657312 TTCGCAAGCACAACAGACAG 59.343 50.000 0.00 0.00 37.18 3.51
2253 2881 3.485394 TGGTCGTAGTTGTACTACCACA 58.515 45.455 13.92 7.53 45.54 4.17
2257 2885 3.190118 ACAGCTGGTCGTAGTTGTACTAC 59.810 47.826 19.93 6.87 45.71 2.73
2258 2886 3.415212 ACAGCTGGTCGTAGTTGTACTA 58.585 45.455 19.93 0.00 39.82 1.82
2259 2887 2.228343 GACAGCTGGTCGTAGTTGTACT 59.772 50.000 19.93 0.00 41.35 2.73
2260 2888 2.593257 GACAGCTGGTCGTAGTTGTAC 58.407 52.381 19.93 0.00 41.35 2.90
2262 2890 3.888093 GACAGCTGGTCGTAGTTGT 57.112 52.632 19.93 6.36 43.49 3.32
2281 2909 6.377429 TGTTAGCTAGTAGCACAGTAATGACT 59.623 38.462 23.77 1.38 45.56 3.41
2286 2914 9.745880 GAATATTGTTAGCTAGTAGCACAGTAA 57.254 33.333 23.77 10.66 45.56 2.24
2288 2916 6.918569 CGAATATTGTTAGCTAGTAGCACAGT 59.081 38.462 23.77 17.60 45.56 3.55
2289 2917 6.129062 GCGAATATTGTTAGCTAGTAGCACAG 60.129 42.308 23.77 8.47 45.56 3.66
2290 2918 5.690409 GCGAATATTGTTAGCTAGTAGCACA 59.310 40.000 23.77 16.70 45.56 4.57
2291 2919 5.164177 CGCGAATATTGTTAGCTAGTAGCAC 60.164 44.000 23.77 14.34 45.56 4.40
2292 2920 4.915667 CGCGAATATTGTTAGCTAGTAGCA 59.084 41.667 23.77 7.49 45.56 3.49
2293 2921 4.323868 CCGCGAATATTGTTAGCTAGTAGC 59.676 45.833 14.62 14.62 42.84 3.58
2294 2922 4.857588 CCCGCGAATATTGTTAGCTAGTAG 59.142 45.833 8.23 0.00 0.00 2.57
2296 2924 3.069158 ACCCGCGAATATTGTTAGCTAGT 59.931 43.478 8.23 0.00 0.00 2.57
2297 2925 3.650139 ACCCGCGAATATTGTTAGCTAG 58.350 45.455 8.23 0.00 0.00 3.42
2299 2927 2.614829 ACCCGCGAATATTGTTAGCT 57.385 45.000 8.23 0.00 0.00 3.32
2765 3409 2.722629 CGCAATTAGGTACGGACGTATG 59.277 50.000 7.89 0.00 32.82 2.39
2767 3411 1.533756 GCGCAATTAGGTACGGACGTA 60.534 52.381 0.30 0.00 0.00 3.57
2769 3413 1.485032 GGCGCAATTAGGTACGGACG 61.485 60.000 10.83 0.00 0.00 4.79
2770 3414 1.485032 CGGCGCAATTAGGTACGGAC 61.485 60.000 10.83 0.00 0.00 4.79
2771 3415 1.227031 CGGCGCAATTAGGTACGGA 60.227 57.895 10.83 0.00 0.00 4.69
2772 3416 2.877974 GCGGCGCAATTAGGTACGG 61.878 63.158 29.21 0.00 0.00 4.02
2773 3417 1.818221 GAGCGGCGCAATTAGGTACG 61.818 60.000 35.02 0.25 0.00 3.67
2774 3418 0.808453 TGAGCGGCGCAATTAGGTAC 60.808 55.000 35.02 12.79 0.00 3.34
2775 3419 0.808453 GTGAGCGGCGCAATTAGGTA 60.808 55.000 35.02 7.45 0.00 3.08
2776 3420 2.106683 GTGAGCGGCGCAATTAGGT 61.107 57.895 35.02 11.56 0.00 3.08
2777 3421 1.643868 TTGTGAGCGGCGCAATTAGG 61.644 55.000 35.02 0.00 41.77 2.69
2778 3422 0.167908 TTTGTGAGCGGCGCAATTAG 59.832 50.000 35.02 0.00 45.59 1.73
2801 3450 1.789751 CGTGTTCGACTGCATGCAT 59.210 52.632 22.97 11.62 39.71 3.96
2802 3451 2.953605 GCGTGTTCGACTGCATGCA 61.954 57.895 21.29 21.29 44.44 3.96
2803 3452 2.202222 GCGTGTTCGACTGCATGC 60.202 61.111 11.82 11.82 39.89 4.06
2804 3453 1.284297 TGAGCGTGTTCGACTGCATG 61.284 55.000 0.00 0.00 39.71 4.06
2876 3529 1.143838 CATCGAGCCGTTGATCCCA 59.856 57.895 0.00 0.00 0.00 4.37
3033 3694 5.985530 TCATCCATTAGCTCGTTGATAACTG 59.014 40.000 0.00 0.00 28.61 3.16
3040 3701 6.082338 GCATAATTCATCCATTAGCTCGTTG 58.918 40.000 0.00 0.00 0.00 4.10
3314 3975 6.097554 ACTGAGATGAGAACCACGAGATTATT 59.902 38.462 0.00 0.00 0.00 1.40
3315 3976 5.596361 ACTGAGATGAGAACCACGAGATTAT 59.404 40.000 0.00 0.00 0.00 1.28
3316 3977 4.950475 ACTGAGATGAGAACCACGAGATTA 59.050 41.667 0.00 0.00 0.00 1.75
3322 3983 2.029918 TCACACTGAGATGAGAACCACG 60.030 50.000 0.00 0.00 0.00 4.94
3478 4139 4.279043 GTTGGTGCCGTTGGTGCC 62.279 66.667 0.00 0.00 0.00 5.01
3479 4140 4.622456 CGTTGGTGCCGTTGGTGC 62.622 66.667 0.00 0.00 0.00 5.01
3480 4141 3.959975 CCGTTGGTGCCGTTGGTG 61.960 66.667 0.00 0.00 0.00 4.17
3482 4143 4.939368 TCCCGTTGGTGCCGTTGG 62.939 66.667 0.00 0.00 0.00 3.77
3483 4144 3.656045 GTCCCGTTGGTGCCGTTG 61.656 66.667 0.00 0.00 0.00 4.10
3706 4386 9.893305 AAATCAAAATAAAGAAACTAGACCGTG 57.107 29.630 0.00 0.00 0.00 4.94
3766 4446 6.079424 AGCTAAAGAGTAATAAGGAGCTCG 57.921 41.667 7.83 0.00 33.92 5.03
3933 4618 5.774179 AGTGTTAGGAGTAGTGGGCTATAA 58.226 41.667 0.00 0.00 0.00 0.98
3935 4620 4.267341 AGTGTTAGGAGTAGTGGGCTAT 57.733 45.455 0.00 0.00 0.00 2.97
3939 4628 4.401837 GGAGTTAGTGTTAGGAGTAGTGGG 59.598 50.000 0.00 0.00 0.00 4.61
3970 4659 0.317854 GGACACGGCACTTTGCTTTC 60.318 55.000 0.00 0.00 44.28 2.62
4173 4874 2.577059 CCAAAGGCTGCCTGCATG 59.423 61.111 24.16 20.16 45.15 4.06
4174 4875 3.387947 GCCAAAGGCTGCCTGCAT 61.388 61.111 24.16 9.10 46.69 3.96
4318 5019 0.473755 TCCTGCACGGCCATGATAAT 59.526 50.000 1.12 0.00 0.00 1.28
4386 5096 2.550830 AGAAATCACAACTGGCGAGT 57.449 45.000 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.