Multiple sequence alignment - TraesCS7A01G312100

Loading Multiple Alignment...

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 TraesCS7A01G312100 chr7A 100.000 1515 0 0 1 1515 442973642 442975156 0.000000e+00 2798
1 TraesCS7A01G312100 chr7A 100.000 616 0 0 1817 2432 442975458 442976073 0.000000e+00 1138
2 TraesCS7A01G312100 chr6A 95.177 1016 21 8 501 1515 13887316 13888304 0.000000e+00 1580
3 TraesCS7A01G312100 chr2A 99.802 505 1 0 1 505 683610340 683609836 0.000000e+00 928
4 TraesCS7A01G312100 chr2A 74.610 898 209 17 524 1412 767304615 767303728 6.350000e-101 377
5 TraesCS7A01G312100 chr6B 99.801 503 1 0 1 503 133554581 133555083 0.000000e+00 924
6 TraesCS7A01G312100 chr5B 99.801 502 1 0 1 502 130273339 130272838 0.000000e+00 922
7 TraesCS7A01G312100 chr3A 99.801 502 1 0 1 502 622441750 622441249 0.000000e+00 922
8 TraesCS7A01G312100 chr5A 99.409 508 1 1 1 508 318334169 318333664 0.000000e+00 920
9 TraesCS7A01G312100 chr3B 99.800 501 1 0 1 501 787419651 787420151 0.000000e+00 920
10 TraesCS7A01G312100 chr7B 99.800 500 1 0 1 500 92918809 92919308 0.000000e+00 918
11 TraesCS7A01G312100 chr7B 93.015 272 10 2 2161 2432 387669720 387669982 2.930000e-104 388
12 TraesCS7A01G312100 chr7B 88.976 254 17 6 1835 2087 387669454 387669697 1.090000e-78 303
13 TraesCS7A01G312100 chr1A 99.800 500 1 0 1 500 26557492 26557991 0.000000e+00 918
14 TraesCS7A01G312100 chr1A 76.250 480 106 8 936 1411 458899564 458899089 5.190000e-62 248
15 TraesCS7A01G312100 chr4B 98.830 513 4 2 1 512 112237756 112237245 0.000000e+00 913
16 TraesCS7A01G312100 chr4D 86.899 603 68 7 914 1515 482960877 482960285 0.000000e+00 665
17 TraesCS7A01G312100 chr7D 91.410 454 23 3 1836 2284 390913871 390914313 2.070000e-170 608
18 TraesCS7A01G312100 chr7D 96.053 152 6 0 2281 2432 390928108 390928259 5.190000e-62 248
19 TraesCS7A01G312100 chr3D 73.880 915 210 26 511 1411 18797270 18796371 3.000000e-89 339
20 TraesCS7A01G312100 chr3D 73.449 919 219 23 507 1411 74444721 74443814 3.020000e-84 322
21 TraesCS7A01G312100 chr5D 77.149 477 101 8 936 1408 27976174 27976646 1.110000e-68 270
22 TraesCS7A01G312100 chrUn 83.486 109 18 0 1044 1152 448731769 448731877 4.280000e-18 102


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 TraesCS7A01G312100 chr7A 442973642 442976073 2431 False 1968.0 2798 100.0000 1 2432 2 chr7A.!!$F1 2431
1 TraesCS7A01G312100 chr6A 13887316 13888304 988 False 1580.0 1580 95.1770 501 1515 1 chr6A.!!$F1 1014
2 TraesCS7A01G312100 chr2A 683609836 683610340 504 True 928.0 928 99.8020 1 505 1 chr2A.!!$R1 504
3 TraesCS7A01G312100 chr2A 767303728 767304615 887 True 377.0 377 74.6100 524 1412 1 chr2A.!!$R2 888
4 TraesCS7A01G312100 chr6B 133554581 133555083 502 False 924.0 924 99.8010 1 503 1 chr6B.!!$F1 502
5 TraesCS7A01G312100 chr5B 130272838 130273339 501 True 922.0 922 99.8010 1 502 1 chr5B.!!$R1 501
6 TraesCS7A01G312100 chr3A 622441249 622441750 501 True 922.0 922 99.8010 1 502 1 chr3A.!!$R1 501
7 TraesCS7A01G312100 chr5A 318333664 318334169 505 True 920.0 920 99.4090 1 508 1 chr5A.!!$R1 507
8 TraesCS7A01G312100 chr3B 787419651 787420151 500 False 920.0 920 99.8000 1 501 1 chr3B.!!$F1 500
9 TraesCS7A01G312100 chr7B 387669454 387669982 528 False 345.5 388 90.9955 1835 2432 2 chr7B.!!$F2 597
10 TraesCS7A01G312100 chr4B 112237245 112237756 511 True 913.0 913 98.8300 1 512 1 chr4B.!!$R1 511
11 TraesCS7A01G312100 chr4D 482960285 482960877 592 True 665.0 665 86.8990 914 1515 1 chr4D.!!$R1 601
12 TraesCS7A01G312100 chr3D 18796371 18797270 899 True 339.0 339 73.8800 511 1411 1 chr3D.!!$R1 900
13 TraesCS7A01G312100 chr3D 74443814 74444721 907 True 322.0 322 73.4490 507 1411 1 chr3D.!!$R2 904

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
58 59 0.810648 CCAACCCAACATCGACCATG 59.189 55.000 0.00 0.0 38.64 3.66 F
506 507 3.823304 GGGCATATTTCCTTCAGATGGAC 59.177 47.826 4.47 0.0 32.65 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1230 1236 0.323908 AGCAGAGTAGGACGAAGGCT 60.324 55.0 0.0 0.0 0.0 4.58 R
2254 2270 0.250124 CACGAGGGGCAACTGTTACA 60.250 55.0 0.0 0.0 0.0 2.41 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
58 59 0.810648 CCAACCCAACATCGACCATG 59.189 55.000 0.00 0.00 38.64 3.66
506 507 3.823304 GGGCATATTTCCTTCAGATGGAC 59.177 47.826 4.47 0.00 32.65 4.02
795 797 4.363990 CGTGGAGGAGTGCGCTGT 62.364 66.667 3.44 0.00 0.00 4.40
1412 1418 0.462225 TGGTTGTCGGTGCTTCGAAA 60.462 50.000 0.00 0.00 41.05 3.46
1413 1419 0.041576 GGTTGTCGGTGCTTCGAAAC 60.042 55.000 0.00 0.00 41.05 2.78
1414 1420 0.653636 GTTGTCGGTGCTTCGAAACA 59.346 50.000 0.00 0.00 41.05 2.83
1423 1438 0.034896 GCTTCGAAACAGGGGTGAGA 59.965 55.000 0.00 0.00 0.00 3.27
1438 1453 4.521256 GGGGTGAGATAGTCTGATGTAGTC 59.479 50.000 0.00 0.00 0.00 2.59
1440 1455 5.240623 GGGTGAGATAGTCTGATGTAGTCTG 59.759 48.000 0.00 0.00 0.00 3.51
1441 1456 6.058833 GGTGAGATAGTCTGATGTAGTCTGA 58.941 44.000 0.00 0.00 33.02 3.27
1442 1457 6.714810 GGTGAGATAGTCTGATGTAGTCTGAT 59.285 42.308 0.00 0.00 37.18 2.90
1443 1458 7.308529 GGTGAGATAGTCTGATGTAGTCTGATG 60.309 44.444 0.00 0.00 37.18 3.07
1444 1459 7.228507 GTGAGATAGTCTGATGTAGTCTGATGT 59.771 40.741 0.00 0.00 37.18 3.06
1445 1460 8.432805 TGAGATAGTCTGATGTAGTCTGATGTA 58.567 37.037 0.00 0.00 37.18 2.29
1446 1461 8.846943 AGATAGTCTGATGTAGTCTGATGTAG 57.153 38.462 0.00 0.00 37.18 2.74
1447 1462 8.436778 AGATAGTCTGATGTAGTCTGATGTAGT 58.563 37.037 0.00 0.00 37.18 2.73
1448 1463 8.988546 ATAGTCTGATGTAGTCTGATGTAGTT 57.011 34.615 0.00 0.00 37.18 2.24
1449 1464 7.328277 AGTCTGATGTAGTCTGATGTAGTTC 57.672 40.000 0.00 0.00 37.18 3.01
1450 1465 7.116075 AGTCTGATGTAGTCTGATGTAGTTCT 58.884 38.462 0.00 0.00 37.18 3.01
1496 1511 6.829298 TCTCCGTCTCTATGTAATCTGACTTT 59.171 38.462 0.00 0.00 0.00 2.66
1498 1513 8.515695 TCCGTCTCTATGTAATCTGACTTTAA 57.484 34.615 0.00 0.00 0.00 1.52
1846 1861 2.760374 CGTCTGGCTCTTTCTTTGTCT 58.240 47.619 0.00 0.00 0.00 3.41
1905 1920 1.081242 GCGTTTGGGTCATGTGCTG 60.081 57.895 0.00 0.00 0.00 4.41
1915 1930 0.321475 TCATGTGCTGCCATGACGAA 60.321 50.000 21.81 7.52 44.70 3.85
1935 1950 0.106369 TGTATCGGGTGATCGGGTCT 60.106 55.000 0.00 0.00 35.99 3.85
1936 1951 0.314302 GTATCGGGTGATCGGGTCTG 59.686 60.000 0.00 0.00 35.99 3.51
1950 1966 1.280421 GGGTCTGGAGTCAAAGCAGAT 59.720 52.381 0.00 0.00 0.00 2.90
1966 1982 5.750352 AGCAGATCCCATTTTGACAAAAT 57.250 34.783 18.41 18.41 41.57 1.82
1967 1983 6.855763 AGCAGATCCCATTTTGACAAAATA 57.144 33.333 22.46 10.62 38.97 1.40
1968 1984 7.243604 AGCAGATCCCATTTTGACAAAATAA 57.756 32.000 22.46 13.21 38.97 1.40
1969 1985 7.678837 AGCAGATCCCATTTTGACAAAATAAA 58.321 30.769 22.46 12.92 38.97 1.40
1970 1986 8.156165 AGCAGATCCCATTTTGACAAAATAAAA 58.844 29.630 22.46 12.63 38.97 1.52
1971 1987 8.445493 GCAGATCCCATTTTGACAAAATAAAAG 58.555 33.333 22.46 12.18 38.97 2.27
1972 1988 9.709495 CAGATCCCATTTTGACAAAATAAAAGA 57.291 29.630 22.46 16.75 38.97 2.52
2009 2025 5.304686 ACACTGAAAAGAATACCCACTGA 57.695 39.130 0.00 0.00 0.00 3.41
2095 2111 2.981909 CAGCCAGCACACACCCAG 60.982 66.667 0.00 0.00 0.00 4.45
2096 2112 4.962836 AGCCAGCACACACCCAGC 62.963 66.667 0.00 0.00 0.00 4.85
2097 2113 4.962836 GCCAGCACACACCCAGCT 62.963 66.667 0.00 0.00 39.63 4.24
2098 2114 2.203394 CCAGCACACACCCAGCTT 60.203 61.111 0.00 0.00 36.26 3.74
2099 2115 2.558286 CCAGCACACACCCAGCTTG 61.558 63.158 0.00 0.00 36.26 4.01
2100 2116 2.908940 AGCACACACCCAGCTTGC 60.909 61.111 0.00 0.00 34.37 4.01
2101 2117 3.982241 GCACACACCCAGCTTGCC 61.982 66.667 0.00 0.00 0.00 4.52
2102 2118 2.519063 CACACACCCAGCTTGCCA 60.519 61.111 0.00 0.00 0.00 4.92
2103 2119 1.904865 CACACACCCAGCTTGCCAT 60.905 57.895 0.00 0.00 0.00 4.40
2104 2120 1.152483 ACACACCCAGCTTGCCATT 60.152 52.632 0.00 0.00 0.00 3.16
2105 2121 1.290955 CACACCCAGCTTGCCATTG 59.709 57.895 0.00 0.00 0.00 2.82
2106 2122 2.263540 CACCCAGCTTGCCATTGC 59.736 61.111 0.00 0.00 38.26 3.56
2107 2123 2.999063 ACCCAGCTTGCCATTGCC 60.999 61.111 0.00 0.00 36.33 4.52
2108 2124 3.777910 CCCAGCTTGCCATTGCCC 61.778 66.667 0.00 0.00 36.33 5.36
2109 2125 4.137872 CCAGCTTGCCATTGCCCG 62.138 66.667 0.00 0.00 36.33 6.13
2110 2126 4.807039 CAGCTTGCCATTGCCCGC 62.807 66.667 0.00 0.00 36.33 6.13
2122 2138 3.747976 GCCCGCCATGAACCACAC 61.748 66.667 0.00 0.00 0.00 3.82
2127 2143 2.625823 GCCATGAACCACACCACGG 61.626 63.158 0.00 0.00 0.00 4.94
2145 2161 4.056125 CAGCGTGCCTGAGGTCGA 62.056 66.667 18.64 0.00 44.64 4.20
2146 2162 3.753434 AGCGTGCCTGAGGTCGAG 61.753 66.667 18.64 2.44 0.00 4.04
2147 2163 4.803426 GCGTGCCTGAGGTCGAGG 62.803 72.222 18.64 3.25 0.00 4.63
2148 2164 4.135153 CGTGCCTGAGGTCGAGGG 62.135 72.222 11.44 0.00 0.00 4.30
2149 2165 3.775654 GTGCCTGAGGTCGAGGGG 61.776 72.222 0.00 0.00 0.00 4.79
2150 2166 3.992641 TGCCTGAGGTCGAGGGGA 61.993 66.667 0.00 0.00 0.00 4.81
2151 2167 2.683933 GCCTGAGGTCGAGGGGAA 60.684 66.667 0.00 0.00 0.00 3.97
2152 2168 2.291043 GCCTGAGGTCGAGGGGAAA 61.291 63.158 0.00 0.00 0.00 3.13
2153 2169 1.901085 CCTGAGGTCGAGGGGAAAG 59.099 63.158 0.00 0.00 0.00 2.62
2154 2170 1.219393 CTGAGGTCGAGGGGAAAGC 59.781 63.158 0.00 0.00 0.00 3.51
2155 2171 1.535444 TGAGGTCGAGGGGAAAGCA 60.535 57.895 0.00 0.00 0.00 3.91
2156 2172 0.909610 TGAGGTCGAGGGGAAAGCAT 60.910 55.000 0.00 0.00 0.00 3.79
2157 2173 0.253327 GAGGTCGAGGGGAAAGCATT 59.747 55.000 0.00 0.00 0.00 3.56
2158 2174 1.485066 GAGGTCGAGGGGAAAGCATTA 59.515 52.381 0.00 0.00 0.00 1.90
2159 2175 1.486726 AGGTCGAGGGGAAAGCATTAG 59.513 52.381 0.00 0.00 0.00 1.73
2166 2182 2.580783 AGGGGAAAGCATTAGTTAGCCA 59.419 45.455 0.00 0.00 0.00 4.75
2203 2219 0.807667 GATGTAGACCTGTGCTGCCG 60.808 60.000 0.00 0.00 0.00 5.69
2213 2229 0.963355 TGTGCTGCCGGTAAAATCCC 60.963 55.000 1.90 0.00 0.00 3.85
2214 2230 1.379309 TGCTGCCGGTAAAATCCCC 60.379 57.895 1.90 0.00 0.00 4.81
2215 2231 1.076995 GCTGCCGGTAAAATCCCCT 60.077 57.895 1.90 0.00 0.00 4.79
2216 2232 0.683179 GCTGCCGGTAAAATCCCCTT 60.683 55.000 1.90 0.00 0.00 3.95
2254 2270 1.303236 TAATTGGCCTGTGCTGCGT 60.303 52.632 3.32 0.00 37.74 5.24
2348 2364 7.201702 TGGAATTACCATCATACTTGTACCA 57.798 36.000 0.00 0.00 44.64 3.25
2372 2388 3.952535 ACTTGCAAAATGAAGTCGACAC 58.047 40.909 19.50 11.83 0.00 3.67
2395 2411 0.692756 TCTGTGGTGGGAGTTGGTGA 60.693 55.000 0.00 0.00 0.00 4.02
2413 2429 2.263540 CCATGCAAGTTGCCCAGC 59.736 61.111 24.59 0.00 44.23 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 2.025131 AGGAGTACTACAGGTGTCTCCC 60.025 54.545 8.10 0.00 43.94 4.30
640 642 4.007644 CCACAGGCGAGCCAGTCA 62.008 66.667 17.18 0.00 38.92 3.41
795 797 5.698741 ATCATCCATCAGTAGTTGGACAA 57.301 39.130 0.00 0.00 44.26 3.18
1166 1172 1.062488 AAGAGACCCAACCACAGCCT 61.062 55.000 0.00 0.00 0.00 4.58
1230 1236 0.323908 AGCAGAGTAGGACGAAGGCT 60.324 55.000 0.00 0.00 0.00 4.58
1412 1418 3.303938 CATCAGACTATCTCACCCCTGT 58.696 50.000 0.00 0.00 0.00 4.00
1413 1419 3.303938 ACATCAGACTATCTCACCCCTG 58.696 50.000 0.00 0.00 0.00 4.45
1414 1420 3.697190 ACATCAGACTATCTCACCCCT 57.303 47.619 0.00 0.00 0.00 4.79
1423 1438 8.988546 AACTACATCAGACTACATCAGACTAT 57.011 34.615 0.00 0.00 0.00 2.12
1438 1453 4.340950 GGGAGAAGAGGAGAACTACATCAG 59.659 50.000 0.00 0.00 0.00 2.90
1440 1455 3.639561 GGGGAGAAGAGGAGAACTACATC 59.360 52.174 0.00 0.00 0.00 3.06
1441 1456 3.273618 AGGGGAGAAGAGGAGAACTACAT 59.726 47.826 0.00 0.00 0.00 2.29
1442 1457 2.655407 AGGGGAGAAGAGGAGAACTACA 59.345 50.000 0.00 0.00 0.00 2.74
1443 1458 3.028130 CAGGGGAGAAGAGGAGAACTAC 58.972 54.545 0.00 0.00 0.00 2.73
1444 1459 2.655407 ACAGGGGAGAAGAGGAGAACTA 59.345 50.000 0.00 0.00 0.00 2.24
1445 1460 1.435168 ACAGGGGAGAAGAGGAGAACT 59.565 52.381 0.00 0.00 0.00 3.01
1446 1461 1.945580 ACAGGGGAGAAGAGGAGAAC 58.054 55.000 0.00 0.00 0.00 3.01
1447 1462 5.377164 AGATATACAGGGGAGAAGAGGAGAA 59.623 44.000 0.00 0.00 0.00 2.87
1448 1463 4.923236 AGATATACAGGGGAGAAGAGGAGA 59.077 45.833 0.00 0.00 0.00 3.71
1449 1464 5.015178 AGAGATATACAGGGGAGAAGAGGAG 59.985 48.000 0.00 0.00 0.00 3.69
1450 1465 4.923236 AGAGATATACAGGGGAGAAGAGGA 59.077 45.833 0.00 0.00 0.00 3.71
1825 1840 1.195674 GACAAAGAAAGAGCCAGACGC 59.804 52.381 0.00 0.00 37.98 5.19
1826 1841 2.760374 AGACAAAGAAAGAGCCAGACG 58.240 47.619 0.00 0.00 0.00 4.18
1827 1842 4.632153 TGTAGACAAAGAAAGAGCCAGAC 58.368 43.478 0.00 0.00 0.00 3.51
1828 1843 4.955811 TGTAGACAAAGAAAGAGCCAGA 57.044 40.909 0.00 0.00 0.00 3.86
1829 1844 7.011857 GGATAATGTAGACAAAGAAAGAGCCAG 59.988 40.741 0.00 0.00 0.00 4.85
1830 1845 6.823689 GGATAATGTAGACAAAGAAAGAGCCA 59.176 38.462 0.00 0.00 0.00 4.75
1831 1846 6.823689 TGGATAATGTAGACAAAGAAAGAGCC 59.176 38.462 0.00 0.00 0.00 4.70
1832 1847 7.849804 TGGATAATGTAGACAAAGAAAGAGC 57.150 36.000 0.00 0.00 0.00 4.09
1838 1853 9.967451 TGGTTATTTGGATAATGTAGACAAAGA 57.033 29.630 0.00 0.00 34.91 2.52
1905 1920 1.148310 CCCGATACATTCGTCATGGC 58.852 55.000 0.00 0.00 46.65 4.40
1915 1930 0.966920 GACCCGATCACCCGATACAT 59.033 55.000 0.00 0.00 29.66 2.29
1928 1943 1.118965 TGCTTTGACTCCAGACCCGA 61.119 55.000 0.00 0.00 0.00 5.14
1929 1944 0.671781 CTGCTTTGACTCCAGACCCG 60.672 60.000 0.00 0.00 0.00 5.28
1935 1950 1.361204 TGGGATCTGCTTTGACTCCA 58.639 50.000 0.00 0.00 0.00 3.86
1936 1951 2.725221 ATGGGATCTGCTTTGACTCC 57.275 50.000 0.00 0.00 0.00 3.85
1982 1998 9.396022 CAGTGGGTATTCTTTTCAGTGTATATT 57.604 33.333 0.00 0.00 0.00 1.28
1987 2003 5.304686 TCAGTGGGTATTCTTTTCAGTGT 57.695 39.130 0.00 0.00 32.44 3.55
1988 2004 4.697352 CCTCAGTGGGTATTCTTTTCAGTG 59.303 45.833 0.00 0.00 0.00 3.66
2009 2025 2.819608 CCAATCAAACACGGTTGATCCT 59.180 45.455 10.61 0.00 45.42 3.24
2019 2035 3.489813 GGCGGAACCAATCAAACAC 57.510 52.632 0.00 0.00 38.86 3.32
2040 2056 4.142160 ACTTTTCCTTGGCAGTTTCTTCAC 60.142 41.667 0.00 0.00 0.00 3.18
2087 2103 1.290955 CAATGGCAAGCTGGGTGTG 59.709 57.895 0.00 0.00 0.00 3.82
2088 2104 2.576832 GCAATGGCAAGCTGGGTGT 61.577 57.895 7.90 0.00 40.72 4.16
2089 2105 2.263540 GCAATGGCAAGCTGGGTG 59.736 61.111 7.90 0.00 40.72 4.61
2090 2106 2.999063 GGCAATGGCAAGCTGGGT 60.999 61.111 13.80 0.00 43.71 4.51
2091 2107 3.777910 GGGCAATGGCAAGCTGGG 61.778 66.667 9.51 0.00 43.71 4.45
2092 2108 4.137872 CGGGCAATGGCAAGCTGG 62.138 66.667 9.51 0.00 43.71 4.85
2093 2109 4.807039 GCGGGCAATGGCAAGCTG 62.807 66.667 16.40 8.79 43.71 4.24
2096 2112 3.463585 ATGGCGGGCAATGGCAAG 61.464 61.111 8.78 3.03 45.55 4.01
2097 2113 3.772281 CATGGCGGGCAATGGCAA 61.772 61.111 8.78 0.00 45.55 4.52
2098 2114 4.755507 TCATGGCGGGCAATGGCA 62.756 61.111 8.78 0.00 46.52 4.92
2099 2115 3.459965 TTCATGGCGGGCAATGGC 61.460 61.111 8.78 0.00 40.13 4.40
2100 2116 2.495866 GTTCATGGCGGGCAATGG 59.504 61.111 8.78 1.46 0.00 3.16
2101 2117 2.349672 TGGTTCATGGCGGGCAATG 61.350 57.895 8.78 7.89 0.00 2.82
2102 2118 2.037049 TGGTTCATGGCGGGCAAT 59.963 55.556 8.78 0.00 0.00 3.56
2103 2119 2.988684 GTGGTTCATGGCGGGCAA 60.989 61.111 8.78 0.00 0.00 4.52
2104 2120 4.277009 TGTGGTTCATGGCGGGCA 62.277 61.111 6.74 6.74 0.00 5.36
2105 2121 3.747976 GTGTGGTTCATGGCGGGC 61.748 66.667 0.00 0.00 0.00 6.13
2106 2122 3.061848 GGTGTGGTTCATGGCGGG 61.062 66.667 0.00 0.00 0.00 6.13
2107 2123 2.282110 TGGTGTGGTTCATGGCGG 60.282 61.111 0.00 0.00 0.00 6.13
2108 2124 2.953821 GTGGTGTGGTTCATGGCG 59.046 61.111 0.00 0.00 0.00 5.69
2109 2125 2.625823 CCGTGGTGTGGTTCATGGC 61.626 63.158 0.00 0.00 33.87 4.40
2110 2126 2.625823 GCCGTGGTGTGGTTCATGG 61.626 63.158 0.00 0.00 41.64 3.66
2111 2127 1.855213 CTGCCGTGGTGTGGTTCATG 61.855 60.000 0.00 0.00 0.00 3.07
2132 2148 3.775654 CCCCTCGACCTCAGGCAC 61.776 72.222 0.00 0.00 0.00 5.01
2134 2150 2.245438 CTTTCCCCTCGACCTCAGGC 62.245 65.000 0.00 0.00 0.00 4.85
2135 2151 1.901085 CTTTCCCCTCGACCTCAGG 59.099 63.158 0.00 0.00 0.00 3.86
2136 2152 1.219393 GCTTTCCCCTCGACCTCAG 59.781 63.158 0.00 0.00 0.00 3.35
2137 2153 0.909610 ATGCTTTCCCCTCGACCTCA 60.910 55.000 0.00 0.00 0.00 3.86
2138 2154 0.253327 AATGCTTTCCCCTCGACCTC 59.747 55.000 0.00 0.00 0.00 3.85
2139 2155 1.486726 CTAATGCTTTCCCCTCGACCT 59.513 52.381 0.00 0.00 0.00 3.85
2140 2156 1.209747 ACTAATGCTTTCCCCTCGACC 59.790 52.381 0.00 0.00 0.00 4.79
2141 2157 2.693267 ACTAATGCTTTCCCCTCGAC 57.307 50.000 0.00 0.00 0.00 4.20
2142 2158 3.431766 GCTAACTAATGCTTTCCCCTCGA 60.432 47.826 0.00 0.00 0.00 4.04
2143 2159 2.872858 GCTAACTAATGCTTTCCCCTCG 59.127 50.000 0.00 0.00 0.00 4.63
2144 2160 3.215151 GGCTAACTAATGCTTTCCCCTC 58.785 50.000 0.00 0.00 0.00 4.30
2145 2161 2.580783 TGGCTAACTAATGCTTTCCCCT 59.419 45.455 0.00 0.00 0.00 4.79
2146 2162 3.012934 TGGCTAACTAATGCTTTCCCC 57.987 47.619 0.00 0.00 0.00 4.81
2147 2163 4.207165 TCATGGCTAACTAATGCTTTCCC 58.793 43.478 0.00 0.00 0.00 3.97
2148 2164 5.532406 TGATCATGGCTAACTAATGCTTTCC 59.468 40.000 0.00 0.00 0.00 3.13
2149 2165 6.433766 GTGATCATGGCTAACTAATGCTTTC 58.566 40.000 0.00 0.00 0.00 2.62
2150 2166 5.008019 CGTGATCATGGCTAACTAATGCTTT 59.992 40.000 7.06 0.00 0.00 3.51
2151 2167 4.512944 CGTGATCATGGCTAACTAATGCTT 59.487 41.667 7.06 0.00 0.00 3.91
2152 2168 4.060900 CGTGATCATGGCTAACTAATGCT 58.939 43.478 7.06 0.00 0.00 3.79
2153 2169 3.809832 ACGTGATCATGGCTAACTAATGC 59.190 43.478 18.97 0.00 0.00 3.56
2154 2170 6.868339 TCATACGTGATCATGGCTAACTAATG 59.132 38.462 18.97 8.85 0.00 1.90
2155 2171 6.993079 TCATACGTGATCATGGCTAACTAAT 58.007 36.000 18.97 0.00 0.00 1.73
2156 2172 6.399639 TCATACGTGATCATGGCTAACTAA 57.600 37.500 18.97 0.00 0.00 2.24
2157 2173 6.590234 ATCATACGTGATCATGGCTAACTA 57.410 37.500 18.97 1.84 41.16 2.24
2158 2174 4.937201 TCATACGTGATCATGGCTAACT 57.063 40.909 18.97 0.00 0.00 2.24
2159 2175 6.545504 AAATCATACGTGATCATGGCTAAC 57.454 37.500 18.97 0.00 44.20 2.34
2166 2182 7.539022 GTCTACATCGAAATCATACGTGATCAT 59.461 37.037 0.00 0.00 44.20 2.45
2203 2219 9.429109 TCATTAAATTAGGAAGGGGATTTTACC 57.571 33.333 0.00 0.00 0.00 2.85
2254 2270 0.250124 CACGAGGGGCAACTGTTACA 60.250 55.000 0.00 0.00 0.00 2.41
2329 2345 7.966339 AGTACTGGTACAAGTATGATGGTAA 57.034 36.000 13.30 0.00 38.70 2.85
2330 2346 7.632028 GCAAGTACTGGTACAAGTATGATGGTA 60.632 40.741 13.30 0.00 38.70 3.25
2333 2349 6.106003 TGCAAGTACTGGTACAAGTATGATG 58.894 40.000 13.30 12.73 38.70 3.07
2348 2364 4.814234 TGTCGACTTCATTTTGCAAGTACT 59.186 37.500 17.92 0.00 32.83 2.73
2372 2388 1.339438 CCAACTCCCACCACAGAGATG 60.339 57.143 0.00 0.00 33.88 2.90
2384 2400 0.539438 TTGCATGGTCACCAACTCCC 60.539 55.000 0.00 0.00 36.95 4.30
2385 2401 0.883833 CTTGCATGGTCACCAACTCC 59.116 55.000 0.00 0.00 36.95 3.85
2386 2402 1.609208 ACTTGCATGGTCACCAACTC 58.391 50.000 0.00 0.00 36.95 3.01
2387 2403 1.682854 CAACTTGCATGGTCACCAACT 59.317 47.619 0.00 0.00 36.95 3.16
2388 2404 1.869342 GCAACTTGCATGGTCACCAAC 60.869 52.381 0.00 0.00 44.26 3.77
2413 2429 3.164011 GAGCCGTCGTTGTCGTCG 61.164 66.667 0.00 0.00 44.85 5.12


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

AutoCloner maintained by Alex Coulton.